Multiple sequence alignment - TraesCS5D01G321600

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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 TraesCS5D01G321600 chr5D 100.000 3447 0 0 1 3447 413569934 413573380 0.000000e+00 6366
1 TraesCS5D01G321600 chr5D 92.019 1278 83 13 346 1616 413437003 413438268 0.000000e+00 1777
2 TraesCS5D01G321600 chr5D 96.111 900 32 2 696 1592 413600456 413601355 0.000000e+00 1465
3 TraesCS5D01G321600 chr5D 96.996 233 7 0 1 233 413599836 413600068 3.220000e-105 392
4 TraesCS5D01G321600 chr5D 94.068 236 12 1 1 234 413570199 413570434 1.180000e-94 357
5 TraesCS5D01G321600 chr5B 95.651 3219 124 10 234 3447 498709524 498712731 0.000000e+00 5155
6 TraesCS5D01G321600 chr5B 94.226 2234 100 8 1217 3447 498784090 498786297 0.000000e+00 3384
7 TraesCS5D01G321600 chr5B 95.131 1869 86 3 1579 3447 498791179 498793042 0.000000e+00 2942
8 TraesCS5D01G321600 chr5B 95.378 1666 72 4 1782 3447 498788018 498789678 0.000000e+00 2645
9 TraesCS5D01G321600 chr5B 94.523 1625 50 18 1 1616 498531261 498532855 0.000000e+00 2471
10 TraesCS5D01G321600 chr5B 92.863 1275 79 9 346 1616 498267300 498268566 0.000000e+00 1840
11 TraesCS5D01G321600 chr5B 95.345 666 27 3 234 896 498783049 498783713 0.000000e+00 1055
12 TraesCS5D01G321600 chr5B 83.667 949 111 22 1286 2227 498802840 498803751 0.000000e+00 854
13 TraesCS5D01G321600 chr5B 94.043 235 14 0 1579 1813 498787788 498788022 1.180000e-94 357
14 TraesCS5D01G321600 chr5B 92.373 236 16 1 1 234 498531504 498531739 5.510000e-88 335
15 TraesCS5D01G321600 chr5A 95.455 1672 69 6 1778 3447 525741556 525743222 0.000000e+00 2660
16 TraesCS5D01G321600 chr5A 95.048 1676 67 9 1778 3447 525928058 525929723 0.000000e+00 2621
17 TraesCS5D01G321600 chr5A 95.209 1628 67 5 845 2469 526281098 526282717 0.000000e+00 2564
18 TraesCS5D01G321600 chr5A 94.387 1657 78 10 1778 3430 525839395 525841040 0.000000e+00 2531
19 TraesCS5D01G321600 chr5A 94.949 1584 67 9 1868 3447 525744513 525746087 0.000000e+00 2470
20 TraesCS5D01G321600 chr5A 94.315 1583 77 8 1868 3447 525747380 525748952 0.000000e+00 2412
21 TraesCS5D01G321600 chr5A 95.965 1388 50 4 236 1618 525740170 525741556 0.000000e+00 2248
22 TraesCS5D01G321600 chr5A 95.890 1387 52 4 236 1618 525838013 525839398 0.000000e+00 2241
23 TraesCS5D01G321600 chr5A 94.949 1386 64 6 236 1618 525926676 525928058 0.000000e+00 2167
24 TraesCS5D01G321600 chr5A 91.358 810 40 13 2 810 526280315 526281095 0.000000e+00 1081
25 TraesCS5D01G321600 chr5A 95.726 234 9 1 1 233 525739962 525740195 3.250000e-100 375
26 TraesCS5D01G321600 chr5A 95.708 233 9 1 1 233 525926470 525926701 1.170000e-99 374
27 TraesCS5D01G321600 chr5A 94.444 234 12 1 1 233 525837805 525838038 3.270000e-95 359
28 TraesCS5D01G321600 chr5A 93.103 232 14 2 1 230 525740200 525740431 4.260000e-89 339
29 TraesCS5D01G321600 chr5A 92.241 232 15 3 1 230 525926706 525926936 3.320000e-85 326
30 TraesCS5D01G321600 chr6D 98.256 172 3 0 1613 1784 406391357 406391528 5.590000e-78 302
31 TraesCS5D01G321600 chr2D 97.674 172 4 0 1613 1784 396613965 396613794 2.600000e-76 296
32 TraesCS5D01G321600 chrUn 97.674 172 3 1 1613 1784 25754363 25754533 9.360000e-76 294


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 TraesCS5D01G321600 chr5D 413569934 413573380 3446 False 3361.500000 6366 97.034000 1 3447 2 chr5D.!!$F2 3446
