Multiple sequence alignment - TraesCS4A01G395000

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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 TraesCS4A01G395000 chr4A 100.000 2384 0 0 1 2384 669899638 669897255 0.000000e+00 4403.0
1 TraesCS4A01G395000 chr4A 98.947 285 3 0 2100 2384 669879895 669879611 5.880000e-141 510.0
2 TraesCS4A01G395000 chr4A 86.765 68 9 0 1456 1523 548645899 548645966 2.540000e-10 76.8
3 TraesCS4A01G395000 chr7D 87.050 1444 135 15 94 1524 54355042 54353638 0.000000e+00 1583.0
4 TraesCS4A01G395000 chr7D 92.100 924 64 2 600 1522 54320464 54319549 0.000000e+00 1293.0
5 TraesCS4A01G395000 chr7D 91.561 865 69 4 600 1462 54311674 54310812 0.000000e+00 1190.0
6 TraesCS4A01G395000 chr7D 89.201 926 88 2 603 1528 54337371 54336458 0.000000e+00 1146.0
7 TraesCS4A01G395000 chr7D 89.624 665 43 10 1574 2215 54353547 54352886 0.000000e+00 822.0
8 TraesCS4A01G395000 chr7D 84.241 514 48 11 80 591 54320985 54320503 9.980000e-129 470.0
9 TraesCS4A01G395000 chr7D 85.561 374 41 10 1635 1998 54310812 54310442 1.730000e-101 379.0
10 TraesCS4A01G395000 chr7D 83.846 390 45 13 1614 1998 54336338 54335962 2.910000e-94 355.0
11 TraesCS4A01G395000 chr7D 85.373 335 39 8 1614 1943 54319427 54319098 2.940000e-89 339.0
12 TraesCS4A01G395000 chr7D 94.776 134 7 0 2243 2376 54352890 54352757 2.400000e-50 209.0
13 TraesCS4A01G395000 chr7A 92.281 868 62 2 600 1464 57865164 57864299 0.000000e+00 1227.0
14 TraesCS4A01G395000 chr7A 92.164 855 64 1 600 1451 57803757 57802903 0.000000e+00 1205.0
15 TraesCS4A01G395000 chr7A 84.912 570 70 7 1 558 57804385 57803820 1.600000e-156 562.0
16 TraesCS4A01G395000 chr7A 82.960 446 52 15 1564 1998 57864188 57863756 4.810000e-102 381.0
17 TraesCS4A01G395000 chr7A 86.755 302 25 5 1577 1875 57802750 57802461 2.960000e-84 322.0
18 TraesCS4A01G395000 chr7A 100.000 30 0 0 1573 1602 693996993 693997022 3.310000e-04 56.5
19 TraesCS4A01G395000 chrUn 91.432 852 72 1 605 1455 49140740 49139889 0.000000e+00 1168.0
20 TraesCS4A01G395000 chrUn 91.197 852 74 1 605 1455 49113901 49113050 0.000000e+00 1157.0
21 TraesCS4A01G395000 chrUn 91.197 852 74 1 605 1455 384623921 384624772 0.000000e+00 1157.0
22 TraesCS4A01G395000 chrUn 99.298 285 2 0 2100 2384 49127507 49127223 1.260000e-142 516.0
23 TraesCS4A01G395000 chrUn 99.034 207 2 0 2100 2306 261595118 261594912 2.890000e-99 372.0
24 TraesCS4A01G395000 chrUn 86.786 280 27 5 1603 1875 49113063 49112787 1.070000e-78 303.0
25 TraesCS4A01G395000 chrUn 86.786 280 27 5 1603 1875 49139902 49139626 1.070000e-78 303.0
26 TraesCS4A01G395000 chrUn 86.786 280 27 5 1603 1875 384624759 384625035 1.070000e-78 303.0
27 TraesCS4A01G395000 chr1A 91.176 68 6 0 1456 1523 510187437 510187370 2.520000e-15 93.5
28 TraesCS4A01G395000 chr4B 88.235 68 8 0 1456 1523 459954439 459954506 5.460000e-12 82.4
29 TraesCS4A01G395000 chr5D 100.000 32 0 0 1573 1604 497839618 497839587 2.560000e-05 60.2
30 TraesCS4A01G395000 chr1B 100.000 31 0 0 1574 1604 158172371 158172401 9.200000e-05 58.4


