Multiple sequence alignment - TraesCS3B01G511200

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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 TraesCS3B01G511200 chr3B 100.000 2612 0 0 1 2612 755044380 755041769 0.000000e+00 4824.0
1 TraesCS3B01G511200 chr3B 87.437 995 71 16 629 1617 756181059 756182005 0.000000e+00 1096.0
2 TraesCS3B01G511200 chr3B 96.063 635 21 4 1 631 395839019 395838385 0.000000e+00 1031.0
3 TraesCS3B01G511200 chr3B 86.659 817 74 19 1635 2433 756181993 756182792 0.000000e+00 872.0
4 TraesCS3B01G511200 chr3B 83.371 445 44 14 687 1120 756135553 756135978 4.080000e-103 385.0
5 TraesCS3B01G511200 chr3B 83.117 231 22 12 2297 2514 754983987 754983761 7.380000e-46 195.0
6 TraesCS3B01G511200 chr3B 97.143 35 1 0 602 636 770740599 770740633 2.810000e-05 60.2
7 TraesCS3B01G511200 chr3B 97.143 35 1 0 602 636 770741491 770741525 2.810000e-05 60.2
8 TraesCS3B01G511200 chr3A 87.889 1445 108 25 859 2263 701864041 701862624 0.000000e+00 1637.0
9 TraesCS3B01G511200 chr3A 93.995 816 42 3 969 1777 700576626 700575811 0.000000e+00 1229.0
10 TraesCS3B01G511200 chr3A 89.725 691 51 11 1907 2584 700575743 700575060 0.000000e+00 865.0
11 TraesCS3B01G511200 chr3A 85.464 399 40 11 123 507 164426129 164425735 1.460000e-107 399.0
12 TraesCS3B01G511200 chr3A 85.250 400 38 9 123 507 6702793 6703186 2.440000e-105 392.0
13 TraesCS3B01G511200 chr3A 85.250 400 38 9 123 507 6757387 6757780 2.440000e-105 392.0
14 TraesCS3B01G511200 chr3A 84.731 334 23 14 2255 2584 701862442 701862133 2.520000e-80 309.0
15 TraesCS3B01G511200 chr3A 92.969 128 9 0 2387 2514 700570369 700570242 1.230000e-43 187.0
16 TraesCS3B01G511200 chr3A 92.188 128 10 0 2387 2514 701858794 701858667 5.740000e-42 182.0
17 TraesCS3B01G511200 chr3A 96.296 81 3 0 1 81 6702722 6702802 1.630000e-27 134.0
18 TraesCS3B01G511200 chr3A 96.296 81 3 0 1 81 6757316 6757396 1.630000e-27 134.0
19 TraesCS3B01G511200 chr3A 96.000 75 2 1 882 955 700576683 700576609 1.270000e-23 121.0
20 TraesCS3B01G511200 chr3D 88.351 970 79 21 1635 2583 567216281 567217237 0.000000e+00 1134.0
21 TraesCS3B01G511200 chr3D 86.406 971 96 23 1635 2584 569547073 569546118 0.000000e+00 1029.0
22 TraesCS3B01G511200 chr3D 87.929 845 67 14 779 1618 567215480 567216294 0.000000e+00 963.0
23 TraesCS3B01G511200 chr3D 91.892 333 27 0 1286 1618 569547392 569547060 1.420000e-127 466.0
24 TraesCS3B01G511200 chr3D 88.354 395 24 7 882 1276 569549347 569548975 3.060000e-124 455.0
25 TraesCS3B01G511200 chr3D 83.117 231 22 12 2298 2514 567221794 567222021 7.380000e-46 195.0
26 TraesCS3B01G511200 chr3D 78.838 241 29 14 2297 2521 567226114 567226348 2.710000e-30 143.0
27 TraesCS3B01G511200 chrUn 86.633 995 79 16 629 1617 41100147 41101093 0.000000e+00 1051.0
28 TraesCS3B01G511200 chrUn 86.925 826 64 23 1635 2433 41101081 41101889 0.000000e+00 887.0
29 TraesCS3B01G511200 chrUn 83.612 659 54 16 629 1281 389811092 389810482 1.050000e-158 569.0
30 TraesCS3B01G511200 chrUn 85.500 400 37 9 123 507 423559760 423559367 5.240000e-107 398.0
31 TraesCS3B01G511200 chrUn 83.559 444 44 14 687 1120 324345885 324346309 3.150000e-104 388.0
