Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004179.1 Hibiscus syriacus cultivar Beakdansim tig00009138_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: 125193
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:423 original size:19 final size:19
Alignment explanation
Indices: 399--437 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
389 GAGTATCGAT
*
399 ACTAGGATGAACAATATCG
1 ACTAGGATAAACAATATCG
418 ACTAGGATAAACAATATCG
1 ACTAGGATAAACAATATCG
437 A
1 A
438 TATTGGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (19 bp):
ACTAGGATAAACAATATCG
Found at i:503 original size:20 final size:20
Alignment explanation
Indices: 478--529 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
468 TCAAGCAGGG
478 AGTATCGATA-TTGCTATGAT
1 AGTATCGATACTT-CTATGAT
*
498 AGTATCGATACTTTTATGAT
1 AGTATCGATACTTCTATGAT
518 AGTATCGATACT
1 AGTATCGATACT
530 GCCCCTTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
AGTATCGATACTTCTATGAT
Found at i:19822 original size:23 final size:23
Alignment explanation
Indices: 19786--19841 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
19776 AAAAAAAATT
* *
19786 GAAAAATGTGCCACAAAGGTAGA
1 GAAAAACGTGCCACAAAAGTAGA
* *
19809 GAAAAACGTTCCACAAAAGTATA
1 GAAAAACGTGCCACAAAAGTAGA
*
19832 GATAAACGTG
1 GAAAAACGTG
19842 TCATAAAGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.16
Consensus pattern (23 bp):
GAAAAACGTGCCACAAAAGTAGA
Found at i:20279 original size:221 final size:224
Alignment explanation
Indices: 19852--20286 Score: 531
Period size: 221 Copynumber: 1.9 Consensus size: 224
19842 TCATAAAGGC
* *
19852 AGAGATAAACATGCAACACAAACAGAGATAAACACGCAACATATGCAGAATTATTTTTATTAAAA
1 AGAGATAAACATGCAACACAAACAGACATAAACACGCAACACATGCAGAATTATTTTTATT-AAA
* * * *
19917 AAATAAAAGAAAAAAACAAAGAGAAAAGAGAATTGACAGTCAGCAACCAGCGTCAAAGCCGATGC
65 AAACAAAAG-AAAAAACAAAGAGAAAAGAGAATTGACAGTCAGCAACCAACGTAAAAGCAGATGC
* * * * *
19982 TGCCACCGGCTAAAGAAAATCGAAGAAGAAAAAGTTCATTTGATCTATAAAACGATACAAACTTA
129 TGCCACCGGCTAAAGAAAATCAAAGAAGAAAAAGTTAATTTGATATATAAAACAATACAAACTCA
*
20047 GAGAAAAAGAAAAA-AAAAGGAAGACAAAAG
194 AAGAAAAAGAAAAAGAAAAGGAAGACAAAAG
* * ** **
20077 AGAGATAAACGTGTAACACATGCAGACATAAATGCGCAACACATGCAGAATTATTTTTATT-AAA
1 AGAGATAAACATGCAACACAAACAGACATAAACACGCAACACATGCAGAATTATTTTTATTAAAA
* * * * * * *
20141 AACAAAAG-TAAAAGAGAGAGAAAAGAGAATTGACAGT-TGACAACCAACATTAAAATCAG-TGT
66 AACAAAAGAAAAAACAAAGAGAAAAGAGAATTGACAGTCAG-CAACCAAC-GTAAAAGCAGATGC
** *
20203 TG-CAGTGGCTAAAGAAAATCAAAGAAGAAAAATTTAATTTGATATATAAAAACAATACAAACTC
129 TGCCACCGGCTAAAGAAAATCAAAGAAGAAAAAGTTAATTTGATATAT-AAAACAATACAAACTC
20267 AAAGAAAAAGAAAAAGAAAA
193 AAAGAAAAAGAAAAAGAAAA
20287 AAAAAGGAAG
Statistics
Matches: 178, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
220 40 0.22
221 65 0.37
222 10 0.06
223 10 0.06
225 53 0.30
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.17
Consensus pattern (224 bp):
AGAGATAAACATGCAACACAAACAGACATAAACACGCAACACATGCAGAATTATTTTTATTAAAA
AACAAAAGAAAAAACAAAGAGAAAAGAGAATTGACAGTCAGCAACCAACGTAAAAGCAGATGCTG
CCACCGGCTAAAGAAAATCAAAGAAGAAAAAGTTAATTTGATATATAAAACAATACAAACTCAAA
GAAAAAGAAAAAGAAAAGGAAGACAAAAG
Found at i:20634 original size:25 final size:25
Alignment explanation
Indices: 20596--20656 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
20586 AATTACTAAA
* *
20596 TTTTACATT-TTATAAGTTTTATAT
1 TTTTATATTATTATAAATTTTATAT
20620 TTTTATATTATTATAAATTTTATAT
1 TTTTATATTATTATAAATTTTATAT
*
20645 TTTTGTATTATT
1 TTTTATATTATT
20657 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 8 0.24
25 25 0.76
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (25 bp):
TTTTATATTATTATAAATTTTATAT
Found at i:28786 original size:22 final size:22
Alignment explanation
Indices: 28748--28789 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28738 TTGTACTAAT
*
28748 TCATTTTTTCTTATTTTTTGGG
1 TCATTTTTTCATATTTTTTGGG
28770 TCATTCTTTTCAT-TTTTTTG
1 TCATT-TTTTCATATTTTTTG
28790 CATTGCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.10, C:0.12, G:0.10, T:0.69
Consensus pattern (22 bp):
TCATTTTTTCATATTTTTTGGG
Found at i:32770 original size:13 final size:12
Alignment explanation
Indices: 32762--32826 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
32752 GCAAAAAATG
32762 AAAAAAAAAAGA
1 AAAAAAAAAAGA
***
32774 TGGAAA-AAAGA
1 AAAAAAAAAAGA
*
32785 AGAAAAAAATAGA
1 A-AAAAAAAAAGA
32798 GAAAAAAAAAAGA
1 -AAAAAAAAAAGA
32811 AAAAAGAAAAAGA
1 AAAAA-AAAAAGA
32824 AAA
1 AAA
32827 TGAATAAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
11 5 0.12
12 11 0.27
13 24 0.59
14 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:32780 original size:23 final size:20
Alignment explanation
Indices: 32754--32826 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 20
32744 AACGAGAGGC
32754 AAAAAATGAAAAAAAAAAGATGG
1 AAAAAA-GAAAAAAAAAAGA--G
32777 AAAAAAGAAGAAAAAAATAGAG
1 AAAAAAGAA-AAAAAAA-AGAG
*
32799 AAAAAA-AAAAGAAAAA-AG
1 AAAAAAGAAAAAAAAAAGAG
32817 -AAAAAGAAAA
1 AAAAAAGAAAA
32827 TGAATAAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.11
18 6 0.13
19 1 0.02
20 6 0.13
21 2 0.04
22 10 0.22
23 13 0.28
24 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAAGAG
