Multiple sequence alignment - TraesCS4D01G231500

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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 TraesCS4D01G231500 chr4D 100.000 4804 0 0 1 4804 391451349 391456152 0.000000e+00 8872
1 TraesCS4D01G231500 chr4D 90.909 341 31 0 1 341 425120908 425121248 4.380000e-125 459
2 TraesCS4D01G231500 chr4B 93.769 2616 102 28 342 2929 481233230 481235812 0.000000e+00 3871
3 TraesCS4D01G231500 chr4B 93.568 1306 52 16 2930 4222 481235975 481237261 0.000000e+00 1917
4 TraesCS4D01G231500 chr4A 91.847 2122 71 25 342 2426 73136273 73138329 0.000000e+00 2867
5 TraesCS4D01G231500 chr4A 92.628 936 38 12 3299 4222 73139567 73140483 0.000000e+00 1317
6 TraesCS4D01G231500 chr4A 93.408 713 32 4 2600 3300 73138825 73139534 0.000000e+00 1042
7 TraesCS4D01G231500 chr4A 87.903 124 7 3 2415 2538 73138524 73138639 6.480000e-29 139
8 TraesCS4D01G231500 chr3D 98.971 583 6 0 4222 4804 532071288 532070706 0.000000e+00 1044
9 TraesCS4D01G231500 chr3D 95.068 588 21 6 4223 4804 523400411 523400996 0.000000e+00 918
10 TraesCS4D01G231500 chr3D 94.228 589 25 8 4223 4804 20288618 20289204 0.000000e+00 891
11 TraesCS4D01G231500 chr3D 94.068 590 25 9 4223 4804 160913034 160913621 0.000000e+00 887
12 TraesCS4D01G231500 chr3D 92.711 343 25 0 1 343 113464662 113465004 3.340000e-136 496
13 TraesCS4D01G231500 chr7D 98.797 582 7 0 4223 4804 526288225 526288806 0.000000e+00 1037
14 TraesCS4D01G231500 chr7D 95.270 592 16 9 4222 4804 540442132 540442720 0.000000e+00 928
15 TraesCS4D01G231500 chr2D 98.110 582 11 0 4223 4804 147381591 147381010 0.000000e+00 1014
16 TraesCS4D01G231500 chr2D 96.115 592 13 7 4221 4804 513034142 513033553 0.000000e+00 957
17 TraesCS4D01G231500 chr2D 90.988 344 29 1 1 342 513541648 513541991 3.390000e-126 462
18 TraesCS4D01G231500 chr6D 95.278 593 17 7 4217 4804 175423678 175424264 0.000000e+00 929
19 TraesCS4D01G231500 chr6D 95.308 341 15 1 1 341 97719922 97719583 1.520000e-149 540
20 TraesCS4D01G231500 chr1D 95.015 341 17 0 1 341 427002831 427002491 1.970000e-148 536
21 TraesCS4D01G231500 chr1D 92.920 339 18 4 9 341 18930659 18930321 5.590000e-134 488
22 TraesCS4D01G231500 chr1D 91.039 279 19 3 62 340 256105685 256105957 5.870000e-99 372
23 TraesCS4D01G231500 chr5D 93.333 345 19 2 1 344 233951828 233951487 1.540000e-139 507
24 TraesCS4D01G231500 chr7A 91.789 341 28 0 1 341 69752840 69753180 4.350000e-130 475
25 TraesCS4D01G231500 chr2A 95.041 121 6 0 1 121 772391798 772391918 1.760000e-44 191


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 TraesCS4D01G231500 chr4D 391451349 391456152 4803 False 8872.00 8872 100.0000 1 4804 1 chr4D.!!$F1 4803
1 TraesCS4D01G231500 chr4B 481233230 481237261 4031 False 2894.00 3871 93.6685 342 4222 2 chr4B.!!$F1 3880
2 TraesCS4D01G231500 chr4A 73136273 73140483 4210 False 1341.25 2867 91.4465 342 4222 4 chr4A.!!$F1 3880
3 TraesCS4D01G231500 chr3D 532070706 532071288 582 True 1044.00 1044 98.9710 4222 4804 1 chr3D.!!$R1 582
4 TraesCS4D01G231500 chr3D 523400411 523400996 585 False 918.00 918 95.0680 4223 4804 1 chr3D.!!$F4 581
5 TraesCS4D01G231500 chr3D 20288618 20289204 586 False 891.00 891 94.2280 4223 4804 1 chr3D.!!$F1 581
6 TraesCS4D01G231500 chr3D 160913034 160913621 587 False 887.00 887 94.0680 4223 4804 1 chr3D.!!$F3 581
7 TraesCS4D01G231500 chr7D 526288225 526288806 581 False 1037.00 1037 98.7970 4223 4804 1 chr7D.!!$F1 581
8 TraesCS4D01G231500 chr7D 540442132 540442720 588 False 928.00 928 95.2700 4222 4804 1 chr7D.!!$F2 582
9 TraesCS4D01G231500 chr2D 147381010 147381591 581 True 1014.00 1014 98.1100 4223 4804 1 chr2D.!!$R1 581
10 TraesCS4D01G231500 chr2D 513033553 513034142 589 True 957.00 957 96.1150 4221 4804 1 chr2D.!!$R2 583
11 TraesCS4D01G231500 chr6D 175423678 175424264 586 False 929.00 929 95.2780 4217 4804 1 chr6D.!!$F1 587

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
282 283 0.035630 AGAGCCAAGCCACATCTGAC 60.036 55.0 0.00 0.0 0.0 3.51 F
1427 1447 0.038166 ATCATCACCCCAACTTGCGT 59.962 50.0 0.00 0.0 0.0 5.24 F
2134 2166 0.027979 CATCGGCGGCAACTAACATG 59.972 55.0 10.53 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1729 0.036010 ACCACCTCCTGAAATCTGCG 60.036 55.0 0.00 0.00 0.00 5.18 R
3366 3955 0.848305 CGCAGCTGCAAAAGAACAAC 59.152 50.0 36.03 4.51 42.21 3.32 R
3961 4560 0.320334 GGGTGTGGGGAAAAATTGCG 60.320 55.0 0.00 0.00 0.00 4.85 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 0.109919 CGGCGACTTAGGGTTTTTGC 60.110 55.000 0.00 0.00 0.00 3.68
20 21 0.242825 GGCGACTTAGGGTTTTTGCC 59.757 55.000 0.00 0.00 0.00 4.52
