Multiple sequence alignment - TraesCS1D01G325200

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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 TraesCS1D01G325200 chr1D 100.000 4732 0 0 1 4732 417577844 417573113 0.000000e+00 8739.0
1 TraesCS1D01G325200 chr1A 91.654 2600 104 51 445 2980 514554439 514551889 0.000000e+00 3494.0
2 TraesCS1D01G325200 chr1A 92.665 1227 52 21 2979 4171 514551850 514550628 0.000000e+00 1733.0
3 TraesCS1D01G325200 chr1A 97.477 555 14 0 4178 4732 514550584 514550030 0.000000e+00 948.0
4 TraesCS1D01G325200 chr1A 78.345 568 78 27 4175 4732 566590106 566590638 4.570000e-85 326.0
5 TraesCS1D01G325200 chr1A 89.831 118 11 1 322 438 585455623 585455506 2.950000e-32 150.0
6 TraesCS1D01G325200 chr1B 90.832 2585 88 45 488 2980 564166042 564163515 0.000000e+00 3323.0
7 TraesCS1D01G325200 chr1B 94.615 1207 36 8 2979 4171 564163474 564162283 0.000000e+00 1842.0
8 TraesCS1D01G325200 chr1B 97.838 555 12 0 4178 4732 564162240 564161686 0.000000e+00 959.0
9 TraesCS1D01G325200 chr1B 90.535 243 23 0 4 246 564166629 564166387 5.910000e-84 322.0
10 TraesCS1D01G325200 chr1B 86.432 199 13 7 288 484 564166318 564166132 6.210000e-49 206.0
11 TraesCS1D01G325200 chr1B 96.875 32 1 0 193 224 433635936 433635967 2.000000e-03 54.7
12 TraesCS1D01G325200 chr2D 78.745 781 106 37 2979 3721 493195387 493194629 7.170000e-128 468.0
13 TraesCS1D01G325200 chr2D 94.545 110 5 1 330 438 76645133 76645024 8.140000e-38 169.0
14 TraesCS1D01G325200 chr2B 78.617 781 106 32 2979 3721 581584897 581584140 1.200000e-125 460.0
15 TraesCS1D01G325200 chr2B 90.881 329 19 8 3844 4171 77877104 77876786 9.410000e-117 431.0
16 TraesCS1D01G325200 chr2B 90.588 85 6 2 4327 4409 331027275 331027359 1.390000e-20 111.0
17 TraesCS1D01G325200 chrUn 90.964 332 13 6 3844 4171 240128728 240128410 9.410000e-117 431.0
18 TraesCS1D01G325200 chrUn 91.159 328 13 5 3847 4171 435744926 435744612 9.410000e-117 431.0
19 TraesCS1D01G325200 chr6B 90.361 332 15 9 3844 4171 91904824 91905142 2.040000e-113 420.0
20 TraesCS1D01G325200 chr6B 90.274 329 21 8 3844 4171 418246684 418246366 2.040000e-113 420.0
21 TraesCS1D01G325200 chr4B 90.361 332 15 6 3844 4171 517726313 517726631 2.040000e-113 420.0
22 TraesCS1D01G325200 chr3B 90.361 332 15 10 3844 4171 170507271 170507589 2.040000e-113 420.0
23 TraesCS1D01G325200 chr5B 89.970 329 22 8 3844 4171 140517300 140516982 9.470000e-112 414.0
24 TraesCS1D01G325200 chr5B 95.122 41 2 0 185 225 642936228 642936268 1.100000e-06 65.8
25 TraesCS1D01G325200 chr5A 89.970 329 22 8 3844 4171 88286341 88286023 9.470000e-112 414.0
26 TraesCS1D01G325200 chr5A 87.255 102 13 0 4332 4433 66049294 66049193 2.990000e-22 117.0
27 TraesCS1D01G325200 chr2A 78.720 578 66 31 3187 3721 733431486 733432049 2.730000e-87 333.0
28 TraesCS1D01G325200 chr2A 81.333 225 26 5 2979 3201 733429797 733430007 8.140000e-38 169.0
29 TraesCS1D01G325200 chr5D 94.495 109 6 0 330 438 101761914 101762022 8.140000e-38 169.0
30 TraesCS1D01G325200 chr5D 92.727 110 7 1 330 438 391820179 391820070 1.760000e-34 158.0
31 TraesCS1D01G325200 chr5D 91.818 110 8 1 330 438 107777129 107777238 8.200000e-33 152.0
