Multiple sequence alignment - TraesCS7A01G093600

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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 TraesCS7A01G093600 chr7A 100.000 2884 0 0 1 2884 57155735 57158618 0.000000e+00 5326.0
1 TraesCS7A01G093600 chr7A 92.139 865 67 1 2019 2882 705603561 705602697 0.000000e+00 1219.0
2 TraesCS7A01G093600 chr7A 90.971 875 68 6 2019 2884 526150135 526149263 0.000000e+00 1168.0
3 TraesCS7A01G093600 chr7A 86.806 955 69 25 910 1828 57095818 57096751 0.000000e+00 1013.0
4 TraesCS7A01G093600 chr7A 84.375 256 30 8 844 1091 57130573 57130826 2.870000e-60 243.0
5 TraesCS7A01G093600 chr7A 84.545 110 17 0 1906 2015 56235664 56235773 3.040000e-20 110.0
6 TraesCS7A01G093600 chr7A 94.737 57 3 0 1 57 694029744 694029688 3.960000e-14 89.8
7 TraesCS7A01G093600 chr7A 94.737 57 3 0 1 57 706442645 706442589 3.960000e-14 89.8
8 TraesCS7A01G093600 chr7D 85.000 1240 113 40 650 1836 53710588 53711807 0.000000e+00 1192.0
9 TraesCS7A01G093600 chr7D 88.618 738 55 17 930 1652 53637739 53638462 0.000000e+00 870.0
10 TraesCS7A01G093600 chr7D 89.247 186 18 2 1411 1595 53558666 53558850 6.210000e-57 231.0
11 TraesCS7A01G093600 chr7D 87.958 191 22 1 1405 1595 53708383 53708572 1.040000e-54 224.0
12 TraesCS7A01G093600 chr7D 97.674 129 3 0 1888 2016 53711806 53711934 3.740000e-54 222.0
13 TraesCS7A01G093600 chr7D 92.969 128 9 0 1883 2010 53577805 53577932 1.360000e-43 187.0
14 TraesCS7A01G093600 chr7D 90.909 110 10 0 1906 2015 53529990 53530099 6.440000e-32 148.0
15 TraesCS7A01G093600 chr1A 91.484 869 67 3 2018 2884 405680223 405679360 0.000000e+00 1188.0
16 TraesCS7A01G093600 chr1A 94.737 57 3 0 1 57 58025518 58025574 3.960000e-14 89.8
17 TraesCS7A01G093600 chr7B 91.284 872 68 5 2015 2884 667413629 667412764 0.000000e+00 1182.0
18 TraesCS7A01G093600 chr7B 94.737 57 3 0 1 57 609753804 609753860 3.960000e-14 89.8
19 TraesCS7A01G093600 chr2B 91.359 868 68 3 2019 2884 371158012 371157150 0.000000e+00 1181.0
20 TraesCS7A01G093600 chr2B 90.185 866 77 4 2019 2882 84423983 84423124 0.000000e+00 1122.0
21 TraesCS7A01G093600 chr4B 91.244 868 69 3 2019 2884 509585730 509584868 0.000000e+00 1175.0
22 TraesCS7A01G093600 chr5D 90.427 867 81 2 2019 2884 138478214 138479079 0.000000e+00 1140.0
23 TraesCS7A01G093600 chr5D 95.833 72 3 0 527 598 350219058 350218987 1.820000e-22 117.0
24 TraesCS7A01G093600 chr6D 92.801 764 53 2 2037 2800 62212442 62213203 0.000000e+00 1105.0
25 TraesCS7A01G093600 chr3A 97.133 593 17 0 1 593 598907592 598908184 0.000000e+00 1002.0
26 TraesCS7A01G093600 chr3A 84.298 726 75 17 950 1664 639620001 639620698 0.000000e+00 673.0
27 TraesCS7A01G093600 chr3A 82.586 379 22 19 1662 2011 639628045 639628408 7.810000e-76 294.0
28 TraesCS7A01G093600 chr4A 84.872 1018 81 32 862 1830 668351659 668352652 0.000000e+00 959.0
29 TraesCS7A01G093600 chr4A 88.021 192 20 3 1405 1595 668285483 668285672 1.040000e-54 224.0
30 TraesCS7A01G093600 chr4A 85.417 144 14 4 1877 2019 668288141 668288278 3.000000e-30 143.0
31 TraesCS7A01G093600 chr4A 85.149 101 6 5 970 1070 668373399 668373490 8.510000e-16 95.3
32 TraesCS7A01G093600 chr6B 91.144 542 46 2 52 593 654600183 654599644 0.000000e+00 734.0
33 TraesCS7A01G093600 chr6B 96.491 57 2 0 1 57 654600924 654600868 8.510000e-16 95.3
34 TraesCS7A01G093600 chr3D 89.706 272 16 7 1328 1594 500110050 500110314 1.280000e-88 337.0
35 TraesCS7A01G093600 chr3D 84.983 293 34 4 950 1237 500109745 500110032 3.640000e-74 289.0
36 TraesCS7A01G093600 chr4D 93.333 225 15 0 369 593 506101152 506101376 1.660000e-87 333.0
