Multiple sequence alignment - TraesCS4A01G260900

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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 TraesCS4A01G260900 chr4A 100.000 4170 0 0 1 4170 573329349 573325180 0.000000e+00 7701.0
1 TraesCS4A01G260900 chr4A 87.324 71 9 0 2372 2442 66338811 66338881 9.610000e-12 82.4
2 TraesCS4A01G260900 chr4B 92.721 1937 102 17 1364 3286 42394487 42396398 0.000000e+00 2760.0
3 TraesCS4A01G260900 chr4B 90.284 844 37 14 3347 4170 42396402 42397220 0.000000e+00 1062.0
4 TraesCS4A01G260900 chr4B 90.160 437 24 7 940 1360 42394013 42394446 6.090000e-153 551.0
5 TraesCS4A01G260900 chr4B 86.686 353 17 12 466 805 42393437 42393772 8.520000e-97 364.0
6 TraesCS4A01G260900 chr4B 100.000 47 0 0 802 848 42393843 42393889 2.070000e-13 87.9
7 TraesCS4A01G260900 chr4B 76.087 184 31 11 2372 2547 471653037 471653215 2.670000e-12 84.2
8 TraesCS4A01G260900 chr4D 95.594 1430 55 4 1860 3281 29828029 29829458 0.000000e+00 2285.0
9 TraesCS4A01G260900 chr4D 96.790 623 15 3 3548 4170 29829815 29830432 0.000000e+00 1035.0
10 TraesCS4A01G260900 chr4D 89.541 784 73 5 1 776 29826122 29826904 0.000000e+00 985.0
11 TraesCS4A01G260900 chr4D 85.833 600 40 26 789 1360 29826972 29827554 2.780000e-166 595.0
12 TraesCS4A01G260900 chr4D 89.461 427 35 4 1364 1790 29827592 29828008 7.940000e-147 531.0
13 TraesCS4A01G260900 chr4D 76.630 184 30 11 2372 2547 384670697 384670875 5.740000e-14 89.8
14 TraesCS4A01G260900 chr1D 84.634 423 59 5 1 418 47844142 47844563 2.320000e-112 416.0
15 TraesCS4A01G260900 chr2B 85.503 338 47 2 1 338 712964499 712964164 6.630000e-93 351.0
16 TraesCS4A01G260900 chrUn 76.510 298 50 15 2361 2645 194663653 194663943 1.210000e-30 145.0
17 TraesCS4A01G260900 chr7A 75.667 300 49 21 2361 2645 35628575 35628865 1.220000e-25 128.0
18 TraesCS4A01G260900 chr7D 77.315 216 38 7 46 250 580031887 580031672 2.630000e-22 117.0
19 TraesCS4A01G260900 chr3A 76.500 200 38 7 14 205 226391708 226391906 2.650000e-17 100.0


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 TraesCS4A01G260900 chr4A 573325180 573329349 4169 True 7701.00 7701 100.0000 1 4170 1 chr4A.!!$R1 4169
1 TraesCS4A01G260900 chr4B 42393437 42397220 3783 False 964.98 2760 91.9702 466 4170 5 chr4B.!!$F2 3704
2 TraesCS4A01G260900 chr4D 29826122 29830432 4310 False 1086.20 2285 91.4438 1 4170 5 chr4D.!!$F2 4169

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
346 347 0.042188 ACGAATTATGATGCGCACGC 60.042 50.0 14.9 9.02 37.87 5.34 F
348 349 0.232046 GAATTATGATGCGCACGCGA 59.768 50.0 14.9 0.00 45.51 5.87 F
559 562 0.324738 ACCTCGATCCTGAGCCTGAA 60.325 55.0 0.0 0.00 34.56 3.02 F
1294 1447 0.539051 CCTTCCTACTGCCACTGGAG 59.461 60.0 0.0 0.00 0.00 3.86 F
2958 3151 0.471780 TCACTCTGTCTGCCCTTGGA 60.472 55.0 0.0 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1282 1434 0.107312 GATGATGCTCCAGTGGCAGT 60.107 55.000 3.51 0.0 43.15 4.40 R
1857 2050 0.177604 ACGTGTCCCACCGTTAACAA 59.822 50.000 6.39 0.0 0.00 2.83 R
1858 2051 0.530211 CACGTGTCCCACCGTTAACA 60.530 55.000 7.58 0.0 0.00 2.41 R
3121 3316 0.469705 AAGCAAACACATGGAGGGCA 60.470 50.000 0.00 0.0 0.00 5.36 R
3772 4138 1.880027 CCTCAACCTAACCTTGTGTGC 59.120 52.381 0.00 0.0 0.00 4.57 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
