Multiple sequence alignment - TraesCS3A01G203500

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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 TraesCS3A01G203500 chr3A 100.000 2870 0 0 1 2870 352469488 352472357 0.000000e+00 5301
1 TraesCS3A01G203500 chr3A 93.943 1915 65 8 969 2870 144697884 144699760 0.000000e+00 2846
2 TraesCS3A01G203500 chr3A 94.144 1810 51 9 1074 2870 126051593 126053360 0.000000e+00 2704
3 TraesCS3A01G203500 chr3A 97.527 647 16 0 1 647 352462613 352463259 0.000000e+00 1107
4 TraesCS3A01G203500 chr3A 93.970 199 9 3 647 844 126038304 126038500 6.010000e-77 298
5 TraesCS3A01G203500 chr7A 97.351 2227 44 4 645 2870 660571907 660574119 0.000000e+00 3771
6 TraesCS3A01G203500 chr7A 94.308 1915 59 9 969 2870 542714768 542716645 0.000000e+00 2887
7 TraesCS3A01G203500 chr7A 80.159 1890 314 44 996 2870 60710784 60708941 0.000000e+00 1356
8 TraesCS3A01G203500 chr7A 97.214 646 15 2 1 646 30105935 30106577 0.000000e+00 1090
9 TraesCS3A01G203500 chr7A 93.564 202 10 3 644 844 542714546 542714745 6.010000e-77 298
10 TraesCS3A01G203500 chr6A 97.034 2225 45 4 647 2870 435090491 435088287 0.000000e+00 3723
11 TraesCS3A01G203500 chr6A 93.928 1927 54 9 969 2870 603905910 603907798 0.000000e+00 2852
12 TraesCS3A01G203500 chr6A 95.542 673 21 7 1 671 527347541 527348206 0.000000e+00 1068
13 TraesCS3A01G203500 chr2D 95.382 1884 46 8 988 2870 618324321 618322478 0.000000e+00 2959
14 TraesCS3A01G203500 chr1A 94.363 1916 57 11 969 2870 564159813 564157935 0.000000e+00 2892
15 TraesCS3A01G203500 chr6B 93.479 1917 59 9 980 2870 18463680 18461804 0.000000e+00 2787
16 TraesCS3A01G203500 chr6B 93.166 1917 65 9 980 2870 18465697 18467573 0.000000e+00 2754
17 TraesCS3A01G203500 chr5D 91.650 2012 106 16 862 2870 34210569 34212521 0.000000e+00 2728
18 TraesCS3A01G203500 chr5D 95.431 197 9 0 647 843 34210286 34210482 5.970000e-82 315
19 TraesCS3A01G203500 chr3B 89.112 1993 152 28 885 2870 821214166 821212232 0.000000e+00 2418
20 TraesCS3A01G203500 chr4B 92.575 1239 30 6 969 2183 167378053 167376853 0.000000e+00 1722
21 TraesCS3A01G203500 chr4B 79.342 881 155 20 993 1864 16676675 16677537 6.850000e-166 593
22 TraesCS3A01G203500 chr4B 96.392 194 7 0 647 840 167378272 167378079 1.280000e-83 320
23 TraesCS3A01G203500 chr4B 95.361 194 9 0 647 840 273959385 273959578 2.780000e-80 309
24 TraesCS3A01G203500 chr4A 93.561 1025 31 3 969 1993 147535731 147534742 0.000000e+00 1495
25 TraesCS3A01G203500 chr4A 96.918 649 18 1 1 649 618202791 618203437 0.000000e+00 1086
26 TraesCS3A01G203500 chr4A 95.812 191 5 3 647 836 410961437 410961249 3.590000e-79 305
27 TraesCS3A01G203500 chr1B 90.486 988 70 8 885 1869 551242054 551241088 0.000000e+00 1282
28 TraesCS3A01G203500 chr5A 97.372 647 15 2 1 647 68419413 68420057 0.000000e+00 1099
29 TraesCS3A01G203500 chr5A 97.063 647 17 2 1 647 322143088 322142444 0.000000e+00 1088
30 TraesCS3A01G203500 chr5A 97.063 647 16 2 1 647 602210434 602211077 0.000000e+00 1086
31 TraesCS3A01G203500 chr2A 97.214 646 16 2 1 646 670419594 670420237 0.000000e+00 1092
