Multiple sequence alignment - TraesCS2D01G109300

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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 TraesCS2D01G109300 chr2D 100.000 2672 0 0 1 2672 60766701 60764030 0.000000e+00 4935.0
1 TraesCS2D01G109300 chr2D 82.143 112 18 2 1850 1960 589757350 589757240 7.870000e-16 95.3
2 TraesCS2D01G109300 chr2A 85.930 1592 103 58 605 2113 61296402 61294849 0.000000e+00 1587.0
3 TraesCS2D01G109300 chr2A 95.224 335 13 3 1 335 61297975 61297644 6.550000e-146 527.0
4 TraesCS2D01G109300 chr2A 87.324 213 21 3 336 544 61296606 61296396 3.440000e-59 239.0
5 TraesCS2D01G109300 chr2B 87.994 1291 111 23 433 1718 95220177 95218926 0.000000e+00 1485.0
6 TraesCS2D01G109300 chr2B 79.231 260 33 15 2429 2672 798538119 798538373 7.650000e-36 161.0
7 TraesCS2D01G109300 chr2B 100.000 32 0 0 1906 1937 649708943 649708912 2.870000e-05 60.2
8 TraesCS2D01G109300 chr3D 87.285 873 86 17 807 1672 355707161 355706307 0.000000e+00 974.0
9 TraesCS2D01G109300 chr3A 86.756 891 83 22 792 1672 474679500 474678635 0.000000e+00 959.0
10 TraesCS2D01G109300 chr3A 89.552 335 16 2 2112 2443 681055639 681055321 8.910000e-110 407.0
11 TraesCS2D01G109300 chr3A 88.889 234 12 3 2443 2672 681055281 681055058 2.620000e-70 276.0
12 TraesCS2D01G109300 chr3A 92.500 40 2 1 1904 1942 488111134 488111095 3.720000e-04 56.5
13 TraesCS2D01G109300 chr3B 86.072 919 88 28 786 1672 456676117 456675207 0.000000e+00 952.0
14 TraesCS2D01G109300 chrUn 89.429 350 18 2 2113 2459 403784757 403785090 8.840000e-115 424.0
15 TraesCS2D01G109300 chrUn 81.765 170 27 3 2105 2271 68081373 68081541 3.590000e-29 139.0
16 TraesCS2D01G109300 chr1A 89.205 352 17 3 2113 2459 558268760 558268425 1.140000e-113 420.0
17 TraesCS2D01G109300 chr1A 88.920 352 18 3 2113 2459 558275071 558274736 5.320000e-112 414.0
18 TraesCS2D01G109300 chr1A 88.636 352 19 3 2113 2459 558273823 558273488 2.480000e-110 409.0
19 TraesCS2D01G109300 chr1A 88.623 334 19 2 2113 2443 558272572 558272255 3.230000e-104 388.0
20 TraesCS2D01G109300 chr1A 82.768 354 18 5 2113 2459 558267507 558267190 2.620000e-70 276.0
21 TraesCS2D01G109300 chr1A 88.158 228 15 2 2447 2672 558267156 558266939 7.340000e-66 261.0
22 TraesCS2D01G109300 chr7D 83.730 252 23 9 2290 2541 199607775 199607542 3.460000e-54 222.0
23 TraesCS2D01G109300 chr7A 86.076 158 19 3 2113 2268 713118194 713118038 1.650000e-37 167.0
24 TraesCS2D01G109300 chr1B 82.609 161 26 2 2112 2271 651700144 651700303 9.970000e-30 141.0
25 TraesCS2D01G109300 chr6B 82.075 106 12 5 1851 1950 1204446 1204550 1.700000e-12 84.2
26 TraesCS2D01G109300 chr5B 97.222 36 1 0 1897 1932 684690191 684690226 7.990000e-06 62.1
27 TraesCS2D01G109300 chr5D 100.000 30 0 0 1796 1825 366745351 366745322 3.720000e-04 56.5


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 TraesCS2D01G109300 chr2D 60764030 60766701 2671 True 4935.000000 4935 100.000000 1 2672 1 chr2D.!!$R1 2671
1 TraesCS2D01G109300 chr2A 61294849 61297975 3126 True 784.333333 1587 89.492667 1 2113 3 chr2A.!!$R1 2112
