Multiple sequence alignment - TraesCS3B01G114400

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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 TraesCS3B01G114400 chr3B 100.000 2679 0 0 1 2679 80202401 80199723 0.000000e+00 4948.0
1 TraesCS3B01G114400 chr3B 95.707 629 22 4 5 628 758628234 758628862 0.000000e+00 1007.0
2 TraesCS3B01G114400 chr3B 94.574 645 27 5 1 639 820889542 820890184 0.000000e+00 990.0
3 TraesCS3B01G114400 chr3B 92.185 627 36 6 933 1557 80659029 80658414 0.000000e+00 874.0
4 TraesCS3B01G114400 chr3B 88.594 640 45 9 1047 1662 59323807 59324442 0.000000e+00 752.0
5 TraesCS3B01G114400 chr3B 84.641 612 42 13 1846 2455 80657970 80657409 1.800000e-156 562.0
6 TraesCS3B01G114400 chr3B 92.213 244 16 2 644 885 80659269 80659027 2.550000e-90 342.0
7 TraesCS3B01G114400 chr3B 86.154 325 30 7 2127 2449 59327543 59327854 1.190000e-88 337.0
8 TraesCS3B01G114400 chr3B 83.019 212 13 13 2471 2679 59327942 59328133 1.280000e-38 171.0
9 TraesCS3B01G114400 chr3B 85.185 162 17 6 2471 2627 80657309 80657150 2.760000e-35 159.0
10 TraesCS3B01G114400 chr3B 96.703 91 3 0 1899 1989 59327437 59327527 4.620000e-33 152.0
11 TraesCS3B01G114400 chr7B 95.880 631 22 3 4 630 217303920 217303290 0.000000e+00 1018.0
12 TraesCS3B01G114400 chr7B 95.707 629 23 3 2 626 608187073 608187701 0.000000e+00 1009.0
13 TraesCS3B01G114400 chr7B 95.694 627 25 1 2 626 453114326 453114952 0.000000e+00 1007.0
14 TraesCS3B01G114400 chr7B 80.729 192 15 13 656 830 661998654 661998840 2.160000e-26 130.0
15 TraesCS3B01G114400 chr4B 95.433 635 26 2 2 633 424285853 424285219 0.000000e+00 1009.0
16 TraesCS3B01G114400 chr5B 95.548 629 24 3 2 626 445178986 445179614 0.000000e+00 1003.0
17 TraesCS3B01G114400 chr3D 95.548 629 25 2 1 626 395834683 395834055 0.000000e+00 1003.0
18 TraesCS3B01G114400 chr3D 91.181 669 25 7 1771 2432 50656469 50655828 0.000000e+00 878.0
19 TraesCS3B01G114400 chr3D 86.916 749 67 18 933 1672 50658558 50657832 0.000000e+00 811.0
20 TraesCS3B01G114400 chr3D 91.667 516 34 6 1047 1557 36822423 36822934 0.000000e+00 706.0
21 TraesCS3B01G114400 chr3D 84.130 586 46 16 1874 2455 36823975 36824517 8.500000e-145 523.0
22 TraesCS3B01G114400 chr3D 95.122 205 10 0 644 848 50658779 50658575 9.250000e-85 324.0
23 TraesCS3B01G114400 chr3D 91.765 170 4 2 2510 2679 50655792 50655633 7.460000e-56 228.0
24 TraesCS3B01G114400 chr3D 84.795 171 14 7 2471 2632 36824584 36824751 7.680000e-36 161.0
25 TraesCS3B01G114400 chr3D 80.800 125 18 4 1770 1893 50657914 50657795 2.840000e-15 93.5
26 TraesCS3B01G114400 chr3D 97.143 35 1 0 2451 2485 50655826 50655792 2.880000e-05 60.2
27 TraesCS3B01G114400 chr1B 95.118 635 26 4 8 638 352332568 352331935 0.000000e+00 996.0
28 TraesCS3B01G114400 chr1B 85.213 399 33 15 2060 2449 633260127 633260508 1.160000e-103 387.0
29 TraesCS3B01G114400 chr3A 83.791 802 86 16 940 1706 47046322 47047114 0.000000e+00 721.0
30 TraesCS3B01G114400 chr3A 85.956 591 55 14 1874 2455 47047566 47048137 8.200000e-170 606.0
31 TraesCS3B01G114400 chr3A 86.239 218 13 7 2471 2679 47048216 47048425 1.250000e-53 220.0
32 TraesCS3B01G114400 chr3A 98.000 50 1 0 885 934 633129689 633129738 1.320000e-13 87.9
33 TraesCS3B01G114400 chrUn 95.047 424 20 1 1033 1456 69444466 69444044 0.000000e+00 665.0
