Multiple sequence alignment - TraesCS1A01G289700

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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 TraesCS1A01G289700 chr1A 100.000 2195 0 0 1 2195 486748007 486745813 0.000000e+00 4054
1 TraesCS1A01G289700 chr1A 80.055 366 55 15 849 1208 486663574 486663221 2.800000e-64 255
2 TraesCS1A01G289700 chr1A 87.817 197 22 2 993 1188 486668134 486667939 1.700000e-56 230
3 TraesCS1A01G289700 chr1A 96.386 83 3 0 2 84 532232296 532232214 1.060000e-28 137
4 TraesCS1A01G289700 chr1D 88.362 1856 112 48 408 2195 386944779 386942960 0.000000e+00 2135
5 TraesCS1A01G289700 chr1D 86.646 322 31 1 83 392 386945085 386944764 1.610000e-91 346
6 TraesCS1A01G289700 chr1D 80.336 417 53 22 907 1314 386896478 386896082 2.760000e-74 289
7 TraesCS1A01G289700 chr1D 91.875 160 13 0 1038 1197 386814052 386813893 7.890000e-55 224
8 TraesCS1A01G289700 chr1D 75.467 428 61 26 725 1125 386941491 386941081 3.750000e-38 169
9 TraesCS1A01G289700 chr1B 85.467 1039 79 31 675 1663 520369041 520368025 0.000000e+00 1016
10 TraesCS1A01G289700 chr1B 84.082 245 32 7 982 1220 520358282 520358039 1.700000e-56 230
11 TraesCS1A01G289700 chr1B 76.905 420 63 22 725 1125 520366731 520366327 7.940000e-50 207
12 TraesCS1A01G289700 chr7A 95.402 87 4 0 1 87 91494688 91494602 2.940000e-29 139
13 TraesCS1A01G289700 chr7A 95.294 85 4 0 1 85 47011220 47011136 3.800000e-28 135
14 TraesCS1A01G289700 chr7A 95.294 85 4 0 1 85 671456623 671456539 3.800000e-28 135
15 TraesCS1A01G289700 chr5A 96.429 84 3 0 1 84 491177434 491177517 2.940000e-29 139
16 TraesCS1A01G289700 chr5A 96.429 84 3 0 1 84 641641142 641641225 2.940000e-29 139
17 TraesCS1A01G289700 chr5A 95.294 85 4 0 1 85 439555568 439555484 3.800000e-28 135
18 TraesCS1A01G289700 chr6A 95.294 85 4 0 1 85 491920146 491920062 3.800000e-28 135
19 TraesCS1A01G289700 chr6A 95.294 85 4 0 1 85 615490921 615491005 3.800000e-28 135


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 TraesCS1A01G289700 chr1A 486745813 486748007 2194 True 4054.000000 4054 100.000000 1 2195 1 chr1A.!!$R3 2194
1 TraesCS1A01G289700 chr1D 386941081 386945085 4004 True 883.333333 2135 83.491667 83 2195 3 chr1D.!!$R3 2112
2 TraesCS1A01G289700 chr1B 520366327 520369041 2714 True 611.500000 1016 81.186000 675 1663 2 chr1B.!!$R2 988

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
29 30 0.458260 TGCTTGATGATGTGGCATGC 59.542 50.0 9.90 9.90 34.46 4.06 F
1016 1041 0.030369 GCGATGGAGTACCGGTACAG 59.970 60.0 38.79 24.38 38.48 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1046 1077 0.972983 CGGAGGCCTCTTCTCCTTGA 60.973 60.000 31.36 0.0 46.43 3.02 R
2016 2326 6.367422 GGTGAACATTTTGAACACAAGTTGAA 59.633 34.615 10.54 0.0 38.30 2.69 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
23 24 3.224884 TGCATGTTGCTTGATGATGTG 57.775 42.857 0.75 0.00 45.31 3.21
24 25 2.094442 TGCATGTTGCTTGATGATGTGG 60.094 45.455 0.75 0.00 45.31 4.17
25 26 2.536365 CATGTTGCTTGATGATGTGGC 58.464 47.619 0.00 0.00 0.00 5.01
26 27 1.618487 TGTTGCTTGATGATGTGGCA 58.382 45.000 0.00 0.00 0.00 4.92
27 28 2.172679 TGTTGCTTGATGATGTGGCAT 58.827 42.857 0.00 0.00 32.87 4.40
28 29 2.094442 TGTTGCTTGATGATGTGGCATG 60.094 45.455 0.00 0.00 32.87 4.06
29 30 0.458260 TGCTTGATGATGTGGCATGC 59.542 50.000 9.90 9.90 34.46 4.06
30 31 0.744874 GCTTGATGATGTGGCATGCT 59.255 50.000 18.92 0.00 32.10 3.79
31 32 1.136305 GCTTGATGATGTGGCATGCTT 59.864 47.619 18.92 0.00 32.10 3.91
