Multiple sequence alignment - TraesCS5B01G441900

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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 TraesCS5B01G441900 chr5B 100.000 5082 0 0 1 5082 615141994 615147075 0.000000e+00 9385.0
1 TraesCS5B01G441900 chr5B 92.209 860 52 7 4185 5043 615154111 615154956 0.000000e+00 1203.0
2 TraesCS5B01G441900 chr5B 98.246 57 1 0 5026 5082 615154966 615155022 3.240000e-17 100.0
3 TraesCS5B01G441900 chr5D 91.099 5213 233 81 1 5082 496572151 496567039 0.000000e+00 6842.0
4 TraesCS5B01G441900 chr5D 89.231 520 42 11 2332 2848 483325749 483326257 5.550000e-179 638.0
5 TraesCS5B01G441900 chr5D 92.308 143 11 0 143 285 456087788 456087930 2.400000e-48 204.0
6 TraesCS5B01G441900 chr5D 85.561 187 22 3 2664 2848 511743165 511742982 1.870000e-44 191.0
7 TraesCS5B01G441900 chr5A 89.791 4349 201 73 822 5081 620490526 620486332 0.000000e+00 5347.0
8 TraesCS5B01G441900 chr5A 88.608 474 46 6 1 468 620491527 620491056 2.050000e-158 569.0
9 TraesCS5B01G441900 chr5A 85.000 220 21 4 605 823 620491067 620490859 3.990000e-51 213.0
10 TraesCS5B01G441900 chr6B 85.868 559 49 19 2309 2848 42540107 42539560 7.380000e-158 568.0
11 TraesCS5B01G441900 chr6B 81.501 373 51 13 2069 2434 59501148 59500787 1.790000e-74 291.0
12 TraesCS5B01G441900 chr4A 83.784 296 36 7 2059 2347 193107221 193106931 2.330000e-68 270.0
13 TraesCS5B01G441900 chr7D 82.624 282 31 13 2157 2434 604109094 604108827 3.060000e-57 233.0
14 TraesCS5B01G441900 chr2D 82.879 257 28 11 2186 2434 50815572 50815324 3.080000e-52 217.0
15 TraesCS5B01G441900 chr7B 82.143 196 21 10 2246 2434 683870486 683870298 6.810000e-34 156.0
16 TraesCS5B01G441900 chr2B 81.726 197 21 10 2246 2434 127021160 127021349 3.170000e-32 150.0
17 TraesCS5B01G441900 chr3A 84.127 126 19 1 155 280 616472724 616472600 2.490000e-23 121.0
18 TraesCS5B01G441900 chr4B 100.000 30 0 0 2557 2586 593392448 593392477 7.110000e-04 56.5


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 TraesCS5B01G441900 chr5B 615141994 615147075 5081 False 9385.0 9385 100.000000 1 5082 1 chr5B.!!$F1 5081
1 TraesCS5B01G441900 chr5B 615154111 615155022 911 False 651.5 1203 95.227500 4185 5082 2 chr5B.!!$F2 897
2 TraesCS5B01G441900 chr5D 496567039 496572151 5112 True 6842.0 6842 91.099000 1 5082 1 chr5D.!!$R1 5081
3 TraesCS5B01G441900 chr5D 483325749 483326257 508 False 638.0 638 89.231000 2332 2848 1 chr5D.!!$F2 516
4 TraesCS5B01G441900 chr5A 620486332 620491527 5195 True 2043.0 5347 87.799667 1 5081 3 chr5A.!!$R1 5080
5 TraesCS5B01G441900 chr6B 42539560 42540107 547 True 568.0 568 85.868000 2309 2848 1 chr6B.!!$R1 539

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
167 170 0.101219 GGCTTGTTCGGCAATCATCC 59.899 55.0 0.00 0.0 36.36 3.51 F
1403 1801 0.036952 ATTCGCACTCACCTCACCAG 60.037 55.0 0.00 0.0 0.00 4.00 F
1994 2416 0.035739 TGTTCCTGGTTCTTACGCCC 59.964 55.0 0.00 0.0 0.00 6.13 F
3280 3762 0.518636 TGCGCATTGCTTCTCTGTTC 59.481 50.0 5.66 0.0 46.63 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 2117 0.318107 CACTTGCAGCCCGTGAAAAG 60.318 55.000 5.46 0.0 0.00 2.27 R
3187 3669 0.459237 CTCAGCCGTGCTAGTTCCAG 60.459 60.000 0.00 0.0 36.40 3.86 R
3378 3865 1.002576 TCAGTGTGTGCATTTGCTTCG 60.003 47.619 3.94 0.0 42.66 3.79 R
4358 4879 0.106519 ATGGCCCAATGCTACTGGAC 60.107 55.000 0.00 0.0 40.92 4.02 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
25 26 6.712095 ACCATGTGCTACCATGAATTATGTAG 59.288 38.462 11.54 0.00 43.99 2.74
