Multiple sequence alignment - TraesCS2D01G210300

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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 TraesCS2D01G210300 chr2D 100.000 2219 0 0 1 2219 166135857 166138075 0.000000e+00 4098
1 TraesCS2D01G210300 chr2B 93.236 961 47 8 371 1324 231658504 231657555 0.000000e+00 1399
2 TraesCS2D01G210300 chr2B 86.913 298 27 8 1 288 231658979 231658684 7.640000e-85 324
3 TraesCS2D01G210300 chr2A 91.331 992 61 14 382 1360 184552646 184551667 0.000000e+00 1332
4 TraesCS2D01G210300 chr2A 91.228 399 35 0 1821 2219 683142009 683142407 5.390000e-151 544
5 TraesCS2D01G210300 chr2A 85.632 174 16 7 1607 1773 683140450 683140621 8.140000e-40 174
6 TraesCS2D01G210300 chr2A 89.831 118 11 1 1360 1477 683140336 683140452 1.370000e-32 150
7 TraesCS2D01G210300 chr2A 91.489 94 5 1 281 371 184552885 184552792 2.310000e-25 126
8 TraesCS2D01G210300 chr1A 92.545 617 42 1 1607 2219 341389531 341390147 0.000000e+00 881
9 TraesCS2D01G210300 chr1A 95.238 126 4 2 1352 1477 341389410 341389533 4.830000e-47 198
10 TraesCS2D01G210300 chr3D 91.332 623 43 7 1607 2219 556616135 556616756 0.000000e+00 841
11 TraesCS2D01G210300 chr3D 95.690 348 15 0 1607 1954 610744547 610744200 5.350000e-156 560
12 TraesCS2D01G210300 chr3D 95.935 123 5 0 1355 1477 610744667 610744545 1.340000e-47 200
13 TraesCS2D01G210300 chr3D 93.388 121 8 0 1357 1477 556616017 556616137 1.750000e-41 180
14 TraesCS2D01G210300 chr4B 89.303 617 60 3 1607 2219 340990103 340990717 0.000000e+00 769
15 TraesCS2D01G210300 chr4B 89.483 542 52 2 1682 2219 402972405 402972945 0.000000e+00 680
16 TraesCS2D01G210300 chr4B 93.600 125 7 1 1353 1477 340989982 340990105 3.760000e-43 185
17 TraesCS2D01G210300 chr4B 94.872 117 6 0 1361 1477 402968664 402968780 1.350000e-42 183
18 TraesCS2D01G210300 chr1D 96.296 135 5 0 1477 1611 409959412 409959546 2.870000e-54 222
19 TraesCS2D01G210300 chr1D 93.162 117 8 0 1360 1476 34848988 34848872 2.930000e-39 172
20 TraesCS2D01G210300 chr7B 97.436 117 3 0 1361 1477 113063581 113063697 1.340000e-47 200
21 TraesCS2D01G210300 chr3B 90.299 134 13 0 1473 1606 448774390 448774523 2.260000e-40 176
22 TraesCS2D01G210300 chr6A 88.356 146 16 1 1470 1614 13121371 13121516 8.140000e-40 174
23 TraesCS2D01G210300 chr6A 88.356 146 16 1 1470 1614 13150748 13150893 8.140000e-40 174
24 TraesCS2D01G210300 chr6A 87.671 146 17 1 1470 1614 13182076 13182221 3.790000e-38 169
25 TraesCS2D01G210300 chr6D 90.551 127 12 0 1479 1605 17368582 17368456 3.790000e-38 169
26 TraesCS2D01G210300 chr6D 98.387 62 1 0 1350 1411 439765488 439765549 2.330000e-20 110


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 TraesCS2D01G210300 chr2D 166135857 166138075 2218 False 4098.000000 4098 100.0000 1 2219 1 chr2D.!!$F1 2218
1 TraesCS2D01G210300 chr2B 231657555 231658979 1424 True 861.500000 1399 90.0745 1 1324 2 chr2B.!!$R1 1323
2 TraesCS2D01G210300 chr2A 184551667 184552885 1218 True 729.000000 1332 91.4100 281 1360 2 chr2A.!!$R1 1079
3 TraesCS2D01G210300 chr2A 683140336 683142407 2071 False 289.333333 544 88.8970 1360 2219 3 chr2A.!!$F1 859
4 TraesCS2D01G210300 chr1A 341389410 341390147 737 False 539.500000 881 93.8915 1352 2219 2 chr1A.!!$F1 867
5 TraesCS2D01G210300 chr3D 556616017 556616756 739 False 510.500000 841 92.3600 1357 2219 2 chr3D.!!$F1 862
