Multiple sequence alignment - TraesCS2B01G147400

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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 TraesCS2B01G147400 chr2B 100.000 4207 0 0 1 4207 113328919 113324713 0.000000e+00 7769.0
1 TraesCS2B01G147400 chr2B 97.297 37 0 1 666 702 113328211 113328176 1.260000e-05 62.1
2 TraesCS2B01G147400 chr2B 97.297 37 0 1 709 744 113328254 113328218 1.260000e-05 62.1
3 TraesCS2B01G147400 chr2D 96.667 1620 29 11 1837 3445 74280699 74279094 0.000000e+00 2669.0
4 TraesCS2B01G147400 chr2D 96.239 904 24 8 944 1843 74281993 74281096 0.000000e+00 1472.0
5 TraesCS2B01G147400 chr2D 85.714 770 110 0 3438 4207 155219238 155220007 0.000000e+00 813.0
6 TraesCS2B01G147400 chr2D 88.326 651 67 6 1 649 74283912 74283269 0.000000e+00 773.0
7 TraesCS2B01G147400 chr3B 91.806 1318 66 13 2058 3355 114144818 114143523 0.000000e+00 1797.0
8 TraesCS2B01G147400 chr3B 92.045 880 54 8 953 1824 114145938 114145067 0.000000e+00 1223.0
9 TraesCS2B01G147400 chr3B 86.753 770 102 0 3438 4207 16844839 16844070 0.000000e+00 857.0
10 TraesCS2B01G147400 chr3B 90.741 108 5 5 3341 3445 114142515 114142410 5.670000e-29 139.0
11 TraesCS2B01G147400 chr3D 88.872 1330 78 23 2054 3355 67711664 67712951 0.000000e+00 1572.0
12 TraesCS2B01G147400 chr3D 91.516 884 55 12 953 1824 67710422 67711297 0.000000e+00 1199.0
13 TraesCS2B01G147400 chr3D 92.784 97 4 2 3342 3437 67713963 67714057 2.040000e-28 137.0
14 TraesCS2B01G147400 chr3A 88.337 1329 81 25 2058 3355 79401536 79402821 0.000000e+00 1528.0
15 TraesCS2B01G147400 chr3A 87.461 638 38 20 821 1419 79400285 79400919 0.000000e+00 697.0
16 TraesCS2B01G147400 chr3A 90.576 382 23 6 1443 1824 79400901 79401269 1.050000e-135 494.0
17 TraesCS2B01G147400 chr3A 78.649 459 63 17 2424 2876 585936700 585936271 5.360000e-69 272.0
18 TraesCS2B01G147400 chr3A 89.583 96 6 3 3343 3437 79403844 79403936 7.390000e-23 119.0
19 TraesCS2B01G147400 chr2A 96.571 904 23 7 944 1843 73557076 73556177 0.000000e+00 1491.0
20 TraesCS2B01G147400 chr2A 96.812 690 20 1 1837 2524 73555924 73555235 0.000000e+00 1151.0
21 TraesCS2B01G147400 chr2A 93.003 686 35 7 2683 3355 73555071 73554386 0.000000e+00 989.0
22 TraesCS2B01G147400 chr2A 86.957 575 73 2 77 649 73558923 73558349 0.000000e+00 645.0
23 TraesCS2B01G147400 chr2A 80.531 678 84 32 2294 2960 383426662 383426022 1.060000e-130 477.0
24 TraesCS2B01G147400 chr2A 90.795 239 19 3 700 936 73557625 73557388 2.440000e-82 316.0
25 TraesCS2B01G147400 chr1B 96.128 594 21 2 3615 4207 328321573 328320981 0.000000e+00 968.0
26 TraesCS2B01G147400 chr1B 85.733 771 107 3 3438 4207 422361563 422360795 0.000000e+00 811.0
27 TraesCS2B01G147400 chr7A 88.052 770 91 1 3438 4207 317901099 317900331 0.000000e+00 911.0
28 TraesCS2B01G147400 chr5D 87.922 770 93 0 3438 4207 6757713 6758482 0.000000e+00 907.0
29 TraesCS2B01G147400 chrUn 87.013 770 99 1 3438 4207 39214482 39213714 0.000000e+00 867.0
30 TraesCS2B01G147400 chrUn 87.013 770 99 1 3438 4207 318357195 318356427 0.000000e+00 867.0
31 TraesCS2B01G147400 chrUn 100.000 52 0 0 1999 2050 45102552 45102501 3.460000e-16 97.1
32 TraesCS2B01G147400 chrUn 100.000 52 0 0 1999 2050 86503864 86503915 3.460000e-16 97.1