34 TraesCS3B01G114400 chrUn 95.024 422 21 0 1030 1451 69362330 69362751 0.000000e+00 664.0
35 TraesCS3B01G114400 chrUn 98.000 50 1 0 885 934 206780330 206780379 1.320000e-13 87.9
36 TraesCS3B01G114400 chr6B 94.749 419 22 0 1033 1451 101325621 101325203 0.000000e+00 652.0
37 TraesCS3B01G114400 chr6B 94.131 426 22 1 1034 1456 35629107 35629532 0.000000e+00 645.0
38 TraesCS3B01G114400 chr1D 84.951 412 28 14 2060 2449 460982002 460982401 1.160000e-103 387.0
39 TraesCS3B01G114400 chr1D 83.333 390 31 14 2060 2449 460995073 460995428 1.990000e-86 329.0
40 TraesCS3B01G114400 chr1D 84.507 213 19 11 2471 2679 460995510 460995712 5.850000e-47 198.0
41 TraesCS3B01G114400 chr1D 88.806 134 8 5 2471 2603 460982483 460982610 9.930000e-35 158.0
42 TraesCS3B01G114400 chr1D 98.000 50 1 0 885 934 420924353 420924402 1.320000e-13 87.9
43 TraesCS3B01G114400 chr1A 83.702 362 34 11 2096 2449 552118845 552119189 4.300000e-83 318.0
44 TraesCS3B01G114400 chr1A 87.678 211 16 8 2471 2679 552119265 552119467 1.240000e-58 237.0
45 TraesCS3B01G114400 chr4A 79.616 417 43 21 2060 2450 686573623 686573223 7.360000e-66 261.0
46 TraesCS3B01G114400 chr4A 83.453 278 36 6 2163 2435 642186194 642186466 1.590000e-62 250.0
47 TraesCS3B01G114400 chr4A 81.724 290 30 10 2163 2450 642903024 642903292 1.250000e-53 220.0
48 TraesCS3B01G114400 chr4A 83.732 209 22 8 2471 2679 642186562 642186758 1.270000e-43 187.0
49 TraesCS3B01G114400 chr4A 82.629 213 19 10 2471 2678 686579173 686578974 3.550000e-39 172.0
50 TraesCS3B01G114400 chr4A 77.990 209 26 17 2471 2679 642653862 642654050 2.180000e-21 113.0
51 TraesCS3B01G114400 chr4A 93.220 59 4 0 2471 2529 686573133 686573075 1.320000e-13 87.9
52 TraesCS3B01G114400 chr7D 82.374 278 42 6 2163 2435 38204538 38204263 4.460000e-58 235.0
53 TraesCS3B01G114400 chr7D 85.401 137 12 5 2543 2679 38005969 38006097 4.650000e-28 135.0
54 TraesCS3B01G114400 chr7D 82.716 162 13 6 656 804 588472119 588471960 2.160000e-26 130.0
55 TraesCS3B01G114400 chr7D 78.947 209 21 10 2471 2679 38204161 38203976 1.300000e-23 121.0
56 TraesCS3B01G114400 chr7D 98.000 50 1 0 885 934 336510324 336510275 1.320000e-13 87.9
57 TraesCS3B01G114400 chr7D 98.000 50 1 0 885 934 606861428 606861477 1.320000e-13 87.9
58 TraesCS3B01G114400 chr7D 97.917 48 1 0 885 932 606931723 606931676 1.710000e-12 84.2
59 TraesCS3B01G114400 chr7D 96.000 50 2 0 2471 2520 38000079 38000128 6.150000e-12 82.4
60 TraesCS3B01G114400 chr6D 85.088 228 18 6 1772 1987 27757896 27758119 4.490000e-53 219.0
61 TraesCS3B01G114400 chr7A 83.732 209 22 8 2471 2679 37938085 37937889 1.270000e-43 187.0
62 TraesCS3B01G114400 chr7A 98.000 50 1 0 885 934 60260986 60261035 1.320000e-13 87.9
63 TraesCS3B01G114400 chr4D 84.672 137 16 2 1771 1907 6775902 6775771 6.020000e-27 132.0
64 TraesCS3B01G114400 chr4D 98.000 50 1 0 885 934 123273744 123273793 1.320000e-13 87.9
65 TraesCS3B01G114400 chr4D 98.000 50 1 0 885 934 123317133 123317182 1.320000e-13 87.9
66 TraesCS3B01G114400 chr6A 82.482 137 19 2 1771 1907 72998825 72998956 6.060000e-22 115.0
67 TraesCS3B01G114400 chr6A 81.752 137 20 2 1771 1907 73017864 73017995 2.820000e-20 110.0
68 TraesCS3B01G114400 chr2B 91.228 57 5 0 1828 1884 247942473 247942417 7.950000e-11 78.7


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 TraesCS3B01G114400 chr3B 80199723 80202401 2678 True 4948.000000 4948 100.000000 1 2679 1 chr3B.!!$R1 2678