1 TraesCS5D01G321600 chr5D 413437003 413438268 1265 False 1777.000000 1777 92.019000 346 1616 1 chr5D.!!$F1 1270
2 TraesCS5D01G321600 chr5D 413599836 413601355 1519 False 928.500000 1465 96.553500 1 1592 2 chr5D.!!$F3 1591
3 TraesCS5D01G321600 chr5B 498709524 498712731 3207 False 5155.000000 5155 95.651000 234 3447 1 chr5B.!!$F2 3213
4 TraesCS5D01G321600 chr5B 498783049 498793042 9993 False 2076.600000 3384 94.824600 234 3447 5 chr5B.!!$F5 3213
5 TraesCS5D01G321600 chr5B 498267300 498268566 1266 False 1840.000000 1840 92.863000 346 1616 1 chr5B.!!$F1 1270
6 TraesCS5D01G321600 chr5B 498531261 498532855 1594 False 1403.000000 2471 93.448000 1 1616 2 chr5B.!!$F4 1615
7 TraesCS5D01G321600 chr5B 498802840 498803751 911 False 854.000000 854 83.667000 1286 2227 1 chr5B.!!$F3 941
8 TraesCS5D01G321600 chr5A 526280315 526282717 2402 False 1822.500000 2564 93.283500 2 2469 2 chr5A.!!$F4 2467
9 TraesCS5D01G321600 chr5A 525739962 525748952 8990 False 1750.666667 2660 94.918833 1 3447 6 chr5A.!!$F1 3446
10 TraesCS5D01G321600 chr5A 525837805 525841040 3235 False 1710.333333 2531 94.907000 1 3430 3 chr5A.!!$F2 3429
11 TraesCS5D01G321600 chr5A 525926470 525929723 3253 False 1372.000000 2621 94.486500 1 3447 4 chr5A.!!$F3 3446

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
452 465 0.859232 AACGTTGACATGCTCGTCAC 59.141 50.000 0.0 4.25 45.36 3.67 F
858 953 1.010294 TGGGCAGTTAAGGGAGGGATA 59.990 52.381 0.0 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1362 0.319211 TACGTGCAAGTTCCCGTCTG 60.319 55.000 11.38 0.0 34.95 3.51 R
2541 5688 1.474077 GTTGTCCATTCTCACCCATGC 59.526 52.381 0.00 0.0 0.00 4.06 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
49 51 8.097038 TGTCCCTTTCTTGATATGTGATATAGC 58.903 37.037 0.00 0.00 0.00 2.97
166 174 8.635328 TGAGGTTATCATTAGCAAACGATACTA 58.365 33.333 0.00 0.00 31.12 1.82
218 226 9.554395 AACTTATTTAAACCCTTTTCACATTGG 57.446 29.630 0.00 0.00 0.00 3.16
219 227 8.710239 ACTTATTTAAACCCTTTTCACATTGGT 58.290 29.630 0.00 0.00 0.00 3.67
223 231 8.894768 TTTAAACCCTTTTCACATTGGTAATG 57.105 30.769 0.28 0.28 44.48 1.90
224 232 4.535526 ACCCTTTTCACATTGGTAATGC 57.464 40.909 1.68 0.00 42.69 3.56
225 233 4.159557 ACCCTTTTCACATTGGTAATGCT 58.840 39.130 1.68 0.00 42.69 3.79
226 234 4.021192 ACCCTTTTCACATTGGTAATGCTG 60.021 41.667 1.68 1.10 42.69 4.41
227 235 4.021192 CCCTTTTCACATTGGTAATGCTGT 60.021 41.667 1.68 0.00 42.69 4.40
228 236 5.184864 CCCTTTTCACATTGGTAATGCTGTA 59.815 40.000 1.68 0.00 42.69 2.74
229 237 6.295011 CCCTTTTCACATTGGTAATGCTGTAA 60.295 38.462 1.68 0.00 42.69 2.41
230 238 7.322664 CCTTTTCACATTGGTAATGCTGTAAT 58.677 34.615 1.68 0.00 42.69 1.89
231 239 8.465999 CCTTTTCACATTGGTAATGCTGTAATA 58.534 33.333 1.68 0.00 42.69 0.98
232 240 9.507280 CTTTTCACATTGGTAATGCTGTAATAG 57.493 33.333 1.68 0.00 42.69 1.73
262 270 9.674068 TTTCACATTGGTAATGCTGTAATAGTA 57.326 29.630 1.68 0.00 42.69 1.82
377 389 6.195244 GTGTTATGAAAAATCAGCGTGCATAG 59.805 38.462 0.00 0.00 0.00 2.23
452 465 0.859232 AACGTTGACATGCTCGTCAC 59.141 50.000 0.00 4.25 45.36 3.67
550 563 9.499479 AGATGTCCATTTCTTGATATATGTGAC 57.501 33.333 0.00 0.00 0.00 3.67
799 813 1.620819 CTATCCGCTTGGGTGCTATCT 59.379 52.381 0.00 0.00 37.00 1.98
858 953 1.010294 TGGGCAGTTAAGGGAGGGATA 59.990 52.381 0.00 0.00 0.00 2.59
995 1094 3.788227 TCTGTAGACATGCCTTTTGGT 57.212 42.857 0.00 0.00 42.99 3.67
