Multiple sequence alignment - TraesCS6D01G070600

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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 TraesCS6D01G070600 chr6D 100.000 3221 0 0 1 3221 35632537 35635757 0.000000e+00 5949.0
1 TraesCS6D01G070600 chr6D 97.619 42 1 0 2491 2532 13290847 13290806 4.460000e-09 73.1
2 TraesCS6D01G070600 chr6B 91.928 2428 162 18 362 2767 75037267 75039682 0.000000e+00 3367.0
3 TraesCS6D01G070600 chr6B 91.256 446 30 7 2763 3202 75039726 75040168 1.650000e-167 599.0
4 TraesCS6D01G070600 chr6B 92.697 178 11 2 1 176 75037077 75037254 4.120000e-64 255.0
5 TraesCS6D01G070600 chr6A 95.562 1307 55 1 904 2207 39507719 39509025 0.000000e+00 2089.0
6 TraesCS6D01G070600 chr6A 87.407 405 30 3 422 822 39507291 39507678 2.280000e-121 446.0
7 TraesCS6D01G070600 chr6A 83.465 508 54 21 2531 3015 39510054 39510554 2.280000e-121 446.0
8 TraesCS6D01G070600 chr6A 88.768 276 27 3 2239 2510 39509027 39509302 5.150000e-88 335.0
9 TraesCS6D01G070600 chr6A 81.481 162 16 7 2769 2917 39509781 39509941 1.570000e-23 121.0
10 TraesCS6D01G070600 chr1B 79.079 239 35 8 2763 2991 57648401 57648168 2.000000e-32 150.0
11 TraesCS6D01G070600 chr1B 81.752 137 18 5 2882 3017 57631637 57631507 1.220000e-19 108.0
12 TraesCS6D01G070600 chr1B 95.238 42 2 0 2487 2528 593924376 593924335 2.070000e-07 67.6
13 TraesCS6D01G070600 chrUn 95.455 44 2 0 2486 2529 313622431 313622388 1.600000e-08 71.3
14 TraesCS6D01G070600 chr1A 95.455 44 2 0 2486 2529 561751115 561751072 1.600000e-08 71.3
15 TraesCS6D01G070600 chr1A 91.667 48 3 1 2488 2534 501030194 501030241 7.460000e-07 65.8
16 TraesCS6D01G070600 chr5D 95.349 43 2 0 2487 2529 464070949 464070907 5.770000e-08 69.4
17 TraesCS6D01G070600 chr2D 95.349 43 2 0 2487 2529 35799970 35800012 5.770000e-08 69.4
18 TraesCS6D01G070600 chr5A 95.238 42 2 0 2488 2529 437207144 437207185 2.070000e-07 67.6


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 TraesCS6D01G070600 chr6D 35632537 35635757 3220 False 5949.0 5949 100.000000 1 3221 1 chr6D.!!$F1 3220
1 TraesCS6D01G070600 chr6B 75037077 75040168 3091 False 1407.0 3367 91.960333 1 3202 3 chr6B.!!$F1 3201
2 TraesCS6D01G070600 chr6A 39507291 39510554 3263 False 687.4 2089 87.336600 422 3015 5 chr6A.!!$F1 2593

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
330 333 0.102844 TCTTATTTCGTACCGGCCCG 59.897 55.0 0.00 3.67 0.0 6.13 F
700 712 0.389296 TCGGACGGTACTGCATGTTG 60.389 55.0 0.23 0.00 0.0 3.33 F
701 713 0.669318 CGGACGGTACTGCATGTTGT 60.669 55.0 0.23 0.00 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 1978 1.122019 ACACCTCGAAGGCCTTGTCT 61.122 55.000 26.25 0.0 39.63 3.41 R
2213 2231 1.148273 AAGCACCGGCAACAGAAGA 59.852 52.632 0.00 0.0 44.61 2.87 R
2224 2242 2.639286 GGTGTGAAGCAAGCACCG 59.361 61.111 0.00 0.0 42.43 4.94 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
45 47 4.227134 CGTGGAGGGCGAGGATGG 62.227 72.222 0.00 0.00 0.00 3.51
94 97 6.603237 TCGCAATCATTGTATTAGGACAAG 57.397 37.500 0.00 0.00 42.38 3.16
95 98 6.345298 TCGCAATCATTGTATTAGGACAAGA 58.655 36.000 0.00 0.00 42.38 3.02
99 102 9.277783 GCAATCATTGTATTAGGACAAGATACT 57.722 33.333 0.00 0.00 42.38 2.12
166 169 2.892334 CGTGGCTCGTGTTGTTGGG 61.892 63.158 0.00 0.00 34.52 4.12
195 198 6.130298 TGACTTTGGTCACAAGTTGTATTG 57.870 37.500 8.49 0.00 46.19 1.90
196 199 5.883115 TGACTTTGGTCACAAGTTGTATTGA 59.117 36.000 8.49 0.00 46.19 2.57
197 200 6.131544 ACTTTGGTCACAAGTTGTATTGAC 57.868 37.500 8.49 11.84 37.97 3.18
198 201 5.650266 ACTTTGGTCACAAGTTGTATTGACA 59.350 36.000 20.46 9.53 40.18 3.58
199 202 5.493133 TTGGTCACAAGTTGTATTGACAC 57.507 39.130 20.46 13.17 40.18 3.67
200 203 4.518249 TGGTCACAAGTTGTATTGACACA 58.482 39.130 20.46 14.86 40.18 3.72
201 204 5.129634 TGGTCACAAGTTGTATTGACACAT 58.870 37.500 20.46 0.00 40.18 3.21
202 205 5.008514 TGGTCACAAGTTGTATTGACACATG 59.991 40.000 20.46 0.00 40.18 3.21
203 206 5.238432 GGTCACAAGTTGTATTGACACATGA 59.762 40.000 20.46 4.89 40.18 3.07
204 207 6.365839 GTCACAAGTTGTATTGACACATGAG 58.634 40.000 8.49 0.00 38.60 2.90
205 208 5.049474 TCACAAGTTGTATTGACACATGAGC 60.049 40.000 8.49 0.00 34.48 4.26
