Multiple sequence alignment - TraesCS6B01G228200

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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 TraesCS6B01G228200 chr6B 100.000 3634 0 0 1 3634 360392858 360396491 0.000000e+00 6711
1 TraesCS6B01G228200 chr6B 90.840 2118 177 15 1526 3634 457477608 457479717 0.000000e+00 2820
2 TraesCS6B01G228200 chr6B 90.986 2008 167 13 1633 3633 372486657 372484657 0.000000e+00 2693
3 TraesCS6B01G228200 chr6B 89.785 1625 128 29 2 1606 132723975 132722369 0.000000e+00 2047
4 TraesCS6B01G228200 chr6B 89.281 1558 133 19 2 1551 372488084 372486553 0.000000e+00 1921
5 TraesCS6B01G228200 chr7B 93.588 2121 128 8 1519 3634 622479612 622477495 0.000000e+00 3157
6 TraesCS6B01G228200 chr7B 89.554 2240 195 23 1398 3634 145082463 145080260 0.000000e+00 2804
7 TraesCS6B01G228200 chr7B 91.107 1698 128 18 5 1688 622481063 622479375 0.000000e+00 2278
8 TraesCS6B01G228200 chr7B 91.508 1625 112 18 2 1618 222672413 222674019 0.000000e+00 2213
9 TraesCS6B01G228200 chr7B 91.679 1394 105 10 2 1389 145091276 145089888 0.000000e+00 1921
10 TraesCS6B01G228200 chr7B 88.384 1584 139 34 2 1574 649485791 649487340 0.000000e+00 1864
11 TraesCS6B01G228200 chr7B 84.630 1607 193 37 11 1581 337179220 337177632 0.000000e+00 1550
12 TraesCS6B01G228200 chr4B 91.354 2082 155 21 1566 3634 324939559 324941628 0.000000e+00 2824
13 TraesCS6B01G228200 chr4B 90.125 2076 181 18 1572 3634 312094983 312092919 0.000000e+00 2676
14 TraesCS6B01G228200 chr4B 91.125 1645 115 19 4 1643 324938135 324939753 0.000000e+00 2200
15 TraesCS6B01G228200 chr5B 91.071 2072 163 20 1566 3628 179190413 179192471 0.000000e+00 2782
16 TraesCS6B01G228200 chr5B 90.959 1648 134 12 2 1643 179188969 179190607 0.000000e+00 2204
17 TraesCS6B01G228200 chr3B 90.034 2077 184 17 1572 3634 317262181 317264248 0.000000e+00 2667
18 TraesCS6B01G228200 chr3B 88.691 1627 145 23 2 1618 317260767 317262364 0.000000e+00 1949
19 TraesCS6B01G228200 chr3B 75.758 429 72 22 3155 3569 17177677 17178087 1.720000e-43 187
20 TraesCS6B01G228200 chr2B 89.776 2054 188 16 1595 3634 589104706 589106751 0.000000e+00 2610
21 TraesCS6B01G228200 chr5A 87.063 1631 142 34 2 1582 148239159 148240770 0.000000e+00 1779
22 TraesCS6B01G228200 chr1D 86.514 1572 165 36 7 1551 165160850 165159299 0.000000e+00 1685
23 TraesCS6B01G228200 chr6D 90.589 1222 103 11 2 1216 370585010 370586226 0.000000e+00 1609


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 TraesCS6B01G228200 chr6B 360392858 360396491 3633 False 6711.0 6711 100.0000 1 3634 1 chr6B.!!$F1 3633
1 TraesCS6B01G228200 chr6B 457477608 457479717 2109 False 2820.0 2820 90.8400 1526 3634 1 chr6B.!!$F2 2108
2 TraesCS6B01G228200 chr6B 372484657 372488084 3427 True 2307.0 2693 90.1335 2 3633 2 chr6B.!!$R2 3631
3 TraesCS6B01G228200 chr6B 132722369 132723975 1606 True 2047.0 2047 89.7850 2 1606 1 chr6B.!!$R1 1604
4 TraesCS6B01G228200 chr7B 145080260 145082463 2203 True 2804.0 2804 89.5540 1398 3634 1 chr7B.!!$R1 2236
5 TraesCS6B01G228200 chr7B 622477495 622481063 3568 True 2717.5 3157 92.3475 5 3634 2 chr7B.!!$R4 3629
6 TraesCS6B01G228200 chr7B 222672413 222674019 1606 False 2213.0 2213 91.5080 2 1618 1 chr7B.!!$F1 1616
7 TraesCS6B01G228200 chr7B 145089888 145091276 1388 True 1921.0 1921 91.6790 2 1389 1 chr7B.!!$R2 1387
8 TraesCS6B01G228200 chr7B 649485791 649487340 1549 False 1864.0 1864 88.3840 2 1574 1 chr7B.!!$F2 1572
9 TraesCS6B01G228200 chr7B 337177632 337179220 1588 True 1550.0 1550 84.6300 11 1581 1 chr7B.!!$R3 1570
10 TraesCS6B01G228200 chr4B 312092919 312094983 2064 True 2676.0 2676 90.1250 1572 3634 1 chr4B.!!$R1 2062
