Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 96 of 125
Found at i:28850479 original size:59 final size:59
Alignment explanation
Indices: 28850323--28850621 Score: 392
Period size: 59 Copynumber: 5.1 Consensus size: 59
28850313 TACCCCGAAT
28850323 CCCCGAATC-TCTAAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTAACC
1 CCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT-A-C
* *
28850382 ACCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC
1 -CCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * *
28850442 CCCCGAATCTTTTAAAATTCCGTTTTTAACCCTGATTTCACACCAAAATTACCATTTT--
1 CCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC-CAAAAATTACCATTTTAC
* * * *
28850500 CCCCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTTACCAAAAATTGCCATTTTAC
1 CCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * * *
28850559 CCCCGAATCTTTTAAAATTCCATTTTTAATCTCGATTACACC-AAAATTACCATTTTTC
1 CCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
28850617 CCCCG
1 CCCCG
28850622 GGTATCCATA
Statistics
Matches: 212, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
57 14 0.07
58 56 0.26
59 72 0.34
60 24 0.11
61 13 0.06
62 33 0.16
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (59 bp):
CCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:28850621 original size:117 final size:116
Alignment explanation
Indices: 28850323--28850621 Score: 408
Period size: 117 Copynumber: 2.5 Consensus size: 116
28850313 TACCCCGAAT
* * *
28850323 CCCCGAATC-TCTAAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTAACCACCC
1 CCCCGAATCTTTTAAAATTCCATTTTTAA-CCCGATTACACC-AAAATTACCATTTT--TC-CCC
*
28850386 CGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC
61 CGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
28850442 CCCCGAATCTTTTAAAATTCCGTTTTTAACCCTGATTTCACACCAAAATTACCA-TTTT-CCCCG
1 CCCCGAATCTTTTAAAATTCCATTTTTAACCC-GA-TT-ACACCAAAATTACCATTTTTCCCCCG
* * *
28850505 AAGCTTCTAAAATTCCGTTTTTAACCCCGATTTTACCAAAAATTGCCATTTTAC
63 AAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
28850559 CCCCGAATCTTTTAAAATTCCATTTTTAATCTCGATTACACCAAAATTACCATTTTTCCCCCG
1 CCCCGAATCTTTTAAAATTCCATTTTTAA-CCCGATTACACCAAAATTACCATTTTTCCCCCG
28850622 GGTATCCATA
Statistics
Matches: 162, Mismatches: 10, Indels: 18
0.85 0.05 0.09
Matches are distributed among these distances:
115 15 0.09
116 6 0.04
117 90 0.56
118 2 0.01
119 9 0.06
120 13 0.08
121 11 0.07
122 12 0.07
123 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (116 bp):
CCCCGAATCTTTTAAAATTCCATTTTTAACCCGATTACACCAAAATTACCATTTTTCCCCCGAAG
CTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:28850640 original size:117 final size:116
Alignment explanation
Indices: 28850323--28850656 Score: 358
Period size: 117 Copynumber: 2.8 Consensus size: 116
28850313 TACCCCGAAT
* * *
28850323 CCCCGAATC-TCTAAAATTCCA-TTTTAACCCCGATTTCAC-CAAAAATTACCATTTTAACCACC
1 CCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACACCAAAATTACCATTTT-----CC
* * * *
28850385 CCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC
61 CCG-AGCTTCCAAAATCCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
28850442 CCCCGAATCTTTTAAAATTCCGTTTTTAACCCTGATTTCACACCAAAATTACCATTTTCCCCGAA
1 CCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACACCAAAATTACCATTTTCCCCG-A
* * * *
28850507 GCTTCTAAAATTCCGTTTTTAACCCCGATTTTACCAAAAATTGCCATTTTAC
65 GCTTCCAAAATCCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
28850559 CCCCGAATCTTTTAAAATTCCATTTTTAA-TCTCGA-TT-ACACCAAAATTACCATTTTTCCCCC
1 CCCCGAATCTTTTAAAATTCCATTTTTAACCCT-GATTTCACACCAAAATTACCA-TTTT-CCCC
* * * *
28850621 G-GGTATCCATAAGTCCCGTTTTTCATCCCGATTTCA
63 GAGCT-TCCA-AAATCCCGTTTTTAACCCCGATTTCA
28850657 TCATTTGTCA
Statistics
Matches: 190, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
115 17 0.09
116 11 0.06
117 111 0.58
119 9 0.05
120 10 0.05
121 17 0.09
122 15 0.08
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (116 bp):
CCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTCACACCAAAATTACCATTTTCCCCGAG
CTTCCAAAATCCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:28862446 original size:161 final size:163
Alignment explanation
Indices: 28862271--28862583 Score: 470
Period size: 162 Copynumber: 1.9 Consensus size: 163
28862261 TTTATAATTT
* * *
28862271 AGTCCTTTGACTGTTTGACTGTACCATAGACTGCCACGTGTCA-CTTTTTGGATCATTTCTGCAT
1 AGTCCTTTGACTGTTTGACTGCACCAGAGACTGCCACGTGTCATCTTTTTGGATCATTTATGCAT
* *
28862335 TTAGTCCTTTTTATTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTACGA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCACAAATCAACTTTTA-TTTAATTACAA
*
28862398 AATTGGCCCAATAATTTTTCAAGGTTTATAAACC
130 AATTGGCCCAAAAATTTTTCAAGGTTTATAAACC
* ** * *
28862432 AGTCCTTTGACTGTTTGACTGCACTAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTATGTAT
1 AGTCCTTTGACTGTTTGACTGCACCAGAGACTGCCACGTGTCATCTTTTTGGATCATTTATGCAT
* *
28862497 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCATAAATCGACTTTTATTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCACAAATCAACTTTTATTTAATTACAAA
*
28862562 ATTGGTCCAAAAATTTTTCAAG
131 ATTGGCCCAAAAATTTTTCAAG
28862584 ATTTTCAAAT
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 38 0.28
162 55 0.41
163 38 0.28
164 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (163 bp):
AGTCCTTTGACTGTTTGACTGCACCAGAGACTGCCACGTGTCATCTTTTTGGATCATTTATGCAT
TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCACAAATCAACTTTTATTTAATTACAAA
ATTGGCCCAAAAATTTTTCAAGGTTTATAAACC
Found at i:28862628 original size:162 final size:161
Alignment explanation
Indices: 28862302--28862637 Score: 412
Period size: 162 Copynumber: 2.1 Consensus size: 161
28862292 TACCATAGAC
* *
28862302 TGCCACGTGTCACTTTTTGGATCATTTCTGCATTTAGTCCTTTTTATTTTTTATTTGTTTTAATT
1 TGCCACGTGTCACTTTTTGGATCATTTATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATT
* * *
28862367 TAATCCCAAATCAACTTTATTTTAATTACGAAATTGGCCCAATAATTTTTCAAGGTTTATAAACC
66 TAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATTTATAAACC
* * * *
28862432 AGTCCTTTGACTGTTTGACTGCACTAGAGGT
131 AGTCCCTTGACTGCTGGACTACACTAGAGGT
* *
28862463 TGCCACGTGTCATCTTTTTGGATTATTTATGTATTTAGTCCTTTTTATTTTTAATTTGTTTTAAT
1 TGCCACGTGTCA-CTTTTTGGATCATTTATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAAT
* * *
28862528 TTAATCCATAAATCGACTTT-TATTTAATTACAAAATTGGTCCAAAAATTTTTCAAGATTT-TCA
65 TTAATCC-CAAATCAACTTTAT-TTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATTTAT-A
*** * *
28862591 AATTGGTCCCTTGACCT-CTGGA-TAC-CTGTGGGGT
127 AACCAGTCCCTTGA-CTGCTGGACTACACT-AGAGGT
28862625 TGCCACGTGTCAC
1 TGCCACGTGTCAC
28862638 CTGTTTATGG
Statistics
Matches: 150, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
161 15 0.10
162 75 0.50
163 58 0.39
164 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.45
Consensus pattern (161 bp):
TGCCACGTGTCACTTTTTGGATCATTTATGCATTTAGTCCTTTTTATTTTTAATTTGTTTTAATT
TAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATTTATAAACC
AGTCCCTTGACTGCTGGACTACACTAGAGGT
Found at i:28862714 original size:30 final size:29
Alignment explanation
Indices: 28862680--28862782 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 29
28862670 AAATTGTCCA
28862680 AAAATTACATTTTGACCCCAAACTTTTCCC
1 AAAATTACATTTTGACCCCAAACTTTT-CC
* *
28862710 AAAATTACATTTTGACCTCAAAACTTTACC
1 AAAATTACATTTTGACC-CCAAACTTTTCC
*
28862740 AAAATTACGTTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCC-AAACTTTTCC
28862770 AAAATTACATTTT
1 AAAATTACATTTT
28862783 TAACCCCGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
29 1 0.02
30 56 0.86
31 8 0.12
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAACTTTTCC
Found at i:28862842 original size:59 final size:59
Alignment explanation
Indices: 28862770--28863166 Score: 571
Period size: 59 Copynumber: 6.7 Consensus size: 59
28862760 AAACTTTTCC
* * * *
28862770 AAAATTACATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTCTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * * *
28862829 AAAATTCCGTTTTTAACCTCGATTTCATCAAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * *
28862888 AAAATTTCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
** *
28862947 AAAATTCTGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATATTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* ** * * *
28863006 AAAATTCTATTTTTAACCCTAATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
*
28863065 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTGCCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * *
28863124 AAAATTCCATTTTTAATCTCGATTACACC-AAAATTACCATTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTT
28863167 GCCTCCGGGT
Statistics
Matches: 301, Mismatches: 37, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
58 13 0.04
59 288 0.96
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
Found at i:28868514 original size:19 final size:18
Alignment explanation
Indices: 28868470--28868518 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
28868460 ATTGTAAATA
*
28868470 TTTTT-ATAATTTTTTAT
1 TTTTTAATAATTTTATAT
**
28868487 TTTAAAATAATATTTATAT
1 TTTTTAATAAT-TTTATAT
28868506 TTTTTAATAATTT
1 TTTTTAATAATTT
28868519 CAAAGTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATAATTTTATAT
Found at i:28884940 original size:30 final size:31
Alignment explanation
Indices: 28884892--28884955 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
28884882 ATAAAAAAAT
* *
28884892 ATTTTTAAAAAAT-TTAAA-ATTAAATTATA
