Multiple sequence alignment - TraesCS7A01G543700

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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 TraesCS7A01G543700 chr7A 100.000 2351 0 0 1 2351 720574606 720576956 0.000000e+00 4342.0
1 TraesCS7A01G543700 chr5D 92.845 1160 75 4 523 1679 54750086 54751240 0.000000e+00 1676.0
2 TraesCS7A01G543700 chr5D 92.255 1162 76 8 523 1679 225859682 225860834 0.000000e+00 1635.0
3 TraesCS7A01G543700 chr5D 86.042 523 51 7 1 504 492174779 492174260 2.060000e-150 542.0
4 TraesCS7A01G543700 chr7D 92.593 1161 77 5 523 1680 589250506 589249352 0.000000e+00 1659.0
5 TraesCS7A01G543700 chr7D 92.388 1156 81 3 525 1679 262289136 262287987 0.000000e+00 1640.0
6 TraesCS7A01G543700 chr7D 96.667 60 2 0 1691 1750 624772969 624773028 1.490000e-17 100.0
7 TraesCS7A01G543700 chr2D 92.380 1168 80 4 523 1687 593127066 593128227 0.000000e+00 1655.0
8 TraesCS7A01G543700 chr2D 92.255 1162 79 6 523 1679 305960576 305959421 0.000000e+00 1637.0
9 TraesCS7A01G543700 chr2D 92.155 1160 79 5 523 1679 157032318 157033468 0.000000e+00 1628.0
10 TraesCS7A01G543700 chr2D 82.265 468 62 12 1873 2323 391864975 391864512 3.670000e-103 385.0
11 TraesCS7A01G543700 chr1D 92.414 1160 79 4 523 1679 4203863 4202710 0.000000e+00 1646.0
12 TraesCS7A01G543700 chr1D 82.201 427 58 9 1874 2286 417783673 417783251 3.720000e-93 351.0
13 TraesCS7A01G543700 chr1D 77.266 651 109 25 1730 2347 59204162 59203518 1.730000e-91 346.0
14 TraesCS7A01G543700 chr1D 79.720 429 65 13 1874 2286 417920063 417919641 8.220000e-75 291.0
15 TraesCS7A01G543700 chrUn 92.148 1159 84 3 523 1679 241760224 241759071 0.000000e+00 1629.0
16 TraesCS7A01G543700 chrUn 86.923 520 46 12 1 500 245881132 245880615 4.390000e-157 564.0
17 TraesCS7A01G543700 chrUn 86.923 520 46 12 1 500 260277787 260278304 4.390000e-157 564.0
18 TraesCS7A01G543700 chrUn 86.923 520 46 12 1 500 452206574 452206057 4.390000e-157 564.0
19 TraesCS7A01G543700 chrUn 78.233 464 76 17 1874 2323 364375062 364374610 8.280000e-70 274.0
20 TraesCS7A01G543700 chrUn 78.199 422 68 18 1874 2286 931163 930757 5.020000e-62 248.0
21 TraesCS7A01G543700 chrUn 78.484 409 66 16 1874 2273 948544 948939 5.020000e-62 248.0
22 TraesCS7A01G543700 chr4A 95.817 502 18 2 1 500 510207820 510207320 0.000000e+00 808.0
23 TraesCS7A01G543700 chr4A 95.652 46 2 0 480 525 510207286 510207241 9.010000e-10 75.0
24 TraesCS7A01G543700 chr4A 95.556 45 2 0 480 524 717012621 717012577 3.240000e-09 73.1
25 TraesCS7A01G543700 chr6A 94.821 502 23 2 1 500 576787617 576788117 0.000000e+00 780.0
26 TraesCS7A01G543700 chr2B 88.294 504 47 9 1 500 499167286 499167781 5.590000e-166 593.0
27 TraesCS7A01G543700 chr2B 88.889 63 4 1 480 539 52699585 52699523 9.010000e-10 75.0
28 TraesCS7A01G543700 chr1B 87.698 504 50 9 1 500 57503374 57502879 5.630000e-161 577.0
29 TraesCS7A01G543700 chr1B 87.205 508 48 14 1 500 128491747 128492245 1.580000e-156 562.0
30 TraesCS7A01G543700 chr1B 74.930 355 57 18 1881 2211 556062600 556062254 1.470000e-27 134.0
31 TraesCS7A01G543700 chr5A 86.957 506 46 12 1 489 346096309 346095807 3.410000e-153 551.0
32 TraesCS7A01G543700 chr7B 81.279 438 59 16 1850 2271 697238058 697237628 1.350000e-87 333.0
33 TraesCS7A01G543700 chr7B 82.973 370 52 6 1877 2237 606333896 606334263 8.100000e-85 324.0
34 TraesCS7A01G543700 chr2A 81.205 415 55 11 1900 2299 528933390 528932984 1.750000e-81 313.0
