Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006657.1 Hibiscus syriacus cultivar Beakdansim tig00016433_pilon, whole genome shotgun sequence
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: 126753
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:70 original size:36 final size:36
Alignment explanation
Indices: 21--136 Score: 141
Period size: 35 Copynumber: 3.3 Consensus size: 36
11 CCATTATCAT
* *
21 TTTTTC-AACAAACATCT-CCAAACTTTGAAAAACTA
1 TTTTTCAAAGAAACAT-TACCAAACTTTGAAAAACAA
*
56 TTTTTCAAAGAAACATTACCAAACTTTG-AAAACCA
1 TTTTTCAAAGAAACATTACCAAACTTTGAAAAACAA
* *
91 -TTTTCAAATAAACATTTACCAAACTTTGAAAACCAA
1 TTTTTCAAAGAAACA-TTACCAAACTTTGAAAAACAA
127 TTTTTCAAAG
1 TTTTTCAAAG
137 TTGGTTGCCA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
34 13 0.19
35 26 0.37
36 23 0.33
37 8 0.11
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
TTTTTCAAAGAAACATTACCAAACTTTGAAAAACAA
Found at i:608 original size:22 final size:25
Alignment explanation
Indices: 567--644 Score: 119
Period size: 24 Copynumber: 3.3 Consensus size: 25
557 ACATATTCTG
*
567 CTTCAGTTGTGGAGAGAGCAACTAT
1 CTTCTGTTGTGGAGAGAGCAACTAT
592 C-TCTGTTGT-G-GAGAGCAACTAT
1 CTTCTGTTGTGGAGAGAGCAACTAT
614 CTTCT-TTGTGGAGAGAGCAACTAT
1 CTTCTGTTGTGGAGAGAGCAACTAT
638 CTTCTGT
1 CTTCTGT
645 AGTTGAAACC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
22 17 0.35
23 5 0.10
24 24 0.50
25 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (25 bp):
CTTCTGTTGTGGAGAGAGCAACTAT
Found at i:3455 original size:15 final size:15
Alignment explanation
Indices: 3435--3466 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3425 AAAATCTTTC
*
3435 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
3450 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
3465 TT
1 TT
3467 CGATCTGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:4243 original size:16 final size:17
Alignment explanation
Indices: 4212--4247 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4202 CGTATCGCTG
*
4212 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
4229 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
4245 ACA
1 ACA
4248 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:4695 original size:36 final size:37
Alignment explanation
Indices: 4651--4755 Score: 110
Period size: 35 Copynumber: 2.9 Consensus size: 37
4641 TCTCATTATC
*
4651 ATTTTTC-AACAATCATCTACCAAACTTTGAAAAATT
1 ATTTTTCAAACAAACATCTACCAAACTTTGAAAAATT
* *
4687 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACA--
1 ATTTTTCAAACAAACATCTACCAAACTTTGAAAA-ATT
* * * *
4723 A-TTTTCAAATAAATATTTACCGAACTTTGAAAA
1 ATTTTTCAAACAAACATCTACCAAACTTTGAAAA
4756 CCAATTTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
35 29 0.48
36 8 0.13
37 23 0.38
38 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (37 bp):
ATTTTTCAAACAAACATCTACCAAACTTTGAAAAATT
Found at i:4761 original size:36 final size:36
Alignment explanation
Indices: 4651--4769 Score: 136
Period size: 37 Copynumber: 3.3 Consensus size: 36
4641 TCTCATTATC
* * *
4651 ATTTTTC-AACAATCATCTACCAAACTTTGAAAA-A
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACA
4685 TTATTTTTCAAAGAAACATTTACCAAACTTTGAAAACA
1 --ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACA
* * *
4723 A-TTTTCAAATAAATATTTACCGAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA-CA
4759 ATTTTTCAAAG
1 ATTTTTCAAAG
4770 TTGGTTGTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
35 29 0.40
36 11 0.15
37 31 0.43
38 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACA
Found at i:17012 original size:10 final size:10
Alignment explanation
Indices: 16997--17036 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
16987 TTTATCACAC
16997 CAAATTCTCT
1 CAAATTCTCT
17007 CAAATTCTCT
1 CAAATTCTCT
17017 -AAATTTCTCT
1 CAAA-TTCTCT
*
17027 CAAATACTCT
1 CAAATTCTCT
17037 TTTTTTAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:17301 original size:110 final size:111
Alignment explanation
Indices: 17161--17381 Score: 390
Period size: 110 Copynumber: 2.0 Consensus size: 111
17151 TGGAAATCAT
* *
17161 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
17226 TATTTAGTT-ATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTAATTCATTTAATGCATGACTATTAGATTAAGAATTAA
17271 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
17336 TAATTAGTTAATTCATTTAATGCATGACTATTAGATTAAGAATTAA
66 TAATTAGTTAATTCATTTAATGCATGACTATTAGATTAAGAATTAA
17382 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTAATTCATTTAATGCATGACTATTAGATTAAGAATTAA
Found at i:19853 original size:11 final size:11
Alignment explanation
Indices: 19807--19884 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
19797 ATAACTATTC
* *
19807 AAATGATTAAA
1 AAATTATTATA
*
19818 AAATTATTATT
1 AAATTATTATA
* *
19829 ACATT-TTATC
1 AAATTATTATA
19839 AAATTATTATA
1 AAATTATTATA
* *
19850 AAATAATTATT
1 AAATTATTATA
19861 AAATTA--ATCA
1 AAATTATTAT-A
19871 AAA-TATTATA
1 AAATTATTATA
19881 AAAT
1 AAAT
19885 AATGCTTAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
9 4 0.08
10 15 0.29
11 32 0.63
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (11 bp):
AAATTATTATA
Found at i:19878 original size:31 final size:31
Alignment explanation
Indices: 19807--19909 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