70 71 2.104331 CACCTACAGCTACGCCGG 59.896 66.667 0.00 0.00 0.00 6.13
72 73 3.833645 CCTACAGCTACGCCGGCA 61.834 66.667 28.98 6.80 0.00 5.69
74 75 1.227263 CTACAGCTACGCCGGCAAT 60.227 57.895 28.98 16.86 0.00 3.56
89 90 1.667154 GCAATCGGAAGGGGAAAGGC 61.667 60.000 0.00 0.00 0.00 4.35
108 109 1.301401 CCGGCGAAGAAGTGGTGAA 60.301 57.895 9.30 0.00 0.00 3.18
120 121 0.980423 GTGGTGAAGAAGCTCCCTCT 59.020 55.000 0.00 0.00 0.00 3.69
123 124 3.008049 GTGGTGAAGAAGCTCCCTCTTAA 59.992 47.826 0.00 0.00 0.00 1.85
126 127 4.500127 GTGAAGAAGCTCCCTCTTAAGTC 58.500 47.826 1.63 0.00 0.00 3.01
129 130 6.017192 TGAAGAAGCTCCCTCTTAAGTCTAA 58.983 40.000 1.63 0.00 0.00 2.10
181 182 2.416547 CGATGAACTGCGGTGATCTTTT 59.583 45.455 0.00 0.00 0.00 2.27
202 203 9.589461 TCTTTTGGATAATGTAAAGTGGGTTTA 57.411 29.630 0.00 0.00 0.00 2.01
208 209 8.082242 GGATAATGTAAAGTGGGTTTATGCATC 58.918 37.037 0.19 0.00 33.11 3.91
216 217 4.641989 AGTGGGTTTATGCATCTCATTGTC 59.358 41.667 0.19 0.00 36.63 3.18
217 218 3.627123 TGGGTTTATGCATCTCATTGTCG 59.373 43.478 0.19 0.00 36.63 4.35
231 232 4.000325 TCATTGTCGGTTTGATGTCGATT 59.000 39.130 0.00 0.00 35.35 3.34
233 234 4.398549 TTGTCGGTTTGATGTCGATTTC 57.601 40.909 0.00 0.00 35.35 2.17
239 240 5.008217 TCGGTTTGATGTCGATTTCTTTGTT 59.992 36.000 0.00 0.00 0.00 2.83
250 251 6.413818 GTCGATTTCTTTGTTCGTTGTTTGAT 59.586 34.615 0.00 0.00 34.60 2.57
255 256 4.093703 TCTTTGTTCGTTGTTTGATCACGT 59.906 37.500 0.00 0.00 0.00 4.49
259 260 4.026393 TGTTCGTTGTTTGATCACGTACAG 60.026 41.667 9.86 0.22 32.27 2.74
261 262 4.857799 TCGTTGTTTGATCACGTACAGTA 58.142 39.130 0.00 0.00 0.00 2.74
267 268 7.716768 TGTTTGATCACGTACAGTATTTCAA 57.283 32.000 0.00 0.79 0.00 2.69
269 270 6.384178 TTGATCACGTACAGTATTTCAACG 57.616 37.500 0.00 0.00 39.37 4.10
279 280 1.317319 GTATTTCAACGCGTTGCATGC 59.683 47.619 39.77 31.19 40.24 4.06
314 315 6.983906 ATATGATGCCGGATATGAGATACA 57.016 37.500 5.05 0.00 0.00 2.29
322 323 4.082190 CCGGATATGAGATACACGGATGTT 60.082 45.833 0.00 0.00 40.48 2.71
323 324 4.859245 CGGATATGAGATACACGGATGTTG 59.141 45.833 0.00 0.00 40.48 3.33
325 326 6.625960 CGGATATGAGATACACGGATGTTGAT 60.626 42.308 0.00 0.00 40.48 2.57
327 328 8.251026 GGATATGAGATACACGGATGTTGATAA 58.749 37.037 0.00 0.00 40.48 1.75
332 333 6.513180 AGATACACGGATGTTGATAACGAAT 58.487 36.000 0.00 0.00 40.48 3.34
335 336 8.827177 ATACACGGATGTTGATAACGAATTAT 57.173 30.769 0.00 0.00 40.48 1.28
343 344 5.007136 TGTTGATAACGAATTATGATGCGCA 59.993 36.000 14.96 14.96 37.87 6.09
345 346 2.367399 AACGAATTATGATGCGCACG 57.633 45.000 14.90 12.24 37.87 5.34
346 347 0.042188 ACGAATTATGATGCGCACGC 60.042 50.000 14.90 9.02 37.87 5.34
348 349 0.232046 GAATTATGATGCGCACGCGA 59.768 50.000 14.90 0.00 45.51 5.87
365 366 1.805945 GATCAGTGTCCGTGTCCGC 60.806 63.158 0.00 0.00 0.00 5.54
395 396 3.059386 GGCCGAATTTGCCCGTCA 61.059 61.111 8.39 0.00 43.33 4.35
397 398 2.478746 CCGAATTTGCCCGTCACG 59.521 61.111 0.00 0.00 0.00 4.35
399 400 2.178273 GAATTTGCCCGTCACGGC 59.822 61.111 12.05 7.27 46.86 5.68
416 417 1.300233 GCCGGAGATGCTCTAACGG 60.300 63.158 5.05 16.96 44.76 4.44
423 424 3.570550 GGAGATGCTCTAACGGAGTACAT 59.429 47.826 0.00 0.00 45.00 2.29
