Multiple sequence alignment - TraesCS6D01G389500

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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 TraesCS6D01G389500 chr6D 100.000 3436 0 0 1 3436 465012650 465009215 0.000000e+00 6346.0
1 TraesCS6D01G389500 chr6D 91.660 1259 65 16 526 1768 464983915 464985149 0.000000e+00 1707.0
2 TraesCS6D01G389500 chr6D 87.970 266 21 5 534 794 101397942 101397683 1.550000e-78 303.0
3 TraesCS6D01G389500 chr6D 95.364 151 7 0 1846 1996 464985273 464985423 1.230000e-59 241.0
4 TraesCS6D01G389500 chr6D 91.279 172 10 4 363 533 101398217 101398050 2.670000e-56 230.0
5 TraesCS6D01G389500 chr6D 97.414 116 2 1 2126 2241 464985535 464985649 2.710000e-46 196.0
6 TraesCS6D01G389500 chr6D 84.091 132 11 5 1 131 464982660 464982782 6.020000e-23 119.0
7 TraesCS6D01G389500 chr6A 87.395 2610 196 65 899 3435 611523414 611520865 0.000000e+00 2874.0
8 TraesCS6D01G389500 chr6A 91.767 1251 78 13 526 1770 611512732 611513963 0.000000e+00 1716.0
9 TraesCS6D01G389500 chr6A 84.220 564 31 28 3 535 611524436 611523900 2.380000e-136 496.0
10 TraesCS6D01G389500 chr6A 84.691 405 36 14 1846 2250 611514080 611514458 6.960000e-102 381.0
11 TraesCS6D01G389500 chr6A 90.909 143 12 1 656 798 611523737 611523596 1.260000e-44 191.0
12 TraesCS6D01G389500 chr6B 91.161 1482 83 29 551 1996 708988247 708989716 0.000000e+00 1967.0
13 TraesCS6D01G389500 chr6B 93.463 1025 46 13 980 1996 709020831 709019820 0.000000e+00 1502.0
14 TraesCS6D01G389500 chr6B 84.786 1124 110 24 2314 3420 709015790 709014711 0.000000e+00 1072.0
15 TraesCS6D01G389500 chr6B 89.087 504 33 12 1 492 709022036 709021543 1.050000e-169 606.0
16 TraesCS6D01G389500 chr6B 89.865 444 33 7 2126 2559 709019741 709019300 8.330000e-156 560.0
17 TraesCS6D01G389500 chr6B 86.486 518 51 7 2345 2854 709017250 709016744 5.010000e-153 551.0
18 TraesCS6D01G389500 chr6B 89.259 270 22 4 534 798 709021391 709021124 7.110000e-87 331.0
19 TraesCS6D01G389500 chr6B 95.726 117 5 0 2125 2241 708989818 708989934 4.530000e-44 189.0
20 TraesCS6D01G389500 chr5D 89.049 831 70 13 949 1771 287571904 287571087 0.000000e+00 1011.0
21 TraesCS6D01G389500 chr5D 87.500 264 16 7 289 535 321682829 321682566 4.340000e-74 289.0
22 TraesCS6D01G389500 chr5D 92.157 153 12 0 1846 1998 287571007 287570855 2.080000e-52 217.0
23 TraesCS6D01G389500 chr5D 92.857 112 7 1 2130 2240 287570755 287570644 9.870000e-36 161.0
24 TraesCS6D01G389500 chr5D 89.091 55 5 1 2120 2174 556272823 556272770 2.210000e-07 67.6
25 TraesCS6D01G389500 chr5B 87.813 878 74 19 899 1771 326613046 326612197 0.000000e+00 998.0
26 TraesCS6D01G389500 chr5B 92.157 153 12 0 1846 1998 326612110 326611958 2.080000e-52 217.0
27 TraesCS6D01G389500 chr5B 93.750 112 6 1 2130 2240 326611867 326611756 2.120000e-37 167.0
28 TraesCS6D01G389500 chr5A 86.961 882 81 19 899 1771 379401700 379400844 0.000000e+00 961.0