32 33 2.359848 GCTTGATGATGTGGCATGCTTA 59.640 45.455 18.92 4.21 32.10 3.09
33 34 3.005472 GCTTGATGATGTGGCATGCTTAT 59.995 43.478 18.92 9.50 32.10 1.73
34 35 4.216902 GCTTGATGATGTGGCATGCTTATA 59.783 41.667 18.92 6.03 32.10 0.98
35 36 5.105877 GCTTGATGATGTGGCATGCTTATAT 60.106 40.000 18.92 10.74 32.10 0.86
36 37 5.890424 TGATGATGTGGCATGCTTATATG 57.110 39.130 18.92 0.00 0.00 1.78
37 38 5.318630 TGATGATGTGGCATGCTTATATGT 58.681 37.500 18.92 0.00 0.00 2.29
38 39 5.771165 TGATGATGTGGCATGCTTATATGTT 59.229 36.000 18.92 0.00 0.00 2.71
39 40 6.941436 TGATGATGTGGCATGCTTATATGTTA 59.059 34.615 18.92 0.00 0.00 2.41
40 41 7.447853 TGATGATGTGGCATGCTTATATGTTAA 59.552 33.333 18.92 0.00 0.00 2.01
41 42 7.205737 TGATGTGGCATGCTTATATGTTAAG 57.794 36.000 18.92 0.00 0.00 1.85
42 43 6.997476 TGATGTGGCATGCTTATATGTTAAGA 59.003 34.615 18.92 0.00 0.00 2.10
43 44 6.866010 TGTGGCATGCTTATATGTTAAGAG 57.134 37.500 18.92 0.00 0.00 2.85
44 45 6.591001 TGTGGCATGCTTATATGTTAAGAGA 58.409 36.000 18.92 0.00 0.00 3.10
45 46 7.053498 TGTGGCATGCTTATATGTTAAGAGAA 58.947 34.615 18.92 0.00 0.00 2.87
46 47 7.555914 TGTGGCATGCTTATATGTTAAGAGAAA 59.444 33.333 18.92 0.00 0.00 2.52
47 48 8.571336 GTGGCATGCTTATATGTTAAGAGAAAT 58.429 33.333 18.92 0.00 0.00 2.17
48 49 9.791801 TGGCATGCTTATATGTTAAGAGAAATA 57.208 29.630 18.92 0.00 0.00 1.40
61 62 8.161425 TGTTAAGAGAAATATATTAGTGGGGGC 58.839 37.037 0.00 0.00 0.00 5.80
62 63 8.383947 GTTAAGAGAAATATATTAGTGGGGGCT 58.616 37.037 0.00 0.00 0.00 5.19
63 64 9.624037 TTAAGAGAAATATATTAGTGGGGGCTA 57.376 33.333 0.00 0.00 0.00 3.93
64 65 7.741554 AGAGAAATATATTAGTGGGGGCTAG 57.258 40.000 0.00 0.00 0.00 3.42
65 66 6.157123 AGAGAAATATATTAGTGGGGGCTAGC 59.843 42.308 6.04 6.04 0.00 3.42
66 67 6.032693 AGAAATATATTAGTGGGGGCTAGCT 58.967 40.000 15.72 0.00 0.00 3.32
67 68 7.196901 AGAAATATATTAGTGGGGGCTAGCTA 58.803 38.462 15.72 0.00 0.00 3.32
68 69 7.851968 AGAAATATATTAGTGGGGGCTAGCTAT 59.148 37.037 15.72 3.75 0.00 2.97
69 70 8.407313 AAATATATTAGTGGGGGCTAGCTATT 57.593 34.615 15.72 3.35 0.00 1.73
70 71 8.407313 AATATATTAGTGGGGGCTAGCTATTT 57.593 34.615 15.72 0.00 0.00 1.40
71 72 9.515440 AATATATTAGTGGGGGCTAGCTATTTA 57.485 33.333 15.72 0.00 0.00 1.40
72 73 5.763876 ATTAGTGGGGGCTAGCTATTTAG 57.236 43.478 15.72 0.00 0.00 1.85
73 74 3.346146 AGTGGGGGCTAGCTATTTAGA 57.654 47.619 15.72 0.00 0.00 2.10
74 75 3.875571 AGTGGGGGCTAGCTATTTAGAT 58.124 45.455 15.72 0.00 0.00 1.98
75 76 5.024803 AGTGGGGGCTAGCTATTTAGATA 57.975 43.478 15.72 0.00 0.00 1.98
76 77 5.604752 AGTGGGGGCTAGCTATTTAGATAT 58.395 41.667 15.72 0.00 0.00 1.63
77 78 6.753134 AGTGGGGGCTAGCTATTTAGATATA 58.247 40.000 15.72 0.00 0.00 0.86
78 79 6.841755 AGTGGGGGCTAGCTATTTAGATATAG 59.158 42.308 15.72 0.00 0.00 1.31
79 80 6.839657 GTGGGGGCTAGCTATTTAGATATAGA 59.160 42.308 15.72 0.00 31.10 1.98
80 81 7.344871 GTGGGGGCTAGCTATTTAGATATAGAA 59.655 40.741 15.72 0.00 31.10 2.10
81 82 7.565398 TGGGGGCTAGCTATTTAGATATAGAAG 59.435 40.741 15.72 0.00 31.10 2.85
112 113 7.611770 TCTAACCTATGTAGCGCATAATCAAT 58.388 34.615 11.47 0.00 39.36 2.57
118 119 3.814842 TGTAGCGCATAATCAATCCTTGG 59.185 43.478 11.47 0.00 0.00 3.61
130 131 3.345808 CCTTGGTCCACACGTGCG 61.346 66.667 17.22 5.90 0.00 5.34
152 153 0.658897 TCGCCCAAAAGTCGTGAAAC 59.341 50.000 0.00 0.00 0.00 2.78
203 204 4.163268 TGGTCCGTGGAAATATCTTCATCA 59.837 41.667 0.00 0.00 0.00 3.07
205 206 5.588648 GGTCCGTGGAAATATCTTCATCAAA 59.411 40.000 0.00 0.00 0.00 2.69
213 214 7.065803 TGGAAATATCTTCATCAAAAGGACGAC 59.934 37.037 0.00 0.00 0.00 4.34
