Multiple sequence alignment - TraesCS7A01G232500

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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 TraesCS7A01G232500 chr7A 100.000 4526 0 0 1 4526 203694218 203698743 0.000000e+00 8359.0
1 TraesCS7A01G232500 chr7A 88.539 1047 72 13 3094 4115 210252672 210253695 0.000000e+00 1225.0
2 TraesCS7A01G232500 chr7A 88.404 940 83 11 3086 3999 131187118 131186179 0.000000e+00 1109.0
3 TraesCS7A01G232500 chr7A 88.614 931 68 14 3087 4005 131108997 131108093 0.000000e+00 1098.0
4 TraesCS7A01G232500 chr7A 100.000 452 0 0 2631 3082 203695518 203695969 0.000000e+00 835.0
5 TraesCS7A01G232500 chr7A 100.000 452 0 0 1301 1752 203696848 203697299 0.000000e+00 835.0
6 TraesCS7A01G232500 chr7A 83.167 701 63 25 612 1298 130891461 130892120 1.400000e-164 590.0
7 TraesCS7A01G232500 chr7A 88.489 278 22 8 946 1219 210252345 210252616 1.210000e-85 327.0
8 TraesCS7A01G232500 chr7A 88.104 269 31 1 612 879 131109917 131109649 7.310000e-83 318.0
9 TraesCS7A01G232500 chr7A 86.508 252 34 0 3903 4154 130783832 130784083 1.240000e-70 278.0
10 TraesCS7A01G232500 chr7A 86.508 252 34 0 3903 4154 131120103 131119852 1.240000e-70 278.0
11 TraesCS7A01G232500 chr1B 98.660 1791 23 1 1294 3083 218957784 218955994 0.000000e+00 3173.0
12 TraesCS7A01G232500 chr2A 97.770 1794 26 3 1301 3080 522570753 522568960 0.000000e+00 3079.0
13 TraesCS7A01G232500 chr1A 97.541 1789 42 2 1300 3086 567831474 567833262 0.000000e+00 3059.0
14 TraesCS7A01G232500 chr1A 98.899 454 5 0 1300 1753 567832805 567833258 0.000000e+00 811.0
15 TraesCS7A01G232500 chr1A 98.894 452 5 0 2631 3082 567831475 567831926 0.000000e+00 808.0
16 TraesCS7A01G232500 chr5B 96.878 1794 33 5 1301 3080 485571914 485573698 0.000000e+00 2981.0
17 TraesCS7A01G232500 chr5B 98.675 453 6 0 2630 3082 485571913 485572365 0.000000e+00 804.0
18 TraesCS7A01G232500 chrUn 99.278 1386 10 0 1301 2686 277735050 277736435 0.000000e+00 2505.0
19 TraesCS7A01G232500 chrUn 99.278 1386 10 0 1301 2686 282947663 282949048 0.000000e+00 2505.0
20 TraesCS7A01G232500 chrUn 98.894 452 5 0 2631 3082 277735050 277735501 0.000000e+00 808.0
21 TraesCS7A01G232500 chrUn 98.894 452 5 0 2631 3082 282947663 282948114 0.000000e+00 808.0
22 TraesCS7A01G232500 chr7D 91.863 1487 78 18 3081 4524 194129802 194131288 0.000000e+00 2036.0
23 TraesCS7A01G232500 chr7D 88.941 1058 65 14 3081 4118 132764135 132763110 0.000000e+00 1258.0
24 TraesCS7A01G232500 chr7D 88.994 1054 64 16 3081 4115 132830454 132829434 0.000000e+00 1256.0
