Multiple sequence alignment - TraesCS1D01G094700

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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 TraesCS1D01G094700 chr1D 100.000 2743 0 0 1 2743 80447325 80450067 0.000000e+00 5066.0
1 TraesCS1D01G094700 chr1D 83.313 833 99 26 942 1750 80540943 80541759 0.000000e+00 732.0
2 TraesCS1D01G094700 chr1D 83.443 761 112 12 1000 1747 80817018 80817777 0.000000e+00 695.0
3 TraesCS1D01G094700 chr1D 90.600 500 47 0 1251 1750 80537384 80537883 0.000000e+00 664.0
4 TraesCS1D01G094700 chr1D 91.286 241 17 3 976 1216 80537068 80537304 2.630000e-85 326.0
5 TraesCS1D01G094700 chr1D 93.500 200 6 4 2233 2431 121242468 121242275 9.610000e-75 291.0
6 TraesCS1D01G094700 chr1D 92.500 200 9 3 2233 2431 465346054 465346248 5.780000e-72 281.0
7 TraesCS1D01G094700 chr1B 91.775 2079 98 41 1 2018 132937252 132939318 0.000000e+00 2824.0
8 TraesCS1D01G094700 chr1B 90.377 769 67 5 989 1750 133032480 133033248 0.000000e+00 1003.0
9 TraesCS1D01G094700 chr1B 84.232 482 74 2 1270 1750 133075966 133076446 4.140000e-128 468.0
10 TraesCS1D01G094700 chr1B 93.226 310 21 0 2431 2740 132940054 132940363 8.950000e-125 457.0
11 TraesCS1D01G094700 chr1B 90.441 272 19 5 960 1231 133075644 133075908 4.350000e-93 351.0
12 TraesCS1D01G094700 chr1A 90.419 2077 120 24 1 2018 99017611 99019667 0.000000e+00 2660.0
13 TraesCS1D01G094700 chr1A 87.084 782 82 11 976 1744 99048754 99049529 0.000000e+00 867.0
14 TraesCS1D01G094700 chr1A 82.940 762 113 13 1000 1747 99234402 99235160 0.000000e+00 671.0
15 TraesCS1D01G094700 chr1A 84.440 482 73 2 1270 1750 99071402 99071882 8.890000e-130 473.0
16 TraesCS1D01G094700 chr1A 94.194 310 17 1 2431 2740 99020409 99020717 3.200000e-129 472.0
17 TraesCS1D01G094700 chr1A 88.660 291 27 5 942 1231 99071059 99071344 1.560000e-92 350.0
18 TraesCS1D01G094700 chr1A 89.637 193 16 1 2045 2233 99020219 99020411 2.730000e-60 243.0
19 TraesCS1D01G094700 chr7B 93.204 206 14 0 1000 1205 95337271 95337476 1.230000e-78 303.0
20 TraesCS1D01G094700 chr7B 81.675 191 33 2 2551 2740 506238589 506238778 1.020000e-34 158.0
21 TraesCS1D01G094700 chr7B 92.105 38 2 1 1947 1983 651494587 651494550 5.000000e-03 52.8
22 TraesCS1D01G094700 chr2D 93.467 199 12 1 2233 2431 600801832 600802029 7.430000e-76 294.0
23 TraesCS1D01G094700 chr2D 91.542 201 9 4 2233 2431 627581144 627580950 1.250000e-68 270.0
24 TraesCS1D01G094700 chr2D 91.000 200 10 4 2234 2432 170610294 170610102 2.090000e-66 263.0
25 TraesCS1D01G094700 chr3D 90.777 206 13 3 2231 2435 597544003 597544203 1.250000e-68 270.0
26 TraesCS1D01G094700 chr2B 90.476 210 13 4 2229 2436 678568545 678568749 1.250000e-68 270.0
27 TraesCS1D01G094700 chr2B 89.796 49 5 0 2473 2521 98672047 98672095 2.280000e-06 63.9
28 TraesCS1D01G094700 chr7D 90.452 199 13 3 2233 2430 114608532 114608725 9.750000e-65 257.0
29 TraesCS1D01G094700 chr7D 82.581 155 26 1 2554 2708 369776842 369776689 4.760000e-28 135.0
30 TraesCS1D01G094700 chr7D 78.534 191 39 2 2554 2743 204338212 204338023 1.030000e-24 124.0
31 TraesCS1D01G094700 chr7D 89.583 48 5 0 2473 2520 204319195 204319148 8.200000e-06 62.1