1 ATTTTTAAAAAATATAAAATATTAAATTAAA
*
28884921 ATTTTTACGAAAATATAAAATATTAAATTAAA
1 ATTTTTA-AAAAATATAAAATATTAAATTAAA
28884953 ATT
1 ATT
28884956 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 5 0.17
31 4 0.14
32 13 0.45
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATTTTTAAAAAATATAAAATATTAAATTAAA
Found at i:28893982 original size:15 final size:14
Alignment explanation
Indices: 28893907--28894011 Score: 68
Period size: 14 Copynumber: 7.4 Consensus size: 14
28893897 TATAAACCTT
* *
28893907 AAACCCTAAATTTA
1 AAACCTTAAATTCA
*
28893921 AAACCTTAAATTCG
1 AAACCTTAAATTCA
** * *
28893935 AATTCATATATTCA
1 AAACCTTAAATTCA
** *
28893949 AAACCTTAAAACCCT
1 AAACCTT-AAATTCA
28893964 AAACCTTAAAATTCA
1 AAACCTT-AAATTCA
*
28893979 AAACCCTT-AATTAA
1 AAA-CCTTAAATTCA
*
28893993 AAACCTTAAATTTA
1 AAACCTTAAATTCA
28894007 AAACC
1 AAACC
28894012 CTATAAATTA
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
13 4 0.06
14 42 0.62
15 18 0.26
16 4 0.06
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.29
Consensus pattern (14 bp):
AAACCTTAAATTCA
Found at i:28893995 original size:14 final size:15
Alignment explanation
Indices: 28893967--28894021 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 15
28893957 AAACCCTAAA
*
28893967 CCTTAAAATTCAAAAC
1 CCTT-AAATTAAAAAC
28893983 CCTT-AATTAAAAA-
1 CCTTAAATTAAAAAC
*
28893996 CCTTAAATTTAAAAC
1 CCTTAAATTAAAAAC
28894011 CCTATAAATTA
1 CCT-TAAATTA
28894022 CAATCTCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.12
14 16 0.48
15 3 0.09
16 10 0.30
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CCTTAAATTAAAAAC
Found at i:28893999 original size:13 final size:14
Alignment explanation
Indices: 28893964--28894021 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
28893954 TTAAAACCCT
28893964 AAACCTTAAAATTCAA
1 AAACCTT-AAATT-AA
*
28893980 AACCCTT-AATTAA
1 AAACCTTAAATTAA
28893993 AAACCTTAAATTTAA
1 AAACCTTAAA-TTAA
*
28894008 AACCCTATAAATTA
1 AAACCT-TAAATTA
28894022 CAATCTCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 8 0.22
14 6 0.17
15 12 0.33
16 10 0.28
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (14 bp):
AAACCTTAAATTAA
Found at i:28895440 original size:24 final size:24
Alignment explanation
Indices: 28895407--28895462 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
28895397 TGGAACCACC
28895407 ATACATGGAGTTGGATATTCATTTT
1 ATAC-TGGAGTTGGATATTCATTTT
* *
28895432 CTACTGGAGTTGGATCTTCATTTT
1 ATACTGGAGTTGGATATTCATTTT
28895456 ATACTGG
1 ATACTGG
28895463 TTCCACATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.43
Consensus pattern (24 bp):
ATACTGGAGTTGGATATTCATTTT
Found at i:28895984 original size:19 final size:19
Alignment explanation
Indices: 28895945--28895983 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28895935 ACCTTTTTAA
28895945 TTCTCCTCTTCTTCTCCTT
1 TTCTCCTCTTCTTCTCCTT
*
28895964 TTCTCCTCTT-TTCTTCTT
1 TTCTCCTCTTCTTCTCCTT
28895982 TT
1 TT
28895984 TATTTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCTCCTCTTCTTCTCCTT
Found at i:28897199 original size:32 final size:30
Alignment explanation
Indices: 28897153--28897220 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
28897143 AGGGTTTTGG
28897153 TTTA-TTACCAAAATAAAATATAAAAAAAATA
1 TTTATTTACCAAAAT--AATATAAAAAAAATA
* * *
28897184 TTTATTTACTAAAATAATATACAAAAATTA
1 TTTATTTACCAAAATAATATAAAAAAAATA
28897214 TTTATTT
1 TTTATTT
28897221 TATTTGACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 20 0.61
31 4 0.12
32 9 0.27
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (30 bp):
TTTATTTACCAAAATAATATAAAAAAAATA
Found at i:28897238 original size:36 final size:35
Alignment explanation
Indices: 28897184--28897256 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 35
28897174 AAAAAAAATA
*
28897184 TTTATTTACTAAAATAATA-TACAAAAATTATTTAT
1 TTTATTTACTAAAATAATATTA-AAAAATTATTAAT
*
28897219 TTTATTTGACTAAAGTAATATTAAAAAATTATTAAT
1 TTTATTT-ACTAAAATAATATTAAAAAATTATTAAT
28897255 TT
1 TT
28897257 AATAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 25 0.74
37 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (35 bp):
TTTATTTACTAAAATAATATTAAAAAATTATTAAT
Found at i:28898339 original size:9 final size:9
Alignment explanation
Indices: 28898325--28898354 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
28898315 ATAACTTGTT
28898325 AAAATAATA
1 AAAATAATA
28898334 AAAATAATA
1 AAAATAATA
28898343 AAAATAATA
1 AAAATAATA
28898352 AAA
1 AAA
28898355 TATGTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:28899520 original size:16 final size:16
Alignment explanation
Indices: 28899499--28899547 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
28899489 GGATGGAGAT
28899499 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
28899515 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
28899530 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
28899545 ATT
1 ATT
28899548 TAGAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:28900191 original size:13 final size:13
Alignment explanation
Indices: 28900173--28900201 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28900163 ACAAATTAAA
28900173 AAATTTTAAAAAT
1 AAATTTTAAAAAT
28900186 AAA-TTTAAAAAT
1 AAATTTTAAAAAT
28900198 AAAT
1 AAAT
28900202 ACATTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:28904398 original size:27 final size:27
Alignment explanation
Indices: 28904357--28904418 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
28904347 TGCGTATCTG
*
28904357 CAAAAACATGCAAATCATTCAT-TCAAA
1 CAAAAACATGAAAATCATTCATAT-AAA
*
28904384 CGAAAACATGAAAATCATTCATATAAA
1 CAAAAACATGAAAATCATTCATATAAA
28904411 CAAAAACA
1 CAAAAACA
28904419 AAGATGTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.19
Consensus pattern (27 bp):
CAAAAACATGAAAATCATTCATATAAA
Found at i:28911941 original size:20 final size:19
Alignment explanation
Indices: 28911918--28911972 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
28911908 TTTTTATACC
*
28911918 TTTTTAATAATTTTAATGAT
1 TTTTTAA-AATTTTAATGAA
**
28911938 TTTTTAAAATGTTTTTTGAA
1 TTTTTAAAAT-TTTAATGAA
28911958 TTTTTAAAATTTTAA
1 TTTTTAAAATTTTAA
28911973 AATTTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTTAAAATTTTAATGAA
Found at i:28913599 original size:30 final size:31
Alignment explanation
Indices: 28913563--28913621 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
28913553 TCTTACATAC
* *
28913563 CAAAAAATATATTTGATATCTTTT-TTGTGT
1 CAAAAAAAATATTTGATAACTTTTATTGTGT
28913593 CAAAAAAAATATTTGATAACTTTTATTGT
1 CAAAAAAAATATTTGATAACTTTTATTGT
28913622 TCTGATAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (31 bp):
CAAAAAAAATATTTGATAACTTTTATTGTGT
Found at i:28913872 original size:30 final size:30
Alignment explanation
Indices: 28913833--28913908 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
28913823 AATAAATTAC
28913833 AAAATATTATAAAAAAT-AT-GGAAATTTATTT
1 AAAA-ATTATAAAAAATCATAGGAAA-TTA-TT
* *
28913864 AAAAATTATTAAAAATCATAGTAAATTATT
1 AAAAATTATAAAAAATCATAGGAAATTATT
28913894 -AAAATTATTAAAAAA
1 AAAAATTA-TAAAAAA
28913909 ACTTAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.18
30 19 0.49
31 9 0.23
32 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAAATTATAAAAAATCATAGGAAATTATT
Found at i:28913877 original size:10 final size:10
Alignment explanation
Indices: 28913862--28913907 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
28913852 GGAAATTTAT
28913862 TTAAAAATTA
1 TTAAAAATTA
*
28913872 TTAAAAATCA
1 TTAAAAATTA
*
28913882 -TAGTAAATTA
1 TTA-AAAATTA
28913892 TT-AAAATTA
1 TTAAAAATTA
28913901 TTAAAAA
1 TTAAAAA
28913908 AACTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 10 0.34
10 18 0.62
11 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:28917964 original size:23 final size:23
Alignment explanation
Indices: 28917927--28917980 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
28917917 ATTTCACTGT
28917927 TTTATAATATATTTA-AAATTAAAA
1 TTTATAATATATTTATAAA-T-AAA
*
28917951 TTTAT-ATATTTTTATAAATAAA
1 TTTATAATATATTTATAAATAAA
28917973 TTTA-AATA
1 TTTATAATA
28917981 AAAATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 10 0.37
23 9 0.33
24 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTATAATATATTTATAAATAAA
Found at i:28930480 original size:27 final size:27
Alignment explanation
Indices: 28930450--28930501 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
28930440 CTTGATTTAG
28930450 ATTCGAAGCATGTTATTCTACTAGTAT
1 ATTCGAAGCATGTTATTCTACTAGTAT
28930477 ATTCGAAGCATGTTATTCTACTAGT
1 ATTCGAAGCATGTTATTCTACTAGT
28930502 TAGCAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (27 bp):
ATTCGAAGCATGTTATTCTACTAGTAT
Found at i:28930511 original size:22 final size:26
Alignment explanation
Indices: 28930453--28930516 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
28930443 GATTTAGATT
*
28930453 CGAAGCATGTTATTCTACTAGTATATT
1 CGAA-CATGTTATTCTACTAGTATATG
28930480 CGAAGCATGTTATTCTACTAGT-TA-G
1 CGAA-CATGTTATTCTACTAGTATATG
28930505 C-AA-ATGTTATTC
1 CGAACATGTTATTC
28930517 CATTGTATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 9 0.25
24 2 0.06
25 1 0.03
26 2 0.06
27 22 0.61
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (26 bp):
CGAACATGTTATTCTACTAGTATATG
Found at i:28932602 original size:18 final size:18
Alignment explanation
Indices: 28932581--28932640 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
28932571 TTGACGACCA
*