206 209 4.821260 ACAAGTTGTATTGACACATGAGCA 59.179 37.500 6.75 0.00 34.48 4.26
207 210 5.149273 CAAGTTGTATTGACACATGAGCAC 58.851 41.667 0.00 0.00 34.48 4.40
208 211 4.645535 AGTTGTATTGACACATGAGCACT 58.354 39.130 0.00 0.00 34.48 4.40
209 212 4.453478 AGTTGTATTGACACATGAGCACTG 59.547 41.667 0.00 0.00 34.48 3.66
210 213 3.337358 TGTATTGACACATGAGCACTGG 58.663 45.455 0.00 0.00 0.00 4.00
211 214 1.171308 ATTGACACATGAGCACTGGC 58.829 50.000 0.00 0.00 41.61 4.85
233 236 5.490139 CGGAGCTATGTGTGATGAAAATT 57.510 39.130 0.00 0.00 0.00 1.82
234 237 5.268544 CGGAGCTATGTGTGATGAAAATTG 58.731 41.667 0.00 0.00 0.00 2.32
235 238 5.585390 GGAGCTATGTGTGATGAAAATTGG 58.415 41.667 0.00 0.00 0.00 3.16
236 239 5.002464 AGCTATGTGTGATGAAAATTGGC 57.998 39.130 0.00 0.00 0.00 4.52
237 240 4.114794 GCTATGTGTGATGAAAATTGGCC 58.885 43.478 0.00 0.00 0.00 5.36
238 241 4.381825 GCTATGTGTGATGAAAATTGGCCA 60.382 41.667 0.00 0.00 0.00 5.36
239 242 4.829872 ATGTGTGATGAAAATTGGCCAT 57.170 36.364 6.09 0.00 0.00 4.40
240 243 3.927854 TGTGTGATGAAAATTGGCCATG 58.072 40.909 6.09 0.00 0.00 3.66
241 244 3.264104 GTGTGATGAAAATTGGCCATGG 58.736 45.455 6.09 7.63 0.00 3.66
242 245 2.282407 GTGATGAAAATTGGCCATGGC 58.718 47.619 29.47 29.47 41.06 4.40
256 259 3.488569 TGGCCCGCCCATCTTAGG 61.489 66.667 0.00 0.00 39.18 2.69
267 270 4.170468 CCCATCTTAGGGCAAATACAGT 57.830 45.455 0.00 0.00 43.10 3.55
268 271 3.885297 CCCATCTTAGGGCAAATACAGTG 59.115 47.826 0.00 0.00 43.10 3.66
269 272 4.526970 CCATCTTAGGGCAAATACAGTGT 58.473 43.478 0.00 0.00 0.00 3.55
270 273 5.397447 CCCATCTTAGGGCAAATACAGTGTA 60.397 44.000 5.24 5.24 43.10 2.90
271 274 5.760253 CCATCTTAGGGCAAATACAGTGTAG 59.240 44.000 9.25 0.00 0.00 2.74
272 275 5.353394 TCTTAGGGCAAATACAGTGTAGG 57.647 43.478 9.25 2.43 0.00 3.18
273 276 4.163458 TCTTAGGGCAAATACAGTGTAGGG 59.837 45.833 9.25 2.09 0.00 3.53
274 277 2.557869 AGGGCAAATACAGTGTAGGGA 58.442 47.619 9.25 0.00 0.00 4.20
275 278 2.238898 AGGGCAAATACAGTGTAGGGAC 59.761 50.000 9.25 2.78 0.00 4.46
276 279 2.238898 GGGCAAATACAGTGTAGGGACT 59.761 50.000 9.25 0.00 46.37 3.85
278 281 3.055385 GGCAAATACAGTGTAGGGACTGA 60.055 47.826 9.25 0.00 45.39 3.41
279 282 4.564821 GGCAAATACAGTGTAGGGACTGAA 60.565 45.833 9.25 0.00 45.39 3.02
280 283 4.631813 GCAAATACAGTGTAGGGACTGAAG 59.368 45.833 9.25 0.00 45.39 3.02
281 284 5.794894 CAAATACAGTGTAGGGACTGAAGT 58.205 41.667 9.25 0.00 45.39 3.01
282 285 6.573680 GCAAATACAGTGTAGGGACTGAAGTA 60.574 42.308 9.25 0.00 45.39 2.24
283 286 7.383687 CAAATACAGTGTAGGGACTGAAGTAA 58.616 38.462 9.25 0.00 45.39 2.24
284 287 7.549147 AATACAGTGTAGGGACTGAAGTAAA 57.451 36.000 9.25 0.00 45.39 2.01
285 288 5.211174 ACAGTGTAGGGACTGAAGTAAAC 57.789 43.478 7.65 0.00 45.39 2.01
286 289 4.900054 ACAGTGTAGGGACTGAAGTAAACT 59.100 41.667 7.65 0.00 45.39 2.66
287 290 5.221461 ACAGTGTAGGGACTGAAGTAAACTG 60.221 44.000 7.65 0.00 45.39 3.16
288 291 4.283722 AGTGTAGGGACTGAAGTAAACTGG 59.716 45.833 0.00 0.00 41.52 4.00
289 292 3.581332 TGTAGGGACTGAAGTAAACTGGG 59.419 47.826 0.00 0.00 41.52 4.45
290 293 2.986050 AGGGACTGAAGTAAACTGGGA 58.014 47.619 0.00 0.00 37.18 4.37
291 294 2.638363 AGGGACTGAAGTAAACTGGGAC 59.362 50.000 0.00 0.00 37.18 4.46
292 295 2.370849 GGGACTGAAGTAAACTGGGACA 59.629 50.000 0.00 0.00 0.00 4.02
293 296 3.400255 GGACTGAAGTAAACTGGGACAC 58.600 50.000 0.00 0.00 0.00 3.67
294 297 3.057734 GACTGAAGTAAACTGGGACACG 58.942 50.000 0.00 0.00 0.00 4.49
295 298 2.696707 ACTGAAGTAAACTGGGACACGA 59.303 45.455 0.00 0.00 0.00 4.35
296 299 3.243771 ACTGAAGTAAACTGGGACACGAG 60.244 47.826 0.00 0.00 0.00 4.18
297 300 2.036733 TGAAGTAAACTGGGACACGAGG 59.963 50.000 0.00 0.00 0.00 4.63
298 301 2.005370 AGTAAACTGGGACACGAGGA 57.995 50.000 0.00 0.00 0.00 3.71
299 302 2.322658 AGTAAACTGGGACACGAGGAA 58.677 47.619 0.00 0.00 0.00 3.36
300 303 2.701951 AGTAAACTGGGACACGAGGAAA 59.298 45.455 0.00 0.00 0.00 3.13
301 304 2.721425 AAACTGGGACACGAGGAAAA 57.279 45.000 0.00 0.00 0.00 2.29
302 305 2.721425 AACTGGGACACGAGGAAAAA 57.279 45.000 0.00 0.00 0.00 1.94
325 328 7.529880 AAAATAGTGGTCTTATTTCGTACCG 57.470 36.000 0.00 0.00 34.60 4.02
