Multiple sequence alignment - TraesCS2D01G073200

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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 TraesCS2D01G073200 chr2D 100.000 3436 0 0 1 3436 30663141 30659706 0.000000e+00 6346
1 TraesCS2D01G073200 chr2D 76.854 890 118 40 1708 2536 630090802 630089940 4.100000e-114 422
2 TraesCS2D01G073200 chr2D 78.816 321 45 19 828 1129 630631973 630632289 9.730000e-46 195
3 TraesCS2D01G073200 chr2D 79.710 276 49 6 859 1129 630091573 630091300 3.500000e-45 193
4 TraesCS2D01G073200 chr2B 92.390 2050 99 21 1431 3436 50483354 50485390 0.000000e+00 2868
5 TraesCS2D01G073200 chr2B 90.236 932 48 13 2537 3436 43804999 43804079 0.000000e+00 1177
6 TraesCS2D01G073200 chr2B 86.430 619 47 13 830 1444 50482750 50483335 0.000000e+00 643
7 TraesCS2D01G073200 chr2B 83.956 455 38 11 3004 3436 50630428 50629987 1.490000e-108 403
8 TraesCS2D01G073200 chr2A 90.639 1079 51 21 736 1792 32922770 32921720 0.000000e+00 1387
9 TraesCS2D01G073200 chr2A 92.655 776 38 8 1844 2619 32921702 32920946 0.000000e+00 1099
10 TraesCS2D01G073200 chr2A 84.792 1131 121 31 1436 2535 33003274 33004384 0.000000e+00 1088
11 TraesCS2D01G073200 chr2A 90.395 354 26 2 3091 3436 32920452 32920099 3.120000e-125 459
12 TraesCS2D01G073200 chr2A 77.374 853 93 44 2629 3436 33021241 33022038 6.860000e-112 414
13 TraesCS2D01G073200 chr2A 85.319 361 23 15 2608 2966 32920912 32920580 2.540000e-91 346
14 TraesCS2D01G073200 chr2A 83.284 341 35 8 3117 3436 33004964 33005303 9.330000e-76 294
15 TraesCS2D01G073200 chr2A 76.654 544 76 18 1 527 32923724 32923215 1.580000e-63 254
16 TraesCS2D01G073200 chr2A 94.253 87 5 0 2533 2619 33004409 33004495 2.150000e-27 134
17 TraesCS2D01G073200 chr2A 87.778 90 8 1 2629 2718 33004536 33004622 6.070000e-18 102


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 TraesCS2D01G073200 chr2D 30659706 30663141 3435 True 6346.0 6346 100.00000 1 3436 1 chr2D.!!$R1 3435
1 TraesCS2D01G073200 chr2D 630089940 630091573 1633 True 307.5 422 78.28200 859 2536 2 chr2D.!!$R2 1677
2 TraesCS2D01G073200 chr2B 50482750 50485390 2640 False 1755.5 2868 89.41000 830 3436 2 chr2B.!!$F1 2606
3 TraesCS2D01G073200 chr2B 43804079 43804999 920 True 1177.0 1177 90.23600 2537 3436 1 chr2B.!!$R1 899
4 TraesCS2D01G073200 chr2A 32920099 32923724 3625 True 709.0 1387 87.13240 1 3436 5 chr2A.!!$R1 3435
5 TraesCS2D01G073200 chr2A 33021241 33022038 797 False 414.0 414 77.37400 2629 3436 1 chr2A.!!$F1 807
6 TraesCS2D01G073200 chr2A 33003274 33005303 2029 False 404.5 1088 87.52675 1436 3436 4 chr2A.!!$F2 2000

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
410 428 0.108585 CGAGAGAGAGAGAGAGGGGG 59.891 65.0 0.00 0.00 0.00 5.40 F
444 462 0.238289 GTGTGAATGGACGGTGCAAG 59.762 55.0 6.39 0.00 0.00 4.01 F
1481 1992 0.037790 TGGTCGCGTGATCATGTTCA 60.038 50.0 8.09 2.22 27.66 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1751 0.174617 GAGGGAGAGACGCTGGAAAG 59.825 60.0 0.0 0.0 41.84 2.62 R
2072 2667 1.652947 GACTTACCCAGTCCCCAAGA 58.347 55.0 0.0 0.0 45.84 3.02 R
2830 3555 0.034337 AAAAGCCATGCAAGTGCCAG 59.966 50.0 0.0 0.0 41.18 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
31 32 3.050275 GTGGTCAGCCAACGCTCC 61.050 66.667 0.00 0.00 43.95 4.70
36 37 0.884704 GTCAGCCAACGCTCCTGAAA 60.885 55.000 0.00 0.00 43.95 2.69
40 41 1.073199 CCAACGCTCCTGAAACCCT 59.927 57.895 0.00 0.00 0.00 4.34
42 43 0.250295 CAACGCTCCTGAAACCCTGA 60.250 55.000 0.00 0.00 0.00 3.86
45 46 2.035442 GCTCCTGAAACCCTGACGC 61.035 63.158 0.00 0.00 0.00 5.19
81 82 1.641577 GCACTATTGACACCGACTCC 58.358 55.000 0.00 0.00 0.00 3.85
88 89 4.417641 ACACCGACTCCTCGATGT 57.582 55.556 0.00 0.00 42.24 3.06
92 93 1.064946 CCGACTCCTCGATGTCAGC 59.935 63.158 11.87 0.00 43.06 4.26
97 98 2.025767 CTCCTCGATGTCAGCCCCTG 62.026 65.000 0.00 0.00 0.00 4.45
111 113 2.785857 AGCCCCTGATAAACCATTAGCT 59.214 45.455 0.00 0.00 0.00 3.32
113 115 3.435026 GCCCCTGATAAACCATTAGCTGA 60.435 47.826 0.00 0.00 30.57 4.26
127 129 5.006358 CCATTAGCTGATTTTTGCAAGATGC 59.994 40.000 0.00 0.30 45.29 3.91
137 139 1.503542 GCAAGATGCAGGTGGTTCG 59.496 57.895 0.00 0.00 44.26 3.95
142 144 0.734889 GATGCAGGTGGTTCGAATGG 59.265 55.000 0.00 0.00 0.00 3.16
144 146 0.888736 TGCAGGTGGTTCGAATGGTG 60.889 55.000 0.00 0.00 0.00 4.17
146 148 1.609580 GCAGGTGGTTCGAATGGTGTA 60.610 52.381 0.00 0.00 0.00 2.90
