Multiple sequence alignment - TraesCS5A01G312300

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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 TraesCS5A01G312300 chr5A 100.000 4786 0 0 1 4786 523867394 523862609 0.000000e+00 8839
1 TraesCS5A01G312300 chr5A 94.952 733 28 5 1815 2539 569167366 569168097 0.000000e+00 1140
2 TraesCS5A01G312300 chr5A 94.498 418 22 1 1323 1740 569166990 569167406 1.120000e-180 643
3 TraesCS5A01G312300 chr4B 94.815 3915 155 18 895 4786 545077154 545081043 0.000000e+00 6061
4 TraesCS5A01G312300 chr4B 94.597 2295 105 13 896 3182 545063838 545066121 0.000000e+00 3533
5 TraesCS5A01G312300 chr4B 95.663 1545 47 4 3257 4786 545066121 545067660 0.000000e+00 2464
6 TraesCS5A01G312300 chr4B 94.498 418 22 1 1323 1740 240148544 240148960 1.120000e-180 643
7 TraesCS5A01G312300 chr4B 91.221 262 21 1 4525 4786 545067538 545067797 5.890000e-94 355
8 TraesCS5A01G312300 chr7A 95.283 2735 100 10 892 3598 343356478 343359211 0.000000e+00 4309
9 TraesCS5A01G312300 chr7A 97.056 1189 30 1 3596 4784 343359666 343360849 0.000000e+00 1997
10 TraesCS5A01G312300 chr7A 94.550 734 30 6 1815 2539 48007091 48006359 0.000000e+00 1125
11 TraesCS5A01G312300 chr7A 92.898 521 22 8 894 1414 48007971 48007466 0.000000e+00 743
12 TraesCS5A01G312300 chr7B 94.799 2442 110 12 894 3328 33834245 33831814 0.000000e+00 3790
13 TraesCS5A01G312300 chr7B 96.089 2148 62 4 2655 4786 78130430 78132571 0.000000e+00 3482
14 TraesCS5A01G312300 chr7B 95.906 1661 65 3 2652 4311 85871363 85869705 0.000000e+00 2687
15 TraesCS5A01G312300 chr7B 95.928 1449 38 3 3354 4786 33831818 33830375 0.000000e+00 2329
16 TraesCS5A01G312300 chr7B 94.341 1025 46 8 1806 2821 78129494 78130515 0.000000e+00 1561
17 TraesCS5A01G312300 chr7B 94.100 1017 52 4 1815 2824 85872288 85871273 0.000000e+00 1539
18 TraesCS5A01G312300 chr7B 79.830 1765 301 45 2904 4639 347326783 347325045 0.000000e+00 1236
19 TraesCS5A01G312300 chr7B 92.611 785 41 9 938 1721 78128756 78129524 0.000000e+00 1112
20 TraesCS5A01G312300 chr7B 91.221 262 21 1 4525 4786 33830497 33830238 5.890000e-94 355
21 TraesCS5A01G312300 chr4A 96.420 1592 52 5 2199 3789 588581849 588580262 0.000000e+00 2619
22 TraesCS5A01G312300 chr4A 93.641 1321 58 14 893 2206 588583078 588581777 0.000000e+00 1951
23 TraesCS5A01G312300 chr6A 96.106 1592 57 5 2199 3788 201629133 201627545 0.000000e+00 2591
24 TraesCS5A01G312300 chr6A 92.955 1320 67 13 893 2206 201630360 201629061 0.000000e+00 1899
25 TraesCS5A01G312300 chr6A 79.660 1765 304 45 2904 4639 358618083 358619821 0.000000e+00 1219
26 TraesCS5A01G312300 chr6B 95.287 1570 67 3 1766 3328 503893718 503892149 0.000000e+00 2483
27 TraesCS5A01G312300 chr6B 95.718 1448 42 2 3354 4786 503892153 503890711 0.000000e+00 2313
28 TraesCS5A01G312300 chr6B 94.598 833 35 9 894 1726 503894524 503893702 0.000000e+00 1280
29 TraesCS5A01G312300 chr6B 94.498 418 22 1 1323 1740 159804336 159803920 1.120000e-180 643
30 TraesCS5A01G312300 chr6B 93.381 423 18 8 894 1315 503895231 503894818 6.810000e-173 617
31 TraesCS5A01G312300 chr3A 82.167 1458 223 29 3201 4644 501730647 501729213 0.000000e+00 1218