1 TraesCS3B01G114400 chr3B 758628234 758628862 628 False 1007.000000 1007 95.707000 5 628 1 chr3B.!!$F1 623
2 TraesCS3B01G114400 chr3B 820889542 820890184 642 False 990.000000 990 94.574000 1 639 1 chr3B.!!$F2 638
3 TraesCS3B01G114400 chr3B 80657150 80659269 2119 True 484.250000 874 88.556000 644 2627 4 chr3B.!!$R2 1983
4 TraesCS3B01G114400 chr3B 59323807 59328133 4326 False 353.000000 752 88.617500 1047 2679 4 chr3B.!!$F3 1632
5 TraesCS3B01G114400 chr7B 217303290 217303920 630 True 1018.000000 1018 95.880000 4 630 1 chr7B.!!$R1 626
6 TraesCS3B01G114400 chr7B 608187073 608187701 628 False 1009.000000 1009 95.707000 2 626 1 chr7B.!!$F2 624
7 TraesCS3B01G114400 chr7B 453114326 453114952 626 False 1007.000000 1007 95.694000 2 626 1 chr7B.!!$F1 624
8 TraesCS3B01G114400 chr4B 424285219 424285853 634 True 1009.000000 1009 95.433000 2 633 1 chr4B.!!$R1 631
9 TraesCS3B01G114400 chr5B 445178986 445179614 628 False 1003.000000 1003 95.548000 2 626 1 chr5B.!!$F1 624
10 TraesCS3B01G114400 chr3D 395834055 395834683 628 True 1003.000000 1003 95.548000 1 626 1 chr3D.!!$R1 625
11 TraesCS3B01G114400 chr3D 36822423 36824751 2328 False 463.333333 706 86.864000 1047 2632 3 chr3D.!!$F1 1585
12 TraesCS3B01G114400 chr3D 50655633 50658779 3146 True 399.116667 878 90.487833 644 2679 6 chr3D.!!$R2 2035
13 TraesCS3B01G114400 chr1B 352331935 352332568 633 True 996.000000 996 95.118000 8 638 1 chr1B.!!$R1 630
14 TraesCS3B01G114400 chr3A 47046322 47048425 2103 False 515.666667 721 85.328667 940 2679 3 chr3A.!!$F2 1739
15 TraesCS3B01G114400 chr1D 460982002 460982610 608 False 272.500000 387 86.878500 2060 2603 2 chr1D.!!$F2 543
16 TraesCS3B01G114400 chr1D 460995073 460995712 639 False 263.500000 329 83.920000 2060 2679 2 chr1D.!!$F3 619
17 TraesCS3B01G114400 chr1A 552118845 552119467 622 False 277.500000 318 85.690000 2096 2679 2 chr1A.!!$F1 583
18 TraesCS3B01G114400 chr4A 642186194 642186758 564 False 218.500000 250 83.592500 2163 2679 2 chr4A.!!$F3 516

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
977 985 0.960364 CCACCACAATTCCTCCCACG 60.96 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 5534 0.107831 TGAAGCCGCCTGTTGTACTT 59.892 50.0 0.0 0.0 0.0 2.24 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
101 103 2.670148 GGTGGATCTCGGCAAGGGT 61.670 63.158 0.00 0.00 0.00 4.34
162 165 1.813513 CTAGGGTTTGTGTCCTGCTG 58.186 55.000 0.00 0.00 34.75 4.41
293 296 1.616865 CCGGCGGATCTATCTTTGGTA 59.383 52.381 24.41 0.00 0.00 3.25
312 315 2.969628 AGATTTGCTCGGATCTCGTT 57.030 45.000 0.00 0.00 40.32 3.85
355 358 5.661458 GTGTCTTCGGATTGGATCTTTCTA 58.339 41.667 0.00 0.00 0.00 2.10
428 431 2.508663 GGCCTTAGCACGACGACC 60.509 66.667 0.00 0.00 42.56 4.79
429 432 2.508663 GCCTTAGCACGACGACCC 60.509 66.667 0.00 0.00 39.53 4.46
695 701 3.051392 CTCAAATTCCCGCCACGGC 62.051 63.158 0.00 0.00 46.86 5.68
696 702 3.369400 CAAATTCCCGCCACGGCA 61.369 61.111 9.11 0.00 46.86 5.69
772 780 4.796231 GCCACGTCAGCGATCCGT 62.796 66.667 0.00 0.00 42.00 4.69
804 812 2.186903 GGGTCGTCCATCGCACAT 59.813 61.111 0.04 0.00 39.67 3.21
848 856 3.014538 ATCCGTGGCACCCATCCA 61.015 61.111 12.86 0.00 35.28 3.41
851 859 2.271821 CGTGGCACCCATCCATCA 59.728 61.111 12.86 0.00 35.28 3.07
