Multiple sequence alignment - TraesCS5B01G034600

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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 TraesCS5B01G034600 chr5B 100.000 4175 0 0 1 4175 37480677 37484851 0.000000e+00 7710.0
1 TraesCS5B01G034600 chr7A 88.178 2766 304 10 904 3665 56174176 56176922 0.000000e+00 3275.0
2 TraesCS5B01G034600 chr7A 81.902 1188 190 20 2489 3664 56206440 56207614 0.000000e+00 979.0
3 TraesCS5B01G034600 chr7A 85.044 341 30 12 534 854 8589266 8589605 1.120000e-85 327.0
4 TraesCS5B01G034600 chr4A 87.315 2767 337 13 904 3665 732058564 732061321 0.000000e+00 3153.0
5 TraesCS5B01G034600 chr4A 81.308 2782 454 39 906 3664 732354794 732357532 0.000000e+00 2196.0
6 TraesCS5B01G034600 chr4A 80.100 2794 484 58 908 3664 731875449 731872691 0.000000e+00 2013.0
7 TraesCS5B01G034600 chr4A 84.827 1707 246 9 908 2607 731616869 731615169 0.000000e+00 1705.0
8 TraesCS5B01G034600 chr4A 83.249 1785 287 11 905 2684 732105438 732107215 0.000000e+00 1629.0
9 TraesCS5B01G034600 chr4A 82.106 1738 305 4 952 2684 731861781 731860045 0.000000e+00 1482.0
10 TraesCS5B01G034600 chr4A 86.364 572 47 14 304 854 732104758 732105319 2.780000e-166 595.0
11 TraesCS5B01G034600 chr4A 83.681 576 67 17 300 854 732057877 732058446 6.190000e-143 518.0
12 TraesCS5B01G034600 chr4A 83.475 587 60 11 296 857 731604943 731604369 2.880000e-141 512.0
13 TraesCS5B01G034600 chr4A 92.230 296 22 1 1 296 732104421 732104715 6.460000e-113 418.0
14 TraesCS5B01G034600 chr4A 90.203 296 29 0 1 296 731605275 731604980 1.820000e-103 387.0
15 TraesCS5B01G034600 chr4A 88.346 266 26 5 443 705 732362001 732362264 8.710000e-82 315.0
16 TraesCS5B01G034600 chr4A 79.661 236 32 11 552 781 731617476 731617251 5.590000e-34 156.0
17 TraesCS5B01G034600 chr7D 82.383 2770 442 34 915 3664 7712562 7715305 0.000000e+00 2370.0
18 TraesCS5B01G034600 chr7D 82.035 2772 455 33 913 3664 7749976 7752724 0.000000e+00 2320.0
19 TraesCS5B01G034600 chr7D 81.221 2785 464 40 907 3664 7597270 7600022 0.000000e+00 2191.0
20 TraesCS5B01G034600 chr7D 82.118 2606 418 41 1079 3665 7606300 7608876 0.000000e+00 2187.0
21 TraesCS5B01G034600 chr7D 83.895 1782 267 17 915 2684 7561054 7562827 0.000000e+00 1683.0
22 TraesCS5B01G034600 chr7D 84.515 1692 251 10 908 2590 7548359 7550048 0.000000e+00 1663.0
23 TraesCS5B01G034600 chr7D 85.393 534 50 13 348 859 7923670 7924197 2.860000e-146 529.0
24 TraesCS5B01G034600 chr7D 82.990 582 50 21 296 852 8256749 8256192 8.120000e-132 481.0
25 TraesCS5B01G034600 chr7D 87.209 430 43 6 296 720 8232822 8233244 2.920000e-131 479.0
26 TraesCS5B01G034600 chr7D 85.235 149 13 3 552 699 7749519 7749659 1.210000e-30 145.0
27 TraesCS5B01G034600 chr7D 82.051 117 13 2 43 159 8037532 8037640 4.440000e-15 93.5
28 TraesCS5B01G034600 chr7D 86.207 87 9 3 14 98 7596585 7596670 1.600000e-14 91.6
29 TraesCS5B01G034600 chr3B 83.907 1771 273 9 908 2669 741463140 741464907 0.000000e+00 1681.0
30 TraesCS5B01G034600 chr3B 80.423 189 28 5 378 559 741456987 741457173 7.280000e-28 135.0
31 TraesCS5B01G034600 chr3B 91.935 62 4 1 103 164 741456834 741456894 7.440000e-13 86.1
32 TraesCS5B01G034600 chr7B 88.650 511 54 4 3666 4175 135408634 135409141 1.650000e-173 619.0
33 TraesCS5B01G034600 chr7B 90.930 441 39 1 3666 4106 450549051 450548612 3.590000e-165 592.0