424 425 4.541779 GAGATGCTCTAACGGAGTACATG 58.458 47.826 0.00 0.00 45.00 3.21
441 442 1.938577 CATGATGAGCGTTTGAGAGGG 59.061 52.381 0.00 0.00 0.00 4.30
513 516 3.615110 GCATCCAGGTAGATACATCACCG 60.615 52.174 0.00 0.00 34.96 4.94
514 517 3.588210 TCCAGGTAGATACATCACCGA 57.412 47.619 0.00 0.00 34.96 4.69
522 525 4.963318 AGATACATCACCGATTCACCAT 57.037 40.909 0.00 0.00 0.00 3.55
529 532 0.461339 ACCGATTCACCATGTACGGC 60.461 55.000 0.00 0.00 43.36 5.68
559 562 0.324738 ACCTCGATCCTGAGCCTGAA 60.325 55.000 0.00 0.00 34.56 3.02
563 566 1.667154 CGATCCTGAGCCTGAACCGA 61.667 60.000 0.00 0.00 0.00 4.69
569 572 1.153147 GAGCCTGAACCGAATCCCC 60.153 63.158 0.00 0.00 0.00 4.81
657 662 1.741394 CGGGTCGGGTAGTTCAAATCC 60.741 57.143 0.00 0.00 0.00 3.01
684 689 1.610327 GGCTCCTTCCTTCCTTCCC 59.390 63.158 0.00 0.00 0.00 3.97
685 690 1.222113 GCTCCTTCCTTCCTTCCCG 59.778 63.158 0.00 0.00 0.00 5.14
765 779 0.598419 GCTTTCCGCTTTGCTTGCTT 60.598 50.000 0.00 0.00 35.14 3.91
778 792 1.004161 GCTTGCTTCCTCTTTCTCCCT 59.996 52.381 0.00 0.00 0.00 4.20
779 793 2.939198 GCTTGCTTCCTCTTTCTCCCTC 60.939 54.545 0.00 0.00 0.00 4.30
780 794 1.280457 TGCTTCCTCTTTCTCCCTCC 58.720 55.000 0.00 0.00 0.00 4.30
850 947 1.552337 AGCTCAACTCACATCATCCGT 59.448 47.619 0.00 0.00 0.00 4.69
880 998 2.803956 CACACCACCACTAGTTAAACCG 59.196 50.000 0.00 0.00 0.00 4.44
881 999 1.802365 CACCACCACTAGTTAAACCGC 59.198 52.381 0.00 0.00 0.00 5.68
882 1000 1.417145 ACCACCACTAGTTAAACCGCA 59.583 47.619 0.00 0.00 0.00 5.69
883 1001 2.073816 CCACCACTAGTTAAACCGCAG 58.926 52.381 0.00 0.00 0.00 5.18
884 1002 1.463444 CACCACTAGTTAAACCGCAGC 59.537 52.381 0.00 0.00 0.00 5.25
956 1092 2.202756 GTACGAGGAAGCGGGCAG 60.203 66.667 0.00 0.00 35.12 4.85
976 1112 0.610687 AAGGGACAAGAAGAGCTCGG 59.389 55.000 8.37 0.00 0.00 4.63
985 1121 2.852431 GAAGAGCTCGGTCGACCACG 62.852 65.000 32.80 22.96 41.26 4.94
1056 1207 2.386660 GCTCTTGCTGCTCGTCCAC 61.387 63.158 0.00 0.00 36.03 4.02
1075 1226 0.671796 CGTCCCGTATGCTGGTATGA 59.328 55.000 0.00 0.00 0.00 2.15
1197 1348 3.069586 TCGACTTTGGAAGCTTCTTCTCA 59.930 43.478 25.05 12.27 0.00 3.27
1282 1434 4.962995 AGATGTTCGATTCCTTCCTTCCTA 59.037 41.667 0.00 0.00 0.00 2.94
1294 1447 0.539051 CCTTCCTACTGCCACTGGAG 59.461 60.000 0.00 0.00 0.00 3.86
1309 1462 1.629353 CTGGAGCATCATCATAGCCCT 59.371 52.381 0.00 0.00 36.25 5.19
1310 1463 1.350019 TGGAGCATCATCATAGCCCTG 59.650 52.381 0.00 0.00 36.25 4.45
1311 1464 1.627329 GGAGCATCATCATAGCCCTGA 59.373 52.381 0.00 0.00 36.25 3.86
1362 1515 7.894708 GGTAGTGTACCTTTTCTTCTTCTACT 58.105 38.462 0.00 0.00 45.52 2.57
1365 1555 8.252624 AGTGTACCTTTTCTTCTTCTACTTCT 57.747 34.615 0.00 0.00 0.00 2.85
1370 1560 7.574607 ACCTTTTCTTCTTCTACTTCTTGGAA 58.425 34.615 0.00 0.00 0.00 3.53
1372 1562 8.510505 CCTTTTCTTCTTCTACTTCTTGGAATG 58.489 37.037 0.00 0.00 0.00 2.67
1410 1600 8.386264 ACAGGGTAACTAAGTACTAGTAACTGA 58.614 37.037 3.61 0.00 40.14 3.41
1486 1676 1.336887 CCTTCGTGTCGACATGGTTCT 60.337 52.381 31.76 0.00 34.89 3.01
1518 1708 2.162681 GGGAAAGAATGTGGGTGACAG 58.837 52.381 0.00 0.00 38.23 3.51
1543 1736 7.604164 AGTGAAATGAACCTACTTACATCTGTG 59.396 37.037 0.00 0.00 0.00 3.66
1581 1774 0.593128 GCTCTCAACCGTGCAACATT 59.407 50.000 0.00 0.00 35.74 2.71
1583 1776 1.603802 CTCTCAACCGTGCAACATTGT 59.396 47.619 0.00 0.00 34.95 2.71