28 29 7.368198 TGTGCTACCATGAATTATGTAGGTA 57.632 36.000 0.00 0.00 34.87 3.08
82 85 4.683334 GCGTTGCTTGACGGTGGC 62.683 66.667 9.25 0.00 42.98 5.01
134 137 0.389426 GGCACAATGTACTCCGTCGT 60.389 55.000 0.00 0.00 0.00 4.34
140 143 2.505557 GTACTCCGTCGTTGGCCG 60.506 66.667 0.00 0.00 38.13 6.13
167 170 0.101219 GGCTTGTTCGGCAATCATCC 59.899 55.000 0.00 0.00 36.36 3.51
193 196 3.007074 TCCGCAAAATACAGGAGTACACA 59.993 43.478 0.00 0.00 31.96 3.72
194 197 3.749088 CCGCAAAATACAGGAGTACACAA 59.251 43.478 0.00 0.00 31.96 3.33
198 201 5.278266 GCAAAATACAGGAGTACACAAAGCA 60.278 40.000 0.00 0.00 31.96 3.91
216 219 2.113139 CCACTTTGGCCACTCCGT 59.887 61.111 3.88 0.00 37.80 4.69
296 299 1.697982 AGGCCCTTAGACAACGTCTTT 59.302 47.619 0.00 0.00 40.28 2.52
303 306 4.814771 CCTTAGACAACGTCTTTCTTGGTT 59.185 41.667 1.36 0.00 40.28 3.67
306 309 2.940410 GACAACGTCTTTCTTGGTTGGA 59.060 45.455 7.55 0.00 42.96 3.53
409 415 1.614413 GGTCGTTCTCTCAAGGTGTCT 59.386 52.381 0.00 0.00 0.00 3.41
460 467 5.676584 GCTCTTCGAGTTTAGCTAGTTGCTA 60.677 44.000 1.90 1.90 41.33 3.49
569 578 4.404640 TCCTACGGAGTACCTATCAATGG 58.595 47.826 0.00 0.00 45.11 3.16
583 592 8.400184 ACCTATCAATGGAATGATACACAATG 57.600 34.615 0.00 0.00 40.44 2.82
631 660 5.696724 TCTTTAGGAGAAGCGAGACAAAAAG 59.303 40.000 0.00 0.00 0.00 2.27
636 665 5.180304 AGGAGAAGCGAGACAAAAAGATTTC 59.820 40.000 0.00 0.00 0.00 2.17
648 677 5.525012 ACAAAAAGATTTCAGCCTGCTTTTC 59.475 36.000 7.82 0.00 37.68 2.29
649 678 3.949842 AAGATTTCAGCCTGCTTTTCC 57.050 42.857 0.00 0.00 0.00 3.13
650 679 1.815003 AGATTTCAGCCTGCTTTTCCG 59.185 47.619 0.00 0.00 0.00 4.30
662 692 2.289565 GCTTTTCCGCATAACTAGGCT 58.710 47.619 0.00 0.00 0.00 4.58
671 701 9.781633 TTTCCGCATAACTAGGCTAATAAATTA 57.218 29.630 0.00 0.00 0.00 1.40
673 703 9.595823 TCCGCATAACTAGGCTAATAAATTATC 57.404 33.333 0.00 0.00 0.00 1.75
848 1216 1.466856 TCAATTGGCAGCTCACATCC 58.533 50.000 5.42 0.00 0.00 3.51
913 1281 4.957296 GGAGGCATAAAATACTCCGAAGA 58.043 43.478 0.00 0.00 40.01 2.87
914 1282 4.991687 GGAGGCATAAAATACTCCGAAGAG 59.008 45.833 0.00 0.00 46.36 2.85
915 1283 5.221461 GGAGGCATAAAATACTCCGAAGAGA 60.221 44.000 0.00 0.00 43.39 3.10
967 1335 2.423538 ACAAGAGCCAAGAACACAACAC 59.576 45.455 0.00 0.00 0.00 3.32
985 1353 2.242043 CACAAGGAAAGAACAGCCCAT 58.758 47.619 0.00 0.00 0.00 4.00
990 1358 0.899717 GAAAGAACAGCCCATGCCCA 60.900 55.000 0.00 0.00 38.69 5.36
1116 1506 5.725362 CGATTACTGATTAATCCTCCTCCC 58.275 45.833 12.90 0.00 42.28 4.30
1118 1508 3.734344 ACTGATTAATCCTCCTCCCCT 57.266 47.619 12.90 0.00 0.00 4.79
1179 1569 8.781951 TCTCTCCACTATTATTCCTTCCAAATT 58.218 33.333 0.00 0.00 0.00 1.82
1183 1574 9.768215 TCCACTATTATTCCTTCCAAATTTCTT 57.232 29.630 0.00 0.00 0.00 2.52
1246 1637 5.635280 GCAGCTCAGTTTTATTTCCCTTTTC 59.365 40.000 0.00 0.00 0.00 2.29
1292 1686 3.036959 TCCTCCCTCCCTCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1293 1687 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1294 1688 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1397 1795 0.616111 AGGAGGATTCGCACTCACCT 60.616 55.000 0.00 0.00 35.45 4.00
1398 1796 0.179097 GGAGGATTCGCACTCACCTC 60.179 60.000 0.00 0.00 44.21 3.85
1402 1800 0.037326 GATTCGCACTCACCTCACCA 60.037 55.000 0.00 0.00 0.00 4.17
1403 1801 0.036952 ATTCGCACTCACCTCACCAG 60.037 55.000 0.00 0.00 0.00 4.00
1404 1802 2.715532 TTCGCACTCACCTCACCAGC 62.716 60.000 0.00 0.00 0.00 4.85
1405 1803 2.359230 GCACTCACCTCACCAGCC 60.359 66.667 0.00 0.00 0.00 4.85
