Multiple sequence alignment - TraesCS5A01G229300

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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 TraesCS5A01G229300 chr5A 100.000 2920 0 0 1 2920 444946174 444943255 0.000000e+00 5393
1 TraesCS5A01G229300 chr5A 98.387 62 1 0 1 62 444946114 444946053 3.080000e-20 110
2 TraesCS5A01G229300 chr5A 98.387 62 1 0 61 122 444946174 444946113 3.080000e-20 110
3 TraesCS5A01G229300 chr5B 93.156 1651 62 29 559 2185 404191625 404190002 0.000000e+00 2375
4 TraesCS5A01G229300 chr5B 90.061 815 56 15 2120 2920 404189995 404189192 0.000000e+00 1033
5 TraesCS5A01G229300 chr5B 86.104 367 36 4 61 427 404192126 404191775 5.900000e-102 381
6 TraesCS5A01G229300 chr5D 94.544 1173 46 11 559 1719 346636336 346637502 0.000000e+00 1796
7 TraesCS5A01G229300 chr5D 89.441 805 48 15 2120 2920 346638033 346638804 0.000000e+00 981
8 TraesCS5A01G229300 chr5D 95.643 459 14 3 1732 2185 346637569 346638026 0.000000e+00 732


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 TraesCS5A01G229300 chr5A 444943255 444946174 2919 True 1871.000000 5393 98.924667 1 2920 3 chr5A.!!$R1 2919
1 TraesCS5A01G229300 chr5B 404189192 404192126 2934 True 1263.000000 2375 89.773667 61 2920 3 chr5B.!!$R1 2859
2 TraesCS5A01G229300 chr5D 346636336 346638804 2468 False 1169.666667 1796 93.209333 559 2920 3 chr5D.!!$F1 2361

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
270 271 0.036388 TGGCAGGATCGAAACTCCAC 60.036 55.0 6.33 0.0 35.08 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2174 0.182775 AAAGTTTCACCACCGGAGCT 59.817 50.0 9.46 0.0 0.0 4.09 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
17 18 3.600843 GCTCTCCGTCGTTACCCT 58.399 61.111 0.00 0.00 0.00 4.34
18 19 1.432657 GCTCTCCGTCGTTACCCTC 59.567 63.158 0.00 0.00 0.00 4.30
19 20 1.031029 GCTCTCCGTCGTTACCCTCT 61.031 60.000 0.00 0.00 0.00 3.69
20 21 1.461559 CTCTCCGTCGTTACCCTCTT 58.538 55.000 0.00 0.00 0.00 2.85
21 22 1.132643 CTCTCCGTCGTTACCCTCTTG 59.867 57.143 0.00 0.00 0.00 3.02
22 23 0.172803 CTCCGTCGTTACCCTCTTGG 59.827 60.000 0.00 0.00 41.37 3.61
32 33 2.266055 CCTCTTGGGTGCCTCGTC 59.734 66.667 0.00 0.00 0.00 4.20
33 34 2.125912 CTCTTGGGTGCCTCGTCG 60.126 66.667 0.00 0.00 0.00 5.12
34 35 3.649277 CTCTTGGGTGCCTCGTCGG 62.649 68.421 0.00 0.00 0.00 4.79
35 36 4.760047 CTTGGGTGCCTCGTCGGG 62.760 72.222 0.00 0.00 0.00 5.14
39 40 4.754667 GGTGCCTCGTCGGGGAAC 62.755 72.222 17.53 16.01 0.00 3.62
40 41 3.692406 GTGCCTCGTCGGGGAACT 61.692 66.667 17.53 0.00 29.89 3.01
41 42 2.920912 TGCCTCGTCGGGGAACTT 60.921 61.111 17.53 0.00 0.00 2.66
42 43 1.607178 TGCCTCGTCGGGGAACTTA 60.607 57.895 17.53 0.00 0.00 2.24
43 44 1.141234 GCCTCGTCGGGGAACTTAG 59.859 63.158 17.53 0.00 0.00 2.18
44 45 1.814527 CCTCGTCGGGGAACTTAGG 59.185 63.158 4.69 0.00 0.00 2.69
45 46 0.969409 CCTCGTCGGGGAACTTAGGT 60.969 60.000 4.69 0.00 0.00 3.08
46 47 1.683011 CCTCGTCGGGGAACTTAGGTA 60.683 57.143 4.69 0.00 0.00 3.08
47 48 2.305009 CTCGTCGGGGAACTTAGGTAT 58.695 52.381 0.00 0.00 0.00 2.73
48 49 2.292845 CTCGTCGGGGAACTTAGGTATC 59.707 54.545 0.00 0.00 0.00 2.24
49 50 2.026641 CGTCGGGGAACTTAGGTATCA 58.973 52.381 0.00 0.00 0.00 2.15
50 51 2.626743 CGTCGGGGAACTTAGGTATCAT 59.373 50.000 0.00 0.00 0.00 2.45
51 52 3.305199 CGTCGGGGAACTTAGGTATCATC 60.305 52.174 0.00 0.00 0.00 2.92
52 53 3.896272 GTCGGGGAACTTAGGTATCATCT 59.104 47.826 0.00 0.00 0.00 2.90
