Multiple sequence alignment - TraesCS3A01G313700

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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 TraesCS3A01G313700 chr3A 100.000 2633 0 0 1 2633 553559982 553562614 0.000000e+00 4863
1 TraesCS3A01G313700 chr3D 88.288 2664 196 64 15 2633 102189632 102187040 0.000000e+00 3085
2 TraesCS3A01G313700 chr3D 76.471 238 38 13 1092 1317 378529511 378529742 2.140000e-21 113
3 TraesCS3A01G313700 chr3B 87.700 2683 210 61 1 2633 152963540 152960928 0.000000e+00 3016
4 TraesCS3A01G313700 chr5A 90.511 137 12 1 1376 1511 568595239 568595103 2.080000e-41 180
5 TraesCS3A01G313700 chr2D 84.971 173 11 4 1294 1466 643732324 643732167 7.540000e-36 161


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 TraesCS3A01G313700 chr3A 553559982 553562614 2632 False 4863 4863 100.000 1 2633 1 chr3A.!!$F1 2632
1 TraesCS3A01G313700 chr3D 102187040 102189632 2592 True 3085 3085 88.288 15 2633 1 chr3D.!!$R1 2618
2 TraesCS3A01G313700 chr3B 152960928 152963540 2612 True 3016 3016 87.700 1 2633 1 chr3B.!!$R1 2632

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
454 455 0.040067 GCCTGCAAACTCGTCCAAAG 60.04 55.0 0.0 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2074 0.109597 GCAAGATGTCAACTTGGGCG 60.11 55.0 20.6 0.4 43.12 6.13 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
28 29 5.401674 GTCCATATCGTTCTAGTAAAAGCCG 59.598 44.000 0.00 0.00 0.00 5.52
31 32 6.919662 CCATATCGTTCTAGTAAAAGCCGTAA 59.080 38.462 0.00 0.00 0.00 3.18
46 47 2.148768 CCGTAAAAACCGAAAGAGCCT 58.851 47.619 0.00 0.00 0.00 4.58
47 48 2.159037 CCGTAAAAACCGAAAGAGCCTC 59.841 50.000 0.00 0.00 0.00 4.70
51 52 4.937201 AAAAACCGAAAGAGCCTCAAAT 57.063 36.364 0.00 0.00 0.00 2.32
53 54 2.859165 ACCGAAAGAGCCTCAAATGA 57.141 45.000 0.00 0.00 0.00 2.57
60 61 5.106396 CGAAAGAGCCTCAAATGAGTGAAAT 60.106 40.000 9.43 0.00 40.48 2.17
62 63 5.640189 AGAGCCTCAAATGAGTGAAATTG 57.360 39.130 9.43 0.00 40.48 2.32
68 69 5.632347 CCTCAAATGAGTGAAATTGAAGCAC 59.368 40.000 9.43 0.00 40.48 4.40
72 73 6.833342 AATGAGTGAAATTGAAGCACAAAC 57.167 33.333 0.00 0.00 42.03 2.93
76 77 4.160252 AGTGAAATTGAAGCACAAACACCT 59.840 37.500 17.63 9.90 42.03 4.00
77 78 4.504097 GTGAAATTGAAGCACAAACACCTC 59.496 41.667 14.08 5.01 42.03 3.85