1408 1806 0.321122 CACTCACCTCACCAGCCTTC 60.321 60.000 0.00 0.00 0.00 3.46
1410 1808 0.689623 CTCACCTCACCAGCCTTCTT 59.310 55.000 0.00 0.00 0.00 2.52
1411 1809 0.397941 TCACCTCACCAGCCTTCTTG 59.602 55.000 0.00 0.00 0.00 3.02
1412 1810 1.073897 ACCTCACCAGCCTTCTTGC 59.926 57.895 0.00 0.00 0.00 4.01
1413 1811 1.377994 CCTCACCAGCCTTCTTGCT 59.622 57.895 0.00 0.00 44.00 3.91
1414 1812 0.251077 CCTCACCAGCCTTCTTGCTT 60.251 55.000 0.00 0.00 40.32 3.91
1415 1813 1.163554 CTCACCAGCCTTCTTGCTTC 58.836 55.000 0.00 0.00 40.32 3.86
1416 1814 0.603707 TCACCAGCCTTCTTGCTTCG 60.604 55.000 0.00 0.00 40.32 3.79
1492 1899 2.496470 GTGACGAGTGGATTACTTCCCT 59.504 50.000 0.00 0.00 44.77 4.20
1602 2009 3.517602 CCGTTTCCAGTTCGATGTATCA 58.482 45.455 0.00 0.00 0.00 2.15
1603 2010 4.119862 CCGTTTCCAGTTCGATGTATCAT 58.880 43.478 0.00 0.00 0.00 2.45
1604 2011 5.286438 CCGTTTCCAGTTCGATGTATCATA 58.714 41.667 0.00 0.00 0.00 2.15
1605 2012 5.926542 CCGTTTCCAGTTCGATGTATCATAT 59.073 40.000 0.00 0.00 0.00 1.78
1606 2013 6.089551 CCGTTTCCAGTTCGATGTATCATATC 59.910 42.308 0.00 0.00 0.00 1.63
1622 2029 8.370940 TGTATCATATCAATCTGTTTCTCTCCC 58.629 37.037 0.00 0.00 0.00 4.30
1656 2063 0.604578 TTTCTGCAGGCAGCCATTTC 59.395 50.000 15.80 0.00 44.83 2.17
1657 2064 0.540133 TTCTGCAGGCAGCCATTTCA 60.540 50.000 15.80 4.52 44.83 2.69
1658 2065 0.323999 TCTGCAGGCAGCCATTTCAT 60.324 50.000 15.80 0.00 44.83 2.57
1659 2066 0.535335 CTGCAGGCAGCCATTTCATT 59.465 50.000 15.80 0.00 44.83 2.57
1660 2067 0.978151 TGCAGGCAGCCATTTCATTT 59.022 45.000 15.80 0.00 44.83 2.32
1702 2109 1.173043 TCGTCAATGCCCAATGGTTC 58.827 50.000 0.00 0.00 0.00 3.62
1710 2117 3.467374 TGCCCAATGGTTCAGTTTTTC 57.533 42.857 0.00 0.00 0.00 2.29
1718 2125 6.237808 CCAATGGTTCAGTTTTTCTTTTCACG 60.238 38.462 0.00 0.00 0.00 4.35
1769 2191 3.243501 TGGATTGCTCTTGTTTTGTGCTC 60.244 43.478 0.00 0.00 0.00 4.26
1884 2306 5.418310 TGTTGACGAAAACTGATCCTTTC 57.582 39.130 0.00 0.00 0.00 2.62
1898 2320 4.161189 TGATCCTTTCTCTGTCCTGATGAC 59.839 45.833 0.00 0.00 44.72 3.06
1927 2349 2.123683 TTGGGTTTCCTTGCGCCA 60.124 55.556 4.18 0.00 0.00 5.69
1936 2358 0.521291 TCCTTGCGCCAGAATTTTCG 59.479 50.000 10.58 0.00 0.00 3.46
1942 2364 1.865725 CGCCAGAATTTTCGTTCGTC 58.134 50.000 0.00 0.00 33.36 4.20
1949 2371 2.681152 ATTTTCGTTCGTCCTTGTGC 57.319 45.000 0.00 0.00 0.00 4.57
1953 2375 1.947146 CGTTCGTCCTTGTGCGTGA 60.947 57.895 0.00 0.00 0.00 4.35
1955 2377 0.865769 GTTCGTCCTTGTGCGTGATT 59.134 50.000 0.00 0.00 0.00 2.57
1962 2384 3.496884 GTCCTTGTGCGTGATTTCTGTTA 59.503 43.478 0.00 0.00 0.00 2.41
1972 2394 5.332656 GCGTGATTTCTGTTAATCGATCTCC 60.333 44.000 0.00 0.00 37.34 3.71
1988 2410 2.408565 TCTCCTGTGTTCCTGGTTCTT 58.591 47.619 0.00 0.00 33.97 2.52
1990 2412 3.323979 TCTCCTGTGTTCCTGGTTCTTAC 59.676 47.826 0.00 0.00 33.97 2.34
1993 2415 1.154197 GTGTTCCTGGTTCTTACGCC 58.846 55.000 0.00 0.00 0.00 5.68
1994 2416 0.035739 TGTTCCTGGTTCTTACGCCC 59.964 55.000 0.00 0.00 0.00 6.13
1995 2417 1.017701 GTTCCTGGTTCTTACGCCCG 61.018 60.000 0.00 0.00 0.00 6.13
1996 2418 1.474332 TTCCTGGTTCTTACGCCCGT 61.474 55.000 0.00 0.00 0.00 5.28
2007 2442 1.259142 TACGCCCGTTGGATCTGGAA 61.259 55.000 0.00 0.00 0.00 3.53
2009 2444 0.748005 CGCCCGTTGGATCTGGAATT 60.748 55.000 0.00 0.00 0.00 2.17
2010 2445 1.474320 CGCCCGTTGGATCTGGAATTA 60.474 52.381 0.00 0.00 0.00 1.40
2028 2467 5.639931 GGAATTAGAGATCGGTTTATCCTGC 59.360 44.000 0.00 0.00 0.00 4.85
2030 2469 3.460857 AGAGATCGGTTTATCCTGCAC 57.539 47.619 0.00 0.00 0.00 4.57