32 TraesCS1D01G325200 chr7B 92.661 109 8 0 330 438 481840666 481840558 1.760000e-34 158.0
33 TraesCS1D01G325200 chr7B 91.228 114 6 2 327 436 741557022 741557135 8.200000e-33 152.0
34 TraesCS1D01G325200 chr4A 91.818 110 8 1 330 438 595373026 595373135 8.200000e-33 152.0
35 TraesCS1D01G325200 chr7D 91.139 79 7 0 4332 4410 326034705 326034627 1.800000e-19 108.0
36 TraesCS1D01G325200 chr7D 96.875 32 1 0 185 216 518566523 518566492 2.000000e-03 54.7
37 TraesCS1D01G325200 chr7A 100.000 32 0 0 193 224 724090375 724090344 5.110000e-05 60.2


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 TraesCS1D01G325200 chr1D 417573113 417577844 4731 True 8739.000000 8739 100.0000 1 4732 1 chr1D.!!$R1 4731
1 TraesCS1D01G325200 chr1A 514550030 514554439 4409 True 2058.333333 3494 93.9320 445 4732 3 chr1A.!!$R2 4287
2 TraesCS1D01G325200 chr1A 566590106 566590638 532 False 326.000000 326 78.3450 4175 4732 1 chr1A.!!$F1 557
3 TraesCS1D01G325200 chr1B 564161686 564166629 4943 True 1330.400000 3323 92.0504 4 4732 5 chr1B.!!$R1 4728
4 TraesCS1D01G325200 chr2D 493194629 493195387 758 True 468.000000 468 78.7450 2979 3721 1 chr2D.!!$R2 742
5 TraesCS1D01G325200 chr2B 581584140 581584897 757 True 460.000000 460 78.6170 2979 3721 1 chr2B.!!$R2 742
6 TraesCS1D01G325200 chr2A 733429797 733432049 2252 False 251.000000 333 80.0265 2979 3721 2 chr2A.!!$F1 742

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
200 201 0.375106 GCAGTCTCGCCAAATAGTGC 59.625 55.000 0.00 0.00 0.00 4.40 F
284 285 0.462759 ATAACTCAGCTGCCCGAAGC 60.463 55.000 9.47 0.00 43.88 3.86 F
946 1113 1.123928 AGGAGGGAGCGGTGAATTAG 58.876 55.000 0.00 0.00 0.00 1.73 F
1570 1803 1.519455 CTCCCTGTTTCTAGGCGCG 60.519 63.158 0.00 0.00 36.47 6.86 F
1805 2053 1.525619 GACAACTTCAGCGCTAACGTT 59.474 47.619 10.99 2.02 42.83 3.99 F
2182 2432 2.029020 TCCCACTCTCGATGACTTGTTG 60.029 50.000 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2181 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49 R
1934 2182 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82 R
2904 3165 0.033405 AGCATTCTGGCCTCTGCAAT 60.033 50.000 17.48 1.97 40.13 3.56 R
3320 5136 2.350772 GGTGATCCACGAAAAACTGCTG 60.351 50.000 0.00 0.00 34.83 4.41 R
3599 5439 3.900601 TGCAACCAAATCACTAACCCAAT 59.099 39.130 0.00 0.00 0.00 3.16 R
3939 5819 1.002430 AGCAGTCCATGTTCATCGTGT 59.998 47.619 0.00 0.00 0.00 4.49 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
25 26 4.335647 CCTCTGGGGCACGCTGTT 62.336 66.667 0.00 0.00 43.80 3.16
26 27 2.743928 CTCTGGGGCACGCTGTTC 60.744 66.667 0.00 0.00 43.80 3.18
83 84 6.825721 AGGATAAGGATAAAGTTGTGAAGCTG 59.174 38.462 0.00 0.00 0.00 4.24
100 101 0.732880 CTGGTTCACAGCGACGGTAG 60.733 60.000 0.00 0.00 40.97 3.18
135 136 3.893763 CGCCTCGCTCCGATCAGT 61.894 66.667 0.00 0.00 34.61 3.41
189 190 2.856032 CAACAAGCGGCAGTCTCG 59.144 61.111 1.45 0.00 0.00 4.04
200 201 0.375106 GCAGTCTCGCCAAATAGTGC 59.625 55.000 0.00 0.00 0.00 4.40
220 221 2.098068 GCGCGTGCACTTTTAAGTTTTC 60.098 45.455 17.66 0.00 42.15 2.29
224 225 4.668289 CGTGCACTTTTAAGTTTTCAGGT 58.332 39.130 16.19 0.00 37.08 4.00
226 227 5.041287 GTGCACTTTTAAGTTTTCAGGTCC 58.959 41.667 10.32 0.00 37.08 4.46
227 228 4.201970 TGCACTTTTAAGTTTTCAGGTCCG 60.202 41.667 0.00 0.00 37.08 4.79