32 TraesCS1D01G094700 chr6A 88.732 213 14 7 2232 2440 595174028 595174234 4.530000e-63 252.0
33 TraesCS1D01G094700 chr6A 84.649 228 22 8 2019 2233 184698197 184698424 5.950000e-52 215.0
34 TraesCS1D01G094700 chr6D 85.333 225 20 9 2022 2233 40079925 40079701 1.280000e-53 220.0
35 TraesCS1D01G094700 chr6D 84.649 228 22 8 2019 2233 40076294 40076067 5.950000e-52 215.0
36 TraesCS1D01G094700 chr6D 84.211 228 23 8 2019 2233 68367780 68368007 2.770000e-50 209.0
37 TraesCS1D01G094700 chr5A 85.022 227 22 8 2019 2233 693941928 693941702 1.280000e-53 220.0
38 TraesCS1D01G094700 chr3A 84.649 228 22 8 2019 2233 354070344 354070571 5.950000e-52 215.0
39 TraesCS1D01G094700 chr7A 84.052 232 22 11 2017 2233 468547797 468548028 2.770000e-50 209.0
40 TraesCS1D01G094700 chr4A 84.211 228 23 7 2019 2233 610657880 610657653 2.770000e-50 209.0
41 TraesCS1D01G094700 chr2A 78.866 194 39 2 2551 2743 227532543 227532735 2.220000e-26 130.0
42 TraesCS1D01G094700 chr4D 80.368 163 30 2 2547 2708 63331795 63331634 3.710000e-24 122.0


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 TraesCS1D01G094700 chr1D 80447325 80450067 2742 False 5066.0 5066 100.000000 1 2743 1 chr1D.!!$F1 2742
1 TraesCS1D01G094700 chr1D 80817018 80817777 759 False 695.0 695 83.443000 1000 1747 1 chr1D.!!$F2 747
2 TraesCS1D01G094700 chr1D 80537068 80541759 4691 False 574.0 732 88.399667 942 1750 3 chr1D.!!$F4 808
3 TraesCS1D01G094700 chr1B 132937252 132940363 3111 False 1640.5 2824 92.500500 1 2740 2 chr1B.!!$F2 2739
4 TraesCS1D01G094700 chr1B 133032480 133033248 768 False 1003.0 1003 90.377000 989 1750 1 chr1B.!!$F1 761
5 TraesCS1D01G094700 chr1B 133075644 133076446 802 False 409.5 468 87.336500 960 1750 2 chr1B.!!$F3 790
6 TraesCS1D01G094700 chr1A 99017611 99020717 3106 False 1125.0 2660 91.416667 1 2740 3 chr1A.!!$F3 2739
7 TraesCS1D01G094700 chr1A 99048754 99049529 775 False 867.0 867 87.084000 976 1744 1 chr1A.!!$F1 768
8 TraesCS1D01G094700 chr1A 99234402 99235160 758 False 671.0 671 82.940000 1000 1747 1 chr1A.!!$F2 747
9 TraesCS1D01G094700 chr1A 99071059 99071882 823 False 411.5 473 86.550000 942 1750 2 chr1A.!!$F4 808
10 TraesCS1D01G094700 chr6D 40076067 40079925 3858 True 217.5 220 84.991000 2019 2233 2 chr6D.!!$R1 214

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
855 885 0.382158 GGACTGCATCGTCGATCAGA 59.618 55.0 26.98 8.63 34.75 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 6659 0.105709 CTGGAACCAAACACCCCCTT 60.106 55.0 0.0 0.0 0.0 3.95 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
53 55 4.778534 ACTTGCATTCTCATGTTCTTGG 57.221 40.909 0.00 0.00 32.28 3.61
55 57 2.799017 TGCATTCTCATGTTCTTGGCT 58.201 42.857 0.00 0.00 32.28 4.75
59 61 4.733815 GCATTCTCATGTTCTTGGCTGATG 60.734 45.833 0.00 0.00 32.28 3.07
66 68 4.829064 TGTTCTTGGCTGATGTTGTAAC 57.171 40.909 0.00 0.00 0.00 2.50
70 72 3.814842 TCTTGGCTGATGTTGTAACTGTG 59.185 43.478 0.00 0.00 0.00 3.66
81 83 5.773575 TGTTGTAACTGTGAAGAGCTCTAG 58.226 41.667 18.59 13.22 0.00 2.43
149 151 3.740832 TGACTGCGTAACATCTTGTTCTG 59.259 43.478 0.00 0.00 40.22 3.02
303 305 3.069300 AGAACATCAGAGATGTCATCCCG 59.931 47.826 12.53 0.00 0.00 5.14
