Multiple sequence alignment - TraesCS5A01G073900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G073900 chr5A 100.000 5035 0 0 853 5887 86658803 86663837 0.000000e+00 9299
1 TraesCS5A01G073900 chr5A 100.000 321 0 0 1 321 86657951 86658271 1.410000e-165 593
2 TraesCS5A01G073900 chr5D 96.601 2118 61 9 1971 4080 93062411 93064525 0.000000e+00 3502
3 TraesCS5A01G073900 chr5D 96.629 1780 47 3 4118 5887 93064523 93066299 0.000000e+00 2942
4 TraesCS5A01G073900 chr5D 94.270 733 34 5 853 1577 93061235 93061967 0.000000e+00 1114
5 TraesCS5A01G073900 chr5D 95.107 327 2 2 1 321 93060839 93061157 2.450000e-138 503
6 TraesCS5A01G073900 chr5D 94.737 76 4 0 1890 1965 93062301 93062376 1.040000e-22 119
7 TraesCS5A01G073900 chr5D 83.582 134 8 3 1701 1827 93061966 93062092 4.820000e-21 113
8 TraesCS5A01G073900 chr5B 96.637 1933 52 5 1701 3629 98660852 98662775 0.000000e+00 3197
9 TraesCS5A01G073900 chr5B 94.316 1777 40 25 3666 5417 98662777 98664517 0.000000e+00 2665
10 TraesCS5A01G073900 chr5B 97.245 726 19 1 853 1577 98660128 98660853 0.000000e+00 1229
11 TraesCS5A01G073900 chr5B 96.904 323 0 3 1 321 98659736 98660050 3.120000e-147 532
12 TraesCS5A01G073900 chr5B 94.925 335 17 0 5553 5887 98664930 98665264 5.230000e-145 525
13 TraesCS5A01G073900 chr7A 94.118 170 8 2 4061 4228 201986994 201987163 2.100000e-64 257
14 TraesCS5A01G073900 chr7A 99.242 132 0 1 1572 1703 170891364 170891234 2.740000e-58 237
15 TraesCS5A01G073900 chr7A 93.590 156 10 0 4069 4224 462978739 462978584 3.550000e-57 233
16 TraesCS5A01G073900 chr7A 99.225 129 1 0 1576 1704 715050950 715051078 3.550000e-57 233
17 TraesCS5A01G073900 chr7B 92.857 168 10 2 4068 4233 155471166 155471333 5.890000e-60 243
18 TraesCS5A01G073900 chr7D 94.231 156 8 1 4069 4224 404056965 404056811 2.740000e-58 237
19 TraesCS5A01G073900 chr7D 94.156 154 8 1 4069 4221 436961948 436961795 3.550000e-57 233
20 TraesCS5A01G073900 chr7D 91.071 168 12 2 4061 4227 192371461 192371626 2.130000e-54 224
21 TraesCS5A01G073900 chr2B 99.242 132 0 1 1572 1702 243084219 243084088 2.740000e-58 237
22 TraesCS5A01G073900 chr2B 93.893 131 6 1 1574 1702 24324156 24324286 4.650000e-46 196
23 TraesCS5A01G073900 chr2A 99.219 128 1 0 1576 1703 43374849 43374976 1.280000e-56 231
24 TraesCS5A01G073900 chr1A 91.667 168 13 1 4062 4228 385659127 385659294 1.280000e-56 231
25 TraesCS5A01G073900 chr1A 98.438 128 2 0 1575 1702 323289626 323289499 5.940000e-55 226
26 TraesCS5A01G073900 chr4A 93.662 142 8 1 1576 1716 674850004 674849863 1.660000e-50 211
27 TraesCS5A01G073900 chr6B 94.656 131 5 2 1572 1702 62005052 62004924 1.000000e-47 202
28 TraesCS5A01G073900 chr6D 94.488 127 7 0 1576 1702 6014157 6014031 4.650000e-46 196


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 TraesCS5A01G073900 chr5A 86657951 86663837 5886 False 4946.000000 9299 100.000000 1 5887 2 chr5A.!!$F1 5886
1 TraesCS5A01G073900 chr5D 93060839 93066299 5460 False 1382.166667 3502 93.487667 1 5887 6 chr5D.!!$F1 5886