27 28 3.689414 GGGTTTTTGCCCCGGTAG 58.311 61.111 0.00 0.00 42.89 3.18
28 29 1.228644 GGGTTTTTGCCCCGGTAGT 60.229 57.895 0.00 0.00 42.89 2.73
29 30 0.828762 GGGTTTTTGCCCCGGTAGTT 60.829 55.000 0.00 0.00 42.89 2.24
30 31 0.315886 GGTTTTTGCCCCGGTAGTTG 59.684 55.000 0.00 0.00 0.00 3.16
31 32 0.315886 GTTTTTGCCCCGGTAGTTGG 59.684 55.000 0.00 0.00 0.00 3.77
32 33 0.828343 TTTTTGCCCCGGTAGTTGGG 60.828 55.000 0.00 0.00 46.93 4.12
39 40 2.368591 CCGGTAGTTGGGACTTGGA 58.631 57.895 0.00 0.00 37.33 3.53
40 41 0.036671 CCGGTAGTTGGGACTTGGAC 60.037 60.000 0.00 0.00 37.33 4.02
41 42 0.389426 CGGTAGTTGGGACTTGGACG 60.389 60.000 0.00 0.00 37.33 4.79
42 43 0.672711 GGTAGTTGGGACTTGGACGC 60.673 60.000 0.00 0.00 37.33 5.19
43 44 0.672711 GTAGTTGGGACTTGGACGCC 60.673 60.000 0.00 0.00 37.33 5.68
44 45 1.122632 TAGTTGGGACTTGGACGCCA 61.123 55.000 0.00 0.00 37.33 5.69
45 46 1.966451 GTTGGGACTTGGACGCCAG 60.966 63.158 0.00 0.00 33.81 4.85
46 47 3.842925 TTGGGACTTGGACGCCAGC 62.843 63.158 0.00 0.00 33.81 4.85
51 52 4.473520 CTTGGACGCCAGCCGGAT 62.474 66.667 5.05 0.00 42.52 4.18
52 53 4.776322 TTGGACGCCAGCCGGATG 62.776 66.667 14.18 14.18 42.52 3.51
55 56 4.778143 GACGCCAGCCGGATGGTT 62.778 66.667 37.37 25.85 42.75 3.67
61 62 3.313874 AGCCGGATGGTTGAGGAG 58.686 61.111 5.05 0.00 37.67 3.69
62 63 2.190578 GCCGGATGGTTGAGGAGG 59.809 66.667 5.05 0.00 37.67 4.30
63 64 2.670148 GCCGGATGGTTGAGGAGGT 61.670 63.158 5.05 0.00 37.67 3.85
64 65 1.221840 CCGGATGGTTGAGGAGGTG 59.778 63.158 0.00 0.00 0.00 4.00
65 66 1.450312 CGGATGGTTGAGGAGGTGC 60.450 63.158 0.00 0.00 0.00 5.01
66 67 1.903877 CGGATGGTTGAGGAGGTGCT 61.904 60.000 0.00 0.00 0.00 4.40
67 68 0.393537 GGATGGTTGAGGAGGTGCTG 60.394 60.000 0.00 0.00 0.00 4.41
68 69 0.326264 GATGGTTGAGGAGGTGCTGT 59.674 55.000 0.00 0.00 0.00 4.40
69 70 0.773644 ATGGTTGAGGAGGTGCTGTT 59.226 50.000 0.00 0.00 0.00 3.16
70 71 0.179020 TGGTTGAGGAGGTGCTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
71 72 0.890996 GGTTGAGGAGGTGCTGTTGG 60.891 60.000 0.00 0.00 0.00 3.77
72 73 0.179018 GTTGAGGAGGTGCTGTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
73 74 0.179020 TTGAGGAGGTGCTGTTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
74 75 1.302832 GAGGAGGTGCTGTTGGTGG 60.303 63.158 0.00 0.00 0.00 4.61
75 76 1.768684 GAGGAGGTGCTGTTGGTGGA 61.769 60.000 0.00 0.00 0.00 4.02
76 77 1.302832 GGAGGTGCTGTTGGTGGAG 60.303 63.158 0.00 0.00 0.00 3.86
77 78 1.302832 GAGGTGCTGTTGGTGGAGG 60.303 63.158 0.00 0.00 0.00 4.30
78 79 2.056906 GAGGTGCTGTTGGTGGAGGT 62.057 60.000 0.00 0.00 0.00 3.85
79 80 1.898574 GGTGCTGTTGGTGGAGGTG 60.899 63.158 0.00 0.00 0.00 4.00
80 81 1.148273 GTGCTGTTGGTGGAGGTGA 59.852 57.895 0.00 0.00 0.00 4.02
81 82 1.148273 TGCTGTTGGTGGAGGTGAC 59.852 57.895 0.00 0.00 0.00 3.67
82 83 1.961277 GCTGTTGGTGGAGGTGACG 60.961 63.158 0.00 0.00 0.00 4.35
83 84 1.301716 CTGTTGGTGGAGGTGACGG 60.302 63.158 0.00 0.00 0.00 4.79
84 85 2.668550 GTTGGTGGAGGTGACGGC 60.669 66.667 0.00 0.00 0.00 5.68
85 86 4.308458 TTGGTGGAGGTGACGGCG 62.308 66.667 4.80 4.80 0.00 6.46
115 116 4.521062 CAGGCGGGCGAGGAGAAG 62.521 72.222 0.00 0.00 0.00 2.85
119 120 3.764466 CGGGCGAGGAGAAGCAGT 61.764 66.667 0.00 0.00 34.54 4.40
120 121 2.125350 GGGCGAGGAGAAGCAGTG 60.125 66.667 0.00 0.00 34.54 3.66
121 122 2.817396 GGCGAGGAGAAGCAGTGC 60.817 66.667 7.13 7.13 34.54 4.40
122 123 3.184683 GCGAGGAGAAGCAGTGCG 61.185 66.667 10.00 0.00 0.00 5.34
123 124 3.184683 CGAGGAGAAGCAGTGCGC 61.185 66.667 10.00 0.00 42.91 6.09
124 125 2.817396 GAGGAGAAGCAGTGCGCC 60.817 66.667 10.00 10.12 44.04 6.53
125 126 4.749310 AGGAGAAGCAGTGCGCCG 62.749 66.667 10.00 0.00 44.04 6.46
188 189 2.496470 GGTTAGCCATACCCTAGGATCG 59.504 54.545 11.48 0.00 34.09 3.69
189 190 3.428532 GTTAGCCATACCCTAGGATCGA 58.571 50.000 11.48 0.00 0.00 3.59
190 191 2.696526 AGCCATACCCTAGGATCGAA 57.303 50.000 11.48 0.00 0.00 3.71
191 192 2.972348 AGCCATACCCTAGGATCGAAA 58.028 47.619 11.48 0.00 0.00 3.46
192 193 2.900546 AGCCATACCCTAGGATCGAAAG 59.099 50.000 11.48 0.00 0.00 2.62
193 194 2.633481 GCCATACCCTAGGATCGAAAGT 59.367 50.000 11.48 0.00 0.00 2.66
194 195 3.306156 GCCATACCCTAGGATCGAAAGTC 60.306 52.174 11.48 0.00 0.00 3.01
195 196 4.153411 CCATACCCTAGGATCGAAAGTCT 58.847 47.826 11.48 0.00 0.00 3.24
196 197 4.021894 CCATACCCTAGGATCGAAAGTCTG 60.022 50.000 11.48 0.58 0.00 3.51
197 198 3.383698 ACCCTAGGATCGAAAGTCTGA 57.616 47.619 11.48 0.00 0.00 3.27
198 199 3.917300 ACCCTAGGATCGAAAGTCTGAT 58.083 45.455 11.48 0.00 0.00 2.90
199 200 5.063017 ACCCTAGGATCGAAAGTCTGATA 57.937 43.478 11.48 0.00 0.00 2.15
200 201 4.828387 ACCCTAGGATCGAAAGTCTGATAC 59.172 45.833 11.48 0.00 0.00 2.24
