Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002602.1 Hibiscus syriacus cultivar Beakdansim tig00005261_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111681
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5907 original size:28 final size:28
Alignment explanation
Indices: 5854--5911 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5844 TCATACAATT
* * *
5854 TTTAAATTTGATATCCTAAATAAATTTC
1 TTTAAATTTAACATCCAAAATAAATTTC
*
5882 TTTAAATTTAACATCTCAAAATAATTTTC
1 TTTAAATTTAACATC-CAAAATAAATTTC
5911 T
1 T
5912 AATTCCGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTAAATTTAACATCCAAAATAAATTTC
Found at i:6389 original size:16 final size:17
Alignment explanation
Indices: 6370--6406 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
6360 ATCTAATCAA
6370 ATTTTTAATCAA-ATT-T
1 ATTTTTAA-CAAGATTAT
6386 ATTTTTAACAAGATTAT
1 ATTTTTAACAAGATTAT
6403 ATTT
1 ATTT
6407 AACTGAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 11 0.58
17 5 0.26
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTTAACAAGATTAT
Found at i:7619 original size:3 final size:3
Alignment explanation
Indices: 7598--7707 Score: 165
Period size: 3 Copynumber: 37.7 Consensus size: 3
7588 ACTGGGAGTA
* *
7598 AAG AAG AAT AAG -AG GAG AAG AAG AAG AAGG AAG AAG AAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG
7642 AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
7688 AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
7708 TAAAGAAAGA
Statistics
Matches: 99, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
2 8 0.08
3 88 0.89
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:7623 original size:20 final size:20
Alignment explanation
Indices: 7613--7703 Score: 145
Period size: 20 Copynumber: 4.8 Consensus size: 20
7603 GAATAAGAGG
7613 AGAAGAAGAAGAAG-GAAGA
1 AGAAGAAGAAGAAGAGAAGA
7632 AGAAGAA-AAG-A-AGAAGA
1 AGAAGAAGAAGAAGAGAAGA
7649 AGAAGAAGAAGAAGAGAAGA
1 AGAAGAAGAAGAAGAGAAGA
*
7669 AGAAGAAGAAGAAAAGAAGA
1 AGAAGAAGAAGAAGAGAAGA
7689 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
7704 AGAATAAAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
17 13 0.20
18 6 0.09
19 8 0.12
20 39 0.59
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAAGAAGAGAAGA
Found at i:7718 original size:20 final size:18
Alignment explanation
Indices: 7598--7707 Score: 165
Period size: 17 Copynumber: 6.3 Consensus size: 18
7588 ACTGGGAGTA
* *
7598 AAGAAGAATAAG-AGGAG
1 AAGAAGAAGAAGAAGAAG
7615 AAGAAGAAGAAGGAAGAAG
1 AAGAAGAAGAA-GAAGAAG
7634 AAGAA-AAGAAGAAGAAG
1 AAGAAGAAGAAGAAGAAG
7651 AAGAAGAAGAAG-AGAAG
1 AAGAAGAAGAAGAAGAAG
7668 AAGAAGAAGAAGAA-AAG
1 AAGAAGAAGAAGAAGAAG
7685 AAGAAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAGAAG
7703 AAGAA
1 AAGAA
7708 TAAAGAAAGA
Statistics
Matches: 86, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
17 56 0.65
18 21 0.24
19 9 0.10
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (18 bp):
AAGAAGAAGAAGAAGAAG
Found at i:9948 original size:56 final size:52
Alignment explanation
Indices: 9866--9980 Score: 167
Period size: 56 Copynumber: 2.1 Consensus size: 52
9856 ATGCTAACAA
* *
9866 ATACATAAATTATTATAAAATAAAGTTAATTATTAATACAATATGATATCAAATAT
1 ATACATAAATTATTATAAAATAAAGTTAATTATT-ATA-AA-A-AAAATCAAATAT
*
9922 ATACATAAATTATTATAAAATCAAGTTAATTATTATAAAAAAAATCAAATAT
1 ATACATAAATTATTATAAAATAAAGTTAATTATTATAAAAAAAATCAAATAT
9974 ATACATA
1 ATACATA
9981 CAAATACATA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
52 17 0.30
53 1 0.02
54 2 0.04
55 3 0.05
56 33 0.59
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (52 bp):
ATACATAAATTATTATAAAATAAAGTTAATTATTATAAAAAAAATCAAATAT
Found at i:12179 original size:21 final size:21
Alignment explanation
Indices: 12155--12208 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
12145 CAGTTTCCAA
12155 ATTCGCAACGCGAATATCT-AG
1 ATTCGCAACGCGAAT-TCTAAG
* *
12176 ATTCTCAACGCG-ATTGTAAG
1 ATTCGCAACGCGAATTCTAAG
12196 ATTCGCAACGCGA
1 ATTCGCAACGCGA
12209 TTTTGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
ATTCGCAACGCGAATTCTAAG
Found at i:12235 original size:22 final size:22
Alignment explanation
Indices: 12210--12272 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 22
12200 GCAACGCGAT
12210 TTTGAAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
12232 TTTGAAAAACGTGTTGTTGCGATAG
1 TTTGAAAAA--TG-TGTTGCGAGAG
12257 --TGAAAAA-GTGTTGCGA
1 TTTGAAAAATGTGTTGCGA
12273 TAGTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
22 9 0.24
23 7 0.19
24 2 0.05
25 10 0.27
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:12270 original size:19 final size:19
Alignment explanation
Indices: 12246--12282 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12236 AAAAACGTGT
12246 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
12265 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
12283 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:12718 original size:21 final size:21
Alignment explanation
Indices: 12694--12905 Score: 193
Period size: 21 Copynumber: 10.4 Consensus size: 21
12684 ATTTTGGAAA
*
12694 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
12715 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
* *
12734 ATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* * *
12755 ATCACAACACGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* **
12776 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
12795 ATCGTAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
12816 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
12837 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
* *
12856 ATTGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
12877 ATCGTAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
12898 ATCGCAAC
1 ATCGCAAC
12906 AAATTTGGAC
Statistics
Matches: 149, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
19 43 0.29
21 106 0.71
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:12748 original size:40 final size:40
Alignment explanation
Indices: 12686--12885 Score: 179
Period size: 40 Copynumber: 5.0 Consensus size: 40
12676 TCGTTGCGAT
*
12686 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAA
* * *
12726 TTTGGAAAATCGCAATGCGAACTTCGACTATCACAACACGAA
1 TTTGGAAAATCGCAACGCGAACTTGGACTATCGC-A-ACGAA
* * ** * ** *
12768 CTTCGACTATCGCAA--CGAATTTGGAAAATCGTAACGCGAA
1 TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAA--CGAA
* ** *
12808 CTTGGACTATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAA
* * *
12848 TTTGGAAAATTGCAACGCGAACTTCGACTATCGTAACG
1 TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACG
12886 TGAACTTGGA
Statistics
Matches: 127, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 94 0.74
41 1 0.01
42 30 0.24
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAA
Found at i:12780 original size:61 final size:61
Alignment explanation
Indices: 12694--12914 Score: 352
Period size: 61 Copynumber: 3.6 Consensus size: 61
12684 ATTTTGGAAA
*
12694 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* ** * * *
