Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 83 of 135
Found at i:25614267 original size:6 final size:6
Alignment explanation
Indices: 25614256--25614320 Score: 62
Period size: 6 Copynumber: 10.8 Consensus size: 6
25614246 TTAAATTTGA
* * *
25614256 TTAAAT TTAAAT TTAAA- GTAATT TTAAAT AGGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
25614304 ATAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
25614321 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
5 7 0.15
6 35 0.74
8 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:25614281 original size:17 final size:17
Alignment explanation
Indices: 25614257--25614331 Score: 84
Period size: 17 Copynumber: 4.6 Consensus size: 17
25614247 TAAATTTGAT
25614257 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
* *
25614274 TAATTTTAAA--T-AGG
1 TAAATTTAAATTTAAAG
*
25614288 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
*
25614305 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
*
25614322 TCAATTTAAA
1 TAAATTTAAA
25614332 CTTTTAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 1 0.02
17 36 0.73
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:25614295 original size:31 final size:31
Alignment explanation
Indices: 25614257--25614315 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
25614247 TAAATTTGAT
* *
25614257 TAAATTTAAATTTAAAGTAATTTTAAATAGG
1 TAAATTTAAATTTAAAATAAATTTAAATAGG
25614288 TAAATTTAAATTTAAAATAAATTTAAAT
1 TAAATTTAAATTTAAAATAAATTTAAAT
25614316 TTAAAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (31 bp):
TAAATTTAAATTTAAAATAAATTTAAATAGG
Found at i:25615238 original size:2 final size:2
Alignment explanation
Indices: 25615231--25615268 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25615221 AGAAAACTTT
25615231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25615269 AAACCATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25619139 original size:25 final size:25
Alignment explanation
Indices: 25619091--25619139 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
25619081 CTACCTTAAT
*
25619091 TAGAGTTTAACTGGAAAACTAAAAA
1 TAGAGTTTAACTGGAAAACGAAAAA
25619116 TAGAGTTTAACTGGAAGAA-GAAAA
1 TAGAGTTTAACTGGAA-AACGAAAA
25619140 GCCAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.22
Consensus pattern (25 bp):
TAGAGTTTAACTGGAAAACGAAAAA
Found at i:25624710 original size:14 final size:14
Alignment explanation
Indices: 25624686--25624719 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
25624676 TTATTTTGTA
25624686 TAAAT-TTTATATT
1 TAAATATTTATATT
25624699 TAAATATTTATATT
1 TAAATATTTATATT
*
25624713 TATATAT
1 TAAATAT
25624720 GCATTCGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATATTTATATT
Found at i:25625685 original size:22 final size:24
Alignment explanation
Indices: 25625660--25625711 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
25625650 CCCTAATTTT
*
25625660 TTGGCTCTT-AAAA-TATTATCTC
1 TTGGCTCTTAAAAATTATTATCTA
*
25625682 TTGGATCTTAAAAATTATTATCTA
1 TTGGCTCTTAAAAATTATTATCTA
25625706 TTGGCT
1 TTGGCT
25625712 ACCATCATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.32
23 4 0.16
24 13 0.52
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (24 bp):
TTGGCTCTTAAAAATTATTATCTA
Found at i:25628185 original size:29 final size:30
Alignment explanation
Indices: 25628132--25628206 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
25628122 AAATAAATAG
*
25628132 AAAATAAAATGAAA-GATTAAGATTTAAGA-
1 AAAATAAAATAAAAGGATTAAGATTTAA-AC
*
25628161 AAAATAAAATAAAAGGATTCA-ATTTAAAC
1 AAAATAAAATAAAAGGATTAAGATTTAAAC
* *
25628190 AAAATAGAACAAAAGGA
1 AAAATAAAATAAAAGGA
25628207 AAATTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 34 0.85
30 5 0.12
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (30 bp):
AAAATAAAATAAAAGGATTAAGATTTAAAC
Found at i:25628360 original size:28 final size:27
Alignment explanation
Indices: 25628329--25628416 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 27
25628319 TAAAAAGAAT
25628329 ATAATAAAAGCGGTTTAATTTTAAAAAA
1 ATAATAAAAG-GGTTTAATTTTAAAAAA
* * * *
25628357 ATAAAAATAAAGGATTAATTTTAAAAAG
1 ATAATAA-AAGGGTTTAATTTTAAAAAA
**
25628385 GGAATAAAAGGGTTTAATTTTAAAAAA
1 ATAATAAAAGGGTTTAATTTTAAAAAA
25628412 A-AATA
1 ATAATA
25628417 GAAATAAAGG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
26 4 0.08
27 17 0.35
28 25 0.52
29 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.12, T:0.30
Consensus pattern (27 bp):
ATAATAAAAGGGTTTAATTTTAAAAAA
Found at i:25628375 original size:57 final size:56
Alignment explanation
Indices: 25628314--25628462 Score: 158
Period size: 57 Copynumber: 2.6 Consensus size: 56
25628304 ATAAGATGAT
* *
25628314 TTAATTAAAAAGAATATAATAAAAGCGGTTTAATTTT-AAAAAAATAAAAATAAAGGA
1 TTAATTAAAAA-AAGAGAATAAAAG-GGTTTAATTTTAAAAAAAATAAAAATAAAGGA
** * *
25628371 TTAATTTTAAAAAGGGAATAAAAGGGTTTAATTTTAAAAAAAAATAGAAATAAAGGA
1 TTAATTAAAAAAAGAGAATAAAAGGGTTTAATTTT-AAAAAAAATAAAAATAAAGGA
* * * *
25628428 TTAATTTAGAAAAA-CGAACAAAAGGATTTAATTTT
1 TTAA-TTAAAAAAAGAGAATAAAAGGGTTTAATTTT
25628463 TTTAAAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
55 11 0.14
56 10 0.13
57 50 0.64
58 7 0.09
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.30
Consensus pattern (56 bp):
TTAATTAAAAAAAGAGAATAAAAGGGTTTAATTTTAAAAAAAATAAAAATAAAGGA
Found at i:25628470 original size:57 final size:57
Alignment explanation
Indices: 25628347--25628472 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 57
25628337 AGCGGTTTAA
** * *
25628347 TTTTAAAAAAATAAAAATAAAGGATTAATTTTAAAAAGGGAATAAAAGGGTTTAATT
1 TTTTAAAAAAATAAAAATAAAGGATTAATTTTAAAAAACGAACAAAAGGATTTAATT
** *
25628404 TTAAAAAAAAATAGAAATAAAGGATTAA-TTTAGAAAAACGAACAAAAGGATTTAATTT
1 TTTTAAAAAAATAAAAATAAAGGATTAATTTTA-AAAAACGAACAAAAGGATTTAA-TT
25628462 TTTTAAAAAAA
1 TTTTAAAAAAA
25628473 AATTGAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 4 0.07
57 43 0.74
58 11 0.19
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (57 bp):
TTTTAAAAAAATAAAAATAAAGGATTAATTTTAAAAAACGAACAAAAGGATTTAATT
Found at i:25629359 original size:16 final size:16
Alignment explanation
Indices: 25629338--25629372 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25629328 TTTCTCACCC
* *
25629338 TTTTATTTATTTATAT
1 TTTTATATATGTATAT
25629354 TTTTATATATGTATAT
1 TTTTATATATGTATAT
25629370 TTT
1 TTT
25629373 CGAATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTATATATGTATAT
Found at i:25630620 original size:45 final size:44
Alignment explanation
Indices: 25630490--25630798 Score: 272
Period size: 46 Copynumber: 7.2 Consensus size: 44
25630480 TGAGATGGTA
*
25630490 GCTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTAGATGATG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATG-TG
25630536 GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATTGTG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGA-TGTG
* * * *
25630582 GCTTTAATTTGCCCCTCTTGATTAGGGGTAAAAGATTGGTTGACG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATG-TG
* * * *
25630627 GCTTCAATGTGTCCCTCTTGATTAGAGGTAAAAGATAGGATG-G
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGTG
* * *
25630670 TCTGT-AATCT-TCCTTC-TGATTA-GGGTAAAAGATTGGA--TG
1 GCT-TCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGTG
* * * *
25630709 GCTTTAATCTG-CTC-CATGATT-GGGGTAAGAGATTGGATG-G
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGTG
* * * *
25630749 TCTTCAATCTG-CCC-CATGA-TCGGGGTAAGAGATTGGA--TG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGTG
25630788 GCTTCAATCTG
1 GCTTCAATCTG
25630799 TTCCATGGTC
Statistics
Matches: 226, Mismatches: 25, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
38 2 0.01
39 40 0.18
40 46 0.20
41 6 0.03
42 5 0.02
43 7 0.03
44 3 0.01
45 55 0.24
46 60 0.27
47 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (44 bp):
GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGTG
Found at i:25630701 original size:40 final size:40
Alignment explanation
Indices: 25630645--25630788 Score: 143
Period size: 40 Copynumber: 3.6 Consensus size: 40
25630635 GTGTCCCTCT
* *
25630645 TGATTAGAGGTAAAAGATAGGATGGTCTGTAATCTTCCTTC-
1 TGATTAG-GGTAAAAGATTGGATGGTCTGTAATC-TCCTCCA
* *
25630686 TGATTAGGGTAAAAGATTGGATGG-CTTTAATCTGCTCCA
1 TGATTAGGGTAAAAGATTGGATGGTCTGTAATCTCCTCCA
* *
25630725 TGATTGGGGTAAGAGATTGGATGGTCT-TCAATCTGCC-CCA
1 TGATTAGGGTAAAAGATTGGATGGTCTGT-AATCT-CCTCCA
** *
25630765 TGATCGGGGTAAGAGATTGGATGG
1 TGATTAGGGTAAAAGATTGGATGG
25630789 CTTCAATCTG
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
38 4 0.04
39 30 0.33
40 49 0.54
41 8 0.09
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.31
Consensus pattern (40 bp):
TGATTAGGGTAAAAGATTGGATGGTCTGTAATCTCCTCCA
Found at i:25630864 original size:42 final size:41
Alignment explanation
Indices: 25630692--25631031 Score: 374
Period size: 42 Copynumber: 8.4 Consensus size: 41
25630682 CTTCTGATTA
* * * *
25630692 GGGTAAAAGATTGGATG-G-CTTTAATCTGCTCCATGATTG
1 GGGTAAGAGATTGGATGTGTCTTCAATCTGCCCCATGATCG
25630731 GGGTAAGAGATTGGATG-GTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGTGTCTTCAATCTGCCCCATGATCG
** *
25630771 GGGTAAGAGATTGGATG-G-CTTCAATCTGTTCCATGGTC-
1 GGGTAAGAGATTGGATGTGTCTTCAATCTGCCCCATGATCG
* * *
25630809 GGTTAAGAGATTGGATGATGTTTTCTATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATG-TGTCTTCAATCTGCCCCATGATCG