37 TraesCS7A01G093600 chr4D 94.937 158 8 0 52 209 506100568 506100725 6.170000e-62 248.0
38 TraesCS7A01G093600 chr4D 93.396 106 7 0 239 344 506100723 506100828 1.070000e-34 158.0
39 TraesCS7A01G093600 chr4D 96.491 57 2 0 1 57 506088154 506088210 8.510000e-16 95.3
40 TraesCS7A01G093600 chrUn 96.296 54 2 0 1 54 94939955 94940008 3.960000e-14 89.8
41 TraesCS7A01G093600 chr1B 94.737 57 3 0 1 57 499019197 499019253 3.960000e-14 89.8


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 TraesCS7A01G093600 chr7A 57155735 57158618 2883 False 5326.000000 5326 100.000000 1 2884 1 chr7A.!!$F4 2883
1 TraesCS7A01G093600 chr7A 705602697 705603561 864 True 1219.000000 1219 92.139000 2019 2882 1 chr7A.!!$R3 863
2 TraesCS7A01G093600 chr7A 526149263 526150135 872 True 1168.000000 1168 90.971000 2019 2884 1 chr7A.!!$R1 865
3 TraesCS7A01G093600 chr7A 57095818 57096751 933 False 1013.000000 1013 86.806000 910 1828 1 chr7A.!!$F2 918
4 TraesCS7A01G093600 chr7D 53637739 53638462 723 False 870.000000 870 88.618000 930 1652 1 chr7D.!!$F4 722
5 TraesCS7A01G093600 chr7D 53708383 53711934 3551 False 546.000000 1192 90.210667 650 2016 3 chr7D.!!$F5 1366
6 TraesCS7A01G093600 chr1A 405679360 405680223 863 True 1188.000000 1188 91.484000 2018 2884 1 chr1A.!!$R1 866
7 TraesCS7A01G093600 chr7B 667412764 667413629 865 True 1182.000000 1182 91.284000 2015 2884 1 chr7B.!!$R1 869
8 TraesCS7A01G093600 chr2B 371157150 371158012 862 True 1181.000000 1181 91.359000 2019 2884 1 chr2B.!!$R2 865
9 TraesCS7A01G093600 chr2B 84423124 84423983 859 True 1122.000000 1122 90.185000 2019 2882 1 chr2B.!!$R1 863
10 TraesCS7A01G093600 chr4B 509584868 509585730 862 True 1175.000000 1175 91.244000 2019 2884 1 chr4B.!!$R1 865
11 TraesCS7A01G093600 chr5D 138478214 138479079 865 False 1140.000000 1140 90.427000 2019 2884 1 chr5D.!!$F1 865
12 TraesCS7A01G093600 chr6D 62212442 62213203 761 False 1105.000000 1105 92.801000 2037 2800 1 chr6D.!!$F1 763
13 TraesCS7A01G093600 chr3A 598907592 598908184 592 False 1002.000000 1002 97.133000 1 593 1 chr3A.!!$F1 592
14 TraesCS7A01G093600 chr3A 639620001 639620698 697 False 673.000000 673 84.298000 950 1664 1 chr3A.!!$F2 714
15 TraesCS7A01G093600 chr4A 668351659 668352652 993 False 959.000000 959 84.872000 862 1830 1 chr4A.!!$F1 968
16 TraesCS7A01G093600 chr6B 654599644 654600924 1280 True 414.650000 734 93.817500 1 593 2 chr6B.!!$R1 592
17 TraesCS7A01G093600 chr3D 500109745 500110314 569 False 313.000000 337 87.344500 950 1594 2 chr3D.!!$F1 644
18 TraesCS7A01G093600 chr4D 506100568 506101376 808 False 246.333333 333 93.888667 52 593 3 chr4D.!!$F2 541

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
609 1599 0.032267 CTCCTAATCTTCCCGCGGAC 59.968 60.0 30.73 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 4019 0.037326 CTACCTCGGCTGCTTGTTGA 60.037 55.0 0.0 0.0 0.0 3.18 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
195 886 9.461312 AGATGAATAGTAGGTGATGAGATAGAC 57.539 37.037 0.00 0.00 0.00 2.59
344 1035 5.008019 TCAAGATTGTGTGAAGCAGAGTTTC 59.992 40.000 0.00 0.00 0.00 2.78
366 1356 1.677552 GGAGGAAACAGGGAAGCGA 59.322 57.895 0.00 0.00 0.00 4.93
367 1357 0.253327 GGAGGAAACAGGGAAGCGAT 59.747 55.000 0.00 0.00 0.00 4.58
564 1554 3.708210 CCTCACCTTAGGCGTGGA 58.292 61.111 1.41 0.00 0.00 4.02
593 1583 1.528129 CTCTGAACCAAACAGCCTCC 58.472 55.000 0.00 0.00 35.61 4.30
595 1585 2.303022 CTCTGAACCAAACAGCCTCCTA 59.697 50.000 0.00 0.00 35.61 2.94
596 1586 2.708861 TCTGAACCAAACAGCCTCCTAA 59.291 45.455 0.00 0.00 35.61 2.69
598 1588 3.686016 TGAACCAAACAGCCTCCTAATC 58.314 45.455 0.00 0.00 0.00 1.75
599 1589 3.330701 TGAACCAAACAGCCTCCTAATCT 59.669 43.478 0.00 0.00 0.00 2.40