90 91 3.375782 AACACCTCAAATGAGCAAAGC 57.624 42.857 4.87 0.00 40.75 3.51
99 100 4.103357 CAAATGAGCAAAGCTAGACATGC 58.897 43.478 0.00 0.00 39.88 4.06
101 102 1.338105 TGAGCAAAGCTAGACATGCGT 60.338 47.619 0.00 0.00 43.39 5.24
102 103 1.061711 GAGCAAAGCTAGACATGCGTG 59.938 52.381 3.82 3.82 43.39 5.34
111 112 1.602323 GACATGCGTGGGGTTTCCA 60.602 57.895 11.36 0.00 44.79 3.53
132 133 2.288825 ACAAAGGATGACACACGTCGAT 60.289 45.455 0.00 0.00 45.80 3.59
134 135 0.098905 AGGATGACACACGTCGATCG 59.901 55.000 9.36 9.36 45.80 3.69
140 141 0.666274 ACACACGTCGATCGCACAAT 60.666 50.000 11.09 0.00 44.19 2.71
141 142 0.246873 CACACGTCGATCGCACAATG 60.247 55.000 11.09 12.31 44.19 2.82
158 159 4.937431 GCTCCCGCCAGGCATACC 62.937 72.222 13.30 0.00 35.76 2.73
159 160 3.479203 CTCCCGCCAGGCATACCA 61.479 66.667 13.30 0.00 39.06 3.25
166 167 0.689623 GCCAGGCATACCAGCTAGAT 59.310 55.000 6.55 0.00 39.06 1.98
190 191 8.947055 ATATGTGCTTATTTTTGGGATGAAAC 57.053 30.769 0.00 0.00 0.00 2.78
193 194 6.172630 GTGCTTATTTTTGGGATGAAACCAT 58.827 36.000 0.00 0.00 37.93 3.55
221 222 6.620733 GCAATAAATTGTACTCACTCGTTGCT 60.621 38.462 4.71 0.00 39.88 3.91
225 226 7.521509 AAATTGTACTCACTCGTTGCTATAC 57.478 36.000 0.00 0.00 0.00 1.47
227 228 4.011698 TGTACTCACTCGTTGCTATACCA 58.988 43.478 0.00 0.00 0.00 3.25
230 231 3.243101 ACTCACTCGTTGCTATACCATCG 60.243 47.826 0.00 0.00 0.00 3.84
232 233 3.043586 CACTCGTTGCTATACCATCGTC 58.956 50.000 0.00 0.00 31.72 4.20
237 238 0.966179 TGCTATACCATCGTCGGCAT 59.034 50.000 0.00 0.00 0.00 4.40
238 239 2.164338 TGCTATACCATCGTCGGCATA 58.836 47.619 0.00 0.00 0.00 3.14
251 252 2.163412 GTCGGCATAAAGGTTTGCATGA 59.837 45.455 0.00 0.00 40.66 3.07
252 253 2.423185 TCGGCATAAAGGTTTGCATGAG 59.577 45.455 0.00 0.00 40.66 2.90
253 254 2.543641 GGCATAAAGGTTTGCATGAGC 58.456 47.619 0.00 0.00 40.66 4.26
255 256 2.159393 GCATAAAGGTTTGCATGAGCGA 60.159 45.455 0.00 0.00 46.23 4.93
321 322 1.612463 GACGGGCGACTCCTATTGTAT 59.388 52.381 0.00 0.00 34.39 2.29
332 333 6.183360 CGACTCCTATTGTATACCGTCCATAG 60.183 46.154 0.00 0.00 0.00 2.23
342 343 3.832615 ACCGTCCATAGGTTTATGTCC 57.167 47.619 0.00 0.00 39.29 4.02
345 346 4.141779 ACCGTCCATAGGTTTATGTCCTTC 60.142 45.833 0.00 0.00 39.29 3.46
346 347 4.377897 CGTCCATAGGTTTATGTCCTTCC 58.622 47.826 0.00 0.00 35.84 3.46
