Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 109 of 193
Found at i:34932170 original size:7 final size:7
Alignment explanation
Indices: 34932158--34932183 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34932148 AATAAAAATG
34932158 ATTTTAA
1 ATTTTAA
34932165 ATTTTAA
1 ATTTTAA
34932172 ATTTTAA
1 ATTTTAA
34932179 ATTTT
1 ATTTT
34932184 TATCTTATAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:34932208 original size:2 final size:2
Alignment explanation
Indices: 34932201--34932229 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34932191 TAATAAGCTC
34932201 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 A
34932230 GAATCAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34935736 original size:29 final size:31
Alignment explanation
Indices: 34935702--34935765 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
34935692 GCAATTGTAT
* * *
34935702 ACATG-AACTTTAATT-TGGTGTAATTATAC
1 ACATGAAACTCTAATTGTGATGTAATCATAC
*
34935731 ACATGAAACTCTAATTGTGATTTAATCATAC
1 ACATGAAACTCTAATTGTGATGTAATCATAC
34935762 ACAT
1 ACAT
34935766 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.17
30 9 0.31
31 15 0.52
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (31 bp):
ACATGAAACTCTAATTGTGATGTAATCATAC
Found at i:34936834 original size:31 final size:31
Alignment explanation
Indices: 34936796--34936858 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
34936786 GAATAACAAA
34936796 TTATTGACTATGTTAATTTATTTTAGATAGT
1 TTATTGACTATGTTAATTTATTTTAGATAGT
34936827 TTATTGACTATGTTAATTTATTTTAGATAGT
1 TTATTGACTATGTTAATTTATTTTAGATAGT
34936858 T
1 T
34936859 GTTTATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.56
Consensus pattern (31 bp):
TTATTGACTATGTTAATTTATTTTAGATAGT
Found at i:34936848 original size:17 final size:17
Alignment explanation
Indices: 34936796--34936848 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
34936786 GAATAACAAA
34936796 TTATTGACTATGTTAAT
1 TTATTGACTATGTTAAT
* * *
34936813 TTATT--TTA-GATAGT
1 TTATTGACTATGTTAAT
34936827 TTATTGACTATGTTAAT
1 TTATTGACTATGTTAAT
34936844 TTATT
1 TTATT
34936849 TTAGATAGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 2 0.07
17 14 0.52
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (17 bp):
TTATTGACTATGTTAAT
Found at i:34937256 original size:28 final size:28
Alignment explanation
Indices: 34937212--34937265 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
34937202 ATCTCTATAT
* *
34937212 TTTTTTTTTGAAAATTT-GTCCTTTTGC
1 TTTTATTTTCAAAATTTAGTCCTTTTGC
*
34937239 TTTTATTTTCAAAGATTTATTCCTTTT
1 TTTTATTTTCAAA-ATTTAGTCCTTTT
34937266 ATTTTTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 4 0.18
29 7 0.32
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (28 bp):
TTTTATTTTCAAAATTTAGTCCTTTTGC
Found at i:34937271 original size:29 final size:27
Alignment explanation
Indices: 34937209--34937271 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
34937199 TAAATCTCTA
* *
34937209 TATTTTTTTTTTGAAAATTTGTCCTTT
1 TATTTTTATTTTCAAAATTTGTCCTTT
** *
34937236 TGCTTTTATTTTCAAAGATTTATTCCTTT
1 TATTTTTATTTTCAAA-ATTT-GTCCTTT
34937265 TATTTTT
1 TATTTTT
34937272 TCAAATTTCA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
27 12 0.44
28 4 0.15
29 11 0.41
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (27 bp):
TATTTTTATTTTCAAAATTTGTCCTTT
Found at i:34938334 original size:20 final size:19
Alignment explanation
Indices: 34938300--34938343 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
34938290 TTTCCCTCAA
34938300 CAAAAATTTAAAAAAAATT
1 CAAAAATTTAAAAAAAATT
*
34938319 CAAAATATTTATAAAAAATT
1 CAAAA-ATTTAAAAAAAATT
*
34938339 TAAAA
1 CAAAA
34938344 CTTATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
CAAAAATTTAAAAAAAATT
Found at i:34941541 original size:39 final size:39
Alignment explanation
Indices: 34941487--34941564 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
34941477 AAAAGTATGA
34941487 ATGTTTCATTCGAGTAGTCTTTCTCTGTTATCCTCAAGC
1 ATGTTTCATTCGAGTAGTCTTTCTCTGTTATCCTCAAGC
34941526 ATGTTTCATTCGAGTAGTCTTTCTCTGTTATCCTCAAGC
1 ATGTTTCATTCGAGTAGTCTTTCTCTGTTATCCTCAAGC
34941565 TCACGTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (39 bp):
ATGTTTCATTCGAGTAGTCTTTCTCTGTTATCCTCAAGC
Found at i:34942019 original size:6 final size:6
Alignment explanation
Indices: 34942008--34942033 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34941998 GGGGCAGGGC
34942008 GGGTGA GGGTGA GGGTGA GGGTGA GG
1 GGGTGA GGGTGA GGGTGA GGGTGA GG
34942034 TGGGTACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (6 bp):
GGGTGA
Found at i:34944747 original size:33 final size:33
Alignment explanation
Indices: 34944705--34944802 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
34944695 CGAGTCTCAA
34944705 CATCATAAACCAACCTAAACATAACACCATCAC
1 CATCATAAACCAACCTAAACATAACACCATCAC
34944738 CATCATAAACCAACCTAAACATAACACCATCAC
1 CATCATAAACCAACCTAAACATAACACCATCAC
*
34944771 CA-CTATAAACCAACCTAAACATAACCCCATCA
1 CATC-ATAAACCAACCTAAACATAACACCATCA
34944803 ACACCGCAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 1 0.02
33 62 0.98
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (33 bp):
CATCATAAACCAACCTAAACATAACACCATCAC
Found at i:34945298 original size:22 final size:20
Alignment explanation
Indices: 34945258--34945316 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 20
34945248 GAAAACCCAA
34945258 AAATTTAAAAAAAAACCTAG
1 AAATTTAAAAAAAAACCTAG
*
34945278 AAATTAAAAAACAGAAACCTAG
1 AAATTTAAAAA-A-AAACCTAG
*
34945300 AAATTTAAAAATAAACC
1 AAATTTAAAAAAAAACC
34945317 CCGCTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.44
21 1 0.03
22 18 0.53
ACGTcount: A:0.64, C:0.12, G:0.05, T:0.19
Consensus pattern (20 bp):
AAATTTAAAAAAAAACCTAG
Found at i:34945537 original size:27 final size:28
Alignment explanation
Indices: 34945491--34945543 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
34945481 GATGATGATA
34945491 ATTTTATAAAAATAAAAAAATAATTTTC
1 ATTTTATAAAAATAAAAAAATAATTTTC
34945519 ATTTTATAAAAAT-AAAAAATAATTT
1 ATTTTATAAAAATAAAAAAATAATTT
34945544 GAATAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTTTATAAAAATAAAAAAATAATTTTC
Found at i:34948429 original size:19 final size:20
Alignment explanation
Indices: 34948397--34948434 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
34948387 ACCTCACTTC
34948397 TCAATAATCCCTTC-ATTCA
1 TCAATAATCCCTTCTATTCA
* *
34948416 TCAATCATCTCTTCTATTC
1 TCAATAATCCCTTCTATTC
34948435 TCTCATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (20 bp):
TCAATAATCCCTTCTATTCA
Found at i:34949287 original size:17 final size:17
Alignment explanation
Indices: 34949245--34949288 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
34949235 ATGCATTTTA
* *
34949245 TTTAGTTGTCATTGCAT
1 TTTATTTGTCAATGCAT
*
34949262 TTCTATTTGTCAATGGAT
1 TT-TATTTGTCAATGCAT
34949280 TTTATTTGT
1 TTTATTTGT
34949289 TAGTTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCAATGCAT
Found at i:34960388 original size:20 final size:20
Alignment explanation
Indices: 34960365--34960405 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
34960355 CCCCAACCCC
34960365 TTCTATTATTTGTCCAAGTG
1 TTCTATTATTTGTCCAAGTG
34960385 TTCTATTATTTGTCCAAGTG
1 TTCTATTATTTGTCCAAGTG
34960405 T
1 T
34960406 ACCACCCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (20 bp):
TTCTATTATTTGTCCAAGTG
Found at i:34962935 original size:12 final size:12
Alignment explanation
Indices: 34962918--34962942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34962908 TGTTATCATG
34962918 ATGAATGCTATT
1 ATGAATGCTATT
34962930 ATGAATGCTATT
1 ATGAATGCTATT
34962942 A
1 A
34962943 ATTCTTTAAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:34978316 original size:29 final size:30
Alignment explanation
Indices: 34978283--34978344 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
34978273 ATATATTTTG
34978283 AAATTTAGTT-TCTATATTTT-TATTTCTAA
1 AAATTTAGTTATCTATATTTTATATTTC-AA
34978312 AAATTTAGTTCATCTATATTTTATATTTCAA
1 AAATTTAGTT-ATCTATATTTTATATTTCAA
34978343 AA
1 AA
34978345 TTCAAGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 10 0.33
31 14 0.47
32 6 0.20
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.53
Consensus pattern (30 bp):
AAATTTAGTTATCTATATTTTATATTTCAA
Found at i:34987889 original size:56 final size:57
Alignment explanation
Indices: 34987823--34987956 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 57
34987813 AACGTAATAG
34987823 TAAATTTTAAAAATATATAAAATAAAAAAAATGATTGTTGA-AAAAAAT-ATAATATA
1 TAAATTTTAAAAATATATAAAA-AAAAAAAATGATTGTTGACAAAAAATAATAATATA
* *
34987879 TAAAATTTAAAAATATATAAAAATAAAAAATGATTGTTGACAAAAAATAATAATATA
1 TAAATTTTAAAAATATATAAAAAAAAAAAATGATTGTTGACAAAAAATAATAATATA
34987936 TAAATTTTAAAAATATATAAA
1 TAAATTTTAAAAATATATAAA
34987957 TTACATAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
55 17 0.23
56 28 0.38
57 28 0.38
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (57 bp):
