Multiple sequence alignment - TraesCS2D01G386300

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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 TraesCS2D01G386300 chr2D 100.000 3330 0 0 1 3330 491428581 491431910 0.000000e+00 6150.0
1 TraesCS2D01G386300 chr2D 82.085 681 84 17 2564 3224 379106630 379105968 6.280000e-152 547.0
2 TraesCS2D01G386300 chr2A 88.526 1621 80 31 456 2005 635722464 635724049 0.000000e+00 1866.0
3 TraesCS2D01G386300 chr2A 87.500 512 34 12 2072 2564 635724074 635724574 6.240000e-157 564.0
4 TraesCS2D01G386300 chr2A 91.818 330 17 8 1 326 635721891 635722214 5.070000e-123 451.0
5 TraesCS2D01G386300 chr2A 81.364 440 61 10 2802 3224 514231291 514230856 4.120000e-89 339.0
6 TraesCS2D01G386300 chr2A 100.000 29 0 0 1814 1842 635723770 635723798 2.000000e-03 54.7
7 TraesCS2D01G386300 chr2B 87.578 1602 102 45 481 2030 575903303 575904859 0.000000e+00 1766.0
8 TraesCS2D01G386300 chr2B 89.228 492 31 12 2082 2564 575904874 575905352 2.210000e-166 595.0
9 TraesCS2D01G386300 chr2B 88.442 398 28 11 1 394 575902777 575903160 6.510000e-127 464.0
10 TraesCS2D01G386300 chr2B 87.805 123 10 1 3107 3224 450368381 450368259 4.480000e-29 139.0
11 TraesCS2D01G386300 chr1D 89.141 792 61 16 2561 3330 468124779 468125567 0.000000e+00 963.0
12 TraesCS2D01G386300 chr4B 88.475 564 48 7 2580 3129 405620469 405619909 0.000000e+00 665.0
13 TraesCS2D01G386300 chr7B 88.206 407 33 6 2566 2959 87011001 87010597 3.890000e-129 472.0
14 TraesCS2D01G386300 chr7B 87.117 163 19 2 998 1159 521578091 521578252 2.040000e-42 183.0
15 TraesCS2D01G386300 chr1A 87.681 414 33 7 2564 2963 584689422 584689013 1.810000e-127 466.0
16 TraesCS2D01G386300 chr6A 80.060 662 74 38 999 1640 449584441 449585064 3.940000e-119 438.0
17 TraesCS2D01G386300 chr6D 78.774 669 79 36 999 1640 312763270 312763902 1.120000e-104 390.0
18 TraesCS2D01G386300 chr6B 78.529 666 86 38 999 1640 514119181 514118549 5.210000e-103 385.0
19 TraesCS2D01G386300 chr4A 88.168 262 19 4 2564 2813 501265791 501266052 5.400000e-78 302.0
20 TraesCS2D01G386300 chr7D 87.730 163 18 2 998 1159 492148816 492148977 4.390000e-44 189.0
21 TraesCS2D01G386300 chr7A 87.730 163 18 2 998 1159 558402769 558402930 4.390000e-44 189.0


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 TraesCS2D01G386300 chr2D 491428581 491431910 3329 False 6150.000000 6150 100.000 1 3330 1 chr2D.!!$F1 3329
1 TraesCS2D01G386300 chr2D 379105968 379106630 662 True 547.000000 547 82.085 2564 3224 1 chr2D.!!$R1 660
2 TraesCS2D01G386300 chr2A 635721891 635724574 2683 False 733.925000 1866 91.961 1 2564 4 chr2A.!!$F1 2563
3 TraesCS2D01G386300 chr2B 575902777 575905352 2575 False 941.666667 1766 88.416 1 2564 3 chr2B.!!$F1 2563
4 TraesCS2D01G386300 chr1D 468124779 468125567 788 False 963.000000 963 89.141 2561 3330 1 chr1D.!!$F1 769
5 TraesCS2D01G386300 chr4B 405619909 405620469 560 True 665.000000 665 88.475 2580 3129 1 chr4B.!!$R1 549
6 TraesCS2D01G386300 chr6A 449584441 449585064 623 False 438.000000 438 80.060 999 1640 1 chr6A.!!$F1 641
7 TraesCS2D01G386300 chr6D 312763270 312763902 632 False 390.000000 390 78.774 999 1640 1 chr6D.!!$F1 641
8 TraesCS2D01G386300 chr6B 514118549 514119181 632 True 385.000000 385 78.529 999 1640 1 chr6B.!!$R1 641