1087 1188 9.607285 CTTACATAAACAATGAGGTAACACAAC 57.393 33.333 0.00 0.00 41.73 3.32
1260 1361 2.597578 GGTTTCCCACCCAACTGTAT 57.402 50.000 0.00 0.00 40.19 2.29
1261 1362 2.443416 GGTTTCCCACCCAACTGTATC 58.557 52.381 0.00 0.00 40.19 2.24
1494 1596 3.389329 AGGCTGGTCAACACAGGATATAG 59.611 47.826 0.00 0.00 36.48 1.31
1538 1640 2.603173 GCTGACTTTGAAACTTCTGCCG 60.603 50.000 3.59 0.00 0.00 5.69
1617 1724 6.435292 AAACTGTGTCCCTTACATTCTACT 57.565 37.500 0.00 0.00 41.10 2.57
1618 1725 5.662674 ACTGTGTCCCTTACATTCTACTC 57.337 43.478 0.00 0.00 41.10 2.59
1619 1726 4.466726 ACTGTGTCCCTTACATTCTACTCC 59.533 45.833 0.00 0.00 41.10 3.85
1620 1727 3.773119 TGTGTCCCTTACATTCTACTCCC 59.227 47.826 0.00 0.00 41.10 4.30
1621 1728 4.031611 GTGTCCCTTACATTCTACTCCCT 58.968 47.826 0.00 0.00 41.10 4.20
1622 1729 4.099727 GTGTCCCTTACATTCTACTCCCTC 59.900 50.000 0.00 0.00 41.10 4.30
1623 1730 3.642377 GTCCCTTACATTCTACTCCCTCC 59.358 52.174 0.00 0.00 0.00 4.30
1624 1731 2.628657 CCCTTACATTCTACTCCCTCCG 59.371 54.545 0.00 0.00 0.00 4.63
1625 1732 3.297736 CCTTACATTCTACTCCCTCCGT 58.702 50.000 0.00 0.00 0.00 4.69
1626 1733 3.705072 CCTTACATTCTACTCCCTCCGTT 59.295 47.826 0.00 0.00 0.00 4.44
1627 1734 4.202131 CCTTACATTCTACTCCCTCCGTTC 60.202 50.000 0.00 0.00 0.00 3.95
1628 1735 2.108970 ACATTCTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
1629 1736 2.292323 ACATTCTACTCCCTCCGTTCCT 60.292 50.000 0.00 0.00 0.00 3.36
1630 1737 3.053095 ACATTCTACTCCCTCCGTTCCTA 60.053 47.826 0.00 0.00 0.00 2.94
1631 1738 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
1632 1739 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
1633 1740 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
1634 1741 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
1635 1742 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
1636 1743 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
1637 1744 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1638 1745 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1639 1746 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1640 1747 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1641 1748 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1642 1749 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1643 1750 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1644 1751 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
1645 1752 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
1646 1753 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
1647 1754 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
1648 1755 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
1659 1766 8.833231 ATTTGTCTTTCTAGAGATTTCGACAA 57.167 30.769 10.14 10.14 38.08 3.18
1660 1767 7.875316 TTGTCTTTCTAGAGATTTCGACAAG 57.125 36.000 10.14 1.62 35.84 3.16
1661 1768 6.982852 TGTCTTTCTAGAGATTTCGACAAGT 58.017 36.000 0.00 0.00 0.00 3.16
1662 1769 6.863645 TGTCTTTCTAGAGATTTCGACAAGTG 59.136 38.462 0.00 0.00 0.00 3.16
1663 1770 7.085116 GTCTTTCTAGAGATTTCGACAAGTGA 58.915 38.462 0.00 0.00 0.00 3.41
1664 1771 7.061326 GTCTTTCTAGAGATTTCGACAAGTGAC 59.939 40.741 0.00 0.00 0.00 3.67
1665 1772 6.576662 TTCTAGAGATTTCGACAAGTGACT 57.423 37.500 0.00 0.00 0.00 3.41
1666 1773 7.683437 TTCTAGAGATTTCGACAAGTGACTA 57.317 36.000 0.00 0.00 0.00 2.59
1667 1774 7.074507 TCTAGAGATTTCGACAAGTGACTAC 57.925 40.000 0.00 0.00 0.00 2.73
