Multiple sequence alignment - TraesCS5D01G342700

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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 TraesCS5D01G342700 chr5D 100.000 3326 0 0 1 3326 430967654 430970979 0.000000e+00 6143.0
1 TraesCS5D01G342700 chr5D 93.328 1334 83 4 993 2326 430985526 430986853 0.000000e+00 1965.0
2 TraesCS5D01G342700 chr5D 79.297 1338 230 33 1001 2322 407517493 407518799 0.000000e+00 893.0
3 TraesCS5D01G342700 chr5D 93.405 561 32 5 2771 3326 128586683 128586123 0.000000e+00 826.0
4 TraesCS5D01G342700 chr5D 76.572 1336 264 36 1001 2322 430164063 430165363 0.000000e+00 688.0
5 TraesCS5D01G342700 chr5D 84.202 652 97 4 1674 2322 430512300 430512948 2.180000e-176 628.0
6 TraesCS5D01G342700 chr5D 83.920 653 95 7 1674 2321 430446197 430446844 1.700000e-172 616.0
7 TraesCS5D01G342700 chr5D 89.623 106 8 3 2598 2702 115608716 115608613 7.490000e-27 132.0
8 TraesCS5D01G342700 chr5A 92.205 2386 137 25 272 2634 546344122 546346481 0.000000e+00 3330.0
9 TraesCS5D01G342700 chr5A 92.125 1346 100 1 993 2338 546360329 546361668 0.000000e+00 1893.0
10 TraesCS5D01G342700 chr5A 76.541 1330 275 25 1001 2322 545984620 545985920 0.000000e+00 693.0
11 TraesCS5D01G342700 chr5A 76.998 1239 238 30 1097 2322 546154313 546155517 0.000000e+00 665.0
12 TraesCS5D01G342700 chr5A 93.269 104 7 0 3 106 546343963 546344066 1.600000e-33 154.0
13 TraesCS5D01G342700 chr5B 93.815 2021 71 10 360 2354 520368954 520370946 0.000000e+00 2990.0
14 TraesCS5D01G342700 chr5B 94.828 1334 69 0 993 2326 520419360 520420693 0.000000e+00 2082.0
15 TraesCS5D01G342700 chr5B 76.343 1340 260 34 1001 2322 519661047 519662347 0.000000e+00 665.0
16 TraesCS5D01G342700 chr5B 76.030 1335 273 33 1001 2322 520036809 520038109 0.000000e+00 649.0
17 TraesCS5D01G342700 chr5B 90.045 221 7 7 2345 2559 520371337 520371548 4.230000e-69 272.0
18 TraesCS5D01G342700 chr6D 93.440 564 33 4 2767 3326 374103600 374104163 0.000000e+00 833.0
19 TraesCS5D01G342700 chr1D 93.393 560 34 3 2769 3326 413227459 413228017 0.000000e+00 826.0
20 TraesCS5D01G342700 chr1D 94.318 88 5 0 2598 2685 219321336 219321423 5.790000e-28 135.0
21 TraesCS5D01G342700 chr1D 94.382 89 4 1 2598 2685 437080431 437080519 5.790000e-28 135.0
22 TraesCS5D01G342700 chr4D 93.202 559 34 4 2771 3326 19347372 19346815 0.000000e+00 819.0
23 TraesCS5D01G342700 chr4D 94.444 90 4 1 2602 2690 371601297 371601208 1.610000e-28 137.0
24 TraesCS5D01G342700 chr2D 93.202 559 34 4 2771 3326 399427343 399427900 0.000000e+00 819.0
25 TraesCS5D01G342700 chr7D 92.718 563 38 3 2767 3326 583072595 583073157 0.000000e+00 809.0
26 TraesCS5D01G342700 chr7D 92.692 561 39 2 2768 3326 40735556 40736116 0.000000e+00 808.0
27 TraesCS5D01G342700 chr7D 92.718 563 36 4 2767 3326 635996871 635996311 0.000000e+00 808.0
28 TraesCS5D01G342700 chr7D 79.292 367 47 11 1623 1989 597267349 597267012 2.580000e-56 230.0
29 TraesCS5D01G342700 chr2B 92.267 569 39 5 2763 3326 117071621 117072189 0.000000e+00 802.0
30 TraesCS5D01G342700 chr3B 85.450 378 54 1 1613 1990 323317038 323316662 3.110000e-105 392.0
31 TraesCS5D01G342700 chr3B 94.565 92 3 2 2602 2691 590683115 590683206 1.240000e-29 141.0
32 TraesCS5D01G342700 chr3B 88.679 106 9 3 2598 2702 329633054 329633157 3.480000e-25 126.0
33 TraesCS5D01G342700 chr1A 89.524 105 9 2 2598 2702 92272706 92272604 7.490000e-27 132.0
34 TraesCS5D01G342700 chr1B 88.679 106 9 3 2598 2702 671106623 671106726 3.480000e-25 126.0
35 TraesCS5D01G342700 chr6B 87.963 108 9 4 2581 2685 416897303 416897409 1.250000e-24 124.0
36 TraesCS5D01G342700 chr6A 86.364 110 13 2 3 112 36401305 36401198 5.830000e-23 119.0
37 TraesCS5D01G342700 chr3A 81.132 106 18 2 8 112 361611369 361611473 2.130000e-12 84.2


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 TraesCS5D01G342700 chr5D 430967654 430970979 3325 False 6143 6143 100.000 1 3326 1 chr5D.!!$F5 3325
1 TraesCS5D01G342700 chr5D 430985526 430986853 1327 False 1965 1965 93.328 993 2326 1 chr5D.!!$F6 1333
2 TraesCS5D01G342700 chr5D 407517493 407518799 1306 False 893 893 79.297 1001 2322 1 chr5D.!!$F1 1321
3 TraesCS5D01G342700 chr5D 128586123 128586683 560 True 826 826 93.405 2771 3326 1 chr5D.!!$R2 555
4 TraesCS5D01G342700 chr5D 430164063 430165363 1300 False 688 688 76.572 1001 2322 1 chr5D.!!$F2 1321
5 TraesCS5D01G342700 chr5D 430512300 430512948 648 False 628 628 84.202 1674 2322 1 chr5D.!!$F4 648
6 TraesCS5D01G342700 chr5D 430446197 430446844 647 False 616 616 83.920 1674 2321 1 chr5D.!!$F3 647
7 TraesCS5D01G342700 chr5A 546360329 546361668 1339 False 1893 1893 92.125 993 2338 1 chr5A.!!$F3 1345
8 TraesCS5D01G342700 chr5A 546343963 546346481 2518 False 1742 3330 92.737 3 2634 2 chr5A.!!$F4 2631
9 TraesCS5D01G342700 chr5A 545984620 545985920 1300 False 693 693 76.541 1001 2322 1 chr5A.!!$F1 1321
10 TraesCS5D01G342700 chr5A 546154313 546155517 1204 False 665 665 76.998 1097 2322 1 chr5A.!!$F2 1225
