Multiple sequence alignment - TraesCS2B01G184300

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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 TraesCS2B01G184300 chr2B 100.000 2207 0 0 1 2207 159299238 159301444 0.000000e+00 4076.0
1 TraesCS2B01G184300 chr2B 85.641 390 43 10 942 1323 159319085 159319469 4.420000e-107 398.0
2 TraesCS2B01G184300 chr2D 96.327 735 26 1 1 734 109802848 109803582 0.000000e+00 1206.0
3 TraesCS2B01G184300 chr2D 93.851 618 32 4 728 1344 109830634 109831246 0.000000e+00 926.0
4 TraesCS2B01G184300 chr2D 91.445 526 33 8 825 1344 109737494 109738013 0.000000e+00 712.0
5 TraesCS2B01G184300 chr2D 94.250 400 20 1 1 397 109736693 109737092 1.870000e-170 608.0
6 TraesCS2B01G184300 chr2D 87.435 382 42 4 932 1312 109793373 109793749 3.370000e-118 435.0
7 TraesCS2B01G184300 chr2D 85.238 420 49 11 174 590 109901359 109901768 9.420000e-114 420.0
8 TraesCS2B01G184300 chr2D 92.632 285 21 0 399 683 109737177 109737461 5.670000e-111 411.0
9 TraesCS2B01G184300 chr2D 86.234 385 43 7 933 1312 109902020 109902399 2.040000e-110 409.0
10 TraesCS2B01G184300 chr2D 92.029 138 11 0 1903 2040 109831235 109831372 6.220000e-46 195.0
11 TraesCS2B01G184300 chr2D 100.000 37 0 0 796 832 545944813 545944849 3.930000e-08 69.4
12 TraesCS2B01G184300 chr7B 96.786 560 11 5 1350 1907 332243373 332243927 0.000000e+00 928.0
13 TraesCS2B01G184300 chr7B 85.897 78 4 2 757 830 677422931 677422857 2.350000e-10 76.8
14 TraesCS2B01G184300 chr5B 96.926 553 12 4 1357 1907 694030886 694030337 0.000000e+00 922.0
15 TraesCS2B01G184300 chr1B 97.248 545 13 1 1365 1907 231934210 231933666 0.000000e+00 922.0
16 TraesCS2B01G184300 chr6B 95.993 549 18 3 1361 1907 25639716 25640262 0.000000e+00 889.0
17 TraesCS2B01G184300 chr6B 95.993 549 18 3 1361 1907 25657114 25657660 0.000000e+00 889.0
18 TraesCS2B01G184300 chrUn 92.687 547 34 4 1361 1905 412452076 412451534 0.000000e+00 784.0
19 TraesCS2B01G184300 chrUn 92.831 544 33 4 1361 1902 471885977 471886516 0.000000e+00 784.0
20 TraesCS2B01G184300 chrUn 92.463 544 35 4 1361 1902 417965335 417965874 0.000000e+00 773.0
21 TraesCS2B01G184300 chrUn 92.279 544 36 4 1361 1902 15290319 15290858 0.000000e+00 767.0
22 TraesCS2B01G184300 chr2A 91.373 510 35 5 834 1342 105531693 105532194 0.000000e+00 689.0
23 TraesCS2B01G184300 chr2A 87.153 576 56 11 184 746 105531100 105531670 2.390000e-179 638.0
24 TraesCS2B01G184300 chr2A 81.660 747 65 27 1 683 105521910 105522648 2.480000e-154 555.0
25 TraesCS2B01G184300 chr2A 85.029 521 65 11 825 1343 105522681 105523190 3.250000e-143 518.0
26 TraesCS2B01G184300 chr2A 87.535 361 37 7 233 591 105540676 105541030 5.670000e-111 411.0
27 TraesCS2B01G184300 chr2A 84.864 403 45 10 921 1312 105541247 105541644 2.050000e-105 392.0
28 TraesCS2B01G184300 chr2A 91.304 138 12 0 1903 2040 105532185 105532322 2.890000e-44 189.0
29 TraesCS2B01G184300 chr2A 91.304 46 3 1 798 842 436008530 436008575 6.580000e-06 62.1
30 TraesCS2B01G184300 chr2A 100.000 32 0 0 725 756 105522650 105522681 2.370000e-05 60.2
31 TraesCS2B01G184300 chr7D 93.960 149 6 3 2043 2189 411022131 411021984 2.850000e-54 222.0
32 TraesCS2B01G184300 chr5D 93.382 136 8 1 2038 2173 302892843 302892977 1.340000e-47 200.0
33 TraesCS2B01G184300 chr5A 85.526 76 4 3 757 831 406535064 406534995 3.040000e-09 73.1
34 TraesCS2B01G184300 chr3D 100.000 37 0 0 796 832 438805124 438805088 3.930000e-08 69.4
35 TraesCS2B01G184300 chr3D 100.000 37 0 0 796 832 517884784 517884820 3.930000e-08 69.4
36 TraesCS2B01G184300 chr4B 95.238 42 2 0 796 837 660583491 660583450 1.410000e-07 67.6
37 TraesCS2B01G184300 chr1D 93.023 43 3 0 796 838 447530713 447530755 1.830000e-06 63.9


