Multiple sequence alignment - TraesCS1B01G318300

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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 TraesCS1B01G318300 chr1B 100.000 2525 0 0 1 2525 542956876 542959400 0.000000e+00 4663.0
1 TraesCS1B01G318300 chr1B 96.614 502 17 0 2024 2525 178183085 178183586 0.000000e+00 833.0
2 TraesCS1B01G318300 chr1D 91.327 1545 80 18 2 1538 403662920 403664418 0.000000e+00 2061.0
3 TraesCS1B01G318300 chr1D 97.778 495 11 0 2031 2525 209337612 209337118 0.000000e+00 854.0
4 TraesCS1B01G318300 chr1D 100.000 30 0 0 857 886 403663680 403663709 3.510000e-04 56.5
5 TraesCS1B01G318300 chr1A 90.380 842 57 10 2 835 499174680 499175505 0.000000e+00 1085.0
6 TraesCS1B01G318300 chr1A 94.072 388 20 3 1151 1538 499176082 499176466 1.010000e-163 586.0
7 TraesCS1B01G318300 chr1A 92.138 318 20 3 810 1124 499175447 499175762 6.410000e-121 444.0
8 TraesCS1B01G318300 chr1A 79.455 477 66 19 1524 1972 499176479 499176951 2.440000e-80 309.0
9 TraesCS1B01G318300 chr1A 78.588 425 78 6 1611 2027 554783403 554782984 4.140000e-68 268.0
10 TraesCS1B01G318300 chr4B 97.760 491 11 0 2035 2525 128330483 128329993 0.000000e+00 846.0
11 TraesCS1B01G318300 chr6B 97.172 495 14 0 2031 2525 171914056 171913562 0.000000e+00 837.0
12 TraesCS1B01G318300 chr4D 97.172 495 14 0 2031 2525 329921054 329921548 0.000000e+00 837.0
13 TraesCS1B01G318300 chr4D 85.890 163 18 3 229 390 439869666 439869508 4.320000e-38 169.0
14 TraesCS1B01G318300 chrUn 96.970 495 15 0 2031 2525 65705374 65705868 0.000000e+00 832.0
15 TraesCS1B01G318300 chr5B 96.976 496 14 1 2030 2525 85557324 85556830 0.000000e+00 832.0
16 TraesCS1B01G318300 chr5B 96.970 495 15 0 2031 2525 302252508 302253002 0.000000e+00 832.0
17 TraesCS1B01G318300 chr5B 76.310 439 61 27 150 572 700337707 700337296 7.130000e-46 195.0
18 TraesCS1B01G318300 chr3B 96.774 496 16 0 2030 2525 250093190 250092695 0.000000e+00 828.0
19 TraesCS1B01G318300 chr3B 79.475 419 71 7 1607 2017 733082093 733081682 1.480000e-72 283.0
20 TraesCS1B01G318300 chr6D 83.245 567 70 12 1 547 105815327 105815888 4.850000e-137 497.0
21 TraesCS1B01G318300 chr6D 81.395 129 21 1 1 129 421548457 421548582 4.440000e-18 102.0
22 TraesCS1B01G318300 chr7D 79.730 592 87 23 1 570 63638915 63639495 5.060000e-107 398.0
23 TraesCS1B01G318300 chr7D 85.075 134 13 3 1 130 602267789 602267659 2.040000e-26 130.0
24 TraesCS1B01G318300 chr7D 84.615 130 16 3 1 130 180258585 180258460 2.640000e-25 126.0
25 TraesCS1B01G318300 chr7D 84.259 108 14 3 585 691 180258029 180257924 4.440000e-18 102.0
26 TraesCS1B01G318300 chr2A 79.884 517 86 13 70 573 90047574 90047063 1.850000e-96 363.0
27 TraesCS1B01G318300 chr7A 77.705 610 84 27 8 573 66605329 66605930 2.420000e-85 326.0
28 TraesCS1B01G318300 chr2B 79.048 420 71 9 1607 2016 758877040 758876628 3.200000e-69 272.0
29 TraesCS1B01G318300 chr2B 80.347 346 56 10 1607 1943 763375780 763375438 4.170000e-63 252.0
30 TraesCS1B01G318300 chr3A 80.055 366 66 6 1641 2003 725107783 725108144 5.360000e-67 265.0
31 TraesCS1B01G318300 chr3A 78.109 402 74 8 1620 2013 560113862 560114257 2.510000e-60 243.0
