Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007315.1 Hibiscus syriacus cultivar Beakdansim tig00019512_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: 44831
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:6298 original size:19 final size:19
Alignment explanation
Indices: 6274--6316 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
6264 AGAAGTGGGT
6274 GAAGTAGGCCATTTTACCA
1 GAAGTAGGCCATTTTACCA
6293 GAAGTAGGCCATTTTACCA
1 GAAGTAGGCCATTTTACCA
6312 GAAGT
1 GAAGT
6317 GGGAGATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
GAAGTAGGCCATTTTACCA
Found at i:6328 original size:19 final size:19
Alignment explanation
Indices: 6274--6328 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
6264 AGAAGTGGGT
* *
6274 GAAGTAGGCCATTTTACCA
1 GAAGTAGGACATGTTACCA
* *
6293 GAAGTAGGCCATTTTACCA
1 GAAGTAGGACATGTTACCA
* *
6312 GAAGTGGGAGATGTTAC
1 GAAGTAGGACATGTTAC
6329 TCTCCAGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (19 bp):
GAAGTAGGACATGTTACCA
Found at i:11093 original size:9 final size:9
Alignment explanation
Indices: 11067--11095 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
11057 GTTAGTCGTA
11067 GTGGTGGTG
1 GTGGTGGTG
11076 GTGGTGGTG
1 GTGGTGGTG
11085 GTGGTGGTG
1 GTGGTGGTG
11094 GT
1 GT
11096 AGTAGTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (9 bp):
GTGGTGGTG
Found at i:11106 original size:9 final size:9
Alignment explanation
Indices: 11094--11391 Score: 339
Period size: 9 Copynumber: 32.3 Consensus size: 9
11084 GGTGGTGGTG
11094 GTAGTAGTA
1 GTAGTAGTA
11103 GTAGTAGTA
1 GTAGTAGTA
11112 GTAGTTAGTA
1 GTAG-TAGTA
*
11122 GTAGTGGTA
1 GTAGTAGTA
*
11131 TTAGTAGTA
1 GTAGTAGTA
*
11140 GTTAGTCGTA
1 G-TAGTAGTA
11150 GTAGTAGTA
1 GTAGTAGTA
*
11159 GTAGTTAGTC
1 GTAG-TAGTA
11169 GTAGTAGTA
1 GTAGTAGTA
*
11178 GTAGTGGTA
1 GTAGTAGTA
*
11187 GTAGTGGTA
1 GTAGTAGTA
11196 GT-GATAGTA
1 GTAG-TAGTA
11205 GTAGTAGTA
1 GTAGTAGTA
11214 GTTAGTAGTA
1 G-TAGTAGTA
11224 GTAGTAGTA
1 GTAGTAGTA
11233 GTAGTAGTA
1 GTAGTAGTA
*
11242 GTAGTTAGTC
1 GTAG-TAGTA
11252 GTAGTAGTA
1 GTAGTAGTA
*
11261 GTAGTGGTA
1 GTAGTAGTA
11270 GTAGT-GATA
1 GTAGTAG-TA
*
11279 GTAGTGGTA
1 GTAGTAGTA
* * *
11288 GTGGTGGTG
1 GTAGTAGTA
11297 GTAGTAGTA
1 GTAGTAGTA
11306 GTAGTAGTA
1 GTAGTAGTA
11315 GTAGTAGTTA
1 GTAGTAG-TA
*
11325 GTCGTAGTA
1 GTAGTAGTA
* *
11334 ATAGTAGTG
1 GTAGTAGTA
*
11343 GTAGTAGTG
1 GTAGTAGTA
*
11352 GTAGTGGTA
1 GTAGTAGTA
*
11361 GTGGTAGTA
1 GTAGTAGTA
11370 GTAGTTAGTA
1 GTAG-TAGTA
11380 GTAGTAGTA
1 GTAGTAGTA
11389 GTA
1 GTA
11392 AAAATATTGA
Statistics
Matches: 250, Mismatches: 28, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
8 2 0.01
9 187 0.75
10 61 0.24
ACGTcount: A:0.28, C:0.01, G:0.36, T:0.35
Consensus pattern (9 bp):
GTAGTAGTA
Found at i:11384 original size:6 final size:6
Alignment explanation
Indices: 8553--11391 Score: 1864
Period size: 6 Copynumber: 470.5 Consensus size: 6
8543 AGTGGTAATG
* * * * * * * *
8553 GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * *
8601 GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * *
8649 GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * *
8697 GTAGTG GTAGTG GTAGTG GTAGTG GTGGTA GTAGTG GTGGTA GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * *
8745 GTGGTG GTAGTA GTGGTA GTGGTG GTAGTG GTAGTA GTGGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * *
8793 GTAGTA GTGGTA -TAGTC GTATTC GTTGTA GTAGTC GTAGTC GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * *
8840 GTGGTA GTAGTG GTAGTA CTGGTA GTAGTG GTAGTA GT-GCTA GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA
* * * * * * *
8888 GTAGTA GTGGTA GTGGTG GTAGTG GTGGTA GTAGTG GTAGTA GTCGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * *
8936 GTAGTC GTAGTA GTCGTA GTGGTA GTAGTG GTAGTA GTGGTA GTAGTC
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
*
8984 GTAGTT GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
9032 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * *
9080 GTAGTA GTAGTC GTAGTA GTCGTA GTAGTA GTAGTA GTAGTG GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * * * * * * *
9128 GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * *
9176 GT-GTG GTGGTG GTGGTG GTGGTG GTAGTA GTGGTG GTAG-G GTTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA G-TAGTA
* * * * * * * * * *
9223 GTGGTA GTGGTG GTAGTG GTGGTA GTGGTG GTAGTG GTAGTA GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * *
9271 GTGGTA GTAGTA GTCGTA GTGGTA GTAGTC GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * *
9319 GTAGTA GTAGTA GTCGTA GTAGTC GTAGTG GTGGTG GTGGTG GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * *
9367 GTGGTG GTCGTA GTGGTA GTGGTA GTAGTCA -TAGTG GTAGTC GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGT-A GTAGTA GTAGTA GTAGTA
* * * * * * * * *
9415 GTCGTA GTGGTA GTGGTG GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * *
9463 GTAGTG GTGGTG GTGGTG GTGGTG GTGGTA GTAGTA GTGGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * *
9511 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * *
9559 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTG GTGGTG GTGGTG GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * * * *
9607 GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTAGTA GTGGTA GAAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * *
9655 GTAGTA GTGGTA GTAGTG GTAGTA GTGGTA GTAGTG GTA-TA GTCGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * *
9702 GTAGTA GTAGTA GTAGTA GTAGTC GTAGTC GTAGTC GTGGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * *
9750 GTAGTG GTAGTA GTGGTA GTAGTC GTAGTA GTCGTA GTAGTA GTAATG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * *
9798 GTAGTA GTGGTA GTAGTC GTAGTA GTGGTG GTAGTG GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
*
9846 GTAGTA GTAGTC GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * *
9894 GTCGTA GTAATA GTAGTG GTAGTA GTAGTG GTGGTG GTGGTG GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * * * * * * *
9942 GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * *
9990 GTGGTG GTGGTG GTGGTA GTAGTT GTAGTA GTGGTA GTAGTT GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * *
10038 GTGGTC GTAGTG GTCGTA GTGGTC GTAGTG GTAGTA GTGGTA GTTGTC
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * *
10086 GTAGTA GTGGTA GTGGTA GTAGTC GTAGTA GTTGTA GTAGTC GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * *
10134 GTAGTA GTCGTA GTTGTA ATAGTC TTAGTG GTAGTG GTAGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * * * * * * *
10182 GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG GTGGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * * * *
10230 GTGGTG GTGGTG GTGGTG GTGGTG GTGGTA GTGGTA GTGGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * *
10278 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTTGTA GTGGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * *
10326 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTAGTA GTTACTC GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA G-TAGTA GTAGTA
* *
10375 GTAGTA GTGGTG GTAGTA GTTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA G-TAGTA GTAGTA GTAGTA GTAGTA GTAGTA
10424 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
*
10472 GTAGTA GTAGTA GTAGTAA TTAGTA GTAGTA GTAGTA GTAGTA GTAGTTA
1 GTAGTA GTAGTA GTAGT-A GTAGTA GTAGTA GTAGTA GTAGTA GTAG-TA
* * * * * *
10522 GTAGTA GTAGTA GTGGTG GTAGTG GTAGTTA GTCGTA GTGGTA GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA GTAGTA GTAGTA
* * * *
10571 GTAGTA GTGGTG GTAGTA GTAGTA GTTAGTCA -TAGTG GTAGTA GTGGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA G-TAGT-A GTAGTA GTAGTA GTAGTA
* * * *
10620 GTAGTG GTAGTA GTGGTG GTAGTA GTAGTTA GTCGTA GTAGTA GTAGTTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA GTAGTA GTAG-TA
* * * *
10670 GTTGTA GTGGTA GTAGTG GTAGTA GTGGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
