Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 89 of 175
Found at i:28263289 original size:7 final size:7
Alignment explanation
Indices: 28263277--28263307 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28263267 TCAAAAAAGT
28263277 ATTTCGA
1 ATTTCGA
28263284 ATTTCGA
1 ATTTCGA
28263291 ATTTCGA
1 ATTTCGA
*
28263298 ATTTCTA
1 ATTTCGA
28263305 ATT
1 ATT
28263308 CTAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (7 bp):
ATTTCGA
Found at i:28263399 original size:27 final size:27
Alignment explanation
Indices: 28263361--28263416 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
28263351 AAAATATGTC
*
28263361 ATAAGTGCTAACGAAAGTGTTCTTTCA
1 ATAAGTGCTAACGAAAGTGTTATTTCA
28263388 ATAAGTGCTAACGAAAGTGTTATTTCA
1 ATAAGTGCTAACGAAAGTGTTATTTCA
28263415 AT
1 AT
28263417 TAGAACCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (27 bp):
ATAAGTGCTAACGAAAGTGTTATTTCA
Found at i:28264293 original size:23 final size:24
Alignment explanation
Indices: 28264232--28264294 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
28264222 CTCAAAACTT
*
28264232 TTTTATATATATTTAGATTTTTATTA
1 TTTTATA-AT-TTTAGATTTTGATTA
* *
28264258 TTTT-TAAAATTTA-ATTTTGATTC
1 TTTTAT-AATTTTAGATTTTGATTA
28264281 TTTTATAATTTTAG
1 TTTTATAATTTTAG
28264295 GATCAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
23 18 0.60
24 5 0.17
25 2 0.07
26 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (24 bp):
TTTTATAATTTTAGATTTTGATTA
Found at i:28265733 original size:21 final size:21
Alignment explanation
Indices: 28265665--28265735 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
28265655 TTTTTTGTAA
* * *
28265665 TATACTTTTTTGTCATAATTT
1 TATAATTTTTTGTTAAAATTT
* * *
28265686 TAGAATTTTTTAAGATTTAAATAT
1 TATAATTTTTT--G-TTAAAATTT
28265710 TATAATTTTTTGTTAAAATTT
1 TATAATTTTTTGTTAAAATTT
28265731 TATAA
1 TATAA
28265736 ATACACATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
21 21 0.55
22 1 0.03
23 1 0.03
24 15 0.39
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (21 bp):
TATAATTTTTTGTTAAAATTT
Found at i:28265796 original size:20 final size:21
Alignment explanation
Indices: 28265753--28265797 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
28265743 TAAGTTATTT
* *
28265753 TTTATAATATAACTTTTTAGAA
1 TTTATAATATAAC-GTTTAAAA
28265775 TTTATAATATAA-GTTTAAAA
1 TTTATAATATAACGTTTAAAA
28265795 TTT
1 TTT
28265798 TTTAACTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTATAATATAACGTTTAAAA
Found at i:28271867 original size:15 final size:15
Alignment explanation
Indices: 28271833--28271867 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28271823 TATATATGCC
28271833 ACAATAATAAATACA
1 ACAATAATAAATACA
* *
28271848 TCAATAATAAATATA
1 ACAATAATAAATACA
28271863 ACAAT
1 ACAAT
28271868 GGCATAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:28272181 original size:11 final size:11
Alignment explanation
Indices: 28272165--28272201 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28272155 ACGTATATAT
28272165 ATAAAATAATA
1 ATAAAATAATA
28272176 ATAAAATAA-A
1 ATAAAATAATA
28272186 ATAAAA-AATA
1 ATAAAATAATA
28272196 AGTAAA
1 A-TAAA
28272202 TATTTAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.08
10 9 0.38
11 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:28272267 original size:24 final size:24
Alignment explanation
Indices: 28272238--28272288 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
28272228 ATATACGTAT
28272238 AAATAT-AAAAATATTCATTTAAAA
1 AAATATAAAAAATATTCA-TTAAAA
28272262 AAATATAGAAAAATATTCATTAAAA
1 AAATATA-AAAAATATTCATTAAAA
28272287 AA
1 AA
28272289 TAGAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.24
25 8 0.32
26 11 0.44
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATATAAAAAATATTCATTAAAA
Found at i:28272291 original size:22 final size:24
Alignment explanation
Indices: 28272238--28272299 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 24
28272228 ATATACGTAT
*
28272238 AAATATAAAAATATTCATTTAAAAA
1 AAATAGAAAAATATTCATTT-AAAA
28272263 AATATAGAAAAATATTCA-TT-AAA
1 AA-ATAGAAAAATATTCATTTAAAA
*
28272286 AAATAGAAATATAT
1 AAATAGAAAAATAT
28272300 ATGCATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 11 0.32
23 5 0.15
25 4 0.12
26 14 0.41
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
AAATAGAAAAATATTCATTTAAAA
Found at i:28272334 original size:19 final size:19
Alignment explanation
Indices: 28272306--28272345 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28272296 ATATATGCAT
28272306 ATATAGATAAAATAATTAC
1 ATATAGATAAAATAATTAC
*
28272325 ATATATATAAAATAATTAC
1 ATATAGATAAAATAATTAC
28272344 AT
1 AT
28272346 TATCAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATAGATAAAATAATTAC
Found at i:28279304 original size:27 final size:26
Alignment explanation
Indices: 28279234--28279306 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
28279224 TTTCATCTCT
*
28279234 ATTTTACCCTGGTAAAA-TTTTGACA
1 ATTTTACCTTGGTAAAATTTTTGACA
* * * *
28279259 ATTTTACCCTCGATGAAATTTTTGACG
1 ATTTTA-CCTTGGTAAAATTTTTGACA
28279286 ATTTTACCTTTGGTAAAATTT
1 ATTTTACC-TTGGTAAAATTT
28279307 CGAGAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 6 0.16
26 9 0.24
27 22 0.59
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (26 bp):
ATTTTACCTTGGTAAAATTTTTGACA
Found at i:28290901 original size:16 final size:17
Alignment explanation
Indices: 28290869--28290903 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28290859 ATTTAATCTT
*
28290869 TATATAACATAACATAA
1 TATATAACATAAAATAA
28290886 TATATAA-ATAAAATAA
1 TATATAACATAAAATAA
28290902 TA
1 TA
28290904 AGTTACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TATATAACATAAAATAA
Found at i:28295327 original size:30 final size:30
Alignment explanation
Indices: 28295271--28295328 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
28295261 AAAATTTTAG
* *
28295271 AATTTAATTCTTATACTTTTATTTTCAATA
1 AATTTAATTCCTATACTTTTAGTTTCAATA
*
28295301 AATTTAA-TCCTATATTTTTCAGTTTCAA
1 AATTTAATTCCTATACTTTT-AGTTTCAA
28295329 AATTCAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTTAATTCCTATACTTTTAGTTTCAATA
Found at i:28295870 original size:15 final size:15
Alignment explanation
Indices: 28295850--28295882 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28295840 ACATTTCACT
*
28295850 TTTATGTCTTTTGTA
1 TTTATGTCTTTTATA
28295865 TTTATGTCTTTTATA
1 TTTATGTCTTTTATA
28295880 TTT
1 TTT
28295883 TGCATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (15 bp):
TTTATGTCTTTTATA
Found at i:28300659 original size:16 final size:17
Alignment explanation
Indices: 28300633--28300676 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
28300623 TATATATATC
*
28300633 TATTATAAAAA-ATGTG
1 TATTTTAAAAACATGTG
28300649 TATTTTGAAAAACATGTG
1 TATTTT-AAAAACATGTG
28300667 TATTTTAAAA
1 TATTTTAAAA
28300677 CGTGCATGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 9 0.36
18 11 0.44
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (17 bp):
TATTTTAAAAACATGTG
Found at i:28301874 original size:23 final size:24
Alignment explanation
Indices: 28301842--28301888 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
28301832 GGAGCGACAA
* *
28301842 GTGTGGCGTGTGGGCGCTGTTGCG
1 GTGTGGCGTGTGGGAGCTGCTGCG
28301866 GTGT-GCGTGTGGGAGCTGCTGCG
1 GTGTGGCGTGTGGGAGCTGCTGCG
28301889 CCTAGGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.02, C:0.17, G:0.53, T:0.28
Consensus pattern (24 bp):
GTGTGGCGTGTGGGAGCTGCTGCG
Found at i:28310202 original size:22 final size:23
Alignment explanation
Indices: 28310177--28310224 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
28310167 CTCTCTAATC
28310177 CTCTTAAATTT-CTTCCAAAATT
1 CTCTTAAATTTCCTTCCAAAATT
*
28310199 CTC-TCAATTTCCTTCCAAAATT
1 CTCTTAAATTTCCTTCCAAAATT
28310221 CTCT
1 CTCT
28310225 GAAACCCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (23 bp):
CTCTTAAATTTCCTTCCAAAATT
Found at i:28310209 original size:21 final size:22
Alignment explanation
Indices: 28310183--28310224 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28310173 AATCCTCTTA
28310183 AATTT-CTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
28310204 AATTTCCTTCCAAAATTCTCT
1 AATTTCCTTCCAAAATTCTCT
28310225 GAAACCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTCCTTCCAAAATTCTCTC
Found at i:28310255 original size:51 final size:51
Alignment explanation
Indices: 28310199--28310311 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 51
28310189 TTCCAAAATT
*
28310199 CTCTCAATTTCCTTCCAAAATTCTCTGAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
** *
28310250 CTCTCAATTTCCTTTGAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
28310301 C-CTTCAATTTC
1 CTC-TCAATTTC
28310312 ATTTTTTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
50 1 0.02
51 56 0.98
ACGTcount: A:0.28, C:0.27, G:0.02, T:0.43
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:28310339 original size:10 final size:10
Alignment explanation
Indices: 28310312--28310377 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
28310302 CTTCAATTTC
*
28310312 ATTTTTTAAA
1 ATTTTTTTAA
**
28310322 ATAATTTTAA
1 ATTTTTTTAA
*
28310332 ATTTTTTTAT
1 ATTTTTTTAA
28310342 ATTTTTTTAAA
1 ATTTTTTT-AA
**
28310353 ATAATTTTAA
1 ATTTTTTTAA
*
28310363 ATTTTTTTAT
1 ATTTTTTTAA
28310373 ATTTT
1 ATTTT
28310378 CATCAATGGC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:28310351 original size:31 final size:31
Alignment explanation
Indices: 28310313--28310377 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
28310303 TTCAATTTCA
28310313 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
28310344 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
28310375 TTT
1 TTT
28310378 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATTTTTTTATAT
Found at i:28311463 original size:7 final size:7
Alignment explanation
Indices: 28311451--28311475 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28311441 AGTCGATTGA
28311451 TATTTAG
1 TATTTAG
28311458 TATTTAG
1 TATTTAG
28311465 TATTTAG
1 TATTTAG
28311472 TATT
1 TATT
28311476 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:28312674 original size:29 final size:28
Alignment explanation
Indices: 28312649--28313280 Score: 352
Period size: 29 Copynumber: 22.2 Consensus size: 28
28312639 TTACTAACAA
*
28312649 TTAACTAACTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
*