12755 ATCACAACACGAACTTCGACTATCGCAACGAATTTGGAAAATCGTAACGCGAACTTGGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
12816 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATTGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* *
12877 ATCGTAACGTGAACTTGGACTATCGCAACAAATTTGGA
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGA
12915 CTAACATAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 144 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (61 bp):
ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:12917 original size:40 final size:39
Alignment explanation
Indices: 12694--12917 Score: 155
Period size: 40 Copynumber: 5.5 Consensus size: 39
12684 ATTTTGGAAA
* * **
12694 ATCGCAACGTGAACTTGGACTATCGCAAC-GAATTTGGAAA
1 ATCGCAAC--GAACTTGGACTATCGTAACGGAACTTGGACT
* ** * *
12734 ATCGCAATGCGAACTTCGACTATCACAACACGAACTTCGACT
1 ATCGCAA--CGAACTTGGACTATCGTAAC-GGAACTTGGACT
* **
12776 ATCGCAACGAATTTGGAAAATCGTAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGACTATCGTAACG-GAACTTGGACT
* * **
12816 ATCGCAACGTGAACTTGGACTATCGCAAC-GAATTTGGAAA
1 ATCGCAAC--GAACTTGGACTATCGTAACGGAACTTGGACT
* *
12856 ATTGCAACGCGAACTTCGACTATCGTAACGTGAACTTGGACT
1 ATCGCAA--CGAACTTGGACTATCGTAACG-GAACTTGGACT
* *
12898 ATCGCAACAAATTTGGACTA
1 ATCGCAACGAACTTGGACTA
12918 ACATAAATTT
Statistics
Matches: 142, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
40 97 0.68
42 45 0.32
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (39 bp):
ATCGCAACGAACTTGGACTATCGTAACGGAACTTGGACT
Found at i:12947 original size:19 final size:19
Alignment explanation
Indices: 12923--12960 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12913 GACTAACATA
*
12923 AATTTGGAAAATTGCAACG
1 AATTTGGAAAATGGCAACG
12942 AATTTGGAAAATGGCAACG
1 AATTTGGAAAATGGCAACG
12961 CGAAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (19 bp):
AATTTGGAAAATGGCAACG
Found at i:12969 original size:21 final size:19
Alignment explanation
Indices: 12926--12970 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12916 TAACATAAAT
* *
12926 TTGGAAAATTGCAACGAAT
1 TTGGAAAATGGCAACGAAA
12945 TTGGAAAATGGCAACGCGAAA
1 TTGGAAAATGGCAA--CGAAA
12966 TTGGA
1 TTGGA
12971 CTATCGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.22
Consensus pattern (19 bp):
TTGGAAAATGGCAACGAAA
Found at i:15799 original size:20 final size:21
Alignment explanation
Indices: 15774--15814 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15764 GATGTGATTG
15774 TTTCTAGTC-GTTGGGGATGA
1 TTTCTAGTCAGTTGGGGATGA
*
15794 TTTCTAGTCATTTGGGGATGA
1 TTTCTAGTCAGTTGGGGATGA
15815 AATCTCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.17, C:0.10, G:0.32, T:0.41
Consensus pattern (21 bp):
TTTCTAGTCAGTTGGGGATGA
Found at i:16920 original size:23 final size:23
Alignment explanation
Indices: 16894--16971 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
16884 CACCACAGCT
16894 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
16917 CATATAATTGCATCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
16940 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
16963 TATAATAAT
1 CAT-ATAAT
16972 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:17149 original size:103 final size:103
Alignment explanation
Indices: 16978--17195 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
16968 TAATGTCCAT
* *
16978 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
17043 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
* * *
17081 AAGGACTACATATCATTCCTTAAGAATCATATACATCTGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
17146 GACTTCACACATATTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
17184 AAGGACCACATA
1 AAGGACCACATA
17196 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:22417 original size:43 final size:43
Alignment explanation
Indices: 22195--22570 Score: 230
Period size: 43 Copynumber: 8.7 Consensus size: 43
22185 TAATTTTAGT
* * * * *
22195 TTTTTATCATTATAATTGAAGTCCCTAATTTTTGT-AATCTTAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTT-TCAATCATAC
* * * * *
22238 TTTTTATCTTTATAATGGAGGCTCTTAATTTTTTTTCAATACCAT-T
1 TTTTTACCTTTATAATTGAGGCCCCTAA--TTTTTTCAAT--CATAC
* * ** * **
22284 TTTTTACATTTATAATTGATGATCCTAAGTTTTTCAATCCCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCATAC
* * ** **
22327 ATTGTACCTTTATAATT-AGGCTTCTGCTTTTTTCAAT-ATCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCAT-AC
*
22369 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCCTA-
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCATAC
* * *
22411 TATTTTA-ATCATATAATTTAGGCCCCTAATTTTTTCAAT-ATCAC
1 T-TTTTACCT-TTATAATTGAGGCCCCTAATTTTTTCAATCAT-AC
* * * * *
22455 TTTTTACCTTTAAAATCGATGCCCCT-ATTTTTTTAAT-ATCAT
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCAT-AC
* * * * *
22497 TTTTTAACTTTATAATTGGGGTCCTTAATTTTTTTAATCATAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCATAC
* * **
22540 TTTTTACTTTTATAATTTAAACCCCTAATTT
1 TTTTTACCTTTATAATTGAGGCCCCTAATTT
22571 AATCATTTTT
Statistics
Matches: 253, Mismatches: 64, Indels: 32
0.72 0.18 0.09
Matches are distributed among these distances:
42 68 0.27
43 138 0.55
44 15 0.06
45 8 0.03
46 22 0.09
47 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCATAC
Found at i:22861 original size:2 final size:2
Alignment explanation
Indices: 22854--22901 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
22844 TAAACGAGTC
22854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22896 TA TA TA
1 TA TA TA
22902 ATGAGTTCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23160 original size:5 final size:5
Alignment explanation
Indices: 23150--23174 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23140 ATTTGATTAA
23150 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
23175 GAGATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:25297 original size:61 final size:59
Alignment explanation
Indices: 25202--25335 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 59
25192 TAAAGTATAT
25202 AAATGGTCCCCGACTATAAGATATTACTTTGTTGAGTCC-TCCGACTATTAAAAGTTTTAAA
1 AAATGGTCCCCGACTATAAGATATTACTTTGTTGAGTCCAT-CGACTATTAAAAG--TTAAA
* * *
25263 AAATGGTCCCCGACTATAAAGA-GTTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACA
1 AAATGGTCCCCGACTAT-AAGATATTACTTTGTTGAGTCCATCGACTATTAAAAGTTAAA
25322 AAATGGTCACCCGA
1 AAATGGTC-CCCGA
25336 TTATTCATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
59 12 0.18
60 5 0.07
61 45 0.67
62 5 0.07
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (59 bp):
AAATGGTCCCCGACTATAAGATATTACTTTGTTGAGTCCATCGACTATTAAAAGTTAAA
Found at i:26578 original size:20 final size:20
Alignment explanation
Indices: 26555--26606 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
26545 AACGCGATCC
26555 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
26575 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
26595 CCAAAATCGCAA
1 CCAGAATCGCAA
26607 CGTGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:26687 original size:20 final size:20
Alignment explanation