310 312 0.541863 AGATGTCATCCCGTTCCCAC 59.458 55.000 9.29 0.00 0.00 4.61
341 343 1.208165 AGGGCCGATCTTTGAAGGGT 61.208 55.000 0.00 0.00 0.00 4.34
393 397 4.143473 CGTCAATTACACTTTCGTTAGCGT 60.143 41.667 0.00 0.00 39.49 5.07
401 405 4.142643 ACACTTTCGTTAGCGTTTTTGGAA 60.143 37.500 0.00 0.00 39.49 3.53
402 406 4.973663 CACTTTCGTTAGCGTTTTTGGAAT 59.026 37.500 0.00 0.00 39.49 3.01
414 418 0.885196 TTTGGAATAGTGTTGGCCGC 59.115 50.000 0.00 0.00 0.00 6.53
460 464 5.681543 CGCATGCTGATATCATTTGATATGC 59.318 40.000 17.13 13.99 45.07 3.14
487 491 4.515191 GTGTCTTGGCTTGTTGTGATTCTA 59.485 41.667 0.00 0.00 0.00 2.10
492 496 7.168135 GTCTTGGCTTGTTGTGATTCTAAAAAG 59.832 37.037 0.00 0.00 0.00 2.27
638 644 4.696479 AGATGCCTTAGTTACATGGAGG 57.304 45.455 0.00 0.00 0.00 4.30
639 645 4.298626 AGATGCCTTAGTTACATGGAGGA 58.701 43.478 0.00 0.00 0.00 3.71
640 646 4.721776 AGATGCCTTAGTTACATGGAGGAA 59.278 41.667 0.00 0.00 0.00 3.36
655 665 4.766375 TGGAGGAAGATGTTAAATCGGTC 58.234 43.478 0.00 0.00 0.00 4.79
829 859 6.583912 AAAAACATCATAGTACGACGATGG 57.416 37.500 14.99 0.07 39.64 3.51
850 880 2.060004 GATCCGGACTGCATCGTCGA 62.060 60.000 6.12 0.00 34.75 4.20
855 885 0.382158 GGACTGCATCGTCGATCAGA 59.618 55.000 26.98 8.63 34.75 3.27
857 887 2.049959 GACTGCATCGTCGATCAGATG 58.950 52.381 26.98 18.22 45.06 2.90
1032 1067 3.617143 GAAGGTGTACGGGTGGGCC 62.617 68.421 0.00 0.00 0.00 5.80
1218 1253 4.091549 TCTTCGGTACACCTACTTCCATT 58.908 43.478 0.00 0.00 0.00 3.16
1252 1347 1.270305 TGGAGCAGGAACGAGTTCTTG 60.270 52.381 19.52 19.52 45.79 3.02
1757 1893 1.218047 GTAGTGATGACTGCCGCCA 59.782 57.895 0.00 0.00 33.21 5.69
1811 1959 0.111001 CTCCGGTTTTGCGTTGTACG 60.111 55.000 0.00 0.00 45.88 3.67
1841 1989 2.561419 GCACCGGCCTATATCTTCTGTA 59.439 50.000 0.00 0.00 0.00 2.74
1861 2009 1.238439 CCAGTGGCTCGTGTTTTGAT 58.762 50.000 0.00 0.00 0.00 2.57
1896 2044 7.706159 TCACGCTTGAATAAAATGCAAGATAT 58.294 30.769 11.13 0.00 41.03 1.63
1897 2045 8.835439 TCACGCTTGAATAAAATGCAAGATATA 58.165 29.630 11.13 0.00 41.03 0.86
1909 2153 3.646162 TGCAAGATATACCCATCGGTTCT 59.354 43.478 0.00 0.00 40.58 3.01
1914 2158 7.095187 GCAAGATATACCCATCGGTTCTAAAAG 60.095 40.741 0.00 0.00 40.58 2.27
1922 2176 6.943718 ACCCATCGGTTCTAAAAGAATTGTTA 59.056 34.615 0.00 0.00 40.58 2.41
2038 2313 9.875708 TTATATGGGTTTTATAGCAAGGACAAT 57.124 29.630 0.00 0.00 0.00 2.71
2042 2317 5.201243 GGTTTTATAGCAAGGACAATCCCT 58.799 41.667 0.00 0.00 37.19 4.20
2103 6530 0.254747 TTGGGGGAATAAGCCGTCAG 59.745 55.000 0.00 0.00 0.00 3.51
2126 6553 4.389374 CTTTGGAAGTTGTTGGAGAGCTA 58.611 43.478 0.00 0.00 0.00 3.32
2131 6558 1.546476 AGTTGTTGGAGAGCTACTCGG 59.454 52.381 0.00 0.00 45.76 4.63
2169 6596 2.615986 TAGCCTAGACACCTTCCACA 57.384 50.000 0.00 0.00 0.00 4.17
2178 6605 2.814336 GACACCTTCCACAAGAATGACC 59.186 50.000 0.00 0.00 32.82 4.02
2230 6658 3.882888 TGAGATTTCTTGCGTTGGAAAGT 59.117 39.130 0.00 0.00 35.37 2.66
2231 6659 5.049680 GTGAGATTTCTTGCGTTGGAAAGTA 60.050 40.000 0.00 0.00 35.37 2.24
2233 6661 6.002062 AGATTTCTTGCGTTGGAAAGTAAG 57.998 37.500 0.00 0.00 35.37 2.34
2234 6662 4.561735 TTTCTTGCGTTGGAAAGTAAGG 57.438 40.909 4.01 0.00 32.24 2.69
