Multiple sequence alignment - TraesCS1B01G064200

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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 TraesCS1B01G064200 chr1B 100.000 2345 0 0 1 2345 48734335 48736679 0.000000e+00 4331
1 TraesCS1B01G064200 chr1B 88.310 1189 59 32 503 1631 48656274 48657442 0.000000e+00 1352
2 TraesCS1B01G064200 chr1B 88.310 1189 59 32 503 1631 48707652 48708820 0.000000e+00 1352
3 TraesCS1B01G064200 chr1B 88.161 1191 59 36 503 1631 48675055 48676225 0.000000e+00 1343
4 TraesCS1B01G064200 chr1B 88.121 1187 63 31 503 1631 48660686 48661852 0.000000e+00 1339
5 TraesCS1B01G064200 chr1B 87.797 1180 66 28 503 1623 48587986 48589146 0.000000e+00 1310
6 TraesCS1B01G064200 chr1B 87.288 1180 72 22 503 1623 48624993 48626153 0.000000e+00 1277
7 TraesCS1B01G064200 chr1B 86.118 814 51 17 863 1631 48563782 48564578 0.000000e+00 821
8 TraesCS1B01G064200 chr1B 88.067 419 37 6 1213 1623 48715787 48716200 3.500000e-133 484
9 TraesCS1B01G064200 chr1B 93.274 223 12 2 503 725 48679479 48679698 2.250000e-85 326
10 TraesCS1B01G064200 chr1A 85.950 1274 103 42 410 1632 30268012 30269260 0.000000e+00 1291
11 TraesCS1B01G064200 chr1A 85.449 1079 89 33 592 1631 30264724 30265773 0.000000e+00 1061
12 TraesCS1B01G064200 chr1A 90.588 510 43 4 1 508 30252775 30253281 0.000000e+00 671
13 TraesCS1B01G064200 chr1A 83.657 618 92 6 1708 2324 50811448 50810839 7.270000e-160 573
14 TraesCS1B01G064200 chrUn 87.726 1108 55 35 585 1631 393542780 393541693 0.000000e+00 1218
15 TraesCS1B01G064200 chrUn 90.438 753 29 19 503 1217 383150927 383150180 0.000000e+00 952
16 TraesCS1B01G064200 chrUn 85.630 508 66 7 1 503 223001795 223002300 5.740000e-146 527
17 TraesCS1B01G064200 chrUn 84.921 504 69 7 9 508 92407330 92406830 9.670000e-139 503
18 TraesCS1B01G064200 chr1D 91.098 865 44 13 794 1631 30124396 30125254 0.000000e+00 1140
19 TraesCS1B01G064200 chr1D 86.602 724 67 19 1 697 30123572 30124292 0.000000e+00 773
20 TraesCS1B01G064200 chr1D 84.808 520 70 7 1 514 293617559 293617043 4.470000e-142 514
21 TraesCS1B01G064200 chr1D 84.598 435 61 5 1650 2080 30175278 30175710 5.990000e-116 427
22 TraesCS1B01G064200 chr6B 84.854 515 68 8 1 507 671719811 671720323 5.780000e-141 510
23 TraesCS1B01G064200 chr6B 84.571 525 66 11 1 516 671726938 671727456 7.480000e-140 507
24 TraesCS1B01G064200 chr7D 84.585 506 68 8 9 508 207314649 207314148 5.820000e-136 494
25 TraesCS1B01G064200 chr7B 84.055 508 72 8 7 508 546383951 546383447 4.530000e-132 481


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 TraesCS1B01G064200 chr1B 48734335 48736679 2344 False 4331.0 4331 100.0000 1 2345 1 chr1B.!!$F6 2344
1 TraesCS1B01G064200 chr1B 48707652 48708820 1168 False 1352.0 1352 88.3100 503 1631 1 chr1B.!!$F4 1128
2 TraesCS1B01G064200 chr1B 48656274 48661852 5578 False 1345.5 1352 88.2155 503 1631 2 chr1B.!!$F7 1128
3 TraesCS1B01G064200 chr1B 48587986 48589146 1160 False 1310.0 1310 87.7970 503 1623 1 chr1B.!!$F2 1120
4 TraesCS1B01G064200 chr1B 48624993 48626153 1160 False 1277.0 1277 87.2880 503 1623 1 chr1B.!!$F3 1120
5 TraesCS1B01G064200 chr1B 48675055 48679698 4643 False 834.5 1343 90.7175 503 1631 2 chr1B.!!$F8 1128
6 TraesCS1B01G064200 chr1B 48563782 48564578 796 False 821.0 821 86.1180 863 1631 1 chr1B.!!$F1 768
7 TraesCS1B01G064200 chr1A 30264724 30269260 4536 False 1176.0 1291 85.6995 410 1632 2 chr1A.!!$F2 1222