Found at i:33399 original size:25 final size:25
Alignment explanation
Indices: 33354--33425 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
33344 AGTAAGGAGC
*
33354 AACATTTTTCAAAATT-CTTCATCA
1 AACATTTTTCAAAATTATTTCATCA
* **
33378 AATATTTTTTGAAATTATTTCATCA
1 AACATTTTTCAAAATTATTTCATCA
33403 AACATTTTTCAAAATTATTTCAT
1 AACATTTTTCAAAATTATTTCAT
33426 TATTCAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 13 0.32
25 27 0.68
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (25 bp):
AACATTTTTCAAAATTATTTCATCA
Found at i:34419 original size:90 final size:90
Alignment explanation
Indices: 34269--34443 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 90
34259 CCGAAAGTGG
* * * *
34269 CCATATCTCTTCAATGTGGATGAACAGTGTCATCTTCAACACCATATTATCTTCATATTGATCCA
1 CCATATCTCTTCAATATGGATGAACAGTGTCATCTTCAACACCAAATTATCTTCAGATTGACCCA
* *
34334 ACTTCCTCAATGAGAAGGAAAGCGA
66 AATTCCTCAATGAAAAGGAAAGCGA
* *
34359 CCATATCTCTTCAATATGGATGAGCAGTGTCATCTTCAGCACCAAATTATC-TCTAGATTGACCC
1 CCATATCTCTTCAATATGGATGAACAGTGTCATCTTCAACACCAAATTATCTTC-AGATTGACCC
34423 AAATTCCTCAATGAAAAGGAA
65 AAATTCCTCAATGAAAAGGAA
34444 CAATGTCATC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 2 0.03
90 74 0.97
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (90 bp):
CCATATCTCTTCAATATGGATGAACAGTGTCATCTTCAACACCAAATTATCTTCAGATTGACCCA
AATTCCTCAATGAAAAGGAAAGCGA
Found at i:34512 original size:212 final size:212
Alignment explanation
Indices: 34142--34565 Score: 539
Period size: 212 Copynumber: 2.0 Consensus size: 212
34132 AATGAGAAAG
** * * * *
34142 AGCGACCAAATCTCTTTGATGTGGATGAGTAGTGTCTTTTTCAACACCAAATTATCTCTAGATTG
1 AGCGACCAAATCTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTATCTCTAGATTG
* ** * * * * * *
34207 ATCTGACTTCCTCAACGAGAAGGAAAATCGTCATCTTCAATAAACAATTTACCCGAAAGTGGCCA
66 ACCCAAATTCCTCAACGAAAAGGAAAATCGTCATCTTCAACAAACAAATTACCCGAAAGCGACCA
* * * * * *
34272 TATCTCTTCAATGTGGATGAACAGTGTCATCTTCAACACCATATTATCTTC-ATATTGATCCAAC
131 TATCTCTTCAATGTAGATGAACAGTGTCATCTTCAACACCAAATTATC-TCAAGATCGACCCAAA
34336 TTCCTCAATGAGAAGGAA
195 TTCCTCAATGAGAAGGAA
* *
34354 AGCGACCATATCTCTTCAATATGGATGAGCAGTGTCATCTTCAGCACCAAATTATCTCTAGATTG
1 AGCGACCAAATCTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTATCTCTAGATTG
* * *
34419 ACCCAAATTCCTCAATGAAAAGGAACAAT-GTCATCTTCAGCAAGA-AAATTACCTGAAAGCGAC
66 ACCCAAATTCCTCAACGAAAAGGAA-AATCGTCATCTTCAACAA-ACAAATTACCCGAAAGCGAC
**
34482 CATATCTCTTCAATGTAGATGATTAGTGTCATCTTCAACACCAAATTATCTCAAGATCGACCCAA
129 CATATCTCTTCAATGTAGATGAACAGTGTCATCTTCAACACCAAATTATCTCAAGATCGACCCAA
*
34547 ATTCCTTAATGAGAAGGAA
194 ATTCCTCAATGAGAAGGAA
34566 TAGTGTTGTC
Statistics
Matches: 180, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
211 2 0.01
212 174 0.97
213 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (212 bp):
AGCGACCAAATCTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTATCTCTAGATTG
ACCCAAATTCCTCAACGAAAAGGAAAATCGTCATCTTCAACAAACAAATTACCCGAAAGCGACCA
TATCTCTTCAATGTAGATGAACAGTGTCATCTTCAACACCAAATTATCTCAAGATCGACCCAAAT
TCCTCAATGAGAAGGAA
Found at i:34543 original size:61 final size:61
Alignment explanation
Indices: 34356--34543 Score: 173
Period size: 61 Copynumber: 3.1 Consensus size: 61
34346 AGAAGGAAAG
* * * *
34356 CGACCATATCTCTTCAATATGGATGAGCAGTGTCATCTTCAGCACCAAATTATCTCTAGAT
1 CGACCATATCTCTTCAATGTAGATGAACAGTGTCATCTTCAGCACCAAATTATCTCAAGAT
* * * * * * * ** * * *
34417 TGACCCAAAT-TCCTCAATGAAAAGGAACAATGTCATCTTCAGCAAGAAAATTACCTGAA-AG
1 CGA-CCATATCTCTTCAATGTAGATGAACAGTGTCATCTTCAGC-ACCAAATTATCTCAAGAT
** *
34478 CGACCATATCTCTTCAATGTAGATGATTAGTGTCATCTTCAACACCAAATTATCTCAAGAT
1 CGACCATATCTCTTCAATGTAGATGAACAGTGTCATCTTCAGCACCAAATTATCTCAAGAT
34539 CGACC
1 CGACC
34544 CAAATTCCTT
Statistics
Matches: 92, Mismatches: 31, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
60 16 0.17
61 61 0.66
62 15 0.16
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (61 bp):
CGACCATATCTCTTCAATGTAGATGAACAGTGTCATCTTCAGCACCAAATTATCTCAAGAT
Found at i:34579 original size:61 final size:61
Alignment explanation
Indices: 34384--34571 Score: 177
Period size: 61 Copynumber: 3.1 Consensus size: 61
34374 ATGGATGAGC
* * * * *
34384 AGTGTCATCTTCAGCACCAAATTATCTCTAGATTGACCCAAATTCCTCAATGAAAAGGAAC
1 AGTGTCATCTTCAGCACCAAATTATCTCAAGATCGACCCAAATTCCTTAATGAGAAGGAAT
* ** * * * * * *
34445 AATGTCATCTTCAGCAAGAAAATTACCTGAA-AGCGA-CCATA-TCTCTTCAATGTAG-ATGATT
1 AGTGTCATCTTCAGC-ACCAAATTATCTCAAGATCGACCCAAATTC-CTT-AATG-AGAAGGAAT
*
34506 AGTGTCATCTTCAACACCAAATTATCTCAAGATCGACCCAAATTCCTTAATGAGAAGGAAT
1 AGTGTCATCTTCAGCACCAAATTATCTCAAGATCGACCCAAATTCCTTAATGAGAAGGAAT
34567 AGTGT
1 AGTGT
34572 TGTCTTCATA
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
59 2 0.02
60 19 0.20
61 54 0.57
62 18 0.19
63 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (61 bp):
AGTGTCATCTTCAGCACCAAATTATCTCAAGATCGACCCAAATTCCTTAATGAGAAGGAAT
Found at i:34813 original size:125 final size:125
Alignment explanation
Indices: 34594--34917 Score: 361
Period size: 125 Copynumber: 2.6 Consensus size: 125
34584 CACAGCTACC
* * * * * * * *
34594 AATTACGACTTAGCGTCTTTTAGAGGAAGGCGTAAGATCATCCCACGA--C-GTGTCTTTCAGAT
1 AATTACGACTTAACATCCTATAGAGGAAAGAGTAAGATCGTCCCACGACTCAGTGTCTTTCAGAG
