Multiple sequence alignment - TraesCS1A01G224800

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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 TraesCS1A01G224800 chr1A 100.000 3359 0 0 1 3359 394850597 394853955 0.000000e+00 6204.0
1 TraesCS1A01G224800 chr1D 92.792 2844 131 23 545 3359 314572979 314575777 0.000000e+00 4048.0
2 TraesCS1A01G224800 chr1D 92.269 401 13 5 1 383 314572574 314572974 1.360000e-153 553.0
3 TraesCS1A01G224800 chr1B 94.284 2152 102 13 547 2682 426071134 426073280 0.000000e+00 3273.0
4 TraesCS1A01G224800 chr1B 84.304 395 10 19 1 384 426070777 426071130 4.150000e-89 339.0
5 TraesCS1A01G224800 chr1B 89.600 250 17 7 2721 2968 426073343 426073585 3.250000e-80 309.0
6 TraesCS1A01G224800 chr1B 80.597 201 9 8 3174 3344 426073591 426073791 9.780000e-26 128.0
7 TraesCS1A01G224800 chr7D 82.597 724 116 4 1681 2394 556640247 556639524 6.120000e-177 630.0
8 TraesCS1A01G224800 chr7A 83.756 671 103 3 1681 2345 642254108 642253438 6.120000e-177 630.0
9 TraesCS1A01G224800 chr7A 90.588 170 16 0 381 550 451519806 451519975 3.370000e-55 226.0
10 TraesCS1A01G224800 chr6B 82.456 456 53 6 1474 1929 22711235 22711663 1.140000e-99 374.0
11 TraesCS1A01G224800 chr6B 86.416 346 40 4 1031 1376 22710840 22711178 4.090000e-99 372.0
12 TraesCS1A01G224800 chr6B 90.698 172 16 0 376 547 172738542 172738371 2.610000e-56 230.0
13 TraesCS1A01G224800 chr6B 78.187 353 50 14 5 334 22710429 22710777 2.040000e-47 200.0
14 TraesCS1A01G224800 chr5A 90.909 176 15 1 380 555 320214410 320214236 5.600000e-58 235.0
15 TraesCS1A01G224800 chr5A 92.500 160 11 1 386 544 120310340 120310499 9.380000e-56 228.0
16 TraesCS1A01G224800 chr2D 92.638 163 11 1 386 547 476515309 476515147 2.020000e-57 233.0
17 TraesCS1A01G224800 chr2D 92.453 159 12 0 386 544 299891554 299891712 9.380000e-56 228.0
18 TraesCS1A01G224800 chr2D 90.000 70 4 2 173 240 80421860 80421928 1.660000e-13 87.9
19 TraesCS1A01G224800 chr5B 92.025 163 12 1 386 548 129721944 129721783 9.380000e-56 228.0
20 TraesCS1A01G224800 chr4D 90.588 170 16 0 386 555 386984829 386984660 3.370000e-55 226.0
21 TraesCS1A01G224800 chr3A 89.773 176 17 1 375 549 600923067 600923242 1.210000e-54 224.0
22 TraesCS1A01G224800 chr6D 79.573 328 43 13 28 334 12344752 12345076 2.630000e-51 213.0
23 TraesCS1A01G224800 chr2B 88.732 71 4 2 173 240 132095949 132096018 2.150000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G224800 chr1A 394850597 394853955 3358 False 6204.000000 6204 100.00000 1 3359 1 chr1A.!!$F1 3358
1 TraesCS1A01G224800 chr1D 314572574 314575777 3203 False 2300.500000 4048 92.53050 1 3359 2 chr1D.!!$F1 3358
2 TraesCS1A01G224800 chr1B 426070777 426073791 3014 False 1012.250000 3273 87.19625 1 3344 4 chr1B.!!$F1 3343
3 TraesCS1A01G224800 chr7D 556639524 556640247 723 True 630.000000 630 82.59700 1681 2394 1 chr7D.!!$R1 713
4 TraesCS1A01G224800 chr7A 642253438 642254108 670 True 630.000000 630 83.75600 1681 2345 1 chr7A.!!$R1 664
5 TraesCS1A01G224800 chr6B 22710429 22711663 1234 False 315.333333 374 82.35300 5 1929 3 chr6B.!!$F1 1924

