Multiple sequence alignment - TraesCS2D01G157100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G157100 chr2D 100.000 2314 0 0 1 2314 100319450 100317137 0.000000e+00 4274
1 TraesCS2D01G157100 chr2D 82.532 790 70 33 912 1680 397962895 397962153 1.170000e-177 632
2 TraesCS2D01G157100 chr2D 81.529 785 78 30 917 1680 54392573 54393311 3.310000e-163 584
3 TraesCS2D01G157100 chr2D 83.616 531 55 16 1165 1680 250920883 250920370 9.680000e-129 470
4 TraesCS2D01G157100 chr3B 86.681 1419 85 48 643 2026 245923253 245921904 0.000000e+00 1478
5 TraesCS2D01G157100 chr2B 84.757 1089 68 45 87 1108 152176914 152175857 0.000000e+00 1002
6 TraesCS2D01G157100 chr2B 83.446 1039 65 35 1191 2177 152175812 152174829 0.000000e+00 867
7 TraesCS2D01G157100 chr2B 83.444 151 7 8 2175 2314 152169347 152169204 8.680000e-25 124
8 TraesCS2D01G157100 chr2A 87.560 828 47 34 298 1095 100130381 100129580 0.000000e+00 907
9 TraesCS2D01G157100 chr2A 88.866 476 24 11 1575 2045 100129144 100128693 2.010000e-155 558
10 TraesCS2D01G157100 chr2A 81.933 238 20 10 2047 2273 100128501 100128276 1.830000e-41 180
11 TraesCS2D01G157100 chr3D 88.889 675 42 14 1376 2039 284205963 284205311 0.000000e+00 800
12 TraesCS2D01G157100 chr3D 86.555 595 24 26 643 1212 284206526 284205963 2.540000e-169 604
13 TraesCS2D01G157100 chr7A 82.868 788 70 31 912 1680 342305584 342304843 0.000000e+00 647
14 TraesCS2D01G157100 chr7A 83.304 569 40 27 912 1465 533367885 533367357 7.480000e-130 473
15 TraesCS2D01G157100 chr1D 82.152 790 73 30 912 1680 465260317 465261059 1.170000e-172 616
16 TraesCS2D01G157100 chr7B 92.978 356 14 5 1698 2053 29703858 29704202 2.050000e-140 508
17 TraesCS2D01G157100 chr7B 86.567 469 21 24 643 1087 29687456 29687906 1.610000e-131 479
18 TraesCS2D01G157100 chr6D 83.992 531 53 17 1165 1680 288070274 288070787 4.470000e-132 481
19 TraesCS2D01G157100 chr7D 82.700 526 59 17 1170 1680 157759022 157759530 2.730000e-119 438


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G157100 chr2D 100317137 100319450 2313 True 4274.000000 4274 100.000000 1 2314 1 chr2D.!!$R1 2313
1 TraesCS2D01G157100 chr2D 397962153 397962895 742 True 632.000000 632 82.532000 912 1680 1 chr2D.!!$R3 768
2 TraesCS2D01G157100 chr2D 54392573 54393311 738 False 584.000000 584 81.529000 917 1680 1 chr2D.!!$F1 763
3 TraesCS2D01G157100 chr2D 250920370 250920883 513 True 470.000000 470 83.616000 1165 1680 1 chr2D.!!$R2 515
4 TraesCS2D01G157100 chr3B 245921904 245923253 1349 True 1478.000000 1478 86.681000 643 2026 1 chr3B.!!$R1 1383
5 TraesCS2D01G157100 chr2B 152174829 152176914 2085 True 934.500000 1002 84.101500 87 2177 2 chr2B.!!$R2 2090
6 TraesCS2D01G157100 chr2A 100128276 100130381 2105 True 548.333333 907 86.119667 298 2273 3 chr2A.!!$R1 1975
7 TraesCS2D01G157100 chr3D 284205311 284206526 1215 True 702.000000 800 87.722000 643 2039 2 chr3D.!!$R1 1396
8 TraesCS2D01G157100 chr7A 342304843 342305584 741 True 647.000000 647 82.868000 912 1680 1 chr7A.!!$R1 768
9 TraesCS2D01G157100 chr7A 533367357 533367885 528 True 473.000000 473 83.304000 912 1465 1 chr7A.!!$R2 553
10 TraesCS2D01G157100 chr1D 465260317 465261059 742 False 616.000000 616 82.152000 912 1680 1 chr1D.!!$F1 768
11 TraesCS2D01G157100 chr6D 288070274 288070787 513 False 481.000000 481 83.992000 1165 1680 1 chr6D.!!$F1 515
12 TraesCS2D01G157100 chr7D 157759022 157759530 508 False 438.000000 438 82.700000 1170 1680 1 chr7D.!!$F1 510

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
51 52 0.107848 ACGGAATAAACAGCCCTCGG 60.108 55.0 0.0 0.0 0.0 4.63 F
52 53 0.107848 CGGAATAAACAGCCCTCGGT 60.108 55.0 0.0 0.0 0.0 4.69 F
56 57 0.175073 ATAAACAGCCCTCGGTCGTC 59.825 55.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1114 1197 0.613853 TAGGACGGGACAGGAACAGG 60.614 60.000 0.0 0.0 0.0 4.00 R
1185 1274 0.687354 ACCAGCAGTCAGTTACCCAG 59.313 55.000 0.0 0.0 0.0 4.45 R
1862 2045 1.569493 CGCGGAGGAACAACACAAG 59.431 57.895 0.0 0.0 0.0 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.776662 CCAACCGTCCTCTAGATCCA 58.223 55.000 0.00 0.00 0.00 3.41
20 21 2.320781 CCAACCGTCCTCTAGATCCAT 58.679 52.381 0.00 0.00 0.00 3.41