149 151 2.569853 AGGTGGTTCGAATGGTGTATGA 59.430 45.455 0.00 0.00 0.00 2.15
151 153 3.945285 GGTGGTTCGAATGGTGTATGAAT 59.055 43.478 0.00 0.00 0.00 2.57
183 186 9.567776 TTCCTCTATGTTTTGTCATAGTTTTCA 57.432 29.630 11.68 0.00 44.25 2.69
192 195 6.723298 TTGTCATAGTTTTCATGTGGGTTT 57.277 33.333 0.00 0.00 0.00 3.27
193 196 7.825331 TTGTCATAGTTTTCATGTGGGTTTA 57.175 32.000 0.00 0.00 0.00 2.01
195 198 7.001674 TGTCATAGTTTTCATGTGGGTTTACT 58.998 34.615 0.00 0.00 0.00 2.24
196 199 7.504238 TGTCATAGTTTTCATGTGGGTTTACTT 59.496 33.333 0.00 0.00 0.00 2.24
198 201 8.919145 TCATAGTTTTCATGTGGGTTTACTTTT 58.081 29.630 0.00 0.00 0.00 2.27
199 202 9.191995 CATAGTTTTCATGTGGGTTTACTTTTC 57.808 33.333 0.00 0.00 0.00 2.29
200 203 7.418337 AGTTTTCATGTGGGTTTACTTTTCT 57.582 32.000 0.00 0.00 0.00 2.52
202 205 7.763985 AGTTTTCATGTGGGTTTACTTTTCTTG 59.236 33.333 0.00 0.00 0.00 3.02
203 206 5.195001 TCATGTGGGTTTACTTTTCTTGC 57.805 39.130 0.00 0.00 0.00 4.01
204 207 3.701532 TGTGGGTTTACTTTTCTTGCG 57.298 42.857 0.00 0.00 0.00 4.85
205 208 2.223618 TGTGGGTTTACTTTTCTTGCGC 60.224 45.455 0.00 0.00 0.00 6.09
206 209 2.025155 TGGGTTTACTTTTCTTGCGCA 58.975 42.857 5.66 5.66 0.00 6.09
207 210 2.427453 TGGGTTTACTTTTCTTGCGCAA 59.573 40.909 23.48 23.48 0.00 4.85
209 212 3.244345 GGGTTTACTTTTCTTGCGCAAAC 59.756 43.478 25.01 15.14 0.00 2.93
211 214 2.392933 TACTTTTCTTGCGCAAACGG 57.607 45.000 25.01 12.96 40.57 4.44
212 215 0.869880 ACTTTTCTTGCGCAAACGGC 60.870 50.000 25.01 0.00 40.57 5.68
213 216 0.594796 CTTTTCTTGCGCAAACGGCT 60.595 50.000 25.01 0.00 41.67 5.52
215 218 0.878416 TTTCTTGCGCAAACGGCTAT 59.122 45.000 25.01 0.00 41.67 2.97
216 219 0.167908 TTCTTGCGCAAACGGCTATG 59.832 50.000 25.01 9.84 41.67 2.23
218 221 1.922135 CTTGCGCAAACGGCTATGGT 61.922 55.000 25.01 0.00 41.67 3.55
219 222 1.519751 TTGCGCAAACGGCTATGGTT 61.520 50.000 22.78 0.00 41.67 3.67
221 224 0.448593 GCGCAAACGGCTATGGTTAA 59.551 50.000 0.30 0.00 41.67 2.01
222 225 1.135632 GCGCAAACGGCTATGGTTAAA 60.136 47.619 0.30 0.00 41.67 1.52
223 226 2.511879 CGCAAACGGCTATGGTTAAAC 58.488 47.619 0.00 0.00 41.67 2.01
224 227 2.160813 CGCAAACGGCTATGGTTAAACT 59.839 45.455 0.00 0.00 41.67 2.66
225 228 3.498082 GCAAACGGCTATGGTTAAACTG 58.502 45.455 0.00 0.00 40.25 3.16
226 229 3.057806 GCAAACGGCTATGGTTAAACTGT 60.058 43.478 0.00 0.00 40.25 3.55
227 230 4.557895 GCAAACGGCTATGGTTAAACTGTT 60.558 41.667 0.00 0.00 40.25 3.16
229 232 5.777850 AACGGCTATGGTTAAACTGTTTT 57.222 34.783 11.48 0.00 0.00 2.43
230 233 5.366829 ACGGCTATGGTTAAACTGTTTTC 57.633 39.130 11.48 5.50 0.00 2.29
231 234 4.083696 ACGGCTATGGTTAAACTGTTTTCG 60.084 41.667 11.48 5.08 0.00 3.46
234 237 6.440436 GGCTATGGTTAAACTGTTTTCGAAA 58.560 36.000 11.48 6.47 0.00 3.46
237 240 8.424731 GCTATGGTTAAACTGTTTTCGAAATTG 58.575 33.333 12.12 7.49 0.00 2.32
238 241 6.576551 TGGTTAAACTGTTTTCGAAATTGC 57.423 33.333 12.12 6.09 0.00 3.56
239 242 6.334202 TGGTTAAACTGTTTTCGAAATTGCT 58.666 32.000 12.12 0.00 0.00 3.91
241 244 7.646130 TGGTTAAACTGTTTTCGAAATTGCTAG 59.354 33.333 12.12 8.30 0.00 3.42
242 245 7.114388 GGTTAAACTGTTTTCGAAATTGCTAGG 59.886 37.037 12.12 1.42 0.00 3.02
243 246 6.385649 AAACTGTTTTCGAAATTGCTAGGA 57.614 33.333 12.12 0.00 0.00 2.94
270 288 4.713321 GGATACCACTGTACTCCTAACCAA 59.287 45.833 0.00 0.00 0.00 3.67
277 295 3.320129 TGTACTCCTAACCAACCAACCT 58.680 45.455 0.00 0.00 0.00 3.50
288 306 0.535102 AACCAACCTTGCGAGTGAGG 60.535 55.000 0.00 0.89 39.02 3.86
289 307 2.328099 CCAACCTTGCGAGTGAGGC 61.328 63.158 0.00 0.00 36.48 4.70
290 308 2.032681 AACCTTGCGAGTGAGGCC 59.967 61.111 0.00 0.00 36.48 5.19
295 313 0.886490 CTTGCGAGTGAGGCCAAACT 60.886 55.000 5.01 7.98 0.00 2.66
296 314 1.165907 TTGCGAGTGAGGCCAAACTG 61.166 55.000 14.55 8.46 0.00 3.16
299 317 1.876416 GCGAGTGAGGCCAAACTGTTA 60.876 52.381 14.55 0.00 0.00 2.41
303 321 4.265073 GAGTGAGGCCAAACTGTTATGAT 58.735 43.478 14.55 0.00 0.00 2.45
307 325 5.126061 GTGAGGCCAAACTGTTATGATGATT 59.874 40.000 5.01 0.00 0.00 2.57
308 326 5.716228 TGAGGCCAAACTGTTATGATGATTT 59.284 36.000 5.01 0.00 0.00 2.17
309 327 6.211184 TGAGGCCAAACTGTTATGATGATTTT 59.789 34.615 5.01 0.00 0.00 1.82
310 328 7.008021 AGGCCAAACTGTTATGATGATTTTT 57.992 32.000 5.01 0.00 0.00 1.94
348 366 5.162794 TGAAACAGAATACATGCATTGCAC 58.837 37.500 14.66 0.00 43.04 4.57
349 367 3.409851 ACAGAATACATGCATTGCACG 57.590 42.857 14.66 8.59 43.04 5.34
