Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007128.1 Hibiscus syriacus cultivar Beakdansim tig00018627_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: 62852
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4714 original size:15 final size:15
Alignment explanation
Indices: 4694--4723 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4684 TGTTAGTAGC
4694 AGTTCTTAATCTTTT
1 AGTTCTTAATCTTTT
4709 AGTTCTTAATCTTTT
1 AGTTCTTAATCTTTT
4724 CTAAGTGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
AGTTCTTAATCTTTT
Found at i:6870 original size:12 final size:12
Alignment explanation
Indices: 6853--6914 Score: 115
Period size: 12 Copynumber: 5.2 Consensus size: 12
6843 CTAGGAGTCA
6853 GTATGTGCGAAT
1 GTATGTGCGAAT
6865 GTATGTGCGAAT
1 GTATGTGCGAAT
6877 GTATGTGCGAAT
1 GTATGTGCGAAT
*
6889 GTATGTGCAAAT
1 GTATGTGCGAAT
6901 GTATGTGCGAAT
1 GTATGTGCGAAT
6913 GT
1 GT
6915 GGATTGAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.26, C:0.08, G:0.32, T:0.34
Consensus pattern (12 bp):
GTATGTGCGAAT
Found at i:12072 original size:185 final size:185
Alignment explanation
Indices: 11755--12144 Score: 606
Period size: 185 Copynumber: 2.1 Consensus size: 185
11745 AACCGAAATT
* * * *
11755 AAATTTTAAATATATTATATATAACATATGGGCTCAGTCCAAACCATTTAAAACTCAATTAATGA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
11820 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
11885 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTTGAATTAAA
*
11940 AAATATTAAATATATTATATATAACATATGGGCTAAG-CTCAAATCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGTC-CAAACCATTTAAAACCCAATTAATA
* * * * * *
12004 ATTTAAGATTCAATAACTTTTAAACTTAAATTAATATTAATTAATTAAAAAATTTATCTGAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
12069 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
* * *
12125 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
12145 AATTAGAAAA
Statistics
Matches: 188, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
184 16 0.09
185 172 0.91
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
Found at i:12295 original size:19 final size:19
Alignment explanation
Indices: 12271--12310 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12261 AAAAAAAAAT
12271 TTAATT-AATTCGGTTATGA
1 TTAATTCAATTCGGTT-TGA
*
12290 TTAATTCGATTCGGTTTGA
1 TTAATTCAATTCGGTTTGA
12309 TT
1 TT
12311 TTAACCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.50
Consensus pattern (19 bp):
TTAATTCAATTCGGTTTGA
Found at i:17703 original size:8 final size:8
Alignment explanation
Indices: 17690--17730 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
17680 CTCATTTTCA
17690 GAGAATTT
1 GAGAATTT
17698 GAGAATTT
1 GAGAATTT
*
17706 -AGAGTTT
1 GAGAATTT
*
17713 GGGAATTT
1 GAGAATTT
17721 GAGAATTT
1 GAGAATTT
17729 GA
1 GA
17731 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:18022 original size:128 final size:128
Alignment explanation
Indices: 17794--18327 Score: 975
Period size: 128 Copynumber: 4.2 Consensus size: 128
17784 GTGTCTATAA
17794 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
1 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
*
17859 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATCTCCC
66 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
17922 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
1 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
17987 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
66 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
18050 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCC-GGGG
1 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
18114 -GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
66 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* ***
18176 TCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAAGGCGCGTTCCCGGGG
