Multiple sequence alignment - TraesCS2D01G155900

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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 TraesCS2D01G155900 chr2D 100.000 2600 0 0 1 2600 99560317 99562916 0.000000e+00 4802.0
1 TraesCS2D01G155900 chr2D 94.586 1496 52 22 616 2105 99572291 99573763 0.000000e+00 2287.0
2 TraesCS2D01G155900 chr2D 87.953 1104 80 30 670 1739 99654294 99655378 0.000000e+00 1253.0
3 TraesCS2D01G155900 chr2D 92.555 497 11 11 1 472 488879649 488880144 0.000000e+00 689.0
4 TraesCS2D01G155900 chr2D 92.683 451 14 3 1 434 92909290 92909738 1.310000e-177 632.0
5 TraesCS2D01G155900 chr2D 91.146 384 24 8 1736 2115 99655403 99655780 1.780000e-141 512.0
6 TraesCS2D01G155900 chr2D 87.727 440 36 14 1311 1739 99360557 99360989 5.000000e-137 497.0
7 TraesCS2D01G155900 chr2D 91.440 257 20 2 1737 1991 99361015 99361271 4.120000e-93 351.0
8 TraesCS2D01G155900 chr2D 81.333 375 41 14 641 1005 99346484 99346839 7.090000e-71 278.0
9 TraesCS2D01G155900 chr2D 89.796 147 12 2 473 617 6811199 6811054 4.420000e-43 185.0
10 TraesCS2D01G155900 chr2A 96.644 1311 27 9 616 1922 98578381 98579678 0.000000e+00 2161.0
11 TraesCS2D01G155900 chr2A 92.616 1422 66 21 618 2014 98603035 98604442 0.000000e+00 2008.0
12 TraesCS2D01G155900 chr2A 91.536 1146 54 16 616 1739 98722323 98723447 0.000000e+00 1539.0
13 TraesCS2D01G155900 chr2A 89.152 1097 68 30 641 1697 98455979 98457064 0.000000e+00 1319.0
14 TraesCS2D01G155900 chr2A 95.018 562 21 6 2044 2600 98620603 98621162 0.000000e+00 876.0
15 TraesCS2D01G155900 chr2A 83.253 830 110 24 884 1693 19913805 19914625 0.000000e+00 736.0
16 TraesCS2D01G155900 chr2A 91.635 263 17 5 1737 1997 98723473 98723732 2.460000e-95 359.0
17 TraesCS2D01G155900 chr2A 91.051 257 19 3 1737 1991 98457184 98457438 6.890000e-91 344.0
18 TraesCS2D01G155900 chr2A 85.000 100 14 1 2482 2580 61477413 61477314 1.650000e-17 100.0
19 TraesCS2D01G155900 chr2B 87.706 1757 134 54 893 2600 151489985 151488262 0.000000e+00 1973.0
20 TraesCS2D01G155900 chr2B 92.794 1138 46 13 616 1739 151486189 151485074 0.000000e+00 1615.0
21 TraesCS2D01G155900 chr2B 82.179 881 108 34 763 1601 30637319 30636446 0.000000e+00 712.0
22 TraesCS2D01G155900 chr2B 90.356 477 27 8 19 478 63115929 63115455 2.210000e-170 608.0
23 TraesCS2D01G155900 chr2B 95.385 65 2 1 1737 1800 151485050 151484986 4.580000e-18 102.0
24 TraesCS2D01G155900 chr2B 88.406 69 8 0 2504 2572 749984917 749984985 1.660000e-12 84.2
25 TraesCS2D01G155900 chr3D 94.274 489 10 2 2 473 562965180 562965667 0.000000e+00 732.0
26 TraesCS2D01G155900 chr3D 92.525 495 18 7 1 477 45437692 45438185 0.000000e+00 691.0
27 TraesCS2D01G155900 chr3D 91.755 473 21 2 19 474 1990376 1990847 2.180000e-180 641.0
28 TraesCS2D01G155900 chr3D 89.474 513 13 2 1 472 526943621 526944133 6.150000e-171 610.0
29 TraesCS2D01G155900 chr3D 88.911 496 10 16 1 472 593771703 593771229 1.040000e-158 569.0
30 TraesCS2D01G155900 chr3D 91.216 148 11 2 473 619 98567047 98566901 1.580000e-47 200.0
31 TraesCS2D01G155900 chr3D 90.541 148 12 2 473 619 59267884 59268030 7.340000e-46 195.0
32 TraesCS2D01G155900 chr3D 91.429 140 11 1 480 619 579738483 579738345 9.500000e-45 191.0
33 TraesCS2D01G155900 chr5D 93.028 459 14 3 31 472 510948969 510948512 0.000000e+00 654.0
34 TraesCS2D01G155900 chr5D 89.933 149 13 2 470 617 518286219 518286366 9.500000e-45 191.0
35 TraesCS2D01G155900 chrUn 82.269 767 95 26 870 1600 24365688 24364927 2.200000e-175 625.0
36 TraesCS2D01G155900 chr7D 89.709 515 10 11 1 473 583039218 583038705 3.680000e-173 617.0
37 TraesCS2D01G155900 chr7D 92.835 321 5 2 153 473 28412847 28412545 1.420000e-122 449.0
38 TraesCS2D01G155900 chr7D 92.617 149 9 2 473 621 185723754 185723900 2.030000e-51 213.0
39 TraesCS2D01G155900 chr7D 91.837 147 11 1 473 619 555439339 555439484 1.220000e-48 204.0
40 TraesCS2D01G155900 chr7D 89.655 145 13 2 473 617 94611237 94611095 1.590000e-42 183.0
41 TraesCS2D01G155900 chr4B 89.431 492 33 4 1 475 660202973 660202484 1.030000e-168 603.0