32 TraesCS3A01G203500 chr2A 97.214 646 16 2 1 646 670435910 670436553 0.000000e+00 1092
33 TraesCS3A01G203500 chr2B 95.876 194 8 0 647 840 311925431 311925238 5.970000e-82 315


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 TraesCS3A01G203500 chr3A 352469488 352472357 2869 False 5301.0 5301 100.0000 1 2870 1 chr3A.!!$F5 2869
1 TraesCS3A01G203500 chr3A 144697884 144699760 1876 False 2846.0 2846 93.9430 969 2870 1 chr3A.!!$F3 1901
2 TraesCS3A01G203500 chr3A 126051593 126053360 1767 False 2704.0 2704 94.1440 1074 2870 1 chr3A.!!$F2 1796
3 TraesCS3A01G203500 chr3A 352462613 352463259 646 False 1107.0 1107 97.5270 1 647 1 chr3A.!!$F4 646
4 TraesCS3A01G203500 chr7A 660571907 660574119 2212 False 3771.0 3771 97.3510 645 2870 1 chr7A.!!$F2 2225
5 TraesCS3A01G203500 chr7A 542714546 542716645 2099 False 1592.5 2887 93.9360 644 2870 2 chr7A.!!$F3 2226
6 TraesCS3A01G203500 chr7A 60708941 60710784 1843 True 1356.0 1356 80.1590 996 2870 1 chr7A.!!$R1 1874
7 TraesCS3A01G203500 chr7A 30105935 30106577 642 False 1090.0 1090 97.2140 1 646 1 chr7A.!!$F1 645
8 TraesCS3A01G203500 chr6A 435088287 435090491 2204 True 3723.0 3723 97.0340 647 2870 1 chr6A.!!$R1 2223
9 TraesCS3A01G203500 chr6A 603905910 603907798 1888 False 2852.0 2852 93.9280 969 2870 1 chr6A.!!$F2 1901
10 TraesCS3A01G203500 chr6A 527347541 527348206 665 False 1068.0 1068 95.5420 1 671 1 chr6A.!!$F1 670
11 TraesCS3A01G203500 chr2D 618322478 618324321 1843 True 2959.0 2959 95.3820 988 2870 1 chr2D.!!$R1 1882
12 TraesCS3A01G203500 chr1A 564157935 564159813 1878 True 2892.0 2892 94.3630 969 2870 1 chr1A.!!$R1 1901
13 TraesCS3A01G203500 chr6B 18461804 18463680 1876 True 2787.0 2787 93.4790 980 2870 1 chr6B.!!$R1 1890
14 TraesCS3A01G203500 chr6B 18465697 18467573 1876 False 2754.0 2754 93.1660 980 2870 1 chr6B.!!$F1 1890
15 TraesCS3A01G203500 chr5D 34210286 34212521 2235 False 1521.5 2728 93.5405 647 2870 2 chr5D.!!$F1 2223
16 TraesCS3A01G203500 chr3B 821212232 821214166 1934 True 2418.0 2418 89.1120 885 2870 1 chr3B.!!$R1 1985
17 TraesCS3A01G203500 chr4B 167376853 167378272 1419 True 1021.0 1722 94.4835 647 2183 2 chr4B.!!$R1 1536
18 TraesCS3A01G203500 chr4B 16676675 16677537 862 False 593.0 593 79.3420 993 1864 1 chr4B.!!$F1 871
19 TraesCS3A01G203500 chr4A 147534742 147535731 989 True 1495.0 1495 93.5610 969 1993 1 chr4A.!!$R1 1024
20 TraesCS3A01G203500 chr4A 618202791 618203437 646 False 1086.0 1086 96.9180 1 649 1 chr4A.!!$F1 648
21 TraesCS3A01G203500 chr1B 551241088 551242054 966 True 1282.0 1282 90.4860 885 1869 1 chr1B.!!$R1 984
22 TraesCS3A01G203500 chr5A 68419413 68420057 644 False 1099.0 1099 97.3720 1 647 1 chr5A.!!$F1 646
23 TraesCS3A01G203500 chr5A 322142444 322143088 644 True 1088.0 1088 97.0630 1 647 1 chr5A.!!$R1 646
24 TraesCS3A01G203500 chr5A 602210434 602211077 643 False 1086.0 1086 97.0630 1 647 1 chr5A.!!$F2 646
25 TraesCS3A01G203500 chr2A 670419594 670420237 643 False 1092.0 1092 97.2140 1 646 1 chr2A.!!$F1 645
26 TraesCS3A01G203500 chr2A 670435910 670436553 643 False 1092.0 1092 97.2140 1 646 1 chr2A.!!$F2 645

