Multiple sequence alignment - TraesCS7D01G013100

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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 TraesCS7D01G013100 chr7D 100.000 6099 0 0 1 6099 5488055 5481957 0.000000e+00 11263.0
1 TraesCS7D01G013100 chr7D 83.260 3871 568 49 1519 5338 5637758 5633917 0.000000e+00 3485.0
2 TraesCS7D01G013100 chr7D 83.466 3756 550 53 1519 5240 5649051 5645333 0.000000e+00 3430.0
3 TraesCS7D01G013100 chr7D 81.945 3650 596 46 1519 5134 5787820 5784200 0.000000e+00 3031.0
4 TraesCS7D01G013100 chr7D 82.690 2721 421 44 2448 5148 5665584 5662894 0.000000e+00 2370.0
5 TraesCS7D01G013100 chr7D 82.952 393 64 3 972 1362 5788202 5787811 9.730000e-93 351.0
6 TraesCS7D01G013100 chr7D 75.123 611 97 33 186 766 5449771 5449186 1.020000e-57 235.0
7 TraesCS7D01G013100 chr4A 96.751 4586 138 6 1518 6093 734730991 734735575 0.000000e+00 7633.0
8 TraesCS7D01G013100 chr4A 96.118 4585 142 15 1518 6091 736571068 736575627 0.000000e+00 7448.0
9 TraesCS7D01G013100 chr4A 84.645 3660 507 39 1519 5151 735316645 735320276 0.000000e+00 3594.0
10 TraesCS7D01G013100 chr4A 84.301 3669 516 32 1519 5151 735562375 735558731 0.000000e+00 3530.0
11 TraesCS7D01G013100 chr4A 84.131 3655 518 45 1519 5151 736756659 736760273 0.000000e+00 3480.0
12 TraesCS7D01G013100 chr4A 83.238 3866 569 50 1519 5339 736470364 736466533 0.000000e+00 3476.0
13 TraesCS7D01G013100 chr4A 83.072 3828 583 40 1518 5309 734385503 734389301 0.000000e+00 3419.0
14 TraesCS7D01G013100 chr4A 83.156 3752 578 43 1519 5240 735747469 735751196 0.000000e+00 3378.0
15 TraesCS7D01G013100 chr4A 82.876 3755 573 49 1519 5240 734585473 734589190 0.000000e+00 3308.0
16 TraesCS7D01G013100 chr4A 83.056 3671 536 58 1522 5151 736412962 736409337 0.000000e+00 3254.0
17 TraesCS7D01G013100 chr4A 83.036 3537 540 44 1635 5140 735689506 735693013 0.000000e+00 3153.0
18 TraesCS7D01G013100 chr4A 81.787 3547 557 56 1677 5195 735662557 735659072 0.000000e+00 2889.0
19 TraesCS7D01G013100 chr4A 95.754 1366 37 8 8 1362 734729646 734731001 0.000000e+00 2182.0
20 TraesCS7D01G013100 chr4A 98.148 594 10 1 2 594 736569801 736570394 0.000000e+00 1035.0
21 TraesCS7D01G013100 chr4A 94.032 687 33 2 684 1362 736570392 736571078 0.000000e+00 1035.0
22 TraesCS7D01G013100 chr4A 91.030 301 27 0 1062 1362 735367886 735367586 2.050000e-109 407.0
23 TraesCS7D01G013100 chr4A 90.365 301 29 0 1062 1362 736896812 736897112 4.430000e-106 396.0
24 TraesCS7D01G013100 chr4A 88.162 321 38 0 1032 1352 736055943 736056263 3.450000e-102 383.0
25 TraesCS7D01G013100 chr4A 87.195 328 42 0 1031 1358 736883975 736884302 2.080000e-99 374.0
26 TraesCS7D01G013100 chr4A 83.461 393 62 3 972 1362 736433901 736433510 4.490000e-96 363.0
27 TraesCS7D01G013100 chr4A 83.206 393 63 3 972 1362 735733821 735734212 2.090000e-94 357.0
28 TraesCS7D01G013100 chr4A 78.571 532 88 21 186 693 736755414 736755943 1.640000e-85 327.0
29 TraesCS7D01G013100 chr4A 77.462 457 82 14 342 789 734996246 734996690 2.820000e-63 254.0
30 TraesCS7D01G013100 chr4A 74.664 596 97 32 186 753 736471540 736470971 1.330000e-51 215.0
31 TraesCS7D01G013100 chr7A 83.130 3770 545 57 1519 5240 7045165 7041439 0.000000e+00 3354.0
