Multiple sequence alignment - TraesCS7D01G200700

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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 TraesCS7D01G200700 chr7D 100.000 2591 0 0 1 2591 159074691 159077281 0.000000e+00 4785.0
1 TraesCS7D01G200700 chr7D 88.043 552 59 6 1 549 598311861 598311314 0.000000e+00 647.0
2 TraesCS7D01G200700 chr7D 87.113 388 41 4 947 1333 159352321 159352700 5.120000e-117 431.0
3 TraesCS7D01G200700 chr7D 87.360 356 33 3 1322 1674 159352723 159353069 5.200000e-107 398.0
4 TraesCS7D01G200700 chr2D 96.508 859 26 3 1736 2591 451010993 451010136 0.000000e+00 1417.0
5 TraesCS7D01G200700 chr2D 84.428 533 78 5 1 528 624029652 624030184 1.060000e-143 520.0
6 TraesCS7D01G200700 chr3D 96.816 848 23 3 1747 2591 396431302 396432148 0.000000e+00 1413.0
7 TraesCS7D01G200700 chr3D 96.357 851 26 3 1744 2591 83388814 83387966 0.000000e+00 1395.0
8 TraesCS7D01G200700 chr3D 96.005 851 19 5 1743 2591 462458070 462457233 0.000000e+00 1369.0
9 TraesCS7D01G200700 chr5D 96.349 849 26 4 1746 2591 45204140 45203294 0.000000e+00 1391.0
10 TraesCS7D01G200700 chr5D 96.118 850 29 4 1744 2591 117834547 117835394 0.000000e+00 1384.0
11 TraesCS7D01G200700 chr6D 96.240 851 25 5 1746 2591 420532791 420531943 0.000000e+00 1387.0
12 TraesCS7D01G200700 chr6D 96.344 848 22 4 1746 2591 388144481 388145321 0.000000e+00 1386.0
13 TraesCS7D01G200700 chr6D 95.423 852 34 5 1743 2591 413508329 413509178 0.000000e+00 1352.0
14 TraesCS7D01G200700 chr6D 83.883 546 73 14 1 540 362624307 362624843 8.270000e-140 507.0
15 TraesCS7D01G200700 chr7B 90.665 632 41 6 825 1456 119727754 119728367 0.000000e+00 824.0
16 TraesCS7D01G200700 chr7B 87.743 669 67 5 1014 1678 119887210 119887867 0.000000e+00 767.0
17 TraesCS7D01G200700 chr7B 86.847 555 62 9 1 549 677402636 677402087 6.130000e-171 610.0
18 TraesCS7D01G200700 chr7B 88.983 236 18 1 1452 1687 119733947 119734174 4.220000e-73 285.0
19 TraesCS7D01G200700 chr7B 90.323 155 13 2 672 825 119712128 119712281 4.370000e-48 202.0
20 TraesCS7D01G200700 chr7A 89.878 573 51 2 672 1243 159513484 159512918 0.000000e+00 730.0
21 TraesCS7D01G200700 chr7A 81.989 533 86 10 1 527 584382636 584382108 6.580000e-121 444.0
22 TraesCS7D01G200700 chr7A 87.845 362 40 2 1239 1599 159507451 159507093 3.080000e-114 422.0
23 TraesCS7D01G200700 chr7A 95.000 60 3 0 1686 1745 15786955 15787014 7.630000e-16 95.3
24 TraesCS7D01G200700 chr7A 95.000 60 3 0 1686 1745 15814838 15814897 7.630000e-16 95.3
25 TraesCS7D01G200700 chr1A 86.131 548 65 8 1 545 300562971 300563510 4.810000e-162 580.0
26 TraesCS7D01G200700 chr1A 93.220 59 3 1 1690 1747 397087439 397087497 4.590000e-13 86.1
27 TraesCS7D01G200700 chr1B 84.489 548 70 9 1 543 330835649 330836186 6.350000e-146 527.0
28 TraesCS7D01G200700 chr1B 81.536 547 86 13 1 540 65787905 65787367 1.100000e-118 436.0
29 TraesCS7D01G200700 chr1D 84.211 532 77 5 2 528 423891325 423891854 6.400000e-141 510.0
30 TraesCS7D01G200700 chrUn 95.000 60 3 0 1686 1745 318851228 318851287 7.630000e-16 95.3
