Multiple sequence alignment - TraesCS6D01G124500

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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 TraesCS6D01G124500 chr6D 100.000 3759 0 0 1 3759 89059111 89062869 0.000000e+00 6942.0
1 TraesCS6D01G124500 chr6D 80.488 492 80 11 2908 3397 89061505 89061982 2.760000e-96 363.0
2 TraesCS6D01G124500 chr6D 80.488 492 80 11 2395 2872 89062018 89062507 2.760000e-96 363.0
3 TraesCS6D01G124500 chr6D 91.379 58 4 1 3396 3452 450552216 450552273 1.120000e-10 78.7
4 TraesCS6D01G124500 chr6A 93.967 2619 113 13 1068 3662 107205853 107208450 0.000000e+00 3919.0
5 TraesCS6D01G124500 chr6A 87.404 389 16 13 707 1086 107205453 107205817 2.090000e-112 416.0
6 TraesCS6D01G124500 chr6A 80.933 493 77 10 2908 3397 107207203 107207681 1.270000e-99 374.0
7 TraesCS6D01G124500 chr6A 91.403 221 10 5 453 665 107205152 107205371 1.020000e-75 294.0
8 TraesCS6D01G124500 chr6A 85.135 148 12 4 322 461 107204799 107204944 3.910000e-30 143.0
9 TraesCS6D01G124500 chr6A 100.000 59 0 0 3701 3759 107208448 107208506 3.970000e-20 110.0
10 TraesCS6D01G124500 chr2D 92.776 2104 104 13 1071 3140 488565445 488563356 0.000000e+00 3000.0
11 TraesCS6D01G124500 chr2D 86.649 382 24 14 706 1086 488565839 488565484 7.570000e-107 398.0
12 TraesCS6D01G124500 chr2D 79.310 493 86 12 2908 3397 488564099 488563620 7.780000e-87 331.0
13 TraesCS6D01G124500 chr2D 89.542 153 12 4 166 315 409579185 409579336 1.380000e-44 191.0
14 TraesCS6D01G124500 chr2D 88.125 160 17 2 158 315 166582254 166582095 4.960000e-44 189.0
15 TraesCS6D01G124500 chr2D 91.176 136 10 2 532 665 488566055 488565920 2.310000e-42 183.0
16 TraesCS6D01G124500 chr2D 86.747 166 20 1 160 323 623514854 623515019 2.310000e-42 183.0
17 TraesCS6D01G124500 chr2D 83.417 199 25 5 2438 2628 488563554 488563356 1.070000e-40 178.0
18 TraesCS6D01G124500 chr6B 86.761 1775 187 21 1071 2800 169479978 169481749 0.000000e+00 1932.0
19 TraesCS6D01G124500 chr6B 92.326 417 29 3 2908 3323 169481335 169481749 1.160000e-164 590.0
20 TraesCS6D01G124500 chr6B 88.252 349 18 11 706 1050 169479484 169479813 2.720000e-106 396.0
21 TraesCS6D01G124500 chr6B 73.945 687 142 29 1618 2287 711756702 711757368 3.750000e-60 243.0
22 TraesCS6D01G124500 chr6B 86.395 147 4 5 511 657 169479265 169479395 3.030000e-31 147.0
23 TraesCS6D01G124500 chr6B 91.379 58 4 1 3396 3452 562557585 562557528 1.120000e-10 78.7
24 TraesCS6D01G124500 chr3D 91.333 150 11 2 167 315 475555215 475555067 1.770000e-48 204.0
25 TraesCS6D01G124500 chr3D 96.154 52 2 0 658 709 546252930 546252981 6.690000e-13 86.1
26 TraesCS6D01G124500 chr7A 90.541 148 12 2 169 315 390272867 390272721 1.070000e-45 195.0
27 TraesCS6D01G124500 chr7A 89.610 154 11 4 167 315 730830674 730830827 1.380000e-44 191.0
28 TraesCS6D01G124500 chr7A 86.957 69 8 1 85 152 640451821 640451889 4.030000e-10 76.8
29 TraesCS6D01G124500 chr7A 87.692 65 7 1 3389 3452 49640447 49640511 1.450000e-09 75.0
30 TraesCS6D01G124500 chr4A 90.476 147 14 0 169 315 127974798 127974652 1.070000e-45 195.0
31 TraesCS6D01G124500 chr3A 90.541 148 12 1 170 315 447565410 447565557 1.070000e-45 195.0
32 TraesCS6D01G124500 chr3A 94.118 51 3 0 3396 3446 148615085 148615035 1.120000e-10 78.7
33 TraesCS6D01G124500 chr2A 88.961 154 13 3 166 315 713644558 713644405 1.780000e-43 187.0
34 TraesCS6D01G124500 chr2A 87.059 85 6 4 3 83 138154752 138154835 1.440000e-14 91.6
35 TraesCS6D01G124500 chr2A 94.118 51 3 0 3396 3446 1217664 1217614 1.120000e-10 78.7
36 TraesCS6D01G124500 chr5B 85.227 88 13 0 3479 3566 382781985 382782072 1.440000e-14 91.6
37 TraesCS6D01G124500 chr2B 78.616 159 16 11 3396 3538 540438808 540438964 5.170000e-14 89.8
38 TraesCS6D01G124500 chr5D 91.379 58 4 1 3396 3452 370443974 370443917 1.120000e-10 78.7
39 TraesCS6D01G124500 chr5D 94.286 35 1 1 2098 2131 551416130 551416164 7.000000e-03 52.8
40 TraesCS6D01G124500 chr4B 88.525 61 5 2 3396 3455 537367311 537367370 5.210000e-09 73.1


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 TraesCS6D01G124500 chr6D 89059111 89062869 3758 False 2556.00 6942 86.9920 1 3759 3 chr6D.!!$F2 3758
1 TraesCS6D01G124500 chr6A 107204799 107208506 3707 False 876.00 3919 89.8070 322 3759 6 chr6A.!!$F1 3437
2 TraesCS6D01G124500 chr2D 488563356 488566055 2699 True 818.00 3000 86.6656 532 3397 5 chr2D.!!$R2 2865
3 TraesCS6D01G124500 chr6B 169479265 169481749 2484 False 766.25 1932 88.4335 511 3323 4 chr6B.!!$F2 2812
4 TraesCS6D01G124500 chr6B 711756702 711757368 666 False 243.00 243 73.9450 1618 2287 1 chr6B.!!$F1 669

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
793 1068 0.179124 CGCTTCCTGTCTGCCTACTC 60.179 60.0 0.0 0.0 0.00 2.59 F
797 1072 0.251787 TCCTGTCTGCCTACTCTGCA 60.252 55.0 0.0 0.0 37.17 4.41 F
807 1082 0.671251 CTACTCTGCATCCCCTCGAC 59.329 60.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 2211 1.202592 TGCTCAACTTTCAGCACGGTA 60.203 47.619 0.0 0.0 40.8 4.02 R
2629 3104 2.819552 GCGGCACTTGTCACACGTT 61.820 57.895 0.0 0.0 0.0 3.99 R