34 TraesCS5B01G034600 chr7B 90.847 437 37 3 3671 4106 450528010 450527576 2.160000e-162 582.0
35 TraesCS5B01G034600 chr6B 88.499 513 53 5 3666 4175 313393041 313393550 2.130000e-172 616.0
36 TraesCS5B01G034600 chr6B 88.258 511 40 10 3665 4175 623052641 623053131 9.990000e-166 593.0
37 TraesCS5B01G034600 chr1B 88.258 511 46 13 3666 4175 428798445 428798942 2.150000e-167 599.0
38 TraesCS5B01G034600 chr1B 90.455 440 38 4 3666 4104 473637402 473637838 1.010000e-160 577.0
39 TraesCS5B01G034600 chr1B 82.779 511 58 18 3671 4175 300609001 300609487 2.980000e-116 429.0
40 TraesCS5B01G034600 chr1B 80.492 528 71 15 3665 4175 636906120 636906632 3.940000e-100 375.0
41 TraesCS5B01G034600 chr4B 90.205 439 40 3 3666 4103 395659081 395659517 1.680000e-158 569.0
42 TraesCS5B01G034600 chr4B 89.414 444 45 2 3666 4109 183830689 183831130 3.650000e-155 558.0
43 TraesCS5B01G034600 chr4B 95.000 80 4 0 4096 4175 142898425 142898346 4.380000e-25 126.0
44 TraesCS5B01G034600 chr2B 85.305 524 56 9 3671 4175 687792486 687791965 4.780000e-144 521.0
45 TraesCS5B01G034600 chr3D 78.656 506 69 17 3680 4175 282822173 282822649 2.440000e-77 300.0
46 TraesCS5B01G034600 chr6A 84.889 225 24 9 3951 4171 416308719 416308937 7.030000e-53 219.0
47 TraesCS5B01G034600 chr1A 79.503 322 45 14 3872 4175 512565875 512565557 4.230000e-50 209.0


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 TraesCS5B01G034600 chr5B 37480677 37484851 4174 False 7710.000000 7710 100.000 1 4175 1 chr5B.!!$F1 4174
1 TraesCS5B01G034600 chr7A 56174176 56176922 2746 False 3275.000000 3275 88.178 904 3665 1 chr7A.!!$F2 2761
2 TraesCS5B01G034600 chr7A 56206440 56207614 1174 False 979.000000 979 81.902 2489 3664 1 chr7A.!!$F3 1175
3 TraesCS5B01G034600 chr4A 732354794 732357532 2738 False 2196.000000 2196 81.308 906 3664 1 chr4A.!!$F1 2758
4 TraesCS5B01G034600 chr4A 731872691 731875449 2758 True 2013.000000 2013 80.100 908 3664 1 chr4A.!!$R2 2756
5 TraesCS5B01G034600 chr4A 732057877 732061321 3444 False 1835.500000 3153 85.498 300 3665 2 chr4A.!!$F3 3365
6 TraesCS5B01G034600 chr4A 731860045 731861781 1736 True 1482.000000 1482 82.106 952 2684 1 chr4A.!!$R1 1732
7 TraesCS5B01G034600 chr4A 731615169 731617476 2307 True 930.500000 1705 82.244 552 2607 2 chr4A.!!$R4 2055
8 TraesCS5B01G034600 chr4A 732104421 732107215 2794 False 880.666667 1629 87.281 1 2684 3 chr4A.!!$F4 2683
9 TraesCS5B01G034600 chr4A 731604369 731605275 906 True 449.500000 512 86.839 1 857 2 chr4A.!!$R3 856
10 TraesCS5B01G034600 chr7D 7712562 7715305 2743 False 2370.000000 2370 82.383 915 3664 1 chr7D.!!$F4 2749
11 TraesCS5B01G034600 chr7D 7606300 7608876 2576 False 2187.000000 2187 82.118 1079 3665 1 chr7D.!!$F3 2586
12 TraesCS5B01G034600 chr7D 7561054 7562827 1773 False 1683.000000 1683 83.895 915 2684 1 chr7D.!!$F2 1769
13 TraesCS5B01G034600 chr7D 7548359 7550048 1689 False 1663.000000 1663 84.515 908 2590 1 chr7D.!!$F1 1682
14 TraesCS5B01G034600 chr7D 7749519 7752724 3205 False 1232.500000 2320 83.635 552 3664 2 chr7D.!!$F9 3112
15 TraesCS5B01G034600 chr7D 7596585 7600022 3437 False 1141.300000 2191 83.714 14 3664 2 chr7D.!!$F8 3650
16 TraesCS5B01G034600 chr7D 7923670 7924197 527 False 529.000000 529 85.393 348 859 1 chr7D.!!$F5 511
17 TraesCS5B01G034600 chr7D 8256192 8256749 557 True 481.000000 481 82.990 296 852 1 chr7D.!!$R1 556
