Multiple sequence alignment - TraesCS1B01G290100

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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 TraesCS1B01G290100 chr1B 100.000 3536 0 0 1 3536 506332905 506336440 0.000000e+00 6530
1 TraesCS1B01G290100 chr4A 94.916 3147 137 8 399 3536 624293815 624290683 0.000000e+00 4903
2 TraesCS1B01G290100 chr4A 87.900 281 20 4 101 367 624294079 624293799 5.700000e-83 318
3 TraesCS1B01G290100 chr5A 93.736 3145 159 15 397 3536 638407806 638404695 0.000000e+00 4682
4 TraesCS1B01G290100 chr5A 95.680 1713 73 1 1824 3536 631794045 631792334 0.000000e+00 2752
5 TraesCS1B01G290100 chr5A 87.234 940 68 15 100 1021 631794978 631794073 0.000000e+00 1024
6 TraesCS1B01G290100 chr5B 95.964 2676 106 2 862 3536 669738618 669741292 0.000000e+00 4342
7 TraesCS1B01G290100 chr5B 91.697 277 23 0 403 679 669738321 669738597 5.540000e-103 385
8 TraesCS1B01G290100 chr5B 91.386 267 17 4 100 360 669738064 669738330 9.330000e-96 361
9 TraesCS1B01G290100 chr5B 95.833 96 4 0 1 96 602300578 602300673 4.730000e-34 156
10 TraesCS1B01G290100 chr7A 94.811 2621 120 6 405 3022 659714016 659716623 0.000000e+00 4072
11 TraesCS1B01G290100 chr7A 81.522 276 33 13 100 360 659713753 659714025 9.940000e-51 211
12 TraesCS1B01G290100 chr6B 92.382 2573 194 2 962 3534 294340994 294343564 0.000000e+00 3664
13 TraesCS1B01G290100 chr7B 90.799 2304 204 6 1196 3499 712180106 712177811 0.000000e+00 3073
14 TraesCS1B01G290100 chr7B 95.960 99 3 1 1 98 389517499 389517597 3.650000e-35 159
15 TraesCS1B01G290100 chr2B 91.756 1868 149 5 1671 3536 397051321 397053185 0.000000e+00 2591
16 TraesCS1B01G290100 chr2B 93.195 1543 102 3 962 2504 122981055 122982594 0.000000e+00 2265
17 TraesCS1B01G290100 chr2B 92.964 867 61 0 2670 3536 122982608 122983474 0.000000e+00 1264
18 TraesCS1B01G290100 chr2B 88.731 914 69 12 97 1000 581621489 581622378 0.000000e+00 1086
19 TraesCS1B01G290100 chr2B 91.981 212 17 0 3141 3352 800217273 800217062 7.420000e-77 298
20 TraesCS1B01G290100 chr2B 88.636 132 15 0 3384 3515 800217067 800216936 1.020000e-35 161
21 TraesCS1B01G290100 chr2B 84.906 106 15 1 3411 3515 221542348 221542243 4.830000e-19 106
22 TraesCS1B01G290100 chr5D 90.152 1909 175 10 961 2867 441937340 441935443 0.000000e+00 2471
23 TraesCS1B01G290100 chr7D 95.960 99 3 1 1 98 429544008 429543910 3.650000e-35 159
24 TraesCS1B01G290100 chr7D 80.690 145 27 1 100 243 623721245 623721101 1.040000e-20 111
25 TraesCS1B01G290100 chr6D 95.960 99 3 1 1 98 65663563 65663465 3.650000e-35 159
26 TraesCS1B01G290100 chr4D 95.960 99 3 1 1 98 160029241 160029143 3.650000e-35 159
27 TraesCS1B01G290100 chr3B 95.960 99 3 1 1 98 538450965 538451063 3.650000e-35 159
28 TraesCS1B01G290100 chrUn 94.949 99 4 1 1 98 18881869 18881771 1.700000e-33 154
29 TraesCS1B01G290100 chrUn 94.949 99 4 1 1 98 63128600 63128698 1.700000e-33 154
30 TraesCS1B01G290100 chrUn 94.949 99 4 1 1 98 163367035 163366937 1.700000e-33 154


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 TraesCS1B01G290100 chr1B 506332905 506336440 3535 False 6530.0 6530 100.000000 1 3536 1 chr1B.!!$F1 3535
