Multiple sequence alignment - TraesCS6A01G204800

Loading Multiple Alignment...

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 TraesCS6A01G204800 chr6A 100.000 5043 0 0 1 5043 356974919 356979961 0.000000e+00 9313.0
1 TraesCS6A01G204800 chr6A 88.098 857 98 4 4189 5043 29983622 29984476 0.000000e+00 1014.0
2 TraesCS6A01G204800 chr6A 97.398 538 14 0 4506 5043 444679273 444679810 0.000000e+00 917.0
3 TraesCS6A01G204800 chr6A 90.181 387 23 2 4184 4555 444678895 444679281 1.630000e-134 490.0
4 TraesCS6A01G204800 chr6B 94.871 3373 87 33 852 4188 347224682 347221360 0.000000e+00 5192.0
5 TraesCS6A01G204800 chr6B 86.559 558 42 16 294 839 347225276 347224740 7.280000e-163 584.0
6 TraesCS6A01G204800 chr6B 86.928 306 33 5 2 306 347227012 347226713 2.250000e-88 337.0
7 TraesCS6A01G204800 chr6D 93.884 3401 104 49 852 4188 262776627 262779987 0.000000e+00 5033.0
8 TraesCS6A01G204800 chr6D 86.762 559 45 20 303 844 262776026 262776572 3.360000e-166 595.0
9 TraesCS6A01G204800 chr4A 93.228 886 28 4 4186 5043 176810977 176811858 0.000000e+00 1275.0
10 TraesCS6A01G204800 chr4A 90.569 668 48 2 4376 5043 1480961 1481613 0.000000e+00 870.0
11 TraesCS6A01G204800 chr5D 92.669 682 49 1 4362 5043 481532339 481533019 0.000000e+00 981.0
12 TraesCS6A01G204800 chr5D 88.710 62 7 0 1072 1133 356979294 356979233 5.410000e-10 76.8
13 TraesCS6A01G204800 chr1A 97.403 539 13 1 4506 5043 21149753 21150291 0.000000e+00 917.0
14 TraesCS6A01G204800 chr1A 93.294 343 22 1 4186 4528 21149353 21149694 5.830000e-139 505.0
15 TraesCS6A01G204800 chr5A 97.212 538 15 0 4506 5043 442427694 442428231 0.000000e+00 911.0
16 TraesCS6A01G204800 chr5A 96.840 538 17 0 4506 5043 459488952 459489489 0.000000e+00 900.0
17 TraesCS6A01G204800 chr5A 93.842 341 21 0 4188 4528 459488566 459488906 9.680000e-142 514.0
18 TraesCS6A01G204800 chr4B 95.676 555 22 2 4488 5041 99007977 99008530 0.000000e+00 891.0
19 TraesCS6A01G204800 chr1D 89.766 684 65 5 4362 5043 27472942 27472262 0.000000e+00 870.0
20 TraesCS6A01G204800 chr1D 88.921 343 38 0 4186 4528 373424615 373424957 1.680000e-114 424.0
21 TraesCS6A01G204800 chr2A 81.737 1002 107 39 1056 2010 701485084 701486056 0.000000e+00 767.0
22 TraesCS6A01G204800 chr2A 85.812 733 87 13 2635 3357 701486586 701487311 0.000000e+00 761.0
23 TraesCS6A01G204800 chr2A 90.816 392 19 3 4179 4555 766420914 766421303 4.500000e-140 508.0
24 TraesCS6A01G204800 chr2A 80.556 504 61 15 2004 2499 701486084 701486558 2.230000e-93 353.0
25 TraesCS6A01G204800 chr2A 82.934 334 37 11 3741 4065 701487715 701488037 2.970000e-72 283.0
26 TraesCS6A01G204800 chr2B 85.675 733 88 13 2635 3357 670835977 670836702 0.000000e+00 756.0
27 TraesCS6A01G204800 chr2B 81.076 1004 118 35 1052 2010 670834476 670835452 0.000000e+00 736.0
28 TraesCS6A01G204800 chr2B 86.866 434 45 7 2932 3357 670840100 670840529 4.570000e-130 475.0
29 TraesCS6A01G204800 chr2B 80.198 505 60 13 2004 2500 670835478 670835950 4.830000e-90 342.0
30 TraesCS6A01G204800 chr2B 79.959 484 56 29 3594 4065 670841183 670841637 8.150000e-83 318.0