TAAATTTTAAAAATATATAAAAAAAAAAAATGATTGTTGACAAAAAATAATAATATA
Found at i:34987907 original size:17 final size:17
Alignment explanation
Indices: 34987873--34987909 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34987863 AAAAAAATAT
* *
34987873 AATATATAAAATTTAAA
1 AATATATAAAAATAAAA
34987890 AATATATAAAAATAAAA
1 AATATATAAAAATAAAA
34987907 AAT
1 AAT
34987910 GATTGTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATATAAAAATAAAA
Found at i:34987924 original size:57 final size:56
Alignment explanation
Indices: 34987823--34987956 Score: 209
Period size: 57 Copynumber: 2.4 Consensus size: 56
34987813 AACGTAATAG
34987823 TAAATTTTAAAAATATATAAAATAAAAAAAATGATTGTTGAAAAAA-ATATAATATA
1 TAAATTTTAAAAATATATAAAATAAAAAAAATGATTGTTGAAAAAATA-ATAATATA
* *
34987879 TAAAATTTAAAAATATATAAAA-ATAAAAAATGATTGTTGACAAAAAATAATAATATA
1 TAAATTTTAAAAATATATAAAATAAAAAAAATGATTGTTG--AAAAAATAATAATATA
34987936 TAAATTTTAAAAATATATAAA
1 TAAATTTTAAAAATATATAAA
34987957 TTACATAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
55 16 0.22
56 21 0.29
57 34 0.47
58 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (56 bp):
TAAATTTTAAAAATATATAAAATAAAAAAAATGATTGTTGAAAAAATAATAATATA
Found at i:34987966 original size:17 final size:17
Alignment explanation
Indices: 34987930--34987968 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
34987920 AAAAAATAAT
**
34987930 AATATATAAATTTTAAA
1 AATATATAAATTACAAA
*
34987947 AATATATAAATTACATA
1 AATATATAAATTACAAA
34987964 AATAT
1 AATAT
34987969 TTTTAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATATAAATTACAAA
Found at i:34994126 original size:62 final size:62
Alignment explanation
Indices: 34993922--34994242 Score: 497
Period size: 62 Copynumber: 5.2 Consensus size: 62
34993912 GTAAATGCAA
* * * *
34993922 AAAGGTCTGATGACTTTGTGTCATTGTGAGTATTAAATGAGAAATGATTCCTATTACGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
* *
34993984 AAAGGTTCGATGAC-TTGTGTCATCATGAGTATTAAATGAGAAATGAATCC---TATGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
* * *
34994042 AAAGGTCTGATGACTTTGTGTTATCGTGAGTATTAAATGAGAAATGAATCCTATTGTGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
*
34994104 AAAGGTCCGATGACTTTGTGTTATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
*
34994166 AAAGGTCCGATGACTTTGTGTCATCATGAGTATTAAATGAGAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
* *
34994228 TAAGGTCCAATGACT
1 AAAGGTCCGATGACT
34994243 CTATATCATC
Statistics
Matches: 238, Mismatches: 17, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
58 19 0.08
59 34 0.14
61 33 0.14
62 152 0.64
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.35
Consensus pattern (62 bp):
AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAGAAATGAATCCTATTATGGATT
Found at i:34997807 original size:14 final size:13
Alignment explanation
Indices: 34997788--34997818 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
34997778 AAAATCAACA
34997788 AATAATAATACAAT
1 AATAATAATA-AAT
34997802 AATAATAATAAAT
1 AATAATAATAAAT
34997815 AATA
1 AATA
34997819 GCAATGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:35005620 original size:4 final size:4
Alignment explanation
Indices: 35005599--35005651 Score: 60
Period size: 4 Copynumber: 14.0 Consensus size: 4
35005589 AGTTTCTTGG
35005599 ATAA ATAA GA-AA AT-A ATAA ATAA ATAA ATAA ATAA AT-A A-AA ATAA
1 ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
35005644 AAAA ATAA
1 ATAA ATAA
35005652 TTGGGTTGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
3 8 0.19
4 33 0.79
5 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:35011266 original size:50 final size:50
Alignment explanation
Indices: 35011203--35011423 Score: 164
Period size: 50 Copynumber: 4.4 Consensus size: 50
35011193 TGTATTATCA
* * *
35011203 GGGATATATGATTTGATGTTGTAGCTTCACCTTG-CTCCACTGCATCTTCAG
1 GGGA-ATAAGATTTGATGTTGTAGCTTCACCTTGAC-CCACTGCAACTTTAG
* *
35011254 GGGAATAAGATTTGCTTTTGTAGCTTCAATCC--GACCCACTGCAACTTTAG
1 GGGAATAAGATTTGATGTTGTAGCTTC-A-CCTTGACCCACTGCAACTTTAG
* * * * * * * *
35011304 GAGTATAGGATTTTATGTTGTAGCTTTATCTTG-CTCCATTGCATCTTTA-
1 GGGAATAAGATTTGATGTTGTAGCTTCACCTTGAC-CCACTGCAACTTTAG
* * ** *
35011353 GGGAGATAAGATTTGTTTTTTGTAGCTTCAATTTGACCCACTGTAACTTTAG
1 GGGA-ATAAGATTTG-ATGTTGTAGCTTCACCTTGACCCACTGCAACTTTAG
* *
35011405 GGGTATAGGATTTGATGTT
1 GGGAATAAGATTTGATGTT
35011424 ATATTAATCT
Statistics
Matches: 129, Mismatches: 31, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
48 1 0.01
49 4 0.03
50 78 0.60
51 40 0.31
52 6 0.05
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (50 bp):
GGGAATAAGATTTGATGTTGTAGCTTCACCTTGACCCACTGCAACTTTAG
Found at i:35011362 original size:100 final size:101
Alignment explanation
Indices: 35011207--35011423 Score: 312
Period size: 100 Copynumber: 2.2 Consensus size: 101
35011197 TTATCAGGGA
*
35011207 TATATGATTTGATGTTGTAGCTTCACCTTGCTCCACTGCATCTTCAGGGGAATAAGATTTG-CTT
1 TATAGGATTTGATGTTGTAGCTTCACCTTGCTCCACTGCATCTTCAGGGGAATAAGATTTGTCTT
35011271 TTGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
66 TTGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
* * * * * *
35011307 TATAGGATTTTATGTTGTAGCTTTATCTTGCTCCATTGCATCTTTA-GGGAGATAAGATTTGTTT
1 TATAGGATTTGATGTTGTAGCTTCACCTTGCTCCACTGCATCTTCAGGGGA-ATAAGATTTGTCT
** * *
35011371 TTTGTAGCTTCAATTTGACCCACTGTAACTTTAGGGG
65 TTTGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
35011408 TATAGGATTTGATGTT
1 TATAGGATTTGATGTT
35011424 ATATTAATCT
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
99 4 0.04
100 50 0.49
101 49 0.48
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (101 bp):
TATAGGATTTGATGTTGTAGCTTCACCTTGCTCCACTGCATCTTCAGGGGAATAAGATTTGTCTT
TTGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
Found at i:35011444 original size:101 final size:99
Alignment explanation
Indices: 35011207--35011433 Score: 260
Period size: 101 Copynumber: 2.3 Consensus size: 99
35011197 TTATCAGGGA
* * * * * *
35011207 TATATGATTTGATGTTGTAGCTTCACCTTGCTCCACTGCATCTTCAGGGGAATAAGATTTGCTTT
1 TATAGGATTTGATGTTATA-CTTAATCTTGCGCCATTGCATCTTCAGGGGAATAAGATTTGCTTT
35011272 TGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
65 TGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
* * * * * *
35011307 TATAGGATTTTATGTTGTAGCTTTATCTTGCTCCATTGCATCTTTA-GGGAGATAAGATTTGTTT
1 TATAGGATTTGATGTTATA-CTTAATCTTGCGCCATTGCATCTTCAGGGGA-ATAAGATTTG-CT
** * *
35011371 TTTGTAGCTTCAATTTGACCCACTGTAACTTTAGGGG
63 TTTGTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
35011408 TATAGGATTTGATGTTATA-TTAATCT
1 TATAGGATTTGATGTTATACTTAATCT
35011434 CTATCGCCAT
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
99 10 0.09
100 50 0.45
101 51 0.46
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (99 bp):
TATAGGATTTGATGTTATACTTAATCTTGCGCCATTGCATCTTCAGGGGAATAAGATTTGCTTTT
GTAGCTTCAATCCGACCCACTGCAACTTTAGGAG
Found at i:35028586 original size:192 final size:194
Alignment explanation
Indices: 35028256--35028641 Score: 717
Period size: 192 Copynumber: 2.0 Consensus size: 194
35028246 GGGAAAATAA
35028256 GAGAGTCAAGCCGTAAGTCGATTATTTTTTTATCTTTCTTGTTGAAAATTTCAAATTCAATTTAA
1 GAGAGTCAAGCCGTAAGTCGATTATTTTTTTATCTTTCTTGTTGAAAATTTCAAATTCAATTTAA
35028321 TTTAATTTGTGATCCTTTGCATTCATTTTTTGTGATTTATATGTTTGTTGTGATTATAACATGTT
66 TTTAATTTGTGATCCTTTGCATTCATTTTTTGTGATTTATATGTTTGTTGTGATTATAACATGTT
*
35028386 TTATATTGTATGTTTTATATTTTTGCATACATGCATTTGTTACTACAACGCTTAAGTGGAAGCG
131 TGATATTGTATGTTTTATATTTTTGCATACATGCATTTGTTACTACAACGCTTAAGTGGAAGCG
35028450 GAGAGTCAAGCCGTAAGTCGATTA-TTTTTTATCTTTC-TGTTGAAAATTTC-AATTCAATTTAA
1 GAGAGTCAAGCCGTAAGTCGATTATTTTTTTATCTTTCTTGTTGAAAATTTCAAATTCAATTTAA
35028512 TTTAATTTGTGATCCTTTGCATTTCATTTTTTGTGATTTATATGTTTTGTTGTGATTATAACATG
66 TTTAATTTGTGATCCTTTGCA-TTCATTTTTTGTGATTTATATG-TTTGTTGTGATTATAACATG
35028577 -TTGATATTGTATGTTTTATATTTTTGCATACATGCATTTGTTACTACAACGCTTAAGTGGAAGC
129 TTTGATATTGTATGTTTTATATTTTTGCATACATGCATTTGTTACTACAACGCTTAAGTGGAAGC
35028641 G
194 G
35028642 AGAAGCTACT
Statistics
Matches: 189, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
191 33 0.17
192 99 0.52
193 33 0.17
194 24 0.13
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.48
Consensus pattern (194 bp):
GAGAGTCAAGCCGTAAGTCGATTATTTTTTTATCTTTCTTGTTGAAAATTTCAAATTCAATTTAA
TTTAATTTGTGATCCTTTGCATTCATTTTTTGTGATTTATATGTTTGTTGTGATTATAACATGTT
TGATATTGTATGTTTTATATTTTTGCATACATGCATTTGTTACTACAACGCTTAAGTGGAAGCG
Found at i:35039847 original size:80 final size:80
Alignment explanation
Indices: 35039536--35040533 Score: 1764
Period size: 80 Copynumber: 12.5 Consensus size: 80
35039526 AGTTACAACC
* *
35039536 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCAAT-CGA-CTTTTACCCCGATCGTG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACC-ATCCGATCTTTTACCCCGATCATG
35039599 GGGCAGATTGAAGAAA
65 GGGCAGATTGAAGAAA
*
35039615 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCAAT-CGA-CTTTTACCCCGATCATG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACC-ATCCGATCTTTTACCCCGATCATG