19797 ATAACTATTC
* * *
19807 AAATGATTAAAAAATTATTATTACATTTTATCA
1 AAAT-ATTATAAAATAATTATTA-AATTTATCA
* *
19840 AATTATTATAAAATAATTATTAAATTAATCA
1 AAATATTATAAAATAATTATTAAATTTATCA
**
19871 AAATATTATAAAATAATGCTTAAATTTATCA
1 AAATATTATAAAATAATTATTAAATTTATCA
19902 AAAT-TTAT
1 AAATATTAT
19910 TATTTTTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
30 4 0.07
31 38 0.62
32 16 0.26
33 3 0.05
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (31 bp):
AAATATTATAAAATAATTATTAAATTTATCA
Found at i:19934 original size:22 final size:22
Alignment explanation
Indices: 19908--19952 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
19898 ATCAAAATTT
19908 ATTATTTTTATAATA-TATAATA
1 ATTA-TTTTATAATAGTATAATA
*
19930 ATTATTTTATAATAGTTTAATA
1 ATTATTTTATAATAGTATAATA
19952 A
1 A
19953 ATTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTATTTTATAATAGTATAATA
Found at i:19979 original size:19 final size:19
Alignment explanation
Indices: 19928--19990 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
19918 TAATATATAA
*
19928 TAATTATTTTATAATAGTT
1 TAATAATTTTATAATAGTT
* *
19947 TAATAAATTAATAATTA-TT
1 TAATAATTTTATAA-TAGTT
* *
19966 TTATAATTTTATAA-ATTT
1 TAATAATTTTATAATAGTT
19984 TAATAAT
1 TAATAAT
19991 AAAAAATATC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 1 0.03
18 8 0.23
19 24 0.69
20 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATAATTTTATAATAGTT
Found at i:21201 original size:26 final size:26
Alignment explanation
Indices: 21171--21225 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
21161 AAGATGTGTA
21171 AGTTTTTTCAAGGATCTCAGTTTTAT
1 AGTTTTTTCAAGGATCTCAGTTTTAT
21197 AGTTTTTTCAAGGATCTCAGTTTTAT
1 AGTTTTTTCAAGGATCTCAGTTTTAT
21223 AGT
1 AGT
21226 CATAGGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (26 bp):
AGTTTTTTCAAGGATCTCAGTTTTAT
Found at i:26325 original size:15 final size:15
Alignment explanation
Indices: 26299--26346 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
26289 TTCAAACATC
*
26299 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
26315 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
26332 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
26347 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:35164 original size:23 final size:23
Alignment explanation
Indices: 35134--35217 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
35124 CTCATATAAA
* *
35134 TGCACCGAAGTGCAATGTAGATT
1 TGCACCGAAGTGCCACGTAGATT
*
35157 TGCACCGAAATGCCACGTAGATT
1 TGCACCGAAGTGCCACGTAGATT
**
35180 TGCATTGAAGTGCCACGTAGATT
1 TGCACCGAAGTGCCACGTAGATT
*
35203 TGCATCGAAGTGCCA
1 TGCACCGAAGTGCCA
35218 TATAAGATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGATT
Found at i:37915 original size:60 final size:60
Alignment explanation
Indices: 37841--38004 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
37831 TTTGGATGAC
* * *
37841 TTTGGGAATGAAATTGAAAGATTCAAAAGTTTATGGATCAATTTAGAATGAGAA-TCATAG
1 TTTGGGGATGAAATTGAAAGATTCAAAAGTTTAAGGATAAATTTAGAATGA-AAGTCATAG
* *
37901 TTTGGGGATGAAATTGAAATG-TTCAAAGGTTTAAGGATTAATTTAGAATGAAAGTCATAG
1 TTTGGGGATGAAATTGAAA-GATTCAAAAGTTTAAGGATAAATTTAGAATGAAAGTCATAG
** * * *
37961 TTTAAGGATGGAA-TGGAATATTCAAAAGTTTAAGGATAAATTTA
1 TTTGGGGATGAAATTGAAAGATTCAAAAGTTTAAGGATAAATTTA
38005 AAGTAGGGAT
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
59 28 0.31
60 61 0.68
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (60 bp):
TTTGGGGATGAAATTGAAAGATTCAAAAGTTTAAGGATAAATTTAGAATGAAAGTCATAG
Found at i:39849 original size:35 final size:35
Alignment explanation
Indices: 39798--39866 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
39788 ATATAATTTG
*
39798 GATAAATTAATCGATTAATATAAATTTGGATATCT
1 GATAAATTAATCGATTAATATAAATTTAGATATCT
* *
39833 GATATATTAATCGATTAATGTAAATTTAGATATC
1 GATAAATTAATCGATTAATATAAATTTAGATATC
39867 GCAGAGATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.41
Consensus pattern (35 bp):
GATAAATTAATCGATTAATATAAATTTAGATATCT
Found at i:43418 original size:73 final size:73
Alignment explanation
Indices: 43305--43444 Score: 262
Period size: 73 Copynumber: 1.9 Consensus size: 73
43295 TTGTACAATT
*
43305 TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
1 TTTCTTACAATTCAATTATAAAATAGGCCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
43370 CGGTACAA
66 CGGTACAA
*
43378 TTTCTTACAATTCAATTATAAAATAGGCCCCCCATTTATTTAATAAGTACTATGGCAGACATGAA
1 TTTCTTACAATTCAATTATAAAATAGGCCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
43443 CG
66 CG
43445 TTATTGTACC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (73 bp):
TTTCTTACAATTCAATTATAAAATAGGCCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
CGGTACAA
Found at i:51500 original size:37 final size:37
Alignment explanation
Indices: 51447--51551 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
51437 CATTTTCGTC
51447 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT-AAAGTT
* *
51485 -TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
* * * *
51521 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
51552 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
Found at i:51947 original size:18 final size:17
Alignment explanation
Indices: 51908--51950 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
