Multiple sequence alignment - TraesCS2A01G400700

Loading Multiple Alignment...

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 TraesCS2A01G400700 chr2A 100.000 2372 0 0 1 2372 654610650 654613021 0.000000e+00 4381.0
1 TraesCS2A01G400700 chr2A 94.503 1528 56 6 819 2345 654603390 654604890 0.000000e+00 2331.0
2 TraesCS2A01G400700 chr2A 93.587 842 37 11 1 826 654602090 654602930 0.000000e+00 1240.0
3 TraesCS2A01G400700 chr2A 90.560 911 45 16 490 1386 301198717 301199600 0.000000e+00 1168.0
4 TraesCS2A01G400700 chr2A 90.981 887 41 8 514 1386 300946822 300947683 0.000000e+00 1158.0
5 TraesCS2A01G400700 chr2A 88.841 923 60 13 479 1386 300954736 300955630 0.000000e+00 1094.0
6 TraesCS2A01G400700 chr2A 95.174 518 21 4 1 515 498414170 498413654 0.000000e+00 815.0
7 TraesCS2A01G400700 chr2A 95.174 518 20 5 1 515 498422155 498421640 0.000000e+00 813.0
8 TraesCS2A01G400700 chr2A 93.629 518 28 5 1 515 445318252 445318767 0.000000e+00 769.0
9 TraesCS2A01G400700 chr2A 89.785 558 26 15 1697 2242 181569024 181568486 0.000000e+00 686.0
10 TraesCS2A01G400700 chr2A 89.504 524 28 11 1697 2212 141255009 141255513 2.570000e-179 638.0
11 TraesCS2A01G400700 chr2A 88.398 543 33 13 1697 2231 141246799 141247319 5.570000e-176 627.0
12 TraesCS2A01G400700 chr2A 78.017 232 25 22 1630 1838 184231095 184231323 3.200000e-24 122.0
13 TraesCS2A01G400700 chr3A 91.954 1044 70 6 514 1544 667920725 667919683 0.000000e+00 1450.0
14 TraesCS2A01G400700 chr3A 92.004 1038 71 7 514 1544 667908828 667907796 0.000000e+00 1447.0
15 TraesCS2A01G400700 chr3A 93.436 518 29 5 1 515 626413688 626413173 0.000000e+00 763.0
16 TraesCS2A01G400700 chr3A 90.146 548 29 10 1706 2245 399958067 399958597 0.000000e+00 689.0
17 TraesCS2A01G400700 chr3A 81.431 657 72 35 1698 2344 632057644 632058260 2.120000e-135 492.0
18 TraesCS2A01G400700 chr3A 81.155 658 73 36 1698 2345 632049477 632050093 4.590000e-132 481.0
19 TraesCS2A01G400700 chr3A 82.940 551 55 21 1697 2233 659172214 659172739 5.970000e-126 460.0
20 TraesCS2A01G400700 chr3A 79.577 568 72 29 1695 2245 559188725 559188185 1.340000e-97 366.0
21 TraesCS2A01G400700 chr3A 77.580 562 74 39 1706 2243 422489399 422488866 2.310000e-75 292.0
22 TraesCS2A01G400700 chr3A 87.817 197 17 4 1280 1469 328781715 328781519 8.530000e-55 224.0
23 TraesCS2A01G400700 chr3A 76.623 231 30 19 1630 1838 68680285 68680513 3.220000e-19 106.0
24 TraesCS2A01G400700 chr3A 97.436 39 0 1 2334 2371 616566931 616566893 5.470000e-07 65.8
25 TraesCS2A01G400700 chr6A 92.126 1016 63 9 547 1548 328975944 328976956 0.000000e+00 1417.0
