Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 71 of 206
Found at i:20067564 original size:22 final size:22
Alignment explanation
Indices: 20067539--20067591 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20067529 TTTTTTATTT
20067539 ATTTTAAAGATT-TT-TTAAAAA
1 ATTTTAAA-ATTATTGTTAAAAA
* *
20067560 AATTTACAATTATTGTTAAAAA
1 ATTTTAAAATTATTGTTAAAAA
20067582 ATTTTAAAAT
1 ATTTTAAAAT
20067592 GTCAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
22 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTTAAAATTATTGTTAAAAA
Found at i:20072842 original size:10 final size:10
Alignment explanation
Indices: 20072819--20072862 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
20072809 TTCATTCTTT
20072819 AAAATTTT-A
1 AAAATTTTAA
20072828 AAAATTTTAA
1 AAAATTTTAA
*
20072838 AAAATTATAA
1 AAAATTTTAA
20072848 AACAACTTTTAA
1 AA-AA-TTTTAA
20072860 AAA
1 AAA
20072863 TTAGAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.27
10 12 0.40
11 3 0.10
12 7 0.23
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:20072933 original size:27 final size:27
Alignment explanation
Indices: 20072854--20072933 Score: 65
Period size: 29 Copynumber: 2.9 Consensus size: 27
20072844 ATAAAACAAC
* * * *
20072854 TTTTAAAAATTAGAAATCACTAAA-AA
1 TTTTTAAAATTAAAAATAATTAAATAA
* *
20072880 TTTTT-AAATTATAAAATATATAAAAATAT
1 TTTTTAAAATTA-AAAATA-AT-TAAATAA
20072909 TTTTTAAAATTAAAAATAATTAAAT
1 TTTTTAAAATTAAAAATAATTAAAT
20072934 GATGATGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
25 6 0.14
26 8 0.19
27 5 0.12
28 5 0.12
29 12 0.29
30 6 0.14
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (27 bp):
TTTTTAAAATTAAAAATAATTAAATAA
Found at i:20075332 original size:12 final size:13
Alignment explanation
Indices: 20075304--20075333 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20075294 TCTAGTCATA
20075304 TAATAAATTATTT
1 TAATAAATTATTT
20075317 TAATAAATTA-TT
1 TAATAAATTATTT
20075329 TAATA
1 TAATA
20075334 TTTCAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAAATTATTT
Found at i:20075438 original size:15 final size:15
Alignment explanation
Indices: 20075418--20075474 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
20075408 ATTGAGTATT
20075418 AATATTTTAATAATA
1 AATATTTTAATAATA
*
20075433 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
* *
20075452 AATATATTAATAAAA
1 AATATTTTAATAATA
20075467 AATATTTT
1 AATATTTT
20075475 GTAATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:20078179 original size:21 final size:20
Alignment explanation
Indices: 20078130--20078179 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
20078120 AAATTTGAAT
* *
20078130 CTATCGATACTTAACAAAAT
1 CTATCGATACTTAAAAAAAA
*
20078150 CTATTGATACTTGAAAAAAAA
1 CTATCGATACTT-AAAAAAAA
*
20078171 GTATCGATA
1 CTATCGATA
20078180 TAGGATCGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (20 bp):
CTATCGATACTTAAAAAAAA
Found at i:20078640 original size:2 final size:2
Alignment explanation
Indices: 20078633--20078672 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20078623 CTTGCTTTTA
20078633 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20078673 CCTTTTTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20081183 original size:19 final size:20
Alignment explanation
Indices: 20081150--20081203 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
20081140 AACCCAATAG
*
20081150 GTATCGATAATTTTTTGT-AA
1 GTATCGAT-ATTTTTTATAAA
20081170 GTATCGATATTTTTTATAAA
1 GTATCGATATTTTTTATAAA
*
20081190 GTGTCGATATTTTT
1 GTATCGATATTTTT
20081204 GTATCGGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.52
Consensus pattern (20 bp):
GTATCGATATTTTTTATAAA
Found at i:20081216 original size:20 final size:19
Alignment explanation
Indices: 20081150--20081219 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 19
20081140 AACCCAATAG
20081150 GTATCGATAATTTTTTGTA-A
1 GTATCGAT-A-TTTTTGTATA
20081170 GTATCGATATTTTT-TATAAA
1 GTATCGATATTTTTGTAT--A
* *
20081190 GTGTCGATATTTTTGTATCG
1 GTATCGATATTTTTGTAT-A
20081210 GTATCGATAT
1 GTATCGATAT
20081220 CAAATGCCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.05
18 5 0.12
19 1 0.02
20 31 0.74
21 3 0.07
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (19 bp):
GTATCGATATTTTTGTATA
Found at i:20087331 original size:20 final size:20
Alignment explanation
Indices: 20087287--20087336 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
20087277 AAATTTGAAT
*
20087287 CTATCGATACTCAACAAAAT
1 CTATCGATACTCAACAAAAA
**
20087307 CTATCGATACTTTACAAAAA
1 CTATCGATACTCAACAAAAA
* *
20087327 GTATCCATAC
1 CTATCGATAC
20087337 AGGACGGATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (20 bp):
CTATCGATACTCAACAAAAA
Found at i:20088144 original size:31 final size:31
Alignment explanation
Indices: 20088106--20088176 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
20088096 TTAAATCAAT
* * *
20088106 TTAAATTAAATTATTATATAATGTGATTAAA
1 TTAAATTAAAATATTACATAATGTAATTAAA
20088137 TTAAATTAAAATATTACATAATGTAATTAAA
1 TTAAATTAAAATATTACATAATGTAATTAAA
*
20088168 TTGAATTAA
1 TTAAATTAA
20088177 TAATGAGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (31 bp):
TTAAATTAAAATATTACATAATGTAATTAAA
Found at i:20089647 original size:20 final size:20
Alignment explanation
Indices: 20089624--20089670 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20089614 AATTAGAGAA
20089624 ATATATAAAAACATATATAT
1 ATATATAAAAACATATATAT
** *
20089644 ATATATAAAAGTATGTATAT
1 ATATATAAAAACATATATAT
20089664 ATATATA
1 ATATATA
20089671 TATGTGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
ATATATAAAAACATATATAT
Found at i:20092249 original size:217 final size:219
Alignment explanation
Indices: 20091950--20092422 Score: 699
Period size: 217 Copynumber: 2.2 Consensus size: 219
20091940 CTATGGTTTT
* * * * * *
20091950 AATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TG-ATTTCTTTCGTCTGCTCCACTGTAACC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTCGTCTACTCCACTGTAACC
* *
20092013 TCAGGGAGATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTGTTATT
66 TCAGGAAAATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATT
20092077 TTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCT
130 TTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCT
*
20092142 CAGGGAGATAAGACTCTG-GC-C-TC
195 CAGGGAGATAAGA-TCTGAACTCTTC
20092165 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTC-TTCAGTCTACTCCACTGTAAC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTC-GTCTACTCCACTGTAAC
* * *
20092229 CTTAGGAAAATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATT
65 CTCAGGAAAATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT
*
20092294 TTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCT
130 TTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCT
20092359 CAGGGAGATAAGATCTGAAACTCTTC
195 CAGGGAGATAAGATCTG-AACTCTTC
** * * *
20092385 GGTCTACTCCACTGTGACCTCAGGGAGATAAGACCTGA
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
20092423 TGCAATCTAC
Statistics
Matches: 232, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
215 30 0.13
216 9 0.04
217 154 0.66
218 3 0.01
219 1 0.00
220 35 0.15
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (219 bp):
AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTCGTCTACTCCACTGTAACC
TCAGGAAAATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTT
TAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
AGGGAGATAAGATCTGAACTCTTC
Found at i:20092286 original size:87 final size:87
Alignment explanation
Indices: 20092176--20092460 Score: 283
Period size: 87 Copynumber: 3.3 Consensus size: 87
20092166 ATCTGCTCCA
* * * *
20092176 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTTAGGAAAATA
1 CTGTAACTTCAGAGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTTAGGGAGATA
20092241 AGACCTGATGCGATCTACTCTG
66 AGACCTGATGCGATCTACTCTG
** * **
20092263 CTGTAACTTCAGAGAGATAAGATCCT-TTATT-TT-AATCCGCTCCACTGTAA-CTTCAGGGAGA
1 CTGTAACTTCAGAGAGATAAGAT-CTGAAATTCTTCAGTCTACTCCACTGTAACCTT-AGGGAGA
* ** * * * *
20092324 TAGGATAGTGTCTTCGATCTGCTCCG
64 TAAGA-CCTG-ATGCGATCTACTCTG
* * * * *
20092350 CTGTAA-TCTCAGGGAGATAAGATCTGAAACTCTTCGGTCTACTCCACTGTGACCTCAGGGAGAT
1 CTGTAACT-TCAGAGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTTAGGGAGAT
* *
20092414 AAGACCTGATGCAATCTACTCTA
65 AAGACCTGATGCGATCTACTCTG
20092437 CTGTAACTTCAGAGAGATAAGATC
1 CTGTAACTTCAGAGAGATAAGATC
20092461 CTTTATTTTA
Statistics
Matches: 152, Mismatches: 36, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
84 3 0.02
85 23 0.15
86 7 0.05
87 87 0.57
88 7 0.05
89 23 0.15
90 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (87 bp):
CTGTAACTTCAGAGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTTAGGGAGATA
AGACCTGATGCGATCTACTCTG
Found at i:20092365 original size:174 final size:174
Alignment explanation
Indices: 20091907--20092548 Score: 707
Period size: 174 Copynumber: 3.7 Consensus size: 174
20091897 ATTTGTTACG
** *
20091907 ATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTATGGTTTTAATCCGCTCCACTGCAACTTC
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAACTTC
* * * *
20091971 AGGGAGATAGGATTGATTTCTTTCG-TCTGCTCCACTGTAACCTCAGGGAGATAAAACCTG--AT
65 AGGGAGATAGGATAG-TGTC-TTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
* * * * **
20092033 GC--GA-TCTACTCTACTGTAA-CTTCA-GAGAGATAAGATCTGTTATTTTA
128 TCTTCAGTCTACTCCACTGTAACCTT-AGGA-AGATAAGACCTG--A-TGCA
** * * ** * * ** * *
20092080 ATCCGCTCCACTGTAACTTCA-AGGAGATAGGATAGTGT-CTTCGATCTGCTCCGCTGTAA-TCT
1 ATCTACTCTACTGTAACTTCAGA-GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACT-T
* * * * *
20092142 CAGGGAGATAAGACT-CTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
64 CAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
* *
20092206 TCTTCAGTCTACTCCACTGTAACCTTAGGAAAATAAGACCTGATGCG
128 TCTTCAGTCTACTCCACTGTAACCTTAGGAAGATAAGACCTGATGCA
*
20092253 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
* * *
20092318 GGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACTCT
66 GGGAGATAGGATAGTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCT
* * * *
20092383 TCGGTCTACTCCACTGTGACCTCAGGGAGATAAGACCTGATGCA
131 TCAGTCTACTCCACTGTAACCTTAGGAAGATAAGACCTGATGCA
20092427 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
* * *
20092492 GGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
66 GGGAGATAGGATAGTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
20092549 CTGGCTTCAA
Statistics
Matches: 395, Mismatches: 58, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
170 2 0.01
171 36 0.09
172 29 0.07
173 61 0.15
174 235 0.59
175 2 0.01
176 25 0.06