35 TraesCS7A01G543700 chr1A 77.962 422 68 18 1874 2286 514594382 514593977 8.400000e-60 241.0
36 TraesCS7A01G543700 chr3A 81.385 231 28 9 1901 2118 750717965 750717737 8.640000e-40 174.0
37 TraesCS7A01G543700 chr3A 100.000 28 0 0 494 521 700694045 700694072 4.000000e-03 52.8
38 TraesCS7A01G543700 chr3B 78.061 196 33 4 1893 2079 761848147 761848341 5.310000e-22 115.0
39 TraesCS7A01G543700 chr4B 100.000 28 0 0 494 521 657513685 657513712 4.000000e-03 52.8


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 TraesCS7A01G543700 chr7A 720574606 720576956 2350 False 4342.0 4342 100.0000 1 2351 1 chr7A.!!$F1 2350
1 TraesCS7A01G543700 chr5D 54750086 54751240 1154 False 1676.0 1676 92.8450 523 1679 1 chr5D.!!$F1 1156
2 TraesCS7A01G543700 chr5D 225859682 225860834 1152 False 1635.0 1635 92.2550 523 1679 1 chr5D.!!$F2 1156
3 TraesCS7A01G543700 chr5D 492174260 492174779 519 True 542.0 542 86.0420 1 504 1 chr5D.!!$R1 503
4 TraesCS7A01G543700 chr7D 589249352 589250506 1154 True 1659.0 1659 92.5930 523 1680 1 chr7D.!!$R2 1157
5 TraesCS7A01G543700 chr7D 262287987 262289136 1149 True 1640.0 1640 92.3880 525 1679 1 chr7D.!!$R1 1154
6 TraesCS7A01G543700 chr2D 593127066 593128227 1161 False 1655.0 1655 92.3800 523 1687 1 chr2D.!!$F2 1164
7 TraesCS7A01G543700 chr2D 305959421 305960576 1155 True 1637.0 1637 92.2550 523 1679 1 chr2D.!!$R1 1156
8 TraesCS7A01G543700 chr2D 157032318 157033468 1150 False 1628.0 1628 92.1550 523 1679 1 chr2D.!!$F1 1156
9 TraesCS7A01G543700 chr1D 4202710 4203863 1153 True 1646.0 1646 92.4140 523 1679 1 chr1D.!!$R1 1156
10 TraesCS7A01G543700 chr1D 59203518 59204162 644 True 346.0 346 77.2660 1730 2347 1 chr1D.!!$R2 617
11 TraesCS7A01G543700 chrUn 241759071 241760224 1153 True 1629.0 1629 92.1480 523 1679 1 chrUn.!!$R2 1156
12 TraesCS7A01G543700 chrUn 245880615 245881132 517 True 564.0 564 86.9230 1 500 1 chrUn.!!$R3 499
13 TraesCS7A01G543700 chrUn 260277787 260278304 517 False 564.0 564 86.9230 1 500 1 chrUn.!!$F2 499
14 TraesCS7A01G543700 chrUn 452206057 452206574 517 True 564.0 564 86.9230 1 500 1 chrUn.!!$R5 499
15 TraesCS7A01G543700 chr4A 510207241 510207820 579 True 441.5 808 95.7345 1 525 2 chr4A.!!$R2 524
16 TraesCS7A01G543700 chr6A 576787617 576788117 500 False 780.0 780 94.8210 1 500 1 chr6A.!!$F1 499
17 TraesCS7A01G543700 chr5A 346095807 346096309 502 True 551.0 551 86.9570 1 489 1 chr5A.!!$R1 488

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
562 598 0.028505 CTTTGATGATGAAGCCGGCG 59.971 55.0 23.2 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1754 0.032678 CGACGGCATCCTCAGCTTAT 59.967 55.0 0.0 0.0 0.0 1.73 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
161 162 8.518430 ACTGCTATGATGTAGATACATAGAGG 57.482 38.462 16.52 12.12 46.20 3.69
185 218 8.154856 AGGTGAACTGTGTAATGTTGTACTTAT 58.845 33.333 0.00 0.00 0.00 1.73
266 299 5.903198 AAAATGGGTTGAAAGAAATGGGA 57.097 34.783 0.00 0.00 0.00 4.37
285 318 1.594862 GATAATGTGCTCAGCCACGAC 59.405 52.381 0.00 0.00 38.55 4.34
313 346 7.931578 TTTTGTGACGGAAAATACTATCCAT 57.068 32.000 0.00 0.00 35.34 3.41
314 347 6.918892 TTGTGACGGAAAATACTATCCATG 57.081 37.500 0.00 0.00 35.34 3.66
470 504 8.978874 TGTAAGGTATGCTGTCAAATTATGAT 57.021 30.769 0.00 0.00 40.97 2.45
493 529 5.293560 TGCGATATACATGACGGATCAAAA 58.706 37.500 0.00 0.00 38.69 2.44
504 540 3.921677 ACGGATCAAAACTGTCACGTAT 58.078 40.909 0.00 0.00 0.00 3.06
505 541 4.312443 ACGGATCAAAACTGTCACGTATT 58.688 39.130 0.00 0.00 0.00 1.89