51898 ATTATATGGA
51908 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
51924 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
51942 TATTATTAT
1 TATTATTAT
51951 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:52257 original size:11 final size:11
Alignment explanation
Indices: 52241--52265 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52231 TTTTTTATTC
52241 ATTATTATTAT
1 ATTATTATTAT
52252 ATTATTATTAT
1 ATTATTATTAT
52263 ATT
1 ATT
52266 TTTCTTTTTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:56829 original size:183 final size:183
Alignment explanation
Indices: 56521--57057 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
56511 ATTAAATCCG
* *
56521 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATAA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
56586 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
56651 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
56704 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
56769 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
56834 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCCGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
56887 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
56952 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
57016 TTTTTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
57058 TAAACCTGAT
Statistics
Matches: 339, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 338 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:58226 original size:36 final size:34
Alignment explanation
Indices: 58186--58299 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 34
58176 CACTCAAATT
58186 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
58222 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
58258 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
58294 TGTTTT
1 TGTTTT
58300 CACTCGAAAG
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 50 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:58262 original size:72 final size:76
Alignment explanation
Indices: 58170--58331 Score: 228
Period size: 72 Copynumber: 2.2 Consensus size: 76
58160 ATGCAGATGA
* * *
58170 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACTGTTTTCACTC
58232 GAAAGAA-G-AT
65 GAAAGAAGGCAT
*
58242 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACTGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTGTTTTCACTCG
58306 AAAGAAGGCAT
66 AAAGAAGGCAT
58317 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
58332 GCTATTTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
71 1 0.01
72 51 0.64
73 11 0.14
74 1 0.01
75 4 0.05
76 12 0.15
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTGTTTTCACTCG
AAAGAAGGCAT
Found at i:58381 original size:73 final size:72
Alignment explanation
Indices: 58209--58366 Score: 178
Period size: 72 Copynumber: 2.2 Consensus size: 72
58199 ACATACTTTG
* * * *
58209 TCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTCACTCAAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGACTGTTTTCACTCGAAAGAAGATTTATTTCACTCAAGACTATTTTTCTT-AAAC
*
58273 AAGATTTG
65 AAGATTTA
*
58281 TCTCGCTTGAGACTGTTTTCACTCGAAAGAAGGCATTTCATTTCACTCAAGGCTATTTTT-TT-A
1 TCTCGCTTGAGACTGTTTTCACTCGAAAGAA-G-ATTT-ATTTCACTCAAGACTATTTTTCTTAA
*
58344 AGAAGATTTTA
63 ACAAGA-TTTA
*
58355 TCTTGCTTGAGA
1 TCTCGCTTGAGA
58367 TAGTTTCCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
72 18 0.25
73 16 0.22
74 15 0.21
75 6 0.08
76 18 0.25
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (72 bp):
TCTCGCTTGAGACTGTTTTCACTCGAAAGAAGATTTATTTCACTCAAGACTATTTTTCTTAAACA
AGATTTA
Found at i:58403 original size:39 final size:39
Alignment explanation
Indices: 58360--58495 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 39
58350 TTTTATCTTG
58360 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* ** * *
58399 CTTGAGACAGTTTCTTTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGATAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
58451 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
58489 CTTGAGA
1 CTTGAGA
58496 CAATTTCTCT
Statistics
Matches: 73, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
38 2 0.03
39 30 0.41
40 5 0.07
41 2 0.03
42 1 0.01
48 1 0.01
49 2 0.03
50 5 0.07
51 23 0.32
52 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (39 bp):
CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:58523 original size:104 final size:104
Alignment explanation
Indices: 58415--58732 Score: 516
Period size: 104 Copynumber: 3.1 Consensus size: 104
58405 ACAGTTTCTT
* *
58415 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
58480 TTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
58519 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
58584 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
58623 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
* ** *
58685 TTTATCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
58724 TTGAAAACA
1 TTGAAAACA
58733 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 154 0.76
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:58679 original size:36 final size:36
Alignment explanation
Indices: 58632--58707 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
