Multiple sequence alignment - TraesCS5A01G524200

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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 TraesCS5A01G524200 chr5A 100.000 2744 0 0 1 2744 684937953 684940696 0.000000e+00 5068.0
1 TraesCS5A01G524200 chr5A 85.484 992 91 34 947 1886 684704789 684703799 0.000000e+00 985.0
2 TraesCS5A01G524200 chr5A 92.509 267 19 1 2095 2361 281122094 281122359 5.540000e-102 381.0
3 TraesCS5A01G524200 chr5A 94.372 231 13 0 702 932 684941504 684941274 3.360000e-94 355.0
4 TraesCS5A01G524200 chr5A 92.181 243 16 1 702 941 661214474 661214232 9.410000e-90 340.0
5 TraesCS5A01G524200 chr4D 90.842 1223 57 21 702 1911 502066824 502065644 0.000000e+00 1587.0
6 TraesCS5A01G524200 chr4D 94.026 703 37 4 4 704 3854803 3855502 0.000000e+00 1061.0
7 TraesCS5A01G524200 chr4D 85.371 957 78 28 1014 1910 502055542 502054588 0.000000e+00 935.0
8 TraesCS5A01G524200 chr4D 93.487 261 17 0 2096 2356 483175803 483176063 3.310000e-104 388.0
9 TraesCS5A01G524200 chr4D 91.701 241 17 3 702 939 502063714 502063954 5.660000e-87 331.0
10 TraesCS5A01G524200 chr4B 90.000 1200 64 23 775 1957 646182389 646183549 0.000000e+00 1500.0
11 TraesCS5A01G524200 chr4B 86.429 980 83 23 948 1886 646146732 646145762 0.000000e+00 1027.0
12 TraesCS5A01G524200 chr4B 92.123 584 46 0 1014 1597 646175251 646174668 0.000000e+00 824.0
13 TraesCS5A01G524200 chr4B 91.143 350 27 3 2399 2744 646162052 646161703 3.200000e-129 472.0
14 TraesCS5A01G524200 chr4B 89.941 338 30 3 2399 2732 646183742 646184079 1.510000e-117 433.0
15 TraesCS5A01G524200 chr4B 89.720 321 12 3 2427 2744 646186382 646186684 9.210000e-105 390.0
16 TraesCS5A01G524200 chr4B 93.033 244 16 1 702 944 646187503 646187260 3.360000e-94 355.0
17 TraesCS5A01G524200 chr4B 81.556 347 22 13 1648 1957 646162584 646162243 5.870000e-62 248.0
18 TraesCS5A01G524200 chr4B 92.683 82 4 1 1920 1999 646184210 646184291 1.730000e-22 117.0
19 TraesCS5A01G524200 chr4B 93.243 74 5 0 1985 2058 646185882 646185955 2.890000e-20 110.0
20 TraesCS5A01G524200 chr4B 91.935 62 4 1 2033 2093 646162214 646162153 4.870000e-13 86.1
21 TraesCS5A01G524200 chr4B 91.935 62 4 1 2033 2093 646183578 646183639 4.870000e-13 86.1
22 TraesCS5A01G524200 chr6D 94.444 702 35 3 3 702 413010390 413009691 0.000000e+00 1077.0
23 TraesCS5A01G524200 chr6D 95.802 262 11 0 2096 2357 450529004 450529265 9.080000e-115 424.0
24 TraesCS5A01G524200 chr6D 93.893 262 15 1 2095 2356 444471234 444470974 7.120000e-106 394.0
25 TraesCS5A01G524200 chr7D 94.437 701 34 4 4 702 133217541 133218238 0.000000e+00 1074.0
26 TraesCS5A01G524200 chr7D 83.607 61 4 6 1265 1325 538603023 538603077 5.000000e-03 52.8
27 TraesCS5A01G524200 chrUn 94.294 701 37 2 4 702 27172217 27171518 0.000000e+00 1070.0
28 TraesCS5A01G524200 chr3D 94.151 701 38 2 4 702 509240155 509240854 0.000000e+00 1064.0
29 TraesCS5A01G524200 chr2D 94.043 705 37 4 4 706 105651093 105650392 0.000000e+00 1064.0