177 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (174 bp):
ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
GGGAGATAGGATAGTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCT
TCAGTCTACTCCACTGTAACCTTAGGAAGATAAGACCTGATGCA
Found at i:20092409 original size:46 final size:46
Alignment explanation
Indices: 20092117--20092854 Score: 274
Period size: 44 Copynumber: 16.8 Consensus size: 46
20092107 TAGGATAGTG
* * * *
20092117 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGACTCTG--GC
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGAC-CTGAAAC
* * * *
20092162 -C-TCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* * *
20092206 TCTTC-AGTCTACTCCACTGTAACCTTAGGAAAATAAGACCTG--A-
1 TCTTCGA-TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* ** * * **
20092249 --TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCT-TTA-
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTGAAAC
** ** * * ***
20092292 T-TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA--T-AGTG
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* * * *
20092334 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAC
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* *
20092380 TCTTCGGTCTACTCCACTGTGACCTCAGGGAGATAAGACCTG--A-
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* * * * * **
20092423 --TGCAATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTA-
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTGAAAC
** ** * * ***
20092466 T-TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA--T-AGTG
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* * * *
20092508 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTG----
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTGAAAC
* * * * * *
20092552 GCTTCAATCTGCTCCACTGTAACCTCAGGGAGAGAAGATCTGAAAT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* *
20092598 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTG--A-
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* ** * * * **
20092641 --TGCGATCTACTCTGCTATAACTTCAGAGAGATAAGATCCT-TTA-
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTGAAAC
** * * * ***
20092684 T-TTTAAT-TCGCTCCACTGTAACTTCAGGGAGATAGGA--T-AGTG
1 TCTTCGATCT-ACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* * *
20092726 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTG----
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTGAAAC
* * * * *
20092770 GCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
* *
20092816 TCTTTGGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGAC
20092855 TTGATGCGAT
Statistics
Matches: 525, Mismatches: 121, Indels: 93
0.71 0.16 0.13
Matches are distributed among these distances:
41 87 0.17
42 21 0.04
43 123 0.23
44 152 0.29
45 3 0.01
46 137 0.26
47 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGAAAC
Found at i:20092528 original size:87 final size:87
Alignment explanation
Indices: 20092251--20092584 Score: 302
Period size: 87 Copynumber: 3.8 Consensus size: 87
20092241 AGACCTGATG
* *
20092251 CGATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAAC
1 CGATCTACTCCGCTGTAATC-TCAGAGAGATAAGATCTC-TTATTTCAATCCGCTCCACTGTAAC
*
20092314 TTCAGGGAGATAGGATAGTGTCTT
64 CTCAGGGAGATAGGATAGTGTCTT
* * *** ** ** *
20092338 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACTCTTCGGTCTACTCCACTGTGAC
1 CGATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTTA-T-TTCAATCCGCTCCACTGTAAC
* ** * *
20092403 CTCAGGGAGATAAGA-CCTG-ATG
64 CTCAGGGAGATAGGATAGTGTCTT
* ** *
20092425 CAATCTACTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAAC
1 CGATCTACTCCGCTGTAATC-TCAGAGAGATAAGATCTC-TTATTTCAATCCGCTCCACTGTAAC
*
20092488 TTCAGGGAGATAGGATAGTGTCTT
64 CTCAGGGAGATAGGATAGTGTCTT
* * * *** *
20092512 TGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTTATTTCAATCCGCTCCACTGTAACCT
20092577 CAGGGAGA
66 CAGGGAGA
20092585 GAAGATCTGA
Statistics
Matches: 187, Mismatches: 50, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
85 28 0.15
86 4 0.02
87 121 0.65
88 6 0.03
89 28 0.15
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTTATTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:20092592 original size:218 final size:218
Alignment explanation
Indices: 20092301--20092939 Score: 1075
Period size: 218 Copynumber: 2.9 Consensus size: 218
20092291 ATTTTAATCC
* * ** * * * *
20092301 GCTCCACTGTAA-CTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGG
1 GCTCCGCTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
* * * *
20092364 AGATAAGATCTGAAACTCTTCGGTCTACTCCACTGTGACCTCAGGGAGATAAGACCTGATGCAAT
65 AGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGAT
*
20092429 CTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGG
130 CTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGG
*
20092494 GAGATAGGATAGTGTCTTTGATCT
195 GAGATAGGATAGTGTCTTCGATCT
20092518 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
1 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
*
20092583 GAGAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATC
66 GATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATC
* *
20092648 TACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATTCGCTCCACTGTAACTTCAGGG
131 TACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGG
20092713 AGATAGGATAGTGTCTTCGATCT
196 AGATAGGATAGTGTCTTCGATCT
20092736 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
1 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
*
20092801 GATAAGATCTGAAATTCTTTGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATC
66 GATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATC
* *
20092866 TACTCTGCTGTAACTTTAGAGAGATAAGATCCTTTACTTTAATCCGCTCCACTGTAACTTCAGGG
131 TACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGG
20092931 AGATAGGAT
196 AGATAGGAT
20092940 CTGAAATTCT
Statistics
Matches: 397, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
217 25 0.06
218 372 0.94
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (218 bp):
GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
GATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATC
TACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGG
AGATAGGATAGTGTCTTCGATCT
Found at i:20092664 original size:174 final size:172
Alignment explanation
Indices: 20091907--20092807 Score: 526
Period size: 174 Copynumber: 5.2 Consensus size: 172
20091897 ATTTGTTACG
* * * * * ** * **
20091907 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGACCT-TGATTGCAATCCACTCCACTATAACTTCA
* * * * * * *
20091972 GGGAGATAGGATTGATTTCTTTCG-TCTGCTCCACTGTAACCTCAGGGAGATAA-AAC-CTGATG
65 GGGAGATAGGATAG-TGTCTTT-GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGCTT
* * * * *
20092034 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTTAT-TTTA
128 CGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG--ATCTTCA
** * * * *** * * ** * *
20092080 ATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTG-TCTTCGATCTGCTCCGCTGTAA-TCTC
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGACCTTGAT-TGCAATCCACTCCACTATAACT-TC
* * * * ** * * * *
20092143 AGGGAGATAAGACT-CTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
64 AGGGAGATAGGA-TAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT---CTG
* * * * * * *
20092207 CTTC-AGTCTACTCCACTGTAACCTTAGGAAAATAAGACCTGA--TGCG
125 CTTCGA-TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGATCTTCA
** * * * ** * *
20092253 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTTGATTGCAATCCACTCCACTATAACTTCA
*
20092318 GGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACT-C
65 GGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT----CTGC
* * * * *
20092382 TTCGGTCTACTCCACTGTGACCTCAGGGAGATAAGACCTGA--TGCA
126 TTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGATCTTCA
* * * * ** * *
20092427 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTTGATTGCAATCCACTCCACTATAACTTCA
20092492 GGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
65 GGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT-GCTTC
* * *
20092557 AATCTGCTCCACTGTAACCTCAGGGAGAGAAGATCTGAAATTCTTCG
129 GATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG--A-TCTTCA
* * * **
20092604 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CTTGA-TGCGATCTACTCTGCTATAACTTCAG
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGACCTTGATTGCAATCCACTCCACTATAACTTCAG
* * ** * * * * * **
20092667 AGAGATAAGATCCTTTATTTTAAT-TCGCTCCACTGTAA-CTTCAGGGAGATAGGAT-AGTGTCT
66 GGAGATAGGATAGTGT-CTTTGATCT-GCTCCGCTGTAATC-TCAGGGAGATAAGATCTCTG-CT
* * *
20092729 TCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTG-GCTTCA
127 TCGATCTGCTCCACTGTAACCTCAGGGAGATAAGA--TCTGATCTTCA
*
20092776 ATCTGCTCCACTGTAACCTCAGGGAGATAAGA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGA
20092808 TCTGAAATTC
Statistics
Matches: 592, Mismatches: 107, Indels: 59
0.78 0.14 0.08
Matches are distributed among these distances:
170 2 0.00
171 34 0.06
172 101 0.17
173 56 0.09
174 294 0.50
175 40 0.07
176 35 0.06
177 30 0.05
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (172 bp):
ATCTACTCCACTGTAACCTCAGGGAGATAAGACCTTGATTGCAATCCACTCCACTATAACTTCAG
GGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGCTTCGA
TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGATCTTCA
Found at i:20092723 original size:392 final size:388
Alignment explanation
Indices: 20091995--20092812 Score: 1397
Period size: 392 Copynumber: 2.1 Consensus size: 388
20091985 GATTTCTTTC
* *
20091995 GTCTGCTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAG
1 GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCAATCTACTCTACTGTAACTTCAGAG
20092060 AGATAAGATCTGTTATTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGAT
66 AGATAAGATCTGTTATTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGAT
20092125 CTGCTCCGCTGTAATCTCAGGGAGATAAGACTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGG
131 CTGCTCCGCTGTAATCTCAGGGAGATAAGACTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGG
* *
20092190 AGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTTAGGAAAATAAGACCTGATGCGAT
196 AGAGAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGAAAATAAGACCTGATGCGAT
*
20092255 CTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGG
261 CTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGG
20092320 GAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACT-CTT
326 GAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT----CTGCTT
*
20092384 CG
387 CA
* *
20092386 GTCTACTCCACTGTGACCTCAGGGAGATAAGACCTGATGCAATCTACTCTACTGTAACTTCAGAG
1 GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCAATCTACTCTACTGTAACTTCAGAG