31 TraesCS6A01G204800 chr2B 82.029 345 37 17 3739 4071 670837115 670837446 2.310000e-68 270.0
32 TraesCS6A01G204800 chr2B 86.275 204 23 3 2629 2828 670838672 670838874 3.060000e-52 217.0
33 TraesCS6A01G204800 chr2B 79.688 192 28 11 2329 2512 670838420 670838608 1.470000e-25 128.0
34 TraesCS6A01G204800 chr2D 80.857 1003 117 41 1055 2010 561838830 561839804 0.000000e+00 719.0
35 TraesCS6A01G204800 chr2D 89.907 535 46 7 2663 3195 561843691 561844219 0.000000e+00 682.0
36 TraesCS6A01G204800 chr2D 86.130 447 50 9 2627 3068 561840326 561840765 5.910000e-129 472.0
37 TraesCS6A01G204800 chr2D 79.633 491 62 12 2016 2500 561839844 561840302 8.150000e-83 318.0
38 TraesCS6A01G204800 chr2D 85.574 305 36 6 3058 3357 561840866 561841167 3.790000e-81 313.0
39 TraesCS6A01G204800 chr2D 84.024 338 31 16 3740 4065 561844507 561844833 2.280000e-78 303.0
40 TraesCS6A01G204800 chr2D 83.172 309 32 13 3741 4040 561841583 561841880 1.080000e-66 265.0
41 TraesCS6A01G204800 chr2D 79.897 194 28 7 2329 2516 561843001 561843189 1.140000e-26 132.0
42 TraesCS6A01G204800 chr7A 93.860 342 21 0 4187 4528 562700712 562700371 2.690000e-142 516.0
43 TraesCS6A01G204800 chr7A 94.277 332 19 0 4186 4517 286528464 286528133 4.500000e-140 508.0


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 TraesCS6A01G204800 chr6A 356974919 356979961 5042 False 9313.000000 9313 100.000000 1 5043 1 chr6A.!!$F2 5042
1 TraesCS6A01G204800 chr6A 29983622 29984476 854 False 1014.000000 1014 88.098000 4189 5043 1 chr6A.!!$F1 854
2 TraesCS6A01G204800 chr6A 444678895 444679810 915 False 703.500000 917 93.789500 4184 5043 2 chr6A.!!$F3 859
3 TraesCS6A01G204800 chr6B 347221360 347227012 5652 True 2037.666667 5192 89.452667 2 4188 3 chr6B.!!$R1 4186
4 TraesCS6A01G204800 chr6D 262776026 262779987 3961 False 2814.000000 5033 90.323000 303 4188 2 chr6D.!!$F1 3885
5 TraesCS6A01G204800 chr4A 176810977 176811858 881 False 1275.000000 1275 93.228000 4186 5043 1 chr4A.!!$F2 857
6 TraesCS6A01G204800 chr4A 1480961 1481613 652 False 870.000000 870 90.569000 4376 5043 1 chr4A.!!$F1 667
7 TraesCS6A01G204800 chr5D 481532339 481533019 680 False 981.000000 981 92.669000 4362 5043 1 chr5D.!!$F1 681
8 TraesCS6A01G204800 chr1A 21149353 21150291 938 False 711.000000 917 95.348500 4186 5043 2 chr1A.!!$F1 857
9 TraesCS6A01G204800 chr5A 442427694 442428231 537 False 911.000000 911 97.212000 4506 5043 1 chr5A.!!$F1 537
10 TraesCS6A01G204800 chr5A 459488566 459489489 923 False 707.000000 900 95.341000 4188 5043 2 chr5A.!!$F2 855
11 TraesCS6A01G204800 chr4B 99007977 99008530 553 False 891.000000 891 95.676000 4488 5041 1 chr4B.!!$F1 553
12 TraesCS6A01G204800 chr1D 27472262 27472942 680 True 870.000000 870 89.766000 4362 5043 1 chr1D.!!$R1 681
13 TraesCS6A01G204800 chr2A 701485084 701488037 2953 False 541.000000 767 82.759750 1056 4065 4 chr2A.!!$F2 3009
14 TraesCS6A01G204800 chr2B 670834476 670841637 7161 False 405.250000 756 82.720750 1052 4071 8 chr2B.!!$F1 3019
15 TraesCS6A01G204800 chr2D 561838830 561844833 6003 False 400.500000 719 83.649250 1055 4065 8 chr2D.!!$F1 3010