506 542 5.472148 ACGGATCAAAACTGTCACGTATTA 58.528 37.500 0.00 0.00 0.00 0.98
507 543 5.927689 ACGGATCAAAACTGTCACGTATTAA 59.072 36.000 0.00 0.00 0.00 1.40
508 544 6.128742 ACGGATCAAAACTGTCACGTATTAAC 60.129 38.462 0.00 0.00 0.00 2.01
509 545 6.128769 CGGATCAAAACTGTCACGTATTAACA 60.129 38.462 0.00 0.00 0.00 2.41
510 546 7.412563 CGGATCAAAACTGTCACGTATTAACAT 60.413 37.037 0.00 0.00 0.00 2.71
511 547 8.875803 GGATCAAAACTGTCACGTATTAACATA 58.124 33.333 0.00 0.00 0.00 2.29
519 555 9.431887 ACTGTCACGTATTAACATATTTCTTGT 57.568 29.630 0.00 0.00 0.00 3.16
539 575 1.556564 AATGTCGTAATCAGCGTCGG 58.443 50.000 0.00 0.00 0.00 4.79
552 588 1.153168 CGTCGGGGCCTTTGATGAT 60.153 57.895 0.84 0.00 0.00 2.45
562 598 0.028505 CTTTGATGATGAAGCCGGCG 59.971 55.000 23.20 0.00 0.00 6.46
563 599 0.676466 TTTGATGATGAAGCCGGCGT 60.676 50.000 23.20 20.21 0.00 5.68
564 600 1.368345 TTGATGATGAAGCCGGCGTG 61.368 55.000 22.76 0.00 0.00 5.34
565 601 2.514592 ATGATGAAGCCGGCGTGG 60.515 61.111 22.76 0.00 42.50 4.94
782 818 0.320771 GCGAAGAGACAAAGGCCAGA 60.321 55.000 5.01 0.00 0.00 3.86
822 859 1.138568 CCTGGATGGCAGAGAGGATT 58.861 55.000 2.99 0.00 0.00 3.01
867 904 1.303317 GTGTTCCGGGTTGATGGCT 60.303 57.895 0.00 0.00 0.00 4.75
884 921 3.665675 CTGGGCCGTGGACTGTAGC 62.666 68.421 0.00 0.00 0.00 3.58
893 930 0.613572 TGGACTGTAGCGATGACCCA 60.614 55.000 0.00 0.00 0.00 4.51
908 945 0.612732 ACCCACGGAGGACACGATAA 60.613 55.000 0.00 0.00 41.22 1.75
927 964 2.060050 ACGAACCATCAACAAACCCA 57.940 45.000 0.00 0.00 0.00 4.51
943 980 1.333636 CCCAAGGAGAGATCGGCTGT 61.334 60.000 0.00 0.00 0.00 4.40
990 1027 2.224209 CCAGAACAAGTAGTTGTCCGGT 60.224 50.000 16.16 0.67 46.68 5.28
991 1028 3.006110 CCAGAACAAGTAGTTGTCCGGTA 59.994 47.826 16.16 0.00 46.68 4.02
995 1032 4.877378 ACAAGTAGTTGTCCGGTATGAA 57.123 40.909 10.24 0.00 43.88 2.57
1066 1103 0.680921 GCCAGCAGCAGGGACAATTA 60.681 55.000 5.89 0.00 42.97 1.40
1070 1107 0.744414 GCAGCAGGGACAATTAGCGA 60.744 55.000 0.00 0.00 0.00 4.93
1145 1182 2.831366 CGATCGGGATCACGACCGT 61.831 63.158 26.02 9.04 44.43 4.83
1214 1251 2.443952 TGAGGTCGCCGGGATGAT 60.444 61.111 2.18 0.00 0.00 2.45
1309 1346 4.077184 GTGACGGTGGGATCGGCA 62.077 66.667 0.00 0.00 44.02 5.69
1328 1365 2.746472 GCACTGAAAATAGGGAGCCGAT 60.746 50.000 0.00 0.00 0.00 4.18
1369 1406 3.695606 GCACTGACGGAGCCAGGA 61.696 66.667 0.00 0.00 36.03 3.86
1381 1420 2.283966 CCAGGACGAGGTGGGAGT 60.284 66.667 0.00 0.00 0.00 3.85
1384 1423 1.263356 CAGGACGAGGTGGGAGTTTA 58.737 55.000 0.00 0.00 0.00 2.01
1416 1455 2.838225 CCACGCGGGGATAGACCT 60.838 66.667 27.22 0.00 38.98 3.85
1456 1495 4.849310 TAAGCGGTGATGGCGCCC 62.849 66.667 26.77 10.34 41.79 6.13
1495 1543 2.677765 TTAGGGTTTTGGTGCGGCGA 62.678 55.000 12.98 0.00 0.00 5.54
1557 1608 6.924060 AGACTCGATACCATGTAAAACATAGC 59.076 38.462 0.00 0.00 36.53 2.97
1657 1714 8.262227 CCAATAAGGTATGGTTTACACAGTAGA 58.738 37.037 0.00 0.00 31.84 2.59
1667 1724 7.544622 TGGTTTACACAGTAGAGCTACAATAG 58.455 38.462 10.04 0.56 38.48 1.73
1680 1737 8.135382 AGAGCTACAATAGGAAGTCTAACAAA 57.865 34.615 0.00 0.00 0.00 2.83
1681 1738 8.763601 AGAGCTACAATAGGAAGTCTAACAAAT 58.236 33.333 0.00 0.00 0.00 2.32
1683 1740 7.770897 AGCTACAATAGGAAGTCTAACAAATGG 59.229 37.037 0.00 0.00 0.00 3.16
1684 1741 6.759497 ACAATAGGAAGTCTAACAAATGGC 57.241 37.500 0.00 0.00 0.00 4.40
1685 1742 6.485171 ACAATAGGAAGTCTAACAAATGGCT 58.515 36.000 0.00 0.00 0.00 4.75
1686 1743 6.375455 ACAATAGGAAGTCTAACAAATGGCTG 59.625 38.462 0.00 0.00 0.00 4.85