1 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTCACATGAAGGCGCGTTCCCGGGG
* *
18240 GCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
65 GCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
18304 TCGGGGACACTAGATATATCAGTA
1 TCGGGGACACTAGATATATCAGTA
18328 AATCGGGTAA
Statistics
Matches: 396, Mismatches: 7, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
125 1 0.00
126 116 0.29
127 8 0.02
128 271 0.68
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
Found at i:18245 original size:254 final size:256
Alignment explanation
Indices: 17794--18327 Score: 975
Period size: 254 Copynumber: 2.1 Consensus size: 256
17784 GTGTCTATAA
17794 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
1 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
17859 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATCTCCCTC
66 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATCTCCCTC
**
17924 GGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCG
131 GGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCCGGGGGCG
17989 CGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
196 CGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
18050 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCC-GGGG
1 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
*
18114 -GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
66 CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATCTCCCTC
* *
18178 GGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAAGGCGCGTTCCCGGGGGC
131 GGGGACACTAGATATATCAGTACCTATTATTTCACTA-GGCACATGAAGGCGCGTTCCCGGGGGC
* *
18242 GCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
195 GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
18304 TCGGGGACACTAGATATATCAGTA
1 TCGGGGACACTAGATATATCAGTA
18328 AATCGGGTAA
Statistics
Matches: 270, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
253 1 0.00
254 205 0.76
255 4 0.01
256 60 0.22
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (256 bp):
TCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGG
CGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATCTCCCTC
GGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCCGGGGGCG
CGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
Found at i:18491 original size:13 final size:13
Alignment explanation
Indices: 18473--18497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18463 ATAAGTTGAT
18473 TGTGACATTGAAA
1 TGTGACATTGAAA
18486 TGTGACATTGAA
1 TGTGACATTGAA
18498 TAAATTGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
TGTGACATTGAAA
Found at i:18751 original size:27 final size:28
Alignment explanation
Indices: 18721--18801 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 28
18711 TTCGAATACT
*
18721 ATAATTTATATTTTAATTTAAATTT-GA
1 ATAATTTATATTTTATTTTAAATTTCGA
18748 ATAATATTATTTTATTTTTATTTTAAATTTCGA
1 ATAAT-TTA---TA-TTTTATTTTAAATTTCGA
18781 ATAA--TATATTTGTATTTTAAA
1 ATAATTTATATTT-TATTTTAAA
18802 AACATTTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
26 3 0.07
27 16 0.35
28 3 0.07
30 2 0.04
31 2 0.04
32 14 0.30
33 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (28 bp):
ATAATTTATATTTTATTTTAAATTTCGA
Found at i:18767 original size:32 final size:32
Alignment explanation
Indices: 18698--18798 Score: 132
Period size: 33 Copynumber: 3.1 Consensus size: 32
18688 TAAGTTGAAA
* *
18698 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATATTTTAT-T
18732 TTTAATTTAAATTT-GAATAATATTATTTTATT
1 TTTAATTTAAATTTCGAATAATA-TATTTTATT
*
18764 TTTATTTTAAATTTCGAATAATATATTTGTATT
1 TTTAATTTAAATTTCGAATAATATATTT-TATT
18797 TT
1 TT
18799 AAAAACATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
32 26 0.43
33 29 0.48
34 6 0.10
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (32 bp):
TTTAATTTAAATTTCGAATAATATATTTTATT
Found at i:18799 original size:32 final size:31
Alignment explanation