354 372 4.875536 AGAATACATGCATTGCACGTAAGA 59.124 37.500 19.96 1.54 40.46 2.10
361 379 3.120234 TGCATTGCACGTAAGATTGTCTG 60.120 43.478 7.38 0.00 43.62 3.51
406 424 2.093711 TGTGGTCGAGAGAGAGAGAGAG 60.094 54.545 0.00 0.00 43.49 3.20
408 426 1.202651 GGTCGAGAGAGAGAGAGAGGG 60.203 61.905 0.00 0.00 43.49 4.30
410 428 0.108585 CGAGAGAGAGAGAGAGGGGG 59.891 65.000 0.00 0.00 0.00 5.40
412 430 1.421646 GAGAGAGAGAGAGAGGGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
413 431 1.010793 AGAGAGAGAGAGAGGGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
414 432 1.421646 GAGAGAGAGAGAGGGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
416 434 1.421646 GAGAGAGAGAGGGGGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
417 435 1.010793 AGAGAGAGAGGGGGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
418 436 1.421646 GAGAGAGAGGGGGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
420 438 1.421646 GAGAGAGGGGGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
421 439 1.010793 AGAGAGGGGGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
422 440 1.421646 GAGAGGGGGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
424 442 1.421646 GAGGGGGAGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
425 443 0.478507 GGGGGAGAGAGAGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
426 444 1.222567 GGGGAGAGAGAGAGAGAGGT 58.777 60.000 0.00 0.00 0.00 3.85
427 445 1.133792 GGGGAGAGAGAGAGAGAGGTG 60.134 61.905 0.00 0.00 0.00 4.00
428 446 1.564348 GGGAGAGAGAGAGAGAGGTGT 59.436 57.143 0.00 0.00 0.00 4.16
429 447 2.643551 GGAGAGAGAGAGAGAGGTGTG 58.356 57.143 0.00 0.00 0.00 3.82
430 448 2.238646 GGAGAGAGAGAGAGAGGTGTGA 59.761 54.545 0.00 0.00 0.00 3.58
431 449 3.308117 GGAGAGAGAGAGAGAGGTGTGAA 60.308 52.174 0.00 0.00 0.00 3.18
432 450 4.526970 GAGAGAGAGAGAGAGGTGTGAAT 58.473 47.826 0.00 0.00 0.00 2.57
433 451 4.272489 AGAGAGAGAGAGAGGTGTGAATG 58.728 47.826 0.00 0.00 0.00 2.67
434 452 3.364549 AGAGAGAGAGAGGTGTGAATGG 58.635 50.000 0.00 0.00 0.00 3.16
435 453 3.011144 AGAGAGAGAGAGGTGTGAATGGA 59.989 47.826 0.00 0.00 0.00 3.41
436 454 3.096092 AGAGAGAGAGGTGTGAATGGAC 58.904 50.000 0.00 0.00 0.00 4.02
437 455 1.821753 AGAGAGAGGTGTGAATGGACG 59.178 52.381 0.00 0.00 0.00 4.79
438 456 0.898320 AGAGAGGTGTGAATGGACGG 59.102 55.000 0.00 0.00 0.00 4.79
439 457 0.608640 GAGAGGTGTGAATGGACGGT 59.391 55.000 0.00 0.00 0.00 4.83
440 458 0.321671 AGAGGTGTGAATGGACGGTG 59.678 55.000 0.00 0.00 0.00 4.94
441 459 1.298859 GAGGTGTGAATGGACGGTGC 61.299 60.000 0.00 0.00 0.00 5.01
442 460 1.599518 GGTGTGAATGGACGGTGCA 60.600 57.895 4.40 4.40 0.00 4.57
443 461 1.169661 GGTGTGAATGGACGGTGCAA 61.170 55.000 6.39 0.00 0.00 4.08
444 462 0.238289 GTGTGAATGGACGGTGCAAG 59.762 55.000 6.39 0.00 0.00 4.01
466 484 4.870426 AGCACATTTAGTAATGACGTGGAG 59.130 41.667 0.00 0.00 43.12 3.86
486 504 3.256704 AGTGATGGACCACCTTTCCTTA 58.743 45.455 0.00 0.00 37.76 2.69
494 512 1.351017 CCACCTTTCCTTACAGCCAGA 59.649 52.381 0.00 0.00 0.00 3.86
506 524 1.202855 ACAGCCAGAGTTGAACATGCT 60.203 47.619 0.00 0.00 0.00 3.79
507 525 1.467734 CAGCCAGAGTTGAACATGCTC 59.532 52.381 0.00 0.00 0.00 4.26
536 554 6.371809 TGCGAACAAGAAACTACAAAATCT 57.628 33.333 0.00 0.00 0.00 2.40
537 555 6.791303 TGCGAACAAGAAACTACAAAATCTT 58.209 32.000 0.00 0.00 32.55 2.40
538 556 7.921787 TGCGAACAAGAAACTACAAAATCTTA 58.078 30.769 0.00 0.00 31.25 2.10
539 557 8.399425 TGCGAACAAGAAACTACAAAATCTTAA 58.601 29.630 0.00 0.00 31.25 1.85
540 558 9.228636 GCGAACAAGAAACTACAAAATCTTAAA 57.771 29.630 0.00 0.00 31.25 1.52
591 609 4.810191 GAGATATCTCACCACCCATACC 57.190 50.000 24.93 0.00 42.42 2.73
592 610 3.165875 AGATATCTCACCACCCATACCG 58.834 50.000 0.00 0.00 0.00 4.02
629 650 5.948742 AAAGTGAAACAATTGGGAGGAAA 57.051 34.783 10.83 0.00 41.43 3.13
630 651 6.499106 AAAGTGAAACAATTGGGAGGAAAT 57.501 33.333 10.83 0.00 41.43 2.17
633 654 6.524734 AGTGAAACAATTGGGAGGAAATTTC 58.475 36.000 10.83 9.83 41.43 2.17
634 655 6.099557 AGTGAAACAATTGGGAGGAAATTTCA 59.900 34.615 19.49 10.76 41.43 2.69
635 656 6.765512 GTGAAACAATTGGGAGGAAATTTCAA 59.234 34.615 19.49 6.15 36.78 2.69
636 657 7.281999 GTGAAACAATTGGGAGGAAATTTCAAA 59.718 33.333 19.49 6.30 36.78 2.69
638 659 5.308014 ACAATTGGGAGGAAATTTCAAAGC 58.692 37.500 19.49 2.51 0.00 3.51
649 952 5.463392 GGAAATTTCAAAGCTCACAAAGACC 59.537 40.000 19.49 0.00 0.00 3.85