2 TraesCS5A01G073900 chr5B 98659736 98665264 5528 False 1629.600000 3197 96.005400 1 5887 5 chr5B.!!$F1 5886

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
131 132 0.327576 TCAAATCCCCTCCCTCCTCC 60.328 60.000 0.00 0.00 0.00 4.30 F
132 133 0.624500 CAAATCCCCTCCCTCCTCCA 60.625 60.000 0.00 0.00 0.00 3.86 F
133 134 0.624795 AAATCCCCTCCCTCCTCCAC 60.625 60.000 0.00 0.00 0.00 4.02 F
954 964 0.829333 ATGCTCGCTGGATTCTCTGT 59.171 50.000 0.00 0.00 0.00 3.41 F
1342 1352 0.925466 GACAAATGATGCGCAATGCC 59.075 50.000 17.11 4.72 45.60 4.40 F
2229 2454 0.901827 TGGCCGTCTTCTCAAGCATA 59.098 50.000 0.00 0.00 0.00 3.14 F
2826 3051 3.199508 AGGAACTGAGATCATCCAGGTTG 59.800 47.826 12.37 0.00 37.18 3.77 F
4067 4295 2.554370 TGGGTCAAGGAGGTAAAACG 57.446 50.000 0.00 0.00 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1701 1.356738 TCTTCTACTCCCTCCGTTCCA 59.643 52.381 0.00 0.00 0.00 3.53 R
1687 1702 2.140839 TCTTCTACTCCCTCCGTTCC 57.859 55.000 0.00 0.00 0.00 3.62 R
1880 2067 3.186001 GTGCAAGATATCGATGCTTCCTG 59.814 47.826 26.34 3.92 40.66 3.86 R
2208 2433 0.179032 TGCTTGAGAAGACGGCCAAA 60.179 50.000 2.24 0.00 0.00 3.28 R
3294 3519 1.339291 AGCTTGGCTGCAAAAACTCTC 59.661 47.619 0.50 0.00 37.57 3.20 R
3747 3975 3.119352 GGCTTGGGAATAACTGCTTTGAG 60.119 47.826 0.00 0.00 0.00 3.02 R
4450 4678 3.302365 AAAATGGAATTCAGCACCACG 57.698 42.857 7.93 0.00 33.67 4.94 R
5830 6397 2.301346 CAAGTTTCTGCCAGTTCACCT 58.699 47.619 0.00 0.00 0.00 4.00 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
126 127 2.023984 GGTCAAATCAAATCCCCTCCCT 60.024 50.000 0.00 0.00 0.00 4.20
127 128 3.291584 GTCAAATCAAATCCCCTCCCTC 58.708 50.000 0.00 0.00 0.00 4.30
128 129 2.244769 TCAAATCAAATCCCCTCCCTCC 59.755 50.000 0.00 0.00 0.00 4.30
129 130 2.245806 CAAATCAAATCCCCTCCCTCCT 59.754 50.000 0.00 0.00 0.00 3.69
130 131 1.826447 ATCAAATCCCCTCCCTCCTC 58.174 55.000 0.00 0.00 0.00 3.71
131 132 0.327576 TCAAATCCCCTCCCTCCTCC 60.328 60.000 0.00 0.00 0.00 4.30
132 133 0.624500 CAAATCCCCTCCCTCCTCCA 60.625 60.000 0.00 0.00 0.00 3.86
133 134 0.624795 AAATCCCCTCCCTCCTCCAC 60.625 60.000 0.00 0.00 0.00 4.02
954 964 0.829333 ATGCTCGCTGGATTCTCTGT 59.171 50.000 0.00 0.00 0.00 3.41
1286 1296 2.435805 GGGATGATGTAGTGGCTTGAGA 59.564 50.000 0.00 0.00 0.00 3.27
1321 1331 8.947115 GCTTTAGAGTTTAGACAACATAATGGT 58.053 33.333 0.00 0.00 0.00 3.55
1342 1352 0.925466 GACAAATGATGCGCAATGCC 59.075 50.000 17.11 4.72 45.60 4.40
1374 1384 3.115554 GTGACTTTTGCAGCAATTTCGT 58.884 40.909 9.12 3.85 0.00 3.85
1375 1385 3.180387 GTGACTTTTGCAGCAATTTCGTC 59.820 43.478 9.12 12.83 0.00 4.20
1564 1579 2.026636 AGCTGCGGAAACCACCTATTTA 60.027 45.455 0.00 0.00 0.00 1.40
1577 1592 7.836479 ACCACCTATTTAGTCTCCTGTATAC 57.164 40.000 0.00 0.00 0.00 1.47
1578 1593 7.593653 ACCACCTATTTAGTCTCCTGTATACT 58.406 38.462 4.17 0.00 0.00 2.12
1579 1594 7.724951 ACCACCTATTTAGTCTCCTGTATACTC 59.275 40.741 4.17 0.00 0.00 2.59
1580 1595 7.177041 CCACCTATTTAGTCTCCTGTATACTCC 59.823 44.444 4.17 0.00 0.00 3.85