26 TraesCS2A01G400700 chr6A 91.667 1008 67 9 547 1539 328989916 328990921 0.000000e+00 1380.0
27 TraesCS2A01G400700 chr6A 95.367 518 20 4 1 515 357146247 357145731 0.000000e+00 821.0
28 TraesCS2A01G400700 chr6A 94.981 518 22 4 1 515 357154255 357153739 0.000000e+00 809.0
29 TraesCS2A01G400700 chr6A 93.243 518 31 4 1 515 357138297 357137781 0.000000e+00 760.0
30 TraesCS2A01G400700 chr6A 85.027 561 58 15 1693 2245 239087103 239087645 4.460000e-152 547.0
31 TraesCS2A01G400700 chr6A 75.980 816 103 61 1475 2233 461344467 461345246 3.780000e-88 335.0
32 TraesCS2A01G400700 chr6A 77.488 613 93 25 1740 2344 154827953 154828528 2.270000e-85 326.0
33 TraesCS2A01G400700 chr6A 83.019 318 39 10 1876 2190 511361589 511361894 8.350000e-70 274.0
34 TraesCS2A01G400700 chr6A 90.625 128 9 3 2217 2344 582048208 582048084 1.460000e-37 167.0
35 TraesCS2A01G400700 chr7A 91.437 1016 60 11 547 1548 378456604 378457606 0.000000e+00 1369.0
36 TraesCS2A01G400700 chr7A 94.574 516 24 4 1 513 335602024 335602538 0.000000e+00 795.0
37 TraesCS2A01G400700 chr7A 89.031 392 24 12 479 855 350851969 350851582 3.570000e-128 468.0
38 TraesCS2A01G400700 chr7A 88.391 379 29 8 490 855 190563369 190562993 2.160000e-120 442.0
39 TraesCS2A01G400700 chr7A 87.724 391 31 10 479 855 350835295 350834908 7.780000e-120 440.0
40 TraesCS2A01G400700 chr7A 75.970 799 115 50 1475 2243 423924332 423925083 8.120000e-90 340.0
41 TraesCS2A01G400700 chr7A 78.807 486 65 28 1876 2345 444480234 444480697 2.310000e-75 292.0
42 TraesCS2A01G400700 chr7A 75.420 655 99 39 1615 2245 423931007 423931623 6.500000e-66 261.0
43 TraesCS2A01G400700 chr7A 93.893 131 5 3 1593 1721 165398892 165399021 6.690000e-46 195.0
44 TraesCS2A01G400700 chr7A 95.726 117 3 2 2229 2345 359514224 359514110 1.120000e-43 187.0
45 TraesCS2A01G400700 chr7A 95.690 116 3 2 2229 2344 312127984 312127871 4.030000e-43 185.0
46 TraesCS2A01G400700 chr7A 92.188 128 8 2 2231 2358 628623919 628624044 1.870000e-41 180.0
47 TraesCS2A01G400700 chr7A 90.411 73 4 3 1631 1702 52542655 52542585 2.510000e-15 93.5
48 TraesCS2A01G400700 chr5A 88.563 682 57 15 479 1145 136739030 136738355 0.000000e+00 808.0
49 TraesCS2A01G400700 chr5A 90.347 518 24 12 1721 2233 588130401 588130897 0.000000e+00 656.0
50 TraesCS2A01G400700 chr5A 89.071 549 26 20 1721 2263 588122306 588122826 0.000000e+00 651.0
51 TraesCS2A01G400700 chr5A 83.540 565 49 32 1697 2245 614290324 614290860 2.740000e-134 488.0
52 TraesCS2A01G400700 chr5A 92.254 142 10 1 2231 2372 341844279 341844419 1.440000e-47 200.0
53 TraesCS2A01G400700 chr5A 97.222 36 1 0 2337 2372 418400731 418400766 7.080000e-06 62.1