28312677 CTAATCTAATTTAATTAAAAACCCTAACCC
1 TTAA-CTAATTTAATTAAAAACCCTAA-CC
* *
28312707 TAAACTAATTTAATTAAAAACCCTAA-T
1 TTAACTAATTTAATTAAAAACCCTAACC
* *****
28312734 TTAATTTTACTAATAATTAACTAATTTAATTAAAAACC
1 TT-A----ACTAAT--TTAATTAA---AAACCCTAACC
*
28312772 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCC
1 TTAA--CTAA--T---TTAATTAAAAACCCTAA-CC
28312808 TAACCTAACCTAATTTAATTAAAAACCCTAA-C
1 T----TAA-CTAATTTAATTAAAAACCCTAACC
28312840 TCTAACCTAATTTAATTAAAAACCCTAACCC
1 T-TAA-CTAATTTAATTAAAAACCCTAA-CC
*
28312871 TAAACTAATTTAATTAAAAACCCTAA--
1 TTAACTAATTTAATTAAAAACCCTAACC
* * * *
28312897 TT---TAATTTTACTAACAA--TTAA-C
1 TTAACTAATTTAATTAAAAACCCTAACC
** **
28312919 -TAACTTAA-TTAAAAACCCTAACCCTAA-C
1 TTAAC-TAATTTAATTA--AAAACCCTAACC
28312947 ----CTAATTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
*
28312971 CTAATCTAATTTAATTAAAAACCCTAACC
1 TTAA-CTAATTTAATTAAAAACCCTAACC
* * *
28313000 CTAACCTAACTTAATTAAAAACCATAACCC
1 TTAA-CTAATTTAATTAAAAACCCTAA-CC
* *
28313030 TAAACTAACTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
*
28313058 CTAACCTAATTTAATTAAAAACCCTAACCC
1 TTAA-CTAATTTAATTAAAAACCCTAA-CC
*
28313088 TAAACTAATTTAATTAAAAACCCTAA--
1 TTAACTAATTTAATTAAAAACCCTAACC
**
28313114 TT---TAA-TT--TTACTAACCCTAA-C
1 TTAACTAATTTAATTAAAAACCCTAACC
28313135 ----CTAATTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
*
28313159 CTAACCTAATTTAATTAAAAACCCTAACC
1 TTAA-CTAATTTAATTAAAAACCCTAACC
* *
28313188 CTAACCTAACTTAATTAAAAACCCTAACCC
1 TTAA-CTAATTTAATTAAAAACCCTAA-CC
* * *
28313218 TAAACTAACTTAACTAAAAACCCTAACCC
1 TTAACTAATTTAATTAAAAACCCTAA-CC
*
28313247 TAAACTAATTTAATTAAAAACCCTAACC
1 TTAACTAATTTAATTAAAAACCCTAACC
28313275 ATTAAC
1 -TTAAC
28313281 ACCATTTTTG
Statistics
Matches: 486, Mismatches: 61, Indels: 113
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.03
21 6 0.01
22 2 0.00
23 34 0.07
24 9 0.02
25 9 0.02
26 4 0.01
27 1 0.00
28 14 0.03
29 306 0.63
30 18 0.04
31 2 0.00
32 8 0.02
33 1 0.00
34 24 0.05
35 8 0.02
36 2 0.00
37 7 0.01
38 9 0.02
39 5 0.01
40 3 0.01
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (28 bp):
TTAACTAATTTAATTAAAAACCCTAACC
Found at i:28312714 original size:58 final size:58
Alignment explanation
Indices: 28312651--28313274 Score: 535
Period size: 58 Copynumber: 10.4 Consensus size: 58
28312641 ACTAACAATT
* *
28312651 AACTAACTTAATTAAAAACCCTAACCCTAATCTAATTTAATTAAAAACCCTAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
** * * *
28312709 AACTAATTTAATTAAAAACCCTAA-TTTAATTTTACTAATAATTAACTAATTTAATTAAAAACCC
1 AACTAATTTAATTAAAAACCCTAACCCT-A----AC--CTAATT---TAA-TT-A--AAAACCCT
* *
28312773 TAACCCTA
52 AAC-CCTA
* *
28312781 ACCTAATTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACTCTA
1 AACTAATTTAATTAAAAACCCTAA--C---CCTAACCTAATTTAATTAAAAACCCTAACCCTA
* * **
28312844 ACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAA-TTTA
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
* ** *
28312901 ATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCC
1 A----ACT---AATT---TAA-TT-A--AAAACCCTAACC-CTAACCTAATTTAATTAAAAACCC
28312966 TAACCCTA
51 TAACCCTA
* * *
28312974 ATCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
*
28313032 AACTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
* **
28313090 AACTAATTTAATTAAAAACCCTAA---T---TTAA-TT--TTACTAACCCTAA--C--
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
28313135 --CTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
* * * * *
28313191 ACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAACTAAAAACCCTAACCCTA
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
28313249 AACTAATTTAATTAAAAACCCTAACC
1 AACTAATTTAATTAAAAACCCTAACC
28313275 ATTAACACCA
Statistics
Matches: 462, Mismatches: 52, Indels: 104
0.75 0.08 0.17
Matches are distributed among these distances:
43 22 0.05
46 1 0.00
47 1 0.00
49 14 0.03
50 2 0.00
51 2 0.00
52 14 0.03
54 1 0.00
55 1 0.00
57 5 0.01
58 234 0.51
59 8 0.02
61 4 0.01
62 3 0.01
63 30 0.06
64 16 0.03
66 5 0.01
67 8 0.02
68 7 0.02
69 4 0.01
71 20 0.04
72 53 0.11
73 5 0.01
77 1 0.00
78 1 0.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (58 bp):
AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
Found at i:28312795 original size:101 final size:104
Alignment explanation
Indices: 28312620--28313214 Score: 528
Period size: 101 Copynumber: 6.1 Consensus size: 104
28312610 TTTGATGTCA
*
28312620 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAATCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
28312685 ATTTAATTAAAAACCCTAACCCT-A-AA-CTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAACAACCTAATTTAAT
* *
28312721 TAAAAACCCTAATTTAATTTTACTAATAATTAACTAATTTAATTAAAAACCCTAACCCTAACCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
28312786 ATTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAA-C-AACCTAATTTAAT
* * *
28312827 TAAAAACCC-----TAA--CT-CTAAC------CTAATTTAATTAAAAACCCTAACCCTAAACTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
** ** *
28312878 ATTTAATTAAAAACCCTAA-TTTAATTTTA-CTAA--CAAT
66 ATTTAATTAAAAACCCTAACCCTAA--CAACCTAATTTAAT
* * ***** ** * * * *
28312915 TAACTAA-CTTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATCT
1 TAA-AAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCT
*
28312978 AATTTAATTAAAAACCCTAACCCT---AACCTAACTTAAT
65 AATTTAATTAAAAACCCTAACCCTAACAACCTAATTTAAT
* *
28313015 TAAAAA-CC--A--T-A----AC---C-CTAAACTAACTTAATTAAAAACCCTAACCCTAACCTA
1 TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
28313066 ATTTAATTAAAAACCCTAACCCT-A-AA-CTAATTTAAT
66 ATTTAATTAAAAACCCTAACCCTAACAACCTAATTTAAT
** *
28313102 TAAAAACCCTAATTTAATTTTACTAAC-CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCT
1 TAAAAACCCTAATTTAATTTTACTAACAATTAA-CTAACTTAATTAAAAACCCTAACCCTAACCT
*
28313166 AATTTAATTAAAAACCCTAACCCT---AACCTAACTTAAT
65 AATTTAATTAAAAACCCTAACCCTAACAACCTAATTTAAT
28313203 TAAAAACCCTAA
1 TAAAAACCCTAA
28313215 CCCTAAACTA
Statistics
Matches: 422, Mismatches: 32, Indels: 80
0.79 0.06 0.15
Matches are distributed among these distances:
87 72 0.17
88 12 0.03
89 2 0.00
90 5 0.01
91 5 0.01
92 54 0.13
93 1 0.00
95 6 0.01
96 1 0.00
97 4 0.01
98 8 0.02
99 4 0.01
100 12 0.03
101 213 0.50
102 2 0.00
105 2 0.00
106 19 0.05
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (104 bp):
TAAAAACCCTAATTTAATTTTACTAACAATTAACTAACTTAATTAAAAACCCTAACCCTAACCTA
ATTTAATTAAAAACCCTAACCCTAACAACCTAATTTAAT
Found at i:28312801 original size:130 final size:130
Alignment explanation
Indices: 28312653--28313243 Score: 691
Period size: 130 Copynumber: 4.6 Consensus size: 130
28312643 TAACAATTAA
*
28312653 CTAACTTAATTAAAAACCCTAACCCTAATCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
1 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
28312718 AATTAAAAACCCTAATTTAATTTTACTAATAATTAA-CTAATTTAATTAAAAACCCTAACCCTAA
66 AATTAAAAACCCTAATTTAATTTTACTAATAA-TAACCTAATTTAATTAAAAACCCTAACCCTAA
28312782 C
130 C
* * *
28312783 CTAATTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACTCTAACCT
1 CTAACTTAATTAAAAACCCTAA--C---CCTAACCTAATTTAATTAAAAACCCTAACCCTAAACT
** ** * * * **
28312848 AATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAATTTAATT--TTA--CT
61 AATTTAATTAAAAACCCTAA-TTTAATTTTA-CTAA-TAATAA-CCTAATTTAATTAAAAACCCT
**
28312909 AACAATTAA-
122 AAC-CCTAAC
*
28312918 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATCTAATTT
1 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
** * * *
28312983 AATTAAAAACCC-----T-A----AC----CCTAACCTAACTTAATTAAAAACCATAACCCTAAA
66 AATTAAAAACCCTAATTTAATTTTACTAATAATAACCTAATTTAATTAAAAACCCTAACCCTAAC
28313034 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
1 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
***
28313099 AATTAAAAACCCTAATTTAATTTTACTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAC
66 AATTAAAAACCCTAATTTAATTTTACTAATAATAACCTAATTTAATTAAAAACCCTAACCCTAAC
* * *
28313164 CTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTT
1 CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
*
28313229 AACTAAAAACCCTAA
66 AATTAAAAACCCTAA
28313244 CCCTAAACTA
Statistics
Matches: 395, Mismatches: 36, Indels: 60
0.80 0.07 0.12
Matches are distributed among these distances:
112 11 0.03
113 2 0.01
114 1 0.00
115 3 0.01
116 80 0.20
119 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 1 0.00
126 2 0.01
130 181 0.46
132 1 0.00
133 1 0.00
135 80 0.20
136 8 0.02
137 6 0.02
138 3 0.01
139 11 0.03
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (130 bp):
CTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTT
AATTAAAAACCCTAATTTAATTTTACTAATAATAACCTAATTTAATTAAAAACCCTAACCCTAAC
Found at i:28313015 original size:87 final size:86
Alignment explanation
Indices: 28312752--28313274 Score: 484
Period size: 87 Copynumber: 6.3 Consensus size: 86
28312742 ACTAATAATT
*
28312752 AACTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAC
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAA--C---CCTAA-
*
28312817 CTAATTTAATTAAAAACCCTAACTCTA
60 CTAATTTAATTAAAAACCCTAACCCTA
* * * *
28312844 ACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAA---T--TTAATT
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACTAATT
* * * *
28312904 TTACTAACAA--TTAA--CT-
66 TAATTAAAAACCCTAACCCTA
28312920 AACTTAA-TTAA--AAACCCTAACCCTAA-CCTAA--T---TTAATTAAAAACCCTAACCCTAAT
1 AAC-TAATTTAATTAAA----AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA-
28312976 CTAATTTAATTAAAAACCCTAACCCTA
60 CTAATTTAATTAAAAACCCTAACCCTA
* * * *
28313003 ACCTAACTTAATTAAAAACCATAACCCTAAACTAACTTAATTAAAAACCCTAACCCTAACCTAAT
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA-CTAAT
28313068 TTAATTAAAAACCCTAACCCTA
65 TTAATTAAAAACCCTAACCCTA
* ** *
28313090 AACTAATTTAATTAAAAACCCTAA---T---TTAA-TT--TTACTAACCCTAA-CCTAATTTAA-
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA-CTAAT
28313144 TT----AAAAACCCTAACCCTA
65 TTAATTAAAAACCCTAACCCTA
* *
28313162 ACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAAACTAAC
1 AACTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCT-AACTAAT
*
28313227 TTAACTAAAAACCCTAACCCTA
65 TTAATTAAAAACCCTAACCCTA
28313249 AACTAATTTAATTAAAAACCCTAACC
1 AACTAATTTAATTAAAAACCCTAACC
28313275 ATTAACACCA
Statistics
Matches: 360, Mismatches: 30, Indels: 87
0.75 0.06 0.18
Matches are distributed among these distances:
72 56 0.16
74 3 0.01
75 3 0.01
76 8 0.02
77 18 0.05
78 34 0.09
79 5 0.01