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
820 2300 0.106918 CTCCTCTCCACCTACGCTCT 60.107 60.0 0.0 0.0 0.00 4.09 F
848 2328 0.110678 TCGATCCCCGAGTGCTATCT 59.889 55.0 0.0 0.0 43.23 1.98 F
849 2329 0.962489 CGATCCCCGAGTGCTATCTT 59.038 55.0 0.0 0.0 41.76 2.40 F
3107 4899 1.209621 GTGTAGGTTGGCCCCAGATA 58.790 55.0 0.0 0.0 34.57 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 3857 1.587547 TGCTGATAACACGTGCACAA 58.412 45.000 17.22 0.0 0.00 3.33 R
2715 4394 2.596923 TGCAAGCACGGCAATGGA 60.597 55.556 0.00 0.0 38.54 3.41 R
3240 5037 9.777008 AACCCCTTGATTTCCTTTACAAATATA 57.223 29.630 0.00 0.0 0.00 0.86 R
4609 11383 0.616395 TGCTTATCCACCTCCACCGA 60.616 55.000 0.00 0.0 0.00 4.69 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
27 28 7.015195 AGGATATGGTTACATGGCATTTAAACC 59.985 37.037 16.53 18.80 37.97 3.27
34 35 7.279090 GGTTACATGGCATTTAAACCCAAATAC 59.721 37.037 18.26 8.67 32.09 1.89
46 47 1.750778 CCCAAATACGCAAAGCTCCAT 59.249 47.619 0.00 0.00 0.00 3.41
55 56 2.483877 CGCAAAGCTCCATGTAAGAACA 59.516 45.455 0.00 0.00 40.69 3.18
69 71 4.819088 TGTAAGAACACATGTGCTTAGCAA 59.181 37.500 25.68 11.02 44.49 3.91
94 96 8.786826 ATTGACCGACAATTTTGAGATTAGTA 57.213 30.769 0.00 0.00 45.60 1.82
95 97 7.591006 TGACCGACAATTTTGAGATTAGTAC 57.409 36.000 0.00 0.00 0.00 2.73
96 98 7.156000 TGACCGACAATTTTGAGATTAGTACA 58.844 34.615 0.00 0.00 0.00 2.90
97 99 7.822334 TGACCGACAATTTTGAGATTAGTACAT 59.178 33.333 0.00 0.00 0.00 2.29
98 100 8.197988 ACCGACAATTTTGAGATTAGTACATC 57.802 34.615 0.00 0.00 0.00 3.06
103 105 6.851222 ATTTTGAGATTAGTACATCTGGCG 57.149 37.500 0.64 0.00 33.36 5.69
124 126 6.024049 GGCGAAAGAATACATCTGAAAACAG 58.976 40.000 0.00 0.00 38.79 3.16
141 143 7.514721 TGAAAACAGAGGGTGATAAAGTAACT 58.485 34.615 0.00 0.00 0.00 2.24
145 147 5.103000 CAGAGGGTGATAAAGTAACTCGTG 58.897 45.833 0.00 0.00 0.00 4.35
159 161 4.830826 AACTCGTGACATATAGATCGCA 57.169 40.909 0.00 0.00 0.00 5.10
166 168 5.284897 CGTGACATATAGATCGCAGATCAAC 59.715 44.000 16.97 0.00 45.12 3.18
170 172 7.928167 TGACATATAGATCGCAGATCAACTTTT 59.072 33.333 16.97 2.66 45.12 2.27
171 173 8.668510 ACATATAGATCGCAGATCAACTTTTT 57.331 30.769 16.97 2.12 45.12 1.94
178 180 6.528014 TCGCAGATCAACTTTTTAACGTTA 57.472 33.333 3.29 3.29 0.00 3.18
181 183 6.299966 CGCAGATCAACTTTTTAACGTTACTG 59.700 38.462 7.70 8.89 0.00 2.74
182 184 6.086371 GCAGATCAACTTTTTAACGTTACTGC 59.914 38.462 18.29 18.29 37.12 4.40
212 214 3.350219 TTCCAGTGCTTCTAATCACCC 57.650 47.619 0.00 0.00 33.90 4.61
213 215 1.207089 TCCAGTGCTTCTAATCACCCG 59.793 52.381 0.00 0.00 33.90 5.28
234 236 6.094464 ACCCGCTTGAAGTTTATATTTGTACC 59.906 38.462 0.00 0.00 0.00 3.34
251 253 3.265737 TGTACCCCAGTAATCATGTTGCT 59.734 43.478 0.00 0.00 0.00 3.91
255 257 5.518865 ACCCCAGTAATCATGTTGCTAATT 58.481 37.500 0.00 0.00 0.00 1.40
273 275 8.464770 TGCTAATTCAGTTTGCAAAATACATC 57.535 30.769 14.67 0.00 43.75 3.06
352 1804 2.890814 AGTAGCTCACTGGTTACCTGT 58.109 47.619 8.14 8.14 35.62 4.00
373 1825 7.863877 ACCTGTTTCGTTAATTATTTTGGTGTC 59.136 33.333 0.00 0.00 0.00 3.67