2802 3287 4.013728 TGGAACTGCAACACAAACTAACT 58.986 39.130 0.0 0.0 0.0 2.24 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
22 23 5.938438 GGAATCATAGAAAGTGAGATGGC 57.062 43.478 0.00 0.00 0.00 4.40
23 24 5.371526 GGAATCATAGAAAGTGAGATGGCA 58.628 41.667 0.00 0.00 0.00 4.92
24 25 6.002704 GGAATCATAGAAAGTGAGATGGCAT 58.997 40.000 0.00 0.00 0.00 4.40
25 26 6.072618 GGAATCATAGAAAGTGAGATGGCATG 60.073 42.308 3.81 0.00 0.00 4.06
26 27 5.363562 TCATAGAAAGTGAGATGGCATGT 57.636 39.130 3.81 0.00 0.00 3.21
27 28 6.484364 TCATAGAAAGTGAGATGGCATGTA 57.516 37.500 3.81 0.00 0.00 2.29
28 29 7.071069 TCATAGAAAGTGAGATGGCATGTAT 57.929 36.000 3.81 0.00 0.00 2.29
29 30 7.157347 TCATAGAAAGTGAGATGGCATGTATC 58.843 38.462 3.81 0.45 0.00 2.24
30 31 5.627182 AGAAAGTGAGATGGCATGTATCT 57.373 39.130 3.81 12.53 37.59 1.98
31 32 5.609423 AGAAAGTGAGATGGCATGTATCTC 58.391 41.667 23.83 23.83 46.82 2.75
39 40 7.507733 GAGATGGCATGTATCTCAATTTTCT 57.492 36.000 24.83 0.00 46.22 2.52
40 41 8.613060 GAGATGGCATGTATCTCAATTTTCTA 57.387 34.615 24.83 0.00 46.22 2.10
41 42 9.228949 GAGATGGCATGTATCTCAATTTTCTAT 57.771 33.333 24.83 0.00 46.22 1.98
68 69 8.418597 AAAAGATATCATTTGATGCATAGGCT 57.581 30.769 0.00 0.00 41.91 4.58
69 70 9.524496 AAAAGATATCATTTGATGCATAGGCTA 57.476 29.630 0.00 0.00 41.91 3.93
70 71 9.524496 AAAGATATCATTTGATGCATAGGCTAA 57.476 29.630 0.00 0.00 41.91 3.09
71 72 8.734218 AGATATCATTTGATGCATAGGCTAAG 57.266 34.615 0.00 0.00 41.91 2.18
72 73 8.546322 AGATATCATTTGATGCATAGGCTAAGA 58.454 33.333 0.00 0.00 41.91 2.10
73 74 9.170734 GATATCATTTGATGCATAGGCTAAGAA 57.829 33.333 0.00 0.00 41.91 2.52
74 75 9.696572 ATATCATTTGATGCATAGGCTAAGAAT 57.303 29.630 0.00 0.00 41.91 2.40
75 76 7.828508 TCATTTGATGCATAGGCTAAGAATT 57.171 32.000 0.00 0.00 41.91 2.17
76 77 8.241497 TCATTTGATGCATAGGCTAAGAATTT 57.759 30.769 0.00 0.00 41.91 1.82
77 78 8.698210 TCATTTGATGCATAGGCTAAGAATTTT 58.302 29.630 0.00 0.00 41.91 1.82
78 79 9.321562 CATTTGATGCATAGGCTAAGAATTTTT 57.678 29.630 0.00 0.00 41.91 1.94
121 122 9.447157 AATGTTTTCTTTCCTTTGAAATGTGAA 57.553 25.926 0.00 0.00 39.65 3.18
122 123 8.477984 TGTTTTCTTTCCTTTGAAATGTGAAG 57.522 30.769 0.00 0.00 39.65 3.02
123 124 7.548780 TGTTTTCTTTCCTTTGAAATGTGAAGG 59.451 33.333 0.00 0.00 39.65 3.46
124 125 5.200368 TCTTTCCTTTGAAATGTGAAGGC 57.800 39.130 0.00 0.00 39.65 4.35
125 126 4.895297 TCTTTCCTTTGAAATGTGAAGGCT 59.105 37.500 0.00 0.00 39.65 4.58
126 127 5.363580 TCTTTCCTTTGAAATGTGAAGGCTT 59.636 36.000 0.00 0.00 39.65 4.35
127 128 4.589216 TCCTTTGAAATGTGAAGGCTTG 57.411 40.909 3.46 0.00 39.78 4.01
128 129 3.321682 TCCTTTGAAATGTGAAGGCTTGG 59.678 43.478 3.46 0.00 39.78 3.61
129 130 3.070015 CCTTTGAAATGTGAAGGCTTGGT 59.930 43.478 3.46 0.00 34.12 3.67
130 131 4.443315 CCTTTGAAATGTGAAGGCTTGGTT 60.443 41.667 3.46 0.00 34.12 3.67
131 132 4.751767 TTGAAATGTGAAGGCTTGGTTT 57.248 36.364 3.46 0.00 0.00 3.27
132 133 4.320608 TGAAATGTGAAGGCTTGGTTTC 57.679 40.909 3.46 9.87 0.00 2.78
133 134 3.960102 TGAAATGTGAAGGCTTGGTTTCT 59.040 39.130 3.46 0.00 0.00 2.52
134 135 5.136828 TGAAATGTGAAGGCTTGGTTTCTA 58.863 37.500 3.46 0.00 0.00 2.10
135 136 5.774690 TGAAATGTGAAGGCTTGGTTTCTAT 59.225 36.000 3.46 0.00 0.00 1.98
136 137 6.267471 TGAAATGTGAAGGCTTGGTTTCTATT 59.733 34.615 3.46 0.00 0.00 1.73
137 138 5.904362 ATGTGAAGGCTTGGTTTCTATTC 57.096 39.130 3.46 0.00 0.00 1.75
138 139 4.985538 TGTGAAGGCTTGGTTTCTATTCT 58.014 39.130 3.46 0.00 0.00 2.40
139 140 6.121776 TGTGAAGGCTTGGTTTCTATTCTA 57.878 37.500 3.46 0.00 0.00 2.10
140 141 6.539173 TGTGAAGGCTTGGTTTCTATTCTAA 58.461 36.000 3.46 0.00 0.00 2.10
141 142 7.001674 TGTGAAGGCTTGGTTTCTATTCTAAA 58.998 34.615 3.46 0.00 0.00 1.85
142 143 7.669722 TGTGAAGGCTTGGTTTCTATTCTAAAT 59.330 33.333 3.46 0.00 0.00 1.40
143 144 9.174166 GTGAAGGCTTGGTTTCTATTCTAAATA 57.826 33.333 3.46 0.00 0.00 1.40
144 145 9.396022 TGAAGGCTTGGTTTCTATTCTAAATAG 57.604 33.333 3.46 1.11 0.00 1.73
145 146 8.753497 AAGGCTTGGTTTCTATTCTAAATAGG 57.247 34.615 0.00 0.00 0.00 2.57
146 147 8.102484 AGGCTTGGTTTCTATTCTAAATAGGA 57.898 34.615 6.82 0.00 0.00 2.94
147 148 8.557450 AGGCTTGGTTTCTATTCTAAATAGGAA 58.443 33.333 6.82 2.38 0.00 3.36
148 149 9.185680 GGCTTGGTTTCTATTCTAAATAGGAAA 57.814 33.333 2.69 2.75 0.00 3.13
192 193 9.950496 AACAGTTTGTCTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
193 194 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
210 211 9.039870 CATCTAGATGTTTTCTAAGGATGTCAC 57.960 37.037 22.42 0.00 36.15 3.67
211 212 8.134202 TCTAGATGTTTTCTAAGGATGTCACA 57.866 34.615 0.00 0.00 36.50 3.58
212 213 8.762645 TCTAGATGTTTTCTAAGGATGTCACAT 58.237 33.333 0.00 0.00 36.50 3.21
213 214 9.388506 CTAGATGTTTTCTAAGGATGTCACATT 57.611 33.333 0.00 0.00 36.50 2.71
214 215 8.641498 AGATGTTTTCTAAGGATGTCACATTT 57.359 30.769 0.00 0.00 30.96 2.32
215 216 9.739276 AGATGTTTTCTAAGGATGTCACATTTA 57.261 29.630 0.00 0.00 30.96 1.40
222 223 9.823647 TTCTAAGGATGTCACATTTAATCTCTC 57.176 33.333 0.00 0.00 0.00 3.20
223 224 8.981659 TCTAAGGATGTCACATTTAATCTCTCA 58.018 33.333 0.00 0.00 0.00 3.27