32 TraesCS1B01G318300 chr5D 79.265 381 71 5 1639 2016 556094131 556093756 2.490000e-65 259.0
33 TraesCS1B01G318300 chr7B 79.058 382 71 7 1639 2016 418045351 418045727 1.160000e-63 254.0
34 TraesCS1B01G318300 chr7B 79.474 380 50 14 210 573 4144926 4145293 6.980000e-61 244.0
35 TraesCS1B01G318300 chr5A 77.698 417 77 13 1611 2016 502215676 502216087 9.030000e-60 241.0
36 TraesCS1B01G318300 chr5A 95.000 40 1 1 640 678 13323022 13322983 7.540000e-06 62.1
37 TraesCS1B01G318300 chr4A 80.899 267 36 9 136 397 620195882 620195626 1.980000e-46 196.0


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 TraesCS1B01G318300 chr1B 542956876 542959400 2524 False 4663.00 4663 100.00000 1 2525 1 chr1B.!!$F2 2524
1 TraesCS1B01G318300 chr1B 178183085 178183586 501 False 833.00 833 96.61400 2024 2525 1 chr1B.!!$F1 501
2 TraesCS1B01G318300 chr1D 403662920 403664418 1498 False 1058.75 2061 95.66350 2 1538 2 chr1D.!!$F1 1536
3 TraesCS1B01G318300 chr1A 499174680 499176951 2271 False 606.00 1085 89.01125 2 1972 4 chr1A.!!$F1 1970
4 TraesCS1B01G318300 chr6D 105815327 105815888 561 False 497.00 497 83.24500 1 547 1 chr6D.!!$F1 546
5 TraesCS1B01G318300 chr7D 63638915 63639495 580 False 398.00 398 79.73000 1 570 1 chr7D.!!$F1 569
6 TraesCS1B01G318300 chr2A 90047063 90047574 511 True 363.00 363 79.88400 70 573 1 chr2A.!!$R1 503
7 TraesCS1B01G318300 chr7A 66605329 66605930 601 False 326.00 326 77.70500 8 573 1 chr7A.!!$F1 565

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
987 1049 0.037697 AGAGAAACCGTGCGCACATA 60.038 50.0 37.03 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2435 0.172352 CAGGACTCTCTCGCTTGTCC 59.828 60.0 0.0 0.0 46.67 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
68 69 4.357142 TCGCTATATGACCGACAAGAAAC 58.643 43.478 0.00 0.00 0.00 2.78
199 207 5.414765 GTGGGAGGTGAAGACGAAAATAAAT 59.585 40.000 0.00 0.00 0.00 1.40
354 392 8.132362 TGTTGTATTAGAAAAGTTGCGATTGTT 58.868 29.630 0.00 0.00 0.00 2.83
522 583 8.471609 ACATGATTGAATTTAATCAGCACATGA 58.528 29.630 24.52 5.19 46.70 3.07
661 722 5.365314 AGAAGCTATCAACTCCCTCTTTAGG 59.635 44.000 0.00 0.00 43.25 2.69
745 806 4.508861 CACAATCTTGCAAAAGAAGGTTGG 59.491 41.667 11.90 0.00 43.18 3.77
775 836 4.096682 GCGAGGAGAGTTAGTACATCACTT 59.903 45.833 0.00 0.00 38.80 3.16
776 837 5.574082 CGAGGAGAGTTAGTACATCACTTG 58.426 45.833 0.00 0.00 38.80 3.16
802 863 9.066892 GTCCTAAATTAATGCATCACTTATCCA 57.933 33.333 0.00 0.00 0.00 3.41
803 864 9.812347 TCCTAAATTAATGCATCACTTATCCAT 57.188 29.630 0.00 0.00 0.00 3.41
804 865 9.850628 CCTAAATTAATGCATCACTTATCCATG 57.149 33.333 0.00 0.00 0.00 3.66
807 868 7.828508 ATTAATGCATCACTTATCCATGTGT 57.171 32.000 0.00 0.00 35.82 3.72
808 869 8.922931 ATTAATGCATCACTTATCCATGTGTA 57.077 30.769 0.00 0.00 35.82 2.90
809 870 8.744568 TTAATGCATCACTTATCCATGTGTAA 57.255 30.769 0.00 0.00 35.82 2.41
810 871 7.828508 AATGCATCACTTATCCATGTGTAAT 57.171 32.000 0.00 0.00 35.82 1.89
811 872 6.866010 TGCATCACTTATCCATGTGTAATC 57.134 37.500 0.00 0.00 35.82 1.75
812 873 5.764686 TGCATCACTTATCCATGTGTAATCC 59.235 40.000 0.00 0.00 35.82 3.01
943 1005 6.419116 GCGACCTATATGCAGTATATGTGATG 59.581 42.308 1.40 0.00 33.96 3.07
987 1049 0.037697 AGAGAAACCGTGCGCACATA 60.038 50.000 37.03 0.00 0.00 2.29