* * * * *
34656 GAAATAGTGAGATCGTAACCATATTCAACATCCTTCAGTAAAAGGAGTGGATCGACCCCG
66 GAAAGAGTGAGATCGTAACCAGATTCAACATCCTTCAGTAAAAGAAGTAGATCAACCCCG
* * *
34716 AATTATGAC-TAAGCATCCT-TCAGAGGAAAGAGTAAGATCGTCCCATGACTCAGTGTCTTTTAG
1 AATTACGACTTAA-CATCCTAT-AGAGGAAAGAGTAAGATCGTCCCACGACTCAGTGTCTTTCAG
* * * * * *
34779 AGGAAAGAGTGAGATCGTAACCGGGTTTAACATCCTTTAGTCAAAGAAGTAGATCAACCTCG
64 AGGAAAGAGTGAGATCGTAACCAGATTCAACATCCTTCAGTAAAAGAAGTAGATCAACCCCG
* **
34841 AATTACGACTTAACGTCCTATAGAGGAAAGAGTAAGATCGTCCCACGACTCAACGTCTTTCAGAG
1 AATTACGACTTAACATCCTATAGAGGAAAGAGTAAGATCGTCCCACGACTCAGTGTCTTTCAGAG
*
34906 GAAAGACTGAGA
66 GAAAGAGTGAGA
34918 CCATTACCGG
Statistics
Matches: 167, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
121 3 0.02
122 35 0.21
124 1 0.01
125 124 0.74
126 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (125 bp):
AATTACGACTTAACATCCTATAGAGGAAAGAGTAAGATCGTCCCACGACTCAGTGTCTTTCAGAG
GAAAGAGTGAGATCGTAACCAGATTCAACATCCTTCAGTAAAAGAAGTAGATCAACCCCG
Found at i:35600 original size:46 final size:46
Alignment explanation
Indices: 35533--35621 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
35523 AAACTCGTTG
*
35533 TCTTTTTATCTTTACCCTATTCTTGTAAACACAATAATGGGTATTA
1 TCTTTTTATCTTTACCCTATTCTTGTAAACACAAGAATGGGTATTA
*
35579 TCTTTTTATCTTTGCCCTATTCTTGTAAACACAAGAATGGGTA
1 TCTTTTTATCTTTACCCTATTCTTGTAAACACAAGAATGGGTA
35622 AAGAGGGGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (46 bp):
TCTTTTTATCTTTACCCTATTCTTGTAAACACAAGAATGGGTATTA
Found at i:38217 original size:7 final size:7
Alignment explanation
Indices: 38205--38232 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
38195 TCCTCCTCCT
38205 CCTCTTC
1 CCTCTTC
38212 CCTCTTC
1 CCTCTTC
38219 CCTCTTC
1 CCTCTTC
38226 CCTCTTC
1 CCTCTTC
38233 ATCTCCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
CCTCTTC
Found at i:41734 original size:2 final size:2
Alignment explanation
Indices: 41727--41760 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41717 TACTCAAGTA
41727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41761 TCATCAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45070 original size:37 final size:37
Alignment explanation
Indices: 45022--45101 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
45012 CCCATAGTTA
* * * *
45022 ATATATATTTATGTTTATATTATA-ATATTTTATAAT
1 ATATAAATTTATGTTTATATAATATAGATTATATAAT
*
45058 ATTATAAATTTATTTTTATATAATATAGATTATATAAT
1 A-TATAAATTTATGTTTATATAATATAGATTATATAAT
45096 ATATAA
1 ATATAA
45102 TAAAATAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 1 0.03
37 25 0.68
38 11 0.30
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (37 bp):
ATATAAATTTATGTTTATATAATATAGATTATATAAT
Found at i:47651 original size:25 final size:23
Alignment explanation
Indices: 47600--47654 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
47590 ATACCTTGAC
47600 TCAATACCGATACTATATAAATA
1 TCAATACCGATACTATATAAATA
* *
47623 -CAATACTGATACTAATATATAGTA
1 TCAATACCGATACT-ATATA-AATA
47647 TCAATACC
1 TCAATACC
47655 CTATCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 12 0.46
23 5 0.19
24 3 0.12
25 6 0.23
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.31
Consensus pattern (23 bp):
TCAATACCGATACTATATAAATA
Found at i:49078 original size:4 final size:4
Alignment explanation
Indices: 49069--49100 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
49059 TGTGATTTTT
49069 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
49101 ATGAAACGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:49947 original size:20 final size:20
Alignment explanation
Indices: 49922--49988 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
49912 TTTTCCGACT
49922 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
* *
49942 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGAATATGACA
* * *
49962 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
49982 ATCGCAA
1 ATCGCAA
49989 CGTAATTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATATGACA
Found at i:49986 original size:40 final size:40
Alignment explanation
Indices: 49918--50030 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
49908 GCGATTTTCC
* * * * *
49918 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTAT
1 GACTATCGCAATGCGATTCTG-ACTATCGCAACGCAATTAT
* *
49958 GACTATCGCAATGCGATTCTGACTATCGCAACGTAATTCT
1 GACTATCGCAATGCGATTCTGACTATCGCAACGCAATTAT
* * *
49998 GACTATCGCAACGAGATTCTAACTATCGCAACG
1 GACTATCGCAATGCGATTCTGACTATCGCAACG
50031 AGATTCTTAC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
39 1 0.02
40 61 0.98
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (40 bp):
GACTATCGCAATGCGATTCTGACTATCGCAACGCAATTAT
Found at i:49996 original size:20 final size:20
Alignment explanation
Indices: 49942--50049 Score: 128
Period size: 20 Copynumber: 5.4 Consensus size: 20
49932 GAATATGTAA
* * *
49942 ATCGCAATGCGATTATGACT
1 ATCGCAACGAGATTCTGACT
* *
49962 ATCGCAATGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
49982 ATCGCAACGTA-ATTCTGACT
1 ATCGCAACG-AGATTCTGACT
*
50002 ATCGCAACGAGATTCTAACT
1 ATCGCAACGAGATTCTGACT
*
50022 ATCGCAACGAGATTCTTACT
1 ATCGCAACGAGATTCTGACT
*
50042 GTCGCAAC
1 ATCGCAAC
50050 ACTGAATTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.99