2033 2472 1.859080 GATCGGTTTATCCTGCACGAC 59.141 52.381 0.00 0.00 32.90 4.34
2034 2473 0.604073 TCGGTTTATCCTGCACGACA 59.396 50.000 0.00 0.00 0.00 4.35
2052 2491 4.211374 ACGACATGTTTACTTCTGTTCTGC 59.789 41.667 0.00 0.00 0.00 4.26
2053 2492 4.211164 CGACATGTTTACTTCTGTTCTGCA 59.789 41.667 0.00 0.00 0.00 4.41
2055 2494 6.246420 ACATGTTTACTTCTGTTCTGCATC 57.754 37.500 0.00 0.00 0.00 3.91
2077 2523 6.385649 TCTGTGTTAAAGGTGTCCAATTTC 57.614 37.500 0.00 0.00 0.00 2.17
2078 2524 5.300792 TCTGTGTTAAAGGTGTCCAATTTCC 59.699 40.000 0.00 0.00 0.00 3.13
2081 2527 5.983118 GTGTTAAAGGTGTCCAATTTCCTTG 59.017 40.000 0.00 0.00 39.77 3.61
2083 2529 6.155393 TGTTAAAGGTGTCCAATTTCCTTGTT 59.845 34.615 0.00 0.00 39.77 2.83
2088 2534 4.141824 GGTGTCCAATTTCCTTGTTTTCCA 60.142 41.667 0.00 0.00 32.61 3.53
2131 2577 3.037431 TGAGCAGCTCTTCTTGTTCTC 57.963 47.619 23.15 0.00 0.00 2.87
2133 2579 3.181462 TGAGCAGCTCTTCTTGTTCTCAA 60.181 43.478 23.15 0.00 0.00 3.02
2143 2589 5.833667 TCTTCTTGTTCTCAACTCCTACAGA 59.166 40.000 0.00 0.00 0.00 3.41
2155 2601 6.101881 TCAACTCCTACAGAGAGATGGATCTA 59.898 42.308 0.00 0.00 46.50 1.98
2170 2616 7.861629 AGATGGATCTAAATTGGTGTTGACTA 58.138 34.615 0.00 0.00 34.85 2.59
2176 2622 9.559958 GATCTAAATTGGTGTTGACTATTTGTG 57.440 33.333 0.00 0.00 0.00 3.33
2177 2623 8.458573 TCTAAATTGGTGTTGACTATTTGTGT 57.541 30.769 0.00 0.00 0.00 3.72
2203 2649 5.956068 TTCAGTTTAACTGCATGCACATA 57.044 34.783 18.46 9.95 45.54 2.29
2205 2651 5.882553 TCAGTTTAACTGCATGCACATATG 58.117 37.500 18.46 9.49 45.54 1.78
2226 2675 9.961265 CATATGCACATACAATCAGAATTCTTT 57.039 29.630 4.86 0.00 0.00 2.52
2287 2739 4.857130 TGGCAGTAGACTAGTCCTCTTA 57.143 45.455 19.38 2.36 0.00 2.10
2293 2745 6.072893 GCAGTAGACTAGTCCTCTTATGCTAC 60.073 46.154 19.38 11.30 30.74 3.58
2294 2746 6.993308 CAGTAGACTAGTCCTCTTATGCTACA 59.007 42.308 19.38 0.00 0.00 2.74
2295 2747 7.172532 CAGTAGACTAGTCCTCTTATGCTACAG 59.827 44.444 19.38 5.41 0.00 2.74
2296 2748 4.825085 AGACTAGTCCTCTTATGCTACAGC 59.175 45.833 19.38 0.00 42.50 4.40
2318 2770 8.900781 ACAGCCATATTCAGATATTTGCATATC 58.099 33.333 0.00 0.00 41.25 1.63
2377 2830 8.432805 TCCAATAAGGGAGAACAAGATTAGATC 58.567 37.037 0.00 0.00 38.24 2.75
2409 2863 4.024809 GTCTTTTCGTTCTAACTGCTGCTT 60.025 41.667 0.00 0.00 0.00 3.91
2435 2889 3.758023 TGGTGCATATCTTGACCTTGTTG 59.242 43.478 0.00 0.00 0.00 3.33
2436 2890 3.758554 GGTGCATATCTTGACCTTGTTGT 59.241 43.478 0.00 0.00 0.00 3.32
2439 2893 6.314784 GTGCATATCTTGACCTTGTTGTTAC 58.685 40.000 0.00 0.00 0.00 2.50
2440 2894 6.149474 GTGCATATCTTGACCTTGTTGTTACT 59.851 38.462 0.00 0.00 0.00 2.24
2441 2895 6.714810 TGCATATCTTGACCTTGTTGTTACTT 59.285 34.615 0.00 0.00 0.00 2.24
2519 2974 2.710902 CGATCACGGTGCAGAGGGA 61.711 63.158 2.51 0.00 35.72 4.20
2894 3366 9.071276 AGTTCATACTCTTTCATGATGTTTGTT 57.929 29.630 0.00 0.00 31.50 2.83
2895 3367 9.683069 GTTCATACTCTTTCATGATGTTTGTTT 57.317 29.630 0.00 0.00 31.50 2.83
2896 3368 9.897744 TTCATACTCTTTCATGATGTTTGTTTC 57.102 29.630 0.00 0.00 31.50 2.78
2897 3369 9.288576 TCATACTCTTTCATGATGTTTGTTTCT 57.711 29.630 0.00 0.00 0.00 2.52
2898 3370 9.338291 CATACTCTTTCATGATGTTTGTTTCTG 57.662 33.333 0.00 0.00 0.00 3.02
2899 3371 6.742109 ACTCTTTCATGATGTTTGTTTCTGG 58.258 36.000 0.00 0.00 0.00 3.86
2900 3372 6.322201 ACTCTTTCATGATGTTTGTTTCTGGT 59.678 34.615 0.00 0.00 0.00 4.00
2901 3373 6.738114 TCTTTCATGATGTTTGTTTCTGGTC 58.262 36.000 0.00 0.00 0.00 4.02
2902 3374 6.320926 TCTTTCATGATGTTTGTTTCTGGTCA 59.679 34.615 0.00 0.00 0.00 4.02