25 TraesCS7A01G232500 chr7D 88.480 1033 62 23 3081 4093 132136082 132137077 0.000000e+00 1195.0
26 TraesCS7A01G232500 chr7D 87.327 1081 70 18 3086 4154 132741553 132742578 0.000000e+00 1175.0
27 TraesCS7A01G232500 chr7D 88.516 984 59 18 3096 4062 132748462 132749408 0.000000e+00 1142.0
28 TraesCS7A01G232500 chr7D 89.136 718 37 24 594 1297 194129113 194129803 0.000000e+00 856.0
29 TraesCS7A01G232500 chr7D 86.013 622 56 14 2 597 194128314 194128930 4.940000e-179 638.0
30 TraesCS7A01G232500 chr7D 86.577 596 55 22 709 1300 132764705 132764131 6.390000e-178 634.0
31 TraesCS7A01G232500 chr7D 84.346 543 53 18 774 1300 132830976 132830450 1.880000e-138 503.0
32 TraesCS7A01G232500 chr7D 82.593 540 40 21 738 1264 132156998 132157496 1.160000e-115 427.0
33 TraesCS7A01G232500 chr7D 84.561 421 27 9 4105 4491 132749405 132749821 2.550000e-102 383.0
34 TraesCS7A01G232500 chr7D 87.879 330 33 2 975 1298 132741222 132741550 9.190000e-102 381.0
35 TraesCS7A01G232500 chr7D 78.788 363 46 24 691 1051 133193438 133193771 9.860000e-52 215.0
36 TraesCS7A01G232500 chr7B 96.592 1203 27 2 1453 2641 610361871 610363073 0.000000e+00 1982.0
37 TraesCS7A01G232500 chr7B 89.536 1529 73 33 3081 4524 157808859 157810385 0.000000e+00 1857.0
38 TraesCS7A01G232500 chr7B 91.554 817 41 11 3094 3884 94185920 94185106 0.000000e+00 1101.0
39 TraesCS7A01G232500 chr7B 90.629 811 56 5 3081 3885 93864989 93865785 0.000000e+00 1059.0
40 TraesCS7A01G232500 chr7B 91.366 776 39 11 3135 3884 94143107 94142334 0.000000e+00 1037.0
41 TraesCS7A01G232500 chr7B 91.445 713 30 17 612 1300 157808158 157808863 0.000000e+00 950.0
42 TraesCS7A01G232500 chr7B 87.221 673 61 16 639 1298 94118623 94117963 0.000000e+00 743.0
43 TraesCS7A01G232500 chr7B 86.944 674 63 16 639 1298 94051067 94050405 0.000000e+00 734.0
44 TraesCS7A01G232500 chr7B 87.859 626 71 5 1753 2376 696908082 696907460 0.000000e+00 730.0
45 TraesCS7A01G232500 chr7B 85.978 542 48 10 3 520 157807010 157807547 5.120000e-154 555.0
46 TraesCS7A01G232500 chr7B 87.187 359 39 5 612 967 93650368 93650722 7.050000e-108 401.0
47 TraesCS7A01G232500 chr7B 77.704 601 88 30 4 591 94051642 94051075 4.370000e-85 326.0
48 TraesCS7A01G232500 chr7B 76.441 590 99 25 14 591 94119192 94118631 2.670000e-72 283.0
49 TraesCS7A01G232500 chr7B 88.479 217 21 3 3903 4115 94049142 94048926 4.490000e-65 259.0
50 TraesCS7A01G232500 chr7B 78.385 421 61 18 3723 4115 94185333 94184915 3.500000e-61 246.0
51 TraesCS7A01G232500 chr7B 78.147 421 62 18 3723 4115 94142561 94142143 1.630000e-59 241.0
