Multiple sequence alignment - TraesCS6B01G393200

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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 TraesCS6B01G393200 chr6B 100.000 2618 0 0 1 2618 668031019 668028402 0.000000e+00 4835.0
1 TraesCS6B01G393200 chr6B 77.744 328 30 19 998 1298 668136660 668136349 7.500000e-36 161.0
2 TraesCS6B01G393200 chr6B 90.541 74 1 2 802 874 668137074 668137006 2.770000e-15 93.5
3 TraesCS6B01G393200 chr6A 87.492 1503 72 53 301 1758 591381868 591380437 0.000000e+00 1628.0
4 TraesCS6B01G393200 chr6A 83.178 321 31 11 1802 2105 591380319 591380005 3.320000e-69 272.0
5 TraesCS6B01G393200 chr6A 86.638 232 10 12 80 302 591382141 591381922 1.210000e-58 237.0
6 TraesCS6B01G393200 chr6A 84.388 237 18 6 2382 2618 591379573 591379356 5.670000e-52 215.0
7 TraesCS6B01G393200 chr6A 95.420 131 6 0 2241 2371 591379910 591379780 2.640000e-50 209.0
8 TraesCS6B01G393200 chr6A 79.835 243 20 15 490 729 591406806 591406590 1.620000e-32 150.0
9 TraesCS6B01G393200 chr6A 92.473 93 6 1 2141 2232 591379916 591380008 5.880000e-27 132.0
10 TraesCS6B01G393200 chr6D 87.794 1319 73 43 499 1758 443741851 443740562 0.000000e+00 1463.0
11 TraesCS6B01G393200 chr6D 82.195 747 63 36 1802 2517 443740441 443739734 1.750000e-161 579.0
12 TraesCS6B01G393200 chr6D 88.329 377 23 9 1 369 443742417 443742054 1.440000e-117 433.0
13 TraesCS6B01G393200 chr6D 84.130 460 34 22 998 1427 443754011 443753561 2.430000e-110 409.0
14 TraesCS6B01G393200 chr6D 80.488 246 17 18 490 729 443754455 443754235 2.700000e-35 159.0
15 TraesCS6B01G393200 chr6D 88.660 97 5 1 1527 1617 443753516 443753420 2.130000e-21 113.0
16 TraesCS6B01G393200 chr6D 91.892 74 0 2 802 874 443754204 443754136 5.960000e-17 99.0
17 TraesCS6B01G393200 chr6D 100.000 47 0 0 2551 2597 443739733 443739687 1.290000e-13 87.9
18 TraesCS6B01G393200 chr7D 88.580 324 21 9 283 598 359083849 359084164 1.900000e-101 379.0
19 TraesCS6B01G393200 chr7D 79.743 311 45 16 1000 1308 94005549 94005843 2.640000e-50 209.0
20 TraesCS6B01G393200 chr7D 80.198 303 39 18 999 1298 93949387 93949103 9.500000e-50 207.0
21 TraesCS6B01G393200 chr7A 74.961 647 96 49 1000 1622 97266936 97267540 1.210000e-58 237.0
22 TraesCS6B01G393200 chr7B 79.470 302 44 17 999 1298 47737265 47737550 5.720000e-47 198.0
23 TraesCS6B01G393200 chr2D 92.562 121 7 2 1178 1297 598712894 598713013 3.460000e-39 172.0
24 TraesCS6B01G393200 chr2B 91.736 121 8 2 1178 1297 726546001 726546120 1.610000e-37 167.0
25 TraesCS6B01G393200 chr2B 88.462 78 9 0 1012 1089 726135854 726135931 7.710000e-16 95.3
26 TraesCS6B01G393200 chr2A 90.909 121 9 2 1178 1297 732580516 732580635 7.500000e-36 161.0
27 TraesCS6B01G393200 chr5D 88.235 51 2 4 1311 1360 553238038 553237991 1.010000e-04 58.4


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 TraesCS6B01G393200 chr6B 668028402 668031019 2617 True 4835.000 4835 100.0000 1 2618 1 chr6B.!!$R1 2617
1 TraesCS6B01G393200 chr6A 591379356 591382141 2785 True 512.200 1628 87.4232 80 2618 5 chr6A.!!$R2 2538
2 TraesCS6B01G393200 chr6D 443739687 443742417 2730 True 640.725 1463 89.5795 1 2597 4 chr6D.!!$R1 2596
3 TraesCS6B01G393200 chr7A 97266936 97267540 604 False 237.000 237 74.9610 1000 1622 1 chr7A.!!$F1 622

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
547 786 0.179004 ATGTCGAACCCAAGCCACAA 60.179 50.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 2060 0.028505 TACACTAAGCGGCGATCGAC 59.971 55.0 21.57 17.0 42.43 4.2 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
