Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004705.1 Hibiscus syriacus cultivar Beakdansim tig00010574_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: 80106
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:6174 original size:19 final size:19
Alignment explanation
Indices: 6145--6190 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
6135 GATTATATAG
*
6145 AATATTTTAAAAT-TTCAAT
1 AATAATTTAAAATATT-AAT
*
6164 ACTAATTTAAAATATTAAT
1 AATAATTTAAAATATTAAT
6183 AATAATTT
1 AATAATTT
6191 GGTGACCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTTAAAATATTAAT
Found at i:13808 original size:2 final size:2
Alignment explanation
Indices: 13797--13825 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13787 AAGTTTAAGA
13797 AT AT -T 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
13826 TGTATACGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:15182 original size:29 final size:29
Alignment explanation
Indices: 15148--15221 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
15138 TATTTAACTA
15148 ATTAGGATTTTATTTTGCTAAAGAATTTT
1 ATTAGGATTTTATTTTGCTAAAGAATTTT
*
15177 ATTAGGATTTTATTTTGCTAAAGAGTTTT
1 ATTAGGATTTTATTTTGCTAAAGAATTTT
15206 ATTAGGATTTTATTTT
1 ATTAGGATTTTATTTT
15222 CTTTAGGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (29 bp):
ATTAGGATTTTATTTTGCTAAAGAATTTT
Found at i:15235 original size:18 final size:18
Alignment explanation
Indices: 15207--15247 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
15197 AAGAGTTTTA
*
15207 TTAGG-ATTTTATTTTCT
1 TTAGGTATTTTATTTTCC
15224 TTAGGTATTTTATTTTCC
1 TTAGGTATTTTATTTTCC
15242 TTAGGT
1 TTAGGT
15248 TTTCTCAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.17, C:0.07, G:0.15, T:0.61
Consensus pattern (18 bp):
TTAGGTATTTTATTTTCC
Found at i:15996 original size:18 final size:18
Alignment explanation
Indices: 15973--16010 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15963 TTTCTACAAT
*
15973 TTACTTTTC-TTATTTTTA
1 TTAC-TTTCGTTACTTTTA
15991 TTACTTTCGTTACTTTTA
1 TTACTTTCGTTACTTTTA
16009 TT
1 TT
16011 TTATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (18 bp):
TTACTTTCGTTACTTTTA
Found at i:22217 original size:6 final size:6
Alignment explanation
Indices: 22206--24017 Score: 737
Period size: 6 Copynumber: 302.0 Consensus size: 6
22196 TATGTGTTTG
* ** *
22206 AGAAGA AGAAGA AGAAGA AAAAGA AGAAGA AGAATG- AGAA-A TTTATATA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA -AGA-AGA
* * * * *
22255 ATAAGA AGAAGA AGAAGG AGAAGA AGAAGG AGAAGA AGGAGA AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * *
22303 AGAAGG AGAATA AGGAGA AGGAGA ATAAGG AGAAGG AGAAGA AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * * *
22351 AGAAGC AGGAGA AGGAGA AGGAGG AGGAGA AGAAGG AGAAGG AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * ** * *
22399 AGGAGA AGGAGG AGAAGG AGAAGG AGGAGA AGGAGA AGGGGA AGGAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * *
22447 AGAAGG AGAAGG AGAAGG AGAAGG AGAATG- AGGAGG AGAAGG AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA AGAAGA AGAAGA
* * * * * *
22495 AGGAGA AGGAGA AGGAGA AGAAGA AGGAGA AGAAGA AGGAGA AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
22543 AGAATG- AGGAGG AGAAGA AGAAG- AGGAGG AGGAGA AGAAGA AGGAGGA
1 AGAA-GA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA
* * * * * * * * *
22591 GGGAGT AGGAGA AGGAGG AGGAGA AGAAGA AGGAGG AGAAGA AGAAG-
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
22638 AGAAGA AGAAGA AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAATG-
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA
* * * * * * * *
22686 AGAAGG AGAA-A GAGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGGAGG
1 AGAAGA AGAAGA -AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * * * *
22734 AGAAGA AGAAGG AGGAGG AGAAGA AGAAGG AGGAG- GGAGGA GGGAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
22781 AGGAGG AGGAGG AGAAGA AGAAGA AGAAGG AGAAGA AGGAGA AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * *
22829 AGGAGA AGGAGA AGGAGA AGGAGA ATG-AGA AGGAGG AGAAGG AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
22877 AGAAGA AGAAGA AGAAGA AGGAGGA TG-AGG AGGAGG AGGAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
22925 AGGAGGA GGAGGA TAGAAGA AG-AGA AGGAGA AGGAGA AGGAGA AGGAGA
1 A-GAAGA AGAAGA -AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
22974 AGGAGA AGGAGA ATG-AGA AGAAGG AGAAGG AGAAGA AGAAGA AGAAAA
1 AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
*
23022 AGAAGA AGAAGA AGAAGA AGAA-A GAGAATGA TA-AA-A AGAAGG AGAA-A
1 AGAAGA AGAAGA AGAAGA AGAAGA -AGAA-GA -AGAAGA AGAAGA AGAAGA
* * * * * * *
23069 GAGAAGA ATAAGT AGGAGA AGAAGA A-AGAGA ATAATA AGTAGG AGAAGA
1 -AGAAGA AGAAGA AGAAGA AGAAGA AGA-AGA AGAAGA AGAAGA AGAAGA
* * * ** * * *
23118 AGAAGG AGAAGG AGAAGG AGAATT AGAAGG AGAAGT AGAAGA AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* *
23166 AGAAGA AGAATG- AGAATG- AGAAGG AGAATG- AGAAGA AGAAGG AGAA-A
1 AGAAGA AGAA-GA AGAA-GA AGAAGA AGAA-GA AGAAGA AGAAGA AGAAGA
* * * * * * *
23213 GAGAAGA AGAAGA AGGAGA AGAAGA ATGATGA TG-AGG AGGAGG AGAAGG
1 -AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
23262 AGGAGG AGGAGG AGAAGA AGAATA AGAAGA AGAAGG GGAATG- AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA
* *
23310 AGAAGA AGAAGA ATG-GGA ATG-AGA AGAAGA AGAAGA AGAAGA AGGAGA
1 AGAAGA AGAAGA A-GAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* ** * * ** *
23358 AGGAGA ATG-AGA AGGGGA ATG-AGA AGGAGA AGGAGA AGGGGA AGGAGA
1 AGAAGA A-GAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * ** * * * ** **
23406 AGGAGA AGGAGA AGGGGA AGGAGA AGGAGA AGGAGA AGGGGA AGGGGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * * *
23454 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGAACA AGGAGG AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * ** *
23502 AGAAGGA A-AAGA AGAAGA AGAAGG AGAATA AGGAGG AGGAGA AGGGGG
1 AGAA-GA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
23550 ATAAGA AGAAGA AGGAGA AGAAGG AGGAGA AGGAGG AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
23598 AGAAGG AGAACA AGAAGG AGAAGG AGAATG- AGAA-A GAGAATG- AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA -AGAA-GA AGAAGA
* * * * * * * * *
23646 AGAAGG GGAAGG AGAAGG AGAAGG GGAAGG AGAAGG AGAAGGA A-AAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA
* * * * * * * *
23694 GGAAGA AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
23742 AGAAGG AGAAGA ACAAGG AGGAGA AGGAGA AGGAA-A AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA
* * * * * * * *
23790 AGAAGA AGGAGA ATAAGA AGGAGG AGAAGG AGGATA AGAAGA AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
23838 AGAAGA AGGAGG AGAATG- AGGATA AGAAGA AGAAGA AGGAGA AGAAGA
1 AGAAGA AGAAGA AGAA-GA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * *
23886 AGGAGA AGGAGA AGGAGA AGGAGA AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
23934 AGAAGG AGGAGG AGAAGA AGGAGA A-ACAGG AGAAGG AGAAGG AGAATG-
1 AGAAGA AGAAGA AGAAGA AGAAGA AGA-AGA AGAAGA AGAAGA AGAA-GA
* *
23982 AGGAGG AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
24018 GGATTTAACA
Statistics
Matches: 1485, Mismatches: 252, Indels: 138
0.79 0.13 0.07