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
897 1048 0.035598 CCGAGAGAGAGCCCGAGATA 59.964 60.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2764 3079 0.251297 CAATGGGCAACTGGTGGAGA 60.251 55.0 0.0 0.0 0.0 3.71 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
64 66 3.684305 TGTCTGTATGTGCCTTGATTTCG 59.316 43.478 0.00 0.00 0.00 3.46
71 74 2.552315 TGTGCCTTGATTTCGTTCCTTC 59.448 45.455 0.00 0.00 0.00 3.46
74 77 4.093556 GTGCCTTGATTTCGTTCCTTCTAG 59.906 45.833 0.00 0.00 0.00 2.43
79 82 6.350612 CCTTGATTTCGTTCCTTCTAGAGAGT 60.351 42.308 0.00 0.00 0.00 3.24
222 227 8.964420 TTAAAGCATGATAGCAACTAAAACAC 57.036 30.769 0.00 0.00 36.85 3.32
279 284 4.482386 CGTTTTCAGATCTACTCCGTCAA 58.518 43.478 0.00 0.00 0.00 3.18
280 285 4.921515 CGTTTTCAGATCTACTCCGTCAAA 59.078 41.667 0.00 0.00 0.00 2.69
294 299 6.331061 ACTCCGTCAAAGATATAACTGTGAC 58.669 40.000 18.84 18.84 46.03 3.67
303 308 9.376075 CAAAGATATAACTGTGACTGTGATCTT 57.624 33.333 15.50 15.50 33.64 2.40
312 317 5.185454 TGTGACTGTGATCTTGTTGTTTCT 58.815 37.500 0.00 0.00 0.00 2.52
351 359 8.932945 CTTTTCAAAAAGGAGTTTAAGCTTCT 57.067 30.769 0.00 0.00 41.23 2.85
353 361 6.300354 TCAAAAAGGAGTTTAAGCTTCTCG 57.700 37.500 0.00 0.00 0.00 4.04
357 365 1.338769 GGAGTTTAAGCTTCTCGGCCA 60.339 52.381 0.00 0.00 0.00 5.36
389 398 4.496507 GCGAAACTGATGGGAGCTTTATTC 60.497 45.833 0.00 0.00 0.00 1.75
427 476 3.321968 TCTGCTCATTCATACCGCAGTAT 59.678 43.478 9.09 0.00 46.00 2.12
451 501 0.807496 GCCTCTGCACCATCTTGTTC 59.193 55.000 0.00 0.00 37.47 3.18
466 599 0.183492 TGTTCTCCTTGGCTGTGCTT 59.817 50.000 0.00 0.00 0.00 3.91
467 600 0.877743 GTTCTCCTTGGCTGTGCTTC 59.122 55.000 0.00 0.00 0.00 3.86
477 610 2.358898 TGGCTGTGCTTCAAAGAAGTTC 59.641 45.455 8.39 0.00 0.00 3.01
515 650 8.856247 GTGTGAAAATTTGAACTTCTTTTACGT 58.144 29.630 0.00 0.00 0.00 3.57
548 688 5.587844 AGAGTACGAATAGGTCACAACGTAT 59.412 40.000 0.00 0.00 37.92 3.06
626 766 3.990959 TGCATCCACCAATGTGTACTA 57.009 42.857 0.00 0.00 41.09 1.82
636 776 6.767423 CCACCAATGTGTACTATCATGATTCA 59.233 38.462 14.65 6.06 41.09 2.57
716 857 2.448961 TCCTCCAAAGTCAAAATCCCCA 59.551 45.455 0.00 0.00 0.00 4.96
802 946 3.710722 CACCGCCCTCTCTGCCTT 61.711 66.667 0.00 0.00 0.00 4.35
804 948 4.168291 CCGCCCTCTCTGCCTTCC 62.168 72.222 0.00 0.00 0.00 3.46
806 950 1.758514 CGCCCTCTCTGCCTTCCTA 60.759 63.158 0.00 0.00 0.00 2.94
807 951 1.330655 CGCCCTCTCTGCCTTCCTAA 61.331 60.000 0.00 0.00 0.00 2.69
808 952 0.179234 GCCCTCTCTGCCTTCCTAAC 59.821 60.000 0.00 0.00 0.00 2.34
809 953 1.573108 CCCTCTCTGCCTTCCTAACA 58.427 55.000 0.00 0.00 0.00 2.41
826 970 4.408921 CCTAACATTACCATGTCCTCCTGA 59.591 45.833 0.00 0.00 43.34 3.86
896 1047 1.228124 CCGAGAGAGAGCCCGAGAT 60.228 63.158 0.00 0.00 0.00 2.75
897 1048 0.035598 CCGAGAGAGAGCCCGAGATA 59.964 60.000 0.00 0.00 0.00 1.98
898 1049 1.543650 CCGAGAGAGAGCCCGAGATAA 60.544 57.143 0.00 0.00 0.00 1.75
899 1050 1.533731 CGAGAGAGAGCCCGAGATAAC 59.466 57.143 0.00 0.00 0.00 1.89
900 1051 2.808933 CGAGAGAGAGCCCGAGATAACT 60.809 54.545 0.00 0.00 0.00 2.24
901 1052 2.812011 GAGAGAGAGCCCGAGATAACTC 59.188 54.545 0.00 0.00 39.54 3.01
968 1127 1.098129 TCCATCTCTCTCTCGCGTGG 61.098 60.000 5.77 2.67 0.00 4.94
1149 1311 2.122729 CTGTCCCTCCTCCACCCA 59.877 66.667 0.00 0.00 0.00 4.51
1217 1388 2.909006 ACATCTGCCAGGTGGGATATAG 59.091 50.000 10.24 0.00 40.01 1.31