33 TraesCS2B01G147400 chrUn 100.000 52 0 0 1999 2050 171018759 171018708 3.460000e-16 97.1
34 TraesCS2B01G147400 chrUn 100.000 52 0 0 1999 2050 186165539 186165488 3.460000e-16 97.1
35 TraesCS2B01G147400 chrUn 100.000 52 0 0 1999 2050 341859544 341859493 3.460000e-16 97.1
36 TraesCS2B01G147400 chrUn 100.000 52 0 0 1999 2050 425818309 425818258 3.460000e-16 97.1
37 TraesCS2B01G147400 chr5A 86.658 772 100 2 3438 4207 11554305 11555075 0.000000e+00 852.0
38 TraesCS2B01G147400 chr6B 79.699 798 126 27 2168 2957 116891589 116892358 1.030000e-150 544.0
39 TraesCS2B01G147400 chr6B 83.855 415 58 8 2168 2580 28008629 28009036 1.830000e-103 387.0
40 TraesCS2B01G147400 chr4A 75.000 568 88 35 2418 2964 151642121 151642655 3.290000e-51 213.0
41 TraesCS2B01G147400 chr4D 100.000 52 0 0 1999 2050 6637549 6637600 3.460000e-16 97.1


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 TraesCS2B01G147400 chr2B 113324713 113328919 4206 True 2631.066667 7769 98.198000 1 4207 3 chr2B.!!$R1 4206
1 TraesCS2B01G147400 chr2D 74279094 74283912 4818 True 1638.000000 2669 93.744000 1 3445 3 chr2D.!!$R1 3444
2 TraesCS2B01G147400 chr2D 155219238 155220007 769 False 813.000000 813 85.714000 3438 4207 1 chr2D.!!$F1 769
3 TraesCS2B01G147400 chr3B 114142410 114145938 3528 True 1053.000000 1797 91.530667 953 3445 3 chr3B.!!$R2 2492
4 TraesCS2B01G147400 chr3B 16844070 16844839 769 True 857.000000 857 86.753000 3438 4207 1 chr3B.!!$R1 769
5 TraesCS2B01G147400 chr3D 67710422 67714057 3635 False 969.333333 1572 91.057333 953 3437 3 chr3D.!!$F1 2484
6 TraesCS2B01G147400 chr3A 79400285 79403936 3651 False 709.500000 1528 88.989250 821 3437 4 chr3A.!!$F1 2616
7 TraesCS2B01G147400 chr2A 73554386 73558923 4537 True 918.400000 1491 92.827600 77 3355 5 chr2A.!!$R2 3278
8 TraesCS2B01G147400 chr2A 383426022 383426662 640 True 477.000000 477 80.531000 2294 2960 1 chr2A.!!$R1 666
9 TraesCS2B01G147400 chr1B 328320981 328321573 592 True 968.000000 968 96.128000 3615 4207 1 chr1B.!!$R1 592
10 TraesCS2B01G147400 chr1B 422360795 422361563 768 True 811.000000 811 85.733000 3438 4207 1 chr1B.!!$R2 769
11 TraesCS2B01G147400 chr7A 317900331 317901099 768 True 911.000000 911 88.052000 3438 4207 1 chr7A.!!$R1 769
12 TraesCS2B01G147400 chr5D 6757713 6758482 769 False 907.000000 907 87.922000 3438 4207 1 chr5D.!!$F1 769
13 TraesCS2B01G147400 chrUn 39213714 39214482 768 True 867.000000 867 87.013000 3438 4207 1 chrUn.!!$R1 769
14 TraesCS2B01G147400 chrUn 318356427 318357195 768 True 867.000000 867 87.013000 3438 4207 1 chrUn.!!$R5 769
15 TraesCS2B01G147400 chr5A 11554305 11555075 770 False 852.000000 852 86.658000 3438 4207 1 chr5A.!!$F1 769
16 TraesCS2B01G147400 chr6B 116891589 116892358 769 False 544.000000 544 79.699000 2168 2957 1 chr6B.!!$F2 789
17 TraesCS2B01G147400 chr4A 151642121 151642655 534 False 213.000000 213 75.000000 2418 2964 1 chr4A.!!$F1 546

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
570 574 0.034283 TGCCACCTTAGATGCATGCA 60.034 50.0 25.04 25.04 0.00 3.96 F
679 683 0.249073 GATGACGGAGGATGGTGTCG 60.249 60.0 0.00 0.00 34.11 4.35 F
682 686 0.736325 GACGGAGGATGGTGTCGTTG 60.736 60.0 0.00 0.00 34.06 4.10 F
1333 2350 1.021202 CCACTGGTGCTTTTCGTGAA 58.979 50.0 0.00 0.00 0.00 3.18 F