885 893 1.684983 CGCCTCCCTCCTCGTATAAAA 59.315 52.381 0.00 0.00 0.00 1.52
886 894 2.288273 CGCCTCCCTCCTCGTATAAAAG 60.288 54.545 0.00 0.00 0.00 2.27
887 895 2.548280 GCCTCCCTCCTCGTATAAAAGC 60.548 54.545 0.00 0.00 0.00 3.51
888 896 2.966516 CCTCCCTCCTCGTATAAAAGCT 59.033 50.000 0.00 0.00 0.00 3.74
889 897 3.243907 CCTCCCTCCTCGTATAAAAGCTG 60.244 52.174 0.00 0.00 0.00 4.24
890 898 2.102588 TCCCTCCTCGTATAAAAGCTGC 59.897 50.000 0.00 0.00 0.00 5.25
891 899 2.103263 CCCTCCTCGTATAAAAGCTGCT 59.897 50.000 0.00 0.00 0.00 4.24
892 900 3.385577 CCTCCTCGTATAAAAGCTGCTC 58.614 50.000 1.00 0.00 0.00 4.26
893 901 3.385577 CTCCTCGTATAAAAGCTGCTCC 58.614 50.000 1.00 0.00 0.00 4.70
894 902 2.128035 CCTCGTATAAAAGCTGCTCCG 58.872 52.381 1.00 0.00 0.00 4.63
895 903 2.223735 CCTCGTATAAAAGCTGCTCCGA 60.224 50.000 1.00 3.76 0.00 4.55
896 904 2.789893 CTCGTATAAAAGCTGCTCCGAC 59.210 50.000 1.00 0.00 0.00 4.79
897 905 2.426024 TCGTATAAAAGCTGCTCCGACT 59.574 45.455 1.00 0.00 0.00 4.18
898 906 3.628942 TCGTATAAAAGCTGCTCCGACTA 59.371 43.478 1.00 0.00 0.00 2.59
899 907 3.729716 CGTATAAAAGCTGCTCCGACTAC 59.270 47.826 1.00 1.38 0.00 2.73
900 908 2.273370 TAAAAGCTGCTCCGACTACG 57.727 50.000 1.00 0.00 39.43 3.51
920 928 1.682740 GGAACCACAAGGAAAACGGA 58.317 50.000 0.00 0.00 38.69 4.69
921 929 2.025898 GGAACCACAAGGAAAACGGAA 58.974 47.619 0.00 0.00 38.69 4.30
922 930 2.223641 GGAACCACAAGGAAAACGGAAC 60.224 50.000 0.00 0.00 38.69 3.62
923 931 2.131776 ACCACAAGGAAAACGGAACA 57.868 45.000 0.00 0.00 38.69 3.18
924 932 1.746787 ACCACAAGGAAAACGGAACAC 59.253 47.619 0.00 0.00 38.69 3.32
925 933 1.268335 CCACAAGGAAAACGGAACACG 60.268 52.381 0.00 0.00 43.29 4.49
926 934 3.571703 CCACAAGGAAAACGGAACACGA 61.572 50.000 0.00 0.00 40.97 4.35
927 935 5.372090 CCACAAGGAAAACGGAACACGAG 62.372 52.174 0.00 0.00 40.97 4.18
977 985 0.960364 CCACCACAATTCCTCCCACG 60.960 60.000 0.00 0.00 0.00 4.94
1014 1025 1.149174 CACCACACCAGAGCACCTT 59.851 57.895 0.00 0.00 0.00 3.50
1015 1026 0.886490 CACCACACCAGAGCACCTTC 60.886 60.000 0.00 0.00 0.00 3.46
1023 1034 4.452733 GAGCACCTTCCCCCGTCG 62.453 72.222 0.00 0.00 0.00 5.12
1131 1142 2.970639 CGGAGAAGAAGGTGCCGA 59.029 61.111 0.00 0.00 44.43 5.54
1182 1202 4.503991 GGAAGAAGAAGTCCAAGAAGAGCA 60.504 45.833 0.00 0.00 33.79 4.26
1267 1287 0.034186 TCCAAGGCCATGTCCATCAC 60.034 55.000 5.01 0.00 0.00 3.06
1486 1510 1.527311 GTCGTCTGTGTCTTCTTTGGC 59.473 52.381 0.00 0.00 0.00 4.52
1487 1511 1.138069 TCGTCTGTGTCTTCTTTGGCA 59.862 47.619 0.00 0.00 0.00 4.92
1488 1512 1.528586 CGTCTGTGTCTTCTTTGGCAG 59.471 52.381 0.00 0.00 0.00 4.85
1489 1513 2.803133 CGTCTGTGTCTTCTTTGGCAGA 60.803 50.000 0.00 0.00 0.00 4.26
1490 1514 3.406764 GTCTGTGTCTTCTTTGGCAGAT 58.593 45.455 0.00 0.00 35.77 2.90
1491 1515 3.434984 GTCTGTGTCTTCTTTGGCAGATC 59.565 47.826 0.00 0.00 35.77 2.75
1492 1516 3.071457 TCTGTGTCTTCTTTGGCAGATCA 59.929 43.478 0.00 0.00 0.00 2.92
1500 1524 3.725490 TCTTTGGCAGATCAGATCGATG 58.275 45.455 0.54 0.28 33.17 3.84
1502 1526 0.034476 TGGCAGATCAGATCGATGGC 59.966 55.000 15.67 15.67 33.17 4.40
1503 1527 1.013005 GGCAGATCAGATCGATGGCG 61.013 60.000 0.54 0.00 33.17 5.69
1531 1565 3.754850 TCTGTAGTTAGCTGTTCGTGCTA 59.245 43.478 0.00 0.00 41.46 3.49
1591 1648 6.934210 AGAAATAGTAACAGCGCTTATTTCG 58.066 36.000 28.56 14.59 37.46 3.46
1598 1655 2.812011 ACAGCGCTTATTTCGGTTCTTT 59.188 40.909 7.50 0.00 35.32 2.52