1218 1389 2.795291 TCTGCCAGGTGGGATATAGT 57.205 50.000 0.00 0.00 40.01 2.12
1219 1390 3.915346 TCTGCCAGGTGGGATATAGTA 57.085 47.619 0.00 0.00 40.01 1.82
1244 1415 8.955061 ACAAATCAAGAACGTTTTCAGATATG 57.045 30.769 0.46 0.00 33.72 1.78
1499 1707 4.753662 CAGCACCAGCCCCTGCAT 62.754 66.667 0.00 0.00 43.56 3.96
1587 1801 0.029567 GCATCTCCGAGTACCTGACG 59.970 60.000 0.00 0.00 0.00 4.35
1677 1903 1.557099 AGCCGTATCAGGTCAGTTCA 58.443 50.000 0.00 0.00 0.00 3.18
1689 1915 1.795286 GTCAGTTCAAGACTTCCAGCG 59.205 52.381 0.00 0.00 36.10 5.18
1723 1955 6.301169 ACTGCTACTTTTACTAGGCAATCT 57.699 37.500 0.00 0.00 0.00 2.40
1732 1964 7.606839 ACTTTTACTAGGCAATCTAAGACAACC 59.393 37.037 0.00 0.00 0.00 3.77
1742 1974 0.391228 TAAGACAACCTGCGAGCACA 59.609 50.000 0.00 0.00 0.00 4.57
1750 1982 0.877071 CCTGCGAGCACAATGAAACT 59.123 50.000 0.00 0.00 0.00 2.66
1753 2008 1.946081 TGCGAGCACAATGAAACTTGA 59.054 42.857 0.00 0.00 0.00 3.02
1762 2017 5.333568 GCACAATGAAACTTGATTTTGAGCC 60.334 40.000 0.00 0.00 0.00 4.70
1764 2019 4.541973 ATGAAACTTGATTTTGAGCCCC 57.458 40.909 0.00 0.00 0.00 5.80
1773 2028 2.619697 TTTTGAGCCCCCAATCATCA 57.380 45.000 0.00 0.00 0.00 3.07
1775 2030 2.852714 TTGAGCCCCCAATCATCATT 57.147 45.000 0.00 0.00 0.00 2.57
1777 2032 2.390696 TGAGCCCCCAATCATCATTTG 58.609 47.619 0.00 0.00 0.00 2.32
1807 2067 4.716784 TCATCTGCTCTAACCAGTAACCAT 59.283 41.667 0.00 0.00 0.00 3.55
1821 2081 4.528039 CCATGCCCCGCTCCCAAT 62.528 66.667 0.00 0.00 0.00 3.16
1822 2082 3.221389 CATGCCCCGCTCCCAATG 61.221 66.667 0.00 0.00 0.00 2.82
1843 2103 3.248266 GCTTTTGAGCTCGCAATCATTT 58.752 40.909 9.64 0.00 0.00 2.32
1877 2137 2.740438 TGCTCGCAACTAGCACCA 59.260 55.556 0.00 0.00 44.78 4.17
1913 2181 3.742640 GCAGGGTGTCAGGATAATGTCTC 60.743 52.174 0.00 0.00 0.00 3.36
1946 2221 3.809832 ACCAACATATGATGCTCTAACGC 59.190 43.478 10.38 0.00 0.00 4.84
1999 2277 1.787012 CCACTTTTGGCATTGCAGAC 58.213 50.000 11.39 0.00 35.56 3.51
2011 2289 4.199310 GCATTGCAGACTTAACCCATCTA 58.801 43.478 3.15 0.00 0.00 1.98
2014 2292 4.202245 TGCAGACTTAACCCATCTACAC 57.798 45.455 0.00 0.00 0.00 2.90
2015 2293 3.838317 TGCAGACTTAACCCATCTACACT 59.162 43.478 0.00 0.00 0.00 3.55
2016 2294 5.020795 TGCAGACTTAACCCATCTACACTA 58.979 41.667 0.00 0.00 0.00 2.74
2017 2295 5.105473 TGCAGACTTAACCCATCTACACTAC 60.105 44.000 0.00 0.00 0.00 2.73
2018 2296 5.105473 GCAGACTTAACCCATCTACACTACA 60.105 44.000 0.00 0.00 0.00 2.74
2021 2299 7.331193 CAGACTTAACCCATCTACACTACAAAC 59.669 40.741 0.00 0.00 0.00 2.93
2023 2301 7.511268 ACTTAACCCATCTACACTACAAACAA 58.489 34.615 0.00 0.00 0.00 2.83
2024 2302 7.660208 ACTTAACCCATCTACACTACAAACAAG 59.340 37.037 0.00 0.00 0.00 3.16
2025 2303 5.818678 ACCCATCTACACTACAAACAAGA 57.181 39.130 0.00 0.00 0.00 3.02
2026 2304 6.182507 ACCCATCTACACTACAAACAAGAA 57.817 37.500 0.00 0.00 0.00 2.52
2027 2305 6.597562 ACCCATCTACACTACAAACAAGAAA 58.402 36.000 0.00 0.00 0.00 2.52
2028 2306 7.231467 ACCCATCTACACTACAAACAAGAAAT 58.769 34.615 0.00 0.00 0.00 2.17
2029 2307 7.174946 ACCCATCTACACTACAAACAAGAAATG 59.825 37.037 0.00 0.00 0.00 2.32
2030 2308 7.023575 CCATCTACACTACAAACAAGAAATGC 58.976 38.462 0.00 0.00 0.00 3.56
2031 2309 7.308529 CCATCTACACTACAAACAAGAAATGCA 60.309 37.037 0.00 0.00 0.00 3.96
2032 2310 7.189693 TCTACACTACAAACAAGAAATGCAG 57.810 36.000 0.00 0.00 0.00 4.41