32 TraesCS3B01G511200 chrUn 81.919 271 39 6 2030 2294 41108413 41108679 1.220000e-53 220.0
33 TraesCS3B01G511200 chrUn 81.304 230 28 9 2298 2514 41108618 41108845 3.460000e-39 172.0
34 TraesCS3B01G511200 chr5B 84.565 771 71 25 1653 2407 619015323 619014585 0.000000e+00 721.0
35 TraesCS3B01G511200 chr2B 84.367 774 72 26 1650 2407 726561928 726562668 0.000000e+00 713.0
36 TraesCS3B01G511200 chr2B 97.561 41 0 1 2571 2611 10382784 10382745 4.660000e-08 69.4
37 TraesCS3B01G511200 chr2B 88.462 52 4 2 2562 2611 598960828 598960879 7.810000e-06 62.1
38 TraesCS3B01G511200 chr7B 84.176 771 74 25 1653 2407 611463201 611462463 0.000000e+00 704.0
39 TraesCS3B01G511200 chr6D 91.549 426 35 1 1 425 86935331 86935756 1.040000e-163 586.0
40 TraesCS3B01G511200 chr6D 87.931 58 2 3 2556 2612 144029422 144029475 2.170000e-06 63.9
41 TraesCS3B01G511200 chr6A 84.358 537 51 11 1 507 369411574 369411041 1.810000e-136 496.0
42 TraesCS3B01G511200 chr5A 86.717 399 35 10 123 507 617938037 617938431 6.680000e-116 427.0
43 TraesCS3B01G511200 chr5A 96.296 81 3 0 1 81 617937966 617938046 1.630000e-27 134.0
44 TraesCS3B01G511200 chr1D 89.855 276 20 5 1 275 386377417 386377149 5.350000e-92 348.0
45 TraesCS3B01G511200 chr1D 82.203 236 33 6 2060 2288 66185331 66185564 7.380000e-46 195.0
46 TraesCS3B01G511200 chr1A 82.203 236 33 6 2060 2288 64713169 64713402 7.380000e-46 195.0
47 TraesCS3B01G511200 chr1A 97.561 41 0 1 2571 2611 387038974 387039013 4.660000e-08 69.4
48 TraesCS3B01G511200 chr1A 89.091 55 3 3 2561 2612 13315707 13315653 6.030000e-07 65.8
49 TraesCS3B01G511200 chr4B 97.500 40 0 1 2573 2611 11930380 11930341 1.680000e-07 67.6
50 TraesCS3B01G511200 chr7D 97.368 38 1 0 2575 2612 436663767 436663730 6.030000e-07 65.8
51 TraesCS3B01G511200 chr7D 90.000 50 3 2 585 632 197180176 197180127 2.170000e-06 63.9
52 TraesCS3B01G511200 chr6B 93.333 45 1 2 2569 2611 631196713 631196669 6.030000e-07 65.8
53 TraesCS3B01G511200 chr1B 93.182 44 2 1 2568 2611 571434286 571434328 2.170000e-06 63.9
54 TraesCS3B01G511200 chr1B 100.000 31 0 0 602 632 63469512 63469482 1.010000e-04 58.4
55 TraesCS3B01G511200 chr1B 96.970 33 0 1 601 632 63480750 63480718 1.000000e-03 54.7
56 TraesCS3B01G511200 chr7A 94.444 36 1 1 595 629 322579 322544 1.000000e-03 54.7


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 TraesCS3B01G511200 chr3B 755041769 755044380 2611 True 4824.000000 4824 100.000000 1 2612 1 chr3B.!!$R3 2611
1 TraesCS3B01G511200 chr3B 395838385 395839019 634 True 1031.000000 1031 96.063000 1 631 1 chr3B.!!$R1 630
2 TraesCS3B01G511200 chr3B 756181059 756182792 1733 False 984.000000 1096 87.048000 629 2433 2 chr3B.!!$F2 1804
3 TraesCS3B01G511200 chr3A 700575060 700576683 1623 True 738.333333 1229 93.240000 882 2584 3 chr3A.!!$R3 1702
4 TraesCS3B01G511200 chr3A 701858667 701864041 5374 True 709.333333 1637 88.269333 859 2584 3 chr3A.!!$R4 1725
5 TraesCS3B01G511200 chr3D 567215480 567217237 1757 False 1048.500000 1134 88.140000 779 2583 2 chr3D.!!$F3 1804
6 TraesCS3B01G511200 chr3D 569546118 569549347 3229 True 650.000000 1029 88.884000 882 2584 3 chr3D.!!$R1 1702