1 TraesCS1B01G290100 chr4A 624290683 624294079 3396 True 2610.5 4903 91.408000 101 3536 2 chr4A.!!$R1 3435
2 TraesCS1B01G290100 chr5A 638404695 638407806 3111 True 4682.0 4682 93.736000 397 3536 1 chr5A.!!$R1 3139
3 TraesCS1B01G290100 chr5A 631792334 631794978 2644 True 1888.0 2752 91.457000 100 3536 2 chr5A.!!$R2 3436
4 TraesCS1B01G290100 chr5B 669738064 669741292 3228 False 1696.0 4342 93.015667 100 3536 3 chr5B.!!$F2 3436
5 TraesCS1B01G290100 chr7A 659713753 659716623 2870 False 2141.5 4072 88.166500 100 3022 2 chr7A.!!$F1 2922
6 TraesCS1B01G290100 chr6B 294340994 294343564 2570 False 3664.0 3664 92.382000 962 3534 1 chr6B.!!$F1 2572
7 TraesCS1B01G290100 chr7B 712177811 712180106 2295 True 3073.0 3073 90.799000 1196 3499 1 chr7B.!!$R1 2303
8 TraesCS1B01G290100 chr2B 397051321 397053185 1864 False 2591.0 2591 91.756000 1671 3536 1 chr2B.!!$F1 1865
9 TraesCS1B01G290100 chr2B 122981055 122983474 2419 False 1764.5 2265 93.079500 962 3536 2 chr2B.!!$F3 2574
10 TraesCS1B01G290100 chr2B 581621489 581622378 889 False 1086.0 1086 88.731000 97 1000 1 chr2B.!!$F2 903
11 TraesCS1B01G290100 chr5D 441935443 441937340 1897 True 2471.0 2471 90.152000 961 2867 1 chr5D.!!$R1 1906

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
98 99 0.605589 GCACAACCTCGGTTTAGCCT 60.606 55.0 0.00 0.0 36.00 4.58 F
441 459 0.653636 TTTGTTTCTCACGCACGACC 59.346 50.0 0.00 0.0 0.00 4.79 F
602 628 0.753262 GGCTTCGGATCAGCTTCCTA 59.247 55.0 2.99 0.0 37.43 2.94 F
1643 1683 0.667993 CAAGGCTTGGCTTTTCGTGA 59.332 50.0 19.55 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1100 1.071699 TGGTTGTGCCTCCACTTCTAC 59.928 52.381 0.0 0.0 42.54 2.59 R
1357 1397 1.177401 GCCCTTCCAGGTTGCTTAAG 58.823 55.000 0.0 0.0 31.93 1.85 R
1741 1783 1.263217 GTGCAATTTCTTCGACCACGT 59.737 47.619 0.0 0.0 40.69 4.49 R
3361 3411 2.565391 TGACTTGAATAACTCCCGCTCA 59.435 45.455 0.0 0.0 0.00 4.26 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
20 21 2.143876 TGGCCAAAGAAAGCTATCCC 57.856 50.000 0.61 0.00 0.00 3.85
21 22 1.640670 TGGCCAAAGAAAGCTATCCCT 59.359 47.619 0.61 0.00 0.00 4.20
22 23 2.849943 TGGCCAAAGAAAGCTATCCCTA 59.150 45.455 0.61 0.00 0.00 3.53
23 24 3.215151 GGCCAAAGAAAGCTATCCCTAC 58.785 50.000 0.00 0.00 0.00 3.18
24 25 3.371595 GGCCAAAGAAAGCTATCCCTACA 60.372 47.826 0.00 0.00 0.00 2.74
25 26 4.270008 GCCAAAGAAAGCTATCCCTACAA 58.730 43.478 0.00 0.00 0.00 2.41
26 27 4.705023 GCCAAAGAAAGCTATCCCTACAAA 59.295 41.667 0.00 0.00 0.00 2.83
27 28 5.185056 GCCAAAGAAAGCTATCCCTACAAAA 59.815 40.000 0.00 0.00 0.00 2.44
28 29 6.127338 GCCAAAGAAAGCTATCCCTACAAAAT 60.127 38.462 0.00 0.00 0.00 1.82
29 30 7.484140 CCAAAGAAAGCTATCCCTACAAAATC 58.516 38.462 0.00 0.00 0.00 2.17
30 31 7.122650 CCAAAGAAAGCTATCCCTACAAAATCA 59.877 37.037 0.00 0.00 0.00 2.57
31 32 8.689972 CAAAGAAAGCTATCCCTACAAAATCAT 58.310 33.333 0.00 0.00 0.00 2.45
32 33 9.920946 AAAGAAAGCTATCCCTACAAAATCATA 57.079 29.630 0.00 0.00 0.00 2.15
38 39 9.554053 AGCTATCCCTACAAAATCATATAGTCT 57.446 33.333 0.00 0.00 0.00 3.24
39 40 9.593134 GCTATCCCTACAAAATCATATAGTCTG 57.407 37.037 0.00 0.00 0.00 3.51
41 42 6.769512 TCCCTACAAAATCATATAGTCTGGC 58.230 40.000 0.00 0.00 0.00 4.85