224 225 9.775854 CTAAGGATGTCACATTTAATCTCTCAT 57.224 33.333 0.00 0.00 0.00 2.90
240 241 8.942338 AATCTCTCATAATTAACGTAGCAACA 57.058 30.769 0.00 0.00 0.00 3.33
241 242 8.942338 ATCTCTCATAATTAACGTAGCAACAA 57.058 30.769 0.00 0.00 0.00 2.83
242 243 8.766000 TCTCTCATAATTAACGTAGCAACAAA 57.234 30.769 0.00 0.00 0.00 2.83
243 244 8.869897 TCTCTCATAATTAACGTAGCAACAAAG 58.130 33.333 0.00 0.00 0.00 2.77
244 245 8.766000 TCTCATAATTAACGTAGCAACAAAGA 57.234 30.769 0.00 0.00 0.00 2.52
245 246 9.210329 TCTCATAATTAACGTAGCAACAAAGAA 57.790 29.630 0.00 0.00 0.00 2.52
246 247 9.820229 CTCATAATTAACGTAGCAACAAAGAAA 57.180 29.630 0.00 0.00 0.00 2.52
289 290 6.877611 AAAACAGACCACAAACATAGTAGG 57.122 37.500 0.00 0.00 0.00 3.18
290 291 3.939066 ACAGACCACAAACATAGTAGGC 58.061 45.455 0.00 0.00 0.00 3.93
291 292 3.326588 ACAGACCACAAACATAGTAGGCA 59.673 43.478 0.00 0.00 0.00 4.75
292 293 4.019321 ACAGACCACAAACATAGTAGGCAT 60.019 41.667 0.00 0.00 0.00 4.40
293 294 4.572389 CAGACCACAAACATAGTAGGCATC 59.428 45.833 0.00 0.00 0.00 3.91
294 295 4.471386 AGACCACAAACATAGTAGGCATCT 59.529 41.667 0.00 0.00 0.00 2.90
295 296 4.517285 ACCACAAACATAGTAGGCATCTG 58.483 43.478 0.00 0.00 0.00 2.90
296 297 3.879295 CCACAAACATAGTAGGCATCTGG 59.121 47.826 0.00 0.00 0.00 3.86
297 298 4.517285 CACAAACATAGTAGGCATCTGGT 58.483 43.478 0.00 0.00 0.00 4.00
298 299 4.943705 CACAAACATAGTAGGCATCTGGTT 59.056 41.667 0.00 0.00 0.00 3.67
299 300 6.112734 CACAAACATAGTAGGCATCTGGTTA 58.887 40.000 0.00 0.00 0.00 2.85
300 301 6.258727 CACAAACATAGTAGGCATCTGGTTAG 59.741 42.308 0.00 0.00 0.00 2.34
301 302 6.156256 ACAAACATAGTAGGCATCTGGTTAGA 59.844 38.462 0.00 0.00 37.35 2.10
302 303 7.147479 ACAAACATAGTAGGCATCTGGTTAGAT 60.147 37.037 0.00 0.00 44.45 1.98
316 317 8.768501 ATCTGGTTAGATGTGACATAACTAGA 57.231 34.615 21.54 21.54 45.22 2.43
317 318 8.768501 TCTGGTTAGATGTGACATAACTAGAT 57.231 34.615 17.77 0.00 40.14 1.98
318 319 8.633561 TCTGGTTAGATGTGACATAACTAGATG 58.366 37.037 17.77 0.00 40.14 2.90
319 320 8.306313 TGGTTAGATGTGACATAACTAGATGT 57.694 34.615 10.13 0.00 42.82 3.06
320 321 8.197439 TGGTTAGATGTGACATAACTAGATGTG 58.803 37.037 10.13 0.00 40.18 3.21
332 333 9.642343 ACATAACTAGATGTGTCTTATAGACCA 57.358 33.333 0.00 3.18 44.44 4.02
337 338 7.839705 ACTAGATGTGTCTTATAGACCAAAGGA 59.160 37.037 0.00 0.00 44.44 3.36
371 372 9.476202 AAAGTTTCTTTTCAAAATCTTATCCGG 57.524 29.630 0.00 0.00 0.00 5.14
394 395 8.493547 CCGGTAAAATTCCTATAATTTCTCGTC 58.506 37.037 0.00 0.00 0.00 4.20
428 429 2.614057 CGGAGAAAGGATCAATTTCCCG 59.386 50.000 22.64 22.64 40.57 5.14
474 700 4.338710 CCCGACCCAAGGCCGAAA 62.339 66.667 0.00 0.00 0.00 3.46
497 727 0.627170 TGACCATCCCCCACATCCAT 60.627 55.000 0.00 0.00 0.00 3.41
520 750 3.056328 GCCCGGTGCAGTTCTTCC 61.056 66.667 9.72 0.00 40.77 3.46
523 753 2.429930 CGGTGCAGTTCTTCCCCA 59.570 61.111 0.00 0.00 0.00 4.96
665 897 1.590932 CTCTCATCCAAAGCCATCGG 58.409 55.000 0.00 0.00 0.00 4.18
666 898 1.139654 CTCTCATCCAAAGCCATCGGA 59.860 52.381 0.00 0.00 0.00 4.55
668 900 2.149578 CTCATCCAAAGCCATCGGATC 58.850 52.381 0.00 0.00 37.44 3.36
669 901 1.490069 TCATCCAAAGCCATCGGATCA 59.510 47.619 0.00 0.00 37.44 2.92
672 904 0.956633 CCAAAGCCATCGGATCATGG 59.043 55.000 7.55 7.55 45.70 3.66
676 908 3.957260 CCATCGGATCATGGCGAC 58.043 61.111 0.00 0.00 37.12 5.19
677 909 2.023771 CCATCGGATCATGGCGACG 61.024 63.158 0.00 0.00 37.12 5.12
744 1019 2.009681 AGAGGCGGGGAAACAAAAAT 57.990 45.000 0.00 0.00 0.00 1.82
788 1063 0.729690 GAAATCGCTTCCTGTCTGCC 59.270 55.000 0.00 0.00 0.00 4.85
789 1064 0.326264 AAATCGCTTCCTGTCTGCCT 59.674 50.000 0.00 0.00 0.00 4.75
790 1065 1.195115 AATCGCTTCCTGTCTGCCTA 58.805 50.000 0.00 0.00 0.00 3.93
791 1066 0.461961 ATCGCTTCCTGTCTGCCTAC 59.538 55.000 0.00 0.00 0.00 3.18
792 1067 0.612174 TCGCTTCCTGTCTGCCTACT 60.612 55.000 0.00 0.00 0.00 2.57
793 1068 0.179124 CGCTTCCTGTCTGCCTACTC 60.179 60.000 0.00 0.00 0.00 2.59
794 1069 1.190643 GCTTCCTGTCTGCCTACTCT 58.809 55.000 0.00 0.00 0.00 3.24
795 1070 1.134848 GCTTCCTGTCTGCCTACTCTG 60.135 57.143 0.00 0.00 0.00 3.35
796 1071 0.898320 TTCCTGTCTGCCTACTCTGC 59.102 55.000 0.00 0.00 0.00 4.26
797 1072 0.251787 TCCTGTCTGCCTACTCTGCA 60.252 55.000 0.00 0.00 37.17 4.41
807 1082 0.671251 CTACTCTGCATCCCCTCGAC 59.329 60.000 0.00 0.00 0.00 4.20
821 1097 2.183858 CTCGACGCTTGTCCGAGTCA 62.184 60.000 0.00 0.00 39.56 3.41
973 1254 1.898574 ACTCCCGCTGGCTGTTTTG 60.899 57.895 0.00 0.00 0.00 2.44
1058 1429 2.412089 CCGTTTCCTTTCGTCAGTGATC 59.588 50.000 0.00 0.00 0.00 2.92
1059 1430 3.057019 CGTTTCCTTTCGTCAGTGATCA 58.943 45.455 0.00 0.00 0.00 2.92
1060 1431 3.493129 CGTTTCCTTTCGTCAGTGATCAA 59.507 43.478 0.00 0.00 0.00 2.57
1109 1541 5.641636 TGTCGAAATTGCAGCTTTCATACTA 59.358 36.000 18.38 8.27 33.20 1.82
1110 1542 6.148645 TGTCGAAATTGCAGCTTTCATACTAA 59.851 34.615 18.38 4.63 33.20 2.24
1187 1619 2.777832 AGCAGGAAGACAATGGAGAC 57.222 50.000 0.00 0.00 0.00 3.36
1211 1643 1.584380 GGCTCAGCAACTTGCCTGAG 61.584 60.000 24.44 24.44 46.52 3.35
1344 1776 7.610305 TGATAAATGTTTGGGACTTCTTAGACC 59.390 37.037 0.00 0.00 35.75 3.85