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 TraesCS2B01G184300 chr2B 159299238 159301444 2206 False 4076.000000 4076 100.000000 1 2207 1 chr2B.!!$F1 2206
1 TraesCS2B01G184300 chr2D 109802848 109803582 734 False 1206.000000 1206 96.327000 1 734 1 chr2D.!!$F2 733
2 TraesCS2B01G184300 chr2D 109736693 109738013 1320 False 577.000000 712 92.775667 1 1344 3 chr2D.!!$F4 1343
3 TraesCS2B01G184300 chr2D 109830634 109831372 738 False 560.500000 926 92.940000 728 2040 2 chr2D.!!$F5 1312
4 TraesCS2B01G184300 chr2D 109901359 109902399 1040 False 414.500000 420 85.736000 174 1312 2 chr2D.!!$F6 1138
5 TraesCS2B01G184300 chr7B 332243373 332243927 554 False 928.000000 928 96.786000 1350 1907 1 chr7B.!!$F1 557
6 TraesCS2B01G184300 chr5B 694030337 694030886 549 True 922.000000 922 96.926000 1357 1907 1 chr5B.!!$R1 550
7 TraesCS2B01G184300 chr1B 231933666 231934210 544 True 922.000000 922 97.248000 1365 1907 1 chr1B.!!$R1 542
8 TraesCS2B01G184300 chr6B 25639716 25640262 546 False 889.000000 889 95.993000 1361 1907 1 chr6B.!!$F1 546
9 TraesCS2B01G184300 chr6B 25657114 25657660 546 False 889.000000 889 95.993000 1361 1907 1 chr6B.!!$F2 546
10 TraesCS2B01G184300 chrUn 412451534 412452076 542 True 784.000000 784 92.687000 1361 1905 1 chrUn.!!$R1 544
11 TraesCS2B01G184300 chrUn 471885977 471886516 539 False 784.000000 784 92.831000 1361 1902 1 chrUn.!!$F3 541
12 TraesCS2B01G184300 chrUn 417965335 417965874 539 False 773.000000 773 92.463000 1361 1902 1 chrUn.!!$F2 541
13 TraesCS2B01G184300 chrUn 15290319 15290858 539 False 767.000000 767 92.279000 1361 1902 1 chrUn.!!$F1 541
14 TraesCS2B01G184300 chr2A 105531100 105532322 1222 False 505.333333 689 89.943333 184 2040 3 chr2A.!!$F3 1856
15 TraesCS2B01G184300 chr2A 105540676 105541644 968 False 401.500000 411 86.199500 233 1312 2 chr2A.!!$F4 1079
16 TraesCS2B01G184300 chr2A 105521910 105523190 1280 False 377.733333 555 88.896333 1 1343 3 chr2A.!!$F2 1342

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
143 144 0.387565 ACGCTTTGACCCGCAATTTT 59.612 45.0 0.0 0.0 36.15 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2429 0.035739 TGTTGGCTTCGTAACTCCCC 59.964 55.0 0.0 0.0 0.0 4.81 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
115 116 3.181499 CGTCAAGCTATCACGTCCTAACT 60.181 47.826 4.31 0.00 0.00 2.24
128 129 2.615912 GTCCTAACTATACGGTCACGCT 59.384 50.000 0.00 0.00 46.04 5.07
143 144 0.387565 ACGCTTTGACCCGCAATTTT 59.612 45.000 0.00 0.00 36.15 1.82
166 167 4.025229 TGCATCACACACTAGAAAAACGTC 60.025 41.667 0.00 0.00 0.00 4.34
354 393 2.142319 CACGTGAATGTGTGTGGATGA 58.858 47.619 10.90 0.00 35.12 2.92
383 423 3.807631 TTGCGCAGACACGGCTTCT 62.808 57.895 11.31 0.00 0.00 2.85
688 925 5.054477 TGTTCTCTTTTTGGTACTCCTTCG 58.946 41.667 0.00 0.00 34.23 3.79
694 931 0.604578 TTGGTACTCCTTCGGTTCCG 59.395 55.000 4.74 4.74 34.23 4.30
703 940 3.592059 TCCTTCGGTTCCGAAATACTTG 58.408 45.455 23.59 12.93 45.78 3.16
707 944 3.319755 TCGGTTCCGAAATACTTGTCAC 58.680 45.455 11.66 0.00 35.41 3.67
838 1124 1.038280 CGGAGGGAGTACCGCTTATT 58.962 55.000 0.00 0.00 46.96 1.40
867 1154 8.349568 ACTTATAAAGGAAAAGGTTAAGCTGG 57.650 34.615 8.16 0.00 0.00 4.85
954 1243 7.472334 AAATTCATTAAGCTGATGTTGACCT 57.528 32.000 9.44 0.00 0.00 3.85
962 1251 2.719739 CTGATGTTGACCTGGAAGCAT 58.280 47.619 0.00 1.77 0.00 3.79
1010 1301 1.001487 CGTTTCCAACATGAGCAAGCA 60.001 47.619 0.00 0.00 0.00 3.91
1029 1326 3.692406 GGCGACGGTCCCAAGACT 61.692 66.667 1.91 0.00 43.05 3.24
1146 1446 4.153117 GGAAGTATTGTGACAGCAGACTTG 59.847 45.833 2.39 0.00 31.15 3.16
1248 1550 3.364549 TCACTGAAATAAAGGCCCATGG 58.635 45.455 4.14 4.14 0.00 3.66