42 43 6.558775 TCCCTACAAAATCATATAGTCTGGCT 59.441 38.462 0.00 0.00 0.00 4.75
43 44 7.733047 TCCCTACAAAATCATATAGTCTGGCTA 59.267 37.037 0.00 0.00 0.00 3.93
44 45 8.543774 CCCTACAAAATCATATAGTCTGGCTAT 58.456 37.037 7.03 7.03 42.63 2.97
45 46 9.376075 CCTACAAAATCATATAGTCTGGCTATG 57.624 37.037 11.91 0.00 40.41 2.23
46 47 7.678947 ACAAAATCATATAGTCTGGCTATGC 57.321 36.000 11.91 0.00 40.41 3.14
47 48 7.456725 ACAAAATCATATAGTCTGGCTATGCT 58.543 34.615 11.91 0.00 40.41 3.79
48 49 7.605691 ACAAAATCATATAGTCTGGCTATGCTC 59.394 37.037 11.91 0.00 40.41 4.26
49 50 7.493499 AAATCATATAGTCTGGCTATGCTCT 57.507 36.000 11.91 0.00 40.41 4.09
50 51 8.601047 AAATCATATAGTCTGGCTATGCTCTA 57.399 34.615 11.91 0.00 40.41 2.43
51 52 8.780616 AATCATATAGTCTGGCTATGCTCTAT 57.219 34.615 11.91 0.00 40.41 1.98
52 53 7.815840 TCATATAGTCTGGCTATGCTCTATC 57.184 40.000 11.91 0.00 40.41 2.08
53 54 7.581814 TCATATAGTCTGGCTATGCTCTATCT 58.418 38.462 11.91 0.00 40.41 1.98
54 55 8.058235 TCATATAGTCTGGCTATGCTCTATCTT 58.942 37.037 11.91 0.00 40.41 2.40
55 56 9.348476 CATATAGTCTGGCTATGCTCTATCTTA 57.652 37.037 11.91 0.00 40.41 2.10
56 57 9.928618 ATATAGTCTGGCTATGCTCTATCTTAA 57.071 33.333 11.91 0.00 40.41 1.85
57 58 8.837099 ATAGTCTGGCTATGCTCTATCTTAAT 57.163 34.615 0.05 0.00 38.86 1.40
58 59 7.169158 AGTCTGGCTATGCTCTATCTTAATC 57.831 40.000 0.00 0.00 0.00 1.75
59 60 6.723515 AGTCTGGCTATGCTCTATCTTAATCA 59.276 38.462 0.00 0.00 0.00 2.57
60 61 6.811170 GTCTGGCTATGCTCTATCTTAATCAC 59.189 42.308 0.00 0.00 0.00 3.06
61 62 6.494835 TCTGGCTATGCTCTATCTTAATCACA 59.505 38.462 0.00 0.00 0.00 3.58
62 63 7.179872 TCTGGCTATGCTCTATCTTAATCACAT 59.820 37.037 0.00 0.00 0.00 3.21
63 64 8.366359 TGGCTATGCTCTATCTTAATCACATA 57.634 34.615 0.00 0.00 0.00 2.29
64 65 8.815912 TGGCTATGCTCTATCTTAATCACATAA 58.184 33.333 0.00 0.00 0.00 1.90
65 66 9.658799 GGCTATGCTCTATCTTAATCACATAAA 57.341 33.333 0.00 0.00 0.00 1.40
89 90 8.633075 AATTATTTAAATCATGCACAACCTCG 57.367 30.769 3.39 0.00 0.00 4.63
90 91 4.433186 TTTAAATCATGCACAACCTCGG 57.567 40.909 0.00 0.00 0.00 4.63
91 92 1.909700 AAATCATGCACAACCTCGGT 58.090 45.000 0.00 0.00 0.00 4.69
92 93 1.909700 AATCATGCACAACCTCGGTT 58.090 45.000 0.00 0.00 39.13 4.44
93 94 1.909700 ATCATGCACAACCTCGGTTT 58.090 45.000 0.00 0.00 36.00 3.27
94 95 2.552599 TCATGCACAACCTCGGTTTA 57.447 45.000 0.00 0.00 36.00 2.01
95 96 2.422597 TCATGCACAACCTCGGTTTAG 58.577 47.619 0.00 0.00 36.00 1.85
98 99 0.605589 GCACAACCTCGGTTTAGCCT 60.606 55.000 0.00 0.00 36.00 4.58
103 104 1.125711 ACCTCGGTTTAGCCTGTGGT 61.126 55.000 0.00 0.00 34.92 4.16
134 135 3.570212 AGCGACCCTGGGCACTTT 61.570 61.111 14.08 0.00 0.00 2.66
135 136 2.597510 GCGACCCTGGGCACTTTT 60.598 61.111 14.08 0.00 0.00 2.27
139 140 2.406002 GACCCTGGGCACTTTTCCGA 62.406 60.000 14.08 0.00 0.00 4.55
171 172 3.816994 TCCTAGTAGCAGCGATAGACAA 58.183 45.455 0.00 0.00 39.76 3.18
247 248 2.108952 ACTGGGCCTTTGTTTCTCTCAT 59.891 45.455 4.53 0.00 0.00 2.90
275 277 2.124122 GCCCAACAATCAACAAACGAC 58.876 47.619 0.00 0.00 0.00 4.34
276 278 2.480416 GCCCAACAATCAACAAACGACA 60.480 45.455 0.00 0.00 0.00 4.35
277 279 3.798548 GCCCAACAATCAACAAACGACAT 60.799 43.478 0.00 0.00 0.00 3.06