21 22 2.036475 CCAACCGTCCTCTAGATCCATG 59.964 54.545 0.00 0.00 0.00 3.66
22 23 2.959030 CAACCGTCCTCTAGATCCATGA 59.041 50.000 0.00 0.00 0.00 3.07
23 24 2.870175 ACCGTCCTCTAGATCCATGAG 58.130 52.381 0.00 0.00 0.00 2.90
24 25 2.443632 ACCGTCCTCTAGATCCATGAGA 59.556 50.000 0.00 0.00 0.00 3.27
25 26 3.117474 ACCGTCCTCTAGATCCATGAGAA 60.117 47.826 0.00 0.00 0.00 2.87
26 27 3.254657 CCGTCCTCTAGATCCATGAGAAC 59.745 52.174 0.00 0.00 0.00 3.01
27 28 3.885901 CGTCCTCTAGATCCATGAGAACA 59.114 47.826 0.00 0.00 0.00 3.18
28 29 4.522405 CGTCCTCTAGATCCATGAGAACAT 59.478 45.833 0.00 0.00 37.19 2.71
36 37 3.157727 CATGAGAACATGCCACGGA 57.842 52.632 0.00 0.00 45.51 4.69
37 38 1.452110 CATGAGAACATGCCACGGAA 58.548 50.000 0.00 0.00 45.51 4.30
38 39 2.019249 CATGAGAACATGCCACGGAAT 58.981 47.619 0.00 0.00 45.51 3.01
39 40 3.205338 CATGAGAACATGCCACGGAATA 58.795 45.455 0.00 0.00 45.51 1.75
40 41 3.342377 TGAGAACATGCCACGGAATAA 57.658 42.857 0.00 0.00 0.00 1.40
41 42 3.680490 TGAGAACATGCCACGGAATAAA 58.320 40.909 0.00 0.00 0.00 1.40
42 43 3.438781 TGAGAACATGCCACGGAATAAAC 59.561 43.478 0.00 0.00 0.00 2.01
43 44 3.417101 AGAACATGCCACGGAATAAACA 58.583 40.909 0.00 0.00 0.00 2.83
44 45 3.440173 AGAACATGCCACGGAATAAACAG 59.560 43.478 0.00 0.00 0.00 3.16
45 46 1.472480 ACATGCCACGGAATAAACAGC 59.528 47.619 0.00 0.00 0.00 4.40
46 47 1.102978 ATGCCACGGAATAAACAGCC 58.897 50.000 0.00 0.00 0.00 4.85
47 48 0.963355 TGCCACGGAATAAACAGCCC 60.963 55.000 0.00 0.00 0.00 5.19
48 49 0.679960 GCCACGGAATAAACAGCCCT 60.680 55.000 0.00 0.00 0.00 5.19
49 50 1.379527 CCACGGAATAAACAGCCCTC 58.620 55.000 0.00 0.00 0.00 4.30
50 51 1.006832 CACGGAATAAACAGCCCTCG 58.993 55.000 0.00 0.00 0.00 4.63
51 52 0.107848 ACGGAATAAACAGCCCTCGG 60.108 55.000 0.00 0.00 0.00 4.63
52 53 0.107848 CGGAATAAACAGCCCTCGGT 60.108 55.000 0.00 0.00 0.00 4.69
53 54 1.664873 GGAATAAACAGCCCTCGGTC 58.335 55.000 0.00 0.00 0.00 4.79
54 55 1.287425 GAATAAACAGCCCTCGGTCG 58.713 55.000 0.00 0.00 0.00 4.79
55 56 0.611714 AATAAACAGCCCTCGGTCGT 59.388 50.000 0.00 0.00 0.00 4.34
56 57 0.175073 ATAAACAGCCCTCGGTCGTC 59.825 55.000 0.00 0.00 0.00 4.20
57 58 0.896940 TAAACAGCCCTCGGTCGTCT 60.897 55.000 0.00 0.00 0.00 4.18
58 59 2.156051 AAACAGCCCTCGGTCGTCTC 62.156 60.000 0.00 0.00 0.00 3.36
59 60 2.752238 CAGCCCTCGGTCGTCTCT 60.752 66.667 0.00 0.00 0.00 3.10
60 61 2.752238 AGCCCTCGGTCGTCTCTG 60.752 66.667 0.00 0.00 0.00 3.35
61 62 2.750637 GCCCTCGGTCGTCTCTGA 60.751 66.667 0.00 0.00 0.00 3.27
62 63 2.122167 GCCCTCGGTCGTCTCTGAT 61.122 63.158 0.00 0.00 0.00 2.90
63 64 2.026522 CCCTCGGTCGTCTCTGATC 58.973 63.158 0.00 0.00 0.00 2.92
64 65 1.448922 CCCTCGGTCGTCTCTGATCC 61.449 65.000 0.00 0.00 0.00 3.36
65 66 1.448922 CCTCGGTCGTCTCTGATCCC 61.449 65.000 0.00 0.00 0.00 3.85
66 67 1.777030 CTCGGTCGTCTCTGATCCCG 61.777 65.000 0.00 0.00 36.83 5.14
67 68 2.413765 GGTCGTCTCTGATCCCGC 59.586 66.667 0.00 0.00 0.00 6.13
68 69 2.024871 GTCGTCTCTGATCCCGCG 59.975 66.667 0.00 0.00 0.00 6.46
69 70 3.889044 TCGTCTCTGATCCCGCGC 61.889 66.667 0.00 0.00 0.00 6.86
71 72 4.194720 GTCTCTGATCCCGCGCGT 62.195 66.667 29.95 10.71 0.00 6.01
72 73 2.515290 TCTCTGATCCCGCGCGTA 60.515 61.111 29.95 17.16 0.00 4.42
73 74 2.050895 CTCTGATCCCGCGCGTAG 60.051 66.667 29.95 19.79 0.00 3.51
91 92 4.793071 CGTAGCTCTCTCTGGTCATAATG 58.207 47.826 0.00 0.00 0.00 1.90
92 93 3.749665 AGCTCTCTCTGGTCATAATGC 57.250 47.619 0.00 0.00 0.00 3.56
95 96 3.305950 GCTCTCTCTGGTCATAATGCGAT 60.306 47.826 0.00 0.00 0.00 4.58
103 104 5.476945 TCTGGTCATAATGCGATCTTAGCTA 59.523 40.000 0.00 0.00 35.28 3.32
105 106 6.159293 TGGTCATAATGCGATCTTAGCTAAG 58.841 40.000 24.90 24.90 35.28 2.18
117 118 5.667539 TCTTAGCTAAGCTCAGTTGTCAT 57.332 39.130 25.83 0.00 40.44 3.06
118 119 6.775594 TCTTAGCTAAGCTCAGTTGTCATA 57.224 37.500 25.83 3.85 40.44 2.15
119 120 7.353414 TCTTAGCTAAGCTCAGTTGTCATAT 57.647 36.000 25.83 0.00 40.44 1.78
120 121 7.786030 TCTTAGCTAAGCTCAGTTGTCATATT 58.214 34.615 25.83 0.00 40.44 1.28
122 123 5.046529 AGCTAAGCTCAGTTGTCATATTCG 58.953 41.667 0.00 0.00 30.62 3.34
123 124 4.806247 GCTAAGCTCAGTTGTCATATTCGT 59.194 41.667 0.00 0.00 0.00 3.85
124 125 5.292101 GCTAAGCTCAGTTGTCATATTCGTT 59.708 40.000 0.00 0.00 0.00 3.85