6 TraesCS2D01G210300 chr4B 340989982 340990717 735 False 477.000000 769 91.4515 1353 2219 2 chr4B.!!$F1 866
7 TraesCS2D01G210300 chr4B 402968664 402972945 4281 False 431.500000 680 92.1775 1361 2219 2 chr4B.!!$F2 858

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
121 125 0.868406 CCTGACCAGAAAGCAACGAC 59.132 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1791 0.179065 CAGCTCCATGAATCTGGCGA 60.179 55.0 0.0 0.0 36.16 5.54 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
41 42 9.898152 AAGTCCAAAGGATAACAAATTTTGAAA 57.102 25.926 15.81 3.74 32.73 2.69
42 43 9.898152 AGTCCAAAGGATAACAAATTTTGAAAA 57.102 25.926 15.81 0.00 32.73 2.29
88 92 2.365941 TGACGGTGACATCCACTTGTAA 59.634 45.455 0.00 0.00 45.03 2.41
121 125 0.868406 CCTGACCAGAAAGCAACGAC 59.132 55.000 0.00 0.00 0.00 4.34
123 127 1.261619 CTGACCAGAAAGCAACGACAC 59.738 52.381 0.00 0.00 0.00 3.67
190 206 3.329743 ACACGACGTACCTGATAATCG 57.670 47.619 0.00 0.00 35.74 3.34
193 209 4.751600 ACACGACGTACCTGATAATCGATA 59.248 41.667 0.00 0.00 33.88 2.92
194 210 5.237127 ACACGACGTACCTGATAATCGATAA 59.763 40.000 0.00 0.00 33.88 1.75
195 211 6.072838 ACACGACGTACCTGATAATCGATAAT 60.073 38.462 0.00 0.00 33.88 1.28
196 212 6.465149 CACGACGTACCTGATAATCGATAATC 59.535 42.308 0.00 0.00 33.88 1.75
197 213 6.370994 ACGACGTACCTGATAATCGATAATCT 59.629 38.462 0.00 0.00 33.88 2.40
198 214 7.547019 ACGACGTACCTGATAATCGATAATCTA 59.453 37.037 0.00 0.00 33.88 1.98
199 215 8.549548 CGACGTACCTGATAATCGATAATCTAT 58.450 37.037 0.00 0.00 0.00 1.98
200 216 9.653067 GACGTACCTGATAATCGATAATCTATG 57.347 37.037 0.00 0.00 0.00 2.23
201 217 8.129840 ACGTACCTGATAATCGATAATCTATGC 58.870 37.037 0.00 0.00 0.00 3.14
202 218 7.321509 CGTACCTGATAATCGATAATCTATGCG 59.678 40.741 0.00 0.00 0.00 4.73
203 219 5.980116 ACCTGATAATCGATAATCTATGCGC 59.020 40.000 0.00 0.00 0.00 6.09
204 220 6.183360 ACCTGATAATCGATAATCTATGCGCT 60.183 38.462 9.73 0.00 0.00 5.92
214 230 7.976175 TCGATAATCTATGCGCTTATCTTCAAT 59.024 33.333 18.52 1.52 32.27 2.57
216 232 9.311916 GATAATCTATGCGCTTATCTTCAATCT 57.688 33.333 9.73 0.00 31.92 2.40
266 282 4.098914 AGTTTGACCCAGCAACTAATCA 57.901 40.909 0.00 0.00 0.00 2.57
313 371 6.189677 TGTTGATTCTTTAGCCGGTTAATG 57.810 37.500 11.86 13.80 0.00 1.90
314 372 5.124776 TGTTGATTCTTTAGCCGGTTAATGG 59.875 40.000 19.38 12.51 0.00 3.16
357 415 2.487762 CAACTAAGCAAAGGCATCCGAA 59.512 45.455 0.00 0.00 44.61 4.30
493 689 4.693566 CCAATGGCAAACTAGTACGAAGAA 59.306 41.667 0.00 0.00 0.00 2.52
580 776 2.672098 ACAAGCTCGGACTAGGATGAT 58.328 47.619 0.00 0.00 0.00 2.45
582 778 2.625314 CAAGCTCGGACTAGGATGATGA 59.375 50.000 0.00 0.00 0.00 2.92
634 830 4.020218 ACACCAGTAACAGTATCTGCATGT 60.020 41.667 0.00 0.00 34.37 3.21
740 936 2.290847 TCAGGATGAGGAGCCACAC 58.709 57.895 0.00 0.00 42.56 3.82
741 937 1.222936 CAGGATGAGGAGCCACACC 59.777 63.158 0.00 0.00 39.69 4.16
742 938 1.997874 AGGATGAGGAGCCACACCC 60.998 63.158 0.00 0.00 0.00 4.61
743 939 2.300967 GGATGAGGAGCCACACCCA 61.301 63.158 0.00 0.00 0.00 4.51
744 940 1.078143 GATGAGGAGCCACACCCAC 60.078 63.158 0.00 0.00 0.00 4.61
745 941 1.841302 GATGAGGAGCCACACCCACA 61.841 60.000 0.00 0.00 0.00 4.17
746 942 1.845627 ATGAGGAGCCACACCCACAG 61.846 60.000 0.00 0.00 0.00 3.66
747 943 2.122413 AGGAGCCACACCCACAGA 60.122 61.111 0.00 0.00 0.00 3.41
850 1046 4.908687 TGTTGTCGCAGCGGCTGT 62.909 61.111 28.88 0.00 38.10 4.40