2 TraesCS2D01G109300 chr2B 95218926 95220177 1251 True 1485.000000 1485 87.994000 433 1718 1 chr2B.!!$R1 1285
3 TraesCS2D01G109300 chr3D 355706307 355707161 854 True 974.000000 974 87.285000 807 1672 1 chr3D.!!$R1 865
4 TraesCS2D01G109300 chr3A 474678635 474679500 865 True 959.000000 959 86.756000 792 1672 1 chr3A.!!$R1 880
5 TraesCS2D01G109300 chr3A 681055058 681055639 581 True 341.500000 407 89.220500 2112 2672 2 chr3A.!!$R3 560
6 TraesCS2D01G109300 chr3B 456675207 456676117 910 True 952.000000 952 86.072000 786 1672 1 chr3B.!!$R1 886
7 TraesCS2D01G109300 chr1A 558266939 558275071 8132 True 361.333333 420 87.718333 2113 2672 6 chr1A.!!$R1 559

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
725 1771 0.035439 GCCGGAAATCTGACTCCCAA 60.035 55.0 5.05 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 2867 0.093026 GAATACTCACACGCACGCAC 59.907 55.0 0.0 0.0 0.0 5.34 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
57 58 6.211515 TCAGAACCGTCTACTTTACAAACTC 58.788 40.000 0.00 0.00 30.85 3.01
58 59 5.116680 CAGAACCGTCTACTTTACAAACTCG 59.883 44.000 0.00 0.00 30.85 4.18
232 233 5.711976 ACAAGAATCAATCCTGAACCGATTT 59.288 36.000 0.00 0.00 34.49 2.17
296 297 2.171237 TCAGCATCCAGGGTTGTATCTG 59.829 50.000 0.00 0.00 0.00 2.90
300 301 3.072184 GCATCCAGGGTTGTATCTGAGAT 59.928 47.826 0.00 0.00 33.11 2.75
314 315 3.807553 TCTGAGATATTGCGGCAATTCA 58.192 40.909 30.74 25.16 35.54 2.57
315 316 3.811497 TCTGAGATATTGCGGCAATTCAG 59.189 43.478 31.38 31.38 37.47 3.02
318 319 4.823442 TGAGATATTGCGGCAATTCAGAAT 59.177 37.500 30.74 18.64 35.54 2.40
320 321 6.148315 TGAGATATTGCGGCAATTCAGAATAG 59.852 38.462 30.74 0.00 35.54 1.73
322 323 4.989279 ATTGCGGCAATTCAGAATAGTT 57.011 36.364 21.87 0.00 28.76 2.24
323 324 4.355543 TTGCGGCAATTCAGAATAGTTC 57.644 40.909 12.11 0.00 0.00 3.01
325 326 3.126858 TGCGGCAATTCAGAATAGTTCAC 59.873 43.478 0.00 0.00 0.00 3.18
348 349 9.767684 TCACTATTAACTTATTTTGACAATGCG 57.232 29.630 0.00 0.00 0.00 4.73
359 1399 1.234821 GACAATGCGTTCAGTGGGAA 58.765 50.000 0.00 0.00 42.13 3.97
369 1409 3.372206 CGTTCAGTGGGAAGATGTCAATC 59.628 47.826 0.00 0.00 35.82 2.67
382 1422 7.930325 GGAAGATGTCAATCTCAAGATGATGTA 59.070 37.037 0.00 0.00 42.60 2.29
389 1429 6.209391 TCAATCTCAAGATGATGTATCGGCTA 59.791 38.462 0.00 0.00 40.86 3.93
398 1438 5.592104 TGATGTATCGGCTAAGTCTTTCA 57.408 39.130 0.00 0.00 0.00 2.69
399 1439 5.592054 TGATGTATCGGCTAAGTCTTTCAG 58.408 41.667 0.00 0.00 0.00 3.02
418 1458 4.148079 TCAGAGATGCTCATAGGTGTAGG 58.852 47.826 0.00 0.00 32.06 3.18
423 1463 5.208890 AGATGCTCATAGGTGTAGGTTGTA 58.791 41.667 0.00 0.00 0.00 2.41
443 1485 0.992072 CGTGCGTGTTCATAGAGGTG 59.008 55.000 0.00 0.00 0.00 4.00
450 1492 4.663166 CGTGTTCATAGAGGTGAGTGTAG 58.337 47.826 0.00 0.00 0.00 2.74
451 1493 4.438880 CGTGTTCATAGAGGTGAGTGTAGG 60.439 50.000 0.00 0.00 0.00 3.18
473 1515 1.453524 GCGTATGTATGAGCTTCTGCG 59.546 52.381 0.00 0.00 45.42 5.18
474 1516 2.732366 CGTATGTATGAGCTTCTGCGT 58.268 47.619 0.00 0.00 45.42 5.24
535 1579 3.014623 GGAATTGGTTGGGCTGTACTAC 58.985 50.000 0.00 0.00 0.00 2.73
540 1584 1.673923 GGTTGGGCTGTACTACCGAAC 60.674 57.143 18.00 18.00 42.14 3.95