358 359 2.223745 TGTCCTTCCCTTACGCAAAAC 58.776 47.619 0.00 0.00 0.00 2.43
372 373 2.258755 GCAAAACGACACAGTGCTTTT 58.741 42.857 0.00 0.00 32.43 2.27
415 416 2.029739 CCGTCCATGTATACACGCCATA 60.030 50.000 7.96 0.00 0.00 2.74
438 439 0.820871 TTTGGTGCGAAAAGTTGCCT 59.179 45.000 0.00 0.00 0.00 4.75
441 442 1.065600 GTGCGAAAAGTTGCCTGCA 59.934 52.632 0.00 0.00 0.00 4.41
444 445 0.576798 GCGAAAAGTTGCCTGCAAAC 59.423 50.000 6.07 1.66 37.70 2.93
447 448 2.119457 GAAAAGTTGCCTGCAAACTCG 58.881 47.619 6.07 0.00 37.70 4.18
448 449 1.102978 AAAGTTGCCTGCAAACTCGT 58.897 45.000 6.07 0.00 37.70 4.18
449 450 0.663153 AAGTTGCCTGCAAACTCGTC 59.337 50.000 6.07 0.00 37.70 4.20
450 451 1.166531 AGTTGCCTGCAAACTCGTCC 61.167 55.000 6.07 0.00 37.70 4.79
452 453 0.749818 TTGCCTGCAAACTCGTCCAA 60.750 50.000 1.31 0.00 32.44 3.53
453 454 0.749818 TGCCTGCAAACTCGTCCAAA 60.750 50.000 0.00 0.00 0.00 3.28
454 455 0.040067 GCCTGCAAACTCGTCCAAAG 60.040 55.000 0.00 0.00 0.00 2.77
455 456 0.040067 CCTGCAAACTCGTCCAAAGC 60.040 55.000 0.00 0.00 0.00 3.51
456 457 0.040067 CTGCAAACTCGTCCAAAGCC 60.040 55.000 0.00 0.00 0.00 4.35
457 458 1.285950 GCAAACTCGTCCAAAGCCC 59.714 57.895 0.00 0.00 0.00 5.19
458 459 1.956802 CAAACTCGTCCAAAGCCCC 59.043 57.895 0.00 0.00 0.00 5.80
459 460 0.537371 CAAACTCGTCCAAAGCCCCT 60.537 55.000 0.00 0.00 0.00 4.79
460 461 1.061546 AAACTCGTCCAAAGCCCCTA 58.938 50.000 0.00 0.00 0.00 3.53
461 462 1.286248 AACTCGTCCAAAGCCCCTAT 58.714 50.000 0.00 0.00 0.00 2.57
462 463 2.170012 ACTCGTCCAAAGCCCCTATA 57.830 50.000 0.00 0.00 0.00 1.31
463 464 2.040178 ACTCGTCCAAAGCCCCTATAG 58.960 52.381 0.00 0.00 0.00 1.31
472 473 6.379417 GTCCAAAGCCCCTATAGTATATACGT 59.621 42.308 7.23 0.00 0.00 3.57
493 494 1.751437 AATCCTAACTTTGGAGGCGC 58.249 50.000 0.00 0.00 36.99 6.53
494 495 0.912486 ATCCTAACTTTGGAGGCGCT 59.088 50.000 7.64 0.00 36.99 5.92
495 496 0.249398 TCCTAACTTTGGAGGCGCTC 59.751 55.000 7.64 2.45 32.40 5.03
496 497 1.084370 CCTAACTTTGGAGGCGCTCG 61.084 60.000 7.64 0.00 0.00 5.03
498 499 0.535335 TAACTTTGGAGGCGCTCGAT 59.465 50.000 7.64 0.00 0.00 3.59
499 500 1.021390 AACTTTGGAGGCGCTCGATG 61.021 55.000 7.64 2.78 0.00 3.84
501 502 0.531532 CTTTGGAGGCGCTCGATGAT 60.532 55.000 7.64 0.00 0.00 2.45