10718 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * *
10766 GTCGTA GTAGTA GTAGTG GTAGTA GTGGTA GTAGTG GTAGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * *
10814 GTAGTG GTAGTA GTGGTG GTAGTG GTAGTA GTGGTG GTAGTG GTAGTG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * *
10862 GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTGGTG GTGGTG GT-GATG
1 GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAG-TA
* * * * *
10910 GTGGTA GTAGTA GTTAGTA GTAGTG GTAGTA GTGGTA GTAGTG GTATTA
1 GTAGTA GTAGTA G-TAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * *
10959 GTGGTA TTAGTA GTAGTTA GTCGTA GTAGTA GTGGTG GTAGTA GTGGTA
1 GTAGTA GTAGTA GTAG-TA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
*
11008 GTAGTA GTGGTA GTAGTA GTTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
1 GTAGTA GTAGTA GTAGTA G-TAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * * * * * * * * *
11057 GTTAGTC GTAGTG GTGGTG GTGGTG GTGGTG GTGGTG GTAGTA GTAGTA
1 G-TAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* * *
11106 GTAGTA GTAGTTA GTAGTA GTGGTA TTAGTA GTAGTTA GTCGTA GTAGTA
1 GTAGTA GTAG-TA GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA GTAGTA
* * *
11156 GTAGTA GTTAGTC GTAGTA GTAGTA GTGGTA GTAGTG GTAGT- GATAGTA
1 GTAGTA G-TAGTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTA G-TAGTA
*
11205 GTAGTA GTAGTTA GTAGTA GTAGTA GTAGTA GTAGTA GTAGTTA GTCGTA
1 GTAGTA GTAG-TA GTAGTA GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA
* * * * *
11255 GTAGTA GTAGTG GTAGTA GT-GATA GTAGTG GTAGTG GTGGTG GTAGTA
1 GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA GTAGTA GTAGTA GTAGTA
* * * *
11303 GTAGTA GTAGTA GTAGTA GTTAGTC GTAGTA ATAGTA GTGGTA GTAGTG
1 GTAGTA GTAGTA GTAGTA G-TAGTA GTAGTA GTAGTA GTAGTA GTAGTA
* *
11352 GTAGTG GTAGTG GTAGTA GTAGTTA GTAGTA GTAGTA GTA
1 GTAGTA GTAGTA GTAGTA GTAG-TA GTAGTA GTAGTA GTA
11392 AAAATATTGA
Statistics
Matches: 2471, Mismatches: 326, Indels: 72
0.86 0.11 0.03
Matches are distributed among these distances:
5 17 0.01
6 2347 0.95
7 106 0.04
8 1 0.00
ACGTcount: A:0.20, C:0.02, G:0.44, T:0.34
Consensus pattern (6 bp):
GTAGTA
Found at i:12946 original size:13 final size:13
Alignment explanation
Indices: 12928--12953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12918 GAATAATTCA
12928 ATTTTTTGGCACT
1 ATTTTTTGGCACT
12941 ATTTTTTGGCACT
1 ATTTTTTGGCACT
12954 CGTTGTGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTTTTTGGCACT
Found at i:13839 original size:29 final size:28
Alignment explanation
Indices: 13807--13884 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 28
13797 CTATTATAAC
13807 TTATAAAAGGTTTTATCCTTAATTTTAAT
1 TTATAAAA-GTTTTATCCTTAATTTTAAT
*
13836 TTATAAAAAGTTTTTTCCTTAATTTTAAT
1 TTAT-AAAAGTTTTATCCTTAATTTTAAT
*
13865 TTATATAAAGTTTTGTCCTT
1 TTATA-AAAGTTTTATCCTT
13885 TTACTAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 1 0.02
29 40 0.89
30 4 0.09
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (28 bp):
TTATAAAAGTTTTATCCTTAATTTTAAT
Found at i:15210 original size:31 final size:31
Alignment explanation
Indices: 15172--15234 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
15162 TAGAGAAGAA
15172 TCAACCTCTCATACCTTAAAGCAACCAATTC
1 TCAACCTCTCATACCTTAAAGCAACCAATTC
15203 TCAACCTCTCATACCTTAAAGCAACCAATTC
1 TCAACCTCTCATACCTTAAAGCAACCAATTC
15234 T
1 T
15235 TACTCCAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (31 bp):
TCAACCTCTCATACCTTAAAGCAACCAATTC
Found at i:26924 original size:27 final size:27
Alignment explanation
Indices: 26893--26945 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
26883 TAGCTGAGGT
*
26893 TGTGTCTTTT-GAATTTGTATTGATTTA
1 TGTGTCTTTTCCAATTTGT-TTGATTTA
*
26920 TGTGTTTTTTCCAATTTGTTTGATTT
1 TGTGTCTTTTCCAATTTGTTTGATTT
26946 TTTTATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.15, C:0.06, G:0.17, T:0.62
Consensus pattern (27 bp):