52 TraesCS7A01G232500 chr7B 85.443 158 20 2 408 562 93647630 93647787 1.300000e-35 161.0
53 TraesCS7A01G232500 chr4B 95.572 926 22 8 1748 2657 647675105 647676027 0.000000e+00 1465.0
54 TraesCS7A01G232500 chr4B 88.508 583 57 7 1710 2291 537797641 537797068 0.000000e+00 697.0
55 TraesCS7A01G232500 chr6B 95.366 928 24 8 1746 2657 317750293 317749369 0.000000e+00 1458.0
56 TraesCS7A01G232500 chr6B 88.651 608 64 5 1747 2352 697538750 697539354 0.000000e+00 736.0
57 TraesCS7A01G232500 chr6B 92.220 437 33 1 1832 2267 442919622 442920058 6.430000e-173 617.0
58 TraesCS7A01G232500 chr6B 89.744 78 7 1 975 1051 207104569 207104492 1.040000e-16 99.0
59 TraesCS7A01G232500 chr3A 95.645 574 22 3 2229 2801 395756159 395756730 0.000000e+00 918.0
60 TraesCS7A01G232500 chr4A 87.707 724 70 11 2090 2797 457583656 457584376 0.000000e+00 826.0
61 TraesCS7A01G232500 chr4A 86.602 724 78 11 2090 2797 456352356 456353076 0.000000e+00 782.0
62 TraesCS7A01G232500 chr2B 92.072 555 31 9 2229 2783 757831277 757831818 0.000000e+00 769.0
63 TraesCS7A01G232500 chr2B 88.953 344 36 2 1999 2340 8824023 8824366 1.510000e-114 424.0
64 TraesCS7A01G232500 chr5D 94.231 52 2 1 985 1035 526706272 526706323 1.350000e-10 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 TraesCS7A01G232500 chr7A 203694218 203698743 4525 False 3343.000000 8359 100.000000 1 4526 3 chr7A.!!$F3 4525
1 TraesCS7A01G232500 chr7A 131186179 131187118 939 True 1109.000000 1109 88.404000 3086 3999 1 chr7A.!!$R2 913
2 TraesCS7A01G232500 chr7A 210252345 210253695 1350 False 776.000000 1225 88.514000 946 4115 2 chr7A.!!$F4 3169
3 TraesCS7A01G232500 chr7A 131108093 131109917 1824 True 708.000000 1098 88.359000 612 4005 2 chr7A.!!$R3 3393
4 TraesCS7A01G232500 chr7A 130891461 130892120 659 False 590.000000 590 83.167000 612 1298 1 chr7A.!!$F2 686
5 TraesCS7A01G232500 chr1B 218955994 218957784 1790 True 3173.000000 3173 98.660000 1294 3083 1 chr1B.!!$R1 1789
6 TraesCS7A01G232500 chr2A 522568960 522570753 1793 True 3079.000000 3079 97.770000 1301 3080 1 chr2A.!!$R1 1779
7 TraesCS7A01G232500 chr1A 567831474 567833262 1788 False 1559.333333 3059 98.444667 1300 3086 3 chr1A.!!$F1 1786
8 TraesCS7A01G232500 chr5B 485571913 485573698 1785 False 1892.500000 2981 97.776500 1301 3082 2 chr5B.!!$F1 1781
9 TraesCS7A01G232500 chrUn 277735050 277736435 1385 False 1656.500000 2505 99.086000 1301 3082 2 chrUn.!!$F1 1781
10 TraesCS7A01G232500 chrUn 282947663 282949048 1385 False 1656.500000 2505 99.086000 1301 3082 2 chrUn.!!$F2 1781