32 TraesCS5A01G312300 chr5D 87.542 899 101 9 1 896 412118624 412117734 0.000000e+00 1029
33 TraesCS5A01G312300 chr3B 92.500 520 24 9 895 1414 477327416 477326912 0.000000e+00 730
34 TraesCS5A01G312300 chr2B 92.322 521 24 9 895 1414 198096415 198095910 0.000000e+00 726
35 TraesCS5A01G312300 chr5B 86.854 426 51 3 471 896 495225011 495224591 5.610000e-129 472
36 TraesCS5A01G312300 chr5B 88.571 315 35 1 1 314 495446979 495446665 9.720000e-102 381


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 TraesCS5A01G312300 chr5A 523862609 523867394 4785 True 8839.000000 8839 100.000000 1 4786 1 chr5A.!!$R1 4785
1 TraesCS5A01G312300 chr5A 569166990 569168097 1107 False 891.500000 1140 94.725000 1323 2539 2 chr5A.!!$F1 1216
2 TraesCS5A01G312300 chr4B 545077154 545081043 3889 False 6061.000000 6061 94.815000 895 4786 1 chr4B.!!$F2 3891
3 TraesCS5A01G312300 chr4B 545063838 545067797 3959 False 2117.333333 3533 93.827000 896 4786 3 chr4B.!!$F3 3890
4 TraesCS5A01G312300 chr7A 343356478 343360849 4371 False 3153.000000 4309 96.169500 892 4784 2 chr7A.!!$F1 3892
5 TraesCS5A01G312300 chr7A 48006359 48007971 1612 True 934.000000 1125 93.724000 894 2539 2 chr7A.!!$R1 1645
6 TraesCS5A01G312300 chr7B 33830238 33834245 4007 True 2158.000000 3790 93.982667 894 4786 3 chr7B.!!$R2 3892
7 TraesCS5A01G312300 chr7B 85869705 85872288 2583 True 2113.000000 2687 95.003000 1815 4311 2 chr7B.!!$R3 2496
8 TraesCS5A01G312300 chr7B 78128756 78132571 3815 False 2051.666667 3482 94.347000 938 4786 3 chr7B.!!$F1 3848
9 TraesCS5A01G312300 chr7B 347325045 347326783 1738 True 1236.000000 1236 79.830000 2904 4639 1 chr7B.!!$R1 1735
10 TraesCS5A01G312300 chr4A 588580262 588583078 2816 True 2285.000000 2619 95.030500 893 3789 2 chr4A.!!$R1 2896
11 TraesCS5A01G312300 chr6A 201627545 201630360 2815 True 2245.000000 2591 94.530500 893 3788 2 chr6A.!!$R1 2895
12 TraesCS5A01G312300 chr6A 358618083 358619821 1738 False 1219.000000 1219 79.660000 2904 4639 1 chr6A.!!$F1 1735
13 TraesCS5A01G312300 chr6B 503890711 503895231 4520 True 1673.250000 2483 94.746000 894 4786 4 chr6B.!!$R2 3892
14 TraesCS5A01G312300 chr3A 501729213 501730647 1434 True 1218.000000 1218 82.167000 3201 4644 1 chr3A.!!$R1 1443
15 TraesCS5A01G312300 chr5D 412117734 412118624 890 True 1029.000000 1029 87.542000 1 896 1 chr5D.!!$R1 895
16 TraesCS5A01G312300 chr3B 477326912 477327416 504 True 730.000000 730 92.500000 895 1414 1 chr3B.!!$R1 519
17 TraesCS5A01G312300 chr2B 198095910 198096415 505 True 726.000000 726 92.322000 895 1414 1 chr2B.!!$R1 519

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
552 555 0.106708 GTCCATGAGCGGCCTATCAA 59.893 55.0 10.43 0.0 0.00 2.57 F
728 731 0.181114 AAGCTGACAACACTGCCTCA 59.819 50.0 0.00 0.0 35.80 3.86 F
1175 1889 0.250513 GACCAATCCTCCTGTCGCTT 59.749 55.0 0.00 0.0 0.00 4.68 F
2127 3150 0.192566 TACCACTCCCAACAGGACCT 59.807 55.0 0.00 0.0 40.93 3.85 F
2829 4022 0.322277 CTGCAGAACATCACAGGCCT 60.322 55.0 8.42 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 2586 0.542333 TCGGAACCAACAGGTCACAA 59.458 50.000 0.00 0.00 33.53 3.33 R
2127 3150 1.301716 GCGTCCTGCTTGAAGTGGA 60.302 57.895 5.27 5.27 41.73 4.02 R
