Multiple sequence alignment - TraesCS3D01G175200

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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 TraesCS3D01G175200 chr3D 100.000 2543 0 0 1 2543 157103655 157101113 0.000000e+00 4697
1 TraesCS3D01G175200 chr3D 96.784 964 26 4 1 963 21801333 21800374 0.000000e+00 1604
2 TraesCS3D01G175200 chr3D 83.601 561 50 15 993 1545 157179974 157179448 2.940000e-134 488
3 TraesCS3D01G175200 chr7D 97.921 962 15 4 1 962 219914682 219915638 0.000000e+00 1661
4 TraesCS3D01G175200 chr7D 97.092 963 23 2 1 962 136194164 136193206 0.000000e+00 1618
5 TraesCS3D01G175200 chr7D 96.985 962 25 4 1 962 534866254 534867211 0.000000e+00 1613
6 TraesCS3D01G175200 chr7D 96.778 962 26 4 1 962 372820899 372819943 0.000000e+00 1600
7 TraesCS3D01G175200 chr1D 97.619 966 19 3 1 965 112417467 112416505 0.000000e+00 1653
8 TraesCS3D01G175200 chr1D 93.407 182 10 2 2037 2218 250661797 250661976 4.170000e-68 268
9 TraesCS3D01G175200 chr1D 87.975 158 10 5 1398 1546 486014976 486015133 7.230000e-41 178
10 TraesCS3D01G175200 chr5D 97.510 964 19 4 1 962 265672427 265671467 0.000000e+00 1642
11 TraesCS3D01G175200 chr5D 92.605 311 23 0 993 1303 62528173 62528483 4.990000e-122 448
12 TraesCS3D01G175200 chr5D 97.006 167 5 0 2040 2206 368995523 368995357 5.360000e-72 281
13 TraesCS3D01G175200 chr4D 97.404 963 21 2 1 962 21730199 21731158 0.000000e+00 1637
14 TraesCS3D01G175200 chr4D 93.407 182 10 2 2037 2218 144738810 144738631 4.170000e-68 268
15 TraesCS3D01G175200 chr4D 93.407 182 10 2 2037 2218 452926132 452926311 4.170000e-68 268
16 TraesCS3D01G175200 chr2D 97.401 962 21 3 1 962 625510058 625509101 0.000000e+00 1635
17 TraesCS3D01G175200 chr2D 96.000 175 6 1 2039 2213 560959650 560959477 1.490000e-72 283
18 TraesCS3D01G175200 chr2D 95.402 174 8 0 2031 2204 516708303 516708476 6.930000e-71 278
19 TraesCS3D01G175200 chr3B 92.719 1085 49 12 964 2035 228209373 228208306 0.000000e+00 1539
20 TraesCS3D01G175200 chr3B 96.815 314 10 0 2230 2543 228208282 228207969 2.240000e-145 525
21 TraesCS3D01G175200 chr3B 81.152 573 81 20 993 1552 228300735 228300177 3.890000e-118 435
22 TraesCS3D01G175200 chr3A 91.076 1087 50 12 962 2036 171173773 171174824 0.000000e+00 1426
23 TraesCS3D01G175200 chr3A 87.723 505 47 12 986 1490 171137934 171138423 2.190000e-160 575
24 TraesCS3D01G175200 chr3A 94.006 317 12 2 2230 2543 171174847 171175159 8.230000e-130 473
25 TraesCS3D01G175200 chr3A 97.006 167 5 0 2040 2206 744921111 744920945 5.360000e-72 281
26 TraesCS3D01G175200 chr6B 91.483 317 24 1 996 1309 6194818 6194502 1.400000e-117 433
27 TraesCS3D01G175200 chr6B 80.838 334 38 13 1397 1706 6194340 6194009 3.270000e-59 239
28 TraesCS3D01G175200 chr6A 91.667 312 23 1 996 1304 1961150 1961461 1.810000e-116 429
29 TraesCS3D01G175200 chr6A 78.446 399 38 22 1407 1759 1961530 1961926 1.530000e-52 217
30 TraesCS3D01G175200 chr6D 91.167 317 25 1 996 1309 3025620 3025304 6.500000e-116 427
31 TraesCS3D01G175200 chr6D 81.791 335 33 15 1397 1706 3025142 3024811 3.250000e-64 255
32 TraesCS3D01G175200 chr1B 81.285 529 68 20 984 1506 676746661 676747164 1.420000e-107 399
33 TraesCS3D01G175200 chr1A 87.500 320 34 3 993 1306 583604864 583605183 5.170000e-97 364
34 TraesCS3D01G175200 chr5A 94.505 182 8 2 2037 2218 349787519 349787340 1.930000e-71 279