1668 1775 5.707242 AGAGATTTCGACAAGTGACTACA 57.293 39.130 0.00 0.00 0.00 2.74
1669 1776 6.274157 AGAGATTTCGACAAGTGACTACAT 57.726 37.500 0.00 0.00 0.00 2.29
1670 1777 7.392494 AGAGATTTCGACAAGTGACTACATA 57.608 36.000 0.00 0.00 0.00 2.29
1671 1778 7.251994 AGAGATTTCGACAAGTGACTACATAC 58.748 38.462 0.00 0.00 0.00 2.39
1672 1779 6.920817 AGATTTCGACAAGTGACTACATACA 58.079 36.000 0.00 0.00 0.00 2.29
1673 1780 7.030165 AGATTTCGACAAGTGACTACATACAG 58.970 38.462 0.00 0.00 0.00 2.74
1674 1781 5.952526 TTCGACAAGTGACTACATACAGA 57.047 39.130 0.00 0.00 0.00 3.41
1675 1782 5.547181 TCGACAAGTGACTACATACAGAG 57.453 43.478 0.00 0.00 0.00 3.35
1676 1783 4.099120 CGACAAGTGACTACATACAGAGC 58.901 47.826 0.00 0.00 0.00 4.09
1677 1784 4.379499 CGACAAGTGACTACATACAGAGCA 60.379 45.833 0.00 0.00 0.00 4.26
1678 1785 5.468540 ACAAGTGACTACATACAGAGCAA 57.531 39.130 0.00 0.00 0.00 3.91
1679 1786 5.853936 ACAAGTGACTACATACAGAGCAAA 58.146 37.500 0.00 0.00 0.00 3.68
1680 1787 6.288294 ACAAGTGACTACATACAGAGCAAAA 58.712 36.000 0.00 0.00 0.00 2.44
1681 1788 6.936900 ACAAGTGACTACATACAGAGCAAAAT 59.063 34.615 0.00 0.00 0.00 1.82
1682 1789 6.974932 AGTGACTACATACAGAGCAAAATG 57.025 37.500 0.00 0.00 0.00 2.32
1683 1790 6.701340 AGTGACTACATACAGAGCAAAATGA 58.299 36.000 0.00 0.00 0.00 2.57
1684 1791 6.815641 AGTGACTACATACAGAGCAAAATGAG 59.184 38.462 0.00 0.00 0.00 2.90
1685 1792 6.591834 GTGACTACATACAGAGCAAAATGAGT 59.408 38.462 0.00 0.00 0.00 3.41
1686 1793 6.591448 TGACTACATACAGAGCAAAATGAGTG 59.409 38.462 0.00 0.00 0.00 3.51
1687 1794 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
1688 1795 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
1689 1796 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
1690 1797 7.081526 ACATACAGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.00 0.00 2.52
1691 1798 6.883217 ACATACAGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.00 0.00 2.40
1692 1799 8.043113 ACATACAGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.00 0.00 1.98
1693 1800 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
1694 1801 5.349817 ACAGAGCAAAATGAGTGAATCTACG 59.650 40.000 0.00 0.00 0.00 3.51
1695 1802 4.331168 AGAGCAAAATGAGTGAATCTACGC 59.669 41.667 0.00 0.00 0.00 4.42
1696 1803 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
1697 1804 4.331168 AGCAAAATGAGTGAATCTACGCTC 59.669 41.667 0.00 0.00 44.55 5.03
1698 1805 4.331168 GCAAAATGAGTGAATCTACGCTCT 59.669 41.667 0.00 0.00 44.58 4.09
1699 1806 5.520288 GCAAAATGAGTGAATCTACGCTCTA 59.480 40.000 0.00 0.00 44.58 2.43
1700 1807 6.036083 GCAAAATGAGTGAATCTACGCTCTAA 59.964 38.462 0.00 0.00 44.58 2.10
1701 1808 7.413000 GCAAAATGAGTGAATCTACGCTCTAAA 60.413 37.037 0.00 0.00 44.58 1.85
1702 1809 8.443160 CAAAATGAGTGAATCTACGCTCTAAAA 58.557 33.333 0.00 0.00 44.58 1.52
1703 1810 8.723942 AAATGAGTGAATCTACGCTCTAAAAT 57.276 30.769 0.00 0.00 44.58 1.82
1704 1811 9.817809 AAATGAGTGAATCTACGCTCTAAAATA 57.182 29.630 0.00 0.00 44.58 1.40
1705 1812 9.988815 AATGAGTGAATCTACGCTCTAAAATAT 57.011 29.630 0.00 0.00 44.58 1.28
1706 1813 8.803201 TGAGTGAATCTACGCTCTAAAATATG 57.197 34.615 0.00 0.00 44.58 1.78
1707 1814 8.414003 TGAGTGAATCTACGCTCTAAAATATGT 58.586 33.333 0.00 0.00 44.58 2.29
1708 1815 8.804688 AGTGAATCTACGCTCTAAAATATGTC 57.195 34.615 0.00 0.00 0.00 3.06
1709 1816 8.634444 AGTGAATCTACGCTCTAAAATATGTCT 58.366 33.333 0.00 0.00 0.00 3.41
