Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001556.1 Hibiscus syriacus cultivar Beakdansim tig00003076_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: 53960
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:3762 original size:2 final size:2
Alignment explanation
Indices: 3755--3780 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3745 AAATAGTCAT
3755 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
3781 AGTAATTTTT
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):
TA
Found at i:4415 original size:59 final size:56
Alignment explanation
Indices: 4312--4431 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 56
4302 GAGTGATCAT
* * *
4312 TTTGTAACTTTTAATAGTGTGACTCAACAAAGCAACATCCTATAGTCGAAGGATTA
1 TTTGTAACTTTTAATAGTGAGACTCAACAAAGCAACACCCTATAGTCGAAGGACTA
** *
4368 TTTGTAACTTTTAATAGTTGAGAGACTCAACAAAAG-ATTACCCTATAGTCGAGGGACTA
1 TTTGTAACTTTTAATAG-T--GAGACTCAAC-AAAGCAACACCCTATAGTCGAAGGACTA
4427 TTTGT
1 TTTGT
4432 GTACTCTACC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 17 0.31
57 1 0.02
59 32 0.59
60 4 0.07
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (56 bp):
TTTGTAACTTTTAATAGTGAGACTCAACAAAGCAACACCCTATAGTCGAAGGACTA
Found at i:6219 original size:18 final size:17
Alignment explanation
Indices: 6193--6226 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6183 TTGAATTGCA
*
6193 TTTATTTTCCATTTTTAC
1 TTTAATTTCC-TTTTTAC
6211 TTTAATTTCCTTTTTA
1 TTTAATTTCCTTTTTA
6227 TATGTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTCCTTTTTAC
Found at i:10185 original size:8 final size:8
Alignment explanation
Indices: 10174--10230 Score: 80
Period size: 8 Copynumber: 7.1 Consensus size: 8
10164 AGAGAGAGAG
10174 AAAAGAAA
1 AAAAGAAA
10182 AAAAGAAA
1 AAAAGAAA
10190 AAAAGAAA
1 AAAAGAAA
10198 GAAAA-AAA
1 -AAAAGAAA
*
10206 GAAAGAAA
1 AAAAGAAA
10214 AAAAGAAA
1 AAAAGAAA
*
10222 AAAGGAAA
1 AAAAGAAA
10230 A
1 A
10231 CAAATACTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
7 3 0.07
8 37 0.84
9 4 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:10200 original size:4 final size:4
Alignment explanation
Indices: 10154--10225 Score: 65
Period size: 4 Copynumber: 18.0 Consensus size: 4
10144 AAAAAACATA
* * * * * *
10154 AAAG AGAG AAAG AGAG AGAG AAAAG AAAA AAAG AAAA AAAG AAAG AAAA
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
10203 AAAG AAAG AAAA AAAG AAA- AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG
10226 GAAAACAAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
3 3 0.06
4 48 0.89
5 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:10200 original size:12 final size:12
Alignment explanation
Indices: 10153--10221 Score: 84
Period size: 12 Copynumber: 5.7 Consensus size: 12
10143 GAAAAAACAT
*
10153 AAAAGAGAGAAA
1 AAAAGAAAGAAA
* * *
10165 GAGAGAGAGAAA
1 AAAAGAAAGAAA
*
10177 AGAAAAAAAGAAA
1 A-AAAGAAAGAAA
10190 AAAAGAAAGAAA
1 AAAAGAAAGAAA
10202 AAAAGAAAGAAA
1 AAAAGAAAGAAA
10214 AAAAGAAA
1 AAAAGAAA
10222 AAAGGAAAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
12 40 0.82
13 9 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:10200 original size:20 final size:19
Alignment explanation
Indices: 10174--10230 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
10164 AGAGAGAGAG
10174 AAAAGAAAAAAAGAAAAAA
1 AAAAGAAAAAAAGAAAAAA
10193 AGAAAGAAAAAAAGAAAGAAA
1 A-AAAGAAAAAAAGAAA-AAA
*
10214 AAAAGAAAAAAGGAAAA
1 AAAAGAAAAAAAGAAAA
10231 CAAATACTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.83
21 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAGAAAAAA
Found at i:10999 original size:28 final size:28
Alignment explanation
Indices: 10955--11036 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
10945 CACAAGAAGC
* *
10955 CAACCTGAAAAATATTACCTTCCCAAAT
1 CAACCTGAAACACATTACCTTCCCAAAT
