Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001275.1 Hibiscus syriacus cultivar Beakdansim tig00002503_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: 67812
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5179 original size:21 final size:21
Alignment explanation
Indices: 5167--5215 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
5157 TATCGGTACC
5167 CCTTCATAGGGTATCAATACA
1 CCTTCATAGGGTATCAATACA
5188 CCTTCATAGGGTATCAATACA
1 CCTTCATAGGGTATCAATACA
5209 CCTTCAT
1 CCTTCAT
5216 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
CCTTCATAGGGTATCAATACA
Found at i:6034 original size:15 final size:17
Alignment explanation
Indices: 5962--6031 Score: 56
Period size: 18 Copynumber: 4.2 Consensus size: 17
5952 TATTATATTA
* *
5962 TAAC-TATATTAAAAAT
1 TAACATATAATAATAAT
**
5978 T-ACATATAATAATTCT
1 TAACATATAATAATAAT
*
5994 AAAC-TACTAATAATAAT
1 TAACATA-TAATAATAAT
6011 TAATCATATAATAATAAT
1 TAA-CATATAATAATAAT
6029 TAA
1 TAA
6032 TATTTAAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
15 2 0.05
16 11 0.27
17 12 0.29
18 14 0.34
19 2 0.05
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
TAACATATAATAATAAT
Found at i:6045 original size:18 final size:17
Alignment explanation
Indices: 6005--6061 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
5995 AACTACTAAT
* *
6005 AATAATTAATCATATAAT
1 AATAATTAAT-ATTTAAA
6023 AATAATTAATATTTAAA
1 AATAATTAATATTTAAA
6040 ACATAA--AATA-TTAAA
1 A-ATAATTAATATTTAAA
6055 AATAATT
1 AATAATT
6062 CTCTTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 4 0.12
17 6 0.18
18 14 0.41
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAATTAATATTTAAA
Found at i:6385 original size:18 final size:16
Alignment explanation
Indices: 6353--6384 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6343 ATTTCTTCTC
6353 TCTCTCTAAAAGAGAG
1 TCTCTCTAAAAGAGAG
6369 TCTCTCTAAAAGAGAG
1 TCTCTCTAAAAGAGAG
6385 AACCTCTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
TCTCTCTAAAAGAGAG
Found at i:6712 original size:12 final size:12
Alignment explanation
Indices: 6692--6725 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6682 TGTTTCTGTT
*
6692 TGTTTTTGTTGC
1 TGTTGTTGTTGC
*
6704 TGTTGTTGTTGG
1 TGTTGTTGTTGC
6716 TGTTGTTGTT
1 TGTTGTTGTT
6726 TGTTTGCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.65
Consensus pattern (12 bp):
TGTTGTTGTTGC
Found at i:9394 original size:3 final size:3
Alignment explanation
Indices: 9386--9471 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
9376 TTTTTACCCA
9386 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9434 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
9472 AATATATTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:11567 original size:6 final size:7
Alignment explanation
Indices: 11546--11570 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11536 TGTCTCTATT
11546 AATTAAA
1 AATTAAA
11553 AATTAAA
1 AATTAAA
11560 AATTAAA
1 AATTAAA
11567 AATT
1 AATT
11571 CATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:11626 original size:18 final size:17
Alignment explanation
Indices: 11603--11653 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
11593 TTCTTGTCAA
11603 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
11620 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
11638 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
11654 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:20479 original size:174 final size:174
Alignment explanation
Indices: 20169--20519 Score: 654
Period size: 174 Copynumber: 2.0 Consensus size: 174
20159 TATCTGAGCA
20169 AGAAATTTACTGATTGTGAAATTCGATATCCACCAATACAAAAATTATGTTGTGCTTTGGTGTGG
1 AGAAATTTACTGATTGTGAAATTCGATATCCACCAATACAAAAATTATGTTGTGCTTTGGTGTGG
20234 GCTACTCGAAGACTCAGACAATATATGTTGTACCATACTACTTGGTTGATATCCAAACTTGATCC
66 GCTACTCGAAGACTCAGACAATATATGTTGTACCATACTACTTGGTTGATATCCAAACTTGATCC
20299 TTTGAAATTCTTAAT-GAATCACCAGCTTTGACAGGCAGAATGGCT
131 TTTGAAATTCTTAATGGAATCACCAGC--TGACAGGCAGAATGGCT
20344 AGAAATTTACTGATTGTGAAATTCGATATCCACCAATACAAAAAATTATGTTGTGCTTTGGTGTG
1 AGAAATTTACTGATTGTGAAATTCGATATCCACCAATAC-AAAAATTATGTTGTGCTTTGGTGTG
20409 GGCTACTCGAAGACTCAGAC-A-ATATGTTGTACCATACTACTTGGTTGATATCCAAACTTGATC