Matches are distributed among these distances:
4 1 0.00
5 45 0.03
6 1386 0.93
7 50 0.03
8 3 0.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (6 bp):
AGAAGA
Found at i:22229 original size:15 final size:15
Alignment explanation
Indices: 22206--24017 Score: 737
Period size: 15 Copynumber: 120.8 Consensus size: 15
22196 TATGTGTTTG
22206 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
*
22221 AGAAAAAGAAGAAGA
1 AGAAGAAGAAGAAGA
**
22236 AGAATG-AGAA-ATTTA
1 AGAA-GAAGAAGA-AGA
* *
22251 TATAATAAGAAGAAGA
1 -AGAAGAAGAAGAAGA
*
22267 AGAAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
* *
22282 AGGAGAAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
22297 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
22312 ATAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
22327 ATAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
22342 AGAAGAAGGAGAAGC
1 AGAAGAAGAAGAAGA
* * *
22357 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
22372 AGGAGGAGAAGAAGG
1 AGAAGAAGAAGAAGA
* * *
22387 AGAAGGAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
22402 AGAAGGAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
22417 AGAAGGAGGAGAAGG
1 AGAAGAAGAAGAAGA
** * *
22432 AGAAGGGGAAGGAGG
1 AGAAGAAGAAGAAGA
* *
22447 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
22462 AGGAGAAGGAGAATG-
1 AGAAGAAGAAGAA-GA
* * * *
22477 AGGAGGAGAAGGAGG
1 AGAAGAAGAAGAAGA
* *
22492 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
22507 AGGAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
*
22522 AGAAGAAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
22537 AGGAGAAGAATG-AGG
1 AGAAGAAGAA-GAAGA
*
22552 AGGAGAAGAAGAAG-
1 AGAAGAAGAAGAAGA
* * *
22566 AGGAGGAGGAGAAGA
1 AGAAGAAGAAGAAGA
* * * *
22581 AGAAGGAGGAGGGAGT
1 AGAA-GAAGAAGAAGA
* * * *
22597 AGGAGAAGGAGGAGG
1 AGAAGAAGAAGAAGA
* *
22612 AGAAGAAGAAGGAGG
1 AGAAGAAGAAGAAGA
22627 AGAAGAAGAAG-AGA
1 AGAAGAAGAAGAAGA
*
22641 AGAAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
* *
22656 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
22671 AGGAGAAGGAGAATG-
1 AGAAGAAGAAGAA-GA
*
22686 AGAAGGAGAA-AGAGA
1 AGAAGAAGAAGA-AGA
* * *
22701 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
22716 AGAAGGAGAAGGAGG
1 AGAAGAAGAAGAAGA
* *
22731 AGGAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
* *
22746 AGGAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * * *
22761 AGGAGGAG-GGAGGA
1 AGAAGAAGAAGAAGA
* * * * * *
22775 GGGAGGAGGAGGAGG
1 AGAAGAAGAAGAAGA
*
22790 AGGAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
* *
22805 AGAAGGAGAAGAAGG
1 AGAAGAAGAAGAAGA
* *
22820 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
22835 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
22850 AGAATG-AGAAGGAGG
1 AGAA-GAAGAAGAAGA
* *
22865 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
22880 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * * *
22895 AGGAGGATG-AGGAGG
1 A-GAAGAAGAAGAAGA
* *
22910 AGGAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * *
22925 AGGAGGAGGAGGATAGA
1 A-GAAGAAGAAGA-AGA
*
22942 AGAAG-AGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
22956 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
22971 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
*
22986 ATG-AGAAGAAGGAGA
1 A-GAAGAAGAAGAAGA
*
23001 AGGAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
*
23016 AGAAAAAGAAGAAGA
1 AGAAGAAGAAGAAGA
23031 AGAAGAAGAAGAA-A
1 AGAAGAAGAAGAAGA
23045 GAGAATGATA-AA-AAGA
1 -AGAA-GA-AGAAGAAGA
*
23061 AGGAGAA-AGAGAAGA
1 AGAAGAAGA-AGAAGA
* * *
23076 ATAAGTAGGAGAAGA
1 AGAAGAAGAAGAAGA