1623 1681 5.886960 ATGATCCTGTTTGTGCTACTTTC 57.113 39.130 0.00 0.00 0.00 2.62
1627 1685 4.632153 TCCTGTTTGTGCTACTTTCTCTC 58.368 43.478 0.00 0.00 0.00 3.20
1632 1690 3.026630 TGTGCTACTTTCTCTCGGTTG 57.973 47.619 0.00 0.00 0.00 3.77
1633 1691 2.364324 TGTGCTACTTTCTCTCGGTTGT 59.636 45.455 0.00 0.00 0.00 3.32
1637 1695 5.062308 GTGCTACTTTCTCTCGGTTGTATTG 59.938 44.000 0.00 0.00 0.00 1.90
1649 1707 2.050691 GTTGTATTGGTTGTGCAAGCG 58.949 47.619 9.16 0.00 41.36 4.68
1667 1727 1.201566 GCGCGCGTTCTCTATAAATCG 60.202 52.381 32.35 0.00 0.00 3.34
1672 1732 2.794910 GCGTTCTCTATAAATCGCTGCA 59.205 45.455 0.00 0.00 40.39 4.41
1677 1737 2.983136 CTCTATAAATCGCTGCAGACGG 59.017 50.000 20.43 5.65 0.00 4.79
1695 1755 1.230324 GGCGGAGATATGAACTTGCC 58.770 55.000 0.00 0.00 34.16 4.52
1707 1767 2.807967 TGAACTTGCCGAGATGTTTCTG 59.192 45.455 0.00 0.00 30.30 3.02
1708 1768 2.839486 ACTTGCCGAGATGTTTCTGA 57.161 45.000 0.00 0.00 30.30 3.27
1709 1769 2.417719 ACTTGCCGAGATGTTTCTGAC 58.582 47.619 0.00 0.00 30.30 3.51
1710 1770 2.224281 ACTTGCCGAGATGTTTCTGACA 60.224 45.455 0.00 0.00 43.71 3.58
1717 1812 3.141398 GAGATGTTTCTGACAAGCACCA 58.859 45.455 0.00 0.00 42.62 4.17
1718 1813 3.144506 AGATGTTTCTGACAAGCACCAG 58.855 45.455 0.00 0.00 42.62 4.00
1758 1853 6.045318 CGGAAGTGTTGATATCTTCAGACAT 58.955 40.000 3.98 0.00 39.19 3.06
1760 1855 7.706607 CGGAAGTGTTGATATCTTCAGACATAA 59.293 37.037 3.98 0.00 39.19 1.90
1763 1858 9.725019 AAGTGTTGATATCTTCAGACATAAACA 57.275 29.630 3.98 0.00 35.27 2.83
1764 1859 9.155975 AGTGTTGATATCTTCAGACATAAACAC 57.844 33.333 16.32 16.32 36.80 3.32
1765 1860 8.935844 GTGTTGATATCTTCAGACATAAACACA 58.064 33.333 18.16 0.00 36.66 3.72
1766 1861 9.154847 TGTTGATATCTTCAGACATAAACACAG 57.845 33.333 3.98 0.00 35.27 3.66
1767 1862 7.776933 TGATATCTTCAGACATAAACACAGC 57.223 36.000 3.98 0.00 0.00 4.40
1768 1863 6.476706 TGATATCTTCAGACATAAACACAGCG 59.523 38.462 3.98 0.00 0.00 5.18
1769 1864 4.251543 TCTTCAGACATAAACACAGCGA 57.748 40.909 0.00 0.00 0.00 4.93
1779 5130 1.668419 AACACAGCGAGTTCTTGCTT 58.332 45.000 11.39 2.37 40.03 3.91
1786 5137 1.131315 GCGAGTTCTTGCTTTGATCCC 59.869 52.381 4.93 0.00 0.00 3.85
1795 5146 0.598065 GCTTTGATCCCGTTTGTGCT 59.402 50.000 0.00 0.00 0.00 4.40
1918 5273 2.260844 TGAACTCTGAACTTGCAGGG 57.739 50.000 0.00 0.00 42.18 4.45
1942 5297 2.304761 TGGGGTGGTGAGTCTATTTCAC 59.695 50.000 0.00 0.00 43.25 3.18
2096 5463 0.640768 GTCATGACGTCAAGCGCTAC 59.359 55.000 24.13 5.01 46.11 3.58
2156 5530 6.072508 TGGTTTCTTTCTAGCTTTGTATGCTG 60.073 38.462 0.00 0.00 41.32 4.41
2157 5531 6.072452 GGTTTCTTTCTAGCTTTGTATGCTGT 60.072 38.462 0.00 0.00 41.32 4.40
2158 5532 7.119262 GGTTTCTTTCTAGCTTTGTATGCTGTA 59.881 37.037 0.00 0.00 41.32 2.74
2159 5533 7.596749 TTCTTTCTAGCTTTGTATGCTGTAC 57.403 36.000 0.00 0.00 41.32 2.90
2160 5534 6.697395 TCTTTCTAGCTTTGTATGCTGTACA 58.303 36.000 0.00 0.00 41.32 2.90
2161 5535 7.158697 TCTTTCTAGCTTTGTATGCTGTACAA 58.841 34.615 10.06 10.06 41.32 2.41
2248 5629 4.804139 TGATCGAACGAGGAAAGAATTAGC 59.196 41.667 2.94 0.00 0.00 3.09
2255 5641 3.017442 GAGGAAAGAATTAGCCCCACAC 58.983 50.000 0.00 0.00 0.00 3.82
2256 5642 1.743394 GGAAAGAATTAGCCCCACACG 59.257 52.381 0.00 0.00 0.00 4.49
2257 5643 1.132453 GAAAGAATTAGCCCCACACGC 59.868 52.381 0.00 0.00 0.00 5.34