11 TraesCS5D01G342700 chr5B 520419360 520420693 1333 False 2082 2082 94.828 993 2326 1 chr5B.!!$F3 1333
12 TraesCS5D01G342700 chr5B 520368954 520371548 2594 False 1631 2990 91.930 360 2559 2 chr5B.!!$F4 2199
13 TraesCS5D01G342700 chr5B 519661047 519662347 1300 False 665 665 76.343 1001 2322 1 chr5B.!!$F1 1321
14 TraesCS5D01G342700 chr5B 520036809 520038109 1300 False 649 649 76.030 1001 2322 1 chr5B.!!$F2 1321
15 TraesCS5D01G342700 chr6D 374103600 374104163 563 False 833 833 93.440 2767 3326 1 chr6D.!!$F1 559
16 TraesCS5D01G342700 chr1D 413227459 413228017 558 False 826 826 93.393 2769 3326 1 chr1D.!!$F2 557
17 TraesCS5D01G342700 chr4D 19346815 19347372 557 True 819 819 93.202 2771 3326 1 chr4D.!!$R1 555
18 TraesCS5D01G342700 chr2D 399427343 399427900 557 False 819 819 93.202 2771 3326 1 chr2D.!!$F1 555
19 TraesCS5D01G342700 chr7D 583072595 583073157 562 False 809 809 92.718 2767 3326 1 chr7D.!!$F2 559
20 TraesCS5D01G342700 chr7D 40735556 40736116 560 False 808 808 92.692 2768 3326 1 chr7D.!!$F1 558
21 TraesCS5D01G342700 chr7D 635996311 635996871 560 True 808 808 92.718 2767 3326 1 chr7D.!!$R2 559
22 TraesCS5D01G342700 chr2B 117071621 117072189 568 False 802 802 92.267 2763 3326 1 chr2B.!!$F1 563

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
326 366 0.099436 GCAACGAAGATGGGATGCAC 59.901 55.0 0.0 0.0 34.1 4.57 F
643 686 0.523072 CGGCAACAAGATCCAACTGG 59.477 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1646 2.506472 GGAAGAGATCGGGGTGGC 59.494 66.667 0.0 0.0 0.0 5.01 R
2595 3109 1.202794 GGGACGGAGGGAGTACTAGAG 60.203 61.905 0.0 0.0 0.0 2.43 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
68 69 7.348201 CAACCTTAATCAATAGCTCACGATTC 58.652 38.462 7.47 0.00 30.94 2.52
80 81 5.168569 AGCTCACGATTCGTCTTTATTTCA 58.831 37.500 9.11 0.00 38.32 2.69
83 84 7.043325 AGCTCACGATTCGTCTTTATTTCATAC 60.043 37.037 9.11 0.00 38.32 2.39
86 87 5.461078 ACGATTCGTCTTTATTTCATACCGG 59.539 40.000 5.75 0.00 33.69 5.28
88 89 6.561533 CGATTCGTCTTTATTTCATACCGGTG 60.562 42.308 19.93 0.25 0.00 4.94
118 158 5.349270 CCGAATTGAAAATCAACATGCATGT 59.651 36.000 26.61 26.61 39.45 3.21
125 165 0.321475 TCAACATGCATGTCTCGGCA 60.321 50.000 31.45 10.02 45.23 5.69
126 166 0.522626 CAACATGCATGTCTCGGCAA 59.477 50.000 31.45 0.00 44.20 4.52
127 167 1.068402 CAACATGCATGTCTCGGCAAA 60.068 47.619 31.45 0.00 44.20 3.68
128 168 1.246649 ACATGCATGTCTCGGCAAAA 58.753 45.000 26.61 0.00 44.20 2.44
129 169 1.068333 ACATGCATGTCTCGGCAAAAC 60.068 47.619 26.61 0.00 44.20 2.43
130 170 0.527565 ATGCATGTCTCGGCAAAACC 59.472 50.000 0.00 0.00 44.20 3.27
131 171 0.537143 TGCATGTCTCGGCAAAACCT 60.537 50.000 0.00 0.00 37.03 3.50
132 172 0.169009 GCATGTCTCGGCAAAACCTC 59.831 55.000 0.00 0.00 35.61 3.85
133 173 0.804989 CATGTCTCGGCAAAACCTCC 59.195 55.000 0.00 0.00 35.61 4.30
134 174 0.400213 ATGTCTCGGCAAAACCTCCA 59.600 50.000 0.00 0.00 35.61 3.86
135 175 0.250295 TGTCTCGGCAAAACCTCCAG 60.250 55.000 0.00 0.00 35.61 3.86
136 176 0.955919 GTCTCGGCAAAACCTCCAGG 60.956 60.000 0.00 0.00 42.17 4.45
164 204 6.579666 AAAAGAAAGCACTCATCTTATGCA 57.420 33.333 0.00 0.00 41.97 3.96
165 205 6.770746 AAAGAAAGCACTCATCTTATGCAT 57.229 33.333 3.79 3.79 41.97 3.96
166 206 7.870509 AAAGAAAGCACTCATCTTATGCATA 57.129 32.000 1.16 1.16 41.97 3.14
167 207 7.493743 AAGAAAGCACTCATCTTATGCATAG 57.506 36.000 6.50 0.00 41.97 2.23
168 208 6.824553 AGAAAGCACTCATCTTATGCATAGA 58.175 36.000 6.50 7.33 41.97 1.98
169 209 6.930164 AGAAAGCACTCATCTTATGCATAGAG 59.070 38.462 15.55 15.55 41.97 2.43
170 210 6.416631 AAGCACTCATCTTATGCATAGAGA 57.583 37.500 21.30 18.59 41.97 3.10
171 211 6.608539 AGCACTCATCTTATGCATAGAGAT 57.391 37.500 21.30 19.61 41.97 2.75
172 212 7.715266 AGCACTCATCTTATGCATAGAGATA 57.285 36.000 21.30 13.02 41.97 1.98
173 213 7.774134 AGCACTCATCTTATGCATAGAGATAG 58.226 38.462 21.30 19.44 41.97 2.08
174 214 7.614974 AGCACTCATCTTATGCATAGAGATAGA 59.385 37.037 21.30 14.93 41.97 1.98
175 215 7.916977 GCACTCATCTTATGCATAGAGATAGAG 59.083 40.741 26.41 26.41 39.23 2.43
176 216 9.176460 CACTCATCTTATGCATAGAGATAGAGA 57.824 37.037 29.49 21.56 33.81 3.10
177 217 9.925545 ACTCATCTTATGCATAGAGATAGAGAT 57.074 33.333 29.49 22.28 33.81 2.75
232 272 9.479549 AGAGAGAGAGAGAGAGATGTTAAAATT 57.520 33.333 0.00 0.00 0.00 1.82
233 273 9.520204 GAGAGAGAGAGAGAGATGTTAAAATTG 57.480 37.037 0.00 0.00 0.00 2.32
234 274 9.253832 AGAGAGAGAGAGAGATGTTAAAATTGA 57.746 33.333 0.00 0.00 0.00 2.57
235 275 9.520204 GAGAGAGAGAGAGATGTTAAAATTGAG 57.480 37.037 0.00 0.00 0.00 3.02
236 276 7.981225 AGAGAGAGAGAGATGTTAAAATTGAGC 59.019 37.037 0.00 0.00 0.00 4.26
237 277 7.619050 AGAGAGAGAGATGTTAAAATTGAGCA 58.381 34.615 0.00 0.00 0.00 4.26
238 278 7.548780 AGAGAGAGAGATGTTAAAATTGAGCAC 59.451 37.037 0.00 0.00 0.00 4.40
239 279 7.164122 AGAGAGAGATGTTAAAATTGAGCACA 58.836 34.615 0.00 0.00 0.00 4.57
240 280 7.828223 AGAGAGAGATGTTAAAATTGAGCACAT 59.172 33.333 0.00 0.00 0.00 3.21
241 281 8.345724 AGAGAGATGTTAAAATTGAGCACATT 57.654 30.769 0.00 0.00 0.00 2.71