* * * *
25630851 GGGTAAGATATTGGATG-G-CTTCAATCTGCACCATGGTCA
1 GGGTAAGAGATTGGATGTGTCTTCAATCTGCCCCATGATCG
*
25630890 AGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATG-TGTCTTCAATCTGCCCCATGATCG
* * * * *
25630932 GGGTATGAGATTGGATG-GTGCTTCAATGTACCCTATGGTCG
1 GGGTAAGAGATTGGATGTGT-CTTCAATCTGCCCCATGATCG
* * *
25630973 GGGAAAGAGATTGGATGATGTCTTCAATTTGCCCCATGATTG
1 GGGTAAGAGATTGGATG-TGTCTTCAATCTGCCCCATGATCG
25631015 GGGTAAGAGATTGGATG
1 GGGTAAGAGATTGGATG
25631032 GTGCTTGATA
Statistics
Matches: 251, Mismatches: 39, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
38 16 0.06
39 65 0.26
40 40 0.16
41 48 0.19
42 80 0.32
43 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (41 bp):
GGGTAAGAGATTGGATGTGTCTTCAATCTGCCCCATGATCG
Found at i:25631037 original size:83 final size:79
Alignment explanation
Indices: 25630692--25631032 Score: 418
Period size: 83 Copynumber: 4.2 Consensus size: 79
25630682 CTTCTGATTA
* * * * *
25630692 GGGTAAAAGATTGGATGGCTTTAATCTGCTCCATGATTGGGGTAAGAGATTGGATG--GTCTTCA
1 GGGTAAGAGATTGGATGGCTTCAATGT-C-CCATGGTCGGGGTAAGAGATTGGATGATGTCTTCA
25630755 ATCTGCCCCATGATCG
64 ATCTGCCCCATGATCG
* * * *
25630771 GGGTAAGAGATTGGATGGCTTCAATCTGTTCCATGGTC-GGTTAAGAGATTGGATGATGTTTTCT
1 GGGTAAGAGATTGGATGGCTTCAA--TGTCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCA
25630835 ATCTGCCCCATGATCG
64 ATCTGCCCCATGATCG
* * **
25630851 GGGTAAGATATTGGATGGCTTCAATCTGCACCATGGTCAAGGTAAGAGATTGGATGATGTCTTCA
1 GGGTAAGAGATTGGATGGCTTCAATGT-C-CCATGGTCGGGGTAAGAGATTGGATGATGTCTTCA
25630916 ATCTGCCCCATGATCG
64 ATCTGCCCCATGATCG
* *
25630932 GGGTATGAGATTGGATGGTGCTTCAATGTACCCTATGGTCGGGGAAAGAGATTGGATGATGTCTT
1 GGGTAAGAGATTGGAT-G-GCTTCAATGT-CCC-ATGGTCGGGGTAAGAGATTGGATGATGTCTT
* *
25630997 CAATTTGCCCCATGATTG
62 CAATCTGCCCCATGATCG
25631015 GGGTAAGAGATTGGATGG
1 GGGTAAGAGATTGGATGG
25631033 TGCTTGATAG
Statistics
Matches: 226, Mismatches: 26, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
78 18 0.08
79 28 0.12
80 52 0.23
81 55 0.24
82 4 0.02
83 69 0.31
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (79 bp):
GGGTAAGAGATTGGATGGCTTCAATGTCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAAT
CTGCCCCATGATCG
Found at i:25641396 original size:42 final size:42
Alignment explanation
Indices: 25641328--25641734 Score: 456
Period size: 42 Copynumber: 9.9 Consensus size: 42
25641318 ACCATTAGTG
* * * * * * *
25641328 CTTCAATCTGCCCCATGGTTGAGGTAAAAAATTAGATGATAT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * *
25641370 CTTCAATTTACCCCATTATCGGGGTAAGAGATTGGATG--G-
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * * *
25641409 CTTCAATCTGCCTCATGGTCGGGGTAAGAGATTAGATAATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
25641451 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGGTGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * * *
25641493 CTTCAATCTGCTCTATGATCGGGATAAGAGATT--A-GATGG
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
25641532 CTTCAATCTACCCCATGGTCGGGGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * * *
25641574 CTTCAATCTGCTCCATGATTGGGGCAAGAGATTGGATGGTAG-
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGAT-GT
* *
25641616 CTTCAATCTGCCCCATGGTAGGGGTAAGAGATTGGATGATG-
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
*
25641657 --TCAATCTACCCCATGATCGGGGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
25641697 CTTCAATTTGCCTCATGATCGGGGTAAGAGATTGGATG
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG
25641735 GTTTTGCTCT
Statistics
Matches: 303, Mismatches: 52, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
39 99 0.33
41 3 0.01
42 200 0.66
43 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (42 bp):
CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
Found at i:25641465 original size:81 final size:81
Alignment explanation
Indices: 25641327--25641735 Score: 427
Period size: 81 Copynumber: 5.0 Consensus size: 81
25641317 TACCATTAGT
* * * * * * * * *
25641327 GCTTCAATCTGCCCCATGGTTGAGGTAAAAAATTAGATGATATCTTCAATTTACCCCATTATCGG
1 GCTTCAATCTGCCTCATGATCGGGGTAAGAGATTAGATGATGTCTTCAATTTGCCCCATGATCGG
25641392 GGTAAGAGATTGGATG
66 GGTAAGAGATTGGATG
* *
25641408 GCTTCAATCTGCCTCATGGTCGGGGTAAGAGATTAGATAATGTCTTCAATTTGCCCCATGATCGG
1 GCTTCAATCTGCCTCATGATCGGGGTAAGAGATTAGATGATGTCTTCAATTTGCCCCATGATCGG
25641473 GGTAAGAGATTGGGTGATG
66 GGTAAGAGATT--G-GATG
* * * * *
25641492 TCTTCAATCTG-CTCTATGATCGGGATAAGAGATTAGATG--G-CTTCAATCTACCCCATGGTCG
1 GCTTCAATCTGCCTC-ATGATCGGGGTAAGAGATTAGATGATGTCTTCAATTTGCCCCATGATCG
25641553 GGGTAAGAGATTGGATG
65 GGGTAAGAGATTGGATG
* * * * *
25641570 ATGTCTTCAATCTG-CTCCATGATTGGGGCAAGAGATTGGATGGTAG-CTTCAATCTGCCCCATG
1 --G-CTTCAATCTGCCT-CATGATCGGGGTAAGAGATTAGATGAT-GTCTTCAATTTGCCCCATG
* *
25641633 GTAGGGGTAAGAGATTGGAT-
61 ATCGGGGTAAGAGATTGGATG
* * * * *
25641653 GATGTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATTTGCCTCATGATCG
1 GCT-TCAATCTGCCTCATGATCGGGGTAAGAGATTAGATGATGTCTTCAATTTGCCCCATGATCG
25641718 GGGTAAGAGATTGGATG
65 GGGTAAGAGATTGGATG
25641735 G
1 G
25641736 TTTTGCTCTA
Statistics
Matches: 280, Mismatches: 33, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
78 4 0.01
79 1 0.00
80 2 0.01
81 194 0.69
82 4 0.01
83 4 0.01
84 71 0.25
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (81 bp):
GCTTCAATCTGCCTCATGATCGGGGTAAGAGATTAGATGATGTCTTCAATTTGCCCCATGATCGG
GGTAAGAGATTGGATG
Found at i:25641549 original size:123 final size:123
Alignment explanation
Indices: 25641328--25641734 Score: 512
Period size: 123 Copynumber: 3.3 Consensus size: 123
25641318 ACCATTAGTG
* * * * * * * * * * *
25641328 CTTCAATCTGCCCCATGGTTGAGGTAAAAAATTAGATGATATCTTCAATTTACCCCATTATCGGG
1 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCGGG
* * * *
25641393 GTAAGAGATTGGATGGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATTAGATAATGT
66 GTAAGAGATTGGATGGCTTCAATCTACCCCATGGTCGGGGTAAGAGATTGGATGATGT
* * *
25641451 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGGTGAT-GTCTTCAATCTGCTCTATGATCGG
1 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGATCGG
* *
25641515 GATAAGAGATTAGATGGCTTCAATCTACCCCATGGTCGGGGTAAGAGATTGGATGATGT
65 GGTAAGAGATTGGATGGCTTCAATCTACCCCATGGTCGGGGTAAGAGATTGGATGATGT
* * * * * * *
25641574 CTTCAATCTGCTCCATGATTGGGGCAAGAGATTGGATGGTAGCTTCAATCTGCCCCATGGTAGGG
1 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCGGG
* *
25641639 GTAAGAGATTGGAT-GATGTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGATGT
66 GTAAGAGATTGGATGGCT-TCAATCTACCCCATGGTCGGGGTAAGAGATTGGATGATGT
*
25641697 CTTCAATTTGCCTCATGATCGGGGTAAGAGATTGGATG
1 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATG
25641735 GTTTTGCTCT
Statistics
Matches: 242, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
122 2 0.01
123 239 0.99
124 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (123 bp):
CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGATAGCTTCAATCTGCCCCATGATCGGG
GTAAGAGATTGGATGGCTTCAATCTACCCCATGGTCGGGGTAAGAGATTGGATGATGT
Found at i:25642619 original size:20 final size:20
Alignment explanation
Indices: 25642582--25642625 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25642572 AATTGTAAAA
* *
25642582 ATTGGTAAAGAATGGCGAAT
1 ATTGGTAAAGAATAGCGAAC
25642602 ATTGGTAAA-ATATAGCGAAC
1 ATTGGTAAAGA-ATAGCGAAC
25642622 ATTG
1 ATTG
25642626 ATCAAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (20 bp):
ATTGGTAAAGAATAGCGAAC
Found at i:25642922 original size:13 final size:13
Alignment explanation
Indices: 25642903--25642962 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 13
25642893 CGACCTCTCA
25642903 TTTTTCTTT-TTC
1 TTTTTCTTTCTTC
*
25642915 TTTCTTCTTTTTTCC
1 TTT-TTCTTTCTT-C
25642930 TTTTTCCTTTCTTC
1 TTTTT-CTTTCTTC
25642944 -TTTTCTTTTCTTC
1 TTTTTC-TTTCTTC
25642957 TCTTTT
1 T-TTTT
25642963 TCCTTCGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 4 0.10
13 17 0.43
14 5 0.12
15 14 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTCTTC
Found at i:25642932 original size:21 final size:21
Alignment explanation
Indices: 25642903--25642947 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
25642893 CGACCTCTCA
25642903 TTTTTCTTTTT-CTTTCTTCT
1 TTTTTCTTTTTCCTTTCTTCT
25642923 TTTTTCCTTTTTCCTTTCTTCT
1 TTTTT-CTTTTTCCTTTCTTCT
25642945 TTT
1 TTT
25642948 CTTTTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.22
21 6 0.26
22 12 0.52
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTTTCCTTTCTTCT
Found at i:25642961 original size:22 final size:21
Alignment explanation
Indices: 25642903--25642961 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
25642893 CGACCTCTCA
25642903 TTTTTCTTTTTCTT-TC-TTCT
1 TTTTTC-TTTTCTTCTCTTTCT
*
25642923 TTTTTCCTTT-TTC-CTTTCT
1 TTTTTCTTTTCTTCTCTTTCT
25642942 TCTTTTCTTTTCTTCTCTTT
1 T-TTTTCTTTTCTTCTCTTT
25642962 TTCCTTCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.09
19 8 0.25
20 14 0.44
21 3 0.09
22 4 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTTCTTCTCTTTCT
Found at i:25647398 original size:31 final size:28
Alignment explanation
Indices: 25647361--25647559 Score: 104
Period size: 29 Copynumber: 7.0 Consensus size: 28
25647351 GATGATTTAA
25647361 TTAAAAAGAATATAATAAAAGGGGTTTAATT
1 TTAAAAA-AA-ATAATAAAA-GGGTTTAATT
* * *
