Multiple sequence alignment - TraesCS2D01G355600

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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 TraesCS2D01G355600 chr2D 100.000 2345 0 0 1 2345 457888341 457890685 0.000000e+00 4331.0
1 TraesCS2D01G355600 chr2A 94.695 886 24 11 744 1609 601481410 601482292 0.000000e+00 1354.0
2 TraesCS2D01G355600 chr2A 88.390 646 47 16 116 752 601480374 601481000 0.000000e+00 752.0
3 TraesCS2D01G355600 chr2A 90.944 519 41 6 119 633 734360 733844 0.000000e+00 693.0
4 TraesCS2D01G355600 chr2A 90.580 138 13 0 635 772 719746 719609 1.430000e-42 183.0
5 TraesCS2D01G355600 chr2A 89.855 138 14 0 635 772 719261 719124 6.660000e-41 178.0
6 TraesCS2D01G355600 chr2A 97.059 68 2 0 3 70 601444134 601444201 5.300000e-22 115.0
7 TraesCS2D01G355600 chr2A 94.231 52 3 0 66 117 601448556 601448607 1.930000e-11 80.5
8 TraesCS2D01G355600 chr2B 93.962 679 19 8 862 1518 539089701 539090379 0.000000e+00 1007.0
9 TraesCS2D01G355600 chr2B 91.111 405 31 5 138 540 683079937 683079536 5.700000e-151 544.0
10 TraesCS2D01G355600 chr2B 90.379 343 29 4 116 456 686096254 686095914 4.600000e-122 448.0
11 TraesCS2D01G355600 chr2B 81.361 338 53 8 1017 1349 685502910 685503242 1.380000e-67 267.0
12 TraesCS2D01G355600 chr2B 81.361 338 53 8 1017 1349 685518192 685518524 1.380000e-67 267.0
13 TraesCS2D01G355600 chr2B 89.326 178 4 4 769 933 539089453 539089628 2.360000e-50 209.0
14 TraesCS2D01G355600 chr2B 94.737 114 6 0 4 117 539088537 539088650 6.660000e-41 178.0
15 TraesCS2D01G355600 chr2B 98.611 72 1 0 862 933 539089629 539089700 6.800000e-26 128.0
16 TraesCS2D01G355600 chr4A 90.385 624 51 9 119 737 726695641 726695022 0.000000e+00 811.0
17 TraesCS2D01G355600 chr3D 91.343 566 47 2 1782 2345 39206351 39205786 0.000000e+00 773.0
18 TraesCS2D01G355600 chr3D 84.892 556 81 2 1784 2336 436370278 436370833 2.040000e-155 558.0
19 TraesCS2D01G355600 chr3A 88.182 660 51 11 119 772 517660243 517660881 0.000000e+00 761.0
20 TraesCS2D01G355600 chr3A 86.151 556 76 1 1782 2336 427783253 427783808 1.200000e-167 599.0
21 TraesCS2D01G355600 chr7A 88.770 561 62 1 1786 2345 519684981 519685541 0.000000e+00 686.0
22 TraesCS2D01G355600 chr5A 86.775 552 70 3 1784 2333 572395942 572396492 1.540000e-171 612.0
23 TraesCS2D01G355600 chr4D 91.429 420 32 4 119 536 425940126 425939709 7.270000e-160 573.0
24 TraesCS2D01G355600 chr4D 84.972 539 75 5 1783 2318 333611811 333612346 2.050000e-150 542.0
25 TraesCS2D01G355600 chr7D 85.582 541 73 4 1781 2318 46817760 46817222 1.570000e-156 562.0
26 TraesCS2D01G355600 chr6B 84.324 555 86 1 1783 2336 650499715 650499161 2.050000e-150 542.0
27 TraesCS2D01G355600 chr6B 89.873 316 25 7 119 432 87922073 87921763 1.310000e-107 399.0
28 TraesCS2D01G355600 chr6D 84.144 555 86 2 1778 2330 327367331 327367885 9.540000e-149 536.0
29 TraesCS2D01G355600 chr4B 88.439 346 33 6 116 456 44918932 44919275 6.030000e-111 411.0
30 TraesCS2D01G355600 chr5B 89.815 324 24 8 116 437 425182063 425181747 7.800000e-110 407.0
31 TraesCS2D01G355600 chr5B 94.828 58 2 1 702 759 670783779 670783835 3.210000e-14 89.8