125 126 6.475727 GCTAAGCTCAGTTGTCATATTCGTTA 59.524 38.462 0.00 0.00 0.00 3.18
126 127 6.648725 AAGCTCAGTTGTCATATTCGTTAC 57.351 37.500 0.00 0.00 0.00 2.50
127 128 4.798907 AGCTCAGTTGTCATATTCGTTACG 59.201 41.667 0.00 0.00 0.00 3.18
130 131 6.252015 GCTCAGTTGTCATATTCGTTACGTTA 59.748 38.462 4.24 0.00 0.00 3.18
131 132 7.496704 TCAGTTGTCATATTCGTTACGTTAC 57.503 36.000 4.24 0.00 0.00 2.50
132 133 7.083230 TCAGTTGTCATATTCGTTACGTTACA 58.917 34.615 4.24 0.00 0.00 2.41
133 134 7.060979 TCAGTTGTCATATTCGTTACGTTACAC 59.939 37.037 4.24 0.00 0.00 2.90
134 135 6.308766 AGTTGTCATATTCGTTACGTTACACC 59.691 38.462 4.24 0.00 0.00 4.16
135 136 5.707931 TGTCATATTCGTTACGTTACACCA 58.292 37.500 4.24 0.00 0.00 4.17
137 138 6.089283 TGTCATATTCGTTACGTTACACCAAC 59.911 38.462 4.24 0.00 0.00 3.77
168 169 2.547218 GCGTCTAACAAGTGGTCTCCAA 60.547 50.000 0.00 0.00 34.18 3.53
170 171 3.679980 CGTCTAACAAGTGGTCTCCAATG 59.320 47.826 0.00 0.00 34.18 2.82
173 174 5.049405 GTCTAACAAGTGGTCTCCAATGTTG 60.049 44.000 21.02 13.88 42.12 3.33
187 188 3.712907 GTTGGTAGCCCGGCCTCA 61.713 66.667 5.55 0.00 0.00 3.86
189 190 3.916438 TTGGTAGCCCGGCCTCAGA 62.916 63.158 5.55 0.00 0.00 3.27
190 191 3.541713 GGTAGCCCGGCCTCAGAG 61.542 72.222 5.55 0.00 0.00 3.35
200 201 0.814812 GGCCTCAGAGCTCTTGCATC 60.815 60.000 23.67 10.31 42.74 3.91
206 207 4.130857 CTCAGAGCTCTTGCATCATTGAT 58.869 43.478 15.27 0.00 42.74 2.57
207 208 4.524053 TCAGAGCTCTTGCATCATTGATT 58.476 39.130 15.27 0.00 42.74 2.57
215 216 4.703093 TCTTGCATCATTGATTGAGCTTCA 59.297 37.500 0.00 0.00 37.89 3.02
224 225 4.564782 TGATTGAGCTTCAGACCATTCT 57.435 40.909 0.00 0.00 0.00 2.40
244 245 1.649271 GGAGGGAACAGGCCATGGAT 61.649 60.000 18.40 0.00 0.00 3.41
245 246 0.466922 GAGGGAACAGGCCATGGATG 60.467 60.000 18.40 15.81 0.00 3.51
255 256 3.339042 CATGGATGGACCCCTGCT 58.661 61.111 0.00 0.00 38.00 4.24
256 257 2.543569 CATGGATGGACCCCTGCTA 58.456 57.895 0.00 0.00 38.00 3.49
257 258 0.399454 CATGGATGGACCCCTGCTAG 59.601 60.000 0.00 0.00 38.00 3.42
258 259 1.422161 ATGGATGGACCCCTGCTAGC 61.422 60.000 8.10 8.10 38.00 3.42
259 260 1.768077 GGATGGACCCCTGCTAGCT 60.768 63.158 17.23 0.00 0.00 3.32
260 261 1.449353 GATGGACCCCTGCTAGCTG 59.551 63.158 17.23 15.65 0.00 4.24
261 262 1.307343 ATGGACCCCTGCTAGCTGT 60.307 57.895 17.23 7.83 0.00 4.40
262 263 0.916358 ATGGACCCCTGCTAGCTGTT 60.916 55.000 17.23 1.82 0.00 3.16
263 264 0.252513 TGGACCCCTGCTAGCTGTTA 60.253 55.000 17.23 0.00 0.00 2.41
264 265 0.178301 GGACCCCTGCTAGCTGTTAC 59.822 60.000 17.23 6.54 0.00 2.50
265 266 1.196012 GACCCCTGCTAGCTGTTACT 58.804 55.000 17.23 0.00 0.00 2.24
266 267 2.385803 GACCCCTGCTAGCTGTTACTA 58.614 52.381 17.23 0.00 0.00 1.82
267 268 2.101082 GACCCCTGCTAGCTGTTACTAC 59.899 54.545 17.23 1.33 0.00 2.73
268 269 2.292323 ACCCCTGCTAGCTGTTACTACT 60.292 50.000 17.23 0.00 0.00 2.57
269 270 3.053095 ACCCCTGCTAGCTGTTACTACTA 60.053 47.826 17.23 0.00 0.00 1.82
270 271 3.318557 CCCCTGCTAGCTGTTACTACTAC 59.681 52.174 17.23 0.00 0.00 2.73
271 272 3.952323 CCCTGCTAGCTGTTACTACTACA 59.048 47.826 17.23 0.00 0.00 2.74
283 284 7.430502 GCTGTTACTACTACAACTACGTAATGG 59.569 40.741 11.45 0.00 0.00 3.16
285 286 4.913376 ACTACTACAACTACGTAATGGCG 58.087 43.478 11.45 5.57 37.94 5.69
286 287 2.533266 ACTACAACTACGTAATGGCGC 58.467 47.619 0.00 0.00 34.88 6.53
371 372 2.844362 CCCCGGATGCCTGCTCTA 60.844 66.667 0.73 0.00 0.00 2.43
387 394 2.806019 GCTCTACTCTGTGGCATGATGG 60.806 54.545 0.00 0.00 0.00 3.51
526 537 3.858868 AAGTGCATGGCGACGTCGT 62.859 57.895 35.48 16.56 42.22 4.34
560 578 2.424956 CAAATTTGGCTGAGAGGGTAGC 59.575 50.000 10.49 0.00 39.17 3.58
598 623 6.647895 TCCAGATAACCTTCAACGTTAAGTTC 59.352 38.462 0.00 1.22 42.02 3.01
599 624 6.425721 CCAGATAACCTTCAACGTTAAGTTCA 59.574 38.462 0.00 0.00 42.02 3.18
600 625 7.288672 CAGATAACCTTCAACGTTAAGTTCAC 58.711 38.462 0.00 1.42 42.02 3.18
601 626 6.987992 AGATAACCTTCAACGTTAAGTTCACA 59.012 34.615 0.00 0.00 42.02 3.58
611 636 0.584396 TAAGTTCACAAAGGCGCGTG 59.416 50.000 8.43 4.93 34.34 5.34
738 763 2.138320 CGATTCTTCCCACATGATCCG 58.862 52.381 0.00 0.00 0.00 4.18
745 770 2.108976 CACATGATCCGACCCCCG 59.891 66.667 0.00 0.00 38.18 5.73