2308 3332 2.142356 TTGGGTCCGCAAATCATGAT 57.858 45.000 1.18 1.18 0.00 2.45 R
3387 4619 1.699634 CAAGGTTCTGGTCTCCCAAGA 59.300 52.381 0.00 0.00 41.27 3.02 R
3906 5601 2.046009 TACACCTGTTCCTGCCGCAA 62.046 55.000 0.00 0.00 0.00 4.85 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 3.969802 GCCATACATGCCCTGCGC 61.970 66.667 0.00 0.00 38.31 6.09
58 60 3.698289 AGATAGACGGACTTCTTCACCA 58.302 45.455 0.00 0.00 0.00 4.17
60 62 4.527038 AGATAGACGGACTTCTTCACCAAA 59.473 41.667 0.00 0.00 0.00 3.28
70 72 5.821204 ACTTCTTCACCAAAATCAAGTTCG 58.179 37.500 0.00 0.00 0.00 3.95
74 76 3.815809 TCACCAAAATCAAGTTCGACCT 58.184 40.909 0.00 0.00 0.00 3.85
96 99 7.738847 ACCTTGATCAAGTTCATGGAAAAATT 58.261 30.769 29.03 0.00 41.29 1.82
97 100 8.212995 ACCTTGATCAAGTTCATGGAAAAATTT 58.787 29.630 29.03 0.00 41.29 1.82
111 114 6.389091 TGGAAAAATTTGTCCATGAATCTCG 58.611 36.000 23.85 0.00 39.04 4.04
114 117 3.931907 ATTTGTCCATGAATCTCGGGA 57.068 42.857 0.00 0.00 0.00 5.14
121 124 2.208431 CATGAATCTCGGGAGCTCAAC 58.792 52.381 17.19 6.83 0.00 3.18
127 130 1.833630 TCTCGGGAGCTCAACATCAAT 59.166 47.619 17.19 0.00 0.00 2.57
128 131 1.938577 CTCGGGAGCTCAACATCAATG 59.061 52.381 17.19 0.00 0.00 2.82
139 142 2.105006 ACATCAATGTTGCTCTCGCT 57.895 45.000 0.00 0.00 37.90 4.93
140 143 2.005451 ACATCAATGTTGCTCTCGCTC 58.995 47.619 0.00 0.00 37.90 5.03
144 147 0.244994 AATGTTGCTCTCGCTCGACT 59.755 50.000 0.00 0.00 36.97 4.18
145 148 0.457509 ATGTTGCTCTCGCTCGACTG 60.458 55.000 0.00 0.00 36.97 3.51
154 157 2.085262 CGCTCGACTGTGCAGAGTG 61.085 63.158 22.83 13.43 36.40 3.51
159 162 1.066136 CGACTGTGCAGAGTGACATG 58.934 55.000 22.83 1.99 0.00 3.21
164 167 2.479275 CTGTGCAGAGTGACATGAACAG 59.521 50.000 12.66 12.66 44.53 3.16
165 168 2.158914 TGTGCAGAGTGACATGAACAGT 60.159 45.455 0.00 2.00 29.75 3.55
166 169 2.222678 GTGCAGAGTGACATGAACAGTG 59.777 50.000 0.00 0.64 0.00 3.66
169 172 3.867600 GCAGAGTGACATGAACAGTGGAT 60.868 47.826 0.00 0.00 0.00 3.41
170 173 4.321718 CAGAGTGACATGAACAGTGGATT 58.678 43.478 0.00 0.00 0.00 3.01
178 181 5.060506 ACATGAACAGTGGATTCGTTTACA 58.939 37.500 0.00 0.00 0.00 2.41
209 212 0.400213 TCCTCGAGCATTGTTTGGGT 59.600 50.000 6.99 0.00 0.00 4.51
232 235 0.602905 CCCTTCGACCGGATTATGCC 60.603 60.000 9.46 0.00 0.00 4.40
238 241 4.074627 TCGACCGGATTATGCCAAATTA 57.925 40.909 9.46 0.00 0.00 1.40
242 245 5.560183 CGACCGGATTATGCCAAATTAAGTC 60.560 44.000 9.46 0.00 0.00 3.01
251 254 5.699097 TGCCAAATTAAGTCTACAACCAC 57.301 39.130 0.00 0.00 0.00 4.16
253 256 5.594725 TGCCAAATTAAGTCTACAACCACAA 59.405 36.000 0.00 0.00 0.00 3.33
255 258 6.586082 GCCAAATTAAGTCTACAACCACAATG 59.414 38.462 0.00 0.00 0.00 2.82
264 267 7.425606 AGTCTACAACCACAATGTCAAATTTC 58.574 34.615 0.00 0.00 32.27 2.17
265 268 7.068103 AGTCTACAACCACAATGTCAAATTTCA 59.932 33.333 0.00 0.00 32.27 2.69
268 271 5.691305 ACAACCACAATGTCAAATTTCATCG 59.309 36.000 0.00 0.00 0.00 3.84
274 277 7.025365 CACAATGTCAAATTTCATCGTGATCT 58.975 34.615 5.43 0.00 32.70 2.75
337 340 2.108168 TCGAATCTGGACGGAAATCCT 58.892 47.619 0.00 0.00 39.75 3.24
364 367 3.259625 AGTTTGGAAGGAGTCTAGCTGAC 59.740 47.826 0.00 2.01 45.67 3.51
381 384 1.202604 TGACGACACCCTTTGGAAGAC 60.203 52.381 0.00 0.00 34.81 3.01