53 54 3.895656 TCGGGGAACTTAGGTATCATCTG 59.104 47.826 0.00 0.00 0.00 2.90
54 55 3.006967 CGGGGAACTTAGGTATCATCTGG 59.993 52.174 0.00 0.00 0.00 3.86
55 56 3.974642 GGGGAACTTAGGTATCATCTGGT 59.025 47.826 0.00 0.00 0.00 4.00
56 57 4.412528 GGGGAACTTAGGTATCATCTGGTT 59.587 45.833 0.00 0.00 0.00 3.67
57 58 5.605488 GGGGAACTTAGGTATCATCTGGTTA 59.395 44.000 0.00 0.00 0.00 2.85
58 59 6.272558 GGGGAACTTAGGTATCATCTGGTTAT 59.727 42.308 0.00 0.00 0.00 1.89
59 60 7.456902 GGGGAACTTAGGTATCATCTGGTTATA 59.543 40.741 0.00 0.00 0.00 0.98
60 61 8.532819 GGGAACTTAGGTATCATCTGGTTATAG 58.467 40.741 0.00 0.00 0.00 1.31
61 62 8.035984 GGAACTTAGGTATCATCTGGTTATAGC 58.964 40.741 0.00 0.00 0.00 2.97
62 63 8.728596 AACTTAGGTATCATCTGGTTATAGCT 57.271 34.615 0.00 0.00 37.59 3.32
63 64 8.356000 ACTTAGGTATCATCTGGTTATAGCTC 57.644 38.462 0.00 0.00 35.93 4.09
64 65 8.174085 ACTTAGGTATCATCTGGTTATAGCTCT 58.826 37.037 0.00 0.00 35.93 4.09
65 66 8.582657 TTAGGTATCATCTGGTTATAGCTCTC 57.417 38.462 0.00 0.00 35.93 3.20
66 67 5.955355 AGGTATCATCTGGTTATAGCTCTCC 59.045 44.000 0.00 0.00 30.21 3.71
67 68 5.163602 GGTATCATCTGGTTATAGCTCTCCG 60.164 48.000 0.00 0.00 0.00 4.63
68 69 3.833732 TCATCTGGTTATAGCTCTCCGT 58.166 45.455 0.00 0.00 0.00 4.69
69 70 3.821600 TCATCTGGTTATAGCTCTCCGTC 59.178 47.826 0.00 0.00 0.00 4.79
70 71 2.219458 TCTGGTTATAGCTCTCCGTCG 58.781 52.381 0.00 0.00 0.00 5.12
118 119 5.308237 GGGAACTCAGGTATCATCTGGTTAT 59.692 44.000 0.00 0.00 31.11 1.89
122 123 5.184096 ACTCAGGTATCATCTGGTTATAGCG 59.816 44.000 0.00 0.00 33.36 4.26
123 124 5.077564 TCAGGTATCATCTGGTTATAGCGT 58.922 41.667 0.00 0.00 33.36 5.07
125 126 3.927142 GGTATCATCTGGTTATAGCGTGC 59.073 47.826 0.00 0.00 0.00 5.34
129 130 1.191535 TCTGGTTATAGCGTGCTGGT 58.808 50.000 4.25 0.00 0.00 4.00
148 149 0.320073 TGCCTTCATGCTTGCTTTGC 60.320 50.000 0.00 0.00 0.00 3.68
151 152 1.614385 CTTCATGCTTGCTTTGCTCG 58.386 50.000 0.00 0.00 0.00 5.03
155 156 1.174712 ATGCTTGCTTTGCTCGTGGT 61.175 50.000 0.00 0.00 0.00 4.16
171 172 0.884704 TGGTGTGAAGCTTCTTCGGC 60.885 55.000 26.09 14.82 0.00 5.54
182 183 0.250727 TTCTTCGGCTTTGGGTGGAG 60.251 55.000 0.00 0.00 0.00 3.86
189 190 1.177401 GCTTTGGGTGGAGTGGATTC 58.823 55.000 0.00 0.00 0.00 2.52
190 191 1.547675 GCTTTGGGTGGAGTGGATTCA 60.548 52.381 0.00 0.00 0.00 2.57
201 202 3.711704 GGAGTGGATTCATTGGTCTCCTA 59.288 47.826 1.13 0.00 37.55 2.94
211 212 8.682936 ATTCATTGGTCTCCTATCATTTACAC 57.317 34.615 0.00 0.00 0.00 2.90
229 230 0.885879 ACGTATCCTCGCAGTCACAA 59.114 50.000 0.00 0.00 0.00 3.33
232 233 2.474816 GTATCCTCGCAGTCACAATCC 58.525 52.381 0.00 0.00 0.00 3.01
262 263 0.673985 CTATCCGTTGGCAGGATCGA 59.326 55.000 11.22 0.00 44.68 3.59
270 271 0.036388 TGGCAGGATCGAAACTCCAC 60.036 55.000 6.33 0.00 35.08 4.02
273 274 1.084370 CAGGATCGAAACTCCACGGC 61.084 60.000 6.33 0.00 35.08 5.68
297 298 2.806856 GCGAGAGGACATGCGCTTG 61.807 63.158 20.60 20.60 45.41 4.01
298 299 2.806856 CGAGAGGACATGCGCTTGC 61.807 63.158 21.93 14.48 39.78 4.01
299 300 1.449246 GAGAGGACATGCGCTTGCT 60.449 57.895 21.93 12.45 40.12 3.91
300 301 1.427592 GAGAGGACATGCGCTTGCTC 61.428 60.000 21.93 19.39 40.12 4.26
301 302 1.449246 GAGGACATGCGCTTGCTCT 60.449 57.895 21.93 18.28 40.12 4.09
302 303 0.179100 GAGGACATGCGCTTGCTCTA 60.179 55.000 21.93 0.00 40.12 2.43
303 304 0.467384 AGGACATGCGCTTGCTCTAT 59.533 50.000 21.93 3.14 40.12 1.98
304 305 0.864455 GGACATGCGCTTGCTCTATC 59.136 55.000 21.93 11.85 40.12 2.08