326 329 3.515330 AGTGGTCTTATTTCGTACCGG 57.485 47.619 0.00 0.00 34.60 5.28
327 330 1.929169 GTGGTCTTATTTCGTACCGGC 59.071 52.381 0.00 0.00 34.60 6.13
328 331 1.134729 TGGTCTTATTTCGTACCGGCC 60.135 52.381 0.00 0.00 34.60 6.13
329 332 1.575244 GTCTTATTTCGTACCGGCCC 58.425 55.000 0.00 0.00 0.00 5.80
330 333 0.102844 TCTTATTTCGTACCGGCCCG 59.897 55.000 0.00 3.67 0.00 6.13
331 334 1.493134 CTTATTTCGTACCGGCCCGC 61.493 60.000 0.00 0.00 0.00 6.13
332 335 2.921692 TTATTTCGTACCGGCCCGCC 62.922 60.000 0.00 0.00 0.00 6.13
349 352 2.246719 GCCCAACTCTGGCTACATAG 57.753 55.000 0.00 0.00 45.70 2.23
350 353 1.811941 GCCCAACTCTGGCTACATAGC 60.812 57.143 2.06 2.06 45.70 2.97
358 361 4.345337 GCTACATAGCTCCGCCAC 57.655 61.111 3.56 0.00 45.62 5.01
359 362 1.742768 GCTACATAGCTCCGCCACT 59.257 57.895 3.56 0.00 45.62 4.00
360 363 0.598680 GCTACATAGCTCCGCCACTG 60.599 60.000 3.56 0.00 45.62 3.66
375 378 1.271379 CCACTGCACATGAGCATTGTT 59.729 47.619 25.71 8.27 44.68 2.83
378 381 3.058085 CACTGCACATGAGCATTGTTACA 60.058 43.478 21.78 0.00 44.68 2.41
381 384 2.489329 GCACATGAGCATTGTTACAGGT 59.511 45.455 10.48 0.00 0.00 4.00
382 385 3.689161 GCACATGAGCATTGTTACAGGTA 59.311 43.478 10.48 0.00 0.00 3.08
389 392 6.341316 TGAGCATTGTTACAGGTATCTCTTC 58.659 40.000 0.00 0.00 0.00 2.87
390 393 5.352284 AGCATTGTTACAGGTATCTCTTCG 58.648 41.667 0.00 0.00 0.00 3.79
392 395 5.232414 GCATTGTTACAGGTATCTCTTCGAC 59.768 44.000 0.00 0.00 0.00 4.20
405 408 4.065088 TCTCTTCGACCTGGTTCATTTTG 58.935 43.478 0.00 0.00 0.00 2.44
410 413 4.452825 TCGACCTGGTTCATTTTGTAACA 58.547 39.130 0.00 0.00 0.00 2.41
411 414 4.513692 TCGACCTGGTTCATTTTGTAACAG 59.486 41.667 0.00 0.00 0.00 3.16
412 415 4.274950 CGACCTGGTTCATTTTGTAACAGT 59.725 41.667 0.00 0.00 0.00 3.55
417 420 9.357161 ACCTGGTTCATTTTGTAACAGTTATAA 57.643 29.630 0.00 0.00 0.00 0.98
499 504 3.632604 TCGAATGCAAACTTGTTTACCCA 59.367 39.130 0.00 0.00 0.00 4.51
527 535 2.793272 TGCGAGCCATTGCAATCG 59.207 55.556 9.53 12.37 43.07 3.34
561 569 8.635765 AGTGGACAGAAGAATATATCTCTCTC 57.364 38.462 0.00 0.00 37.42 3.20
562 570 8.448008 AGTGGACAGAAGAATATATCTCTCTCT 58.552 37.037 0.00 0.00 37.42 3.10
564 572 9.733556 TGGACAGAAGAATATATCTCTCTCTAC 57.266 37.037 0.00 0.00 37.42 2.59
604 612 6.375377 TCATACGTCCAACAAAACTTTATGC 58.625 36.000 0.00 0.00 0.00 3.14
605 613 4.640789 ACGTCCAACAAAACTTTATGCA 57.359 36.364 0.00 0.00 0.00 3.96
619 627 2.847959 TATGCACAACATTGCCATCG 57.152 45.000 0.00 0.00 42.25 3.84
620 628 0.458889 ATGCACAACATTGCCATCGC 60.459 50.000 0.00 0.00 42.25 4.58
640 648 4.628333 TCGCTACCAAAAGTATAGCAACAC 59.372 41.667 3.63 0.00 41.18 3.32
691 703 0.392998 TCCTAGGTGTCGGACGGTAC 60.393 60.000 9.08 0.00 0.00 3.34
697 709 1.076533 GTGTCGGACGGTACTGCATG 61.077 60.000 0.23 0.00 0.00 4.06
698 710 1.214589 GTCGGACGGTACTGCATGT 59.785 57.895 0.23 0.00 0.00 3.21
700 712 0.389296 TCGGACGGTACTGCATGTTG 60.389 55.000 0.23 0.00 0.00 3.33
701 713 0.669318 CGGACGGTACTGCATGTTGT 60.669 55.000 0.23 0.00 0.00 3.32
702 714 1.403116 CGGACGGTACTGCATGTTGTA 60.403 52.381 0.23 0.00 0.00 2.41
703 715 2.268298 GGACGGTACTGCATGTTGTAG 58.732 52.381 0.23 0.00 36.12 2.74
704 716 1.659098 GACGGTACTGCATGTTGTAGC 59.341 52.381 0.23 14.84 33.13 3.58
731 744 2.702592 AGGGCCGATTTCACGAATTA 57.297 45.000 0.00 0.00 35.09 1.40
750 763 2.035783 GGAAAGGTGGAGGGGCAC 59.964 66.667 0.00 0.00 0.00 5.01
862 875 1.332178 GTCGAGCACGTGAGAGAAAG 58.668 55.000 22.23 2.54 40.69 2.62
878 891 1.402107 AAAGCCCAGCCCAACAACAG 61.402 55.000 0.00 0.00 0.00 3.16
889 902 3.491598 AACAACAGGCCCACGGGAG 62.492 63.158 6.21 0.00 37.50 4.30
915 928 4.161295 TCGCTCGAAGCCCATGGG 62.161 66.667 27.87 27.87 38.18 4.00
1106 1124 4.689549 TCGTCCCGAAGCCCTCCA 62.690 66.667 0.00 0.00 31.06 3.86
1483 1501 2.283388 TACTCCGCCGACAACCCT 60.283 61.111 0.00 0.00 0.00 4.34
1852 1870 1.815421 GATGTGCGTCAAGGGCGAT 60.815 57.895 0.00 0.00 0.00 4.58
1886 1904 3.144657 TCAAGCTGCTTGAGGAAATGA 57.855 42.857 34.40 15.43 44.27 2.57
1960 1978 1.552337 CTCTGCAGGAACAGGAAGCTA 59.448 52.381 15.13 0.00 38.26 3.32
2017 2035 1.964608 CTGGGATGAAGCTCGAGCCA 61.965 60.000 32.94 24.47 43.38 4.75
