Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold337
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: 2178121
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 137747 characters in sequence are not A, C, G, or T
File 1 of 7
Found at i:22 original size:4 final size:4
Alignment explanation
Indices: 13--40 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3 TTTTTACTTA
13 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
41 GTATCCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:5649 original size:51 final size:50
Alignment explanation
Indices: 5587--5684 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
5577 TATTACAGTG
* * *
5587 AATCTTATTTCCCTGGTGTTGCAATGGAACCGATTAAAGCTAAAGGTAAAA
1 AATCTTATTTCCATGGTGTTACAATGGAACAGATTAAAGCT-AAGGTAAAA
* * *
5638 AATCTTGTTTCCATGGTGTTACAGTGGAATAGATTAAAGCTAAGGTA
1 AATCTTATTTCCATGGTGTTACAATGGAACAGATTAAAGCTAAGGTA
5685 GAGCAGATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
50 6 0.15
51 35 0.85
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (50 bp):
AATCTTATTTCCATGGTGTTACAATGGAACAGATTAAAGCTAAGGTAAAA
Found at i:5750 original size:51 final size:51
Alignment explanation
Indices: 5685--5879 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 51
5675 AGCTAAGGTA
* * * * * *
5685 GAGCAGATTAAAGCTGAAGGCAGTGAATCCTATCTCCATGGCGTTACAATG
1 GAGCAGATTAAAGCTAAAAGCAGCGAATCTTATCTCCCTGGCATTACAATG
* * *
5736 GAGCGGATTAAAGCTAAAAGCAGCGAATCATATCTCCTTGGCATTACAATG
1 GAGCAGATTAAAGCTAAAAGCAGCGAATCTTATCTCCCTGGCATTACAATG
** * * * * ** *
5787 GAATAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGTAGTG
1 GAGCAGATTAAAGCTAAAAGCAGCGAATCTTATCTCCCTGGCATTACAATG
* * *
5838 GAGCAGATTAAAGCTGAAAGCAACGAATCTTATATCCCTGGC
1 GAGCAGATTAAAGCTAAAAGCAGCGAATCTTATCTCCCTGGC
5880 GTTAAGACTA
Statistics
Matches: 117, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 117 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (51 bp):
GAGCAGATTAAAGCTAAAAGCAGCGAATCTTATCTCCCTGGCATTACAATG
Found at i:6090 original size:51 final size:51
Alignment explanation
Indices: 6035--6190 Score: 213
Period size: 51 Copynumber: 3.1 Consensus size: 51
6025 CCTATCTCCT
* *
6035 TGGCGTTACAGTGGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCC
1 TGGCGTTACAGCGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCC
*
6086 TGGCGTTACAGCGAAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCC
1 TGGCGTTACAGCGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCC
* * * * * * * *
6137 TGGTGTTGCAACAGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCC
1 TGGCGTTACAGCGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCC
6188 TGG
1 TGG
6191 TGCAGACTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 93 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (51 bp):
TGGCGTTACAGCGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCC
Found at i:6159 original size:312 final size:312
Alignment explanation
Indices: 5582--6190 Score: 817
Period size: 312 Copynumber: 2.0 Consensus size: 312
5572 GAAGTTATTA
** *
5582 CAGTGAATCTTATTTCCCTGGTGTTGCAATGGAACCGATTAAAGCTAAAGGTAAAAAATCTTGTT
1 CAGTGAATCTTATTTCCCTGGCATTGCAATGGAACAGATTAAAGCTAAAGGTAAAAAATCTTGTT
* ** * * **
5647 TCCATGGTGTTACAGTGGAATAGATTAAAGCTAAGGTAGAGCAGATTAAAGCTGAAGGCAGTGAA
66 TCCATAGCATTACAGTGGAATAGATTAAAGATAAGGTAGAGCAGATTAAAGCTGAAGACAACGAA
* * *
5712 TCCTATCTCCATGGCGTTACAATGGAGCGGATTAAAGCTAAAAGCAGCGAATCATATCTCCTTGG
131 TCCTATCTCCATGGCGTTACAATGGAACAGATTAAAGCTAAAAGCAGCGAATCATATCTCCCTGG
* * * * *** *
5777 CATTACAATGGAATAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGTAGTGGAGC
196 CATTACAACGAAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGCAACAGAAC
*
5842 AGATTAAAGCTGAAA-GCAACGAATCTTATATCCCTGGCGTTAAGACTAAAGG
261 AGATTAAAGCT-AAAGGCAACAAATCTTATATCCCTGGCGTTAAGACTAAAGG
* **
5894 CAGTGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTT
1 CAGTGAATCTTATTTCCCTGGCATTGCAATGGAACAGATTAAAGCTAAAGGTAAAAAATCTTGTT
* ** *
5959 TCCCTAGCATTGTAGTGGAATAGATTAAAGATGAA-GTAGAGCGGATTAAAGCTGAAGACAACGA
66 TCCATAGCATTACAGTGGAATAGATTAAAGAT-AAGGTAGAGCAGATTAAAGCTGAAGACAACGA
* * * * * *
6023 ATCCTATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTG
130 ATCCTATCTCCATGGCGTTACAATGGAACAGATTAAAGCTAAAAGCAGCGAATCATATCTCCCTG
* * **
6088 GCGTTACAGCGAAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGTGTTGCAACAGAA
195 GCATTACAACGAAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGCAACAGAA
* *
6153 CAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTGG
260 CAGATTAAAGCTAAAGGCAACAAATCTTATATCCCTGG
6191 TGCAGACTGA
Statistics
Matches: 254, Mismatches: 41, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
311 3 0.01
312 249 0.98
313 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (312 bp):
CAGTGAATCTTATTTCCCTGGCATTGCAATGGAACAGATTAAAGCTAAAGGTAAAAAATCTTGTT
TCCATAGCATTACAGTGGAATAGATTAAAGATAAGGTAGAGCAGATTAAAGCTGAAGACAACGAA
TCCTATCTCCATGGCGTTACAATGGAACAGATTAAAGCTAAAAGCAGCGAATCATATCTCCCTGG
CATTACAACGAAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTGCAACAGAAC
AGATTAAAGCTAAAGGCAACAAATCTTATATCCCTGGCGTTAAGACTAAAGG
Found at i:6314 original size:44 final size:42
Alignment explanation
Indices: 6254--6669 Score: 224
Period size: 44 Copynumber: 9.6 Consensus size: 42
6244 GAAGATGGCG
*
6254 AATCTTATCTCCCTAAAGTTACAGTGAAGCAGATTAAAACCAAT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAA--AAT
* * * **
6298 AATCCTATCTCTCTAAAGTTACAGTGGAGCGGATTAAAGTTAT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAA-AAAT
* * *
6341 AACTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAATAAACC
1 AA-TCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAA-AAA-T
* * *
6386 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAAC
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATT-AAAAAAT
* * * ** * **
6429 AATCCTATCTCCCTGAAGTTGCAGCAGAGTAGATTGAAATGAT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATT-AAAAAAT
* * * ** * *** **
6472 GGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCA-
1 -AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAAAAT
* * * * * **
6514 AGTCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAATAAACC
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGA-TTAA-AAAAT
* * * * *
6558 AATCTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGAAAC
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATT-AAAAAAT
* * * * *
6601 AAT-TCTATCTCTCTGAAGTTGCAGCGGAGCAGATTAAAATGAT
1 AATCT-TATCTCCCTAAAGTTACAGTGGAGCAGATTAAAA-AAT
* * *
6644 GGATCTTATCTCTCTGAAGTTACAGT
1 -AATCTTATCTCCCTAAAGTTACAGT
6670 AGAGAATATC
Statistics
Matches: 292, Mismatches: 67, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
41 25 0.09
42 5 0.02
43 78 0.27
44 179 0.61
45 5 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (42 bp):
AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAAAAT
Found at i:6361 original size:88 final size:87
Alignment explanation
Indices: 6254--6638 Score: 273
Period size: 87 Copynumber: 4.4 Consensus size: 87
6244 GAAGATGGCG
* * * *
6254 AATCTTATCTCCCTAAAGTTACAGTGAAGCAGATTAAA-ACCAA-TAATCCTATCTCTCTAAAGT
1 AATCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATA--AACCAATCCTATCTCCCTAAAGT
* ** *
6317 TACAGTGGAGCGGATTAAAGTTAT
64 TACAGTGGAGCAGATTAAAGAAAC
* * *
6341 AACTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAATAAACCAATCTTATCTCCCTGAAGTT
1 AA-TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATAAACCAATCCTATCTCCCTAAAGTT
*
6406 ACAGTGGAGCAGATTGAAGAAAC
65 ACAGTGGAGCAGATTAAAGAAAC
* * * * * * *** * * *
6429 AATCCTATCTCCCTGAAGTTGCAG-CAGAGTAGATTGAAAT-GATGGATCTTATCTCTCTGAAGT
1 AATCTTATCTCCCTGAAGTTACAGTGA-AGCAGACT-AAATAAACCAATCCTATCTCCCTAAAGT
** * * * *
6492 TGTAGTAGAGCAGA-T--CGCATC
64 TACAGTGGAGCAGATTAAAGAAAC
* * * * *
6513 AAGTCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAATAAACCAATCTTATCTCCCTGAATTT
1 AA-TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATAAACCAATCCTATCTCCCTAAAGTT
* *
6578 GCAGTGGAGCAGATTGAAGAAAC
65 ACAGTGGAGCAGATTAAAGAAAC
* * * * *
6601 AAT-TCTATCTCTCTGAAGTTGCAGCGGAGCAGATTAAA
1 AATCT-TATCTCCCTGAAGTTACAGTGAAGCAGACTAAA
6639 ATGATGGATC
Statistics
Matches: 232, Mismatches: 54, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
84 8 0.03
85 54 0.23
86 4 0.02
87 86 0.37
88 79 0.34
89 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (87 bp):
AATCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATAAACCAATCCTATCTCCCTAAAGTTA
CAGTGGAGCAGATTAAAGAAAC
Found at i:6479 original size:87 final size:87
Alignment explanation
Indices: 6387--6669 Score: 290
Period size: 87 Copynumber: 3.3 Consensus size: 87
6377 AAATAAACCA
6387 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCA
*
6452 GCAGAGTAGATTGAAATGATGG
66 GCAGAGCAGATTGAAATGATGG
* ** * * * * * *
6474 ATCTTATCTCTCTGAAGTTGTAGTAGAGCAGA-T--CGCATCAAGTCTTATCTCCCTGAAGTTAC
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAACAA-TCCTATCTCCCTGAAGTTGC
* * ***
6536 A--ATGAAGCAGACTG-AATAAACCA
65 AGCA-G-AGCAGATTGAAAT-GATGG
* * * *
6559 ATCTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGAAACAATTCTATCTCTCTGAAGTTGCA
1 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCA
* *
6624 GCGGAGCAGATTAAAATGATGG
66 GCAGAGCAGATTGAAATGATGG
*
6646 ATCTTATCTCTCTGAAGTTACAGT
1 ATCTTATCTCCCTGAAGTTACAGT
6670 AGAGAATATC
Statistics
Matches: 150, Mismatches: 36, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
83 1 0.01
84 9 0.06
85 55 0.37
86 2 0.01
87 74 0.49
88 9 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (87 bp):
ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCA
GCAGAGCAGATTGAAATGATGG
Found at i:6533 original size:172 final size:172
Alignment explanation
Indices: 6344--6716 Score: 575
Period size: 172 Copynumber: 2.2 Consensus size: 172
6334 AAGTTATAAC
*
6344 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAATAAACCAATCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATAAACCAATCTTATCTCCCTGAAGTTACA
* *
6409 GTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCAGCAGAGTAGATTGAAATGATGG
66 GTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCAGCAGAGCAGATTAAAATGATGG
** *
6474 ATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCAAG
131 ATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGCATCAAG
* * * *
6516 TCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAATAAACCAATCTTATCTCCCTGAATTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATAAACCAATCTTATCTCCCTGAAGTTACA
* * *
6581 GTGGAGCAGATTGAAGAAACAATTCTATCTCTCTGAAGTTGCAGCGGAGCAGATTAAAATGATGG
66 GTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCAGCAGAGCAGATTAAAATGATGG
* *
6646 ATCTTATCTCTCTGAAGTTACAGTAGAGAATATCGCATCAGG
131 ATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGCATCAAG
* * *
6688 TCTTATTTCCTTGAAATTACAGTTGAAGC
1 TCTTATCTCCCTGAAGTTACAG-TGAAGC
6717 TACAAGTCTT
Statistics
Matches: 181, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
172 175 0.97
173 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (172 bp):
TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTAAATAAACCAATCTTATCTCCCTGAAGTTACA
GTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCAGCAGAGCAGATTAAAATGATGG
ATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGCATCAAG
Found at i:6610 original size:128 final size:127
Alignment explanation
Indices: 6388--6621 Score: 310
Period size: 128 Copynumber: 1.8 Consensus size: 127
6378 AATAAACCAA
* * *
6388 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAAGAAACAATCCTATCTCCCTGAAGTTGCAG
* ***
6453 CAGAGTAGATTGAAATGATGGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCAAG
66 CAGAGCAGATTGAAA-GAACAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCAAG
* * *
6516 TCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAATAAACCAATCTTATCTCCCTGAATTTGCA
1 TCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAAGAAA-CAATCCTATCTCCCTGAAGTTGCA
**
6581 GTGGAGCAGATTG-AAGAAACAAT-TCTATCTCTCTGAAGTTG
65 GCAGAGCAGATTGAAAG-AACAATCT-TATCTCTCTGAAGTTG
6622 CAGCGGAGCA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
127 2 0.02
128 57 0.63
129 32 0.35
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (127 bp):
TCTTATCTCCCTGAAGTTACAATGAAGCAGACTGAAGAAACAATCCTATCTCCCTGAAGTTGCAG
CAGAGCAGATTGAAAGAACAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCAAG
Found at i:9534 original size:3 final size:3
Alignment explanation
Indices: 9528--9568 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
9518 GATTTCGGCA
* * *
9528 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATC CTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9569 CCTTATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:9549 original size:15 final size:15
Alignment explanation
Indices: 9529--9593 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
9519 ATTTCGGCAA
**
9529 TTATTATTATTATTG
1 TTATTATTATTATCC
9544 TTATTATTATTATCC
1 TTATTATTATTATCC
9559 ---TTATTATTATCC
1 TTATTATTATTATCC
* * *
9571 TTATAATTATTGTCG
1 TTATTATTATTATCC
9586 TTATTATT
1 TTATTATT
9594 TATGGATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
12 12 0.29
15 29 0.71
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (15 bp):
TTATTATTATTATCC
Found at i:9562 original size:12 final size:12
Alignment explanation
Indices: 9547--9580 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
9537 ATTATTGTTA
9547 TTATTATTATCC
1 TTATTATTATCC
9559 TTATTATTATCC
1 TTATTATTATCC
*
9571 TTATAATTAT
1 TTATTATTAT
9581 TGTCGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTATTATCC
Found at i:9593 original size:12 final size:12
Alignment explanation
Indices: 9528--9580 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
9518 GATTTCGGCA
*
9528 ATTATTATTATT
1 ATTATCATTATT
* *
9540 ATTGTTATTATT
1 ATTATCATTATT
*
9552 ATTATCCTTATT
1 ATTATCATTATT
* *
9564 ATTATCCTTATA
1 ATTATCATTATT
9576 ATTAT
1 ATTAT
9581 TGTCGTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTATCATTATT
Found at i:11016 original size:21 final size:22
Alignment explanation
Indices: 10986--11040 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
10976 ATTTATTTTT
10986 AAAAAT-TAAAAATAAA-ATTA
1 AAAAATATAAAAATAAATATTA
* *
11006 AAAAATATAAATATAAATATTG
1 AAAAATATAAAAATAAATATTA
*
11028 AAAACTA-AAAAAT
1 AAAAATATAAAAAT
11041 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 14 0.48
22 9 0.31
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAAATATAAAAATAAATATTA
Found at i:15026 original size:26 final size:26
Alignment explanation
Indices: 14992--15041 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
14982 CCCACACACC
* *
14992 AATATTGCAGCATAGCTACCAGTAAT
1 AATAATGCAGCAGAGCTACCAGTAAT
*
15018 AATAATGCAGCAGAGCTGCCAGTA
1 AATAATGCAGCAGAGCTACCAGTA
15042 CAGTATAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
AATAATGCAGCAGAGCTACCAGTAAT
Found at i:15082 original size:27 final size:27
Alignment explanation
Indices: 15052--15127 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
15042 CAGTATAGGC
* *
15052 GGCAAAGCCACCAATAACAGTATTTGT
1 GGCAGAGCCACCAATAACAGTATGTGT
* * *
15079 GGCAGAGCCACCAGTATCAATATGTGT
1 GGCAGAGCCACCAATAACAGTATGTGT
*
15106 GACAGAGCCACCAGA-AACAGTA
1 GGCAGAGCCACCA-ATAACAGTA
15128 CTTCCTCCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (27 bp):
GGCAGAGCCACCAATAACAGTATGTGT
Found at i:15273 original size:27 final size:27
Alignment explanation
Indices: 15227--15516 Score: 330
Period size: 27 Copynumber: 10.8 Consensus size: 27
15217 TCATCTCCTA
** * *
15227 AGGGTATAATGGTCATTTTACCCTTCG
1 AGGGTATTTTGGTAATTTTACCCATCG
** * * *
15254 AGGGTATTTTAATAACTTTACCCTTCA
1 AGGGTATTTTGGTAATTTTACCCATCG
*
15281 AGGGTATTTCGGTAATTTTA-CCATCG
1 AGGGTATTTTGGTAATTTTACCCATCG
* ***
15307 AAGGTATTTCAATAATTTTACCCATCG
1 AGGGTATTTTGGTAATTTTACCCATCG
* * *
15334 AGAGCATTTTGGTAATTTTACCCATCA
1 AGGGTATTTTGGTAATTTTACCCATCG
*
15361 AGGGTATTTTAGTAATTTTACCCATCG
1 AGGGTATTTTGGTAATTTTACCCATCG
* *
15388 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTTGGTAATTTTACCCATCG
* *
15415 AGGGTATTTTGGTAATTTTACCAATCA
1 AGGGTATTTTGGTAATTTTACCCATCG
* * *
15442 AGGGTATTTCGGTAATTTTACCAATTG
1 AGGGTATTTTGGTAATTTTACCCATCG
15469 AGGGTATTTTGGTAATTTTACCCATCG
1 AGGGTATTTTGGTAATTTTACCCATCG
* *
15496 AGGGTATTTCGATAATTTTAC
1 AGGGTATTTTGGTAATTTTAC
15517 GGCCCAAGCC
Statistics
Matches: 220, Mismatches: 42, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 21 0.10
27 199 0.90
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACCCATCG
Found at i:15379 original size:54 final size:54
Alignment explanation
Indices: 15241--15516 Score: 365
Period size: 54 Copynumber: 5.1 Consensus size: 54
15231 TATAATGGTC
* * * * *
15241 ATTTTACCCTTCGAGGGTATTTTAATAACTTTACCCTTCAAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTA
* * * * * *
15295 ATTTTA-CCATCGAAGGTATTTCAATAATTTTACCCATCGAGAGCATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTA
* *
15348 ATTTTACCCATCAAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTA
* * *
15402 ATTTTACCCATCGAGGGTATTTTGGTAATTTTACCAATCAAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTA
* * * *
15456 ATTTTACCAATTGAGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTA
15510 ATTTTAC
1 ATTTTAC
15517 GGCCCAAGCC
Statistics
Matches: 194, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 44 0.23
54 150 0.77
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTA
Found at i:15424 original size:81 final size:81
Alignment explanation
Indices: 15241--15516 Score: 383
Period size: 81 Copynumber: 3.4 Consensus size: 81
15231 TATAATGGTC
* * * *
15241 ATTTTACCCTTCGAGGGTATTTTAATAACTTTACCCTTCAAGGGTATTTCGGTAATTTTA-CCAT
1 ATTTTACCCATCGAGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCAT
* *
15305 CGAAGGTATTTCAATA
66 CGAGGGTATTTCGATA
* * * **
15321 ATTTTACCCATCGAGAGCATTTTGGTAATTTTACCCATCAAGGGTATTTTAGTAATTTTACCCAT
1 ATTTTACCCATCGAGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCAT
15386 CGAGGGTATTTCGATA
66 CGAGGGTATTTCGATA
* * *
15402 ATTTTACCCATCGAGGGTATTTTGGTAATTTTACCAATCAAGGGTATTTCGGTAATTTTACCAAT
1 ATTTTACCCATCGAGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCAT
* * *
15467 TGAGGGTATTTTGGTA
66 CGAGGGTATTTCGATA
*
15483 ATTTTACCCATCGAGGGTATTTCGATAATTTTAC
1 ATTTTACCCATCGAGGGTATTTTGATAATTTTAC
15517 GGCCCAAGCC
Statistics
Matches: 173, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 51 0.29
81 122 0.71
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (81 bp):
ATTTTACCCATCGAGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCAT
CGAGGGTATTTCGATA
Found at i:17484 original size:73 final size:71
Alignment explanation
Indices: 17351--17493 Score: 180
Period size: 73 Copynumber: 2.0 Consensus size: 71
17341 TCGAATGTGG
* * * *
17351 CAATAGCATGTTTTTGATATGTTAAACTATAGTGCAATTAGTATGTTCTAATTAGTTTTATCTGA
1 CAATAGCATGTTTTTGATATATTAAACTATAATGCAACTAGTATGTTCTAATTAGCTTTATCTGA
17416 ATATGC
66 ATATGC
* * *
17422 CAATAGCATGTTTTTTTATCTATTAAACTATATATGCAACTAGTATGTTCTGATCTA-CTTTATC
1 CAATAGCATG-TTTTTGATATATTAAACTATA-ATGCAACTAGTATGTTCTAAT-TAGCTTTATC
*
17486 TGCATATG
63 TGAATATG
17494 GGCATGTCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 10 0.16
72 18 0.30
73 31 0.51
74 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (71 bp):
CAATAGCATGTTTTTGATATATTAAACTATAATGCAACTAGTATGTTCTAATTAGCTTTATCTGA
ATATGC
Found at i:26873 original size:129 final size:130
Alignment explanation
Indices: 26713--26978 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 130
26703 GTTTACAATT
26713 TAAAAGTACTAAACTTAATTAACTTATTTATACTAATATTTATGTTTCTAATTAAATTGGAGTCA
1 TAAAA-TACTAAACTTAATTAACTTATTTATACTAATATTTATGTTTCTAATTAAATTGGAGTCA
26778 CGAGTCAATCGGGATAATTCGGAGATTACCAAAAAAAATATTTTTTTATCTTTTTTATA-TTTAT
65 CGAGTCAATCGGGATAATTCGGAGATTACCAAAAAAAATATTTTTTTATCTTTTTTATATTTTAT
26842 A
130 A
26843 TAAAATACTAAACTTAATTAACTTATTTATACTAATATTTATGTTTCTAATTAAATTGGAGTCAC
1 TAAAATACTAAACTTAATTAACTTATTTATACTAATATTTATGTTTCTAATTAAATTGGAGTCAC
26908 GAGTCAATCGGGATAATTCGGAGATTACCAAAAAAAATATTTTTTTATCTTTTTTATATTTTATA
66 GAGTCAATCGGGATAATTCGGAGATTACCAAAAAAAATATTTTTTTATCTTTTTTATATTTTATA
26973 TAAAAT
1 TAAAAT
26979 TTAAAAATCT
Statistics
Matches: 135, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
129 118 0.87
130 17 0.13
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (130 bp):
TAAAATACTAAACTTAATTAACTTATTTATACTAATATTTATGTTTCTAATTAAATTGGAGTCAC
GAGTCAATCGGGATAATTCGGAGATTACCAAAAAAAATATTTTTTTATCTTTTTTATATTTTATA
Found at i:36072 original size:21 final size:18
Alignment explanation
Indices: 36042--36082 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 18
36032 CATAAGTTTT
36042 AAACAATTAATATAATATTA
1 AAACAATTAA-ATAA-ATTA
36062 AAACTAATTAAATAAATTA
1 AAAC-AATTAAATAAATTA
36081 AA
1 AA
36083 CATCTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 8 0.40
21 6 0.30
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAACAATTAAATAAATTA
Found at i:36747 original size:22 final size:21
Alignment explanation
Indices: 36712--36814 Score: 65
Period size: 19 Copynumber: 5.1 Consensus size: 21
36702 AAAAGGTATC
* *
36712 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
36733 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* * *
36756 TGCATATCATA--TCTAAAAT
1 TACAAATCATATCTCTAAGAT
* *
36775 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
36794 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
36813 TA
1 TA
36815 TATAGTATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 41 0.59
21 3 0.04
22 15 0.22
23 10 0.14
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:36755 original size:23 final size:22
Alignment explanation
Indices: 36712--36769 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
36702 AAAAGGTATC
* *
36712 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
36733 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
36756 TGCATATCATATCT
1 TACAAATCATATCT
36770 AAAATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:36781 original size:19 final size:19
Alignment explanation
Indices: 36748--36911 Score: 204
Period size: 19 Copynumber: 8.6 Consensus size: 19
36738 AATCATATCT
36748 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* **
36767 TCTAAAATTATATATCATA
1 TCTAAGATTGCATATCATA
36786 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
36805 TCTAAGATTATATAGT-ATA
1 TCTAAGATTGCATA-TCATA
*
36824 TTTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
36843 TCTAAGATTGCATATCCCA
1 TCTAAGATTGCATATCATA
** *
36862 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
36881 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
36900 ACTAAGATTGCA
1 TCTAAGATTGCA
36912 CATCCCTGAA
Statistics
Matches: 120, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
18 1 0.01
19 118 0.98
20 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:36794 original size:38 final size:38
Alignment explanation
Indices: 36725--36911 Score: 205
Period size: 38 Copynumber: 4.8 Consensus size: 38
36715 AAATTAAATC
*
36725 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
* *
36767 TCTAAAATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
36805 TCTAAGATTATATAGT-ATATTTAAGATTGCATATCATA
1 TCTAAGATTACATA-TCATATCTAAGATTGCATATCATA
* ** ** *
36843 TCTAAGATTGCATATCCCATCTAAGATTATATATTATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