2235 6663 2.500229 TCTTGCGTTGGAAAGTAAGGG 58.500 47.619 4.01 0.00 32.24 3.95
2236 6664 1.539827 CTTGCGTTGGAAAGTAAGGGG 59.460 52.381 0.00 0.00 0.00 4.79
2237 6665 0.250989 TGCGTTGGAAAGTAAGGGGG 60.251 55.000 0.00 0.00 0.00 5.40
2238 6666 0.251033 GCGTTGGAAAGTAAGGGGGT 60.251 55.000 0.00 0.00 0.00 4.95
2239 6667 1.530323 CGTTGGAAAGTAAGGGGGTG 58.470 55.000 0.00 0.00 0.00 4.61
2240 6668 1.202842 CGTTGGAAAGTAAGGGGGTGT 60.203 52.381 0.00 0.00 0.00 4.16
2241 6669 2.750471 CGTTGGAAAGTAAGGGGGTGTT 60.750 50.000 0.00 0.00 0.00 3.32
2242 6670 3.302161 GTTGGAAAGTAAGGGGGTGTTT 58.698 45.455 0.00 0.00 0.00 2.83
2243 6671 2.952116 TGGAAAGTAAGGGGGTGTTTG 58.048 47.619 0.00 0.00 0.00 2.93
2244 6672 2.244695 GGAAAGTAAGGGGGTGTTTGG 58.755 52.381 0.00 0.00 0.00 3.28
2245 6673 2.425247 GGAAAGTAAGGGGGTGTTTGGT 60.425 50.000 0.00 0.00 0.00 3.67
2246 6674 3.302161 GAAAGTAAGGGGGTGTTTGGTT 58.698 45.455 0.00 0.00 0.00 3.67
2247 6675 2.670019 AGTAAGGGGGTGTTTGGTTC 57.330 50.000 0.00 0.00 0.00 3.62
2248 6676 1.146359 AGTAAGGGGGTGTTTGGTTCC 59.854 52.381 0.00 0.00 0.00 3.62
2249 6677 1.133419 GTAAGGGGGTGTTTGGTTCCA 60.133 52.381 0.00 0.00 0.00 3.53
2250 6678 0.105709 AAGGGGGTGTTTGGTTCCAG 60.106 55.000 0.00 0.00 0.00 3.86
2251 6679 1.533033 GGGGGTGTTTGGTTCCAGG 60.533 63.158 0.00 0.00 0.00 4.45
2252 6680 1.539665 GGGGTGTTTGGTTCCAGGA 59.460 57.895 0.00 0.00 0.00 3.86
2253 6681 0.105913 GGGGTGTTTGGTTCCAGGAA 60.106 55.000 0.00 0.00 0.00 3.36
2254 6682 1.037493 GGGTGTTTGGTTCCAGGAAC 58.963 55.000 22.73 22.73 41.32 3.62
2255 6683 1.411074 GGGTGTTTGGTTCCAGGAACT 60.411 52.381 28.14 0.00 41.70 3.01
2256 6684 2.384828 GGTGTTTGGTTCCAGGAACTT 58.615 47.619 28.14 0.00 41.70 2.66
2257 6685 2.764010 GGTGTTTGGTTCCAGGAACTTT 59.236 45.455 28.14 0.00 41.70 2.66
2258 6686 3.196901 GGTGTTTGGTTCCAGGAACTTTT 59.803 43.478 28.14 0.00 41.70 2.27
2259 6687 4.323180 GGTGTTTGGTTCCAGGAACTTTTT 60.323 41.667 28.14 0.00 41.70 1.94
2297 6725 4.734843 AAAACCCTAAAAGTCCCTAGCA 57.265 40.909 0.00 0.00 0.00 3.49
2298 6726 4.734843 AAACCCTAAAAGTCCCTAGCAA 57.265 40.909 0.00 0.00 0.00 3.91
2299 6727 4.734843 AACCCTAAAAGTCCCTAGCAAA 57.265 40.909 0.00 0.00 0.00 3.68
2300 6728 4.030314 ACCCTAAAAGTCCCTAGCAAAC 57.970 45.455 0.00 0.00 0.00 2.93
2301 6729 3.245158 ACCCTAAAAGTCCCTAGCAAACC 60.245 47.826 0.00 0.00 0.00 3.27
2302 6730 3.245122 CCCTAAAAGTCCCTAGCAAACCA 60.245 47.826 0.00 0.00 0.00 3.67
2303 6731 4.403734 CCTAAAAGTCCCTAGCAAACCAA 58.596 43.478 0.00 0.00 0.00 3.67
2304 6732 4.830600 CCTAAAAGTCCCTAGCAAACCAAA 59.169 41.667 0.00 0.00 0.00 3.28
2305 6733 4.665833 AAAAGTCCCTAGCAAACCAAAC 57.334 40.909 0.00 0.00 0.00 2.93
2306 6734 3.306472 AAGTCCCTAGCAAACCAAACA 57.694 42.857 0.00 0.00 0.00 2.83
2307 6735 2.863809 AGTCCCTAGCAAACCAAACAG 58.136 47.619 0.00 0.00 0.00 3.16
2308 6736 1.886542 GTCCCTAGCAAACCAAACAGG 59.113 52.381 0.00 0.00 45.67 4.00
2309 6737 1.203001 TCCCTAGCAAACCAAACAGGG 60.203 52.381 0.00 0.00 43.52 4.45
2310 6738 1.256812 CCTAGCAAACCAAACAGGGG 58.743 55.000 0.00 0.00 43.89 4.79
2311 6739 1.256812 CTAGCAAACCAAACAGGGGG 58.743 55.000 0.00 0.00 43.89 5.40
2354 6782 7.859613 CTTTTTGCTAAAAGTCCTTAGAAGC 57.140 36.000 20.79 0.00 43.34 3.86