241 254 9.118300 GTGATGAAAATATCTTCAAGAGGATGT 57.882 33.333 5.09 0.00 42.07 3.06
261 274 5.203358 TGTTGTTCGCGAAAGAATATCTG 57.797 39.130 25.24 0.00 32.25 2.90
263 276 5.062183 TGTTGTTCGCGAAAGAATATCTGAG 59.938 40.000 25.24 0.00 32.25 3.35
291 304 8.863049 GTGGAAAGCTGATATTTGTTACATTTG 58.137 33.333 0.00 0.00 0.00 2.32
298 311 2.690173 TTTGTTACATTTGCCGTCCG 57.310 45.000 0.00 0.00 0.00 4.79
302 315 2.288948 TGTTACATTTGCCGTCCGTAGT 60.289 45.455 0.00 0.00 0.00 2.73
327 340 8.333186 GTGTTATATACTTTGGTCGATGGAAAC 58.667 37.037 0.00 0.00 0.00 2.78
334 347 6.884832 ACTTTGGTCGATGGAAACTATATCA 58.115 36.000 0.00 0.00 0.00 2.15
341 354 7.145985 GTCGATGGAAACTATATCAAGTAGCA 58.854 38.462 0.00 0.00 0.00 3.49
345 358 8.613060 ATGGAAACTATATCAAGTAGCATGTG 57.387 34.615 0.00 0.00 0.00 3.21
346 359 7.564793 TGGAAACTATATCAAGTAGCATGTGT 58.435 34.615 0.00 0.00 0.00 3.72
352 365 3.887621 TCAAGTAGCATGTGTCCTACC 57.112 47.619 0.00 0.00 35.63 3.18
353 366 2.165641 TCAAGTAGCATGTGTCCTACCG 59.834 50.000 0.00 0.00 35.63 4.02
355 368 2.453521 AGTAGCATGTGTCCTACCGAA 58.546 47.619 0.00 0.00 35.63 4.30
358 371 1.346395 AGCATGTGTCCTACCGAAACA 59.654 47.619 0.00 0.00 43.08 2.83
370 383 9.104965 TGTCCTACCGAAACATCTTATATTTTG 57.895 33.333 0.00 0.00 0.00 2.44
393 406 9.661954 TTTGATATGGAGAGAGGTAATACTTCT 57.338 33.333 4.65 4.65 37.24 2.85
394 407 9.661954 TTGATATGGAGAGAGGTAATACTTCTT 57.338 33.333 6.50 0.00 34.47 2.52
395 408 9.661954 TGATATGGAGAGAGGTAATACTTCTTT 57.338 33.333 6.50 0.90 34.47 2.52
417 430 5.492855 TTTTTCGAGAATGAGGGAGGTAA 57.507 39.130 0.00 0.00 0.00 2.85
418 431 5.693769 TTTTCGAGAATGAGGGAGGTAAT 57.306 39.130 0.00 0.00 0.00 1.89
419 432 6.801718 TTTTCGAGAATGAGGGAGGTAATA 57.198 37.500 0.00 0.00 0.00 0.98
420 433 5.786264 TTCGAGAATGAGGGAGGTAATAC 57.214 43.478 0.00 0.00 0.00 1.89
421 434 5.063017 TCGAGAATGAGGGAGGTAATACT 57.937 43.478 0.00 0.00 0.00 2.12
422 435 5.455872 TCGAGAATGAGGGAGGTAATACTT 58.544 41.667 0.00 0.00 0.00 2.24
463 476 9.179552 CAGATCAGATGTTTTTATCTAGAGACG 57.820 37.037 0.00 0.00 35.70 4.18
464 477 7.865385 AGATCAGATGTTTTTATCTAGAGACGC 59.135 37.037 0.00 0.00 35.70 5.19
645 660 4.618920 AATTCCTAGTGTGTCCGTTTCT 57.381 40.909 0.00 0.00 0.00 2.52
650 665 5.535333 TCCTAGTGTGTCCGTTTCTAAAAG 58.465 41.667 0.00 0.00 0.00 2.27
652 667 5.987347 CCTAGTGTGTCCGTTTCTAAAAGAA 59.013 40.000 0.00 0.00 31.28 2.52
653 668 5.729974 AGTGTGTCCGTTTCTAAAAGAAC 57.270 39.130 0.00 0.00 33.26 3.01
654 669 5.180271 AGTGTGTCCGTTTCTAAAAGAACA 58.820 37.500 0.00 0.00 33.26 3.18
655 670 5.644636 AGTGTGTCCGTTTCTAAAAGAACAA 59.355 36.000 0.00 0.00 33.26 2.83
708 724 4.466370 TCTGGTGATTTAGTTCCGTGATCT 59.534 41.667 0.00 0.00 0.00 2.75
718 734 2.642139 TCCGTGATCTCGTTTACACC 57.358 50.000 15.34 0.00 0.00 4.16
720 736 2.094906 TCCGTGATCTCGTTTACACCTG 60.095 50.000 15.34 0.00 0.00 4.00
721 737 2.259618 CGTGATCTCGTTTACACCTGG 58.740 52.381 8.97 0.00 0.00 4.45
722 738 2.094906 CGTGATCTCGTTTACACCTGGA 60.095 50.000 8.97 0.00 0.00 3.86
723 739 3.613193 CGTGATCTCGTTTACACCTGGAA 60.613 47.826 8.97 0.00 0.00 3.53
724 740 4.504858 GTGATCTCGTTTACACCTGGAAT 58.495 43.478 0.00 0.00 0.00 3.01
725 741 4.567159 GTGATCTCGTTTACACCTGGAATC 59.433 45.833 0.00 0.00 0.00 2.52
726 742 4.466370 TGATCTCGTTTACACCTGGAATCT 59.534 41.667 0.00 0.00 0.00 2.40
727 743 4.884668 TCTCGTTTACACCTGGAATCTT 57.115 40.909 0.00 0.00 0.00 2.40
728 744 4.566004 TCTCGTTTACACCTGGAATCTTG 58.434 43.478 0.00 0.00 0.00 3.02