545 1589 2.650163 CTGTACTACCGAACAGCGC 58.350 57.895 0.00 0.00 36.96 5.92
565 1609 1.115467 AGTTCCTGTAGCTAGCGCAT 58.885 50.000 11.47 0.00 39.10 4.73
591 1635 2.817396 GAAGCAGCAGAGGTCGCC 60.817 66.667 0.00 0.00 0.00 5.54
617 1661 1.959226 GAACCGAAGAGCACCGCAA 60.959 57.895 0.00 0.00 0.00 4.85
618 1662 1.503818 GAACCGAAGAGCACCGCAAA 61.504 55.000 0.00 0.00 0.00 3.68
619 1663 0.889186 AACCGAAGAGCACCGCAAAT 60.889 50.000 0.00 0.00 0.00 2.32
620 1664 1.135315 CCGAAGAGCACCGCAAATG 59.865 57.895 0.00 0.00 0.00 2.32
621 1665 1.135315 CGAAGAGCACCGCAAATGG 59.865 57.895 0.00 0.00 0.00 3.16
682 1726 2.709475 GCGTCCAGCTATTTGGCG 59.291 61.111 0.00 0.00 44.04 5.69
725 1771 0.035439 GCCGGAAATCTGACTCCCAA 60.035 55.000 5.05 0.00 0.00 4.12
726 1772 1.739067 CCGGAAATCTGACTCCCAAC 58.261 55.000 0.00 0.00 0.00 3.77
763 1809 0.171231 CCTGATCTCGACAGCGACAA 59.829 55.000 0.00 0.00 42.51 3.18
770 1816 2.027625 CGACAGCGACAACCCCTTC 61.028 63.158 0.00 0.00 40.82 3.46
771 1817 1.371558 GACAGCGACAACCCCTTCT 59.628 57.895 0.00 0.00 0.00 2.85
772 1818 0.951040 GACAGCGACAACCCCTTCTG 60.951 60.000 0.00 0.00 0.00 3.02
773 1819 2.032681 AGCGACAACCCCTTCTGC 59.967 61.111 0.00 0.00 0.00 4.26
774 1820 3.423154 GCGACAACCCCTTCTGCG 61.423 66.667 0.00 0.00 0.00 5.18
775 1821 3.423154 CGACAACCCCTTCTGCGC 61.423 66.667 0.00 0.00 0.00 6.09
776 1822 3.423154 GACAACCCCTTCTGCGCG 61.423 66.667 0.00 0.00 0.00 6.86
777 1823 4.250305 ACAACCCCTTCTGCGCGT 62.250 61.111 8.43 0.00 0.00 6.01
778 1824 3.423154 CAACCCCTTCTGCGCGTC 61.423 66.667 8.43 0.00 0.00 5.19
779 1825 3.936203 AACCCCTTCTGCGCGTCA 61.936 61.111 8.43 5.42 0.00 4.35
780 1826 3.254024 AACCCCTTCTGCGCGTCAT 62.254 57.895 8.43 0.00 0.00 3.06
781 1827 2.892425 CCCCTTCTGCGCGTCATC 60.892 66.667 8.43 0.00 0.00 2.92
782 1828 2.125552 CCCTTCTGCGCGTCATCA 60.126 61.111 8.43 0.00 0.00 3.07
783 1829 1.522355 CCCTTCTGCGCGTCATCAT 60.522 57.895 8.43 0.00 0.00 2.45
784 1830 1.493950 CCCTTCTGCGCGTCATCATC 61.494 60.000 8.43 0.00 0.00 2.92
797 1863 2.093973 GTCATCATCGGTTCCTCACTGT 60.094 50.000 0.00 0.00 32.85 3.55
817 1883 2.068519 TCTGTCATGCACGCACTTTAG 58.931 47.619 0.00 0.00 0.00 1.85
896 1991 8.383619 CAACGCAATATGGTCTCTATTTATAGC 58.616 37.037 0.00 0.00 0.00 2.97
971 2074 1.527433 GCCAAACACCAGGGAAGAGC 61.527 60.000 0.00 0.00 0.00 4.09
1458 2595 2.904011 AGAAGAACGAGCTCTACGTG 57.096 50.000 12.85 0.00 43.16 4.49
1464 2601 2.970639 GAGCTCTACGTGGTGCCA 59.029 61.111 20.30 0.00 0.00 4.92
1729 2866 4.385447 TGCTAAATTGATTCTTTTGCGTGC 59.615 37.500 0.00 0.00 37.22 5.34
1730 2867 4.489206 GCTAAATTGATTCTTTTGCGTGCG 60.489 41.667 0.00 0.00 0.00 5.34
1733 2870 0.660005 TGATTCTTTTGCGTGCGTGC 60.660 50.000 0.00 0.00 0.00 5.34
1759 2896 4.754332 CGTGTGAGTATTCGTTCGTTTTT 58.246 39.130 0.00 0.00 0.00 1.94
1809 2949 8.431910 TTGTAATATTATACTCCCTCTGTCCC 57.568 38.462 0.00 0.00 0.00 4.46
1810 2950 7.541074 TGTAATATTATACTCCCTCTGTCCCA 58.459 38.462 0.00 0.00 0.00 4.37
1848 2994 1.929836 CATACTTCGCTCTTGTGCCTC 59.070 52.381 0.00 0.00 0.00 4.70
1854 3000 1.202582 TCGCTCTTGTGCCTCTTACTC 59.797 52.381 0.00 0.00 0.00 2.59
1863 3009 1.964223 TGCCTCTTACTCCATCCGATC 59.036 52.381 0.00 0.00 0.00 3.69