11 TraesCS7A01G232500 chr7D 132136082 132137077 995 False 1195.000000 1195 88.480000 3081 4093 1 chr7D.!!$F1 1012
12 TraesCS7A01G232500 chr7D 194128314 194131288 2974 False 1176.666667 2036 89.004000 2 4524 3 chr7D.!!$F6 4522
13 TraesCS7A01G232500 chr7D 132763110 132764705 1595 True 946.000000 1258 87.759000 709 4118 2 chr7D.!!$R1 3409
14 TraesCS7A01G232500 chr7D 132829434 132830976 1542 True 879.500000 1256 86.670000 774 4115 2 chr7D.!!$R2 3341
15 TraesCS7A01G232500 chr7D 132741222 132742578 1356 False 778.000000 1175 87.603000 975 4154 2 chr7D.!!$F4 3179
16 TraesCS7A01G232500 chr7D 132748462 132749821 1359 False 762.500000 1142 86.538500 3096 4491 2 chr7D.!!$F5 1395
17 TraesCS7A01G232500 chr7B 610361871 610363073 1202 False 1982.000000 1982 96.592000 1453 2641 1 chr7B.!!$F2 1188
18 TraesCS7A01G232500 chr7B 157807010 157810385 3375 False 1120.666667 1857 88.986333 3 4524 3 chr7B.!!$F4 4521
19 TraesCS7A01G232500 chr7B 93864989 93865785 796 False 1059.000000 1059 90.629000 3081 3885 1 chr7B.!!$F1 804
20 TraesCS7A01G232500 chr7B 696907460 696908082 622 True 730.000000 730 87.859000 1753 2376 1 chr7B.!!$R1 623
21 TraesCS7A01G232500 chr7B 94184915 94185920 1005 True 673.500000 1101 84.969500 3094 4115 2 chr7B.!!$R5 1021
22 TraesCS7A01G232500 chr7B 94142143 94143107 964 True 639.000000 1037 84.756500 3135 4115 2 chr7B.!!$R4 980
23 TraesCS7A01G232500 chr7B 94117963 94119192 1229 True 513.000000 743 81.831000 14 1298 2 chr7B.!!$R3 1284
24 TraesCS7A01G232500 chr7B 94048926 94051642 2716 True 439.666667 734 84.375667 4 4115 3 chr7B.!!$R2 4111
25 TraesCS7A01G232500 chr7B 93647630 93650722 3092 False 281.000000 401 86.315000 408 967 2 chr7B.!!$F3 559
26 TraesCS7A01G232500 chr4B 647675105 647676027 922 False 1465.000000 1465 95.572000 1748 2657 1 chr4B.!!$F1 909
27 TraesCS7A01G232500 chr4B 537797068 537797641 573 True 697.000000 697 88.508000 1710 2291 1 chr4B.!!$R1 581
28 TraesCS7A01G232500 chr6B 317749369 317750293 924 True 1458.000000 1458 95.366000 1746 2657 1 chr6B.!!$R2 911
29 TraesCS7A01G232500 chr6B 697538750 697539354 604 False 736.000000 736 88.651000 1747 2352 1 chr6B.!!$F2 605
30 TraesCS7A01G232500 chr3A 395756159 395756730 571 False 918.000000 918 95.645000 2229 2801 1 chr3A.!!$F1 572
31 TraesCS7A01G232500 chr4A 457583656 457584376 720 False 826.000000 826 87.707000 2090 2797 1 chr4A.!!$F2 707
32 TraesCS7A01G232500 chr4A 456352356 456353076 720 False 782.000000 782 86.602000 2090 2797 1 chr4A.!!$F1 707
