Multiple sequence alignment - TraesCS3B01G042700

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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 TraesCS3B01G042700 chr3B 100.000 3049 0 0 1 3049 22102538 22099490 0.000000e+00 5631.0
1 TraesCS3B01G042700 chr3B 87.288 1180 105 24 911 2058 22130547 22129381 0.000000e+00 1306.0
2 TraesCS3B01G042700 chr3B 84.830 646 63 22 3 628 499086861 499086231 4.320000e-173 617.0
3 TraesCS3B01G042700 chr3B 92.602 392 25 3 2383 2772 22086490 22086101 7.380000e-156 560.0
4 TraesCS3B01G042700 chr3B 73.515 623 103 31 1298 1881 757456825 757456226 2.420000e-41 180.0
5 TraesCS3B01G042700 chr3B 79.114 158 16 10 1298 1440 757286069 757285914 3.240000e-15 93.5
6 TraesCS3B01G042700 chr3B 85.294 68 4 1 823 890 22130706 22130645 7.060000e-07 65.8
7 TraesCS3B01G042700 chr3D 93.576 1401 67 13 996 2382 14948684 14947293 0.000000e+00 2067.0
8 TraesCS3B01G042700 chr3D 89.002 1182 92 18 911 2058 14998787 14999964 0.000000e+00 1428.0
9 TraesCS3B01G042700 chr3D 88.262 673 50 21 2382 3047 20746869 20747519 0.000000e+00 778.0
10 TraesCS3B01G042700 chr3D 74.548 719 134 28 1303 1987 569976854 569977557 5.010000e-68 268.0
11 TraesCS3B01G042700 chr3A 90.989 1254 88 15 995 2236 21323905 21325145 0.000000e+00 1666.0
12 TraesCS3B01G042700 chr3A 83.761 234 15 13 661 878 21323561 21323787 1.850000e-47 200.0
13 TraesCS3B01G042700 chr5B 96.000 650 12 2 1 636 507628412 507627763 0.000000e+00 1044.0
14 TraesCS3B01G042700 chr5B 95.064 547 12 5 105 637 507634674 507634129 0.000000e+00 846.0
15 TraesCS3B01G042700 chr4B 95.846 650 13 3 1 636 658529936 658530585 0.000000e+00 1038.0
16 TraesCS3B01G042700 chr4B 95.438 548 9 3 105 637 658523467 658524013 0.000000e+00 859.0
17 TraesCS3B01G042700 chr2B 95.221 544 14 2 105 637 655784950 655784408 0.000000e+00 850.0
18 TraesCS3B01G042700 chr2B 95.266 338 5 1 308 634 655766134 655765797 2.690000e-145 525.0
19 TraesCS3B01G042700 chr6D 89.021 674 46 20 2383 3049 58158530 58159182 0.000000e+00 809.0
20 TraesCS3B01G042700 chr6D 89.924 397 22 6 2657 3049 46863274 46863656 2.110000e-136 496.0
21 TraesCS3B01G042700 chr5D 89.021 674 46 21 2382 3049 57110963 57111614 0.000000e+00 809.0
22 TraesCS3B01G042700 chr5D 90.064 312 26 5 2659 2966 379260444 379260754 1.700000e-107 399.0
23 TraesCS3B01G042700 chr5D 90.064 312 26 5 2659 2966 519285244 519284934 1.700000e-107 399.0
24 TraesCS3B01G042700 chr5D 86.667 375 28 15 2383 2754 57116153 57116508 2.200000e-106 396.0
25 TraesCS3B01G042700 chr5D 85.714 161 22 1 2890 3049 514313181 514313021 5.230000e-38 169.0
26 TraesCS3B01G042700 chr6B 89.660 648 46 13 1 636 52801771 52802409 0.000000e+00 806.0
27 TraesCS3B01G042700 chr6B 91.351 370 28 3 2381 2748 214035696 214036063 1.260000e-138 503.0
28 TraesCS3B01G042700 chr6B 94.265 279 13 2 2773 3048 653309141 653308863 1.010000e-114 424.0
29 TraesCS3B01G042700 chr1B 88.872 647 48 13 1 626 375418658 375419301 0.000000e+00 774.0
30 TraesCS3B01G042700 chr1B 88.603 544 37 11 105 626 566039313 566039853 3.320000e-179 638.0