* *
23091 AGAA-AGAGAATAATA
1 AGAAGA-AGAAGAAGA
* *
23106 AGTAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * *
23121 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
** *
23136 AGAATTAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
23151 AGTAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
23166 AGAAGAAGAATG-AGA
1 AGAAGAAGAA-GAAGA
*
23181 ATG-AGAAGGAGAATG-
1 A-GAAGAAGAAGAA-GA
*
23196 AGAAGAAGAAGGAGA
1 AGAAGAAGAAGAAGA
23211 A-AGAGAAGAAGAAGA
1 AGA-AGAAGAAGAAGA
*
23226 AGGAGAAGAAGAATGA
1 AGAAGAAGAAGAA-GA
* * * * *
23242 TGATG-AGGAGGAGG
1 AGAAGAAGAAGAAGA
* * * *
23256 AGAAGGAGGAGGAGG
1 AGAAGAAGAAGAAGA
* *
23271 AGGAGAAGAAGAATA
1 AGAAGAAGAAGAAGA
**
23286 AGAAGAAGAAGGGGA
1 AGAAGAAGAAGAAGA
23301 ATG-AGAAGAAGAAGA
1 A-GAAGAAGAAGAAGA
*
23316 AGAAGAATG-GGAATG-
1 AGAAGAA-GAAGAA-GA
23331 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
* *
23346 AGAAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
**
23361 AGAATG-AGAAGGGGA
1 AGAA-GAAGAAGAAGA
* *
23376 ATG-AGAAGGAGAAGG
1 A-GAAGAAGAAGAAGA
** *
23391 AGAAGGGGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
23406 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
23421 GGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* ** *
23436 AGGAGAAGGGGAAGG
1 AGAAGAAGAAGAAGA
* * *
23451 GGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
23466 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* * *
23481 AGAAGAACAAGGAGG
1 AGAAGAAGAAGAAGA
*
23496 AGAAGGAGAAGGAA-A
1 AGAAGAAGAA-GAAGA
*
23511 AGAAGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
* * * *
23526 AGAATAAGGAGGAGG
1 AGAAGAAGAAGAAGA
** * *
23541 AGAAGGGGGATAAGA
1 AGAAGAAGAAGAAGA
*
23556 AGAAGAAGGAGAAGA
1 AGAAGAAGAAGAAGA
* * * *
23571 AGGAGGAGAAGGAGG
1 AGAAGAAGAAGAAGA
23586 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * *
23601 AGGAGAACAAGAAGG
1 AGAAGAAGAAGAAGA
*
23616 AGAAGGAGAATG-AGA
1 AGAAGAAGAA-GAAGA
*
23631 A-AGAGAATG-AGAAGG
1 AGA-AGAA-GAAGAAGA
** *
23646 AGAAGGGGAAGGAGA
1 AGAAGAAGAAGAAGA
* ** *
23661 AGGAGAAGGGGAAGG
1 AGAAGAAGAAGAAGA
*
23676 AGAAGGAGAAGGAA-A
1 AGAAGAAGAA-GAAGA
** *
23691 AGGGGAAGAAGAAGG
1 AGAAGAAGAAGAAGA
* *
23706 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
23721 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
23736 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * *
23751 AGAACAAGGAGGAGA
1 AGAAGAAGAAGAAGA
*
23766 AGGAGAAGGAA-AAGA
1 AGAAGAA-GAAGAAGA
23781 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * *
23796 AGGAGAATAAGAAGG
1 AGAAGAAGAAGAAGA
* * * *
23811 AGGAGAAGGAGGATA
1 AGAAGAAGAAGAAGA
*
23826 AGAAGAAGAAGGAGA
1 AGAAGAAGAAGAAGA
* *
23841 AGAAGGAGGAGAATG-
1 AGAAGAAGAAGAA-GA
* *
23856 AGGATAAGAAGAAGA
1 AGAAGAAGAAGAAGA
*
23871 AGAAGGAGAAGAAGA
1 AGAAGAAGAAGAAGA
* * *
23886 AGGAGAAGGAGAAGG
1 AGAAGAAGAAGAAGA
* *
23901 AGAAGGAGAAGAAGG
1 AGAAGAAGAAGAAGA
* *
23916 AGAAGGAGAAGGAGA
1 AGAAGAAGAAGAAGA
* * * *
23931 AGGAGAAGGAGGAGG
1 AGAAGAAGAAGAAGA
*
23946 AGAAGAAGGAGAA-A
1 AGAAGAAGAAGAAGA
* * *
23960 CAGGAGAAGGAGAAGG
1 -AGAAGAAGAAGAAGA
* *
23976 AGAATG-AGGAGGAGA
1 AGAA-GAAGAAGAAGA
23991 AGAAGAAGAAGAAGA
1 AGAAGAAGAAGAAGA
24006 AGAAGAAGAAGA
1 AGAAGAAGAAGA
24018 GGATTTAACA
Statistics
Matches: 1339, Mismatches: 385, Indels: 146
0.72 0.21 0.08
Matches are distributed among these distances:
13 2 0.00
14 84 0.06
15 1182 0.88
16 65 0.05
17 6 0.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (15 bp):
AGAAGAAGAAGAAGA
Found at i:22774 original size:7 final size:7
Alignment explanation
Indices: 22762--22794 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
22752 AGAAGAAGAA