1710 1817 9.894783 GTGAATCTACGCTCTAAAATATGTCTA 57.105 33.333 0.00 0.00 0.00 2.59
1728 1835 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
1730 1837 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
1731 1838 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
1732 1839 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
1733 1840 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
1734 1841 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
1735 1842 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
1736 1843 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
1737 1844 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
1738 1845 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
1739 1846 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
1740 1847 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
1741 1848 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
1742 1849 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
1743 1850 6.094881 CCGTATGTGGTAGTCCATTTGAAATT 59.905 38.462 0.00 0.00 46.20 1.82
1744 1851 7.362574 CCGTATGTGGTAGTCCATTTGAAATTT 60.363 37.037 0.00 0.00 46.20 1.82
1745 1852 7.696453 CGTATGTGGTAGTCCATTTGAAATTTC 59.304 37.037 11.41 11.41 46.20 2.17
1746 1853 7.781324 ATGTGGTAGTCCATTTGAAATTTCT 57.219 32.000 18.64 0.00 46.20 2.52
1747 1854 8.877864 ATGTGGTAGTCCATTTGAAATTTCTA 57.122 30.769 18.64 8.95 46.20 2.10
1748 1855 8.698973 TGTGGTAGTCCATTTGAAATTTCTAA 57.301 30.769 18.64 17.10 46.20 2.10
1749 1856 9.137459 TGTGGTAGTCCATTTGAAATTTCTAAA 57.863 29.630 18.64 15.99 46.20 1.85
1750 1857 9.974980 GTGGTAGTCCATTTGAAATTTCTAAAA 57.025 29.630 18.64 11.98 46.20 1.52
1773 1880 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
1774 1881 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1775 1882 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1776 1883 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1896 2163 8.279970 TCTTACATAAGTACTTACGGCAGTTA 57.720 34.615 17.45 5.37 34.93 2.24
1928 2201 7.904461 CCTTGTTGATTGTTTCATTGTTTGTTC 59.096 33.333 0.00 0.00 33.34 3.18
1934 2207 6.746104 TTGTTTCATTGTTTGTTCGCATAG 57.254 33.333 0.00 0.00 0.00 2.23
2069 2342 8.605746 TGCGTGTTAACTATTGTTTATGTATCC 58.394 33.333 7.22 0.00 37.59 2.59
2263 2541 9.262358 CTTTCTACAGTTAGCATAATCCCTTAC 57.738 37.037 0.00 0.00 0.00 2.34
2352 2630 4.346418 TGTGGGCTTGAAATAAACAATGGT 59.654 37.500 0.00 0.00 0.00 3.55
2380 2658 8.729805 TTCTTTTTGCAGGTTATTTGTTTGAT 57.270 26.923 0.00 0.00 0.00 2.57
2469 5616 2.135933 GCTCGTGCTAGGCGATAAATT 58.864 47.619 1.41 0.00 37.74 1.82
2474 5621 4.033587 TCGTGCTAGGCGATAAATTTTGTC 59.966 41.667 0.00 0.00 33.09 3.18
2541 5688 6.436843 AATTCTTCCTTGCTTATGTTACCG 57.563 37.500 0.00 0.00 0.00 4.02
2791 5942 4.308526 TCTGTTTGGTGGGCATATTACA 57.691 40.909 0.00 0.00 0.00 2.41
2893 6044 4.393062 AGATAAGCAATGTTCTGTTCGGTG 59.607 41.667 0.00 0.00 0.00 4.94
3068 6219 4.278310 TGACTCTCGATCCATGTTCCTTA 58.722 43.478 0.00 0.00 0.00 2.69
3080 6231 0.250166 GTTCCTTAGTGTGTGGGCGT 60.250 55.000 0.00 0.00 0.00 5.68
3375 16141 1.146930 GCATGGGAGGATTCGAGCA 59.853 57.895 0.00 0.00 0.00 4.26
3392 16158 1.445095 CAGAGGAGGAAGATGGCGG 59.555 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 8.200792 AGAGCATTAACTAAAGTGTGGATCTAG 58.799 37.037 0.00 0.00 0.00 2.43
146 154 9.304731 ACGTTTTAGTATCGTTTGCTAATGATA 57.695 29.630 15.89 15.89 39.91 2.15