Indices: 26662--26855 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
26652 GATTTTCCAT
* *
26662 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
26682 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
26702 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
26722 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
26742 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
26762 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
26782 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
26802 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
26823 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
26843 AATCGCAACGCGA
1 AATCGCAACGCGA
26856 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:26707 original size:40 final size:39
Alignment explanation
Indices: 26658--26855 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
26648 TTGCGATTTT
* ** *
26658 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
26696 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
26737 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
26777 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
26816 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
26856 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:26731 original size:60 final size:60
Alignment explanation
Indices: 26662--26855 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
26652 GATTTTCCAT
** * *
26662 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * * *** *
26722 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * **
26782 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
26843 AATCGCAACGCGA
1 AATCGCAACGCGA
26856 TATTTAAAGC
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:27271 original size:33 final size:33
Alignment explanation
Indices: 27232--27302 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
27222 TTCACTTAGA
*
27232 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
27265 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
27298 TTTCA
1 TTTCA
27303 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:27442 original size:14 final size:14
Alignment explanation
Indices: 27423--27477 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
27413 AGAATGACTG
27423 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
27437 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
27456 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
27470 TCGCAACG
1 TCGCAACG
27478 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:27460 original size:33 final size:33
Alignment explanation
Indices: 27423--27493 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
27413 AGAATGACTG
**
27423 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
27456 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
27489 TCGCA
1 TCGCA
27494 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:27511 original size:19 final size:19
Alignment explanation
Indices: 27489--27586 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
27479 GAAACCAAAA
*
27489 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27508 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
27522 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27541 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
27555 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
27574 TCGCGTTGCGATT
1 TCGCGTTGCGATT
27587 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27530 original size:14 final size:14
Alignment explanation
Indices: 27511--27600 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
27501 TTTCATTTCG
27511 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
27525 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
27544 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
27558 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
27575 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
27591 CGTTGCGATT
1 CGTTGCGATT
27601 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:27536 original size:33 final size:33
Alignment explanation
Indices: 27494--27608 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
27484 CAAAATCGCA
27494 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
27527 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
27560 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
27593 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
27609 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:29480 original size:185 final size:186
Alignment explanation
Indices: 29250--29907 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
29240 TAGATTGCTT
*
29250 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29315 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
29380 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
29435 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29500 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
29565 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
29621 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29685 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
29750 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
29806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29871 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
29908 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 131 0.28
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:29564 original size:93 final size:93
Alignment explanation
Indices: 29250--29907 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
29240 TAGATTGCTT
*
29250 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29315 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29343 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29407 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29435 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29500 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29528 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29593 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29621 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29685 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29713 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29778 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29871 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29899 AGTAAATTT
1 AGTAAATTT
29908 ATCCATTCAA
Statistics
Matches: 562, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.33
93 378 0.67
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:29747 original size:278 final size:278
Alignment explanation
Indices: 29250--29907 Score: 1307
Period size: 278 Copynumber: 2.4 Consensus size: 278
29240 TAGATTGCTT
*
29250 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29315 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
29380 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
29445 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