654 957 2.262423 AAGCTCACAAAGACCAGACC 57.738 50.000 0.00 0.00 0.00 3.85
655 958 1.131638 AGCTCACAAAGACCAGACCA 58.868 50.000 0.00 0.00 0.00 4.02
657 991 1.876156 GCTCACAAAGACCAGACCAAG 59.124 52.381 0.00 0.00 0.00 3.61
659 993 1.843851 TCACAAAGACCAGACCAAGGT 59.156 47.619 0.00 0.00 43.46 3.50
664 998 1.600916 GACCAGACCAAGGTGCCAC 60.601 63.158 0.00 0.00 40.09 5.01
688 1022 3.775654 GCCCCAGGGTCGACTCAG 61.776 72.222 19.57 9.95 37.65 3.35
689 1023 2.037367 CCCCAGGGTCGACTCAGA 59.963 66.667 19.57 0.00 0.00 3.27
690 1024 2.055042 CCCCAGGGTCGACTCAGAG 61.055 68.421 19.57 6.89 0.00 3.35
692 1026 1.599606 CCCAGGGTCGACTCAGAGTG 61.600 65.000 19.57 6.82 0.00 3.51
693 1027 0.896019 CCAGGGTCGACTCAGAGTGT 60.896 60.000 19.57 0.00 0.00 3.55
694 1028 0.523966 CAGGGTCGACTCAGAGTGTC 59.476 60.000 19.57 0.00 0.00 3.67
695 1029 0.402504 AGGGTCGACTCAGAGTGTCT 59.597 55.000 19.57 0.00 32.70 3.41
696 1030 1.629353 AGGGTCGACTCAGAGTGTCTA 59.371 52.381 19.57 0.00 32.70 2.59
697 1031 2.040012 AGGGTCGACTCAGAGTGTCTAA 59.960 50.000 19.57 0.00 32.70 2.10
698 1032 2.818432 GGGTCGACTCAGAGTGTCTAAA 59.182 50.000 16.46 0.00 32.70 1.85
699 1033 3.366171 GGGTCGACTCAGAGTGTCTAAAC 60.366 52.174 16.46 0.00 32.70 2.01
700 1034 3.502979 GGTCGACTCAGAGTGTCTAAACT 59.497 47.826 16.46 0.00 32.70 2.66
701 1035 4.468643 GTCGACTCAGAGTGTCTAAACTG 58.531 47.826 8.15 0.00 32.70 3.16
702 1036 4.213694 GTCGACTCAGAGTGTCTAAACTGA 59.786 45.833 8.15 0.00 37.71 3.41
703 1037 4.820173 TCGACTCAGAGTGTCTAAACTGAA 59.180 41.667 8.15 0.00 38.60 3.02
704 1038 4.912766 CGACTCAGAGTGTCTAAACTGAAC 59.087 45.833 8.15 0.00 38.60 3.18
707 1041 3.318275 TCAGAGTGTCTAAACTGAACGCT 59.682 43.478 0.00 0.00 36.63 5.07
715 1049 2.604046 AAACTGAACGCTCACTCACT 57.396 45.000 0.00 0.00 0.00 3.41
716 1050 1.858091 AACTGAACGCTCACTCACTG 58.142 50.000 0.00 0.00 0.00 3.66
720 1054 1.341209 TGAACGCTCACTCACTGTCAT 59.659 47.619 0.00 0.00 0.00 3.06
723 1057 1.073964 CGCTCACTCACTGTCATTGG 58.926 55.000 0.00 0.00 0.00 3.16
724 1058 1.446907 GCTCACTCACTGTCATTGGG 58.553 55.000 0.00 0.00 0.00 4.12
725 1059 1.002430 GCTCACTCACTGTCATTGGGA 59.998 52.381 0.00 0.00 0.00 4.37
754 1088 4.708177 CTTGGAGTGAGAAGAGAAACCAA 58.292 43.478 0.00 0.00 35.38 3.67
814 1157 3.379445 GCGTGGGTCGAGGAGGAA 61.379 66.667 0.00 0.00 42.86 3.36
815 1158 2.885861 CGTGGGTCGAGGAGGAAG 59.114 66.667 0.00 0.00 42.86 3.46
816 1159 2.711922 CGTGGGTCGAGGAGGAAGG 61.712 68.421 0.00 0.00 42.86 3.46
817 1160 2.038975 TGGGTCGAGGAGGAAGGG 59.961 66.667 0.00 0.00 0.00 3.95
818 1161 2.363361 GGGTCGAGGAGGAAGGGA 59.637 66.667 0.00 0.00 0.00 4.20
819 1162 1.758906 GGGTCGAGGAGGAAGGGAG 60.759 68.421 0.00 0.00 0.00 4.30
820 1163 1.758906 GGTCGAGGAGGAAGGGAGG 60.759 68.421 0.00 0.00 0.00 4.30
821 1164 1.306970 GTCGAGGAGGAAGGGAGGA 59.693 63.158 0.00 0.00 0.00 3.71
840 1188 2.373224 GATTGCAAGGGAGGAAAGGAG 58.627 52.381 4.94 0.00 0.00 3.69
1005 1383 0.886490 CGCCTGGGGTGATTATGAGC 60.886 60.000 1.98 0.00 34.74 4.26
1143 1521 0.258484 TCCTCTCCTCCTGCTCTCTG 59.742 60.000 0.00 0.00 0.00 3.35
1196 1589 7.913297 TCTTCCTAGTGTTTCAATTTTGTTTCG 59.087 33.333 0.00 0.00 0.00 3.46
1315 1751 4.439305 TGAATGACTGCATTAGCCAAAC 57.561 40.909 0.00 0.00 44.47 2.93
1347 1783 1.007721 TCTCCCTCTCCCTCTTTCAGG 59.992 57.143 0.00 0.00 43.01 3.86
1370 1806 6.014669 AGGCATAAGTTTGCAGTGGAAATTAA 60.015 34.615 13.24 2.31 44.59 1.40
1372 1808 7.334171 GGCATAAGTTTGCAGTGGAAATTAATT 59.666 33.333 13.24 8.58 44.59 1.40
1373 1809 9.364989 GCATAAGTTTGCAGTGGAAATTAATTA 57.635 29.630 13.24 10.23 42.31 1.40
1395 1831 5.886960 AGTATTGTGTCCTTGAGAAATGC 57.113 39.130 0.00 0.00 0.00 3.56
1417 1887 4.555360 GCTCGTATATATCTGTTCGTGCAG 59.445 45.833 9.14 3.28 37.60 4.41
1425 1895 3.673746 TCTGTTCGTGCAGTTTTTCAG 57.326 42.857 0.00 0.00 37.70 3.02
1481 1992 0.037790 TGGTCGCGTGATCATGTTCA 60.038 50.000 8.09 2.22 27.66 3.18
1653 2203 7.661968 TGACATAGTTATCTAGGCATTCAGTC 58.338 38.462 0.00 0.00 32.01 3.51
1658 2208 7.617041 AGTTATCTAGGCATTCAGTCAAAAC 57.383 36.000 0.00 0.00 0.00 2.43
1811 2377 4.519350 TCAGTATTGGGAGTAGTATCAGCG 59.481 45.833 0.00 0.00 0.00 5.18
1812 2386 4.278669 CAGTATTGGGAGTAGTATCAGCGT 59.721 45.833 0.00 0.00 0.00 5.07
1902 2482 5.762711 TGCTGCTGTTAGAACTCAAAATACA 59.237 36.000 0.00 0.00 0.00 2.29
1930 2521 7.875316 TTTTTCTCTCTTCTGTAGATGAACG 57.125 36.000 0.11 0.00 30.26 3.95