35 TraesCS3D01G175200 chr7A 92.632 190 10 4 2029 2217 431989102 431989288 1.160000e-68 270


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 TraesCS3D01G175200 chr3D 157101113 157103655 2542 True 4697.0 4697 100.0000 1 2543 1 chr3D.!!$R2 2542
1 TraesCS3D01G175200 chr3D 21800374 21801333 959 True 1604.0 1604 96.7840 1 963 1 chr3D.!!$R1 962
2 TraesCS3D01G175200 chr3D 157179448 157179974 526 True 488.0 488 83.6010 993 1545 1 chr3D.!!$R3 552
3 TraesCS3D01G175200 chr7D 219914682 219915638 956 False 1661.0 1661 97.9210 1 962 1 chr7D.!!$F1 961
4 TraesCS3D01G175200 chr7D 136193206 136194164 958 True 1618.0 1618 97.0920 1 962 1 chr7D.!!$R1 961
5 TraesCS3D01G175200 chr7D 534866254 534867211 957 False 1613.0 1613 96.9850 1 962 1 chr7D.!!$F2 961
6 TraesCS3D01G175200 chr7D 372819943 372820899 956 True 1600.0 1600 96.7780 1 962 1 chr7D.!!$R2 961
7 TraesCS3D01G175200 chr1D 112416505 112417467 962 True 1653.0 1653 97.6190 1 965 1 chr1D.!!$R1 964
8 TraesCS3D01G175200 chr5D 265671467 265672427 960 True 1642.0 1642 97.5100 1 962 1 chr5D.!!$R1 961
9 TraesCS3D01G175200 chr4D 21730199 21731158 959 False 1637.0 1637 97.4040 1 962 1 chr4D.!!$F1 961
10 TraesCS3D01G175200 chr2D 625509101 625510058 957 True 1635.0 1635 97.4010 1 962 1 chr2D.!!$R2 961
11 TraesCS3D01G175200 chr3B 228207969 228209373 1404 True 1032.0 1539 94.7670 964 2543 2 chr3B.!!$R2 1579
12 TraesCS3D01G175200 chr3B 228300177 228300735 558 True 435.0 435 81.1520 993 1552 1 chr3B.!!$R1 559
13 TraesCS3D01G175200 chr3A 171173773 171175159 1386 False 949.5 1426 92.5410 962 2543 2 chr3A.!!$F2 1581
14 TraesCS3D01G175200 chr6B 6194009 6194818 809 True 336.0 433 86.1605 996 1706 2 chr6B.!!$R1 710
15 TraesCS3D01G175200 chr6A 1961150 1961926 776 False 323.0 429 85.0565 996 1759 2 chr6A.!!$F1 763
16 TraesCS3D01G175200 chr6D 3024811 3025620 809 True 341.0 427 86.4790 996 1706 2 chr6D.!!$R1 710
17 TraesCS3D01G175200 chr1B 676746661 676747164 503 False 399.0 399 81.2850 984 1506 1 chr1B.!!$F1 522

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
891 895 1.342474 TGCACAAAAAGGTCAGGGGAA 60.342 47.619 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2355 0.708802 TCCCTTTCTACTCCCTCCGT 59.291 55.0 0.0 0.0 0.0 4.69 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
65 66 2.355310 CCGGCCACTTTCAGTATTACCA 60.355 50.000 2.24 0.00 0.00 3.25
111 112 2.231529 CCGGTGTTGTTTGTCCCAATA 58.768 47.619 0.00 0.00 0.00 1.90
564 566 2.487762 GGATTGGTGAAGAAATGCACGA 59.512 45.455 0.00 0.00 35.91 4.35
814 818 2.280552 GCCACGGTGGACTGGAGTA 61.281 63.158 30.65 0.00 40.96 2.59
891 895 1.342474 TGCACAAAAAGGTCAGGGGAA 60.342 47.619 0.00 0.00 0.00 3.97
1319 1327 4.436050 CGTAAGTTTGGCAGCTTGATAGTG 60.436 45.833 14.09 0.00 0.00 2.74
1486 1597 0.519077 CAACTTCCTCGCAAGCTTCC 59.481 55.000 0.00 0.00 37.18 3.46
1515 1638 4.233635 GCTGCTGCATCGGCTTCG 62.234 66.667 14.06 0.00 41.91 3.79
1548 1675 3.071457 TGATGAGAGGAAACTGAAGCACA 59.929 43.478 0.00 0.00 44.43 4.57
1617 1760 7.481275 TTCAGATTTCAAATTGGCTTTTGAC 57.519 32.000 13.34 5.54 43.38 3.18
1625 1768 7.048629 TCAAATTGGCTTTTGACTTCATGTA 57.951 32.000 10.71 0.00 39.91 2.29
1643 1786 7.929941 TCATGTAGTGGCATTACAATGTTTA 57.070 32.000 23.91 2.17 38.65 2.01
1733 1890 6.789262 CAACTTGATTTGGACATCACTATCC 58.211 40.000 0.00 0.00 32.68 2.59