246 247 6.825213 AGGTCCGTATATAACCCAAAGAAAAC 59.175 38.462 0.00 0.00 33.33 2.43
248 249 5.816777 TCCGTATATAACCCAAAGAAAACGG 59.183 40.000 0.00 0.00 45.56 4.44
250 251 6.760770 CCGTATATAACCCAAAGAAAACGGTA 59.239 38.462 0.00 0.00 40.81 4.02
255 256 9.856162 ATATAACCCAAAGAAAACGGTATACAT 57.144 29.630 5.01 0.00 0.00 2.29
262 263 8.388103 CCAAAGAAAACGGTATACATAGTGAAG 58.612 37.037 5.01 0.00 0.00 3.02
264 265 6.636705 AGAAAACGGTATACATAGTGAAGCA 58.363 36.000 5.01 0.00 0.00 3.91
266 267 7.769044 AGAAAACGGTATACATAGTGAAGCAAT 59.231 33.333 5.01 0.00 0.00 3.56
267 268 8.951787 AAAACGGTATACATAGTGAAGCAATA 57.048 30.769 5.01 0.00 0.00 1.90
268 269 8.951787 AAACGGTATACATAGTGAAGCAATAA 57.048 30.769 5.01 0.00 0.00 1.40
269 270 7.941795 ACGGTATACATAGTGAAGCAATAAC 57.058 36.000 5.01 0.00 0.00 1.89
271 272 7.866393 ACGGTATACATAGTGAAGCAATAACTC 59.134 37.037 5.01 0.00 0.00 3.01
272 273 7.865889 CGGTATACATAGTGAAGCAATAACTCA 59.134 37.037 5.01 0.00 0.00 3.41
273 274 9.197694 GGTATACATAGTGAAGCAATAACTCAG 57.802 37.037 5.01 0.00 0.00 3.35
274 275 7.721286 ATACATAGTGAAGCAATAACTCAGC 57.279 36.000 0.00 0.00 0.00 4.26
275 276 5.738909 ACATAGTGAAGCAATAACTCAGCT 58.261 37.500 0.00 0.00 41.03 4.24
276 277 5.583854 ACATAGTGAAGCAATAACTCAGCTG 59.416 40.000 7.63 7.63 38.86 4.24
277 278 2.746362 AGTGAAGCAATAACTCAGCTGC 59.254 45.455 9.47 0.00 38.86 5.25
279 280 1.403323 GAAGCAATAACTCAGCTGCCC 59.597 52.381 9.47 0.00 38.86 5.36
280 281 0.745845 AGCAATAACTCAGCTGCCCG 60.746 55.000 9.47 2.20 37.20 6.13
282 283 1.737838 CAATAACTCAGCTGCCCGAA 58.262 50.000 9.47 0.00 0.00 4.30
284 285 0.462759 ATAACTCAGCTGCCCGAAGC 60.463 55.000 9.47 0.00 43.88 3.86
299 327 3.243201 CCCGAAGCAATAGAGGCAATTTC 60.243 47.826 0.00 0.00 0.00 2.17
307 335 5.278169 GCAATAGAGGCAATTTCGATGACAT 60.278 40.000 0.00 0.00 0.00 3.06
310 338 4.769688 AGAGGCAATTTCGATGACATACA 58.230 39.130 0.00 0.00 0.00 2.29
313 341 3.548818 GGCAATTTCGATGACATACAGCC 60.549 47.826 0.00 0.00 0.00 4.85
381 411 9.828691 TTCCATTCTCTATTATCTAGATCACCA 57.171 33.333 8.95 0.00 0.00 4.17
382 412 9.249053 TCCATTCTCTATTATCTAGATCACCAC 57.751 37.037 8.95 0.00 0.00 4.16
383 413 9.253832 CCATTCTCTATTATCTAGATCACCACT 57.746 37.037 8.95 0.00 0.00 4.00
636 760 3.993081 CACCAGACAAACAAACAAGCAAA 59.007 39.130 0.00 0.00 0.00 3.68
640 764 5.389725 CCAGACAAACAAACAAGCAAACAAG 60.390 40.000 0.00 0.00 0.00 3.16
641 765 5.177327 CAGACAAACAAACAAGCAAACAAGT 59.823 36.000 0.00 0.00 0.00 3.16
642 766 5.177327 AGACAAACAAACAAGCAAACAAGTG 59.823 36.000 0.00 0.00 0.00 3.16
644 768 5.177327 ACAAACAAACAAGCAAACAAGTGAG 59.823 36.000 0.00 0.00 0.00 3.51
645 769 3.253230 ACAAACAAGCAAACAAGTGAGC 58.747 40.909 0.00 0.00 0.00 4.26
646 770 2.584492 AACAAGCAAACAAGTGAGCC 57.416 45.000 0.00 0.00 0.00 4.70
648 772 2.034124 ACAAGCAAACAAGTGAGCCAT 58.966 42.857 0.00 0.00 0.00 4.40
747 897 1.142314 CTCTGCTCTGCTCTGCTCC 59.858 63.158 0.00 0.00 0.00 4.70
749 899 4.447989 TGCTCTGCTCTGCTCCGC 62.448 66.667 0.00 0.00 0.00 5.54
751 901 2.780094 GCTCTGCTCTGCTCCGCTA 61.780 63.158 0.00 0.00 0.00 4.26
767 917 1.518133 CTAGCTGTCTGTCGCTGCC 60.518 63.158 0.00 0.00 37.05 4.85
855 1021 3.775654 CGAGGAGCCCCTTCGCTT 61.776 66.667 0.00 0.00 44.53 4.68
