Multiple sequence alignment - TraesCS6A01G103900

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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 TraesCS6A01G103900 chr6A 100.000 3600 0 0 1 3600 73067424 73071023 0.000000e+00 6649
1 TraesCS6A01G103900 chr6A 93.966 232 9 3 3369 3600 73078152 73077926 2.660000e-91 346
2 TraesCS6A01G103900 chr6A 83.860 285 40 6 2778 3059 100666204 100666485 2.130000e-67 267
3 TraesCS6A01G103900 chr6A 83.219 292 41 8 2772 3059 100664470 100664757 9.910000e-66 261
4 TraesCS6A01G103900 chr6A 82.119 302 47 7 2761 3059 100646425 100646128 5.970000e-63 252
5 TraesCS6A01G103900 chr6B 93.592 2341 132 11 457 2783 129854685 129857021 0.000000e+00 3476
6 TraesCS6A01G103900 chr6B 95.767 189 8 0 112 300 129854500 129854688 4.520000e-79 305
7 TraesCS6A01G103900 chr6B 84.138 290 42 4 2772 3059 159133392 159133679 9.840000e-71 278
8 TraesCS6A01G103900 chr6B 83.000 300 46 5 2762 3059 159061262 159060966 2.130000e-67 267
9 TraesCS6A01G103900 chr6B 82.935 293 40 9 2772 3059 159137922 159138209 4.610000e-64 255
10 TraesCS6A01G103900 chr6B 96.581 117 4 0 1 117 129854284 129854400 1.020000e-45 195
11 TraesCS6A01G103900 chr6B 85.635 181 15 1 2933 3102 129857107 129857287 2.860000e-41 180
12 TraesCS6A01G103900 chr6D 94.275 2201 117 6 459 2658 57898877 57901069 0.000000e+00 3358
13 TraesCS6A01G103900 chr6D 90.754 411 28 4 2687 3097 57901069 57901469 1.140000e-149 540
14 TraesCS6A01G103900 chr6D 96.791 187 5 1 112 297 57898689 57898875 9.710000e-81 311
15 TraesCS6A01G103900 chr6D 84.014 294 35 12 2772 3059 83429709 83429996 4.580000e-69 272
16 TraesCS6A01G103900 chr6D 82.781 302 43 8 2762 3059 83397232 83396936 9.910000e-66 261
17 TraesCS6A01G103900 chr6D 93.642 173 9 2 3194 3365 57903088 57903259 1.280000e-64 257
18 TraesCS6A01G103900 chr6D 97.436 117 3 0 1 117 57898483 57898599 2.190000e-47 200
19 TraesCS6A01G103900 chr1D 94.043 235 12 2 3366 3600 342104926 342105158 4.420000e-94 355
20 TraesCS6A01G103900 chr1D 93.617 235 11 3 3366 3600 342112146 342111916 7.400000e-92 348
21 TraesCS6A01G103900 chr1D 90.678 236 18 4 3366 3600 469585160 469584928 9.710000e-81 311
22 TraesCS6A01G103900 chr1D 90.336 238 16 4 3364 3600 440084964 440084733 4.520000e-79 305
23 TraesCS6A01G103900 chr1D 99.091 110 1 0 351 460 368091078 368090969 7.880000e-47 198
24 TraesCS6A01G103900 chr3A 94.619 223 10 2 3378 3600 658655162 658655382 9.570000e-91 344
25 TraesCS6A01G103900 chr7A 93.191 235 11 4 3366 3600 627113263 627113034 1.240000e-89 340
26 TraesCS6A01G103900 chr7A 92.340 235 14 3 3366 3600 627045018 627044788 7.450000e-87 331
27 TraesCS6A01G103900 chr7A 93.252 163 9 2 296 458 420780776 420780936 4.650000e-59 239
28 TraesCS6A01G103900 chr7A 89.394 132 14 0 540 671 519485732 519485863 2.220000e-37 167
29 TraesCS6A01G103900 chr2A 90.678 236 17 5 3366 3600 593507898 593507667 3.490000e-80 309
30 TraesCS6A01G103900 chr2A 92.121 165 13 0 295 459 144660093 144660257 2.160000e-57 233
31 TraesCS6A01G103900 chr2A 90.152 132 13 0 540 671 748206663 748206794 4.780000e-39 172
32 TraesCS6A01G103900 chr5B 91.566 166 11 2 296 458 411855511 411855346 3.620000e-55 226
33 TraesCS6A01G103900 chr4B 89.412 170 12 1 296 459 586943793 586943962 3.640000e-50 209
34 TraesCS6A01G103900 chr4B 95.763 118 3 2 351 467 149160514 149160398 4.740000e-44 189
35 TraesCS6A01G103900 chr4B 90.152 132 13 0 540 671 238957817 238957686 4.780000e-39 172
36 TraesCS6A01G103900 chr7D 98.214 112 2 0 351 462 150359408 150359297 2.840000e-46 196
37 TraesCS6A01G103900 chr3D 98.214 112 2 0 351 462 67437084 67437195 2.840000e-46 196
38 TraesCS6A01G103900 chr3D 88.028 142 15 2 540 681 25143159 25143298 2.220000e-37 167
39 TraesCS6A01G103900 chr3D 96.875 64 2 0 289 352 606484220 606484157 1.370000e-19 108
40 TraesCS6A01G103900 chr2B 95.041 121 4 2 348 467 262409757 262409638 4.740000e-44 189
41 TraesCS6A01G103900 chr2B 86.228 167 7 11 297 460 772709365 772709212 2.220000e-37 167
42 TraesCS6A01G103900 chr3B 90.845 142 9 1 296 433 140855610 140855469 1.710000e-43 187
43 TraesCS6A01G103900 chr1A 90.152 132 13 0 540 671 50694899 50695030 4.780000e-39 172
44 TraesCS6A01G103900 chr1B 83.951 162 15 6 297 458 194785484 194785634 1.040000e-30 145
45 TraesCS6A01G103900 chr1B 91.304 92 3 4 297 388 630653623 630653537 1.760000e-23 121


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 TraesCS6A01G103900 chr6A 73067424 73071023 3599 False 6649.0 6649 100.00000 1 3600 1 chr6A.!!$F1 3599
1 TraesCS6A01G103900 chr6A 100664470 100666485 2015 False 264.0 267 83.53950 2772 3059 2 chr6A.!!$F2 287
2 TraesCS6A01G103900 chr6B 129854284 129857287 3003 False 1039.0 3476 92.89375 1 3102 4 chr6B.!!$F3 3101
3 TraesCS6A01G103900 chr6D 57898483 57903259 4776 False 933.2 3358 94.57960 1 3365 5 chr6D.!!$F2 3364

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
314 421 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 F