404 1856 6.373774 CAGAAAGTTGTAGCTTCCAATGAGAT 59.626 38.462 0.00 0.00 0.00 2.75
410 1862 5.773575 TGTAGCTTCCAATGAGATATCGTC 58.226 41.667 0.00 0.00 0.00 4.20
473 1925 6.803154 AATCCTAAACTTCCAACGAAAGAG 57.197 37.500 0.00 0.00 0.00 2.85
534 1991 7.062138 GTGCACAAACATAAACTGGTTCATATG 59.938 37.037 13.17 0.00 30.24 1.78
617 2080 0.467290 GGGCACTTCAACCCAGTTCA 60.467 55.000 0.00 0.00 46.22 3.18
647 2110 2.996621 GTCTACCTAAGCAAGCACACAG 59.003 50.000 0.00 0.00 0.00 3.66
659 2128 2.187351 GCACACAGCAAGAACGAAAA 57.813 45.000 0.00 0.00 44.79 2.29
660 2129 1.846175 GCACACAGCAAGAACGAAAAC 59.154 47.619 0.00 0.00 44.79 2.43
661 2130 2.477863 GCACACAGCAAGAACGAAAACT 60.478 45.455 0.00 0.00 44.79 2.66
662 2131 3.242608 GCACACAGCAAGAACGAAAACTA 60.243 43.478 0.00 0.00 44.79 2.24
663 2132 4.271687 CACACAGCAAGAACGAAAACTAC 58.728 43.478 0.00 0.00 0.00 2.73
664 2133 4.034048 CACACAGCAAGAACGAAAACTACT 59.966 41.667 0.00 0.00 0.00 2.57
679 2148 7.543520 ACGAAAACTACTACTAGCAAATACCAC 59.456 37.037 0.00 0.00 0.00 4.16
700 2169 1.457346 AATTTCAGAAGAGCCGCCAG 58.543 50.000 0.00 0.00 0.00 4.85
701 2170 0.326264 ATTTCAGAAGAGCCGCCAGT 59.674 50.000 0.00 0.00 0.00 4.00
703 2172 2.125350 CAGAAGAGCCGCCAGTCC 60.125 66.667 0.00 0.00 0.00 3.85
705 2174 1.992277 AGAAGAGCCGCCAGTCCAT 60.992 57.895 0.00 0.00 0.00 3.41
707 2176 1.965754 GAAGAGCCGCCAGTCCATCT 61.966 60.000 0.00 0.00 0.00 2.90
709 2178 2.685017 AGCCGCCAGTCCATCTGA 60.685 61.111 0.00 0.00 46.27 3.27
710 2179 2.202987 GCCGCCAGTCCATCTGAG 60.203 66.667 0.00 0.00 46.27 3.35
714 2183 2.898738 CCAGTCCATCTGAGCGCT 59.101 61.111 11.27 11.27 46.27 5.92
715 2184 1.220206 CCAGTCCATCTGAGCGCTT 59.780 57.895 13.26 0.00 46.27 4.68
716 2185 1.088340 CCAGTCCATCTGAGCGCTTG 61.088 60.000 13.26 5.42 46.27 4.01
717 2186 1.449246 AGTCCATCTGAGCGCTTGC 60.449 57.895 13.26 0.00 39.58 4.01
755 2235 3.668447 TCTCTGTTGTTTCTCATGCTCC 58.332 45.455 0.00 0.00 0.00 4.70
815 2295 1.001760 TGCCCTCCTCTCCACCTAC 59.998 63.158 0.00 0.00 0.00 3.18
820 2300 0.106918 CTCCTCTCCACCTACGCTCT 60.107 60.000 0.00 0.00 0.00 4.09
847 2327 2.642425 TCGATCCCCGAGTGCTATC 58.358 57.895 0.00 0.00 43.23 2.08
848 2328 0.110678 TCGATCCCCGAGTGCTATCT 59.889 55.000 0.00 0.00 43.23 1.98
849 2329 0.962489 CGATCCCCGAGTGCTATCTT 59.038 55.000 0.00 0.00 41.76 2.40
850 2330 1.341531 CGATCCCCGAGTGCTATCTTT 59.658 52.381 0.00 0.00 41.76 2.52
870 2402 4.796038 TTTCCCCGTTTGTTTGTGTTTA 57.204 36.364 0.00 0.00 0.00 2.01
905 2437 2.124193 CATCGCCATGCCCCTCAA 60.124 61.111 0.00 0.00 0.00 3.02
952 2487 1.882189 ATAGGGGTGGACCGGACAGA 61.882 60.000 9.46 0.00 41.60 3.41
979 2517 2.108970 CCTAACGGTTAAGCCCTCTCT 58.891 52.381 1.79 0.00 0.00 3.10
988 2526 2.835895 GCCCTCTCTCCCCGAGAC 60.836 72.222 0.00 0.00 43.72 3.36
989 2527 2.123640 CCCTCTCTCCCCGAGACC 60.124 72.222 0.00 0.00 43.72 3.85
1334 2892 4.129737 CGGTCGCCGGACAGATGT 62.130 66.667 5.05 0.00 45.28 3.06
1343 2902 1.335872 CCGGACAGATGTTTTTGTGGC 60.336 52.381 0.00 0.00 0.00 5.01
1346 2905 1.606668 GACAGATGTTTTTGTGGCGGA 59.393 47.619 0.00 0.00 0.00 5.54