201 202 4.218852 CCCTAGGATCGAAAGTCTGATACC 59.781 50.000 11.48 0.00 0.00 2.73
202 203 4.827835 CCTAGGATCGAAAGTCTGATACCA 59.172 45.833 1.05 0.00 0.00 3.25
203 204 5.478679 CCTAGGATCGAAAGTCTGATACCAT 59.521 44.000 1.05 0.00 0.00 3.55
204 205 5.207110 AGGATCGAAAGTCTGATACCATG 57.793 43.478 0.00 0.00 0.00 3.66
205 206 4.651503 AGGATCGAAAGTCTGATACCATGT 59.348 41.667 0.00 0.00 0.00 3.21
206 207 5.833667 AGGATCGAAAGTCTGATACCATGTA 59.166 40.000 0.00 0.00 0.00 2.29
207 208 6.015856 AGGATCGAAAGTCTGATACCATGTAG 60.016 42.308 0.00 0.00 0.00 2.74
208 209 6.016192 GGATCGAAAGTCTGATACCATGTAGA 60.016 42.308 0.00 0.00 0.00 2.59
209 210 6.769134 TCGAAAGTCTGATACCATGTAGAA 57.231 37.500 0.00 0.00 0.00 2.10
210 211 7.348080 TCGAAAGTCTGATACCATGTAGAAT 57.652 36.000 0.00 0.00 0.00 2.40
211 212 7.782049 TCGAAAGTCTGATACCATGTAGAATT 58.218 34.615 0.00 0.00 0.00 2.17
212 213 7.706607 TCGAAAGTCTGATACCATGTAGAATTG 59.293 37.037 0.00 0.00 29.25 2.32
213 214 7.492669 CGAAAGTCTGATACCATGTAGAATTGT 59.507 37.037 0.00 0.00 29.25 2.71
214 215 9.817809 GAAAGTCTGATACCATGTAGAATTGTA 57.182 33.333 0.00 0.00 29.25 2.41
217 218 9.770097 AGTCTGATACCATGTAGAATTGTATTG 57.230 33.333 0.00 0.00 0.00 1.90
218 219 9.764363 GTCTGATACCATGTAGAATTGTATTGA 57.236 33.333 0.00 0.00 0.00 2.57
245 246 4.891627 TGTTGATACAATATTGTGCCGG 57.108 40.909 27.62 0.00 42.31 6.13
246 247 4.265893 TGTTGATACAATATTGTGCCGGT 58.734 39.130 27.62 10.66 42.31 5.28
247 248 5.429130 TGTTGATACAATATTGTGCCGGTA 58.571 37.500 27.62 9.82 42.31 4.02
248 249 5.294799 TGTTGATACAATATTGTGCCGGTAC 59.705 40.000 27.62 16.68 42.31 3.34
249 250 5.024785 TGATACAATATTGTGCCGGTACA 57.975 39.130 27.62 22.40 42.31 2.90
250 251 5.429130 TGATACAATATTGTGCCGGTACAA 58.571 37.500 35.22 35.22 43.93 2.41
251 252 5.525745 TGATACAATATTGTGCCGGTACAAG 59.474 40.000 35.61 26.12 43.14 3.16
252 253 3.945346 ACAATATTGTGCCGGTACAAGA 58.055 40.909 35.61 33.06 43.14 3.02
253 254 4.328536 ACAATATTGTGCCGGTACAAGAA 58.671 39.130 35.61 27.71 43.14 2.52
254 255 4.394920 ACAATATTGTGCCGGTACAAGAAG 59.605 41.667 35.61 29.13 43.14 2.85
255 256 2.561478 ATTGTGCCGGTACAAGAAGT 57.439 45.000 35.61 20.99 43.14 3.01
256 257 3.688694 ATTGTGCCGGTACAAGAAGTA 57.311 42.857 35.61 18.03 43.14 2.24
257 258 3.688694 TTGTGCCGGTACAAGAAGTAT 57.311 42.857 31.02 0.00 35.75 2.12
258 259 4.804868 TTGTGCCGGTACAAGAAGTATA 57.195 40.909 31.02 9.60 35.75 1.47
259 260 5.347620 TTGTGCCGGTACAAGAAGTATAT 57.652 39.130 31.02 0.00 35.75 0.86
260 261 6.468333 TTGTGCCGGTACAAGAAGTATATA 57.532 37.500 31.02 8.10 35.75 0.86
261 262 6.659745 TGTGCCGGTACAAGAAGTATATAT 57.340 37.500 23.98 0.00 34.67 0.86
262 263 7.764141 TGTGCCGGTACAAGAAGTATATATA 57.236 36.000 23.98 0.00 34.67 0.86
263 264 8.180706 TGTGCCGGTACAAGAAGTATATATAA 57.819 34.615 23.98 0.00 34.67 0.98
264 265 8.301720 TGTGCCGGTACAAGAAGTATATATAAG 58.698 37.037 23.98 0.00 34.67 1.73
265 266 8.517878 GTGCCGGTACAAGAAGTATATATAAGA 58.482 37.037 18.66 0.00 34.67 2.10
266 267 8.737175 TGCCGGTACAAGAAGTATATATAAGAG 58.263 37.037 1.90 0.00 34.67 2.85
267 268 7.701501 GCCGGTACAAGAAGTATATATAAGAGC 59.298 40.741 1.90 0.00 34.67 4.09
268 269 8.189460 CCGGTACAAGAAGTATATATAAGAGCC 58.811 40.741 0.00 0.00 34.67 4.70
269 270 8.737175 CGGTACAAGAAGTATATATAAGAGCCA 58.263 37.037 0.00 0.00 34.67 4.75
273 274 8.097662 ACAAGAAGTATATATAAGAGCCAAGCC 58.902 37.037 0.00 0.00 0.00 4.35
274 275 7.798710 AGAAGTATATATAAGAGCCAAGCCA 57.201 36.000 0.00 0.00 0.00 4.75
275 276 7.616313 AGAAGTATATATAAGAGCCAAGCCAC 58.384 38.462 0.00 0.00 0.00 5.01
276 277 6.935240 AGTATATATAAGAGCCAAGCCACA 57.065 37.500 0.00 0.00 0.00 4.17
277 278 7.502060 AGTATATATAAGAGCCAAGCCACAT 57.498 36.000 0.00 0.00 0.00 3.21
278 279 7.560368 AGTATATATAAGAGCCAAGCCACATC 58.440 38.462 0.00 0.00 0.00 3.06
279 280 4.989875 ATATAAGAGCCAAGCCACATCT 57.010 40.909 0.00 0.00 0.00 2.90
280 281 2.408271 TAAGAGCCAAGCCACATCTG 57.592 50.000 0.00 0.00 0.00 2.90
281 282 0.694771 AAGAGCCAAGCCACATCTGA 59.305 50.000 0.00 0.00 0.00 3.27
282 283 0.035630 AGAGCCAAGCCACATCTGAC 60.036 55.000 0.00 0.00 0.00 3.51
283 284 1.001641 AGCCAAGCCACATCTGACC 60.002 57.895 0.00 0.00 0.00 4.02
284 285 1.001641 GCCAAGCCACATCTGACCT 60.002 57.895 0.00 0.00 0.00 3.85
285 286 0.253044 GCCAAGCCACATCTGACCTA 59.747 55.000 0.00 0.00 0.00 3.08
286 287 1.745141 GCCAAGCCACATCTGACCTAG 60.745 57.143 0.00 0.00 0.00 3.02
287 288 1.661341 CAAGCCACATCTGACCTAGC 58.339 55.000 0.00 0.00 0.00 3.42
288 289 0.543749 AAGCCACATCTGACCTAGCC 59.456 55.000 0.00 0.00 0.00 3.93
289 290 0.326048 AGCCACATCTGACCTAGCCT 60.326 55.000 0.00 0.00 0.00 4.58
290 291 0.543749 GCCACATCTGACCTAGCCTT 59.456 55.000 0.00 0.00 0.00 4.35