*
35039678 GGGCAGATTGAAAAAA
65 GGGCAGATTGAAGAAA
35039694 TCCAATCTTTTACCCTAACCAGAGGGCAAGA-TGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35039758 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
35039773 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35039838 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
35039853 TCCAATCTTTTA-CCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35039917 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
35039932 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35039997 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
35040012 TCCAATCTTTTACCCTAGCCAGAGGGCAAGATTGAAGACCATCCGATCTTTTCCCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35040077 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
*
35040092 TCCAATCTTTTACCCTAACCAAAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35040157 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
35040172 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35040237 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
*
35040252 TCCAATCTTTTACCCTAACCACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCA
1 TCCAATCTTTTACCCT-A--ACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCA
35040317 TGGGGCAGATTGAAGAAA
63 TGGGGCAGATTGAAGAAA
*
35040335 TCCAATCTTTTACCCTAACCAGA-GGCAAGATTGAAGATCATCC-ATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
35040398 GGCAGATTGAAGAGA
66 GGCAGATTGAAGAAA
*
35040413 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
35040478 GGCAGATTGAA-AAA
66 GGCAGATTGAAGAAA
* *
35040492 TCAAATCTTTTACCCTAACCAGA-GCCAAGATTGAAGACCATC
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATC
35040534 AATCTTCCCG
Statistics
Matches: 894, Mismatches: 16, Indels: 19
0.96 0.02 0.02
Matches are distributed among these distances:
77 2 0.00
78 86 0.10
79 312 0.35
80 414 0.46
81 1 0.00
82 1 0.00
83 78 0.09
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:35040667 original size:39 final size:38
Alignment explanation
Indices: 35040567--35040673 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
35040557 CCGATGATGG
35040567 GGCAGATTGAAA-AATCTAATCTTTTACCCTAACCAAA
1 GGCAGATTGAAACAATCTAATCTTTTACCCTAACCAAA
* * *
35040604 GGCAGATTGAAGACCATC-AGATCTTTTA-CCTCGACCATGA
1 GGCAGATTGAA-ACAATCTA-ATCTTTTACCCT-AACCA-AA
*
35040644 GGCAAATTGAAACAATCTAATCTTTTACCC
1 GGCAGATTGAAACAATCTAATCTTTTACCC
35040674 CTAAAGTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
37 11 0.19
38 5 0.09
39 28 0.48
40 14 0.24
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (38 bp):
GGCAGATTGAAACAATCTAATCTTTTACCCTAACCAAA
Found at i:35044757 original size:15 final size:15
Alignment explanation
Indices: 35044698--35044746 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
35044688 CATTTATTAT
35044698 CTTTTCAGATATAAC
1 CTTTTCAGATATAAC
*
35044713 CTTTTCA-A-ATATC
1 CTTTTCAGATATAAC
35044726 C-TTTCAGATATAAC
1 CTTTTCAGATATAAC
35044740 CTTTTCA
1 CTTTTCA
35044747 ATGATATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 5 0.17
13 6 0.21
14 6 0.21
15 12 0.41
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (15 bp):
CTTTTCAGATATAAC
Found at i:35044780 original size:56 final size:55
Alignment explanation
Indices: 35044703--35044942 Score: 234
Period size: 56 Copynumber: 4.3 Consensus size: 55
35044693 ATTATCTTTT
* * * *
35044703 CAGATATAACCTTTTCA--AATATCCTTTCAGATATAACCTTTTCAATGATATCCTTC
1 CAGATAT-TCCTTTTCATTAATATCCTTGC-GATAT-ACCTTTTCAATAATATCCTTA
* * * * * *
35044759 CGGATATCCCTTTTCA-TAATATTCTTACGAATATAACCTTTTCATTAATATCTTTA
1 CAGATATTCCTTTTCATTAATATCCTTGCG-ATAT-ACCTTTTCAATAATATCCTTA
* * *
35044815 CAAATATTCCTTTTCATTGATATCCTTGCGATATCCCTTTTCAATAATATCCTTA
1 CAGATATTCCTTTTCATTAATATCCTTGCGATATACCTTTTCAATAATATCCTTA
* * * * *
35044870 CGGATATTCCTTTTCATTGATATCCTTGCGGAGATCCCTTTTCAATGATATCCTTA
1 CAGATATTCCTTTTCATTAATATCCTTGC-GATATACCTTTTCAATAATATCCTTA
35044926 CAGATATATCCTTTTCA
1 CAGATAT-TCCTTTTCA
35044943 CATAATTTAG
Statistics
Matches: 157, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
55 54 0.34
56 84 0.54
57 19 0.12
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (55 bp):
CAGATATTCCTTTTCATTAATATCCTTGCGATATACCTTTTCAATAATATCCTTA
Found at i:35044794 original size:83 final size:82
Alignment explanation
Indices: 35044706--35044942 Score: 255
Period size: 83 Copynumber: 2.8 Consensus size: 82
35044696 ATCTTTTCAG
*
35044706 ATATAACCTTTTCA-AATATCCTTTCAGATATAACCTTTTCAATGATATCCTTCCGGATATCCCT
1 ATATAACCTTTTCATAATATCCTTTCAGATAT-ACCTTTTCAATGATATCCTTAC-GATATCCCT
*
35044770 TTTCATAATATTCTTACGA
64 TTTCATAATATCCTTACGA
* * * *
35044789 ATATAACCTTTTCATTAATAT-CTTTACAAATATTCCTTTTCATTGATATCCTTGCGATATCCCT
1 ATATAACCTTTTCA-TAATATCCTTT-CAGATATACCTTTTCAATGATATCCTTACGATATCCCT
*
35044853 TTTCAATAATATCCTTACGG
64 TTTC-ATAATATCCTTACGA
* * * * * * *
35044873 ATAT-TCCTTTTCATTGATATCCTTGCGGAGATCCCTTTTCAATGATATCCTTACAGATATATCC
1 ATATAACCTTTTCA-TAATATCCTTTCAGATATACCTTTTCAATGATATCCTTAC-GATAT-CCC
35044937 TTTTCA
63 TTTTCA
35044943 CATAATTTAG
Statistics
Matches: 131, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
83 64 0.49
84 49 0.37
85 18 0.14
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (82 bp):
ATATAACCTTTTCATAATATCCTTTCAGATATACCTTTTCAATGATATCCTTACGATATCCCTTT
TCATAATATCCTTACGA
Found at i:35044798 original size:28 final size:27
Alignment explanation
Indices: 35044706--35044942 Score: 158
Period size: 28 Copynumber: 8.5 Consensus size: 27
35044696 ATCTTTTCAG
*
35044706 ATATAACCTTTTCA-AATATCCTTTC-A
1 ATAT-ACCTTTTCATAATATCCTTACGA
* * *
35044732 GATATAACCTTTTCAATGATATCCTTCCGG
1 -ATAT-ACCTTTTC-ATAATATCCTTACGA
* *
35044762 ATATCCCTTTTCATAATATTCTTACGA
1 ATATACCTTTTCATAATATCCTTACGA
* *
35044789 ATATAACCTTTTCATTAATATCTTTACAA
1 ATAT-ACCTTTTCA-TAATATCCTTACGA
* * *
35044818 ATATTCCTTTTCATTGATATCCTTGCG-
1 ATATACCTTTTCA-TAATATCCTTACGA
* *
35044845 ATATCCCTTTTCAATAATATCCTTACGG
1 ATATACCTTTTC-ATAATATCCTTACGA
* * * *
35044873 ATATTCCTTTTCATTGATATCCTTGCGG
1 ATATACCTTTTCA-TAATATCCTTACGA
* * *
35044901 AGATCCCTTTTCAATGATATCCTTAC-A
1 ATATACCTTTTC-ATAATATCCTTACGA
35044928 GATATATCCTTTTCA
1 -ATATA-CCTTTTCA
35044943 CATAATTTAG
Statistics
Matches: 170, Mismatches: 29, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
27 51 0.30
28 83 0.49
29 36 0.21
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (27 bp):
ATATACCTTTTCATAATATCCTTACGA
Found at i:35044910 original size:111 final size:114
Alignment explanation
Indices: 35044721--35044942 Score: 272
Period size: 111 Copynumber: 2.0 Consensus size: 114
35044711 ACCTTTTCAA
* * * *
35044721 ATATCCTTTCAGATATAACCTTTTCAATGATATCCTTCCGGATATCCCTTTTCATAATATTCTTA
1 ATATCCTTGCAGATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTTCATAATATCCTTA
* * *
35044786 CGAATATAACCTTTTCATTAATATCTTTACAAATAT-TCCTTTTCATTG
66 CGAAGATAACCTTTTCAATAATATCCTTACAAATATATCCTTTTCATTG
* * *
35044834 ATATCCTTGC-GATAT-CCCTTTTCAATAATATCCTTACGGATATTCCTTTTCATTGATATCCTT
1 ATATCCTTGCAGATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTTCA-TAATATCCTT
* * * * *
35044897 GCGGAGAT-CCCTTTTCAATGATATCCTTACAGATATATCCTTTTCA
65 ACGAAGATAACCTTTTCAATAATATCCTTACAAATATATCCTTTTCA
35044943 CATAATTTAG
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
111 56 0.61
112 27 0.29
113 9 0.10
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.43
Consensus pattern (114 bp):
ATATCCTTGCAGATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTTCATAATATCCTTA
CGAAGATAACCTTTTCAATAATATCCTTACAAATATATCCTTTTCATTG
Found at i:35046408 original size:17 final size:17
Alignment explanation
Indices: 35046394--35046450 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
35046384 TATTTTAAGA
35046394 TTAAATTTGTTTTAAAT
1 TTAAATTTGTTTTAAAT
** * *
35046411 TTAAATTTAATTTGAGT
1 TTAAATTTGTTTTAAAT
*
35046428 TTAAATTTATTTTCAAAT
1 TTAAATTTGTTTT-AAAT
35046446 TTAAA
1 TTAAA
35046451 AGAATAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (17 bp):
TTAAATTTGTTTTAAAT
Found at i:35048290 original size:30 final size:30
Alignment explanation
Indices: 35048254--35048474 Score: 165
Period size: 30 Copynumber: 7.4 Consensus size: 30
35048244 TGCTTTGGAG
* *
35048254 GACCCTAAA-TTTTCCAAAAATTATA-TTTT
1 GACCCTAAACTTCTCC-AAAATTACATTTTT
35048283 GACCCCTAAACTTCTCCAAAATTACATTTTT
1 GA-CCCTAAACTTCTCCAAAATTACATTTTT
**
35048314 GACCCTAAAAACTT-TTAAAAATTACATTTTT
1 GACCCT--AAACTTCTCCAAAATTACATTTTT
*
35048345 -ACCCTCAAAC-T-TCCAAAAATACATTTTT
1 GACCCT-AAACTTCTCCAAAATTACATTTTT
* *
35048373 GACCCTAAAACTT-TCAAAAATTCCATTTTT
1 GACCCT-AAACTTCTCCAAAATTACATTTTT
* * * *
35048403 AACCCCAAAACTTCT-AAAAATTTCATTTTT
1 GA-CCCTAAACTTCTCCAAAATTACATTTTT
* *
35048433 -ACCCTTAAACTTCT-AAAAATTCCATTTTT
1 GACCC-TAAACTTCTCCAAAATTACATTTTT
*
35048462 GACCTCGAAACTT
1 GACC-CTAAACTT
35048475 TTAAATTACC
Statistics
Matches: 162, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.11
29 38 0.23