49 50 6.148976 TCGTGCATAGTTATATCTCGTAAGCT 59.851 38.462 0.00 0.00 37.18 3.74
51 52 6.034044 GTGCATAGTTATATCTCGTAAGCTGC 59.966 42.308 0.00 0.00 37.18 5.25
105 113 4.345962 TTGCATGCACGGTGCTGC 62.346 61.111 31.95 31.95 45.31 5.25
176 184 1.080569 GCCACAGAAAACGCCATGG 60.081 57.895 7.63 7.63 0.00 3.66
246 264 1.078426 AGAACCCGTGCATGGCTAC 60.078 57.895 20.27 11.74 0.00 3.58
249 267 2.514592 CCCGTGCATGGCTACCTG 60.515 66.667 20.27 0.44 0.00 4.00
254 272 1.802880 CGTGCATGGCTACCTGTCTAC 60.803 57.143 0.00 0.00 0.00 2.59
255 273 1.482593 GTGCATGGCTACCTGTCTACT 59.517 52.381 0.00 0.00 0.00 2.57
256 274 1.757118 TGCATGGCTACCTGTCTACTC 59.243 52.381 0.00 0.00 0.00 2.59
279 297 9.026121 ACTCCTACATGTCAATACATATCTACC 57.974 37.037 0.00 0.00 44.70 3.18
281 299 9.374711 TCCTACATGTCAATACATATCTACCAA 57.625 33.333 0.00 0.00 44.70 3.67
334 411 9.952030 CTTTCTATAAGAAAAAGTCTTCCTCCT 57.048 33.333 3.88 0.00 43.49 3.69
337 414 9.543231 TCTATAAGAAAAAGTCTTCCTCCTACA 57.457 33.333 0.00 0.00 43.49 2.74
338 415 9.589111 CTATAAGAAAAAGTCTTCCTCCTACAC 57.411 37.037 0.00 0.00 43.49 2.90
340 417 6.502074 AGAAAAAGTCTTCCTCCTACACTT 57.498 37.500 0.00 0.00 29.66 3.16
342 419 8.030913 AGAAAAAGTCTTCCTCCTACACTTAA 57.969 34.615 0.00 0.00 29.66 1.85
343 420 7.932491 AGAAAAAGTCTTCCTCCTACACTTAAC 59.068 37.037 0.00 0.00 29.66 2.01
344 421 6.742559 AAAGTCTTCCTCCTACACTTAACA 57.257 37.500 0.00 0.00 0.00 2.41
345 422 6.742559 AAGTCTTCCTCCTACACTTAACAA 57.257 37.500 0.00 0.00 0.00 2.83
346 423 6.347859 AGTCTTCCTCCTACACTTAACAAG 57.652 41.667 0.00 0.00 0.00 3.16
347 424 6.075984 AGTCTTCCTCCTACACTTAACAAGA 58.924 40.000 0.00 0.00 0.00 3.02
348 425 6.209788 AGTCTTCCTCCTACACTTAACAAGAG 59.790 42.308 0.00 0.00 0.00 2.85
406 637 1.269257 GCCAGTGCAAAGTTGAGGAAC 60.269 52.381 0.00 0.00 37.47 3.62
411 642 4.741676 CAGTGCAAAGTTGAGGAACAAATC 59.258 41.667 0.00 0.00 40.36 2.17
428 659 6.178239 ACAAATCGTGCCAAGTTATAGTTC 57.822 37.500 0.00 0.00 0.00 3.01
431 662 1.931172 CGTGCCAAGTTATAGTTCGGG 59.069 52.381 0.00 0.00 0.00 5.14
432 663 2.417651 CGTGCCAAGTTATAGTTCGGGA 60.418 50.000 0.00 0.00 0.00 5.14
434 665 3.101437 TGCCAAGTTATAGTTCGGGAGA 58.899 45.455 0.00 0.00 0.00 3.71
484 719 6.513806 TGTATGTCAAAATTGCATGCTAGT 57.486 33.333 20.33 7.93 32.84 2.57
486 721 7.696755 TGTATGTCAAAATTGCATGCTAGTAG 58.303 34.615 20.33 7.38 32.84 2.57
487 722 7.552330 TGTATGTCAAAATTGCATGCTAGTAGA 59.448 33.333 20.33 9.64 32.84 2.59
488 723 6.182039 TGTCAAAATTGCATGCTAGTAGAC 57.818 37.500 20.33 20.03 0.00 2.59
526 761 7.954835 TGAGATTTCAAGTTTCAACCATGAAT 58.045 30.769 0.00 2.29 44.70 2.57
527 762 8.423349 TGAGATTTCAAGTTTCAACCATGAATT 58.577 29.630 0.00 6.29 44.70 2.17
547 786 0.179004 ATGTCGAACCCAAGCCACAA 60.179 50.000 0.00 0.00 0.00 3.33
558 797 2.134346 CAAGCCACAAATTTCGTTGGG 58.866 47.619 10.60 3.70 32.50 4.12
560 799 2.035632 AGCCACAAATTTCGTTGGGAA 58.964 42.857 10.60 0.00 33.46 3.97
691 933 3.281359 GAACATGCACCCAACGCCC 62.281 63.158 0.00 0.00 0.00 6.13
764 1013 1.079127 ATTCCCACTTCCGCAGTCG 60.079 57.895 0.00 0.00 30.92 4.18
787 1036 5.440260 CGCAGCACTTCAATTTAATTTCC 57.560 39.130 0.00 0.00 0.00 3.13
788 1037 4.327087 CGCAGCACTTCAATTTAATTTCCC 59.673 41.667 0.00 0.00 0.00 3.97
789 1038 5.482006 GCAGCACTTCAATTTAATTTCCCT 58.518 37.500 0.00 0.00 0.00 4.20
790 1039 5.578336 GCAGCACTTCAATTTAATTTCCCTC 59.422 40.000 0.00 0.00 0.00 4.30