32 TraesCS7D01G013100 chr7A 75.475 632 113 35 186 797 6929304 6928695 2.800000e-68 270.0
33 TraesCS7D01G013100 chr1A 96.241 133 5 0 1360 1492 545868017 545868149 1.030000e-52 219.0
34 TraesCS7D01G013100 chr6B 93.478 46 3 0 1472 1517 669350011 669350056 1.100000e-07 69.4
35 TraesCS7D01G013100 chr1B 100.000 33 0 0 1485 1517 111051632 111051600 1.840000e-05 62.1


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 TraesCS7D01G013100 chr7D 5481957 5488055 6098 True 11263.000000 11263 100.000000 1 6099 1 chr7D.!!$R2 6098
1 TraesCS7D01G013100 chr7D 5633917 5637758 3841 True 3485.000000 3485 83.260000 1519 5338 1 chr7D.!!$R3 3819
2 TraesCS7D01G013100 chr7D 5645333 5649051 3718 True 3430.000000 3430 83.466000 1519 5240 1 chr7D.!!$R4 3721
3 TraesCS7D01G013100 chr7D 5662894 5665584 2690 True 2370.000000 2370 82.690000 2448 5148 1 chr7D.!!$R5 2700
4 TraesCS7D01G013100 chr7D 5784200 5788202 4002 True 1691.000000 3031 82.448500 972 5134 2 chr7D.!!$R6 4162
5 TraesCS7D01G013100 chr7D 5449186 5449771 585 True 235.000000 235 75.123000 186 766 1 chr7D.!!$R1 580
6 TraesCS7D01G013100 chr4A 734729646 734735575 5929 False 4907.500000 7633 96.252500 8 6093 2 chr4A.!!$F11 6085
7 TraesCS7D01G013100 chr4A 735316645 735320276 3631 False 3594.000000 3594 84.645000 1519 5151 1 chr4A.!!$F4 3632
8 TraesCS7D01G013100 chr4A 735558731 735562375 3644 True 3530.000000 3530 84.301000 1519 5151 1 chr4A.!!$R2 3632
9 TraesCS7D01G013100 chr4A 734385503 734389301 3798 False 3419.000000 3419 83.072000 1518 5309 1 chr4A.!!$F1 3791
10 TraesCS7D01G013100 chr4A 735747469 735751196 3727 False 3378.000000 3378 83.156000 1519 5240 1 chr4A.!!$F7 3721
11 TraesCS7D01G013100 chr4A 734585473 734589190 3717 False 3308.000000 3308 82.876000 1519 5240 1 chr4A.!!$F2 3721
12 TraesCS7D01G013100 chr4A 736409337 736412962 3625 True 3254.000000 3254 83.056000 1522 5151 1 chr4A.!!$R4 3629
13 TraesCS7D01G013100 chr4A 736569801 736575627 5826 False 3172.666667 7448 96.099333 2 6091 3 chr4A.!!$F12 6089
14 TraesCS7D01G013100 chr4A 735689506 735693013 3507 False 3153.000000 3153 83.036000 1635 5140 1 chr4A.!!$F5 3505
15 TraesCS7D01G013100 chr4A 735659072 735662557 3485 True 2889.000000 2889 81.787000 1677 5195 1 chr4A.!!$R3 3518
16 TraesCS7D01G013100 chr4A 736755414 736760273 4859 False 1903.500000 3480 81.351000 186 5151 2 chr4A.!!$F13 4965
17 TraesCS7D01G013100 chr4A 736466533 736471540 5007 True 1845.500000 3476 78.951000 186 5339 2 chr4A.!!$R6 5153
18 TraesCS7D01G013100 chr7A 7041439 7045165 3726 True 3354.000000 3354 83.130000 1519 5240 1 chr7A.!!$R2 3721
19 TraesCS7D01G013100 chr7A 6928695 6929304 609 True 270.000000 270 75.475000 186 797 1 chr7A.!!$R1 611

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
330 339 1.202639 TGCTGTCGTGTGATTCCTGTT 60.203 47.619 0.00 0.0 0.00 3.16 F
1173 1552 0.034186 TGGAGACCACAATCATGCCC 60.034 55.000 0.00 0.0 0.00 5.36 F
1372 1751 0.103026 CATCAGCAGTGCCGTAGCTA 59.897 55.000 12.58 0.0 40.80 3.32 F
1377 1756 0.105039 GCAGTGCCGTAGCTAGGATT 59.895 55.000 14.94 0.0 40.80 3.01 F
1389 1768 0.250338 CTAGGATTAGCCAACGCCCC 60.250 60.000 0.00 0.0 40.02 5.80 F
