Multiple sequence alignment - TraesCS4A01G404200

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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 TraesCS4A01G404200 chr4A 100.000 2354 0 0 1 2354 677970511 677968158 0.000000e+00 4348.0
1 TraesCS4A01G404200 chr4A 91.905 1433 86 10 767 2177 677989115 677987691 0.000000e+00 1977.0
2 TraesCS4A01G404200 chr4A 90.136 1328 112 11 859 2176 677958660 677957342 0.000000e+00 1709.0
3 TraesCS4A01G404200 chr4A 86.026 229 22 4 2130 2354 677975950 677975728 1.470000e-58 237.0
4 TraesCS4A01G404200 chr4A 100.000 97 0 0 3080 3176 677967432 677967336 2.520000e-41 180.0
5 TraesCS4A01G404200 chr4A 91.398 93 8 0 3084 3176 677975501 677975409 9.250000e-26 128.0
6 TraesCS4A01G404200 chr4A 90.789 76 6 1 7 81 678016433 678016358 2.020000e-17 100.0
7 TraesCS4A01G404200 chr4A 85.938 64 4 4 2210 2268 677987643 677987580 2.640000e-06 63.9
8 TraesCS4A01G404200 chr4D 90.408 1814 123 20 567 2354 470138794 470137006 0.000000e+00 2338.0
9 TraesCS4A01G404200 chr4D 92.792 1637 74 10 652 2267 470130679 470129066 0.000000e+00 2329.0
10 TraesCS4A01G404200 chr4D 92.636 258 17 1 152 407 470131243 470130986 1.390000e-98 370.0
11 TraesCS4A01G404200 chr4D 92.593 108 5 3 4 108 470131938 470131831 5.490000e-33 152.0
12 TraesCS4A01G404200 chr4D 95.699 93 3 1 418 510 116821999 116821908 7.100000e-32 148.0
13 TraesCS4A01G404200 chr4D 92.784 97 7 0 3080 3176 470128397 470128301 1.190000e-29 141.0
14 TraesCS4A01G404200 chr4D 83.217 143 3 5 509 638 470130976 470130842 9.310000e-21 111.0
15 TraesCS4A01G404200 chr4D 98.000 50 0 1 105 153 470131814 470131765 5.640000e-13 86.1
16 TraesCS4A01G404200 chr4B 93.298 1328 78 6 853 2177 592079743 592078424 0.000000e+00 1949.0
17 TraesCS4A01G404200 chr4B 88.698 1628 116 29 582 2177 592188462 592186871 0.000000e+00 1925.0
18 TraesCS4A01G404200 chr4B 93.687 1283 79 2 965 2246 591955092 591953811 0.000000e+00 1919.0
19 TraesCS4A01G404200 chr4B 89.197 1333 120 11 859 2177 591909494 591908172 0.000000e+00 1642.0
20 TraesCS4A01G404200 chr4B 88.681 1334 123 16 859 2177 591539796 591538476 0.000000e+00 1602.0
21 TraesCS4A01G404200 chr4B 94.681 94 5 0 417 510 603516257 603516350 2.550000e-31 147.0
22 TraesCS4A01G404200 chr4B 88.158 76 8 1 7 81 592190095 592190020 4.360000e-14 89.8
23 TraesCS4A01G404200 chr6A 96.739 92 3 0 417 508 63583197 63583288 1.530000e-33 154.0
24 TraesCS4A01G404200 chr1B 94.059 101 5 1 417 516 554222429 554222529 5.490000e-33 152.0
25 TraesCS4A01G404200 chr5D 93.000 100 6 1 418 517 418431059 418431157 9.180000e-31 145.0
26 TraesCS4A01G404200 chr3B 92.857 98 7 0 415 512 736889942 736890039 3.300000e-30 143.0
27 TraesCS4A01G404200 chr3B 92.857 98 7 0 415 512 736912136 736912233 3.300000e-30 143.0
28 TraesCS4A01G404200 chr2A 92.157 102 6 2 411 511 189018840 189018940 3.300000e-30 143.0
29 TraesCS4A01G404200 chr1A 91.346 104 9 0 406 509 315264766 315264663 3.300000e-30 143.0


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 TraesCS4A01G404200 chr4A 677967336 677970511 3175 True 2264.000000 4348 100.000000 1 3176 2 chr4A.!!$R3 3175
1 TraesCS4A01G404200 chr4A 677957342 677958660 1318 True 1709.000000 1709 90.136000 859 2176 1 chr4A.!!$R1 1317