29 TraesCS6D01G389500 chr5A 77.635 389 81 6 1381 1766 143552720 143552335 7.420000e-57 231.0
30 TraesCS6D01G389500 chr5A 92.810 153 11 0 1846 1998 379400765 379400613 4.460000e-54 222.0
31 TraesCS6D01G389500 chr5A 92.105 114 6 2 2116 2229 379400523 379400413 1.280000e-34 158.0
32 TraesCS6D01G389500 chr3B 77.267 739 141 21 2624 3343 62306250 62305520 3.190000e-110 409.0
33 TraesCS6D01G389500 chr3D 77.100 738 143 18 2624 3343 569835889 569835160 1.490000e-108 403.0
34 TraesCS6D01G389500 chr3D 76.398 733 149 18 2626 3340 27763026 27763752 1.160000e-99 374.0
35 TraesCS6D01G389500 chr3D 89.177 231 22 3 553 782 478336679 478336451 5.610000e-73 285.0
36 TraesCS6D01G389500 chr1D 76.892 740 148 17 2618 3340 421874390 421875123 6.910000e-107 398.0
37 TraesCS6D01G389500 chr1D 90.530 264 18 4 536 794 339905919 339906180 3.280000e-90 342.0
38 TraesCS6D01G389500 chr1D 86.842 266 18 10 286 535 113493779 113493515 7.260000e-72 281.0
39 TraesCS6D01G389500 chr1D 91.979 187 15 0 349 535 339905628 339905814 2.630000e-66 263.0
40 TraesCS6D01G389500 chr1D 94.737 38 2 0 304 341 339905567 339905604 3.700000e-05 60.2
41 TraesCS6D01G389500 chr2B 76.558 738 146 20 2625 3343 417770851 417770122 2.500000e-101 379.0
42 TraesCS6D01G389500 chr7B 76.366 732 148 18 2625 3338 654009481 654010205 1.510000e-98 370.0
43 TraesCS6D01G389500 chr4A 75.806 744 153 18 2618 3340 677314290 677315027 5.460000e-93 351.0
44 TraesCS6D01G389500 chr2A 77.604 576 102 18 1217 1768 622853694 622853122 1.190000e-84 324.0
45 TraesCS6D01G389500 chr2D 84.967 306 44 2 1466 1770 519134361 519134057 3.330000e-80 309.0
46 TraesCS6D01G389500 chr4D 85.932 263 19 8 289 535 227829283 227829543 7.310000e-67 265.0
47 TraesCS6D01G389500 chr1A 85.375 253 19 7 534 781 234658782 234658543 2.650000e-61 246.0
48 TraesCS6D01G389500 chr1A 84.351 262 24 7 289 535 234659145 234658886 1.230000e-59 241.0
49 TraesCS6D01G389500 chr3A 84.980 253 20 7 534 781 58456637 58456876 1.230000e-59 241.0


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 TraesCS6D01G389500 chr6D 465009215 465012650 3435 True 6346.000000 6346 100.000000 1 3436 1 chr6D.!!$R1 3435
1 TraesCS6D01G389500 chr6D 464982660 464985649 2989 False 565.750000 1707 92.132250 1 2241 4 chr6D.!!$F1 2240
2 TraesCS6D01G389500 chr6D 101397683 101398217 534 True 266.500000 303 89.624500 363 794 2 chr6D.!!$R2 431
3 TraesCS6D01G389500 chr6A 611520865 611524436 3571 True 1187.000000 2874 87.508000 3 3435 3 chr6A.!!$R1 3432
4 TraesCS6D01G389500 chr6A 611512732 611514458 1726 False 1048.500000 1716 88.229000 526 2250 2 chr6A.!!$F1 1724
5 TraesCS6D01G389500 chr6B 708988247 708989934 1687 False 1078.000000 1967 93.443500 551 2241 2 chr6B.!!$F1 1690
6 TraesCS6D01G389500 chr6B 709014711 709022036 7325 True 770.333333 1502 88.824333 1 3420 6 chr6B.!!$R1 3419
7 TraesCS6D01G389500 chr5D 287570644 287571904 1260 True 463.000000 1011 91.354333 949 2240 3 chr5D.!!$R3 1291