1379 1811 3.831911 ACAATGATGAAATTGTTCGGGGT 59.168 39.130 0.00 0.00 46.19 4.95
1381 1813 5.125417 ACAATGATGAAATTGTTCGGGGTAG 59.875 40.000 0.00 0.00 46.19 3.18
1383 1815 2.570415 TGAAATTGTTCGGGGTAGCA 57.430 45.000 0.00 0.00 36.46 3.49
1417 1849 1.004044 AGTGACAAAGAGCATCCTGGG 59.996 52.381 0.00 0.00 33.66 4.45
1467 1899 2.287644 CAGTTTCTGTGCATGACGTTCA 59.712 45.455 0.00 0.00 0.00 3.18
1496 1928 6.013898 TGAGAGAAGATGACCCAATATCCATC 60.014 42.308 0.00 0.00 36.56 3.51
1754 2211 5.808366 TCTATTGTGACTCAGGAAGTTGT 57.192 39.130 0.00 0.00 38.74 3.32
1764 2221 1.045407 AGGAAGTTGTACCGTGCTGA 58.955 50.000 0.00 0.00 0.00 4.26
1849 2306 4.154918 GCTCAACTCATTTCCGAAACTCAT 59.845 41.667 0.00 0.00 0.00 2.90
1909 2369 4.536090 TCCACTATCTTTTGGTGATGTCCT 59.464 41.667 0.00 0.00 34.19 3.85
2035 2495 6.286240 ACTGGGATTTAATTCTGAAAAGGC 57.714 37.500 0.00 0.00 0.00 4.35
2060 2521 7.566709 CATGTCAAAATGCTTTGTTTTCCTAC 58.433 34.615 0.00 0.00 42.26 3.18
2496 2971 3.321111 GCAGAATGGGAATCATCTGCAAT 59.679 43.478 18.67 0.00 45.49 3.56
2527 3002 1.067283 CATCAGAGTCTGGTCACGCTT 60.067 52.381 19.99 0.00 31.51 4.68
2629 3104 4.868171 GCTGTGTTCTTGTATGATCGGTTA 59.132 41.667 0.00 0.00 0.00 2.85
2787 3272 5.711506 TGATCATGTTGATAAGCTGTGGTTT 59.288 36.000 0.00 0.00 37.20 3.27
2802 3287 5.392595 GCTGTGGTTTCTGTAGTGTTTTCAA 60.393 40.000 0.00 0.00 0.00 2.69
2892 3378 1.673920 GTCAAGGTTTTGCCGACAGAA 59.326 47.619 0.00 0.00 43.70 3.02
2994 3480 3.838317 AGTGAGGATAAAGGTGCACAGTA 59.162 43.478 20.43 7.50 0.00 2.74
3035 3522 1.025113 CAGCATCACAGTCTGGCCAG 61.025 60.000 27.87 27.87 0.00 4.85
3038 3525 2.226315 ATCACAGTCTGGCCAGGCA 61.226 57.895 37.48 18.93 34.98 4.75
3040 3527 2.851102 ACAGTCTGGCCAGGCACT 60.851 61.111 37.48 27.82 43.88 4.40
3128 3623 5.596845 GGTCAATCTAGAGGATGTGTTCTC 58.403 45.833 0.00 0.00 34.45 2.87
3143 3638 4.171005 GTGTTCTCGTATGATCGGTTGAA 58.829 43.478 0.00 0.00 0.00 2.69
3156 3651 3.275143 TCGGTTGAAATGTGACAAGTGT 58.725 40.909 0.00 0.00 0.00 3.55
3159 3654 4.967575 CGGTTGAAATGTGACAAGTGTTAC 59.032 41.667 0.00 0.00 35.40 2.50
3164 3659 2.248280 TGTGACAAGTGTTACGGCAT 57.752 45.000 2.40 0.00 37.35 4.40
3169 3664 1.535462 ACAAGTGTTACGGCATGCTTC 59.465 47.619 18.92 0.00 0.00 3.86
3170 3665 1.135689 CAAGTGTTACGGCATGCTTCC 60.136 52.381 18.92 0.00 0.00 3.46
3171 3666 0.036164 AGTGTTACGGCATGCTTCCA 59.964 50.000 18.92 4.89 0.00 3.53
3172 3667 0.878416 GTGTTACGGCATGCTTCCAA 59.122 50.000 18.92 4.13 0.00 3.53
3173 3668 1.268352 GTGTTACGGCATGCTTCCAAA 59.732 47.619 18.92 2.67 0.00 3.28
3174 3669 1.539388 TGTTACGGCATGCTTCCAAAG 59.461 47.619 18.92 3.37 0.00 2.77
3188 3683 1.021202 CCAAAGCCGTCACAGTTTCA 58.979 50.000 0.00 0.00 0.00 2.69
3189 3684 1.403679 CCAAAGCCGTCACAGTTTCAA 59.596 47.619 0.00 0.00 0.00 2.69
3217 3712 2.433446 AGCAGGGCTGTGTGAAGG 59.567 61.111 0.00 0.00 37.57 3.46
3249 3744 0.173708 AAGAGGATCAACTCGTCGGC 59.826 55.000 0.00 0.00 42.37 5.54
3328 3823 4.409574 TGGTTCCTGTAGTGTTTTCAGGTA 59.590 41.667 9.71 0.00 46.04 3.08
3331 3826 5.881923 TCCTGTAGTGTTTTCAGGTAAGT 57.118 39.130 9.71 0.00 46.04 2.24
3353 3848 6.172630 AGTTTGTGTTGCAATTCCTTTCTTT 58.827 32.000 0.59 0.00 36.89 2.52
3354 3849 6.092533 AGTTTGTGTTGCAATTCCTTTCTTTG 59.907 34.615 0.59 0.00 36.89 2.77
3355 3850 3.870419 TGTGTTGCAATTCCTTTCTTTGC 59.130 39.130 0.59 0.00 44.59 3.68
3356 3851 4.122046 GTGTTGCAATTCCTTTCTTTGCT 58.878 39.130 0.59 0.00 44.62 3.91
3369 3864 1.748493 TCTTTGCTGCCTGAAACGTTT 59.252 42.857 14.57 14.57 0.00 3.60
3376 3871 1.202245 TGCCTGAAACGTTTGCTGAAC 60.202 47.619 20.10 3.06 34.82 3.18
3385 3880 1.908065 GTTTGCTGAACGCTTTGTGT 58.092 45.000 0.00 0.00 40.11 3.72
3386 3881 2.258755 GTTTGCTGAACGCTTTGTGTT 58.741 42.857 0.00 0.00 39.06 3.32
3387 3882 1.906757 TTGCTGAACGCTTTGTGTTG 58.093 45.000 1.05 0.00 36.34 3.33
3388 3883 0.525242 TGCTGAACGCTTTGTGTTGC 60.525 50.000 1.05 1.13 36.34 4.17
3417 3912 2.969300 TTTCCAACCGGGCTCACACC 62.969 60.000 6.32 0.00 36.21 4.16
3430 3925 2.492088 GCTCACACCCCTTTCCATTAAC 59.508 50.000 0.00 0.00 0.00 2.01
3454 3949 6.649141 ACTGCTCAACGAAAATATTCAGTACA 59.351 34.615 0.00 0.00 35.15 2.90
3478 3973 5.408604 ACAAATCTTAGCTACAACTGAACCG 59.591 40.000 0.00 0.00 0.00 4.44
3511 4006 1.014564 CGGGAAAGTGGAGAAGCGAC 61.015 60.000 0.00 0.00 0.00 5.19
3560 4055 1.954146 TGCTCGCTGTCGAAACACC 60.954 57.895 0.00 0.00 44.98 4.16
3567 4062 1.415374 CTGTCGAAACACCTACCACG 58.585 55.000 0.00 0.00 0.00 4.94
3571 4066 1.002990 GAAACACCTACCACGGGGG 60.003 63.158 9.50 0.00 44.81 5.40
3575 4070 1.061324 ACACCTACCACGGGGGAAAA 61.061 55.000 9.50 0.00 41.15 2.29
3580 4075 0.110869 TACCACGGGGGAAAAACCTG 59.889 55.000 9.50 0.00 41.15 4.00
3590 4085 3.644265 GGGGAAAAACCTGTTAACACCAT 59.356 43.478 3.59 0.00 38.98 3.55
3628 4123 1.138568 CAGGGCTGGGATCTCAGATT 58.861 55.000 27.21 7.43 36.93 2.40
3629 4124 1.138568 AGGGCTGGGATCTCAGATTG 58.861 55.000 27.21 0.28 36.93 2.67
3632 4127 1.595466 GCTGGGATCTCAGATTGCAG 58.405 55.000 27.21 0.00 36.93 4.41
3635 4130 3.468770 CTGGGATCTCAGATTGCAGAAG 58.531 50.000 18.40 0.00 36.93 2.85