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
194 195 0.887933 GATTCGTGCCAACCCAACAT 59.112 50.000 0.00 0.0 0.00 2.71 F
490 492 1.961394 TGGTCAACGAGCTAGTCAACT 59.039 47.619 0.00 0.0 0.00 3.16 F
1556 1669 1.617357 TGATCATGAGAGCGAGGATGG 59.383 52.381 0.09 0.0 31.29 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1669 0.319727 CATGCTCTCATCCTCGCTCC 60.320 60.00 0.00 0.00 0.0 4.70 R
1809 1994 5.426509 TGTAGAAGCATATATCCTCCATGGG 59.573 44.00 13.02 2.26 36.2 4.00 R
2639 2827 4.792068 TCTTCTTGAAGTTGGACACCAAT 58.208 39.13 6.50 0.00 45.8 3.16 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
57 58 5.464030 AGGCAAGTCTCTTTTACTCGTTA 57.536 39.130 0.00 0.00 0.00 3.18
74 75 4.699637 TCGTTATGTAACACATCATCCCC 58.300 43.478 4.04 0.00 39.88 4.81
194 195 0.887933 GATTCGTGCCAACCCAACAT 59.112 50.000 0.00 0.00 0.00 2.71
214 215 2.674796 ACACTTTCGGAGATACCTGC 57.325 50.000 0.00 0.00 35.04 4.85
467 469 2.027469 GGTCAGGAAACCGTAACCATCT 60.027 50.000 0.00 0.00 0.00 2.90
468 470 3.196254 GGTCAGGAAACCGTAACCATCTA 59.804 47.826 0.00 0.00 0.00 1.98
469 471 4.141779 GGTCAGGAAACCGTAACCATCTAT 60.142 45.833 0.00 0.00 0.00 1.98
470 472 5.425630 GTCAGGAAACCGTAACCATCTATT 58.574 41.667 0.00 0.00 0.00 1.73
471 473 5.293569 GTCAGGAAACCGTAACCATCTATTG 59.706 44.000 0.00 0.00 0.00 1.90
482 484 3.185246 CCATCTATTGGTCAACGAGCT 57.815 47.619 0.00 0.00 40.99 4.09
483 485 4.322080 CCATCTATTGGTCAACGAGCTA 57.678 45.455 0.00 0.00 40.99 3.32
484 486 4.302455 CCATCTATTGGTCAACGAGCTAG 58.698 47.826 0.00 0.00 40.99 3.42
485 487 4.202161 CCATCTATTGGTCAACGAGCTAGT 60.202 45.833 0.00 0.00 40.99 2.57
486 488 4.634184 TCTATTGGTCAACGAGCTAGTC 57.366 45.455 0.00 0.00 0.00 2.59
487 489 4.014406 TCTATTGGTCAACGAGCTAGTCA 58.986 43.478 0.00 0.00 0.00 3.41
488 490 3.678056 ATTGGTCAACGAGCTAGTCAA 57.322 42.857 0.00 0.55 0.00 3.18
489 491 2.433868 TGGTCAACGAGCTAGTCAAC 57.566 50.000 0.00 1.69 0.00 3.18
490 492 1.961394 TGGTCAACGAGCTAGTCAACT 59.039 47.619 0.00 0.00 0.00 3.16
491 493 3.151554 TGGTCAACGAGCTAGTCAACTA 58.848 45.455 0.00 0.00 0.00 2.24
492 494 3.190744 TGGTCAACGAGCTAGTCAACTAG 59.809 47.826 11.99 11.99 46.63 2.57
493 495 3.439476 GGTCAACGAGCTAGTCAACTAGA 59.561 47.826 19.03 0.00 46.80 2.43
494 496 4.437659 GGTCAACGAGCTAGTCAACTAGAG 60.438 50.000 19.03 11.89 46.80 2.43
495 497 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
496 498 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
497 499 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
498 500 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
499 501 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
500 502 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
501 503 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
502 504 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
503 505 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
504 506 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
505 507 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
506 508 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