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
727 779 0.686789 TGTCAGTACTGTGCCAGCAT 59.313 50.0 21.99 0.0 34.37 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 2665 0.535335 AAGCATAGCCCGAAACGAGA 59.465 50.0 0.0 0.0 0.0 4.04 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
105 113 2.758979 ACTTGTCCACCTACCTATGTCG 59.241 50.000 0.00 0.00 0.00 4.35
271 297 9.664332 TTAATTTTGCATAACTTATTGCCATGT 57.336 25.926 0.00 0.00 0.00 3.21
384 435 8.994170 TCTGATTGAATATTTGTCGTTGTTGTA 58.006 29.630 0.00 0.00 0.00 2.41
385 436 9.773328 CTGATTGAATATTTGTCGTTGTTGTAT 57.227 29.630 0.00 0.00 0.00 2.29
390 441 8.875803 TGAATATTTGTCGTTGTTGTATACTCC 58.124 33.333 4.17 0.00 0.00 3.85
391 442 7.781548 ATATTTGTCGTTGTTGTATACTCCC 57.218 36.000 4.17 0.00 0.00 4.30
392 443 4.877378 TTGTCGTTGTTGTATACTCCCT 57.123 40.909 4.17 0.00 0.00 4.20
393 444 4.445452 TGTCGTTGTTGTATACTCCCTC 57.555 45.455 4.17 0.00 0.00 4.30
394 445 3.194116 TGTCGTTGTTGTATACTCCCTCC 59.806 47.826 4.17 0.00 0.00 4.30
395 446 3.194116 GTCGTTGTTGTATACTCCCTCCA 59.806 47.826 4.17 0.00 0.00 3.86
396 447 4.028131 TCGTTGTTGTATACTCCCTCCAT 58.972 43.478 4.17 0.00 0.00 3.41
397 448 4.468510 TCGTTGTTGTATACTCCCTCCATT 59.531 41.667 4.17 0.00 0.00 3.16
398 449 4.809426 CGTTGTTGTATACTCCCTCCATTC 59.191 45.833 4.17 0.00 0.00 2.67
399 450 5.123936 GTTGTTGTATACTCCCTCCATTCC 58.876 45.833 4.17 0.00 0.00 3.01
400 451 4.631234 TGTTGTATACTCCCTCCATTCCT 58.369 43.478 4.17 0.00 0.00 3.36
401 452 5.784023 TGTTGTATACTCCCTCCATTCCTA 58.216 41.667 4.17 0.00 0.00 2.94
402 453 6.206787 TGTTGTATACTCCCTCCATTCCTAA 58.793 40.000 4.17 0.00 0.00 2.69
403 454 6.674861 TGTTGTATACTCCCTCCATTCCTAAA 59.325 38.462 4.17 0.00 0.00 1.85
404 455 7.349859 TGTTGTATACTCCCTCCATTCCTAAAT 59.650 37.037 4.17 0.00 0.00 1.40
405 456 8.877195 GTTGTATACTCCCTCCATTCCTAAATA 58.123 37.037 4.17 0.00 0.00 1.40
406 457 9.629649 TTGTATACTCCCTCCATTCCTAAATAT 57.370 33.333 4.17 0.00 0.00 1.28
410 461 9.860393 ATACTCCCTCCATTCCTAAATATAAGT 57.140 33.333 0.00 0.00 0.00 2.24
411 462 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
412 463 7.237887 ACTCCCTCCATTCCTAAATATAAGTCC 59.762 40.741 0.00 0.00 0.00 3.85
413 464 7.321530 TCCCTCCATTCCTAAATATAAGTCCT 58.678 38.462 0.00 0.00 0.00 3.85
414 465 7.799583 TCCCTCCATTCCTAAATATAAGTCCTT 59.200 37.037 0.00 0.00 0.00 3.36
415 466 8.448816 CCCTCCATTCCTAAATATAAGTCCTTT 58.551 37.037 0.00 0.00 0.00 3.11
416 467 9.868160 CCTCCATTCCTAAATATAAGTCCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
434 485 9.620259 AGTCCTTTTAGAGATTTCAATATGGAC 57.380 33.333 0.00 0.00 38.27 4.02
435 486 9.620259 GTCCTTTTAGAGATTTCAATATGGACT 57.380 33.333 0.00 0.00 35.99 3.85
488 539 8.885494 AGAGTATAGATTCACTCATTTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
489 540 7.930865 AGAGTATAGATTCACTCATTTTGCTCC 59.069 37.037 4.70 0.00 42.99 4.70
490 541 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
491 542 3.942829 AGATTCACTCATTTTGCTCCGA 58.057 40.909 0.00 0.00 0.00 4.55
492 543 4.326826 AGATTCACTCATTTTGCTCCGAA 58.673 39.130 0.00 0.00 0.00 4.30