31 TraesCS3B01G042700 chr1B 88.398 543 38 15 105 626 375403528 375404066 5.550000e-177 630.0
32 TraesCS3B01G042700 chr1B 77.231 650 92 32 1001 1621 340458141 340457519 2.270000e-86 329.0
33 TraesCS3B01G042700 chr7A 87.654 648 53 14 1 627 735831696 735831055 0.000000e+00 728.0
34 TraesCS3B01G042700 chr7A 85.584 659 54 24 1 636 86113421 86112781 0.000000e+00 652.0
35 TraesCS3B01G042700 chr6A 87.561 611 50 14 1 589 608737229 608737835 0.000000e+00 684.0
36 TraesCS3B01G042700 chr6A 85.605 653 53 19 1 628 581721099 581721735 0.000000e+00 647.0
37 TraesCS3B01G042700 chrUn 87.817 591 46 18 2382 2966 326326320 326326890 0.000000e+00 669.0
38 TraesCS3B01G042700 chrUn 87.797 590 48 11 2382 2966 471561162 471560592 0.000000e+00 669.0
39 TraesCS3B01G042700 chrUn 88.403 457 31 9 1 438 83365589 83366042 5.790000e-147 531.0
40 TraesCS3B01G042700 chr4D 86.532 594 39 25 2383 2966 20248741 20248179 1.550000e-172 616.0
41 TraesCS3B01G042700 chr4D 86.243 378 30 13 2383 2757 20243385 20243027 1.020000e-104 390.0
42 TraesCS3B01G042700 chr7D 87.129 404 38 13 2655 3049 554843021 554842623 2.160000e-121 446.0
43 TraesCS3B01G042700 chr1D 85.581 430 36 18 2382 2807 482307388 482307795 7.810000e-116 427.0
44 TraesCS3B01G042700 chr1D 85.714 392 33 15 2383 2771 482312635 482313006 2.850000e-105 392.0
45 TraesCS3B01G042700 chr1D 89.103 312 27 7 2659 2966 491933164 491933472 6.170000e-102 381.0
46 TraesCS3B01G042700 chr2D 87.023 393 28 15 2383 2771 539222272 539222645 3.630000e-114 422.0
47 TraesCS3B01G042700 chr2D 84.663 163 21 4 2890 3049 571185253 571185414 3.150000e-35 159.0
48 TraesCS3B01G042700 chr7B 80.969 289 45 8 2383 2667 654132787 654132505 1.420000e-53 220.0
49 TraesCS3B01G042700 chr7B 94.118 51 3 0 1010 1060 120364659 120364609 9.060000e-11 78.7
50 TraesCS3B01G042700 chr5A 85.475 179 25 1 1216 1393 13331261 13331439 5.190000e-43 185.0
51 TraesCS3B01G042700 chr2A 87.654 162 17 3 2890 3049 39577206 39577046 5.190000e-43 185.0


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 TraesCS3B01G042700 chr3B 22099490 22102538 3048 True 5631.0 5631 100.000 1 3049 1 chr3B.!!$R2 3048
1 TraesCS3B01G042700 chr3B 22129381 22130706 1325 True 685.9 1306 86.291 823 2058 2 chr3B.!!$R6 1235
2 TraesCS3B01G042700 chr3B 499086231 499086861 630 True 617.0 617 84.830 3 628 1 chr3B.!!$R3 625
3 TraesCS3B01G042700 chr3D 14947293 14948684 1391 True 2067.0 2067 93.576 996 2382 1 chr3D.!!$R1 1386
4 TraesCS3B01G042700 chr3D 14998787 14999964 1177 False 1428.0 1428 89.002 911 2058 1 chr3D.!!$F1 1147
5 TraesCS3B01G042700 chr3D 20746869 20747519 650 False 778.0 778 88.262 2382 3047 1 chr3D.!!$F2 665
6 TraesCS3B01G042700 chr3D 569976854 569977557 703 False 268.0 268 74.548 1303 1987 1 chr3D.!!$F3 684
7 TraesCS3B01G042700 chr3A 21323561 21325145 1584 False 933.0 1666 87.375 661 2236 2 chr3A.!!$F1 1575
8 TraesCS3B01G042700 chr5B 507627763 507628412 649 True 1044.0 1044 96.000 1 636 1 chr5B.!!$R1 635
9 TraesCS3B01G042700 chr5B 507634129 507634674 545 True 846.0 846 95.064 105 637 1 chr5B.!!$R2 532