18 TraesCS5B01G034600 chr3B 741463140 741464907 1767 False 1681.000000 1681 83.907 908 2669 1 chr3B.!!$F1 1761
19 TraesCS5B01G034600 chr7B 135408634 135409141 507 False 619.000000 619 88.650 3666 4175 1 chr7B.!!$F1 509
20 TraesCS5B01G034600 chr6B 313393041 313393550 509 False 616.000000 616 88.499 3666 4175 1 chr6B.!!$F1 509
21 TraesCS5B01G034600 chr1B 636906120 636906632 512 False 375.000000 375 80.492 3665 4175 1 chr1B.!!$F4 510
22 TraesCS5B01G034600 chr2B 687791965 687792486 521 True 521.000000 521 85.305 3671 4175 1 chr2B.!!$R1 504

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
694 764 0.758123 GCTTCCATCCTCTCTCCAGG 59.242 60.0 0.00 0.00 34.40 4.45 F
1605 2139 0.178846 TTGGGATGGGAGGTCTTGGA 60.179 55.0 0.00 0.00 0.00 3.53 F
1976 2512 0.815615 CGGTTAAGCCCCATGAGCTC 60.816 60.0 6.82 6.82 40.49 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2485 0.393267 GGGGCTTAACCGTGCACATA 60.393 55.000 18.64 3.72 40.62 2.29 R
3046 3604 1.140652 GAGCTGCTCTATTCCAAGGCT 59.859 52.381 21.93 0.00 0.00 4.58 R
3634 4193 1.115326 ACTTTCAAGCTGGGGGCAAC 61.115 55.000 0.00 0.00 44.79 4.17 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
98 101 2.027192 ACGCCCATAGAACAAGTGACAT 60.027 45.455 0.00 0.00 0.00 3.06
99 102 2.352651 CGCCCATAGAACAAGTGACATG 59.647 50.000 0.00 0.00 0.00 3.21
134 137 0.991146 TGCCTATTCCTGCAGAACCA 59.009 50.000 17.39 0.00 37.29 3.67
143 146 2.002586 CCTGCAGAACCATTAGTGACG 58.997 52.381 17.39 0.00 0.00 4.35
298 350 0.861837 GCTGGCTTGAATATCGGACG 59.138 55.000 0.00 0.00 0.00 4.79
484 541 5.181056 CACTACACTAACACAATGGCAATGA 59.819 40.000 10.01 0.00 0.00 2.57
490 547 8.147058 ACACTAACACAATGGCAATGATAAAAA 58.853 29.630 10.01 0.00 0.00 1.94
491 548 9.153721 CACTAACACAATGGCAATGATAAAAAT 57.846 29.630 10.01 0.00 0.00 1.82
492 549 9.153721 ACTAACACAATGGCAATGATAAAAATG 57.846 29.630 10.01 0.00 0.00 2.32
493 550 9.368674 CTAACACAATGGCAATGATAAAAATGA 57.631 29.630 10.01 0.00 0.00 2.57
494 551 8.795842 AACACAATGGCAATGATAAAAATGAT 57.204 26.923 10.01 0.00 0.00 2.45
495 552 8.428186 ACACAATGGCAATGATAAAAATGATC 57.572 30.769 10.01 0.00 0.00 2.92
629 689 6.037786 CCGGTAGGTACATGTATCAATCAT 57.962 41.667 18.22 1.13 0.00 2.45
633 693 7.655732 CGGTAGGTACATGTATCAATCATTCAA 59.344 37.037 18.22 0.00 0.00 2.69
694 764 0.758123 GCTTCCATCCTCTCTCCAGG 59.242 60.000 0.00 0.00 34.40 4.45
753 873 4.496336 GCAGGGGCAGCGAAGGAT 62.496 66.667 0.00 0.00 40.72 3.24
789 1127 2.892852 CTGCTCTTTCACCAATTTGGGA 59.107 45.455 19.39 10.76 43.37 4.37
799 1137 3.636300 CACCAATTTGGGAGTTGTTGAGA 59.364 43.478 19.39 0.00 43.37 3.27
830 1171 3.806949 ACTCAATCCTTGGCCTTGTTA 57.193 42.857 3.32 0.00 0.00 2.41
854 1198 6.005583 TGCTCTTCTTTGATTGTTCATGTC 57.994 37.500 0.00 0.00 0.00 3.06
859 1203 8.690203 TCTTCTTTGATTGTTCATGTCCTTTA 57.310 30.769 0.00 0.00 0.00 1.85
864 1208 9.778993 CTTTGATTGTTCATGTCCTTTATACAG 57.221 33.333 0.00 0.00 0.00 2.74
866 1210 9.952030 TTGATTGTTCATGTCCTTTATACAGTA 57.048 29.630 0.00 0.00 0.00 2.74
867 1211 9.599866 TGATTGTTCATGTCCTTTATACAGTAG 57.400 33.333 0.00 0.00 0.00 2.57
868 1212 7.843490 TTGTTCATGTCCTTTATACAGTAGC 57.157 36.000 0.00 0.00 0.00 3.58
869 1213 6.346096 TGTTCATGTCCTTTATACAGTAGCC 58.654 40.000 0.00 0.00 0.00 3.93
870 1214 6.070481 TGTTCATGTCCTTTATACAGTAGCCA 60.070 38.462 0.00 0.00 0.00 4.75