1734 1891 6.065976 ACTTGATTTGGACATCACTATCCA 57.934 37.500 0.00 0.00 43.42 3.41
1743 1900 5.045942 TGGACATCACTATCCAAAGTGCTAA 60.046 40.000 0.00 0.00 45.34 3.09
1881 2044 2.859165 TTTGAGCACTGTAGGGAAGG 57.141 50.000 0.00 0.00 0.00 3.46
1901 2064 3.573558 CGTTGCCCACGCTGTTAT 58.426 55.556 0.00 0.00 43.37 1.89
1902 2065 1.873165 CGTTGCCCACGCTGTTATT 59.127 52.632 0.00 0.00 43.37 1.40
1903 2066 0.179200 CGTTGCCCACGCTGTTATTC 60.179 55.000 0.00 0.00 43.37 1.75
1904 2067 0.878416 GTTGCCCACGCTGTTATTCA 59.122 50.000 0.00 0.00 35.36 2.57
1914 2077 6.260050 CCCACGCTGTTATTCATAGTACAAAT 59.740 38.462 0.00 0.00 0.00 2.32
1981 2144 2.086869 CTCCTGTGTCGAAAATGGCAT 58.913 47.619 0.00 0.00 0.00 4.40
2017 2180 5.614308 TGAGAAAACATGAGCTTCAGAAGA 58.386 37.500 14.86 0.00 0.00 2.87
2021 2184 8.627208 AGAAAACATGAGCTTCAGAAGAATTA 57.373 30.769 14.86 0.00 32.31 1.40
2025 2188 7.750229 ACATGAGCTTCAGAAGAATTACAAA 57.250 32.000 14.86 0.00 32.31 2.83
2026 2189 7.588512 ACATGAGCTTCAGAAGAATTACAAAC 58.411 34.615 14.86 0.00 32.31 2.93
2036 2199 6.150140 CAGAAGAATTACAAACCAGCTAAGCT 59.850 38.462 0.00 0.00 40.77 3.74
2037 2200 6.372937 AGAAGAATTACAAACCAGCTAAGCTC 59.627 38.462 0.00 0.00 36.40 4.09
2039 2202 6.183347 AGAATTACAAACCAGCTAAGCTCAT 58.817 36.000 0.00 0.00 36.40 2.90
2040 2203 7.338710 AGAATTACAAACCAGCTAAGCTCATA 58.661 34.615 0.00 0.00 36.40 2.15
2041 2204 6.927294 ATTACAAACCAGCTAAGCTCATAC 57.073 37.500 0.00 0.00 36.40 2.39
2042 2205 4.559862 ACAAACCAGCTAAGCTCATACT 57.440 40.909 0.00 0.00 36.40 2.12
2043 2206 4.508662 ACAAACCAGCTAAGCTCATACTC 58.491 43.478 0.00 0.00 36.40 2.59
2044 2207 3.828875 AACCAGCTAAGCTCATACTCC 57.171 47.619 0.00 0.00 36.40 3.85
2045 2208 2.043227 ACCAGCTAAGCTCATACTCCC 58.957 52.381 0.00 0.00 36.40 4.30
2046 2209 2.324541 CCAGCTAAGCTCATACTCCCT 58.675 52.381 0.00 0.00 36.40 4.20
2047 2210 2.298729 CCAGCTAAGCTCATACTCCCTC 59.701 54.545 0.00 0.00 36.40 4.30
2048 2211 2.298729 CAGCTAAGCTCATACTCCCTCC 59.701 54.545 0.00 0.00 36.40 4.30
2049 2212 1.271102 GCTAAGCTCATACTCCCTCCG 59.729 57.143 0.00 0.00 0.00 4.63
2050 2213 2.588620 CTAAGCTCATACTCCCTCCGT 58.411 52.381 0.00 0.00 0.00 4.69
2051 2214 1.867363 AAGCTCATACTCCCTCCGTT 58.133 50.000 0.00 0.00 0.00 4.44
2052 2215 1.404843 AGCTCATACTCCCTCCGTTC 58.595 55.000 0.00 0.00 0.00 3.95
2053 2216 0.389757 GCTCATACTCCCTCCGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
2054 2217 2.030045 GCTCATACTCCCTCCGTTCCT 61.030 57.143 0.00 0.00 0.00 3.36
2055 2218 2.752154 GCTCATACTCCCTCCGTTCCTA 60.752 54.545 0.00 0.00 0.00 2.94
2056 2219 3.563223 CTCATACTCCCTCCGTTCCTAA 58.437 50.000 0.00 0.00 0.00 2.69
2057 2220 3.958798 CTCATACTCCCTCCGTTCCTAAA 59.041 47.826 0.00 0.00 0.00 1.85
2058 2221 4.553678 TCATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
2059 2222 5.708544 TCATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
2060 2223 6.320518 TCATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
2061 2224 6.785963 TCATACTCCCTCCGTTCCTAAATATT 59.214 38.462 0.00 0.00 0.00 1.28