2903 3375 5.437289 TCATGATGTTTGTTTCTGGTCAC 57.563 39.130 0.00 0.00 0.00 3.67
2904 3376 4.886489 TCATGATGTTTGTTTCTGGTCACA 59.114 37.500 0.00 0.00 0.00 3.58
2905 3377 5.535783 TCATGATGTTTGTTTCTGGTCACAT 59.464 36.000 0.00 0.00 0.00 3.21
2906 3378 5.850557 TGATGTTTGTTTCTGGTCACATT 57.149 34.783 0.00 0.00 0.00 2.71
2907 3379 6.951062 TGATGTTTGTTTCTGGTCACATTA 57.049 33.333 0.00 0.00 0.00 1.90
2908 3380 7.523293 TGATGTTTGTTTCTGGTCACATTAT 57.477 32.000 0.00 0.00 0.00 1.28
2909 3381 7.950512 TGATGTTTGTTTCTGGTCACATTATT 58.049 30.769 0.00 0.00 0.00 1.40
3021 3499 5.874093 AGGAATATGGTCTAGGCATCTTTG 58.126 41.667 0.00 0.00 0.00 2.77
3148 3630 5.659079 AGAGTTCAGTAGATAGTTTCCTGGG 59.341 44.000 0.00 0.00 0.00 4.45
3187 3669 2.546778 CACATGCTTGATGGGCAATTC 58.453 47.619 6.60 0.00 43.14 2.17
3221 3703 2.559440 GCTGAGATGGGATCAACTCAC 58.441 52.381 0.00 0.00 44.37 3.51
3231 3713 3.375299 GGGATCAACTCACCTTGATTTCG 59.625 47.826 0.00 0.00 40.33 3.46
3280 3762 0.518636 TGCGCATTGCTTCTCTGTTC 59.481 50.000 5.66 0.00 46.63 3.18
3282 3764 1.202009 GCGCATTGCTTCTCTGTTCTC 60.202 52.381 0.30 0.00 41.73 2.87
3288 3770 2.603021 TGCTTCTCTGTTCTCCTCTGT 58.397 47.619 0.00 0.00 0.00 3.41
3378 3865 2.433868 TCAACCTGTACGCTCTGAAC 57.566 50.000 0.00 0.00 0.00 3.18
3404 3891 3.364864 GCAAATGCACACACTGACGATAA 60.365 43.478 0.00 0.00 41.59 1.75
3415 3902 5.959527 CACACTGACGATAAATACAACATGC 59.040 40.000 0.00 0.00 0.00 4.06
3455 3942 6.519382 TGAATGAATTGTACAAATTGCCACA 58.481 32.000 13.23 5.61 0.00 4.17
3482 3974 5.674525 TCTCATAATTTGTCCACTGCTAGG 58.325 41.667 0.00 0.00 0.00 3.02
3616 4108 2.762234 GCTGCCTGCTGATGTGCTC 61.762 63.158 0.00 0.00 38.95 4.26
3661 4153 5.941948 AATCGTCCGAAGTTCTTGATTTT 57.058 34.783 0.56 0.00 0.00 1.82
3667 4159 4.451096 TCCGAAGTTCTTGATTTTTCTCCG 59.549 41.667 0.56 0.00 0.00 4.63
4230 4738 2.155279 GTGGAGCTCTCTGTTTTTCCC 58.845 52.381 14.64 0.00 0.00 3.97
4233 4741 3.078097 GGAGCTCTCTGTTTTTCCCTTC 58.922 50.000 14.64 0.00 0.00 3.46
4355 4876 1.599576 GCCTTCCTCCAGTCCAGTC 59.400 63.158 0.00 0.00 0.00 3.51
4356 4877 1.904990 GCCTTCCTCCAGTCCAGTCC 61.905 65.000 0.00 0.00 0.00 3.85
4357 4878 0.545309 CCTTCCTCCAGTCCAGTCCA 60.545 60.000 0.00 0.00 0.00 4.02
4358 4879 0.901124 CTTCCTCCAGTCCAGTCCAG 59.099 60.000 0.00 0.00 0.00 3.86
4359 4880 0.191064 TTCCTCCAGTCCAGTCCAGT 59.809 55.000 0.00 0.00 0.00 4.00
4360 4881 0.251832 TCCTCCAGTCCAGTCCAGTC 60.252 60.000 0.00 0.00 0.00 3.51
4361 4882 1.261238 CCTCCAGTCCAGTCCAGTCC 61.261 65.000 0.00 0.00 0.00 3.85
4362 4883 0.542938 CTCCAGTCCAGTCCAGTCCA 60.543 60.000 0.00 0.00 0.00 4.02
4363 4884 0.542938 TCCAGTCCAGTCCAGTCCAG 60.543 60.000 0.00 0.00 0.00 3.86
4364 4885 0.833834 CCAGTCCAGTCCAGTCCAGT 60.834 60.000 0.00 0.00 0.00 4.00
4435 4959 7.229506 GCCTTGCCTTTCTATCTATGTAAATGT 59.770 37.037 0.00 0.00 0.00 2.71
4436 4960 9.778741 CCTTGCCTTTCTATCTATGTAAATGTA 57.221 33.333 0.00 0.00 0.00 2.29
4479 5006 8.504815 CACTGATCTGCTCCAAGATTATTATTG 58.495 37.037 0.00 0.00 37.03 1.90
4518 5045 4.766375 TCATGTCTCGGTAAAATTCTCCC 58.234 43.478 0.00 0.00 0.00 4.30
4634 5165 1.518572 GGGCACGTGTATGTCTCGG 60.519 63.158 18.38 0.00 37.36 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.785321 CGCACACACACCGAATACC 59.215 57.895 0.00 0.00 0.00 2.73
28 29 3.711842 CGCGCACACACACCGAAT 61.712 61.111 8.75 0.00 0.00 3.34
82 85 3.046087 CACGCCTCACAGCAGTGG 61.046 66.667 9.58 0.34 45.91 4.00
140 143 1.369839 GCCGAACAAGCCCTAAGAGC 61.370 60.000 0.00 0.00 0.00 4.09