8 TraesCS6D01G389500 chr5B 326611756 326613046 1290 True 460.666667 998 91.240000 899 2240 3 chr5B.!!$R1 1341
9 TraesCS6D01G389500 chr5A 379400413 379401700 1287 True 447.000000 961 90.625333 899 2229 3 chr5A.!!$R2 1330
10 TraesCS6D01G389500 chr3B 62305520 62306250 730 True 409.000000 409 77.267000 2624 3343 1 chr3B.!!$R1 719
11 TraesCS6D01G389500 chr3D 569835160 569835889 729 True 403.000000 403 77.100000 2624 3343 1 chr3D.!!$R2 719
12 TraesCS6D01G389500 chr3D 27763026 27763752 726 False 374.000000 374 76.398000 2626 3340 1 chr3D.!!$F1 714
13 TraesCS6D01G389500 chr1D 421874390 421875123 733 False 398.000000 398 76.892000 2618 3340 1 chr1D.!!$F1 722
14 TraesCS6D01G389500 chr1D 339905567 339906180 613 False 221.733333 342 92.415333 304 794 3 chr1D.!!$F2 490
15 TraesCS6D01G389500 chr2B 417770122 417770851 729 True 379.000000 379 76.558000 2625 3343 1 chr2B.!!$R1 718
16 TraesCS6D01G389500 chr7B 654009481 654010205 724 False 370.000000 370 76.366000 2625 3338 1 chr7B.!!$F1 713
17 TraesCS6D01G389500 chr4A 677314290 677315027 737 False 351.000000 351 75.806000 2618 3340 1 chr4A.!!$F1 722
18 TraesCS6D01G389500 chr2A 622853122 622853694 572 True 324.000000 324 77.604000 1217 1768 1 chr2A.!!$R1 551
19 TraesCS6D01G389500 chr1A 234658543 234659145 602 True 243.500000 246 84.863000 289 781 2 chr1A.!!$R1 492

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
678 1648 0.531753 GCTCTCTTTCGGCCCTCATC 60.532 60.000 0.0 0.0 0.0 2.92 F
1078 2217 1.205655 ACACACACATCATCTCCTCCG 59.794 52.381 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 3340 0.613260 TCTTCCTAAGCATGCACGGT 59.387 50.0 21.98 4.4 0.0 4.83 R
2805 7864 0.261991 TCTCCCTGACCGCCTTATCT 59.738 55.0 0.00 0.0 0.0 1.98 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
42 44 2.943978 CGGAGTTGGAGCGGAGGTT 61.944 63.158 0.00 0.00 39.88 3.50
214 235 0.737367 CATCGCCTCTCGCTGTCAAA 60.737 55.000 0.00 0.00 38.27 2.69
235 256 7.222611 GTCAAAGCCATAAACATATTGCGATTT 59.777 33.333 0.00 0.00 0.00 2.17
236 257 7.763528 TCAAAGCCATAAACATATTGCGATTTT 59.236 29.630 0.00 0.00 0.00 1.82
247 268 1.512734 GCGATTTTGCTGAGTGGCG 60.513 57.895 0.00 0.00 34.52 5.69
360 425 1.878948 GCTGTGCTGTTACCCCGTTAA 60.879 52.381 0.00 0.00 0.00 2.01
361 426 2.496111 CTGTGCTGTTACCCCGTTAAA 58.504 47.619 0.00 0.00 0.00 1.52
475 592 5.395768 GGAAGAGGGAGATCGAATTCTTTGA 60.396 44.000 3.52 0.00 0.00 2.69
489 611 7.754924 TCGAATTCTTTGAACCAAATTATCTGC 59.245 33.333 3.52 0.00 32.70 4.26
547 1514 1.271656 GCTGGGCTATGATTCATTGGC 59.728 52.381 20.95 20.95 40.17 4.52
678 1648 0.531753 GCTCTCTTTCGGCCCTCATC 60.532 60.000 0.00 0.00 0.00 2.92
689 1659 2.549754 CGGCCCTCATCATACAACAATC 59.450 50.000 0.00 0.00 0.00 2.67
710 1684 8.424133 ACAATCCAATTCAGATAAATTAAGCCC 58.576 33.333 0.00 0.00 0.00 5.19
725 1699 3.380471 AAGCCCACACATTATTAGCCA 57.620 42.857 0.00 0.00 0.00 4.75
798 1797 7.636326 CCGACTAAACCATTCAATACCATAAC 58.364 38.462 0.00 0.00 0.00 1.89