1687 1744 4.373156 AGGAAGTCTAACAAATGGCTGT 57.627 40.909 0.00 0.00 0.00 4.40
1688 1745 5.499004 AGGAAGTCTAACAAATGGCTGTA 57.501 39.130 0.00 0.00 0.00 2.74
1689 1746 5.491982 AGGAAGTCTAACAAATGGCTGTAG 58.508 41.667 0.00 0.00 0.00 2.74
1690 1747 4.636206 GGAAGTCTAACAAATGGCTGTAGG 59.364 45.833 0.00 0.00 0.00 3.18
1691 1748 4.222124 AGTCTAACAAATGGCTGTAGGG 57.778 45.455 0.00 0.00 0.00 3.53
1692 1749 3.587506 AGTCTAACAAATGGCTGTAGGGT 59.412 43.478 0.00 0.00 0.00 4.34
1693 1750 3.939592 GTCTAACAAATGGCTGTAGGGTC 59.060 47.826 0.00 0.00 0.00 4.46
1694 1751 3.844211 TCTAACAAATGGCTGTAGGGTCT 59.156 43.478 0.00 0.00 0.00 3.85
1695 1752 5.027460 TCTAACAAATGGCTGTAGGGTCTA 58.973 41.667 0.00 0.00 0.00 2.59
1696 1753 4.862641 AACAAATGGCTGTAGGGTCTAT 57.137 40.909 0.00 0.00 0.00 1.98
1697 1754 5.968676 AACAAATGGCTGTAGGGTCTATA 57.031 39.130 0.00 0.00 0.00 1.31
1698 1755 6.515512 AACAAATGGCTGTAGGGTCTATAT 57.484 37.500 0.00 0.00 0.00 0.86
1699 1756 7.626999 AACAAATGGCTGTAGGGTCTATATA 57.373 36.000 0.00 0.00 0.00 0.86
1700 1757 7.626999 ACAAATGGCTGTAGGGTCTATATAA 57.373 36.000 0.00 0.00 0.00 0.98
1701 1758 7.680730 ACAAATGGCTGTAGGGTCTATATAAG 58.319 38.462 0.00 0.00 0.00 1.73
1702 1759 5.941555 ATGGCTGTAGGGTCTATATAAGC 57.058 43.478 0.00 0.00 0.00 3.09
1703 1760 5.011982 TGGCTGTAGGGTCTATATAAGCT 57.988 43.478 0.00 0.00 0.00 3.74
1704 1761 4.772624 TGGCTGTAGGGTCTATATAAGCTG 59.227 45.833 0.00 0.00 0.00 4.24
1705 1762 5.017490 GGCTGTAGGGTCTATATAAGCTGA 58.983 45.833 0.00 0.00 0.00 4.26
1706 1763 5.126384 GGCTGTAGGGTCTATATAAGCTGAG 59.874 48.000 0.00 0.00 0.00 3.35
1707 1764 5.126384 GCTGTAGGGTCTATATAAGCTGAGG 59.874 48.000 0.00 0.00 0.00 3.86
1708 1765 6.464530 TGTAGGGTCTATATAAGCTGAGGA 57.535 41.667 0.00 0.00 0.00 3.71
1709 1766 7.045693 TGTAGGGTCTATATAAGCTGAGGAT 57.954 40.000 0.00 0.00 0.00 3.24
1710 1767 6.892456 TGTAGGGTCTATATAAGCTGAGGATG 59.108 42.308 0.00 0.00 0.00 3.51
1711 1768 4.714308 AGGGTCTATATAAGCTGAGGATGC 59.286 45.833 0.00 0.00 0.00 3.91
1712 1769 4.141824 GGGTCTATATAAGCTGAGGATGCC 60.142 50.000 0.00 0.00 0.00 4.40
1713 1770 4.440802 GGTCTATATAAGCTGAGGATGCCG 60.441 50.000 0.00 0.00 0.00 5.69
1714 1771 4.158764 GTCTATATAAGCTGAGGATGCCGT 59.841 45.833 0.00 0.00 0.00 5.68
1715 1772 3.601443 ATATAAGCTGAGGATGCCGTC 57.399 47.619 0.00 0.00 0.00 4.79
1716 1773 0.032678 ATAAGCTGAGGATGCCGTCG 59.967 55.000 0.00 0.00 0.00 5.12
1717 1774 1.320344 TAAGCTGAGGATGCCGTCGT 61.320 55.000 0.00 0.00 0.00 4.34
1718 1775 2.564553 AAGCTGAGGATGCCGTCGTC 62.565 60.000 0.00 0.00 41.11 4.20
1719 1776 2.885113 CTGAGGATGCCGTCGTCA 59.115 61.111 8.84 8.84 46.37 4.35
1720 1777 1.517257 CTGAGGATGCCGTCGTCAC 60.517 63.158 5.24 0.00 44.39 3.67
1721 1778 2.212900 CTGAGGATGCCGTCGTCACA 62.213 60.000 5.24 0.00 44.39 3.58
1722 1779 1.517257 GAGGATGCCGTCGTCACAG 60.517 63.158 1.85 0.00 40.58 3.66
1723 1780 1.934220 GAGGATGCCGTCGTCACAGA 61.934 60.000 1.85 0.00 40.58 3.41
1724 1781 1.141881 GGATGCCGTCGTCACAGAT 59.858 57.895 0.00 0.00 0.00 2.90
1725 1782 1.148157 GGATGCCGTCGTCACAGATG 61.148 60.000 0.00 0.00 0.00 2.90
1726 1783 1.756375 GATGCCGTCGTCACAGATGC 61.756 60.000 0.00 0.00 0.00 3.91
1727 1784 2.432456 GCCGTCGTCACAGATGCA 60.432 61.111 0.00 0.00 0.00 3.96
1728 1785 2.447887 GCCGTCGTCACAGATGCAG 61.448 63.158 0.00 0.00 0.00 4.41
1734 1791 2.125952 TCACAGATGCAGCCGTCG 60.126 61.111 0.00 0.00 32.12 5.12
1746 1803 3.829044 CCGTCGGCATACGTCCCA 61.829 66.667 0.00 0.00 44.69 4.37