856 1022 2.188207 GAGGAGCCCCTTCGCTTC 59.812 66.667 0.00 0.00 44.53 3.86
946 1113 1.123928 AGGAGGGAGCGGTGAATTAG 58.876 55.000 0.00 0.00 0.00 1.73
1131 1317 3.073062 TCCTTCCCTTCCTTCTTCAACTG 59.927 47.826 0.00 0.00 0.00 3.16
1147 1339 4.758688 TCAACTGCTCCACATACATGTAG 58.241 43.478 11.91 6.29 39.39 2.74
1148 1340 4.222810 TCAACTGCTCCACATACATGTAGT 59.777 41.667 11.91 6.90 39.39 2.73
1149 1341 5.420739 TCAACTGCTCCACATACATGTAGTA 59.579 40.000 11.91 0.00 39.39 1.82
1150 1342 5.263968 ACTGCTCCACATACATGTAGTAC 57.736 43.478 11.91 0.00 39.39 2.73
1203 1406 7.326454 TCTTCTTAGAACAAGACAGATGGATG 58.674 38.462 0.00 0.00 0.00 3.51
1304 1516 8.964772 ACTAGGGAAAAAGAAGATTGATTGATG 58.035 33.333 0.00 0.00 0.00 3.07
1422 1634 9.424319 TCACTCAATTTACTAGCTACTTTTCAG 57.576 33.333 0.00 0.00 0.00 3.02
1466 1685 2.724454 CTAGTCTCCTCCGACTCCAAA 58.276 52.381 0.00 0.00 42.92 3.28
1493 1712 5.819825 GAGTTTATCTCCACCCAACAATC 57.180 43.478 0.00 0.00 37.22 2.67
1494 1713 5.253330 GAGTTTATCTCCACCCAACAATCA 58.747 41.667 0.00 0.00 37.22 2.57
1530 1763 5.316167 TGCTGTCACATGAAACCTCTTAAT 58.684 37.500 0.00 0.00 0.00 1.40
1570 1803 1.519455 CTCCCTGTTTCTAGGCGCG 60.519 63.158 0.00 0.00 36.47 6.86
1571 1804 3.195698 CCCTGTTTCTAGGCGCGC 61.196 66.667 25.94 25.94 36.47 6.86
1572 1805 2.434185 CCTGTTTCTAGGCGCGCA 60.434 61.111 34.42 12.90 0.00 6.09
1573 1806 2.740714 CCTGTTTCTAGGCGCGCAC 61.741 63.158 34.42 21.35 0.00 5.34
1588 1821 1.872468 GCACACACACACACACACA 59.128 52.632 0.00 0.00 0.00 3.72
1613 1846 7.540400 CACACACACACAAAATGACTTTTAGAA 59.460 33.333 0.00 0.00 32.81 2.10
1614 1847 8.085296 ACACACACACAAAATGACTTTTAGAAA 58.915 29.630 0.00 0.00 32.81 2.52
1616 1849 9.482627 ACACACACAAAATGACTTTTAGAAAAA 57.517 25.926 0.00 0.00 32.81 1.94
1677 1918 7.255695 CCCAATATGATGAATAGCTGAAGCAAA 60.256 37.037 4.90 0.00 45.16 3.68
1680 1921 6.710597 ATGATGAATAGCTGAAGCAAATGT 57.289 33.333 4.90 0.00 45.16 2.71
1681 1922 7.812690 ATGATGAATAGCTGAAGCAAATGTA 57.187 32.000 4.90 0.00 45.16 2.29
1683 1924 7.868775 TGATGAATAGCTGAAGCAAATGTATC 58.131 34.615 4.90 6.36 45.16 2.24
1685 1926 9.212641 GATGAATAGCTGAAGCAAATGTATCTA 57.787 33.333 4.90 0.00 45.16 1.98
1750 1998 3.964688 TCGTGCCTTATCCTCCATTTCTA 59.035 43.478 0.00 0.00 0.00 2.10
1805 2053 1.525619 GACAACTTCAGCGCTAACGTT 59.474 47.619 10.99 2.02 42.83 3.99
1860 2108 2.170607 TGGGATACTGCAGGTTAGCTTC 59.829 50.000 19.93 3.72 34.99 3.86
1891 2139 4.441356 CCCCCATTTATGTTATGTGCACAC 60.441 45.833 24.37 10.59 0.00 3.82
1892 2140 4.159321 CCCCATTTATGTTATGTGCACACA 59.841 41.667 24.37 16.59 46.44 3.72
1915 2163 6.492429 ACATGCATGCTAATATCAACATCCTT 59.508 34.615 26.53 0.00 0.00 3.36
1933 2181 5.422214 TCCTTGTTTCCATCTTCTAGTCC 57.578 43.478 0.00 0.00 0.00 3.85
1934 2182 4.081642 TCCTTGTTTCCATCTTCTAGTCCG 60.082 45.833 0.00 0.00 0.00 4.79
2046 2295 5.106237 GGACTATAATAGACTACGCCCACTG 60.106 48.000 0.00 0.00 0.00 3.66
2182 2432 2.029020 TCCCACTCTCGATGACTTGTTG 60.029 50.000 0.00 0.00 0.00 3.33
2295 2545 3.088532 TGGTGTGCCCATAATTCTTGTC 58.911 45.455 0.00 0.00 38.72 3.18
2350 2600 6.040391 GTCTCCTATCTCTGTTATGCTTCTGT 59.960 42.308 0.00 0.00 0.00 3.41
2620 2870 5.680594 TTTGAATTTTATGGAGGCATGCT 57.319 34.783 18.92 3.20 0.00 3.79
2711 2972 2.399916 AGAACCAGCTGAGAGATTGC 57.600 50.000 17.39 0.00 0.00 3.56