36881 TCTAAGATTGCATATCATAACTAAGATTGCA
1 TCTAAGATTACATATCATATCTAAGATTGCA
36912 CATCCCTGAA
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
37 1 0.01
38 107 0.86
39 1 0.01
41 7 0.06
42 9 0.07
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:36917 original size:57 final size:57
Alignment explanation
Indices: 36748--36917 Score: 232
Period size: 57 Copynumber: 3.0 Consensus size: 57
36738 AATCATATCT
** * * ** **
36748 TCTAAGATTGCATATCATATCTAAAATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTATATATTATATCTAAGATTGCATATCATATCTAAGATTGCATATCCCA
* *
36805 TCTAAGATTATATAGTATATTTAAGATTGCATATCATATCTAAGATTGCATATCCCA
1 TCTAAGATTATATATTATATCTAAGATTGCATATCATATCTAAGATTGCATATCCCA
* *
36862 TCTAAGATTATATATTATATCTAAGATTGCATATCATAACTAAGATTGCACATCCC
1 TCTAAGATTATATATTATATCTAAGATTGCATATCATATCTAAGATTGCATATCCC
36918 TGAAGATTAT
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 99 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (57 bp):
TCTAAGATTATATATTATATCTAAGATTGCATATCATATCTAAGATTGCATATCCCA
Found at i:37410 original size:132 final size:132
Alignment explanation
Indices: 37225--37949 Score: 1281
Period size: 132 Copynumber: 5.5 Consensus size: 132
37215 GGGAGATATG
* * *
37225 ATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGTTAAAATCCGCCATCTTCGATCTTCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* * *
37290 CCACTACTGCTTAGAGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCCAGGGAAGTA
37355 GA
131 GA
37357 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* * *
37422 CCACTACTACTTAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCCAGGGAAGTA
37487 GA
131 GA
37489 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
37554 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTG-CCAAGGGAAGT
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCC-AGGGAAGT
37618 AGA
130 AGA
* *
37621 ATTACTGGCTTGAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
*
37686 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGCCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCCAGGGAAGTA
37751 GA
131 GA
* *
37753 ATTACTGGATTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* *
37818 CCACTACTGCTTAGGGAGCTAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCCAGAGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCCAGGGAAGTA
37883 GA
131 GA
*
37885 ATTACTGGCTTCAATGTACTGCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
37950 TCGTTGTCAA
Statistics
Matches: 573, Mismatches: 18, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
131 2 0.00
132 569 0.99
133 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCCATCTATTCCACTGTTGTCCAGGGAAGTA
GA
Found at i:44968 original size:23 final size:22
Alignment explanation
Indices: 44938--44982 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44928 NNNNNNNNNN
44938 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
44961 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
44983 AAGATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:45008 original size:38 final size:38
Alignment explanation
Indices: 44961--45710 Score: 1491
Period size: 38 Copynumber: 19.7 Consensus size: 38
44951 AATCATATCT
44961 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
44999 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45037 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45075 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45113 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45151 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45189 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45227 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45265 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45303 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45341 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45379 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45417 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45455 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45493 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45531 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45569 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45607 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
45645 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
45683 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
45711 GCATATCCCT
Statistics
Matches: 711, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 711 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:46030 original size:99 final size:100
Alignment explanation
Indices: 45859--46063 Score: 403
Period size: 99 Copynumber: 2.1 Consensus size: 100
45849 GCCCAATTTG
45859 TAAAATTTTATTTTTTTTAAATACTTAGTTTAAATTTTTATGTAAATATACAGTCCAAGAGGCCC
1 TAAAATTTTATTTTTTTTAAATACTTAGTTTAAATTTTTATGTAAATATACAGTCCAAGAGGCCC
45924 AATTAAGAGGCCTTGGCCAAATTAACATTT-AAAT
66 AATTAAGAGGCCTTGGCCAAATTAACATTTAAAAT
45958 TAAAATTTTATTTTTTTTAAATACTTAGTTTAAATTTTTATGTAAATATACAGTCCAAGAGGCCC
1 TAAAATTTTATTTTTTTTAAATACTTAGTTTAAATTTTTATGTAAATATACAGTCCAAGAGGCCC
46023 AATTAAGAGGCCTTGGCCAAATTAACATTTAAAAT
66 AATTAAGAGGCCTTGGCCAAATTAACATTTAAAAT
46058 TAAAAT
1 TAAAAT
46064 AATTAGGAGT
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 95 0.90
100 10 0.10
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (100 bp):
TAAAATTTTATTTTTTTTAAATACTTAGTTTAAATTTTTATGTAAATATACAGTCCAAGAGGCCC
AATTAAGAGGCCTTGGCCAAATTAACATTTAAAAT
Found at i:51125 original size:37 final size:37
Alignment explanation
Indices: 51084--51186 Score: 116
Period size: 38 Copynumber: 2.7 Consensus size: 37
51074 TTACTGCCCT
* * * * *
51084 ATTGAGTACATGTTATGCATGTCATTGCCAGTGTTGA
1 ATTGAATACATGTTAAGCATGTCACTGCCAATGTTAA
* *
51121 ATTGAATACATGTTAAGTATGTCCACTGCTAATGTTAA
1 ATTGAATACATGTTAAGCATGT-CACTGCCAATGTTAA
*
51159 ACTGAATACATGTTAAGCATGTCTACTG
1 ATTGAATACATGTTAAGCATGTC-ACTG
51187 TTTTGCATTA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
37 20 0.36
38 35 0.64
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (37 bp):
ATTGAATACATGTTAAGCATGTCACTGCCAATGTTAA
Found at i:63074 original size:217 final size:216
Alignment explanation
Indices: 62689--63099 Score: 533
Period size: 217 Copynumber: 1.9 Consensus size: 216
62679 AGAAAGATTA
* * * * *
62689 TTGAAGAGATTCCATCTAAAGACTCATTTGATTTAACTGATGAACCAGAAACTAAATCAGACCCC
1 TTGAAGAGATTCCATCTAAAGACTCATATAATTCAACTAATGAACCAGAAACAAAATCAGACCCC
*
62754 ACTTTATAGAGGACATACCTCTGAAGGAAATCATCGGTGACAAAACTCGATCCAAGAAGCCAAAT
66 ACTTTATAGAGGACATACCTCTAAAGGAAATCATCGGTGACAAAACTCGATCCAAGAAGCCAAAT
* * * *
62819 GTTCCTATGACTGCACAGCAACGTAATAAGAGGATGAAGCAAGTAGGTGTACCTTCTTTGCTTGT
131 GTGCCTATGACTGCACAGCAACGTAACAAGAAGATGAAGCAAGCAGGTGTACCTTCTTTGCTTGT
62884 TGAAGCTACTGCCAAGGCACC
196 TGAAGCTACTGCCAAGGCACC
** *
62905 TTGAAGAGATTCCA-CTTAAAGACTCATATAATTCAGTTAATGAACCAGAAACAAAATCAGGCCC
1 TTGAAGAGATTCCATC-TAAAGACTCATATAATTCAACTAATGAACCAGAAACAAAATCAGACCC
* * * * **
62969 TAGCTTTGTAGATGG-CATACCTCTAAAGGAAATCATTGGTGGA-AAAGCTCGATCCAAGTGGCC
65 CA-CTTTATAGA-GGACATACCTCTAAAGGAAATCATCGGT-GACAAAACTCGATCCAAGAAGCC
* * * * *
63032 AAATGTGCAC-ATGACTGCACAGTAATGTAACAAGAAGATGAAGTAAGCAGGTGTACTTTCTTTT
127 AAATGTGC-CTATGACTGCACAGCAACGTAACAAGAAGATGAAGCAAGCAGGTGTACCTTCTTTG
63096 CTTG
191 CTTG
63100 CTAAAGATAA
Statistics
Matches: 166, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
215 1 0.01
216 55 0.33
217 105 0.63
218 5 0.03
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (216 bp):
TTGAAGAGATTCCATCTAAAGACTCATATAATTCAACTAATGAACCAGAAACAAAATCAGACCCC
ACTTTATAGAGGACATACCTCTAAAGGAAATCATCGGTGACAAAACTCGATCCAAGAAGCCAAAT
GTGCCTATGACTGCACAGCAACGTAACAAGAAGATGAAGCAAGCAGGTGTACCTTCTTTGCTTGT
TGAAGCTACTGCCAAGGCACC
Found at i:68940 original size:18 final size:18
Alignment explanation
Indices: 68919--68953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68909 TAAAAAATTA
68919 CAAAAAACATAAAAAACG
1 CAAAAAACATAAAAAACG
* *
68937 CAAAAAAGATGAAAAAC
1 CAAAAAACATAAAAAAC
68954 AAAAAGAATA
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:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (18 bp):
CAAAAAACATAAAAAACG
Found at i:84293 original size:402 final size:402
Alignment explanation
Indices: 83549--84354 Score: 1497
Period size: 402 Copynumber: 2.0 Consensus size: 402
83539 AAATAAAACC
83549 ATGAAAATCCAGAACCATGGTCACCGTTGAGTCCTCCGTCGCACCAATCCATCTAGGTCTGGAGA
1 ATGAAAATCCAGAACCATGGTCACCGTTGAGTCCTCCGTCGCACCAATCCATCTAGGTCTGGAGA
* *
83614 TTACCTATGCATATTCAACAGAAGGGGGTGAGTTTACGTAAACTCAGTGTAATCCCACAGAAACA
66 TTACCTATGCATATTCAACAGAAGGGGGTGAGTTTACATAAACTCAGTGTAATCCCACAAAAACA
83679 AACAAACAGCAATCATAATGCACAGTCAGAAGCGGTCTTGGGCCTAAGCCCTTTTCAGTATCAGT
131 AACAAACAGCAATCATAATGCACAGTCAGAAGCGGTCTTGGGCCTAAGCCCTTTTCAGTATCAGT
83744 ATCAGTTTGCACAAGGGCCTTAGCCCATCACAGCATCAGTAACAGATATACAGTATTCAGTAACA
196 ATCAGTTTGCACAAGGGCCTTAGCCCATCACAGCATCAGTAACAGATATACAGTATTCAGTAACA
*
83809 ATGTCCTACCTAACCAGCCTCTACACACCATCTCCGTCCAACCCTACACTCCATGTGGGATTAAA
261 ATGTCCTACCCAACCAGCCTCTACACACCATCTCCGTCCAACCCTACACTCCATGTGGGATTAAA
*
83874 TCAACCCACCCATCCTTACACTCCAGGTAGTACCGAATGCGGCATAACACAGTAATTTGCAGCTG
326 TCAACCCACCCATCCTTACACTCCAGGTAGTACCGAATGCGGCATAAAACAGTAATTTGCAGCTG
*
83939 AGTTGCCAGTAT
391 AGCTGCCAGTAT
83951 ATGAAAATCCAGAACCATGGTCACCGTTGAGTCCTCCGTCGCACCAATCCATCTAGGTCTGGAGA
1 ATGAAAATCCAGAACCATGGTCACCGTTGAGTCCTCCGTCGCACCAATCCATCTAGGTCTGGAGA
*
84016 TTACCTATGCATATTCAATAGAAGGGGGTGAGTTTACATAAACTCAGTGTAATCCCACAAAAACA
66 TTACCTATGCATATTCAACAGAAGGGGGTGAGTTTACATAAACTCAGTGTAATCCCACAAAAACA
*
84081 AACAAACAG-AATCATAATGCACAGTCAGAAGTGGTCTTGGGCCTAAGCCCTTTTTCAGTATCAG
131 AACAAACAGCAATCATAATGCACAGTCAGAAGCGGTCTTGGGCCTAAGCCC-TTTTCAGTATCAG
* *
84145 TATCAGTTTGCACAAGGGCCTTAGCCCATTACAGCATCAGTAACCGATATACAGTATTCAGTAAC
195 TATCAGTTTGCACAAGGGCCTTAGCCCATCACAGCATCAGTAACAGATATACAGTATTCAGTAAC
*
84210 AATGTCCTACCCAACCAGCCTCTACACACCATCTCCGTCCAACCCTACACTTCATGTGGGATTAA
260 AATGTCCTACCCAACCAGCCTCTACACACCATCTCCGTCCAACCCTACACTCCATGTGGGATTAA
*
84275 ATCAACCCACCCATCCTTACACTCCAGGTAGTACCGAATGCGGCATAAAATAGTAATTTGCAGCT
325 ATCAACCCACCCATCCTTACACTCCAGGTAGTACCGAATGCGGCATAAAACAGTAATTTGCAGCT
84340 GAGCTGCCAGTAT
390 GAGCTGCCAGTAT
84353 AT
1 AT
84355 TAGGCTTAAG
Statistics
Matches: 392, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
401 40 0.10
402 352 0.90
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (402 bp):
ATGAAAATCCAGAACCATGGTCACCGTTGAGTCCTCCGTCGCACCAATCCATCTAGGTCTGGAGA
TTACCTATGCATATTCAACAGAAGGGGGTGAGTTTACATAAACTCAGTGTAATCCCACAAAAACA
AACAAACAGCAATCATAATGCACAGTCAGAAGCGGTCTTGGGCCTAAGCCCTTTTCAGTATCAGT
ATCAGTTTGCACAAGGGCCTTAGCCCATCACAGCATCAGTAACAGATATACAGTATTCAGTAACA
ATGTCCTACCCAACCAGCCTCTACACACCATCTCCGTCCAACCCTACACTCCATGTGGGATTAAA
TCAACCCACCCATCCTTACACTCCAGGTAGTACCGAATGCGGCATAAAACAGTAATTTGCAGCTG
AGCTGCCAGTAT
Found at i:86702 original size:30 final size:30
Alignment explanation
Indices: 86655--86712 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
86645 TAGTGTAACT
86655 ATTATAAAAAAAAAATTTAAT-CTCTAAGG
1 ATTATAAAAAAAAAATTTAATCCTCTAAGG
** *
86684 ATTATAGAAAAATGAATTTACTCCTCTAA
1 ATTATA-AAAAAAAAATTTAATCCTCTAA
86713 ATAAAAAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 12 0.50
31 6 0.25
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (30 bp):
ATTATAAAAAAAAAATTTAATCCTCTAAGG
Found at i:92150 original size:42 final size:43
Alignment explanation
Indices: 92095--92185 Score: 166
Period size: 42 Copynumber: 2.1 Consensus size: 43
92085 TTATTTTAAC
92095 TCTTTGATGTCATTTATACTTCTATACAACTTCCCATTTCTT-
1 TCTTTGATGTCATTTATACTTCTATACAACTTCCCATTTCTTA
*