2258 5644 1.024579 AAGAATTAGCCCCACACGCG 61.025 55.000 3.53 3.53 0.00 6.01
2435 5851 3.710722 CAGACCGCCCTGCTTCCT 61.711 66.667 0.00 0.00 0.00 3.36
2436 5852 2.038975 AGACCGCCCTGCTTCCTA 59.961 61.111 0.00 0.00 0.00 2.94
2449 5865 1.964552 CTTCCTATCTTGCCCTGCTG 58.035 55.000 0.00 0.00 0.00 4.41
2545 6048 3.655358 GGGACGGGGATGATTCCA 58.345 61.111 0.00 0.00 44.60 3.53
2581 6084 1.135315 CGATGCTTTCTTGCACCCG 59.865 57.895 0.00 0.00 46.33 5.28
2603 6114 1.066914 CTCGCTCTGTGTCTTTGCTC 58.933 55.000 0.00 0.00 0.00 4.26
2628 6139 5.873179 ATCAATCAATTGGCTTTGCTTTG 57.127 34.783 5.42 0.00 38.30 2.77
2629 6140 3.499157 TCAATCAATTGGCTTTGCTTTGC 59.501 39.130 5.42 0.00 38.30 3.68
2630 6141 2.914695 TCAATTGGCTTTGCTTTGCT 57.085 40.000 5.42 0.00 0.00 3.91
2631 6142 3.196939 TCAATTGGCTTTGCTTTGCTT 57.803 38.095 5.42 0.00 0.00 3.91
2632 6143 3.543665 TCAATTGGCTTTGCTTTGCTTT 58.456 36.364 5.42 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 165 2.100603 CGCCGTCTCGTCTTCCTC 59.899 66.667 0.00 0.00 0.00 3.71
186 189 5.104318 GGAGACCTTTATTCCATCTTCAGGT 60.104 44.000 0.00 0.00 35.82 4.00
293 296 2.093973 ACAACGAGATCCGAGCAAATCT 60.094 45.455 10.05 0.00 41.76 2.40
312 315 1.717113 CGCGAACATAGACGAACAACA 59.283 47.619 0.00 0.00 0.00 3.33
355 358 5.692204 CCGCAGATGAAGAATAACGTAGATT 59.308 40.000 0.00 0.00 0.00 2.40
428 431 1.475682 GTTGTAGTAGACAGTCGGGGG 59.524 57.143 0.00 0.00 39.88 5.40
429 432 2.165167 TGTTGTAGTAGACAGTCGGGG 58.835 52.381 0.00 0.00 39.88 5.73
567 572 6.054941 TCAATCATGGCAGTACAACGAATAT 58.945 36.000 0.00 0.00 0.00 1.28
626 632 5.517770 GCTGCAAACCATCATTATCAACTTC 59.482 40.000 0.00 0.00 0.00 3.01
630 636 4.705991 TCTGCTGCAAACCATCATTATCAA 59.294 37.500 3.02 0.00 0.00 2.57
635 641 4.339872 TTTTCTGCTGCAAACCATCATT 57.660 36.364 3.02 0.00 0.00 2.57
666 672 4.388773 GCGGGAATTTGAGTTCAATTTTCC 59.611 41.667 19.12 19.12 42.12 3.13
695 701 2.427765 CGCGCGCATTGGAGTTTTG 61.428 57.895 32.61 5.79 0.00 2.44
696 702 2.126888 CGCGCGCATTGGAGTTTT 60.127 55.556 32.61 0.00 0.00 2.43
744 752 2.668550 ACGTGGCGGAAAGAAGGC 60.669 61.111 0.00 0.00 0.00 4.35
848 856 0.749454 GCGGGCTCTGATTGGTTGAT 60.749 55.000 0.00 0.00 0.00 2.57
851 859 2.044946 GGCGGGCTCTGATTGGTT 60.045 61.111 0.00 0.00 0.00 3.67
893 901 0.389426 CCTTGTGGTTCCCGTAGTCG 60.389 60.000 0.00 0.00 0.00 4.18
894 902 0.971386 TCCTTGTGGTTCCCGTAGTC 59.029 55.000 0.00 0.00 34.23 2.59
895 903 1.426751 TTCCTTGTGGTTCCCGTAGT 58.573 50.000 0.00 0.00 34.23 2.73
896 904 2.551032 GTTTTCCTTGTGGTTCCCGTAG 59.449 50.000 0.00 0.00 34.23 3.51
897 905 2.574450 GTTTTCCTTGTGGTTCCCGTA 58.426 47.619 0.00 0.00 34.23 4.02
898 906 1.395635 GTTTTCCTTGTGGTTCCCGT 58.604 50.000 0.00 0.00 34.23 5.28
899 907 0.309612 CGTTTTCCTTGTGGTTCCCG 59.690 55.000 0.00 0.00 34.23 5.14
900 908 0.671796 CCGTTTTCCTTGTGGTTCCC 59.328 55.000 0.00 0.00 34.23 3.97
901 909 1.682740 TCCGTTTTCCTTGTGGTTCC 58.317 50.000 0.00 0.00 34.23 3.62
902 910 2.424246 TGTTCCGTTTTCCTTGTGGTTC 59.576 45.455 0.00 0.00 34.23 3.62
903 911 2.164827 GTGTTCCGTTTTCCTTGTGGTT 59.835 45.455 0.00 0.00 34.23 3.67
904 912 1.746787 GTGTTCCGTTTTCCTTGTGGT 59.253 47.619 0.00 0.00 34.23 4.16
905 913 1.268335 CGTGTTCCGTTTTCCTTGTGG 60.268 52.381 0.00 0.00 0.00 4.17
906 914 1.666700 TCGTGTTCCGTTTTCCTTGTG 59.333 47.619 0.00 0.00 37.94 3.33
907 915 1.937899 CTCGTGTTCCGTTTTCCTTGT 59.062 47.619 0.00 0.00 37.94 3.16