3637 4132 4.033009 TGGGATCTCAGATTGCAGAAGTA 58.967 43.478 0.00 0.00 0.00 2.24
3640 4135 6.327365 TGGGATCTCAGATTGCAGAAGTATTA 59.673 38.462 0.00 0.00 0.00 0.98
3659 4154 7.721402 AGTATTACAAAGACTATCTCAGCAGG 58.279 38.462 0.00 0.00 0.00 4.85
3660 4155 3.258971 ACAAAGACTATCTCAGCAGGC 57.741 47.619 0.00 0.00 0.00 4.85
3661 4156 2.568956 ACAAAGACTATCTCAGCAGGCA 59.431 45.455 0.00 0.00 0.00 4.75
3662 4157 3.196463 CAAAGACTATCTCAGCAGGCAG 58.804 50.000 0.00 0.00 0.00 4.85
3663 4158 0.752054 AGACTATCTCAGCAGGCAGC 59.248 55.000 0.00 0.00 46.19 5.25
3673 4168 3.788672 GCAGGCAGCATACCTTAGT 57.211 52.632 0.00 0.00 44.79 2.24
3674 4169 1.303309 GCAGGCAGCATACCTTAGTG 58.697 55.000 0.00 0.00 44.79 2.74
3675 4170 1.134401 GCAGGCAGCATACCTTAGTGA 60.134 52.381 0.00 0.00 44.79 3.41
3676 4171 2.831333 CAGGCAGCATACCTTAGTGAG 58.169 52.381 0.00 0.00 34.42 3.51
3677 4172 2.432146 CAGGCAGCATACCTTAGTGAGA 59.568 50.000 0.00 0.00 34.42 3.27
3678 4173 3.107601 AGGCAGCATACCTTAGTGAGAA 58.892 45.455 0.00 0.00 31.87 2.87
3679 4174 3.118592 AGGCAGCATACCTTAGTGAGAAC 60.119 47.826 0.00 0.00 31.87 3.01
3680 4175 3.118592 GGCAGCATACCTTAGTGAGAACT 60.119 47.826 0.00 0.00 0.00 3.01
3681 4176 4.099573 GGCAGCATACCTTAGTGAGAACTA 59.900 45.833 0.00 0.00 0.00 2.24
3682 4177 5.044558 GCAGCATACCTTAGTGAGAACTAC 58.955 45.833 0.00 0.00 0.00 2.73
3683 4178 5.163499 GCAGCATACCTTAGTGAGAACTACT 60.163 44.000 0.00 0.00 0.00 2.57
3684 4179 6.039493 GCAGCATACCTTAGTGAGAACTACTA 59.961 42.308 0.00 0.00 0.00 1.82
3685 4180 7.416438 GCAGCATACCTTAGTGAGAACTACTAA 60.416 40.741 0.00 0.00 38.06 2.24
3693 4188 8.245701 CTTAGTGAGAACTACTAAGCAAAAGG 57.754 38.462 10.78 0.00 45.98 3.11
3694 4189 4.998033 AGTGAGAACTACTAAGCAAAAGGC 59.002 41.667 0.00 0.00 45.30 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.371526 TGCCATCTCACTTTCTATGATTCC 58.628 41.667 0.00 0.00 0.00 3.01
1 2 6.485984 ACATGCCATCTCACTTTCTATGATTC 59.514 38.462 0.00 0.00 0.00 2.52
2 3 6.363065 ACATGCCATCTCACTTTCTATGATT 58.637 36.000 0.00 0.00 0.00 2.57
3 4 5.938279 ACATGCCATCTCACTTTCTATGAT 58.062 37.500 0.00 0.00 0.00 2.45
4 5 5.363562 ACATGCCATCTCACTTTCTATGA 57.636 39.130 0.00 0.00 0.00 2.15
5 6 7.160049 AGATACATGCCATCTCACTTTCTATG 58.840 38.462 4.89 0.00 0.00 2.23
6 7 7.313740 AGATACATGCCATCTCACTTTCTAT 57.686 36.000 4.89 0.00 0.00 1.98
7 8 6.737720 AGATACATGCCATCTCACTTTCTA 57.262 37.500 4.89 0.00 0.00 2.10
8 9 5.609423 GAGATACATGCCATCTCACTTTCT 58.391 41.667 23.49 1.34 45.17 2.52
9 10 5.921004 GAGATACATGCCATCTCACTTTC 57.079 43.478 23.49 5.43 45.17 2.62
15 16 7.507733 AGAAAATTGAGATACATGCCATCTC 57.492 36.000 22.40 22.40 45.76 2.75
42 43 8.867097 AGCCTATGCATCAAATGATATCTTTTT 58.133 29.630 0.19 6.22 41.13 1.94
43 44 8.418597 AGCCTATGCATCAAATGATATCTTTT 57.581 30.769 0.19 10.06 41.13 2.27
44 45 9.524496 TTAGCCTATGCATCAAATGATATCTTT 57.476 29.630 0.19 0.85 41.13 2.52
45 46 9.175312 CTTAGCCTATGCATCAAATGATATCTT 57.825 33.333 0.19 0.00 41.13 2.40
46 47 8.546322 TCTTAGCCTATGCATCAAATGATATCT 58.454 33.333 0.19 0.00 41.13 1.98
47 48 8.728337 TCTTAGCCTATGCATCAAATGATATC 57.272 34.615 0.19 0.00 41.13 1.63
48 49 9.696572 ATTCTTAGCCTATGCATCAAATGATAT 57.303 29.630 0.19 0.00 41.13 1.63
49 50 9.524496 AATTCTTAGCCTATGCATCAAATGATA 57.476 29.630 0.19 0.00 41.13 2.15
50 51 8.418597 AATTCTTAGCCTATGCATCAAATGAT 57.581 30.769 0.19 0.00 41.13 2.45
51 52 7.828508 AATTCTTAGCCTATGCATCAAATGA 57.171 32.000 0.19 0.00 41.13 2.57
52 53 8.882415 AAAATTCTTAGCCTATGCATCAAATG 57.118 30.769 0.19 0.00 41.13 2.32
95 96 9.447157 TTCACATTTCAAAGGAAAGAAAACATT 57.553 25.926 0.00 0.00 45.58 2.71
96 97 9.101655 CTTCACATTTCAAAGGAAAGAAAACAT 57.898 29.630 0.00 0.00 45.58 2.71
97 98 7.548780 CCTTCACATTTCAAAGGAAAGAAAACA 59.451 33.333 0.00 0.00 45.58 2.83
98 99 7.465916 GCCTTCACATTTCAAAGGAAAGAAAAC 60.466 37.037 4.60 0.00 45.58 2.43
99 100 6.538381 GCCTTCACATTTCAAAGGAAAGAAAA 59.462 34.615 4.60 0.00 45.58 2.29
100 101 6.048509 GCCTTCACATTTCAAAGGAAAGAAA 58.951 36.000 4.60 0.00 45.58 2.52
101 102 5.363580 AGCCTTCACATTTCAAAGGAAAGAA 59.636 36.000 4.60 0.00 45.58 2.52
102 103 4.895297 AGCCTTCACATTTCAAAGGAAAGA 59.105 37.500 4.60 0.00 45.58 2.52
103 104 5.205759 AGCCTTCACATTTCAAAGGAAAG 57.794 39.130 4.60 0.00 45.58 2.62
104 105 5.358922 CAAGCCTTCACATTTCAAAGGAAA 58.641 37.500 4.60 0.00 46.36 3.13
105 106 4.202243 CCAAGCCTTCACATTTCAAAGGAA 60.202 41.667 4.60 0.00 41.78 3.36
106 107 3.321682 CCAAGCCTTCACATTTCAAAGGA 59.678 43.478 4.60 0.00 41.78 3.36
107 108 3.070015 ACCAAGCCTTCACATTTCAAAGG 59.930 43.478 0.00 0.00 42.07 3.11
108 109 4.326504 ACCAAGCCTTCACATTTCAAAG 57.673 40.909 0.00 0.00 0.00 2.77
109 110 4.751767 AACCAAGCCTTCACATTTCAAA 57.248 36.364 0.00 0.00 0.00 2.69
110 111 4.405358 AGAAACCAAGCCTTCACATTTCAA 59.595 37.500 0.00 0.00 0.00 2.69
111 112 3.960102 AGAAACCAAGCCTTCACATTTCA 59.040 39.130 0.00 0.00 0.00 2.69
112 113 4.590850 AGAAACCAAGCCTTCACATTTC 57.409 40.909 0.00 0.00 0.00 2.17
113 114 6.494835 AGAATAGAAACCAAGCCTTCACATTT 59.505 34.615 0.00 0.00 0.00 2.32
114 115 6.012745 AGAATAGAAACCAAGCCTTCACATT 58.987 36.000 0.00 0.00 0.00 2.71