2 TraesCS4A01G404200 chr4A 677987580 677989115 1535 True 1020.450000 1977 88.921500 767 2268 2 chr4A.!!$R5 1501
3 TraesCS4A01G404200 chr4D 470137006 470138794 1788 True 2338.000000 2338 90.408000 567 2354 1 chr4D.!!$R2 1787
4 TraesCS4A01G404200 chr4D 470128301 470131938 3637 True 531.516667 2329 92.003667 4 3176 6 chr4D.!!$R3 3172
5 TraesCS4A01G404200 chr4B 592078424 592079743 1319 True 1949.000000 1949 93.298000 853 2177 1 chr4B.!!$R4 1324
6 TraesCS4A01G404200 chr4B 591953811 591955092 1281 True 1919.000000 1919 93.687000 965 2246 1 chr4B.!!$R3 1281
7 TraesCS4A01G404200 chr4B 591908172 591909494 1322 True 1642.000000 1642 89.197000 859 2177 1 chr4B.!!$R2 1318
8 TraesCS4A01G404200 chr4B 591538476 591539796 1320 True 1602.000000 1602 88.681000 859 2177 1 chr4B.!!$R1 1318
9 TraesCS4A01G404200 chr4B 592186871 592190095 3224 True 1007.400000 1925 88.428000 7 2177 2 chr4B.!!$R5 2170

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
84 86 0.110192 GCCGCTTCTCCTTCGTTTTG 60.110 55.0 0.0 0.0 0.0 2.44 F
430 1639 0.179081 GGCACATACTCCCTCCGTTC 60.179 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 2734 0.686769 GAAGCGGGAGGAGGAGGTTA 60.687 60.0 0.0 0.0 0.0 2.85 R
2286 3829 0.038526 ACCGTACCGCTTGACTTCTG 60.039 55.0 0.0 0.0 0.0 3.02 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
43 45 6.382869 AATCCTTCAAGACAAAAGTCACAG 57.617 37.500 0.00 0.00 0.00 3.66
84 86 0.110192 GCCGCTTCTCCTTCGTTTTG 60.110 55.000 0.00 0.00 0.00 2.44
89 91 4.083484 CCGCTTCTCCTTCGTTTTGTTTAT 60.083 41.667 0.00 0.00 0.00 1.40
91 93 5.564127 CGCTTCTCCTTCGTTTTGTTTATTC 59.436 40.000 0.00 0.00 0.00 1.75
94 98 7.113544 GCTTCTCCTTCGTTTTGTTTATTCAAG 59.886 37.037 0.00 0.00 0.00 3.02
109 138 9.162764 TGTTTATTCAAGAAAGGAGTATGTAGC 57.837 33.333 0.00 0.00 0.00 3.58
110 139 9.384764 GTTTATTCAAGAAAGGAGTATGTAGCT 57.615 33.333 0.00 0.00 0.00 3.32
230 1421 4.745125 CGTCAAAATCGCTATAGTGATGGT 59.255 41.667 25.60 15.71 43.75 3.55
249 1440 8.454106 GTGATGGTAGGCTAAAAATATATGCAG 58.546 37.037 0.00 0.00 0.00 4.41
314 1523 2.742116 GGGCCCACTCGCTAATGGA 61.742 63.158 19.95 0.00 38.34 3.41
344 1553 1.745264 CTCGGCCTCTCTTCCATCC 59.255 63.158 0.00 0.00 0.00 3.51
349 1558 1.826024 CCTCTCTTCCATCCCCACG 59.174 63.158 0.00 0.00 0.00 4.94
350 1559 1.690219 CCTCTCTTCCATCCCCACGG 61.690 65.000 0.00 0.00 0.00 4.94
376 1585 3.694566 GGTGAGGGACCATGTGAATTTAC 59.305 47.826 0.00 0.00 45.34 2.01
391 1600 4.517075 TGAATTTACTTTCATGCCACACGA 59.483 37.500 0.00 0.00 30.82 4.35
403 1612 5.877564 TCATGCCACACGATTTCATAAGTTA 59.122 36.000 0.00 0.00 0.00 2.24
407 1616 5.727791 GCCACACGATTTCATAAGTTAGCAG 60.728 44.000 0.00 0.00 0.00 4.24
408 1617 5.351465 CCACACGATTTCATAAGTTAGCAGT 59.649 40.000 0.00 0.00 0.00 4.40
409 1618 6.128282 CCACACGATTTCATAAGTTAGCAGTT 60.128 38.462 0.00 0.00 0.00 3.16
410 1619 7.298122 CACACGATTTCATAAGTTAGCAGTTT 58.702 34.615 0.00 0.00 0.00 2.66
412 1621 6.742718 CACGATTTCATAAGTTAGCAGTTTGG 59.257 38.462 0.00 0.00 0.00 3.28
414 1623 6.588719 ATTTCATAAGTTAGCAGTTTGGCA 57.411 33.333 0.00 0.00 35.83 4.92
415 1624 5.371115 TTCATAAGTTAGCAGTTTGGCAC 57.629 39.130 0.00 0.00 35.83 5.01
416 1625 4.393834 TCATAAGTTAGCAGTTTGGCACA 58.606 39.130 0.00 0.00 35.83 4.57