54 TraesCS2A01G400700 chr1A 88.536 567 47 9 479 1030 243992660 243992097 0.000000e+00 671.0
55 TraesCS2A01G400700 chr1A 87.544 570 49 15 479 1031 230152950 230153514 7.150000e-180 640.0
56 TraesCS2A01G400700 chr1A 84.199 462 38 12 1794 2245 437811860 437812296 1.310000e-112 416.0
57 TraesCS2A01G400700 chr1A 77.816 586 85 30 1766 2345 142324095 142324641 1.060000e-83 320.0
58 TraesCS2A01G400700 chr1A 86.139 303 18 13 2044 2345 322709425 322709704 2.960000e-79 305.0
59 TraesCS2A01G400700 chr1A 77.830 212 23 21 1630 1820 563463147 563462939 2.490000e-20 110.0
60 TraesCS2A01G400700 chr4A 88.113 530 42 10 1707 2233 313846858 313847369 5.610000e-171 610.0
61 TraesCS2A01G400700 chr4A 82.266 609 64 29 1742 2344 462364503 462365073 9.860000e-134 486.0
62 TraesCS2A01G400700 chr4A 88.747 391 27 10 479 855 171987783 171987396 1.660000e-126 462.0
63 TraesCS2A01G400700 chr4A 75.965 803 113 58 1475 2245 13625116 13625870 8.120000e-90 340.0
64 TraesCS2A01G400700 chr4A 76.702 661 91 38 1559 2189 201323371 201322744 2.290000e-80 309.0
65 TraesCS2A01G400700 chr4A 87.273 220 18 5 1258 1469 297882205 297882422 2.360000e-60 243.0
66 TraesCS2A01G400700 chr4A 91.667 108 6 3 1559 1663 201269523 201269416 1.900000e-31 147.0
67 TraesCS2A01G400700 chr4A 91.589 107 6 2 1559 1662 201316547 201316441 6.830000e-31 145.0
68 TraesCS2A01G400700 chr4A 89.815 108 8 3 1559 1663 201277446 201277339 4.110000e-28 135.0
69 TraesCS2A01G400700 chr4A 76.623 231 30 20 1630 1838 296703916 296704144 3.220000e-19 106.0
70 TraesCS2A01G400700 chr4A 93.750 64 3 1 1410 1472 296542495 296542432 6.980000e-16 95.3
71 TraesCS2A01G400700 chr4A 95.000 60 2 1 1411 1469 296711828 296711887 2.510000e-15 93.5
72 TraesCS2A01G400700 chr4A 96.364 55 1 1 1417 1471 331618342 331618395 3.250000e-14 89.8
73 TraesCS2A01G400700 chr4A 98.000 50 1 0 1417 1466 331626225 331626274 1.170000e-13 87.9
74 TraesCS2A01G400700 chr1B 78.761 565 74 33 1692 2233 274809948 274810489 1.050000e-88 337.0
75 TraesCS2A01G400700 chr1B 94.737 38 2 0 2335 2372 2377236 2377273 2.550000e-05 60.2
76 TraesCS2A01G400700 chr4D 100.000 34 0 0 2339 2372 135158170 135158137 1.970000e-06 63.9
77 TraesCS2A01G400700 chr7D 92.857 42 2 1 2332 2372 513549898 513549857 2.550000e-05 60.2
78 TraesCS2A01G400700 chr6D 92.857 42 2 1 2332 2372 315005760 315005719 2.550000e-05 60.2
79 TraesCS2A01G400700 chr3B 100.000 31 0 0 2342 2372 620720904 620720874 9.160000e-05 58.4


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 TraesCS2A01G400700 chr2A 654610650 654613021 2371 False 4381.0 4381 100.000 1 2372 1 chr2A.!!$F8 2371
1 TraesCS2A01G400700 chr2A 654602090 654604890 2800 False 1785.5 2331 94.045 1 2345 2 chr2A.!!$F9 2344