1865 3011 1.896465 CCTCTTACTCCATCCGATCCC 59.104 57.143 0.00 0.00 0.00 3.85
1866 3012 2.598565 CTCTTACTCCATCCGATCCCA 58.401 52.381 0.00 0.00 0.00 4.37
1871 3017 3.004752 ACTCCATCCGATCCCAAAAAG 57.995 47.619 0.00 0.00 0.00 2.27
1872 3018 2.308866 ACTCCATCCGATCCCAAAAAGT 59.691 45.455 0.00 0.00 0.00 2.66
1873 3019 2.684881 CTCCATCCGATCCCAAAAAGTG 59.315 50.000 0.00 0.00 0.00 3.16
1889 3036 3.919223 AAGTGGCGCGGTTTTAAATTA 57.081 38.095 8.83 0.00 0.00 1.40
1890 3037 4.443913 AAGTGGCGCGGTTTTAAATTAT 57.556 36.364 8.83 0.00 0.00 1.28
1895 3042 4.800993 TGGCGCGGTTTTAAATTATGATTG 59.199 37.500 8.83 0.00 0.00 2.67
1898 3045 6.035112 GGCGCGGTTTTAAATTATGATTGAAA 59.965 34.615 8.83 0.00 0.00 2.69
1932 3079 8.885722 AGTTCAAAACTACGACACTTATTTTGA 58.114 29.630 5.98 5.98 41.69 2.69
1935 3082 9.872757 TCAAAACTACGACACTTATTTTGAATC 57.127 29.630 7.32 0.00 40.93 2.52
1937 3084 6.642683 ACTACGACACTTATTTTGAATCGG 57.357 37.500 0.00 0.00 32.56 4.18
1938 3085 4.939509 ACGACACTTATTTTGAATCGGG 57.060 40.909 0.00 0.00 32.56 5.14
1941 3088 4.266714 GACACTTATTTTGAATCGGGGGA 58.733 43.478 0.00 0.00 0.00 4.81
1950 3097 2.754465 TGAATCGGGGGAAGTAGCTAA 58.246 47.619 0.00 0.00 0.00 3.09
1951 3098 3.314693 TGAATCGGGGGAAGTAGCTAAT 58.685 45.455 0.00 0.00 0.00 1.73
1953 3100 5.091552 TGAATCGGGGGAAGTAGCTAATAT 58.908 41.667 0.00 0.00 0.00 1.28
1955 3102 4.399483 TCGGGGGAAGTAGCTAATATCT 57.601 45.455 0.00 0.00 0.00 1.98
1956 3103 4.342359 TCGGGGGAAGTAGCTAATATCTC 58.658 47.826 0.00 0.00 0.00 2.75
1959 3106 5.892119 CGGGGGAAGTAGCTAATATCTCATA 59.108 44.000 0.00 0.00 0.00 2.15
1961 3108 7.470702 CGGGGGAAGTAGCTAATATCTCATATG 60.471 44.444 0.00 0.00 0.00 1.78
1963 3110 8.982723 GGGGAAGTAGCTAATATCTCATATGAA 58.017 37.037 6.90 0.00 0.00 2.57
2033 3192 4.493547 ACATTTTTGCCATACATGAACGG 58.506 39.130 0.00 0.00 0.00 4.44
2082 3243 8.185506 TGGTGACTACTCTCTGTAAACAAATA 57.814 34.615 0.00 0.00 0.00 1.40
2197 3358 1.434555 TCGTGCAAACTGAATACCCG 58.565 50.000 0.00 0.00 0.00 5.28
2198 3359 0.446222 CGTGCAAACTGAATACCCGG 59.554 55.000 0.00 0.00 0.00 5.73
2199 3360 0.808755 GTGCAAACTGAATACCCGGG 59.191 55.000 22.25 22.25 0.00 5.73
2203 3364 1.212250 AAACTGAATACCCGGGGGCT 61.212 55.000 27.92 7.99 39.32 5.19
2218 3379 3.497763 CGGGGGCTGTATAATGATTTCCA 60.498 47.826 0.00 0.00 0.00 3.53
2272 3433 0.179171 GCATCTGACACATGCAGCAC 60.179 55.000 10.45 0.00 45.19 4.40
2309 3470 4.144297 ACACATGCAATTAACCACTCACT 58.856 39.130 0.00 0.00 0.00 3.41
2319 3480 7.521423 GCAATTAACCACTCACTCATTACAACA 60.521 37.037 0.00 0.00 0.00 3.33
2321 3482 4.689612 ACCACTCACTCATTACAACAGT 57.310 40.909 0.00 0.00 0.00 3.55
2348 3509 3.488778 CAGCATGCTCCTCTCCTTATT 57.511 47.619 19.68 0.00 0.00 1.40
2349 3510 3.818180 CAGCATGCTCCTCTCCTTATTT 58.182 45.455 19.68 0.00 0.00 1.40
2350 3511 3.564644 CAGCATGCTCCTCTCCTTATTTG 59.435 47.826 19.68 0.00 0.00 2.32
2351 3512 2.292845 GCATGCTCCTCTCCTTATTTGC 59.707 50.000 11.37 0.00 0.00 3.68
2352 3513 3.548770 CATGCTCCTCTCCTTATTTGCA 58.451 45.455 0.00 0.00 0.00 4.08
2353 3514 2.991250 TGCTCCTCTCCTTATTTGCAC 58.009 47.619 0.00 0.00 0.00 4.57