28932581 TGATGATGAGCTTGTATC
1 TGATGATGAGTTTGTATC
28932599 TGATGA--A-TTTGATGATC
1 TGATGATGAGTTTG-T-ATC
28932616 TGGATGATGAGTTTGTATC
1 T-GATGATGAGTTTGTATC
28932635 TGATGA
1 TGATGA
28932641 ATTTGATGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 4 0.11
18 16 0.46
19 4 0.11
20 2 0.06
21 4 0.11
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (18 bp):
TGATGATGAGTTTGTATC
Found at i:28932623 original size:21 final size:19
Alignment explanation
Indices: 28932599--28932670 Score: 53
Period size: 21 Copynumber: 3.8 Consensus size: 19
28932589 AGCTTGTATC
28932599 TGATGAATTTGATGATCTGGA
1 TGATGAATTTGATGATC--GA
*
28932620 TGATGAGTTTG-T-ATC--
1 TGATGAATTTGATGATCGA
*
28932635 TGATGAATTTGATGACCAGAA
1 TGATGAATTTGATGATC-G-A
*
28932656 TGATGAGTTTGATGA
1 TGATGAATTTGATGA
28932671 AGTAGAAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 10 0.24
16 1 0.02
17 2 0.05
19 3 0.07
20 1 0.02
21 24 0.59
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.38
Consensus pattern (19 bp):
TGATGAATTTGATGATCGA
Found at i:28932663 original size:36 final size:35
Alignment explanation
Indices: 28932557--28932666 Score: 148
Period size: 36 Copynumber: 3.1 Consensus size: 35
28932547 TGTTGGAAAG
* * *
28932557 TGTATCTGATGAAGTTGACGACCATGATGATGAGCT
1 TGTATCTGATGAATTTGATGACCA-GATGATGAGTT
**
28932593 TGTATCTGATGAATTTGATGATCTGGATGATGAGTT
1 TGTATCTGATGAATTTGATGA-CCAGATGATGAGTT
28932629 TGTATCTGATGAATTTGATGACCAGAATGATGAGTT
1 TGTATCTGATGAATTTGATGACCAG-ATGATGAGTT
28932665 TG
1 TG
28932667 ATGAAGTAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 2 0.03
36 62 0.95
37 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (35 bp):
TGTATCTGATGAATTTGATGACCAGATGATGAGTT
Found at i:28941299 original size:22 final size:22
Alignment explanation
Indices: 28941274--28941328 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 22
28941264 AATTACAACT
*
28941274 ACAAATAATATTCATTCGAATA
1 ACAAAAAATATTCATTCGAATA
28941296 ACAAAAAAAAAATATTCATTCGAATA
1 AC----AAAAAATATTCATTCGAATA
28941322 ACAAAAA
1 ACAAAAA
28941329 GGAGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
22 7 0.25
26 21 0.75
ACGTcount: A:0.60, C:0.13, G:0.04, T:0.24
Consensus pattern (22 bp):
ACAAAAAATATTCATTCGAATA
Found at i:28942358 original size:14 final size:13
Alignment explanation
Indices: 28942335--28942364 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
28942325 CTGTTAAATT
28942335 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
28942348 GAAAGAAAAGAAAA
1 GAAA-AAAAGAAAA
28942362 GAA
1 GAA
28942365 TATTGTCGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:28959590 original size:20 final size:18
Alignment explanation
Indices: 28959559--28959616 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
28959549 TTTTATCAAT
28959559 ATTAAACAATATATTATAA
1 ATTAAACAATAT-TTATAA
28959578 ATTAAAGCAATATTTAT--
1 ATTAAA-CAATATTTATAA
* * *
28959595 ATTAAATAATAATTATGA
1 ATTAAACAATATTTATAA
28959613 ATTA
1 ATTA
28959617 TTAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 4 0.12
19 10 0.29
20 6 0.18
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAACAATATTTATAA
Found at i:28964592 original size:22 final size:22
Alignment explanation
Indices: 28964567--28964608 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28964557 TTGGTGCATG
*
28964567 ATTAACATATGATATAAATTCA
1 ATTAAAATATGATATAAATTCA
* *
28964589 ATTAAAATTTTATATAAATT
1 ATTAAAATATGATATAAATT
28964609 AGATAATAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTAAAATATGATATAAATTCA
Found at i:28966630 original size:19 final size:19
Alignment explanation
Indices: 28966588--28966635 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
28966578 TTTCATTTTT
*
28966588 TTTTTATAAATTTTACAAT-
1 TTTTTA-AAATTTTAAAATA
*
28966607 GTTTTAAAATTTTAAAACTA
1 TTTTTAAAATTTTAAAA-TA
28966627 TTTTTAAAA
1 TTTTTAAAA
28966636 GCTACGTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.42
19 6 0.25
20 8 0.33
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTTAAAATTTTAAAATA
Found at i:28968336 original size:20 final size:20
Alignment explanation
Indices: 28968299--28968338 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28968289 AGGTTTTGAT
*
28968299 TTATTTTTTTAATATTTTAA
1 TTATTTTTTAAATATTTTAA
28968319 TTATTTTTATAAAT-TTTTAA
1 TTATTTTT-TAAATATTTTAA
28968339 AATTTTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTTTAAATATTTTAA
Found at i:28968486 original size:29 final size:31
Alignment explanation
Indices: 28968444--28968502 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
28968434 TATATATATA
* *
28968444 TATATTAATATTATAT-TTTT-ATGTTTTTT
1 TATATAAATATTATATATTTTCAAGTTTTTT
28968473 TATATAAATATTATATATTTTCAAGTTTTT
1 TATATAAATATTATATATTTTCAAGTTTTT
28968503 AAAATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 4 0.15
31 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (31 bp):
TATATAAATATTATATATTTTCAAGTTTTTT
Found at i:28970073 original size:19 final size:19
Alignment explanation
Indices: 28970042--28970092 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
28970032 AATTTTAAAA
*
28970042 ATATATGTTTTTATAATTTT
1 ATATAT-TTTTTATAAATTT
28970062 ATATATTTTTTAATAAATTT
1 ATATATTTTTT-ATAAATTT
*
28970082 A-ATGTTTTTTA
1 ATATATTTTTTA
28970093 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.46
20 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
ATATATTTTTTATAAATTT
Found at i:28970093 original size:19 final size:20
Alignment explanation
Indices: 28970042--28970094 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
28970032 AATTTTAAAA
*
28970042 ATATATGTTTTT-ATAATTTT
1 ATATAT-TTTTTAATAAATTT
28970062 ATATATTTTTTAATAAATTT
1 ATATATTTTTTAATAAATTT
*
28970082 A-ATGTTTTTTAAT
1 ATATATTTTTTAAT
28970095 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATATATTTTTTAATAAATTT
Found at i:28970259 original size:22 final size:24
Alignment explanation
Indices: 28970215--28970261 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
28970205 ATGATTTGAC
**
28970215 AAAAATGTAAATTTAAGATTTAAA
1 AAAAATGTAAATAAAAGATTTAAA
28970239 AAAAAT-TAAATAAAAGA-TTAAA
1 AAAAATGTAAATAAAAGATTTAAA
28970261 A
1 A
28970262 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (24 bp):
AAAAATGTAAATAAAAGATTTAAA
Found at i:28971641 original size:16 final size:16
Alignment explanation
Indices: 28971622--28971664 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
28971612 AATTTTTTAA
28971622 ATTTTAAAAAAATTTT
1 ATTTTAAAAAAATTTT
* *
28971638 ATTTGAAAAAATTTTT
1 ATTTTAAAAAAATTTT
28971654 ATTTTAAAAAA
1 ATTTTAAAAAA
28971665 GATCGAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTTTAAAAAAATTTT
Found at i:28981333 original size:11 final size:12
Alignment explanation
Indices: 28981306--28981338 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28981296 TTAATTAACG
*
28981306 TTTAAATTGATT
1 TTTAAATTTATT
28981318 TTTAAATTTA-T
1 TTTAAATTTATT
28981329 TTTAAATTTA
1 TTTAAATTTA
28981339 AATTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:28981340 original size:17 final size:16
Alignment explanation
Indices: 28981318--28981356 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28981308 TAAATTGATT
*
28981318 TTTAAATTTATTTTAAA
1 TTTAAATTTA-ATTAAA
28981335 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
28981351 TTTAAA
1 TTTAAA
28981357 ATAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:28981365 original size:17 final size:16
Alignment explanation
Indices: 28981330--28981372 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28981320 TAAATTTATT
* *
28981330 TTAAATTTAAATTTAA
1 TTAAATTTAAAATAAA
28981346 TTAAATTTAAAATAATA
1 TTAAATTTAAAATAA-A
*
28981363 TTAAACTTAA
1 TTAAATTTAA
28981373 TACAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:28983349 original size:59 final size:57
Alignment explanation
Indices: 28983220--28983417 Score: 170
Period size: 59 Copynumber: 3.4 Consensus size: 57
28983210 TTTAACCCCA
* * *
28983220 AAACTTTAT-AAAATTACATTTTAACCCCAAAACTTTTAAAAATTACATTGTG-CCTC
1 AAACTTT-TCAAAATTACATTTTAACCCTAAAACTTCTAAAAATTACATTTTGCCCTC
* * * *
28983276 ATAAACATTCCAAAATTATATTCTTGACCCTAAAACTTCTAAAAATTACATTTTTGCCCTC
1 --AAACTTTTCAAAATTACATT-TTAACCCTAAAACTTCTAAAAATTACA-TTTTGCCCTC
* * * *
28983337 AAACTTTTCAAAATTCCATTTTTAA-CCTCAAAACTTCCAAAACTTACAATTTTACCCTC
1 AAACTTTTCAAAATTACA-TTTTAACCCT-AAAACTTCTAAAAATTAC-ATTTTGCCCTC
* *
28983396 GAAC-TTTCAAAAATTTCATTTT
1 AAACTTTTC-AAAATTACATTTT
28983418 TCCTTCAAAC
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
58 27 0.23
59 77 0.67
60 7 0.06
61 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (57 bp):
AAACTTTTCAAAATTACATTTTAACCCTAAAACTTCTAAAAATTACATTTTGCCCTC
Found at i:28983375 original size:88 final size:84
Alignment explanation
Indices: 28983209--28983486 Score: 231
Period size: 88 Copynumber: 3.2 Consensus size: 84
28983199 ATTTATTATG
* * * * * *
28983209 TTTTAACCCCAAAACTTTATAAAATTACATTTTAACCC-CAAAACTTTTAAAAATTACA-TTGTG
1 TTTT-ACCCTAAAACTTTA-AAAATTACATTTT-TCCCTC-AAACTTTTCAAAATTCCATTTTTA
*
28983272 CCTCATAAACATTCCAAAATTA-TA
62 CCTCA-AAAC-TTCCAAAATTACAA
28983296 TTCTTGACCCTAAAACTTCTAAAAATTACATTTTTGCCCTCAAACTTTTCAAAATTCCATTTTTA
1 TT-TT-ACCCTAAAACTT-TAAAAATTACATTTTT-CCCTCAAACTTTTCAAAATTCCATTTTT-
28983361 ACCTCAAAACTTCCAAAACTTACAA
61 ACCTCAAAACTTCCAAAA-TTACAA
** * * *
28983386 TTTTACCCTCGAACTTTCAAAAATTTCATTTTTCCTTCAAAC-TTTCAAAAATACCATTTTTGAC
1 TTTTACCCTAAAACTTT-AAAAATTACATTTTTCCCTCAAACTTTTC-AAAATTCCATTTTT-AC