* *
20092451 AGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTTGA
66 AGATAAGAT-CTGTTATTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGA
*
20092515 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAG
130 TCTGCTCCGCTGTAATCTCAGGGAGATAAGA-CTCTGGCCTCAATCTGCTCCACTGTAACCTCAG
* * * *
20092580 GGAGAGAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCG
194 GGAGAGAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGAAAATAAGACCTGATGCG
*
20092645 ATCTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATTCGCTCCACTGTAACTTCA
259 ATCTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
20092710 GGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
324 GGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT-GCTTC
20092775 A
388 A
* *
20092776 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
1 GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGA
20092813 AATTCTTTGG
Statistics
Matches: 403, Mismatches: 20, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
388 2 0.00
390 37 0.09
391 151 0.37
392 213 0.53
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (388 bp):
GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCAATCTACTCTACTGTAACTTCAGAG
AGATAAGATCTGTTATTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGAT
CTGCTCCGCTGTAATCTCAGGGAGATAAGACTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGG
AGAGAAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGAAAATAAGACCTGATGCGAT
CTACTCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGG
GAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGCTTCA
Found at i:20092877 original size:131 final size:132
Alignment explanation
Indices: 20092694--20092952 Score: 328
Period size: 131 Copynumber: 2.0 Consensus size: 132
20092684 TTTTAATTCG
* * * * * *
20092694 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAG
1 CTCCACTGTAACCTCAGGGAGATAAGATA-TGTATGCGATCTACTCCGCTGTAACT-TCAGAGAG
* *
20092758 ATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTG
64 ATAAGATCCT-TGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTG
20092822 GTCTA
128 GTCTA
* *
20092827 CTCCACTGTAACCTCAGGGAGATAAGACT-TG-ATGCGATCTACTCTGCTGTAACTTTAGAGAGA
1 CTCCACTGTAACCTCAGGGAGATAAGA-TATGTATGCGATCTACTCCGCTGTAACTTCAGAGAGA
* * * *
20092890 TAAGATCCTTTACTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATCTGAAATTCTTTG
65 TAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTG
20092953 ATCTGCTTCG
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
131 78 0.72
132 5 0.05
133 25 0.23
134 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (132 bp):
CTCCACTGTAACCTCAGGGAGATAAGATATGTATGCGATCTACTCCGCTGTAACTTCAGAGAGAT
AAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTC
TA
Found at i:20092879 original size:392 final size:388
Alignment explanation
Indices: 20092000--20092941 Score: 1282
Period size: 392 Copynumber: 2.4 Consensus size: 388
20091990 CTTTCGTCTG
* * * *
20092000 CTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAACCTCAGAGAGATA
* * ** * * *
20092065 AGATCTGTTATTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATAGTGTCTTCGATCTGCT
66 AGACCT-TGATTGCAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTTGATCTGCT
*
20092130 CCGCTGTAATCTCAGGGAGATAAGA-CTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAT
130 CCGCTGTAATCTCAGGGAGATAAGATCTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAG
*
20092194 AAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTTAGGAAAATAAGACCTGATGCGATCTAC
195 AAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGAAAATAAGACCTGATGCGATCTAC
*
20092259 TCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGA
260 TCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGA
**
20092324 TAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACTCTTCGGTC
325 TAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT---ACTCTTCAATC
20092389 TA
387 TA
* * *
20092391 CTCCACTGTGACCTCAGGGAGATAAGACCTGATGCAATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAACCTCAGAGAGATA
* ** *
20092456 AGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTTGATCTGCT
66 AGA-CCTTGATTGCAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTTGATCTGCT
*
20092521 CCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGAG
130 CCGCTGTAATCTCAGGGAGATAAGATCTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAG
* * * *
20092586 AAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATCTAC
195 AAGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGAAAATAAGACCTGATGCGATCTAC
*
20092651 TCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATTCGCTCCACTGTAACTTCAGGGAGA
260 TCTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGA
20092716 TAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCT
325 TAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTACT--CTTCAATCT
*
20092780 G
388 A
* * ** *
20092781 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTACTCCACTGTAACCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG--ATGC---AATCTACTCCACTGTAACCTCAGAG
* * ** * * * ** * *
20092846 AGATAAGA-CTTGA-TGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCCTTTACTTTAAT
61 AGATAAGACCTTGATTGCAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTTGAT
* * *
20092909 CCGCTCCACTGTAA-CTTCAGGGAGATAGGATCT
125 CTGCTCCGCTGTAATC-TCAGGGAGATAAGATCT
20092942 GAAATTCTTT
Statistics
Matches: 496, Mismatches: 44, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
388 2 0.00
390 36 0.07
391 146 0.29
392 246 0.50
393 38 0.08
395 28 0.06
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (388 bp):
CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCAATCTACTCCACTGTAACCTCAGAGAGATA
AGACCTTGATTGCAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTTGATCTGCTC
CGCTGTAATCTCAGGGAGATAAGATCTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAGA
AGATCTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGAAAATAAGACCTGATGCGATCTACT
CTGCTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGAT
AGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTACTCTTCAATCTA
Found at i:20094228 original size:7 final size:7
Alignment explanation
Indices: 20094216--20094253 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
20094206 TAGACTCTCT
20094216 ATTTTTC
1 ATTTTTC
20094223 ATTTTTC
1 ATTTTTC
20094230 ATTTTTC
1 ATTTTTC
*
20094237 A-TTCTC
1 ATTTTTC
20094243 ATTTTTC
1 ATTTTTC
20094250 ATTT
1 ATTT
20094254 ATTTTTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTTTC
Found at i:20094244 original size:13 final size:13
Alignment explanation
Indices: 20094211--20094252 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
20094201 CCCCTTAGAC
20094211 TCTCTATTTTTCATT
1 TCTC-ATTTTTCA-T
*
20094226 TTTCATTTTTCAT
1 TCTCATTTTTCAT
20094239 TCTCATTTTTCAT
1 TCTCATTTTTCAT
20094252 T
1 T
20094253 TATTTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 14 0.56
14 8 0.32
15 3 0.12
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTCATTTTTCAT
Found at i:20095277 original size:6 final size:6
Alignment explanation
Indices: 20095269--20095301 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
20095259 TCATTTTCCC
*
20095269 TTTGAC TTTGAT TTTGAT TTTGAT TTTGAT TTT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTT
20095302 TCTTCCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.67
Consensus pattern (6 bp):
TTTGAT
Found at i:20102618 original size:24 final size:24
Alignment explanation
Indices: 20102573--20102624 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
20102563 TTTCTAGAAG
* *
20102573 ATTTAGTATTTATTAGATTAATAT
1 ATTTAGCATTTATTAGAATAATAT
*
20102597 ATTTAGCATTTATTA-ACATAATTT
1 ATTTAGCATTTATTAGA-ATAATAT
20102621 ATTT
1 ATTT
20102625 GACCTACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGAATAATAT
Found at i:20109349 original size:20 final size:19
Alignment explanation
Indices: 20109302--20109351 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
20109292 CAAGATAAAC
20109302 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
20109319 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
20109339 ATTAAATTAATAA
1 ATTAAATTAATAA
20109352 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 3 0.11
20 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:20130065 original size:40 final size:40
Alignment explanation
Indices: 20130008--20130083 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
20129998 CAATTTGCTC
20130008 TCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAATT
* * * *
20130048 TCAATTTCC-TCTTAAATTTCTTTTAAATCCCTATTT
1 TCAATTTCCTTC-CAAATTTCTCTCAAATCCATATTT
20130084 TTAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 29 0.94
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.49
Consensus pattern (40 bp):
TCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAATT
Found at i:20131236 original size:7 final size:7
Alignment explanation
Indices: 20131224--20131249 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20131214 TAGTCGATTG
20131224 GTATTTA
1 GTATTTA
20131231 GTATTTA
1 GTATTTA
20131238 GTATTTA
1 GTATTTA
20131245 GTATT
1 GTATT
20131250 ATGTATATAA
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:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:20132234 original size:21 final size:21
Alignment explanation
Indices: 20132194--20132234 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20132184 AGATGGCCTA
* * *
20132194 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAACCCCCG
20132215 CCGGAGCAACCACAACCCCC
1 CCGGAGCAACCACAACCCCC
20132235 AACGGAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.46, G:0.22, T:0.02
Consensus pattern (21 bp):
CCGGAGCAACCACAACCCCCG
Found at i:20132512 original size:21 final size:21
Alignment explanation
Indices: 20132488--20132879 Score: 617
Period size: 21 Copynumber: 18.6 Consensus size: 21
20132478 AAACCCTAAC
20132488 AAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132509 AAAACCCTAACCCTTAAGTTA
1 AAAACCCTAACCCTTAACTTA
* *
20132530 AAAACCCAAACCCTTAAGTT-
1 AAAACCCTAACCCTTAACTTA
*
20132550 AAAACCCTAAATCCTTAACTTA
1 AAAACCCT-AACCCTTAACTTA
* *
20132572 AAAACCATAATCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
20132593 AAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132614 AAAACCCTAAGCCATTAACTTA
1 AAAACCCTAA-CCCTTAACTTA
20132636 AAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132657 AAAACTCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
20132678 AAAACCCTAAACCCTTAACTTA
1 AAAACCCT-AACCCTTAACTTA
20132700 AAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
20132721 AAAACCCT-ACCCATTAACTTA