1751 1808 1.374885 CGGCATACGTCCCAACACA 60.375 57.895 0.00 0.00 37.93 3.72
1753 1810 0.732571 GGCATACGTCCCAACACATG 59.267 55.000 0.00 0.00 0.00 3.21
1761 1818 3.384532 CCAACACATGGCCCTGGC 61.385 66.667 13.03 0.00 43.80 4.85
1789 1846 0.035630 GGCAGACAGAAGGCTGACAT 60.036 55.000 1.84 0.00 45.17 3.06
1795 1852 5.181009 CAGACAGAAGGCTGACATCATTAA 58.819 41.667 0.00 0.00 45.17 1.40
1798 1855 7.496920 CAGACAGAAGGCTGACATCATTAAATA 59.503 37.037 0.00 0.00 45.17 1.40
1800 1857 9.494271 GACAGAAGGCTGACATCATTAAATATA 57.506 33.333 0.00 0.00 45.17 0.86
1806 1863 6.316140 GGCTGACATCATTAAATATATGCCGA 59.684 38.462 0.00 0.00 0.00 5.54
1828 1885 4.457496 CTGATGGCGGCCGACAGT 62.457 66.667 39.97 26.56 36.12 3.55
1829 1886 3.071837 TGATGGCGGCCGACAGTA 61.072 61.111 39.97 27.24 36.12 2.74
1830 1887 2.279517 GATGGCGGCCGACAGTAG 60.280 66.667 39.97 2.91 36.12 2.57
1833 1890 1.113517 ATGGCGGCCGACAGTAGTAT 61.114 55.000 39.97 19.56 36.12 2.12
1834 1891 0.466007 TGGCGGCCGACAGTAGTATA 60.466 55.000 34.62 3.71 0.00 1.47
1835 1892 0.886563 GGCGGCCGACAGTAGTATAT 59.113 55.000 33.48 0.00 0.00 0.86
1836 1893 1.135460 GGCGGCCGACAGTAGTATATC 60.135 57.143 33.48 5.54 0.00 1.63
1987 2058 9.311916 TGAATATCCACTTTGTTTCTGTTTTTG 57.688 29.630 0.00 0.00 0.00 2.44
1988 2059 9.528018 GAATATCCACTTTGTTTCTGTTTTTGA 57.472 29.630 0.00 0.00 0.00 2.69
1991 2062 8.614469 ATCCACTTTGTTTCTGTTTTTGAAAA 57.386 26.923 0.00 0.00 35.54 2.29
1992 2063 8.614469 TCCACTTTGTTTCTGTTTTTGAAAAT 57.386 26.923 0.00 0.00 35.54 1.82
1993 2064 9.712305 TCCACTTTGTTTCTGTTTTTGAAAATA 57.288 25.926 0.00 0.00 35.54 1.40
2076 2156 9.491675 TTCATACTTGCATCAATTTTGACAAAT 57.508 25.926 0.50 0.00 40.49 2.32
2122 2204 6.480524 TCTTGAAATGATTCTGTTGGTACG 57.519 37.500 0.00 0.00 36.48 3.67
2123 2205 4.678509 TGAAATGATTCTGTTGGTACGC 57.321 40.909 0.00 0.00 36.48 4.42
2124 2206 4.068599 TGAAATGATTCTGTTGGTACGCA 58.931 39.130 0.00 0.00 36.48 5.24
2127 2209 4.621068 ATGATTCTGTTGGTACGCAATG 57.379 40.909 0.97 0.00 0.00 2.82
2132 2214 4.640789 TCTGTTGGTACGCAATGTTTTT 57.359 36.364 0.97 0.00 0.00 1.94
2138 2220 7.621991 TGTTGGTACGCAATGTTTTTAAATTG 58.378 30.769 0.00 0.00 36.95 2.32
2142 2224 7.042658 TGGTACGCAATGTTTTTAAATTGGAAC 60.043 33.333 2.40 0.00 34.90 3.62
2183 2265 4.332268 GCTTCAAATTTGCAGAAAACACCA 59.668 37.500 20.11 0.00 0.00 4.17
2189 2271 4.734398 TTTGCAGAAAACACCATCTTGT 57.266 36.364 0.00 0.00 0.00 3.16
2233 2316 5.400066 TTTAGTCCTTGGCAAAATTAGGC 57.600 39.130 0.00 0.00 0.00 3.93
2300 2388 1.368641 TCTTACACATGCGATGCCAC 58.631 50.000 0.00 0.00 0.00 5.01
2305 2393 1.003476 ACATGCGATGCCACTCACA 60.003 52.632 0.00 0.00 0.00 3.58
2308 2396 1.068402 CATGCGATGCCACTCACAAAA 60.068 47.619 0.00 0.00 0.00 2.44
2314 2402 2.031258 TGCCACTCACAAAAGTTCGA 57.969 45.000 0.00 0.00 0.00 3.71
2323 2411 5.519206 ACTCACAAAAGTTCGACACTTAGAC 59.481 40.000 11.62 0.00 45.77 2.59
2324 2412 5.412640 TCACAAAAGTTCGACACTTAGACA 58.587 37.500 11.62 1.82 45.77 3.41
2328 2416 2.872732 AGTTCGACACTTAGACAGGGA 58.127 47.619 0.00 0.00 27.32 4.20
2331 2419 4.100498 AGTTCGACACTTAGACAGGGAAAA 59.900 41.667 0.00 0.00 27.32 2.29
2333 2421 3.640029 TCGACACTTAGACAGGGAAAACT 59.360 43.478 0.00 0.00 0.00 2.66
2334 2422 4.828939 TCGACACTTAGACAGGGAAAACTA 59.171 41.667 0.00 0.00 0.00 2.24
2342 2430 1.847737 ACAGGGAAAACTACCACCACA 59.152 47.619 0.00 0.00 0.00 4.17
2347 2435 3.181441 GGGAAAACTACCACCACAGGTAA 60.181 47.826 0.00 0.00 43.24 2.85