1584 1777 1.601903 TCTCAACCGTGCAACATTGTC 59.398 47.619 0.00 0.00 34.95 3.18
1586 1779 1.745653 TCAACCGTGCAACATTGTCAA 59.254 42.857 0.00 0.00 34.95 3.18
1587 1780 1.851666 CAACCGTGCAACATTGTCAAC 59.148 47.619 0.00 0.00 35.74 3.18
1588 1781 1.098869 ACCGTGCAACATTGTCAACA 58.901 45.000 0.00 0.00 35.74 3.33
1589 1782 1.474478 ACCGTGCAACATTGTCAACAA 59.526 42.857 0.00 0.00 40.51 2.83
1590 1783 2.100584 ACCGTGCAACATTGTCAACAAT 59.899 40.909 2.53 2.53 46.62 2.71
1591 1784 3.122297 CCGTGCAACATTGTCAACAATT 58.878 40.909 5.64 0.00 43.48 2.32
1592 1785 3.182173 CCGTGCAACATTGTCAACAATTC 59.818 43.478 5.64 0.00 43.48 2.17
1593 1786 3.121729 CGTGCAACATTGTCAACAATTCG 60.122 43.478 5.64 0.00 43.48 3.34
1634 1827 2.368980 GCGCACTCGTGATAAAATCC 57.631 50.000 0.30 0.00 38.14 3.01
1640 1833 4.026804 GCACTCGTGATAAAATCCTACGTG 60.027 45.833 0.00 0.00 36.28 4.49
1699 1892 0.666577 GCTGTACCGACCTGACACAC 60.667 60.000 0.00 0.00 0.00 3.82
1717 1910 6.128117 TGACACACTTTGTTTTCCAAGTCTAC 60.128 38.462 0.00 0.00 39.17 2.59
1738 1931 8.935844 GTCTACCCATTTGAAATTTTGAATTCC 58.064 33.333 2.27 0.00 0.00 3.01
1783 1976 6.724263 TCACAAGTTTATTTACTGTGCAGTG 58.276 36.000 14.44 0.00 42.52 3.66
1790 1983 7.387948 AGTTTATTTACTGTGCAGTGACCTTAG 59.612 37.037 14.44 0.00 42.52 2.18
1791 1984 3.678056 TTACTGTGCAGTGACCTTAGG 57.322 47.619 14.44 0.00 42.52 2.69
1792 1985 1.717032 ACTGTGCAGTGACCTTAGGA 58.283 50.000 4.77 0.00 40.75 2.94
1793 1986 1.620819 ACTGTGCAGTGACCTTAGGAG 59.379 52.381 4.77 0.00 40.75 3.69
1814 2007 5.449177 GGAGTGCATTTTGCCAACTATACTC 60.449 44.000 0.00 0.00 44.23 2.59
1816 2009 5.653769 AGTGCATTTTGCCAACTATACTCAT 59.346 36.000 0.00 0.00 44.23 2.90
1817 2010 5.745294 GTGCATTTTGCCAACTATACTCATG 59.255 40.000 0.00 0.00 44.23 3.07
1818 2011 5.418524 TGCATTTTGCCAACTATACTCATGT 59.581 36.000 0.00 0.00 44.23 3.21
1820 2013 6.254157 GCATTTTGCCAACTATACTCATGTTG 59.746 38.462 0.00 0.00 37.42 3.33
1821 2014 6.892658 TTTTGCCAACTATACTCATGTTGT 57.107 33.333 0.00 0.00 39.30 3.32
1822 2015 6.892658 TTTGCCAACTATACTCATGTTGTT 57.107 33.333 0.00 0.00 39.30 2.83
1823 2016 6.892658 TTGCCAACTATACTCATGTTGTTT 57.107 33.333 0.00 0.00 39.30 2.83
1824 2017 7.987750 TTGCCAACTATACTCATGTTGTTTA 57.012 32.000 0.00 0.00 39.30 2.01
1826 2019 7.165485 TGCCAACTATACTCATGTTGTTTACT 58.835 34.615 0.00 0.00 39.30 2.24
2086 2279 2.721167 CGACATCCCCTCCTTCGCA 61.721 63.158 0.00 0.00 0.00 5.10
2140 2333 3.450115 CACCTCCCGTCGTCCTCC 61.450 72.222 0.00 0.00 0.00 4.30
2278 2471 2.390599 CGGCATCAAGGTGTCCACG 61.391 63.158 0.00 0.00 0.00 4.94
2440 2633 4.139234 GCGTACCAGGACGACCCC 62.139 72.222 6.60 0.00 45.82 4.95
2441 2634 2.677524 CGTACCAGGACGACCCCA 60.678 66.667 0.00 0.00 45.82 4.96
2803 2996 1.153804 GTCGGAGAAGTCCTTCGGC 60.154 63.158 1.59 0.00 44.04 5.54
2806 2999 1.518302 GGAGAAGTCCTTCGGCCTC 59.482 63.158 0.00 0.00 43.97 4.70
2809 3002 1.276705 GAGAAGTCCTTCGGCCTCTTT 59.723 52.381 0.00 0.00 43.97 2.52
2958 3151 0.471780 TCACTCTGTCTGCCCTTGGA 60.472 55.000 0.00 0.00 0.00 3.53
3165 3360 1.467734 CTTGTTCATGTCTCTGCTGGC 59.532 52.381 0.00 0.00 0.00 4.85
3176 3371 2.530151 TGCTGGCCTGACCTTCCT 60.530 61.111 14.77 0.00 40.22 3.36
3247 3442 3.191162 TCTGCTCATATGTGGTTTTGCAC 59.809 43.478 1.90 0.00 0.00 4.57