65 GGCTACTCGAAGACTCAGACAATATATGTTGTACCATACTACTTGGTTGATATCCAAACTTGATC
20472 CTTTGAAATTCTTAATGGAATCACCAGCTGACAGGCAGAATGGCT
130 CTTTGAAATTCTTAATGGAATCACCAGCTGACAGGCAGAATGGCT
20517 AGA
1 AGA
20520 TGGGCAGATG
Statistics
Matches: 174, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
173 20 0.11
174 58 0.33
175 51 0.29
176 45 0.26
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (174 bp):
AGAAATTTACTGATTGTGAAATTCGATATCCACCAATACAAAAATTATGTTGTGCTTTGGTGTGG
GCTACTCGAAGACTCAGACAATATATGTTGTACCATACTACTTGGTTGATATCCAAACTTGATCC
TTTGAAATTCTTAATGGAATCACCAGCTGACAGGCAGAATGGCT
Found at i:23672 original size:83 final size:83
Alignment explanation
Indices: 23529--23912 Score: 678
Period size: 83 Copynumber: 4.6 Consensus size: 83
23519 AAATGTAATG
23529 TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TGCT-AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
*
23594 TGAATTTAGAAGATGAATT
65 TGAATTTGGAAGATGAATT
* * * *
23613 TGCCAATAGAAACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATT
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
23678 GAATTTGGAAGATGAATT
66 GAATTTGGAAGATGAATT
* * *
23696 TGCTAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
23761 GAATTTGGAAGATGAATT
66 GAATTTGGAAGATGAATT
*
23779 TGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
23844 GAATTTGGAAGATGAATT
66 GAATTTGGAAGATGAATT
23862 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
23913 TAAGAACTAC
Statistics
Matches: 283, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
83 280 0.99
84 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
GAATTTGGAAGATGAATT
Found at i:25086 original size:116 final size:113
Alignment explanation
Indices: 24641--25163 Score: 764
Period size: 116 Copynumber: 4.6 Consensus size: 113
24631 ATTCAAATCT
* *
24641 ATCATTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
24706 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
24754 ATCACTTGATGGATTATTTTTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
24818 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
* * *
24866 ATCAAATTGATGGATTAGCTTTT-CCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 ATC-ACTTGATGGATTA-TTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
24930 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
64 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
* *
24980 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATAAGAAGAACTCGTCATCTGAAGAAG
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
* * * *
25045 GAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
63 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
* * *** * *
25096 ATCATTTGATGGATCAACGTTGTCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCACTTGATGGATTATTTTTGCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
25160 GGAA
62 GGAA
25164 ACCCTAAATC
Statistics
Matches: 377, Mismatches: 25, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
112 91 0.24
113 78 0.21
114 89 0.24
115 2 0.01
116 117 0.31
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (113 bp):
ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
Found at i:31527 original size:46 final size:50
Alignment explanation
Indices: 31460--31551 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 50
31450 AAAAACATAT
* * *
31460 CCTAACCTCATGTTTTCTAGTTC-CATG-CTTTATT-T-AGAATAACAAA
1 CCTAACCACATGATTTCTAGTTCGCATGTATTTATTCTGAGAATAACAAA
31506 CCTAACCACATGATTTCTAGTTCGCATGTATTTATTCTGAGAATAA
1 CCTAACCACATGATTTCTAGTTCGCATGTATTTATTCTGAGAATAA
31552 TAATAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 21 0.54
47 4 0.10
48 6 0.15
49 1 0.03
50 7 0.18
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (50 bp):
CCTAACCACATGATTTCTAGTTCGCATGTATTTATTCTGAGAATAACAAA
Found at i:32630 original size:18 final size:18
Alignment explanation
Indices: 32588--32640 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
32578 TTAAAAATTA
*
32588 CATATAATAAT-TTTAA-
1 CATATAATAATAATTAAT
*
32604 AATACTAATAATAATTAAT
1 CATA-TAATAATAATTAAT
32623 CATATAATAATAATTAAT
1 CATATAATAATAATTAAT
32641 TTTTAAAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 18 0.58
19 3 0.10
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