58622 ATTGAAAACA
* * *
58632 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
58668 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
58704 TTTC
1 TTTC
58708 TCTCCAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:59099 original size:105 final size:105
Alignment explanation
Indices: 58923--59534 Score: 903
Period size: 105 Copynumber: 5.9 Consensus size: 105
58913 GACAACACAA
* * * *
58923 CAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCTAATTTC
1 CAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTC
* *
58987 AACTTCACAACGAAGGATATTGGACTCCAGAAAATGCAAGTT
64 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
59029 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAA
1 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
*
59094 CTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTT
66 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
59134 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAA
1 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
59199 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
66 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
*
59239 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAA
1 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
59304 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
66 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* * *
59344 CAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGTCAATTTCAA
1 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
* * *
59404 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
66 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* * * * * * ** *
59444 CAACTTCACAACGAAGGGACGGCTGGTTATCAACAAAGAATTTCCCGGTTCCAGAGCCAATTTCA
1 CAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCA
* * *
59509 ACTTCACGATGGAGGATATTGGACTC
65 ACTTCACAACGAAGGATATTGGACTC
59535 GGAACAATGC
Statistics
Matches: 470, Mismatches: 29, Indels: 14
0.92 0.06 0.03
Matches are distributed among these distances:
100 81 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 309 0.66
106 65 0.14
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
Found at i:60540 original size:18 final size:17
Alignment explanation
Indices: 60501--60543 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
60491 ATTATATGGA
60501 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
60517 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
60535 TATTATTAT
1 TATTATTAT
60544 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:60851 original size:20 final size:20
Alignment explanation
Indices: 60826--60877 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
60816 TAGTTGAAAA
*
60826 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
60846 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
60866 TCGCGTTGCGAT
1 TCGCGTTGCGAT
60878 AGTCTACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.08, C:0.25, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:61074 original size:2 final size:2
Alignment explanation
Indices: 61067--61110 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
61057 TAATACTTTG
61067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61109 AT
1 AT
61111 TTTTTTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61192 original size:9 final size:9
Alignment explanation
Indices: 61180--61231 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
61170 CTTATCTCAC
61180 TTATTTATT
1 TTATTTATT
61189 TTATTTATT
1 TTATTTATT
61198 TTATTT-TT
1 TTATTTATT
61206 CTCT-TTTATT
1 -T-TATTTATT
*
61216 TTATTTGTT
1 TTATTTATT
*
61225 TTCTTTA
1 TTATTTA
61232 CCTTGTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 3 0.08
9 30 0.83
10 3 0.08
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (9 bp):
TTATTTATT
Found at i:61241 original size:27 final size:27
Alignment explanation
Indices: 61183--61234 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
61173 ATCTCACTTA
**
61183 TTTATTTTATTTATTTTATTTTTCTCT
1 TTTATTTTATTTATTTTATTTACCTCT
* *
61210 TTTATTTTATTTGTTTTCTTTACCT
1 TTTATTTTATTTATTTTATTTACCT
61235 TGTTTATCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.13, C:0.10, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTATTTTATTTATTTTATTTACCTCT
Found at i:68322 original size:22 final size:22
Alignment explanation
Indices: 68294--68356 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
68284 AATATTAAGA
68294 GGTATCGATACCCCTATGAATG
1 GGTATCGATACCCCTATGAATG
68316 GGTATCGATACCCCTATGAATG
1 GGTATCGATACCCCTATGAATG
*
68338 GGTATCAATACCCC-ATGAA
1 GGTATCGATACCCCTATGAA
68357 GGCTCAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 5 0.12
22 35 0.88
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (22 bp):
GGTATCGATACCCCTATGAATG
Found at i:68559 original size:20 final size:20
Alignment explanation
Indices: 68530--68573 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
68520 ATAATCACCA
*
68530 AACGGTTCCAAAACATCCCC
1 AACGGCTCCAAAACATCCCC
68550 AACGGCTCCAAAACATCCCC
1 AACGGCTCCAAAACATCCCC
68570 AACG
1 AACG
68574 ACTATATACG
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:0.36, C:0.41, G:0.11, T:0.11
Consensus pattern (20 bp):
AACGGCTCCAAAACATCCCC
Found at i:69295 original size:60 final size:59