25647392 TTAAAAAAAATAAAAATAAAGGATTAA--
1 TTAAAAAAAATAATAA-AAGGGTTTAATT
*
25647419 TTAAAAAAAAGGAATAAAAGGGTTTAATT
1 TTAAAAAAAA-TAATAAAAGGGTTTAATT
* *
25647448 TTAAAAATAGA-AAT-AAA-GGATTAA-T
1 TTAAAAA-AAATAATAAAAGGGTTTAATT
* ** * *
25647473 TTAGAAAAAGGAACAAAAGGATTTAATTT
1 TTAAAAAAAATAATAAAAGGGTTTAA-TT
* * **
25647502 TTTAAAAAATTGAATAAAAGGGTAAAATT
1 TTAAAAAAAAT-AATAAAAGGGTTTAATT
* ** *
25647531 TAATAAAAAAATAATGTAAGGGTTAAATT
1 TTA-AAAAAAATAATAAAAGGGTTTAATT
25647560 AAAATTAAAA
Statistics
Matches: 127, Mismatches: 29, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
24 1 0.01
25 9 0.07
26 9 0.07
27 26 0.20
28 7 0.06
29 44 0.35
30 24 0.19
31 7 0.06
ACGTcount: A:0.57, C:0.01, G:0.14, T:0.29
Consensus pattern (28 bp):
TTAAAAAAAATAATAAAAGGGTTTAATT
Found at i:25647424 original size:26 final size:26
Alignment explanation
Indices: 25647395--25647473 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
25647385 TTTAATTTTA
*
25647395 AAAAAAATAAAAATAAAGGATTAATT
1 AAAAAAATAGAAATAAAGGATTAATT
* *
25647421 AAAAAAA-AGGAATAAAAGGGTTTAATT
1 AAAAAAATAGAAAT-AAA-GGATTAATT
**
25647448 TTAAAAATAGAAATAAAGGATTAATT
1 AAAAAAATAGAAATAAAGGATTAATT
25647474 TAGAAAAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
25 4 0.09
26 18 0.42
27 16 0.37
28 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (26 bp):
AAAAAAATAGAAATAAAGGATTAATT
Found at i:25647467 original size:53 final size:54
Alignment explanation
Indices: 25647357--25647511 Score: 179
Period size: 53 Copynumber: 2.8 Consensus size: 54
25647347 ACAAGATGAT
*
25647357 TTAATTAAAAAGAATA-TAATAAAAGGGGTTTAATTTTAAAAAAAATAAAAATAAAGGA
1 TTAATTAAAAA-AA-AGGAATAAAA-GGGTTTAATTTT--AAAAAATAAAAATAAAGGA
*
25647415 TTAATTAAAAAAAAGGAATAAAAGGGTTTAATTTT-AAAAATAGAAATAAAGGA
1 TTAATTAAAAAAAAGGAATAAAAGGGTTTAATTTTAAAAAATAAAAATAAAGGA
* * * *
25647468 TTAATTTAGAAAAAGGAACAAAAGGATTTAATTTTTTAAAAAAT
1 TTAATTAAAAAAAAGGAATAAAAGGGTTTAA--TTTTAAAAAAT
25647512 TGAATAAAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
53 44 0.51
55 4 0.05
56 19 0.22
57 9 0.10
58 11 0.13
ACGTcount: A:0.57, C:0.01, G:0.13, T:0.29
Consensus pattern (54 bp):
TTAATTAAAAAAAAGGAATAAAAGGGTTTAATTTTAAAAAATAAAAATAAAGGA
Found at i:25647480 original size:27 final size:26
Alignment explanation
Indices: 25647396--25647481 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
25647386 TTAATTTTAA
*
25647396 AAAAAATAAAAATAAAGGATTAA-TT
1 AAAAAATAGAAATAAAGGATTAATTT
* * *
25647421 AAAAAAAAGGAATAAAAGGGTTTAATTT
1 AAAAAATAGAAAT-AAA-GGATTAATTT
*
25647449 TAAAAATAGAAATAAAGGATTAATTT
1 AAAAAATAGAAATAAAGGATTAATTT
25647475 AGAAAAA
1 A-AAAAA
25647482 GGAACAAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
25 10 0.21
26 12 0.25
27 14 0.29
28 12 0.25
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (26 bp):
AAAAAATAGAAATAAAGGATTAATTT
Found at i:25647498 original size:27 final size:24
Alignment explanation
Indices: 25647409--25647501 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 24
25647399 AAATAAAAAT
*
25647409 AAAGGATTAATTAAAAAAAAGGAATA
1 AAAGGATTAATT-TAAAAAAGGAA-A
*
25647435 AAAGGGTTTAATTTTAAAAATA-GAAA
1 AAA-GGATTAA-TTTAAAAA-AGGAAA
25647461 TAAAGGATTAATTTAGAAAAAGGAACA
1 -AAAGGATTAATTTA-AAAAAGGAA-A
25647488 AAAGGATTTAATTT
1 AAAGGA-TTAATTT
25647502 TTTAAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
25 5 0.09
26 23 0.41
27 25 0.45
28 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAGGATTAATTTAAAAAAGGAAA
Found at i:25648335 original size:19 final size:19
Alignment explanation
Indices: 25648313--25648350 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25648303 GTTATCTGAG
25648313 AAGTGGACCACCCTTCGGT
1 AAGTGGACCACCCTTCGGT
25648332 AAGTGGACCACCCTTCGGT
1 AAGTGGACCACCCTTCGGT
25648351 GGTGGTGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (19 bp):
AAGTGGACCACCCTTCGGT
Found at i:25661039 original size:37 final size:37
Alignment explanation
Indices: 25660997--25661069 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
25660987 TTATTTTGAT
*
25660997 TGAACTT-AATTGTTTTATTGGTATTTATAGATACAAA
1 TGAACTTGAA-TGCTTTATTGGTATTTATAGATACAAA
*
25661034 TGAACTTGAATGCTTTATTGGTATTTTTAGATACAA
1 TGAACTTGAATGCTTTATTGGTATTTATAGATACAA
25661070 GTGATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (37 bp):
TGAACTTGAATGCTTTATTGGTATTTATAGATACAAA
Found at i:25661551 original size:20 final size:20
Alignment explanation
Indices: 25661512--25661606 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 20
25661502 TTTTGAAACA
*
25661512 ATTTTAAAATCAAGTTAAAATG
1 ATTTT-AAA-CAAGTCAAAATG
*
25661534 ATTTTAAACAAGTCAAAATA
1 ATTTTAAACAAGTCAAAATG
* * *
25661554 ATTTCAATCAAGTC--AATC
1 ATTTTAAACAAGTCAAAATG
*
25661572 ATTTTAATAC--TTCAAAATG
1 ATTTTAA-ACAAGTCAAAATG
*
25661591 TTTTTCAAACAAGTCA
1 ATTTT-AAACAAGTCA
25661607 GAATAGCTCC
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
17 2 0.04
18 9 0.16
19 10 0.18
20 24 0.43
21 6 0.11
22 5 0.09
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTTTAAACAAGTCAAAATG
Found at i:25669472 original size:38 final size:38
Alignment explanation
Indices: 25669430--25669516 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
25669420 AATTGAACAT
* *
25669430 AATAACTATAATAATGTTTGACCGAAAAATTA-CATTAC
1 AATAACTATAATAATATTTGACCG-AAAATTATAATTAC
* *
25669468 AATAACTATAATAATATTTGATCGTAAATTATAATTAC
1 AATAACTATAATAATATTTGACCGAAAATTATAATTAC
*
25669506 AATAATTATAA
1 AATAACTATAA
25669517 CAAGGATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 6 0.14
38 37 0.86
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (38 bp):
AATAACTATAATAATATTTGACCGAAAATTATAATTAC
Found at i:25670851 original size:20 final size:20
Alignment explanation
Indices: 25670828--25670892 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
25670818 AGGGGCATCG
*
25670828 AAGTGCAAATAAGGGCACCA
1 AAGTGCAAACAAGGGCACCA
* * *
25670848 AAGTGCAAACAGGGGCATCG
1 AAGTGCAAACAAGGGCACCA
* *
25670868 ATGTGCAAACAAGGACACCA
1 AAGTGCAAACAAGGGCACCA
25670888 AAGTG
1 AAGTG
25670893 TTTACATGGG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.28, T:0.11
Consensus pattern (20 bp):
AAGTGCAAACAAGGGCACCA
Found at i:25670932 original size:39 final size:40
Alignment explanation
Indices: 25670813--25670957 Score: 134
Period size: 40 Copynumber: 3.6 Consensus size: 40
25670803 TAATTACACC
* * * *
25670813 ATACTAGGGGCATC-GAAGTGCAAATAAGGGCACCAAAGTGC
1 ATAC-AGGGGCA-CAGAGGTGCAAACAAGGACACCAAAGTGT
* *
25670854 AAACAGGGGCATC-GATGTGCAAACAAGGACACCAAAGTGT
1 ATACAGGGGCA-CAGAGGTGCAAACAAGGACACCAAAGTGT
* * * *
25670894 TTACATGGGCACAGAGGTGCAAAC-TGGACACCGAAGTGT
1 ATACAGGGGCACAGAGGTGCAAACAAGGACACCAAAGTGT
* *
25670933 ATATAGGGGCACTGAGGTGCAAACA
1 ATACAGGGGCACAGAGGTGCAAACA
25670958 GGGGCACTTT
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 34 0.39
40 50 0.57
41 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (40 bp):
ATACAGGGGCACAGAGGTGCAAACAAGGACACCAAAGTGT
Found at i:25674980 original size:16 final size:16
Alignment explanation
Indices: 25674959--25675004 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
25674949 GCGTGGGAAT
25674959 GAATAGAGAAATGAGA
1 GAATAGAGAAATGAGA
*
25674975 GAATAGA-AGATTGAGA
1 GAATAGAGA-AATGAGA
25674991 GAAT-GAAGAAATGA
1 GAATAG-AGAAATGA
25675005 TGTATTAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.08
16 22 0.88
17 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.30, T:0.15
Consensus pattern (16 bp):
GAATAGAGAAATGAGA
Found at i:25683767 original size:12 final size:12
Alignment explanation
Indices: 25683741--25683790 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
25683731 TCAGGGAGGT
* *
25683741 AAGAGAAGGATG
1 AAGAAAAGGAAG
*
25683753 AAGAAAAAGAAG
1 AAGAAAAGGAAG
*
25683765 AAGGAAAGGAAG
1 AAGAAAAGGAAG
*
25683777 AAGAGAAGGAAG
1 AAGAAAAGGAAG
25683789 AA
1 AA
25683791 ACTGAACCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (12 bp):
AAGAAAAGGAAG
Found at i:25694614 original size:21 final size:21
Alignment explanation
Indices: 25694588--25694627 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
25694578 ACCATCATCC
25694588 AACCAATTGCTTTTTTAAAGA
1 AACCAATTGCTTTTTTAAAGA
25694609 AACCAATTGCTTTTTTAAA
1 AACCAATTGCTTTTTTAAA
25694628 TTTCTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (21 bp):
AACCAATTGCTTTTTTAAAGA
Found at i:25702127 original size:17 final size:19
Alignment explanation
Indices: 25702105--25702143 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
25702095 GAAGAAGAAA
25702105 AAAGAAAAGAA-G-AGAGG
1 AAAGAAAAGAAGGAAGAGG
*
25702122 AAAGAAGAGAAGGAAGAGG
1 AAAGAAAAGAAGGAAGAGG
25702141 AAA
1 AAA
25702144 AAGGAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
AAAGAAAAGAAGGAAGAGG
Found at i:25702564 original size:17 final size:17
Alignment explanation
Indices: 25702539--25702582 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
25702529 CATTCATTTC
25702539 TTTTAATTGTCAT-TGCA
1 TTTTAATTGTC-TCTGCA
*
25702556 TTTTTATTGTCTCTGCA
1 TTTTAATTGTCTCTGCA
*
25702573 TTTTACTTGT
1 TTTTAATTGT
25702583 TTTAGCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTTAATTGTCTCTGCA
Found at i:25703195 original size:18 final size:20
Alignment explanation
Indices: 25703167--25703216 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
25703157 TCAATCGCAT
25703167 AAAGAAAAGAAAAAG-AGA-A