2218 2831 6.150307 AAAACAATTTGGTTTTTGACCCTGAC 59.850 34.615 6.59 0.00 45.89 3.51
2332 2946 1.546773 CCCGGGAAATCACTGTCCAAA 60.547 52.381 18.48 0.00 35.44 3.28
2395 3009 1.143183 GTGTGCCATCCGGTATCGT 59.857 57.895 0.00 0.00 33.95 3.73
2437 3051 7.861872 GGTCTACGAAATACAAAGATCCTAGTC 59.138 40.741 0.00 0.00 0.00 2.59
2441 3055 7.612677 ACGAAATACAAAGATCCTAGTCTGTT 58.387 34.615 0.00 0.00 0.00 3.16
2464 3078 1.133976 ACAAGACTCAGGCTGTTTGCT 60.134 47.619 15.27 5.34 42.39 3.91
2490 3106 2.226437 CAGATCCCTTTGTGACCAAACG 59.774 50.000 0.00 0.00 35.67 3.60
2610 3259 9.144747 GATTTTTCTTTTTCCTTTGAGGATAGC 57.855 33.333 0.00 0.00 45.34 2.97
2733 3433 2.608506 CGTGGTTGTGACCTACGATTGA 60.609 50.000 12.12 0.00 45.21 2.57
2754 3457 9.132521 GATTGACAAATTATCTGTTGTTTCAGG 57.867 33.333 0.00 0.00 38.07 3.86
2755 3458 7.815840 TGACAAATTATCTGTTGTTTCAGGA 57.184 32.000 0.00 0.00 38.07 3.86
2756 3459 7.874940 TGACAAATTATCTGTTGTTTCAGGAG 58.125 34.615 0.00 0.00 38.07 3.69
2814 3539 4.394920 TCAATAGATGGCTTCGGTTTTGAC 59.605 41.667 0.00 0.00 0.00 3.18
2820 3545 2.098443 TGGCTTCGGTTTTGACTGAAAC 59.902 45.455 2.82 0.00 38.49 2.78
2830 3555 6.358118 GTTTTGACTGAAACCCATTTTTCC 57.642 37.500 0.00 0.00 35.01 3.13
2905 3631 2.411547 CGAAACTCATCTTGGACAACGC 60.412 50.000 0.00 0.00 0.00 4.84
3165 3942 7.863375 AGTTATGTGTATTCACTCTCGCTTATC 59.137 37.037 4.01 0.00 44.14 1.75
3196 3973 5.495640 AGATAAGAGGCCTGTGAAGAAAAG 58.504 41.667 12.00 0.00 0.00 2.27
3318 4103 6.848296 GTCAAGCTCATATCGAAATTGCTTAC 59.152 38.462 12.99 9.55 37.20 2.34
3343 4169 4.629200 CGAAGAATCTGATATAAGCCAGGC 59.371 45.833 1.84 1.84 0.00 4.85
3428 4254 6.137794 TCTTCTATTCTGTAGCTTCCTTCG 57.862 41.667 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.738099 CGCGTCAGGGTTTCAGGAG 60.738 63.158 0.00 0.00 0.00 3.69
31 32 3.423154 GGCGCGTCAGGGTTTCAG 61.423 66.667 5.47 0.00 0.00 3.02
81 82 1.332195 TATCAGGGGCTGACATCGAG 58.668 55.000 0.00 0.00 43.63 4.04
88 89 3.435026 GCTAATGGTTTATCAGGGGCTGA 60.435 47.826 0.00 0.00 44.99 4.26
92 93 4.437682 TCAGCTAATGGTTTATCAGGGG 57.562 45.455 0.00 0.00 0.00 4.79
97 98 8.477984 TTGCAAAAATCAGCTAATGGTTTATC 57.522 30.769 0.00 0.00 41.51 1.75
127 129 2.465860 TACACCATTCGAACCACCTG 57.534 50.000 0.00 0.00 0.00 4.00
129 131 2.980568 TCATACACCATTCGAACCACC 58.019 47.619 0.00 0.00 0.00 4.61
131 133 6.826231 ACAATATTCATACACCATTCGAACCA 59.174 34.615 0.00 0.00 0.00 3.67
133 135 9.221775 GAAACAATATTCATACACCATTCGAAC 57.778 33.333 0.00 0.00 0.00 3.95
137 139 9.125026 AGAGGAAACAATATTCATACACCATTC 57.875 33.333 0.00 0.00 0.00 2.67
174 177 9.143155 AGAAAAGTAAACCCACATGAAAACTAT 57.857 29.630 0.00 0.00 0.00 2.12
183 186 3.552068 GCGCAAGAAAAGTAAACCCACAT 60.552 43.478 0.30 0.00 43.02 3.21
187 190 2.785713 TGCGCAAGAAAAGTAAACCC 57.214 45.000 8.16 0.00 43.02 4.11
195 198 0.663688 TAGCCGTTTGCGCAAGAAAA 59.336 45.000 23.68 5.40 44.36 2.29
204 207 3.057806 ACAGTTTAACCATAGCCGTTTGC 60.058 43.478 0.00 0.00 41.71 3.68
205 208 4.759516 ACAGTTTAACCATAGCCGTTTG 57.240 40.909 0.00 0.00 0.00 2.93
206 209 5.777850 AAACAGTTTAACCATAGCCGTTT 57.222 34.783 0.00 0.00 0.00 3.60
207 210 5.561339 CGAAAACAGTTTAACCATAGCCGTT 60.561 40.000 0.00 0.00 0.00 4.44
209 212 4.152759 TCGAAAACAGTTTAACCATAGCCG 59.847 41.667 0.00 0.00 0.00 5.52
211 214 8.424731 CAATTTCGAAAACAGTTTAACCATAGC 58.575 33.333 15.66 0.00 0.00 2.97
212 215 8.424731 GCAATTTCGAAAACAGTTTAACCATAG 58.575 33.333 15.66 0.00 0.00 2.23
213 216 8.138712 AGCAATTTCGAAAACAGTTTAACCATA 58.861 29.630 15.66 0.00 0.00 2.74
215 218 6.334202 AGCAATTTCGAAAACAGTTTAACCA 58.666 32.000 15.66 0.00 0.00 3.67
216 219 6.822073 AGCAATTTCGAAAACAGTTTAACC 57.178 33.333 15.66 0.00 0.00 2.85
218 221 7.932335 TCCTAGCAATTTCGAAAACAGTTTAA 58.068 30.769 15.66 0.00 0.00 1.52
219 222 7.499321 TCCTAGCAATTTCGAAAACAGTTTA 57.501 32.000 15.66 2.91 0.00 2.01
221 224 6.381801 CATCCTAGCAATTTCGAAAACAGTT 58.618 36.000 15.66 8.22 0.00 3.16
222 225 5.106157 CCATCCTAGCAATTTCGAAAACAGT 60.106 40.000 15.66 3.22 0.00 3.55
223 226 5.335127 CCATCCTAGCAATTTCGAAAACAG 58.665 41.667 15.66 8.77 0.00 3.16
224 227 4.157656 CCCATCCTAGCAATTTCGAAAACA 59.842 41.667 15.66 0.00 0.00 2.83
225 228 4.440112 CCCCATCCTAGCAATTTCGAAAAC 60.440 45.833 15.66 7.70 0.00 2.43
226 229 3.699038 CCCCATCCTAGCAATTTCGAAAA 59.301 43.478 15.66 0.00 0.00 2.29
227 230 3.053991 TCCCCATCCTAGCAATTTCGAAA 60.054 43.478 13.91 13.91 0.00 3.46