Alignment explanation
Indices: 69205--69347 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 59
69195 TTTTAAATGT
* * * * *
69205 TTTAATTTCATGCTTAAACTATAAATTTCATTATAA-ATTAGTCCTTAAAC-TTTTGAATA
1 TTTAATTTCAT-CTCAAACTATAAACTTCATT-TAAGATTAATCCTCAAACTTTTTGAACA
* * *
69264 TTTAATTTTCATCCTCAAACTATGACCTTCATTTAAGATTAATTCTCAAACTTTTTGAACA
1 TTTAA-TTTCAT-CTCAAACTATAAACTTCATTTAAGATTAATCCTCAAACTTTTTGAACA
*
69325 TTTCAATTTCATCTCAAATTATA
1 TTT-AATTTCATCTCAAACTATA
69348 TGTATATACT
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 8 0.12
60 42 0.61
61 17 0.25
62 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (59 bp):
TTTAATTTCATCTCAAACTATAAACTTCATTTAAGATTAATCCTCAAACTTTTTGAACA
Found at i:69572 original size:60 final size:59
Alignment explanation
Indices: 69508--69624 Score: 162
Period size: 60 Copynumber: 2.0 Consensus size: 59
69498 TTTGGGGACC
* ** ** *
69508 AATTTAGAATGAGAGTCATAGTTTGGGGATGAAATTGGAATGTTCAAAGGTTTAAGGATT
1 AATTTAGAATGAAAGTCATAGTTTAAGGATGAAA-TGGAATACTCAAAAGTTTAAGGATT
*
69568 AATTTAGAATGAAAGTCATGGTTTAAGGATGAAATGGAATACTCAAAAGTTTAAGGA
1 AATTTAGAATGAAAGTCATAGTTTAAGGATGAAATGGAATACTCAAAAGTTTAAGGA
69625 CCAAATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 20 0.40
60 30 0.60
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (59 bp):
AATTTAGAATGAAAGTCATAGTTTAAGGATGAAATGGAATACTCAAAAGTTTAAGGATT
Found at i:74852 original size:73 final size:73
Alignment explanation
Indices: 74763--74902 Score: 262
Period size: 73 Copynumber: 1.9 Consensus size: 73
74753 GGTACAATAA
*
74763 CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAGA
1 CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
74828 AATTGTAC
66 AATTGTAC
*
74836 CGTTCATGTCTGCCATAGTGCTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
1 CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
74901 AA
66 AA
74903 AATTGTACAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (73 bp):
CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
AATTGTAC
Found at i:84653 original size:18 final size:18
Alignment explanation
Indices: 84553--84662 Score: 61
Period size: 18 Copynumber: 6.2 Consensus size: 18
84543 GATATACATG
84553 ATATTAAG-AAAAA-A-A
1 ATATTAAGAAAAAATATA
*
84568 ATAAT-AGAAAAAA-ATA
1 ATATTAAGAAAAAATATA
* * * *
84584 AAATAAAGTAAAAATAGA
1 ATATTAAGAAAAAATATA
* *
84602 ATATTAAGTAAATATAT-
1 ATATTAAGAAAAAATATA
* *
84619 ATATAAAACATATAAAATATA
1 ATAT-TAAGA-A-AAAATATA
84640 ATATTAAGAAAAAATATA
1 ATATTAAGAAAAAATATA
84658 TATAT
1 -ATAT
84663 ATACATAGTA
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
14 2 0.03
15 10 0.14
16 3 0.04
17 11 0.16
18 25 0.36
19 6 0.09
20 9 0.13
21 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (18 bp):
ATATTAAGAAAAAATATA
Found at i:84719 original size:8 final size:10
Alignment explanation
Indices: 84690--84731 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
84680 AAAAATTAAT
84690 ATATCTATAC
1 ATATCTATAC
84700 ATATCTATAC
1 ATATCTATAC
84710 ATA-C-ATAC
1 ATATCTATAC
*
84718 ATATATATAC
1 ATATCTATAC
84728 ATAT
1 ATAT
84732 ACACATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.24
9 1 0.03
10 21 0.72
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATCTATAC
Found at i:84725 original size:4 final size:4
Alignment explanation
Indices: 84688--84769 Score: 51
Period size: 4 Copynumber: 20.8 Consensus size: 4
84678 AGAAAAATTA
* * * * * * * * *
84688 ATAT ATCT ATAC ATAT CTAT ACAT ACAT ACAT ATAT ATAC ATAT ACAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
84736 ATAT ATAT ATAT ATA- ATGAT ATA- AGAT ATAT ATA
1 ATAT ATAT ATAT ATAT AT-AT ATAT ATAT ATAT ATA
84770 ATAAAAATAA
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
3 4 0.07
4 53 0.90
5 2 0.03
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:84749 original size:18 final size:18
Alignment explanation
Indices: 84695--84750 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
84685 TTAATATATC
*
84695 TATACATATCTATACATA
1 TATACATATATATACATA
*
84713 CATACATATATATACATA
1 TATACATATATATACATA
* *
84731 TACACATATATATATATA
1 TATACATATATATACATA
84749 TA
1 TA
84751 ATGATATAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
TATACATATATATACATA
Found at i:84782 original size:25 final size:25
Alignment explanation
Indices: 84736--84784 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
84726 ACATATACAC
* *
84736 ATATATATATATATAATGATATAAG
1 ATATATATATATAAAATAATATAAG
84761 ATATATATA-ATAAAAATAATATAA
1 ATATATATATAT-AAAATAATATAA
84785 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
ATATATATATATAAAATAATATAAG
Found at i:84810 original size:20 final size:18
Alignment explanation
Indices: 84761--84845 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 18
84751 ATGATATAAG
*
84761 ATATATATAATAAAAATAAT
1 ATATATA-AATAAAAA-AAA
*
84781 ATAATATAAATAAAAAAGGA
1 AT-ATATAAATAAAAAA-AA
84801 ATATAGTAAATAAATAAAAA
1 ATATA-TAAATAAA-AAAAA
* * *
84821 ATATATAATTAAAAATAT
1 ATATATAAATAAAAAAAA
84839 ATATATA
1 ATATATA
84846 GGGGAAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
18 10 0.18
19 11 0.20
20 26 0.47
21 8 0.15
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
ATATATAAATAAAAAAAA
Found at i:86449 original size:106 final size:106
Alignment explanation