827 859 2.026520 GCCGGGCACGTAACGTAAA 61.027 57.895 15.62 0.00 38.32 2.01
841 893 1.620413 CGTAAACCTCGCCAACCGTC 61.620 60.000 0.00 0.00 38.35 4.79
873 927 2.983402 TTATAATCTCGGGCTCGTCG 57.017 50.000 5.57 0.00 37.69 5.12
874 928 1.888215 TATAATCTCGGGCTCGTCGT 58.112 50.000 5.57 0.00 37.69 4.34
875 929 0.592148 ATAATCTCGGGCTCGTCGTC 59.408 55.000 5.57 0.00 37.69 4.20
876 930 0.745486 TAATCTCGGGCTCGTCGTCA 60.745 55.000 5.57 0.00 37.69 4.35
884 938 2.278206 CTCGTCGTCAGGGCATCG 60.278 66.667 0.00 0.00 0.00 3.84
887 941 2.887568 GTCGTCAGGGCATCGCAG 60.888 66.667 0.00 0.00 0.00 5.18
992 1075 3.053619 AGAGAGGGAGAGAGAGAAGGAAC 60.054 52.174 0.00 0.00 0.00 3.62
1109 1192 3.839432 GAGCGCCCGACCTAGCTT 61.839 66.667 2.29 0.00 40.39 3.74
1110 1193 3.372554 GAGCGCCCGACCTAGCTTT 62.373 63.158 2.29 0.00 40.39 3.51
1111 1194 3.195698 GCGCCCGACCTAGCTTTG 61.196 66.667 0.00 0.00 0.00 2.77
1112 1195 2.264794 CGCCCGACCTAGCTTTGT 59.735 61.111 0.00 0.00 0.00 2.83
1113 1196 1.810030 CGCCCGACCTAGCTTTGTC 60.810 63.158 0.00 0.00 0.00 3.18
1114 1197 1.449778 GCCCGACCTAGCTTTGTCC 60.450 63.158 0.00 0.00 0.00 4.02
1119 1202 1.002087 CGACCTAGCTTTGTCCCTGTT 59.998 52.381 0.00 0.00 0.00 3.16
1153 1237 4.868171 CCTAGCTGCATGTTTTACTTCGTA 59.132 41.667 1.02 0.00 0.00 3.43
1161 1245 7.369607 TGCATGTTTTACTTCGTACAGTAGTA 58.630 34.615 0.00 0.00 32.55 1.82
1162 1246 7.866898 TGCATGTTTTACTTCGTACAGTAGTAA 59.133 33.333 10.50 10.50 39.76 2.24
1163 1247 8.371053 GCATGTTTTACTTCGTACAGTAGTAAG 58.629 37.037 12.69 1.73 41.53 2.34
1166 1250 7.592533 TGTTTTACTTCGTACAGTAGTAAGCTG 59.407 37.037 12.69 0.00 41.53 4.24
1167 1251 4.698583 ACTTCGTACAGTAGTAAGCTGG 57.301 45.455 0.00 0.00 38.22 4.85
1185 1274 2.789203 GCGTGATTCCGTCGACAGC 61.789 63.158 17.16 0.00 0.00 4.40
1202 1295 0.322975 AGCTGGGTAACTGACTGCTG 59.677 55.000 0.00 0.00 31.48 4.41
1203 1296 0.674895 GCTGGGTAACTGACTGCTGG 60.675 60.000 0.00 0.00 0.00 4.85
1204 1297 0.687354 CTGGGTAACTGACTGCTGGT 59.313 55.000 0.00 0.00 0.00 4.00
1205 1298 0.396435 TGGGTAACTGACTGCTGGTG 59.604 55.000 0.00 0.00 0.00 4.17
1387 1498 0.613260 CTCGGGGGAACTTGTCATGA 59.387 55.000 0.00 0.00 0.00 3.07
1391 1502 2.356125 CGGGGGAACTTGTCATGATTCT 60.356 50.000 0.00 0.00 0.00 2.40
1396 1507 4.003648 GGAACTTGTCATGATTCTCGGTT 58.996 43.478 0.00 0.00 0.00 4.44
1397 1508 5.175859 GGAACTTGTCATGATTCTCGGTTA 58.824 41.667 0.00 0.00 0.00 2.85
1417 1531 7.705325 TCGGTTATATTTTCTGTTCAGTAGAGC 59.295 37.037 0.00 0.00 0.00 4.09
1486 1611 7.647907 AACAAATATAGTCCGCCGTATTAAG 57.352 36.000 0.00 0.00 0.00 1.85
1491 1616 1.202382 AGTCCGCCGTATTAAGAGCAC 60.202 52.381 0.00 0.00 0.00 4.40
1492 1617 0.818938 TCCGCCGTATTAAGAGCACA 59.181 50.000 0.00 0.00 0.00 4.57
1558 1725 2.481289 GAGGCAGCCTCTTGTTACTT 57.519 50.000 31.54 0.00 46.41 2.24
1559 1726 2.351455 GAGGCAGCCTCTTGTTACTTC 58.649 52.381 31.54 4.18 46.41 3.01
1560 1727 1.003696 AGGCAGCCTCTTGTTACTTCC 59.996 52.381 8.70 0.00 0.00 3.46
1561 1728 1.271379 GGCAGCCTCTTGTTACTTCCA 60.271 52.381 3.29 0.00 0.00 3.53
1562 1729 2.079925 GCAGCCTCTTGTTACTTCCAG 58.920 52.381 0.00 0.00 0.00 3.86
1579 1746 2.568956 TCCAGTTCCATCTCTGTTCCAG 59.431 50.000 0.00 0.00 0.00 3.86
1596 1763 3.251484 TCCAGAAACAGAGGAACCATCT 58.749 45.455 0.00 0.00 0.00 2.90
1597 1764 3.652869 TCCAGAAACAGAGGAACCATCTT 59.347 43.478 0.00 0.00 0.00 2.40
1598 1765 4.104738 TCCAGAAACAGAGGAACCATCTTT 59.895 41.667 0.00 0.00 0.00 2.52
1682 1849 0.405198 TTGTGCCAGGTGATCCATGT 59.595 50.000 0.00 0.00 35.89 3.21
1862 2045 4.345257 AGTGTAGTGTATCCATCCATCCAC 59.655 45.833 0.00 0.00 0.00 4.02
2008 2201 4.083217 CGTTCCATCCGATTGGTTTTGTTA 60.083 41.667 0.00 0.00 38.01 2.41
2059 2446 6.539649 TGGATAAGTTTCAAGTTCGTTCAG 57.460 37.500 0.00 0.00 0.00 3.02
2078 2465 0.460311 GACGGATGTGACGGAGGATT 59.540 55.000 0.00 0.00 35.23 3.01
2163 2562 1.002900 CGCGTTCTCTCTCATCTCTCC 60.003 57.143 0.00 0.00 0.00 3.71
2179 2578 9.883142 CTCATCTCTCCACTTTATTTTTCTACT 57.117 33.333 0.00 0.00 0.00 2.57
2252 2652 1.291877 CCGTTTCCAGAGGCAACGAG 61.292 60.000 19.62 8.30 44.85 4.18
2257 2657 1.118965 TCCAGAGGCAACGAGGACAA 61.119 55.000 0.00 0.00 46.39 3.18
2273 2673 0.032678 ACAAGTGCCAGAGTCACGAG 59.967 55.000 0.00 0.00 39.31 4.18