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 TraesCS4A01G395000 chr4A 669897255 669899638 2383 True 4403.000000 4403 100.000000 1 2384 1 chr4A.!!$R2 2383
1 TraesCS4A01G395000 chr7D 54352757 54355042 2285 True 871.333333 1583 90.483333 94 2376 3 chr7D.!!$R4 2282
2 TraesCS4A01G395000 chr7D 54310442 54311674 1232 True 784.500000 1190 88.561000 600 1998 2 chr7D.!!$R1 1398
3 TraesCS4A01G395000 chr7D 54335962 54337371 1409 True 750.500000 1146 86.523500 603 1998 2 chr7D.!!$R3 1395
4 TraesCS4A01G395000 chr7D 54319098 54320985 1887 True 700.666667 1293 87.238000 80 1943 3 chr7D.!!$R2 1863
5 TraesCS4A01G395000 chr7A 57863756 57865164 1408 True 804.000000 1227 87.620500 600 1998 2 chr7A.!!$R2 1398
6 TraesCS4A01G395000 chr7A 57802461 57804385 1924 True 696.333333 1205 87.943667 1 1875 3 chr7A.!!$R1 1874
7 TraesCS4A01G395000 chrUn 49139626 49140740 1114 True 735.500000 1168 89.109000 605 1875 2 chrUn.!!$R4 1270
8 TraesCS4A01G395000 chrUn 49112787 49113901 1114 True 730.000000 1157 88.991500 605 1875 2 chrUn.!!$R3 1270
9 TraesCS4A01G395000 chrUn 384623921 384625035 1114 False 730.000000 1157 88.991500 605 1875 2 chrUn.!!$F1 1270

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
84 85 0.320247 AGCTCCGCAAACTCAGTCTG 60.32 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1985 0.031178 CTGCAAGTGTTGGTGGCTTC 59.969 55.0 0.0 0.0 0.0 3.86 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
26 27 9.581289 TCTACATTGTGGAAAGAAAAAGGATAA 57.419 29.630 0.00 0.00 0.00 1.75
29 30 9.492973 ACATTGTGGAAAGAAAAAGGATAAATG 57.507 29.630 0.00 0.00 0.00 2.32
53 54 7.598278 TGTATGACGAAAATTATGCCAAGTTT 58.402 30.769 0.00 0.00 0.00 2.66
58 59 6.774717 CGAAAATTATGCCAAGTTTCGTAG 57.225 37.500 23.80 7.31 46.16 3.51
84 85 0.320247 AGCTCCGCAAACTCAGTCTG 60.320 55.000 0.00 0.00 0.00 3.51
92 93 2.813754 GCAAACTCAGTCTGCCATAACA 59.186 45.455 0.00 0.00 0.00 2.41
145 148 3.054878 CGTAAACTTTGCTGAGTACGGT 58.945 45.455 7.18 0.00 31.38 4.83
156 159 1.421410 GAGTACGGTCTGCCAATGCG 61.421 60.000 0.00 0.00 41.78 4.73
161 164 1.699656 CGGTCTGCCAATGCGAGAAG 61.700 60.000 0.00 0.00 41.78 2.85
208 211 5.897050 AGTTTATTTTGTTTGCCGAGTTCA 58.103 33.333 0.00 0.00 0.00 3.18
209 212 6.512297 AGTTTATTTTGTTTGCCGAGTTCAT 58.488 32.000 0.00 0.00 0.00 2.57
214 217 7.961325 ATTTTGTTTGCCGAGTTCATTTTAT 57.039 28.000 0.00 0.00 0.00 1.40
337 349 2.165319 ACGACCAACTTTCCAGTAGC 57.835 50.000 0.00 0.00 30.68 3.58
363 375 3.997021 GGTTGAGATGTCATGTTCGAAGT 59.003 43.478 0.00 0.00 30.85 3.01
372 399 4.975502 TGTCATGTTCGAAGTTGCAAAATC 59.024 37.500 0.00 1.23 0.00 2.17
373 400 5.215160 GTCATGTTCGAAGTTGCAAAATCT 58.785 37.500 0.00 0.00 0.00 2.40
374 401 5.687285 GTCATGTTCGAAGTTGCAAAATCTT 59.313 36.000 0.00 0.00 0.00 2.40
375 402 6.198966 GTCATGTTCGAAGTTGCAAAATCTTT 59.801 34.615 0.00 0.00 0.00 2.52
376 403 5.947503 TGTTCGAAGTTGCAAAATCTTTG 57.052 34.783 0.00 4.93 0.00 2.77
377 404 5.406649 TGTTCGAAGTTGCAAAATCTTTGT 58.593 33.333 0.00 0.00 0.00 2.83
