Multiple sequence alignment - TraesCS2A01G005500

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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 TraesCS2A01G005500 chr2A 100.000 2714 0 0 1 2714 2709888 2707175 0.000000e+00 5012.0
1 TraesCS2A01G005500 chr2D 90.464 1877 117 39 233 2079 3003970 3005814 0.000000e+00 2418.0
2 TraesCS2A01G005500 chr2B 87.707 2115 155 58 233 2320 7684845 7682809 0.000000e+00 2368.0
3 TraesCS2A01G005500 chr2B 83.496 1024 72 42 1725 2714 7682206 7681246 0.000000e+00 865.0
4 TraesCS2A01G005500 chr2B 94.643 56 2 1 178 232 7684946 7684891 4.810000e-13 86.1
5 TraesCS2A01G005500 chr1B 81.744 1227 137 48 563 1774 432379774 432378620 0.000000e+00 944.0
6 TraesCS2A01G005500 chr1D 84.026 939 93 23 840 1772 319618133 319617246 0.000000e+00 850.0
7 TraesCS2A01G005500 chr1A 79.648 1194 122 61 586 1774 403631918 403632995 0.000000e+00 747.0


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 TraesCS2A01G005500 chr2A 2707175 2709888 2713 True 5012.000000 5012 100.000000 1 2714 1 chr2A.!!$R1 2713
1 TraesCS2A01G005500 chr2D 3003970 3005814 1844 False 2418.000000 2418 90.464000 233 2079 1 chr2D.!!$F1 1846
2 TraesCS2A01G005500 chr2B 7681246 7684946 3700 True 1106.366667 2368 88.615333 178 2714 3 chr2B.!!$R1 2536
3 TraesCS2A01G005500 chr1B 432378620 432379774 1154 True 944.000000 944 81.744000 563 1774 1 chr1B.!!$R1 1211
4 TraesCS2A01G005500 chr1D 319617246 319618133 887 True 850.000000 850 84.026000 840 1772 1 chr1D.!!$R1 932
5 TraesCS2A01G005500 chr1A 403631918 403632995 1077 False 747.000000 747 79.648000 586 1774 1 chr1A.!!$F1 1188

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
290 337 0.107703 CGGGCCAGCAAGAATGTCTA 60.108 55.0 4.39 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 3204 0.037303 TGAAGCTTTGAGGCTCCAGG 59.963 55.0 12.86 2.23 42.24 4.45 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 0.788995 CCGATTGCAGATCTGATCGC 59.211 55.000 28.50 20.07 0.00 4.58
20 21 1.604947 CCGATTGCAGATCTGATCGCT 60.605 52.381 28.50 10.89 32.64 4.93
21 22 2.133553 CGATTGCAGATCTGATCGCTT 58.866 47.619 27.04 16.40 32.64 4.68
22 23 2.155347 CGATTGCAGATCTGATCGCTTC 59.845 50.000 27.04 20.27 32.64 3.86
23 24 1.564207 TTGCAGATCTGATCGCTTCG 58.436 50.000 27.04 10.75 32.64 3.79
24 25 0.249197 TGCAGATCTGATCGCTTCGG 60.249 55.000 27.04 0.00 32.64 4.30
25 26 0.943359 GCAGATCTGATCGCTTCGGG 60.943 60.000 27.04 0.00 0.00 5.14
26 27 0.387202 CAGATCTGATCGCTTCGGGT 59.613 55.000 18.34 0.00 0.00 5.28
27 28 1.115467 AGATCTGATCGCTTCGGGTT 58.885 50.000 11.73 0.00 0.00 4.11
28 29 1.482593 AGATCTGATCGCTTCGGGTTT 59.517 47.619 11.73 0.00 0.00 3.27
29 30 2.093447 AGATCTGATCGCTTCGGGTTTT 60.093 45.455 11.73 0.00 0.00 2.43
30 31 1.722011 TCTGATCGCTTCGGGTTTTC 58.278 50.000 0.00 0.00 0.00 2.29
31 32 1.001520 TCTGATCGCTTCGGGTTTTCA 59.998 47.619 0.00 0.00 0.00 2.69
32 33 2.009774 CTGATCGCTTCGGGTTTTCAT 58.990 47.619 0.00 0.00 0.00 2.57
33 34 2.420022 CTGATCGCTTCGGGTTTTCATT 59.580 45.455 0.00 0.00 0.00 2.57
34 35 2.817258 TGATCGCTTCGGGTTTTCATTT 59.183 40.909 0.00 0.00 0.00 2.32
35 36 3.254657 TGATCGCTTCGGGTTTTCATTTT 59.745 39.130 0.00 0.00 0.00 1.82
36 37 3.719173 TCGCTTCGGGTTTTCATTTTT 57.281 38.095 0.00 0.00 0.00 1.94
37 38 3.634283 TCGCTTCGGGTTTTCATTTTTC 58.366 40.909 0.00 0.00 0.00 2.29
38 39 2.729360 CGCTTCGGGTTTTCATTTTTCC 59.271 45.455 0.00 0.00 0.00 3.13
39 40 3.552068 CGCTTCGGGTTTTCATTTTTCCT 60.552 43.478 0.00 0.00 0.00 3.36
40 41 3.987868 GCTTCGGGTTTTCATTTTTCCTC 59.012 43.478 0.00 0.00 0.00 3.71
41 42 4.556233 CTTCGGGTTTTCATTTTTCCTCC 58.444 43.478 0.00 0.00 0.00 4.30
42 43 3.567397 TCGGGTTTTCATTTTTCCTCCA 58.433 40.909 0.00 0.00 0.00 3.86
43 44 4.156477 TCGGGTTTTCATTTTTCCTCCAT 58.844 39.130 0.00 0.00 0.00 3.41
44 45 5.326069 TCGGGTTTTCATTTTTCCTCCATA 58.674 37.500 0.00 0.00 0.00 2.74
45 46 5.955355 TCGGGTTTTCATTTTTCCTCCATAT 59.045 36.000 0.00 0.00 0.00 1.78
46 47 6.042143 CGGGTTTTCATTTTTCCTCCATATG 58.958 40.000 0.00 0.00 0.00 1.78
47 48 5.817296 GGGTTTTCATTTTTCCTCCATATGC 59.183 40.000 0.00 0.00 0.00 3.14
48 49 6.405538 GGTTTTCATTTTTCCTCCATATGCA 58.594 36.000 0.00 0.00 0.00 3.96
49 50 7.049754 GGTTTTCATTTTTCCTCCATATGCAT 58.950 34.615 3.79 3.79 0.00 3.96
50 51 8.203485 GGTTTTCATTTTTCCTCCATATGCATA 58.797 33.333 9.27 9.27 0.00 3.14
51 52 9.252962 GTTTTCATTTTTCCTCCATATGCATAG 57.747 33.333 12.79 0.00 0.00 2.23
52 53 8.765488 TTTCATTTTTCCTCCATATGCATAGA 57.235 30.769 12.79 4.13 0.00 1.98
53 54 8.945195 TTCATTTTTCCTCCATATGCATAGAT 57.055 30.769 12.79 0.00 0.00 1.98
54 55 8.945195 TCATTTTTCCTCCATATGCATAGATT 57.055 30.769 12.79 0.00 0.00 2.40
55 56 9.370930 TCATTTTTCCTCCATATGCATAGATTT 57.629 29.630 12.79 0.00 0.00 2.17
56 57 9.419297 CATTTTTCCTCCATATGCATAGATTTG 57.581 33.333 12.79 5.37 0.00 2.32
57 58 7.528996 TTTTCCTCCATATGCATAGATTTGG 57.471 36.000 15.26 15.26 0.00 3.28
58 59 5.848286 TCCTCCATATGCATAGATTTGGT 57.152 39.130 19.03 0.00 0.00 3.67
59 60 6.204852 TCCTCCATATGCATAGATTTGGTT 57.795 37.500 19.03 0.00 0.00 3.67
60 61 6.613699 TCCTCCATATGCATAGATTTGGTTT 58.386 36.000 19.03 0.00 0.00 3.27
61 62 7.068702 TCCTCCATATGCATAGATTTGGTTTT 58.931 34.615 19.03 0.00 0.00 2.43
62 63 8.224025 TCCTCCATATGCATAGATTTGGTTTTA 58.776 33.333 19.03 4.28 0.00 1.52