1301 1603 6.262273 CCGAATAAATAAGCATGGGTACAGTT 59.738 38.462 0.00 0.00 0.00 3.16
1344 1648 8.709386 TGTGCTATGTAATGTTGTTTTGTTTT 57.291 26.923 0.00 0.00 0.00 2.43
1345 1649 9.155975 TGTGCTATGTAATGTTGTTTTGTTTTT 57.844 25.926 0.00 0.00 0.00 1.94
1346 1650 9.419737 GTGCTATGTAATGTTGTTTTGTTTTTG 57.580 29.630 0.00 0.00 0.00 2.44
1347 1651 9.155975 TGCTATGTAATGTTGTTTTGTTTTTGT 57.844 25.926 0.00 0.00 0.00 2.83
1348 1652 9.980780 GCTATGTAATGTTGTTTTGTTTTTGTT 57.019 25.926 0.00 0.00 0.00 2.83
1417 1723 7.032598 TCTAATGAAAGTTTGGGATCTCCTT 57.967 36.000 0.00 0.00 36.20 3.36
1551 1857 0.249741 CCACGAAACCTTCCTGTCGT 60.250 55.000 0.00 0.00 46.95 4.34
1647 1953 3.242492 ATGCTTGCCACCCCCATGT 62.242 57.895 0.00 0.00 0.00 3.21
1733 2039 1.444672 CATGAGCTCCGCCATCTCA 59.555 57.895 12.15 0.00 40.62 3.27
1746 2052 0.599466 CATCTCAGCATCCACGCGAT 60.599 55.000 15.93 0.00 36.85 4.58
1907 2213 1.889530 GCTGCACCTCCCTCGTAGTT 61.890 60.000 0.00 0.00 0.00 2.24
1908 2214 0.608640 CTGCACCTCCCTCGTAGTTT 59.391 55.000 0.00 0.00 0.00 2.66
1909 2215 1.002087 CTGCACCTCCCTCGTAGTTTT 59.998 52.381 0.00 0.00 0.00 2.43
1910 2216 1.270625 TGCACCTCCCTCGTAGTTTTG 60.271 52.381 0.00 0.00 0.00 2.44
1911 2217 1.270678 GCACCTCCCTCGTAGTTTTGT 60.271 52.381 0.00 0.00 0.00 2.83
1912 2218 2.809299 GCACCTCCCTCGTAGTTTTGTT 60.809 50.000 0.00 0.00 0.00 2.83
1913 2219 3.473625 CACCTCCCTCGTAGTTTTGTTT 58.526 45.455 0.00 0.00 0.00 2.83
1914 2220 3.881089 CACCTCCCTCGTAGTTTTGTTTT 59.119 43.478 0.00 0.00 0.00 2.43
1932 2238 6.691754 TGTTTTTGAGTTGTAAGCATCAGA 57.308 33.333 0.00 0.00 0.00 3.27
1962 2268 3.745975 TCGAGCCACTGTTTATTGTTCAG 59.254 43.478 0.00 0.00 35.60 3.02
2028 2334 3.900971 TCTTGAAGGCCAATGATATGCA 58.099 40.909 5.01 0.00 33.68 3.96
2040 2346 6.377996 GCCAATGATATGCAGGGTATGATTTA 59.622 38.462 0.00 0.00 0.00 1.40
2041 2347 7.069085 GCCAATGATATGCAGGGTATGATTTAT 59.931 37.037 0.00 0.00 0.00 1.40
2042 2348 8.974238 CCAATGATATGCAGGGTATGATTTATT 58.026 33.333 0.00 0.00 0.00 1.40
2082 2388 6.205101 AGGAACTTTCATTGATCAAGCATC 57.795 37.500 14.54 5.23 27.25 3.91
2083 2389 5.032863 GGAACTTTCATTGATCAAGCATCG 58.967 41.667 14.54 4.99 33.61 3.84
2084 2390 5.392380 GGAACTTTCATTGATCAAGCATCGT 60.392 40.000 14.54 5.59 33.61 3.73
2085 2391 4.978186 ACTTTCATTGATCAAGCATCGTG 58.022 39.130 14.54 6.23 33.61 4.35
2086 2392 4.696877 ACTTTCATTGATCAAGCATCGTGA 59.303 37.500 14.54 8.55 33.61 4.35
2087 2393 5.356190 ACTTTCATTGATCAAGCATCGTGAT 59.644 36.000 14.54 0.00 38.44 3.06
2088 2394 5.823209 TTCATTGATCAAGCATCGTGATT 57.177 34.783 14.54 0.00 35.84 2.57
2089 2395 6.923928 TTCATTGATCAAGCATCGTGATTA 57.076 33.333 14.54 0.00 35.84 1.75
2090 2396 6.291067 TCATTGATCAAGCATCGTGATTAC 57.709 37.500 14.54 0.00 35.84 1.89
2091 2397 5.816777 TCATTGATCAAGCATCGTGATTACA 59.183 36.000 14.54 0.00 35.84 2.41
2092 2398 6.315891 TCATTGATCAAGCATCGTGATTACAA 59.684 34.615 14.54 0.00 35.84 2.41
2093 2399 6.682423 TTGATCAAGCATCGTGATTACAAT 57.318 33.333 3.38 0.00 35.84 2.71
2094 2400 6.291067 TGATCAAGCATCGTGATTACAATC 57.709 37.500 0.00 0.00 35.84 2.67
2095 2401 5.237127 TGATCAAGCATCGTGATTACAATCC 59.763 40.000 0.00 0.00 35.84 3.01
2096 2402 3.555547 TCAAGCATCGTGATTACAATCCG 59.444 43.478 0.00 3.70 34.50 4.18
2097 2403 3.452755 AGCATCGTGATTACAATCCGA 57.547 42.857 13.88 13.88 40.06 4.55
2098 2404 3.384668 AGCATCGTGATTACAATCCGAG 58.615 45.455 15.60 11.10 39.56 4.63
2099 2405 3.123804 GCATCGTGATTACAATCCGAGT 58.876 45.455 15.60 6.73 39.56 4.18
2100 2406 3.182572 GCATCGTGATTACAATCCGAGTC 59.817 47.826 15.60 9.41 39.56 3.36
2101 2407 4.359706 CATCGTGATTACAATCCGAGTCA 58.640 43.478 15.60 0.00 39.56 3.41
2102 2408 4.443913 TCGTGATTACAATCCGAGTCAA 57.556 40.909 9.82 0.00 35.07 3.18