3251 3454 4.726416 CTCATATGTGGTTTTGCACTGTC 58.274 43.478 1.90 0.00 0.00 3.51
3258 3461 2.024414 GGTTTTGCACTGTCCAACTCT 58.976 47.619 0.00 0.00 0.00 3.24
3325 3674 5.922053 ACCCTAGTTCGTTAAAGAAACAGT 58.078 37.500 5.37 0.00 38.03 3.55
3326 3675 5.756833 ACCCTAGTTCGTTAAAGAAACAGTG 59.243 40.000 5.37 0.94 38.03 3.66
3327 3676 5.756833 CCCTAGTTCGTTAAAGAAACAGTGT 59.243 40.000 5.37 0.00 38.03 3.55
3328 3677 6.925165 CCCTAGTTCGTTAAAGAAACAGTGTA 59.075 38.462 5.37 0.00 38.03 2.90
3339 3688 6.959639 AAGAAACAGTGTACCAACATCAAT 57.040 33.333 0.00 0.00 38.08 2.57
3345 3694 5.239306 ACAGTGTACCAACATCAATGACAAG 59.761 40.000 0.00 0.00 38.08 3.16
3356 3705 2.028476 TCAATGACAAGGTAGGGACACG 60.028 50.000 0.00 0.00 0.00 4.49
3368 3717 1.509463 GGACACGCCGACAGTCATA 59.491 57.895 0.41 0.00 34.04 2.15
3369 3718 0.525668 GGACACGCCGACAGTCATAG 60.526 60.000 0.41 0.00 34.04 2.23
3404 3761 5.480642 AGAATCATCATCCGAAGCATACT 57.519 39.130 0.00 0.00 0.00 2.12
3405 3762 5.236282 AGAATCATCATCCGAAGCATACTG 58.764 41.667 0.00 0.00 0.00 2.74
3436 3793 7.591006 TTTGTTGGCGTACAAATAACAAAAA 57.409 28.000 17.61 3.70 43.84 1.94
3486 3843 2.224159 CCAGGCCCTACACACTGGT 61.224 63.158 0.00 0.00 44.21 4.00
3523 3880 2.295349 AGAAACAACAATCTGCAGGCAG 59.705 45.455 15.13 14.97 44.86 4.85
3597 3954 5.425217 TCTCAGCATACCACCATCTTAGAAA 59.575 40.000 0.00 0.00 0.00 2.52
3628 3988 1.403249 GCAAAGGCAGCATCGAACAAT 60.403 47.619 0.00 0.00 40.72 2.71
3772 4138 2.286872 CTCCACCTGCAGCATAAGAAG 58.713 52.381 8.66 0.00 0.00 2.85
3789 4155 3.214328 AGAAGCACACAAGGTTAGGTTG 58.786 45.455 0.00 0.00 0.00 3.77
3953 4319 0.462047 AGCCGAAGTAATGGAAGCGG 60.462 55.000 0.00 0.00 41.51 5.52
3961 4327 0.546122 TAATGGAAGCGGCCAGTGAT 59.454 50.000 2.24 0.00 42.15 3.06
4134 4503 3.314553 ACACTTTTAGACCGATGACACG 58.685 45.455 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.005539 GAGGAGGTGGAGCTGCCA 61.006 66.667 1.53 1.36 46.96 4.92
70 71 1.667154 GCCTTTCCCCTTCCGATTGC 61.667 60.000 0.00 0.00 0.00 3.56
72 73 1.306633 GGCCTTTCCCCTTCCGATT 59.693 57.895 0.00 0.00 0.00 3.34
89 90 2.725203 TTCACCACTTCTTCGCCGGG 62.725 60.000 2.18 0.00 0.00 5.73
93 94 1.195674 GCTTCTTCACCACTTCTTCGC 59.804 52.381 0.00 0.00 0.00 4.70
97 98 1.349357 GGGAGCTTCTTCACCACTTCT 59.651 52.381 0.00 0.00 0.00 2.85
108 109 8.791298 ATAATTAGACTTAAGAGGGAGCTTCT 57.209 34.615 10.09 1.38 0.00 2.85
181 182 6.892456 TGCATAAACCCACTTTACATTATCCA 59.108 34.615 0.00 0.00 0.00 3.41
202 203 3.346315 TCAAACCGACAATGAGATGCAT 58.654 40.909 0.00 0.00 39.43 3.96
208 209 2.993220 TCGACATCAAACCGACAATGAG 59.007 45.455 0.00 0.00 0.00 2.90
216 217 4.783242 ACAAAGAAATCGACATCAAACCG 58.217 39.130 0.00 0.00 0.00 4.44
217 218 5.339611 CGAACAAAGAAATCGACATCAAACC 59.660 40.000 0.00 0.00 38.82 3.27
231 232 5.025190 CGTGATCAAACAACGAACAAAGAA 58.975 37.500 0.00 0.00 0.00 2.52
233 234 4.339429 ACGTGATCAAACAACGAACAAAG 58.661 39.130 9.36 0.00 0.00 2.77
239 240 3.708890 ACTGTACGTGATCAAACAACGA 58.291 40.909 9.36 0.00 0.00 3.85
250 251 2.657848 CGCGTTGAAATACTGTACGTGA 59.342 45.455 0.00 0.00 43.19 4.35
255 256 2.801111 TGCAACGCGTTGAAATACTGTA 59.199 40.909 45.98 21.36 42.93 2.74
259 260 1.317319 GCATGCAACGCGTTGAAATAC 59.683 47.619 45.98 30.36 42.93 1.89