115 116 5.574188 AGAATAGAAACCAAGCCTTCACAT 58.426 37.500 0.00 0.00 0.00 3.21
116 117 4.985538 AGAATAGAAACCAAGCCTTCACA 58.014 39.130 0.00 0.00 0.00 3.58
117 118 7.448748 TTTAGAATAGAAACCAAGCCTTCAC 57.551 36.000 0.00 0.00 0.00 3.18
118 119 9.396022 CTATTTAGAATAGAAACCAAGCCTTCA 57.604 33.333 2.28 0.00 0.00 3.02
119 120 8.841300 CCTATTTAGAATAGAAACCAAGCCTTC 58.159 37.037 8.81 0.00 0.00 3.46
120 121 8.557450 TCCTATTTAGAATAGAAACCAAGCCTT 58.443 33.333 8.81 0.00 0.00 4.35
121 122 8.102484 TCCTATTTAGAATAGAAACCAAGCCT 57.898 34.615 8.81 0.00 0.00 4.58
122 123 8.747538 TTCCTATTTAGAATAGAAACCAAGCC 57.252 34.615 8.81 0.00 0.00 4.35
166 167 9.950496 ATCTAGATGTGAATTAGACAAACTGTT 57.050 29.630 3.89 0.00 0.00 3.16
167 168 9.376075 CATCTAGATGTGAATTAGACAAACTGT 57.624 33.333 22.42 0.00 34.23 3.55
184 185 9.039870 GTGACATCCTTAGAAAACATCTAGATG 57.960 37.037 27.63 27.63 42.94 2.90
185 186 8.762645 TGTGACATCCTTAGAAAACATCTAGAT 58.237 33.333 0.00 0.00 41.59 1.98
186 187 8.134202 TGTGACATCCTTAGAAAACATCTAGA 57.866 34.615 0.00 0.00 41.59 2.43
187 188 8.954950 ATGTGACATCCTTAGAAAACATCTAG 57.045 34.615 0.00 0.00 41.59 2.43
188 189 9.739276 AAATGTGACATCCTTAGAAAACATCTA 57.261 29.630 0.00 0.00 39.71 1.98
189 190 8.641498 AAATGTGACATCCTTAGAAAACATCT 57.359 30.769 0.00 0.00 42.48 2.90
196 197 9.823647 GAGAGATTAAATGTGACATCCTTAGAA 57.176 33.333 0.00 0.00 0.00 2.10
197 198 8.981659 TGAGAGATTAAATGTGACATCCTTAGA 58.018 33.333 0.00 0.00 0.00 2.10
198 199 9.775854 ATGAGAGATTAAATGTGACATCCTTAG 57.224 33.333 0.00 0.00 0.00 2.18
215 216 8.942338 TGTTGCTACGTTAATTATGAGAGATT 57.058 30.769 0.00 0.00 0.00 2.40
216 217 8.942338 TTGTTGCTACGTTAATTATGAGAGAT 57.058 30.769 0.00 0.00 0.00 2.75
217 218 8.766000 TTTGTTGCTACGTTAATTATGAGAGA 57.234 30.769 0.00 0.00 0.00 3.10
218 219 8.869897 TCTTTGTTGCTACGTTAATTATGAGAG 58.130 33.333 0.00 0.00 0.00 3.20
219 220 8.766000 TCTTTGTTGCTACGTTAATTATGAGA 57.234 30.769 0.00 0.00 0.00 3.27
220 221 9.820229 TTTCTTTGTTGCTACGTTAATTATGAG 57.180 29.630 0.00 0.00 0.00 2.90
265 266 6.238925 GCCTACTATGTTTGTGGTCTGTTTTT 60.239 38.462 0.00 0.00 0.00 1.94
266 267 5.240844 GCCTACTATGTTTGTGGTCTGTTTT 59.759 40.000 0.00 0.00 0.00 2.43
267 268 4.760204 GCCTACTATGTTTGTGGTCTGTTT 59.240 41.667 0.00 0.00 0.00 2.83
268 269 4.202419 TGCCTACTATGTTTGTGGTCTGTT 60.202 41.667 0.00 0.00 0.00 3.16
269 270 3.326588 TGCCTACTATGTTTGTGGTCTGT 59.673 43.478 0.00 0.00 0.00 3.41
270 271 3.937814 TGCCTACTATGTTTGTGGTCTG 58.062 45.455 0.00 0.00 0.00 3.51
271 272 4.471386 AGATGCCTACTATGTTTGTGGTCT 59.529 41.667 0.00 0.00 0.00 3.85
272 273 4.572389 CAGATGCCTACTATGTTTGTGGTC 59.428 45.833 0.00 0.00 0.00 4.02
273 274 4.517285 CAGATGCCTACTATGTTTGTGGT 58.483 43.478 0.00 0.00 0.00 4.16
274 275 3.879295 CCAGATGCCTACTATGTTTGTGG 59.121 47.826 0.00 0.00 0.00 4.17
275 276 4.517285 ACCAGATGCCTACTATGTTTGTG 58.483 43.478 0.00 0.00 0.00 3.33
276 277 4.844349 ACCAGATGCCTACTATGTTTGT 57.156 40.909 0.00 0.00 0.00 2.83
277 278 6.582636 TCTAACCAGATGCCTACTATGTTTG 58.417 40.000 0.00 0.00 0.00 2.93
278 279 6.808321 TCTAACCAGATGCCTACTATGTTT 57.192 37.500 0.00 0.00 0.00 2.83
291 292 8.768501 TCTAGTTATGTCACATCTAACCAGAT 57.231 34.615 0.00 0.00 42.52 2.90
292 293 8.633561 CATCTAGTTATGTCACATCTAACCAGA 58.366 37.037 0.00 0.00 31.13 3.86
293 294 8.417106 ACATCTAGTTATGTCACATCTAACCAG 58.583 37.037 0.00 0.00 35.08 4.00
294 295 8.197439 CACATCTAGTTATGTCACATCTAACCA 58.803 37.037 0.00 0.00 38.01 3.67
295 296 8.198109 ACACATCTAGTTATGTCACATCTAACC 58.802 37.037 0.00 0.00 38.01 2.85
296 297 9.239002 GACACATCTAGTTATGTCACATCTAAC 57.761 37.037 7.24 0.00 40.95 2.34
297 298 9.190317 AGACACATCTAGTTATGTCACATCTAA 57.810 33.333 13.32 0.00 43.19 2.10
298 299 8.753497 AGACACATCTAGTTATGTCACATCTA 57.247 34.615 13.32 0.00 43.19 1.98
299 300 7.652524 AGACACATCTAGTTATGTCACATCT 57.347 36.000 13.32 4.15 43.19 2.90
300 301 9.973450 ATAAGACACATCTAGTTATGTCACATC 57.027 33.333 13.32 2.38 43.19 3.06
306 307 9.642343 TGGTCTATAAGACACATCTAGTTATGT 57.358 33.333 9.15 0.00 46.79 2.29
310 311 8.478877 CCTTTGGTCTATAAGACACATCTAGTT 58.521 37.037 9.15 0.00 46.79 2.24
311 312 7.839705 TCCTTTGGTCTATAAGACACATCTAGT 59.160 37.037 9.15 0.00 46.79 2.57
312 313 8.138712 GTCCTTTGGTCTATAAGACACATCTAG 58.861 40.741 9.15 0.00 46.79 2.43
313 314 7.839705 AGTCCTTTGGTCTATAAGACACATCTA 59.160 37.037 9.15 0.00 46.79 1.98
314 315 6.670027 AGTCCTTTGGTCTATAAGACACATCT 59.330 38.462 9.15 0.00 46.79 2.90
315 316 6.879400 AGTCCTTTGGTCTATAAGACACATC 58.121 40.000 9.15 0.00 46.79 3.06
316 317 6.875972 AGTCCTTTGGTCTATAAGACACAT 57.124 37.500 9.15 0.00 46.79 3.21
317 318 7.786046 TTAGTCCTTTGGTCTATAAGACACA 57.214 36.000 9.15 2.55 46.79 3.72
318 319 9.498176 TTTTTAGTCCTTTGGTCTATAAGACAC 57.502 33.333 9.15 0.00 46.79 3.67
345 346 9.476202 CCGGATAAGATTTTGAAAAGAAACTTT 57.524 29.630 0.00 0.00 0.00 2.66
356 357 8.817092 AGGAATTTTACCGGATAAGATTTTGA 57.183 30.769 9.46 0.00 29.86 2.69
370 371 8.781196 GGGACGAGAAATTATAGGAATTTTACC 58.219 37.037 0.00 0.00 30.68 2.85
371 372 9.333724 TGGGACGAGAAATTATAGGAATTTTAC 57.666 33.333 0.00 0.00 30.68 2.01