42 TraesCS2D01G155900 chr4B 87.629 97 12 0 2482 2578 509764284 509764188 2.110000e-21 113.0
43 TraesCS2D01G155900 chr1D 88.825 519 12 17 1 474 473971071 473970554 1.720000e-166 595.0
44 TraesCS2D01G155900 chr1D 88.889 153 13 4 473 623 466486873 466487023 4.420000e-43 185.0
45 TraesCS2D01G155900 chr5B 87.975 474 39 7 16 472 535213545 535214017 6.330000e-151 544.0
46 TraesCS2D01G155900 chr5B 86.344 227 31 0 2354 2580 18246838 18247064 5.560000e-62 248.0
47 TraesCS2D01G155900 chr5B 88.235 153 16 2 2124 2274 158940204 158940052 5.720000e-42 182.0
48 TraesCS2D01G155900 chr5B 84.524 84 12 1 2482 2565 421506406 421506488 5.960000e-12 82.4
49 TraesCS2D01G155900 chr7B 83.810 105 16 1 2475 2578 66507307 66507411 5.920000e-17 99.0
50 TraesCS2D01G155900 chr6B 87.500 80 7 3 2482 2560 176254833 176254756 3.560000e-14 89.8
51 TraesCS2D01G155900 chr6D 95.455 44 2 0 2352 2395 38238469 38238426 1.290000e-08 71.3


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 TraesCS2D01G155900 chr2D 99560317 99562916 2599 False 4802.0 4802 100.000000 1 2600 1 chr2D.!!$F3 2599
1 TraesCS2D01G155900 chr2D 99572291 99573763 1472 False 2287.0 2287 94.586000 616 2105 1 chr2D.!!$F4 1489
2 TraesCS2D01G155900 chr2D 99654294 99655780 1486 False 882.5 1253 89.549500 670 2115 2 chr2D.!!$F7 1445
3 TraesCS2D01G155900 chr2D 99360557 99361271 714 False 424.0 497 89.583500 1311 1991 2 chr2D.!!$F6 680
4 TraesCS2D01G155900 chr2A 98578381 98579678 1297 False 2161.0 2161 96.644000 616 1922 1 chr2A.!!$F2 1306
5 TraesCS2D01G155900 chr2A 98603035 98604442 1407 False 2008.0 2008 92.616000 618 2014 1 chr2A.!!$F3 1396
6 TraesCS2D01G155900 chr2A 98722323 98723732 1409 False 949.0 1539 91.585500 616 1997 2 chr2A.!!$F6 1381
7 TraesCS2D01G155900 chr2A 98620603 98621162 559 False 876.0 876 95.018000 2044 2600 1 chr2A.!!$F4 556
8 TraesCS2D01G155900 chr2A 98455979 98457438 1459 False 831.5 1319 90.101500 641 1991 2 chr2A.!!$F5 1350
9 TraesCS2D01G155900 chr2A 19913805 19914625 820 False 736.0 736 83.253000 884 1693 1 chr2A.!!$F1 809
10 TraesCS2D01G155900 chr2B 151484986 151489985 4999 True 1230.0 1973 91.961667 616 2600 3 chr2B.!!$R3 1984
11 TraesCS2D01G155900 chr2B 30636446 30637319 873 True 712.0 712 82.179000 763 1601 1 chr2B.!!$R1 838
12 TraesCS2D01G155900 chr3D 526943621 526944133 512 False 610.0 610 89.474000 1 472 1 chr3D.!!$F4 471
13 TraesCS2D01G155900 chrUn 24364927 24365688 761 True 625.0 625 82.269000 870 1600 1 chrUn.!!$R1 730
14 TraesCS2D01G155900 chr7D 583038705 583039218 513 True 617.0 617 89.709000 1 473 1 chr7D.!!$R3 472
15 TraesCS2D01G155900 chr1D 473970554 473971071 517 True 595.0 595 88.825000 1 474 1 chr1D.!!$R1 473

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
592 596 0.026285 CGATTTTTAGCGCCTCGTGG 59.974 55.0 2.29 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 5467 0.239879 CGTACCAACATTGCACACCC 59.76 55.0 0.0 0.0 0.0 4.61 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
99 103 2.772224 TGGCAACATCCATGGGCT 59.228 55.556 13.02 0.00 46.17 5.19
148 152 1.881973 CATAGATTTGCCATCCCACGG 59.118 52.381 0.00 0.00 0.00 4.94
149 153 1.208706 TAGATTTGCCATCCCACGGA 58.791 50.000 0.00 0.00 35.55 4.69
150 154 0.552848 AGATTTGCCATCCCACGGAT 59.447 50.000 0.00 0.00 44.21 4.18
151 155 0.954452 GATTTGCCATCCCACGGATC 59.046 55.000 0.00 0.00 40.98 3.36
152 156 0.819259 ATTTGCCATCCCACGGATCG 60.819 55.000 0.00 0.00 40.98 3.69
153 157 2.884997 TTTGCCATCCCACGGATCGG 62.885 60.000 0.00 0.00 40.98 4.18
155 159 4.969196 CCATCCCACGGATCGGCG 62.969 72.222 0.00 0.00 40.98 6.46
156 160 3.911698 CATCCCACGGATCGGCGA 61.912 66.667 13.87 13.87 40.98 5.54
157 161 3.606662 ATCCCACGGATCGGCGAG 61.607 66.667 17.22 4.14 38.09 5.03
172 176 3.520268 GAGCGACGCAGATCGATG 58.480 61.111 23.70 0.00 41.59 3.84
173 177 1.009562 GAGCGACGCAGATCGATGA 60.010 57.895 23.70 0.00 41.59 2.92
174 178 1.265462 GAGCGACGCAGATCGATGAC 61.265 60.000 23.70 0.00 41.59 3.06
