Multiple sequence alignment - TraesCS2D01G384900

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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 TraesCS2D01G384900 chr2D 100.000 1948 0 0 718 2665 489637190 489639137 0.000000e+00 3598.0
1 TraesCS2D01G384900 chr2D 93.202 662 31 10 869 1525 489593356 489594008 0.000000e+00 961.0
2 TraesCS2D01G384900 chr2D 100.000 365 0 0 1 365 489636473 489636837 0.000000e+00 675.0
3 TraesCS2D01G384900 chr2D 89.683 504 36 9 1962 2465 489595071 489595558 1.740000e-176 628.0
4 TraesCS2D01G384900 chr2D 89.835 423 29 6 1103 1524 489574390 489574799 5.050000e-147 531.0
5 TraesCS2D01G384900 chr2D 89.318 337 25 5 36 362 489592878 489593213 1.910000e-111 412.0
6 TraesCS2D01G384900 chr2D 90.909 275 16 3 2220 2493 489590629 489590895 7.010000e-96 361.0
7 TraesCS2D01G384900 chr2D 86.528 193 12 10 884 1073 489574230 489574411 1.620000e-47 200.0
8 TraesCS2D01G384900 chr2D 82.482 137 19 5 175 311 531470622 531470491 6.030000e-22 115.0
9 TraesCS2D01G384900 chr2D 84.404 109 6 1 36 133 489592698 489592806 2.180000e-16 97.1
10 TraesCS2D01G384900 chr2D 82.828 99 9 7 1685 1779 489594206 489594300 6.110000e-12 82.4
11 TraesCS2D01G384900 chr2A 97.358 757 17 3 1902 2658 633229433 633230186 0.000000e+00 1284.0
12 TraesCS2D01G384900 chr2A 92.611 609 34 4 1902 2500 633223832 633224439 0.000000e+00 865.0
13 TraesCS2D01G384900 chr2A 90.016 611 36 11 874 1476 633222776 633223369 0.000000e+00 767.0
14 TraesCS2D01G384900 chr2A 95.109 368 13 3 1163 1525 633228727 633229094 2.300000e-160 575.0
15 TraesCS2D01G384900 chr2A 87.616 323 27 4 38 349 633228016 633228336 1.950000e-96 363.0
16 TraesCS2D01G384900 chr2A 89.320 206 12 3 869 1073 633228505 633228701 1.580000e-62 250.0
17 TraesCS2D01G384900 chr2A 84.906 212 16 6 36 237 633222163 633222368 1.620000e-47 200.0
18 TraesCS2D01G384900 chr2A 95.349 43 2 0 778 820 392756200 392756158 4.760000e-08 69.4
19 TraesCS2D01G384900 chr2A 87.500 56 4 3 1685 1739 633223603 633223656 7.970000e-06 62.1
20 TraesCS2D01G384900 chr2B 95.325 770 25 4 1902 2661 573199122 573199890 0.000000e+00 1212.0
21 TraesCS2D01G384900 chr2B 89.314 758 57 15 718 1471 573197840 573198577 0.000000e+00 929.0
22 TraesCS2D01G384900 chr2B 87.424 819 57 20 718 1525 573186362 573187145 0.000000e+00 900.0
23 TraesCS2D01G384900 chr2B 87.317 820 60 23 718 1525 573183596 573184383 0.000000e+00 898.0
24 TraesCS2D01G384900 chr2B 87.781 311 25 3 36 334 573197428 573197737 4.220000e-93 351.0
25 TraesCS2D01G384900 chr2B 88.850 287 23 6 884 1168 573182279 573182558 7.060000e-91 344.0
26 TraesCS2D01G384900 chr2B 94.928 138 6 1 2192 2329 573187643 573187779 5.780000e-52 215.0
27 TraesCS2D01G384900 chr2B 85.030 167 21 3 2327 2493 573189922 573190084 1.640000e-37 167.0
28 TraesCS2D01G384900 chr2B 98.529 68 1 0 1902 1969 573187572 573187639 1.300000e-23 121.0
29 TraesCS2D01G384900 chr5D 82.320 181 23 9 142 320 3899239 3899066 5.940000e-32 148.0
30 TraesCS2D01G384900 chr6B 78.378 259 33 15 83 331 590140626 590140381 2.140000e-31 147.0
31 TraesCS2D01G384900 chr6B 97.674 43 1 0 1524 1566 195182989 195183031 1.020000e-09 75.0
32 TraesCS2D01G384900 chr6A 84.564 149 16 6 147 294 449812489 449812347 9.950000e-30 141.0
33 TraesCS2D01G384900 chr7A 79.902 204 29 10 78 276 681719207 681719403 3.580000e-29 139.0
34 TraesCS2D01G384900 chr1A 77.567 263 33 16 39 282 500371847 500372102 4.630000e-28 135.0