2062 2225 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2063 2226 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2064 2227 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2065 2228 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2066 2229 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2067 2230 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2068 2231 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2069 2232 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2070 2233 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2071 2234 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2072 2235 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2073 2236 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2086 2249 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2087 2250 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2088 2251 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2089 2252 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2090 2253 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2091 2254 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2092 2255 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2093 2256 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2094 2257 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2096 2259 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2097 2260 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2098 2261 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
2099 2262 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
2100 2263 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
2101 2264 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
2102 2265 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
2103 2266 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2104 2267 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2105 2268 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
2106 2269 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
2107 2270 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2108 2271 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2109 2272 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
2110 2273 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
2111 2274 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2112 2275 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2113 2276 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2114 2277 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2115 2278 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2116 2279 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2117 2280 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2118 2281 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2119 2282 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2120 2283 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2155 2318 9.616156 AAGTCTATATACATCCGTCTATGGTAG 57.384 37.037 0.00 0.00 0.00 3.18
2156 2319 8.770322 AGTCTATATACATCCGTCTATGGTAGT 58.230 37.037 0.00 0.00 0.00 2.73
2157 2320 9.044150 GTCTATATACATCCGTCTATGGTAGTC 57.956 40.741 0.00 0.00 0.00 2.59
2158 2321 8.209584 TCTATATACATCCGTCTATGGTAGTCC 58.790 40.741 0.00 0.00 0.00 3.85
2180 2343 9.753674 AGTCCATTTGAAATATCTAAAAGGACA 57.246 29.630 22.14 0.00 43.52 4.02
2195 2358 9.169592 TCTAAAAGGACAAATATTTAGGAACGG 57.830 33.333 0.00 0.00 36.48 4.44
2196 2359 9.169592 CTAAAAGGACAAATATTTAGGAACGGA 57.830 33.333 0.00 0.00 33.69 4.69