383 386 0.107831 CGACACCCTTTGGAAGACCA 59.892 55.000 0.00 0.00 45.34 4.02
427 430 0.909610 CTCCTGGCTACAACCCCTCA 60.910 60.000 0.00 0.00 0.00 3.86
452 455 7.807433 CACAATTTCAATTTGATCGGACTGTTA 59.193 33.333 0.00 0.00 0.00 2.41
458 461 4.610605 TTTGATCGGACTGTTAACTCCA 57.389 40.909 12.86 2.84 0.00 3.86
469 472 2.148768 GTTAACTCCAGGAAACACCCG 58.851 52.381 0.00 0.00 40.05 5.28
470 473 1.719529 TAACTCCAGGAAACACCCGA 58.280 50.000 0.00 0.00 40.05 5.14
488 491 2.589014 CGAGAAGTGCTTCAATTTGCC 58.411 47.619 13.58 0.00 41.84 4.52
499 502 6.196910 GTGCTTCAATTTGCCAATTTGTTTTC 59.803 34.615 10.78 2.53 29.41 2.29
502 505 6.998968 TCAATTTGCCAATTTGTTTTCTGT 57.001 29.167 10.78 0.00 29.41 3.41
504 507 4.612932 TTTGCCAATTTGTTTTCTGTGC 57.387 36.364 0.00 0.00 0.00 4.57
518 521 2.422597 TCTGTGCGAAACAAATCCGAT 58.577 42.857 0.00 0.00 38.67 4.18
540 543 3.260632 TCCGAGTTCATCTTTGTCCATGA 59.739 43.478 0.00 0.00 0.00 3.07
546 549 0.749454 ATCTTTGTCCATGAGCGGCC 60.749 55.000 0.00 0.00 0.00 6.13
552 555 0.106708 GTCCATGAGCGGCCTATCAA 59.893 55.000 10.43 0.00 0.00 2.57
567 570 6.465084 GGCCTATCAAACGACCTCTTATTAT 58.535 40.000 0.00 0.00 0.00 1.28
605 608 4.256920 GGTGATGTGCTATGTTCTCAAGT 58.743 43.478 0.00 0.00 0.00 3.16
606 609 4.093998 GGTGATGTGCTATGTTCTCAAGTG 59.906 45.833 0.00 0.00 0.00 3.16
654 657 1.860078 GTGCTAACCACTGTCGTGC 59.140 57.895 0.00 0.00 41.35 5.34
670 673 2.903350 GCCGTTTTCACACCGGGT 60.903 61.111 6.32 0.00 41.96 5.28
674 677 1.554042 CGTTTTCACACCGGGTCGAG 61.554 60.000 6.32 0.00 0.00 4.04
711 714 0.325933 TCTGACCACATGGCTCCAAG 59.674 55.000 0.00 0.00 39.32 3.61
714 717 1.303888 ACCACATGGCTCCAAGCTG 60.304 57.895 0.00 0.00 41.99 4.24
716 719 1.310933 CCACATGGCTCCAAGCTGAC 61.311 60.000 0.00 0.00 41.99 3.51
717 720 0.607217 CACATGGCTCCAAGCTGACA 60.607 55.000 0.00 0.00 41.99 3.58
721 724 0.819259 TGGCTCCAAGCTGACAACAC 60.819 55.000 0.00 0.00 41.99 3.32
722 725 0.536006 GGCTCCAAGCTGACAACACT 60.536 55.000 0.00 0.00 41.99 3.55
725 728 0.819259 TCCAAGCTGACAACACTGCC 60.819 55.000 0.00 0.00 35.80 4.85
727 730 0.590195 CAAGCTGACAACACTGCCTC 59.410 55.000 0.00 0.00 35.80 4.70
728 731 0.181114 AAGCTGACAACACTGCCTCA 59.819 50.000 0.00 0.00 35.80 3.86
751 754 2.506217 CGACACCATCGTCCCGTG 60.506 66.667 0.00 0.00 46.25 4.94
780 783 0.807667 CCTCCTTCAACATCTCCGCG 60.808 60.000 0.00 0.00 0.00 6.46
788 791 4.758251 CATCTCCGCGCCACCACA 62.758 66.667 0.00 0.00 0.00 4.17
789 792 4.015406 ATCTCCGCGCCACCACAA 62.015 61.111 0.00 0.00 0.00 3.33
790 793 3.329542 ATCTCCGCGCCACCACAAT 62.330 57.895 0.00 0.00 0.00 2.71
801 804 2.209315 ACCACAATGCCAAGCCACC 61.209 57.895 0.00 0.00 0.00 4.61
805 808 3.055719 AATGCCAAGCCACCGTCG 61.056 61.111 0.00 0.00 0.00 5.12
821 824 1.456145 TCGGCGCCCAGTCCTTATA 60.456 57.895 23.46 0.00 0.00 0.98
885 888 2.892373 TTTTACTTCGGCTCGCATTG 57.108 45.000 0.00 0.00 0.00 2.82
886 889 0.446222 TTTACTTCGGCTCGCATTGC 59.554 50.000 0.00 0.00 0.00 3.56
887 890 0.391130 TTACTTCGGCTCGCATTGCT 60.391 50.000 7.12 0.00 0.00 3.91
888 891 0.391130 TACTTCGGCTCGCATTGCTT 60.391 50.000 7.12 0.00 0.00 3.91
889 892 1.237285 ACTTCGGCTCGCATTGCTTT 61.237 50.000 7.12 0.00 0.00 3.51