2054 2072 0.677731 CATCAGGGCATTGTGTCGGT 60.678 55.000 0.00 0.00 0.00 4.69
2056 2074 2.040544 CAGGGCATTGTGTCGGTCC 61.041 63.158 0.00 0.00 0.00 4.46
2098 2116 4.295141 TGAGGTGTTTGATTACGGGATT 57.705 40.909 0.00 0.00 0.00 3.01
2140 2158 2.432628 GCCGCGTACAGTGAGCTT 60.433 61.111 4.92 0.00 0.00 3.74
2175 2193 2.101770 GCTGCGCAAGATGAAGGC 59.898 61.111 13.05 4.64 43.02 4.35
2224 2242 2.409948 AGCCATAGTCTTCTGTTGCC 57.590 50.000 0.00 0.00 0.00 4.52
2262 2283 3.504906 CCTGATTCAGTGAGTTGCATTGT 59.495 43.478 12.54 0.00 35.84 2.71
2283 2304 4.887071 TGTCTGGCTTGTTTTGATACAGTT 59.113 37.500 0.00 0.00 0.00 3.16
2336 2357 4.935205 TGTGTTTGTATGGAGTGATACTGC 59.065 41.667 0.00 0.00 37.06 4.40
2373 2394 9.793252 AATCAGAATGTAAGATGAAATTTTCGG 57.207 29.630 4.76 0.00 37.40 4.30
2424 2445 3.691498 GTGTGTCAAACTTTGGTAGCAC 58.309 45.455 0.00 6.95 0.00 4.40
2499 2525 6.115446 TGAATTAGCTTGTAATCCCTCTGTG 58.885 40.000 0.00 0.00 0.00 3.66
2510 2536 9.967451 TTGTAATCCCTCTGTGTCAAAATATAA 57.033 29.630 0.00 0.00 0.00 0.98
2594 2815 3.513515 AGACAGGCTCTTCTAAGTTCTGG 59.486 47.826 0.00 0.00 0.00 3.86
2626 2850 6.410540 AGCAAACTGGTTTTAAATGTTCCAA 58.589 32.000 0.00 0.00 0.00 3.53
2640 2864 7.427989 AAATGTTCCAAGAGCATATCCAATT 57.572 32.000 0.00 0.00 32.59 2.32
2645 2876 5.263599 TCCAAGAGCATATCCAATTGTGTT 58.736 37.500 4.43 0.00 0.00 3.32
2646 2877 5.357878 TCCAAGAGCATATCCAATTGTGTTC 59.642 40.000 4.43 3.81 0.00 3.18
2648 2879 6.459298 CCAAGAGCATATCCAATTGTGTTCTC 60.459 42.308 11.71 7.30 32.14 2.87
2660 2891 6.149474 CCAATTGTGTTCTCCTAGGTACAAAG 59.851 42.308 9.08 0.00 32.58 2.77
2693 3463 2.305635 TCTCCTGCACCTTCAGCAAATA 59.694 45.455 0.00 0.00 42.17 1.40
2699 3469 4.025360 TGCACCTTCAGCAAATATTCCAT 58.975 39.130 0.00 0.00 39.39 3.41
2740 3510 7.120579 AGAGTCAGTGTAGGATTGATCGATATC 59.879 40.741 0.00 0.00 0.00 1.63
2741 3511 6.024664 GTCAGTGTAGGATTGATCGATATCG 58.975 44.000 19.14 19.14 41.45 2.92
2796 3639 3.513517 TCTCGGAAAGACCCCTAAGAAA 58.486 45.455 0.00 0.00 34.64 2.52
2806 3649 3.451540 GACCCCTAAGAAACAGAGGTAGG 59.548 52.174 0.00 0.00 0.00 3.18
2850 3693 7.175104 TCCTTTTAGCTATTTTCATGGTGACT 58.825 34.615 0.00 0.00 0.00 3.41
2851 3694 8.325787 TCCTTTTAGCTATTTTCATGGTGACTA 58.674 33.333 0.00 0.00 0.00 2.59
3031 3880 0.043334 AGCAGGGAGGTCTGGTATGT 59.957 55.000 0.00 0.00 42.80 2.29
3058 3907 6.007076 TGCCTCCTGAAGATCATACTACTAG 58.993 44.000 0.00 0.00 0.00 2.57
3060 3909 6.150474 GCCTCCTGAAGATCATACTACTAGAC 59.850 46.154 0.00 0.00 0.00 2.59
3066 3915 8.502105 TGAAGATCATACTACTAGACGAACAA 57.498 34.615 0.00 0.00 0.00 2.83
3067 3916 8.396390 TGAAGATCATACTACTAGACGAACAAC 58.604 37.037 0.00 0.00 0.00 3.32
3072 3921 2.164427 CTACTAGACGAACAACGCGAC 58.836 52.381 15.93 0.00 46.94 5.19
3073 3922 0.308684 ACTAGACGAACAACGCGACA 59.691 50.000 15.93 0.00 46.94 4.35
3074 3923 0.975544 CTAGACGAACAACGCGACAG 59.024 55.000 15.93 4.09 46.94 3.51
3083 3932 0.642291 CAACGCGACAGCACTATCTG 59.358 55.000 15.93 0.00 45.49 2.90
3097 3946 6.868864 CAGCACTATCTGTAGTTGTAACTTGT 59.131 38.462 2.20 0.00 39.12 3.16
3122 3971 3.054878 GCAACTGGAGAAGCATGTTTTG 58.945 45.455 0.00 0.00 0.00 2.44
3124 3973 1.615392 ACTGGAGAAGCATGTTTTGGC 59.385 47.619 0.00 0.00 0.00 4.52
3149 3998 2.294233 GCAAGTTCCAGCACATCTTGAA 59.706 45.455 7.28 0.00 38.06 2.69
3170 4019 3.402110 AGAAACAGCGACACATTCATCA 58.598 40.909 0.00 0.00 0.00 3.07
3171 4020 4.005650 AGAAACAGCGACACATTCATCAT 58.994 39.130 0.00 0.00 0.00 2.45
3202 4051 2.954989 TGTTGCTTACCTGCATGACAAA 59.045 40.909 0.00 0.00 42.96 2.83
3203 4052 3.573538 TGTTGCTTACCTGCATGACAAAT 59.426 39.130 0.00 0.00 42.96 2.32
3204 4053 4.039004 TGTTGCTTACCTGCATGACAAATT 59.961 37.500 0.00 0.00 42.96 1.82
3205 4054 4.177165 TGCTTACCTGCATGACAAATTG 57.823 40.909 0.00 0.00 38.12 2.32
3206 4055 3.825585 TGCTTACCTGCATGACAAATTGA 59.174 39.130 0.00 0.00 38.12 2.57
3207 4056 4.168760 GCTTACCTGCATGACAAATTGAC 58.831 43.478 0.00 0.00 0.00 3.18
3208 4057 4.321156 GCTTACCTGCATGACAAATTGACA 60.321 41.667 0.00 0.00 0.00 3.58
3209 4058 5.771469 CTTACCTGCATGACAAATTGACAA 58.229 37.500 0.00 0.00 0.00 3.18
3210 4059 3.981211 ACCTGCATGACAAATTGACAAC 58.019 40.909 0.00 0.00 0.00 3.32