30 69 0.43
31 31 0.19
32 6 0.04
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
GACCCTAAACTTCTCCAAAATTACATTTTT
Found at i:35048364 original size:29 final size:30
Alignment explanation
Indices: 35048265--35048474 Score: 200
Period size: 29 Copynumber: 7.1 Consensus size: 30
35048255 ACCCTAAATT
*
35048265 TTCCAAAAATTATA-TTTTGACCC-CTAAAC
1 TTCCAAAAATTACATTTTTGACCCTC-AAAC
* *
35048294 TTCTCCAAAATTACATTTTTGACCCTAAAAAC
1 TTC-CAAAAATTACATTTTTGACCCT-CAAAC
**
35048326 TTTTAAAAATTACATTTTT-ACCCTCAAAC
1 TTCCAAAAATTACATTTTTGACCCTCAAAC
*
35048355 TTCCAAAAA-TACATTTTTGACCCTAAAAC
1 TTCCAAAAATTACATTTTTGACCCTCAAAC
* * *
35048384 TTTCAAAAATTCCATTTTTAACCC-CAAAAC
1 TTCCAAAAATTACATTTTTGACCCTC-AAAC
* * *
35048414 TTCTAAAAATTTCATTTTT-ACCCTTAAAC
1 TTCCAAAAATTACATTTTTGACCCTCAAAC
* *
35048443 TTCTAAAAATTCCATTTTTGA-CCTCGAAAC
1 TTCCAAAAATTACATTTTTGACCCTC-AAAC
35048473 TT
1 TT
35048475 TTAAATTACC
Statistics
Matches: 151, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
28 9 0.06
29 60 0.40
30 53 0.35
31 23 0.15
32 6 0.04
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
TTCCAAAAATTACATTTTTGACCCTCAAAC
Found at i:35048473 original size:59 final size:58
Alignment explanation
Indices: 35048279--35048479 Score: 228
Period size: 59 Copynumber: 3.4 Consensus size: 58
35048269 AAAAATTATA
* *
35048279 TTTTGACCCCTAAACTTCTCCAAAATTACATTTTTGACCCTAAAAACTTTTAAAAATTACAT
1 TTTTGACCCC-AAACTTCT-AAAAATTACATTTTTGACCCT-AAAAC-TTTAAAAATTCCAT
*
35048341 TTTT-ACCCTCAAACTTCCAAAAA-TACATTTTTGACCCTAAAACTTTCAAAAATTCCAT
1 TTTTGACCC-CAAACTTCTAAAAATTACATTTTTGACCCTAAAACTTT-AAAAATTCCAT
* * *
35048399 TTTTAACCCCAAAACTTCTAAAAATTTCATTTTT-ACCCTTAAACTTCTAAAAATTCCAT
1 TTTTGACCCC-AAACTTCTAAAAATTACATTTTTGACCCTAAAACTT-TAAAAATTCCAT
* *
35048458 TTTTGACCTCGAAACTTTTAAA
1 TTTTGACC-CCAAACTTCTAAA
35048480 TTACCATTTT
Statistics
Matches: 123, Mismatches: 9, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
57 3 0.02
58 20 0.16
59 70 0.57
60 14 0.11
61 11 0.09
62 5 0.04
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (58 bp):
TTTTGACCCCAAACTTCTAAAAATTACATTTTTGACCCTAAAACTTTAAAAATTCCAT
Found at i:35048625 original size:28 final size:28
Alignment explanation
Indices: 35048592--35048653 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
35048582 CCAAATTTTC
* * *
35048592 CCAAAATTACCATTTTGCCCTCGAATGT
1 CCAAAATTACCATTTTACCCCCGAATAT
*
35048620 CCAAAATTACCATTTTACCCCCGAGTAT
1 CCAAAATTACCATTTTACCCCCGAATAT
35048648 CCAAAA
1 CCAAAA
35048654 AATCTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAATAT
Found at i:35061073 original size:16 final size:14
Alignment explanation
Indices: 35061047--35061088 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 14
35061037 TATTAATTAA
35061047 ATTTTTT-AATAAT
1 ATTTTTTAAATAAT
35061060 ATTTTAATTAAATAAT
1 ATTTT--TTAAATAAT
35061076 ATTTTTTAAATAA
1 ATTTTTTAAATAA
35061089 ATCGAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 2 0.08
16 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAATAAT
Found at i:35065064 original size:29 final size:29
Alignment explanation
Indices: 35065031--35065102 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
35065021 ATAAAAGGAG
* *
35065031 GATATTGAATAAATCTATGGGGCAATATA
1 GATATGGAATAAATCTATGGGGAAATATA
*
35065060 GATATGGAATAAATCTATTGGGAAATATA
1 GATATGGAATAAATCTATGGGGAAATATA
35065089 GATATGGAATAAAT
1 GATATGGAATAAAT
35065103 GGCTAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (29 bp):
GATATGGAATAAATCTATGGGGAAATATA
Found at i:35068409 original size:12 final size:12
Alignment explanation
Indices: 35068392--35068416 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35068382 CAGAGGCTAT
35068392 TAACAATATTTA
1 TAACAATATTTA
35068404 TAACAATATTTA
1 TAACAATATTTA
35068416 T
1 T
35068417 GTTATAAAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:35077558 original size:18 final size:18
Alignment explanation
Indices: 35077535--35077591 Score: 51
Period size: 24 Copynumber: 2.8 Consensus size: 18
35077525 CATATTATTA
35077535 AGGTTCGCATAACAACAT
1 AGGTTCGCATAACAACAT
*
35077553 AGGTTCACATACATCATACAACAT
1 AGGTT--C--GCAT-A-ACAACAT
35077577 AGGTTCGCATAACAA
1 AGGTTCGCATAACAA
35077592 AACATCACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
18 9 0.29
19 1 0.03
20 4 0.13
22 4 0.13
23 1 0.03
24 12 0.39
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (18 bp):
AGGTTCGCATAACAACAT
Found at i:35084662 original size:25 final size:24
Alignment explanation
Indices: 35084625--35084679 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
35084615 AGGATGTATC
**
35084625 CGAAAAGAATATCCAATGAAAAGGT
1 CGAAAAGAATAT-CAACAAAAAGGT
**
35084650 CGAAAAGGGTATCAACAAAAAGGT
1 CGAAAAGAATATCAACAAAAAGGT
35084674 CGAAAA
1 CGAAAA
35084680 AAGATAGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.53, C:0.13, G:0.22, T:0.13
Consensus pattern (24 bp):
CGAAAAGAATATCAACAAAAAGGT
Found at i:35084690 original size:25 final size:24
Alignment explanation
Indices: 35084643--35084690 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
35084633 ATATCCAATG
* * *
35084643 AAAAGGTCGAAAAGGGTATCAACA
1 AAAAGGTCGAAAAAGATAGCAACA
35084667 AAAAGGTCGAAAAAAGATAGCAAC
1 AAAAGGTCG-AAAAAGATAGCAAC
35084691 GAAAGTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.10
Consensus pattern (24 bp):
AAAAGGTCGAAAAAGATAGCAACA
Found at i:35090518 original size:2 final size:2
Alignment explanation
Indices: 35090511--35090552 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
35090501 CACTGGACTC
35090511 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
35090553 TGGGCTTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35092201 original size:2 final size:2
Alignment explanation
Indices: 35092163--35092191 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35092153 TTATTATTAA
35092163 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 A
35092192 GTTTTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35094193 original size:26 final size:26
Alignment explanation
Indices: 35094157--35094206 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
35094147 GAAACAACTG
*
35094157 AATTAATGCGTTTAATTGTTAATCTA
1 AATTAACGCGTTTAATTGTTAATCTA
35094183 AATTAACGCGTTTAATTGTTAATC
1 AATTAACGCGTTTAATTGTTAATC
35094207 GGATTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (26 bp):
AATTAACGCGTTTAATTGTTAATCTA
Found at i:35117355 original size:22 final size:22
Alignment explanation
Indices: 35117317--35117363 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
35117307 AAAATATTAA
35117317 AAATAAGTGAGATTAATTAAAGCT
1 AAATAAGT-AGATTAATT-AAGCT
35117341 AAATAAGT-GATTAATTAAGCT
1 AAATAAGTAGATTAATTAAGCT
35117362 AA
1 AA
35117364 TTATGAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
24 8 0.35
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
AAATAAGTAGATTAATTAAGCT
Found at i:35130762 original size:15 final size:15
Alignment explanation
Indices: 35130742--35130787 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
35130732 AAATTCAAAT
*
35130742 ATATATATTTTAGAA
1 ATATATAATTTAGAA
35130757 ATATATAATTTAGAA
1 ATATATAATTTAGAA
* *
35130772 AAATAAAATTTAGAA
1 ATATATAATTTAGAA
35130787 A
1 A
35130788 AAAAACACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
ATATATAATTTAGAA
Found at i:35130851 original size:19 final size:19
Alignment explanation
Indices: 35130829--35130868 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35130819 AAGTACTAAT
*
35130829 ATTATTAAAAACTA-TAAAA
1 ATTA-TAAAAAATATTAAAA
35130848 ATTATAAAAAATATTAAAA
1 ATTATAAAAAATATTAAAA
35130867 AT
1 AT
35130869 ATTTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTATAAAAAATATTAAAA
Found at i:35130961 original size:19 final size:19
Alignment explanation
Indices: 35130937--35130986 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
35130927 GAAATTTAAT
35130937 ATTTTTATAAAAAATTTTA
1 ATTTTTATAAAAAATTTTA
** *
35130956 ATTTTTATATATTATTTTTA
1 ATTTTTATA-AAAAATTTTA
35130976 ATTTTT-TAAAA
1 ATTTTTATAAAA
35130987 TTTATAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAAAATTTTA
Found at i:35132265 original size:44 final size:44
Alignment explanation
Indices: 35132197--35132290 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
35132187 AAAACCACAA
35132197 TATAAAGGTTTTACTATCAAAATGCACTCTTACAATAATATTAC
1 TATAAAGGTTTTACTATCAAAATGCACTCTTACAATAATATTAC
*
35132241 TATAAAGGTTTTACTATCAGAATGCACTCTTACAATAATATTAC
1 TATAAAGGTTTTACTATCAAAATGCACTCTTACAATAATATTAC
35132285 TCATAA
1 T-ATAA
35132291 GAATAGAGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 44 0.92
45 4 0.08
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (44 bp):
TATAAAGGTTTTACTATCAAAATGCACTCTTACAATAATATTAC
Found at i:35134624 original size:27 final size:27
Alignment explanation
Indices: 35134540--35134680 Score: 115
Period size: 27 Copynumber: 5.2 Consensus size: 27
35134530 AGAATATCGC
* * *
35134540 TCATTTGAGCTAGATACATAATATTGCT
1 TCATTCGAGCCAGATACAAAATATTG-T