493 544 4.946157 AGATTCACTCATTTTGCTCCGAAT 59.054 37.500 0.00 0.00 0.00 3.34
494 545 4.424061 TTCACTCATTTTGCTCCGAATG 57.576 40.909 0.00 0.00 35.18 2.67
495 546 3.411446 TCACTCATTTTGCTCCGAATGT 58.589 40.909 0.00 0.00 35.35 2.71
496 547 4.574892 TCACTCATTTTGCTCCGAATGTA 58.425 39.130 0.00 0.00 35.35 2.29
497 548 4.631377 TCACTCATTTTGCTCCGAATGTAG 59.369 41.667 0.00 0.00 35.35 2.74
498 549 4.393062 CACTCATTTTGCTCCGAATGTAGT 59.607 41.667 0.00 0.00 35.35 2.73
499 550 4.631813 ACTCATTTTGCTCCGAATGTAGTC 59.368 41.667 0.00 0.00 35.35 2.59
500 551 4.832248 TCATTTTGCTCCGAATGTAGTCT 58.168 39.130 0.00 0.00 35.35 3.24
501 552 4.870426 TCATTTTGCTCCGAATGTAGTCTC 59.130 41.667 0.00 0.00 35.35 3.36
502 553 4.537135 TTTTGCTCCGAATGTAGTCTCT 57.463 40.909 0.00 0.00 0.00 3.10
503 554 5.654603 TTTTGCTCCGAATGTAGTCTCTA 57.345 39.130 0.00 0.00 0.00 2.43
504 555 5.854010 TTTGCTCCGAATGTAGTCTCTAT 57.146 39.130 0.00 0.00 0.00 1.98
505 556 5.854010 TTGCTCCGAATGTAGTCTCTATT 57.146 39.130 0.00 0.00 0.00 1.73
506 557 5.188327 TGCTCCGAATGTAGTCTCTATTG 57.812 43.478 0.00 0.00 0.00 1.90
507 558 4.645136 TGCTCCGAATGTAGTCTCTATTGT 59.355 41.667 0.00 0.00 0.00 2.71
508 559 5.826208 TGCTCCGAATGTAGTCTCTATTGTA 59.174 40.000 0.00 0.00 0.00 2.41
509 560 6.320418 TGCTCCGAATGTAGTCTCTATTGTAA 59.680 38.462 0.00 0.00 0.00 2.41
510 561 7.014326 TGCTCCGAATGTAGTCTCTATTGTAAT 59.986 37.037 0.00 0.00 0.00 1.89
511 562 8.512956 GCTCCGAATGTAGTCTCTATTGTAATA 58.487 37.037 0.00 0.00 0.00 0.98
542 593 9.907229 AAAAGACTTATATTTAGGAACAGAGGG 57.093 33.333 0.00 0.00 0.00 4.30
543 594 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
544 595 8.855804 AGACTTATATTTAGGAACAGAGGGAA 57.144 34.615 0.00 0.00 0.00 3.97
545 596 9.453830 AGACTTATATTTAGGAACAGAGGGAAT 57.546 33.333 0.00 0.00 0.00 3.01
573 624 3.863142 ATTCTGCTTTAGCTGCCAAAG 57.137 42.857 14.88 14.88 42.66 2.77
591 642 4.940046 CCAAAGAGCACCTATATGGCTATG 59.060 45.833 0.00 0.00 38.15 2.23
664 716 3.506398 TGACTGACAGATACTGGGAACA 58.494 45.455 10.08 0.00 35.51 3.18
673 725 2.198827 TACTGGGAACACATGGCTTG 57.801 50.000 0.00 0.00 35.60 4.01
724 776 2.233676 TGGTATGTCAGTACTGTGCCAG 59.766 50.000 21.99 0.00 37.52 4.85
727 779 0.686789 TGTCAGTACTGTGCCAGCAT 59.313 50.000 21.99 0.00 34.37 3.79
728 780 1.338105 TGTCAGTACTGTGCCAGCATC 60.338 52.381 21.99 4.43 34.37 3.91
737 789 1.003476 TGCCAGCATCGTGTCACAT 60.003 52.632 3.42 0.00 0.00 3.21
751 803 6.198687 TCGTGTCACATGAAAAGATTTGTTC 58.801 36.000 0.00 0.00 0.00 3.18
757 809 4.901250 ACATGAAAAGATTTGTTCCCCACT 59.099 37.500 0.00 0.00 0.00 4.00
760 813 4.714308 TGAAAAGATTTGTTCCCCACTTGT 59.286 37.500 0.00 0.00 0.00 3.16
788 841 7.093552 CCAACCCAGAAATTACCATTTGACATA 60.094 37.037 0.00 0.00 32.35 2.29
850 903 8.585881 TGTTTAGTCTTTAGTTACAGAGATGCT 58.414 33.333 0.00 0.00 0.00 3.79
879 932 7.118680 GTGAAGTCGGGAAAGTATTCATGTTTA 59.881 37.037 0.00 0.00 37.29 2.01
880 933 7.333423 TGAAGTCGGGAAAGTATTCATGTTTAG 59.667 37.037 0.00 0.00 37.29 1.85
884 937 7.333672 GTCGGGAAAGTATTCATGTTTAGTTCT 59.666 37.037 0.00 0.00 37.29 3.01