764 780 2.394708 CCGGTATGCAGATACGTTCAG 58.605 52.381 0.00 0.00 36.08 3.02
769 785 4.740695 GGTATGCAGATACGTTCAGACTTC 59.259 45.833 0.00 0.00 36.08 3.01
945 963 1.419762 TGGCTTCACCACACAGTACAT 59.580 47.619 0.00 0.00 46.36 2.29
947 965 3.000727 GGCTTCACCACACAGTACATAC 58.999 50.000 0.00 0.00 38.86 2.39
955 973 0.999406 CACAGTACATACGGTGCAGC 59.001 55.000 5.64 5.64 43.28 5.25
976 994 2.599973 CACACAACACAAAAGAAGCAGC 59.400 45.455 0.00 0.00 0.00 5.25
1016 1041 0.030369 GCGATGGAGTACCGGTACAG 59.970 60.000 38.79 24.38 38.48 2.74
1089 1120 0.907230 AGAGGGGTCAGGTCAAGCTC 60.907 60.000 0.00 0.00 0.00 4.09
1125 1156 0.827925 TGAGCAACCTCGTGTCTCCT 60.828 55.000 0.00 0.00 41.13 3.69
1129 1160 1.837051 AACCTCGTGTCTCCTGGCA 60.837 57.895 0.00 0.00 0.00 4.92
1167 1198 2.986306 GCAGGCAAATCGCAGCAGT 61.986 57.895 0.00 0.00 45.17 4.40
1201 1233 5.741388 AACAAGCTACAACTGAACAAGAG 57.259 39.130 0.00 0.00 0.00 2.85
1203 1235 5.615289 ACAAGCTACAACTGAACAAGAGAT 58.385 37.500 0.00 0.00 0.00 2.75
1222 1254 1.961793 TTTAGATGGGTATGGTGCGC 58.038 50.000 0.00 0.00 0.00 6.09
1230 1262 2.046411 TATGGTGCGCCTGTGTGG 60.046 61.111 18.96 0.00 39.35 4.17
1231 1263 3.620419 TATGGTGCGCCTGTGTGGG 62.620 63.158 18.96 0.00 36.00 4.61
1277 1335 5.066593 CCTATTGAGGGTTTTAGCAGGATC 58.933 45.833 0.00 0.00 39.48 3.36
1316 1374 1.902508 GGAGAACCTGTCTGATCCACA 59.097 52.381 0.00 0.00 36.41 4.17
1317 1375 2.503356 GGAGAACCTGTCTGATCCACAT 59.497 50.000 0.00 0.00 36.41 3.21
1318 1376 3.706594 GGAGAACCTGTCTGATCCACATA 59.293 47.826 0.00 0.00 36.41 2.29
1323 1381 4.610333 ACCTGTCTGATCCACATACACTA 58.390 43.478 0.00 0.00 33.27 2.74
1343 1401 6.014499 ACACTATACTGTAACTTGGCTTGAGT 60.014 38.462 0.00 0.00 0.00 3.41
1365 1423 1.135170 GGAAATGCTCCAAGCTTGAGC 60.135 52.381 28.90 28.90 44.67 4.26
1373 1431 0.731514 CCAAGCTTGAGCGTGCATTG 60.732 55.000 28.05 2.79 46.61 2.82
1432 1490 6.558009 ACATACAAGCTTTTGAGTATGCATG 58.442 36.000 24.09 10.53 44.64 4.06
1442 1500 0.462581 AGTATGCATGACACCCAGCG 60.463 55.000 10.16 0.00 0.00 5.18
1531 1595 5.731599 TTGCACATTTTGGCAAGTTAAAG 57.268 34.783 0.00 0.00 44.41 1.85
1534 1598 5.523188 TGCACATTTTGGCAAGTTAAAGAAG 59.477 36.000 0.00 0.00 37.03 2.85
1570 1634 5.512942 TGAGGGATCCAAAATAAGTGTCA 57.487 39.130 15.23 0.00 0.00 3.58
1571 1635 5.500234 TGAGGGATCCAAAATAAGTGTCAG 58.500 41.667 15.23 0.00 0.00 3.51
1572 1636 5.014123 TGAGGGATCCAAAATAAGTGTCAGT 59.986 40.000 15.23 0.00 0.00 3.41
1573 1637 5.892348 AGGGATCCAAAATAAGTGTCAGTT 58.108 37.500 15.23 0.00 0.00 3.16
1575 1639 5.710099 GGGATCCAAAATAAGTGTCAGTTCA 59.290 40.000 15.23 0.00 0.00 3.18
1576 1640 6.349363 GGGATCCAAAATAAGTGTCAGTTCAC 60.349 42.308 15.23 0.00 38.46 3.18
1577 1641 6.206634 GGATCCAAAATAAGTGTCAGTTCACA 59.793 38.462 6.95 0.00 40.37 3.58
1582 1655 9.097257 CCAAAATAAGTGTCAGTTCACAAAAAT 57.903 29.630 0.00 0.00 40.37 1.82
1615 1691 6.550843 AGTTTTGTTTTTGCTAAATGTTGGC 58.449 32.000 0.00 0.00 37.69 4.52
1620 1696 5.645497 TGTTTTTGCTAAATGTTGGCTTGTT 59.355 32.000 0.00 0.00 38.08 2.83
1623 1699 7.849804 TTTTGCTAAATGTTGGCTTGTTAAA 57.150 28.000 0.00 0.00 38.08 1.52
1697 1779 2.991540 AAAAAGGCCTCCCGCTGC 60.992 61.111 5.23 0.00 37.74 5.25
1767 2069 5.594317 GCCCTATTCAGTTTGGTGATGTATT 59.406 40.000 0.00 0.00 0.00 1.89
1800 2106 1.247567 CTTCACTTGCCCGTTCCAAT 58.752 50.000 0.00 0.00 0.00 3.16
1810 2116 3.574396 TGCCCGTTCCAATGATTTGTTTA 59.426 39.130 0.00 0.00 0.00 2.01
1811 2117 4.173256 GCCCGTTCCAATGATTTGTTTAG 58.827 43.478 0.00 0.00 0.00 1.85
1835 2141 4.411256 TTCTTTCAGGTTGTTCCGTAGT 57.589 40.909 0.00 0.00 41.99 2.73