* * * * **
35134568 T-ATTCAAGCTAGATACAGAATACTAC
1 TCATTCGAGCCAGATACAAAATATTGT
* *
35134594 TCATTCGAGCCAGATATAGAATATT-T
1 TCATTCGAGCCAGATACAAAATATTGT
* *
35134620 ATCATTTGAGCCAAATACAAAATATTGT
1 -TCATTCGAGCCAGATACAAAATATTGT
* *
35134648 TCATTCGAGCCAGATACGAAATATTGG
1 TCATTCGAGCCAGATACAAAATATTGT
35134675 TCATTC
1 TCATTC
35134681 CATAGACCTT
Statistics
Matches: 91, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 88 0.97
28 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (27 bp):
TCATTCGAGCCAGATACAAAATATTGT
Found at i:35135884 original size:53 final size:53
Alignment explanation
Indices: 35135798--35135904 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
35135788 ACACTACTGG
* *
35135798 AAAACGGGTTGTTACAGCATCAAACTAGGAAGAAAAGAGTATACTTAGAAAGA
1 AAAACGGGTTGTTACAGCATCAAACCAGAAAGAAAAGAGTATACTTAGAAAGA
* *
35135851 AAAATGGGTTGTTACAGTATCAAACCAGAAAGAAAAGAGTATACTTAGAAAGA
1 AAAACGGGTTGTTACAGCATCAAACCAGAAAGAAAAGAGTATACTTAGAAAGA
35135904 A
1 A
35135905 GGGATAAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (53 bp):
AAAACGGGTTGTTACAGCATCAAACCAGAAAGAAAAGAGTATACTTAGAAAGA
Found at i:35140656 original size:6 final size:6
Alignment explanation
Indices: 35140642--35140707 Score: 96
Period size: 6 Copynumber: 10.8 Consensus size: 6
35140632 AGGTTTCTCA
* *
35140642 AAATAG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
*
35140690 AAATGA AAATGAG AAATG
1 AAATGG AAATG-G AAATG
35140708 ATTCATTTGC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 51 0.91
7 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:35157551 original size:13 final size:13
Alignment explanation
Indices: 35157533--35157559 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35157523 AGACTGTTAG
35157533 TATGGTTATCAGT
1 TATGGTTATCAGT
35157546 TATGGTTATCAGT
1 TATGGTTATCAGT
35157559 T
1 T
35157560 GTATAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TATGGTTATCAGT
Found at i:35163206 original size:14 final size:15
Alignment explanation
Indices: 35163187--35163232 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
35163177 AAGTAAATTA
35163187 TTTAATAATATAT-T
1 TTTAATAATATATAT
*
35163201 TTTAAT-TTATTATAT
1 TTTAATAATA-TATAT
35163216 TTTAA-AATATATAT
1 TTTAATAATATATAT
35163230 TTT
1 TTT
35163233 TTAGAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 17 0.63
15 8 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATAATATATAT
Found at i:35163664 original size:24 final size:25
Alignment explanation
Indices: 35163636--35163682 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
35163626 GAAAAATTAT
*
35163636 TTATGAGATCTA-TTAAATTTTTAC
1 TTATGAAATCTATTTAAATTTTTAC
*
35163660 TTATGAAATCTATTTTAATTTTT
1 TTATGAAATCTATTTAAATTTTT
35163683 TAAAAAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (25 bp):
TTATGAAATCTATTTAAATTTTTAC
Found at i:35163708 original size:32 final size:32
Alignment explanation
Indices: 35163672--35163733 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
35163662 ATGAAATCTA
*
35163672 TTTTAATTTTTTA-AAAAA-GTGTTTTAATTTTG
1 TTTT-ATTATTTAGAAAAATGT-TTTTAATTTTG
*
35163704 TTTTATTATTTAGAAACATGTTTTTAATTT
1 TTTTATTATTTAGAAAAATGTTTTTAATTT
35163734 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 7 0.27
32 17 0.65
33 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (32 bp):
TTTTATTATTTAGAAAAATGTTTTTAATTTTG
Found at i:35165797 original size:12 final size:12
Alignment explanation
Indices: 35165780--35165815 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35165770 TTTTGAGAGC
35165780 ATAAAATAAAAG
1 ATAAAATAAAAG
*
35165792 ATAAAATAAAAT
1 ATAAAATAAAAG
*
35165804 AGAAAATAAAAG
1 ATAAAATAAAAG
35165816 CAAAAGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:35165802 original size:17 final size:17
Alignment explanation
Indices: 35165780--35165814 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35165770 TTTTGAGAGC
35165780 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
35165797 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
35165814 A
1 A
35165815 GCAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:35168686 original size:69 final size:68
Alignment explanation
Indices: 35168596--35168737 Score: 248
Period size: 69 Copynumber: 2.1 Consensus size: 68
35168586 ATTGCTCTAG
*
35168596 GTCGCAACAAAGGGACCAGACTTGAAGAATCTGGGAACTGACTTCTTTGTCACGACATACATCAC
1 GTCGCAACAAAGGGACCAGACTTGAAGAAGCTGGGAACTGAC-TCTTTGTCACGACATACATCAC
35168661 CTAT
65 CTAT
**
35168665 GTCGCAACAAAGGGACCAGACTTGAAGAAGCTGGGAACTGACTCTTTGTCGTGACATACATCACC
1 GTCGCAACAAAGGGACCAGACTTGAAGAAGCTGGGAACTGACTCTTTGTCACGACATACATCACC
35168730 TAT
66 TAT
35168733 GTCGC
1 GTCGC
35168738 GAAAATGCTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
68 29 0.41
69 41 0.59
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (68 bp):
GTCGCAACAAAGGGACCAGACTTGAAGAAGCTGGGAACTGACTCTTTGTCACGACATACATCACC
TAT
Found at i:35171453 original size:19 final size:19
Alignment explanation
Indices: 35171374--35171531 Score: 153
Period size: 19 Copynumber: 8.5 Consensus size: 19
35171364 AATATCATAT
*
35171374 TGGCTCGT-TGAGCAATAC
1 TGGCTCGTAAGAGCAATAC
*
35171392 TGGCTCGT-TGAGCAATAC
1 TGGCTCGTAAGAGCAATAC
* * * *
35171410 TGGTTTGT-TGAGCAGTAC
1 TGGCTCGTAAGAGCAATAC
* *
35171428 CGGCTCGTAAGACCAATAC
1 TGGCTCGTAAGAGCAATAC
* *
35171447 TGGCTCGT-TGTGCAATAC
1 TGGCTCGTAAGAGCAATAC
35171465 TGGCTCGTAAGAGCAATAC
1 TGGCTCGTAAGAGCAATAC
* * *
35171484 TGACTCGTGAGAGCCATAC
1 TGGCTCGTAAGAGCAATAC
*
35171503 TGGCTCGTAAGAGCAATAT
1 TGGCTCGTAAGAGCAATAC
*
35171522 TGGATCGTAA
1 TGGCTCGTAA
35171532 TGAGTTATTT
Statistics
Matches: 115, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
18 53 0.46
19 62 0.54
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (19 bp):
TGGCTCGTAAGAGCAATAC
Found at i:35171470 original size:37 final size:37
Alignment explanation
Indices: 35171374--35171529 Score: 188
Period size: 37 Copynumber: 4.2 Consensus size: 37
35171364 AATATCATAT
*
35171374 TGGCTCGTTGAGCAATACTGGCTCGT-TGAGCAATAC
1 TGGCTCGTTGAGCAATACTGGCTCGTAAGAGCAATAC
* * * * *
35171410 TGGTTTGTTGAGCAGTACCGGCTCGTAAGACCAATAC
1 TGGCTCGTTGAGCAATACTGGCTCGTAAGAGCAATAC
*
35171447 TGGCTCGTTGTGCAATACTGGCTCGTAAGAGCAATAC
1 TGGCTCGTTGAGCAATACTGGCTCGTAAGAGCAATAC
* * * *
35171484 TGACTCGTGAGAGCCATACTGGCTCGTAAGAGCAATAT
1 TGGCTCGT-TGAGCAATACTGGCTCGTAAGAGCAATAC
*
35171522 TGGATCGT
1 TGGCTCGT
35171530 AATGAGTTAT
Statistics
Matches: 99, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
36 22 0.22
37 46 0.46
38 31 0.31
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (37 bp):
TGGCTCGTTGAGCAATACTGGCTCGTAAGAGCAATAC
Found at i:35172259 original size:21 final size:21
Alignment explanation
Indices: 35172235--35172302 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
35172225 CATGTTTCGA
* *
35172235 TAGAAGAGACACTTATATCGG
1 TAGAAGAGTCACTTGTATCGG
*
35172256 TAGAAGAGTCACTTGTATCAG
1 TAGAAGAGTCACTTGTATCGG
**
35172277 TAGAACTGTCACTTGTATCGG
1 TAGAAGAGTCACTTGTATCGG
35172298 TAGAA
1 TAGAA
35172303 ATCTGTAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (21 bp):
TAGAAGAGTCACTTGTATCGG
Found at i:35176245 original size:17 final size:17
Alignment explanation
Indices: 35176223--35176258 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35176213 CTCGTAGGAA
35176223 AGGGAAATTAGAAGAAT
1 AGGGAAATTAGAAGAAT
*
35176240 AGGGAAATTAGCAGAAT
1 AGGGAAATTAGAAGAAT
35176257 AG
1 AG
35176259 TCCCTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.31, T:0.17
Consensus pattern (17 bp):
AGGGAAATTAGAAGAAT
Found at i:35177714 original size:43 final size:43
Alignment explanation
Indices: 35177653--35177747 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
35177643 TTTATTTAAA
* * *
35177653 AAAATCATATTCAAAATAAATTGGTAGCTTGATTAATCAATCC
1 AAAATCGTCTTCAAAATAAATTGGTAGCTCGATTAATCAATCC
35177696 AAAATCGTCTTCAAAATAAATTGGTAGCTCGATTAATCAATCC
1 AAAATCGTCTTCAAAATAAATTGGTAGCTCGATTAATCAATCC
35177739 AAAATCGTC
1 AAAATCGTC
35177748 AAGAGAGGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (43 bp):
AAAATCGTCTTCAAAATAAATTGGTAGCTCGATTAATCAATCC
Found at i:35178675 original size:134 final size:134
Alignment explanation
Indices: 35178418--35178676 Score: 290
Period size: 134 Copynumber: 1.9 Consensus size: 134
35178408 CCAAATAGAA
* * * ** ** *
35178418 GGTATTGATACCGTGTTGATACATGATAAATACTTTGAAAGCCCGAATGCCAATTTCATATTGAT
1 GGTATTGATACAGTATCGATACATGATAAATACTTTGAAAAACAAAATGCCAATTTCATATCGAT
** * ** *
35178483 ATAACAAAAGGTATCGATAAAAGTGTCCCACTATCGATACTTGAAAAATTTTATTGATACCAAGC
66 ATAACAAAAGGTATCGATAAAAGTGTCAAACTATCGATACTTAAAAAAACTTACTGATACCAAGC
35178548 GAAG
131 GAAG
* * * * *
35178552 GGTATTGATACAGTATCGATACTTGATAAATACTTTGAAAAATAAAATGTCATTTTCGTATCGAT
1 GGTATTGATACAGTATCGATACATGATAAATACTTTGAAAAACAAAATGCCAATTTCATATCGAT
*
35178617 ATCAA-AAAATGTATCGATAAAAGTGT-AAATCTATCGATAC-TAAACAAAACTTACTGATAC
66 AT-AACAAAAGGTATCGATAAAAGTGTCAAA-CTATCGATACTTAAA-AAAACTTACTGATAC