151 154 0.810648 GCTGGATGATTGCCGAACAA 59.189 50.000 0.00 0.00 44.01 2.83
194 197 1.076044 AGTGGCCAAAGTGGTGCTT 60.076 52.632 7.24 0.00 40.46 3.91
198 201 2.113139 CGGAGTGGCCAAAGTGGT 59.887 61.111 7.24 0.00 40.46 4.16
216 219 3.918544 GCCCGCAGCCTATTTTCA 58.081 55.556 0.00 0.00 34.35 2.69
296 299 3.931907 ATCATTCGGATCCAACCAAGA 57.068 42.857 13.41 1.83 0.00 3.02
303 306 0.250295 GCGGGAATCATTCGGATCCA 60.250 55.000 13.41 0.00 34.28 3.41
306 309 0.474184 AAGGCGGGAATCATTCGGAT 59.526 50.000 0.00 0.00 38.05 4.18
419 425 1.443194 GCACAAAGGCTGCATCACG 60.443 57.895 0.50 0.00 34.56 4.35
460 467 2.659610 GTGCTCAGCCCTCGAACT 59.340 61.111 0.00 0.00 0.00 3.01
524 531 6.347079 GGAGATAACGTTGACGAGATAGAGAG 60.347 46.154 11.99 0.00 43.02 3.20
525 532 5.466058 GGAGATAACGTTGACGAGATAGAGA 59.534 44.000 11.99 0.00 43.02 3.10
526 533 5.467399 AGGAGATAACGTTGACGAGATAGAG 59.533 44.000 11.99 0.00 43.02 2.43
527 534 5.366460 AGGAGATAACGTTGACGAGATAGA 58.634 41.667 11.99 0.00 43.02 1.98
530 537 4.025061 CGTAGGAGATAACGTTGACGAGAT 60.025 45.833 11.99 2.84 43.02 2.75
598 624 2.751166 TCTCCTAAAGAGCAGTGTGC 57.249 50.000 0.00 0.00 45.46 4.57
602 628 2.165437 CTCGCTTCTCCTAAAGAGCAGT 59.835 50.000 0.00 0.00 42.90 4.40
631 660 1.733718 GCGGAAAAGCAGGCTGAAATC 60.734 52.381 20.86 9.87 37.05 2.17
648 677 8.540492 CGATAATTTATTAGCCTAGTTATGCGG 58.460 37.037 0.00 0.00 0.00 5.69
649 678 9.084164 ACGATAATTTATTAGCCTAGTTATGCG 57.916 33.333 0.00 0.00 0.00 4.73
671 701 5.618640 GCTCTTTGCAATTCAGAAAGACGAT 60.619 40.000 0.00 0.00 42.31 3.73
673 703 3.910767 GCTCTTTGCAATTCAGAAAGACG 59.089 43.478 0.00 0.00 42.31 4.18
848 1216 3.973657 GCATTGGCTAATGGAGATGTTG 58.026 45.455 22.46 0.00 43.12 3.33
876 1244 8.756486 TTTATGCCTCCTTAAAATAGGTTACC 57.244 34.615 0.00 0.00 36.63 2.85
967 1335 1.067354 GCATGGGCTGTTCTTTCCTTG 60.067 52.381 0.00 0.00 36.96 3.61
996 1364 2.036098 TGCTTGCTGATGGGTGGG 59.964 61.111 0.00 0.00 0.00 4.61
997 1365 2.707849 GCTGCTTGCTGATGGGTGG 61.708 63.158 3.71 0.00 38.95 4.61
1116 1506 2.660064 CGACCAACCTGGGAGGAGG 61.660 68.421 12.86 0.83 43.37 4.30
1118 1508 3.319198 GCGACCAACCTGGGAGGA 61.319 66.667 12.86 0.00 43.37 3.71
1179 1569 4.998051 ACCCCAAGAATAGAAAGCAAGAA 58.002 39.130 0.00 0.00 0.00 2.52
1183 1574 3.343617 CGAACCCCAAGAATAGAAAGCA 58.656 45.455 0.00 0.00 0.00 3.91
1246 1637 4.504097 GCAGCACTTGTTTCTGGTAAAAAG 59.496 41.667 0.00 0.00 0.00 2.27
1397 1795 0.603707 CGAAGCAAGAAGGCTGGTGA 60.604 55.000 0.00 0.00 45.07 4.02
1398 1796 0.886490 ACGAAGCAAGAAGGCTGGTG 60.886 55.000 0.00 0.00 45.07 4.17
1416 1814 1.313091 GCCAATCCCAGGAACGGAAC 61.313 60.000 8.56 0.00 31.75 3.62
1492 1899 8.339344 TCTCATCAAGATGCAGAAATTAAACA 57.661 30.769 5.19 0.00 38.65 2.83
1602 2009 5.600484 AGTCGGGAGAGAAACAGATTGATAT 59.400 40.000 0.00 0.00 41.26 1.63
1603 2010 4.956700 AGTCGGGAGAGAAACAGATTGATA 59.043 41.667 0.00 0.00 41.26 2.15
1604 2011 3.772025 AGTCGGGAGAGAAACAGATTGAT 59.228 43.478 0.00 0.00 41.26 2.57
1605 2012 3.056536 CAGTCGGGAGAGAAACAGATTGA 60.057 47.826 0.00 0.00 41.26 2.57
1606 2013 3.257393 CAGTCGGGAGAGAAACAGATTG 58.743 50.000 0.00 0.00 41.26 2.67
1622 2029 2.600792 GCAGAAACAACAAGAGCAGTCG 60.601 50.000 0.00 0.00 0.00 4.18
1656 2063 0.461135 CCATCAAAGGCCGGGAAATG 59.539 55.000 2.18 0.00 0.00 2.32
1657 2064 2.900547 CCATCAAAGGCCGGGAAAT 58.099 52.632 2.18 0.00 0.00 2.17
1658 2065 4.432601 CCATCAAAGGCCGGGAAA 57.567 55.556 2.18 0.00 0.00 3.13
1702 2109 3.115554 CAGCCCGTGAAAAGAAAAACTG 58.884 45.455 0.00 0.00 0.00 3.16