2348 2436 4.507869 GGGAAAACTACCACCACAGGTAAT 60.508 45.833 0.00 0.00 43.24 1.89
2349 2437 5.280624 GGGAAAACTACCACCACAGGTAATA 60.281 44.000 0.00 0.00 43.24 0.98
2350 2438 6.420638 GGAAAACTACCACCACAGGTAATAT 58.579 40.000 0.00 0.00 43.24 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 8.984764 TGATAAGTACAACATTACACAGTTCAC 58.015 33.333 0.00 0.00 0.00 3.18
247 280 6.673537 ACATTATCCCATTTCTTTCAACCCAT 59.326 34.615 0.00 0.00 0.00 4.00
252 285 6.436847 TGAGCACATTATCCCATTTCTTTCAA 59.563 34.615 0.00 0.00 0.00 2.69
266 299 1.656652 GTCGTGGCTGAGCACATTAT 58.343 50.000 6.82 0.00 0.00 1.28
285 318 7.638683 GGATAGTATTTTCCGTCACAAAATTCG 59.361 37.037 0.00 0.00 35.52 3.34
313 346 4.193865 TCGAATGACGTGTCTACCTATCA 58.806 43.478 0.00 0.00 43.13 2.15
314 347 4.808077 TCGAATGACGTGTCTACCTATC 57.192 45.455 0.00 0.00 43.13 2.08
470 504 4.513198 TTGATCCGTCATGTATATCGCA 57.487 40.909 0.00 0.00 33.56 5.10
493 529 9.431887 ACAAGAAATATGTTAATACGTGACAGT 57.568 29.630 0.00 0.00 0.00 3.55
508 544 9.586150 GCTGATTACGACATTACAAGAAATATG 57.414 33.333 0.00 0.00 0.00 1.78
509 545 8.487970 CGCTGATTACGACATTACAAGAAATAT 58.512 33.333 0.00 0.00 0.00 1.28
510 546 7.490079 ACGCTGATTACGACATTACAAGAAATA 59.510 33.333 0.00 0.00 0.00 1.40
511 547 6.312918 ACGCTGATTACGACATTACAAGAAAT 59.687 34.615 0.00 0.00 0.00 2.17
512 548 5.636121 ACGCTGATTACGACATTACAAGAAA 59.364 36.000 0.00 0.00 0.00 2.52
513 549 5.165676 ACGCTGATTACGACATTACAAGAA 58.834 37.500 0.00 0.00 0.00 2.52
514 550 4.740268 ACGCTGATTACGACATTACAAGA 58.260 39.130 0.00 0.00 0.00 3.02
515 551 4.316446 CGACGCTGATTACGACATTACAAG 60.316 45.833 0.00 0.00 0.00 3.16
516 552 3.544682 CGACGCTGATTACGACATTACAA 59.455 43.478 0.00 0.00 0.00 2.41
517 553 3.103007 CGACGCTGATTACGACATTACA 58.897 45.455 0.00 0.00 0.00 2.41
518 554 2.466571 CCGACGCTGATTACGACATTAC 59.533 50.000 0.00 0.00 0.00 1.89
519 555 2.542205 CCCGACGCTGATTACGACATTA 60.542 50.000 0.00 0.00 0.00 1.90
520 556 1.556564 CCGACGCTGATTACGACATT 58.443 50.000 0.00 0.00 0.00 2.71
521 557 0.248907 CCCGACGCTGATTACGACAT 60.249 55.000 0.00 0.00 0.00 3.06
529 565 3.717294 AAAGGCCCCGACGCTGAT 61.717 61.111 0.00 0.00 0.00 2.90
539 575 0.749049 GGCTTCATCATCAAAGGCCC 59.251 55.000 0.00 0.00 40.97 5.80
607 643 2.045926 GAAGGTGCTGGCGGACAT 60.046 61.111 0.00 0.00 32.44 3.06
831 868 2.398554 CCGTATGTGGGTGCAGCAC 61.399 63.158 17.97 17.97 0.00 4.40
867 904 3.702048 GCTACAGTCCACGGCCCA 61.702 66.667 0.00 0.00 0.00 5.36
879 916 1.663379 CTCCGTGGGTCATCGCTACA 61.663 60.000 0.00 0.00 0.00 2.74
884 921 2.348104 TGTCCTCCGTGGGTCATCG 61.348 63.158 0.00 0.00 36.20 3.84
893 930 1.135575 GTTCGTTATCGTGTCCTCCGT 60.136 52.381 0.00 0.00 38.33 4.69
908 945 2.060050 TGGGTTTGTTGATGGTTCGT 57.940 45.000 0.00 0.00 0.00 3.85
927 964 2.028130 CTACACAGCCGATCTCTCCTT 58.972 52.381 0.00 0.00 0.00 3.36
943 980 0.613853 AAGGTCCTACCGCTGCTACA 60.614 55.000 0.00 0.00 44.90 2.74
1070 1107 2.597805 ATCCTATCGCGGCTCCGT 60.598 61.111 6.13 0.00 42.09 4.69
1082 1119 2.124612 TCGCGGTCGTGGATCCTA 60.125 61.111 14.23 0.00 36.96 2.94
1197 1234 2.443952 ATCATCCCGGCGACCTCA 60.444 61.111 9.30 0.00 0.00 3.86
1214 1251 2.838748 ATCCTCCTCGACACTCGCCA 62.839 60.000 0.00 0.00 40.21 5.69
1237 1274 4.115199 GCCCGTGATGGCCTCCTT 62.115 66.667 3.32 0.00 46.11 3.36
1288 1325 3.771160 GATCCCACCGTCACCGCT 61.771 66.667 0.00 0.00 0.00 5.52
1309 1346 2.158755 CCATCGGCTCCCTATTTTCAGT 60.159 50.000 0.00 0.00 0.00 3.41
1369 1406 1.900486 CTCCTTAAACTCCCACCTCGT 59.100 52.381 0.00 0.00 0.00 4.18