80 5 0.01
81 33 0.09
82 16 0.04
83 10 0.03
84 3 0.01
85 3 0.01
87 112 0.31
92 51 0.14
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (86 bp):
AACTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACTAATT
TAATTAAAAACCCTAACCCTA
Found at i:28313130 original size:188 final size:188
Alignment explanation
Indices: 28312651--28313274 Score: 918
Period size: 188 Copynumber: 3.3 Consensus size: 188
28312641 ACTAACAATT
*
28312651 AACTAACTTAATTAAAAACCCTAACCCTAATCTAATTTAATTAAAAACCCTAACCCTAAACTAAT
1 AACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCCTAAACTAAT
***
28312716 TTAATTAAAAACCCTAATTTAATTTTACTAATAATTAA-CTAATTTAATTAAAAACCCTAACCCT
66 TTAATTAAAAACCCTAATTTAATTTTACTAA-CCCTAACCTAATTTAATTAAAAACCCTAACCCT
*
28312780 AACCTAATTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACTCTA
130 AACCTAATTTAATTAAAAACCCTAACCCTAACCTAA-C----TTAATTAAAAACCCTAACCCTA
* * **
28312844 ACCTAATTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAA-TTTAATTTTAC
1 AACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCCTAA----AC
* * * *****
28312908 TAA--CAATTAACTAA-CTTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
62 TAATTTAATTAA-AAACCCTAATTTAATTTTACTAACCCTAACCTAATTTAATTAAAAACCCTAA
* *
28312969 CCCTAATCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCCTA
126 CCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTA
*
28313032 AACTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTAAT
1 AACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCCTAAACTAAT
28313097 TTAATTAAAAACCCTAATTTAATTTTACTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
66 TTAATTAAAAACCCTAATTTAATTTTACTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
28313162 ACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTA
131 ACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTA
*
28313220 AACTAACTTAACTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACC
1 AACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACC
28313275 ATTAACACCA
Statistics
Matches: 384, Mismatches: 36, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
185 5 0.01
186 2 0.01
187 10 0.03
188 221 0.58
189 3 0.01
192 7 0.02
193 119 0.31
194 10 0.03
195 2 0.01
196 5 0.01
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (188 bp):
AACTAACTTAATTAAAAACCCTAACCCTAAACTAATTTAATTAAAAACCCTAACCCTAAACTAAT
TTAATTAAAAACCCTAATTTAATTTTACTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
ACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTA
Found at i:28313215 original size:159 final size:159
Alignment explanation
Indices: 28312965--28313272 Score: 553
Period size: 159 Copynumber: 1.9 Consensus size: 159
28312955 ATTAAAAACC
*
28312965 CTAACCCTAATCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCC
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCC
* * *
28313030 TAAACTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAACTA
66 TAAACTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAACTAAAAACCCTAACCCTAAACTA
28313095 ATTTAATTAAAAACCCTAATTTAATTTTA
131 ATTTAATTAAAAACCCTAATTTAATTTTA
* *
28313124 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCC
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCC
*
28313189 TAACCTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAACTAAAAACCCTAACCCTAAACTA
66 TAAACTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAACTAAAAACCCTAACCCTAAACTA
28313254 ATTTAATTAAAAACCCTAA
131 ATTTAATTAAAAACCCTAA
28313273 CCATTAACAC
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 142 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (159 bp):
CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCC
TAAACTAACTTAATTAAAAACCCTAACCCTAAACTAACTTAACTAAAAACCCTAACCCTAAACTA
ATTTAATTAAAAACCCTAATTTAATTTTA
Found at i:28313337 original size:55 final size:55
Alignment explanation
Indices: 28313269--28313420 Score: 234
Period size: 55 Copynumber: 2.7 Consensus size: 55
28313259 ATTAAAAACC
* *
28313269 CTAACCATTAACACCATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTA
1 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATGTTA
*
28313324 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATATTTTGATAATGTTA
1 CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATGTTA
* *
28313379 CTAAGCATTAACAAAAATTTTTTGG-CTTAATAATTTTACATA
1 CTAACCATTAAC-ACAA-TTTTTGGACTTAATAATTTTACATA
28313421 CTTTTACATA
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
55 63 0.70
56 20 0.22
57 7 0.08
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.43
Consensus pattern (55 bp):
CTAACCATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATGTTA
Found at i:28314411 original size:13 final size:13
Alignment explanation
Indices: 28314393--28314417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28314383 TATTTTAATA
28314393 TTATTTTGTGTGT
1 TTATTTTGTGTGT
28314406 TTATTTTGTGTG
1 TTATTTTGTGTG
28314418 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:28315960 original size:84 final size:80
Alignment explanation
Indices: 28315828--28315978 Score: 196
Period size: 84 Copynumber: 1.8 Consensus size: 80
28315818 GTAAGAATGT
* ** *
28315828 TATATATATATAAGATTTGAAAATGTATATATATATGTATAAGATTTTGAATTTAATTAAAGGTA
1 TATATATATATAAGATTTGAAAATATATATATATATGTATAAGATTTTGAATAGAATTAAAAGTA
28315893 TGGACGATATATTTA
66 TGGACGATATATTTA
* *
28315908 TATATATATATAAGGTTT-AAATATATATATGTATATATAGGTATAAGTTTTTGAATAGAATTAA
1 TATATATATATAAGATTTGAAA-ATATATA--TATATAT--GTATAAGATTTTGAATAGAATTAA
28315972 AAGTATG
61 AAGTATG
28315979 AATTATATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 23 0.38
82 7 0.12
84 27 0.45
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (80 bp):
TATATATATATAAGATTTGAAAATATATATATATATGTATAAGATTTTGAATAGAATTAAAAGTA
TGGACGATATATTTA
Found at i:28316419 original size:27 final size:27
Alignment explanation
Indices: 28316378--28316432 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
28316368 AAATCAGGTT
* *
28316378 ATAAACCTAGTAGGCTATGTGCCGGTG
1 ATAAACCTAGCAGGCTAAGTGCCGGTG
*
28316405 ATAAGCCTAGCAGGCTAAGTGCCGGTG
1 ATAAACCTAGCAGGCTAAGTGCCGGTG
28316432 A
1 A
28316433 ATATGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (27 bp):
ATAAACCTAGCAGGCTAAGTGCCGGTG
Found at i:28317774 original size:13 final size:13
Alignment explanation
Indices: 28317756--28317780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28317746 TAATGGTATA
28317756 TTGAATCCATGAC
1 TTGAATCCATGAC
28317769 TTGAATCCATGA
1 TTGAATCCATGA
28317781 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:28318361 original size:27 final size:27
Alignment explanation
Indices: 28318326--28318504 Score: 182
Period size: 27 Copynumber: 6.6 Consensus size: 27
28318316 TTAAATTGTA
28318326 TAGCACTAAGTGTGCGATATGACTATG
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
28318353 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATATGACTATG
* *
28318380 -ATGCACTAAGCGTGCGA-ATTGACCATG
1 TA-GCACTAAGTGTGCGATA-TGACTATG
** *
28318407 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TATGACTATG
* * *
28318435 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATATGACTATG
* * *
28318462 TAGCACTAAGTGTGCGAGATGATTATA
1 TAGCACTAAGTGTGCGATATGACTATG
*
28318489 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
28318505 GGCTCAATAT
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 104 0.82
28 22 0.17
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATATGACTATG
Found at i:28318468 original size:82 final size:81
Alignment explanation
Indices: 28318328--28318478 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
28318318 AAATTGTATA
* *
28318328 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGCGT
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGCGT
28318393 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** * *
28318409 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGC
28318473 GTGCGA
64 GTGCGA
28318479 GATGATTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 16 0.26
82 45 0.74
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGCGT
GCGAATTGACCATGCG
Found at i:28318495 original size:82 final size:81
Alignment explanation
Indices: 28318324--28318504 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
28318314 GATTAAATTG
* *
28318324 TATAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28318389 GCGTGCGAATTGACCA
66 GCGTGCGAATTGACCA
*** * ** *
28318405 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TATAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28318469 AAGTGTGCGAGA-TGATTA
64 AAGCGTGCGA-ATTGACCA
*
28318487 TATAGCACTGAGTGTGCG
1 TATAGCACTAAGTGTGCG
28318505 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
81 17 0.21
82 63 0.78
83 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TATAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GCGTGCGAATTGACCA
Found at i:28338354 original size:45 final size:45
Alignment explanation
Indices: 28338303--28338428 Score: 200
Period size: 45 Copynumber: 2.8 Consensus size: 45
28338293 ATCATTTCAT
28338303 CGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCAC
1 CGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCAC
* * *
28338348 CGGCATTATAGCCTACTAGGCCCAAAGGCCCGAATAGTGTCTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
*
28338393 CGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
28338429 TAATACCAGC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
44 3 0.04
45 71 0.96
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (45 bp):
CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
Found at i:28338469 original size:38 final size:38
Alignment explanation
Indices: 28338421--28338591 Score: 252
Period size: 38 Copynumber: 4.5 Consensus size: 38
28338411 GGCTCAAAGG
* * *
28338421 CCCGAATATAATACCAGCACTAGGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
* *
28338459 CCCGGATATAATACCAGCACGAAGCCTGCGGGAATTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
* * *
28338497 CTCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
*
28338535 CCCGGATATATTACCAGCACGAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
*
28338573 CCCGGATATAATTCCAGCA
1 CCCGGATATAATACCAGCA
28338592 TATAGCCTGC
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 121 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
Found at i:28338610 original size:38 final size:38
Alignment explanation