316 423 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.0 5.23 0.0 44.66 1.40 F
318 425 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
2476 2588 0.038021 TTGCCTATGTGCAGCAGGAA 59.962 50.0 11.47 0.0 43.21 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2211 0.237498 CGTAGCTCAGTGTGTCGTCA 59.763 55.000 0.00 0.0 0.00 4.35 R
2548 2666 1.195900 GATAGCTCTCCGCAGTAGTCG 59.804 57.143 0.00 0.0 42.61 4.18 R
2572 2690 2.214216 TTGGTACTCTGCCGGCACT 61.214 57.895 29.03 13.6 0.00 4.40 R
3491 5971 0.237235 TTCAATCAGACGCGCCAAAC 59.763 50.000 5.73 0.0 0.00 2.93 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
24 25 1.355381 TGCAGGGACCTGTCATCAAAT 59.645 47.619 18.86 0.00 45.24 2.32
32 33 3.270877 ACCTGTCATCAAATAACCTCGC 58.729 45.455 0.00 0.00 0.00 5.03
123 229 6.759272 TGCTTCCTAATTAGTACTATGCAGG 58.241 40.000 11.50 10.04 0.00 4.85
243 350 0.036105 ATGTGCTGCGTGATCTTCCA 60.036 50.000 0.00 0.00 0.00 3.53
261 368 7.311092 TCTTCCACTGAAAGACCTGTAATTA 57.689 36.000 0.00 0.00 37.43 1.40
300 407 6.007703 ACAGATACCTCCTTAGCTCATACTC 58.992 44.000 0.00 0.00 0.00 2.59
301 408 5.417580 CAGATACCTCCTTAGCTCATACTCC 59.582 48.000 0.00 0.00 0.00 3.85
302 409 2.965562 ACCTCCTTAGCTCATACTCCC 58.034 52.381 0.00 0.00 0.00 4.30
303 410 2.520549 ACCTCCTTAGCTCATACTCCCT 59.479 50.000 0.00 0.00 0.00 4.20
304 411 3.161866 CCTCCTTAGCTCATACTCCCTC 58.838 54.545 0.00 0.00 0.00 4.30
305 412 3.161866 CTCCTTAGCTCATACTCCCTCC 58.838 54.545 0.00 0.00 0.00 4.30
306 413 1.889829 CCTTAGCTCATACTCCCTCCG 59.110 57.143 0.00 0.00 0.00 4.63
307 414 2.588620 CTTAGCTCATACTCCCTCCGT 58.411 52.381 0.00 0.00 0.00 4.69
308 415 2.273538 TAGCTCATACTCCCTCCGTC 57.726 55.000 0.00 0.00 0.00 4.79
309 416 0.468400 AGCTCATACTCCCTCCGTCC 60.468 60.000 0.00 0.00 0.00 4.79
310 417 1.797211 GCTCATACTCCCTCCGTCCG 61.797 65.000 0.00 0.00 0.00 4.79
311 418 1.152819 TCATACTCCCTCCGTCCGG 60.153 63.158 0.00 0.00 0.00 5.14
312 419 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
314 421 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
315 422 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
316 423 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
317 424 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
318 425 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
319 426 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
320 427 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
321 428 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
322 429 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
323 430 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
324 431 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
325 432 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
326 433 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
327 434 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
328 435 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
329 436 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
330 437 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
331 438 7.201574 CGTCCGGAAATACTTGTCATCAAAATA 60.202 37.037 5.23 0.00 32.87 1.40
332 439 8.122952 GTCCGGAAATACTTGTCATCAAAATAG 58.877 37.037 5.23 0.00 32.87 1.73
333 440 8.044309 TCCGGAAATACTTGTCATCAAAATAGA 58.956 33.333 0.00 0.00 32.87 1.98
334 441 8.840321 CCGGAAATACTTGTCATCAAAATAGAT 58.160 33.333 0.00 0.00 32.87 1.98
367 474 9.334947 AGATGTATCTACTTGTCATCAAAATGG 57.665 33.333 0.00 0.00 37.80 3.16
368 475 9.330063 GATGTATCTACTTGTCATCAAAATGGA 57.670 33.333 0.00 0.00 36.11 3.41
369 476 9.857656 ATGTATCTACTTGTCATCAAAATGGAT 57.142 29.630 0.00 0.00 33.42 3.41
375 482 9.793252 CTACTTGTCATCAAAATGGATAAAAGG 57.207 33.333 0.00 0.00 33.42 3.11
376 483 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
377 484 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
378 485 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
379 486 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
380 487 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
381 488 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
382 489 8.064389 TCATCAAAATGGATAAAAGGGGATGTA 58.936 33.333 0.00 0.00 33.42 2.29
383 490 8.873144 CATCAAAATGGATAAAAGGGGATGTAT 58.127 33.333 0.00 0.00 0.00 2.29
384 491 8.477419 TCAAAATGGATAAAAGGGGATGTATC 57.523 34.615 0.00 0.00 0.00 2.24
385 492 8.288812 TCAAAATGGATAAAAGGGGATGTATCT 58.711 33.333 0.00 0.00 0.00 1.98
386 493 9.586732 CAAAATGGATAAAAGGGGATGTATCTA 57.413 33.333 0.00 0.00 0.00 1.98
387 494 9.813826 AAAATGGATAAAAGGGGATGTATCTAG 57.186 33.333 0.00 0.00 0.00 2.43
388 495 8.757307 AATGGATAAAAGGGGATGTATCTAGA 57.243 34.615 0.00 0.00 0.00 2.43
389 496 8.940012 ATGGATAAAAGGGGATGTATCTAGAT 57.060 34.615 10.73 10.73 0.00 1.98
390 497 8.150827 TGGATAAAAGGGGATGTATCTAGATG 57.849 38.462 15.79 0.00 0.00 2.90
391 498 7.739444 TGGATAAAAGGGGATGTATCTAGATGT 59.261 37.037 15.79 1.25 0.00 3.06
392 499 9.268282 GGATAAAAGGGGATGTATCTAGATGTA 57.732 37.037 15.79 4.44 0.00 2.29
399 506 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