2197 2360 7.625828 AAAGGACAAATATTTAGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
2198 2361 5.681639 AGGACAAATATTTAGGAACGGAGG 58.318 41.667 0.00 0.00 0.00 4.30
2199 2362 4.820173 GGACAAATATTTAGGAACGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
2200 2363 5.397109 GGACAAATATTTAGGAACGGAGGGA 60.397 44.000 0.00 0.00 0.00 4.20
2201 2364 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2206 2369 3.744940 TTAGGAACGGAGGGAGTAGAA 57.255 47.619 0.00 0.00 0.00 2.10
2233 2396 9.892130 AGGGAAATTATCTTACTTGTAGACTTG 57.108 33.333 0.00 0.00 0.00 3.16
2234 2397 9.668497 GGGAAATTATCTTACTTGTAGACTTGT 57.332 33.333 0.00 0.00 0.00 3.16
2243 2406 9.007901 TCTTACTTGTAGACTTGTAGTACCTTC 57.992 37.037 0.00 0.00 0.00 3.46
2251 2414 9.786105 GTAGACTTGTAGTACCTTCATAACTTC 57.214 37.037 0.00 0.00 0.00 3.01
2470 2636 1.202428 GGTCCGTGTATGAGAAGAGCC 60.202 57.143 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.819229 CTATGTCGGTGGAGCAGCT 59.181 57.895 0.00 0.00 0.00 4.24
111 112 3.071874 TGGTTTGGCTTCTCGATGATT 57.928 42.857 0.00 0.00 0.00 2.57
193 194 4.099573 TCTTGCATGTAGTAGGCCTACTTC 59.900 45.833 42.51 36.93 43.35 3.01
564 566 4.020218 TCCTTCAGATCTGACGATTTGGTT 60.020 41.667 26.25 0.00 39.66 3.67
576 578 3.715834 CCTCTCCCAAATCCTTCAGATCT 59.284 47.826 0.00 0.00 32.47 2.75
688 692 0.983467 TGTGACTTAGATGCCAGCCA 59.017 50.000 0.00 0.00 0.00 4.75
814 818 2.660064 CCTAGCTCTGGGGCGTTGT 61.660 63.158 0.00 0.00 37.29 3.32
932 936 3.546724 TGACAATTTTGACCTCGGAACA 58.453 40.909 0.00 0.00 0.00 3.18
989 993 0.969409 AGGCTTCATCCCTGCAAAGC 60.969 55.000 9.56 9.56 42.60 3.51
990 994 1.101331 GAGGCTTCATCCCTGCAAAG 58.899 55.000 0.00 0.00 31.41 2.77
1198 1205 0.535102 CAGTGCCGGAACTTGAAGGT 60.535 55.000 14.25 0.00 0.00 3.50
1267 1274 1.714794 CAGACGCCAAAGAACTCGAT 58.285 50.000 0.00 0.00 0.00 3.59
1319 1327 4.622701 ACTCTGAACAAAAGTTGACTGC 57.377 40.909 0.00 0.00 0.00 4.40
1548 1675 6.741992 TGATATGAGCGACATGTTTCTTTT 57.258 33.333 0.00 0.00 39.77 2.27
1617 1760 6.441093 ACATTGTAATGCCACTACATGAAG 57.559 37.500 0.00 0.00 40.04 3.02
1733 1890 6.602179 TCGAGTCATTTCATTTAGCACTTTG 58.398 36.000 0.00 0.00 0.00 2.77
1734 1891 6.801539 TCGAGTCATTTCATTTAGCACTTT 57.198 33.333 0.00 0.00 0.00 2.66
1783 1946 5.828859 TCTAGCTCGAAAATAAGTAGGCTCT 59.171 40.000 0.00 0.00 0.00 4.09
1892 2055 7.843490 ACATTTGTACTATGAATAACAGCGT 57.157 32.000 13.28 0.00 0.00 5.07
1960 2123 1.202758 TGCCATTTTCGACACAGGAGT 60.203 47.619 0.00 0.00 0.00 3.85
2017 2180 7.112779 AGTATGAGCTTAGCTGGTTTGTAATT 58.887 34.615 13.01 0.00 39.88 1.40
2021 2184 4.508662 GAGTATGAGCTTAGCTGGTTTGT 58.491 43.478 13.01 0.00 39.88 2.83
2025 2188 2.043227 GGGAGTATGAGCTTAGCTGGT 58.957 52.381 13.01 1.97 39.88 4.00
2026 2189 2.298729 GAGGGAGTATGAGCTTAGCTGG 59.701 54.545 13.01 0.00 39.88 4.85
2036 2199 3.675348 TTAGGAACGGAGGGAGTATGA 57.325 47.619 0.00 0.00 0.00 2.15
2037 2200 4.957684 ATTTAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