1472 1851 0.663153 AAAGAGTTTCACTGCCACGC 59.337 50.000 0.00 0.0 0.00 5.34 F
1473 1852 1.166531 AAGAGTTTCACTGCCACGCC 61.167 55.000 0.00 0.0 0.00 5.68 F
3038 3486 2.092968 TCTGTTGGTGAGTTGAAGCACT 60.093 45.455 0.00 0.0 35.43 4.40 F
4095 4569 3.063704 CATTGGGCCGCTGCTGAA 61.064 61.111 0.00 0.0 37.74 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1732 0.103026 TAGCTACGGCACTGCTGATG 59.897 55.000 17.08 9.23 41.70 3.07 R
2253 2652 2.005451 CCAAGAACTGAGCATCTTCCG 58.995 52.381 0.00 0.00 33.73 4.30 R
2999 3447 4.833390 ACAGATTCTGGCAACTTACTACC 58.167 43.478 17.66 0.00 35.51 3.18 R
3038 3486 9.389755 TGTTCTGATGATATTCAAATACCGAAA 57.610 29.630 0.00 0.00 0.00 3.46 R
3416 3879 3.302968 GCAAGCTGCGAAGATGAAC 57.697 52.632 0.00 0.00 31.71 3.18 R
3648 4121 7.397192 AGCAATTTCCAAATAGTCCAGTATTGT 59.603 33.333 0.00 0.00 0.00 2.71 R
3765 4239 6.036083 CCCATCGTTGGAGATAAATATAAGCG 59.964 42.308 14.27 0.00 46.92 4.68 R
4293 4768 1.061033 AGCCCCCTAATGACCTGAGAT 60.061 52.381 0.00 0.00 0.00 2.75 R
5728 6253 0.163146 GCAGCGTCGTAACAAACTCC 59.837 55.000 0.00 0.00 0.00 3.85 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
85 86 4.800023 TCAGAATGATGGATTCCTGCAAT 58.200 39.130 3.95 0.00 42.56 3.56
330 339 1.202639 TGCTGTCGTGTGATTCCTGTT 60.203 47.619 0.00 0.00 0.00 3.16
925 1063 4.529716 ACCCACCTTCTAACAGGAAAAA 57.470 40.909 0.00 0.00 37.39 1.94
1173 1552 0.034186 TGGAGACCACAATCATGCCC 60.034 55.000 0.00 0.00 0.00 5.36
1192 1571 1.207089 CCCAACTCGAGCTGGTGATTA 59.793 52.381 28.41 0.00 29.47 1.75
1354 1733 4.738998 CGCCCAATGCCTCCACCA 62.739 66.667 0.00 0.00 36.24 4.17
1355 1734 2.042639 GCCCAATGCCTCCACCAT 60.043 61.111 0.00 0.00 0.00 3.55
1356 1735 2.129785 GCCCAATGCCTCCACCATC 61.130 63.158 0.00 0.00 0.00 3.51
1357 1736 1.307309 CCCAATGCCTCCACCATCA 59.693 57.895 0.00 0.00 0.00 3.07
1358 1737 0.754217 CCCAATGCCTCCACCATCAG 60.754 60.000 0.00 0.00 0.00 2.90
1359 1738 1.389609 CCAATGCCTCCACCATCAGC 61.390 60.000 0.00 0.00 0.00 4.26
1360 1739 0.681887 CAATGCCTCCACCATCAGCA 60.682 55.000 0.00 0.00 37.94 4.41
1361 1740 0.395311 AATGCCTCCACCATCAGCAG 60.395 55.000 0.00 0.00 36.80 4.24
1362 1741 1.569030 ATGCCTCCACCATCAGCAGT 61.569 55.000 0.00 0.00 36.80 4.40
1363 1742 1.748122 GCCTCCACCATCAGCAGTG 60.748 63.158 0.00 0.00 0.00 3.66
1364 1743 1.748122 CCTCCACCATCAGCAGTGC 60.748 63.158 7.13 7.13 32.48 4.40
1365 1744 1.748122 CTCCACCATCAGCAGTGCC 60.748 63.158 12.58 0.00 32.48 5.01
1366 1745 3.129502 CCACCATCAGCAGTGCCG 61.130 66.667 12.58 0.38 32.48 5.69
1367 1746 2.359107 CACCATCAGCAGTGCCGT 60.359 61.111 12.58 0.00 0.00 5.68
1368 1747 1.079197 CACCATCAGCAGTGCCGTA 60.079 57.895 12.58 0.00 0.00 4.02
1369 1748 1.086067 CACCATCAGCAGTGCCGTAG 61.086 60.000 12.58 0.00 0.00 3.51
1370 1749 2.176273 CCATCAGCAGTGCCGTAGC 61.176 63.158 12.58 0.00 40.48 3.58
1371 1750 1.153489 CATCAGCAGTGCCGTAGCT 60.153 57.895 12.58 0.00 40.80 3.32
1372 1751 0.103026 CATCAGCAGTGCCGTAGCTA 59.897 55.000 12.58 0.00 40.80 3.32
1373 1752 0.387202 ATCAGCAGTGCCGTAGCTAG 59.613 55.000 12.58 0.00 40.80 3.42
1374 1753 1.227089 CAGCAGTGCCGTAGCTAGG 60.227 63.158 12.58 6.46 40.80 3.02
1375 1754 1.379977 AGCAGTGCCGTAGCTAGGA 60.380 57.895 12.58 0.00 40.80 2.94