1710 2117 0.318107 CACTTGCAGCCCGTGAAAAG 60.318 55.000 5.46 0.00 0.00 2.27
1718 2125 2.991540 GGGGAACACTTGCAGCCC 60.992 66.667 0.00 0.00 38.08 5.19
1898 2320 2.480587 GGAAACCCAACAAACCAAGTCG 60.481 50.000 0.00 0.00 0.00 4.18
1927 2349 3.303791 GCACAAGGACGAACGAAAATTCT 60.304 43.478 0.14 0.00 0.00 2.40
1936 2358 0.865769 AATCACGCACAAGGACGAAC 59.134 50.000 0.00 0.00 0.00 3.95
1942 2364 4.481930 TTAACAGAAATCACGCACAAGG 57.518 40.909 0.00 0.00 0.00 3.61
1949 2371 5.980116 AGGAGATCGATTAACAGAAATCACG 59.020 40.000 0.00 0.00 35.93 4.35
1953 2375 6.644347 ACACAGGAGATCGATTAACAGAAAT 58.356 36.000 0.00 0.00 0.00 2.17
1955 2377 5.661056 ACACAGGAGATCGATTAACAGAA 57.339 39.130 0.00 0.00 0.00 3.02
1962 2384 2.169352 CCAGGAACACAGGAGATCGATT 59.831 50.000 0.00 0.00 0.00 3.34
1972 2394 1.798813 GCGTAAGAACCAGGAACACAG 59.201 52.381 0.00 0.00 43.02 3.66
1988 2410 1.259142 TTCCAGATCCAACGGGCGTA 61.259 55.000 0.00 0.00 0.00 4.42
1990 2412 0.748005 AATTCCAGATCCAACGGGCG 60.748 55.000 0.00 0.00 0.00 6.13
1993 2415 4.672587 TCTCTAATTCCAGATCCAACGG 57.327 45.455 0.00 0.00 0.00 4.44
1994 2416 4.920340 CGATCTCTAATTCCAGATCCAACG 59.080 45.833 15.93 6.19 41.41 4.10
1995 2417 5.221541 ACCGATCTCTAATTCCAGATCCAAC 60.222 44.000 15.93 0.00 41.41 3.77
1996 2418 4.901849 ACCGATCTCTAATTCCAGATCCAA 59.098 41.667 15.93 0.00 41.41 3.53
2007 2442 5.542779 GTGCAGGATAAACCGATCTCTAAT 58.457 41.667 0.00 0.00 44.74 1.73
2009 2444 3.004419 CGTGCAGGATAAACCGATCTCTA 59.996 47.826 0.00 0.00 44.74 2.43
2010 2445 2.223829 CGTGCAGGATAAACCGATCTCT 60.224 50.000 0.00 0.00 44.74 3.10
2028 2467 5.670097 CAGAACAGAAGTAAACATGTCGTG 58.330 41.667 0.00 0.00 0.00 4.35
2030 2469 4.211164 TGCAGAACAGAAGTAAACATGTCG 59.789 41.667 0.00 0.00 0.00 4.35
2033 2472 6.072838 ACAGATGCAGAACAGAAGTAAACATG 60.073 38.462 0.00 0.00 0.00 3.21
2034 2473 6.000219 ACAGATGCAGAACAGAAGTAAACAT 59.000 36.000 0.00 0.00 0.00 2.71
2052 2491 5.964958 ATTGGACACCTTTAACACAGATG 57.035 39.130 0.00 0.00 0.00 2.90
2053 2492 6.015434 GGAAATTGGACACCTTTAACACAGAT 60.015 38.462 0.00 0.00 0.00 2.90
2055 2494 5.301805 AGGAAATTGGACACCTTTAACACAG 59.698 40.000 0.00 0.00 0.00 3.66
2078 2524 5.804979 AGTTTCATCAACGTTGGAAAACAAG 59.195 36.000 31.64 14.78 40.75 3.16
2081 2527 6.020678 CAGAAGTTTCATCAACGTTGGAAAAC 60.021 38.462 27.69 27.69 40.75 2.43
2083 2529 5.355630 TCAGAAGTTTCATCAACGTTGGAAA 59.644 36.000 27.02 23.74 40.75 3.13
2088 2534 7.479980 TCAAATTCAGAAGTTTCATCAACGTT 58.520 30.769 0.00 0.00 40.75 3.99
2131 2577 5.139727 AGATCCATCTCTCTGTAGGAGTTG 58.860 45.833 0.00 0.00 42.40 3.16
2133 2579 6.523035 TTAGATCCATCTCTCTGTAGGAGT 57.477 41.667 0.00 0.00 42.40 3.85
2143 2589 6.825721 GTCAACACCAATTTAGATCCATCTCT 59.174 38.462 0.00 0.00 38.32 3.10
2155 2601 7.106439 TGACACAAATAGTCAACACCAATTT 57.894 32.000 0.00 0.00 42.57 1.82
2203 2649 8.308931 ACAAAAGAATTCTGATTGTATGTGCAT 58.691 29.630 26.42 9.51 36.03 3.96
2205 2651 9.282247 CTACAAAAGAATTCTGATTGTATGTGC 57.718 33.333 29.08 0.00 37.89 4.57
2273 2722 4.825085 GCTGTAGCATAAGAGGACTAGTCT 59.175 45.833 21.88 8.54 41.59 3.24
2287 2739 7.148120 GCAAATATCTGAATATGGCTGTAGCAT 60.148 37.037 6.18 0.86 44.36 3.79
2293 2745 8.899771 TGATATGCAAATATCTGAATATGGCTG 58.100 33.333 8.42 0.00 35.21 4.85
2294 2746 9.642343 ATGATATGCAAATATCTGAATATGGCT 57.358 29.630 8.42 0.00 35.21 4.75
2295 2747 9.894783 GATGATATGCAAATATCTGAATATGGC 57.105 33.333 8.42 0.00 35.21 4.40
2389 2843 4.597079 CAAAGCAGCAGTTAGAACGAAAA 58.403 39.130 0.00 0.00 0.00 2.29