Indices: 86185--86666 Score: 575
Period size: 106 Copynumber: 4.6 Consensus size: 106
86175 AATTGGCTCT
* * * *
86185 GGAAATTGTTTGTTGACAGTCAACCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTC
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * * *
86250 TAATATCATTCGTTGTGAAGTTGAAATTGACTCTG-AA-T-
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * *
86288 -GAAA-T-TTTATTGACAATCAGCCTCCCCTTCG-TCGCGAAGTTGAGCTTGTGTTGTCTTGGGT
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCT-GTGAAGTTGAGCTTGTGTTGTCTTGAGT
*
86349 CCAATATCCTTCGCT-TGGAAGTTGAAATTGGCCCTGAAATTG
65 CCAATATCCTTCGCTGT-GAAGTTGAAATTGGCTCTGAAATTG
* * * *
86391 GGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTTGAGTC
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
86456 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * ** * ** * *
86497 GGAAGTTGTTTGTTGACAACCAGTCGTTCCTTCGTTGTGAAGTTGAATTTGTGTTGTCTCGAATC
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
86562 CAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAACTG
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * * * *
86603 GGAAATTGTTTGTTGACAACCAGTCGTCACTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGT
86667 GGCACGATAT
Statistics
Matches: 327, Mismatches: 42, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
99 2 0.01
100 75 0.23
101 3 0.01
102 5 0.02
104 3 0.01
105 1 0.00
106 236 0.72
107 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (106 bp):
GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
Found at i:87508 original size:65 final size:67
Alignment explanation
Indices: 87313--87511 Score: 244
Period size: 67 Copynumber: 3.0 Consensus size: 67
87303 AATTCATTTC
* * * * *
87313 AAGGGAAAT-GATCTCAAAGATATCTGTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTT
1 AAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
87376 TTTTT
63 GTTTT
**
87381 AAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
87446 TT
66 TT
* * *
87448 AGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
87511 T
66 T
87512 CAAGAGAGAC
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
65 39 0.34
66 12 0.10
67 48 0.41
68 15 0.13
69 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (67 bp):
AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
TT
Found at i:87634 original size:123 final size:123
Alignment explanation
Indices: 87415--87638 Score: 331
Period size: 123 Copynumber: 1.8 Consensus size: 123
87405 GTGTTTCAAG
* ** * * *
87415 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
87480 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
* * * * *
87538 AGAAACTGTCTTAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
87603 GGAAATTGTCTTAAGAGAGACAAAATTTGTTTCAAG
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
87639 GGAAACTGTC
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
123 88 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (123 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:87637 original size:36 final size:36
Alignment explanation
Indices: 87590--87868 Score: 212
Period size: 36 Copynumber: 8.1 Consensus size: 36
87580 ATATTCAAAT
* *
87590 AATTTGTTTCAAGGGAAATTGTCTTAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
87626 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * ** *
87662 AATTTATTTCAAGGGAAA-TGTTTTTA-A-TG----
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* *
87691 -TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
87727 AATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 AA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * **
87764 AATTCGTTTCAAGGGAAA-TGTTTTCAA-TG-TTC--
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* *
87796 -A--TGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * *
87829 TATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAA
1 -AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
87866 AAT
1 AAT
87869 CTTCTTTTTA
Statistics
Matches: 187, Mismatches: 36, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.01
29 29 0.16
30 8 0.04
31 3 0.02
32 1 0.01
33 1 0.01
34 2 0.01
35 7 0.04
36 72 0.39
37 60 0.32
38 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:87659 original size:101 final size:100
Alignment explanation
Indices: 87511--87862 Score: 384
Period size: 102 Copynumber: 3.5 Consensus size: 100
87501 AAAATTTGTT
* * ** * * * ***
87511 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGACGAAATTTGTTTCAAATA
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGG
** * *
87576 AAACATATTCAAATAATT-TGTTTCAAGGGAAATTGTC
66 AAATGT-TTC-AAT-ATTATGTTTCAAGAGAAACTGTC
* * *
87613 TTAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGG
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGG
* *
87677 AAATGTTTTTAATGTTTATGTTTCAAGAGAAACTGTC
66 AAATG-TTTCAAT-ATTATGTTTCAAGAGAAACTGTC
* * *
87714 TCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGG
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGG
*
87779 AAATGTTTTCAATGTTCATGTTTCAAGAGAAACTGTC
66 AAATG-TTTCAATATT-ATGTTTCAAGAGAAACTGTC
* * * *
87816 TCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
87863 TAAAATCTTC
Statistics
Matches: 218, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
100 5 0.02
101 77 0.35