504 505 0.530650 TGGAGGCGCTCGATGATTTC 60.531 55.000 7.64 0.00 0.00 2.17
521 522 1.670791 TTCGTTTTTCTTGCGAGGGT 58.329 45.000 0.00 0.00 36.00 4.34
526 527 0.108585 TTTTCTTGCGAGGGTGCTCT 59.891 50.000 0.00 0.00 35.36 4.09
532 533 0.901827 TGCGAGGGTGCTCTATGAAA 59.098 50.000 0.00 0.00 35.36 2.69
533 534 1.291132 GCGAGGGTGCTCTATGAAAC 58.709 55.000 0.00 0.00 0.00 2.78
534 535 1.405526 GCGAGGGTGCTCTATGAAACA 60.406 52.381 0.00 0.00 0.00 2.83
539 540 5.584649 CGAGGGTGCTCTATGAAACATTTTA 59.415 40.000 0.00 0.00 0.00 1.52
540 541 6.456988 CGAGGGTGCTCTATGAAACATTTTAC 60.457 42.308 0.00 0.00 0.00 2.01
541 542 5.652452 AGGGTGCTCTATGAAACATTTTACC 59.348 40.000 0.00 0.00 0.00 2.85
542 543 5.417580 GGGTGCTCTATGAAACATTTTACCA 59.582 40.000 0.00 0.00 0.00 3.25
543 544 6.096846 GGGTGCTCTATGAAACATTTTACCAT 59.903 38.462 0.00 0.00 0.00 3.55
546 558 7.912250 GTGCTCTATGAAACATTTTACCATGAG 59.088 37.037 0.00 0.00 0.00 2.90
563 575 7.568199 ACCATGAGGAAATAATAAGAAACCG 57.432 36.000 0.00 0.00 38.69 4.44
564 576 6.546034 ACCATGAGGAAATAATAAGAAACCGG 59.454 38.462 0.00 0.00 38.69 5.28
572 584 8.847196 GGAAATAATAAGAAACCGGCTTTCTAT 58.153 33.333 23.46 17.38 46.80 1.98
619 631 3.159472 GTTTTATTGGAAGGACGGGGTT 58.841 45.455 0.00 0.00 0.00 4.11
632 649 1.696884 ACGGGGTTGGCATCAAAATTT 59.303 42.857 0.00 0.00 34.28 1.82
633 650 2.289382 ACGGGGTTGGCATCAAAATTTC 60.289 45.455 0.00 0.00 34.28 2.17
638 655 5.243507 GGGGTTGGCATCAAAATTTCAAAAT 59.756 36.000 0.00 0.00 34.28 1.82
640 657 6.238981 GGGTTGGCATCAAAATTTCAAAATGT 60.239 34.615 0.00 0.00 34.28 2.71
650 667 7.543868 TCAAAATTTCAAAATGTATACAGCCCG 59.456 33.333 11.91 0.67 0.00 6.13
710 733 1.204941 GAGTGGTGTACTGGTAGCAGG 59.795 57.143 24.84 8.17 40.53 4.85
713 736 0.824759 GGTGTACTGGTAGCAGGAGG 59.175 60.000 24.84 2.07 0.00 4.30
911 938 0.679960 AGCCCATAAAACCCACGCTC 60.680 55.000 0.00 0.00 0.00 5.03
912 939 1.988834 GCCCATAAAACCCACGCTCG 61.989 60.000 0.00 0.00 0.00 5.03
913 940 1.427819 CCATAAAACCCACGCTCGC 59.572 57.895 0.00 0.00 0.00 5.03
914 941 1.427819 CATAAAACCCACGCTCGCC 59.572 57.895 0.00 0.00 0.00 5.54
915 942 1.747745 ATAAAACCCACGCTCGCCC 60.748 57.895 0.00 0.00 0.00 6.13
916 943 2.193087 ATAAAACCCACGCTCGCCCT 62.193 55.000 0.00 0.00 0.00 5.19
917 944 2.791501 TAAAACCCACGCTCGCCCTC 62.792 60.000 0.00 0.00 0.00 4.30