31 TraesCS7D01G200700 chrUn 98.039 51 1 0 1697 1747 45616115 45616165 3.550000e-14 89.8
32 TraesCS7D01G200700 chr2A 94.915 59 2 1 1689 1747 63805900 63805843 9.870000e-15 91.6
33 TraesCS7D01G200700 chr6B 93.333 60 3 1 1689 1747 538070307 538070248 1.280000e-13 87.9
34 TraesCS7D01G200700 chr6A 94.545 55 2 1 1693 1747 21147830 21147777 1.650000e-12 84.2
35 TraesCS7D01G200700 chr3A 90.323 62 6 0 1700 1761 229171085 229171146 5.940000e-12 82.4


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 TraesCS7D01G200700 chr7D 159074691 159077281 2590 False 4785.0 4785 100.0000 1 2591 1 chr7D.!!$F1 2590
1 TraesCS7D01G200700 chr7D 598311314 598311861 547 True 647.0 647 88.0430 1 549 1 chr7D.!!$R1 548
2 TraesCS7D01G200700 chr7D 159352321 159353069 748 False 414.5 431 87.2365 947 1674 2 chr7D.!!$F2 727
3 TraesCS7D01G200700 chr2D 451010136 451010993 857 True 1417.0 1417 96.5080 1736 2591 1 chr2D.!!$R1 855
4 TraesCS7D01G200700 chr2D 624029652 624030184 532 False 520.0 520 84.4280 1 528 1 chr2D.!!$F1 527
5 TraesCS7D01G200700 chr3D 396431302 396432148 846 False 1413.0 1413 96.8160 1747 2591 1 chr3D.!!$F1 844
6 TraesCS7D01G200700 chr3D 83387966 83388814 848 True 1395.0 1395 96.3570 1744 2591 1 chr3D.!!$R1 847
7 TraesCS7D01G200700 chr3D 462457233 462458070 837 True 1369.0 1369 96.0050 1743 2591 1 chr3D.!!$R2 848
8 TraesCS7D01G200700 chr5D 45203294 45204140 846 True 1391.0 1391 96.3490 1746 2591 1 chr5D.!!$R1 845
9 TraesCS7D01G200700 chr5D 117834547 117835394 847 False 1384.0 1384 96.1180 1744 2591 1 chr5D.!!$F1 847
10 TraesCS7D01G200700 chr6D 420531943 420532791 848 True 1387.0 1387 96.2400 1746 2591 1 chr6D.!!$R1 845
11 TraesCS7D01G200700 chr6D 388144481 388145321 840 False 1386.0 1386 96.3440 1746 2591 1 chr6D.!!$F2 845
12 TraesCS7D01G200700 chr6D 413508329 413509178 849 False 1352.0 1352 95.4230 1743 2591 1 chr6D.!!$F3 848
13 TraesCS7D01G200700 chr6D 362624307 362624843 536 False 507.0 507 83.8830 1 540 1 chr6D.!!$F1 539
14 TraesCS7D01G200700 chr7B 119727754 119728367 613 False 824.0 824 90.6650 825 1456 1 chr7B.!!$F2 631
15 TraesCS7D01G200700 chr7B 119887210 119887867 657 False 767.0 767 87.7430 1014 1678 1 chr7B.!!$F4 664
16 TraesCS7D01G200700 chr7B 677402087 677402636 549 True 610.0 610 86.8470 1 549 1 chr7B.!!$R1 548
17 TraesCS7D01G200700 chr7A 159512918 159513484 566 True 730.0 730 89.8780 672 1243 1 chr7A.!!$R2 571
18 TraesCS7D01G200700 chr7A 584382108 584382636 528 True 444.0 444 81.9890 1 527 1 chr7A.!!$R3 526
19 TraesCS7D01G200700 chr1A 300562971 300563510 539 False 580.0 580 86.1310 1 545 1 chr1A.!!$F1 544
20 TraesCS7D01G200700 chr1B 330835649 330836186 537 False 527.0 527 84.4890 1 543 1 chr1B.!!$F1 542
21 TraesCS7D01G200700 chr1B 65787367 65787905 538 True 436.0 436 81.5360 1 540 1 chr1B.!!$R1 539
22 TraesCS7D01G200700 chr1D 423891325 423891854 529 False 510.0 510 84.2110 2 528 1 chr1D.!!$F1 526

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
998 1035 0.17691 CACCACCACCAAACCAAACC 59.823 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1906 1.209383 GGCGAAAAACGGGCTTCTC 59.791 57.895 0.0 0.0 42.83 2.87 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