890 893 0.726827 CTTCGGCTCGCATTGCTTTA 59.273 50.000 7.12 0.00 0.00 1.85
995 998 1.839994 TGGAGGGTCAAGATAAGCCTG 59.160 52.381 0.00 0.00 44.46 4.85
996 999 1.840635 GGAGGGTCAAGATAAGCCTGT 59.159 52.381 0.00 0.00 44.46 4.00
1027 1031 6.317893 GGGATCTAACCGTGAATACACAAAAT 59.682 38.462 0.00 0.00 46.20 1.82
1039 1043 3.495434 ACACAAAATTACCCCTGACGA 57.505 42.857 0.00 0.00 0.00 4.20
1059 1063 5.345702 ACGATGTACGCTAAGCAATTTAGA 58.654 37.500 0.00 0.00 46.94 2.10
1175 1889 0.250513 GACCAATCCTCCTGTCGCTT 59.749 55.000 0.00 0.00 0.00 4.68
1282 2036 4.429212 CCCGCGACATCCACGACA 62.429 66.667 8.23 0.00 0.00 4.35
1452 2296 0.379669 CATCCGTTCATTGCTCCTGC 59.620 55.000 0.00 0.00 40.20 4.85
1492 2336 7.611467 AGTTCTGCATAAATAGTGAAACCATGA 59.389 33.333 0.00 0.00 37.80 3.07
1623 2467 4.163268 TGAAATCATACCACGGATCCTCAA 59.837 41.667 10.75 0.00 0.00 3.02
1626 2470 2.835156 TCATACCACGGATCCTCAACAA 59.165 45.455 10.75 0.00 0.00 2.83
1630 2474 1.665679 CCACGGATCCTCAACAAATCG 59.334 52.381 10.75 0.00 0.00 3.34
1972 2989 1.538047 TGCATGAGGCCTCTTGAAAC 58.462 50.000 39.25 26.49 43.89 2.78
1973 2990 1.074405 TGCATGAGGCCTCTTGAAACT 59.926 47.619 39.25 13.79 43.89 2.66
1994 3011 6.111768 ACTGACAATTGCGATTGAATCTAC 57.888 37.500 29.52 14.40 44.37 2.59
2070 3087 6.237901 TGGTCTTGCGCTCCATTAAATATAT 58.762 36.000 9.73 0.00 0.00 0.86
2127 3150 0.192566 TACCACTCCCAACAGGACCT 59.807 55.000 0.00 0.00 40.93 3.85
2133 3156 0.401395 TCCCAACAGGACCTCCACTT 60.401 55.000 0.00 0.00 40.93 3.16
2135 3158 0.764890 CCAACAGGACCTCCACTTCA 59.235 55.000 0.00 0.00 38.89 3.02
2190 3213 6.158598 AGCAACAACCAAACATCATGTATTC 58.841 36.000 0.00 0.00 0.00 1.75
2320 3344 4.201841 TGCTGAACTGTATCATGATTTGCG 60.202 41.667 14.65 3.22 0.00 4.85
2417 3444 4.546570 GCGTGAAGCCTACAAAAGAAAAT 58.453 39.130 0.00 0.00 40.81 1.82
2421 3448 7.328493 GCGTGAAGCCTACAAAAGAAAATAAAT 59.672 33.333 0.00 0.00 40.81 1.40
2458 3487 1.134037 TGGCCTACAAAACGGAACACT 60.134 47.619 3.32 0.00 0.00 3.55
2646 3676 3.767630 AACGCCAAACCCGTGAGCT 62.768 57.895 0.00 0.00 39.13 4.09
2648 3678 2.388232 CGCCAAACCCGTGAGCTAC 61.388 63.158 0.00 0.00 0.00 3.58
2663 3693 8.737175 CCCGTGAGCTACATAGAAATATTACTA 58.263 37.037 0.00 0.00 0.00 1.82
2829 4022 0.322277 CTGCAGAACATCACAGGCCT 60.322 55.000 8.42 0.00 0.00 5.19
2949 4142 4.855105 TGCGTACCAGATGCATCC 57.145 55.556 23.06 6.45 45.41 3.51
2951 4144 0.469494 TGCGTACCAGATGCATCCAT 59.531 50.000 23.06 11.23 45.41 3.41
2979 4172 4.130118 AGAAGAATGACACTCACACAACC 58.870 43.478 0.00 0.00 0.00 3.77
3223 4422 0.604073 TTATCAGGCAACGACCACGA 59.396 50.000 0.00 0.00 46.39 4.35
3328 4560 8.772250 CCTCTACCCCAATAATATGTGTCATAT 58.228 37.037 0.00 0.00 0.00 1.78
3361 4593 4.180817 CGTGACCTTGTGCATCATAACTA 58.819 43.478 0.00 0.00 0.00 2.24
3469 4704 5.499004 TGTTTGCTAGACCAGGTAGATTT 57.501 39.130 0.00 0.00 0.00 2.17
3723 5418 1.912971 GGTTCCAATACGAGGGGCT 59.087 57.895 0.00 0.00 0.00 5.19
3824 5519 3.949754 TCAGGATGATGAGGATGCAAAAC 59.050 43.478 0.00 0.00 42.56 2.43
3906 5601 1.202348 CCTTGATCGTCGAGTCAGCAT 60.202 52.381 0.00 0.00 0.00 3.79
4061 5757 2.164624 CACAGAGTTAAGAGGTCTCCGG 59.835 54.545 0.00 0.00 0.00 5.14
4339 6050 6.051717 CCTGTATATTAGAGCATACCATGGC 58.948 44.000 13.04 0.00 0.00 4.40