1016 1078 2.890371 CATGGAGGCCAAGCTTGC 59.110 61.111 21.43 15.56 36.95 4.01
1032 1094 2.437359 GCAGTCATCCTTGCGGCT 60.437 61.111 0.00 0.00 0.00 5.52
1046 1108 1.202510 TGCGGCTTGCTTGTTGATTTT 60.203 42.857 0.00 0.00 46.63 1.82
1050 1112 3.426525 CGGCTTGCTTGTTGATTTTCTTC 59.573 43.478 0.00 0.00 0.00 2.87
1052 1114 4.209911 GGCTTGCTTGTTGATTTTCTTCAC 59.790 41.667 0.00 0.00 0.00 3.18
1080 1145 5.537295 TGGAGGTACGCATGTATACAGTATT 59.463 40.000 11.91 2.06 32.11 1.89
1085 1150 7.223971 AGGTACGCATGTATACAGTATTGTTTG 59.776 37.037 11.91 3.29 38.76 2.93
1090 1155 5.463499 TGTATACAGTATTGTTTGCGCAG 57.537 39.130 11.31 0.00 38.76 5.18
1106 1171 2.420022 GCGCAGACAAATACCTGAACAT 59.580 45.455 0.30 0.00 32.37 2.71
1109 1174 5.220854 GCGCAGACAAATACCTGAACATATT 60.221 40.000 0.30 0.00 32.37 1.28
1112 1177 6.183360 GCAGACAAATACCTGAACATATTGCT 60.183 38.462 0.00 0.00 32.37 3.91
1129 1331 8.711457 ACATATTGCTTACTTTGCATTGAAAAC 58.289 29.630 0.00 0.00 40.34 2.43
1164 1523 5.460748 TCCATTTCATAAGTATGCACGTACG 59.539 40.000 15.01 15.01 33.76 3.67
1177 1536 1.212490 CGTACGCCGGGAACTAACA 59.788 57.895 2.18 0.00 0.00 2.41
1186 1545 1.657094 CGGGAACTAACAAATCGGACG 59.343 52.381 0.00 0.00 0.00 4.79
1216 1575 0.589729 CGCACAGTGCACAGTGAAAC 60.590 55.000 37.37 22.44 45.36 2.78
1276 1635 0.739561 AGAGACGTACCCGAAGCATC 59.260 55.000 0.00 0.00 37.88 3.91
1416 1775 1.001641 GCTCTGCACCCTCAATGGT 60.002 57.895 0.00 0.00 39.96 3.55
1528 1887 3.527533 TGTTCCGTAGCACCATAATGTC 58.472 45.455 0.00 0.00 0.00 3.06
1566 1966 7.696992 AACCATGGAAAAGTATACAATTCGT 57.303 32.000 21.47 0.58 0.00 3.85
1569 1969 8.044908 ACCATGGAAAAGTATACAATTCGTAGT 58.955 33.333 21.47 3.06 32.28 2.73
1571 1971 8.879759 CATGGAAAAGTATACAATTCGTAGTGT 58.120 33.333 5.50 0.00 36.42 3.55
1585 1985 8.395633 CAATTCGTAGTGTAGGAAATAAAAGGG 58.604 37.037 0.00 0.00 36.33 3.95
1595 1997 4.090819 GGAAATAAAAGGGGTACTTGCCA 58.909 43.478 0.00 0.00 39.96 4.92
1616 2019 9.935241 TTGCCAACTCTATTTATTTATTTTGCA 57.065 25.926 0.00 0.00 0.00 4.08
1629 2032 7.832503 ATTTATTTTGCAGGAAATCTTTCGG 57.167 32.000 0.00 0.00 38.06 4.30
1630 2033 4.871933 ATTTTGCAGGAAATCTTTCGGT 57.128 36.364 0.00 0.00 38.06 4.69
1631 2034 3.915437 TTTGCAGGAAATCTTTCGGTC 57.085 42.857 0.00 0.00 38.06 4.79
1633 2036 3.973206 TGCAGGAAATCTTTCGGTCTA 57.027 42.857 0.00 0.00 38.06 2.59
1634 2037 4.487714 TGCAGGAAATCTTTCGGTCTAT 57.512 40.909 0.00 0.00 38.06 1.98
1636 2039 4.876107 TGCAGGAAATCTTTCGGTCTATTC 59.124 41.667 0.00 0.00 38.06 1.75
1637 2040 4.876107 GCAGGAAATCTTTCGGTCTATTCA 59.124 41.667 0.00 0.00 38.06 2.57
1638 2041 5.529060 GCAGGAAATCTTTCGGTCTATTCAT 59.471 40.000 0.00 0.00 38.06 2.57
1645 2054 8.438676 AATCTTTCGGTCTATTCATGTTAAGG 57.561 34.615 0.00 0.00 0.00 2.69
1651 2060 7.934457 TCGGTCTATTCATGTTAAGGTAGTAC 58.066 38.462 0.00 0.00 0.00 2.73
1652 2061 7.557358 TCGGTCTATTCATGTTAAGGTAGTACA 59.443 37.037 2.06 0.00 0.00 2.90
1698 2107 9.988815 AAAAATACATCTAGATTCGTAGAGCAT 57.011 29.630 1.33 0.00 38.43 3.79
1724 2133 2.416566 CGATGAGCACAAGCACTAGAGT 60.417 50.000 0.00 0.00 45.49 3.24
1752 2161 2.736995 CACACCGCCGTCATCGTT 60.737 61.111 0.00 0.00 35.01 3.85
1756 2165 1.445582 ACCGCCGTCATCGTTTCTC 60.446 57.895 0.00 0.00 35.01 2.87