2394 2848 2.351157 CCAGCAAAGCAGCAGTTAGAAC 60.351 50.000 0.00 0.00 36.85 3.01
2397 2851 1.068748 CACCAGCAAAGCAGCAGTTAG 60.069 52.381 0.00 0.00 36.85 2.34
2401 2855 2.049433 GCACCAGCAAAGCAGCAG 60.049 61.111 0.00 0.00 41.58 4.24
2435 2889 2.749621 CTGCACAATGGGAGGAAGTAAC 59.250 50.000 0.00 0.00 0.00 2.50
2436 2890 3.071874 CTGCACAATGGGAGGAAGTAA 57.928 47.619 0.00 0.00 0.00 2.24
3021 3499 2.553911 AGTCCTCCCCTTCTACTTCC 57.446 55.000 0.00 0.00 0.00 3.46
3148 3630 6.860023 GCATGTGGACTTGATATAAGCATTTC 59.140 38.462 0.00 0.00 0.00 2.17
3187 3669 0.459237 CTCAGCCGTGCTAGTTCCAG 60.459 60.000 0.00 0.00 36.40 3.86
3221 3703 6.128172 ACTCATCAAAAGTAGCGAAATCAAGG 60.128 38.462 0.00 0.00 0.00 3.61
3231 3713 5.112686 CCTCCACTACTCATCAAAAGTAGC 58.887 45.833 9.59 0.00 46.67 3.58
3280 3762 5.854010 TGGTAGCTACATTTACAGAGGAG 57.146 43.478 24.75 0.00 0.00 3.69
3282 3764 4.811557 GCTTGGTAGCTACATTTACAGAGG 59.188 45.833 24.75 8.62 44.27 3.69
3378 3865 1.002576 TCAGTGTGTGCATTTGCTTCG 60.003 47.619 3.94 0.00 42.66 3.79
3404 3891 2.029110 GTGCCAACCAGCATGTTGTATT 60.029 45.455 8.84 0.00 46.24 1.89
3455 3942 7.472334 AGCAGTGGACAAATTATGAGATTTT 57.528 32.000 0.00 0.00 0.00 1.82
3505 3997 4.659111 TGAACAGTCGGAAGAAAGTGTA 57.341 40.909 0.00 0.00 45.01 2.90
3616 4108 3.197333 TCCTCTTCTTGCCTGATCTTCTG 59.803 47.826 0.00 0.00 0.00 3.02
3661 4153 3.907260 CTGGCTTGGCTGCGGAGAA 62.907 63.158 8.65 0.00 0.00 2.87
3667 4159 1.002868 TCTTCTCTGGCTTGGCTGC 60.003 57.895 0.00 0.00 0.00 5.25
3911 4412 2.594962 CCAGTTCGTGCACGTCCAC 61.595 63.158 35.74 28.29 40.80 4.02
3912 4413 2.279851 CCAGTTCGTGCACGTCCA 60.280 61.111 35.74 19.92 40.80 4.02
3913 4414 2.022129 CTCCAGTTCGTGCACGTCC 61.022 63.158 35.74 26.38 40.80 4.79
3914 4415 2.658707 GCTCCAGTTCGTGCACGTC 61.659 63.158 35.74 27.97 40.80 4.34
3925 4426 2.037367 TACGCCTCCAGCTCCAGT 59.963 61.111 0.00 0.00 40.39 4.00
4230 4738 4.022849 ACAAAATTCTTCTCTTGCCGGAAG 60.023 41.667 5.05 6.46 39.94 3.46
4233 4741 3.923017 ACAAAATTCTTCTCTTGCCGG 57.077 42.857 0.00 0.00 0.00 6.13
4355 4876 0.749454 GCCCAATGCTACTGGACTGG 60.749 60.000 1.37 0.00 35.85 4.00
4356 4877 0.749454 GGCCCAATGCTACTGGACTG 60.749 60.000 0.00 0.00 40.92 3.51
4357 4878 1.207488 TGGCCCAATGCTACTGGACT 61.207 55.000 0.00 0.00 40.92 3.85
4358 4879 0.106519 ATGGCCCAATGCTACTGGAC 60.107 55.000 0.00 0.00 40.92 4.02
4359 4880 0.630673 AATGGCCCAATGCTACTGGA 59.369 50.000 0.00 0.00 40.92 3.86
4360 4881 0.748450 CAATGGCCCAATGCTACTGG 59.252 55.000 0.00 0.00 40.92 4.00
4361 4882 1.406539 GTCAATGGCCCAATGCTACTG 59.593 52.381 0.00 0.00 40.92 2.74
4362 4883 1.285962 AGTCAATGGCCCAATGCTACT 59.714 47.619 0.00 0.00 40.92 2.57
4363 4884 1.678101 GAGTCAATGGCCCAATGCTAC 59.322 52.381 0.00 0.00 40.92 3.58
4364 4885 1.565759 AGAGTCAATGGCCCAATGCTA 59.434 47.619 0.00 0.00 40.92 3.49
4435 4959 9.647918 AGATCAGTGAGTAGATGGATTTAGTTA 57.352 33.333 0.00 0.00 0.00 2.24
4436 4960 8.420222 CAGATCAGTGAGTAGATGGATTTAGTT 58.580 37.037 0.00 0.00 0.00 2.24
4437 4961 7.471260 GCAGATCAGTGAGTAGATGGATTTAGT 60.471 40.741 0.00 0.00 0.00 2.24
4438 4962 6.867816 GCAGATCAGTGAGTAGATGGATTTAG 59.132 42.308 0.00 0.00 0.00 1.85
4492 5019 8.311836 GGGAGAATTTTACCGAGACATGATATA 58.688 37.037 0.00 0.00 0.00 0.86
4518 5045 5.120830 CAGAGAGTAACAAAAGTTGATCCCG 59.879 44.000 0.00 0.00 0.00 5.14
4593 5124 2.165301 GGCCGGACGATCGAGTTTG 61.165 63.158 24.34 7.06 0.00 2.93
4749 5280 2.125753 CACGGGAGCAGAGCAGAC 60.126 66.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.