80 83 8.836413 TGTGAAATAAGTTAGTGGAAAGTGAAG 58.164 33.333 0.00 0.00 0.00 3.02
106 109 8.784043 GTGTAGGTTCTGAATTGTGAAATAGTT 58.216 33.333 0.00 0.00 0.00 2.24
163 178 7.384660 TGTGAAACTGATTATTTGGAAATGTGC 59.615 33.333 0.00 0.00 38.04 4.57
421 449 6.930722 AGGTTTTAATGCAAGGAGTTCAAATG 59.069 34.615 0.00 0.00 0.00 2.32
423 454 7.307337 GGTTTTAATGCAAGGAGTTCAAATGTG 60.307 37.037 0.00 0.00 0.00 3.21
471 504 8.199449 ACATGGTTTAAAAGATATGGATGCTTG 58.801 33.333 0.00 0.00 0.00 4.01
530 565 1.476488 GTGGGAGAAGAGAGAGAGTGC 59.524 57.143 0.00 0.00 0.00 4.40
549 584 1.529152 CTCTGCCACATTGCTGCCAA 61.529 55.000 0.00 0.00 35.01 4.52
550 585 0.901114 TCTGCCACATTGCTGCCAAT 60.901 50.000 0.00 0.00 42.26 3.16
551 586 0.818938 CTGCCACATTGCTGCCAATA 59.181 50.000 0.00 0.00 39.60 1.90
552 587 1.411246 CTGCCACATTGCTGCCAATAT 59.589 47.619 0.00 0.00 39.60 1.28
553 588 1.832366 TGCCACATTGCTGCCAATATT 59.168 42.857 0.00 0.00 39.60 1.28
554 589 2.159071 TGCCACATTGCTGCCAATATTC 60.159 45.455 0.00 0.00 39.60 1.75
555 590 2.101917 GCCACATTGCTGCCAATATTCT 59.898 45.455 0.00 0.00 39.60 2.40
556 591 3.431207 GCCACATTGCTGCCAATATTCTT 60.431 43.478 0.00 0.00 39.60 2.52
557 592 4.761975 CCACATTGCTGCCAATATTCTTT 58.238 39.130 0.00 0.00 39.60 2.52
558 593 5.681954 GCCACATTGCTGCCAATATTCTTTA 60.682 40.000 0.00 0.00 39.60 1.85
559 594 6.339730 CCACATTGCTGCCAATATTCTTTAA 58.660 36.000 0.00 0.00 39.60 1.52
560 595 6.817641 CCACATTGCTGCCAATATTCTTTAAA 59.182 34.615 0.00 0.00 39.60 1.52
561 596 7.201548 CCACATTGCTGCCAATATTCTTTAAAC 60.202 37.037 0.00 0.00 39.60 2.01
562 597 7.331440 CACATTGCTGCCAATATTCTTTAAACA 59.669 33.333 0.00 0.00 39.60 2.83
563 598 8.042515 ACATTGCTGCCAATATTCTTTAAACAT 58.957 29.630 0.00 0.00 39.60 2.71
564 599 7.830940 TTGCTGCCAATATTCTTTAAACATG 57.169 32.000 0.00 0.00 0.00 3.21
565 600 6.339730 TGCTGCCAATATTCTTTAAACATGG 58.660 36.000 0.00 0.00 0.00 3.66
566 601 5.754890 GCTGCCAATATTCTTTAAACATGGG 59.245 40.000 0.00 0.00 0.00 4.00
567 602 6.406849 GCTGCCAATATTCTTTAAACATGGGA 60.407 38.462 0.00 0.00 0.00 4.37
568 603 7.487822 TGCCAATATTCTTTAAACATGGGAA 57.512 32.000 0.00 0.00 0.00 3.97
569 604 7.911651 TGCCAATATTCTTTAAACATGGGAAA 58.088 30.769 0.00 0.00 0.00 3.13
570 605 8.378565 TGCCAATATTCTTTAAACATGGGAAAA 58.621 29.630 0.00 0.00 0.00 2.29
571 606 9.225436 GCCAATATTCTTTAAACATGGGAAAAA 57.775 29.630 0.00 0.00 0.00 1.94
610 645 9.617975 GAAAGAGAATATATGCAGTTAAATGGC 57.382 33.333 4.91 0.00 0.00 4.40
611 646 8.696043 AAGAGAATATATGCAGTTAAATGGCA 57.304 30.769 4.91 3.97 42.43 4.92
612 647 8.103948 AGAGAATATATGCAGTTAAATGGCAC 57.896 34.615 4.91 0.00 40.83 5.01
613 648 7.941238 AGAGAATATATGCAGTTAAATGGCACT 59.059 33.333 4.91 0.00 40.83 4.40
614 649 9.219603 GAGAATATATGCAGTTAAATGGCACTA 57.780 33.333 4.91 0.96 40.83 2.74
615 650 9.224267 AGAATATATGCAGTTAAATGGCACTAG 57.776 33.333 4.91 0.00 40.83 2.57
616 651 5.695851 ATATGCAGTTAAATGGCACTAGC 57.304 39.130 4.91 0.00 40.83 3.42
617 652 3.071874 TGCAGTTAAATGGCACTAGCT 57.928 42.857 4.91 0.00 41.70 3.32