10 TraesCS3B01G042700 chr4B 658529936 658530585 649 False 1038.0 1038 95.846 1 636 1 chr4B.!!$F2 635
11 TraesCS3B01G042700 chr4B 658523467 658524013 546 False 859.0 859 95.438 105 637 1 chr4B.!!$F1 532
12 TraesCS3B01G042700 chr2B 655784408 655784950 542 True 850.0 850 95.221 105 637 1 chr2B.!!$R2 532
13 TraesCS3B01G042700 chr6D 58158530 58159182 652 False 809.0 809 89.021 2383 3049 1 chr6D.!!$F2 666
14 TraesCS3B01G042700 chr5D 57110963 57111614 651 False 809.0 809 89.021 2382 3049 1 chr5D.!!$F1 667
15 TraesCS3B01G042700 chr6B 52801771 52802409 638 False 806.0 806 89.660 1 636 1 chr6B.!!$F1 635
16 TraesCS3B01G042700 chr1B 375418658 375419301 643 False 774.0 774 88.872 1 626 1 chr1B.!!$F2 625
17 TraesCS3B01G042700 chr1B 566039313 566039853 540 False 638.0 638 88.603 105 626 1 chr1B.!!$F3 521
18 TraesCS3B01G042700 chr1B 375403528 375404066 538 False 630.0 630 88.398 105 626 1 chr1B.!!$F1 521
19 TraesCS3B01G042700 chr1B 340457519 340458141 622 True 329.0 329 77.231 1001 1621 1 chr1B.!!$R1 620
20 TraesCS3B01G042700 chr7A 735831055 735831696 641 True 728.0 728 87.654 1 627 1 chr7A.!!$R2 626
21 TraesCS3B01G042700 chr7A 86112781 86113421 640 True 652.0 652 85.584 1 636 1 chr7A.!!$R1 635
22 TraesCS3B01G042700 chr6A 608737229 608737835 606 False 684.0 684 87.561 1 589 1 chr6A.!!$F2 588
23 TraesCS3B01G042700 chr6A 581721099 581721735 636 False 647.0 647 85.605 1 628 1 chr6A.!!$F1 627
24 TraesCS3B01G042700 chrUn 326326320 326326890 570 False 669.0 669 87.817 2382 2966 1 chrUn.!!$F2 584
25 TraesCS3B01G042700 chrUn 471560592 471561162 570 True 669.0 669 87.797 2382 2966 1 chrUn.!!$R1 584
26 TraesCS3B01G042700 chr4D 20248179 20248741 562 True 616.0 616 86.532 2383 2966 1 chr4D.!!$R2 583

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
908 1043 0.032403 TTGGTTGGACCGTCTACGTG 59.968 55.0 0.0 0.0 42.58 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2448 0.166597 TCATTCGCGTCGTACTTCGT 59.833 50.0 5.77 0.0 40.8 3.85 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
217 239 0.324943 CCCTTGATCCCAACTCACGT 59.675 55.000 0.00 0.00 0.00 4.49
263 292 0.397816 CAAGTGGTTTTGGTCCCCCA 60.398 55.000 0.00 0.00 39.65 4.96
502 546 3.390521 ATCGAGCAGGCACGGGAA 61.391 61.111 10.96 0.00 0.00 3.97
639 689 8.197592 TCCTACTGGATTAAGACTAACAAACA 57.802 34.615 0.00 0.00 37.46 2.83
640 690 8.822805 TCCTACTGGATTAAGACTAACAAACAT 58.177 33.333 0.00 0.00 37.46 2.71
653 703 9.396022 AGACTAACAAACATATCAATGGTTAGG 57.604 33.333 0.00 0.00 41.19 2.69
654 704 9.174166 GACTAACAAACATATCAATGGTTAGGT 57.826 33.333 0.00 0.00 41.19 3.08
687 737 6.357367 AGAGGATGTAAACACACAAGAACTT 58.643 36.000 0.00 0.00 30.84 2.66
703 753 9.261180 CACAAGAACTTGACTAGAAGTATCAAA 57.739 33.333 19.35 0.00 42.93 2.69
730 780 9.386010 ACTGTAAACACACACAAAAATACTCTA 57.614 29.630 0.00 0.00 0.00 2.43
791 855 4.060900 TGCAAGATCTTGGATAATCTCGC 58.939 43.478 31.41 16.49 40.74 5.03
806 870 0.443869 CTCGCATGGACTTTGAACGG 59.556 55.000 0.00 0.00 0.00 4.44
819 887 3.694043 TTGAACGGGAATCATCTGTGA 57.306 42.857 0.00 0.00 39.04 3.58