507 509 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
508 510 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
509 511 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
510 512 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
511 513 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
512 514 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
513 515 3.206866 AGAGGCTTACTAGGGACATGGTA 59.793 47.826 0.00 0.00 0.00 3.25
514 516 4.140663 AGAGGCTTACTAGGGACATGGTAT 60.141 45.833 0.00 0.00 0.00 2.73
515 517 4.567857 AGGCTTACTAGGGACATGGTATT 58.432 43.478 0.00 0.00 0.00 1.89
516 518 4.348168 AGGCTTACTAGGGACATGGTATTG 59.652 45.833 0.00 0.00 0.00 1.90
517 519 4.102681 GGCTTACTAGGGACATGGTATTGT 59.897 45.833 0.00 0.00 0.00 2.71
518 520 5.298347 GCTTACTAGGGACATGGTATTGTC 58.702 45.833 0.00 0.00 44.27 3.18
519 521 5.070580 GCTTACTAGGGACATGGTATTGTCT 59.929 44.000 0.00 0.00 44.39 3.41
520 522 6.267014 GCTTACTAGGGACATGGTATTGTCTA 59.733 42.308 0.00 0.00 44.39 2.59
521 523 7.038941 GCTTACTAGGGACATGGTATTGTCTAT 60.039 40.741 0.00 0.00 44.39 1.98
522 524 6.672266 ACTAGGGACATGGTATTGTCTATG 57.328 41.667 0.00 0.00 44.39 2.23
523 525 6.143915 ACTAGGGACATGGTATTGTCTATGT 58.856 40.000 0.00 0.00 44.39 2.29
524 526 7.302948 ACTAGGGACATGGTATTGTCTATGTA 58.697 38.462 0.00 0.00 44.39 2.29
525 527 7.956315 ACTAGGGACATGGTATTGTCTATGTAT 59.044 37.037 0.00 0.00 44.39 2.29
526 528 7.246171 AGGGACATGGTATTGTCTATGTATC 57.754 40.000 0.00 0.00 44.39 2.24
527 529 6.213600 AGGGACATGGTATTGTCTATGTATCC 59.786 42.308 0.00 0.00 44.39 2.59
528 530 6.013725 GGGACATGGTATTGTCTATGTATCCA 60.014 42.308 0.00 0.00 44.39 3.41
529 531 6.874134 GGACATGGTATTGTCTATGTATCCAC 59.126 42.308 0.00 0.00 44.39 4.02
530 532 7.373617 ACATGGTATTGTCTATGTATCCACA 57.626 36.000 0.00 0.00 37.66 4.17
531 533 7.217200 ACATGGTATTGTCTATGTATCCACAC 58.783 38.462 0.00 0.00 37.66 3.82
532 534 6.800072 TGGTATTGTCTATGTATCCACACA 57.200 37.500 0.00 0.00 37.54 3.72
533 535 7.373617 TGGTATTGTCTATGTATCCACACAT 57.626 36.000 0.00 0.00 41.88 3.21
534 536 7.216494 TGGTATTGTCTATGTATCCACACATG 58.784 38.462 0.00 0.00 39.46 3.21
535 537 7.147567 TGGTATTGTCTATGTATCCACACATGT 60.148 37.037 0.00 0.00 39.46 3.21
536 538 8.364894 GGTATTGTCTATGTATCCACACATGTA 58.635 37.037 0.00 0.00 39.46 2.29
537 539 9.929180 GTATTGTCTATGTATCCACACATGTAT 57.071 33.333 0.00 0.00 39.46 2.29
539 541 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
540 542 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
541 543 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
542 544 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
543 545 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
544 546 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
545 547 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
546 548 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
547 549 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
548 550 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
549 551 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