2355 6783 6.952773 TTTTGCTAAAAGTCCTTAGAAGCA 57.047 33.333 6.73 6.73 31.59 3.91
2356 6784 5.941948 TTGCTAAAAGTCCTTAGAAGCAC 57.058 39.130 9.21 0.00 31.59 4.40
2357 6785 4.324267 TGCTAAAAGTCCTTAGAAGCACC 58.676 43.478 6.73 0.00 31.59 5.01
2358 6786 4.041691 TGCTAAAAGTCCTTAGAAGCACCT 59.958 41.667 6.73 0.00 31.59 4.00
2359 6787 4.632251 GCTAAAAGTCCTTAGAAGCACCTC 59.368 45.833 0.00 0.00 31.59 3.85
2360 6788 3.704800 AAAGTCCTTAGAAGCACCTCC 57.295 47.619 0.00 0.00 0.00 4.30
2361 6789 2.632763 AGTCCTTAGAAGCACCTCCT 57.367 50.000 0.00 0.00 0.00 3.69
2362 6790 2.909217 AGTCCTTAGAAGCACCTCCTT 58.091 47.619 0.00 0.00 0.00 3.36
2363 6791 4.062490 AGTCCTTAGAAGCACCTCCTTA 57.938 45.455 0.00 0.00 0.00 2.69
2364 6792 4.426704 AGTCCTTAGAAGCACCTCCTTAA 58.573 43.478 0.00 0.00 0.00 1.85
2365 6793 4.468153 AGTCCTTAGAAGCACCTCCTTAAG 59.532 45.833 0.00 0.00 0.00 1.85
2366 6794 4.466726 GTCCTTAGAAGCACCTCCTTAAGA 59.533 45.833 3.36 0.00 0.00 2.10
2367 6795 4.712337 TCCTTAGAAGCACCTCCTTAAGAG 59.288 45.833 3.36 0.00 42.83 2.85
2368 6796 4.468153 CCTTAGAAGCACCTCCTTAAGAGT 59.532 45.833 3.36 0.00 41.47 3.24
2369 6797 5.394773 CCTTAGAAGCACCTCCTTAAGAGTC 60.395 48.000 3.36 0.00 41.47 3.36
2370 6798 3.785364 AGAAGCACCTCCTTAAGAGTCT 58.215 45.455 3.36 0.00 41.47 3.24
2371 6799 4.164204 AGAAGCACCTCCTTAAGAGTCTT 58.836 43.478 10.87 10.87 41.47 3.01
2372 6800 4.595350 AGAAGCACCTCCTTAAGAGTCTTT 59.405 41.667 11.40 0.00 41.47 2.52
2373 6801 4.984146 AGCACCTCCTTAAGAGTCTTTT 57.016 40.909 11.40 0.00 41.47 2.27
2374 6802 5.311844 AGCACCTCCTTAAGAGTCTTTTT 57.688 39.130 11.40 0.00 41.47 1.94
2424 6852 6.342338 GTCCTAAGACTAGAGAACCAAACA 57.658 41.667 0.00 0.00 40.10 2.83
2425 6853 6.157904 GTCCTAAGACTAGAGAACCAAACAC 58.842 44.000 0.00 0.00 40.10 3.32
2426 6854 5.245526 TCCTAAGACTAGAGAACCAAACACC 59.754 44.000 0.00 0.00 0.00 4.16
2427 6855 5.011738 CCTAAGACTAGAGAACCAAACACCA 59.988 44.000 0.00 0.00 0.00 4.17
2428 6856 4.338379 AGACTAGAGAACCAAACACCAC 57.662 45.455 0.00 0.00 0.00 4.16
2429 6857 3.071167 AGACTAGAGAACCAAACACCACC 59.929 47.826 0.00 0.00 0.00 4.61
2451 6879 7.029563 CACCTAAATTTGATGTAGTTTCTGGC 58.970 38.462 0.00 0.00 0.00 4.85
2453 6881 4.701956 AATTTGATGTAGTTTCTGGCGG 57.298 40.909 0.00 0.00 0.00 6.13
2457 6885 3.792401 TGATGTAGTTTCTGGCGGTATG 58.208 45.455 0.00 0.00 0.00 2.39
2659 7087 4.082733 CCTTTCTTGGAGAAAATTCGTCCC 60.083 45.833 4.84 3.57 42.95 4.46
2741 7172 8.827832 AAGGGAAAGATGAATAATCATGTGAA 57.172 30.769 0.00 0.00 46.30 3.18
2742 7173 8.827832 AGGGAAAGATGAATAATCATGTGAAA 57.172 30.769 0.00 0.00 46.30 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 4.377841 GCTCTTCACAGTTACAACATCAGC 60.378 45.833 0.00 0.00 0.00 4.26
55 57 4.960938 AGCTCTTCACAGTTACAACATCA 58.039 39.130 0.00 0.00 0.00 3.07
59 61 6.015027 TCTAGAGCTCTTCACAGTTACAAC 57.985 41.667 23.84 0.00 0.00 3.32
66 68 9.677567 GTATTCTTTATCTAGAGCTCTTCACAG 57.322 37.037 23.84 13.35 0.00 3.66
106 108 5.645497 GTCAGCTCACAGGTCATAAAGAAAT 59.355 40.000 0.00 0.00 0.00 2.17
149 151 3.150767 AGATCTGCGTCCAGTATCCTAC 58.849 50.000 0.00 0.00 40.09 3.18
165 167 0.032615 ACGGCTCCAGAGGAAGATCT 60.033 55.000 0.00 0.00 0.00 2.75