1836 2142 3.986277 TCTTTCAGGTTGTTCCGTAGTC 58.014 45.455 0.00 0.00 41.99 2.59
1837 2143 3.385433 TCTTTCAGGTTGTTCCGTAGTCA 59.615 43.478 0.00 0.00 41.99 3.41
1911 2217 9.790389 AATGAACACTGTTTTAATTACACGAAA 57.210 25.926 0.00 0.00 0.00 3.46
1912 2218 8.829514 TGAACACTGTTTTAATTACACGAAAG 57.170 30.769 0.00 0.00 0.00 2.62
2048 2358 6.071896 TGTGTTCAAAATGTTCACCTTGTACA 60.072 34.615 0.00 0.00 32.36 2.90
2062 2372 7.051623 TCACCTTGTACATAAAACTGTTCACT 58.948 34.615 0.00 0.00 0.00 3.41
2063 2373 7.011950 TCACCTTGTACATAAAACTGTTCACTG 59.988 37.037 0.00 0.00 0.00 3.66
2064 2374 6.826741 ACCTTGTACATAAAACTGTTCACTGT 59.173 34.615 0.00 0.72 0.00 3.55
2065 2375 7.012044 ACCTTGTACATAAAACTGTTCACTGTC 59.988 37.037 0.00 0.00 0.00 3.51
2066 2376 7.226720 CCTTGTACATAAAACTGTTCACTGTCT 59.773 37.037 0.00 0.00 0.00 3.41
2067 2377 9.256477 CTTGTACATAAAACTGTTCACTGTCTA 57.744 33.333 0.00 0.00 0.00 2.59
2068 2378 8.812147 TGTACATAAAACTGTTCACTGTCTAG 57.188 34.615 0.00 0.00 0.00 2.43
2072 2382 9.174166 ACATAAAACTGTTCACTGTCTAGTTTT 57.826 29.630 15.06 15.06 46.87 2.43
2146 2468 8.794335 ACTACTGAAAATAGGAGGAAATGAAC 57.206 34.615 0.00 0.00 32.64 3.18
2152 2474 9.762933 TGAAAATAGGAGGAAATGAACAAAAAG 57.237 29.630 0.00 0.00 0.00 2.27
2157 2479 7.379059 AGGAGGAAATGAACAAAAAGGAAAT 57.621 32.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.536365 CCACATCATCAAGCAACATGC 58.464 47.619 0.00 0.00 45.46 4.06
5 6 2.094442 TGCCACATCATCAAGCAACATG 60.094 45.455 0.00 0.00 0.00 3.21
6 7 2.172679 TGCCACATCATCAAGCAACAT 58.827 42.857 0.00 0.00 0.00 2.71
7 8 1.618487 TGCCACATCATCAAGCAACA 58.382 45.000 0.00 0.00 0.00 3.33
8 9 2.536365 CATGCCACATCATCAAGCAAC 58.464 47.619 0.00 0.00 36.95 4.17
9 10 1.134936 GCATGCCACATCATCAAGCAA 60.135 47.619 6.36 0.00 36.95 3.91
10 11 0.458260 GCATGCCACATCATCAAGCA 59.542 50.000 6.36 0.00 37.94 3.91
11 12 0.744874 AGCATGCCACATCATCAAGC 59.255 50.000 15.66 0.00 0.00 4.01
12 13 4.848562 ATAAGCATGCCACATCATCAAG 57.151 40.909 15.66 0.00 0.00 3.02
13 14 5.771165 ACATATAAGCATGCCACATCATCAA 59.229 36.000 15.66 0.00 0.00 2.57
14 15 5.318630 ACATATAAGCATGCCACATCATCA 58.681 37.500 15.66 0.00 0.00 3.07
15 16 5.892160 ACATATAAGCATGCCACATCATC 57.108 39.130 15.66 0.00 0.00 2.92
16 17 7.666804 TCTTAACATATAAGCATGCCACATCAT 59.333 33.333 15.66 1.45 0.00 2.45
17 18 6.997476 TCTTAACATATAAGCATGCCACATCA 59.003 34.615 15.66 0.00 0.00 3.07
18 19 7.388776 TCTCTTAACATATAAGCATGCCACATC 59.611 37.037 15.66 0.00 0.00 3.06
19 20 7.226441 TCTCTTAACATATAAGCATGCCACAT 58.774 34.615 15.66 7.78 0.00 3.21
20 21 6.591001 TCTCTTAACATATAAGCATGCCACA 58.409 36.000 15.66 0.00 0.00 4.17
21 22 7.496529 TTCTCTTAACATATAAGCATGCCAC 57.503 36.000 15.66 0.00 0.00 5.01
22 23 8.696043 ATTTCTCTTAACATATAAGCATGCCA 57.304 30.769 15.66 2.46 0.00 4.92
35 36 8.161425 GCCCCCACTAATATATTTCTCTTAACA 58.839 37.037 2.68 0.00 0.00 2.41
36 37 8.383947 AGCCCCCACTAATATATTTCTCTTAAC 58.616 37.037 2.68 0.00 0.00 2.01
37 38 8.520119 AGCCCCCACTAATATATTTCTCTTAA 57.480 34.615 2.68 0.00 0.00 1.85
38 39 9.268282 CTAGCCCCCACTAATATATTTCTCTTA 57.732 37.037 2.68 0.00 0.00 2.10
39 40 7.311360 GCTAGCCCCCACTAATATATTTCTCTT 60.311 40.741 2.29 0.00 0.00 2.85
40 41 6.157123 GCTAGCCCCCACTAATATATTTCTCT 59.843 42.308 2.29 0.00 0.00 3.10
41 42 6.157123 AGCTAGCCCCCACTAATATATTTCTC 59.843 42.308 12.13 0.00 0.00 2.87
42 43 6.032693 AGCTAGCCCCCACTAATATATTTCT 58.967 40.000 12.13 0.00 0.00 2.52
43 44 6.314899 AGCTAGCCCCCACTAATATATTTC 57.685 41.667 12.13 0.00 0.00 2.17