305 306 0.864455 GACATGCGCTTGCTCTATCC 59.136 55.000 21.93 1.07 40.12 2.59
306 307 0.178767 ACATGCGCTTGCTCTATCCA 59.821 50.000 21.93 0.00 40.12 3.41
311 312 0.924090 CGCTTGCTCTATCCAACGAC 59.076 55.000 0.00 0.00 0.00 4.34
318 319 3.126831 GCTCTATCCAACGACATCTTGG 58.873 50.000 0.00 0.00 39.79 3.61
323 324 1.414550 TCCAACGACATCTTGGTGTGA 59.585 47.619 2.09 0.00 39.48 3.58
328 329 1.404181 CGACATCTTGGTGTGATCGGT 60.404 52.381 0.00 0.00 31.16 4.69
330 331 0.729116 CATCTTGGTGTGATCGGTGC 59.271 55.000 0.00 0.00 0.00 5.01
340 341 4.430765 ATCGGTGCGTCGGTGTCC 62.431 66.667 0.00 0.00 0.00 4.02
363 364 0.741221 GGTTTCTCTAGGCAGTGCGG 60.741 60.000 9.45 1.97 0.00 5.69
364 365 0.037232 GTTTCTCTAGGCAGTGCGGT 60.037 55.000 9.45 0.96 0.00 5.68
365 366 0.685097 TTTCTCTAGGCAGTGCGGTT 59.315 50.000 9.45 0.00 0.00 4.44
366 367 0.246635 TTCTCTAGGCAGTGCGGTTC 59.753 55.000 9.45 0.00 0.00 3.62
367 368 0.898326 TCTCTAGGCAGTGCGGTTCA 60.898 55.000 9.45 0.00 0.00 3.18
374 375 1.208642 GCAGTGCGGTTCAGTTTTGC 61.209 55.000 0.00 0.00 0.00 3.68
377 378 1.065551 AGTGCGGTTCAGTTTTGCTTC 59.934 47.619 0.00 0.00 0.00 3.86
398 399 2.549563 CGGTAGTCTAGGTCGCCTCATA 60.550 54.545 1.46 0.00 34.61 2.15
407 408 2.365617 AGGTCGCCTCATATTAGTGTGG 59.634 50.000 0.00 0.00 36.17 4.17
410 411 2.526304 GCCTCATATTAGTGTGGCGA 57.474 50.000 4.49 0.00 45.40 5.54
411 412 3.045601 GCCTCATATTAGTGTGGCGAT 57.954 47.619 4.49 0.00 45.40 4.58
412 413 3.403038 GCCTCATATTAGTGTGGCGATT 58.597 45.455 4.49 0.00 45.40 3.34
413 414 3.433615 GCCTCATATTAGTGTGGCGATTC 59.566 47.826 4.49 0.00 45.40 2.52
414 415 3.997021 CCTCATATTAGTGTGGCGATTCC 59.003 47.826 0.00 0.00 0.00 3.01
415 416 4.262635 CCTCATATTAGTGTGGCGATTCCT 60.263 45.833 0.00 0.00 35.26 3.36
416 417 5.290493 TCATATTAGTGTGGCGATTCCTT 57.710 39.130 0.00 0.00 35.26 3.36
417 418 5.680619 TCATATTAGTGTGGCGATTCCTTT 58.319 37.500 0.00 0.00 35.26 3.11
418 419 6.119536 TCATATTAGTGTGGCGATTCCTTTT 58.880 36.000 0.00 0.00 35.26 2.27
419 420 6.601613 TCATATTAGTGTGGCGATTCCTTTTT 59.398 34.615 0.00 0.00 35.26 1.94
464 465 5.217895 ACGCGATTCCTATTTTCTTGTTC 57.782 39.130 15.93 0.00 0.00 3.18
471 472 2.476185 CCTATTTTCTTGTTCGGCTGCG 60.476 50.000 0.00 0.00 0.00 5.18
507 508 1.017177 GCCGCGACTGGTTTGTATGA 61.017 55.000 8.23 0.00 0.00 2.15
508 509 1.434555 CCGCGACTGGTTTGTATGAA 58.565 50.000 8.23 0.00 0.00 2.57
525 533 6.693466 TGTATGAAGTTTCACCTTGTATCGA 58.307 36.000 0.00 0.00 40.49 3.59
529 537 5.347635 TGAAGTTTCACCTTGTATCGATTCG 59.652 40.000 1.71 0.00 31.01 3.34
533 541 2.756207 TCACCTTGTATCGATTCGACCA 59.244 45.455 11.56 8.44 39.18 4.02
539 547 5.463499 TTGTATCGATTCGACCATTTGTG 57.537 39.130 11.56 0.00 39.18 3.33
544 552 5.176407 TCGATTCGACCATTTGTGTTTTT 57.824 34.783 4.29 0.00 0.00 1.94
565 621 4.724279 TTCTAGGGAGAAAGCCTGTTTT 57.276 40.909 0.00 0.00 38.80 2.43
567 623 1.332195 AGGGAGAAAGCCTGTTTTGC 58.668 50.000 0.00 0.00 0.00 3.68
577 633 0.040067 CCTGTTTTGCGTGGAAGAGC 60.040 55.000 0.00 0.00 0.00 4.09
606 662 1.110442 CAAGCAAACAGACCAACCCA 58.890 50.000 0.00 0.00 0.00 4.51
702 758 0.105964 TTCCCCGACCAATAGCGATG 59.894 55.000 0.00 0.00 0.00 3.84
787 843 2.896685 GGTCCATCTATCCAGTCTCCAG 59.103 54.545 0.00 0.00 0.00 3.86
788 844 2.896685 GTCCATCTATCCAGTCTCCAGG 59.103 54.545 0.00 0.00 0.00 4.45
945 1003 1.453015 GGCAGAACCACCACACACA 60.453 57.895 0.00 0.00 38.86 3.72
946 1004 1.724582 GGCAGAACCACCACACACAC 61.725 60.000 0.00 0.00 38.86 3.82