983 1016 4.110656 GCGAAGGCGACGTTTTTC 57.889 55.556 0.00 0.00 40.82 2.29
988 1021 2.033151 CGAAGGCGACGTTTTTCTTCTT 60.033 45.455 14.93 3.83 40.82 2.52
1074 1107 4.175489 CAGATGCAGCTGCCGCAC 62.175 66.667 34.64 21.67 43.35 5.34
1410 1443 4.767255 CTGGAGGTGCTGTCGCCC 62.767 72.222 0.00 0.00 43.91 6.13
1539 1572 3.737122 GGGTTCTACCTCCACCCC 58.263 66.667 0.00 0.00 44.16 4.95
1542 1575 1.328430 GGTTCTACCTCCACCCCTCG 61.328 65.000 0.00 0.00 34.73 4.63
1656 1689 2.911143 CCCGCTCCTTGCTGGTAT 59.089 61.111 0.00 0.00 40.58 2.73
1657 1690 1.524621 CCCGCTCCTTGCTGGTATG 60.525 63.158 0.00 0.00 40.58 2.39
1658 1691 2.182842 CCGCTCCTTGCTGGTATGC 61.183 63.158 0.00 0.00 40.11 3.14
1659 1692 1.153289 CGCTCCTTGCTGGTATGCT 60.153 57.895 0.00 0.00 40.11 3.79
1660 1693 1.156645 CGCTCCTTGCTGGTATGCTC 61.157 60.000 0.00 0.00 40.11 4.26
1661 1694 0.179936 GCTCCTTGCTGGTATGCTCT 59.820 55.000 0.00 0.00 38.95 4.09
1662 1695 1.950828 CTCCTTGCTGGTATGCTCTG 58.049 55.000 0.00 0.00 37.07 3.35
1663 1696 0.107508 TCCTTGCTGGTATGCTCTGC 60.108 55.000 0.00 0.00 37.07 4.26
1664 1697 0.107312 CCTTGCTGGTATGCTCTGCT 60.107 55.000 0.00 0.00 0.00 4.24
1665 1698 1.297664 CTTGCTGGTATGCTCTGCTC 58.702 55.000 0.00 0.00 0.00 4.26
1679 1716 2.125188 GCTCTGCTCTGCTCACCC 60.125 66.667 0.00 0.00 0.00 4.61
1690 1727 3.449227 CTCACCCGGTCGCTGCTA 61.449 66.667 0.00 0.00 0.00 3.49
1705 1742 2.225467 CTGCTAAAATGCTAGGCTCCC 58.775 52.381 0.00 0.00 0.00 4.30
1756 1793 1.280457 TTTGCTCCTCTTCTCTCCCC 58.720 55.000 0.00 0.00 0.00 4.81
1845 1882 3.815401 GGGATTAATTGATCACTCCACCG 59.185 47.826 11.86 0.00 0.00 4.94
1849 1886 2.270874 ATTGATCACTCCACCGGCCC 62.271 60.000 0.00 0.00 0.00 5.80
1899 1936 6.099125 TGGCTATTAGTAGTTTCATACTGGCA 59.901 38.462 0.00 0.00 37.73 4.92
1900 1937 6.647067 GGCTATTAGTAGTTTCATACTGGCAG 59.353 42.308 14.16 14.16 37.73 4.85
1901 1938 6.146347 GCTATTAGTAGTTTCATACTGGCAGC 59.854 42.308 15.89 0.00 37.73 5.25
1938 1975 3.087781 AGCTTGGCATTTTCCTCTTCTC 58.912 45.455 0.00 0.00 0.00 2.87
1948 1985 1.244816 TCCTCTTCTCGCTTCGTGAA 58.755 50.000 4.14 4.14 37.10 3.18
1976 2013 8.771920 TGTCTTGTCATATTACTAGTTTGGTG 57.228 34.615 0.00 0.00 0.00 4.17
2017 2054 7.546250 TTAAAGCTGTTGGAATTGGGATTTA 57.454 32.000 0.00 0.00 0.00 1.40