303 305 2.502577 CCGGGGTATCGTGGGAAC 59.497 66.667 0.00 0.00 0.00 3.62
393 397 2.288518 GCGGCCAACACTATTCCAAAAA 60.289 45.455 2.24 0.00 0.00 1.94
401 405 4.483243 CCGGGCGGCCAACACTAT 62.483 66.667 29.19 0.00 0.00 2.12
414 418 7.654568 TGCGTATATATATCAATCTAACCGGG 58.345 38.462 6.32 0.00 0.00 5.73
460 464 0.588252 CAACAAGCCAAGACACGAGG 59.412 55.000 0.00 0.00 0.00 4.63
487 491 9.696917 CATAAAACAAGCCTGATACTTCTTTTT 57.303 29.630 0.00 0.00 30.91 1.94
575 579 1.683385 GGCATAAGATCCAAACAGGGC 59.317 52.381 0.00 0.00 38.24 5.19
638 644 5.420409 AGGTGAGACCGATTTAACATCTTC 58.580 41.667 0.00 0.00 44.90 2.87
639 645 5.422214 AGGTGAGACCGATTTAACATCTT 57.578 39.130 0.00 0.00 44.90 2.40
640 646 5.420409 GAAGGTGAGACCGATTTAACATCT 58.580 41.667 0.00 0.00 44.90 2.90
655 665 1.656652 CTATTGTGGGCGAAGGTGAG 58.343 55.000 0.00 0.00 0.00 3.51
829 859 2.029666 CGATGCAGTCCGGATCCC 59.970 66.667 7.81 0.00 39.20 3.85
850 880 0.538584 TGCTTGCGTCCTCATCTGAT 59.461 50.000 0.00 0.00 0.00 2.90
855 885 0.671781 GTCACTGCTTGCGTCCTCAT 60.672 55.000 0.00 0.00 0.00 2.90
857 887 2.375766 CGTCACTGCTTGCGTCCTC 61.376 63.158 0.00 0.00 0.00 3.71
1056 1091 2.527624 TCCTCCAGGCACAGCAGT 60.528 61.111 0.00 0.00 34.44 4.40
1218 1253 3.436325 CCTGCTCCAGAGAAGAGAGGATA 60.436 52.174 4.06 0.00 36.10 2.59
1252 1347 2.159517 GCGTGTGGGATTTCAGATTGTC 60.160 50.000 0.00 0.00 0.00 3.18
1484 1599 0.892814 GCACCTTCTTGAGCTTGGCT 60.893 55.000 0.00 0.00 43.88 4.75
1757 1893 0.389948 GCTCGATCCTGGTGAACGTT 60.390 55.000 0.00 0.00 39.93 3.99
1841 1989 0.107410 TCAAAACACGAGCCACTGGT 60.107 50.000 0.00 0.00 0.00 4.00
1861 2009 7.485418 TTTATTCAAGCGTGAGACTAAAACA 57.515 32.000 1.81 0.00 34.49 2.83
2018 2293 4.341235 GGGATTGTCCTTGCTATAAAACCC 59.659 45.833 0.00 0.00 36.57 4.11
2020 2295 6.775594 AAGGGATTGTCCTTGCTATAAAAC 57.224 37.500 0.00 0.00 44.78 2.43
2021 2296 7.060421 CCTAAGGGATTGTCCTTGCTATAAAA 58.940 38.462 6.41 0.00 45.87 1.52
2022 2297 6.159751 ACCTAAGGGATTGTCCTTGCTATAAA 59.840 38.462 6.41 0.00 45.87 1.40
2023 2298 5.670361 ACCTAAGGGATTGTCCTTGCTATAA 59.330 40.000 6.41 0.00 45.87 0.98
2024 2299 5.071788 CACCTAAGGGATTGTCCTTGCTATA 59.928 44.000 6.41 0.00 45.87 1.31
2025 2300 4.047883 ACCTAAGGGATTGTCCTTGCTAT 58.952 43.478 6.41 0.00 45.87 2.97
2031 2306 2.915869 TCACACCTAAGGGATTGTCCT 58.084 47.619 0.00 0.00 36.57 3.85
2038 2313 8.485578 AATTTAACATTTTCACACCTAAGGGA 57.514 30.769 0.00 0.00 36.25 4.20
2103 6530 2.287849 GCTCTCCAACAACTTCCAAAGC 60.288 50.000 0.00 0.00 0.00 3.51
2126 6553 1.359459 GGCTTCGCGAATTTCCGAGT 61.359 55.000 23.67 0.00 34.68 4.18
2131 6558 2.832672 ATCAAGGCTTCGCGAATTTC 57.167 45.000 23.67 14.27 0.00 2.17
2150 6577 2.615986 TGTGGAAGGTGTCTAGGCTA 57.384 50.000 0.00 0.00 0.00 3.93
2169 6596 2.808543 GTCAAGCGTTCTGGTCATTCTT 59.191 45.455 0.00 0.00 0.00 2.52
2178 6605 2.221981 GGAGTTTGAGTCAAGCGTTCTG 59.778 50.000 13.26 0.00 30.10 3.02
2230 6658 1.146152 CTGGAACCAAACACCCCCTTA 59.854 52.381 0.00 0.00 0.00 2.69
2231 6659 0.105709 CTGGAACCAAACACCCCCTT 60.106 55.000 0.00 0.00 0.00 3.95
2233 6661 1.533033 CCTGGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
2234 6662 0.105913 TTCCTGGAACCAAACACCCC 60.106 55.000 4.68 0.00 0.00 4.95
