Multiple sequence alignment - TraesCS1D01G378300

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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 TraesCS1D01G378300 chr1D 100.000 5503 0 0 1 5503 454233828 454228326 0.000000e+00 10163.0
1 TraesCS1D01G378300 chr1A 94.934 4027 147 25 1517 5503 548567785 548563776 0.000000e+00 6253.0
2 TraesCS1D01G378300 chr1A 94.957 1408 57 9 1 1398 548569186 548567783 0.000000e+00 2194.0
3 TraesCS1D01G378300 chr1B 93.459 1697 97 9 2531 4226 624733709 624732026 0.000000e+00 2507.0
4 TraesCS1D01G378300 chr1B 92.308 1092 48 15 1479 2538 624734816 624733729 0.000000e+00 1519.0
5 TraesCS1D01G378300 chr1B 91.732 508 20 10 877 1368 624735413 624734912 0.000000e+00 686.0
6 TraesCS1D01G378300 chr1B 85.090 389 38 10 85 455 624736175 624735789 4.020000e-101 379.0
7 TraesCS1D01G378300 chr1B 92.754 207 12 1 5297 5503 624731199 624730996 4.170000e-76 296.0
8 TraesCS1D01G378300 chr1B 95.775 71 3 0 5087 5157 624731329 624731259 1.250000e-21 115.0
9 TraesCS1D01G378300 chr5B 89.855 138 5 3 1230 1362 149454486 149454619 9.480000e-38 169.0
10 TraesCS1D01G378300 chr6D 100.000 31 0 0 1782 1812 194246734 194246704 2.140000e-04 58.4
11 TraesCS1D01G378300 chr6D 100.000 30 0 0 1782 1811 82584685 82584656 7.700000e-04 56.5
12 TraesCS1D01G378300 chr6D 100.000 28 0 0 1782 1809 194198365 194198338 1.000000e-02 52.8
13 TraesCS1D01G378300 chr6B 100.000 31 0 0 1782 1812 387142856 387142826 2.140000e-04 58.4
14 TraesCS1D01G378300 chr6B 100.000 30 0 0 1782 1811 387098904 387098875 7.700000e-04 56.5
15 TraesCS1D01G378300 chr7A 96.970 33 1 0 608 640 102328886 102328918 7.700000e-04 56.5
16 TraesCS1D01G378300 chr6A 100.000 30 0 0 1782 1811 268952964 268952935 7.700000e-04 56.5


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 TraesCS1D01G378300 chr1D 454228326 454233828 5502 True 10163.0 10163 100.0000 1 5503 1 chr1D.!!$R1 5502
1 TraesCS1D01G378300 chr1A 548563776 548569186 5410 True 4223.5 6253 94.9455 1 5503 2 chr1A.!!$R1 5502
2 TraesCS1D01G378300 chr1B 624730996 624736175 5179 True 917.0 2507 91.8530 85 5503 6 chr1B.!!$R1 5418

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
846 893 0.320421 TACTGTTCGCCCAAGCTCAC 60.320 55.0 0.0 0.0 36.60 3.51 F
1541 1689 0.108585 ACCTTGTTCGTGGAGCACAT 59.891 50.0 0.0 0.0 33.40 3.21 F
1668 1818 0.908910 TTCGCTGAATCCAAGCCCTA 59.091 50.0 0.0 0.0 0.00 3.53 F
3222 3438 0.094730 GACGTTTGCTCCGAATTCCG 59.905 55.0 0.0 0.0 38.18 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2165 0.804989 GGCCGCCATACAGAATATGC 59.195 55.000 3.91 0.0 0.00 3.14 R
3191 3407 1.002792 GCAAACGTCCAACCTTCAGAC 60.003 52.381 0.00 0.0 0.00 3.51 R
3558 3774 1.275291 CGTAAGGGCAGGACTTCTCAA 59.725 52.381 0.00 0.0 0.00 3.02 R
5199 5507 0.106719 CACACCTGGTCTGGTTTGGT 60.107 55.000 0.00 0.0 38.45 3.67 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
36 37 0.759346 AGTCAACTCACAGTCCACCC 59.241 55.000 0.00 0.00 0.00 4.61
50 51 2.813754 GTCCACCCCGGTTAAGTTTTAC 59.186 50.000 0.00 0.00 35.57 2.01
55 56 4.579753 CACCCCGGTTAAGTTTTACTTTCA 59.420 41.667 0.00 0.00 39.51 2.69
187 199 4.069304 CGGGTTGAGTTGGATAAAAGACA 58.931 43.478 0.00 0.00 0.00 3.41
423 446 9.823647 ATATATAGAGGTCGCCTTTTCAATATG 57.176 33.333 0.00 0.00 31.76 1.78
456 479 3.041946 ACCGATTAGATGAGGCCTTCTT 58.958 45.455 12.22 1.64 0.00 2.52