417 1626 5.009631 TCATAAGTTAGCAGTTTGGCACAT 58.990 37.500 0.00 0.00 39.30 3.21
418 1627 6.176896 TCATAAGTTAGCAGTTTGGCACATA 58.823 36.000 0.00 0.00 39.30 2.29
419 1628 4.766404 AAGTTAGCAGTTTGGCACATAC 57.234 40.909 0.00 0.00 40.56 2.39
426 1635 1.751437 GTTTGGCACATACTCCCTCC 58.249 55.000 0.00 0.00 39.30 4.30
427 1636 0.251916 TTTGGCACATACTCCCTCCG 59.748 55.000 0.00 0.00 39.30 4.63
428 1637 0.907704 TTGGCACATACTCCCTCCGT 60.908 55.000 0.00 0.00 39.30 4.69
429 1638 0.907704 TGGCACATACTCCCTCCGTT 60.908 55.000 0.00 0.00 0.00 4.44
430 1639 0.179081 GGCACATACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
431 1640 0.179081 GCACATACTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
432 1641 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
433 1642 1.553248 CACATACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
434 1643 2.027561 CACATACTCCCTCCGTTCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
435 1644 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
436 1645 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
437 1646 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
438 1647 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
439 1648 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
440 1649 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
441 1650 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
442 1651 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
443 1652 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
444 1653 4.757149 CCCTCCGTTCCAAAATAGATGATC 59.243 45.833 0.00 0.00 0.00 2.92
445 1654 4.757149 CCTCCGTTCCAAAATAGATGATCC 59.243 45.833 0.00 0.00 0.00 3.36
446 1655 5.366482 TCCGTTCCAAAATAGATGATCCA 57.634 39.130 0.00 0.00 0.00 3.41
447 1656 5.750524 TCCGTTCCAAAATAGATGATCCAA 58.249 37.500 0.00 0.00 0.00 3.53
448 1657 5.588648 TCCGTTCCAAAATAGATGATCCAAC 59.411 40.000 0.00 0.00 0.00 3.77
449 1658 5.590259 CCGTTCCAAAATAGATGATCCAACT 59.410 40.000 0.00 0.00 0.00 3.16
450 1659 6.095440 CCGTTCCAAAATAGATGATCCAACTT 59.905 38.462 0.00 0.00 0.00 2.66
451 1660 7.362920 CCGTTCCAAAATAGATGATCCAACTTT 60.363 37.037 0.00 0.00 0.00 2.66
452 1661 8.673711 CGTTCCAAAATAGATGATCCAACTTTA 58.326 33.333 0.00 0.00 0.00 1.85
476 1685 9.715121 TTATACTAAAGTCAGTACAAAGTTGGG 57.285 33.333 0.00 0.00 33.94 4.12
477 1686 5.997843 ACTAAAGTCAGTACAAAGTTGGGT 58.002 37.500 0.00 0.00 0.00 4.51
478 1687 6.053650 ACTAAAGTCAGTACAAAGTTGGGTC 58.946 40.000 0.00 0.00 0.00 4.46
479 1688 4.497291 AAGTCAGTACAAAGTTGGGTCA 57.503 40.909 0.00 0.00 0.00 4.02
480 1689 4.706842 AGTCAGTACAAAGTTGGGTCAT 57.293 40.909 0.00 0.00 0.00 3.06
481 1690 4.642429 AGTCAGTACAAAGTTGGGTCATC 58.358 43.478 0.00 0.00 0.00 2.92
482 1691 4.348168 AGTCAGTACAAAGTTGGGTCATCT 59.652 41.667 0.00 0.00 0.00 2.90
483 1692 5.542635 AGTCAGTACAAAGTTGGGTCATCTA 59.457 40.000 0.00 0.00 0.00 1.98
484 1693 6.213600 AGTCAGTACAAAGTTGGGTCATCTAT 59.786 38.462 0.00 0.00 0.00 1.98
485 1694 6.879458 GTCAGTACAAAGTTGGGTCATCTATT 59.121 38.462 0.00 0.00 0.00 1.73
486 1695 7.390718 GTCAGTACAAAGTTGGGTCATCTATTT 59.609 37.037 0.00 0.00 0.00 1.40
487 1696 7.942341 TCAGTACAAAGTTGGGTCATCTATTTT 59.058 33.333 0.00 0.00 0.00 1.82