2887 4541 0.987294 AGTGGCATGCCTAGTTCACT 59.013 50.0 35.53 25.82 36.94 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 2438 1.141234 GTACAGTAGTGCCCCGAGC 59.859 63.158 0.00 0.00 44.14 5.03 R
1927 3376 2.041081 TGGTGGTATGGTTTGCTAAGCT 59.959 45.455 11.21 0.52 32.98 3.74 R
1928 3377 2.442413 TGGTGGTATGGTTTGCTAAGC 58.558 47.619 3.02 3.02 0.00 3.09 R
2995 4660 0.687354 AGAGTGGAAGACCGTGCATT 59.313 50.000 0.00 0.00 39.42 3.56 R
3816 6597 9.955208 AATTGCCAAAAGAAAATCTTGATTTTC 57.045 25.926 27.87 27.87 45.81 2.29 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
33 34 2.361610 ATGACTTGGGCCCTTGCG 60.362 61.111 25.70 10.93 38.85 4.85
42 43 2.409870 GGCCCTTGCGGTCAATCTG 61.410 63.158 0.00 0.00 35.67 2.90
51 52 0.742281 CGGTCAATCTGCCACTCCTG 60.742 60.000 0.00 0.00 0.00 3.86
56 57 0.323178 AATCTGCCACTCCTGCTTGG 60.323 55.000 0.00 0.00 35.81 3.61
101 102 2.916702 TCTTCCGATCCATCACCATG 57.083 50.000 0.00 0.00 0.00 3.66
122 123 6.379703 CCATGGTTTCTATGGGTAATGTTCAA 59.620 38.462 2.57 0.00 41.11 2.69
130 131 4.396357 TGGGTAATGTTCAATCCACCTT 57.604 40.909 0.00 0.00 0.00 3.50
132 133 3.377172 GGGTAATGTTCAATCCACCTTCG 59.623 47.826 0.00 0.00 0.00 3.79
139 140 0.613260 CAATCCACCTTCGTCTGGGA 59.387 55.000 0.00 0.00 0.00 4.37
169 171 2.039348 GGCTACCCAACTCCACTAACAA 59.961 50.000 0.00 0.00 0.00 2.83
170 172 3.308188 GGCTACCCAACTCCACTAACAAT 60.308 47.826 0.00 0.00 0.00 2.71
176 178 3.560025 CCAACTCCACTAACAATCTGGCT 60.560 47.826 0.00 0.00 0.00 4.75
181 183 3.072330 TCCACTAACAATCTGGCTGTTCA 59.928 43.478 0.00 0.00 38.05 3.18
189 191 2.673775 TCTGGCTGTTCATTTCCCAA 57.326 45.000 0.00 0.00 0.00 4.12
193 195 1.337118 GCTGTTCATTTCCCAACCCA 58.663 50.000 0.00 0.00 0.00 4.51
205 207 2.983192 TCCCAACCCATTTCTCACACTA 59.017 45.455 0.00 0.00 0.00 2.74
208 210 4.335416 CCAACCCATTTCTCACACTACAT 58.665 43.478 0.00 0.00 0.00 2.29
239 242 0.395311 CCTCTGTGGCTCGGGTACTA 60.395 60.000 0.00 0.00 0.00 1.82
243 246 1.035932 TGTGGCTCGGGTACTAGCTC 61.036 60.000 12.80 8.61 37.44 4.09
247 250 1.272037 GGCTCGGGTACTAGCTCCTAT 60.272 57.143 12.80 0.00 37.44 2.57
249 252 2.552591 GCTCGGGTACTAGCTCCTATGA 60.553 54.545 0.00 0.00 35.16 2.15
274 277 6.681729 ACTTAACCTAGACCTCACAAATCA 57.318 37.500 0.00 0.00 0.00 2.57
284 287 7.856145 AGACCTCACAAATCAATTATCTCAC 57.144 36.000 0.00 0.00 0.00 3.51
289 292 3.242739 ACAAATCAATTATCTCACGCGGC 60.243 43.478 12.47 0.00 0.00 6.53
319 322 1.376609 CTGGGGGAATTGCGTGCTAC 61.377 60.000 0.00 0.00 0.00 3.58
353 356 9.979578 ACAATTAACTTGAATTTGCAGATACAA 57.020 25.926 0.00 0.00 38.29 2.41
358 361 7.275888 ACTTGAATTTGCAGATACAAGACAA 57.724 32.000 22.61 9.57 38.30 3.18
370 373 2.787994 ACAAGACAAGAGGATTGGCAG 58.212 47.619 0.00 0.00 0.00 4.85
380 383 1.566298 GGATTGGCAGACAGGGAGGT 61.566 60.000 0.00 0.00 0.00 3.85
411 414 2.495669 ACAACCAAAATGGCCTATTCGG 59.504 45.455 3.32 9.08 42.67 4.30
425 428 1.369091 ATTCGGTGCTTTGGCTAGCG 61.369 55.000 9.00 0.00 44.18 4.26
471 474 3.631250 ACCATTTGGAGGAATTATGCGT 58.369 40.909 3.01 0.00 38.94 5.24
473 476 3.631686 CCATTTGGAGGAATTATGCGTCA 59.368 43.478 0.00 0.00 37.39 4.35
486 489 7.487829 GGAATTATGCGTCAAATAAAAGCAGAA 59.512 33.333 0.00 0.00 42.02 3.02
504 508 4.612033 GCAGAATTTTCATTTGGCTTGCAC 60.612 41.667 0.00 0.00 0.00 4.57
518 522 1.436195 TTGCACGCAAGGACTGTGTC 61.436 55.000 0.00 0.00 45.91 3.67