30 TraesCS5A01G524200 chr2D 94.151 701 36 4 4 702 571223875 571223178 0.000000e+00 1062.0
31 TraesCS5A01G524200 chr2D 94.253 261 15 0 2096 2356 535240032 535240292 1.530000e-107 399.0
32 TraesCS5A01G524200 chr5D 93.454 718 43 3 4 718 236156579 236155863 0.000000e+00 1062.0
33 TraesCS5A01G524200 chr1D 93.785 708 40 3 1 706 72673030 72673735 0.000000e+00 1061.0
34 TraesCS5A01G524200 chr6A 95.038 262 13 0 2096 2357 187738694 187738955 1.970000e-111 412.0
35 TraesCS5A01G524200 chr6B 94.656 262 14 0 2096 2357 248353912 248354173 9.150000e-110 407.0
36 TraesCS5A01G524200 chr2A 94.275 262 15 0 2096 2357 625120490 625120229 4.260000e-108 401.0
37 TraesCS5A01G524200 chr2A 93.585 265 16 1 2090 2354 631201666 631201929 7.120000e-106 394.0


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 TraesCS5A01G524200 chr5A 684937953 684940696 2743 False 5068.00 5068 100.000000 1 2744 1 chr5A.!!$F2 2743
1 TraesCS5A01G524200 chr5A 684703799 684704789 990 True 985.00 985 85.484000 947 1886 1 chr5A.!!$R2 939
2 TraesCS5A01G524200 chr4D 502065644 502066824 1180 True 1587.00 1587 90.842000 702 1911 1 chr4D.!!$R2 1209
3 TraesCS5A01G524200 chr4D 3854803 3855502 699 False 1061.00 1061 94.026000 4 704 1 chr4D.!!$F1 700
4 TraesCS5A01G524200 chr4D 502054588 502055542 954 True 935.00 935 85.371000 1014 1910 1 chr4D.!!$R1 896
5 TraesCS5A01G524200 chr4B 646145762 646146732 970 True 1027.00 1027 86.429000 948 1886 1 chr4B.!!$R1 938
6 TraesCS5A01G524200 chr4B 646174668 646175251 583 True 824.00 824 92.123000 1014 1597 1 chr4B.!!$R2 583
7 TraesCS5A01G524200 chr4B 646182389 646186684 4295 False 439.35 1500 91.253667 775 2744 6 chr4B.!!$F1 1969
8 TraesCS5A01G524200 chr4B 646161703 646162584 881 True 268.70 472 88.211333 1648 2744 3 chr4B.!!$R4 1096
9 TraesCS5A01G524200 chr6D 413009691 413010390 699 True 1077.00 1077 94.444000 3 702 1 chr6D.!!$R1 699
10 TraesCS5A01G524200 chr7D 133217541 133218238 697 False 1074.00 1074 94.437000 4 702 1 chr7D.!!$F1 698
11 TraesCS5A01G524200 chrUn 27171518 27172217 699 True 1070.00 1070 94.294000 4 702 1 chrUn.!!$R1 698
12 TraesCS5A01G524200 chr3D 509240155 509240854 699 False 1064.00 1064 94.151000 4 702 1 chr3D.!!$F1 698
13 TraesCS5A01G524200 chr2D 105650392 105651093 701 True 1064.00 1064 94.043000 4 706 1 chr2D.!!$R1 702
14 TraesCS5A01G524200 chr2D 571223178 571223875 697 True 1062.00 1062 94.151000 4 702 1 chr2D.!!$R2 698
15 TraesCS5A01G524200 chr5D 236155863 236156579 716 True 1062.00 1062 93.454000 4 718 1 chr5D.!!$R1 714
16 TraesCS5A01G524200 chr1D 72673030 72673735 705 False 1061.00 1061 93.785000 1 706 1 chr1D.!!$F1 705

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
572 577 0.248289 AGCCATGGTAGCGTTACGTT 59.752 50.0 14.67 2.32 34.64 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 5314 0.889186 GAGTGCCGTGGACCAAATGT 60.889 55.0 0.0 0.0 0.0 2.71 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
59 60 2.037620 GCTGGGCCACGATCTGAGAT 62.038 60.000 0.00 0.00 0.00 2.75