618 653 2.749076 TGCAGTTAAATGGCACTAGCTG 59.251 45.455 14.32 14.32 41.70 4.24
619 654 3.009723 GCAGTTAAATGGCACTAGCTGA 58.990 45.455 19.85 0.00 41.70 4.26
620 655 3.629398 GCAGTTAAATGGCACTAGCTGAT 59.371 43.478 19.85 0.00 41.70 2.90
621 656 4.096984 GCAGTTAAATGGCACTAGCTGATT 59.903 41.667 19.85 0.00 41.70 2.57
622 657 5.575957 CAGTTAAATGGCACTAGCTGATTG 58.424 41.667 13.73 0.00 41.70 2.67
623 658 4.641989 AGTTAAATGGCACTAGCTGATTGG 59.358 41.667 0.00 0.00 41.70 3.16
624 659 1.396653 AATGGCACTAGCTGATTGGC 58.603 50.000 0.00 3.39 41.70 4.52
625 660 0.549950 ATGGCACTAGCTGATTGGCT 59.450 50.000 15.51 0.00 45.29 4.75
626 661 1.203237 TGGCACTAGCTGATTGGCTA 58.797 50.000 15.51 0.00 42.97 3.93
632 667 1.403814 TAGCTGATTGGCTAGAGCGT 58.596 50.000 0.00 0.00 42.97 5.07
633 668 0.539051 AGCTGATTGGCTAGAGCGTT 59.461 50.000 0.00 0.00 41.16 4.84
634 669 0.654683 GCTGATTGGCTAGAGCGTTG 59.345 55.000 0.00 0.00 43.26 4.10
635 670 0.654683 CTGATTGGCTAGAGCGTTGC 59.345 55.000 0.00 0.00 43.26 4.17
636 671 0.744414 TGATTGGCTAGAGCGTTGCC 60.744 55.000 7.47 7.47 46.26 4.52
640 675 2.493030 GCTAGAGCGTTGCCGGTA 59.507 61.111 1.90 0.00 46.32 4.02
641 676 1.877165 GCTAGAGCGTTGCCGGTAC 60.877 63.158 1.90 0.36 46.32 3.34
642 677 1.226888 CTAGAGCGTTGCCGGTACC 60.227 63.158 1.90 0.16 46.32 3.34
643 678 2.931713 CTAGAGCGTTGCCGGTACCG 62.932 65.000 27.68 27.68 46.32 4.02
662 697 2.905959 GGTAGTAACCGCGCAATTTT 57.094 45.000 8.75 0.00 35.62 1.82
663 698 3.206034 GGTAGTAACCGCGCAATTTTT 57.794 42.857 8.75 0.00 35.62 1.94
664 699 3.165890 GGTAGTAACCGCGCAATTTTTC 58.834 45.455 8.75 0.00 35.62 2.29
665 700 3.365164 GGTAGTAACCGCGCAATTTTTCA 60.365 43.478 8.75 0.00 35.62 2.69
666 701 2.928694 AGTAACCGCGCAATTTTTCAG 58.071 42.857 8.75 0.00 0.00 3.02
667 702 2.292292 AGTAACCGCGCAATTTTTCAGT 59.708 40.909 8.75 0.00 0.00 3.41
668 703 2.217429 AACCGCGCAATTTTTCAGTT 57.783 40.000 8.75 0.00 0.00 3.16
669 704 2.217429 ACCGCGCAATTTTTCAGTTT 57.783 40.000 8.75 0.00 0.00 2.66
670 705 3.357166 ACCGCGCAATTTTTCAGTTTA 57.643 38.095 8.75 0.00 0.00 2.01
693 729 5.066593 AGAAATTCCTTCGCTTTCTTCTGT 58.933 37.500 0.00 0.00 36.14 3.41
695 731 6.710744 AGAAATTCCTTCGCTTTCTTCTGTTA 59.289 34.615 0.00 0.00 36.14 2.41
761 797 1.872313 AGGTTCGATACGATCTCGACC 59.128 52.381 6.60 9.58 44.18 4.79
769 805 1.226888 CGATCTCGACCCGGGTTTC 60.227 63.158 30.89 15.69 43.02 2.78
807 843 0.963856 ATAGACACGACTCACCGCCA 60.964 55.000 0.00 0.00 0.00 5.69
808 844 0.963856 TAGACACGACTCACCGCCAT 60.964 55.000 0.00 0.00 0.00 4.40
826 862 4.272504 CGCCATCGGTATCTTACAACAATT 59.727 41.667 0.00 0.00 0.00 2.32
998 1035 0.176910 CACCACCACCAAACCAAACC 59.823 55.000 0.00 0.00 0.00 3.27
1131 1168 0.815734 CCGGTACCACGACTGAAGAT 59.184 55.000 13.54 0.00 35.47 2.40
1156 1193 2.509512 CTGCGGAGGAGGATCAAGA 58.490 57.895 0.00 0.00 44.33 3.02
1164 1201 1.153549 GAGGATCAAGACGGCGCTT 60.154 57.895 6.90 8.91 33.17 4.68
1213 1250 1.144936 GCAGCCGAGTTGGAGCTAT 59.855 57.895 0.00 0.00 42.00 2.97
1253 1290 2.232298 GAGTCCAAGCCCGAGACCAG 62.232 65.000 0.00 0.00 0.00 4.00
1263 1300 2.665603 GAGACCAGGTCTGTGGCC 59.334 66.667 27.94 8.20 43.53 5.36