551 555 1.482593 AGACGCTTCCGGAGATCAATT 59.517 47.619 3.34 0.00 39.22 2.32
559 563 1.683011 CCGGAGATCAATTGCCACCTT 60.683 52.381 0.00 0.00 0.00 3.50
565 569 3.887716 AGATCAATTGCCACCTTAGATGC 59.112 43.478 0.00 0.00 0.00 3.91
566 570 3.084536 TCAATTGCCACCTTAGATGCA 57.915 42.857 0.00 0.00 0.00 3.96
568 572 3.382227 TCAATTGCCACCTTAGATGCATG 59.618 43.478 2.46 0.00 33.08 4.06
570 574 0.034283 TGCCACCTTAGATGCATGCA 60.034 50.000 25.04 25.04 0.00 3.96
609 613 4.327627 GCGAAAGTATCACTCACCTTCTTC 59.672 45.833 0.00 0.00 0.00 2.87
614 618 6.279513 AGTATCACTCACCTTCTTCTTCAG 57.720 41.667 0.00 0.00 0.00 3.02
618 622 2.703007 ACTCACCTTCTTCTTCAGTGCT 59.297 45.455 0.00 0.00 0.00 4.40
621 625 3.641436 TCACCTTCTTCTTCAGTGCTACA 59.359 43.478 0.00 0.00 0.00 2.74
623 627 4.391216 CACCTTCTTCTTCAGTGCTACATG 59.609 45.833 0.00 0.00 0.00 3.21
635 639 4.627467 CAGTGCTACATGTTGTTACCTCTC 59.373 45.833 2.30 0.00 0.00 3.20
649 653 1.364328 ACCTCTCTGGGATGAACTCCT 59.636 52.381 0.00 0.00 44.28 3.69
650 654 2.225753 ACCTCTCTGGGATGAACTCCTT 60.226 50.000 0.00 0.00 44.28 3.36
651 655 2.433970 CCTCTCTGGGATGAACTCCTTC 59.566 54.545 0.00 0.00 44.28 3.46
654 658 0.807667 CTGGGATGAACTCCTTCGCG 60.808 60.000 0.00 0.00 44.28 5.87
655 659 1.521681 GGGATGAACTCCTTCGCGG 60.522 63.158 6.13 0.00 44.28 6.46
656 660 2.174319 GGATGAACTCCTTCGCGGC 61.174 63.158 6.13 0.00 41.29 6.53
658 662 2.579684 GATGAACTCCTTCGCGGCCT 62.580 60.000 6.13 0.00 0.00 5.19
659 663 2.509561 GAACTCCTTCGCGGCCTC 60.510 66.667 6.13 0.00 0.00 4.70
664 668 4.207281 CCTTCGCGGCCTCGATGA 62.207 66.667 27.07 10.59 38.37 2.92
665 669 2.956964 CTTCGCGGCCTCGATGAC 60.957 66.667 22.57 0.00 38.37 3.06
666 670 4.847516 TTCGCGGCCTCGATGACG 62.848 66.667 20.06 11.97 38.37 4.35
669 673 4.933064 GCGGCCTCGATGACGGAG 62.933 72.222 17.83 0.00 40.21 4.63
670 674 4.271816 CGGCCTCGATGACGGAGG 62.272 72.222 8.21 3.49 40.21 4.30
672 676 2.203771 GGCCTCGATGACGGAGGAT 61.204 63.158 11.83 0.00 38.28 3.24
673 677 1.006805 GCCTCGATGACGGAGGATG 60.007 63.158 11.83 0.00 38.28 3.51
674 678 1.662608 CCTCGATGACGGAGGATGG 59.337 63.158 1.59 0.00 38.28 3.51
675 679 1.109920 CCTCGATGACGGAGGATGGT 61.110 60.000 1.59 0.00 38.28 3.55
679 683 0.249073 GATGACGGAGGATGGTGTCG 60.249 60.000 0.00 0.00 34.11 4.35
680 684 0.970937 ATGACGGAGGATGGTGTCGT 60.971 55.000 0.00 0.00 36.74 4.34
681 685 1.183030 TGACGGAGGATGGTGTCGTT 61.183 55.000 0.00 0.00 34.06 3.85
682 686 0.736325 GACGGAGGATGGTGTCGTTG 60.736 60.000 0.00 0.00 34.06 4.10
684 688 1.745489 GGAGGATGGTGTCGTTGGC 60.745 63.158 0.00 0.00 0.00 4.52
685 689 2.047274 AGGATGGTGTCGTTGGCG 60.047 61.111 0.00 0.00 39.92 5.69
686 690 2.047655 GGATGGTGTCGTTGGCGA 60.048 61.111 0.00 0.00 45.79 5.54
743 1423 3.554692 GCGAGATGGCAACCGTCG 61.555 66.667 0.00 0.00 43.76 5.12
778 1458 3.467374 AAGAATGATCTTCTCCCGCTC 57.533 47.619 7.57 0.00 42.26 5.03
779 1459 1.691434 AGAATGATCTTCTCCCGCTCC 59.309 52.381 0.00 0.00 29.15 4.70
785 1465 2.994995 TTCTCCCGCTCCGCTTCA 60.995 61.111 0.00 0.00 0.00 3.02
793 1473 1.150567 CGCTCCGCTTCATCTCCTTG 61.151 60.000 0.00 0.00 0.00 3.61
802 1482 4.499696 CGCTTCATCTCCTTGGTTTTTGTT 60.500 41.667 0.00 0.00 0.00 2.83
807 1488 2.116366 CTCCTTGGTTTTTGTTTCGCG 58.884 47.619 0.00 0.00 0.00 5.87