1376 1755 0.757188 AGCAGTGCCGTAGCTAGGAT 60.757 55.000 12.58 0.00 40.80 3.24
1377 1756 0.105039 GCAGTGCCGTAGCTAGGATT 59.895 55.000 14.94 0.00 40.80 3.01
1378 1757 1.340248 GCAGTGCCGTAGCTAGGATTA 59.660 52.381 14.94 0.00 40.80 1.75
1379 1758 2.608261 GCAGTGCCGTAGCTAGGATTAG 60.608 54.545 14.94 0.00 40.80 1.73
1387 1766 2.618165 GCTAGGATTAGCCAACGCC 58.382 57.895 0.00 0.00 45.34 5.68
1388 1767 0.885150 GCTAGGATTAGCCAACGCCC 60.885 60.000 0.00 0.00 45.34 6.13
1389 1768 0.250338 CTAGGATTAGCCAACGCCCC 60.250 60.000 0.00 0.00 40.02 5.80
1390 1769 2.035237 TAGGATTAGCCAACGCCCCG 62.035 60.000 0.00 0.00 40.02 5.73
1391 1770 2.900337 GATTAGCCAACGCCCCGG 60.900 66.667 0.00 0.00 34.57 5.73
1392 1771 4.499633 ATTAGCCAACGCCCCGGG 62.500 66.667 15.80 15.80 34.57 5.73
1432 1811 7.818997 ACAGTAATATAGTAGCTACAGTGCA 57.181 36.000 25.28 6.42 34.99 4.57
1433 1812 7.649973 ACAGTAATATAGTAGCTACAGTGCAC 58.350 38.462 25.28 9.40 34.99 4.57
1434 1813 7.502895 ACAGTAATATAGTAGCTACAGTGCACT 59.497 37.037 25.28 15.25 34.99 4.40
1435 1814 9.000486 CAGTAATATAGTAGCTACAGTGCACTA 58.000 37.037 25.28 9.54 34.12 2.74
1436 1815 9.001542 AGTAATATAGTAGCTACAGTGCACTAC 57.998 37.037 25.28 13.14 36.16 2.73
1437 1816 9.001542 GTAATATAGTAGCTACAGTGCACTACT 57.998 37.037 25.28 19.76 45.44 2.57
1438 1817 8.466617 AATATAGTAGCTACAGTGCACTACTT 57.533 34.615 25.28 9.52 41.93 2.24
1439 1818 6.777213 ATAGTAGCTACAGTGCACTACTTT 57.223 37.500 25.28 10.44 41.93 2.66
1440 1819 5.470047 AGTAGCTACAGTGCACTACTTTT 57.530 39.130 25.28 8.24 41.93 2.27
1441 1820 5.230942 AGTAGCTACAGTGCACTACTTTTG 58.769 41.667 25.28 9.63 41.93 2.44
1442 1821 2.808543 AGCTACAGTGCACTACTTTTGC 59.191 45.455 21.20 16.81 37.60 3.68
1443 1822 2.808543 GCTACAGTGCACTACTTTTGCT 59.191 45.455 21.20 0.96 40.86 3.91
1444 1823 3.994392 GCTACAGTGCACTACTTTTGCTA 59.006 43.478 21.20 2.05 40.86 3.49
1445 1824 4.143094 GCTACAGTGCACTACTTTTGCTAC 60.143 45.833 21.20 0.00 40.86 3.58
1446 1825 3.804036 ACAGTGCACTACTTTTGCTACA 58.196 40.909 21.20 0.00 40.86 2.74
1447 1826 3.809832 ACAGTGCACTACTTTTGCTACAG 59.190 43.478 21.20 4.67 40.86 2.74
1448 1827 3.809832 CAGTGCACTACTTTTGCTACAGT 59.190 43.478 21.20 0.00 40.86 3.55
1449 1828 4.058817 AGTGCACTACTTTTGCTACAGTC 58.941 43.478 20.16 0.00 40.86 3.51
1450 1829 4.058817 GTGCACTACTTTTGCTACAGTCT 58.941 43.478 10.32 0.00 40.86 3.24
1451 1830 4.150804 GTGCACTACTTTTGCTACAGTCTC 59.849 45.833 10.32 0.00 40.86 3.36
1452 1831 3.680458 GCACTACTTTTGCTACAGTCTCC 59.320 47.826 0.00 0.00 37.00 3.71
1453 1832 4.799586 GCACTACTTTTGCTACAGTCTCCA 60.800 45.833 0.00 0.00 37.00 3.86
1454 1833 5.297547 CACTACTTTTGCTACAGTCTCCAA 58.702 41.667 0.00 0.00 0.00 3.53
1455 1834 5.758296 CACTACTTTTGCTACAGTCTCCAAA 59.242 40.000 0.00 0.00 0.00 3.28
1456 1835 5.992217 ACTACTTTTGCTACAGTCTCCAAAG 59.008 40.000 0.00 0.00 0.00 2.77
1457 1836 5.036117 ACTTTTGCTACAGTCTCCAAAGA 57.964 39.130 0.00 0.00 0.00 2.52
1458 1837 5.059833 ACTTTTGCTACAGTCTCCAAAGAG 58.940 41.667 0.00 0.00 41.93 2.85
1459 1838 4.689612 TTTGCTACAGTCTCCAAAGAGT 57.310 40.909 0.00 0.00 41.26 3.24
1460 1839 4.689612 TTGCTACAGTCTCCAAAGAGTT 57.310 40.909 0.00 0.00 41.26 3.01
1461 1840 4.689612 TGCTACAGTCTCCAAAGAGTTT 57.310 40.909 0.00 0.00 41.26 2.66