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 TraesCS2D01G355600 chr2D 457888341 457890685 2344 False 4331.0 4331 100.0000 1 2345 1 chr2D.!!$F1 2344
1 TraesCS2D01G355600 chr2A 601480374 601482292 1918 False 1053.0 1354 91.5425 116 1609 2 chr2A.!!$F3 1493
2 TraesCS2D01G355600 chr2A 733844 734360 516 True 693.0 693 90.9440 119 633 1 chr2A.!!$R1 514
3 TraesCS2D01G355600 chr2B 539088537 539090379 1842 False 380.5 1007 94.1590 4 1518 4 chr2B.!!$F3 1514
4 TraesCS2D01G355600 chr4A 726695022 726695641 619 True 811.0 811 90.3850 119 737 1 chr4A.!!$R1 618
5 TraesCS2D01G355600 chr3D 39205786 39206351 565 True 773.0 773 91.3430 1782 2345 1 chr3D.!!$R1 563
6 TraesCS2D01G355600 chr3D 436370278 436370833 555 False 558.0 558 84.8920 1784 2336 1 chr3D.!!$F1 552
7 TraesCS2D01G355600 chr3A 517660243 517660881 638 False 761.0 761 88.1820 119 772 1 chr3A.!!$F2 653
8 TraesCS2D01G355600 chr3A 427783253 427783808 555 False 599.0 599 86.1510 1782 2336 1 chr3A.!!$F1 554
9 TraesCS2D01G355600 chr7A 519684981 519685541 560 False 686.0 686 88.7700 1786 2345 1 chr7A.!!$F1 559
10 TraesCS2D01G355600 chr5A 572395942 572396492 550 False 612.0 612 86.7750 1784 2333 1 chr5A.!!$F1 549
11 TraesCS2D01G355600 chr4D 333611811 333612346 535 False 542.0 542 84.9720 1783 2318 1 chr4D.!!$F1 535
12 TraesCS2D01G355600 chr7D 46817222 46817760 538 True 562.0 562 85.5820 1781 2318 1 chr7D.!!$R1 537
13 TraesCS2D01G355600 chr6B 650499161 650499715 554 True 542.0 542 84.3240 1783 2336 1 chr6B.!!$R2 553
14 TraesCS2D01G355600 chr6D 327367331 327367885 554 False 536.0 536 84.1440 1778 2330 1 chr6D.!!$F1 552

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
84 85 0.036294 CTTCGGAAGGTCCAAGGGTC 60.036 60.0 9.93 0.0 35.91 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 2710 0.036306 GGTCGAGCTCCCCAAGAAAA 59.964 55.0 8.47 0.0 0.0 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
35 36 6.915544 TGATCAATGATGACTTAGTGAAGC 57.084 37.500 0.00 0.00 38.69 3.86
68 69 3.550437 TTATCAGAGCAGCCTTCCTTC 57.450 47.619 0.00 0.00 0.00 3.46
84 85 0.036294 CTTCGGAAGGTCCAAGGGTC 60.036 60.000 9.93 0.00 35.91 4.46
86 87 0.903454 TCGGAAGGTCCAAGGGTCTC 60.903 60.000 0.00 0.00 35.91 3.36
104 105 1.065410 TCCCTCCAAAGACCTGGCAA 61.065 55.000 0.00 0.00 36.32 4.52
176 299 5.233263 CGTGTTTTCAAATTTTGTTCCGGAT 59.767 36.000 4.15 0.00 0.00 4.18
943 1887 1.289066 CTCGAGACCACAAGCCGAA 59.711 57.895 6.58 0.00 0.00 4.30
972 1916 2.019249 CTGGCTCACCACCACATATTG 58.981 52.381 0.00 0.00 42.67 1.90
1346 2290 4.082625 TGCCATGCTGAACTTGAAATAGTG 60.083 41.667 0.00 0.00 0.00 2.74
1352 2296 6.054941 TGCTGAACTTGAAATAGTGTCTTCA 58.945 36.000 0.00 0.00 0.00 3.02
1500 2466 7.375106 AGCTGCTAGTATTATTCATGCAATC 57.625 36.000 0.00 0.00 0.00 2.67
1590 2556 4.099266 GTCAGAGAGGCATCAGTTGTATCT 59.901 45.833 0.00 0.00 0.00 1.98
1609 2575 0.109458 TAGCGCACGAGTACTGTTGG 60.109 55.000 11.47 0.00 0.00 3.77
1610 2576 3.011760 GCGCACGAGTACTGTTGGC 62.012 63.158 0.30 0.00 0.00 4.52
1611 2577 1.663388 CGCACGAGTACTGTTGGCA 60.663 57.895 0.00 0.00 0.00 4.92
1612 2578 1.014044 CGCACGAGTACTGTTGGCAT 61.014 55.000 0.00 0.00 0.00 4.40