166 174 5.545658 AATGACGAGCATATCAACGTTTT 57.454 34.783 0.00 0.00 39.04 2.43
224 232 6.515272 ACCAATGTGAAAAGGCTATTACAG 57.485 37.500 0.00 0.00 0.00 2.74
225 233 8.465999 CATTACCAATGTGAAAAGGCTATTACA 58.534 33.333 0.00 0.00 34.18 2.41
226 234 7.435192 GCATTACCAATGTGAAAAGGCTATTAC 59.565 37.037 0.00 0.00 41.01 1.89
227 235 7.341769 AGCATTACCAATGTGAAAAGGCTATTA 59.658 33.333 0.00 0.00 41.01 0.98
228 236 6.155049 AGCATTACCAATGTGAAAAGGCTATT 59.845 34.615 0.00 0.00 41.01 1.73
229 237 5.658190 AGCATTACCAATGTGAAAAGGCTAT 59.342 36.000 0.00 0.00 41.01 2.97
230 238 5.016173 AGCATTACCAATGTGAAAAGGCTA 58.984 37.500 0.00 0.00 41.01 3.93
231 239 3.834231 AGCATTACCAATGTGAAAAGGCT 59.166 39.130 1.24 0.00 41.01 4.58
232 240 3.928375 CAGCATTACCAATGTGAAAAGGC 59.072 43.478 1.24 0.00 41.01 4.35
377 389 7.054124 TGTCATCTATGAGGTTAAAATGGACC 58.946 38.462 0.00 0.00 37.51 4.46
799 813 1.202830 ACCACTCCACCAATAAACGCA 60.203 47.619 0.00 0.00 0.00 5.24
827 922 4.263156 CCTTAACTGCCCACTGTTAGGTAA 60.263 45.833 0.00 0.00 40.12 2.85
858 953 2.124312 AGGGCTAAAGGGGGACGT 59.876 61.111 0.00 0.00 0.00 4.34
995 1094 1.522668 CTCAAAACCAGTCATCCGCA 58.477 50.000 0.00 0.00 0.00 5.69
1087 1188 7.693969 AGTCTTAATGAGGAACAAGGAATTG 57.306 36.000 0.00 0.00 0.00 2.32
1149 1250 5.647658 TGTAAAGATGCACCAGGTCAAATAG 59.352 40.000 0.00 0.00 0.00 1.73
1179 1280 6.530120 TGTGGCTCATAAGAACTAACAGAAA 58.470 36.000 0.00 0.00 0.00 2.52
1187 1288 4.472833 AGGAAGATGTGGCTCATAAGAACT 59.527 41.667 1.43 0.00 36.83 3.01
1260 1361 1.300620 CGTGCAAGTTCCCGTCTGA 60.301 57.895 0.00 0.00 0.00 3.27
1261 1362 0.319211 TACGTGCAAGTTCCCGTCTG 60.319 55.000 11.38 0.00 34.95 3.51
1532 1634 1.593787 CAGAGAAGGCTTCGGCAGA 59.406 57.895 20.78 0.00 43.96 4.26
1538 1640 2.015587 CTTCATGGCAGAGAAGGCTTC 58.984 52.381 19.53 19.53 38.03 3.86
1617 1724 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1618 1725 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1619 1726 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1620 1727 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1621 1728 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1622 1729 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1633 1740 9.923143 TTGTCGAAATCTCTAGAAAGACAAATA 57.077 29.630 15.51 2.34 42.14 1.40
1634 1741 8.833231 TTGTCGAAATCTCTAGAAAGACAAAT 57.167 30.769 15.51 0.00 42.14 2.32
1635 1742 7.926555 ACTTGTCGAAATCTCTAGAAAGACAAA 59.073 33.333 17.13 8.26 43.67 2.83
1636 1743 7.382488 CACTTGTCGAAATCTCTAGAAAGACAA 59.618 37.037 16.28 16.28 42.63 3.18
1637 1744 6.863645 CACTTGTCGAAATCTCTAGAAAGACA 59.136 38.462 0.00 1.29 35.86 3.41
1638 1745 7.061326 GTCACTTGTCGAAATCTCTAGAAAGAC 59.939 40.741 0.00 0.00 0.00 3.01
1639 1746 7.040340 AGTCACTTGTCGAAATCTCTAGAAAGA 60.040 37.037 0.00 0.00 0.00 2.52
1640 1747 7.087639 AGTCACTTGTCGAAATCTCTAGAAAG 58.912 38.462 0.00 0.00 0.00 2.62
1641 1748 6.982852 AGTCACTTGTCGAAATCTCTAGAAA 58.017 36.000 0.00 0.00 0.00 2.52
1642 1749 6.576662 AGTCACTTGTCGAAATCTCTAGAA 57.423 37.500 0.00 0.00 0.00 2.10
1643 1750 6.653740 TGTAGTCACTTGTCGAAATCTCTAGA 59.346 38.462 0.00 0.00 0.00 2.43
1644 1751 6.843208 TGTAGTCACTTGTCGAAATCTCTAG 58.157 40.000 0.00 0.00 0.00 2.43
1645 1752 6.812879 TGTAGTCACTTGTCGAAATCTCTA 57.187 37.500 0.00 0.00 0.00 2.43
1646 1753 5.707242 TGTAGTCACTTGTCGAAATCTCT 57.293 39.130 0.00 0.00 0.00 3.10