2762 3023 6.648725 GACTCGTGTCTTTTAGTATTGCAT 57.351 37.500 10.29 0.00 39.94 3.96
2964 3225 6.219473 CAGTGACTAGACATCAGTTTGAACT 58.781 40.000 0.00 0.00 40.60 3.01
3176 3482 5.652014 TGCTTTGTACCTGATTCCCAATTAG 59.348 40.000 0.00 0.00 0.00 1.73
3320 5136 4.246458 GTTAATAGATCTGCGGGATGACC 58.754 47.826 5.18 0.00 34.33 4.02
3591 5431 6.674573 TCCTAGTAGTGAAGAAGAAGGCTAT 58.325 40.000 0.00 0.00 0.00 2.97
3592 5432 6.773685 TCCTAGTAGTGAAGAAGAAGGCTATC 59.226 42.308 0.00 0.00 0.00 2.08
3599 5439 7.120051 AGTGAAGAAGAAGGCTATCTGTAGTA 58.880 38.462 0.00 0.00 0.00 1.82
3733 5583 4.708726 AAGGATGCAGCATCTTGTAAAC 57.291 40.909 30.20 14.74 40.39 2.01
3734 5584 3.960571 AGGATGCAGCATCTTGTAAACT 58.039 40.909 30.20 16.57 40.39 2.66
3735 5585 5.102953 AGGATGCAGCATCTTGTAAACTA 57.897 39.130 30.20 0.00 40.39 2.24
3736 5586 5.121811 AGGATGCAGCATCTTGTAAACTAG 58.878 41.667 30.20 0.00 40.39 2.57
3737 5587 4.260948 GGATGCAGCATCTTGTAAACTAGC 60.261 45.833 30.20 9.27 40.39 3.42
3738 5588 3.942829 TGCAGCATCTTGTAAACTAGCT 58.057 40.909 0.00 0.00 0.00 3.32
3739 5589 3.935203 TGCAGCATCTTGTAAACTAGCTC 59.065 43.478 0.00 0.00 0.00 4.09
3740 5590 3.935203 GCAGCATCTTGTAAACTAGCTCA 59.065 43.478 0.00 0.00 0.00 4.26
3926 5806 3.875727 CAGCTCATGATGAACTTGGGTAG 59.124 47.826 0.00 0.00 0.00 3.18
3939 5819 8.715190 TGAACTTGGGTAGTGTGCTATATATA 57.285 34.615 0.00 0.00 37.12 0.86
3940 5820 8.582437 TGAACTTGGGTAGTGTGCTATATATAC 58.418 37.037 0.00 0.00 37.12 1.47
4019 5900 4.270808 GCTGCTTATTTGTTTGTTTGTGCT 59.729 37.500 0.00 0.00 0.00 4.40
4020 5901 5.220643 GCTGCTTATTTGTTTGTTTGTGCTT 60.221 36.000 0.00 0.00 0.00 3.91
4120 6001 6.017605 ACTGACAGACTGTTTGAATAGCAAAG 60.018 38.462 10.01 0.00 46.48 2.77
4171 6052 3.039252 AGGGTGTCTCTGCTAGCTTAT 57.961 47.619 17.23 0.00 0.00 1.73
4172 6053 3.379452 AGGGTGTCTCTGCTAGCTTATT 58.621 45.455 17.23 0.00 0.00 1.40
4173 6054 3.386402 AGGGTGTCTCTGCTAGCTTATTC 59.614 47.826 17.23 4.71 0.00 1.75
4230 6148 1.466851 AAGCAGCCAAGGCAAAGGAC 61.467 55.000 14.40 0.00 44.88 3.85
4234 6152 1.896660 GCCAAGGCAAAGGACGTGA 60.897 57.895 6.14 0.00 41.49 4.35
4294 6212 2.930019 TGGTGCAGGAGAGGGTGG 60.930 66.667 0.00 0.00 0.00 4.61
4593 6519 1.092348 CGTAGACCTCGGTGATGTCA 58.908 55.000 0.00 0.00 31.33 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.976701 ATCCGGCAAGGGAACAGCG 62.977 63.158 0.00 0.00 40.09 5.18
21 22 0.527565 CAAATCCGGCAAGGGAACAG 59.472 55.000 0.00 0.00 40.09 3.16
25 26 0.395586 CCATCAAATCCGGCAAGGGA 60.396 55.000 0.00 0.00 41.52 4.20
26 27 0.395586 TCCATCAAATCCGGCAAGGG 60.396 55.000 0.00 0.00 41.52 3.95
83 84 2.092882 GCTACCGTCGCTGTGAACC 61.093 63.158 0.00 0.00 0.00 3.62
93 94 4.771356 TCACGCGCTGCTACCGTC 62.771 66.667 5.73 0.00 32.18 4.79
97 98 2.667318 TTTGCTCACGCGCTGCTAC 61.667 57.895 5.73 0.00 39.65 3.58
121 122 2.186076 GTGTTTACTGATCGGAGCGAG 58.814 52.381 9.00 0.00 39.91 5.03
131 132 0.970640 TAGCGCCAGGTGTTTACTGA 59.029 50.000 2.29 0.00 38.20 3.41
135 136 0.036765 CCACTAGCGCCAGGTGTTTA 60.037 55.000 18.76 0.00 0.00 2.01
189 190 2.576847 GCACGCGCACTATTTGGC 60.577 61.111 5.73 0.00 38.36 4.52
200 201 3.102276 TGAAAACTTAAAAGTGCACGCG 58.898 40.909 12.01 3.53 39.66 6.01