242 282 8.457261 AGAGAGATGTTAAAATTGAGCACATTC 58.543 33.333 0.00 0.00 0.00 2.67
243 283 8.114331 AGAGATGTTAAAATTGAGCACATTCA 57.886 30.769 0.00 0.00 0.00 2.57
244 284 8.579006 AGAGATGTTAAAATTGAGCACATTCAA 58.421 29.630 0.00 0.00 41.00 2.69
245 285 9.195411 GAGATGTTAAAATTGAGCACATTCAAA 57.805 29.630 0.00 0.00 40.21 2.69
246 286 9.545105 AGATGTTAAAATTGAGCACATTCAAAA 57.455 25.926 0.00 0.00 40.21 2.44
252 292 8.665643 AAAATTGAGCACATTCAAAATTCTCA 57.334 26.923 0.00 0.00 40.21 3.27
253 293 8.842358 AAATTGAGCACATTCAAAATTCTCAT 57.158 26.923 0.00 0.00 40.21 2.90
254 294 7.827819 ATTGAGCACATTCAAAATTCTCATG 57.172 32.000 0.00 0.00 40.21 3.07
255 295 6.578163 TGAGCACATTCAAAATTCTCATGA 57.422 33.333 0.00 0.00 0.00 3.07
256 296 7.165460 TGAGCACATTCAAAATTCTCATGAT 57.835 32.000 0.00 0.00 0.00 2.45
257 297 7.608153 TGAGCACATTCAAAATTCTCATGATT 58.392 30.769 0.00 0.00 0.00 2.57
258 298 7.544217 TGAGCACATTCAAAATTCTCATGATTG 59.456 33.333 0.00 0.00 33.14 2.67
259 299 7.383687 AGCACATTCAAAATTCTCATGATTGT 58.616 30.769 0.00 0.00 37.86 2.71
261 301 7.117236 GCACATTCAAAATTCTCATGATTGTGT 59.883 33.333 21.24 0.00 46.61 3.72
262 302 8.432359 CACATTCAAAATTCTCATGATTGTGTG 58.568 33.333 16.09 11.91 43.50 3.82
263 303 8.361889 ACATTCAAAATTCTCATGATTGTGTGA 58.638 29.630 0.00 0.00 36.72 3.58
264 304 8.860128 CATTCAAAATTCTCATGATTGTGTGAG 58.140 33.333 0.00 0.00 42.46 3.51
265 305 6.384224 TCAAAATTCTCATGATTGTGTGAGC 58.616 36.000 0.00 0.00 41.21 4.26
266 306 5.970317 AAATTCTCATGATTGTGTGAGCA 57.030 34.783 0.00 0.00 41.21 4.26
267 307 6.525578 AAATTCTCATGATTGTGTGAGCAT 57.474 33.333 0.00 0.00 41.21 3.79
268 308 5.752892 ATTCTCATGATTGTGTGAGCATC 57.247 39.130 0.00 0.00 41.21 3.91
269 309 3.192466 TCTCATGATTGTGTGAGCATCG 58.808 45.455 0.00 0.00 41.21 3.84
270 310 3.119029 TCTCATGATTGTGTGAGCATCGA 60.119 43.478 0.00 0.00 41.21 3.59
271 311 3.192466 TCATGATTGTGTGAGCATCGAG 58.808 45.455 0.00 0.00 38.61 4.04
272 312 2.014335 TGATTGTGTGAGCATCGAGG 57.986 50.000 0.00 0.00 38.61 4.63
273 313 0.654683 GATTGTGTGAGCATCGAGGC 59.345 55.000 15.45 15.45 38.61 4.70
288 328 2.508663 GGCTACCGTCGACAAGGC 60.509 66.667 17.16 16.87 0.00 4.35
299 339 0.318441 CGACAAGGCTGAGAAGGACA 59.682 55.000 0.00 0.00 0.00 4.02
304 344 4.985538 ACAAGGCTGAGAAGGACAATAAA 58.014 39.130 0.00 0.00 0.00 1.40
309 349 3.334691 CTGAGAAGGACAATAAACGGCA 58.665 45.455 0.00 0.00 0.00 5.69
325 365 1.031571 GGCAACGAAGATGGGATGCA 61.032 55.000 0.00 0.00 35.57 3.96
326 366 0.099436 GCAACGAAGATGGGATGCAC 59.901 55.000 0.00 0.00 34.10 4.57
333 373 1.078497 GATGGGATGCACGTGGACA 60.078 57.895 18.88 9.59 0.00 4.02
335 375 0.836606 ATGGGATGCACGTGGACATA 59.163 50.000 18.88 2.57 0.00 2.29
342 382 1.882623 TGCACGTGGACATATTGCAAA 59.117 42.857 18.88 0.00 40.15 3.68
365 405 1.557651 CGGGCTCTTTCGCTAGTAAC 58.442 55.000 0.00 0.00 0.00 2.50
366 406 1.134560 CGGGCTCTTTCGCTAGTAACT 59.865 52.381 0.00 0.00 0.00 2.24
367 407 2.357009 CGGGCTCTTTCGCTAGTAACTA 59.643 50.000 0.00 0.00 0.00 2.24
369 409 4.499357 CGGGCTCTTTCGCTAGTAACTATT 60.499 45.833 0.00 0.00 0.00 1.73
455 495 1.680735 GATGAATTGGCCGGTTATGCA 59.319 47.619 1.90 0.00 0.00 3.96
508 548 4.433877 GCACGTACCCGGCCGTAA 62.434 66.667 26.12 5.71 38.78 3.18
510 550 1.153588 CACGTACCCGGCCGTAAAT 60.154 57.895 26.12 8.70 38.78 1.40
549 589 1.664965 GCGATGAGATACACGGCCC 60.665 63.158 0.00 0.00 0.00 5.80
614 654 3.059044 CGCGACACTGTGTGATTTACTAC 59.941 47.826 19.62 0.00 36.96 2.73
616 659 5.396484 GCGACACTGTGTGATTTACTACTA 58.604 41.667 19.62 0.00 36.96 1.82
628 671 8.198778 TGTGATTTACTACTAATTATCACGGCA 58.801 33.333 0.00 0.00 42.81 5.69
643 686 0.523072 CGGCAACAAGATCCAACTGG 59.477 55.000 0.00 0.00 0.00 4.00
660 703 7.047891 TCCAACTGGAAATATACAGTAAGCTG 58.952 38.462 7.73 0.00 46.49 4.24
680 723 2.597510 GCCGCACAAAAGGACCCT 60.598 61.111 0.00 0.00 0.00 4.34
715 758 4.848562 ATCCATGACATGCATCATTCAC 57.151 40.909 10.10 0.00 37.20 3.18
716 759 3.622630 TCCATGACATGCATCATTCACA 58.377 40.909 10.10 0.00 37.20 3.58
717 760 4.017808 TCCATGACATGCATCATTCACAA 58.982 39.130 10.10 0.00 37.20 3.33
718 761 4.109766 CCATGACATGCATCATTCACAAC 58.890 43.478 10.10 0.00 37.20 3.32
719 762 4.142249 CCATGACATGCATCATTCACAACT 60.142 41.667 10.10 0.00 37.20 3.16
720 763 4.428615 TGACATGCATCATTCACAACTG 57.571 40.909 0.00 0.00 0.00 3.16
721 764 4.073549 TGACATGCATCATTCACAACTGA 58.926 39.130 0.00 0.00 0.00 3.41
722 765 4.519730 TGACATGCATCATTCACAACTGAA 59.480 37.500 0.00 0.00 40.77 3.02
723 766 4.801891 ACATGCATCATTCACAACTGAAC 58.198 39.130 0.00 0.00 39.28 3.18
724 767 3.921119 TGCATCATTCACAACTGAACC 57.079 42.857 0.00 0.00 39.28 3.62
725 768 3.220940 TGCATCATTCACAACTGAACCA 58.779 40.909 0.00 0.00 39.28 3.67
726 769 3.635836 TGCATCATTCACAACTGAACCAA 59.364 39.130 0.00 0.00 39.28 3.67
727 770 4.281435 TGCATCATTCACAACTGAACCAAT 59.719 37.500 0.00 0.00 39.28 3.16
728 771 4.624024 GCATCATTCACAACTGAACCAATG 59.376 41.667 0.00 0.00 39.28 2.82
729 772 4.852134 TCATTCACAACTGAACCAATGG 57.148 40.909 0.00 0.00 39.28 3.16