600 1590 4.202567 TGAACCAAACAGCCTCCTAATCTT 60.203 41.667 0.00 0.00 0.00 2.40
601 1591 3.956744 ACCAAACAGCCTCCTAATCTTC 58.043 45.455 0.00 0.00 0.00 2.87
603 1593 3.282885 CAAACAGCCTCCTAATCTTCCC 58.717 50.000 0.00 0.00 0.00 3.97
605 1595 0.250081 CAGCCTCCTAATCTTCCCGC 60.250 60.000 0.00 0.00 0.00 6.13
606 1596 1.301009 GCCTCCTAATCTTCCCGCG 60.301 63.158 0.00 0.00 0.00 6.46
607 1597 1.367840 CCTCCTAATCTTCCCGCGG 59.632 63.158 21.04 21.04 0.00 6.46
608 1598 1.113517 CCTCCTAATCTTCCCGCGGA 61.114 60.000 30.73 10.38 0.00 5.54
609 1599 0.032267 CTCCTAATCTTCCCGCGGAC 59.968 60.000 30.73 0.00 0.00 4.79
611 1601 1.299926 CTAATCTTCCCGCGGACCG 60.300 63.158 30.73 10.29 0.00 4.79
612 1602 1.731433 CTAATCTTCCCGCGGACCGA 61.731 60.000 30.73 19.32 40.02 4.69
613 1603 2.008268 TAATCTTCCCGCGGACCGAC 62.008 60.000 30.73 8.22 40.02 4.79
632 1622 3.458579 CGCCGACGACAACGAGTG 61.459 66.667 0.00 0.00 43.93 3.51
633 1623 2.050714 GCCGACGACAACGAGTGA 60.051 61.111 0.00 0.00 42.66 3.41
634 1624 1.659335 GCCGACGACAACGAGTGAA 60.659 57.895 0.00 0.00 42.66 3.18
635 1625 1.210545 GCCGACGACAACGAGTGAAA 61.211 55.000 0.00 0.00 42.66 2.69
636 1626 0.501435 CCGACGACAACGAGTGAAAC 59.499 55.000 0.00 0.00 42.66 2.78
637 1627 0.501435 CGACGACAACGAGTGAAACC 59.499 55.000 0.00 0.00 42.66 3.27
638 1628 0.501435 GACGACAACGAGTGAAACCG 59.499 55.000 0.00 0.00 42.66 4.44
640 1630 1.568025 GACAACGAGTGAAACCGGC 59.432 57.895 0.00 0.00 37.80 6.13
642 1632 2.663852 AACGAGTGAAACCGGCGG 60.664 61.111 27.06 27.06 37.80 6.13
655 1645 3.430862 GGCGGCGCTTGTGATCAA 61.431 61.111 32.30 0.00 0.00 2.57
664 2221 2.730090 CGCTTGTGATCAAATCAGCACC 60.730 50.000 9.68 0.00 40.53 5.01
684 2241 4.092968 CACCGTTGTGCCTAACTTTAGATC 59.907 45.833 0.00 0.00 35.31 2.75
687 2244 4.031426 CGTTGTGCCTAACTTTAGATCGAC 59.969 45.833 0.00 0.00 32.47 4.20
709 2266 4.223032 ACCGAGATCTCCTTTTTCTTGCTA 59.777 41.667 17.13 0.00 0.00 3.49
713 2270 6.552445 AGATCTCCTTTTTCTTGCTAGCTA 57.448 37.500 17.23 7.59 0.00 3.32
714 2271 6.581712 AGATCTCCTTTTTCTTGCTAGCTAG 58.418 40.000 18.70 18.70 0.00 3.42
725 2282 2.009888 CTAGCTAGCTTTGGCACGC 58.990 57.895 24.88 0.00 41.70 5.34
729 2299 0.318614 GCTAGCTTTGGCACGCAAAA 60.319 50.000 7.70 0.00 41.70 2.44
746 2316 0.691332 AAAAAGGACGAGGGAGGACC 59.309 55.000 0.00 0.00 40.67 4.46
747 2317 1.542187 AAAAGGACGAGGGAGGACCG 61.542 60.000 0.00 0.00 46.96 4.79
748 2318 3.959329 AAGGACGAGGGAGGACCGG 62.959 68.421 0.00 0.00 46.96 5.28
749 2319 4.437587 GGACGAGGGAGGACCGGA 62.438 72.222 9.46 0.00 46.96 5.14
750 2320 2.829458 GACGAGGGAGGACCGGAG 60.829 72.222 9.46 0.00 46.96 4.63
773 2343 4.764823 GGATACCTCCAACAAACAACATCA 59.235 41.667 0.00 0.00 41.64 3.07
784 2354 4.405358 ACAAACAACATCAAATCCTGTGGT 59.595 37.500 0.00 0.00 30.74 4.16
785 2355 4.853924 AACAACATCAAATCCTGTGGTC 57.146 40.909 0.00 0.00 28.08 4.02
787 2357 3.822735 ACAACATCAAATCCTGTGGTCTG 59.177 43.478 0.00 0.00 0.00 3.51
788 2358 3.795688 ACATCAAATCCTGTGGTCTGT 57.204 42.857 0.00 0.00 0.00 3.41
789 2359 3.415212 ACATCAAATCCTGTGGTCTGTG 58.585 45.455 0.00 0.00 0.00 3.66
790 2360 2.566833 TCAAATCCTGTGGTCTGTGG 57.433 50.000 0.00 0.00 0.00 4.17
791 2361 2.054021 TCAAATCCTGTGGTCTGTGGA 58.946 47.619 0.00 0.00 0.00 4.02
792 2362 2.644299 TCAAATCCTGTGGTCTGTGGAT 59.356 45.455 0.00 0.00 40.65 3.41
794 2364 3.814504 AATCCTGTGGTCTGTGGATTT 57.185 42.857 0.00 0.00 44.16 2.17
795 2365 2.859165 TCCTGTGGTCTGTGGATTTC 57.141 50.000 0.00 0.00 0.00 2.17
796 2366 1.351017 TCCTGTGGTCTGTGGATTTCC 59.649 52.381 0.00 0.00 0.00 3.13
797 2367 1.073763 CCTGTGGTCTGTGGATTTCCA 59.926 52.381 0.00 0.00 45.30 3.53