29510 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
29528 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29593 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
29658 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
29723 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
29788 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
29806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29871 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
29908 ATCCATTCAA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 379 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:29991 original size:19 final size:19
Alignment explanation
Indices: 29951--30079 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
29941 TAGTTTACTT
* *
29951 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
29971 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
29990 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
30009 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
30023 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
30042 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
30056 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
30075 TCGCA
1 TCGCA
30080 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:30030 original size:33 final size:32
Alignment explanation
Indices: 29987--30079 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
29977 CGCGAAACCA
**
29987 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
30019 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
30052 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
30080 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:30077 original size:52 final size:52
Alignment explanation
Indices: 29951--30079 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
29941 TAGTTTACTT
**
29951 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
30003 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
30056 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
30080 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:30097 original size:19 final size:19
Alignment explanation
Indices: 30075--30209 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
30065 GAAACCAAAA
*
30075 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
30094 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
30110 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
30127 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
30143 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
30160 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
30179 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
30199 TCGTGTTGCGA
1 TCGCGTTGCGA
30210 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:30116 original size:14 final size:14
Alignment explanation
Indices: 30097--30153 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
30087 TTTCATTTCG
30097 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
30111 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
30128 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
30144 CGTTGCGATT
1 CGTTGCGATT
30154 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:30122 original size:33 final size:33
Alignment explanation
Indices: 30080--30172 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
30070 CAAAATCGCA
*
30080 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
30113 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
30146 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
30173 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:32132 original size:14 final size:14
Alignment explanation
Indices: 32113--32148 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32103 ATTGTTTAAT
32113 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
32127 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
32141 TGATTTGT
1 TGATTTGT
32149 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:32271 original size:19 final size:19
Alignment explanation
Indices: 32255--32356 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
32245 AAAAATGACT
32255 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32274 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32293 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
32307 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32326 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
32346 ATCGCAATGCG
1 ATCGCAATGCG
32357 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32405 original size:33 final size:35
Alignment explanation
Indices: 32363--32604 Score: 197
Period size: 33 Copynumber: 6.9 Consensus size: 35
32353 TGCGTTTATA
32363 ATTTCGCATTGCGATT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
32396 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
32432 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
* *
32467 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
* *
32503 -TGTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTCATCTCG-ATTGCGATTTTC
32537 ATTTCGCATTGCGATTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
32570 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATT
32605 CTCTCGTTGC
Statistics
Matches: 182, Mismatches: 7, Indels: 35
0.81 0.03 0.16
Matches are distributed among these distances:
32 17 0.09
33 70 0.38
34 3 0.02
35 25 0.14
36 23 0.13
37 6 0.03
38 38 0.21
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
Found at i:32409 original size:19 final size:19
Alignment explanation
Indices: 32385--32671 Score: 329
Period size: 19 Copynumber: 16.4 Consensus size: 19
32375 GATTATCTCG
32385 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32404 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32423 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
32437 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32456 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32475 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32494 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
32508 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32526 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32545 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
32559 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32578 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
32597 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
32611 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
32631 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
32645 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
32664 TTGCGATT
1 TTGCGATT
32672 GTATTTTCCG
Statistics
Matches: 232, Mismatches: 10, Indels: 52
0.79 0.03 0.18
Matches are distributed among these distances:
14 35 0.15
15 3 0.01
16 32 0.14
17 23 0.10
18 9 0.04
19 118 0.51
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:32425 original size:52 final size:49
Alignment explanation
Indices: 32363--32671 Score: 289