278 280 4.367450 CCCAACAATCAACAAACGACATT 58.633 39.130 0.00 0.00 0.00 2.71
302 318 3.305619 ATGCAATCAGCCCAGGCCA 62.306 57.895 5.01 0.00 44.83 5.36
360 376 2.634600 GTCGCTCCAACTCTCTCTCTA 58.365 52.381 0.00 0.00 0.00 2.43
361 377 3.211045 GTCGCTCCAACTCTCTCTCTAT 58.789 50.000 0.00 0.00 0.00 1.98
362 378 3.250040 GTCGCTCCAACTCTCTCTCTATC 59.750 52.174 0.00 0.00 0.00 2.08
363 379 3.135712 TCGCTCCAACTCTCTCTCTATCT 59.864 47.826 0.00 0.00 0.00 1.98
364 380 4.345547 TCGCTCCAACTCTCTCTCTATCTA 59.654 45.833 0.00 0.00 0.00 1.98
365 381 5.012664 TCGCTCCAACTCTCTCTCTATCTAT 59.987 44.000 0.00 0.00 0.00 1.98
366 382 5.351465 CGCTCCAACTCTCTCTCTATCTATC 59.649 48.000 0.00 0.00 0.00 2.08
367 383 6.476378 GCTCCAACTCTCTCTCTATCTATCT 58.524 44.000 0.00 0.00 0.00 1.98
368 384 7.578763 CGCTCCAACTCTCTCTCTATCTATCTA 60.579 44.444 0.00 0.00 0.00 1.98
369 385 8.267894 GCTCCAACTCTCTCTCTATCTATCTAT 58.732 40.741 0.00 0.00 0.00 1.98
370 386 9.823647 CTCCAACTCTCTCTCTATCTATCTATC 57.176 40.741 0.00 0.00 0.00 2.08
371 387 9.560860 TCCAACTCTCTCTCTATCTATCTATCT 57.439 37.037 0.00 0.00 0.00 1.98
441 459 0.653636 TTTGTTTCTCACGCACGACC 59.346 50.000 0.00 0.00 0.00 4.79
544 564 4.519730 GGCTACCATGTAGTCTATTCGTCT 59.480 45.833 3.45 0.00 0.00 4.18
581 601 2.515853 TCTCCTTCCTCTCATCTGGCTA 59.484 50.000 0.00 0.00 0.00 3.93
591 611 1.756950 ATCTGGCTACGGCTTCGGA 60.757 57.895 0.00 0.00 38.73 4.55
602 628 0.753262 GGCTTCGGATCAGCTTCCTA 59.247 55.000 2.99 0.00 37.43 2.94
609 635 2.543238 CGGATCAGCTTCCTACGGTAAC 60.543 54.545 2.99 0.00 33.30 2.50
619 645 4.730949 TCCTACGGTAACAAATCTCCAG 57.269 45.455 0.00 0.00 0.00 3.86
655 681 5.832595 CCAAGGATCTCTCATCTCTGAAGTA 59.167 44.000 0.00 0.00 0.00 2.24
686 720 6.443849 AGTTTGTCTGGGAAGTAGGATTGATA 59.556 38.462 0.00 0.00 0.00 2.15
762 796 7.067129 CAGACTTAGGGTTTAGGGCTTAAATTC 59.933 40.741 5.05 1.79 33.99 2.17
806 840 9.941325 GGTGATCATGAATTCATTACTAGAGAT 57.059 33.333 18.41 14.93 33.61 2.75
896 936 8.147058 ACACTGTGGTATTCATGCAAATTTTTA 58.853 29.630 13.09 0.00 0.00 1.52
1023 1063 9.620259 GAGATGAGGAGATTTTTGGTTAATAGT 57.380 33.333 0.00 0.00 0.00 2.12
1191 1231 5.480642 TTCAAGATCAAGTGAGAAGAGCT 57.519 39.130 0.00 0.00 0.00 4.09
1207 1247 7.344612 TGAGAAGAGCTTATGTATTGAAGGGTA 59.655 37.037 0.00 0.00 0.00 3.69
1216 1256 5.895636 TGTATTGAAGGGTACAATGCAAG 57.104 39.130 0.00 0.00 43.30 4.01
1230 1270 7.221452 GGTACAATGCAAGCAGATTTGAATAAG 59.779 37.037 12.31 0.00 0.00 1.73
1234 1274 7.591006 ATGCAAGCAGATTTGAATAAGTTTG 57.409 32.000 0.00 0.00 0.00 2.93
1258 1298 8.177119 TGCTTGTACTAAATTTGGAAGTTCAT 57.823 30.769 8.72 0.00 0.00 2.57
1267 1307 7.951530 AAATTTGGAAGTTCATGTTCATCAC 57.048 32.000 5.01 0.00 0.00 3.06
1333 1373 1.490490 ACAGTGAGTGGAAGAAGGCAA 59.510 47.619 0.00 0.00 0.00 4.52
1357 1397 8.490355 CAACTTATTGTTTTCATTGCTTTCTCC 58.510 33.333 0.00 0.00 36.63 3.71
1466 1506 6.125029 CCTTCAAAGATCATATTGGTGGTCT 58.875 40.000 0.00 0.00 41.22 3.85
1489 1529 3.181459 TGGTAGTAAGCACAACTCTTGCA 60.181 43.478 0.00 0.00 42.83 4.08
1595 1635 6.869695 TGTATAAGATCCGCTTGACTTGTTA 58.130 36.000 0.00 0.00 37.42 2.41
1643 1683 0.667993 CAAGGCTTGGCTTTTCGTGA 59.332 50.000 19.55 0.00 0.00 4.35