10983 CAACCTGAAACACATTACC-TCCTCAAAT
1 CAACCTGAAACACATTACCTTCC-CAAAT
* * *
11011 TAATCTGAAACAC-TCTACTTTCCCAA
1 CAACCTGAAACACAT-TACCTTCCCAA
11037 GGTAGCCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 4 0.09
28 39 0.85
29 3 0.07
ACGTcount: A:0.39, C:0.32, G:0.04, T:0.26
Consensus pattern (28 bp):
CAACCTGAAACACATTACCTTCCCAAAT
Found at i:12269 original size:55 final size:55
Alignment explanation
Indices: 12208--12679 Score: 450
Period size: 55 Copynumber: 8.8 Consensus size: 55
12198 GTGTTTTTTT
* *
12208 AGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAGTGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * *
12263 AGAAACTAAGTCTGATTTTCAGAAGTTTCCTGATTA-TTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * *
12317 AGAAACTAAGTCTGATTTTCGGAAGTTTCTTGATCATTTTTAAATGATCTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * * * *
12372 AGAAACTAAGTTTGATTTTCAGAGGTTTCCTGATG-GTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * *
12426 AGAAACTAAGTCCGATTTT-TGAAAGTTTATTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * *
12481 AGAAACGAAGTCTGATTTTTAGAAGTTTCCTGATGATTTTAAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * * * *
12536 AGAAATTAAGTCTGATTTTTAGAGGTTTC-T--TGA--CTT-AATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * ** * * *
12584 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
* * * * * *
12637 AGAAGCTAAGCCTAATTTTTAG-GGTTTCTTGATG-TTTTCAAAT
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAAT
12680 TAATTTGAAA
Statistics
Matches: 355, Mismatches: 52, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
48 29 0.08
49 6 0.02
50 1 0.00
51 2 0.01
52 25 0.07
53 33 0.09
54 91 0.26
55 167 0.47
56 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAA
Found at i:12391 original size:109 final size:109
Alignment explanation
Indices: 12208--12568 Score: 508
Period size: 109 Copynumber: 3.3 Consensus size: 109
12198 GTGTTTTTTT
* * *
12208 AGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAGTGAGCTTTCAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCATTTTTAAATGAGCTTTCAAAGAAACTAAG
*
12273 TCTGATTTTCAGAAGTTTCCTGATTATTTTAAATGAGTTTTTAA
66 TCTGATTTTCAGAAGTTTCCTGATGATTTTAAATGAGTTTTTAA
* * *
12317 AGAAACTAAGTCTGATTTTCGGAAGTTTCTTGATCATTTTTAAATGATCTTTTAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCATTTTTAAATGAGCTTTCAAAGAAACTAAG
* * *
12382 TTTGATTTTCAGAGGTTTCCTGATGGTTTTAAATGAGTTTTTAA
66 TCTGATTTTCAGAAGTTTCCTGATGATTTTAAATGAGTTTTTAA
* * * * *
12426 AGAAACTAAGTCCGATTTT-TGAAAGTTTATTGATTATTTTTAAATGAGCTTTCAAAGAAACGAA
1 AGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATCATTTTTAAATGAGCTTTCAAAGAAACTAA
* * *
12490 GTCTGATTTTTAGAAGTTTCCTGATGATTTTAAAATGAGCTTTCAA
65 GTCTGATTTTCAGAAGTTTCCTGATGATTTT-AAATGAGTTTTTAA
* * *
12536 AGAAATTAAGTCTGATTTTTAGAGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
12569 CTTAATGAAT
Statistics
Matches: 221, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
108 1 0.00
109 181 0.82
110 38 0.17
111 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (109 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCATTTTTAAATGAGCTTTCAAAGAAACTAAG
TCTGATTTTCAGAAGTTTCCTGATGATTTTAAATGAGTTTTTAA
Found at i:12485 original size:164 final size:164
Alignment explanation
Indices: 12208--12564 Score: 475
Period size: 164 Copynumber: 2.2 Consensus size: 164
12198 GTGTTTTTTT
* * * *
12208 AGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAGTGAGCTTTCAAAGAAACTAAG
1 AGAAACTAAGTTTGATTTTCAGAGGTTTCCTGATGAGTTTTAAATGAGCTTTCAAAGAAACTAAG
* * * * * *
12273 TCTGATTTTCAGAAGTTTCCTGATTATTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCG
66 TCCGATTTTCAGAAGTTTACTGATTATTTTAAATGAGCTTTCAAAGAAACGAAGTCTGATTTTCA
* * * *
12338 GAAGTTTCTTGATCATTTTTAAATGATCTTTTAA
131 GAAGTTTCCTGATCATTTTAAAATGAGCTTTCAA
* *