1581 1596 7.177041 CACCTATTTAGTCTCCTGTATACTCCC 59.823 44.444 4.17 0.00 0.00 4.30
1582 1597 7.075267 ACCTATTTAGTCTCCTGTATACTCCCT 59.925 40.741 4.17 0.00 0.00 4.20
1583 1598 7.612633 CCTATTTAGTCTCCTGTATACTCCCTC 59.387 44.444 4.17 0.00 0.00 4.30
1584 1599 3.887916 AGTCTCCTGTATACTCCCTCC 57.112 52.381 4.17 0.00 0.00 4.30
1585 1600 2.106857 AGTCTCCTGTATACTCCCTCCG 59.893 54.545 4.17 0.00 0.00 4.63
1586 1601 2.133520 TCTCCTGTATACTCCCTCCGT 58.866 52.381 4.17 0.00 0.00 4.69
1587 1602 2.512896 TCTCCTGTATACTCCCTCCGTT 59.487 50.000 4.17 0.00 0.00 4.44
1588 1603 2.885894 CTCCTGTATACTCCCTCCGTTC 59.114 54.545 4.17 0.00 0.00 3.95
1589 1604 1.962100 CCTGTATACTCCCTCCGTTCC 59.038 57.143 4.17 0.00 0.00 3.62
1590 1605 2.662866 CTGTATACTCCCTCCGTTCCA 58.337 52.381 4.17 0.00 0.00 3.53
1591 1606 3.028850 CTGTATACTCCCTCCGTTCCAA 58.971 50.000 4.17 0.00 0.00 3.53
1592 1607 3.443052 TGTATACTCCCTCCGTTCCAAA 58.557 45.455 4.17 0.00 0.00 3.28
1593 1608 4.035112 TGTATACTCCCTCCGTTCCAAAT 58.965 43.478 4.17 0.00 0.00 2.32
1594 1609 4.472108 TGTATACTCCCTCCGTTCCAAATT 59.528 41.667 4.17 0.00 0.00 1.82
1595 1610 5.662208 TGTATACTCCCTCCGTTCCAAATTA 59.338 40.000 4.17 0.00 0.00 1.40
1596 1611 3.629142 ACTCCCTCCGTTCCAAATTAG 57.371 47.619 0.00 0.00 0.00 1.73
1597 1612 3.178865 ACTCCCTCCGTTCCAAATTAGA 58.821 45.455 0.00 0.00 0.00 2.10
1598 1613 3.780850 ACTCCCTCCGTTCCAAATTAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1599 1614 4.130118 CTCCCTCCGTTCCAAATTAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1600 1615 3.778075 TCCCTCCGTTCCAAATTAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1601 1616 3.877508 CCCTCCGTTCCAAATTAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1602 1617 4.384208 CCCTCCGTTCCAAATTAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1603 1618 5.186198 CCTCCGTTCCAAATTAGATGACTT 58.814 41.667 0.00 0.00 0.00 3.01
1604 1619 5.648092 CCTCCGTTCCAAATTAGATGACTTT 59.352 40.000 0.00 0.00 0.00 2.66
1605 1620 6.183360 CCTCCGTTCCAAATTAGATGACTTTC 60.183 42.308 0.00 0.00 0.00 2.62
1606 1621 6.234920 TCCGTTCCAAATTAGATGACTTTCA 58.765 36.000 0.00 0.00 0.00 2.69
1607 1622 6.884295 TCCGTTCCAAATTAGATGACTTTCAT 59.116 34.615 0.00 0.00 40.34 2.57
1608 1623 7.393234 TCCGTTCCAAATTAGATGACTTTCATT 59.607 33.333 0.00 0.00 37.20 2.57
1609 1624 8.028938 CCGTTCCAAATTAGATGACTTTCATTT 58.971 33.333 0.00 0.00 37.20 2.32
1610 1625 8.853345 CGTTCCAAATTAGATGACTTTCATTTG 58.147 33.333 0.00 0.00 37.20 2.32
1611 1626 9.696917 GTTCCAAATTAGATGACTTTCATTTGT 57.303 29.630 0.00 0.00 37.20 2.83
1612 1627 9.912634 TTCCAAATTAGATGACTTTCATTTGTC 57.087 29.630 0.00 0.00 37.20 3.18
1613 1628 9.300681 TCCAAATTAGATGACTTTCATTTGTCT 57.699 29.630 0.00 0.00 37.20 3.41
1620 1635 8.945481 AGATGACTTTCATTTGTCTAGAGATG 57.055 34.615 0.00 0.00 37.20 2.90
1621 1636 7.986320 AGATGACTTTCATTTGTCTAGAGATGG 59.014 37.037 0.00 0.00 37.20 3.51
1622 1637 7.244886 TGACTTTCATTTGTCTAGAGATGGA 57.755 36.000 0.00 0.00 34.57 3.41
1623 1638 7.855375 TGACTTTCATTTGTCTAGAGATGGAT 58.145 34.615 0.00 0.00 34.57 3.41