291 292 1.762957 GCCACATCTGACCTAGCCTTA 59.237 52.381 0.00 0.00 0.00 2.69
292 293 2.370189 GCCACATCTGACCTAGCCTTAT 59.630 50.000 0.00 0.00 0.00 1.73
293 294 3.181450 GCCACATCTGACCTAGCCTTATT 60.181 47.826 0.00 0.00 0.00 1.40
294 295 4.040461 GCCACATCTGACCTAGCCTTATTA 59.960 45.833 0.00 0.00 0.00 0.98
295 296 5.542779 CCACATCTGACCTAGCCTTATTAC 58.457 45.833 0.00 0.00 0.00 1.89
296 297 5.070446 CCACATCTGACCTAGCCTTATTACA 59.930 44.000 0.00 0.00 0.00 2.41
297 298 6.408092 CCACATCTGACCTAGCCTTATTACAA 60.408 42.308 0.00 0.00 0.00 2.41
298 299 7.047891 CACATCTGACCTAGCCTTATTACAAA 58.952 38.462 0.00 0.00 0.00 2.83
299 300 7.011482 CACATCTGACCTAGCCTTATTACAAAC 59.989 40.741 0.00 0.00 0.00 2.93
300 301 5.985911 TCTGACCTAGCCTTATTACAAACC 58.014 41.667 0.00 0.00 0.00 3.27
301 302 4.761975 TGACCTAGCCTTATTACAAACCG 58.238 43.478 0.00 0.00 0.00 4.44
302 303 4.467082 TGACCTAGCCTTATTACAAACCGA 59.533 41.667 0.00 0.00 0.00 4.69
303 304 5.019785 ACCTAGCCTTATTACAAACCGAG 57.980 43.478 0.00 0.00 0.00 4.63
304 305 4.468868 ACCTAGCCTTATTACAAACCGAGT 59.531 41.667 0.00 0.00 0.00 4.18
305 306 5.658190 ACCTAGCCTTATTACAAACCGAGTA 59.342 40.000 0.00 0.00 0.00 2.59
306 307 6.183360 ACCTAGCCTTATTACAAACCGAGTAG 60.183 42.308 0.00 0.00 0.00 2.57
307 308 5.927281 AGCCTTATTACAAACCGAGTAGA 57.073 39.130 0.00 0.00 0.00 2.59
308 309 6.290294 AGCCTTATTACAAACCGAGTAGAA 57.710 37.500 0.00 0.00 0.00 2.10
309 310 6.338937 AGCCTTATTACAAACCGAGTAGAAG 58.661 40.000 0.00 0.00 0.00 2.85
310 311 6.070938 AGCCTTATTACAAACCGAGTAGAAGT 60.071 38.462 0.00 0.00 0.00 3.01
311 312 6.255237 GCCTTATTACAAACCGAGTAGAAGTC 59.745 42.308 0.00 0.00 0.00 3.01
312 313 7.545489 CCTTATTACAAACCGAGTAGAAGTCT 58.455 38.462 0.00 0.00 0.00 3.24
313 314 8.033626 CCTTATTACAAACCGAGTAGAAGTCTT 58.966 37.037 0.00 0.00 0.00 3.01
317 318 8.976986 TTACAAACCGAGTAGAAGTCTTAATC 57.023 34.615 0.00 0.00 0.00 1.75
318 319 6.396450 ACAAACCGAGTAGAAGTCTTAATCC 58.604 40.000 0.00 0.00 0.00 3.01
319 320 6.210984 ACAAACCGAGTAGAAGTCTTAATCCT 59.789 38.462 0.00 0.00 0.00 3.24
320 321 7.395489 ACAAACCGAGTAGAAGTCTTAATCCTA 59.605 37.037 0.00 0.00 0.00 2.94
321 322 7.951347 AACCGAGTAGAAGTCTTAATCCTAA 57.049 36.000 0.00 0.00 0.00 2.69
322 323 8.536340 AACCGAGTAGAAGTCTTAATCCTAAT 57.464 34.615 0.00 0.00 0.00 1.73
323 324 9.638176 AACCGAGTAGAAGTCTTAATCCTAATA 57.362 33.333 0.00 0.00 0.00 0.98
324 325 9.065798 ACCGAGTAGAAGTCTTAATCCTAATAC 57.934 37.037 0.00 0.00 0.00 1.89
325 326 9.064706 CCGAGTAGAAGTCTTAATCCTAATACA 57.935 37.037 0.00 0.00 0.00 2.29
371 372 1.349067 ACACTACCAGACTGGAACCC 58.651 55.000 28.56 0.00 40.96 4.11
399 400 1.567357 ACCCCAAACAAAAGCACACT 58.433 45.000 0.00 0.00 0.00 3.55
475 476 1.464997 GTTGGATGGACTCACTTTCGC 59.535 52.381 0.00 0.00 0.00 4.70
701 710 2.092323 GCTTTTATCCCCACTGTCACC 58.908 52.381 0.00 0.00 0.00 4.02
704 713 2.233605 TTATCCCCACTGTCACCGCG 62.234 60.000 0.00 0.00 0.00 6.46
733 743 1.602771 CCCCTTTCTTCCCGTCTCC 59.397 63.158 0.00 0.00 0.00 3.71
799 809 1.615124 ATCCGGTCACATCCACCCA 60.615 57.895 0.00 0.00 0.00 4.51
800 810 1.204786 ATCCGGTCACATCCACCCAA 61.205 55.000 0.00 0.00 0.00 4.12
1059 1079 1.705873 ACCCTCTCGATCCGCTTTAT 58.294 50.000 0.00 0.00 0.00 1.40
1080 1100 1.227674 CGGCCCTAGCTAGCTTTGG 60.228 63.158 24.88 23.05 39.73 3.28
1119 1139 1.153188 CTGTGCATATGGTGGCGGA 60.153 57.895 4.56 0.00 0.00 5.54
1377 1397 1.671054 AATCAGCGACCACCAACCG 60.671 57.895 0.00 0.00 0.00 4.44
1402 1422 4.440826 TGCTTAGGCTCTAGCTAGTAGT 57.559 45.455 20.10 6.75 41.70 2.73
1403 1423 5.563876 TGCTTAGGCTCTAGCTAGTAGTA 57.436 43.478 20.10 5.84 41.70 1.82
1404 1424 5.553123 TGCTTAGGCTCTAGCTAGTAGTAG 58.447 45.833 20.10 11.24 41.70 2.57
1427 1447 0.038166 ATCATCACCCCAACTTGCGT 59.962 50.000 0.00 0.00 0.00 5.24
1435 1455 4.368808 CAACTTGCGTCGTGGCGG 62.369 66.667 0.00 0.00 35.06 6.13
1616 1636 2.703409 CGTCCTCGGGTACGTACG 59.297 66.667 18.98 15.01 41.85 3.67
1617 1637 2.100631 CGTCCTCGGGTACGTACGT 61.101 63.158 25.98 25.98 41.85 3.57
1618 1638 0.804544 CGTCCTCGGGTACGTACGTA 60.805 60.000 23.60 23.60 41.85 3.57
1619 1639 0.931005 GTCCTCGGGTACGTACGTAG 59.069 60.000 27.48 17.16 41.85 3.51
1620 1640 0.821517 TCCTCGGGTACGTACGTAGA 59.178 55.000 27.48 19.44 41.85 2.59
1689 1709 4.699735 TGTGGATGCATGGTTAGTAACAAG 59.300 41.667 14.81 5.05 0.00 3.16
1695 1726 3.694072 GCATGGTTAGTAACAAGATGGCA 59.306 43.478 14.81 0.00 0.00 4.92
1698 1729 3.694072 TGGTTAGTAACAAGATGGCATGC 59.306 43.478 9.90 9.90 0.00 4.06
1784 1815 2.434884 ATGCGGTGGAACGAGCTG 60.435 61.111 0.00 0.00 40.89 4.24
2134 2166 0.027979 CATCGGCGGCAACTAACATG 59.972 55.000 10.53 0.00 0.00 3.21
2155 2187 0.807496 GATTCAACTCTGTGCAGGGC 59.193 55.000 0.00 0.00 30.10 5.19