947 1005 2.013807 CAGAACCACCACACACACG 58.986 57.895 0.00 0.00 0.00 4.49
948 1006 1.817941 AGAACCACCACACACACGC 60.818 57.895 0.00 0.00 0.00 5.34
1188 1246 3.701604 CTACCTCGACGGCAGGTGC 62.702 68.421 19.10 0.00 44.51 5.01
1190 1248 4.457496 CCTCGACGGCAGGTGCAT 62.457 66.667 4.01 0.00 44.36 3.96
1191 1249 3.190849 CTCGACGGCAGGTGCATG 61.191 66.667 4.01 0.00 44.36 4.06
1217 1275 7.257003 GGAACATAACAATAACACATGATGCA 58.743 34.615 0.00 0.00 0.00 3.96
1218 1276 7.758980 GGAACATAACAATAACACATGATGCAA 59.241 33.333 0.00 0.00 0.00 4.08
1219 1277 8.464770 AACATAACAATAACACATGATGCAAC 57.535 30.769 0.00 0.00 0.00 4.17
1220 1278 6.746822 ACATAACAATAACACATGATGCAACG 59.253 34.615 0.00 0.00 0.00 4.10
1223 1281 2.610219 TAACACATGATGCAACGCAC 57.390 45.000 0.00 0.00 43.04 5.34
1224 1282 0.667453 AACACATGATGCAACGCACA 59.333 45.000 0.00 0.00 43.04 4.57
1225 1283 0.883153 ACACATGATGCAACGCACAT 59.117 45.000 0.00 0.00 43.04 3.21
1226 1284 1.264672 CACATGATGCAACGCACATG 58.735 50.000 20.16 20.16 44.81 3.21
1227 1285 0.457166 ACATGATGCAACGCACATGC 60.457 50.000 21.00 0.00 44.03 4.06
1228 1286 0.179148 CATGATGCAACGCACATGCT 60.179 50.000 14.19 0.00 43.04 3.79
1229 1287 0.179148 ATGATGCAACGCACATGCTG 60.179 50.000 1.82 0.00 43.04 4.41
1231 1289 0.447406 GATGCAACGCACATGCTGTA 59.553 50.000 1.82 0.00 43.04 2.74
1233 1291 0.447406 TGCAACGCACATGCTGTATC 59.553 50.000 1.82 0.00 44.14 2.24
1263 1332 6.543465 TGCTAATACTCTTTGTTGGATGGATG 59.457 38.462 0.00 0.00 0.00 3.51
1265 1334 5.715439 ATACTCTTTGTTGGATGGATGGA 57.285 39.130 0.00 0.00 0.00 3.41
1288 1363 2.282816 TTGGCGGGTGACAATGGG 60.283 61.111 0.00 0.00 38.51 4.00
1615 1690 3.849951 CCCCACGAGTGCGGCTAT 61.850 66.667 0.00 0.00 43.17 2.97
1694 1769 3.366739 CTCGCCAACGGTACCTCCC 62.367 68.421 10.90 0.00 40.63 4.30
1772 1900 8.795786 TCTTGTTAATCTTTGGATGTTTTTCG 57.204 30.769 0.00 0.00 31.75 3.46
2207 2409 9.565090 TGATGATAGCAATAGTAAATCAAAGCT 57.435 29.630 0.00 0.00 30.90 3.74
2221 2423 9.677567 GTAAATCAAAGCTGAACTTCATACAAA 57.322 29.630 0.00 0.00 37.75 2.83
2222 2424 8.579682 AAATCAAAGCTGAACTTCATACAAAC 57.420 30.769 0.00 0.00 37.75 2.93
2223 2425 6.691754 TCAAAGCTGAACTTCATACAAACA 57.308 33.333 0.00 0.00 37.75 2.83
2225 2427 5.438761 AAGCTGAACTTCATACAAACACC 57.561 39.130 0.00 0.00 30.77 4.16
2228 2430 4.062293 CTGAACTTCATACAAACACCGGA 58.938 43.478 9.46 0.00 0.00 5.14
2229 2431 3.810941 TGAACTTCATACAAACACCGGAC 59.189 43.478 9.46 0.00 0.00 4.79
2230 2432 3.478857 ACTTCATACAAACACCGGACA 57.521 42.857 9.46 0.00 0.00 4.02
2245 2448 2.231478 CCGGACACAGATGTAGAACAGT 59.769 50.000 0.00 0.00 39.95 3.55
2290 2498 5.541868 AGGATCCAGTATATCAAGTCACAGG 59.458 44.000 15.82 0.00 0.00 4.00
2321 2529 7.391148 ACATCAGTCACAAAACTACAACTTT 57.609 32.000 0.00 0.00 0.00 2.66
2329 2537 7.581600 GTCACAAAACTACAACTTTGTCGTATC 59.418 37.037 0.00 0.00 42.41 2.24
2339 2547 3.367932 ACTTTGTCGTATCGAATGTGCAG 59.632 43.478 0.00 0.00 37.72 4.41
2372 2580 2.050144 AGAGTCCTTCAAGGCTCAACA 58.950 47.619 22.47 0.00 39.44 3.33
2445 2654 4.150451 GCCAACTGATTCAACCGAAAATTG 59.850 41.667 0.00 0.00 34.01 2.32
2455 2664 8.970691 ATTCAACCGAAAATTGAGAACTAATG 57.029 30.769 0.00 0.00 37.38 1.90
2487 2698 5.349817 CCACATGAGCTTATCCTAATTAGCG 59.650 44.000 6.99 1.18 41.36 4.26
2502 2713 0.457853 TAGCGGCTGCAAGTAACTCG 60.458 55.000 21.93 0.00 46.23 4.18
2518 2729 3.626028 ACTCGGCACATTTCTTTTGTC 57.374 42.857 0.00 0.00 0.00 3.18
2541 2752 1.205064 CACTGCAGAAAACTCGGCG 59.795 57.895 23.35 0.00 33.59 6.46