448 555 7.922505 TTTTGATGACAAGTATTTTTGGACG 57.077 32.000 0.00 0.00 37.32 4.79
449 556 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
450 557 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
451 558 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
452 559 4.069304 TGACAAGTATTTTTGGACGGAGG 58.931 43.478 0.00 0.00 32.32 4.30
453 560 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
454 561 3.073356 ACAAGTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 32.32 4.20
455 562 3.629142 AGTATTTTTGGACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
456 563 2.910977 AGTATTTTTGGACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
457 564 4.098894 AGTATTTTTGGACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
458 565 2.845363 TTTTTGGACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
459 566 2.019807 TTTTGGACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
460 567 1.263356 TTTGGACGGAGGGAGTACTG 58.737 55.000 0.00 0.00 0.00 2.74
461 568 0.113776 TTGGACGGAGGGAGTACTGT 59.886 55.000 0.00 0.00 0.00 3.55
462 569 0.611062 TGGACGGAGGGAGTACTGTG 60.611 60.000 0.00 0.00 0.00 3.66
463 570 0.323178 GGACGGAGGGAGTACTGTGA 60.323 60.000 0.00 0.00 0.00 3.58
464 571 1.542492 GACGGAGGGAGTACTGTGAA 58.458 55.000 0.00 0.00 0.00 3.18
465 572 1.891150 GACGGAGGGAGTACTGTGAAA 59.109 52.381 0.00 0.00 0.00 2.69
466 573 1.617357 ACGGAGGGAGTACTGTGAAAC 59.383 52.381 0.00 0.00 37.35 2.78
467 574 1.402456 CGGAGGGAGTACTGTGAAACG 60.402 57.143 0.00 0.00 42.39 3.60
520 627 2.126467 CAAAATCCTGCGTGTTGTTGG 58.874 47.619 0.00 0.00 0.00 3.77
611 718 5.235616 TGATTCTGTGAACGTTTACAGGAAC 59.764 40.000 37.50 31.65 43.40 3.62
626 733 3.138304 CAGGAACGTGGAGAACAATCAA 58.862 45.455 0.00 0.00 0.00 2.57
629 736 4.827284 AGGAACGTGGAGAACAATCAATTT 59.173 37.500 0.00 0.00 0.00 1.82
638 745 5.334724 AGAACAATCAATTTGCAGGATCC 57.665 39.130 2.48 2.48 39.03 3.36
658 765 2.950309 CCATCCCAAAGAAGATGCTCAG 59.050 50.000 0.00 0.00 38.85 3.35
709 816 7.384660 CCATCCTCTTTTATCGAGATTCAAGAG 59.615 40.741 18.03 18.03 36.50 2.85
734 841 3.618690 AAGAGCTTGGCTAACTACTGG 57.381 47.619 0.00 0.00 39.88 4.00
743 850 2.104963 GGCTAACTACTGGCTGCCTAAT 59.895 50.000 21.03 7.66 37.58 1.73
753 860 8.386264 ACTACTGGCTGCCTAATAAATCAATAT 58.614 33.333 21.03 0.00 0.00 1.28
755 862 8.482852 ACTGGCTGCCTAATAAATCAATATTT 57.517 30.769 21.03 0.00 38.80 1.40
797 904 0.391228 AAACGGCAACCATTTCACCC 59.609 50.000 0.00 0.00 0.00 4.61
808 915 0.551396 ATTTCACCCTTCCGATCCCC 59.449 55.000 0.00 0.00 0.00 4.81
853 960 1.153667 GTCTCCTTCTCCAGCTGCG 60.154 63.158 8.66 1.56 0.00 5.18
878 985 6.356556 CATCCTCACATTACTGTAATTCCCA 58.643 40.000 10.25 0.00 33.14 4.37
907 1014 0.944311 CACAGGACACTACACACGGC 60.944 60.000 0.00 0.00 0.00 5.68
912 1019 3.998672 CACTACACACGGCGGGGT 61.999 66.667 16.11 11.48 0.00 4.95
913 1020 3.688159 ACTACACACGGCGGGGTC 61.688 66.667 16.11 0.00 0.00 4.46
914 1021 3.379445 CTACACACGGCGGGGTCT 61.379 66.667 16.11 0.00 0.00 3.85
917 1024 4.308458 CACACGGCGGGGTCTTCA 62.308 66.667 16.11 0.00 0.00 3.02
936 1044 2.123897 AGGCACGCCAACAAGGTT 60.124 55.556 11.35 0.00 40.61 3.50
1000 1108 7.361371 CCAGTTTATTAACCATTGCTGTCGTTA 60.361 37.037 0.00 0.00 34.71 3.18
1045 1153 1.599047 CGGCAGGAGATGTCCACTT 59.401 57.895 12.14 0.00 46.80 3.16
1075 1183 0.038744 CCTGAGGGCAATTGTGAGGT 59.961 55.000 7.40 0.00 0.00 3.85
1141 1249 1.871039 CCTACCCTGACAAACAACACG 59.129 52.381 0.00 0.00 0.00 4.49
1214 1322 7.772332 GAACCTACACGTTCTGATATCAATT 57.228 36.000 6.90 0.00 39.27 2.32
1225 1333 7.201723 CGTTCTGATATCAATTCCCATTGTTGA 60.202 37.037 6.90 0.00 40.78 3.18
1307 1415 0.390603 TGACGGGTTTATCGGCACAG 60.391 55.000 0.00 0.00 41.09 3.66
1364 1472 6.902341 TGTTTCAGATAAGAATGTTCAGTGC 58.098 36.000 0.00 0.00 0.00 4.40
1538 1646 8.788325 AGGTAAATTGAACTGTATGTAGAACC 57.212 34.615 0.00 0.00 0.00 3.62
1540 1648 8.880750 GGTAAATTGAACTGTATGTAGAACCTC 58.119 37.037 0.00 0.00 0.00 3.85
1562 1670 7.503566 ACCTCCATTCCTAATTGTGTCATATTG 59.496 37.037 0.00 0.00 0.00 1.90
1658 1766 7.675161 TCCCATGATCACATTTCTTCTAGTA 57.325 36.000 0.00 0.00 34.15 1.82
1729 1837 1.803334 TTTGGAGAATGTTCGGACCG 58.197 50.000 7.84 7.84 0.00 4.79
1821 1929 3.183574 TCGTGTACAAACATTTCAGCGAG 59.816 43.478 0.00 0.00 38.08 5.03
1950 2058 1.065928 CGAGTACCTCCATGACGGC 59.934 63.158 0.00 0.00 33.14 5.68
2103 2211 1.033574 GAGCTACTACGGACTGGCAT 58.966 55.000 0.00 0.00 0.00 4.40
2110 2218 1.245376 TACGGACTGGCATGACGACA 61.245 55.000 10.97 0.00 0.00 4.35
2125 2233 0.237498 CGACACACTGAGCTACGTCA 59.763 55.000 0.00 0.00 0.00 4.35
2430 2539 2.476997 GTCTCTGGTTTCTCGTTTGCTC 59.523 50.000 0.00 0.00 0.00 4.26
2472 2584 1.167851 GAGTTTGCCTATGTGCAGCA 58.832 50.000 0.00 0.00 43.21 4.41
2476 2588 0.038021 TTGCCTATGTGCAGCAGGAA 59.962 50.000 11.47 0.00 43.21 3.36
2572 2690 2.833121 TGCGGAGAGCTATCGCCA 60.833 61.111 20.07 9.67 45.12 5.69
2622 2741 2.793790 CTGCTCGCTCTGATTGACATAC 59.206 50.000 0.00 0.00 0.00 2.39