851 1047 2.736995 GTTGTCGCAGCGGCTGTA 60.737 61.111 28.88 16.18 38.10 2.74
879 1075 4.385405 GCTCGCCTGTCACCTGCT 62.385 66.667 0.00 0.00 0.00 4.24
918 1114 2.910688 ACACTCCAGAAACGTCACAT 57.089 45.000 0.00 0.00 0.00 3.21
927 1123 4.151335 CCAGAAACGTCACATTTGAGAGAG 59.849 45.833 0.00 0.00 30.10 3.20
929 1125 4.985409 AGAAACGTCACATTTGAGAGAGAC 59.015 41.667 0.00 0.00 30.10 3.36
930 1126 4.592485 AACGTCACATTTGAGAGAGACT 57.408 40.909 0.00 0.00 30.10 3.24
931 1127 4.592485 ACGTCACATTTGAGAGAGACTT 57.408 40.909 0.00 0.00 30.10 3.01
935 1135 3.742882 TCACATTTGAGAGAGACTTTGCG 59.257 43.478 0.00 0.00 0.00 4.85
951 1151 1.658994 TGCGTCGGAAGTTTGAGTTT 58.341 45.000 0.00 0.00 0.00 2.66
952 1152 1.329292 TGCGTCGGAAGTTTGAGTTTG 59.671 47.619 0.00 0.00 0.00 2.93
953 1153 1.920272 GCGTCGGAAGTTTGAGTTTGC 60.920 52.381 0.00 0.00 0.00 3.68
954 1154 1.329292 CGTCGGAAGTTTGAGTTTGCA 59.671 47.619 0.00 0.00 0.00 4.08
956 1156 1.946768 TCGGAAGTTTGAGTTTGCAGG 59.053 47.619 0.00 0.00 0.00 4.85
957 1157 1.676006 CGGAAGTTTGAGTTTGCAGGT 59.324 47.619 0.00 0.00 0.00 4.00
959 1159 2.223805 GGAAGTTTGAGTTTGCAGGTGG 60.224 50.000 0.00 0.00 0.00 4.61
960 1160 2.143876 AGTTTGAGTTTGCAGGTGGT 57.856 45.000 0.00 0.00 0.00 4.16
961 1161 3.290948 AGTTTGAGTTTGCAGGTGGTA 57.709 42.857 0.00 0.00 0.00 3.25
983 1190 6.259608 GGTAGAAGTAGAACTAGCACGTATCA 59.740 42.308 0.00 0.00 37.16 2.15
1267 1491 5.617252 TGACTTTTCTTTTGAGACGGGTAT 58.383 37.500 0.00 0.00 0.00 2.73
1296 1520 0.321671 CTGGAGTTCTGGCCGAAAGA 59.678 55.000 10.87 0.00 32.41 2.52
1308 1532 2.678336 GGCCGAAAGAATCTCGTGATTT 59.322 45.455 13.50 0.00 42.43 2.17
1312 1536 5.616866 GCCGAAAGAATCTCGTGATTTTGAA 60.617 40.000 13.50 0.00 42.43 2.69
1345 1569 6.839124 AACTGTTATTGAATTCATGCTCCA 57.161 33.333 9.40 2.52 0.00 3.86
1347 1571 5.948162 ACTGTTATTGAATTCATGCTCCAGT 59.052 36.000 9.40 13.93 0.00 4.00
1474 1699 7.561356 CCACCTAATCCATGAATTTAGGAAACT 59.439 37.037 23.74 8.33 43.03 2.66
1475 1700 8.971073 CACCTAATCCATGAATTTAGGAAACTT 58.029 33.333 23.74 8.08 43.03 2.66
1480 1705 7.391148 TCCATGAATTTAGGAAACTTACTGC 57.609 36.000 0.00 0.00 43.67 4.40
1481 1706 6.377146 TCCATGAATTTAGGAAACTTACTGCC 59.623 38.462 0.00 0.00 43.67 4.85
1482 1707 6.405842 CCATGAATTTAGGAAACTTACTGCCC 60.406 42.308 0.00 0.00 43.67 5.36
1483 1708 4.698304 TGAATTTAGGAAACTTACTGCCCG 59.302 41.667 0.00 0.00 43.67 6.13
1484 1709 3.775261 TTTAGGAAACTTACTGCCCGT 57.225 42.857 0.00 0.00 43.67 5.28
1485 1710 3.775261 TTAGGAAACTTACTGCCCGTT 57.225 42.857 0.00 0.00 43.67 4.44
1486 1711 2.180432 AGGAAACTTACTGCCCGTTC 57.820 50.000 0.00 0.00 37.44 3.95
1487 1712 0.794473 GGAAACTTACTGCCCGTTCG 59.206 55.000 0.00 0.00 0.00 3.95
1488 1713 0.794473 GAAACTTACTGCCCGTTCGG 59.206 55.000 4.08 4.08 0.00 4.30
1489 1714 0.393820 AAACTTACTGCCCGTTCGGA 59.606 50.000 13.08 0.00 0.00 4.55
1490 1715 0.037605 AACTTACTGCCCGTTCGGAG 60.038 55.000 13.08 5.67 0.00 4.63
1491 1716 1.153628 CTTACTGCCCGTTCGGAGG 60.154 63.158 13.08 4.94 0.00 4.30
1508 1733 4.021925 GCCCTCCGCTCCACAACT 62.022 66.667 0.00 0.00 0.00 3.16
1509 1734 2.266055 CCCTCCGCTCCACAACTC 59.734 66.667 0.00 0.00 0.00 3.01
1510 1735 2.266055 CCTCCGCTCCACAACTCC 59.734 66.667 0.00 0.00 0.00 3.85
1511 1736 2.583441 CCTCCGCTCCACAACTCCA 61.583 63.158 0.00 0.00 0.00 3.86
1512 1737 1.374758 CTCCGCTCCACAACTCCAC 60.375 63.158 0.00 0.00 0.00 4.02
1513 1738 2.358737 CCGCTCCACAACTCCACC 60.359 66.667 0.00 0.00 0.00 4.61