102 136 0.62
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (100 bp):
TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGG
AAATGTTTCAATATTATGTTTCAAGAGAAACTGTC
Found at i:87746 original size:37 final size:37
Alignment explanation
Indices: 87695--87868 Score: 152
Period size: 37 Copynumber: 4.9 Consensus size: 37
87685 TTAATGTTTA
*
87695 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
87732 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * **
87768 CGTTTCAAGGGAAA-TGTTTTCAA-TG-TTC---A---
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
87797 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
87834 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
87869 CTTCTTTTTA
Statistics
Matches: 108, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
29 17 0.16
30 3 0.03
31 2 0.02
34 2 0.02
35 2 0.02
36 20 0.19
37 62 0.57
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:87767 original size:102 final size:102
Alignment explanation
Indices: 87594--87868 Score: 426
Period size: 102 Copynumber: 2.7 Consensus size: 102
87584 TCAAATAATT
* * * *
87594 TGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* * * *
87658 ACGAAATTTATTTCAAGGGAAATGTTTTTAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTCA
87695 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
87760 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTCA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTCA
* * *
87797 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
87862 ATAAAAT
66 ACAAAAT
87869 CTTCTTTTTA
Statistics
Matches: 160, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 31 0.19
102 129 0.81
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTCA
Found at i:89395 original size:69 final size:69
Alignment explanation
Indices: 89280--89417 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
89270 TGTCTCTCTC
*
89280 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
89345 TCAT
66 TCAT
* * *
89349 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
89414 TCAT
66 TCAT
89418 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
TCAT
Found at i:89505 original size:12 final size:13
Alignment explanation
Indices: 89490--89550 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 13
89480 TTTTCTTCAA
89490 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
89502 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
89514 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
* *
89529 TTTTCTCTCT-CT
1 TTTTCTCTTTGTT
89541 TTTTCTCTTT
1 TTTTCTCTTT
89551 TTGTTCTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.40
13 14 0.33
14 9 0.21
15 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:89531 original size:26 final size:27
Alignment explanation
Indices: 89489--89550 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
89479 TTTTTCTTCA
* *
89489 ATTTTC-CTTTG-TTTTTTCTCTTTTT
1 ATTTTCTCTTTGCTTTTTTCTCTCTCT
89514 ATTTTCTCTTTGCTTTTTTCTCTCTCT
1 ATTTTCTCTTTGCTTTTTTCTCTCTCT
89541 -TTTTCTCTTT
1 ATTTTCTCTTT
89551 TTGTTCTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 6 0.18
26 15 0.45
27 12 0.36
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (27 bp):
ATTTTCTCTTTGCTTTTTTCTCTCTCT
Found at i:91142 original size:28 final size:27
Alignment explanation
Indices: 91111--91208 Score: 102
Period size: 28 Copynumber: 3.8 Consensus size: 27
91101 AAAAAAAATA
91111 AAATAAAGTAAAAATATAATATATATAT
1 AAATAAAGT-AAAATATAATATATATAT
91139 AAATAAA-TAAAA-ATAA-A-A-ATAT
1 AAATAAAGTAAAATATAATATATATAT
*
91161 AATATTAAG-AAAATATATATATATATAT
1 AA-ATAAAGTAAAATATA-ATATATATAT
*
91189 AAA-AAAATAAAATATAATAT
1 AAATAAAGTAAAATATAATAT
91209 TAAGAAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
22 6 0.10
23 9 0.15
24 4 0.07
25 5 0.08
26 11 0.19
27 11 0.19
28 13 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AAATAAAGTAAAATATAATATATATAT
Found at i:91191 original size:42 final size:42
Alignment explanation
Indices: 91102--91228 Score: 159
Period size: 44 Copynumber: 3.0 Consensus size: 42
91092 AATAATAGAA
** * *
91102 AAAAAAATAAAATA-AAGTAAAAATATAATATATATATAAATA-
1 AAAAAAATAAAATATAA-TATTAAGA-AATATATATATATATAT
91144 AATAAAAATAAAAATATAATATTAAGAAAATATATATATATATAT
1 AA-AAAAAT-AAAATATAATATTAAG-AAATATATATATATATAT
91189 AAAAAAATAAAATATAATATTAAGAAATATATATATATAT
1 AAAAAAATAAAATATAATATTAAGAAATATATATATATAT
91229 GGTAAATGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
42 18 0.24
43 22 0.29
44 31 0.41
45 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (42 bp):
AAAAAAATAAAATATAATATTAAGAAATATATATATATATAT
Found at i:91250 original size:43 final size:42
Alignment explanation
Indices: 91131--91228 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
91121 AAAATATAAT
* * *
91131 ATATATATAAATAAATAAAAATAAAAATATAATATTAAGAAA
1 ATATATATATATATATAAAAAAAAAAATATAATATTAAGAAA
91173 ATATATATATATATATAAAAAAATAAAATATAATATTAAG-AA
1 ATATATATATATATATAAAAAAA-AAAATATAATATTAAGAAA
91215 ATATATATATATAT
1 ATATATATATATAT
91229 GGTAAATGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
42 36 0.69
43 16 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (42 bp):
ATATATATATATATATAAAAAAAAAAATATAATATTAAGAAA
Found at i:91321 original size:14 final size:14
Alignment explanation