1462 1841 4.632153 TGCTACAGTCTCCAAAGAGTTTC 58.368 43.478 0.00 0.00 41.26 2.78
1463 1842 4.100963 TGCTACAGTCTCCAAAGAGTTTCA 59.899 41.667 0.00 0.00 41.26 2.69
1464 1843 4.449405 GCTACAGTCTCCAAAGAGTTTCAC 59.551 45.833 0.00 0.00 41.26 3.18
1465 1844 4.762289 ACAGTCTCCAAAGAGTTTCACT 57.238 40.909 0.00 0.00 41.26 3.41
1466 1845 4.446371 ACAGTCTCCAAAGAGTTTCACTG 58.554 43.478 7.65 7.65 42.64 3.66
1467 1846 3.249559 CAGTCTCCAAAGAGTTTCACTGC 59.750 47.826 0.00 0.00 41.26 4.40
1468 1847 2.550180 GTCTCCAAAGAGTTTCACTGCC 59.450 50.000 0.00 0.00 41.26 4.85
1469 1848 2.172505 TCTCCAAAGAGTTTCACTGCCA 59.827 45.455 0.00 0.00 41.26 4.92
1470 1849 2.291741 CTCCAAAGAGTTTCACTGCCAC 59.708 50.000 0.00 0.00 35.21 5.01
1471 1850 1.002468 CCAAAGAGTTTCACTGCCACG 60.002 52.381 0.00 0.00 0.00 4.94
1472 1851 0.663153 AAAGAGTTTCACTGCCACGC 59.337 50.000 0.00 0.00 0.00 5.34
1473 1852 1.166531 AAGAGTTTCACTGCCACGCC 61.167 55.000 0.00 0.00 0.00 5.68
1474 1853 2.594592 AGTTTCACTGCCACGCCC 60.595 61.111 0.00 0.00 0.00 6.13
1475 1854 3.670377 GTTTCACTGCCACGCCCC 61.670 66.667 0.00 0.00 0.00 5.80
1766 2156 3.513912 AGTGATTGGTCGTGACAAGGATA 59.486 43.478 2.00 0.00 0.00 2.59
1783 2173 8.709386 ACAAGGATAGCGATCATATAATTGAC 57.291 34.615 9.15 0.00 33.27 3.18
1797 2187 3.366052 AATTGACCGCCTTACCAAGAT 57.634 42.857 0.00 0.00 0.00 2.40
1870 2263 3.355378 CATTGTTGGAGTTGGAGGCATA 58.645 45.455 0.00 0.00 0.00 3.14
2092 2487 9.339492 CTGCAAGAATCAAAGAAATTTCTACTC 57.661 33.333 20.76 12.31 33.28 2.59
2253 2652 2.919228 AGTGTGTCCTCTGGAAAACAC 58.081 47.619 18.46 18.46 44.80 3.32
2774 3222 5.105117 CAGAATCACTCTCCAAAGGGAACC 61.105 50.000 0.00 0.00 44.38 3.62
2792 3240 2.911484 ACCGCTTCAGATTGGAAGATC 58.089 47.619 7.08 0.00 45.66 2.75
2999 3447 8.691727 GCGTACTATATTTGTCATCTTACAGTG 58.308 37.037 0.00 0.00 0.00 3.66
3038 3486 2.092968 TCTGTTGGTGAGTTGAAGCACT 60.093 45.455 0.00 0.00 35.43 4.40
3416 3879 9.403110 CCTTGAAATCAAAGTTGTATCAGAAAG 57.597 33.333 0.00 0.00 35.15 2.62
3468 3932 3.701040 AGTTGCAAGGATGACACAAACTT 59.299 39.130 0.00 0.00 0.00 2.66
3472 3945 4.341806 TGCAAGGATGACACAAACTTTGAT 59.658 37.500 8.55 0.00 0.00 2.57
3765 4239 5.609533 TTAGTAGTAGAGAAATGCCCACC 57.390 43.478 0.00 0.00 0.00 4.61
3952 4426 8.117813 TGATGATATTAATGCATGCTGATGTT 57.882 30.769 20.33 8.41 31.50 2.71
4095 4569 3.063704 CATTGGGCCGCTGCTGAA 61.064 61.111 0.00 0.00 37.74 3.02
4124 4598 6.176183 CCATCAGGACTTCATGAACTTACTT 58.824 40.000 3.38 0.00 40.22 2.24
4152 4626 8.655935 TCTTCATGCTATATTACAGATGGAGA 57.344 34.615 0.00 0.00 0.00 3.71
4293 4768 3.760738 TGGACATCAAACATTGCTGGTA 58.239 40.909 0.00 0.00 31.37 3.25
4733 5214 1.603456 TGCGGCTGAAGATTTCACAA 58.397 45.000 0.00 0.00 35.46 3.33
4771 5254 1.533625 TTGAAGGATGCAAGGAACCG 58.466 50.000 0.00 0.00 0.00 4.44
4834 5317 5.573337 AGATCCTGTGCTTCTTTAATTGC 57.427 39.130 0.00 0.00 0.00 3.56
4857 5340 3.683365 AATGATTTCCCTGCCAACAAC 57.317 42.857 0.00 0.00 0.00 3.32
4893 5376 7.531857 TCTCCAATCTGAAGGATCTACATAC 57.468 40.000 3.12 0.00 32.76 2.39
4991 5476 1.977129 AGCTCTTGAAGGAGAGTTGCT 59.023 47.619 4.08 0.00 44.03 3.91
5438 5960 4.423732 CAAGGCTGGTAATTATGCAACAC 58.576 43.478 0.00 0.00 0.00 3.32