1762 2171 1.630148 CGTCATCGTTTCTCCCTCAC 58.370 55.000 0.00 0.00 0.00 3.51
1763 2172 1.736032 CGTCATCGTTTCTCCCTCACC 60.736 57.143 0.00 0.00 0.00 4.02
1764 2173 0.530744 TCATCGTTTCTCCCTCACCG 59.469 55.000 0.00 0.00 0.00 4.94
1804 2214 3.233507 TGTAGTAGACAACCGGGAAGTT 58.766 45.455 6.32 0.00 34.15 2.66
1811 2221 1.890510 AACCGGGAAGTTGTCGTGC 60.891 57.895 6.32 0.00 0.00 5.34
1813 2223 1.290955 CCGGGAAGTTGTCGTGCTA 59.709 57.895 0.00 0.00 0.00 3.49
1820 2230 0.037232 AGTTGTCGTGCTAAGGCCTC 60.037 55.000 5.23 0.00 37.74 4.70
1841 2251 2.167398 TAGGACCAGCGCACCAGAAC 62.167 60.000 11.47 0.00 0.00 3.01
1844 2254 1.639298 GACCAGCGCACCAGAACATC 61.639 60.000 11.47 0.00 0.00 3.06
1850 2260 0.238289 CGCACCAGAACATCAACCAC 59.762 55.000 0.00 0.00 0.00 4.16
1852 2262 0.874390 CACCAGAACATCAACCACCG 59.126 55.000 0.00 0.00 0.00 4.94
1853 2263 0.472471 ACCAGAACATCAACCACCGT 59.528 50.000 0.00 0.00 0.00 4.83
1863 2273 1.067846 TCAACCACCGTCGATGAAGAG 60.068 52.381 6.11 0.00 0.00 2.85
1865 2275 0.811915 ACCACCGTCGATGAAGAGAG 59.188 55.000 6.11 0.00 0.00 3.20
1866 2276 1.095600 CCACCGTCGATGAAGAGAGA 58.904 55.000 6.11 0.00 0.00 3.10
1867 2277 1.472878 CCACCGTCGATGAAGAGAGAA 59.527 52.381 6.11 0.00 0.00 2.87
1871 2281 4.035792 CACCGTCGATGAAGAGAGAAGTAT 59.964 45.833 6.11 0.00 0.00 2.12
1873 2283 5.467399 ACCGTCGATGAAGAGAGAAGTATAG 59.533 44.000 6.11 0.00 0.00 1.31
1874 2284 5.697178 CCGTCGATGAAGAGAGAAGTATAGA 59.303 44.000 6.11 0.00 0.00 1.98
1875 2285 6.370442 CCGTCGATGAAGAGAGAAGTATAGAT 59.630 42.308 6.11 0.00 0.00 1.98
1876 2286 7.412563 CCGTCGATGAAGAGAGAAGTATAGATC 60.413 44.444 6.11 0.00 0.00 2.75
1877 2287 7.117092 CGTCGATGAAGAGAGAAGTATAGATCA 59.883 40.741 0.00 0.00 0.00 2.92
1902 2312 9.708222 CAAAAGAATCCAATCTATAGAAACACG 57.292 33.333 6.52 0.00 0.00 4.49
1909 2319 6.761242 TCCAATCTATAGAAACACGAACATGG 59.239 38.462 6.52 3.58 0.00 3.66
1916 2326 1.223187 AACACGAACATGGACGAACC 58.777 50.000 17.79 0.00 39.54 3.62
1927 2340 1.294138 GACGAACCACCGGATCCAA 59.706 57.895 9.46 0.00 0.00 3.53
1928 2341 0.739813 GACGAACCACCGGATCCAAG 60.740 60.000 9.46 4.76 0.00 3.61
1930 2343 2.046314 AACCACCGGATCCAAGCG 60.046 61.111 9.46 0.00 0.00 4.68
1962 2375 1.727467 CAAATGCCGACCGAATCCC 59.273 57.895 0.00 0.00 0.00 3.85
1963 2376 1.817941 AAATGCCGACCGAATCCCG 60.818 57.895 0.00 0.00 38.18 5.14
1964 2377 4.910585 ATGCCGACCGAATCCCGC 62.911 66.667 0.00 0.00 36.84 6.13
1981 2394 2.900273 CGGGATCCGCTGGAGAAA 59.100 61.111 5.45 0.00 41.17 2.52
1982 2395 1.220749 CGGGATCCGCTGGAGAAAA 59.779 57.895 5.45 0.00 41.17 2.29
1983 2396 0.392461 CGGGATCCGCTGGAGAAAAA 60.392 55.000 5.45 0.00 41.17 1.94
1984 2397 1.747206 CGGGATCCGCTGGAGAAAAAT 60.747 52.381 5.45 0.00 41.17 1.82
1985 2398 1.950216 GGGATCCGCTGGAGAAAAATC 59.050 52.381 5.45 0.00 34.05 2.17
1986 2399 2.422093 GGGATCCGCTGGAGAAAAATCT 60.422 50.000 5.45 0.00 34.05 2.40
1987 2400 2.875317 GGATCCGCTGGAGAAAAATCTC 59.125 50.000 0.00 0.00 34.05 2.75
1995 2408 2.902065 GAGAAAAATCTCCACACGCC 57.098 50.000 0.00 0.00 0.00 5.68
1996 2409 1.468914 GAGAAAAATCTCCACACGCCC 59.531 52.381 0.00 0.00 0.00 6.13
1997 2410 1.202879 AGAAAAATCTCCACACGCCCA 60.203 47.619 0.00 0.00 0.00 5.36