175 179 2.630714 GCGACGCAGATCGATGACG 61.631 63.158 16.42 6.18 45.13 4.35
176 180 1.297672 CGACGCAGATCGATGACGT 60.298 57.895 14.58 14.58 45.13 4.34
177 181 1.524179 CGACGCAGATCGATGACGTG 61.524 60.000 18.29 8.91 45.13 4.49
178 182 1.202973 GACGCAGATCGATGACGTGG 61.203 60.000 18.29 0.13 41.67 4.94
182 186 2.658593 GATCGATGACGTGGCGGG 60.659 66.667 0.54 0.00 40.69 6.13
185 189 4.201679 CGATGACGTGGCGGGCTA 62.202 66.667 0.00 0.00 34.56 3.93
186 190 2.421739 GATGACGTGGCGGGCTAT 59.578 61.111 0.00 0.00 0.00 2.97
187 191 1.956170 GATGACGTGGCGGGCTATG 60.956 63.158 0.00 0.00 0.00 2.23
188 192 4.830765 TGACGTGGCGGGCTATGC 62.831 66.667 0.00 0.00 0.00 3.14
223 227 2.099831 CCGTCGGCGTAGACTGAC 59.900 66.667 9.28 0.00 38.90 3.51
230 234 2.865308 CGTAGACTGACGCCGTCA 59.135 61.111 20.04 20.04 40.50 4.35
232 236 0.386352 CGTAGACTGACGCCGTCAAA 60.386 55.000 21.56 4.37 42.26 2.69
234 238 1.719780 GTAGACTGACGCCGTCAAAAG 59.280 52.381 21.56 12.15 42.26 2.27
235 239 0.600255 AGACTGACGCCGTCAAAAGG 60.600 55.000 21.56 11.78 42.26 3.11
244 248 1.082366 CGTCAAAAGGCCGTTTCCG 60.082 57.895 14.18 14.68 0.00 4.30
245 249 1.371267 GTCAAAAGGCCGTTTCCGC 60.371 57.895 14.18 3.79 0.00 5.54
246 250 2.049526 CAAAAGGCCGTTTCCGCC 60.050 61.111 14.18 0.00 0.00 6.13
247 251 3.299977 AAAAGGCCGTTTCCGCCC 61.300 61.111 11.18 0.00 32.77 6.13
253 257 4.825252 CCGTTTCCGCCCGGGTAG 62.825 72.222 24.63 16.77 40.54 3.18
269 273 3.961225 TAGCCGGGCCCACGTTCTA 62.961 63.158 24.92 11.64 0.00 2.10
270 274 4.171103 GCCGGGCCCACGTTCTAT 62.171 66.667 24.92 0.00 0.00 1.98
271 275 2.203015 CCGGGCCCACGTTCTATG 60.203 66.667 24.92 0.78 0.00 2.23
272 276 2.895372 CGGGCCCACGTTCTATGC 60.895 66.667 24.92 0.00 0.00 3.14
273 277 2.516225 GGGCCCACGTTCTATGCC 60.516 66.667 19.95 0.00 41.42 4.40
274 278 2.895372 GGCCCACGTTCTATGCCG 60.895 66.667 0.00 0.00 31.55 5.69
275 279 2.185867 GCCCACGTTCTATGCCGA 59.814 61.111 0.00 0.00 0.00 5.54
276 280 2.171725 GCCCACGTTCTATGCCGAC 61.172 63.158 0.00 0.00 0.00 4.79
277 281 1.876714 CCCACGTTCTATGCCGACG 60.877 63.158 0.00 0.00 42.13 5.12
278 282 1.876714 CCACGTTCTATGCCGACGG 60.877 63.158 10.29 10.29 40.82 4.79
290 294 3.123674 CCGACGGGCTTATCTATGC 57.876 57.895 5.81 0.00 0.00 3.14
296 300 3.123674 GGCTTATCTATGCCGACGG 57.876 57.895 10.29 10.29 39.71 4.79
319 323 1.060713 CCGTAGGCATATTTCTCGCG 58.939 55.000 0.00 0.00 46.14 5.87
320 324 1.335597 CCGTAGGCATATTTCTCGCGA 60.336 52.381 9.26 9.26 46.14 5.87
321 325 1.714460 CGTAGGCATATTTCTCGCGAC 59.286 52.381 3.71 0.00 0.00 5.19
322 326 1.714460 GTAGGCATATTTCTCGCGACG 59.286 52.381 3.71 1.32 0.00 5.12
324 328 1.201825 GCATATTTCTCGCGACGCC 59.798 57.895 15.34 0.00 0.00 5.68
325 329 1.482955 CATATTTCTCGCGACGCCG 59.517 57.895 15.34 9.76 39.16 6.46
326 330 0.933047 CATATTTCTCGCGACGCCGA 60.933 55.000 15.34 13.61 38.22 5.54
327 331 0.933509 ATATTTCTCGCGACGCCGAC 60.934 55.000 15.34 0.00 38.22 4.79
339 343 3.793144 GCCGACGGCTGAGCTTTG 61.793 66.667 31.30 0.00 46.69 2.77
345 349 3.793144 GGCTGAGCTTTGCCGACG 61.793 66.667 13.84 0.00 39.71 5.12
346 350 3.793144 GCTGAGCTTTGCCGACGG 61.793 66.667 10.29 10.29 0.00 4.79
347 351 3.121030 CTGAGCTTTGCCGACGGG 61.121 66.667 17.22 0.00 0.00 5.28
372 376 3.618698 CGTCGGCATAGATGGATATACG 58.381 50.000 0.00 0.00 0.00 3.06
374 378 2.361119 TCGGCATAGATGGATATACGCC 59.639 50.000 0.00 0.00 34.91 5.68
376 380 2.361119 GGCATAGATGGATATACGCCGA 59.639 50.000 0.00 0.00 0.00 5.54
377 381 3.372954 GCATAGATGGATATACGCCGAC 58.627 50.000 0.00 0.00 0.00 4.79
379 383 0.809385 AGATGGATATACGCCGACGG 59.191 55.000 10.29 10.29 46.04 4.79
380 384 0.801067 GATGGATATACGCCGACGGC 60.801 60.000 29.10 29.10 46.75 5.68
402 406 4.301027 GCTGGGCCGTCGGGATAG 62.301 72.222 14.38 0.00 34.06 2.08
403 407 3.616721 CTGGGCCGTCGGGATAGG 61.617 72.222 14.38 0.00 34.06 2.57
407 411 3.857038 GCCGTCGGGATAGGCCAA 61.857 66.667 14.38 0.00 44.80 4.52
408 412 3.148084 CCGTCGGGATAGGCCAAT 58.852 61.111 5.01 0.00 38.95 3.16
409 413 1.004918 CCGTCGGGATAGGCCAATC 60.005 63.158 5.01 0.00 38.95 2.67