1613 2579 1.734377 CGCACGAGTACTGTTGGCATA 60.734 52.381 0.00 0.00 0.00 3.14
1614 2580 1.659098 GCACGAGTACTGTTGGCATAC 59.341 52.381 0.00 0.00 0.00 2.39
1615 2581 2.674177 GCACGAGTACTGTTGGCATACT 60.674 50.000 0.00 0.00 31.79 2.12
1616 2582 3.179830 CACGAGTACTGTTGGCATACTC 58.820 50.000 13.52 13.52 40.88 2.59
1618 2584 3.505464 GAGTACTGTTGGCATACTCGT 57.495 47.619 0.00 5.78 36.50 4.18
1619 2585 3.846360 GAGTACTGTTGGCATACTCGTT 58.154 45.455 0.00 0.00 36.50 3.85
1620 2586 4.243270 GAGTACTGTTGGCATACTCGTTT 58.757 43.478 0.00 0.00 36.50 3.60
1621 2587 5.395682 AGTACTGTTGGCATACTCGTTTA 57.604 39.130 0.00 0.00 0.00 2.01
1622 2588 5.974108 AGTACTGTTGGCATACTCGTTTAT 58.026 37.500 0.00 0.00 0.00 1.40
1623 2589 6.040878 AGTACTGTTGGCATACTCGTTTATC 58.959 40.000 0.00 0.00 0.00 1.75
1624 2590 5.086104 ACTGTTGGCATACTCGTTTATCT 57.914 39.130 0.00 0.00 0.00 1.98
1625 2591 5.488341 ACTGTTGGCATACTCGTTTATCTT 58.512 37.500 0.00 0.00 0.00 2.40
1626 2592 5.581085 ACTGTTGGCATACTCGTTTATCTTC 59.419 40.000 0.00 0.00 0.00 2.87
1627 2593 5.730550 TGTTGGCATACTCGTTTATCTTCT 58.269 37.500 0.00 0.00 0.00 2.85
1628 2594 6.170506 TGTTGGCATACTCGTTTATCTTCTT 58.829 36.000 0.00 0.00 0.00 2.52
1629 2595 6.312918 TGTTGGCATACTCGTTTATCTTCTTC 59.687 38.462 0.00 0.00 0.00 2.87
1630 2596 6.222038 TGGCATACTCGTTTATCTTCTTCT 57.778 37.500 0.00 0.00 0.00 2.85
1631 2597 6.640518 TGGCATACTCGTTTATCTTCTTCTT 58.359 36.000 0.00 0.00 0.00 2.52
1632 2598 7.103641 TGGCATACTCGTTTATCTTCTTCTTT 58.896 34.615 0.00 0.00 0.00 2.52
1633 2599 7.606456 TGGCATACTCGTTTATCTTCTTCTTTT 59.394 33.333 0.00 0.00 0.00 2.27
1634 2600 8.451748 GGCATACTCGTTTATCTTCTTCTTTTT 58.548 33.333 0.00 0.00 0.00 1.94
1657 2623 9.649024 TTTTTAGAAAAGTACAACCGTTTATCG 57.351 29.630 0.00 0.00 39.52 2.92
1658 2624 7.945033 TTAGAAAAGTACAACCGTTTATCGT 57.055 32.000 0.00 0.00 37.94 3.73
1659 2625 6.849588 AGAAAAGTACAACCGTTTATCGTT 57.150 33.333 0.00 0.00 37.94 3.85
1660 2626 6.881017 AGAAAAGTACAACCGTTTATCGTTC 58.119 36.000 0.00 0.00 37.94 3.95
1661 2627 5.596268 AAAGTACAACCGTTTATCGTTCC 57.404 39.130 0.00 0.00 37.94 3.62
1662 2628 3.244976 AGTACAACCGTTTATCGTTCCG 58.755 45.455 0.00 0.00 37.94 4.30
1663 2629 0.792031 ACAACCGTTTATCGTTCCGC 59.208 50.000 0.00 0.00 37.94 5.54
1664 2630 0.095762 CAACCGTTTATCGTTCCGCC 59.904 55.000 0.00 0.00 37.94 6.13
1665 2631 1.020861 AACCGTTTATCGTTCCGCCC 61.021 55.000 0.00 0.00 37.94 6.13
1666 2632 1.448189 CCGTTTATCGTTCCGCCCA 60.448 57.895 0.00 0.00 37.94 5.36
1667 2633 1.020333 CCGTTTATCGTTCCGCCCAA 61.020 55.000 0.00 0.00 37.94 4.12
1668 2634 1.011333 CGTTTATCGTTCCGCCCAAT 58.989 50.000 0.00 0.00 34.52 3.16
1669 2635 1.004292 CGTTTATCGTTCCGCCCAATC 60.004 52.381 0.00 0.00 34.52 2.67
1670 2636 1.004292 GTTTATCGTTCCGCCCAATCG 60.004 52.381 0.00 0.00 0.00 3.34
1671 2637 0.176219 TTATCGTTCCGCCCAATCGT 59.824 50.000 0.00 0.00 0.00 3.73
1672 2638 0.249155 TATCGTTCCGCCCAATCGTC 60.249 55.000 0.00 0.00 0.00 4.20
1673 2639 1.956629 ATCGTTCCGCCCAATCGTCT 61.957 55.000 0.00 0.00 0.00 4.18
1674 2640 1.740296 CGTTCCGCCCAATCGTCTT 60.740 57.895 0.00 0.00 0.00 3.01