820 888 2.972625 TGAACGGGAATCATCTGTGAC 58.027 47.619 0.00 0.00 37.14 3.67
821 889 2.280628 GAACGGGAATCATCTGTGACC 58.719 52.381 0.00 0.00 37.14 4.02
826 894 2.271800 GGAATCATCTGTGACCGTGAC 58.728 52.381 0.00 0.00 37.14 3.67
849 917 5.933463 ACCGATAACGTAGAAAATTGGAACA 59.067 36.000 0.00 0.00 37.88 3.18
850 918 6.128472 ACCGATAACGTAGAAAATTGGAACAC 60.128 38.462 0.00 0.00 36.22 3.32
851 919 6.091713 CCGATAACGTAGAAAATTGGAACACT 59.908 38.462 0.00 0.00 36.22 3.55
852 920 7.276218 CCGATAACGTAGAAAATTGGAACACTA 59.724 37.037 0.00 0.00 36.22 2.74
853 921 8.106348 CGATAACGTAGAAAATTGGAACACTAC 58.894 37.037 0.00 0.00 33.93 2.73
854 922 9.148104 GATAACGTAGAAAATTGGAACACTACT 57.852 33.333 0.00 0.00 39.29 2.57
904 1039 0.687920 TGCATTGGTTGGACCGTCTA 59.312 50.000 0.00 0.00 42.58 2.59
905 1040 1.084289 GCATTGGTTGGACCGTCTAC 58.916 55.000 0.00 0.00 42.58 2.59
906 1041 1.355971 CATTGGTTGGACCGTCTACG 58.644 55.000 0.00 0.00 42.58 3.51
908 1043 0.032403 TTGGTTGGACCGTCTACGTG 59.968 55.000 0.00 0.00 42.58 4.49
909 1044 1.735559 GGTTGGACCGTCTACGTGC 60.736 63.158 0.00 0.00 37.74 5.34
918 1079 4.633126 GGACCGTCTACGTGCATATATAGA 59.367 45.833 0.00 0.00 37.74 1.98
921 1082 5.106396 ACCGTCTACGTGCATATATAGAACC 60.106 44.000 0.00 0.00 37.74 3.62
937 1098 2.030490 AACCCACGTACGTGCCTTCA 62.030 55.000 36.76 0.00 44.16 3.02
947 1108 0.592637 CGTGCCTTCATTCACAGCAA 59.407 50.000 0.00 0.00 34.79 3.91
948 1109 1.400629 CGTGCCTTCATTCACAGCAAG 60.401 52.381 0.00 0.00 34.79 4.01
953 1114 2.753452 CCTTCATTCACAGCAAGCATCT 59.247 45.455 0.00 0.00 0.00 2.90
955 1116 4.397103 CCTTCATTCACAGCAAGCATCTTA 59.603 41.667 0.00 0.00 0.00 2.10
962 1129 3.254166 CACAGCAAGCATCTTACCAAAGT 59.746 43.478 0.00 0.00 34.13 2.66
963 1130 3.254166 ACAGCAAGCATCTTACCAAAGTG 59.746 43.478 0.00 0.00 34.13 3.16
972 1139 5.390991 GCATCTTACCAAAGTGTAAGCTGAC 60.391 44.000 15.19 0.00 42.98 3.51
975 1142 3.127425 ACCAAAGTGTAAGCTGACCTC 57.873 47.619 0.00 0.00 0.00 3.85
985 1157 2.261671 CTGACCTCCCCAACGACG 59.738 66.667 0.00 0.00 0.00 5.12
1096 1274 2.429930 CGAAGGTCACCAAGGGCA 59.570 61.111 0.00 0.00 0.00 5.36
1230 1412 3.000819 TCCGCCAACTCCACCGAT 61.001 61.111 0.00 0.00 0.00 4.18
2049 2302 3.549433 TTCACCAGGGCGGGGTAGA 62.549 63.158 0.00 0.00 40.26 2.59
2053 2306 2.511452 CCAGGGCGGGGTAGAGATG 61.511 68.421 0.00 0.00 0.00 2.90
2058 2311 1.227380 GCGGGGTAGAGATGCACAG 60.227 63.158 0.00 0.00 0.00 3.66
2182 2457 9.406298 CAGATATATATCACGTAACGAAGTACG 57.594 37.037 21.95 13.66 40.98 3.67
2183 2458 9.358872 AGATATATATCACGTAACGAAGTACGA 57.641 33.333 21.95 4.34 39.46 3.43
2184 2459 9.402657 GATATATATCACGTAACGAAGTACGAC 57.597 37.037 16.41 0.00 39.46 4.34
2185 2460 2.211449 TCACGTAACGAAGTACGACG 57.789 50.000 19.44 11.78 45.00 5.12
2196 2471 2.342910 AGTACGACGCGAATGAAGTT 57.657 45.000 15.93 0.00 0.00 2.66
2279 2554 1.470098 GCCAACATCATGAGTGTGACC 59.530 52.381 0.09 0.00 0.00 4.02
2280 2555 2.877300 GCCAACATCATGAGTGTGACCT 60.877 50.000 0.09 0.00 0.00 3.85
2325 2600 1.156736 AAATGAGTTGAAGACGCCCG 58.843 50.000 0.00 0.00 0.00 6.13