2039 2202 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2040 2203 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2041 2204 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2042 2205 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2043 2206 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2044 2207 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2045 2208 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2046 2209 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2047 2210 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2060 2223 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2061 2224 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2062 2225 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2063 2226 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2064 2227 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2065 2228 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2066 2229 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2067 2230 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2068 2231 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2069 2232 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2070 2233 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2071 2234 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2072 2235 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
2073 2236 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
2074 2237 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
2075 2238 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
2076 2239 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
2077 2240 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
2078 2241 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
2079 2242 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
2080 2243 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
2081 2244 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
2082 2245 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2083 2246 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2084 2247 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2085 2248 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2086 2249 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2087 2250 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2088 2251 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2089 2252 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2090 2253 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2091 2254 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2092 2255 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2093 2256 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2094 2257 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2095 2258 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2096 2259 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2097 2260 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2129 2292 9.616156 CTACCATAGACGGATGTATATAGACTT 57.384 37.037 0.00 0.00 30.94 3.01
2130 2293 8.770322 ACTACCATAGACGGATGTATATAGACT 58.230 37.037 0.00 0.00 30.94 3.24
2131 2294 8.961294 ACTACCATAGACGGATGTATATAGAC 57.039 38.462 0.00 0.00 30.94 2.59
2132 2295 8.209584 GGACTACCATAGACGGATGTATATAGA 58.790 40.741 0.00 0.00 30.94 1.98
2133 2296 7.991460 TGGACTACCATAGACGGATGTATATAG 59.009 40.741 0.00 0.00 41.77 1.31
2134 2297 7.864770 TGGACTACCATAGACGGATGTATATA 58.135 38.462 0.00 0.00 41.77 0.86
2135 2298 6.728411 TGGACTACCATAGACGGATGTATAT 58.272 40.000 0.00 0.00 41.77 0.86
2136 2299 6.130692 TGGACTACCATAGACGGATGTATA 57.869 41.667 0.00 0.00 41.77 1.47