1624 1639 7.767659 TGACTTTCATTTGTCTAGAGATGGATG 59.232 37.037 0.00 0.00 34.57 3.51
1625 1640 7.628234 ACTTTCATTTGTCTAGAGATGGATGT 58.372 34.615 0.00 0.00 0.00 3.06
1626 1641 8.762645 ACTTTCATTTGTCTAGAGATGGATGTA 58.237 33.333 0.00 0.00 0.00 2.29
1627 1642 9.775854 CTTTCATTTGTCTAGAGATGGATGTAT 57.224 33.333 0.00 0.00 0.00 2.29
1634 1649 8.996651 TGTCTAGAGATGGATGTATTTAGACA 57.003 34.615 6.86 6.86 41.79 3.41
1635 1650 8.851145 TGTCTAGAGATGGATGTATTTAGACAC 58.149 37.037 6.86 0.00 40.19 3.67
1636 1651 9.073475 GTCTAGAGATGGATGTATTTAGACACT 57.927 37.037 0.00 0.00 37.06 3.55
1641 1656 9.817809 GAGATGGATGTATTTAGACACTAAACA 57.182 33.333 6.17 3.20 30.52 2.83
1644 1659 9.959721 ATGGATGTATTTAGACACTAAACAAGT 57.040 29.630 6.17 0.00 39.81 3.16
1673 1688 5.296151 ACATCCATATGTAGACAAGTGGG 57.704 43.478 13.56 3.00 44.66 4.61
1674 1689 4.103153 ACATCCATATGTAGACAAGTGGGG 59.897 45.833 13.56 10.14 44.66 4.96
1675 1690 3.045634 TCCATATGTAGACAAGTGGGGG 58.954 50.000 13.56 0.00 36.04 5.40
1676 1691 2.777692 CCATATGTAGACAAGTGGGGGT 59.222 50.000 1.24 0.00 33.48 4.95
1677 1692 3.181454 CCATATGTAGACAAGTGGGGGTC 60.181 52.174 1.24 0.00 33.48 4.46
1678 1693 2.038863 ATGTAGACAAGTGGGGGTCA 57.961 50.000 0.00 0.00 36.50 4.02
1679 1694 1.809133 TGTAGACAAGTGGGGGTCAA 58.191 50.000 0.00 0.00 36.50 3.18
1680 1695 1.697432 TGTAGACAAGTGGGGGTCAAG 59.303 52.381 0.00 0.00 36.50 3.02
1681 1696 1.697982 GTAGACAAGTGGGGGTCAAGT 59.302 52.381 0.00 0.00 36.50 3.16
1682 1697 2.112279 AGACAAGTGGGGGTCAAGTA 57.888 50.000 0.00 0.00 36.50 2.24
1683 1698 2.632537 AGACAAGTGGGGGTCAAGTAT 58.367 47.619 0.00 0.00 36.50 2.12
1684 1699 2.986728 AGACAAGTGGGGGTCAAGTATT 59.013 45.455 0.00 0.00 36.50 1.89
1685 1700 3.397955 AGACAAGTGGGGGTCAAGTATTT 59.602 43.478 0.00 0.00 36.50 1.40
1686 1701 4.141018 AGACAAGTGGGGGTCAAGTATTTT 60.141 41.667 0.00 0.00 36.50 1.82
1687 1702 3.895041 ACAAGTGGGGGTCAAGTATTTTG 59.105 43.478 0.00 0.00 0.00 2.44
1688 1703 3.169512 AGTGGGGGTCAAGTATTTTGG 57.830 47.619 0.00 0.00 0.00 3.28
1689 1704 2.719705 AGTGGGGGTCAAGTATTTTGGA 59.280 45.455 0.00 0.00 0.00 3.53
1690 1705 3.141272 AGTGGGGGTCAAGTATTTTGGAA 59.859 43.478 0.00 0.00 0.00 3.53
1691 1706 3.257375 GTGGGGGTCAAGTATTTTGGAAC 59.743 47.826 0.00 0.00 0.00 3.62
1692 1707 2.490509 GGGGGTCAAGTATTTTGGAACG 59.509 50.000 0.00 0.00 0.00 3.95
1693 1708 2.490509 GGGGTCAAGTATTTTGGAACGG 59.509 50.000 0.00 0.00 0.00 4.44
1694 1709 3.414269 GGGTCAAGTATTTTGGAACGGA 58.586 45.455 0.00 0.00 0.00 4.69
1695 1710 3.439129 GGGTCAAGTATTTTGGAACGGAG 59.561 47.826 0.00 0.00 0.00 4.63
1696 1711 3.439129 GGTCAAGTATTTTGGAACGGAGG 59.561 47.826 0.00 0.00 0.00 4.30
1697 1712 3.439129 GTCAAGTATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
1698 1713 3.328343 TCAAGTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
1699 1714 3.629142 AGTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1726 1741 4.465886 AGATAAGTAGACACGAGGATGCT 58.534 43.478 0.00 0.00 0.00 3.79
1727 1742 4.890581 AGATAAGTAGACACGAGGATGCTT 59.109 41.667 0.00 0.00 0.00 3.91