2330 2605 2.098607 TGAGTTGAAGACGCCCGTATAG 59.901 50.000 0.00 0.00 0.00 1.31
2331 2606 1.202382 AGTTGAAGACGCCCGTATAGC 60.202 52.381 0.00 0.00 0.00 2.97
2351 2630 3.824443 AGCTATGGTGTGTTTGGTAAACC 59.176 43.478 2.36 0.00 40.67 3.27
2361 2640 2.306341 TTGGTAAACCGAACACGACA 57.694 45.000 0.00 0.00 39.43 4.35
2368 2647 1.879430 CCGAACACGACAACACGGT 60.879 57.895 0.00 0.00 36.38 4.83
2392 2671 7.066645 GGTAATTAGTTAGGCTTGTTAGGTTGG 59.933 40.741 0.00 0.00 0.00 3.77
2426 2706 2.361610 CCAACGGCTCATTGGGCT 60.362 61.111 8.71 0.00 42.57 5.19
2477 2757 2.203538 CAAGCAAGGCTGGTGGGT 60.204 61.111 0.00 0.00 39.62 4.51
2485 2765 3.249189 GCTGGTGGGTCCCTGTCA 61.249 66.667 10.00 3.98 34.77 3.58
2488 2768 3.239253 GGTGGGTCCCTGTCACGT 61.239 66.667 10.00 0.00 32.65 4.49
2509 2789 4.579340 CGTAGTGCTATAAAGAGGAGGTGA 59.421 45.833 0.00 0.00 0.00 4.02
2528 2809 4.752594 ACCAGGGGCACGGGGTAT 62.753 66.667 11.55 0.00 38.94 2.73
2541 2822 1.192428 GGGGTATGAGGTTCGTCACT 58.808 55.000 0.00 0.00 0.00 3.41
2556 2837 1.075482 CACTGCCACTGTTCCCCAT 59.925 57.895 0.00 0.00 0.00 4.00
2579 2860 3.336997 TCCTAACCCTATCCGATCCAGAT 59.663 47.826 0.00 0.00 0.00 2.90
2605 2886 1.098050 GCAATGAAGCGATGGGAAGT 58.902 50.000 0.00 0.00 0.00 3.01
2648 2929 2.108976 CTGCCATCACCGCCGTAT 59.891 61.111 0.00 0.00 0.00 3.06
2652 2933 1.594293 CCATCACCGCCGTATCCAC 60.594 63.158 0.00 0.00 0.00 4.02
2653 2934 1.142965 CATCACCGCCGTATCCACA 59.857 57.895 0.00 0.00 0.00 4.17
2654 2935 0.461163 CATCACCGCCGTATCCACAA 60.461 55.000 0.00 0.00 0.00 3.33
2655 2936 0.461339 ATCACCGCCGTATCCACAAC 60.461 55.000 0.00 0.00 0.00 3.32
2656 2937 2.104253 CACCGCCGTATCCACAACC 61.104 63.158 0.00 0.00 0.00 3.77
2657 2938 2.266372 CCGCCGTATCCACAACCA 59.734 61.111 0.00 0.00 0.00 3.67
2658 2939 2.104253 CCGCCGTATCCACAACCAC 61.104 63.158 0.00 0.00 0.00 4.16
2659 2940 2.104253 CGCCGTATCCACAACCACC 61.104 63.158 0.00 0.00 0.00 4.61
2660 2941 2.104253 GCCGTATCCACAACCACCG 61.104 63.158 0.00 0.00 0.00 4.94
2661 2942 1.448893 CCGTATCCACAACCACCGG 60.449 63.158 0.00 0.00 0.00 5.28
2662 2943 2.104253 CGTATCCACAACCACCGGC 61.104 63.158 0.00 0.00 0.00 6.13
2663 2944 1.747745 GTATCCACAACCACCGGCC 60.748 63.158 0.00 0.00 0.00 6.13
2664 2945 2.224877 TATCCACAACCACCGGCCA 61.225 57.895 0.00 0.00 0.00 5.36
2665 2946 2.472414 TATCCACAACCACCGGCCAC 62.472 60.000 0.00 0.00 0.00 5.01
2667 2948 4.885270 CACAACCACCGGCCACCA 62.885 66.667 0.00 0.00 0.00 4.17
2668 2949 3.897122 ACAACCACCGGCCACCAT 61.897 61.111 0.00 0.00 0.00 3.55
2683 2964 2.520020 CATCACCATGGCCGGCAT 60.520 61.111 30.85 17.04 0.00 4.40
2702 2983 4.131088 GGGACGTCCTCGAGCCAC 62.131 72.222 32.52 10.90 40.62 5.01
2703 2984 3.371063 GGACGTCCTCGAGCCACA 61.371 66.667 27.64 0.00 40.62 4.17
2704 2985 2.179517 GACGTCCTCGAGCCACAG 59.820 66.667 6.99 5.22 40.62 3.66
2707 2988 1.153939 CGTCCTCGAGCCACAGAAG 60.154 63.158 6.99 0.00 39.71 2.85
2714 2995 1.544691 TCGAGCCACAGAAGAAGGTAC 59.455 52.381 0.00 0.00 0.00 3.34
2742 3023 0.251564 ACCATTGTTGCCGGAATCCA 60.252 50.000 5.05 0.00 0.00 3.41