494 517 1.656818 CCTTCCTACGGACGCGGTTA 61.657 60.000 12.47 0.00 0.00 2.85
586 617 7.481275 ACAAATTGTGCCTAACATTGAAAAG 57.519 32.000 0.00 0.00 38.99 2.27
645 691 1.674322 ATGGAAAACGTGGCCTCCG 60.674 57.895 3.32 9.27 0.00 4.63
701 747 4.267690 GTCGCATCTTTCACGAATGTCATA 59.732 41.667 0.00 0.00 37.60 2.15
846 893 0.320421 TACTGTTCGCCCAAGCTCAC 60.320 55.000 0.00 0.00 36.60 3.51
870 917 2.106338 TGGGATGAGAACAGCACTTTCA 59.894 45.455 0.00 0.00 36.71 2.69
969 1037 1.985662 AAGCCCACACGTCCCGATA 60.986 57.895 0.00 0.00 0.00 2.92
1101 1169 4.845580 ATGCTTCCGGCGCTGAGG 62.846 66.667 20.25 14.27 45.43 3.86
1177 1245 4.521062 CTTCCGGCGAGGGAGCTG 62.521 72.222 9.30 0.00 39.17 4.24
1353 1433 3.709653 AGGAGTTCGGGTGAGCATTATTA 59.290 43.478 0.00 0.00 0.00 0.98
1395 1543 0.307760 CTCGTTGCAAGGTTGTCACC 59.692 55.000 17.96 0.00 44.67 4.02
1405 1553 2.264005 GGTTGTCACCATACACCACA 57.736 50.000 0.00 0.00 43.61 4.17
1406 1554 1.877443 GGTTGTCACCATACACCACAC 59.123 52.381 0.00 0.00 43.61 3.82
1407 1555 1.877443 GTTGTCACCATACACCACACC 59.123 52.381 0.00 0.00 0.00 4.16
1408 1556 1.132500 TGTCACCATACACCACACCA 58.868 50.000 0.00 0.00 0.00 4.17
1409 1557 1.071542 TGTCACCATACACCACACCAG 59.928 52.381 0.00 0.00 0.00 4.00
1410 1558 1.071699 GTCACCATACACCACACCAGT 59.928 52.381 0.00 0.00 0.00 4.00
1411 1559 2.300723 GTCACCATACACCACACCAGTA 59.699 50.000 0.00 0.00 0.00 2.74
1412 1560 2.565391 TCACCATACACCACACCAGTAG 59.435 50.000 0.00 0.00 0.00 2.57
1413 1561 1.906574 ACCATACACCACACCAGTAGG 59.093 52.381 0.00 0.00 42.21 3.18
1414 1562 2.184533 CCATACACCACACCAGTAGGA 58.815 52.381 0.00 0.00 38.69 2.94
1415 1563 2.771943 CCATACACCACACCAGTAGGAT 59.228 50.000 0.00 0.00 38.69 3.24
1416 1564 3.199946 CCATACACCACACCAGTAGGATT 59.800 47.826 0.00 0.00 38.69 3.01
1417 1565 2.859165 ACACCACACCAGTAGGATTG 57.141 50.000 0.00 0.00 38.69 2.67
1418 1566 2.334977 ACACCACACCAGTAGGATTGA 58.665 47.619 0.00 0.00 38.69 2.57
1419 1567 2.912956 ACACCACACCAGTAGGATTGAT 59.087 45.455 0.00 0.00 38.69 2.57
1420 1568 4.101114 ACACCACACCAGTAGGATTGATA 58.899 43.478 0.00 0.00 38.69 2.15
1421 1569 4.721776 ACACCACACCAGTAGGATTGATAT 59.278 41.667 0.00 0.00 38.69 1.63
1422 1570 5.059161 CACCACACCAGTAGGATTGATATG 58.941 45.833 0.00 0.00 38.69 1.78
1423 1571 4.721776 ACCACACCAGTAGGATTGATATGT 59.278 41.667 0.00 0.00 38.69 2.29
1424 1572 5.059161 CCACACCAGTAGGATTGATATGTG 58.941 45.833 0.00 0.00 38.69 3.21
1425 1573 5.163311 CCACACCAGTAGGATTGATATGTGA 60.163 44.000 0.00 0.00 37.67 3.58
1426 1574 6.464892 CCACACCAGTAGGATTGATATGTGAT 60.465 42.308 0.00 0.00 37.67 3.06
1427 1575 6.426025 CACACCAGTAGGATTGATATGTGATG 59.574 42.308 0.00 0.00 37.67 3.07
1428 1576 6.327365 ACACCAGTAGGATTGATATGTGATGA 59.673 38.462 0.00 0.00 38.69 2.92
1429 1577 7.016957 ACACCAGTAGGATTGATATGTGATGAT 59.983 37.037 0.00 0.00 38.69 2.45
1430 1578 7.333672 CACCAGTAGGATTGATATGTGATGATG 59.666 40.741 0.00 0.00 38.69 3.07
1431 1579 6.822170 CCAGTAGGATTGATATGTGATGATGG 59.178 42.308 0.00 0.00 36.89 3.51
1432 1580 6.822170 CAGTAGGATTGATATGTGATGATGGG 59.178 42.308 0.00 0.00 0.00 4.00
1433 1581 6.732390 AGTAGGATTGATATGTGATGATGGGA 59.268 38.462 0.00 0.00 0.00 4.37
1434 1582 6.653790 AGGATTGATATGTGATGATGGGAT 57.346 37.500 0.00 0.00 0.00 3.85
1435 1583 6.424032 AGGATTGATATGTGATGATGGGATG 58.576 40.000 0.00 0.00 0.00 3.51
1436 1584 5.593095 GGATTGATATGTGATGATGGGATGG 59.407 44.000 0.00 0.00 0.00 3.51