1514 1739 2.425592 CGCTCCACAACTCCACCA 59.574 61.111 0.00 0.00 0.00 4.17
1515 1740 1.961277 CGCTCCACAACTCCACCAC 60.961 63.158 0.00 0.00 0.00 4.16
1516 1741 1.961277 GCTCCACAACTCCACCACG 60.961 63.158 0.00 0.00 0.00 4.94
1517 1742 1.301716 CTCCACAACTCCACCACGG 60.302 63.158 0.00 0.00 0.00 4.94
1518 1743 1.754380 CTCCACAACTCCACCACGGA 61.754 60.000 0.00 0.00 43.61 4.69
1538 1763 3.146783 CGGAGCGGGTTGTAATTCA 57.853 52.632 0.00 0.00 0.00 2.57
1539 1764 1.444836 CGGAGCGGGTTGTAATTCAA 58.555 50.000 0.00 0.00 0.00 2.69
1540 1765 1.807742 CGGAGCGGGTTGTAATTCAAA 59.192 47.619 0.00 0.00 37.81 2.69
1541 1766 2.422127 CGGAGCGGGTTGTAATTCAAAT 59.578 45.455 0.00 0.00 37.81 2.32
1542 1767 3.486875 CGGAGCGGGTTGTAATTCAAATC 60.487 47.826 0.00 0.00 37.81 2.17
1543 1768 3.694566 GGAGCGGGTTGTAATTCAAATCT 59.305 43.478 0.00 0.00 37.81 2.40
1544 1769 4.157840 GGAGCGGGTTGTAATTCAAATCTT 59.842 41.667 0.00 0.00 37.81 2.40
1545 1770 5.310720 AGCGGGTTGTAATTCAAATCTTC 57.689 39.130 0.00 0.00 37.81 2.87
1546 1771 4.764823 AGCGGGTTGTAATTCAAATCTTCA 59.235 37.500 0.00 0.00 37.81 3.02
1547 1772 5.095490 GCGGGTTGTAATTCAAATCTTCAG 58.905 41.667 0.00 0.00 37.81 3.02
1548 1773 5.106317 GCGGGTTGTAATTCAAATCTTCAGA 60.106 40.000 0.00 0.00 37.81 3.27
1549 1774 6.546395 CGGGTTGTAATTCAAATCTTCAGAG 58.454 40.000 0.00 0.00 37.81 3.35
1550 1775 6.325596 GGGTTGTAATTCAAATCTTCAGAGC 58.674 40.000 0.00 0.00 37.81 4.09
1551 1776 6.024049 GGTTGTAATTCAAATCTTCAGAGCG 58.976 40.000 0.00 0.00 37.81 5.03
1552 1777 5.801350 TGTAATTCAAATCTTCAGAGCGG 57.199 39.130 0.00 0.00 0.00 5.52
1553 1778 5.245531 TGTAATTCAAATCTTCAGAGCGGT 58.754 37.500 0.00 0.00 0.00 5.68
1554 1779 4.691860 AATTCAAATCTTCAGAGCGGTG 57.308 40.909 0.00 0.00 0.00 4.94
1555 1780 2.099141 TCAAATCTTCAGAGCGGTGG 57.901 50.000 0.00 0.00 0.00 4.61
1556 1781 1.623311 TCAAATCTTCAGAGCGGTGGA 59.377 47.619 0.00 0.00 0.00 4.02
1557 1782 2.038426 TCAAATCTTCAGAGCGGTGGAA 59.962 45.455 0.00 0.00 0.00 3.53
1558 1783 3.012518 CAAATCTTCAGAGCGGTGGAAT 58.987 45.455 0.00 0.00 0.00 3.01
1559 1784 2.322355 ATCTTCAGAGCGGTGGAATG 57.678 50.000 0.00 0.00 0.00 2.67
1560 1785 0.250234 TCTTCAGAGCGGTGGAATGG 59.750 55.000 0.00 0.00 0.00 3.16
1561 1786 0.745845 CTTCAGAGCGGTGGAATGGG 60.746 60.000 0.00 0.00 0.00 4.00
1562 1787 1.488705 TTCAGAGCGGTGGAATGGGT 61.489 55.000 0.00 0.00 0.00 4.51
1563 1788 1.746615 CAGAGCGGTGGAATGGGTG 60.747 63.158 0.00 0.00 0.00 4.61
1564 1789 3.134127 GAGCGGTGGAATGGGTGC 61.134 66.667 0.00 0.00 0.00 5.01
1565 1790 3.628646 GAGCGGTGGAATGGGTGCT 62.629 63.158 0.00 0.00 34.96 4.40
1566 1791 2.676471 GCGGTGGAATGGGTGCTT 60.676 61.111 0.00 0.00 0.00 3.91
1567 1792 2.700773 GCGGTGGAATGGGTGCTTC 61.701 63.158 0.00 0.00 0.00 3.86
1568 1793 2.398554 CGGTGGAATGGGTGCTTCG 61.399 63.158 0.00 0.00 0.00 3.79
1569 1794 2.700773 GGTGGAATGGGTGCTTCGC 61.701 63.158 0.00 0.00 0.00 4.70
1570 1795 2.361104 TGGAATGGGTGCTTCGCC 60.361 61.111 0.00 0.00 0.00 5.54
1571 1796 2.361104 GGAATGGGTGCTTCGCCA 60.361 61.111 0.00 0.00 35.42 5.69
1572 1797 2.409870 GGAATGGGTGCTTCGCCAG 61.410 63.158 0.00 0.00 35.42 4.85
1573 1798 1.377202 GAATGGGTGCTTCGCCAGA 60.377 57.895 0.00 0.00 35.42 3.86
1574 1799 0.749454 GAATGGGTGCTTCGCCAGAT 60.749 55.000 0.00 0.00 35.42 2.90
1575 1800 0.323725 AATGGGTGCTTCGCCAGATT 60.324 50.000 0.00 0.00 35.42 2.40
1576 1801 0.749454 ATGGGTGCTTCGCCAGATTC 60.749 55.000 0.00 0.00 35.42 2.52