35 TraesCS2D01G384900 chr3D 100.000 43 0 0 1525 1567 26204675 26204633 2.200000e-11 80.5
36 TraesCS2D01G384900 chr1D 100.000 43 0 0 1525 1567 199069165 199069207 2.200000e-11 80.5


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 TraesCS2D01G384900 chr2D 489636473 489639137 2664 False 2136.500000 3598 100.000000 1 2665 2 chr2D.!!$F3 2664
1 TraesCS2D01G384900 chr2D 489590629 489595558 4929 False 423.583333 961 88.390667 36 2493 6 chr2D.!!$F2 2457
2 TraesCS2D01G384900 chr2D 489574230 489574799 569 False 365.500000 531 88.181500 884 1524 2 chr2D.!!$F1 640
3 TraesCS2D01G384900 chr2A 633222163 633230186 8023 False 545.762500 1284 90.554500 36 2658 8 chr2A.!!$F1 2622
4 TraesCS2D01G384900 chr2B 573197428 573199890 2462 False 830.666667 1212 90.806667 36 2661 3 chr2B.!!$F2 2625
5 TraesCS2D01G384900 chr2B 573182279 573190084 7805 False 440.833333 900 90.346333 718 2493 6 chr2B.!!$F1 1775

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
840 6934 0.036765 TAAGGCACCGCAACCACTAG 60.037 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 9000 0.036875 CACAGGAGGTTCCCTTGTCC 59.963 60.0 0.0 0.0 37.19 4.02 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
21 22 3.081804 ACTTAGTTGCTATGTTGTGGGC 58.918 45.455 0.00 0.00 0.00 5.36
22 23 3.244911 ACTTAGTTGCTATGTTGTGGGCT 60.245 43.478 0.00 0.00 0.00 5.19
25 26 1.068333 GTTGCTATGTTGTGGGCTGTG 60.068 52.381 0.00 0.00 0.00 3.66
26 27 0.608856 TGCTATGTTGTGGGCTGTGG 60.609 55.000 0.00 0.00 0.00 4.17
30 31 1.494960 ATGTTGTGGGCTGTGGTTTT 58.505 45.000 0.00 0.00 0.00 2.43
33 34 2.832129 TGTTGTGGGCTGTGGTTTTTAA 59.168 40.909 0.00 0.00 0.00 1.52
34 35 3.452627 TGTTGTGGGCTGTGGTTTTTAAT 59.547 39.130 0.00 0.00 0.00 1.40
364 6455 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
769 6860 2.487428 CCAGTCTCGTGCTCCTCG 59.513 66.667 0.00 0.00 0.00 4.63
798 6889 0.459585 GCCCTACATCTCGCGTCAAA 60.460 55.000 5.77 0.00 0.00 2.69
813 6904 0.800683 TCAAACGAGACATAGGCGCG 60.801 55.000 0.00 0.00 34.71 6.86
834 6928 2.388232 CCTCGTAAGGCACCGCAAC 61.388 63.158 0.00 0.00 35.37 4.17
835 6929 2.357760 TCGTAAGGCACCGCAACC 60.358 61.111 0.00 0.00 38.47 3.77
839 6933 0.320946 GTAAGGCACCGCAACCACTA 60.321 55.000 0.00 0.00 0.00 2.74
840 6934 0.036765 TAAGGCACCGCAACCACTAG 60.037 55.000 0.00 0.00 0.00 2.57
846 6940 2.857104 GCACCGCAACCACTAGTTTTTC 60.857 50.000 0.00 0.00 36.18 2.29
848 6942 3.066203 CACCGCAACCACTAGTTTTTCTT 59.934 43.478 0.00 0.00 36.18 2.52
849 6943 3.697542 ACCGCAACCACTAGTTTTTCTTT 59.302 39.130 0.00 0.00 36.18 2.52
850 6944 4.158949 ACCGCAACCACTAGTTTTTCTTTT 59.841 37.500 0.00 0.00 36.18 2.27
854 6948 6.530181 CGCAACCACTAGTTTTTCTTTTCTTT 59.470 34.615 0.00 0.00 36.18 2.52
855 6949 7.062956 CGCAACCACTAGTTTTTCTTTTCTTTT 59.937 33.333 0.00 0.00 36.18 2.27
922 7018 2.745100 TCTCGTCGACCACTCCGG 60.745 66.667 10.58 0.00 42.50 5.14
1032 7132 5.047021 TGTGAGATTTTCTGATTCGAGACCT 60.047 40.000 0.00 0.00 0.00 3.85
1044 7144 5.591472 TGATTCGAGACCTTAGATCCGTTTA 59.409 40.000 0.00 0.00 0.00 2.01
1168 7325 1.082300 GACGAAGCAGACGACGACA 60.082 57.895 0.00 0.00 34.70 4.35
1241 7398 3.362797 ACGAGTTCGAGCTGCCGA 61.363 61.111 15.47 8.74 43.02 5.54
1371 7528 3.499737 CGCCATGGTGAAGACGGC 61.500 66.667 21.19 0.00 39.45 5.68
1394 7551 2.387445 CGAGCGCCGTTTGATTCCA 61.387 57.895 2.29 0.00 0.00 3.53
1423 7580 2.124570 CCCATCCTCGGCTGGTTG 60.125 66.667 5.22 0.00 30.04 3.77