5638 6163 1.463444 GCGGTACCATGACTGAACAAC 59.537 52.381 13.54 0.00 0.00 3.32
5701 6226 6.565234 TGTTGCTTAGCTCTGATACTACTTC 58.435 40.000 5.60 0.00 0.00 3.01
5728 6253 4.695455 AGTTTTGTATGTCTTGTCATCCCG 59.305 41.667 0.00 0.00 0.00 5.14
5748 6273 0.179282 GAGTTTGTTACGACGCTGCG 60.179 55.000 21.91 21.91 37.29 5.18
5862 6387 2.897350 GTATCCAGCGGCTGTGCC 60.897 66.667 26.79 9.42 46.75 5.01
5891 6416 2.884012 TCCAATGGCTAAGTTGTGTGTG 59.116 45.455 0.00 0.00 0.00 3.82
5925 6457 2.711542 AGAGAAAAGGCATACAACCGG 58.288 47.619 0.00 0.00 0.00 5.28
5996 6528 0.529378 GAAATGGAGCCTGCCAACTG 59.471 55.000 0.00 0.00 42.16 3.16
6000 6532 1.228245 GGAGCCTGCCAACTGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
6022 6554 7.916914 TCATATTGATGGTGCTATCTTGATG 57.083 36.000 0.00 0.00 33.49 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.679898 GGAGGTGGGAGTGGACTTG 59.320 63.158 0.00 0.00 0.00 3.16
2 3 2.049792 AAGGGAGGTGGGAGTGGACT 62.050 60.000 0.00 0.00 0.00 3.85
3 4 1.539124 AAGGGAGGTGGGAGTGGAC 60.539 63.158 0.00 0.00 0.00 4.02
388 423 0.698238 AGCAACATTGTAGGAGCCCA 59.302 50.000 0.00 0.00 0.00 5.36
875 1013 3.964031 AGGCTGGAAGAGAGTATAAGTGG 59.036 47.826 0.00 0.00 34.07 4.00
882 1020 4.317530 TTCACTAGGCTGGAAGAGAGTA 57.682 45.455 4.33 0.00 34.07 2.59
1164 1543 0.749454 GCTCGAGTTGGGGCATGATT 60.749 55.000 15.13 0.00 0.00 2.57
1192 1571 2.419990 GGTTTCCCTTGTTTGCTGCTTT 60.420 45.455 0.00 0.00 0.00 3.51
1352 1731 2.176273 GCTACGGCACTGCTGATGG 61.176 63.158 17.08 6.92 38.46 3.51
1353 1732 0.103026 TAGCTACGGCACTGCTGATG 59.897 55.000 17.08 9.23 41.70 3.07
1354 1733 0.387202 CTAGCTACGGCACTGCTGAT 59.613 55.000 17.08 3.79 41.70 2.90
1355 1734 1.667154 CCTAGCTACGGCACTGCTGA 61.667 60.000 17.08 0.00 41.70 4.26
1356 1735 1.227089 CCTAGCTACGGCACTGCTG 60.227 63.158 8.40 8.40 41.70 4.41
1357 1736 0.757188 ATCCTAGCTACGGCACTGCT 60.757 55.000 0.00 0.00 41.70 4.24
1358 1737 0.105039 AATCCTAGCTACGGCACTGC 59.895 55.000 0.00 0.00 41.70 4.40
1359 1738 2.608261 GCTAATCCTAGCTACGGCACTG 60.608 54.545 0.00 0.00 46.12 3.66
1360 1739 1.614413 GCTAATCCTAGCTACGGCACT 59.386 52.381 0.00 0.00 46.12 4.40
1361 1740 2.067414 GCTAATCCTAGCTACGGCAC 57.933 55.000 0.00 0.00 46.12 5.01
1370 1749 0.250338 GGGGCGTTGGCTAATCCTAG 60.250 60.000 4.55 0.00 39.81 3.02
1371 1750 1.834301 GGGGCGTTGGCTAATCCTA 59.166 57.895 4.55 0.00 39.81 2.94
1372 1751 2.595655 GGGGCGTTGGCTAATCCT 59.404 61.111 4.55 0.00 39.81 3.24
1373 1752 2.900337 CGGGGCGTTGGCTAATCC 60.900 66.667 0.00 0.00 39.81 3.01
1374 1753 2.900337 CCGGGGCGTTGGCTAATC 60.900 66.667 0.00 0.00 39.81 1.75
1375 1754 4.499633 CCCGGGGCGTTGGCTAAT 62.500 66.667 14.71 0.00 39.81 1.73
1406 1785 9.000486 TGCACTGTAGCTACTATATTACTGTAG 58.000 37.037 23.84 10.94 37.36 2.74
1407 1786 8.781196 GTGCACTGTAGCTACTATATTACTGTA 58.219 37.037 23.84 5.26 34.99 2.74
1408 1787 7.502895 AGTGCACTGTAGCTACTATATTACTGT 59.497 37.037 20.97 5.65 34.99 3.55
1409 1788 7.877003 AGTGCACTGTAGCTACTATATTACTG 58.123 38.462 20.97 5.02 34.99 2.74
1410 1789 9.001542 GTAGTGCACTGTAGCTACTATATTACT 57.998 37.037 29.57 20.01 33.78 2.24
1411 1790 9.001542 AGTAGTGCACTGTAGCTACTATATTAC 57.998 37.037 29.57 12.87 41.36 1.89
1412 1791 9.570468 AAGTAGTGCACTGTAGCTACTATATTA 57.430 33.333 29.57 0.00 42.04 0.98