1998 2411 0.958822 AAAAATCTCCACACGCCCAC 59.041 50.000 0.00 0.00 0.00 4.61
1999 2412 0.893727 AAAATCTCCACACGCCCACC 60.894 55.000 0.00 0.00 0.00 4.61
2000 2413 2.063015 AAATCTCCACACGCCCACCA 62.063 55.000 0.00 0.00 0.00 4.17
2001 2414 2.063015 AATCTCCACACGCCCACCAA 62.063 55.000 0.00 0.00 0.00 3.67
2002 2415 2.748058 ATCTCCACACGCCCACCAAC 62.748 60.000 0.00 0.00 0.00 3.77
2003 2416 4.920112 TCCACACGCCCACCAACG 62.920 66.667 0.00 0.00 0.00 4.10
2004 2417 4.920112 CCACACGCCCACCAACGA 62.920 66.667 0.00 0.00 0.00 3.85
2005 2418 2.897846 CACACGCCCACCAACGAA 60.898 61.111 0.00 0.00 0.00 3.85
2006 2419 2.590575 ACACGCCCACCAACGAAG 60.591 61.111 0.00 0.00 0.00 3.79
2007 2420 4.025401 CACGCCCACCAACGAAGC 62.025 66.667 0.00 0.00 0.00 3.86
2008 2421 4.250305 ACGCCCACCAACGAAGCT 62.250 61.111 0.00 0.00 0.00 3.74
2009 2422 2.047655 CGCCCACCAACGAAGCTA 60.048 61.111 0.00 0.00 0.00 3.32
2010 2423 2.100631 CGCCCACCAACGAAGCTAG 61.101 63.158 0.00 0.00 0.00 3.42
2011 2424 1.295423 GCCCACCAACGAAGCTAGA 59.705 57.895 0.00 0.00 0.00 2.43
2012 2425 0.321298 GCCCACCAACGAAGCTAGAA 60.321 55.000 0.00 0.00 0.00 2.10
2013 2426 1.726853 CCCACCAACGAAGCTAGAAG 58.273 55.000 0.00 0.00 0.00 2.85
2014 2427 1.079503 CCACCAACGAAGCTAGAAGC 58.920 55.000 0.00 0.00 42.84 3.86
2015 2428 1.608025 CCACCAACGAAGCTAGAAGCA 60.608 52.381 1.22 0.00 45.56 3.91
2016 2429 2.350522 CACCAACGAAGCTAGAAGCAT 58.649 47.619 1.22 0.00 45.56 3.79
2017 2430 2.744202 CACCAACGAAGCTAGAAGCATT 59.256 45.455 1.22 0.00 45.56 3.56
2018 2431 2.744202 ACCAACGAAGCTAGAAGCATTG 59.256 45.455 1.22 0.00 45.56 2.82
2019 2432 2.744202 CCAACGAAGCTAGAAGCATTGT 59.256 45.455 1.22 0.00 45.56 2.71
2020 2433 3.181516 CCAACGAAGCTAGAAGCATTGTC 60.182 47.826 1.22 0.00 45.56 3.18
2021 2434 2.263077 ACGAAGCTAGAAGCATTGTCG 58.737 47.619 1.22 7.11 45.56 4.35
2022 2435 1.590238 CGAAGCTAGAAGCATTGTCGG 59.410 52.381 1.22 0.00 45.56 4.79
2033 2446 3.450507 TTGTCGGGACAAGCGAGA 58.549 55.556 10.04 0.00 45.42 4.04
2057 2470 0.759346 CCTGGATTAAGGGGTCCTCG 59.241 60.000 0.00 0.00 35.49 4.63
2079 2492 5.972107 GGACAGCCGGACTATATACTTTA 57.028 43.478 5.05 0.00 0.00 1.85
2121 2534 7.818493 TGAAGATACAAGATTGAAGACTTCG 57.182 36.000 10.56 0.00 34.37 3.79
2125 2538 4.608948 ACAAGATTGAAGACTTCGTCCT 57.391 40.909 10.56 4.33 32.18 3.85
2130 2543 3.536956 TTGAAGACTTCGTCCTGTGTT 57.463 42.857 10.56 0.00 32.18 3.32
2137 2550 0.963225 TTCGTCCTGTGTTCGGATGA 59.037 50.000 0.00 0.00 43.08 2.92
2222 2635 2.458620 GACTCTGTGTAACCCTAGCCT 58.541 52.381 0.00 0.00 34.36 4.58
2376 2789 2.912956 TCAATCAAGCAGGAAGTAGGGT 59.087 45.455 0.00 0.00 0.00 4.34
2389 2802 5.102783 AGGAAGTAGGGTATTACCTCCATCA 60.103 44.000 16.39 0.00 42.09 3.07
2418 2831 2.419667 CGAACCTGGGTAAAACATCGT 58.580 47.619 0.00 0.00 0.00 3.73
2462 2875 0.388134 GCCTTAGACGCACAGTTCGA 60.388 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.719246 CGTGGACGCGGTCATATTATG 59.281 52.381 12.47 0.00 33.68 1.90
448 498 5.763698 TGTATACGTGAGATCACCTTCCTAG 59.236 44.000 7.37 0.00 43.66 3.02
573 634 2.578940 CACACCACCCCCTCCTATTAAA 59.421 50.000 0.00 0.00 0.00 1.52
574 635 2.201830 CACACCACCCCCTCCTATTAA 58.798 52.381 0.00 0.00 0.00 1.40
575 636 1.366787 TCACACCACCCCCTCCTATTA 59.633 52.381 0.00 0.00 0.00 0.98