1454 7613 1.541147 CACGTTGATGCACCTCCAATT 59.459 47.619 0.00 0.00 0.00 2.32
1525 7689 6.663734 TGTAGTTGATGGACTCTAGAGATGA 58.336 40.000 26.57 9.06 0.00 2.92
1526 7690 6.770303 TGTAGTTGATGGACTCTAGAGATGAG 59.230 42.308 26.57 0.04 37.55 2.90
1527 7691 6.012337 AGTTGATGGACTCTAGAGATGAGA 57.988 41.667 26.57 5.57 35.66 3.27
1528 7692 6.430864 AGTTGATGGACTCTAGAGATGAGAA 58.569 40.000 26.57 8.45 35.66 2.87
1529 7693 6.894654 AGTTGATGGACTCTAGAGATGAGAAA 59.105 38.462 26.57 10.45 35.66 2.52
1530 7694 7.564660 AGTTGATGGACTCTAGAGATGAGAAAT 59.435 37.037 26.57 9.15 35.66 2.17
1532 7696 7.724287 TGATGGACTCTAGAGATGAGAAATTG 58.276 38.462 26.57 0.00 35.66 2.32
1534 7698 6.197903 TGGACTCTAGAGATGAGAAATTGGA 58.802 40.000 26.57 0.00 35.66 3.53
1535 7699 6.843333 TGGACTCTAGAGATGAGAAATTGGAT 59.157 38.462 26.57 0.00 35.66 3.41
1537 7701 7.233348 GGACTCTAGAGATGAGAAATTGGATCT 59.767 40.741 26.57 0.00 35.66 2.75
1538 7702 8.551682 ACTCTAGAGATGAGAAATTGGATCTT 57.448 34.615 26.57 0.00 35.66 2.40
1539 7703 8.991275 ACTCTAGAGATGAGAAATTGGATCTTT 58.009 33.333 26.57 0.00 35.66 2.52
1540 7704 9.835389 CTCTAGAGATGAGAAATTGGATCTTTT 57.165 33.333 15.05 0.00 33.68 2.27
1542 7706 7.098074 AGAGATGAGAAATTGGATCTTTTGC 57.902 36.000 0.00 0.00 0.00 3.68
1543 7707 6.096564 AGAGATGAGAAATTGGATCTTTTGCC 59.903 38.462 0.00 0.00 0.00 4.52
1545 7709 5.649782 TGAGAAATTGGATCTTTTGCCTC 57.350 39.130 0.00 0.00 0.00 4.70
1547 7711 5.047802 TGAGAAATTGGATCTTTTGCCTCAC 60.048 40.000 0.00 0.00 0.00 3.51
1548 7712 5.082425 AGAAATTGGATCTTTTGCCTCACT 58.918 37.500 0.00 0.00 0.00 3.41
1549 7713 5.541484 AGAAATTGGATCTTTTGCCTCACTT 59.459 36.000 0.00 0.00 0.00 3.16
1551 7715 5.813513 ATTGGATCTTTTGCCTCACTTTT 57.186 34.783 0.00 0.00 0.00 2.27
1552 7716 4.853924 TGGATCTTTTGCCTCACTTTTC 57.146 40.909 0.00 0.00 0.00 2.29
1553 7717 4.473444 TGGATCTTTTGCCTCACTTTTCT 58.527 39.130 0.00 0.00 0.00 2.52
1555 7719 5.010012 TGGATCTTTTGCCTCACTTTTCTTC 59.990 40.000 0.00 0.00 0.00 2.87
1556 7720 5.242615 GGATCTTTTGCCTCACTTTTCTTCT 59.757 40.000 0.00 0.00 0.00 2.85
1557 7721 6.431234 GGATCTTTTGCCTCACTTTTCTTCTA 59.569 38.462 0.00 0.00 0.00 2.10
1558 7722 7.040409 GGATCTTTTGCCTCACTTTTCTTCTAA 60.040 37.037 0.00 0.00 0.00 2.10
1559 7723 7.027778 TCTTTTGCCTCACTTTTCTTCTAAC 57.972 36.000 0.00 0.00 0.00 2.34
1560 7724 6.828785 TCTTTTGCCTCACTTTTCTTCTAACT 59.171 34.615 0.00 0.00 0.00 2.24
1561 7725 7.339466 TCTTTTGCCTCACTTTTCTTCTAACTT 59.661 33.333 0.00 0.00 0.00 2.66
1562 7726 7.404671 TTTGCCTCACTTTTCTTCTAACTTT 57.595 32.000 0.00 0.00 0.00 2.66
1563 7727 6.377327 TGCCTCACTTTTCTTCTAACTTTG 57.623 37.500 0.00 0.00 0.00 2.77
1564 7728 6.119536 TGCCTCACTTTTCTTCTAACTTTGA 58.880 36.000 0.00 0.00 0.00 2.69
1565 7729 6.772716 TGCCTCACTTTTCTTCTAACTTTGAT 59.227 34.615 0.00 0.00 0.00 2.57
1566 7730 7.041098 TGCCTCACTTTTCTTCTAACTTTGATC 60.041 37.037 0.00 0.00 0.00 2.92
1567 7731 7.574030 GCCTCACTTTTCTTCTAACTTTGATCC 60.574 40.741 0.00 0.00 0.00 3.36
1568 7732 7.445402 CCTCACTTTTCTTCTAACTTTGATCCA 59.555 37.037 0.00 0.00 0.00 3.41
1569 7733 8.746052 TCACTTTTCTTCTAACTTTGATCCAA 57.254 30.769 0.00 0.00 0.00 3.53
1571 7735 8.405531 CACTTTTCTTCTAACTTTGATCCAACA 58.594 33.333 0.00 0.00 0.00 3.33
1572 7736 8.406297 ACTTTTCTTCTAACTTTGATCCAACAC 58.594 33.333 0.00 0.00 0.00 3.32
1573 7737 6.877611 TTCTTCTAACTTTGATCCAACACC 57.122 37.500 0.00 0.00 0.00 4.16
1574 7738 5.313712 TCTTCTAACTTTGATCCAACACCC 58.686 41.667 0.00 0.00 0.00 4.61