1577 1802 1.377202 GGGTGCTTCGCCAGATTCA 60.377 57.895 0.00 0.00 35.42 2.57
1578 1803 0.749454 GGGTGCTTCGCCAGATTCAT 60.749 55.000 0.00 0.00 35.42 2.57
1579 1804 0.379669 GGTGCTTCGCCAGATTCATG 59.620 55.000 0.00 0.00 33.65 3.07
1580 1805 0.379669 GTGCTTCGCCAGATTCATGG 59.620 55.000 0.00 0.00 43.72 3.66
1581 1806 0.252761 TGCTTCGCCAGATTCATGGA 59.747 50.000 0.00 0.00 43.57 3.41
1582 1807 0.942962 GCTTCGCCAGATTCATGGAG 59.057 55.000 0.00 0.00 43.57 3.86
1583 1808 0.942962 CTTCGCCAGATTCATGGAGC 59.057 55.000 0.00 0.00 43.57 4.70
1584 1809 0.543277 TTCGCCAGATTCATGGAGCT 59.457 50.000 0.00 0.00 43.57 4.09
1585 1810 0.179065 TCGCCAGATTCATGGAGCTG 60.179 55.000 12.58 12.58 43.57 4.24
1588 1813 1.676746 CCAGATTCATGGAGCTGGTG 58.323 55.000 27.47 5.65 43.57 4.17
1589 1814 1.676746 CAGATTCATGGAGCTGGTGG 58.323 55.000 11.68 0.00 0.00 4.61
1590 1815 1.211212 CAGATTCATGGAGCTGGTGGA 59.789 52.381 11.68 0.00 0.00 4.02
1591 1816 2.133520 AGATTCATGGAGCTGGTGGAT 58.866 47.619 0.00 0.00 0.00 3.41
1592 1817 2.512896 AGATTCATGGAGCTGGTGGATT 59.487 45.455 0.00 0.00 0.00 3.01
1593 1818 3.718434 AGATTCATGGAGCTGGTGGATTA 59.282 43.478 0.00 0.00 0.00 1.75
1594 1819 3.281727 TTCATGGAGCTGGTGGATTAC 57.718 47.619 0.00 0.00 0.00 1.89
1656 1881 5.854866 GGTTTGTGGAAAAACGACTATTAGC 59.145 40.000 0.00 0.00 40.29 3.09
1774 5575 7.011382 ACTTCAGGATATAAGTCCTTCGGTAT 58.989 38.462 0.00 0.00 46.45 2.73
1831 6972 2.114616 ACCTTCAGGCAGGTGATAGAG 58.885 52.381 0.00 0.00 46.22 2.43
1928 7069 1.679153 TCACGAGTTATGCGATGCCTA 59.321 47.619 0.00 0.00 0.00 3.93
1933 7074 0.868406 GTTATGCGATGCCTAGGTGC 59.132 55.000 11.31 10.26 0.00 5.01
1961 7102 0.729116 CATTCGCATCAAAGACGGCT 59.271 50.000 0.00 0.00 0.00 5.52
2019 7160 1.078918 CATGCTGGAAGTGCGAGGA 60.079 57.895 0.00 0.00 35.30 3.71
2085 7228 2.406002 GACCTCGGTGCCAGGGAAAA 62.406 60.000 0.00 0.00 35.01 2.29
2192 7336 1.134965 AGCTTGGTCATGTACTCTCGC 60.135 52.381 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.642343 AGAAAGTTTGTTACTCTCCCTAATTTT 57.358 29.630 0.00 0.00 35.54 1.82
42 43 9.067986 CAGAAAGTTTGTTACTCTCCCTAATTT 57.932 33.333 0.00 0.00 35.54 1.82
43 44 8.437575 TCAGAAAGTTTGTTACTCTCCCTAATT 58.562 33.333 0.00 0.00 35.54 1.40
44 45 7.878644 GTCAGAAAGTTTGTTACTCTCCCTAAT 59.121 37.037 0.00 0.00 35.54 1.73
47 48 5.612351 GTCAGAAAGTTTGTTACTCTCCCT 58.388 41.667 0.00 0.00 35.54 4.20
49 50 4.448060 CCGTCAGAAAGTTTGTTACTCTCC 59.552 45.833 0.00 0.00 35.54 3.71
51 52 4.809426 CACCGTCAGAAAGTTTGTTACTCT 59.191 41.667 0.00 0.00 35.54 3.24
53 54 4.569564 GTCACCGTCAGAAAGTTTGTTACT 59.430 41.667 0.00 0.00 39.32 2.24
94 98 2.616510 GCTTTCTGGTCAGGTGCTACAT 60.617 50.000 0.00 0.00 0.00 2.29
95 99 1.270839 GCTTTCTGGTCAGGTGCTACA 60.271 52.381 0.00 0.00 0.00 2.74
96 100 1.270839 TGCTTTCTGGTCAGGTGCTAC 60.271 52.381 0.00 0.00 0.00 3.58
97 101 1.055849 TGCTTTCTGGTCAGGTGCTA 58.944 50.000 0.00 0.00 0.00 3.49
121 125 6.019237 CCGAATCTCATCTTGTAACATCAGTG 60.019 42.308 0.00 0.00 0.00 3.66
123 127 6.276091 TCCGAATCTCATCTTGTAACATCAG 58.724 40.000 0.00 0.00 0.00 2.90
193 209 6.933521 ACAGATTGAAGATAAGCGCATAGATT 59.066 34.615 11.47 0.40 0.00 2.40
194 210 6.368243 CACAGATTGAAGATAAGCGCATAGAT 59.632 38.462 11.47 0.00 0.00 1.98
195 211 5.693555 CACAGATTGAAGATAAGCGCATAGA 59.306 40.000 11.47 0.00 0.00 1.98
196 212 5.614231 GCACAGATTGAAGATAAGCGCATAG 60.614 44.000 11.47 0.00 0.00 2.23