2754 3035 1.300481 GGAATCCAAGCCTAAGCGAC 58.700 55.000 0.00 0.00 46.67 5.19
2842 3125 3.625853 GAAATCCCCTTCCTCCAAGAAG 58.374 50.000 0.00 0.00 42.46 2.85
2887 3172 4.202461 GGGGAAAAGAAGGGCAAAGAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
2979 3265 1.192146 ACCACCGGAGCTAGCTCAAA 61.192 55.000 38.32 0.00 44.40 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 292 1.024046 TTTATGTGTGCGCTGGCGAT 61.024 50.000 19.31 5.35 44.10 4.58
502 546 0.107897 TTGGTGTAGGCGATGCGAAT 60.108 50.000 0.00 0.00 0.00 3.34
659 709 7.639113 TCTTGTGTGTTTACATCCTCTTTTT 57.361 32.000 0.00 0.00 39.39 1.94
660 710 7.339466 AGTTCTTGTGTGTTTACATCCTCTTTT 59.661 33.333 0.00 0.00 39.39 2.27
661 711 6.828785 AGTTCTTGTGTGTTTACATCCTCTTT 59.171 34.615 0.00 0.00 39.39 2.52
662 712 6.357367 AGTTCTTGTGTGTTTACATCCTCTT 58.643 36.000 0.00 0.00 39.39 2.85
663 713 5.930135 AGTTCTTGTGTGTTTACATCCTCT 58.070 37.500 0.00 0.00 39.39 3.69
664 714 6.260050 TCAAGTTCTTGTGTGTTTACATCCTC 59.740 38.462 11.52 0.00 39.39 3.71
665 715 6.038271 GTCAAGTTCTTGTGTGTTTACATCCT 59.962 38.462 11.52 0.00 39.39 3.24
666 716 6.038271 AGTCAAGTTCTTGTGTGTTTACATCC 59.962 38.462 11.52 0.00 39.39 3.51
667 717 7.016361 AGTCAAGTTCTTGTGTGTTTACATC 57.984 36.000 11.52 0.00 39.39 3.06
668 718 7.985184 TCTAGTCAAGTTCTTGTGTGTTTACAT 59.015 33.333 11.52 0.00 39.39 2.29
669 719 7.324935 TCTAGTCAAGTTCTTGTGTGTTTACA 58.675 34.615 11.52 0.00 0.00 2.41
670 720 7.766219 TCTAGTCAAGTTCTTGTGTGTTTAC 57.234 36.000 11.52 2.37 0.00 2.01
703 753 8.736244 AGAGTATTTTTGTGTGTGTTTACAGTT 58.264 29.630 0.00 0.00 37.52 3.16
791 855 3.081061 TGATTCCCGTTCAAAGTCCATG 58.919 45.455 0.00 0.00 0.00 3.66
806 870 2.271800 GTCACGGTCACAGATGATTCC 58.728 52.381 0.00 0.00 37.14 3.01
819 887 1.737838 TCTACGTTATCGGTCACGGT 58.262 50.000 7.39 0.00 40.84 4.83
820 888 2.830772 TTCTACGTTATCGGTCACGG 57.169 50.000 7.39 0.00 40.84 4.94
821 889 5.478001 CAATTTTCTACGTTATCGGTCACG 58.522 41.667 0.00 0.00 42.29 4.35
826 894 6.091713 AGTGTTCCAATTTTCTACGTTATCGG 59.908 38.462 0.00 0.00 41.85 4.18
849 917 6.742109 TGTTGCTTAACGAACTAGAAGTAGT 58.258 36.000 0.00 0.00 41.61 2.73
850 918 7.813852 ATGTTGCTTAACGAACTAGAAGTAG 57.186 36.000 0.00 0.00 0.00 2.57
851 919 7.868922 TCAATGTTGCTTAACGAACTAGAAGTA 59.131 33.333 0.00 0.00 0.00 2.24
852 920 6.704493 TCAATGTTGCTTAACGAACTAGAAGT 59.296 34.615 0.00 0.00 0.00 3.01
853 921 7.010023 GTCAATGTTGCTTAACGAACTAGAAG 58.990 38.462 0.00 0.00 0.00 2.85
854 922 6.073440 GGTCAATGTTGCTTAACGAACTAGAA 60.073 38.462 0.00 0.00 0.00 2.10
904 1039 3.319972 ACGTGGGTTCTATATATGCACGT 59.680 43.478 0.00 0.00 41.05 4.49
905 1040 3.909430 ACGTGGGTTCTATATATGCACG 58.091 45.455 0.00 0.00 39.11 5.34
906 1041 4.855388 CGTACGTGGGTTCTATATATGCAC 59.145 45.833 7.22 0.00 0.00 4.57
908 1043 4.855388 CACGTACGTGGGTTCTATATATGC 59.145 45.833 35.09 0.00 42.00 3.14
909 1044 4.855388 GCACGTACGTGGGTTCTATATATG 59.145 45.833 40.17 17.31 45.49 1.78
918 1079 1.301165 GAAGGCACGTACGTGGGTT 60.301 57.895 40.17 14.34 45.49 4.11
921 1082 0.719465 GAATGAAGGCACGTACGTGG 59.281 55.000 40.17 25.91 45.49 4.94