1728 1743 6.062749 AGATAAGTAGACACGAGGATGCTTA 58.937 40.000 0.00 0.00 0.00 3.09
1729 1744 6.717540 AGATAAGTAGACACGAGGATGCTTAT 59.282 38.462 8.63 8.63 32.62 1.73
1730 1745 4.576216 AGTAGACACGAGGATGCTTATG 57.424 45.455 0.00 0.00 0.00 1.90
1731 1746 4.207955 AGTAGACACGAGGATGCTTATGA 58.792 43.478 5.80 0.00 0.00 2.15
1732 1747 4.830046 AGTAGACACGAGGATGCTTATGAT 59.170 41.667 5.80 0.00 0.00 2.45
1788 1809 2.507484 TGCCTTGATTGTTCAGTGAGG 58.493 47.619 0.00 0.00 32.61 3.86
1840 2027 5.470098 CAGACAGTTTGTACAGTAAGCCATT 59.530 40.000 0.00 0.00 0.00 3.16
1880 2067 9.635520 TGCAACTACTCTAGTTTTCTATGTTAC 57.364 33.333 0.00 0.00 46.27 2.50
1929 2116 4.693566 TGTTTAGAATTGGGAACTGCTACG 59.306 41.667 0.00 0.00 0.00 3.51
2092 2311 3.375782 GCATCCCAATGGCTTTGTATC 57.624 47.619 11.60 0.00 33.15 2.24
2096 2315 2.852449 TCCCAATGGCTTTGTATCTCCT 59.148 45.455 11.60 0.00 33.15 3.69
2208 2433 1.559682 ACGTGCTTCCACCCTCATTAT 59.440 47.619 0.00 0.00 38.79 1.28
2229 2454 0.901827 TGGCCGTCTTCTCAAGCATA 59.098 50.000 0.00 0.00 0.00 3.14
2420 2645 5.722021 TTGCACTTCCCTTTAATCCTTTC 57.278 39.130 0.00 0.00 0.00 2.62
2456 2681 3.656651 TTTTAATCGATCGCTGCACTG 57.343 42.857 11.09 0.00 0.00 3.66
2826 3051 3.199508 AGGAACTGAGATCATCCAGGTTG 59.800 47.826 12.37 0.00 37.18 3.77
3294 3519 4.320456 ACTGCAGGTGACAGCCCG 62.320 66.667 19.93 0.00 43.15 6.13
3464 3690 3.446873 TGGTGAAACACTCAACTGCAAAT 59.553 39.130 0.00 0.00 42.83 2.32
3547 3773 4.947388 GGTGTCAAGAGGCAACCAATATTA 59.053 41.667 0.00 0.00 37.17 0.98
3550 3776 4.338400 GTCAAGAGGCAACCAATATTACCC 59.662 45.833 0.00 0.00 37.17 3.69
3578 3805 6.780457 ACCTTTTGCAGAAATGTATAGCAT 57.220 33.333 0.00 0.00 40.03 3.79
4067 4295 2.554370 TGGGTCAAGGAGGTAAAACG 57.446 50.000 0.00 0.00 0.00 3.60
4078 4306 2.827921 GAGGTAAAACGTACTCCCTCCA 59.172 50.000 11.30 0.00 33.85 3.86
4219 4447 6.371278 TCTTATAATAGTGAACGGAGGGAGT 58.629 40.000 0.00 0.00 0.00 3.85
4220 4448 7.520798 TCTTATAATAGTGAACGGAGGGAGTA 58.479 38.462 0.00 0.00 0.00 2.59
4235 4463 9.575868 ACGGAGGGAGTATATATATCACTATTG 57.424 37.037 0.00 0.88 0.00 1.90
4298 4526 7.377662 GCATTTCTTTTCTTTTTGCCATTTCAG 59.622 33.333 0.00 0.00 0.00 3.02
4450 4678 5.351465 TGCTGAAAAAGTATAGCTGTACTGC 59.649 40.000 22.15 18.93 35.20 4.40
4473 4701 5.410067 CGTGGTGCTGAATTCCATTTTATT 58.590 37.500 2.27 0.00 33.68 1.40
5469 5966 0.105760 ATGCTGGTTGGTGGGTTGAA 60.106 50.000 0.00 0.00 0.00 2.69
5487 5984 6.094881 GGGTTGAACAGCAGCAGTTTATAATA 59.905 38.462 4.46 0.00 0.00 0.98
5674 6241 3.243839 GGGCAGAACACATCAACACAAAT 60.244 43.478 0.00 0.00 0.00 2.32
5773 6340 7.801280 AACTACAGTTCATCGCTAGCAAGCA 62.801 44.000 16.45 0.00 40.61 3.91
5806 6373 2.506438 GGGAAGACGACGAAGGCG 60.506 66.667 0.00 0.00 44.79 5.52
5830 6397 1.081442 CAGCGGCGCGACATAGATA 60.081 57.895 27.59 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 2.637640 GGGAGGGAGGAGTGGAGGA 61.638 68.421 0.00 0.00 0.00 3.71
127 128 2.041405 GGGAGGGAGGAGTGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