* * **
28983450 CCCAAAATTTCCCAAAATTACGT
63 CTCAAAACTT-CCAAAATTACAA
28983473 TTTTACCCTCAAAA
1 TTTTACCCT-AAAA
28983487 TTCCAAAAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
86 4 0.03
87 47 0.30
88 85 0.53
89 15 0.09
90 8 0.05
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (84 bp):
TTTTACCCTAAAACTTTAAAAATTACATTTTTCCCTCAAACTTTTCAAAATTCCATTTTTACCTC
AAAACTTCCAAAATTACAA
Found at i:28983377 original size:29 final size:30
Alignment explanation
Indices: 28983209--28983534 Score: 162
Period size: 29 Copynumber: 11.1 Consensus size: 30
28983199 ATTTATTATG
* **
28983209 TTTTAACCCCAAAACTTTATAAAATTACA-
1 TTTTAACCTCAAAACTTTCCAAAATTACAT
* **
28983238 TTTTAACCCCAAAACTTTTAAAAATTACA-
1 TTTTAACCTCAAAACTTTCCAAAATTACAT
* * * *
28983267 TTGT-GCCTCATAAACATTCCAAAATTATAT
1 TTTTAACCTCA-AAACTTTCCAAAATTACAT
* * *
28983297 TCTTGACC-CTAAAAC-TTCTAAAAATTACAT
1 TTTTAACCTC-AAAACTTTC-CAAAATTACAT
** * *
28983327 TTTTGCCCTC-AAACTTTTCAAAATTCCAT
1 TTTTAACCTCAAAACTTTCCAAAATTACAT
*
28983356 TTTTAACCTCAAAAC-TTCCAAAACTTACAA
1 TTTTAACCTCAAAACTTTCCAAAA-TTACAT
* * * *
28983386 TTTTACCCTC-GAACTTTCAAAAATTTCAT
1 TTTTAACCTCAAAACTTTCCAAAATTACAT
*
28983415 TTTT--CCTTC-AAACTTT-CAAAAATACCAT
1 TTTTAACC-TCAAAACTTTCCAAAATTA-CAT
* * *
28983443 TTTTGACCCCAAAA-TTTCCCAAAATTACGT
1 TTTTAACCTCAAAACTTT-CCAAAATTACAT
* * *
28983473 TTTTACCCTCAAAA--TTCCAAAAATTTCAC
1 TTTTAACCTCAAAACTTTCC-AAAATTACAT
* * * *
28983502 TTTAAACCCCGACACTTT-CAAAATTACCAT
1 TTTTAACCTCAAAACTTTCCAAAATTA-CAT
28983532 TTT
1 TTT
28983535 AGCCCGAATA
Statistics
Matches: 227, Mismatches: 49, Indels: 41
0.72 0.15 0.13
Matches are distributed among these distances:
27 7 0.03
28 21 0.09
29 114 0.50
30 72 0.32
31 13 0.06
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTTAACCTCAAAACTTTCCAAAATTACAT
Found at i:28983418 original size:59 final size:59
Alignment explanation
Indices: 28983307--28983497 Score: 171
Period size: 59 Copynumber: 3.3 Consensus size: 59
28983297 TCTTGACCCT
* * *
28983307 AAAACTTCTAAAAATTACATTTTTGCCCTCAAACTTTTCAAAATTCCATTTTTAACCTC
1 AAAACTTCCAAAAATTACAATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACCTC
* * *
28983366 AAAACTTCCAAAACTTACAATTTTACCCTCGAAC-TTTCAAAAATTTCATTTTT--CCTTC
1 AAAACTTCCAAAAATTACAATTTTACCCTCAAACTTTTC-AAAATTCCATTTTTAACC-TC
* * * * * * *
28983424 -AAACTTTCAAAAA-TACCATTTTTGACCC-CAAAATTTCCCAAAATTACGTTTTTACCCTC
1 AAAACTTCCAAAAATTA-CAATTTT-ACCCTCAAACTTT-TCAAAATTCCATTTTTAACCTC
28983483 AAAA-TTCCAAAAATT
1 AAAACTTCCAAAAATT
28983498 TCACTTTAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
56 2 0.02
57 22 0.21
58 24 0.22
59 53 0.50
60 6 0.06
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAACTTCCAAAAATTACAATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACCTC
Found at i:28983477 original size:87 final size:88
Alignment explanation
Indices: 28983302--28983500 Score: 235
Period size: 87 Copynumber: 2.3 Consensus size: 88
28983292 TATATTCTTG
* * * *
28983302 ACCCT-AAAACTTCTAAAAATTACATTTTTGCCCTCAAACTTTTCAAAATTCCATTTTTAACCTC
1 ACCCTCAAAA-TTCCAAAAATTTCATTTTTGCCCTCAAACTTTTCAAAATACCATTTTTAACCCC
28983366 AAAACTTCCAAAACTTACAATTTT
65 AAAACTTCCAAAACTTACAATTTT
* * * * *
28983390 ACCCTCGAACTTTCAAAAATTTCATTTTT-CCTTCAAAC-TTTCAAAAATACCATTTTTGACCCC
1 ACCCTCAAAATTCCAAAAATTTCATTTTTGCCCTCAAACTTTTC-AAAATACCATTTTTAACCCC
* **
28983453 AAAATTTCCCAAAA-TTACGTTTTT
65 AAAACTT-CCAAAACTTACAATTTT
28983477 ACCCTCAAAATTCCAAAAATTTCA
1 ACCCTCAAAATTCCAAAAATTTCA
28983501 CTTTAAACCC
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
86 4 0.04
87 60 0.65
88 27 0.29
89 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (88 bp):
ACCCTCAAAATTCCAAAAATTTCATTTTTGCCCTCAAACTTTTCAAAATACCATTTTTAACCCCA
AAACTTCCAAAACTTACAATTTT
Found at i:28990462 original size:12 final size:12
Alignment explanation
Indices: 28990428--28990559 Score: 100
Period size: 12 Copynumber: 11.2 Consensus size: 12
28990418 TTCAATAAAT
28990428 AAAAGAAAAGAAA
1 AAAAGAAAAG-AA
*
28990441 AAAAGAAAAAAA
1 AAAAGAAAAGAA
28990453 GAAAAGAAAA-ATA
1 -AAAAGAAAAGA-A
*
28990466 AGAAGAAAA-AA
1 AAAAGAAAAGAA
*
28990477 AAGAGAAAAGAA
1 AAAAGAAAAGAA
28990489 AAAAG--AAGAA
1 AAAAGAAAAGAA
*
28990499 AAAAG-AAGGAGA
1 AAAAGAAAAGA-A
28990511 AAAAGAAAA-AGA
1 AAAAGAAAAGA-A
*
28990523 GAAAGAAAA-AA
1 AAAAGAAAAGAA
*
28990534 CAAA-AAAAGAGA
1 AAAAGAAAAGA-A
28990546 AAAAGAAAAGAA
1 AAAAGAAAAGAA
28990558 AA
1 AA
28990560 GGAGAGGTCG
Statistics
Matches: 100, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
10 14 0.14
11 16 0.16
12 43 0.43
13 27 0.27
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:28990475 original size:26 final size:25
Alignment explanation
Indices: 28990428--28990552 Score: 98
Period size: 27 Copynumber: 4.8 Consensus size: 25
28990418 TTCAATAAAT
28990428 AAAAGAAAAG--AAAAA-AAG-AAA
1 AAAAGAAAAGAAAAAAAGAAGAAAA
28990449 AAAAGAAAAGAAAAATAAGAAGAAAA
1 AAAAGAAAAGAAAAA-AAGAAGAAAA
28990475 AAAAGAGAAA-AGAAAAAAGAAGAAAAA
1 AAAAGA-AAAGA-AAAAAAGAAG-AAAA
*
28990502 AGAAGGAGAAAAAGAAAAAGAGAAAGAAAA
1 A-AA--AG-AAAAGAAAAAAAG-AAGAAAA
* *
28990532 AACAAAAAAAGAGAAAAAGAA
1 AA-AAGAAAAGAAAAAAAGAA
28990553 AAGAAAAGGA
Statistics
Matches: 85, Mismatches: 4, Indels: 25
0.75 0.04 0.22
Matches are distributed among these distances:
21 10 0.12
23 3 0.04
24 2 0.02
25 3 0.04
26 18 0.21
27 23 0.27
28 3 0.04
29 1 0.01
30 17 0.20
31 5 0.06
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (25 bp):
AAAAGAAAAGAAAAAAAGAAGAAAA
Found at i:28990486 original size:28 final size:27
Alignment explanation
Indices: 28990428--28990552 Score: 109
Period size: 26 Copynumber: 4.6 Consensus size: 27
28990418 TTCAATAAAT
28990428 AAAAGAAAAGAAA-AA-AAGAAAA-AAAG
1 AAAAGAAAA-AAAGAAGAA-AAAACAAAG
28990454 AAAAGAAAAATAAGAAGAAAAAA-AAGAG
1 AAAAGAAAAA-AAGAAGAAAAAACAA-AG
*
28990482 AAAAG-AAAAAAGAAGAAAAAAGAAGGAG
1 AAAAGAAAAAAAGAAGAAAAAACAA--AG
*
28990510 AAAAAGAAAAAGAGAAAGAAAAAACAAA-
1 -AAAAGAAAAAAAG-AAGAAAAAACAAAG
*
28990538 AAAAGAGAAAAAGAA
1 AAAAGAAAAAAAGAA
28990553 AAGAAAAGGA
Statistics
Matches: 86, Mismatches: 4, Indels: 18
0.80 0.04 0.17
Matches are distributed among these distances:
25 1 0.01
26 25 0.29
27 25 0.29
28 12 0.14
29 6 0.07
30 6 0.07
31 11 0.13
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (27 bp):
AAAAGAAAAAAAGAAGAAAAAACAAAG
Found at i:28990517 original size:48 final size:48
Alignment explanation
Indices: 28990431--28990559 Score: 133
Period size: 47 Copynumber: 2.6 Consensus size: 48
28990421 AATAAATAAA
28990431 AGAAAAG-AAAAAAAGAAAAAAAGAAAAGAAAAATAAGAAGAAA-AAAAAG
1 AGAAAAGAAAAAAAAG-AAAAAAG-AAAGAAAAATAAGAA-AAAGAAAAAG
* * *
28990480 AGAAAAGAAAAAAGAAGAAAAAAGAAGGAGAAA-AAGAAAAAGAGAAAG
1 AGAAAAGAAAAAA-AAGAAAAAAGAAAGAAAAATAAGAAAAAGAAAAAG
28990528 A-AAAA-ACAAAAAAAGAGAAAAAGAAAAGAAAA
1 AGAAAAGA-AAAAAAAGA-AAAAAG-AAAGAAAA
28990560 GGAGAGGTCG
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
46 5 0.07
47 18 0.26
48 17 0.25
49 14 0.20
50 12 0.17
51 3 0.04
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.01
Consensus pattern (48 bp):
AGAAAAGAAAAAAAAGAAAAAAGAAAGAAAAATAAGAAAAAGAAAAAG
Found at i:28990555 original size:28 final size:28
Alignment explanation
Indices: 28990429--28990559 Score: 110
Period size: 29 Copynumber: 4.5 Consensus size: 28
28990419 TCAATAAATA
28990429 AAAGAAAAGAAAAAAAGAAAAAA-AG-A
1 AAAGAAAAGAAAAAAAGAAAAAAGAGAA
28990455 AAAGAAAA-ATAAGAAGAA-AAAAAAGAGAA
1 AAAGAAAAGA-AA-AA-AAGAAAAAAGAGAA
* *
28990484 AAGAAAAAAGAAGAAAAAAGAAGGAGAAAAAGAA
1 AA-AGAAAAG-A-AAAAAAGAA--A-AAAGAGAA
28990518 AAAGAGAAAGAAAAAACA-AAAAAAGAGAA
1 AAAGA-AAAGAAAAAA-AGAAAAAAGAGAA
28990547 AAAGAAAAGAAAA
1 AAAGAAAAGAAAA
28990560 GGAGAGGTCG
Statistics
Matches: 86, Mismatches: 5, Indels: 26
0.74 0.04 0.22
Matches are distributed among these distances:
25 1 0.01
26 10 0.12
27 8 0.09
28 12 0.14
29 15 0.17
30 8 0.09
31 4 0.05
32 10 0.12
33 5 0.06
34 13 0.15
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (28 bp):
AAAGAAAAGAAAAAAAGAAAAAAGAGAA
Found at i:28990565 original size:21 final size:19
Alignment explanation
Indices: 28990429--28990564 Score: 86
Period size: 19 Copynumber: 7.1 Consensus size: 19
28990419 TCAATAAATA
28990429 AAAGAAAAGAA-AAAAAGA-
1 AAAGAAAA-AAGAAAAAGAG
* *
28990447 AAAAAAGAAAAGAAAAATAAG
1 AAAGAA-AAAAGAAAAA-GAG
* *
28990468 AAGAAAAAAAAGAGAAA-AG
1 AA-AGAAAAAAGAAAAAGAG
*
28990487 AAA-AAAGAAGAAAAA-AG
1 AAAGAAAAAAGAAAAAGAG
*
28990504 AAGGAGAAAAAGAAAAAGAG
1 AAAGA-AAAAAGAAAAAGAG
*
28990524 AAAGAAAAAACAAAAAAAGAG
1 AAAG-AAAAA-AGAAAAAGAG
*
28990545 AAA-AAGAAAAGAAAAGGAG
1 AAAGAA-AAAAGAAAAAGAG
28990564 A
1 A
28990565 GGTCGAGGTG
Statistics
Matches: 96, Mismatches: 11, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
17 14 0.15
18 9 0.09
19 32 0.33
20 13 0.14
21 24 0.25
22 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.01
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAAGAG
Found at i:28992300 original size:78 final size:78
Alignment explanation
Indices: 28992210--28992379 Score: 182
Period size: 78 Copynumber: 2.2 Consensus size: 78
28992200 GAAGATTCTG
* * * * ** * * *
28992210 ATCTCTTGCCCCGAGCCTGGGGCAGATTGA-AGCCATTTGATCTCTTACCCCGAGTTTGGGGCAG
1 ATCTCTTACCCCGAGCCAGAGGCAGATT-ACAACCATCCGACCTCTTACCCCGAGCTTGGAGCAG
*
28992274 ATCATCATCAATCA
65 ATCATCATCAACCA
* * * *
28992288 ATCTCTTACCCCGAGCCAGAGGTAGATTACAACCATCCGACCTTTTACTCCGAGCTTGGAGCAGT
1 ATCTCTTACCCCGAGCCAGAGGCAGATTACAACCATCCGACCTCTTACCCCGAGCTTGGAGCAGA
28992353 TCATCATCAACCA