2 TraesCS2A01G400700 chr2A 301198717 301199600 883 False 1168.0 1168 90.560 490 1386 1 chr2A.!!$F6 896
3 TraesCS2A01G400700 chr2A 300946822 300947683 861 False 1158.0 1158 90.981 514 1386 1 chr2A.!!$F4 872
4 TraesCS2A01G400700 chr2A 300954736 300955630 894 False 1094.0 1094 88.841 479 1386 1 chr2A.!!$F5 907
5 TraesCS2A01G400700 chr2A 498413654 498414170 516 True 815.0 815 95.174 1 515 1 chr2A.!!$R2 514
6 TraesCS2A01G400700 chr2A 498421640 498422155 515 True 813.0 813 95.174 1 515 1 chr2A.!!$R3 514
7 TraesCS2A01G400700 chr2A 445318252 445318767 515 False 769.0 769 93.629 1 515 1 chr2A.!!$F7 514
8 TraesCS2A01G400700 chr2A 181568486 181569024 538 True 686.0 686 89.785 1697 2242 1 chr2A.!!$R1 545
9 TraesCS2A01G400700 chr2A 141255009 141255513 504 False 638.0 638 89.504 1697 2212 1 chr2A.!!$F2 515
10 TraesCS2A01G400700 chr2A 141246799 141247319 520 False 627.0 627 88.398 1697 2231 1 chr2A.!!$F1 534
11 TraesCS2A01G400700 chr3A 667919683 667920725 1042 True 1450.0 1450 91.954 514 1544 1 chr3A.!!$R7 1030
12 TraesCS2A01G400700 chr3A 667907796 667908828 1032 True 1447.0 1447 92.004 514 1544 1 chr3A.!!$R6 1030
13 TraesCS2A01G400700 chr3A 626413173 626413688 515 True 763.0 763 93.436 1 515 1 chr3A.!!$R5 514
14 TraesCS2A01G400700 chr3A 399958067 399958597 530 False 689.0 689 90.146 1706 2245 1 chr3A.!!$F2 539
15 TraesCS2A01G400700 chr3A 632057644 632058260 616 False 492.0 492 81.431 1698 2344 1 chr3A.!!$F4 646
16 TraesCS2A01G400700 chr3A 632049477 632050093 616 False 481.0 481 81.155 1698 2345 1 chr3A.!!$F3 647
17 TraesCS2A01G400700 chr3A 659172214 659172739 525 False 460.0 460 82.940 1697 2233 1 chr3A.!!$F5 536
18 TraesCS2A01G400700 chr3A 559188185 559188725 540 True 366.0 366 79.577 1695 2245 1 chr3A.!!$R3 550
19 TraesCS2A01G400700 chr3A 422488866 422489399 533 True 292.0 292 77.580 1706 2243 1 chr3A.!!$R2 537
20 TraesCS2A01G400700 chr6A 328975944 328976956 1012 False 1417.0 1417 92.126 547 1548 1 chr6A.!!$F3 1001
21 TraesCS2A01G400700 chr6A 328989916 328990921 1005 False 1380.0 1380 91.667 547 1539 1 chr6A.!!$F4 992
22 TraesCS2A01G400700 chr6A 357145731 357146247 516 True 821.0 821 95.367 1 515 1 chr6A.!!$R2 514
23 TraesCS2A01G400700 chr6A 357153739 357154255 516 True 809.0 809 94.981 1 515 1 chr6A.!!$R3 514
24 TraesCS2A01G400700 chr6A 357137781 357138297 516 True 760.0 760 93.243 1 515 1 chr6A.!!$R1 514
25 TraesCS2A01G400700 chr6A 239087103 239087645 542 False 547.0 547 85.027 1693 2245 1 chr6A.!!$F2 552
26 TraesCS2A01G400700 chr6A 461344467 461345246 779 False 335.0 335 75.980 1475 2233 1 chr6A.!!$F5 758