2371 2403 1.133598 CACGAGTAAGTACATCGCCCA 59.866 52.381 8.96 0.00 40.02 5.36
2486 2741 6.844388 ACACCCATTCCTCTCACATAAGTATA 59.156 38.462 0.00 0.00 0.00 1.47
2828 3216 2.040544 CCAGCCAGCCAGTTTACCG 61.041 63.158 0.00 0.00 0.00 4.02
2855 3243 4.820897 ACACACGTATTGATCATGTCACT 58.179 39.130 0.00 0.00 36.32 3.41
2953 3506 1.040646 TCTATGCCAGACCGGTGATC 58.959 55.000 14.63 0.00 36.97 2.92
2954 3507 0.034059 CTATGCCAGACCGGTGATCC 59.966 60.000 14.63 0.00 36.97 3.36
3063 3619 1.738099 CTGACAAAGACGGCTCGGG 60.738 63.158 0.00 0.00 0.00 5.14
3290 3846 3.195396 ACAAATTCAACCAGCACACAACT 59.805 39.130 0.00 0.00 0.00 3.16
3294 3850 2.778299 TCAACCAGCACACAACTATCC 58.222 47.619 0.00 0.00 0.00 2.59
3327 3916 7.463469 ACAAAACACGAGGAAATTCAAATTC 57.537 32.000 0.00 0.00 0.00 2.17
3328 3917 7.038659 ACAAAACACGAGGAAATTCAAATTCA 58.961 30.769 0.00 0.00 0.00 2.57
3329 3918 7.547370 ACAAAACACGAGGAAATTCAAATTCAA 59.453 29.630 0.00 0.00 0.00 2.69
3330 3919 8.386606 CAAAACACGAGGAAATTCAAATTCAAA 58.613 29.630 0.00 0.00 0.00 2.69
3331 3920 8.661352 AAACACGAGGAAATTCAAATTCAAAT 57.339 26.923 0.00 0.00 0.00 2.32
3771 4360 4.065281 GGGAGGACGACCACACGG 62.065 72.222 6.71 0.00 38.94 4.94
3836 4431 0.530211 GCAATGGCTGTGCACAAACA 60.530 50.000 21.98 21.44 41.80 2.83
3875 4472 8.619146 AAAATCATTTTCGTCGATAGTACGTA 57.381 30.769 0.00 0.00 41.08 3.57
3920 4519 5.936372 CCATCTGTTCTGTTTCTTCTGATCA 59.064 40.000 0.00 0.00 0.00 2.92
3961 4560 1.854227 GCACAAGCTAGGATACGGAC 58.146 55.000 0.00 0.00 39.07 4.79
3970 4569 3.311596 GCTAGGATACGGACGCAATTTTT 59.688 43.478 0.00 0.00 46.39 1.94
4109 4710 2.349886 GAGTTGTCGCTGCTAAATCCTG 59.650 50.000 0.00 0.00 0.00 3.86
4139 4740 0.321564 TGGGACTTTGTCGCCATGAG 60.322 55.000 11.27 0.00 43.42 2.90
4151 4752 2.158769 TCGCCATGAGCAACCTTCATAT 60.159 45.455 0.00 0.00 44.04 1.78
4263 4874 8.473358 ACTACTAATTTACAGGCTTTGGTTTT 57.527 30.769 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.109919 GCAAAAACCCTAAGTCGCCG 60.110 55.000 0.00 0.00 0.00 6.46
2 3 3.786809 GGCAAAAACCCTAAGTCGC 57.213 52.632 0.00 0.00 0.00 5.19
11 12 0.315886 CAACTACCGGGGCAAAAACC 59.684 55.000 6.32 0.00 0.00 3.27
12 13 0.315886 CCAACTACCGGGGCAAAAAC 59.684 55.000 6.32 0.00 0.00 2.43
13 14 0.828343 CCCAACTACCGGGGCAAAAA 60.828 55.000 6.32 0.00 40.35 1.94
14 15 1.228613 CCCAACTACCGGGGCAAAA 60.229 57.895 6.32 0.00 40.35 2.44
15 16 2.154747 TCCCAACTACCGGGGCAAA 61.155 57.895 6.32 0.00 44.62 3.68
16 17 2.529643 TCCCAACTACCGGGGCAA 60.530 61.111 6.32 0.00 44.62 4.52
19 20 1.298667 CAAGTCCCAACTACCGGGG 59.701 63.158 6.32 0.00 44.62 5.73
20 21 1.196104 TCCAAGTCCCAACTACCGGG 61.196 60.000 6.32 0.00 46.03 5.73
21 22 0.036671 GTCCAAGTCCCAACTACCGG 60.037 60.000 0.00 0.00 33.48 5.28
22 23 0.389426 CGTCCAAGTCCCAACTACCG 60.389 60.000 0.00 0.00 33.48 4.02
23 24 0.672711 GCGTCCAAGTCCCAACTACC 60.673 60.000 0.00 0.00 33.48 3.18
24 25 0.672711 GGCGTCCAAGTCCCAACTAC 60.673 60.000 0.00 0.00 33.48 2.73
25 26 1.122632 TGGCGTCCAAGTCCCAACTA 61.123 55.000 0.00 0.00 33.48 2.24
26 27 2.397413 CTGGCGTCCAAGTCCCAACT 62.397 60.000 0.35 0.00 37.32 3.16
27 28 1.966451 CTGGCGTCCAAGTCCCAAC 60.966 63.158 0.35 0.00 30.80 3.77
28 29 2.429930 CTGGCGTCCAAGTCCCAA 59.570 61.111 0.35 0.00 30.80 4.12
29 30 4.329545 GCTGGCGTCCAAGTCCCA 62.330 66.667 0.35 0.00 30.80 4.37
34 35 4.473520 ATCCGGCTGGCGTCCAAG 62.474 66.667 22.22 6.67 30.80 3.61
35 36 4.776322 CATCCGGCTGGCGTCCAA 62.776 66.667 22.22 5.37 30.80 3.53
38 39 4.778143 AACCATCCGGCTGGCGTC 62.778 66.667 24.24 0.00 40.15 5.19
40 41 4.776322 TCAACCATCCGGCTGGCG 62.776 66.667 24.24 17.39 40.15 5.69
41 42 2.825836 CTCAACCATCCGGCTGGC 60.826 66.667 24.24 0.00 40.15 4.85
42 43 2.124570 CCTCAACCATCCGGCTGG 60.125 66.667 22.80 22.80 42.35 4.85
43 44 1.153289 CTCCTCAACCATCCGGCTG 60.153 63.158 0.00 0.00 34.57 4.85
44 45 2.370445 CCTCCTCAACCATCCGGCT 61.370 63.158 0.00 0.00 34.57 5.52
45 46 2.190578 CCTCCTCAACCATCCGGC 59.809 66.667 0.00 0.00 34.57 6.13
46 47 1.221840 CACCTCCTCAACCATCCGG 59.778 63.158 0.00 0.00 38.77 5.14
47 48 1.450312 GCACCTCCTCAACCATCCG 60.450 63.158 0.00 0.00 0.00 4.18
48 49 0.393537 CAGCACCTCCTCAACCATCC 60.394 60.000 0.00 0.00 0.00 3.51
49 50 0.326264 ACAGCACCTCCTCAACCATC 59.674 55.000 0.00 0.00 0.00 3.51
50 51 0.773644 AACAGCACCTCCTCAACCAT 59.226 50.000 0.00 0.00 0.00 3.55
51 52 0.179020 CAACAGCACCTCCTCAACCA 60.179 55.000 0.00 0.00 0.00 3.67
52 53 0.890996 CCAACAGCACCTCCTCAACC 60.891 60.000 0.00 0.00 0.00 3.77
53 54 0.179018 ACCAACAGCACCTCCTCAAC 60.179 55.000 0.00 0.00 0.00 3.18
54 55 0.179020 CACCAACAGCACCTCCTCAA 60.179 55.000 0.00 0.00 0.00 3.02
55 56 1.451504 CACCAACAGCACCTCCTCA 59.548 57.895 0.00 0.00 0.00 3.86