2274 2674 0.032678 CAAGTGCCAGAGTCACGAGT 59.967 55.000 0.00 0.00 39.31 4.18
2275 2675 0.032678 AAGTGCCAGAGTCACGAGTG 59.967 55.000 0.00 0.00 39.31 3.51
2276 2676 1.373497 GTGCCAGAGTCACGAGTGG 60.373 63.158 3.19 0.00 0.00 4.00
2279 2679 2.807045 CAGAGTCACGAGTGGCGC 60.807 66.667 0.00 0.00 46.04 6.53
2280 2680 3.295273 AGAGTCACGAGTGGCGCA 61.295 61.111 10.83 0.00 46.04 6.09
2281 2681 3.106407 GAGTCACGAGTGGCGCAC 61.106 66.667 10.83 5.73 46.04 5.34
2282 2682 3.841379 GAGTCACGAGTGGCGCACA 62.841 63.158 10.83 1.22 46.04 4.57
2283 2683 2.964925 GTCACGAGTGGCGCACAA 60.965 61.111 10.83 0.00 46.04 3.33
2284 2684 2.661537 TCACGAGTGGCGCACAAG 60.662 61.111 10.83 6.47 46.04 3.16
2285 2685 3.716006 CACGAGTGGCGCACAAGG 61.716 66.667 10.83 0.00 46.04 3.61
2293 2693 3.730761 GCGCACAAGGCCTCACAG 61.731 66.667 5.23 0.00 40.31 3.66
2294 2694 3.730761 CGCACAAGGCCTCACAGC 61.731 66.667 5.23 7.60 40.31 4.40
2295 2695 2.282040 GCACAAGGCCTCACAGCT 60.282 61.111 5.23 0.00 36.11 4.24
2296 2696 2.331132 GCACAAGGCCTCACAGCTC 61.331 63.158 5.23 0.00 36.11 4.09
2297 2697 1.071987 CACAAGGCCTCACAGCTCA 59.928 57.895 5.23 0.00 0.00 4.26
2298 2698 1.072159 ACAAGGCCTCACAGCTCAC 59.928 57.895 5.23 0.00 0.00 3.51
2299 2699 1.673665 CAAGGCCTCACAGCTCACC 60.674 63.158 5.23 0.00 0.00 4.02
2300 2700 2.900106 AAGGCCTCACAGCTCACCC 61.900 63.158 5.23 0.00 0.00 4.61
2301 2701 3.325753 GGCCTCACAGCTCACCCT 61.326 66.667 0.00 0.00 0.00 4.34
2302 2702 2.046507 GCCTCACAGCTCACCCTG 60.047 66.667 0.00 0.00 38.78 4.45
2303 2703 2.667418 CCTCACAGCTCACCCTGG 59.333 66.667 0.00 0.00 37.16 4.45
2304 2704 2.046507 CTCACAGCTCACCCTGGC 60.047 66.667 0.00 0.00 37.16 4.85
2305 2705 3.947132 CTCACAGCTCACCCTGGCG 62.947 68.421 0.00 0.00 37.16 5.69
2310 2710 4.537433 GCTCACCCTGGCGCCTAG 62.537 72.222 29.70 21.88 0.00 3.02
2311 2711 3.077556 CTCACCCTGGCGCCTAGT 61.078 66.667 29.70 18.99 0.00 2.57
2312 2712 3.376935 CTCACCCTGGCGCCTAGTG 62.377 68.421 29.70 28.38 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.776662 TGGATCTAGAGGACGGTTGG 58.223 55.000 0.00 0.00 0.00 3.77
5 6 3.885901 TGTTCTCATGGATCTAGAGGACG 59.114 47.826 12.93 0.00 40.11 4.79
6 7 5.782047 CATGTTCTCATGGATCTAGAGGAC 58.218 45.833 11.64 11.64 45.30 3.85
19 20 2.425143 ATTCCGTGGCATGTTCTCAT 57.575 45.000 5.89 0.00 34.21 2.90
20 21 3.342377 TTATTCCGTGGCATGTTCTCA 57.658 42.857 5.89 0.00 0.00 3.27
21 22 3.438781 TGTTTATTCCGTGGCATGTTCTC 59.561 43.478 5.89 0.00 0.00 2.87
22 23 3.417101 TGTTTATTCCGTGGCATGTTCT 58.583 40.909 5.89 0.00 0.00 3.01
23 24 3.758300 CTGTTTATTCCGTGGCATGTTC 58.242 45.455 5.89 0.00 0.00 3.18
24 25 2.094752 GCTGTTTATTCCGTGGCATGTT 60.095 45.455 5.89 0.00 0.00 2.71
25 26 1.472480 GCTGTTTATTCCGTGGCATGT 59.528 47.619 5.89 0.00 0.00 3.21
26 27 1.202290 GGCTGTTTATTCCGTGGCATG 60.202 52.381 0.00 0.00 0.00 4.06
27 28 1.102978 GGCTGTTTATTCCGTGGCAT 58.897 50.000 0.00 0.00 0.00 4.40
28 29 0.963355 GGGCTGTTTATTCCGTGGCA 60.963 55.000 0.00 0.00 0.00 4.92
29 30 0.679960 AGGGCTGTTTATTCCGTGGC 60.680 55.000 0.00 0.00 0.00 5.01
30 31 1.379527 GAGGGCTGTTTATTCCGTGG 58.620 55.000 0.00 0.00 0.00 4.94
31 32 1.006832 CGAGGGCTGTTTATTCCGTG 58.993 55.000 0.00 0.00 0.00 4.94
32 33 0.107848 CCGAGGGCTGTTTATTCCGT 60.108 55.000 0.00 0.00 0.00 4.69
33 34 0.107848 ACCGAGGGCTGTTTATTCCG 60.108 55.000 0.00 0.00 0.00 4.30
34 35 1.664873 GACCGAGGGCTGTTTATTCC 58.335 55.000 0.00 0.00 0.00 3.01
35 36 1.287425 CGACCGAGGGCTGTTTATTC 58.713 55.000 0.00 0.00 0.00 1.75
36 37 0.611714 ACGACCGAGGGCTGTTTATT 59.388 50.000 0.00 0.00 0.00 1.40
37 38 0.175073 GACGACCGAGGGCTGTTTAT 59.825 55.000 0.00 0.00 0.00 1.40
38 39 0.896940 AGACGACCGAGGGCTGTTTA 60.897 55.000 0.00 0.00 0.00 2.01
39 40 2.156051 GAGACGACCGAGGGCTGTTT 62.156 60.000 0.00 0.00 0.00 2.83
40 41 2.600769 AGACGACCGAGGGCTGTT 60.601 61.111 0.00 0.00 0.00 3.16
41 42 3.063084 GAGACGACCGAGGGCTGT 61.063 66.667 0.00 0.00 0.00 4.40
42 43 2.752238 AGAGACGACCGAGGGCTG 60.752 66.667 0.00 0.00 0.00 4.85
43 44 2.559922 ATCAGAGACGACCGAGGGCT 62.560 60.000 0.00 0.00 0.00 5.19
44 45 2.065906 GATCAGAGACGACCGAGGGC 62.066 65.000 0.00 0.00 0.00 5.19
45 46 1.448922 GGATCAGAGACGACCGAGGG 61.449 65.000 0.00 0.00 0.00 4.30