1381 1420 1.677633 GCTTGCCGCCCTCCTTAAA 60.678 57.895 0.00 0.00 0.00 1.52
1400 1439 1.672854 TTCAGGTCTATCCCCGCGTG 61.673 60.000 4.92 0.00 36.75 5.34
1462 1501 0.988678 CCCTAAACCCTAGGGCTGCT 60.989 60.000 28.88 11.99 46.81 4.24
1557 1608 1.341209 GTTGAGCCAGTTCCCCAAAAG 59.659 52.381 0.00 0.00 0.00 2.27
1657 1714 7.770897 CCATTTGTTAGACTTCCTATTGTAGCT 59.229 37.037 0.00 0.00 0.00 3.32
1667 1724 4.636206 CCTACAGCCATTTGTTAGACTTCC 59.364 45.833 0.00 0.00 32.56 3.46
1680 1737 5.423610 CAGCTTATATAGACCCTACAGCCAT 59.576 44.000 0.00 0.00 0.00 4.40
1681 1738 4.772624 CAGCTTATATAGACCCTACAGCCA 59.227 45.833 0.00 0.00 0.00 4.75
1683 1740 5.126384 CCTCAGCTTATATAGACCCTACAGC 59.874 48.000 0.00 0.00 0.00 4.40
1684 1741 6.486056 TCCTCAGCTTATATAGACCCTACAG 58.514 44.000 0.00 0.00 0.00 2.74
1685 1742 6.464530 TCCTCAGCTTATATAGACCCTACA 57.535 41.667 0.00 0.00 0.00 2.74
1686 1743 6.183360 GCATCCTCAGCTTATATAGACCCTAC 60.183 46.154 0.00 0.00 0.00 3.18
1687 1744 5.894393 GCATCCTCAGCTTATATAGACCCTA 59.106 44.000 0.00 0.00 0.00 3.53
1688 1745 4.714308 GCATCCTCAGCTTATATAGACCCT 59.286 45.833 0.00 0.00 0.00 4.34
1689 1746 4.141824 GGCATCCTCAGCTTATATAGACCC 60.142 50.000 0.00 0.00 0.00 4.46
1690 1747 4.440802 CGGCATCCTCAGCTTATATAGACC 60.441 50.000 0.00 0.00 0.00 3.85
1691 1748 4.158764 ACGGCATCCTCAGCTTATATAGAC 59.841 45.833 0.00 0.00 0.00 2.59
1692 1749 4.344978 ACGGCATCCTCAGCTTATATAGA 58.655 43.478 0.00 0.00 0.00 1.98
1693 1750 4.677584 GACGGCATCCTCAGCTTATATAG 58.322 47.826 0.00 0.00 0.00 1.31
1694 1751 3.128764 CGACGGCATCCTCAGCTTATATA 59.871 47.826 0.00 0.00 0.00 0.86
1695 1752 2.094494 CGACGGCATCCTCAGCTTATAT 60.094 50.000 0.00 0.00 0.00 0.86
1696 1753 1.269723 CGACGGCATCCTCAGCTTATA 59.730 52.381 0.00 0.00 0.00 0.98
1697 1754 0.032678 CGACGGCATCCTCAGCTTAT 59.967 55.000 0.00 0.00 0.00 1.73
1698 1755 1.320344 ACGACGGCATCCTCAGCTTA 61.320 55.000 0.00 0.00 0.00 3.09
1699 1756 2.185350 CGACGGCATCCTCAGCTT 59.815 61.111 0.00 0.00 0.00 3.74
1700 1757 3.069980 GACGACGGCATCCTCAGCT 62.070 63.158 0.00 0.00 0.00 4.24
1701 1758 2.583593 GACGACGGCATCCTCAGC 60.584 66.667 0.00 0.00 0.00 4.26
1702 1759 1.517257 GTGACGACGGCATCCTCAG 60.517 63.158 6.69 0.00 0.00 3.35
1703 1760 2.212900 CTGTGACGACGGCATCCTCA 62.213 60.000 6.69 0.00 0.00 3.86
1704 1761 1.517257 CTGTGACGACGGCATCCTC 60.517 63.158 6.69 0.00 0.00 3.71
1705 1762 1.323271 ATCTGTGACGACGGCATCCT 61.323 55.000 6.69 0.00 0.00 3.24
1706 1763 1.141881 ATCTGTGACGACGGCATCC 59.858 57.895 6.69 0.00 0.00 3.51
1707 1764 1.756375 GCATCTGTGACGACGGCATC 61.756 60.000 6.69 0.97 0.00 3.91
1708 1765 1.811266 GCATCTGTGACGACGGCAT 60.811 57.895 6.69 0.00 0.00 4.40
1709 1766 2.432456 GCATCTGTGACGACGGCA 60.432 61.111 0.00 0.00 0.00 5.69
1710 1767 2.432456 TGCATCTGTGACGACGGC 60.432 61.111 0.00 0.00 0.00 5.68
1711 1768 2.447887 GCTGCATCTGTGACGACGG 61.448 63.158 0.00 0.00 0.00 4.79
1712 1769 2.447887 GGCTGCATCTGTGACGACG 61.448 63.158 0.50 0.00 0.00 5.12
1713 1770 2.447887 CGGCTGCATCTGTGACGAC 61.448 63.158 0.50 0.00 0.00 4.34
1714 1771 2.125952 CGGCTGCATCTGTGACGA 60.126 61.111 0.50 0.00 0.00 4.20
1715 1772 2.433145 ACGGCTGCATCTGTGACG 60.433 61.111 0.15 0.00 0.00 4.35
1716 1773 2.447887 CGACGGCTGCATCTGTGAC 61.448 63.158 6.78 0.00 0.00 3.67
1717 1774 2.125952 CGACGGCTGCATCTGTGA 60.126 61.111 6.78 0.00 0.00 3.58
1718 1775 3.190849 CCGACGGCTGCATCTGTG 61.191 66.667 6.78 0.00 0.00 3.66
1734 1791 0.732571 CATGTGTTGGGACGTATGCC 59.267 55.000 0.00 0.00 36.69 4.40