92137 TCTTTGATGTCATTTATACTTCTATACAACTTCTCATTTCTTA
1 TCTTTGATGTCATTTATACTTCTATACAACTTCCCATTTCTTA
92180 TCTTTG
1 TCTTTG
92186 GGTTCCTAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 41 0.87
43 6 0.13
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.52
Consensus pattern (43 bp):
TCTTTGATGTCATTTATACTTCTATACAACTTCCCATTTCTTA
Found at i:100099 original size:2 final size:2
Alignment explanation
Indices: 100092--100119 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
100082 TTAAGTTTTC
100092 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
100120 CTTTTTACAT
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:100607 original size:73 final size:71
Alignment explanation
Indices: 100489--100630 Score: 216
Period size: 73 Copynumber: 2.0 Consensus size: 71
100479 TCTTTTCAAA
*
100489 CTCAAGTTTTAAACAGTCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGG-CATGATCC
1 CTCAAGTTTTAAACAGTCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGTC-TGAT-C
100553 CCTTTTTC
64 CCTTTTTC
*
100561 CTCAAGTTTTTAAAC-GATCTTGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGTCTGATC
1 CTCAAG-TTTTAAACAG-TCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGTCTGATC
100625 CCTTTT
64 CCTTTT
100631 CTAAACCCTA
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
72 14 0.22
73 50 0.77
74 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (71 bp):
CTCAAGTTTTAAACAGTCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGTCTGATCCC
TTTTTC
Found at i:103056 original size:60 final size:60
Alignment explanation
Indices: 102930--103059 Score: 138
Period size: 60 Copynumber: 2.2 Consensus size: 60
102920 TTTAATGGTC
* * * *
102930 GTTCATATAAAAATCAAATCTTTCAAAATGGTCAAATAATAGTCTAATCTTTATAAAAGT
1 GTTCAAATAAAAACCAAATCTTTCAAAATGGTCAAATAAGAGCCTAATCTTTATAAAAGT
** * * * *
102990 ACTCAAATAAAGACCAAATCTTTCAAAATGTTTAAATAAGA-CCTAA-CTTTTTTCAAAAGT
1 GTTCAAATAAAAACCAAATCTTTCAAAATGGTCAAATAAGAGCCTAATC-TTTAT-AAAAGT
103050 GTTCAAATAA
1 GTTCAAATAA
103060 GGGCTTTTCA
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
58 1 0.02
59 8 0.14
60 47 0.84
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (60 bp):
GTTCAAATAAAAACCAAATCTTTCAAAATGGTCAAATAAGAGCCTAATCTTTATAAAAGT
Found at i:106637 original size:522 final size:522
Alignment explanation
Indices: 105653--106696 Score: 2063
Period size: 522 Copynumber: 2.0 Consensus size: 522
105643 AAATTGATGA
105653 ATAACAAGGGAAAGAGAAGAAAGAAGAAAGAACCCAAAATAAGATATGACAATGTTGACCTCTTA
1 ATAACAAGGGAAAGAGAAGAAAGAAGAAAGAACCCAAAATAAGATATGACAATGTTGACCTCTTA
105718 AAATGTAAATTAAATTTTCAAGAAATCAAGTCTATAAAATAGGAGAAAGAATGATAAAAGAAAAT
66 AAATGTAAATTAAATTTTCAAGAAATCAAGTCTATAAAATAGGAGAAAGAATGATAAAAGAAAAT
105783 AAAACCCTAAAACGTATAGGGAAGAAAAAAATTCGAAAACCATATATCTAGATTCAAGAACTCAA
131 AAAACCCTAAAACGTATAGGGAAGAAAAAAATTCGAAAACCATATATCTAGATTCAAGAACTCAA
105848 AGGATAACGAGAGTGAAAAGCAAAAAGTTGTGTATTAAGACTGTAATACTGAGGTGTTAAAGTTA
196 AGGATAACGAGAGTGAAAAGCAAAAAGTTGTGTATTAAGACTGTAATACTGAGGTGTTAAAGTTA
105913 AAACCCGAGCTTGACGACTTATTTTATTATAAAAATATTAAAGTAATATTATATTACATATATTT
261 AAACCCGAGCTTGACGACTTATTTTATTATAAAAATATTAAAGTAATATTATATTACATATATTT
105978 TATAATTGATTTAAGTAAAAAAATTTATTACACAACAGTAATTAAAATAGTAATTTAGATAGATC
326 TATAATTGATTTAAGTAAAAAAATTTATTACACAACAGTAATTAAAATAGTAATTTAGATAGATC
106043 TTGAAATTTGTAAAATCTATCCAACACTACTACTTTTTTTTTTTAGAATTTTTATACAGTTTCAA
391 TTGAAATTTGTAAAATCTATCCAACACTACTACTTTTTTTTTTTAGAATTTTTATACAGTTTCAA
106108 TAAAATTAATTATTATATAAACAACAATAATCAAAATATTTGTAGACTCAAATGATAAATTAATA
456 TAAAATTAATTATTATATAAACAACAATAATCAAAATATTTGTAGACTCAAATGATAAATTAATA
106173 TT
521 TT
*
106175 ATAACAAGTGAAAGAGAAGAAAGAAGAAAGAACCCAAAATAAGATATGACAATGTTGACCTCTTA
1 ATAACAAGGGAAAGAGAAGAAAGAAGAAAGAACCCAAAATAAGATATGACAATGTTGACCTCTTA
106240 AAATGTAAATTAAATTTTCAAGAAATCAAGTCTATAAAATAGGAGAAAGAATGATAAAAGAAAAT
66 AAATGTAAATTAAATTTTCAAGAAATCAAGTCTATAAAATAGGAGAAAGAATGATAAAAGAAAAT
106305 AAAACCCTAAAACGTATAGGGAAGAAAAAAATTCGAAAACCATATATCTAGATTCAAGAACTCAA
131 AAAACCCTAAAACGTATAGGGAAGAAAAAAATTCGAAAACCATATATCTAGATTCAAGAACTCAA
106370 AGGATAACGAGAGTGAAAAGCAAAAAGTTGTGTATTAAGACTGTAATACTGAGGTGTTAAAGTTA
196 AGGATAACGAGAGTGAAAAGCAAAAAGTTGTGTATTAAGACTGTAATACTGAGGTGTTAAAGTTA
106435 AAACCCGAGCTTGACGACTTATTTTATTATAAAAATATTAAAGTAATATTATATTACATATATTT
261 AAACCCGAGCTTGACGACTTATTTTATTATAAAAATATTAAAGTAATATTATATTACATATATTT
106500 TATAATTGATTTAAGTAAAAAAATTTATTACACAACAGTAATTAAAATAGTAATTTAGATTAGAT
326 TATAATTGATTTAAGTAAAAAAATTTATTACACAACAGTAATTAAAATAGTAATTTAGA-TAGAT
106565 CTTG-AATTTGTAAAATCTATCCAACACTACTACTTTTTTTTTTTAGAATTTTTATACAGTTTCA
390 CTTGAAATTTGTAAAATCTATCCAACACTACTACTTTTTTTTTTTAGAATTTTTATACAGTTTCA
106629 ATAAAATTAATTATTATATAAACAACAATAATCAAAATATTTGTAGACTCAAATGATAAATTAAT
455 ATAAAATTAATTATTATATAAACAACAATAATCAAAATATTTGTAGACTCAAATGATAAATTAAT
106694 ATT
520 ATT
106697 TATTTATAAA
Statistics
Matches: 520, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
522 511 0.98
523 9 0.02
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (522 bp):
ATAACAAGGGAAAGAGAAGAAAGAAGAAAGAACCCAAAATAAGATATGACAATGTTGACCTCTTA
AAATGTAAATTAAATTTTCAAGAAATCAAGTCTATAAAATAGGAGAAAGAATGATAAAAGAAAAT
AAAACCCTAAAACGTATAGGGAAGAAAAAAATTCGAAAACCATATATCTAGATTCAAGAACTCAA
AGGATAACGAGAGTGAAAAGCAAAAAGTTGTGTATTAAGACTGTAATACTGAGGTGTTAAAGTTA
AAACCCGAGCTTGACGACTTATTTTATTATAAAAATATTAAAGTAATATTATATTACATATATTT
TATAATTGATTTAAGTAAAAAAATTTATTACACAACAGTAATTAAAATAGTAATTTAGATAGATC
TTGAAATTTGTAAAATCTATCCAACACTACTACTTTTTTTTTTTAGAATTTTTATACAGTTTCAA
TAAAATTAATTATTATATAAACAACAATAATCAAAATATTTGTAGACTCAAATGATAAATTAATA
TT
Found at i:118786 original size:43 final size:43
Alignment explanation
Indices: 118719--119048 Score: 317
Period size: 43 Copynumber: 7.3 Consensus size: 43
118709 TTTTTGAAAT
*
118719 AAACGCCGCTATAGACCA-TGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
*
118762 AAACGCCGCTAAAGACCAGTACCTTTAGCGGCGCTATT-CCAC
1 AAACGCCGCTAAAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
*
118804 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
* *
118847 AAACGCCGCTATAGACCAATACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
* * *
118890 AAACGCCGCTATAGACCATGACCTATAGCGGTCTATAGCGGCGCTTTTTCCCGC
1 AAACGCCGCTAAAGACCA-G-----TA-C---CTTTAGCGGCGC-TTTTCCCAC
* * * *
118944 AAACGCTGCTAAAGA-CAATGACCTTTAGCGGCGCTTTTCACAA
1 AAACGCCGCTAAAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
* * *
118987 AAACGCCGCTAAAAACTTAGACCA-TGACCTTTAGCGACGCTTTTCACAA
1 AAACGCCGCT---AA---AGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
119036 AAACGCCGCTAAA
1 AAACGCCGCTAAA
119049 AACTTATCTT
Statistics
Matches: 249, Mismatches: 17, Indels: 42
0.81 0.06 0.14
Matches are distributed among these distances:
42 40 0.16
43 114 0.46
44 12 0.05
46 4 0.02
47 2 0.01
48 1 0.00
49 39 0.16
50 3 0.01
53 13 0.05
54 21 0.08
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
Found at i:118863 original size:85 final size:86
Alignment explanation
Indices: 118719--119048 Score: 369
Period size: 85 Copynumber: 3.7 Consensus size: 86
118709 TTTTTGAAAT
*
118719 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGTAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATAC
118784 CTTTAGCGGCGCTATT-CCAC
66 CTTTAGCGGCGCTATTCCCAC
*
118804 AAACGCCGCTATAGACCA-GTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCAATA
1 AAACGCCGCTATAGACCATG-ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATA
*
118868 CCTTTAGCGGCGCTTTTCCCAC
65 CCTTTAGCGGCGCTATTCCCAC
* *
118890 AAACGCCGCTATAGACCATGACCTATAGCGGTCTATAGCGGCGCTTTTTCCCGCAAACGCTGCTA
1 AAACGCCGCTATAGACCATGA-C-----C--T-T-TAGCGGCGC-TTTTCCCACAAACGCCGCTA
* * *
118955 AAGA-CAATGACCTTTAGCGGCGCTTTTCACAA
55 AAGACCAAT-ACCTTTAGCGGCGCTATTCCCAC
* * *
118987 AAACGCCGCTAAAAACTTAGACCATGACCTTTAGCGACGCTTTTCACAAAAACGCCGCTAAA
1 AAACGCCGCT----A--TAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
119049 AACTTATCTT
Statistics
Matches: 211, Mismatches: 13, Indels: 35
0.81 0.05 0.14
Matches are distributed among these distances:
84 1 0.00
85 76 0.36
86 23 0.11
87 2 0.01
92 19 0.09
93 8 0.04
94 2 0.01
95 2 0.01
96 13 0.06
97 53 0.25
101 1 0.00
102 1 0.00
103 10 0.05
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATAC
CTTTAGCGGCGCTATTCCCAC
Found at i:118948 original size:54 final size:53
Alignment explanation
Indices: 118872--118974 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 53
118862 CCAATACCTT
* *
118872 TAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCATGACCTATAGCGGTCTA
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAATGACCTATAGCGGTCTA
* * *
118925 TAGCGGCGCTTTTTCCCGCAAACGCTGCTAAAGACAATGACCTTTAGCGG
1 TAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACAATGACCTATAGCGG
118975 CGCTTTTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 9 0.20
54 35 0.80
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.23
Consensus pattern (53 bp):
TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAATGACCTATAGCGGTCTA
Found at i:119371 original size:43 final size:43
Alignment explanation
Indices: 119323--119417 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
119313 ACATATGCAA
* * * *
119323 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
119366 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
119409 GGTAATAAA
1 GGTAATAAA
119418 GTATCCTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:125193 original size:7 final size:7
Alignment explanation
Indices: 125177--125218 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
125167 TTAAATCACT
125177 AACCCCA
1 AACCCCA
*
125184 AACTCCA
1 AACCCCA
125191 AACCCCA
1 AACCCCA
*
125198 AACCCCT
1 AACCCCA
*
125205 AA-CCCT
1 AACCCCA
125211 AACCCCA
1 AACCCCA
125218 A
1 A
125219 CGCTGCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.40, C:0.52, G:0.00, T:0.07
Consensus pattern (7 bp):
AACCCCA
Found at i:125762 original size:41 final size:41
Alignment explanation
Indices: 125217--125742 Score: 1000
Period size: 41 Copynumber: 12.8 Consensus size: 41
125207 CCCTAACCCC
125217 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125258 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125299 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125340 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125381 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125422 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125463 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125504 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125545 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125586 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125627 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
125668 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCTCCA-AA
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTC-CCAGAA
* * * *
125709 AACGCCGCTAAAGACCCGAGAATTAGCGCCGCTT
1 AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTT
125743 TTATAAAAAC
Statistics
Matches: 480, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
41 477 0.99
42 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (41 bp):
AACGCTGCTAAAGACCTGAGCATTAGCGGCGCTTCCCAGAA
Found at i:134997 original size:21 final size:23
Alignment explanation
Indices: 134971--135012 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
134961 GGATGTATAA
134971 AAAATAAAT-AAAAT-ATTTTAT
1 AAAATAAATGAAAATAATTTTAT
134992 AAAATAAATGAAAATAATTTT
1 AAAATAAATGAAAATAATTTT
135013 TATTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATAAATGAAAATAATTTTAT
Found at i:138682 original size:15 final size:15
Alignment explanation