872 1216 7.136822 TCATGTCCTTTATACAGTAGCCAAT 57.863 36.000 0.00 0.00 0.00 3.16
873 1217 7.573710 TCATGTCCTTTATACAGTAGCCAATT 58.426 34.615 0.00 0.00 0.00 2.32
969 1496 4.585955 ACGTCTCTTCTTTCTTGTGCTA 57.414 40.909 0.00 0.00 0.00 3.49
997 1526 2.806945 TATTCCTCCAACCAGCAAGG 57.193 50.000 0.00 0.00 45.67 3.61
1022 1551 1.889454 CAGAGTCGCTGCTTCTCCT 59.111 57.895 14.13 3.61 37.90 3.69
1073 1602 3.438088 CGCACTCGTCGAGACAAC 58.562 61.111 28.33 12.66 33.32 3.32
1109 1638 1.886861 CTTGACGACGACCGCCAAAG 61.887 60.000 0.00 0.00 40.00 2.77
1191 1720 4.810790 AGACAAACGACTATGTCAAGAGG 58.189 43.478 8.43 0.00 46.55 3.69
1221 1750 1.407258 GAGCTCAAGTCTGTCGCCTAT 59.593 52.381 9.40 0.00 0.00 2.57
1254 1783 3.186909 CGTGCTCGATGATTTCCAGTAA 58.813 45.455 1.00 0.00 39.71 2.24
1258 1787 5.294306 GTGCTCGATGATTTCCAGTAATGAA 59.706 40.000 0.00 0.00 0.00 2.57
1282 1811 0.812549 TGCGTCGCCAGTGTAAGATA 59.187 50.000 15.88 0.00 0.00 1.98
1285 1814 1.674441 CGTCGCCAGTGTAAGATAGGA 59.326 52.381 0.00 0.00 0.00 2.94
1314 1843 3.165606 CCCTTAAGGTGCTCAGCTG 57.834 57.895 20.22 7.63 39.39 4.24
1318 1847 2.420547 CCTTAAGGTGCTCAGCTGCATA 60.421 50.000 13.83 0.00 45.23 3.14
1325 1854 0.677731 GCTCAGCTGCATAACCCACA 60.678 55.000 9.47 0.00 0.00 4.17
1378 1907 5.809001 AGCAAGAAACTCATGAATGTCCTA 58.191 37.500 0.00 0.00 0.00 2.94
1407 1941 8.497910 AGATCAATAAGCTGGTTAAGGAGATA 57.502 34.615 3.16 0.00 0.00 1.98
1439 1973 6.325993 TGGATTGGAGAATTCTGTCCATAA 57.674 37.500 14.00 1.74 44.16 1.90
1447 1981 4.657969 AGAATTCTGTCCATAAGGAGGAGG 59.342 45.833 7.30 0.00 46.92 4.30
1465 1999 2.361610 AGCAACATCCTTGGCGGG 60.362 61.111 0.00 0.00 0.00 6.13
1481 2015 1.535226 GCGGGAAACACACTCAAAACC 60.535 52.381 0.00 0.00 0.00 3.27
1490 2024 1.134610 ACACTCAAAACCGGACGACTT 60.135 47.619 9.46 0.00 0.00 3.01
1545 2079 2.890945 GGTGGTGGTGAAGTTATTGCTT 59.109 45.455 0.00 0.00 0.00 3.91
1546 2080 4.076394 GGTGGTGGTGAAGTTATTGCTTA 58.924 43.478 0.00 0.00 0.00 3.09
1605 2139 0.178846 TTGGGATGGGAGGTCTTGGA 60.179 55.000 0.00 0.00 0.00 3.53
1626 2160 3.409026 AAGACGACTCTTGCCAAGATT 57.591 42.857 7.75 1.70 35.24 2.40
1643 2177 6.095440 GCCAAGATTGTGTATAATGACCAAGT 59.905 38.462 0.00 0.00 0.00 3.16
1679 2213 2.637382 TCCAGTTGAAGATGTGGCACTA 59.363 45.455 19.83 5.69 0.00 2.74
1711 2246 3.863142 ACTTTGATGCCATTGCTCTTC 57.137 42.857 0.00 0.00 38.71 2.87
1777 2312 3.492656 GCCTGGTAGCATCGAACTATTGA 60.493 47.826 0.00 0.00 0.00 2.57
1788 2323 5.264060 TCGAACTATTGAAAAAGCGACTG 57.736 39.130 0.00 0.00 0.00 3.51
1809 2344 2.407090 GAGCAAGTCATTGGCCAAAAC 58.593 47.619 24.71 22.50 36.88 2.43
1869 2405 0.978146 AGAGGAAGTGGGGGATGTCG 60.978 60.000 0.00 0.00 0.00 4.35
1925 2461 5.590259 AGGAAGTGTTATATTGGTCACATGC 59.410 40.000 0.00 0.00 33.84 4.06
1945 2481 0.954452 CGAAGCAAGAAAGTGGCCTT 59.046 50.000 3.32 0.00 0.00 4.35
1949 2485 2.601905 AGCAAGAAAGTGGCCTTCATT 58.398 42.857 3.32 0.00 0.00 2.57
1976 2512 0.815615 CGGTTAAGCCCCATGAGCTC 60.816 60.000 6.82 6.82 40.49 4.09
1992 2528 7.363181 CCCATGAGCTCATATTTTTGAGTGAAA 60.363 37.037 28.27 0.00 44.10 2.69
2016 2553 6.923199 AAGATTCATGGGAGTTGTTTTCAT 57.077 33.333 0.00 0.00 0.00 2.57
2017 2554 6.276832 AGATTCATGGGAGTTGTTTTCATG 57.723 37.500 0.00 0.00 37.23 3.07
2044 2584 5.567138 GCATTTAGCAATGGTGTAGAAGT 57.433 39.130 0.00 0.00 44.79 3.01