12372 AGAAACTAAGTTTGATTTTCAGAGGTTTCCTGATG-GTTTTAAATGAGTTTTTAAAGAAACTAAG
1 AGAAACTAAGTTTGATTTTCAGAGGTTTCCTGATGAGTTTTAAATGAGCTTTCAAAGAAACTAAG
* *
12436 TCCGATTTT-TGAAAGTTTATTGATTATTTTTAAATGAGCTTTCAAAGAAACGAAGTCTGATTTT
66 TCCGATTTTCAG-AAGTTTACTGATTA-TTTTAAATGAGCTTTCAAAGAAACGAAGTCTGATTTT
* *
12500 TAGAAGTTTCCTGATGATTTTAAAATGAGCTTTCAA
129 CAGAAGTTTCCTGATCATTTTAAAATGAGCTTTCAA
* * *
12536 AGAAATTAAGTCTGATTTTTAGAGGTTTC
1 AGAAACTAAGTTTGATTTTCAGAGGTTTC
12565 TTGACTTAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
162 1 0.01
163 45 0.27
164 122 0.73
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.41
Consensus pattern (164 bp):
AGAAACTAAGTTTGATTTTCAGAGGTTTCCTGATGAGTTTTAAATGAGCTTTCAAAGAAACTAAG
TCCGATTTTCAGAAGTTTACTGATTATTTTAAATGAGCTTTCAAAGAAACGAAGTCTGATTTTCA
GAAGTTTCCTGATCATTTTAAAATGAGCTTTCAA
Found at i:12642 original size:53 final size:53
Alignment explanation
Indices: 12208--12940 Score: 441
Period size: 55 Copynumber: 13.7 Consensus size: 53
12198 GTGTTTTTTT
** ** * * * *
12208 AGAAACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTAAGTGAGCTTTCAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
* ** * * * *
12263 AGAAACTAAGTCTGATTTTCAGAAGTTTCCTGAT-TATTTTAAATGAGTTTTTAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGT-TTTCAAATGA-ATTTGAA
* * * * * *
12317 AGAAACTAAGTCTGATTTTC-GGAAGTTTCTTGATCATTTTTAAATGATCTTTTAA
1 AGAAACTAAGCCTGATTTTCAGG-GGTTTCTTGAT-GTTTTCAAATGA-ATTTGAA
** * * * *
12372 AGAAACTAAGTTTGATTTTCAGAGGTTTCCTGATGGTTTT-AAATGAGTTTTTAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGAT-GTTTTCAAATGA-ATTTGAA
* ** * * * * *
12426 AGAAACTAAGTCC-GATTTT-TGAAAGTTTATTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAG-CCTGATTTTCAG-GGGTTTCTTGA-TGTTTTCAAATGA-ATTTGAA
* * * ** * * * *
12481 AGAAACGAAGTCTGATTTTTAGAAGTTTCCTGATGATTTTAAAATGAGCTTTCAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
* * * * *
12536 AGAAATTAAGTCTGATTTTTAGAGGTTTCTTGA---CTT--AATGAATTTGAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
*
12584 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * * *
12637 AGAAGCTAAGCCTAATTTTTA-GGGTTTCTTGATGTTTTCAAATTAATTTGAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * * *
12689 AGAAGCTAAGCCTAATAGTT-AAGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTGAT-TTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * *
12742 AGAAGCTAAGCCTAATAGTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTGAT-TTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
** *** * * * *
12795 AGAAGTTAAATTTGATTTTCAAGGGTTTCTTGATATTTTCAAATGAAATTTTAT
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATG-AATTTGAA
* * * * * * **
12849 AGAAGCTAAGCCTAATTTTTAGGGGTTTTCTATGATAATTGT-AAACGAAAGTTTTTA
1 AGAAACTAAGCCTGATTTTCAGGGG-TTTCT-TGAT-GTTTTCAAATG-AA-TTTGAA
* *
12906 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATG
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
12941 AGTAAGTTCT
Statistics
Matches: 574, Mismatches: 79, Indels: 51
0.82 0.11 0.07
Matches are distributed among these distances:
48 33 0.06
49 5 0.01
51 4 0.01
52 49 0.09
53 152 0.26
54 111 0.19
55 173 0.30
56 19 0.03
57 28 0.05
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (53 bp):
AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
Found at i:12698 original size:105 final size:105
Alignment explanation
Indices: 12572--12940 Score: 463
Period size: 105 Copynumber: 3.4 Consensus size: 105
12562 TTCTTGACTT
*
12572 AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTGAA
12637 AGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTTTTCA
66 AGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTTTTCA
* * *
12677 AATTAATTTGAAAGAAGCTAAGCCTAATAGTT-AAGGGTTTCTTGATGTTTTCAAATGAATTTGA
1 AATGAATTTGAAAGAAGCTAAGCCTGAT-TTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTGA
**
12741 AAGAAGCTAAGCCTAATAGTTAGGGGTTTCTTGATGTTTTCA
65 AAGAAGCTAAGCCTAATTTTTA-GGGTTTCTTGATGTTTTCA
* *** * *
12783 AATGAATTTGAAAGAAGTTAAATTTGATTTTCAAGGGTTTCTTGATATTTTCAAATGAAATTTTA
1 AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATG-AATTTGA
* * *
12848 TAGAAGCTAAGCCTAATTTTTAGGGGTTTTCTATGATAATTGT-A
65 AAGAAGCTAAGCCTAATTTTTA-GGG-TTTCT-TGAT-GTTTTCA
* ** * *
12892 AACGAAAGTTTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATG
1 AATG-AA-TTTGAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATG
12941 AGTAAGTTCT
Statistics
Matches: 227, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
105 79 0.35
106 67 0.30
107 29 0.13
108 5 0.02
109 8 0.04
110 5 0.02
111 34 0.15
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (105 bp):
AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTGAA
AGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTTTTCA
Found at i:12734 original size:158 final size:162
Alignment explanation
Indices: 12572--12940 Score: 453
Period size: 158 Copynumber: 2.3 Consensus size: 162
12562 TTCTTGACTT
12572 AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * * *
12637 AGAAGCTAAGCCTAATTTT-TAGGGTTTCTTGATGTTTTCAAAT-TAATTTGAAAGAAGCTAAGC
66 AGAAGCTAAACCTAATTTTCAAGGGTTTCTTGATATTTTCAAATGAAATTTGAAAGAAGCTAAGC
* *
12700 CTAATAGTTAAGGG-TTTCT-TGAT-GTTTTCA
131 CTAATAGTTAAGGGTTTTCTATGATAATTGT-A
* *
12730 AATGAATTTGAAAGAAGCTAAGCCTAATAGTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTGA
1 AATGAATTTGAAAGAAGCTAAGCCTGAT-TTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGA
* ** * * *
12794 AAGAAGTTAAATTTGATTTTCAAGGGTTTCTTGATATTTTCAAATGAAATTTTATAGAAGCTAAG
65 AAGAAGCTAAACCTAATTTTCAAGGGTTTCTTGATATTTTCAAATGAAATTTGAAAGAAGCTAAG
** *
12859 CCTAATTTTTAGGGGTTTTCTATGATAATTGTA
130 CCTAATAGTTAAGGGTTTTCTATGATAATTGTA
* ** * * *
12892 AACGAAAGTTTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATG
1 AATG-AA-TTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG
12941 AGTAAGTTCT
Statistics
Matches: 177, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
158 74 0.42
159 24 0.14
160 28 0.16
161 5 0.03
162 8 0.05
163 7 0.04
164 31 0.18
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (162 bp):
AATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
AGAAGCTAAACCTAATTTTCAAGGGTTTCTTGATATTTTCAAATGAAATTTGAAAGAAGCTAAGC
CTAATAGTTAAGGGTTTTCTATGATAATTGTA
Found at i:13017 original size:20 final size:22
Alignment explanation
Indices: 12963--13017 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
12953 GAGCCATCAA
12963 TAAGTCTTTCGAGTGCGATGCT
1 TAAGTCTTTCGAGTGCGATGCT
* *
12985 TAAATCCTTCGAGT-C-AT-CT
1 TAAGTCTTTCGAGTGCGATGCT
13004 GTAAGTCTTTCGAG
1 -TAAGTCTTTCGAG
13018 CAAGATGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 13 0.46
21 1 0.04
22 12 0.43
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (22 bp):
TAAGTCTTTCGAGTGCGATGCT
Found at i:13292 original size:41 final size:41
Alignment explanation
Indices: 13183--13292 Score: 105
Period size: 42 Copynumber: 2.7 Consensus size: 41
13173 GTTTCTTAAT
* *
13183 TGATAAGTCCTTCGGACCAT-CAGTAAGGATTTCGAGCATGA
1 TGATAAGTCCTTCGGGCCATCCA-TAAGGATTTCGAGCAAGA
* * * * * **
13224 TGCTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGA
1 TG-ATAAGTCCTTCGGGCCATCCATAAGGATTTCGAGCAAGA
*
13266 TGATAAGTCCTTTGGGCCATCCATAAG
1 TGATAAGTCCTTCGGGCCATCCATAAG
13293 ACCTACGGGC
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
41 21 0.40
42 30 0.58
43 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (41 bp):
TGATAAGTCCTTCGGGCCATCCATAAGGATTTCGAGCAAGA
Found at i:14081 original size:139 final size:139
Alignment explanation
Indices: 13812--14177 Score: 601
Period size: 139 Copynumber: 2.6 Consensus size: 139
13802 GATAAACCAG
*