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:50921 original size:24 final size:24
Alignment explanation
Indices: 50870--50923 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
50860 GTATTCGAAA
*
50870 TTTGATCTTGGTCAATACCCGTAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
50894 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
50918 TTTGAT
1 TTTGAT
50924 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:51136 original size:13 final size:13
Alignment explanation
Indices: 51120--51151 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
51110 GAAGAAGAAA
51120 AAAATCCCCGAAG
1 AAAATCCCCGAAG
51133 AAAAGTCCCCGAAG
1 AAAA-TCCCCGAAG
51147 AAAAT
1 AAAAT
51152 GCCACGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAATCCCCGAAG
Found at i:53486 original size:140 final size:140
Alignment explanation
Indices: 53234--53503 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
53224 AAACGTTGTA
*
53234 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
53299 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
53364 TATGTGTATT
131 TATGTGTATT
53374 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
53439 TGATGTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
53504 CGCAACGCGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:53499 original size:20 final size:20
Alignment explanation
Indices: 53474--53772 Score: 231
Period size: 20 Copynumber: 15.8 Consensus size: 20
53464 TTACACATTC
*
53474 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
53494 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
53514 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
53533 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
53548 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
53568 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
53587 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* * *
53602 ATTTGTCTATCGCAATGTGA
1 ATTTGACTATCGCAACGCGA
*
53622 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* * *
53642 ATTTGATTATTGCAACAGC-T
1 ATTTGACTATCGCAAC-GCGA
* *
53662 ATTTGACTATCACAACGAGA
1 ATTTGACTATCGCAACGCGA
*
53682 A----A--ATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
53696 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
53716 ATTTGACTATCACAACACGA
1 ATTTGACTATCGCAACGCGA
* * * * *
53736 ATTTGATTATGGCAAAGGGT
1 ATTTGACTATCGCAACGCGA
53756 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
53773 AGAAAATCGC
Statistics
Matches: 216, Mismatches: 43, Indels: 40
0.72 0.14 0.13
Matches are distributed among these distances:
14 28 0.13
15 6 0.03
16 1 0.00
18 1 0.00
19 6 0.03
20 172 0.80
21 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:53569 original size:54 final size:54
Alignment explanation
Indices: 53482--53636 Score: 238
Period size: 54 Copynumber: 2.9 Consensus size: 54
53472 TCATTTGAAT
* *
53482 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
53536 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* * * *
53590 ATCGCAACACGAATTTGTCTATCGCAATGTGAATTTGACTATCGCAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAA
53637 TGCGAATTTG
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:53657 original size:94 final size:93
Alignment explanation
Indices: 53536--53811 Score: 333
Period size: 94 Copynumber: 2.9 Consensus size: 93
53526 CAACTCAAAA
* * *
53536 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAATCGCAACAC
1 ATCGCAACGCGAATTTGATTATCGCAACA-GTATTTGACTATCGCAACG-AGAAAATCGCAACAC
* * *
53600 GAATTTGTCTATCGCAATGTGAATTTGACT
64 GAATTTGACTATCGCAACGCGAATTTGACT
* * *
53630 ATCGCAATGCGAATTTGATTATTGCAACAGCTATTTGACTATCACAACGAGAAAATCGCAACACG
1 ATCGCAACGCGAATTTGATTATCGCAACAG-TATTTGACTATCGCAACGAGAAAATCGCAACACG
53695 AATTTGACTATCGCAACGCGAATTTGACT
65 AATTTGACTATCGCAACGCGAATTTGACT
* * *
53724 ATCACAACACGAATTTGATTATGGCAA-AGGGTATTTGACTATCGCAACGAGAAAATCGCAA-AG
1 ATCGCAACGCGAATTTGATTATCGCAACA--GTATTTGACTATCGCAACGAGAAAATCGCAACA-
* * * *
53787 TGTATTAGACTATCGCAATGCGAAT
63 CGAATTTGACTATCGCAACGCGAAT
53812 AAACTTTCAC
Statistics
Matches: 159, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
93 4 0.03
94 154 0.97
95 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGATTATCGCAACAGTATTTGACTATCGCAACGAGAAAATCGCAACACGA
ATTTGACTATCGCAACGCGAATTTGACT
Found at i:53732 original size:74 final size:74
Alignment explanation
Indices: 53474--53741 Score: 238
Period size: 74 Copynumber: 3.6 Consensus size: 74
53464 TTACACATTC
* * * *
53474 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCACAAC-CAGAAAAT
53538 CGCAACGCGA
65 CGCAACGCGA
* * * * * *** ***
53548 ATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCG-C-AACACGAATTTGTCTA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AAATTTGACTATCAC-AACCAGAAAA
* *
53611 TCGCAATGTGA
64 TCGCAACGCGA
* * * * *
53622 ATTTGACTATCGCAATGCGAATTTGATTATTGCAACAGC-TATTTGACTATCACAACGAGAAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GCAAATTTGACTATCACAACCAGAAAAT
*
53686 CGCAACACGA
65 CGCAACGCGA
* * *
53696 ATTTGACTATCGCAACGCGAATTTGACTATCACAACACGAATTTGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGA
53742 TTATGGCAAA