933 991 4.263594 GGTTTATTCTGTAGGTGGGTTGGA 60.264 45.833 0.00 0.00 0.00 3.53
985 1043 7.951530 ATCAAAATCCTTTAAAACTGTGCTG 57.048 32.000 0.00 0.00 0.00 4.41
1143 1204 4.101430 AGGGTTGCAGACAAACAAATCAAT 59.899 37.500 0.00 0.00 45.87 2.57
1155 1216 6.070824 ACAAACAAATCAATAAGGATCACCCC 60.071 38.462 0.00 0.00 36.73 4.95
1188 1249 2.095212 TGACTCATCGGAACAAGAGACG 60.095 50.000 0.00 0.00 32.59 4.18
1429 1518 3.181451 ACTTGTTGAGTCAGATGGCAAGA 60.181 43.478 20.06 0.00 36.38 3.02
1430 1519 3.708403 TGTTGAGTCAGATGGCAAGAT 57.292 42.857 0.00 0.00 0.00 2.40
1458 1547 2.795231 CAGTGGATGGAACTGGTGAT 57.205 50.000 0.00 0.00 41.13 3.06
1610 1699 5.983720 GCAAGGATGATGATGAGAAAAATGG 59.016 40.000 0.00 0.00 0.00 3.16
1623 1712 5.051891 AGAAAAATGGTGAAGCTGAATCG 57.948 39.130 0.00 0.00 0.00 3.34
1626 1715 0.911769 ATGGTGAAGCTGAATCGGGA 59.088 50.000 0.00 0.00 0.00 5.14
2139 2231 5.451520 GCTCATTCTGAATGCAAGCCTTTAT 60.452 40.000 23.37 0.00 38.77 1.40
2151 2243 4.096833 GCAAGCCTTTATGATGACATGACA 59.903 41.667 0.00 0.00 37.87 3.58
2327 2422 1.300620 CGGACACGCCAAAGACTCA 60.301 57.895 0.00 0.00 35.94 3.41
2431 2530 2.041115 GGCGTTCCTTGCTCTTCCC 61.041 63.158 0.00 0.00 0.00 3.97
2438 2537 1.153745 CTTGCTCTTCCCGGAGTCG 60.154 63.158 0.73 0.00 35.89 4.18
2440 2539 1.874345 TTGCTCTTCCCGGAGTCGTC 61.874 60.000 0.73 0.00 35.89 4.20
2490 2591 1.228657 GGTTTCTGGCGTGTCCTGTC 61.229 60.000 0.00 0.00 35.49 3.51
2564 2665 4.105697 TCTTGGTAAACTGGAGAAATGGGT 59.894 41.667 0.00 0.00 0.00 4.51
2599 2702 2.207590 TGCTTCTTCTGCTATGCGATG 58.792 47.619 0.00 0.00 0.00 3.84
2604 2707 4.590850 TCTTCTGCTATGCGATGTGTAT 57.409 40.909 0.00 0.00 0.00 2.29
2636 2739 7.067129 TCAGTAGTAATGTATTTGAGCGAGTCT 59.933 37.037 0.00 0.00 0.00 3.24
2637 2740 7.166638 CAGTAGTAATGTATTTGAGCGAGTCTG 59.833 40.741 0.00 0.00 0.00 3.51
2644 2747 0.750249 TTGAGCGAGTCTGTCACCAA 59.250 50.000 0.00 0.00 0.00 3.67
2645 2748 0.315251 TGAGCGAGTCTGTCACCAAG 59.685 55.000 0.00 0.00 0.00 3.61
2769 2901 5.711506 TGGCTTGTCTGTATTGTGAATTCAT 59.288 36.000 12.12 0.00 0.00 2.57
2830 2963 4.331108 TGCCATCATGCACTAGTTTTACA 58.669 39.130 0.00 0.00 36.04 2.41
2870 3003 5.964758 TCTTTTGAACTTGCAACATGAGTT 58.035 33.333 0.00 0.00 38.88 3.01
2878 3011 6.168164 ACTTGCAACATGAGTTTTTGTTTG 57.832 33.333 0.00 0.00 35.28 2.93
2968 3102 0.315251 GAGCCTGTTTGAACTTGGGC 59.685 55.000 13.74 13.74 38.75 5.36
2971 3105 0.030638 CCTGTTTGAACTTGGGCGTG 59.969 55.000 0.00 0.00 0.00 5.34
2975 3109 1.002792 GTTTGAACTTGGGCGTGTCTC 60.003 52.381 0.00 0.00 0.00 3.36
3003 3137 8.933653 AGAACCCTTTTGATCCAATTCTTTTTA 58.066 29.630 0.00 0.00 0.00 1.52
3078 3212 0.242825 TGGGTCGCTTTCGTACTCAG 59.757 55.000 0.00 0.00 36.96 3.35
3108 3242 2.319025 TTTTCCTTTCCCATGGACCC 57.681 50.000 15.22 0.00 31.24 4.46
3110 3244 0.778078 TTCCTTTCCCATGGACCCCA 60.778 55.000 15.22 0.00 38.19 4.96
3116 3250 1.380380 CCCATGGACCCCAAGCTTC 60.380 63.158 15.22 0.00 36.95 3.86
3117 3251 1.383799 CCATGGACCCCAAGCTTCA 59.616 57.895 5.56 0.00 36.95 3.02
3143 3277 6.147164 GGAAATGTTCTTTCATGTCTACGACA 59.853 38.462 0.00 0.00 46.90 4.35