2649 2768 1.895131 GCCAAACATGTCCTCACCATT 59.105 47.619 0.00 0.00 0.00 3.16
2652 2771 4.335416 CCAAACATGTCCTCACCATTAGT 58.665 43.478 0.00 0.00 0.00 2.24
2663 2782 7.016563 TGTCCTCACCATTAGTATAGAATGCAT 59.983 37.037 0.00 0.00 33.70 3.96
2664 2783 7.547370 GTCCTCACCATTAGTATAGAATGCATC 59.453 40.741 0.00 0.00 33.70 3.91
2665 2784 7.455953 TCCTCACCATTAGTATAGAATGCATCT 59.544 37.037 0.00 1.57 42.48 2.90
2723 2842 2.035530 CCTTTGATCTCAGGCTGGAC 57.964 55.000 15.73 4.59 0.00 4.02
2793 2912 2.153547 GATTTGGTTGGGGTGTGCCG 62.154 60.000 0.00 0.00 34.97 5.69
2833 2952 1.663739 CCCGGACGACACTTGAAGA 59.336 57.895 0.73 0.00 0.00 2.87
2846 2965 3.826157 CACTTGAAGACCCCAATAGCAAA 59.174 43.478 0.00 0.00 0.00 3.68
2864 2983 3.496331 CAAACTATTGTGGTGGACCCTT 58.504 45.455 0.00 0.00 34.29 3.95
2869 2988 4.029809 GTGGTGGACCCTTCCCCG 62.030 72.222 0.00 0.00 42.01 5.73
2958 3077 7.889873 ACAGATACTACACTTGATCTTAGCT 57.110 36.000 0.00 0.00 0.00 3.32
3018 3137 6.353082 CCTTCCTCTCCTTTTATGGCTTCTTA 60.353 42.308 0.00 0.00 0.00 2.10
3030 3149 2.426842 GCTTCTTAGGCCAACTCCAT 57.573 50.000 5.01 0.00 0.00 3.41
3108 3265 0.987294 ACCTGTATCTGCCTGTGCTT 59.013 50.000 0.00 0.00 38.71 3.91
3114 3271 2.116983 ATCTGCCTGTGCTTCCACGT 62.117 55.000 0.00 0.00 45.04 4.49
3140 3297 3.387962 TGGGCCTGATGATAAGAAGTCT 58.612 45.455 4.53 0.00 0.00 3.24
3142 3299 4.345257 TGGGCCTGATGATAAGAAGTCTAC 59.655 45.833 4.53 0.00 0.00 2.59
3152 3309 9.575783 GATGATAAGAAGTCTACGAAGAAAGTT 57.424 33.333 0.00 0.00 32.16 2.66
3153 3310 8.967552 TGATAAGAAGTCTACGAAGAAAGTTC 57.032 34.615 0.00 0.00 32.16 3.01
3156 3313 5.451039 AGAAGTCTACGAAGAAAGTTCGAC 58.549 41.667 13.69 2.33 43.97 4.20
3160 3317 1.273455 ACGAAGAAAGTTCGACGGCG 61.273 55.000 2.87 2.87 43.97 6.46
3161 3318 1.779683 GAAGAAAGTTCGACGGCGG 59.220 57.895 12.58 0.00 38.28 6.13
3162 3319 0.942884 GAAGAAAGTTCGACGGCGGT 60.943 55.000 12.58 0.00 38.28 5.68
3163 3320 1.219522 AAGAAAGTTCGACGGCGGTG 61.220 55.000 12.58 2.47 38.28 4.94
3165 3322 1.216941 GAAAGTTCGACGGCGGTGAA 61.217 55.000 12.58 12.06 38.28 3.18
3169 3326 1.952133 TTCGACGGCGGTGAAAGTG 60.952 57.895 12.58 0.00 38.28 3.16
3170 3327 2.632136 TTCGACGGCGGTGAAAGTGT 62.632 55.000 12.58 0.00 38.28 3.55
3172 3329 1.568025 GACGGCGGTGAAAGTGTTC 59.432 57.895 13.24 0.00 0.00 3.18
3253 5727 1.412710 TGCTCTCCATCGTTACCCATC 59.587 52.381 0.00 0.00 0.00 3.51
3254 5728 1.270358 GCTCTCCATCGTTACCCATCC 60.270 57.143 0.00 0.00 0.00 3.51
3304 5778 3.226777 CTCAGCTACAGCCTACAGGTAT 58.773 50.000 0.00 0.00 43.38 2.73
3310 5784 4.098960 GCTACAGCCTACAGGTATGTACAA 59.901 45.833 0.00 0.00 37.72 2.41
3340 5820 0.314935 ACAAAAGGCCAGCATCAACG 59.685 50.000 5.01 0.00 0.00 4.10
3365 5845 1.142748 GTGACATCGGAGCCTGGAG 59.857 63.158 0.00 0.00 0.00 3.86
3367 5847 1.039785 TGACATCGGAGCCTGGAGAG 61.040 60.000 0.00 0.00 0.00 3.20
3368 5848 1.000993 ACATCGGAGCCTGGAGAGT 59.999 57.895 0.00 0.00 0.00 3.24
3370 5850 1.342076 ACATCGGAGCCTGGAGAGTAA 60.342 52.381 0.00 0.00 0.00 2.24
3371 5851 1.757118 CATCGGAGCCTGGAGAGTAAA 59.243 52.381 0.00 0.00 0.00 2.01
3372 5852 2.160721 TCGGAGCCTGGAGAGTAAAT 57.839 50.000 0.00 0.00 0.00 1.40
3373 5853 2.467880 TCGGAGCCTGGAGAGTAAATT 58.532 47.619 0.00 0.00 0.00 1.82
3375 5855 2.293170 GGAGCCTGGAGAGTAAATTGC 58.707 52.381 0.00 0.00 0.00 3.56
3377 5857 3.347216 GAGCCTGGAGAGTAAATTGCAA 58.653 45.455 0.00 0.00 0.00 4.08
3379 5859 4.151883 AGCCTGGAGAGTAAATTGCAAAA 58.848 39.130 1.71 0.00 0.00 2.44
3398 5878 3.621682 AAAAACCACCACATTAGGGGA 57.378 42.857 0.00 0.00 32.15 4.81
3399 5879 2.597578 AAACCACCACATTAGGGGAC 57.402 50.000 0.00 0.00 32.15 4.46
3400 5880 0.326927 AACCACCACATTAGGGGACG 59.673 55.000 0.00 0.00 32.15 4.79
3401 5881 1.451387 CCACCACATTAGGGGACGC 60.451 63.158 0.00 0.00 32.15 5.19
3402 5882 1.602237 CACCACATTAGGGGACGCT 59.398 57.895 0.00 0.00 32.15 5.07
3403 5883 0.828022 CACCACATTAGGGGACGCTA 59.172 55.000 0.00 0.00 32.15 4.26
3404 5884 1.208535 CACCACATTAGGGGACGCTAA 59.791 52.381 10.64 10.64 32.15 3.09
3405 5885 1.910671 ACCACATTAGGGGACGCTAAA 59.089 47.619 11.99 0.00 0.00 1.85
3406 5886 2.306512 ACCACATTAGGGGACGCTAAAA 59.693 45.455 11.99 0.00 0.00 1.52
3407 5887 2.681344 CCACATTAGGGGACGCTAAAAC 59.319 50.000 11.99 0.00 0.00 2.43
3408 5888 3.340034 CACATTAGGGGACGCTAAAACA 58.660 45.455 11.99 0.00 0.00 2.83
3409 5889 3.754323 CACATTAGGGGACGCTAAAACAA 59.246 43.478 11.99 0.00 0.00 2.83
3410 5890 4.216687 CACATTAGGGGACGCTAAAACAAA 59.783 41.667 11.99 0.00 0.00 2.83
3411 5891 4.828387 ACATTAGGGGACGCTAAAACAAAA 59.172 37.500 11.99 0.00 0.00 2.44
3412 5892 5.302313 ACATTAGGGGACGCTAAAACAAAAA 59.698 36.000 11.99 0.00 0.00 1.94
3463 5943 5.388408 AAAAACCACCACGTTTAAGTTGA 57.612 34.783 0.00 0.00 34.89 3.18
3464 5944 4.359971 AAACCACCACGTTTAAGTTGAC 57.640 40.909 0.00 0.00 34.21 3.18
3465 5945 2.988570 ACCACCACGTTTAAGTTGACA 58.011 42.857 0.00 0.00 0.00 3.58
3467 5947 2.940410 CCACCACGTTTAAGTTGACAGT 59.060 45.455 0.00 0.00 0.00 3.55
3468 5948 3.375922 CCACCACGTTTAAGTTGACAGTT 59.624 43.478 0.00 0.00 0.00 3.16