2137 2300 4.994282 TGGACTACCATAGACGGATGTAT 58.006 43.478 0.00 0.00 41.77 2.29
2138 2301 4.442401 TGGACTACCATAGACGGATGTA 57.558 45.455 0.00 0.00 41.77 2.29
2139 2302 3.308035 TGGACTACCATAGACGGATGT 57.692 47.619 0.00 0.00 41.77 3.06
2154 2317 9.753674 TGTCCTTTTAGATATTTCAAATGGACT 57.246 29.630 24.27 3.40 46.43 3.85
2169 2332 9.169592 CCGTTCCTAAATATTTGTCCTTTTAGA 57.830 33.333 11.05 0.00 34.90 2.10
2170 2333 9.169592 TCCGTTCCTAAATATTTGTCCTTTTAG 57.830 33.333 11.05 0.00 33.47 1.85
2171 2334 9.169592 CTCCGTTCCTAAATATTTGTCCTTTTA 57.830 33.333 11.05 0.00 0.00 1.52
2172 2335 7.122204 CCTCCGTTCCTAAATATTTGTCCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2173 2336 6.602009 CCTCCGTTCCTAAATATTTGTCCTTT 59.398 38.462 11.05 0.00 0.00 3.11
2174 2337 6.120220 CCTCCGTTCCTAAATATTTGTCCTT 58.880 40.000 11.05 0.00 0.00 3.36
2175 2338 5.397559 CCCTCCGTTCCTAAATATTTGTCCT 60.398 44.000 11.05 0.00 0.00 3.85
2176 2339 4.820173 CCCTCCGTTCCTAAATATTTGTCC 59.180 45.833 11.05 0.00 0.00 4.02
2177 2340 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2178 2341 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2179 2342 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2180 2343 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2181 2344 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2182 2345 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2183 2346 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2184 2347 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2185 2348 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2186 2349 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
2187 2350 3.626729 CCTTTCTACTCCCTCCGTTCCTA 60.627 52.174 0.00 0.00 0.00 2.94
2188 2351 2.458620 CTTTCTACTCCCTCCGTTCCT 58.541 52.381 0.00 0.00 0.00 3.36
2189 2352 1.481363 CCTTTCTACTCCCTCCGTTCC 59.519 57.143 0.00 0.00 0.00 3.62
2190 2353 1.481363 CCCTTTCTACTCCCTCCGTTC 59.519 57.143 0.00 0.00 0.00 3.95
2191 2354 1.078324 TCCCTTTCTACTCCCTCCGTT 59.922 52.381 0.00 0.00 0.00 4.44
2192 2355 0.708802 TCCCTTTCTACTCCCTCCGT 59.291 55.000 0.00 0.00 0.00 4.69
2193 2356 1.861982 TTCCCTTTCTACTCCCTCCG 58.138 55.000 0.00 0.00 0.00 4.63
2194 2357 4.864483 AATTTCCCTTTCTACTCCCTCC 57.136 45.455 0.00 0.00 0.00 4.30
2195 2358 7.381789 AGATAATTTCCCTTTCTACTCCCTC 57.618 40.000 0.00 0.00 0.00 4.30
2196 2359 7.773099 AAGATAATTTCCCTTTCTACTCCCT 57.227 36.000 0.00 0.00 0.00 4.20
2197 2360 8.715842 AGTAAGATAATTTCCCTTTCTACTCCC 58.284 37.037 0.00 0.00 0.00 4.30
2229 2392 7.458409 TCGAAGTTATGAAGGTACTACAAGT 57.542 36.000 0.00 0.00 38.49 3.16
2230 2393 8.928270 AATCGAAGTTATGAAGGTACTACAAG 57.072 34.615 0.00 0.00 38.49 3.16
2231 2394 9.715121 AAAATCGAAGTTATGAAGGTACTACAA 57.285 29.630 0.00 0.00 38.49 2.41
2232 2395 9.146984 CAAAATCGAAGTTATGAAGGTACTACA 57.853 33.333 0.00 0.00 38.49 2.74
2233 2396 8.114905 GCAAAATCGAAGTTATGAAGGTACTAC 58.885 37.037 0.00 0.00 38.49 2.73
2234 2397 7.009815 CGCAAAATCGAAGTTATGAAGGTACTA 59.990 37.037 0.00 0.00 38.49 1.82
2236 2399 5.957796 CGCAAAATCGAAGTTATGAAGGTAC 59.042 40.000 0.00 0.00 0.00 3.34
2243 2406 4.335082 TGTCCGCAAAATCGAAGTTATG 57.665 40.909 0.00 0.00 0.00 1.90
2251 2414 3.201726 ACAAGATTGTCCGCAAAATCG 57.798 42.857 0.00 0.00 36.50 3.34
2470 2636 5.494724 TCTGGAAAGATGACAAAGGATCTG 58.505 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.