Indices: 138662--138695 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
138652 TAGAATTACA
138662 AAAAATTAAGATATT
1 AAAAATTAAGATATT
**
138677 AAAAATTTTGATATT
1 AAAAATTAAGATATT
138692 AAAA
1 AAAA
138696 CAAATTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
AAAAATTAAGATATT
Found at i:142448 original size:24 final size:24
Alignment explanation
Indices: 142403--142448 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
142393 ATACCTCTAA
*
142403 AATAATAGCAAAATTAATAATAAT
1 AATAATAGCAAAATTAACAATAAT
*
142427 AATAATAG-AAAGTTATACAATA
1 AATAATAGCAAAATTA-ACAATA
142449 TTCAAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (24 bp):
AATAATAGCAAAATTAACAATAAT
Found at i:163299 original size:347 final size:348
Alignment explanation
Indices: 162664--163356 Score: 1370
Period size: 347 Copynumber: 2.0 Consensus size: 348
162654 TTTTAGTCTA
162664 TCTACCTTAATTGGTTAGTCTCCTCTTTATTTCCAAGAATTTATCATTTTTTTACTTTTTCAGAT
1 TCTACCTTAATTGGTTAGTCTCCTCTTTATTTCCAAGAATTTATCATTTTTTTACTTTTTCAGAT
162729 CTAATTATTAACACTCTTGAAATTATTTTATTAAATTCAAGTTTATTATAATGTCCTATTGTTAA
66 CTAATTATTAACACTCTTGAAATTATTTTATTAAATTCAAGTTTATTATAATGTCCTATTGTTAA
162794 TTATATTGTTACCAAGTGAACTTTTTTATTTTAAAATGTCACATCAATAAATTTAACATTATGTA
131 TTATATTGTTACCAAGTGAACTTTTTTATTTTAAAATGTCACATCAATAAATTTAACATTATGTA
162859 TTTTTTTAAGAAATAAACTATATTAGGATCATCCTAAAAAGTATAGTTTTTAGGCACCAATAAAC
196 TTTTTTTAAGAAATAAACTATATTAGGATCATCCTAAAAAGTATAGTTTTTAGGCACCAATAAAC
162924 GTCGTTAAATTTTAAAGATAACGAAGTATTATTATACGCTCATCTATATCTAATATTTTCTCTCA
261 GTCGTTAAATTTTAAAGATAACGAAGTATTATTATACGCTCATCTATATCTAATATTTTCTCTCA
*
162989 CTTAATTTAA-TTTAATTAAAAT
326 CTAAATTTAATTTTAATTAAAAT
163011 TCTACCTTAATTGGTTAGTCTCCTCTTTATTTCCAAGAATTTATCATTTTTTTACTTTTTCAGAT
1 TCTACCTTAATTGGTTAGTCTCCTCTTTATTTCCAAGAATTTATCATTTTTTTACTTTTTCAGAT
163076 CTAATTATTAACACTCTTGAAATTATTTTATTAAATTCAAGTTTATTATAATGTCCTATTGTTAA
66 CTAATTATTAACACTCTTGAAATTATTTTATTAAATTCAAGTTTATTATAATGTCCTATTGTTAA
163141 TTATATTGTTACCAAGTGAACTTTTTTATTTTAAAATGTCACATCAATAAATTTAACATTATGTA
131 TTATATTGTTACCAAGTGAACTTTTTTATTTTAAAATGTCACATCAATAAATTTAACATTATGTA
163206 TTTTTTTAAGAAATAAACTATATTAGGATCATCCTAAAAAGTATAGTTTTTAGGCACCAATAAAC
196 TTTTTTTAAGAAATAAACTATATTAGGATCATCCTAAAAAGTATAGTTTTTAGGCACCAATAAAC
163271 GTCGTTAAATTTTAAAGATAACGAAGTATTATTATACGCTCATCTATATCTAATATTTTCTCTCA
261 GTCGTTAAATTTTAAAGATAACGAAGTATTATTATACGCTCATCTATATCTAATATTTTCTCTCA
163336 CTAAATTTAATTTTAATTAAA
326 CTAAATTTAATTTTAATTAAA
163357 TTACTTAAAA
Statistics
Matches: 344, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
347 334 0.97
348 10 0.03
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (348 bp):
TCTACCTTAATTGGTTAGTCTCCTCTTTATTTCCAAGAATTTATCATTTTTTTACTTTTTCAGAT
CTAATTATTAACACTCTTGAAATTATTTTATTAAATTCAAGTTTATTATAATGTCCTATTGTTAA
TTATATTGTTACCAAGTGAACTTTTTTATTTTAAAATGTCACATCAATAAATTTAACATTATGTA
TTTTTTTAAGAAATAAACTATATTAGGATCATCCTAAAAAGTATAGTTTTTAGGCACCAATAAAC
GTCGTTAAATTTTAAAGATAACGAAGTATTATTATACGCTCATCTATATCTAATATTTTCTCTCA
CTAAATTTAATTTTAATTAAAAT
Found at i:173166 original size:7 final size:8
Alignment explanation
Indices: 173146--173172 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
173136 TTGAATCAGG
173146 ATTTTTTA
1 ATTTTTTA
173154 ATTTTTTA
1 ATTTTTTA
173162 ATTTTTTA
1 ATTTTTTA
173170 ATT
1 ATT
173173 AAATTGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTA
Found at i:174543 original size:16 final size:18
Alignment explanation
Indices: 174504--174537 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
174494 AAAGTTTATA
174504 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
174521 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
174538 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:175327 original size:119 final size:119
Alignment explanation
Indices: 175116--175483 Score: 736
Period size: 119 Copynumber: 3.1 Consensus size: 119
175106 AAACCGAAAA
175116 AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
1 AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
175181 GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
66 GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
175235 AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
1 AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
175300 GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
66 GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
175354 AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
1 AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
175419 GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
66 GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
175473 AATTCGGTTAA
1 AATTCGGTTAA
175484 TGTTATTTCG
Statistics
Matches: 249, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 249 1.00
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (119 bp):
AATTCGGTTAACCGACCGAATTCGGTTAATCGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCG
GTTAATTATTTTTTGATTTTTCGGTTAACGGTTAAAGATTTTGAAAGGTCGGTT
Found at i:177028 original size:15 final size:17
Alignment explanation
Indices: 176997--177028 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
176987 GTCCTGTTTG
176997 TTCTTAATTTCATAAAT
1 TTCTTAATTTCATAAAT
177014 TTCTT-ATTT-ATAAAT
1 TTCTTAATTTCATAAAT
177029 CTTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCTTAATTTCATAAAT
Found at i:177885 original size:28 final size:28
Alignment explanation
Indices: 177854--177914 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
177844 CTCGAAGTTC
**
177854 AAAACCTCAAATCCGCAATTTGAAATTT
1 AAAACCTCAAATCCAAAATTTGAAATTT
* *
177882 AAAACTTCAAATCTAAAATTTGAAATTT
1 AAAACCTCAAATCCAAAATTTGAAATTT
177910 AAAAC
1 AAAAC
177915 TTAAAACCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAACCTCAAATCCAAAATTTGAAATTT
Found at i:177893 original size:14 final size:14
Alignment explanation
Indices: 177876--177916 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
177866 CCGCAATTTG
177876 AAATTTAAAACTTC
1 AAATTTAAAACTTC
* * *
177890 AAATCTAAAATTTG
1 AAATTTAAAACTTC
177904 AAATTTAAAACTT
1 AAATTTAAAACTT
177917 AAAACCCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATTTAAAACTTC
Found at i:177927 original size:28 final size:28
Alignment explanation
Indices: 177870--177927 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
177860 TCAAATCCGC
* * *
177870 AATTTGAAATTTAAAACTTCAAATCTAA
1 AATTTGAAATTTAAAACTTAAAACCCAA
177898 AATTTGAAATTTAAAACTTAAAACCCAA
1 AATTTGAAATTTAAAACTTAAAACCCAA
177926 AA
1 AA
177928 AAAATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (28 bp):
AATTTGAAATTTAAAACTTAAAACCCAA
Found at i:178860 original size:29 final size:29
Alignment explanation
Indices: 178826--178881 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
178816 CGCGGAAAAT
178826 GGCCCATTCCGGTAAATAATT-AAAAAACC
1 GGCCCATTCCGGTAAAT-ATTGAAAAAACC
**
178855 GGCCCATTTTGGTAAATATTGAAAAAA
1 GGCCCATTCCGGTAAATATTGAAAAAA
178882 AGGGCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATATTGAAAAAACC
Found at i:184955 original size:22 final size:22
Alignment explanation
Indices: 184927--184971 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
184917 CTACAAGGGG
184927 TATGCTTTACTTTATTTATCTA
1 TATGCTTTACTTTATTTATCTA
184949 TATGCTTTACTTTATTTATCTA
1 TATGCTTTACTTTATTTATCTA
184971 T
1 T
184972 CTTTCGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.60
Consensus pattern (22 bp):
TATGCTTTACTTTATTTATCTA
Found at i:196931 original size:23 final size:23
Alignment explanation
Indices: 196892--196936 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
196882 TTAAAATCTA
*
196892 AAAAATAGAAAGATTAATTTTCT
1 AAAAATAGAAAGATTAAATTTCT
*
196915 AAAAATA-AAAGGCTTAAATTTC
1 AAAAATAGAAA-GATTAAATTTC
196937 AAATGCACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (23 bp):
AAAAATAGAAAGATTAAATTTCT
Found at i:202757 original size:21 final size:18
Alignment explanation
Indices: 202733--202778 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
202723 ATATAAAAAC
202733 TATAATATTTTTATGAATAAA
1 TATAATATTTTTAT-AAT--A
*
202754 TATATTATTTTTATAATA
1 TATAATATTTTTATAATA
202772 TATAATA
1 TATAATA
202779 CAGATACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 7 0.30
20 3 0.13
21 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATAATATTTTTATAATA
Found at i:202771 original size:20 final size:21
Alignment explanation
Indices: 202724--202771 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
202714 TAAGTTATGA
202724 TATAA-AAACTATAATATTTT
1 TATAATAAACTATAATATTTT
*
202744 TATGAATAAA-TATATTATTTT
1 TAT-AATAAACTATAATATTTT
202765 TATAATA
1 TATAATA
202772 TATAATACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TATAATAAACTATAATATTTT
Found at i:206059 original size:24 final size:24
Alignment explanation
Indices: 206031--206082 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
206021 TTCGTAGGTC
* *
206031 AAATAAATTATGCTAATAAATATT
1 AAATAAATTATACTAATAAATACT
*
206055 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
206079 AAAT
1 AAAT
206083 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:206507 original size:18 final size:17
Alignment explanation
Indices: 206484--206517 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
206474 TCATATTATT
206484 AATAATTATACATTTAAA
1 AATAATTATA-ATTTAAA
206502 AATAATTATAATTTAA
1 AATAATTATAATTTAA
206518 TAGAAGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATTATAATTTAAA
Found at i:222778 original size:91 final size:91
Alignment explanation
Indices: 222636--222840 Score: 256
Period size: 91 Copynumber: 2.3 Consensus size: 91
222626 CACTCAAGTT
* * * * * *
222636 TTTTCAAAAAAAGCAATTAAGTCCCTGTTTTTTTTTTTGCACTCATTTGGGTACTTGAACTTTCA
1 TTTTCAAAAAAAGCAATTAAGCCCCTGCTCTTTTTTTTGCAATCAATTGGGTACTTGAACTTCCA
222701 AAATG-TATCAAAAAAGCCCTTAAACC
66 AAATGCT-TCAAAAAAGCCCTTAAACC
222727 TTTTCAAGAAAAAGCAATTAAGCCCCTGCTCTTTTTTTT-CAATCAATTGGGTACTTGAACTTCC
1 TTTTCAA-AAAAAGCAATTAAGCCCCTGCTCTTTTTTTTGCAATCAATTGGGTACTTGAACTTCC
* ***
222791 AAAATGCTTC-AAAAAGACCCTCAATTTT
65 AAAATGCTTCAAAAAAG-CCCTTAA-ACC
222819 TTTTC-AAAAAAGCAATTAAGCC
1 TTTTCAAAAAAAGCAATTAAGCC
222841 TCTGATTTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
90 22 0.22
91 44 0.44
92 34 0.34
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (91 bp):
TTTTCAAAAAAAGCAATTAAGCCCCTGCTCTTTTTTTTGCAATCAATTGGGTACTTGAACTTCCA
AAATGCTTCAAAAAAGCCCTTAAACC
Found at i:223156 original size:20 final size:20
Alignment explanation
Indices: 223131--223187 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
223121 TACAATAATT
223131 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
223151 TTTAT-ATTTCTTTA-GATT
1 TTTATAATTTTTTTACGAAA
*
223169 TTGTATAATTTTCTTACGA
1 TT-TATAATTTTTTTACGA
223188 CTTTATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 12 0.41
21 2 0.07
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:223411 original size:88 final size:89
Alignment explanation
Indices: 223319--223525 Score: 245
Period size: 88 Copynumber: 2.3 Consensus size: 89
223309 GTAAAAGCAT
* * * * *
223319 GGGCTTAATTGTTTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAATTCAATTAC
1 GGGCTTAATTGTTTTTTTTGAAAAATTTTGAGGGTATTTTTAATACATTCTGAAAATTCAAGTAC
* *
223384 CCAATTGAGTG-AAAAAAAAGTAG
66 CCAATTGAGTGAAAAAAAAAGGAA
* * * * *
223407 GGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGTATTTTTAATACGTTCTGAAAATTCAAGTGC
1 GGGCTTAATTGTTTTTTTTGAAAAATTTTGAGGGTATTTTTAATACATTCTGAAAATTCAAGTAC
**
223472 TTAATTGAGTGAAAAAAAAAGGAA
66 CCAATTGAGTGAAAAAAAAAGGAA
* *
223496 GGGCTTAATTACTTTTCTTTTTAAAAATTT
1 GGGCTTAATT-GTTTT-TTTTGAAAAATTT
223526 GAGAACTTTT
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