Indices: 91265--91336 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
91255 TATACATATC
* *
91265 TATATATACATATA
1 TATATATATATAAA
*
91279 TATATATATATATA
1 TATATATATATAAA
91293 TATATAATGATATAAGA
1 TATAT-AT-ATATAA-A
91310 TATATATA-ATAAA
1 TATATATATATAAA
*
91323 AAT-TATATAATAAA
1 TATATATAT-ATAAA
91337 AATAAAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
12 4 0.08
13 3 0.06
14 27 0.54
15 3 0.06
16 7 0.14
17 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (14 bp):
TATATATATATAAA
Found at i:91330 original size:25 final size:27
Alignment explanation
Indices: 91282--91332 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
91272 ACATATATAT
*
91282 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATGATATAAG
*
91309 ATATATATA-ATA-AAAATTATATAA
1 ATATATATATATATAAAATGATATAA
91333 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
ATATATATATATATAAAATGATATAAG
Found at i:91331 original size:2 final size:2
Alignment explanation
Indices: 91255--91317 Score: 67
Period size: 2 Copynumber: 32.0 Consensus size: 2
91245 TTAATACATC
* * *
91255 TA TA CA TA TC TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
91297 TA -A TGA TA TA -A GA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA
91318 ATAAAAATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:91337 original size:14 final size:14
Alignment explanation
Indices: 91312--91339 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
91302 ATATAAGATA
91312 TATATAATAAAAAT
1 TATATAATAAAAAT
91326 TATATAATAAAAAT
1 TATATAATAAAAAT
91340 AAAAAAGGAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATATAATAAAAAT
Found at i:91342 original size:20 final size:20
Alignment explanation
Indices: 91317--91385 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
91307 AGATATATAT
*
91317 AATAAAAATTATATAATAAA
1 AATAAAAAATATATAATAAA
* *
91337 AATAAAAAAGGAATATAGTAAATA
1 AATAAAAAA--TATATAAT-AA-A
91361 AATAAAAAATATATAATTAAA
1 AATAAAAAATATATAA-TAAA
91382 AATA
1 AATA
91386 TATATATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.21
21 5 0.13
22 13 0.33
23 3 0.08
24 10 0.26
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (20 bp):
AATAAAAAATATATAATAAA
Found at i:91851 original size:23 final size:23
Alignment explanation
Indices: 91825--91877 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
91815 CCTTGCTCGA
*
91825 TTGTTGCACGTTTGTTGGTGTGG
1 TTGTTGCACGTTTGTTGGTATGG
91848 TTGTTGCACGTTTGTTGGTATGG
1 TTGTTGCACGTTTGTTGGTATGG
91871 TTGTTGC
1 TTGTTGC
91878 TTTAAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.06, C:0.09, G:0.36, T:0.49
Consensus pattern (23 bp):
TTGTTGCACGTTTGTTGGTATGG
Found at i:95571 original size:3 final size:3
Alignment explanation
Indices: 95563--95595 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
95553 TATGTTATCT
95563 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
95596 ATGGTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:97177 original size:73 final size:73
Alignment explanation
Indices: 97088--97227 Score: 262
Period size: 73 Copynumber: 1.9 Consensus size: 73
97078 GGTACAATAA
*
97088 CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAGA
1 CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
97153 AATTGTAC
66 AATTGTAC
*
97161 CGTTCATGTCTGCCATAGTGCTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
1 CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
97226 AA
66 AA
97228 AATTGTACAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (73 bp):
CGTTCATGTCTGCCATAGTACTTATTAAATAAATGGGGGCCCTATTTTATAATTGAATTGTAAGA
AATTGTAC
Found at i:98311 original size:6 final size:6
Alignment explanation
Indices: 98300--98336 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
98290 TCCAAAGCTT
98300 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA T
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA T
98337 GGACTGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:104716 original size:20 final size:20
Alignment explanation
Indices: 104649--104721 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
104639 AATATTTTTA
* *
104649 TGAATAGTAT-TATACTGTA
1 TGAATAGTATCGATACTGTG
* *
104668 TGAATAGTATCAATACTATG
1 TGAATAGTATCGATACTGTG
*
104688 TAAATAGTATCGATACTGTG
1 TGAATAGTATCGATACTGTG
* *
104708 TGAACAGTACCGAT
1 TGAATAGTATCGAT
104722 GCACAAAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 10 0.23
20 34 0.77
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TGAATAGTATCGATACTGTG
Found at i:109287 original size:2 final size:2
Alignment explanation
Indices: 109280--109307 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109270 ACAGTTGATA
109280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109308 GTTTATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121102 original size:26 final size:26
Alignment explanation
Indices: 121059--121109 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
121049 GTATTGGGAG
*
121059 AAAGCTAGAATGATTTAGGATGATTTT
1 AAAGCTAGAATGAGTTAGGAT-ATTTT
*
121086 AAAGCTA-AATGGGTTAGGATATTT
1 AAAGCTAGAATGAGTTAGGATATTT
121110 ATAGTTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 11 0.50
27 7 0.32
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (26 bp):
AAAGCTAGAATGAGTTAGGATATTTT
Done.