7 TraesCS3B01G511200 chrUn 41100147 41101889 1742 False 969.000000 1051 86.779000 629 2433 2 chrUn.!!$F2 1804
8 TraesCS3B01G511200 chrUn 389810482 389811092 610 True 569.000000 569 83.612000 629 1281 1 chrUn.!!$R1 652
9 TraesCS3B01G511200 chr5B 619014585 619015323 738 True 721.000000 721 84.565000 1653 2407 1 chr5B.!!$R1 754
10 TraesCS3B01G511200 chr2B 726561928 726562668 740 False 713.000000 713 84.367000 1650 2407 1 chr2B.!!$F2 757
11 TraesCS3B01G511200 chr7B 611462463 611463201 738 True 704.000000 704 84.176000 1653 2407 1 chr7B.!!$R1 754
12 TraesCS3B01G511200 chr6A 369411041 369411574 533 True 496.000000 496 84.358000 1 507 1 chr6A.!!$R1 506

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
952 991 0.041238 TGGTAGCTAGCACCACCTCT 59.959 55.0 25.71 4.79 41.17 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 3820 0.249489 CGAAGCCATAGAACGGGAGG 60.249 60.0 0.0 0.0 0.0 4.3 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
236 253 1.726853 ACATACAAGCAGGCGAAGAC 58.273 50.000 0.00 0.00 0.00 3.01
373 390 3.997021 AGACTTCGGCACATACTTCAAAG 59.003 43.478 0.00 0.00 0.00 2.77
399 416 8.793592 GTTTGAGAGGTAACCAAAATAGTTGAT 58.206 33.333 0.00 0.00 32.44 2.57
404 421 9.975218 AGAGGTAACCAAAATAGTTGATACAAT 57.025 29.630 0.00 0.00 37.17 2.71
552 582 1.021202 ATGGACGTGTTGTTGTGTGG 58.979 50.000 0.00 0.00 0.00 4.17
578 609 0.802494 GAGGGTGTGTATGTTTGGCG 59.198 55.000 0.00 0.00 0.00 5.69
580 611 1.154301 GGTGTGTATGTTTGGCGCG 60.154 57.895 0.00 0.00 0.00 6.86
625 657 2.027385 TGCAACGCATGGGCATATTTA 58.973 42.857 10.10 0.00 41.24 1.40
626 658 2.223688 TGCAACGCATGGGCATATTTAC 60.224 45.455 10.10 0.00 41.24 2.01
627 659 2.034558 GCAACGCATGGGCATATTTACT 59.965 45.455 10.10 0.00 41.24 2.24
667 699 9.764363 ATAAAGTAATGAAGCGATGTTGATCTA 57.236 29.630 0.00 0.00 0.00 1.98
674 706 7.468922 TGAAGCGATGTTGATCTATAAACAG 57.531 36.000 3.17 0.00 39.50 3.16
680 712 7.201522 GCGATGTTGATCTATAAACAGACAACA 60.202 37.037 0.00 0.00 43.04 3.33
693 725 3.560068 ACAGACAACACGAAATGGTCTTC 59.440 43.478 0.00 0.00 36.74 2.87
710 742 2.866156 TCTTCAGCGCAATAAGGAATCG 59.134 45.455 11.47 0.00 0.00 3.34
761 793 4.713792 TTTGGGCCCAAAATACAACAAT 57.286 36.364 41.59 0.00 42.16 2.71
762 794 3.971245 TGGGCCCAAAATACAACAATC 57.029 42.857 26.33 0.00 0.00 2.67
764 796 2.267426 GGCCCAAAATACAACAATCGC 58.733 47.619 0.00 0.00 0.00 4.58
765 797 2.353208 GGCCCAAAATACAACAATCGCA 60.353 45.455 0.00 0.00 0.00 5.10
767 799 3.932089 GCCCAAAATACAACAATCGCAAT 59.068 39.130 0.00 0.00 0.00 3.56
769 801 5.231991 GCCCAAAATACAACAATCGCAATAG 59.768 40.000 0.00 0.00 0.00 1.73
777 811 9.769093 AATACAACAATCGCAATAGTAAAAGAC 57.231 29.630 0.00 0.00 0.00 3.01
783 817 8.677300 ACAATCGCAATAGTAAAAGACATCAAT 58.323 29.630 0.00 0.00 0.00 2.57
801 835 4.318332 TCAATGAGCACGAATCTCAAAGT 58.682 39.130 9.28 0.00 43.01 2.66
816 850 3.745799 TCAAAGTAGAAATCAACGGCCA 58.254 40.909 2.24 0.00 0.00 5.36
818 852 4.215399 TCAAAGTAGAAATCAACGGCCAAG 59.785 41.667 2.24 0.00 0.00 3.61
835 869 2.618053 CAAGATAACCGACTGACCCAC 58.382 52.381 0.00 0.00 0.00 4.61
841 875 2.762535 ACCGACTGACCCACATTTAG 57.237 50.000 0.00 0.00 0.00 1.85
937 976 5.335261 TGGTACTCCAACATTAGACTGGTA 58.665 41.667 0.00 0.00 41.25 3.25