11 TraesCS6B01G228200 chr4B 324938135 324941628 3493 False 2512.0 2824 91.2395 4 3634 2 chr4B.!!$F1 3630
12 TraesCS6B01G228200 chr5B 179188969 179192471 3502 False 2493.0 2782 91.0150 2 3628 2 chr5B.!!$F1 3626
13 TraesCS6B01G228200 chr3B 317260767 317264248 3481 False 2308.0 2667 89.3625 2 3634 2 chr3B.!!$F2 3632
14 TraesCS6B01G228200 chr2B 589104706 589106751 2045 False 2610.0 2610 89.7760 1595 3634 1 chr2B.!!$F1 2039
15 TraesCS6B01G228200 chr5A 148239159 148240770 1611 False 1779.0 1779 87.0630 2 1582 1 chr5A.!!$F1 1580
16 TraesCS6B01G228200 chr1D 165159299 165160850 1551 True 1685.0 1685 86.5140 7 1551 1 chr1D.!!$R1 1544
17 TraesCS6B01G228200 chr6D 370585010 370586226 1216 False 1609.0 1609 90.5890 2 1216 1 chr6D.!!$F1 1214

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
889 902 0.324943 AAGCATTACGTGAGCCTGGT 59.675 50.0 0.0 0.0 0.0 4.00 F
2108 2487 0.323360 AATGGGACGGGATTGTGTGG 60.323 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2575 0.036590 GTTTGTGGCCCCAATGCATT 59.963 50.0 5.99 5.99 0.0 3.56 R
3464 3864 0.478072 AGGTGCAATGGTTGTGGAGA 59.522 50.0 0.00 0.00 0.0 3.71 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
78 79 6.590656 AGAATGGTCCAAATATTGTCCCTA 57.409 37.500 0.00 0.00 0.00 3.53
165 166 2.099427 GGCAAAGTACCGTAGAGAGAGG 59.901 54.545 0.00 0.00 0.00 3.69
270 271 0.894184 ACGATGAGGACCGTGTCAGT 60.894 55.000 6.41 0.00 37.64 3.41
318 319 7.119262 GCTACAAGAAGAGCCTACAAACATTTA 59.881 37.037 0.00 0.00 32.25 1.40
326 327 7.101054 AGAGCCTACAAACATTTACGTGATTA 58.899 34.615 0.00 0.00 0.00 1.75
402 403 9.247861 GCTCCATTCATAGGAATAAATAACCAT 57.752 33.333 1.67 0.00 41.78 3.55
545 548 1.534595 CCAGGATTTTAGCATGCGCAC 60.535 52.381 14.90 0.00 42.27 5.34
546 549 1.132834 CAGGATTTTAGCATGCGCACA 59.867 47.619 14.90 0.00 42.27 4.57
761 772 2.919228 AGTCCAAGACAACAAGACACC 58.081 47.619 0.00 0.00 34.60 4.16
777 788 2.488153 GACACCAAATAGCTTGTGGGAC 59.512 50.000 12.96 2.80 36.69 4.46
889 902 0.324943 AAGCATTACGTGAGCCTGGT 59.675 50.000 0.00 0.00 0.00 4.00
916 929 0.464870 TGTTGCAGTTTGCCAAGCAT 59.535 45.000 0.00 0.00 44.23 3.79
952 965 5.163713 GCAACAGAAAATACTGGGATCTGAC 60.164 44.000 7.98 0.00 39.85 3.51
1184 1219 5.899120 TTGAAGCTAACATCTCTAGTCGT 57.101 39.130 0.00 0.00 0.00 4.34
1210 1252 7.909121 TCACATGAATGCAAAACAAAAATGAAC 59.091 29.630 0.00 0.00 0.00 3.18
1228 1285 8.801715 AAATGAACAAACTATGTAGTTGCAAG 57.198 30.769 0.00 0.00 45.17 4.01
1248 1305 5.003778 GCAAGAACAAATATTAGTTGCTGCG 59.996 40.000 3.89 0.00 36.68 5.18
1374 1433 6.413052 AGATGAACTTATGTGCATTGAGAGT 58.587 36.000 3.82 0.00 42.29 3.24
1439 1525 9.743057 TCTTTTGACATGTTGATCGTTTTAAAT 57.257 25.926 0.00 0.00 0.00 1.40
1443 1529 9.952188 TTGACATGTTGATCGTTTTAAATACAA 57.048 25.926 0.00 0.00 0.00 2.41
1465 1579 7.839907 ACAATAGTTGCCATGTGAAAATACAT 58.160 30.769 0.00 0.00 41.77 2.29
1486 1623 6.424176 CATTGCATTTGCCATGTGAAAATA 57.576 33.333 8.12 0.00 38.80 1.40
1489 1626 4.689812 TGCATTTGCCATGTGAAAATACAC 59.310 37.500 0.00 0.00 41.18 2.90
1507 1644 4.540359 ACACTGCATTTGCCATGTAAAT 57.460 36.364 6.92 0.00 41.18 1.40
1515 1652 6.017852 TGCATTTGCCATGTAAATATGCAATG 60.018 34.615 13.87 10.69 41.18 2.82
1516 1653 5.987777 TTTGCCATGTAAATATGCAATGC 57.012 34.783 0.00 0.00 30.26 3.56
1517 1654 4.667519 TGCCATGTAAATATGCAATGCA 57.332 36.364 11.44 11.44 44.86 3.96
1532 1669 4.955925 CAATGCATTTGCCATGTGAAAT 57.044 36.364 9.83 0.00 41.18 2.17
1534 1671 6.424176 CAATGCATTTGCCATGTGAAATAA 57.576 33.333 9.83 0.00 41.18 1.40
1535 1672 6.843208 CAATGCATTTGCCATGTGAAATAAA 58.157 32.000 9.83 0.00 41.18 1.40