Period size: 52 Copynumber: 5.9 Consensus size: 49
32353 TGCGTTTATA
*
32363 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
*
32415 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-T-TTTCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
** * *
32467 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTCTGTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATTTC-G-CGTTGCGATTTTC
* * * *
32518 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * * *
32570 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
*
32622 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTC--GTTGCGA-TTTCATTTCGCGTTGCGATT
32672 GTATTTTCCG
Statistics
Matches: 232, Mismatches: 12, Indels: 25
0.86 0.04 0.09
Matches are distributed among these distances:
50 13 0.06
51 48 0.21
52 129 0.56
53 31 0.13
54 5 0.02
55 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (49 bp):
ATTTCGCATTGCGATTTTCGTTGCGATTTCATTTCGCGTTGCGATTTTC
Found at i:32565 original size:122 final size:124
Alignment explanation
Indices: 32347--32604 Score: 459
Period size: 122 Copynumber: 2.1 Consensus size: 124
32337 GAAATGAAAA
*
32347 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
*
32411 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
32470 TCGCATTGCGATTT-TAATTTCGCATTGCGATTCTGTCGTTGCGA-TTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
32533 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
32592 TCGCATTGCGATT
1 TCGCATTGCGATT
32605 CTCTCGTTGC
Statistics
Matches: 130, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
122 90 0.69
123 37 0.28
124 3 0.02
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (124 bp):
TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:32615 original size:33 final size:33
Alignment explanation
Indices: 32404--32671 Score: 249
Period size: 33 Copynumber: 7.8 Consensus size: 33
32394 TCATTTCGCA
*
32404 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32437 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
32473 CATTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32508 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
32543 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
32578 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32611 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
32645 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
32672 GTATTTTCCG
Statistics
Matches: 198, Mismatches: 18, Indels: 38
0.78 0.07 0.15
Matches are distributed among these distances:
31 9 0.05
32 22 0.11
33 68 0.34
34 32 0.16
35 14 0.07
36 8 0.04
37 8 0.04
38 25 0.13
39 3 0.02
40 9 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:34971 original size:12 final size:12
Alignment explanation
Indices: 34954--34978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34944 TCTTCGGGGA
34954 CTTTTTCTTCTT
1 CTTTTTCTTCTT
34966 CTTTTTCTTCTT
1 CTTTTTCTTCTT
34978 C
1 C
34979 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:35187 original size:24 final size:24
Alignment explanation
Indices: 35153--35199 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35143 CTGAAACATC
35153 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
35177 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
35200 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:35910 original size:20 final size:20
Alignment explanation
Indices: 35882--36250 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
35872 AAATTTCAGT
* * * *
35882 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
35902 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
35922 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
35942 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
35962 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
35982 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
36002 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
36022 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36042 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36062 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
36082 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
36102 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
36122 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
36142 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
36162 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
36182 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
36202 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
36222 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
36242 GTTGCGATT
1 GTTGCGATT
36251 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:37077 original size:13 final size:14
Alignment explanation
Indices: 37054--37083 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
37044 TTCCCATTAC
37054 AGACGTGCATATGA
1 AGACGTGCATATGA
37068 AGAC-TGCATATGA
1 AGACGTGCATATGA
37081 AGA
1 AGA
37084 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:41880 original size:22 final size:20
Alignment explanation
Indices: 41859--41926 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
41849 GCAAAGAAAT
41859 TAAAAATATAATGAAAATAAA
1 TAAAAATATAAT-AAAATAAA
*
41880 TAAATAGTATAAATAAAAT-AA
1 TAAA-AATAT-AATAAAATAAA
*
41901 TAAAAATATATATAAAA-ATA
1 TAAAAATATA-ATAAAATAAA
41921 TAAAAA
1 TAAAAA
41927 AATGTATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.03
20 17 0.43
21 10 0.25
22 9 0.22
23 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
TAAAAATATAATAAAATAAA
Found at i:41883 original size:21 final size:22
Alignment explanation
Indices: 41859--42002 Score: 72
Period size: 21 Copynumber: 6.5 Consensus size: 22
41849 GCAAAGAAAT
41859 TAAAAATATAATG-AAAATAAA
1 TAAAAATATAATGTAAAATAAA
* *
41880 TAAATAGTATAA-ATAAAAT-AA
1 TAAA-AATATAATGTAAAATAAA
*
41901 TAAAAATATATAT-AAAAATATAA
1 TAAAAATATA-ATGTAAAATA-AA
* *
41924 -AAAAATGT-ATGTATAATATAA
1 TAAAAATATAATGTAAAATA-AA
41945 T-AAAATACTAAATAGTAATAAT-AA
1 TAAAAATA-T-AAT-GTAA-AATAAA
*
41969 TAATAAATA-AATGAAAAATAAA
1 TAA-AAATATAATGTAAAATAAA
* *
41991 TATACATATAAT
1 TAAAAATATAAT
42003 ATTAACTAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 33
0.68 0.09 0.24
Matches are distributed among these distances:
20 7 0.07
21 36 0.38
22 29 0.31
23 5 0.05
24 5 0.05
25 4 0.04
26 8 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (22 bp):
TAAAAATATAATGTAAAATAAA
Found at i:41929 original size:22 final size:20
Alignment explanation
Indices: 41860--41927 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
41850 CAAAGAAATT
*
41860 AAAAATATA-ATGAAAATAA
1 AAAAATATATATAAAAATAA
* *
41879 ATAAATAGTATAAATAAAATAA
1 AAAAATA-TATATA-AAAATAA
41901 TAAAAATATATATAAAAATATA
1 -AAAAATATATATAAAAATA-A
41923 AAAAA
1 AAAAA
41928 ATGTATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.15
20 2 0.05
21 12 0.31
22 13 0.33
23 6 0.15
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAATATATATAAAAATAA
Found at i:41938 original size:24 final size:24
Alignment explanation