799 1798 7.281324 CCGACTAAACCATTCAATACCATAACA 59.719 37.037 0.00 0.00 0.00 2.41
830 1861 1.490490 AGGTGAGGTGACACAACACAT 59.510 47.619 24.77 19.38 41.56 3.21
930 2018 4.612264 ATCAAGAAGTGGCAGCAAAAAT 57.388 36.364 0.00 0.00 0.00 1.82
1045 2184 2.711009 TCCCTCTCCTCATCTCTCTCTC 59.289 54.545 0.00 0.00 0.00 3.20
1046 2185 2.713167 CCCTCTCCTCATCTCTCTCTCT 59.287 54.545 0.00 0.00 0.00 3.10
1047 2186 3.244700 CCCTCTCCTCATCTCTCTCTCTC 60.245 56.522 0.00 0.00 0.00 3.20
1048 2187 3.649981 CCTCTCCTCATCTCTCTCTCTCT 59.350 52.174 0.00 0.00 0.00 3.10
1049 2188 4.262808 CCTCTCCTCATCTCTCTCTCTCTC 60.263 54.167 0.00 0.00 0.00 3.20
1050 2189 4.560739 TCTCCTCATCTCTCTCTCTCTCT 58.439 47.826 0.00 0.00 0.00 3.10
1051 2190 4.590647 TCTCCTCATCTCTCTCTCTCTCTC 59.409 50.000 0.00 0.00 0.00 3.20
1052 2191 4.297768 TCCTCATCTCTCTCTCTCTCTCA 58.702 47.826 0.00 0.00 0.00 3.27
1054 2193 4.141642 CCTCATCTCTCTCTCTCTCTCACA 60.142 50.000 0.00 0.00 0.00 3.58
1078 2217 1.205655 ACACACACATCATCTCCTCCG 59.794 52.381 0.00 0.00 0.00 4.63
1858 3117 1.477553 TGAAATTGCAGATCCTGGCC 58.522 50.000 0.00 0.00 31.21 5.36
1885 3144 1.418342 CGATCGGATTCGCGGTGTTT 61.418 55.000 7.38 0.00 36.13 2.83
2005 3305 6.540914 GGGACGACCATGTAAGAATCAATTTA 59.459 38.462 6.20 0.00 39.85 1.40
2035 3340 9.816354 TCAATCATTCATCAGTTAATTACTCGA 57.184 29.630 0.00 0.00 33.85 4.04
2036 3341 9.855361 CAATCATTCATCAGTTAATTACTCGAC 57.145 33.333 0.00 0.00 33.85 4.20
2037 3342 8.594881 ATCATTCATCAGTTAATTACTCGACC 57.405 34.615 0.00 0.00 33.85 4.79
2038 3343 6.695713 TCATTCATCAGTTAATTACTCGACCG 59.304 38.462 0.00 0.00 33.85 4.79
2039 3344 5.571784 TCATCAGTTAATTACTCGACCGT 57.428 39.130 0.00 0.00 33.85 4.83
2040 3345 5.337554 TCATCAGTTAATTACTCGACCGTG 58.662 41.667 0.00 0.00 33.85 4.94
2041 3346 3.504863 TCAGTTAATTACTCGACCGTGC 58.495 45.455 0.00 0.00 33.85 5.34
2042 3347 3.057386 TCAGTTAATTACTCGACCGTGCA 60.057 43.478 0.00 0.00 33.85 4.57
2043 3348 3.863424 CAGTTAATTACTCGACCGTGCAT 59.137 43.478 0.00 0.00 33.85 3.96
2044 3349 3.863424 AGTTAATTACTCGACCGTGCATG 59.137 43.478 0.00 0.00 28.23 4.06
2045 3350 1.006832 AATTACTCGACCGTGCATGC 58.993 50.000 11.82 11.82 0.00 4.06
2046 3351 0.175760 ATTACTCGACCGTGCATGCT 59.824 50.000 20.33 0.00 0.00 3.79
2047 3352 0.037697 TTACTCGACCGTGCATGCTT 60.038 50.000 20.33 0.00 0.00 3.91
2048 3353 0.812549 TACTCGACCGTGCATGCTTA 59.187 50.000 20.33 0.00 0.00 3.09
2049 3354 0.458543 ACTCGACCGTGCATGCTTAG 60.459 55.000 20.33 9.47 0.00 2.18
2050 3355 1.148157 CTCGACCGTGCATGCTTAGG 61.148 60.000 20.33 20.06 0.00 2.69
2051 3356 1.153647 CGACCGTGCATGCTTAGGA 60.154 57.895 25.57 2.29 0.00 2.94
2052 3357 0.739462 CGACCGTGCATGCTTAGGAA 60.739 55.000 25.57 1.58 0.00 3.36
2053 3358 1.009829 GACCGTGCATGCTTAGGAAG 58.990 55.000 25.57 7.18 0.00 3.46
2054 3359 0.613260 ACCGTGCATGCTTAGGAAGA 59.387 50.000 25.57 0.15 0.00 2.87