2235 6663 1.037493 GTTCCTGGAACCAAACACCC 58.963 55.000 25.74 0.44 36.65 4.61
2236 6664 2.067365 AGTTCCTGGAACCAAACACC 57.933 50.000 30.69 8.42 42.85 4.16
2237 6665 4.465632 AAAAGTTCCTGGAACCAAACAC 57.534 40.909 30.69 9.86 42.85 3.32
2275 6703 5.069518 TGCTAGGGACTTTTAGGGTTTTT 57.930 39.130 0.00 0.00 41.75 1.94
2276 6704 4.734843 TGCTAGGGACTTTTAGGGTTTT 57.265 40.909 0.00 0.00 41.75 2.43
2277 6705 4.734843 TTGCTAGGGACTTTTAGGGTTT 57.265 40.909 0.00 0.00 41.75 3.27
2278 6706 4.404640 GTTTGCTAGGGACTTTTAGGGTT 58.595 43.478 0.00 0.00 41.75 4.11
2279 6707 3.245158 GGTTTGCTAGGGACTTTTAGGGT 60.245 47.826 0.00 0.00 41.75 4.34
2280 6708 3.245122 TGGTTTGCTAGGGACTTTTAGGG 60.245 47.826 0.00 0.00 41.75 3.53
2281 6709 4.028993 TGGTTTGCTAGGGACTTTTAGG 57.971 45.455 0.00 0.00 41.75 2.69
2282 6710 5.300792 TGTTTGGTTTGCTAGGGACTTTTAG 59.699 40.000 0.00 0.00 41.75 1.85
2283 6711 5.202004 TGTTTGGTTTGCTAGGGACTTTTA 58.798 37.500 0.00 0.00 41.75 1.52
2284 6712 4.027437 TGTTTGGTTTGCTAGGGACTTTT 58.973 39.130 0.00 0.00 41.75 2.27
2285 6713 3.636764 CTGTTTGGTTTGCTAGGGACTTT 59.363 43.478 0.00 0.00 41.75 2.66
2286 6714 3.222603 CTGTTTGGTTTGCTAGGGACTT 58.777 45.455 0.00 0.00 41.75 3.01
2287 6715 2.489073 CCTGTTTGGTTTGCTAGGGACT 60.489 50.000 0.00 0.00 46.37 3.85
2288 6716 1.886542 CCTGTTTGGTTTGCTAGGGAC 59.113 52.381 0.00 0.00 0.00 4.46
2289 6717 1.203001 CCCTGTTTGGTTTGCTAGGGA 60.203 52.381 0.00 0.00 46.19 4.20
2290 6718 1.256812 CCCTGTTTGGTTTGCTAGGG 58.743 55.000 0.00 0.00 38.96 3.53
2291 6719 1.256812 CCCCTGTTTGGTTTGCTAGG 58.743 55.000 0.00 0.00 0.00 3.02
2292 6720 1.256812 CCCCCTGTTTGGTTTGCTAG 58.743 55.000 0.00 0.00 0.00 3.42
2293 6721 3.448469 CCCCCTGTTTGGTTTGCTA 57.552 52.632 0.00 0.00 0.00 3.49
2294 6722 4.293610 CCCCCTGTTTGGTTTGCT 57.706 55.556 0.00 0.00 0.00 3.91
2331 6759 7.200455 GTGCTTCTAAGGACTTTTAGCAAAAA 58.800 34.615 7.07 0.00 43.15 1.94
2332 6760 6.238925 GGTGCTTCTAAGGACTTTTAGCAAAA 60.239 38.462 13.12 0.00 45.42 2.44
2333 6761 5.240844 GGTGCTTCTAAGGACTTTTAGCAAA 59.759 40.000 13.12 0.00 45.42 3.68
2334 6762 4.760204 GGTGCTTCTAAGGACTTTTAGCAA 59.240 41.667 13.12 1.75 45.42 3.91
2335 6763 4.041691 AGGTGCTTCTAAGGACTTTTAGCA 59.958 41.667 13.12 9.74 45.42 3.49
2336 6764 4.580868 AGGTGCTTCTAAGGACTTTTAGC 58.419 43.478 13.12 0.00 45.42 3.09
2337 6765 5.046231 AGGAGGTGCTTCTAAGGACTTTTAG 60.046 44.000 13.12 0.00 45.42 1.85
2338 6766 4.844655 AGGAGGTGCTTCTAAGGACTTTTA 59.155 41.667 13.12 0.00 45.42 1.52
2339 6767 3.653352 AGGAGGTGCTTCTAAGGACTTTT 59.347 43.478 13.12 1.47 45.42 2.27
2340 6768 3.252351 AGGAGGTGCTTCTAAGGACTTT 58.748 45.455 13.12 3.63 45.42 2.66
2341 6769 2.909217 AGGAGGTGCTTCTAAGGACTT 58.091 47.619 13.12 6.52 45.42 3.01
2342 6770 2.632763 AGGAGGTGCTTCTAAGGACT 57.367 50.000 13.12 1.24 45.42 3.85
2343 6771 4.466726 TCTTAAGGAGGTGCTTCTAAGGAC 59.533 45.833 1.85 5.86 45.39 3.85
2344 6772 4.684724 TCTTAAGGAGGTGCTTCTAAGGA 58.315 43.478 1.85 0.00 0.00 3.36
2345 6773 4.468153 ACTCTTAAGGAGGTGCTTCTAAGG 59.532 45.833 1.85 0.00 45.83 2.69
2346 6774 5.420739 AGACTCTTAAGGAGGTGCTTCTAAG 59.579 44.000 1.85 0.00 45.83 2.18
2347 6775 5.334421 AGACTCTTAAGGAGGTGCTTCTAA 58.666 41.667 1.85 0.00 45.83 2.10