2565 2776 2.143876 ACCCTTGGCACATACAATCC 57.856 50.000 0.00 0.00 39.30 3.01
2683 2894 1.081892 CCACTCCATGCTCTTGTTCG 58.918 55.000 0.00 0.00 0.00 3.95
2727 2938 3.689161 TCATGTTTGGCCTTATCGTCTTG 59.311 43.478 3.32 0.00 0.00 3.02
2793 3004 6.407202 TCTAGTCAGGACCAATAAAGAAAGC 58.593 40.000 0.00 0.00 0.00 3.51
2797 3008 3.756434 CAGGACCAATAAAGAAAGCGGAA 59.244 43.478 0.00 0.00 0.00 4.30
2829 3040 0.764890 TACAGCAGAAGCCAACAGGT 59.235 50.000 0.00 0.00 43.56 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.904466 CCAAGAGGGTAACGACGG 57.096 61.111 0.00 0.00 37.60 4.79
15 16 2.266055 GACGAGGCACCCAAGAGG 59.734 66.667 0.00 0.00 43.78 3.69
16 17 2.125912 CGACGAGGCACCCAAGAG 60.126 66.667 0.00 0.00 0.00 2.85
17 18 3.691342 CCGACGAGGCACCCAAGA 61.691 66.667 0.00 0.00 0.00 3.02
18 19 4.760047 CCCGACGAGGCACCCAAG 62.760 72.222 0.00 0.00 39.21 3.61
22 23 4.754667 GTTCCCCGACGAGGCACC 62.755 72.222 0.00 0.00 39.21 5.01
23 24 1.880819 TAAGTTCCCCGACGAGGCAC 61.881 60.000 0.00 0.00 39.21 5.01
24 25 1.601419 CTAAGTTCCCCGACGAGGCA 61.601 60.000 0.00 0.00 39.21 4.75
25 26 1.141234 CTAAGTTCCCCGACGAGGC 59.859 63.158 0.00 0.00 39.21 4.70
26 27 0.969409 ACCTAAGTTCCCCGACGAGG 60.969 60.000 0.00 0.00 40.63 4.63
27 28 1.755179 TACCTAAGTTCCCCGACGAG 58.245 55.000 0.00 0.00 0.00 4.18
28 29 2.301346 GATACCTAAGTTCCCCGACGA 58.699 52.381 0.00 0.00 0.00 4.20
29 30 2.026641 TGATACCTAAGTTCCCCGACG 58.973 52.381 0.00 0.00 0.00 5.12
30 31 3.896272 AGATGATACCTAAGTTCCCCGAC 59.104 47.826 0.00 0.00 0.00 4.79
31 32 3.895656 CAGATGATACCTAAGTTCCCCGA 59.104 47.826 0.00 0.00 0.00 5.14
32 33 3.006967 CCAGATGATACCTAAGTTCCCCG 59.993 52.174 0.00 0.00 0.00 5.73
33 34 3.974642 ACCAGATGATACCTAAGTTCCCC 59.025 47.826 0.00 0.00 0.00 4.81
34 35 5.632034 AACCAGATGATACCTAAGTTCCC 57.368 43.478 0.00 0.00 0.00 3.97
35 36 8.035984 GCTATAACCAGATGATACCTAAGTTCC 58.964 40.741 0.00 0.00 0.00 3.62
36 37 8.808092 AGCTATAACCAGATGATACCTAAGTTC 58.192 37.037 0.00 0.00 0.00 3.01
37 38 8.728596 AGCTATAACCAGATGATACCTAAGTT 57.271 34.615 0.00 0.00 0.00 2.66
38 39 8.174085 AGAGCTATAACCAGATGATACCTAAGT 58.826 37.037 0.00 0.00 0.00 2.24
39 40 8.588290 AGAGCTATAACCAGATGATACCTAAG 57.412 38.462 0.00 0.00 0.00 2.18
40 41 7.616150 GGAGAGCTATAACCAGATGATACCTAA 59.384 40.741 0.00 0.00 0.00 2.69
41 42 7.120051 GGAGAGCTATAACCAGATGATACCTA 58.880 42.308 0.00 0.00 0.00 3.08
42 43 5.955355 GGAGAGCTATAACCAGATGATACCT 59.045 44.000 0.00 0.00 0.00 3.08
43 44 5.163602 CGGAGAGCTATAACCAGATGATACC 60.164 48.000 0.00 0.00 0.00 2.73
44 45 5.416326 ACGGAGAGCTATAACCAGATGATAC 59.584 44.000 0.00 0.00 0.00 2.24
45 46 5.571285 ACGGAGAGCTATAACCAGATGATA 58.429 41.667 0.00 0.00 0.00 2.15
46 47 4.411927 ACGGAGAGCTATAACCAGATGAT 58.588 43.478 0.00 0.00 0.00 2.45
47 48 3.821600 GACGGAGAGCTATAACCAGATGA 59.178 47.826 0.00 0.00 0.00 2.92
48 49 3.365465 CGACGGAGAGCTATAACCAGATG 60.365 52.174 0.00 0.00 0.00 2.90
49 50 2.814919 CGACGGAGAGCTATAACCAGAT 59.185 50.000 0.00 0.00 0.00 2.90
50 51 2.219458 CGACGGAGAGCTATAACCAGA 58.781 52.381 0.00 0.00 0.00 3.86
51 52 1.948145 ACGACGGAGAGCTATAACCAG 59.052 52.381 0.00 0.00 0.00 4.00
52 53 2.048444 ACGACGGAGAGCTATAACCA 57.952 50.000 0.00 0.00 0.00 3.67
53 54 3.304324 GGTAACGACGGAGAGCTATAACC 60.304 52.174 0.00 0.00 0.00 2.85
54 55 3.304324 GGGTAACGACGGAGAGCTATAAC 60.304 52.174 0.00 0.00 37.60 1.89
55 56 2.880890 GGGTAACGACGGAGAGCTATAA 59.119 50.000 0.00 0.00 37.60 0.98