1 AAAACCCTAACCC-TTAACTTA
20132742 AAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132763 AAAACCCTAATCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132784 AATACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132805 AACACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132826 AATACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
*
20132847 AACACCCTAACCCTTAACTTA
1 AAAACCCTAACCCTTAACTTA
20132868 AAAACCCTAACC
1 AAAACCCTAACC
20132880 GTATTCCTTA
Statistics
Matches: 346, Mismatches: 19, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
20 11 0.03
21 283 0.82
22 52 0.15
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (21 bp):
AAAACCCTAACCCTTAACTTA
Found at i:20132953 original size:18 final size:18
Alignment explanation
Indices: 20132919--20132953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20132909 TCCAAGCCCT
* *
20132919 AAAACCCTAATCTTAACA
1 AAAACCCTAACCCTAACA
20132937 AAAACCCTAACCCTAAC
1 AAAACCCTAACCCTAAC
20132954 CCTAATATGA
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:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAACCCTAACCCTAACA
Found at i:20133143 original size:21 final size:22
Alignment explanation
Indices: 20133099--20133144 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20133089 TTTTCTCTAA
**
20133099 AACCCTAAAAACCTTAAACTCT
1 AACCCTAAAAACCCAAAACTCT
*
20133121 AACCCTAAAACCCCAAAAC-CT
1 AACCCTAAAAACCCAAAACTCT
20133142 AAC
1 AAC
20133145 GTTGGAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (22 bp):
AACCCTAAAAACCCAAAACTCT
Found at i:20135840 original size:43 final size:43
Alignment explanation
Indices: 20135769--20135850 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 43
20135759 GATTCTGTTA
20135769 TGTGTTATCGTGTAAGACCACGTTTGGGAC-GTTGGCATCAACC
1 TGTGTTATCGTGTAAGACCACGTTTGGGACAG-TGGCATCAACC
20135812 TGTGTT-TACGTGTAAGACC-C-TATCTGGGACAGTGGCATC
1 TGTGTTAT-CGTGTAAGACCACGT-T-TGGGACAGTGGCATC
20135851 GTTATATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
41 1 0.03
42 3 0.09
43 30 0.86
44 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (43 bp):
TGTGTTATCGTGTAAGACCACGTTTGGGACAGTGGCATCAACC
Found at i:20144318 original size:17 final size:18
Alignment explanation
Indices: 20144282--20144325 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20144272 AAATAAAATT
20144282 TATTTTATAATAAGATAA
1 TATTTTATAATAAGATAA
20144300 TATTTTATAATAA-ATAA
1 TATTTTATAATAAGATAA
*
20144317 TATATTATA
1 TATTTTATA
20144326 TAGATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTTATAATAAGATAA
Found at i:20145101 original size:23 final size:23
Alignment explanation
Indices: 20145050--20145102 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
20145040 AGATTTAAAC
* *
20145050 AAATACTCATATTTATATTATTA
1 AAATATTCATATTTATACTATTA
*
20145073 ATATATTCATATTTTATACTA-TA
1 AAATATTCATA-TTTATACTATTA
20145096 AAATATT
1 AAATATT
20145103 TTACTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATATTCATATTTATACTATTA
Found at i:20145208 original size:18 final size:19
Alignment explanation
Indices: 20145185--20145224 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
20145175 ATATTACTTC
20145185 AAATTTAAAA-CTATTATT
1 AAATTTAAAATCTATTATT
*
20145203 AAATTTAAAATTTATTATT
1 AAATTTAAAATCTATTATT
20145222 AAA
1 AAA
20145225 ATAAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTAAAATCTATTATT
Found at i:20145220 original size:19 final size:19
Alignment explanation
Indices: 20145185--20145245 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
20145175 ATATTACTTC
*
20145185 AAATTTAAAA-CTATTATT
1 AAATTTAAAATTTATTATT
20145203 AAATTTAAAATTTATTATT
1 AAATTTAAAATTTATTATT
* * *
20145222 AAAATAAAAATTGTAATATT
1 AAATTTAAAATT-TATTATT
20145242 AAAT
1 AAAT
20145246 AAACTTGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
18 10 0.28
19 17 0.47
20 9 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATTTAAAATTTATTATT
Found at i:20145794 original size:14 final size:14
Alignment explanation
Indices: 20145770--20145803 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
20145760 AATAATCATG
20145770 TATTTTTTTT-AAA
1 TATTTTTTTTAAAA
20145783 TATTTATTTTTAAAA
1 TATTT-TTTTTAAAA
20145798 TATTTT
1 TATTTT
20145804 ACTATTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 6 0.32
15 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTTTAAAA
Found at i:20152116 original size:12 final size:11
Alignment explanation
Indices: 20152090--20152114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20152080 TTCTTTTAAC
20152090 TTTCTTTTTTT
1 TTTCTTTTTTT
20152101 TTTCTTTTTTT
1 TTTCTTTTTTT
20152112 TTT
1 TTT
20152115 TCCATTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:20152410 original size:25 final size:25
Alignment explanation
Indices: 20152369--20152430 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
20152359 GGAAAAAAGA
**
20152369 AAAAG-AAAAAAGTTTAAAGAACAT
1 AAAAGAAAAAAAAATTAAAGAACAT
** *
20152393 AAAAGAAAAAAAAATTAAATTACTT
1 AAAAGAAAAAAAAATTAAAGAACAT
*
20152418 AAAACAAAAAAAA
1 AAAAGAAAAAAAA
20152431 TATGGGGATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.16
Consensus pattern (25 bp):
AAAAGAAAAAAAAATTAAAGAACAT
Found at i:20153281 original size:50 final size:50
Alignment explanation
Indices: 20153179--20153285 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
20153169 GTAAAAACAT
* * * * *
20153179 ATAAATATTTTTAAATATATATAATGATAAAATTTAAATTTTAAAATTAA
1 ATAAATATATTTAAAAATATATAATAATAAAATATAAATATTAAAATTAA
*
20153229 ATAAATATATTTAAAAATATATAATAAT-AAATAT-AATATTAATATTAA
1 ATAAATATATTTAAAAATATATAATAATAAAATATAAATATTAAAATTAA
20153277 A-AATATATA
1 ATAA-ATATA
20153286 ATTATATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 2 0.04
48 18 0.36
49 5 0.10
50 25 0.50
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (50 bp):
ATAAATATATTTAAAAATATATAATAATAAAATATAAATATTAAAATTAA
Found at i:20154310 original size:22 final size:23
Alignment explanation
Indices: 20154284--20154544 Score: 109
Period size: 22 Copynumber: 11.0 Consensus size: 23
20154274 ATTTTCACAC
*
20154284 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
*
20154306 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTTGGACAGCA--TATACAT
20154331 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
20154353 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
20154378 CAAAATTT-GATAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
**
20154400 -ATATAA-TTGGACTCCATTTATTTATACAT
1 CA-A-AATTTGGA---CA-GCA--TATACAT
*
20154429 CAAAATTT-GACAGCATACACAT
1 CAAAATTTGGACAGCATATACAT
* *
20154451 -ATATAA-TTGGACTGCATCTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
20154476 CAAAATTT-GACAGCATACACAT
1 CAAAATTTGGACAGCATATACAT
**
20154498 -ATATAA-TTGGACTCCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
20154523 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
20154545 TCATTTACTC
Statistics
Matches: 179, Mismatches: 25, Indels: 70
0.65 0.09 0.26
Matches are distributed among these distances:
21 4 0.02
22 58 0.32
23 27 0.15
24 34 0.19
25 36 0.20
26 4 0.02
27 1 0.01
28 4 0.02
29 10 0.06
30 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:20154337 original size:47 final size:45
Alignment explanation
Indices: 20154284--20154541 Score: 300
Period size: 47 Copynumber: 5.4 Consensus size: 45
20154274 ATTTTCACAC
* *
20154284 CAAAATTTGGACAGCATATATACAAAATTTGGACTGCATTTATACAT
1 CAAAATTT-GACAGCATATATATATAA-TTGGACTGCATTTATACAT
*
20154331 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATAT--ATATATAATTGGACTGCATTTATACAT
* *
20154378 CAAAATTTGATAGCATATACATATATAATTGGACTCCATTTATTTATACAT
1 CAAAATTTGACAGCATAT--ATATATAATTGGACTGC----ATTTATACAT
* * *
20154429 CAAAATTTGACAGCATACACATATATAATTGGACTGCATCTGTACAT
1 CAAAATTTGACAGCAT--ATATATATAATTGGACTGCATTTATACAT
* *
20154476 CAAAATTTGACAGCATACACATATATAATTGGACTCCATTTATACAT
1 CAAAATTTGACAGCAT--ATATATATAATTGGACTGCATTTATACAT
20154523 CAAAATTTGACAGCATATA
1 CAAAATTTGACAGCATATA
20154542 CATTCATTTA
Statistics
Matches: 188, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
45 2 0.01
46 10 0.05
47 129 0.69
48 6 0.03
51 40 0.21
53 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (45 bp):
CAAAATTTGACAGCATATATATATAATTGGACTGCATTTATACAT
Found at i:20154441 original size:98 final size:94
Alignment explanation
Indices: 20154312--20154544 Score: 385
Period size: 98 Copynumber: 2.4 Consensus size: 94
20154302 TATACAAAAT
* *
20154312 TTGGACTGCATTTATACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACA
1 TTGGACTCCATTTATACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATCTGTACA
* *
20154377 TCAAAATTTGATAGCATATACATATATAA
66 TCAAAATTTGACAGCATACACATATATAA
*
20154406 TTGGACTCCATTTATTTATACATCAAAATTTGACAGCATACACATATATAATTGGACTGCATCTG
1 TTGGACTCC----ATTTATACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATCTG
20154471 TACATCAAAATTTGACAGCATACACATATATAA
62 TACATCAAAATTTGACAGCATACACATATATAA
20154504 TTGGACTCCATTTATACATCAAAATTTGACAGCATATACAT
1 TTGGACTCCATTTATACATCAAAATTTGACAGCATATACAT
20154545 TCATTTACTC
Statistics
Matches: 129, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
94 39 0.30
98 90 0.70
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (94 bp):
TTGGACTCCATTTATACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATCTGTACA
TCAAAATTTGACAGCATACACATATATAA
Found at i:20154817 original size:14 final size:15
Alignment explanation
Indices: 20154779--20154827 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
20154769 TCACCATGCA
* *
20154779 CATATATATACATTAC
1 CATATAAATAC-TAAC
20154795 CATATAAATACTAAC
1 CATATAAATACTAAC
20154810 CATA-AAATACTAATC
1 CATATAAATACTAA-C
20154825 CAT
1 CAT
20154828 GATTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CATATAAATACTAAC
Found at i:20155563 original size:43 final size:43
Alignment explanation
Indices: 20155474--20155597 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
20155464 AGCTAGTACA
* * * *
20155474 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAC-A-TACCG
1 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACAAGTA--G
20155517 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAAACACAAGTAG
1 ATGCCGAC-GTCCCAGAC-GTGGTCTTACACGAAAACACAAGTAG
20155560 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
20155598 TATCGGAGTC
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
42 3 0.04
43 63 0.88
44 4 0.06
45 2 0.03
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACAAGTAG
Found at i:20159395 original size:32 final size:32
Alignment explanation
Indices: 20159358--20159448 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 32
20159348 TAACCACATT
*