1303 1340 4.036498 GGTTCTCGAATGAAGAGATCCGTA 59.964 45.833 7.35 0.00 43.39 4.02
1312 1349 4.023980 TGAAGAGATCCGTATCTGGTTGT 58.976 43.478 0.00 0.00 42.73 3.32
1313 1350 4.098044 TGAAGAGATCCGTATCTGGTTGTC 59.902 45.833 0.00 0.00 42.73 3.18
1314 1351 2.959707 AGAGATCCGTATCTGGTTGTCC 59.040 50.000 0.00 0.00 42.73 4.02
1338 1409 2.284405 AAGACCCCCACCGTCGAT 60.284 61.111 0.00 0.00 35.33 3.59
1402 1473 4.410481 TGGATCCACCAGAGAGCTATAT 57.590 45.455 11.44 0.00 44.64 0.86
1411 1482 8.122481 TCCACCAGAGAGCTATATTATTGGATA 58.878 37.037 0.00 0.00 0.00 2.59
1482 1553 2.307934 TCCGCATCGATTTGATCACA 57.692 45.000 0.00 0.00 34.13 3.58
1493 1564 2.851263 TTGATCACAAAGGGCTACGT 57.149 45.000 0.00 0.00 32.73 3.57
1531 1602 2.418910 ATGAGCCCTGACTCGGACG 61.419 63.158 0.00 0.00 39.68 4.79
1563 1634 2.735151 TGCTACGAATCTGAGGAGGAA 58.265 47.619 0.00 0.00 0.00 3.36
1582 1653 0.112606 AGTGACTTCTGTCCTCCGGA 59.887 55.000 2.93 2.93 42.28 5.14
1605 1680 8.028938 CGGAAGGAATAAATGAAAAGATGTTGT 58.971 33.333 0.00 0.00 0.00 3.32
1606 1681 9.143631 GGAAGGAATAAATGAAAAGATGTTGTG 57.856 33.333 0.00 0.00 0.00 3.33
1607 1682 8.538409 AAGGAATAAATGAAAAGATGTTGTGC 57.462 30.769 0.00 0.00 0.00 4.57
1608 1683 6.808212 AGGAATAAATGAAAAGATGTTGTGCG 59.192 34.615 0.00 0.00 0.00 5.34
1609 1684 6.034898 GGAATAAATGAAAAGATGTTGTGCGG 59.965 38.462 0.00 0.00 0.00 5.69
1610 1685 4.320608 AAATGAAAAGATGTTGTGCGGT 57.679 36.364 0.00 0.00 0.00 5.68
1611 1686 5.446143 AAATGAAAAGATGTTGTGCGGTA 57.554 34.783 0.00 0.00 0.00 4.02
1612 1687 3.889196 TGAAAAGATGTTGTGCGGTAC 57.111 42.857 0.00 0.00 0.00 3.34
1659 1734 1.064758 CGATGAATCCAACCAAGGGGA 60.065 52.381 0.00 0.00 38.05 4.81
1678 1753 2.223745 GAACCGCTTTGTCAACCCTAA 58.776 47.619 0.00 0.00 0.00 2.69
1679 1754 1.601166 ACCGCTTTGTCAACCCTAAC 58.399 50.000 0.00 0.00 0.00 2.34
1680 1755 1.142262 ACCGCTTTGTCAACCCTAACT 59.858 47.619 0.00 0.00 0.00 2.24
1681 1756 2.227194 CCGCTTTGTCAACCCTAACTT 58.773 47.619 0.00 0.00 0.00 2.66
1682 1757 3.181452 ACCGCTTTGTCAACCCTAACTTA 60.181 43.478 0.00 0.00 0.00 2.24
1683 1758 4.007659 CCGCTTTGTCAACCCTAACTTAT 58.992 43.478 0.00 0.00 0.00 1.73
1684 1759 5.180271 CCGCTTTGTCAACCCTAACTTATA 58.820 41.667 0.00 0.00 0.00 0.98
1685 1760 5.820947 CCGCTTTGTCAACCCTAACTTATAT 59.179 40.000 0.00 0.00 0.00 0.86
1686 1761 6.987992 CCGCTTTGTCAACCCTAACTTATATA 59.012 38.462 0.00 0.00 0.00 0.86
1687 1762 7.170998 CCGCTTTGTCAACCCTAACTTATATAG 59.829 40.741 0.00 0.00 0.00 1.31
1688 1763 7.924412 CGCTTTGTCAACCCTAACTTATATAGA 59.076 37.037 0.00 0.00 0.00 1.98
1689 1764 9.780186 GCTTTGTCAACCCTAACTTATATAGAT 57.220 33.333 0.00 0.00 0.00 1.98
1738 1813 9.910267 ATATCTAGATGTGCCATAAATATTGCA 57.090 29.630 15.79 0.00 32.69 4.08
2001 2083 2.361230 CCCCGCTTTTCCCCAGTC 60.361 66.667 0.00 0.00 0.00 3.51
2083 2165 0.739813 ATGGCACCGAAGAAGTACGC 60.740 55.000 0.00 0.00 0.00 4.42
2356 2456 1.302033 GCGCGGGGATGATGAATCT 60.302 57.895 8.83 0.00 35.43 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 7.070322 ACCTACACTTCACTTTCCACTAACTTA 59.930 37.037 0.00 0.00 0.00 2.24