937 1098 3.689347 TGGTAAGATGCTTGCTGTGAAT 58.311 40.909 0.00 0.00 0.00 2.57
953 1114 4.504340 GGAGGTCAGCTTACACTTTGGTAA 60.504 45.833 0.00 0.00 0.00 2.85
955 1116 2.224548 GGAGGTCAGCTTACACTTTGGT 60.225 50.000 0.00 0.00 0.00 3.67
962 1129 0.690762 GTTGGGGAGGTCAGCTTACA 59.309 55.000 0.00 0.00 0.00 2.41
963 1130 0.391263 CGTTGGGGAGGTCAGCTTAC 60.391 60.000 0.00 0.00 0.00 2.34
972 1139 3.047877 GTTGCGTCGTTGGGGAGG 61.048 66.667 0.00 0.00 0.00 4.30
975 1142 3.656045 GGTGTTGCGTCGTTGGGG 61.656 66.667 0.00 0.00 0.00 4.96
985 1157 2.126502 CATTTCGGCCGGTGTTGC 60.127 61.111 27.83 0.00 0.00 4.17
1019 1197 1.614824 AGCAGGAGGAAGACCAGGG 60.615 63.158 0.00 0.00 38.94 4.45
1778 2022 1.742880 CAGCATCACGTCCACCTGG 60.743 63.158 0.00 0.00 0.00 4.45
1928 2181 3.618351 CAGCTTGTTCTCCATCTGGAAT 58.382 45.455 0.00 0.00 44.91 3.01
2049 2302 1.676916 CCGATGTGGAACTGTGCATCT 60.677 52.381 0.00 0.00 42.00 2.90
2053 2306 0.517316 GAACCGATGTGGAACTGTGC 59.483 55.000 0.00 0.00 42.00 4.57
2058 2311 1.821216 ACCATGAACCGATGTGGAAC 58.179 50.000 0.00 0.00 42.00 3.62
2171 2446 2.159720 TCATTCGCGTCGTACTTCGTTA 60.160 45.455 5.77 0.00 40.80 3.18
2172 2447 0.979811 CATTCGCGTCGTACTTCGTT 59.020 50.000 5.77 0.00 40.80 3.85
2173 2448 0.166597 TCATTCGCGTCGTACTTCGT 59.833 50.000 5.77 0.00 40.80 3.85
2174 2449 1.249491 CTTCATTCGCGTCGTACTTCG 59.751 52.381 5.77 0.00 41.41 3.79
2175 2450 2.248487 ACTTCATTCGCGTCGTACTTC 58.752 47.619 5.77 0.00 0.00 3.01
2176 2451 2.342910 ACTTCATTCGCGTCGTACTT 57.657 45.000 5.77 0.00 0.00 2.24
2177 2452 2.342910 AACTTCATTCGCGTCGTACT 57.657 45.000 5.77 0.00 0.00 2.73
2178 2453 4.089065 ACTTAAACTTCATTCGCGTCGTAC 59.911 41.667 5.77 0.00 0.00 3.67
2179 2454 4.229096 ACTTAAACTTCATTCGCGTCGTA 58.771 39.130 5.77 0.00 0.00 3.43
2180 2455 3.054878 ACTTAAACTTCATTCGCGTCGT 58.945 40.909 5.77 0.00 0.00 4.34
2181 2456 3.700130 ACTTAAACTTCATTCGCGTCG 57.300 42.857 5.77 0.00 0.00 5.12
2182 2457 6.195798 ACAAAAACTTAAACTTCATTCGCGTC 59.804 34.615 5.77 0.00 0.00 5.19
2183 2458 6.031471 ACAAAAACTTAAACTTCATTCGCGT 58.969 32.000 5.77 0.00 0.00 6.01
2184 2459 6.490877 ACAAAAACTTAAACTTCATTCGCG 57.509 33.333 0.00 0.00 0.00 5.87
2185 2460 8.166066 ACAAACAAAAACTTAAACTTCATTCGC 58.834 29.630 0.00 0.00 0.00 4.70
2225 2500 4.331717 CCGTACTTGGTTATGATGGACAAC 59.668 45.833 0.00 0.00 0.00 3.32
2226 2501 4.509616 CCGTACTTGGTTATGATGGACAA 58.490 43.478 0.00 0.00 0.00 3.18
2263 2538 4.081972 GTCAGTAGGTCACACTCATGATGT 60.082 45.833 0.00 0.20 0.00 3.06
2269 2544 1.961394 GGTGTCAGTAGGTCACACTCA 59.039 52.381 0.00 0.00 40.32 3.41
2279 2554 1.331138 GAGATCGGTCGGTGTCAGTAG 59.669 57.143 0.00 0.00 0.00 2.57
2280 2555 1.065636 AGAGATCGGTCGGTGTCAGTA 60.066 52.381 3.73 0.00 0.00 2.74
2325 2600 7.201670 GGTTTACCAAACACACCATAGCTATAC 60.202 40.741 5.77 0.00 43.15 1.47
2330 2605 3.365565 CGGTTTACCAAACACACCATAGC 60.366 47.826 4.35 0.00 43.15 2.97
2331 2606 4.066490 TCGGTTTACCAAACACACCATAG 58.934 43.478 4.35 0.00 43.15 2.23
2351 2630 1.198767 TTACCGTGTTGTCGTGTTCG 58.801 50.000 0.00 0.00 38.55 3.95
2361 2640 5.554070 ACAAGCCTAACTAATTACCGTGTT 58.446 37.500 0.00 0.00 0.00 3.32