Indices: 28338421--28338618 Score: 247
Period size: 38 Copynumber: 5.2 Consensus size: 38
28338411 GGCTCAAAGG
* * * * *
28338421 CCCGAATATAATACCAGCACTAGGCCTGCAGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
28338459 CCCGGATATAATACCAGCACGAAGCCTGCGGGAATTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
28338497 CTCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
28338535 CCCGGATATATTACCAGCACGAAGCCTGCAGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* **
28338573 CCCGGATATAATT-CCAGCA-TATAGCCTGCGGTCTTTAA
1 CCCGGATAT-ATTACCAGCACGA-AGCCTGCGGGATTTAA
*
28338611 GCCGGATA
1 CCCGGATA
28338619 CAAATATCAT
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
37 1 0.01
38 139 0.97
39 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:28339013 original size:43 final size:44
Alignment explanation
Indices: 28338888--28339006 Score: 170
Period size: 45 Copynumber: 2.7 Consensus size: 44
28338878 ACATAACATT
*
28338888 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GC-CCAATAA
* * *
28338934 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCCAA-AA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCAATAA
28338976 TCATTTCACCGGCATTATAGCCTGCTAGGCT
1 TCATTTCACCGGCATTATAGCCTGCTAGGCT
28339007 TGAAGCCTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
42 3 0.05
43 29 0.45
44 2 0.03
45 30 0.46
46 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (44 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCAATAA
Found at i:28360555 original size:12 final size:12
Alignment explanation
Indices: 28360538--28360568 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28360528 AACCTTGTGG
28360538 AGGACACGGCCT
1 AGGACACGGCCT
28360550 AGGACACGGCCT
1 AGGACACGGCCT
*
28360562 AGCACAC
1 AGGACAC
28360569 AGGTGTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.35, G:0.29, T:0.06
Consensus pattern (12 bp):
AGGACACGGCCT
Found at i:28364002 original size:14 final size:14
Alignment explanation
Indices: 28363983--28364011 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28363973 GTTTAGTCAG
28363983 TTCTCGGACTAACC
1 TTCTCGGACTAACC
28363997 TTCTCGGACTAACC
1 TTCTCGGACTAACC
28364011 T
1 T
28364012 AGTATGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (14 bp):
TTCTCGGACTAACC
Found at i:28365828 original size:15 final size:15
Alignment explanation
Indices: 28365795--28365868 Score: 78
Period size: 15 Copynumber: 4.9 Consensus size: 15
28365785 TTTCCTCATC
* * *
28365795 TTGGATCTCTCTATC
1 TTGGATTTCTTTATT
*
28365810 TTGGATTTCTTTACT
1 TTGGATTTCTTTATT
28365825 TTGGATTTC-TTATT
1 TTGGATTTCTTTATT
* *
28365839 TATGGGTTTCTTCATT
1 T-TGGATTTCTTTATT
28365855 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
28365869 CATGGTTTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
14 5 0.10
15 38 0.79
16 5 0.10
ACGTcount: A:0.14, C:0.14, G:0.15, T:0.58
Consensus pattern (15 bp):
TTGGATTTCTTTATT
Found at i:28365829 original size:30 final size:29
Alignment explanation
Indices: 28365795--28365879 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
28365785 TTTCCTCATC
* *
28365795 TTGGATCTCTCTATCTTGGATTTCTTTACT
1 TTGGATTTCT-TATCTTGGATTTCTTCACT
* * *
28365825 TTGGATTTCTTATTTATGGGTTTCTTCATT
1 TTGGATTTCTTATCT-TGGATTTCTTCACT
* *
28365855 TTGGATTTCTTTATCATGGTTTTCT
1 TTGGATTTC-TTATCTTGGATTTCT
28365880 AGTCATCTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 4 0.09
30 37 0.82
31 4 0.09
ACGTcount: A:0.13, C:0.14, G:0.15, T:0.58
Consensus pattern (29 bp):
TTGGATTTCTTATCTTGGATTTCTTCACT
Found at i:28380630 original size:13 final size:13
Alignment explanation
Indices: 28380614--28380639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28380604 GAAATGATTT
28380614 TTTGAAAATTTCG
1 TTTGAAAATTTCG
28380627 TTTGAAAATTTCG
1 TTTGAAAATTTCG
28380640 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGAAAATTTCG
Found at i:28385824 original size:27 final size:27
Alignment explanation
Indices: 28385793--28385970 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28385783 TAAATTGTAC
28385793 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28385820 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28385846 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28385874 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28385902 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28385929 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28385956 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28385971 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28385907 original size:82 final size:81
Alignment explanation
Indices: 28385794--28385949 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28385784 AAATTGTACA
* *
28385794 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28385858 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28385875 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28385940 TGCGAGTTGA
65 TGCGAATTGA
28385950 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28385961 original size:82 final size:81
Alignment explanation
Indices: 28385790--28385970 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28385780 GATTAAATTG
* *
28385790 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28385855 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28385871 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28385935 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28385953 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28385971 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28385981 original size:27 final size:27
Alignment explanation
Indices: 28385875--28385981 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
28385865 TGACCATGCG
* * * *
28385875 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
28385903 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
28385930 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
28385957 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
28385982 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:28395194 original size:48 final size:48
Alignment explanation
Indices: 28395066--28395391 Score: 347
Period size: 48 Copynumber: 6.8 Consensus size: 48
28395056 TGACACCGTA
** *
28395066 ATATATGTGCCTTTGTAAGACCATGTCTGGGACATGGCATCGGCGATT
1 ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* ** * * * * *
28395114 ATATATGTACTTGTGT-A-ACCATCTCTGGGACATGGAATTGGCAACG
1 ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* * *
28395160 ATACATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGACGATG
1 ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* * *
28395208 ATATGTGTGCCAATGTAAGACCATGTCTGGGACATGGCATCGGTGATG
1 ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* * * * *
28395256 ATATGTGTGCCAGTATAAGACCATGTTTGGGACATGGCATCAGTGATG
1 ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* **
28395304 ATATATCTGCCAGTGTAAGACCATGTCTGGTCCATGGCATCGGCGAT-
1 ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* *
28395351 -TATATGTGCATTCA-TGTAAGACCATGTCGGGGACATAGCAT
1 ATATATGTGC---CAGTGTAAGACCATGTCTGGGACATGGCAT
28395392 TGGTACTTAA
Statistics
Matches: 232, Mismatches: 41, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
46 44 0.19
47 2 0.01
48 184 0.79
49 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (48 bp):
ATATATGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
Found at i:28402834 original size:48 final size:48
Alignment explanation
Indices: 28402753--28403032 Score: 339
Period size: 48 Copynumber: 5.8 Consensus size: 48
28402743 TGACACCGTA
* * *
28402753 ATATATGTGCCTGTGCAAGACCATGTCTAGGACATGGCATCGGCGATG
1 ATATGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* *
28402801 ATACT-TGTGCCTGTGTAAGACCACGTCTGGGACATGGCATCGGCGACG
1 ATA-TGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* * *
28402849 ATATATGTGCCTTTGTAAGACCATGTCTCGGACATGGCATCGGCGATG
1 ATATGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
** * * *
28402897 ATATGTGTGCCAATGTAAGACCATGCCTGGGACCTGGCATCGACGATG
1 ATATGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
* * * *
28402945 ATATGTGTGCCAGTGTAAGACCATGTCTGGTACGTGGCATCGGTGATG
1 ATATGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
** * *
28402993 ATATGTG-GATTCATGTAAGACCATGTCGGGGACATGGCAT
1 ATATGTGTGCCT-GTGTAAGACCATGTCTGGGACATGGCAT
28403033 TGGTACTTAA
Statistics
Matches: 201, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
47 2 0.01
48 198 0.99
49 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (48 bp):
ATATGTGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATG
Found at i:28407454 original size:16 final size:16
Alignment explanation
Indices: 28407433--28407465 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28407423 ATGTAACGCC
*
28407433 CCAAAAATCCCGAAAT
1 CCAAAAATCCCAAAAT
28407449 CCAAAAATCCCAAAAT
1 CCAAAAATCCCAAAAT
28407465 C
1 C
28407466 TTGAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.33, G:0.03, T:0.12
Consensus pattern (16 bp):
CCAAAAATCCCAAAAT
Found at i:28409032 original size:29 final size:28
Alignment explanation
Indices: 28408935--28409037 Score: 120
Period size: 28 Copynumber: 3.6 Consensus size: 28
28408925 GCGAGCATGA
* *
28408935 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
28408963 ATATAAATGTGATTTGGGCCT-ATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
*
28408991 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGA-TTGGGCCTAATGGGCC
*
28409020 ATATGAATATGATTGGGC
1 ATATGAATGTGATTGGGC
28409038 TTTGTAACGC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 41 0.63
29 22 0.34
30 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:28410514 original size:46 final size:46
Alignment explanation
Indices: 28410346--28410662 Score: 295
Period size: 46 Copynumber: 6.8 Consensus size: 46
28410336 TGTAACCCAC
* * * ** *
28410346 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCAT
* * * *
28410392 CCATCAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTAGCAT
* * * *
28410438 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCAT
*
28410485 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCAT-TT-GCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGTTAGCAT
* *
28410531 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTAGCAT
* * * * * * *
28410577 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGAACGTTCGTAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCAT
*
28410624 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
28410663 CCCAAATATC
Statistics
Matches: 220, Mismatches: 37, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
44 2 0.01
45 6 0.03
46 133 0.60
47 72 0.33
48 7 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCAT
Found at i:28410596 original size:139 final size:139
Alignment explanation
Indices: 28410346--28410651 Score: 540
Period size: 139 Copynumber: 2.2 Consensus size: 139
28410336 TGTAACCCAC
* * * *
28410346 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTTGCATCCATCAGTGAACTCAGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCAGACT
*
28410411 CAACTCAACGAGTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACGAGTTCGGA
66 CAACTCAACGAGTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACGAGTTCGAA
*
28410476 TGTTCGCAT
131 CGTTCGCAT
*
28410485 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCGGACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCAGACT
28410550 CAACTCAACGAGTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACGAGTTCGAA
66 CAACTCAACGAGTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACGAGTTCGAA
*
28410615 CGTTCGTAT
131 CGTTCGCAT
28410624 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
28410652 AAGTTCGGAT
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 159 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (139 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCAGACT
CAACTCAACGAGTTCGGATGCCTAGTTACATTTCACGAACTCGGACTCAACTCAACGAGTTCGAA
CGTTCGCAT
Found at i:28410600 original size:93 final size:93
Alignment explanation
Indices: 28410493--28410664 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
28410483 ATCCATAAGT
** *
28410493 GAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28410558 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CAAGTTCGGATGCCTAGTTACATTTCAC
* * *
28410586 GAACTCGGACTCAACTCAACGAGTTCGAACGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28410651 CAAGTTCGGATGCC
66 CAAGTTCGGATGCC
28410665 CAAATATCCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATTTCAC
Found at i:28413112 original size:30 final size:30
Alignment explanation
Indices: 28413068--28413136 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
28413058 TAAAGATAAC
* *
28413068 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCAGAATAAAGAAATCCAAAATA
*
28413097 GAGAAACCCAGAATAAAGAAATCCAAAATA
1 AAGAAACCCAGAATAAAGAAATCCAAAATA
28413127 AAGAAACCCA
1 AAGAAACCCA
28413137 AGATACGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 7 0.20
30 28 0.80
ACGTcount: A:0.61, C:0.17, G:0.13, T:0.09
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCCAAAATA
Found at i:28413116 original size:15 final size:15
Alignment explanation
Indices: 28413068--28413136 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
28413058 TAAAGATAAC
*
28413068 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
*
28413082 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
*
28413097 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
* *
28413112 AAGAAATCCAAAATA
1 AAGAAACCCAGAATA
28413127 AAGAAACCCA
1 AAGAAACCCA
28413137 AGATACGATA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.20
15 35 0.78
16 1 0.02
ACGTcount: A:0.61, C:0.17, G:0.13, T:0.09
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:28413137 original size:15 final size:15
Alignment explanation
Indices: 28413078--28413137 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
28413068 AAGAAAACCG
*
28413078 AATAAAGAAATCCAA
1 AATAAAGAAACCCAA
* * *
28413093 GATAGAGAAACCCAG
1 AATAAAGAAACCCAA
*
28413108 AATAAAGAAATCCAA
1 AATAAAGAAACCCAA
28413123 AATAAAGAAACCCAA
1 AATAAAGAAACCCAA
28413138 GATACGATAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.62, C:0.17, G:0.12, T:0.10
Consensus pattern (15 bp):
AATAAAGAAACCCAA
Found at i:28414508 original size:12 final size:12
Alignment explanation
Indices: 28414491--28414517 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28414481 TATATCATAA
28414491 ACTTTTATCCAT
1 ACTTTTATCCAT
28414503 ACTTTTATCCAT
1 ACTTTTATCCAT
28414515 ACT
1 ACT
28414518 CTTCTGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (12 bp):
ACTTTTATCCAT
Found at i:28424669 original size:29 final size:29
Alignment explanation
Indices: 28424606--28424673 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
28424596 TAATCAACCG
28424606 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
28424635 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
28424664 CGCACACTTA
1 CGCACACTTA
28424674 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:28424786 original size:174 final size:174
Alignment explanation
Indices: 28424495--28424822 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
28424485 AACTCAAGGT
* *
28424495 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
28424560 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
28424625 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
28424669 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
28424734 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
28424799 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
28424823 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:28424814 original size:29 final size:30
Alignment explanation
Indices: 28424775--28424853 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
28424765 CTTAATAATC
28424775 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
28424805 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
28424834 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28424854 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28432813 original size:29 final size:29
Alignment explanation
Indices: 28432750--28432817 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
28432740 TAATCAACCG
28432750 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
28432779 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
28432808 CGCACACTTA
1 CGCACACTTA
28432818 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:28432930 original size:174 final size:174
Alignment explanation
Indices: 28432639--28432966 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
28432629 AACTCAAGGT
* *
28432639 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
28432704 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
28432769 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
28432813 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
28432878 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
* *
28432943 ACTTTAAACTCGCGCACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
28432967 TGTACAATTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:28432962 original size:29 final size:30
Alignment explanation
Indices: 28432919--28432997 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
28432909 CTTAATAATC
28432919 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
* *
28432949 AACTCGCGCACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
28432978 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28432998 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 31 0.76
30 4 0.10
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:28437242 original size:25 final size:25
Alignment explanation
Indices: 28437205--28437263 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
28437195 CTCTTACATT
* *
28437205 TTAATTTACTTATCTAAT-TTTTAAA
1 TTAATTAAATTAT-TAATATTTTAAA
* *
28437230 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTAAA
28437255 TTAATTAAA
1 TTAATTAAA
28437264 ATTTTGAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTAAA
Found at i:28439445 original size:19 final size:20
Alignment explanation
Indices: 28439421--28439459 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28439411 AAAATGCTTG
* *
28439421 TTAAAA-AAAGCACATGTAC
1 TTAAAAGAAAACAAATGTAC
28439440 TTAAAAGAAAACAAATGTAC
1 TTAAAAGAAAACAAATGTAC
28439460 AAAGGAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (20 bp):
TTAAAAGAAAACAAATGTAC
Found at i:28441962 original size:37 final size:37
Alignment explanation
Indices: 28441918--28442074 Score: 289
Period size: 37 Copynumber: 4.3 Consensus size: 37
28441908 ACATGAAGTT
*
28441918 ATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
*
28441955 ATTGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
28441992 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
28442029 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
28442066 ATC-GGTCTT
1 ATCGGGTCTT
28442075 TAGAGCTCGG
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
36 6 0.05
37 111 0.95
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (37 bp):
ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
Found at i:28442271 original size:47 final size:47
Alignment explanation
Indices: 28442193--28442597 Score: 702
Period size: 47 Copynumber: 8.6 Consensus size: 47
28442183 CCATTCGGGA
* * * * * *
28442193 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28442240 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28442287 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28442334 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28442381 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28442430 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28442477 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28442524 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28442571 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28442598 TATTCAAATA
Statistics
Matches: 342, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 296 0.87
49 46 0.13
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28442527 original size:190 final size:190
Alignment explanation
Indices: 28442193--28442597 Score: 701
Period size: 190 Copynumber: 2.2 Consensus size: 190
28442183 CCATTCGGGA
* * * * *
28442193 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATAC
28442256 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
28442321 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28442381 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATAC
*
28442446 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