2033 2311 6.989759 TCTACACTACAAACAAGAAATGCAGA 59.010 34.615 0.00 0.00 0.00 4.26
2034 2312 6.639632 ACACTACAAACAAGAAATGCAGAT 57.360 33.333 0.00 0.00 0.00 2.90
2035 2313 7.042797 ACACTACAAACAAGAAATGCAGATT 57.957 32.000 0.00 0.00 0.00 2.40
2036 2314 7.491682 ACACTACAAACAAGAAATGCAGATTT 58.508 30.769 0.00 0.00 34.29 2.17
2037 2315 7.649306 ACACTACAAACAAGAAATGCAGATTTC 59.351 33.333 4.88 4.88 45.50 2.17
2047 2325 6.753897 GAAATGCAGATTTCGTGTTTCTTT 57.246 33.333 0.00 0.00 38.50 2.52
2048 2326 7.165427 GAAATGCAGATTTCGTGTTTCTTTT 57.835 32.000 0.00 0.00 38.50 2.27
2049 2327 7.538303 AAATGCAGATTTCGTGTTTCTTTTT 57.462 28.000 0.00 0.00 0.00 1.94
2050 2328 6.753897 ATGCAGATTTCGTGTTTCTTTTTC 57.246 33.333 0.00 0.00 0.00 2.29
2051 2329 5.890334 TGCAGATTTCGTGTTTCTTTTTCT 58.110 33.333 0.00 0.00 0.00 2.52
2052 2330 6.329496 TGCAGATTTCGTGTTTCTTTTTCTT 58.671 32.000 0.00 0.00 0.00 2.52
2053 2331 6.811170 TGCAGATTTCGTGTTTCTTTTTCTTT 59.189 30.769 0.00 0.00 0.00 2.52
2054 2332 7.330700 TGCAGATTTCGTGTTTCTTTTTCTTTT 59.669 29.630 0.00 0.00 0.00 2.27
2055 2333 7.632132 GCAGATTTCGTGTTTCTTTTTCTTTTG 59.368 33.333 0.00 0.00 0.00 2.44
2056 2334 8.859156 CAGATTTCGTGTTTCTTTTTCTTTTGA 58.141 29.630 0.00 0.00 0.00 2.69
2057 2335 9.076596 AGATTTCGTGTTTCTTTTTCTTTTGAG 57.923 29.630 0.00 0.00 0.00 3.02
2058 2336 6.626199 TTCGTGTTTCTTTTTCTTTTGAGC 57.374 33.333 0.00 0.00 0.00 4.26
2061 2339 6.811170 TCGTGTTTCTTTTTCTTTTGAGCAAT 59.189 30.769 0.00 0.00 0.00 3.56
2063 2341 8.261908 CGTGTTTCTTTTTCTTTTGAGCAATAG 58.738 33.333 0.00 0.00 0.00 1.73
2090 2371 6.449698 AGATATTGTTTTGTTGCTTGGACTG 58.550 36.000 0.00 0.00 0.00 3.51
2104 2386 2.942804 TGGACTGATTTGGCAACTTGA 58.057 42.857 0.00 0.00 37.61 3.02
2105 2387 2.622942 TGGACTGATTTGGCAACTTGAC 59.377 45.455 0.00 0.00 37.61 3.18
2106 2388 2.622942 GGACTGATTTGGCAACTTGACA 59.377 45.455 0.00 0.00 30.30 3.58
2107 2389 3.550842 GGACTGATTTGGCAACTTGACAC 60.551 47.826 0.00 0.00 33.32 3.67
2108 2390 3.290710 ACTGATTTGGCAACTTGACACT 58.709 40.909 0.00 0.00 33.32 3.55
2114 2396 1.134521 TGGCAACTTGACACTCGTCTT 60.135 47.619 0.00 0.00 39.51 3.01
2121 2406 0.888619 TGACACTCGTCTTAGCAGGG 59.111 55.000 0.00 0.00 43.06 4.45
2122 2407 1.174783 GACACTCGTCTTAGCAGGGA 58.825 55.000 0.00 0.00 39.22 4.20
2123 2408 1.133407 GACACTCGTCTTAGCAGGGAG 59.867 57.143 0.00 0.00 39.22 4.30
2124 2409 0.457851 CACTCGTCTTAGCAGGGAGG 59.542 60.000 0.00 0.00 0.00 4.30
2135 2420 3.368501 AGGGAGGAGGGCTGGCTA 61.369 66.667 0.00 0.00 0.00 3.93
2158 2443 4.660938 GGTGGGCCGCAAGAAGGT 62.661 66.667 20.39 0.00 43.02 3.50
2159 2444 3.365265 GTGGGCCGCAAGAAGGTG 61.365 66.667 13.30 0.00 43.02 4.00
2160 2445 3.565214 TGGGCCGCAAGAAGGTGA 61.565 61.111 0.00 0.00 43.02 4.02
2161 2446 2.282180 GGGCCGCAAGAAGGTGAA 60.282 61.111 0.00 0.00 43.02 3.18
2162 2447 2.335712 GGGCCGCAAGAAGGTGAAG 61.336 63.158 0.00 0.00 43.02 3.02
2163 2448 2.335712 GGCCGCAAGAAGGTGAAGG 61.336 63.158 0.00 0.00 43.02 3.46
2164 2449 1.600916 GCCGCAAGAAGGTGAAGGT 60.601 57.895 0.00 0.00 43.02 3.50
2203 2488 2.866085 AAGAGCAGCTGATCGGTGGC 62.866 60.000 25.12 12.98 41.38 5.01
2319 2607 1.751162 CGTCTCTCGGCTCCTCCTT 60.751 63.158 0.00 0.00 35.71 3.36
2359 2647 3.522553 GCTTTGCAGTACCAGTACTAGG 58.477 50.000 10.04 2.26 43.98 3.02
2416 2715 6.128472 GGACCATGAATTTTTGTTTGATCTGC 60.128 38.462 0.00 0.00 0.00 4.26