201 202 3.485743 CCTGAAAACTTAAAAGTGCACGC 59.514 43.478 12.01 0.00 39.66 5.34
202 203 4.668289 ACCTGAAAACTTAAAAGTGCACG 58.332 39.130 12.01 0.00 39.66 5.34
220 221 5.540400 TCTTTGGGTTATATACGGACCTG 57.460 43.478 2.80 0.00 33.90 4.00
224 225 5.816777 CCGTTTTCTTTGGGTTATATACGGA 59.183 40.000 0.00 0.00 45.46 4.69
226 227 6.667007 ACCGTTTTCTTTGGGTTATATACG 57.333 37.500 0.00 0.00 0.00 3.06
246 247 7.865889 TGAGTTATTGCTTCACTATGTATACCG 59.134 37.037 0.00 0.00 0.00 4.02
248 249 8.704234 GCTGAGTTATTGCTTCACTATGTATAC 58.296 37.037 0.00 0.00 0.00 1.47
250 251 7.440556 CAGCTGAGTTATTGCTTCACTATGTAT 59.559 37.037 8.42 0.00 34.51 2.29
253 254 5.503683 GCAGCTGAGTTATTGCTTCACTATG 60.504 44.000 20.43 0.00 34.51 2.23
254 255 4.574013 GCAGCTGAGTTATTGCTTCACTAT 59.426 41.667 20.43 0.00 34.51 2.12
255 256 3.935203 GCAGCTGAGTTATTGCTTCACTA 59.065 43.478 20.43 0.00 34.51 2.74
256 257 2.746362 GCAGCTGAGTTATTGCTTCACT 59.254 45.455 20.43 0.00 34.51 3.41
262 263 0.744414 TCGGGCAGCTGAGTTATTGC 60.744 55.000 20.43 0.00 35.87 3.56
264 265 2.014068 GCTTCGGGCAGCTGAGTTATT 61.014 52.381 20.43 0.00 41.35 1.40
266 267 1.079127 GCTTCGGGCAGCTGAGTTA 60.079 57.895 20.43 0.00 41.35 2.24
267 268 2.359230 GCTTCGGGCAGCTGAGTT 60.359 61.111 20.43 0.00 41.35 3.01
276 277 0.748005 TTGCCTCTATTGCTTCGGGC 60.748 55.000 0.00 0.00 42.22 6.13
277 278 1.972872 ATTGCCTCTATTGCTTCGGG 58.027 50.000 0.00 0.00 0.00 5.14
279 280 3.309682 TCGAAATTGCCTCTATTGCTTCG 59.690 43.478 0.00 0.00 36.11 3.79
280 281 4.882671 TCGAAATTGCCTCTATTGCTTC 57.117 40.909 0.00 0.00 0.00 3.86
282 283 4.274459 GTCATCGAAATTGCCTCTATTGCT 59.726 41.667 0.00 0.00 0.00 3.91
284 285 5.739752 TGTCATCGAAATTGCCTCTATTG 57.260 39.130 0.00 0.00 0.00 1.90
285 286 6.992123 TGTATGTCATCGAAATTGCCTCTATT 59.008 34.615 0.00 0.00 0.00 1.73
286 287 6.524734 TGTATGTCATCGAAATTGCCTCTAT 58.475 36.000 0.00 0.00 0.00 1.98
292 320 3.065233 TGGCTGTATGTCATCGAAATTGC 59.935 43.478 0.00 0.00 0.00 3.56
299 327 1.863454 GCTTCTGGCTGTATGTCATCG 59.137 52.381 0.00 0.00 38.06 3.84
372 402 7.857456 TGAGGCTTTATTTAAGTGGTGATCTA 58.143 34.615 0.00 0.00 36.19 1.98
373 403 6.721318 TGAGGCTTTATTTAAGTGGTGATCT 58.279 36.000 0.00 0.00 36.19 2.75
374 404 7.573968 ATGAGGCTTTATTTAAGTGGTGATC 57.426 36.000 0.00 0.00 36.19 2.92
375 405 8.903820 GTTATGAGGCTTTATTTAAGTGGTGAT 58.096 33.333 0.00 0.00 36.19 3.06
376 406 8.107095 AGTTATGAGGCTTTATTTAAGTGGTGA 58.893 33.333 0.00 0.00 36.19 4.02
377 407 8.281212 AGTTATGAGGCTTTATTTAAGTGGTG 57.719 34.615 0.00 0.00 36.19 4.17
378 408 8.107095 TGAGTTATGAGGCTTTATTTAAGTGGT 58.893 33.333 0.00 0.00 36.19 4.16
379 409 8.506168 TGAGTTATGAGGCTTTATTTAAGTGG 57.494 34.615 0.00 0.00 36.19 4.00
380 410 8.125448 GCTGAGTTATGAGGCTTTATTTAAGTG 58.875 37.037 0.00 0.00 36.19 3.16
381 411 8.049721 AGCTGAGTTATGAGGCTTTATTTAAGT 58.950 33.333 0.00 0.00 36.19 2.24
382 412 8.341173 CAGCTGAGTTATGAGGCTTTATTTAAG 58.659 37.037 8.42 0.00 36.90 1.85
383 413 7.201732 GCAGCTGAGTTATGAGGCTTTATTTAA 60.202 37.037 20.43 0.00 0.00 1.52
491 607 9.618890 TCTCTCTTTCATTTGACCCTTAATATG 57.381 33.333 0.00 0.00 0.00 1.78
493 609 8.267894 CCTCTCTCTTTCATTTGACCCTTAATA 58.732 37.037 0.00 0.00 0.00 0.98
636 760 1.211457 GGAGATGGATGGCTCACTTGT 59.789 52.381 0.00 0.00 32.83 3.16