1437 1585 3.959293 TGATATGTGATGATGGGATGGC 58.041 45.455 0.00 0.00 0.00 4.40
1438 1586 3.331294 TGATATGTGATGATGGGATGGCA 59.669 43.478 0.00 0.00 0.00 4.92
1439 1587 2.759839 ATGTGATGATGGGATGGCAA 57.240 45.000 0.00 0.00 0.00 4.52
1440 1588 2.759839 TGTGATGATGGGATGGCAAT 57.240 45.000 0.00 0.00 0.00 3.56
1441 1589 3.880168 TGTGATGATGGGATGGCAATA 57.120 42.857 0.00 0.00 0.00 1.90
1442 1590 4.181799 TGTGATGATGGGATGGCAATAA 57.818 40.909 0.00 0.00 0.00 1.40
1443 1591 4.544683 TGTGATGATGGGATGGCAATAAA 58.455 39.130 0.00 0.00 0.00 1.40
1444 1592 4.961099 TGTGATGATGGGATGGCAATAAAA 59.039 37.500 0.00 0.00 0.00 1.52
1445 1593 5.603395 TGTGATGATGGGATGGCAATAAAAT 59.397 36.000 0.00 0.00 0.00 1.82
1446 1594 5.929992 GTGATGATGGGATGGCAATAAAATG 59.070 40.000 0.00 0.00 0.00 2.32
1447 1595 5.603395 TGATGATGGGATGGCAATAAAATGT 59.397 36.000 0.00 0.00 0.00 2.71
1448 1596 5.954153 TGATGGGATGGCAATAAAATGTT 57.046 34.783 0.00 0.00 0.00 2.71
1449 1597 7.289549 TGATGATGGGATGGCAATAAAATGTTA 59.710 33.333 0.00 0.00 0.00 2.41
1450 1598 7.429374 TGATGGGATGGCAATAAAATGTTAA 57.571 32.000 0.00 0.00 0.00 2.01
1451 1599 7.855375 TGATGGGATGGCAATAAAATGTTAAA 58.145 30.769 0.00 0.00 0.00 1.52
1452 1600 8.324306 TGATGGGATGGCAATAAAATGTTAAAA 58.676 29.630 0.00 0.00 0.00 1.52
1453 1601 9.341078 GATGGGATGGCAATAAAATGTTAAAAT 57.659 29.630 0.00 0.00 0.00 1.82
1454 1602 9.697990 ATGGGATGGCAATAAAATGTTAAAATT 57.302 25.926 0.00 0.00 0.00 1.82
1455 1603 9.525826 TGGGATGGCAATAAAATGTTAAAATTT 57.474 25.926 0.00 0.00 0.00 1.82
1477 1625 7.650834 TTTATTGGCAATTCCTTTTCTTTCG 57.349 32.000 19.21 0.00 35.26 3.46
1492 1640 4.934075 TCTTTCGCTGATGTCTGATTTG 57.066 40.909 0.00 0.00 0.00 2.32
1493 1641 4.318332 TCTTTCGCTGATGTCTGATTTGT 58.682 39.130 0.00 0.00 0.00 2.83
1494 1642 5.478407 TCTTTCGCTGATGTCTGATTTGTA 58.522 37.500 0.00 0.00 0.00 2.41
1541 1689 0.108585 ACCTTGTTCGTGGAGCACAT 59.891 50.000 0.00 0.00 33.40 3.21
1549 1697 2.038659 TCGTGGAGCACATATCATGGA 58.961 47.619 0.00 0.00 33.40 3.41
1567 1716 7.780008 TCATGGAAAAATCATGATGCATTTC 57.220 32.000 21.91 21.91 43.98 2.17
1668 1818 0.908910 TTCGCTGAATCCAAGCCCTA 59.091 50.000 0.00 0.00 0.00 3.53
1687 1837 5.065346 GCCCTAAGAGGATTTTCTTTTCTCG 59.935 44.000 0.00 0.00 37.67 4.04
1772 1944 4.010349 GGAAAGTTCCCCATGTGTTCTAG 58.990 47.826 0.00 0.00 41.62 2.43
1814 1986 6.259550 ACAAGTTGCATATTTCCTCAGAAC 57.740 37.500 1.81 0.00 0.00 3.01
1822 1994 5.665459 CATATTTCCTCAGAACGAGAAGGT 58.335 41.667 0.00 0.00 45.45 3.50
1825 1997 1.887198 TCCTCAGAACGAGAAGGTGAC 59.113 52.381 0.00 0.00 45.45 3.67
1839 2011 6.915300 CGAGAAGGTGACACTAAGATCAATAG 59.085 42.308 5.39 0.00 0.00 1.73
1952 2129 6.753744 GGAGCATTCAATCTGTAACATTTTCC 59.246 38.462 0.00 0.00 0.00 3.13
1977 2154 4.202090 GGAATGCTGGTTTTGGAGATGATC 60.202 45.833 0.00 0.00 0.00 2.92
1996 2173 6.161855 TGATCTCCGTTACAAGCATATTCT 57.838 37.500 0.00 0.00 0.00 2.40
1997 2174 5.985530 TGATCTCCGTTACAAGCATATTCTG 59.014 40.000 0.00 0.00 0.00 3.02
1998 2175 5.339008 TCTCCGTTACAAGCATATTCTGT 57.661 39.130 0.00 0.00 0.00 3.41
2110 2287 9.349713 TCACTAGGTTTGTTTCATGATAAACTT 57.650 29.630 20.57 17.79 39.57 2.66
2157 2337 5.149973 TGGGATGTCAAATGTGAAATTGG 57.850 39.130 0.00 0.00 31.32 3.16
3191 3407 6.358118 TCAAGTTGTACAAACAGTTGCTAG 57.642 37.500 10.51 0.00 38.39 3.42
3222 3438 0.094730 GACGTTTGCTCCGAATTCCG 59.905 55.000 0.00 0.00 38.18 4.30