550 552 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
551 553 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
552 554 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
553 555 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
554 556 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
555 557 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
556 558 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
557 559 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
565 567 9.547753 TGAGTTTCCTATCAATACAATTCTAGC 57.452 33.333 0.00 0.00 0.00 3.42
566 568 9.547753 GAGTTTCCTATCAATACAATTCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
569 571 8.853077 TTCCTATCAATACAATTCTAGCATGG 57.147 34.615 0.00 0.00 0.00 3.66
570 572 8.206126 TCCTATCAATACAATTCTAGCATGGA 57.794 34.615 0.00 0.00 0.00 3.41
571 573 8.829746 TCCTATCAATACAATTCTAGCATGGAT 58.170 33.333 0.00 0.00 0.00 3.41
1387 1470 8.837389 ACAACATAGAACAAGATGATGATGATG 58.163 33.333 0.00 0.00 32.06 3.07
1388 1471 9.052759 CAACATAGAACAAGATGATGATGATGA 57.947 33.333 0.00 0.00 29.81 2.92
1389 1472 9.794719 AACATAGAACAAGATGATGATGATGAT 57.205 29.630 0.00 0.00 0.00 2.45
1390 1473 9.220767 ACATAGAACAAGATGATGATGATGATG 57.779 33.333 0.00 0.00 0.00 3.07
1391 1474 9.436957 CATAGAACAAGATGATGATGATGATGA 57.563 33.333 0.00 0.00 0.00 2.92
1393 1476 8.329203 AGAACAAGATGATGATGATGATGATG 57.671 34.615 0.00 0.00 0.00 3.07
1394 1477 8.157476 AGAACAAGATGATGATGATGATGATGA 58.843 33.333 0.00 0.00 0.00 2.92
1395 1478 8.870075 AACAAGATGATGATGATGATGATGAT 57.130 30.769 0.00 0.00 0.00 2.45
1396 1479 8.273780 ACAAGATGATGATGATGATGATGATG 57.726 34.615 0.00 0.00 0.00 3.07
1397 1480 8.103305 ACAAGATGATGATGATGATGATGATGA 58.897 33.333 0.00 0.00 0.00 2.92
1398 1481 9.118300 CAAGATGATGATGATGATGATGATGAT 57.882 33.333 0.00 0.00 0.00 2.45
1424 1525 4.161565 TGATTATCTTCGCAACCCAGTACT 59.838 41.667 0.00 0.00 0.00 2.73
1518 1619 7.852263 TGGTTCCTTGTTCCAATAAAGAAAAA 58.148 30.769 0.00 0.00 0.00 1.94
1556 1669 1.617357 TGATCATGAGAGCGAGGATGG 59.383 52.381 0.09 0.00 31.29 3.51
1809 1994 5.431765 TCAAGAAGGGATGAAGATAAGTGC 58.568 41.667 0.00 0.00 0.00 4.40
2215 2403 4.846779 TTGGGATACAAGCTTTGACAAC 57.153 40.909 0.00 0.00 33.18 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.713824 ACGAGATTGAACAAGGTATCGA 57.286 40.909 10.57 0.00 33.43 3.59
194 195 3.093814 TGCAGGTATCTCCGAAAGTGTA 58.906 45.455 0.00 0.00 41.99 2.90
214 215 3.199071 TGGGTGGCTATAAAGGTACACTG 59.801 47.826 0.00 0.00 0.00 3.66
256 257 1.542547 CGTAGGAGTGCTTTGGGTGTT 60.543 52.381 0.00 0.00 0.00 3.32
467 469 4.219944 AGTTGACTAGCTCGTTGACCAATA 59.780 41.667 0.00 0.00 0.00 1.90
468 470 3.006967 AGTTGACTAGCTCGTTGACCAAT 59.993 43.478 0.00 0.00 0.00 3.16
469 471 2.364324 AGTTGACTAGCTCGTTGACCAA 59.636 45.455 0.00 0.00 0.00 3.67
470 472 1.961394 AGTTGACTAGCTCGTTGACCA 59.039 47.619 0.00 0.00 0.00 4.02
471 473 2.726832 AGTTGACTAGCTCGTTGACC 57.273 50.000 0.00 0.00 0.00 4.02
472 474 4.437659 CCTCTAGTTGACTAGCTCGTTGAC 60.438 50.000 12.30 0.00 44.24 3.18
473 475 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