410 414 1.472662 CCGTCGGGATAGGCCAATCT 61.473 60.000 5.01 0.00 38.95 2.40
411 415 1.254026 CGTCGGGATAGGCCAATCTA 58.746 55.000 5.01 0.00 38.95 1.98
412 416 1.825474 CGTCGGGATAGGCCAATCTAT 59.175 52.381 5.01 0.00 38.95 1.98
421 425 1.961277 GCCAATCTATGCCGACGGG 60.961 63.158 17.22 0.00 0.00 5.28
423 427 1.301716 CAATCTATGCCGACGGGGG 60.302 63.158 17.22 0.00 35.78 5.40
424 428 1.764854 AATCTATGCCGACGGGGGT 60.765 57.895 17.22 0.00 35.78 4.95
435 439 4.280494 CGGGGGTCGTCGGCATAG 62.280 72.222 0.00 0.00 0.00 2.23
436 440 3.925090 GGGGGTCGTCGGCATAGG 61.925 72.222 0.00 0.00 0.00 2.57
437 441 3.152400 GGGGTCGTCGGCATAGGT 61.152 66.667 0.00 0.00 0.00 3.08
439 443 1.227176 GGGTCGTCGGCATAGGTTC 60.227 63.158 0.00 0.00 0.00 3.62
440 444 1.588139 GGTCGTCGGCATAGGTTCG 60.588 63.158 0.00 0.00 0.00 3.95
441 445 1.588139 GTCGTCGGCATAGGTTCGG 60.588 63.158 0.00 0.00 0.00 4.30
442 446 2.960129 CGTCGGCATAGGTTCGGC 60.960 66.667 0.00 0.00 0.00 5.54
448 452 2.279252 CATAGGTTCGGCCGTCGG 60.279 66.667 27.15 6.99 43.70 4.79
479 483 4.164221 AGTTATTCTGGTAGTGATGTGGGG 59.836 45.833 0.00 0.00 0.00 4.96
480 484 0.618458 TTCTGGTAGTGATGTGGGGC 59.382 55.000 0.00 0.00 0.00 5.80
481 485 1.224592 CTGGTAGTGATGTGGGGCC 59.775 63.158 0.00 0.00 0.00 5.80
482 486 2.189521 GGTAGTGATGTGGGGCCG 59.810 66.667 0.00 0.00 0.00 6.13
483 487 2.189521 GTAGTGATGTGGGGCCGG 59.810 66.667 0.00 0.00 0.00 6.13
484 488 2.039787 TAGTGATGTGGGGCCGGA 59.960 61.111 5.05 0.00 0.00 5.14
485 489 1.383943 TAGTGATGTGGGGCCGGAT 60.384 57.895 5.05 0.00 0.00 4.18
486 490 0.986019 TAGTGATGTGGGGCCGGATT 60.986 55.000 5.05 0.00 0.00 3.01
488 492 0.970427 GTGATGTGGGGCCGGATTTT 60.970 55.000 5.05 0.00 0.00 1.82
491 495 0.544120 ATGTGGGGCCGGATTTTGTT 60.544 50.000 5.05 0.00 0.00 2.83
494 498 1.132500 TGGGGCCGGATTTTGTTTTT 58.868 45.000 5.05 0.00 0.00 1.94
495 499 1.070914 TGGGGCCGGATTTTGTTTTTC 59.929 47.619 5.05 0.00 0.00 2.29
497 501 2.485657 GGGGCCGGATTTTGTTTTTCAA 60.486 45.455 5.05 0.00 0.00 2.69
498 502 3.206964 GGGCCGGATTTTGTTTTTCAAA 58.793 40.909 5.05 0.00 43.24 2.69
511 515 6.292389 TGTTTTTCAAAAATAACATGGGCG 57.708 33.333 0.00 0.00 33.27 6.13
512 516 4.999751 TTTTCAAAAATAACATGGGCGC 57.000 36.364 0.00 0.00 0.00 6.53
516 520 2.606155 AAAATAACATGGGCGCGGCG 62.606 55.000 27.12 19.62 0.00 6.46
517 521 4.539083 ATAACATGGGCGCGGCGA 62.539 61.111 28.54 24.29 0.00 5.54
528 532 3.917760 GCGGCGACTAGGGAGCAT 61.918 66.667 12.98 0.00 0.00 3.79
529 533 2.336809 CGGCGACTAGGGAGCATC 59.663 66.667 0.00 0.00 0.00 3.91
530 534 2.490148 CGGCGACTAGGGAGCATCA 61.490 63.158 0.00 0.00 36.25 3.07
531 535 1.068250 GGCGACTAGGGAGCATCAC 59.932 63.158 8.27 0.00 40.51 3.06
539 543 4.864334 GGAGCATCACGCCCCCAG 62.864 72.222 0.00 0.00 44.04 4.45
551 555 2.040544 CCCCCAGCACGCAGTTTAG 61.041 63.158 0.00 0.00 41.61 1.85
552 556 2.690778 CCCCAGCACGCAGTTTAGC 61.691 63.158 0.00 0.00 41.61 3.09
560 564 3.087176 GCAGTTTAGCGCCGGTAC 58.913 61.111 2.29 0.00 0.00 3.34
561 565 1.738830 GCAGTTTAGCGCCGGTACA 60.739 57.895 2.29 0.00 0.00 2.90
562 566 1.963190 GCAGTTTAGCGCCGGTACAC 61.963 60.000 2.29 4.55 0.00 2.90
564 568 2.102438 GTTTAGCGCCGGTACACCC 61.102 63.158 2.29 0.00 0.00 4.61
566 570 1.829523 TTTAGCGCCGGTACACCCTT 61.830 55.000 2.29 0.00 0.00 3.95
567 571 0.969917 TTAGCGCCGGTACACCCTTA 60.970 55.000 2.29 0.00 0.00 2.69
568 572 1.386525 TAGCGCCGGTACACCCTTAG 61.387 60.000 2.29 0.00 0.00 2.18
569 573 2.497770 CGCCGGTACACCCTTAGG 59.502 66.667 1.90 0.00 40.04 2.69
570 574 2.188731 GCCGGTACACCCTTAGGC 59.811 66.667 1.90 0.12 36.11 3.93
571 575 2.497770 CCGGTACACCCTTAGGCG 59.502 66.667 0.00 0.00 36.11 5.52
572 576 2.497770 CGGTACACCCTTAGGCGG 59.502 66.667 0.00 0.00 36.11 6.13
573 577 2.188731 GGTACACCCTTAGGCGGC 59.811 66.667 0.00 0.00 36.11 6.53
574 578 2.202837 GTACACCCTTAGGCGGCG 60.203 66.667 0.51 0.51 36.11 6.46
575 579 2.362760 TACACCCTTAGGCGGCGA 60.363 61.111 12.98 0.00 36.11 5.54
576 580 1.759299 TACACCCTTAGGCGGCGAT 60.759 57.895 12.98 0.00 36.11 4.58
577 581 1.332144 TACACCCTTAGGCGGCGATT 61.332 55.000 12.98 0.00 36.11 3.34