66 TCATCATCAACCA
28992366 ATCT-TCTACCCCGA
1 ATCTCT-TACCCCGA
28992380 TCACGTGGCG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
77 2 0.03
78 74 0.97
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCAGAGGCAGATTACAACCATCCGACCTCTTACCCCGAGCTTGGAGCAGA
TCATCATCAACCA
Found at i:28993038 original size:204 final size:205
Alignment explanation
Indices: 28992404--28993481 Score: 1342
Period size: 204 Copynumber: 5.3 Consensus size: 205
28992394 ACGATTATTG
* * * * *
28992404 AAACAAACGATGCGATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATTAAACCCAACGCT
1 AAACAAACGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCC-ACGCT
* ** * * * *
28992469 CGATATGAGCAAATTTTCGAACCCTAGCTTCTTGATGAGACACTAAGAAGCAGGTCTAAGCAATA
65 CAATGCGAGCAAATCTTCGAA-CCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATA
* * *
28992534 AAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACGG
129 AAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATCCAG
*
28992599 AGAAGC-AAGTTG
194 AGAAGCGAA-TTA
* * * * *
28992611 AAACAAGCGAGGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
1 AAACAAACGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCACGCTC
* ** * * * *
28992676 GATATGAGCAAATCTTCGAACCTTCGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAA
66 AATGCGAGCAAATCTTCGAACC-TAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAA
* * * *
28992741 AATGGTTAGCTTCCTGATGAGATACAGAAAAGTGGACCAAATTCGTCTTCCTAAGGAGATCCAGA
130 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATCCAGA
28992806 GAAGCGAATTA
195 GAAGCGAATTA
* * *
28992817 AAACAAGCGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTC
1 AAACAAACGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
28992882 AATGCGAGCAAATCTTCGAACCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AA
66 AATGCGAGCAAATCTTCGAACCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAA
* * * *
28992946 ATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTTCTGAGGAGATCCAAAG
131 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATCCAGAG
28993011 AAGCGAATTA
196 AAGCGAATTA
* ** * * *
28993021 AAACAAATGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACTTAATCAAACGCAGGTTC
1 AAACAAACGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * *
28993086 AATGCGAGCAAATCTTTGAACCCAGCTTCCTGATGAGATACTAAGACGCAGGTCGAAGCAATAAA
66 AATGCGAGCAAATCTTCGAACCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAA
* * *
28993151 ATGGTTAGCTTCTTGATGAGATA-TAGAGAAGTGGACCAAATTCGCCTTCCTGATGAGA--CACA
131 ATGGTTAGCTTCCTGATGAGATACT-GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATCCAGA
* *
28993213 GAAGTGAATTG
195 GAAGCGAATTA
** * *
28993224 AAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAAGCTC
1 AAACAAACGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * *
28993289 AATGCGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAA
66 AATGCGAGCAAATCTTCGAA-CCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAA
* * * * * * * *
28993354 AGTGATCAGCTTCCTGATGAGACACAGAGAAGTGAACCAAATCCGTCTTCCTGATGA-AACACAG
130 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATC-CAG
* * *
28993418 AGAAGTGGATCA
194 AGAAGCGAATTA
* * * * *
28993430 CAACAAACGACA-CGGTCATCTTCTTGATGAAATACTGAGAAGAAGGCCAAAT
1 AAACAAACGA-AGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAAT
28993482 TAATGAAATC
Statistics
Matches: 773, Mismatches: 88, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
203 89 0.12
204 277 0.36
205 92 0.12
206 261 0.34
207 54 0.07
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
AAACAAACGAAGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCACGCTC
AATGCGAGCAAATCTTCGAACCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAA
ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATCCAGAG
AAGCGAATTA
Found at i:28993848 original size:6 final size:6
Alignment explanation
Indices: 28993828--28993897 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
28993818 TATATTGATT
* * *
28993828 TTTAAA TTT-AT TTTAAA TTTAAA TTTACCTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
28993876 TTTAAA TTT-AA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
28993898 ATAATATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 18 0.34
6 30 0.57
8 5 0.09
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:28993875 original size:11 final size:11
Alignment explanation
Indices: 28993843--28993897 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
28993833 ATTTATTTTA
28993843 AATTTAAATTT
1 AATTTAAATTT
28993854 ACCTATTTAAATTT
1 A---ATTTAAATTT
*
28993868 ACTTTAAATTT
1 AATTTAAATTT
28993879 AAATTT-AATTT
1 -AATTTAAATTT
28993890 AATTTAAA
1 AATTTAAA
28993898 ATAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 5 0.14
11 17 0.46
12 4 0.11
14 11 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:28993899 original size:17 final size:16
Alignment explanation
Indices: 28993805--28993897 Score: 73
Period size: 17 Copynumber: 5.7 Consensus size: 16
28993795 AACTTTTGAT
*
28993805 TTTAATTAAAATTTATA
1 TTTAATTTAAATTTA-A
* * *
28993822 TTGATTTTTAAATTTAT
1 TTTA-ATTTAAATTTAA
28993839 TTTAAATTTAAATTT-A
1 TTT-AATTTAAATTTAA
** *
28993855 CCT-ATTTAAATTTAC
1 TTTAATTTAAATTTAA
28993870 TTTAAATTTAAATTTAA
1 TTT-AATTTAAATTTAA
28993887 TTTAATTTAAA
1 TTTAATTTAAA
28993898 ATAATATTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 9 0.16
17 28 0.48
18 10 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTAATTTAAATTTAA
Found at i:28995980 original size:29 final size:29
Alignment explanation
Indices: 28995948--28996028 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
28995938 TTGACCTCGA
* **
28995948 AACTTCCAAAAATTCCATTTTTGCCTTTG
1 AACTTCCAAAAATTCCAATTTTGCCTCCG
*
28995977 AACTTTCAAAAATTCCAATTTTGCCTCCG
1 AACTTCCAAAAATTCCAATTTTGCCTCCG
28996006 AACTTCCAAAAATTCCAATTTTG
1 AACTTCCAAAAATTCCAATTTTG
28996029 ACCCTAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (29 bp):
AACTTCCAAAAATTCCAATTTTGCCTCCG
Found at i:28996020 original size:58 final size:59
Alignment explanation
Indices: 28995916--28996028 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 59
28995906 TTTTGACCCC
* * * * *
28995916 TGAACTTTCCATAATTGCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTGCCTT
1 TGAACTTTCAAAAATTCCAATTTTGACCTCGAAACTTCCAAAAATTCCAATTTTGCCTT
28995975 TGAACTTTCAAAAATTCCAATTTTG-CCTCCG-AACTTCCAAAAATTCCAATTTTG
1 TGAACTTTCAAAAATTCCAATTTTGACCT-CGAAACTTCCAAAAATTCCAATTTTG
28996029 ACCCTAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 25 0.52
59 23 0.48
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (59 bp):
TGAACTTTCAAAAATTCCAATTTTGACCTCGAAACTTCCAAAAATTCCAATTTTGCCTT
Found at i:28996085 original size:29 final size:29
Alignment explanation
Indices: 28995928--28996090 Score: 91
Period size: 29 Copynumber: 5.6 Consensus size: 29
28995918 AACTTTCCAT
* * *
28995928 AATTGCATTTTTGACCTCGAAACTTCCAAA
1 AATTCCATTTTTTACCCCGAAA-TTCCAAA
* ** * *
28995958 AATTCCA-TTTTTGCCTTTGAACTTTCAAA
1 AATTCCATTTTTTACC-CCGAAATTCCAAA
* * *
28995987 AATTCCA-ATTTTGCCTCCGAACTTCCAAA
1 AATTCCATTTTTTACC-CCGAAATTCCAAA
* * ** *
28996016 AATTCCAATTTTGACCCTAAAATTTCCCAA
1 AATTCCATTTTTTACCCCGAAA-TTCCAAA
28996046 AATT--ATGTTTTTACCCCGAAATTCCAAA
1 AATTCCAT-TTTTTACCCCGAAATTCCAAA
* *
28996074 AATTTCATTTTTAACCC
1 AATTCCATTTTTTACCC
28996091 GTATACTTTC
Statistics
Matches: 104, Mismatches: 23, Indels: 13
0.74 0.16 0.09
Matches are distributed among these distances:
28 11 0.11
29 66 0.63
30 27 0.26
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.37
Consensus pattern (29 bp):
AATTCCATTTTTTACCCCGAAATTCCAAA
Found at i:28996142 original size:28 final size:28
Alignment explanation
Indices: 28996072--28996142 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 28
28996062 CGAAATTCCA
*
28996072 AAAATTTCATTTTTAACCCGTATACTTTC
1 AAAATTTCATTTTTAACCCGGATAC-TTC
* * *
28996101 AAAATTACCA-TTTTACCCCGGATGC-TC
1 AAAATT-TCATTTTTAACCCGGATACTTC
28996128 GAAAATTTCATTTTT
1 -AAAATTTCATTTTT
28996143 GTTCTCGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
27 4 0.12
28 10 0.29
29 18 0.53
30 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (28 bp):
AAAATTTCATTTTTAACCCGGATACTTC
Found at i:29000851 original size:41 final size:40
Alignment explanation
Indices: 29000806--29000885 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
29000796 GCATTTTTAA
29000806 CGGTGTTTGGACAGAAAACGCCGCAAAAGGCAAAGCAATAG
1 CGGTGTTTGGACA-AAAACGCCGCAAAAGGCAAAGCAATAG
** * * * *
29000847 CGGTGTTTTTACATAAACGCCGTAAAAGGTAGAGCAATA
1 CGGTGTTTGGACAAAAACGCCGCAAAAGGCAAAGCAATA
29000886 ACGGCGCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (40 bp):
CGGTGTTTGGACAAAAACGCCGCAAAAGGCAAAGCAATAG
Found at i:29001902 original size:45 final size:45
Alignment explanation
Indices: 29001828--29001991 Score: 197
Period size: 45 Copynumber: 3.7 Consensus size: 45
29001818 CTCATTTTTG
*
29001828 TATGAATCCGCATGTATGAGTTCGA-CATATCTATGAATCTTCTTC
1 TATGAATCCGCATGTATGAG-TCCACCATATCTATGAATCTTCTTC
* *
29001873 TATGAATCCGCATGTATAAGTCCACCATATTTATGAATCTTCTTC
1 TATGAATCCGCATGTATGAGTCCACCATATCTATGAATCTTCTTC
* * ** *
29001918 TATGAATCTGCATGTATGATTCTGCCATATCTATGAATCTTCTTT
1 TATGAATCCGCATGTATGAGTCCACCATATCTATGAATCTTCTTC
* * * *
29001963 TACGAATTCACATGTATGAGTTCA-CATAT
1 TATGAATCCGCATGTATGAGTCCACCATAT
29001992 AAGAATCCAC
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
44 8 0.08
45 92 0.92
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (45 bp):