63 64 9.028284 CCTCCATATGCATAGATTTGGTTTTAT 57.972 33.333 19.03 0.00 0.00 1.40
71 72 9.851686 TGCATAGATTTGGTTTTATATGACTCT 57.148 29.630 0.00 0.00 0.00 3.24
84 85 9.472361 TTTTATATGACTCTTATACTTGTCGGC 57.528 33.333 0.00 0.00 32.64 5.54
85 86 6.650427 ATATGACTCTTATACTTGTCGGCA 57.350 37.500 0.00 0.00 32.64 5.69
86 87 4.794278 TGACTCTTATACTTGTCGGCAA 57.206 40.909 0.91 0.91 32.64 4.52
87 88 5.339008 TGACTCTTATACTTGTCGGCAAT 57.661 39.130 1.35 0.00 33.65 3.56
88 89 5.730550 TGACTCTTATACTTGTCGGCAATT 58.269 37.500 1.35 0.00 33.65 2.32
89 90 6.869695 TGACTCTTATACTTGTCGGCAATTA 58.130 36.000 1.35 1.78 33.65 1.40
90 91 6.755141 TGACTCTTATACTTGTCGGCAATTAC 59.245 38.462 1.35 0.00 33.65 1.89
91 92 6.636705 ACTCTTATACTTGTCGGCAATTACA 58.363 36.000 1.35 0.00 33.65 2.41
92 93 7.272978 ACTCTTATACTTGTCGGCAATTACAT 58.727 34.615 1.35 0.00 33.65 2.29
93 94 8.418662 ACTCTTATACTTGTCGGCAATTACATA 58.581 33.333 1.35 0.00 33.65 2.29
94 95 9.424319 CTCTTATACTTGTCGGCAATTACATAT 57.576 33.333 1.35 0.00 33.65 1.78
95 96 9.419297 TCTTATACTTGTCGGCAATTACATATC 57.581 33.333 1.35 0.00 33.65 1.63
96 97 9.424319 CTTATACTTGTCGGCAATTACATATCT 57.576 33.333 1.35 0.00 33.65 1.98
97 98 9.772973 TTATACTTGTCGGCAATTACATATCTT 57.227 29.630 1.35 0.00 33.65 2.40
98 99 6.604735 ACTTGTCGGCAATTACATATCTTC 57.395 37.500 1.35 0.00 33.65 2.87
99 100 6.349300 ACTTGTCGGCAATTACATATCTTCT 58.651 36.000 1.35 0.00 33.65 2.85
100 101 6.823689 ACTTGTCGGCAATTACATATCTTCTT 59.176 34.615 1.35 0.00 33.65 2.52
101 102 7.985184 ACTTGTCGGCAATTACATATCTTCTTA 59.015 33.333 1.35 0.00 33.65 2.10
102 103 8.725405 TTGTCGGCAATTACATATCTTCTTAA 57.275 30.769 0.00 0.00 0.00 1.85
103 104 8.902540 TGTCGGCAATTACATATCTTCTTAAT 57.097 30.769 0.00 0.00 0.00 1.40
104 105 8.773645 TGTCGGCAATTACATATCTTCTTAATG 58.226 33.333 0.00 0.00 0.00 1.90
105 106 7.746475 GTCGGCAATTACATATCTTCTTAATGC 59.254 37.037 0.00 0.00 0.00 3.56
106 107 7.661437 TCGGCAATTACATATCTTCTTAATGCT 59.339 33.333 0.00 0.00 0.00 3.79
107 108 7.959651 CGGCAATTACATATCTTCTTAATGCTC 59.040 37.037 0.00 0.00 0.00 4.26
108 109 9.007901 GGCAATTACATATCTTCTTAATGCTCT 57.992 33.333 0.00 0.00 0.00 4.09
118 119 8.894768 ATCTTCTTAATGCTCTATTTTACGCT 57.105 30.769 0.00 0.00 0.00 5.07
119 120 9.982651 ATCTTCTTAATGCTCTATTTTACGCTA 57.017 29.630 0.00 0.00 0.00 4.26
120 121 9.245962 TCTTCTTAATGCTCTATTTTACGCTAC 57.754 33.333 0.00 0.00 0.00 3.58
121 122 9.250624 CTTCTTAATGCTCTATTTTACGCTACT 57.749 33.333 0.00 0.00 0.00 2.57
122 123 9.595823 TTCTTAATGCTCTATTTTACGCTACTT 57.404 29.630 0.00 0.00 0.00 2.24
123 124 9.245962 TCTTAATGCTCTATTTTACGCTACTTC 57.754 33.333 0.00 0.00 0.00 3.01
124 125 6.846325 AATGCTCTATTTTACGCTACTTCC 57.154 37.500 0.00 0.00 0.00 3.46
125 126 5.593679 TGCTCTATTTTACGCTACTTCCT 57.406 39.130 0.00 0.00 0.00 3.36
126 127 5.589192 TGCTCTATTTTACGCTACTTCCTC 58.411 41.667 0.00 0.00 0.00 3.71
127 128 5.360144 TGCTCTATTTTACGCTACTTCCTCT 59.640 40.000 0.00 0.00 0.00 3.69
128 129 6.544931 TGCTCTATTTTACGCTACTTCCTCTA 59.455 38.462 0.00 0.00 0.00 2.43
129 130 7.079475 GCTCTATTTTACGCTACTTCCTCTAG 58.921 42.308 0.00 0.00 0.00 2.43
130 131 7.255208 GCTCTATTTTACGCTACTTCCTCTAGT 60.255 40.741 0.00 0.00 0.00 2.57
131 132 8.517062 TCTATTTTACGCTACTTCCTCTAGTT 57.483 34.615 0.00 0.00 0.00 2.24
132 133 8.619546 TCTATTTTACGCTACTTCCTCTAGTTC 58.380 37.037 0.00 0.00 0.00 3.01
133 134 6.579666 TTTTACGCTACTTCCTCTAGTTCA 57.420 37.500 0.00 0.00 0.00 3.18
134 135 6.770746 TTTACGCTACTTCCTCTAGTTCAT 57.229 37.500 0.00 0.00 0.00 2.57
135 136 7.870509 TTTACGCTACTTCCTCTAGTTCATA 57.129 36.000 0.00 0.00 0.00 2.15
136 137 8.461249 TTTACGCTACTTCCTCTAGTTCATAT 57.539 34.615 0.00 0.00 0.00 1.78
137 138 6.563222 ACGCTACTTCCTCTAGTTCATATC 57.437 41.667 0.00 0.00 0.00 1.63
138 139 6.062749 ACGCTACTTCCTCTAGTTCATATCA 58.937 40.000 0.00 0.00 0.00 2.15
139 140 6.205853 ACGCTACTTCCTCTAGTTCATATCAG 59.794 42.308 0.00 0.00 0.00 2.90
140 141 6.205853 CGCTACTTCCTCTAGTTCATATCAGT 59.794 42.308 0.00 0.00 0.00 3.41
141 142 7.367285 GCTACTTCCTCTAGTTCATATCAGTG 58.633 42.308 0.00 0.00 0.00 3.66
142 143 7.229707 GCTACTTCCTCTAGTTCATATCAGTGA 59.770 40.741 0.00 0.00 0.00 3.41
143 144 7.341445 ACTTCCTCTAGTTCATATCAGTGAC 57.659 40.000 0.00 0.00 0.00 3.67
144 145 6.892456 ACTTCCTCTAGTTCATATCAGTGACA 59.108 38.462 0.00 0.00 0.00 3.58
145 146 7.397476 ACTTCCTCTAGTTCATATCAGTGACAA 59.603 37.037 0.00 0.00 0.00 3.18
146 147 7.904558 TCCTCTAGTTCATATCAGTGACAAT 57.095 36.000 0.00 0.00 0.00 2.71
147 148 8.311395 TCCTCTAGTTCATATCAGTGACAATT 57.689 34.615 0.00 0.00 0.00 2.32
148 149 9.421399 TCCTCTAGTTCATATCAGTGACAATTA 57.579 33.333 0.00 0.00 0.00 1.40
161 162 9.730705 ATCAGTGACAATTAATATGGATCGAAT 57.269 29.630 0.00 0.00 0.00 3.34
162 163 8.992073 TCAGTGACAATTAATATGGATCGAATG 58.008 33.333 0.00 0.00 0.00 2.67
163 164 8.992073 CAGTGACAATTAATATGGATCGAATGA 58.008 33.333 0.00 0.00 0.00 2.57
164 165 9.559732 AGTGACAATTAATATGGATCGAATGAA 57.440 29.630 0.00 0.00 0.00 2.57
165 166 9.817365 GTGACAATTAATATGGATCGAATGAAG 57.183 33.333 0.00 0.00 0.00 3.02
166 167 9.559732 TGACAATTAATATGGATCGAATGAAGT 57.440 29.630 0.00 0.00 0.00 3.01
197 198 7.775397 ATTCACCTTTTGTCAAAAACATCTG 57.225 32.000 11.73 0.00 37.82 2.90
198 199 6.522625 TCACCTTTTGTCAAAAACATCTGA 57.477 33.333 11.73 5.73 37.82 3.27