1536 1673 5.859521 TGCATTTGCCATGTGAAATAAAC 57.140 34.783 0.00 0.00 41.18 2.01
1537 1674 5.549347 TGCATTTGCCATGTGAAATAAACT 58.451 33.333 0.00 0.00 41.18 2.66
1538 1675 6.695429 TGCATTTGCCATGTGAAATAAACTA 58.305 32.000 0.00 0.00 41.18 2.24
1539 1676 6.589523 TGCATTTGCCATGTGAAATAAACTAC 59.410 34.615 0.00 0.00 41.18 2.73
1540 1677 6.589523 GCATTTGCCATGTGAAATAAACTACA 59.410 34.615 0.00 0.00 34.31 2.74
1541 1678 7.278424 GCATTTGCCATGTGAAATAAACTACAT 59.722 33.333 0.00 0.00 34.31 2.29
1542 1679 9.153721 CATTTGCCATGTGAAATAAACTACATT 57.846 29.630 0.00 0.00 31.84 2.71
1543 1680 9.723601 ATTTGCCATGTGAAATAAACTACATTT 57.276 25.926 0.00 0.00 31.84 2.32
1544 1681 8.531622 TTGCCATGTGAAATAAACTACATTTG 57.468 30.769 0.00 0.00 31.84 2.32
1545 1682 6.589523 TGCCATGTGAAATAAACTACATTTGC 59.410 34.615 0.00 0.00 31.84 3.68
1546 1683 6.035975 GCCATGTGAAATAAACTACATTTGCC 59.964 38.462 0.00 0.00 31.84 4.52
1547 1684 7.095910 CCATGTGAAATAAACTACATTTGCCA 58.904 34.615 0.00 0.00 31.84 4.92
1548 1685 7.765360 CCATGTGAAATAAACTACATTTGCCAT 59.235 33.333 0.00 0.00 31.84 4.40
1549 1686 8.597227 CATGTGAAATAAACTACATTTGCCATG 58.403 33.333 0.00 0.00 31.84 3.66
1550 1687 7.665690 TGTGAAATAAACTACATTTGCCATGT 58.334 30.769 4.21 4.21 36.13 3.21
1551 1688 7.598118 TGTGAAATAAACTACATTTGCCATGTG 59.402 33.333 8.54 2.73 33.76 3.21
1552 1689 7.812191 GTGAAATAAACTACATTTGCCATGTGA 59.188 33.333 8.54 0.00 33.76 3.58
1553 1690 7.812191 TGAAATAAACTACATTTGCCATGTGAC 59.188 33.333 8.54 0.00 33.76 3.67
1554 1691 6.832520 ATAAACTACATTTGCCATGTGACA 57.167 33.333 8.54 0.00 33.76 3.58
1555 1692 5.726980 AAACTACATTTGCCATGTGACAT 57.273 34.783 8.54 0.00 33.76 3.06
1556 1693 6.832520 AAACTACATTTGCCATGTGACATA 57.167 33.333 0.00 0.00 33.76 2.29
1557 1694 6.832520 AACTACATTTGCCATGTGACATAA 57.167 33.333 0.00 0.00 33.76 1.90
1558 1695 6.832520 ACTACATTTGCCATGTGACATAAA 57.167 33.333 0.00 0.00 33.76 1.40
1559 1696 6.620678 ACTACATTTGCCATGTGACATAAAC 58.379 36.000 0.00 0.00 33.76 2.01
1560 1697 5.726980 ACATTTGCCATGTGACATAAACT 57.273 34.783 0.00 0.00 0.00 2.66
1620 1919 7.035004 GTGAAATAAACTGCATTTGCCATCTA 58.965 34.615 0.00 0.00 41.18 1.98
1639 2009 6.389091 CATCTAAAATAAACTGCAGTTGCCA 58.611 36.000 31.73 19.90 41.18 4.92
1640 2010 6.588719 TCTAAAATAAACTGCAGTTGCCAT 57.411 33.333 31.73 21.13 41.18 4.40
1641 2011 6.389091 TCTAAAATAAACTGCAGTTGCCATG 58.611 36.000 31.73 17.82 41.18 3.66
1642 2012 4.605640 AAATAAACTGCAGTTGCCATGT 57.394 36.364 31.73 17.59 41.18 3.21
1643 2013 4.605640 AATAAACTGCAGTTGCCATGTT 57.394 36.364 31.73 17.39 41.18 2.71
1644 2014 5.720371 AATAAACTGCAGTTGCCATGTTA 57.280 34.783 31.73 18.45 41.18 2.41
1645 2015 5.720371 ATAAACTGCAGTTGCCATGTTAA 57.280 34.783 31.73 9.91 41.18 2.01
1646 2016 4.605640 AAACTGCAGTTGCCATGTTAAT 57.394 36.364 31.73 9.99 41.18 1.40
1647 2017 5.720371 AAACTGCAGTTGCCATGTTAATA 57.280 34.783 31.73 0.00 41.18 0.98
1648 2018 4.970662 ACTGCAGTTGCCATGTTAATAG 57.029 40.909 15.25 0.00 41.18 1.73
1649 2019 4.335416 ACTGCAGTTGCCATGTTAATAGT 58.665 39.130 15.25 0.00 41.18 2.12
1650 2020 4.396166 ACTGCAGTTGCCATGTTAATAGTC 59.604 41.667 15.25 0.00 41.18 2.59
1651 2021 4.588899 TGCAGTTGCCATGTTAATAGTCT 58.411 39.130 1.06 0.00 41.18 3.24
1652 2022 4.395854 TGCAGTTGCCATGTTAATAGTCTG 59.604 41.667 1.06 0.00 41.18 3.51
1653 2023 4.731773 GCAGTTGCCATGTTAATAGTCTGC 60.732 45.833 0.00 0.00 37.87 4.26
1654 2024 4.395854 CAGTTGCCATGTTAATAGTCTGCA 59.604 41.667 0.00 0.00 0.00 4.41
1655 2025 4.637534 AGTTGCCATGTTAATAGTCTGCAG 59.362 41.667 7.63 7.63 0.00 4.41
1656 2026 4.220693 TGCCATGTTAATAGTCTGCAGT 57.779 40.909 14.67 0.00 0.00 4.40