27 TraesCS2A01G400700 chr6A 154827953 154828528 575 False 326.0 326 77.488 1740 2344 1 chr6A.!!$F1 604
28 TraesCS2A01G400700 chr7A 378456604 378457606 1002 False 1369.0 1369 91.437 547 1548 1 chr7A.!!$F3 1001
29 TraesCS2A01G400700 chr7A 335602024 335602538 514 False 795.0 795 94.574 1 513 1 chr7A.!!$F2 512
30 TraesCS2A01G400700 chr7A 423924332 423925083 751 False 340.0 340 75.970 1475 2243 1 chr7A.!!$F4 768
31 TraesCS2A01G400700 chr7A 423931007 423931623 616 False 261.0 261 75.420 1615 2245 1 chr7A.!!$F5 630
32 TraesCS2A01G400700 chr5A 136738355 136739030 675 True 808.0 808 88.563 479 1145 1 chr5A.!!$R1 666
33 TraesCS2A01G400700 chr5A 588122306 588122826 520 False 651.0 651 89.071 1721 2263 1 chr5A.!!$F3 542
34 TraesCS2A01G400700 chr5A 614290324 614290860 536 False 488.0 488 83.540 1697 2245 1 chr5A.!!$F5 548
35 TraesCS2A01G400700 chr1A 243992097 243992660 563 True 671.0 671 88.536 479 1030 1 chr1A.!!$R1 551
36 TraesCS2A01G400700 chr1A 230152950 230153514 564 False 640.0 640 87.544 479 1031 1 chr1A.!!$F2 552
37 TraesCS2A01G400700 chr1A 142324095 142324641 546 False 320.0 320 77.816 1766 2345 1 chr1A.!!$F1 579
38 TraesCS2A01G400700 chr4A 313846858 313847369 511 False 610.0 610 88.113 1707 2233 1 chr4A.!!$F5 526
39 TraesCS2A01G400700 chr4A 462364503 462365073 570 False 486.0 486 82.266 1742 2344 1 chr4A.!!$F8 602
40 TraesCS2A01G400700 chr4A 13625116 13625870 754 False 340.0 340 75.965 1475 2245 1 chr4A.!!$F1 770
41 TraesCS2A01G400700 chr4A 201322744 201323371 627 True 309.0 309 76.702 1559 2189 1 chr4A.!!$R5 630
42 TraesCS2A01G400700 chr1B 274809948 274810489 541 False 337.0 337 78.761 1692 2233 1 chr1B.!!$F2 541

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
706 709 0.45395 CACACGAGGGTAGACGAACG 60.454 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 2052 1.004758 CCTCCCTCAATCCCCCTCA 59.995 63.158 0.0 0.0 0.0 3.86 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
53 54 3.350612 CGGCGGCGAAACAGGAAA 61.351 61.111 29.19 0.00 0.00 3.13
201 202 1.115326 GGTGGCAAGGCAAAAGAGGT 61.115 55.000 0.00 0.00 0.00 3.85
264 266 5.404946 GTGCATCTCATACAACTGCATTTT 58.595 37.500 0.00 0.00 43.89 1.82
425 428 2.289444 CGTAGGTGTTCAGGGTCAACAT 60.289 50.000 0.00 0.00 36.19 2.71
593 596 1.066716 CGTGGTAATTGGGGTCTTCGA 60.067 52.381 0.00 0.00 0.00 3.71
625 628 1.403647 CCGTTCTTGCGATGGTAGTCA 60.404 52.381 0.00 0.00 0.00 3.41
653 656 4.556104 CGTTCGTTCAGAGAGGTACTTGAA 60.556 45.833 0.00 0.00 41.55 2.69
706 709 0.453950 CACACGAGGGTAGACGAACG 60.454 60.000 0.00 0.00 0.00 3.95
767 770 2.100197 TCCGGGTCTTGAGACATACTG 58.900 52.381 12.76 1.55 46.47 2.74