938 977 5.421056 TGGTACTCCAACATTAGACTGGTAG 59.579 44.000 0.00 0.00 41.25 3.18
939 978 4.473477 ACTCCAACATTAGACTGGTAGC 57.527 45.455 0.00 0.00 0.00 3.58
940 979 4.097418 ACTCCAACATTAGACTGGTAGCT 58.903 43.478 0.00 0.00 0.00 3.32
941 980 5.269991 ACTCCAACATTAGACTGGTAGCTA 58.730 41.667 0.00 0.00 0.00 3.32
942 981 5.361285 ACTCCAACATTAGACTGGTAGCTAG 59.639 44.000 0.00 0.00 0.00 3.42
943 982 4.099573 TCCAACATTAGACTGGTAGCTAGC 59.900 45.833 16.08 16.08 0.00 3.42
944 983 4.141937 CCAACATTAGACTGGTAGCTAGCA 60.142 45.833 23.39 23.39 0.00 3.49
945 984 4.657436 ACATTAGACTGGTAGCTAGCAC 57.343 45.455 21.35 12.87 0.00 4.40
946 985 3.385111 ACATTAGACTGGTAGCTAGCACC 59.615 47.826 21.35 20.93 36.54 5.01
947 986 2.820728 TAGACTGGTAGCTAGCACCA 57.179 50.000 26.85 26.85 43.82 4.17
948 987 1.187087 AGACTGGTAGCTAGCACCAC 58.813 55.000 25.71 19.54 41.17 4.16
949 988 0.175989 GACTGGTAGCTAGCACCACC 59.824 60.000 25.71 23.16 41.17 4.61
950 989 0.252284 ACTGGTAGCTAGCACCACCT 60.252 55.000 25.71 15.60 41.17 4.00
951 990 0.461961 CTGGTAGCTAGCACCACCTC 59.538 60.000 25.71 8.45 41.17 3.85
952 991 0.041238 TGGTAGCTAGCACCACCTCT 59.959 55.000 25.71 4.79 41.17 3.69
953 992 1.196012 GGTAGCTAGCACCACCTCTT 58.804 55.000 23.37 2.65 36.01 2.85
954 993 1.555533 GGTAGCTAGCACCACCTCTTT 59.444 52.381 23.37 1.99 36.01 2.52
955 994 2.622436 GTAGCTAGCACCACCTCTTTG 58.378 52.381 18.83 0.00 0.00 2.77
956 995 1.059913 AGCTAGCACCACCTCTTTGT 58.940 50.000 18.83 0.00 0.00 2.83
957 996 1.421646 AGCTAGCACCACCTCTTTGTT 59.578 47.619 18.83 0.00 0.00 2.83
958 997 2.158608 AGCTAGCACCACCTCTTTGTTT 60.159 45.455 18.83 0.00 0.00 2.83
959 998 2.226674 GCTAGCACCACCTCTTTGTTTC 59.773 50.000 10.63 0.00 0.00 2.78
960 999 2.435372 AGCACCACCTCTTTGTTTCA 57.565 45.000 0.00 0.00 0.00 2.69
961 1000 2.733956 AGCACCACCTCTTTGTTTCAA 58.266 42.857 0.00 0.00 0.00 2.69
962 1001 3.096092 AGCACCACCTCTTTGTTTCAAA 58.904 40.909 0.00 0.00 0.00 2.69
963 1002 3.513515 AGCACCACCTCTTTGTTTCAAAA 59.486 39.130 0.00 0.00 0.00 2.44
964 1003 4.020662 AGCACCACCTCTTTGTTTCAAAAA 60.021 37.500 0.00 0.00 0.00 1.94
1081 1151 1.472201 GCGTCTGCTTCATCATCTCCA 60.472 52.381 0.00 0.00 38.39 3.86
1091 1161 1.000274 CATCATCTCCATCGCCGTACA 60.000 52.381 0.00 0.00 0.00 2.90
1109 1182 2.681778 CCTCCTCCTCGCTGTGGT 60.682 66.667 0.00 0.00 0.00 4.16
1110 1183 2.286523 CCTCCTCCTCGCTGTGGTT 61.287 63.158 0.00 0.00 0.00 3.67
1120 1193 2.587753 CTGTGGTTGTCGCCGTGT 60.588 61.111 0.00 0.00 0.00 4.49
1593 3242 2.049156 CAGAGCTCGTCGTGCCAA 60.049 61.111 15.17 0.00 0.00 4.52
1665 3315 8.962679 TGGTTAGCGATATTTGGATTAGTTTTT 58.037 29.630 0.00 0.00 0.00 1.94
1672 3322 9.158364 CGATATTTGGATTAGTTTTTGTGATCG 57.842 33.333 0.00 0.00 0.00 3.69
1746 3400 5.055812 TCTGGCCAAGCTTTTATTGTTTTG 58.944 37.500 7.01 0.00 0.00 2.44
1818 3482 3.740115 TCTAGTTTTTGGGTGCTGTCTC 58.260 45.455 0.00 0.00 0.00 3.36
1819 3483 2.736670 AGTTTTTGGGTGCTGTCTCT 57.263 45.000 0.00 0.00 0.00 3.10
1820 3484 2.576615 AGTTTTTGGGTGCTGTCTCTC 58.423 47.619 0.00 0.00 0.00 3.20
1822 3486 0.250295 TTTTGGGTGCTGTCTCTCCG 60.250 55.000 0.00 0.00 0.00 4.63
1830 3494 2.612212 GTGCTGTCTCTCCGAACAAAAA 59.388 45.455 0.00 0.00 0.00 1.94