3342 3558 4.937620 TGGCACTTGATAGATTCTTGTCAC 59.062 41.667 0.00 0.00 0.00 3.67
3355 3571 4.471904 TCTTGTCACGATATGAAAGGCT 57.528 40.909 0.00 0.00 39.72 4.58
3554 3770 4.454504 GTCGTTAAGGAAATTGCAGAGGAA 59.545 41.667 0.00 0.00 0.00 3.36
3558 3774 6.868339 CGTTAAGGAAATTGCAGAGGAAAAAT 59.132 34.615 0.00 0.00 0.00 1.82
3665 3881 3.365472 TGGAAGTGATAGTCAGCTAGCA 58.635 45.455 18.83 0.00 40.81 3.49
3685 3901 5.181748 AGCATCAGTCAAGATTAAGGACAC 58.818 41.667 0.00 0.00 34.04 3.67
3750 3966 0.323629 TAAACGGGACAGAGGCAAGG 59.676 55.000 0.00 0.00 0.00 3.61
3836 4052 6.488344 TGTGTTGTAGCCATCAGTTCAATTTA 59.512 34.615 0.00 0.00 0.00 1.40
3837 4053 7.176515 TGTGTTGTAGCCATCAGTTCAATTTAT 59.823 33.333 0.00 0.00 0.00 1.40
3842 4058 7.715249 TGTAGCCATCAGTTCAATTTATAGTCC 59.285 37.037 0.00 0.00 0.00 3.85
3849 4065 8.014070 TCAGTTCAATTTATAGTCCGTGGATA 57.986 34.615 0.00 0.00 0.00 2.59
3872 4088 2.373502 GGCAAAGGGCTAGATCAGGTAT 59.626 50.000 0.00 0.00 44.01 2.73
4099 4315 9.636965 GAATTACATTTTTCAAAGTTGCAAGTC 57.363 29.630 7.36 0.00 0.00 3.01
4142 4358 3.715628 ACGCATATCCATTTTTCTGGC 57.284 42.857 0.00 0.00 36.16 4.85
4304 4520 7.423844 ACTGATGTATTATTGTCTCTGGTGA 57.576 36.000 0.00 0.00 0.00 4.02
4327 4543 2.613691 ACCGCAATGTACCTAACTTCG 58.386 47.619 0.00 0.00 0.00 3.79
4329 4545 2.613691 CGCAATGTACCTAACTTCGGT 58.386 47.619 0.00 0.00 38.55 4.69
4334 4550 5.870978 GCAATGTACCTAACTTCGGTTCTTA 59.129 40.000 0.00 0.00 39.17 2.10
4360 4580 9.499369 ACCTCTGAAATACATATATATGGCTCT 57.501 33.333 23.44 7.96 38.00 4.09
4369 4589 7.308450 ACATATATATGGCTCTGTGTTGAGT 57.692 36.000 23.44 0.00 38.00 3.41
4393 4613 6.481644 GTCAGAATTCCTTGTATCATCTGTCC 59.518 42.308 0.65 0.00 35.50 4.02
4400 4620 6.542821 TCCTTGTATCATCTGTCCTTTTTGT 58.457 36.000 0.00 0.00 0.00 2.83
4401 4621 6.430925 TCCTTGTATCATCTGTCCTTTTTGTG 59.569 38.462 0.00 0.00 0.00 3.33
4407 4627 3.011566 TCTGTCCTTTTTGTGCTTCCA 57.988 42.857 0.00 0.00 0.00 3.53
4408 4628 3.565307 TCTGTCCTTTTTGTGCTTCCAT 58.435 40.909 0.00 0.00 0.00 3.41
4410 4630 5.136828 TCTGTCCTTTTTGTGCTTCCATTA 58.863 37.500 0.00 0.00 0.00 1.90
4411 4631 5.009610 TCTGTCCTTTTTGTGCTTCCATTAC 59.990 40.000 0.00 0.00 0.00 1.89
4416 4638 6.071616 TCCTTTTTGTGCTTCCATTACCATAC 60.072 38.462 0.00 0.00 0.00 2.39
4460 4682 9.350951 GGTTTATATATGTTTTTGTAGGAGGCT 57.649 33.333 0.00 0.00 0.00 4.58
4462 4684 8.918202 TTATATATGTTTTTGTAGGAGGCTGG 57.082 34.615 0.00 0.00 0.00 4.85
4475 4697 2.159379 GGAGGCTGGCGAGTTTAATTTG 60.159 50.000 0.00 0.00 0.00 2.32
4477 4699 1.135112 GGCTGGCGAGTTTAATTTGGG 60.135 52.381 0.00 0.00 0.00 4.12
4485 4707 4.083565 CGAGTTTAATTTGGGGGAAGGAA 58.916 43.478 0.00 0.00 0.00 3.36
4502 4724 6.258068 GGGAAGGAATGTAATACTTGTCGAAG 59.742 42.308 0.00 0.00 35.07 3.79
4508 4730 8.718734 GGAATGTAATACTTGTCGAAGAACTTT 58.281 33.333 0.00 0.00 39.69 2.66
4512 4734 8.922676 TGTAATACTTGTCGAAGAACTTTCATC 58.077 33.333 0.00 0.00 39.69 2.92
4781 5008 6.774656 AGATTCATCATGGAAAAGGTGTATCC 59.225 38.462 0.00 0.00 0.00 2.59
4819 5046 3.613030 ACAACAACCTTCGGTTTACACT 58.387 40.909 0.00 0.00 44.33 3.55
4833 5060 6.816640 TCGGTTTACACTGATTTAGGAGATTG 59.183 38.462 0.00 0.00 32.93 2.67
4857 5084 0.391130 CCACACCCACTATGACCACG 60.391 60.000 0.00 0.00 0.00 4.94
4858 5085 1.019278 CACACCCACTATGACCACGC 61.019 60.000 0.00 0.00 0.00 5.34
4860 5087 2.202878 CCCACTATGACCACGCCG 60.203 66.667 0.00 0.00 0.00 6.46