2429 2728 0.373024 GATCTGCAGTTGCTCGCTTC 59.627 55.000 14.67 0.00 42.66 3.86
2430 2729 0.321034 ATCTGCAGTTGCTCGCTTCA 60.321 50.000 14.67 0.00 42.66 3.02
2431 2730 0.947660 TCTGCAGTTGCTCGCTTCAG 60.948 55.000 14.67 0.00 42.66 3.02
2434 2733 0.588252 GCAGTTGCTCGCTTCAGAAA 59.412 50.000 0.00 0.00 38.21 2.52
2435 2734 1.198637 GCAGTTGCTCGCTTCAGAAAT 59.801 47.619 0.00 0.00 38.21 2.17
2441 2740 3.664107 TGCTCGCTTCAGAAATTACTGT 58.336 40.909 0.00 0.00 38.79 3.55
2511 2815 3.070018 CTGGATCACTGGACTGTTTGAC 58.930 50.000 0.00 0.00 0.00 3.18
2535 2839 1.079503 GAAGTACTCTGCGCCTTTGG 58.920 55.000 4.18 0.00 0.00 3.28
2635 2942 1.174783 TCTCCGAGCTAACACACTCC 58.825 55.000 0.00 0.00 0.00 3.85
2638 2945 1.585006 CGAGCTAACACACTCCGGT 59.415 57.895 0.00 0.00 0.00 5.28
2686 2994 3.333680 AGATTTCAAGCAACCCTCCCTAA 59.666 43.478 0.00 0.00 0.00 2.69
2687 2995 3.825908 TTTCAAGCAACCCTCCCTAAT 57.174 42.857 0.00 0.00 0.00 1.73
2732 3040 3.737172 GCGTCGCACCCAAGCAAT 61.737 61.111 13.44 0.00 0.00 3.56
2744 3052 3.330701 ACCCAAGCAATCCTAAAGTCTGA 59.669 43.478 0.00 0.00 0.00 3.27
2865 3180 6.409704 TCGAGAATGATCCTCTGAACATTTT 58.590 36.000 0.00 0.00 42.15 1.82
2866 3181 6.881065 TCGAGAATGATCCTCTGAACATTTTT 59.119 34.615 0.00 0.00 42.15 1.94
2882 3197 4.022416 ACATTTTTAGTTCATTCGCCAGCA 60.022 37.500 0.00 0.00 0.00 4.41
2886 3201 1.538047 AGTTCATTCGCCAGCAACAT 58.462 45.000 0.00 0.00 0.00 2.71
2889 3204 0.608856 TCATTCGCCAGCAACATGGT 60.609 50.000 0.00 0.00 42.75 3.55
2938 3253 0.824109 CTGCATCGTGGGTAGAAGGA 59.176 55.000 0.00 0.00 0.00 3.36
3028 3347 3.562557 ACGTTCACCTTTGATAAAGCGTT 59.437 39.130 0.00 0.00 37.18 4.84
3031 3350 5.278604 GTTCACCTTTGATAAAGCGTTGTT 58.721 37.500 0.00 0.00 37.18 2.83
3034 3353 3.562557 ACCTTTGATAAAGCGTTGTTCGT 59.437 39.130 0.00 0.00 42.13 3.85
3053 3372 0.324738 TGTTTGCTTTGACCCACCCA 60.325 50.000 0.00 0.00 0.00 4.51
3059 3378 0.392998 CTTTGACCCACCCATCCTCG 60.393 60.000 0.00 0.00 0.00 4.63
3090 3410 1.773496 CTTTCGCGTTCTGTCGTCC 59.227 57.895 5.77 0.00 0.00 4.79
3274 3600 2.435586 CTTGCCGAGCCACTCCAG 60.436 66.667 0.00 0.00 0.00 3.86
3301 3627 3.692406 ACGAAGTCCCTCCGTGGC 61.692 66.667 0.00 0.00 29.74 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.703007 CAGGAGGATAAGGCTTGCTAGT 59.297 50.000 10.69 0.00 0.00 2.57
64 66 4.401202 AGCTAAGCACTCTCTAGAAGGAAC 59.599 45.833 0.00 0.00 0.00 3.62
71 74 2.034558 GGAGCAGCTAAGCACTCTCTAG 59.965 54.545 0.00 0.00 35.39 2.43
74 77 0.534412 TGGAGCAGCTAAGCACTCTC 59.466 55.000 0.00 0.00 35.39 3.20
79 82 1.275666 TACCTTGGAGCAGCTAAGCA 58.724 50.000 0.00 0.00 34.06 3.91
159 163 9.090692 CAAATGCAGAAGAAAAAGAGAAAAAGA 57.909 29.630 0.00 0.00 0.00 2.52
161 165 8.776376 ACAAATGCAGAAGAAAAAGAGAAAAA 57.224 26.923 0.00 0.00 0.00 1.94
199 203 6.863126 GTGTGTTTTAGTTGCTATCATGCTTT 59.137 34.615 0.00 0.00 0.00 3.51
220 225 6.488683 TCCTTTCTAGGGTTTTATTGTGTGTG 59.511 38.462 0.00 0.00 42.26 3.82
221 226 6.489022 GTCCTTTCTAGGGTTTTATTGTGTGT 59.511 38.462 0.00 0.00 42.26 3.72
222 227 6.488683 TGTCCTTTCTAGGGTTTTATTGTGTG 59.511 38.462 0.00 0.00 42.26 3.82
252 257 4.184629 GGAGTAGATCTGAAAACGCACAT 58.815 43.478 5.18 0.00 0.00 3.21
253 258 3.585862 GGAGTAGATCTGAAAACGCACA 58.414 45.455 5.18 0.00 0.00 4.57
279 284 8.535335 ACAAGATCACAGTCACAGTTATATCTT 58.465 33.333 0.00 0.00 32.81 2.40