2103 2409 4.171005 TCGTGATTACAATCCGAGTCAAC 58.829 43.478 9.82 0.00 35.07 3.18
2104 2410 4.082408 TCGTGATTACAATCCGAGTCAACT 60.082 41.667 9.82 0.00 35.07 3.16
2105 2411 5.124297 TCGTGATTACAATCCGAGTCAACTA 59.876 40.000 9.82 0.00 35.07 2.24
2106 2412 5.977725 CGTGATTACAATCCGAGTCAACTAT 59.022 40.000 0.00 0.00 33.72 2.12
2107 2413 6.074835 CGTGATTACAATCCGAGTCAACTATG 60.075 42.308 0.00 0.00 33.72 2.23
2108 2414 6.201044 GTGATTACAATCCGAGTCAACTATGG 59.799 42.308 0.00 0.00 34.50 2.74
2109 2415 5.670792 TTACAATCCGAGTCAACTATGGT 57.329 39.130 0.00 0.00 0.00 3.55
2110 2416 6.778834 TTACAATCCGAGTCAACTATGGTA 57.221 37.500 0.00 0.00 0.00 3.25
2111 2417 5.263968 ACAATCCGAGTCAACTATGGTAG 57.736 43.478 0.00 0.00 0.00 3.18
2112 2418 4.051922 CAATCCGAGTCAACTATGGTAGC 58.948 47.826 0.00 0.00 0.00 3.58
2113 2419 3.014304 TCCGAGTCAACTATGGTAGCT 57.986 47.619 0.00 0.00 0.00 3.32
2114 2420 4.160642 TCCGAGTCAACTATGGTAGCTA 57.839 45.455 0.00 0.00 0.00 3.32
2115 2421 4.726583 TCCGAGTCAACTATGGTAGCTAT 58.273 43.478 0.00 0.00 0.00 2.97
2116 2422 4.760715 TCCGAGTCAACTATGGTAGCTATC 59.239 45.833 0.00 0.00 0.00 2.08
2117 2423 4.762765 CCGAGTCAACTATGGTAGCTATCT 59.237 45.833 5.42 0.00 0.00 1.98
2118 2424 5.106475 CCGAGTCAACTATGGTAGCTATCTC 60.106 48.000 5.42 0.00 0.00 2.75
2119 2425 5.106475 CGAGTCAACTATGGTAGCTATCTCC 60.106 48.000 5.42 0.00 0.00 3.71
2120 2426 5.706447 AGTCAACTATGGTAGCTATCTCCA 58.294 41.667 5.42 4.74 35.64 3.86
2121 2427 6.318913 AGTCAACTATGGTAGCTATCTCCAT 58.681 40.000 16.25 16.25 43.30 3.41
2122 2428 7.471041 AGTCAACTATGGTAGCTATCTCCATA 58.529 38.462 16.65 16.65 41.45 2.74
2126 2432 3.474798 TGGTAGCTATCTCCATAGGGG 57.525 52.381 5.42 0.00 33.61 4.79
2127 2433 3.001086 TGGTAGCTATCTCCATAGGGGA 58.999 50.000 5.42 0.00 45.89 4.81
2137 2443 2.037144 TCCATAGGGGAGTTACGAAGC 58.963 52.381 0.00 0.00 42.15 3.86
2138 2444 1.070289 CCATAGGGGAGTTACGAAGCC 59.930 57.143 0.00 0.00 40.01 4.35
2139 2445 1.760613 CATAGGGGAGTTACGAAGCCA 59.239 52.381 0.00 0.00 0.00 4.75
2140 2446 1.941377 TAGGGGAGTTACGAAGCCAA 58.059 50.000 0.00 0.00 0.00 4.52
2141 2447 0.323957 AGGGGAGTTACGAAGCCAAC 59.676 55.000 0.00 0.00 0.00 3.77
2142 2448 0.035739 GGGGAGTTACGAAGCCAACA 59.964 55.000 0.00 0.00 0.00 3.33
2143 2449 1.439679 GGGAGTTACGAAGCCAACAG 58.560 55.000 0.00 0.00 0.00 3.16
2144 2450 0.796927 GGAGTTACGAAGCCAACAGC 59.203 55.000 0.00 0.00 44.25 4.40
2145 2451 0.796927 GAGTTACGAAGCCAACAGCC 59.203 55.000 0.00 0.00 45.47 4.85
2146 2452 0.107831 AGTTACGAAGCCAACAGCCA 59.892 50.000 0.00 0.00 45.47 4.75
2147 2453 0.517316 GTTACGAAGCCAACAGCCAG 59.483 55.000 0.00 0.00 45.47 4.85
2148 2454 0.107831 TTACGAAGCCAACAGCCAGT 59.892 50.000 0.00 0.00 45.47 4.00
2149 2455 0.970640 TACGAAGCCAACAGCCAGTA 59.029 50.000 0.00 0.00 45.47 2.74
2150 2456 0.602905 ACGAAGCCAACAGCCAGTAC 60.603 55.000 0.00 0.00 45.47 2.73
2151 2457 1.626654 CGAAGCCAACAGCCAGTACG 61.627 60.000 0.00 0.00 45.47 3.67
2152 2458 0.602905 GAAGCCAACAGCCAGTACGT 60.603 55.000 0.00 0.00 45.47 3.57
2153 2459 0.179029 AAGCCAACAGCCAGTACGTT 60.179 50.000 0.00 0.00 45.47 3.99
2154 2460 0.884704 AGCCAACAGCCAGTACGTTG 60.885 55.000 0.00 4.21 45.47 4.10
2155 2461 1.164041 GCCAACAGCCAGTACGTTGT 61.164 55.000 0.00 0.00 38.65 3.32
2156 2462 1.305201 CCAACAGCCAGTACGTTGTT 58.695 50.000 0.00 0.00 38.65 2.83
2157 2463 1.002900 CCAACAGCCAGTACGTTGTTG 60.003 52.381 17.54 17.54 46.06 3.33
2158 2464 0.661020 AACAGCCAGTACGTTGTTGC 59.339 50.000 0.00 0.00 32.90 4.17
2159 2465 1.204062 CAGCCAGTACGTTGTTGCG 59.796 57.895 0.00 0.00 37.94 4.85
2160 2466 1.068417 AGCCAGTACGTTGTTGCGA 59.932 52.632 0.00 0.00 35.59 5.10
2161 2467 0.944311 AGCCAGTACGTTGTTGCGAG 60.944 55.000 0.00 0.00 35.59 5.03