1350 2909 3.190327 CAGATGTTTTTGTGGCGGATGTA 59.810 43.478 0.00 0.00 0.00 2.29
1351 2910 3.823873 AGATGTTTTTGTGGCGGATGTAA 59.176 39.130 0.00 0.00 0.00 2.41
1352 2911 3.357166 TGTTTTTGTGGCGGATGTAAC 57.643 42.857 0.00 0.00 0.00 2.50
1353 2912 2.688446 TGTTTTTGTGGCGGATGTAACA 59.312 40.909 0.00 0.00 0.00 2.41
1354 2913 3.130516 TGTTTTTGTGGCGGATGTAACAA 59.869 39.130 0.00 0.00 0.00 2.83
1357 2916 1.518325 TGTGGCGGATGTAACAAGTG 58.482 50.000 0.00 0.00 0.00 3.16
1377 2936 2.700407 TTTCGGCGGGTTGGGTTGAT 62.700 55.000 7.21 0.00 0.00 2.57
1378 2937 3.439540 CGGCGGGTTGGGTTGATG 61.440 66.667 0.00 0.00 0.00 3.07
1379 2938 2.034999 GGCGGGTTGGGTTGATGA 59.965 61.111 0.00 0.00 0.00 2.92
1561 3129 2.505557 GCACATTCGCTGCTTGCC 60.506 61.111 0.00 0.00 38.78 4.52
1582 3150 3.518590 CTGCTTTCTTGATGGAAATGGC 58.481 45.455 0.00 0.00 35.12 4.40
1730 3298 8.948631 AATCAACTTCGAATTTAGCTCTGATA 57.051 30.769 0.00 0.00 0.00 2.15
1731 3299 8.948631 ATCAACTTCGAATTTAGCTCTGATAA 57.051 30.769 0.00 0.00 0.00 1.75
1790 3397 1.937899 GTGTTAGCTCCACGTTGTTGT 59.062 47.619 0.00 0.00 0.00 3.32
1791 3398 2.353579 GTGTTAGCTCCACGTTGTTGTT 59.646 45.455 0.00 0.00 0.00 2.83
1904 3511 4.843220 ATTCCAGTGCAGAAAACAGAAG 57.157 40.909 0.00 0.00 0.00 2.85
2012 3619 8.828688 AGTAGTTATCCAGTTGTTTTACTGAC 57.171 34.615 5.39 0.00 46.72 3.51
2013 3620 8.426489 AGTAGTTATCCAGTTGTTTTACTGACA 58.574 33.333 5.39 0.00 46.72 3.58
2050 3694 5.268387 TGCCCAACATCCTGTAACATTTAT 58.732 37.500 0.00 0.00 0.00 1.40
2145 3789 6.907206 TTTTCTTCAAATTTTGACCAGCAG 57.093 33.333 11.30 6.41 39.87 4.24
2213 3857 4.765273 TGGTCTCGCATGTTACATTATGT 58.235 39.130 2.58 2.58 0.00 2.29
2313 3957 8.226543 TGTTTTTGTGAGATCAATTTATTCGC 57.773 30.769 0.00 0.00 0.00 4.70
2409 4055 6.649141 CGTATGTGTATGCCCTGTTGTTATAT 59.351 38.462 0.00 0.00 0.00 0.86
2617 4268 6.876257 AGAGTTGTTTTATGAGGTCATCAGAC 59.124 38.462 0.00 0.00 42.53 3.51
2633 4284 5.363580 TCATCAGACCAGTATTAGTGATGCA 59.636 40.000 5.44 0.00 40.62 3.96
2673 4335 6.992715 AGGGTCAAATTAATTCTATGGAGACG 59.007 38.462 0.10 0.00 0.00 4.18
2715 4394 8.778358 CAAAGAAGTTTAGAGCTAACTCATTGT 58.222 33.333 0.91 0.00 46.09 2.71
2895 4575 9.965824 ATGAACTTTCAGTACTTAAAACCATTG 57.034 29.630 3.93 0.00 41.08 2.82
3107 4899 1.209621 GTGTAGGTTGGCCCCAGATA 58.790 55.000 0.00 0.00 34.57 1.98
3449 9657 4.943705 ACCAAGGTACACTTTATGCATCAG 59.056 41.667 0.19 3.01 37.29 2.90
3475 9886 5.647589 CTGTCCATTTGACTCAATCCATTG 58.352 41.667 0.00 0.00 44.75 2.82
3533 9947 4.280174 ACATTGCTGCTTCATTCTGTTCTT 59.720 37.500 0.00 0.00 0.00 2.52
3701 10301 1.421382 CAACAAAGCATTTCCCGCTG 58.579 50.000 0.00 0.00 40.35 5.18
3731 10331 1.681229 TGCCTTCCCATCTAAACCCT 58.319 50.000 0.00 0.00 0.00 4.34
3732 10332 2.853430 TGCCTTCCCATCTAAACCCTA 58.147 47.619 0.00 0.00 0.00 3.53
4070 10688 2.217750 TGTATCCATATTGCCGTGTGC 58.782 47.619 0.00 0.00 41.77 4.57
4095 10713 5.333581 TGCCAGTATATGCTACCTCAGTAT 58.666 41.667 0.00 0.00 33.66 2.12
4105 10723 3.637229 GCTACCTCAGTATCTTGCTACCA 59.363 47.826 0.00 0.00 0.00 3.25
4172 10790 2.083774 TCAGTTTTTATGCTGGCCTCG 58.916 47.619 3.32 0.00 33.81 4.63