8 TraesCS1B01G064200 chr1A 30252775 30253281 506 False 671.0 671 90.5880 1 508 1 chr1A.!!$F1 507
9 TraesCS1B01G064200 chr1A 50810839 50811448 609 True 573.0 573 83.6570 1708 2324 1 chr1A.!!$R1 616
10 TraesCS1B01G064200 chrUn 393541693 393542780 1087 True 1218.0 1218 87.7260 585 1631 1 chrUn.!!$R3 1046
11 TraesCS1B01G064200 chrUn 383150180 383150927 747 True 952.0 952 90.4380 503 1217 1 chrUn.!!$R2 714
12 TraesCS1B01G064200 chrUn 223001795 223002300 505 False 527.0 527 85.6300 1 503 1 chrUn.!!$F1 502
13 TraesCS1B01G064200 chrUn 92406830 92407330 500 True 503.0 503 84.9210 9 508 1 chrUn.!!$R1 499
14 TraesCS1B01G064200 chr1D 30123572 30125254 1682 False 956.5 1140 88.8500 1 1631 2 chr1D.!!$F2 1630
15 TraesCS1B01G064200 chr1D 293617043 293617559 516 True 514.0 514 84.8080 1 514 1 chr1D.!!$R1 513
16 TraesCS1B01G064200 chr6B 671719811 671720323 512 False 510.0 510 84.8540 1 507 1 chr6B.!!$F1 506
17 TraesCS1B01G064200 chr6B 671726938 671727456 518 False 507.0 507 84.5710 1 516 1 chr6B.!!$F2 515
18 TraesCS1B01G064200 chr7D 207314148 207314649 501 True 494.0 494 84.5850 9 508 1 chr7D.!!$R1 499
19 TraesCS1B01G064200 chr7B 546383447 546383951 504 True 481.0 481 84.0550 7 508 1 chr7B.!!$R1 501

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
365 371 0.041312 CGTGCGGGTGAAAAAGTGAG 60.041 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 8752 0.031716 AGGCCATCTCTAGCTGGTCA 60.032 55.0 5.01 0.0 38.32 4.02 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
82 84 2.171870 TCCTCTCGTTCTTTTGGTGGTT 59.828 45.455 0.00 0.00 0.00 3.67
250 256 0.251653 ACGACCTGCACTTCTAGGGA 60.252 55.000 0.00 0.00 38.42 4.20
285 291 6.153756 TCTCAAGTACGTTCATCGATCAAAA 58.846 36.000 0.00 0.00 42.86 2.44
365 371 0.041312 CGTGCGGGTGAAAAAGTGAG 60.041 55.000 0.00 0.00 0.00 3.51
371 377 3.243401 GCGGGTGAAAAAGTGAGAACATT 60.243 43.478 0.00 0.00 0.00 2.71
402 408 6.497259 TCCAGTCCAATTGTAGACTCTTTACT 59.503 38.462 12.74 0.00 41.38 2.24
408 414 8.429641 TCCAATTGTAGACTCTTTACTGAAGTT 58.570 33.333 4.43 0.00 36.70 2.66
415 2882 7.555306 AGACTCTTTACTGAAGTTTTTGGAC 57.445 36.000 0.00 0.00 36.70 4.02
431 2898 7.603024 AGTTTTTGGACTATTTCTTCGAGTAGG 59.397 37.037 0.00 0.00 0.00 3.18
432 2899 6.845758 TTTGGACTATTTCTTCGAGTAGGA 57.154 37.500 0.00 0.00 0.00 2.94
451 3331 2.480419 GGAATTGATACCGCGAAGATGG 59.520 50.000 8.23 0.00 0.00 3.51
458 3338 1.600023 ACCGCGAAGATGGTTTCAAA 58.400 45.000 8.23 0.00 34.08 2.69
758 3695 3.077556 ACTCCCCGCGAGCTGATT 61.078 61.111 8.23 0.00 43.01 2.57
942 3904 2.697654 CAGAGGCTCTTGGAACAGAAG 58.302 52.381 15.90 0.00 42.39 2.85
943 3905 2.301296 CAGAGGCTCTTGGAACAGAAGA 59.699 50.000 15.90 0.00 42.39 2.87
944 3906 2.975489 AGAGGCTCTTGGAACAGAAGAA 59.025 45.455 12.24 0.00 42.39 2.52
963 3925 1.827399 AAGGTCGAGCCATCAACGGT 61.827 55.000 11.73 0.00 40.61 4.83
1072 4052 4.033776 CCAAGAAGAGGGCGGCCA 62.034 66.667 31.59 0.00 0.00 5.36
1080 4060 4.678743 AGGGCGGCCAAAGGAACC 62.679 66.667 31.59 0.00 0.00 3.62
1174 4154 4.889856 TCATGGCCGCATCCGACG 62.890 66.667 0.00 0.00 36.29 5.12
1276 4274 1.222115 ACAAGCAAACTCGACGCTCC 61.222 55.000 0.00 0.00 34.11 4.70
1278 4276 0.320771 AAGCAAACTCGACGCTCCAT 60.321 50.000 0.00 0.00 34.11 3.41
1289 4287 6.688578 ACTCGACGCTCCATATTATTTATGT 58.311 36.000 0.00 0.00 0.00 2.29
1296 4294 7.118390 ACGCTCCATATTATTTATGTTCTCTGC 59.882 37.037 0.00 0.00 0.00 4.26
1318 4316 5.299028 TGCTTGCTCTTCTTGTTTGTATCAA 59.701 36.000 0.00 0.00 0.00 2.57