20159358 AAAGTTGATATTTGTTATCGTTTCACAAAATTG
1 AAAGTTGATATTTGTTATCATTTCACAAAA-TG
*
20159391 -AAGTTG-TAATTTGTTAGT-ATTTCATAAAATG
1 AAAGTTGAT-ATTTGTTA-TCATTTCACAAAATG
20159422 AAAGTTGATATTTGTTATCATTTCACA
1 AAAGTTGATATTTGTTATCATTTCACA
20159449 GAACTGCGCG
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
31 4 0.08
32 44 0.88
33 2 0.04
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (32 bp):
AAAGTTGATATTTGTTATCATTTCACAAAATG
Found at i:20160101 original size:12 final size:12
Alignment explanation
Indices: 20160084--20160108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20160074 GGGGAAGGGG
20160084 AGAGAGAAACAA
1 AGAGAGAAACAA
20160096 AGAGAGAAACAA
1 AGAGAGAAACAA
20160108 A
1 A
20160109 AGAAAGCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAGAGAAACAA
Found at i:20166671 original size:14 final size:14
Alignment explanation
Indices: 20166631--20166662 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
20166621 GAAAAAGGAA
20166631 TAATATATAATTTC
1 TAATATATAATTTC
20166645 TAATATATAATTTC
1 TAATATATAATTTC
20166659 TAAT
1 TAAT
20166663 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATATAATTTC
Found at i:20166769 original size:28 final size:27
Alignment explanation
Indices: 20166737--20166805 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
20166727 AATAAAAAAA
*
20166737 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
20166765 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
20166792 TTACCAAAATATAT
1 TTACCAAAATATAT
20166806 CAAAAAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.59
28 10 0.27
29 5 0.14
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:20166820 original size:10 final size:9
Alignment explanation
Indices: 20166806--20166839 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
20166796 CAAAATATAT
20166806 CAAAAAAAA
1 CAAAAAAAA
20166815 CAAAAAAAA
1 CAAAAAAAA
20166824 CAAAAAAAA
1 CAAAAAAAA
*
20166833 TAAAAAA
1 CAAAAAA
20166840 CAGAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:20166830 original size:16 final size:16
Alignment explanation
Indices: 20166808--20166848 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
20166798 AAATATATCA
*
20166808 AAAAAAACAAAAAAAAC
1 AAAAAAA-ATAAAAAAC
20166825 AAAAAAAATAAAAAAC
1 AAAAAAAATAAAAAAC
20166841 AGAAAAAA
1 A-AAAAAA
20166849 GAAATCTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.88, C:0.07, G:0.02, T:0.02
Consensus pattern (16 bp):
AAAAAAAATAAAAAAC
Found at i:20166921 original size:27 final size:27
Alignment explanation
Indices: 20166883--20166959 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
20166873 CCCTGGGTGG
20166883 AGGGAAGCAGGTTGGCGGCACCAAACA
1 AGGGAAGCAGGTTGGCGGCACCAAACA
****
20166910 AGGGAAGCAGGTTGGCGGCACCAGTGG
1 AGGGAAGCAGGTTGGCGGCACCAAACA
* *
20166937 AGGGAACCAAGTTGGCGGCACCA
1 AGGGAAGCAGGTTGGCGGCACCA
20166960 CCCTTGAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.29, C:0.22, G:0.40, T:0.09
Consensus pattern (27 bp):
AGGGAAGCAGGTTGGCGGCACCAAACA
Found at i:20167086 original size:56 final size:56
Alignment explanation
Indices: 20167008--20167139 Score: 160
Period size: 56 Copynumber: 2.4 Consensus size: 56
20166998 AGGAGAGGGG
* * * *
20167008 AAGAAGAAGAAAGAAAGGAAGAAAGAA-AAAGAAGGAAAAGG-AATGGAGAGGAAAGA
1 AAGAAAAAGAAGGAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAATGG-GAGGAAAGA
* *
20167064 AAGAAAAAGAAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAATTGGAGGAAAGA
1 AAGAAAAAGAAGGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAATGGGAGGAAAGA
**
20167120 AAGAAAATTAAGGAAAGAAA
1 AAGAAAAAGAAGGAAAGAAA
20167140 AGGAAAGGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
55 2 0.03
56 60 0.91
57 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (56 bp):
AAGAAAAAGAAGGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAATGGGAGGAAAGA
Found at i:20167104 original size:10 final size:10
Alignment explanation
Indices: 20167028--20167146 Score: 58
Period size: 10 Copynumber: 12.5 Consensus size: 10
20167018 AAGAAAGGAA
*
20167028 GAAAGAAAAA
1 GAAAGAAAAG
*
20167038 GAAGGAAAAG
1 GAAAGAAAAG
* * *
20167048 GAATGGAGAG
1 GAAAGAAAAG
20167058 GAAAG-AAA-
1 GAAAGAAAAG
20167066 GAAA-AAGAAG
1 GAAAGAA-AAG
20167076 GAAAG-AAA-
1 GAAAGAAAAG
20167084 GAAA-AAGAAG
1 GAAAGAA-AAG
20167094 GAAAGAAAAG
1 GAAAGAAAAG
****
20167104 GAAATTGGAG
1 GAAAGAAAAG
20167114 GAAAG-AAA-
1 GAAAGAAAAG
*
20167122 GAAA-ATTAAG
1 GAAAGA-AAAG
20167132 GAAAGAAAAG
1 GAAAGAAAAG
20167142 GAAAG
1 GAAAG
20167147 GAGAAGAGAA
Statistics
Matches: 81, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
8 14 0.17
9 11 0.14
10 53 0.65
11 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:20167122 original size:38 final size:35
Alignment explanation
Indices: 20167056--20167210 Score: 124
Period size: 38 Copynumber: 4.3 Consensus size: 35
20167046 AGGAATGGAG
* *
20167056 AGGAAAG-AAAGAAAAAGAAGGAAAGAAAGAAAAAGA
1 AGGAAAGAAAAG-GAAAGGAGGAAAGAAAGAAAAA-A
*
20167092 AGGAAAGAAAAGGAAATTGGAGGAAAGAAAGAAAATTA
1 AGGAAAGAAAAGGAAA--GGAGGAAAGAAAGAAAA-AA
20167130 AGGAAAGAAAAGGAAAGGA-GAAGAGAAA-AAAAAA
1 AGGAAAGAAAAGGAAAGGAGGAA-AGAAAGAAAAAA
* * *
20167164 A-GAAAGAAGAA-GAAGAAGAGGGAAAG-AAGGAAAGA
1 AGGAAAGAA-AAGGAA-AGGA-GGAAAGAAAGAAAAAA
*
20167199 AGGAAAAAAAAG
1 AGGAAAGAAAAG
20167211 AAAATAAGGT
Statistics
Matches: 99, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
33 10 0.10
34 9 0.09
35 16 0.16
36 27 0.27
37 4 0.04
38 33 0.33
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (35 bp):
AGGAAAGAAAAGGAAAGGAGGAAAGAAAGAAAAAA
Found at i:20167125 original size:28 final size:28
Alignment explanation
Indices: 20167035--20167125 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
20167025 GAAGAAAGAA
*
20167035 AAAGAAGGAAAAGG-AATGGAGAGGAAAG
1 AAAGAAAGAAAAGGAAAT-GAGAGGAAAG
* *
20167063 AAAGAAA-AAGAAGGAAA-GAAAGAAAAAG
1 AAAGAAAGAA-AAGGAAATGAGAG-GAAAG
*
20167091 AAGGAAAGAAAAGGAAATTG-GAGGAAAG
1 AAAGAAAGAAAAGGAAA-TGAGAGGAAAG
20167119 AAAGAAA
1 AAAGAAA
20167126 ATTAAGGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
27 6 0.12
28 37 0.74
29 6 0.12
30 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (28 bp):
AAAGAAAGAAAAGGAAATGAGAGGAAAG
Found at i:20167133 original size:18 final size:18
Alignment explanation
Indices: 20167011--20167206 Score: 121
Period size: 18 Copynumber: 10.4 Consensus size: 18
20167001 AGAGGGGAAG
20167011 AAGAAGAAAGAAAGG-AAGA
1 AAGAA-AAAG-AAGGAAAGA
20167030 AAGAAAAAGAAGG--A-A
1 AAGAAAAAGAAGGAAAGA
* **
20167045 AAGGAATGGAGAGGAAAGA
1 AAGAAAAAGA-AGGAAAGA
20167064 AAGAAAAAGAAGGAAAGA
1 AAGAAAAAGAAGGAAAGA
20167082 AAGAAAAAGAAGGAAAGAA
1 AAGAAAAAGAAGGAAAG-A
** *
20167101 AAGGAAATTGGAGGAAAGA
1 AA-GAAAAAGAAGGAAAGA
**
20167120 AAGAAAATTAAGGAAAGAA
1 AAGAAAAAGAAGGAAAG-A
* *
20167139 AAGGAAAGGAGAAGAGAAAAA
1 AA-GAAA-AAGAAG-GAAAGA
* *
20167160 AAAAAGAAAGAAGAAGAAGA
1 AAGAA-AAAGAAGGA-AAGA
**
20167180 AGAGGGAAAGAAGGAAAGA
1 A-AGAAAAAGAAGGAAAGA
*
20167199 AGGAAAAA
1 AAGAAAAA
20167207 AAAGAAAATA
Statistics
Matches: 137, Mismatches: 27, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
15 8 0.06
16 4 0.03
17 4 0.03
18 46 0.34
19 28 0.20
20 35 0.26
21 8 0.06
22 4 0.03
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
AAGAAAAAGAAGGAAAGA
Found at i:20167157 original size:56 final size:56
Alignment explanation
Indices: 20167008--20167158 Score: 157
Period size: 56 Copynumber: 2.7 Consensus size: 56
20166998 AGGAGAGGGG
* * * *
20167008 AAGAAGAAGAAAGAAAGGAAGAAAGAAAAAGAAG-GAAAAGGAATGGAGAGGAAAGA
1 AAGAAAAAGAAGGAAAGAAAGAAA-AAGAAGAAGAGAAAAGGAATGGAGAGGAAAGA
*
20167064 AAGAAAAAGAAGGAAAGAAAGAAAAAGAAGGAA-AGAAAAGGAAATTG-GAGGAAAGA
1 AAGAAAAAGAAGGAAAGAAAGAAAAAGAA-GAAGAGAAAAGG-AATGGAGAGGAAAGA
** * *
20167120 AAGAAAATTAAGGAAAGAAA-AGGAAAGGAGAAGAGAAAA
1 AAGAAAAAGAAGGAAAGAAAGA-AAAAGAAGAAGAGAAAA
20167159 AAAAAAGAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
55 8 0.10
56 69 0.85
57 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (56 bp):
AAGAAAAAGAAGGAAAGAAAGAAAAAGAAGAAGAGAAAAGGAATGGAGAGGAAAGA
Found at i:20167941 original size:19 final size:19
Alignment explanation
Indices: 20167893--20167944 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
20167883 TAAAAAAAAA
** *
20167893 TAATATTTTGGTATTTTTT
1 TAATATTTTATTATTTTTG
20167912 TAATATTTTATTATTTTTG
1 TAATATTTTATTATTTTTG
*
20167931 TAATGTTTTATTAT
1 TAATATTTTATTAT
20167945 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:20167969 original size:13 final size:13
Alignment explanation
Indices: 20167951--20167976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20167941 TTATGGGTTT
20167951 TATAAAAAAATAA
1 TATAAAAAAATAA
20167964 TATAAAAAAATAA
1 TATAAAAAAATAA
20167977 AAAATTATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:20168031 original size:28 final size:29
Alignment explanation
Indices: 20167985--20168051 Score: 111
Period size: 28 Copynumber: 2.3 Consensus size: 29
20167975 AAAAAATTAT
20167985 CAAAATAT-TATAACTTTTTTTTTATTTAC
1 CAAAATATATATAAC-TTTTTTTTATTTAC
20168014 CAAAATATATATAA-TTTTTTTTATTTAC
1 CAAAATATATATAACTTTTTTTTATTTAC
20168042 CAAAATATAT
1 CAAAATATAT
20168052 CAAAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
28 24 0.65
29 8 0.22
30 5 0.14
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (29 bp):
CAAAATATATATAACTTTTTTTTATTTAC
Found at i:20169416 original size:17 final size:17
Alignment explanation
Indices: 20169394--20169430 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
20169384 ATGGGGTAAG
20169394 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
20169411 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
20169428 ATG
1 ATG
20169431 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:20170353 original size:15 final size:14
Alignment explanation
Indices: 20170313--20170341 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20170303 TTTTTGTATC
20170313 AATTTAATTATTCT
1 AATTTAATTATTCT
20170327 AATTTAATTATTCT
1 AATTTAATTATTCT
20170341 A
1 A
20170342 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:20170504 original size:20 final size:20
Alignment explanation
Indices: 20170481--20170524 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
20170471 CTTATTTTTC
20170481 TTTCTTTCCTCTCATTTCCT
1 TTTCTTTCCTCTCATTTCCT
*
20170501 TTTCTTTCCTCTCCTTTCCT
1 TTTCTTTCCTCTCATTTCCT
20170521 TTTC
1 TTTC
20170525 CTTCTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTTTCCTCTCATTTCCT
Found at i:20170515 original size:15 final size:14
Alignment explanation
Indices: 20170496--20170550 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
20170486 TTCCTCTCAT
20170496 TTCCTTTTCTTTCC
1 TTCCTTTTCTTTCC
*