95 96 4.648626 ACGGACTCGGACGTGGGA 62.649 66.667 0.00 0.00 42.39 4.37
100 101 3.812019 CTCGGACGTGGGACGAGG 61.812 72.222 16.24 3.55 46.05 4.63
151 154 0.753867 TGTGTGCGGTGTCTCCTAAA 59.246 50.000 0.00 0.00 0.00 1.85
168 171 3.927163 AACCTAGCCGCCACGAACG 62.927 63.158 0.00 0.00 0.00 3.95
221 224 1.900498 GTTCCCTTGCTGCTGCTGT 60.900 57.895 17.00 0.00 40.48 4.40
237 240 2.264794 GTCGCCGGTGACTCCATT 59.735 61.111 35.30 0.00 35.95 3.16
287 290 1.366366 CAGGTCTCCGAAACCACGT 59.634 57.895 0.00 0.00 39.39 4.49
299 302 0.834612 AACCACGTCCTTCTGGTTCA 59.165 50.000 0.30 0.00 45.94 3.18
362 365 1.139734 GACTGCTCGCTTCCGATCA 59.860 57.895 0.00 0.00 43.47 2.92
492 495 4.204028 AGCCACCAAAGCCACGGT 62.204 61.111 0.00 0.00 35.27 4.83
495 498 1.528309 CCACCAAAGCCACGGTCTT 60.528 57.895 0.00 0.00 31.41 3.01
546 549 2.403252 ATCCCGCTCCTACTGTTTTG 57.597 50.000 0.00 0.00 0.00 2.44
560 563 4.692228 ACTGTTTTGTGTTTTAGCCATGG 58.308 39.130 7.63 7.63 0.00 3.66
572 577 0.248289 AGCCATGGTAGCGTTACGTT 59.752 50.000 14.67 2.32 34.64 3.99
582 587 5.106197 TGGTAGCGTTACGTTGATCTTTCTA 60.106 40.000 6.63 0.00 0.00 2.10
609 614 2.128035 GCGTAGTATGTGCTAGCTTGG 58.872 52.381 17.23 0.00 0.00 3.61
723 729 0.536006 AGCTGGTGCAGAAGGTTGTC 60.536 55.000 0.00 0.00 42.74 3.18
724 730 0.819259 GCTGGTGCAGAAGGTTGTCA 60.819 55.000 0.00 0.00 39.41 3.58
741 747 2.103373 GTCATGGAGCTCTCACCTGTA 58.897 52.381 14.64 0.00 0.00 2.74
745 751 1.007118 TGGAGCTCTCACCTGTATGGA 59.993 52.381 14.64 0.00 39.71 3.41
885 895 7.581213 TCTTATCTTCTCTGTCTGAGGATTC 57.419 40.000 6.87 0.00 42.86 2.52
929 939 1.065564 AGCCATGAGAACTTGAGCCTC 60.066 52.381 0.00 0.00 0.00 4.70
965 975 0.397564 TAAAACCCCACCACCTCGAC 59.602 55.000 0.00 0.00 0.00 4.20
989 1001 3.160047 CCTGCGCTCTCCCATCCT 61.160 66.667 9.73 0.00 0.00 3.24
990 1002 2.420890 CTGCGCTCTCCCATCCTC 59.579 66.667 9.73 0.00 0.00 3.71
991 1003 3.157252 TGCGCTCTCCCATCCTCC 61.157 66.667 9.73 0.00 0.00 4.30
992 1004 4.292178 GCGCTCTCCCATCCTCCG 62.292 72.222 0.00 0.00 0.00 4.63
993 1005 2.519541 CGCTCTCCCATCCTCCGA 60.520 66.667 0.00 0.00 0.00 4.55
1356 1377 1.013596 TGCAGACCAACTTGTTCGTG 58.986 50.000 0.00 0.00 0.00 4.35
1407 1428 0.966370 AACTCCCCTTCGACTCCTCG 60.966 60.000 0.00 0.00 41.65 4.63
1746 1817 4.212214 GCCGAAGCTGGTAAAGATTAGATG 59.788 45.833 0.00 0.00 33.71 2.90
1798 1895 4.350816 ACCAGCCATGTGGAATTAGCTATA 59.649 41.667 9.25 0.00 40.44 1.31
1811 1921 9.326489 TGGAATTAGCTATACTATCTTGGTCAT 57.674 33.333 0.00 0.00 0.00 3.06
1816 1946 5.098893 GCTATACTATCTTGGTCATGAGCG 58.901 45.833 19.36 6.92 0.00 5.03
1817 1947 2.231215 ACTATCTTGGTCATGAGCGC 57.769 50.000 19.36 0.00 0.00 5.92
1850 2000 5.835257 AGATTCATGAATTATTTGCCGTGG 58.165 37.500 21.57 0.00 0.00 4.94
1911 2065 9.248291 ACACTTGTTTTTCTTAATGTTGCATAG 57.752 29.630 0.00 0.00 0.00 2.23
1922 2076 9.079833 TCTTAATGTTGCATAGTACGTTTAGAC 57.920 33.333 0.00 0.00 29.18 2.59
1930 2085 7.198390 TGCATAGTACGTTTAGACAATACTCC 58.802 38.462 0.00 0.00 32.51 3.85
1952 2107 8.652290 ACTCCTATAATAACAGAGATTGAACCC 58.348 37.037 0.00 0.00 0.00 4.11