908 916 1.333791 GCTCGTGTTCCGTTTTCCTTG 60.334 52.381 0.00 0.00 37.94 3.61
909 917 0.942252 GCTCGTGTTCCGTTTTCCTT 59.058 50.000 0.00 0.00 37.94 3.36
910 918 1.219522 CGCTCGTGTTCCGTTTTCCT 61.220 55.000 0.00 0.00 37.94 3.36
911 919 1.203313 CGCTCGTGTTCCGTTTTCC 59.797 57.895 0.00 0.00 37.94 3.13
912 920 1.203313 CCGCTCGTGTTCCGTTTTC 59.797 57.895 0.00 0.00 37.94 2.29
913 921 2.248835 CCCGCTCGTGTTCCGTTTT 61.249 57.895 0.00 0.00 37.94 2.43
914 922 2.647680 TTCCCGCTCGTGTTCCGTTT 62.648 55.000 0.00 0.00 37.94 3.60
915 923 2.647680 TTTCCCGCTCGTGTTCCGTT 62.648 55.000 0.00 0.00 37.94 4.44
916 924 3.154584 TTTCCCGCTCGTGTTCCGT 62.155 57.895 0.00 0.00 37.94 4.69
917 925 2.356553 TTTCCCGCTCGTGTTCCG 60.357 61.111 0.00 0.00 38.13 4.30
918 926 1.289800 GAGTTTCCCGCTCGTGTTCC 61.290 60.000 0.00 0.00 0.00 3.62
919 927 2.151295 GAGTTTCCCGCTCGTGTTC 58.849 57.895 0.00 0.00 0.00 3.18
920 928 4.355925 GAGTTTCCCGCTCGTGTT 57.644 55.556 0.00 0.00 0.00 3.32
965 973 0.322546 GCTGGAACGTGGGAGGAATT 60.323 55.000 0.00 0.00 0.00 2.17
991 999 2.421314 CTCTGGTGTGGTGTGCGA 59.579 61.111 0.00 0.00 0.00 5.10
1045 1056 2.425592 CCTTCGGCGCCATGGATA 59.574 61.111 28.98 5.96 0.00 2.59
1182 1202 6.065374 AGATGTAGATCTTGTACGTCTCCAT 58.935 40.000 11.52 0.00 41.07 3.41
1267 1287 2.672714 TGTCGTTGATGAAGGAGTTCG 58.327 47.619 0.00 0.00 35.17 3.95
1486 1510 0.038435 AGCGCCATCGATCTGATCTG 60.038 55.000 15.16 7.81 34.13 2.90
1487 1511 0.243365 GAGCGCCATCGATCTGATCT 59.757 55.000 15.16 0.00 46.50 2.75
1488 1512 2.735634 GAGCGCCATCGATCTGATC 58.264 57.895 2.29 7.60 46.50 2.92
1489 1513 4.983628 GAGCGCCATCGATCTGAT 57.016 55.556 2.29 0.00 46.50 2.90
1500 1524 0.592754 CTAACTACAGAGCGAGCGCC 60.593 60.000 11.66 3.34 43.17 6.53
1502 1526 0.378962 AGCTAACTACAGAGCGAGCG 59.621 55.000 0.00 0.00 43.72 5.03
1503 1527 1.133407 ACAGCTAACTACAGAGCGAGC 59.867 52.381 0.00 0.00 43.72 5.03
1531 1565 3.494626 CAGCACAAGTTACAAGACGACAT 59.505 43.478 0.00 0.00 0.00 3.06
1591 1648 6.623767 GCACAAACAGGATCATAGAAAGAACC 60.624 42.308 0.00 0.00 0.00 3.62
1598 1655 5.939764 AGTAGCACAAACAGGATCATAGA 57.060 39.130 0.00 0.00 0.00 1.98
1623 1681 2.159627 GCACAACCAATACAACCGAGAG 59.840 50.000 0.00 0.00 0.00 3.20
1627 1685 2.660490 CTTGCACAACCAATACAACCG 58.340 47.619 0.00 0.00 0.00 4.44
1632 1690 1.065031 CGCGCTTGCACAACCAATAC 61.065 55.000 5.56 0.00 39.07 1.89
1633 1691 1.208870 CGCGCTTGCACAACCAATA 59.791 52.632 5.56 0.00 39.07 1.90
1649 1707 2.472696 GCGATTTATAGAGAACGCGC 57.527 50.000 5.73 0.00 37.06 6.86
1653 1711 4.147306 CGTCTGCAGCGATTTATAGAGAAC 59.853 45.833 21.01 3.92 0.00 3.01
1656 1714 2.983136 CCGTCTGCAGCGATTTATAGAG 59.017 50.000 25.33 7.41 0.00 2.43
1667 1727 2.427540 ATATCTCCGCCGTCTGCAGC 62.428 60.000 9.47 3.23 41.33 5.25
1672 1732 1.693627 AGTTCATATCTCCGCCGTCT 58.306 50.000 0.00 0.00 0.00 4.18
1677 1737 0.861837 CGGCAAGTTCATATCTCCGC 59.138 55.000 0.00 0.00 0.00 5.54
1680 1740 4.626042 ACATCTCGGCAAGTTCATATCTC 58.374 43.478 0.00 0.00 0.00 2.75
1681 1741 4.679373 ACATCTCGGCAAGTTCATATCT 57.321 40.909 0.00 0.00 0.00 1.98
1682 1742 5.525378 AGAAACATCTCGGCAAGTTCATATC 59.475 40.000 0.00 0.00 0.00 1.63
1685 1745 3.438087 CAGAAACATCTCGGCAAGTTCAT 59.562 43.478 0.00 0.00 0.00 2.57
1695 1755 2.158449 GGTGCTTGTCAGAAACATCTCG 59.842 50.000 0.00 0.00 37.82 4.04