2162 2468 1.491563 CCAGTACGTTGTTGCGAGC 59.508 57.895 0.00 0.00 35.59 5.03
2163 2469 1.127817 CAGTACGTTGTTGCGAGCG 59.872 57.895 0.00 0.00 35.59 5.03
2164 2470 1.008194 AGTACGTTGTTGCGAGCGA 60.008 52.632 0.00 0.00 35.59 4.93
2165 2471 1.127225 GTACGTTGTTGCGAGCGAC 59.873 57.895 8.45 8.45 35.59 5.19
2166 2472 2.017783 TACGTTGTTGCGAGCGACC 61.018 57.895 12.43 0.00 35.59 4.79
2167 2473 2.410638 TACGTTGTTGCGAGCGACCT 62.411 55.000 12.43 0.00 35.59 3.85
2168 2474 1.731613 CGTTGTTGCGAGCGACCTA 60.732 57.895 12.43 0.00 0.00 3.08
2169 2475 1.076533 CGTTGTTGCGAGCGACCTAT 61.077 55.000 12.43 0.00 0.00 2.57
2170 2476 1.796253 CGTTGTTGCGAGCGACCTATA 60.796 52.381 12.43 0.00 0.00 1.31
2171 2477 1.852895 GTTGTTGCGAGCGACCTATAG 59.147 52.381 12.43 0.00 0.00 1.31
2172 2478 1.385528 TGTTGCGAGCGACCTATAGA 58.614 50.000 12.43 0.00 0.00 1.98
2173 2479 1.954382 TGTTGCGAGCGACCTATAGAT 59.046 47.619 12.43 0.00 0.00 1.98
2174 2480 2.287608 TGTTGCGAGCGACCTATAGATG 60.288 50.000 12.43 0.00 0.00 2.90
2175 2481 0.241213 TGCGAGCGACCTATAGATGC 59.759 55.000 0.00 2.07 0.00 3.91
2176 2482 0.241213 GCGAGCGACCTATAGATGCA 59.759 55.000 0.00 0.00 0.00 3.96
2177 2483 1.335964 GCGAGCGACCTATAGATGCAA 60.336 52.381 0.00 0.00 0.00 4.08
2178 2484 2.590073 CGAGCGACCTATAGATGCAAG 58.410 52.381 0.00 0.00 0.00 4.01
2179 2485 2.669670 CGAGCGACCTATAGATGCAAGG 60.670 54.545 0.00 0.00 36.42 3.61
2180 2486 1.620819 AGCGACCTATAGATGCAAGGG 59.379 52.381 0.00 0.00 34.52 3.95
2181 2487 1.344763 GCGACCTATAGATGCAAGGGT 59.655 52.381 0.00 1.49 34.52 4.34
2182 2488 2.561419 GCGACCTATAGATGCAAGGGTA 59.439 50.000 0.00 0.00 34.52 3.69
2183 2489 3.195825 GCGACCTATAGATGCAAGGGTAT 59.804 47.826 0.00 0.00 34.52 2.73
2184 2490 4.748892 CGACCTATAGATGCAAGGGTATG 58.251 47.826 0.00 0.00 34.52 2.39
2185 2491 4.462834 CGACCTATAGATGCAAGGGTATGA 59.537 45.833 0.00 0.00 34.52 2.15
2186 2492 5.622460 CGACCTATAGATGCAAGGGTATGAC 60.622 48.000 0.00 0.00 34.52 3.06
2187 2493 5.407049 ACCTATAGATGCAAGGGTATGACT 58.593 41.667 0.00 0.00 34.52 3.41
2188 2494 5.482175 ACCTATAGATGCAAGGGTATGACTC 59.518 44.000 0.00 0.00 34.52 3.36
2189 2495 2.898729 AGATGCAAGGGTATGACTCG 57.101 50.000 0.00 0.00 0.00 4.18
2190 2496 1.202580 AGATGCAAGGGTATGACTCGC 60.203 52.381 0.00 0.00 0.00 5.03
2191 2497 0.179045 ATGCAAGGGTATGACTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
2192 2498 1.220749 GCAAGGGTATGACTCGCCA 59.779 57.895 0.00 0.00 0.00 5.69
2193 2499 0.179045 GCAAGGGTATGACTCGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
2194 2500 1.070134 GCAAGGGTATGACTCGCCATA 59.930 52.381 0.00 0.00 0.00 2.74
2195 2501 2.289694 GCAAGGGTATGACTCGCCATAT 60.290 50.000 0.00 0.00 32.33 1.78
2196 2502 3.807209 GCAAGGGTATGACTCGCCATATT 60.807 47.826 0.00 0.00 32.33 1.28
2197 2503 3.963428 AGGGTATGACTCGCCATATTC 57.037 47.619 0.00 0.00 32.33 1.75
2198 2504 2.231478 AGGGTATGACTCGCCATATTCG 59.769 50.000 0.00 0.00 32.33 3.34
2199 2505 1.993370 GGTATGACTCGCCATATTCGC 59.007 52.381 0.00 0.00 32.33 4.70
2205 2511 2.967076 CGCCATATTCGCGTGCCT 60.967 61.111 5.77 0.00 44.55 4.75
2206 2512 1.663388 CGCCATATTCGCGTGCCTA 60.663 57.895 5.77 0.00 44.55 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.335532 TGTATCTATTTTTCTGACCACTTTGG 57.664 34.615 0.00 0.00 45.02 3.28
34 35 9.226606 ACGGTGAAAATGTATCTATTTTTCTGA 57.773 29.630 8.34 0.00 39.60 3.27
143 144 3.874543 ACGTTTTTCTAGTGTGTGATGCA 59.125 39.130 0.00 0.00 0.00 3.96
297 333 3.445096 GCTATTGTCAACATTTCAGGCCT 59.555 43.478 0.00 0.00 0.00 5.19
688 925 3.319755 TCGTGACAAGTATTTCGGAACC 58.680 45.455 0.00 0.00 0.00 3.62
954 1243 3.609853 CCTGCAAGTAGTAATGCTTCCA 58.390 45.455 9.78 0.00 42.97 3.53
962 1251 2.803956 GACAAACGCCTGCAAGTAGTAA 59.196 45.455 0.00 0.00 0.00 2.24