1675 2641 1.296056 CGTTCCGCCCAATCGTCTTT 61.296 55.000 0.00 0.00 0.00 2.52
1676 2642 0.446616 GTTCCGCCCAATCGTCTTTC 59.553 55.000 0.00 0.00 0.00 2.62
1677 2643 0.675522 TTCCGCCCAATCGTCTTTCC 60.676 55.000 0.00 0.00 0.00 3.13
1678 2644 1.078426 CCGCCCAATCGTCTTTCCT 60.078 57.895 0.00 0.00 0.00 3.36
1679 2645 0.676782 CCGCCCAATCGTCTTTCCTT 60.677 55.000 0.00 0.00 0.00 3.36
1680 2646 1.165270 CGCCCAATCGTCTTTCCTTT 58.835 50.000 0.00 0.00 0.00 3.11
1681 2647 1.130561 CGCCCAATCGTCTTTCCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
1682 2648 1.130561 GCCCAATCGTCTTTCCTTTCG 59.869 52.381 0.00 0.00 0.00 3.46
1683 2649 2.695359 CCCAATCGTCTTTCCTTTCGA 58.305 47.619 0.00 0.00 36.77 3.71
1684 2650 3.071479 CCCAATCGTCTTTCCTTTCGAA 58.929 45.455 0.00 0.00 35.99 3.71
1685 2651 3.500680 CCCAATCGTCTTTCCTTTCGAAA 59.499 43.478 10.71 10.71 38.16 3.46
1686 2652 4.464112 CCAATCGTCTTTCCTTTCGAAAC 58.536 43.478 6.47 0.00 35.49 2.78
1687 2653 4.213482 CCAATCGTCTTTCCTTTCGAAACT 59.787 41.667 6.47 0.00 35.49 2.66
1688 2654 5.407387 CCAATCGTCTTTCCTTTCGAAACTA 59.593 40.000 6.47 0.00 35.49 2.24
1689 2655 6.401153 CCAATCGTCTTTCCTTTCGAAACTAG 60.401 42.308 6.47 0.00 35.49 2.57
1690 2656 3.985925 TCGTCTTTCCTTTCGAAACTAGC 59.014 43.478 6.47 0.00 35.49 3.42
1691 2657 3.988517 CGTCTTTCCTTTCGAAACTAGCT 59.011 43.478 6.47 0.00 35.49 3.32
1692 2658 4.090210 CGTCTTTCCTTTCGAAACTAGCTC 59.910 45.833 6.47 0.00 35.49 4.09
1693 2659 4.989168 GTCTTTCCTTTCGAAACTAGCTCA 59.011 41.667 6.47 0.00 35.49 4.26
1694 2660 5.465724 GTCTTTCCTTTCGAAACTAGCTCAA 59.534 40.000 6.47 0.00 35.49 3.02
1695 2661 5.465724 TCTTTCCTTTCGAAACTAGCTCAAC 59.534 40.000 6.47 0.00 35.49 3.18
1696 2662 4.602340 TCCTTTCGAAACTAGCTCAACT 57.398 40.909 6.47 0.00 0.00 3.16
1697 2663 4.307432 TCCTTTCGAAACTAGCTCAACTG 58.693 43.478 6.47 0.00 0.00 3.16
1698 2664 3.120511 CCTTTCGAAACTAGCTCAACTGC 60.121 47.826 6.47 0.00 0.00 4.40
1699 2665 3.386768 TTCGAAACTAGCTCAACTGCT 57.613 42.857 0.00 0.00 46.11 4.24
1700 2666 2.947852 TCGAAACTAGCTCAACTGCTC 58.052 47.619 0.00 0.00 42.97 4.26
1701 2667 2.296190 TCGAAACTAGCTCAACTGCTCA 59.704 45.455 0.00 0.00 42.97 4.26
1702 2668 3.056536 TCGAAACTAGCTCAACTGCTCAT 60.057 43.478 0.00 0.00 42.97 2.90
1703 2669 3.681897 CGAAACTAGCTCAACTGCTCATT 59.318 43.478 0.00 0.00 42.97 2.57
1704 2670 4.153117 CGAAACTAGCTCAACTGCTCATTT 59.847 41.667 0.00 0.00 42.97 2.32
1705 2671 5.368256 AAACTAGCTCAACTGCTCATTTG 57.632 39.130 0.00 0.00 42.97 2.32
1706 2672 4.013267 ACTAGCTCAACTGCTCATTTGT 57.987 40.909 0.00 0.00 42.97 2.83
1707 2673 5.152623 ACTAGCTCAACTGCTCATTTGTA 57.847 39.130 0.00 0.00 42.97 2.41
1708 2674 5.174395 ACTAGCTCAACTGCTCATTTGTAG 58.826 41.667 0.00 0.00 42.97 2.74
1709 2675 4.277515 AGCTCAACTGCTCATTTGTAGA 57.722 40.909 0.95 0.00 39.34 2.59
1710 2676 4.645535 AGCTCAACTGCTCATTTGTAGAA 58.354 39.130 0.95 0.00 39.34 2.10
1711 2677 5.065914 AGCTCAACTGCTCATTTGTAGAAA 58.934 37.500 0.00 0.00 39.34 2.52
1712 2678 5.532406 AGCTCAACTGCTCATTTGTAGAAAA 59.468 36.000 0.00 0.00 39.34 2.29
1713 2679 5.626955 GCTCAACTGCTCATTTGTAGAAAAC 59.373 40.000 0.00 0.00 0.00 2.43
1714 2680 6.691754 TCAACTGCTCATTTGTAGAAAACA 57.308 33.333 0.00 0.00 35.88 2.83