1953 2108 8.561536 TCCTATAATAACAGAGATTGAACCCA 57.438 34.615 0.00 0.00 0.00 4.51
1954 2109 9.170890 TCCTATAATAACAGAGATTGAACCCAT 57.829 33.333 0.00 0.00 0.00 4.00
1959 2114 8.511604 AATAACAGAGATTGAACCCATAACTG 57.488 34.615 0.00 0.00 0.00 3.16
1960 2115 5.505181 ACAGAGATTGAACCCATAACTGT 57.495 39.130 0.00 0.00 0.00 3.55
1961 2116 5.491982 ACAGAGATTGAACCCATAACTGTC 58.508 41.667 0.00 0.00 31.87 3.51
1962 2117 5.013079 ACAGAGATTGAACCCATAACTGTCA 59.987 40.000 0.00 0.00 31.87 3.58
1963 2118 5.939883 CAGAGATTGAACCCATAACTGTCAA 59.060 40.000 0.00 0.00 0.00 3.18
1964 2119 6.430925 CAGAGATTGAACCCATAACTGTCAAA 59.569 38.462 0.00 0.00 0.00 2.69
1965 2120 7.004086 AGAGATTGAACCCATAACTGTCAAAA 58.996 34.615 0.00 0.00 0.00 2.44
1966 2121 7.505585 AGAGATTGAACCCATAACTGTCAAAAA 59.494 33.333 0.00 0.00 0.00 1.94
2012 2167 7.946381 TTATTAGTGCAAAATACATGGACCA 57.054 32.000 0.00 0.00 39.65 4.02
2013 2168 5.637006 TTAGTGCAAAATACATGGACCAC 57.363 39.130 0.00 0.00 39.65 4.16
2014 2169 3.495331 AGTGCAAAATACATGGACCACA 58.505 40.909 0.00 0.00 39.65 4.17
2015 2170 4.088634 AGTGCAAAATACATGGACCACAT 58.911 39.130 0.00 0.00 39.65 3.21
2016 2171 5.260424 AGTGCAAAATACATGGACCACATA 58.740 37.500 0.00 0.00 39.65 2.29
2017 2172 5.714333 AGTGCAAAATACATGGACCACATAA 59.286 36.000 0.00 0.00 39.65 1.90
2018 2173 6.210385 AGTGCAAAATACATGGACCACATAAA 59.790 34.615 0.00 0.00 39.65 1.40
2019 2174 6.870965 GTGCAAAATACATGGACCACATAAAA 59.129 34.615 0.00 0.00 37.84 1.52
2020 2175 7.548780 GTGCAAAATACATGGACCACATAAAAT 59.451 33.333 0.00 0.00 37.84 1.82
2021 2176 8.753133 TGCAAAATACATGGACCACATAAAATA 58.247 29.630 0.00 0.00 37.84 1.40
2022 2177 9.030301 GCAAAATACATGGACCACATAAAATAC 57.970 33.333 0.00 0.00 37.84 1.89
2023 2178 9.232082 CAAAATACATGGACCACATAAAATACG 57.768 33.333 0.00 0.00 37.84 3.06
2024 2179 8.514330 AAATACATGGACCACATAAAATACGT 57.486 30.769 0.00 0.00 37.84 3.57
2025 2180 5.811399 ACATGGACCACATAAAATACGTG 57.189 39.130 0.00 0.00 37.84 4.49
2082 2237 4.850347 AACGTATCTCCTTCCCTATTCG 57.150 45.455 0.00 0.00 0.00 3.34
2083 2238 3.155501 ACGTATCTCCTTCCCTATTCGG 58.844 50.000 0.00 0.00 0.00 4.30
2107 2262 2.916702 AAAAACGTACTCCCTCCGTT 57.083 45.000 0.00 0.00 45.76 4.44
2110 2265 2.916702 AACGTACTCCCTCCGTTTTT 57.083 45.000 0.00 0.00 41.58 1.94
2112 2267 4.541973 AACGTACTCCCTCCGTTTTTAT 57.458 40.909 0.00 0.00 41.58 1.40
2113 2268 4.541973 ACGTACTCCCTCCGTTTTTATT 57.458 40.909 0.00 0.00 0.00 1.40
2114 2269 4.898320 ACGTACTCCCTCCGTTTTTATTT 58.102 39.130 0.00 0.00 0.00 1.40
2115 2270 6.036577 ACGTACTCCCTCCGTTTTTATTTA 57.963 37.500 0.00 0.00 0.00 1.40
2116 2271 5.869344 ACGTACTCCCTCCGTTTTTATTTAC 59.131 40.000 0.00 0.00 0.00 2.01
2117 2272 6.101997 CGTACTCCCTCCGTTTTTATTTACT 58.898 40.000 0.00 0.00 0.00 2.24
2118 2273 6.591448 CGTACTCCCTCCGTTTTTATTTACTT 59.409 38.462 0.00 0.00 0.00 2.24
2119 2274 7.201470 CGTACTCCCTCCGTTTTTATTTACTTC 60.201 40.741 0.00 0.00 0.00 3.01
2120 2275 5.640783 ACTCCCTCCGTTTTTATTTACTTCG 59.359 40.000 0.00 0.00 0.00 3.79