1925 3621 1.305201 TTCCAACTCGCAGGTTTGAC 58.695 50.000 0.00 0.00 0.00 3.18
1962 3658 7.554118 AGCATGAGCAACAAATAACTATAGTGT 59.446 33.333 6.06 0.00 45.49 3.55
1966 3670 9.448438 TGAGCAACAAATAACTATAGTGTGAAT 57.552 29.630 6.06 0.00 0.00 2.57
2018 3722 2.362736 AGCAACATGAGGCTGTACATG 58.637 47.619 13.61 11.82 46.11 3.21
2116 3820 0.309922 TCGTGTGACCTTCGACTGAC 59.690 55.000 0.00 0.00 0.00 3.51
2147 3851 6.422776 TCTATGGCTTCGAAACTCAAATTC 57.577 37.500 0.00 0.00 0.00 2.17
2164 3868 5.885352 TCAAATTCCCGATGCTTAAGAATCA 59.115 36.000 21.17 4.23 30.22 2.57
2249 3958 3.441572 ACTATTTTGGTGATGTGCTGAGC 59.558 43.478 0.00 0.00 0.00 4.26
2252 3961 2.046892 GGTGATGTGCTGAGCCGT 60.047 61.111 0.23 0.00 0.00 5.68
2270 4169 4.406003 AGCCGTAGATGAAAATGTAGAGGT 59.594 41.667 0.00 0.00 0.00 3.85
2316 4215 2.177394 TTTGGCGATGTGCTGAGTTA 57.823 45.000 0.00 0.00 45.43 2.24
2318 4217 0.735978 TGGCGATGTGCTGAGTTACG 60.736 55.000 0.00 0.00 45.43 3.18
2323 4222 1.594862 GATGTGCTGAGTTACGGATGC 59.405 52.381 0.00 0.00 0.00 3.91
2368 4267 5.793026 TTCAAAGCACCAATTTGTTTCAC 57.207 34.783 0.00 0.00 38.50 3.18
2372 4271 2.168106 AGCACCAATTTGTTTCACTGCA 59.832 40.909 0.00 0.00 0.00 4.41
2384 4283 4.094887 TGTTTCACTGCAGTTTCTTGTCTC 59.905 41.667 18.94 1.95 0.00 3.36
2407 4309 5.420104 TCTCAGAAACATGCAGACTATCAGA 59.580 40.000 0.00 0.00 0.00 3.27
2408 4310 5.414360 TCAGAAACATGCAGACTATCAGAC 58.586 41.667 0.00 0.00 0.00 3.51
2409 4311 4.569966 CAGAAACATGCAGACTATCAGACC 59.430 45.833 0.00 0.00 0.00 3.85
2410 4312 4.469227 AGAAACATGCAGACTATCAGACCT 59.531 41.667 0.00 0.00 0.00 3.85
2411 4313 3.815856 ACATGCAGACTATCAGACCTG 57.184 47.619 0.00 0.00 0.00 4.00
2416 4318 3.162202 CAGACTATCAGACCTGCAGTG 57.838 52.381 13.81 4.59 0.00 3.66
2417 4319 2.757314 CAGACTATCAGACCTGCAGTGA 59.243 50.000 13.81 10.51 0.00 3.41
2418 4320 3.194329 CAGACTATCAGACCTGCAGTGAA 59.806 47.826 13.81 1.13 0.00 3.18
2419 4321 4.029520 AGACTATCAGACCTGCAGTGAAT 58.970 43.478 13.81 0.57 0.00 2.57
2420 4322 4.099266 AGACTATCAGACCTGCAGTGAATC 59.901 45.833 13.81 9.33 0.00 2.52
2421 4323 3.771479 ACTATCAGACCTGCAGTGAATCA 59.229 43.478 13.81 0.00 0.00 2.57
2422 4324 2.756840 TCAGACCTGCAGTGAATCAG 57.243 50.000 13.81 2.11 0.00 2.90
2423 4325 2.250924 TCAGACCTGCAGTGAATCAGA 58.749 47.619 13.81 4.45 32.26 3.27
2424 4326 2.634453 TCAGACCTGCAGTGAATCAGAA 59.366 45.455 13.81 0.00 32.26 3.02
2425 4327 2.740981 CAGACCTGCAGTGAATCAGAAC 59.259 50.000 13.81 0.00 32.26 3.01
2514 4416 7.755591 ACTATCATCACAAGTTAATGTTGCAG 58.244 34.615 0.00 0.00 0.00 4.41
2584 4491 2.368548 TGCCTCGCATTCACCATATACT 59.631 45.455 0.00 0.00 31.71 2.12
2585 4492 2.996621 GCCTCGCATTCACCATATACTC 59.003 50.000 0.00 0.00 0.00 2.59
2586 4493 3.589988 CCTCGCATTCACCATATACTCC 58.410 50.000 0.00 0.00 0.00 3.85
2587 4494 3.589988 CTCGCATTCACCATATACTCCC 58.410 50.000 0.00 0.00 0.00 4.30
2589 4496 3.258372 TCGCATTCACCATATACTCCCTC 59.742 47.826 0.00 0.00 0.00 4.30
2590 4497 3.617531 CGCATTCACCATATACTCCCTCC 60.618 52.174 0.00 0.00 0.00 4.30
2592 4499 3.323774 TTCACCATATACTCCCTCCGT 57.676 47.619 0.00 0.00 0.00 4.69
2593 4500 2.872732 TCACCATATACTCCCTCCGTC 58.127 52.381 0.00 0.00 0.00 4.79