20170510 TCTCCTTTCCTTTTCC
1 T-TCCTTTTC-TTTCC
*
20170526 TTCTTTTTCTTT-C
1 TTCCTTTTCTTTCC
20170539 TTCC-TTTCTTTC
1 TTCCTTTTCTTTC
20170551 TTCTTCTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
12 7 0.21
13 4 0.12
14 4 0.12
15 13 0.38
16 6 0.18
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCCTTTTCTTTCC
Found at i:20170549 original size:18 final size:17
Alignment explanation
Indices: 20170522--20170560 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
20170512 TCCTTTCCTT
20170522 TTCCTTCTTT-TTCTTTC
1 TTCCTTCTTTCTTC-TTC
20170539 TTCCTTTCTTTCTTCTTC
1 TTCC-TTCTTTCTTCTTC
20170557 TTCC
1 TTCC
20170561 CCTCTCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 13 0.65
19 3 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCCTTCTTTCTTCTTC
Found at i:20170551 original size:22 final size:23
Alignment explanation
Indices: 20170516--20170558 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
20170506 TTCCTCTCCT
*
20170516 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
20170539 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
20170559 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:20170645 original size:27 final size:27
Alignment explanation
Indices: 20170607--20170660 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20170597 AATTCAAGGG
*
20170607 TGGTGCCGCCAACCTGGTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
20170634 TGGTGCCGCCAACCTGCTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
20170661 CTAGGGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.46, G:0.20, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCAACCTGCTTCCCTCCAC
Found at i:20170745 original size:23 final size:23
Alignment explanation
Indices: 20170715--20170761 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20170705 TTTGTTTTTT
20170715 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
20170738 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
20170761 A
1 A
20170762 GTTATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
ATATATTTTGGTAAATAAAAAAA
Found at i:20171706 original size:35 final size:35
Alignment explanation
Indices: 20171655--20171729 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
20171645 TACAAAGAGG
* *
20171655 AAAAAAAATAGCTTGTTTAACAAAACTAGAGAGAA
1 AAAAAAAAGAGCTTGTTTAACAAAACGAGAGAGAA
* * *
20171690 AAAAAAAAGAGTTTGTTTGACAAAACGGGAGAGAA
1 AAAAAAAAGAGCTTGTTTAACAAAACGAGAGAGAA
20171725 AAAAA
1 AAAAA
20171730 GCTGTTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (35 bp):
AAAAAAAAGAGCTTGTTTAACAAAACGAGAGAGAA
Found at i:20174493 original size:19 final size:19
Alignment explanation
Indices: 20174438--20174495 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
20174428 TGGCATCGGA
* *
20174438 GTGCATCTTGACGTACAAG
1 GTGCATCTTGGCGCACAAG
* * *
20174457 ATGCATACCTGGCACACAAG
1 GTGCAT-CTTGGCGCACAAG
20174477 GTGCATCTTGGCGCACAAG
1 GTGCATCTTGGCGCACAAG
20174496 CGTATATCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (19 bp):
GTGCATCTTGGCGCACAAG
Found at i:20174856 original size:243 final size:243
Alignment explanation
Indices: 20174426--20174900 Score: 693
Period size: 243 Copynumber: 2.0 Consensus size: 243
20174416 TATTAACTTG
* * * * * *
20174426 ACTGGCATCGGAGTGCATCTTGACGTACAAGATGCATACCTGGCACACAAGGTGCATCTTGGCGC
1 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGCGC
* * *
20174491 ACAAGCGTATATCTAGTACATGAAATGCATCCTGGCGTATAAGCACATAATCCCGTACTTAATCC
66 ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAGCACATAATCCCATACTCAATCC
* *
20174556 AATCCTATGGCATGCCAACTATATCCAACTCAATCCCACTAGTTAATATGATATCAAATTTCAAT
131 AATCCTATGACATGCCAACTATATCCAACTCAATCCCACTAGTTAATAGGATATCAAATTTCAAT
*
20174621 TCCATTTAAAATATAATACACATATCAATTTTTCAATGAACACACCAA
196 TCCATTTAAAATATAATACACATATCAAATTTTCAATGAACACACCAA
*
20174669 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGTGC
1 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGCGC
* * * *
20174734 ATAAGTGTATATCTAGCACATGAAATGCATCCTGGGGTATAAG-AGCATAATCTCATACTCAATC
66 ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAGCA-CATAATCCCATACTCAATC
* * * *
20174798 CACTCCTATGACATGCCAACTATATCCAACTCAA-CTCGACTAGTTAATAGGGTATCAAATTTTA
130 CAATCCTATGACATGCCAACTATATCCAACTCAATC-CCACTAGTTAATAGGATATCAAATTTCA
** * *
20174862 ATTCTGTTTAGAGTATAATACACATATCAAATTTTCAAT
194 ATTCCATTTAAAATATAATACACATATCAAATTTTCAAT
20174901 CCTATACACT
Statistics
Matches: 205, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
242 2 0.01
243 203 0.99
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (243 bp):
ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGCGC
ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAGCACATAATCCCATACTCAATCC
AATCCTATGACATGCCAACTATATCCAACTCAATCCCACTAGTTAATAGGATATCAAATTTCAAT
TCCATTTAAAATATAATACACATATCAAATTTTCAATGAACACACCAA
Found at i:20175857 original size:20 final size:20
Alignment explanation
Indices: 20175834--20175873 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20175824 TTAATTAACA
*
20175834 TAATTAACCTTACTTTAATT
1 TAATAAACCTTACTTTAATT
*
20175854 TAATAAACCTTATTTTAATT
1 TAATAAACCTTACTTTAATT
20175874 AAGTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAACCTTACTTTAATT
Found at i:20182552 original size:39 final size:40
Alignment explanation
Indices: 20182424--20182660 Score: 274
Period size: 40 Copynumber: 6.0 Consensus size: 40
20182414 AGTTGAAATA
*
20182424 CTATCGAGCCATACCTACTGAATCTACTGAAATGTATG-T
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* *
20182463 GCTATTGAGCCATACCTAATGAATT-TACTGAAATGTATGCGT
1 -CTATCGAGCCATACCTACTG-ATTCTACTGAAATGTATGC-T
* *
20182505 -TATTGAGCCATACCTACTGATTCTAATGAAA-GTATGCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* * * *
20182543 TTAGCGAGCCATACCTACGGAATT-TACTGAAATGTATGCG
1 CTATCGAGCCATACCTACTG-ATTCTACTGAAATGTATGCT
* *
20182583 CTATCAAGCCATACCTACTAATTCTACTGAAA-GTATGCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
*
20182622 CTATCGAGCCATACCTACTGATTCTATTGAAA-GTA-GCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
20182660 C
1 C
20182661 AAACGAGCAT
Statistics
Matches: 170, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
38 5 0.03
39 73 0.43
40 89 0.52
41 2 0.01
42 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (40 bp):
CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
Found at i:20182566 original size:79 final size:79
Alignment explanation
Indices: 20182424--20182639 Score: 308
Period size: 79 Copynumber: 2.7 Consensus size: 79
20182414 AGTTGAAATA
* * **
20182424 CTATCGAGCCATACCTACTGAATCTACTGAAATGTATG-TGCTATTGAGCCATACCTAATGAATT
1 CTATCGAGCCATACCTACTGATTCTACTGAAA-GTATGCT-CTATCGAGCCATACCTACGGAATT
20182488 TACTGAAATGTATGCG
64 TACTGAAATGTATGCG
* * * * *
20182504 TTATTGAGCCATACCTACTGATTCTAATGAAAGTATGCTTTAGCGAGCCATACCTACGGAATTTA
1 CTATCGAGCCATACCTACTGATTCTACTGAAAGTATGCTCTATCGAGCCATACCTACGGAATTTA
20182569 CTGAAATGTATGCG
66 CTGAAATGTATGCG
* *
20182583 CTATCAAGCCATACCTACTAATTCTACTGAAAGTATGCTCTATCGAGCCATACCTAC
1 CTATCGAGCCATACCTACTGATTCTACTGAAAGTATGCTCTATCGAGCCATACCTAC
20182640 TGATTCTATT
Statistics
Matches: 119, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 90 0.76
80 29 0.24
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (79 bp):
CTATCGAGCCATACCTACTGATTCTACTGAAAGTATGCTCTATCGAGCCATACCTACGGAATTTA
CTGAAATGTATGCG
Found at i:20184611 original size:24 final size:24
Alignment explanation
Indices: 20184579--20184636 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
20184569 GCAAACAGTT
20184579 ATTAAACACTATTTGTTTGCTTTC
1 ATTAAACACTATTTGTTTGCTTTC
*
20184603 ATTAAACACTATTTGTTTGCTTTT
1 ATTAAACACTATTTGTTTGCTTTC
*
20184627 AGTAAACACT
1 ATTAAACACT
20184637 TAAGAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTAAACACTATTTGTTTGCTTTC
Found at i:20187579 original size:29 final size:28
Alignment explanation
Indices: 20187547--20187611 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
20187537 TATGAAAAAA
20187547 TATTATGAATATAAAGTTATAATTA-TAAT
1 TATTATGAATA-AAA-TTATAATTATTAAT
*
20187576 TATTTTATTAATAAAATTATAATTATTAAT
1 TA--TTATGAATAAAATTATAATTATTAAT
*
20187606 TCTTAT
1 TATTAT
20187612 AGTTATCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 4 0.13
29 11 0.35
30 8 0.26
31 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
TATTATGAATAAAATTATAATTATTAAT
Found at i:20189213 original size:19 final size:18
Alignment explanation
Indices: 20189189--20189232 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
20189179 TAATGATTAC
20189189 TTAAATTAATTATATAAAA
1 TTAAATTAATTAT-TAAAA
**
20189208 TTAAATTTTTTATTAAAA
1 TTAAATTAATTATTAAAA
20189226 -TAAATTA
1 TTAAATTA
20189233 TATAAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTAATTATTAAAA
Found at i:20190114 original size:26 final size:24
Alignment explanation
Indices: 20190062--20190107 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
20190052 AAGGTCAGTA
20190062 ATTCATATTTCTCTCTCTCTCTTT
1 ATTCATATTTCTCTCTCTCTCTTT
20190086 ATTCATATTTCTCTCTCTCTCT
1 ATTCATATTTCTCTCTCTCTCT
20190108 CTTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTCATATTTCTCTCTCTCTCTTT
Found at i:20200197 original size:17 final size:18
Alignment explanation
Indices: 20200166--20200199 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20200156 AATTTAACTT
20200166 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
20200184 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
20200200 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:20200463 original size:21 final size:21
Alignment explanation
Indices: 20200404--20200463 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
20200394 CCGAACCCCG
*
20200404 AGATTTAAGGTTT-GGGTTTA
1 AGATTTAAGGTTTAGGGTTGA
*
20200424 AGATTTAAGATTTTA-GGTTCGA
1 AGATTTAAG-GTTTAGGGTT-GA
20200446 A-ATTTAAGGTTTAGGGTT
1 AGATTTAAGGTTTAGGGTT
20200464 ATGAATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 13 0.39
21 18 0.55
22 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (21 bp):
AGATTTAAGGTTTAGGGTTGA
Found at i:20203255 original size:3 final size:3
Alignment explanation
Indices: 20203247--20203299 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
20203237 TTGCTATAAA
20203247 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20203295 TAT TA
1 TAT TA
20203300 AGTGTAGAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20205947 original size:20 final size:18
Alignment explanation
Indices: 20205897--20205948 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
20205887 CTTGTAGATA
20205897 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
20205914 AATAGTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
20205934 AATATTAAATTAATA