3469 5949 4.142556 CCACCACGTTTAAGTTGACAGTTT 60.143 41.667 0.00 0.00 0.00 2.66
3470 5950 5.395642 CACCACGTTTAAGTTGACAGTTTT 58.604 37.500 0.00 0.00 0.00 2.43
3471 5951 5.510323 CACCACGTTTAAGTTGACAGTTTTC 59.490 40.000 0.00 0.00 0.00 2.29
3473 5953 6.087522 CCACGTTTAAGTTGACAGTTTTCAA 58.912 36.000 0.00 0.00 32.94 2.69
3474 5954 6.583050 CCACGTTTAAGTTGACAGTTTTCAAA 59.417 34.615 0.00 0.00 37.24 2.69
3475 5955 7.115095 CCACGTTTAAGTTGACAGTTTTCAAAA 59.885 33.333 0.00 0.00 37.24 2.44
3476 5956 8.480853 CACGTTTAAGTTGACAGTTTTCAAAAA 58.519 29.630 0.00 0.00 37.24 1.94
3492 5972 1.305201 AAAAACACTGATCGCACGGT 58.695 45.000 0.00 0.00 0.00 4.83
3493 5973 1.305201 AAAACACTGATCGCACGGTT 58.695 45.000 0.00 0.00 0.00 4.44
3496 5976 1.227999 ACACTGATCGCACGGTTTGG 61.228 55.000 0.00 0.00 0.00 3.28
3497 5977 2.325082 ACTGATCGCACGGTTTGGC 61.325 57.895 0.00 0.00 0.00 4.52
3504 5984 4.368808 CACGGTTTGGCGCGTCTG 62.369 66.667 13.81 0.00 0.00 3.51
3505 5985 4.595538 ACGGTTTGGCGCGTCTGA 62.596 61.111 13.81 0.00 0.00 3.27
3507 5987 2.677003 CGGTTTGGCGCGTCTGATT 61.677 57.895 13.81 0.00 0.00 2.57
3509 5989 1.573829 GGTTTGGCGCGTCTGATTGA 61.574 55.000 13.81 0.00 0.00 2.57
3512 5992 0.947960 TTGGCGCGTCTGATTGAAAA 59.052 45.000 13.81 0.00 0.00 2.29
3513 5993 0.947960 TGGCGCGTCTGATTGAAAAA 59.052 45.000 13.81 0.00 0.00 1.94
3514 5994 1.327507 GGCGCGTCTGATTGAAAAAC 58.672 50.000 8.43 0.00 0.00 2.43
3515 5995 1.069227 GGCGCGTCTGATTGAAAAACT 60.069 47.619 8.43 0.00 0.00 2.66
3517 5997 2.574322 CGCGTCTGATTGAAAAACTGG 58.426 47.619 0.00 0.00 0.00 4.00
3518 5998 2.319472 GCGTCTGATTGAAAAACTGGC 58.681 47.619 0.00 0.00 0.00 4.85
3519 5999 2.922335 GCGTCTGATTGAAAAACTGGCC 60.922 50.000 0.00 0.00 0.00 5.36
3523 6003 3.960102 TCTGATTGAAAAACTGGCCTGTT 59.040 39.130 21.28 21.28 0.00 3.16
3524 6004 4.053295 CTGATTGAAAAACTGGCCTGTTG 58.947 43.478 26.56 8.73 0.00 3.33
3525 6005 2.977772 TTGAAAAACTGGCCTGTTGG 57.022 45.000 26.56 3.97 0.00 3.77
3526 6006 1.118838 TGAAAAACTGGCCTGTTGGG 58.881 50.000 26.56 2.23 38.36 4.12
3535 6015 3.698765 CCTGTTGGGCCCAATGTC 58.301 61.111 39.03 26.42 38.28 3.06
3536 6016 1.228831 CCTGTTGGGCCCAATGTCA 60.229 57.895 39.03 29.33 38.28 3.58
3537 6017 1.252904 CCTGTTGGGCCCAATGTCAG 61.253 60.000 39.03 35.16 38.28 3.51
3538 6018 1.228831 TGTTGGGCCCAATGTCAGG 60.229 57.895 39.03 0.00 38.28 3.86
3544 6024 3.685435 CCCAATGTCAGGCACCAC 58.315 61.111 0.00 0.00 0.00 4.16
3545 6025 2.334946 CCCAATGTCAGGCACCACG 61.335 63.158 0.00 0.00 0.00 4.94
3546 6026 1.600636 CCAATGTCAGGCACCACGT 60.601 57.895 0.00 0.00 0.00 4.49
3547 6027 1.575922 CAATGTCAGGCACCACGTG 59.424 57.895 9.08 9.08 36.51 4.49
3548 6028 1.600636 AATGTCAGGCACCACGTGG 60.601 57.895 32.83 32.83 42.17 4.94
3549 6029 2.050836 AATGTCAGGCACCACGTGGA 62.051 55.000 40.21 16.38 38.94 4.02
3550 6030 2.665185 GTCAGGCACCACGTGGAC 60.665 66.667 40.21 28.84 38.94 4.02
3552 6032 2.666190 CAGGCACCACGTGGACAG 60.666 66.667 40.21 27.42 38.94 3.51
3553 6033 3.941188 AGGCACCACGTGGACAGG 61.941 66.667 40.21 24.82 38.94 4.00
3557 6037 4.567597 ACCACGTGGACAGGGGGA 62.568 66.667 40.21 0.00 42.12 4.81
3558 6038 3.706373 CCACGTGGACAGGGGGAG 61.706 72.222 31.31 0.00 42.12 4.30
3559 6039 2.603473 CACGTGGACAGGGGGAGA 60.603 66.667 7.95 0.00 0.00 3.71
3560 6040 2.603776 ACGTGGACAGGGGGAGAC 60.604 66.667 0.00 0.00 0.00 3.36
3596 6076 3.530104 CGTTAGACGGCGTCGCAC 61.530 66.667 31.59 28.10 38.08 5.34
3597 6077 2.126580 GTTAGACGGCGTCGCACT 60.127 61.111 31.59 18.41 40.63 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 229 5.422650 ACAAACTACCAGGAAGAGAGTATCC 59.577 44.000 0.00 0.00 33.66 2.59
198 305 0.250553 TCCCGGTTAGCCTGTTGTTG 60.251 55.000 0.00 0.00 0.00 3.33
243 350 8.434392 TGGTAAAGTAATTACAGGTCTTTCAGT 58.566 33.333 17.65 0.00 44.77 3.41
261 368 7.827729 GGAGGTATCTGTGTAAATTGGTAAAGT 59.172 37.037 0.00 0.00 0.00 2.66
300 407 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
301 408 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
302 409 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
303 410 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
304 411 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
305 412 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
306 413 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
307 414 8.044309 TCTATTTTGATGACAAGTATTTCCGGA 58.956 33.333 0.00 0.00 37.32 5.14
308 415 8.208718 TCTATTTTGATGACAAGTATTTCCGG 57.791 34.615 0.00 0.00 37.32 5.14
341 448 9.334947 CCATTTTGATGACAAGTAGATACATCT 57.665 33.333 0.00 0.00 38.36 2.90
342 449 9.330063 TCCATTTTGATGACAAGTAGATACATC 57.670 33.333 0.00 0.00 37.32 3.06
343 450 9.857656 ATCCATTTTGATGACAAGTAGATACAT 57.142 29.630 0.00 0.00 37.32 2.29
349 456 9.793252 CCTTTTATCCATTTTGATGACAAGTAG 57.207 33.333 0.00 0.00 37.32 2.57
350 457 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
351 458 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
352 459 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