229 232 2.123589 TCCCCATCCTAGCAATTTCGA 58.876 47.619 0.00 0.00 0.00 3.71
230 233 2.638480 TCCCCATCCTAGCAATTTCG 57.362 50.000 0.00 0.00 0.00 3.46
231 234 4.202567 TGGTATCCCCATCCTAGCAATTTC 60.203 45.833 0.00 0.00 38.72 2.17
234 237 3.004126 TGGTATCCCCATCCTAGCAAT 57.996 47.619 0.00 0.00 38.72 3.56
253 271 4.062991 GTTGGTTGGTTAGGAGTACAGTG 58.937 47.826 0.00 0.00 0.00 3.66
259 277 2.751816 GCAAGGTTGGTTGGTTAGGAGT 60.752 50.000 0.00 0.00 0.00 3.85
263 281 1.535462 CTCGCAAGGTTGGTTGGTTAG 59.465 52.381 0.00 0.00 38.47 2.34
270 288 1.071471 CCTCACTCGCAAGGTTGGT 59.929 57.895 0.00 0.00 38.47 3.67
277 295 1.148273 AGTTTGGCCTCACTCGCAA 59.852 52.632 3.32 0.00 0.00 4.85
320 338 8.871862 GCAATGCATGTATTCTGTTTCATTAAA 58.128 29.630 6.00 0.00 0.00 1.52
321 339 8.033626 TGCAATGCATGTATTCTGTTTCATTAA 58.966 29.630 2.72 0.00 31.71 1.40
322 340 7.488792 GTGCAATGCATGTATTCTGTTTCATTA 59.511 33.333 12.38 0.00 41.91 1.90
323 341 6.311935 GTGCAATGCATGTATTCTGTTTCATT 59.688 34.615 12.38 0.00 41.91 2.57
348 366 4.500545 CCAGGATCTCCAGACAATCTTACG 60.501 50.000 0.00 0.00 38.89 3.18
349 367 4.651503 TCCAGGATCTCCAGACAATCTTAC 59.348 45.833 0.00 0.00 38.89 2.34
354 372 2.406559 CCTCCAGGATCTCCAGACAAT 58.593 52.381 0.00 0.00 38.89 2.71
361 379 2.046292 CTTTCTCCCTCCAGGATCTCC 58.954 57.143 0.00 0.00 46.33 3.71
406 424 0.478507 CCTCTCTCTCTCTCTCCCCC 59.521 65.000 0.00 0.00 0.00 5.40
408 426 1.564348 ACACCTCTCTCTCTCTCTCCC 59.436 57.143 0.00 0.00 0.00 4.30
410 428 3.627395 TCACACCTCTCTCTCTCTCTC 57.373 52.381 0.00 0.00 0.00 3.20
412 430 3.381272 CCATTCACACCTCTCTCTCTCTC 59.619 52.174 0.00 0.00 0.00 3.20
413 431 3.011144 TCCATTCACACCTCTCTCTCTCT 59.989 47.826 0.00 0.00 0.00 3.10
414 432 3.130340 GTCCATTCACACCTCTCTCTCTC 59.870 52.174 0.00 0.00 0.00 3.20
416 434 2.159310 CGTCCATTCACACCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
417 435 1.821753 CGTCCATTCACACCTCTCTCT 59.178 52.381 0.00 0.00 0.00 3.10
418 436 1.134965 CCGTCCATTCACACCTCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
420 438 0.608640 ACCGTCCATTCACACCTCTC 59.391 55.000 0.00 0.00 0.00 3.20
421 439 0.321671 CACCGTCCATTCACACCTCT 59.678 55.000 0.00 0.00 0.00 3.69
422 440 1.298859 GCACCGTCCATTCACACCTC 61.299 60.000 0.00 0.00 0.00 3.85
424 442 1.169661 TTGCACCGTCCATTCACACC 61.170 55.000 0.00 0.00 0.00 4.16
425 443 0.238289 CTTGCACCGTCCATTCACAC 59.762 55.000 0.00 0.00 0.00 3.82
426 444 1.514678 GCTTGCACCGTCCATTCACA 61.515 55.000 0.00 0.00 0.00 3.58
427 445 1.210155 GCTTGCACCGTCCATTCAC 59.790 57.895 0.00 0.00 0.00 3.18
428 446 1.228094 TGCTTGCACCGTCCATTCA 60.228 52.632 0.00 0.00 0.00 2.57
429 447 1.210155 GTGCTTGCACCGTCCATTC 59.790 57.895 14.17 0.00 0.00 2.67
430 448 0.895100 ATGTGCTTGCACCGTCCATT 60.895 50.000 21.01 0.00 0.00 3.16
431 449 0.895100 AATGTGCTTGCACCGTCCAT 60.895 50.000 21.01 6.56 0.00 3.41
432 450 1.106351 AAATGTGCTTGCACCGTCCA 61.106 50.000 21.01 4.49 0.00 4.02
433 451 0.878416 TAAATGTGCTTGCACCGTCC 59.122 50.000 21.01 0.00 0.00 4.79
434 452 1.535462 ACTAAATGTGCTTGCACCGTC 59.465 47.619 21.01 0.00 0.00 4.79
435 453 1.604604 ACTAAATGTGCTTGCACCGT 58.395 45.000 21.01 8.75 0.00 4.83
436 454 3.822594 TTACTAAATGTGCTTGCACCG 57.177 42.857 21.01 8.38 0.00 4.94
437 455 5.095490 GTCATTACTAAATGTGCTTGCACC 58.905 41.667 21.01 5.89 42.66 5.01
438 456 4.788100 CGTCATTACTAAATGTGCTTGCAC 59.212 41.667 17.73 17.73 42.66 4.57
439 457 4.454161 ACGTCATTACTAAATGTGCTTGCA 59.546 37.500 0.00 0.00 42.66 4.08
440 458 4.788100 CACGTCATTACTAAATGTGCTTGC 59.212 41.667 0.00 0.00 42.66 4.01
441 459 5.121611 TCCACGTCATTACTAAATGTGCTTG 59.878 40.000 0.00 0.00 42.66 4.01
442 460 5.242434 TCCACGTCATTACTAAATGTGCTT 58.758 37.500 0.00 0.00 42.66 3.91
443 461 4.827692 TCCACGTCATTACTAAATGTGCT 58.172 39.130 0.00 0.00 42.66 4.40
444 462 4.630069 ACTCCACGTCATTACTAAATGTGC 59.370 41.667 0.00 0.00 42.66 4.57
453 471 3.187700 GTCCATCACTCCACGTCATTAC 58.812 50.000 0.00 0.00 0.00 1.89
455 473 1.066143 GGTCCATCACTCCACGTCATT 60.066 52.381 0.00 0.00 0.00 2.57
466 484 2.586648 AAGGAAAGGTGGTCCATCAC 57.413 50.000 4.57 0.00 37.65 3.06
477 495 3.077359 CAACTCTGGCTGTAAGGAAAGG 58.923 50.000 0.00 0.00 0.00 3.11
486 504 1.202855 AGCATGTTCAACTCTGGCTGT 60.203 47.619 0.00 0.00 0.00 4.40
494 512 2.417933 GCAAGATCGAGCATGTTCAACT 59.582 45.455 10.36 2.82 0.00 3.16
570 588 3.193691 CGGTATGGGTGGTGAGATATCTC 59.806 52.174 23.47 23.47 43.15 2.75