35178677 TAGACAAAAA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
133 4 0.04
134 96 0.94
135 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (134 bp):
GGTATTGATACAGTATCGATACATGATAAATACTTTGAAAAACAAAATGCCAATTTCATATCGAT
ATAACAAAAGGTATCGATAAAAGTGTCAAACTATCGATACTTAAAAAAACTTACTGATACCAAGC
GAAG
Found at i:35178695 original size:20 final size:20
Alignment explanation
Indices: 35178648--35178696 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
35178638 AGTGTAAATC
**
35178648 TATCGATACTAAACAAAACT
1 TATCGATACTAAACAAAAAG
*
35178668 TA-CTGATACTAGACAAAAAG
1 TATC-GATACTAAACAAAAAG
35178688 TATCGATAC
1 TATCGATAC
35178697 CAAATCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.24
Consensus pattern (20 bp):
TATCGATACTAAACAAAAAG
Found at i:35179311 original size:69 final size:69
Alignment explanation
Indices: 35179229--35179364 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
35179219 TCAATGATTT
* *
35179229 ATCCAAGACACAAAATCACTACTCTGTAGAAAATTGGGTGATCCCACACCAAATTCAAATAATAT
1 ATCCAAGACACAAAATCACCACTCTGTAGAAAATTAGGTGATCCCACACCAAATTCAAATAATAT
35179294 GGCC
66 GGCC
* * *
35179298 ATCCAAGACACAAAATCACCACTCTTTAGAAATTTAGGTGATCCCACACGAAATTCAAATAATAT
1 ATCCAAGACACAAAATCACCACTCTGTAGAAAATTAGGTGATCCCACACCAAATTCAAATAATAT
35179363 GG
66 GG
35179365 GACCTCCAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (69 bp):
ATCCAAGACACAAAATCACCACTCTGTAGAAAATTAGGTGATCCCACACCAAATTCAAATAATAT
GGCC
Found at i:35202578 original size:23 final size:25
Alignment explanation
Indices: 35202552--35202597 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35202542 CCAATTAGGG
35202552 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
35202575 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
35202598 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:35203013 original size:15 final size:15
Alignment explanation
Indices: 35202976--35203014 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
35202966 TTATGTGTGC
*
35202976 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
35202991 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
35203005 TTAATTCTTG
1 TTAATTCTTG
35203015 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:35214667 original size:20 final size:20
Alignment explanation
Indices: 35214642--35214681 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35214632 TTTTTCGAAA
*
35214642 AAAGTCAATGATCAACGGTC
1 AAAGTCAACGATCAACGGTC
*
35214662 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGATCAACGGTC
35214682 GGTCAACAGT
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:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGATCAACGGTC
Found at i:35214810 original size:33 final size:33
Alignment explanation
Indices: 35214735--35214811 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
35214725 GGGTTTAGGC
*
35214735 TTAAAGGTTGTTAAAGGGTTTGGGTTATTGGGT
1 TTAAAGGTTTTTAAAGGGTTTGGGTTATTGGGT
35214768 TTAAAGGTTTTTAAAGGGTTTGGGTTATTGGGT
1 TTAAAGGTTTTTAAAGGGTTTGGGTTATTGGGT
35214801 TTAAAGGTTTT
1 TTAAAGGTTTT
35214812 GGGTTAGGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.45
Consensus pattern (33 bp):
TTAAAGGTTTTTAAAGGGTTTGGGTTATTGGGT
Found at i:35215902 original size:12 final size:12
Alignment explanation
Indices: 35215885--35215959 Score: 89
Period size: 12 Copynumber: 6.3 Consensus size: 12
35215875 ATAACATCCA
35215885 AACAACAAAAAT
1 AACAACAAAAAT
*
35215897 AACAACCAAAAT
1 AACAACAAAAAT
*
35215909 AGCAACAAAAAT
1 AACAACAAAAAT
* * *
35215921 AATAGC-AAAAC
1 AACAACAAAAAT
35215932 AACAACAAAAAT
1 AACAACAAAAAT
*
35215944 AGCAACAAAAAT
1 AACAACAAAAAT
35215956 AACA
1 AACA
35215960 GCAAGAACAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
11 8 0.16
12 42 0.84
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:35215924 original size:15 final size:15
Alignment explanation
Indices: 35215906--35215963 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
35215896 TAACAACCAA
35215906 AATAGCAACAAAAAT
1 AATAGCAACAAAAAT
*
35215921 AATAGCAAAACAACAACAAA
1 AATAGC--AAC-A-AA-AAT
35215941 AATAGCAACAAAAAT
1 AATAGCAACAAAAAT
*
35215956 AACAGCAA
1 AATAGCAA
35215964 GAACAACACT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 15 0.43
16 2 0.06
17 4 0.11
18 4 0.11
19 2 0.06
20 8 0.23
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (15 bp):
AATAGCAACAAAAAT
Found at i:35215936 original size:20 final size:20
Alignment explanation
Indices: 35215911--35215948 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35215901 ACCAAAATAG
35215911 CAACAA-AAATAATAGCAAAA
1 CAACAACAAA-AATAGCAAAA
35215931 CAACAACAAAAATAGCAA
1 CAACAACAAAAATAGCAA
35215949 CAAAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.08
Consensus pattern (20 bp):
CAACAACAAAAATAGCAAAA
Found at i:35215943 original size:35 final size:35
Alignment explanation
Indices: 35215892--35215971 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
35215882 CCAAACAACA
* * *
35215892 AAAATAACAACCAAAATAGCAACAAAAATAATAGC
1 AAAACAACAACAAAAATAGCAACAAAAATAACAGC
35215927 AAAACAACAACAAAAATAGCAACAAAAATAACAGC
1 AAAACAACAACAAAAATAGCAACAAAAATAACAGC
35215962 AAGAACAACA
1 AA-AACAACA
35215972 CTAAAACAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 34 0.83
36 7 0.17
ACGTcount: A:0.68, C:0.19, G:0.06, T:0.07
Consensus pattern (35 bp):
AAAACAACAACAAAAATAGCAACAAAAATAACAGC
Found at i:35215978 original size:47 final size:47
Alignment explanation
Indices: 35215885--35215988 Score: 113
Period size: 47 Copynumber: 2.2 Consensus size: 47
35215875 ATAACATCCA
* * * *
35215885 AACAACAAAAATAACAACCAAAATAGCAACAAAAATAATAGCAAAAC
1 AACAACAAAAATAACAACAAAAATAACAACAAAAACAACAGCAAAAC
* * *
35215932 AACAACAAAAATAGCAACAAAAATAACAGCAAGAACAACA-CTAAAAC
1 AACAACAAAAATAACAACAAAAATAACAACAAAAACAACAGC-AAAAC
*
35215979 AATAA-AAAAA
1 AACAACAAAAA
35215989 GCATCAAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
46 6 0.12
47 42 0.88
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (47 bp):
AACAACAAAAATAACAACAAAAATAACAACAAAAACAACAGCAAAAC
Found at i:35216028 original size:31 final size:32
Alignment explanation
Indices: 35215974--35216073 Score: 94
Period size: 35 Copynumber: 2.9 Consensus size: 32
35215964 GAACAACACT
* * *
35215974 AAAACAATAAAAAAAGCATCAAAACAG-CAACC
1 AAAACAGTAAAAAAA-CACCAAAACAGAAAACC
*
35216006 GAAACAGTAAAAAAACACCAAAACAGTAAAAAACC
1 AAAACAGTAAAAAAACACCAAAACAG---AAAACC
35216041 AAAACAGTAAAAACAACAACCAAAACAGTAAAA
1 AAAACAGTAAAAA-AAC-ACCAAAACAG-AAAA
35216074 AACAACACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
31 10 0.18
32 13 0.23
35 20 0.36
36 3 0.05
37 10 0.18
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.06
Consensus pattern (32 bp):
AAAACAGTAAAAAAACACCAAAACAGAAAACC
Found at i:35216070 original size:37 final size:35
Alignment explanation
Indices: 35216002--35216076 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 35
35215992 TCAAAACAGC
*
35216002 AACCGAAACAGTAAAAAAACACCAAAACAGTAAAA
1 AACCAAAACAGTAAAAAAACACCAAAACAGTAAAA
35216037 AACCAAAACAGTAAAAACAACAACCAAAACAGTAAAA
1 AACCAAAACAGTAAAAA-AAC-ACCAAAACAGTAAAA
35216074 AAC
1 AAC
35216077 AACACAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 16 0.43
36 3 0.08
37 18 0.49
ACGTcount: A:0.67, C:0.21, G:0.07, T:0.05
Consensus pattern (35 bp):
AACCAAAACAGTAAAAAAACACCAAAACAGTAAAA
Found at i:35216077 original size:22 final size:21
Alignment explanation
Indices: 35215994--35216088 Score: 98
Period size: 21 Copynumber: 4.9 Consensus size: 21
35215984 AAAAAGCATC
* *
35215994 AAAACAGCAACCGAAACAGTA
1 AAAACAACAACCAAAACAGTA
35216015 AAAA-AAC-ACCAAAACAGT-
1 AAAACAACAACCAAAACAGTA
35216033 --AA-AA-AACCAAAACAGTA
1 AAAACAACAACCAAAACAGTA
35216050 AAAACAACAACCAAAACAGTAA
1 AAAACAACAACCAAAACAGT-A
*
35216072 AAAACAAC-ACAAAAACA
1 AAAACAACAACCAAAACA
35216089 ACAATATAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
16 15 0.23
19 12 0.19
20 4 0.06
21 24 0.38
22 9 0.14
ACGTcount: A:0.67, C:0.22, G:0.06, T:0.04
Consensus pattern (21 bp):
AAAACAACAACCAAAACAGTA
Found at i:35216079 original size:19 final size:19
Alignment explanation
Indices: 35216001--35216085 Score: 97
Period size: 19 Copynumber: 4.5 Consensus size: 19
35215991 ATCAAAACAG
*
35216001 CAACCGAAACAGTAAAAAA
1 CAACCAAAACAGTAAAAAA
35216020 -ACACCAAAACAGT--AAAA
1 CA-ACCAAAACAGTAAAAAA
35216037 -AACCAAAACAGTAAAAACAA
1 CAACCAAAACAGT-AAAA-AA
35216057 CAACCAAAACAGTAAAAAA
1 CAACCAAAACAGTAAAAAA
35216076 CAACACAAAA
1 CAAC-CAAAA
35216086 ACAACAATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
16 11 0.19
17 5 0.09
18 1 0.02
19 18 0.31
20 11 0.19
21 12 0.21
ACGTcount: A:0.67, C:0.22, G:0.06, T:0.05
Consensus pattern (19 bp):
CAACCAAAACAGTAAAAAA
Found at i:35216088 original size:21 final size:19
Alignment explanation
Indices: 35216007--35216075 Score: 99
Period size: 21 Copynumber: 3.7 Consensus size: 19
35215997 ACAGCAACCG
35216007 AAACAGTAAAAAAACACCA
1 AAACAGTAAAAAAACACCA
35216026 AAACAGT--AAAAA-ACCA