488 1697 8.023128 CAGTACAAAGTTGGGTCATCTATTTTG 58.977 37.037 0.00 0.00 0.00 2.44
489 1698 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
490 1699 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
491 1700 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
492 1701 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
493 1702 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
494 1703 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
495 1704 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
496 1705 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
497 1706 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
498 1707 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
499 1708 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
500 1709 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
501 1710 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
502 1711 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
503 1712 5.974108 TCTATTTTGAAACGGAGGGAGTAG 58.026 41.667 0.00 0.00 0.00 2.57
504 1713 4.903045 ATTTTGAAACGGAGGGAGTAGA 57.097 40.909 0.00 0.00 0.00 2.59
505 1714 4.903045 TTTTGAAACGGAGGGAGTAGAT 57.097 40.909 0.00 0.00 0.00 1.98
506 1715 3.887621 TTGAAACGGAGGGAGTAGATG 57.112 47.619 0.00 0.00 0.00 2.90
507 1716 1.480954 TGAAACGGAGGGAGTAGATGC 59.519 52.381 0.00 0.00 0.00 3.91
537 1746 2.355946 GCTCGGAGGCCAGATATGA 58.644 57.895 5.01 0.00 0.00 2.15
565 1787 4.404640 TCTAATAGTGACTCATACGGGGG 58.595 47.826 0.00 0.00 0.00 5.40
634 1857 7.319646 TGATGGTTATTATGAAGTTTTGGTGC 58.680 34.615 0.00 0.00 0.00 5.01
657 2028 6.826612 GCTTTTAGCAACTCTTCTCTTACAG 58.173 40.000 0.00 0.00 41.89 2.74
668 2039 7.846066 ACTCTTCTCTTACAGATAGCAAACAT 58.154 34.615 0.00 0.00 0.00 2.71
669 2040 7.763528 ACTCTTCTCTTACAGATAGCAAACATG 59.236 37.037 0.00 0.00 0.00 3.21
670 2041 7.840931 TCTTCTCTTACAGATAGCAAACATGA 58.159 34.615 0.00 0.00 0.00 3.07
672 2043 9.107177 CTTCTCTTACAGATAGCAAACATGAAT 57.893 33.333 0.00 0.00 0.00 2.57
709 2088 6.101650 TGTAGATGAACGCAAGATATGGAT 57.898 37.500 0.00 0.00 43.62 3.41
762 2144 4.093408 CGCTTCGGGACAAATATATCATGG 59.907 45.833 0.00 0.00 0.00 3.66
763 2145 5.003804 GCTTCGGGACAAATATATCATGGT 58.996 41.667 0.00 0.00 0.00 3.55
764 2146 6.170506 GCTTCGGGACAAATATATCATGGTA 58.829 40.000 0.00 0.00 0.00 3.25
765 2147 6.653320 GCTTCGGGACAAATATATCATGGTAA 59.347 38.462 0.00 0.00 0.00 2.85
808 2190 5.363939 GGAGAGCTCATTGTTAACTGCTAT 58.636 41.667 17.77 6.15 0.00 2.97
827 2209 4.642885 GCTATGTGTGTACTTCTCTCCTCT 59.357 45.833 0.00 0.00 0.00 3.69
964 2374 2.333581 TCGTGAGCGAAACTGCGA 59.666 55.556 0.00 0.00 44.92 5.10
965 2375 1.299544 TCGTGAGCGAAACTGCGAA 60.300 52.632 0.00 0.00 44.92 4.70
966 2376 0.872451 TCGTGAGCGAAACTGCGAAA 60.872 50.000 0.00 0.00 44.92 3.46
967 2377 0.449507 CGTGAGCGAAACTGCGAAAG 60.450 55.000 0.00 0.00 41.33 2.62
968 2378 0.582005 GTGAGCGAAACTGCGAAAGT 59.418 50.000 0.00 0.00 42.60 2.66
969 2379 1.790623 GTGAGCGAAACTGCGAAAGTA 59.209 47.619 0.00 0.00 38.56 2.24
970 2380 5.502563 CGTGAGCGAAACTGCGAAAGTAG 62.503 52.174 0.00 0.00 44.74 2.57
979 2389 1.136690 TGCGAAAGTAGCAGAACACG 58.863 50.000 0.00 0.00 40.01 4.49
980 2390 0.179248 GCGAAAGTAGCAGAACACGC 60.179 55.000 0.00 0.00 38.23 5.34