247 294 3.059868 CGGCAATACGCGTTCAAGAATAT 60.060 43.478 20.78 0.00 43.84 1.28
252 299 6.482835 CAATACGCGTTCAAGAATATGGAAA 58.517 36.000 20.78 0.00 0.00 3.13
290 337 0.107703 CGGGCCAGCAAGAATGTCTA 60.108 55.000 4.39 0.00 0.00 2.59
314 361 4.638421 TGGTTCCTTAGCCATGAATTAACG 59.362 41.667 0.00 0.00 0.00 3.18
344 391 2.576083 CGTGCTTTGCGCTTTTTCA 58.424 47.368 9.73 0.00 40.11 2.69
345 392 0.499761 CGTGCTTTGCGCTTTTTCAG 59.500 50.000 9.73 0.00 40.11 3.02
376 424 4.760047 GCGCGGCTTCTCTTCCCA 62.760 66.667 8.83 0.00 0.00 4.37
421 469 6.713762 ATTTTCAGTTTCTCACATTCACCA 57.286 33.333 0.00 0.00 0.00 4.17
422 470 5.756195 TTTCAGTTTCTCACATTCACCAG 57.244 39.130 0.00 0.00 0.00 4.00
423 471 4.422073 TCAGTTTCTCACATTCACCAGT 57.578 40.909 0.00 0.00 0.00 4.00
424 472 4.780815 TCAGTTTCTCACATTCACCAGTT 58.219 39.130 0.00 0.00 0.00 3.16
425 473 4.816385 TCAGTTTCTCACATTCACCAGTTC 59.184 41.667 0.00 0.00 0.00 3.01
428 476 2.054021 TCTCACATTCACCAGTTCCCA 58.946 47.619 0.00 0.00 0.00 4.37
429 477 2.154462 CTCACATTCACCAGTTCCCAC 58.846 52.381 0.00 0.00 0.00 4.61
430 478 0.874390 CACATTCACCAGTTCCCACG 59.126 55.000 0.00 0.00 0.00 4.94
487 536 5.689514 CAGAAATCAGTATCGATGGTGAGTC 59.310 44.000 8.54 11.38 0.00 3.36
495 544 5.639506 AGTATCGATGGTGAGTCAGTTTTTG 59.360 40.000 8.54 0.00 0.00 2.44
511 560 6.255453 TCAGTTTTTGCTACATTGTTTTGCTC 59.745 34.615 0.00 0.00 0.00 4.26
517 566 4.097741 TGCTACATTGTTTTGCTCAAGTGT 59.902 37.500 0.00 0.00 0.00 3.55
583 634 4.277423 TGTTTTGCTTAACTTAGTGGGAGC 59.723 41.667 7.60 7.60 0.00 4.70
685 750 1.064463 TCTAAAGCAGGCCCCAATCAG 60.064 52.381 0.00 0.00 0.00 2.90
714 779 1.301087 CCACACCACGTCGCCTTTA 60.301 57.895 0.00 0.00 0.00 1.85
715 780 1.562575 CCACACCACGTCGCCTTTAC 61.563 60.000 0.00 0.00 0.00 2.01
723 788 1.449070 GTCGCCTTTACCCCCGAAG 60.449 63.158 0.00 0.00 0.00 3.79
751 816 1.831106 GGTGGAAATGGGAATGGGAAC 59.169 52.381 0.00 0.00 0.00 3.62
824 900 1.212935 GCTGCCTCTTTATCCCTTCCA 59.787 52.381 0.00 0.00 0.00 3.53
833 909 7.507277 GCCTCTTTATCCCTTCCATCTTTATTT 59.493 37.037 0.00 0.00 0.00 1.40
834 910 9.426534 CCTCTTTATCCCTTCCATCTTTATTTT 57.573 33.333 0.00 0.00 0.00 1.82
836 912 8.695456 TCTTTATCCCTTCCATCTTTATTTTGC 58.305 33.333 0.00 0.00 0.00 3.68
837 913 8.608185 TTTATCCCTTCCATCTTTATTTTGCT 57.392 30.769 0.00 0.00 0.00 3.91
838 914 8.608185 TTATCCCTTCCATCTTTATTTTGCTT 57.392 30.769 0.00 0.00 0.00 3.91
871 956 3.840124 ATTAGCCTCCTTTTACCTCCG 57.160 47.619 0.00 0.00 0.00 4.63
889 974 0.794473 CGTTACTTCGTTCCCTTGGC 59.206 55.000 0.00 0.00 0.00 4.52
923 1010 1.700739 TCCCGTTTGGACACCATACTT 59.299 47.619 9.00 0.00 38.61 2.24
949 1036 2.622977 GGCTTCTTCTCCTCTCCTCTCA 60.623 54.545 0.00 0.00 0.00 3.27
1128 1243 1.819632 GCCGCCGTCCAAGATCATT 60.820 57.895 0.00 0.00 0.00 2.57
1138 1253 1.660167 CAAGATCATTCTGCAGCCGA 58.340 50.000 9.47 5.38 30.72 5.54
1236 1351 3.078097 CCTCGTCATCCTCATCGTCTAT 58.922 50.000 0.00 0.00 0.00 1.98
1368 1483 0.856982 ACATCTCCAACCCCAACCAA 59.143 50.000 0.00 0.00 0.00 3.67
1396 1511 2.678580 TCGTCATCCAGTCCGGCA 60.679 61.111 0.00 0.00 33.14 5.69
1742 1878 3.311048 GGTTTCTGGATCGATGCTCTTTC 59.689 47.826 18.23 6.05 0.00 2.62
1743 1879 4.187694 GTTTCTGGATCGATGCTCTTTCT 58.812 43.478 18.23 0.00 0.00 2.52
1744 1880 4.478206 TTCTGGATCGATGCTCTTTCTT 57.522 40.909 18.23 0.00 0.00 2.52
1788 1930 1.177401 GAGGAATTGGGTCAAGGCAC 58.823 55.000 0.00 0.00 0.00 5.01
1789 1931 0.482446 AGGAATTGGGTCAAGGCACA 59.518 50.000 0.00 0.00 0.00 4.57
1790 1932 1.077663 AGGAATTGGGTCAAGGCACAT 59.922 47.619 0.00 0.00 0.00 3.21
1791 1933 2.311542 AGGAATTGGGTCAAGGCACATA 59.688 45.455 0.00 0.00 0.00 2.29
1811 3117 5.817296 ACATATAGCAAAGCAAACAGATCGA 59.183 36.000 0.00 0.00 0.00 3.59
1825 3131 7.701078 GCAAACAGATCGACTAGTATGACTTAA 59.299 37.037 0.00 0.00 0.00 1.85
1826 3132 9.737427 CAAACAGATCGACTAGTATGACTTAAT 57.263 33.333 0.00 0.00 0.00 1.40
1842 3155 7.429636 TGACTTAATTACTAGTGTGGTTTGC 57.570 36.000 5.39 0.00 0.00 3.68
1852 3165 2.832661 TGGTTTGCGCTTGTGGCT 60.833 55.556 9.73 0.00 39.13 4.75
1876 3189 6.721571 TTCACATTCTTGTTTACTCGATCC 57.278 37.500 0.00 0.00 32.34 3.36
1882 3195 3.441222 TCTTGTTTACTCGATCCGTAGCA 59.559 43.478 0.00 0.00 0.00 3.49
1885 3198 0.666913 TTACTCGATCCGTAGCAGCC 59.333 55.000 0.00 0.00 0.00 4.85
1887 3200 1.038130 ACTCGATCCGTAGCAGCCTT 61.038 55.000 0.00 0.00 0.00 4.35
1888 3201 0.596083 CTCGATCCGTAGCAGCCTTG 60.596 60.000 0.00 0.00 0.00 3.61
1897 3210 2.438075 GCAGCCTTGCTCCTGGAG 60.438 66.667 19.55 19.55 46.95 3.86
1910 3223 0.037303 CCTGGAGCCTCAAAGCTTCA 59.963 55.000 0.00 0.00 46.38 3.02
1932 3245 2.040544 AACATGTACAGCGGCAGGC 61.041 57.895 0.00 0.00 44.05 4.85
2003 3316 9.243105 TCGTGAATCTCATATATGGTGAATAGA 57.757 33.333 12.78 7.34 0.00 1.98
2044 3357 9.710900 CTTGTTGCAGACATATAATAGATGGTA 57.289 33.333 0.00 0.00 38.26 3.25
2069 3382 3.432749 GGTGCTGATTCTGATAGCCTTGA 60.433 47.826 0.00 0.00 36.64 3.02
2085 3398 1.751351 CTTGACGACTCTCCATGGCTA 59.249 52.381 6.96 0.00 0.00 3.93
2088 3401 2.235016 GACGACTCTCCATGGCTATCT 58.765 52.381 6.96 0.00 0.00 1.98
2134 3447 2.596904 TTATGAAGGCTGGTACGAGC 57.403 50.000 20.51 20.51 38.34 5.03
2143 3456 2.201436 CTGGTACGAGCGCTCACACT 62.201 60.000 34.69 17.03 0.00 3.55