791 1040 6.101997 CAGCACTTCAATTTAATTTCCCTCC 58.898 40.000 0.00 0.00 0.00 4.30
844 1099 4.025401 CCGCCACAACGCACTTCC 62.025 66.667 0.00 0.00 0.00 3.46
878 1135 4.410743 GCCAAGCTTGCTCGCCAC 62.411 66.667 21.43 0.12 0.00 5.01
879 1136 4.093952 CCAAGCTTGCTCGCCACG 62.094 66.667 21.43 0.62 0.00 4.94
880 1137 4.748679 CAAGCTTGCTCGCCACGC 62.749 66.667 14.65 0.00 38.87 5.34
1089 1347 2.743718 CACCCTCTCCTGTGCGTT 59.256 61.111 0.00 0.00 0.00 4.84
1152 1418 1.337354 TGCGCTTACGGTGATTCTTGA 60.337 47.619 9.73 0.00 40.57 3.02
1621 1984 1.063183 GGAGATCTGCCATTAGCCCT 58.937 55.000 0.00 0.00 42.71 5.19
1622 1985 2.260822 GGAGATCTGCCATTAGCCCTA 58.739 52.381 0.00 0.00 42.71 3.53
1625 1988 1.981495 GATCTGCCATTAGCCCTACCT 59.019 52.381 0.00 0.00 42.71 3.08
1626 1989 1.893315 TCTGCCATTAGCCCTACCTT 58.107 50.000 0.00 0.00 42.71 3.50
1627 1990 3.054779 TCTGCCATTAGCCCTACCTTA 57.945 47.619 0.00 0.00 42.71 2.69
1628 1991 2.972713 TCTGCCATTAGCCCTACCTTAG 59.027 50.000 0.00 0.00 42.71 2.18
1629 1992 1.420138 TGCCATTAGCCCTACCTTAGC 59.580 52.381 0.00 0.00 42.71 3.09
1631 1994 2.904434 GCCATTAGCCCTACCTTAGCTA 59.096 50.000 0.00 0.00 38.06 3.32
1633 1996 3.055747 CCATTAGCCCTACCTTAGCTAGC 60.056 52.174 6.62 6.62 40.05 3.42
1634 1997 2.305858 TAGCCCTACCTTAGCTAGCC 57.694 55.000 12.13 0.00 38.06 3.93
1635 1998 0.264955 AGCCCTACCTTAGCTAGCCA 59.735 55.000 12.13 0.00 34.38 4.75
1636 1999 0.682292 GCCCTACCTTAGCTAGCCAG 59.318 60.000 12.13 7.87 0.00 4.85
1667 2030 1.616091 GCTTCCTCTGCCTCTGCTCT 61.616 60.000 0.00 0.00 38.71 4.09
1669 2032 1.408702 CTTCCTCTGCCTCTGCTCTAC 59.591 57.143 0.00 0.00 38.71 2.59
1674 2037 1.733402 CTGCCTCTGCTCTACCTCCG 61.733 65.000 0.00 0.00 38.71 4.63
1679 2042 0.107116 TCTGCTCTACCTCCGTCTCC 60.107 60.000 0.00 0.00 0.00 3.71
1685 2048 0.455005 CTACCTCCGTCTCCGTTTCC 59.545 60.000 0.00 0.00 0.00 3.13
1697 2060 4.084888 GTTTCCTGGCGCGAACGG 62.085 66.667 12.10 6.70 40.57 4.44
1712 2075 2.726180 CGGTCGATCGCCGCTTAG 60.726 66.667 28.60 10.60 42.82 2.18
1713 2076 2.412112 GGTCGATCGCCGCTTAGT 59.588 61.111 11.09 0.00 38.37 2.24
1715 2078 1.226603 GTCGATCGCCGCTTAGTGT 60.227 57.895 11.09 0.00 38.37 3.55
1716 2079 0.028505 GTCGATCGCCGCTTAGTGTA 59.971 55.000 11.09 0.00 38.37 2.90
1717 2080 0.306840 TCGATCGCCGCTTAGTGTAG 59.693 55.000 11.09 0.00 38.37 2.74
1718 2081 0.029035 CGATCGCCGCTTAGTGTAGT 59.971 55.000 0.26 0.00 0.00 2.73
1723 2104 1.557651 GCCGCTTAGTGTAGTGTAGC 58.442 55.000 0.00 0.00 0.00 3.58
1760 2194 6.775594 ATTACAGTCAGTGAGCTATGTACA 57.224 37.500 0.00 0.00 0.00 2.90
1762 2196 3.119814 ACAGTCAGTGAGCTATGTACACG 60.120 47.826 0.00 0.00 39.19 4.49
1769 2203 4.399618 AGTGAGCTATGTACACGAGTGATT 59.600 41.667 10.50 0.00 39.19 2.57
1797 2231 7.854934 CAGAATAACTGTACCTCGTATTAGC 57.145 40.000 0.00 0.00 41.30 3.09
1798 2232 6.577800 CAGAATAACTGTACCTCGTATTAGCG 59.422 42.308 0.00 0.00 41.30 4.26
1799 2233 6.261826 AGAATAACTGTACCTCGTATTAGCGT 59.738 38.462 0.00 0.00 0.00 5.07
1800 2234 3.959573 ACTGTACCTCGTATTAGCGTC 57.040 47.619 0.00 0.00 0.00 5.19
1801 2235 3.539604 ACTGTACCTCGTATTAGCGTCT 58.460 45.455 0.00 0.00 0.00 4.18
1802 2236 4.697514 ACTGTACCTCGTATTAGCGTCTA 58.302 43.478 0.00 0.00 0.00 2.59
1803 2237 5.303971 ACTGTACCTCGTATTAGCGTCTAT 58.696 41.667 0.00 0.00 0.00 1.98
1804 2238 5.407995 ACTGTACCTCGTATTAGCGTCTATC 59.592 44.000 0.00 0.00 0.00 2.08
1805 2239 4.692625 TGTACCTCGTATTAGCGTCTATCC 59.307 45.833 0.00 0.00 0.00 2.59
1806 2240 3.748083 ACCTCGTATTAGCGTCTATCCA 58.252 45.455 0.00 0.00 0.00 3.41