1740 1797 3.061848 GGGCCATGTGTTGGGACG 61.062 66.667 4.39 0.00 46.55 4.79
1741 1798 1.978617 CAGGGCCATGTGTTGGGAC 60.979 63.158 9.85 0.00 46.55 4.46
1745 1802 3.751246 CGCCAGGGCCATGTGTTG 61.751 66.667 17.55 1.39 37.98 3.33
1764 1821 1.672356 CCTTCTGTCTGCCAACGGG 60.672 63.158 0.00 0.00 37.18 5.28
1765 1822 2.328099 GCCTTCTGTCTGCCAACGG 61.328 63.158 0.00 0.00 0.00 4.44
1773 1830 3.996921 AATGATGTCAGCCTTCTGTCT 57.003 42.857 0.00 0.00 41.10 3.41
1777 1834 8.954350 GCATATATTTAATGATGTCAGCCTTCT 58.046 33.333 0.00 0.00 0.00 2.85
1779 1836 7.148188 CGGCATATATTTAATGATGTCAGCCTT 60.148 37.037 0.00 0.00 33.96 4.35
1780 1837 6.317140 CGGCATATATTTAATGATGTCAGCCT 59.683 38.462 0.00 0.00 33.96 4.58
1812 1869 3.071837 TACTGTCGGCCGCCATCA 61.072 61.111 23.51 15.32 0.00 3.07
1813 1870 1.731433 TACTACTGTCGGCCGCCATC 61.731 60.000 23.51 11.27 0.00 3.51
1814 1871 1.113517 ATACTACTGTCGGCCGCCAT 61.114 55.000 23.51 8.36 0.00 4.40
1815 1872 0.466007 TATACTACTGTCGGCCGCCA 60.466 55.000 23.51 16.47 0.00 5.69
1816 1873 0.886563 ATATACTACTGTCGGCCGCC 59.113 55.000 23.51 10.90 0.00 6.13
1818 1875 5.814764 ATAAGATATACTACTGTCGGCCG 57.185 43.478 22.12 22.12 0.00 6.13
1996 2067 7.185318 TCTATTTGCATCATGTCCCATTTTT 57.815 32.000 0.00 0.00 0.00 1.94
1997 2068 6.795144 TCTATTTGCATCATGTCCCATTTT 57.205 33.333 0.00 0.00 0.00 1.82
2001 2072 4.105217 AGGATCTATTTGCATCATGTCCCA 59.895 41.667 0.00 0.00 0.00 4.37
2002 2073 4.660168 AGGATCTATTTGCATCATGTCCC 58.340 43.478 0.00 0.00 0.00 4.46
2003 2074 7.934855 ATAAGGATCTATTTGCATCATGTCC 57.065 36.000 0.00 0.00 0.00 4.02
2004 2075 9.664332 AGTATAAGGATCTATTTGCATCATGTC 57.336 33.333 0.00 0.00 0.00 3.06
2008 2079 9.851686 ACAAAGTATAAGGATCTATTTGCATCA 57.148 29.630 0.00 0.00 31.12 3.07
2010 2081 9.851686 TGACAAAGTATAAGGATCTATTTGCAT 57.148 29.630 0.00 0.00 31.12 3.96
2011 2082 9.679661 TTGACAAAGTATAAGGATCTATTTGCA 57.320 29.630 0.00 0.00 31.12 4.08
2107 2189 3.407698 ACATTGCGTACCAACAGAATCA 58.592 40.909 0.00 0.00 35.99 2.57
2112 2194 6.814076 TTTAAAAACATTGCGTACCAACAG 57.186 33.333 0.00 0.00 35.99 3.16
2121 2203 7.907563 AGTTTGTTCCAATTTAAAAACATTGCG 59.092 29.630 4.48 0.00 32.16 4.85
2154 2236 6.680874 TTTCTGCAAATTTGAAGCAAACAT 57.319 29.167 22.31 0.00 36.13 2.71
2156 2238 6.249050 GTGTTTTCTGCAAATTTGAAGCAAAC 59.751 34.615 31.52 31.52 44.83 2.93
2159 2241 4.332268 GGTGTTTTCTGCAAATTTGAAGCA 59.668 37.500 22.31 8.50 33.64 3.91
2164 2246 6.037391 ACAAGATGGTGTTTTCTGCAAATTTG 59.963 34.615 14.03 14.03 0.00 2.32
2169 2251 4.734398 AACAAGATGGTGTTTTCTGCAA 57.266 36.364 0.00 0.00 38.60 4.08
2215 2298 3.676291 TTGCCTAATTTTGCCAAGGAC 57.324 42.857 0.00 0.00 0.00 3.85
2277 2365 2.355756 GGCATCGCATGTGTAAGAACAT 59.644 45.455 6.09 0.00 41.50 2.71
2278 2366 1.737236 GGCATCGCATGTGTAAGAACA 59.263 47.619 6.09 0.00 0.00 3.18
2279 2367 1.737236 TGGCATCGCATGTGTAAGAAC 59.263 47.619 6.09 0.00 0.00 3.01
2282 2370 1.328680 GAGTGGCATCGCATGTGTAAG 59.671 52.381 6.09 0.00 0.00 2.34
2292 2380 2.662791 CGAACTTTTGTGAGTGGCATCG 60.663 50.000 0.00 0.00 0.00 3.84
2294 2382 2.290641 GTCGAACTTTTGTGAGTGGCAT 59.709 45.455 0.00 0.00 0.00 4.40
2308 2396 2.872732 TCCCTGTCTAAGTGTCGAACT 58.127 47.619 0.00 0.00 42.60 3.01
2314 2402 4.657039 TGGTAGTTTTCCCTGTCTAAGTGT 59.343 41.667 0.00 0.00 0.00 3.55
2323 2411 2.504367 CTGTGGTGGTAGTTTTCCCTG 58.496 52.381 0.00 0.00 0.00 4.45
2324 2412 1.423921 CCTGTGGTGGTAGTTTTCCCT 59.576 52.381 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.