1 AAAG-AAAGAAAAAGCAGATA
*
25703186 AAAGAAAG-AAAAGCTGATA
1 AAAGAAAGAAAAAGCAGATA
25703205 AAAGAAAGAAAA
1 AAAGAAAGAAAA
25703217 GGAAAGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 13 0.48
20 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAGAAAGAAAAAGCAGATA
Found at i:25703571 original size:13 final size:13
Alignment explanation
Indices: 25703553--25703577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25703543 CCTTTTGTAT
25703553 CATTTTTAGCATG
1 CATTTTTAGCATG
25703566 CATTTTTAGCAT
1 CATTTTTAGCAT
25703578 TTCATACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:25714393 original size:16 final size:15
Alignment explanation
Indices: 25714372--25714401 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25714362 AAGAGAGAAA
25714372 TGAGAGAATAGAAGAT
1 TGAGAGAAT-GAAGAT
25714388 TGAGAGAATGAAGA
1 TGAGAGAATGAAGA
25714402 AATGATGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
TGAGAGAATGAAGAT
Found at i:25717470 original size:12 final size:12
Alignment explanation
Indices: 25717453--25717495 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
25717443 AATTCTTATT
25717453 TATCAAACATAA
1 TATCAAACATAA
* *
25717465 TATCAAA-TTATT
1 TATCAAACATA-A
25717477 TATCAAACATAA
1 TATCAAACATAA
25717489 TATCAAA
1 TATCAAA
25717496 TTAACTAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (12 bp):
TATCAAACATAA
Found at i:25717476 original size:24 final size:24
Alignment explanation
Indices: 25717448--25717498 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
25717438 AATATAATTC
25717448 TTATTTATCAAACATAATATCAAA
1 TTATTTATCAAACATAATATCAAA
25717472 TTATTTATCAAACATAATATCAAA
1 TTATTTATCAAACATAATATCAAA
25717496 TTA
1 TTA
25717499 ACTAACAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (24 bp):
TTATTTATCAAACATAATATCAAA
Found at i:25721569 original size:25 final size:25
Alignment explanation
Indices: 25721532--25721608 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 25
25721522 ATACTGGTTA
* * *
25721532 AACTCTATTTGGGCTCGTAAGAGTT
1 AACTTTATCTGGGCTCGTAAGAGCT
25721557 AACTTTATCTGGGCTCGTAAGAGCT
1 AACTTTATCTGGGCTCGTAAGAGCT
* * * *
25721582 AACCTCATCTAGGCTCGTATGAGCT
1 AACTTTATCTGGGCTCGTAAGAGCT
25721607 AA
1 AA
25721609 ATTATGGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (25 bp):
AACTTTATCTGGGCTCGTAAGAGCT
Found at i:25723084 original size:55 final size:55
Alignment explanation
Indices: 25722981--25723109 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 55
25722971 CAAGCAAAGG
* * ***
25722981 CCATGTCGTGTAAGACCTAGTCTGGGACTATGGAATTATATGGGGTATGTGAAAA
1 CCATATCGTGTAAGACCTAGTCTGGGACTATGGAATCATATAACGTATGTGAAAA
* **
25723036 CCATATCGTGTAAGACCTAGTCTGGGACTATGGCATCATATAACGTATGTGAAGT
1 CCATATCGTGTAAGACCTAGTCTGGGACTATGGAATCATATAACGTATGTGAAAA
* *
25723091 CCATATAGTGTAAGGCCTA
1 CCATATCGTGTAAGACCTA
25723110 CCAATATTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (55 bp):
CCATATCGTGTAAGACCTAGTCTGGGACTATGGAATCATATAACGTATGTGAAAA
Found at i:25724737 original size:19 final size:19
Alignment explanation
Indices: 25724701--25724738 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25724691 GACTATAAAA
*
25724701 TTCATATATTCTTGTATTT
1 TTCATATATGCTTGTATTT
25724720 TTCACTATATGCTT-TATTT
1 TTCA-TATATGCTTGTATTT
25724739 ATCAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (19 bp):
TTCATATATGCTTGTATTT
Found at i:25726400 original size:28 final size:30
Alignment explanation
Indices: 25726322--25726401 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 30
25726312 TGTGGCAGAA
* *
25726322 TCTGATGTGCGAGCCCTTATGGTTGGAACT
1 TCTGATATGTGAGCCCTTATGGTTGGAACT
* **
25726352 TGTGATATGTGAG-CCTCTATGGTT-GTTC-
1 TCTGATATGTGAGCCCT-TATGGTTGGAACT
25726380 TCTGATATGTGAGCCCTTATGG
1 TCTGATATGTGAGCCCTTATGG
25726402 AGAAACCTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 17 0.40
29 8 0.19
30 17 0.40
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.38
Consensus pattern (30 bp):
TCTGATATGTGAGCCCTTATGGTTGGAACT
Found at i:25727390 original size:49 final size:49
Alignment explanation
Indices: 25727336--25727434 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
25727326 AAGATTATTT
*
25727336 TACTCATGAATACTATACTATACCTTAAGGAATGGAGAGAAAAGGAATG
1 TACTCATGAATACTATACTATACCTTAAGGAATGAAGAGAAAAGGAATG
* *
25727385 TACTCATGAATATTATACTATACCTTAAGGAATGAAGAGAAAATGAATG
1 TACTCATGAATACTATACTATACCTTAAGGAATGAAGAGAAAAGGAATG
25727434 T
1 T
25727435 GAGAGAAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.27
Consensus pattern (49 bp):
TACTCATGAATACTATACTATACCTTAAGGAATGAAGAGAAAAGGAATG
Found at i:25728315 original size:22 final size:22
Alignment explanation
Indices: 25728288--25728337 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
25728278 TTCAAAGTTG
*
25728288 TGTGTCGCGACACGCATAAGCT
1 TGTGTCGCGACACGCATAAGCA
* *
25728310 TGTGTCGTGACATGCATAAGCA
1 TGTGTCGCGACACGCATAAGCA
25728332 TGTGTC
1 TGTGTC
25728338 ATAACACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (22 bp):
TGTGTCGCGACACGCATAAGCA
Found at i:25729387 original size:291 final size:291
Alignment explanation
Indices: 25728863--25729445 Score: 1148
Period size: 291 Copynumber: 2.0 Consensus size: 291
25728853 AATGTGGGAG
*
25728863 TAATTAACGGAAAAATGAGGGTTTATCTTAGAATTAGTTGGCTTAAATTTGTATGTTTAAACCTT
1 TAATTAACGGAAAAACGAGGGTTTATCTTAGAATTAGTTGGCTTAAATTTGTATGTTTAAACCTT
25728928 AGGATTGACGACCCTAAGAAGTAATCCAAGCAGATAGGCCGAAAGATAAGTCTATCGAACACCTC
66 AGGATTGACGACCCTAAGAAGTAATCCAAGCAGATAGGCCGAAAGATAAGTCTATCGAACACCTC
25728993 ATAATTTATCCTGATTTTAAACGGTGAGGTCGAAAGATAAGTGGGTTTTTACCGTTTAATTAATC
131 ATAATTTATCCTGATTTTAAACGGTGAGGTCGAAAGATAAGTGGGTTTTTACCGTTTAATTAATC
25729058 AGTTAAAGGTCGAAAGGTAATAATTAGTTAGTTATTAGCTAATTCACTAAAACCCAAGTTTTGAA
196 AGTTAAAGGTCGAAAGGTAATAATTAGTTAGTTATTAGCTAATTCACTAAAACCCAAGTTTTGAA
25729123 GTTAATTATGAACACTGAAGTGAATTAATCT
261 GTTAATTATGAACACTGAAGTGAATTAATCT
25729154 TAATTAACGGAAAAACGAGGGTTTATCTTAGAATTAGTTGGCTTAAATTTGTATGTTTAAACCTT
1 TAATTAACGGAAAAACGAGGGTTTATCTTAGAATTAGTTGGCTTAAATTTGTATGTTTAAACCTT
*
25729219 AGGATTGACGACCCTAAGAAGTAATCCAAGCAGATAGGCCGAAAGATAAGTTTATCGAACACCTC
66 AGGATTGACGACCCTAAGAAGTAATCCAAGCAGATAGGCCGAAAGATAAGTCTATCGAACACCTC
25729284 ATAATTTATCCTGATTTTAAACGGTGAGGTCGAAAGATAAGTGGGTTTTTACCGTTTAATTAATC
131 ATAATTTATCCTGATTTTAAACGGTGAGGTCGAAAGATAAGTGGGTTTTTACCGTTTAATTAATC
25729349 AGTTAAAGGTCGAAAGGTAATAATTAGTTAGTTATTAGCTAATTCACTAAAACCCAAGTTTTGAA
196 AGTTAAAGGTCGAAAGGTAATAATTAGTTAGTTATTAGCTAATTCACTAAAACCCAAGTTTTGAA
25729414 GTTAATTATGAACACTGAAGTGAATTAATCT
261 GTTAATTATGAACACTGAAGTGAATTAATCT
25729445 T
1 T
25729446 TTGTTTGTTA
Statistics
Matches: 290, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
291 290 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (291 bp):
TAATTAACGGAAAAACGAGGGTTTATCTTAGAATTAGTTGGCTTAAATTTGTATGTTTAAACCTT
AGGATTGACGACCCTAAGAAGTAATCCAAGCAGATAGGCCGAAAGATAAGTCTATCGAACACCTC
ATAATTTATCCTGATTTTAAACGGTGAGGTCGAAAGATAAGTGGGTTTTTACCGTTTAATTAATC
AGTTAAAGGTCGAAAGGTAATAATTAGTTAGTTATTAGCTAATTCACTAAAACCCAAGTTTTGAA
GTTAATTATGAACACTGAAGTGAATTAATCT
Found at i:25730230 original size:21 final size:20
Alignment explanation
Indices: 25730204--25730261 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 20
25730194 TTTTTAACAC
25730204 TTTTAATATTTTTAAAACA-TA
1 TTTTAA-ATTTTTAAAA-AGTA
25730225 TTTTAAATGTTTTATAAAAGTA
1 TTTTAAAT-TTTTA-AAAAGTA
25730247 TTTTAAACTTTTTAA
1 TTTTAAA-TTTTTAA
25730262 CTCTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 2 0.06
21 13 0.39
22 17 0.52
23 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTAAATTTTTAAAAAGTA
Found at i:25734556 original size:155 final size:155
Alignment explanation
Indices: 25734274--25734571 Score: 587
Period size: 155 Copynumber: 1.9 Consensus size: 155
25734264 CCACCAAGAT
25734274 TATTGATACAGACCAAGCCACTCAATGCCCAGTAACTTAGATATGGGTTCTCATGATCCAGGGAT
1 TATTGATACAGACCAAGCCACTCAATGCCCAGTAACTTAGATATGGGTTCTCATGATCCAGGGAT
25734339 AGGCTGATTGGTTTGATAAAAGAAAACCTAGAAGGAAACCAAAAGGAAGAGAATCTGGAGGCTAG
66 AGGCTGATTGGTTTGATAAAAGAAAACCTAGAAGGAAACCAAAAGGAAGAGAATCTGGAGGCTAG
25734404 TGGCGCAGATATTGGAAGCACCTCG
131 TGGCGCAGATATTGGAAGCACCTCG
25734429 TATTGATACAGACCAAGCCACTCAATGCCCAGTAACTTAGATATGGGTTCTCATGATCCAGGGAT
1 TATTGATACAGACCAAGCCACTCAATGCCCAGTAACTTAGATATGGGTTCTCATGATCCAGGGAT
25734494 AGGCTGATTGGTTTGATAAAAGAAAACCTAGAAGGAAACCAAAAGGAAGAGAATCTGGAGGCTAG
66 AGGCTGATTGGTTTGATAAAAGAAAACCTAGAAGGAAACCAAAAGGAAGAGAATCTGGAGGCTAG
*
25734559 TTGCGCAGATATT
131 TGGCGCAGATATT
25734572 ATATTAAAGA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 142 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (155 bp):
TATTGATACAGACCAAGCCACTCAATGCCCAGTAACTTAGATATGGGTTCTCATGATCCAGGGAT
AGGCTGATTGGTTTGATAAAAGAAAACCTAGAAGGAAACCAAAAGGAAGAGAATCTGGAGGCTAG
TGGCGCAGATATTGGAAGCACCTCG
Found at i:25736194 original size:22 final size:21
Alignment explanation
Indices: 25736169--25736209 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
25736159 TCTTTTAAAA
*
25736169 AATATTTATATTATTTTATATT
1 AATATTTA-ATAATTTTATATT
25736191 AATATTTAATAATTTTATA
1 AATATTTAATAATTTTATA
25736210 CAATAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATATTTAATAATTTTATATT
Found at i:25737763 original size:23 final size:23
Alignment explanation
Indices: 25737736--25737782 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