378 405 5.866633 TGTTCGAAGTTGCAAAATCTTTGTT 59.133 32.000 0.00 0.00 0.00 2.83
379 406 6.034470 TGTTCGAAGTTGCAAAATCTTTGTTC 59.966 34.615 0.00 3.88 0.00 3.18
380 407 5.645624 TCGAAGTTGCAAAATCTTTGTTCA 58.354 33.333 0.00 0.00 0.00 3.18
381 408 6.096036 TCGAAGTTGCAAAATCTTTGTTCAA 58.904 32.000 0.00 0.00 0.00 2.69
382 409 6.587990 TCGAAGTTGCAAAATCTTTGTTCAAA 59.412 30.769 0.00 0.00 0.00 2.69
383 410 7.116948 TCGAAGTTGCAAAATCTTTGTTCAAAA 59.883 29.630 0.00 0.00 0.00 2.44
384 411 7.214263 CGAAGTTGCAAAATCTTTGTTCAAAAC 59.786 33.333 0.00 0.00 0.00 2.43
385 412 7.432350 AGTTGCAAAATCTTTGTTCAAAACA 57.568 28.000 0.00 0.00 40.21 2.83
386 413 7.297391 AGTTGCAAAATCTTTGTTCAAAACAC 58.703 30.769 0.00 0.00 41.97 3.32
396 423 4.009798 TGTTCAAAACACGTTACAGCAG 57.990 40.909 0.00 0.00 36.25 4.24
458 485 3.067106 GCAGCACAGTTACACATGTAGT 58.933 45.455 0.00 1.92 0.00 2.73
462 489 3.608506 GCACAGTTACACATGTAGTCGAG 59.391 47.826 0.00 0.00 0.00 4.04
491 518 3.678072 CGTTGGCGAGAATTGAACTAAGA 59.322 43.478 0.00 0.00 41.33 2.10
535 563 7.472334 ACAATGATGGATGCTAAAAGAAAGT 57.528 32.000 0.00 0.00 0.00 2.66
539 567 5.415701 TGATGGATGCTAAAAGAAAGTCCAC 59.584 40.000 0.00 0.00 37.13 4.02
555 583 2.477754 GTCCACACTTTACAGCGGTAAC 59.522 50.000 9.06 0.00 39.14 2.50
556 584 2.366266 TCCACACTTTACAGCGGTAACT 59.634 45.455 9.06 0.00 39.14 2.24
572 600 0.392193 AACTCTCGCTTGCAGGATGG 60.392 55.000 0.00 0.00 35.86 3.51
591 619 2.231964 TGGAAGCAAACAATGGAGATGC 59.768 45.455 0.00 0.00 37.28 3.91
593 621 3.306225 GGAAGCAAACAATGGAGATGCAA 60.306 43.478 0.00 0.00 39.42 4.08
594 622 3.308438 AGCAAACAATGGAGATGCAAC 57.692 42.857 0.00 0.00 39.42 4.17
595 623 2.629137 AGCAAACAATGGAGATGCAACA 59.371 40.909 0.00 0.00 39.42 3.33
598 626 4.142988 GCAAACAATGGAGATGCAACAATG 60.143 41.667 0.00 0.00 37.00 2.82
630 711 2.933495 AGTAGTAGTTGATTGCGCGA 57.067 45.000 12.10 0.00 0.00 5.87
672 753 2.599281 TCGCCGGTCTTGACCTCA 60.599 61.111 16.60 0.00 0.00 3.86
753 834 0.955428 CGTTGTCCACCACCATCCTG 60.955 60.000 0.00 0.00 0.00 3.86
839 920 4.617253 TGTTGTAGTACTGCTTGTCCAT 57.383 40.909 12.42 0.00 0.00 3.41
843 924 3.576550 TGTAGTACTGCTTGTCCATGTCA 59.423 43.478 12.42 0.00 0.00 3.58
879 960 2.033448 TGCATCACCGTTGGGTCC 59.967 61.111 0.00 0.00 46.01 4.46
956 1037 2.322212 CGTCGATGTCGGAGGAGAT 58.678 57.895 2.25 0.00 40.29 2.75
1041 1122 1.906824 GACCAGGTCCTCCACGTCA 60.907 63.158 8.65 0.00 35.47 4.35
1086 1167 1.901085 GAGGTCGCTGAGGTTGGAT 59.099 57.895 0.00 0.00 0.00 3.41
1088 1169 2.109126 GGTCGCTGAGGTTGGATGC 61.109 63.158 0.00 0.00 0.00 3.91
1109 1190 2.125512 CGGGGCGAGGAACTTGAG 60.126 66.667 0.00 0.00 44.22 3.02
1236 1317 1.519234 GATGTCGGCGCATGAGACA 60.519 57.895 22.50 22.50 46.99 3.41
1240 1321 3.112075 CGGCGCATGAGACAACGT 61.112 61.111 10.83 0.00 0.00 3.99
1274 1355 0.982852 TCGAGGGCATCCTTGATGGT 60.983 55.000 6.24 0.00 46.14 3.55
1329 1410 3.780173 GGCGGGCTGAGCTTCTCT 61.780 66.667 3.72 0.00 34.52 3.10
1465 1549 7.280428 TGCATTGCAATTTATTATTGTTGAGGG 59.720 33.333 9.83 0.00 34.76 4.30
1485 1569 3.369157 GGGAATCGTTAACTGGTAGCTGT 60.369 47.826 3.71 0.00 0.00 4.40