578 582 1.451387 CACCCTTAGGCGGCGATTT 60.451 57.895 12.98 0.00 36.11 2.17
579 583 1.029947 CACCCTTAGGCGGCGATTTT 61.030 55.000 12.98 0.00 36.11 1.82
580 584 0.323087 ACCCTTAGGCGGCGATTTTT 60.323 50.000 12.98 0.00 36.11 1.94
581 585 1.065272 ACCCTTAGGCGGCGATTTTTA 60.065 47.619 12.98 0.00 36.11 1.52
582 586 1.602377 CCCTTAGGCGGCGATTTTTAG 59.398 52.381 12.98 0.00 0.00 1.85
584 588 0.653636 TTAGGCGGCGATTTTTAGCG 59.346 50.000 12.98 0.00 0.00 4.26
589 593 4.571257 GCGATTTTTAGCGCCTCG 57.429 55.556 2.29 4.74 46.93 4.63
590 594 1.713830 GCGATTTTTAGCGCCTCGT 59.286 52.632 2.29 0.00 46.93 4.18
591 595 0.586502 GCGATTTTTAGCGCCTCGTG 60.587 55.000 2.29 0.00 46.93 4.35
592 596 0.026285 CGATTTTTAGCGCCTCGTGG 59.974 55.000 2.29 0.00 0.00 4.94
593 597 0.377203 GATTTTTAGCGCCTCGTGGG 59.623 55.000 2.29 0.00 38.36 4.61
594 598 0.035820 ATTTTTAGCGCCTCGTGGGA 60.036 50.000 2.29 0.00 37.23 4.37
595 599 0.672401 TTTTTAGCGCCTCGTGGGAG 60.672 55.000 2.29 1.23 40.14 4.30
603 607 4.760047 CTCGTGGGAGGCCAACGG 62.760 72.222 12.97 1.25 36.61 4.44
614 618 2.042831 GCCAACGGCTGAAGATGCT 61.043 57.895 0.00 0.00 46.69 3.79
934 4175 1.153249 CCACCACAACACGACCTGT 60.153 57.895 0.00 0.00 32.89 4.00
944 4218 0.109086 CACGACCTGTCTGGCACTAG 60.109 60.000 0.00 0.00 40.22 2.57
1722 5214 3.435327 GGTTGCTTGTGTATCATTGTCGA 59.565 43.478 0.00 0.00 0.00 4.20
1857 5379 9.685276 TCACATATAGTCTCACCAAAAATCATT 57.315 29.630 0.00 0.00 0.00 2.57
1944 5467 2.019951 ACGGTTGCAGTTACGCGAG 61.020 57.895 15.93 0.00 33.35 5.03
1977 5502 1.212688 TGGTACGGTCGGATCCTAGAA 59.787 52.381 10.75 0.00 0.00 2.10
2003 5528 1.568504 AAGGCAAGGTGGATCGTCTA 58.431 50.000 0.00 0.00 0.00 2.59
2029 5554 0.609131 ACCAACTGCTTCAATCCCCG 60.609 55.000 0.00 0.00 0.00 5.73
2030 5555 1.315257 CCAACTGCTTCAATCCCCGG 61.315 60.000 0.00 0.00 0.00 5.73
2031 5556 1.678970 AACTGCTTCAATCCCCGGC 60.679 57.895 0.00 0.00 0.00 6.13
2045 5570 1.228793 CCGGCCCATCCATTTGGTA 59.771 57.895 0.00 0.00 34.77 3.25
2061 5586 6.601613 CCATTTGGTATGGTGTCTAGCTTAAA 59.398 38.462 0.00 0.00 34.56 1.52
2263 5790 5.428253 TCTTCCATGTGGCACTACTTATTC 58.572 41.667 19.83 0.00 34.44 1.75
2343 5870 2.094762 AAGACTTTGGCGACGCTTAT 57.905 45.000 20.77 0.89 0.00 1.73
2356 5883 2.949644 GACGCTTATGGGGCACTATTTT 59.050 45.455 0.00 0.00 33.88 1.82
2396 5923 1.607801 CCCACGTCCTCTGCATCTCA 61.608 60.000 0.00 0.00 0.00 3.27
2443 5971 9.581099 TTAAAAATTGAGGTTCAGAACAAAGTC 57.419 29.630 15.36 6.46 0.00 3.01
2457 5985 5.755861 AGAACAAAGTCTCAAAGAGTAGTGC 59.244 40.000 0.00 0.00 0.00 4.40
2467 5995 6.020971 TCAAAGAGTAGTGCGAAACTCATA 57.979 37.500 12.82 0.00 43.74 2.15
2491 6019 0.808453 ATAATCCGTCACAACCGGCG 60.808 55.000 0.00 0.00 45.09 6.46
2507 6035 2.802816 CCGGCGAAAATAGGAAGAGATG 59.197 50.000 9.30 0.00 0.00 2.90
2563 6093 2.185663 ACCGGTTGTAGGTATCCCAT 57.814 50.000 0.00 0.00 40.80 4.00
2587 6117 1.414181 ACCATCTCCCATCAGCTTACG 59.586 52.381 0.00 0.00 0.00 3.18
2591 6121 2.203209 CCCATCAGCTTACGGGGC 60.203 66.667 0.00 0.00 34.81 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 131 1.267806 CGTGGGATGGCAAATCTATGC 59.732 52.381 0.00 0.00 45.67 3.14
128 132 1.881973 CCGTGGGATGGCAAATCTATG 59.118 52.381 0.00 0.00 0.00 2.23
129 133 1.774254 TCCGTGGGATGGCAAATCTAT 59.226 47.619 0.00 0.00 0.00 1.98
131 135 0.552848 ATCCGTGGGATGGCAAATCT 59.447 50.000 0.00 0.00 41.43 2.40
132 136 0.954452 GATCCGTGGGATGGCAAATC 59.046 55.000 1.07 0.00 43.27 2.17
133 137 0.819259 CGATCCGTGGGATGGCAAAT 60.819 55.000 1.07 0.00 43.27 2.32
134 138 1.451207 CGATCCGTGGGATGGCAAA 60.451 57.895 1.07 0.00 43.27 3.68
135 139 2.189257 CGATCCGTGGGATGGCAA 59.811 61.111 1.07 0.00 43.27 4.52
138 142 4.969196 CGCCGATCCGTGGGATGG 62.969 72.222 1.07 0.57 43.27 3.51
139 143 3.848347 CTCGCCGATCCGTGGGATG 62.848 68.421 1.07 0.00 43.27 3.51
140 144 3.606662 CTCGCCGATCCGTGGGAT 61.607 66.667 0.00 0.00 46.28 3.85
154 158 2.051793 ATCGATCTGCGTCGCTCG 60.052 61.111 19.50 18.70 41.22 5.03
155 159 1.009562 TCATCGATCTGCGTCGCTC 60.010 57.895 19.50 6.84 41.22 5.03