261 262 2.433637 GCATGCAACGCGTTGAAAT 58.566 47.368 45.98 35.08 42.93 2.17
279 280 3.737774 CGGCATCATATATCCATGCTACG 59.262 47.826 19.09 13.84 42.24 3.51
280 281 4.060900 CCGGCATCATATATCCATGCTAC 58.939 47.826 19.09 8.31 42.24 3.58
284 285 6.704310 TCATATCCGGCATCATATATCCATG 58.296 40.000 0.00 0.00 0.00 3.66
294 295 3.119495 CGTGTATCTCATATCCGGCATCA 60.119 47.826 0.00 0.00 0.00 3.07
314 315 7.571244 GCATCATAATTCGTTATCAACATCCGT 60.571 37.037 0.00 0.00 0.00 4.69
322 323 4.375908 CGTGCGCATCATAATTCGTTATCA 60.376 41.667 15.91 0.00 0.00 2.15
323 324 4.074949 CGTGCGCATCATAATTCGTTATC 58.925 43.478 15.91 0.00 0.00 1.75
325 326 2.348125 GCGTGCGCATCATAATTCGTTA 60.348 45.455 15.91 0.00 41.49 3.18
327 328 0.042188 GCGTGCGCATCATAATTCGT 60.042 50.000 15.91 0.00 41.49 3.85
332 333 0.873743 TGATCGCGTGCGCATCATAA 60.874 50.000 15.91 0.00 42.06 1.90
335 336 3.256833 CTGATCGCGTGCGCATCA 61.257 61.111 15.91 12.33 42.06 3.07
343 344 2.126463 CACGGACACTGATCGCGT 60.126 61.111 5.77 0.00 0.00 6.01
345 346 1.805945 GGACACGGACACTGATCGC 60.806 63.158 0.00 0.00 0.00 4.58
346 347 1.514228 CGGACACGGACACTGATCG 60.514 63.158 0.00 0.00 36.18 3.69
348 349 2.261671 GCGGACACGGACACTGAT 59.738 61.111 0.00 0.00 41.36 2.90
368 369 1.873270 AAATTCGGCCTCCCAAACGC 61.873 55.000 0.00 0.00 0.00 4.84
416 417 4.424626 TCTCAAACGCTCATCATGTACTC 58.575 43.478 0.00 0.00 0.00 2.59
419 420 3.430790 CCCTCTCAAACGCTCATCATGTA 60.431 47.826 0.00 0.00 0.00 2.29
423 424 0.391661 GCCCTCTCAAACGCTCATCA 60.392 55.000 0.00 0.00 0.00 3.07
424 425 1.424493 CGCCCTCTCAAACGCTCATC 61.424 60.000 0.00 0.00 0.00 2.92
441 442 2.278142 GCACGATGGCAAATCCGC 60.278 61.111 0.00 0.00 37.80 5.54
452 453 4.373727 TGTCCTCTGTGTTAGAGCACGAT 61.374 47.826 0.00 0.00 45.52 3.73
513 516 1.014352 GTGGCCGTACATGGTGAATC 58.986 55.000 0.00 0.00 0.00 2.52
514 517 0.393808 GGTGGCCGTACATGGTGAAT 60.394 55.000 0.00 0.00 0.00 2.57
559 562 2.041301 TGGGATCGGGGATTCGGT 60.041 61.111 0.00 0.00 0.00 4.69
563 566 2.043772 TGGGTGGGATCGGGGATT 59.956 61.111 0.00 0.00 0.00 3.01
569 572 4.530857 GCTCCGTGGGTGGGATCG 62.531 72.222 0.00 0.00 31.99 3.69
765 779 1.396594 GGGGGAGGGAGAAAGAGGA 59.603 63.158 0.00 0.00 0.00 3.71
929 1065 4.135153 CCTCGTACTGCTGCCGCT 62.135 66.667 0.70 0.00 36.97 5.52
930 1066 3.642778 TTCCTCGTACTGCTGCCGC 62.643 63.158 0.00 0.00 0.00 6.53
931 1067 1.517257 CTTCCTCGTACTGCTGCCG 60.517 63.158 0.00 0.00 0.00 5.69
932 1068 1.811679 GCTTCCTCGTACTGCTGCC 60.812 63.158 0.00 0.00 0.00 4.85
933 1069 2.161486 CGCTTCCTCGTACTGCTGC 61.161 63.158 0.00 0.00 0.00 5.25
934 1070 1.517257 CCGCTTCCTCGTACTGCTG 60.517 63.158 0.00 0.00 0.00 4.41
956 1092 1.404851 CCGAGCTCTTCTTGTCCCTTC 60.405 57.143 12.85 0.00 0.00 3.46
1023 1174 4.101077 AGCCCCAGGAGGAGGAGG 62.101 72.222 0.00 0.00 38.24 4.30
1075 1226 1.033746 TAACCGACGGAGCCGAAGAT 61.034 55.000 23.38 1.28 42.83 2.40
1168 1319 1.333791 GCTTCCAAAGTCGAAACACCG 60.334 52.381 0.00 0.00 0.00 4.94
1174 1325 4.058817 GAGAAGAAGCTTCCAAAGTCGAA 58.941 43.478 22.81 0.00 0.00 3.71
1176 1327 3.185391 GTGAGAAGAAGCTTCCAAAGTCG 59.815 47.826 22.81 0.00 0.00 4.18
1282 1434 0.107312 GATGATGCTCCAGTGGCAGT 60.107 55.000 3.51 0.00 43.15 4.40
1294 1447 2.556144 TGTCAGGGCTATGATGATGC 57.444 50.000 0.00 0.00 0.00 3.91