2348 6776 4.936802 AGACTCTTAAGGAGGTGCTTCTA 58.063 43.478 1.85 0.00 45.83 2.10
2349 6777 3.785364 AGACTCTTAAGGAGGTGCTTCT 58.215 45.455 1.85 0.00 45.83 2.85
2350 6778 4.545208 AAGACTCTTAAGGAGGTGCTTC 57.455 45.455 1.85 0.00 45.83 3.86
2351 6779 4.984146 AAAGACTCTTAAGGAGGTGCTT 57.016 40.909 1.85 2.98 45.83 3.91
2352 6780 4.984146 AAAAGACTCTTAAGGAGGTGCT 57.016 40.909 1.85 0.00 45.83 4.40
2401 6829 6.157904 GTGTTTGGTTCTCTAGTCTTAGGAC 58.842 44.000 0.00 0.00 42.41 3.85
2402 6830 5.245526 GGTGTTTGGTTCTCTAGTCTTAGGA 59.754 44.000 0.00 0.00 0.00 2.94
2403 6831 5.011738 TGGTGTTTGGTTCTCTAGTCTTAGG 59.988 44.000 0.00 0.00 0.00 2.69
2404 6832 5.927115 GTGGTGTTTGGTTCTCTAGTCTTAG 59.073 44.000 0.00 0.00 0.00 2.18
2405 6833 5.221581 GGTGGTGTTTGGTTCTCTAGTCTTA 60.222 44.000 0.00 0.00 0.00 2.10
2406 6834 4.444449 GGTGGTGTTTGGTTCTCTAGTCTT 60.444 45.833 0.00 0.00 0.00 3.01
2407 6835 3.071167 GGTGGTGTTTGGTTCTCTAGTCT 59.929 47.826 0.00 0.00 0.00 3.24
2408 6836 3.071167 AGGTGGTGTTTGGTTCTCTAGTC 59.929 47.826 0.00 0.00 0.00 2.59
2409 6837 3.046374 AGGTGGTGTTTGGTTCTCTAGT 58.954 45.455 0.00 0.00 0.00 2.57
2410 6838 3.771577 AGGTGGTGTTTGGTTCTCTAG 57.228 47.619 0.00 0.00 0.00 2.43
2411 6839 5.633655 TTTAGGTGGTGTTTGGTTCTCTA 57.366 39.130 0.00 0.00 0.00 2.43
2412 6840 4.513406 TTTAGGTGGTGTTTGGTTCTCT 57.487 40.909 0.00 0.00 0.00 3.10
2413 6841 5.784578 AATTTAGGTGGTGTTTGGTTCTC 57.215 39.130 0.00 0.00 0.00 2.87
2414 6842 5.659079 TCAAATTTAGGTGGTGTTTGGTTCT 59.341 36.000 0.00 0.00 32.26 3.01
2415 6843 5.908341 TCAAATTTAGGTGGTGTTTGGTTC 58.092 37.500 0.00 0.00 32.26 3.62
2416 6844 5.941555 TCAAATTTAGGTGGTGTTTGGTT 57.058 34.783 0.00 0.00 32.26 3.67
2417 6845 5.365314 ACATCAAATTTAGGTGGTGTTTGGT 59.635 36.000 0.00 0.00 35.55 3.67
2418 6846 5.852827 ACATCAAATTTAGGTGGTGTTTGG 58.147 37.500 0.00 0.00 35.55 3.28
2419 6847 7.657336 ACTACATCAAATTTAGGTGGTGTTTG 58.343 34.615 0.00 0.00 39.72 2.93
2420 6848 7.833285 ACTACATCAAATTTAGGTGGTGTTT 57.167 32.000 0.00 0.00 39.72 2.83
2421 6849 7.833285 AACTACATCAAATTTAGGTGGTGTT 57.167 32.000 0.00 4.44 39.72 3.32
2422 6850 7.724061 AGAAACTACATCAAATTTAGGTGGTGT 59.276 33.333 0.00 0.00 41.82 4.16
2423 6851 8.023128 CAGAAACTACATCAAATTTAGGTGGTG 58.977 37.037 6.04 0.00 31.88 4.17
2424 6852 7.176690 CCAGAAACTACATCAAATTTAGGTGGT 59.823 37.037 0.00 0.00 0.00 4.16
2425 6853 7.538575 CCAGAAACTACATCAAATTTAGGTGG 58.461 38.462 0.00 0.00 0.00 4.61
2426 6854 7.029563 GCCAGAAACTACATCAAATTTAGGTG 58.970 38.462 0.00 0.00 0.00 4.00
2427 6855 6.128007 CGCCAGAAACTACATCAAATTTAGGT 60.128 38.462 0.00 0.00 0.00 3.08
2428 6856 6.258160 CGCCAGAAACTACATCAAATTTAGG 58.742 40.000 0.00 0.00 0.00 2.69
2429 6857 6.128007 ACCGCCAGAAACTACATCAAATTTAG 60.128 38.462 0.00 0.00 0.00 1.85
2461 6889 6.542005 TCGATGAAGTATTTGTGTTGCCATAT 59.458 34.615 0.00 0.00 0.00 1.78
2484 6912 5.739161 GGTGAAAGCTAAACTTATGCATTCG 59.261 40.000 3.54 0.00 37.75 3.34
2567 6995 9.326413 CTACGTGGAAATATTAGTTGAAAGGAT 57.674 33.333 0.00 0.00 0.00 3.24
2606 7034 5.242171 TGATATGAACATGATCATGGTTGCC 59.758 40.000 33.31 19.39 39.18 4.52


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

AutoCloner maintained by Alex Coulton.