28442511 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28442571 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
28442598 TATTCAAATA
Statistics
Matches: 206, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
188 29 0.14
189 1 0.00
190 176 0.85
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (190 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28451746 original size:23 final size:23
Alignment explanation
Indices: 28451716--28451760 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28451706 ATTTATGCCT
28451716 AAATCTTATTTATTTAGTATGTA
1 AAATCTTATTTATTTAGTATGTA
28451739 AAATCTTATTTATTTAGTATGT
1 AAATCTTATTTATTTAGTATGT
28451761 GCGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
AAATCTTATTTATTTAGTATGTA
Found at i:28455728 original size:41 final size:41
Alignment explanation
Indices: 28455671--28455814 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
28455661 GGAAAAATGA
* * **
28455671 TGAATTGCACATACGTGCCACTGTTTGTACTTCAGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCC
*
28455712 TGAATTGAACATACGTGCCCCTATTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCC
* * *
28455753 TAAATTCCACATACATGCCCCTATTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCC
*
28455794 TGAATTGCACACACGT-CCCCT
1 TGAATTGCACATACGTGCCCCT
28455815 GTTTAAGCTT
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 5 0.06
41 85 0.94
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.32
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCC
Found at i:28471485 original size:26 final size:25
Alignment explanation
Indices: 28471436--28471557 Score: 129
Period size: 26 Copynumber: 4.7 Consensus size: 25
28471426 ATAATGGGCC
* * * *
28471436 TAAATTACCGGAATAACCTTGATGG
1 TAAATTACTGAAATACCCTCGATGG
*
28471461 ATAAATTACTGATATACCCTCGATGG
1 -TAAATTACTGAAATACCCTCGATGG
* *
28471487 CTAGATTATTGAAATACCCTCGATGGG
1 -TAAATTACTGAAATACCCTCGAT-GG
28471514 TAAATTA-TCGAAATACCCTCGATAGG
1 TAAATTACT-GAAATACCCTCGAT-GG
28471540 TAAATTACTGAAATACCC
1 TAAATTACTGAAATACCC
28471558 CCGAAGGGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.01
26 78 0.95
27 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
TAAATTACTGAAATACCCTCGATGG
Found at i:28471534 original size:52 final size:52
Alignment explanation
Indices: 28471436--28471567 Score: 142
Period size: 52 Copynumber: 2.5 Consensus size: 52
28471426 ATAATGGGCC
* * * * * *
28471436 TAAATTACCGGAATAACCTTGATGGATAAATTACTGATATACCCTCGAT-GG
1 TAAATTACTGAAATACCCTCGATGGGTAAATTACTGAAATACCCTCGATAGG
* *
28471487 CTAGATTATTGAAATACCCTCGATGGGTAAATTA-TCGAAATACCCTCGATAGG
1 -TAAATTACTGAAATACCCTCGATGGGTAAATTACT-GAAATACCCTCGATAGG
* *
28471540 TAAATTACTGAAATACCCCCGAAGGGTA
1 TAAATTACTGAAATACCCTCGATGGGTA
28471568 GAACGACCGT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
51 1 0.02
52 63 0.95
53 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (52 bp):
TAAATTACTGAAATACCCTCGATGGGTAAATTACTGAAATACCCTCGATAGG
Found at i:28471627 original size:26 final size:27
Alignment explanation
Indices: 28471597--28471658 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
28471587 AGGAGATAAG
*
28471597 ATGACTGTTATGGCTTTAT-A-CTTTGT
1 ATGACTGTTAT-GCTTTATGATCTTTAT
* *
28471623 ATGACCG-TATGCTTTATGATTTTTAT
1 ATGACTGTTATGCTTTATGATCTTTAT
28471649 ATGACTGTTA
1 ATGACTGTTA
28471659 CTGAGTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 7 0.24
25 4 0.14
26 16 0.55
27 2 0.07
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (27 bp):
ATGACTGTTATGCTTTATGATCTTTAT
Found at i:28472355 original size:18 final size:19
Alignment explanation
Indices: 28472340--28472375 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28472330 AGTTTTCACA
28472340 ACAAACAC-TATTTTCAAG
1 ACAAACACGTATTTTCAAG
28472358 ACAAACACGTATTTTCAA
1 ACAAACACGTATTTTCAA
28472376 CTACAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (19 bp):
ACAAACACGTATTTTCAAG
Found at i:28477867 original size:16 final size:17
Alignment explanation
Indices: 28477836--28477869 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28477826 CAATTCAGTC
*
28477836 CAAAATTCATACTTTTA
1 CAAAATTCACACTTTTA
28477853 CAAAATT-ACACTTTTA
1 CAAAATTCACACTTTTA
28477869 C
1 C
28477870 CCCTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
CAAAATTCACACTTTTA
Found at i:28479257 original size:80 final size:80
Alignment explanation
Indices: 28479124--28479283 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
28479114 AGATTCATAG
*
28479124 GATGTATGTAAGTCTGTTTTAGTCCCGTTTCAAGTACTTTTTATGTTTTTGAGATCGTTGCTATT
1 GATGTATGTAAGTCTGTTTTAGTCCCGTTTCAAGTAATTTTTATGTTTTTGAGATCGTTGCTATT
28479189 AGATCCAACTAGCCT
66 AGATCCAACTAGCCT
*
28479204 GATGTATGTAAGTCTGTTTTAGTCCCGTTTCTAGTAATTTTTATGTTTTTGAGATCGTTGCTATT
1 GATGTATGTAAGTCTGTTTTAGTCCCGTTTCAAGTAATTTTTATGTTTTTGAGATCGTTGCTATT
28479269 AGATCCAACTAGCCT
66 AGATCCAACTAGCCT
28479284 ATACCTTTGA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (80 bp):
GATGTATGTAAGTCTGTTTTAGTCCCGTTTCAAGTAATTTTTATGTTTTTGAGATCGTTGCTATT
AGATCCAACTAGCCT
Found at i:28480099 original size:25 final size:25
Alignment explanation
Indices: 28480036--28480091 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
28480026 TAGGCCCATT
28480036 TTCACAGCTTGTGTGAGCACACTTA
1 TTCACAGCTTGTGTGAGCACACTTA
*
28480061 TTCACAGCTTGTGTGAGCACAGTTA
1 TTCACAGCTTGTGTGAGCACACTTA
28480086 TTCACA
1 TTCACA
28480092 ACTCGTGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
TTCACAGCTTGTGTGAGCACACTTA
Found at i:28486325 original size:27 final size:27
Alignment explanation
Indices: 28486290--28486352 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
28486280 CATTTAGATT
28486290 TAATTTCATATATTATTTAACCTCTAA
1 TAATTTCATATATTATTTAACCTCTAA
28486317 TAATTTCATATATTATTTAACCTCTAA
1 TAATTTCATATATTATTTAACCTCTAA
28486344 TAATTTCAT
1 TAATTTCAT
28486353 CCACCATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (27 bp):
TAATTTCATATATTATTTAACCTCTAA
Found at i:28486361 original size:27 final size:27
Alignment explanation
Indices: 28486290--28486361 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
28486280 CATTTAGATT
* **
28486290 TAATTTCATATATTATTTAACCTCTAA
1 TAATTTCATACACCATTTAACCTCTAA
* **
28486317 TAATTTCATATATTATTTAACCTCTAA
1 TAATTTCATACACCATTTAACCTCTAA
*
28486344 TAATTTCATCCACCATTT
1 TAATTTCATACACCATTT
28486362 TTGATGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATTTCATACACCATTTAACCTCTAA
Found at i:28491101 original size:50 final size:50
Alignment explanation
Indices: 28490973--28491211 Score: 198
Period size: 50 Copynumber: 4.7 Consensus size: 50
28490963 GATAATAACA
* * *
28490973 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTT-TCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA-GTTCTCATAT-CGG
* * * *
28491022 TACCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATCGG
* ** *
28491072 TGCCCATGCCATGTCCCAGACATGGTCTTACA-GAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGA-GAGTTCTCATATCGG
* * * ** **
28491122 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCAT-A--TC---GG
*
28491178 TGCAAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
28491212 GGATCTCATC
Statistics
Matches: 154, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
48 4 0.03
49 38 0.25
50 78 0.51
51 1 0.01
53 2 0.01
56 31 0.20
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATCGG
Found at i:28493518 original size:50 final size:50
Alignment explanation
Indices: 28493438--28493579 Score: 160
Period size: 50 Copynumber: 2.8 Consensus size: 50
28493428 TTTCCTTTAC
* * ** *
28493438 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
* * * * * *
28493488 TGCCCATTCCATGTCTCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGA
*
28493538 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28493580 TTGCCCAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
49 1 0.01
50 72 0.97
51 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
Found at i:28493962 original size:30 final size:29
Alignment explanation
Indices: 28493914--28493971 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
28493904 TCATTGACTC
*
28493914 AAACTTTAGCAAAATTACATTTTTACCCCT
1 AAACTTTAGCAAAATTACACTTTT-CCCCT
* * *
28493944 AAACTTTTGCATATTTACACTTTTCCCC
1 AAACTTTAGCAAAATTACACTTTTCCCC
28493972 AAAGCTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (29 bp):
AAACTTTAGCAAAATTACACTTTTCCCCT
Found at i:28502335 original size:50 final size:50
Alignment explanation
Indices: 28502233--28502423 Score: 170
Period size: 50 Copynumber: 3.7 Consensus size: 50
28502223 GGTAAAGATA
* * *
28502233 TCCCATGTAAGGCCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGAGACATGGCATTGGCA-C--CGAG---ATGAGAGG
28502289 TCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGG
** * * **
28502339 TCCCCCGTAAGACCATGGCT-AGGACATGGCA-TGGACACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGA-GACATGGCATTGG-CACCGAGATGAGAGG
* * * * *
28502389 TCTCATGTAAGACCATATTTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGAGACATGGCATTGG
28502424 TAGTAAAGGA
Statistics
Matches: 114, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
49 4 0.04
50 68 0.60
51 3 0.03
53 3 0.03
55 1 0.01
56 35 0.31
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28506552 original size:21 final size:21
Alignment explanation
Indices: 28506511--28506552 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28506501 CATCTGAGTG
**
28506511 TGTTGATTGTAGTTCTGTTGT
1 TGTTGATTGTAGTTCCCTTGT
28506532 TGTTGATTGTAGTTCCCTTGT
1 TGTTGATTGTAGTTCCCTTGT
28506553 CTGGGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.55
Consensus pattern (21 bp):
TGTTGATTGTAGTTCCCTTGT
Found at i:28524726 original size:41 final size:41
Alignment explanation
Indices: 28524688--28524773 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
28524678 TGACACTTCA
* ** *
28524688 CCTGATAGGCTTATAGTTTAATTCCGTTAACCGGCACTTAG
1 CCTGATAGGCCTATAGCCTAATTCAGTTAACCGGCACTTAG
* * *
28524729 CCTGCTAGGCCTATAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGATAGGCCTATAGCCTAATTCAGTTAACCGGCACTTAG
28524770 CCTG
1 CCTG
28524774 CTAGACGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (41 bp):
CCTGATAGGCCTATAGCCTAATTCAGTTAACCGGCACTTAG
Found at i:28524785 original size:41 final size:41
Alignment explanation
Indices: 28524708--28524790 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
28524698 TTATAGTTTA
* *
28524708 ATTCCGTTAACCGGCACTTAGCCTGCTAGGCCTATAGCCTG