837 2424 3.178539 CGCTCCCGGAAAGAAAGC 58.821 61.111 0.73 0.71 0.00 3.51
838 2425 3.178539 GCTCCCGGAAAGAAAGCG 58.821 61.111 0.73 0.00 0.00 4.68
839 2426 1.671379 GCTCCCGGAAAGAAAGCGT 60.671 57.895 0.73 0.00 0.00 5.07
840 2427 1.912371 GCTCCCGGAAAGAAAGCGTG 61.912 60.000 0.73 0.00 0.00 5.34
841 2428 1.912371 CTCCCGGAAAGAAAGCGTGC 61.912 60.000 0.73 0.00 0.00 5.34
842 2429 2.258013 CCCGGAAAGAAAGCGTGCA 61.258 57.895 0.73 0.00 0.00 4.57
843 2430 1.207593 CCGGAAAGAAAGCGTGCAG 59.792 57.895 0.00 0.00 0.00 4.41
844 2431 1.507141 CCGGAAAGAAAGCGTGCAGT 61.507 55.000 0.00 0.00 0.00 4.40
845 2432 0.384725 CGGAAAGAAAGCGTGCAGTG 60.385 55.000 0.00 0.00 0.00 3.66
846 2433 0.040067 GGAAAGAAAGCGTGCAGTGG 60.040 55.000 0.00 0.00 0.00 4.00
847 2434 0.661483 GAAAGAAAGCGTGCAGTGGC 60.661 55.000 0.00 0.00 41.68 5.01
878 2465 2.341846 TTCCCACCAACTCAGTTCAC 57.658 50.000 0.00 0.00 0.00 3.18
882 2469 1.134098 CCACCAACTCAGTTCACCACT 60.134 52.381 0.00 0.00 35.35 4.00
883 2470 2.213499 CACCAACTCAGTTCACCACTC 58.787 52.381 0.00 0.00 30.92 3.51
884 2471 1.141053 ACCAACTCAGTTCACCACTCC 59.859 52.381 0.00 0.00 30.92 3.85
885 2472 1.140852 CCAACTCAGTTCACCACTCCA 59.859 52.381 0.00 0.00 30.92 3.86
886 2473 2.421388 CCAACTCAGTTCACCACTCCAA 60.421 50.000 0.00 0.00 30.92 3.53
904 2491 2.484264 CCAATCCAAGTCCAAACGAGTC 59.516 50.000 0.00 0.00 0.00 3.36
961 2554 2.650778 CCGCCACCTTTTTGCTCC 59.349 61.111 0.00 0.00 0.00 4.70
978 2571 6.696042 TTGCTCCCTATAAATACATGGCTA 57.304 37.500 0.00 0.00 0.00 3.93
991 2585 0.825840 ATGGCTAGCTCCTCGTCCTC 60.826 60.000 15.72 0.00 0.00 3.71
1029 2623 3.806667 GCCAGCCAGCCCATCTCT 61.807 66.667 0.00 0.00 0.00 3.10
1071 2672 0.463654 TTGTGCTGAGCCGTTTCTGT 60.464 50.000 0.23 0.00 0.00 3.41
1075 2676 1.071605 GCTGAGCCGTTTCTGTACAG 58.928 55.000 17.17 17.17 0.00 2.74
1170 2776 1.025812 CTGCTCCAGAGGTACGTAGG 58.974 60.000 0.00 0.00 32.44 3.18
1173 2779 2.308690 GCTCCAGAGGTACGTAGGAAT 58.691 52.381 0.00 0.00 0.00 3.01
1220 2826 2.016318 TCAGTTCAGCCAAGTTGTGTG 58.984 47.619 1.45 0.00 0.00 3.82
1251 2862 4.633126 TCTGACACTAGCAATGCATTTCTC 59.367 41.667 15.06 5.05 0.00 2.87
1257 2868 7.885297 ACACTAGCAATGCATTTCTCTTTTTA 58.115 30.769 15.06 0.00 0.00 1.52
1341 2952 2.280797 GTGCCAACGGTGAGCTCA 60.281 61.111 13.74 13.74 0.00 4.26
1352 2963 1.078759 GTGAGCTCATCCGTCCAACG 61.079 60.000 21.47 0.00 42.11 4.10
1386 3019 0.678950 TCATGCACGTTGGACTCTGA 59.321 50.000 0.00 0.00 0.00 3.27
1399 3032 3.069586 TGGACTCTGATTTTCGTGACTGT 59.930 43.478 0.00 0.00 0.00 3.55
1400 3033 4.058817 GGACTCTGATTTTCGTGACTGTT 58.941 43.478 0.00 0.00 0.00 3.16
1401 3034 5.221362 TGGACTCTGATTTTCGTGACTGTTA 60.221 40.000 0.00 0.00 0.00 2.41
1404 3040 7.009357 GGACTCTGATTTTCGTGACTGTTATAC 59.991 40.741 0.00 0.00 0.00 1.47
1407 3047 7.599171 TCTGATTTTCGTGACTGTTATACTCA 58.401 34.615 0.00 0.00 0.00 3.41
1414 3054 3.557595 GTGACTGTTATACTCATGCAGCC 59.442 47.826 0.00 0.00 0.00 4.85
1598 3241 0.178861 AGGACACCTCCTTCCATGGT 60.179 55.000 12.58 0.00 45.77 3.55
1665 3311 5.931146 CCTTGAGCTAGTATTATCCTGCTTG 59.069 44.000 0.00 0.00 0.00 4.01
1760 3439 4.316205 TCTGACGCCGAAATGTATGTAT 57.684 40.909 0.00 0.00 0.00 2.29
1776 3462 9.639601 AATGTATGTATATCCGTGTACTGAATG 57.360 33.333 0.00 0.00 0.00 2.67
1807 3493 4.080863 GGGCTCGATCCTGGTTTCATATAT 60.081 45.833 5.10 0.00 0.00 0.86
1834 3520 4.676018 GTGTACGACAGACTTCAGAAGTTC 59.324 45.833 17.19 9.91 43.03 3.01
1835 3521 4.337274 TGTACGACAGACTTCAGAAGTTCA 59.663 41.667 17.19 4.80 43.03 3.18
1836 3522 3.971150 ACGACAGACTTCAGAAGTTCAG 58.029 45.455 17.19 11.99 43.03 3.02
1837 3523 3.632604 ACGACAGACTTCAGAAGTTCAGA 59.367 43.478 17.19 0.00 43.03 3.27