383 384 4.007659 GCCTTTTCTGGGACGAGAAATTA 58.992 43.478 9.74 0.00 40.74 1.40
386 387 1.876416 CGCCTTTTCTGGGACGAGAAA 60.876 52.381 5.55 5.55 39.64 2.52
389 390 2.391389 GCGCCTTTTCTGGGACGAG 61.391 63.158 0.00 0.00 0.00 4.18
390 391 2.358247 GCGCCTTTTCTGGGACGA 60.358 61.111 0.00 0.00 0.00 4.20
394 395 3.127533 CTCCGCGCCTTTTCTGGG 61.128 66.667 0.00 0.00 0.00 4.45
461 469 1.674322 CACGATTTCGGCCTTGGGT 60.674 57.895 0.00 0.00 44.95 4.51
464 690 0.953471 TGGTCACGATTTCGGCCTTG 60.953 55.000 0.00 0.00 44.95 3.61
474 700 0.988145 ATGTGGGGGATGGTCACGAT 60.988 55.000 0.00 0.00 34.43 3.73
520 750 2.105821 TGCCCTAGATCCGTTTATTGGG 59.894 50.000 0.00 0.00 36.63 4.12
523 753 4.102524 TCACATGCCCTAGATCCGTTTATT 59.897 41.667 0.00 0.00 0.00 1.40
701 933 2.038557 GGAAACTTCACAGGAGGCAGTA 59.961 50.000 0.00 0.00 0.00 2.74
702 934 1.202818 GGAAACTTCACAGGAGGCAGT 60.203 52.381 0.00 0.00 0.00 4.40
704 936 0.250295 CGGAAACTTCACAGGAGGCA 60.250 55.000 0.00 0.00 0.00 4.75
744 1019 0.244994 GCAGCTCGAGGAAGAACTGA 59.755 55.000 15.58 0.00 36.69 3.41
786 1061 1.751563 GAGGGGATGCAGAGTAGGC 59.248 63.158 0.00 0.00 0.00 3.93
787 1062 0.468214 TCGAGGGGATGCAGAGTAGG 60.468 60.000 0.00 0.00 0.00 3.18
788 1063 0.671251 GTCGAGGGGATGCAGAGTAG 59.329 60.000 0.00 0.00 0.00 2.57
789 1064 1.101635 CGTCGAGGGGATGCAGAGTA 61.102 60.000 0.00 0.00 0.00 2.59
790 1065 2.418910 CGTCGAGGGGATGCAGAGT 61.419 63.158 0.00 0.00 0.00 3.24
791 1066 2.415010 CGTCGAGGGGATGCAGAG 59.585 66.667 0.00 0.00 0.00 3.35
796 1071 1.519455 GACAAGCGTCGAGGGGATG 60.519 63.158 7.31 0.00 31.07 3.51
797 1072 2.722201 GGACAAGCGTCGAGGGGAT 61.722 63.158 7.31 0.00 43.61 3.85
807 1082 0.455295 GAGAGTGACTCGGACAAGCG 60.455 60.000 6.99 0.00 35.84 4.68
867 1143 5.220989 GCTCGGGCGTATATATAACTGATCA 60.221 44.000 0.00 0.00 0.00 2.92
896 1177 3.284449 GGTTCGGTGGTGTGTGGC 61.284 66.667 0.00 0.00 0.00 5.01
901 1182 1.354101 TCTTATGGGTTCGGTGGTGT 58.646 50.000 0.00 0.00 0.00 4.16
963 1244 0.183492 AGGACAGAGCAAAACAGCCA 59.817 50.000 0.00 0.00 34.23 4.75
968 1249 1.268079 GCCAAGAGGACAGAGCAAAAC 59.732 52.381 0.00 0.00 36.89 2.43
973 1254 2.484594 GGATTAGCCAAGAGGACAGAGC 60.485 54.545 0.00 0.00 36.89 4.09
1058 1429 6.313411 TCTGAAAAATGCAACTTTTCCTGTTG 59.687 34.615 23.90 14.14 45.23 3.33
1059 1430 6.313658 GTCTGAAAAATGCAACTTTTCCTGTT 59.686 34.615 23.90 2.02 34.70 3.16
1060 1431 5.812127 GTCTGAAAAATGCAACTTTTCCTGT 59.188 36.000 23.90 2.32 34.70 4.00
1135 1567 7.264221 ACTGTCATTCTGCATTTAGAGTAGAG 58.736 38.462 0.00 0.00 0.00 2.43
1187 1619 1.864862 CAAGTTGCTGAGCCTGTCG 59.135 57.895 0.23 0.00 0.00 4.35
1344 1776 4.236147 TCATCATTGTTGCAATTGAACGG 58.764 39.130 10.34 5.41 0.00 4.44
1379 1811 4.274950 GTCACTTTAACCACAGCTTTGCTA 59.725 41.667 0.00 0.00 36.40 3.49
1381 1813 3.181491 TGTCACTTTAACCACAGCTTTGC 60.181 43.478 0.00 0.00 0.00 3.68
1383 1815 5.417580 TCTTTGTCACTTTAACCACAGCTTT 59.582 36.000 0.00 0.00 0.00 3.51
1417 1849 1.922570 TCGGCTTAAATCTCTGCGTC 58.077 50.000 0.00 0.00 0.00 5.19
1467 1899 5.972327 ATTGGGTCATCTTCTCTCAAGAT 57.028 39.130 0.00 0.00 37.47 2.40
1754 2211 1.202592 TGCTCAACTTTCAGCACGGTA 60.203 47.619 0.00 0.00 40.80 4.02
1764 2221 3.622459 GTTGTGCGTGCTCAACTTT 57.378 47.368 24.57 0.00 43.15 2.66
1836 2293 3.591023 TGATGCGTATGAGTTTCGGAAA 58.409 40.909 0.00 0.00 0.00 3.13
1849 2306 3.270027 CAACCCTCAAAGATGATGCGTA 58.730 45.455 0.00 0.00 34.37 4.42
1902 2362 4.256920 ACAGTATCAAGCAACAGGACATC 58.743 43.478 0.00 0.00 0.00 3.06
2035 2495 6.607735 AGGAAAACAAAGCATTTTGACATG 57.392 33.333 5.51 0.00 45.21 3.21
2060 2521 4.753233 CAGATAAGAAGTGTGACCAGAGG 58.247 47.826 0.00 0.00 0.00 3.69
2607 3082 6.453791 CGTTAACCGATCATACAAGAACACAG 60.454 42.308 0.00 0.00 39.56 3.66
2629 3104 2.819552 GCGGCACTTGTCACACGTT 61.820 57.895 0.00 0.00 0.00 3.99
2787 3272 8.447833 CACAAACTAACTTGAAAACACTACAGA 58.552 33.333 0.00 0.00 0.00 3.41
2802 3287 4.013728 TGGAACTGCAACACAAACTAACT 58.986 39.130 0.00 0.00 0.00 2.24
2892 3378 3.388024 TGCCCGTAAGAAGCTCTTATGAT 59.612 43.478 18.81 0.00 44.66 2.45
2994 3480 4.828939 TGGAAACAGTTGCAGATGATTTCT 59.171 37.500 7.19 0.00 35.01 2.52
3035 3522 2.627699 TGAAACCCAAAGATGAAGTGCC 59.372 45.455 0.00 0.00 0.00 5.01
3038 3525 4.218312 AGCTTGAAACCCAAAGATGAAGT 58.782 39.130 0.00 0.00 33.76 3.01
3040 3527 3.253188 CGAGCTTGAAACCCAAAGATGAA 59.747 43.478 0.00 0.00 33.76 2.57
3128 3623 4.328712 TGTCACATTTCAACCGATCATACG 59.671 41.667 0.00 0.00 0.00 3.06
3143 3638 2.566913 TGCCGTAACACTTGTCACATT 58.433 42.857 0.00 0.00 0.00 2.71
3169 3664 1.021202 TGAAACTGTGACGGCTTTGG 58.979 50.000 0.00 0.00 0.00 3.28
3170 3665 2.450160 GTTGAAACTGTGACGGCTTTG 58.550 47.619 0.00 0.00 0.00 2.77
3171 3666 1.404035 GGTTGAAACTGTGACGGCTTT 59.596 47.619 0.00 0.00 0.00 3.51
3172 3667 1.021968 GGTTGAAACTGTGACGGCTT 58.978 50.000 0.00 0.00 0.00 4.35
3173 3668 0.180406 AGGTTGAAACTGTGACGGCT 59.820 50.000 0.00 0.00 0.00 5.52
3174 3669 1.873698 TAGGTTGAAACTGTGACGGC 58.126 50.000 0.00 0.00 0.00 5.68
3180 3675 3.214328 CTGCCACTTAGGTTGAAACTGT 58.786 45.455 0.00 0.00 40.61 3.55