46 47 1.448922 GGGATCAGAGACGACCGAGG 61.449 65.000 0.00 0.00 0.00 4.63
47 48 1.777030 CGGGATCAGAGACGACCGAG 61.777 65.000 0.00 0.00 43.69 4.63
48 49 1.818363 CGGGATCAGAGACGACCGA 60.818 63.158 0.00 0.00 43.69 4.69
49 50 2.716244 CGGGATCAGAGACGACCG 59.284 66.667 0.00 0.00 35.01 4.79
50 51 2.413765 GCGGGATCAGAGACGACC 59.586 66.667 0.00 0.00 0.00 4.79
51 52 2.024871 CGCGGGATCAGAGACGAC 59.975 66.667 0.00 0.00 0.00 4.34
52 53 3.889044 GCGCGGGATCAGAGACGA 61.889 66.667 8.83 0.00 0.00 4.20
54 55 2.718993 CTACGCGCGGGATCAGAGAC 62.719 65.000 35.22 0.00 0.00 3.36
55 56 2.515290 TACGCGCGGGATCAGAGA 60.515 61.111 35.22 4.15 0.00 3.10
56 57 2.050895 CTACGCGCGGGATCAGAG 60.051 66.667 35.22 14.41 0.00 3.35
57 58 4.266070 GCTACGCGCGGGATCAGA 62.266 66.667 35.22 8.67 0.00 3.27
58 59 4.271816 AGCTACGCGCGGGATCAG 62.272 66.667 35.22 21.51 45.59 2.90
59 60 4.266070 GAGCTACGCGCGGGATCA 62.266 66.667 35.22 12.21 45.59 2.92
60 61 3.882835 GAGAGCTACGCGCGGGATC 62.883 68.421 35.22 30.28 45.59 3.36
61 62 3.967335 GAGAGCTACGCGCGGGAT 61.967 66.667 35.22 24.48 45.59 3.85
63 64 4.615834 GAGAGAGCTACGCGCGGG 62.616 72.222 35.22 25.77 45.59 6.13
64 65 3.578272 AGAGAGAGCTACGCGCGG 61.578 66.667 35.22 18.64 45.59 6.46
65 66 2.351774 CAGAGAGAGCTACGCGCG 60.352 66.667 30.96 30.96 45.59 6.86
66 67 2.025441 CCAGAGAGAGCTACGCGC 59.975 66.667 5.73 0.00 39.57 6.86
67 68 1.353804 GACCAGAGAGAGCTACGCG 59.646 63.158 3.53 3.53 0.00 6.01
68 69 1.028905 ATGACCAGAGAGAGCTACGC 58.971 55.000 0.00 0.00 0.00 4.42
69 70 4.793071 CATTATGACCAGAGAGAGCTACG 58.207 47.826 0.00 0.00 0.00 3.51
70 71 4.555262 GCATTATGACCAGAGAGAGCTAC 58.445 47.826 0.00 0.00 0.00 3.58
71 72 3.254411 CGCATTATGACCAGAGAGAGCTA 59.746 47.826 0.00 0.00 0.00 3.32
72 73 2.035704 CGCATTATGACCAGAGAGAGCT 59.964 50.000 0.00 0.00 0.00 4.09
73 74 2.035193 TCGCATTATGACCAGAGAGAGC 59.965 50.000 0.00 0.00 0.00 4.09
74 75 3.998099 TCGCATTATGACCAGAGAGAG 57.002 47.619 0.00 0.00 0.00 3.20
75 76 4.148079 AGATCGCATTATGACCAGAGAGA 58.852 43.478 0.00 0.00 0.00 3.10
76 77 4.517952 AGATCGCATTATGACCAGAGAG 57.482 45.455 0.00 0.00 0.00 3.20
77 78 4.944619 AAGATCGCATTATGACCAGAGA 57.055 40.909 0.00 0.00 0.00 3.10
78 79 4.624882 GCTAAGATCGCATTATGACCAGAG 59.375 45.833 0.00 0.00 0.00 3.35
79 80 4.281941 AGCTAAGATCGCATTATGACCAGA 59.718 41.667 0.00 0.00 0.00 3.86
80 81 4.564041 AGCTAAGATCGCATTATGACCAG 58.436 43.478 0.00 0.00 0.00 4.00
81 82 4.607293 AGCTAAGATCGCATTATGACCA 57.393 40.909 0.00 0.00 0.00 4.02
82 83 5.062809 GCTTAGCTAAGATCGCATTATGACC 59.937 44.000 32.88 9.46 35.33 4.02
83 84 5.866633 AGCTTAGCTAAGATCGCATTATGAC 59.133 40.000 32.88 12.89 36.99 3.06
84 85 6.030548 AGCTTAGCTAAGATCGCATTATGA 57.969 37.500 32.88 0.00 36.99 2.15
85 86 6.329838 GAGCTTAGCTAAGATCGCATTATG 57.670 41.667 32.88 7.08 39.88 1.90
95 96 5.667539 ATGACAACTGAGCTTAGCTAAGA 57.332 39.130 32.88 14.29 39.42 2.10
103 104 5.288712 CGTAACGAATATGACAACTGAGCTT 59.711 40.000 0.00 0.00 0.00 3.74
105 106 4.561606 ACGTAACGAATATGACAACTGAGC 59.438 41.667 0.00 0.00 0.00 4.26
127 128 3.624900 GCCTTTCTTTCGTTGGTGTAAC 58.375 45.455 0.00 0.00 35.90 2.50
130 131 0.661020 CGCCTTTCTTTCGTTGGTGT 59.339 50.000 0.00 0.00 0.00 4.16
131 132 0.661020 ACGCCTTTCTTTCGTTGGTG 59.339 50.000 0.00 0.00 31.89 4.17
132 133 0.942252 GACGCCTTTCTTTCGTTGGT 59.058 50.000 0.00 0.00 36.50 3.67
133 134 1.226746 AGACGCCTTTCTTTCGTTGG 58.773 50.000 0.00 0.00 36.50 3.77
134 135 3.246699 TGTTAGACGCCTTTCTTTCGTTG 59.753 43.478 0.00 0.00 36.50 4.10
135 136 3.460103 TGTTAGACGCCTTTCTTTCGTT 58.540 40.909 0.00 0.00 36.50 3.85
137 138 3.493503 ACTTGTTAGACGCCTTTCTTTCG 59.506 43.478 0.00 0.00 0.00 3.46
145 146 1.272769 GAGACCACTTGTTAGACGCCT 59.727 52.381 0.00 0.00 0.00 5.52
146 147 1.672145 GGAGACCACTTGTTAGACGCC 60.672 57.143 0.00 0.00 0.00 5.68
168 169 3.015145 AGGCCGGGCTACCAACAT 61.015 61.111 31.90 1.55 36.13 2.71
170 171 3.682292 CTGAGGCCGGGCTACCAAC 62.682 68.421 32.93 18.68 36.13 3.77
173 174 3.541713 CTCTGAGGCCGGGCTACC 61.542 72.222 32.93 20.29 0.00 3.18
175 176 4.465446 AGCTCTGAGGCCGGGCTA 62.465 66.667 32.93 15.26 0.00 3.93
187 188 4.524053 TCAATCAATGATGCAAGAGCTCT 58.476 39.130 11.45 11.45 35.72 4.09