25737726 ATTATTAAGT
*
25737736 AGTTGTAATTAATTGCTGGAAGC
1 AGTTGTAACTAATTGCTGGAAGC
* *
25737759 AGTTGTAACTAATTGTTGTAAGC
1 AGTTGTAACTAATTGCTGGAAGC
25737782 A
1 A
25737783 ATAGTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (23 bp):
AGTTGTAACTAATTGCTGGAAGC
Found at i:25738025 original size:23 final size:23
Alignment explanation
Indices: 25737999--25738046 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
25737989 TACATATTTA
* *
25737999 TACAGCAACTGATTACAACTGCT
1 TACAGCAACTAATTACAACTACT
*
25738022 TACAGTAACTAATTACAACTACT
1 TACAGCAACTAATTACAACTACT
25738045 TA
1 TA
25738047 GTAACTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (23 bp):
TACAGCAACTAATTACAACTACT
Found at i:25743139 original size:102 final size:102
Alignment explanation
Indices: 25742936--25743132 Score: 313
Period size: 102 Copynumber: 1.9 Consensus size: 102
25742926 CGTTACAGGA
** * * *
25742936 AAGAAACCCGCAAATATGGATAAATTAGAATAGGAAGAATTTGATGAAAAGGCTCTATTAGTTAT
1 AAGAAACCCGCAAATATGGATAAATTAGAATAAAAAGAACTCGATGAAAAGGCTCTATCAGTTAT
25743001 TCAATTATGCCTCACGAATAATGTGTTACAAGAGGTT
66 TCAATTATGCCTCACGAATAATGTGTTACAAGAGGTT
* * *
25743038 AAGAAACCCGCAAATATGGATCAGTTAGAATAAAAAGAACTCGATGAAAAGGCTCTATCCGTTAT
1 AAGAAACCCGCAAATATGGATAAATTAGAATAAAAAGAACTCGATGAAAAGGCTCTATCAGTTAT
*
25743103 TCAATTATGCCTTACGAATAATGTGTTACA
66 TCAATTATGCCTCACGAATAATGTGTTACA
25743133 GAAGGTTCTG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 86 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (102 bp):
AAGAAACCCGCAAATATGGATAAATTAGAATAAAAAGAACTCGATGAAAAGGCTCTATCAGTTAT
TCAATTATGCCTCACGAATAATGTGTTACAAGAGGTT
Found at i:25766437 original size:65 final size:65
Alignment explanation
Indices: 25766328--25766472 Score: 281
Period size: 65 Copynumber: 2.2 Consensus size: 65
25766318 GATACACGAA
*
25766328 TCTCCAACACACCAAATGAATCGAAGAGTCGAGCATATCCCAAAAGCGTAGCATAAAGCTAACAC
1 TCTCTAACACACCAAATGAATCGAAGAGTCGAGCATATCCCAAAAGCGTAGCATAAAGCTAACAC
25766393 TCTCTAACACACCAAATGAATCGAAGAGTCGAGCATATCCCAAAAGCGTAGCATAAAGCTAACAC
1 TCTCTAACACACCAAATGAATCGAAGAGTCGAGCATATCCCAAAAGCGTAGCATAAAGCTAACAC
25766458 TCTCTAACACACCAA
1 TCTCTAACACACCAA
25766473 CATGTCCCGA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 79 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (65 bp):
TCTCTAACACACCAAATGAATCGAAGAGTCGAGCATATCCCAAAAGCGTAGCATAAAGCTAACAC
Found at i:25774482 original size:28 final size:28
Alignment explanation
Indices: 25774442--25774498 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
25774432 GACAATGATT
25774442 ATTCAAATGGTATTGGTTGTATAGGAGA
1 ATTCAAATGGTATTGGTTGTATAGGAGA
25774470 ATTCAAATGGTATTGGTTGTATAGGAGA
1 ATTCAAATGGTATTGGTTGTATAGGAGA
25774498 A
1 A
25774499 AGGTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (28 bp):
ATTCAAATGGTATTGGTTGTATAGGAGA
Found at i:25779353 original size:32 final size:31
Alignment explanation
Indices: 25779311--25779439 Score: 115
Period size: 32 Copynumber: 4.2 Consensus size: 31
25779301 ATGTAATAGT
*
25779311 TATATGCGTGAGTCTTGTATTATTATATTATA
1 TATATGCGTGAGTCTT-TATTATTATATAATA
* *
25779343 TATAGGCGTGA--CTTTATTATATAGATAATA
1 TATATGCGTGAGTCTTTATTAT-TATATAATA
*
25779373 TATATGTGTGAGT-TTTATT-TTATATAATA
1 TATATGCGTGAGTCTTTATTATTATATAATA
* * * *
25779402 TATATGCATGGGTTTTGGTGTTA-TATATAATA
1 TATATGCGTGAGTCTT--TATTATTATATAATA
25779434 TATATG
1 TATATG
25779440 AATGGGGTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
29 24 0.30
30 22 0.28
31 6 0.08
32 28 0.35
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (31 bp):
TATATGCGTGAGTCTTTATTATTATATAATA
Found at i:25779478 original size:20 final size:21
Alignment explanation
Indices: 25779453--25779527 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 21
25779443 GGGGTTGATA
* *
25779453 AATATATATGC-ATGGGTCTT
1 AATATATATACTATCGGTCTT
25779473 AATATATATACTTATCGGTCTT
1 AATATATATAC-TATCGGTCTT
25779495 AATATATATACTTATCGGTCTTAT
1 AATATATATAC-TATCGGTC-T-T
25779519 AATATATAT
1 AATATATAT
25779528 TTATGGGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.20
22 28 0.57
23 1 0.02
24 10 0.20
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (21 bp):
AATATATATACTATCGGTCTT
Found at i:25779531 original size:22 final size:22
Alignment explanation
Indices: 25779467--25779531 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
25779457 TATATGCATG
25779467 GGTCTTAATATATATACTTATC
1 GGTCTTAATATATATACTTATC
25779489 GGTCTTAATATATATACTTATC
1 GGTCTTAATATATATACTTATC
*
25779511 GGTCTT-ATAATATATATTTAT
1 GGTCTTAAT-ATATATACTTAT
25779532 GGGATATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (22 bp):
GGTCTTAATATATATACTTATC
Found at i:25789818 original size:25 final size:25
Alignment explanation
Indices: 25789761--25789810 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
25789751 CTAATCACAT
25789761 GCAAAACATCATTTGCTGTATGTCC
1 GCAAAACATCATTTGCTGTATGTCC
*
25789786 GCAAAACATCATTTGTTGTATGTCC
1 GCAAAACATCATTTGCTGTATGTCC
25789811 TCAGAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (25 bp):
GCAAAACATCATTTGCTGTATGTCC
Found at i:25812580 original size:20 final size:20
Alignment explanation
Indices: 25812555--25812594 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25812545 AATCATACAC
25812555 ATTTAACGGAATAAATATAT
1 ATTTAACGGAATAAATATAT
25812575 ATTTAACGGAATAAATATAT
1 ATTTAACGGAATAAATATAT
25812595 CAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
ATTTAACGGAATAAATATAT
Found at i:25812743 original size:29 final size:30
Alignment explanation
Indices: 25812711--25812777 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
25812701 TCAAAATTTA
*
25812711 ATGTATAAAATTGTACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAATCAAAGTTC
* *
25812740 ATGTGTACAATTGCACATTAAATCAAAGTTC
1 ATGTATAAAATTGCACA-TAAATCAAAGTTC
*
25812771 ATCTATA
1 ATGTATA
25812778 GTTTTGAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAATCAAAGTTC
Found at i:25823633 original size:19 final size:20
Alignment explanation
Indices: 25823609--25823646 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
25823599 CATTGTATCA
25823609 GATTTTTATTC-GATTTTAG
1 GATTTTTATTCTGATTTTAG
*
25823628 GATTTTTTTTCTGATTTTA
1 GATTTTTATTCTGATTTTA
25823647 AAAGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.63
Consensus pattern (20 bp):
GATTTTTATTCTGATTTTAG
Found at i:25834851 original size:9 final size:9
Alignment explanation
Indices: 25834837--25834861 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25834827 ACTTTCTCTT
25834837 AAAGAATAC
1 AAAGAATAC
25834846 AAAGAATAC
1 AAAGAATAC
25834855 AAAGAAT
1 AAAGAAT
25834862 GGAATGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.12, T:0.12
Consensus pattern (9 bp):
AAAGAATAC
Found at i:25837200 original size:12 final size:12
Alignment explanation
Indices: 25837165--25837203 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25837155 ATAAATACAA
*
25837165 TATAAATCAACC
1 TATAAATCAGCC
* *
25837177 TATTAATTAGCC
1 TATAAATCAGCC
25837189 TATAAATCAGCC
1 TATAAATCAGCC
25837201 TAT
1 TAT
25837204 GATTCTATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (12 bp):
TATAAATCAGCC
Found at i:25845299 original size:14 final size:14
Alignment explanation
Indices: 25845280--25845320 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
25845270 TTGTTTCATT
25845280 GAAAATGATTATCG
1 GAAAATGATTATCG
* *
25845294 GAAAATGATTTTTG
1 GAAAATGATTATCG
25845308 GAAAATGACTTAT
1 GAAAATGA-TTAT
25845321 TTTTCTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (14 bp):
GAAAATGATTATCG
Found at i:25845378 original size:33 final size:32
Alignment explanation
Indices: 25845336--25845407 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
25845326 TGGAAAAACT
*
25845336 AATATTTTCTGGTGTTTGGATAAATTT-GTGTAA
1 AATATTTTCTGGTGTTT-GATAAATTTCTTG-AA
* *
25845369 AATATTTTCTGTTGTTTGATAGATTTCTTGAA
1 AATATTTTCTGGTGTTTGATAAATTTCTTGAA
25845401 AATATTT
1 AATATTT
25845408 CATAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 17 0.49
33 18 0.51
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (32 bp):
AATATTTTCTGGTGTTTGATAAATTTCTTGAA
Found at i:25845799 original size:15 final size:16
Alignment explanation
Indices: 25845778--25845825 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
25845768 TATACTACAA
25845778 AATATTTATTATTAAT
1 AATATTTATTATTAAT
*
25845794 -ATATTTATAATTGTAAT
1 AATATTTATTA-T-TAAT
25845811 AAATATTTATTATTA
1 -AATATTTATTATTA
25845826 GAATATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 9 0.35
16 1 0.04
17 6 0.23
18 1 0.04
19 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AATATTTATTATTAAT
Found at i:25845896 original size:13 final size:14
Alignment explanation
Indices: 25845863--25845906 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
25845853 ATATGTGAAG
*
25845863 AATATTATT-TAAA
1 AATATTATTATTAA
*
25845876 AATATTATTTTTAA
1 AATATTATTATTAA
25845890 AAT-TTATTATTAA
1 AATATTATTATTAA
25845903 AATA
1 AATA
25845907 AAATTGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:25845897 original size:16 final size:16
Alignment explanation
Indices: 25845865--25845904 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
25845855 ATGTGAAGAA
25845865 TATTATTTAAAAATAT
1 TATTATTTAAAAATAT
25845881 TATT-TTT-AAAAT-T
1 TATTATTTAAAAATAT