1324 4322 6.631971 TCTTCTTGTTTGTATCAATGTGCA 57.368 33.333 0.00 0.00 0.00 4.57
1325 4323 7.218228 TCTTCTTGTTTGTATCAATGTGCAT 57.782 32.000 0.00 0.00 0.00 3.96
1334 4332 7.628769 TTGTATCAATGTGCATGTTAGTGAT 57.371 32.000 11.52 11.52 0.00 3.06
1335 4333 7.250445 TGTATCAATGTGCATGTTAGTGATC 57.750 36.000 10.57 0.00 0.00 2.92
1336 4334 7.049754 TGTATCAATGTGCATGTTAGTGATCT 58.950 34.615 10.57 0.00 0.00 2.75
1348 4346 9.098355 GCATGTTAGTGATCTTGTTGTAATCTA 57.902 33.333 0.00 0.00 0.00 1.98
1454 4456 8.499162 CGAATTTAAATATTGGCAGACTAGGAG 58.501 37.037 0.01 0.00 0.00 3.69
1455 4457 9.561069 GAATTTAAATATTGGCAGACTAGGAGA 57.439 33.333 0.01 0.00 0.00 3.71
1457 4459 9.732130 ATTTAAATATTGGCAGACTAGGAGATC 57.268 33.333 0.00 0.00 0.00 2.75
1529 4548 2.771943 AGAAACCACACTCCTGACTTGA 59.228 45.455 0.00 0.00 0.00 3.02
1564 4585 4.839121 TGACCGCAGTTGGAGTTAATTAT 58.161 39.130 0.00 0.00 0.00 1.28
1615 4636 2.030274 GCATAAAACCACCAAGTCGCTT 60.030 45.455 0.00 0.00 0.00 4.68
1654 4675 2.793278 AACACCGCAATTTGTTCTCC 57.207 45.000 0.00 0.00 29.75 3.71
1655 4676 1.981256 ACACCGCAATTTGTTCTCCT 58.019 45.000 0.00 0.00 0.00 3.69
1658 4679 4.079253 ACACCGCAATTTGTTCTCCTATT 58.921 39.130 0.00 0.00 0.00 1.73
1659 4680 5.250200 ACACCGCAATTTGTTCTCCTATTA 58.750 37.500 0.00 0.00 0.00 0.98
1662 4683 7.554835 ACACCGCAATTTGTTCTCCTATTATAA 59.445 33.333 0.00 0.00 0.00 0.98
1663 4684 8.402472 CACCGCAATTTGTTCTCCTATTATAAA 58.598 33.333 0.00 0.00 0.00 1.40
1664 4685 8.962679 ACCGCAATTTGTTCTCCTATTATAAAA 58.037 29.630 0.00 0.00 0.00 1.52
1665 4686 9.450807 CCGCAATTTGTTCTCCTATTATAAAAG 57.549 33.333 0.00 0.00 0.00 2.27
1666 4687 8.958043 CGCAATTTGTTCTCCTATTATAAAAGC 58.042 33.333 0.00 0.00 0.00 3.51
1667 4688 8.958043 GCAATTTGTTCTCCTATTATAAAAGCG 58.042 33.333 0.00 0.00 0.00 4.68
1668 4689 8.958043 CAATTTGTTCTCCTATTATAAAAGCGC 58.042 33.333 0.00 0.00 0.00 5.92
1669 4690 6.613755 TTGTTCTCCTATTATAAAAGCGCC 57.386 37.500 2.29 0.00 0.00 6.53
1671 4692 5.526111 TGTTCTCCTATTATAAAAGCGCCAC 59.474 40.000 2.29 0.00 0.00 5.01
1672 4693 5.546621 TCTCCTATTATAAAAGCGCCACT 57.453 39.130 2.29 0.00 0.00 4.00
1673 4694 5.925509 TCTCCTATTATAAAAGCGCCACTT 58.074 37.500 2.29 0.00 41.70 3.16
1675 4696 5.061179 TCCTATTATAAAAGCGCCACTTCC 58.939 41.667 2.29 0.00 37.75 3.46
1676 4697 5.063880 CCTATTATAAAAGCGCCACTTCCT 58.936 41.667 2.29 0.00 37.75 3.36
1677 4698 4.900635 ATTATAAAAGCGCCACTTCCTG 57.099 40.909 2.29 0.00 37.75 3.86
1678 4699 1.463674 ATAAAAGCGCCACTTCCTGG 58.536 50.000 2.29 0.00 44.08 4.45
1679 4700 0.109723 TAAAAGCGCCACTTCCTGGT 59.890 50.000 2.29 0.00 42.99 4.00
1680 4701 1.172812 AAAAGCGCCACTTCCTGGTC 61.173 55.000 2.29 0.00 42.99 4.02
1681 4702 2.337879 AAAGCGCCACTTCCTGGTCA 62.338 55.000 2.29 0.00 42.99 4.02
1682 4703 2.281484 GCGCCACTTCCTGGTCAA 60.281 61.111 0.00 0.00 42.99 3.18
1683 4704 2.328099 GCGCCACTTCCTGGTCAAG 61.328 63.158 0.00 0.00 42.99 3.02
1699 4720 7.721286 CTGGTCAAGGAAGATATAATGTGTC 57.279 40.000 0.00 0.00 0.00 3.67
1700 4721 6.591935 TGGTCAAGGAAGATATAATGTGTCC 58.408 40.000 0.00 0.00 0.00 4.02
1701 4722 6.157820 TGGTCAAGGAAGATATAATGTGTCCA 59.842 38.462 0.00 0.00 0.00 4.02
1702 4723 7.147320 TGGTCAAGGAAGATATAATGTGTCCAT 60.147 37.037 0.00 0.00 0.00 3.41
1703 4724 7.721399 GGTCAAGGAAGATATAATGTGTCCATT 59.279 37.037 0.00 0.00 43.62 3.16
1705 4726 9.123902 TCAAGGAAGATATAATGTGTCCATTTG 57.876 33.333 0.00 0.00 41.50 2.32
1707 4728 8.455903 AGGAAGATATAATGTGTCCATTTGTG 57.544 34.615 0.00 0.00 41.50 3.33