353 460 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
354 461 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
355 462 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
356 463 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
357 464 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
358 465 9.093458 GATACATCCCCTTTTATCCATTTTGAT 57.907 33.333 0.00 0.00 0.00 2.57
359 466 8.288812 AGATACATCCCCTTTTATCCATTTTGA 58.711 33.333 0.00 0.00 0.00 2.69
360 467 8.482852 AGATACATCCCCTTTTATCCATTTTG 57.517 34.615 0.00 0.00 0.00 2.44
361 468 9.813826 CTAGATACATCCCCTTTTATCCATTTT 57.186 33.333 0.00 0.00 0.00 1.82
362 469 9.182642 TCTAGATACATCCCCTTTTATCCATTT 57.817 33.333 0.00 0.00 0.00 2.32
363 470 8.757307 TCTAGATACATCCCCTTTTATCCATT 57.243 34.615 0.00 0.00 0.00 3.16
364 471 8.776119 CATCTAGATACATCCCCTTTTATCCAT 58.224 37.037 4.54 0.00 0.00 3.41
365 472 7.739444 ACATCTAGATACATCCCCTTTTATCCA 59.261 37.037 4.54 0.00 0.00 3.41
366 473 8.152023 ACATCTAGATACATCCCCTTTTATCC 57.848 38.462 4.54 0.00 0.00 2.59
373 480 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
422 529 9.619316 CGTCCAAAAATACTTGTCATCAAAATA 57.381 29.630 0.00 0.00 32.87 1.40
423 530 7.598493 CCGTCCAAAAATACTTGTCATCAAAAT 59.402 33.333 0.00 0.00 32.87 1.82
424 531 6.920758 CCGTCCAAAAATACTTGTCATCAAAA 59.079 34.615 0.00 0.00 32.87 2.44
425 532 6.263392 TCCGTCCAAAAATACTTGTCATCAAA 59.737 34.615 0.00 0.00 32.87 2.69
426 533 5.765677 TCCGTCCAAAAATACTTGTCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
427 534 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
428 535 5.163754 CCTCCGTCCAAAAATACTTGTCATC 60.164 44.000 0.00 0.00 0.00 2.92
429 536 4.700213 CCTCCGTCCAAAAATACTTGTCAT 59.300 41.667 0.00 0.00 0.00 3.06
430 537 4.069304 CCTCCGTCCAAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
431 538 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
432 539 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
433 540 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
434 541 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
435 542 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
436 543 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
437 544 4.081309 CAGTACTCCCTCCGTCCAAAAATA 60.081 45.833 0.00 0.00 0.00 1.40
438 545 2.910977 AGTACTCCCTCCGTCCAAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
439 546 2.038033 CAGTACTCCCTCCGTCCAAAAA 59.962 50.000 0.00 0.00 0.00 1.94
440 547 1.621814 CAGTACTCCCTCCGTCCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
441 548 1.263356 CAGTACTCCCTCCGTCCAAA 58.737 55.000 0.00 0.00 0.00 3.28
442 549 0.113776 ACAGTACTCCCTCCGTCCAA 59.886 55.000 0.00 0.00 0.00 3.53
443 550 0.611062 CACAGTACTCCCTCCGTCCA 60.611 60.000 0.00 0.00 0.00 4.02
444 551 0.323178 TCACAGTACTCCCTCCGTCC 60.323 60.000 0.00 0.00 0.00 4.79
445 552 1.542492 TTCACAGTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
446 553 1.617357 GTTTCACAGTACTCCCTCCGT 59.383 52.381 0.00 0.00 0.00 4.69
447 554 1.402456 CGTTTCACAGTACTCCCTCCG 60.402 57.143 0.00 0.00 0.00 4.63
448 555 1.891150 TCGTTTCACAGTACTCCCTCC 59.109 52.381 0.00 0.00 0.00 4.30
449 556 3.512680 CATCGTTTCACAGTACTCCCTC 58.487 50.000 0.00 0.00 0.00 4.30
450 557 2.233922 CCATCGTTTCACAGTACTCCCT 59.766 50.000 0.00 0.00 0.00 4.20
451 558 2.028385 ACCATCGTTTCACAGTACTCCC 60.028 50.000 0.00 0.00 0.00 4.30
452 559 3.251571 GACCATCGTTTCACAGTACTCC 58.748 50.000 0.00 0.00 0.00 3.85
453 560 3.673809 GTGACCATCGTTTCACAGTACTC 59.326 47.826 0.00 0.00 41.58 2.59
454 561 3.069016 TGTGACCATCGTTTCACAGTACT 59.931 43.478 0.31 0.00 45.63 2.73
455 562 3.386486 TGTGACCATCGTTTCACAGTAC 58.614 45.455 0.31 0.00 45.63 2.73
456 563 3.737032 TGTGACCATCGTTTCACAGTA 57.263 42.857 0.31 0.00 45.63 2.74
457 564 2.613026 TGTGACCATCGTTTCACAGT 57.387 45.000 0.31 0.00 45.63 3.55
460 567 3.650139 AGTAGTGTGACCATCGTTTCAC 58.350 45.455 0.00 0.00 42.18 3.18
461 568 3.305813 GGAGTAGTGTGACCATCGTTTCA 60.306 47.826 0.00 0.00 0.00 2.69
462 569 3.056749 AGGAGTAGTGTGACCATCGTTTC 60.057 47.826 0.00 0.00 0.00 2.78
463 570 2.897969 AGGAGTAGTGTGACCATCGTTT 59.102 45.455 0.00 0.00 0.00 3.60
464 571 2.526432 AGGAGTAGTGTGACCATCGTT 58.474 47.619 0.00 0.00 0.00 3.85
465 572 2.217510 AGGAGTAGTGTGACCATCGT 57.782 50.000 0.00 0.00 0.00 3.73
466 573 2.492088 TCAAGGAGTAGTGTGACCATCG 59.508 50.000 0.00 0.00 0.00 3.84
467 574 3.673594 CGTCAAGGAGTAGTGTGACCATC 60.674 52.174 0.00 0.00 37.66 3.51
611 718 3.899734 TGCAAATTGATTGTTCTCCACG 58.100 40.909 0.00 0.00 41.32 4.94
626 733 2.852714 TTGGGATGGATCCTGCAAAT 57.147 45.000 14.23 0.00 46.35 2.32
629 736 1.297968 TCTTTGGGATGGATCCTGCA 58.702 50.000 14.23 0.00 46.35 4.41
638 745 2.358267 GCTGAGCATCTTCTTTGGGATG 59.642 50.000 0.00 0.00 41.36 3.51
658 765 6.691508 AGTTCTTACAGAAATTTTGGGATGC 58.308 36.000 0.00 0.00 35.75 3.91
692 799 6.878923 TCTTTTGGCTCTTGAATCTCGATAAA 59.121 34.615 0.00 0.00 0.00 1.40
734 841 8.498358 GGCAAAAATATTGATTTATTAGGCAGC 58.502 33.333 0.00 0.00 34.01 5.25