4442 6153 3.560068 AGTCGATGACACAAACCAAGTTC 59.440 43.478 0.00 0.00 34.60 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.422479 TCCGTCTATCTTGAGTTCACCG 59.578 50.000 0.00 0.00 0.00 4.94
74 76 8.961294 ACAAATTTTTCCATGAACTTGATCAA 57.039 26.923 8.12 8.12 32.06 2.57
96 99 1.134401 GCTCCCGAGATTCATGGACAA 60.134 52.381 0.00 0.00 0.00 3.18
97 100 0.465705 GCTCCCGAGATTCATGGACA 59.534 55.000 0.00 0.00 0.00 4.02
105 108 1.833630 TGATGTTGAGCTCCCGAGATT 59.166 47.619 12.15 0.00 0.00 2.40
139 142 0.961753 ATGTCACTCTGCACAGTCGA 59.038 50.000 0.00 0.00 0.00 4.20
140 143 1.066136 CATGTCACTCTGCACAGTCG 58.934 55.000 0.00 0.00 0.00 4.18
144 147 2.158914 ACTGTTCATGTCACTCTGCACA 60.159 45.455 0.00 0.00 0.00 4.57
145 148 2.222678 CACTGTTCATGTCACTCTGCAC 59.777 50.000 0.00 0.00 0.00 4.57
154 157 4.749245 AAACGAATCCACTGTTCATGTC 57.251 40.909 0.00 0.00 0.00 3.06
159 162 4.201685 CCGATGTAAACGAATCCACTGTTC 60.202 45.833 0.00 0.00 31.90 3.18
164 167 1.329599 GGCCGATGTAAACGAATCCAC 59.670 52.381 0.00 0.00 31.90 4.02
165 168 1.066071 TGGCCGATGTAAACGAATCCA 60.066 47.619 0.00 0.00 31.90 3.41
166 169 1.329599 GTGGCCGATGTAAACGAATCC 59.670 52.381 0.00 0.00 31.90 3.01
169 172 1.628447 GCGTGGCCGATGTAAACGAA 61.628 55.000 13.13 0.00 36.38 3.85
170 173 2.095847 GCGTGGCCGATGTAAACGA 61.096 57.895 13.13 0.00 36.38 3.85
209 212 2.076207 TAATCCGGTCGAAGGGATCA 57.924 50.000 16.43 2.33 42.14 2.92
221 224 6.485313 TGTAGACTTAATTTGGCATAATCCGG 59.515 38.462 0.00 0.00 0.00 5.14
222 225 7.490962 TGTAGACTTAATTTGGCATAATCCG 57.509 36.000 0.00 0.00 0.00 4.18
232 235 8.349245 TGACATTGTGGTTGTAGACTTAATTTG 58.651 33.333 0.00 0.00 0.00 2.32
238 241 6.959639 ATTTGACATTGTGGTTGTAGACTT 57.040 33.333 0.00 0.00 0.00 3.01
242 245 7.060979 CGATGAAATTTGACATTGTGGTTGTAG 59.939 37.037 0.00 0.00 0.00 2.74
251 254 7.245604 TCAGATCACGATGAAATTTGACATTG 58.754 34.615 0.00 0.46 34.97 2.82
253 256 6.990341 TCAGATCACGATGAAATTTGACAT 57.010 33.333 0.00 0.00 0.00 3.06
255 258 6.183360 ACCATCAGATCACGATGAAATTTGAC 60.183 38.462 20.85 0.00 42.39 3.18
264 267 1.413812 TCCCACCATCAGATCACGATG 59.586 52.381 14.99 14.99 40.01 3.84
265 268 1.793414 TCCCACCATCAGATCACGAT 58.207 50.000 0.00 0.00 0.00 3.73
268 271 3.217626 GGAAATCCCACCATCAGATCAC 58.782 50.000 0.00 0.00 34.14 3.06
308 311 2.106683 CCAGATTCGACAACGCCCC 61.107 63.158 0.00 0.00 39.58 5.80
314 317 2.823924 TTTCCGTCCAGATTCGACAA 57.176 45.000 0.00 0.00 0.00 3.18
320 323 1.473434 GCGAGGATTTCCGTCCAGATT 60.473 52.381 0.00 0.00 40.90 2.40
321 324 0.105039 GCGAGGATTTCCGTCCAGAT 59.895 55.000 0.00 0.00 40.90 2.90
337 340 0.038526 GACTCCTTCCAAACTCGCGA 60.039 55.000 9.26 9.26 0.00 5.87
364 367 0.107831 TGGTCTTCCAAAGGGTGTCG 59.892 55.000 0.00 0.00 41.25 4.35
401 404 3.536570 GGTTGTAGCCAGGAGAATTCTC 58.463 50.000 24.68 24.68 42.14 2.87
408 411 0.909610 TGAGGGGTTGTAGCCAGGAG 60.910 60.000 0.00 0.00 37.54 3.69
411 414 0.400213 TTGTGAGGGGTTGTAGCCAG 59.600 55.000 0.00 0.00 37.54 4.85
427 430 6.331369 ACAGTCCGATCAAATTGAAATTGT 57.669 33.333 0.00 0.00 0.00 2.71
452 455 0.396811 CTCGGGTGTTTCCTGGAGTT 59.603 55.000 0.00 0.00 42.62 3.01
458 461 0.250338 GCACTTCTCGGGTGTTTCCT 60.250 55.000 0.00 0.00 37.07 3.36