1807 2241 4.333690 ACCTCGTATTAGCGTCTATCCAT 58.666 43.478 0.00 0.00 0.00 3.41
1808 2242 5.494724 ACCTCGTATTAGCGTCTATCCATA 58.505 41.667 0.00 0.00 0.00 2.74
1809 2243 5.585445 ACCTCGTATTAGCGTCTATCCATAG 59.415 44.000 0.00 0.00 0.00 2.23
1811 2245 5.183969 TCGTATTAGCGTCTATCCATAGCT 58.816 41.667 0.00 0.00 41.45 3.32
1814 2274 7.498239 TCGTATTAGCGTCTATCCATAGCTTAT 59.502 37.037 0.00 0.00 39.14 1.73
1859 2325 8.215050 TGATCCTCTCTGTTTTTACCTTTTACA 58.785 33.333 0.00 0.00 0.00 2.41
1867 2333 5.585445 TGTTTTTACCTTTTACAGTGCTCGA 59.415 36.000 0.00 0.00 0.00 4.04
1872 2338 2.731976 CCTTTTACAGTGCTCGACTCAC 59.268 50.000 5.22 5.22 29.75 3.51
1898 2364 4.174009 TGATTCTAGTCTACGTGCTTTGC 58.826 43.478 0.00 0.00 0.00 3.68
1936 2402 2.281345 CCATCTGATCTGCCGCCC 60.281 66.667 0.00 0.00 0.00 6.13
1937 2403 2.815945 CCATCTGATCTGCCGCCCT 61.816 63.158 0.00 0.00 0.00 5.19
1938 2404 1.301558 CATCTGATCTGCCGCCCTC 60.302 63.158 0.00 0.00 0.00 4.30
1939 2405 2.865598 ATCTGATCTGCCGCCCTCG 61.866 63.158 0.00 0.00 0.00 4.63
1940 2406 3.531207 CTGATCTGCCGCCCTCGA 61.531 66.667 0.00 0.00 38.10 4.04
1941 2407 3.781770 CTGATCTGCCGCCCTCGAC 62.782 68.421 0.00 0.00 38.10 4.20
1959 2425 2.937149 CGACCTCGAGAGTCAAGACATA 59.063 50.000 24.42 0.00 43.02 2.29
1994 2465 1.423845 CAAGGTAACGTGCGATGCC 59.576 57.895 0.00 0.00 39.79 4.40
1995 2466 2.098233 AAGGTAACGTGCGATGCCG 61.098 57.895 0.00 0.00 46.39 5.69
1998 2469 1.426041 GGTAACGTGCGATGCCGAAT 61.426 55.000 0.00 0.00 38.22 3.34
1999 2470 1.202203 GTAACGTGCGATGCCGAATA 58.798 50.000 0.00 0.00 38.22 1.75
2002 2473 0.032130 ACGTGCGATGCCGAATAGAT 59.968 50.000 0.00 0.00 38.22 1.98
2003 2474 0.710567 CGTGCGATGCCGAATAGATC 59.289 55.000 0.00 0.00 38.22 2.75
2004 2475 1.783284 GTGCGATGCCGAATAGATCA 58.217 50.000 0.00 0.00 38.22 2.92
2008 2482 1.337167 CGATGCCGAATAGATCAGCCA 60.337 52.381 0.00 0.00 38.22 4.75
2013 2487 2.740981 GCCGAATAGATCAGCCAATCAG 59.259 50.000 0.00 0.00 0.00 2.90
2029 2504 0.038251 TCAGTGGCGTGCTAACTGAG 60.038 55.000 19.74 4.11 44.01 3.35
2076 2559 3.411446 TGGATTTGCTAGCCGGATAATG 58.589 45.455 13.29 0.00 0.00 1.90
2082 2565 4.350368 TGCTAGCCGGATAATGAATCAA 57.650 40.909 13.29 0.00 36.20 2.57
2090 2573 4.368315 CGGATAATGAATCAACCAGACGA 58.632 43.478 0.00 0.00 36.20 4.20
2095 2578 1.347707 TGAATCAACCAGACGAGCCTT 59.652 47.619 0.00 0.00 0.00 4.35
2098 2581 0.033504 TCAACCAGACGAGCCTTGTC 59.966 55.000 3.73 3.73 36.60 3.18
2110 2593 1.556911 AGCCTTGTCGATGAACCATCT 59.443 47.619 5.54 0.00 38.59 2.90
2124 2607 3.659183 ACCATCTTCCTGGGAAATCAG 57.341 47.619 3.55 0.00 40.85 2.90
2129 2612 1.815003 CTTCCTGGGAAATCAGTGCAC 59.185 52.381 9.40 9.40 33.34 4.57
2131 2614 1.171308 CCTGGGAAATCAGTGCACTG 58.829 55.000 36.07 36.07 45.08 3.66
2133 2616 1.236616 TGGGAAATCAGTGCACTGCG 61.237 55.000 36.76 18.97 43.46 5.18
2134 2617 0.955428 GGGAAATCAGTGCACTGCGA 60.955 55.000 36.76 24.04 43.46 5.10
2135 2618 0.166814 GGAAATCAGTGCACTGCGAC 59.833 55.000 36.76 25.89 43.46 5.19
2136 2619 1.151668 GAAATCAGTGCACTGCGACT 58.848 50.000 36.76 22.38 43.46 4.18
2137 2620 2.337583 GAAATCAGTGCACTGCGACTA 58.662 47.619 36.76 22.61 43.46 2.59
2138 2621 2.001812 AATCAGTGCACTGCGACTAG 57.998 50.000 36.76 16.05 43.46 2.57
2139 2622 0.174389 ATCAGTGCACTGCGACTAGG 59.826 55.000 36.76 15.32 43.46 3.02
2140 2623 1.179174 TCAGTGCACTGCGACTAGGT 61.179 55.000 36.76 1.68 43.46 3.08
2141 2624 0.526211 CAGTGCACTGCGACTAGGTA 59.474 55.000 32.39 0.00 37.15 3.08