2144 3457 1.514443 GGTACGAGCGCTCACACTC 60.514 63.158 34.69 20.02 0.00 3.51
2148 3461 2.563942 GAGCGCTCACACTCGTCT 59.436 61.111 31.91 0.00 0.00 4.18
2149 3462 1.794864 GAGCGCTCACACTCGTCTA 59.205 57.895 31.91 0.00 0.00 2.59
2150 3463 0.168348 GAGCGCTCACACTCGTCTAA 59.832 55.000 31.91 0.00 0.00 2.10
2151 3464 0.596577 AGCGCTCACACTCGTCTAAA 59.403 50.000 2.64 0.00 0.00 1.85
2152 3465 1.202582 AGCGCTCACACTCGTCTAAAT 59.797 47.619 2.64 0.00 0.00 1.40
2153 3466 1.993370 GCGCTCACACTCGTCTAAATT 59.007 47.619 0.00 0.00 0.00 1.82
2154 3467 3.119602 AGCGCTCACACTCGTCTAAATTA 60.120 43.478 2.64 0.00 0.00 1.40
2155 3468 3.240861 GCGCTCACACTCGTCTAAATTAG 59.759 47.826 0.00 0.00 0.00 1.73
2156 3469 4.659088 CGCTCACACTCGTCTAAATTAGA 58.341 43.478 0.00 0.00 0.00 2.10
2166 3479 4.780546 GTCTAAATTAGACGCTGGCTTC 57.219 45.455 16.26 0.00 44.90 3.86
2167 3480 4.434520 GTCTAAATTAGACGCTGGCTTCT 58.565 43.478 16.26 6.79 44.90 2.85
2177 3490 1.447945 GCTGGCTTCTCCTCAGTTTC 58.552 55.000 0.00 0.00 35.26 2.78
2217 3533 6.038603 CAGTTGATTTGGTTCGATATCCACAT 59.961 38.462 0.00 4.20 33.12 3.21
2229 3545 7.595311 TCGATATCCACATTTCATATTTCCG 57.405 36.000 0.00 0.00 0.00 4.30
2230 3546 7.158697 TCGATATCCACATTTCATATTTCCGT 58.841 34.615 0.00 0.00 0.00 4.69
2231 3547 8.308207 TCGATATCCACATTTCATATTTCCGTA 58.692 33.333 0.00 0.00 0.00 4.02
2232 3548 9.098355 CGATATCCACATTTCATATTTCCGTAT 57.902 33.333 0.00 0.00 0.00 3.06
2236 3552 8.560355 TCCACATTTCATATTTCCGTATATGG 57.440 34.615 4.41 4.41 38.47 2.74
2237 3553 7.120579 TCCACATTTCATATTTCCGTATATGGC 59.879 37.037 6.06 0.00 38.47 4.40
2239 3555 8.514594 CACATTTCATATTTCCGTATATGGCTT 58.485 33.333 6.06 0.00 38.47 4.35
2267 3606 2.879103 TCCCTCAAGTGGTCCATTTC 57.121 50.000 0.00 0.00 0.00 2.17
2300 3639 7.775053 AAGAATTAAACATAGGGACTTGCAA 57.225 32.000 0.00 0.00 41.75 4.08
2302 3641 8.366359 AGAATTAAACATAGGGACTTGCAATT 57.634 30.769 0.00 0.00 41.75 2.32
2328 3667 7.680442 TTTGCATTTATTAGTCACTAGTGCA 57.320 32.000 18.45 5.10 38.18 4.57
2329 3668 6.662414 TGCATTTATTAGTCACTAGTGCAC 57.338 37.500 18.45 9.40 35.41 4.57
2330 3669 6.406370 TGCATTTATTAGTCACTAGTGCACT 58.594 36.000 25.12 25.12 35.41 4.40
2331 3670 6.535150 TGCATTTATTAGTCACTAGTGCACTC 59.465 38.462 25.56 8.69 35.41 3.51
2332 3671 6.018669 GCATTTATTAGTCACTAGTGCACTCC 60.019 42.308 25.56 7.43 0.00 3.85
2335 3674 2.595750 AGTCACTAGTGCACTCCTCT 57.404 50.000 25.56 12.72 0.00 3.69
2336 3675 2.442413 AGTCACTAGTGCACTCCTCTC 58.558 52.381 25.56 12.42 0.00 3.20
2337 3676 1.474879 GTCACTAGTGCACTCCTCTCC 59.525 57.143 25.56 4.59 0.00 3.71
2338 3677 1.075536 TCACTAGTGCACTCCTCTCCA 59.924 52.381 25.56 2.30 0.00 3.86
2339 3678 1.476085 CACTAGTGCACTCCTCTCCAG 59.524 57.143 25.56 15.71 0.00 3.86
2340 3679 1.356059 ACTAGTGCACTCCTCTCCAGA 59.644 52.381 25.56 0.59 0.00 3.86
2341 3680 2.225142 ACTAGTGCACTCCTCTCCAGAA 60.225 50.000 25.56 0.00 0.00 3.02
2342 3681 1.722034 AGTGCACTCCTCTCCAGAAA 58.278 50.000 15.25 0.00 0.00 2.52
2343 3682 1.622811 AGTGCACTCCTCTCCAGAAAG 59.377 52.381 15.25 0.00 0.00 2.62
2344 3683 0.322975 TGCACTCCTCTCCAGAAAGC 59.677 55.000 0.00 0.00 0.00 3.51
2345 3684 0.392327 GCACTCCTCTCCAGAAAGCC 60.392 60.000 0.00 0.00 0.00 4.35
2346 3685 0.979665 CACTCCTCTCCAGAAAGCCA 59.020 55.000 0.00 0.00 0.00 4.75
2347 3686 1.349026 CACTCCTCTCCAGAAAGCCAA 59.651 52.381 0.00 0.00 0.00 4.52
2348 3687 2.057922 ACTCCTCTCCAGAAAGCCAAA 58.942 47.619 0.00 0.00 0.00 3.28
2362 3701 7.758528 CCAGAAAGCCAAATAATTTTCTCAGAG 59.241 37.037 0.00 0.00 37.68 3.35
2363 3702 8.517878 CAGAAAGCCAAATAATTTTCTCAGAGA 58.482 33.333 0.00 0.00 37.68 3.10
2397 3736 1.259507 GCGCGGCGATCAGTATTAAAA 59.740 47.619 28.54 0.00 0.00 1.52
2424 3763 4.396478 TCATGTACACTCCTCTCGAGAAAG 59.604 45.833 17.36 17.97 41.63 2.62
2426 3765 1.917872 ACACTCCTCTCGAGAAAGCT 58.082 50.000 17.36 5.42 41.63 3.74
2429 3768 2.230025 CACTCCTCTCGAGAAAGCTGAA 59.770 50.000 17.36 0.00 41.63 3.02
2431 3770 4.097135 CACTCCTCTCGAGAAAGCTGAATA 59.903 45.833 17.36 0.00 41.63 1.75
2432 3771 4.707448 ACTCCTCTCGAGAAAGCTGAATAA 59.293 41.667 17.36 0.00 41.63 1.40
2433 3772 5.362430 ACTCCTCTCGAGAAAGCTGAATAAT 59.638 40.000 17.36 0.00 41.63 1.28
2434 3773 6.547880 ACTCCTCTCGAGAAAGCTGAATAATA 59.452 38.462 17.36 0.00 41.63 0.98
2435 3774 7.232534 ACTCCTCTCGAGAAAGCTGAATAATAT 59.767 37.037 17.36 0.00 41.63 1.28
2436 3775 7.957002 TCCTCTCGAGAAAGCTGAATAATATT 58.043 34.615 17.36 0.00 0.00 1.28
2437 3776 8.424918 TCCTCTCGAGAAAGCTGAATAATATTT 58.575 33.333 17.36 0.00 0.00 1.40
2438 3777 8.494347 CCTCTCGAGAAAGCTGAATAATATTTG 58.506 37.037 17.36 0.00 0.00 2.32
2439 3778 8.948631 TCTCGAGAAAGCTGAATAATATTTGT 57.051 30.769 14.01 0.00 0.00 2.83
2440 3779 9.383519 TCTCGAGAAAGCTGAATAATATTTGTT 57.616 29.630 14.01 0.00 0.00 2.83
2441 3780 9.430838 CTCGAGAAAGCTGAATAATATTTGTTG 57.569 33.333 6.58 0.00 0.00 3.33
2442 3781 8.946085 TCGAGAAAGCTGAATAATATTTGTTGT 58.054 29.630 0.00 0.00 0.00 3.32
2447 3786 9.793252 AAAGCTGAATAATATTTGTTGTAGCAG 57.207 29.630 0.00 0.00 0.00 4.24
2479 3818 3.961408 AGATGGTAACCAACTCGATAGCT 59.039 43.478 0.00 0.00 36.95 3.32
2487 3826 3.197766 ACCAACTCGATAGCTGAAATCCA 59.802 43.478 0.00 0.00 0.00 3.41
2503 3842 7.094634 GCTGAAATCCAAGTCAAAACTCTGATA 60.095 37.037 0.00 0.00 33.48 2.15