88 64 0.66
89 20 0.21
90 3 0.03
91 10 0.10
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (89 bp):
GGGCTTAATTGTTTTTTTTGAAAAATTTTGAGGGTATTTTTAATACATTCTGAAAATTCAAGTAC
CCAATTGAGTGAAAAAAAAAGGAA
Found at i:224776 original size:36 final size:36
Alignment explanation
Indices: 224730--224810 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
224720 AAGCCGCAAA
*
224730 TTTACATATAAGTT-TATCAAGATTTAATTATATGTG
1 TTTAAATATAA-TTATATCAAGATTTAATTATATGTG
* * *
224766 TTTAAATATAATTATCTCTATATTTAATTATATGTG
1 TTTAAATATAATTATATCAAGATTTAATTATATGTG
*
224802 TTTGAATAT
1 TTTAAATAT
224811 CAAATTGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 2 0.05
36 37 0.95
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.51
Consensus pattern (36 bp):
TTTAAATATAATTATATCAAGATTTAATTATATGTG
Found at i:225031 original size:33 final size:33
Alignment explanation
Indices: 224980--225046 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
224970 ACAAAGTTAG
* *
224980 AAATGATCTAAAACGTAAGTAATCAAAATAAAA
1 AAATAATCTAAAACGTAAGTAACCAAAATAAAA
* *
225013 AAATAATCTAAAATGTAAGTGACCAAAATAAAA
1 AAATAATCTAAAACGTAAGTAACCAAAATAAAA
225046 A
1 A
225047 CGATCTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (33 bp):
AAATAATCTAAAACGTAAGTAACCAAAATAAAA
Found at i:225053 original size:31 final size:32
Alignment explanation
Indices: 224984--225066 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 32
224974 AGTTAGAAAT
* *
224984 GATCTAAAACGTAAGTAATCAAAATAAAAAAAT
1 GATCTAAAACGTAAGTAACCAAAAT-AAAAAAC
* * *
225017 AATCTAAAATGTAAGTGACCAAAAT-AAAAAC
1 GATCTAAAACGTAAGTAACCAAAATAAAAAAC
* *
225048 GATCTAAAACATTAGTAAC
1 GATCTAAAACGTAAGTAAC
225067 TGAATTGAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 19 0.47
33 21 0.52
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.22
Consensus pattern (32 bp):
GATCTAAAACGTAAGTAACCAAAATAAAAAAC
Found at i:230208 original size:21 final size:21
Alignment explanation
Indices: 230182--230237 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
230172 AATAGCAGTG
230182 GCGGTGAGATTA-ATTACTGTA
1 GCGGTGAGATTAGA-TACTGTA
230203 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
230224 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
230238 AACAGTGGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:237282 original size:14 final size:13
Alignment explanation
Indices: 237242--237284 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
237232 TAACAAAAAG
237242 AAAAAAATTAGAA
1 AAAAAAATTAGAA
* *
237255 ATTAGAAATTAGAA
1 A-AAAAAATTAGAA
237269 AAAAAAATTCAGAA
1 AAAAAAATT-AGAA
237283 AA
1 AA
237285 TCTCAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (13 bp):
AAAAAAATTAGAA
Found at i:240152 original size:17 final size:17
Alignment explanation
Indices: 240130--240163 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
240120 ACTTGTTTTC
240130 GCAAATCAGTGTGATAA
1 GCAAATCAGTGTGATAA
240147 GCAAATCAGTGTGATAA
1 GCAAATCAGTGTGATAA
240164 AGAATAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
GCAAATCAGTGTGATAA
Found at i:245848 original size:29 final size:31
Alignment explanation
Indices: 245816--245892 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
245806 TTTAGTTCAG
* *
245816 GTTACATTTTAGTCATTTATGTT-TGA-AAT
1 GTTACATTTTAGTCACTTATGTTATCATAAT
* *
245845 GTTACGTTTTAGTCACTTATGTTATCATGAT
1 GTTACATTTTAGTCACTTATGTTATCATAAT
*
245876 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
245893 GAGCCGTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
30 2 0.05
31 17 0.43
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTATGTTATCATAAT
Found at i:259323 original size:27 final size:28
Alignment explanation
Indices: 259305--259357 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 28
259295 GCGGCACCAG
* * *
259305 TGGTGCCAGTGGCAGAGGCGGCACC-GA
1 TGGTGCCACTGCCACAGGCGGCACCAGA
*
259332 TGGTGCTACTGCCACAGGCGGCACCA
1 TGGTGCCACTGCCACAGGCGGCACCA
259358 ACCCCTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.38, T:0.13
Consensus pattern (28 bp):
TGGTGCCACTGCCACAGGCGGCACCAGA
Found at i:259900 original size:157 final size:155
Alignment explanation
Indices: 259732--260617 Score: 1299
Period size: 155 Copynumber: 5.7 Consensus size: 155
259722 ATAAAATCCG
* *
259732 AAAA-AATGTAAAATAATAAAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGG
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGG
*
259795 AAAAAAATATGAACAAAGGGCCGAAATAAGGGTTATTTTTTGAAATTTATTTAAAAAACACACTA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTT-TTTTTT-AAATTTATTTAAAAAACACACTA
* *
259860 AATTAATAAACTTCAAACATAATGTACT
128 AATTAATACATTTCAAACATAATGTACT
*
259888 AAAATAATGTAAAATAATAAAATTAGAAAATAATATAATTTT-TT-AAAGTAATAAAATCCAAGG
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCC--GG
* ** * *
259951 G-AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAATTTA-AAAAAAAACAGAAGT
64 GAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT-TTAAATTTATTTAAAAAACA-CACT
260014 -AATTAATACATTTCAAACATAATGTACT
127 AAATTAATACATTTCAAACATAATGTACT
* * *
260042 AAAATAATGTAAAATAATAAAA-TACAAAAATAATATATTTTTATTGGAAGTAATAAAATCCAGG
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGG
* * *
260106 AAAAAAATACGAACAAATGGTCGAAATAA-GGTTTTTTTT-AATTTATTTAAAAAACACAGTAAA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAA
*
260169 TTAATATATTTCAAACATAATGTACT
130 TTAATACATTTCAAACATAATGTACT
* * *
260195 AAACTAATGTAAAATAATAAAATTAGGAAATAATATATTTTTATTGAAAGTAATAAAATCGGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGA
* *
260260 AAAAAATACGAACAAAGGGCTGAAATAAGGGGTTTTTTTAAATTTATTTAAAAAACACACTAAAT
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
260325 TAATACATTTCAAACATAATGTACT
131 TAATACATTTCAAACATAATGTACT
* *
260350 AAAATAATGTAAAATAATAAAATTAGAAAATAAAATATTTTTATTGAAAGTAATAAAATCCAGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGA
*
260415 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTGTAAATTTATTTAAAACACACACTAA
66 AAAAAATACGAACAAAGGGCCGAAATAAGGG-TTTTTTT-TAAATTTATTTAAAAAACACACTAA
260480 ATTAATACATTTCAAACATAATGGT-CT
129 ATTAATACATTTCAAACATAAT-GTACT
* * * **
260507 AAACTAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATAGAAAGTAATAAATTTTGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGA
*
260572 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAATTT
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT-TTAAATTT
260618 GTTTTGAAGT
Statistics
Matches: 661, Mismatches: 50, Indels: 38
0.88 0.07 0.05
Matches are distributed among these distances:
152 9 0.01
153 119 0.18
154 92 0.14
155 193 0.29
156 72 0.11
157 172 0.26
158 4 0.01
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (155 bp):
AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGA
AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
TAATACATTTCAAACATAATGTACT
Found at i:260390 original size:308 final size:309
Alignment explanation
Indices: 259732--260617 Score: 1351
Period size: 308 Copynumber: 2.9 Consensus size: 309
259722 ATAAAATCCG
* *
259732 AAAA-AATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCAGGA
*
259796 AAAAAATATGAACAAAGGGCCGAAATAAGGGTTATTTTTTGAAATTTATTTAAAAAACACACTAA
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTT-TTTTTT-AAATTTATTTAAAAAACACACTAA
* * *
259861 ATTAATAAACTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATAA
129 ATTAATAAATTTCAAACATAATGTACTAAACTAATGTAAAATAATAAAATTAGAAAATAATATAT
259926 TTTT-TT-AAAGTAATAAAATCCAAGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
194 TTTTATTGAAAGTAATAAAAT-C-AGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
*
259988 TACTAAATTTAAAAAAAAACAGAAGTAATTAATACATTTCAAACATAATGTACT
257 TA-TAAATTTAAAAAAAAACAGAACTAATTAATACATTTCAAACATAATGTACT
*
260042 AAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGGAAGTAATAAAATCCAGGA
1 AAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCAGGA
* * *
260107 AAAAAATACGAACAAATGGTCGAAATAA-GGTTTTTTTT-AATTTATTTAAAAAACACAGTAAAT
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
* *
260170 TAATATATTTCAAACATAATGTACTAAACTAATGTAAAATAATAAAATTAGGAAATAATATATTT
131 TAATAAATTTCAAACATAATGTACTAAACTAATGTAAAATAATAAAATTAGAAAATAATATATTT
* *
260235 TTATTGAAAGTAATAAAATCGGGGAAAAAAATACGAACAAAGGGCTGAAATAAGGGGTTTTTT-T
196 TTATTGAAAGTAATAAAATCAGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGGTTTTTTAT
** *
260299 AAATTTATTTAAAAAACA-CACTAAATTAATACATTTCAAACATAATGTACT
260 AAATTTA-AAAAAAAACAGAACT-AATTAATACATTTCAAACATAATGTACT
* *
260350 AAAATAATGTAAAATAATAAAATTA-GAAAATAAAATATTTTTATTGAAAGTAATAAAATCCAGG
1 AAAATAATGTAAAATAATAAAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCAGG
*
260414 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTGTAAATTTATTTAAAACACACACTA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGG-TTTTTTT-TAAATTTATTTAAAAAACACACTA
*
260479 AATTAATACATTTCAAACATAATGGT-CTAAACTAATGTAAAATAATAAAATTAGAAAATAATAT
128 AATTAATAAATTTCAAACATAAT-GTACTAAACTAATGTAAAATAATAAAATTAGAAAATAATAT
* * **
260543 ATTTTTATAGAAAGTAATAAATTTTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
192 ATTTTTATTGAAAGTAATAAAATCAGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
260608 TACTAAATTT
257 TA-TAAATTT
260618 GTTTTGAAGT
Statistics
Matches: 529, Mismatches: 32, Indels: 27
0.90 0.05 0.05
Matches are distributed among these distances:
307 99 0.19
308 151 0.29
309 32 0.06
310 15 0.03
311 92 0.17
312 131 0.25
313 9 0.02
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (309 bp):
AAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCAGGA
AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
TAATAAATTTCAAACATAATGTACTAAACTAATGTAAAATAATAAAATTAGAAAATAATATATTT
TTATTGAAAGTAATAAAATCAGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTATA
AATTTAAAAAAAAACAGAACTAATTAATACATTTCAAACATAATGTACT
Found at i:260555 original size:20 final size:20
Alignment explanation
Indices: 260530--260567 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
260520 ATAATAAAAT
*
260530 TAGAAAATAATATATTTTTA
1 TAGAAAATAATAAATTTTTA
*
260550 TAGAAAGTAATAAATTTT
1 TAGAAAATAATAAATTTT
260568 GGGAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (20 bp):
TAGAAAATAATAAATTTTTA
Found at i:266396 original size:18 final size:19
Alignment explanation
Indices: 266365--266408 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
266355 AAATAAAAAA
*
266365 TTTTATATTATTTTGGTAT
1 TTTTTTATTATTTTGGTAT
*
266384 TTTTTTATT-TTTTTGTAT
1 TTTTTTATTATTTTGGTAT
*
266402 TATTTTA
1 TTTTTTA
266409 GTAAAATACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTTTTATTATTTTGGTAT
Found at i:273946 original size:23 final size:23
Alignment explanation
Indices: 273920--273967 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
273910 TTTTGTACAA
*
273920 TTCTGATTTGAACTTAGATTATT
1 TTCTAATTTGAACTTAGATTATT
*
273943 TTCTAATTTGAATTTAGATTATT
1 TTCTAATTTGAACTTAGATTATT
273966 TT
1 TT
273968 TAAAGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (23 bp):
TTCTAATTTGAACTTAGATTATT
Found at i:275735 original size:21 final size:21
Alignment explanation
Indices: 275610--275774 Score: 115
Period size: 21 Copynumber: 8.0 Consensus size: 21
275600 GTACATCGTT
* *
275610 AACAGAAGCTC-GAA-AGCTA
1 AACAGAAGCTCATAAGAGCTG
*
275629 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * * *
275650 AAC-GAAAACTCATATGAGTTA
1 AACAG-AAGCTCATAAGAGCTG
* *
275671 AACAGAAGCTCACAAGAGCCG
1 AACAGAAGCTCATAAGAGCTG
* *
275692 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
275713 AACAGAAGCTCGA-AAGAGCTG
1 AACAGAAGCTC-ATAAGAGCTG
** * * * *
275734 AATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTG
275755 AACAGAAGCTCGA-AAGAGCT