2368 2647 7.692172 ACCAACCTAACAAGCCTAACTAATTA 58.308 34.615 0.00 0.00 0.00 1.40
2392 2671 2.592308 GGCCCATGGTGGAGAGAC 59.408 66.667 11.73 0.00 40.96 3.36
2426 2706 1.899437 GATCAGGGCGTGGGTCAAGA 61.899 60.000 7.42 0.00 0.00 3.02
2477 2757 2.139323 ATAGCACTACGTGACAGGGA 57.861 50.000 0.00 0.00 35.23 4.20
2485 2765 4.338682 CACCTCCTCTTTATAGCACTACGT 59.661 45.833 0.00 0.00 0.00 3.57
2488 2768 5.828859 GTCTCACCTCCTCTTTATAGCACTA 59.171 44.000 0.00 0.00 0.00 2.74
2528 2809 1.069090 GTGGCAGTGACGAACCTCA 59.931 57.895 0.00 0.00 0.00 3.86
2541 2822 1.076549 GGAATGGGGAACAGTGGCA 59.923 57.895 0.00 0.00 0.00 4.92
2556 2837 3.141460 TCTGGATCGGATAGGGTTAGGAA 59.859 47.826 0.00 0.00 0.00 3.36
2579 2860 1.925285 ATCGCTTCATTGCCCCTCCA 61.925 55.000 0.00 0.00 0.00 3.86
2583 2864 2.492773 CCCATCGCTTCATTGCCCC 61.493 63.158 0.00 0.00 0.00 5.80
2584 2865 1.037030 TTCCCATCGCTTCATTGCCC 61.037 55.000 0.00 0.00 0.00 5.36
2589 2870 1.281867 TGGAACTTCCCATCGCTTCAT 59.718 47.619 5.30 0.00 35.03 2.57
2648 2929 4.572571 GTGGCCGGTGGTTGTGGA 62.573 66.667 1.90 0.00 0.00 4.02
2652 2933 3.061848 GATGGTGGCCGGTGGTTG 61.062 66.667 1.90 0.00 0.00 3.77
2653 2934 3.575247 TGATGGTGGCCGGTGGTT 61.575 61.111 1.90 0.00 0.00 3.67
2654 2935 4.344865 GTGATGGTGGCCGGTGGT 62.345 66.667 1.90 0.00 0.00 4.16
2656 2937 3.643595 ATGGTGATGGTGGCCGGTG 62.644 63.158 1.90 0.00 0.00 4.94
2657 2938 3.338250 ATGGTGATGGTGGCCGGT 61.338 61.111 1.90 0.00 0.00 5.28
2658 2939 2.829914 CATGGTGATGGTGGCCGG 60.830 66.667 0.00 0.00 0.00 6.13
2659 2940 2.829914 CCATGGTGATGGTGGCCG 60.830 66.667 2.57 0.00 43.98 6.13
2666 2947 2.520020 ATGCCGGCCATGGTGATG 60.520 61.111 26.77 0.88 31.48 3.07
2667 2948 2.203394 GATGCCGGCCATGGTGAT 60.203 61.111 26.77 8.72 33.29 3.06
2668 2949 4.854924 CGATGCCGGCCATGGTGA 62.855 66.667 26.77 2.60 33.29 4.02
2679 2960 4.570663 CGAGGACGTCCCGATGCC 62.571 72.222 30.82 11.98 40.87 4.40
2680 2961 3.471244 CTCGAGGACGTCCCGATGC 62.471 68.421 33.42 18.75 40.87 3.91
2689 2970 1.153939 CTTCTGTGGCTCGAGGACG 60.154 63.158 15.58 0.00 41.26 4.79
2690 2971 0.603569 TTCTTCTGTGGCTCGAGGAC 59.396 55.000 15.58 0.00 0.00 3.85
2697 2978 2.832733 GGTAGTACCTTCTTCTGTGGCT 59.167 50.000 12.41 0.00 34.73 4.75
2714 2995 2.365582 GGCAACAATGGTGGTAGGTAG 58.634 52.381 0.00 0.00 0.00 3.18
2721 3002 0.173255 GATTCCGGCAACAATGGTGG 59.827 55.000 0.00 0.00 0.00 4.61
2727 3008 1.531739 GGCTTGGATTCCGGCAACAA 61.532 55.000 18.01 0.00 0.00 2.83
2742 3023 0.960861 GCTTTGGGTCGCTTAGGCTT 60.961 55.000 0.00 0.00 36.09 4.35
2754 3035 6.491062 TGATACCATTGATAGATTGCTTTGGG 59.509 38.462 0.00 0.00 0.00 4.12
2831 3114 0.620700 GGGGTAGGCTTCTTGGAGGA 60.621 60.000 0.00 0.00 0.00 3.71
2834 3117 1.451449 TTTGGGGTAGGCTTCTTGGA 58.549 50.000 0.00 0.00 0.00 3.53
2842 3125 4.322725 CCTCTTTTTCATTTTGGGGTAGGC 60.323 45.833 0.00 0.00 0.00 3.93
2947 3232 1.373873 GGTGGTTCTTCGTCCGACC 60.374 63.158 0.00 0.00 0.00 4.79
2979 3265 1.341209 CTTTTCTTTTCCGGCAAGCCT 59.659 47.619 9.73 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.