981 2391 1.136690 CGAAAGTAGCAGAACACGCA 58.863 50.000 0.00 0.00 0.00 5.24
982 2392 1.726791 CGAAAGTAGCAGAACACGCAT 59.273 47.619 0.00 0.00 0.00 4.73
1026 2455 1.303309 CCATAACTGCTAGTGCCAGC 58.697 55.000 0.00 0.00 42.15 4.85
1500 2929 1.816863 TTCGCTTCACGCCCTTCTCT 61.817 55.000 0.00 0.00 43.23 3.10
1548 2977 4.988598 CCGGCAGTGCTCGGTGTT 62.989 66.667 27.11 0.00 37.51 3.32
1653 3082 2.659610 GGACTCGTGCTGCCTCTT 59.340 61.111 0.00 0.00 0.00 2.85
1659 3088 0.179059 TCGTGCTGCCTCTTGTTGAA 60.179 50.000 0.00 0.00 0.00 2.69
1669 3098 2.416747 CTCTTGTTGAAGTCGCCATGA 58.583 47.619 0.00 0.00 0.00 3.07
1680 3109 4.750460 GCCATGAAGCGATACGGA 57.250 55.556 0.00 0.00 0.00 4.69
1752 3181 3.405093 GATGCAGGCCGTGATGGGA 62.405 63.158 0.00 0.00 38.63 4.37
1959 3388 2.667536 GCCGGCATCATGATCGCT 60.668 61.111 24.80 0.00 0.00 4.93
2096 3525 1.135141 CGAGAAGGTCCAGCAGAAGAG 60.135 57.143 0.00 0.00 0.00 2.85
2115 3544 4.135153 GCGGAGGCGCAGAAGAGA 62.135 66.667 10.83 0.00 34.62 3.10
2190 3638 4.441495 GCCCCTTGAAATTATTGGTGTAGC 60.441 45.833 0.00 0.00 0.00 3.58
2280 3823 8.547967 TTGTTTCATTCTAAACTAGCTAGGTG 57.452 34.615 24.35 7.73 39.57 4.00
2297 3840 2.706636 TGGCACACAGAAGTCAAGC 58.293 52.632 0.00 0.00 0.00 4.01
3126 4669 6.735678 TTTACAAGAATATGAGAAGCGCAA 57.264 33.333 11.47 0.00 0.00 4.85
3134 4677 1.167851 TGAGAAGCGCAAGGGATTTG 58.832 50.000 11.47 0.00 39.88 2.32
3135 4678 1.271325 TGAGAAGCGCAAGGGATTTGA 60.271 47.619 11.47 0.00 39.21 2.69
3170 4713 8.229811 GTCAAATTTTGATCTTTGGGCAATAAC 58.770 33.333 14.54 0.00 42.47 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.525290 AGGATTTGGTACCTTCATTTTATCTG 57.475 34.615 14.36 0.00 31.95 2.90
43 45 1.359459 GACCGAGTCATTGGAACGCC 61.359 60.000 0.00 0.00 33.61 5.68
75 77 8.850454 TCCTTTCTTGAATAAACAAAACGAAG 57.150 30.769 0.00 0.00 0.00 3.79
84 86 9.384764 AGCTACATACTCCTTTCTTGAATAAAC 57.615 33.333 0.00 0.00 0.00 2.01
89 91 6.381420 AGCTAGCTACATACTCCTTTCTTGAA 59.619 38.462 17.69 0.00 0.00 2.69
91 93 6.155475 AGCTAGCTACATACTCCTTTCTTG 57.845 41.667 17.69 0.00 0.00 3.02
94 98 5.336134 GCCTAGCTAGCTACATACTCCTTTC 60.336 48.000 20.67 0.00 0.00 2.62
108 137 6.869388 CCACTAAATTACTAAGCCTAGCTAGC 59.131 42.308 15.74 6.62 38.25 3.42
109 138 8.179509 TCCACTAAATTACTAAGCCTAGCTAG 57.820 38.462 14.20 14.20 38.25 3.42
110 139 7.255871 GCTCCACTAAATTACTAAGCCTAGCTA 60.256 40.741 0.00 0.00 38.25 3.32
111 140 6.463190 GCTCCACTAAATTACTAAGCCTAGCT 60.463 42.308 0.00 0.00 42.56 3.32
195 1385 4.027991 GCGATTTTGACGATCGACTTTTTG 59.972 41.667 24.34 6.98 46.93 2.44
201 1391 4.910456 ACTATAGCGATTTTGACGATCGAC 59.090 41.667 24.34 17.11 46.93 4.20
249 1440 7.936584 AGGCTAGAATATATAGCGATTCTGAC 58.063 38.462 13.67 8.51 45.38 3.51
344 1553 3.706373 CCCTCACCTCACCGTGGG 61.706 72.222 0.00 0.00 34.36 4.61
349 1558 1.201429 ACATGGTCCCTCACCTCACC 61.201 60.000 0.00 0.00 46.98 4.02
350 1559 0.036010 CACATGGTCCCTCACCTCAC 60.036 60.000 0.00 0.00 46.98 3.51
376 1585 3.557577 TGAAATCGTGTGGCATGAAAG 57.442 42.857 0.00 0.00 32.88 2.62
391 1600 6.015519 TGTGCCAAACTGCTAACTTATGAAAT 60.016 34.615 0.00 0.00 0.00 2.17
403 1612 1.614317 GGGAGTATGTGCCAAACTGCT 60.614 52.381 0.00 0.00 36.40 4.24
407 1616 1.751437 GGAGGGAGTATGTGCCAAAC 58.249 55.000 0.00 0.00 39.84 2.93