1715 2681 7.094508 TCAACTGCTCATTTGTAGAAAACAA 57.905 32.000 0.00 0.00 46.41 2.83
1733 2699 9.921637 AGAAAACAATAGAACTGTTGAAAAACA 57.078 25.926 15.87 0.00 37.10 2.83
1742 2708 7.193595 AGAACTGTTGAAAAACAATTCTACCG 58.806 34.615 12.16 0.00 44.37 4.02
1743 2709 6.445357 ACTGTTGAAAAACAATTCTACCGT 57.555 33.333 0.00 0.00 40.76 4.83
1744 2710 6.859017 ACTGTTGAAAAACAATTCTACCGTT 58.141 32.000 0.00 0.00 40.76 4.44
1745 2711 7.317390 ACTGTTGAAAAACAATTCTACCGTTT 58.683 30.769 0.00 0.00 40.76 3.60
1746 2712 7.815549 ACTGTTGAAAAACAATTCTACCGTTTT 59.184 29.630 0.00 0.00 42.91 2.43
1752 2718 7.764695 AAAACAATTCTACCGTTTTTCTTGG 57.235 32.000 0.00 0.00 39.21 3.61
1753 2719 5.447624 ACAATTCTACCGTTTTTCTTGGG 57.552 39.130 0.00 0.00 0.00 4.12
1754 2720 4.279922 ACAATTCTACCGTTTTTCTTGGGG 59.720 41.667 0.00 0.00 0.00 4.96
1755 2721 3.860968 TTCTACCGTTTTTCTTGGGGA 57.139 42.857 0.00 0.00 0.00 4.81
1756 2722 3.412237 TCTACCGTTTTTCTTGGGGAG 57.588 47.619 0.00 0.00 0.00 4.30
1757 2723 1.810755 CTACCGTTTTTCTTGGGGAGC 59.189 52.381 0.00 0.00 0.00 4.70
1758 2724 0.185175 ACCGTTTTTCTTGGGGAGCT 59.815 50.000 0.00 0.00 0.00 4.09
1759 2725 0.881796 CCGTTTTTCTTGGGGAGCTC 59.118 55.000 4.71 4.71 0.00 4.09
1760 2726 0.517316 CGTTTTTCTTGGGGAGCTCG 59.483 55.000 7.83 0.00 0.00 5.03
1761 2727 1.876416 CGTTTTTCTTGGGGAGCTCGA 60.876 52.381 7.83 0.00 0.00 4.04
1762 2728 1.535896 GTTTTTCTTGGGGAGCTCGAC 59.464 52.381 7.83 3.32 0.00 4.20
1763 2729 0.036306 TTTTCTTGGGGAGCTCGACC 59.964 55.000 16.79 16.79 0.00 4.79
1769 2735 2.417936 GGGAGCTCGACCCGAATC 59.582 66.667 7.83 0.00 37.85 2.52
1770 2736 2.417936 GGAGCTCGACCCGAATCC 59.582 66.667 7.83 0.00 35.65 3.01
1771 2737 2.417936 GAGCTCGACCCGAATCCC 59.582 66.667 0.00 0.00 34.74 3.85
1772 2738 2.042843 AGCTCGACCCGAATCCCT 60.043 61.111 0.00 0.00 34.74 4.20
1773 2739 0.822532 GAGCTCGACCCGAATCCCTA 60.823 60.000 0.00 0.00 34.74 3.53
1774 2740 0.178958 AGCTCGACCCGAATCCCTAT 60.179 55.000 0.00 0.00 34.74 2.57
1775 2741 0.038159 GCTCGACCCGAATCCCTATG 60.038 60.000 0.00 0.00 34.74 2.23
1776 2742 0.038159 CTCGACCCGAATCCCTATGC 60.038 60.000 0.00 0.00 34.74 3.14
1777 2743 1.372997 CGACCCGAATCCCTATGCG 60.373 63.158 0.00 0.00 33.54 4.73
1778 2744 1.668151 GACCCGAATCCCTATGCGC 60.668 63.158 0.00 0.00 32.27 6.09
1779 2745 2.358737 CCCGAATCCCTATGCGCC 60.359 66.667 4.18 0.00 32.27 6.53
1851 2817 4.042271 ACAGGGACGGATGGTAAATTTT 57.958 40.909 0.00 0.00 0.00 1.82
1872 2838 2.081462 CGGGATGTCCTAACCAAACAC 58.919 52.381 0.00 0.00 35.95 3.32
2031 2999 3.077359 CTCGCCAAATTCTCCTTCTGTT 58.923 45.455 0.00 0.00 0.00 3.16
2038 3006 6.003950 CCAAATTCTCCTTCTGTTTGTCCTA 58.996 40.000 0.00 0.00 0.00 2.94
2047 3015 2.093869 TCTGTTTGTCCTATACCACCGC 60.094 50.000 0.00 0.00 0.00 5.68
2057 3025 0.324943 ATACCACCGCTTTGCAGTCT 59.675 50.000 0.00 0.00 0.00 3.24
2091 3059 3.232213 TGCGTCTCAAATAGAGGTCAC 57.768 47.619 0.00 0.00 44.81 3.67
2105 3073 1.301716 GTCACCAGCCAAAGCGAGA 60.302 57.895 0.00 0.00 46.67 4.04
2143 3111 2.170817 GAGCTTCTAAAGTCGGGGGATT 59.829 50.000 0.00 0.00 0.00 3.01
2219 3187 2.575735 TCTGCATATGACCCCAACTGAA 59.424 45.455 6.97 0.00 0.00 3.02