1413 1792 8.466617 AAGTAGTGCACTGTAGCTACTATATT 57.533 34.615 29.57 5.53 42.04 1.28
1414 1793 8.466617 AAAGTAGTGCACTGTAGCTACTATAT 57.533 34.615 29.57 10.20 42.04 0.86
1415 1794 7.876936 AAAGTAGTGCACTGTAGCTACTATA 57.123 36.000 29.57 1.01 42.04 1.31
1416 1795 6.777213 AAAGTAGTGCACTGTAGCTACTAT 57.223 37.500 29.57 9.78 42.04 2.12
1417 1796 6.387465 CAAAAGTAGTGCACTGTAGCTACTA 58.613 40.000 29.57 10.11 42.04 1.82
1418 1797 5.230942 CAAAAGTAGTGCACTGTAGCTACT 58.769 41.667 29.57 19.66 43.96 2.57
1419 1798 4.143094 GCAAAAGTAGTGCACTGTAGCTAC 60.143 45.833 29.57 17.65 41.80 3.58
1420 1799 3.994392 GCAAAAGTAGTGCACTGTAGCTA 59.006 43.478 29.57 4.96 41.80 3.32
1421 1800 2.808543 GCAAAAGTAGTGCACTGTAGCT 59.191 45.455 29.57 17.51 41.80 3.32
1422 1801 2.808543 AGCAAAAGTAGTGCACTGTAGC 59.191 45.455 29.57 21.32 44.74 3.58
1423 1802 4.988540 TGTAGCAAAAGTAGTGCACTGTAG 59.011 41.667 29.57 13.31 44.74 2.74
1424 1803 4.951254 TGTAGCAAAAGTAGTGCACTGTA 58.049 39.130 29.57 7.53 44.74 2.74
1425 1804 3.804036 TGTAGCAAAAGTAGTGCACTGT 58.196 40.909 29.57 13.63 44.74 3.55
1426 1805 3.809832 ACTGTAGCAAAAGTAGTGCACTG 59.190 43.478 29.57 13.26 44.74 3.66
1427 1806 4.058817 GACTGTAGCAAAAGTAGTGCACT 58.941 43.478 25.12 25.12 44.74 4.40
1428 1807 4.058817 AGACTGTAGCAAAAGTAGTGCAC 58.941 43.478 9.40 9.40 44.74 4.57
1429 1808 4.307432 GAGACTGTAGCAAAAGTAGTGCA 58.693 43.478 0.00 0.00 44.74 4.57
1430 1809 3.680458 GGAGACTGTAGCAAAAGTAGTGC 59.320 47.826 0.00 0.00 42.55 4.40
1431 1810 4.883083 TGGAGACTGTAGCAAAAGTAGTG 58.117 43.478 0.00 0.00 0.00 2.74
1432 1811 5.546621 TTGGAGACTGTAGCAAAAGTAGT 57.453 39.130 0.00 0.00 0.00 2.73
1433 1812 6.223852 TCTTTGGAGACTGTAGCAAAAGTAG 58.776 40.000 8.31 0.00 0.00 2.57
1434 1813 6.169557 TCTTTGGAGACTGTAGCAAAAGTA 57.830 37.500 8.31 0.00 0.00 2.24
1435 1814 5.036117 TCTTTGGAGACTGTAGCAAAAGT 57.964 39.130 8.31 0.00 0.00 2.66
1436 1815 5.059833 ACTCTTTGGAGACTGTAGCAAAAG 58.940 41.667 0.00 3.91 41.86 2.27
1437 1816 5.036117 ACTCTTTGGAGACTGTAGCAAAA 57.964 39.130 0.00 0.00 41.86 2.44
1438 1817 4.689612 ACTCTTTGGAGACTGTAGCAAA 57.310 40.909 0.00 0.00 41.86 3.68
1439 1818 4.689612 AACTCTTTGGAGACTGTAGCAA 57.310 40.909 0.00 0.00 41.86 3.91
1440 1819 4.100963 TGAAACTCTTTGGAGACTGTAGCA 59.899 41.667 0.00 0.00 41.86 3.49
1441 1820 4.449405 GTGAAACTCTTTGGAGACTGTAGC 59.551 45.833 0.00 0.00 41.86 3.58
1458 1837 3.670377 GGGGCGTGGCAGTGAAAC 61.670 66.667 0.00 0.00 0.00 2.78
1506 1885 1.443407 CTGATGGTCAGGGGCGTAG 59.557 63.158 0.00 0.00 40.71 3.51
1507 1886 2.731571 GCTGATGGTCAGGGGCGTA 61.732 63.158 8.85 0.00 44.43 4.42
1508 1887 4.101448 GCTGATGGTCAGGGGCGT 62.101 66.667 8.85 0.00 44.43 5.68
1509 1888 4.100084 TGCTGATGGTCAGGGGCG 62.100 66.667 8.85 0.00 44.43 6.13
1510 1889 2.124403 CTGCTGATGGTCAGGGGC 60.124 66.667 8.85 0.00 44.43 5.80
1511 1890 2.124403 GCTGCTGATGGTCAGGGG 60.124 66.667 8.85 0.00 44.43 4.79
1512 1891 1.748122 GTGCTGCTGATGGTCAGGG 60.748 63.158 8.85 0.00 44.43 4.45
1513 1892 0.322277 AAGTGCTGCTGATGGTCAGG 60.322 55.000 8.85 0.00 44.43 3.86
1514 1893 1.531423 AAAGTGCTGCTGATGGTCAG 58.469 50.000 0.00 2.65 46.90 3.51
1515 1894 1.985473 AAAAGTGCTGCTGATGGTCA 58.015 45.000 0.00 0.00 0.00 4.02