22762 GGAGGAG
1 GGAGGAG
22769 GGAGGAG
1 GGAGGAG
22776 GGAGGA-
1 GGAGGAG
22782 GGAGGA-
1 GGAGGAG
22788 GGAGGAG
1 GGAGGAG
22795 AAGAAGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (7 bp):
GGAGGAG
Found at i:26807 original size:15 final size:14
Alignment explanation
Indices: 26769--26798 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
26759 TTACTAATTG
26769 AATCCAATTAGCTA
1 AATCCAATTAGCTA
26783 AATCCAATTAGCTA
1 AATCCAATTAGCTA
26797 AA
1 AA
26799 ATTGAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (14 bp):
AATCCAATTAGCTA
Found at i:28065 original size:9 final size:9
Alignment explanation
Indices: 28051--28093 Score: 77
Period size: 9 Copynumber: 4.7 Consensus size: 9
28041 CTGCTGGAAA
28051 ACCGGTTTG
1 ACCGGTTTG
28060 ACCGGTTCTG
1 ACCGGTT-TG
28070 ACCGGTTTG
1 ACCGGTTTG
28079 ACCGGTTTG
1 ACCGGTTTG
28088 ACCGGT
1 ACCGGT
28094 CATACCCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 24 0.73
10 9 0.27
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:28075 original size:19 final size:18
Alignment explanation
Indices: 28051--28093 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 18
28041 CTGCTGGAAA
28051 ACCGGTTTGACCGGTTCTG
1 ACCGGTTTGACCGGTT-TG
28070 ACCGGTTTGACCGGTTTG
1 ACCGGTTTGACCGGTTTG
28088 ACCGGT
1 ACCGGT
28094 CATACCCGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.30
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:31014 original size:3 final size:3
Alignment explanation
Indices: 31002--31066 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
30992 TTTTTTCAAA
*
31002 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31050 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
31067 AGAGATTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52119 original size:22 final size:23
Alignment explanation
Indices: 52094--52139 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
52084 TTATAAACTC
52094 AATTAAACT-CATATATTTAATT
1 AATTAAACTACATATATTTAATT
*
52116 AATTAAACTGACATGTATTTAATT
1 AATTAAACT-ACATATATTTAATT
52140 TTTCTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTAAACTACATATATTTAATT
Found at i:60590 original size:14 final size:14
Alignment explanation
Indices: 60565--60600 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
60555 TCACAACTTT
60565 TTTTACTTTAATCAC
1 TTTTA-TTTAATCAC
*
60580 TTTTATTTAATCAT
1 TTTTATTTAATCAC
60594 TTTTATT
1 TTTTATT
60601 ACTACTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTAATCAC
Found at i:60802 original size:18 final size:18
Alignment explanation
Indices: 60779--60814 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
60769 TGACATCAAA
60779 ACGACAGTTGTCAAATTG
1 ACGACAGTTGTCAAATTG
60797 ACGACAGTTGTCAAATTG
1 ACGACAGTTGTCAAATTG
60815 GCGCCGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (18 bp):
ACGACAGTTGTCAAATTG
Found at i:69136 original size:17 final size:17
Alignment explanation
Indices: 69116--69158 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
69106 ATGTTGAATG
69116 AAAAAAAAGCAGTTCGA
1 AAAAAAAAGCAGTTCGA
**
69133 AAAAAAAAGTTGTTCGA
1 AAAAAAAAGCAGTTCGA
69150 AAGAAAAAA
1 AA-AAAAAA
69159 TGGAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.63, C:0.07, G:0.16, T:0.14
Consensus pattern (17 bp):
AAAAAAAAGCAGTTCGA
Found at i:77763 original size:16 final size:17
Alignment explanation
Indices: 77742--77773 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
77732 TACTATTTAT
77742 ATGAATAGT-AAATTTC
1 ATGAATAGTGAAATTTC
77758 ATGAATAGTGAAATTT
1 ATGAATAGTGAAATTT
77774 TGTCGGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (17 bp):
ATGAATAGTGAAATTTC
Done.