1708 4729 8.274322 AGGAAGATATAATGTGTCCATTTGTGA 58.726 33.333 0.00 0.00 41.50 3.58
1709 4730 9.071276 GGAAGATATAATGTGTCCATTTGTGAT 57.929 33.333 0.00 0.00 41.50 3.06
1710 4731 9.888878 GAAGATATAATGTGTCCATTTGTGATG 57.111 33.333 0.00 0.00 41.50 3.07
1711 4732 9.631257 AAGATATAATGTGTCCATTTGTGATGA 57.369 29.630 0.00 0.00 41.50 2.92
1712 4733 9.281371 AGATATAATGTGTCCATTTGTGATGAG 57.719 33.333 0.00 0.00 41.50 2.90
1714 4735 9.803507 ATATAATGTGTCCATTTGTGATGAGAT 57.196 29.630 0.00 0.00 41.50 2.75
1715 4736 5.830000 ATGTGTCCATTTGTGATGAGATG 57.170 39.130 0.00 0.00 0.00 2.90
1716 4737 4.654915 TGTGTCCATTTGTGATGAGATGT 58.345 39.130 0.00 0.00 0.00 3.06
1723 4744 5.295292 CCATTTGTGATGAGATGTGGACTAC 59.705 44.000 0.00 0.00 0.00 2.73
1737 4758 4.067972 TGGACTACACAGTTGAAAGGAC 57.932 45.455 0.00 0.00 34.21 3.85
1738 5921 3.709653 TGGACTACACAGTTGAAAGGACT 59.290 43.478 0.00 0.00 34.21 3.85
1739 5922 4.202223 TGGACTACACAGTTGAAAGGACTC 60.202 45.833 0.00 0.00 34.21 3.36
1740 5923 4.202223 GGACTACACAGTTGAAAGGACTCA 60.202 45.833 0.00 0.00 34.21 3.41
1743 5926 2.222027 CACAGTTGAAAGGACTCACCC 58.778 52.381 0.00 0.00 40.05 4.61
1745 5928 2.222027 CAGTTGAAAGGACTCACCCAC 58.778 52.381 0.00 0.00 40.05 4.61
1748 5931 3.650942 AGTTGAAAGGACTCACCCACATA 59.349 43.478 0.00 0.00 40.05 2.29
1751 5934 5.255397 TGAAAGGACTCACCCACATAATT 57.745 39.130 0.00 0.00 40.05 1.40
1761 5944 8.038862 ACTCACCCACATAATTTAGATGAGAT 57.961 34.615 4.54 0.00 35.95 2.75
1764 5947 8.375506 TCACCCACATAATTTAGATGAGATACC 58.624 37.037 0.00 0.00 0.00 2.73
1792 5975 7.751768 AGAAAACTGAAGGAATGAGTTTAGG 57.248 36.000 0.00 0.00 38.64 2.69
1798 6218 4.597507 TGAAGGAATGAGTTTAGGACCTGT 59.402 41.667 3.53 0.00 0.00 4.00
1803 6223 1.891150 TGAGTTTAGGACCTGTCGACC 59.109 52.381 14.12 0.00 0.00 4.79
1804 6224 2.169330 GAGTTTAGGACCTGTCGACCT 58.831 52.381 14.12 4.80 37.76 3.85
1807 6227 0.679002 TTAGGACCTGTCGACCTCGG 60.679 60.000 14.12 13.12 40.29 4.63
1811 6231 0.179134 GACCTGTCGACCTCGGAATG 60.179 60.000 14.12 0.00 40.29 2.67
1837 6257 6.677781 TGATAAATTTCAAGATGGGTCGTC 57.322 37.500 0.00 0.00 0.00 4.20
1838 6258 6.176896 TGATAAATTTCAAGATGGGTCGTCA 58.823 36.000 0.00 0.00 0.00 4.35
1840 6260 2.920724 TTTCAAGATGGGTCGTCACA 57.079 45.000 0.00 0.00 0.00 3.58
1859 6736 6.263344 GTCACAACGTACTCATATAGCAGAA 58.737 40.000 0.00 0.00 0.00 3.02
1861 6738 7.274904 GTCACAACGTACTCATATAGCAGAAAA 59.725 37.037 0.00 0.00 0.00 2.29
1875 6752 2.669391 GCAGAAAAGCAATTCAGGGTCG 60.669 50.000 4.59 0.00 0.00 4.79
1876 6753 1.541588 AGAAAAGCAATTCAGGGTCGC 59.458 47.619 4.59 0.00 0.00 5.19
1880 6757 1.377202 GCAATTCAGGGTCGCCTCA 60.377 57.895 0.00 0.00 0.00 3.86
1883 6760 0.181350 AATTCAGGGTCGCCTCATCC 59.819 55.000 0.00 0.00 0.00 3.51
1888 6765 4.530857 GGTCGCCTCATCCCACGG 62.531 72.222 0.00 0.00 0.00 4.94
1896 6773 0.824109 CTCATCCCACGGCTTCACTA 59.176 55.000 0.00 0.00 0.00 2.74
1908 6785 1.561643 CTTCACTAGCTCCCACCTCA 58.438 55.000 0.00 0.00 0.00 3.86
1909 6786 1.205893 CTTCACTAGCTCCCACCTCAC 59.794 57.143 0.00 0.00 0.00 3.51
1934 6811 2.201708 TCACACACCGCCGGTTAGA 61.202 57.895 5.76 0.00 31.02 2.10
1950 7027 0.893727 TAGAGGCAGCACTCGTGTCA 60.894 55.000 0.00 0.00 42.31 3.58
1953 7030 1.669115 GGCAGCACTCGTGTCATGT 60.669 57.895 0.00 0.00 0.00 3.21
1954 7031 1.494628 GCAGCACTCGTGTCATGTG 59.505 57.895 0.00 0.00 35.08 3.21
1970 7047 0.758123 TGTGTCACCTCACTCATGCA 59.242 50.000 0.00 0.00 38.90 3.96
2000 7770 2.349580 CGCAGACTCCACATGTATGTTG 59.650 50.000 0.00 1.56 39.39 3.33