2595 4502 1.203149 ACCATATACTCCCTCCGTCCC 60.203 57.143 0.00 0.00 0.00 4.46
2597 4504 2.605257 CATATACTCCCTCCGTCCCAA 58.395 52.381 0.00 0.00 0.00 4.12
2602 4509 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2603 4510 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2604 4511 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2605 4512 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2606 4513 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2607 4514 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2608 4515 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2610 4517 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2611 4518 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 253 5.640357 AGAAAACATGCAAATACATTGGCTG 59.360 36.000 3.12 2.22 39.54 4.85
325 342 8.839310 ATACATTTAATCTACTGGATGTCTGC 57.161 34.615 0.00 0.00 34.45 4.26
373 390 8.161699 TCAACTATTTTGGTTACCTCTCAAAC 57.838 34.615 2.07 0.00 31.21 2.93
399 416 7.595819 ATTCTGTTTGTCTCCCAAAATTGTA 57.404 32.000 0.00 0.00 44.36 2.41
404 421 7.654022 AAAGTATTCTGTTTGTCTCCCAAAA 57.346 32.000 0.00 0.00 44.36 2.44
425 442 8.811378 CAAAAGAAAAGGAGCTTCAAGTAAAAG 58.189 33.333 0.00 0.00 0.00 2.27
509 539 8.607459 CATGTACTCTATTTCAACAGAACATCC 58.393 37.037 0.00 0.00 0.00 3.51
512 542 7.602644 GTCCATGTACTCTATTTCAACAGAACA 59.397 37.037 0.00 0.00 0.00 3.18
552 582 0.474184 CATACACACCCTCATCCCCC 59.526 60.000 0.00 0.00 0.00 5.40
646 678 9.798885 GTTTATAGATCAACATCGCTTCATTAC 57.201 33.333 0.00 0.00 33.75 1.89
656 688 8.110612 CGTGTTGTCTGTTTATAGATCAACATC 58.889 37.037 17.93 13.64 42.87 3.06
657 689 7.817478 TCGTGTTGTCTGTTTATAGATCAACAT 59.183 33.333 17.93 0.00 42.87 2.71
661 693 8.655970 CATTTCGTGTTGTCTGTTTATAGATCA 58.344 33.333 0.00 0.00 0.00 2.92
663 695 7.606456 ACCATTTCGTGTTGTCTGTTTATAGAT 59.394 33.333 0.00 0.00 0.00 1.98
667 699 5.763204 AGACCATTTCGTGTTGTCTGTTTAT 59.237 36.000 0.00 0.00 35.12 1.40
674 706 3.607078 GCTGAAGACCATTTCGTGTTGTC 60.607 47.826 0.00 0.00 0.00 3.18
680 712 0.602638 TGCGCTGAAGACCATTTCGT 60.603 50.000 9.73 0.00 0.00 3.85
693 725 1.261619 GGTCGATTCCTTATTGCGCTG 59.738 52.381 9.73 0.00 0.00 5.18
710 742 0.464916 ACCACTGTTTTGGGTCGGTC 60.465 55.000 0.00 0.00 41.49 4.79
753 785 8.312896 TGTCTTTTACTATTGCGATTGTTGTA 57.687 30.769 6.34 0.00 0.00 2.41
754 786 7.197071 TGTCTTTTACTATTGCGATTGTTGT 57.803 32.000 6.34 0.00 0.00 3.32
759 791 8.892723 TCATTGATGTCTTTTACTATTGCGATT 58.107 29.630 0.00 0.00 0.00 3.34
761 793 7.465916 GCTCATTGATGTCTTTTACTATTGCGA 60.466 37.037 0.00 0.00 0.00 5.10
762 794 6.630443 GCTCATTGATGTCTTTTACTATTGCG 59.370 38.462 0.00 0.00 0.00 4.85
764 796 7.637519 CGTGCTCATTGATGTCTTTTACTATTG 59.362 37.037 0.00 0.00 0.00 1.90
765 797 7.549134 TCGTGCTCATTGATGTCTTTTACTATT 59.451 33.333 0.00 0.00 0.00 1.73
767 799 6.394809 TCGTGCTCATTGATGTCTTTTACTA 58.605 36.000 0.00 0.00 0.00 1.82
769 801 5.530519 TCGTGCTCATTGATGTCTTTTAC 57.469 39.130 0.00 0.00 0.00 2.01
775 809 3.867493 TGAGATTCGTGCTCATTGATGTC 59.133 43.478 0.00 0.00 37.46 3.06
777 811 4.870221 TTGAGATTCGTGCTCATTGATG 57.130 40.909 0.00 0.00 41.60 3.07
783 817 4.783764 TCTACTTTGAGATTCGTGCTCA 57.216 40.909 0.00 0.00 40.41 4.26