1575 7739 4.028993 TCTAACTTTGATCCAACACCCC 57.971 45.455 0.00 0.00 0.00 4.95
1580 7758 2.352561 TTGATCCAACACCCCCTCTA 57.647 50.000 0.00 0.00 0.00 2.43
1591 7769 4.227197 ACACCCCCTCTAGAGATGTATTG 58.773 47.826 21.76 11.79 0.00 1.90
1607 7785 7.615403 AGATGTATTGCTCAGAGAAAAGTGTA 58.385 34.615 0.00 0.00 0.00 2.90
1609 7787 7.658179 TGTATTGCTCAGAGAAAAGTGTAAG 57.342 36.000 0.00 0.00 0.00 2.34
1618 7923 6.868864 TCAGAGAAAAGTGTAAGTATGTCTGC 59.131 38.462 0.00 0.00 31.08 4.26
1643 7948 7.677276 GCAACGAAGTGTAAAGATTGATAGCAT 60.677 37.037 0.00 0.00 45.00 3.79
1644 7949 7.470289 ACGAAGTGTAAAGATTGATAGCATC 57.530 36.000 0.00 0.00 42.51 3.91
1679 7984 6.515043 AATGTTTCTTTCAGAAATTGCACG 57.485 33.333 2.36 0.00 44.94 5.34
1682 7987 6.734137 TGTTTCTTTCAGAAATTGCACGTAT 58.266 32.000 2.36 0.00 44.94 3.06
1683 7988 6.636447 TGTTTCTTTCAGAAATTGCACGTATG 59.364 34.615 2.36 0.00 44.94 2.39
1687 7992 7.866729 TCTTTCAGAAATTGCACGTATGTAAA 58.133 30.769 0.00 0.00 33.83 2.01
1692 7997 6.855914 CAGAAATTGCACGTATGTAAACTTGT 59.144 34.615 0.00 0.00 33.83 3.16
1693 7998 8.012809 CAGAAATTGCACGTATGTAAACTTGTA 58.987 33.333 0.00 0.00 33.83 2.41
1694 7999 8.013378 AGAAATTGCACGTATGTAAACTTGTAC 58.987 33.333 0.00 0.00 33.83 2.90
1723 8188 1.208535 TGGAAACAGACGAACACACCT 59.791 47.619 0.00 0.00 35.01 4.00
1724 8189 1.865340 GGAAACAGACGAACACACCTC 59.135 52.381 0.00 0.00 0.00 3.85
1735 8200 4.478699 CGAACACACCTCGTACTATCAAA 58.521 43.478 0.00 0.00 0.00 2.69
1736 8201 4.322804 CGAACACACCTCGTACTATCAAAC 59.677 45.833 0.00 0.00 0.00 2.93
1738 8203 5.464030 ACACACCTCGTACTATCAAACTT 57.536 39.130 0.00 0.00 0.00 2.66
1739 8204 6.579666 ACACACCTCGTACTATCAAACTTA 57.420 37.500 0.00 0.00 0.00 2.24
1740 8205 6.385033 ACACACCTCGTACTATCAAACTTAC 58.615 40.000 0.00 0.00 0.00 2.34
1741 8206 6.016024 ACACACCTCGTACTATCAAACTTACA 60.016 38.462 0.00 0.00 0.00 2.41
1742 8207 6.527023 CACACCTCGTACTATCAAACTTACAG 59.473 42.308 0.00 0.00 0.00 2.74
1743 8208 6.432162 ACACCTCGTACTATCAAACTTACAGA 59.568 38.462 0.00 0.00 0.00 3.41
1745 8210 7.974501 CACCTCGTACTATCAAACTTACAGAAT 59.025 37.037 0.00 0.00 0.00 2.40
1746 8211 8.189460 ACCTCGTACTATCAAACTTACAGAATC 58.811 37.037 0.00 0.00 0.00 2.52
1747 8212 8.407064 CCTCGTACTATCAAACTTACAGAATCT 58.593 37.037 0.00 0.00 0.00 2.40
1748 8213 9.790389 CTCGTACTATCAAACTTACAGAATCTT 57.210 33.333 0.00 0.00 0.00 2.40
1761 8226 9.725019 ACTTACAGAATCTTACATGTTTGATCA 57.275 29.630 2.30 0.00 0.00 2.92
1767 8234 5.497464 TCTTACATGTTTGATCACCCAGA 57.503 39.130 2.30 0.00 0.00 3.86
1768 8235 5.491070 TCTTACATGTTTGATCACCCAGAG 58.509 41.667 2.30 0.00 0.00 3.35
1798 8882 3.257393 AGAGCTTCTGAACGCATTACAG 58.743 45.455 12.20 0.00 0.00 2.74
1813 8902 6.420903 ACGCATTACAGTATCATACACACATC 59.579 38.462 0.00 0.00 0.00 3.06
1814 8903 6.420604 CGCATTACAGTATCATACACACATCA 59.579 38.462 0.00 0.00 0.00 3.07
1826 8917 2.086869 CACACATCAAAGGGCCTACAG 58.913 52.381 6.41 0.00 0.00 2.74
1845 8941 6.647067 CCTACAGGCTATAACTAACAATGCTC 59.353 42.308 0.00 0.00 0.00 4.26
1846 8942 5.368989 ACAGGCTATAACTAACAATGCTCC 58.631 41.667 0.00 0.00 0.00 4.70
1862 8970 8.449423 ACAATGCTCCTATAATTCTATACCCA 57.551 34.615 0.00 0.00 0.00 4.51
1864 8972 6.869206 TGCTCCTATAATTCTATACCCACC 57.131 41.667 0.00 0.00 0.00 4.61
1866 8974 6.790461 TGCTCCTATAATTCTATACCCACCAA 59.210 38.462 0.00 0.00 0.00 3.67
1867 8975 7.038302 TGCTCCTATAATTCTATACCCACCAAG 60.038 40.741 0.00 0.00 0.00 3.61