128 129 1.297409 TAGGGGAGGGAGGAGTGGAG 61.297 65.000 0.00 0.00 0.00 3.86
129 130 0.858598 TTAGGGGAGGGAGGAGTGGA 60.859 60.000 0.00 0.00 0.00 4.02
130 131 0.269173 ATTAGGGGAGGGAGGAGTGG 59.731 60.000 0.00 0.00 0.00 4.00
131 132 1.723288 GATTAGGGGAGGGAGGAGTG 58.277 60.000 0.00 0.00 0.00 3.51
132 133 0.568697 GGATTAGGGGAGGGAGGAGT 59.431 60.000 0.00 0.00 0.00 3.85
133 134 0.178888 GGGATTAGGGGAGGGAGGAG 60.179 65.000 0.00 0.00 0.00 3.69
954 964 2.438614 CTCCTGCTCCGTCCTCGA 60.439 66.667 0.00 0.00 39.71 4.04
1321 1331 1.994074 GCATTGCGCATCATTTGTCAA 59.006 42.857 12.75 0.00 41.79 3.18
1342 1352 2.288395 GCAAAAGTCACATCCCACAAGG 60.288 50.000 0.00 0.00 0.00 3.61
1374 1384 3.992943 ACCCATCAAGTTATTCACCGA 57.007 42.857 0.00 0.00 0.00 4.69
1375 1385 4.457603 TCAAACCCATCAAGTTATTCACCG 59.542 41.667 0.00 0.00 0.00 4.94
1564 1579 2.106857 CGGAGGGAGTATACAGGAGACT 59.893 54.545 5.50 0.00 46.44 3.24
1577 1592 3.906720 TCTAATTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1578 1593 3.778075 TCATCTAATTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1579 1594 3.877508 GTCATCTAATTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1580 1595 4.770795 AGTCATCTAATTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1581 1596 6.371548 TGAAAGTCATCTAATTTGGAACGGAG 59.628 38.462 0.00 0.00 0.00 4.63
1582 1597 6.234920 TGAAAGTCATCTAATTTGGAACGGA 58.765 36.000 0.00 0.00 0.00 4.69
1583 1598 6.494893 TGAAAGTCATCTAATTTGGAACGG 57.505 37.500 0.00 0.00 0.00 4.44
1584 1599 8.853345 CAAATGAAAGTCATCTAATTTGGAACG 58.147 33.333 0.00 0.00 35.76 3.95
1585 1600 9.696917 ACAAATGAAAGTCATCTAATTTGGAAC 57.303 29.630 9.85 0.00 35.76 3.62
1586 1601 9.912634 GACAAATGAAAGTCATCTAATTTGGAA 57.087 29.630 9.85 0.00 35.76 3.53
1587 1602 9.300681 AGACAAATGAAAGTCATCTAATTTGGA 57.699 29.630 9.85 0.00 35.76 3.53
1595 1610 7.986320 CCATCTCTAGACAAATGAAAGTCATCT 59.014 37.037 6.59 0.00 35.76 2.90
1596 1611 7.984050 TCCATCTCTAGACAAATGAAAGTCATC 59.016 37.037 6.59 0.00 35.76 2.92
1597 1612 7.855375 TCCATCTCTAGACAAATGAAAGTCAT 58.145 34.615 6.59 0.00 39.09 3.06
1598 1613 7.244886 TCCATCTCTAGACAAATGAAAGTCA 57.755 36.000 6.59 0.00 37.23 3.41
1599 1614 7.768120 ACATCCATCTCTAGACAAATGAAAGTC 59.232 37.037 6.59 0.00 35.02 3.01
1600 1615 7.628234 ACATCCATCTCTAGACAAATGAAAGT 58.372 34.615 6.59 0.00 0.00 2.66
1601 1616 9.775854 ATACATCCATCTCTAGACAAATGAAAG 57.224 33.333 6.59 0.80 0.00 2.62
1608 1623 9.421399 TGTCTAAATACATCCATCTCTAGACAA 57.579 33.333 6.22 0.00 40.41 3.18
1609 1624 8.851145 GTGTCTAAATACATCCATCTCTAGACA 58.149 37.037 4.86 4.86 40.83 3.41
1610 1625 9.073475 AGTGTCTAAATACATCCATCTCTAGAC 57.927 37.037 0.00 0.00 36.26 2.59
1615 1630 9.817809 TGTTTAGTGTCTAAATACATCCATCTC 57.182 33.333 5.46 0.00 0.00 2.75
1618 1633 9.959721 ACTTGTTTAGTGTCTAAATACATCCAT 57.040 29.630 5.46 0.00 35.19 3.41
1646 1661 9.025041 CCACTTGTCTACATATGGATGTATCTA 57.975 37.037 7.80 0.00 45.42 1.98
1647 1662 7.038729 CCCACTTGTCTACATATGGATGTATCT 60.039 40.741 7.80 0.00 45.42 1.98