280 285 8.072321 ACAAGATCACAGTCACAGTTATATCT 57.928 34.615 0.00 0.00 0.00 1.98
294 299 6.857777 AAGAGAGAAACAACAAGATCACAG 57.142 37.500 0.00 0.00 0.00 3.66
326 331 8.932945 AGAAGCTTAAACTCCTTTTTGAAAAG 57.067 30.769 0.00 8.83 43.82 2.27
364 373 0.254178 AGCTCCCATCAGTTTCGCAT 59.746 50.000 0.00 0.00 0.00 4.73
389 398 3.094572 AGCAGAAATCCTCCATGTTTGG 58.905 45.455 0.00 0.00 45.15 3.28
451 501 1.268899 CTTTGAAGCACAGCCAAGGAG 59.731 52.381 0.00 0.00 0.00 3.69
487 622 9.068008 GTAAAAGAAGTTCAAATTTTCACACGA 57.932 29.630 5.50 0.00 0.00 4.35
522 657 5.159209 CGTTGTGACCTATTCGTACTCTTT 58.841 41.667 0.00 0.00 0.00 2.52
537 677 6.472808 GGAATGAAGTCTCTATACGTTGTGAC 59.527 42.308 0.00 1.75 0.00 3.67
548 688 6.381133 TGAATGCAGTAGGAATGAAGTCTCTA 59.619 38.462 0.00 0.00 0.00 2.43
626 766 9.482175 TCTCTGATAGATCTGATGAATCATGAT 57.518 33.333 5.18 1.18 36.02 2.45
716 857 1.678970 GCCTTGTTCCTTGGGCGAT 60.679 57.895 0.00 0.00 35.08 4.58
793 937 4.101114 TGGTAATGTTAGGAAGGCAGAGA 58.899 43.478 0.00 0.00 0.00 3.10
797 941 4.584638 ACATGGTAATGTTAGGAAGGCA 57.415 40.909 0.00 0.00 44.94 4.75
826 970 4.379186 CGCGAGAGGTGTTTATATATCGGT 60.379 45.833 0.00 0.00 0.00 4.69
1219 1390 8.567948 ACATATCTGAAAACGTTCTTGATTTGT 58.432 29.630 0.00 11.29 36.34 2.83
1283 1462 3.357079 CCTGCAGCCCACAACGAC 61.357 66.667 8.66 0.00 0.00 4.34
1677 1903 1.963338 GCAGTGCGCTGGAAGTCTT 60.963 57.895 27.56 0.00 42.78 3.01
1703 1929 7.980099 TGTCTTAGATTGCCTAGTAAAAGTAGC 59.020 37.037 0.00 0.00 0.00 3.58
1713 1945 3.873952 GCAGGTTGTCTTAGATTGCCTAG 59.126 47.826 2.25 0.00 0.00 3.02
1723 1955 0.391228 TGTGCTCGCAGGTTGTCTTA 59.609 50.000 0.00 0.00 0.00 2.10
1732 1964 2.031769 TCAAGTTTCATTGTGCTCGCAG 60.032 45.455 0.00 0.00 0.00 5.18
1742 1974 4.263025 GGGGGCTCAAAATCAAGTTTCATT 60.263 41.667 0.00 0.00 0.00 2.57
1750 1982 2.899975 TGATTGGGGGCTCAAAATCAA 58.100 42.857 11.14 0.00 36.40 2.57
1753 2008 3.119009 TGATGATTGGGGGCTCAAAAT 57.881 42.857 0.00 0.00 0.00 1.82
1762 2017 5.834742 TGAACTATCCAAATGATGATTGGGG 59.165 40.000 0.00 0.00 45.97 4.96
1773 2028 6.995091 GGTTAGAGCAGATGAACTATCCAAAT 59.005 38.462 0.00 0.00 36.40 2.32
1775 2030 5.425217 TGGTTAGAGCAGATGAACTATCCAA 59.575 40.000 0.00 0.00 36.40 3.53
1777 2032 5.069781 ACTGGTTAGAGCAGATGAACTATCC 59.930 44.000 13.44 0.00 45.98 2.59
1843 2103 4.242475 CGAGCATGACAACAAACTACCTA 58.758 43.478 0.00 0.00 0.00 3.08
1877 2137 2.558359 CACCCTGCTTCGGATTTTTCTT 59.442 45.455 0.00 0.00 0.00 2.52
1925 2200 3.187227 GGCGTTAGAGCATCATATGTTGG 59.813 47.826 14.19 2.13 37.82 3.77
1928 2203 3.751479 TGGCGTTAGAGCATCATATGT 57.249 42.857 1.90 0.00 37.82 2.29
1929 2204 5.422666 TTTTGGCGTTAGAGCATCATATG 57.577 39.130 0.00 0.00 37.82 1.78
1946 2221 7.177878 AGTAGATATTCCTATGGCCATTTTGG 58.822 38.462 26.37 22.33 41.55 3.28
1959 2234 4.043059 TGGTAGGAGCGAGTAGATATTCCT 59.957 45.833 0.00 0.00 38.52 3.36
1994 2272 4.473477 AGTGTAGATGGGTTAAGTCTGC 57.527 45.455 0.00 0.00 0.00 4.26
1999 2277 7.876068 TCTTGTTTGTAGTGTAGATGGGTTAAG 59.124 37.037 0.00 0.00 0.00 1.85
2011 2289 6.639632 ATCTGCATTTCTTGTTTGTAGTGT 57.360 33.333 0.00 0.00 0.00 3.55
2014 2292 6.857964 ACGAAATCTGCATTTCTTGTTTGTAG 59.142 34.615 10.27 0.00 44.11 2.74
2015 2293 6.636447 CACGAAATCTGCATTTCTTGTTTGTA 59.364 34.615 10.27 0.00 44.11 2.41