33 TraesCS7A01G232500 chr2B 757831277 757831818 541 False 769.000000 769 92.072000 2229 2783 1 chr2B.!!$F2 554

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
192 209 0.249120 CACACTAGCCAATCCGGTGA 59.751 55.000 0.00 0.00 36.97 4.02 F
194 211 0.537188 CACTAGCCAATCCGGTGAGT 59.463 55.000 0.00 0.00 36.97 3.41 F
1161 4758 0.574454 GCTACGACGACGACGACTAT 59.426 55.000 25.15 6.28 42.66 2.12 F
1190 4793 2.022240 GACCTCGTCATCCCCAGCTC 62.022 65.000 0.00 0.00 32.09 4.09 F
1298 4906 2.415625 CAGCCTTCTGATGAGCTTTTGC 60.416 50.000 0.00 0.00 42.95 3.68 F
1498 5106 3.389983 ACTACATCGCCTGGCCTTTATAA 59.610 43.478 14.12 0.00 0.00 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 4996 0.034059 CCTGTGTCCACCTGTGTCTC 59.966 60.000 0.0 0.0 0.0 3.36 R
1671 5279 1.835267 TGTGTGTCGCTGGGTAGGT 60.835 57.895 0.0 0.0 0.0 3.08 R
2718 6343 0.034059 CCTGTGTCCACCTGTGTCTC 59.966 60.000 0.0 0.0 0.0 3.36 R
3001 6626 1.835267 TGTGTGTCGCTGGGTAGGT 60.835 57.895 0.0 0.0 0.0 3.08 R
3074 6699 2.290641 ACATCAGGGACGGCAATGTTAA 60.291 45.455 0.0 0.0 0.0 2.01 R
4497 8917 0.830023 GGGCAAAACTAAGCACCCCA 60.830 55.000 0.0 0.0 0.0 4.96 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
99 102 7.601886 TGCCATGTACTGAAAACCAATAATTTG 59.398 33.333 0.00 0.00 0.00 2.32
160 177 0.760945 GAGGATCACGGGTCTCCCAT 60.761 60.000 5.64 0.00 38.37 4.00
168 185 0.394352 CGGGTCTCCCATTTGAAGGG 60.394 60.000 5.64 0.00 45.83 3.95
192 209 0.249120 CACACTAGCCAATCCGGTGA 59.751 55.000 0.00 0.00 36.97 4.02
194 211 0.537188 CACTAGCCAATCCGGTGAGT 59.463 55.000 0.00 0.00 36.97 3.41
199 216 4.722193 CAATCCGGTGAGTGGCTT 57.278 55.556 0.00 0.00 33.03 4.35
201 218 2.107950 CAATCCGGTGAGTGGCTTTA 57.892 50.000 0.00 0.00 33.03 1.85
202 219 2.432444 CAATCCGGTGAGTGGCTTTAA 58.568 47.619 0.00 0.00 33.03 1.52
214 231 6.152831 GTGAGTGGCTTTAATTGGTTAGGATT 59.847 38.462 0.00 0.00 0.00 3.01
252 273 7.858879 GCTTTTATTCCTTACAAGTTTCGAACA 59.141 33.333 0.00 0.00 0.00 3.18
260 281 6.073276 CCTTACAAGTTTCGAACATGATGTGA 60.073 38.462 0.00 0.00 34.42 3.58
290 311 3.132111 TCTTGTGCTAAGATCCGTGCATA 59.868 43.478 7.26 2.89 37.76 3.14
305 326 1.770061 TGCATATGATCTGGTGGCAGA 59.230 47.619 6.97 0.00 35.46 4.26
317 338 1.208052 GGTGGCAGAGTAGAGCATTCA 59.792 52.381 0.00 0.00 0.00 2.57
320 341 3.131223 GTGGCAGAGTAGAGCATTCACTA 59.869 47.826 0.00 0.00 0.00 2.74
325 346 5.587289 CAGAGTAGAGCATTCACTAGAACC 58.413 45.833 0.00 0.00 36.39 3.62
327 348 6.544197 CAGAGTAGAGCATTCACTAGAACCTA 59.456 42.308 0.00 0.00 36.39 3.08
331 352 8.221944 AGTAGAGCATTCACTAGAACCTACTAT 58.778 37.037 0.00 0.00 36.04 2.12