Statistics
Matches: 146, Mismatches: 41, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
73 7 0.05
74 129 0.88
75 10 0.07
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCACAACCAGAAAATC
GCAACGCGA
Found at i:53866 original size:20 final size:20
Alignment explanation
Indices: 53821--53868 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
53811 TAAACTTTCA
*
53821 CGTTGCGATTTTGGCTTTCG
1 CGTTGCGATTTTGGCTTTAG
*
53841 CATTGCGATTTTGAG-TTTAG
1 CGTTGCGATTTTG-GCTTTAG
53861 CGTTGCGA
1 CGTTGCGA
53869 AAGTGTACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTGGCTTTAG
Found at i:54027 original size:14 final size:14
Alignment explanation
Indices: 53967--54028 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
53957 CACAAATAAG
*
53967 AATTATTTACACATC
1 AATT-TTTACAAATC
**
53982 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
53997 AACTTTTACAAATC
1 AATTTTTACAAATC
*
54011 AATTTTTATAAATC
1 AATTTTTACAAATC
54025 AATT
1 AATT
54029 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:55468 original size:21 final size:18
Alignment explanation
Indices: 55444--55488 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
55434 GAACGGTGGG
55444 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
55465 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
55483 AGGGGA
1 AGGGGA
55489 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:56031 original size:20 final size:20
Alignment explanation
Indices: 56006--56080 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
55996 TCACAACACG
*
56006 AATGACTATCGCAAAGCGAA
1 AATGACTATCGCAACGCGAA
56026 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
56046 AATGACTATCGTAACGCGAA
1 AATGACTATCGCAACGCGAA
** *
56066 TTTGACTATCACAAC
1 AATGACTATCGCAAC
56081 AAGAGAATCG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:58061 original size:20 final size:20
Alignment explanation
Indices: 58038--58094 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
58028 TCTGAAACTT
58038 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
58058 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
58078 ACTATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
58095 CTAAAACCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:58738 original size:20 final size:20
Alignment explanation
Indices: 58708--58845 Score: 170
Period size: 20 Copynumber: 6.9 Consensus size: 20
58698 GCGCTTTGAA
58708 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
58728 CATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
58748 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
58768 AATCACATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
58788 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* *
58808 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
*
58828 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
58846 GGAAAATCGC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 101 0.98
21 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:58837 original size:60 final size:60
Alignment explanation
Indices: 58708--58845 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 60
58698 GCGCTTTGAA
* * *
58708 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATAGTCAG
* * * *
58768 AATCACATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATAGT-CAG
*
58828 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
58846 GGAAAATCGC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 67 0.99
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATAGTCAG
Found at i:60455 original size:27 final size:26
Alignment explanation
Indices: 60424--60493 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
60414 TATTGATAAC
60424 TTAATATAAATAATTACATAACCATAT
1 TTAATATAAATAATTA-ATAACCATAT
* * *
60451 TTAATAGAAAT-ATTAATAATCTTAT
1 TTAATATAAATAATTAATAACCATAT
60476 TATAATATTAAAT-ATTAA
1 T-TAATA-TAAATAATTAA
60494 AACTATACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.24
26 9 0.24
27 19 0.51
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (26 bp):
TTAATATAAATAATTAATAACCATAT
Found at i:60505 original size:26 final size:27
Alignment explanation
Indices: 60458--60511 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
60448 TATTTAATAG
* *
60458 AAATATTAATAATCTTATTATAATATT
1 AAATATTAATAATCTTACTATAAAATT
60485 AAATATTAA-AA-CTATACTATAAAATT
1 AAATATTAATAATCT-TACTATAAAATT
60511 A
1 A
60512 TCTTAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 13 0.54
27 9 0.38
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATATTAATAATCTTACTATAAAATT
Found at i:60525 original size:18 final size:18
Alignment explanation
Indices: 60502--60552 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
60492 AAAACTATAC
60502 TATAAAATTATCTTAATA
1 TATAAAATTATCTTAATA
*
60520 TATAAAAATATAC-TAATA
1 TATAAAATTAT-CTTAATA
*
60538 T-TATAATTAATCTTA
1 TATAAAATT-ATCTTA
60553 TAATAATAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAAAATTATCTTAATA
Found at i:61870 original size:6 final size:7
Alignment explanation
Indices: 61851--61944 Score: 86
Period size: 8 Copynumber: 12.7 Consensus size: 7
61841 GTAACATTTG
61851 TAATATAA
1 TAATAT-A
61859 TAATAT-