2018 2055 5.405935 AAGCTGTTGGAATTGGGATTTAC 57.594 39.130 0.00 0.00 0.00 2.01
2035 2072 1.570857 TACCATGGGAGGCAAGTGGG 61.571 60.000 18.09 0.00 34.27 4.61
2036 2073 2.615465 CCATGGGAGGCAAGTGGGA 61.615 63.158 2.85 0.00 0.00 4.37
2037 2074 1.379044 CATGGGAGGCAAGTGGGAC 60.379 63.158 0.00 0.00 0.00 4.46
2083 2123 6.070824 AGGCTGGTAAAATATTCAAAACCTGG 60.071 38.462 12.81 0.00 0.00 4.45
2100 2140 2.149578 CTGGACTTGAACTGAGCCTTG 58.850 52.381 0.00 0.00 0.00 3.61
2104 2144 1.952296 ACTTGAACTGAGCCTTGCTTG 59.048 47.619 0.00 0.00 39.88 4.01
2113 2153 2.684843 GCCTTGCTTGCTCAGGACG 61.685 63.158 13.28 0.00 0.00 4.79
2136 2176 2.801342 GCTGATTTCTAGAGGACGGCTG 60.801 54.545 14.40 0.00 0.00 4.85
2153 2209 1.269309 GCTGCTCCAGTACTCCGTATG 60.269 57.143 0.00 0.00 33.43 2.39
2202 2260 2.573941 GCCAGAGGCTGCATTTTTAG 57.426 50.000 0.50 0.00 46.69 1.85
2219 2283 4.408182 TTTAGCTCCTCTCAGGCATTAC 57.592 45.455 0.00 0.00 34.61 1.89
2235 2306 9.555727 TCAGGCATTACAGTAAGTTATTATTCC 57.444 33.333 0.00 0.00 0.00 3.01
2270 2341 0.738762 CACACACTCGCTGATCAGGG 60.739 60.000 28.91 28.91 42.08 4.45
2290 2361 5.470437 CAGGGTCAGTTAAGAAGAAGAAACC 59.530 44.000 0.00 0.00 0.00 3.27
2301 2372 3.244033 AGAAGAAACCTGATCTGAGCG 57.756 47.619 0.38 0.00 0.00 5.03
2307 2378 2.506061 CCTGATCTGAGCGGAGGGG 61.506 68.421 2.75 0.00 0.00 4.79
2334 2405 2.221981 GTCTCACTTCAGCCTTGTTTCG 59.778 50.000 0.00 0.00 0.00 3.46
2366 2437 1.202568 GCTCAAAGCAGGGCACTTTTT 60.203 47.619 0.00 0.00 41.89 1.94
2373 2444 1.408702 GCAGGGCACTTTTTCTGAACA 59.591 47.619 0.00 0.00 0.00 3.18
2422 2493 5.473162 CCAACAAAATCTTCCCAAAAATCCC 59.527 40.000 0.00 0.00 0.00 3.85
2430 2501 6.481434 TCTTCCCAAAAATCCCGTTAAAAA 57.519 33.333 0.00 0.00 0.00 1.94
2434 2505 6.459923 TCCCAAAAATCCCGTTAAAAATCTG 58.540 36.000 0.00 0.00 0.00 2.90
2443 2519 4.542735 CCGTTAAAAATCTGGGAACACAC 58.457 43.478 0.00 0.00 35.60 3.82
2444 2520 4.036971 CCGTTAAAAATCTGGGAACACACA 59.963 41.667 0.00 0.00 35.60 3.72
2445 2521 4.973663 CGTTAAAAATCTGGGAACACACAC 59.026 41.667 0.00 0.00 35.60 3.82
2447 2523 4.385358 AAAAATCTGGGAACACACACAC 57.615 40.909 0.00 0.00 35.60 3.82
2448 2524 3.297134 AAATCTGGGAACACACACACT 57.703 42.857 0.00 0.00 35.60 3.55
2449 2525 2.260844 ATCTGGGAACACACACACTG 57.739 50.000 0.00 0.00 35.60 3.66