197 213 4.212004 GCACAGATTGAAGATAAGCGCATA 59.788 41.667 11.47 0.97 0.00 3.14
198 214 3.003068 GCACAGATTGAAGATAAGCGCAT 59.997 43.478 11.47 0.00 0.00 4.73
199 215 2.352651 GCACAGATTGAAGATAAGCGCA 59.647 45.455 11.47 0.00 0.00 6.09
200 216 2.286654 GGCACAGATTGAAGATAAGCGC 60.287 50.000 0.00 0.00 0.00 5.92
201 217 2.938451 TGGCACAGATTGAAGATAAGCG 59.062 45.455 0.00 0.00 0.00 4.68
202 218 3.944015 AGTGGCACAGATTGAAGATAAGC 59.056 43.478 21.41 0.00 41.80 3.09
203 219 6.506500 AAAGTGGCACAGATTGAAGATAAG 57.493 37.500 21.41 0.00 41.80 1.73
204 220 7.994425 TTAAAGTGGCACAGATTGAAGATAA 57.006 32.000 21.41 0.00 41.80 1.75
214 230 4.980573 ACCAGTAATTAAAGTGGCACAGA 58.019 39.130 21.41 0.74 42.80 3.41
216 232 8.865420 TTATTACCAGTAATTAAAGTGGCACA 57.135 30.769 21.41 0.00 42.80 4.57
266 282 7.552687 ACATCGTCCATATTGTTCATTAACTGT 59.447 33.333 0.00 0.00 36.51 3.55
313 371 1.826385 AAACTAGCATCACTGGCACC 58.174 50.000 0.00 0.00 0.00 5.01
314 372 2.554032 ACAAAACTAGCATCACTGGCAC 59.446 45.455 0.00 0.00 0.00 5.01
441 637 8.507249 AGTTAAACAAGTGAGATAAGCATCAAC 58.493 33.333 0.00 0.00 33.21 3.18
580 776 1.480212 AACCGTGCTGACCTGGATCA 61.480 55.000 0.00 0.00 0.00 2.92
582 778 0.537188 CTAACCGTGCTGACCTGGAT 59.463 55.000 0.00 0.00 0.00 3.41
658 854 2.460669 TGTCTTCTCTGCAGCATCCTA 58.539 47.619 9.47 0.00 0.00 2.94
659 855 1.273759 TGTCTTCTCTGCAGCATCCT 58.726 50.000 9.47 0.00 0.00 3.24
740 936 1.604378 GATCCAGTGGGTCTGTGGG 59.396 63.158 15.71 0.00 42.19 4.61
741 937 1.219124 CGATCCAGTGGGTCTGTGG 59.781 63.158 20.28 0.61 42.19 4.17
742 938 1.219124 CCGATCCAGTGGGTCTGTG 59.781 63.158 20.28 4.89 42.19 3.66
743 939 1.990060 CCCGATCCAGTGGGTCTGT 60.990 63.158 20.28 0.00 42.19 3.41
744 940 2.903357 CCCGATCCAGTGGGTCTG 59.097 66.667 20.28 13.66 40.76 3.51
760 956 0.108756 GAGTAGACCACTGGTTCGCC 60.109 60.000 1.13 0.00 37.72 5.54
761 957 0.456312 CGAGTAGACCACTGGTTCGC 60.456 60.000 1.13 0.00 37.72 4.70
850 1046 5.237996 GTGACAGGCGAGCCGTATATATATA 59.762 44.000 8.63 0.00 41.95 0.86
851 1047 4.036498 GTGACAGGCGAGCCGTATATATAT 59.964 45.833 8.63 0.00 41.95 0.86
879 1075 3.117701 TGTTTGATGTGTGGAGGGAGAAA 60.118 43.478 0.00 0.00 0.00 2.52
927 1123 1.595794 TCAAACTTCCGACGCAAAGTC 59.404 47.619 12.44 0.00 46.16 3.01
929 1125 1.597663 ACTCAAACTTCCGACGCAAAG 59.402 47.619 6.66 6.66 0.00 2.77
930 1126 1.658994 ACTCAAACTTCCGACGCAAA 58.341 45.000 0.00 0.00 0.00 3.68
931 1127 1.658994 AACTCAAACTTCCGACGCAA 58.341 45.000 0.00 0.00 0.00 4.85
935 1135 2.287009 CCTGCAAACTCAAACTTCCGAC 60.287 50.000 0.00 0.00 0.00 4.79
942 1142 3.211045 TCTACCACCTGCAAACTCAAAC 58.789 45.455 0.00 0.00 0.00 2.93
951 1151 3.507411 AGTTCTACTTCTACCACCTGCA 58.493 45.455 0.00 0.00 0.00 4.41
952 1152 4.440387 GCTAGTTCTACTTCTACCACCTGC 60.440 50.000 0.00 0.00 0.00 4.85
953 1153 4.705507 TGCTAGTTCTACTTCTACCACCTG 59.294 45.833 0.00 0.00 0.00 4.00
954 1154 4.705991 GTGCTAGTTCTACTTCTACCACCT 59.294 45.833 0.00 0.00 0.00 4.00
956 1156 4.155644 ACGTGCTAGTTCTACTTCTACCAC 59.844 45.833 0.00 0.00 0.00 4.16
957 1157 4.330250 ACGTGCTAGTTCTACTTCTACCA 58.670 43.478 0.00 0.00 0.00 3.25
959 1159 7.244166 TGATACGTGCTAGTTCTACTTCTAC 57.756 40.000 0.00 0.00 0.00 2.59
960 1160 8.447924 AATGATACGTGCTAGTTCTACTTCTA 57.552 34.615 0.00 0.00 0.00 2.10
961 1161 6.945938 ATGATACGTGCTAGTTCTACTTCT 57.054 37.500 0.00 0.00 0.00 2.85
983 1190 3.516700 CCTCATTTCCTTGCCCTGAAAAT 59.483 43.478 0.00 0.00 34.43 1.82