2055 3360 1.003118 ACCGTGCATGCTTAGGAAGAA 59.997 47.619 25.57 0.00 0.00 2.52
2056 3361 2.292267 CCGTGCATGCTTAGGAAGAAT 58.708 47.619 20.33 0.00 0.00 2.40
2057 3362 2.289002 CCGTGCATGCTTAGGAAGAATC 59.711 50.000 20.33 0.00 0.00 2.52
2058 3363 2.938451 CGTGCATGCTTAGGAAGAATCA 59.062 45.455 20.33 0.00 0.00 2.57
2059 3364 3.374988 CGTGCATGCTTAGGAAGAATCAA 59.625 43.478 20.33 0.00 0.00 2.57
2060 3365 4.142622 CGTGCATGCTTAGGAAGAATCAAA 60.143 41.667 20.33 0.00 0.00 2.69
2061 3366 5.338365 GTGCATGCTTAGGAAGAATCAAAG 58.662 41.667 20.33 0.00 0.00 2.77
2094 3399 4.271661 TGATCATGCATGTTTTGGAGCTA 58.728 39.130 25.43 3.20 0.00 3.32
2115 3426 6.430925 AGCTAGCTAGAGACTAATCAGTGATG 59.569 42.308 25.15 0.00 34.21 3.07
2117 3428 7.255451 GCTAGCTAGAGACTAATCAGTGATGTT 60.255 40.741 25.15 0.00 34.21 2.71
2122 3433 7.678947 AGAGACTAATCAGTGATGTTTTTGG 57.321 36.000 6.34 0.00 34.21 3.28
2123 3434 6.150140 AGAGACTAATCAGTGATGTTTTTGGC 59.850 38.462 6.34 0.00 34.21 4.52
2128 3439 4.933505 TCAGTGATGTTTTTGGCATTGA 57.066 36.364 0.00 0.00 0.00 2.57
2257 3570 1.134699 TCAATCTGCCGACTGTGGATC 60.135 52.381 0.00 0.00 0.00 3.36
2278 3591 4.119862 TCGAGTCTTCTTGTTTCTGTTGG 58.880 43.478 0.00 0.00 0.00 3.77
2307 3621 7.383102 TCTCCTTGCTCTTGAAATGTATTTC 57.617 36.000 9.78 9.78 44.83 2.17
2316 3630 8.800332 GCTCTTGAAATGTATTTCCCATCATAT 58.200 33.333 13.19 0.00 44.16 1.78
2387 5972 6.197981 CAAATTTGCAAAGCACGGTAAAATT 58.802 32.000 18.19 0.00 38.71 1.82
2463 6048 8.809468 AATTCCTGGTAAATCTTAAAGGTCTC 57.191 34.615 0.00 0.00 0.00 3.36
2485 6077 6.215841 TCTCTGTGGGGTTTTATAACATGGTA 59.784 38.462 0.00 0.00 35.92 3.25
2515 6107 8.934023 ATTTAGTACCAACCTGATTTTGAAGA 57.066 30.769 0.00 0.00 0.00 2.87
2549 6141 8.207545 AGACCAAAATATAAGAGCAACTCTAGG 58.792 37.037 0.00 0.00 40.28 3.02
2579 6183 4.260194 GTCGTATTCGCAGTCGCTATATTC 59.740 45.833 0.00 0.00 36.96 1.75
2611 6215 7.309438 GGAGAGTTGAGACCAAAATTGCTAATT 60.309 37.037 0.00 0.00 33.49 1.40
2701 6306 3.822167 ACAATGAAACCGAACCCGTTTAT 59.178 39.130 0.00 0.00 0.00 1.40
2725 7778 5.298276 TGGATGTTCACTTTAAGTGTTGGTC 59.702 40.000 22.36 16.05 46.03 4.02
2751 7808 2.440539 AACTGTCTTGTGGCTACGAG 57.559 50.000 11.16 11.16 39.31 4.18
2799 7858 1.753073 CCCAACAGAATGATTGCTCCC 59.247 52.381 0.00 0.00 39.69 4.30
2802 7861 2.947652 CAACAGAATGATTGCTCCCGAT 59.052 45.455 0.00 0.00 39.69 4.18
2805 7864 3.208594 CAGAATGATTGCTCCCGATCAA 58.791 45.455 0.00 0.00 43.34 2.57
2808 7867 3.784511 ATGATTGCTCCCGATCAAGAT 57.215 42.857 0.00 0.00 43.34 2.40
2815 7874 0.679505 TCCCGATCAAGATAAGGCGG 59.320 55.000 0.00 0.00 38.54 6.13
2851 7910 0.523072 CATCTTTGTGGGAGCCGTTG 59.477 55.000 0.00 0.00 0.00 4.10
2891 7950 4.634184 AGCTAGTTGACACATACCTACG 57.366 45.455 0.00 0.00 0.00 3.51
2952 8011 0.532115 AATTTGGCTCAACCGATGCC 59.468 50.000 0.00 0.00 46.26 4.40
2975 8034 2.332063 AGCGAGTTGTATTCCATGGG 57.668 50.000 13.02 0.00 0.00 4.00
3045 8105 5.474189 TCAGACTCATGAAAACAATGCATCA 59.526 36.000 0.00 0.00 0.00 3.07