156 160 1.298713 GTCATCGATCTGCGTCGCT 60.299 57.895 19.50 0.00 41.22 4.93
157 161 2.630714 CGTCATCGATCTGCGTCGC 61.631 63.158 11.10 11.10 41.22 5.19
160 164 1.226688 CCACGTCATCGATCTGCGT 60.227 57.895 11.18 11.18 41.80 5.24
162 166 2.580470 CGCCACGTCATCGATCTGC 61.580 63.158 0.00 0.00 40.62 4.26
163 167 1.946156 CCGCCACGTCATCGATCTG 60.946 63.158 0.00 0.00 40.62 2.90
164 168 2.413351 CCGCCACGTCATCGATCT 59.587 61.111 0.00 0.00 40.62 2.75
166 170 4.891727 GCCCGCCACGTCATCGAT 62.892 66.667 0.00 0.00 40.62 3.59
168 172 3.499929 ATAGCCCGCCACGTCATCG 62.500 63.158 0.00 0.00 43.34 3.84
170 174 2.108976 CATAGCCCGCCACGTCAT 59.891 61.111 0.00 0.00 0.00 3.06
171 175 4.830765 GCATAGCCCGCCACGTCA 62.831 66.667 0.00 0.00 0.00 4.35
205 209 3.129502 TCAGTCTACGCCGACGGG 61.130 66.667 17.22 8.43 46.04 5.28
213 217 0.386352 TTTGACGGCGTCAGTCTACG 60.386 55.000 36.94 0.00 43.69 3.51
214 218 1.719780 CTTTTGACGGCGTCAGTCTAC 59.280 52.381 36.94 13.88 43.69 2.59
215 219 1.336517 CCTTTTGACGGCGTCAGTCTA 60.337 52.381 36.94 23.35 43.69 2.59
216 220 0.600255 CCTTTTGACGGCGTCAGTCT 60.600 55.000 36.94 3.60 43.69 3.24
217 221 1.860078 CCTTTTGACGGCGTCAGTC 59.140 57.895 36.94 15.75 43.69 3.51
218 222 2.251642 GCCTTTTGACGGCGTCAGT 61.252 57.895 36.94 4.91 43.69 3.41
219 223 2.556287 GCCTTTTGACGGCGTCAG 59.444 61.111 36.94 27.64 43.69 3.51
225 229 1.284715 GGAAACGGCCTTTTGACGG 59.715 57.895 12.63 0.00 0.00 4.79
226 230 4.935630 GGAAACGGCCTTTTGACG 57.064 55.556 12.63 0.00 0.00 4.35
251 255 3.961225 TAGAACGTGGGCCCGGCTA 62.961 63.158 19.37 10.82 0.00 3.93
253 257 4.171103 ATAGAACGTGGGCCCGGC 62.171 66.667 19.37 12.01 0.00 6.13
255 259 2.895372 GCATAGAACGTGGGCCCG 60.895 66.667 19.37 8.84 0.00 6.13
256 260 2.516225 GGCATAGAACGTGGGCCC 60.516 66.667 17.59 17.59 38.70 5.80
257 261 2.895372 CGGCATAGAACGTGGGCC 60.895 66.667 0.00 0.00 41.20 5.80
258 262 2.171725 GTCGGCATAGAACGTGGGC 61.172 63.158 0.00 0.00 0.00 5.36
259 263 1.876714 CGTCGGCATAGAACGTGGG 60.877 63.158 0.00 0.00 0.00 4.61
261 265 1.876714 CCCGTCGGCATAGAACGTG 60.877 63.158 5.50 0.00 0.00 4.49
262 266 2.493030 CCCGTCGGCATAGAACGT 59.507 61.111 5.50 0.00 0.00 3.99
272 276 0.389948 GGCATAGATAAGCCCGTCGG 60.390 60.000 3.60 3.60 45.18 4.79
273 277 3.123674 GGCATAGATAAGCCCGTCG 57.876 57.895 0.00 0.00 45.18 5.12
297 301 2.927014 GCGAGAAATATGCCTACGGAGG 60.927 54.545 10.25 10.25 46.93 4.30
299 303 1.335597 CGCGAGAAATATGCCTACGGA 60.336 52.381 0.00 0.00 0.00 4.69
300 304 1.060713 CGCGAGAAATATGCCTACGG 58.939 55.000 0.00 0.00 0.00 4.02
301 305 1.714460 GTCGCGAGAAATATGCCTACG 59.286 52.381 10.24 0.00 45.01 3.51
303 307 1.929038 GCGTCGCGAGAAATATGCCTA 60.929 52.381 10.24 0.00 45.01 3.93
304 308 1.215655 GCGTCGCGAGAAATATGCCT 61.216 55.000 10.24 0.00 45.01 4.75
306 310 1.201825 GGCGTCGCGAGAAATATGC 59.798 57.895 10.24 3.53 45.01 3.14
308 312 0.933509 GTCGGCGTCGCGAGAAATAT 60.934 55.000 10.24 0.00 45.01 1.28
309 313 1.584483 GTCGGCGTCGCGAGAAATA 60.584 57.895 10.24 0.00 45.01 1.40
310 314 2.879462 GTCGGCGTCGCGAGAAAT 60.879 61.111 10.24 0.00 45.01 2.17
324 328 3.793144 GGCAAAGCTCAGCCGTCG 61.793 66.667 12.94 0.00 41.70 5.12
330 334 3.121030 CCCGTCGGCAAAGCTCAG 61.121 66.667 5.50 0.00 0.00 3.35
331 335 4.697756 CCCCGTCGGCAAAGCTCA 62.698 66.667 5.50 0.00 0.00 4.26
351 355 3.618698 CGTATATCCATCTATGCCGACG 58.381 50.000 0.00 0.00 0.00 5.12
352 356 3.372954 GCGTATATCCATCTATGCCGAC 58.627 50.000 0.00 0.00 0.00 4.79
353 357 2.361119 GGCGTATATCCATCTATGCCGA 59.639 50.000 0.73 0.00 39.52 5.54
355 359 2.361119 TCGGCGTATATCCATCTATGCC 59.639 50.000 6.85 5.49 43.59 4.40
357 361 3.548214 CCGTCGGCGTATATCCATCTATG 60.548 52.174 9.28 0.00 36.15 2.23
358 362 2.617308 CCGTCGGCGTATATCCATCTAT 59.383 50.000 9.28 0.00 36.15 1.98
360 364 0.809385 CCGTCGGCGTATATCCATCT 59.191 55.000 9.28 0.00 36.15 2.90
361 365 0.801067 GCCGTCGGCGTATATCCATC 60.801 60.000 22.50 0.00 39.62 3.51
362 366 1.214589 GCCGTCGGCGTATATCCAT 59.785 57.895 22.50 0.00 39.62 3.41
386 390 3.616721 CCTATCCCGACGGCCCAG 61.617 72.222 8.86 4.13 0.00 4.45