1838 3524 4.279671 ACGACAGACTTCAGAAGTTCAGAT 59.720 41.667 17.19 2.20 43.03 2.90
1839 3525 5.473846 ACGACAGACTTCAGAAGTTCAGATA 59.526 40.000 17.19 0.00 43.03 1.98
1840 3526 6.151985 ACGACAGACTTCAGAAGTTCAGATAT 59.848 38.462 17.19 0.00 43.03 1.63
1841 3527 6.690957 CGACAGACTTCAGAAGTTCAGATATC 59.309 42.308 17.19 7.63 43.03 1.63
1842 3528 6.559810 ACAGACTTCAGAAGTTCAGATATCG 58.440 40.000 17.19 2.15 43.03 2.92
1843 3529 6.375736 ACAGACTTCAGAAGTTCAGATATCGA 59.624 38.462 17.19 0.00 43.03 3.59
1844 3530 6.690957 CAGACTTCAGAAGTTCAGATATCGAC 59.309 42.308 17.19 0.15 43.03 4.20
1845 3531 5.574082 ACTTCAGAAGTTCAGATATCGACG 58.426 41.667 10.27 0.00 39.04 5.12
1846 3532 5.354513 ACTTCAGAAGTTCAGATATCGACGA 59.645 40.000 10.27 0.00 39.04 4.20
1847 3533 5.813080 TCAGAAGTTCAGATATCGACGAA 57.187 39.130 0.00 0.00 0.00 3.85
1848 3534 5.811588 TCAGAAGTTCAGATATCGACGAAG 58.188 41.667 0.00 0.00 0.00 3.79
1849 3535 5.585047 TCAGAAGTTCAGATATCGACGAAGA 59.415 40.000 0.00 0.00 0.00 2.87
1850 3536 6.093633 TCAGAAGTTCAGATATCGACGAAGAA 59.906 38.462 0.00 0.00 0.00 2.52
1851 3537 6.413526 CAGAAGTTCAGATATCGACGAAGAAG 59.586 42.308 0.00 0.00 0.00 2.85
1852 3538 6.316640 AGAAGTTCAGATATCGACGAAGAAGA 59.683 38.462 0.00 0.00 0.00 2.87
1853 3539 6.627395 AGTTCAGATATCGACGAAGAAGAT 57.373 37.500 0.00 0.00 0.00 2.40
1854 3540 6.434596 AGTTCAGATATCGACGAAGAAGATG 58.565 40.000 0.00 0.00 0.00 2.90
1855 3541 5.363979 TCAGATATCGACGAAGAAGATGG 57.636 43.478 0.00 0.00 0.00 3.51
1856 3542 4.216472 TCAGATATCGACGAAGAAGATGGG 59.784 45.833 0.00 0.00 0.00 4.00
1857 3543 4.216472 CAGATATCGACGAAGAAGATGGGA 59.784 45.833 0.00 0.00 0.00 4.37
1858 3544 5.013547 AGATATCGACGAAGAAGATGGGAT 58.986 41.667 0.00 0.00 0.00 3.85
1859 3545 3.651803 ATCGACGAAGAAGATGGGATC 57.348 47.619 0.00 0.00 0.00 3.36
1860 3546 2.375146 TCGACGAAGAAGATGGGATCA 58.625 47.619 0.00 0.00 0.00 2.92
1861 3547 2.959030 TCGACGAAGAAGATGGGATCAT 59.041 45.455 0.00 0.00 36.09 2.45
1862 3548 4.142038 TCGACGAAGAAGATGGGATCATA 58.858 43.478 0.00 0.00 32.98 2.15
1863 3549 4.767409 TCGACGAAGAAGATGGGATCATAT 59.233 41.667 0.00 0.00 32.98 1.78
1864 3550 5.944007 TCGACGAAGAAGATGGGATCATATA 59.056 40.000 0.00 0.00 32.98 0.86
1865 3551 6.433093 TCGACGAAGAAGATGGGATCATATAA 59.567 38.462 0.00 0.00 32.98 0.98
1866 3552 7.122799 TCGACGAAGAAGATGGGATCATATAAT 59.877 37.037 0.00 0.00 32.98 1.28
1867 3553 8.406297 CGACGAAGAAGATGGGATCATATAATA 58.594 37.037 0.00 0.00 32.98 0.98
2016 3702 2.501128 GCTGCCGCAGTCTCCATA 59.499 61.111 21.29 0.00 33.43 2.74
2017 3703 1.593750 GCTGCCGCAGTCTCCATAG 60.594 63.158 21.29 0.00 33.43 2.23
2074 3762 8.109705 TCAATTAGATTAAGCAGAAAACAGCA 57.890 30.769 0.00 0.00 0.00 4.41
2088 3776 6.310956 CAGAAAACAGCAGAAAAACAACATGA 59.689 34.615 0.00 0.00 0.00 3.07
2089 3777 6.873076 AGAAAACAGCAGAAAAACAACATGAA 59.127 30.769 0.00 0.00 0.00 2.57
2127 3822 6.337356 TCAAAGAGAAAAGAAAAACGGCAAT 58.663 32.000 0.00 0.00 0.00 3.56
2162 3857 4.501915 CCGAACAACACTACCCTTACAAGA 60.502 45.833 0.00 0.00 0.00 3.02
2200 3896 2.666190 GCAGGACAACGCAGCTCA 60.666 61.111 0.00 0.00 0.00 4.26
2206 3902 0.038709 GACAACGCAGCTCAGACTCT 60.039 55.000 0.00 0.00 0.00 3.24
2223 3919 2.367567 ACTCTGGCGGAGAACTACAAAA 59.632 45.455 29.39 0.00 44.45 2.44
2231 3927 4.261031 GCGGAGAACTACAAAAAGCAAAGA 60.261 41.667 0.00 0.00 0.00 2.52
2282 3978 0.033504 ACCACTTGTCGCTCGTCATT 59.966 50.000 0.00 0.00 0.00 2.57
2323 4019 1.016130 CCGCAGCTTCGACTTCACAT 61.016 55.000 7.52 0.00 0.00 3.21
2348 4044 0.612174 AGCAGCCGAGGTAGTCTCAA 60.612 55.000 0.00 0.00 42.55 3.02
2352 4048 1.063567 AGCCGAGGTAGTCTCAAGGAT 60.064 52.381 0.00 0.00 42.55 3.24