947 1663 2.154798 TTGTCAGCCTCCTCGTTCCG 62.155 60.000 0.00 0.00 0.00 4.30
948 1664 2.035155 TCAGCCTCCTCGTTCCGA 59.965 61.111 0.00 0.00 0.00 4.55
950 1666 1.066587 CAGCCTCCTCGTTCCGATC 59.933 63.158 0.00 0.00 34.61 3.69
951 1667 1.076632 AGCCTCCTCGTTCCGATCT 60.077 57.895 0.00 0.00 34.61 2.75
966 1978 1.535028 CGATCTCTGTCCCGATCTCTG 59.465 57.143 0.00 0.00 35.13 3.35
998 2012 3.812019 GCTCGTTCGAGGCTCGGA 61.812 66.667 33.93 25.95 40.88 4.55
1251 2265 3.706373 CAGTACAGGTGCGCCCCT 61.706 66.667 14.07 5.25 34.57 4.79
1258 2272 3.394836 GGTGCGCCCCTCTCTCTT 61.395 66.667 4.45 0.00 0.00 2.85
1319 2336 3.339253 TCCATGAGATGTGTTCCACTG 57.661 47.619 0.00 0.00 35.11 3.66
1333 2350 1.021202 CCACTGGTGCTTTTCGTGAA 58.979 50.000 0.00 0.00 0.00 3.18
1418 2435 5.460091 GCTCTGTTTCAGTTGTTTTTGATCC 59.540 40.000 0.00 0.00 32.61 3.36
1421 2438 4.048504 GTTTCAGTTGTTTTTGATCCGGG 58.951 43.478 0.00 0.00 0.00 5.73
1496 2520 1.809271 CGTTCTGATCCATGGAGCCAG 60.809 57.143 28.19 28.19 33.22 4.85
1527 2551 3.820467 TGTCCACCAATTGTCTGATGTTC 59.180 43.478 4.43 0.00 0.00 3.18
1828 2853 9.270640 ACTAAGTGTCTAACTATACATACTCCG 57.729 37.037 0.00 0.00 38.56 4.63
1843 3272 7.375106 ACATACTCCGTCCGTAAAGATATAG 57.625 40.000 0.00 0.00 0.00 1.31
1926 3375 9.719355 ACCATTTCAAAATAAACAAGATAACCC 57.281 29.630 0.00 0.00 0.00 4.11
1927 3376 9.717942 CCATTTCAAAATAAACAAGATAACCCA 57.282 29.630 0.00 0.00 0.00 4.51
1930 3379 7.775053 TCAAAATAAACAAGATAACCCAGCT 57.225 32.000 0.00 0.00 0.00 4.24
1931 3380 8.189119 TCAAAATAAACAAGATAACCCAGCTT 57.811 30.769 0.00 0.00 31.44 3.74
1932 3381 9.303116 TCAAAATAAACAAGATAACCCAGCTTA 57.697 29.630 0.00 0.00 29.80 3.09
1933 3382 9.573133 CAAAATAAACAAGATAACCCAGCTTAG 57.427 33.333 0.00 0.00 29.80 2.18
1934 3383 6.944234 ATAAACAAGATAACCCAGCTTAGC 57.056 37.500 0.00 0.00 29.80 3.09
1935 3384 4.301072 AACAAGATAACCCAGCTTAGCA 57.699 40.909 7.07 0.00 29.80 3.49
1936 3385 4.301072 ACAAGATAACCCAGCTTAGCAA 57.699 40.909 7.07 0.00 29.80 3.91
1937 3386 4.662278 ACAAGATAACCCAGCTTAGCAAA 58.338 39.130 7.07 0.00 29.80 3.68
1938 3387 4.459337 ACAAGATAACCCAGCTTAGCAAAC 59.541 41.667 7.07 0.00 29.80 2.93
1939 3388 3.621558 AGATAACCCAGCTTAGCAAACC 58.378 45.455 7.07 0.00 0.00 3.27
1940 3389 2.961531 TAACCCAGCTTAGCAAACCA 57.038 45.000 7.07 0.00 0.00 3.67
1941 3390 2.309136 AACCCAGCTTAGCAAACCAT 57.691 45.000 7.07 0.00 0.00 3.55
1942 3391 3.449746 AACCCAGCTTAGCAAACCATA 57.550 42.857 7.07 0.00 0.00 2.74
1943 3392 2.723273 ACCCAGCTTAGCAAACCATAC 58.277 47.619 7.07 0.00 0.00 2.39
1967 3426 7.872138 ACCACCATGATATTTTTCCTCTTCTA 58.128 34.615 0.00 0.00 0.00 2.10
2183 3758 4.584327 ATGCTGTTTAACTGTTTCCCAC 57.416 40.909 0.00 0.00 0.00 4.61
2450 4026 5.546499 AGGGACTTATGTTGGTCTACAGAAA 59.454 40.000 0.00 0.00 27.25 2.52
2820 4470 4.403113 TGTTTGCCTTGCATCATATGACAT 59.597 37.500 7.78 0.00 38.76 3.06
2887 4541 0.987294 AGTGGCATGCCTAGTTCACT 59.013 50.000 35.53 25.82 36.94 3.41
2995 4660 6.364165 GTGAGCACACGTAATCTTTAAGTGTA 59.636 38.462 15.26 2.19 43.21 2.90
3179 4844 2.297701 GTTGTCTCCCAGCTTGAAACA 58.702 47.619 0.00 0.00 0.00 2.83
3377 6154 9.727627 TTTGCGAAAATTTAAGCAATTTGAAAT 57.272 22.222 24.39 0.00 46.92 2.17
3387 6164 9.903682 TTTAAGCAATTTGAAATGAAGAGAGAG 57.096 29.630 0.00 0.00 0.00 3.20
3455 6232 2.440247 CATGGGGGCGAAGTTCCC 60.440 66.667 0.00 0.00 43.15 3.97