56 57 2.105477 AGGGTAACGACGGAGAGCTATA 59.895 50.000 0.00 0.00 37.60 1.31
57 58 1.133853 AGGGTAACGACGGAGAGCTAT 60.134 52.381 0.00 0.00 37.60 2.97
58 59 0.254178 AGGGTAACGACGGAGAGCTA 59.746 55.000 0.00 0.00 37.60 3.32
59 60 1.001145 AGGGTAACGACGGAGAGCT 60.001 57.895 0.00 0.00 37.60 4.09
60 61 1.031029 AGAGGGTAACGACGGAGAGC 61.031 60.000 0.00 0.00 37.60 4.09
61 62 1.132643 CAAGAGGGTAACGACGGAGAG 59.867 57.143 0.00 0.00 37.60 3.20
62 63 1.171308 CAAGAGGGTAACGACGGAGA 58.829 55.000 0.00 0.00 37.60 3.71
63 64 0.172803 CCAAGAGGGTAACGACGGAG 59.827 60.000 0.00 0.00 37.60 4.63
64 65 2.269978 CCAAGAGGGTAACGACGGA 58.730 57.895 0.00 0.00 37.60 4.69
65 66 4.904466 CCAAGAGGGTAACGACGG 57.096 61.111 0.00 0.00 37.60 4.79
87 88 0.679002 TACCTGAGTTCCCCGACGAG 60.679 60.000 0.00 0.00 0.00 4.18
118 119 2.047274 GAAGGCACCAGCACGCTA 60.047 61.111 0.00 0.00 44.61 4.26
122 123 1.530013 AAGCATGAAGGCACCAGCAC 61.530 55.000 0.00 0.00 44.61 4.40
123 124 1.228644 AAGCATGAAGGCACCAGCA 60.229 52.632 0.00 0.00 44.61 4.41
125 126 1.214589 GCAAGCATGAAGGCACCAG 59.785 57.895 0.00 0.00 35.83 4.00
129 130 0.320073 GCAAAGCAAGCATGAAGGCA 60.320 50.000 0.00 0.00 35.83 4.75
148 149 1.795286 GAAGAAGCTTCACACCACGAG 59.205 52.381 27.57 0.00 0.00 4.18
151 152 0.868406 CCGAAGAAGCTTCACACCAC 59.132 55.000 27.57 10.83 0.00 4.16
171 172 2.584835 TGAATCCACTCCACCCAAAG 57.415 50.000 0.00 0.00 0.00 2.77
182 183 5.296151 TGATAGGAGACCAATGAATCCAC 57.704 43.478 0.00 0.00 34.08 4.02
189 190 6.049149 ACGTGTAAATGATAGGAGACCAATG 58.951 40.000 0.00 0.00 0.00 2.82
190 191 6.235231 ACGTGTAAATGATAGGAGACCAAT 57.765 37.500 0.00 0.00 0.00 3.16
201 202 4.202121 ACTGCGAGGATACGTGTAAATGAT 60.202 41.667 0.00 0.00 46.39 2.45
211 212 2.120232 GATTGTGACTGCGAGGATACG 58.880 52.381 0.00 0.00 46.39 3.06
229 230 1.545875 CGGATAGTGAGGACCGAGGAT 60.546 57.143 0.00 0.00 46.94 3.24
232 233 1.065701 CAACGGATAGTGAGGACCGAG 59.934 57.143 11.27 0.27 46.94 4.63
262 263 4.016706 CTCCGGGCCGTGGAGTTT 62.017 66.667 26.84 0.00 46.49 2.66
273 274 2.835431 ATGTCCTCTCGCTCCGGG 60.835 66.667 0.00 0.00 0.00 5.73
297 298 3.126831 CCAAGATGTCGTTGGATAGAGC 58.873 50.000 0.00 0.00 46.53 4.09
298 299 4.115516 CACCAAGATGTCGTTGGATAGAG 58.884 47.826 8.83 0.00 46.53 2.43
299 300 3.513912 ACACCAAGATGTCGTTGGATAGA 59.486 43.478 8.83 0.00 46.53 1.98
300 301 3.618594 CACACCAAGATGTCGTTGGATAG 59.381 47.826 8.83 1.54 46.53 2.08
301 302 3.259625 TCACACCAAGATGTCGTTGGATA 59.740 43.478 8.83 0.00 46.53 2.59
302 303 2.038426 TCACACCAAGATGTCGTTGGAT 59.962 45.455 8.83 0.00 46.53 3.41
303 304 1.414550 TCACACCAAGATGTCGTTGGA 59.585 47.619 8.83 0.00 46.53 3.53
305 306 2.092681 CGATCACACCAAGATGTCGTTG 59.907 50.000 0.00 0.00 0.00 4.10
306 307 2.337583 CGATCACACCAAGATGTCGTT 58.662 47.619 0.00 0.00 0.00 3.85
311 312 0.729116 GCACCGATCACACCAAGATG 59.271 55.000 0.00 0.00 0.00 2.90
318 319 3.179265 CCGACGCACCGATCACAC 61.179 66.667 0.00 0.00 0.00 3.82
323 324 4.430765 GGACACCGACGCACCGAT 62.431 66.667 0.00 0.00 0.00 4.18
340 341 0.608640 ACTGCCTAGAGAAACCACGG 59.391 55.000 0.00 0.00 0.00 4.94
341 342 1.714794 CACTGCCTAGAGAAACCACG 58.285 55.000 0.00 0.00 0.00 4.94
348 349 0.898326 TGAACCGCACTGCCTAGAGA 60.898 55.000 0.00 0.00 0.00 3.10
350 351 1.185618 ACTGAACCGCACTGCCTAGA 61.186 55.000 0.00 0.00 0.00 2.43
363 364 3.808174 AGACTACCGAAGCAAAACTGAAC 59.192 43.478 0.00 0.00 0.00 3.18
364 365 4.067972 AGACTACCGAAGCAAAACTGAA 57.932 40.909 0.00 0.00 0.00 3.02