4301 10924 4.403734 TCTTGGCCGAAATAGGACTTTTT 58.596 39.130 0.00 0.00 40.90 1.94
4359 10982 4.280019 GGCCGAAGTGGTGGGGTT 62.280 66.667 0.00 0.00 41.21 4.11
4404 11027 4.039366 GGTCAAGTCTAGGCCGAAATAGAT 59.961 45.833 0.00 0.00 31.05 1.98
4447 11070 6.515043 CGAAAAGTACTTTTTGGTCTCGTA 57.485 37.500 29.54 0.00 42.26 3.43
4609 11383 8.401955 TCCTCTGTATCTATAAAAACCCCTTT 57.598 34.615 0.00 0.00 0.00 3.11
5000 11774 0.460311 CGCTTCCGGGTTCTACATCT 59.540 55.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.036220 CGTATTTGGGTTTAAATGCCATGTAA 58.964 34.615 0.00 0.00 31.53 2.41
14 15 4.081420 TGCGTATTTGGGTTTAAATGCCAT 60.081 37.500 0.00 0.00 31.53 4.40
17 18 5.670094 GCTTTGCGTATTTGGGTTTAAATGC 60.670 40.000 0.00 0.00 32.79 3.56
27 28 2.164219 ACATGGAGCTTTGCGTATTTGG 59.836 45.455 0.00 0.00 0.00 3.28
34 35 2.483877 TGTTCTTACATGGAGCTTTGCG 59.516 45.455 0.00 0.00 0.00 4.85
46 47 4.384940 TGCTAAGCACATGTGTTCTTACA 58.615 39.130 26.01 19.41 33.74 2.41
55 56 2.162208 CGGTCAATTGCTAAGCACATGT 59.838 45.455 0.00 0.00 38.71 3.21
59 60 1.804151 TGTCGGTCAATTGCTAAGCAC 59.196 47.619 0.00 0.00 38.71 4.40
60 61 2.177394 TGTCGGTCAATTGCTAAGCA 57.823 45.000 0.00 0.00 36.47 3.91
81 83 5.972935 TCGCCAGATGTACTAATCTCAAAA 58.027 37.500 0.00 0.00 34.60 2.44
87 89 7.652105 TGTATTCTTTCGCCAGATGTACTAATC 59.348 37.037 0.00 0.00 0.00 1.75
90 92 6.459670 TGTATTCTTTCGCCAGATGTACTA 57.540 37.500 0.00 0.00 0.00 1.82
91 93 5.339008 TGTATTCTTTCGCCAGATGTACT 57.661 39.130 0.00 0.00 0.00 2.73
92 94 5.986135 AGATGTATTCTTTCGCCAGATGTAC 59.014 40.000 0.00 0.00 0.00 2.90
94 96 4.813161 CAGATGTATTCTTTCGCCAGATGT 59.187 41.667 0.00 0.00 29.93 3.06
95 97 5.052481 TCAGATGTATTCTTTCGCCAGATG 58.948 41.667 0.00 0.00 29.93 2.90
96 98 5.282055 TCAGATGTATTCTTTCGCCAGAT 57.718 39.130 0.00 0.00 29.93 2.90
97 99 4.736126 TCAGATGTATTCTTTCGCCAGA 57.264 40.909 0.00 0.00 29.93 3.86
98 100 5.801350 TTTCAGATGTATTCTTTCGCCAG 57.199 39.130 0.00 0.00 29.93 4.85
124 126 5.100943 GTCACGAGTTACTTTATCACCCTC 58.899 45.833 0.00 0.00 0.00 4.30
141 143 4.695455 TGATCTGCGATCTATATGTCACGA 59.305 41.667 15.99 0.00 0.00 4.35
145 147 7.881643 AAAGTTGATCTGCGATCTATATGTC 57.118 36.000 15.99 1.90 0.00 3.06
157 159 6.086371 GCAGTAACGTTAAAAAGTTGATCTGC 59.914 38.462 18.29 18.29 39.89 4.26
159 161 7.225931 TCTGCAGTAACGTTAAAAAGTTGATCT 59.774 33.333 14.67 0.00 32.92 2.75
166 168 4.024387 TGCCTCTGCAGTAACGTTAAAAAG 60.024 41.667 14.67 5.97 44.23 2.27
170 172 2.823924 TGCCTCTGCAGTAACGTTAA 57.176 45.000 14.67 0.00 44.23 2.01
181 183 1.375098 GCACTGGAATCTGCCTCTGC 61.375 60.000 0.00 0.00 38.26 4.26
182 184 0.252479 AGCACTGGAATCTGCCTCTG 59.748 55.000 0.00 0.00 33.57 3.35
194 196 1.656652 CGGGTGATTAGAAGCACTGG 58.343 55.000 10.22 0.00 44.29 4.00
212 214 6.094325 TGGGGTACAAATATAAACTTCAAGCG 59.906 38.462 0.00 0.00 0.00 4.68
213 215 7.122204 ACTGGGGTACAAATATAAACTTCAAGC 59.878 37.037 0.00 0.00 0.00 4.01
234 236 6.319658 ACTGAATTAGCAACATGATTACTGGG 59.680 38.462 0.00 0.00 0.00 4.45
246 248 8.071122 TGTATTTTGCAAACTGAATTAGCAAC 57.929 30.769 12.39 0.00 43.94 4.17