2016 2294 5.459762 CACGAAATCTGCATTTCTTGTTTGT 59.540 36.000 10.27 0.00 44.11 2.83
2017 2295 5.897133 CACGAAATCTGCATTTCTTGTTTG 58.103 37.500 10.27 0.00 44.11 2.93
2021 2299 5.916883 AGAAACACGAAATCTGCATTTCTTG 59.083 36.000 14.39 14.39 46.48 3.02
2023 2301 5.695851 AGAAACACGAAATCTGCATTTCT 57.304 34.783 10.27 5.93 44.11 2.52
2024 2302 6.753897 AAAGAAACACGAAATCTGCATTTC 57.246 33.333 3.17 3.17 43.21 2.17
2025 2303 7.492344 AGAAAAAGAAACACGAAATCTGCATTT 59.508 29.630 0.00 0.00 34.70 2.32
2026 2304 6.980397 AGAAAAAGAAACACGAAATCTGCATT 59.020 30.769 0.00 0.00 0.00 3.56
2027 2305 6.507023 AGAAAAAGAAACACGAAATCTGCAT 58.493 32.000 0.00 0.00 0.00 3.96
2028 2306 5.890334 AGAAAAAGAAACACGAAATCTGCA 58.110 33.333 0.00 0.00 0.00 4.41
2029 2307 6.812481 AAGAAAAAGAAACACGAAATCTGC 57.188 33.333 0.00 0.00 0.00 4.26
2030 2308 8.859156 TCAAAAGAAAAAGAAACACGAAATCTG 58.141 29.630 0.00 0.00 0.00 2.90
2031 2309 8.980143 TCAAAAGAAAAAGAAACACGAAATCT 57.020 26.923 0.00 0.00 0.00 2.40
2032 2310 7.841277 GCTCAAAAGAAAAAGAAACACGAAATC 59.159 33.333 0.00 0.00 0.00 2.17
2033 2311 7.330700 TGCTCAAAAGAAAAAGAAACACGAAAT 59.669 29.630 0.00 0.00 0.00 2.17
2034 2312 6.642950 TGCTCAAAAGAAAAAGAAACACGAAA 59.357 30.769 0.00 0.00 0.00 3.46
2035 2313 6.153067 TGCTCAAAAGAAAAAGAAACACGAA 58.847 32.000 0.00 0.00 0.00 3.85
2036 2314 5.704888 TGCTCAAAAGAAAAAGAAACACGA 58.295 33.333 0.00 0.00 0.00 4.35
2037 2315 6.388259 TTGCTCAAAAGAAAAAGAAACACG 57.612 33.333 0.00 0.00 0.00 4.49
2038 2316 9.301153 TCTATTGCTCAAAAGAAAAAGAAACAC 57.699 29.630 0.00 0.00 0.00 3.32
2056 2334 9.956720 GCAACAAAACAATATCTATCTATTGCT 57.043 29.630 0.00 0.00 40.99 3.91
2057 2335 9.956720 AGCAACAAAACAATATCTATCTATTGC 57.043 29.630 0.00 0.00 40.99 3.56
2061 2339 9.679661 TCCAAGCAACAAAACAATATCTATCTA 57.320 29.630 0.00 0.00 0.00 1.98
2063 2341 8.462016 AGTCCAAGCAACAAAACAATATCTATC 58.538 33.333 0.00 0.00 0.00 2.08
2066 2344 6.265196 TCAGTCCAAGCAACAAAACAATATCT 59.735 34.615 0.00 0.00 0.00 1.98
2067 2345 6.446318 TCAGTCCAAGCAACAAAACAATATC 58.554 36.000 0.00 0.00 0.00 1.63
2068 2346 6.403866 TCAGTCCAAGCAACAAAACAATAT 57.596 33.333 0.00 0.00 0.00 1.28
2070 2351 4.734398 TCAGTCCAAGCAACAAAACAAT 57.266 36.364 0.00 0.00 0.00 2.71
2073 2354 4.270808 CCAAATCAGTCCAAGCAACAAAAC 59.729 41.667 0.00 0.00 0.00 2.43
2078 2359 1.340889 TGCCAAATCAGTCCAAGCAAC 59.659 47.619 0.00 0.00 0.00 4.17
2090 2371 2.290641 ACGAGTGTCAAGTTGCCAAATC 59.709 45.455 0.00 0.00 0.00 2.17
2104 2386 1.178276 CTCCCTGCTAAGACGAGTGT 58.822 55.000 0.00 0.00 0.00 3.55
2105 2387 0.457851 CCTCCCTGCTAAGACGAGTG 59.542 60.000 0.00 0.00 0.00 3.51
2106 2388 0.331954 TCCTCCCTGCTAAGACGAGT 59.668 55.000 0.00 0.00 0.00 4.18
2107 2389 1.028905 CTCCTCCCTGCTAAGACGAG 58.971 60.000 0.00 0.00 0.00 4.18
2108 2390 0.395862 CCTCCTCCCTGCTAAGACGA 60.396 60.000 0.00 0.00 0.00 4.20
2114 2396 2.041508 CAGCCCTCCTCCCTGCTA 60.042 66.667 0.00 0.00 31.69 3.49
2121 2406 1.152139 ATCCTAGCCAGCCCTCCTC 60.152 63.158 0.00 0.00 0.00 3.71
2122 2407 1.152139 GATCCTAGCCAGCCCTCCT 60.152 63.158 0.00 0.00 0.00 3.69
2123 2408 2.578714 CGATCCTAGCCAGCCCTCC 61.579 68.421 0.00 0.00 0.00 4.30
2124 2409 2.578714 CCGATCCTAGCCAGCCCTC 61.579 68.421 0.00 0.00 0.00 4.30
2179 2464 1.077930 GATCAGCTGCTCTTGGCCA 60.078 57.895 9.47 0.00 40.92 5.36
2185 2470 2.898738 CCACCGATCAGCTGCTCT 59.101 61.111 15.15 0.00 0.00 4.09