2259 3227 1.792367 CAGCGTCGATGTTGAACTTCA 59.208 47.619 15.65 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.397103 TCATCATTGATCAAGCTTGACACC 59.603 41.667 30.66 21.40 40.49 4.16
2 3 5.123502 AGTCATCATTGATCAAGCTTGACAC 59.876 40.000 30.66 25.11 40.49 3.67
35 36 3.558746 GCTCTGATAATCCCCCATGACAG 60.559 52.174 0.00 0.00 0.00 3.51
68 69 1.597461 GAGACCCTTGGACCTTCCG 59.403 63.158 0.00 0.00 40.17 4.30
84 85 1.301293 GCCAGGTCTTTGGAGGGAG 59.699 63.158 0.00 0.00 40.87 4.30
86 87 0.895559 GTTGCCAGGTCTTTGGAGGG 60.896 60.000 0.00 0.00 40.87 4.30
129 130 8.503626 CACGAACAAAATTTTGAAAATCAAACG 58.496 29.630 32.20 22.25 45.03 3.60
286 596 5.224109 CCGAACAAAATTTCAAAACGCAAAC 59.776 36.000 0.00 0.00 0.00 2.93
290 600 3.552294 TCCCGAACAAAATTTCAAAACGC 59.448 39.130 0.00 0.00 0.00 4.84
328 638 7.709149 AATTCCAAACAAAATTGAAAACCCA 57.291 28.000 0.00 0.00 31.84 4.51
400 712 7.589954 ACTCCGAACAAATTCAAAATAACGAAG 59.410 33.333 0.00 0.00 34.14 3.79
407 719 8.485976 TTTGAAACTCCGAACAAATTCAAAAT 57.514 26.923 8.53 0.00 41.26 1.82
622 993 1.675219 GGGCACTGTAGAAACCCGA 59.325 57.895 0.00 0.00 0.00 5.14
943 1887 0.904865 TGGTGAGCCAGAGAACGGAT 60.905 55.000 0.00 0.00 40.46 4.18
972 1916 2.483583 TCATTGTTTCGTTGGTGTGC 57.516 45.000 0.00 0.00 0.00 4.57
1399 2345 9.414295 TCATATACTGTACTGTACAACAACAAC 57.586 33.333 20.09 0.00 38.38 3.32
1435 2401 7.447374 TGAGTGTACAAGTGGAAATTAATGG 57.553 36.000 0.00 0.00 0.00 3.16
1441 2407 9.167311 GAAATCTATGAGTGTACAAGTGGAAAT 57.833 33.333 0.00 0.00 0.00 2.17
1500 2466 0.952497 ACAGCACAAGCCAGACATCG 60.952 55.000 0.00 0.00 43.56 3.84
1590 2556 0.109458 CCAACAGTACTCGTGCGCTA 60.109 55.000 9.73 0.00 0.00 4.26
1631 2597 9.649024 CGATAAACGGTTGTACTTTTCTAAAAA 57.351 29.630 0.00 0.00 38.46 1.94
1634 2600 8.487176 GAACGATAAACGGTTGTACTTTTCTAA 58.513 33.333 0.00 0.00 44.13 2.10
1635 2601 7.116233 GGAACGATAAACGGTTGTACTTTTCTA 59.884 37.037 0.00 0.00 44.13 2.10
1636 2602 6.073602 GGAACGATAAACGGTTGTACTTTTCT 60.074 38.462 0.00 0.00 44.13 2.52
1637 2603 6.073369 GGAACGATAAACGGTTGTACTTTTC 58.927 40.000 0.00 0.00 44.13 2.29
1638 2604 5.989249 GGAACGATAAACGGTTGTACTTTT 58.011 37.500 0.00 0.00 44.13 2.27
1639 2605 5.596268 GGAACGATAAACGGTTGTACTTT 57.404 39.130 0.00 0.00 44.13 2.66
1657 2623 0.446616 GAAAGACGATTGGGCGGAAC 59.553 55.000 0.00 0.00 35.12 3.62
1658 2624 0.675522 GGAAAGACGATTGGGCGGAA 60.676 55.000 0.00 0.00 35.12 4.30
1659 2625 1.078708 GGAAAGACGATTGGGCGGA 60.079 57.895 0.00 0.00 35.12 5.54
1660 2626 0.676782 AAGGAAAGACGATTGGGCGG 60.677 55.000 0.00 0.00 35.12 6.13
1661 2627 1.130561 GAAAGGAAAGACGATTGGGCG 59.869 52.381 0.00 0.00 37.29 6.13
1662 2628 1.130561 CGAAAGGAAAGACGATTGGGC 59.869 52.381 0.00 0.00 0.00 5.36
1663 2629 2.695359 TCGAAAGGAAAGACGATTGGG 58.305 47.619 0.00 0.00 0.00 4.12
1664 2630 4.213482 AGTTTCGAAAGGAAAGACGATTGG 59.787 41.667 11.66 0.00 44.95 3.16
1665 2631 5.344207 AGTTTCGAAAGGAAAGACGATTG 57.656 39.130 11.66 0.00 44.95 2.67
1666 2632 5.120363 GCTAGTTTCGAAAGGAAAGACGATT 59.880 40.000 11.66 0.00 44.95 3.34
1667 2633 4.626172 GCTAGTTTCGAAAGGAAAGACGAT 59.374 41.667 11.66 0.00 44.95 3.73