3144 3278 6.712241 AATGTTCTTTCATGTCTACGACAG 57.288 37.500 2.96 0.00 46.04 3.51
3158 3292 1.340889 ACGACAGCCATGCATGTTTTT 59.659 42.857 24.58 6.87 0.00 1.94
3168 3302 4.624024 CCATGCATGTTTTTAGACAGCTTG 59.376 41.667 24.58 0.22 33.68 4.01
3169 3303 5.463286 CATGCATGTTTTTAGACAGCTTGA 58.537 37.500 18.91 0.00 34.59 3.02
3240 3382 2.280628 CATGGACGCTTTTCCTACTCC 58.719 52.381 0.00 0.00 36.51 3.85
3241 3383 1.640917 TGGACGCTTTTCCTACTCCT 58.359 50.000 0.00 0.00 36.51 3.69
3262 3412 1.687368 GGAATCCTGCCAAGAGCCAAT 60.687 52.381 0.00 0.00 42.71 3.16
3282 3432 6.458888 GCCAATAAAACATTCTCTAGTGGAGC 60.459 42.308 0.00 0.00 41.60 4.70
3284 3434 7.201679 CCAATAAAACATTCTCTAGTGGAGCAG 60.202 40.741 0.00 0.00 41.60 4.24
3285 3435 4.899352 AAACATTCTCTAGTGGAGCAGT 57.101 40.909 0.00 0.00 41.60 4.40
3286 3436 6.360370 AAAACATTCTCTAGTGGAGCAGTA 57.640 37.500 0.00 0.00 41.60 2.74
3324 3487 5.605908 AGTCATGACTGGACATCCTATCAAT 59.394 40.000 27.37 0.00 40.75 2.57
3332 3499 7.405292 ACTGGACATCCTATCAATCTTTTTCA 58.595 34.615 0.00 0.00 36.82 2.69
3339 3506 9.321562 CATCCTATCAATCTTTTTCATTTTGGG 57.678 33.333 0.00 0.00 0.00 4.12
3346 3513 8.090214 TCAATCTTTTTCATTTTGGGATCACTC 58.910 33.333 0.00 0.00 0.00 3.51
3347 3514 6.975196 TCTTTTTCATTTTGGGATCACTCA 57.025 33.333 0.00 0.00 0.00 3.41
3348 3515 7.543359 TCTTTTTCATTTTGGGATCACTCAT 57.457 32.000 0.00 0.00 0.00 2.90
3349 3516 7.605449 TCTTTTTCATTTTGGGATCACTCATC 58.395 34.615 0.00 0.00 0.00 2.92
3350 3517 6.914654 TTTTCATTTTGGGATCACTCATCA 57.085 33.333 0.00 0.00 32.33 3.07
3351 3518 7.484993 TTTTCATTTTGGGATCACTCATCAT 57.515 32.000 0.00 0.00 32.33 2.45
3352 3519 7.484993 TTTCATTTTGGGATCACTCATCATT 57.515 32.000 0.00 0.00 32.33 2.57
3353 3520 6.704289 TCATTTTGGGATCACTCATCATTC 57.296 37.500 0.00 0.00 32.33 2.67
3354 3521 6.189133 TCATTTTGGGATCACTCATCATTCA 58.811 36.000 0.00 0.00 32.33 2.57
3355 3522 6.664384 TCATTTTGGGATCACTCATCATTCAA 59.336 34.615 0.00 0.00 32.33 2.69
3356 3523 6.519679 TTTTGGGATCACTCATCATTCAAG 57.480 37.500 0.00 0.00 32.33 3.02
3357 3524 4.849813 TGGGATCACTCATCATTCAAGT 57.150 40.909 0.00 0.00 32.33 3.16
3358 3525 4.774124 TGGGATCACTCATCATTCAAGTC 58.226 43.478 0.00 0.00 32.33 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 113 7.162082 ACTATAATACTGGACATTAGCCAAGC 58.838 38.462 0.00 0.00 34.44 4.01
192 202 9.995003 AAAATGGCAAACTTATGTGAATAGAAA 57.005 25.926 0.00 0.00 0.00 2.52
271 297 2.544277 GCTGCAGTGCAAACTTGATTGA 60.544 45.455 20.22 0.00 38.41 2.57
376 427 5.104485 AGGAATGGAGGGAGTATACAACAAC 60.104 44.000 5.50 0.00 0.00 3.32
384 435 9.860393 ACTTATATTTAGGAATGGAGGGAGTAT 57.140 33.333 0.00 0.00 0.00 2.12
385 436 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
386 437 7.237887 GGACTTATATTTAGGAATGGAGGGAGT 59.762 40.741 0.00 0.00 0.00 3.85
387 438 7.459444 AGGACTTATATTTAGGAATGGAGGGAG 59.541 40.741 0.00 0.00 0.00 4.30
389 440 7.575499 AGGACTTATATTTAGGAATGGAGGG 57.425 40.000 0.00 0.00 0.00 4.30
390 441 9.868160 AAAAGGACTTATATTTAGGAATGGAGG 57.132 33.333 0.00 0.00 0.00 4.30
408 459 9.620259 GTCCATATTGAAATCTCTAAAAGGACT 57.380 33.333 0.00 0.00 37.06 3.85