1 AATATTAAATTAATA
20205949 AACTACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:20209412 original size:2 final size:2
Alignment explanation
Indices: 20209396--20209436 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
20209386 ACTCGAATGC
* *
20209396 AT AT AT GT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20209437 AGTTTTTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20209831 original size:75 final size:75
Alignment explanation
Indices: 20209694--20209833 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 75
20209684 CTTACATATA
* * * * * **
20209694 TGTATATGTTCTTTTATTGAATTTAGGTAGGACATTTATATAAGTTTATATGAGGTTTGATTATG
1 TGTATATGTTCTTGTAATGAATTTAAGTAGGAAATTTATATAAGTGTATATGAAATTTGATTATG
20209759 CAAGATTATG
66 CAAGATTATG
* *
20209769 TGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATGTGAAAATTTCGATTA
1 TGTATATGTTCTTGTAATGAATTTAAGTAGGAAATTTATATAAGTGTATATG-AAATTT-GATTA
20209832 TG
64 TG
20209834 TATGTATATT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.11
74 5 0.09
75 43 0.80
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (75 bp):
TGTATATGTTCTTGTAATGAATTTAAGTAGGAAATTTATATAAGTGTATATGAAATTTGATTATG
CAAGATTATG
Found at i:20209990 original size:41 final size:41
Alignment explanation
Indices: 20209920--20210083 Score: 172
Period size: 41 Copynumber: 4.0 Consensus size: 41
20209910 GAATGTAATA
* * * **
20209920 CAGACTTCACGTCTAGCAGGCT-TGATGCCGGTGAAAT-AATT
1 CAGACTTTACGCCTAGCAGGCTAAG-TGCCGGTGATCTGAA-T
*
20209961 CAGACTTTACGTCTAGCAGGCTAAGTGCCGGTGATCTGAAT
1 CAGACTTTACGCCTAGCAGGCTAAGTGCCGGTGATCTGAAT
* *
20210002 CAGGCTATGA-GCCTAGCAGGCTAAGTGCCGGTGATCTGAAT
1 CAGACT-TTACGCCTAGCAGGCTAAGTGCCGGTGATCTGAAT
* * * *
20210043 CAGGCTATAAGCCTAGCAGGCTAAGCGCCGGTGATCTGAAT
1 CAGACTTTACGCCTAGCAGGCTAAGTGCCGGTGATCTGAAT
20210084 ATGTTAAATT
Statistics
Matches: 109, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
40 1 0.01
41 103 0.94
42 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
CAGACTTTACGCCTAGCAGGCTAAGTGCCGGTGATCTGAAT
Found at i:20211920 original size:9 final size:9
Alignment explanation
Indices: 20211906--20211932 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
20211896 TATAATATTA
20211906 AATTTAATT
1 AATTTAATT
20211915 AATTTAATT
1 AATTTAATT
20211924 AATTTAATT
1 AATTTAATT
20211933 TTACTTGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTAATT
Found at i:20214148 original size:21 final size:21
Alignment explanation
Indices: 20214122--20214165 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20214112 TACAAAAAAC
20214122 AAAATAGTGAAATGTGAAATT
1 AAAATAGTGAAATGTGAAATT
20214143 AAAATAGTGAAATGTGAAATT
1 AAAATAGTGAAATGTGAAATT
20214164 AA
1 AA
20214166 CTTTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (21 bp):
AAAATAGTGAAATGTGAAATT
Found at i:20231502 original size:6 final size:6
Alignment explanation
Indices: 20231420--20231501 Score: 155
Period size: 6 Copynumber: 13.7 Consensus size: 6
20231410 AATTCAAAAA
20231420 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
*
20231468 AAAATC AAAATC AAAATC AAAATC AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
20231502 AGAAGAAAGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.70, C:0.16, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:20231535 original size:41 final size:41
Alignment explanation
Indices: 20231432--20231554 Score: 124
Period size: 41 Copynumber: 3.0 Consensus size: 41
20231422 AATCAAAATC
* ** *
20231432 AAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAA-A-ATC
1 AAAATCAAAATCAAAATCAAAAACAAAAAGAAAA--AAGAGA-A
*
20231474 AAAATCAAAATCAAAATCAAAAACAAAAAGAAGAAAGAGAA
1 AAAATCAAAATCAAAATCAAAAACAAAAAGAAAAAAGAGAA
* ** *
20231515 AAAATCAAAATCAAAGTCAAAATGAAAATGAAAAAAGAGA
1 AAAATCAAAATCAAAATCAAAAACAAAAAGAAAAAAGAGA
20231555 GAAGGAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.03
41 36 0.52
42 31 0.45
ACGTcount: A:0.69, C:0.11, G:0.07, T:0.12
Consensus pattern (41 bp):
AAAATCAAAATCAAAATCAAAAACAAAAAGAAAAAAGAGAA
Found at i:20231571 original size:53 final size:53
Alignment explanation
Indices: 20231420--20231572 Score: 148
Period size: 54 Copynumber: 2.8 Consensus size: 53
20231410 AATTCAAAAA
* * ** **
20231420 AAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAAAA-TCAAAATCAAAATC
1 AAAATCAAAATCAAAATCAAAAACAAAA--AGAAGAAAAAGAAAAAATCAAAATC
*
20231474 AAAATCAAAATCAAAATCAAAAACAAAAAGAAGAAAGAGAAAAAATCAAAATC
1 AAAATCAAAATCAAAATCAAAAACAAAAAGAAGAAAAAGAAAAAATCAAAATC
* * * * *
20231527 AAAGTCAAAATGAAAATGAAAAA-AGAGAGAAGGAAAAAAGAAAAAA
1 AAAATCAAAATCAAAATCAAAAACAAAAAGAA-G-AAAAAGAAAAAA
20231573 GAAAAATGAG
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
52 12 0.14
53 33 0.40
54 38 0.46
ACGTcount: A:0.70, C:0.10, G:0.08, T:0.11
Consensus pattern (53 bp):
AAAATCAAAATCAAAATCAAAAACAAAAAGAAGAAAAAGAAAAAATCAAAATC
Found at i:20232585 original size:42 final size:41
Alignment explanation
Indices: 20232517--20232634 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 41
20232507 AAAGGGCGGC
* * *
20232517 TCAAATATTGATCAGAATTGGACATGAGGTGATTAGAGCAAT
1 TCAAAT-TTGATCAGAATGGGGCATGAGGTGATCAGAGCAAT
* *
20232559 TCAAATTCTGATCAGAGTGGGGCATGAAGTGATCAGAGCAAT
1 TCAAATT-TGATCAGAATGGGGCATGAGGTGATCAGAGCAAT
* * *
20232601 TTAAATTTTGATCAGATTGGGGCATGTGGTGATC
1 TCAAA-TTTGATCAGAATGGGGCATGAGGTGATC
20232635 TTGTTATACC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.95
43 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (41 bp):
TCAAATTTGATCAGAATGGGGCATGAGGTGATCAGAGCAAT
Found at i:20233918 original size:44 final size:44
Alignment explanation
Indices: 20233781--20233918 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
20233771 AAAGCAAAGC
*
20233781 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
* * * * * * * * * * *
20233825 CTTGCCTTC-TTGCATCGACAGCGAAGCAGATCAAA-AGTA-AAG-C
1 CTTGCCTCCATCG-GTTG-CAGTGGAGCTGGTTAAAGA-TAGCAGAT
20233868 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
20233912 CTTGCCT
1 CTTGCCT
20233919 TCCTGCATTG
Statistics
Matches: 64, Mismatches: 23, Indels: 14
0.63 0.23 0.14
Matches are distributed among these distances:
42 14 0.22
43 15 0.23
44 22 0.34
45 13 0.20
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
Found at i:20234087 original size:88 final size:88
Alignment explanation
Indices: 20233726--20234341 Score: 784
Period size: 88 Copynumber: 7.0 Consensus size: 88
20233716 CAGATCAGTG
* * * *
20233726 AAGATAGCAGATCTTGCCTTCTTGCATCGACAGCGAAGCAGATCGAAAG-CA-AAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAGACACCAGCCTTGCCTC
* *
20233789 CATCGGTTGTAGTGGAGCTGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* * *
20233813 AAGATAGCAGATCTTGCCTTCTTGCATCGACAGCGAAGCAGATCAAAAGTA-A--AGCCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAG-ACACCAGCCTTGCCT
*
20233875 CCATCGGTTGCAGTGGAGCTGGTTA
64 CCATCGGTTGCAGTGGAGCAGGTTA
* * * *
20233900 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAA-ACA-AAGCCTTGCC-C
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAGACACCAGCCTTGCCTC
*
20233962 CCTCGGTTGCAGTGGAGCAGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* *
20233986 AAAATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* *
20234051 CTCAGTTGCAGTGGAGCAGGTTGA
66 ATCGGTTGCAGTGGAGCAGGTT-A
*
20234075 AA-ATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTC-
* *
20234139 C-TTGGTTGCAGTGGAGCGGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* * * *
20234162 AAGATAGCAGATCTTGCCTTTCTGCGTAGACAACGAAGCAGATCGAAGACTCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* * *
20234227 ATCGATTGCAGTGAAGCGGGTTA
66 ATCGGTTGCAGTGGAGCAGGTTA
* * * *
20234250 AAGATAGCAGATCTTGCCTTTCTGCGTAGAAAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* * *
20234315 GTCGGTTACAGTGGAGCAGGTTG
66 ATCGGTTGCAGTGGAGCAGGTTA
20234338 AAGA
1 AAGA
20234342 GTCCTATATC
Statistics
Matches: 482, Mismatches: 36, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
85 4 0.01
86 67 0.14
87 147 0.30
88 260 0.54
89 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCAGGTTA
Found at i:20240288 original size:52 final size:53
Alignment explanation
Indices: 20240186--20240291 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
20240176 ATATGTATGG
20240186 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
20240239 TAGTTTTTGTGTATATCTCTTTC-TTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
20240291 T
1 T
20240292 TAGGAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.57
53 23 0.43
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.51
Consensus pattern (53 bp):
TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:20244859 original size:52 final size:53
Alignment explanation
Indices: 20244757--20244862 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
20244747 ATATGTATGG
20244757 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
20244810 TAGTTTTTGTGTATATCTCTTTC-TTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
20244862 T
1 T
20244863 TAGGAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.57
53 23 0.43
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.51
Consensus pattern (53 bp):
TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:20245803 original size:40 final size:40
Alignment explanation
Indices: 20245748--20245825 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 40
20245738 GAAGTTCGGG
20245748 ACATATATATTTGTTGGTTCTAGC-GACTAGTGTTGGGCAC
1 ACATATATATTTGTTGGTT-TAGCTGACTAGTGTTGGGCAC
*
20245788 ACATATGATA-TTGTTGGTTTATCTGACTAGTGTTGGGC
1 ACATAT-ATATTTGTTGGTTTAGCTGACTAGTGTTGGGC
20245826 GCAAACCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
39 3 0.09
40 29 0.83
41 3 0.09
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.40
Consensus pattern (40 bp):
ACATATATATTTGTTGGTTTAGCTGACTAGTGTTGGGCAC
Found at i:20245970 original size:70 final size:70
Alignment explanation
Indices: 20245804--20245975 Score: 184
Period size: 70 Copynumber: 2.5 Consensus size: 70
20245794 GATATTGTTG
* * * *
20245804 GTTTA-TCTGACTAGTGTTGGGCGCAAACCATTGTCGGTTATCCGACTAGTGCAAGATACACCTA
1 GTTTATTC-GACTAGCGTTGGGCGCAAAACATTATCGGTTATCCGACTAGTGCAAGACACACCTA
* *
20245868 TCGTCG
65 TCATCA
* ** * * * * * *
20245874 GTTTATCCGACTAGCACTAGGCGCAAAATATTATCGGTTATCTGACTAGTGCAGGGCACACTTAT
1 GTTTATTCGACTAGCGTTGGGCGCAAAACATTATCGGTTATCCGACTAGTGCAAGACACACCTAT
20245939 CATCA
66 CATCA
*
20245944 GTTTATTCGACTAGCGTTGGGTGCAAAACATT
1 GTTTATTCGACTAGCGTTGGGCGCAAAACATT
20245976 GTCGATTTAA
Statistics
Matches: 80, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
70 79 0.99
71 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (70 bp):
GTTTATTCGACTAGCGTTGGGCGCAAAACATTATCGGTTATCCGACTAGTGCAAGACACACCTAT