2319 2607 1.493772 CGCACGTTTTCACCAGTAGA 58.506 50.000 0.00 0.00 0.00 2.59
2359 2647 8.644318 TTTTCTGATTTTATCCGCTACTAGTC 57.356 34.615 0.00 0.00 0.00 2.59
2416 2715 3.549299 AATTTCTGAAGCGAGCAACTG 57.451 42.857 0.00 0.00 0.00 3.16
2451 2750 1.959899 GCGACACATTGAGGACGCAG 61.960 60.000 18.12 0.00 44.29 5.18
2452 2751 2.027073 GCGACACATTGAGGACGCA 61.027 57.895 18.12 0.00 44.29 5.24
2453 2752 1.291877 AAGCGACACATTGAGGACGC 61.292 55.000 16.44 16.44 45.03 5.19
2454 2753 0.716108 GAAGCGACACATTGAGGACG 59.284 55.000 0.00 0.00 0.00 4.79
2455 2754 1.728971 CAGAAGCGACACATTGAGGAC 59.271 52.381 0.00 0.00 0.00 3.85
2456 2755 1.618343 TCAGAAGCGACACATTGAGGA 59.382 47.619 0.00 0.00 0.00 3.71
2457 2756 1.998315 CTCAGAAGCGACACATTGAGG 59.002 52.381 0.00 0.00 0.00 3.86
2459 2758 2.297315 AGACTCAGAAGCGACACATTGA 59.703 45.455 0.00 0.00 0.00 2.57
2460 2759 2.681706 AGACTCAGAAGCGACACATTG 58.318 47.619 0.00 0.00 0.00 2.82
2461 2760 3.393089 AAGACTCAGAAGCGACACATT 57.607 42.857 0.00 0.00 0.00 2.71
2462 2761 3.062763 CAAAGACTCAGAAGCGACACAT 58.937 45.455 0.00 0.00 0.00 3.21
2463 2762 2.473816 CAAAGACTCAGAAGCGACACA 58.526 47.619 0.00 0.00 0.00 3.72
2464 2763 1.795286 CCAAAGACTCAGAAGCGACAC 59.205 52.381 0.00 0.00 0.00 3.67
2465 2764 1.270305 CCCAAAGACTCAGAAGCGACA 60.270 52.381 0.00 0.00 0.00 4.35
2511 2815 1.079503 GGCGCAGAGTACTTCAAAGG 58.920 55.000 10.83 0.00 0.00 3.11
2578 2882 8.174422 GCGTTAAACATTGAATAAAATGGCAAT 58.826 29.630 0.00 0.00 41.06 3.56
2635 2942 1.134401 ACTTGGCTCCATGTATCACCG 60.134 52.381 5.74 0.00 33.44 4.94
2638 2945 5.172687 TGTAAACTTGGCTCCATGTATCA 57.827 39.130 7.72 5.59 34.54 2.15
2686 2994 2.380084 AATGTCGCACACGTCCTAAT 57.620 45.000 0.00 0.00 41.18 1.73
2687 2995 3.513680 ATAATGTCGCACACGTCCTAA 57.486 42.857 0.00 0.00 41.18 2.69
2732 3040 7.461749 ACTTGGATCATTTTCAGACTTTAGGA 58.538 34.615 0.00 0.00 0.00 2.94
2744 3052 9.566432 GTGGAGAAGATATACTTGGATCATTTT 57.434 33.333 0.00 0.00 39.13 1.82
2764 3079 0.251297 CAATGGGCAACTGGTGGAGA 60.251 55.000 0.00 0.00 0.00 3.71
2786 3101 8.082672 TCATGAATGAATAGAAGGACTTCTCA 57.917 34.615 17.16 10.62 40.30 3.27
2800 3115 4.464951 TGGCAAGAAAGCTCATGAATGAAT 59.535 37.500 0.00 0.00 36.18 2.57
2838 3153 4.097135 TGTTCAGAGGATCATTCTCGAGAC 59.903 45.833 16.36 2.68 37.82 3.36
2865 3180 2.499197 TGTTGCTGGCGAATGAACTAA 58.501 42.857 0.00 0.00 0.00 2.24
2866 3181 2.177394 TGTTGCTGGCGAATGAACTA 57.823 45.000 0.00 0.00 0.00 2.24
2954 3272 1.675310 CCATGGCGAGTTCTTGGCA 60.675 57.895 16.58 16.58 45.22 4.92
3006 3325 3.135994 ACGCTTTATCAAAGGTGAACGT 58.864 40.909 1.19 0.00 38.93 3.99
3028 3347 1.133407 GGGTCAAAGCAAACACGAACA 59.867 47.619 0.00 0.00 0.00 3.18
3031 3350 0.736053 GTGGGTCAAAGCAAACACGA 59.264 50.000 0.00 0.00 0.00 4.35
3034 3353 0.324738 TGGGTGGGTCAAAGCAAACA 60.325 50.000 0.00 0.00 0.00 2.83
3053 3372 1.977293 GCTGGAAGAAGCCCGAGGAT 61.977 60.000 0.00 0.00 37.20 3.24
3059 3378 2.175236 CGAAAGCTGGAAGAAGCCC 58.825 57.895 0.00 0.00 44.68 5.19
3090 3410 1.170290 GGTGGTTGTTCGTCAAGGGG 61.170 60.000 0.00 0.00 36.66 4.79
3117 3438 2.673523 CTGGGGAGTGGAAGGCTG 59.326 66.667 0.00 0.00 0.00 4.85
3274 3600 1.359459 GGGACTTCGTGCGTGGATTC 61.359 60.000 0.00 0.00 0.00 2.52
3301 3627 5.182570 CCACATGCACCATCTTATATTCAGG 59.817 44.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.