2060 2601 4.078639 AGAAGTGCAAGCAGAGTTAGTT 57.921 40.909 0.00 0.00 0.00 2.24
2073 2614 4.159879 CAGAGTTAGTTACCATCGGAAGGT 59.840 45.833 10.11 10.11 43.14 3.50
2103 2646 3.767309 ATAAATGTGGGGGTTTGCCTA 57.233 42.857 0.00 0.00 34.45 3.93
2182 2725 6.183360 TGGAAGGTCATTGAACAAAGTAACAC 60.183 38.462 4.20 0.00 0.00 3.32
2233 2782 6.911308 AGGTCATGCCCATACTAAAGTTAAT 58.089 36.000 0.00 0.00 38.26 1.40
2313 2862 8.567198 TCCCAAGGATTATGAAATAGAGAAGA 57.433 34.615 0.00 0.00 0.00 2.87
2389 2938 3.219281 TGGGTTTAACACAGAAAGGAGC 58.781 45.455 0.00 0.00 0.00 4.70
2462 3011 5.098211 GTGGTAGTCAAATACGGTGTCTAC 58.902 45.833 0.00 0.00 37.09 2.59
2556 3105 5.361135 CACAGATGAATGTGCAAGTACAA 57.639 39.130 0.00 0.00 43.69 2.41
2559 3108 6.864685 CACAGATGAATGTGCAAGTACAAAAT 59.135 34.615 0.00 0.00 43.69 1.82
2620 3172 4.988540 TCACGTGAAAGTGTTAGATTCTGG 59.011 41.667 17.62 0.00 42.40 3.86
2732 3287 4.384056 AGTTGCTACATGTATCAGCATCC 58.616 43.478 19.69 14.07 44.29 3.51
2750 3305 4.684485 GCATCCCTAAGAGCATTACACTGT 60.684 45.833 0.00 0.00 0.00 3.55
2755 3310 1.958288 AGAGCATTACACTGTCCCCT 58.042 50.000 0.00 0.00 0.00 4.79
2934 3492 5.250313 AGAAGACATGGGAAGACTGAGAAAT 59.750 40.000 0.00 0.00 0.00 2.17
2988 3546 5.997746 TGGTCTCAAAAGTATGTCTCCAAAG 59.002 40.000 0.00 0.00 0.00 2.77
3079 3637 3.012518 GAGCAGCTCAAAGGCTTATCAA 58.987 45.455 18.17 0.00 41.00 2.57
3083 3641 3.507233 CAGCTCAAAGGCTTATCAAACCA 59.493 43.478 0.00 0.00 41.00 3.67
3109 3667 7.219484 AGAAATAGGTTGGAACTGTTCAATG 57.781 36.000 21.01 0.00 0.00 2.82
3124 3682 7.715657 ACTGTTCAATGTGAGCAAGATAAAAA 58.284 30.769 0.00 0.00 37.16 1.94
3215 3773 3.371917 GGGACCAAGGATGTCATGATGAA 60.372 47.826 0.00 0.00 34.36 2.57
3309 3868 6.274436 TGGATATGGTGGCCTAGAAATATCAA 59.726 38.462 3.32 1.27 31.54 2.57
3544 4103 6.034591 AGACGATGGAGTTGATTAAGTTACG 58.965 40.000 0.00 0.00 0.00 3.18
3549 4108 5.484715 TGGAGTTGATTAAGTTACGAAGGG 58.515 41.667 0.00 0.00 0.00 3.95
3561 4120 1.056660 ACGAAGGGTGGAGATGTTGT 58.943 50.000 0.00 0.00 0.00 3.32
3596 4155 3.676291 GGAGATCCCAGTGATAGCTTC 57.324 52.381 0.00 0.00 32.41 3.86
3617 4176 3.616821 TCGTAACATTTCCGATGCTTGAG 59.383 43.478 0.00 0.00 0.00 3.02
3634 4193 4.865776 CTTGAGAAGCTAAGGATCGTAGG 58.134 47.826 0.00 0.00 0.00 3.18
3669 4228 5.545063 TGAAAGTATTCCAGTGACTGACA 57.455 39.130 15.33 0.00 34.49 3.58
3674 4233 2.936919 TTCCAGTGACTGACAATGCT 57.063 45.000 15.33 0.00 42.30 3.79
3690 4249 5.966684 ACAATGCTATAGACCTAGGGTAGT 58.033 41.667 14.81 0.00 35.25 2.73
3692 4251 5.602291 ATGCTATAGACCTAGGGTAGTGT 57.398 43.478 14.81 0.00 35.25 3.55
3701 4260 3.305720 CCTAGGGTAGTGTTCATAGGCA 58.694 50.000 0.00 0.00 0.00 4.75
3728 4287 4.278513 CGCCCCACCCAAGGTCAA 62.279 66.667 0.00 0.00 31.02 3.18
3760 4319 5.841957 AGCAAAGACATTCAAAGAACAGT 57.158 34.783 0.00 0.00 0.00 3.55
3796 4358 0.317160 AGTCGTCGAGTGCAATCCAA 59.683 50.000 8.83 0.00 0.00 3.53
3827 4394 1.223501 TCTCACTCGGATACCCCTCT 58.776 55.000 0.00 0.00 0.00 3.69
3828 4395 1.133761 TCTCACTCGGATACCCCTCTG 60.134 57.143 0.00 0.00 0.00 3.35
3913 4481 3.019799 GACCAGGAGTCACTCAGGATA 57.980 52.381 19.46 0.00 45.55 2.59
3914 4482 3.366396 GACCAGGAGTCACTCAGGATAA 58.634 50.000 19.46 0.00 45.55 1.75
3915 4483 3.964031 GACCAGGAGTCACTCAGGATAAT 59.036 47.826 19.46 0.24 45.55 1.28
3919 4487 5.363868 CCAGGAGTCACTCAGGATAATAACA 59.636 44.000 7.24 0.00 31.68 2.41