1868 8976 7.581658 GCTCCTATAATTCTATACCCACCAAGG 60.582 44.444 0.00 0.00 37.03 3.61
1869 8977 6.214819 TCCTATAATTCTATACCCACCAAGGC 59.785 42.308 0.00 0.00 35.39 4.35
1871 8979 1.868713 TTCTATACCCACCAAGGCGA 58.131 50.000 0.00 0.00 35.39 5.54
1872 8980 1.410004 TCTATACCCACCAAGGCGAG 58.590 55.000 0.00 0.00 35.39 5.03
1873 8981 0.393077 CTATACCCACCAAGGCGAGG 59.607 60.000 0.00 0.00 35.39 4.63
1874 8982 0.325860 TATACCCACCAAGGCGAGGT 60.326 55.000 0.00 0.00 40.85 3.85
1879 8987 2.526873 ACCAAGGCGAGGTGAGGT 60.527 61.111 3.04 0.00 38.13 3.85
1880 8988 2.046892 CCAAGGCGAGGTGAGGTG 60.047 66.667 0.00 0.00 0.00 4.00
1881 8989 2.046892 CAAGGCGAGGTGAGGTGG 60.047 66.667 0.00 0.00 0.00 4.61
1882 8990 3.322466 AAGGCGAGGTGAGGTGGG 61.322 66.667 0.00 0.00 0.00 4.61
1886 8994 3.706373 CGAGGTGAGGTGGGGGTG 61.706 72.222 0.00 0.00 0.00 4.61
1887 8995 3.330720 GAGGTGAGGTGGGGGTGG 61.331 72.222 0.00 0.00 0.00 4.61
1898 9006 3.339093 GGGGTGGGGGAGGACAAG 61.339 72.222 0.00 0.00 0.00 3.16
1899 9007 3.339093 GGGTGGGGGAGGACAAGG 61.339 72.222 0.00 0.00 0.00 3.61
1900 9008 3.339093 GGTGGGGGAGGACAAGGG 61.339 72.222 0.00 0.00 0.00 3.95
2323 9441 3.405831 TGCAGAGAAGTGAGAAATGTGG 58.594 45.455 0.00 0.00 0.00 4.17
2350 11613 3.248602 CCTTGAAACCAGAGAAGTGTTCG 59.751 47.826 0.00 0.00 34.02 3.95
2379 11642 1.666888 GCCACGACTTTGCTTTCCATG 60.667 52.381 0.00 0.00 0.00 3.66
2389 11652 0.741927 GCTTTCCATGCCACCATTGC 60.742 55.000 0.00 0.00 0.00 3.56
2541 11804 4.699257 AGGTCAATGATCTCTTGCTGTTTC 59.301 41.667 0.00 0.00 0.00 2.78
2616 11879 0.888619 CTAGTCCAACGCTCCTGACA 59.111 55.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.068333 CACAGCCCACAACATAGCAAC 60.068 52.381 0.00 0.00 0.00 4.17
8 9 0.609131 ACCACAGCCCACAACATAGC 60.609 55.000 0.00 0.00 0.00 2.97
10 11 2.373335 AAACCACAGCCCACAACATA 57.627 45.000 0.00 0.00 0.00 2.29
12 13 1.270907 AAAAACCACAGCCCACAACA 58.729 45.000 0.00 0.00 0.00 3.33
17 18 1.346068 GGCATTAAAAACCACAGCCCA 59.654 47.619 0.00 0.00 34.71 5.36
18 19 1.623311 AGGCATTAAAAACCACAGCCC 59.377 47.619 0.00 0.00 41.45 5.19
20 21 5.749596 AAAAAGGCATTAAAAACCACAGC 57.250 34.783 0.00 0.00 0.00 4.40
33 34 9.995003 TGTTCATCAAGTATTTTAAAAAGGCAT 57.005 25.926 4.44 0.00 0.00 4.40
34 35 9.995003 ATGTTCATCAAGTATTTTAAAAAGGCA 57.005 25.926 4.44 0.00 0.00 4.75
331 6422 3.963383 CACACCAGTGGAAGTTACAAC 57.037 47.619 18.40 0.00 42.13 3.32
717 6808 2.032681 GGAGCCACAGCCTCGTTT 59.967 61.111 0.00 0.00 41.25 3.60
718 6809 4.021925 GGGAGCCACAGCCTCGTT 62.022 66.667 0.00 0.00 41.25 3.85
721 6812 3.791586 GAGGGGAGCCACAGCCTC 61.792 72.222 0.00 0.00 41.25 4.70
727 6818 2.583472 CCATTTTGAGGGGAGCCAC 58.417 57.895 0.00 0.00 0.00 5.01
798 6889 4.570663 GGCGCGCCTATGTCTCGT 62.571 66.667 41.71 0.00 0.00 4.18
827 6921 2.927028 AGAAAAACTAGTGGTTGCGGT 58.073 42.857 0.00 0.00 38.29 5.68
830 6924 7.827819 AAAGAAAAGAAAAACTAGTGGTTGC 57.172 32.000 0.00 0.00 38.29 4.17
858 6952 5.652994 AACTAGTGGTTGCAAGTCAAAAA 57.347 34.783 0.00 0.00 36.70 1.94
859 6953 5.652994 AAACTAGTGGTTGCAAGTCAAAA 57.347 34.783 0.00 0.00 38.29 2.44
860 6954 5.652994 AAAACTAGTGGTTGCAAGTCAAA 57.347 34.783 0.00 0.00 38.29 2.69
861 6955 6.761099 TTAAAACTAGTGGTTGCAAGTCAA 57.239 33.333 0.00 0.00 38.29 3.18
862 6956 6.293190 CGATTAAAACTAGTGGTTGCAAGTCA 60.293 38.462 0.00 0.00 38.29 3.41
863 6957 6.077838 CGATTAAAACTAGTGGTTGCAAGTC 58.922 40.000 0.00 0.00 38.29 3.01
864 6958 5.529800 ACGATTAAAACTAGTGGTTGCAAGT 59.470 36.000 0.00 0.00 38.29 3.16