469 472 3.648339 TGGCAAATTGAAGCACTTCTC 57.352 42.857 11.44 0.00 40.14 2.87
470 473 4.612264 ATTGGCAAATTGAAGCACTTCT 57.388 36.364 3.01 0.00 40.14 2.85
499 502 2.476185 GGATCGGATTTGTTTCGCACAG 60.476 50.000 0.00 0.00 36.48 3.66
502 505 0.724549 CGGATCGGATTTGTTTCGCA 59.275 50.000 0.00 0.00 0.00 5.10
504 507 2.268298 ACTCGGATCGGATTTGTTTCG 58.732 47.619 3.13 0.00 0.00 3.46
518 521 3.260632 TCATGGACAAAGATGAACTCGGA 59.739 43.478 0.00 0.00 0.00 4.55
540 543 1.153429 GGTCGTTTGATAGGCCGCT 60.153 57.895 0.00 0.00 0.00 5.52
546 549 8.577296 TCTCCATAATAAGAGGTCGTTTGATAG 58.423 37.037 0.00 0.00 0.00 2.08
592 595 4.095932 ACATGCATGCACTTGAGAACATAG 59.904 41.667 25.37 1.02 0.00 2.23
605 608 4.520111 AGAGTCAAACTTTACATGCATGCA 59.480 37.500 26.53 25.04 0.00 3.96
606 609 5.051891 AGAGTCAAACTTTACATGCATGC 57.948 39.130 26.53 11.82 0.00 4.06
652 655 2.902846 CCCGGTGTGAAAACGGCA 60.903 61.111 0.00 0.00 45.93 5.69
653 656 2.900167 GACCCGGTGTGAAAACGGC 61.900 63.158 0.00 0.00 45.93 5.68
654 657 2.600475 CGACCCGGTGTGAAAACGG 61.600 63.158 0.00 0.00 46.79 4.44
699 702 0.111061 TTGTCAGCTTGGAGCCATGT 59.889 50.000 4.59 0.00 43.77 3.21
702 705 0.819259 GTGTTGTCAGCTTGGAGCCA 60.819 55.000 0.00 0.00 43.77 4.75
711 714 0.520404 CATGAGGCAGTGTTGTCAGC 59.480 55.000 0.00 0.00 0.00 4.26
714 717 1.499056 CGCATGAGGCAGTGTTGTC 59.501 57.895 0.00 0.00 45.17 3.18
716 719 2.177531 GCGCATGAGGCAGTGTTG 59.822 61.111 0.30 0.00 45.17 3.33
717 720 3.058160 GGCGCATGAGGCAGTGTT 61.058 61.111 18.09 0.00 45.17 3.32
725 728 2.512286 ATGGTGTCGGCGCATGAG 60.512 61.111 10.83 0.00 0.00 2.90
727 730 3.928769 CGATGGTGTCGGCGCATG 61.929 66.667 10.83 0.00 46.47 4.06
759 762 1.480954 GCGGAGATGTTGAAGGAGGTA 59.519 52.381 0.00 0.00 0.00 3.08
766 769 2.032634 GTGGCGCGGAGATGTTGAA 61.033 57.895 8.83 0.00 0.00 2.69
780 783 2.047939 GCTTGGCATTGTGGTGGC 60.048 61.111 0.00 0.00 44.24 5.01
788 791 3.055719 CGACGGTGGCTTGGCATT 61.056 61.111 0.00 0.00 0.00 3.56
805 808 2.271944 AAATATAAGGACTGGGCGCC 57.728 50.000 21.18 21.18 0.00 6.53
865 868 2.667171 GCAATGCGAGCCGAAGTAAAAA 60.667 45.455 0.00 0.00 0.00 1.94
866 869 1.135803 GCAATGCGAGCCGAAGTAAAA 60.136 47.619 0.00 0.00 0.00 1.52
867 870 0.446222 GCAATGCGAGCCGAAGTAAA 59.554 50.000 0.00 0.00 0.00 2.01
868 871 0.391130 AGCAATGCGAGCCGAAGTAA 60.391 50.000 0.00 0.00 0.00 2.24
869 872 0.391130 AAGCAATGCGAGCCGAAGTA 60.391 50.000 0.00 0.00 0.00 2.24
870 873 1.237285 AAAGCAATGCGAGCCGAAGT 61.237 50.000 0.00 0.00 0.00 3.01
871 874 0.726827 TAAAGCAATGCGAGCCGAAG 59.273 50.000 0.00 0.00 0.00 3.79
872 875 1.063912 CATAAAGCAATGCGAGCCGAA 59.936 47.619 0.00 0.00 0.00 4.30
873 876 0.657312 CATAAAGCAATGCGAGCCGA 59.343 50.000 0.00 0.00 0.00 5.54
874 877 0.378257 ACATAAAGCAATGCGAGCCG 59.622 50.000 0.00 0.00 0.00 5.52
875 878 3.499918 AGATACATAAAGCAATGCGAGCC 59.500 43.478 0.00 0.00 0.00 4.70
876 879 4.450419 AGAGATACATAAAGCAATGCGAGC 59.550 41.667 0.00 0.00 0.00 5.03
877 880 6.865726 AGTAGAGATACATAAAGCAATGCGAG 59.134 38.462 0.00 0.00 0.00 5.03
878 881 6.749139 AGTAGAGATACATAAAGCAATGCGA 58.251 36.000 0.00 0.00 0.00 5.10
879 882 7.810282 AGTAGTAGAGATACATAAAGCAATGCG 59.190 37.037 0.00 0.00 0.00 4.73