1647 1754 7.027760 TGTATGTAGTCACTTGTCGAAATCTC 58.972 38.462 0.00 0.00 0.00 2.75
1648 1755 6.920817 TGTATGTAGTCACTTGTCGAAATCT 58.079 36.000 0.00 0.00 0.00 2.40
1649 1756 7.027760 TCTGTATGTAGTCACTTGTCGAAATC 58.972 38.462 0.00 0.00 0.00 2.17
1650 1757 6.920817 TCTGTATGTAGTCACTTGTCGAAAT 58.079 36.000 0.00 0.00 0.00 2.17
1651 1758 6.321848 TCTGTATGTAGTCACTTGTCGAAA 57.678 37.500 0.00 0.00 0.00 3.46
1652 1759 5.619309 GCTCTGTATGTAGTCACTTGTCGAA 60.619 44.000 0.00 0.00 0.00 3.71
1653 1760 4.142665 GCTCTGTATGTAGTCACTTGTCGA 60.143 45.833 0.00 0.00 0.00 4.20
1654 1761 4.099120 GCTCTGTATGTAGTCACTTGTCG 58.901 47.826 0.00 0.00 0.00 4.35
1655 1762 5.060662 TGCTCTGTATGTAGTCACTTGTC 57.939 43.478 0.00 0.00 0.00 3.18
1656 1763 5.468540 TTGCTCTGTATGTAGTCACTTGT 57.531 39.130 0.00 0.00 0.00 3.16
1657 1764 6.785488 TTTTGCTCTGTATGTAGTCACTTG 57.215 37.500 0.00 0.00 0.00 3.16
1658 1765 7.161404 TCATTTTGCTCTGTATGTAGTCACTT 58.839 34.615 0.00 0.00 0.00 3.16
1659 1766 6.701340 TCATTTTGCTCTGTATGTAGTCACT 58.299 36.000 0.00 0.00 0.00 3.41
1660 1767 6.591834 ACTCATTTTGCTCTGTATGTAGTCAC 59.408 38.462 0.00 0.00 0.00 3.67
1661 1768 6.591448 CACTCATTTTGCTCTGTATGTAGTCA 59.409 38.462 0.00 0.00 0.00 3.41
1662 1769 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
1663 1770 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
1664 1771 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
1665 1772 8.043113 AGATTCACTCATTTTGCTCTGTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
1666 1773 6.883217 AGATTCACTCATTTTGCTCTGTATGT 59.117 34.615 0.00 0.00 0.00 2.29
1667 1774 7.317842 AGATTCACTCATTTTGCTCTGTATG 57.682 36.000 0.00 0.00 0.00 2.39
1668 1775 7.223582 CGTAGATTCACTCATTTTGCTCTGTAT 59.776 37.037 0.00 0.00 0.00 2.29
1669 1776 6.531594 CGTAGATTCACTCATTTTGCTCTGTA 59.468 38.462 0.00 0.00 0.00 2.74
1670 1777 5.349817 CGTAGATTCACTCATTTTGCTCTGT 59.650 40.000 0.00 0.00 0.00 3.41
1671 1778 5.726138 GCGTAGATTCACTCATTTTGCTCTG 60.726 44.000 0.00 0.00 0.00 3.35
1672 1779 4.331168 GCGTAGATTCACTCATTTTGCTCT 59.669 41.667 0.00 0.00 0.00 4.09
1673 1780 4.331168 AGCGTAGATTCACTCATTTTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
1674 1781 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
1675 1782 4.331168 AGAGCGTAGATTCACTCATTTTGC 59.669 41.667 0.00 0.00 0.00 3.68
1676 1783 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
1677 1784 8.547967 TTTTAGAGCGTAGATTCACTCATTTT 57.452 30.769 0.00 0.00 0.00 1.82
1678 1785 8.723942 ATTTTAGAGCGTAGATTCACTCATTT 57.276 30.769 0.00 0.00 0.00 2.32
1679 1786 9.988815 ATATTTTAGAGCGTAGATTCACTCATT 57.011 29.630 0.00 0.00 0.00 2.57
1680 1787 9.416794 CATATTTTAGAGCGTAGATTCACTCAT 57.583 33.333 0.00 0.00 0.00 2.90
1681 1788 8.414003 ACATATTTTAGAGCGTAGATTCACTCA 58.586 33.333 0.00 0.00 0.00 3.41
1682 1789 8.804688 ACATATTTTAGAGCGTAGATTCACTC 57.195 34.615 0.00 0.00 0.00 3.51
1683 1790 8.634444 AGACATATTTTAGAGCGTAGATTCACT 58.366 33.333 0.00 0.00 0.00 3.41
1684 1791 8.804688 AGACATATTTTAGAGCGTAGATTCAC 57.195 34.615 0.00 0.00 0.00 3.18
1702 1809 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
1704 1811 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
1705 1812 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
1706 1813 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
1707 1814 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