4868 5095 4.309950 GACCACGCCGACAAGGGT 62.310 66.667 0.00 0.00 41.48 4.34
4871 5098 3.411351 CACGCCGACAAGGGTTCG 61.411 66.667 0.00 0.00 41.48 3.95
4947 5174 0.396060 CTAGGGCTGCTTCTCCATCC 59.604 60.000 0.00 0.00 0.00 3.51
4966 5193 0.179124 CGCAAGTGCCTAGAGGAGTC 60.179 60.000 0.00 0.00 37.91 3.36
5012 5239 1.812571 GGCTACAATTGACAGTGTGGG 59.187 52.381 13.59 0.00 32.24 4.61
5039 5266 1.263217 CCAGTAACAACTTGACGCCAC 59.737 52.381 0.00 0.00 0.00 5.01
5190 5498 0.393402 TTGCGCCTTGCTCATCAGAT 60.393 50.000 4.18 0.00 46.63 2.90
5195 5503 2.211806 GCCTTGCTCATCAGATCAGAC 58.788 52.381 0.00 0.00 0.00 3.51
5196 5504 2.836262 CCTTGCTCATCAGATCAGACC 58.164 52.381 0.00 0.00 0.00 3.85
5197 5505 2.169978 CCTTGCTCATCAGATCAGACCA 59.830 50.000 0.00 0.00 0.00 4.02
5198 5506 3.459145 CTTGCTCATCAGATCAGACCAG 58.541 50.000 0.00 0.00 0.00 4.00
5199 5507 2.743553 TGCTCATCAGATCAGACCAGA 58.256 47.619 0.00 0.00 0.00 3.86
5363 5672 0.099436 GCTGCCTGCGACCAAAATAG 59.901 55.000 0.00 0.00 0.00 1.73
5475 5784 1.553704 CTGAAACCTAGGTAACCCGCT 59.446 52.381 16.67 0.00 35.12 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.902196 ATGTTAATGAAAGTAAAACTTAACCGG 57.098 29.630 0.00 0.00 37.47 5.28
50 51 9.784531 AGTCCACTATATCCATGTTAATGAAAG 57.215 33.333 0.00 0.00 35.67 2.62
120 121 6.682423 TCTATCTAATTTGTACCGTCGTCA 57.318 37.500 0.00 0.00 0.00 4.35
121 122 7.699812 AGTTTCTATCTAATTTGTACCGTCGTC 59.300 37.037 0.00 0.00 0.00 4.20
122 123 7.542025 AGTTTCTATCTAATTTGTACCGTCGT 58.458 34.615 0.00 0.00 0.00 4.34
123 124 7.982371 AGTTTCTATCTAATTTGTACCGTCG 57.018 36.000 0.00 0.00 0.00 5.12
187 199 7.710676 AGATTTATAGAGACCATAGCGACAT 57.289 36.000 0.00 0.00 0.00 3.06
317 333 4.202111 GCTCTGGATTCTACAACCTCTCTC 60.202 50.000 0.00 0.00 0.00 3.20
423 446 8.129211 CCTCATCTAATCGGTAATTTTGGTTTC 58.871 37.037 0.00 0.00 0.00 2.78
456 479 2.525368 GGCCTCCTCTTTGCCTAAAAA 58.475 47.619 0.00 0.00 42.01 1.94
494 517 2.166907 ACTCACCTCGGGATCAGAAT 57.833 50.000 0.00 0.00 0.00 2.40
627 658 1.674322 CGGAGGCCACGTTTTCCAT 60.674 57.895 5.01 0.00 0.00 3.41
681 727 4.908156 GCATATGACATTCGTGAAAGATGC 59.092 41.667 6.97 0.00 0.00 3.91
846 893 0.798776 GTGCTGTTCTCATCCCAACG 59.201 55.000 0.00 0.00 0.00 4.10
870 917 0.773644 AGTGCAGAACATGGGAAGGT 59.226 50.000 0.00 0.00 0.00 3.50
1353 1433 6.433441 AGACTAGTTACTATGGTTACTGCCT 58.567 40.000 10.71 3.06 36.25 4.75
1373 1521 1.134521 TGACAACCTTGCAACGAGACT 60.135 47.619 0.00 0.00 0.00 3.24
1395 1543 4.081142 TCAATCCTACTGGTGTGGTGTATG 60.081 45.833 0.00 0.00 34.23 2.39
1396 1544 4.101114 TCAATCCTACTGGTGTGGTGTAT 58.899 43.478 0.00 0.00 34.23 2.29
1397 1545 3.512496 TCAATCCTACTGGTGTGGTGTA 58.488 45.455 0.00 0.00 34.23 2.90
1398 1546 2.334977 TCAATCCTACTGGTGTGGTGT 58.665 47.619 0.00 0.00 34.23 4.16
1399 1547 3.634397 ATCAATCCTACTGGTGTGGTG 57.366 47.619 0.00 0.00 34.23 4.17
1400 1548 4.721776 ACATATCAATCCTACTGGTGTGGT 59.278 41.667 0.00 0.00 34.23 4.16
1401 1549 5.059161 CACATATCAATCCTACTGGTGTGG 58.941 45.833 0.00 0.00 32.91 4.17
1402 1550 5.917462 TCACATATCAATCCTACTGGTGTG 58.083 41.667 0.00 0.00 36.64 3.82
1403 1551 6.327365 TCATCACATATCAATCCTACTGGTGT 59.673 38.462 0.00 0.00 34.23 4.16
1404 1552 6.762333 TCATCACATATCAATCCTACTGGTG 58.238 40.000 0.00 0.00 34.23 4.17
1405 1553 7.392418 CATCATCACATATCAATCCTACTGGT 58.608 38.462 0.00 0.00 34.23 4.00