189 190 3.066900 GCTCAATCAATGATGCAAGAGCT 59.933 43.478 21.84 0.00 38.73 4.09
190 191 3.066900 AGCTCAATCAATGATGCAAGAGC 59.933 43.478 21.71 21.71 40.40 4.09
200 201 5.357314 AGAATGGTCTGAAGCTCAATCAATG 59.643 40.000 0.00 0.00 30.83 2.82
224 225 2.615465 CCATGGCCTGTTCCCTCCA 61.615 63.158 3.32 0.00 0.00 3.86
244 245 0.252513 TAACAGCTAGCAGGGGTCCA 60.253 55.000 18.83 0.00 0.00 4.02
245 246 0.178301 GTAACAGCTAGCAGGGGTCC 59.822 60.000 18.83 0.00 0.00 4.46
246 247 1.196012 AGTAACAGCTAGCAGGGGTC 58.804 55.000 18.83 2.73 0.00 4.46
247 248 2.108970 GTAGTAACAGCTAGCAGGGGT 58.891 52.381 18.83 7.18 0.00 4.95
248 249 2.389715 AGTAGTAACAGCTAGCAGGGG 58.610 52.381 18.83 5.83 0.00 4.79
249 250 3.952323 TGTAGTAGTAACAGCTAGCAGGG 59.048 47.826 18.83 8.51 0.00 4.45
250 251 5.125739 AGTTGTAGTAGTAACAGCTAGCAGG 59.874 44.000 18.83 11.24 36.75 4.85
251 252 6.197364 AGTTGTAGTAGTAACAGCTAGCAG 57.803 41.667 18.83 12.15 36.75 4.24
252 253 6.183360 CGTAGTTGTAGTAGTAACAGCTAGCA 60.183 42.308 18.83 0.00 40.07 3.49
253 254 6.183360 ACGTAGTTGTAGTAGTAACAGCTAGC 60.183 42.308 6.62 6.62 37.78 3.42
254 255 7.301068 ACGTAGTTGTAGTAGTAACAGCTAG 57.699 40.000 0.00 0.00 37.78 3.42
255 256 8.771920 TTACGTAGTTGTAGTAGTAACAGCTA 57.228 34.615 0.00 0.00 37.78 3.32
256 257 7.672983 TTACGTAGTTGTAGTAGTAACAGCT 57.327 36.000 0.00 0.00 37.78 4.24
257 258 7.430502 CCATTACGTAGTTGTAGTAGTAACAGC 59.569 40.741 0.00 0.00 37.78 4.40
258 259 7.430502 GCCATTACGTAGTTGTAGTAGTAACAG 59.569 40.741 0.00 0.00 37.78 3.16
259 260 7.250569 GCCATTACGTAGTTGTAGTAGTAACA 58.749 38.462 0.00 0.00 37.78 2.41
260 261 6.412072 CGCCATTACGTAGTTGTAGTAGTAAC 59.588 42.308 0.00 0.00 37.78 2.50
261 262 6.486248 CGCCATTACGTAGTTGTAGTAGTAA 58.514 40.000 0.00 0.00 37.78 2.24
262 263 5.504010 GCGCCATTACGTAGTTGTAGTAGTA 60.504 44.000 0.00 0.00 37.78 1.82
263 264 4.731773 GCGCCATTACGTAGTTGTAGTAGT 60.732 45.833 0.00 0.00 37.78 2.73
264 265 3.727723 GCGCCATTACGTAGTTGTAGTAG 59.272 47.826 0.00 0.00 37.78 2.57
265 266 3.694734 GCGCCATTACGTAGTTGTAGTA 58.305 45.455 0.00 0.00 37.78 1.82
266 267 2.533266 GCGCCATTACGTAGTTGTAGT 58.467 47.619 0.00 0.00 37.78 2.73
267 268 1.515631 CGCGCCATTACGTAGTTGTAG 59.484 52.381 0.00 0.00 37.78 2.74
268 269 1.132073 TCGCGCCATTACGTAGTTGTA 59.868 47.619 0.00 0.00 37.78 2.41
269 270 0.109179 TCGCGCCATTACGTAGTTGT 60.109 50.000 0.00 0.00 37.78 3.32
270 271 1.189446 GATCGCGCCATTACGTAGTTG 59.811 52.381 0.00 0.00 37.78 3.16
271 272 1.484356 GATCGCGCCATTACGTAGTT 58.516 50.000 0.00 0.00 37.78 2.24
285 286 3.176708 TCTTAGTGTTTAGTGCGATCGC 58.823 45.455 32.48 32.48 42.35 4.58
286 287 4.857588 AGTTCTTAGTGTTTAGTGCGATCG 59.142 41.667 11.69 11.69 0.00 3.69
371 372 1.611419 CCCCATCATGCCACAGAGT 59.389 57.895 0.00 0.00 0.00 3.24
387 394 3.733960 GACGCACGAAAAGCCCCC 61.734 66.667 0.00 0.00 0.00 5.40
391 398 1.952266 CTACCGGACGCACGAAAAGC 61.952 60.000 9.46 0.00 35.47 3.51
392 399 0.387622 TCTACCGGACGCACGAAAAG 60.388 55.000 9.46 0.00 35.47 2.27
526 537 4.099881 AGCCAAATTTGACTGCTCAAGAAA 59.900 37.500 19.86 0.00 37.70 2.52
569 594 3.179830 CGTTGAAGGTTATCTGGACTCG 58.820 50.000 0.00 0.00 0.00 4.18
598 623 2.801996 CATGCACGCGCCTTTGTG 60.802 61.111 5.73 5.15 39.10 3.33
599 624 4.705519 GCATGCACGCGCCTTTGT 62.706 61.111 14.21 0.00 37.32 2.83
600 625 4.703799 TGCATGCACGCGCCTTTG 62.704 61.111 18.46 0.00 37.32 2.77
601 626 4.409218 CTGCATGCACGCGCCTTT 62.409 61.111 18.46 0.00 37.32 3.11
611 636 3.830192 CCCGCTTTCCCTGCATGC 61.830 66.667 11.82 11.82 0.00 4.06
841 893 3.886549 AGATTATAAAGACGACGAGGCG 58.113 45.455 0.00 0.00 37.29 5.52
848 900 3.058432 CGAGCCCGAGATTATAAAGACGA 60.058 47.826 0.00 0.00 38.22 4.20
873 927 3.503363 GTGCTGCGATGCCCTGAC 61.503 66.667 0.00 0.00 0.00 3.51
874 928 4.783621 GGTGCTGCGATGCCCTGA 62.784 66.667 0.00 0.00 0.00 3.86
884 938 1.066573 AGTAGAGTGATGTGGTGCTGC 60.067 52.381 0.00 0.00 0.00 5.25
887 941 1.550524 TGGAGTAGAGTGATGTGGTGC 59.449 52.381 0.00 0.00 0.00 5.01
976 1041 2.021457 CCTCGTTCCTTCTCTCTCTCC 58.979 57.143 0.00 0.00 0.00 3.71
992 1075 2.278857 CGTCCGCCATCTTCCTCG 60.279 66.667 0.00 0.00 0.00 4.63
1104 1187 2.038557 GACAGGAACAGGGACAAAGCTA 59.961 50.000 0.00 0.00 0.00 3.32