1657 2027 4.588899 TGCCATGTTAATAGTCTGCAGTT 58.411 39.130 14.67 6.17 0.00 3.16
1658 2028 4.395854 TGCCATGTTAATAGTCTGCAGTTG 59.604 41.667 14.67 0.00 0.00 3.16
1659 2029 4.731773 GCCATGTTAATAGTCTGCAGTTGC 60.732 45.833 14.67 5.62 42.50 4.17
1660 2030 4.201950 CCATGTTAATAGTCTGCAGTTGCC 60.202 45.833 14.67 0.48 41.18 4.52
1661 2031 4.014569 TGTTAATAGTCTGCAGTTGCCA 57.985 40.909 14.67 0.00 41.18 4.92
1662 2032 4.588899 TGTTAATAGTCTGCAGTTGCCAT 58.411 39.130 14.67 0.00 41.18 4.40
1663 2033 4.635765 TGTTAATAGTCTGCAGTTGCCATC 59.364 41.667 14.67 0.86 41.18 3.51
1664 2034 3.641434 AATAGTCTGCAGTTGCCATCT 57.359 42.857 14.67 4.97 41.18 2.90
1665 2035 2.391616 TAGTCTGCAGTTGCCATCTG 57.608 50.000 14.67 0.00 41.18 2.90
1666 2036 0.689055 AGTCTGCAGTTGCCATCTGA 59.311 50.000 14.67 0.00 41.18 3.27
1667 2037 1.072806 AGTCTGCAGTTGCCATCTGAA 59.927 47.619 14.67 0.00 41.18 3.02
1668 2038 1.881973 GTCTGCAGTTGCCATCTGAAA 59.118 47.619 14.67 0.00 41.18 2.69
1669 2039 2.490903 GTCTGCAGTTGCCATCTGAAAT 59.509 45.455 14.67 0.00 41.18 2.17
1670 2040 3.691118 GTCTGCAGTTGCCATCTGAAATA 59.309 43.478 14.67 0.00 41.18 1.40
1671 2041 4.156556 GTCTGCAGTTGCCATCTGAAATAA 59.843 41.667 14.67 0.00 41.18 1.40
1672 2042 4.766373 TCTGCAGTTGCCATCTGAAATAAA 59.234 37.500 14.67 0.00 41.18 1.40
1673 2043 4.808558 TGCAGTTGCCATCTGAAATAAAC 58.191 39.130 6.96 0.00 41.18 2.01
1674 2044 4.523943 TGCAGTTGCCATCTGAAATAAACT 59.476 37.500 6.96 0.00 41.18 2.66
1675 2045 4.860907 GCAGTTGCCATCTGAAATAAACTG 59.139 41.667 6.96 16.12 43.60 3.16
1676 2046 5.565439 GCAGTTGCCATCTGAAATAAACTGT 60.565 40.000 19.06 0.00 43.02 3.55
1677 2047 6.449698 CAGTTGCCATCTGAAATAAACTGTT 58.550 36.000 13.85 0.00 38.65 3.16
1678 2048 6.364165 CAGTTGCCATCTGAAATAAACTGTTG 59.636 38.462 13.85 0.00 38.65 3.33
1679 2049 6.040842 AGTTGCCATCTGAAATAAACTGTTGT 59.959 34.615 0.00 0.00 0.00 3.32
1680 2050 6.403866 TGCCATCTGAAATAAACTGTTGTT 57.596 33.333 0.00 0.00 38.16 2.83
1681 2051 6.215121 TGCCATCTGAAATAAACTGTTGTTG 58.785 36.000 0.00 0.00 36.39 3.33
1682 2052 5.119125 GCCATCTGAAATAAACTGTTGTTGC 59.881 40.000 0.00 0.00 36.39 4.17
1683 2053 5.634859 CCATCTGAAATAAACTGTTGTTGCC 59.365 40.000 0.00 0.00 36.39 4.52
1684 2054 5.843673 TCTGAAATAAACTGTTGTTGCCA 57.156 34.783 0.00 0.00 36.39 4.92
1685 2055 6.403866 TCTGAAATAAACTGTTGTTGCCAT 57.596 33.333 0.00 0.00 36.39 4.40
1686 2056 6.215121 TCTGAAATAAACTGTTGTTGCCATG 58.785 36.000 0.00 0.00 36.39 3.66
1687 2057 5.911752 TGAAATAAACTGTTGTTGCCATGT 58.088 33.333 0.00 0.00 36.39 3.21
1688 2058 6.344500 TGAAATAAACTGTTGTTGCCATGTT 58.656 32.000 0.00 0.00 36.39 2.71
1689 2059 7.492524 TGAAATAAACTGTTGTTGCCATGTTA 58.507 30.769 0.00 0.00 36.39 2.41
1690 2060 7.981789 TGAAATAAACTGTTGTTGCCATGTTAA 59.018 29.630 0.00 0.00 36.39 2.01
1691 2061 8.900983 AAATAAACTGTTGTTGCCATGTTAAT 57.099 26.923 0.00 0.00 36.39 1.40
1692 2062 9.988815 AAATAAACTGTTGTTGCCATGTTAATA 57.011 25.926 0.00 0.00 36.39 0.98
1693 2063 9.638239 AATAAACTGTTGTTGCCATGTTAATAG 57.362 29.630 0.00 0.00 36.39 1.73
1694 2064 6.648879 AACTGTTGTTGCCATGTTAATAGT 57.351 33.333 0.00 0.00 34.71 2.12
1695 2065 6.254281 ACTGTTGTTGCCATGTTAATAGTC 57.746 37.500 0.00 0.00 0.00 2.59
1696 2066 6.003950 ACTGTTGTTGCCATGTTAATAGTCT 58.996 36.000 0.00 0.00 0.00 3.24
1697 2067 6.072508 ACTGTTGTTGCCATGTTAATAGTCTG 60.073 38.462 0.00 0.00 0.00 3.51
1698 2068 4.963276 TGTTGCCATGTTAATAGTCTGC 57.037 40.909 0.00 0.00 0.00 4.26
1699 2069 4.331108 TGTTGCCATGTTAATAGTCTGCA 58.669 39.130 0.00 0.00 0.00 4.41
1700 2070 4.395854 TGTTGCCATGTTAATAGTCTGCAG 59.604 41.667 7.63 7.63 0.00 4.41
1701 2071 4.220693 TGCCATGTTAATAGTCTGCAGT 57.779 40.909 14.67 0.00 0.00 4.40