1668 2634 3.985925 GCTAGTTTCGAAAGGAAAGACGA 59.014 43.478 11.66 0.00 44.95 4.20
1669 2635 3.988517 AGCTAGTTTCGAAAGGAAAGACG 59.011 43.478 11.66 0.00 44.95 4.18
1670 2636 4.989168 TGAGCTAGTTTCGAAAGGAAAGAC 59.011 41.667 11.66 0.00 44.95 3.01
1671 2637 5.209818 TGAGCTAGTTTCGAAAGGAAAGA 57.790 39.130 11.66 0.00 44.95 2.52
1672 2638 5.467063 AGTTGAGCTAGTTTCGAAAGGAAAG 59.533 40.000 11.66 7.49 44.95 2.62
1673 2639 5.236478 CAGTTGAGCTAGTTTCGAAAGGAAA 59.764 40.000 11.66 0.00 42.23 3.13
1674 2640 4.750098 CAGTTGAGCTAGTTTCGAAAGGAA 59.250 41.667 11.66 0.00 0.00 3.36
1675 2641 4.307432 CAGTTGAGCTAGTTTCGAAAGGA 58.693 43.478 11.66 0.95 0.00 3.36
1676 2642 3.120511 GCAGTTGAGCTAGTTTCGAAAGG 60.121 47.826 11.66 6.00 0.00 3.11
1677 2643 3.743396 AGCAGTTGAGCTAGTTTCGAAAG 59.257 43.478 11.66 0.25 44.50 2.62
1678 2644 3.728845 AGCAGTTGAGCTAGTTTCGAAA 58.271 40.909 6.47 6.47 44.50 3.46
1679 2645 3.243737 TGAGCAGTTGAGCTAGTTTCGAA 60.244 43.478 0.00 0.00 46.75 3.71
1680 2646 2.296190 TGAGCAGTTGAGCTAGTTTCGA 59.704 45.455 0.00 0.00 46.75 3.71
1681 2647 2.677199 TGAGCAGTTGAGCTAGTTTCG 58.323 47.619 0.00 0.00 46.75 3.46
1682 2648 5.049129 ACAAATGAGCAGTTGAGCTAGTTTC 60.049 40.000 16.34 0.00 46.75 2.78
1683 2649 4.823989 ACAAATGAGCAGTTGAGCTAGTTT 59.176 37.500 16.34 0.00 46.75 2.66
1684 2650 4.392940 ACAAATGAGCAGTTGAGCTAGTT 58.607 39.130 16.34 0.00 46.75 2.24
1685 2651 4.013267 ACAAATGAGCAGTTGAGCTAGT 57.987 40.909 16.34 0.00 46.75 2.57
1686 2652 5.414360 TCTACAAATGAGCAGTTGAGCTAG 58.586 41.667 16.34 8.50 46.75 3.42
1687 2653 5.405935 TCTACAAATGAGCAGTTGAGCTA 57.594 39.130 16.34 0.00 46.75 3.32
1688 2654 8.811403 TGTTTTCTACAAATGAGCAGTTGAGCT 61.811 37.037 16.34 0.00 39.97 4.09
1689 2655 5.362556 TTTCTACAAATGAGCAGTTGAGC 57.637 39.130 16.34 0.00 38.53 4.26
1690 2656 6.728200 TGTTTTCTACAAATGAGCAGTTGAG 58.272 36.000 16.34 9.69 38.53 3.02
1691 2657 6.691754 TGTTTTCTACAAATGAGCAGTTGA 57.308 33.333 16.34 1.33 38.53 3.18
1707 2673 9.921637 TGTTTTTCAACAGTTCTATTGTTTTCT 57.078 25.926 0.00 0.00 38.03 2.52
1719 2685 6.859017 ACGGTAGAATTGTTTTTCAACAGTT 58.141 32.000 0.00 0.00 43.92 3.16
1720 2686 6.445357 ACGGTAGAATTGTTTTTCAACAGT 57.555 33.333 0.00 0.00 43.92 3.55
1721 2687 7.749539 AAACGGTAGAATTGTTTTTCAACAG 57.250 32.000 0.00 0.00 43.92 3.16
1722 2688 8.535690 AAAAACGGTAGAATTGTTTTTCAACA 57.464 26.923 8.70 0.00 46.91 3.33
1728 2694 6.759356 CCCAAGAAAAACGGTAGAATTGTTTT 59.241 34.615 0.00 0.00 45.00 2.43
1729 2695 6.277605 CCCAAGAAAAACGGTAGAATTGTTT 58.722 36.000 0.00 0.00 37.41 2.83
1730 2696 5.221362 CCCCAAGAAAAACGGTAGAATTGTT 60.221 40.000 0.00 0.00 0.00 2.83
1731 2697 4.279922 CCCCAAGAAAAACGGTAGAATTGT 59.720 41.667 0.00 0.00 0.00 2.71
1732 2698 4.521256 TCCCCAAGAAAAACGGTAGAATTG 59.479 41.667 0.00 0.00 0.00 2.32
1733 2699 4.732065 TCCCCAAGAAAAACGGTAGAATT 58.268 39.130 0.00 0.00 0.00 2.17
1734 2700 4.332828 CTCCCCAAGAAAAACGGTAGAAT 58.667 43.478 0.00 0.00 0.00 2.40
1735 2701 3.746940 CTCCCCAAGAAAAACGGTAGAA 58.253 45.455 0.00 0.00 0.00 2.10
1736 2702 2.551504 GCTCCCCAAGAAAAACGGTAGA 60.552 50.000 0.00 0.00 0.00 2.59
1737 2703 1.810755 GCTCCCCAAGAAAAACGGTAG 59.189 52.381 0.00 0.00 0.00 3.18