13812 TCAACATTTCCAGTGGAGA-TTCATAATAAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * ** *
13876 ATGAGAAGAACTTGTTCAACCTTAGCTTGAATCATGGCATATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAACTCGAATCATCACATATAGAGTTGAATCAGCAACACCTCA
13941 CTCGAGGGA
131 CTCGAGGGA
* *
13950 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* *
14015 ATGAGAAGAACTTGTTCAACCTTAACTCGATTTATCACATATAGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAACTCGAATCATCACATATAGAGTTGAATCAGCAACACCTCA
14080 CTCGAGGGA
131 CTCGAGGGA
* *
14089 TCAACATGTT-CAGGGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
1 TCAACAT-TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
14153 AATGAGAAGAACTTGTTCAACCTTA
65 AATGAGAAGAACTTGTTCAACCTTA
14178 GCTTGTTTCC
Statistics
Matches: 212, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
138 19 0.09
139 191 0.90
140 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAACTCGAATCATCACATATAGAGTTGAATCAGCAACACCTCA
CTCGAGGGA
Found at i:14170 original size:20 final size:19
Alignment explanation
Indices: 14108--14171 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
14098 TCAGGGGAGA
14108 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
14127 CATCCGATAAGGGAGAAGAA--
1 -GTTC-ATAA-TGAGAAGAACT
14147 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
14167 GTTCA
1 GTTCA
14172 ACCTTAGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:16127 original size:18 final size:18
Alignment explanation
Indices: 16099--16136 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
16089 TAGCATTGAG
16099 TTGCATTTAATTTCCATTT
1 TTGCATTTAATTTCC-TTT
16118 TTGC-TTTAATTTCCTTT
1 TTGCATTTAATTTCCTTT
16135 TT
1 TT
16137 ATTTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (18 bp):
TTGCATTTAATTTCCTTT
Found at i:27939 original size:37 final size:36
Alignment explanation
Indices: 27880--27999 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
27870 ATCCCATTAT
* *
27880 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
27916 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
27952 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
27987 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
28000 TTGGTTATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:27955 original size:21 final size:21
Alignment explanation
Indices: 27931--27991 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
27921 TTCAAAGAAA
27931 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
27952 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
27966 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
27987 CATTT
1 CATTT
27992 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:29055 original size:21 final size:21
Alignment explanation
Indices: 29023--29064 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29013 TGTCATTATC
29023 TATATATGTTTATTATATTTT
1 TATATATGTTTATTATATTTT
*
29044 TATA-ATGTTTTATTTTATTTT
1 TATATATG-TTTATTATATTTT
29065 AATTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TATATATGTTTATTATATTTT
Found at i:29489 original size:62 final size:62
Alignment explanation
Indices: 29419--29538 Score: 181
Period size: 62 Copynumber: 1.9 Consensus size: 62
29409 TAGCCACATA
*
29419 TTTATACGTGCAATA-TTTTCTAAATTTTAGTTTCCTAAACTAAGGCACTAA-CCACTAATATT
1 TTTATACGTGCAATACTTTT-TAAATTTTAATTTCC-AAACTAAGGCACTAATCCACTAATATT
* *
29481 TTTATACGTGGAATACTTTTTAAATTTTAATTTCCAAACTAAGGTACTAATCCACTAA
1 TTTATACGTGCAATACTTTTTAAATTTTAATTTCCAAACTAAGGCACTAATCCACTAA
29539 GGCAATACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
61 14 0.26
62 35 0.66
63 4 0.08
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (62 bp):
TTTATACGTGCAATACTTTTTAAATTTTAATTTCCAAACTAAGGCACTAATCCACTAATATT
Found at i:33250 original size:2 final size:2
Alignment explanation