2532 3871 4.373116 GGCCAGCGGAGTCGTCAA 62.373 66.667 0.00 0.00 38.89 3.18
2540 3879 2.029290 AGCGGAGTCGTCAACATAAACT 60.029 45.455 0.00 0.00 38.89 2.66
2561 3900 3.947834 CTCAAAGGGTTGACAAAGTCACT 59.052 43.478 0.00 0.00 42.60 3.41
2630 3969 5.331098 CGTAAAGCAATCATGTATGCACAA 58.669 37.500 21.54 8.20 44.95 3.33
2649 3988 5.062558 GCACAACAAATCTTGGCATGTAATC 59.937 40.000 0.00 0.00 34.12 1.75
2661 4000 5.438833 TGGCATGTAATCATCTCAATCACA 58.561 37.500 0.00 0.00 31.15 3.58
2685 4024 6.442541 TCCAAGTTAGTTCCTATGGACAAA 57.557 37.500 0.00 0.00 32.28 2.83
2697 4036 1.075542 TGGACAAATCTACGCAAGCG 58.924 50.000 13.50 13.50 46.03 4.68
2699 4038 0.247695 GACAAATCTACGCAAGCGCC 60.248 55.000 15.09 0.00 44.19 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.788995 GCGATCAGATCTGCAATCGG 59.211 55.000 31.65 20.63 37.61 4.18
1 2 1.780806 AGCGATCAGATCTGCAATCG 58.219 50.000 29.07 29.07 39.10 3.34
2 3 2.155347 CGAAGCGATCAGATCTGCAATC 59.845 50.000 18.36 14.86 33.42 2.67
3 4 2.133553 CGAAGCGATCAGATCTGCAAT 58.866 47.619 18.36 7.24 33.42 3.56
4 5 1.564207 CGAAGCGATCAGATCTGCAA 58.436 50.000 18.36 1.80 33.42 4.08
5 6 0.249197 CCGAAGCGATCAGATCTGCA 60.249 55.000 18.36 7.53 33.42 4.41
6 7 0.943359 CCCGAAGCGATCAGATCTGC 60.943 60.000 18.36 15.40 0.00 4.26
7 8 0.387202 ACCCGAAGCGATCAGATCTG 59.613 55.000 17.07 17.07 0.00 2.90
8 9 1.115467 AACCCGAAGCGATCAGATCT 58.885 50.000 8.82 0.00 0.00 2.75
9 10 1.941325 AAACCCGAAGCGATCAGATC 58.059 50.000 0.00 0.00 0.00 2.75
10 11 2.280628 GAAAACCCGAAGCGATCAGAT 58.719 47.619 0.00 0.00 0.00 2.90
11 12 1.001520 TGAAAACCCGAAGCGATCAGA 59.998 47.619 0.00 0.00 0.00 3.27
12 13 1.438651 TGAAAACCCGAAGCGATCAG 58.561 50.000 0.00 0.00 0.00 2.90
13 14 2.107950 ATGAAAACCCGAAGCGATCA 57.892 45.000 0.00 0.00 0.00 2.92
14 15 3.487563 AAATGAAAACCCGAAGCGATC 57.512 42.857 0.00 0.00 0.00 3.69
15 16 3.934457 AAAATGAAAACCCGAAGCGAT 57.066 38.095 0.00 0.00 0.00 4.58
16 17 3.551250 GGAAAAATGAAAACCCGAAGCGA 60.551 43.478 0.00 0.00 0.00 4.93
17 18 2.729360 GGAAAAATGAAAACCCGAAGCG 59.271 45.455 0.00 0.00 0.00 4.68
18 19 3.987868 GAGGAAAAATGAAAACCCGAAGC 59.012 43.478 0.00 0.00 0.00 3.86
19 20 4.038642 TGGAGGAAAAATGAAAACCCGAAG 59.961 41.667 0.00 0.00 0.00 3.79
20 21 3.961408 TGGAGGAAAAATGAAAACCCGAA 59.039 39.130 0.00 0.00 0.00 4.30
21 22 3.567397 TGGAGGAAAAATGAAAACCCGA 58.433 40.909 0.00 0.00 0.00 5.14
22 23 4.535526 ATGGAGGAAAAATGAAAACCCG 57.464 40.909 0.00 0.00 0.00 5.28
23 24 5.817296 GCATATGGAGGAAAAATGAAAACCC 59.183 40.000 4.56 0.00 0.00 4.11
24 25 6.405538 TGCATATGGAGGAAAAATGAAAACC 58.594 36.000 4.56 0.00 0.00 3.27
25 26 9.252962 CTATGCATATGGAGGAAAAATGAAAAC 57.747 33.333 6.92 0.00 0.00 2.43
26 27 9.199645 TCTATGCATATGGAGGAAAAATGAAAA 57.800 29.630 6.92 0.00 0.00 2.29
27 28 8.765488 TCTATGCATATGGAGGAAAAATGAAA 57.235 30.769 6.92 0.00 0.00 2.69
28 29 8.945195 ATCTATGCATATGGAGGAAAAATGAA 57.055 30.769 6.92 0.00 0.00 2.57
29 30 8.945195 AATCTATGCATATGGAGGAAAAATGA 57.055 30.769 6.92 0.00 0.00 2.57
30 31 9.419297 CAAATCTATGCATATGGAGGAAAAATG 57.581 33.333 6.92 0.00 0.00 2.32
31 32 8.591072 CCAAATCTATGCATATGGAGGAAAAAT 58.409 33.333 16.08 0.00 0.00 1.82
32 33 7.564660 ACCAAATCTATGCATATGGAGGAAAAA 59.435 33.333 24.44 0.00 0.00 1.94
33 34 7.068702 ACCAAATCTATGCATATGGAGGAAAA 58.931 34.615 24.44 0.00 0.00 2.29
34 35 6.613699 ACCAAATCTATGCATATGGAGGAAA 58.386 36.000 24.44 0.00 0.00 3.13
35 36 6.204852 ACCAAATCTATGCATATGGAGGAA 57.795 37.500 24.44 0.00 0.00 3.36
36 37 5.848286 ACCAAATCTATGCATATGGAGGA 57.152 39.130 24.44 11.87 0.00 3.71
37 38 6.906157 AAACCAAATCTATGCATATGGAGG 57.094 37.500 24.44 16.74 0.00 4.30
45 46 9.851686 AGAGTCATATAAAACCAAATCTATGCA 57.148 29.630 0.00 0.00 0.00 3.96
58 59 9.472361 GCCGACAAGTATAAGAGTCATATAAAA 57.528 33.333 0.00 0.00 0.00 1.52
59 60 8.635328 TGCCGACAAGTATAAGAGTCATATAAA 58.365 33.333 0.00 0.00 0.00 1.40
60 61 8.173542 TGCCGACAAGTATAAGAGTCATATAA 57.826 34.615 0.00 0.00 0.00 0.98
61 62 7.754851 TGCCGACAAGTATAAGAGTCATATA 57.245 36.000 0.00 0.00 0.00 0.86
62 63 6.650427 TGCCGACAAGTATAAGAGTCATAT 57.350 37.500 0.00 0.00 0.00 1.78
63 64 6.459670 TTGCCGACAAGTATAAGAGTCATA 57.540 37.500 0.00 0.00 0.00 2.15
64 65 5.339008 TTGCCGACAAGTATAAGAGTCAT 57.661 39.130 0.00 0.00 0.00 3.06
65 66 4.794278 TTGCCGACAAGTATAAGAGTCA 57.206 40.909 0.00 0.00 0.00 3.41
66 67 6.755141 TGTAATTGCCGACAAGTATAAGAGTC 59.245 38.462 0.00 0.00 38.48 3.36
67 68 6.636705 TGTAATTGCCGACAAGTATAAGAGT 58.363 36.000 0.00 0.00 38.48 3.24
68 69 7.715265 ATGTAATTGCCGACAAGTATAAGAG 57.285 36.000 0.00 0.00 38.48 2.85
69 70 9.419297 GATATGTAATTGCCGACAAGTATAAGA 57.581 33.333 0.00 0.00 38.48 2.10
70 71 9.424319 AGATATGTAATTGCCGACAAGTATAAG 57.576 33.333 0.00 0.00 38.48 1.73
71 72 9.772973 AAGATATGTAATTGCCGACAAGTATAA 57.227 29.630 0.00 0.00 38.48 0.98
72 73 9.419297 GAAGATATGTAATTGCCGACAAGTATA 57.581 33.333 0.00 0.00 38.48 1.47
73 74 8.150945 AGAAGATATGTAATTGCCGACAAGTAT 58.849 33.333 0.00 0.00 38.48 2.12
74 75 7.497595 AGAAGATATGTAATTGCCGACAAGTA 58.502 34.615 0.00 0.00 39.69 2.24
75 76 6.349300 AGAAGATATGTAATTGCCGACAAGT 58.651 36.000 0.00 0.00 39.69 3.16
76 77 6.851222 AGAAGATATGTAATTGCCGACAAG 57.149 37.500 0.00 0.00 39.69 3.16
77 78 8.725405 TTAAGAAGATATGTAATTGCCGACAA 57.275 30.769 0.00 0.00 40.87 3.18