474 476 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
475 477 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
476 478 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
477 479 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
478 480 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
479 481 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
480 482 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
481 483 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
482 484 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
483 485 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
484 486 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
485 487 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
486 488 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
487 489 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
488 490 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
489 491 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
490 492 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
491 493 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
492 494 2.399580 ACCATGTCCCTAGTAAGCCTC 58.600 52.381 0.00 0.00 0.00 4.70
493 495 2.570386 ACCATGTCCCTAGTAAGCCT 57.430 50.000 0.00 0.00 0.00 4.58
494 496 4.102681 ACAATACCATGTCCCTAGTAAGCC 59.897 45.833 0.00 0.00 0.00 4.35
495 497 5.291905 ACAATACCATGTCCCTAGTAAGC 57.708 43.478 0.00 0.00 0.00 3.09
502 504 8.140082 TGGATACATAGACAATACCATGTCCCT 61.140 40.741 3.95 0.00 46.44 4.20
503 505 6.013725 TGGATACATAGACAATACCATGTCCC 60.014 42.308 3.95 0.00 46.44 4.46
504 506 7.004555 TGGATACATAGACAATACCATGTCC 57.995 40.000 3.95 0.00 46.44 4.02
522 524 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
523 525 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
524 526 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
525 527 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
526 528 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
527 529 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
528 530 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
529 531 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
530 532 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
531 533 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
539 541 9.547753 GCTAGAATTGTATTGATAGGAAACTCA 57.452 33.333 0.00 0.00 43.67 3.41
540 542 9.547753 TGCTAGAATTGTATTGATAGGAAACTC 57.452 33.333 0.00 0.00 43.67 3.01
543 545 9.288576 CCATGCTAGAATTGTATTGATAGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
544 546 8.659527 TCCATGCTAGAATTGTATTGATAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
545 547 8.206126 TCCATGCTAGAATTGTATTGATAGGA 57.794 34.615 0.00 0.00 0.00 2.94
624 626 4.392940 CTGTTGGAAATATGCCCTAGAGG 58.607 47.826 0.00 0.00 39.47 3.69
625 627 3.817647 GCTGTTGGAAATATGCCCTAGAG 59.182 47.826 0.00 0.00 0.00 2.43
626 628 3.459598 AGCTGTTGGAAATATGCCCTAGA 59.540 43.478 0.00 0.00 0.00 2.43
627 629 3.825328 AGCTGTTGGAAATATGCCCTAG 58.175 45.455 0.00 0.00 0.00 3.02