2142 2625 0.526662 AGTGCACTGCGACTAGGTAC 59.473 55.000 20.97 0.00 0.00 3.34
2143 2626 0.797249 GTGCACTGCGACTAGGTACG 60.797 60.000 10.32 0.00 0.00 3.67
2175 2658 1.010574 GGCTCGATCGTCGACAGAG 60.011 63.158 17.16 18.95 44.82 3.35
2177 2660 0.315544 GCTCGATCGTCGACAGAGTC 60.316 60.000 22.07 14.39 44.82 3.36
2178 2661 0.302288 CTCGATCGTCGACAGAGTCC 59.698 60.000 17.16 6.73 44.82 3.85
2179 2662 1.088340 TCGATCGTCGACAGAGTCCC 61.088 60.000 17.16 4.64 44.82 4.46
2212 2695 2.424601 ACATGCCATGGACTGAATTTCG 59.575 45.455 18.40 0.00 33.60 3.46
2228 2715 2.356313 CGCTGTGTCGTTGGCTCT 60.356 61.111 0.00 0.00 0.00 4.09
2232 2719 1.143305 CTGTGTCGTTGGCTCTTCAG 58.857 55.000 0.00 0.00 0.00 3.02
2236 2723 1.664649 TCGTTGGCTCTTCAGTGCG 60.665 57.895 0.00 0.00 35.57 5.34
2238 2725 2.032528 TTGGCTCTTCAGTGCGGG 59.967 61.111 0.00 0.00 35.57 6.13
2372 2859 2.749839 CCAATTCCGGGCAGCGAA 60.750 61.111 0.00 0.00 0.00 4.70
2373 2860 2.764314 CCAATTCCGGGCAGCGAAG 61.764 63.158 0.00 0.00 0.00 3.79
2376 2863 4.735132 TTCCGGGCAGCGAAGACG 62.735 66.667 0.00 0.00 42.93 4.18
2378 2865 4.735132 CCGGGCAGCGAAGACGAA 62.735 66.667 0.00 0.00 42.66 3.85
2380 2867 2.815647 GGGCAGCGAAGACGAAGG 60.816 66.667 0.00 0.00 42.66 3.46
2410 3093 1.594269 CGTCGTGTGTCCGTCGAAAG 61.594 60.000 0.00 0.00 40.80 2.62
2417 3100 4.011517 TCCGTCGAAAGCCCCACC 62.012 66.667 0.00 0.00 0.00 4.61
2432 3115 3.168528 ACCGCCACCACCTTCAGT 61.169 61.111 0.00 0.00 0.00 3.41
2440 3123 1.270550 CACCACCTTCAGTTTGGATGC 59.729 52.381 0.00 0.00 34.24 3.91
2445 3128 2.154462 CCTTCAGTTTGGATGCGTTCT 58.846 47.619 0.00 0.00 0.00 3.01
2446 3129 2.095567 CCTTCAGTTTGGATGCGTTCTG 60.096 50.000 0.00 0.00 0.00 3.02
2447 3130 1.522668 TCAGTTTGGATGCGTTCTGG 58.477 50.000 0.00 0.00 0.00 3.86
2448 3131 0.523072 CAGTTTGGATGCGTTCTGGG 59.477 55.000 0.00 0.00 0.00 4.45
2449 3132 1.212751 GTTTGGATGCGTTCTGGGC 59.787 57.895 0.00 0.00 0.00 5.36
2450 3133 1.074775 TTTGGATGCGTTCTGGGCT 59.925 52.632 0.00 0.00 0.00 5.19
2451 3134 0.539438 TTTGGATGCGTTCTGGGCTT 60.539 50.000 0.00 0.00 0.00 4.35
2452 3135 0.960364 TTGGATGCGTTCTGGGCTTC 60.960 55.000 0.00 0.00 34.77 3.86
2465 3148 2.266055 GCTTCAGGTCCACCGAGG 59.734 66.667 0.00 0.00 42.08 4.63
2466 3149 2.283529 GCTTCAGGTCCACCGAGGA 61.284 63.158 0.00 0.00 46.75 3.71
2480 3163 2.705658 ACCGAGGATGAATGGCTGATTA 59.294 45.455 0.00 0.00 0.00 1.75
2522 3205 4.202706 ACTGGAGGAGATGAGCTGATAGAT 60.203 45.833 0.00 0.00 0.00 1.98
2525 3208 4.527816 GGAGGAGATGAGCTGATAGATTGT 59.472 45.833 0.00 0.00 0.00 2.71
2531 3214 4.684484 TGAGCTGATAGATTGTCATGCT 57.316 40.909 0.00 0.00 34.82 3.79
2532 3215 4.377897 TGAGCTGATAGATTGTCATGCTG 58.622 43.478 0.00 0.00 33.41 4.41
2542 3225 1.913778 TGTCATGCTGCCATTTCTGT 58.086 45.000 0.00 0.00 0.00 3.41
2546 3229 2.229543 TCATGCTGCCATTTCTGTTGAC 59.770 45.455 0.00 0.00 0.00 3.18
2547 3230 0.961019 TGCTGCCATTTCTGTTGACC 59.039 50.000 0.00 0.00 0.00 4.02
2548 3231 0.244721 GCTGCCATTTCTGTTGACCC 59.755 55.000 0.00 0.00 0.00 4.46
2549 3232 1.619654 CTGCCATTTCTGTTGACCCA 58.380 50.000 0.00 0.00 0.00 4.51
2603 3286 0.101939 GTATCCCCCTGTTCGTCGAC 59.898 60.000 5.18 5.18 0.00 4.20
2611 3294 1.990563 CCTGTTCGTCGACATGGTTAC 59.009 52.381 17.16 4.31 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.511454 GTGCTATCGATAAATCAACCAGCA 59.489 41.667 6.58 8.02 34.36 4.41
51 52 4.376413 GCGTGCTATCGATAAATCAACCAG 60.376 45.833 6.58 0.00 0.00 4.00
105 113 1.859427 AACAAGCTCACATGCAGGCG 61.859 55.000 0.00 0.00 34.99 5.52