251 253 9.409312 CTGTGATGTATTTTGCAAACTGAATTA 57.591 29.630 12.39 0.00 0.00 1.40
255 257 5.534278 TCCTGTGATGTATTTTGCAAACTGA 59.466 36.000 12.39 0.00 0.00 3.41
336 1788 1.798813 CGAAACAGGTAACCAGTGAGC 59.201 52.381 0.00 0.00 37.17 4.26
373 1825 4.261614 GGAAGCTACAACTTTCTGGTTTGG 60.262 45.833 0.00 0.00 0.00 3.28
404 1856 0.107361 TCAGAGAGTGGCGGACGATA 60.107 55.000 0.00 0.00 0.00 2.92
410 1862 2.672961 TACATTTCAGAGAGTGGCGG 57.327 50.000 0.00 0.00 0.00 6.13
508 1965 4.677584 TGAACCAGTTTATGTTTGTGCAC 58.322 39.130 10.75 10.75 0.00 4.57
534 1991 3.567478 ATGCACTTCCTCCATAGTTCC 57.433 47.619 0.00 0.00 0.00 3.62
539 2002 5.645056 TTGGATAATGCACTTCCTCCATA 57.355 39.130 11.48 0.66 32.02 2.74
544 2007 3.443681 CGGTTTTGGATAATGCACTTCCT 59.556 43.478 11.48 0.00 0.00 3.36
586 2049 6.775629 GGGTTGAAGTGCCCATCTTAATATTA 59.224 38.462 0.00 0.00 44.23 0.98
606 2069 4.763793 AGACAGATGAAATGAACTGGGTTG 59.236 41.667 0.00 0.00 35.08 3.77
613 2076 6.818644 TGCTTAGGTAGACAGATGAAATGAAC 59.181 38.462 0.00 0.00 0.00 3.18
617 2080 5.819901 GCTTGCTTAGGTAGACAGATGAAAT 59.180 40.000 0.00 0.00 0.00 2.17
647 2110 5.632347 TGCTAGTAGTAGTTTTCGTTCTTGC 59.368 40.000 6.47 0.00 0.00 4.01
659 2128 9.734984 AAATTTGTGGTATTTGCTAGTAGTAGT 57.265 29.630 6.47 0.00 0.00 2.73
661 2130 9.727859 TGAAATTTGTGGTATTTGCTAGTAGTA 57.272 29.630 0.00 0.00 0.00 1.82
662 2131 8.630054 TGAAATTTGTGGTATTTGCTAGTAGT 57.370 30.769 0.00 0.00 0.00 2.73
663 2132 8.946085 TCTGAAATTTGTGGTATTTGCTAGTAG 58.054 33.333 0.00 0.00 0.00 2.57
664 2133 8.856153 TCTGAAATTTGTGGTATTTGCTAGTA 57.144 30.769 0.00 0.00 0.00 1.82
679 2148 1.541147 TGGCGGCTCTTCTGAAATTTG 59.459 47.619 11.43 0.00 0.00 2.32
700 2169 2.467826 GGCAAGCGCTCAGATGGAC 61.468 63.158 12.06 0.00 38.60 4.02
701 2170 2.124983 GGCAAGCGCTCAGATGGA 60.125 61.111 12.06 0.00 38.60 3.41
703 2172 1.428219 CAAGGCAAGCGCTCAGATG 59.572 57.895 12.06 6.38 38.60 2.90
705 2174 3.052082 GCAAGGCAAGCGCTCAGA 61.052 61.111 12.06 0.00 38.60 3.27
707 2176 4.648626 AGGCAAGGCAAGCGCTCA 62.649 61.111 12.06 0.00 38.60 4.26
709 2178 4.341783 AGAGGCAAGGCAAGCGCT 62.342 61.111 2.64 2.64 38.60 5.92
710 2179 4.112341 CAGAGGCAAGGCAAGCGC 62.112 66.667 0.00 0.00 37.44 5.92
714 2183 0.767375 AGAGAACAGAGGCAAGGCAA 59.233 50.000 0.00 0.00 0.00 4.52
715 2184 0.767375 AAGAGAACAGAGGCAAGGCA 59.233 50.000 0.00 0.00 0.00 4.75
716 2185 1.003003 AGAAGAGAACAGAGGCAAGGC 59.997 52.381 0.00 0.00 0.00 4.35
717 2186 2.566724 AGAGAAGAGAACAGAGGCAAGG 59.433 50.000 0.00 0.00 0.00 3.61
839 2319 3.081804 CAAACGGGGAAAAGATAGCACT 58.918 45.455 0.00 0.00 0.00 4.40
844 2324 4.645588 ACACAAACAAACGGGGAAAAGATA 59.354 37.500 0.00 0.00 0.00 1.98
845 2325 3.449377 ACACAAACAAACGGGGAAAAGAT 59.551 39.130 0.00 0.00 0.00 2.40
847 2327 3.239587 ACACAAACAAACGGGGAAAAG 57.760 42.857 0.00 0.00 0.00 2.27
848 2328 3.679824 AACACAAACAAACGGGGAAAA 57.320 38.095 0.00 0.00 0.00 2.29
849 2329 3.679824 AAACACAAACAAACGGGGAAA 57.320 38.095 0.00 0.00 0.00 3.13
850 2330 3.429135 GCTAAACACAAACAAACGGGGAA 60.429 43.478 0.00 0.00 0.00 3.97
905 2437 6.157994 AGGGCTAGGTTTTTCCTTTTCTTTTT 59.842 34.615 0.00 0.00 45.67 1.94