640 764 1.698532 AGATGGAGATGGATGGCTCAC 59.301 52.381 0.00 0.00 32.83 3.51
641 765 1.976404 GAGATGGAGATGGATGGCTCA 59.024 52.381 0.00 0.00 32.83 4.26
642 766 1.278699 GGAGATGGAGATGGATGGCTC 59.721 57.143 0.00 0.00 0.00 4.70
644 768 1.062364 TGGAGATGGAGATGGATGGC 58.938 55.000 0.00 0.00 0.00 4.40
645 769 3.182976 AGATGGAGATGGAGATGGATGG 58.817 50.000 0.00 0.00 0.00 3.51
646 770 3.838903 TGAGATGGAGATGGAGATGGATG 59.161 47.826 0.00 0.00 0.00 3.51
648 772 3.116823 ACTGAGATGGAGATGGAGATGGA 60.117 47.826 0.00 0.00 0.00 3.41
747 897 1.871345 CAGCGACAGACAGCTAGCG 60.871 63.158 9.55 7.05 42.52 4.26
749 899 1.518133 GGCAGCGACAGACAGCTAG 60.518 63.158 0.00 0.00 42.52 3.42
751 901 4.731612 CGGCAGCGACAGACAGCT 62.732 66.667 0.00 0.00 45.74 4.24
767 917 1.639280 GAAGGAAGAAGCTCAGCTCG 58.361 55.000 0.00 0.00 38.25 5.03
852 1018 1.550327 CAAAGGAAGGGAAGGGAAGC 58.450 55.000 0.00 0.00 0.00 3.86
853 1019 1.429299 ACCAAAGGAAGGGAAGGGAAG 59.571 52.381 0.00 0.00 0.00 3.46
854 1020 1.427753 GACCAAAGGAAGGGAAGGGAA 59.572 52.381 0.00 0.00 0.00 3.97
855 1021 1.073098 GACCAAAGGAAGGGAAGGGA 58.927 55.000 0.00 0.00 0.00 4.20
856 1022 0.039764 GGACCAAAGGAAGGGAAGGG 59.960 60.000 0.00 0.00 0.00 3.95
946 1113 9.201127 CCCTTTCTTTCTTTCTTGAATTCAATC 57.799 33.333 20.76 0.00 35.02 2.67
1150 1342 9.699410 GGGGATCTATCTATCTATCTATCCATG 57.301 40.741 0.00 0.00 34.58 3.66
1228 1431 8.404000 ACAAAGCAAGTAATCATGATTCATCTC 58.596 33.333 23.95 11.86 32.50 2.75
1248 1451 3.765026 TCGGTTGAACTGAAAACAAAGC 58.235 40.909 4.00 0.00 28.96 3.51
1304 1516 1.549203 ACCTCCAACACAATCCATGC 58.451 50.000 0.00 0.00 0.00 4.06
1490 1709 7.658167 TGTGACAGCAATTGATTTGATTTGATT 59.342 29.630 10.34 0.00 37.53 2.57
1491 1710 7.156000 TGTGACAGCAATTGATTTGATTTGAT 58.844 30.769 10.34 0.00 37.53 2.57
1492 1711 6.514063 TGTGACAGCAATTGATTTGATTTGA 58.486 32.000 10.34 0.00 37.53 2.69
1493 1712 6.772770 TGTGACAGCAATTGATTTGATTTG 57.227 33.333 10.34 0.00 37.53 2.32
1494 1713 7.156000 TCATGTGACAGCAATTGATTTGATTT 58.844 30.769 10.34 0.00 37.53 2.17
1530 1763 0.197661 AGGGAGGGAGGGGTTAACAA 59.802 55.000 8.10 0.00 0.00 2.83
1570 1803 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
1571 1804 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1572 1805 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1573 1806 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1588 1821 7.151999 TCTAAAAGTCATTTTGTGTGTGTGT 57.848 32.000 0.00 0.00 39.01 3.72
1614 1847 4.330620 TGAACGAACGCAGTAGAACTTTTT 59.669 37.500 0.00 0.00 45.00 1.94
1616 1849 3.450578 TGAACGAACGCAGTAGAACTTT 58.549 40.909 0.00 0.00 45.00 2.66
1617 1850 3.088194 TGAACGAACGCAGTAGAACTT 57.912 42.857 0.00 0.00 45.00 2.66
1618 1851 2.787601 TGAACGAACGCAGTAGAACT 57.212 45.000 0.00 0.00 45.00 3.01
1619 1852 3.243336 AGATGAACGAACGCAGTAGAAC 58.757 45.455 0.00 0.00 45.00 3.01
1677 1918 7.864108 TTGCTTGCTGTACATTTAGATACAT 57.136 32.000 0.00 0.00 31.10 2.29
1680 1921 7.390440 AGTGTTTGCTTGCTGTACATTTAGATA 59.610 33.333 0.00 0.00 0.00 1.98
1681 1922 6.207417 AGTGTTTGCTTGCTGTACATTTAGAT 59.793 34.615 0.00 0.00 0.00 1.98
1683 1924 5.762045 AGTGTTTGCTTGCTGTACATTTAG 58.238 37.500 0.00 0.00 0.00 1.85
1685 1926 4.654091 AGTGTTTGCTTGCTGTACATTT 57.346 36.364 0.00 0.00 0.00 2.32