1 AAACAGTAAAAAAACACCA
35216042 AAACAGTAAAAACAACAACCA
1 AAACAGTAAAAA-AAC-ACCA
35216063 AAACAGTAAAAAA
1 AAACAGTAAAAAA
35216076 CAACACAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.24
17 5 0.11
18 3 0.07
19 9 0.20
20 1 0.02
21 16 0.36
ACGTcount: A:0.70, C:0.19, G:0.06, T:0.06
Consensus pattern (19 bp):
AAACAGTAAAAAAACACCA
Found at i:35220066 original size:25 final size:26
Alignment explanation
Indices: 35220031--35220093 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 26
35220021 AGAAATAAGA
*
35220031 GAATATTTAGCAGGCTTCGAGCCAGT
1 GAATGTTTAGCAGGCTTCGAGCCAGT
*
35220057 GAATG-TTAGCAGGCTTCGAGCCGGT
1 GAATGTTTAGCAGGCTTCGAGCCAGT
*
35220082 GAGTGTTTAGCA
1 GAATGTTTAGCA
35220094 AGTACTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (26 bp):
GAATGTTTAGCAGGCTTCGAGCCAGT
Found at i:35227277 original size:26 final size:26
Alignment explanation
Indices: 35227248--35227338 Score: 119
Period size: 26 Copynumber: 3.5 Consensus size: 26
35227238 AAATAAGAGA
*
35227248 ATATTTAGTAGGCTTCAAGCCGGTGT
1 ATATTTAGCAGGCTTCAAGCCGGTGT
*
35227274 ATATTTAGCAGGCTTCGAGCCGGTGT
1 ATATTTAGCAGGCTTCAAGCCGGTGT
* * * *
35227300 ATATTTAGCAAGCTTCGAGCCAGTGA
1 ATATTTAGCAGGCTTCAAGCCGGTGT
*
35227326 ATGTTTAGCAGGC
1 ATATTTAGCAGGC
35227339 CTTGAGCCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (26 bp):
ATATTTAGCAGGCTTCAAGCCGGTGT
Found at i:35236491 original size:24 final size:24
Alignment explanation
Indices: 35236458--35236508 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35236448 AAAGCGCTCC
* *
35236458 AAGGACAAGAAGCGTAGAAAGAAA
1 AAGGACAAGAAGAGAAGAAAGAAA
* *
35236482 AAGGAGAAGAAGAGAAGGAAGAAA
1 AAGGACAAGAAGAGAAGAAAGAAA
35236506 AAG
1 AAG
35236509 TACCATCCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.33, T:0.02
Consensus pattern (24 bp):
AAGGACAAGAAGAGAAGAAAGAAA
Found at i:35236640 original size:17 final size:17
Alignment explanation
Indices: 35236618--35236689 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
35236608 TATTAATAAG
* *
35236618 CATTGTCATCGCATTCC
1 CATTGTCATCACATTTC
* *
35236635 CATTGTCATTACATTTT
1 CATTGTCATCACATTTC
* *
35236652 AATTGTCATCACATTTG
1 CATTGTCATCACATTTC
**
35236669 CATTGTCATTGCATTTC
1 CATTGTCATCACATTTC
35236686 CATT
1 CATT
35236690 TGTCCTTATA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (17 bp):
CATTGTCATCACATTTC
Found at i:35236673 original size:34 final size:34
Alignment explanation
Indices: 35236619--35236684 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
35236609 ATTAATAAGC
*
35236619 ATTGTCATCGCATTCCCATTGTCATTACATTTTA
1 ATTGTCATCACATTCCCATTGTCATTACATTTTA
** *
35236653 ATTGTCATCACATTTGCATTGTCATTGCATTT
1 ATTGTCATCACATTCCCATTGTCATTACATTT
35236685 CCATTTGTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (34 bp):
ATTGTCATCACATTCCCATTGTCATTACATTTTA
Found at i:35237787 original size:26 final size:26
Alignment explanation
Indices: 35237746--35237803 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
35237736 TTGCGCCCAA
35237746 AATTGTCACTGCATGA-CGATGTCTAG
1 AATTGTCACTGCATGAGC-ATGTCTAG
* * *
35237772 AGTTGTCGCTGTATGAGCATGTCTAG
1 AATTGTCACTGCATGAGCATGTCTAG
35237798 AATTGT
1 AATTGT
35237804 GCCCAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (26 bp):
AATTGTCACTGCATGAGCATGTCTAG
Found at i:35245951 original size:3 final size:3
Alignment explanation
Indices: 35245943--35245968 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35245933 ATTCGATCTT
35245943 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
35245969 TAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35246618 original size:16 final size:15
Alignment explanation
Indices: 35246597--35246641 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
35246587 TGTGTAAAAA
35246597 AAACATAAATATAAAT
1 AAACATAAA-ATAAAT
35246613 AAACATTAAAATAAAT
1 AAACA-TAAAATAAAT
*
35246629 AAAGATAAAATAA
1 AAACATAAAATAA
35246642 GAATAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 15 0.56
17 4 0.15
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (15 bp):
AAACATAAAATAAAT
Found at i:35247395 original size:22 final size:22
Alignment explanation
Indices: 35247343--35247398 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 22
35247333 AAATGTAAAC
*
35247343 TTTTTTTTAAAGAAAATCACTA
1 TTTTTCTTAAAGAAAATCACTA
35247365 TATTTTCTTAAAGAAAATCACTA
1 T-TTTTCTTAAAGAAAATCACTA
35247388 TTTTTCTTAAA
1 TTTTTCTTAAA
35247399 ATTTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTTTCTTAAAGAAAATCACTA
Found at i:35247572 original size:141 final size:145
Alignment explanation
Indices: 35247367--35247722 Score: 526
Period size: 141 Copynumber: 2.5 Consensus size: 145
35247357 AATCACTATA
* * * * *
35247367 TTTTCTTAAAGAAAATCACTATTTTTCTTAAAATTTAAAA-TTTTATTTTGAAATAGTTTAAAAA
1 TTTTTTTAAAGAAAATCACTATTTTT-TTAAAACTCAAAACTTTTATTTCGAAATAGTTAAAAAA
*
35247431 ATCAAAACTTTGTTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAA-A-AAAATTA-TTTT
65 ATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATATAAAATTATTTTT
35247493 AAAAATCGAAACTTTC
130 AAAAATCGAAACTTTC
35247509 TTTTTTTAAAGAAAATCACTATTTTTTT-AAACTCAAAACTTTTATTTCGAAATAGTTAAAAAAA
1 TTTTTTTAAAGAAAATCACTATTTTTTTAAAACTCAAAACTTTTATTTCGAAATAGTTAAAAAAA
* * ***
35247573 TTAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAATATATTTTTATTTTTA
66 TCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATATAAAATTATTTTTA
*
35247638 AAAATCTAAACTTTC
131 AAAATCGAAACTTTC
* *
35247653 TTTTTTGAAA-AAAATCACTATTTTTTTTAAAACTCAAAACTTTTATTTCGAAATTGTTAAAAAA
1 TTTTTTTAAAGAAAATCACTA-TTTTTTTAAAACTCAAAACTTTTATTTCGAAATAGTTAAAAAA
35247717 ATCAAA
65 ATCAAA
35247723 TTTTTTTCCC
Statistics
Matches: 193, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
140 8 0.04
141 71 0.37
142 26 0.13
143 14 0.07
144 35 0.18
145 39 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (145 bp):
TTTTTTTAAAGAAAATCACTATTTTTTTAAAACTCAAAACTTTTATTTCGAAATAGTTAAAAAAA
TCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATATAAAATTATTTTTA
AAAATCGAAACTTTC
Found at i:35248169 original size:12 final size:12
Alignment explanation
Indices: 35248148--35248187 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
35248138 AAAAATTAAA
35248148 TAATAATAATAG
1 TAATAATAATAG
*
35248160 TAATAGTAATAG
1 TAATAATAATAG
* *
35248172 TAATGATAATAA
1 TAATAATAATAG
35248184 TAAT
1 TAAT
35248188 TTGGGCCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:35258472 original size:4 final size:4
Alignment explanation
Indices: 35258445--35258487 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
35258435 AATATATATA
*
35258445 TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
35258488 ATGAGAGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:35262973 original size:21 final size:21
Alignment explanation
Indices: 35262921--35262974 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
35262911 ACCTACAAAA
*
35262921 CATTATGTTTGTAACTCTCCT
1 CATTATGTTTGTAACTCTCAT
* *
35262942 -AATAAGTTTTGTAACTCTCAT
1 CATTATG-TTTGTAACTCTCAT
35262963 CATTATGTTTGT
1 CATTATGTTTGT
35262975 TTTAAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (21 bp):
CATTATGTTTGTAACTCTCAT
Found at i:35265269 original size:11 final size:11
Alignment explanation
Indices: 35265253--35265283 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
35265243 TCTAAAAGGT
35265253 ATCGATACCGA
1 ATCGATACCGA
35265264 ATCGATACCGA
1 ATCGATACCGA
35265275 ATCGATACC
1 ATCGATACC
35265284 TCCTAGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.19
Consensus pattern (11 bp):
ATCGATACCGA
Found at i:35265583 original size:20 final size:20
Alignment explanation
Indices: 35265536--35265589 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
35265526 ATTTTGAAGT
* * *
35265536 GTTAAAATGATTTTGACTTG
1 GTTAAAATCATTTTGACATA
* *
35265556 GTTCAAATTATTTTGACATA
1 GTTAAAATCATTTTGACATA
*
35265576 TTTAAAATCATTTT
1 GTTAAAATCATTTT
35265590 AACTTTTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (20 bp):
GTTAAAATCATTTTGACATA
Found at i:35267337 original size:2 final size:2
Alignment explanation
Indices: 35267330--35267363 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
35267320 ATCACAAAAC
*
35267330 AT AT AT AT AT AC AT AT AT AT -T 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 A
35267364 AATTCTTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35270702 original size:20 final size:20
Alignment explanation
Indices: 35270679--35270729 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35270669 AGCACACTTA
* *
35270679 TATCGGTAGAACTGTAGTTG
1 TATCGGTAGAACAGTAGTTC
* *
35270699 TATCAGTAGAAGAGTAGTTC
1 TATCGGTAGAACAGTAGTTC
*
35270719 TACCGGTAGAA
1 TATCGGTAGAA
35270730 GTCCCAAGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGGTAGAACAGTAGTTC
Found at i:35273764 original size:20 final size:20
Alignment explanation
Indices: 35273711--35273779 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
35273701 TTAATTGTTC
*
35273711 CAGTAGAAGCA-TACTTGTAT