56 57 1.302832 CCACCAACAGCACCTCCTC 60.303 63.158 0.00 0.00 0.00 3.71
57 58 1.770110 TCCACCAACAGCACCTCCT 60.770 57.895 0.00 0.00 0.00 3.69
58 59 1.302832 CTCCACCAACAGCACCTCC 60.303 63.158 0.00 0.00 0.00 4.30
59 60 1.302832 CCTCCACCAACAGCACCTC 60.303 63.158 0.00 0.00 0.00 3.85
60 61 2.078665 ACCTCCACCAACAGCACCT 61.079 57.895 0.00 0.00 0.00 4.00
61 62 1.898574 CACCTCCACCAACAGCACC 60.899 63.158 0.00 0.00 0.00 5.01
62 63 1.148273 TCACCTCCACCAACAGCAC 59.852 57.895 0.00 0.00 0.00 4.40
63 64 1.148273 GTCACCTCCACCAACAGCA 59.852 57.895 0.00 0.00 0.00 4.41
64 65 1.961277 CGTCACCTCCACCAACAGC 60.961 63.158 0.00 0.00 0.00 4.40
65 66 1.301716 CCGTCACCTCCACCAACAG 60.302 63.158 0.00 0.00 0.00 3.16
66 67 2.825982 CCGTCACCTCCACCAACA 59.174 61.111 0.00 0.00 0.00 3.33
67 68 2.668550 GCCGTCACCTCCACCAAC 60.669 66.667 0.00 0.00 0.00 3.77
68 69 4.308458 CGCCGTCACCTCCACCAA 62.308 66.667 0.00 0.00 0.00 3.67
98 99 4.521062 CTTCTCCTCGCCCGCCTG 62.521 72.222 0.00 0.00 0.00 4.85
102 103 3.764466 ACTGCTTCTCCTCGCCCG 61.764 66.667 0.00 0.00 0.00 6.13
103 104 2.125350 CACTGCTTCTCCTCGCCC 60.125 66.667 0.00 0.00 0.00 6.13
104 105 2.817396 GCACTGCTTCTCCTCGCC 60.817 66.667 0.00 0.00 0.00 5.54
105 106 3.184683 CGCACTGCTTCTCCTCGC 61.185 66.667 0.00 0.00 0.00 5.03
106 107 3.184683 GCGCACTGCTTCTCCTCG 61.185 66.667 0.30 0.00 41.73 4.63
107 108 2.817396 GGCGCACTGCTTCTCCTC 60.817 66.667 10.83 0.00 45.43 3.71
108 109 4.749310 CGGCGCACTGCTTCTCCT 62.749 66.667 10.83 0.00 45.43 3.69
163 164 2.112507 GGGTATGGCTAACCCGCC 59.887 66.667 11.36 0.00 46.95 6.13
167 168 2.496470 CGATCCTAGGGTATGGCTAACC 59.504 54.545 9.46 0.73 34.60 2.85
168 169 3.428532 TCGATCCTAGGGTATGGCTAAC 58.571 50.000 9.46 0.00 0.00 2.34
169 170 3.820195 TCGATCCTAGGGTATGGCTAA 57.180 47.619 9.46 0.00 0.00 3.09
170 171 3.820195 TTCGATCCTAGGGTATGGCTA 57.180 47.619 9.46 0.00 0.00 3.93
171 172 2.696526 TTCGATCCTAGGGTATGGCT 57.303 50.000 9.46 0.00 0.00 4.75
172 173 2.633481 ACTTTCGATCCTAGGGTATGGC 59.367 50.000 9.46 0.00 0.00 4.40
173 174 4.021894 CAGACTTTCGATCCTAGGGTATGG 60.022 50.000 9.46 0.00 0.00 2.74
174 175 4.827835 TCAGACTTTCGATCCTAGGGTATG 59.172 45.833 9.46 4.70 0.00 2.39
175 176 5.063017 TCAGACTTTCGATCCTAGGGTAT 57.937 43.478 9.46 0.00 0.00 2.73
176 177 4.515028 TCAGACTTTCGATCCTAGGGTA 57.485 45.455 9.46 0.00 0.00 3.69
177 178 3.383698 TCAGACTTTCGATCCTAGGGT 57.616 47.619 9.46 0.00 0.00 4.34
178 179 4.218852 GGTATCAGACTTTCGATCCTAGGG 59.781 50.000 9.46 0.00 0.00 3.53
179 180 4.827835 TGGTATCAGACTTTCGATCCTAGG 59.172 45.833 0.82 0.82 0.00 3.02
180 181 6.015856 ACATGGTATCAGACTTTCGATCCTAG 60.016 42.308 0.00 0.00 0.00 3.02
181 182 5.833667 ACATGGTATCAGACTTTCGATCCTA 59.166 40.000 0.00 0.00 0.00 2.94
182 183 4.651503 ACATGGTATCAGACTTTCGATCCT 59.348 41.667 0.00 0.00 0.00 3.24
183 184 4.950050 ACATGGTATCAGACTTTCGATCC 58.050 43.478 0.00 0.00 0.00 3.36
184 185 6.971602 TCTACATGGTATCAGACTTTCGATC 58.028 40.000 0.00 0.00 0.00 3.69
185 186 6.961360 TCTACATGGTATCAGACTTTCGAT 57.039 37.500 0.00 0.00 0.00 3.59
186 187 6.769134 TTCTACATGGTATCAGACTTTCGA 57.231 37.500 0.00 0.00 0.00 3.71
187 188 7.492669 ACAATTCTACATGGTATCAGACTTTCG 59.507 37.037 0.00 0.00 0.00 3.46
188 189 8.723942 ACAATTCTACATGGTATCAGACTTTC 57.276 34.615 0.00 0.00 0.00 2.62
191 192 9.770097 CAATACAATTCTACATGGTATCAGACT 57.230 33.333 0.00 0.00 0.00 3.24
192 193 9.764363 TCAATACAATTCTACATGGTATCAGAC 57.236 33.333 0.00 0.00 0.00 3.51
224 225 4.265893 ACCGGCACAATATTGTATCAACA 58.734 39.130 20.39 0.00 39.91 3.33
225 226 4.893424 ACCGGCACAATATTGTATCAAC 57.107 40.909 20.39 8.15 39.91 3.18
226 227 5.429130 TGTACCGGCACAATATTGTATCAA 58.571 37.500 20.39 2.63 39.91 2.57
227 228 5.024785 TGTACCGGCACAATATTGTATCA 57.975 39.130 20.39 9.27 39.91 2.15
228 229 5.756347 TCTTGTACCGGCACAATATTGTATC 59.244 40.000 20.40 14.47 39.91 2.24
229 230 5.676552 TCTTGTACCGGCACAATATTGTAT 58.323 37.500 20.40 7.13 39.91 2.29
230 231 5.087391 TCTTGTACCGGCACAATATTGTA 57.913 39.130 20.40 1.55 39.91 2.41
231 232 3.945346 TCTTGTACCGGCACAATATTGT 58.055 40.909 20.40 15.47 43.36 2.71
232 233 4.394920 ACTTCTTGTACCGGCACAATATTG 59.605 41.667 20.40 14.01 37.75 1.90
233 234 4.585879 ACTTCTTGTACCGGCACAATATT 58.414 39.130 20.40 4.12 37.75 1.28
234 235 4.216411 ACTTCTTGTACCGGCACAATAT 57.784 40.909 20.40 4.20 37.75 1.28
235 236 3.688694 ACTTCTTGTACCGGCACAATA 57.311 42.857 20.40 11.02 37.75 1.90
236 237 2.561478 ACTTCTTGTACCGGCACAAT 57.439 45.000 20.40 3.07 37.75 2.71
237 238 3.688694 ATACTTCTTGTACCGGCACAA 57.311 42.857 19.09 19.09 36.94 3.33
238 239 6.659745 ATATATACTTCTTGTACCGGCACA 57.340 37.500 2.48 2.48 33.45 4.57