1741 1783 5.589855 TGAACAAGTGAGAGATGCTTTTGAA 59.410 36.000 0.00 0.00 0.00 2.69
1748 1790 2.808543 AGAGATGCTTTTGAACGTGGTC 59.191 45.455 0.00 0.00 0.00 4.02
1772 1814 5.471556 AAGAAATTGCACAATGACATCCA 57.528 34.783 0.00 0.00 0.00 3.41
1989 2033 5.646606 TGTTGTGCACTAACCTTCTTTTTC 58.353 37.500 19.41 0.00 0.00 2.29
1991 2037 5.243426 TGTGCACTAACCTTCTTTTTCAC 57.757 39.130 19.41 0.00 0.00 3.18
1997 2043 6.430000 GCACTAACCTTCTTTTTCACATAGGA 59.570 38.462 0.00 0.00 0.00 2.94
2051 2097 4.439305 TTTATTGCTCTTCACCATGTGC 57.561 40.909 0.00 0.00 32.98 4.57
2054 2100 1.913778 TGCTCTTCACCATGTGCAAT 58.086 45.000 0.00 0.00 32.98 3.56
2157 2203 4.498682 GCAAGGATATGATGGTGCTTCAAC 60.499 45.833 0.00 0.00 0.00 3.18
2178 2224 6.094048 TCAACTATGAGAGGCAAGTTTAATGC 59.906 38.462 0.00 0.00 43.08 3.56
2277 2324 5.163343 TGGTTGTCTCTGTTGCTAGTAGTTT 60.163 40.000 0.00 0.00 0.00 2.66
2374 2421 1.068748 GCATTGACAGAGGCACAACAG 60.069 52.381 0.00 0.00 0.00 3.16
2573 2623 1.675310 CGTGGGCCATCTCAAGCAA 60.675 57.895 10.70 0.00 0.00 3.91
2649 2699 4.044336 TGTTGAAGTTGTTTGGCATCAG 57.956 40.909 0.00 0.00 0.00 2.90
2732 2782 2.165030 GTGGATGATGTCAAAGCTTGGG 59.835 50.000 0.00 0.00 0.00 4.12
2736 2786 1.133513 TGATGTCAAAGCTTGGGTGGT 60.134 47.619 0.00 0.00 0.00 4.16
2763 2813 1.577736 AGAGAGAGTGGTTGGGATGG 58.422 55.000 0.00 0.00 0.00 3.51
2893 2943 4.439057 TCACTAATCTTCACCATTACCGC 58.561 43.478 0.00 0.00 0.00 5.68
2895 2945 2.396590 AATCTTCACCATTACCGCGT 57.603 45.000 4.92 0.00 0.00 6.01
3058 3108 4.205792 GCGCATCTTGCTGAAATTTATCAC 59.794 41.667 0.30 0.00 42.25 3.06
3099 3149 4.160439 TGATCGTGGAACAATAAGAGAGCT 59.840 41.667 0.00 0.00 44.16 4.09
3121 3171 7.961351 AGCTGCTTCTCACTTATATAAGTCAT 58.039 34.615 22.60 2.05 44.19 3.06
3135 3185 9.625747 TTATATAAGTCATGTGAAAAGGCATGA 57.374 29.630 0.00 3.45 46.16 3.07
3172 3222 6.154203 TGTGATGATGTTAAAAGTTTGGCA 57.846 33.333 0.00 0.00 0.00 4.92
3190 3240 3.244976 GGCAATGAAGATGGTTGAAACG 58.755 45.455 0.00 0.00 0.00 3.60
3281 3331 4.377841 CGGCATCTGTTGAGAGAACTTTTC 60.378 45.833 0.00 0.00 0.00 2.29
3429 3479 3.245229 ACATTTACTGCAATGGGGTCTCA 60.245 43.478 1.44 0.00 38.32 3.27
3441 3491 1.683319 GGGGTCTCAGAAAGGGCATTC 60.683 57.143 0.00 0.00 0.00 2.67
3469 3519 8.299570 CCTCATAATTTTCTTTAGTGCACTGTT 58.700 33.333 29.57 5.90 0.00 3.16
3471 3521 8.845227 TCATAATTTTCTTTAGTGCACTGTTGA 58.155 29.630 29.57 19.26 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.640670 AGGGATAGCTTTCTTTGGCCA 59.359 47.619 0.00 0.00 0.00 5.36
2 3 2.443958 AGGGATAGCTTTCTTTGGCC 57.556 50.000 0.00 0.00 0.00 5.36
3 4 3.886123 TGTAGGGATAGCTTTCTTTGGC 58.114 45.455 4.10 0.00 0.00 4.52
4 5 6.834168 TTTTGTAGGGATAGCTTTCTTTGG 57.166 37.500 4.10 0.00 0.00 3.28
5 6 8.055279 TGATTTTGTAGGGATAGCTTTCTTTG 57.945 34.615 4.10 0.00 0.00 2.77
6 7 8.829373 ATGATTTTGTAGGGATAGCTTTCTTT 57.171 30.769 4.10 0.00 0.00 2.52
12 13 9.554053 AGACTATATGATTTTGTAGGGATAGCT 57.446 33.333 0.00 0.00 0.00 3.32
13 14 9.593134 CAGACTATATGATTTTGTAGGGATAGC 57.407 37.037 0.00 0.00 0.00 2.97
15 16 8.540388 GCCAGACTATATGATTTTGTAGGGATA 58.460 37.037 0.00 0.00 0.00 2.59
16 17 7.238514 AGCCAGACTATATGATTTTGTAGGGAT 59.761 37.037 0.00 0.00 0.00 3.85