365 366 3.746045 AGACTACCGAAGCAAAACTGA 57.254 42.857 0.00 0.00 0.00 3.41
366 367 3.927142 CCTAGACTACCGAAGCAAAACTG 59.073 47.826 0.00 0.00 0.00 3.16
367 368 3.577415 ACCTAGACTACCGAAGCAAAACT 59.423 43.478 0.00 0.00 0.00 2.66
374 375 0.662085 GGCGACCTAGACTACCGAAG 59.338 60.000 0.00 0.00 0.00 3.79
377 378 0.463295 TGAGGCGACCTAGACTACCG 60.463 60.000 0.00 0.00 31.76 4.02
433 434 5.873179 AATAGGAATCGCGTTCTCAAAAA 57.127 34.783 5.77 0.00 37.01 1.94
434 435 5.873179 AAATAGGAATCGCGTTCTCAAAA 57.127 34.783 5.77 0.00 37.01 2.44
435 436 5.642063 AGAAAATAGGAATCGCGTTCTCAAA 59.358 36.000 5.77 0.00 37.01 2.69
436 437 5.175859 AGAAAATAGGAATCGCGTTCTCAA 58.824 37.500 5.77 0.52 37.01 3.02
437 438 4.755411 AGAAAATAGGAATCGCGTTCTCA 58.245 39.130 5.77 2.51 37.01 3.27
438 439 5.063564 ACAAGAAAATAGGAATCGCGTTCTC 59.936 40.000 5.77 0.76 37.01 2.87
439 440 4.935808 ACAAGAAAATAGGAATCGCGTTCT 59.064 37.500 5.77 0.98 37.01 3.01
440 441 5.217895 ACAAGAAAATAGGAATCGCGTTC 57.782 39.130 5.77 9.40 36.04 3.95
441 442 5.622770 AACAAGAAAATAGGAATCGCGTT 57.377 34.783 5.77 0.00 0.00 4.84
442 443 4.201685 CGAACAAGAAAATAGGAATCGCGT 60.202 41.667 5.77 0.00 0.00 6.01
443 444 4.263800 CGAACAAGAAAATAGGAATCGCG 58.736 43.478 0.00 0.00 0.00 5.87
499 500 7.658167 TCGATACAAGGTGAAACTTCATACAAA 59.342 33.333 0.00 0.00 39.73 2.83
507 508 5.347907 GTCGAATCGATACAAGGTGAAACTT 59.652 40.000 9.10 0.00 38.42 2.66
508 509 4.863131 GTCGAATCGATACAAGGTGAAACT 59.137 41.667 9.10 0.00 38.42 2.66
544 552 4.398319 CAAAACAGGCTTTCTCCCTAGAA 58.602 43.478 0.00 0.00 40.03 2.10
546 554 2.489722 GCAAAACAGGCTTTCTCCCTAG 59.510 50.000 0.00 0.00 0.00 3.02
547 555 2.514803 GCAAAACAGGCTTTCTCCCTA 58.485 47.619 0.00 0.00 0.00 3.53
551 559 1.600413 CCACGCAAAACAGGCTTTCTC 60.600 52.381 0.00 0.00 0.00 2.87
552 560 0.385390 CCACGCAAAACAGGCTTTCT 59.615 50.000 0.00 0.00 0.00 2.52
553 561 0.383949 TCCACGCAAAACAGGCTTTC 59.616 50.000 0.00 0.00 0.00 2.62
555 563 0.385390 CTTCCACGCAAAACAGGCTT 59.615 50.000 0.00 0.00 0.00 4.35
556 564 0.465460 TCTTCCACGCAAAACAGGCT 60.465 50.000 0.00 0.00 0.00 4.58
557 565 0.040067 CTCTTCCACGCAAAACAGGC 60.040 55.000 0.00 0.00 0.00 4.85
565 621 1.229428 CTTTCAAGCTCTTCCACGCA 58.771 50.000 0.00 0.00 0.00 5.24
567 623 2.872245 TGAACTTTCAAGCTCTTCCACG 59.128 45.455 0.00 0.00 33.55 4.94
625 681 1.133598 TCGATCCGTCATGGTGTACAC 59.866 52.381 18.01 18.01 39.52 2.90
702 758 2.947448 AATGCGGAATCAAAAGGAGC 57.053 45.000 0.00 0.00 0.00 4.70
865 921 0.673437 GGTGATTTGTGGGTGTGGTG 59.327 55.000 0.00 0.00 0.00 4.17
945 1003 2.049985 GAGTGAGAGTGCGTGCGT 60.050 61.111 0.00 0.00 0.00 5.24
946 1004 1.799519 GAGAGTGAGAGTGCGTGCG 60.800 63.158 0.00 0.00 0.00 5.34
947 1005 1.445238 GGAGAGTGAGAGTGCGTGC 60.445 63.158 0.00 0.00 0.00 5.34
948 1006 0.109365 CAGGAGAGTGAGAGTGCGTG 60.109 60.000 0.00 0.00 0.00 5.34
995 1053 0.243907 ACTGACCGACGACATCTTGG 59.756 55.000 0.00 0.00 0.00 3.61
1188 1246 7.770201 TCATGTGTTATTGTTATGTTCCCATG 58.230 34.615 0.00 0.00 32.29 3.66
1189 1247 7.953005 TCATGTGTTATTGTTATGTTCCCAT 57.047 32.000 0.00 0.00 34.97 4.00
1190 1248 7.630297 GCATCATGTGTTATTGTTATGTTCCCA 60.630 37.037 0.00 0.00 0.00 4.37
1191 1249 6.697019 GCATCATGTGTTATTGTTATGTTCCC 59.303 38.462 0.00 0.00 0.00 3.97
1220 1278 7.412346 GTATTAGCATACAGATACAGCATGTGC 60.412 40.741 0.00 0.00 41.86 4.57
1223 1281 8.249638 AGAGTATTAGCATACAGATACAGCATG 58.750 37.037 0.00 0.00 39.25 4.06