25845894 TATTA-TTAAAA
1 TATTATTTAAAA
25845905 TAAAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 3 0.14
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTTAAAAATAT
Found at i:25845940 original size:16 final size:19
Alignment explanation
Indices: 25845915--25845970 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
25845905 TAAAATTGAA
25845915 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAT
25845934 A-A-TAATAAATTGTATTAATT
1 ATATTAAT-AATT-TATTAA-T
25845954 ATATTAATAATTTATTA
1 ATATTAATAATTTATTA
25845971 TATGACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 7 0.23
19 1 0.03
20 6 0.19
21 5 0.16
22 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTAATAATTTATTAAT
Found at i:25848539 original size:19 final size:19
Alignment explanation
Indices: 25848515--25848560 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
25848505 GTTGGGTAAT
*
25848515 GTGACACTGAGCTGATGTC
1 GTGACACTAAGCTGATGTC
25848534 GTGACACTAAGCTGATGTC
1 GTGACACTAAGCTGATGTC
25848553 GTGACACT
1 GTGACACT
25848561 TGGCTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (19 bp):
GTGACACTAAGCTGATGTC
Found at i:25866874 original size:21 final size:21
Alignment explanation
Indices: 25866848--25866901 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
25866838 TGTGTTTTTA
*
25866848 GTATCGGTAGATG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
*
25866869 GTATCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTCATACTT
25866890 GTATCGGTAGAA
1 GTATCGGTAGAA
25866902 CTAGCACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:25879843 original size:12 final size:12
Alignment explanation
Indices: 25879828--25879859 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25879818 AAAGAAGAGA
25879828 AAGAAGAAAAGG
1 AAGAAGAAAAGG
*
25879840 AAGAAGAGAAGG
1 AAGAAGAAAAGG
25879852 AAGAAGAA
1 AAGAAGAA
25879860 GAAAGCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAGG
Found at i:25880910 original size:10 final size:10
Alignment explanation
Indices: 25880883--25880942 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
25880873 TCAGTCGCAT
25880883 AAAGAAAAGAA
1 AAAG-AAAGAA
25880894 AAA-AAAGAA
1 AAAGAAAGAA
25880903 AAAGAAAG-A
1 AAAGAAAGAA
** *
25880912 AAAGTTGATAA
1 AAAG-AAAGAA
25880923 AAAGAAAGAA
1 AAAGAAAGAA
25880933 AAAGAAAGAA
1 AAAGAAAGAA
25880943 TATATACATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 14 0.35
10 18 0.45
11 8 0.20
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:25887088 original size:22 final size:22
Alignment explanation
Indices: 25887063--25887119 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
25887053 TAAAAATTCA
25887063 AAATAAAATAATTAGAGCT-A-AT
1 AAATAAAAT-ATTAG-GCTCATAT
*
25887085 AAATATAATATTAGGCTCATAT
1 AAATAAAATATTAGGCTCATAT
25887107 ATAATAAAA-ATTA
1 A-AATAAAATATTA
25887120 AGCCTAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 6 0.20
22 15 0.50
23 6 0.20
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
AAATAAAATATTAGGCTCATAT
Found at i:25888354 original size:24 final size:24
Alignment explanation
Indices: 25888323--25888397 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
25888313 CCAGACAAAA
*
25888323 TTAGCTCTTACGAGCTCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
25888347 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
25888371 TTAGCTCTTACAAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
25888395 TTA
1 TTA
25888398 ACCAATATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:25898748 original size:18 final size:18
Alignment explanation
Indices: 25898719--25898762 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
25898709 AAATGTACAA
* *
25898719 ACAAAT-AAAATGTAGTG
1 ACAAATAAAAATGCAATG
25898736 ACAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
*
25898754 ACAACTAAA
1 ACAAATAAA
25898763 TGAGATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:25899194 original size:12 final size:12
Alignment explanation
Indices: 25899159--25899213 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
25899149 TATCGGGGCA
25899159 TCTTCCTTCTCT
1 TCTTCCTTCTCT
* *
25899171 TCACTCTTCTTCTTT
1 T--CT-TCCTTCTCT
25899186 TCTTCCTTCTCT
1 TCTTCCTTCTCT
25899198 TCTTCCTTCTCT
1 TCTTCCTTCTCT
25899210 TCTT
1 TCTT
25899214 TAGTTTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 24 0.67
13 2 0.06
14 2 0.06
15 8 0.22
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTTCCTTCTCT
Found at i:25903564 original size:17 final size:18
Alignment explanation
Indices: 25903542--25903576 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25903532 GTTCTGTTTC
25903542 TTCCTTC-TCTTCTTTTT
1 TTCCTTCATCTTCTTTTT
*
25903559 TTCCTTCATTTTCTTTTT
1 TTCCTTCATCTTCTTTTT
25903577 CTTCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCCTTCATCTTCTTTTT
Found at i:25903591 original size:18 final size:18
Alignment explanation
Indices: 25903542--25903591 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
25903532 GTTCTGTTTC
*
25903542 TTCCTTC-TCTTCTTTTT
1 TTCCTTCATCTTCTCTTT
25903559 TTCCTTCAT-TT-TCTTT
1 TTCCTTCATCTTCTCTTT
25903575 TT-CTTCATCCTTCTCTT
1 TTCCTTCAT-CTTCTCTT
25903592 GGTCACCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 11 0.39
18 5 0.18
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCCTTCATCTTCTCTTT
Found at i:25924253 original size:24 final size:24
Alignment explanation
Indices: 25924226--25924271 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
25924216 TTGGAGCTTT
*
25924226 GATTAATTAATATACCTTTTTTGG
1 GATTAATTAACATACCTTTTTTGG
*
25924250 GATTAATTAACATACTTTTTTT
1 GATTAATTAACATACCTTTTTT
25924272 TACTAACCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (24 bp):
GATTAATTAACATACCTTTTTTGG
Found at i:25924314 original size:29 final size:30
Alignment explanation
Indices: 25924282--25924348 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
25924272 TACTAACCCG
* *
25924282 TTTAAT-TTTT-TTAATTTTAATTTAATTTA
1 TTTAATATTTTATTAATATTAATTTAA-TAA
25924311 TTTAATAATTTTAATTAATATTAATTTAATAA
1 TTTAAT-ATTTT-ATTAATATTAATTTAATAA
25924343 TTTAAT
1 TTTAAT
25924349 CCAAGAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
31 4 0.12
32 8 0.25
33 14 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTAATATTTTATTAATATTAATTTAATAA
Found at i:25924335 original size:33 final size:31
Alignment explanation
Indices: 25924284--25924348 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
25924274 CTAACCCGTT
* * *
25924284 TAATTTTTTTAATTTTAATTTAATTTATTTAA
1 TAATTTTATTAATATTAATTTAA-TAATTTAA
25924316 TAATTTTAATTAATATTAATTTAATAATTTAA
1 TAATTTT-ATTAATATTAATTTAATAATTTAA
25924348 T
1 T
25924349 CCAAGAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TAATTTTATTAATATTAATTTAATAATTTAA
Found at i:25924342 original size:24 final size:23
Alignment explanation
Indices: 25924282--25924345 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
25924272 TACTAACCCG
25924282 TTTAATTT-TTT--TAATTTTAA
1 TTTAATTTATTTAATAATTTTAA
25924302 TTTAATTTATTTAATAATTTTAA
1 TTTAATTTATTTAATAATTTTAA
25924325 -TTAATATTAATTTAATAATTT
1 TTTAAT-TT-ATTTAATAATTT
25924346 AATCCAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.21
21 3 0.08
22 5 0.13
23 11 0.28
24 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAATTTATTTAATAATTTTAA
Found at i:25924347 original size:13 final size:13
Alignment explanation
Indices: 25924304--25924348 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
25924294 AATTTTAATT
25924304 TAATTT-ATTTAA
1 TAATTTAATTTAA
25924316 TAATTTTAA-TTAA
1 TAA-TTTAATTTAA
25924329 T-A-TTAATTTAA
1 TAATTTAATTTAA
25924340 TAATTTAAT
1 TAATTTAAT
25924349 CCAAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.14
11 5 0.18
12 5 0.18
13 13 0.46
14 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTAATTTAA
Found at i:25928371 original size:41 final size:41
Alignment explanation
Indices: 25928325--25928403 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
25928315 GAAAAAAGAA
*
25928325 ATTCAAACAAAAAAATCCAAGAAATGCGATTCAATGTACAG
1 ATTCAAACAAAAAAATCCAAGAAATGCCATTCAATGTACAG
*** *
25928366 ATTCAAACCCTAATATCCAAGAAATGCCATTCAATGTA
1 ATTCAAACAAAAAAATCCAAGAAATGCCATTCAATGTA
25928404 TCCTTTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (41 bp):
ATTCAAACAAAAAAATCCAAGAAATGCCATTCAATGTACAG
Found at i:25930226 original size:195 final size:195
Alignment explanation
Indices: 25929893--25930328 Score: 556
Period size: 195 Copynumber: 2.2 Consensus size: 195
25929883 ACGTGATAAA
* * * * *
25929893 TGAGGTATCGCATATGTTTCGAGTCCTCGACAGTTCGTGTGAGTAGCATCATGAGTCCAAAAATG
1 TGAGGTACCGCATATGTTACGAGTCCTCGATAGCTCGTGTGAGCAGCATCATGAGTCCAAAAATG
* * **
25929958 AGTAAAGAATCCAAGAATGGATTACAAGCCTTACAATGGTTGAGATTTATGCATAAGTGCATATT
66 AGTAAAGAATCCAAGAATGGATTACAAGCCTTACAATGGCTGAGACTTATGCATAAGTGCATACA
* * ** * *
25930023 CTCGACAGCTCATGTGAGCAGCATCGTTAAGGA-ACAGTTATATGCACAGATACCATATCAATGG
131 CCCGACAGCTCATGTGAGCAGCATCGTT-AGGAGACAATTATATAAACAGACACCATACCAATGG
25930087 C
195 C
* * *
25930088 TGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTCATGTGAGCAGCATCATGAGTCTGAAAAAT
1 TGAGGTACCGCATATGTTACGAGTCCTCGATAGCTCGTGTGAGCAGCATCATGAGTC-CAAAAAT
* * * * *
25930153 -AG-ATATGAATCCTAGAATGGATTACAGGCCTTGCGATGGCTGAGACTTATGCATAAGTGCATA
65 GAGTA-AAGAATCCAAGAATGGATTACAAGCCTTACAATGGCTGAGACTTATGCATAAGTGCATA