2547 4243 2.615227 GATGCCCCAAGAGGTGCGAT 62.615 60.000 0.00 0.00 35.27 4.58
2571 4267 4.789075 CGCCGTCATCGTCCGGTT 62.789 66.667 0.00 0.00 45.91 4.44
2646 4342 1.667830 CCTCAGCGACGCCTTCAAA 60.668 57.895 17.79 0.00 0.00 2.69
2755 4452 1.002134 CAAACCCGAGCCAGACCAT 60.002 57.895 0.00 0.00 0.00 3.55
2760 4457 2.659063 CCGAGCCAGACCATCACCA 61.659 63.158 0.00 0.00 0.00 4.17
2821 4518 3.283684 CGCCGCAACCACCTTCAA 61.284 61.111 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 886 4.169508 CAATAGTAATCTCCGCCATCTCG 58.830 47.826 0.00 0.00 0.00 4.04
344 1035 2.198304 CTTCCCTGTTTCCTCCCCCG 62.198 65.000 0.00 0.00 0.00 5.73
366 1356 3.821033 GCGGGCCTGATTAATAAAGTCAT 59.179 43.478 18.31 0.00 0.00 3.06
367 1357 3.211045 GCGGGCCTGATTAATAAAGTCA 58.789 45.455 18.31 0.00 0.00 3.41
499 1489 5.313712 GTTTGGTTCTCCATCAAGGTTAGA 58.686 41.667 0.00 0.00 43.91 2.10
593 1583 1.299926 CGGTCCGCGGGAAGATTAG 60.300 63.158 27.83 4.61 31.38 1.73
595 1585 3.072468 TCGGTCCGCGGGAAGATT 61.072 61.111 27.83 0.00 31.38 2.40
596 1586 3.834799 GTCGGTCCGCGGGAAGAT 61.835 66.667 27.83 0.00 31.38 2.40
615 1605 3.458579 CACTCGTTGTCGTCGGCG 61.459 66.667 1.15 1.15 38.33 6.46
616 1606 1.210545 TTTCACTCGTTGTCGTCGGC 61.211 55.000 0.00 0.00 38.33 5.54
618 1608 0.501435 GGTTTCACTCGTTGTCGTCG 59.499 55.000 0.00 0.00 38.33 5.12
619 1609 0.501435 CGGTTTCACTCGTTGTCGTC 59.499 55.000 0.00 0.00 38.33 4.20
621 1611 1.850640 CCGGTTTCACTCGTTGTCG 59.149 57.895 0.00 0.00 38.55 4.35
622 1612 1.568025 GCCGGTTTCACTCGTTGTC 59.432 57.895 1.90 0.00 0.00 3.18
623 1613 2.241880 CGCCGGTTTCACTCGTTGT 61.242 57.895 1.90 0.00 0.00 3.32
624 1614 2.549282 CGCCGGTTTCACTCGTTG 59.451 61.111 1.90 0.00 0.00 4.10
625 1615 2.663852 CCGCCGGTTTCACTCGTT 60.664 61.111 1.90 0.00 0.00 3.85
638 1628 2.270297 ATTTGATCACAAGCGCCGCC 62.270 55.000 4.98 0.00 37.32 6.13
640 1630 0.447406 TGATTTGATCACAAGCGCCG 59.553 50.000 2.29 0.00 37.32 6.46
642 1632 1.135603 TGCTGATTTGATCACAAGCGC 60.136 47.619 0.00 0.00 37.32 5.92
644 1634 2.730090 CGGTGCTGATTTGATCACAAGC 60.730 50.000 0.00 3.02 37.32 4.01
645 1635 2.485426 ACGGTGCTGATTTGATCACAAG 59.515 45.455 0.00 0.00 37.32 3.16
646 1636 2.503331 ACGGTGCTGATTTGATCACAA 58.497 42.857 0.00 0.00 35.06 3.33
647 1637 2.183478 ACGGTGCTGATTTGATCACA 57.817 45.000 0.00 0.00 35.06 3.58
648 1638 2.226437 ACAACGGTGCTGATTTGATCAC 59.774 45.455 0.00 0.00 35.06 3.06
664 2221 4.031426 GTCGATCTAAAGTTAGGCACAACG 59.969 45.833 0.00 0.00 33.50 4.10
684 2241 3.512033 AGAAAAAGGAGATCTCGGTCG 57.488 47.619 16.46 0.00 0.00 4.79
687 2244 3.604582 AGCAAGAAAAAGGAGATCTCGG 58.395 45.455 16.46 0.00 0.00 4.63
709 2266 1.172180 TTTGCGTGCCAAAGCTAGCT 61.172 50.000 12.68 12.68 38.46 3.32
729 2299 1.982938 CGGTCCTCCCTCGTCCTTT 60.983 63.158 0.00 0.00 0.00 3.11
732 2302 4.437587 TCCGGTCCTCCCTCGTCC 62.438 72.222 0.00 0.00 0.00 4.79
749 2319 4.447138 TGTTGTTTGTTGGAGGTATCCT 57.553 40.909 0.00 0.00 46.80 3.24
750 2320 4.764823 TGATGTTGTTTGTTGGAGGTATCC 59.235 41.667 0.00 0.00 46.87 2.59
751 2321 5.957842 TGATGTTGTTTGTTGGAGGTATC 57.042 39.130 0.00 0.00 0.00 2.24
752 2322 6.723298 TTTGATGTTGTTTGTTGGAGGTAT 57.277 33.333 0.00 0.00 0.00 2.73
753 2323 6.239176 GGATTTGATGTTGTTTGTTGGAGGTA 60.239 38.462 0.00 0.00 0.00 3.08
756 2326 5.693104 CAGGATTTGATGTTGTTTGTTGGAG 59.307 40.000 0.00 0.00 0.00 3.86
757 2327 5.128499 ACAGGATTTGATGTTGTTTGTTGGA 59.872 36.000 0.00 0.00 0.00 3.53
758 2328 5.234757 CACAGGATTTGATGTTGTTTGTTGG 59.765 40.000 0.00 0.00 0.00 3.77
759 2329 5.234757 CCACAGGATTTGATGTTGTTTGTTG 59.765 40.000 0.00 0.00 0.00 3.33
760 2330 5.104982 ACCACAGGATTTGATGTTGTTTGTT 60.105 36.000 0.00 0.00 0.00 2.83