CATATAATAATAATTAAT
Found at i:33310 original size:15 final size:15
Alignment explanation
Indices: 33276--33320 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
33266 TTTCTTGCTC
* *
33276 TTGTTTCTGTTTGTTT
1 TTGTTGCTG-TTGTTG
33292 TTGTTGCTGTTGTTG
1 TTGTTGCTGTTGTTG
33307 TTGTTGCTGTTGTT
1 TTGTTGCTGTTGTT
33321 TGTTTGCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.00, C:0.07, G:0.27, T:0.67
Consensus pattern (15 bp):
TTGTTGCTGTTGTTG
Found at i:34012 original size:18 final size:19
Alignment explanation
Indices: 33965--34021 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
33955 ATGTTTAATG
33965 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
33984 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
34004 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
34022 GGAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:36400 original size:21 final size:21
Alignment explanation
Indices: 36375--36415 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36365 CCATAACAGG
*
36375 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACACCTTCATA
*
36396 GGGTATTGGTACACCTTCAT
1 GGGTATCGGTACACCTTCAT
36416 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (21 bp):
GGGTATCGGTACACCTTCATA
Found at i:37747 original size:3 final size:3
Alignment explanation
Indices: 37741--37794 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
37731 GATGATGATG
37741 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
37789 ATA ATA
1 ATA ATA
37795 TTTTATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:37870 original size:17 final size:17
Alignment explanation
Indices: 37848--37880 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37838 AAAAATAAGA
37848 ATATTACATTA-TTAATT
1 ATATTA-ATTACTTAATT
37865 ATATTAATTACTTAAT
1 ATATTAATTACTTAAT
37881 ATTATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTAATTACTTAATT
Found at i:38915 original size:20 final size:20
Alignment explanation
Indices: 38890--38932 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
38880 ACCATAGAAT
*
38890 GTTCTAGAACATTATGGAAG
1 GTTCTAGAACATCATGGAAG
*
38910 GTTCTAGAACATCCTGGAAG
1 GTTCTAGAACATCATGGAAG
38930 GTT
1 GTT
38933 ATAAAACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (20 bp):
GTTCTAGAACATCATGGAAG
Found at i:48256 original size:2 final size:2
Alignment explanation
Indices: 48249--48280 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
48239 AATAATCCAT
48249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48281 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49219 original size:3 final size:3
Alignment explanation
Indices: 49211--49265 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
49201 TATGTGAATG
* * *
49211 TAA TAA TAA TAA TCA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
49259 TAA TAA T
1 TAA TAA T
49266 TTATTATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:49272 original size:3 final size:3
Alignment explanation
Indices: 49266--49293 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49256 TAATAATAAT
49266 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49294 ATTTTTTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52795 original size:21 final size:21
Alignment explanation
Indices: 52749--52795 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
52739 AATATAAAAT
*
52749 TATTAAAAATCATTAATATAA
1 TATTAAAAATCATAAATATAA
* *
52770 AATTAAAAAT-ATAAAATTTAA
1 TATTAAAAATCAT-AAATATAA
52791 TATTA
1 TATTA
52796 TAAGTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTAAAAATCATAAATATAA
Found at i:53466 original size:3 final size:3
Alignment explanation
Indices: 53458--53499 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
53448 TGGTACACCC
53458 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
53500 AGATCTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:62014 original size:21 final size:21
Alignment explanation
Indices: 61984--62024 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
61974 AATTGTTAAA
*
61984 AAATATTAATGTTTTAGGTAG
1 AAATAATAATGTTTTAGGTAG
62005 AAATAATAATGTTTTAGGTA
1 AAATAATAATGTTTTAGGTA
62025 ATTTTTACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTTAGGTAG
Done.