614 675 6.886459 TCTCCTCATTGGTTTATTTTCCTCTG 59.114 38.462 0.00 0.00 37.07 3.35
618 679 6.153510 AGCTTCTCCTCATTGGTTTATTTTCC 59.846 38.462 0.00 0.00 37.07 3.13
628 689 5.033589 AGTTGATAGCTTCTCCTCATTGG 57.966 43.478 0.00 0.00 37.10 3.16
631 692 3.645687 GGGAGTTGATAGCTTCTCCTCAT 59.354 47.826 16.85 0.00 43.97 2.90
694 755 5.079689 TGCATTTGAGAGTCACCGTATAA 57.920 39.130 0.00 0.00 0.00 0.98
775 836 9.066892 GGATAAGTGATGCATTAATTTAGGACA 57.933 33.333 9.52 0.00 0.00 4.02
776 837 9.066892 TGGATAAGTGATGCATTAATTTAGGAC 57.933 33.333 9.52 0.00 29.57 3.85
803 864 9.407380 AGTGATGCATTAATTTAGGATTACACA 57.593 29.630 0.00 0.00 0.00 3.72
809 870 9.812347 TGGATAAGTGATGCATTAATTTAGGAT 57.188 29.630 9.52 0.00 29.57 3.24
810 871 9.812347 ATGGATAAGTGATGCATTAATTTAGGA 57.188 29.630 9.52 0.00 43.59 2.94
811 872 9.850628 CATGGATAAGTGATGCATTAATTTAGG 57.149 33.333 9.52 0.00 43.59 2.69
972 1034 2.095213 CACTAATATGTGCGCACGGTTT 59.905 45.455 33.22 25.96 0.00 3.27
987 1049 3.395607 TGGCCTCCATGCTAATCACTAAT 59.604 43.478 3.32 0.00 0.00 1.73
1032 1094 5.336150 TGGTGAAGAAAATCAACAAGCAA 57.664 34.783 0.00 0.00 43.75 3.91
1046 1108 1.066430 GCGTACCTCCATTGGTGAAGA 60.066 52.381 6.33 0.00 41.05 2.87
1050 1112 1.016627 CATGCGTACCTCCATTGGTG 58.983 55.000 1.86 0.00 41.05 4.17
1052 1114 2.613026 TACATGCGTACCTCCATTGG 57.387 50.000 0.00 0.00 0.00 3.16
1080 1145 2.031245 CAGGTATTTGTCTGCGCAAACA 60.031 45.455 13.60 13.60 40.58 2.83
1085 1150 1.804151 TGTTCAGGTATTTGTCTGCGC 59.196 47.619 0.00 0.00 0.00 6.09
1090 1155 8.893727 AGTAAGCAATATGTTCAGGTATTTGTC 58.106 33.333 0.00 0.00 0.00 3.18
1106 1171 7.441017 AGGTTTTCAATGCAAAGTAAGCAATA 58.559 30.769 0.00 0.00 46.27 1.90
1164 1523 0.730840 CCGATTTGTTAGTTCCCGGC 59.269 55.000 0.00 0.00 0.00 6.13
1177 1536 0.824109 TCTCCTGCATCGTCCGATTT 59.176 50.000 0.00 0.00 31.62 2.17
1186 1545 1.079543 ACTGTGCGTCTCCTGCATC 60.080 57.895 0.00 0.00 45.34 3.91
1216 1575 4.778415 CTGGGCGACGACGAGGTG 62.778 72.222 12.29 0.00 42.66 4.00
1276 1635 1.217882 GTGTTCTTCACCGTCACCAG 58.782 55.000 0.00 0.00 40.84 4.00
1299 1658 1.571215 CGTTGAGCTGCATGCAGACA 61.571 55.000 44.02 36.16 46.30 3.41
1416 1775 0.899253 TTCCATACACCGGACGACCA 60.899 55.000 9.46 0.00 35.59 4.02
1528 1887 7.996098 TTTCCATGGTTTTTAGAGTCCTTAG 57.004 36.000 12.58 0.00 0.00 2.18
1561 1947 7.052248 CCCCTTTTATTTCCTACACTACGAAT 58.948 38.462 0.00 0.00 0.00 3.34
1562 1948 6.013466 ACCCCTTTTATTTCCTACACTACGAA 60.013 38.462 0.00 0.00 0.00 3.85
1566 1966 8.323567 CAAGTACCCCTTTTATTTCCTACACTA 58.676 37.037 0.00 0.00 0.00 2.74
1569 1969 5.947566 GCAAGTACCCCTTTTATTTCCTACA 59.052 40.000 0.00 0.00 0.00 2.74
1571 1971 5.015391 TGGCAAGTACCCCTTTTATTTCCTA 59.985 40.000 0.00 0.00 0.00 2.94
1582 1982 2.337359 TAGAGTTGGCAAGTACCCCT 57.663 50.000 7.71 3.48 0.00 4.79
1615 2018 6.540189 ACATGAATAGACCGAAAGATTTCCTG 59.460 38.462 0.00 0.00 33.68 3.86
1616 2019 6.653989 ACATGAATAGACCGAAAGATTTCCT 58.346 36.000 0.00 0.00 33.68 3.36
1619 2022 8.893727 CCTTAACATGAATAGACCGAAAGATTT 58.106 33.333 0.00 0.00 0.00 2.17
1622 2025 6.942976 ACCTTAACATGAATAGACCGAAAGA 58.057 36.000 0.00 0.00 0.00 2.52
1627 2030 7.709947 TGTACTACCTTAACATGAATAGACCG 58.290 38.462 0.00 0.00 0.00 4.79