597 3763 8.710239 TGCTTCCATGTAGTCTACCAAAATATA 58.290 33.333 7.56 0.00 0.00 0.86
637 3993 3.439129 CACCAAACGGTAGGAATTCTTCC 59.561 47.826 5.23 4.94 42.03 3.46
670 4026 4.279169 TCCAACTCTGAAAAGCAAATCAGG 59.721 41.667 11.28 6.33 42.62 3.86
714 4071 2.436417 TCAAAAGCTAGCACCATCCAC 58.564 47.619 18.83 0.00 0.00 4.02
736 4098 3.610821 CGTCGCCCTGATCGTATATCAAA 60.611 47.826 0.00 0.00 0.00 2.69
747 4109 6.478673 TGATCGTATATCAAACAGCACGAATT 59.521 34.615 0.00 0.00 41.17 2.17
760 4122 5.523916 ACAGCACGAATTGTAAAGCTATAGG 59.476 40.000 1.04 0.00 0.00 2.57
800 4162 4.271816 CGAGAGCCCACCCGATCG 62.272 72.222 8.51 8.51 0.00 3.69
981 4359 7.232118 AGGAGAGAGAAAGAGAAAGAGAAAG 57.768 40.000 0.00 0.00 0.00 2.62
982 4360 7.010160 AGGAGAGAGAAAGAGAAAGAGAAAGA 58.990 38.462 0.00 0.00 0.00 2.52
997 4393 5.189180 AGAGAAAGAAGAGAGAGAGAGAGC 58.811 45.833 0.00 0.00 0.00 4.09
1161 4758 0.574454 GCTACGACGACGACGACTAT 59.426 55.000 25.15 6.28 42.66 2.12
1190 4793 2.022240 GACCTCGTCATCCCCAGCTC 62.022 65.000 0.00 0.00 32.09 4.09
1296 4904 3.430042 TCAGCCTTCTGATGAGCTTTT 57.570 42.857 0.00 0.00 43.95 2.27
1297 4905 3.079578 TCAGCCTTCTGATGAGCTTTTG 58.920 45.455 0.00 0.00 43.95 2.44
1298 4906 2.415625 CAGCCTTCTGATGAGCTTTTGC 60.416 50.000 0.00 0.00 42.95 3.68
1388 4996 4.780554 AGGTAGAAGAAGAAGGGAAGAAGG 59.219 45.833 0.00 0.00 0.00 3.46
1498 5106 3.389983 ACTACATCGCCTGGCCTTTATAA 59.610 43.478 14.12 0.00 0.00 0.98
2718 6343 4.780554 AGGTAGAAGAAGAAGGGAAGAAGG 59.219 45.833 0.00 0.00 0.00 3.46
2828 6453 3.389983 ACTACATCGCCTGGCCTTTATAA 59.610 43.478 14.12 0.00 0.00 0.98
3089 6714 4.565166 GCTTATTTTTAACATTGCCGTCCC 59.435 41.667 0.00 0.00 0.00 4.46
3175 6800 0.247460 TCTGATGGAGGACGTTGCAG 59.753 55.000 0.00 0.00 0.00 4.41
3243 6883 2.722201 GGCCAAGGAGGACGACGAT 61.722 63.158 0.00 0.00 41.22 3.73
3322 6962 1.826385 GGACAAGAACATCCTGGTGG 58.174 55.000 0.00 0.00 31.75 4.61
3627 7801 2.861462 TCCTTGTTTTGCTTCGTTGG 57.139 45.000 0.00 0.00 0.00 3.77
3849 8054 2.941453 GTGCTGGACGAATCTAGTGA 57.059 50.000 0.00 0.00 35.88 3.41
3944 8149 3.381908 TCTCGCCTGTCTATCTTTTCTCC 59.618 47.826 0.00 0.00 0.00 3.71
4014 8220 5.649395 TCATGCCTACTCTCTGAAAAATTGG 59.351 40.000 0.00 0.00 0.00 3.16
4088 8426 6.932400 TGATTGATGATTCTTGCTTGCTTTTT 59.068 30.769 0.00 0.00 0.00 1.94
4104 8443 4.328440 TGCTTTTTCGTGAATTTTGTGTGG 59.672 37.500 0.00 0.00 0.00 4.17
4197 8549 5.518487 CGTTTGTTTGTTTATGTCCTGCTTT 59.482 36.000 0.00 0.00 0.00 3.51
4207 8559 7.768120 TGTTTATGTCCTGCTTTGTTGATTTTT 59.232 29.630 0.00 0.00 0.00 1.94
4245 8617 2.354328 ACCTGATTTGGTGGTTCCCTA 58.646 47.619 0.00 0.00 39.17 3.53