1 CAGTAGAAG-AGTAGTTGTAT
* **
35273731 CGGTAGAACTGTAGTTGTAT
1 CAGTAGAAGAGTAGTTGTAT
* *
35273751 CAGTAGAAGAGTAGTTCTAC
1 CAGTAGAAGAGTAGTTGTAT
35273771 CAGTAGAAG
1 CAGTAGAAG
35273780 TCTCAGGGCA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
CAGTAGAAGAGTAGTTGTAT
Found at i:35275529 original size:14 final size:14
Alignment explanation
Indices: 35275510--35275536 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35275500 TGATATTAGT
35275510 GAAAAAGGAAAGAG
1 GAAAAAGGAAAGAG
35275524 GAAAAAGGAAAGA
1 GAAAAAGGAAAGA
35275537 AAAACGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAAAAGGAAAGAG
Found at i:35277764 original size:198 final size:200
Alignment explanation
Indices: 35277408--35277779 Score: 504
Period size: 198 Copynumber: 1.9 Consensus size: 200
35277398 CCTATTTACT
* * * * *
35277408 CTTAAATTTGTCCTGTTTTGGTATTGATGTCACTGCATAAGTAATTTCAGATTGCGTCCAGGATT
1 CTTAAATTTGTCCTCTTTTGCTACTGATGTCACTGCATAAGTAATTTCAGATTACGTCCAAGATT
* * * *
35277473 TTCCTCGCATCTGAAAATTTTCTGGATAAGAACAGAAATGTGTGAGCTGGCTAGTCTGGTATAAC
66 TTCCTCGCATCTGAAAATGTTCTGGATAAAAACAAAAATGTGTGAGCTGGCTAGTCTAGTATAAC
* *
35277538 CAACTTGTACGACCAACAACAGCTTGATT-TAT-GAAAGGACACCTGCACAAGGACAACTTATAC
131 CAACTTGTACGACCAACAACAACTTGATTCTATAGAAAAGACACCTGCACAAGGACAACTTATAC
35277601 TTGCC
196 TTGCC
* *
35277606 CTTAAATTTGTCCTCTTTTTCTACTGATGTCGCTGCATAAGTAATTTCAGATTACGTCCAAGATT
1 CTTAAATTTGTCCTCTTTTGCTACTGATGTCACTGCATAAGTAATTTCAGATTACGTCCAAGATT
* * * *
35277671 ATTGC-CGCATCT-AATAGCTGTT-TGGATAAAAACAAAAATGTGTTAGCTGTCTAGTCTAGTAT
66 -TTCCTCGCATCTGAA-A-ATGTTCTGGATAAAAACAAAAATGTGTGAGCTGGCTAGTCTAGTAT
*
35277733 AACCAACTTGTATGACCAA-AGACAACTTGATTCTATAGAAAAGACAC
128 AACCAACTTGTACGACCAACA-ACAACTTGATTCTATAGAAAAGACAC
35277780 TTGTACAATT
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
197 3 0.02
198 129 0.86
199 9 0.06
200 9 0.06
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (200 bp):
CTTAAATTTGTCCTCTTTTGCTACTGATGTCACTGCATAAGTAATTTCAGATTACGTCCAAGATT
TTCCTCGCATCTGAAAATGTTCTGGATAAAAACAAAAATGTGTGAGCTGGCTAGTCTAGTATAAC
CAACTTGTACGACCAACAACAACTTGATTCTATAGAAAAGACACCTGCACAAGGACAACTTATAC
TTGCC
Found at i:35279289 original size:51 final size:51
Alignment explanation
Indices: 35279229--35279377 Score: 226
Period size: 51 Copynumber: 2.9 Consensus size: 51
35279219 CCAAAAATAA
* *
35279229 CAGAGGATTTTCCTCAATTGAAAATATTCTGAAAGTATTTTTTGCAACAGT
1 CAGAGGATTTTCCTCAACTGAAAATATTCTGAAAATATTTTTTGCAACAGT
* * * *
35279280 CAGAGGATTTTCCTCAACTAAAAATATTTTGAAAATATTTTCTACAACAGT
1 CAGAGGATTTTCCTCAACTGAAAATATTCTGAAAATATTTTTTGCAACAGT
*
35279331 CAGAGGATTTTTCTCAACTGAAAATATTCTGAAAATATTATTTTGCA
1 CAGAGGATTTTCCTCAACTGAAAATATTCTGAAAATATT-TTTTGCA
35279378 TTATCAACAA
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 81 0.94
52 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (51 bp):
CAGAGGATTTTCCTCAACTGAAAATATTCTGAAAATATTTTTTGCAACAGT
Found at i:35291317 original size:21 final size:21
Alignment explanation
Indices: 35291293--35291343 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
35291283 GTTTGCATGT
35291293 ATTTTTATTTGTTGTCACTGC
1 ATTTTTATTTGTTGTCACTGC
*
35291314 A-TTTTA-TT-TTGTCATTGC
1 ATTTTTATTTGTTGTCACTGC
*
35291332 ATTTCT-TTTGTT
1 ATTTTTATTTGTT
35291344 AATTTAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 7 0.28
21 1 0.04
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.63
Consensus pattern (21 bp):
ATTTTTATTTGTTGTCACTGC
Found at i:35291934 original size:15 final size:15
Alignment explanation
Indices: 35291902--35291949 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
35291892 TCAGTCACAT
*
35291902 GAAAAAGGAA-AATGA
1 GAAAAAGGAAGAA-AA
35291917 GAAAAAGGAAGAAAA
1 GAAAAAGGAAGAAAA
35291932 GAAAAA-GAAGAAAA
1 GAAAAAGGAAGAAAA
35291946 -AAAA
1 GAAAA
35291950 TTTATGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 4 0.13
14 8 0.26
15 17 0.55
16 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (15 bp):
GAAAAAGGAAGAAAA
Found at i:35294179 original size:51 final size:51
Alignment explanation
Indices: 35294119--35294230 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
35294109 TTTTCTCAAT
* ** * *
35294119 TGAAAATATTTTCTACAACAGTTTGAGGATTTTCCTCAACTGAAAATATTC
1 TGAAAATATTTTCTACAACAATAAGAGAATTTTCCTCAACTGAAAACATTC
** * *
35294170 TGAAAATATTTTCTGTAACAATAAGAGAATTTTTCTCAACTGAAAACATTT
1 TGAAAATATTTTCTACAACAATAAGAGAATTTTCCTCAACTGAAAACATTC
35294221 TGAAAATATT
1 TGAAAATATT
35294231 ATTTTGCATT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (51 bp):
TGAAAATATTTTCTACAACAATAAGAGAATTTTCCTCAACTGAAAACATTC
Found at i:35304638 original size:13 final size:13
Alignment explanation
Indices: 35304615--35304656 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
35304605 AAATATCATT
35304615 TATTCAATTAATTA
1 TATT-AATTAATTA
35304629 TATTAATTAATTA
1 TATTAATTAATTA
35304642 -ACTTAATTAAATTA
1 TA-TTAATT-AATTA
35304656 T
1 T
35304657 TTTCTCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 15 0.60
14 9 0.36
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTAATTAATTA
Found at i:35305961 original size:24 final size:25
Alignment explanation
Indices: 35305934--35305981 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
35305924 TTACATTTTT
*
35305934 ATAATTTAT-TTTATATTTTAAAAA
1 ATAATTTATATATATATTTTAAAAA
*
35305958 ATAATTTATATATATTTTTTAAAA
1 ATAATTTATATATATATTTTAAAA
35305982 TTTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAATTTATATATATATTTTAAAAA
Found at i:35306237 original size:14 final size:14
Alignment explanation
Indices: 35306218--35306290 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 14
35306208 ATATAAATCC
35306218 ATATAATATTATTT
1 ATATAATATTATTT
*
35306232 ATATAA-ATTATGT
1 ATATAATATTATTT
*
35306245 ATA-AATAATA-TT
1 ATATAATATTATTT
** *
35306257 ATATTTTATAATTT
1 ATATAATATTATTT
*
35306271 TTATAATATATCATTT
1 ATATAATAT-T-ATTT
35306287 ATAT
1 ATAT
35306291 TTATTATATG
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
12 6 0.14
13 15 0.36
14 14 0.33
16 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (14 bp):
ATATAATATTATTT
Found at i:35306253 original size:29 final size:26
Alignment explanation
Indices: 35306220--35306290 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
35306210 ATAAATCCAT
35306220 ATAATATTATTTATATAAATTATGTATAA
1 ATAATATTATTTATAT-AATT-TGTAT-A
* *
35306249 ATAATATTATATTTTATAATTTTTATA
1 ATAATATTAT-TTATATAATTTGTATA
*
35306276 AT-ATATCATTTATAT
1 ATAATATTATTTATAT
35306291 TTATTATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 5 0.14
26 6 0.16
27 3 0.08
28 4 0.11
29 14 0.38
30 5 0.14
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
ATAATATTATTTATATAATTTGTATA
Found at i:35306425 original size:21 final size:21
Alignment explanation
Indices: 35306384--35306427 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35306374 AAATTGATAG
*
35306384 AATATATTAATATTATGATTA
1 AATATATTAATATTATAATTA
*
35306405 AATATATTATTA-TATCAATTA
1 AATATATTAATATTAT-AATTA
35306426 AA
1 AA
35306428 AAAATCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATATATTAATATTATAATTA
Found at i:35311290 original size:39 final size:39
Alignment explanation
Indices: 35311247--35311331 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
35311237 GTTATCAAAT
*
35311247 TACTGAACTGGCAGTGACACTATAAACATTGCAATACAA
1 TACTGAACTGGCAGTGACACTATAAACACTGCAATACAA
* * *
35311286 TACTGAACTTGCAGTGACACTGTAAATACTGCAATACAA
1 TACTGAACTGGCAGTGACACTATAAACACTGCAATACAA
*
35311325 TAATGAA
1 TACTGAA
35311332 TTGACTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (39 bp):
TACTGAACTGGCAGTGACACTATAAACACTGCAATACAA
Found at i:35312148 original size:19 final size:19
Alignment explanation
Indices: 35312124--35312162 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35312114 AATAAACATG
35312124 AGATGTTGTGACATATGCT
1 AGATGTTGTGACATATGCT
35312143 AGATGTTGTGACATATGCT
1 AGATGTTGTGACATATGCT
35312162 A
1 A
35312163 TAAGCTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (19 bp):
AGATGTTGTGACATATGCT
Found at i:35312221 original size:36 final size:36
Alignment explanation
Indices: 35312181--35312254 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
35312171 TGATGACTGT
**
35312181 TGTGAAAGTGAATATGTGGGTATGTTATTCATGCCA
1 TGTGAAAGAAAATATGTGGGTATGTTATTCATGCCA
*
35312217 TGTGACAGAAAATATGTGGGTATGTTATTCATGCCA
1 TGTGAAAGAAAATATGTGGGTATGTTATTCATGCCA
35312253 TG
1 TG
35312255 AGACTGATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.35
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGGGTATGTTATTCATGCCA
Found at i:35321761 original size:24 final size:24
Alignment explanation
Indices: 35321713--35321757 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
35321703 GGACCAAATT
*
35321713 AAATTGTAATTTTTACGATAATAA
1 AAATTGTAATTTTTACAATAATAA
35321737 AAATT-TAATTTTTTA-AATAAT
1 AAATTGTAA-TTTTTACAATAAT
35321758 TAAATCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
AAATTGTAATTTTTACAATAATAA
Done.