3063 8123 4.457257 GCATCACTAAGGAGCTTGAACTTT 59.543 41.667 0.00 0.00 0.00 2.66
3189 8251 3.221771 CTCAGTTGGGGTTGTCATCAAA 58.778 45.455 0.00 0.00 35.20 2.69
3212 8274 7.814264 AACATCTGAGTGTTGAAGAGAATTT 57.186 32.000 5.18 0.00 40.60 1.82
3245 8307 2.113139 ACACTCCAAAGGTGCCGG 59.887 61.111 0.00 0.00 38.14 6.13
3304 8374 9.087424 ACTTACAAAAGTTCAAGAAAAGAATGC 57.913 29.630 0.00 0.00 43.60 3.56
3309 8379 4.137543 AGTTCAAGAAAAGAATGCGGTCT 58.862 39.130 0.00 0.00 0.00 3.85
3349 8420 6.645306 AGAAGAGGGTAAGAATAACAAGAGC 58.355 40.000 0.00 0.00 0.00 4.09
3355 8426 6.069381 AGGGTAAGAATAACAAGAGCCAAGAT 60.069 38.462 0.00 0.00 0.00 2.40
3358 8429 9.343539 GGTAAGAATAACAAGAGCCAAGATAAT 57.656 33.333 0.00 0.00 0.00 1.28
3402 8480 2.035066 GTGCTGATATTGGACATTGGGC 59.965 50.000 0.00 0.00 0.00 5.36
3435 8513 1.831389 CGACGCAAGGTGAAGGTGTG 61.831 60.000 0.00 0.00 46.39 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 17 4.410400 CCAACTCCGGCCTCACCC 62.410 72.222 0.00 0.00 33.26 4.61
130 143 7.412020 CCGACGAAAATAGAAGAAGAAAAGAGG 60.412 40.741 0.00 0.00 0.00 3.69
214 235 5.463061 GCAAAATCGCAATATGTTTATGGCT 59.537 36.000 0.00 0.00 33.23 4.75
225 246 2.159393 GCCACTCAGCAAAATCGCAATA 60.159 45.455 0.00 0.00 0.00 1.90
235 256 4.299547 ACGAGCGCCACTCAGCAA 62.300 61.111 2.29 0.00 46.63 3.91
247 268 3.414700 CACACGCCCTTCACGAGC 61.415 66.667 0.00 0.00 0.00 5.03
360 425 8.552296 AGAAAAGTATGGATAGAGGTGACATTT 58.448 33.333 0.00 0.00 0.00 2.32
361 426 8.095452 AGAAAAGTATGGATAGAGGTGACATT 57.905 34.615 0.00 0.00 0.00 2.71
450 552 3.647636 AGAATTCGATCTCCCTCTTCCA 58.352 45.455 0.00 0.00 0.00 3.53
475 592 3.088532 TCGCAAGGCAGATAATTTGGTT 58.911 40.909 0.00 0.00 38.47 3.67
489 611 1.216710 GAGTCACTCCCTCGCAAGG 59.783 63.158 0.00 0.00 42.95 3.61
541 1508 2.038952 TCTATCCCTTCATCGGCCAATG 59.961 50.000 2.24 0.00 0.00 2.82
547 1514 5.317808 TCTTCTACTCTATCCCTTCATCGG 58.682 45.833 0.00 0.00 0.00 4.18
689 1659 6.980397 GTGTGGGCTTAATTTATCTGAATTGG 59.020 38.462 0.00 0.00 31.96 3.16
756 1734 1.733360 TCGGCGGTTGTTAATTAGCAC 59.267 47.619 7.21 0.00 0.00 4.40
798 1797 2.745821 CACCTCACCTGTCATGTCAATG 59.254 50.000 0.00 0.00 34.88 2.82
799 1798 2.639347 TCACCTCACCTGTCATGTCAAT 59.361 45.455 0.00 0.00 0.00 2.57
830 1861 6.650807 TGAAAAATGTTTGTGGCTTGTTTACA 59.349 30.769 0.00 0.00 0.00 2.41
1045 2184 2.196749 GTGTGTGTGTGTGTGAGAGAG 58.803 52.381 0.00 0.00 0.00 3.20
1046 2185 1.548269 TGTGTGTGTGTGTGTGAGAGA 59.452 47.619 0.00 0.00 0.00 3.10
1047 2186 2.008752 TGTGTGTGTGTGTGTGAGAG 57.991 50.000 0.00 0.00 0.00 3.20
1048 2187 2.093764 TGATGTGTGTGTGTGTGTGAGA 60.094 45.455 0.00 0.00 0.00 3.27
1049 2188 2.278854 TGATGTGTGTGTGTGTGTGAG 58.721 47.619 0.00 0.00 0.00 3.51
1050 2189 2.393271 TGATGTGTGTGTGTGTGTGA 57.607 45.000 0.00 0.00 0.00 3.58
1051 2190 2.874086 AGATGATGTGTGTGTGTGTGTG 59.126 45.455 0.00 0.00 0.00 3.82
1052 2191 3.133691 GAGATGATGTGTGTGTGTGTGT 58.866 45.455 0.00 0.00 0.00 3.72