1 AACAGAAGCTC-ATAAGAGCT
275775 AAACGGAAAG
Statistics
Matches: 109, Mismatches: 30, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
19 11 0.10
20 4 0.04
21 91 0.83
22 3 0.03
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:275783 original size:42 final size:42
Alignment explanation
Indices: 275627--275783 Score: 226
Period size: 42 Copynumber: 3.7 Consensus size: 42
275617 GCTCGAAAGC
* *
275627 TAAACAGAAGCTCGTAAGAGCTGAACGAAAACTCATATGAGT
1 TAAACAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGT
* * *
275669 TAAACAGAAGCTC-ACAAGAGCCGAACAGAAACTCATAAGAGT
1 TAAACAGAAGCTCGA-AAGAGCTGAACGGAAACTCATATGAGT
* *
275711 TGAACAGAAGCTCGAAAGAGCTGAATGGAAACTCATATGAGT
1 TAAACAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGT
*
275753 TAAACAGAAGCTCGAAAGAGCTAAACGGAAA
1 TAAACAGAAGCTCGAAAGAGCTGAACGGAAA
275784 GTAAAATACA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
42 99 0.99
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (42 bp):
TAAACAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGT
Found at i:276675 original size:32 final size:32
Alignment explanation
Indices: 276639--276699 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
276629 CAATGGCAAT
*
276639 ATCCAAAATCTTTAACAAAATCAAAAACTCAA
1 ATCCAAAATCTGTAACAAAATCAAAAACTCAA
276671 ATCCAAAATCTGTAACAAAATCAAAAACT
1 ATCCAAAATCTGTAACAAAATCAAAAACT
276700 AAAGTAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.21
Consensus pattern (32 bp):
ATCCAAAATCTGTAACAAAATCAAAAACTCAA
Found at i:277927 original size:305 final size:305
Alignment explanation
Indices: 277376--277984 Score: 1200
Period size: 305 Copynumber: 2.0 Consensus size: 305
277366 ACTTAGGTTG
277376 CGTTCACTTTGTGTTCTGAAAGTGCTTCTTAAGCCAAAAACAATATAAACAGATAAATTTTCTAT
1 CGTTCACTTTGTGTTCTGAAAGTGCTTCTTAAGCCAAAAACAATATAAACAGATAAATTTTCTAT
277441 TTAGCTTTTCAGGCCAAACTAAAATTTCTAACATGAATCCAACCATACATATGGAAATTTAACCC
66 TTAGCTTTTCAGGCCAAACTAAAATTTCTAACATGAATCCAACCATACATATGGAAATTTAACCC
277506 TCCAAGAATCTTCCAAGTAAACTTGAAAAAATTGAATATATAGTCCGGTCAAACACATCCATATC
131 TCCAAGAATCTTCCAAGTAAACTTGAAAAAATTGAATATATAGTCCGGTCAAACACATCCATATC
*
277571 CGACACCTATTCTCATTCCCGAGTCCGAGTAATATTGGGCAGAACTTGACTGAACTTATTGCTGC
196 CGACACCTATTCTCATTCCCGAGTCCGAGTAACATTGGGCAGAACTTGACTGAACTTATTGCTGC
277636 TGCTGGAGTTGTTGTTGCTGCTATTGCCTCAACTGTTAGAGGCCT
261 TGCTGGAGTTGTTGTTGCTGCTATTGCCTCAACTGTTAGAGGCCT
277681 CGTTCACTTTGTGTTCTGAAAGTGCTTCTTAAGCCAAAAACAATATAAACAGATAAATTTTCTAT
1 CGTTCACTTTGTGTTCTGAAAGTGCTTCTTAAGCCAAAAACAATATAAACAGATAAATTTTCTAT
277746 TTAGCTTTTCAGGCCAAACTAAAATTTCTAACATGAATCCAACCATACATATGGAAATTTAACCC
66 TTAGCTTTTCAGGCCAAACTAAAATTTCTAACATGAATCCAACCATACATATGGAAATTTAACCC
*
277811 TCCAAGAATCTTCCAAGTAAACTTGAAAAAATTGAATATATAGTCCGGTCAAACACATCCGTATC
131 TCCAAGAATCTTCCAAGTAAACTTGAAAAAATTGAATATATAGTCCGGTCAAACACATCCATATC
277876 CGACACCTATTCTCATTCCCGAGTCCGAGTAACATTGGGCAGAACTTGACTGAACTTATTGCTGC
196 CGACACCTATTCTCATTCCCGAGTCCGAGTAACATTGGGCAGAACTTGACTGAACTTATTGCTGC
277941 TGCTGGAGTTGTTGTTGCTGCTATTGCCTCAACTGTTAGAGGCC
261 TGCTGGAGTTGTTGTTGCTGCTATTGCCTCAACTGTTAGAGGCC
277985 CTCTTGTCTA
Statistics
Matches: 302, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 302 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (305 bp):
CGTTCACTTTGTGTTCTGAAAGTGCTTCTTAAGCCAAAAACAATATAAACAGATAAATTTTCTAT
TTAGCTTTTCAGGCCAAACTAAAATTTCTAACATGAATCCAACCATACATATGGAAATTTAACCC
TCCAAGAATCTTCCAAGTAAACTTGAAAAAATTGAATATATAGTCCGGTCAAACACATCCATATC
CGACACCTATTCTCATTCCCGAGTCCGAGTAACATTGGGCAGAACTTGACTGAACTTATTGCTGC
TGCTGGAGTTGTTGTTGCTGCTATTGCCTCAACTGTTAGAGGCCT
Found at i:286667 original size:39 final size:38
Alignment explanation
Indices: 286599--286681 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 38
286589 ACCTCGTCCT
** * *
286599 TGCGAGGTTTACGCGAGCTCCCTCTTGCGACCTTGTCTC
1 TGCGAGGCCTACGCGAGCTCCCTCATGCGACC-TATCTC
*
286638 TGCGAGGCCTACGCGAGCT-CCTCCATGCGAGCTATCTC
1 TGCGAGGCCTACGCGAGCTCCCT-CATGCGACCTATCTC
286676 TGCGAG
1 TGCGAG
286682 CATCTTGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 14 0.37
39 24 0.63
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.25
Consensus pattern (38 bp):
TGCGAGGCCTACGCGAGCTCCCTCATGCGACCTATCTC
Found at i:289751 original size:93 final size:93
Alignment explanation
Indices: 289622--290116 Score: 990
Period size: 93 Copynumber: 5.3 Consensus size: 93
289612 AGACCCTACT
289622 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
1 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
289687 TTTAATAAAAAAATTTAATTATTAAAAA
66 TTTAATAAAAAAATTTAATTATTAAAAA
289715 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
1 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
289780 TTTAATAAAAAAATTTAATTATTAAAAA
66 TTTAATAAAAAAATTTAATTATTAAAAA
289808 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
1 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
289873 TTTAATAAAAAAATTTAATTATTAAAAA
66 TTTAATAAAAAAATTTAATTATTAAAAA
289901 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
1 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
289966 TTTAATAAAAAAATTTAATTATTAAAAA
66 TTTAATAAAAAAATTTAATTATTAAAAA
289994 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
1 TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
290059 TTTAATAAAAAAATTTAATTATTAAAAA
66 TTTAATAAAAAAATTTAATTATTAAAAA
290087 TTTATTAAAAATTAGAAAAAAATATAAAAA
1 TTTATTAAAAATTAGAAAAAAATATAAAAA
290117 TCATAAAAAA
Statistics
Matches: 402, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 402 1.00
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (93 bp):
TTTATTAAAAATTAGAAAAAAATATAAAAAATTAATATCCATAAAATCTATAAATATTGTTAAAT
TTTAATAAAAAAATTTAATTATTAAAAA
Found at i:290114 original size:19 final size:19
Alignment explanation
Indices: 290092--290136 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
290082 AAAAATTTAT
*
290092 TAAAAATTAGAAAAAAATA
1 TAAAAATCAGAAAAAAATA
*
290111 TAAAAATCATAAAAAAATA
1 TAAAAATCAGAAAAAAATA
290130 TATAAAA
1 TA-AAAA
290137 AATTGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
TAAAAATCAGAAAAAAATA
Found at i:290146 original size:10 final size:11
Alignment explanation
Indices: 290082--290139 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
290072 TTTAATTATT
* *
290082 AAAAATTTATT
1 AAAAATATATA
*
290093 AAAAAT-TAGA
1 AAAAATATATA
290103 AAAAA-ATAT-
1 AAAAATATATA
290112 AAAAATCATA-A
1 AAAAAT-ATATA
290123 AAAAATATATA
1 AAAAATATATA
290134 AAAAAT
1 AAAAAT
290140 TGTAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 5 0.13
10 12 0.31
11 22 0.56
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
AAAAATATATA
Found at i:290169 original size:21 final size:21
Alignment explanation
Indices: 290143--290187 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
290133 AAAAAATTGT
* *
290143 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
290164 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
290185 AAA
1 AAA
290188 TATAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:290444 original size:27 final size:30
Alignment explanation
Indices: 290414--290476 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
290404 AAAAAGTTCT
290414 AATTTTTAAT-AAATTT-TAATTTTTTT-A
1 AATTTTTAATAAAATTTATAATTTTTTTGA
*
290441 AATTTTTATTAAAATTTAATAATTTTTTTGA
1 AATTTTTAATAAAATTT-ATAATTTTTTTGA
290472 AATTT
1 AATTT
290477 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.29
28 6 0.19
30 10 0.32
31 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
AATTTTTAATAAAATTTATAATTTTTTTGA
Found at i:290448 original size:17 final size:17
Alignment explanation
Indices: 290413--290446 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
290403 TAAAAAGTTC
290413 TAATTTTTAATAAATTT
1 TAATTTTTAATAAATTT
*
290430 TAATTTTT-TTAAATTT
1 TAATTTTTAATAAATTT
290446 T
1 T
290447 TATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTTAATAAATTT
Found at i:290674 original size:42 final size:41
Alignment explanation
Indices: 290591--290672 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
290581 GAAAAAAGTA
290591 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
1 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
290632 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
1 GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
290673 TGATGCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.44
Consensus pattern (41 bp):
GGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTT
Found at i:290739 original size:129 final size:127
Alignment explanation
Indices: 290505--290740 Score: 330
Period size: 129 Copynumber: 1.8 Consensus size: 127
290495 ATGAGAGCAA
*
290505 GGGCTTAATTGCTTTTTTGAAAAATTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
1 GGGCCTAATTGCTTTTTTGAAAAATTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
** ** *
290570 CAATTGAGTGGGAAAAAAGTAGGGGCCTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTTG
66 CAATTGAGTGCAAAAAAAAAAGGGGCCTAATTAC-TTTTTTGAAGAAGTTTGAGGGTCTTTTG
* *
290633 GGGCCTAATTGCTTTTTTTGAAGAAGTTT-GAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTG
1 GGGCCTAATTGC-TTTTTTGAA-AAATTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
* *
290697 CTCAATTGAGTGCAAAAAAAAAAGAGGGACTTAATTACTTTTTT
64 CCCAATTGAGTGCAAAAAAAAAAG-GGG-CCTAATTACTTTTTT
290741 TTTTATTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
128 11 0.12
129 62 0.66
130 14 0.15
131 7 0.07
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (127 bp):
GGGCCTAATTGCTTTTTTGAAAAATTTGGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
CAATTGAGTGCAAAAAAAAAAGGGGCCTAATTACTTTTTTGAAGAAGTTTGAGGGTCTTTTG
Found at i:292312 original size:26 final size:25
Alignment explanation
Indices: 292283--292346 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
292273 ATCATTCTTC
292283 ATATATTTGAAAACTTATTTTAAAAA
1 ATAT-TTTGAAAACTTATTTTAAAAA
*
292309 ATATTTATGAAAACTTATTTTAAAGA
1 ATATTT-TGAAAACTTATTTTAAAAA
*
292335 ATATTTTTAAAA
1 ATATTTTGAAAA
292347 GTAATTAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 7 0.20
26 28 0.80
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (25 bp):
ATATTTTGAAAACTTATTTTAAAAA
Found at i:292327 original size:14 final size:13
Alignment explanation
Indices: 292288--292329 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
292278 TCTTCATATA
292288 TTTGAAAACTTAT
1 TTTGAAAACTTAT
**
292301 TTT-AAAAAATAT
1 TTTGAAAACTTAT
292313 TTATGAAAACTTAT
1 TT-TGAAAACTTAT
292327 TTT
1 TTT
292330 AAAGAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 9 0.39
13 5 0.22
14 9 0.39
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (13 bp):
TTTGAAAACTTAT
Found at i:297902 original size:26 final size:25
Alignment explanation
Indices: 297873--297936 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
297863 ATCATTCTTC
297873 ATATATTTGAAAACTTATTTTAAAAA
1 ATAT-TTTGAAAACTTATTTTAAAAA
*
297899 ATATTTATGAAAACTTATTTTAAAGA
1 ATATTT-TGAAAACTTATTTTAAAAA
*
297925 ATATTTTTAAAA
1 ATATTTTGAAAA
297937 GTAATTAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 7 0.20
26 28 0.80
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (25 bp):
ATATTTTGAAAACTTATTTTAAAAA
Found at i:297917 original size:14 final size:13
Alignment explanation
Indices: 297878--297919 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
297868 TCTTCATATA
297878 TTTGAAAACTTAT
1 TTTGAAAACTTAT
**
297891 TTT-AAAAAATAT
1 TTTGAAAACTTAT
297903 TTATGAAAACTTAT
1 TT-TGAAAACTTAT
297917 TTT
1 TTT
297920 AAAGAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 9 0.39
13 5 0.22
14 9 0.39
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (13 bp):
TTTGAAAACTTAT
Found at i:302627 original size:64 final size:64