3188 3683 1.380302 CCCTGCTGCCACTTAGGTT 59.620 57.895 0.00 0.00 40.61 3.50
3189 3684 3.081554 CCCTGCTGCCACTTAGGT 58.918 61.111 0.00 0.00 40.61 3.08
3217 3712 5.028549 TGATCCTCTTGGTGATTTAGCTC 57.971 43.478 0.00 0.00 34.23 4.09
3249 3744 4.214119 CGGCTGTATGGAAGTGAATTATGG 59.786 45.833 0.00 0.00 0.00 2.74
3328 3823 5.733676 AGAAAGGAATTGCAACACAAACTT 58.266 33.333 0.00 0.00 42.86 2.66
3331 3826 5.163774 GCAAAGAAAGGAATTGCAACACAAA 60.164 36.000 0.00 0.00 46.57 2.83
3353 3848 1.065600 GCAAACGTTTCAGGCAGCA 59.934 52.632 11.37 0.00 0.00 4.41
3354 3849 0.936297 CAGCAAACGTTTCAGGCAGC 60.936 55.000 19.96 15.20 0.00 5.25
3355 3850 0.662619 TCAGCAAACGTTTCAGGCAG 59.337 50.000 19.96 13.91 0.00 4.85
3356 3851 1.098869 TTCAGCAAACGTTTCAGGCA 58.901 45.000 19.96 2.16 0.00 4.75
3376 3871 0.944386 AGTACTGGCAACACAAAGCG 59.056 50.000 0.00 0.00 46.17 4.68
3377 3872 3.436700 AAAGTACTGGCAACACAAAGC 57.563 42.857 0.00 0.00 46.17 3.51
3417 3912 3.119849 CGTTGAGCAGTTAATGGAAAGGG 60.120 47.826 0.00 0.00 0.00 3.95
3430 3925 6.955963 GTGTACTGAATATTTTCGTTGAGCAG 59.044 38.462 0.00 0.00 34.39 4.24
3454 3949 5.408604 CGGTTCAGTTGTAGCTAAGATTTGT 59.591 40.000 0.00 0.00 0.00 2.83
3478 3973 2.361230 CCCGCCCCCTTTTCTGTC 60.361 66.667 0.00 0.00 0.00 3.51
3511 4006 1.824852 GTTTCCTGTTAATGCCCCAGG 59.175 52.381 3.23 3.23 45.81 4.45
3560 4055 0.402887 AGGTTTTTCCCCCGTGGTAG 59.597 55.000 0.00 0.00 36.75 3.18
3567 4062 2.366266 GGTGTTAACAGGTTTTTCCCCC 59.634 50.000 8.98 0.00 36.75 5.40
3571 4066 6.569780 AGTTGATGGTGTTAACAGGTTTTTC 58.430 36.000 8.98 1.78 0.00 2.29
3575 4070 4.753107 CGTAGTTGATGGTGTTAACAGGTT 59.247 41.667 8.98 0.00 0.00 3.50
3580 4075 3.991773 TGCTCGTAGTTGATGGTGTTAAC 59.008 43.478 0.00 0.00 0.00 2.01
3590 4085 1.883926 TGTGCTACTGCTCGTAGTTGA 59.116 47.619 12.99 0.00 45.97 3.18
3628 4123 8.749354 TGAGATAGTCTTTGTAATACTTCTGCA 58.251 33.333 0.00 0.00 0.00 4.41
3629 4124 9.243637 CTGAGATAGTCTTTGTAATACTTCTGC 57.756 37.037 0.00 0.00 0.00 4.26
3632 4127 9.243637 CTGCTGAGATAGTCTTTGTAATACTTC 57.756 37.037 0.00 0.00 0.00 3.01
3635 4130 6.422400 GCCTGCTGAGATAGTCTTTGTAATAC 59.578 42.308 0.00 0.00 0.00 1.89
3637 4132 5.104776 TGCCTGCTGAGATAGTCTTTGTAAT 60.105 40.000 0.00 0.00 0.00 1.89
3640 4135 2.568956 TGCCTGCTGAGATAGTCTTTGT 59.431 45.455 0.00 0.00 0.00 2.83
3659 4154 4.130286 AGTTCTCACTAAGGTATGCTGC 57.870 45.455 0.00 0.00 0.00 5.25
3660 4155 6.458232 AGTAGTTCTCACTAAGGTATGCTG 57.542 41.667 0.00 0.00 37.24 4.41
3661 4156 8.228035 CTTAGTAGTTCTCACTAAGGTATGCT 57.772 38.462 12.39 0.00 46.16 3.79
3669 4164 6.649557 GCCTTTTGCTTAGTAGTTCTCACTAA 59.350 38.462 0.00 0.00 35.56 2.24
3670 4165 6.164176 GCCTTTTGCTTAGTAGTTCTCACTA 58.836 40.000 0.00 0.00 36.87 2.74
3671 4166 4.998033 GCCTTTTGCTTAGTAGTTCTCACT 59.002 41.667 0.00 0.00 36.87 3.41
3672 4167 4.755123 TGCCTTTTGCTTAGTAGTTCTCAC 59.245 41.667 0.00 0.00 42.00 3.51
3673 4168 4.755123 GTGCCTTTTGCTTAGTAGTTCTCA 59.245 41.667 0.00 0.00 42.00 3.27
3674 4169 4.755123 TGTGCCTTTTGCTTAGTAGTTCTC 59.245 41.667 0.00 0.00 42.00 2.87
3675 4170 4.714632 TGTGCCTTTTGCTTAGTAGTTCT 58.285 39.130 0.00 0.00 42.00 3.01
3676 4171 5.432885 TTGTGCCTTTTGCTTAGTAGTTC 57.567 39.130 0.00 0.00 42.00 3.01
3677 4172 5.736207 GCTTTGTGCCTTTTGCTTAGTAGTT 60.736 40.000 0.00 0.00 42.00 2.24
3678 4173 4.261614 GCTTTGTGCCTTTTGCTTAGTAGT 60.262 41.667 0.00 0.00 42.00 2.73
3679 4174 4.229876 GCTTTGTGCCTTTTGCTTAGTAG 58.770 43.478 0.00 0.00 42.00 2.57
3680 4175 3.634448 TGCTTTGTGCCTTTTGCTTAGTA 59.366 39.130 0.00 0.00 42.00 1.82
3681 4176 2.430332 TGCTTTGTGCCTTTTGCTTAGT 59.570 40.909 0.00 0.00 42.00 2.24
3682 4177 3.096489 TGCTTTGTGCCTTTTGCTTAG 57.904 42.857 0.00 0.00 42.00 2.18
3683 4178 3.749665 ATGCTTTGTGCCTTTTGCTTA 57.250 38.095 0.00 0.00 42.00 3.09
3684 4179 2.625695 ATGCTTTGTGCCTTTTGCTT 57.374 40.000 0.00 0.00 42.00 3.91
3685 4180 3.967332 ATATGCTTTGTGCCTTTTGCT 57.033 38.095 0.00 0.00 42.00 3.91
3686 4181 4.997565 TCTATATGCTTTGTGCCTTTTGC 58.002 39.130 0.00 0.00 42.00 3.68
3687 4182 5.807011 GGTTCTATATGCTTTGTGCCTTTTG 59.193 40.000 0.00 0.00 42.00 2.44
3688 4183 5.480073 TGGTTCTATATGCTTTGTGCCTTTT 59.520 36.000 0.00 0.00 42.00 2.27
3689 4184 5.016173 TGGTTCTATATGCTTTGTGCCTTT 58.984 37.500 0.00 0.00 42.00 3.11
3690 4185 4.599041 TGGTTCTATATGCTTTGTGCCTT 58.401 39.130 0.00 0.00 42.00 4.35
3691 4186 4.080356 TCTGGTTCTATATGCTTTGTGCCT 60.080 41.667 0.00 0.00 42.00 4.75
3692 4187 4.199310 TCTGGTTCTATATGCTTTGTGCC 58.801 43.478 0.00 0.00 42.00 5.01
3693 4188 4.260948 GCTCTGGTTCTATATGCTTTGTGC 60.261 45.833 0.00 0.00 43.25 4.57
3694 4189 4.877823 TGCTCTGGTTCTATATGCTTTGTG 59.122 41.667 0.00 0.00 0.00 3.33
3695 4190 5.102953 TGCTCTGGTTCTATATGCTTTGT 57.897 39.130 0.00 0.00 0.00 2.83
3696 4191 6.128336 GCTATGCTCTGGTTCTATATGCTTTG 60.128 42.308 0.00 0.00 0.00 2.77
3697 4192 5.936956 GCTATGCTCTGGTTCTATATGCTTT 59.063 40.000 0.00 0.00 0.00 3.51
3698 4193 5.012458 TGCTATGCTCTGGTTCTATATGCTT 59.988 40.000 0.00 0.00 0.00 3.91
3699 4194 4.529769 TGCTATGCTCTGGTTCTATATGCT 59.470 41.667 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.