2354 3515 2.293170 GCTCCTCTCCTTATTTGCACC 58.707 52.381 0.00 0.00 0.00 5.01
2355 3516 2.356125 GCTCCTCTCCTTATTTGCACCA 60.356 50.000 0.00 0.00 0.00 4.17
2356 3517 3.274288 CTCCTCTCCTTATTTGCACCAC 58.726 50.000 0.00 0.00 0.00 4.16
2357 3518 2.009774 CCTCTCCTTATTTGCACCACG 58.990 52.381 0.00 0.00 0.00 4.94
2358 3519 2.615493 CCTCTCCTTATTTGCACCACGT 60.615 50.000 0.00 0.00 0.00 4.49
2359 3520 3.074412 CTCTCCTTATTTGCACCACGTT 58.926 45.455 0.00 0.00 0.00 3.99
2413 3577 1.432807 TCCCCTGCCCAATTTTCTTCT 59.567 47.619 0.00 0.00 0.00 2.85
2421 3585 6.261826 CCTGCCCAATTTTCTTCTACTCTATG 59.738 42.308 0.00 0.00 0.00 2.23
2473 11231 3.193479 ACACACACTCTAGCATCGAATCA 59.807 43.478 0.00 0.00 0.00 2.57
2483 11241 1.681780 GCATCGAATCAACCCCTTCCA 60.682 52.381 0.00 0.00 0.00 3.53
2533 11291 0.908198 GCTCTCCACCACCTTCATCT 59.092 55.000 0.00 0.00 0.00 2.90
2534 11292 1.134551 GCTCTCCACCACCTTCATCTC 60.135 57.143 0.00 0.00 0.00 2.75
2535 11293 2.182827 CTCTCCACCACCTTCATCTCA 58.817 52.381 0.00 0.00 0.00 3.27
2536 11294 1.902508 TCTCCACCACCTTCATCTCAC 59.097 52.381 0.00 0.00 0.00 3.51
2537 11295 0.608130 TCCACCACCTTCATCTCACG 59.392 55.000 0.00 0.00 0.00 4.35
2538 11296 0.321671 CCACCACCTTCATCTCACGT 59.678 55.000 0.00 0.00 0.00 4.49
2539 11297 1.673033 CCACCACCTTCATCTCACGTC 60.673 57.143 0.00 0.00 0.00 4.34
2540 11298 1.000843 CACCACCTTCATCTCACGTCA 59.999 52.381 0.00 0.00 0.00 4.35
2541 11299 1.273606 ACCACCTTCATCTCACGTCAG 59.726 52.381 0.00 0.00 0.00 3.51
2542 11300 1.273606 CCACCTTCATCTCACGTCAGT 59.726 52.381 0.00 0.00 0.00 3.41
2583 11343 1.643286 ACCTCCCTCTCATCACTCTCA 59.357 52.381 0.00 0.00 0.00 3.27
2584 11344 2.309613 CCTCCCTCTCATCACTCTCAG 58.690 57.143 0.00 0.00 0.00 3.35
2596 11356 0.600557 ACTCTCAGTGCTCTGGTTCG 59.399 55.000 15.39 5.16 41.59 3.95
2609 11369 1.890510 GGTTCGTTTCGGGCACTGT 60.891 57.895 0.00 0.00 35.30 3.55
2616 11376 0.400213 TTTCGGGCACTGTCCTCAAT 59.600 50.000 0.00 0.00 35.30 2.57
2619 11379 1.077429 GGGCACTGTCCTCAATCCC 60.077 63.158 0.00 0.00 0.00 3.85
2644 11404 5.586643 GGGAGGAATTTCTACAAGTGTGATC 59.413 44.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.215160 TCGAGTTTGTAAAGTAGACGGTTC 58.785 41.667 0.00 0.00 0.00 3.62
71 72 2.711009 TCAGGGTTGATTCTTGTCTGGT 59.289 45.455 0.00 0.00 0.00 4.00
232 233 9.505995 GTCAAAATAAGTTAAAAAGACGGTTGA 57.494 29.630 0.00 0.00 0.00 3.18
270 271 1.833630 CAACCCTGGATGCTGACTAGA 59.166 52.381 0.00 0.00 0.00 2.43
296 297 4.818534 TTCTGAATTGCCGCAATATCTC 57.181 40.909 18.80 13.11 32.43 2.75
300 301 5.588246 TGAACTATTCTGAATTGCCGCAATA 59.412 36.000 18.80 3.54 32.43 1.90
322 323 9.767684 CGCATTGTCAAAATAAGTTAATAGTGA 57.232 29.630 0.00 0.00 0.00 3.41
323 324 9.554724 ACGCATTGTCAAAATAAGTTAATAGTG 57.445 29.630 0.00 0.00 0.00 2.74
329 330 7.589587 CACTGAACGCATTGTCAAAATAAGTTA 59.410 33.333 0.00 0.00 0.00 2.24
335 336 3.552684 CCCACTGAACGCATTGTCAAAAT 60.553 43.478 0.00 0.00 0.00 1.82
337 338 1.336440 CCCACTGAACGCATTGTCAAA 59.664 47.619 0.00 0.00 0.00 2.69
340 341 1.197721 CTTCCCACTGAACGCATTGTC 59.802 52.381 0.00 0.00 0.00 3.18
342 343 1.522668 TCTTCCCACTGAACGCATTG 58.477 50.000 0.00 0.00 0.00 2.82