1702 2072 4.588899 TGCCATGTTAATAGTCTGCAGTT 58.411 39.130 14.67 6.17 0.00 3.16
1703 2073 4.395854 TGCCATGTTAATAGTCTGCAGTTG 59.604 41.667 14.67 0.00 0.00 3.16
1704 2074 4.731773 GCCATGTTAATAGTCTGCAGTTGC 60.732 45.833 14.67 5.62 42.50 4.17
1705 2075 4.637534 CCATGTTAATAGTCTGCAGTTGCT 59.362 41.667 14.67 12.72 42.66 3.91
1743 2114 5.651576 TGCATTTGCCATGTTAATAGTCTGA 59.348 36.000 0.00 0.00 41.18 3.27
1866 2241 4.464597 ACCTCAACAAAAGGTGCTACAAAA 59.535 37.500 0.00 0.00 45.50 2.44
1867 2242 5.046950 ACCTCAACAAAAGGTGCTACAAAAA 60.047 36.000 0.00 0.00 45.50 1.94
1868 2243 5.519927 CCTCAACAAAAGGTGCTACAAAAAG 59.480 40.000 0.00 0.00 0.00 2.27
1993 2372 2.305635 TGTGTACTCTCATGGGCATGTT 59.694 45.455 0.00 0.00 39.72 2.71
2042 2421 4.969484 AGGGACGAAACTACTTTGTCAAT 58.031 39.130 7.08 0.00 46.63 2.57
2108 2487 0.323360 AATGGGACGGGATTGTGTGG 60.323 55.000 0.00 0.00 0.00 4.17
2181 2560 0.462937 TTTCATACGATGGCGGTGGG 60.463 55.000 0.00 0.00 43.17 4.61
2196 2575 0.323360 GTGGGCTTGGGATGCTAACA 60.323 55.000 0.00 0.00 0.00 2.41
2249 2628 5.241506 AGTTTTGGTTGTACATGATGACAGG 59.758 40.000 0.00 0.00 0.00 4.00
2325 2704 4.321718 TGAGCTAATAGATGAAGCATGCC 58.678 43.478 15.66 0.00 38.75 4.40
2392 2771 5.335504 CCCTGAAAAGAAAGCTTGATGAGAC 60.336 44.000 0.00 0.00 33.79 3.36
2519 2898 1.959042 CAAGCACACAGACTCAGGTT 58.041 50.000 0.00 0.00 0.00 3.50
2563 2942 1.605753 AAAGGGCGTCCAAAAGAGAC 58.394 50.000 9.71 0.00 34.83 3.36
2600 2979 4.510571 GGATGGAAATTCAAGCAAAGCAT 58.489 39.130 0.00 0.00 0.00 3.79
2699 3080 7.972832 TTGTAACGTAGATGATCAAGGTTTT 57.027 32.000 0.00 0.00 0.00 2.43
2902 3285 8.549777 TTTGTTTCACACGTATTGAATTGTAC 57.450 30.769 11.45 8.08 33.03 2.90
2993 3378 3.886505 ACAACCATGCTTACCGAAAAAGA 59.113 39.130 0.00 0.00 0.00 2.52
3000 3385 6.912591 CCATGCTTACCGAAAAAGATATCAAC 59.087 38.462 5.32 0.00 0.00 3.18
3061 3450 8.364894 ACTAACCATGCGTGATCAACTATATTA 58.635 33.333 7.72 0.00 0.00 0.98
3249 3644 0.323360 TACAGCAAAGGGGGATGCAC 60.323 55.000 0.00 0.00 44.95 4.57
3267 3662 4.768583 TGCACTCATAACATAGCACATGA 58.231 39.130 0.00 0.00 0.00 3.07
3318 3713 5.396772 CCTTACATTCCTCAGCCACAGAATA 60.397 44.000 0.00 0.00 0.00 1.75
3464 3864 9.300681 CCAGTTCCATGTGTATATTTTATGGAT 57.699 33.333 0.00 0.00 44.72 3.41
3493 3893 1.741706 CCATTGCACCTGTGATCACTC 59.258 52.381 25.55 10.58 0.00 3.51
3601 4004 8.746922 ACACATGCAAACAGAAACATAATAAG 57.253 30.769 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 3.055819 TGTCTTCTATGTCAGCCAACCTC 60.056 47.826 0.00 0.00 0.00 3.85
270 271 4.531854 CACCATCCACCCAATACATGTTA 58.468 43.478 2.30 0.00 0.00 2.41
318 319 4.491924 GCGTCGAATGAAATGTAATCACGT 60.492 41.667 0.00 0.00 0.00 4.49
326 327 1.424403 TGTCGCGTCGAATGAAATGT 58.576 45.000 5.77 0.00 37.72 2.71
402 403 2.301870 ACCGAACTGCAAGGACTGATTA 59.698 45.455 4.48 0.00 39.30 1.75
451 452 3.561143 TGAACAGCCAAGTGTAACCATT 58.439 40.909 0.00 0.00 37.80 3.16
545 548 3.737850 GGAAAGACCTCCTCTATGCATG 58.262 50.000 10.16 0.00 35.41 4.06
546 549 2.366916 CGGAAAGACCTCCTCTATGCAT 59.633 50.000 3.79 3.79 36.31 3.96
587 590 5.183904 GCCTTCTTAATAATATGCCACCTGG 59.816 44.000 0.00 0.00 38.53 4.45
697 705 1.543429 CCAGCTCCGTTCAAACTCCTT 60.543 52.381 0.00 0.00 0.00 3.36
777 788 1.732259 GACACCCAGTACATTCGCTTG 59.268 52.381 0.00 0.00 0.00 4.01
916 929 8.359642 AGTATTTTCTGTTGCAAAGCTGAATAA 58.640 29.630 0.00 4.32 0.00 1.40
952 965 2.030805 GGTGTTTGCTTCTTGCTGTAGG 60.031 50.000 0.00 0.00 43.37 3.18
1002 1015 0.249657 CTGCCTCTCCATCGGTAAGC 60.250 60.000 0.00 0.00 0.00 3.09
1149 1183 9.282569 GATGTTAGCTTCAAATCAGGAGATATT 57.717 33.333 0.00 0.00 33.08 1.28