1 TAATATA
61865 TAATATA
1 TAATATA
61872 TAA-ATA
1 TAATATA
61878 TAATGATA
1 TAAT-ATA
61886 TTAATATA
1 -TAATATA
*
61894 TAATAAA
1 TAATATA
61901 TAATATA
1 TAATATA
61908 GTAATATA
1 -TAATATA
61916 GTAATAATA
1 -TAAT-ATA
61925 TAATAATA
1 TAAT-ATA
61933 GTAATA-A
1 -TAATATA
61940 TAATA
1 TAATA
61945 CAATAATATC
Statistics
Matches: 77, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
6 17 0.22
7 16 0.21
8 33 0.43
9 11 0.14
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (7 bp):
TAATATA
Found at i:61870 original size:14 final size:15
Alignment explanation
Indices: 61851--61953 Score: 99
Period size: 14 Copynumber: 6.9 Consensus size: 15
61841 GTAACATTTG
61851 TAATATAATAATAT-
1 TAATATAATAATATA
61865 TAATAT-ATAA-ATA
1 TAATATAATAATATA
*
61878 TAATGATATTAATATA
1 TAAT-ATAATAATATA
61894 TAATA-AATAATATA
1 TAATATAATAATATA
*
61908 GTAATATAGTAATAATA
1 -TAATATAATAAT-ATA
*
61925 TAATAATAGTAATA-A
1 TAAT-ATAATAATATA
*
61940 TAATACAATAATAT
1 TAATATAATAATAT
61954 CAACTCGGAC
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.03
13 8 0.11
14 23 0.31
15 14 0.19
16 17 0.23
17 11 0.15
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (15 bp):
TAATATAATAATATA
Found at i:61880 original size:22 final size:21
Alignment explanation
Indices: 61851--61953 Score: 102
Period size: 22 Copynumber: 4.7 Consensus size: 21
61841 GTAACATTTG
61851 TAATATAATAATATTAATATA
1 TAATATAATAATATTAATATA
*
61872 TAAATATAATGATATTAATATA
1 T-AATATAATAATATTAATATA
61894 TAATA-AATAATATAGTAATATAGTAA
1 TAATATAATAATAT--T-A-ATA-T-A
*
61920 TAATATAATAATAGTAATA-A
1 TAATATAATAATATTAATATA
*
61940 TAATACAATAATAT
1 TAATATAATAATAT
61954 CAACTCGGAC
Statistics
Matches: 69, Mismatches: 5, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
20 20 0.29
21 5 0.07
22 21 0.30
23 4 0.06
24 4 0.06
25 2 0.03
26 6 0.09
27 7 0.10
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (21 bp):
TAATATAATAATATTAATATA
Found at i:61952 original size:3 final size:3
Alignment explanation
Indices: 61851--61944 Score: 63
Period size: 3 Copynumber: 31.7 Consensus size: 3
61841 GTAACATTTG
* * *
61851 TAA T-A TAA TAA TAT TAA TATA TAA -ATA TAA TGA TAT TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TA-A TAA
* * *
61897 TAAA TAA T-A TAG TAA T-A TAG TAA TAA T-A TAA TAA TAG TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61940 TAA TA
1 TAA TA
61945 CAATAATATC
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
2 9 0.13
3 51 0.73
4 10 0.14
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:62242 original size:20 final size:20
Alignment explanation
Indices: 62214--62267 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
62204 AAAACATCCT
* *
62214 ACCCTGAGGTTTTACAAATG
1 ACCCAGAGGTTTTACAAATC
62234 ACCCAGAGGTTTTACAAATC
1 ACCCAGAGGTTTTACAAATC
* *
62254 ACCCGGAGGATTTA
1 ACCCAGAGGTTTTA
62268 ATTTTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (20 bp):
ACCCAGAGGTTTTACAAATC
Found at i:62296 original size:119 final size:119
Alignment explanation
Indices: 62085--62490 Score: 661
Period size: 119 Copynumber: 3.4 Consensus size: 119
62075 ATAAAAAATA
* ** * *
62085 AAAACATCATACCCTGAGGTTTTACAGATGACATGGAGGCTTTGCAAATCACCC-GACGGATTTA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGA-GGATTTA
* * *
62149 ATTTTCTATAACTTTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCG
65 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATTTTCATGCG
* *
62204 AAAACATCCTACCCTGAGGTTTTACAAATGACCCAGAGGTTTTACAAATCACCCGGAGGATTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAA
* *
62269 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGTTTTCTCATTTTCATGTG
66 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATTTTCATGCG
* * *
62323 AAAACATCCTACCCTAAGGTTTTACAGATGACCCGGAGGTTTTACAAATCATCCGGATGATTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAA
62388 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATTTTCATGCG
66 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATTTTCATGCG
62442 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAAT
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAAT
62491 TCGTGGAAAT
Statistics
Matches: 267, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
119 265 0.99
120 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (119 bp):
AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTAA
TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATTTTCATGCG
Found at i:62378 original size:20 final size:20
Alignment explanation
Indices: 62339--62379 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62329 TCCTACCCTA
* *
62339 AGGTTTTACAGATGACCCGG
1 AGGTTTTACAAATCACCCGG
*
62359 AGGTTTTACAAATCATCCGG
1 AGGTTTTACAAATCACCCGG
62379 A
1 A
62380 TGATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
AGGTTTTACAAATCACCCGG
Found at i:63145 original size:22 final size:22
Alignment explanation
Indices: 63120--63204 Score: 134
Period size: 22 Copynumber: 3.8 Consensus size: 22
63110 AGCTTCCATT
*
63120 TTTGAAAAGAGAATCTATCATC
1 TTTGAAAAGAGAATATATCATC
63142 TTTGAAAAGAGAATATATCATC
1 TTTGAAAAGAGAATATATCATC
* *
63164 TTTGAAAAAAAAATATATCATC
1 TTTGAAAAGAGAATATATCATC
63186 TTTGAAAAGAGATATATAT
1 TTTGAAAAGAGA-ATATAT