1338 1491 9.409312 GAAGTAGAAGAAGAAAAGGTACACTAC 57.591 37.037 0.00 0.00 0.00 2.73
1339 1492 9.364653 AGAAGTAGAAGAAGAAAAGGTACACTA 57.635 33.333 0.00 0.00 0.00 2.74
1360 1513 5.003096 ACCTGAATTCCATTCCAAGAAGT 57.997 39.130 2.27 0.00 38.50 3.01
1362 1515 4.766891 GTGACCTGAATTCCATTCCAAGAA 59.233 41.667 2.27 0.00 38.50 2.52
1365 1555 4.081406 CTGTGACCTGAATTCCATTCCAA 58.919 43.478 2.27 0.00 38.50 3.53
1370 1560 1.995542 ACCCTGTGACCTGAATTCCAT 59.004 47.619 2.27 0.00 0.00 3.41
1372 1562 3.009143 AGTTACCCTGTGACCTGAATTCC 59.991 47.826 2.27 0.00 0.00 3.01
1380 1570 5.948758 ACTAGTACTTAGTTACCCTGTGACC 59.051 44.000 0.00 0.00 39.64 4.02
1381 1571 8.454894 GTTACTAGTACTTAGTTACCCTGTGAC 58.545 40.741 0.00 0.00 42.57 3.67
1466 1656 1.068474 GAACCATGTCGACACGAAGG 58.932 55.000 22.71 21.18 37.72 3.46
1486 1676 2.660670 TCTTTCCCGGGCTAAAAACA 57.339 45.000 18.49 0.00 0.00 2.83
1518 1708 7.148407 CCACAGATGTAAGTAGGTTCATTTCAC 60.148 40.741 0.00 0.00 0.00 3.18
1543 1736 0.316689 CGCAGACACCGTTGTTTTCC 60.317 55.000 0.00 0.00 35.47 3.13
1600 1793 3.549997 GCGCGTGCATAATTGGATT 57.450 47.368 17.66 0.00 42.15 3.01
1634 1827 2.645014 CGACGAGCGAGCACGTAG 60.645 66.667 19.16 15.58 42.66 3.51
1640 1833 4.738345 ACGACACGACGAGCGAGC 62.738 66.667 0.00 0.00 44.57 5.03
1699 1892 6.405278 AATGGGTAGACTTGGAAAACAAAG 57.595 37.500 0.00 0.00 38.91 2.77
1717 1910 5.630061 GCGGAATTCAAAATTTCAAATGGG 58.370 37.500 7.93 0.00 0.00 4.00
1738 1931 1.982073 GAGCACAAGAAATCCCCGCG 61.982 60.000 0.00 0.00 0.00 6.46
1783 1976 3.494045 GCAAAATGCACTCCTAAGGTC 57.506 47.619 0.00 0.00 44.26 3.85
1839 2032 9.449550 CGTTAACAACACAAGTATATATACGGA 57.550 33.333 15.57 0.00 38.28 4.69
1841 2034 9.236691 ACCGTTAACAACACAAGTATATATACG 57.763 33.333 15.57 6.71 38.28 3.06
1843 2036 9.531942 CCACCGTTAACAACACAAGTATATATA 57.468 33.333 6.39 0.00 0.00 0.86
1844 2037 7.496591 CCCACCGTTAACAACACAAGTATATAT 59.503 37.037 6.39 0.00 0.00 0.86
1845 2038 6.817641 CCCACCGTTAACAACACAAGTATATA 59.182 38.462 6.39 0.00 0.00 0.86
1848 2041 3.816523 CCCACCGTTAACAACACAAGTAT 59.183 43.478 6.39 0.00 0.00 2.12
1849 2042 3.118482 TCCCACCGTTAACAACACAAGTA 60.118 43.478 6.39 0.00 0.00 2.24
1850 2043 2.018515 CCCACCGTTAACAACACAAGT 58.981 47.619 6.39 0.00 0.00 3.16
1851 2044 2.032426 GTCCCACCGTTAACAACACAAG 59.968 50.000 6.39 0.00 0.00 3.16
1852 2045 2.015587 GTCCCACCGTTAACAACACAA 58.984 47.619 6.39 0.00 0.00 3.33
1853 2046 1.065636 TGTCCCACCGTTAACAACACA 60.066 47.619 6.39 0.00 0.00 3.72
1854 2047 1.331447 GTGTCCCACCGTTAACAACAC 59.669 52.381 6.39 6.12 0.00 3.32
1855 2048 1.666054 GTGTCCCACCGTTAACAACA 58.334 50.000 6.39 0.00 0.00 3.33
1856 2049 0.582960 CGTGTCCCACCGTTAACAAC 59.417 55.000 6.39 0.00 0.00 3.32
1857 2050 0.177604 ACGTGTCCCACCGTTAACAA 59.822 50.000 6.39 0.00 0.00 2.83
1858 2051 0.530211 CACGTGTCCCACCGTTAACA 60.530 55.000 7.58 0.00 0.00 2.41
1960 2153 1.021390 CGATGGTGGTGGACTTCAGC 61.021 60.000 0.00 0.00 43.68 4.26
1963 2156 1.745489 GCCGATGGTGGTGGACTTC 60.745 63.158 0.00 0.00 0.00 3.01
2256 2449 2.045926 ACACCTTGATGCCGGAGC 60.046 61.111 5.05 0.00 40.48 4.70
2278 2471 2.358247 ACGTCCATGGCGTTCACC 60.358 61.111 22.94 0.00 39.79 4.02
2806 2999 1.284982 CGGTGAGCGTGGTCTGAAAG 61.285 60.000 0.00 0.00 0.00 2.62