Indices: 41872--41944 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
41862 AAATATAATG
*
41872 AAAATAA-ATAAATA-GTATAAAT
1 AAAATAATAAAAATATGTATAAAT
*
41894 AAAATAATAAAAATATATATAAA-
1 AAAATAATAAAAATATGTATAAAT
*
41917 AATATAA-AAAAATGTATGTATAATAT
1 AAAATAATAAAAA--TATGTATAA-AT
41943 AA
1 AA
41945 TAAAATACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 14 0.34
25 1 0.02
26 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAATAATAAAAATATGTATAAAT
Found at i:41945 original size:44 final size:42
Alignment explanation
Indices: 41859--41949 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 42
41849 GCAAAGAAAT
* *
41859 TAAAAATATAATGAAAATAAATAAATAGTATAAATAAAATAA
1 TAAAAATATAATAAAAATAAAAAAATAGTATAAATAAAATAA
** *
41901 TAAAAATATATATAAAAATATAAAAAA-ATGTATGTATAATATAA
1 TAAAAATATA-ATAAAAATA-AAAAAATA-GTATAAATAAAATAA
41945 TAAAA
1 TAAAA
41950 TACTAAATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 10 0.24
43 9 0.22
44 22 0.54
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (42 bp):
TAAAAATATAATAAAAATAAAAAAATAGTATAAATAAAATAA
Found at i:42731 original size:37 final size:37
Alignment explanation
Indices: 42638--42739 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
42628 ATGCTTGTAA
* * * * *
42638 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATACTAGCAAAACTCT
*
42675 ATCCTATTTTTAGGAGTTTGAATACTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATACTAGCAAAACTCT
* *
42712 ATCTTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATACTAG
42740 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATACTAGCAAAACTCT
Found at i:43677 original size:106 final size:106
Alignment explanation
Indices: 43492--44762 Score: 2013
Period size: 106 Copynumber: 12.0 Consensus size: 106
43482 GCATTGTTCC
* * * * * * *
43492 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
43557 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
43598 GAGTCCAATATCCTTTGTTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
43663 CCAGCAGTCTCTTCGTCGTGAAGTTGAACTTGCGTTATCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
43704 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
43769 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
43810 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
43875 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
43916 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
43981 CCAGCGGTCCGTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
44022 GAGTCCAATATCTTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
44087 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
44128 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
44193 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
44234 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
44299 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
44340 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGGCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
44405 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
44446 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
44511 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
44552 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
44617 CCAGTGGTCCCTTCGTCGTGAAGTTGAATTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
44658 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * **
44723 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTATGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
44763 CAAGTGGCAC
Statistics
Matches: 1082, Mismatches: 82, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
105 1 0.00
106 1081 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:45768 original size:21 final size:22
Alignment explanation
Indices: 45730--45784 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
45720 TTGTGTTTGG
45730 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
45752 TCAAAGGTTTG-CATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
45773 TCAAAGGTTTGA
1 TCAAAGGTTTGA
45785 TGGGGTAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:46419 original size:17 final size:16
Alignment explanation
Indices: 46385--46445 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
46375 TTTTTGTCCC
*
46385 TTTTTCTTTTTGATT-T
1 TTTTTCTTTTT-TTTCT
* *
46401 TTGTTCTTTTTTTTGT
1 TTTTTCTTTTTTTTCT
*
46417 TTTCTTCTTTGTTTTCT
1 TTT-TTCTTTTTTTTCT
46434 TCTTTTCTTTTT
1 T-TTTTCTTTTT
46446 GTTTTTTCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 13 0.36
17 19 0.53
18 2 0.06
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCT
Found at i:46427 original size:12 final size:12
Alignment explanation
Indices: 46412--46438 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46402 TGTTCTTTTT
46412 TTTGTTTTCTTC
1 TTTGTTTTCTTC
46424 TTTGTTTTCTTC
1 TTTGTTTTCTTC
46436 TTT
1 TTT
46439 TCTTTTTGTT
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:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTGTTTTCTTC
Found at i:46431 original size:20 final size:19
Alignment explanation
Indices: 46408--46452 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
46398 TTTTTGTTCT
*
46408 TTTTTTTGTTTTCTTCTTTG
1 TTTTTTTCTTTTCTT-TTTG
*
46428 TTTTCTTCTTTTCTTTTTG
1 TTTTTTTCTTTTCTTTTTG
46447 TTTTTT
1 TTTTTT
46453 CCCTTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTTTTCTTTTTG
Found at i:46460 original size:29 final size:29
Alignment explanation
Indices: 46398--46465 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
46388 TTCTTTTTGA
**
46398 TTTTTGTTC-TTTTTTTTGTTTTCTTCTT
1 TTTTTGTTCTTTTTTTTTGTTTTCTTCCC
*
46426 TGTTTTCTTCTTTTCTTTTTGTTTT-TTCCC
1 T-TTTTGTTCTTTT-TTTTTGTTTTCTTCCC
46456 TTTTTGTTCT
1 TTTTTGTTCT
46466 GATTGAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 15 0.45
30 7 0.21
31 10 0.30
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (29 bp):
TTTTTGTTCTTTTTTTTTGTTTTCTTCCC
Found at i:50789 original size:20 final size:20
Alignment explanation
Indices: 50739--50793 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
50729 AACCAATAAT
50739 AATAAACATAAAAT--AATTG
1 AATAAA-ATAAAATAAAATTG
*
50758 GATGAAAA-AAAATAAAATTG
1 AAT-AAAATAAAATAAAATTG
50778 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
50794 TGAAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 18 0.60
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (20 bp):
AATAAAATAAAATAAAATTG
Found at i:50910 original size:22 final size:21
Alignment explanation
Indices: 50884--51000 Score: 74
Period size: 26 Copynumber: 4.9 Consensus size: 21
50874 AAACTAAAAA
50884 TATAATGAAAATAAATAAATAG
1 TATAAT-AAAATAAATAAATAG
*
50906 TATAAATAAAAT-AATAAAATATA
1 TAT-AATAAAATAAAT-AAATA-G
*
50929 TATATATATAAATATAAAAATATATG
1 TATA-ATA-AAATA-AATAA-ATA-G
50955 TATAATAAAATAAAATACTAAATAG
1 TATAATAAAAT--AA-A-TAAATAG
50980 TAATAATAAAAATAAATAAAT
1 T-ATAAT-AAAATAAATAAAT
51001 GAAAAATAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 27
0.71 0.04 0.25
Matches are distributed among these distances:
21 3 0.04