1490 1574 2.344025 GTTAACTGGTAGCTGTTCGGG 58.656 52.381 18.78 0.00 0.00 5.14
1494 1578 1.827399 CTGGTAGCTGTTCGGGTGGT 61.827 60.000 0.00 0.00 0.00 4.16
1497 1581 0.250166 GTAGCTGTTCGGGTGGTTGT 60.250 55.000 0.00 0.00 0.00 3.32
1506 1590 1.700739 TCGGGTGGTTGTTGAATAGGT 59.299 47.619 0.00 0.00 0.00 3.08
1514 1634 7.558444 GGGTGGTTGTTGAATAGGTGATTAATA 59.442 37.037 0.00 0.00 0.00 0.98
1517 1637 8.682710 TGGTTGTTGAATAGGTGATTAATAAGC 58.317 33.333 0.00 0.00 0.00 3.09
1564 1684 4.751600 TCGGCTATTCGATAACTCTACGAA 59.248 41.667 0.00 0.00 46.83 3.85
1610 1773 3.964909 ACGAATTCTTGAACAAGGCAAC 58.035 40.909 13.46 4.48 38.88 4.17
1631 1794 4.504858 ACTTATTTCTTGCCGTGAGTAGG 58.495 43.478 0.00 0.00 0.00 3.18
1821 1987 3.914579 GAGCAGCAGCAGGGCAGAA 62.915 63.158 3.17 0.00 45.49 3.02
1833 1999 4.164258 GCAGAAGCCACCAACACT 57.836 55.556 0.00 0.00 33.58 3.55
1844 2010 1.027357 ACCAACACTTGCAGCTTCTG 58.973 50.000 0.00 0.00 34.12 3.02
1865 2034 3.679738 ACCCGCCGCCATTGTTTG 61.680 61.111 0.00 0.00 0.00 2.93
1905 2084 6.464180 GCCTGACTAAGATTGGAAGATGAGAT 60.464 42.308 0.00 0.00 0.00 2.75
1917 2096 2.114616 AGATGAGATGTGGGAGGTGAC 58.885 52.381 0.00 0.00 0.00 3.67
1922 2101 0.179073 GATGTGGGAGGTGACCGATG 60.179 60.000 0.00 0.00 0.00 3.84
1924 2103 1.987855 GTGGGAGGTGACCGATGGA 60.988 63.158 0.00 0.00 0.00 3.41
1949 2128 1.225704 GGGAATGCCTGCTAGCTGT 59.774 57.895 17.23 0.00 0.00 4.40
1958 2137 4.883083 TGCCTGCTAGCTGTTGTATATAC 58.117 43.478 17.23 5.89 0.00 1.47
1972 2151 7.433680 TGTTGTATATACTTCGAGCATGATGT 58.566 34.615 13.89 0.00 0.00 3.06
2009 2191 3.283256 GCATTCGAAGCATATGTTGTCG 58.717 45.455 3.35 14.71 0.00 4.35
2017 2199 2.695666 AGCATATGTTGTCGACTAGCCT 59.304 45.455 17.92 2.79 0.00 4.58
2020 2202 4.433615 CATATGTTGTCGACTAGCCTTGT 58.566 43.478 17.92 0.00 0.00 3.16
2034 2216 2.431247 GCCTTGTGCTTCATGGGAACA 61.431 52.381 13.11 0.00 40.43 3.18
2058 2242 4.860261 GCTACGTACACCGGCCGG 62.860 72.222 42.17 42.17 42.24 6.13
2124 2308 1.202533 AGAGGGCGTCGGTAATGAATG 60.203 52.381 0.96 0.00 0.00 2.67
2152 2346 3.611766 ACACAAATAGCGAGCTAACCT 57.388 42.857 9.00 0.00 31.73 3.50
2153 2347 3.939066 ACACAAATAGCGAGCTAACCTT 58.061 40.909 9.00 0.99 31.73 3.50
2171 2365 8.231161 GCTAACCTTGAGTTTTTAGAAGATGAC 58.769 37.037 0.00 0.00 40.05 3.06
2178 2372 6.870965 TGAGTTTTTAGAAGATGACAGCTCTC 59.129 38.462 0.00 0.00 0.00 3.20
2215 2409 1.774254 ACATGGGGTTGACTTGACTGA 59.226 47.619 0.00 0.00 0.00 3.41
2216 2410 2.376518 ACATGGGGTTGACTTGACTGAT 59.623 45.455 0.00 0.00 0.00 2.90
2218 2412 1.774254 TGGGGTTGACTTGACTGATGT 59.226 47.619 0.00 0.00 0.00 3.06
2219 2413 2.976185 TGGGGTTGACTTGACTGATGTA 59.024 45.455 0.00 0.00 0.00 2.29
2220 2414 3.587061 TGGGGTTGACTTGACTGATGTAT 59.413 43.478 0.00 0.00 0.00 2.29
2221 2415 3.941483 GGGGTTGACTTGACTGATGTATG 59.059 47.826 0.00 0.00 0.00 2.39
2222 2416 4.323485 GGGGTTGACTTGACTGATGTATGA 60.323 45.833 0.00 0.00 0.00 2.15
2223 2417 5.245531 GGGTTGACTTGACTGATGTATGAA 58.754 41.667 0.00 0.00 0.00 2.57