1010 1301 2.920912 TCTTGGGACCGTCGCCTT 60.921 61.111 12.65 0.00 0.00 4.35
1146 1446 1.511254 GCGAACGCGGTTCAAATCC 60.511 57.895 12.47 0.00 42.05 3.01
1167 1467 4.612412 GCCACCGTGTCGACCCAA 62.612 66.667 14.12 0.00 0.00 4.12
1226 1528 3.962718 CCATGGGCCTTTATTTCAGTGAT 59.037 43.478 2.85 0.00 0.00 3.06
1227 1529 3.011144 TCCATGGGCCTTTATTTCAGTGA 59.989 43.478 13.02 0.00 0.00 3.41
1233 1535 4.281657 GAGACTTCCATGGGCCTTTATTT 58.718 43.478 13.02 0.00 0.00 1.40
1363 1667 2.354821 GCGGCGAGTTATCCTCAAAAAT 59.645 45.455 12.98 0.00 40.48 1.82
1417 1723 4.102524 ACTTTGTGTTAGATGTGGTCTCCA 59.897 41.667 0.00 0.00 38.42 3.86
1551 1857 1.672363 GCAGATGATGCGTGGATTCAA 59.328 47.619 0.00 0.00 46.99 2.69
1647 1953 1.608055 TTACACCTCGAGACGGACAA 58.392 50.000 15.71 0.00 0.00 3.18
1733 2039 0.179076 TTGATGATCGCGTGGATGCT 60.179 50.000 5.77 0.00 34.82 3.79
1746 2052 1.199789 GGCGTGCACTTTCATTGATGA 59.800 47.619 16.19 0.00 34.44 2.92
1907 2213 7.542890 TCTGATGCTTACAACTCAAAAACAAA 58.457 30.769 0.00 0.00 0.00 2.83
1908 2214 7.094508 TCTGATGCTTACAACTCAAAAACAA 57.905 32.000 0.00 0.00 0.00 2.83
1909 2215 6.691754 TCTGATGCTTACAACTCAAAAACA 57.308 33.333 0.00 0.00 0.00 2.83
1910 2216 7.985634 TTTCTGATGCTTACAACTCAAAAAC 57.014 32.000 0.00 0.00 0.00 2.43
1914 2220 9.453572 AGAATATTTCTGATGCTTACAACTCAA 57.546 29.630 0.00 0.00 38.91 3.02
1932 2238 7.336931 ACAATAAACAGTGGCTCGAGAATATTT 59.663 33.333 18.75 10.32 0.00 1.40
1939 2245 3.745975 TGAACAATAAACAGTGGCTCGAG 59.254 43.478 8.45 8.45 0.00 4.04
2047 2353 5.413309 TGAAAGTTCCTTTCCTGCAAAAA 57.587 34.783 12.73 0.00 46.36 1.94
2048 2354 5.612725 ATGAAAGTTCCTTTCCTGCAAAA 57.387 34.783 12.73 0.00 46.36 2.44
2049 2355 5.128499 TCAATGAAAGTTCCTTTCCTGCAAA 59.872 36.000 12.73 0.00 46.36 3.68
2050 2356 4.648762 TCAATGAAAGTTCCTTTCCTGCAA 59.351 37.500 12.73 0.00 46.36 4.08
2051 2357 4.214310 TCAATGAAAGTTCCTTTCCTGCA 58.786 39.130 12.73 0.00 46.36 4.41
2052 2358 4.853924 TCAATGAAAGTTCCTTTCCTGC 57.146 40.909 12.73 0.00 46.36 4.85
2053 2359 6.579666 TGATCAATGAAAGTTCCTTTCCTG 57.420 37.500 12.73 10.38 46.36 3.86
2054 2360 6.294955 GCTTGATCAATGAAAGTTCCTTTCCT 60.295 38.462 8.96 2.26 46.36 3.36
2055 2361 5.866092 GCTTGATCAATGAAAGTTCCTTTCC 59.134 40.000 8.96 0.00 46.36 3.13
2056 2362 6.449698 TGCTTGATCAATGAAAGTTCCTTTC 58.550 36.000 8.96 9.27 46.88 2.62
2057 2363 6.409524 TGCTTGATCAATGAAAGTTCCTTT 57.590 33.333 8.96 0.00 36.29 3.11
2058 2364 6.600882 ATGCTTGATCAATGAAAGTTCCTT 57.399 33.333 8.96 0.00 0.00 3.36
2059 2365 5.163683 CGATGCTTGATCAATGAAAGTTCCT 60.164 40.000 8.96 0.00 0.00 3.36
2060 2366 5.032863 CGATGCTTGATCAATGAAAGTTCC 58.967 41.667 8.96 0.00 0.00 3.62
2061 2367 5.510674 CACGATGCTTGATCAATGAAAGTTC 59.489 40.000 8.96 0.00 0.00 3.01
2062 2368 5.181811 TCACGATGCTTGATCAATGAAAGTT 59.818 36.000 8.96 0.00 0.00 2.66
2063 2369 4.696877 TCACGATGCTTGATCAATGAAAGT 59.303 37.500 8.96 4.56 0.00 2.66
2064 2370 5.225899 TCACGATGCTTGATCAATGAAAG 57.774 39.130 8.96 3.94 0.00 2.62
2065 2371 5.823209 ATCACGATGCTTGATCAATGAAA 57.177 34.783 8.96 0.00 32.30 2.69
2066 2372 5.823209 AATCACGATGCTTGATCAATGAA 57.177 34.783 8.96 0.00 32.29 2.57
2067 2373 5.816777 TGTAATCACGATGCTTGATCAATGA 59.183 36.000 8.96 9.02 32.29 2.57
2068 2374 6.051646 TGTAATCACGATGCTTGATCAATG 57.948 37.500 8.96 3.32 32.29 2.82
2069 2375 6.682423 TTGTAATCACGATGCTTGATCAAT 57.318 33.333 8.96 0.00 32.29 2.57
2070 2376 6.238456 GGATTGTAATCACGATGCTTGATCAA 60.238 38.462 8.12 8.12 34.78 2.57
2071 2377 5.237127 GGATTGTAATCACGATGCTTGATCA 59.763 40.000 6.90 0.00 34.78 2.92
2072 2378 5.613360 CGGATTGTAATCACGATGCTTGATC 60.613 44.000 6.90 0.00 35.32 2.92
2073 2379 4.212004 CGGATTGTAATCACGATGCTTGAT 59.788 41.667 6.90 0.00 35.32 2.57