865 6959 5.997385 ACGATTAAAACTAGTGGTTGCAAG 58.003 37.500 0.00 0.00 38.29 4.01
866 6960 7.675962 ATACGATTAAAACTAGTGGTTGCAA 57.324 32.000 0.00 0.00 38.29 4.08
867 6961 7.388224 TGAATACGATTAAAACTAGTGGTTGCA 59.612 33.333 0.00 0.00 38.29 4.08
872 6966 8.928270 ACTCTGAATACGATTAAAACTAGTGG 57.072 34.615 0.00 0.00 0.00 4.00
922 7018 0.883370 GGTATCGGTTTGGCGGGATC 60.883 60.000 0.00 0.00 0.00 3.36
951 7049 4.081862 GCTGTATATTATGGTACCTCGGCA 60.082 45.833 14.36 0.00 0.00 5.69
953 7051 5.408356 GTGCTGTATATTATGGTACCTCGG 58.592 45.833 14.36 0.45 0.00 4.63
954 7052 5.408356 GGTGCTGTATATTATGGTACCTCG 58.592 45.833 14.36 0.00 31.64 4.63
955 7053 5.184479 TCGGTGCTGTATATTATGGTACCTC 59.816 44.000 14.36 0.00 32.04 3.85
956 7054 5.081728 TCGGTGCTGTATATTATGGTACCT 58.918 41.667 14.36 1.08 32.04 3.08
957 7055 5.395682 TCGGTGCTGTATATTATGGTACC 57.604 43.478 4.43 4.43 0.00 3.34
958 7056 5.742453 CGATCGGTGCTGTATATTATGGTAC 59.258 44.000 7.38 0.00 0.00 3.34
959 7057 5.677852 GCGATCGGTGCTGTATATTATGGTA 60.678 44.000 18.30 0.00 0.00 3.25
960 7058 4.744570 CGATCGGTGCTGTATATTATGGT 58.255 43.478 7.38 0.00 0.00 3.55
1010 7110 5.667539 AGGTCTCGAATCAGAAAATCTCA 57.332 39.130 0.00 0.00 0.00 3.27
1079 7233 2.046314 CACCAAGGGAACGCCGAT 60.046 61.111 0.00 0.00 33.83 4.18
1122 7276 2.515996 GAAGAACCCCATGGCGTCGA 62.516 60.000 6.09 0.00 33.59 4.20
1241 7398 2.509336 GCTGCGTAGGTGCGATGT 60.509 61.111 1.76 0.00 37.81 3.06
1423 7580 0.388649 ATCAACGTGACCGAGCTGAC 60.389 55.000 0.00 0.00 37.88 3.51
1525 7689 5.082425 AGTGAGGCAAAAGATCCAATTTCT 58.918 37.500 0.00 0.00 0.00 2.52
1526 7690 5.397142 AGTGAGGCAAAAGATCCAATTTC 57.603 39.130 0.00 0.00 0.00 2.17
1527 7691 5.813513 AAGTGAGGCAAAAGATCCAATTT 57.186 34.783 0.00 0.00 0.00 1.82
1528 7692 5.813513 AAAGTGAGGCAAAAGATCCAATT 57.186 34.783 0.00 0.00 0.00 2.32
1529 7693 5.541484 AGAAAAGTGAGGCAAAAGATCCAAT 59.459 36.000 0.00 0.00 0.00 3.16
1530 7694 4.895297 AGAAAAGTGAGGCAAAAGATCCAA 59.105 37.500 0.00 0.00 0.00 3.53
1532 7696 5.242615 AGAAGAAAAGTGAGGCAAAAGATCC 59.757 40.000 0.00 0.00 0.00 3.36
1534 7698 7.503902 AGTTAGAAGAAAAGTGAGGCAAAAGAT 59.496 33.333 0.00 0.00 0.00 2.40
1535 7699 6.828785 AGTTAGAAGAAAAGTGAGGCAAAAGA 59.171 34.615 0.00 0.00 0.00 2.52
1537 7701 7.404671 AAGTTAGAAGAAAAGTGAGGCAAAA 57.595 32.000 0.00 0.00 0.00 2.44
1538 7702 7.122055 TCAAAGTTAGAAGAAAAGTGAGGCAAA 59.878 33.333 0.00 0.00 0.00 3.68
1539 7703 6.601613 TCAAAGTTAGAAGAAAAGTGAGGCAA 59.398 34.615 0.00 0.00 0.00 4.52
1540 7704 6.119536 TCAAAGTTAGAAGAAAAGTGAGGCA 58.880 36.000 0.00 0.00 0.00 4.75
1542 7706 7.445402 TGGATCAAAGTTAGAAGAAAAGTGAGG 59.555 37.037 0.00 0.00 0.00 3.86
1543 7707 8.383318 TGGATCAAAGTTAGAAGAAAAGTGAG 57.617 34.615 0.00 0.00 0.00 3.51
1545 7709 8.405531 TGTTGGATCAAAGTTAGAAGAAAAGTG 58.594 33.333 0.00 0.00 0.00 3.16
1547 7711 7.862873 GGTGTTGGATCAAAGTTAGAAGAAAAG 59.137 37.037 0.00 0.00 0.00 2.27
1548 7712 7.201875 GGGTGTTGGATCAAAGTTAGAAGAAAA 60.202 37.037 0.00 0.00 0.00 2.29
1549 7713 6.264518 GGGTGTTGGATCAAAGTTAGAAGAAA 59.735 38.462 0.00 0.00 0.00 2.52
1551 7715 5.313712 GGGTGTTGGATCAAAGTTAGAAGA 58.686 41.667 0.00 0.00 0.00 2.87
1552 7716 4.459337 GGGGTGTTGGATCAAAGTTAGAAG 59.541 45.833 0.00 0.00 0.00 2.85
1553 7717 4.403734 GGGGTGTTGGATCAAAGTTAGAA 58.596 43.478 0.00 0.00 0.00 2.10
1555 7719 3.089284 GGGGGTGTTGGATCAAAGTTAG 58.911 50.000 0.00 0.00 0.00 2.34
1556 7720 2.719705 AGGGGGTGTTGGATCAAAGTTA 59.280 45.455 0.00 0.00 0.00 2.24