2224 2418 5.882557 GGGTTGACTTGACTGATGTATGAAT 59.117 40.000 0.00 0.00 0.00 2.57
2225 2419 6.037610 GGGTTGACTTGACTGATGTATGAATC 59.962 42.308 0.00 0.00 0.00 2.52
2226 2420 6.237942 GGTTGACTTGACTGATGTATGAATCG 60.238 42.308 0.00 0.00 0.00 3.34
2227 2421 5.351458 TGACTTGACTGATGTATGAATCGG 58.649 41.667 0.00 0.00 38.65 4.18
2228 2422 4.122776 ACTTGACTGATGTATGAATCGGC 58.877 43.478 0.00 0.00 36.55 5.54
2229 2423 3.111853 TGACTGATGTATGAATCGGCC 57.888 47.619 0.00 0.00 36.55 6.13
2230 2424 2.433970 TGACTGATGTATGAATCGGCCA 59.566 45.455 2.24 0.00 36.55 5.36
2231 2425 3.071457 TGACTGATGTATGAATCGGCCAT 59.929 43.478 2.24 0.00 36.55 4.40
2232 2426 3.405831 ACTGATGTATGAATCGGCCATG 58.594 45.455 2.24 0.00 36.55 3.66
2233 2427 3.181451 ACTGATGTATGAATCGGCCATGT 60.181 43.478 2.24 0.00 36.55 3.21
2234 2428 4.040339 ACTGATGTATGAATCGGCCATGTA 59.960 41.667 2.24 0.00 36.55 2.29
2235 2429 5.164620 TGATGTATGAATCGGCCATGTAT 57.835 39.130 2.24 0.00 0.00 2.29
2236 2430 6.070824 ACTGATGTATGAATCGGCCATGTATA 60.071 38.462 2.24 0.00 36.55 1.47
2237 2431 6.706295 TGATGTATGAATCGGCCATGTATAA 58.294 36.000 2.24 0.00 0.00 0.98
2238 2432 6.818142 TGATGTATGAATCGGCCATGTATAAG 59.182 38.462 2.24 0.00 0.00 1.73
2239 2433 4.935205 TGTATGAATCGGCCATGTATAAGC 59.065 41.667 2.24 0.00 0.00 3.09
2240 2434 3.769739 TGAATCGGCCATGTATAAGCT 57.230 42.857 2.24 0.00 0.00 3.74
2241 2435 3.402110 TGAATCGGCCATGTATAAGCTG 58.598 45.455 2.24 0.00 0.00 4.24
2242 2436 2.479566 ATCGGCCATGTATAAGCTGG 57.520 50.000 2.24 0.00 33.58 4.85
2243 2437 1.419381 TCGGCCATGTATAAGCTGGA 58.581 50.000 2.24 0.00 33.58 3.86
2244 2438 1.070134 TCGGCCATGTATAAGCTGGAC 59.930 52.381 2.24 0.00 34.52 4.02
2245 2439 1.070758 CGGCCATGTATAAGCTGGACT 59.929 52.381 2.24 0.00 35.81 3.85
2246 2440 2.498167 GGCCATGTATAAGCTGGACTG 58.502 52.381 0.00 0.00 35.05 3.51
2247 2441 2.498167 GCCATGTATAAGCTGGACTGG 58.502 52.381 0.00 0.00 31.38 4.00
2248 2442 2.811873 GCCATGTATAAGCTGGACTGGG 60.812 54.545 0.00 0.00 31.38 4.45
2249 2443 2.498167 CATGTATAAGCTGGACTGGGC 58.502 52.381 0.00 0.00 0.00 5.36
2260 2454 2.173569 CTGGACTGGGCCTAGCTATTTT 59.826 50.000 17.38 0.00 0.00 1.82
2266 2460 4.130118 CTGGGCCTAGCTATTTTGTACTG 58.870 47.826 1.92 0.00 0.00 2.74
2269 2463 5.605069 TGGGCCTAGCTATTTTGTACTGATA 59.395 40.000 4.53 0.00 0.00 2.15
2337 2531 1.212751 GGACGCATGTTTTCCTGGC 59.787 57.895 0.00 0.00 0.00 4.85
2354 2548 0.398318 GGCTGTTGAGAGGTCAGGTT 59.602 55.000 0.00 0.00 32.98 3.50
2361 2555 6.488769 TGTTGAGAGGTCAGGTTAGTTAAA 57.511 37.500 0.00 0.00 32.98 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.771183 ACTTGGCATAATTTTCGTCATACATT 58.229 30.769 0.00 0.00 0.00 2.71
29 30 7.044966 CGAAACTTGGCATAATTTTCGTCATAC 60.045 37.037 20.10 0.00 42.13 2.39
33 34 5.664870 CGAAACTTGGCATAATTTTCGTC 57.335 39.130 20.10 0.00 42.13 4.20
40 41 4.616181 GCACTACGAAACTTGGCATAAT 57.384 40.909 0.00 0.00 0.00 1.28
70 71 1.725641 TATGGCAGACTGAGTTTGCG 58.274 50.000 19.87 0.00 43.26 4.85
71 72 2.813754 TGTTATGGCAGACTGAGTTTGC 59.186 45.455 18.67 18.67 41.91 3.68