2809 3002 2.596338 TCGGTGAGCGTGGTCTGA 60.596 61.111 3.30 0.00 0.00 3.27
2941 3134 0.908198 GATCCAAGGGCAGACAGAGT 59.092 55.000 0.00 0.00 0.00 3.24
2942 3135 1.202330 AGATCCAAGGGCAGACAGAG 58.798 55.000 0.00 0.00 0.00 3.35
2945 3138 1.067295 ACAAGATCCAAGGGCAGACA 58.933 50.000 0.00 0.00 0.00 3.41
2946 3139 2.206576 AACAAGATCCAAGGGCAGAC 57.793 50.000 0.00 0.00 0.00 3.51
2958 3151 6.136541 AGAAACTTCGAAAGCAAACAAGAT 57.863 33.333 0.00 0.00 0.00 2.40
3082 3277 1.812922 AGCAGCACTACGAGCATGC 60.813 57.895 10.51 10.51 39.74 4.06
3121 3316 0.469705 AAGCAAACACATGGAGGGCA 60.470 50.000 0.00 0.00 0.00 5.36
3124 3319 3.068590 AGAAACAAGCAAACACATGGAGG 59.931 43.478 0.00 0.00 0.00 4.30
3165 3360 3.406764 CAGACAGAAAAGGAAGGTCAGG 58.593 50.000 0.00 0.00 0.00 3.86
3176 3371 6.712095 ACATTACAGAGATTGCAGACAGAAAA 59.288 34.615 0.00 0.00 0.00 2.29
3247 3442 4.108336 CACATCGTATCAGAGTTGGACAG 58.892 47.826 0.00 0.00 0.00 3.51
3251 3454 4.494484 TGTTCACATCGTATCAGAGTTGG 58.506 43.478 0.00 0.00 0.00 3.77
3289 3633 4.081309 CGAACTAGGGTTCCCAACTGATTA 60.081 45.833 10.73 0.00 46.46 1.75
3296 3640 4.347583 TCTTTAACGAACTAGGGTTCCCAA 59.652 41.667 10.73 0.00 46.46 4.12
3298 3642 4.541973 TCTTTAACGAACTAGGGTTCCC 57.458 45.455 0.00 0.00 46.46 3.97
3300 3644 6.481313 ACTGTTTCTTTAACGAACTAGGGTTC 59.519 38.462 0.00 0.00 45.91 3.62
3302 3646 5.756833 CACTGTTTCTTTAACGAACTAGGGT 59.243 40.000 0.00 0.00 39.72 4.34
3303 3647 5.756833 ACACTGTTTCTTTAACGAACTAGGG 59.243 40.000 0.00 0.43 39.72 3.53
3305 3649 7.436080 TGGTACACTGTTTCTTTAACGAACTAG 59.564 37.037 0.00 0.00 39.72 2.57
3306 3650 7.264221 TGGTACACTGTTTCTTTAACGAACTA 58.736 34.615 0.00 0.00 39.72 2.24
3325 3674 4.724399 ACCTTGTCATTGATGTTGGTACA 58.276 39.130 0.00 0.00 38.95 2.90
3326 3675 5.354234 CCTACCTTGTCATTGATGTTGGTAC 59.646 44.000 0.00 0.00 0.00 3.34
3327 3676 5.496556 CCTACCTTGTCATTGATGTTGGTA 58.503 41.667 0.00 1.02 0.00 3.25
3328 3677 4.335416 CCTACCTTGTCATTGATGTTGGT 58.665 43.478 0.00 0.00 0.00 3.67
3339 3688 1.669440 GCGTGTCCCTACCTTGTCA 59.331 57.895 0.00 0.00 0.00 3.58
3345 3694 3.352338 CTGTCGGCGTGTCCCTACC 62.352 68.421 6.85 0.00 0.00 3.18
3356 3705 3.303881 TGATATGCTATGACTGTCGGC 57.696 47.619 2.98 8.08 0.00 5.54
3369 3718 9.499585 CGGATGATGATTCTTTTTATGATATGC 57.500 33.333 0.00 0.00 0.00 3.14
3392 3741 6.170506 ACAAAATACTTCAGTATGCTTCGGA 58.829 36.000 0.07 0.00 40.78 4.55
3404 3761 5.752892 TTGTACGCCAACAAAATACTTCA 57.247 34.783 0.00 0.00 36.45 3.02
3435 3792 3.230134 TCCTTGCACTTGCTTGGTATTT 58.770 40.909 2.33 0.00 42.66 1.40
3436 3793 2.875296 TCCTTGCACTTGCTTGGTATT 58.125 42.857 2.33 0.00 42.66 1.89
3475 3832 4.379813 GCCATTCATTTGACCAGTGTGTAG 60.380 45.833 0.00 0.00 0.00 2.74
3486 3843 5.787953 TGTTTCTCTTGCCATTCATTTGA 57.212 34.783 0.00 0.00 0.00 2.69
3628 3988 1.454201 TTTTGTGTGTGGCTGTTCGA 58.546 45.000 0.00 0.00 0.00 3.71
3772 4138 1.880027 CCTCAACCTAACCTTGTGTGC 59.120 52.381 0.00 0.00 0.00 4.57
3789 4155 2.990066 ACACATAAGCTACAGGCCTC 57.010 50.000 0.00 0.00 43.05 4.70
3953 4319 4.574599 ACTTGAACAAAGAATCACTGGC 57.425 40.909 0.00 0.00 39.38 4.85
3961 4327 7.227910 GGGTGTCAGTTATACTTGAACAAAGAA 59.772 37.037 0.00 0.00 39.38 2.52
4134 4503 5.869888 AGGTACTCGATTGTTCTGTGAATTC 59.130 40.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.