2005 7775 4.690748 AGACTCCACATGTATGTTGTTTCG 59.309 41.667 0.00 0.00 39.39 3.46
2010 7780 2.158841 ACATGTATGTTGTTTCGCCGTC 59.841 45.455 0.00 0.00 37.90 4.79
2047 7817 1.287730 GCTCTCGTGTGCTGTCTTGG 61.288 60.000 4.40 0.00 0.00 3.61
2075 7955 1.541588 GCTCATCTTGGCTCGGTTTTT 59.458 47.619 0.00 0.00 0.00 1.94
2076 7956 2.414691 GCTCATCTTGGCTCGGTTTTTC 60.415 50.000 0.00 0.00 0.00 2.29
2085 7965 5.523438 TGGCTCGGTTTTTCTTTAACAAT 57.477 34.783 0.00 0.00 0.00 2.71
2104 7984 4.039124 ACAATTTTTCATCTTGGCTCCGTT 59.961 37.500 0.00 0.00 0.00 4.44
2148 8028 2.746277 GCGACGGGAGGCACAATT 60.746 61.111 0.00 0.00 38.29 2.32
2173 8336 1.743996 CTTCCTACAAAGCTCCAGCC 58.256 55.000 0.00 0.00 43.38 4.85
2202 8388 0.608640 GAAGAAGTCGGCAAGGAGGA 59.391 55.000 0.00 0.00 0.00 3.71
2212 8398 1.376037 CAAGGAGGAGTTGGCGGTC 60.376 63.158 0.00 0.00 0.00 4.79
2213 8399 1.841556 AAGGAGGAGTTGGCGGTCA 60.842 57.895 0.00 0.00 0.00 4.02
2217 8403 3.056328 GGAGTTGGCGGTCAAGGC 61.056 66.667 0.00 0.00 35.80 4.35
2240 8426 1.066143 CCGAAGTAGTGGGCATGAACT 60.066 52.381 0.00 0.00 0.00 3.01
2269 8752 1.000993 AGAGGTCTCCACGCTCCAT 59.999 57.895 0.00 0.00 0.00 3.41
2278 8761 1.517361 CACGCTCCATGACCAGCTA 59.483 57.895 0.00 0.00 33.09 3.32
2293 8776 2.094286 CCAGCTAGAGATGGCCTATTCG 60.094 54.545 3.32 0.00 45.25 3.34
2302 8785 2.391926 TGGCCTATTCGGAGATGGTA 57.608 50.000 3.32 0.00 35.04 3.25
2304 8787 3.248024 TGGCCTATTCGGAGATGGTATT 58.752 45.455 3.32 0.00 35.04 1.89
2305 8788 3.007940 TGGCCTATTCGGAGATGGTATTG 59.992 47.826 3.32 0.00 35.04 1.90
2312 8795 2.362397 TCGGAGATGGTATTGCACTCTC 59.638 50.000 0.00 0.00 33.24 3.20
2315 8798 1.482182 AGATGGTATTGCACTCTCGCA 59.518 47.619 0.00 0.00 41.03 5.10
2324 8807 1.893062 CACTCTCGCACCATCCAGA 59.107 57.895 0.00 0.00 0.00 3.86
2325 8808 0.179116 CACTCTCGCACCATCCAGAG 60.179 60.000 0.00 0.00 38.71 3.35
2326 8809 1.326213 ACTCTCGCACCATCCAGAGG 61.326 60.000 0.00 0.00 37.33 3.69
2329 8812 2.249413 CTCGCACCATCCAGAGGCTT 62.249 60.000 0.00 0.00 0.00 4.35
2330 8813 2.110967 CGCACCATCCAGAGGCTTG 61.111 63.158 0.00 0.00 0.00 4.01
2332 8815 1.310933 GCACCATCCAGAGGCTTGTG 61.311 60.000 0.00 0.00 0.00 3.33
2333 8816 0.325933 CACCATCCAGAGGCTTGTGA 59.674 55.000 0.00 0.00 0.00 3.58
2334 8817 0.326264 ACCATCCAGAGGCTTGTGAC 59.674 55.000 0.00 0.00 0.00 3.67
2336 8819 1.833630 CCATCCAGAGGCTTGTGACTA 59.166 52.381 0.00 0.00 0.00 2.59
2337 8820 2.419297 CCATCCAGAGGCTTGTGACTAC 60.419 54.545 0.00 0.00 0.00 2.73
2338 8821 0.888619 TCCAGAGGCTTGTGACTACG 59.111 55.000 0.00 0.00 0.00 3.51
2339 8822 0.737715 CCAGAGGCTTGTGACTACGC 60.738 60.000 0.00 0.00 0.00 4.42
2340 8823 0.038251 CAGAGGCTTGTGACTACGCA 60.038 55.000 0.00 0.00 34.56 5.24
2341 8824 0.244994 AGAGGCTTGTGACTACGCAG 59.755 55.000 0.00 0.00 37.81 5.18
2342 8825 0.737715 GAGGCTTGTGACTACGCAGG 60.738 60.000 0.00 0.00 37.81 4.85
2344 8827 1.292223 GCTTGTGACTACGCAGGGA 59.708 57.895 0.00 0.00 37.81 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.807304 GTCGTTGACAAGAACAAAGAGGTA 59.193 41.667 0.00 0.00 36.71 3.08
82 84 8.478877 GGACAGAAAACTCTCTAATCTTATGGA 58.521 37.037 0.00 0.00 0.00 3.41
136 138 4.644685 AGGCTGACACAACAACATAAACTT 59.355 37.500 0.00 0.00 0.00 2.66
216 222 2.544686 AGGTCGTCGAATCACTCTATCG 59.455 50.000 0.00 0.00 37.90 2.92
250 256 8.246430 TGAACGTACTTGAGATAGGGATTATT 57.754 34.615 0.00 0.00 0.00 1.40
260 266 5.500645 TGATCGATGAACGTACTTGAGAT 57.499 39.130 0.54 0.00 43.13 2.75