939 2474 1.509703 GTCTTTTCTGTCCGGTCCAC 58.490 55.000 0.00 0.00 0.00 4.02
979 2517 4.257810 TTGTGGGGGTCTCGGGGA 62.258 66.667 0.00 0.00 0.00 4.81
1118 2665 3.839432 GGCTTCTCTACGGCGGCT 61.839 66.667 13.24 0.00 0.00 5.52
1334 2892 3.381908 ACTTGTTACATCCGCCACAAAAA 59.618 39.130 0.00 0.00 0.00 1.94
1343 2902 2.412325 GCCGAAACACTTGTTACATCCG 60.412 50.000 0.00 0.00 37.25 4.18
1346 2905 1.533731 CCGCCGAAACACTTGTTACAT 59.466 47.619 0.00 0.00 37.25 2.29
1350 2909 1.033202 AACCCGCCGAAACACTTGTT 61.033 50.000 0.00 0.00 40.50 2.83
1351 2910 1.452470 AACCCGCCGAAACACTTGT 60.452 52.632 0.00 0.00 0.00 3.16
1352 2911 1.008995 CAACCCGCCGAAACACTTG 60.009 57.895 0.00 0.00 0.00 3.16
1353 2912 2.190841 CCAACCCGCCGAAACACTT 61.191 57.895 0.00 0.00 0.00 3.16
1354 2913 2.593436 CCAACCCGCCGAAACACT 60.593 61.111 0.00 0.00 0.00 3.55
1357 2916 2.908428 AACCCAACCCGCCGAAAC 60.908 61.111 0.00 0.00 0.00 2.78
1561 3129 3.194968 AGCCATTTCCATCAAGAAAGCAG 59.805 43.478 0.00 0.00 39.04 4.24
1582 3150 2.029623 CTTCATCCCATGGAAGGCAAG 58.970 52.381 15.22 4.74 37.46 4.01
1886 3493 2.575532 TCCTTCTGTTTTCTGCACTGG 58.424 47.619 0.00 0.00 0.00 4.00
1904 3511 4.855340 TGACCATCCAAAGGTAAAGATCC 58.145 43.478 0.00 0.00 40.09 3.36
2010 3617 6.318648 TGTTGGGCATTAGTAGATGAATTGTC 59.681 38.462 0.00 0.00 0.00 3.18
2011 3618 6.186957 TGTTGGGCATTAGTAGATGAATTGT 58.813 36.000 0.00 0.00 0.00 2.71
2012 3619 6.698008 TGTTGGGCATTAGTAGATGAATTG 57.302 37.500 0.00 0.00 0.00 2.32
2013 3620 6.491403 GGATGTTGGGCATTAGTAGATGAATT 59.509 38.462 0.00 0.00 38.06 2.17
2145 3789 2.550830 TCAAGAGTTTCCAGTGAGGC 57.449 50.000 0.00 0.00 37.29 4.70
2213 3857 1.587547 TGCTGATAACACGTGCACAA 58.412 45.000 17.22 0.00 0.00 3.33
2296 3940 8.219546 TGGTAAATGCGAATAAATTGATCTCA 57.780 30.769 0.00 0.00 0.00 3.27
2313 3957 5.866633 ACCAATTAAACGCACATGGTAAATG 59.133 36.000 0.00 0.00 39.29 2.32
2409 4055 3.213506 GCATCACACCCACATGCTAATA 58.786 45.455 0.00 0.00 39.92 0.98
2512 4161 6.660949 AGGTTTCCATTAACTTGGATCTCTTG 59.339 38.462 0.00 0.00 45.08 3.02
2715 4394 2.596923 TGCAAGCACGGCAATGGA 60.597 55.556 0.00 0.00 38.54 3.41
3240 5037 9.777008 AACCCCTTGATTTCCTTTACAAATATA 57.223 29.630 0.00 0.00 0.00 0.86
3533 9947 3.712733 AGGTAGTTAGGTCCAACACAACA 59.287 43.478 0.00 0.00 0.00 3.33
3586 10001 4.100189 AGCAAGATACCAGACTATGTCACC 59.900 45.833 0.46 0.00 34.60 4.02
3701 10301 1.084289 GGGAAGGCATACACGAACAC 58.916 55.000 0.00 0.00 0.00 3.32
3731 10331 4.534500 TCTGCTCCAAATAAACAGACCCTA 59.466 41.667 0.00 0.00 32.65 3.53
3732 10332 3.330701 TCTGCTCCAAATAAACAGACCCT 59.669 43.478 0.00 0.00 32.65 4.34
4070 10688 4.039730 ACTGAGGTAGCATATACTGGCAAG 59.960 45.833 0.00 0.00 0.00 4.01
4095 10713 0.758734 ACACACAGCTGGTAGCAAGA 59.241 50.000 19.93 0.00 45.56 3.02
4447 11070 1.103398 GCCATGCAACTTCGGCCTAT 61.103 55.000 0.00 0.00 38.67 2.57
4609 11383 0.616395 TGCTTATCCACCTCCACCGA 60.616 55.000 0.00 0.00 0.00 4.69
4811 11585 2.359975 GTCCTTTCAGGCCACCCG 60.360 66.667 5.01 0.00 34.61 5.28
5000 11774 1.878102 GCAGAACTCTTGCCCTTCGAA 60.878 52.381 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.