3211 4060 3.384146 ACCTGCATGACAAATTGACAACA 59.616 39.130 0.00 2.46 0.00 3.33
3212 4061 4.141981 ACCTGCATGACAAATTGACAACAA 60.142 37.500 0.00 0.00 40.42 2.83
3213 4062 4.809958 CCTGCATGACAAATTGACAACAAA 59.190 37.500 0.00 0.00 39.54 2.83
3214 4063 5.276963 CCTGCATGACAAATTGACAACAAAC 60.277 40.000 0.00 0.00 39.54 2.93
3215 4064 4.569966 TGCATGACAAATTGACAACAAACC 59.430 37.500 0.00 0.00 39.54 3.27
3216 4065 4.569966 GCATGACAAATTGACAACAAACCA 59.430 37.500 0.00 0.00 39.54 3.67
3217 4066 5.236911 GCATGACAAATTGACAACAAACCAT 59.763 36.000 0.00 0.00 39.54 3.55
3218 4067 6.651308 CATGACAAATTGACAACAAACCATG 58.349 36.000 0.00 0.00 39.54 3.66
3219 4068 5.728471 TGACAAATTGACAACAAACCATGT 58.272 33.333 0.00 0.00 46.82 3.21
3220 4069 5.579904 TGACAAATTGACAACAAACCATGTG 59.420 36.000 0.00 0.00 42.99 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.136695 TGCAATTCATGAAATCGGGCC 59.863 47.619 13.09 0.00 0.00 5.80
16 17 2.403259 CCCTCCACGTTTTTGCAATTC 58.597 47.619 0.00 0.00 0.00 2.17
57 59 3.387699 TGATTGCGATAGGATGGTGAGAA 59.612 43.478 0.00 0.00 35.16 2.87
112 115 7.517320 ACTTGCATGGTGGTATTATCTAATGA 58.483 34.615 4.44 0.00 0.00 2.57
128 131 3.436704 ACGAGTGAATGTTACTTGCATGG 59.563 43.478 4.44 0.00 33.68 3.66
176 179 5.416013 TGTGTCAATACAACTTGTGACCAAA 59.584 36.000 4.57 0.00 39.72 3.28
177 180 4.944317 TGTGTCAATACAACTTGTGACCAA 59.056 37.500 4.57 0.00 39.72 3.67
178 181 4.518249 TGTGTCAATACAACTTGTGACCA 58.482 39.130 4.57 2.58 39.72 4.02
179 182 5.238432 TCATGTGTCAATACAACTTGTGACC 59.762 40.000 4.57 0.39 39.72 4.02
180 183 6.299023 TCATGTGTCAATACAACTTGTGAC 57.701 37.500 4.57 4.65 40.64 3.67
181 184 5.049474 GCTCATGTGTCAATACAACTTGTGA 60.049 40.000 4.57 0.00 37.36 3.58
184 187 5.049198 AGTGCTCATGTGTCAATACAACTTG 60.049 40.000 0.00 0.00 37.36 3.16
185 188 5.049198 CAGTGCTCATGTGTCAATACAACTT 60.049 40.000 0.00 0.00 37.36 2.66
186 189 4.453478 CAGTGCTCATGTGTCAATACAACT 59.547 41.667 0.00 0.00 37.36 3.16
187 190 4.378770 CCAGTGCTCATGTGTCAATACAAC 60.379 45.833 0.00 0.00 37.36 3.32
188 191 3.752747 CCAGTGCTCATGTGTCAATACAA 59.247 43.478 0.00 0.00 37.36 2.41
189 192 3.337358 CCAGTGCTCATGTGTCAATACA 58.663 45.455 0.00 0.00 34.63 2.29
190 193 2.096496 GCCAGTGCTCATGTGTCAATAC 59.904 50.000 0.00 0.00 33.53 1.89
191 194 2.358957 GCCAGTGCTCATGTGTCAATA 58.641 47.619 0.00 0.00 33.53 1.90
192 195 1.171308 GCCAGTGCTCATGTGTCAAT 58.829 50.000 0.00 0.00 33.53 2.57
193 196 1.229975 CGCCAGTGCTCATGTGTCAA 61.230 55.000 0.00 0.00 34.43 3.18
194 197 1.668793 CGCCAGTGCTCATGTGTCA 60.669 57.895 0.00 0.00 34.43 3.58
195 198 2.393768 CCGCCAGTGCTCATGTGTC 61.394 63.158 0.00 0.00 34.43 3.67
196 199 2.359107 CCGCCAGTGCTCATGTGT 60.359 61.111 0.00 0.00 34.43 3.72
197 200 2.046988 TCCGCCAGTGCTCATGTG 60.047 61.111 0.00 0.00 34.43 3.21
198 201 2.267006 CTCCGCCAGTGCTCATGT 59.733 61.111 0.00 0.00 34.43 3.21
199 202 2.302199 TAGCTCCGCCAGTGCTCATG 62.302 60.000 0.00 0.00 44.07 3.07
200 203 1.406065 ATAGCTCCGCCAGTGCTCAT 61.406 55.000 0.00 0.00 44.07 2.90
201 204 2.060383 ATAGCTCCGCCAGTGCTCA 61.060 57.895 0.00 0.00 44.07 4.26
202 205 1.593750 CATAGCTCCGCCAGTGCTC 60.594 63.158 0.00 0.00 44.07 4.26
203 206 2.362369 ACATAGCTCCGCCAGTGCT 61.362 57.895 0.00 3.75 46.70 4.40
204 207 2.176273 CACATAGCTCCGCCAGTGC 61.176 63.158 0.00 0.00 35.13 4.40
205 208 1.086067 CACACATAGCTCCGCCAGTG 61.086 60.000 0.00 0.00 33.52 3.66
206 209 1.219124 CACACATAGCTCCGCCAGT 59.781 57.895 0.00 0.00 0.00 4.00
207 210 0.105593 ATCACACATAGCTCCGCCAG 59.894 55.000 0.00 0.00 0.00 4.85
208 211 0.179076 CATCACACATAGCTCCGCCA 60.179 55.000 0.00 0.00 0.00 5.69
209 212 0.104855 TCATCACACATAGCTCCGCC 59.895 55.000 0.00 0.00 0.00 6.13
210 213 1.939974 TTCATCACACATAGCTCCGC 58.060 50.000 0.00 0.00 0.00 5.54
211 214 5.268544 CAATTTTCATCACACATAGCTCCG 58.731 41.667 0.00 0.00 0.00 4.63
212 215 5.585390 CCAATTTTCATCACACATAGCTCC 58.415 41.667 0.00 0.00 0.00 4.70
213 216 5.039333 GCCAATTTTCATCACACATAGCTC 58.961 41.667 0.00 0.00 0.00 4.09
214 217 4.142093 GGCCAATTTTCATCACACATAGCT 60.142 41.667 0.00 0.00 0.00 3.32
215 218 4.114794 GGCCAATTTTCATCACACATAGC 58.885 43.478 0.00 0.00 0.00 2.97