770 773 2.188817 GGGTCTTGAGACATACTGGGT 58.811 52.381 12.76 0.00 46.47 4.51
771 774 2.168728 GGGTCTTGAGACATACTGGGTC 59.831 54.545 12.76 0.00 46.47 4.46
779 796 3.764434 GAGACATACTGGGTCTTGACTCA 59.236 47.826 3.15 3.15 45.21 3.41
780 797 4.160329 AGACATACTGGGTCTTGACTCAA 58.840 43.478 4.80 0.00 42.77 3.02
923 1408 1.019673 GGCAGGCTACATCACACATG 58.980 55.000 0.00 0.00 0.00 3.21
1055 1540 1.519719 GAGAGGGTGCAGTAGCTGG 59.480 63.158 0.00 0.00 42.74 4.85
1249 1734 3.665675 GACTTCGGCCTGGCACGAT 62.666 63.158 25.38 15.80 39.06 3.73
1469 1956 1.380515 CGAGGAGGGAGAAGGCAGA 60.381 63.158 0.00 0.00 0.00 4.26
1531 2018 1.544759 GGGAGAGGGAGAGATCGAGAC 60.545 61.905 0.00 0.00 0.00 3.36
1565 2052 3.854669 CGGCGCTGGAGGAAGGAT 61.855 66.667 8.83 0.00 0.00 3.24
1575 2066 1.700576 GGAGGAAGGATGAGGGGGATT 60.701 57.143 0.00 0.00 0.00 3.01
1823 2396 6.003326 TCTTGGACTCACAAAAATATGCTCA 58.997 36.000 0.00 0.00 0.00 4.26
2214 2842 6.600882 AGAAAAAGAAATGACATGATGGCT 57.399 33.333 0.00 0.00 0.00 4.75
2345 2979 2.029964 GTCTCGGGGCGTCACAAA 59.970 61.111 0.00 0.00 0.00 2.83
2346 2980 2.027625 GTCTCGGGGCGTCACAAAG 61.028 63.158 0.00 0.00 0.00 2.77
2347 2981 2.204461 TCTCGGGGCGTCACAAAGA 61.204 57.895 0.00 0.00 0.00 2.52
2348 2982 1.738099 CTCGGGGCGTCACAAAGAG 60.738 63.158 0.00 0.00 0.00 2.85
2349 2983 2.030562 CGGGGCGTCACAAAGAGT 59.969 61.111 0.00 0.00 0.00 3.24
2350 2984 2.027625 CGGGGCGTCACAAAGAGTC 61.028 63.158 0.00 0.00 0.00 3.36
2351 2985 1.070786 GGGGCGTCACAAAGAGTCA 59.929 57.895 0.00 0.00 0.00 3.41
2352 2986 1.228657 GGGGCGTCACAAAGAGTCAC 61.229 60.000 0.00 0.00 0.00 3.67
2353 2987 0.249911 GGGCGTCACAAAGAGTCACT 60.250 55.000 0.00 0.00 0.00 3.41
2354 2988 1.140816 GGCGTCACAAAGAGTCACTC 58.859 55.000 0.00 0.00 0.00 3.51
2355 2989 1.140816 GCGTCACAAAGAGTCACTCC 58.859 55.000 0.00 0.00 0.00 3.85
2356 2990 1.538204 GCGTCACAAAGAGTCACTCCA 60.538 52.381 0.00 0.00 0.00 3.86
2357 2991 2.821546 CGTCACAAAGAGTCACTCCAA 58.178 47.619 0.00 0.00 0.00 3.53
2358 2992 3.194861 CGTCACAAAGAGTCACTCCAAA 58.805 45.455 0.00 0.00 0.00 3.28
2359 2993 3.246226 CGTCACAAAGAGTCACTCCAAAG 59.754 47.826 0.00 0.00 0.00 2.77
2360 2994 4.192317 GTCACAAAGAGTCACTCCAAAGT 58.808 43.478 0.00 0.00 35.60 2.66
2361 2995 4.271291 GTCACAAAGAGTCACTCCAAAGTC 59.729 45.833 0.00 0.00 31.71 3.01
2362 2996 4.081142 TCACAAAGAGTCACTCCAAAGTCA 60.081 41.667 0.00 0.00 31.71 3.41
2363 2997 4.034510 CACAAAGAGTCACTCCAAAGTCAC 59.965 45.833 0.00 0.00 31.71 3.67
2364 2998 4.080863 ACAAAGAGTCACTCCAAAGTCACT 60.081 41.667 0.00 0.00 39.88 3.41
2365 2999 5.128827 ACAAAGAGTCACTCCAAAGTCACTA 59.871 40.000 0.00 0.00 36.91 2.74
2366 3000 5.871396 AAGAGTCACTCCAAAGTCACTAA 57.129 39.130 0.00 0.00 36.91 2.24