285 291 3.766051 GCCCATCCAAAAAGATGAGAAGT 59.234 43.478 3.14 0.00 45.43 3.01
329 335 5.410132 CCCGCACGAATATTACCAATAATGA 59.590 40.000 0.00 0.00 32.98 2.57
365 371 2.229792 TGGACTGGAGCAACAATGTTC 58.770 47.619 0.00 0.00 36.17 3.18
371 377 2.363306 ACAATTGGACTGGAGCAACA 57.637 45.000 10.83 0.00 0.00 3.33
402 408 7.497909 ACTCGAAGAAATAGTCCAAAAACTTCA 59.502 33.333 0.00 0.00 34.09 3.02
408 414 7.235935 TCCTACTCGAAGAAATAGTCCAAAA 57.764 36.000 0.00 0.00 34.09 2.44
415 2882 9.413048 GGTATCAATTCCTACTCGAAGAAATAG 57.587 37.037 0.00 0.00 34.09 1.73
431 2898 3.131396 ACCATCTTCGCGGTATCAATTC 58.869 45.455 6.13 0.00 32.31 2.17
432 2899 3.194005 ACCATCTTCGCGGTATCAATT 57.806 42.857 6.13 0.00 32.31 2.32
559 3462 7.926018 GCCTTGTTATTAATGGAAAGGGTAATG 59.074 37.037 18.81 2.50 35.71 1.90
609 3512 6.360414 GCTTTTAAACGTGTATACAAACCCAC 59.640 38.462 7.25 0.00 0.00 4.61
618 3521 9.171701 GTTCACATTTGCTTTTAAACGTGTATA 57.828 29.630 0.00 0.00 35.79 1.47
619 3522 7.702772 TGTTCACATTTGCTTTTAAACGTGTAT 59.297 29.630 0.00 0.00 35.79 2.29
710 3627 2.403987 CGTACGCGTCCTGAGAGG 59.596 66.667 18.63 0.00 36.46 3.69
754 3691 3.618594 GTGATCAACGCTCAGCTTAATCA 59.381 43.478 0.00 0.00 0.00 2.57
758 3695 1.550524 AGGTGATCAACGCTCAGCTTA 59.449 47.619 4.80 0.00 46.34 3.09
942 3904 0.721718 CGTTGATGGCTCGACCTTTC 59.278 55.000 5.77 4.10 40.22 2.62
943 3905 0.673644 CCGTTGATGGCTCGACCTTT 60.674 55.000 5.77 0.00 40.22 3.11
944 3906 1.079127 CCGTTGATGGCTCGACCTT 60.079 57.895 5.77 0.06 40.22 3.50
963 3925 2.884012 GTGTTTGGTGGTGTGATGATCA 59.116 45.455 0.00 0.00 0.00 2.92
1072 4052 3.343421 GTCGCGCACGGTTCCTTT 61.343 61.111 8.75 0.00 40.63 3.11
1080 4060 2.792290 CTTCTCCATGTCGCGCACG 61.792 63.158 8.75 0.00 42.01 5.34
1174 4154 2.420466 GACGGCCTTATCGACCCC 59.580 66.667 0.00 0.00 0.00 4.95
1276 4274 9.823098 GAGCAAGCAGAGAACATAAATAATATG 57.177 33.333 0.00 0.00 0.00 1.78
1278 4276 9.618890 AAGAGCAAGCAGAGAACATAAATAATA 57.381 29.630 0.00 0.00 0.00 0.98
1289 4287 3.482156 ACAAGAAGAGCAAGCAGAGAA 57.518 42.857 0.00 0.00 0.00 2.87
1296 4294 7.325338 CACATTGATACAAACAAGAAGAGCAAG 59.675 37.037 0.00 0.00 0.00 4.01
1318 4316 5.474532 ACAACAAGATCACTAACATGCACAT 59.525 36.000 0.00 0.00 0.00 3.21
1334 4332 8.602424 TGAGGAAGGAAATAGATTACAACAAGA 58.398 33.333 0.00 0.00 0.00 3.02
1335 4333 8.792830 TGAGGAAGGAAATAGATTACAACAAG 57.207 34.615 0.00 0.00 0.00 3.16
1336 4334 8.383175 ACTGAGGAAGGAAATAGATTACAACAA 58.617 33.333 0.00 0.00 0.00 2.83
1348 4346 6.310149 ACATCAGAAAACTGAGGAAGGAAAT 58.690 36.000 16.56 0.00 38.37 2.17
1393 4395 3.149005 TGAAGTACATGGGGTGTTTCC 57.851 47.619 0.00 0.00 42.29 3.13
1454 4456 6.959671 AGTGTCAAAGAAGATTTCTCGATC 57.040 37.500 0.00 0.00 39.61 3.69
1455 4457 7.095017 GGAAAGTGTCAAAGAAGATTTCTCGAT 60.095 37.037 0.00 0.00 39.61 3.59
1456 4458 6.202954 GGAAAGTGTCAAAGAAGATTTCTCGA 59.797 38.462 0.00 0.00 39.61 4.04
1457 4459 6.017934 TGGAAAGTGTCAAAGAAGATTTCTCG 60.018 38.462 0.00 0.00 39.61 4.04
1529 4548 1.244019 GCGGTCATGCCCAAGAACTT 61.244 55.000 0.00 0.00 0.00 2.66
1564 4585 5.797051 AGCCGTAAATGTGGTAGTTTCTTA 58.203 37.500 0.00 0.00 0.00 2.10
1640 4661 8.958043 GCTTTTATAATAGGAGAACAAATTGCG 58.042 33.333 5.27 0.00 0.00 4.85
1642 4663 8.958043 GCGCTTTTATAATAGGAGAACAAATTG 58.042 33.333 0.00 0.00 0.00 2.32
1648 4669 5.758784 AGTGGCGCTTTTATAATAGGAGAAC 59.241 40.000 7.64 0.00 0.00 3.01
1654 4675 5.049405 CCAGGAAGTGGCGCTTTTATAATAG 60.049 44.000 15.41 0.00 40.39 1.73