392 396 1.254026 TAGATTGGCCTATCCCGACG 58.746 55.000 21.62 0.00 0.00 5.12
393 397 2.678190 GCATAGATTGGCCTATCCCGAC 60.678 54.545 21.62 7.65 0.00 4.79
395 399 1.407437 GGCATAGATTGGCCTATCCCG 60.407 57.143 21.62 12.34 46.74 5.14
396 400 2.426842 GGCATAGATTGGCCTATCCC 57.573 55.000 21.62 12.82 46.74 3.85
405 409 1.301716 CCCCCGTCGGCATAGATTG 60.302 63.158 5.50 0.00 0.00 2.67
406 410 1.755393 GACCCCCGTCGGCATAGATT 61.755 60.000 5.50 0.00 0.00 2.40
407 411 2.122989 ACCCCCGTCGGCATAGAT 60.123 61.111 5.50 0.00 0.00 1.98
408 412 2.836360 GACCCCCGTCGGCATAGA 60.836 66.667 5.50 0.00 0.00 1.98
421 425 1.227176 GAACCTATGCCGACGACCC 60.227 63.158 0.00 0.00 0.00 4.46
423 427 1.588139 CCGAACCTATGCCGACGAC 60.588 63.158 0.00 0.00 0.00 4.34
424 428 2.802792 CCGAACCTATGCCGACGA 59.197 61.111 0.00 0.00 0.00 4.20
429 433 2.588034 GACGGCCGAACCTATGCC 60.588 66.667 35.90 4.89 41.85 4.40
430 434 2.960129 CGACGGCCGAACCTATGC 60.960 66.667 35.90 8.88 41.76 3.14
431 435 2.279252 CCGACGGCCGAACCTATG 60.279 66.667 35.90 12.24 41.76 2.23
432 436 4.217159 GCCGACGGCCGAACCTAT 62.217 66.667 35.90 8.10 44.06 2.57
455 459 5.118990 CCCACATCACTACCAGAATAACTG 58.881 45.833 0.00 0.00 45.36 3.16
456 460 4.164221 CCCCACATCACTACCAGAATAACT 59.836 45.833 0.00 0.00 0.00 2.24
457 461 4.451900 CCCCACATCACTACCAGAATAAC 58.548 47.826 0.00 0.00 0.00 1.89
458 462 3.118038 GCCCCACATCACTACCAGAATAA 60.118 47.826 0.00 0.00 0.00 1.40
460 464 1.212935 GCCCCACATCACTACCAGAAT 59.787 52.381 0.00 0.00 0.00 2.40
461 465 0.618458 GCCCCACATCACTACCAGAA 59.382 55.000 0.00 0.00 0.00 3.02
462 466 1.271840 GGCCCCACATCACTACCAGA 61.272 60.000 0.00 0.00 0.00 3.86
463 467 1.224592 GGCCCCACATCACTACCAG 59.775 63.158 0.00 0.00 0.00 4.00
464 468 2.665089 CGGCCCCACATCACTACCA 61.665 63.158 0.00 0.00 0.00 3.25
465 469 2.189521 CGGCCCCACATCACTACC 59.810 66.667 0.00 0.00 0.00 3.18
466 470 1.696097 ATCCGGCCCCACATCACTAC 61.696 60.000 0.00 0.00 0.00 2.73
467 471 0.986019 AATCCGGCCCCACATCACTA 60.986 55.000 0.00 0.00 0.00 2.74
468 472 1.863155 AAATCCGGCCCCACATCACT 61.863 55.000 0.00 0.00 0.00 3.41
469 473 0.970427 AAAATCCGGCCCCACATCAC 60.970 55.000 0.00 0.00 0.00 3.06
470 474 0.969917 CAAAATCCGGCCCCACATCA 60.970 55.000 0.00 0.00 0.00 3.07
471 475 0.970427 ACAAAATCCGGCCCCACATC 60.970 55.000 0.00 0.00 0.00 3.06
472 476 0.544120 AACAAAATCCGGCCCCACAT 60.544 50.000 0.00 0.00 0.00 3.21
473 477 0.760945 AAACAAAATCCGGCCCCACA 60.761 50.000 0.00 0.00 0.00 4.17
474 478 0.394938 AAAACAAAATCCGGCCCCAC 59.605 50.000 0.00 0.00 0.00 4.61
476 480 1.070914 TGAAAAACAAAATCCGGCCCC 59.929 47.619 0.00 0.00 0.00 5.80
486 490 7.189512 CGCCCATGTTATTTTTGAAAAACAAA 58.810 30.769 5.08 0.98 45.22 2.83
488 492 5.277538 GCGCCCATGTTATTTTTGAAAAACA 60.278 36.000 5.08 0.68 0.00 2.83
491 495 3.430218 CGCGCCCATGTTATTTTTGAAAA 59.570 39.130 0.00 0.00 0.00 2.29
494 498 1.135257 CCGCGCCCATGTTATTTTTGA 60.135 47.619 0.00 0.00 0.00 2.69
495 499 1.276415 CCGCGCCCATGTTATTTTTG 58.724 50.000 0.00 0.00 0.00 2.44
497 501 1.140804 GCCGCGCCCATGTTATTTT 59.859 52.632 0.00 0.00 0.00 1.82
498 502 2.804856 GCCGCGCCCATGTTATTT 59.195 55.556 0.00 0.00 0.00 1.40
499 503 3.582120 CGCCGCGCCCATGTTATT 61.582 61.111 0.00 0.00 0.00 1.40
500 504 4.539083 TCGCCGCGCCCATGTTAT 62.539 61.111 8.21 0.00 0.00 1.89
511 515 3.850095 GATGCTCCCTAGTCGCCGC 62.850 68.421 0.00 0.00 0.00 6.53
512 516 2.336809 GATGCTCCCTAGTCGCCG 59.663 66.667 0.00 0.00 0.00 6.46
516 520 1.068250 GGCGTGATGCTCCCTAGTC 59.932 63.158 0.00 0.00 45.43 2.59
517 521 2.435693 GGGCGTGATGCTCCCTAGT 61.436 63.158 0.00 0.00 45.43 2.57
518 522 2.423446 GGGCGTGATGCTCCCTAG 59.577 66.667 0.00 0.00 45.43 3.02
534 538 2.690778 GCTAAACTGCGTGCTGGGG 61.691 63.158 3.77 0.00 0.00 4.96
543 547 1.738830 TGTACCGGCGCTAAACTGC 60.739 57.895 7.64 0.00 0.00 4.40
544 548 1.356527 GGTGTACCGGCGCTAAACTG 61.357 60.000 7.64 0.00 0.00 3.16
545 549 1.079612 GGTGTACCGGCGCTAAACT 60.080 57.895 7.64 0.00 0.00 2.66
547 551 1.829523 AAGGGTGTACCGGCGCTAAA 61.830 55.000 7.64 0.00 46.96 1.85