CATCA
Found at i:20246368 original size:12 final size:12
Alignment explanation
Indices: 20246347--20246384 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
20246337 TTACGAGAAT
*
20246347 ATTGTGTACTAA
1 ATTGTATACTAA
20246359 ATTGTATACTAA
1 ATTGTATACTAA
*
20246371 ATTGTATATTAA
1 ATTGTATACTAA
20246383 AT
1 AT
20246385 AGAATCGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (12 bp):
ATTGTATACTAA
Found at i:20247663 original size:12 final size:12
Alignment explanation
Indices: 20247646--20247672 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20247636 GTTTGAATAT
20247646 GATGAAGTTGGA
1 GATGAAGTTGGA
20247658 GATGAAGTTGGA
1 GATGAAGTTGGA
20247670 GAT
1 GAT
20247673 TAAAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (12 bp):
GATGAAGTTGGA
Found at i:20263106 original size:34 final size:33
Alignment explanation
Indices: 20263032--20263106 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
20263022 AATATTGTTT
*
20263032 AATATAAATTAATTTTAATATTTTTCATTAATCA
1 AATATAAATTAATTTAAATATTTTT-ATTAATCA
*
20263066 ATTATAAA-TAATTTAAATAATTATTT-TTAATACA
1 AATATAAATTAATTTAAAT-ATT-TTTATTAAT-CA
20263100 AATATAA
1 AATATAA
20263107 TTTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 14 0.40
34 18 0.51
35 3 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (33 bp):
AATATAAATTAATTTAAATATTTTTATTAATCA
Found at i:20264115 original size:31 final size:31
Alignment explanation
Indices: 20264049--20264115 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
20264039 CCTAGGGAAG
** **
20264049 AGGCGGCACGTAGTGGTGGAGGAGGCAGCTT
1 AGGCGGCACCCAGTGGTGGAGGAGGCAGCGC
* *
20264080 AGGCGGCACCCAGTGGTGGAGGCGGCGGCGC
1 AGGCGGCACCCAGTGGTGGAGGAGGCAGCGC
20264111 AGGCG
1 AGGCG
20264116 ACACAAGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.51, T:0.10
Consensus pattern (31 bp):
AGGCGGCACCCAGTGGTGGAGGAGGCAGCGC
Found at i:20266329 original size:14 final size:14
Alignment explanation
Indices: 20266310--20266337 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20266300 TTTTTTTAAT
20266310 GATACTATTCTAAC
1 GATACTATTCTAAC
20266324 GATACTATTCTAAC
1 GATACTATTCTAAC
20266338 ATGCAATTTG
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:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
GATACTATTCTAAC
Found at i:20267663 original size:62 final size:62
Alignment explanation
Indices: 20267519--20267752 Score: 333
Period size: 62 Copynumber: 3.7 Consensus size: 62
20267509 CAACATTACA
* * * *
20267519 ACATTAGAACACTAAAACTTGTAACAAAATTTGTAATATAAATTTTGTTTGTAATATAAATTAAA
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTG--T-T-ATATAAATTAAA
20267584 T
62 T
*
20267585 ACATTACAACACTAAAAATTGGAACAAACTTTATAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* *
20267647 ACATTACAACATTAAAAATTGGAACAAACTTTGTAACATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* * * *
20267709 ACATTAGAGCATTAAAAATTAGAACAAACTTTGTAATATAAATT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATT
20267753 AGGTACATTG
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
62 112 0.72
63 1 0.01
64 1 0.01
66 42 0.27
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (62 bp):
ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:20281257 original size:21 final size:21
Alignment explanation
Indices: 20281233--20281290 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
20281223 CATTGTTTCT
* *
20281233 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
20281254 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
*
20281275 AATCTCACCGCCACAG
1 AATCTCACCGCTACAG
20281291 CTGTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.36, G:0.10, T:0.22
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:20281450 original size:45 final size:45
Alignment explanation
Indices: 20281386--20281473 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
20281376 ACAGATACTC
*
20281386 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
* *
20281431 GGTGGAATT-AGCACATAGCAGCCACTTTACTAATCAATGATGT
1 GGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
20281474 TCAGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 36 0.92
46 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (45 bp):
GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
Found at i:20281538 original size:51 final size:50
Alignment explanation
Indices: 20281480--20281667 Score: 236
Period size: 51 Copynumber: 3.7 Consensus size: 50
20281470 ATGTTCAGTT
* *
20281480 CACATAGTAGCCTGCACATAGTACTACACATGTGACAATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACAA-TACCATCCGGTA
* *
20281531 CACATAGTAGCTTGCACATAGTACTACACACGTGATCGAA-ACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-C-AATACCATCCGGTA
* * * * *
20281582 CGCATAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACAATACCA-TCCGGTA
*
20281632 CACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGAC
20281668 CATCACTTTC
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 73 0.62
52 1 0.01
53 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACAATACCATCCGGTA
Found at i:20281661 original size:101 final size:101
Alignment explanation
Indices: 20281482--20281666 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
20281472 GTTCAGTTCA
* * *
20281482 CATAGTAGCCTGCACATAGTACTACACATGTGACAATTACCATCCGATACACATAGTAGCTTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGAC-ACTACCATCCGATACACATAGTAGCCTGCA
20281547 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
20281584 CATAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACACTACCA-TCCGATACACATAGTAGCCTGCA
20281648 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
20281667 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACACTACCATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:20283301 original size:62 final size:62
Alignment explanation
Indices: 20283235--20283530 Score: 448
Period size: 62 Copynumber: 4.7 Consensus size: 62
20283225 CAATGTACCT
*
20283235 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
* * *
20283297 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATCTATATAACGA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
20283359 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
* * *
20283421 AACTTATATTATAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATTACAAAGA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATA-TA-ACA-A
* * * * *
20283486 AATTTTATATTATAAATTTTGTTACAAGTTTTAGTGTTTTAATGT
1 AA-TTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGT
20283531 TGTAATGTTG
Statistics
Matches: 217, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
62 173 0.80
63 2 0.01
64 2 0.01
65 3 0.01
66 37 0.17
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
Found at i:20284111 original size:18 final size:17
Alignment explanation
Indices: 20284090--20284158 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 17
20284080 GCGAGAGGTG
* *
20284090 TGGCTCGAGCTTTGGCTC
1 TGGCTCG-GCTCTGGTTC
20284108 TGGCTCGGGCTCTGGTTC
1 TGGCTC-GGCTCTGGTTC
20284126 TGGCTCTGGCTCTGGTTC
1 TGGCTC-GGCTCTGGTTC
20284144 TGGCTCTGGCTCTGG
1 TGGCTC-GGCTCTGG
20284159 CTCGGCCTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 46 0.98
19 1 0.02
ACGTcount: A:0.01, C:0.28, G:0.36, T:0.35
Consensus pattern (17 bp):
TGGCTCGGCTCTGGTTC
Found at i:20284113 original size:6 final size:6
Alignment explanation
Indices: 20284102--20284161 Score: 93
Period size: 6 Copynumber: 10.0 Consensus size: 6
20284092 GCTCGAGCTT
* * *
20284102 TGGCTC TGGCTC GGGCTC TGGTTC TGGCTC TGGCTC TGGTTC TGGCTC
1 TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC
20284150 TGGCTC TGGCTC
1 TGGCTC TGGCTC
20284162 GGCCTCTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.30, G:0.35, T:0.35
Consensus pattern (6 bp):
TGGCTC
Found at i:20284821 original size:14 final size:14
Alignment explanation
Indices: 20284802--20284836 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
20284792 CAAATTACAT
20284802 GTTAGAATAGTATC
1 GTTAGAATAGTATC
20284816 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
20284830 ATTAGAA
1 GTTAGAA
20284837 AAAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:20287062 original size:14 final size:14
Alignment explanation
Indices: 20287043--20287078 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
20287033 AAACATTTTT
*
20287043 ACTTTTCCCCCAAA
1 ACTTTTACCCCAAA
20287057 ACTTTTACCCCAAA
1 ACTTTTACCCCAAA
20287071 ACTTTTAC
1 ACTTTTAC
20287079 TCTTCTCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (14 bp):
ACTTTTACCCCAAA
Found at i:20287762 original size:24 final size:24
Alignment explanation
Indices: 20287730--20287782 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
20287720 ACAAAGATTT
* *
20287730 TTATACTAATAAAT-ATCAAATATA
1 TTATACTAACAAATGCT-AAATATA
*
20287754 TTATGCTAACAAATGCTAAATATA
1 TTATACTAACAAATGCTAAATATA
20287778 TTATA
1 TTATA
20287783 TTAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TTATACTAACAAATGCTAAATATA
Found at i:20287789 original size:14 final size:14
Alignment explanation
Indices: 20287769--20287802 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
20287759 CTAACAAATG
20287769 CTAAATATATTATA
1 CTAAATATATTATA
*
20287783 TTAAATATATTATA
1 CTAAATATATTATA
20287797 CTAAAT
1 CTAAAT
20287803 CTTCTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
CTAAATATATTATA
Found at i:20288450 original size:12 final size:12
Alignment explanation
Indices: 20288435--20288464 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20288425 CAAAACCTTC
*
20288435 ATCTTCATCTTT
1 ATCTTCAACTTT
20288447 ATCTTCAACTTT
1 ATCTTCAACTTT
20288459 ATCTTC
1 ATCTTC
20288465 TCAATTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (12 bp):
ATCTTCAACTTT
Found at i:20294733 original size:24 final size:24
Alignment explanation
Indices: 20294706--20294757 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
20294696 TTTTTGGTTA
20294706 TTGGGCTAATTATGT-TTTTGTAAT
1 TTGGGCTAA-TATGTATTTTGTAAT
*
20294730 TTGGGCTAATATTTATTTTGTAAT
1 TTGGGCTAATATGTATTTTGTAAT
20294754 TTGG
1 TTGG
20294758 ACTATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (24 bp):
TTGGGCTAATATGTATTTTGTAAT
Found at i:20298401 original size:28 final size:29
Alignment explanation
Indices: 20298370--20298429 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
20298360 CCTAAACCTT
20298370 AAAATCCTAAACCCAAATTTA-ATTTTCA
1 AAAATCCTAAACCCAAATTTATATTTTCA
** *
20298398 AAAATCCTAAACCTTAATTTATTTTTTCA
1 AAAATCCTAAACCCAAATTTATATTTTCA
20298427 AAA
1 AAA
20298430 GCCTTACCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATCCTAAACCCAAATTTATATTTTCA
Done.