409 460 9.620259 AGTCCATATTGAAATCTCTAAAAGGAC 57.380 33.333 0.00 0.00 39.53 3.85
462 513 9.973450 GAGCAAAATGAGTGAATCTATACTCTA 57.027 33.333 0.00 0.00 42.86 2.43
463 514 7.930865 GGAGCAAAATGAGTGAATCTATACTCT 59.069 37.037 0.00 0.00 42.86 3.24
464 515 7.095857 CGGAGCAAAATGAGTGAATCTATACTC 60.096 40.741 0.00 0.00 42.77 2.59
465 516 6.703607 CGGAGCAAAATGAGTGAATCTATACT 59.296 38.462 0.00 0.00 0.00 2.12
466 517 6.701841 TCGGAGCAAAATGAGTGAATCTATAC 59.298 38.462 0.00 0.00 0.00 1.47
467 518 6.816136 TCGGAGCAAAATGAGTGAATCTATA 58.184 36.000 0.00 0.00 0.00 1.31
468 519 5.674525 TCGGAGCAAAATGAGTGAATCTAT 58.325 37.500 0.00 0.00 0.00 1.98
469 520 5.084818 TCGGAGCAAAATGAGTGAATCTA 57.915 39.130 0.00 0.00 0.00 1.98
470 521 3.942829 TCGGAGCAAAATGAGTGAATCT 58.057 40.909 0.00 0.00 0.00 2.40
471 522 4.685169 TTCGGAGCAAAATGAGTGAATC 57.315 40.909 0.00 0.00 0.00 2.52
472 523 4.460382 ACATTCGGAGCAAAATGAGTGAAT 59.540 37.500 2.36 0.00 36.57 2.57
473 524 3.820467 ACATTCGGAGCAAAATGAGTGAA 59.180 39.130 2.36 0.00 36.57 3.18
474 525 3.411446 ACATTCGGAGCAAAATGAGTGA 58.589 40.909 2.36 0.00 36.57 3.41
475 526 3.837213 ACATTCGGAGCAAAATGAGTG 57.163 42.857 2.36 0.00 36.57 3.51
476 527 4.579869 ACTACATTCGGAGCAAAATGAGT 58.420 39.130 2.36 0.09 36.57 3.41
477 528 4.872691 AGACTACATTCGGAGCAAAATGAG 59.127 41.667 2.36 0.00 36.57 2.90
478 529 4.832248 AGACTACATTCGGAGCAAAATGA 58.168 39.130 2.36 0.00 36.57 2.57
479 530 4.872691 AGAGACTACATTCGGAGCAAAATG 59.127 41.667 0.00 0.00 38.54 2.32
480 531 5.091261 AGAGACTACATTCGGAGCAAAAT 57.909 39.130 0.00 0.00 0.00 1.82
481 532 4.537135 AGAGACTACATTCGGAGCAAAA 57.463 40.909 0.00 0.00 0.00 2.44
482 533 5.854010 ATAGAGACTACATTCGGAGCAAA 57.146 39.130 0.00 0.00 0.00 3.68
483 534 5.127194 ACAATAGAGACTACATTCGGAGCAA 59.873 40.000 0.00 0.00 0.00 3.91
484 535 4.645136 ACAATAGAGACTACATTCGGAGCA 59.355 41.667 0.00 0.00 0.00 4.26
485 536 5.189659 ACAATAGAGACTACATTCGGAGC 57.810 43.478 0.00 0.00 0.00 4.70
516 567 9.907229 CCCTCTGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
517 568 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
518 569 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
519 570 8.855804 TTCCCTCTGTTCCTAAATATAAGTCT 57.144 34.615 0.00 0.00 0.00 3.24
544 595 9.300681 TGGCAGCTAAAGCAGAATAATTTATAT 57.699 29.630 4.54 0.00 45.16 0.86
545 596 8.690203 TGGCAGCTAAAGCAGAATAATTTATA 57.310 30.769 4.54 0.00 45.16 0.98
546 597 7.587037 TGGCAGCTAAAGCAGAATAATTTAT 57.413 32.000 4.54 0.00 45.16 1.40
547 598 7.403312 TTGGCAGCTAAAGCAGAATAATTTA 57.597 32.000 4.54 0.00 45.16 1.40
569 620 5.555017 ACATAGCCATATAGGTGCTCTTTG 58.445 41.667 4.06 4.64 40.61 2.77
573 624 5.413309 AAGACATAGCCATATAGGTGCTC 57.587 43.478 4.06 0.00 40.61 4.26
652 704 2.684881 CAAGCCATGTGTTCCCAGTATC 59.315 50.000 0.00 0.00 0.00 2.24
661 713 2.304180 AGAGAGCTACAAGCCATGTGTT 59.696 45.455 3.13 0.00 43.77 3.32
664 716 2.697751 CCTAGAGAGCTACAAGCCATGT 59.302 50.000 0.00 0.00 43.77 3.21
673 725 5.811190 TGGTATCATCTCCTAGAGAGCTAC 58.189 45.833 0.32 2.56 42.26 3.58