1648 1663 7.099764 CCCACTTGTCTACATATGGATGTATC 58.900 42.308 7.80 0.00 45.42 2.24
1649 1664 6.013379 CCCCACTTGTCTACATATGGATGTAT 60.013 42.308 7.80 0.00 45.42 2.29
1650 1665 5.306937 CCCCACTTGTCTACATATGGATGTA 59.693 44.000 7.80 0.00 44.77 2.29
1652 1667 4.505566 CCCCCACTTGTCTACATATGGATG 60.506 50.000 7.80 0.00 39.16 3.51
1653 1668 3.652869 CCCCCACTTGTCTACATATGGAT 59.347 47.826 7.80 0.00 34.75 3.41
1654 1669 3.045634 CCCCCACTTGTCTACATATGGA 58.954 50.000 7.80 0.00 34.75 3.41
1655 1670 2.777692 ACCCCCACTTGTCTACATATGG 59.222 50.000 7.80 6.28 33.41 2.74
1656 1671 3.454447 TGACCCCCACTTGTCTACATATG 59.546 47.826 0.00 0.00 32.67 1.78
1657 1672 3.731431 TGACCCCCACTTGTCTACATAT 58.269 45.455 0.00 0.00 32.67 1.78
1658 1673 3.193395 TGACCCCCACTTGTCTACATA 57.807 47.619 0.00 0.00 32.67 2.29
1659 1674 2.038863 TGACCCCCACTTGTCTACAT 57.961 50.000 0.00 0.00 32.67 2.29
1660 1675 1.697432 CTTGACCCCCACTTGTCTACA 59.303 52.381 0.00 0.00 32.67 2.74
1661 1676 1.697982 ACTTGACCCCCACTTGTCTAC 59.302 52.381 0.00 0.00 32.67 2.59
1662 1677 2.112279 ACTTGACCCCCACTTGTCTA 57.888 50.000 0.00 0.00 32.67 2.59
1663 1678 2.112279 TACTTGACCCCCACTTGTCT 57.888 50.000 0.00 0.00 32.67 3.41
1664 1679 3.434940 AATACTTGACCCCCACTTGTC 57.565 47.619 0.00 0.00 0.00 3.18
1665 1680 3.895041 CAAAATACTTGACCCCCACTTGT 59.105 43.478 0.00 0.00 0.00 3.16
1666 1681 3.258123 CCAAAATACTTGACCCCCACTTG 59.742 47.826 0.00 0.00 0.00 3.16
1667 1682 3.141272 TCCAAAATACTTGACCCCCACTT 59.859 43.478 0.00 0.00 0.00 3.16
1668 1683 2.719705 TCCAAAATACTTGACCCCCACT 59.280 45.455 0.00 0.00 0.00 4.00
1669 1684 3.163616 TCCAAAATACTTGACCCCCAC 57.836 47.619 0.00 0.00 0.00 4.61
1670 1685 3.502356 GTTCCAAAATACTTGACCCCCA 58.498 45.455 0.00 0.00 0.00 4.96
1671 1686 2.490509 CGTTCCAAAATACTTGACCCCC 59.509 50.000 0.00 0.00 0.00 5.40
1672 1687 2.490509 CCGTTCCAAAATACTTGACCCC 59.509 50.000 0.00 0.00 0.00 4.95
1673 1688 3.414269 TCCGTTCCAAAATACTTGACCC 58.586 45.455 0.00 0.00 0.00 4.46
1674 1689 3.439129 CCTCCGTTCCAAAATACTTGACC 59.561 47.826 0.00 0.00 0.00 4.02
1675 1690 3.439129 CCCTCCGTTCCAAAATACTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
1676 1691 3.328343 TCCCTCCGTTCCAAAATACTTGA 59.672 43.478 0.00 0.00 0.00 3.02
1677 1692 3.681593 TCCCTCCGTTCCAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
1678 1693 3.329814 ACTCCCTCCGTTCCAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
1679 1694 2.910977 ACTCCCTCCGTTCCAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
1680 1695 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
1681 1696 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
1682 1697 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
1683 1698 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
1684 1699 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
1685 1700 2.176889 CTTCTACTCCCTCCGTTCCAA 58.823 52.381 0.00 0.00 0.00 3.53
1686 1701 1.356738 TCTTCTACTCCCTCCGTTCCA 59.643 52.381 0.00 0.00 0.00 3.53
1687 1702 2.140839 TCTTCTACTCCCTCCGTTCC 57.859 55.000 0.00 0.00 0.00 3.62