768 2338 3.415212 CACAGACCACAGGATTTGATGT 58.585 45.455 0.00 0.00 0.00 3.06
773 2343 3.814504 AATCCACAGACCACAGGATTT 57.185 42.857 0.00 0.00 45.91 2.17
788 2358 5.736951 CCAAAACTATGGTTGGAAATCCA 57.263 39.130 0.00 0.00 46.11 3.41
795 2365 5.394115 GCAGGTTATCCAAAACTATGGTTGG 60.394 44.000 0.00 0.00 44.82 3.77
796 2366 5.394115 GGCAGGTTATCCAAAACTATGGTTG 60.394 44.000 0.00 0.00 41.46 3.77
797 2367 4.709886 GGCAGGTTATCCAAAACTATGGTT 59.290 41.667 0.00 0.00 41.46 3.67
802 2372 2.026636 AGCGGCAGGTTATCCAAAACTA 60.027 45.455 1.45 0.00 35.89 2.24
847 2434 3.589542 TGGGAAAGGCAGGGGGTG 61.590 66.667 0.00 0.00 0.00 4.61
848 2435 3.590574 GTGGGAAAGGCAGGGGGT 61.591 66.667 0.00 0.00 0.00 4.95
849 2436 4.382541 GGTGGGAAAGGCAGGGGG 62.383 72.222 0.00 0.00 0.00 5.40
850 2437 3.159104 TTGGTGGGAAAGGCAGGGG 62.159 63.158 0.00 0.00 0.00 4.79
851 2438 1.908299 GTTGGTGGGAAAGGCAGGG 60.908 63.158 0.00 0.00 0.00 4.45
852 2439 0.895559 GAGTTGGTGGGAAAGGCAGG 60.896 60.000 0.00 0.00 0.00 4.85
853 2440 0.178992 TGAGTTGGTGGGAAAGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
857 2444 2.618709 GTGAACTGAGTTGGTGGGAAAG 59.381 50.000 0.90 0.00 0.00 2.62
858 2445 2.650322 GTGAACTGAGTTGGTGGGAAA 58.350 47.619 0.90 0.00 0.00 3.13
860 2447 0.472471 GGTGAACTGAGTTGGTGGGA 59.528 55.000 0.90 0.00 0.00 4.37
878 2465 2.558359 GTTTGGACTTGGATTGGAGTGG 59.442 50.000 0.00 0.00 0.00 4.00
882 2469 2.105821 ACTCGTTTGGACTTGGATTGGA 59.894 45.455 0.00 0.00 0.00 3.53
883 2470 2.484264 GACTCGTTTGGACTTGGATTGG 59.516 50.000 0.00 0.00 0.00 3.16
884 2471 3.138304 TGACTCGTTTGGACTTGGATTG 58.862 45.455 0.00 0.00 0.00 2.67
885 2472 3.403038 CTGACTCGTTTGGACTTGGATT 58.597 45.455 0.00 0.00 0.00 3.01
886 2473 2.872038 GCTGACTCGTTTGGACTTGGAT 60.872 50.000 0.00 0.00 0.00 3.41
904 2491 0.034896 AAACCGTGGGTACTCTGCTG 59.965 55.000 0.00 0.00 33.12 4.41
961 2554 6.552445 AGGAGCTAGCCATGTATTTATAGG 57.448 41.667 12.13 0.00 0.00 2.57
991 2585 0.455633 GGCTGTTGCTTGATGCTTCG 60.456 55.000 0.00 0.00 43.37 3.79
1029 2623 1.745653 AGTGCGATGATCGAGTGAGAA 59.254 47.619 20.25 0.00 43.74 2.87
1071 2672 1.067060 CATCTTCGCCGTGATCCTGTA 59.933 52.381 0.00 0.00 0.00 2.74
1075 2676 1.209275 CGACATCTTCGCCGTGATCC 61.209 60.000 0.00 0.00 41.87 3.36
1124 2727 1.293498 GAGGGCGAGCTTGTTCTCA 59.707 57.895 16.03 0.00 33.41 3.27
1170 2776 5.104982 ACTCTGAAGAAGTGGATCCTGATTC 60.105 44.000 14.23 13.62 0.00 2.52
1173 2779 3.784178 ACTCTGAAGAAGTGGATCCTGA 58.216 45.455 14.23 0.00 0.00 3.86
1220 2826 4.377839 TTGCTAGTGTCAGACTATCAGC 57.622 45.455 1.31 6.16 35.28 4.26
1251 2862 5.622233 CGCCTCTGGGGAAGATTTTAAAAAG 60.622 44.000 4.44 0.00 37.91 2.27
1257 2868 0.991920 TCGCCTCTGGGGAAGATTTT 59.008 50.000 0.00 0.00 41.69 1.82
1352 2963 4.168760 GTGCATGAAAATCAGCAACTACC 58.831 43.478 0.00 0.00 34.25 3.18
1354 2965 3.501828 ACGTGCATGAAAATCAGCAACTA 59.498 39.130 14.17 0.00 34.25 2.24
1386 3019 6.593770 TGCATGAGTATAACAGTCACGAAAAT 59.406 34.615 0.00 0.00 39.44 1.82
1399 3032 0.599991 CGCCGGCTGCATGAGTATAA 60.600 55.000 26.68 0.00 41.33 0.98
1400 3033 1.006220 CGCCGGCTGCATGAGTATA 60.006 57.895 26.68 0.00 41.33 1.47
1401 3034 2.280389 CGCCGGCTGCATGAGTAT 60.280 61.111 26.68 0.00 41.33 2.12
1702 3367 3.222603 GGTTTCTTGGGACACTGACAAT 58.777 45.455 0.00 0.00 39.29 2.71
1760 3439 6.275494 TCTGTTTCATTCAGTACACGGATA 57.725 37.500 0.00 0.00 34.86 2.59
1776 3462 0.827368 AGGATCGAGCCCTCTGTTTC 59.173 55.000 17.84 0.00 0.00 2.78
1834 3520 4.216472 TCCCATCTTCTTCGTCGATATCTG 59.784 45.833 0.00 0.00 0.00 2.90
1835 3521 4.399219 TCCCATCTTCTTCGTCGATATCT 58.601 43.478 0.00 0.00 0.00 1.98
1836 3522 4.768130 TCCCATCTTCTTCGTCGATATC 57.232 45.455 0.00 0.00 0.00 1.63