4263 8635 6.783708 TCCCTAAATGTTTTGTGTTTGTCT 57.216 33.333 0.00 0.00 0.00 3.41
4266 8638 6.198216 CCCTAAATGTTTTGTGTTTGTCTTCG 59.802 38.462 0.00 0.00 0.00 3.79
4294 8666 9.880157 TGTTTACTTCTTGTAAGAACAGTAACT 57.120 29.630 14.12 0.00 41.55 2.24
4317 8690 4.624024 TGTTTCAGTATGTAGTTGTAGCGC 59.376 41.667 0.00 0.00 37.40 5.92
4497 8917 8.637196 TTCAGTTTTACCCCAAAAATGTTTTT 57.363 26.923 9.02 0.00 46.93 1.94
4516 8937 0.830023 TGGGGTGCTTAGTTTTGCCC 60.830 55.000 0.00 0.00 35.52 5.36
4524 8945 3.569701 TGCTTAGTTTTGCCCTTCTTCTG 59.430 43.478 0.00 0.00 0.00 3.02
4525 8946 3.570125 GCTTAGTTTTGCCCTTCTTCTGT 59.430 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 72 5.344743 TGGTTTTCAGTACATGGCAAAAA 57.655 34.783 0.00 0.00 0.00 1.94
70 73 5.344743 TTGGTTTTCAGTACATGGCAAAA 57.655 34.783 0.00 0.00 0.00 2.44
71 74 5.543507 ATTGGTTTTCAGTACATGGCAAA 57.456 34.783 0.00 0.00 0.00 3.68
99 102 6.426633 ACTTTTACAAGGTGGCAAAAATATGC 59.573 34.615 0.00 0.00 38.78 3.14
160 177 4.139038 GGCTAGTGTGTAAACCCTTCAAA 58.861 43.478 0.00 0.00 0.00 2.69
168 185 2.676342 CCGGATTGGCTAGTGTGTAAAC 59.324 50.000 0.00 0.00 0.00 2.01
192 209 5.105351 GCAATCCTAACCAATTAAAGCCACT 60.105 40.000 0.00 0.00 0.00 4.00
194 211 4.142271 CGCAATCCTAACCAATTAAAGCCA 60.142 41.667 0.00 0.00 0.00 4.75
199 216 4.437659 GCGAACGCAATCCTAACCAATTAA 60.438 41.667 14.26 0.00 41.49 1.40
201 218 2.159435 GCGAACGCAATCCTAACCAATT 60.159 45.455 14.26 0.00 41.49 2.32
202 219 1.400494 GCGAACGCAATCCTAACCAAT 59.600 47.619 14.26 0.00 41.49 3.16
234 251 5.995282 ACATCATGTTCGAAACTTGTAAGGA 59.005 36.000 0.00 0.00 37.68 3.36
290 311 2.964464 CTCTACTCTGCCACCAGATCAT 59.036 50.000 0.00 0.00 46.44 2.45
305 326 6.428295 AGTAGGTTCTAGTGAATGCTCTACT 58.572 40.000 0.00 0.00 34.28 2.57
320 341 8.583296 GGGAACGTCATATTTATAGTAGGTTCT 58.417 37.037 0.00 0.00 32.78 3.01
327 348 8.877195 ACTATTGGGGAACGTCATATTTATAGT 58.123 33.333 0.00 0.00 0.00 2.12
535 1141 2.935849 TGCTTATGCCAATACAGTGTCG 59.064 45.455 0.00 0.00 38.71 4.35
567 1182 4.041075 TGGTAGACTACATGGAAGCAACAA 59.959 41.667 14.48 0.00 0.00 2.83
597 3763 0.677288 TGGACTTGATGTCGTCGGTT 59.323 50.000 0.00 0.00 46.24 4.44
637 3993 2.575532 TCAGAGTTGGACTGCTTTTGG 58.424 47.619 0.00 0.00 35.61 3.28
644 4000 4.637483 TTTGCTTTTCAGAGTTGGACTG 57.363 40.909 0.00 0.00 36.80 3.51
714 4071 1.467342 TGATATACGATCAGGGCGACG 59.533 52.381 0.00 0.00 0.00 5.12
736 4098 5.523916 CCTATAGCTTTACAATTCGTGCTGT 59.476 40.000 0.00 0.00 32.72 4.40
981 4359 2.435372 TGGGCTCTCTCTCTCTCTTC 57.565 55.000 0.00 0.00 0.00 2.87