2121 2276 4.392754 TCCCTCCGTTTTTATTTACTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
2122 2277 4.154556 CCCTCCGTTTTTATTTACTTCGCA 59.845 41.667 0.00 0.00 0.00 5.10
2123 2278 5.163693 CCCTCCGTTTTTATTTACTTCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
2124 2279 6.037391 CCCTCCGTTTTTATTTACTTCGCATA 59.963 38.462 0.00 0.00 0.00 3.14
2125 2280 7.255001 CCCTCCGTTTTTATTTACTTCGCATAT 60.255 37.037 0.00 0.00 0.00 1.78
2126 2281 8.126700 CCTCCGTTTTTATTTACTTCGCATATT 58.873 33.333 0.00 0.00 0.00 1.28
2129 2284 8.889000 CCGTTTTTATTTACTTCGCATATTAGC 58.111 33.333 0.00 0.00 0.00 3.09
2130 2285 9.646336 CGTTTTTATTTACTTCGCATATTAGCT 57.354 29.630 0.00 0.00 0.00 3.32
2134 2289 9.944663 TTTATTTACTTCGCATATTAGCTTTGG 57.055 29.630 0.00 0.00 0.00 3.28
2135 2290 6.995511 TTTACTTCGCATATTAGCTTTGGT 57.004 33.333 0.00 0.00 0.00 3.67
2136 2291 6.598753 TTACTTCGCATATTAGCTTTGGTC 57.401 37.500 0.00 0.00 0.00 4.02
2137 2292 4.513442 ACTTCGCATATTAGCTTTGGTCA 58.487 39.130 0.00 0.00 0.00 4.02
2138 2293 4.941263 ACTTCGCATATTAGCTTTGGTCAA 59.059 37.500 0.00 0.00 0.00 3.18
2139 2294 5.414454 ACTTCGCATATTAGCTTTGGTCAAA 59.586 36.000 0.00 0.00 0.00 2.69
2229 2384 9.764870 CAATACCATTAGATTCATTATTGAGCG 57.235 33.333 0.00 0.00 32.27 5.03
2230 2385 6.246420 ACCATTAGATTCATTATTGAGCGC 57.754 37.500 0.00 0.00 32.27 5.92
2231 2386 5.764686 ACCATTAGATTCATTATTGAGCGCA 59.235 36.000 11.47 0.00 32.27 6.09
2232 2387 6.082338 CCATTAGATTCATTATTGAGCGCAC 58.918 40.000 11.47 3.13 32.27 5.34
2233 2388 6.072838 CCATTAGATTCATTATTGAGCGCACT 60.073 38.462 11.47 0.00 32.27 4.40
2234 2389 6.925610 TTAGATTCATTATTGAGCGCACTT 57.074 33.333 11.47 0.00 32.27 3.16
2235 2390 5.824904 AGATTCATTATTGAGCGCACTTT 57.175 34.783 11.47 0.00 32.27 2.66
2236 2391 5.814783 AGATTCATTATTGAGCGCACTTTC 58.185 37.500 11.47 0.00 32.27 2.62
2237 2392 3.656651 TCATTATTGAGCGCACTTTCG 57.343 42.857 11.47 0.00 0.00 3.46
2251 2406 6.974677 CGCACTTTCGCATCATATAAAATT 57.025 33.333 0.00 0.00 0.00 1.82
2252 2407 6.790247 CGCACTTTCGCATCATATAAAATTG 58.210 36.000 0.00 0.00 0.00 2.32
2253 2408 6.414694 CGCACTTTCGCATCATATAAAATTGT 59.585 34.615 0.00 0.00 0.00 2.71
2254 2409 7.044117 CGCACTTTCGCATCATATAAAATTGTT 60.044 33.333 0.00 0.00 0.00 2.83
2255 2410 9.232082 GCACTTTCGCATCATATAAAATTGTTA 57.768 29.630 0.00 0.00 0.00 2.41
2335 2490 8.700051 ACTTCAGTCAACTATAATATGCAGAGT 58.300 33.333 0.00 0.00 0.00 3.24
2351 2508 6.817765 TGCAGAGTAAATAAAAACAGAGGG 57.182 37.500 0.00 0.00 0.00 4.30
2352 2509 6.539173 TGCAGAGTAAATAAAAACAGAGGGA 58.461 36.000 0.00 0.00 0.00 4.20
2378 2535 1.962807 TCCTTCCCACAAACAAGCATG 59.037 47.619 0.00 0.00 0.00 4.06
2392 2555 5.018539 ACAAGCATGCCTACTACGAATAA 57.981 39.130 15.66 0.00 0.00 1.40
2398 2561 5.107065 GCATGCCTACTACGAATAATGTTCC 60.107 44.000 6.36 0.00 0.00 3.62
2423 2586 4.202409 GGTATCTTCATTCTCCCCCTCTTG 60.202 50.000 0.00 0.00 0.00 3.02
2429 5238 3.457380 TCATTCTCCCCCTCTTGAATGAG 59.543 47.826 11.63 0.00 45.29 2.90
2432 5241 3.044156 TCTCCCCCTCTTGAATGAGATG 58.956 50.000 0.00 0.00 36.23 2.90