730 773 3.005684 TCATTCACAACTGAACCAATGGC 59.994 43.478 0.00 0.00 39.28 4.40
731 774 2.363306 TCACAACTGAACCAATGGCT 57.637 45.000 0.00 0.00 0.00 4.75
732 775 3.500448 TCACAACTGAACCAATGGCTA 57.500 42.857 0.00 0.00 0.00 3.93
954 1035 1.588404 CACGGTAGATCGCATCAACAC 59.412 52.381 0.00 0.00 0.00 3.32
1212 1293 4.388499 CTGGCCGTGTACCGCCTT 62.388 66.667 13.94 0.00 34.92 4.35
1491 1572 2.743928 GCCACCAGCGACTTCCTG 60.744 66.667 0.00 0.00 0.00 3.86
2295 2397 2.661537 CAGCACAACCTCGACGCA 60.662 61.111 0.00 0.00 0.00 5.24
2328 2430 3.462021 CTGCTACTCCATGGACTAAAGC 58.538 50.000 11.44 16.55 0.00 3.51
2572 3086 5.627499 ATTGTTTGCACAGACGATTATGT 57.373 34.783 0.00 0.00 33.22 2.29
2575 3089 4.090786 TGTTTGCACAGACGATTATGTACG 59.909 41.667 0.00 0.00 0.00 3.67
2582 3096 5.806502 CACAGACGATTATGTACGGGTTTTA 59.193 40.000 0.00 0.00 0.00 1.52
2595 3109 5.638596 ACGGGTTTTAATTCCATGTTCTC 57.361 39.130 0.00 0.00 0.00 2.87
2600 3114 7.011482 CGGGTTTTAATTCCATGTTCTCTCTAG 59.989 40.741 0.00 0.00 0.00 2.43
2613 3132 2.699846 TCTCTCTAGTACTCCCTCCGTC 59.300 54.545 0.00 0.00 0.00 4.79
2627 3146 6.156554 TCCCTCCGTCCCATAATATAAGTA 57.843 41.667 0.00 0.00 0.00 2.24
2629 3148 5.163581 CCCTCCGTCCCATAATATAAGTACG 60.164 48.000 0.00 0.00 0.00 3.67
2634 3153 7.652909 TCCGTCCCATAATATAAGTACGTTTTG 59.347 37.037 0.00 0.00 0.00 2.44
2635 3154 7.095523 CCGTCCCATAATATAAGTACGTTTTGG 60.096 40.741 0.00 0.00 0.00 3.28
2636 3155 7.569957 CGTCCCATAATATAAGTACGTTTTGGC 60.570 40.741 0.00 0.00 0.00 4.52
2637 3156 7.227116 GTCCCATAATATAAGTACGTTTTGGCA 59.773 37.037 0.00 0.00 0.00 4.92
2638 3157 7.227116 TCCCATAATATAAGTACGTTTTGGCAC 59.773 37.037 0.00 0.00 0.00 5.01
2639 3158 7.227910 CCCATAATATAAGTACGTTTTGGCACT 59.772 37.037 0.00 0.00 0.00 4.40
2640 3159 9.263538 CCATAATATAAGTACGTTTTGGCACTA 57.736 33.333 0.00 0.00 0.00 2.74
2642 3161 9.820725 ATAATATAAGTACGTTTTGGCACTACA 57.179 29.630 0.00 0.00 0.00 2.74
2643 3162 8.550710 AATATAAGTACGTTTTGGCACTACAA 57.449 30.769 0.00 0.00 0.00 2.41
2644 3163 8.726870 ATATAAGTACGTTTTGGCACTACAAT 57.273 30.769 0.00 0.00 0.00 2.71
2645 3164 9.820725 ATATAAGTACGTTTTGGCACTACAATA 57.179 29.630 0.00 0.00 0.00 1.90
2646 3165 6.476243 AAGTACGTTTTGGCACTACAATAG 57.524 37.500 0.00 0.00 0.00 1.73
2647 3166 5.544650 AGTACGTTTTGGCACTACAATAGT 58.455 37.500 0.00 0.00 40.28 2.12
2676 3195 9.677567 CAAAAATGTTCTTATATTATGGGACGG 57.322 33.333 0.00 0.00 0.00 4.79
2677 3196 9.635404 AAAAATGTTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
2678 3197 8.848474 AAATGTTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
2679 3198 6.354794 TGTTCTTATATTATGGGACGGAGG 57.645 41.667 0.00 0.00 0.00 4.30
2680 3199 6.079336 TGTTCTTATATTATGGGACGGAGGA 58.921 40.000 0.00 0.00 0.00 3.71
2681 3200 6.555738 TGTTCTTATATTATGGGACGGAGGAA 59.444 38.462 0.00 0.00 0.00 3.36
2682 3201 6.852420 TCTTATATTATGGGACGGAGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
2683 3202 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
2684 3203 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
2685 3204 7.614583 TCTTATATTATGGGACGGAGGAAGTAG 59.385 40.741 0.00 0.00 0.00 2.57
2686 3205 3.393426 TTATGGGACGGAGGAAGTAGT 57.607 47.619 0.00 0.00 0.00 2.73
2687 3206 4.524802 TTATGGGACGGAGGAAGTAGTA 57.475 45.455 0.00 0.00 0.00 1.82
2688 3207 2.905415 TGGGACGGAGGAAGTAGTAA 57.095 50.000 0.00 0.00 0.00 2.24
2689 3208 3.393426 TGGGACGGAGGAAGTAGTAAT 57.607 47.619 0.00 0.00 0.00 1.89
2690 3209 3.716431 TGGGACGGAGGAAGTAGTAATT 58.284 45.455 0.00 0.00 0.00 1.40
2691 3210 4.870636 TGGGACGGAGGAAGTAGTAATTA 58.129 43.478 0.00 0.00 0.00 1.40
2692 3211 5.271598 TGGGACGGAGGAAGTAGTAATTAA 58.728 41.667 0.00 0.00 0.00 1.40
2693 3212 5.361857 TGGGACGGAGGAAGTAGTAATTAAG 59.638 44.000 0.00 0.00 0.00 1.85
2694 3213 5.362143 GGGACGGAGGAAGTAGTAATTAAGT 59.638 44.000 0.00 0.00 0.00 2.24
2695 3214 6.547510 GGGACGGAGGAAGTAGTAATTAAGTA 59.452 42.308 0.00 0.00 0.00 2.24
2696 3215 7.255416 GGGACGGAGGAAGTAGTAATTAAGTAG 60.255 44.444 0.00 0.00 0.00 2.57
2697 3216 7.500559 GGACGGAGGAAGTAGTAATTAAGTAGA 59.499 40.741 0.00 0.00 0.00 2.59
2698 3217 8.449251 ACGGAGGAAGTAGTAATTAAGTAGAG 57.551 38.462 0.00 0.00 0.00 2.43
2699 3218 8.052141 ACGGAGGAAGTAGTAATTAAGTAGAGT 58.948 37.037 0.00 0.00 0.00 3.24
2700 3219 9.553064 CGGAGGAAGTAGTAATTAAGTAGAGTA 57.447 37.037 0.00 0.00 0.00 2.59
2717 3236 8.350852 AGTAGAGTAGTAGTATGTTTGCTTGT 57.649 34.615 0.00 0.00 0.00 3.16
2718 3237 8.244802 AGTAGAGTAGTAGTATGTTTGCTTGTG 58.755 37.037 0.00 0.00 0.00 3.33
2719 3238 6.994221 AGAGTAGTAGTATGTTTGCTTGTGT 58.006 36.000 0.00 0.00 0.00 3.72
2720 3239 7.442656 AGAGTAGTAGTATGTTTGCTTGTGTT 58.557 34.615 0.00 0.00 0.00 3.32
2721 3240 7.385205 AGAGTAGTAGTATGTTTGCTTGTGTTG 59.615 37.037 0.00 0.00 0.00 3.33
2722 3241 6.990349 AGTAGTAGTATGTTTGCTTGTGTTGT 59.010 34.615 0.00 0.00 0.00 3.32
2723 3242 6.300354 AGTAGTATGTTTGCTTGTGTTGTC 57.700 37.500 0.00 0.00 0.00 3.18
2724 3243 4.209452 AGTATGTTTGCTTGTGTTGTCG 57.791 40.909 0.00 0.00 0.00 4.35