106 114 0.316204 AAACAAGCTCACATGCAGGC 59.684 50.000 0.00 0.00 34.99 4.85
107 115 1.338973 ACAAACAAGCTCACATGCAGG 59.661 47.619 0.00 0.00 34.99 4.85
176 184 0.957395 TGCTGCTGCTAAAGACTGGC 60.957 55.000 17.00 0.00 40.48 4.85
200 218 3.919973 TTTCCCGTCTACGCACGCC 62.920 63.158 0.00 0.00 38.52 5.68
203 221 1.017701 CCCTTTTCCCGTCTACGCAC 61.018 60.000 0.00 0.00 38.18 5.34
207 225 1.450025 CTTGCCCTTTTCCCGTCTAC 58.550 55.000 0.00 0.00 0.00 2.59
246 264 5.860941 ATTGACATGTAGGAGTAGACAGG 57.139 43.478 0.00 0.00 33.69 4.00
254 272 9.025041 TGGTAGATATGTATTGACATGTAGGAG 57.975 37.037 0.00 0.00 46.11 3.69
255 273 8.950007 TGGTAGATATGTATTGACATGTAGGA 57.050 34.615 0.00 0.00 46.11 2.94
328 405 4.748701 ACCTCTTGTTAAGTGTAGGAGGA 58.251 43.478 12.23 0.00 40.68 3.71
334 411 2.895404 AGGCGACCTCTTGTTAAGTGTA 59.105 45.455 0.00 0.00 0.00 2.90
335 412 1.692519 AGGCGACCTCTTGTTAAGTGT 59.307 47.619 0.00 0.00 0.00 3.55
336 413 2.457366 AGGCGACCTCTTGTTAAGTG 57.543 50.000 0.00 0.00 0.00 3.16
337 414 2.550208 CCAAGGCGACCTCTTGTTAAGT 60.550 50.000 0.00 0.00 39.78 2.24
338 415 2.076863 CCAAGGCGACCTCTTGTTAAG 58.923 52.381 0.00 0.00 39.78 1.85
340 417 0.321298 GCCAAGGCGACCTCTTGTTA 60.321 55.000 0.00 0.00 39.78 2.41
342 419 2.032681 GCCAAGGCGACCTCTTGT 59.967 61.111 0.00 0.00 39.78 3.16
398 629 1.974265 TGGCACGATTTGTTCCTCAA 58.026 45.000 0.00 0.00 34.60 3.02
406 637 5.255596 CGAACTATAACTTGGCACGATTTG 58.744 41.667 0.00 0.00 0.00 2.32
411 642 1.931172 CCCGAACTATAACTTGGCACG 59.069 52.381 0.00 0.00 0.00 5.34
484 719 8.212995 TGAAATCTCATATGCCAAATGAGTCTA 58.787 33.333 15.58 2.72 46.84 2.59
486 721 7.268199 TGAAATCTCATATGCCAAATGAGTC 57.732 36.000 15.58 9.47 46.84 3.36
487 722 7.341256 ACTTGAAATCTCATATGCCAAATGAGT 59.659 33.333 15.58 5.29 46.84 3.41
526 761 1.072489 TGTGGCTTGGGTTCGACATAA 59.928 47.619 0.00 0.00 0.00 1.90
527 762 0.687920 TGTGGCTTGGGTTCGACATA 59.312 50.000 0.00 0.00 0.00 2.29
547 786 6.042208 TGGGTTATCTTTTTCCCAACGAAATT 59.958 34.615 0.00 0.00 45.66 1.82
558 797 4.864704 TGTGGCTTGGGTTATCTTTTTC 57.135 40.909 0.00 0.00 0.00 2.29
560 799 3.055891 GCATGTGGCTTGGGTTATCTTTT 60.056 43.478 0.00 0.00 40.25 2.27
694 936 0.231790 GACTACTAGGCGCTACGACG 59.768 60.000 7.64 0.00 41.28 5.12
695 937 0.231790 CGACTACTAGGCGCTACGAC 59.768 60.000 7.64 0.00 41.27 4.34
696 938 2.598045 CGACTACTAGGCGCTACGA 58.402 57.895 7.64 0.00 41.27 3.43
703 945 3.999051 CGCAAGCGACTACTAGGC 58.001 61.111 9.11 0.00 42.83 3.93
764 1013 4.201618 GGAAATTAAATTGAAGTGCTGCGC 60.202 41.667 4.76 4.76 0.00 6.09
768 1017 6.019108 AGGAGGGAAATTAAATTGAAGTGCT 58.981 36.000 0.00 0.00 0.00 4.40
781 1030 7.475798 CGGGAGGTATAAATAAGGAGGGAAATT 60.476 40.741 0.00 0.00 0.00 1.82
782 1031 6.012771 CGGGAGGTATAAATAAGGAGGGAAAT 60.013 42.308 0.00 0.00 0.00 2.17
783 1032 5.308759 CGGGAGGTATAAATAAGGAGGGAAA 59.691 44.000 0.00 0.00 0.00 3.13
784 1033 4.842380 CGGGAGGTATAAATAAGGAGGGAA 59.158 45.833 0.00 0.00 0.00 3.97
786 1035 3.055312 GCGGGAGGTATAAATAAGGAGGG 60.055 52.174 0.00 0.00 0.00 4.30
787 1036 3.368116 CGCGGGAGGTATAAATAAGGAGG 60.368 52.174 0.00 0.00 0.00 4.30
788 1037 3.846360 CGCGGGAGGTATAAATAAGGAG 58.154 50.000 0.00 0.00 0.00 3.69
789 1038 2.028748 GCGCGGGAGGTATAAATAAGGA 60.029 50.000 8.83 0.00 0.00 3.36
790 1039 2.344025 GCGCGGGAGGTATAAATAAGG 58.656 52.381 8.83 0.00 0.00 2.69
791 1040 2.289195 TGGCGCGGGAGGTATAAATAAG 60.289 50.000 8.83 0.00 0.00 1.73
840 1095 2.041928 AGCAGGAGGGGAGGGAAG 59.958 66.667 0.00 0.00 0.00 3.46