1109 1192 1.764571 CGGGACAGGAACAGGGACAA 61.765 60.000 0.00 0.00 0.00 3.18
1110 1193 2.214216 CGGGACAGGAACAGGGACA 61.214 63.158 0.00 0.00 0.00 4.02
1111 1194 2.168666 GACGGGACAGGAACAGGGAC 62.169 65.000 0.00 0.00 0.00 4.46
1112 1195 1.911766 GACGGGACAGGAACAGGGA 60.912 63.158 0.00 0.00 0.00 4.20
1113 1196 2.663196 GACGGGACAGGAACAGGG 59.337 66.667 0.00 0.00 0.00 4.45
1114 1197 0.613853 TAGGACGGGACAGGAACAGG 60.614 60.000 0.00 0.00 0.00 4.00
1119 1202 1.379977 CAGCTAGGACGGGACAGGA 60.380 63.158 0.00 0.00 0.00 3.86
1153 1237 1.254026 TCACGCCAGCTTACTACTGT 58.746 50.000 0.00 0.00 33.09 3.55
1161 1245 1.741770 GACGGAATCACGCCAGCTT 60.742 57.895 0.00 0.00 37.37 3.74
1162 1246 2.125512 GACGGAATCACGCCAGCT 60.126 61.111 0.00 0.00 37.37 4.24
1163 1247 3.554692 CGACGGAATCACGCCAGC 61.555 66.667 0.00 0.00 37.37 4.85
1166 1250 2.126228 TGTCGACGGAATCACGCC 60.126 61.111 11.62 0.00 37.37 5.68
1167 1251 2.789203 GCTGTCGACGGAATCACGC 61.789 63.158 28.38 4.33 37.37 5.34
1185 1274 0.687354 ACCAGCAGTCAGTTACCCAG 59.313 55.000 0.00 0.00 0.00 4.45
1202 1295 2.591715 ACGTTCAGCAGCACCACC 60.592 61.111 0.00 0.00 0.00 4.61
1203 1296 2.633657 CACGTTCAGCAGCACCAC 59.366 61.111 0.00 0.00 0.00 4.16
1204 1297 2.591429 CCACGTTCAGCAGCACCA 60.591 61.111 0.00 0.00 0.00 4.17
1205 1298 1.724582 AAACCACGTTCAGCAGCACC 61.725 55.000 0.00 0.00 0.00 5.01
1391 1502 7.705325 GCTCTACTGAACAGAAAATATAACCGA 59.295 37.037 8.87 0.00 0.00 4.69
1396 1507 8.982723 AGAAGGCTCTACTGAACAGAAAATATA 58.017 33.333 8.87 0.00 0.00 0.86
1397 1508 7.768120 CAGAAGGCTCTACTGAACAGAAAATAT 59.232 37.037 8.87 0.00 34.07 1.28
1417 1531 9.696917 AATTGCTTTTGTAAATTCTACAGAAGG 57.303 29.630 20.06 11.72 38.97 3.46
1486 1611 3.615496 GGATGCATCATTTTGTTGTGCTC 59.385 43.478 27.25 1.72 36.78 4.26
1491 1616 4.459390 TGGAGGATGCATCATTTTGTTG 57.541 40.909 27.25 0.00 0.00 3.33
1492 1617 4.622220 GCTTGGAGGATGCATCATTTTGTT 60.622 41.667 27.25 4.27 35.22 2.83
1557 1724 2.978978 TGGAACAGAGATGGAACTGGAA 59.021 45.455 0.00 0.00 38.30 3.53
1558 1725 2.619931 TGGAACAGAGATGGAACTGGA 58.380 47.619 0.00 0.00 38.30 3.86
1638 1805 2.282745 GCAGAGCAAGCAGGGGTT 60.283 61.111 0.00 0.00 0.00 4.11
1682 1849 2.167693 ACCAGACACAGAACAAGTTCGA 59.832 45.455 7.25 0.00 43.97 3.71
1862 2045 1.569493 CGCGGAGGAACAACACAAG 59.431 57.895 0.00 0.00 0.00 3.16
1944 2131 4.552961 GCTCGAGAACAACTGAAAACTTCC 60.553 45.833 18.75 0.00 0.00 3.46
1978 2165 4.141801 ACCAATCGGATGGAACGAGAATTA 60.142 41.667 13.38 0.00 44.24 1.40
2059 2446 0.460311 AATCCTCCGTCACATCCGTC 59.540 55.000 0.00 0.00 0.00 4.79
2078 2465 1.594833 CCGTCCGTGATTTCCTCCA 59.405 57.895 0.00 0.00 0.00 3.86
2147 2543 7.969690 AATAAAGTGGAGAGATGAGAGAGAA 57.030 36.000 0.00 0.00 0.00 2.87
2229 2628 2.433436 GTTGCCTCTGGAAACGGTATT 58.567 47.619 0.00 0.00 38.16 1.89
2252 2652 0.946221 CGTGACTCTGGCACTTGTCC 60.946 60.000 1.94 0.00 34.18 4.02
2257 2657 1.662608 CACTCGTGACTCTGGCACT 59.337 57.895 1.94 0.00 34.18 4.40
2276 2676 3.730761 CTGTGAGGCCTTGTGCGC 61.731 66.667 6.77 0.00 42.61 6.09
2277 2677 3.730761 GCTGTGAGGCCTTGTGCG 61.731 66.667 6.77 0.00 42.61 5.34
2278 2678 2.282040 AGCTGTGAGGCCTTGTGC 60.282 61.111 6.77 9.84 40.16 4.57
2279 2679 1.071987 TGAGCTGTGAGGCCTTGTG 59.928 57.895 6.77 0.00 0.00 3.33
2280 2680 1.072159 GTGAGCTGTGAGGCCTTGT 59.928 57.895 6.77 0.00 0.00 3.16
2281 2681 1.673665 GGTGAGCTGTGAGGCCTTG 60.674 63.158 6.77 0.00 0.00 3.61
2282 2682 2.753029 GGTGAGCTGTGAGGCCTT 59.247 61.111 6.77 0.00 0.00 4.35
2283 2683 3.325753 GGGTGAGCTGTGAGGCCT 61.326 66.667 3.86 3.86 0.00 5.19
2284 2684 3.325753 AGGGTGAGCTGTGAGGCC 61.326 66.667 0.00 0.00 0.00 5.19
2285 2685 2.046507 CAGGGTGAGCTGTGAGGC 60.047 66.667 0.00 0.00 0.00 4.70
2286 2686 2.667418 CCAGGGTGAGCTGTGAGG 59.333 66.667 0.00 0.00 0.00 3.86
2287 2687 2.046507 GCCAGGGTGAGCTGTGAG 60.047 66.667 0.00 0.00 0.00 3.51
2288 2688 4.007644 CGCCAGGGTGAGCTGTGA 62.008 66.667 0.00 0.00 0.00 3.58
2293 2693 4.537433 CTAGGCGCCAGGGTGAGC 62.537 72.222 31.54 0.00 0.00 4.26
2294 2694 3.077556 ACTAGGCGCCAGGGTGAG 61.078 66.667 31.54 16.94 0.00 3.51
2295 2695 3.390521 CACTAGGCGCCAGGGTGA 61.391 66.667 31.54 5.06 0.00 4.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.