1557 7721 1.503347 AGGGGGTGTTGGATCAAAGTT 59.497 47.619 0.00 0.00 0.00 2.66
1558 7722 1.075536 GAGGGGGTGTTGGATCAAAGT 59.924 52.381 0.00 0.00 0.00 2.66
1559 7723 1.355720 AGAGGGGGTGTTGGATCAAAG 59.644 52.381 0.00 0.00 0.00 2.77
1560 7724 1.455822 AGAGGGGGTGTTGGATCAAA 58.544 50.000 0.00 0.00 0.00 2.69
1561 7725 2.196595 CTAGAGGGGGTGTTGGATCAA 58.803 52.381 0.00 0.00 0.00 2.57
1562 7726 1.364678 TCTAGAGGGGGTGTTGGATCA 59.635 52.381 0.00 0.00 0.00 2.92
1563 7727 2.043227 CTCTAGAGGGGGTGTTGGATC 58.957 57.143 12.27 0.00 0.00 3.36
1564 7728 1.651770 TCTCTAGAGGGGGTGTTGGAT 59.348 52.381 19.67 0.00 0.00 3.41
1565 7729 1.089978 TCTCTAGAGGGGGTGTTGGA 58.910 55.000 19.67 0.00 0.00 3.53
1566 7730 1.765314 CATCTCTAGAGGGGGTGTTGG 59.235 57.143 19.67 0.00 0.00 3.77
1567 7731 2.472029 ACATCTCTAGAGGGGGTGTTG 58.528 52.381 19.67 8.58 0.00 3.33
1568 7732 2.950990 ACATCTCTAGAGGGGGTGTT 57.049 50.000 19.67 3.33 0.00 3.32
1569 7733 4.227197 CAATACATCTCTAGAGGGGGTGT 58.773 47.826 19.67 18.77 0.00 4.16
1571 7735 3.116551 AGCAATACATCTCTAGAGGGGGT 60.117 47.826 19.67 16.14 0.00 4.95
1572 7736 3.513515 GAGCAATACATCTCTAGAGGGGG 59.486 52.174 19.67 11.48 0.00 5.40
1573 7737 4.155709 TGAGCAATACATCTCTAGAGGGG 58.844 47.826 19.67 13.83 0.00 4.79
1574 7738 5.076182 TCTGAGCAATACATCTCTAGAGGG 58.924 45.833 19.67 14.17 0.00 4.30
1575 7739 6.003326 TCTCTGAGCAATACATCTCTAGAGG 58.997 44.000 19.67 7.17 36.45 3.69
1580 7758 6.817641 CACTTTTCTCTGAGCAATACATCTCT 59.182 38.462 0.00 0.00 0.00 3.10
1591 7769 7.062839 CAGACATACTTACACTTTTCTCTGAGC 59.937 40.741 0.00 0.00 0.00 4.26
1607 7785 3.728845 ACACTTCGTTGCAGACATACTT 58.271 40.909 0.00 0.00 0.00 2.24
1609 7787 5.404366 TCTTTACACTTCGTTGCAGACATAC 59.596 40.000 0.00 0.00 0.00 2.39
1618 7923 7.060600 TGCTATCAATCTTTACACTTCGTTG 57.939 36.000 0.00 0.00 0.00 4.10
1666 7971 6.795098 AGTTTACATACGTGCAATTTCTGA 57.205 33.333 0.00 0.00 0.00 3.27
1669 7974 8.013378 AGTACAAGTTTACATACGTGCAATTTC 58.987 33.333 0.00 0.00 31.81 2.17
1687 7992 7.873505 GTCTGTTTCCAAAGAGATAGTACAAGT 59.126 37.037 2.51 0.00 39.96 3.16
1692 7997 6.829229 TCGTCTGTTTCCAAAGAGATAGTA 57.171 37.500 2.51 0.00 39.96 1.82
1693 7998 5.723672 TCGTCTGTTTCCAAAGAGATAGT 57.276 39.130 2.51 0.00 39.96 2.12
1694 7999 5.926542 TGTTCGTCTGTTTCCAAAGAGATAG 59.073 40.000 2.51 1.61 39.96 2.08
1735 8200 9.725019 TGATCAAACATGTAAGATTCTGTAAGT 57.275 29.630 12.58 0.00 33.76 2.24
1736 8201 9.979270 GTGATCAAACATGTAAGATTCTGTAAG 57.021 33.333 12.58 0.00 0.00 2.34
1738 8203 7.552687 GGGTGATCAAACATGTAAGATTCTGTA 59.447 37.037 12.58 0.00 0.00 2.74
1739 8204 6.375455 GGGTGATCAAACATGTAAGATTCTGT 59.625 38.462 12.58 0.00 0.00 3.41
1740 8205 6.375174 TGGGTGATCAAACATGTAAGATTCTG 59.625 38.462 12.58 0.00 0.00 3.02
1741 8206 6.484288 TGGGTGATCAAACATGTAAGATTCT 58.516 36.000 12.58 0.00 0.00 2.40
1742 8207 6.599244 TCTGGGTGATCAAACATGTAAGATTC 59.401 38.462 12.58 9.64 0.00 2.52
1743 8208 6.484288 TCTGGGTGATCAAACATGTAAGATT 58.516 36.000 12.58 0.00 0.00 2.40
1745 8210 5.491070 CTCTGGGTGATCAAACATGTAAGA 58.509 41.667 0.00 0.00 0.00 2.10
1746 8211 4.095483 GCTCTGGGTGATCAAACATGTAAG 59.905 45.833 0.00 0.00 0.00 2.34
1747 8212 4.009675 GCTCTGGGTGATCAAACATGTAA 58.990 43.478 0.00 0.00 0.00 2.41
1748 8213 3.008923 TGCTCTGGGTGATCAAACATGTA 59.991 43.478 0.00 0.00 0.00 2.29
1749 8214 2.224843 TGCTCTGGGTGATCAAACATGT 60.225 45.455 0.00 0.00 0.00 3.21