1054 2193 2.369860 AGGAGATGATGTGTGTGTGTGT 59.630 45.455 0.00 0.00 0.00 3.72
1078 2217 0.250901 TCTTGGCTTGGTTGAGAGGC 60.251 55.000 0.00 0.00 38.78 4.70
1368 2543 4.323477 CCGCACTTGGACCCCGAA 62.323 66.667 0.00 0.00 0.00 4.30
1873 3132 1.852067 GCACCAGAAACACCGCGAAT 61.852 55.000 8.23 0.00 0.00 3.34
1885 3144 4.314440 GTCGCCAGGTGCACCAGA 62.314 66.667 36.39 25.05 41.33 3.86
2010 3310 9.855361 GTCGAGTAATTAACTGATGAATGATTG 57.145 33.333 0.00 0.00 39.07 2.67
2021 3321 3.247442 TGCACGGTCGAGTAATTAACTG 58.753 45.455 0.00 0.00 39.07 3.16
2031 3336 1.148157 CCTAAGCATGCACGGTCGAG 61.148 60.000 21.98 5.57 0.00 4.04
2032 3337 1.153647 CCTAAGCATGCACGGTCGA 60.154 57.895 21.98 0.00 0.00 4.20
2033 3338 0.739462 TTCCTAAGCATGCACGGTCG 60.739 55.000 21.98 1.72 0.00 4.79
2034 3339 1.009829 CTTCCTAAGCATGCACGGTC 58.990 55.000 21.98 0.00 0.00 4.79
2035 3340 0.613260 TCTTCCTAAGCATGCACGGT 59.387 50.000 21.98 4.40 0.00 4.83
2036 3341 1.737838 TTCTTCCTAAGCATGCACGG 58.262 50.000 21.98 16.31 0.00 4.94
2037 3342 2.938451 TGATTCTTCCTAAGCATGCACG 59.062 45.455 21.98 7.19 0.00 5.34
2038 3343 4.970662 TTGATTCTTCCTAAGCATGCAC 57.029 40.909 21.98 0.00 0.00 4.57
2039 3344 5.255687 TCTTTGATTCTTCCTAAGCATGCA 58.744 37.500 21.98 0.00 0.00 3.96
2040 3345 5.732810 GCTCTTTGATTCTTCCTAAGCATGC 60.733 44.000 10.51 10.51 0.00 4.06
2041 3346 5.589452 AGCTCTTTGATTCTTCCTAAGCATG 59.411 40.000 0.00 0.00 0.00 4.06
2042 3347 5.753716 AGCTCTTTGATTCTTCCTAAGCAT 58.246 37.500 0.00 0.00 0.00 3.79
2043 3348 5.171339 AGCTCTTTGATTCTTCCTAAGCA 57.829 39.130 0.00 0.00 0.00 3.91
2044 3349 5.645497 TCAAGCTCTTTGATTCTTCCTAAGC 59.355 40.000 0.00 0.00 40.82 3.09
2056 3361 5.008712 GCATGATCATCATCAAGCTCTTTGA 59.991 40.000 4.86 0.00 46.08 2.69
2057 3362 5.215903 GCATGATCATCATCAAGCTCTTTG 58.784 41.667 4.86 0.00 46.08 2.77
2058 3363 5.440234 GCATGATCATCATCAAGCTCTTT 57.560 39.130 4.86 0.00 46.08 2.52
2084 3389 6.607600 TGATTAGTCTCTAGCTAGCTCCAAAA 59.392 38.462 23.26 8.23 0.00 2.44
2094 3399 7.416964 AAACATCACTGATTAGTCTCTAGCT 57.583 36.000 0.00 0.00 34.07 3.32
2115 3426 2.137523 CCACTGCTCAATGCCAAAAAC 58.862 47.619 0.00 0.00 42.00 2.43
2117 3428 1.702182 TCCACTGCTCAATGCCAAAA 58.298 45.000 0.00 0.00 42.00 2.44
2122 3433 2.355132 CAGAAGATCCACTGCTCAATGC 59.645 50.000 4.26 0.00 43.25 3.56
2123 3434 2.943690 CCAGAAGATCCACTGCTCAATG 59.056 50.000 10.18 0.00 30.80 2.82
2128 3439 1.004044 CAACCCAGAAGATCCACTGCT 59.996 52.381 10.18 0.00 34.18 4.24
2204 3515 1.524849 GCGGCTCTTGAAGGGGATC 60.525 63.158 0.00 0.00 0.00 3.36
2257 3570 4.119862 TCCAACAGAAACAAGAAGACTCG 58.880 43.478 0.00 0.00 0.00 4.18
2278 3591 6.685657 ACATTTCAAGAGCAAGGAGAAAATC 58.314 36.000 0.00 0.00 32.65 2.17
2316 3630 9.582648 AACCTTCCAAAACTAGAAAATAAGCTA 57.417 29.630 0.00 0.00 0.00 3.32
2318 3632 9.542462 AAAACCTTCCAAAACTAGAAAATAAGC 57.458 29.630 0.00 0.00 0.00 3.09
2387 5972 5.010415 TGCAATCCACACACATTTTACATCA 59.990 36.000 0.00 0.00 0.00 3.07