1655 4676 4.819630 CCAGGAAGTGGCGCTTTTATAATA 59.180 41.667 15.41 0.00 40.39 0.98
1658 4679 2.639065 CCAGGAAGTGGCGCTTTTATA 58.361 47.619 15.41 0.00 40.39 0.98
1659 4680 1.463674 CCAGGAAGTGGCGCTTTTAT 58.536 50.000 15.41 1.20 40.39 1.40
1675 4696 6.708054 GGACACATTATATCTTCCTTGACCAG 59.292 42.308 0.00 0.00 0.00 4.00
1676 4697 6.157820 TGGACACATTATATCTTCCTTGACCA 59.842 38.462 0.00 0.00 0.00 4.02
1677 4698 6.591935 TGGACACATTATATCTTCCTTGACC 58.408 40.000 0.00 0.00 0.00 4.02
1678 4699 8.682936 AATGGACACATTATATCTTCCTTGAC 57.317 34.615 0.00 0.00 45.17 3.18
1679 4700 9.123902 CAAATGGACACATTATATCTTCCTTGA 57.876 33.333 0.00 0.00 46.25 3.02
1680 4701 8.906867 ACAAATGGACACATTATATCTTCCTTG 58.093 33.333 0.00 0.00 46.25 3.61
1681 4702 8.906867 CACAAATGGACACATTATATCTTCCTT 58.093 33.333 0.00 0.00 46.25 3.36
1682 4703 8.274322 TCACAAATGGACACATTATATCTTCCT 58.726 33.333 0.00 0.00 46.25 3.36
1683 4704 8.450578 TCACAAATGGACACATTATATCTTCC 57.549 34.615 0.00 0.00 46.25 3.46
1686 4707 9.281371 CTCATCACAAATGGACACATTATATCT 57.719 33.333 0.00 0.00 46.25 1.98
1687 4708 9.276590 TCTCATCACAAATGGACACATTATATC 57.723 33.333 0.00 0.00 46.25 1.63
1688 4709 9.803507 ATCTCATCACAAATGGACACATTATAT 57.196 29.630 0.00 0.00 46.25 0.86
1689 4710 9.059260 CATCTCATCACAAATGGACACATTATA 57.941 33.333 0.00 0.00 46.25 0.98
1690 4711 7.558807 ACATCTCATCACAAATGGACACATTAT 59.441 33.333 0.00 0.00 46.25 1.28
1693 4714 5.124936 CACATCTCATCACAAATGGACACAT 59.875 40.000 0.00 0.00 39.54 3.21
1694 4715 4.456566 CACATCTCATCACAAATGGACACA 59.543 41.667 0.00 0.00 0.00 3.72
1695 4716 4.142534 CCACATCTCATCACAAATGGACAC 60.143 45.833 0.00 0.00 0.00 3.67
1697 4718 4.095483 GTCCACATCTCATCACAAATGGAC 59.905 45.833 4.46 4.46 45.76 4.02
1698 4719 4.019051 AGTCCACATCTCATCACAAATGGA 60.019 41.667 0.00 0.00 32.62 3.41
1699 4720 4.267536 AGTCCACATCTCATCACAAATGG 58.732 43.478 0.00 0.00 0.00 3.16
1700 4721 5.876460 TGTAGTCCACATCTCATCACAAATG 59.124 40.000 0.00 0.00 30.04 2.32
1701 4722 5.877012 GTGTAGTCCACATCTCATCACAAAT 59.123 40.000 0.00 0.00 43.92 2.32
1702 4723 5.237815 GTGTAGTCCACATCTCATCACAAA 58.762 41.667 0.00 0.00 43.92 2.83
1703 4724 4.820897 GTGTAGTCCACATCTCATCACAA 58.179 43.478 0.00 0.00 43.92 3.33
1715 4736 3.808174 GTCCTTTCAACTGTGTAGTCCAC 59.192 47.826 0.00 0.00 44.78 4.02
1716 4737 3.709653 AGTCCTTTCAACTGTGTAGTCCA 59.290 43.478 0.00 0.00 35.69 4.02
1723 4744 2.222027 GGGTGAGTCCTTTCAACTGTG 58.778 52.381 0.00 0.00 35.12 3.66
1731 4752 7.027874 TCTAAATTATGTGGGTGAGTCCTTT 57.972 36.000 0.00 0.00 36.25 3.11
1735 4756 7.500992 TCTCATCTAAATTATGTGGGTGAGTC 58.499 38.462 8.54 0.00 33.96 3.36
1737 4758 9.429359 GTATCTCATCTAAATTATGTGGGTGAG 57.571 37.037 2.96 2.96 33.65 3.51
1738 5921 8.375506 GGTATCTCATCTAAATTATGTGGGTGA 58.624 37.037 0.00 0.00 0.00 4.02
1739 5922 8.156820 TGGTATCTCATCTAAATTATGTGGGTG 58.843 37.037 0.00 0.00 0.00 4.61
1740 5923 8.275187 TGGTATCTCATCTAAATTATGTGGGT 57.725 34.615 0.00 0.00 0.00 4.51
1751 5934 9.035890 TCAGTTTTCTTCTGGTATCTCATCTAA 57.964 33.333 0.00 0.00 34.15 2.10
1761 5944 6.837312 TCATTCCTTCAGTTTTCTTCTGGTA 58.163 36.000 0.00 0.00 34.15 3.25
1764 5947 6.874288 ACTCATTCCTTCAGTTTTCTTCTG 57.126 37.500 0.00 0.00 0.00 3.02
1772 5955 5.310857 AGGTCCTAAACTCATTCCTTCAGTT 59.689 40.000 0.00 0.00 31.48 3.16
1792 5975 0.179134 CATTCCGAGGTCGACAGGTC 60.179 60.000 18.91 9.64 43.02 3.85
1798 6218 5.777850 TTTATCATACATTCCGAGGTCGA 57.222 39.130 0.00 0.00 43.02 4.20
1811 6231 8.154649 ACGACCCATCTTGAAATTTATCATAC 57.845 34.615 0.00 0.00 0.00 2.39