841 1096 2.041265 GAGCAGGAGGGGAGGGAA 59.959 66.667 0.00 0.00 0.00 3.97
842 1097 4.095400 GGAGCAGGAGGGGAGGGA 62.095 72.222 0.00 0.00 0.00 4.20
1089 1347 1.482553 GCATGGGCTAGGTAGGTAGGA 60.483 57.143 0.00 0.00 36.96 2.94
1123 1384 0.317854 CCGTAAGCGCATCGATCAGA 60.318 55.000 11.47 0.00 36.67 3.27
1636 1999 3.426568 GGAAGCAGAGCACCACGC 61.427 66.667 0.00 0.00 42.91 5.34
1637 2000 1.739562 GAGGAAGCAGAGCACCACG 60.740 63.158 7.67 0.00 31.94 4.94
1638 2001 0.673022 CAGAGGAAGCAGAGCACCAC 60.673 60.000 7.67 2.57 31.94 4.16
1639 2002 1.675801 CAGAGGAAGCAGAGCACCA 59.324 57.895 7.67 0.00 31.94 4.17
1640 2003 1.744741 GCAGAGGAAGCAGAGCACC 60.745 63.158 0.00 0.00 0.00 5.01
1674 2037 3.119096 GCGCCAGGAAACGGAGAC 61.119 66.667 0.00 0.00 0.00 3.36
1679 2042 4.424430 CGTTCGCGCCAGGAAACG 62.424 66.667 12.93 12.93 0.00 3.60
1697 2060 0.028505 TACACTAAGCGGCGATCGAC 59.971 55.000 21.57 17.00 42.43 4.20
1704 2067 1.557651 GCTACACTACACTAAGCGGC 58.442 55.000 0.00 0.00 0.00 6.53
1708 2071 5.523188 AGCTACTACGCTACACTACACTAAG 59.477 44.000 0.00 0.00 38.76 2.18
1710 2073 4.807834 CAGCTACTACGCTACACTACACTA 59.192 45.833 0.00 0.00 38.41 2.74
1712 2075 3.788135 GCAGCTACTACGCTACACTACAC 60.788 52.174 0.00 0.00 38.41 2.90
1713 2076 2.353889 GCAGCTACTACGCTACACTACA 59.646 50.000 0.00 0.00 38.41 2.74
1715 2078 1.596260 CGCAGCTACTACGCTACACTA 59.404 52.381 0.00 0.00 38.41 2.74
1716 2079 0.377554 CGCAGCTACTACGCTACACT 59.622 55.000 0.00 0.00 38.41 3.55
1717 2080 0.098376 ACGCAGCTACTACGCTACAC 59.902 55.000 0.00 0.00 38.41 2.90
1718 2081 1.655484 TACGCAGCTACTACGCTACA 58.345 50.000 0.00 0.00 38.41 2.74
1723 2104 4.206698 ACTGTAATACGCAGCTACTACG 57.793 45.455 0.00 0.00 37.47 3.51
1735 2116 7.644551 GTGTACATAGCTCACTGACTGTAATAC 59.355 40.741 0.00 0.00 0.00 1.89
1795 2229 4.645588 GGGTATAAGCTATGGATAGACGCT 59.354 45.833 0.00 0.00 32.05 5.07
1796 2230 4.645588 AGGGTATAAGCTATGGATAGACGC 59.354 45.833 0.00 0.00 32.05 5.19
1797 2231 6.018098 CGTAGGGTATAAGCTATGGATAGACG 60.018 46.154 0.00 0.00 32.05 4.18
1798 2232 7.261829 CGTAGGGTATAAGCTATGGATAGAC 57.738 44.000 0.00 0.00 32.05 2.59
1814 2274 7.848846 GAGGATCAAATTTGTTACCGTAGGGTA 60.849 40.741 17.47 10.28 46.28 3.69
1830 2290 8.712228 AAAGGTAAAAACAGAGAGGATCAAAT 57.288 30.769 0.00 0.00 37.82 2.32
1834 2294 8.617290 TGTAAAAGGTAAAAACAGAGAGGATC 57.383 34.615 0.00 0.00 0.00 3.36
1859 2325 0.250945 TCAGAGGTGAGTCGAGCACT 60.251 55.000 15.50 0.00 38.45 4.40
1867 2333 5.120399 CGTAGACTAGAATCAGAGGTGAGT 58.880 45.833 0.00 0.00 35.66 3.41
1872 2338 3.880490 AGCACGTAGACTAGAATCAGAGG 59.120 47.826 0.00 0.00 0.00 3.69
1898 2364 3.234386 GCTGGCTAAAACAAAAGCTACG 58.766 45.455 0.00 0.00 38.80 3.51
1903 2369 4.022068 TCAGATGGCTGGCTAAAACAAAAG 60.022 41.667 2.00 0.00 42.53 2.27
1938 2404 1.157585 TGTCTTGACTCTCGAGGTCG 58.842 55.000 21.41 12.78 41.45 4.79
1939 2405 4.966965 TTATGTCTTGACTCTCGAGGTC 57.033 45.455 20.62 20.62 0.00 3.85
1940 2406 5.010719 TGTTTTATGTCTTGACTCTCGAGGT 59.989 40.000 13.56 9.47 0.00 3.85
1941 2407 5.470368 TGTTTTATGTCTTGACTCTCGAGG 58.530 41.667 13.56 5.96 0.00 4.63
1959 2425 9.187455 CGTTACCTTGTGCTATTTTTATGTTTT 57.813 29.630 0.00 0.00 0.00 2.43
1994 2465 3.744942 CCACTGATTGGCTGATCTATTCG 59.255 47.826 0.00 0.00 39.07 3.34
2008 2482 1.001974 TCAGTTAGCACGCCACTGATT 59.998 47.619 14.63 0.00 41.60 2.57
2013 2487 1.344942 CGTCTCAGTTAGCACGCCAC 61.345 60.000 0.00 0.00 0.00 5.01
2076 2559 1.734465 CAAGGCTCGTCTGGTTGATTC 59.266 52.381 0.00 0.00 0.00 2.52