408 1617 0.251916 CGGAGGGAGTATGTGCCAAA 59.748 55.000 0.00 0.00 39.84 3.28
409 1618 0.907704 ACGGAGGGAGTATGTGCCAA 60.908 55.000 0.00 0.00 39.84 4.52
410 1619 0.907704 AACGGAGGGAGTATGTGCCA 60.908 55.000 0.00 0.00 39.84 4.92
412 1621 0.179081 GGAACGGAGGGAGTATGTGC 60.179 60.000 0.00 0.00 0.00 4.57
414 1623 1.946984 TTGGAACGGAGGGAGTATGT 58.053 50.000 0.00 0.00 0.00 2.29
415 1624 3.343941 TTTTGGAACGGAGGGAGTATG 57.656 47.619 0.00 0.00 0.00 2.39
416 1625 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
417 1626 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
418 1627 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
419 1628 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
420 1629 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
421 1630 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
422 1631 4.757149 GGATCATCTATTTTGGAACGGAGG 59.243 45.833 0.00 0.00 0.00 4.30
423 1632 5.368145 TGGATCATCTATTTTGGAACGGAG 58.632 41.667 0.00 0.00 0.00 4.63
424 1633 5.366482 TGGATCATCTATTTTGGAACGGA 57.634 39.130 0.00 0.00 0.00 4.69
425 1634 5.590259 AGTTGGATCATCTATTTTGGAACGG 59.410 40.000 0.00 0.00 0.00 4.44
426 1635 6.683974 AGTTGGATCATCTATTTTGGAACG 57.316 37.500 0.00 0.00 0.00 3.95
450 1659 9.715121 CCCAACTTTGTACTGACTTTAGTATAA 57.285 33.333 0.00 0.00 35.75 0.98
451 1660 8.873144 ACCCAACTTTGTACTGACTTTAGTATA 58.127 33.333 0.00 0.00 35.75 1.47
452 1661 7.742767 ACCCAACTTTGTACTGACTTTAGTAT 58.257 34.615 0.00 0.00 35.75 2.12
453 1662 7.128234 ACCCAACTTTGTACTGACTTTAGTA 57.872 36.000 0.00 0.00 32.19 1.82
454 1663 5.997843 ACCCAACTTTGTACTGACTTTAGT 58.002 37.500 0.00 0.00 34.71 2.24
455 1664 6.053005 TGACCCAACTTTGTACTGACTTTAG 58.947 40.000 0.00 0.00 0.00 1.85
456 1665 5.991861 TGACCCAACTTTGTACTGACTTTA 58.008 37.500 0.00 0.00 0.00 1.85
457 1666 4.850680 TGACCCAACTTTGTACTGACTTT 58.149 39.130 0.00 0.00 0.00 2.66
458 1667 4.497291 TGACCCAACTTTGTACTGACTT 57.503 40.909 0.00 0.00 0.00 3.01
459 1668 4.348168 AGATGACCCAACTTTGTACTGACT 59.652 41.667 0.00 0.00 0.00 3.41
460 1669 4.642429 AGATGACCCAACTTTGTACTGAC 58.358 43.478 0.00 0.00 0.00 3.51
461 1670 4.974645 AGATGACCCAACTTTGTACTGA 57.025 40.909 0.00 0.00 0.00 3.41
462 1671 7.687941 AAATAGATGACCCAACTTTGTACTG 57.312 36.000 0.00 0.00 0.00 2.74
463 1672 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
464 1673 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
465 1674 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
466 1675 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
467 1676 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
468 1677 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
469 1678 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
470 1679 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
471 1680 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
472 1681 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
473 1682 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
474 1683 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
475 1684 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
476 1685 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
477 1686 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