2725 3244 2.490328 ATGTTTGCTTGTGTTGTCGG 57.510 45.000 0.00 0.00 0.00 4.79
2726 3245 1.454201 TGTTTGCTTGTGTTGTCGGA 58.546 45.000 0.00 0.00 0.00 4.55
2727 3246 2.020720 TGTTTGCTTGTGTTGTCGGAT 58.979 42.857 0.00 0.00 0.00 4.18
2728 3247 2.223456 TGTTTGCTTGTGTTGTCGGATG 60.223 45.455 0.00 0.00 0.00 3.51
2729 3248 0.310543 TTGCTTGTGTTGTCGGATGC 59.689 50.000 0.00 0.00 0.00 3.91
2730 3249 0.534877 TGCTTGTGTTGTCGGATGCT 60.535 50.000 0.00 0.00 0.00 3.79
2731 3250 0.110056 GCTTGTGTTGTCGGATGCTG 60.110 55.000 0.00 0.00 0.00 4.41
2732 3251 1.229428 CTTGTGTTGTCGGATGCTGT 58.771 50.000 0.00 0.00 0.00 4.40
2733 3252 0.943673 TTGTGTTGTCGGATGCTGTG 59.056 50.000 0.00 0.00 0.00 3.66
2734 3253 0.884259 TGTGTTGTCGGATGCTGTGG 60.884 55.000 0.00 0.00 0.00 4.17
2735 3254 1.965930 TGTTGTCGGATGCTGTGGC 60.966 57.895 0.00 0.00 39.26 5.01
2744 3263 4.306767 TGCTGTGGCATAGCAGTG 57.693 55.556 31.41 0.00 45.52 3.66
2745 3264 1.377594 TGCTGTGGCATAGCAGTGG 60.378 57.895 31.41 0.00 45.52 4.00
2746 3265 2.117156 GCTGTGGCATAGCAGTGGG 61.117 63.158 28.35 0.00 40.81 4.61
2747 3266 1.603842 CTGTGGCATAGCAGTGGGA 59.396 57.895 0.00 0.00 0.00 4.37
2748 3267 0.035152 CTGTGGCATAGCAGTGGGAA 60.035 55.000 0.00 0.00 0.00 3.97
2749 3268 0.625316 TGTGGCATAGCAGTGGGAAT 59.375 50.000 0.00 0.00 0.00 3.01
2750 3269 1.312815 GTGGCATAGCAGTGGGAATC 58.687 55.000 0.00 0.00 0.00 2.52
2751 3270 0.918258 TGGCATAGCAGTGGGAATCA 59.082 50.000 0.00 0.00 0.00 2.57
2752 3271 1.284491 TGGCATAGCAGTGGGAATCAA 59.716 47.619 0.00 0.00 0.00 2.57
2753 3272 2.291475 TGGCATAGCAGTGGGAATCAAA 60.291 45.455 0.00 0.00 0.00 2.69
2754 3273 2.961062 GGCATAGCAGTGGGAATCAAAT 59.039 45.455 0.00 0.00 0.00 2.32
2755 3274 3.005155 GGCATAGCAGTGGGAATCAAATC 59.995 47.826 0.00 0.00 0.00 2.17
2756 3275 3.887716 GCATAGCAGTGGGAATCAAATCT 59.112 43.478 0.00 0.00 0.00 2.40
2757 3276 4.023365 GCATAGCAGTGGGAATCAAATCTC 60.023 45.833 0.00 0.00 0.00 2.75
2758 3277 5.374921 CATAGCAGTGGGAATCAAATCTCT 58.625 41.667 0.00 0.00 0.00 3.10
2759 3278 4.313020 AGCAGTGGGAATCAAATCTCTT 57.687 40.909 0.00 0.00 0.00 2.85
2760 3279 4.015084 AGCAGTGGGAATCAAATCTCTTG 58.985 43.478 0.00 0.00 0.00 3.02
2761 3280 4.012374 GCAGTGGGAATCAAATCTCTTGA 58.988 43.478 0.00 0.00 0.00 3.02
2813 3332 4.307432 GTGTGGTATATTAGACATGCGCT 58.693 43.478 9.73 0.00 0.00 5.92
2881 3400 3.055021 TGTGTGGGCGGACATTAGAATTA 60.055 43.478 0.00 0.00 0.00 1.40
2886 3405 3.497942 GGGCGGACATTAGAATTACCCAT 60.498 47.826 0.00 0.00 34.82 4.00
2939 3459 3.308188 GCCCAACAAGTACTACCCATCTT 60.308 47.826 0.00 0.00 0.00 2.40
3054 3579 4.586001 GGTTGGTAGATGTAGTTATCCGGA 59.414 45.833 6.61 6.61 0.00 5.14
3162 3688 0.519961 AATCAAACCGTAGTTGCCGC 59.480 50.000 0.00 0.00 35.97 6.53
3174 3701 0.453782 GTTGCCGCGTGTGATTAACC 60.454 55.000 4.92 0.00 0.00 2.85
3175 3702 0.604243 TTGCCGCGTGTGATTAACCT 60.604 50.000 4.92 0.00 0.00 3.50
3234 3763 1.330234 TACCTAGTTGCCACGTGTGA 58.670 50.000 15.65 0.00 0.00 3.58
3236 3765 1.078709 CCTAGTTGCCACGTGTGATG 58.921 55.000 15.65 0.00 0.00 3.07
3293 3822 3.505680 GCCATGTGTGTTTATCTGGTTGA 59.494 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 6.267817 TCTACACCGGTATGAAATAAAGACG 58.732 40.000 6.87 0.00 0.00 4.18
83 84 9.009557 TTGATTTTCAATTCGGATCTACACCGG 62.010 40.741 0.00 0.00 40.07 5.28
86 87 7.526608 TGTTGATTTTCAATTCGGATCTACAC 58.473 34.615 0.00 0.00 38.79 2.90
88 89 7.166473 GCATGTTGATTTTCAATTCGGATCTAC 59.834 37.037 0.00 0.00 38.79 2.59
106 107 0.321475 TGCCGAGACATGCATGTTGA 60.321 50.000 31.82 10.80 41.95 3.18
107 108 0.522626 TTGCCGAGACATGCATGTTG 59.477 50.000 31.82 22.99 41.95 3.33
118 158 1.374947 CCTGGAGGTTTTGCCGAGA 59.625 57.895 0.00 0.00 43.70 4.04
140 180 6.985117 TGCATAAGATGAGTGCTTTCTTTTT 58.015 32.000 0.00 0.00 39.52 1.94
141 181 6.579666 TGCATAAGATGAGTGCTTTCTTTT 57.420 33.333 0.00 0.00 39.52 2.27
142 182 6.770746 ATGCATAAGATGAGTGCTTTCTTT 57.229 33.333 0.00 0.00 39.52 2.52
143 183 7.278135 TCTATGCATAAGATGAGTGCTTTCTT 58.722 34.615 8.00 0.00 39.52 2.52
144 184 6.824553 TCTATGCATAAGATGAGTGCTTTCT 58.175 36.000 8.00 0.00 39.52 2.52
145 185 6.927936 TCTCTATGCATAAGATGAGTGCTTTC 59.072 38.462 16.18 0.00 39.52 2.62
146 186 6.824553 TCTCTATGCATAAGATGAGTGCTTT 58.175 36.000 16.18 0.00 39.52 3.51
147 187 6.416631 TCTCTATGCATAAGATGAGTGCTT 57.583 37.500 16.18 0.00 39.52 3.91
148 188 6.608539 ATCTCTATGCATAAGATGAGTGCT 57.391 37.500 20.92 8.08 39.52 4.40
149 189 7.770201 TCTATCTCTATGCATAAGATGAGTGC 58.230 38.462 25.59 0.00 39.26 4.40
150 190 9.176460 TCTCTATCTCTATGCATAAGATGAGTG 57.824 37.037 25.59 20.35 32.53 3.51
151 191 9.925545 ATCTCTATCTCTATGCATAAGATGAGT 57.074 33.333 25.59 19.12 32.53 3.41
206 246 9.479549 AATTTTAACATCTCTCTCTCTCTCTCT 57.520 33.333 0.00 0.00 0.00 3.10
207 247 9.520204 CAATTTTAACATCTCTCTCTCTCTCTC 57.480 37.037 0.00 0.00 0.00 3.20
208 248 9.253832 TCAATTTTAACATCTCTCTCTCTCTCT 57.746 33.333 0.00 0.00 0.00 3.10
209 249 9.520204 CTCAATTTTAACATCTCTCTCTCTCTC 57.480 37.037 0.00 0.00 0.00 3.20