216 219 5.327616 TGGCCAATTTTCATCACACATAG 57.672 39.130 0.61 0.00 0.00 2.23
217 220 5.395435 CCATGGCCAATTTTCATCACACATA 60.395 40.000 10.96 0.00 0.00 2.29
218 221 4.509616 CATGGCCAATTTTCATCACACAT 58.490 39.130 10.96 0.00 0.00 3.21
219 222 3.306849 CCATGGCCAATTTTCATCACACA 60.307 43.478 10.96 0.00 0.00 3.72
220 223 3.264104 CCATGGCCAATTTTCATCACAC 58.736 45.455 10.96 0.00 0.00 3.82
221 224 2.354906 GCCATGGCCAATTTTCATCACA 60.355 45.455 27.24 0.00 34.56 3.58
222 225 2.282407 GCCATGGCCAATTTTCATCAC 58.718 47.619 27.24 0.00 34.56 3.06
223 226 2.695127 GCCATGGCCAATTTTCATCA 57.305 45.000 27.24 0.00 34.56 3.07
236 239 3.132029 TAAGATGGGCGGGCCATGG 62.132 63.158 37.16 7.63 37.98 3.66
237 240 1.601759 CTAAGATGGGCGGGCCATG 60.602 63.158 37.16 20.52 37.98 3.66
238 241 2.833913 CCTAAGATGGGCGGGCCAT 61.834 63.158 33.40 33.40 37.98 4.40
239 242 3.488569 CCTAAGATGGGCGGGCCA 61.489 66.667 26.51 26.51 37.98 5.36
240 243 4.271016 CCCTAAGATGGGCGGGCC 62.271 72.222 14.65 14.65 40.84 5.80
247 250 4.526970 ACACTGTATTTGCCCTAAGATGG 58.473 43.478 0.00 0.00 0.00 3.51
248 251 5.760253 CCTACACTGTATTTGCCCTAAGATG 59.240 44.000 0.00 0.00 0.00 2.90
249 252 5.163195 CCCTACACTGTATTTGCCCTAAGAT 60.163 44.000 0.00 0.00 0.00 2.40
250 253 4.163458 CCCTACACTGTATTTGCCCTAAGA 59.837 45.833 0.00 0.00 0.00 2.10
251 254 4.163458 TCCCTACACTGTATTTGCCCTAAG 59.837 45.833 0.00 0.00 0.00 2.18
252 255 4.080751 GTCCCTACACTGTATTTGCCCTAA 60.081 45.833 0.00 0.00 0.00 2.69
253 256 3.453353 GTCCCTACACTGTATTTGCCCTA 59.547 47.826 0.00 0.00 0.00 3.53
254 257 2.238898 GTCCCTACACTGTATTTGCCCT 59.761 50.000 0.00 0.00 0.00 5.19
255 258 2.238898 AGTCCCTACACTGTATTTGCCC 59.761 50.000 0.00 0.00 0.00 5.36
256 259 3.055385 TCAGTCCCTACACTGTATTTGCC 60.055 47.826 0.74 0.00 43.80 4.52
257 260 4.202245 TCAGTCCCTACACTGTATTTGC 57.798 45.455 0.74 0.00 43.80 3.68
258 261 5.794894 ACTTCAGTCCCTACACTGTATTTG 58.205 41.667 0.74 0.00 43.80 2.32
259 262 7.549147 TTACTTCAGTCCCTACACTGTATTT 57.451 36.000 0.74 0.00 43.80 1.40
260 263 7.234988 AGTTTACTTCAGTCCCTACACTGTATT 59.765 37.037 0.74 0.00 43.80 1.89
261 264 6.724905 AGTTTACTTCAGTCCCTACACTGTAT 59.275 38.462 0.74 0.00 43.80 2.29
262 265 6.015688 CAGTTTACTTCAGTCCCTACACTGTA 60.016 42.308 0.74 0.00 43.80 2.74
263 266 4.900054 AGTTTACTTCAGTCCCTACACTGT 59.100 41.667 0.74 0.00 43.80 3.55
264 267 5.230942 CAGTTTACTTCAGTCCCTACACTG 58.769 45.833 0.00 0.00 44.61 3.66
265 268 4.283722 CCAGTTTACTTCAGTCCCTACACT 59.716 45.833 0.00 0.00 0.00 3.55
266 269 4.562963 CCCAGTTTACTTCAGTCCCTACAC 60.563 50.000 0.00 0.00 0.00 2.90
267 270 3.581332 CCCAGTTTACTTCAGTCCCTACA 59.419 47.826 0.00 0.00 0.00 2.74
268 271 3.836562 TCCCAGTTTACTTCAGTCCCTAC 59.163 47.826 0.00 0.00 0.00 3.18
269 272 3.836562 GTCCCAGTTTACTTCAGTCCCTA 59.163 47.826 0.00 0.00 0.00 3.53
270 273 2.638363 GTCCCAGTTTACTTCAGTCCCT 59.362 50.000 0.00 0.00 0.00 4.20
271 274 2.370849 TGTCCCAGTTTACTTCAGTCCC 59.629 50.000 0.00 0.00 0.00 4.46
272 275 3.400255 GTGTCCCAGTTTACTTCAGTCC 58.600 50.000 0.00 0.00 0.00 3.85
273 276 3.057734 CGTGTCCCAGTTTACTTCAGTC 58.942 50.000 0.00 0.00 0.00 3.51
274 277 2.696707 TCGTGTCCCAGTTTACTTCAGT 59.303 45.455 0.00 0.00 0.00 3.41
275 278 3.318017 CTCGTGTCCCAGTTTACTTCAG 58.682 50.000 0.00 0.00 0.00 3.02
276 279 2.036733 CCTCGTGTCCCAGTTTACTTCA 59.963 50.000 0.00 0.00 0.00 3.02
277 280 2.298163 TCCTCGTGTCCCAGTTTACTTC 59.702 50.000 0.00 0.00 0.00 3.01
278 281 2.322658 TCCTCGTGTCCCAGTTTACTT 58.677 47.619 0.00 0.00 0.00 2.24
279 282 2.005370 TCCTCGTGTCCCAGTTTACT 57.995 50.000 0.00 0.00 0.00 2.24
280 283 2.825861 TTCCTCGTGTCCCAGTTTAC 57.174 50.000 0.00 0.00 0.00 2.01
281 284 3.842007 TTTTCCTCGTGTCCCAGTTTA 57.158 42.857 0.00 0.00 0.00 2.01
282 285 2.721425 TTTTCCTCGTGTCCCAGTTT 57.279 45.000 0.00 0.00 0.00 2.66
283 286 2.721425 TTTTTCCTCGTGTCCCAGTT 57.279 45.000 0.00 0.00 0.00 3.16
331 334 2.246719 GCTATGTAGCCAGAGTTGGG 57.753 55.000 0.48 0.00 45.16 4.12
350 353 2.046988 TCATGTGCAGTGGCGGAG 60.047 61.111 0.00 0.00 45.35 4.63
351 354 2.046988 CTCATGTGCAGTGGCGGA 60.047 61.111 0.00 0.00 45.35 5.54