TATGAATCCGCATGTATGAGTCCACCATATCTATGAATCTTCTTC
Found at i:29003053 original size:6 final size:6
Alignment explanation
Indices: 29003035--29003100 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
29003025 TCAAATTGAT
* *
29003035 TTTAAA TTT--A TTTAAA TTTAAA TTTAATTA TTTAAA TTT-AC CTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA
*
29003082 TTTAAA TACTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA
29003101 CATTAAAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
4 4 0.08
5 3 0.06
6 30 0.62
7 5 0.10
8 6 0.12
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:29003083 original size:20 final size:20
Alignment explanation
Indices: 29003036--29003074 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29003026 CAAATTGATT
29003036 TTAAATTTATTTAAATTTAAA
1 TTAAA-TTATTTAAATTTAAA
*
29003057 TTTAATTATTTAAATTTA
1 TTAAATTATTTAAATTTA
29003075 CCTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTATTTAAATTTAAA
Found at i:29003098 original size:30 final size:29
Alignment explanation
Indices: 29003035--29003100 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
29003025 TCAAATTGAT
* *
29003035 TTTAAATTTATTTAAATTTAAATTTAATTA
1 TTTAAATTTACTTAAATTTAAATCTAA-TA
29003065 TTTAAATTTACCTTAAATTTAAATACTAA-A
1 TTTAAATTTA-CTTAAATTTAAAT-CTAATA
29003095 TTTAAA
1 TTTAAA
29003101 CATTAAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 17 0.53
31 12 0.38
32 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTAAATTTACTTAAATTTAAATCTAATA
Found at i:29004934 original size:162 final size:163
Alignment explanation
Indices: 29004758--29005092 Score: 462
Period size: 163 Copynumber: 2.1 Consensus size: 163
29004748 AATTTAATCA
* *
29004758 TTTGACTGTTTGACTGCACCAAAAGCTGCCACGTGTCACTTTTTGGCTTATTTATGTATCTGA-T
1 TTTGACTGTTTGACTGCACCAAAAGCTACCACGTGTCACTTTTTGGCTTATTTATGCAT-TGAGT
** * * **
29004822 CCCTGTTA-TTTTTAATTTG-TCTTAATTTAATCC-CTAAATCAACTTTTGCTTAATTATGAAAT
65 CCCTGGCATTTTTTAATATGCT-TTAATTTAATCCTC-AAATCAACTTTTACTTAATTACAAAAT
*
29004884 TGGCCCAAGAATTTTTCAAGATTTATAAATTAGTCC
128 TGGCCCAAGAATTTTTCAAGATTTACAAATTAGTCC
* * *
29004920 TTTGACTGTTTGACTGCACCAGAGGCTACCACGTGTCACTTTTTGGCTTATTTATGCATTTAGTC
1 TTTGACTGTTTGACTGCACCAAAAGCTACCACGTGTCACTTTTTGGCTTATTTATGCATTGAGTC
*
29004985 CCTGGCATTTTTTAATATGCTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAATTGG
66 CCTGGCATTTTTTAATATGCTTTAATTTAATCCTCAAATCAACTTTTACTTAATTACAAAATTGG
* * *
29005050 CCCAATAGTTTTTCAAGATTTACAATTTAGTCC
131 CCCAAGAATTTTTCAAGATTTACAAATTAGTCC
*
29005083 CTTGACTGTT
1 TTTGACTGTT
29005093 GGATGCCTGT
Statistics
Matches: 152, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 2 0.01
162 62 0.41
163 86 0.57
164 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (163 bp):
TTTGACTGTTTGACTGCACCAAAAGCTACCACGTGTCACTTTTTGGCTTATTTATGCATTGAGTC
CCTGGCATTTTTTAATATGCTTTAATTTAATCCTCAAATCAACTTTTACTTAATTACAAAATTGG
CCCAAGAATTTTTCAAGATTTACAAATTAGTCC
Found at i:29005184 original size:30 final size:30
Alignment explanation
Indices: 29005149--29005254 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
29005139 GTTTATAGGT
*
29005149 CCCCAAACAGTCCAAAAATTACCATTTTAC
1 CCCCAAACATTCCAAAAATTACCATTTTAC
* *
29005179 CCCCAAACTTTCC-AAAATT-CCATTTTTAA
1 CCCCAAACATTCCAAAAATTACCA-TTTTAC
* *
29005208 CCCC-GA-TTTCACCAAAAATTACCATTTTAC
1 CCCCAAACATT--CCAAAAATTACCATTTTAC
* *
29005238 CTCCAAACTTTCCAAAA
1 CCCCAAACATTCCAAAA
29005255 TTCCTTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.05
28 4 0.06
29 17 0.27
30 31 0.50
31 4 0.06
32 3 0.05
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.28
Consensus pattern (30 bp):
CCCCAAACATTCCAAAAATTACCATTTTAC
Found at i:29005196 original size:29 final size:28
Alignment explanation
Indices: 29005163--29005410 Score: 142
Period size: 29 Copynumber: 8.5 Consensus size: 28
29005153 AAACAGTCCA
*
29005163 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTAACCCC-AACTTTCC
*
29005192 AAAATT-CCATTTTTAACCCCGA-TTTCACC
1 AAAATTACCA-TTTTAACCCCAACTTT--CC
29005221 AAAAATTACCATTTT-ACCTCCAAACTTTCC
1 -AAAATTACCATTTTAACC-CC-AACTTTCC
* *
29005251 AAAATT-CCTTTTTTAACCCCGA-TTTCACC
1 AAAATTACC-ATTTTAACCCCAACTTT--CC
* *
29005280 AAAAATCACCATTTT-ACCCTCGAACTTTTC
1 -AAAATTACCATTTTAACCC-C-AACTTTCC
* *
29005310 AAAATT-CCATTTTTAACCTCGA-TTTCACC
1 AAAATTACCA-TTTTAACCCCAACTTT--CC
29005339 AAAAATTACCA-TTT-ACCCCTGAACTTTCC
1 -AAAATTACCATTTTAACCCC--AACTTTCC
29005368 AAAATT-CCATTTTTAACCCCAA-TTTCACC
1 AAAATTACCA-TTTTAACCCCAACTTT--CC
29005397 AAAATTACCATTTT
1 AAAATTACCATTTT
29005411 GCCCTCGGGT
Statistics
Matches: 172, Mismatches: 15, Indels: 64
0.69 0.06 0.25
Matches are distributed among these distances:
27 15 0.09
28 23 0.13
29 69 0.40
30 46 0.27
31 13 0.08
32 6 0.03
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTAACCCCAACTTTCC
Found at i:29005252 original size:59 final size:58
Alignment explanation
Indices: 29005160--29005410 Score: 389
Period size: 59 Copynumber: 4.3 Consensus size: 58
29005150 CCCAAACAGT
29005160 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
29005219 CCAAAAATTACCATTTTACCTCCAAACTTTCCAAAATTCCTTTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACC-CCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
29005278 CCAAAAATCACCATTTTACCCTCGAACTTTTCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
29005337 CCAAAAATTACCA-TTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
29005395 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
29005411 GCCCTCGGGT
Statistics
Matches: 178, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
57 11 0.06
58 48 0.27
59 119 0.67
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:29013000 original size:2 final size:2
Alignment explanation
Indices: 29012993--29013028 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29012983 TTTCAGAGTC
29012993 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29013029 TCTTTAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29014085 original size:24 final size:24
Alignment explanation
Indices: 29014058--29014104 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
29014048 GGTTACTATG
29014058 TCATATTTTTTTTAATAATTTCAA
1 TCATATTTTTTTTAATAATTTCAA
*
29014082 TCATATTTTTTTTAGTAATTTCA
1 TCATATTTTTTTTAATAATTTCA
29014105 TTATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (24 bp):
TCATATTTTTTTTAATAATTTCAA
Found at i:29019288 original size:27 final size:29
Alignment explanation
Indices: 29019236--29019297 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
29019226 TAAAAATATA
29019236 AATTTTGAAAATTTTATAAA-TATTTTG-
1 AATTTTGAAAATTTTATAAATTATTTTGT
* *
29019263 AATTTTGAAAATTATTTTGAATT-TTTTGT
1 AATTTTGAAAATT-TTATAAATTATTTTGT
29019292 AATTTT
1 AATTTT
29019298 TGTTTAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.43
28 10 0.33
29 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (29 bp):
AATTTTGAAAATTTTATAAATTATTTTGT
Found at i:29019461 original size:14 final size:14
Alignment explanation
Indices: 29019442--29019471 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29019432 TGACTTGAAT
29019442 AATTCAAATAACTC
1 AATTCAAATAACTC
*
29019456 AATTCAATTAACTC
1 AATTCAAATAACTC
29019470 AA
1 AA
29019472 AGCTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTCAAATAACTC
Found at i:29019706 original size:19 final size:19
Alignment explanation
Indices: 29019678--29019718 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
29019668 TTTAAGATTG
*
29019678 AAAAGGAAAGAAAAAGAAA
1 AAAAGAAAAGAAAAAGAAA
* *
29019697 AAAAGAAAAGGAAAGGAAA
1 AAAAGAAAAGAAAAAGAAA
29019716 AAA
1 AAA
29019719 GTCGCTTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAGAAA
Found at i:29020053 original size:3 final size:3
Alignment explanation
Indices: 29020045--29020081 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
29020035 AACAACCCAC
*
29020045 ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
29020082 AGAGACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:29023629 original size:15 final size:15
Alignment explanation
Indices: 29023609--29023652 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29023599 CTAAAAAATA
29023609 TTTTTATATTTACTT
1 TTTTTATATTTACTT
* * *
29023624 TTTTTAAATTAATTT
1 TTTTTATATTTACTT
29023639 TTTTTATAATTTAC
1 TTTTTAT-ATTTAC
29023653 ATTTACTTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTATATTTACTT
Found at i:29025892 original size:18 final size:18
Alignment explanation
Indices: 29025869--29025911 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
29025859 AAAATTTACT
29025869 ATAATTATATATTTAA-AA
1 ATAATTATA-ATTTAATAA
*
29025887 ATAATTAGAATTTAATAA
1 ATAATTATAATTTAATAA
29025905 A-AATTAT
1 ATAATTAT
29025912 GATAATTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAATTATAATTTAATAA
Found at i:29025899 original size:17 final size:19
Alignment explanation
Indices: 29025869--29025915 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
29025859 AAAATTTACT
*
29025869 ATAATTATATATTTAA-AA
1 ATAATTAGATATTTAATAA
29025887 ATAATTAGA-ATTTAATAA
1 ATAATTAGATATTTAATAA
29025905 A-AATTATGATA
1 ATAATTA-GATA
29025916 ATTACATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 11 0.44
18 13 0.52
19 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
ATAATTAGATATTTAATAA
Found at i:29026324 original size:23 final size:22
Alignment explanation
Indices: 29026264--29026324 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
29026254 GATTGTCCAT