63205 ATGTGAAACT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 51 0.89
23 6 0.11
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (22 bp):
TTTGAAAAGAGAATATATCATC
Found at i:63436 original size:57 final size:57
Alignment explanation
Indices: 63271--63440 Score: 272
Period size: 57 Copynumber: 3.0 Consensus size: 57
63261 TCTTGAAACA
* * *
63271 TATT-ACAAGAAGGA-TTTATCCTAATTCCTTTCATGTATCCACATCTAATCAAATA
1 TATTCACAAGAAGGATTTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAGATC
* *
63326 TTTTCACAAGAAGGATTTTATCCTAATTCCTTTCATTTCTCCACATCTAATCAGATC
1 TATTCACAAGAAGGATTTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAGATC
*
63383 TATTCACAAGAAGGATTTTATCCTAATTCCTTTCATGTCTCCATATCTAATCAGATC
1 TATTCACAAGAAGGATTTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAGATC
63440 T
1 T
63441 CGAATAAGGT
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 3 0.03
56 10 0.10
57 92 0.88
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (57 bp):
TATTCACAAGAAGGATTTTATCCTAATTCCTTTCATGTCTCCACATCTAATCAGATC
Found at i:65308 original size:24 final size:24
Alignment explanation
Indices: 65264--65313 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
65254 ATAAAGAACC
*
65264 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
65288 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
65312 AA
1 AA
65314 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:75542 original size:24 final size:24
Alignment explanation
Indices: 75498--75547 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
75488 ATAAAGAACC
*
75498 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
75522 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
75546 AA
1 AA
75548 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:82332 original size:26 final size:26
Alignment explanation
Indices: 82276--82383 Score: 91
Period size: 26 Copynumber: 4.1 Consensus size: 26
82266 ATTGATAATT
* *
82276 TAATATAAATAATTACATAACCATATT-
1 TAATATAAAT-ATTA-ATAAACTTATTA
* *
82303 TAATAGAAATATTAATAATCTTATTA
1 TAATATAAATATTAATAAACTTATTA
82329 TAATATTAAATA-TAA-AAACTATATTA
1 TAATA-TAAATATTAATAAACT-TATTA
82355 TAATATTAAATA-TAA-AAACTATATTA
1 TAATA-TAAATATTAATAAACT-TATTA
82381 TAA
1 TAA
82384 AATTATCTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
25 13 0.18
26 46 0.63
27 14 0.19
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (26 bp):
TAATATAAATATTAATAAACTTATTA
Found at i:82384 original size:14 final size:14
Alignment explanation
Indices: 82339--82385 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
82329 TAATATTAAA
82339 TATAAAAACTATAT
1 TATAAAAACTATAT
* * *
82353 TAT-AATATTA-AA
1 TATAAAAACTATAT
82365 TATAAAAACTATAT
1 TATAAAAACTATAT
82379 TATAAAA
1 TATAAAA
82386 TTATCTTAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
12 4 0.16
13 10 0.40
14 11 0.44
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (14 bp):
TATAAAAACTATAT
Found at i:82388 original size:26 final size:26
Alignment explanation
Indices: 82324--82388 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
82314 TTAATAATCT
82324 TATTATAATATTAAATATAAAAACTA
1 TATTATAATATTAAATATAAAAACTA
82350 TATTATAATATTAAATATAAAAACTA
1 TATTATAATATTAAATATAAAAACTA
*
82376 TATTATAAAATTA
1 TATTATAATATTA
82389 TCTTAATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (26 bp):
TATTATAATATTAAATATAAAAACTA
Found at i:83741 original size:8 final size:8
Alignment explanation
Indices: 83728--83807 Score: 60
Period size: 8 Copynumber: 9.8 Consensus size: 8
83718 GTAACATTTG
83728 TAATATAA
1 TAATATAA
83736 TAATAT--
1 TAATATAA
83742 TAATAT-A
1 TAATATAA
83749 TAAATATAA
1 T-AATATAA
*
83758 TGATATTAA
1 TAATA-TAA
83767 T-ATATAA
1 TAATATAA
83774 TAATAATAA
1 TAAT-ATAA
83783 TATAGTAATAA
1 TA-A-T-ATAA
*
83794 TAATACAA
1 TAATATAA
83802 TAATAT
1 TAATAT
83808 CAACTCGGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
6 6 0.10
7 5 0.08
8 27 0.44
9 13 0.21
10 2 0.03
11 8 0.13
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (8 bp):
TAATATAA
Found at i:83747 original size:6 final size:7
Alignment explanation
Indices: 83728--83798 Score: 67
Period size: 8 Copynumber: 9.7 Consensus size: 7
83718 GTAACATTTG
83728 TAATATAA
1 TAATAT-A
83736 TAATAT-
1 TAATATA
83742 TAATATA
1 TAATATA
83749 TAA-ATA
1 TAATATA
83755 TAATGATA
1 TAAT-ATA
83763 TTAATATA
1 -TAATATA
83771 TAATAATAA
1 TAAT-AT-A
83780 TAATATA
1 TAATATA
83787 GTAATA-A
1 -TAATATA
83794 TAATA
1 TAATA
83799 CAATAATATC
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
6 17 0.30
7 9 0.16
8 21 0.38
9 9 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (7 bp):
TAATATA
Found at i:83747 original size:14 final size:16
Alignment explanation
Indices: 83728--83798 Score: 80
Period size: 16 Copynumber: 4.7 Consensus size: 16
83718 GTAACATTTG
83728 TAAT-ATAATAATAT-
1 TAATAATAATAATATA
83742 TAAT-AT-ATAA-ATA
1 TAATAATAATAATATA
* *
83755 TAATGATATTAATATA
1 TAATAATAATAATATA
83771 TAATAATAATAATATA
1 TAATAATAATAATATA
83787 GTAATAATAATA
1 -TAATAATAATA
83799 CAATAATATC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
12 2 0.04
13 8 0.16
14 8 0.16
15 3 0.06
16 17 0.35
17 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATAATAATAATATA
Found at i:83757 original size:22 final size:21
Alignment explanation
Indices: 83728--83807 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 21
83718 GTAACATTTG
83728 TAATATAATAATATTAATATA
1 TAATATAATAATATTAATATA
*
83749 TAAATATAATGATATTAATATA
1 T-AATATAATAATATTAATATA
83771 TAATAATAATAATATAGTAATA-A
1 TAAT-ATAATAATAT--TAATATA
*
83794 TAATACAATAATAT
1 TAATATAATAATAT
83808 CAACTCGGAC
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.08
22 38 0.73
23 5 0.10
24 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (21 bp):
TAATATAATAATATTAATATA
Found at i:83805 original size:14 final size:14
Alignment explanation
Indices: 83772--83806 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
83762 ATTAATATAT
*
83772 AATAATAATAATAT
1 AATAATAATAATAC
*
83786 AGTAATAATAATAC
1 AATAATAATAATAC
83800 AATAATA
1 AATAATA
83807 TCAACTCGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (14 bp):
AATAATAATAATAC
Found at i:84681 original size:57 final size:58
Alignment explanation
Indices: 84571--84685 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
84561 GTCCCCACCT
* * * * *
84571 TTAACCTATATTAAACCCTAAGACATCAACCCCAACATACCACAAATCAACTAAACCA
1 TTAAACTACATTAAACCCAAAGACATCAACCCCAACACACCACAAATAAACTAAACCA
* *
84629 TTAAACTACATTAACCCCAAAGACATCAA-CCCAACACACCATAAATAAACTAAACCA
1 TTAAACTACATTAAACCCAAAGACATCAACCCCAACACACCACAAATAAACTAAACCA
84686 ACATCAAGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 25 0.50
58 25 0.50
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.17
Consensus pattern (58 bp):
TTAAACTACATTAAACCCAAAGACATCAACCCCAACACACCACAAATAAACTAAACCA
Found at i:85540 original size:43 final size:42
Alignment explanation
Indices: 85481--85603 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
85471 TTGAGAACAA
* *
85481 AAAAGCCGCAATAGGTCAAGATCTATAGCGGTGTTTTTGGAAC
1 AAAAGCCGCAA-AGGTCAATATCTATAACGGTGTTTTTGGAAC
* **
85524 AAATGCCGCAGAAGGTCAATATCTATAACGG-CATTTTGGAAC
1 AAAAGCCGCA-AAGGTCAATATCTATAACGGTGTTTTTGGAAC
* * * *
85566 AAAAGCCGCAAAAGGCCGATATCTATATCAGTGTTTTT
1 AAAAGCCGC-AAAGGTCAATATCTATAACGGTGTTTTT
85604 TTCAAAAGGT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
42 33 0.51
43 31 0.48
44 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AAAAGCCGCAAAGGTCAATATCTATAACGGTGTTTTTGGAAC
Found at i:85622 original size:32 final size:32
Alignment explanation
Indices: 85574--85637 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
85564 ACAAAAGCCG
* *
85574 CAAAAGGCCGATATCTATA-TCAGTGTTTTTTT
1 CAAAAGGCCGAGATCTATAGT-AGCGTTTTTTT
*
85606 CAAAAGGTCGAGATCTATAGTAGCGTTTTTTT
1 CAAAAGGCCGAGATCTATAGTAGCGTTTTTTT
85638 ATACAAACGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
CAAAAGGCCGAGATCTATAGTAGCGTTTTTTT
Found at i:85718 original size:44 final size:43
Alignment explanation
Indices: 85607--85743 Score: 134
Period size: 43 Copynumber: 3.2 Consensus size: 43
85597 TGTTTTTTTC
* ***
85607 AAAAGGTCGAGATCTATAGTAGCGTTTTTTTATACAAACGCCGA
1 AAAAGGTCGAGATCTATAGTGGCGTTTTAGAATA-AAACGCCGA
** * *
85651 AAAAGGTC-AGATCTATAACGGCGTTTTCAGAATAAAACGTCGT
1 AAAAGGTCGAGATCTATAGTGGCGTTTT-AGAATAAAACGCCGA
* * *
85694 AAAATGTCGAGATCTATAGTGGCGTTTTAAGAAT-AAACGCTGC
1 AAAAGGTCGAGATCTATAGTGGCGTTTT-AGAATAAAACGCCGA
85737 AAAAGGT
1 AAAAGGT
85744 TATATATATA
Statistics
Matches: 75, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
43 42 0.56
44 33 0.44
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (43 bp):
AAAAGGTCGAGATCTATAGTGGCGTTTTAGAATAAAACGCCGA
Found at i:101909 original size:15 final size:15
Alignment explanation
Indices: 101889--101922 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
101879 ATAATATCCC
*
101889 ATTATTCGTATTATT
1 ATTATTCGTATCATT
*
101904 ATTATTCTTATCATT
1 ATTATTCGTATCATT
101919 ATTA
1 ATTA
101923 GCATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTATTCGTATCATT
Found at i:102314 original size:21 final size:21
Alignment explanation
Indices: 102288--102344 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
102278 AATAAGTGTA
*
102288 CCAAAGTATCACATATATGTT
1 CCAAAGGATCACATATATGTT
** *
102309 CCAAAGGATTGCATATATGTC
1 CCAAAGGATCACATATATGTT
* *
102330 CCGAAGGACCACATA
1 CCAAAGGATCACATA
102345 GAACCCTCGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.25
Consensus pattern (21 bp):
CCAAAGGATCACATATATGTT
Found at i:106563 original size:27 final size:27
Alignment explanation
Indices: 106528--106591 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
106518 AATTCATGAC
* *
106528 TTCATAAATCACCAAAAAATTAACTAAA
1 TTCA-AAATAACCAAAAAATTAACCAAA
* * *
106556 TTCAAAATAATCAAATATTTAACCAAA
1 TTCAAAATAACCAAAAAATTAACCAAA
106583 TGTCAAAAT
1 T-TCAAAAT
106592 TGTATACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.28
Consensus pattern (27 bp):
TTCAAAATAACCAAAAAATTAACCAAA
Found at i:118514 original size:21 final size:20
Alignment explanation
Indices: 118477--118516 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
118467 TCAATTGATA
* *
118477 TAAAATATTTTATTATTATT
1 TAAAACATTTTAATATTATT
118497 TAAAACATATTTAATATTAT
1 TAAAACAT-TTTAATATTAT
118517 CTGAATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAACATTTTAATATTATT
Done.