Alignment explanation
Indices: 302548--302685 Score: 240
Period size: 64 Copynumber: 2.2 Consensus size: 64
302538 ACAAAGCAAA
* *
302548 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTACATTGGGCATTAGTTTATAAGGAAC
1 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
302612 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
1 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
**
302676 ACCAATAACA
1 GGCAATAACA
302686 GTATTTTCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (64 bp):
GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGAAAC
Found at i:306774 original size:15 final size:15
Alignment explanation
Indices: 306754--306800 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
306744 GTTGACCCAG
306754 AAAATAATTTTTTTA
1 AAAATAATTTTTTTA
* **
306769 AAAATAGTTGCTTT-
1 AAAATAATTTTTTTA
306783 AAAATATATTTTTTTA
1 AAAATA-ATTTTTTTA
306799 AA
1 AA
306801 TTGTAAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (15 bp):
AAAATAATTTTTTTA
Found at i:306866 original size:18 final size:19
Alignment explanation
Indices: 306843--306882 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
306833 ATTGTAAAAA
306843 TATTTTATA-AAAATAAAT
1 TATTTTATAGAAAATAAAT
306861 TATTTTATAGGAAAATAAAT
1 TATTTTATA-GAAAATAAAT
306881 TA
1 TA
306883 ATCTTTTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TATTTTATAGAAAATAAAT
Found at i:308866 original size:16 final size:16
Alignment explanation
Indices: 308845--308914 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
308835 TTTGGTTCGC
* *
308845 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
308861 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
308877 TATAATGGAATAGAGG
1 TGTAATGGAATAGAGG
308893 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
308909 TGTAAT
1 TGTAAT
308915 AGCATAATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:309086 original size:18 final size:18
Alignment explanation
Indices: 309063--309114 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
309053 TTATTATTAA
309063 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
309081 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
309098 ATATGAATTTACTAAAA
1 ATAT-AATTTAATAAAA
309115 CCATAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 9 0.29
18 19 0.61
19 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:314554 original size:15 final size:14
Alignment explanation
Indices: 314534--314564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
314524 CAATCAACTC
314534 CACATATTCTTATAT
1 CACATATTCTTA-AT
314549 CACATATTCTTAAT
1 CACATATTCTTAAT
314563 CA
1 CA
314565 ACAGAGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (14 bp):
CACATATTCTTAAT
Found at i:314930 original size:29 final size:29
Alignment explanation
Indices: 314891--314953 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
314881 GTCTGGCCCA
314891 TGTGGCCCACACGGCCTAGCACATAGTCG
1 TGTGGCCCACACGGCCTAGCACATAGTCG
* * * *
314920 TGTGGCTCACACGGCCTCGCATATGGTCG
1 TGTGGCCCACACGGCCTAGCACATAGTCG
314949 TGTGG
1 TGTGG
314954 TCGTAAATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (29 bp):
TGTGGCCCACACGGCCTAGCACATAGTCG
Found at i:315263 original size:24 final size:24
Alignment explanation
Indices: 315236--315284 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
315226 AAAACTTTCG
*
315236 AAACAAACCCAAAATTGAATTTAA
1 AAACAAACCCAAAATCGAATTTAA
315260 AAACAAACCCAAAATCGAATTTAA
1 AAACAAACCCAAAATCGAATTTAA
315284 A
1 A
315285 CTTTTCCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.18
Consensus pattern (24 bp):
AAACAAACCCAAAATCGAATTTAA
Found at i:315964 original size:15 final size:15
Alignment explanation
Indices: 315944--315974 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
315934 TAGTTAGATG
*
315944 AATTTGCATGGATTA
1 AATTTGCATGAATTA
315959 AATTTGCATGAATTA
1 AATTTGCATGAATTA
315974 A
1 A
315975 GAGTAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (15 bp):
AATTTGCATGAATTA
Found at i:317242 original size:40 final size:39
Alignment explanation
Indices: 317121--317261 Score: 126
Period size: 40 Copynumber: 3.6 Consensus size: 39
317111 ACTTCGAGTT
* ** *
317121 GATGAGACACTGGGTGTCAATTTACTACTTCGAATTAATTC
1 GATGAGGCACTGGGTGTCAAACTATTACTTCGAATT-A-TC
* **
317162 GATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGTC
1 GATGAGGCACTGGGTGTCAAACTATTACTTCGAATTA-TC
*
317199 GATGAGGCACTGGGTGTCAAACTATTACTTTGAATTATCC
1 GATGAGGCACTGGGTGTCAAACTATTACTTCGAATTAT-C
* * *
317239 GATGAGGTATTGGGTGCCAAACT
1 GATGAGGCACTGGGTGTCAAACT
317262 GGTGTGTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 19 0.23
38 12 0.15
39 3 0.04
40 33 0.40
41 15 0.18
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (39 bp):
GATGAGGCACTGGGTGTCAAACTATTACTTCGAATTATC
Found at i:325750 original size:21 final size:23
Alignment explanation
Indices: 325703--325752 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
325693 ACGAGGCAAC
*
325703 TAAAAT-ATATATTTTTATCTTT
1 TAAAATAAAATATTTTTATCTTT
325725 T-AAATAAAATATTTTT-T-TTT
1 TAAAATAAAATATTTTTATCTTT
325745 TAAAATAA
1 TAAAATAA
325753 CCCTAATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TAAAATAAAATATTTTTATCTTT
Found at i:325901 original size:27 final size:30
Alignment explanation
Indices: 325867--325928 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
325857 TATTATTGAT
325867 TTTTTATTCAT-AAA-A-TTATTTTTATAA
1 TTTTTATTCATAAAACATTTATTTTTATAA
** *
325894 TTTTTATTTTTAAAACATTTTTTTTTATAA
1 TTTTTATTCATAAAACATTTATTTTTATAA
325924 TTTTT
1 TTTTT
325929 GGATATGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.31
28 3 0.10
29 1 0.03
30 16 0.55
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTTATTCATAAAACATTTATTTTTATAA
Found at i:325902 original size:15 final size:15
Alignment explanation
Indices: 325882--325928 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
325872 ATTCATAAAA
325882 TTATTTTTATAATTT
1 TTATTTTTATAATTT
* *
325897 TTATTTTTAAAACATT
1 TTATTTTTATAA-TTT
325913 TT-TTTTTATAATTT
1 TTATTTTTATAATTT
325927 TT
1 TT
325929 GGATATGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTTATAATTT
Found at i:326205 original size:24 final size:25
Alignment explanation
Indices: 326178--326226 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
326168 AACAAACTTA
326178 TGTTTACAAA-TAAACTTAAAAATT
1 TGTTTACAAATTAAACTTAAAAATT
* *
326202 TGTTTATAAATTAAATTTAAAAATT
1 TGTTTACAAATTAAACTTAAAAATT
326227 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
TGTTTACAAATTAAACTTAAAAATT
Found at i:331458 original size:17 final size:17
Alignment explanation
Indices: 331436--331468 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
331426 CACTAACATG
*
331436 AAAATGGAATGACAATA
1 AAAATGCAATGACAATA
331453 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
331469 GTGTACTTAT
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:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:332052 original size:7 final size:7
Alignment explanation
Indices: 332040--332065 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
332030 AATTTATTTT
332040 AAAAATA
1 AAAAATA
332047 AAAAATA
1 AAAAATA
332054 AAAAATA
1 AAAAATA
332061 AAAAA
1 AAAAA
332066 AAGTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:332385 original size:21 final size:21
Alignment explanation
Indices: 332361--332408 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
332351 TCATCTTCAG
*
332361 CAACTTCTTATTCTTCAGCAA
1 CAACTTCTTATTCTGCAGCAA
* *
332382 CAACTTCTTCTTCTGCAGCAG
1 CAACTTCTTATTCTGCAGCAA
332403 CAACTT
1 CAACTT
332409 TCTTCTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (21 bp):
CAACTTCTTATTCTGCAGCAA
Found at i:332392 original size:18 final size:18
Alignment explanation
Indices: 332354--332394 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
332344 TTCTTTTTCA
**
332354 TCTTCAGCAACTTCTTAT
1 TCTTCAGCAACAACTTAT
*
332372 TCTTCAGCAACAACTTCT
1 TCTTCAGCAACAACTTAT
332390 TCTTC
1 TCTTC
332395 TGCAGCAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAGCAACAACTTAT
Found at i:342411 original size:40 final size:40
Alignment explanation
Indices: 342356--342637 Score: 350
Period size: 40 Copynumber: 7.0 Consensus size: 40
342346 TTATTGGATT
*
342356 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTATTCCC-G
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTA-CCCCTG
* * * *
342396 ATTGCACTTACGTGCCCCTATTTGTACTTTGGTACTCATG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * *
342436 GTTGCAGTTCCGTGCCCCTGTTTGTACTTTGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * *
342476 ATTACACTTACGTGCCCCTATTTGTACTTCGGTACTCCTA
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
*
342516 ATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * *
342556 ATTGCACTTATGTGCCCATATTTGTACTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* * * * *
342596 GTTACACTTACGTACCCTTGTTTGCACTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
342636 AT
1 AT
342638 CACACTTTGG
Statistics
Matches: 207, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.00
40 206 1.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (40 bp):
ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:342475 original size:20 final size:20
Alignment explanation
Indices: 342357--342635 Score: 136
Period size: 20 Copynumber: 13.9 Consensus size: 20
342347 TATTGGATTA
*
342357 TTGCACTTAC-GTGCCCCTGT
1 TTGCACTT-CGGTACCCCTGT
* * *
342377 TTGTACTTCGGTATTCCC-GA
1 TTGCACTTCGGTA-CCCCTGT
* *
342397 TTGCACTTAC-GTGCCCCTAT
1 TTGCACTT-CGGTACCCCTGT
* * * * *
342417 TTGTACTTTGGTACTCATGG
1 TTGCACTTCGGTACCCCTGT
* * *
342437 TTGCAGTTCCGTGCCCCTGT
1 TTGCACTTCGGTACCCCTGT
* * *
342457 TTGTACTTTGGTACCCCTGA
1 TTGCACTTCGGTACCCCTGT
* * *
342477 TTACACTTAC-GTGCCCCTAT
1 TTGCACTT-CGGTACCCCTGT
* * **
342497 TTGTACTTCGGTACTCCTAA
1 TTGCACTTCGGTACCCCTGT
** *
342517 TTGCACTTATGTGCCCCTGT
1 TTGCACTTCGGTACCCCTGT
* *
342537 TTGTACTTCGGTACCCCTGA
1 TTGCACTTCGGTACCCCTGT
** * * *
342557 TTGCACTTATGTGCCCATAT
1 TTGCACTTCGGTACCCCTGT
* *
342577 TTGTACTTCGGTACCCCTGG
1 TTGCACTTCGGTACCCCTGT
* *
342597 TTACACTTAC-GTACCCTTGT
1 TTGCACTT-CGGTACCCCTGT
342617 TTGCACTTCGGTACCCCTG
1 TTGCACTTCGGTACCCCTG
342636 ATCACACTTT
Statistics
Matches: 177, Mismatches: 73, Indels: 18
0.66 0.27 0.07
Matches are distributed among these distances:
19 6 0.03
20 166 0.94
21 5 0.03
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCACTTCGGTACCCCTGT
Found at i:342490 original size:80 final size:80
Alignment explanation
Indices: 342357--342644 Score: 389
Period size: 80 Copynumber: 3.6 Consensus size: 80
342347 TATTGGATTA
* *
342357 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTATTCCC-GATTGCACTTACGTGCCCCTATTTGT
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTA-CCCCTGATTACACTTACGTGCCCCTATTTGT
* *
342421 ACTTTGGTACTCATGG
65 ACTTCGGTACTCCTGG
* * *
342437 TTGCAGTTCCGTGCCCCTGTTTGTACTTTGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
**
342502 CTTCGGTACTCCTAA
66 CTTCGGTACTCCTGG
* * * *
342517 TTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGCACTTATGTGCCCATATTTGTA
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
*
342582 CTTCGGTACCCCTGG
66 CTTCGGTACTCCTGG
* * * * *
342597 TTACACTTACGTACCCTTGTTTGCACTTCGGTACCCCTGATCACACTT
1 TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTT
342645 TGGTTCCCCT
Statistics
Matches: 181, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
79 3 0.02
80 178 0.98
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.38
Consensus pattern (80 bp):
TTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTATTTGTA
CTTCGGTACTCCTGG
Done.