78 79 8.773645 CATTAAGAAGATATGTAATTGCCGACA 58.226 33.333 0.00 0.00 0.00 4.35
79 80 7.746475 GCATTAAGAAGATATGTAATTGCCGAC 59.254 37.037 0.00 0.00 0.00 4.79
80 81 7.661437 AGCATTAAGAAGATATGTAATTGCCGA 59.339 33.333 0.00 0.00 0.00 5.54
81 82 7.810658 AGCATTAAGAAGATATGTAATTGCCG 58.189 34.615 0.00 0.00 0.00 5.69
82 83 9.007901 AGAGCATTAAGAAGATATGTAATTGCC 57.992 33.333 0.00 0.00 0.00 4.52
92 93 9.982651 AGCGTAAAATAGAGCATTAAGAAGATA 57.017 29.630 0.00 0.00 0.00 1.98
93 94 8.894768 AGCGTAAAATAGAGCATTAAGAAGAT 57.105 30.769 0.00 0.00 0.00 2.40
94 95 9.245962 GTAGCGTAAAATAGAGCATTAAGAAGA 57.754 33.333 0.00 0.00 0.00 2.87
95 96 9.250624 AGTAGCGTAAAATAGAGCATTAAGAAG 57.749 33.333 0.00 0.00 0.00 2.85
96 97 9.595823 AAGTAGCGTAAAATAGAGCATTAAGAA 57.404 29.630 0.00 0.00 0.00 2.52
97 98 9.245962 GAAGTAGCGTAAAATAGAGCATTAAGA 57.754 33.333 0.00 0.00 0.00 2.10
98 99 8.488764 GGAAGTAGCGTAAAATAGAGCATTAAG 58.511 37.037 0.00 0.00 0.00 1.85
99 100 8.202137 AGGAAGTAGCGTAAAATAGAGCATTAA 58.798 33.333 0.00 0.00 0.00 1.40
100 101 7.723324 AGGAAGTAGCGTAAAATAGAGCATTA 58.277 34.615 0.00 0.00 0.00 1.90
101 102 6.583562 AGGAAGTAGCGTAAAATAGAGCATT 58.416 36.000 0.00 0.00 0.00 3.56
102 103 6.041069 AGAGGAAGTAGCGTAAAATAGAGCAT 59.959 38.462 0.00 0.00 0.00 3.79
103 104 5.360144 AGAGGAAGTAGCGTAAAATAGAGCA 59.640 40.000 0.00 0.00 0.00 4.26
104 105 5.834169 AGAGGAAGTAGCGTAAAATAGAGC 58.166 41.667 0.00 0.00 0.00 4.09
105 106 8.156994 ACTAGAGGAAGTAGCGTAAAATAGAG 57.843 38.462 0.00 0.00 0.00 2.43
106 107 8.517062 AACTAGAGGAAGTAGCGTAAAATAGA 57.483 34.615 0.00 0.00 0.00 1.98
107 108 8.404000 TGAACTAGAGGAAGTAGCGTAAAATAG 58.596 37.037 0.00 0.00 0.00 1.73
108 109 8.284945 TGAACTAGAGGAAGTAGCGTAAAATA 57.715 34.615 0.00 0.00 0.00 1.40
109 110 7.166691 TGAACTAGAGGAAGTAGCGTAAAAT 57.833 36.000 0.00 0.00 0.00 1.82
110 111 6.579666 TGAACTAGAGGAAGTAGCGTAAAA 57.420 37.500 0.00 0.00 0.00 1.52
111 112 6.770746 ATGAACTAGAGGAAGTAGCGTAAA 57.229 37.500 0.00 0.00 0.00 2.01
112 113 7.718314 TGATATGAACTAGAGGAAGTAGCGTAA 59.282 37.037 0.00 0.00 0.00 3.18
113 114 7.222161 TGATATGAACTAGAGGAAGTAGCGTA 58.778 38.462 0.00 0.00 0.00 4.42
114 115 6.062749 TGATATGAACTAGAGGAAGTAGCGT 58.937 40.000 0.00 0.00 0.00 5.07
115 116 6.205853 ACTGATATGAACTAGAGGAAGTAGCG 59.794 42.308 0.00 0.00 0.00 4.26
116 117 7.229707 TCACTGATATGAACTAGAGGAAGTAGC 59.770 40.741 0.00 0.00 0.00 3.58
117 118 8.564574 GTCACTGATATGAACTAGAGGAAGTAG 58.435 40.741 0.00 0.00 0.00 2.57
118 119 8.053355 TGTCACTGATATGAACTAGAGGAAGTA 58.947 37.037 0.00 0.00 0.00 2.24
119 120 6.892456 TGTCACTGATATGAACTAGAGGAAGT 59.108 38.462 0.00 0.00 0.00 3.01
120 121 7.340122 TGTCACTGATATGAACTAGAGGAAG 57.660 40.000 0.00 0.00 0.00 3.46
121 122 7.718334 TTGTCACTGATATGAACTAGAGGAA 57.282 36.000 0.00 0.00 0.00 3.36
122 123 7.904558 ATTGTCACTGATATGAACTAGAGGA 57.095 36.000 0.00 0.00 0.00 3.71
135 136 9.730705 ATTCGATCCATATTAATTGTCACTGAT 57.269 29.630 0.00 0.00 0.00 2.90
136 137 8.992073 CATTCGATCCATATTAATTGTCACTGA 58.008 33.333 0.00 0.00 0.00 3.41
137 138 8.992073 TCATTCGATCCATATTAATTGTCACTG 58.008 33.333 0.00 0.00 0.00 3.66
138 139 9.559732 TTCATTCGATCCATATTAATTGTCACT 57.440 29.630 0.00 0.00 0.00 3.41
139 140 9.817365 CTTCATTCGATCCATATTAATTGTCAC 57.183 33.333 0.00 0.00 0.00 3.67
140 141 9.559732 ACTTCATTCGATCCATATTAATTGTCA 57.440 29.630 0.00 0.00 0.00 3.58
153 154 9.665264 GGTGAATTTTATTACTTCATTCGATCC 57.335 33.333 0.00 0.00 32.05 3.36
170 171 9.230122 AGATGTTTTTGACAAAAGGTGAATTTT 57.770 25.926 12.84 0.00 42.62 1.82
171 172 8.667463 CAGATGTTTTTGACAAAAGGTGAATTT 58.333 29.630 12.84 0.00 42.62 1.82
172 173 8.040132 TCAGATGTTTTTGACAAAAGGTGAATT 58.960 29.630 12.84 0.00 42.62 2.17
173 174 7.492344 GTCAGATGTTTTTGACAAAAGGTGAAT 59.508 33.333 12.84 4.87 42.62 2.57
174 175 6.811170 GTCAGATGTTTTTGACAAAAGGTGAA 59.189 34.615 12.84 0.00 42.62 3.18
175 176 6.329496 GTCAGATGTTTTTGACAAAAGGTGA 58.671 36.000 12.84 9.78 42.62 4.02
176 177 6.573617 GTCAGATGTTTTTGACAAAAGGTG 57.426 37.500 12.84 7.99 42.62 4.00
197 198 2.683968 TCTGCCACGTGAATTAGTGTC 58.316 47.619 19.30 0.00 36.69 3.67
198 199 2.831685 TCTGCCACGTGAATTAGTGT 57.168 45.000 19.30 0.00 36.69 3.55
228 229 5.651172 TCCATATTCTTGAACGCGTATTG 57.349 39.130 14.46 3.42 0.00 1.90
229 230 6.315393 ACTTTCCATATTCTTGAACGCGTATT 59.685 34.615 14.46 0.00 0.00 1.89
231 232 5.172934 ACTTTCCATATTCTTGAACGCGTA 58.827 37.500 14.46 0.00 0.00 4.42
278 325 5.008118 GCTAAGGAACCATAGACATTCTTGC 59.992 44.000 7.21 0.00 0.00 4.01
344 391 1.971695 GCGCAGGTTGCTTAACCCT 60.972 57.895 0.30 0.00 43.87 4.34
345 392 2.566529 GCGCAGGTTGCTTAACCC 59.433 61.111 0.30 0.00 43.87 4.11
360 407 2.815647 GTGGGAAGAGAAGCCGCG 60.816 66.667 0.00 0.00 0.00 6.46
421 469 3.434940 AGCTTAATTTCCGTGGGAACT 57.565 42.857 0.00 0.00 41.87 3.01
422 470 3.504520 TCAAGCTTAATTTCCGTGGGAAC 59.495 43.478 0.00 0.00 41.87 3.62
423 471 3.756434 CTCAAGCTTAATTTCCGTGGGAA 59.244 43.478 0.00 0.00 40.27 3.97
424 472 3.343617 CTCAAGCTTAATTTCCGTGGGA 58.656 45.455 0.00 0.00 0.00 4.37
425 473 2.159379 GCTCAAGCTTAATTTCCGTGGG 60.159 50.000 0.00 0.00 38.21 4.61
487 536 6.035866 TGAGCAAAACAATGTAGCAAAAACTG 59.964 34.615 7.84 0.00 0.00 3.16
495 544 4.442073 CACACTTGAGCAAAACAATGTAGC 59.558 41.667 0.00 0.00 0.00 3.58