1708 1815 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
1709 1816 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
1710 1817 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
1711 1818 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
1712 1819 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
1713 1820 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
1747 1854 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
1748 1855 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
1749 1856 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1750 1857 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1751 1858 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1752 1859 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1753 1860 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1754 1861 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1755 1862 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1756 1863 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
1757 1864 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1758 1865 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1759 1866 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1760 1867 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1761 1868 4.803329 ATACTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
1762 1869 4.414846 AGAATACTACTCCCTCCGTTCCTA 59.585 45.833 0.00 0.00 0.00 2.94
1763 1870 3.204831 AGAATACTACTCCCTCCGTTCCT 59.795 47.826 0.00 0.00 0.00 3.36
1764 1871 3.564264 AGAATACTACTCCCTCCGTTCC 58.436 50.000 0.00 0.00 0.00 3.62
1765 1872 6.374053 GGTATAGAATACTACTCCCTCCGTTC 59.626 46.154 0.00 0.00 0.00 3.95
1766 1873 6.045341 AGGTATAGAATACTACTCCCTCCGTT 59.955 42.308 0.00 0.00 0.00 4.44
1767 1874 5.551189 AGGTATAGAATACTACTCCCTCCGT 59.449 44.000 0.00 0.00 0.00 4.69
1768 1875 5.881443 CAGGTATAGAATACTACTCCCTCCG 59.119 48.000 0.00 0.00 0.00 4.63
1769 1876 7.030234 TCAGGTATAGAATACTACTCCCTCC 57.970 44.000 0.00 0.00 0.00 4.30
1770 1877 9.617523 GTATCAGGTATAGAATACTACTCCCTC 57.382 40.741 0.00 0.00 0.00 4.30
1771 1878 9.354108 AGTATCAGGTATAGAATACTACTCCCT 57.646 37.037 0.00 0.00 0.00 4.20
1772 1879 9.978336 AAGTATCAGGTATAGAATACTACTCCC 57.022 37.037 0.00 0.00 0.00 4.30
1928 2201 4.033358 CAGTAAGAACAGGAAAGCTATGCG 59.967 45.833 0.00 0.00 0.00 4.73
1934 2207 3.669536 AGCTCAGTAAGAACAGGAAAGC 58.330 45.455 0.00 0.00 0.00 3.51
2069 2342 7.134815 GCTACACTTATATTTGCAAGATGTGG 58.865 38.462 0.00 1.71 0.00 4.17
2263 2541 5.063204 TGGGATAGTGAGACACAAACAAAG 58.937 41.667 4.75 0.00 36.74 2.77
2352 2630 5.669477 ACAAATAACCTGCAAAAAGAAGCA 58.331 33.333 0.00 0.00 39.25 3.91
2469 5616 9.745880 GATATATAAGAAACTGAGACCGACAAA 57.254 33.333 0.00 0.00 0.00 2.83
2541 5688 1.474077 GTTGTCCATTCTCACCCATGC 59.526 52.381 0.00 0.00 0.00 4.06
2880 6031 1.960417 TCATTGCACCGAACAGAACA 58.040 45.000 0.00 0.00 0.00 3.18
2893 6044 4.211794 CCCAACAACAGAAAACATCATTGC 59.788 41.667 0.00 0.00 32.43 3.56
3080 6231 4.308458 CACTCCAACCCCGCGTGA 62.308 66.667 4.92 0.00 0.00 4.35
3348 12750 0.029163 TCCTCCCATGCCCCATTCTA 60.029 55.000 0.00 0.00 0.00 2.10
3375 16141 1.764054 CCCGCCATCTTCCTCCTCT 60.764 63.158 0.00 0.00 0.00 3.69
3392 16158 4.090761 TCACCATTAAGGCTCATCATCC 57.909 45.455 0.00 0.00 43.14 3.51


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

AutoCloner maintained by Alex Coulton.