TGTGTCTTTTCCAATTTGTTTGATTTA
Found at i:29621 original size:21 final size:21
Alignment explanation
Indices: 29584--29653 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
29574 TAAACTTTGA
*
29584 TTTATTATTATTG-ATTTCAAG
1 TTTATTGTTA-TGAATTTCAAG
* *
29605 TTTCTTGTTATGAATTTCAAA
1 TTTATTGTTATGAATTTCAAG
* *
29626 TTTATTGTTATGGATGTCAAG
1 TTTATTGTTATGAATTTCAAG
29647 TTTATTG
1 TTTATTG
29654 GATAATGCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.05
21 39 0.95
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (21 bp):
TTTATTGTTATGAATTTCAAG
Found at i:29972 original size:44 final size:46
Alignment explanation
Indices: 29879--29973 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 46
29869 TACATTCCCA
*
29879 AAAACG-TCACTATATGACATAACATTTAGCAGCGTTTTTTGGAAC
1 AAAACGCTCACTATATGACAGAACATTTAGCAGCGTTTTTTGGAAC
* **
29924 -AAACGCT-ACTATATGTCAGAACATTTAGC-G-GTATTTTTGGGGC
1 AAAACGCTCACTATATGACAGAACATTTAGCAGCGT-TTTTTGGAAC
29967 AAAACGC
1 AAAACGC
29974 CACAAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.05
43 9 0.21
44 31 0.72
45 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (46 bp):
AAAACGCTCACTATATGACAGAACATTTAGCAGCGTTTTTTGGAAC
Found at i:32479 original size:21 final size:21
Alignment explanation
Indices: 32453--32564 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
32443 TTCCATTTCG
32453 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
32474 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
* *
32492 CACGTTACAATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
32515 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
32533 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
32556 CGTTGCGAT
1 CGTTGCGAT
32565 TTTCCATTTC
Statistics
Matches: 65, Mismatches: 16, Indels: 20
0.64 0.16 0.20
Matches are distributed among these distances:
18 4 0.06
19 8 0.12
20 16 0.25
21 25 0.38
22 8 0.12
23 4 0.06
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:32490 original size:41 final size:41
Alignment explanation
Indices: 32433--32587 Score: 274
Period size: 41 Copynumber: 3.8 Consensus size: 41
32423 CGCAAATTCG
*
32433 CGTTGCGGTTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
* * *
32474 CGTTGCGATTTTCCATTTCACGTTACAATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
32515 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
32556 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT
32588 TTTAAAAATG
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:32540 original size:20 final size:20
Alignment explanation
Indices: 32515--32584 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
32505 TCTACAGTGT
32515 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
32535 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
32555 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
32576 CGTTGCGAT
1 CGTTGCGAT
32585 AGTTTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:32720 original size:5 final size:6
Alignment explanation
Indices: 32670--32717 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
32660 GACACGTATT
32670 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
32715 ACC
1 ACC
32718 CGAGACGGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:33560 original size:20 final size:20
Alignment explanation
Indices: 33535--33648 Score: 74
Period size: 20 Copynumber: 5.6 Consensus size: 20
33525 TTTTAAAACT
33535 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
33555 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
33576 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
* **
33596 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
33617 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
33637 ACCGCAACGCGA
1 ATCGCAACGCGA
33649 TTTTCAACTA
Statistics
Matches: 69, Mismatches: 15, Indels: 20
0.66 0.14 0.19
Matches are distributed among these distances:
18 6 0.09
19 6 0.09
20 28 0.41
21 17 0.25
22 6 0.09
23 6 0.09