2082 2565 1.251527 ATCGACAAGGCTCGTCTGGT 61.252 55.000 3.79 0.00 35.10 4.00
2090 2573 1.556911 AGATGGTTCATCGACAAGGCT 59.443 47.619 0.00 0.00 44.67 4.58
2095 2578 2.093500 CCAGGAAGATGGTTCATCGACA 60.093 50.000 0.00 0.00 44.67 4.35
2098 2581 1.486310 TCCCAGGAAGATGGTTCATCG 59.514 52.381 0.00 0.00 44.67 3.84
2110 2593 1.425066 AGTGCACTGATTTCCCAGGAA 59.575 47.619 20.97 0.00 38.44 3.36
2124 2607 0.797249 CGTACCTAGTCGCAGTGCAC 60.797 60.000 16.83 9.40 0.00 4.57
2133 2616 1.866496 CGTGCGTGCGTACCTAGTC 60.866 63.158 7.19 0.00 0.00 2.59
2134 2617 2.177531 CGTGCGTGCGTACCTAGT 59.822 61.111 7.19 0.00 0.00 2.57
2135 2618 3.245315 GCGTGCGTGCGTACCTAG 61.245 66.667 7.19 0.00 0.00 3.02
2136 2619 4.040636 TGCGTGCGTGCGTACCTA 62.041 61.111 7.19 0.00 37.81 3.08
2139 2622 3.773630 ATGTGCGTGCGTGCGTAC 61.774 61.111 12.88 12.88 45.26 3.67
2140 2623 3.772560 CATGTGCGTGCGTGCGTA 61.773 61.111 3.11 0.00 37.81 4.42
2179 2662 0.776810 TGGCATGTATGGTATGGGGG 59.223 55.000 0.00 0.00 0.00 5.40
2212 2695 0.880278 TGAAGAGCCAACGACACAGC 60.880 55.000 0.00 0.00 0.00 4.40
2238 2725 0.107848 CCACGAGTTGATGGTACCCC 60.108 60.000 10.07 1.60 0.00 4.95
2250 2737 4.704833 AATGCTGCGCCCACGAGT 62.705 61.111 4.18 0.00 43.93 4.18
2251 2738 3.386867 GAAATGCTGCGCCCACGAG 62.387 63.158 4.18 0.00 43.93 4.18
2270 2757 5.403246 TCATGTTAACAAACACACCACAAC 58.597 37.500 13.23 0.00 35.22 3.32
2371 2858 0.905357 CCTGATGTCCCCTTCGTCTT 59.095 55.000 0.00 0.00 0.00 3.01
2372 2859 1.617947 GCCTGATGTCCCCTTCGTCT 61.618 60.000 0.00 0.00 0.00 4.18
2373 2860 1.153349 GCCTGATGTCCCCTTCGTC 60.153 63.158 0.00 0.00 0.00 4.20
2376 2863 1.153349 GACGCCTGATGTCCCCTTC 60.153 63.158 0.00 0.00 0.00 3.46
2377 2864 2.990479 GACGCCTGATGTCCCCTT 59.010 61.111 0.00 0.00 0.00 3.95
2378 2865 3.461773 CGACGCCTGATGTCCCCT 61.462 66.667 0.00 0.00 32.68 4.79
2380 2867 2.509336 CACGACGCCTGATGTCCC 60.509 66.667 0.00 0.00 32.68 4.46
2417 3100 1.654220 CAAACTGAAGGTGGTGGCG 59.346 57.895 0.00 0.00 0.00 5.69
2418 3101 0.467290 TCCAAACTGAAGGTGGTGGC 60.467 55.000 3.14 0.00 35.23 5.01
2432 3115 0.539438 AAGCCCAGAACGCATCCAAA 60.539 50.000 0.00 0.00 0.00 3.28
2440 3123 1.376037 GGACCTGAAGCCCAGAACG 60.376 63.158 5.38 0.00 45.78 3.95
2445 3128 3.636231 CGGTGGACCTGAAGCCCA 61.636 66.667 0.00 0.00 0.00 5.36
2446 3129 3.316573 CTCGGTGGACCTGAAGCCC 62.317 68.421 0.00 0.00 0.00 5.19
2447 3130 2.266055 CTCGGTGGACCTGAAGCC 59.734 66.667 0.00 0.00 0.00 4.35
2448 3131 2.266055 CCTCGGTGGACCTGAAGC 59.734 66.667 0.00 0.00 38.35 3.86
2449 3132 4.113617 TCCTCGGTGGACCTGAAG 57.886 61.111 0.00 0.00 40.56 3.02
2465 3148 3.571401 CCCCAACTAATCAGCCATTCATC 59.429 47.826 0.00 0.00 0.00 2.92
2466 3149 3.569491 CCCCAACTAATCAGCCATTCAT 58.431 45.455 0.00 0.00 0.00 2.57
2467 3150 2.358090 CCCCCAACTAATCAGCCATTCA 60.358 50.000 0.00 0.00 0.00 2.57
2525 3208 2.229543 GTCAACAGAAATGGCAGCATGA 59.770 45.455 0.00 0.00 39.69 3.07
2531 3214 1.133513 ACTGGGTCAACAGAAATGGCA 60.134 47.619 0.00 0.00 40.97 4.92
2532 3215 1.270550 CACTGGGTCAACAGAAATGGC 59.729 52.381 0.00 0.00 40.97 4.40
2546 3229 1.228245 CACCAACTGGGACACTGGG 60.228 63.158 0.00 0.00 39.76 4.45
2547 3230 1.228245 CCACCAACTGGGACACTGG 60.228 63.158 0.00 0.00 40.88 4.00
2548 3231 0.535102 GACCACCAACTGGGACACTG 60.535 60.000 0.00 0.00 45.78 3.66
2549 3232 0.694444 AGACCACCAACTGGGACACT 60.694 55.000 0.00 0.00 45.78 3.55


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

AutoCloner maintained by Alex Coulton.