84 85 5.350640 GGTAGTTTGTGTACTCTGTTATGGC 59.649 44.000 0.00 0.00 0.00 4.40
92 93 5.365619 CAACAAGGGTAGTTTGTGTACTCT 58.634 41.667 0.00 0.00 38.67 3.24
125 128 4.150098 CAGACCGTACTCAGCAAAGTTTAC 59.850 45.833 0.00 0.00 0.00 2.01
145 148 0.742281 GAGCTTCTCGCATTGGCAGA 60.742 55.000 0.00 0.00 42.61 4.26
169 172 1.919956 AACTCGGCTCGTACGGACTG 61.920 60.000 16.52 12.71 0.00 3.51
178 181 3.360758 GCAAACAAAATAAACTCGGCTCG 59.639 43.478 0.00 0.00 0.00 5.03
179 182 3.673338 GGCAAACAAAATAAACTCGGCTC 59.327 43.478 0.00 0.00 0.00 4.70
208 211 5.619981 GCCGTTGTTGAGAGCAAGATAAAAT 60.620 40.000 0.00 0.00 34.01 1.82
209 212 4.320202 GCCGTTGTTGAGAGCAAGATAAAA 60.320 41.667 0.00 0.00 34.01 1.52
214 217 0.179059 TGCCGTTGTTGAGAGCAAGA 60.179 50.000 0.00 0.00 34.01 3.02
298 301 0.317160 TGCCGAGAGTCAAATCACGT 59.683 50.000 0.00 0.00 32.33 4.49
299 302 1.126846 GTTGCCGAGAGTCAAATCACG 59.873 52.381 0.00 0.00 33.75 4.35
337 349 0.253044 ACATGACATCTCAACCCCCG 59.747 55.000 0.00 0.00 0.00 5.73
363 375 6.073548 ACGTGTTTTGAACAAAGATTTTGCAA 60.074 30.769 0.00 0.00 44.16 4.08
372 399 4.854291 TGCTGTAACGTGTTTTGAACAAAG 59.146 37.500 0.00 0.00 44.16 2.77
373 400 4.795268 TGCTGTAACGTGTTTTGAACAAA 58.205 34.783 0.00 0.00 44.16 2.83
374 401 4.154375 TCTGCTGTAACGTGTTTTGAACAA 59.846 37.500 0.00 0.00 44.16 2.83
375 402 3.685272 TCTGCTGTAACGTGTTTTGAACA 59.315 39.130 0.00 0.00 39.52 3.18
376 403 4.267357 TCTGCTGTAACGTGTTTTGAAC 57.733 40.909 0.00 0.00 0.00 3.18
377 404 4.393680 ACTTCTGCTGTAACGTGTTTTGAA 59.606 37.500 0.00 0.00 0.00 2.69
378 405 3.936453 ACTTCTGCTGTAACGTGTTTTGA 59.064 39.130 0.00 0.00 0.00 2.69
379 406 4.028383 CACTTCTGCTGTAACGTGTTTTG 58.972 43.478 0.00 0.00 0.00 2.44
380 407 3.687698 ACACTTCTGCTGTAACGTGTTTT 59.312 39.130 0.00 0.00 32.23 2.43
381 408 3.267483 ACACTTCTGCTGTAACGTGTTT 58.733 40.909 0.00 0.00 32.23 2.83
382 409 2.901249 ACACTTCTGCTGTAACGTGTT 58.099 42.857 0.00 0.00 32.23 3.32
383 410 2.596904 ACACTTCTGCTGTAACGTGT 57.403 45.000 0.00 0.00 0.00 4.49
384 411 4.370620 GTTACACTTCTGCTGTAACGTG 57.629 45.455 9.38 6.51 42.35 4.49
414 441 6.765036 TGCAAGCCAATGTTCTTTTATTTTGA 59.235 30.769 0.00 0.00 0.00 2.69
416 443 7.193377 CTGCAAGCCAATGTTCTTTTATTTT 57.807 32.000 0.00 0.00 0.00 1.82
458 485 2.387445 CGCCAACGGAATTGCTCGA 61.387 57.895 0.00 0.00 36.93 4.04
462 489 0.451783 ATTCTCGCCAACGGAATTGC 59.548 50.000 0.00 0.00 36.45 3.56
509 537 9.023962 ACTTTCTTTTAGCATCCATCATTGTTA 57.976 29.630 0.00 0.00 0.00 2.41
533 561 0.756903 ACCGCTGTAAAGTGTGGACT 59.243 50.000 0.00 0.00 37.30 3.85
535 563 2.366266 AGTTACCGCTGTAAAGTGTGGA 59.634 45.455 1.99 0.00 38.62 4.02
539 567 2.915463 CGAGAGTTACCGCTGTAAAGTG 59.085 50.000 1.99 0.00 38.62 3.16
555 583 0.107993 TTCCATCCTGCAAGCGAGAG 60.108 55.000 0.00 0.00 0.00 3.20
556 584 0.107993 CTTCCATCCTGCAAGCGAGA 60.108 55.000 0.00 0.00 0.00 4.04
572 600 3.581024 TGCATCTCCATTGTTTGCTTC 57.419 42.857 0.00 0.00 34.47 3.86
591 619 4.740268 ACTAAGTGCATGCATCATTGTTG 58.260 39.130 25.64 14.58 0.00 3.33
593 621 5.188434 ACTACTAAGTGCATGCATCATTGT 58.812 37.500 25.64 19.85 33.57 2.71