801 835 4.879545 GGTTATCTTGGCCGTTGATTTCTA 59.120 41.667 9.66 0.00 0.00 2.10
816 850 2.253610 TGTGGGTCAGTCGGTTATCTT 58.746 47.619 0.00 0.00 0.00 2.40
818 852 2.981859 ATGTGGGTCAGTCGGTTATC 57.018 50.000 0.00 0.00 0.00 1.75
847 881 4.499472 AGCTACATGTAATAAGCCCCCTA 58.501 43.478 13.48 0.00 35.69 3.53
848 882 3.327439 AGCTACATGTAATAAGCCCCCT 58.673 45.455 13.48 0.00 35.69 4.79
851 885 6.204882 CCAACTTAGCTACATGTAATAAGCCC 59.795 42.308 24.32 1.87 35.69 5.19
852 886 6.204882 CCCAACTTAGCTACATGTAATAAGCC 59.795 42.308 24.32 7.92 35.69 4.35
854 888 7.506114 TCCCCAACTTAGCTACATGTAATAAG 58.494 38.462 23.49 23.49 0.00 1.73
855 889 7.440505 TCCCCAACTTAGCTACATGTAATAA 57.559 36.000 7.06 8.23 0.00 1.40
856 890 7.440505 TTCCCCAACTTAGCTACATGTAATA 57.559 36.000 7.06 0.40 0.00 0.98
857 891 5.968676 TCCCCAACTTAGCTACATGTAAT 57.031 39.130 7.06 1.38 0.00 1.89
937 976 1.059913 ACAAAGAGGTGGTGCTAGCT 58.940 50.000 17.23 0.00 0.00 3.32
938 977 1.897560 AACAAAGAGGTGGTGCTAGC 58.102 50.000 8.10 8.10 0.00 3.42
939 978 3.476552 TGAAACAAAGAGGTGGTGCTAG 58.523 45.455 0.00 0.00 0.00 3.42
940 979 3.569194 TGAAACAAAGAGGTGGTGCTA 57.431 42.857 0.00 0.00 0.00 3.49
941 980 2.435372 TGAAACAAAGAGGTGGTGCT 57.565 45.000 0.00 0.00 0.00 4.40
942 981 3.518634 TTTGAAACAAAGAGGTGGTGC 57.481 42.857 0.00 0.00 0.00 5.01
964 1003 0.482887 AGGGGTGGTGCTAGCTTTTT 59.517 50.000 17.23 0.00 0.00 1.94
965 1004 0.482887 AAGGGGTGGTGCTAGCTTTT 59.517 50.000 17.23 0.00 0.00 2.27
966 1005 0.482887 AAAGGGGTGGTGCTAGCTTT 59.517 50.000 17.23 2.30 0.00 3.51
967 1006 0.038310 GAAAGGGGTGGTGCTAGCTT 59.962 55.000 17.23 0.00 0.00 3.74
981 1020 1.901591 TGCTTGCTCTCTTGGAAAGG 58.098 50.000 0.00 0.00 46.24 3.11
1081 1151 2.125961 GGAGGAGGTGTACGGCGAT 61.126 63.158 16.62 0.00 0.00 4.58
1091 1161 2.681778 CCACAGCGAGGAGGAGGT 60.682 66.667 0.00 0.00 0.00 3.85
1109 1182 1.004320 ATGGCTAACACGGCGACAA 60.004 52.632 16.62 0.00 0.00 3.18
1110 1183 1.447140 GATGGCTAACACGGCGACA 60.447 57.895 16.62 0.72 0.00 4.35
1284 2933 1.375098 GGTAGTAGACCTCAGCGCGT 61.375 60.000 8.43 0.00 45.89 6.01
1593 3242 2.748388 AGCTAGAACTTGGTCCGGTAT 58.252 47.619 0.00 0.00 0.00 2.73
1630 3279 5.854010 AATATCGCTAACCAGAACTCTGA 57.146 39.130 8.33 0.00 46.59 3.27
1746 3400 1.134699 TGTCTGCAGAATCACCGATCC 60.135 52.381 20.19 2.06 0.00 3.36
1798 3452 3.744660 AGAGACAGCACCCAAAAACTAG 58.255 45.455 0.00 0.00 0.00 2.57
1830 3494 8.237267 CCTTCGTTCTCTTATTAGCAATGTTTT 58.763 33.333 0.00 0.00 0.00 2.43
1831 3495 7.606456 TCCTTCGTTCTCTTATTAGCAATGTTT 59.394 33.333 0.00 0.00 0.00 2.83
1832 3496 7.103641 TCCTTCGTTCTCTTATTAGCAATGTT 58.896 34.615 0.00 0.00 0.00 2.71
1833 3497 6.640518 TCCTTCGTTCTCTTATTAGCAATGT 58.359 36.000 0.00 0.00 0.00 2.71
1834 3498 7.064609 TGTTCCTTCGTTCTCTTATTAGCAATG 59.935 37.037 0.00 0.00 0.00 2.82
1835 3499 7.103641 TGTTCCTTCGTTCTCTTATTAGCAAT 58.896 34.615 0.00 0.00 0.00 3.56
1838 3502 6.963049 TTGTTCCTTCGTTCTCTTATTAGC 57.037 37.500 0.00 0.00 0.00 3.09
1842 3506 8.391075 TGAAATTTGTTCCTTCGTTCTCTTAT 57.609 30.769 0.00 0.00 0.00 1.73
1852 3519 6.392354 TGAGCATCATGAAATTTGTTCCTTC 58.608 36.000 0.00 0.00 42.56 3.46