239 240 8.517878 TCTTATATATACTTCTTGTACCGGCAC 58.482 37.037 0.00 0.00 33.45 5.01
240 241 8.640063 TCTTATATATACTTCTTGTACCGGCA 57.360 34.615 0.00 0.00 33.45 5.69
241 242 7.701501 GCTCTTATATATACTTCTTGTACCGGC 59.298 40.741 0.00 0.00 33.45 6.13
242 243 8.189460 GGCTCTTATATATACTTCTTGTACCGG 58.811 40.741 0.00 0.00 33.45 5.28
243 244 8.737175 TGGCTCTTATATATACTTCTTGTACCG 58.263 37.037 0.00 0.00 33.45 4.02
247 248 8.097662 GGCTTGGCTCTTATATATACTTCTTGT 58.902 37.037 0.00 0.00 0.00 3.16
248 249 8.097038 TGGCTTGGCTCTTATATATACTTCTTG 58.903 37.037 0.00 0.00 0.00 3.02
249 250 8.097662 GTGGCTTGGCTCTTATATATACTTCTT 58.902 37.037 0.00 0.00 0.00 2.52
250 251 7.235606 TGTGGCTTGGCTCTTATATATACTTCT 59.764 37.037 0.00 0.00 0.00 2.85
251 252 7.386851 TGTGGCTTGGCTCTTATATATACTTC 58.613 38.462 0.00 0.00 0.00 3.01
252 253 7.316393 TGTGGCTTGGCTCTTATATATACTT 57.684 36.000 0.00 0.00 0.00 2.24
253 254 6.935240 TGTGGCTTGGCTCTTATATATACT 57.065 37.500 0.00 0.00 0.00 2.12
254 255 7.493971 CAGATGTGGCTTGGCTCTTATATATAC 59.506 40.741 0.00 0.00 0.00 1.47
255 256 7.400052 TCAGATGTGGCTTGGCTCTTATATATA 59.600 37.037 0.00 0.00 0.00 0.86
256 257 6.214208 TCAGATGTGGCTTGGCTCTTATATAT 59.786 38.462 0.00 0.00 0.00 0.86
257 258 5.543790 TCAGATGTGGCTTGGCTCTTATATA 59.456 40.000 0.00 0.00 0.00 0.86
258 259 4.349048 TCAGATGTGGCTTGGCTCTTATAT 59.651 41.667 0.00 0.00 0.00 0.86
259 260 3.711190 TCAGATGTGGCTTGGCTCTTATA 59.289 43.478 0.00 0.00 0.00 0.98
260 261 2.507058 TCAGATGTGGCTTGGCTCTTAT 59.493 45.455 0.00 0.00 0.00 1.73
261 262 1.908619 TCAGATGTGGCTTGGCTCTTA 59.091 47.619 0.00 0.00 0.00 2.10
262 263 0.694771 TCAGATGTGGCTTGGCTCTT 59.305 50.000 0.00 0.00 0.00 2.85
263 264 0.035630 GTCAGATGTGGCTTGGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
264 265 1.028868 GGTCAGATGTGGCTTGGCTC 61.029 60.000 0.00 0.00 0.00 4.70
265 266 1.001641 GGTCAGATGTGGCTTGGCT 60.002 57.895 0.00 0.00 0.00 4.75
266 267 0.253044 TAGGTCAGATGTGGCTTGGC 59.747 55.000 0.00 0.00 0.00 4.52
267 268 1.745141 GCTAGGTCAGATGTGGCTTGG 60.745 57.143 0.00 0.00 0.00 3.61
268 269 1.661341 GCTAGGTCAGATGTGGCTTG 58.339 55.000 0.00 0.00 0.00 4.01
269 270 0.543749 GGCTAGGTCAGATGTGGCTT 59.456 55.000 0.00 0.00 0.00 4.35
270 271 0.326048 AGGCTAGGTCAGATGTGGCT 60.326 55.000 0.00 0.00 0.00 4.75
271 272 0.543749 AAGGCTAGGTCAGATGTGGC 59.456 55.000 0.00 0.00 0.00 5.01
272 273 4.696479 AATAAGGCTAGGTCAGATGTGG 57.304 45.455 0.00 0.00 0.00 4.17
273 274 6.161855 TGTAATAAGGCTAGGTCAGATGTG 57.838 41.667 0.00 0.00 0.00 3.21
274 275 6.808321 TTGTAATAAGGCTAGGTCAGATGT 57.192 37.500 0.00 0.00 0.00 3.06
275 276 6.483640 GGTTTGTAATAAGGCTAGGTCAGATG 59.516 42.308 0.00 0.00 0.00 2.90
276 277 6.592870 GGTTTGTAATAAGGCTAGGTCAGAT 58.407 40.000 0.00 0.00 0.00 2.90
277 278 5.394883 CGGTTTGTAATAAGGCTAGGTCAGA 60.395 44.000 0.00 0.00 0.00 3.27
278 279 4.809426 CGGTTTGTAATAAGGCTAGGTCAG 59.191 45.833 0.00 0.00 0.00 3.51
279 280 4.467082 TCGGTTTGTAATAAGGCTAGGTCA 59.533 41.667 0.00 0.00 0.00 4.02
280 281 5.014808 TCGGTTTGTAATAAGGCTAGGTC 57.985 43.478 0.00 0.00 0.00 3.85
281 282 4.468868 ACTCGGTTTGTAATAAGGCTAGGT 59.531 41.667 0.00 0.00 0.00 3.08
282 283 5.019785 ACTCGGTTTGTAATAAGGCTAGG 57.980 43.478 0.00 0.00 0.00 3.02
283 284 7.035840 TCTACTCGGTTTGTAATAAGGCTAG 57.964 40.000 0.00 0.00 0.00 3.42
284 285 7.123247 ACTTCTACTCGGTTTGTAATAAGGCTA 59.877 37.037 0.00 0.00 0.00 3.93
285 286 5.927281 TCTACTCGGTTTGTAATAAGGCT 57.073 39.130 0.00 0.00 0.00 4.58
286 287 6.104665 ACTTCTACTCGGTTTGTAATAAGGC 58.895 40.000 0.00 0.00 0.00 4.35
287 288 7.545489 AGACTTCTACTCGGTTTGTAATAAGG 58.455 38.462 0.00 0.00 0.00 2.69
288 289 8.983307 AAGACTTCTACTCGGTTTGTAATAAG 57.017 34.615 0.00 0.00 0.00 1.73
291 292 9.583765 GATTAAGACTTCTACTCGGTTTGTAAT 57.416 33.333 0.00 0.00 0.00 1.89
292 293 8.031277 GGATTAAGACTTCTACTCGGTTTGTAA 58.969 37.037 0.00 0.00 0.00 2.41
293 294 7.395489 AGGATTAAGACTTCTACTCGGTTTGTA 59.605 37.037 0.00 0.00 0.00 2.41
294 295 6.210984 AGGATTAAGACTTCTACTCGGTTTGT 59.789 38.462 0.00 0.00 0.00 2.83
295 296 6.631962 AGGATTAAGACTTCTACTCGGTTTG 58.368 40.000 0.00 0.00 0.00 2.93
296 297 6.854091 AGGATTAAGACTTCTACTCGGTTT 57.146 37.500 0.00 0.00 0.00 3.27
297 298 7.951347 TTAGGATTAAGACTTCTACTCGGTT 57.049 36.000 0.00 0.00 0.00 4.44
298 299 9.065798 GTATTAGGATTAAGACTTCTACTCGGT 57.934 37.037 0.00 0.00 30.25 4.69
299 300 9.064706 TGTATTAGGATTAAGACTTCTACTCGG 57.935 37.037 0.00 0.00 33.27 4.63
328 329 9.137459 TGTTCTGGGAATTTTGTTAGAATACAA 57.863 29.630 0.00 0.00 36.30 2.41
329 330 8.573035 GTGTTCTGGGAATTTTGTTAGAATACA 58.427 33.333 0.00 0.00 36.73 2.29
330 331 8.793592 AGTGTTCTGGGAATTTTGTTAGAATAC 58.206 33.333 0.00 0.00 36.88 1.89