*
29026264 AATTATAA-AAATATATAGAAA
1 AATTATAATAAATATAAAGAAA
* *
29026285 AATTA-CATAAA-ATTAAATTAAA
1 AATTATAATAAATA-TAAA-GAAA
29026307 AATTATAATAAATATAAA
1 AATTATAATAAATATAAA
29026325 AAATTACTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
22 8 0.26
23 9 0.29
24 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AATTATAATAAATATAAAGAAA
Found at i:29032971 original size:34 final size:34
Alignment explanation
Indices: 29032932--29032997 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
29032922 AAGTGCTAAA
*
29032932 AAGTAATATGTTTTAATTGTTTTTATTGCGTTAG
1 AAGTAATATATTTTAATTGTTTTTATTGCGTTAG
29032966 AAGTAATATATTTTAATTGTTTTTATTGCGTT
1 AAGTAATATATTTTAATTGTTTTTATTGCGTT
29032998 TTTGGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (34 bp):
AAGTAATATATTTTAATTGTTTTTATTGCGTTAG
Found at i:29036041 original size:31 final size:32
Alignment explanation
Indices: 29036003--29036080 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 32
29035993 CAAACATTTC
29036003 AAAGTGCTCAAATAAAG-GCCAAAACTTTTTG
1 AAAGTGCTCAAATAAAGAGCCAAAACTTTTTG
* *
29036034 AAAGTGCTCAAAT-AAGAGCTAAACCTTTTTG
1 AAAGTGCTCAAATAAAGAGCCAAAACTTTTTG
29036065 AAAGTGCTCAAATAAA
1 AAAGTGCTCAAATAAA
29036081 AGCTTCTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 3 0.07
31 38 0.88
32 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (32 bp):
AAAGTGCTCAAATAAAGAGCCAAAACTTTTTG
Found at i:29046450 original size:18 final size:19
Alignment explanation
Indices: 29046407--29046452 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
29046397 TATCATTAAT
*
29046407 AATTCAATTTTAATATAAA
1 AATTCAATATTAATATAAA
* *
29046426 TATTCAATATTATTA-AAA
1 AATTCAATATTAATATAAA
29046444 AATTCAATA
1 AATTCAATA
29046453 ATATAAATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAATATTAATATAAA
Found at i:29054452 original size:29 final size:30
Alignment explanation
Indices: 29054420--29054476 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
29054410 TGATTTAATA
*
29054420 TGTAATTGTATATAT-AAACTTTTATTTTG
1 TGTAATTGTATACATGAAACTTTTATTTTG
* *
29054449 TGTAATTTTATACATGAAATTTTTATTT
1 TGTAATTGTATACATGAAACTTTTATTT
29054477 GATCCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.56
Consensus pattern (30 bp):
TGTAATTGTATACATGAAACTTTTATTTTG
Found at i:29056477 original size:20 final size:21
Alignment explanation
Indices: 29056447--29056487 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29056437 CTGAATTTAT
*
29056447 ATTTAATATATGGTTAGTCTA
1 ATTTAATATATGGTTAATCTA
*
29056468 ATTT-ATATATTGTTAATCTA
1 ATTTAATATATGGTTAATCTA
29056488 TATATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (21 bp):
ATTTAATATATGGTTAATCTA
Found at i:29056880 original size:2 final size:2
Alignment explanation
Indices: 29056875--29056901 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29056865 TTTCCTTTTT
29056875 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29056902 TTATGTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29057363 original size:111 final size:113
Alignment explanation
Indices: 29057243--29057453 Score: 254
Period size: 112 Copynumber: 1.9 Consensus size: 113
29057233 CCCTCACATC
* * *
29057243 CCATGGTCGACACCATCTTTTTTACA-T-AAAATTTTTTTTT-GAGTGTTTGCCAAAC-CATAGC
1 CCATGGTCGACACC-CCTTTTTCA-AGTCAAAATTTTTTTTTGGA-TGTTTACC-AACTCATAGC
*
29057304 CGACACTCAA-AAAATACGAAT-AAAAAATTATTTTTTAGGTGTCTATCAAG
62 CGACACCCAATAAAATACGAATAAAAAAATTATTTTTTAGGTGTCTATCAAG
* * * *
29057354 CCATGGTCGACACCCCTTTTTCAAGTCCCAAATTTTTTTTTGGATGTTTACCAACTCATGGCTGG
1 CCATGGTCGACACCCCTTTTTCAAGT-CAAAATTTTTTTTTGGATGTTTACCAACTCATAGCCGA
*
29057419 CACCCAATAAATTACGAATAAAAAAATTATTTTTT
65 CACCCAATAAAATACGAATAAAAAAATTATTTTTT
29057454 TTGTGTGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
109 1 0.01
110 8 0.10
111 17 0.20
112 31 0.37
113 12 0.14
114 15 0.18
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (113 bp):
CCATGGTCGACACCCCTTTTTCAAGTCAAAATTTTTTTTTGGATGTTTACCAACTCATAGCCGAC
ACCCAATAAAATACGAATAAAAAAATTATTTTTTAGGTGTCTATCAAG
Found at i:29057865 original size:55 final size:54
Alignment explanation
Indices: 29057694--29057847 Score: 191
Period size: 55 Copynumber: 2.8 Consensus size: 54
29057684 TATTGGATGA
* * * *
29057694 AAAAAAATATTTTTAAATCTGAAAAATGTGGTTTAGGTCATTGGGTGACAAACAC
1 AAAAAAATATTTTTAAATTTGGAAAATGTGATGTAGGTCATT-GGTGACAAACAC
* * * *
29057749 AAAAAAATACTTTTAAAATTGGAAAAGGTAATGTAGGTCATTAGGTGACAAACAC
1 AAAAAAATATTTTTAAATTTGGAAAATGTGATGTAGGTCATT-GGTGACAAACAC
** *
29057804 TTAAAAATATTTTTAAATTTGGAAAATGTGATGTAAGTCATTGG
1 AAAAAAATATTTTTAAATTTGGAAAATGTGATGTAGGTCATTGG
29057848 ATGGCAAATT
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 2 0.02
55 81 0.98
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (54 bp):
AAAAAAATATTTTTAAATTTGGAAAATGTGATGTAGGTCATTGGTGACAAACAC
Found at i:29069524 original size:12 final size:12
Alignment explanation
Indices: 29069509--29069533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29069499 TTTCTATATT
29069509 ATAGATTATAGG
1 ATAGATTATAGG
29069521 ATAGATTATAGG
1 ATAGATTATAGG
29069533 A
1 A
29069534 AAACGGGTCA
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATAGATTATAGG
Found at i:29070322 original size:12 final size:12
Alignment explanation
Indices: 29070305--29070329 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29070295 CAGAGGCTAT
29070305 TAACAATATTTA
1 TAACAATATTTA
29070317 TAACAATATTTA
1 TAACAATATTTA
29070329 T
1 T
29070330 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:29082911 original size:21 final size:22
Alignment explanation
Indices: 29082885--29082938 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
29082875 TAAAAAATTC
29082885 TTTATTGTTTTCTTG-T-TGTTT
1 TTTATTGTTTTCTTGCTAT-TTT
* *
29082906 TTTATTTTTTTGTTGCTATTTT
1 TTTATTGTTTTCTTGCTATTTT
29082928 TTTATTGTTTT
1 TTTATTGTTTT
29082939 TTCACTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.46
22 14 0.50
23 1 0.04
ACGTcount: A:0.07, C:0.04, G:0.11, T:0.78
Consensus pattern (22 bp):
TTTATTGTTTTCTTGCTATTTT
Found at i:29082946 original size:22 final size:22
Alignment explanation
Indices: 29082903--29082949 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
29082893 TTTCTTGTTG
**
29082903 TTTTTTATTTTTTTGTTGCTAT
1 TTTTTTATTTTTTTGTCACTAT
29082925 TTTTTTATTGTTTTT-TCACTAT
1 TTTTTTATT-TTTTTGTCACTAT
29082947 TTT
1 TTT
29082950 GCTACCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTTTATTTTTTTGTCACTAT
Found at i:29083023 original size:19 final size:17
Alignment explanation
Indices: 29082999--29083033 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
29082989 ATTGTTTGTA
29082999 TATTGTATAATTCTTGTTT
1 TATTGT-TAATT-TTGTTT
29083018 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
29083034 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:29105048 original size:2 final size:2
Alignment explanation
Indices: 29105041--29105073 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29105031 AATATAAAAC
29105041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29105074 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29105078 original size:2 final size:2
Alignment explanation
Indices: 29105073--29105111 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29105063 ATATATATAT
29105073 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29105112 AAGCATTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29106732 original size:26 final size:26
Alignment explanation
Indices: 29106684--29106735 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
29106674 TTTTTTATCG
*
29106684 AATTTTTCGAATCGAATTTGATTTAT
1 AATTTTTCGAATCGAATTGGATTTAT
29106710 AATTTTTCGAATCGAATTGGATTTAT
1 AATTTTTCGAATCGAATTGGATTTAT
29106736 CTCACCCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (26 bp):
AATTTTTCGAATCGAATTGGATTTAT
Found at i:29107508 original size:16 final size:17
Alignment explanation
Indices: 29107489--29107521 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29107479 TAATGTTTGA
29107489 ATTTTTAAAT-AATTTT
1 ATTTTTAAATAAATTTT
*
29107505 ATTTTTTAATAAATTTT
1 ATTTTTAAATAAATTTT
29107522 TTAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTAAATAAATTTT
Found at i:29112155 original size:26 final size:26
Alignment explanation
Indices: 29112070--29112158 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 26
29112060 ATGTAATAAT
* * *
29112070 ATGTGAACATAAATTTAAAAGTGAAC
1 ATGTGAAAATAAAGTTAAAAGTAAAC
* * * *
29112096 ATGTG-AATTAAGTGTTAAAA-TATAT
1 ATGTGAAAATAA-AGTTAAAAGTAAAC
29112121 ATGTGAAAATAAAGTTAAAAGTAAAC
1 ATGTGAAAATAAAGTTAAAAGTAAAC
29112147 ATGTGAAAATAA
1 ATGTGAAAATAA
29112159 TAAAATTTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
25 18 0.37
26 31 0.63
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (26 bp):
ATGTGAAAATAAAGTTAAAAGTAAAC
Found at i:29112198 original size:11 final size:12
Alignment explanation
Indices: 29112175--29112208 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
29112165 TTTAGAGGTT
29112175 AATAATAAAATG
1 AATAATAAAATG
*
29112187 AA-AATAAGATG
1 AATAATAAAATG
29112198 AATAATAAAAT
1 AATAATAAAAT
29112209 ATTTTCGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AATAATAAAATG
Found at i:29114310 original size:28 final size:27
Alignment explanation
Indices: 29114268--29114323 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
29114258 TAATGTCTTG
29114268 TTACTATGATAAAGTTCATTCACTAGCT
1 TTACTATGATAAAGTTCA-TCACTAGCT
*