210 250 7.981225 GCTCAATTTTAACATCTCTCTCTCTCT 59.019 37.037 0.00 0.00 0.00 3.10
211 251 7.763528 TGCTCAATTTTAACATCTCTCTCTCTC 59.236 37.037 0.00 0.00 0.00 3.20
212 252 7.548780 GTGCTCAATTTTAACATCTCTCTCTCT 59.451 37.037 0.00 0.00 0.00 3.10
213 253 7.332926 TGTGCTCAATTTTAACATCTCTCTCTC 59.667 37.037 0.00 0.00 0.00 3.20
214 254 7.164122 TGTGCTCAATTTTAACATCTCTCTCT 58.836 34.615 0.00 0.00 0.00 3.10
215 255 7.369803 TGTGCTCAATTTTAACATCTCTCTC 57.630 36.000 0.00 0.00 0.00 3.20
216 256 7.934855 ATGTGCTCAATTTTAACATCTCTCT 57.065 32.000 0.00 0.00 0.00 3.10
217 257 8.239314 TGAATGTGCTCAATTTTAACATCTCTC 58.761 33.333 0.00 0.00 31.29 3.20
218 258 8.114331 TGAATGTGCTCAATTTTAACATCTCT 57.886 30.769 0.00 0.00 31.29 3.10
219 259 8.746922 TTGAATGTGCTCAATTTTAACATCTC 57.253 30.769 0.00 0.00 31.29 2.75
220 260 9.545105 TTTTGAATGTGCTCAATTTTAACATCT 57.455 25.926 0.00 0.00 35.31 2.90
226 266 9.761504 TGAGAATTTTGAATGTGCTCAATTTTA 57.238 25.926 0.00 0.00 35.31 1.52
227 267 8.665643 TGAGAATTTTGAATGTGCTCAATTTT 57.334 26.923 0.00 0.00 35.31 1.82
228 268 8.717821 CATGAGAATTTTGAATGTGCTCAATTT 58.282 29.630 0.00 0.00 35.31 1.82
229 269 8.092068 TCATGAGAATTTTGAATGTGCTCAATT 58.908 29.630 0.00 0.00 35.31 2.32
230 270 7.608153 TCATGAGAATTTTGAATGTGCTCAAT 58.392 30.769 0.00 0.00 35.31 2.57
231 271 6.983984 TCATGAGAATTTTGAATGTGCTCAA 58.016 32.000 0.00 0.00 34.95 3.02
232 272 6.578163 TCATGAGAATTTTGAATGTGCTCA 57.422 33.333 0.00 0.00 35.65 4.26
233 273 7.544566 ACAATCATGAGAATTTTGAATGTGCTC 59.455 33.333 11.90 0.00 33.46 4.26
234 274 7.330946 CACAATCATGAGAATTTTGAATGTGCT 59.669 33.333 11.90 0.00 41.60 4.40
235 275 7.453034 CACAATCATGAGAATTTTGAATGTGC 58.547 34.615 11.90 0.00 41.60 4.57
237 277 8.361889 TCACACAATCATGAGAATTTTGAATGT 58.638 29.630 11.90 5.14 34.66 2.71
238 278 8.751302 TCACACAATCATGAGAATTTTGAATG 57.249 30.769 11.90 9.30 0.00 2.67
239 279 7.544566 GCTCACACAATCATGAGAATTTTGAAT 59.455 33.333 11.90 0.00 44.32 2.57
240 280 6.864685 GCTCACACAATCATGAGAATTTTGAA 59.135 34.615 11.90 0.00 44.32 2.69
241 281 6.016108 TGCTCACACAATCATGAGAATTTTGA 60.016 34.615 11.90 4.75 44.32 2.69
242 282 6.153756 TGCTCACACAATCATGAGAATTTTG 58.846 36.000 0.09 2.90 44.32 2.44
243 283 6.335471 TGCTCACACAATCATGAGAATTTT 57.665 33.333 0.09 0.00 44.32 1.82
244 284 5.970317 TGCTCACACAATCATGAGAATTT 57.030 34.783 0.09 0.00 44.32 1.82
245 285 5.220796 CGATGCTCACACAATCATGAGAATT 60.221 40.000 0.09 0.00 40.70 2.17
246 286 4.272748 CGATGCTCACACAATCATGAGAAT 59.727 41.667 0.09 0.00 42.90 2.40
247 287 3.619929 CGATGCTCACACAATCATGAGAA 59.380 43.478 0.09 0.00 44.32 2.87
248 288 3.119029 TCGATGCTCACACAATCATGAGA 60.119 43.478 0.09 0.00 44.32 3.27
249 289 3.192466 TCGATGCTCACACAATCATGAG 58.808 45.455 0.09 0.00 44.37 2.90
250 290 3.192466 CTCGATGCTCACACAATCATGA 58.808 45.455 0.00 0.00 0.00 3.07
251 291 2.287103 CCTCGATGCTCACACAATCATG 59.713 50.000 0.00 0.00 0.00 3.07
252 292 2.558378 CCTCGATGCTCACACAATCAT 58.442 47.619 0.00 0.00 0.00 2.45
253 293 2.008543 GCCTCGATGCTCACACAATCA 61.009 52.381 5.34 0.00 0.00 2.57
254 294 0.654683 GCCTCGATGCTCACACAATC 59.345 55.000 5.34 0.00 0.00 2.67
255 295 0.251354 AGCCTCGATGCTCACACAAT 59.749 50.000 9.61 0.00 36.75 2.71
256 296 0.894835 TAGCCTCGATGCTCACACAA 59.105 50.000 18.89 0.00 41.68 3.33
257 297 0.173481 GTAGCCTCGATGCTCACACA 59.827 55.000 18.89 0.00 41.68 3.72
258 298 0.528684 GGTAGCCTCGATGCTCACAC 60.529 60.000 18.89 11.50 41.68 3.82
259 299 1.816537 GGTAGCCTCGATGCTCACA 59.183 57.895 18.89 0.00 41.68 3.58
260 300 1.299468 CGGTAGCCTCGATGCTCAC 60.299 63.158 18.89 14.12 41.68 3.51
261 301 1.725557 GACGGTAGCCTCGATGCTCA 61.726 60.000 18.89 3.41 41.68 4.26
262 302 1.008309 GACGGTAGCCTCGATGCTC 60.008 63.158 18.89 10.39 41.68 4.26
263 303 2.835705 CGACGGTAGCCTCGATGCT 61.836 63.158 19.26 19.26 45.38 3.79
264 304 2.353607 CGACGGTAGCCTCGATGC 60.354 66.667 4.31 4.31 31.24 3.91
265 305 1.009900 GTCGACGGTAGCCTCGATG 60.010 63.158 16.85 0.00 40.81 3.84
266 306 1.028330 TTGTCGACGGTAGCCTCGAT 61.028 55.000 16.85 0.00 40.81 3.59
267 307 1.642037 CTTGTCGACGGTAGCCTCGA 61.642 60.000 11.62 11.19 36.58 4.04
268 308 1.226323 CTTGTCGACGGTAGCCTCG 60.226 63.158 11.62 6.95 0.00 4.63
269 309 1.139095 CCTTGTCGACGGTAGCCTC 59.861 63.158 11.62 0.00 0.00 4.70
270 310 3.003113 GCCTTGTCGACGGTAGCCT 62.003 63.158 11.62 0.00 0.00 4.58
271 311 2.508663 GCCTTGTCGACGGTAGCC 60.509 66.667 11.62 0.00 0.00 3.93
272 312 1.805945 CAGCCTTGTCGACGGTAGC 60.806 63.158 11.62 11.01 0.00 3.58
273 313 0.179161 CTCAGCCTTGTCGACGGTAG 60.179 60.000 11.62 8.02 0.00 3.18
274 314 0.607217 TCTCAGCCTTGTCGACGGTA 60.607 55.000 11.62 0.00 0.00 4.02
284 324 4.003648 CGTTTATTGTCCTTCTCAGCCTT 58.996 43.478 0.00 0.00 0.00 4.35
288 328 3.334691 TGCCGTTTATTGTCCTTCTCAG 58.665 45.455 0.00 0.00 0.00 3.35
299 339 2.422127 CCCATCTTCGTTGCCGTTTATT 59.578 45.455 0.00 0.00 35.01 1.40
304 344 0.744414 CATCCCATCTTCGTTGCCGT 60.744 55.000 0.00 0.00 35.01 5.68
309 349 0.036388 ACGTGCATCCCATCTTCGTT 60.036 50.000 0.00 0.00 0.00 3.85