1022 1246 2.186826 GTCACCGCCATGTATGCCC 61.187 63.158 0.00 0.00 0.00 5.36
1267 1491 4.284490 GGCCAGAACTCCAGATCATGTATA 59.716 45.833 0.00 0.00 0.00 1.47
1316 1540 9.624373 AGCATGAATTCAATAACAGTTAGATCT 57.376 29.630 13.09 0.00 0.00 2.75
1326 1550 6.441093 TGACTGGAGCATGAATTCAATAAC 57.559 37.500 13.09 5.04 0.00 1.89
1340 1564 3.674410 GCCTTAAAGCAATTGACTGGAGC 60.674 47.826 10.34 0.00 0.00 4.70
1345 1569 3.317993 ACAACGCCTTAAAGCAATTGACT 59.682 39.130 10.34 2.94 34.30 3.41
1347 1571 4.314740 AACAACGCCTTAAAGCAATTGA 57.685 36.364 10.34 0.00 34.30 2.57
1424 1648 6.127814 GGAGTAGCCAAACAAGGTTTTATACC 60.128 42.308 0.00 0.00 41.30 2.73
1474 1699 2.975536 CCTCCGAACGGGCAGTAA 59.024 61.111 13.29 0.00 34.94 2.24
1475 1700 3.766691 GCCTCCGAACGGGCAGTA 61.767 66.667 13.29 0.00 46.84 2.74
1491 1716 3.959991 GAGTTGTGGAGCGGAGGGC 62.960 68.421 0.00 0.00 44.05 5.19
1492 1717 2.266055 GAGTTGTGGAGCGGAGGG 59.734 66.667 0.00 0.00 0.00 4.30
1493 1718 2.266055 GGAGTTGTGGAGCGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
1494 1719 1.374758 GTGGAGTTGTGGAGCGGAG 60.375 63.158 0.00 0.00 0.00 4.63
1495 1720 2.741092 GTGGAGTTGTGGAGCGGA 59.259 61.111 0.00 0.00 0.00 5.54
1496 1721 2.358737 GGTGGAGTTGTGGAGCGG 60.359 66.667 0.00 0.00 0.00 5.52
1497 1722 1.961277 GTGGTGGAGTTGTGGAGCG 60.961 63.158 0.00 0.00 0.00 5.03
1498 1723 1.961277 CGTGGTGGAGTTGTGGAGC 60.961 63.158 0.00 0.00 0.00 4.70
1499 1724 1.301716 CCGTGGTGGAGTTGTGGAG 60.302 63.158 0.00 0.00 42.00 3.86
1500 1725 1.762858 TCCGTGGTGGAGTTGTGGA 60.763 57.895 0.00 0.00 43.74 4.02
1501 1726 2.825982 TCCGTGGTGGAGTTGTGG 59.174 61.111 0.00 0.00 43.74 4.17
1516 1741 2.588856 ATTACAACCCGCTCCGCTCC 62.589 60.000 0.00 0.00 0.00 4.70
1517 1742 0.743345 AATTACAACCCGCTCCGCTC 60.743 55.000 0.00 0.00 0.00 5.03
1518 1743 0.743345 GAATTACAACCCGCTCCGCT 60.743 55.000 0.00 0.00 0.00 5.52
1519 1744 1.022451 TGAATTACAACCCGCTCCGC 61.022 55.000 0.00 0.00 0.00 5.54
1520 1745 1.444836 TTGAATTACAACCCGCTCCG 58.555 50.000 0.00 0.00 33.18 4.63
1521 1746 3.694566 AGATTTGAATTACAACCCGCTCC 59.305 43.478 0.00 0.00 38.29 4.70
1522 1747 4.965119 AGATTTGAATTACAACCCGCTC 57.035 40.909 0.00 0.00 38.29 5.03
1523 1748 4.764823 TGAAGATTTGAATTACAACCCGCT 59.235 37.500 0.00 0.00 38.29 5.52
1524 1749 5.054390 TGAAGATTTGAATTACAACCCGC 57.946 39.130 0.00 0.00 38.29 6.13
1525 1750 6.494893 TCTGAAGATTTGAATTACAACCCG 57.505 37.500 0.00 0.00 38.29 5.28
1526 1751 6.325596 GCTCTGAAGATTTGAATTACAACCC 58.674 40.000 0.00 0.00 38.29 4.11
1527 1752 6.024049 CGCTCTGAAGATTTGAATTACAACC 58.976 40.000 0.00 0.00 38.29 3.77
1528 1753 6.024049 CCGCTCTGAAGATTTGAATTACAAC 58.976 40.000 0.00 0.00 38.29 3.32
1529 1754 5.705441 ACCGCTCTGAAGATTTGAATTACAA 59.295 36.000 0.00 0.00 36.65 2.41
1530 1755 5.122239 CACCGCTCTGAAGATTTGAATTACA 59.878 40.000 0.00 0.00 0.00 2.41
1531 1756 5.447818 CCACCGCTCTGAAGATTTGAATTAC 60.448 44.000 0.00 0.00 0.00 1.89
1532 1757 4.635765 CCACCGCTCTGAAGATTTGAATTA 59.364 41.667 0.00 0.00 0.00 1.40
1533 1758 3.441572 CCACCGCTCTGAAGATTTGAATT 59.558 43.478 0.00 0.00 0.00 2.17
1534 1759 3.012518 CCACCGCTCTGAAGATTTGAAT 58.987 45.455 0.00 0.00 0.00 2.57
1535 1760 2.038426 TCCACCGCTCTGAAGATTTGAA 59.962 45.455 0.00 0.00 0.00 2.69
1536 1761 1.623311 TCCACCGCTCTGAAGATTTGA 59.377 47.619 0.00 0.00 0.00 2.69
1537 1762 2.099141 TCCACCGCTCTGAAGATTTG 57.901 50.000 0.00 0.00 0.00 2.32