345 346 0.396435 ACATCTTCCCACTGAACGCA 59.604 50.000 0.00 0.00 0.00 5.24
347 348 2.455674 TGACATCTTCCCACTGAACG 57.544 50.000 0.00 0.00 0.00 3.95
348 349 4.583871 AGATTGACATCTTCCCACTGAAC 58.416 43.478 0.00 0.00 36.18 3.18
359 1399 7.813627 CGATACATCATCTTGAGATTGACATCT 59.186 37.037 0.90 0.00 43.03 2.90
369 1409 5.777802 ACTTAGCCGATACATCATCTTGAG 58.222 41.667 0.00 0.00 0.00 3.02
382 1422 4.739137 GCATCTCTGAAAGACTTAGCCGAT 60.739 45.833 0.00 0.00 38.67 4.18
389 1429 5.424895 ACCTATGAGCATCTCTGAAAGACTT 59.575 40.000 0.00 0.00 38.67 3.01
398 1438 4.191804 ACCTACACCTATGAGCATCTCT 57.808 45.455 0.00 0.00 34.92 3.10
399 1439 4.100189 ACAACCTACACCTATGAGCATCTC 59.900 45.833 0.00 0.00 34.92 2.75
418 1458 2.981805 TCTATGAACACGCACGTACAAC 59.018 45.455 0.00 0.00 0.00 3.32
423 1463 0.601558 ACCTCTATGAACACGCACGT 59.398 50.000 0.00 0.00 0.00 4.49
443 1485 4.537965 CTCATACATACGCACCTACACTC 58.462 47.826 0.00 0.00 0.00 3.51
450 1492 2.797156 CAGAAGCTCATACATACGCACC 59.203 50.000 0.00 0.00 0.00 5.01
451 1493 2.219674 GCAGAAGCTCATACATACGCAC 59.780 50.000 0.00 0.00 37.91 5.34
473 1515 9.646336 CTATTCTTTTTAACACAGTACACACAC 57.354 33.333 0.00 0.00 0.00 3.82
474 1516 8.339714 GCTATTCTTTTTAACACAGTACACACA 58.660 33.333 0.00 0.00 0.00 3.72
535 1579 2.357517 AGGAACTGCGCTGTTCGG 60.358 61.111 37.34 14.24 45.11 4.30
565 1609 2.156917 CTCTGCTGCTTCCATTTGTGA 58.843 47.619 0.00 0.00 0.00 3.58
591 1635 1.784062 CTCTTCGGTTCAAGCTGCG 59.216 57.895 0.00 0.00 0.00 5.18
617 1661 1.154454 ATGCCCATCCGCATCCATT 59.846 52.632 0.00 0.00 46.55 3.16
618 1662 2.848784 ATGCCCATCCGCATCCAT 59.151 55.556 0.00 0.00 46.55 3.41
682 1726 2.335011 GGGTTCTGGCGTTTGTGC 59.665 61.111 0.00 0.00 0.00 4.57
725 1771 2.035626 CACCATTTGGCCTCGGGT 59.964 61.111 3.32 3.46 39.32 5.28
726 1772 3.451894 GCACCATTTGGCCTCGGG 61.452 66.667 3.32 2.73 39.32 5.14
747 1793 0.802607 GGGTTGTCGCTGTCGAGATC 60.803 60.000 0.00 0.00 46.46 2.75
763 1809 3.665675 GATGACGCGCAGAAGGGGT 62.666 63.158 5.73 0.00 0.00 4.95
770 1816 2.082437 GAACCGATGATGACGCGCAG 62.082 60.000 5.73 2.42 0.00 5.18
771 1817 2.125713 AACCGATGATGACGCGCA 60.126 55.556 5.73 5.73 0.00 6.09
772 1818 2.621000 GAACCGATGATGACGCGC 59.379 61.111 5.73 0.00 0.00 6.86
773 1819 1.209275 GAGGAACCGATGATGACGCG 61.209 60.000 3.53 3.53 0.00 6.01
774 1820 0.179111 TGAGGAACCGATGATGACGC 60.179 55.000 0.00 0.00 0.00 5.19
775 1821 1.135139 AGTGAGGAACCGATGATGACG 59.865 52.381 0.00 0.00 0.00 4.35
776 1822 2.093973 ACAGTGAGGAACCGATGATGAC 60.094 50.000 0.00 0.00 0.00 3.06
777 1823 2.166459 GACAGTGAGGAACCGATGATGA 59.834 50.000 0.00 0.00 0.00 2.92
778 1824 2.167281 AGACAGTGAGGAACCGATGATG 59.833 50.000 0.00 0.00 0.00 3.07
779 1825 2.167281 CAGACAGTGAGGAACCGATGAT 59.833 50.000 0.00 0.00 0.00 2.45
780 1826 1.546029 CAGACAGTGAGGAACCGATGA 59.454 52.381 0.00 0.00 0.00 2.92
781 1827 1.273606 ACAGACAGTGAGGAACCGATG 59.726 52.381 0.00 0.00 0.00 3.84
782 1828 1.546476 GACAGACAGTGAGGAACCGAT 59.454 52.381 0.00 0.00 0.00 4.18
783 1829 0.959553 GACAGACAGTGAGGAACCGA 59.040 55.000 0.00 0.00 0.00 4.69
784 1830 0.673985 TGACAGACAGTGAGGAACCG 59.326 55.000 0.00 0.00 0.00 4.44