17 18 6.558775 AGCCAGACTATATGATTTTGTAGGGA 59.441 38.462 0.00 0.00 0.00 4.20
18 19 6.773638 AGCCAGACTATATGATTTTGTAGGG 58.226 40.000 0.00 0.00 0.00 3.53
19 20 9.376075 CATAGCCAGACTATATGATTTTGTAGG 57.624 37.037 0.00 0.00 39.71 3.18
20 21 8.877779 GCATAGCCAGACTATATGATTTTGTAG 58.122 37.037 5.95 0.00 39.71 2.74
21 22 8.597167 AGCATAGCCAGACTATATGATTTTGTA 58.403 33.333 5.95 0.00 39.71 2.41
22 23 7.456725 AGCATAGCCAGACTATATGATTTTGT 58.543 34.615 5.95 0.00 39.71 2.83
23 24 7.823310 AGAGCATAGCCAGACTATATGATTTTG 59.177 37.037 5.95 0.00 39.71 2.44
24 25 7.915930 AGAGCATAGCCAGACTATATGATTTT 58.084 34.615 5.95 0.00 39.71 1.82
25 26 7.493499 AGAGCATAGCCAGACTATATGATTT 57.507 36.000 5.95 0.00 39.71 2.17
26 27 8.780616 ATAGAGCATAGCCAGACTATATGATT 57.219 34.615 5.95 0.00 39.71 2.57
27 28 8.226810 AGATAGAGCATAGCCAGACTATATGAT 58.773 37.037 5.95 0.63 39.71 2.45
28 29 7.581814 AGATAGAGCATAGCCAGACTATATGA 58.418 38.462 5.95 0.00 39.71 2.15
29 30 7.822161 AGATAGAGCATAGCCAGACTATATG 57.178 40.000 0.00 0.00 39.71 1.78
30 31 9.928618 TTAAGATAGAGCATAGCCAGACTATAT 57.071 33.333 0.00 0.00 39.71 0.86
31 32 9.928618 ATTAAGATAGAGCATAGCCAGACTATA 57.071 33.333 0.00 0.00 39.71 1.31
32 33 8.837099 ATTAAGATAGAGCATAGCCAGACTAT 57.163 34.615 0.00 0.00 42.62 2.12
33 34 7.890655 TGATTAAGATAGAGCATAGCCAGACTA 59.109 37.037 0.00 0.00 34.64 2.59
34 35 6.723515 TGATTAAGATAGAGCATAGCCAGACT 59.276 38.462 0.00 0.00 0.00 3.24
35 36 6.811170 GTGATTAAGATAGAGCATAGCCAGAC 59.189 42.308 0.00 0.00 0.00 3.51
36 37 6.494835 TGTGATTAAGATAGAGCATAGCCAGA 59.505 38.462 0.00 0.00 0.00 3.86
37 38 6.695429 TGTGATTAAGATAGAGCATAGCCAG 58.305 40.000 0.00 0.00 0.00 4.85
38 39 6.670695 TGTGATTAAGATAGAGCATAGCCA 57.329 37.500 0.00 0.00 0.00 4.75
39 40 9.658799 TTTATGTGATTAAGATAGAGCATAGCC 57.341 33.333 0.00 0.00 0.00 3.93
63 64 9.086336 CGAGGTTGTGCATGATTTAAATAATTT 57.914 29.630 0.00 0.00 0.00 1.82
64 65 7.706179 CCGAGGTTGTGCATGATTTAAATAATT 59.294 33.333 0.00 0.00 0.00 1.40
65 66 7.147915 ACCGAGGTTGTGCATGATTTAAATAAT 60.148 33.333 0.00 0.00 0.00 1.28
66 67 6.151985 ACCGAGGTTGTGCATGATTTAAATAA 59.848 34.615 0.00 0.00 0.00 1.40
67 68 5.650266 ACCGAGGTTGTGCATGATTTAAATA 59.350 36.000 0.00 0.00 0.00 1.40
68 69 4.462483 ACCGAGGTTGTGCATGATTTAAAT 59.538 37.500 0.00 0.00 0.00 1.40
69 70 3.823873 ACCGAGGTTGTGCATGATTTAAA 59.176 39.130 0.00 0.00 0.00 1.52
70 71 3.417101 ACCGAGGTTGTGCATGATTTAA 58.583 40.909 0.00 0.00 0.00 1.52
71 72 3.066291 ACCGAGGTTGTGCATGATTTA 57.934 42.857 0.00 0.00 0.00 1.40
72 73 1.909700 ACCGAGGTTGTGCATGATTT 58.090 45.000 0.00 0.00 0.00 2.17
73 74 1.909700 AACCGAGGTTGTGCATGATT 58.090 45.000 6.73 0.00 36.91 2.57
74 75 1.909700 AAACCGAGGTTGTGCATGAT 58.090 45.000 8.43 0.00 38.47 2.45
75 76 2.422597 CTAAACCGAGGTTGTGCATGA 58.577 47.619 8.43 0.00 38.47 3.07
76 77 1.135689 GCTAAACCGAGGTTGTGCATG 60.136 52.381 19.97 0.00 38.47 4.06
77 78 1.165270 GCTAAACCGAGGTTGTGCAT 58.835 50.000 19.97 4.97 38.47 3.96
78 79 0.887387 GGCTAAACCGAGGTTGTGCA 60.887 55.000 23.55 0.00 38.47 4.57
79 80 0.605589 AGGCTAAACCGAGGTTGTGC 60.606 55.000 17.97 17.97 46.52 4.57
80 81 1.156736 CAGGCTAAACCGAGGTTGTG 58.843 55.000 8.43 5.81 46.52 3.33