2446 5255 1.339535 TGAGATGTGTTAATGCCGCCA 60.340 47.619 0.00 0.00 0.00 5.69
2452 5261 4.727507 TGTGTTAATGCCGCCATATTTT 57.272 36.364 0.00 0.00 0.00 1.82
2505 5314 2.099652 CTGGGTGCCTTGTCACTCGA 62.100 60.000 0.00 0.00 40.26 4.04
2712 5526 5.536161 ACCATTGTTATGCTTTAGCCTATGG 59.464 40.000 13.33 13.33 41.18 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.994995 ACAGCCCACGATCCGACA 60.995 61.111 0.00 0.00 0.00 4.35
95 96 3.063084 GGAGAGACGTGGCCTCGT 61.063 66.667 31.20 31.20 46.88 4.18
130 133 0.246360 TAGGAGACACCGCACACATG 59.754 55.000 0.00 0.00 44.74 3.21
131 134 0.973632 TTAGGAGACACCGCACACAT 59.026 50.000 0.00 0.00 44.74 3.21
132 135 0.753867 TTTAGGAGACACCGCACACA 59.246 50.000 0.00 0.00 44.74 3.72
151 154 4.430765 CGTTCGTGGCGGCTAGGT 62.431 66.667 11.43 0.00 0.00 3.08
199 202 1.597854 CAGCAGCAAGGGAACGACA 60.598 57.895 0.00 0.00 0.00 4.35
221 224 2.577059 GAATGGAGTCACCGGCGA 59.423 61.111 9.30 0.00 42.61 5.54
287 290 1.553248 CCCGTACATGAACCAGAAGGA 59.447 52.381 0.00 0.00 38.69 3.36
299 302 3.087906 GCCCCTCACCCCGTACAT 61.088 66.667 0.00 0.00 0.00 2.29
362 365 2.220313 GCGGACGTAGAGGAAGTAGAT 58.780 52.381 0.00 0.00 0.00 1.98
473 476 2.906897 CGTGGCTTTGGTGGCTGT 60.907 61.111 0.00 0.00 0.00 4.40
475 478 4.204028 ACCGTGGCTTTGGTGGCT 62.204 61.111 0.00 0.00 37.02 4.75
492 495 0.991146 TCCAGTAGGCCATGCAAAGA 59.009 50.000 5.01 0.00 33.74 2.52
495 498 1.609239 CCTCCAGTAGGCCATGCAA 59.391 57.895 5.01 0.00 38.97 4.08
546 549 2.081462 ACGCTACCATGGCTAAAACAC 58.919 47.619 13.04 0.00 0.00 3.32
560 563 5.796935 TGTAGAAAGATCAACGTAACGCTAC 59.203 40.000 0.00 0.00 0.00 3.58
572 577 9.678941 CATACTACGCTAATTGTAGAAAGATCA 57.321 33.333 7.11 0.00 41.44 2.92
582 587 4.982916 GCTAGCACATACTACGCTAATTGT 59.017 41.667 10.63 0.00 37.77 2.71
678 683 8.177119 TGTGTTGAGTAAATAGGCAATTTCTT 57.823 30.769 0.00 0.00 38.71 2.52
723 729 2.224233 CCATACAGGTGAGAGCTCCATG 60.224 54.545 10.93 5.82 0.00 3.66
724 730 2.045524 CCATACAGGTGAGAGCTCCAT 58.954 52.381 10.93 0.00 0.00 3.41
885 895 0.872388 GTTTACAACAGGAGGCCACG 59.128 55.000 5.01 0.00 0.00 4.94
907 917 1.339438 GGCTCAAGTTCTCATGGCTGA 60.339 52.381 0.00 0.00 0.00 4.26
929 939 4.925646 GGTTTTAAGAAGGAATGCAGCTTG 59.074 41.667 0.00 0.00 0.00 4.01
932 942 3.368427 GGGGTTTTAAGAAGGAATGCAGC 60.368 47.826 0.00 0.00 0.00 5.25
933 943 3.831911 TGGGGTTTTAAGAAGGAATGCAG 59.168 43.478 0.00 0.00 0.00 4.41
940 950 2.158370 AGGTGGTGGGGTTTTAAGAAGG 60.158 50.000 0.00 0.00 0.00 3.46
941 951 3.154710 GAGGTGGTGGGGTTTTAAGAAG 58.845 50.000 0.00 0.00 0.00 2.85
1706 1756 1.529309 GCATCAACCTCCTCCTCCC 59.471 63.158 0.00 0.00 0.00 4.30
1798 1895 1.759445 AGCGCTCATGACCAAGATAGT 59.241 47.619 2.64 0.00 0.00 2.12
1811 1921 3.439825 TGAATCTTTTATTGCAGCGCTCA 59.560 39.130 7.13 6.15 0.00 4.26
1850 2000 5.866633 TGTGTGTGTTTCATTGTTTTTCCTC 59.133 36.000 0.00 0.00 0.00 3.71
1940 2095 5.762179 TGACAGTTATGGGTTCAATCTCT 57.238 39.130 0.00 0.00 0.00 3.10
1941 2096 6.817765 TTTGACAGTTATGGGTTCAATCTC 57.182 37.500 0.00 0.00 0.00 2.75