2367 3001 6.426646 AAGAGTCACTCCAAAGTCACTAAT 57.573 37.500 0.00 0.00 36.91 1.73
2368 3002 7.540474 AAGAGTCACTCCAAAGTCACTAATA 57.460 36.000 0.00 0.00 36.91 0.98
2369 3003 7.164230 AGAGTCACTCCAAAGTCACTAATAG 57.836 40.000 0.00 0.00 36.91 1.73
2370 3004 5.725362 AGTCACTCCAAAGTCACTAATAGC 58.275 41.667 0.00 0.00 34.73 2.97
2371 3005 4.563184 GTCACTCCAAAGTCACTAATAGCG 59.437 45.833 0.00 0.00 31.71 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.237268 TGTTGCCATGGTAACTTTCCT 57.763 42.857 35.72 0.00 40.52 3.36
50 51 4.494484 GGAATGTTGCCATGGTAACTTTC 58.506 43.478 38.37 38.37 45.07 2.62
53 54 2.091541 CGGAATGTTGCCATGGTAACT 58.908 47.619 35.72 22.90 40.52 2.24
264 266 0.589223 GACGACGCCCATGAACAAAA 59.411 50.000 0.00 0.00 0.00 2.44
267 269 1.080093 GAGACGACGCCCATGAACA 60.080 57.895 0.00 0.00 0.00 3.18
415 418 1.620822 GCAAGTTCCATGTTGACCCT 58.379 50.000 0.00 0.00 0.00 4.34
425 428 2.280524 CGTGGACGGCAAGTTCCA 60.281 61.111 0.00 0.00 35.37 3.53
593 596 2.281276 GAACGGGACCGGCAAGTT 60.281 61.111 15.92 2.66 44.69 2.66
625 628 2.296471 ACCTCTCTGAACGAACGTGAAT 59.704 45.455 0.00 0.00 0.00 2.57
706 709 3.140225 GAGCCCTCGGATCCGTCAC 62.140 68.421 32.15 19.87 40.74 3.67
767 770 1.499049 GACACGTTGAGTCAAGACCC 58.501 55.000 5.62 0.00 36.06 4.46
770 773 2.971660 TTGGACACGTTGAGTCAAGA 57.028 45.000 5.62 0.00 37.74 3.02
771 774 3.680789 GTTTTGGACACGTTGAGTCAAG 58.319 45.455 5.62 3.44 37.74 3.02
923 1408 4.394712 CCTCTCCGTGGGCCACAC 62.395 72.222 34.11 10.91 46.78 3.82
1031 1516 4.056125 CTGCACCCTCTCGACGCA 62.056 66.667 0.00 0.00 0.00 5.24
1249 1734 1.681666 CTCCTCTGCTTTGCCTCCA 59.318 57.895 0.00 0.00 0.00 3.86
1330 1817 2.147387 ACCGCTCAAACCAGACCCT 61.147 57.895 0.00 0.00 0.00 4.34
1469 1956 2.044353 AGAGAAAGGGAGAGGAGCTTCT 59.956 50.000 0.00 0.00 0.00 2.85
1565 2052 1.004758 CCTCCCTCAATCCCCCTCA 59.995 63.158 0.00 0.00 0.00 3.86
1575 2066 1.306997 ATTCCCTTCGCCTCCCTCA 60.307 57.895 0.00 0.00 0.00 3.86
1823 2396 6.773976 TGGCCATTTCTATTTTCTTCGAAT 57.226 33.333 0.00 0.00 0.00 3.34
2136 2760 5.955355 TGATCCATTTAAACCGAGGGAATTT 59.045 36.000 0.00 0.00 0.00 1.82
2214 2842 6.458232 TTCATCATTGCATCATGTCATCAA 57.542 33.333 0.00 0.00 0.00 2.57
2345 2979 6.350612 GCTATTAGTGACTTTGGAGTGACTCT 60.351 42.308 12.92 0.00 45.55 3.24
2346 2980 5.808030 GCTATTAGTGACTTTGGAGTGACTC 59.192 44.000 3.47 3.47 45.55 3.36
2348 2982 4.563184 CGCTATTAGTGACTTTGGAGTGAC 59.437 45.833 0.00 0.00 39.91 3.67
2349 2983 4.744570 CGCTATTAGTGACTTTGGAGTGA 58.255 43.478 0.00 0.00 35.88 3.41


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

AutoCloner maintained by Alex Coulton.