594 622 5.746307 ACTACTAAGTGCATGCATCATTG 57.254 39.130 25.64 15.45 33.57 2.82
595 623 6.586344 ACTACTACTAAGTGCATGCATCATT 58.414 36.000 25.64 20.12 36.36 2.57
598 626 6.042777 TCAACTACTACTAAGTGCATGCATC 58.957 40.000 25.64 17.07 36.36 3.91
672 753 1.754234 GGTGAAGATGGCCGGCATT 60.754 57.895 30.85 16.87 0.00 3.56
777 858 3.573772 CTTCACCTCTGACGCGGCA 62.574 63.158 17.01 17.01 0.00 5.69
930 1011 4.814294 GACATCGACGGCGGCCTT 62.814 66.667 12.58 7.81 38.28 4.35
1041 1122 1.172812 GCTTTGTCGTCAAGGGCCTT 61.173 55.000 14.48 14.48 34.88 4.35
1096 1177 3.491652 GCCGCTCAAGTTCCTCGC 61.492 66.667 0.00 0.00 0.00 5.03
1152 1233 2.741092 GTGGACTTCGAGGTGCCA 59.259 61.111 16.35 14.20 0.00 4.92
1230 1311 1.367471 CTGCCCAGACGTTGTCTCA 59.633 57.895 0.00 0.00 41.37 3.27
1263 1344 2.484417 GCTGATCGACACCATCAAGGAT 60.484 50.000 0.00 0.00 41.22 3.24
1305 1386 3.365265 CTCAGCCCGCCCAACAAC 61.365 66.667 0.00 0.00 0.00 3.32
1316 1397 2.511145 CGCCAGAGAAGCTCAGCC 60.511 66.667 0.00 0.00 31.33 4.85
1456 1540 4.069304 CCAGTTAACGATTCCCTCAACAA 58.931 43.478 0.00 0.00 0.00 2.83
1465 1549 4.031426 CGAACAGCTACCAGTTAACGATTC 59.969 45.833 0.00 0.00 0.00 2.52
1485 1569 2.106857 ACCTATTCAACAACCACCCGAA 59.893 45.455 0.00 0.00 0.00 4.30
1540 1660 4.151335 TCGTAGAGTTATCGAATAGCCGAC 59.849 45.833 0.00 0.00 41.70 4.79
1564 1684 9.543783 GTTCGATTAATCAGTTAACTTCCCTAT 57.456 33.333 15.57 0.00 32.91 2.57
1610 1773 4.567159 GTCCTACTCACGGCAAGAAATAAG 59.433 45.833 0.00 0.00 0.00 1.73
1631 1794 0.520827 CTGCTTCGTCGAGGTACGTC 60.521 60.000 6.22 5.47 43.31 4.34
1819 1985 0.031178 CTGCAAGTGTTGGTGGCTTC 59.969 55.000 0.00 0.00 0.00 3.86
1821 1987 2.492773 GCTGCAAGTGTTGGTGGCT 61.493 57.895 0.00 0.00 35.30 4.75
1829 1995 2.626582 GCTCAGAAGCTGCAAGTGT 58.373 52.632 1.02 0.00 45.55 3.55
1849 2018 2.817470 CTTCAAACAATGGCGGCGGG 62.817 60.000 9.78 0.00 0.00 6.13
1851 2020 2.088178 GCTTCAAACAATGGCGGCG 61.088 57.895 0.51 0.51 0.00 6.46
1865 2034 0.527385 CAGGCACTCGAGCTAGCTTC 60.527 60.000 20.42 11.11 34.60 3.86
1905 2084 2.290287 CCATCGGTCACCTCCCACA 61.290 63.158 0.00 0.00 0.00 4.17
1922 2101 2.203351 GGCATTCCCGACCCATCC 60.203 66.667 0.00 0.00 0.00 3.51
1924 2103 2.597340 CAGGCATTCCCGACCCAT 59.403 61.111 0.00 0.00 39.21 4.00
1949 2128 7.095649 GCAACATCATGCTCGAAGTATATACAA 60.096 37.037 15.18 0.00 43.06 2.41
1972 2151 4.041075 TCGAATGCCCACCTATATAAGCAA 59.959 41.667 0.00 0.00 33.35 3.91
2017 2199 4.406456 AGTAATGTTCCCATGAAGCACAA 58.594 39.130 0.00 0.00 0.00 3.33
2020 2202 4.080356 AGCTAGTAATGTTCCCATGAAGCA 60.080 41.667 0.00 0.00 30.54 3.91
2026 2208 5.595542 TGTACGTAGCTAGTAATGTTCCCAT 59.404 40.000 0.00 0.00 0.00 4.00
2028 2210 5.277047 GTGTACGTAGCTAGTAATGTTCCC 58.723 45.833 0.00 0.00 0.00 3.97
2034 2216 2.291741 GCCGGTGTACGTAGCTAGTAAT 59.708 50.000 1.90 0.00 42.24 1.89
2058 2242 0.719465 CGACGATTGGTGGCAACTAC 59.281 55.000 3.27 0.00 37.61 2.73
2124 2308 8.587950 GTTAGCTCGCTATTTGTGTATCATATC 58.412 37.037 0.00 0.00 0.00 1.63
2152 2346 7.220030 AGAGCTGTCATCTTCTAAAAACTCAA 58.780 34.615 0.00 0.00 0.00 3.02