1406 1554 6.822170 CCATCATCACATATCAATCCTACTGG 59.178 42.308 0.00 0.00 0.00 4.00
1407 1555 6.822170 CCCATCATCACATATCAATCCTACTG 59.178 42.308 0.00 0.00 0.00 2.74
1408 1556 6.732390 TCCCATCATCACATATCAATCCTACT 59.268 38.462 0.00 0.00 0.00 2.57
1409 1557 6.950842 TCCCATCATCACATATCAATCCTAC 58.049 40.000 0.00 0.00 0.00 3.18
1410 1558 7.366191 CCATCCCATCATCACATATCAATCCTA 60.366 40.741 0.00 0.00 0.00 2.94
1411 1559 6.424032 CATCCCATCATCACATATCAATCCT 58.576 40.000 0.00 0.00 0.00 3.24
1412 1560 5.593095 CCATCCCATCATCACATATCAATCC 59.407 44.000 0.00 0.00 0.00 3.01
1413 1561 5.067413 GCCATCCCATCATCACATATCAATC 59.933 44.000 0.00 0.00 0.00 2.67
1414 1562 4.954202 GCCATCCCATCATCACATATCAAT 59.046 41.667 0.00 0.00 0.00 2.57
1415 1563 4.202588 TGCCATCCCATCATCACATATCAA 60.203 41.667 0.00 0.00 0.00 2.57
1416 1564 3.331294 TGCCATCCCATCATCACATATCA 59.669 43.478 0.00 0.00 0.00 2.15
1417 1565 3.959293 TGCCATCCCATCATCACATATC 58.041 45.455 0.00 0.00 0.00 1.63
1418 1566 4.391683 TTGCCATCCCATCATCACATAT 57.608 40.909 0.00 0.00 0.00 1.78
1419 1567 3.880168 TTGCCATCCCATCATCACATA 57.120 42.857 0.00 0.00 0.00 2.29
1420 1568 2.759839 TTGCCATCCCATCATCACAT 57.240 45.000 0.00 0.00 0.00 3.21
1421 1569 2.759839 ATTGCCATCCCATCATCACA 57.240 45.000 0.00 0.00 0.00 3.58
1422 1570 5.534207 TTTTATTGCCATCCCATCATCAC 57.466 39.130 0.00 0.00 0.00 3.06
1423 1571 5.603395 ACATTTTATTGCCATCCCATCATCA 59.397 36.000 0.00 0.00 0.00 3.07
1424 1572 6.105397 ACATTTTATTGCCATCCCATCATC 57.895 37.500 0.00 0.00 0.00 2.92
1425 1573 6.503560 AACATTTTATTGCCATCCCATCAT 57.496 33.333 0.00 0.00 0.00 2.45
1426 1574 5.954153 AACATTTTATTGCCATCCCATCA 57.046 34.783 0.00 0.00 0.00 3.07
1427 1575 8.729805 TTTTAACATTTTATTGCCATCCCATC 57.270 30.769 0.00 0.00 0.00 3.51
1428 1576 9.697990 AATTTTAACATTTTATTGCCATCCCAT 57.302 25.926 0.00 0.00 0.00 4.00
1429 1577 9.525826 AAATTTTAACATTTTATTGCCATCCCA 57.474 25.926 0.00 0.00 0.00 4.37
1451 1599 8.720562 CGAAAGAAAAGGAATTGCCAATAAATT 58.279 29.630 0.00 0.00 40.02 1.82
1452 1600 7.148423 GCGAAAGAAAAGGAATTGCCAATAAAT 60.148 33.333 0.00 0.00 40.02 1.40
1453 1601 6.147000 GCGAAAGAAAAGGAATTGCCAATAAA 59.853 34.615 0.00 0.00 40.02 1.40
1454 1602 5.637387 GCGAAAGAAAAGGAATTGCCAATAA 59.363 36.000 0.00 0.00 40.02 1.40
1455 1603 5.047377 AGCGAAAGAAAAGGAATTGCCAATA 60.047 36.000 0.00 0.00 40.02 1.90
1456 1604 3.996363 GCGAAAGAAAAGGAATTGCCAAT 59.004 39.130 0.00 0.00 40.02 3.16
1457 1605 3.069443 AGCGAAAGAAAAGGAATTGCCAA 59.931 39.130 0.00 0.00 40.02 4.52
1458 1606 2.627699 AGCGAAAGAAAAGGAATTGCCA 59.372 40.909 0.00 0.00 40.02 4.92
1459 1607 2.989166 CAGCGAAAGAAAAGGAATTGCC 59.011 45.455 0.00 0.00 0.00 4.52
1460 1608 3.900941 TCAGCGAAAGAAAAGGAATTGC 58.099 40.909 0.00 0.00 0.00 3.56
1461 1609 5.464168 ACATCAGCGAAAGAAAAGGAATTG 58.536 37.500 0.00 0.00 0.00 2.32
1462 1610 5.474876 AGACATCAGCGAAAGAAAAGGAATT 59.525 36.000 0.00 0.00 0.00 2.17
1463 1611 5.006386 AGACATCAGCGAAAGAAAAGGAAT 58.994 37.500 0.00 0.00 0.00 3.01
1464 1612 4.214119 CAGACATCAGCGAAAGAAAAGGAA 59.786 41.667 0.00 0.00 0.00 3.36
1465 1613 3.748048 CAGACATCAGCGAAAGAAAAGGA 59.252 43.478 0.00 0.00 0.00 3.36
1466 1614 3.748048 TCAGACATCAGCGAAAGAAAAGG 59.252 43.478 0.00 0.00 0.00 3.11
1467 1615 4.997905 TCAGACATCAGCGAAAGAAAAG 57.002 40.909 0.00 0.00 0.00 2.27
1468 1616 5.947228 AATCAGACATCAGCGAAAGAAAA 57.053 34.783 0.00 0.00 0.00 2.29