Indices: 18698--18800 Score: 127
Period size: 32 Copynumber: 3.2 Consensus size: 31
18688 TAAGTTGAAA
*
18698 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATAT-ATTT-TAT
18732 TTTAATTTAAATTT-GAATAATATTATTTTATT
1 TTTAATTTAAATTTCGAATAATA-TATTTTA-T
*
18764 TTTATTTTAAATTTCGAATAATATATTTGTAT
1 TTTAATTTAAATTTCGAATAATATATTT-TAT
18796 TTTAA
1 TTTAA
18801 AAACATTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
31 2 0.03
32 35 0.56
33 19 0.31
34 6 0.10
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
TTTAATTTAAATTTCGAATAATATATTTTAT
Found at i:19405 original size:21 final size:21
Alignment explanation
Indices: 19317--19410 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
19307 TATGGTATAA
*
19317 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
19338 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* * *
19359 AACCCTGTGGGCTCGAAATGT
1 AACCCTGCGGGCTAGGAATGT
*
19380 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
19401 AACCCTGCGG
1 AACCCTGCGG
19411 AGATGGCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.05
21 59 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:19440 original size:21 final size:21
Alignment explanation
Indices: 19414--19461 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19404 CCTGCGGAGA
*
19414 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
19435 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
19456 GGGCAT
1 TGGCAT
19462 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:21171 original size:17 final size:19
Alignment explanation
Indices: 21149--21192 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21139 ATAATTATAT
21149 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
21166 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
21185 ATATATTA
1 AAATATTA
21193 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:21184 original size:19 final size:18
Alignment explanation
Indices: 21136--21223 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
21126 TTCTAAATAA
* *
21136 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
21153 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
21170 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
21189 ATTAATA--T-A-AAAAAT
1 A-TAATATTTAATAAAAAT
21204 AATAACTATTTAA-AAAAAT
1 -ATAA-TATTTAATAAAAAT
21223 A
1 A
21224 CTAACATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 8 0.14
16 6 0.11
17 15 0.27
18 7 0.12
19 15 0.27
20 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:21233 original size:34 final size:34
Alignment explanation
Indices: 21164--21235 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
21154 TTATTTTAAT
* * *
21164 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAAAATACTAACATA
21198 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATA
21232 AAAA
1 AAAA
21236 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATACTAACATA
Found at i:29619 original size:36 final size:36
Alignment explanation
Indices: 29571--29686 Score: 128
Period size: 36 Copynumber: 3.2 Consensus size: 36
29561 CCAACTTTGA
* *
29571 AAAAATGATTTTCAAAGTTTGATAAATGTTTTTTTT
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTTCTTT
*
29607 AAAAATGGTTTTCAAAGTTTGGTAAATG-TTTCTTT
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTTCTTT
* * * * * *
29642 GAAAATAGTTTTTTAAAGTTTGGTAGATG-TTTGTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTTCTTT
29678 AAAAATGAT
1 AAAAATGAT
29687 AATGAGATCA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 13 0.19
36 55 0.81
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTTCTTT
Found at i:34166 original size:21 final size:20
Alignment explanation
Indices: 34142--34207 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
34132 AACTTTGAAA
34142 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
* * *
34163 AAATGTTTT----TTTTTGA
1 AAATGTTTTCAAAGTTTGGT