511 560 3.557207 GCAAGAGGCAACACACTTG 57.443 52.632 0.00 0.00 43.97 3.16
583 634 3.405831 TGTCTTCTGGAATGTGCTCTTG 58.594 45.455 0.00 0.00 0.00 3.02
705 770 1.449070 CTTCGGGGGTAAAGGCGAC 60.449 63.158 0.00 0.00 0.00 5.19
709 774 2.555325 GTTGAAACTTCGGGGGTAAAGG 59.445 50.000 0.00 0.00 0.00 3.11
711 776 2.220313 CGTTGAAACTTCGGGGGTAAA 58.780 47.619 0.00 0.00 0.00 2.01
714 779 1.228033 CCGTTGAAACTTCGGGGGT 60.228 57.895 0.00 0.00 40.49 4.95
715 780 3.663202 CCGTTGAAACTTCGGGGG 58.337 61.111 0.00 0.00 40.49 5.40
723 788 1.957877 TCCCATTTCCACCGTTGAAAC 59.042 47.619 0.12 0.00 34.77 2.78
751 816 1.651240 CTGCCATTGCCTCAACTCCG 61.651 60.000 0.00 0.00 36.33 4.63
824 900 8.782339 AGCTAATGCAAAAGCAAAATAAAGAT 57.218 26.923 21.56 0.00 41.32 2.40
849 925 4.718276 ACGGAGGTAAAAGGAGGCTAATAA 59.282 41.667 0.00 0.00 0.00 1.40
871 956 1.162698 GGCCAAGGGAACGAAGTAAC 58.837 55.000 0.00 0.00 45.00 2.50
889 974 0.539669 ACGGGAAAGCAAAAGGGAGG 60.540 55.000 0.00 0.00 0.00 4.30
923 1010 1.277557 GAGAGGAGAAGAAGCCAAGCA 59.722 52.381 0.00 0.00 0.00 3.91
949 1036 2.104111 TCACCAACGAAACCACAGAGAT 59.896 45.455 0.00 0.00 0.00 2.75
1114 1229 1.938577 CTGCAGAATGATCTTGGACGG 59.061 52.381 8.42 0.00 39.69 4.79
1115 1230 1.329906 GCTGCAGAATGATCTTGGACG 59.670 52.381 20.43 0.00 39.69 4.79
1116 1231 1.674962 GGCTGCAGAATGATCTTGGAC 59.325 52.381 20.43 0.00 39.69 4.02
1368 1483 0.462047 GGATGACGACGCCCATCTTT 60.462 55.000 22.03 0.00 39.19 2.52
1396 1511 1.884444 GGAAGAAGAGCTCGACGGT 59.116 57.895 8.37 0.55 0.00 4.83
1530 1663 3.535629 CTGGTTGAGCAGGTCCGCA 62.536 63.158 8.15 0.00 0.00 5.69
1717 1850 3.009723 GAGCATCGATCCAGAAACCAAA 58.990 45.455 0.00 0.00 0.00 3.28
1788 1930 6.018425 AGTCGATCTGTTTGCTTTGCTATATG 60.018 38.462 0.00 0.00 0.00 1.78
1789 1931 6.051717 AGTCGATCTGTTTGCTTTGCTATAT 58.948 36.000 0.00 0.00 0.00 0.86
1790 1932 5.419542 AGTCGATCTGTTTGCTTTGCTATA 58.580 37.500 0.00 0.00 0.00 1.31
1791 1933 4.256920 AGTCGATCTGTTTGCTTTGCTAT 58.743 39.130 0.00 0.00 0.00 2.97
1825 3131 3.053831 AGCGCAAACCACACTAGTAAT 57.946 42.857 11.47 0.00 0.00 1.89
1826 3132 2.536761 AGCGCAAACCACACTAGTAA 57.463 45.000 11.47 0.00 0.00 2.24
1827 3133 2.139917 CAAGCGCAAACCACACTAGTA 58.860 47.619 11.47 0.00 0.00 1.82
1828 3134 0.944386 CAAGCGCAAACCACACTAGT 59.056 50.000 11.47 0.00 0.00 2.57
1829 3135 0.944386 ACAAGCGCAAACCACACTAG 59.056 50.000 11.47 0.00 0.00 2.57
1852 3165 6.128661 CGGATCGAGTAAACAAGAATGTGAAA 60.129 38.462 0.00 0.00 40.46 2.69
1889 3202 0.327591 AAGCTTTGAGGCTCCAGGAG 59.672 55.000 12.81 12.81 42.24 3.69
1890 3203 0.326264 GAAGCTTTGAGGCTCCAGGA 59.674 55.000 12.86 0.00 42.24 3.86
1891 3204 0.037303 TGAAGCTTTGAGGCTCCAGG 59.963 55.000 12.86 2.23 42.24 4.45
1892 3205 1.743958 CATGAAGCTTTGAGGCTCCAG 59.256 52.381 12.86 9.19 42.24 3.86
1893 3206 1.830279 CATGAAGCTTTGAGGCTCCA 58.170 50.000 12.86 0.00 42.24 3.86
1894 3207 0.455005 GCATGAAGCTTTGAGGCTCC 59.545 55.000 12.86 0.00 42.24 4.70
1895 3208 1.171308 TGCATGAAGCTTTGAGGCTC 58.829 50.000 7.79 7.79 45.94 4.70
1896 3209 1.271656 GTTGCATGAAGCTTTGAGGCT 59.728 47.619 14.65 0.00 45.94 4.58
1897 3210 1.000060 TGTTGCATGAAGCTTTGAGGC 60.000 47.619 0.00 4.70 45.94 4.70
1901 3214 4.548494 TGTACATGTTGCATGAAGCTTTG 58.452 39.130 15.03 0.00 45.94 2.77
1910 3223 0.959867 TGCCGCTGTACATGTTGCAT 60.960 50.000 2.30 0.00 0.00 3.96
1932 3245 6.561614 AGACAAGTACTACATACGACCATTG 58.438 40.000 0.00 0.00 38.97 2.82
1964 3277 7.272037 TGAGATTCACGATGTACAAGCTATA 57.728 36.000 0.00 0.00 0.00 1.31
1965 3278 6.149129 TGAGATTCACGATGTACAAGCTAT 57.851 37.500 0.00 0.00 0.00 2.97
1967 3280 4.456280 TGAGATTCACGATGTACAAGCT 57.544 40.909 0.00 0.00 0.00 3.74
1968 3281 8.590470 CATATATGAGATTCACGATGTACAAGC 58.410 37.037 6.92 0.00 0.00 4.01
1969 3282 9.080915 CCATATATGAGATTCACGATGTACAAG 57.919 37.037 14.54 0.00 0.00 3.16
2003 3316 9.516314 GTCTGCAACAAGTTAATAAAGTTTTCT 57.484 29.630 0.00 0.00 0.00 2.52
2005 3318 9.816354 ATGTCTGCAACAAGTTAATAAAGTTTT 57.184 25.926 5.94 0.00 42.37 2.43
2026 3339 7.676043 AGCACCACTACCATCTATTATATGTCT 59.324 37.037 0.00 0.00 0.00 3.41
2035 3348 4.904251 AGAATCAGCACCACTACCATCTAT 59.096 41.667 0.00 0.00 0.00 1.98
2036 3349 4.100035 CAGAATCAGCACCACTACCATCTA 59.900 45.833 0.00 0.00 0.00 1.98
2037 3350 3.110705 AGAATCAGCACCACTACCATCT 58.889 45.455 0.00 0.00 0.00 2.90
2044 3357 2.158842 GGCTATCAGAATCAGCACCACT 60.159 50.000 4.85 0.00 37.02 4.00
2069 3382 2.235016 GAGATAGCCATGGAGAGTCGT 58.765 52.381 18.40 0.00 0.00 4.34
2085 3398 3.398920 CGCATTCGCAACGGAGAT 58.601 55.556 0.00 0.00 38.40 2.75
2124 3437 1.801913 GTGTGAGCGCTCGTACCAG 60.802 63.158 30.75 0.00 0.00 4.00
2134 3447 4.496183 GTCTAATTTAGACGAGTGTGAGCG 59.504 45.833 18.22 0.00 44.90 5.03
2145 3458 6.470737 GGAGAAGCCAGCGTCTAATTTAGAC 61.471 48.000 21.62 21.62 43.14 2.59
2146 3459 4.441634 GGAGAAGCCAGCGTCTAATTTAGA 60.442 45.833 8.09 1.90 35.07 2.10
2147 3460 3.804873 GGAGAAGCCAGCGTCTAATTTAG 59.195 47.826 8.09 0.00 35.07 1.85
2148 3461 3.451178 AGGAGAAGCCAGCGTCTAATTTA 59.549 43.478 8.09 0.00 40.02 1.40
2149 3462 2.237392 AGGAGAAGCCAGCGTCTAATTT 59.763 45.455 8.09 0.00 40.02 1.82
2150 3463 1.834263 AGGAGAAGCCAGCGTCTAATT 59.166 47.619 8.09 0.00 40.02 1.40
2151 3464 1.410882 GAGGAGAAGCCAGCGTCTAAT 59.589 52.381 8.09 0.35 40.02 1.73