1893 3561 5.048083 TGCGAGTTGGAATCAGCTTAAATTT 60.048 36.000 0.00 0.00 34.53 1.82
1925 3621 2.076100 TGCTCATGCTTTAGGTGTTCG 58.924 47.619 0.00 0.00 40.48 3.95
1986 3690 4.867047 CCTCATGTTGCTAACTGACTACTG 59.133 45.833 0.00 0.00 0.00 2.74
2018 3722 8.893219 TCACAAGATCCATATGTGAGAATAAC 57.107 34.615 13.91 0.00 46.11 1.89
2116 3820 0.249489 CGAAGCCATAGAACGGGAGG 60.249 60.000 0.00 0.00 0.00 4.30
2147 3851 8.322906 TGTTATATTGATTCTTAAGCATCGGG 57.677 34.615 10.01 0.00 0.00 5.14
2249 3958 7.611213 AAAACCTCTACATTTTCATCTACGG 57.389 36.000 0.00 0.00 0.00 4.02
2252 3961 8.662141 GCGTTAAAACCTCTACATTTTCATCTA 58.338 33.333 0.00 0.00 30.80 1.98
2290 4189 2.031245 CAGCACATCGCCAAAACTAACA 60.031 45.455 0.00 0.00 44.04 2.41
2316 4215 2.158900 CCCTCTCTACATTTGCATCCGT 60.159 50.000 0.00 0.00 0.00 4.69
2318 4217 3.567478 ACCCTCTCTACATTTGCATCC 57.433 47.619 0.00 0.00 0.00 3.51
2323 4222 4.935808 AGCGTTAAACCCTCTCTACATTTG 59.064 41.667 0.00 0.00 0.00 2.32
2361 4260 4.009675 AGACAAGAAACTGCAGTGAAACA 58.990 39.130 22.49 0.00 41.43 2.83
2368 4267 3.987547 TCTGAGAGACAAGAAACTGCAG 58.012 45.455 13.48 13.48 0.00 4.41
2372 4271 5.238214 GCATGTTTCTGAGAGACAAGAAACT 59.762 40.000 22.00 10.28 41.44 2.66
2384 4283 5.519566 GTCTGATAGTCTGCATGTTTCTGAG 59.480 44.000 0.00 0.00 0.00 3.35
2407 4309 1.070758 ACGTTCTGATTCACTGCAGGT 59.929 47.619 19.93 0.24 33.05 4.00
2408 4310 1.462283 CACGTTCTGATTCACTGCAGG 59.538 52.381 19.93 7.28 33.05 4.85
2409 4311 2.407090 TCACGTTCTGATTCACTGCAG 58.593 47.619 13.48 13.48 0.00 4.41
2410 4312 2.524569 TCACGTTCTGATTCACTGCA 57.475 45.000 0.00 0.00 0.00 4.41
2411 4313 3.425359 CCATTCACGTTCTGATTCACTGC 60.425 47.826 0.00 0.00 0.00 4.40
2412 4314 3.748048 ACCATTCACGTTCTGATTCACTG 59.252 43.478 0.00 0.00 0.00 3.66
2414 4316 4.749245 AACCATTCACGTTCTGATTCAC 57.251 40.909 0.00 0.00 0.00 3.18
2415 4317 6.567701 GCTTTAACCATTCACGTTCTGATTCA 60.568 38.462 0.00 0.00 0.00 2.57
2416 4318 5.795441 GCTTTAACCATTCACGTTCTGATTC 59.205 40.000 0.00 0.00 0.00 2.52
2417 4319 5.240623 TGCTTTAACCATTCACGTTCTGATT 59.759 36.000 0.00 0.00 0.00 2.57
2418 4320 4.759693 TGCTTTAACCATTCACGTTCTGAT 59.240 37.500 0.00 0.00 0.00 2.90
2419 4321 4.024387 GTGCTTTAACCATTCACGTTCTGA 60.024 41.667 0.00 0.00 0.00 3.27
2420 4322 4.219033 GTGCTTTAACCATTCACGTTCTG 58.781 43.478 0.00 0.00 0.00 3.02
2421 4323 3.880490 TGTGCTTTAACCATTCACGTTCT 59.120 39.130 0.00 0.00 0.00 3.01
2422 4324 4.024387 TCTGTGCTTTAACCATTCACGTTC 60.024 41.667 0.00 0.00 0.00 3.95
2423 4325 3.880490 TCTGTGCTTTAACCATTCACGTT 59.120 39.130 0.00 0.00 0.00 3.99
2424 4326 3.250040 GTCTGTGCTTTAACCATTCACGT 59.750 43.478 0.00 0.00 0.00 4.49
2425 4327 3.249799 TGTCTGTGCTTTAACCATTCACG 59.750 43.478 0.00 0.00 0.00 4.35
2514 4416 4.560716 GCCCACATTCTTTGTTAACCCTTC 60.561 45.833 2.48 0.00 36.00 3.46
2565 4467 3.589988 GGAGTATATGGTGAATGCGAGG 58.410 50.000 0.00 0.00 0.00 4.63
2584 4491 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2585 4492 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2586 4493 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2587 4494 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2589 4496 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.