352 355 3.807538 GCTCATGTGCAGTGGCGG 61.808 66.667 14.66 0.00 45.35 6.13
353 356 1.929806 AATGCTCATGTGCAGTGGCG 61.930 55.000 24.89 0.00 46.71 5.69
354 357 1.888018 AATGCTCATGTGCAGTGGC 59.112 52.632 24.89 5.88 46.71 5.01
357 360 3.148412 TGTAACAATGCTCATGTGCAGT 58.852 40.909 24.89 20.79 46.71 4.40
358 361 3.427098 CCTGTAACAATGCTCATGTGCAG 60.427 47.826 24.89 15.89 46.71 4.41
360 363 2.489329 ACCTGTAACAATGCTCATGTGC 59.511 45.455 12.78 12.78 0.00 4.57
378 381 2.830651 ACCAGGTCGAAGAGATACCT 57.169 50.000 0.00 0.00 44.54 3.08
381 384 5.677319 AAATGAACCAGGTCGAAGAGATA 57.323 39.130 0.00 0.00 36.95 1.98
382 385 4.559862 AAATGAACCAGGTCGAAGAGAT 57.440 40.909 0.00 0.00 36.95 2.75
389 392 4.274950 ACTGTTACAAAATGAACCAGGTCG 59.725 41.667 0.00 0.00 0.00 4.79
390 393 5.767816 ACTGTTACAAAATGAACCAGGTC 57.232 39.130 0.00 0.00 0.00 3.85
410 413 9.099454 GTCCTTCAATTGAGTTCGATTATAACT 57.901 33.333 8.41 0.00 39.84 2.24
411 414 8.879759 TGTCCTTCAATTGAGTTCGATTATAAC 58.120 33.333 8.41 0.00 0.00 1.89
412 415 9.613428 ATGTCCTTCAATTGAGTTCGATTATAA 57.387 29.630 8.41 0.00 0.00 0.98
417 420 5.491070 TCATGTCCTTCAATTGAGTTCGAT 58.509 37.500 8.41 0.00 0.00 3.59
419 422 5.611796 TTCATGTCCTTCAATTGAGTTCG 57.388 39.130 8.41 0.00 0.00 3.95
452 457 5.841810 TCTTGCCTAAACTTTGATGTTTGG 58.158 37.500 0.00 0.00 40.00 3.28
461 466 4.083271 GCATTCGACTCTTGCCTAAACTTT 60.083 41.667 0.00 0.00 0.00 2.66
464 469 2.742053 TGCATTCGACTCTTGCCTAAAC 59.258 45.455 6.42 0.00 35.51 2.01
499 504 0.107897 TGGCTCGCATACAAACCGAT 60.108 50.000 0.00 0.00 0.00 4.18
553 561 7.070447 TGGATTTGCAAGTATGTAGAGAGAGAT 59.930 37.037 0.00 0.00 0.00 2.75
561 569 7.171508 ACGTATGATGGATTTGCAAGTATGTAG 59.828 37.037 0.00 0.00 0.00 2.74
562 570 6.989759 ACGTATGATGGATTTGCAAGTATGTA 59.010 34.615 0.00 0.00 0.00 2.29
564 572 6.304356 ACGTATGATGGATTTGCAAGTATG 57.696 37.500 0.00 0.00 0.00 2.39
566 574 4.814234 GGACGTATGATGGATTTGCAAGTA 59.186 41.667 0.00 0.00 0.00 2.24
567 575 3.627577 GGACGTATGATGGATTTGCAAGT 59.372 43.478 0.00 0.00 0.00 3.16
568 576 3.627123 TGGACGTATGATGGATTTGCAAG 59.373 43.478 0.00 0.00 0.00 4.01
569 577 3.615155 TGGACGTATGATGGATTTGCAA 58.385 40.909 0.00 0.00 0.00 4.08
570 578 3.274095 TGGACGTATGATGGATTTGCA 57.726 42.857 0.00 0.00 0.00 4.08
604 612 1.202177 GGTAGCGATGGCAATGTTGTG 60.202 52.381 1.50 0.00 43.41 3.33
605 613 1.094785 GGTAGCGATGGCAATGTTGT 58.905 50.000 1.50 0.00 43.41 3.32
619 627 5.642063 TCTGTGTTGCTATACTTTTGGTAGC 59.358 40.000 0.00 0.00 40.85 3.58
620 628 7.063544 GTCTCTGTGTTGCTATACTTTTGGTAG 59.936 40.741 0.00 0.00 33.51 3.18
640 648 2.229062 AGTGTGTATGGTCACGTCTCTG 59.771 50.000 0.00 0.00 40.74 3.35
698 710 0.326927 GGCCCTAGGTTGTGCTACAA 59.673 55.000 8.29 0.00 35.42 2.41
700 712 1.153429 CGGCCCTAGGTTGTGCTAC 60.153 63.158 8.29 0.00 0.00 3.58
701 713 0.689745 ATCGGCCCTAGGTTGTGCTA 60.690 55.000 8.29 0.00 0.00 3.49
702 714 1.562672 AATCGGCCCTAGGTTGTGCT 61.563 55.000 8.29 0.00 0.00 4.40
703 715 0.679960 AAATCGGCCCTAGGTTGTGC 60.680 55.000 8.29 3.41 0.00 4.57
704 716 1.339631 TGAAATCGGCCCTAGGTTGTG 60.340 52.381 8.29 0.00 0.00 3.33
731 744 3.647771 GCCCCTCCACCTTTCCGT 61.648 66.667 0.00 0.00 0.00 4.69
734 747 2.359975 CGTGCCCCTCCACCTTTC 60.360 66.667 0.00 0.00 32.10 2.62
831 844 2.345991 CTCGACGGGGCAGGAAAA 59.654 61.111 0.00 0.00 0.00 2.29
862 875 3.305516 CCTGTTGTTGGGCTGGGC 61.306 66.667 0.00 0.00 0.00 5.36
878 891 3.647771 AGAAACCTCCCGTGGGCC 61.648 66.667 0.00 0.00 34.68 5.80
889 902 1.960994 GCTTCGAGCGAGCAGAAACC 61.961 60.000 2.70 0.00 0.00 3.27
891 904 1.738099 GGCTTCGAGCGAGCAGAAA 60.738 57.895 9.64 0.00 43.62 2.52
915 928 3.914426 TCAGCCCAAGGTAAGAAGATC 57.086 47.619 0.00 0.00 0.00 2.75
954 967 3.670377 GTGTCGGGTGGGCTTTGC 61.670 66.667 0.00 0.00 0.00 3.68
968 981 0.611714 GGAATACGACTGTGGGGTGT 59.388 55.000 0.00 0.00 0.00 4.16
1159 1177 1.818959 CGTGGGGAGGTTTACCGTCA 61.819 60.000 0.00 0.00 42.08 4.35
1696 1714 1.338973 GTGTTGTAGGTGACGAGGTCA 59.661 52.381 0.00 0.00 40.50 4.02
1886 1904 2.361610 CTCGCACCCATTGGCCTT 60.362 61.111 3.32 0.00 33.59 4.35
1960 1978 1.122019 ACACCTCGAAGGCCTTGTCT 61.122 55.000 26.25 0.00 39.63 3.41