2152 3465 0.818296 GAGGAGAAGCCAGCGTCTAA 59.182 55.000 8.09 0.00 40.02 2.10
2153 3466 0.323451 TGAGGAGAAGCCAGCGTCTA 60.323 55.000 8.09 0.00 40.02 2.59
2154 3467 1.603236 CTGAGGAGAAGCCAGCGTCT 61.603 60.000 7.84 7.84 40.02 4.18
2155 3468 1.153667 CTGAGGAGAAGCCAGCGTC 60.154 63.158 0.00 0.00 40.02 5.19
2156 3469 1.476007 AACTGAGGAGAAGCCAGCGT 61.476 55.000 0.00 0.00 40.02 5.07
2157 3470 0.321122 AAACTGAGGAGAAGCCAGCG 60.321 55.000 0.00 0.00 40.02 5.18
2158 3471 1.447945 GAAACTGAGGAGAAGCCAGC 58.552 55.000 0.00 0.00 40.02 4.85
2159 3472 1.627834 AGGAAACTGAGGAGAAGCCAG 59.372 52.381 0.00 0.00 41.13 4.85
2160 3473 1.625818 GAGGAAACTGAGGAGAAGCCA 59.374 52.381 0.00 0.00 44.43 4.75
2161 3474 1.905894 AGAGGAAACTGAGGAGAAGCC 59.094 52.381 0.00 0.00 44.43 4.35
2162 3475 5.351948 AATAGAGGAAACTGAGGAGAAGC 57.648 43.478 0.00 0.00 44.43 3.86
2163 3476 6.928492 GCATAATAGAGGAAACTGAGGAGAAG 59.072 42.308 0.00 0.00 44.43 2.85
2164 3477 6.183361 GGCATAATAGAGGAAACTGAGGAGAA 60.183 42.308 0.00 0.00 44.43 2.87
2165 3478 5.305644 GGCATAATAGAGGAAACTGAGGAGA 59.694 44.000 0.00 0.00 44.43 3.71
2166 3479 5.306678 AGGCATAATAGAGGAAACTGAGGAG 59.693 44.000 0.00 0.00 44.43 3.69
2167 3480 5.219739 AGGCATAATAGAGGAAACTGAGGA 58.780 41.667 0.00 0.00 44.43 3.71
2177 3490 4.963318 TCAACTGGAGGCATAATAGAGG 57.037 45.455 0.00 0.00 0.00 3.69
2229 3545 7.231467 TGAGGGAAGGAAATAAAGCCATATAC 58.769 38.462 0.00 0.00 0.00 1.47
2230 3546 7.401060 TGAGGGAAGGAAATAAAGCCATATA 57.599 36.000 0.00 0.00 0.00 0.86
2231 3547 6.279813 TGAGGGAAGGAAATAAAGCCATAT 57.720 37.500 0.00 0.00 0.00 1.78
2232 3548 5.725551 TGAGGGAAGGAAATAAAGCCATA 57.274 39.130 0.00 0.00 0.00 2.74
2233 3549 4.608170 TGAGGGAAGGAAATAAAGCCAT 57.392 40.909 0.00 0.00 0.00 4.40
2235 3551 4.158579 CACTTGAGGGAAGGAAATAAAGCC 59.841 45.833 0.00 0.00 35.78 4.35
2236 3552 4.158579 CCACTTGAGGGAAGGAAATAAAGC 59.841 45.833 0.00 0.00 35.78 3.51
2237 3553 5.325239 ACCACTTGAGGGAAGGAAATAAAG 58.675 41.667 0.00 0.00 35.78 1.85
2239 3555 4.263771 GGACCACTTGAGGGAAGGAAATAA 60.264 45.833 0.00 0.00 35.78 1.40
2277 3616 7.961326 ATTGCAAGTCCCTATGTTTAATTCT 57.039 32.000 4.94 0.00 0.00 2.40
2302 3641 9.389755 TGCACTAGTGACTAATAAATGCAAATA 57.610 29.630 27.08 0.00 37.59 1.40
2304 3643 7.390440 AGTGCACTAGTGACTAATAAATGCAAA 59.610 33.333 27.08 0.00 41.76 3.68
2313 3652 4.605183 AGAGGAGTGCACTAGTGACTAAT 58.395 43.478 27.08 16.11 0.00 1.73
2321 3660 2.136298 TCTGGAGAGGAGTGCACTAG 57.864 55.000 21.73 11.86 0.00 2.57
2327 3666 0.979665 TGGCTTTCTGGAGAGGAGTG 59.020 55.000 0.00 0.00 0.00 3.51
2328 3667 1.734655 TTGGCTTTCTGGAGAGGAGT 58.265 50.000 0.00 0.00 0.00 3.85
2329 3668 2.867109 TTTGGCTTTCTGGAGAGGAG 57.133 50.000 0.00 0.00 0.00 3.69
2330 3669 4.927267 TTATTTGGCTTTCTGGAGAGGA 57.073 40.909 0.00 0.00 0.00 3.71
2331 3670 6.535963 AAATTATTTGGCTTTCTGGAGAGG 57.464 37.500 0.00 0.00 0.00 3.69
2332 3671 7.834803 AGAAAATTATTTGGCTTTCTGGAGAG 58.165 34.615 0.00 0.00 36.89 3.20
2335 3674 7.451255 TCTGAGAAAATTATTTGGCTTTCTGGA 59.549 33.333 0.90 0.00 38.05 3.86
2336 3675 7.605449 TCTGAGAAAATTATTTGGCTTTCTGG 58.395 34.615 0.90 0.00 38.05 3.86
2337 3676 8.517878 TCTCTGAGAAAATTATTTGGCTTTCTG 58.482 33.333 4.57 0.00 38.05 3.02
2338 3677 8.641498 TCTCTGAGAAAATTATTTGGCTTTCT 57.359 30.769 4.57 0.00 40.06 2.52
2339 3678 9.866798 AATCTCTGAGAAAATTATTTGGCTTTC 57.133 29.630 12.00 0.00 0.00 2.62
2340 3679 9.649167 CAATCTCTGAGAAAATTATTTGGCTTT 57.351 29.630 12.00 0.00 0.00 3.51
2341 3680 8.810041 ACAATCTCTGAGAAAATTATTTGGCTT 58.190 29.630 12.00 0.00 0.00 4.35
2342 3681 8.358582 ACAATCTCTGAGAAAATTATTTGGCT 57.641 30.769 12.00 0.00 0.00 4.75
2343 3682 8.465201 AGACAATCTCTGAGAAAATTATTTGGC 58.535 33.333 12.00 11.48 0.00 4.52
2362 3701 1.514136 CGCGCTCGAAAAAGACAATC 58.486 50.000 5.56 0.00 38.10 2.67
2363 3702 0.165944 CCGCGCTCGAAAAAGACAAT 59.834 50.000 5.56 0.00 38.10 2.71
2370 3709 3.550992 GATCGCCGCGCTCGAAAA 61.551 61.111 21.79 3.95 39.54 2.29
2375 3714 0.386858 TAATACTGATCGCCGCGCTC 60.387 55.000 8.21 9.00 0.00 5.03
2397 3736 5.419155 TCTCGAGAGGAGTGTACATGAAAAT 59.581 40.000 12.08 0.00 43.60 1.82
2409 3748 2.208132 TCAGCTTTCTCGAGAGGAGT 57.792 50.000 15.94 6.28 43.60 3.85
2424 3763 7.166473 GCACTGCTACAACAAATATTATTCAGC 59.834 37.037 0.00 0.00 0.00 4.26
2426 3765 8.183536 CAGCACTGCTACAACAAATATTATTCA 58.816 33.333 2.39 0.00 36.40 2.57
2447 3786 2.280628 GGTTACCATCTGTAGCAGCAC 58.719 52.381 0.00 0.00 32.70 4.40
2479 3818 8.156820 TCTATCAGAGTTTTGACTTGGATTTCA 58.843 33.333 0.00 0.00 0.00 2.69
2487 3826 9.902684 ATGAATGATCTATCAGAGTTTTGACTT 57.097 29.630 7.04 0.00 40.64 3.01
2503 3842 1.002888 CCGCTGGCCTATGAATGATCT 59.997 52.381 3.32 0.00 0.00 2.75
2532 3871 6.379988 ACTTTGTCAACCCTTTGAGTTTATGT 59.620 34.615 0.00 0.00 42.60 2.29
2540 3879 3.694072 CAGTGACTTTGTCAACCCTTTGA 59.306 43.478 1.73 0.00 44.49 2.69
2630 3969 6.604396 TGAGATGATTACATGCCAAGATTTGT 59.396 34.615 0.00 0.00 36.82 2.83
2649 3988 7.201679 GGAACTAACTTGGATGTGATTGAGATG 60.202 40.741 0.00 0.00 0.00 2.90
2661 4000 6.636454 TTGTCCATAGGAACTAACTTGGAT 57.364 37.500 0.00 0.00 45.69 3.41
2685 4024 0.461870 TCAATGGCGCTTGCGTAGAT 60.462 50.000 16.38 3.70 40.46 1.98


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

AutoCloner maintained by Alex Coulton.