1 ATTCAGTTAACCGGCACTTAGCCTGCTAGACCTATAGCCTG
* * *
28524749 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGTCTG
1 ATTCAGTTAACCGGCACTTAGCCTGCTAGACCTATAGCCTG
28524790 A
1 A
28524791 ATAATTTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (41 bp):
ATTCAGTTAACCGGCACTTAGCCTGCTAGACCTATAGCCTG
Found at i:28524800 original size:41 final size:41
Alignment explanation
Indices: 28524717--28524805 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
28524707 AATTCCGTTA
* * *
28524717 ACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAGTTC
1 ACCGGCACTTAGCCTGCTAGACCTATAGCCTGAATAAGTTC
* * *
28524758 ACCGGCACTTAGCCTGCTAGACGTATAGTCTGAATAATTTC
1 ACCGGCACTTAGCCTGCTAGACCTATAGCCTGAATAAGTTC
*
28524799 ACTGGCA
1 ACCGGCA
28524806 ATAAATCCGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (41 bp):
ACCGGCACTTAGCCTGCTAGACCTATAGCCTGAATAAGTTC
Found at i:28532741 original size:41 final size:41
Alignment explanation
Indices: 28532573--28532718 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
28532563 TTTAAACAGA
* * * ** * *
28532573 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCCTATAGCCTGATTCAG
28532614 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
28532655 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
28532696 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
28532719 ACGTATAGTC
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 96 0.99
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
Found at i:28532741 original size:82 final size:82
Alignment explanation
Indices: 28532573--28532746 Score: 215
Period size: 82 Copynumber: 2.1 Consensus size: 82
28532563 TTTAAACAGA
* ** * *
28532573 TTCACTGGCACTTCACCTGATAGGCTTATAGTTTAATTCCGTTCACCGGCACTTAGCCTGCTAGG
1 TTCACTGGCACTTCACCTGATAGGCCTATAGCCTAATTCAGTTCACCGGCACTTAGCCTGCTAGA
* *
28532638 CCTATAGCCTGATTCAG
66 CCTATAGCCTGAATAAG
* * *
28532655 TTCACCGGCACTT-AGCCTGCTAGGCCTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAG
1 TTCACTGGCACTTCA-CCTGATAGGCCTATAGCCTAATTCAGTTCACCGGCACTTAGCCTGCTAG
* * *
28532719 ACGTATAGTCTGAATAAT
65 ACCTATAGCCTGAATAAG
28532737 TTCACTGGCA
1 TTCACTGGCA
28532747 ATAAATCCGA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
81 1 0.01
82 76 0.99
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (82 bp):
TTCACTGGCACTTCACCTGATAGGCCTATAGCCTAATTCAGTTCACCGGCACTTAGCCTGCTAGA
CCTATAGCCTGAATAAG
Found at i:28535088 original size:21 final size:20
Alignment explanation
Indices: 28535064--28535114 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 20
28535054 CACTGTTATT
28535064 GAGAAGGAGGTTGTTGCAGAA
1 GAGAA-GAGGTTGTTGCAGAA
*
28535085 GAGAA-A-GTTGTTGCTGAA
1 GAGAAGAGGTTGTTGCAGAA
28535103 GAAGAAGAGGTT
1 G-AGAAGAGGTT
28535115 TCTGAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 12 0.46
19 5 0.19
20 1 0.04
21 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.39, T:0.22
Consensus pattern (20 bp):
GAGAAGAGGTTGTTGCAGAA
Found at i:28539913 original size:23 final size:23
Alignment explanation
Indices: 28539879--28539923 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28539869 ACCCCCTCTC
*
28539879 TGTAATATCCCGAAAAGTACTAT
1 TGTAATACCCCGAAAAGTACTAT
*
28539902 TGTAATACCCCGAAAATTACTA
1 TGTAATACCCCGAAAAGTACTA
28539924 CAGTAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAAGTACTAT
Found at i:28539929 original size:23 final size:23
Alignment explanation
Indices: 28539880--28539929 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
28539870 CCCCCTCTCT
* **
28539880 GTAATATCCCGAAAAGTACTATT
1 GTAATACCCCGAAAAGTACTACA
*
28539903 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAAGTACTACA
28539926 GTAA
1 GTAA
28539930 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (23 bp):
GTAATACCCCGAAAAGTACTACA
Found at i:28544171 original size:5 final size:5
Alignment explanation
Indices: 28544163--28544188 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28544153 CTTTGTCATA
28544163 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
28544189 ATTTTATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:28550145 original size:29 final size:28
Alignment explanation
Indices: 28550109--28550186 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
28550099 TCATGAGATT
28550109 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
28550139 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
28550166 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
28550187 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:28550404 original size:174 final size:174
Alignment explanation
Indices: 28550139--28550466 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
28550129 AAATTGTACA
* *
28550139 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTCTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
28550204 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCAAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
28550269 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
28550313 GCACTAAGTGTGTGAGTCTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTCTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
28550378 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGGAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
28550443 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
28550467 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTCTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:28568467 original size:41 final size:40
Alignment explanation
Indices: 28568421--28568778 Score: 374
Period size: 41 Copynumber: 8.6 Consensus size: 40
28568411 CTTTGAATGT
* * * *
28568421 AAGGGGTTGCTAAGTGCAGATTCCCTGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAT-TAA
* * *
28568462 AAGGGGTTGCTATGTGCTGATTCCCCATATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* *
28568502 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* *
28568546 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* * *
28568586 AAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* *
28568630 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* * * * *
28568670 AAGGTGGTTGGTAAGTGCTAATTCCACCATATGATTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* *
28568714 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
*
28568754 AAGGTGGTTGCTAAGTGTTGATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
28568779 ACCGGGATCC
Statistics
Matches: 262, Mismatches: 42, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
40 20 0.08
41 107 0.41
42 63 0.24
43 57 0.22
44 15 0.06
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
Found at i:28568564 original size:84 final size:84
Alignment explanation
Indices: 28568461--28568782 Score: 572
Period size: 84 Copynumber: 3.8 Consensus size: 84
28568451 CATTGATCAA
*
28568461 AAAGGGGTTGCTATGTGCTGATTCCCCATATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28568526 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
*
28568545 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28568610 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
* *
28568629 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGGTAAGTGCTAATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
* **
28568694 CACCATATGATTGATTGTG
66 CACCGTATCCTTGATTGTG
*
28568713 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28568778 CACCG
66 CACCG
28568783 GGATCCTTTG
Statistics
Matches: 226, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 226 1.00
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
CACCGTATCCTTGATTGTG
Found at i:28574862 original size:30 final size:30
Alignment explanation
Indices: 28574806--28574864 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28574796 CTTTTTAAAA
* * *
28574806 ATATTTACAAAATGAGGCATCTAATTTTTC
1 ATATTTACAAAAAGAGGCACCAAATTTTTC
28574836 ATATTTACAAAAAGA-GCAACCAAATTTTT
1 ATATTTACAAAAAGAGGC-ACCAAATTTTT
28574865 AAAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (30 bp):
ATATTTACAAAAAGAGGCACCAAATTTTTC
Found at i:28586043 original size:223 final size:223
Alignment explanation
Indices: 28585648--28586083 Score: 640
Period size: 223 Copynumber: 2.0 Consensus size: 223
28585638 TAAACTGAAT
* * * * * * *
28585648 CTAATTCTGAAAAGGTTGGATTTGTTGGATTGAAATTGAATGATATAAGCGTGTATTTGACCGAA
1 CTAATTCTAAAAAGGTTGGATTAGTTAGACTGAAATTGAATGATACAAGCGGGTATTCGACCGAA
* * *
28585713 TACTTGCAGCAGACTCTAAACATAGAGCAGCGTTTGTATAGAACGAAGACAAAATAGTGCAGGGT
66 TACTTGCAGCAGACTCTAAACATAAAGCAGCGTTTGTATAGAACGAAGACAAAATAGTACACGGT
* * * * * * *
28585778 ATCGTGCTAAGGCCTGTAGACATAGGCCAGGTAACTTGAGATCTTGC-TCTTGAAAGAAGCAAGT
131 ACCATGCTAAGGACTATAGACACAGGCCAGGTAACGTGAGATCTTGCTTC-CGAAAGAAGCAAGT
28585842 CACTTTAGGTCTCTTCTAAACCCTAAACC
195 CACTTTAGGTCTCTTCTAAACCCTAAACC
*
28585871 CTAATTCTAAAAAGGTTGGATTAGTTAGACTGAAATTGAATGATACAAGCGGGTATTCGACTGAA
1 CTAATTCTAAAAAGGTTGGATTAGTTAGACTGAAATTGAATGATACAAGCGGGTATTCGACCGAA
* ** *
28585936 TACTTGCAGCAGACTCTAGACATAAAGCAGCGTTTGTATAGAATTAAGACAAAATATTACACGGT
66 TACTTGCAGCAGACTCTAAACATAAAGCAGCGTTTGTATAGAACGAAGACAAAATAGTACACGGT
* *
28586001 ACCATGCTAAGGACTATAGACACAGGCCAGGTAACGTGAGATCTTGCTTCCGAAAGAATCAGGTC
131 ACCATGCTAAGGACTATAGACACAGGCCAGGTAACGTGAGATCTTGCTTCCGAAAGAAGCAAGTC
28586066 ACTTTAGGTCTCTTCTAA
196 ACTTTAGGTCTCTTCTAA
28586084 GTAGTAGAAT
Statistics
Matches: 188, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
223 186 0.99
224 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (223 bp):
CTAATTCTAAAAAGGTTGGATTAGTTAGACTGAAATTGAATGATACAAGCGGGTATTCGACCGAA
TACTTGCAGCAGACTCTAAACATAAAGCAGCGTTTGTATAGAACGAAGACAAAATAGTACACGGT
ACCATGCTAAGGACTATAGACACAGGCCAGGTAACGTGAGATCTTGCTTCCGAAAGAAGCAAGTC
ACTTTAGGTCTCTTCTAAACCCTAAACC
Found at i:28586589 original size:26 final size:26
Alignment explanation
Indices: 28586543--28586668 Score: 155
Period size: 26 Copynumber: 4.8 Consensus size: 26
28586533 GGCACATTCC
* *
28586543 ATCATAGTATCACAGCC-AAGTGTGTA
1 ATCACAGTATCACA-CCGAAGTGTGCA
* * * **
28586569 ATCTCAATATCACATCGAAGTACGCA
1 ATCACAGTATCACACCGAAGTGTGCA
28586595 ATCACAGTATCACACCGAAGTGTGCA
1 ATCACAGTATCACACCGAAGTGTGCA
*
28586621 ATCACAGTATCGCACCGAAGTGTGCA
1 ATCACAGTATCACACCGAAGTGTGCA
*
28586647 ATCACAGTATCGCACCGAAGTG
1 ATCACAGTATCACACCGAAGTG
28586669 CTCATCAATT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
25 1 0.01
26 85 0.99