* *
25930216 CACCCGACAGCTCGTGTGAGCAGCATCGTTAGGAGACAATTATATAAACAGACACCGTACCAATG
129 CACCCGACAGCTCATGTGAGCAGCATCGTTAGGAGACAATTATATAAACAGACACCATACCAATG
*
25930281 GT
194 GC
* * *
25930283 TG-GGTACCGCATATGTTATGAGTCATCGATAGCTCGTGTGACCAGC
1 TGAGGTACCGCATATGTTACGAGTCCTCGATAGCTCGTGTGAGCAGC
25930329 TTCGAGTACT
Statistics
Matches: 208, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
194 44 0.21
195 158 0.76
196 6 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (195 bp):
TGAGGTACCGCATATGTTACGAGTCCTCGATAGCTCGTGTGAGCAGCATCATGAGTCCAAAAATG
AGTAAAGAATCCAAGAATGGATTACAAGCCTTACAATGGCTGAGACTTATGCATAAGTGCATACA
CCCGACAGCTCATGTGAGCAGCATCGTTAGGAGACAATTATATAAACAGACACCATACCAATGGC
Found at i:25931131 original size:21 final size:21
Alignment explanation
Indices: 25931079--25931132 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
25931069 GGATTTTTTA
*
25931079 GTATCGATAGAAGCATGCATT
1 GTATCGATAGAAGCATGCACT
* * *
25931100 ATTTCGGTAGAAGTCAT-CACT
1 GTATCGATAGAAG-CATGCACT
25931121 GTATCGATAGAA
1 GTATCGATAGAA
25931133 CCATCACCAC
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (21 bp):
GTATCGATAGAAGCATGCACT
Found at i:25934142 original size:42 final size:42
Alignment explanation
Indices: 25934084--25934168 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
25934074 TTAAAATGCG
*
25934084 ATAATTTGTTAAAATAGTTATCGGAGCAATAACTTGAAAATA
1 ATAATTTGTGAAAATAGTTATCGGAGCAATAACTTGAAAATA
* *
25934126 ATAATTTGTGATAATAGTTGTCGGAGCAATAACTTGAAAATA
1 ATAATTTGTGAAAATAGTTATCGGAGCAATAACTTGAAAATA
25934168 A
1 A
25934169 AAACGAACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (42 bp):
ATAATTTGTGAAAATAGTTATCGGAGCAATAACTTGAAAATA
Found at i:25935535 original size:15 final size:15
Alignment explanation
Indices: 25935511--25935545 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25935501 TATACATATT
*
25935511 TTTTTTTCTTTTCCC
1 TTTTTCTCTTTTCCC
*
25935526 TTTTTCTCTTTTCTC
1 TTTTTCTCTTTTCCC
25935541 TTTTT
1 TTTTT
25935546 TTTATATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTCTTTTCCC
Found at i:25950091 original size:12 final size:12
Alignment explanation
Indices: 25950071--25950106 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
25950061 TACATTGTAG
25950071 TATTATATATTT
1 TATTATATATTT
*
25950083 TATTTTATATTT
1 TATTATATATTT
25950095 TA-TATATATTT
1 TATTATATATTT
25950106 T
1 T
25950107 TATATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATATATTT
Found at i:25950116 original size:21 final size:21
Alignment explanation
Indices: 25950073--25950116 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25950063 CATTGTAGTA
*
25950073 TTATATATTTTATTTTATATT
1 TTATATATTTTATTATATATT
*
25950094 TTATATATATTT-TTATATGTT
1 TTATATAT-TTTATTATATATT
25950115 TT
1 TT
25950117 TTTAAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATATATTTTATTATATATT
Found at i:25953010 original size:37 final size:37
Alignment explanation
Indices: 25952959--25953029 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
25952949 TTCCGGCTTA
*
25952959 TAGACATCTTTTCTATGAATATATAAAGCATTCAAAT
1 TAGACATCTGTTCTATGAATATATAAAGCATTCAAAT
25952996 TAGACATCTGTTCTATGAATATATAAAGCATTCA
1 TAGACATCTGTTCTATGAATATATAAAGCATTCA
25953030 TATTTCATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (37 bp):
TAGACATCTGTTCTATGAATATATAAAGCATTCAAAT
Found at i:25955727 original size:136 final size:135
Alignment explanation
Indices: 25955424--25955802 Score: 542
Period size: 136 Copynumber: 2.8 Consensus size: 135
25955414 GTTTGTTCAC
* *
25955424 AATCAACAGTAAGAAAGAAAAATATGGAATACCCACAAAGGGATTATGGGTAAACAAGCCGATAC
1 AATCAACAGTAAGAAAGAAAAATATGGAATACCCACAAAGGGATTGTGGGTAAACAAGCCGATTC
* * * *
25955489 AGATCAGAAAAAATCGGATTGAGAAACTAATTATTCGAGAACCTGGAATACAACAAAGGTAAATC
66 AGAT-A-AAAAAATCGAATTGAGAAACCAATTATTCAAGAACCTGGAATAAAACAAAGGTAAATC
*
25955554 GGCACAA
129 AGCACAA
* * * *
25955561 AATTAGCAGTAAGAAAGAAAAATTTGGAATACCCACAAAGTGATTGTGGGTAAACAAGCCGATTC
1 AATCAACAGTAAGAAAGAAAAATATGGAATACCCACAAAGGGATTGTGGGTAAACAAGCCGATTC
* * *
25955626 AGATAAAAAAATCGAATTAAGAAACCAATTATTCAAGAACCTGTAGTAAACACAAAGGTAAATCA
66 AGATAAAAAAATCGAATTGAGAAACCAATTATTCAAGAACCTGGAATAAA-ACAAAGGTAAATCA
25955691 GCACAA
130 GCACAA
* * * ***
25955697 AATCAACAGTAAGAAAGAAAAATCTAGAATAACCACAAAGGGATTGTGAACAAACAAGCCGATTC
1 AATCAACAGTAAGAAAGAAAAATATGGAATACCCACAAAGGGATTGTGGGTAAACAAGCCGATTC
*
25955762 AGGTAAAAAAATCGAATTGAGAAACCAATTATTCAAGAACC
66 AGATAAAAAAATCGAATTGAGAAACCAATTATTCAAGAACC
25955803 GTGAAAGAAG
Statistics
Matches: 216, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
135 38 0.18
136 115 0.53
137 63 0.29
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (135 bp):
AATCAACAGTAAGAAAGAAAAATATGGAATACCCACAAAGGGATTGTGGGTAAACAAGCCGATTC
AGATAAAAAAATCGAATTGAGAAACCAATTATTCAAGAACCTGGAATAAAACAAAGGTAAATCAG
CACAA
Found at i:25956030 original size:14 final size:14
Alignment explanation
Indices: 25956011--25956038 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25956001 GTTTAAAATT
25956011 TTTATTTAATTAAA
1 TTTATTTAATTAAA
25956025 TTTATTTAATTAAA
1 TTTATTTAATTAAA
25956039 AATCTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTTAATTAAA
Found at i:25967994 original size:21 final size:21
Alignment explanation
Indices: 25967957--25967996 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25967947 ATTTCTACCG
*
25967957 ATACAAGTGATAGTTCTACTT
1 ATACAAGTGATACTTCTACTT
25967978 ATACAAGTG-TCACTTCTAC
1 ATACAAGTGAT-ACTTCTAC
25967997 CAAAACAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (21 bp):
ATACAAGTGATACTTCTACTT
Found at i:25975111 original size:21 final size:21
Alignment explanation
Indices: 25975067--25975114 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
25975057 CTTGTGATTG
* *
25975067 TTCTACCGATACAAGTGTGAC
1 TTCTACCGAAACAAGTATGAC
25975088 TTCTACCGAAACAAGTCATG-C
1 TTCTACCGAAACAAGT-ATGAC
25975109 TTCTAC
1 TTCTAC
25975115 TGATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAC
Found at i:25977251 original size:20 final size:21
Alignment explanation
Indices: 25977226--25977264 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25977216 TAGACTTTTA
25977226 TCATTAA-CTTAATTAATCAC
1 TCATTAACCTTAATTAATCAC
25977246 TCATTAACCTTAATTAATC
1 TCATTAACCTTAATTAATC
25977265 CTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (21 bp):
TCATTAACCTTAATTAATCAC
Found at i:25979537 original size:34 final size:34
Alignment explanation
Indices: 25979492--25979594 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 34
25979482 AGAATATGAA
*
25979492 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAGGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
* *
25979526 ATGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
*
25979560 AAGTTAAGGAAGATGGAAGGTTAAAAGATGAAAGG
1 AAGTTAAGGAAGATGGAAGGTT-AAAGATCAAAGG
25979595 TTGAACATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
34 52 0.84
35 10 0.16
ACGTcount: A:0.45, C:0.02, G:0.35, T:0.18
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
Found at i:25982337 original size:34 final size:34
Alignment explanation
Indices: 25982292--25982394 Score: 145
Period size: 34 Copynumber: 3.0 Consensus size: 34
25982282 AGAATATGAA
25982292 AAGTTAAGGAAGATGGAAGGTTAAAGATC-AAGAG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAG-G
* *
25982326 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
* *
25982360 AAGTTAAGAAAGATGGAAGGTTAAAAGATGAAAGG
1 AAGTTAAGGAAGATGGAAGGTT-AAAGATCAAAGG
25982395 TTGAACATCC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 48 0.79
35 13 0.21
ACGTcount: A:0.47, C:0.02, G:0.34, T:0.17
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
Found at i:25982346 original size:17 final size:17
Alignment explanation
Indices: 25982294--25982396 Score: 74
Period size: 17 Copynumber: 6.2 Consensus size: 17
25982284 AATATGAAAA
25982294 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
* ** *
25982311 GTTAAAGATCA-AGAGAG
1 GTTAAGGAAGATGGA-AG
25982328 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
25982345 GTTAAAGGTCAA-A-GGAA-
1 GTT-AAGG--AAGATGGAAG
*
25982362 GTTAAGAAAGATGGAAG
1 GTTAAGGAAGATGGAAG
*
25982379 GTTAA--AAGATGAAAG
1 GTTAAGGAAGATGGAAG
25982394 GTT
1 GTT
25982397 GAACATCCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.03
15 13 0.19
16 9 0.13
17 31 0.46
18 10 0.15
19 1 0.01
20 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.34, T:0.19
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:25987039 original size:30 final size:31
Alignment explanation
Indices: 25986990--25987084 Score: 99
Period size: 30 Copynumber: 3.1 Consensus size: 31
25986980 TTATGTTTTA
* * *
25986990 ACCCTCAAACTGTCTAAAAATTTC-AATTTG
1 ACCCTCGAACTTTCCAAAAATTTCAAATTTG
25987020 ACTCCT-GAACTTTCCAAAAA-TTCAAATTTG
1 AC-CCTCGAACTTTCCAAAAATTTCAAATTTG
* *
25987050 ACCTTCGAACTTTTCAAAAA-TTCAAATTTTG
1 ACCCTCGAACTTTCCAAAAATTTCAAA-TTTG
25987081 ACCC
1 ACCC
25987085 GGTTTCAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 5 0.09
30 40 0.73
31 10 0.18
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (31 bp):
ACCCTCGAACTTTCCAAAAATTTCAAATTTG
Found at i:25997770 original size:30 final size:29
Alignment explanation
Indices: 25997695--25997780 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