1688 1703 4.888823 ACTTATCTTCTACTCCCTCCGTTC 59.111 45.833 0.00 0.00 0.00 3.95
1689 1704 4.869451 ACTTATCTTCTACTCCCTCCGTT 58.131 43.478 0.00 0.00 0.00 4.44
1690 1705 4.523168 ACTTATCTTCTACTCCCTCCGT 57.477 45.455 0.00 0.00 0.00 4.69
1691 1706 5.702209 GTCTACTTATCTTCTACTCCCTCCG 59.298 48.000 0.00 0.00 0.00 4.63
1692 1707 6.487668 GTGTCTACTTATCTTCTACTCCCTCC 59.512 46.154 0.00 0.00 0.00 4.30
1693 1708 6.203338 CGTGTCTACTTATCTTCTACTCCCTC 59.797 46.154 0.00 0.00 0.00 4.30
1694 1709 6.056884 CGTGTCTACTTATCTTCTACTCCCT 58.943 44.000 0.00 0.00 0.00 4.20
1695 1710 6.054295 TCGTGTCTACTTATCTTCTACTCCC 58.946 44.000 0.00 0.00 0.00 4.30
1696 1711 6.203338 CCTCGTGTCTACTTATCTTCTACTCC 59.797 46.154 0.00 0.00 0.00 3.85
1697 1712 6.985645 TCCTCGTGTCTACTTATCTTCTACTC 59.014 42.308 0.00 0.00 0.00 2.59
1698 1713 6.887013 TCCTCGTGTCTACTTATCTTCTACT 58.113 40.000 0.00 0.00 0.00 2.57
1699 1714 7.577979 CATCCTCGTGTCTACTTATCTTCTAC 58.422 42.308 0.00 0.00 0.00 2.59
1788 1809 8.382875 GGCTTGAACAAAATATGCAACTAATTC 58.617 33.333 0.00 0.00 0.00 2.17
1863 2050 7.903145 TGCTTCCTGTAACATAGAAAACTAGA 58.097 34.615 0.00 0.00 0.00 2.43
1880 2067 3.186001 GTGCAAGATATCGATGCTTCCTG 59.814 47.826 26.34 3.92 40.66 3.86
2170 2392 9.480538 GAAGCACGTAAAATAAAATAATCGTCA 57.519 29.630 0.00 0.00 0.00 4.35
2174 2399 9.016623 GGTGGAAGCACGTAAAATAAAATAATC 57.983 33.333 0.00 0.00 0.00 1.75
2192 2417 2.101415 GCCAAATAATGAGGGTGGAAGC 59.899 50.000 0.00 0.00 0.00 3.86
2208 2433 0.179032 TGCTTGAGAAGACGGCCAAA 60.179 50.000 2.24 0.00 0.00 3.28
2258 2483 9.685276 TGATTGACTGGACAAATTATACAATCT 57.315 29.630 2.39 0.00 40.52 2.40
2406 2631 9.869757 AAATAAAACATCGAAAGGATTAAAGGG 57.130 29.630 0.00 0.00 31.28 3.95
2456 2681 2.113860 TACAAGCCTCTGCACATTCC 57.886 50.000 0.00 0.00 41.13 3.01
2580 2805 8.624701 AAGCAAATGACTTCAAATCATAATCG 57.375 30.769 0.00 0.00 35.72 3.34
2826 3051 4.756084 ATGTTTGTTTAGCTGCTCTGAC 57.244 40.909 4.91 4.20 0.00 3.51
3294 3519 1.339291 AGCTTGGCTGCAAAAACTCTC 59.661 47.619 0.50 0.00 37.57 3.20
3423 3648 7.558161 TCACCACATCATTCTATCACATTTC 57.442 36.000 0.00 0.00 0.00 2.17
3547 3773 5.071653 ACATTTCTGCAAAAGGTATTTGGGT 59.928 36.000 9.01 0.00 0.00 4.51
3550 3776 9.023967 GCTATACATTTCTGCAAAAGGTATTTG 57.976 33.333 23.49 19.38 32.51 2.32
3746 3974 3.674410 GCTTGGGAATAACTGCTTTGAGC 60.674 47.826 0.00 0.00 42.82 4.26
3747 3975 3.119352 GGCTTGGGAATAACTGCTTTGAG 60.119 47.826 0.00 0.00 0.00 3.02
4067 4295 9.310449 TCTTATAATAGTGAATGGAGGGAGTAC 57.690 37.037 0.00 0.00 0.00 2.73
4450 4678 3.302365 AAAATGGAATTCAGCACCACG 57.698 42.857 7.93 0.00 33.67 4.94
5469 5966 8.960591 ACAGAAATTATTATAAACTGCTGCTGT 58.039 29.630 6.33 6.33 0.00 4.40
5541 6038 9.939802 GAGGTTGTCTCCTACTTTATAAGAAAA 57.060 33.333 0.00 0.00 38.02 2.29
5605 6172 9.598517 AACAAATTCACAATAAAGAAAAGCTCA 57.401 25.926 0.00 0.00 0.00 4.26
5773 6340 3.267812 TCTTCCCAGATTTTGAGGCTGAT 59.732 43.478 0.00 0.00 0.00 2.90
5830 6397 2.301346 CAAGTTTCTGCCAGTTCACCT 58.699 47.619 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.