22 14 0.18
23 14 0.18
24 9 0.12
25 10 0.13
26 20 0.26
27 7 0.09
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (21 bp):
TATAATAAAATAAATAAATAG
Found at i:50925 original size:26 final size:26
Alignment explanation
Indices: 50896--50999 Score: 78
Period size: 26 Copynumber: 4.1 Consensus size: 26
50886 TAATGAAAAT
50896 AAATAAATAGTATAAATAAAATAATA
1 AAATAAATAGTATAAATAAAATAATA
* *
50922 AAATATATA-TATATAT-AAAT-ATA
1 AAATAAATAGTATAAATAAAATAATA
*
50945 AAA-ATATATGTAT-AATAAAATAA-A
1 AAATAAATA-GTATAAATAAAATAATA
*
50969 ATACTAAATAGTA-ATAATAAAAATAAATA
1 A-AATAAATAGTATA-AAT-AAAAT-AATA
50998 AA
1 AA
51000 TGAAAAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
22 5 0.08
23 8 0.13
24 13 0.21
25 11 0.18
26 15 0.24
27 5 0.08
28 3 0.05
29 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
AAATAAATAGTATAAATAAAATAATA
Found at i:50935 original size:8 final size:8
Alignment explanation
Indices: 50892--50953 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
50882 AATATAATGA
*
50892 AAATAAAT
1 AAATATAT
50900 AAATAGTAT
1 AAATA-TAT
50909 -AA-ATA-
1 AAATATAT
50914 AAATA-AT
1 AAATATAT
50921 AAAATATAT
1 -AAATATAT
*
50930 ATATATAT
1 AAATATAT
*
50938 AAATATAA
1 AAATATAT
50946 AAATATAT
1 AAATATAT
50954 GTATAATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 32 0.74
9 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (8 bp):
AAATATAT
Found at i:50948 original size:24 final size:22
Alignment explanation
Indices: 50883--51023 Score: 93
Period size: 24 Copynumber: 6.4 Consensus size: 22
50873 GAAACTAAAA
50883 ATATAATGAAAATAAATAA-ATAGT
1 ATATAAT-AAAATAAA-AATATA-T
50907 ATA-AATAAAATAATAAAATATAT
1 ATATAATAAAAT-A-AAAATATAT
50930 ATATATATAAATATAAAAATATAT
1 ATATA-ATAAA-ATAAAAATATAT
*
50954 GTATAATAAAAT-AAAATACTA-
1 ATATAATAAAATAAAAATA-TAT
*
50975 A-ATAGTAATAATAAAAATA-A-
1 ATATAATAA-AATAAAAATATAT
* *
50995 ATA-AATGAAAA-ATAAATATAC
1 ATATAAT-AAAATAAAAATATAT
51016 ATATAATA
1 ATATAATA
51024 TTAATTAAAA
Statistics
Matches: 98, Mismatches: 5, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
19 6 0.06
20 13 0.13
21 16 0.16
22 18 0.18
23 15 0.15
24 22 0.22
25 6 0.06
26 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (22 bp):
ATATAATAAAATAAAAATATAT
Found at i:51033 original size:43 final size:43
Alignment explanation
Indices: 50907--51034 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 43
50897 AATAAATAGT
* * *
50907 ATAAATAAAATAATAAAATATATATATATATAAATATAAAAATAT
1 ATAAATAAAA-AATAAAATACATATA-ATATTAATATAAAAATAA
** *
50952 ATGTATAATAAAATAAAATAC-TA-AATAGTAATAATAAAAATAA
1 ATAAATAA-AAAATAAAATACATATAATATTAAT-ATAAAAATAA
*
50995 ATAAATGAAAAATAAATATACATATAATATTAAT-TAAAAA
1 ATAAATAAAAAATAAA-ATACATATAATATTAATATAAAAA
51035 AATAGTAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
42 14 0.21
43 25 0.37
44 4 0.06
45 23 0.34
46 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (43 bp):
ATAAATAAAAAATAAAATACATATAATATTAATATAAAAATAA
Found at i:51170 original size:16 final size:15
Alignment explanation
Indices: 51140--51191 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
51130 GTAAACATAG
*
51140 ATAAAAAAATAATAAT
1 ATAAAATAAT-ATAAT
*
51156 ATAATATATATATAAT
1 ATAAAATA-ATATAAT
*
51172 AGGAAAATAATATAAT
1 A-TAAAATAATATAAT
51188 ATAA
1 ATAA
51192 CGCAAAGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.07
16 20 0.69
17 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
ATAAAATAATATAAT
Found at i:51236 original size:23 final size:24
Alignment explanation
Indices: 51201--51248 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
51191 ACGCAAAGAA
51201 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
51225 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
51248 A
1 A
51249 TATACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:51715 original size:37 final size:37
Alignment explanation
Indices: 51674--51758 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
51664 AAATCATATC
* *
51674 TTTAGGAGTTTAAATAATAGTATAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
* ** * *
51711 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTGTT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
51748 TTTAGGAGTTT
1 TTTAGGAGTTT
51759 GAATCCTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Found at i:57819 original size:19 final size:20
Alignment explanation
Indices: 57778--57819 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
57768 AAAGCAGATA
*
57778 AAAGAAAAAGGACAATTAGC
1 AAAGAAAAAGGACAATTACC
* *
57798 AAAGAAGAA-GACGATTACC
1 AAAGAAAAAGGACAATTACC
57817 AAA
1 AAA
57820 AACAAAAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.60, C:0.12, G:0.19, T:0.10
Consensus pattern (20 bp):
AAAGAAAAAGGACAATTACC
Found at i:58228 original size:2 final size:2
Alignment explanation
Indices: 58223--58259 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
58213 ATAGACACAC
58223 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
58260 CGGAGGGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58268 original size:4 final size:4
Alignment explanation
Indices: 58261--58291 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
58251 AGAGAGAGAC
58261 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGA
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGA
58292 AATTATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:58654 original size:3 final size:3
Alignment explanation
Indices: 58643--58708 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
58633 TTTTTTTCCG
**
58643 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58688 TT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
58709 CAAATTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 8 0.15
3 43 0.80
4 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58704 original size:26 final size:29
Alignment explanation
Indices: 58643--58708 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
58633 TTTTTTTCCG
* *
58643 TTATTTTATTATTATTATTATTATTATCG
1 TTATATTATTATTATTATTATTATTATCA
*
58672 TTATATTATTATT-TTATT-TTATTATTA
1 TTATATTATTATTATTATTATTATTATCA
58699 TT-TATTATTA
1 TTATATTATTA
58709 CAAATTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.24
27 9 0.26
28 5 0.15
29 12 0.35
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (29 bp):
TTATATTATTATTATTATTATTATTATCA
Found at i:72093 original size:16 final size:16
Alignment explanation
Indices: 72074--72108 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
72064 AAAAAAAAGG
72074 AAATGAAAAA-AATGAA
1 AAATGAAAAAGAA-GAA
72090 AAATGAAAAAGAAGAA
1 AAATGAAAAAGAAGAA
72106 AAA
1 AAA
72109 ATAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATGAAAAAGAAGAA
Found at i:72107 original size:15 final size:14
Alignment explanation
Indices: 72065--72107 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
72055 ATACTTAAAA
*
72065 AAAAAAAGGAAATG
1 AAAAAAAGAAAATG
72079 AAAAAAATGAAAAATG
1 AAAAAAA-G-AAAATG
72095 AAAAAGAAGAAAA
1 AAAAA-AAGAAAA
72108 AATAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 11 0.44