3922 4490 6.670027 AGGAGTCACTCAGGATAATAACAGTT 59.330 38.462 7.24 0.00 31.08 3.16
3925 4493 8.824756 AGTCACTCAGGATAATAACAGTTAGA 57.175 34.615 0.00 0.00 0.00 2.10
3943 4511 5.711036 AGTTAGACGTTCACTCCATAGTCTT 59.289 40.000 1.18 0.00 39.36 3.01
4028 4597 2.666098 CCCCTGTAACGGAGGTGGG 61.666 68.421 0.00 0.00 34.68 4.61
4042 4611 4.369591 TGGGATGGGGTCCTGGCT 62.370 66.667 0.00 0.00 46.91 4.75
4087 4657 2.397413 CTGGGACAAGGGTTCGCACT 62.397 60.000 0.00 0.00 38.70 4.40
4133 4729 4.036144 CACACACACACACACATATTCCAA 59.964 41.667 0.00 0.00 0.00 3.53
4135 4731 5.301551 ACACACACACACACATATTCCAATT 59.698 36.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 1.065998 GGCACACGGACCTGGTAATTA 60.066 52.381 0.00 0.00 0.00 1.40
134 137 3.990092 TGTTCTCACTTGCGTCACTAAT 58.010 40.909 0.00 0.00 0.00 1.73
143 146 3.873952 ACTGAAGACTTGTTCTCACTTGC 59.126 43.478 0.00 0.00 31.02 4.01
153 156 3.118629 TGCTGTGAAGACTGAAGACTTGT 60.119 43.478 0.00 0.00 30.73 3.16
223 226 2.988010 TGCCTGTACCATCATGACTC 57.012 50.000 0.00 0.00 0.00 3.36
298 350 6.178239 AGAGCGTGGAAATGTTGTATTTAC 57.822 37.500 0.00 0.00 0.00 2.01
355 407 3.067461 TGTGGAAGGAAACATTTTGGTCG 59.933 43.478 0.00 0.00 0.00 4.79
464 521 6.832520 TTATCATTGCCATTGTGTTAGTGT 57.167 33.333 0.00 0.00 0.00 3.55
490 547 9.632638 ACCTATATGCAACAGTTTTTAGATCAT 57.367 29.630 0.00 0.00 0.00 2.45
579 638 7.125507 TGGTCCCTCATTTATTTGCAACAATAT 59.874 33.333 0.00 0.00 0.00 1.28
583 642 4.021544 GTGGTCCCTCATTTATTTGCAACA 60.022 41.667 0.00 0.00 0.00 3.33
625 685 9.011095 CCAAGAGCTGTATATTGATTGAATGAT 57.989 33.333 0.00 0.00 0.00 2.45
629 689 8.985315 AATCCAAGAGCTGTATATTGATTGAA 57.015 30.769 0.00 0.00 0.00 2.69
633 693 6.274200 AGGGAATCCAAGAGCTGTATATTGAT 59.726 38.462 0.09 0.00 34.83 2.57
694 764 4.335594 GGCTACTATGGAATTGTGTGGTTC 59.664 45.833 0.00 0.00 33.47 3.62
744 863 1.827969 ACTAGTGCTTGATCCTTCGCT 59.172 47.619 0.00 0.00 0.00 4.93
753 873 0.888619 AGCAGCGTACTAGTGCTTGA 59.111 50.000 5.39 0.00 45.31 3.02
830 1171 6.349944 GGACATGAACAATCAAAGAAGAGCAT 60.350 38.462 0.00 0.00 39.49 3.79
898 1295 9.794719 ACCTTGTAATCCTCCTATTTTAATAGC 57.205 33.333 4.33 0.00 37.61 2.97
902 1299 9.816787 AACAACCTTGTAATCCTCCTATTTTAA 57.183 29.630 0.00 0.00 41.31 1.52
969 1496 5.316987 CTGGTTGGAGGAATAAGAAACTGT 58.683 41.667 0.00 0.00 0.00 3.55
997 1526 3.791539 CAGCGACTCTGCCATGAC 58.208 61.111 0.00 0.00 35.78 3.06
1022 1551 2.048597 CCACACCGCGCACTAGAA 60.049 61.111 8.75 0.00 0.00 2.10
1072 1601 2.738521 GCCACACATGCGAGTCGT 60.739 61.111 15.08 0.00 0.00 4.34
1073 1602 3.490759 GGCCACACATGCGAGTCG 61.491 66.667 8.54 8.54 0.00 4.18
1109 1638 3.328189 GCAGCTAGCGCTCCAATC 58.672 61.111 16.34 0.00 45.15 2.67
1120 1649 0.173481 CACTCAACGGCTAGCAGCTA 59.827 55.000 18.24 1.13 41.99 3.32
1191 1720 2.235898 AGACTTGAGCTCCTTCATCCAC 59.764 50.000 12.15 0.00 0.00 4.02
1221 1750 3.268965 GAGCACGTCGTCAGCCTCA 62.269 63.158 0.00 0.00 0.00 3.86
1314 1843 0.951558 CGGGCTATTGTGGGTTATGC 59.048 55.000 0.00 0.00 0.00 3.14
1318 1847 1.378514 CAGCGGGCTATTGTGGGTT 60.379 57.895 0.00 0.00 0.00 4.11
1368 1897 9.466497 AGCTTATTGATCTTTTTAGGACATTCA 57.534 29.630 0.00 0.00 0.00 2.57
1378 1907 8.650143 TCCTTAACCAGCTTATTGATCTTTTT 57.350 30.769 0.00 0.00 0.00 1.94
1393 1927 7.447238 TCCAAACTTGTTTATCTCCTTAACCAG 59.553 37.037 0.00 0.00 0.00 4.00
1407 1941 7.147672 ACAGAATTCTCCAATCCAAACTTGTTT 60.148 33.333 4.57 0.00 0.00 2.83