25997685 AAAATTATAT
* *
25997695 TTTGACCCCTAAACTATCCAAAAATTTGAA
1 TTTGA-CCCTAAACTTTCCAAAAATTTCAA
25997725 TTTGACCCTCAAACTTTCCAAAAATTTCAA
1 TTTGACCCT-AAACTTTCCAAAAATTTCAA
* *
25997755 TTT-ATTCCCTGAACTTCCCAAAAATT
1 TTTGA--CCCTAAACTTTCCAAAAATT
25997781 CAAATTCAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.10
30 40 0.82
31 4 0.08
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTGACCCTAAACTTTCCAAAAATTTCAA
Found at i:25997799 original size:30 final size:31
Alignment explanation
Indices: 25997712--25997800 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 31
25997702 CCTAAACTAT
* * *
25997712 CCAAAAATTTGAATT--TGACCCTCAAACTTT
1 CCAAAAATTTCAATTCAT-ACCCTCGAACTTC
* *
25997742 CCAAAAATTTCAATTTATTCCCT-GAACTTC
1 CCAAAAATTTCAATTCATACCCTCGAACTTC
25997772 CCAAAAA-TTCAAATTCA-ACCCTCGAACTT
1 CCAAAAATTTC-AATTCATACCCTCGAACTT
25997801 TTCAAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
29 7 0.14
30 37 0.76
31 4 0.08
32 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (31 bp):
CCAAAAATTTCAATTCATACCCTCGAACTTC
Found at i:25997807 original size:30 final size:31
Alignment explanation
Indices: 25997729--25997816 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 31
25997719 TTTGAATTTG
* *
25997729 ACCCTCAAACTTTCCAAAAATTTC-AATTTAT
1 ACCCTCGAACTTTCCAAAAA-TTCAAATTCAT
* *
25997760 TCCCT-GAACTTCCCAAAAATTCAAATTCA-
1 ACCCTCGAACTTTCCAAAAATTCAAATTCAT
* * *
25997789 ACCCTCGAACTTTTCAAAATTTTAAATT
1 ACCCTCGAACTTTCCAAAAATTCAAATT
25997817 TTGACCCGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 7 0.15
30 35 0.76
31 4 0.09
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (31 bp):
ACCCTCGAACTTTCCAAAAATTCAAATTCAT
Found at i:25999020 original size:18 final size:18
Alignment explanation
Indices: 25998997--25999031 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25998987 TTTCATGGTT
25998997 AATAAAA-AAAATATTTAA
1 AATAAAATAAAAT-TTTAA
25999015 AATAAAATAAAATTTTA
1 AATAAAATAAAATTTTA
25999032 TTTCAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAATAAAATTTTAA
Found at i:26003705 original size:41 final size:41
Alignment explanation
Indices: 26003622--26003869 Score: 347
Period size: 41 Copynumber: 6.1 Consensus size: 41
26003612 AAACGCTGCA
* *
26003622 AAAGGT-AGGGCAATAGCGGCGCTTAT-GGGAAGCGCCACT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
* *
26003661 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGTCGTT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
26003702 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
** *
26003743 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAACCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
* * ** *
26003784 AAAGGTTAGAGTAATAGCGGCGCTTATTAGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
* * *
26003825 AAAGGTCAGAGCATTAGCGGCGCTTATGAGGAAGCCCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
26003866 AAAG
1 AAAG
26003870 CTCAATAATA
Statistics
Matches: 186, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 6 0.03
40 19 0.10
41 161 0.87
ACGTcount: A:0.29, C:0.21, G:0.33, T:0.17
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGGGAAGCGCCGCT
Found at i:26004003 original size:34 final size:36
Alignment explanation
Indices: 26003926--26004003 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 36
26003916 ATAATATTAA
*
26003926 AAATTATTTTAAAACTTATATATACTAAAAAAAATT
1 AAATTATTTTAAAACTTATATAAACTAAAAAAAATT
26003962 AAA--ATTTTAAAACTTATATAAACT-AAAAAAA-T
1 AAATTATTTTAAAACTTATATAAACTAAAAAAAATT
26003994 AAATTATTTT
1 AAATTATTTT
26004004 GGTTTTATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
32 4 0.10
33 7 0.18
34 25 0.64
36 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (36 bp):
AAATTATTTTAAAACTTATATAAACTAAAAAAAATT
Found at i:26008489 original size:86 final size:86
Alignment explanation
Indices: 26008339--26008561 Score: 290
Period size: 86 Copynumber: 2.6 Consensus size: 86
26008329 TTTGTTAATG
* * * *
26008339 TTAGTGGTGTTTGTGGGAAAAGCACTGCTAAAGA-TCATGTTCTTTAGCAGCGTTTGTAGGAAAA
1 TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACT-ATGTTCTTTAGCGGCGTTTGTAGGAAAA
26008403 GCGTCGTTAAAGAACATGGTCT
65 GCGTCGTTAAAGAACATGGTCT
* * *
26008425 TTAGCGGTGTTTGTGAGAAAAGCGCCGTTAAAGACTATGTTCTTTAGCGGTGTTTGT-GAGAAAA
1 TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACTATGTTCTTTAGCGGCGTTTGTAG-GAAAA
* * *
26008489 GCGTTGTTAAAGACCATGTTCT
65 GCGTCGTTAAAGAACATGGTCT
**
26008511 TTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGAAC-ATGTTCTTTAGCGGC
1 TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAG-ACTATGTTCTTTAGCGGC
26008562 ATTTTTTCAA
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
85 1 0.01
86 115 0.97
87 3 0.03
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.31
Consensus pattern (86 bp):
TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACTATGTTCTTTAGCGGCGTTTGTAGGAAAAG
CGTCGTTAAAGAACATGGTCT
Found at i:26008565 original size:43 final size:43
Alignment explanation
Indices: 26008347--26008561 Score: 261
Period size: 43 Copynumber: 5.0 Consensus size: 43
26008337 TGTTAGTGGT
* * * * *
26008347 GTTTGTGGGAAAAGCACTGCTAAAGATCATGTTCTTTAGCAGC
1 GTTTGTGGGAAAAGCGCCGTTAAAGAACATGTTCTTTAGCGGC
* * * *
26008390 GTTTGTAGGAAAAGCGTCGTTAAAGAACATGGTCTTTAGCGGT
1 GTTTGTGGGAAAAGCGCCGTTAAAGAACATGTTCTTTAGCGGC
* *
26008433 GTTTGTGAGAAAAGCGCCGTTAAAG-ACTATGTTCTTTAGCGGT
1 GTTTGTGGGAAAAGCGCCGTTAAAGAAC-ATGTTCTTTAGCGGC
* ** *
26008476 GTTTGTGAGAAAAGCGTTGTTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGTTAAAGAACATGTTCTTTAGCGGC
* *
26008519 ATTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGTTAAAGAACATGTTCTTTAGCGGC
26008562 ATTTTTTCAA
Statistics
Matches: 147, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
42 2 0.01
43 144 0.98
44 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (43 bp):
GTTTGTGGGAAAAGCGCCGTTAAAGAACATGTTCTTTAGCGGC
Found at i:26010297 original size:25 final size:25
Alignment explanation
Indices: 26010269--26010327 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
26010259 TAAAGAGTCA
* * * *
26010269 TACACGGCATTCTTTTATAGTTCCT
1 TACACGCCATTATTTCATAGCTCCT
*
26010294 TACATGCCATTATTTCATAGCTCCT
1 TACACGCCATTATTTCATAGCTCCT
26010319 TACACGCCA
1 TACACGCCA
26010328 ATCATTTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (25 bp):
TACACGCCATTATTTCATAGCTCCT
Found at i:26010662 original size:58 final size:58
Alignment explanation
Indices: 26010577--26010731 Score: 138
Period size: 58 Copynumber: 2.7 Consensus size: 58
26010567 GTCATGAAGA
* * * * *
26010577 CTTTCCT-TTCAGAGGTTTACCATAAAGGC-TATCTTTTAACAAAGATCACCACAAAGG
1 CTTTCCTATCCAGAGTTTTGCCACAAAGGCAT-TCCTTTAACAAAGATCACCACAAAGG
* * * * * * *
26010634 CTTTCTTGTCTATG-GTTTTGCCACAAAGGCATTCCTTTAATAGAGATCGCCACAAAGT
1 CTTTCCTATCCA-GAGTTTTGCCACAAAGGCATTCCTTTAACAAAGATCACCACAAAGG
*
26010692 CTTTCCTATCCAGAGTTTTGCCACAAAAG-ATTTCCTTTAA
1 CTTTCCTATCCAGAGTTTTGCCACAAAGGCA-TTCCTTTAA
26010732 GAGGTTCGCC
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
57 8 0.10
58 68 0.87
59 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (58 bp):
CTTTCCTATCCAGAGTTTTGCCACAAAGGCATTCCTTTAACAAAGATCACCACAAAGG
Found at i:26012015 original size:6 final size:7
Alignment explanation
Indices: 26011999--26012024 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
26011989 AAAGCCATCC
26011999 AAAATTA
1 AAAATTA
26012006 AAAATTA
1 AAAATTA
26012013 AAAATTA
1 AAAATTA
26012020 AAAAT
1 AAAAT
26012025 GTCCAAGTCC
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:26027448 original size:17 final size:17
Alignment explanation
Indices: 26027415--26027510 Score: 102
Period size: 17 Copynumber: 5.6 Consensus size: 17
26027405 CTAACTTTTA
*
26027415 ATTTTAAAATTTTAATTT
1 ATTTT-AAATTTAAATTT
* *
26027433 ATTTTAGATTTGAATTT
1 ATTTTAAATTTAAATTT
*
26027450 ATTTTAAATTTAAATTC
1 ATTTTAAATTTAAATTT
***
26027467 ATTTTGGGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
26027484 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
*
26027501 ATTTTGAATT
1 ATTTTAAATT
26027511 AAAAATTGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
17 59 0.92
18 5 0.08
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:26027471 original size:34 final size:34
Alignment explanation
Indices: 26027415--26027513 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
26027405 CTAACTTTTA
* *
26027415 ATTTTAAAATTTTAATTTATTTTAGATTTGAATTT
1 ATTTT-AAATTTAAATTTATTTTAGATTTAAATTT
* * *
26027450 ATTTTAAATTTAAATTCATTTTGGGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTTAGATTTAAATTT
* *
26027484 ATTTTAAATTTGAATTTATTTT-GAATTAAA
1 ATTTTAAATTTAAATTTATTTTAGATTTAAA
26027514 AATTGTTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 6 0.11
34 44 0.80
35 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTTAGATTTAAATTT
Found at i:26028278 original size:20 final size:21
Alignment explanation
Indices: 26028229--26028295 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
26028219 CATAATATTA
* *
26028229 AATAATAATAACTATTTTGAT
1 AATAATAATAAATATTTAGAT
* *
26028250 AATAGTAATAAATGTTTAG-T
1 AATAATAATAAATATTTAGAT
26028270 AATAATAATAAATACTTTA-AT
1 AATAATAATAAATA-TTTAGAT
26028291 AATAA
1 AATAA
26028296 AAAGAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (21 bp):
AATAATAATAAATATTTAGAT
Done.