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (26 bp):
ATCACAGTATCACACCGAAGTGTGCA
Found at i:28593316 original size:50 final size:50
Alignment explanation
Indices: 28593193--28593333 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 50
28593183 CACTATCCAA
* *
28593193 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCAAGCTATTTGG
* * * * *
28593244 TACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCT-TTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAGCTATT-TGG
* **
28593294 TACACGTAGTAGCTTGCACATAGTGTTACACATGTGACCA
1 TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
28593334 TCACTTTCAC
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.03
50 40 0.53
51 33 0.44
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAGCTATTTGG
Found at i:28609140 original size:40 final size:40
Alignment explanation
Indices: 28609095--28609286 Score: 190
Period size: 40 Copynumber: 4.8 Consensus size: 40
28609085 ATAACCACAA
* * * *
28609095 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAAATC
* *
28609135 GCACAAATGCCTTTGGGTCTTAGCCCGGATATATCAAATC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAAATC
* * * *
28609175 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAAATC
* * * * * *
28609215 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAAATC
* *
28609255 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
28609287 CATTCAAATG
Statistics
Matches: 138, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 133 0.96
41 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAAATC
Found at i:28609223 original size:80 final size:81
Alignment explanation
Indices: 28609094--28609285 Score: 228
Period size: 80 Copynumber: 2.4 Consensus size: 81
28609084 TATAACCACA
* * * * * * *
28609094 AGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTTGGGTCTTAG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAGCAACTAGCACAAATGCCTTCGGGACTTAG
*
28609158 CCCGGAT-ATATCAAAT
66 CCCGGATAAAATC-AAT
* * *
28609174 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCATAAATGCCTTCGGGACTTAG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAGCAACTAGCACAAATGCCTTCGGGACTTAG
*
28609238 CCCGGATAAAATCACT
66 CCCGGATAAAATCAAT
* *
28609254 AGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA
28609286 TCATTCAAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 88 0.93
81 7 0.07
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (81 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAGCAACTAGCACAAATGCCTTCGGGACTTAG
CCCGGATAAAATCAAT
Found at i:28611583 original size:23 final size:23
Alignment explanation
Indices: 28611516--28611583 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
28611506 TTGTCGATTC
* *
28611516 TGTGGAAGCCTTTATGGCTATTA
1 TGTGGAAGCCTTTGTGGCTGTTA
* *
28611539 TGTGGAAGCCTTTGTGGTTGTTT
1 TGTGGAAGCCTTTGTGGCTGTTA
*
28611562 TGTGGAAGCCTTTGTAGCTGTT
1 TGTGGAAGCCTTTGTGGCTGTT
28611584 CTAAATTGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.43
Consensus pattern (23 bp):
TGTGGAAGCCTTTGTGGCTGTTA
Found at i:28611810 original size:29 final size:30
Alignment explanation
Indices: 28611750--28611811 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
28611740 CTTGTTACAC
*
28611750 GTGAGCCCTTGTGGTAGAAATCTGGTATAT
1 GTGAGCCCTTGTGGTAGAAACCTGGTATAT
* * * *
28611780 GTGAGCCTTTGTGGT-GGAACCTGTTGTAT
1 GTGAGCCCTTGTGGTAGAAACCTGGTATAT
28611809 GTG
1 GTG
28611812 GAAGTCTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.35
Consensus pattern (30 bp):
GTGAGCCCTTGTGGTAGAAACCTGGTATAT
Found at i:28612279 original size:4 final size:4
Alignment explanation
Indices: 28612238--28612307 Score: 56
Period size: 4 Copynumber: 17.5 Consensus size: 4
28612228 AGATTTGATG
* * *
28612238 TGTA TGGA TGAA TGT- TGTGA TGT- TGTA TGTT TGTTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGT-A TGTA TGTA TGTA TG-TA TGTA TGTA TGTA
*
28612286 TATAA TGT- TGTA TGTA TGTA TG
1 TGT-A TGTA TGTA TGTA TGTA TG
28612308 ATAATGCCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
3 9 0.17
4 35 0.66
5 9 0.17
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:28612297 original size:20 final size:21
Alignment explanation
Indices: 28612274--28612313 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28612264 ATGTTTGTTA
28612274 TGTATGTATGTAT-ATAATGT
1 TGTATGTATGTATGATAATGT
28612294 TGTATGTATGTATGATAATG
1 TGTATGTATGTATGATAATG
28612314 CCTTGCTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
TGTATGTATGTATGATAATGT
Found at i:28613679 original size:30 final size:30
Alignment explanation
Indices: 28613645--28613711 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
28613635 AGAAAGATGG
*
28613645 AAAATGGCAACTCTGTTATGTCTGTAACAA
1 AAAATGGCAACTCTGTTATGTCTATAACAA
* ** * *
28613675 AAAATGGTAGTTTTGTTATGTCTATAACGA
1 AAAATGGCAACTCTGTTATGTCTATAACAA
28613705 AAAATGG
1 AAAATGG
28613712 TTAGTGTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (30 bp):
AAAATGGCAACTCTGTTATGTCTATAACAA
Found at i:28614688 original size:21 final size:21
Alignment explanation
Indices: 28614664--28614708 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28614654 AAATAAAAAC
* *
28614664 AAAATAATA-ATGACAATACTA
1 AAAATAAAATATG-CAATAATA
28614685 AAAATAAAATATGCAATAATA
1 AAAATAAAATATGCAATAATA
28614706 AAA
1 AAA
28614709 GCATGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAATAAAATATGCAATAATA
Found at i:28614969 original size:61 final size:62
Alignment explanation
Indices: 28614898--28615016 Score: 186
Period size: 61 Copynumber: 1.9 Consensus size: 62
28614888 TTTAAATATT
28614898 AAAAGAAGCGAAGGAATAATAAATAAG-TAAATAAATAAACAAATAAAAGAATGAAAATAAG
1 AAAAGAAGCGAAGGAATAATAAATAAGATAAATAAATAAACAAATAAAAGAATGAAAATAAG
* *
28614959 AAAATAAGCGAAGGAATAATAAATAAGAAAATAAGTAAATAAACAAATAAAAGAATGA
1 AAAAGAAGCGAAGGAATAATAAATAAG---ATAAATAAATAAACAAATAAAAGAATGA
28615017 TAATGAATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 26 0.50
65 26 0.50
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.15
Consensus pattern (62 bp):
AAAAGAAGCGAAGGAATAATAAATAAGATAAATAAATAAACAAATAAAAGAATGAAAATAAG
Found at i:28616258 original size:23 final size:23
Alignment explanation
Indices: 28616228--28616285 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
28616218 CATCTATTTT
*
28616228 TTTGTTTGGGTTGATTGGTTTGG
1 TTTGTTTGGGCTGATTGGTTTGG
28616251 TTTGTTTGGGCTGATTGGTTTGG
1 TTTGTTTGGGCTGATTGGTTTGG
28616274 TTTGTTTGGGCT
1 TTTGTTTGGGCT
28616286 CAGAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.03, C:0.03, G:0.38, T:0.55
Consensus pattern (23 bp):
TTTGTTTGGGCTGATTGGTTTGG
Found at i:28616697 original size:44 final size:44
Alignment explanation
Indices: 28616648--28616910 Score: 260
Period size: 44 Copynumber: 5.8 Consensus size: 44
28616638 AGATGTATAT
* * *
28616648 GATTTGTCGCTTCAATCTGCTCCACCT-CAACTTCAGGGAGATAA
1 GATTTGTAGCTTTAATCTGCTCCA-CTGCAACTTCAGGGAAATAA
* **
28616692 GATTTGTAAATCGTAGCTTTAATCTGTTCCACTGCAACTTTTTGGGAAATAA
1 GA--T-T---T-GTAGCTTTAATCTGCTCCACTGCAAC-TTCAGGGAAATAA
* * *
28616744 GATTTGTAGCTTTAATCTACT-CACTACAACTTTCAAGGAAATAA
1 GATTTGTAGCTTTAATCTGCTCCACTGCAAC-TTCAGGGAAATAA
* * *
28616788 GGTTTGTAGCTTTAATCTGCTCCACTGCAAATTCAGGGAGATAA
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAA
* *
28616832 GATTTGTAGCTTTAATATGCTCCACTGTAACTTCAGGGAAATAA
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAA
* * * *
28616876 GATTCGCAACTTTAATCCGCTCCACTGCAACTTCA
1 GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCA
28616911 AAGAGATAAG
Statistics
Matches: 180, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
44 119 0.66
45 21 0.12
46 2 0.01
47 1 0.01
49 1 0.01
50 4 0.02
51 20 0.11
52 12 0.07
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
GATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAA
Found at i:28616937 original size:132 final size:137
Alignment explanation
Indices: 28616660--28616939 Score: 295
Period size: 132 Copynumber: 2.1 Consensus size: 137
28616650 TTTGTCGCTT
* * *
28616660 CAATCTGCTCCACCTCAACTTCAGGGAGATAAGATTTGTAAATCGTAGCTTTAATCTGTTCCACT
1 CAATCTGCTCCACCTCAAATTCAGGGAGATAAGA-TTGT--ATCGTAGCTTTAATATGCTCCACT
** * * * * * *
28616725 GCAACTTTTTGGGAAATAAGATTTGTAGCTTTAATCTACTCACTACAACTTTCAAGGAAATAAGG
63 GCAACTTTCAGGGAAATAAGATTCGCAACTTTAATCCACTCACTACAACTTTCAAAGAAATAAGA
* * *
28616790 TTTGTAGCTT
128 TTGGTAACTC
* *
28616800 TAATCTGCTCCA-CTGCAAATTCAGGGAGATAAGA-T-T-T-GTAGCTTTAATATGCTCCACTGT
1 CAATCTGCTCCACCT-CAAATTCAGGGAGATAAGATTGTATCGTAGCTTTAATATGCTCCACTGC
* * *
28616860 AAC-TTCAGGGAAATAAGATTCGCAACTTTAATCCGCTCCACTGCAAC-TTCAAAGAGATAAGAT
65 AACTTTCAGGGAAATAAGATTCGCAACTTTAATCCACT-CACTACAACTTTCAAAGAAATAAGAT
28616923 TGGTAACTC
129 TGGTAACTC
28616932 CAATCTGC
1 CAATCTGC
28616940 GAACCTTTCA
Statistics
Matches: 118, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
132 53 0.45
133 31 0.26
134 1 0.01
137 1 0.01
138 1 0.01
139 2 0.02
140 29 0.25
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (137 bp):
CAATCTGCTCCACCTCAAATTCAGGGAGATAAGATTGTATCGTAGCTTTAATATGCTCCACTGCA
ACTTTCAGGGAAATAAGATTCGCAACTTTAATCCACTCACTACAACTTTCAAAGAAATAAGATTG
GTAACTC
Found at i:28620736 original size:26 final size:26
Alignment explanation
Indices: 28620700--28620751 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28620690 CATGGGGAAG
28620700 AAGATGATAATTCCTCATCTTTCCTT
1 AAGATGATAATTCCTCATCTTTCCTT
28620726 AAGATGATAATTCCTCATCTTTCCTT
1 AAGATGATAATTCCTCATCTTTCCTT
28620752 TCATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (26 bp):
AAGATGATAATTCCTCATCTTTCCTT
Found at i:28620807 original size:11 final size:13
Alignment explanation
Indices: 28620787--28620818 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28620777 AATAAATTAA
28620787 TAAAATATCAT-T
1 TAAAATATCATAT
28620799 TAAAA-ATCATAT
1 TAAAATATCATAT
28620811 TAAAATAT
1 TAAAATAT
28620819 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:28624752 original size:20 final size:20
Alignment explanation
Indices: 28624701--28624757 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
28624691 AACAACATCA
28624701 AAAAAATA-AA-AATAAAAT
1 AAAAAATACAATAATAAAAT
* *
28624719 -AATAATGACGATAATAAAAT
1 AAAAAAT-ACAATAATAAAAT
28624739 AAAAAATACAATAATAAAA
1 AAAAAATACAATAATAAAA
28624758 GCATGTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 1 0.03
20 19 0.61
21 5 0.16
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (20 bp):
AAAAAATACAATAATAAAAT
Done.