724 776 3.811722 TCTTTTCATGTGACACGATGC 57.188 42.857 0.22 0.00 0.00 3.91
727 779 5.749596 ACAAATCTTTTCATGTGACACGA 57.250 34.783 0.22 0.00 0.00 4.35
728 780 5.399301 GGAACAAATCTTTTCATGTGACACG 59.601 40.000 0.22 0.00 0.00 4.49
737 789 4.714308 ACAAGTGGGGAACAAATCTTTTCA 59.286 37.500 0.00 0.00 0.00 2.69
757 809 8.104265 AAATGGTAATTTCTGGGTTGGCACAA 62.104 38.462 0.00 0.00 35.54 3.33
760 813 2.685106 TGGTAATTTCTGGGTTGGCA 57.315 45.000 0.00 0.00 0.00 4.92
788 841 7.906327 AGGAAAACTATGTTGCCAATAACAAT 58.094 30.769 0.00 0.00 43.13 2.71
796 849 4.211125 TGTGAAGGAAAACTATGTTGCCA 58.789 39.130 0.00 0.00 0.00 4.92
850 903 1.719529 TACTTTCCCGACTTCACCCA 58.280 50.000 0.00 0.00 0.00 4.51
879 932 8.523658 AGCAAACTAAAAAGTTGAAAGAGAACT 58.476 29.630 0.00 0.00 35.08 3.01
880 933 8.689251 AGCAAACTAAAAAGTTGAAAGAGAAC 57.311 30.769 0.00 0.00 31.64 3.01
933 991 6.015180 TGCAGATTCCTTCTTTTTGTATTGCT 60.015 34.615 0.00 0.00 29.93 3.91
967 1025 6.373774 CAGAGATCAGCACAGTTTTAAAGGAT 59.626 38.462 0.00 0.00 0.00 3.24
985 1043 5.121811 AGTAACCATGCAACATCAGAGATC 58.878 41.667 0.00 0.00 0.00 2.75
1059 1120 8.644374 TCCTTACAAGTTTTGGCTACATTAAT 57.356 30.769 0.00 0.00 34.12 1.40
1143 1204 1.048724 CAGGCTCGGGGTGATCCTTA 61.049 60.000 0.00 0.00 40.34 2.69
1155 1216 2.816204 ATGAGTCATCATCAGGCTCG 57.184 50.000 0.00 0.00 42.76 5.03
1188 1249 7.390718 TCTTCACTAGCTTTCTTAAATGTTCCC 59.609 37.037 0.00 0.00 0.00 3.97
1270 1331 4.217118 TGCAGAGAAAGGATTTGAAGAAGC 59.783 41.667 0.00 0.00 39.27 3.86
1337 1398 1.003646 AGGTGGAGGCTCTGAGACTA 58.996 55.000 14.21 0.00 30.20 2.59
1387 1476 3.391296 AGTTGAGAGGGTGCTTCAGTTAA 59.609 43.478 0.00 0.00 0.00 2.01
1429 1518 6.352222 CCAGTTCCATCCACTGTAACTTCTAT 60.352 42.308 0.00 0.00 40.19 1.98
1430 1519 5.046591 CCAGTTCCATCCACTGTAACTTCTA 60.047 44.000 0.00 0.00 40.19 2.10
1568 1657 6.173339 TCCTTGCTAACTTTATCTTCACCTG 58.827 40.000 0.00 0.00 0.00 4.00
1610 1699 1.087501 GGTTCCCGATTCAGCTTCAC 58.912 55.000 0.00 0.00 0.00 3.18
1623 1712 2.444766 AGATGATCCATCCTTGGTTCCC 59.555 50.000 3.55 0.00 44.06 3.97
1626 1715 3.434739 GCTCAGATGATCCATCCTTGGTT 60.435 47.826 3.55 0.00 44.06 3.67
2139 2231 3.324556 TGTCCTTCAGTGTCATGTCATCA 59.675 43.478 0.00 0.00 0.00 3.07
2151 2243 3.244700 CCTTCTTGTCCATGTCCTTCAGT 60.245 47.826 0.00 0.00 0.00 3.41
2327 2422 2.770048 CCTTCGGGGAGCCCTCAT 60.770 66.667 5.38 0.00 42.67 2.90
2347 2442 1.650363 GTGGGTTTCAAACGTCGGG 59.350 57.895 0.00 0.00 0.00 5.14
2431 2530 4.985044 ATGTTTTAACTTGACGACTCCG 57.015 40.909 0.00 0.00 42.50 4.63
2438 2537 7.599630 TGGGTACGATATGTTTTAACTTGAC 57.400 36.000 0.00 0.00 0.00 3.18
2440 2539 7.981142 ACATGGGTACGATATGTTTTAACTTG 58.019 34.615 0.00 0.00 31.38 3.16
2490 2591 2.738521 CACCGTTCCAGACCAGCG 60.739 66.667 0.00 0.00 0.00 5.18
2564 2665 0.535335 AAGCATAGCCCGAAACGAGA 59.465 50.000 0.00 0.00 0.00 4.04
2573 2674 2.918712 TAGCAGAAGAAGCATAGCCC 57.081 50.000 0.00 0.00 0.00 5.19
2616 2719 5.805486 TGACAGACTCGCTCAAATACATTAC 59.195 40.000 0.00 0.00 0.00 1.89
2617 2720 5.805486 GTGACAGACTCGCTCAAATACATTA 59.195 40.000 0.00 0.00 0.00 1.90