Indices: 33243--33278 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33233 AACATGAACC
33243 AT 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 AT
33279 GCATGTGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36812 original size:2 final size:2
Alignment explanation
Indices: 36805--36831 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36795 CATTGTTAAT
36805 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
36832 TGAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39540 original size:20 final size:20
Alignment explanation
Indices: 39511--39558 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
39501 AATGATTTTC
* *
39511 TTTT-AAAAGCAAAATTAGA
1 TTTTGAAAAGCAAAATGAAA
39530 TTTTGAAAAGCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
39550 TTTTGAAAA
1 TTTTGAAAA
39559 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:43893 original size:22 final size:22
Alignment explanation
Indices: 43859--43926 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
43849 CTCATTTCAG
* *
43859 TGCTAA-GTCACTTT-GTATTAG
1 TGCTAATG-CACTTTAGTATCAA
**
43880 TGCATAATGCACTTTCTTATCAA
1 TGC-TAATGCACTTTAGTATCAA
43903 TGCTAATGCACTTTAGTATCAA
1 TGCTAATGCACTTTAGTATCAA
43925 TG
1 TG
43927 GCAAGGCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 28 0.72
23 8 0.21
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (22 bp):
TGCTAATGCACTTTAGTATCAA
Found at i:43935 original size:22 final size:22
Alignment explanation
Indices: 43859--43937 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
43849 CTCATTTCAG
* * *
43859 TGCTAAGTCACTTT-GTATTAG
1 TGCTAAGGCACTTTAGTATCAA
* **
43880 TGCATAATGCACTTTCTTATCAA
1 TGC-TAAGGCACTTTAGTATCAA
*
43903 TGCTAATGCACTTTAGTATCAA
1 TGCTAAGGCACTTTAGTATCAA
43925 TGGC-AAGGCACTT
1 T-GCTAAGGCACTT
43938 CCGTTAATCG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 3 0.06
22 35 0.74
23 9 0.19
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (22 bp):
TGCTAAGGCACTTTAGTATCAA
Found at i:46542 original size:31 final size:31
Alignment explanation
Indices: 46504--46574 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
46494 CTTTTAAAAC
* *
46504 TTACAATATAATCCCCCAATATTTAGTCCGT
1 TTACAATATAATCCCCCAACATTTAGTCCAT
** * *
46535 TTACAATATGGTTCCCCAACATTTAGTCTAT
1 TTACAATATAATCCCCCAACATTTAGTCCAT
46566 TTACAATAT
1 TTACAATAT
46575 GGTCCCCGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
TTACAATATAATCCCCCAACATTTAGTCCAT
Found at i:46575 original size:31 final size:30
Alignment explanation
Indices: 46517--46581 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
46507 CAATATAATC
* *
46517 CCCCAATATTTAGTCCGTTTACAATATGGTT
1 CCCCAACATTTAGTCCATTTACAATATGG-T
*
46548 CCCCAACATTTAGTCTATTTACAATATGGT
1 CCCCAACATTTAGTCCATTTACAATATGGT
46578 CCCC
1 CCCC
46582 GACGTAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (30 bp):
CCCCAACATTTAGTCCATTTACAATATGGT
Found at i:53735 original size:3 final size:3
Alignment explanation
Indices: 53729--53773 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
53719 TGTTGTCGTC
*
53729 ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATTT ATT CATG ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT -ATT ATT ATT
53774 GATTTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 29 0.78
4 8 0.22
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:53780 original size:19 final size:18
Alignment explanation
Indices: 53727--53781 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
53717 GTTGTTGTCG
53727 TCATTATTATTTATTATTAT
1 TCATTATTA-TTATT-TTAT
53747 T-ATTATTATTA-TTTAT
1 TCATTATTATTATTTTAT
*
53763 TCATGATTATTGATTTTAT
1 TCATTATTATT-ATTTTAT
53782 ATTTGTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.16
17 9 0.29
18 4 0.13
19 12 0.39
20 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TCATTATTATTATTTTAT
Done.