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:33581 original size:21 final size:21
Alignment explanation
Indices: 33555--33625 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
33545 GAAATGGAAA
33555 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
33576 ATCGCAACG-CGAAATG-A-AAA
1 ATCGCAACGAC--ACTGTAGACT
33596 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
33617 ATCGCAACG
1 ATCGCAACG
33626 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 21 0.54
22 3 0.08
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:33665 original size:21 final size:21
Alignment explanation
Indices: 33639--33689 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
33629 AATGGAAAAC
*
33639 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTCCAACTAT
33660 CGCAACGCGATTTCCAACTAT
1 CGCAACGCGATTTCCAACTAT
33681 CGCAACGCG
1 CGCAACGCG
33690 GAATGCAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (21 bp):
CGCAACGCGATTTCCAACTAT
Found at i:33669 original size:41 final size:41
Alignment explanation
Indices: 33532--33645 Score: 210
Period size: 41 Copynumber: 2.8 Consensus size: 41
33522 CATTTTTAAA
33532 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
33573 ACTATCGCAACGCGAAATGAAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
33614 ACTATCGCAACGCGAAATGGAAAACCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
33646 CGATTTTCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.13
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:37497 original size:204 final size:206
Alignment explanation
Indices: 37050--37497 Score: 548
Period size: 206 Copynumber: 2.2 Consensus size: 206
37040 TTATTTTGAT
* * * *
37050 GATGGCACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATTTGGTGTTGAAGATGACATTGCTAAT
1 GATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATTTGATGTTGAAGACGACACTGCTAAT
* * * * *
37115 CCTTGTTGAAGAGATTTGATCACTTTCAGATGAATTATTTATTGGAGATGACGTTGTTCCTTCAC
66 CCGTGTTAAAGAGATCTGATCACTTTCAGATAAATTATTTATTGAAGATGACGTTGTTCCTTCAC
* * *
37180 GTTGAGGAAATCAGATCCATCAGAGATAATTTGGAGGCAATACGGTTCCCTTGTTAAGGAAGTCT
131 GTTGAGGAAATCAGATCAATCAGAGATAATTTGGAGACAACACGGTTCCCTTGTTAAGGAAGTCT
37245 GATTGTCAGAG
196 GATTGTCAGAG
* * * *
37256 GATGACGCTGCTCCTTCGCGTTGAGGAGCTAGGGTCAATTTGATGTTGAAGACGTA-ACTGCTTA
1 GATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATTTGATGTTGAAGACG-ACACTGCTAA
* ** * *
37320 TCCGTGTTAAAGAGATCT-ATTC-GTTTTGGGTAAATTATTTGTTGAAGATGACGTTGTTCCTTC
65 TCCGTGTTAAAGAGATCTGA-TCACTTTCAGATAAATTATTTATTGAAGATGACGTTGTTCCTTC
** * * ** *
37383 GTGTTGAGGAAATCAGGTCAATCAGGCGATAA-TTGGAGACAACATTGTT-CCTTCG-TGAGGAA
129 ACGTTGAGGAAATCAGATCAATCA-GAGATAATTTGGAGACAACACGGTTCCCTT-GTTAAGGAA
*
37445 GTCTGATTGTCTGAG
192 GTCTGATTGTCAGAG
*
37460 GATGACACTGCTCCTTCGCATTGAGGAGATCGGGTCAA
1 GATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAA
37498 ACTGGAGATA
Statistics
Matches: 205, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
204 58 0.28
205 69 0.34
206 77 0.38
207 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (206 bp):
GATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATTTGATGTTGAAGACGACACTGCTAAT
CCGTGTTAAAGAGATCTGATCACTTTCAGATAAATTATTTATTGAAGATGACGTTGTTCCTTCAC
GTTGAGGAAATCAGATCAATCAGAGATAATTTGGAGACAACACGGTTCCCTTGTTAAGGAAGTCT
GATTGTCAGAG
Found at i:37761 original size:3 final size:3
Alignment explanation
Indices: 37753--37782 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
37743 ATGTTGTAAC
37753 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37783 TTTTTGTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39202 original size:19 final size:19
Alignment explanation
Indices: 39178--39217 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
39168 GCTTCTTGTC
* *
39178 TTCTTTTTCTTTGCTTTTT
1 TTCTTTTTCGTTGATTTTT
39197 TTCTTTTTCGTTGATTTTT
1 TTCTTTTTCGTTGATTTTT
39216 TT
1 TT
39218 GTTTCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCGTTGATTTTT
Done.