1439 1973 0.043940 AGGATGTTGCTCCTCCTCCT 59.956 55.000 1.89 0.00 42.12 3.69
1447 1981 2.409870 CCCGCCAAGGATGTTGCTC 61.410 63.158 0.00 0.00 45.00 4.26
1465 1999 2.538132 CGTCCGGTTTTGAGTGTGTTTC 60.538 50.000 0.00 0.00 0.00 2.78
1481 2015 5.389516 CCAAAGATCTTTGTAAAGTCGTCCG 60.390 44.000 34.83 18.20 46.19 4.79
1490 2024 5.001232 CGTCCCTTCCAAAGATCTTTGTAA 58.999 41.667 34.83 28.07 46.19 2.41
1509 2043 2.040178 ACCACCTCCTTATCATCGTCC 58.960 52.381 0.00 0.00 0.00 4.79
1512 2046 1.762957 ACCACCACCTCCTTATCATCG 59.237 52.381 0.00 0.00 0.00 3.84
1545 2079 1.375908 CCGCTGAGCTTGCTGGTTA 60.376 57.895 1.78 0.00 0.00 2.85
1546 2080 2.670934 CCGCTGAGCTTGCTGGTT 60.671 61.111 1.78 0.00 0.00 3.67
1556 2090 2.435586 CCTGCACCTTCCGCTGAG 60.436 66.667 0.00 0.00 0.00 3.35
1605 2139 2.910688 TCTTGGCAAGAGTCGTCTTT 57.089 45.000 25.38 0.00 41.40 2.52
1643 2177 1.216678 ACTGGAAATGTTGGTGGACCA 59.783 47.619 0.00 0.00 45.94 4.02
1679 2213 3.188460 GGCATCAAAGTTGTATGACACGT 59.812 43.478 2.64 0.00 0.00 4.49
1687 2221 4.081406 AGAGCAATGGCATCAAAGTTGTA 58.919 39.130 0.00 0.00 44.61 2.41
1711 2246 4.401519 AGCCAACTCAATGATGGATTTCAG 59.598 41.667 7.05 0.00 40.62 3.02
1761 2296 5.579119 TCGCTTTTTCAATAGTTCGATGCTA 59.421 36.000 0.00 0.00 0.00 3.49
1777 2312 1.604278 GACTTGCTCCAGTCGCTTTTT 59.396 47.619 0.00 0.00 34.12 1.94
1788 2323 0.968405 TTTGGCCAATGACTTGCTCC 59.032 50.000 21.26 0.00 0.00 4.70
1809 2344 2.076100 TCAAGCACGAGCATAAACCTG 58.924 47.619 7.77 0.00 45.49 4.00
1925 2461 0.890996 AGGCCACTTTCTTGCTTCGG 60.891 55.000 5.01 0.00 0.00 4.30
1945 2481 2.680841 GGCTTAACCGTGCACATAATGA 59.319 45.455 18.64 0.00 0.00 2.57
1949 2485 0.393267 GGGGCTTAACCGTGCACATA 60.393 55.000 18.64 3.72 40.62 2.29
1992 2528 6.729690 TGAAAACAACTCCCATGAATCTTT 57.270 33.333 0.00 0.00 0.00 2.52
2016 2553 3.244146 ACACCATTGCTAAATGCTTTGCA 60.244 39.130 0.00 0.00 44.86 4.08
2017 2554 3.328505 ACACCATTGCTAAATGCTTTGC 58.671 40.909 0.00 0.00 41.66 3.68
2044 2584 3.762407 TGGTAACTAACTCTGCTTGCA 57.238 42.857 0.00 0.00 37.61 4.08
2060 2601 3.770388 TGACAATACACCTTCCGATGGTA 59.230 43.478 5.67 0.00 35.80 3.25
2073 2614 5.584913 ACCCCCACATTTATTGACAATACA 58.415 37.500 7.41 1.94 0.00 2.29
2103 2646 3.087031 CACCCATTGTCTTGAGAGCAAT 58.913 45.455 0.00 0.00 33.12 3.56
2182 2725 1.215173 TGCCTCCAACATTATCCCCAG 59.785 52.381 0.00 0.00 0.00 4.45
2233 2782 8.539544 TCATTTCTGATGACAGGTATTTGTAGA 58.460 33.333 0.00 0.00 43.60 2.59
2346 2895 7.177392 ACCCATTGTTCCTTCTTCTTGAATAAG 59.823 37.037 2.68 2.68 33.71 1.73
2389 2938 7.441760 TCCAAACCAACTCATTGAAAATGAATG 59.558 33.333 4.38 6.37 38.15 2.67
2433 2982 5.347907 CACCGTATTTGACTACCACTTTCTC 59.652 44.000 0.00 0.00 0.00 2.87
2520 3069 8.849168 ACATTCATCTGTGACATCTTTTGTTAA 58.151 29.630 0.00 0.00 39.18 2.01
2523 3072 6.889301 ACATTCATCTGTGACATCTTTTGT 57.111 33.333 0.00 0.00 42.79 2.83
2556 3105 6.211587 TGCTTTATGCTGCATCAGTTATTT 57.788 33.333 19.90 0.00 43.37 1.40
2620 3172 7.765360 TGCATAACCCATTGATCTTTTTCATTC 59.235 33.333 0.00 0.00 0.00 2.67
2656 3208 7.959175 AGTACCTAATAAAGTGCCGATGAATA 58.041 34.615 0.00 0.00 0.00 1.75
2664 3216 6.315642 GGTGAAGAAGTACCTAATAAAGTGCC 59.684 42.308 0.00 0.00 34.11 5.01
2732 3287 3.432326 GGGGACAGTGTAATGCTCTTAGG 60.432 52.174 0.00 0.00 0.00 2.69
2750 3305 3.115390 CAAAGGATAACTGGAGAGGGGA 58.885 50.000 0.00 0.00 0.00 4.81