80 83 8.324163 ACTATTTCACAATTCAGAACCTACAC 57.676 34.615 0.00 0.00 0.00 2.90
131 139 9.642327 TTCCAAATAATCAGTTTCACAATGATG 57.358 29.630 0.00 0.00 34.02 3.07
271 292 8.008513 TCACTTTCTGTAGTTACTCTTTCACT 57.991 34.615 0.00 0.00 0.00 3.41
342 367 4.626604 ACCATGTTTAAATTCAAGCGCATG 59.373 37.500 11.47 8.69 34.14 4.06
403 431 5.534207 TTCACATTTGAACTCCTTGCATT 57.466 34.783 0.00 0.00 36.79 3.56
530 565 2.882876 GGCAGCAATGTGGCAGAG 59.117 61.111 0.00 0.00 42.50 3.35
584 619 9.617975 GCCATTTAACTGCATATATTCTCTTTC 57.382 33.333 0.00 0.00 0.00 2.62
585 620 9.135189 TGCCATTTAACTGCATATATTCTCTTT 57.865 29.630 0.00 0.00 0.00 2.52
586 621 8.571336 GTGCCATTTAACTGCATATATTCTCTT 58.429 33.333 0.00 0.00 37.34 2.85
587 622 7.941238 AGTGCCATTTAACTGCATATATTCTCT 59.059 33.333 0.00 0.00 37.34 3.10
588 623 8.103948 AGTGCCATTTAACTGCATATATTCTC 57.896 34.615 0.00 0.00 37.34 2.87
589 624 9.224267 CTAGTGCCATTTAACTGCATATATTCT 57.776 33.333 0.00 0.00 37.34 2.40
590 625 7.965107 GCTAGTGCCATTTAACTGCATATATTC 59.035 37.037 0.00 0.00 37.34 1.75
591 626 7.667219 AGCTAGTGCCATTTAACTGCATATATT 59.333 33.333 0.00 0.00 40.80 1.28
592 627 7.120285 CAGCTAGTGCCATTTAACTGCATATAT 59.880 37.037 0.00 0.00 40.80 0.86
593 628 6.427853 CAGCTAGTGCCATTTAACTGCATATA 59.572 38.462 0.00 0.00 40.80 0.86
594 629 5.240183 CAGCTAGTGCCATTTAACTGCATAT 59.760 40.000 0.00 0.00 40.80 1.78
595 630 4.576053 CAGCTAGTGCCATTTAACTGCATA 59.424 41.667 0.00 0.00 40.80 3.14
596 631 3.379372 CAGCTAGTGCCATTTAACTGCAT 59.621 43.478 0.00 0.00 40.80 3.96
597 632 2.749076 CAGCTAGTGCCATTTAACTGCA 59.251 45.455 0.00 0.00 40.80 4.41
598 633 3.009723 TCAGCTAGTGCCATTTAACTGC 58.990 45.455 0.00 0.00 40.80 4.40
599 634 5.449588 CCAATCAGCTAGTGCCATTTAACTG 60.450 44.000 0.00 0.00 40.80 3.16
600 635 4.641989 CCAATCAGCTAGTGCCATTTAACT 59.358 41.667 0.00 0.00 40.80 2.24
601 636 4.734695 GCCAATCAGCTAGTGCCATTTAAC 60.735 45.833 0.00 0.00 40.80 2.01
602 637 3.381272 GCCAATCAGCTAGTGCCATTTAA 59.619 43.478 0.00 0.00 40.80 1.52
603 638 2.951642 GCCAATCAGCTAGTGCCATTTA 59.048 45.455 0.00 0.00 40.80 1.40
604 639 1.753073 GCCAATCAGCTAGTGCCATTT 59.247 47.619 0.00 0.00 40.80 2.32
605 640 1.064166 AGCCAATCAGCTAGTGCCATT 60.064 47.619 0.00 0.00 42.70 3.16
606 641 0.549950 AGCCAATCAGCTAGTGCCAT 59.450 50.000 0.00 0.00 42.70 4.40
607 642 1.203237 TAGCCAATCAGCTAGTGCCA 58.797 50.000 0.00 0.00 42.70 4.92
608 643 4.972875 AGCCAATCAGCTAGTGCC 57.027 55.556 0.00 0.00 42.70 5.01
613 648 1.403814 ACGCTCTAGCCAATCAGCTA 58.596 50.000 0.00 0.00 42.70 3.32
615 650 0.654683 CAACGCTCTAGCCAATCAGC 59.345 55.000 0.00 0.00 37.91 4.26
616 651 0.654683 GCAACGCTCTAGCCAATCAG 59.345 55.000 0.00 0.00 37.91 2.90
617 652 2.767536 GCAACGCTCTAGCCAATCA 58.232 52.632 0.00 0.00 37.91 2.57
643 678 2.905959 AAAATTGCGCGGTTACTACC 57.094 45.000 8.83 0.00 41.33 3.18
644 679 3.812656 TGAAAAATTGCGCGGTTACTAC 58.187 40.909 8.83 0.00 0.00 2.73
645 680 3.499157 ACTGAAAAATTGCGCGGTTACTA 59.501 39.130 8.83 0.00 0.00 1.82
646 681 2.292292 ACTGAAAAATTGCGCGGTTACT 59.708 40.909 8.83 0.00 0.00 2.24
647 682 2.657184 ACTGAAAAATTGCGCGGTTAC 58.343 42.857 8.83 0.00 0.00 2.50