331 332 8.934023 AGTGTTCTGGGAATTTTGTTAGAATA 57.066 30.769 0.00 0.00 0.00 1.75
332 333 7.839680 AGTGTTCTGGGAATTTTGTTAGAAT 57.160 32.000 0.00 0.00 0.00 2.40
333 334 7.229907 GGTAGTGTTCTGGGAATTTTGTTAGAA 59.770 37.037 0.00 0.00 0.00 2.10
334 335 6.713450 GGTAGTGTTCTGGGAATTTTGTTAGA 59.287 38.462 0.00 0.00 0.00 2.10
335 336 6.488683 TGGTAGTGTTCTGGGAATTTTGTTAG 59.511 38.462 0.00 0.00 0.00 2.34
336 337 6.366340 TGGTAGTGTTCTGGGAATTTTGTTA 58.634 36.000 0.00 0.00 0.00 2.41
337 338 5.205056 TGGTAGTGTTCTGGGAATTTTGTT 58.795 37.500 0.00 0.00 0.00 2.83
338 339 4.798882 TGGTAGTGTTCTGGGAATTTTGT 58.201 39.130 0.00 0.00 0.00 2.83
339 340 5.048713 GTCTGGTAGTGTTCTGGGAATTTTG 60.049 44.000 0.00 0.00 0.00 2.44
340 341 5.070685 GTCTGGTAGTGTTCTGGGAATTTT 58.929 41.667 0.00 0.00 0.00 1.82
371 372 4.814234 GCTTTTGTTTGGGGTTAGGAAAAG 59.186 41.667 0.00 0.00 33.86 2.27
399 400 4.380531 AGAGTTGCTCTTGATCGTTTTCA 58.619 39.130 0.00 0.00 37.60 2.69
475 476 2.901840 ACTGGTGTGCTGTTGCCG 60.902 61.111 0.00 0.00 38.71 5.69
704 713 0.691413 AGAAAGGGGGAGGATCGGTC 60.691 60.000 0.00 0.00 34.37 4.79
799 809 0.796312 CAAATCGTGCCACTACGCTT 59.204 50.000 0.00 0.00 43.40 4.68
800 810 0.320421 ACAAATCGTGCCACTACGCT 60.320 50.000 0.00 0.00 43.40 5.07
1059 1079 2.891307 AAAGCTAGCTAGGGCCGGGA 62.891 60.000 19.70 0.00 39.73 5.14
1119 1139 2.743718 CTCGGCCACAGAACCTGT 59.256 61.111 2.24 0.00 46.51 4.00
1349 1369 1.207390 GTCGCTGATTGAGCTAGCAG 58.793 55.000 18.83 5.24 46.64 4.24
1402 1422 4.686944 GCAAGTTGGGGTGATGATGATCTA 60.687 45.833 4.75 0.00 0.00 1.98
1403 1423 3.894759 CAAGTTGGGGTGATGATGATCT 58.105 45.455 0.00 0.00 0.00 2.75
1404 1424 2.360165 GCAAGTTGGGGTGATGATGATC 59.640 50.000 4.75 0.00 0.00 2.92
1435 1455 0.681175 AAAAACCAGCATGCACTCCC 59.319 50.000 21.98 0.00 31.97 4.30
1616 1636 3.933332 ACTGCTCGCTTGGTAATTTCTAC 59.067 43.478 0.00 0.00 0.00 2.59
1617 1637 3.932710 CACTGCTCGCTTGGTAATTTCTA 59.067 43.478 0.00 0.00 0.00 2.10
1618 1638 2.744202 CACTGCTCGCTTGGTAATTTCT 59.256 45.455 0.00 0.00 0.00 2.52
1619 1639 2.742053 TCACTGCTCGCTTGGTAATTTC 59.258 45.455 0.00 0.00 0.00 2.17
1620 1640 2.484264 GTCACTGCTCGCTTGGTAATTT 59.516 45.455 0.00 0.00 0.00 1.82
1689 1709 0.382873 TGAAATCTGCGCATGCCATC 59.617 50.000 12.24 6.98 41.78 3.51
1695 1726 0.254178 ACCTCCTGAAATCTGCGCAT 59.746 50.000 12.24 0.00 0.00 4.73
1698 1729 0.036010 ACCACCTCCTGAAATCTGCG 60.036 55.000 0.00 0.00 0.00 5.18
2134 2166 2.354259 CCCTGCACAGAGTTGAATCTC 58.646 52.381 0.00 0.00 34.96 2.75
2155 2187 4.657824 AACCTCACGGACACGGCG 62.658 66.667 4.80 4.80 46.48 6.46
2371 2403 1.467374 GGCACGCACGAAAATAATGCT 60.467 47.619 0.00 0.00 37.20 3.79
2458 2713 1.548719 TGTGAGAGGAATGGGTGTACG 59.451 52.381 0.00 0.00 0.00 3.67
2521 2776 3.610637 CCAAATGTTGGCAAGGGTG 57.389 52.632 0.00 0.00 45.17 4.61
2732 3110 1.084289 GTGCAACCACCGGATAAGAC 58.916 55.000 9.46 0.00 35.92 3.01
2828 3216 4.566759 ACATGATCAATACGTGTGTACAGC 59.433 41.667 0.00 0.00 36.35 4.40
2855 3243 3.117812 CGTGCCTACGTGCATGCA 61.118 61.111 18.46 18.46 44.30 3.96
2953 3506 4.837093 TTTCATACTACCACTTCCCTGG 57.163 45.455 0.00 0.00 37.33 4.45
2954 3507 7.016661 AGGATATTTCATACTACCACTTCCCTG 59.983 40.741 0.00 0.00 0.00 4.45
3045 3601 1.738099 CCCGAGCCGTCTTTGTCAG 60.738 63.158 0.00 0.00 0.00 3.51
3089 3645 1.471676 GGTCAAGGTCTACCGCATCAG 60.472 57.143 0.00 0.00 42.08 2.90
3247 3803 1.374758 CTGGTCGTTGTCCAGGAGC 60.375 63.158 0.00 0.00 46.03 4.70
3290 3846 8.095792 TCCTCGTGTTTTGTAATAAGTTGGATA 58.904 33.333 0.00 0.00 0.00 2.59
3294 3850 9.458374 AATTTCCTCGTGTTTTGTAATAAGTTG 57.542 29.630 0.00 0.00 0.00 3.16
3344 3933 7.929245 ACAACCAAATCACCCATAAGTTTTTAC 59.071 33.333 0.00 0.00 0.00 2.01
3366 3955 0.848305 CGCAGCTGCAAAAGAACAAC 59.152 50.000 36.03 4.51 42.21 3.32
3509 4098 0.673644 GCTTCAGCTTGTCGCCCTTA 60.674 55.000 0.00 0.00 40.39 2.69
3782 4371 1.860950 CAAACATCCTCGGCGTATCTG 59.139 52.381 6.85 3.79 0.00 2.90
3875 4472 5.529289 TGGAGGATGGATCTTTACTACTGT 58.471 41.667 0.00 0.00 0.00 3.55
3920 4519 4.098654 GCTGTAGACATGTATGGACACTCT 59.901 45.833 2.50 0.00 38.76 3.24
3961 4560 0.320334 GGGTGTGGGGAAAAATTGCG 60.320 55.000 0.00 0.00 0.00 4.85
3970 4569 3.869934 AGGGACAGGGTGTGGGGA 61.870 66.667 0.00 0.00 0.00 4.81
4100 4699 4.697352 CCCATATTTCCTCGCAGGATTTAG 59.303 45.833 5.83 0.00 45.34 1.85
4109 4710 3.279434 ACAAAGTCCCATATTTCCTCGC 58.721 45.455 0.00 0.00 0.00 5.03
4139 4740 7.502120 ACATCAACTGATATATGAAGGTTGC 57.498 36.000 0.00 0.00 35.48 4.17
4151 4752 6.127451 ACCACTCATTCGTACATCAACTGATA 60.127 38.462 0.00 0.00 32.63 2.15


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

AutoCloner maintained by Alex Coulton.