1469 1617 5.239306 ACAAATCAGACATCAGCGAAAGAAA 59.761 36.000 0.00 0.00 0.00 2.52
1470 1618 4.756642 ACAAATCAGACATCAGCGAAAGAA 59.243 37.500 0.00 0.00 0.00 2.52
1471 1619 4.318332 ACAAATCAGACATCAGCGAAAGA 58.682 39.130 0.00 0.00 0.00 2.52
1472 1620 4.675190 ACAAATCAGACATCAGCGAAAG 57.325 40.909 0.00 0.00 0.00 2.62
1473 1621 5.478407 TCTACAAATCAGACATCAGCGAAA 58.522 37.500 0.00 0.00 0.00 3.46
1474 1622 5.072040 TCTACAAATCAGACATCAGCGAA 57.928 39.130 0.00 0.00 0.00 4.70
1475 1623 4.718940 TCTACAAATCAGACATCAGCGA 57.281 40.909 0.00 0.00 0.00 4.93
1476 1624 5.752472 AGATTCTACAAATCAGACATCAGCG 59.248 40.000 1.07 0.00 0.00 5.18
1477 1625 6.538021 ACAGATTCTACAAATCAGACATCAGC 59.462 38.462 1.07 0.00 0.00 4.26
1492 1640 5.220491 GCCGAACTCAAATGACAGATTCTAC 60.220 44.000 0.00 0.00 0.00 2.59
1493 1641 4.870426 GCCGAACTCAAATGACAGATTCTA 59.130 41.667 0.00 0.00 0.00 2.10
1494 1642 3.686726 GCCGAACTCAAATGACAGATTCT 59.313 43.478 0.00 0.00 0.00 2.40
1549 1697 9.590451 AATAGAACGAAATGCATCATGATTTTT 57.410 25.926 5.16 6.60 0.00 1.94
1567 1716 9.781834 TGATTTATAGGCAAACAAAATAGAACG 57.218 29.630 0.00 0.00 0.00 3.95
1668 1818 7.442656 TCAGTACGAGAAAAGAAAATCCTCTT 58.557 34.615 0.00 0.00 37.24 2.85
1687 1837 3.292460 AGGAGTCACATAGCCTCAGTAC 58.708 50.000 0.00 0.00 0.00 2.73
1814 1986 4.703645 TGATCTTAGTGTCACCTTCTCG 57.296 45.455 0.00 0.00 0.00 4.04
1822 1994 7.228108 CCCGTACTACTATTGATCTTAGTGTCA 59.772 40.741 15.17 0.62 32.35 3.58
1825 1997 7.094720 CCTCCCGTACTACTATTGATCTTAGTG 60.095 44.444 15.17 9.77 32.35 2.74
1839 2011 4.886489 AGAAACTATGACCTCCCGTACTAC 59.114 45.833 0.00 0.00 0.00 2.73
1952 2129 2.517959 TCTCCAAAACCAGCATTCCAG 58.482 47.619 0.00 0.00 0.00 3.86
1977 2154 6.146184 CCATACAGAATATGCTTGTAACGGAG 59.854 42.308 0.00 0.00 0.00 4.63
1988 2165 0.804989 GGCCGCCATACAGAATATGC 59.195 55.000 3.91 0.00 0.00 3.14
2383 2564 7.924947 TGAAAACAAGTTGCATCATAATGTTCA 59.075 29.630 1.81 0.00 35.18 3.18
2394 2575 9.037737 GCATTGATATATGAAAACAAGTTGCAT 57.962 29.630 1.81 0.95 31.32 3.96
2828 3044 9.650539 CTGATAGCATTAATAGTAGAGTGCAAT 57.349 33.333 0.00 0.00 35.17 3.56
3191 3407 1.002792 GCAAACGTCCAACCTTCAGAC 60.003 52.381 0.00 0.00 0.00 3.51
3342 3558 8.826710 TGTTTACTGAATAAGCCTTTCATATCG 58.173 33.333 0.00 0.00 32.94 2.92
3378 3594 5.471456 CCTGAGACAAGCAACATAAAACTCT 59.529 40.000 0.00 0.00 0.00 3.24
3554 3770 3.532641 AGGGCAGGACTTCTCAATTTT 57.467 42.857 0.00 0.00 0.00 1.82
3558 3774 1.275291 CGTAAGGGCAGGACTTCTCAA 59.725 52.381 0.00 0.00 0.00 3.02
3665 3881 5.762179 TGGTGTCCTTAATCTTGACTGAT 57.238 39.130 0.00 0.00 0.00 2.90
3685 3901 3.406764 GGAGCATTAGTAGCATCCTTGG 58.593 50.000 0.00 0.00 0.00 3.61
3750 3966 6.012658 TCAACTATTTGACTCACCATTTGC 57.987 37.500 0.00 0.00 36.79 3.68
3776 3992 1.300080 CAAGCACCCCAAAACAGCG 60.300 57.895 0.00 0.00 0.00 5.18
3836 4052 3.181454 CCTTTGCCTTATCCACGGACTAT 60.181 47.826 0.00 0.00 0.00 2.12
3837 4053 2.169769 CCTTTGCCTTATCCACGGACTA 59.830 50.000 0.00 0.00 0.00 2.59
3842 4058 0.394352 AGCCCTTTGCCTTATCCACG 60.394 55.000 0.00 0.00 42.71 4.94
3849 4065 1.213926 CCTGATCTAGCCCTTTGCCTT 59.786 52.381 0.00 0.00 42.71 4.35
3872 4088 6.379703 TGTTCTCCATCAAAAAGAAAAGGTGA 59.620 34.615 0.00 0.00 31.26 4.02
3889 4105 5.809001 AGAAATGATGCTAACTGTTCTCCA 58.191 37.500 0.00 0.00 0.00 3.86
4078 4294 6.397272 TGAGACTTGCAACTTTGAAAAATGT 58.603 32.000 0.00 0.00 0.00 2.71
4099 4315 7.908601 GCGTACAATTATTTTCCTAGGTTTGAG 59.091 37.037 9.08 0.00 0.00 3.02