2153 2347 6.763355 AGAGCTGTCATCTTCTAAAAACTCA 58.237 36.000 0.00 0.00 0.00 3.41
2171 2365 2.158986 CCATCAGGGTTAGTGAGAGCTG 60.159 54.545 0.00 0.00 0.00 4.24
2215 2409 5.586243 GCTTATACATGGCCGATTCATACAT 59.414 40.000 0.00 0.00 0.00 2.29
2216 2410 4.935205 GCTTATACATGGCCGATTCATACA 59.065 41.667 0.00 0.00 0.00 2.29
2218 2412 5.178061 CAGCTTATACATGGCCGATTCATA 58.822 41.667 0.00 0.00 0.00 2.15
2219 2413 4.005650 CAGCTTATACATGGCCGATTCAT 58.994 43.478 0.00 0.00 0.00 2.57
2220 2414 3.402110 CAGCTTATACATGGCCGATTCA 58.598 45.455 0.00 0.00 0.00 2.57
2221 2415 2.744202 CCAGCTTATACATGGCCGATTC 59.256 50.000 0.00 0.00 0.00 2.52
2222 2416 2.371841 TCCAGCTTATACATGGCCGATT 59.628 45.455 0.00 0.00 33.92 3.34
2223 2417 1.977854 TCCAGCTTATACATGGCCGAT 59.022 47.619 0.00 0.00 33.92 4.18
2224 2418 1.070134 GTCCAGCTTATACATGGCCGA 59.930 52.381 0.00 0.00 33.92 5.54
2225 2419 1.070758 AGTCCAGCTTATACATGGCCG 59.929 52.381 0.00 0.00 33.92 6.13
2226 2420 2.498167 CAGTCCAGCTTATACATGGCC 58.502 52.381 0.00 0.00 33.92 5.36
2227 2421 2.498167 CCAGTCCAGCTTATACATGGC 58.502 52.381 0.00 0.00 33.92 4.40
2228 2422 2.811873 GCCCAGTCCAGCTTATACATGG 60.812 54.545 0.00 0.00 35.30 3.66
2229 2423 2.498167 GCCCAGTCCAGCTTATACATG 58.502 52.381 0.00 0.00 0.00 3.21
2230 2424 1.421646 GGCCCAGTCCAGCTTATACAT 59.578 52.381 0.00 0.00 0.00 2.29
2231 2425 0.837272 GGCCCAGTCCAGCTTATACA 59.163 55.000 0.00 0.00 0.00 2.29
2232 2426 1.132500 AGGCCCAGTCCAGCTTATAC 58.868 55.000 0.00 0.00 0.00 1.47
2233 2427 2.609747 CTAGGCCCAGTCCAGCTTATA 58.390 52.381 0.00 0.00 0.00 0.98
2234 2428 1.428869 CTAGGCCCAGTCCAGCTTAT 58.571 55.000 0.00 0.00 0.00 1.73
2235 2429 1.338136 GCTAGGCCCAGTCCAGCTTA 61.338 60.000 0.00 0.00 31.80 3.09
2236 2430 2.674220 GCTAGGCCCAGTCCAGCTT 61.674 63.158 0.00 0.00 31.80 3.74
2237 2431 2.243774 TAGCTAGGCCCAGTCCAGCT 62.244 60.000 0.00 6.96 40.79 4.24
2238 2432 1.124477 ATAGCTAGGCCCAGTCCAGC 61.124 60.000 0.00 0.00 33.43 4.85
2239 2433 1.428869 AATAGCTAGGCCCAGTCCAG 58.571 55.000 0.00 0.00 0.00 3.86
2240 2434 1.893315 AAATAGCTAGGCCCAGTCCA 58.107 50.000 0.00 0.00 0.00 4.02
2241 2435 2.092375 ACAAAATAGCTAGGCCCAGTCC 60.092 50.000 0.00 0.00 0.00 3.85
2242 2436 3.283259 ACAAAATAGCTAGGCCCAGTC 57.717 47.619 0.00 0.00 0.00 3.51
2243 2437 3.780850 AGTACAAAATAGCTAGGCCCAGT 59.219 43.478 0.00 0.00 0.00 4.00
2244 2438 4.130118 CAGTACAAAATAGCTAGGCCCAG 58.870 47.826 0.00 0.00 0.00 4.45
2245 2439 3.778075 TCAGTACAAAATAGCTAGGCCCA 59.222 43.478 0.00 0.00 0.00 5.36
2246 2440 4.417426 TCAGTACAAAATAGCTAGGCCC 57.583 45.455 0.00 0.00 0.00 5.80
2247 2441 8.532819 ACTATATCAGTACAAAATAGCTAGGCC 58.467 37.037 0.00 0.00 34.98 5.19
2260 2454 7.390996 GCTTGGTCTAGCTACTATATCAGTACA 59.609 40.741 0.00 0.00 38.80 2.90
2266 2460 5.417580 AGCTGCTTGGTCTAGCTACTATATC 59.582 44.000 0.00 0.00 45.30 1.63
2269 2463 3.320541 CAGCTGCTTGGTCTAGCTACTAT 59.679 47.826 0.00 0.00 45.37 2.12
2337 2531 4.608948 AACTAACCTGACCTCTCAACAG 57.391 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.