753 860 5.021033 TCTGCAGAAAATTCAGGCAAAAA 57.979 34.783 15.67 0.00 38.60 1.94
755 862 4.341806 TCTTCTGCAGAAAATTCAGGCAAA 59.658 37.500 28.16 3.23 38.60 3.68
831 938 0.251386 AGCTGGAGAAGGAGACGACA 60.251 55.000 0.00 0.00 0.00 4.35
853 960 5.239525 GGGAATTACAGTAATGTGAGGATGC 59.760 44.000 5.98 0.00 0.00 3.91
878 985 2.679082 AGTGTCCTGTGGAGTAACTGT 58.321 47.619 0.00 0.00 29.39 3.55
907 1014 2.266055 GTGCCTCTGAAGACCCCG 59.734 66.667 0.00 0.00 0.00 5.73
912 1019 1.301716 GTTGGCGTGCCTCTGAAGA 60.302 57.895 12.84 0.00 36.94 2.87
913 1020 1.165907 TTGTTGGCGTGCCTCTGAAG 61.166 55.000 12.84 0.00 36.94 3.02
914 1021 1.153066 TTGTTGGCGTGCCTCTGAA 60.153 52.632 12.84 0.00 36.94 3.02
917 1024 2.281761 CCTTGTTGGCGTGCCTCT 60.282 61.111 12.84 0.00 36.94 3.69
1000 1108 1.453155 GAGGTTGCGAACATGGTCAT 58.547 50.000 12.13 0.00 0.00 3.06
1045 1153 2.935481 CCTCAGGTGCCCTTCCCA 60.935 66.667 0.00 0.00 0.00 4.37
1075 1183 1.228094 TTGTCCAGATTGCCACGCA 60.228 52.632 0.00 0.00 36.47 5.24
1141 1249 5.861787 GCATTGTTTTTCATGTACCTGTACC 59.138 40.000 5.07 0.00 35.26 3.34
1199 1307 6.624352 ACAATGGGAATTGATATCAGAACG 57.376 37.500 5.39 0.00 35.60 3.95
1200 1308 7.999679 TCAACAATGGGAATTGATATCAGAAC 58.000 34.615 5.39 1.59 35.60 3.01
1214 1322 6.854091 TCAATGATCAAATCAACAATGGGA 57.146 33.333 0.00 0.00 43.50 4.37
1225 1333 5.142061 TGCAGCAACTTCAATGATCAAAT 57.858 34.783 0.00 0.00 0.00 2.32
1290 1398 0.390735 GTCTGTGCCGATAAACCCGT 60.391 55.000 0.00 0.00 0.00 5.28
1307 1415 3.005897 TGCTGTAGTTCTTGAGAGGTGTC 59.994 47.826 0.00 0.00 0.00 3.67
1364 1472 0.875059 GTTTGCCTTCTTCTGACCCG 59.125 55.000 0.00 0.00 0.00 5.28
1387 1495 3.553828 AGAACTTGAAGGAAACCGTCA 57.446 42.857 0.00 2.62 40.01 4.35
1538 1646 8.681486 TCAATATGACACAATTAGGAATGGAG 57.319 34.615 0.00 0.00 0.00 3.86
1540 1648 8.455903 ACTCAATATGACACAATTAGGAATGG 57.544 34.615 0.00 0.00 0.00 3.16
1578 1686 7.663043 ACAGGAAAAAGGGATAGTACTCTAG 57.337 40.000 0.00 0.00 0.00 2.43
1658 1766 2.393768 CGAAGCTTCAGCACCGCAT 61.394 57.895 25.47 0.00 45.16 4.73
1711 1819 0.682852 ACGGTCCGAACATTCTCCAA 59.317 50.000 20.51 0.00 0.00 3.53
1737 1845 1.066430 TCTATGTTGGGGTGTCGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
1821 1929 1.155889 TCATGTCGTCCAATGTGTGC 58.844 50.000 0.00 0.00 0.00 4.57
2069 2177 2.651361 CTCCTGACGCTGACGGTT 59.349 61.111 0.00 0.00 46.04 4.44
2103 2211 0.237498 CGTAGCTCAGTGTGTCGTCA 59.763 55.000 0.00 0.00 0.00 4.35
2548 2666 1.195900 GATAGCTCTCCGCAGTAGTCG 59.804 57.143 0.00 0.00 42.61 4.18
2572 2690 2.214216 TTGGTACTCTGCCGGCACT 61.214 57.895 29.03 13.60 0.00 4.40
2622 2741 3.181477 TGAGGACATGTTTGGCAGTTTTG 60.181 43.478 0.00 0.00 29.63 2.44
2652 2771 9.533831 TGAGTACCATAGAAGATGCATTCTATA 57.466 33.333 17.97 5.10 46.13 1.31
2663 2782 5.516044 TGGCTTAGTGAGTACCATAGAAGA 58.484 41.667 0.00 0.00 0.00 2.87
2664 2783 5.854010 TGGCTTAGTGAGTACCATAGAAG 57.146 43.478 0.00 0.00 0.00 2.85
2665 2784 6.808321 AATGGCTTAGTGAGTACCATAGAA 57.192 37.500 0.00 0.00 40.20 2.10
2671 2790 5.581085 CACAGTAAATGGCTTAGTGAGTACC 59.419 44.000 7.98 0.00 41.69 3.34
2723 2842 5.827568 AATAATTTGCTTGAAACAGTGCG 57.172 34.783 0.00 0.00 0.00 5.34
2793 2912 2.124507 TTGCACTACAGCCCAGACCC 62.125 60.000 0.00 0.00 0.00 4.46
2846 2965 1.633945 GGAAGGGTCCACCACAATAGT 59.366 52.381 0.00 0.00 44.26 2.12
2900 3019 8.004215 AGTTTAATATCTGATATGTGGGCCAAA 58.996 33.333 8.40 1.64 0.00 3.28
2966 3085 7.867403 GCAAAGTTTCAAATCATACCTTTCTCA 59.133 33.333 0.00 0.00 0.00 3.27
3043 3162 2.701951 AGTTTCGTTTAGTCCCACCTCA 59.298 45.455 0.00 0.00 0.00 3.86
3108 3265 1.122632 TCAGGCCCAACTTACGTGGA 61.123 55.000 0.00 0.00 0.00 4.02
3114 3271 5.191722 ACTTCTTATCATCAGGCCCAACTTA 59.808 40.000 0.00 0.00 0.00 2.24
3140 3297 1.689959 GCCGTCGAACTTTCTTCGTA 58.310 50.000 0.00 0.00 42.09 3.43
3142 3299 1.411089 CGCCGTCGAACTTTCTTCG 59.589 57.895 0.00 0.00 42.74 3.79
3152 3309 2.355363 CACTTTCACCGCCGTCGA 60.355 61.111 0.00 0.00 38.10 4.20
3153 3310 2.154427 GAACACTTTCACCGCCGTCG 62.154 60.000 0.00 0.00 0.00 5.12
3156 3313 2.549282 CGAACACTTTCACCGCCG 59.451 61.111 0.00 0.00 0.00 6.46
3160 3317 2.540157 CGGAAAACCGAACACTTTCACC 60.540 50.000 2.30 0.00 31.93 4.02
3161 3318 2.096335 ACGGAAAACCGAACACTTTCAC 59.904 45.455 15.45 0.00 36.94 3.18
3162 3319 2.352342 GACGGAAAACCGAACACTTTCA 59.648 45.455 15.45 0.00 36.94 2.69
3163 3320 2.610833 AGACGGAAAACCGAACACTTTC 59.389 45.455 15.45 0.93 36.94 2.62
3165 3322 2.320745 AGACGGAAAACCGAACACTT 57.679 45.000 15.45 0.00 36.94 3.16
3169 3326 5.405797 ACTATTCTAGACGGAAAACCGAAC 58.594 41.667 15.45 8.64 36.94 3.95
3170 3327 5.649782 ACTATTCTAGACGGAAAACCGAA 57.350 39.130 15.45 0.00 36.94 4.30
3172 3329 6.129053 AGTACTATTCTAGACGGAAAACCG 57.871 41.667 7.12 7.12 39.31 4.44
3182 3345 7.770433 TGGCGTACAACTTAGTACTATTCTAGA 59.230 37.037 2.79 0.00 41.65 2.43
3230 4883 0.824759 GGTAACGATGGAGAGCAGGT 59.175 55.000 0.00 0.00 0.00 4.00
3253 5727 6.654161 CCTAGATTATCTTGAGCTCAAATGGG 59.346 42.308 28.16 17.28 35.15 4.00
3254 5728 6.149142 GCCTAGATTATCTTGAGCTCAAATGG 59.851 42.308 28.16 17.63 35.15 3.16