1738 2704 1.422402 AGCTCCCCAAGAAAAACGGTA 59.578 47.619 0.00 0.00 0.00 4.02
1739 2705 0.185175 AGCTCCCCAAGAAAAACGGT 59.815 50.000 0.00 0.00 0.00 4.83
1740 2706 0.881796 GAGCTCCCCAAGAAAAACGG 59.118 55.000 0.87 0.00 0.00 4.44
1741 2707 0.517316 CGAGCTCCCCAAGAAAAACG 59.483 55.000 8.47 0.00 0.00 3.60
1742 2708 1.535896 GTCGAGCTCCCCAAGAAAAAC 59.464 52.381 8.47 0.00 0.00 2.43
1743 2709 1.544759 GGTCGAGCTCCCCAAGAAAAA 60.545 52.381 8.47 0.00 0.00 1.94
1744 2710 0.036306 GGTCGAGCTCCCCAAGAAAA 59.964 55.000 8.47 0.00 0.00 2.29
1745 2711 1.677552 GGTCGAGCTCCCCAAGAAA 59.322 57.895 8.47 0.00 0.00 2.52
1746 2712 2.291043 GGGTCGAGCTCCCCAAGAA 61.291 63.158 20.03 0.00 40.88 2.52
1747 2713 2.683933 GGGTCGAGCTCCCCAAGA 60.684 66.667 20.03 3.84 40.88 3.02
1748 2714 4.148825 CGGGTCGAGCTCCCCAAG 62.149 72.222 23.28 11.45 41.30 3.61
1749 2715 4.689549 TCGGGTCGAGCTCCCCAA 62.690 66.667 23.28 6.72 41.30 4.12
1750 2716 3.976490 ATTCGGGTCGAGCTCCCCA 62.976 63.158 23.28 9.12 41.30 4.96
1751 2717 3.153270 GATTCGGGTCGAGCTCCCC 62.153 68.421 16.13 16.13 41.78 4.81
1752 2718 2.417936 GATTCGGGTCGAGCTCCC 59.582 66.667 15.18 7.07 41.41 4.30
1753 2719 2.417936 GGATTCGGGTCGAGCTCC 59.582 66.667 15.18 9.66 37.14 4.70
1754 2720 0.822532 TAGGGATTCGGGTCGAGCTC 60.823 60.000 15.18 2.73 37.14 4.09
1755 2721 0.178958 ATAGGGATTCGGGTCGAGCT 60.179 55.000 15.18 0.00 37.14 4.09
1756 2722 0.038159 CATAGGGATTCGGGTCGAGC 60.038 60.000 5.93 5.93 37.14 5.03
1757 2723 0.038159 GCATAGGGATTCGGGTCGAG 60.038 60.000 0.00 0.00 37.14 4.04
1758 2724 1.802337 CGCATAGGGATTCGGGTCGA 61.802 60.000 0.00 0.00 0.00 4.20
1759 2725 1.372997 CGCATAGGGATTCGGGTCG 60.373 63.158 0.00 0.00 0.00 4.79
1760 2726 1.668151 GCGCATAGGGATTCGGGTC 60.668 63.158 0.30 0.00 0.00 4.46
1761 2727 2.426023 GCGCATAGGGATTCGGGT 59.574 61.111 0.30 0.00 0.00 5.28
1762 2728 2.358737 GGCGCATAGGGATTCGGG 60.359 66.667 10.83 0.00 0.00 5.14
1763 2729 0.606401 AATGGCGCATAGGGATTCGG 60.606 55.000 10.83 0.00 0.00 4.30
1764 2730 1.238439 AAATGGCGCATAGGGATTCG 58.762 50.000 10.83 0.00 0.00 3.34
1765 2731 3.733443 AAAAATGGCGCATAGGGATTC 57.267 42.857 10.83 0.00 0.00 2.52
1851 2817 1.979308 TGTTTGGTTAGGACATCCCGA 59.021 47.619 0.00 0.00 40.87 5.14
1961 2927 6.763355 AGTAGATCACTCTTCAGCTTTTGAA 58.237 36.000 0.00 0.00 43.24 2.69
2031 2999 2.937873 GCAAAGCGGTGGTATAGGACAA 60.938 50.000 0.00 0.00 0.00 3.18
2057 3025 2.153645 AGACGCATTCAAGTTGCATCA 58.846 42.857 0.00 0.00 40.14 3.07
2091 3059 2.046507 AGCTCTCGCTTTGGCTGG 60.047 61.111 0.00 0.00 46.47 4.85
2105 3073 1.653094 CTCTCGCCGTCAGAGAAGCT 61.653 60.000 0.00 0.00 43.30 3.74
2116 3084 1.551145 GACTTTAGAAGCTCTCGCCG 58.449 55.000 0.00 0.00 36.60 6.46
2129 3097 3.009695 ACATTGTGAATCCCCCGACTTTA 59.990 43.478 0.00 0.00 0.00 1.85
2143 3111 4.136796 CCTTTCCTTCAGACACATTGTGA 58.863 43.478 23.12 0.00 36.96 3.58
2219 3187 5.296780 CGCTGTTGTATCCAGATATTTTGGT 59.703 40.000 6.99 0.00 37.02 3.67
2248 3216 3.286353 TCAGGCAATGTGAAGTTCAACA 58.714 40.909 7.25 8.68 0.00 3.33
2259 3227 1.149174 CCCCGCTATCAGGCAATGT 59.851 57.895 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.