4142 4358 4.640364 ACCAATAAACATGTTTTGGCCAG 58.360 39.130 29.66 17.56 35.10 4.85
4230 4446 2.293170 TCTGGTTGTGCGTGAAAATCA 58.707 42.857 0.00 0.00 0.00 2.57
4231 4447 3.347958 TTCTGGTTGTGCGTGAAAATC 57.652 42.857 0.00 0.00 0.00 2.17
4238 4454 3.880490 TCTTACAAATTCTGGTTGTGCGT 59.120 39.130 0.18 0.00 39.50 5.24
4304 4520 4.807304 CGAAGTTAGGTACATTGCGGTTAT 59.193 41.667 0.00 0.00 0.00 1.89
4334 4550 9.499369 AGAGCCATATATATGTATTTCAGAGGT 57.501 33.333 19.11 7.79 31.82 3.85
4360 4580 4.780815 ACAAGGAATTCTGACTCAACACA 58.219 39.130 5.23 0.00 0.00 3.72
4369 4589 6.385176 AGGACAGATGATACAAGGAATTCTGA 59.615 38.462 5.23 0.00 34.62 3.27
4393 4613 6.099341 GGTATGGTAATGGAAGCACAAAAAG 58.901 40.000 0.00 0.00 0.00 2.27
4400 4620 3.117550 AGCATGGTATGGTAATGGAAGCA 60.118 43.478 0.00 0.00 39.58 3.91
4401 4621 3.490348 AGCATGGTATGGTAATGGAAGC 58.510 45.455 0.00 0.00 39.58 3.86
4437 4659 7.447238 GCCAGCCTCCTACAAAAACATATATAA 59.553 37.037 0.00 0.00 0.00 0.98
4460 4682 1.075698 TCCCCCAAATTAAACTCGCCA 59.924 47.619 0.00 0.00 0.00 5.69
4461 4683 1.842052 TCCCCCAAATTAAACTCGCC 58.158 50.000 0.00 0.00 0.00 5.54
4462 4684 2.165641 CCTTCCCCCAAATTAAACTCGC 59.834 50.000 0.00 0.00 0.00 5.03
4475 4697 5.125367 ACAAGTATTACATTCCTTCCCCC 57.875 43.478 0.00 0.00 0.00 5.40
4477 4699 5.667466 TCGACAAGTATTACATTCCTTCCC 58.333 41.667 0.00 0.00 0.00 3.97
4485 4707 8.827177 TGAAAGTTCTTCGACAAGTATTACAT 57.173 30.769 0.00 0.00 0.00 2.29
4502 4724 6.980397 TCAAAGAAAAAGGCAGATGAAAGTTC 59.020 34.615 0.00 0.00 0.00 3.01
4508 4730 6.061441 TGTACTCAAAGAAAAAGGCAGATGA 58.939 36.000 0.00 0.00 0.00 2.92
4512 4734 9.696917 AAATATTGTACTCAAAGAAAAAGGCAG 57.303 29.630 0.00 0.00 37.11 4.85
4595 4819 8.099364 CTGAAAGAGGTTTTCAGTGCTATAAA 57.901 34.615 17.27 0.00 46.17 1.40
4781 5008 8.478877 AGGTTGTTGTATCCTTCTATTAGTGAG 58.521 37.037 0.00 0.00 0.00 3.51
4819 5046 2.580322 TGGTGGCCAATCTCCTAAATCA 59.420 45.455 7.24 0.00 0.00 2.57
4833 5060 1.378514 CATAGTGGGTGTGGTGGCC 60.379 63.158 0.00 0.00 0.00 5.36
4857 5084 0.952010 TAAAGCGAACCCTTGTCGGC 60.952 55.000 0.00 0.00 0.00 5.54
4858 5085 0.794473 GTAAAGCGAACCCTTGTCGG 59.206 55.000 0.00 0.00 0.00 4.79
4860 5087 1.804748 CAGGTAAAGCGAACCCTTGTC 59.195 52.381 2.04 0.00 37.77 3.18
4947 5174 0.179124 GACTCCTCTAGGCACTTGCG 60.179 60.000 0.00 0.00 43.26 4.85
4966 5193 0.670546 AATTGGTCAGACACTCGCCG 60.671 55.000 2.17 0.00 0.00 6.46
5012 5239 4.387862 CGTCAAGTTGTTACTGGTACATCC 59.612 45.833 2.11 0.00 38.20 3.51
5190 5498 1.416401 GTCTGGTTTGGTCTGGTCTGA 59.584 52.381 0.00 0.00 0.00 3.27
5195 5503 0.250901 CCTGGTCTGGTTTGGTCTGG 60.251 60.000 0.00 0.00 0.00 3.86
5196 5504 0.474184 ACCTGGTCTGGTTTGGTCTG 59.526 55.000 0.00 0.00 36.89 3.51
5197 5505 0.474184 CACCTGGTCTGGTTTGGTCT 59.526 55.000 0.00 0.00 38.45 3.85
5198 5506 0.182775 ACACCTGGTCTGGTTTGGTC 59.817 55.000 0.00 0.00 38.45 4.02
5199 5507 0.106719 CACACCTGGTCTGGTTTGGT 60.107 55.000 0.00 0.00 38.45 3.67
5363 5672 1.218316 CCCCGAGGTGACAAGCTAC 59.782 63.158 0.00 0.00 33.19 3.58
5403 5712 1.944024 GTGTCGATCGTCAGGAGATCT 59.056 52.381 15.28 0.00 41.59 2.75
5411 5720 0.723459 CGTCGTTGTGTCGATCGTCA 60.723 55.000 15.94 13.37 41.78 4.35
5475 5784 2.082629 TTTCAGACTCTGCCGTCGCA 62.083 55.000 0.62 0.00 44.78 5.10


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

AutoCloner maintained by Alex Coulton.