34179 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
34200 AAATGTTT
1 AAATGTTT
34208 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 11
0.67 0.12 0.22
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
20 8 0.24
21 13 0.38
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:34231 original size:37 final size:37
Alignment explanation
Indices: 34134--34254 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 37
34124 TGACAACCAA
34134 CTTTGAAAAA-ATGATTTTCAAAGTTTGGTAAATGTTTTT
1 CTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATG--TTT
* *
34173 TTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
* * * *
34208 CTTTGAAAAATAGTTTTTTAAAGTTTGATAGATGTTT
1 CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
34245 -GTTGAAAAAT
1 CTTTGAAAAAT
34255 GATAATGGGA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
35 7 0.10
36 14 0.20
37 42 0.59
38 4 0.06
39 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.46
Consensus pattern (37 bp):
CTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Found at i:36498 original size:19 final size:19
Alignment explanation
Indices: 36474--36531 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
36464 AAAACCGAAA
36474 TCGGTTTTTTTGGTTCGGT
1 TCGGTTTTTTTGGTTCGGT
**
36493 TCGGTTTTTTT--AACGGT
1 TCGGTTTTTTTGGTTCGGT
* *
36510 TCGGGTTTTTCGGTTCGGT
1 TCGGTTTTTTTGGTTCGGT
36529 TCG
1 TCG
36532 ATTCAGTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 13 0.42
19 18 0.58
ACGTcount: A:0.03, C:0.14, G:0.31, T:0.52
Consensus pattern (19 bp):
TCGGTTTTTTTGGTTCGGT
Found at i:38028 original size:25 final size:25
Alignment explanation
Indices: 37988--38053 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
37978 ACCTAGGATG
37988 AACATAAAAATTTATGTTGAGGTACA
1 AACATAAAAA-TTATGTTGAGGTACA
38014 AACATAAAAATTATGTTGAGGTACA
1 AACATAAAAATTATGTTGAGGTACA
38039 AACATAACAAATTAT
1 AACATAA-AAATTAT
38054 ATTAAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 22 0.56
26 17 0.44
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (25 bp):
AACATAAAAATTATGTTGAGGTACA
Found at i:42967 original size:46 final size:45
Alignment explanation
Indices: 42884--42970 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
42874 TATAACAAAT
* *
42884 ATTTCATGTTCTTTTCATTTGTATATATTTCAAAACTTTCATTTC
1 ATTTCATATTCTTTTCATTTGTAGATATTTCAAAACTTTCATTTC
*
42929 ATTTCCATATTCTTTTC-TTT-TAGATACTTGTCATAACTTTCA
1 ATTT-CATATTCTTTTCATTTGTAGATA-TT-TCAAAACTTTCA
42971 CATTTACTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 5 0.14
45 9 0.25
46 22 0.61
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.54
Consensus pattern (45 bp):
ATTTCATATTCTTTTCATTTGTAGATATTTCAAAACTTTCATTTC
Found at i:49026 original size:24 final size:24
Alignment explanation
Indices: 48990--49196 Score: 163
Period size: 24 Copynumber: 8.5 Consensus size: 24
48980 TTTAAATATT
48990 TAAT-ATTATTAAATCATTATTAG
1 TAATAATTATTAAATCATTATTAG
49013 TAATAATTATTAAATCATTATTAG
1 TAATAATTATTAAATCATTATTAG
* *
49037 TAATTATTA-TAATTTCATTATTAG
1 TAATAATTATTAA-ATCATTATTAG
* *
49061 TAATCATTATTAAATCATTAGTA-
1 TAATAATTATTAAATCATTATTAG
* * * *
49084 TCA-AATCATTAAAT-ATTAATAA
1 TAATAATTATTAAATCATTATTAG
* * *
49106 TAAAACATTATTAGTAATCATTACTAAA
1 TAATA-ATTATTA--AATCATTA-TTAG
* * *
49134 TCATTAAATATTAAATCATTAAATTAA
1 T-AATAATTATTAAATCATT--ATTAG
*
49161 TAATAATTAATAAATCATTATTAG
1 TAATAATTATTAAATCATTATTAG
*
49185 TAATCATTATTA
1 TAATAATTATTA
49197 CTAATCATAT
Statistics
Matches: 148, Mismatches: 23, Indels: 25
0.76 0.12 0.13
Matches are distributed among these distances:
21 6 0.04
22 11 0.07
23 10 0.07
24 73 0.49
25 3 0.02
26 25 0.17
27 8 0.05
28 10 0.07
29 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (24 bp):
TAATAATTATTAAATCATTATTAG
Found at i:49251 original size:13 final size:13
Alignment explanation
Indices: 49233--49257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49223 TAAAAAATAA