2074 2380 3.555547 CGGATTGTAATCACGATGCTTGA 59.444 43.478 6.90 0.00 35.32 3.02
2075 2381 3.555547 TCGGATTGTAATCACGATGCTTG 59.444 43.478 6.90 0.00 35.32 4.01
2076 2382 3.792401 TCGGATTGTAATCACGATGCTT 58.208 40.909 6.90 0.00 35.32 3.91
2077 2383 3.181475 ACTCGGATTGTAATCACGATGCT 60.181 43.478 14.16 3.61 37.42 3.79
2078 2384 3.123804 ACTCGGATTGTAATCACGATGC 58.876 45.455 14.16 0.00 37.42 3.91
2079 2385 4.359706 TGACTCGGATTGTAATCACGATG 58.640 43.478 14.16 11.80 37.42 3.84
2080 2386 4.649088 TGACTCGGATTGTAATCACGAT 57.351 40.909 14.16 8.23 37.42 3.73
2081 2387 4.082408 AGTTGACTCGGATTGTAATCACGA 60.082 41.667 13.52 13.52 37.15 4.35
2082 2388 4.174009 AGTTGACTCGGATTGTAATCACG 58.826 43.478 6.90 7.71 37.15 4.35
2083 2389 6.201044 CCATAGTTGACTCGGATTGTAATCAC 59.799 42.308 6.90 0.00 37.15 3.06
2084 2390 6.127168 ACCATAGTTGACTCGGATTGTAATCA 60.127 38.462 6.90 0.00 37.15 2.57
2085 2391 6.281405 ACCATAGTTGACTCGGATTGTAATC 58.719 40.000 6.54 0.00 34.66 1.75
2086 2392 6.235231 ACCATAGTTGACTCGGATTGTAAT 57.765 37.500 6.54 0.00 0.00 1.89
2087 2393 5.670792 ACCATAGTTGACTCGGATTGTAA 57.329 39.130 6.54 0.00 0.00 2.41
2088 2394 5.221185 GCTACCATAGTTGACTCGGATTGTA 60.221 44.000 6.54 0.00 0.00 2.41
2089 2395 4.441634 GCTACCATAGTTGACTCGGATTGT 60.442 45.833 6.54 0.00 0.00 2.71
2090 2396 4.051922 GCTACCATAGTTGACTCGGATTG 58.948 47.826 6.54 0.00 0.00 2.67
2091 2397 3.961408 AGCTACCATAGTTGACTCGGATT 59.039 43.478 6.54 0.00 0.00 3.01
2092 2398 3.567397 AGCTACCATAGTTGACTCGGAT 58.433 45.455 6.54 0.00 0.00 4.18
2093 2399 3.014304 AGCTACCATAGTTGACTCGGA 57.986 47.619 6.54 0.00 0.00 4.55
2094 2400 4.762765 AGATAGCTACCATAGTTGACTCGG 59.237 45.833 0.00 0.00 0.00 4.63
2095 2401 5.106475 GGAGATAGCTACCATAGTTGACTCG 60.106 48.000 0.00 0.00 0.00 4.18
2096 2402 5.770663 TGGAGATAGCTACCATAGTTGACTC 59.229 44.000 0.00 0.00 0.00 3.36
2097 2403 5.706447 TGGAGATAGCTACCATAGTTGACT 58.294 41.667 0.00 0.00 0.00 3.41
2098 2404 6.597832 ATGGAGATAGCTACCATAGTTGAC 57.402 41.667 11.65 0.00 41.77 3.18
2104 2410 4.799579 TCCCCTATGGAGATAGCTACCATA 59.200 45.833 16.65 16.65 43.11 2.74
2105 2411 3.602922 TCCCCTATGGAGATAGCTACCAT 59.397 47.826 16.25 16.25 44.94 3.55
2106 2412 3.001086 TCCCCTATGGAGATAGCTACCA 58.999 50.000 4.18 4.18 38.61 3.25
2107 2413 3.759815 TCCCCTATGGAGATAGCTACC 57.240 52.381 0.00 0.00 38.61 3.18
2117 2423 2.037144 GCTTCGTAACTCCCCTATGGA 58.963 52.381 0.00 0.00 42.41 3.41
2118 2424 1.070289 GGCTTCGTAACTCCCCTATGG 59.930 57.143 0.00 0.00 0.00 2.74
2119 2425 1.760613 TGGCTTCGTAACTCCCCTATG 59.239 52.381 0.00 0.00 0.00 2.23
2120 2426 2.169978 GTTGGCTTCGTAACTCCCCTAT 59.830 50.000 0.00 0.00 0.00 2.57
2121 2427 1.551883 GTTGGCTTCGTAACTCCCCTA 59.448 52.381 0.00 0.00 0.00 3.53
2122 2428 0.323957 GTTGGCTTCGTAACTCCCCT 59.676 55.000 0.00 0.00 0.00 4.79
2123 2429 0.035739 TGTTGGCTTCGTAACTCCCC 59.964 55.000 0.00 0.00 0.00 4.81
2124 2430 1.439679 CTGTTGGCTTCGTAACTCCC 58.560 55.000 0.00 0.00 0.00 4.30
2125 2431 0.796927 GCTGTTGGCTTCGTAACTCC 59.203 55.000 0.00 0.00 38.06 3.85
2126 2432 0.796927 GGCTGTTGGCTTCGTAACTC 59.203 55.000 0.00 0.00 41.46 3.01
2127 2433 0.107831 TGGCTGTTGGCTTCGTAACT 59.892 50.000 0.00 0.00 41.46 2.24
2128 2434 0.517316 CTGGCTGTTGGCTTCGTAAC 59.483 55.000 0.00 0.00 41.46 2.50
2129 2435 0.107831 ACTGGCTGTTGGCTTCGTAA 59.892 50.000 0.00 0.00 41.46 3.18
2130 2436 0.970640 TACTGGCTGTTGGCTTCGTA 59.029 50.000 1.31 0.00 41.46 3.43
2131 2437 0.602905 GTACTGGCTGTTGGCTTCGT 60.603 55.000 1.31 0.00 41.46 3.85
2132 2438 1.626654 CGTACTGGCTGTTGGCTTCG 61.627 60.000 1.31 0.00 41.46 3.79
2133 2439 0.602905 ACGTACTGGCTGTTGGCTTC 60.603 55.000 1.31 0.00 41.46 3.86