995 998 3.869065 TCACGGTTAGATCCCATTGAAC 58.131 45.455 0.00 0.00 0.00 3.18
996 999 4.561500 TTCACGGTTAGATCCCATTGAA 57.438 40.909 0.00 0.00 0.00 2.69
1027 1031 0.457035 GCGTACATCGTCAGGGGTAA 59.543 55.000 0.00 0.00 42.13 2.85
1039 1043 5.470098 CCCATCTAAATTGCTTAGCGTACAT 59.530 40.000 0.00 0.00 37.51 2.29
1059 1063 1.079127 CAGAGTTTCGTCCGCCCAT 60.079 57.895 0.00 0.00 0.00 4.00
1181 1895 1.658114 GTTTCGGTGGAGGGCAAAC 59.342 57.895 0.00 0.00 0.00 2.93
1182 1896 1.894756 CGTTTCGGTGGAGGGCAAA 60.895 57.895 0.00 0.00 0.00 3.68
1452 2296 4.596801 GCAGAACTATGCAGAACAGAAG 57.403 45.455 0.00 0.00 45.77 2.85
1623 2467 7.391148 AATTTTCAGTACCATAGCGATTTGT 57.609 32.000 0.00 0.00 0.00 2.83
1626 2470 7.624360 TCAAATTTTCAGTACCATAGCGATT 57.376 32.000 0.00 0.00 0.00 3.34
1630 2474 8.129211 GTGGTATCAAATTTTCAGTACCATAGC 58.871 37.037 17.10 7.27 42.28 2.97
1742 2586 0.542333 TCGGAACCAACAGGTCACAA 59.458 50.000 0.00 0.00 33.53 3.33
1751 2595 9.268268 TCATATAGATTAATGTTCGGAACCAAC 57.732 33.333 17.62 4.46 0.00 3.77
1892 2909 9.136323 GGGGACATCTTTGTAATAGATTCAATT 57.864 33.333 0.00 0.00 35.79 2.32
1972 2989 6.355397 AGTAGATTCAATCGCAATTGTCAG 57.645 37.500 7.40 0.00 42.46 3.51
1973 2990 6.816140 TGTAGTAGATTCAATCGCAATTGTCA 59.184 34.615 7.40 0.00 42.46 3.58
2070 3087 7.453393 ACTCCTGTAAAAAGATGTGAGATCAA 58.547 34.615 0.00 0.00 0.00 2.57
2127 3150 1.301716 GCGTCCTGCTTGAAGTGGA 60.302 57.895 5.27 5.27 41.73 4.02
2133 3156 2.357034 GGTTCGCGTCCTGCTTGA 60.357 61.111 5.77 0.00 43.27 3.02
2135 3158 4.699522 GGGGTTCGCGTCCTGCTT 62.700 66.667 18.58 0.00 43.27 3.91
2190 3213 2.826428 CGTCCTGACTGGGTTATGATG 58.174 52.381 0.00 0.00 36.20 3.07
2308 3332 2.142356 TTGGGTCCGCAAATCATGAT 57.858 45.000 1.18 1.18 0.00 2.45
2320 3344 3.006537 GCCTTTTTAGTTCCTTTGGGTCC 59.993 47.826 0.00 0.00 0.00 4.46
2374 3399 7.014711 TCACGCCTTCTCTTATTAATCTCATCT 59.985 37.037 0.00 0.00 0.00 2.90
2417 3444 6.299141 GCCATCTATTTCCTCAGTGGATTTA 58.701 40.000 0.00 0.00 45.68 1.40
2421 3448 2.439507 GGCCATCTATTTCCTCAGTGGA 59.560 50.000 0.00 0.00 44.51 4.02
2947 4140 5.624159 AGTGTCATTCTTCTTGAACATGGA 58.376 37.500 0.00 0.00 37.52 3.41
2949 4142 6.017687 TGTGAGTGTCATTCTTCTTGAACATG 60.018 38.462 0.00 0.00 37.52 3.21
2951 4144 5.294306 GTGTGAGTGTCATTCTTCTTGAACA 59.706 40.000 0.00 0.00 37.52 3.18
3223 4422 4.299155 CAGTATTCCATACGCATCTTCGT 58.701 43.478 0.00 0.00 45.49 3.85
3387 4619 1.699634 CAAGGTTCTGGTCTCCCAAGA 59.300 52.381 0.00 0.00 41.27 3.02
3399 4631 2.777692 TCACCAGTTTCTCCAAGGTTCT 59.222 45.455 0.00 0.00 0.00 3.01
3469 4704 8.978539 GTCGTATTCATAACTCATGATAGCAAA 58.021 33.333 0.00 0.00 43.26 3.68
3515 4752 9.828852 AATTGCATTATTTAAAGTTTGTGCATG 57.171 25.926 13.56 0.00 40.52 4.06
3516 4753 9.828852 CAATTGCATTATTTAAAGTTTGTGCAT 57.171 25.926 13.56 2.70 40.52 3.96
3678 5373 2.280389 CACAGTGGCAGCAGTCGT 60.280 61.111 0.00 0.00 0.00 4.34
3906 5601 2.046009 TACACCTGTTCCTGCCGCAA 62.046 55.000 0.00 0.00 0.00 4.85
4061 5757 4.142271 CCGTATGAGATCCAGCCTAAGATC 60.142 50.000 0.00 0.00 39.38 2.75
4415 6126 4.055360 TGGTTTGTGTCATCGACTAACTG 58.945 43.478 0.00 0.00 33.15 3.16
4442 6153 5.181811 TCTGTTGTGCAAATTCATCTACTGG 59.818 40.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.