648 683 3.357166 AACTGAAAAATTGCGCGGTTA 57.643 38.095 8.83 0.00 0.00 2.85
649 684 2.217429 AACTGAAAAATTGCGCGGTT 57.783 40.000 8.83 0.00 0.00 4.44
650 685 2.217429 AAACTGAAAAATTGCGCGGT 57.783 40.000 8.83 0.00 0.00 5.68
651 686 3.560503 TCTAAACTGAAAAATTGCGCGG 58.439 40.909 8.83 0.00 0.00 6.46
652 687 5.553692 TTTCTAAACTGAAAAATTGCGCG 57.446 34.783 0.00 0.00 33.59 6.86
653 688 7.009440 GGAATTTCTAAACTGAAAAATTGCGC 58.991 34.615 0.00 0.00 39.08 6.09
654 689 8.298030 AGGAATTTCTAAACTGAAAAATTGCG 57.702 30.769 0.00 0.00 41.45 4.85
657 692 8.978539 GCGAAGGAATTTCTAAACTGAAAAATT 58.021 29.630 0.00 0.00 39.08 1.82
658 693 8.360390 AGCGAAGGAATTTCTAAACTGAAAAAT 58.640 29.630 0.00 0.00 39.08 1.82
659 694 7.712797 AGCGAAGGAATTTCTAAACTGAAAAA 58.287 30.769 0.00 0.00 39.08 1.94
660 695 7.272037 AGCGAAGGAATTTCTAAACTGAAAA 57.728 32.000 0.00 0.00 39.08 2.29
661 696 6.877611 AGCGAAGGAATTTCTAAACTGAAA 57.122 33.333 0.00 0.00 39.79 2.69
662 697 6.877611 AAGCGAAGGAATTTCTAAACTGAA 57.122 33.333 0.00 0.00 33.44 3.02
663 698 6.710744 AGAAAGCGAAGGAATTTCTAAACTGA 59.289 34.615 0.00 0.00 40.54 3.41
664 699 6.903419 AGAAAGCGAAGGAATTTCTAAACTG 58.097 36.000 0.00 0.00 40.54 3.16
665 700 7.445707 AGAAGAAAGCGAAGGAATTTCTAAACT 59.554 33.333 0.28 0.00 41.25 2.66
666 701 7.535599 CAGAAGAAAGCGAAGGAATTTCTAAAC 59.464 37.037 0.28 0.00 41.25 2.01
667 702 7.228706 ACAGAAGAAAGCGAAGGAATTTCTAAA 59.771 33.333 0.28 0.00 41.25 1.85
668 703 6.710744 ACAGAAGAAAGCGAAGGAATTTCTAA 59.289 34.615 0.28 0.00 41.25 2.10
669 704 6.231211 ACAGAAGAAAGCGAAGGAATTTCTA 58.769 36.000 0.28 0.00 41.25 2.10
670 705 5.066593 ACAGAAGAAAGCGAAGGAATTTCT 58.933 37.500 0.00 0.00 43.33 2.52
682 717 1.519408 TGGCGGTAACAGAAGAAAGC 58.481 50.000 0.00 0.00 0.00 3.51
693 729 1.301874 CCAGAACGGTTGGCGGTAA 60.302 57.895 0.00 0.00 0.00 2.85
695 731 4.636435 CCCAGAACGGTTGGCGGT 62.636 66.667 0.00 0.00 34.26 5.68
790 826 2.214181 GATGGCGGTGAGTCGTGTCT 62.214 60.000 0.00 0.00 0.00 3.41
793 829 2.880879 CGATGGCGGTGAGTCGTG 60.881 66.667 0.00 0.00 0.00 4.35
807 843 5.054477 CGGGAATTGTTGTAAGATACCGAT 58.946 41.667 0.00 0.00 39.92 4.18
808 844 4.160065 TCGGGAATTGTTGTAAGATACCGA 59.840 41.667 0.00 0.00 43.51 4.69
908 944 1.304962 AAAAATCACCCTCCCGGCC 60.305 57.895 0.00 0.00 33.26 6.13
1033 1070 1.256812 CTTTTGCCCTTCGGTGGAAT 58.743 50.000 0.00 0.00 0.00 3.01
1066 1103 4.577246 GCGCGGCTTCTCCTCGAT 62.577 66.667 8.83 0.00 45.46 3.59
1197 1234 0.752009 TCGATAGCTCCAACTCGGCT 60.752 55.000 0.00 0.00 39.74 5.52
1199 1236 2.034685 TCAATCGATAGCTCCAACTCGG 59.965 50.000 0.00 0.00 0.00 4.63
1200 1237 3.355626 TCAATCGATAGCTCCAACTCG 57.644 47.619 0.00 0.00 0.00 4.18
1213 1250 7.295322 ACTCCTTCATGATTCTATCAATCGA 57.705 36.000 0.00 0.00 43.50 3.59
1312 1349 0.918983 GTGGGGGTCTTCATCATGGA 59.081 55.000 0.00 0.00 0.00 3.41
1313 1350 0.106519 GGTGGGGGTCTTCATCATGG 60.107 60.000 0.00 0.00 0.00 3.66
1314 1351 0.464373 CGGTGGGGGTCTTCATCATG 60.464 60.000 0.00 0.00 0.00 3.07
1338 1409 1.538204 GCTTCAACGCCGAGGATATCA 60.538 52.381 4.83 0.00 0.00 2.15
1402 1473 4.642437 TCGTTGGCATTGCTTATCCAATAA 59.358 37.500 8.82 0.00 40.29 1.40