49233 TAATCATTATTAG
1 TAATCATTATTAG
49246 TAATCATTATTA
1 TAATCATTATTA
49258 AATTATTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TAATCATTATTAG
Found at i:49282 original size:22 final size:21
Alignment explanation
Indices: 49238--49287 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
49228 AATAATAATC
*
49238 ATTATTAGTAATCATTATTAA
1 ATTATTAGTAATCATCATTAA
49259 ATTATTAGT-ATCAAATCATTAA
1 ATTATTAGTAATC--ATCATTAA
49281 ATTATTA
1 ATTATTA
49288 TTATTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 14 0.54
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTATTAGTAATCATCATTAA
Found at i:49557 original size:5 final size:5
Alignment explanation
Indices: 49549--49581 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
49539 AATTGAATCG
*
49549 AATAT AATAT AATAT AATAG AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AAT
49582 CTACAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:49676 original size:11 final size:11
Alignment explanation
Indices: 49660--49721 Score: 61
Period size: 11 Copynumber: 5.0 Consensus size: 11
49650 AATTAGAAGT
49660 AATCATTATTA
1 AATCATTATTA
49671 AATCATTAAAGTTCA
1 AATCATT--A-TT-A
49686 AATCATTATTA
1 AATCATTATTA
49697 AATCATTATTATCA
1 AATCATTA-T-T-A
49711 AATCATTATTA
1 AATCATTATTA
49722 TCAAATCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
11 17 0.39
12 4 0.09
13 4 0.09
14 11 0.25
15 8 0.18
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (11 bp):
AATCATTATTA
Found at i:49689 original size:26 final size:25
Alignment explanation
Indices: 49660--49721 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 25
49650 AATTAGAAGT
49660 AATCATTATTAAATCATTAAAGT-TCA
1 AATCATTATTAAATCATT--AGTATCA
*
49686 AATCATTATTAAATCATTATTATCA
1 AATCATTATTAAATCATTAGTATCA
49711 AATCATTATTA
1 AATCATTATTA
49722 TCAAATCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 2 0.06
25 14 0.41
26 18 0.53
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (25 bp):
AATCATTATTAAATCATTAGTATCA
Found at i:49713 original size:14 final size:14
Alignment explanation
Indices: 49683--49732 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
49673 TCATTAAAGT
49683 TCAAATCATTA-T-
1 TCAAATCATTATTA
49695 T-AAATCATTATTA
1 TCAAATCATTATTA
49708 TCAAATCATTATTA
1 TCAAATCATTATTA
49722 TCAAATCATTA
1 TCAAATCATTA
49733 AAACATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.26
12 2 0.06
13 1 0.03
14 23 0.66
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (14 bp):
TCAAATCATTATTA
Found at i:49732 original size:25 final size:24
Alignment explanation
Indices: 49683--49756 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 24
49673 TCATTAAAGT
*
49683 TCAAATCATTATTA-AATCATTATTA
1 TCAAATCATTATTATAA--ATCATTA
49708 TCAAATCATTATTATCAAATCATTA
1 TCAAATCATTATTAT-AAATCATTA
49733 --AAA-CATTATTAATAAATCA-TA
1 TCAAATCATTATT-ATAAATCATTA
49754 TCA
1 TCA
49757 TTACTATTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 2 0.05
22 13 0.30
23 6 0.14
25 20 0.47
27 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (24 bp):
TCAAATCATTATTATAAATCATTA
Found at i:49864 original size:2 final size:2
Alignment explanation
Indices: 49857--49898 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
49847 ACTTTAAGTA
49857 AT AT AT 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 AT AT AT
49899 TCGAGTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50065 original size:14 final size:14
Alignment explanation
Indices: 50022--50156 Score: 72
Period size: 14 Copynumber: 10.8 Consensus size: 14
50012 TCATTAAAGT
50022 TCAAATCATTATTA
1 TCAAATCATTATTA
*
50036 T-TAATCATTA-T-
1 TCAAATCATTATTA
*
50047 T-AAATTATTATTA
1 TCAAATCATTATTA
*
50060 TCAAATCATTAATA
1 TCAAATCATTATTA
50074 TCAAATC---A-T-
1 TCAAATCATTATTA
50083 T-AAATCATTATTA
1 TCAAATCATTATTA
* *
50096 TTAAATCATTAGTA
1 TCAAATCATTATTA