1837 3523 4.767409 TGATCCCATCTTCTTCGTCGATAT 59.233 41.667 0.00 0.00 0.00 1.63
1838 3524 4.142038 TGATCCCATCTTCTTCGTCGATA 58.858 43.478 0.00 0.00 0.00 2.92
1839 3525 2.959030 TGATCCCATCTTCTTCGTCGAT 59.041 45.455 0.00 0.00 0.00 3.59
1840 3526 2.375146 TGATCCCATCTTCTTCGTCGA 58.625 47.619 0.00 0.00 0.00 4.20
1841 3527 2.871182 TGATCCCATCTTCTTCGTCG 57.129 50.000 0.00 0.00 0.00 5.12
1862 3548 8.835734 TGGATGGGAATACACAGCTTATATTAT 58.164 33.333 0.00 0.00 35.98 1.28
1863 3549 8.213489 TGGATGGGAATACACAGCTTATATTA 57.787 34.615 0.00 0.00 35.98 0.98
1864 3550 7.090319 TGGATGGGAATACACAGCTTATATT 57.910 36.000 0.00 0.00 35.98 1.28
1865 3551 6.702449 TGGATGGGAATACACAGCTTATAT 57.298 37.500 0.00 0.00 35.98 0.86
1866 3552 6.702449 ATGGATGGGAATACACAGCTTATA 57.298 37.500 0.00 0.00 35.98 0.98
1867 3553 5.589367 ATGGATGGGAATACACAGCTTAT 57.411 39.130 0.00 0.00 35.98 1.73
1868 3554 5.132502 CAATGGATGGGAATACACAGCTTA 58.867 41.667 0.00 0.00 35.98 3.09
1869 3555 3.956199 CAATGGATGGGAATACACAGCTT 59.044 43.478 0.00 0.00 35.98 3.74
1870 3556 3.559069 CAATGGATGGGAATACACAGCT 58.441 45.455 0.00 0.00 35.98 4.24
1871 3557 2.035066 GCAATGGATGGGAATACACAGC 59.965 50.000 0.00 0.00 34.82 4.40
1872 3558 3.289836 TGCAATGGATGGGAATACACAG 58.710 45.455 0.00 0.00 30.90 3.66
1873 3559 3.289836 CTGCAATGGATGGGAATACACA 58.710 45.455 0.00 0.00 0.00 3.72
1874 3560 2.035066 GCTGCAATGGATGGGAATACAC 59.965 50.000 0.00 0.00 0.00 2.90
1875 3561 2.091720 AGCTGCAATGGATGGGAATACA 60.092 45.455 1.02 0.00 0.00 2.29
1876 3562 2.590821 AGCTGCAATGGATGGGAATAC 58.409 47.619 1.02 0.00 0.00 1.89
1877 3563 3.317455 AAGCTGCAATGGATGGGAATA 57.683 42.857 1.02 0.00 0.00 1.75
1878 3564 2.170012 AAGCTGCAATGGATGGGAAT 57.830 45.000 1.02 0.00 0.00 3.01
1879 3565 2.824689 TAAGCTGCAATGGATGGGAA 57.175 45.000 1.02 0.00 0.00 3.97
1880 3566 2.589720 CATAAGCTGCAATGGATGGGA 58.410 47.619 1.02 0.00 0.00 4.37
1901 3587 3.742882 TCAAGATCAAGTTTCAGCAGTCG 59.257 43.478 0.00 0.00 0.00 4.18
2069 3757 5.581874 CCTTTTCATGTTGTTTTTCTGCTGT 59.418 36.000 0.00 0.00 0.00 4.40
2074 3762 7.123355 TGGATCCTTTTCATGTTGTTTTTCT 57.877 32.000 14.23 0.00 0.00 2.52
2088 3776 8.482852 TTTCTCTTTGATCTTTGGATCCTTTT 57.517 30.769 14.23 0.00 45.62 2.27
2089 3777 8.482852 TTTTCTCTTTGATCTTTGGATCCTTT 57.517 30.769 14.23 0.00 45.62 3.11
2127 3822 2.186602 TTGTTCGGCGGCCAATAGGA 62.187 55.000 20.71 4.50 36.89 2.94
2162 3857 2.264794 GAGTGGATGGCGTTCCGT 59.735 61.111 2.32 0.00 38.74 4.69
2178 3874 1.595109 CTGCGTTGTCCTGCTGTGA 60.595 57.895 0.00 0.00 0.00 3.58
2200 3896 1.271982 TGTAGTTCTCCGCCAGAGTCT 60.272 52.381 0.00 0.00 43.71 3.24
2206 3902 1.877443 GCTTTTTGTAGTTCTCCGCCA 59.123 47.619 0.00 0.00 0.00 5.69
2223 3919 5.104374 CGTGATGCCAATATTTCTTTGCTT 58.896 37.500 0.00 0.00 0.00 3.91
2231 3927 5.009010 GTGATCTTCCGTGATGCCAATATTT 59.991 40.000 0.00 0.00 0.00 1.40
2323 4019 0.037326 CTACCTCGGCTGCTTGTTGA 60.037 55.000 0.00 0.00 0.00 3.18
2348 4044 1.457009 GCTCTTCTCCGGCGTATCCT 61.457 60.000 6.01 0.00 0.00 3.24
2352 4048 3.515286 CGGCTCTTCTCCGGCGTA 61.515 66.667 6.01 0.00 42.99 4.42
2558 4254 0.384669 CCCTAGAACCGGACGATGAC 59.615 60.000 9.46 0.00 0.00 3.06
2569 4265 3.371702 GGAAACCCTTGATCCCCTAGAAC 60.372 52.174 0.00 0.00 0.00 3.01
2571 4267 2.488836 GGAAACCCTTGATCCCCTAGA 58.511 52.381 0.00 0.00 0.00 2.43
2694 4390 2.982744 GAAGACTTTGCTGCCGGCC 61.983 63.158 26.77 10.34 40.92 6.13
2755 4452 1.440060 GACCGTGTGTCTGTGGTGA 59.560 57.895 0.00 0.00 41.03 4.02
2760 4457 4.640855 CGCCGACCGTGTGTCTGT 62.641 66.667 0.00 0.00 42.13 3.41
2839 4536 1.437573 CGGCAGCGATGAAGACCTA 59.562 57.895 4.02 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.