1411 1482 1.334960 CGTCTTTCGTTGGCATTGCTT 60.335 47.619 8.82 0.00 34.52 3.91
1432 1503 2.618709 CCAAGATTATTTCGCCACCCTC 59.381 50.000 0.00 0.00 0.00 4.30
1482 1553 1.607251 CGGAACTCAACGTAGCCCTTT 60.607 52.381 0.00 0.00 0.00 3.11
1493 1564 1.203087 TGTACTCCTCCCGGAACTCAA 60.203 52.381 0.73 0.00 39.29 3.02
1513 1584 2.418910 CGTCCGAGTCAGGGCTCAT 61.419 63.158 1.46 0.00 35.33 2.90
1531 1602 0.594028 TCGTAGCATTCATCGTCCGC 60.594 55.000 0.00 0.00 0.00 5.54
1582 1653 7.329226 CGCACAACATCTTTTCATTTATTCCTT 59.671 33.333 0.00 0.00 0.00 3.36
1587 1658 6.024552 ACCGCACAACATCTTTTCATTTAT 57.975 33.333 0.00 0.00 0.00 1.40
1591 1662 4.072131 AGTACCGCACAACATCTTTTCAT 58.928 39.130 0.00 0.00 0.00 2.57
1592 1663 3.249799 CAGTACCGCACAACATCTTTTCA 59.750 43.478 0.00 0.00 0.00 2.69
1593 1664 3.810373 CAGTACCGCACAACATCTTTTC 58.190 45.455 0.00 0.00 0.00 2.29
1608 1683 1.000506 TCTCAGAACAACGGCAGTACC 59.999 52.381 0.00 0.00 0.00 3.34
1609 1684 2.433868 TCTCAGAACAACGGCAGTAC 57.566 50.000 0.00 0.00 0.00 2.73
1610 1685 2.626266 TCTTCTCAGAACAACGGCAGTA 59.374 45.455 0.00 0.00 0.00 2.74
1611 1686 1.412710 TCTTCTCAGAACAACGGCAGT 59.587 47.619 0.00 0.00 0.00 4.40
1612 1687 2.154854 TCTTCTCAGAACAACGGCAG 57.845 50.000 0.00 0.00 0.00 4.85
1659 1734 1.951602 GTTAGGGTTGACAAAGCGGTT 59.048 47.619 0.00 0.00 34.50 4.44
1704 1779 5.163426 ATGGCACATCTAGATATGCTCTAGC 60.163 44.000 29.70 16.46 46.36 3.42
1723 1798 7.308770 GCTCTTAGATGTGCAATATTTATGGCA 60.309 37.037 0.00 0.00 40.19 4.92
1724 1799 7.025963 GCTCTTAGATGTGCAATATTTATGGC 58.974 38.462 0.00 0.00 33.16 4.40
1725 1800 8.102800 TGCTCTTAGATGTGCAATATTTATGG 57.897 34.615 0.00 0.00 34.19 2.74
1726 1801 9.770503 GATGCTCTTAGATGTGCAATATTTATG 57.229 33.333 0.00 0.00 39.39 1.90
1727 1802 9.736414 AGATGCTCTTAGATGTGCAATATTTAT 57.264 29.630 0.00 0.00 39.39 1.40
1728 1803 9.212641 GAGATGCTCTTAGATGTGCAATATTTA 57.787 33.333 0.00 0.00 39.39 1.40
1729 1804 7.174599 GGAGATGCTCTTAGATGTGCAATATTT 59.825 37.037 0.00 0.00 39.39 1.40
1730 1805 6.654161 GGAGATGCTCTTAGATGTGCAATATT 59.346 38.462 0.00 0.00 39.39 1.28
1731 1806 6.171921 GGAGATGCTCTTAGATGTGCAATAT 58.828 40.000 0.00 0.00 39.39 1.28
1732 1807 5.070847 TGGAGATGCTCTTAGATGTGCAATA 59.929 40.000 0.00 0.00 39.39 1.90
1733 1808 4.141551 TGGAGATGCTCTTAGATGTGCAAT 60.142 41.667 0.00 0.00 39.39 3.56
1734 1809 3.198417 TGGAGATGCTCTTAGATGTGCAA 59.802 43.478 0.00 0.00 39.39 4.08
1735 1810 2.767960 TGGAGATGCTCTTAGATGTGCA 59.232 45.455 0.00 0.00 40.07 4.57
1736 1811 3.391965 CTGGAGATGCTCTTAGATGTGC 58.608 50.000 0.00 0.00 0.00 4.57
1737 1812 3.391965 GCTGGAGATGCTCTTAGATGTG 58.608 50.000 0.00 0.00 0.00 3.21
1738 1813 2.368221 GGCTGGAGATGCTCTTAGATGT 59.632 50.000 0.00 0.00 0.00 3.06
1739 1814 2.609984 CGGCTGGAGATGCTCTTAGATG 60.610 54.545 0.00 0.00 0.00 2.90
1773 1848 2.774633 AAAAACGCCTGGGGAGGGT 61.775 57.895 18.53 0.00 0.00 4.34
1830 1906 1.209383 GGCGAAAAACGGGCTTCTC 59.791 57.895 0.00 0.00 42.83 2.87
2001 2083 3.268072 AGGAAAGGAGAAAATGAGAGGGG 59.732 47.826 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.