3459 6236 3.393106 GGGGCGAAGTTCCCGGTA 61.393 66.667 0.00 0.00 44.86 4.02
3543 6320 3.303791 CCCGTTTCAGACAGCTGTTTAAC 60.304 47.826 22.65 19.17 42.84 2.01
3558 6337 3.067461 TGTTTAACATTGCGCTTGAACCT 59.933 39.130 9.73 0.00 0.00 3.50
3589 6368 4.766088 CGCAAGCTTTGGCCGAGC 62.766 66.667 20.13 20.13 39.73 5.03
3760 6540 0.747852 CTCCCTTTACCGAGCTCTCC 59.252 60.000 12.85 0.00 0.00 3.71
3810 6590 2.486796 GCTTTGGAAGGCTAGGCTG 58.513 57.895 20.99 7.15 0.00 4.85
3983 6764 1.603455 CCCGGTTTGCATGGAGTGT 60.603 57.895 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.356535 GCCCAAGTCATGAACCAGAGAT 60.357 50.000 0.00 0.00 0.00 2.75
10 11 1.076549 GGGCCCAAGTCATGAACCA 59.923 57.895 19.95 0.00 0.00 3.67
11 12 0.251787 AAGGGCCCAAGTCATGAACC 60.252 55.000 27.56 0.00 0.00 3.62
33 34 1.028868 GCAGGAGTGGCAGATTGACC 61.029 60.000 0.00 0.00 0.00 4.02
51 52 0.316841 TTGAAAATGTCCCGCCAAGC 59.683 50.000 0.00 0.00 0.00 4.01
56 57 0.389817 GGCCTTTGAAAATGTCCCGC 60.390 55.000 0.00 0.00 0.00 6.13
101 102 6.605594 TGGATTGAACATTACCCATAGAAACC 59.394 38.462 0.00 0.00 0.00 3.27
108 109 4.608170 AGGTGGATTGAACATTACCCAT 57.392 40.909 0.00 0.00 0.00 4.00
118 119 1.003118 CCCAGACGAAGGTGGATTGAA 59.997 52.381 0.00 0.00 37.89 2.69
122 123 2.287829 GTCCCAGACGAAGGTGGAT 58.712 57.895 0.00 0.00 37.89 3.41
132 133 1.671379 GCCAAAGGTCGTCCCAGAC 60.671 63.158 0.00 0.00 40.25 3.51
139 140 0.250597 GTTGGGTAGCCAAAGGTCGT 60.251 55.000 27.24 0.00 0.00 4.34
141 142 1.613520 GGAGTTGGGTAGCCAAAGGTC 60.614 57.143 27.24 21.55 0.00 3.85
169 171 2.827921 GTTGGGAAATGAACAGCCAGAT 59.172 45.455 0.00 0.00 0.00 2.90
170 172 2.238521 GTTGGGAAATGAACAGCCAGA 58.761 47.619 0.00 0.00 0.00 3.86
176 178 4.230455 AGAAATGGGTTGGGAAATGAACA 58.770 39.130 0.00 0.00 0.00 3.18
181 183 3.578282 GTGTGAGAAATGGGTTGGGAAAT 59.422 43.478 0.00 0.00 0.00 2.17
189 191 3.347216 GCATGTAGTGTGAGAAATGGGT 58.653 45.455 0.00 0.00 0.00 4.51
193 195 3.334583 ACCGCATGTAGTGTGAGAAAT 57.665 42.857 0.00 0.00 40.86 2.17
236 239 8.060075 TCTAGGTTAAGTTTCATAGGAGCTAGT 58.940 37.037 0.00 0.00 36.01 2.57
239 242 6.098552 GGTCTAGGTTAAGTTTCATAGGAGCT 59.901 42.308 0.00 0.00 0.00 4.09
243 246 7.093465 TGTGAGGTCTAGGTTAAGTTTCATAGG 60.093 40.741 0.00 0.00 0.00 2.57
247 250 6.488769 TTGTGAGGTCTAGGTTAAGTTTCA 57.511 37.500 0.00 0.00 0.00 2.69
249 252 7.514721 TGATTTGTGAGGTCTAGGTTAAGTTT 58.485 34.615 0.00 0.00 0.00 2.66
274 277 1.933853 GTTCAGCCGCGTGAGATAATT 59.066 47.619 4.92 0.00 0.00 1.40
289 292 1.764571 TTCCCCCAGACCACGTTCAG 61.765 60.000 0.00 0.00 0.00 3.02
298 301 2.700773 GCACGCAATTCCCCCAGAC 61.701 63.158 0.00 0.00 0.00 3.51
319 322 7.376601 GCAAATTCAAGTTAATTGTTGCCAAAG 59.623 33.333 7.62 0.00 40.16 2.77
330 333 9.846248 GTCTTGTATCTGCAAATTCAAGTTAAT 57.154 29.630 16.18 0.00 36.20 1.40
353 356 1.980765 TGTCTGCCAATCCTCTTGTCT 59.019 47.619 0.00 0.00 0.00 3.41
358 361 0.252881 TCCCTGTCTGCCAATCCTCT 60.253 55.000 0.00 0.00 0.00 3.69
380 383 5.011227 GGCCATTTTGGTTGTAAGAGGTTTA 59.989 40.000 0.00 0.00 40.46 2.01
411 414 2.482374 CTGCGCTAGCCAAAGCAC 59.518 61.111 9.73 0.00 42.91 4.40
433 436 1.153549 GTAGGAGCGAGCTGGTTGG 60.154 63.158 0.84 0.00 0.00 3.77
435 438 0.978146 ATGGTAGGAGCGAGCTGGTT 60.978 55.000 0.84 0.00 0.00 3.67
473 476 9.070179 AGCCAAATGAAAATTCTGCTTTTATTT 57.930 25.926 0.00 0.00 0.00 1.40