1750 8215 2.422479 CTGCTCTGGGTGATCAAACATG 59.578 50.000 0.00 0.00 0.00 3.21
1751 8216 2.040813 ACTGCTCTGGGTGATCAAACAT 59.959 45.455 0.00 0.00 0.00 2.71
1754 8219 3.055819 GTCTACTGCTCTGGGTGATCAAA 60.056 47.826 0.00 0.00 0.00 2.69
1755 8220 2.497675 GTCTACTGCTCTGGGTGATCAA 59.502 50.000 0.00 0.00 0.00 2.57
1757 8222 2.100584 CTGTCTACTGCTCTGGGTGATC 59.899 54.545 0.00 0.00 0.00 2.92
1758 8223 2.106566 CTGTCTACTGCTCTGGGTGAT 58.893 52.381 0.00 0.00 0.00 3.06
1760 8225 1.476085 CTCTGTCTACTGCTCTGGGTG 59.524 57.143 0.00 0.00 0.00 4.61
1761 8226 1.846007 CTCTGTCTACTGCTCTGGGT 58.154 55.000 0.00 0.00 0.00 4.51
1767 8234 2.801483 TCAGAAGCTCTGTCTACTGCT 58.199 47.619 11.37 0.00 44.58 4.24
1768 8235 3.249917 GTTCAGAAGCTCTGTCTACTGC 58.750 50.000 11.37 0.00 44.58 4.40
1786 8832 6.254804 TGTGTGTATGATACTGTAATGCGTTC 59.745 38.462 4.03 0.00 0.00 3.95
1789 8835 6.420604 TGATGTGTGTATGATACTGTAATGCG 59.579 38.462 4.03 0.00 0.00 4.73
1790 8836 7.713764 TGATGTGTGTATGATACTGTAATGC 57.286 36.000 4.03 0.00 0.00 3.56
1792 8838 9.330063 CCTTTGATGTGTGTATGATACTGTAAT 57.670 33.333 4.03 0.00 0.00 1.89
1798 8882 4.275936 GGCCCTTTGATGTGTGTATGATAC 59.724 45.833 0.00 0.00 0.00 2.24
1826 8917 9.892130 ATTATAGGAGCATTGTTAGTTATAGCC 57.108 33.333 0.00 0.00 0.00 3.93
1845 8941 6.415573 GCCTTGGTGGGTATAGAATTATAGG 58.584 44.000 0.00 0.00 36.00 2.57
1846 8942 6.070995 TCGCCTTGGTGGGTATAGAATTATAG 60.071 42.308 0.00 0.00 36.00 1.31
1862 8970 2.526873 ACCTCACCTCGCCTTGGT 60.527 61.111 0.00 0.00 38.53 3.67
1864 8972 2.046892 CCACCTCACCTCGCCTTG 60.047 66.667 0.00 0.00 0.00 3.61
1869 8977 3.706373 CACCCCCACCTCACCTCG 61.706 72.222 0.00 0.00 0.00 4.63
1881 8989 3.339093 CTTGTCCTCCCCCACCCC 61.339 72.222 0.00 0.00 0.00 4.95
1882 8990 3.339093 CCTTGTCCTCCCCCACCC 61.339 72.222 0.00 0.00 0.00 4.61
1883 8991 3.339093 CCCTTGTCCTCCCCCACC 61.339 72.222 0.00 0.00 0.00 4.61
1884 8992 1.850755 TTCCCTTGTCCTCCCCCAC 60.851 63.158 0.00 0.00 0.00 4.61
1885 8993 1.850755 GTTCCCTTGTCCTCCCCCA 60.851 63.158 0.00 0.00 0.00 4.96
1886 8994 2.613482 GGTTCCCTTGTCCTCCCCC 61.613 68.421 0.00 0.00 0.00 5.40
1887 8995 1.541620 AGGTTCCCTTGTCCTCCCC 60.542 63.158 0.00 0.00 0.00 4.81
1888 8996 1.992037 GAGGTTCCCTTGTCCTCCC 59.008 63.158 0.00 0.00 41.09 4.30
1890 8998 0.615850 CAGGAGGTTCCCTTGTCCTC 59.384 60.000 0.00 0.00 44.78 3.71
1891 8999 0.104409 ACAGGAGGTTCCCTTGTCCT 60.104 55.000 0.00 0.00 37.19 3.85
1892 9000 0.036875 CACAGGAGGTTCCCTTGTCC 59.963 60.000 0.00 0.00 37.19 4.02
1893 9001 0.765510 ACACAGGAGGTTCCCTTGTC 59.234 55.000 0.00 0.00 37.19 3.18
1894 9002 1.143073 GAACACAGGAGGTTCCCTTGT 59.857 52.381 0.00 0.00 38.92 3.16
1895 9003 1.142870 TGAACACAGGAGGTTCCCTTG 59.857 52.381 0.00 0.00 43.05 3.61
1896 9004 1.518367 TGAACACAGGAGGTTCCCTT 58.482 50.000 0.00 0.00 43.05 3.95
1897 9005 1.747444 ATGAACACAGGAGGTTCCCT 58.253 50.000 0.00 0.00 43.05 4.20
1898 9006 2.558359 CAAATGAACACAGGAGGTTCCC 59.442 50.000 0.00 0.00 43.05 3.97
1899 9007 2.029918 GCAAATGAACACAGGAGGTTCC 60.030 50.000 0.00 0.00 43.05 3.62
1900 9008 2.622942 TGCAAATGAACACAGGAGGTTC 59.377 45.455 0.00 0.00 43.78 3.62
2038 9146 4.350620 CGATTGATCGGCCTCCTG 57.649 61.111 0.00 0.00 45.93 3.86
2290 9398 4.993584 CACTTCTCTGCATTACAACACTCT 59.006 41.667 0.00 0.00 0.00 3.24
2323 9441 4.214332 CACTTCTCTGGTTTCAAGGTAAGC 59.786 45.833 0.00 0.00 0.00 3.09
2541 11804 1.272092 TGGCCACTGGAATTTGAGAGG 60.272 52.381 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.