1628 2031 9.880157 TTTGTACTACCTTAACATGAATAGACC 57.120 33.333 0.00 0.00 0.00 3.85
1683 2092 4.566987 TCGCTAGATGCTCTACGAATCTA 58.433 43.478 0.00 0.00 40.11 1.98
1698 2107 0.532115 TGCTTGTGCTCATCGCTAGA 59.468 50.000 0.00 0.00 40.48 2.43
1706 2115 1.963515 TCACTCTAGTGCTTGTGCTCA 59.036 47.619 5.21 0.00 45.25 4.26
1710 2119 1.719600 GGCTCACTCTAGTGCTTGTG 58.280 55.000 5.21 0.00 45.25 3.33
1736 2145 2.025418 GAAACGATGACGGCGGTGT 61.025 57.895 13.24 0.00 44.46 4.16
1741 2150 0.806492 GAGGGAGAAACGATGACGGC 60.806 60.000 0.00 0.00 44.46 5.68
1763 2172 1.170290 AAAAGGTTTGTCCGGCTCCG 61.170 55.000 0.00 0.48 41.99 4.63
1764 2173 1.037493 AAAAAGGTTTGTCCGGCTCC 58.963 50.000 0.00 0.00 41.99 4.70
1799 2209 0.796927 GGCCTTAGCACGACAACTTC 59.203 55.000 0.00 0.00 42.56 3.01
1804 2214 1.409064 CTATGAGGCCTTAGCACGACA 59.591 52.381 6.77 0.00 42.56 4.35
1808 2218 1.070914 GGTCCTATGAGGCCTTAGCAC 59.929 57.143 6.77 1.09 42.56 4.40
1811 2221 1.346068 GCTGGTCCTATGAGGCCTTAG 59.654 57.143 6.77 5.46 34.61 2.18
1813 2223 1.690219 CGCTGGTCCTATGAGGCCTT 61.690 60.000 6.77 0.00 34.61 4.35
1820 2230 1.522355 CTGGTGCGCTGGTCCTATG 60.522 63.158 9.73 0.00 0.00 2.23
1830 2240 1.210155 GGTTGATGTTCTGGTGCGC 59.790 57.895 0.00 0.00 0.00 6.09
1844 2254 1.067846 TCTCTTCATCGACGGTGGTTG 60.068 52.381 8.51 0.00 0.00 3.77
1850 2260 4.822036 ATACTTCTCTCTTCATCGACGG 57.178 45.455 0.00 0.00 0.00 4.79
1852 2262 8.317891 TGATCTATACTTCTCTCTTCATCGAC 57.682 38.462 0.00 0.00 0.00 4.20
1853 2263 8.910351 TTGATCTATACTTCTCTCTTCATCGA 57.090 34.615 0.00 0.00 0.00 3.59
1876 2286 9.708222 CGTGTTTCTATAGATTGGATTCTTTTG 57.292 33.333 2.58 0.00 0.00 2.44
1877 2287 9.667107 TCGTGTTTCTATAGATTGGATTCTTTT 57.333 29.630 2.58 0.00 0.00 2.27
1881 2291 8.420374 TGTTCGTGTTTCTATAGATTGGATTC 57.580 34.615 2.58 0.00 0.00 2.52
1882 2292 8.830580 CATGTTCGTGTTTCTATAGATTGGATT 58.169 33.333 2.58 0.00 0.00 3.01
1892 2302 4.182693 TCGTCCATGTTCGTGTTTCTAT 57.817 40.909 6.65 0.00 0.00 1.98
1895 2305 2.349155 GGTTCGTCCATGTTCGTGTTTC 60.349 50.000 6.65 0.00 35.97 2.78
1909 2319 0.739813 CTTGGATCCGGTGGTTCGTC 60.740 60.000 7.39 0.00 0.00 4.20
1930 2343 0.740737 CATTTGCCTTCGGTGGATCC 59.259 55.000 4.20 4.20 0.00 3.36
1943 2356 1.064134 GGATTCGGTCGGCATTTGC 59.936 57.895 0.00 0.00 41.14 3.68
1965 2378 1.950216 GATTTTTCTCCAGCGGATCCC 59.050 52.381 6.06 0.00 0.00 3.85
1966 2379 2.875317 GAGATTTTTCTCCAGCGGATCC 59.125 50.000 0.00 0.00 0.00 3.36
1976 2389 1.468914 GGGCGTGTGGAGATTTTTCTC 59.531 52.381 0.00 0.00 36.08 2.87
1977 2390 1.202879 TGGGCGTGTGGAGATTTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
1978 2391 1.068541 GTGGGCGTGTGGAGATTTTTC 60.069 52.381 0.00 0.00 0.00 2.29
1979 2392 0.958822 GTGGGCGTGTGGAGATTTTT 59.041 50.000 0.00 0.00 0.00 1.94
1980 2393 0.893727 GGTGGGCGTGTGGAGATTTT 60.894 55.000 0.00 0.00 0.00 1.82
1981 2394 1.303317 GGTGGGCGTGTGGAGATTT 60.303 57.895 0.00 0.00 0.00 2.17
1982 2395 2.063015 TTGGTGGGCGTGTGGAGATT 62.063 55.000 0.00 0.00 0.00 2.40
1983 2396 2.525124 TTGGTGGGCGTGTGGAGAT 61.525 57.895 0.00 0.00 0.00 2.75
1984 2397 3.164977 TTGGTGGGCGTGTGGAGA 61.165 61.111 0.00 0.00 0.00 3.71
1985 2398 2.978010 GTTGGTGGGCGTGTGGAG 60.978 66.667 0.00 0.00 0.00 3.86