486 489 1.799994 GCGTGCAAGCCAAATGAAAAT 59.200 42.857 14.16 0.00 0.00 1.82
504 508 1.419374 GTGTAGACACAGTCCTTGCG 58.581 55.000 7.93 0.00 45.75 4.85
518 522 2.949451 AGCGTCTCTCATTGGTGTAG 57.051 50.000 0.00 0.00 0.00 2.74
551 555 0.034283 TGCATGCATCTAAGGTGGCA 60.034 50.000 18.46 0.00 41.00 4.92
609 613 4.997395 AGGTAACAACATGTAGCACTGAAG 59.003 41.667 0.00 0.00 41.41 3.02
614 618 4.627467 CAGAGAGGTAACAACATGTAGCAC 59.373 45.833 0.00 0.00 41.41 4.40
618 622 4.422057 TCCCAGAGAGGTAACAACATGTA 58.578 43.478 0.00 0.00 41.41 2.29
621 625 4.104086 TCATCCCAGAGAGGTAACAACAT 58.896 43.478 0.00 0.00 41.41 2.71
623 627 4.020128 AGTTCATCCCAGAGAGGTAACAAC 60.020 45.833 0.00 0.00 41.41 3.32
649 653 4.847516 CGTCATCGAGGCCGCGAA 62.848 66.667 34.86 17.69 44.22 4.70
654 658 2.203771 ATCCTCCGTCATCGAGGCC 61.204 63.158 0.00 0.00 39.71 5.19
655 659 1.006805 CATCCTCCGTCATCGAGGC 60.007 63.158 0.00 0.00 39.71 4.70
656 660 1.109920 ACCATCCTCCGTCATCGAGG 61.110 60.000 0.00 0.00 39.71 4.63
658 662 0.683179 ACACCATCCTCCGTCATCGA 60.683 55.000 0.00 0.00 39.71 3.59
659 663 0.249073 GACACCATCCTCCGTCATCG 60.249 60.000 0.00 0.00 0.00 3.84
664 668 1.292223 CAACGACACCATCCTCCGT 59.708 57.895 0.00 0.00 34.74 4.69
665 669 1.447838 CCAACGACACCATCCTCCG 60.448 63.158 0.00 0.00 0.00 4.63
666 670 1.745489 GCCAACGACACCATCCTCC 60.745 63.158 0.00 0.00 0.00 4.30
668 672 2.047274 CGCCAACGACACCATCCT 60.047 61.111 0.00 0.00 43.93 3.24
669 673 2.047655 TCGCCAACGACACCATCC 60.048 61.111 0.00 0.00 45.12 3.51
670 674 0.460284 ATCTCGCCAACGACACCATC 60.460 55.000 0.00 0.00 45.12 3.51
672 676 1.374125 CATCTCGCCAACGACACCA 60.374 57.895 0.00 0.00 45.12 4.17
673 677 2.100631 CCATCTCGCCAACGACACC 61.101 63.158 0.00 0.00 45.12 4.16
674 678 2.740714 GCCATCTCGCCAACGACAC 61.741 63.158 0.00 0.00 45.12 3.67
675 679 2.434185 GCCATCTCGCCAACGACA 60.434 61.111 0.00 0.00 45.12 4.35
684 688 2.885644 CGACGGTTGGCCATCTCG 60.886 66.667 6.09 13.80 34.09 4.04
685 689 3.195698 GCGACGGTTGGCCATCTC 61.196 66.667 6.09 0.00 34.09 2.75
698 1377 3.210528 ATCCTCCGAGACCGCGAC 61.211 66.667 8.23 0.40 0.00 5.19
705 1384 0.611062 AACGACACCATCCTCCGAGA 60.611 55.000 0.00 0.00 0.00 4.04
709 1388 1.745489 GCCAACGACACCATCCTCC 60.745 63.158 0.00 0.00 0.00 4.30
751 1431 1.221414 GAAGATCATTCTTCGGGGCG 58.779 55.000 0.00 0.00 46.17 6.13
778 1458 1.826385 AAACCAAGGAGATGAAGCGG 58.174 50.000 0.00 0.00 0.00 5.52
779 1459 3.004734 ACAAAAACCAAGGAGATGAAGCG 59.995 43.478 0.00 0.00 0.00 4.68
785 1465 3.550030 CGCGAAACAAAAACCAAGGAGAT 60.550 43.478 0.00 0.00 0.00 2.75
793 1473 2.719046 CACTGATCGCGAAACAAAAACC 59.281 45.455 15.24 0.00 0.00 3.27
807 1488 2.583593 GAGACGGCGCCACTGATC 60.584 66.667 28.98 14.88 0.00 2.92
928 1623 1.671742 GGAACGAGGAGGCTGACAA 59.328 57.895 0.00 0.00 0.00 3.18
947 1663 2.552315 GACAGAGATCGGGACAGAGATC 59.448 54.545 0.00 0.00 42.52 2.75
948 1664 2.174639 AGACAGAGATCGGGACAGAGAT 59.825 50.000 0.00 0.00 0.00 2.75
950 1666 1.946768 GAGACAGAGATCGGGACAGAG 59.053 57.143 0.00 0.00 0.00 3.35
951 1667 1.562008 AGAGACAGAGATCGGGACAGA 59.438 52.381 0.00 0.00 0.00 3.41
966 1978 3.783588 GAGCGAGCGAGCGAGAGAC 62.784 68.421 1.41 0.00 43.00 3.36
998 2012 0.249398 GAAGTGGTAGTCCGCCATGT 59.751 55.000 0.00 0.00 44.61 3.21