2618 2721 4.627467 GTGACAGACTCGCTCAAATACATT 59.373 41.667 0.00 0.00 0.00 2.71
2630 2733 1.338337 AGTGACTTGGTGACAGACTCG 59.662 52.381 0.00 0.00 44.54 4.18
2636 2739 4.036262 GCATAAAACAGTGACTTGGTGACA 59.964 41.667 0.00 0.00 39.83 3.58
2637 2740 4.036262 TGCATAAAACAGTGACTTGGTGAC 59.964 41.667 0.00 0.00 0.00 3.67
2644 2747 4.515191 ACGAACATGCATAAAACAGTGACT 59.485 37.500 0.00 0.00 0.00 3.41
2645 2748 4.783242 ACGAACATGCATAAAACAGTGAC 58.217 39.130 0.00 0.00 0.00 3.67
2769 2901 3.057586 TGGTAAAACCTCCCCAAGAGAA 58.942 45.455 0.00 0.00 46.50 2.87
2830 2963 5.652014 TCAAAAGAACCTGAAGTGTGTCAAT 59.348 36.000 0.00 0.00 0.00 2.57
2895 3028 5.488645 TCGACCTGGTAAAAACACTTTTC 57.511 39.130 0.00 0.00 36.20 2.29
2909 3043 1.812922 GTGCAGATGCTCGACCTGG 60.813 63.158 6.35 0.00 42.66 4.45
2953 3087 0.738389 ACACGCCCAAGTTCAAACAG 59.262 50.000 0.00 0.00 0.00 3.16
2968 3102 4.252971 TCAAAAGGGTTCTAGAGACACG 57.747 45.455 0.00 0.00 0.00 4.49
2971 3105 5.422214 TGGATCAAAAGGGTTCTAGAGAC 57.578 43.478 0.00 0.00 0.00 3.36
2975 3109 7.709149 AAGAATTGGATCAAAAGGGTTCTAG 57.291 36.000 0.00 0.00 0.00 2.43
3017 3151 6.371825 GGATTCTAGTCCTGTAAACCAAACAG 59.628 42.308 0.00 0.00 43.26 3.16
3034 3168 6.595716 ACGTGAGAATTTTCCAAGGATTCTAG 59.404 38.462 3.99 2.87 39.52 2.43
3044 3178 2.500229 GACCCACGTGAGAATTTTCCA 58.500 47.619 19.30 0.00 0.00 3.53
3050 3184 0.034896 AAAGCGACCCACGTGAGAAT 59.965 50.000 19.30 0.00 44.60 2.40
3053 3187 2.372690 CGAAAGCGACCCACGTGAG 61.373 63.158 19.30 6.24 44.60 3.51
3078 3212 5.610398 TGGGAAAGGAAAATTCTTTTGAGC 58.390 37.500 7.83 0.00 36.73 4.26
3101 3235 0.846427 TCCTGAAGCTTGGGGTCCAT 60.846 55.000 2.10 0.00 31.53 3.41
3108 3242 4.861102 AAGAACATTTCCTGAAGCTTGG 57.139 40.909 2.10 0.00 0.00 3.61
3110 3244 6.041296 ACATGAAAGAACATTTCCTGAAGCTT 59.959 34.615 0.00 0.00 31.46 3.74
3116 3250 6.368791 TCGTAGACATGAAAGAACATTTCCTG 59.631 38.462 0.00 4.69 30.21 3.86
3117 3251 6.464222 TCGTAGACATGAAAGAACATTTCCT 58.536 36.000 0.00 0.00 30.21 3.36
3143 3277 3.367703 GCTGTCTAAAAACATGCATGGCT 60.368 43.478 29.41 14.20 0.00 4.75
3144 3278 2.925563 GCTGTCTAAAAACATGCATGGC 59.074 45.455 29.41 15.30 0.00 4.40
3168 3302 9.710979 TGCAAACGTACTAGCAATAAATAATTC 57.289 29.630 0.00 0.00 33.48 2.17
3169 3303 9.716507 CTGCAAACGTACTAGCAATAAATAATT 57.283 29.630 0.00 0.00 36.44 1.40
3240 3382 0.750911 GGCTCTTGGCAGGATTCCAG 60.751 60.000 5.29 0.00 44.01 3.86
3241 3383 1.304282 GGCTCTTGGCAGGATTCCA 59.696 57.895 5.29 0.00 44.01 3.53
3262 3412 6.360370 ACTGCTCCACTAGAGAATGTTTTA 57.640 37.500 0.00 0.00 46.50 1.52
3282 3432 8.383619 GTCATGACTTGCAAATTAGTACTACTG 58.616 37.037 18.83 2.03 0.00 2.74
3284 3434 8.383619 CAGTCATGACTTGCAAATTAGTACTAC 58.616 37.037 25.84 0.00 40.20 2.73
3285 3435 7.549134 CCAGTCATGACTTGCAAATTAGTACTA 59.451 37.037 25.84 0.00 40.20 1.82
3286 3436 6.372659 CCAGTCATGACTTGCAAATTAGTACT 59.627 38.462 25.84 0.00 40.20 2.73
3324 3487 6.975196 TGAGTGATCCCAAAATGAAAAAGA 57.025 33.333 0.00 0.00 0.00 2.52
3332 3499 6.666546 ACTTGAATGATGAGTGATCCCAAAAT 59.333 34.615 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.