1156 1190 7.271511 ACTAGAGATGTTAGCTTCAAATCAGG 58.728 38.462 0.00 0.00 0.00 3.86
1184 1219 7.549615 TCATTTTTGTTTTGCATTCATGTGA 57.450 28.000 0.00 0.00 0.00 3.58
1210 1252 8.801715 ATTTGTTCTTGCAACTACATAGTTTG 57.198 30.769 9.09 0.49 43.57 2.93
1228 1285 5.390613 ACACGCAGCAACTAATATTTGTTC 58.609 37.500 11.62 7.79 0.00 3.18
1248 1305 6.416750 GGCAGTTATACTTTGTTTCACAACAC 59.583 38.462 0.00 0.00 42.87 3.32
1439 1525 8.341892 TGTATTTTCACATGGCAACTATTGTA 57.658 30.769 0.00 0.00 37.61 2.41
1465 1579 5.178996 GTGTATTTTCACATGGCAAATGCAA 59.821 36.000 14.45 0.00 39.25 4.08
1486 1623 4.540359 ATTTACATGGCAAATGCAGTGT 57.460 36.364 15.78 15.78 44.36 3.55
1489 1626 5.051153 TGCATATTTACATGGCAAATGCAG 58.949 37.500 16.19 8.65 44.36 4.41
1515 1652 6.589523 TGTAGTTTATTTCACATGGCAAATGC 59.410 34.615 12.23 0.00 41.14 3.56
1516 1653 8.706492 ATGTAGTTTATTTCACATGGCAAATG 57.294 30.769 12.23 0.00 30.64 2.32
1517 1654 9.723601 AAATGTAGTTTATTTCACATGGCAAAT 57.276 25.926 0.00 3.60 32.15 2.32
1518 1655 8.986847 CAAATGTAGTTTATTTCACATGGCAAA 58.013 29.630 0.00 0.00 32.15 3.68
1519 1656 7.117523 GCAAATGTAGTTTATTTCACATGGCAA 59.882 33.333 0.00 0.00 34.86 4.52
1520 1657 6.589523 GCAAATGTAGTTTATTTCACATGGCA 59.410 34.615 0.00 0.00 34.86 4.92
1521 1658 6.035975 GGCAAATGTAGTTTATTTCACATGGC 59.964 38.462 0.00 0.00 34.40 4.40
1522 1659 7.095910 TGGCAAATGTAGTTTATTTCACATGG 58.904 34.615 0.00 0.00 32.15 3.66
1523 1660 8.597227 CATGGCAAATGTAGTTTATTTCACATG 58.403 33.333 0.00 0.00 35.16 3.21
1524 1661 8.313292 ACATGGCAAATGTAGTTTATTTCACAT 58.687 29.630 2.62 0.00 33.12 3.21
1525 1662 7.598118 CACATGGCAAATGTAGTTTATTTCACA 59.402 33.333 4.14 0.00 0.00 3.58
1526 1663 7.812191 TCACATGGCAAATGTAGTTTATTTCAC 59.188 33.333 4.14 0.00 0.00 3.18
1527 1664 7.812191 GTCACATGGCAAATGTAGTTTATTTCA 59.188 33.333 4.14 0.00 0.00 2.69
1528 1665 7.812191 TGTCACATGGCAAATGTAGTTTATTTC 59.188 33.333 4.14 0.00 0.00 2.17
1529 1666 7.665690 TGTCACATGGCAAATGTAGTTTATTT 58.334 30.769 4.14 0.00 0.00 1.40
1530 1667 7.225784 TGTCACATGGCAAATGTAGTTTATT 57.774 32.000 4.14 0.00 0.00 1.40
1531 1668 6.832520 TGTCACATGGCAAATGTAGTTTAT 57.167 33.333 4.14 0.00 0.00 1.40
1532 1669 6.832520 ATGTCACATGGCAAATGTAGTTTA 57.167 33.333 4.14 0.00 31.21 2.01
1533 1670 5.726980 ATGTCACATGGCAAATGTAGTTT 57.273 34.783 4.14 0.00 31.21 2.66
1534 1671 6.832520 TTATGTCACATGGCAAATGTAGTT 57.167 33.333 0.00 0.00 31.21 2.24
1535 1672 6.434028 AGTTTATGTCACATGGCAAATGTAGT 59.566 34.615 0.00 0.00 31.21 2.73
1536 1673 6.748658 CAGTTTATGTCACATGGCAAATGTAG 59.251 38.462 0.00 0.99 31.21 2.74
1537 1674 6.619744 CAGTTTATGTCACATGGCAAATGTA 58.380 36.000 0.00 0.00 31.21 2.29
1538 1675 5.472148 CAGTTTATGTCACATGGCAAATGT 58.528 37.500 0.00 0.00 31.21 2.71
1539 1676 4.327898 GCAGTTTATGTCACATGGCAAATG 59.672 41.667 0.00 1.75 31.21 2.32
1540 1677 4.021280 TGCAGTTTATGTCACATGGCAAAT 60.021 37.500 0.00 0.00 31.21 2.32
1541 1678 3.320256 TGCAGTTTATGTCACATGGCAAA 59.680 39.130 0.00 0.00 31.21 3.68
1542 1679 2.889678 TGCAGTTTATGTCACATGGCAA 59.110 40.909 0.00 0.00 31.21 4.52
1543 1680 2.512705 TGCAGTTTATGTCACATGGCA 58.487 42.857 0.00 0.00 0.00 4.92
1544 1681 3.788333 ATGCAGTTTATGTCACATGGC 57.212 42.857 0.00 0.00 0.00 4.40
1545 1682 4.327898 GCAAATGCAGTTTATGTCACATGG 59.672 41.667 0.00 0.00 41.59 3.66
1546 1683 4.327898 GGCAAATGCAGTTTATGTCACATG 59.672 41.667 0.00 0.00 44.36 3.21
1547 1684 4.021280 TGGCAAATGCAGTTTATGTCACAT 60.021 37.500 7.80 0.00 44.36 3.21
1548 1685 3.320256 TGGCAAATGCAGTTTATGTCACA 59.680 39.130 7.80 0.00 44.36 3.58
1549 1686 3.911868 TGGCAAATGCAGTTTATGTCAC 58.088 40.909 7.80 0.00 44.36 3.67