44 45 8.407313 AATAGCTAGCCCCCACTAATATATTT 57.593 34.615 12.13 0.00 0.00 1.40
45 46 8.407313 AAATAGCTAGCCCCCACTAATATATT 57.593 34.615 12.13 2.97 0.00 1.28
46 47 9.160412 CTAAATAGCTAGCCCCCACTAATATAT 57.840 37.037 12.13 0.00 0.00 0.86
47 48 8.349118 TCTAAATAGCTAGCCCCCACTAATATA 58.651 37.037 12.13 0.00 0.00 0.86
48 49 7.196901 TCTAAATAGCTAGCCCCCACTAATAT 58.803 38.462 12.13 0.00 0.00 1.28
49 50 6.567854 TCTAAATAGCTAGCCCCCACTAATA 58.432 40.000 12.13 0.00 0.00 0.98
50 51 5.412384 TCTAAATAGCTAGCCCCCACTAAT 58.588 41.667 12.13 0.00 0.00 1.73
51 52 4.823107 TCTAAATAGCTAGCCCCCACTAA 58.177 43.478 12.13 0.00 0.00 2.24
52 53 4.480777 TCTAAATAGCTAGCCCCCACTA 57.519 45.455 12.13 0.00 0.00 2.74
53 54 3.346146 TCTAAATAGCTAGCCCCCACT 57.654 47.619 12.13 0.00 0.00 4.00
54 55 5.959583 ATATCTAAATAGCTAGCCCCCAC 57.040 43.478 12.13 0.00 0.00 4.61
55 56 6.993408 TCTATATCTAAATAGCTAGCCCCCA 58.007 40.000 12.13 0.00 30.79 4.96
56 57 7.785506 TCTTCTATATCTAAATAGCTAGCCCCC 59.214 40.741 12.13 0.00 30.79 5.40
57 58 8.770010 TCTTCTATATCTAAATAGCTAGCCCC 57.230 38.462 12.13 0.00 30.79 5.80
75 76 9.250246 GCTACATAGGTTAGAGGAATCTTCTAT 57.750 37.037 2.88 0.00 28.79 1.98
76 77 7.390996 CGCTACATAGGTTAGAGGAATCTTCTA 59.609 40.741 0.00 0.00 28.79 2.10
77 78 6.207810 CGCTACATAGGTTAGAGGAATCTTCT 59.792 42.308 0.00 0.00 28.79 2.85
78 79 6.383415 CGCTACATAGGTTAGAGGAATCTTC 58.617 44.000 0.00 0.00 28.79 2.87
79 80 5.279056 GCGCTACATAGGTTAGAGGAATCTT 60.279 44.000 0.00 0.00 28.79 2.40
80 81 4.218852 GCGCTACATAGGTTAGAGGAATCT 59.781 45.833 0.00 0.00 31.63 2.40
81 82 4.022242 TGCGCTACATAGGTTAGAGGAATC 60.022 45.833 9.73 0.00 0.00 2.52
89 90 6.816640 GGATTGATTATGCGCTACATAGGTTA 59.183 38.462 9.73 0.00 42.20 2.85
112 113 2.110213 GCACGTGTGGACCAAGGA 59.890 61.111 18.38 0.00 0.00 3.36
130 131 2.668550 ACGACTTTTGGGCGAGGC 60.669 61.111 0.00 0.00 0.00 4.70
133 134 0.658897 GTTTCACGACTTTTGGGCGA 59.341 50.000 0.00 0.00 0.00 5.54
134 135 0.656205 CGTTTCACGACTTTTGGGCG 60.656 55.000 0.00 0.00 46.05 6.13
158 159 1.446907 GTGGTCGACCGAGAGTCTAA 58.553 55.000 28.70 5.71 43.91 2.10
160 161 1.674980 GGTGGTCGACCGAGAGTCT 60.675 63.158 28.70 0.00 43.91 3.24
203 204 2.536761 TTCATCACCGTCGTCCTTTT 57.463 45.000 0.00 0.00 0.00 2.27
205 206 2.536761 TTTTCATCACCGTCGTCCTT 57.463 45.000 0.00 0.00 0.00 3.36
213 214 6.763135 TCCTCTTGAAGATATTTTCATCACCG 59.237 38.462 9.31 0.00 36.97 4.94
241 254 5.407502 TCTCAGATATTCTTTCGCGAACAA 58.592 37.500 23.33 17.44 0.00 2.83
261 274 6.749923 AACAAATATCAGCTTTCCACTCTC 57.250 37.500 0.00 0.00 0.00 3.20
263 276 7.377766 TGTAACAAATATCAGCTTTCCACTC 57.622 36.000 0.00 0.00 0.00 3.51
291 304 4.756084 AGTATATAACACTACGGACGGC 57.244 45.455 0.00 0.00 0.00 5.68
298 311 8.355169 TCCATCGACCAAAGTATATAACACTAC 58.645 37.037 0.00 0.00 0.00 2.73
302 315 8.262227 AGTTTCCATCGACCAAAGTATATAACA 58.738 33.333 0.00 0.00 0.00 2.41
327 340 7.316640 GGTAGGACACATGCTACTTGATATAG 58.683 42.308 6.03 0.00 46.24 1.31
334 347 2.453521 TCGGTAGGACACATGCTACTT 58.546 47.619 6.03 0.00 46.24 2.24
341 354 4.553330 AAGATGTTTCGGTAGGACACAT 57.447 40.909 0.00 0.00 46.11 3.21
345 358 9.321562 TCAAAATATAAGATGTTTCGGTAGGAC 57.678 33.333 0.00 0.00 0.00 3.85
395 408 5.492855 TTACCTCCCTCATTCTCGAAAAA 57.507 39.130 0.00 0.00 0.00 1.94
396 409 5.693769 ATTACCTCCCTCATTCTCGAAAA 57.306 39.130 0.00 0.00 0.00 2.29
397 410 5.897824 AGTATTACCTCCCTCATTCTCGAAA 59.102 40.000 0.00 0.00 0.00 3.46
398 411 5.455872 AGTATTACCTCCCTCATTCTCGAA 58.544 41.667 0.00 0.00 0.00 3.71