797 1863 2.068519 CTAAAGTGCGTGCATGACAGA 58.931 47.619 10.93 0.00 0.00 3.41
817 1883 2.435410 CGGCGGTTTACTGGGTCC 60.435 66.667 0.00 0.00 0.00 4.46
908 2003 2.282110 TGGTGGTGCCATTGTCCG 60.282 61.111 0.00 0.00 43.61 4.79
929 2027 0.950555 GTGGAATCGCAGTGTGCTGA 60.951 55.000 0.00 0.00 45.28 4.26
930 2028 1.499056 GTGGAATCGCAGTGTGCTG 59.501 57.895 0.00 0.00 42.25 4.41
931 2029 2.029288 CGTGGAATCGCAGTGTGCT 61.029 57.895 0.00 0.00 42.25 4.40
952 2050 1.527433 GCTCTTCCCTGGTGTTTGGC 61.527 60.000 0.00 0.00 0.00 4.52
971 2074 0.164647 GCTTACACGAGCTGCAACTG 59.835 55.000 1.02 0.00 39.57 3.16
984 2087 1.136305 GCCATCGGTCAGTAGCTTACA 59.864 52.381 0.00 0.00 0.00 2.41
1011 2148 2.203112 TGGAGCATCATGGAGCGC 60.203 61.111 0.00 0.00 36.25 5.92
1378 2515 2.501610 GACCATGACCTCGCCCTC 59.498 66.667 0.00 0.00 0.00 4.30
1719 2856 3.378042 CACGCACGCACGCAAAAG 61.378 61.111 0.00 0.00 36.19 2.27
1729 2866 1.614227 AATACTCACACGCACGCACG 61.614 55.000 0.00 0.00 39.50 5.34
1730 2867 0.093026 GAATACTCACACGCACGCAC 59.907 55.000 0.00 0.00 0.00 5.34
1733 2870 1.057285 GAACGAATACTCACACGCACG 59.943 52.381 0.00 0.00 0.00 5.34
1737 2874 4.364817 AAAACGAACGAATACTCACACG 57.635 40.909 0.14 0.00 0.00 4.49
1828 2971 1.929836 GAGGCACAAGAGCGAAGTATG 59.070 52.381 0.00 0.00 34.64 2.39
1837 2983 3.431486 GGATGGAGTAAGAGGCACAAGAG 60.431 52.174 0.00 0.00 0.00 2.85
1848 2994 3.838244 TTTGGGATCGGATGGAGTAAG 57.162 47.619 0.00 0.00 0.00 2.34
1854 3000 1.750778 CCACTTTTTGGGATCGGATGG 59.249 52.381 0.00 0.00 42.54 3.51
1865 3011 1.841450 TAAAACCGCGCCACTTTTTG 58.159 45.000 0.00 0.00 0.00 2.44
1866 3012 2.580966 TTAAAACCGCGCCACTTTTT 57.419 40.000 0.00 5.04 0.00 1.94
1871 3017 3.760537 TCATAATTTAAAACCGCGCCAC 58.239 40.909 0.00 0.00 0.00 5.01
1872 3018 4.640789 ATCATAATTTAAAACCGCGCCA 57.359 36.364 0.00 0.00 0.00 5.69
1873 3019 5.038033 TCAATCATAATTTAAAACCGCGCC 58.962 37.500 0.00 0.00 0.00 6.53
1874 3020 6.561945 TTCAATCATAATTTAAAACCGCGC 57.438 33.333 0.00 0.00 0.00 6.86
1898 3045 9.538508 AGTGTCGTAGTTTTGAACTAAGTTTAT 57.461 29.630 11.57 0.00 44.95 1.40
1915 3062 5.006358 CCCCGATTCAAAATAAGTGTCGTAG 59.994 44.000 0.00 0.00 0.00 3.51
1917 3064 3.687698 CCCCGATTCAAAATAAGTGTCGT 59.312 43.478 0.00 0.00 0.00 4.34
1919 3066 4.266714 TCCCCCGATTCAAAATAAGTGTC 58.733 43.478 0.00 0.00 0.00 3.67
1921 3068 4.705023 ACTTCCCCCGATTCAAAATAAGTG 59.295 41.667 0.00 0.00 0.00 3.16
1932 3079 5.342866 AGATATTAGCTACTTCCCCCGATT 58.657 41.667 0.00 0.00 0.00 3.34
1935 3082 4.087182 TGAGATATTAGCTACTTCCCCCG 58.913 47.826 0.00 0.00 0.00 5.73
1937 3084 8.540507 TCATATGAGATATTAGCTACTTCCCC 57.459 38.462 0.00 0.00 0.00 4.81
2008 3167 6.756074 CCGTTCATGTATGGCAAAAATGTTAT 59.244 34.615 0.00 0.00 0.00 1.89
2010 3169 4.928615 CCGTTCATGTATGGCAAAAATGTT 59.071 37.500 0.00 0.00 0.00 2.71
2033 3192 7.095607 CCATTCGTTTGCTGATAGGTCTAATAC 60.096 40.741 0.00 0.00 0.00 1.89
2105 3266 6.087820 GTCCACTCGTGATTATTCGCTATAAC 59.912 42.308 0.00 0.00 31.69 1.89
2108 3269 4.037565 TGTCCACTCGTGATTATTCGCTAT 59.962 41.667 0.00 0.00 0.00 2.97
2122 3283 4.758251 TGGCCGCATGTCCACTCG 62.758 66.667 0.00 0.00 0.00 4.18