1550 1687 4.021280 ACATGGCAAATGCAGTTTATGTCA 60.021 37.500 12.63 5.02 44.36 3.58
1551 1688 4.327898 CACATGGCAAATGCAGTTTATGTC 59.672 41.667 14.54 0.94 44.36 3.06
1552 1689 4.021280 TCACATGGCAAATGCAGTTTATGT 60.021 37.500 12.63 12.63 44.36 2.29
1553 1690 4.496360 TCACATGGCAAATGCAGTTTATG 58.504 39.130 7.80 5.41 44.36 1.90
1554 1691 4.804868 TCACATGGCAAATGCAGTTTAT 57.195 36.364 7.80 0.00 44.36 1.40
1555 1692 4.597404 TTCACATGGCAAATGCAGTTTA 57.403 36.364 7.80 0.00 44.36 2.01
1556 1693 3.472283 TTCACATGGCAAATGCAGTTT 57.528 38.095 7.80 0.00 44.36 2.66
1557 1694 3.472283 TTTCACATGGCAAATGCAGTT 57.528 38.095 7.80 0.00 44.36 3.16
1558 1695 3.688694 ATTTCACATGGCAAATGCAGT 57.311 38.095 7.80 0.00 44.36 4.40
1559 1696 5.640357 AGTTTATTTCACATGGCAAATGCAG 59.360 36.000 7.80 0.00 44.36 4.41
1560 1697 5.408909 CAGTTTATTTCACATGGCAAATGCA 59.591 36.000 7.80 0.00 44.36 3.96
1620 1919 4.959723 ACATGGCAACTGCAGTTTATTTT 58.040 34.783 29.23 10.73 44.36 1.82
1639 2009 4.588899 TGGCAACTGCAGACTATTAACAT 58.411 39.130 23.35 0.00 44.36 2.71
1640 2010 4.014569 TGGCAACTGCAGACTATTAACA 57.985 40.909 23.35 3.78 44.36 2.41
1641 2011 4.878397 AGATGGCAACTGCAGACTATTAAC 59.122 41.667 23.35 5.42 44.36 2.01
1642 2012 4.877823 CAGATGGCAACTGCAGACTATTAA 59.122 41.667 23.35 0.00 44.36 1.40
1643 2013 4.162131 TCAGATGGCAACTGCAGACTATTA 59.838 41.667 23.35 2.13 44.36 0.98
1644 2014 3.054875 TCAGATGGCAACTGCAGACTATT 60.055 43.478 23.35 0.04 44.36 1.73
1645 2015 2.502947 TCAGATGGCAACTGCAGACTAT 59.497 45.455 23.35 12.42 44.36 2.12
1646 2016 1.901833 TCAGATGGCAACTGCAGACTA 59.098 47.619 23.35 7.71 44.36 2.59
1647 2017 0.689055 TCAGATGGCAACTGCAGACT 59.311 50.000 23.35 3.66 44.36 3.24
1648 2018 1.527034 TTCAGATGGCAACTGCAGAC 58.473 50.000 23.35 9.20 44.36 3.51
1649 2019 2.275134 TTTCAGATGGCAACTGCAGA 57.725 45.000 23.35 0.00 44.36 4.26
1650 2020 4.707030 TTATTTCAGATGGCAACTGCAG 57.293 40.909 18.88 13.48 44.36 4.41
1651 2021 4.523943 AGTTTATTTCAGATGGCAACTGCA 59.476 37.500 18.88 6.44 44.36 4.41
1652 2022 4.860907 CAGTTTATTTCAGATGGCAACTGC 59.139 41.667 18.88 4.31 34.86 4.40
1653 2023 6.017400 ACAGTTTATTTCAGATGGCAACTG 57.983 37.500 17.76 17.76 43.40 3.16
1654 2024 6.040842 ACAACAGTTTATTTCAGATGGCAACT 59.959 34.615 0.00 0.00 37.61 3.16
1655 2025 6.215845 ACAACAGTTTATTTCAGATGGCAAC 58.784 36.000 0.00 0.00 0.00 4.17
1656 2026 6.403866 ACAACAGTTTATTTCAGATGGCAA 57.596 33.333 0.00 0.00 0.00 4.52
1657 2027 6.215121 CAACAACAGTTTATTTCAGATGGCA 58.785 36.000 0.00 0.00 0.00 4.92
1658 2028 5.119125 GCAACAACAGTTTATTTCAGATGGC 59.881 40.000 0.00 0.00 0.00 4.40
1659 2029 5.634859 GGCAACAACAGTTTATTTCAGATGG 59.365 40.000 0.00 0.00 0.00 3.51
1660 2030 6.695292 GGCAACAACAGTTTATTTCAGATG 57.305 37.500 0.00 0.00 0.00 2.90
1678 2048 4.396166 ACTGCAGACTATTAACATGGCAAC 59.604 41.667 23.35 0.00 0.00 4.17
1679 2049 4.588899 ACTGCAGACTATTAACATGGCAA 58.411 39.130 23.35 0.00 0.00 4.52
1680 2050 4.220693 ACTGCAGACTATTAACATGGCA 57.779 40.909 23.35 0.00 0.00 4.92
1681 2051 4.731773 GCAACTGCAGACTATTAACATGGC 60.732 45.833 23.35 0.00 41.59 4.40
1682 2052 4.637534 AGCAACTGCAGACTATTAACATGG 59.362 41.667 23.35 0.00 45.16 3.66
1683 2053 5.808042 AGCAACTGCAGACTATTAACATG 57.192 39.130 23.35 4.42 45.16 3.21
1684 2054 7.011763 CACATAGCAACTGCAGACTATTAACAT 59.988 37.037 23.35 1.32 45.16 2.71
1685 2055 6.313658 CACATAGCAACTGCAGACTATTAACA 59.686 38.462 23.35 0.00 45.16 2.41
1686 2056 6.535150 TCACATAGCAACTGCAGACTATTAAC 59.465 38.462 23.35 0.00 45.16 2.01
1687 2057 6.639563 TCACATAGCAACTGCAGACTATTAA 58.360 36.000 23.35 8.68 45.16 1.40
1688 2058 6.220726 TCACATAGCAACTGCAGACTATTA 57.779 37.500 23.35 6.46 45.16 0.98