1986 2399 4.920112 CGTTGGTGGGCGTGTGGA 62.920 66.667 0.00 0.00 0.00 4.02
1987 2400 4.920112 TCGTTGGTGGGCGTGTGG 62.920 66.667 0.00 0.00 0.00 4.17
1988 2401 2.892334 CTTCGTTGGTGGGCGTGTG 61.892 63.158 0.00 0.00 0.00 3.82
1989 2402 2.590575 CTTCGTTGGTGGGCGTGT 60.591 61.111 0.00 0.00 0.00 4.49
1990 2403 4.025401 GCTTCGTTGGTGGGCGTG 62.025 66.667 0.00 0.00 0.00 5.34
1991 2404 2.781595 CTAGCTTCGTTGGTGGGCGT 62.782 60.000 0.00 0.00 0.00 5.68
1992 2405 2.047655 TAGCTTCGTTGGTGGGCG 60.048 61.111 0.00 0.00 0.00 6.13
1993 2406 0.321298 TTCTAGCTTCGTTGGTGGGC 60.321 55.000 0.00 0.00 0.00 5.36
1994 2407 1.726853 CTTCTAGCTTCGTTGGTGGG 58.273 55.000 0.00 0.00 0.00 4.61
1995 2408 1.079503 GCTTCTAGCTTCGTTGGTGG 58.920 55.000 0.00 0.00 38.45 4.61
1996 2409 1.795768 TGCTTCTAGCTTCGTTGGTG 58.204 50.000 0.00 0.00 42.97 4.17
1997 2410 2.744202 CAATGCTTCTAGCTTCGTTGGT 59.256 45.455 0.00 0.00 42.97 3.67
1998 2411 2.744202 ACAATGCTTCTAGCTTCGTTGG 59.256 45.455 0.00 0.00 42.97 3.77
1999 2412 3.482598 CGACAATGCTTCTAGCTTCGTTG 60.483 47.826 0.00 0.00 42.97 4.10
2000 2413 2.668457 CGACAATGCTTCTAGCTTCGTT 59.332 45.455 0.00 0.00 42.97 3.85
2001 2414 2.263077 CGACAATGCTTCTAGCTTCGT 58.737 47.619 0.00 0.00 42.97 3.85
2002 2415 1.590238 CCGACAATGCTTCTAGCTTCG 59.410 52.381 0.00 0.00 42.97 3.79
2003 2416 1.936547 CCCGACAATGCTTCTAGCTTC 59.063 52.381 0.00 0.00 42.97 3.86
2004 2417 1.555075 TCCCGACAATGCTTCTAGCTT 59.445 47.619 0.00 0.00 42.97 3.74
2005 2418 1.134670 GTCCCGACAATGCTTCTAGCT 60.135 52.381 0.00 0.00 42.97 3.32
2006 2419 1.291132 GTCCCGACAATGCTTCTAGC 58.709 55.000 0.00 0.00 42.82 3.42
2007 2420 2.672961 TGTCCCGACAATGCTTCTAG 57.327 50.000 0.00 0.00 38.56 2.43
2017 2430 1.587043 CTCTCTCGCTTGTCCCGACA 61.587 60.000 0.00 0.00 39.98 4.35
2018 2431 1.137825 CTCTCTCGCTTGTCCCGAC 59.862 63.158 0.00 0.00 0.00 4.79
2019 2432 1.303398 ACTCTCTCGCTTGTCCCGA 60.303 57.895 0.00 0.00 0.00 5.14
2020 2433 1.137825 GACTCTCTCGCTTGTCCCG 59.862 63.158 0.00 0.00 0.00 5.14
2021 2434 1.513622 GGACTCTCTCGCTTGTCCC 59.486 63.158 0.00 0.00 42.11 4.46
2022 2435 0.172352 CAGGACTCTCTCGCTTGTCC 59.828 60.000 0.00 0.00 46.67 4.02
2029 2442 2.625790 CCCTTAATCCAGGACTCTCTCG 59.374 54.545 0.00 0.00 35.71 4.04
2033 2446 2.629909 GGACCCCTTAATCCAGGACTCT 60.630 54.545 0.00 0.00 35.71 3.24
2057 2470 4.868314 AAAGTATATAGTCCGGCTGTCC 57.132 45.455 0.00 0.00 0.00 4.02
2079 2492 0.537188 CATAGTCCAACAGTCCGGCT 59.463 55.000 0.00 0.00 0.00 5.52
2121 2534 1.546476 AGTCTCATCCGAACACAGGAC 59.454 52.381 0.00 0.00 41.10 3.85
2125 2538 1.819288 GGAGAGTCTCATCCGAACACA 59.181 52.381 21.53 0.00 31.08 3.72
2130 2543 1.478510 GCAAAGGAGAGTCTCATCCGA 59.521 52.381 21.53 0.00 40.73 4.55
2137 2550 1.001406 CTTCCACGCAAAGGAGAGTCT 59.999 52.381 0.00 0.00 36.33 3.24
2262 2675 8.388484 AGCCTATGATTATGATTGTTCTTGTC 57.612 34.615 0.00 0.00 0.00 3.18
2389 2802 3.330720 CCAGGTTCGGGCCCTCTT 61.331 66.667 22.43 3.59 0.00 2.85
2418 2831 1.159905 TAACAGGAGGCAGGGGACA 59.840 57.895 0.00 0.00 0.00 4.02
2462 2875 1.542679 GATCTCGGGTAGGGGGTCT 59.457 63.158 0.00 0.00 0.00 3.85
2501 2914 3.569701 GGAACTCTCAATGAAAGCACCAA 59.430 43.478 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.