1538 1763 2.859165 TTCCACCGCTCTGAAGATTT 57.141 45.000 0.00 0.00 0.00 2.17
1539 1764 2.636830 CATTCCACCGCTCTGAAGATT 58.363 47.619 0.00 0.00 0.00 2.40
1540 1765 1.134280 CCATTCCACCGCTCTGAAGAT 60.134 52.381 0.00 0.00 0.00 2.40
1541 1766 0.250234 CCATTCCACCGCTCTGAAGA 59.750 55.000 0.00 0.00 0.00 2.87
1542 1767 0.745845 CCCATTCCACCGCTCTGAAG 60.746 60.000 0.00 0.00 0.00 3.02
1543 1768 1.299648 CCCATTCCACCGCTCTGAA 59.700 57.895 0.00 0.00 0.00 3.02
1544 1769 1.918293 ACCCATTCCACCGCTCTGA 60.918 57.895 0.00 0.00 0.00 3.27
1545 1770 1.746615 CACCCATTCCACCGCTCTG 60.747 63.158 0.00 0.00 0.00 3.35
1546 1771 2.671070 CACCCATTCCACCGCTCT 59.329 61.111 0.00 0.00 0.00 4.09
1547 1772 3.134127 GCACCCATTCCACCGCTC 61.134 66.667 0.00 0.00 0.00 5.03
1548 1773 3.210012 AAGCACCCATTCCACCGCT 62.210 57.895 0.00 0.00 0.00 5.52
1549 1774 2.676471 AAGCACCCATTCCACCGC 60.676 61.111 0.00 0.00 0.00 5.68
1550 1775 2.398554 CGAAGCACCCATTCCACCG 61.399 63.158 0.00 0.00 0.00 4.94
1551 1776 3.590824 CGAAGCACCCATTCCACC 58.409 61.111 0.00 0.00 0.00 4.61
1564 1789 0.942962 GCTCCATGAATCTGGCGAAG 59.057 55.000 0.00 0.00 36.16 3.79
1565 1790 0.543277 AGCTCCATGAATCTGGCGAA 59.457 50.000 0.00 0.00 36.16 4.70
1566 1791 0.179065 CAGCTCCATGAATCTGGCGA 60.179 55.000 0.00 0.00 36.16 5.54
1567 1792 1.164662 CCAGCTCCATGAATCTGGCG 61.165 60.000 12.09 0.00 39.53 5.69
1568 1793 2.716814 CCAGCTCCATGAATCTGGC 58.283 57.895 12.09 0.56 39.53 4.85
1570 1795 1.211212 TCCACCAGCTCCATGAATCTG 59.789 52.381 0.00 0.00 0.00 2.90
1571 1796 1.588239 TCCACCAGCTCCATGAATCT 58.412 50.000 0.00 0.00 0.00 2.40
1572 1797 2.653234 ATCCACCAGCTCCATGAATC 57.347 50.000 0.00 0.00 0.00 2.52
1573 1798 3.825328 GTAATCCACCAGCTCCATGAAT 58.175 45.455 0.00 0.00 0.00 2.57
1574 1799 3.281727 GTAATCCACCAGCTCCATGAA 57.718 47.619 0.00 0.00 0.00 2.57
1586 1811 2.215942 AGGCCTGTTTGGTAATCCAC 57.784 50.000 3.11 0.00 44.22 4.02
1587 1812 2.990740 AAGGCCTGTTTGGTAATCCA 57.009 45.000 5.69 0.00 42.66 3.41
1588 1813 4.341487 ACTAAAGGCCTGTTTGGTAATCC 58.659 43.478 5.69 0.00 38.35 3.01
1589 1814 5.977489 AACTAAAGGCCTGTTTGGTAATC 57.023 39.130 5.69 0.00 38.35 1.75
1590 1815 5.245301 GGAAACTAAAGGCCTGTTTGGTAAT 59.755 40.000 20.95 7.73 38.35 1.89
1591 1816 4.585581 GGAAACTAAAGGCCTGTTTGGTAA 59.414 41.667 20.95 0.00 38.35 2.85
1592 1817 4.146564 GGAAACTAAAGGCCTGTTTGGTA 58.853 43.478 20.95 0.00 38.35 3.25
1593 1818 2.963101 GGAAACTAAAGGCCTGTTTGGT 59.037 45.455 20.95 11.70 38.35 3.67
1594 1819 2.962421 TGGAAACTAAAGGCCTGTTTGG 59.038 45.455 20.95 11.09 34.55 3.28
1595 1820 3.888930 TCTGGAAACTAAAGGCCTGTTTG 59.111 43.478 20.95 13.62 34.55 2.93
1596 1821 4.178956 TCTGGAAACTAAAGGCCTGTTT 57.821 40.909 17.17 17.17 36.73 2.83
1597 1822 3.876309 TCTGGAAACTAAAGGCCTGTT 57.124 42.857 5.69 2.91 0.00 3.16
1598 1823 3.876309 TTCTGGAAACTAAAGGCCTGT 57.124 42.857 5.69 1.77 0.00 4.00
1599 1824 4.505313 GTTTCTGGAAACTAAAGGCCTG 57.495 45.455 5.69 0.00 45.26 4.85
1774 5575 2.225791 CTCGTGGTCGCCAATGGAGA 62.226 60.000 2.05 1.15 34.18 3.71
1870 7011 3.770040 CCTGACGTCCATGGCGGA 61.770 66.667 25.35 14.42 43.61 5.54
1961 7102 0.885596 CGTTTACCTTGGTGGCCGAA 60.886 55.000 0.00 0.00 40.22 4.30
2065 7206 4.631740 TCCCTGGCACCGAGGTCA 62.632 66.667 0.00 0.00 0.00 4.02
2192 7336 2.047061 TCTTCCCCTATCGTCCATTGG 58.953 52.381 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.