571 589 3.165875 CGGTATGGGTGGTGAGATATCT 58.834 50.000 4.47 4.47 0.00 1.98
572 590 3.162666 TCGGTATGGGTGGTGAGATATC 58.837 50.000 0.00 0.00 0.00 1.63
573 591 3.254093 TCGGTATGGGTGGTGAGATAT 57.746 47.619 0.00 0.00 0.00 1.63
574 592 2.759839 TCGGTATGGGTGGTGAGATA 57.240 50.000 0.00 0.00 0.00 1.98
575 593 1.874129 TTCGGTATGGGTGGTGAGAT 58.126 50.000 0.00 0.00 0.00 2.75
576 594 1.484653 CATTCGGTATGGGTGGTGAGA 59.515 52.381 0.00 0.00 0.00 3.27
577 595 1.953559 CATTCGGTATGGGTGGTGAG 58.046 55.000 0.00 0.00 0.00 3.51
613 634 6.262944 GCTTTGAAATTTCCTCCCAATTGTTT 59.737 34.615 15.48 0.00 0.00 2.83
614 635 5.764686 GCTTTGAAATTTCCTCCCAATTGTT 59.235 36.000 15.48 0.00 0.00 2.83
622 643 4.853924 TGTGAGCTTTGAAATTTCCTCC 57.146 40.909 15.48 8.88 0.00 4.30
623 644 6.419116 GTCTTTGTGAGCTTTGAAATTTCCTC 59.581 38.462 15.48 13.81 0.00 3.71
629 650 4.889409 TCTGGTCTTTGTGAGCTTTGAAAT 59.111 37.500 0.00 0.00 43.13 2.17
630 651 4.096382 GTCTGGTCTTTGTGAGCTTTGAAA 59.904 41.667 0.00 0.00 43.13 2.69
633 654 2.291741 GGTCTGGTCTTTGTGAGCTTTG 59.708 50.000 0.00 0.00 43.13 2.77
634 655 2.092429 TGGTCTGGTCTTTGTGAGCTTT 60.092 45.455 0.00 0.00 43.13 3.51
635 656 1.490490 TGGTCTGGTCTTTGTGAGCTT 59.510 47.619 0.00 0.00 43.13 3.74
636 657 1.131638 TGGTCTGGTCTTTGTGAGCT 58.868 50.000 0.00 0.00 43.13 4.09
638 659 2.158755 ACCTTGGTCTGGTCTTTGTGAG 60.159 50.000 0.00 0.00 31.03 3.51
649 952 2.111043 ACGTGGCACCTTGGTCTG 59.889 61.111 12.86 0.00 0.00 3.51
671 1005 3.775654 CTGAGTCGACCCTGGGGC 61.776 72.222 18.88 14.46 39.32 5.80
679 1013 4.213694 TCAGTTTAGACACTCTGAGTCGAC 59.786 45.833 7.70 7.70 40.84 4.20
680 1014 4.386711 TCAGTTTAGACACTCTGAGTCGA 58.613 43.478 7.49 0.00 40.84 4.20
683 1017 4.793353 GCGTTCAGTTTAGACACTCTGAGT 60.793 45.833 4.06 4.06 38.03 3.41
684 1018 3.670991 GCGTTCAGTTTAGACACTCTGAG 59.329 47.826 2.45 2.45 38.03 3.35
685 1019 3.318275 AGCGTTCAGTTTAGACACTCTGA 59.682 43.478 0.00 0.00 35.54 3.27
686 1020 3.643763 AGCGTTCAGTTTAGACACTCTG 58.356 45.455 0.00 0.00 0.00 3.35
687 1021 3.318275 TGAGCGTTCAGTTTAGACACTCT 59.682 43.478 0.00 0.00 0.00 3.24
688 1022 3.425858 GTGAGCGTTCAGTTTAGACACTC 59.574 47.826 0.73 0.00 32.98 3.51
689 1023 3.068307 AGTGAGCGTTCAGTTTAGACACT 59.932 43.478 0.73 0.00 33.08 3.55
690 1024 3.381949 AGTGAGCGTTCAGTTTAGACAC 58.618 45.455 0.73 0.00 33.08 3.67
692 1026 3.425858 GTGAGTGAGCGTTCAGTTTAGAC 59.574 47.826 11.14 3.07 37.11 2.59
693 1027 3.318275 AGTGAGTGAGCGTTCAGTTTAGA 59.682 43.478 11.14 0.00 37.11 2.10
694 1028 3.426859 CAGTGAGTGAGCGTTCAGTTTAG 59.573 47.826 11.14 0.00 37.11 1.85
695 1029 3.181479 ACAGTGAGTGAGCGTTCAGTTTA 60.181 43.478 11.14 1.37 37.11 2.01
696 1030 2.205074 CAGTGAGTGAGCGTTCAGTTT 58.795 47.619 11.14 0.00 37.11 2.66
697 1031 1.137086 ACAGTGAGTGAGCGTTCAGTT 59.863 47.619 11.14 0.00 37.11 3.16
698 1032 0.747255 ACAGTGAGTGAGCGTTCAGT 59.253 50.000 9.57 9.57 39.70 3.41
699 1033 1.269257 TGACAGTGAGTGAGCGTTCAG 60.269 52.381 0.73 0.00 32.98 3.02
700 1034 0.744281 TGACAGTGAGTGAGCGTTCA 59.256 50.000 0.00 0.00 0.00 3.18
701 1035 2.071688 ATGACAGTGAGTGAGCGTTC 57.928 50.000 0.00 0.00 0.00 3.95
702 1036 2.138320 CAATGACAGTGAGTGAGCGTT 58.862 47.619 0.00 0.00 0.00 4.84
703 1037 1.606480 CCAATGACAGTGAGTGAGCGT 60.606 52.381 4.07 0.00 0.00 5.07
704 1038 1.073964 CCAATGACAGTGAGTGAGCG 58.926 55.000 4.07 0.00 0.00 5.03
707 1041 2.839486 GTCCCAATGACAGTGAGTGA 57.161 50.000 4.07 0.00 43.85 3.41
716 1050 2.501723 TCCAAGCTAGAGTCCCAATGAC 59.498 50.000 0.00 0.00 44.82 3.06
720 1054 1.902508 CACTCCAAGCTAGAGTCCCAA 59.097 52.381 14.75 0.00 42.69 4.12
723 1057 2.729194 TCTCACTCCAAGCTAGAGTCC 58.271 52.381 14.75 0.00 42.69 3.85
724 1058 4.013728 TCTTCTCACTCCAAGCTAGAGTC 58.986 47.826 14.75 0.00 42.69 3.36
725 1059 4.016444 CTCTTCTCACTCCAAGCTAGAGT 58.984 47.826 12.42 12.42 45.45 3.24
726 1060 4.269183 TCTCTTCTCACTCCAAGCTAGAG 58.731 47.826 11.24 11.24 37.39 2.43
727 1061 4.308526 TCTCTTCTCACTCCAAGCTAGA 57.691 45.455 0.00 0.00 0.00 2.43
728 1062 5.167845 GTTTCTCTTCTCACTCCAAGCTAG 58.832 45.833 0.00 0.00 0.00 3.42
729 1063 4.021016 GGTTTCTCTTCTCACTCCAAGCTA 60.021 45.833 0.00 0.00 0.00 3.32
730 1064 3.244387 GGTTTCTCTTCTCACTCCAAGCT 60.244 47.826 0.00 0.00 0.00 3.74
731 1065 3.070748 GGTTTCTCTTCTCACTCCAAGC 58.929 50.000 0.00 0.00 0.00 4.01
732 1066 4.342862 TGGTTTCTCTTCTCACTCCAAG 57.657 45.455 0.00 0.00 0.00 3.61