1942 2097 7.595819 TTTTTGACAGTTATGGGTTCAATCT 57.404 32.000 0.00 0.00 0.00 2.40
2012 2167 8.700722 TCGTATTAACCACACGTATTTTATGT 57.299 30.769 0.00 0.00 37.02 2.29
2013 2168 9.575702 CATCGTATTAACCACACGTATTTTATG 57.424 33.333 0.00 0.00 37.02 1.90
2014 2169 9.531942 TCATCGTATTAACCACACGTATTTTAT 57.468 29.630 0.00 0.00 37.02 1.40
2015 2170 8.923609 TCATCGTATTAACCACACGTATTTTA 57.076 30.769 0.00 0.00 37.02 1.52
2016 2171 7.830940 TCATCGTATTAACCACACGTATTTT 57.169 32.000 0.00 0.00 37.02 1.82
2017 2172 7.042321 CCATCATCGTATTAACCACACGTATTT 60.042 37.037 0.00 0.00 37.02 1.40
2018 2173 6.422701 CCATCATCGTATTAACCACACGTATT 59.577 38.462 0.00 0.00 37.02 1.89
2019 2174 5.924254 CCATCATCGTATTAACCACACGTAT 59.076 40.000 0.00 0.00 37.02 3.06
2020 2175 5.163530 ACCATCATCGTATTAACCACACGTA 60.164 40.000 0.00 0.00 37.02 3.57
2021 2176 4.116961 CCATCATCGTATTAACCACACGT 58.883 43.478 0.00 0.00 37.02 4.49
2022 2177 4.116961 ACCATCATCGTATTAACCACACG 58.883 43.478 0.00 0.00 37.03 4.49
2023 2178 5.357257 AGACCATCATCGTATTAACCACAC 58.643 41.667 0.00 0.00 0.00 3.82
2024 2179 5.607939 AGACCATCATCGTATTAACCACA 57.392 39.130 0.00 0.00 0.00 4.17
2025 2180 6.046593 TGAAGACCATCATCGTATTAACCAC 58.953 40.000 0.00 0.00 0.00 4.16
2058 2213 5.619533 CGAATAGGGAAGGAGATACGTTAGC 60.620 48.000 0.00 0.00 0.00 3.09
2093 2248 6.101997 AGTAAATAAAAACGGAGGGAGTACG 58.898 40.000 0.00 0.00 0.00 3.67
2094 2249 7.201470 CGAAGTAAATAAAAACGGAGGGAGTAC 60.201 40.741 0.00 0.00 0.00 2.73
2095 2250 6.813152 CGAAGTAAATAAAAACGGAGGGAGTA 59.187 38.462 0.00 0.00 0.00 2.59
2096 2251 5.640783 CGAAGTAAATAAAAACGGAGGGAGT 59.359 40.000 0.00 0.00 0.00 3.85
2097 2252 5.446875 GCGAAGTAAATAAAAACGGAGGGAG 60.447 44.000 0.00 0.00 0.00 4.30
2098 2253 4.392754 GCGAAGTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
2099 2254 4.154556 TGCGAAGTAAATAAAAACGGAGGG 59.845 41.667 0.00 0.00 0.00 4.30
2100 2255 5.285798 TGCGAAGTAAATAAAAACGGAGG 57.714 39.130 0.00 0.00 0.00 4.30
2103 2258 8.889000 GCTAATATGCGAAGTAAATAAAAACGG 58.111 33.333 0.00 0.00 0.00 4.44
2104 2259 9.646336 AGCTAATATGCGAAGTAAATAAAAACG 57.354 29.630 0.00 0.00 38.13 3.60
2108 2263 9.944663 CCAAAGCTAATATGCGAAGTAAATAAA 57.055 29.630 0.00 0.00 38.13 1.40
2109 2264 9.116067 ACCAAAGCTAATATGCGAAGTAAATAA 57.884 29.630 0.00 0.00 38.13 1.40
2110 2265 8.671384 ACCAAAGCTAATATGCGAAGTAAATA 57.329 30.769 0.00 0.00 38.13 1.40
2111 2266 7.282224 TGACCAAAGCTAATATGCGAAGTAAAT 59.718 33.333 0.00 0.00 38.13 1.40
2112 2267 6.596106 TGACCAAAGCTAATATGCGAAGTAAA 59.404 34.615 0.00 0.00 38.13 2.01
2113 2268 6.110033 TGACCAAAGCTAATATGCGAAGTAA 58.890 36.000 0.00 0.00 38.13 2.24
2114 2269 5.666462 TGACCAAAGCTAATATGCGAAGTA 58.334 37.500 0.00 0.00 38.13 2.24
2115 2270 4.513442 TGACCAAAGCTAATATGCGAAGT 58.487 39.130 0.00 0.00 38.13 3.01
2116 2271 5.484173 TTGACCAAAGCTAATATGCGAAG 57.516 39.130 0.00 0.00 38.13 3.79
2117 2272 5.879237 CTTTGACCAAAGCTAATATGCGAA 58.121 37.500 9.25 0.00 40.94 4.70