399 412 5.063017 AGTATTACCTCCCTCATTCTCGA 57.937 43.478 0.00 0.00 0.00 4.04
400 413 5.793030 AAGTATTACCTCCCTCATTCTCG 57.207 43.478 0.00 0.00 0.00 4.04
411 424 8.558700 GTGACTAGCACTAGTAAGTATTACCTC 58.441 40.741 10.25 0.00 47.00 3.85
412 425 8.449251 GTGACTAGCACTAGTAAGTATTACCT 57.551 38.462 10.25 0.00 47.00 3.08
415 428 9.848710 ATCTGTGACTAGCACTAGTAAGTATTA 57.151 33.333 10.25 0.00 45.63 0.98
416 429 8.754991 ATCTGTGACTAGCACTAGTAAGTATT 57.245 34.615 10.25 0.00 45.63 1.89
417 430 7.993758 TGATCTGTGACTAGCACTAGTAAGTAT 59.006 37.037 10.25 2.07 45.63 2.12
418 431 7.336396 TGATCTGTGACTAGCACTAGTAAGTA 58.664 38.462 10.25 0.00 45.63 2.24
419 432 6.181190 TGATCTGTGACTAGCACTAGTAAGT 58.819 40.000 10.25 0.00 45.63 2.24
420 433 6.540551 TCTGATCTGTGACTAGCACTAGTAAG 59.459 42.308 10.25 8.74 45.63 2.34
421 434 6.415573 TCTGATCTGTGACTAGCACTAGTAA 58.584 40.000 10.25 0.35 45.63 2.24
422 435 5.990668 TCTGATCTGTGACTAGCACTAGTA 58.009 41.667 10.25 0.00 45.63 1.82
463 476 0.831307 CCCCCTGAGTAAGTAGGTGC 59.169 60.000 0.00 0.00 31.99 5.01
464 477 1.831736 CACCCCCTGAGTAAGTAGGTG 59.168 57.143 0.00 0.00 39.49 4.00
574 589 1.799403 CAACAGCACAGCAAGAGAGAG 59.201 52.381 0.00 0.00 0.00 3.20
575 590 1.541889 CCAACAGCACAGCAAGAGAGA 60.542 52.381 0.00 0.00 0.00 3.10
645 660 9.757227 CACACTGGGAATATTTTTGTTCTTTTA 57.243 29.630 0.00 0.00 0.00 1.52
650 665 5.537188 TGCACACTGGGAATATTTTTGTTC 58.463 37.500 0.00 0.00 0.00 3.18
652 667 4.021192 CCTGCACACTGGGAATATTTTTGT 60.021 41.667 0.00 0.00 0.00 2.83
653 668 4.497300 CCTGCACACTGGGAATATTTTTG 58.503 43.478 0.00 0.00 0.00 2.44
654 669 3.055891 GCCTGCACACTGGGAATATTTTT 60.056 43.478 0.00 0.00 35.49 1.94
655 670 2.497273 GCCTGCACACTGGGAATATTTT 59.503 45.455 0.00 0.00 35.49 1.82
687 702 4.676986 CGAGATCACGGAACTAAATCACCA 60.677 45.833 4.47 0.00 0.00 4.17
708 724 3.325425 TCCAAGATTCCAGGTGTAAACGA 59.675 43.478 0.00 0.00 0.00 3.85
718 734 6.874288 GAATCCAACTATCCAAGATTCCAG 57.126 41.667 0.00 0.00 37.79 3.86
721 737 5.073428 GGGGAATCCAACTATCCAAGATTC 58.927 45.833 0.09 0.00 41.24 2.52
722 738 4.140924 GGGGGAATCCAACTATCCAAGATT 60.141 45.833 0.09 0.00 37.22 2.40
723 739 3.399305 GGGGGAATCCAACTATCCAAGAT 59.601 47.826 0.09 0.00 37.22 2.40
724 740 2.783510 GGGGGAATCCAACTATCCAAGA 59.216 50.000 0.09 0.00 37.22 3.02
725 741 2.487265 CGGGGGAATCCAACTATCCAAG 60.487 54.545 0.09 0.00 37.22 3.61
726 742 1.493022 CGGGGGAATCCAACTATCCAA 59.507 52.381 0.09 0.00 37.22 3.53
727 743 1.136828 CGGGGGAATCCAACTATCCA 58.863 55.000 0.09 0.00 37.22 3.41
728 744 0.400594 CCGGGGGAATCCAACTATCC 59.599 60.000 0.09 0.00 37.22 2.59
764 780 1.305930 GGGCCATGGTGTTCGAAGTC 61.306 60.000 14.67 0.00 0.00 3.01
769 785 1.467678 TTTTGGGGCCATGGTGTTCG 61.468 55.000 14.67 0.00 0.00 3.95
955 973 2.599973 GCTGCTTCTTTTGTGTTGTGTG 59.400 45.455 0.00 0.00 0.00 3.82
1033 1058 3.793144 CTTGACGAAGCTGCCGCC 61.793 66.667 8.47 0.00 36.60 6.13
1034 1059 3.793144 CCTTGACGAAGCTGCCGC 61.793 66.667 8.47 0.00 0.00 6.53
1035 1060 2.048222 TCCTTGACGAAGCTGCCG 60.048 61.111 7.16 7.16 0.00 5.69
1046 1077 0.972983 CGGAGGCCTCTTCTCCTTGA 60.973 60.000 31.36 0.00 46.43 3.02
1077 1108 1.759445 GCTATCTGGAGCTTGACCTGA 59.241 52.381 2.57 2.57 39.50 3.86
1137 1168 4.704833 GCCTGCTTGGAGCCGTCA 62.705 66.667 0.49 0.00 41.51 4.35
1146 1177 1.804326 GCTGCGATTTGCCTGCTTG 60.804 57.895 0.00 0.00 45.60 4.01
1167 1198 4.787551 TGTAGCTTGTTTCCCTTCTGAAA 58.212 39.130 0.00 0.00 32.02 2.69