81 82 0.763035 ACAGGCTAAACCGAGGTTGT 59.237 50.000 8.43 0.00 46.52 3.32
82 83 1.156736 CACAGGCTAAACCGAGGTTG 58.843 55.000 8.43 0.00 46.52 3.77
83 84 0.036306 CCACAGGCTAAACCGAGGTT 59.964 55.000 0.93 0.93 46.52 3.50
84 85 1.125711 ACCACAGGCTAAACCGAGGT 61.126 55.000 0.00 0.00 46.52 3.85
85 86 0.673644 CACCACAGGCTAAACCGAGG 60.674 60.000 0.00 0.00 46.52 4.63
86 87 0.673644 CCACCACAGGCTAAACCGAG 60.674 60.000 0.00 0.00 46.52 4.63
87 88 1.122632 TCCACCACAGGCTAAACCGA 61.123 55.000 0.00 0.00 46.52 4.69
88 89 0.673644 CTCCACCACAGGCTAAACCG 60.674 60.000 0.00 0.00 46.52 4.44
89 90 0.960861 GCTCCACCACAGGCTAAACC 60.961 60.000 0.00 0.00 39.61 3.27
90 91 0.960861 GGCTCCACCACAGGCTAAAC 60.961 60.000 0.00 0.00 38.86 2.01
91 92 1.378762 GGCTCCACCACAGGCTAAA 59.621 57.895 0.00 0.00 38.86 1.85
92 93 1.845664 TGGCTCCACCACAGGCTAA 60.846 57.895 0.00 0.00 46.36 3.09
93 94 2.203922 TGGCTCCACCACAGGCTA 60.204 61.111 0.00 0.00 46.36 3.93
134 135 2.261671 GAACCAGCGAGCTCGGAA 59.738 61.111 35.10 0.00 40.23 4.30
135 136 2.831894 TAGGAACCAGCGAGCTCGGA 62.832 60.000 35.10 1.86 40.23 4.55
139 140 1.394618 CTACTAGGAACCAGCGAGCT 58.605 55.000 0.00 0.00 0.00 4.09
236 237 3.141398 GGCTGTGAACATGAGAGAAACA 58.859 45.455 0.00 0.00 0.00 2.83
247 248 2.064434 TGATTGTTGGGCTGTGAACA 57.936 45.000 0.00 0.00 0.00 3.18
302 318 3.118920 CCCCTTTGTTTCTTTGTTTCGGT 60.119 43.478 0.00 0.00 0.00 4.69
338 354 0.968393 AGAGAGAGTTGGAGCGACCC 60.968 60.000 0.00 0.00 38.00 4.46
380 396 9.420118 GAGAGAGAGAGAGAGAGATAGATAGAT 57.580 40.741 0.00 0.00 0.00 1.98
381 397 8.619281 AGAGAGAGAGAGAGAGAGATAGATAGA 58.381 40.741 0.00 0.00 0.00 1.98
382 398 8.821686 AGAGAGAGAGAGAGAGAGATAGATAG 57.178 42.308 0.00 0.00 0.00 2.08
383 399 8.619281 AGAGAGAGAGAGAGAGAGAGATAGATA 58.381 40.741 0.00 0.00 0.00 1.98
384 400 7.477864 AGAGAGAGAGAGAGAGAGAGATAGAT 58.522 42.308 0.00 0.00 0.00 1.98
388 406 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
471 489 0.325296 TCTAGGGTTCATCCGCCACT 60.325 55.000 0.00 0.00 37.00 4.00
581 601 1.153549 GAAGCTGATCCGAAGCCGT 60.154 57.895 0.14 0.00 41.82 5.68
602 628 1.274167 TCGCTGGAGATTTGTTACCGT 59.726 47.619 0.00 0.00 0.00 4.83
609 635 4.035675 GGACCTAAATTCGCTGGAGATTTG 59.964 45.833 0.00 0.00 0.00 2.32
619 645 3.809905 AGATCCTTGGACCTAAATTCGC 58.190 45.455 0.00 0.00 0.00 4.70
655 681 6.443849 TCCTACTTCCCAGACAAACTATTCAT 59.556 38.462 0.00 0.00 0.00 2.57
665 691 4.341235 CGTATCAATCCTACTTCCCAGACA 59.659 45.833 0.00 0.00 0.00 3.41
686 720 3.493877 CAGTATCTCGATCCGTACTTCGT 59.506 47.826 8.82 0.00 36.74 3.85
762 796 0.398948 CCCCCAATGATTTCCCCCTG 60.399 60.000 0.00 0.00 0.00 4.45
859 897 1.386525 CCACAGTGTGCAAGTTGCCT 61.387 55.000 24.59 12.00 44.23 4.75
871 909 7.424227 AAAAATTTGCATGAATACCACAGTG 57.576 32.000 0.00 0.00 0.00 3.66
936 976 4.003648 GAGCTACAACTGGCTACAACAAT 58.996 43.478 0.00 0.00 39.05 2.71
1023 1063 3.797451 TTCACATTTTCAGTGCTTGCA 57.203 38.095 0.00 0.00 36.93 4.08
1057 1097 3.477530 GTTGTGCCTCCACTTCTACTTT 58.522 45.455 0.00 0.00 42.54 2.66
1060 1100 1.071699 TGGTTGTGCCTCCACTTCTAC 59.928 52.381 0.00 0.00 42.54 2.59
1191 1231 7.416213 GCTTGCATTGTACCCTTCAATACATAA 60.416 37.037 0.00 0.00 34.34 1.90