50110 GT-AAATC---A-T-
1 -TCAAATCATTATTA
50119 T-AAATCATTATTA
1 TCAAATCATTATTA
*
50132 TTAAATCATTATTA
1 TCAAATCATTATTA
50146 GT-AAATCATTA
1 -TCAAATCATTA
50157 AATCATTATT
Statistics
Matches: 98, Mismatches: 6, Indels: 34
0.71 0.04 0.25
Matches are distributed among these distances:
8 11 0.11
9 1 0.01
10 2 0.02
11 12 0.12
12 4 0.04
13 11 0.11
14 55 0.56
15 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (14 bp):
TCAAATCATTATTA
Found at i:50087 original size:22 final size:22
Alignment explanation
Indices: 50062--50106 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
50052 TATTATTATC
50062 AAATCATTAATATCAAATCATT
1 AAATCATTAATATCAAATCATT
* *
50084 AAATCATTATTATTAAATCATT
1 AAATCATTAATATCAAATCATT
50106 A
1 A
50107 GTAGTAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATCATTAATATCAAATCATT
Found at i:50093 original size:36 final size:36
Alignment explanation
Indices: 50022--50176 Score: 197
Period size: 36 Copynumber: 4.2 Consensus size: 36
50012 TCATTAAAGT
* * *
50022 TCAAATCATTATTATTAATCATTATTAAATTATTATTA
1 TCAAATCATTATTAGTAA--ATCATTAAATCATTATTA
*
50060 TCAAATCATTAATA-TCAAATCATTAAATCATTATTA
1 TCAAATCATTATTAGT-AAATCATTAAATCATTATTA
* *
50096 TTAAATCATTAGTAGTAAATCATTAAATCATTATTA
1 TCAAATCATTATTAGTAAATCATTAAATCATTATTA
*
50132 TTAAATCATTATTAGTAAATCATTAAATCATTATTAA
1 TCAAATCATTATTAGTAAATCATTAAATCATTATT-A
50169 T-AAATCAT
1 TCAAATCAT
50177 ATCATTACTA
Statistics
Matches: 108, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
36 89 0.82
37 4 0.04
38 15 0.14
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (36 bp):
TCAAATCATTATTAGTAAATCATTAAATCATTATTA
Found at i:50120 original size:22 final size:22
Alignment explanation
Indices: 50095--50142 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
50085 AATCATTATT
50095 ATTAAATCATTAGTAGTAAATC
1 ATTAAATCATTAGTAGTAAATC
* *
50117 ATTAAATCATTATTATTAAATC
1 ATTAAATCATTAGTAGTAAATC
50139 ATTA
1 ATTA
50143 TTAGTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (22 bp):
ATTAAATCATTAGTAGTAAATC
Found at i:50156 original size:22 final size:22
Alignment explanation
Indices: 50131--50176 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
50121 AATCATTATT
*
50131 ATTAAATCATTATTAGTAAATC
1 ATTAAATCATTATTAATAAATC
50153 ATTAAATCATTATTAATAAATC
1 ATTAAATCATTATTAATAAATC
50175 AT
1 AT
50177 ATCATTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTAAATCATTATTAATAAATC
Found at i:50176 original size:14 final size:14
Alignment explanation
Indices: 50083--50156 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
50073 ATCAAATCAT
*
50083 TAAATCATTATTAT
1 TAAATCATTATTAG
*
50097 TAAATCATTAGTAG
1 TAAATCATTATTAG
50111 TAAATC---A-T--
1 TAAATCATTATTAG
*
50119 TAAATCATTATTAT
1 TAAATCATTATTAG
50133 TAAATCATTATTAG
1 TAAATCATTATTAG
50147 TAAATCATTA
1 TAAATCATTA
50157 AATCATTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
8 6 0.12
10 1 0.02
11 2 0.04
12 1 0.02
14 41 0.80
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (14 bp):
TAAATCATTATTAG
Found at i:58612 original size:33 final size:33
Alignment explanation
Indices: 58575--58656 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
58565 CCAACTACTA
* *
58575 AAGATTAATTTTCCAATAAGTTAGCCACAAACC
1 AAGATGAATTTTCCAATAAATTAGCCACAAACC
* * *
58608 AAGATGAATTTTCTAATAAATTGGCCATAAACC
1 AAGATGAATTTTCCAATAAATTAGCCACAAACC
58641 AAGATGAATTTTCCAA
1 AAGATGAATTTTCCAA
58657 CTTGCCAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (33 bp):
AAGATGAATTTTCCAATAAATTAGCCACAAACC
Found at i:61232 original size:22 final size:22
Alignment explanation
Indices: 61204--61245 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
61194 GCACTTTATT
61204 TTTAGACTTCATCGGATACATC
1 TTTAGACTTCATCGGATACATC
61226 TTTAGACTTCATCGGATACA
1 TTTAGACTTCATCGGATACA
61246 CCAAACTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (22 bp):
TTTAGACTTCATCGGATACATC
Done.