1837 6257 7.520119 TTTTCTGCTATATGAGTACGTTGTG 57.480 36.000 0.00 0.00 0.00 3.33
1838 6258 6.255887 GCTTTTCTGCTATATGAGTACGTTGT 59.744 38.462 0.00 0.00 0.00 3.32
1840 6260 6.338146 TGCTTTTCTGCTATATGAGTACGTT 58.662 36.000 0.00 0.00 0.00 3.99
1846 6266 7.361127 CCTGAATTGCTTTTCTGCTATATGAG 58.639 38.462 0.00 0.00 0.00 2.90
1852 6729 3.758554 GACCCTGAATTGCTTTTCTGCTA 59.241 43.478 0.00 0.00 0.00 3.49
1854 6731 2.669391 CGACCCTGAATTGCTTTTCTGC 60.669 50.000 0.00 0.00 0.00 4.26
1859 6736 0.251341 AGGCGACCCTGAATTGCTTT 60.251 50.000 0.00 0.00 40.94 3.51
1861 6738 1.078143 GAGGCGACCCTGAATTGCT 60.078 57.895 0.00 0.00 43.12 3.91
1876 6753 1.450312 GTGAAGCCGTGGGATGAGG 60.450 63.158 0.00 0.00 0.00 3.86
1880 6757 1.522569 GCTAGTGAAGCCGTGGGAT 59.477 57.895 0.00 0.00 46.25 3.85
1914 6791 3.518419 TAACCGGCGGTGTGTGACC 62.518 63.158 34.87 0.00 42.07 4.02
1920 6797 4.078516 GCCTCTAACCGGCGGTGT 62.079 66.667 34.87 23.59 37.87 4.16
1934 6811 1.375140 CATGACACGAGTGCTGCCT 60.375 57.895 2.76 0.00 0.00 4.75
1939 6970 0.508641 GTGACACATGACACGAGTGC 59.491 55.000 0.00 0.00 36.76 4.40
1950 7027 1.348696 TGCATGAGTGAGGTGACACAT 59.651 47.619 8.08 0.00 42.45 3.21
1953 7030 0.321034 GCTGCATGAGTGAGGTGACA 60.321 55.000 0.00 0.00 0.00 3.58
1954 7031 0.036577 AGCTGCATGAGTGAGGTGAC 60.037 55.000 1.02 0.00 0.00 3.67
1981 7058 5.389830 CGAAACAACATACATGTGGAGTCTG 60.390 44.000 9.11 7.83 41.61 3.51
2010 7780 2.110967 CCAAGATGAGCAGGCCACG 61.111 63.158 5.01 0.00 0.00 4.94
2047 7817 1.503542 CCAAGATGAGCAACGTGGC 59.496 57.895 6.88 6.88 0.00 5.01
2075 7955 7.872483 GGAGCCAAGATGAAAAATTGTTAAAGA 59.128 33.333 0.00 0.00 0.00 2.52
2076 7956 7.148755 CGGAGCCAAGATGAAAAATTGTTAAAG 60.149 37.037 0.00 0.00 0.00 1.85
2085 7965 2.955660 ACAACGGAGCCAAGATGAAAAA 59.044 40.909 0.00 0.00 0.00 1.94
2104 7984 2.284921 CTCCCCTCCTCCTGCACA 60.285 66.667 0.00 0.00 0.00 4.57
2133 8013 2.877691 GCAATTGTGCCTCCCGTC 59.122 61.111 7.40 0.00 45.68 4.79
2185 8371 0.543174 ACTCCTCCTTGCCGACTTCT 60.543 55.000 0.00 0.00 0.00 2.85
2195 8381 1.415672 TTGACCGCCAACTCCTCCTT 61.416 55.000 0.00 0.00 0.00 3.36
2212 8398 2.100631 CACTACTTCGGGCGCCTTG 61.101 63.158 28.56 19.56 0.00 3.61
2213 8399 2.264794 CACTACTTCGGGCGCCTT 59.735 61.111 28.56 8.32 0.00 4.35
2222 8408 3.451178 TCCTAGTTCATGCCCACTACTTC 59.549 47.826 0.00 0.00 0.00 3.01
2234 8420 6.678547 AGACCTCTGAAGTATCCTAGTTCAT 58.321 40.000 5.20 0.00 44.54 2.57
2240 8426 4.686396 CGTGGAGACCTCTGAAGTATCCTA 60.686 50.000 18.11 5.28 44.33 2.94
2261 8744 0.684479 TCTAGCTGGTCATGGAGCGT 60.684 55.000 0.00 0.00 40.34 5.07
2262 8745 0.031857 CTCTAGCTGGTCATGGAGCG 59.968 60.000 0.00 0.00 40.34 5.03
2269 8752 0.031716 AGGCCATCTCTAGCTGGTCA 60.032 55.000 5.01 0.00 38.32 4.02
2278 8761 2.685106 TCTCCGAATAGGCCATCTCT 57.315 50.000 5.01 0.00 40.77 3.10
2293 8776 2.748605 CGAGAGTGCAATACCATCTCC 58.251 52.381 0.00 0.00 34.26 3.71
2304 8787 2.265739 GGATGGTGCGAGAGTGCA 59.734 61.111 0.00 0.00 43.95 4.57
2305 8788 1.812922 CTGGATGGTGCGAGAGTGC 60.813 63.158 0.00 0.00 0.00 4.40
2312 8795 2.110967 CAAGCCTCTGGATGGTGCG 61.111 63.158 0.00 0.00 0.00 5.34
2315 8798 0.326264 GTCACAAGCCTCTGGATGGT 59.674 55.000 0.00 0.00 0.00 3.55
2324 8807 1.293498 CCTGCGTAGTCACAAGCCT 59.707 57.895 0.00 0.00 0.00 4.58
2325 8808 1.741770 CCCTGCGTAGTCACAAGCC 60.742 63.158 0.00 0.00 0.00 4.35
2326 8809 1.292223 TCCCTGCGTAGTCACAAGC 59.708 57.895 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.