2446 6031 5.880887 CCCCACAGAGACCTTTAAGATTTAC 59.119 44.000 0.00 0.00 0.00 2.01
2447 6032 5.550403 ACCCCACAGAGACCTTTAAGATTTA 59.450 40.000 0.00 0.00 0.00 1.40
2463 6048 6.887545 TCTTACCATGTTATAAAACCCCACAG 59.112 38.462 0.00 0.00 34.49 3.66
2485 6077 9.981114 CAAAATCAGGTTGGTACTAAATTTCTT 57.019 29.630 0.00 0.00 0.00 2.52
2515 6107 8.103305 TGCTCTTATATTTTGGTCTCAACTCTT 58.897 33.333 0.00 0.00 31.78 2.85
2549 6141 2.847133 GACTGCGAATACGACAACTCTC 59.153 50.000 0.00 0.00 42.66 3.20
2555 6147 4.066769 GCGACTGCGAATACGACA 57.933 55.556 0.00 0.00 42.66 4.35
2559 6151 6.918569 ATATGGAATATAGCGACTGCGAATAC 59.081 38.462 0.00 0.00 37.86 1.89
2579 6183 4.760530 TTGGTCTCAACTCTCCATATGG 57.239 45.455 16.25 16.25 0.00 2.74
2725 7778 3.131396 AGCCACAAGACAGTTTTAGTCG 58.869 45.455 0.00 0.00 40.84 4.18
2751 7808 1.021390 CAGCGACCCAGACACATTCC 61.021 60.000 0.00 0.00 0.00 3.01
2799 7858 2.398498 CTGACCGCCTTATCTTGATCG 58.602 52.381 0.00 0.00 0.00 3.69
2802 7861 0.830648 CCCTGACCGCCTTATCTTGA 59.169 55.000 0.00 0.00 0.00 3.02
2805 7864 0.261991 TCTCCCTGACCGCCTTATCT 59.738 55.000 0.00 0.00 0.00 1.98
2808 7867 4.029472 GTCTCCCTGACCGCCTTA 57.971 61.111 0.00 0.00 39.69 2.69
2815 7874 1.201429 ATGGTGGTGGTCTCCCTGAC 61.201 60.000 0.00 0.00 44.63 3.51
2851 7910 7.206687 ACTAGCTTGTCTCTAATCATGCTTAC 58.793 38.462 9.92 0.00 42.26 2.34
2891 7950 1.070786 TCCTTGTCAAGCCGGACAC 59.929 57.895 5.05 0.00 46.76 3.67
2895 7954 2.247790 CAAGTCCTTGTCAAGCCGG 58.752 57.895 7.09 0.00 35.92 6.13
2952 8011 2.004583 TGGAATACAACTCGCTTCCG 57.995 50.000 0.00 0.00 40.04 4.30
2975 8034 9.979270 CAATCATTTTGTAGTCATAGAACTGAC 57.021 33.333 0.00 0.00 44.78 3.51
3045 8105 7.556635 ACACTTAAAAAGTTCAAGCTCCTTAGT 59.443 33.333 0.00 0.00 40.46 2.24
3063 8123 7.614124 ACTTTTTCGGTAACTCACACTTAAA 57.386 32.000 0.00 0.00 0.00 1.52
3143 8205 2.101750 TCACGTCTCTGGTGCTTTACAA 59.898 45.455 0.00 0.00 35.39 2.41
3145 8207 2.433868 TCACGTCTCTGGTGCTTTAC 57.566 50.000 0.00 0.00 35.39 2.01
3189 8251 6.994496 TCAAATTCTCTTCAACACTCAGATGT 59.006 34.615 0.00 0.00 0.00 3.06
3212 8274 3.005897 GGAGTGTGAGTACTTTGCTCTCA 59.994 47.826 17.69 0.00 35.11 3.27
3245 8307 2.290960 ACATTGGCACTAGAAGTTCCCC 60.291 50.000 0.00 0.00 30.00 4.81
3304 8374 6.392625 TCTTGAAGATGGTATTCTAGACCG 57.607 41.667 0.00 0.00 40.09 4.79
3309 8379 6.903534 ACCCTCTTCTTGAAGATGGTATTCTA 59.096 38.462 27.19 1.34 43.16 2.10
3331 8401 5.497474 TCTTGGCTCTTGTTATTCTTACCC 58.503 41.667 0.00 0.00 0.00 3.69
3335 8405 8.897752 GTCATTATCTTGGCTCTTGTTATTCTT 58.102 33.333 0.00 0.00 0.00 2.52
3340 8411 7.994425 TTTGTCATTATCTTGGCTCTTGTTA 57.006 32.000 0.00 0.00 0.00 2.41
3382 8453 2.309613 GCCCAATGTCCAATATCAGCA 58.690 47.619 0.00 0.00 0.00 4.41
3402 8480 0.165944 GCGTCGTGGAAACTTGGATG 59.834 55.000 0.00 0.00 0.00 3.51
3411 8489 0.878523 CTTCACCTTGCGTCGTGGAA 60.879 55.000 7.79 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.