1207 1247 6.694447 ACTTATTCAAATCTGCTTGCATTGT 58.306 32.000 0.00 0.00 0.00 2.71
1216 1256 7.809806 AGTACAAGCAAACTTATTCAAATCTGC 59.190 33.333 0.00 0.00 33.74 4.26
1230 1270 8.642908 AACTTCCAAATTTAGTACAAGCAAAC 57.357 30.769 0.00 0.00 0.00 2.93
1234 1274 8.082242 ACATGAACTTCCAAATTTAGTACAAGC 58.918 33.333 0.00 0.00 0.00 4.01
1258 1298 6.552859 TTTAGAAAATGCTCGTGATGAACA 57.447 33.333 0.00 0.00 0.00 3.18
1267 1307 7.072177 TGTACCAAGATTTAGAAAATGCTCG 57.928 36.000 0.00 0.00 0.00 5.03
1333 1373 7.955918 AGGAGAAAGCAATGAAAACAATAAGT 58.044 30.769 0.00 0.00 0.00 2.24
1357 1397 1.177401 GCCCTTCCAGGTTGCTTAAG 58.823 55.000 0.00 0.00 31.93 1.85
1466 1506 3.813166 GCAAGAGTTGTGCTTACTACCAA 59.187 43.478 0.00 0.00 39.00 3.67
1595 1635 9.254133 CGATGAGATATCTTGAACAACTTACAT 57.746 33.333 6.70 0.98 0.00 2.29
1643 1683 5.654650 AGAGAAGTAGAGGATTCGTCATGTT 59.345 40.000 8.91 0.00 0.00 2.71
1709 1751 7.446625 AGCATCTCTCACTTGTTCATTTTTAGT 59.553 33.333 0.00 0.00 0.00 2.24
1741 1783 1.263217 GTGCAATTTCTTCGACCACGT 59.737 47.619 0.00 0.00 40.69 4.49
1748 1790 4.560035 GGATGTCATTGTGCAATTTCTTCG 59.440 41.667 0.00 0.00 0.00 3.79
1772 1814 3.070018 CGAGCTCCTTTTGAATGTCACT 58.930 45.455 8.47 0.00 0.00 3.41
1837 1880 8.049117 AGCATAGAGAATTGTTTATCACCAAGA 58.951 33.333 0.00 0.00 0.00 3.02
1989 2033 7.829725 TCCTTTGTCATTCAAAATCCTATGTG 58.170 34.615 0.00 0.00 44.08 3.21
1991 2037 9.362539 CTTTCCTTTGTCATTCAAAATCCTATG 57.637 33.333 0.00 0.00 44.08 2.23
1997 2043 7.280652 CACAACCTTTCCTTTGTCATTCAAAAT 59.719 33.333 0.00 0.00 44.08 1.82
2130 2176 2.754186 GCACCATCATATCCTTGCCCTT 60.754 50.000 0.00 0.00 0.00 3.95
2157 2203 6.690194 AAGCATTAAACTTGCCTCTCATAG 57.310 37.500 0.00 0.00 41.06 2.23
2374 2421 6.927936 TCTCAAGTCTATGCAGAATATCTTGC 59.072 38.462 0.00 4.83 35.21 4.01
2504 2551 4.412843 TGTAACACAGAGGACCACATCTA 58.587 43.478 0.00 0.00 35.33 1.98
2506 2553 3.678056 TGTAACACAGAGGACCACATC 57.322 47.619 0.00 0.00 0.00 3.06
2649 2699 5.152804 GCAAGACTTTTGAGAGCTCATTTC 58.847 41.667 17.77 5.44 39.64 2.17
2681 2731 9.737844 TTCTATGGCATGCACAATATTAAGATA 57.262 29.630 21.36 0.96 0.00 1.98
2697 2747 6.787170 ACATCATCCACTAATTCTATGGCAT 58.213 36.000 4.88 4.88 33.20 4.40
2704 2754 6.421485 AGCTTTGACATCATCCACTAATTCT 58.579 36.000 0.00 0.00 0.00 2.40
2732 2782 6.038997 ACCACTCTCTCTTAATGTTACCAC 57.961 41.667 0.00 0.00 0.00 4.16
2736 2786 5.783360 TCCCAACCACTCTCTCTTAATGTTA 59.217 40.000 0.00 0.00 0.00 2.41
2859 2909 6.325286 GTGAAGATTAGTGATAGTCCTCCCTT 59.675 42.308 0.00 0.00 0.00 3.95
3058 3108 5.007039 ACGATCATCATTGGAAAAGTCATCG 59.993 40.000 0.00 0.00 0.00 3.84
3099 3149 8.695456 TCACATGACTTATATAAGTGAGAAGCA 58.305 33.333 28.61 19.65 45.84 3.91
3121 3171 6.819284 AGAAAAAGAATCATGCCTTTTCACA 58.181 32.000 15.56 0.00 40.49 3.58
3172 3222 4.651778 TCTCCGTTTCAACCATCTTCATT 58.348 39.130 0.00 0.00 0.00 2.57
3281 3331 6.939132 AGTCTTGATAATCTTCATTGCTGG 57.061 37.500 0.00 0.00 0.00 4.85
3338 3388 8.877808 TCAGTGTAACATATCATCAAGTCATC 57.122 34.615 0.00 0.00 41.43 2.92
3361 3411 2.565391 TGACTTGAATAACTCCCGCTCA 59.435 45.455 0.00 0.00 0.00 4.26
3441 3491 5.739161 GTGCACTAAAGAAAATTATGAGGCG 59.261 40.000 10.32 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.