2068 2086 5.428496 AATCAAACACCTCATATGCATCG 57.572 39.130 0.19 0.00 0.00 3.84
2123 2141 2.432628 AAGCTCACTGTACGCGGC 60.433 61.111 12.47 3.05 0.00 6.53
2140 2158 1.627329 AGCCATTTGAGTGAGCTCTCA 59.373 47.619 16.19 8.49 42.13 3.27
2175 2193 1.592669 CTCGGGCCTTCATGCTACG 60.593 63.158 0.84 0.00 34.55 3.51
2180 2198 1.153086 CCTTCCTCGGGCCTTCATG 60.153 63.158 0.84 0.00 0.00 3.07
2211 2229 1.598130 GCACCGGCAACAGAAGACT 60.598 57.895 0.00 0.00 40.72 3.24
2213 2231 1.148273 AAGCACCGGCAACAGAAGA 59.852 52.632 0.00 0.00 44.61 2.87
2224 2242 2.639286 GGTGTGAAGCAAGCACCG 59.361 61.111 0.00 0.00 42.43 4.94
2262 2283 5.129634 TCAACTGTATCAAAACAAGCCAGA 58.870 37.500 0.00 0.00 0.00 3.86
2296 2317 7.193595 ACAAACACAGTAGTAGTTTCAAATGC 58.806 34.615 0.00 0.00 33.54 3.56
2336 2357 8.272545 TCTTACATTCTGATTGATTGAACAGG 57.727 34.615 6.56 0.00 32.24 4.00
2489 2515 6.986817 CGTCTTATATTTTGACACAGAGGGAT 59.013 38.462 0.00 0.00 0.00 3.85
2547 2767 8.958060 TCTATAGGCTACCAACATTATTCTCT 57.042 34.615 0.00 0.00 0.00 3.10
2551 2771 8.492415 TGTCTCTATAGGCTACCAACATTATT 57.508 34.615 0.00 0.00 0.00 1.40
2611 2835 8.250332 TGGATATGCTCTTGGAACATTTAAAAC 58.750 33.333 0.00 0.00 39.30 2.43
2616 2840 7.093201 ACAATTGGATATGCTCTTGGAACATTT 60.093 33.333 10.83 0.00 39.30 2.32
2621 2845 5.263599 ACACAATTGGATATGCTCTTGGAA 58.736 37.500 10.83 0.00 0.00 3.53
2626 2850 5.104193 AGGAGAACACAATTGGATATGCTCT 60.104 40.000 10.83 5.00 0.00 4.09
2640 2864 3.901844 AGCTTTGTACCTAGGAGAACACA 59.098 43.478 17.98 8.80 0.00 3.72
2645 2876 6.839134 TCATATTCAGCTTTGTACCTAGGAGA 59.161 38.462 17.98 0.00 0.00 3.71
2646 2877 7.055667 TCATATTCAGCTTTGTACCTAGGAG 57.944 40.000 17.98 2.45 0.00 3.69
2648 2879 8.153550 AGAATCATATTCAGCTTTGTACCTAGG 58.846 37.037 7.41 7.41 0.00 3.02
2660 2891 3.501445 GGTGCAGGAGAATCATATTCAGC 59.499 47.826 0.00 2.23 36.25 4.26
2699 3469 4.649674 ACTGACTCTTAACAGTCCAACTCA 59.350 41.667 8.23 0.00 42.61 3.41
2740 3510 0.960861 GGGGAAGGCAAGAAACCTCG 60.961 60.000 0.00 0.00 36.14 4.63
2741 3511 0.405973 AGGGGAAGGCAAGAAACCTC 59.594 55.000 0.00 0.00 36.14 3.85
2796 3639 9.102453 ACTAGATAAAAGAAAACCTACCTCTGT 57.898 33.333 0.00 0.00 0.00 3.41
2825 3668 7.175104 AGTCACCATGAAAATAGCTAAAAGGA 58.825 34.615 0.00 0.00 0.00 3.36
2845 3688 2.389715 AGATGCTGGTACCCTAGTCAC 58.610 52.381 10.07 0.00 0.00 3.67
2850 3693 2.840511 TGGAAAGATGCTGGTACCCTA 58.159 47.619 10.07 0.00 0.00 3.53
2851 3694 1.668826 TGGAAAGATGCTGGTACCCT 58.331 50.000 10.07 0.00 0.00 4.34
2872 3719 7.617041 TTGTTTTCAACTTTTAACCAATGGG 57.383 32.000 3.55 0.00 36.00 4.00
3018 3866 0.107654 GGCACCACATACCAGACCTC 60.108 60.000 0.00 0.00 0.00 3.85
3025 3873 0.618458 TTCAGGAGGCACCACATACC 59.382 55.000 3.18 0.00 42.04 2.73
3031 3880 1.588239 ATGATCTTCAGGAGGCACCA 58.412 50.000 3.18 0.00 42.04 4.17
3058 3907 2.167918 GCTGTCGCGTTGTTCGTC 59.832 61.111 5.77 0.00 42.13 4.20
3060 3909 1.272784 TAGTGCTGTCGCGTTGTTCG 61.273 55.000 5.77 0.00 39.65 3.95
3066 3915 1.064208 CTACAGATAGTGCTGTCGCGT 59.936 52.381 5.77 0.00 45.54 6.01
3067 3916 1.064208 ACTACAGATAGTGCTGTCGCG 59.936 52.381 0.00 0.00 45.54 5.87
3072 3921 6.868864 ACAAGTTACAACTACAGATAGTGCTG 59.131 38.462 0.00 0.00 41.00 4.41
3073 3922 6.994221 ACAAGTTACAACTACAGATAGTGCT 58.006 36.000 0.00 0.00 41.00 4.40
3074 3923 8.752766 TTACAAGTTACAACTACAGATAGTGC 57.247 34.615 0.00 0.00 41.00 4.40
3083 3932 6.293244 CCAGTTGCCTTACAAGTTACAACTAC 60.293 42.308 15.82 0.00 44.21 2.73
3097 3946 2.040278 ACATGCTTCTCCAGTTGCCTTA 59.960 45.455 0.00 0.00 0.00 2.69
3122 3971 3.435186 GCTGGAACTTGCTCCGCC 61.435 66.667 0.00 0.00 38.44 6.13
3124 3973 0.957395 ATGTGCTGGAACTTGCTCCG 60.957 55.000 0.00 0.00 38.44 4.63
3139 3988 3.248363 TGTCGCTGTTTCTTCAAGATGTG 59.752 43.478 0.00 0.00 0.00 3.21
3140 3989 3.248602 GTGTCGCTGTTTCTTCAAGATGT 59.751 43.478 0.00 0.00 0.00 3.06
3149 3998 3.402110 TGATGAATGTGTCGCTGTTTCT 58.598 40.909 0.00 0.00 0.00 2.52
3170 4019 2.489329 GGTAAGCAACATCACACTGCAT 59.511 45.455 0.00 0.00 38.58 3.96
3171 4020 1.879380 GGTAAGCAACATCACACTGCA 59.121 47.619 0.00 0.00 38.58 4.41


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

AutoCloner maintained by Alex Coulton.