29114296 TTACTATGATGAAGTTCATCACTAGCT
1 TTACTATGATAAAGTTCATCACTAGCT
29114323 T
1 T
29114324 GAAAAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (27 bp):
TTACTATGATAAAGTTCATCACTAGCT
Found at i:29118106 original size:26 final size:26
Alignment explanation
Indices: 29118068--29118124 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
29118058 GTACTTGACA
* *
29118068 TTTTTTCCTAATTTGATACCTAAATG
1 TTTTTACCCAATTTGATACCTAAATG
* *
29118094 TTTTTACCCAATTTGGTACCTAAATT
1 TTTTTACCCAATTTGATACCTAAATG
29118120 TTTTT
1 TTTTT
29118125 GGATCCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTTTACCCAATTTGATACCTAAATG
Found at i:29121030 original size:16 final size:17
Alignment explanation
Indices: 29121009--29121048 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
29120999 TAATGATATA
29121009 TTAATCAATA-TAATAG
1 TTAATCAATATTAATAG
29121025 TTAATCAATATTTAATAG
1 TTAATCAATA-TTAATAG
29121043 TTAATC
1 TTAATC
29121049 GACTCAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.45
18 12 0.55
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (17 bp):
TTAATCAATATTAATAG
Found at i:29123760 original size:18 final size:20
Alignment explanation
Indices: 29123739--29123781 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29123729 AAATGATACT
29123739 AAATAAATT-TCAA-ATATA
1 AAATAAATTATCAATATATA
29123757 AAAT-AATTATCAATTATATA
1 AAATAAATTATCAA-TATATA
29123777 AAATA
1 AAATA
29123782 TTCATTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 8 0.38
20 9 0.43
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAAATTATCAATATATA
Found at i:29131860 original size:14 final size:14
Alignment explanation
Indices: 29131841--29131868 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29131831 GGAAAAGGCT
29131841 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
29131855 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
29131869 AGTAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
GAAAAGCTTTTACA
Found at i:29133774 original size:22 final size:22
Alignment explanation
Indices: 29133749--29133797 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
29133739 AAAATATATT
29133749 ATTT-TAGTTTAATATTTAAAAA
1 ATTTATAGTTTAATA-TTAAAAA
* **
29133771 ATTTATATTTTTTTATTAAAAA
1 ATTTATAGTTTAATATTAAAAA
29133793 ATTTA
1 ATTTA
29133798 AACATACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTATAGTTTAATATTAAAAA
Found at i:29133789 original size:29 final size:30
Alignment explanation
Indices: 29133720--29133789 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
29133710 GTTTTAAATC
* *
29133720 TTTTTATATTATTTTTTAAAAAATATATTA
1 TTTTTATATTAATATTTAAAAAATATATTA
*
29133750 -TTTTAGT-TTAATATTTAAAAAATTTA-TA
1 TTTTTA-TATTAATATTTAAAAAATATATTA
*
29133778 TTTTTTTATTAA
1 TTTTTATATTAA
29133790 AAAATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
28 3 0.09
29 29 0.88
30 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTTTATATTAATATTTAAAAAATATATTA
Found at i:29134464 original size:33 final size:32
Alignment explanation
Indices: 29134427--29134490 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
29134417 CAGAACCCCA
29134427 AGCTTTTGAGACTACTGGTTTTTTAAACTCTCG
1 AGCTTTTGAGACTACTGG-TTTTTAAACTCTCG
* * *
29134460 AGCTTTTGGGACTCCTGGTTTTTAAATTCTC
1 AGCTTTTGAGACTACTGGTTTTTAAACTCTC
29134491 TCTCTCTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (32 bp):
AGCTTTTGAGACTACTGGTTTTTAAACTCTCG
Found at i:29138756 original size:32 final size:32
Alignment explanation
Indices: 29138715--29138777 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
29138705 TAAACCATAA
29138715 ACCTTAACTAAAAAAACCCTAAACCCATTTTC
1 ACCTTAACTAAAAAAACCCTAAACCCATTTTC
* * *
29138747 ACCTTAACTAAAAAAATCTTAAACTCATTTT
1 ACCTTAACTAAAAAAACCCTAAACCCATTTT
29138778 AACACACCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.30
Consensus pattern (32 bp):
ACCTTAACTAAAAAAACCCTAAACCCATTTTC
Found at i:29139221 original size:31 final size:30
Alignment explanation
Indices: 29139186--29139251 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
29139176 TGATCACTTC
29139186 GTAACAAAATAATAACATAAGTGACTAAAAT
1 GTAACAAAATAA-AACATAAGTGACTAAAAT
** * *
29139217 GTAAC-ATTTCAAACATAAGTGACTATAAT
1 GTAACAAAATAAAACATAAGTGACTAAAAT
29139246 GTAACA
1 GTAACA
29139252 TGAGGCAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 22 0.73
30 3 0.10
31 5 0.17
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.26
Consensus pattern (30 bp):
GTAACAAAATAAAACATAAGTGACTAAAAT
Found at i:29144375 original size:6 final size:6
Alignment explanation
Indices: 29144366--29144397 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
29144356 GACTAAGAAT
29144366 TAGATA TAGATA TAGATA TAGATA TAGATA TA
1 TAGATA TAGATA TAGATA TAGATA TAGATA TA
29144398 AATGATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
TAGATA
Found at i:29146098 original size:31 final size:31
Alignment explanation
Indices: 29146060--29146124 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
29146050 GTCCCCCAAC
*
29146060 TATGAGAGTGATTCTATTTTGGTCA-CTCAAT
1 TATGAGAGTGATTCTATTTCGGTCACCT-AAT
29146091 TATGAGAGTGATTCTATTTCGGTCACCTAAT
1 TATGAGAGTGATTCTATTTCGGTCACCTAAT
29146122 TAT
1 TAT
29146125 AAAGTTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (31 bp):
TATGAGAGTGATTCTATTTCGGTCACCTAAT
Found at i:29148801 original size:24 final size:24
Alignment explanation
Indices: 29148761--29148905 Score: 110
Period size: 24 Copynumber: 5.8 Consensus size: 24
29148751 ACATATATAT
* *
29148761 AAGCTGAAGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTAC
* * *
29148785 AAGTTGACGAGCGTAAACGCATATATAT
1 AAGCTGACGAGCGTAAACG----TGTAC
* *
29148813 AAGCTGACGAGCATAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTAC
* * * *
29148837 AAGCTGGCGAGCGTAAATGCATATAT
1 AAGCTGACGAGCGTAAA--CGTGTAC
*
29148863 AAGCTGACGAGCGTAAACGTGTCC
1 AAGCTGACGAGCGTAAACGTGTAC
* *
29148887 AAGCTGGCTAGCGTAAACG
1 AAGCTGACGAGCGTAAACG
29148906 CATATATAGC
Statistics
Matches: 92, Mismatches: 23, Indels: 12
0.72 0.18 0.09
Matches are distributed among these distances:
24 54 0.59
26 19 0.21
28 19 0.21
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTAC
Found at i:29148809 original size:50 final size:50
Alignment explanation
Indices: 29148755--29148930 Score: 246
Period size: 50 Copynumber: 3.5 Consensus size: 50
29148745 ATATACACAT
* * *
29148755 ATATATAAGCTGAAGAGCGTAAACGTGTGCAAGTTGACGAGCGTAAACGC
1 ATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGC
* *
29148805 ATATATATAAGCTGACGAGCATAAACGTGTGCAAGCTGGCGAGCGTAAATGC
1 --ATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGC
* *
29148857 ATATATAAGCTGACGAGCGTAAACGTGTCCAAGCTGGCTAGCGTAAACGC
1 ATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGC
* *
29148907 ATATAT-AGCTGACAAGCATAAACG
1 ATATATAAGCTGACGAGCGTAAACG
29148931 CAATGATCAT
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
49 16 0.14
50 52 0.46
52 45 0.40
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (50 bp):
ATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGC
Found at i:29148809 original size:52 final size:52
Alignment explanation
Indices: 29148752--29148913 Score: 247
Period size: 52 Copynumber: 3.2 Consensus size: 52
29148742 TATATATACA
* * *
29148752 CATATATATAAGCTGAAGAGCGTAAACGTGTGCAAGTTGACGAGCGTAAACG
1 CATATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* *
29148804 CATATATATAAGCTGACGAGCATAAACGTGTGCAAGCTGGCGAGCGTAAATG
1 CATATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* *
29148856 C--ATATATAAGCTGACGAGCGTAAACGTGTCCAAGCTGGCTAGCGTAAACG
1 CATATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
29148906 CATATATA
1 CATATATA
29148914 GCTGACAAGC
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
50 46 0.46
52 53 0.54
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (52 bp):
CATATATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
Found at i:29151008 original size:29 final size:29
Alignment explanation
Indices: 29150966--29151046 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
29150956 TACAAAAGAA
* *
29150966 TGACAGGTGTGGCAACCCGACCACGTTGT
1 TGACAAGTATGGCAACCCGACCACGTTGT
* * *
29150995 TGACAAGTATGGCAACTCGACTAGGTTGT
1 TGACAAGTATGGCAACCCGACCACGTTGT
** * *
29151024 TGATGAGTATGGCGACCTGACCA
1 TGACAAGTATGGCAACCCGACCA
29151047 ATAAAACAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (29 bp):
TGACAAGTATGGCAACCCGACCACGTTGT
Found at i:29161523 original size:2 final size:2
Alignment explanation
Indices: 29161516--29161546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29161506 TGCAAGTAAT
29161516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29161547 CCTTGATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29164042 original size:58 final size:58
Alignment explanation
Indices: 29163926--29164046 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 58
29163916 AAACTCATCA
* * *
29163926 ATAAACTAAACCCAAATTTTTTTAAACTCAAATATAATTTCATTCTTCAAAAATACTC
1 ATAAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTCAAAAACACTC
* *
29163984 ATAAACTAAACCCAAATATTTTTAAACTCATATATAA-TTCTATTCCT-AAATAGCACTC
1 ATAAACTAAACCCAAATATTTTTAAACTCAAATATAATTTC-ATTCCTCAAA-AACACTC
29164042 ATAAA
1 ATAAA
29164047 TAATTCCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
57 6 0.11
58 50 0.89
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (58 bp):
ATAAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTCAAAAACACTC
Done.