478 1687 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
479 1688 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
480 1689 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
481 1690 5.974108 TCTACTCCCTCCGTTTCAAAATAG 58.026 41.667 0.00 0.00 0.00 1.73
482 1691 6.346096 CATCTACTCCCTCCGTTTCAAAATA 58.654 40.000 0.00 0.00 0.00 1.40
483 1692 4.903045 TCTACTCCCTCCGTTTCAAAAT 57.097 40.909 0.00 0.00 0.00 1.82
484 1693 4.575885 CATCTACTCCCTCCGTTTCAAAA 58.424 43.478 0.00 0.00 0.00 2.44
485 1694 3.618997 GCATCTACTCCCTCCGTTTCAAA 60.619 47.826 0.00 0.00 0.00 2.69
486 1695 2.093658 GCATCTACTCCCTCCGTTTCAA 60.094 50.000 0.00 0.00 0.00 2.69
487 1696 1.480954 GCATCTACTCCCTCCGTTTCA 59.519 52.381 0.00 0.00 0.00 2.69
488 1697 1.757699 AGCATCTACTCCCTCCGTTTC 59.242 52.381 0.00 0.00 0.00 2.78
489 1698 1.867363 AGCATCTACTCCCTCCGTTT 58.133 50.000 0.00 0.00 0.00 3.60
490 1699 2.750141 TAGCATCTACTCCCTCCGTT 57.250 50.000 0.00 0.00 0.00 4.44
491 1700 2.750141 TTAGCATCTACTCCCTCCGT 57.250 50.000 0.00 0.00 0.00 4.69
492 1701 5.419155 TCATATTTAGCATCTACTCCCTCCG 59.581 44.000 0.00 0.00 0.00 4.63
493 1702 6.859112 TCATATTTAGCATCTACTCCCTCC 57.141 41.667 0.00 0.00 0.00 4.30
494 1703 7.327214 CCTTCATATTTAGCATCTACTCCCTC 58.673 42.308 0.00 0.00 0.00 4.30
495 1704 6.296145 GCCTTCATATTTAGCATCTACTCCCT 60.296 42.308 0.00 0.00 0.00 4.20
496 1705 5.877564 GCCTTCATATTTAGCATCTACTCCC 59.122 44.000 0.00 0.00 0.00 4.30
497 1706 6.706295 AGCCTTCATATTTAGCATCTACTCC 58.294 40.000 0.00 0.00 0.00 3.85
498 1707 6.529829 CGAGCCTTCATATTTAGCATCTACTC 59.470 42.308 0.00 0.00 0.00 2.59
499 1708 6.393990 CGAGCCTTCATATTTAGCATCTACT 58.606 40.000 0.00 0.00 0.00 2.57
500 1709 5.578727 CCGAGCCTTCATATTTAGCATCTAC 59.421 44.000 0.00 0.00 0.00 2.59
501 1710 5.480422 TCCGAGCCTTCATATTTAGCATCTA 59.520 40.000 0.00 0.00 0.00 1.98
502 1711 4.284490 TCCGAGCCTTCATATTTAGCATCT 59.716 41.667 0.00 0.00 0.00 2.90
503 1712 4.569943 TCCGAGCCTTCATATTTAGCATC 58.430 43.478 0.00 0.00 0.00 3.91
504 1713 4.564406 CCTCCGAGCCTTCATATTTAGCAT 60.564 45.833 0.00 0.00 0.00 3.79
505 1714 3.244215 CCTCCGAGCCTTCATATTTAGCA 60.244 47.826 0.00 0.00 0.00 3.49
506 1715 3.330267 CCTCCGAGCCTTCATATTTAGC 58.670 50.000 0.00 0.00 0.00 3.09
507 1716 3.330267 GCCTCCGAGCCTTCATATTTAG 58.670 50.000 0.00 0.00 0.00 1.85
537 1746 6.487331 CCGTATGAGTCACTATTAGAGTCCTT 59.513 42.308 0.00 0.00 35.64 3.36
672 2043 9.031360 GCGTTCATCTACAGTAGATATTTTTCA 57.969 33.333 20.72 0.53 43.41 2.69
732 2114 2.583593 GTCCCGAAGCGCTGCTAG 60.584 66.667 12.58 2.19 38.25 3.42
762 2144 7.938715 TCCGGTCTATATCTTCTGAACTTTAC 58.061 38.462 0.00 0.00 0.00 2.01
763 2145 7.997223 TCTCCGGTCTATATCTTCTGAACTTTA 59.003 37.037 0.00 0.00 0.00 1.85
764 2146 6.834451 TCTCCGGTCTATATCTTCTGAACTTT 59.166 38.462 0.00 0.00 0.00 2.66
765 2147 6.366340 TCTCCGGTCTATATCTTCTGAACTT 58.634 40.000 0.00 0.00 0.00 2.66
808 2190 4.281182 GGAAAGAGGAGAGAAGTACACACA 59.719 45.833 0.00 0.00 0.00 3.72
827 2209 3.205733 AGGTGGGTCAAACCTAAAGGAAA 59.794 43.478 2.23 0.00 46.44 3.13
922 2329 0.315251 GTTTGGAGGCTCCTGTTTGC 59.685 55.000 32.28 13.74 37.46 3.68
961 2371 0.179248 GCGTGTTCTGCTACTTTCGC 60.179 55.000 0.00 0.00 36.06 4.70
962 2372 1.136690 TGCGTGTTCTGCTACTTTCG 58.863 50.000 0.00 0.00 0.00 3.46