982 4360 2.669781 CATGGGCTCTCTCTCTCTCTT 58.330 52.381 0.00 0.00 0.00 2.85
1118 4709 2.352805 CCTCCTTGACCTGGGTGC 59.647 66.667 0.00 0.00 0.00 5.01
1190 4793 4.445699 GCATACCCTGCGAGAAGG 57.554 61.111 0.00 0.00 41.97 3.46
1295 4903 0.179043 TAGTCGGCAACAACAGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
1296 4904 0.602638 CTAGTCGGCAACAACAGGCA 60.603 55.000 0.00 0.00 0.00 4.75
1297 4905 1.912371 GCTAGTCGGCAACAACAGGC 61.912 60.000 0.00 0.00 0.00 4.85
1298 4906 1.298859 GGCTAGTCGGCAACAACAGG 61.299 60.000 0.00 0.00 38.25 4.00
1388 4996 0.034059 CCTGTGTCCACCTGTGTCTC 59.966 60.000 0.00 0.00 0.00 3.36
1498 5106 2.511600 GCCGCTGCGTTACCTGAT 60.512 61.111 21.59 0.00 0.00 2.90
1671 5279 1.835267 TGTGTGTCGCTGGGTAGGT 60.835 57.895 0.00 0.00 0.00 3.08
1744 5352 5.428457 TCATGGCTTAGGAGGAGAATGTTAA 59.572 40.000 0.00 0.00 0.00 2.01
2594 6218 4.856607 GGTTCGGAGGAGCTCGCG 62.857 72.222 7.83 0.00 0.00 5.87
2718 6343 0.034059 CCTGTGTCCACCTGTGTCTC 59.966 60.000 0.00 0.00 0.00 3.36
2828 6453 2.511600 GCCGCTGCGTTACCTGAT 60.512 61.111 21.59 0.00 0.00 2.90
3001 6626 1.835267 TGTGTGTCGCTGGGTAGGT 60.835 57.895 0.00 0.00 0.00 3.08
3074 6699 2.290641 ACATCAGGGACGGCAATGTTAA 60.291 45.455 0.00 0.00 0.00 2.01
3089 6714 2.998670 ACGTCTGCAGAATCAACATCAG 59.001 45.455 20.19 2.93 0.00 2.90
3175 6800 3.844090 GGAGAGGCCGGTCTGAGC 61.844 72.222 16.74 0.00 0.00 4.26
3627 7801 1.067776 ACCAACTCGATCCAAGACGAC 60.068 52.381 0.00 0.00 34.82 4.34
3839 8044 8.442632 TCATGACCAATTTCATCACTAGATTC 57.557 34.615 0.00 0.00 33.74 2.52
3843 8048 7.120285 ACAGTTCATGACCAATTTCATCACTAG 59.880 37.037 0.00 0.00 33.74 2.57
3849 8054 6.040729 TCAACACAGTTCATGACCAATTTCAT 59.959 34.615 0.00 0.00 36.62 2.57
3900 8105 7.149047 CGAGACTAGCTTAAGATAATCAAAGCG 60.149 40.741 11.37 5.90 46.92 4.68
3944 8149 5.860716 GCTTAAAGCAAAACAGATCAAGGAG 59.139 40.000 0.00 0.00 41.89 3.69
4014 8220 2.917971 CGTCAAACTCGAGGAGATCAAC 59.082 50.000 18.41 4.62 33.32 3.18
4088 8426 5.067273 AGGATAACCACACAAAATTCACGA 58.933 37.500 0.00 0.00 38.94 4.35
4245 8617 5.347364 CACCGAAGACAAACACAAAACATTT 59.653 36.000 0.00 0.00 0.00 2.32
4263 8635 6.817641 TGTTCTTACAAGAAGTAAACACCGAA 59.182 34.615 4.66 0.00 45.01 4.30
4266 8638 7.549615 ACTGTTCTTACAAGAAGTAAACACC 57.450 36.000 4.66 0.00 45.01 4.16
4294 8666 4.624024 GCGCTACAACTACATACTGAAACA 59.376 41.667 0.00 0.00 0.00 2.83
4317 8690 5.981315 CAGATAAACAAGCAAATGCCCATAG 59.019 40.000 0.94 0.00 43.38 2.23
4497 8917 0.830023 GGGCAAAACTAAGCACCCCA 60.830 55.000 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.