2197 3358 4.112634 TGGAAATCATTATACAGCCCCC 57.887 45.455 0.00 0.00 0.00 5.40
2198 3359 5.574188 AGATGGAAATCATTATACAGCCCC 58.426 41.667 0.00 0.00 35.97 5.80
2199 3360 6.150140 GTGAGATGGAAATCATTATACAGCCC 59.850 42.308 0.00 0.00 35.97 5.19
2218 3379 8.420222 GCTATACTGAATGCTATATGGTGAGAT 58.580 37.037 0.00 0.00 0.00 2.75
2309 3470 5.244755 TGCTGCAGATAACTGTTGTAATGA 58.755 37.500 20.43 0.00 45.04 2.57
2344 3505 4.339814 AGGAGAAAAACGTGGTGCAAATAA 59.660 37.500 0.00 0.00 0.00 1.40
2345 3506 3.886505 AGGAGAAAAACGTGGTGCAAATA 59.113 39.130 0.00 0.00 0.00 1.40
2346 3507 2.693074 AGGAGAAAAACGTGGTGCAAAT 59.307 40.909 0.00 0.00 0.00 2.32
2347 3508 2.096248 AGGAGAAAAACGTGGTGCAAA 58.904 42.857 0.00 0.00 0.00 3.68
2348 3509 1.673920 GAGGAGAAAAACGTGGTGCAA 59.326 47.619 0.00 0.00 0.00 4.08
2349 3510 1.134220 AGAGGAGAAAAACGTGGTGCA 60.134 47.619 0.00 0.00 0.00 4.57
2350 3511 1.594331 AGAGGAGAAAAACGTGGTGC 58.406 50.000 0.00 0.00 0.00 5.01
2351 3512 5.744666 TTAAAGAGGAGAAAAACGTGGTG 57.255 39.130 0.00 0.00 0.00 4.17
2352 3513 6.544564 TGATTTAAAGAGGAGAAAAACGTGGT 59.455 34.615 0.00 0.00 0.00 4.16
2353 3514 6.856426 GTGATTTAAAGAGGAGAAAAACGTGG 59.144 38.462 0.00 0.00 0.00 4.94
2354 3515 7.639945 AGTGATTTAAAGAGGAGAAAAACGTG 58.360 34.615 0.00 0.00 0.00 4.49
2355 3516 7.715686 AGAGTGATTTAAAGAGGAGAAAAACGT 59.284 33.333 0.00 0.00 0.00 3.99
2356 3517 8.012241 CAGAGTGATTTAAAGAGGAGAAAAACG 58.988 37.037 0.00 0.00 0.00 3.60
2357 3518 8.293157 CCAGAGTGATTTAAAGAGGAGAAAAAC 58.707 37.037 0.00 0.00 0.00 2.43
2358 3519 7.040409 GCCAGAGTGATTTAAAGAGGAGAAAAA 60.040 37.037 0.00 0.00 0.00 1.94
2359 3520 6.431234 GCCAGAGTGATTTAAAGAGGAGAAAA 59.569 38.462 0.00 0.00 0.00 2.29
2413 3577 6.077993 AGAGAGAGAGAGAGAGCATAGAGTA 58.922 44.000 0.00 0.00 0.00 2.59
2421 3585 3.386078 TGAGAGAGAGAGAGAGAGAGAGC 59.614 52.174 0.00 0.00 0.00 4.09
2473 11231 0.560688 ACATGGTTGTGGAAGGGGTT 59.439 50.000 0.00 0.00 33.85 4.11
2483 11241 3.499338 ACATGGATGAACACATGGTTGT 58.501 40.909 9.17 0.00 46.60 3.32
2536 11294 8.287941 CAAACTATTGGACATGACGACTGACG 62.288 46.154 0.00 0.00 39.23 4.35
2537 11295 4.111375 ACTATTGGACATGACGACTGAC 57.889 45.455 0.00 0.00 0.00 3.51
2538 11296 4.801330 AACTATTGGACATGACGACTGA 57.199 40.909 0.00 0.00 0.00 3.41
2539 11297 4.436050 GCAAACTATTGGACATGACGACTG 60.436 45.833 0.00 0.00 37.02 3.51
2540 11298 3.684788 GCAAACTATTGGACATGACGACT 59.315 43.478 0.00 0.00 37.02 4.18
2541 11299 3.435327 TGCAAACTATTGGACATGACGAC 59.565 43.478 0.00 0.00 37.02 4.34
2542 11300 3.669536 TGCAAACTATTGGACATGACGA 58.330 40.909 0.00 0.00 37.02 4.20
2583 11343 0.600255 CCGAAACGAACCAGAGCACT 60.600 55.000 0.00 0.00 0.00 4.40
2584 11344 1.566018 CCCGAAACGAACCAGAGCAC 61.566 60.000 0.00 0.00 0.00 4.40
2596 11356 0.534203 TTGAGGACAGTGCCCGAAAC 60.534 55.000 0.00 0.00 0.00 2.78
2616 11376 2.257391 TGTAGAAATTCCTCCCGGGA 57.743 50.000 25.06 25.06 43.41 5.14
2619 11379 3.684788 CACACTTGTAGAAATTCCTCCCG 59.315 47.826 0.00 0.00 0.00 5.14
2628 11388 3.394674 TGGCGATCACACTTGTAGAAA 57.605 42.857 0.00 0.00 0.00 2.52
2644 11404 4.591202 GAATATGAACTCACAACATGGCG 58.409 43.478 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.