2118 2273 5.484173 CTTTGACCAAAGCTAATATGCGA 57.516 39.130 9.25 0.00 40.94 5.10
2203 2358 9.764870 CGCTCAATAATGAATCTAATGGTATTG 57.235 33.333 0.00 0.00 34.49 1.90
2204 2359 8.454106 GCGCTCAATAATGAATCTAATGGTATT 58.546 33.333 0.00 0.00 34.49 1.89
2205 2360 7.607607 TGCGCTCAATAATGAATCTAATGGTAT 59.392 33.333 9.73 0.00 34.49 2.73
2206 2361 6.934083 TGCGCTCAATAATGAATCTAATGGTA 59.066 34.615 9.73 0.00 34.49 3.25
2207 2362 5.764686 TGCGCTCAATAATGAATCTAATGGT 59.235 36.000 9.73 0.00 34.49 3.55
2208 2363 6.072838 AGTGCGCTCAATAATGAATCTAATGG 60.073 38.462 9.73 0.00 34.49 3.16
2209 2364 6.895898 AGTGCGCTCAATAATGAATCTAATG 58.104 36.000 9.73 0.00 34.49 1.90
2210 2365 7.502120 AAGTGCGCTCAATAATGAATCTAAT 57.498 32.000 9.73 0.00 34.49 1.73
2211 2366 6.925610 AAGTGCGCTCAATAATGAATCTAA 57.074 33.333 9.73 0.00 34.49 2.10
2212 2367 6.292328 CGAAAGTGCGCTCAATAATGAATCTA 60.292 38.462 9.73 0.00 34.49 1.98
2213 2368 5.503031 CGAAAGTGCGCTCAATAATGAATCT 60.503 40.000 9.73 0.00 34.49 2.40
2214 2369 4.667948 CGAAAGTGCGCTCAATAATGAATC 59.332 41.667 9.73 0.00 34.49 2.52
2215 2370 4.591202 CGAAAGTGCGCTCAATAATGAAT 58.409 39.130 9.73 0.00 34.49 2.57
2216 2371 4.002267 CGAAAGTGCGCTCAATAATGAA 57.998 40.909 9.73 0.00 34.49 2.57
2217 2372 3.656651 CGAAAGTGCGCTCAATAATGA 57.343 42.857 9.73 0.00 0.00 2.57
2228 2383 6.414694 ACAATTTTATATGATGCGAAAGTGCG 59.585 34.615 0.00 0.00 37.81 5.34
2229 2384 7.684062 ACAATTTTATATGATGCGAAAGTGC 57.316 32.000 0.00 0.00 30.93 4.40
2308 2463 9.190858 CTCTGCATATTATAGTTGACTGAAGTC 57.809 37.037 3.41 3.41 44.97 3.01
2309 2464 8.700051 ACTCTGCATATTATAGTTGACTGAAGT 58.300 33.333 0.00 0.00 0.00 3.01
2325 2480 9.125026 CCCTCTGTTTTTATTTACTCTGCATAT 57.875 33.333 0.00 0.00 0.00 1.78
2326 2481 8.325787 TCCCTCTGTTTTTATTTACTCTGCATA 58.674 33.333 0.00 0.00 0.00 3.14
2327 2482 7.175104 TCCCTCTGTTTTTATTTACTCTGCAT 58.825 34.615 0.00 0.00 0.00 3.96
2328 2483 6.539173 TCCCTCTGTTTTTATTTACTCTGCA 58.461 36.000 0.00 0.00 0.00 4.41
2329 2484 6.655425 ACTCCCTCTGTTTTTATTTACTCTGC 59.345 38.462 0.00 0.00 0.00 4.26
2330 2485 9.892130 ATACTCCCTCTGTTTTTATTTACTCTG 57.108 33.333 0.00 0.00 0.00 3.35
2351 2508 4.553330 TGTTTGTGGGAAGGAGATACTC 57.447 45.455 0.00 0.00 0.00 2.59
2352 2509 4.807643 GCTTGTTTGTGGGAAGGAGATACT 60.808 45.833 0.00 0.00 0.00 2.12
2378 2535 4.989168 CCAGGAACATTATTCGTAGTAGGC 59.011 45.833 0.00 0.00 0.00 3.93
2392 2555 5.163152 GGGAGAATGAAGATACCAGGAACAT 60.163 44.000 0.00 0.00 0.00 2.71
2398 2561 3.321950 AGGGGGAGAATGAAGATACCAG 58.678 50.000 0.00 0.00 0.00 4.00
2423 2586 3.548818 GGCGGCATTAACACATCTCATTC 60.549 47.826 3.07 0.00 0.00 2.67
2429 5238 4.503741 AATATGGCGGCATTAACACATC 57.496 40.909 30.54 0.00 0.00 3.06
2432 5241 6.526674 GCTATAAAATATGGCGGCATTAACAC 59.473 38.462 30.54 7.40 0.00 3.32
2505 5314 0.889186 GAGTGCCGTGGACCAAATGT 60.889 55.000 0.00 0.00 0.00 2.71
2645 5455 5.531287 GTGAAGGAAACTATTGTCCACAGTT 59.469 40.000 0.00 0.00 42.68 3.16
2712 5526 2.159827 GGAGACGACGAAAAAGCACATC 60.160 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.