628 630 3.951563 AGCTGTTGGAAATATGCCCTA 57.048 42.857 0.00 0.00 0.00 3.53
629 631 2.834638 AGCTGTTGGAAATATGCCCT 57.165 45.000 0.00 0.00 0.00 5.19
630 632 3.287222 TGTAGCTGTTGGAAATATGCCC 58.713 45.455 0.00 0.00 0.00 5.36
631 633 4.823989 AGATGTAGCTGTTGGAAATATGCC 59.176 41.667 0.00 0.00 0.00 4.40
632 634 5.755813 CAGATGTAGCTGTTGGAAATATGC 58.244 41.667 0.00 0.00 0.00 3.14
633 635 5.530171 AGCAGATGTAGCTGTTGGAAATATG 59.470 40.000 0.00 0.00 41.61 1.78
634 636 5.688807 AGCAGATGTAGCTGTTGGAAATAT 58.311 37.500 0.00 0.00 41.61 1.28
635 637 5.102953 AGCAGATGTAGCTGTTGGAAATA 57.897 39.130 0.00 0.00 41.61 1.40
636 638 3.960571 AGCAGATGTAGCTGTTGGAAAT 58.039 40.909 0.00 0.00 41.61 2.17
637 639 3.423539 AGCAGATGTAGCTGTTGGAAA 57.576 42.857 0.00 0.00 41.61 3.13
638 640 3.076621 CAAGCAGATGTAGCTGTTGGAA 58.923 45.455 0.00 0.00 42.53 3.53
639 641 2.038952 ACAAGCAGATGTAGCTGTTGGA 59.961 45.455 0.00 0.00 42.53 3.53
640 642 2.417933 GACAAGCAGATGTAGCTGTTGG 59.582 50.000 0.00 3.17 42.53 3.77
641 643 3.332919 AGACAAGCAGATGTAGCTGTTG 58.667 45.455 0.00 5.31 42.53 3.33
642 644 3.692257 AGACAAGCAGATGTAGCTGTT 57.308 42.857 0.00 0.00 42.53 3.16
894 964 0.673437 AACCCATGTGCAAAAGACCG 59.327 50.000 0.00 0.00 0.00 4.79
1062 1142 8.246180 TCAAAACAGAAGCATTTGATATCCTTC 58.754 33.333 0.00 5.53 37.95 3.46
1134 1214 3.609475 CGAGTACTGCTCTACGATTGAC 58.391 50.000 0.00 0.00 41.98 3.18
1159 1239 5.528043 ACATGTGCAACTTCCAAATAACA 57.472 34.783 0.00 0.00 38.04 2.41
1387 1470 8.277018 GCGAAGATAATCATCATCATCATCATC 58.723 37.037 0.00 0.00 33.21 2.92
1388 1471 7.769044 TGCGAAGATAATCATCATCATCATCAT 59.231 33.333 0.00 0.00 33.21 2.45
1389 1472 7.101054 TGCGAAGATAATCATCATCATCATCA 58.899 34.615 0.00 0.00 33.21 3.07
1390 1473 7.535489 TGCGAAGATAATCATCATCATCATC 57.465 36.000 0.00 0.00 33.21 2.92
1391 1474 7.148289 GGTTGCGAAGATAATCATCATCATCAT 60.148 37.037 0.00 0.00 33.21 2.45
1392 1475 6.148315 GGTTGCGAAGATAATCATCATCATCA 59.852 38.462 0.00 0.00 33.21 3.07
1393 1476 6.402983 GGGTTGCGAAGATAATCATCATCATC 60.403 42.308 0.00 0.00 33.21 2.92
1394 1477 5.413833 GGGTTGCGAAGATAATCATCATCAT 59.586 40.000 0.00 0.00 33.21 2.45
1395 1478 4.756642 GGGTTGCGAAGATAATCATCATCA 59.243 41.667 0.00 0.00 33.21 3.07
1396 1479 4.756642 TGGGTTGCGAAGATAATCATCATC 59.243 41.667 0.00 0.00 33.21 2.92
1397 1480 4.717877 TGGGTTGCGAAGATAATCATCAT 58.282 39.130 0.00 0.00 33.21 2.45
1398 1481 4.129380 CTGGGTTGCGAAGATAATCATCA 58.871 43.478 0.00 0.00 33.21 3.07
1424 1525 3.489355 ACACCAACATGCTCATTCTCAA 58.511 40.909 0.00 0.00 0.00 3.02
1518 1619 6.611613 TGATCAGGAACATAGTCTTTGTCT 57.388 37.500 0.00 0.00 0.00 3.41
1556 1669 0.319727 CATGCTCTCATCCTCGCTCC 60.320 60.000 0.00 0.00 0.00 4.70
1809 1994 5.426509 TGTAGAAGCATATATCCTCCATGGG 59.573 44.000 13.02 2.26 36.20 4.00
1890 2075 9.206870 CCAAAAATTAAGCACACATGAGTAAAT 57.793 29.630 0.00 0.00 0.00 1.40
2215 2403 5.957842 TTTGTGCCTTGAAACTATACAGG 57.042 39.130 0.00 0.00 0.00 4.00
2639 2827 4.792068 TCTTCTTGAAGTTGGACACCAAT 58.208 39.130 6.50 0.00 45.80 3.16


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

AutoCloner maintained by Alex Coulton.