1689 2059 5.089970 TCACATAGCAACTGCAGACTATT 57.910 39.130 23.35 0.04 45.16 1.73
1690 2060 4.743057 TCACATAGCAACTGCAGACTAT 57.257 40.909 23.35 19.42 45.16 2.12
1691 2061 4.535526 TTCACATAGCAACTGCAGACTA 57.464 40.909 23.35 18.07 45.16 2.59
1692 2062 3.407424 TTCACATAGCAACTGCAGACT 57.593 42.857 23.35 16.46 45.16 3.24
1693 2063 3.748048 TCTTTCACATAGCAACTGCAGAC 59.252 43.478 23.35 9.43 45.16 3.51
1694 2064 4.006780 TCTTTCACATAGCAACTGCAGA 57.993 40.909 23.35 0.00 45.16 4.26
1695 2065 4.754372 TTCTTTCACATAGCAACTGCAG 57.246 40.909 13.48 13.48 45.16 4.41
1696 2066 4.580167 AGTTTCTTTCACATAGCAACTGCA 59.420 37.500 4.22 0.00 45.16 4.41
1697 2067 4.913924 CAGTTTCTTTCACATAGCAACTGC 59.086 41.667 0.00 0.00 39.03 4.40
1698 2068 4.913924 GCAGTTTCTTTCACATAGCAACTG 59.086 41.667 9.86 9.86 44.40 3.16
1699 2069 4.580167 TGCAGTTTCTTTCACATAGCAACT 59.420 37.500 0.00 0.00 30.82 3.16
1700 2070 4.858935 TGCAGTTTCTTTCACATAGCAAC 58.141 39.130 0.00 0.00 0.00 4.17
1701 2071 5.710513 ATGCAGTTTCTTTCACATAGCAA 57.289 34.783 0.00 0.00 32.83 3.91
1702 2072 5.710513 AATGCAGTTTCTTTCACATAGCA 57.289 34.783 0.00 0.00 0.00 3.49
1703 2073 5.164022 GCAAATGCAGTTTCTTTCACATAGC 60.164 40.000 0.00 0.00 41.59 2.97
1704 2074 5.346822 GGCAAATGCAGTTTCTTTCACATAG 59.653 40.000 7.80 0.00 44.36 2.23
1705 2075 5.221402 TGGCAAATGCAGTTTCTTTCACATA 60.221 36.000 7.80 0.00 44.36 2.29
1743 2114 1.786937 TGTTTCCCACATGGCAACTT 58.213 45.000 0.00 0.00 31.64 2.66
1993 2372 3.408634 GGGTCTTCAGGTTTTGAATCGA 58.591 45.455 0.00 0.00 44.48 3.59
2042 2421 1.626321 TCACCTTCGGTTATTGAGGCA 59.374 47.619 0.00 0.00 31.02 4.75
2070 2449 5.401550 CCATTCGTATTTGCAACATTGACT 58.598 37.500 0.00 0.00 0.00 3.41
2108 2487 4.941263 TCCATTACTTTGAGTATGTGGCAC 59.059 41.667 11.55 11.55 37.05 5.01
2181 2560 1.477700 TGCATTGTTAGCATCCCAAGC 59.522 47.619 0.00 0.00 37.02 4.01
2196 2575 0.036590 GTTTGTGGCCCCAATGCATT 59.963 50.000 5.99 5.99 0.00 3.56
2325 2704 2.354503 CCCTGGTTGTCTCATCACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
2379 2758 4.565236 CCTCTTCTTGGTCTCATCAAGCTT 60.565 45.833 0.00 0.00 40.82 3.74
2392 2771 2.304180 TCTTCAGCCTTCCTCTTCTTGG 59.696 50.000 0.00 0.00 0.00 3.61
2420 2799 2.668632 GTGCGGGGGAACAGATGA 59.331 61.111 0.00 0.00 0.00 2.92
2425 2804 3.172106 TTGAGGTGCGGGGGAACA 61.172 61.111 0.00 0.00 0.00 3.18
2460 2839 2.234908 CCGAGTTTTCAGAGGATGGACT 59.765 50.000 0.00 0.00 0.00 3.85
2519 2898 3.395630 GAACAGGGCGGGTTCCTA 58.604 61.111 8.26 0.00 38.92 2.94
2532 2911 1.440938 CGCCCTTTTGTGACGGAACA 61.441 55.000 0.00 0.00 0.00 3.18
2580 2959 6.938507 TCTTATGCTTTGCTTGAATTTCCAT 58.061 32.000 0.00 0.00 0.00 3.41
2600 2979 2.525368 GCCCCTTTCTTTGCCTTCTTA 58.475 47.619 0.00 0.00 0.00 2.10
2699 3080 5.240623 ACCAACATTCACTCTCGCATTTTTA 59.759 36.000 0.00 0.00 0.00 1.52
2902 3285 6.839033 TCAACTAGTTCGTACAGAGTATGTG 58.161 40.000 4.77 0.00 43.80 3.21
2993 3378 5.360591 TGTTTTGGGTTTTTGCGTTGATAT 58.639 33.333 0.00 0.00 0.00 1.63
3000 3385 4.606457 TCATTTGTTTTGGGTTTTTGCG 57.394 36.364 0.00 0.00 0.00 4.85
3249 3644 8.599055 ACTATGTTCATGTGCTATGTTATGAG 57.401 34.615 0.00 0.00 31.85 2.90
3267 3662 7.639113 TCACCTTGTTCTTTGAAACTATGTT 57.361 32.000 0.00 0.00 0.00 2.71
3318 3713 4.225042 TCTTCACACACATGCCTACCTTAT 59.775 41.667 0.00 0.00 0.00 1.73
3464 3864 0.478072 AGGTGCAATGGTTGTGGAGA 59.522 50.000 0.00 0.00 0.00 3.71
3493 3893 4.125695 GGAAGGTCGACGGGTCCG 62.126 72.222 9.92 7.97 46.03 4.79
3601 4004 7.149569 TCTTTTCCATGTCTTCATCAATGTC 57.850 36.000 0.00 0.00 31.15 3.06


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

AutoCloner maintained by Alex Coulton.