312 352 0.107703 TCCACGTGCATCCCATCTTC 60.108 55.000 10.91 0.00 0.00 2.87
313 353 0.392998 GTCCACGTGCATCCCATCTT 60.393 55.000 10.91 0.00 0.00 2.40
319 359 1.002468 GCAATATGTCCACGTGCATCC 60.002 52.381 10.91 0.00 35.28 3.51
325 365 1.130373 CGCTTTGCAATATGTCCACGT 59.870 47.619 0.00 0.00 0.00 4.49
326 366 1.813896 CGCTTTGCAATATGTCCACG 58.186 50.000 0.00 0.00 0.00 4.94
333 373 2.120909 AGCCCGCGCTTTGCAATAT 61.121 52.632 5.56 0.00 45.55 1.28
455 495 1.867233 GCACACACATTGACGTCTTCT 59.133 47.619 17.92 0.00 0.00 2.85
549 589 2.964911 CTCTTTAGCGAGCTTCCCG 58.035 57.895 1.86 0.00 0.00 5.14
614 654 5.527214 TGGATCTTGTTGCCGTGATAATTAG 59.473 40.000 0.00 0.00 0.00 1.73
616 659 4.269183 TGGATCTTGTTGCCGTGATAATT 58.731 39.130 0.00 0.00 0.00 1.40
622 665 1.069022 CAGTTGGATCTTGTTGCCGTG 60.069 52.381 0.00 0.00 0.00 4.94
625 668 1.909700 TCCAGTTGGATCTTGTTGCC 58.090 50.000 0.00 0.00 39.78 4.52
628 671 8.109634 ACTGTATATTTCCAGTTGGATCTTGTT 58.890 33.333 0.93 0.00 44.98 2.83
643 686 4.084328 CGGCAGCAGCTTACTGTATATTTC 60.084 45.833 13.62 0.00 46.30 2.17
660 703 2.050077 GTCCTTTTGTGCGGCAGC 60.050 61.111 1.18 0.31 45.41 5.25
680 723 4.161377 TGTCATGGATTTGGTCAGACGATA 59.839 41.667 0.00 0.00 31.38 2.92
715 758 2.749621 GAGGTAGCCATTGGTTCAGTTG 59.250 50.000 4.26 0.00 0.00 3.16
716 759 2.644798 AGAGGTAGCCATTGGTTCAGTT 59.355 45.455 4.26 0.00 0.00 3.16
717 760 2.237392 GAGAGGTAGCCATTGGTTCAGT 59.763 50.000 4.26 0.00 0.00 3.41
718 761 2.739932 CGAGAGGTAGCCATTGGTTCAG 60.740 54.545 4.26 0.00 0.00 3.02
719 762 1.207089 CGAGAGGTAGCCATTGGTTCA 59.793 52.381 4.26 0.00 0.00 3.18
720 763 1.480954 TCGAGAGGTAGCCATTGGTTC 59.519 52.381 4.26 0.00 0.00 3.62
721 764 1.568504 TCGAGAGGTAGCCATTGGTT 58.431 50.000 4.26 0.04 0.00 3.67
722 765 1.689273 GATCGAGAGGTAGCCATTGGT 59.311 52.381 4.26 0.00 0.00 3.67
723 766 1.001406 GGATCGAGAGGTAGCCATTGG 59.999 57.143 0.00 0.00 0.00 3.16
724 767 1.688735 TGGATCGAGAGGTAGCCATTG 59.311 52.381 0.00 0.00 0.00 2.82
725 768 2.088104 TGGATCGAGAGGTAGCCATT 57.912 50.000 0.00 0.00 0.00 3.16
726 769 1.689273 GTTGGATCGAGAGGTAGCCAT 59.311 52.381 0.00 0.00 0.00 4.40
727 770 1.112113 GTTGGATCGAGAGGTAGCCA 58.888 55.000 0.00 0.00 0.00 4.75
728 771 1.067821 CTGTTGGATCGAGAGGTAGCC 59.932 57.143 0.00 0.00 0.00 3.93
729 772 2.025155 TCTGTTGGATCGAGAGGTAGC 58.975 52.381 0.00 0.00 0.00 3.58
730 773 3.283751 AGTCTGTTGGATCGAGAGGTAG 58.716 50.000 0.00 0.00 0.00 3.18
731 774 3.367646 AGTCTGTTGGATCGAGAGGTA 57.632 47.619 0.00 0.00 0.00 3.08
732 775 2.223803 AGTCTGTTGGATCGAGAGGT 57.776 50.000 0.00 0.00 0.00 3.85
954 1035 6.737254 AGTACGGTTGATGTATTTTCTTGG 57.263 37.500 0.00 0.00 0.00 3.61
1559 1646 2.506472 GGAAGAGATCGGGGTGGC 59.494 66.667 0.00 0.00 0.00 5.01
2103 2205 4.954118 TCCAGGTCCGGGCACAGT 62.954 66.667 9.07 0.00 0.00 3.55
2572 3086 6.478129 AGAGAACATGGAATTAAAACCCGTA 58.522 36.000 0.00 0.00 0.00 4.02
2575 3089 7.829706 ACTAGAGAGAACATGGAATTAAAACCC 59.170 37.037 0.00 0.00 0.00 4.11
2582 3096 6.325286 GGGAGTACTAGAGAGAACATGGAATT 59.675 42.308 0.00 0.00 0.00 2.17
2595 3109 1.202794 GGGACGGAGGGAGTACTAGAG 60.203 61.905 0.00 0.00 0.00 2.43
2600 3114 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2613 3132 7.227910 AGTGCCAAAACGTACTTATATTATGGG 59.772 37.037 0.00 0.00 0.00 4.00
2650 3169 9.677567 CCGTCCCATAATATAAGAACATTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
2651 3170 9.635404 TCCGTCCCATAATATAAGAACATTTTT 57.365 29.630 0.00 0.00 0.00 1.94
2652 3171 9.284968 CTCCGTCCCATAATATAAGAACATTTT 57.715 33.333 0.00 0.00 0.00 1.82
2653 3172 7.883311 CCTCCGTCCCATAATATAAGAACATTT 59.117 37.037 0.00 0.00 0.00 2.32
2654 3173 7.236847 TCCTCCGTCCCATAATATAAGAACATT 59.763 37.037 0.00 0.00 0.00 2.71
2655 3174 6.729100 TCCTCCGTCCCATAATATAAGAACAT 59.271 38.462 0.00 0.00 0.00 2.71
2656 3175 6.079336 TCCTCCGTCCCATAATATAAGAACA 58.921 40.000 0.00 0.00 0.00 3.18
2657 3176 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
2658 3177 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
2659 3178 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
2660 3179 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
2661 3180 7.243824 ACTACTTCCTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
2662 3181 6.797707 ACTACTTCCTCCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
2663 3182 5.652324 ACTACTTCCTCCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
2664 3183 5.070823 ACTACTTCCTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
2665 3184 3.924922 ACTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
2666 3185 3.393426 ACTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
2667 3186 4.524802 TTACTACTTCCTCCGTCCCATA 57.475 45.455 0.00 0.00 0.00 2.74
2668 3187 3.393426 TTACTACTTCCTCCGTCCCAT 57.607 47.619 0.00 0.00 0.00 4.00
2669 3188 2.905415 TTACTACTTCCTCCGTCCCA 57.095 50.000 0.00 0.00 0.00 4.37
2670 3189 5.362143 ACTTAATTACTACTTCCTCCGTCCC 59.638 44.000 0.00 0.00 0.00 4.46
2671 3190 6.462552 ACTTAATTACTACTTCCTCCGTCC 57.537 41.667 0.00 0.00 0.00 4.79