1707 1767 1.680338 ACTGAAACCTGGTGCTTGTC 58.320 50.000 0.00 0.00 0.00 3.18
1708 1768 2.143876 AACTGAAACCTGGTGCTTGT 57.856 45.000 0.00 0.00 0.00 3.16
1709 1769 2.030805 GCTAACTGAAACCTGGTGCTTG 60.031 50.000 0.00 0.00 0.00 4.01
1710 1770 2.158608 AGCTAACTGAAACCTGGTGCTT 60.159 45.455 0.00 0.00 0.00 3.91
1734 1829 5.410924 TGTCTGAAGATATCAACACTTCCG 58.589 41.667 5.32 0.00 39.14 4.30
1735 1830 8.948631 TTATGTCTGAAGATATCAACACTTCC 57.051 34.615 5.32 0.00 39.14 3.46
1743 1838 6.476706 CGCTGTGTTTATGTCTGAAGATATCA 59.523 38.462 5.32 0.00 36.38 2.15
1758 1853 2.833794 AGCAAGAACTCGCTGTGTTTA 58.166 42.857 0.00 0.00 37.02 2.01
1760 1855 1.668419 AAGCAAGAACTCGCTGTGTT 58.332 45.000 0.00 0.00 38.82 3.32
1762 1857 1.599071 TCAAAGCAAGAACTCGCTGTG 59.401 47.619 0.00 0.00 43.61 3.66
1763 1858 1.953559 TCAAAGCAAGAACTCGCTGT 58.046 45.000 0.00 0.00 38.82 4.40
1764 1859 2.159599 GGATCAAAGCAAGAACTCGCTG 60.160 50.000 0.00 0.00 38.82 5.18
1765 1860 2.079925 GGATCAAAGCAAGAACTCGCT 58.920 47.619 0.00 0.00 41.20 4.93
1766 1861 1.131315 GGGATCAAAGCAAGAACTCGC 59.869 52.381 0.00 0.00 0.00 5.03
1767 1862 1.394917 CGGGATCAAAGCAAGAACTCG 59.605 52.381 0.00 0.00 0.00 4.18
1768 1863 2.427506 ACGGGATCAAAGCAAGAACTC 58.572 47.619 0.00 0.00 0.00 3.01
1769 1864 2.568623 ACGGGATCAAAGCAAGAACT 57.431 45.000 0.00 0.00 0.00 3.01
1779 5130 2.851263 AGTAGCACAAACGGGATCAA 57.149 45.000 0.00 0.00 0.00 2.57
1786 5137 3.064820 ACCAAGACAAAGTAGCACAAACG 59.935 43.478 0.00 0.00 0.00 3.60
1795 5146 6.585695 AGTAGATCGAACCAAGACAAAGTA 57.414 37.500 0.00 0.00 0.00 2.24
1824 5175 1.139989 CAGAGAAACGCGAGCTTCAA 58.860 50.000 15.93 0.00 38.61 2.69
1918 5273 1.614241 ATAGACTCACCACCCCACGC 61.614 60.000 0.00 0.00 0.00 5.34
2092 5459 5.048013 ACTTGGATAAGCTTTGGTTTGTAGC 60.048 40.000 3.20 0.00 37.43 3.58
2093 5460 6.575162 ACTTGGATAAGCTTTGGTTTGTAG 57.425 37.500 3.20 0.00 37.43 2.74
2096 5463 7.542130 GTGATTACTTGGATAAGCTTTGGTTTG 59.458 37.037 3.20 0.00 37.43 2.93
2156 5530 0.794473 GCCGCCTGTTGTACTTGTAC 59.206 55.000 4.14 4.14 0.00 2.90
2157 5531 0.682852 AGCCGCCTGTTGTACTTGTA 59.317 50.000 0.00 0.00 0.00 2.41
2158 5532 0.179029 AAGCCGCCTGTTGTACTTGT 60.179 50.000 0.00 0.00 0.00 3.16
2159 5533 0.517316 GAAGCCGCCTGTTGTACTTG 59.483 55.000 0.00 0.00 0.00 3.16
2160 5534 0.107831 TGAAGCCGCCTGTTGTACTT 59.892 50.000 0.00 0.00 0.00 2.24
2161 5535 0.320771 CTGAAGCCGCCTGTTGTACT 60.321 55.000 0.00 0.00 0.00 2.73
2289 5692 0.602638 TGTGCCACTGATCGGTGAAC 60.603 55.000 32.02 27.01 39.34 3.18
2435 5851 0.469917 GGCTACAGCAGGGCAAGATA 59.530 55.000 3.24 0.00 44.36 1.98
2436 5852 1.225704 GGCTACAGCAGGGCAAGAT 59.774 57.895 3.24 0.00 44.36 2.40
2480 5980 0.839946 GGCCTTCTCCATCCTAAGCA 59.160 55.000 0.00 0.00 0.00 3.91
2484 5984 0.326522 TGCTGGCCTTCTCCATCCTA 60.327 55.000 3.32 0.00 35.22 2.94
2581 6084 0.510359 CAAAGACACAGAGCGAGTGC 59.490 55.000 6.20 1.01 40.59 4.40
2628 6139 1.731969 CCGAGCAAGCAAGCAAAGC 60.732 57.895 3.19 0.00 36.85 3.51
2629 6140 1.080974 CCCGAGCAAGCAAGCAAAG 60.081 57.895 3.19 0.00 36.85 2.77
2630 6141 1.391157 AACCCGAGCAAGCAAGCAAA 61.391 50.000 3.19 0.00 36.85 3.68
2631 6142 1.827789 AACCCGAGCAAGCAAGCAA 60.828 52.632 3.19 0.00 36.85 3.91
2632 6143 2.203337 AACCCGAGCAAGCAAGCA 60.203 55.556 3.19 0.00 36.85 3.91


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

AutoCloner maintained by Alex Coulton.