2865 3423 5.747197 GCAATGTATGAGCCTCAAAATCTTG 59.253 40.000 0.00 1.18 0.00 3.02
2866 3424 5.655532 AGCAATGTATGAGCCTCAAAATCTT 59.344 36.000 0.00 0.00 0.00 2.40
2870 3428 5.726980 AAAGCAATGTATGAGCCTCAAAA 57.273 34.783 0.00 0.00 0.00 2.44
2871 3429 6.681120 GCATAAAGCAATGTATGAGCCTCAAA 60.681 38.462 0.00 0.00 44.79 2.69
2988 3546 6.183360 TGTGAAGGTTGTTCAATAGACCAAAC 60.183 38.462 0.00 0.00 34.39 2.93
3036 3594 6.166984 TCTATTCCAAGGCTATCTCTTGTG 57.833 41.667 0.00 0.00 39.78 3.33
3046 3604 1.140652 GAGCTGCTCTATTCCAAGGCT 59.859 52.381 21.93 0.00 0.00 4.58
3079 3637 6.790319 ACAGTTCCAACCTATTTCTATGGTT 58.210 36.000 0.00 0.00 43.98 3.67
3083 3641 8.960591 CATTGAACAGTTCCAACCTATTTCTAT 58.039 33.333 10.93 0.00 0.00 1.98
3124 3682 5.594926 CTTCTTTTGCATTCTCCACACTTT 58.405 37.500 0.00 0.00 0.00 2.66
3125 3683 4.500375 GCTTCTTTTGCATTCTCCACACTT 60.500 41.667 0.00 0.00 0.00 3.16
3215 3773 4.042187 AGCACTTCTTCCACATCTTTAGGT 59.958 41.667 0.00 0.00 0.00 3.08
3267 3825 4.806640 ATCCACGCATCTCCAAATTTTT 57.193 36.364 0.00 0.00 0.00 1.94
3419 3978 7.070571 AGGTTATCCATCTTCTTGAAGACTAGG 59.929 40.741 14.36 15.31 35.89 3.02
3422 3981 6.882768 AGGTTATCCATCTTCTTGAAGACT 57.117 37.500 14.36 3.33 35.89 3.24
3428 3987 6.414732 TGTGGTTAGGTTATCCATCTTCTTG 58.585 40.000 0.00 0.00 35.89 3.02
3481 4040 2.091720 TGCTGATGGGTAATGCATCCTT 60.092 45.455 0.00 0.00 0.00 3.36
3544 4103 2.303022 TCAGACAACATCTCCACCCTTC 59.697 50.000 0.00 0.00 34.41 3.46
3549 4108 6.428159 ACACTATTTTCAGACAACATCTCCAC 59.572 38.462 0.00 0.00 34.41 4.02
3561 4120 5.359194 GGATCTCCCACACTATTTTCAGA 57.641 43.478 0.00 0.00 34.14 3.27
3596 4155 3.616821 TCTCAAGCATCGGAAATGTTACG 59.383 43.478 0.00 0.00 0.00 3.18
3617 4176 3.124560 GCAACCTACGATCCTTAGCTTC 58.875 50.000 0.00 0.00 0.00 3.86
3634 4193 1.115326 ACTTTCAAGCTGGGGGCAAC 61.115 55.000 0.00 0.00 44.79 4.17
3669 4228 5.966684 ACACTACCCTAGGTCTATAGCATT 58.033 41.667 8.29 0.00 37.09 3.56
3674 4233 7.696981 CCTATGAACACTACCCTAGGTCTATA 58.303 42.308 8.29 0.00 37.09 1.31
3701 4260 1.125711 GGGTGGGGCGTATAGGTCAT 61.126 60.000 0.00 0.00 0.00 3.06
3728 4287 6.313519 TGAATGTCTTTGCTTCTAGGGTAT 57.686 37.500 0.00 0.00 0.00 2.73
3760 4319 5.163784 CGACGACTTCAATTGGTACTCTCTA 60.164 44.000 5.42 0.00 0.00 2.43
3796 4358 1.673400 CGAGTGAGATGACTGGTCGAT 59.327 52.381 0.00 0.00 0.00 3.59
3827 4394 4.282449 TCTTGGTCGAGTGAAATTAGGACA 59.718 41.667 0.00 0.00 0.00 4.02
3828 4395 4.626172 GTCTTGGTCGAGTGAAATTAGGAC 59.374 45.833 0.00 0.00 0.00 3.85
3913 4481 6.092955 TGGAGTGAACGTCTAACTGTTATT 57.907 37.500 0.00 0.00 0.00 1.40
3914 4482 5.717078 TGGAGTGAACGTCTAACTGTTAT 57.283 39.130 0.00 0.00 0.00 1.89
3915 4483 5.717078 ATGGAGTGAACGTCTAACTGTTA 57.283 39.130 0.00 0.00 0.00 2.41
3919 4487 5.254901 AGACTATGGAGTGAACGTCTAACT 58.745 41.667 0.00 0.00 35.45 2.24
3922 4490 7.692460 TTAAAGACTATGGAGTGAACGTCTA 57.308 36.000 0.00 0.00 35.45 2.59
3925 4493 6.989659 TCTTTAAAGACTATGGAGTGAACGT 58.010 36.000 13.99 0.00 35.45 3.99
3986 4554 5.172687 TCAATGTACATTAAGACAGGGCA 57.827 39.130 20.39 0.00 0.00 5.36
4028 4597 1.977293 GAGTGAGCCAGGACCCCATC 61.977 65.000 0.00 0.00 0.00 3.51
4042 4611 3.144125 AGGGGGTGGCTTATATAGAGTGA 59.856 47.826 0.00 0.00 0.00 3.41
4087 4657 3.388350 TGTGTGTGTGTGTGTTATAGGGA 59.612 43.478 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.