963 2373 5.470845 AATATGCGTGTTCTGCTACTTTC 57.529 39.130 0.00 0.00 0.00 2.62
964 2374 4.332819 GGAATATGCGTGTTCTGCTACTTT 59.667 41.667 14.18 0.00 0.00 2.66
965 2375 3.871594 GGAATATGCGTGTTCTGCTACTT 59.128 43.478 14.18 0.00 0.00 2.24
966 2376 3.458189 GGAATATGCGTGTTCTGCTACT 58.542 45.455 14.18 0.00 0.00 2.57
967 2377 2.544267 GGGAATATGCGTGTTCTGCTAC 59.456 50.000 14.18 0.00 0.00 3.58
968 2378 2.169561 TGGGAATATGCGTGTTCTGCTA 59.830 45.455 14.18 0.00 0.00 3.49
969 2379 1.065491 TGGGAATATGCGTGTTCTGCT 60.065 47.619 14.18 0.00 0.00 4.24
970 2380 1.331756 CTGGGAATATGCGTGTTCTGC 59.668 52.381 14.18 0.12 0.00 4.26
971 2381 1.331756 GCTGGGAATATGCGTGTTCTG 59.668 52.381 14.18 7.14 0.00 3.02
972 2382 1.210478 AGCTGGGAATATGCGTGTTCT 59.790 47.619 14.18 0.00 0.00 3.01
973 2383 1.331756 CAGCTGGGAATATGCGTGTTC 59.668 52.381 5.57 6.85 0.00 3.18
974 2384 1.065491 TCAGCTGGGAATATGCGTGTT 60.065 47.619 15.13 0.00 0.00 3.32
975 2385 0.541392 TCAGCTGGGAATATGCGTGT 59.459 50.000 15.13 0.00 0.00 4.49
976 2386 1.224075 CTCAGCTGGGAATATGCGTG 58.776 55.000 8.28 0.00 0.00 5.34
977 2387 0.533755 GCTCAGCTGGGAATATGCGT 60.534 55.000 20.53 0.00 0.00 5.24
978 2388 0.250209 AGCTCAGCTGGGAATATGCG 60.250 55.000 20.53 0.00 37.57 4.73
979 2389 1.878734 GAAGCTCAGCTGGGAATATGC 59.121 52.381 20.53 9.02 39.62 3.14
980 2390 3.204306 TGAAGCTCAGCTGGGAATATG 57.796 47.619 20.53 0.00 39.62 1.78
981 2391 3.498121 CCATGAAGCTCAGCTGGGAATAT 60.498 47.826 20.53 2.28 39.62 1.28
982 2392 2.158711 CCATGAAGCTCAGCTGGGAATA 60.159 50.000 20.53 0.00 39.62 1.75
1026 2455 2.890371 GCTTCTTGCATGGCTGGG 59.110 61.111 0.00 0.00 42.31 4.45
1298 2727 1.404843 GAGGAGGAGGTTAGCGATGT 58.595 55.000 0.00 0.00 0.00 3.06
1305 2734 0.686769 GAAGCGGGAGGAGGAGGTTA 60.687 60.000 0.00 0.00 0.00 2.85
1465 2894 0.737715 CGAAGCCCAACGAAGAGGAG 60.738 60.000 0.00 0.00 0.00 3.69
1500 2929 2.593148 AACATGACGGCGTTGGCA 60.593 55.556 16.19 8.40 42.47 4.92
1638 3067 0.882042 CAACAAGAGGCAGCACGAGT 60.882 55.000 0.00 0.00 0.00 4.18
1650 3079 2.542020 TCATGGCGACTTCAACAAGA 57.458 45.000 0.00 0.00 33.34 3.02
1653 3082 0.874390 GCTTCATGGCGACTTCAACA 59.126 50.000 0.00 0.00 0.00 3.33
1959 3388 2.680352 GAGACCGGCAGGAGGACA 60.680 66.667 10.86 0.00 41.02 4.02
1972 3401 1.098712 ACGGCGAGGATCTCAGAGAC 61.099 60.000 16.62 0.00 0.00 3.36
2268 3726 1.276421 CTGTGTGCCACCTAGCTAGTT 59.724 52.381 19.31 1.83 32.73 2.24
2280 3823 1.571460 CGCTTGACTTCTGTGTGCC 59.429 57.895 0.00 0.00 0.00 5.01
2286 3829 0.038526 ACCGTACCGCTTGACTTCTG 60.039 55.000 0.00 0.00 0.00 3.02
2291 3834 0.319297 ACTCAACCGTACCGCTTGAC 60.319 55.000 0.00 0.00 30.09 3.18
2297 3840 4.259530 CGCTTTATTAACTCAACCGTACCG 60.260 45.833 0.00 0.00 0.00 4.02
2303 3846 8.193250 TCTGAATACGCTTTATTAACTCAACC 57.807 34.615 0.00 0.00 0.00 3.77
3100 4643 6.371548 TGCGCTTCTCATATTCTTGTAAAACT 59.628 34.615 9.73 0.00 0.00 2.66
3108 4651 3.118261 TCCCTTGCGCTTCTCATATTCTT 60.118 43.478 9.73 0.00 0.00 2.52
3134 4677 5.474876 AGATCAAAATTTGACAGTCTGGGTC 59.525 40.000 10.91 1.67 43.48 4.46
3135 4678 5.388654 AGATCAAAATTTGACAGTCTGGGT 58.611 37.500 10.91 0.00 43.48 4.51


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

AutoCloner maintained by Alex Coulton.