1516 1895 3.691118 TCATAAAAGTGCTGCTGATGGTC 59.309 43.478 0.00 0.00 0.00 4.02
1783 2173 1.940613 GCAGTTATCTTGGTAAGGCGG 59.059 52.381 0.00 0.00 0.00 6.13
1797 2187 5.806818 ACTCAGACTCAGTAGTAGCAGTTA 58.193 41.667 0.00 0.00 35.56 2.24
1870 2263 3.788227 TGTGCTAATGTGGACTTTCCT 57.212 42.857 0.00 0.00 37.46 3.36
2092 2487 3.641437 AACCAAACATCATCCAACACG 57.359 42.857 0.00 0.00 0.00 4.49
2253 2652 2.005451 CCAAGAACTGAGCATCTTCCG 58.995 52.381 0.00 0.00 33.73 4.30
2774 3222 5.178996 CCTTATGATCTTCCAATCTGAAGCG 59.821 44.000 0.00 0.00 41.23 4.68
2999 3447 4.833390 ACAGATTCTGGCAACTTACTACC 58.167 43.478 17.66 0.00 35.51 3.18
3038 3486 9.389755 TGTTCTGATGATATTCAAATACCGAAA 57.610 29.630 0.00 0.00 0.00 3.46
3416 3879 3.302968 GCAAGCTGCGAAGATGAAC 57.697 52.632 0.00 0.00 31.71 3.18
3648 4121 7.397192 AGCAATTTCCAAATAGTCCAGTATTGT 59.603 33.333 0.00 0.00 0.00 2.71
3765 4239 6.036083 CCCATCGTTGGAGATAAATATAAGCG 59.964 42.308 14.27 0.00 46.92 4.68
3878 4352 7.984050 AGATGAGAACGCATTCCTAATATATGG 59.016 37.037 0.00 0.00 35.18 2.74
3920 4394 6.183360 GCATGCATTAATATCATCAGCTGCTA 60.183 38.462 14.21 0.00 0.00 3.49
3952 4426 5.652014 ACTTTCAAGGTTCTGAACATGTGAA 59.348 36.000 21.01 20.32 35.07 3.18
3991 4465 7.013274 TCCTCTTTTACCAACACTTCATCTTTG 59.987 37.037 0.00 0.00 0.00 2.77
4095 4569 3.117745 TCATGAAGTCCTGATGGTGGAT 58.882 45.455 0.00 0.00 35.87 3.41
4152 4626 4.460948 CCATCAAGGCAAACAGCTAAAT 57.539 40.909 0.00 0.00 44.79 1.40
4293 4768 1.061033 AGCCCCCTAATGACCTGAGAT 60.061 52.381 0.00 0.00 0.00 2.75
4625 5106 1.196104 TCGGGGGTGAGTTTCGGAAT 61.196 55.000 0.00 0.00 0.00 3.01
4733 5214 5.255397 TCAAAACAGAGGTATGGTGGAAT 57.745 39.130 0.00 0.00 0.00 3.01
4834 5317 2.302445 TGTTGGCAGGGAAATCATTTGG 59.698 45.455 0.00 0.00 0.00 3.28
4857 5340 3.933955 CAGATTGGAGAAGCACTTCAGAG 59.066 47.826 12.65 0.00 41.84 3.35
4893 5376 5.808366 TGATATGTTAGGGCAGTTAGAGG 57.192 43.478 0.00 0.00 0.00 3.69
5038 5523 7.681939 AATCACGCTTGAACTAATTTCCTTA 57.318 32.000 0.00 0.00 34.61 2.69
5110 5615 2.664402 ATTGAGAGTGCAAAGGTGGT 57.336 45.000 0.00 0.00 0.00 4.16
5438 5960 4.819630 ACATACATAATAAACTGGTGCCCG 59.180 41.667 0.00 0.00 0.00 6.13
5638 6163 1.817099 GCAAGTGATGGAGGCTCCG 60.817 63.158 27.58 13.00 40.17 4.63
5701 6226 7.301054 GGATGACAAGACATACAAAACTTGAG 58.699 38.462 0.00 0.00 41.16 3.02
5715 6240 2.076863 CAAACTCCGGGATGACAAGAC 58.923 52.381 0.00 0.00 0.00 3.01
5728 6253 0.163146 GCAGCGTCGTAACAAACTCC 59.837 55.000 0.00 0.00 0.00 3.85
5748 6273 3.365565 CCAATTAGGCCAACAACACGTAC 60.366 47.826 5.01 0.00 0.00 3.67
5862 6387 0.174845 TTAGCCATTGGACTCGACCG 59.825 55.000 6.95 0.00 0.00 4.79
5901 6433 5.175859 CGGTTGTATGCCTTTTCTCTAGAA 58.824 41.667 0.00 0.00 0.00 2.10
5904 6436 3.869065 CCGGTTGTATGCCTTTTCTCTA 58.131 45.455 0.00 0.00 0.00 2.43
5972 6504 0.750911 GGCAGGCTCCATTTCTCCTG 60.751 60.000 2.94 2.94 46.63 3.86
5996 6528 7.734924 TCAAGATAGCACCATCAATATGAAC 57.265 36.000 0.00 0.00 34.84 3.18
6000 6532 6.787170 ACCATCAAGATAGCACCATCAATAT 58.213 36.000 0.00 0.00 0.00 1.28
6022 6554 3.798202 GTGAGGGTCATCACTTCATACC 58.202 50.000 8.30 0.00 45.03 2.73


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

AutoCloner maintained by Alex Coulton.