733 1067 4.080582 TGTTGGTTTCTCTTCTCACTCCAA 60.081 41.667 0.00 0.00 0.00 3.53
734 1068 3.454447 TGTTGGTTTCTCTTCTCACTCCA 59.546 43.478 0.00 0.00 0.00 3.86
754 1088 2.628657 AGAAGTACCTTGCTTCGTCTGT 59.371 45.455 0.00 0.00 44.97 3.41
814 1157 1.284841 CCTCCCTTGCAATCCTCCCT 61.285 60.000 0.00 0.00 0.00 4.20
815 1158 1.228510 CCTCCCTTGCAATCCTCCC 59.771 63.158 0.00 0.00 0.00 4.30
816 1159 0.625849 TTCCTCCCTTGCAATCCTCC 59.374 55.000 0.00 0.00 0.00 4.30
817 1160 2.373224 CTTTCCTCCCTTGCAATCCTC 58.627 52.381 0.00 0.00 0.00 3.71
818 1161 1.006400 CCTTTCCTCCCTTGCAATCCT 59.994 52.381 0.00 0.00 0.00 3.24
819 1162 1.005924 TCCTTTCCTCCCTTGCAATCC 59.994 52.381 0.00 0.00 0.00 3.01
820 1163 2.025887 TCTCCTTTCCTCCCTTGCAATC 60.026 50.000 0.00 0.00 0.00 2.67
821 1164 1.995542 TCTCCTTTCCTCCCTTGCAAT 59.004 47.619 0.00 0.00 0.00 3.56
840 1188 2.507547 TACAACCGCGGCATCGTC 60.508 61.111 28.58 0.00 38.89 4.20
910 1258 2.592993 GCCCCTGCACCTGTCACTA 61.593 63.158 0.00 0.00 37.47 2.74
1143 1521 1.685355 GGAGCAGGAGAGGAGAAGGC 61.685 65.000 0.00 0.00 0.00 4.35
1196 1589 1.467920 AGCTACTGCAAATTGGCTCC 58.532 50.000 6.34 0.00 42.74 4.70
1240 1663 7.895759 TGAAGAATAACCCCTGAAAAATTCTG 58.104 34.615 0.00 0.00 34.73 3.02
1315 1751 0.174617 GAGGGAGAGACGCTGGAAAG 59.825 60.000 0.00 0.00 41.84 2.62
1347 1783 7.832503 ATTAATTTCCACTGCAAACTTATGC 57.167 32.000 0.00 0.00 46.58 3.14
1370 1806 7.831193 AGCATTTCTCAAGGACACAATACTAAT 59.169 33.333 0.00 0.00 0.00 1.73
1372 1808 6.711277 AGCATTTCTCAAGGACACAATACTA 58.289 36.000 0.00 0.00 0.00 1.82
1373 1809 5.564550 AGCATTTCTCAAGGACACAATACT 58.435 37.500 0.00 0.00 0.00 2.12
1374 1810 5.446473 CGAGCATTTCTCAAGGACACAATAC 60.446 44.000 0.00 0.00 41.98 1.89
1375 1811 4.631377 CGAGCATTTCTCAAGGACACAATA 59.369 41.667 0.00 0.00 41.98 1.90
1386 1822 7.750903 CGAACAGATATATACGAGCATTTCTCA 59.249 37.037 0.00 0.00 41.98 3.27
1395 1831 5.690816 ACTGCACGAACAGATATATACGAG 58.309 41.667 14.74 0.00 40.25 4.18
1401 1871 6.649141 ACTGAAAAACTGCACGAACAGATATA 59.351 34.615 14.74 0.00 40.25 0.86
1402 1872 5.470098 ACTGAAAAACTGCACGAACAGATAT 59.530 36.000 14.74 0.00 40.25 1.63
1403 1873 4.814234 ACTGAAAAACTGCACGAACAGATA 59.186 37.500 14.74 0.00 40.25 1.98
1404 1874 3.627577 ACTGAAAAACTGCACGAACAGAT 59.372 39.130 14.74 2.01 40.25 2.90
1417 1887 3.052745 GCTGCCAAGCTAACTGAAAAAC 58.947 45.455 0.00 0.00 46.60 2.43
1658 2208 3.958704 TCAGCGTACACAACAAAAATGG 58.041 40.909 0.00 0.00 0.00 3.16
1698 2252 7.567250 TCATACTATCCTGAATTCTGGTAACCA 59.433 37.037 25.50 10.78 36.48 3.67
1742 2296 5.221185 CCTCAAGGAAGGAAATGTATGCATG 60.221 44.000 10.16 0.00 38.87 4.06
1743 2297 4.891756 CCTCAAGGAAGGAAATGTATGCAT 59.108 41.667 3.79 3.79 38.87 3.96
1811 2377 9.649167 AATGTACCATACTAGTACTTGTTTCAC 57.351 33.333 15.11 7.56 40.61 3.18
1902 2482 8.372877 TCATCTACAGAAGAGAGAAAAATCCT 57.627 34.615 0.00 0.00 37.74 3.24
1930 2521 5.523369 AGCTGCTCAAAAGAACAACAATAC 58.477 37.500 0.00 0.00 0.00 1.89
2072 2667 1.652947 GACTTACCCAGTCCCCAAGA 58.347 55.000 0.00 0.00 45.84 3.02
2218 2831 2.742053 CCTGTGACCTATGGACAAAACG 59.258 50.000 0.00 0.00 0.00 3.60
2332 2946 3.442996 GCGGTAGCAGTCATGAAGT 57.557 52.632 0.00 0.00 44.35 3.01
2437 3051 4.130118 ACAGCCTGAGTCTTGTTTAACAG 58.870 43.478 0.00 0.00 0.00 3.16
2441 3055 3.315191 GCAAACAGCCTGAGTCTTGTTTA 59.685 43.478 0.00 0.00 37.23 2.01
2464 3078 2.224769 GGTCACAAAGGGATCTGGTTGA 60.225 50.000 8.97 0.00 0.00 3.18
2490 3106 0.882042 CTGCGCTATGATGTGTCCCC 60.882 60.000 9.73 0.00 0.00 4.81
2733 3433 6.294731 GCCTCCTGAAACAACAGATAATTTGT 60.295 38.462 0.00 0.00 39.94 2.83
2754 3457 2.182030 CGACAACTCGAGGGCCTC 59.818 66.667 24.06 24.06 43.06 4.70
2755 3458 2.282958 TCGACAACTCGAGGGCCT 60.283 61.111 18.41 5.25 44.14 5.19
2814 3539 2.368221 TGCCAGGAAAAATGGGTTTCAG 59.632 45.455 0.00 0.00 38.93 3.02
2820 3545 1.608801 GCAAGTGCCAGGAAAAATGGG 60.609 52.381 0.00 0.00 38.33 4.00
2830 3555 0.034337 AAAAGCCATGCAAGTGCCAG 59.966 50.000 0.00 0.00 41.18 4.85
2905 3631 2.561733 TTAGCTGATCGACGTCTTGG 57.438 50.000 14.70 0.00 0.00 3.61
3030 3776 0.320247 ACTTGCACTTCTCCAGCGAG 60.320 55.000 0.00 0.00 43.74 5.03
3165 3942 3.450457 ACAGGCCTCTTATCTCTTCACAG 59.550 47.826 0.00 0.00 0.00 3.66
3318 4103 6.098679 CCTGGCTTATATCAGATTCTTCGAG 58.901 44.000 0.00 0.00 33.11 4.04


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

AutoCloner maintained by Alex Coulton.