548 552 0.969917 TAAGGGTGTACCGGCGCTAA 60.970 55.000 7.64 0.00 46.96 3.09
549 553 1.379710 TAAGGGTGTACCGGCGCTA 60.380 57.895 7.64 0.00 46.96 4.26
551 555 2.202837 CTAAGGGTGTACCGGCGC 60.203 66.667 0.00 0.00 46.96 6.53
552 556 2.497770 CCTAAGGGTGTACCGGCG 59.502 66.667 0.00 0.00 46.96 6.46
553 557 2.188731 GCCTAAGGGTGTACCGGC 59.811 66.667 0.00 2.61 46.96 6.13
555 559 2.497770 CCGCCTAAGGGTGTACCG 59.502 66.667 0.00 0.00 46.96 4.02
556 560 2.188731 GCCGCCTAAGGGTGTACC 59.811 66.667 0.00 0.00 41.26 3.34
558 562 1.332144 AATCGCCGCCTAAGGGTGTA 61.332 55.000 0.00 0.00 41.26 2.90
559 563 2.193087 AAATCGCCGCCTAAGGGTGT 62.193 55.000 0.00 0.00 41.26 4.16
560 564 1.029947 AAAATCGCCGCCTAAGGGTG 61.030 55.000 0.00 0.00 42.41 4.61
561 565 0.323087 AAAAATCGCCGCCTAAGGGT 60.323 50.000 0.00 0.00 34.45 4.34
562 566 1.602377 CTAAAAATCGCCGCCTAAGGG 59.398 52.381 0.00 0.00 0.00 3.95
564 568 1.332904 CGCTAAAAATCGCCGCCTAAG 60.333 52.381 0.00 0.00 0.00 2.18
566 570 1.768112 GCGCTAAAAATCGCCGCCTA 61.768 55.000 0.00 0.00 45.01 3.93
567 571 3.098555 CGCTAAAAATCGCCGCCT 58.901 55.556 0.00 0.00 0.00 5.52
568 572 2.650917 GCGCTAAAAATCGCCGCC 60.651 61.111 0.00 0.00 45.01 6.13
573 577 0.026285 CCACGAGGCGCTAAAAATCG 59.974 55.000 7.64 10.38 39.22 3.34
574 578 0.377203 CCCACGAGGCGCTAAAAATC 59.623 55.000 7.64 0.00 0.00 2.17
575 579 0.035820 TCCCACGAGGCGCTAAAAAT 60.036 50.000 7.64 0.00 34.51 1.82
576 580 0.672401 CTCCCACGAGGCGCTAAAAA 60.672 55.000 7.64 0.00 34.51 1.94
577 581 1.079405 CTCCCACGAGGCGCTAAAA 60.079 57.895 7.64 0.00 34.51 1.52
578 582 2.577059 CTCCCACGAGGCGCTAAA 59.423 61.111 7.64 0.00 34.51 1.85
586 590 4.760047 CCGTTGGCCTCCCACGAG 62.760 72.222 15.92 5.58 41.97 4.18
597 601 2.093216 GAGCATCTTCAGCCGTTGG 58.907 57.895 0.00 0.00 0.00 3.77
610 614 0.978146 AGCGTCCCAGGTTAGAGCAT 60.978 55.000 0.00 0.00 0.00 3.79
611 615 1.605058 GAGCGTCCCAGGTTAGAGCA 61.605 60.000 0.00 0.00 0.00 4.26
614 618 1.303888 ACGAGCGTCCCAGGTTAGA 60.304 57.895 0.00 0.00 0.00 2.10
934 4175 3.634448 GACAAGCTAGATCTAGTGCCAGA 59.366 47.826 26.73 0.00 35.65 3.86
1052 4354 2.203126 CCATGCCGAGGAGAAGCC 60.203 66.667 0.00 0.00 0.00 4.35
1095 4400 3.386237 GGGCTGCTGGAGACGACT 61.386 66.667 0.00 0.00 0.00 4.18
1722 5214 7.732996 ACAGTAAAGATACTTATGGGCGTATT 58.267 34.615 0.00 0.00 40.44 1.89
1857 5379 7.207383 CGTGACTAATATGTTATGGTGGAGAA 58.793 38.462 0.00 0.00 0.00 2.87
1922 5445 1.567537 CGTAACTGCAACCGTGTGG 59.432 57.895 0.00 0.00 42.84 4.17
1944 5467 0.239879 CGTACCAACATTGCACACCC 59.760 55.000 0.00 0.00 0.00 4.61
1977 5502 3.443681 CGATCCACCTTGCCTTAAATGTT 59.556 43.478 0.00 0.00 0.00 2.71
2003 5528 4.762251 GGATTGAAGCAGTTGGTTAGAACT 59.238 41.667 0.00 0.00 36.58 3.01
2029 5554 1.341080 CCATACCAAATGGATGGGCC 58.659 55.000 16.76 0.00 45.18 5.80
2030 5555 1.688197 CACCATACCAAATGGATGGGC 59.312 52.381 23.22 0.00 45.18 5.36
2031 5556 2.958355 GACACCATACCAAATGGATGGG 59.042 50.000 23.22 15.87 45.18 4.00
2045 5570 6.775708 TGTAGGTTTTTAAGCTAGACACCAT 58.224 36.000 0.00 0.00 41.68 3.55
2061 5586 1.599797 GCGCCACCACTGTAGGTTT 60.600 57.895 0.00 0.00 40.77 3.27
2178 5704 9.590451 CCAATGATTAATTAGCATGACAAGTTT 57.410 29.630 0.00 0.00 0.00 2.66
2263 5790 7.715657 AGTATTCTCTCTACAGCTTGATCAAG 58.284 38.462 27.82 27.82 41.24 3.02
2343 5870 7.663493 CCTTTTCAAAAATAAAATAGTGCCCCA 59.337 33.333 0.00 0.00 0.00 4.96
2356 5883 7.094118 CGTGGGTATTCCTCCTTTTCAAAAATA 60.094 37.037 0.00 0.00 36.20 1.40
2424 5951 5.097742 TGAGACTTTGTTCTGAACCTCAA 57.902 39.130 17.26 7.27 0.00 3.02
2432 5960 6.292596 GCACTACTCTTTGAGACTTTGTTCTG 60.293 42.308 1.25 0.00 33.32 3.02
2443 5971 4.299155 TGAGTTTCGCACTACTCTTTGAG 58.701 43.478 9.60 0.00 41.05 3.02
2478 6006 0.791422 TATTTTCGCCGGTTGTGACG 59.209 50.000 1.90 0.00 31.91 4.35
2491 6019 9.436957 TGTGTTTAGTCATCTCTTCCTATTTTC 57.563 33.333 0.00 0.00 0.00 2.29
2507 6035 8.827677 GTCCAACAATAGGATATGTGTTTAGTC 58.172 37.037 0.00 0.00 37.52 2.59
2563 6093 1.918262 AGCTGATGGGAGATGGTTTCA 59.082 47.619 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.