1209 2223 1.136984 GAAGCGGTCATCGTCGAGT 59.863 57.895 0.00 0.00 41.72 4.18
1251 2265 1.265454 GGCCGAGGGGAAAAGAGAGA 61.265 60.000 0.00 0.00 34.06 3.10
1319 2336 4.545610 TCAAATCATTCACGAAAAGCACC 58.454 39.130 0.00 0.00 0.00 5.01
1395 2412 5.682862 CGGATCAAAAACAACTGAAACAGAG 59.317 40.000 5.76 1.02 35.18 3.35
1421 2438 1.141234 GTACAGTAGTGCCCCGAGC 59.859 63.158 0.00 0.00 44.14 5.03
1496 2520 5.047092 AGACAATTGGTGGACATGGATTTTC 60.047 40.000 10.83 0.00 0.00 2.29
1527 2551 2.877786 TGTAAGCACACCACAACATCAG 59.122 45.455 0.00 0.00 0.00 2.90
1776 2801 5.747197 ACGAATAAAGTTCTACCTACATGCG 59.253 40.000 0.00 0.00 0.00 4.73
1784 2809 9.631452 ACACTTAGTTACGAATAAAGTTCTACC 57.369 33.333 0.00 0.00 0.00 3.18
1828 2853 8.470040 TTCAACACAACTATATCTTTACGGAC 57.530 34.615 0.00 0.00 0.00 4.79
1843 3272 5.181690 TGCCAGAACTATTTCAACACAAC 57.818 39.130 0.00 0.00 33.72 3.32
1926 3375 2.423538 GGTGGTATGGTTTGCTAAGCTG 59.576 50.000 11.21 0.00 32.98 4.24
1927 3376 2.041081 TGGTGGTATGGTTTGCTAAGCT 59.959 45.455 11.21 0.52 32.98 3.74
1928 3377 2.442413 TGGTGGTATGGTTTGCTAAGC 58.558 47.619 3.02 3.02 0.00 3.09
1930 3379 4.308526 TCATGGTGGTATGGTTTGCTAA 57.691 40.909 0.00 0.00 0.00 3.09
1931 3380 4.518278 ATCATGGTGGTATGGTTTGCTA 57.482 40.909 0.00 0.00 0.00 3.49
1932 3381 2.897271 TCATGGTGGTATGGTTTGCT 57.103 45.000 0.00 0.00 0.00 3.91
1933 3382 5.789643 AATATCATGGTGGTATGGTTTGC 57.210 39.130 0.00 0.00 0.00 3.68
1934 3383 7.710475 GGAAAAATATCATGGTGGTATGGTTTG 59.290 37.037 0.00 0.00 0.00 2.93
1935 3384 7.623278 AGGAAAAATATCATGGTGGTATGGTTT 59.377 33.333 0.00 0.00 0.00 3.27
1936 3385 7.132128 AGGAAAAATATCATGGTGGTATGGTT 58.868 34.615 0.00 0.00 0.00 3.67
1937 3386 6.682537 AGGAAAAATATCATGGTGGTATGGT 58.317 36.000 0.00 0.00 0.00 3.55
1938 3387 7.006509 AGAGGAAAAATATCATGGTGGTATGG 58.993 38.462 0.00 0.00 0.00 2.74
1939 3388 8.469309 AAGAGGAAAAATATCATGGTGGTATG 57.531 34.615 0.00 0.00 0.00 2.39
1940 3389 8.506083 AGAAGAGGAAAAATATCATGGTGGTAT 58.494 33.333 0.00 0.00 0.00 2.73
1941 3390 7.872138 AGAAGAGGAAAAATATCATGGTGGTA 58.128 34.615 0.00 0.00 0.00 3.25
1942 3391 6.735556 AGAAGAGGAAAAATATCATGGTGGT 58.264 36.000 0.00 0.00 0.00 4.16
1943 3392 8.930846 ATAGAAGAGGAAAAATATCATGGTGG 57.069 34.615 0.00 0.00 0.00 4.61
1967 3426 6.034591 CGTGTGGAGTAAATCGAAGTAGAAT 58.965 40.000 0.00 0.00 0.00 2.40
2183 3758 8.668510 AGTCATTTCTGTATTATAAGCACCTG 57.331 34.615 0.00 0.00 0.00 4.00
2450 4026 2.890311 TGTGCATTTCTTTCCACCGAAT 59.110 40.909 0.00 0.00 0.00 3.34
2995 4660 0.687354 AGAGTGGAAGACCGTGCATT 59.313 50.000 0.00 0.00 39.42 3.56
3179 4844 3.303461 CGCTATCATCTTCGTCTTCTCGT 60.303 47.826 0.00 0.00 0.00 4.18
3377 6154 3.887110 TCACGTGGTTTACTCTCTCTTCA 59.113 43.478 17.00 0.00 0.00 3.02
3386 6163 1.944032 ACGCTTTCACGTGGTTTACT 58.056 45.000 17.00 0.00 46.28 2.24
3455 6232 0.107703 TGAGCAGCCATCCTTTACCG 60.108 55.000 0.00 0.00 0.00 4.02
3516 6293 0.534203 GCTGTCTGAAACGGGACCAA 60.534 55.000 0.00 0.00 34.56 3.67
3543 6320 0.592637 TGTGAGGTTCAAGCGCAATG 59.407 50.000 11.47 8.75 0.00 2.82
3558 6337 1.850377 CTTGCGCCACAAAAATGTGA 58.150 45.000 4.18 0.00 42.02 3.58
3816 6597 9.955208 AATTGCCAAAAGAAAATCTTGATTTTC 57.045 25.926 27.87 27.87 45.81 2.29


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

AutoCloner maintained by Alex Coulton.