2672 3191 8.443953 TCTACTTAATTACTACTTCCTCCGTC 57.556 38.462 0.00 0.00 0.00 4.79
2673 3192 8.052141 ACTCTACTTAATTACTACTTCCTCCGT 58.948 37.037 0.00 0.00 0.00 4.69
2674 3193 8.449251 ACTCTACTTAATTACTACTTCCTCCG 57.551 38.462 0.00 0.00 0.00 4.63
2691 3210 8.804204 ACAAGCAAACATACTACTACTCTACTT 58.196 33.333 0.00 0.00 0.00 2.24
2692 3211 8.244802 CACAAGCAAACATACTACTACTCTACT 58.755 37.037 0.00 0.00 0.00 2.57
2693 3212 8.027771 ACACAAGCAAACATACTACTACTCTAC 58.972 37.037 0.00 0.00 0.00 2.59
2694 3213 8.118976 ACACAAGCAAACATACTACTACTCTA 57.881 34.615 0.00 0.00 0.00 2.43
2695 3214 6.994221 ACACAAGCAAACATACTACTACTCT 58.006 36.000 0.00 0.00 0.00 3.24
2696 3215 7.170998 ACAACACAAGCAAACATACTACTACTC 59.829 37.037 0.00 0.00 0.00 2.59
2697 3216 6.990349 ACAACACAAGCAAACATACTACTACT 59.010 34.615 0.00 0.00 0.00 2.57
2698 3217 7.186021 ACAACACAAGCAAACATACTACTAC 57.814 36.000 0.00 0.00 0.00 2.73
2699 3218 6.144886 CGACAACACAAGCAAACATACTACTA 59.855 38.462 0.00 0.00 0.00 1.82
2700 3219 5.050363 CGACAACACAAGCAAACATACTACT 60.050 40.000 0.00 0.00 0.00 2.57
2701 3220 5.137403 CGACAACACAAGCAAACATACTAC 58.863 41.667 0.00 0.00 0.00 2.73
2702 3221 4.212425 CCGACAACACAAGCAAACATACTA 59.788 41.667 0.00 0.00 0.00 1.82
2703 3222 3.003275 CCGACAACACAAGCAAACATACT 59.997 43.478 0.00 0.00 0.00 2.12
2704 3223 3.002862 TCCGACAACACAAGCAAACATAC 59.997 43.478 0.00 0.00 0.00 2.39
2705 3224 3.206964 TCCGACAACACAAGCAAACATA 58.793 40.909 0.00 0.00 0.00 2.29
2706 3225 2.020720 TCCGACAACACAAGCAAACAT 58.979 42.857 0.00 0.00 0.00 2.71
2707 3226 1.454201 TCCGACAACACAAGCAAACA 58.546 45.000 0.00 0.00 0.00 2.83
2708 3227 2.384382 CATCCGACAACACAAGCAAAC 58.616 47.619 0.00 0.00 0.00 2.93
2709 3228 1.268999 GCATCCGACAACACAAGCAAA 60.269 47.619 0.00 0.00 0.00 3.68
2710 3229 0.310543 GCATCCGACAACACAAGCAA 59.689 50.000 0.00 0.00 0.00 3.91
2711 3230 0.534877 AGCATCCGACAACACAAGCA 60.535 50.000 0.00 0.00 0.00 3.91
2712 3231 0.110056 CAGCATCCGACAACACAAGC 60.110 55.000 0.00 0.00 0.00 4.01
2713 3232 1.069703 CACAGCATCCGACAACACAAG 60.070 52.381 0.00 0.00 0.00 3.16
2714 3233 0.943673 CACAGCATCCGACAACACAA 59.056 50.000 0.00 0.00 0.00 3.33
2715 3234 0.884259 CCACAGCATCCGACAACACA 60.884 55.000 0.00 0.00 0.00 3.72
2716 3235 1.868997 CCACAGCATCCGACAACAC 59.131 57.895 0.00 0.00 0.00 3.32
2717 3236 1.965930 GCCACAGCATCCGACAACA 60.966 57.895 0.00 0.00 39.53 3.33
2718 3237 1.965930 TGCCACAGCATCCGACAAC 60.966 57.895 0.00 0.00 46.52 3.32
2719 3238 2.429494 TGCCACAGCATCCGACAA 59.571 55.556 0.00 0.00 46.52 3.18
2728 3247 2.117156 CCCACTGCTATGCCACAGC 61.117 63.158 0.00 0.00 37.42 4.40
2729 3248 0.035152 TTCCCACTGCTATGCCACAG 60.035 55.000 0.00 0.00 39.86 3.66
2730 3249 0.625316 ATTCCCACTGCTATGCCACA 59.375 50.000 0.00 0.00 0.00 4.17
2731 3250 1.312815 GATTCCCACTGCTATGCCAC 58.687 55.000 0.00 0.00 0.00 5.01
2732 3251 0.918258 TGATTCCCACTGCTATGCCA 59.082 50.000 0.00 0.00 0.00 4.92
2733 3252 2.057137 TTGATTCCCACTGCTATGCC 57.943 50.000 0.00 0.00 0.00 4.40
2734 3253 3.887716 AGATTTGATTCCCACTGCTATGC 59.112 43.478 0.00 0.00 0.00 3.14
2735 3254 5.374921 AGAGATTTGATTCCCACTGCTATG 58.625 41.667 0.00 0.00 0.00 2.23
2736 3255 5.643421 AGAGATTTGATTCCCACTGCTAT 57.357 39.130 0.00 0.00 0.00 2.97
2737 3256 5.045651 TCAAGAGATTTGATTCCCACTGCTA 60.046 40.000 0.00 0.00 0.00 3.49
2738 3257 4.015084 CAAGAGATTTGATTCCCACTGCT 58.985 43.478 0.00 0.00 0.00 4.24
2739 3258 4.012374 TCAAGAGATTTGATTCCCACTGC 58.988 43.478 0.00 0.00 0.00 4.40
2740 3259 7.278135 TCTATCAAGAGATTTGATTCCCACTG 58.722 38.462 7.60 0.00 39.59 3.66
2741 3260 7.443302 TCTATCAAGAGATTTGATTCCCACT 57.557 36.000 7.60 0.00 39.59 4.00
2742 3261 8.688747 AATCTATCAAGAGATTTGATTCCCAC 57.311 34.615 7.60 0.00 42.33 4.61
2752 3271 5.529060 GGCGTCCAAAATCTATCAAGAGATT 59.471 40.000 0.00 0.00 46.02 2.40
2753 3272 5.059833 GGCGTCCAAAATCTATCAAGAGAT 58.940 41.667 0.00 0.00 37.81 2.75
2754 3273 4.442706 GGCGTCCAAAATCTATCAAGAGA 58.557 43.478 0.00 0.00 34.49 3.10
2755 3274 3.246226 CGGCGTCCAAAATCTATCAAGAG 59.754 47.826 0.00 0.00 34.49 2.85
2756 3275 3.118920 TCGGCGTCCAAAATCTATCAAGA 60.119 43.478 6.85 0.00 35.80 3.02
2757 3276 3.194861 TCGGCGTCCAAAATCTATCAAG 58.805 45.455 6.85 0.00 0.00 3.02
2758 3277 3.254470 TCGGCGTCCAAAATCTATCAA 57.746 42.857 6.85 0.00 0.00 2.57
2759 3278 2.971660 TCGGCGTCCAAAATCTATCA 57.028 45.000 6.85 0.00 0.00 2.15
2760 3279 4.567159 GGATATCGGCGTCCAAAATCTATC 59.433 45.833 6.85 1.69 34.57 2.08
2761 3280 4.020573 TGGATATCGGCGTCCAAAATCTAT 60.021 41.667 14.48 0.00 41.36 1.98
2858 3377 0.687920 TCTAATGTCCGCCCACACAA 59.312 50.000 0.00 0.00 0.00 3.33
2972 3493 4.314440 GCTGCCCAGGACGTGTGA 62.314 66.667 0.00 0.00 0.00 3.58
3054 3579 6.709018 ACTTTTACAACTACACTTGCCATT 57.291 33.333 0.00 0.00 0.00 3.16
3162 3688 2.159627 GTGGCAAGAGGTTAATCACACG 59.840 50.000 0.00 0.00 0.00 4.49
3293 3822 3.698463 GCAGTTGCGCGTACGTGT 61.698 61.111 27.72 7.25 42.83 4.49


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

AutoCloner maintained by Alex Coulton.