3304 5778 6.559810 CCTTTTGTTCTGTTCATGTTGTACA 58.440 36.000 0.00 0.00 0.00 2.90
3310 5784 3.030291 TGGCCTTTTGTTCTGTTCATGT 58.970 40.909 3.32 0.00 0.00 3.21
3340 5820 0.737715 GCTCCGATGTCACACTGGAC 60.738 60.000 0.00 0.00 38.29 4.02
3379 5859 2.816337 CGTCCCCTAATGTGGTGGTTTT 60.816 50.000 0.00 0.00 0.00 2.43
3382 5862 1.988015 CGTCCCCTAATGTGGTGGT 59.012 57.895 0.00 0.00 0.00 4.16
3383 5863 1.451387 GCGTCCCCTAATGTGGTGG 60.451 63.158 0.00 0.00 0.00 4.61
3384 5864 0.828022 TAGCGTCCCCTAATGTGGTG 59.172 55.000 0.00 0.00 0.00 4.17
3386 5866 2.681344 GTTTTAGCGTCCCCTAATGTGG 59.319 50.000 0.00 0.00 0.00 4.17
3387 5867 3.340034 TGTTTTAGCGTCCCCTAATGTG 58.660 45.455 0.00 0.00 0.00 3.21
3388 5868 3.706600 TGTTTTAGCGTCCCCTAATGT 57.293 42.857 0.00 0.00 0.00 2.71
3389 5869 5.379732 TTTTGTTTTAGCGTCCCCTAATG 57.620 39.130 0.00 0.00 0.00 1.90
3441 5921 5.162794 GTCAACTTAAACGTGGTGGTTTTT 58.837 37.500 0.00 0.00 40.41 1.94
3443 5923 3.757493 TGTCAACTTAAACGTGGTGGTTT 59.243 39.130 0.00 0.00 42.42 3.27
3444 5924 3.345414 TGTCAACTTAAACGTGGTGGTT 58.655 40.909 0.00 0.00 0.00 3.67
3445 5925 2.940410 CTGTCAACTTAAACGTGGTGGT 59.060 45.455 0.00 0.00 0.00 4.16
3446 5926 2.940410 ACTGTCAACTTAAACGTGGTGG 59.060 45.455 0.00 0.00 0.00 4.61
3447 5927 4.609691 AACTGTCAACTTAAACGTGGTG 57.390 40.909 0.00 0.00 0.00 4.17
3448 5928 5.181622 TGAAAACTGTCAACTTAAACGTGGT 59.818 36.000 0.00 0.00 0.00 4.16
3449 5929 5.632959 TGAAAACTGTCAACTTAAACGTGG 58.367 37.500 0.00 0.00 0.00 4.94
3450 5930 7.555639 TTTGAAAACTGTCAACTTAAACGTG 57.444 32.000 0.00 0.00 37.24 4.49
3451 5931 8.576936 TTTTTGAAAACTGTCAACTTAAACGT 57.423 26.923 0.00 0.00 37.24 3.99
3473 5953 1.305201 ACCGTGCGATCAGTGTTTTT 58.695 45.000 0.00 0.00 0.00 1.94
3474 5954 1.305201 AACCGTGCGATCAGTGTTTT 58.695 45.000 0.00 0.00 0.00 2.43
3475 5955 1.002900 CAAACCGTGCGATCAGTGTTT 60.003 47.619 0.00 0.00 31.27 2.83
3476 5956 0.586319 CAAACCGTGCGATCAGTGTT 59.414 50.000 0.00 0.00 0.00 3.32
3478 5958 1.497278 CCAAACCGTGCGATCAGTG 59.503 57.895 0.00 0.00 0.00 3.66
3479 5959 2.325082 GCCAAACCGTGCGATCAGT 61.325 57.895 0.00 0.00 0.00 3.41
3480 5960 2.480555 GCCAAACCGTGCGATCAG 59.519 61.111 0.00 0.00 0.00 2.90
3488 5968 3.876589 ATCAGACGCGCCAAACCGT 62.877 57.895 5.73 0.00 40.85 4.83
3489 5969 2.677003 AATCAGACGCGCCAAACCG 61.677 57.895 5.73 0.00 0.00 4.44
3490 5970 1.154225 CAATCAGACGCGCCAAACC 60.154 57.895 5.73 0.00 0.00 3.27
3491 5971 0.237235 TTCAATCAGACGCGCCAAAC 59.763 50.000 5.73 0.00 0.00 2.93
3492 5972 0.947960 TTTCAATCAGACGCGCCAAA 59.052 45.000 5.73 0.00 0.00 3.28
3493 5973 0.947960 TTTTCAATCAGACGCGCCAA 59.052 45.000 5.73 0.00 0.00 4.52
3496 5976 1.971962 CAGTTTTTCAATCAGACGCGC 59.028 47.619 5.73 0.00 0.00 6.86
3497 5977 2.574322 CCAGTTTTTCAATCAGACGCG 58.426 47.619 3.53 3.53 0.00 6.01
3499 5979 2.554032 AGGCCAGTTTTTCAATCAGACG 59.446 45.455 5.01 0.00 0.00 4.18
3500 5980 3.319122 ACAGGCCAGTTTTTCAATCAGAC 59.681 43.478 5.01 0.00 0.00 3.51
3501 5981 3.565307 ACAGGCCAGTTTTTCAATCAGA 58.435 40.909 5.01 0.00 0.00 3.27
3503 5983 3.181467 CCAACAGGCCAGTTTTTCAATCA 60.181 43.478 11.38 0.00 0.00 2.57
3504 5984 3.392882 CCAACAGGCCAGTTTTTCAATC 58.607 45.455 11.38 0.00 0.00 2.67
3505 5985 2.104622 CCCAACAGGCCAGTTTTTCAAT 59.895 45.455 11.38 0.00 0.00 2.57
3507 5987 1.118838 CCCAACAGGCCAGTTTTTCA 58.881 50.000 11.38 0.00 0.00 2.69
3518 5998 1.228831 TGACATTGGGCCCAACAGG 60.229 57.895 39.44 30.47 38.88 4.00
3519 5999 1.252904 CCTGACATTGGGCCCAACAG 61.253 60.000 39.44 35.24 38.88 3.16
3529 6009 1.575922 CACGTGGTGCCTGACATTG 59.424 57.895 7.95 0.00 0.00 2.82
3530 6010 1.600636 CCACGTGGTGCCTGACATT 60.601 57.895 26.95 0.00 31.34 2.71
3531 6011 2.032528 CCACGTGGTGCCTGACAT 59.967 61.111 26.95 0.00 31.34 3.06
3532 6012 3.157949 TCCACGTGGTGCCTGACA 61.158 61.111 32.74 9.47 36.34 3.58
3533 6013 2.665185 GTCCACGTGGTGCCTGAC 60.665 66.667 32.74 19.23 36.34 3.51
3534 6014 3.157949 TGTCCACGTGGTGCCTGA 61.158 61.111 32.74 11.09 36.34 3.86
3535 6015 2.666190 CTGTCCACGTGGTGCCTG 60.666 66.667 32.74 20.40 36.34 4.85
3536 6016 3.941188 CCTGTCCACGTGGTGCCT 61.941 66.667 32.74 0.00 36.34 4.75
3539 6019 4.329545 CCCCCTGTCCACGTGGTG 62.330 72.222 32.74 22.45 36.34 4.17
3541 6021 3.706373 CTCCCCCTGTCCACGTGG 61.706 72.222 29.26 29.26 0.00 4.94
3542 6022 2.603473 TCTCCCCCTGTCCACGTG 60.603 66.667 9.08 9.08 0.00 4.49
3543 6023 2.603776 GTCTCCCCCTGTCCACGT 60.604 66.667 0.00 0.00 0.00 4.49
3544 6024 3.760035 CGTCTCCCCCTGTCCACG 61.760 72.222 0.00 0.00 0.00 4.94
3545 6025 3.391382 CCGTCTCCCCCTGTCCAC 61.391 72.222 0.00 0.00 0.00 4.02
3579 6059 3.530104 GTGCGACGCCGTCTAACG 61.530 66.667 18.69 3.51 42.11 3.18
3580 6060 2.126580 AGTGCGACGCCGTCTAAC 60.127 61.111 18.69 12.73 38.24 2.34
3581 6061 2.126618 CAGTGCGACGCCGTCTAA 60.127 61.111 18.69 0.00 38.24 2.10
3582 6062 3.051479 TCAGTGCGACGCCGTCTA 61.051 61.111 18.69 1.07 38.24 2.59


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

AutoCloner maintained by Alex Coulton.