17 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAAAAAGAAAATG
Found at i:73356 original size:87 final size:90
Alignment explanation
Indices: 73192--73403 Score: 295
Period size: 89 Copynumber: 2.4 Consensus size: 90
73182 GTCATCCCCA
* *
73192 GACCAGACCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
* **
73257 GGAACCGTGTTATCA-CCTTTAGAT
66 GGAACCGAGTTATCACCCTAAAGAT
* * *
73281 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATTACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
73344 GGAACCGAGTTATCATCCCTAAAGAT
66 GGAACCGAGTTATCA-CCCTAAAGAT
* * *
73370 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
73404 CCCTTAGACG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 37 0.34
88 1 0.01
89 71 0.65
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (90 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTAAAGAT
Found at i:73613 original size:3 final size:3
Alignment explanation
Indices: 73602--73666 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
73592 TTTTTTTCCG
**
73602 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
73647 TTA TTA TTTA TTTA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA
73667 CAAATTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.11
3 41 0.76
4 7 0.13
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:73616 original size:11 final size:11
Alignment explanation
Indices: 73602--73665 Score: 76
Period size: 11 Copynumber: 5.5 Consensus size: 11
73592 TTTTTTTCCG
73602 TTATTTTATTA
1 TTATTTTATTA
73613 TTATTATTATTA
1 TTATT-TTATTA
73625 TTATCGTTATATTA
1 TTAT--TT-TATTA
73639 TTATTTTATTA
1 TTATTTTATTA
73650 TTA-TTTATTTA
1 TTATTTTA-TTA
73661 TTATT
1 TTATT
73666 ACAAATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.09
11 19 0.40
12 13 0.28
13 1 0.02
14 10 0.21
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:73666 original size:14 final size:13
Alignment explanation
Indices: 73607--73666 Score: 70
Period size: 14 Copynumber: 4.5 Consensus size: 13
73597 TTCCGTTATT
73607 TTATTATTA-TTA
1 TTATTATTATTTA
73619 TTATTATTATCGTTA
1 TTATTATTAT--TTA
73634 -TATTATTATTTTA
1 TTATTATTA-TTTA
73647 TTATTATTTATTTA
1 TTATTA-TTATTTA
73661 TTATTA
1 TTATTA
73667 CAAATTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.21
13 3 0.07
14 23 0.55
15 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:84493 original size:25 final size:25
Alignment explanation
Indices: 84460--84511 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
84450 TATTTGAGAT
84460 TGAGATCTGAAATGAATAAAACTAA
1 TGAGATCTGAAATGAATAAAACTAA
84485 TGAGATCTGAAATGAATAAAACTAA
1 TGAGATCTGAAATGAATAAAACTAA
84510 TG
1 TG
84512 GAAATTTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (25 bp):
TGAGATCTGAAATGAATAAAACTAA
Found at i:86795 original size:19 final size:19
Alignment explanation
Indices: 86736--86795 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 19
86726 GATTTAAGAT
*
86736 ATTAATATTTT-CAATAATA
1 ATTAATTTTTTACAATAA-A
86755 ATT-ATTTATTAATACAAATAAA
1 ATTAATTT-TT--TAC-AATAAA
86777 ATTAATTTTTTACAATAAA
1 ATTAATTTTTTACAATAAA
86796 TTTCTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 3 0.09
19 11 0.32
20 3 0.09
21 1 0.03
22 7 0.21
23 9 0.26
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAATTTTTTACAATAAA
Found at i:97370 original size:2 final size:2
Alignment explanation
Indices: 97363--97388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
97353 GTTTTAAGAA
97363 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
97389 CCATCTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98649 original size:20 final size:20
Alignment explanation
Indices: 98626--98667 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
98616 TGATGAAATA
98626 TATTAAATTTTAAATTTTGT
1 TATTAAATTTTAAATTTTGT
98646 TATTAAATTTTAAATTTTGT
1 TATTAAATTTTAAATTTTGT
98666 TA
1 TA
98668 ATGATATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TATTAAATTTTAAATTTTGT
Found at i:98982 original size:49 final size:49
Alignment explanation
Indices: 98925--99018 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
98915 ACACTTGTGA
** *
98925 AGGGGTTGCTTGGGATACCCTGGGCACCATGGAGGTCCACCCCTGGATG
1 AGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGATG
* *
98974 AGGGGTTGCCCGGGATACCCCGGGCTCCATGGAGGTCCGCCCCTG
1 AGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCACCCCTG
99019 ACTGACGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.14, C:0.31, G:0.37, T:0.18
Consensus pattern (49 bp):
AGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGATG
Found at i:99825 original size:28 final size:28
Alignment explanation
Indices: 99769--99822 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
99759 TATAAATAAT
*
99769 ATATATTATATAGATTATATTTTATTTA
1 ATATATTATATAGATAATATTTTATTTA
99797 ATATATTA-ATA-ATAATATTATTATTT
1 ATATATTATATAGATAATATT-TTATTT
99823 TAAATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 9 0.38
28 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATATTATATAGATAATATTTTATTTA
Found at i:99831 original size:32 final size:30
Alignment explanation
Indices: 99761--99832 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 30
99751 TATAAACATA
*
99761 TAAATAATATATATTATATAGATTATATTT
1 TAAATAATATATATAATATAGATTATATTT
** *
99791 TATTTAATATAT-TAATAATAATATTATTATTT
1 TAAATAATATATATAAT-AT-AGATTA-TATTT
99823 TAAATAATAT
1 TAAATAATAT
99833 GAAGTGATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 3 0.09
30 12 0.36
31 5 0.15
32 13 0.39
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TAAATAATATATATAATATAGATTATATTT
Found at i:100013 original size:12 final size:11
Alignment explanation
Indices: 99996--100050 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
99986 AATTAATTAA
99996 AATATTTTTATT
1 AATATTTTTA-T
100008 AATATTTTTAT
1 AATATTTTTAT
*
100019 AATATTATTA-
1 AATATTTTTAT
* *
100029 AAGATATTTA-
1 AATATTTTTAT
*
100039 AATATTATTAT
1 AATATTTTTAT
100050 A
1 A
100051 TTTATATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
10 14 0.40
11 11 0.31
12 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATATTTTTAT
Found at i:100028 original size:20 final size:20
Alignment explanation
Indices: 100003--100058 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
99993 TAAAATATTT
100003 TTATTAATATTTTTATAATA
1 TTATTAATATTTTTATAATA
* *
100023 TTATTAAAGATATTTA-AATA
1 TTATT-AATATTTTTATAATA
*
100043 TTATT-ATATTTATATA
1 TTATTAATATTTTTATA
100059 TAATCCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.21
19 1 0.03
20 14 0.48
21 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTAATATTTTTATAATA
Found at i:110600 original size:27 final size:27
Alignment explanation
Indices: 110577--110632 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
110567 TAATCTCCAG
110577 TTTCTTCAAGGCCTCAGCCTTCTCAAA
1 TTTCTTCAAGGCCTCAGCCTTCTCAAA
* *
110604 TTTCTTTAAGGCCTCAGCCTTCTCGAA
1 TTTCTTCAAGGCCTCAGCCTTCTCAAA
110631 TT
1 TT
110633 CGTCATCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (27 bp):
TTTCTTCAAGGCCTCAGCCTTCTCAAA
Done.