1224 1282 8.359875 AGAGTATTAGCATACAGATACAGCAT 57.640 34.615 0.00 0.00 38.24 3.79
1225 1283 7.767250 AGAGTATTAGCATACAGATACAGCA 57.233 36.000 0.00 0.00 38.24 4.41
1226 1284 8.920665 CAAAGAGTATTAGCATACAGATACAGC 58.079 37.037 0.00 0.00 38.24 4.40
1227 1285 9.973450 ACAAAGAGTATTAGCATACAGATACAG 57.027 33.333 0.00 0.00 38.24 2.74
1231 1289 8.486210 TCCAACAAAGAGTATTAGCATACAGAT 58.514 33.333 0.00 0.00 38.24 2.90
1233 1291 8.554528 CATCCAACAAAGAGTATTAGCATACAG 58.445 37.037 0.00 0.00 38.24 2.74
1263 1332 2.825836 CACCCGCCAAGCTGATCC 60.826 66.667 0.00 0.00 0.00 3.36
1265 1334 2.045926 GTCACCCGCCAAGCTGAT 60.046 61.111 0.00 0.00 0.00 2.90
1615 1690 3.621805 TTGAAGACGCTGCCGGGA 61.622 61.111 2.18 0.00 39.22 5.14
1695 1770 2.266554 CAAGCAGAGAACGATGGACTC 58.733 52.381 0.00 0.00 0.00 3.36
1701 1776 2.072298 GTGAAGCAAGCAGAGAACGAT 58.928 47.619 0.00 0.00 0.00 3.73
1704 1779 1.597742 TGGTGAAGCAAGCAGAGAAC 58.402 50.000 0.00 0.00 0.00 3.01
1706 1781 1.673923 CGATGGTGAAGCAAGCAGAGA 60.674 52.381 0.00 0.00 0.00 3.10
1772 1900 1.740718 GCCAGTCTCCCTGAACGAATC 60.741 57.143 0.00 0.00 44.49 2.52
2041 2174 0.182775 AAAGTTTCACCACCGGAGCT 59.817 50.000 9.46 0.00 0.00 4.09
2099 2232 4.024893 CACGCATGGGTGATATTACAAGTC 60.025 45.833 32.85 0.00 40.38 3.01
2165 2298 1.253800 CATCACAGCGAATTCGAGACG 59.746 52.381 31.01 16.56 43.02 4.18
2177 2310 8.315391 TGATTTACTATTGCTATCATCACAGC 57.685 34.615 0.00 0.00 38.31 4.40
2207 2409 3.810941 GTCCGGTGTTTGTATGAAGTTCA 59.189 43.478 8.27 8.27 0.00 3.18
2221 2423 1.919240 TCTACATCTGTGTCCGGTGT 58.081 50.000 0.00 0.00 39.77 4.16
2222 2424 2.029380 TGTTCTACATCTGTGTCCGGTG 60.029 50.000 0.00 0.00 39.77 4.94
2223 2425 2.231478 CTGTTCTACATCTGTGTCCGGT 59.769 50.000 0.00 0.00 39.77 5.28
2225 2427 3.245797 CACTGTTCTACATCTGTGTCCG 58.754 50.000 0.00 0.00 39.77 4.79
2228 2430 4.955811 TTCCACTGTTCTACATCTGTGT 57.044 40.909 0.00 0.00 42.39 3.72
2229 2431 5.482006 TGATTCCACTGTTCTACATCTGTG 58.518 41.667 0.00 0.00 34.75 3.66
2230 2432 5.745312 TGATTCCACTGTTCTACATCTGT 57.255 39.130 0.00 0.00 0.00 3.41
2245 2448 7.896383 TCCTTTTTCTTCTTCTTTGATTCCA 57.104 32.000 0.00 0.00 0.00 3.53
2290 2498 8.984764 TGTAGTTTTGTGACTGATGTTGTATAC 58.015 33.333 0.00 0.00 0.00 1.47
2321 2529 1.277326 GCTGCACATTCGATACGACA 58.723 50.000 0.00 0.00 34.89 4.35
2339 2547 3.258971 AGGACTCTAATCTTGTGCTGC 57.741 47.619 0.00 0.00 31.41 5.25
2372 2580 8.101654 TCTTAACCAATTTTTACGCACTGTAT 57.898 30.769 0.00 0.00 31.81 2.29
2487 2698 1.671054 TGCCGAGTTACTTGCAGCC 60.671 57.895 6.45 0.00 0.00 4.85
2502 2713 2.393764 CACCGACAAAAGAAATGTGCC 58.606 47.619 0.00 0.00 0.00 5.01
2518 2729 0.040958 GAGTTTTCTGCAGTGCACCG 60.041 55.000 15.37 5.78 33.79 4.94
2541 2752 3.838244 TGTATGTGCCAAGGGTAGATC 57.162 47.619 0.00 0.00 0.00 2.75
2565 2776 5.299782 GTCTATCTATACTTATCCTGCCCCG 59.700 48.000 0.00 0.00 0.00 5.73
2683 2894 2.383368 TTGCTTGGCCACATATTTGC 57.617 45.000 3.88 1.96 0.00 3.68
2727 2938 0.255033 ACCGGGCCTACAGGAATTTC 59.745 55.000 6.32 0.00 37.90 2.17
2797 3008 5.416013 GCTTCTGCTGTATTCCCTAGTTTTT 59.584 40.000 0.00 0.00 36.03 1.94
2801 3012 2.436173 GGCTTCTGCTGTATTCCCTAGT 59.564 50.000 0.00 0.00 39.59 2.57
2804 3015 1.289160 TGGCTTCTGCTGTATTCCCT 58.711 50.000 0.00 0.00 39.59 4.20
2806 3017 2.421424 CTGTTGGCTTCTGCTGTATTCC 59.579 50.000 0.00 0.00 39.59 3.01


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

AutoCloner maintained by Alex Coulton.