1805 2053 2.110213 GTGCTCCCGTCAACCACA 59.890 61.111 0.00 0.00 0.00 4.17
1891 2139 6.510879 AGGATGTTGATATTAGCATGCATG 57.489 37.500 22.70 22.70 33.27 4.06
1892 2140 6.492429 ACAAGGATGTTGATATTAGCATGCAT 59.508 34.615 21.98 8.19 35.91 3.96
1893 2141 5.829391 ACAAGGATGTTGATATTAGCATGCA 59.171 36.000 21.98 0.00 35.91 3.96
1894 2142 6.323203 ACAAGGATGTTGATATTAGCATGC 57.677 37.500 10.51 10.51 35.91 4.06
1933 2181 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
1934 2182 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2046 2295 2.491022 ATCGGCACCTCGGTAGCTC 61.491 63.158 0.00 0.00 0.00 4.09
2295 2545 2.290641 GCATATACCAAGCTTTGTCCCG 59.709 50.000 6.43 0.00 0.00 5.14
2568 2818 2.096248 TGCTTTCCGTTCAACCAAGTT 58.904 42.857 0.00 0.00 0.00 2.66
2620 2870 6.184068 TGTATTAGAAAGTATTGGGCAGCAA 58.816 36.000 0.00 0.00 0.00 3.91
2685 2935 4.924625 TCTCTCAGCTGGTTCTTAGTAGT 58.075 43.478 15.13 0.00 0.00 2.73
2711 2972 6.701400 CCATTTTCTTGTTTAAGGACCAACAG 59.299 38.462 0.00 0.00 34.43 3.16
2771 3032 9.014297 AGGATCTCAAGTTTTCGAATTAACAAT 57.986 29.630 13.63 1.61 0.00 2.71
2772 3033 8.391075 AGGATCTCAAGTTTTCGAATTAACAA 57.609 30.769 13.63 0.00 0.00 2.83
2904 3165 0.033405 AGCATTCTGGCCTCTGCAAT 60.033 50.000 17.48 1.97 40.13 3.56
2913 3174 4.725790 ACAAAGGAAATAGCATTCTGGC 57.274 40.909 0.00 0.00 0.00 4.85
2964 3225 7.395489 ACAGACCTCGGTAGAAACTAATCTTAA 59.605 37.037 0.00 0.00 0.00 1.85
3017 3321 7.621428 ACATCAAGAATTTCTGTCATACTGG 57.379 36.000 0.00 0.00 0.00 4.00
3126 3432 4.573900 CAACTCAATCTCAAGTGGCTACT 58.426 43.478 0.00 0.00 39.32 2.57
3176 3482 5.698545 AGACAGCATTTCTTACAGTCAACTC 59.301 40.000 0.00 0.00 0.00 3.01
3320 5136 2.350772 GGTGATCCACGAAAAACTGCTG 60.351 50.000 0.00 0.00 34.83 4.41
3591 5431 7.037873 ACCAAATCACTAACCCAATACTACAGA 60.038 37.037 0.00 0.00 0.00 3.41
3592 5432 7.110155 ACCAAATCACTAACCCAATACTACAG 58.890 38.462 0.00 0.00 0.00 2.74
3599 5439 3.900601 TGCAACCAAATCACTAACCCAAT 59.099 39.130 0.00 0.00 0.00 3.16
3733 5583 6.900568 CTCACTCTACCATTTTTGAGCTAG 57.099 41.667 0.00 0.00 0.00 3.42
3736 5586 4.348198 GCTCACTCTACCATTTTTGAGC 57.652 45.455 5.69 5.69 46.51 4.26
3737 5587 5.240891 TCAGCTCACTCTACCATTTTTGAG 58.759 41.667 0.00 0.00 34.77 3.02
3738 5588 5.227569 TCAGCTCACTCTACCATTTTTGA 57.772 39.130 0.00 0.00 0.00 2.69
3739 5589 4.394300 CCTCAGCTCACTCTACCATTTTTG 59.606 45.833 0.00 0.00 0.00 2.44
3740 5590 4.287067 TCCTCAGCTCACTCTACCATTTTT 59.713 41.667 0.00 0.00 0.00 1.94
3926 5806 8.587111 CATGTTCATCGTGTATATATAGCACAC 58.413 37.037 15.60 15.60 39.32 3.82
3939 5819 1.002430 AGCAGTCCATGTTCATCGTGT 59.998 47.619 0.00 0.00 0.00 4.49
3940 5820 1.662629 GAGCAGTCCATGTTCATCGTG 59.337 52.381 0.00 0.00 38.88 4.35
4054 5935 8.743085 TCATTTTTCAAAACATTTGGGATTCA 57.257 26.923 3.25 0.00 0.00 2.57
4151 6032 2.534042 TAAGCTAGCAGAGACACCCT 57.466 50.000 18.83 0.00 0.00 4.34
4171 6052 8.653191 CCTCCTCTAGTCTAGTCTAGTAATGAA 58.347 40.741 19.35 3.30 38.66 2.57
4172 6053 8.011883 TCCTCCTCTAGTCTAGTCTAGTAATGA 58.988 40.741 19.35 12.35 38.66 2.57
4173 6054 8.197592 TCCTCCTCTAGTCTAGTCTAGTAATG 57.802 42.308 19.35 11.02 38.66 1.90
4230 6148 4.778415 CTCACCGCCGGAGTCACG 62.778 72.222 11.71 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.