1201 1233 2.484264 GCGCACCATACCCATCTAAATC 59.516 50.000 0.30 0.00 0.00 2.17
1203 1235 1.476110 GGCGCACCATACCCATCTAAA 60.476 52.381 10.83 0.00 35.26 1.85
1222 1254 2.159085 GCTAGCTAGTAACCCACACAGG 60.159 54.545 21.62 0.00 37.03 4.00
1230 1262 8.202811 AGGTAATAAAACAGCTAGCTAGTAACC 58.797 37.037 18.86 15.61 0.00 2.85
1257 1315 3.054361 ACGATCCTGCTAAAACCCTCAAT 60.054 43.478 0.00 0.00 0.00 2.57
1277 1335 5.424757 TCTCCATTTATAAACTGGGACACG 58.575 41.667 18.59 8.88 0.00 4.49
1316 1374 8.074613 TCAAGCCAAGTTACAGTATAGTGTAT 57.925 34.615 18.86 4.89 32.92 2.29
1317 1375 7.177921 ACTCAAGCCAAGTTACAGTATAGTGTA 59.822 37.037 15.13 15.13 31.46 2.90
1318 1376 6.014499 ACTCAAGCCAAGTTACAGTATAGTGT 60.014 38.462 17.14 17.14 34.21 3.55
1323 1381 4.565652 CCCACTCAAGCCAAGTTACAGTAT 60.566 45.833 0.00 0.00 0.00 2.12
1343 1401 1.203038 TCAAGCTTGGAGCATTTCCCA 60.203 47.619 25.73 0.00 45.56 4.37
1411 1469 5.704978 TGTCATGCATACTCAAAAGCTTGTA 59.295 36.000 0.00 0.00 34.79 2.41
1412 1470 4.520111 TGTCATGCATACTCAAAAGCTTGT 59.480 37.500 0.00 0.00 34.79 3.16
1414 1472 4.082571 GGTGTCATGCATACTCAAAAGCTT 60.083 41.667 0.00 0.00 0.00 3.74
1415 1473 3.441572 GGTGTCATGCATACTCAAAAGCT 59.558 43.478 0.00 0.00 0.00 3.74
1416 1474 3.428045 GGGTGTCATGCATACTCAAAAGC 60.428 47.826 0.00 0.00 0.00 3.51
1417 1475 3.758023 TGGGTGTCATGCATACTCAAAAG 59.242 43.478 0.00 0.00 0.00 2.27
1418 1476 3.758023 CTGGGTGTCATGCATACTCAAAA 59.242 43.478 0.00 0.00 0.00 2.44
1442 1500 2.675348 GAGCACTCCTAATCAAGCACAC 59.325 50.000 0.00 0.00 0.00 3.82
1488 1552 4.942761 AGACAAATGTTGGCATCAAACT 57.057 36.364 1.83 0.00 42.71 2.66
1531 1595 5.202004 TCCCTCATCCAGTTAGTAGTCTTC 58.798 45.833 0.00 0.00 0.00 2.87
1534 1598 5.715434 GATCCCTCATCCAGTTAGTAGTC 57.285 47.826 0.00 0.00 0.00 2.59
1572 1636 9.930693 ACAAAACTTACCAGTTATTTTTGTGAA 57.069 25.926 13.62 0.00 42.89 3.18
1573 1637 9.930693 AACAAAACTTACCAGTTATTTTTGTGA 57.069 25.926 14.56 0.00 42.89 3.58
1582 1655 9.924650 TTTAGCAAAAACAAAACTTACCAGTTA 57.075 25.926 0.00 0.00 42.89 2.24
1585 1658 8.878769 ACATTTAGCAAAAACAAAACTTACCAG 58.121 29.630 0.00 0.00 0.00 4.00
1691 1773 3.470567 GACAGAACGACGCAGCGG 61.471 66.667 21.15 4.41 35.12 5.52
1693 1775 1.291877 AATGGACAGAACGACGCAGC 61.292 55.000 0.00 0.00 0.00 5.25
1697 1779 4.637968 CATGTTTAATGGACAGAACGACG 58.362 43.478 0.00 0.00 0.00 5.12
1745 2047 6.828273 TGGAATACATCACCAAACTGAATAGG 59.172 38.462 0.00 0.00 0.00 2.57
1747 2049 8.821686 AATGGAATACATCACCAAACTGAATA 57.178 30.769 0.00 0.00 39.40 1.75
1792 2098 8.574196 AGAAAACTAAACAAATCATTGGAACG 57.426 30.769 0.00 0.00 41.01 3.95
1800 2106 9.364989 CAACCTGAAAGAAAACTAAACAAATCA 57.635 29.630 0.00 0.00 34.07 2.57
1810 2116 4.014406 ACGGAACAACCTGAAAGAAAACT 58.986 39.130 0.00 0.00 34.07 2.66
1811 2117 4.365899 ACGGAACAACCTGAAAGAAAAC 57.634 40.909 0.00 0.00 34.07 2.43
1885 2191 9.790389 TTTCGTGTAATTAAAACAGTGTTCATT 57.210 25.926 9.40 10.42 0.00 2.57
1890 2196 9.628746 AAAACTTTCGTGTAATTAAAACAGTGT 57.371 25.926 0.00 0.00 0.00 3.55
2016 2326 6.367422 GGTGAACATTTTGAACACAAGTTGAA 59.633 34.615 10.54 0.00 38.30 2.69
2036 2346 7.554835 AGTGAACAGTTTTATGTACAAGGTGAA 59.445 33.333 0.00 0.00 31.70 3.18
2112 2422 9.813446 CCTCCTATTTTCAGTAGTAAAATACGT 57.187 33.333 0.00 0.00 37.61 3.57
2132 2454 7.906199 TTTCCTTTTTGTTCATTTCCTCCTA 57.094 32.000 0.00 0.00 0.00 2.94
2133 2455 6.806668 TTTCCTTTTTGTTCATTTCCTCCT 57.193 33.333 0.00 0.00 0.00 3.69
2163 2485 9.601810 AGTTTTCTTCCTGGTTTATTTATCCTT 57.398 29.630 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.