2134 2440 0.179029 AACGTACTGGCTGTTGGCTT 60.179 50.000 1.31 0.00 41.46 4.35
2135 2441 0.884704 CAACGTACTGGCTGTTGGCT 60.885 55.000 1.31 0.00 39.36 4.75
2136 2442 1.164041 ACAACGTACTGGCTGTTGGC 61.164 55.000 13.03 0.00 45.48 4.52
2137 2443 1.002900 CAACAACGTACTGGCTGTTGG 60.003 52.381 16.96 0.00 45.48 3.77
2138 2444 2.383298 CAACAACGTACTGGCTGTTG 57.617 50.000 12.59 12.59 46.36 3.33
2139 2445 0.661020 GCAACAACGTACTGGCTGTT 59.339 50.000 1.31 0.00 32.31 3.16
2140 2446 1.495584 CGCAACAACGTACTGGCTGT 61.496 55.000 1.74 1.74 0.00 4.40
2141 2447 1.204062 CGCAACAACGTACTGGCTG 59.796 57.895 0.00 0.00 0.00 4.85
2142 2448 0.944311 CTCGCAACAACGTACTGGCT 60.944 55.000 0.00 0.00 0.00 4.75
2143 2449 1.491563 CTCGCAACAACGTACTGGC 59.508 57.895 0.00 0.00 0.00 4.85
2144 2450 1.491563 GCTCGCAACAACGTACTGG 59.508 57.895 0.00 0.00 0.00 4.00
2145 2451 1.127817 CGCTCGCAACAACGTACTG 59.872 57.895 0.00 0.00 0.00 2.74
2146 2452 1.008194 TCGCTCGCAACAACGTACT 60.008 52.632 0.00 0.00 0.00 2.73
2147 2453 1.127225 GTCGCTCGCAACAACGTAC 59.873 57.895 0.00 0.00 0.00 3.67
2148 2454 2.017783 GGTCGCTCGCAACAACGTA 61.018 57.895 0.00 0.00 0.00 3.57
2149 2455 2.410638 TAGGTCGCTCGCAACAACGT 62.411 55.000 0.00 0.00 0.00 3.99
2150 2456 1.076533 ATAGGTCGCTCGCAACAACG 61.077 55.000 0.00 0.00 0.00 4.10
2151 2457 1.852895 CTATAGGTCGCTCGCAACAAC 59.147 52.381 0.00 0.00 0.00 3.32
2152 2458 1.746787 TCTATAGGTCGCTCGCAACAA 59.253 47.619 0.00 0.00 0.00 2.83
2153 2459 1.385528 TCTATAGGTCGCTCGCAACA 58.614 50.000 0.00 0.00 0.00 3.33
2154 2460 2.320367 CATCTATAGGTCGCTCGCAAC 58.680 52.381 0.00 0.00 0.00 4.17
2155 2461 1.335964 GCATCTATAGGTCGCTCGCAA 60.336 52.381 0.00 0.00 0.00 4.85
2156 2462 0.241213 GCATCTATAGGTCGCTCGCA 59.759 55.000 0.00 0.00 0.00 5.10
2157 2463 0.241213 TGCATCTATAGGTCGCTCGC 59.759 55.000 0.00 0.00 0.00 5.03
2158 2464 2.590073 CTTGCATCTATAGGTCGCTCG 58.410 52.381 0.00 0.00 0.00 5.03
2159 2465 2.353208 CCCTTGCATCTATAGGTCGCTC 60.353 54.545 0.00 0.00 0.00 5.03
2160 2466 1.620819 CCCTTGCATCTATAGGTCGCT 59.379 52.381 0.00 0.00 0.00 4.93
2161 2467 1.344763 ACCCTTGCATCTATAGGTCGC 59.655 52.381 0.00 0.45 0.00 5.19
2162 2468 4.462834 TCATACCCTTGCATCTATAGGTCG 59.537 45.833 0.00 0.00 0.00 4.79
2163 2469 5.482175 AGTCATACCCTTGCATCTATAGGTC 59.518 44.000 0.00 0.00 0.00 3.85
2164 2470 5.407049 AGTCATACCCTTGCATCTATAGGT 58.593 41.667 0.00 0.00 0.00 3.08
2165 2471 5.393569 CGAGTCATACCCTTGCATCTATAGG 60.394 48.000 0.00 0.00 0.00 2.57
2166 2472 5.645624 CGAGTCATACCCTTGCATCTATAG 58.354 45.833 0.00 0.00 0.00 1.31
2167 2473 4.082190 GCGAGTCATACCCTTGCATCTATA 60.082 45.833 0.00 0.00 38.87 1.31
2168 2474 3.306364 GCGAGTCATACCCTTGCATCTAT 60.306 47.826 0.00 0.00 38.87 1.98
2169 2475 2.035961 GCGAGTCATACCCTTGCATCTA 59.964 50.000 0.00 0.00 38.87 1.98
2170 2476 1.202580 GCGAGTCATACCCTTGCATCT 60.203 52.381 0.00 0.00 38.87 2.90
2171 2477 1.221414 GCGAGTCATACCCTTGCATC 58.779 55.000 0.00 0.00 38.87 3.91
2172 2478 0.179045 GGCGAGTCATACCCTTGCAT 60.179 55.000 0.00 0.00 40.47 3.96
2173 2479 1.220749 GGCGAGTCATACCCTTGCA 59.779 57.895 0.00 0.00 40.47 4.08
2174 2480 0.179045 ATGGCGAGTCATACCCTTGC 60.179 55.000 0.00 0.00 38.40 4.01
2175 2481 3.685139 ATATGGCGAGTCATACCCTTG 57.315 47.619 0.00 0.00 33.08 3.61
2176 2482 3.306088 CGAATATGGCGAGTCATACCCTT 60.306 47.826 0.00 0.00 33.08 3.95
2177 2483 2.231478 CGAATATGGCGAGTCATACCCT 59.769 50.000 0.00 0.00 33.08 4.34
2178 2484 2.607187 CGAATATGGCGAGTCATACCC 58.393 52.381 0.00 0.00 33.08 3.69
2179 2485 1.993370 GCGAATATGGCGAGTCATACC 59.007 52.381 0.00 0.00 33.08 2.73
2189 2495 4.354155 TAGGCACGCGAATATGGC 57.646 55.556 15.93 13.68 41.52 4.40


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

AutoCloner maintained by Alex Coulton.