2450 2526 1.199615 TCTGGGAACACACACACTGA 58.800 50.000 0.00 0.00 35.60 3.41
2451 2527 1.768275 TCTGGGAACACACACACTGAT 59.232 47.619 0.00 0.00 35.60 2.90
2452 2528 2.146342 CTGGGAACACACACACTGATC 58.854 52.381 0.00 0.00 35.60 2.92
2453 2529 1.768275 TGGGAACACACACACTGATCT 59.232 47.619 0.00 0.00 33.40 2.75
2454 2530 2.146342 GGGAACACACACACTGATCTG 58.854 52.381 0.00 0.00 0.00 2.90
2465 2541 1.671328 CACTGATCTGCTGCATTGGAG 59.329 52.381 1.31 0.03 0.00 3.86
2535 2612 3.449746 AATCAAATTCGTCCTGGGGAA 57.550 42.857 0.00 0.00 31.38 3.97
2538 2615 2.907696 TCAAATTCGTCCTGGGGAACTA 59.092 45.455 0.00 0.00 31.38 2.24
2585 2664 4.262808 GGGAGTGGGAATATGAGACTGATG 60.263 50.000 0.00 0.00 0.00 3.07
2594 2673 6.017275 GGAATATGAGACTGATGAAAAGGCAG 60.017 42.308 0.00 0.00 35.81 4.85
2595 2674 3.063510 TGAGACTGATGAAAAGGCAGG 57.936 47.619 0.00 0.00 34.05 4.85
2596 2675 2.290514 TGAGACTGATGAAAAGGCAGGG 60.291 50.000 0.00 0.00 34.05 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.287226 ACGGCTTTTACTAGAACGATATGG 58.713 41.667 0.00 0.00 0.00 2.74
7 8 7.919313 TTACGGCTTTTACTAGAACGATATG 57.081 36.000 0.00 0.00 0.00 1.78
13 14 6.073369 CGGTTTTTACGGCTTTTACTAGAAC 58.927 40.000 0.00 0.00 0.00 3.01
28 29 4.823790 TTGAGGCTCTTTCGGTTTTTAC 57.176 40.909 16.72 0.00 0.00 2.01
31 32 3.888930 TCATTTGAGGCTCTTTCGGTTTT 59.111 39.130 16.72 0.00 0.00 2.43
46 47 6.146601 TGTGCTTCAATTTCACTCATTTGA 57.853 33.333 0.00 0.00 0.00 2.69
47 48 6.831727 TTGTGCTTCAATTTCACTCATTTG 57.168 33.333 0.00 0.00 0.00 2.32
51 52 5.101628 GTGTTTGTGCTTCAATTTCACTCA 58.898 37.500 0.00 0.00 35.84 3.41
53 54 4.160252 AGGTGTTTGTGCTTCAATTTCACT 59.840 37.500 15.82 0.00 35.84 3.41
60 61 4.159321 TCATTTGAGGTGTTTGTGCTTCAA 59.841 37.500 0.00 0.00 0.00 2.69
62 63 4.293415 CTCATTTGAGGTGTTTGTGCTTC 58.707 43.478 0.00 0.00 38.48 3.86
68 69 3.492011 GCTTTGCTCATTTGAGGTGTTTG 59.508 43.478 9.49 0.00 42.29 2.93
72 73 4.005650 TCTAGCTTTGCTCATTTGAGGTG 58.994 43.478 9.49 0.00 42.29 4.00
76 77 4.142534 GCATGTCTAGCTTTGCTCATTTGA 60.143 41.667 0.00 0.00 40.44 2.69
77 78 4.103357 GCATGTCTAGCTTTGCTCATTTG 58.897 43.478 0.00 0.00 40.44 2.32
90 91 1.369625 GAAACCCCACGCATGTCTAG 58.630 55.000 0.00 0.00 0.00 2.43
111 112 1.067974 TCGACGTGTGTCATCCTTTGT 59.932 47.619 0.00 0.00 45.80 2.83
113 114 2.607187 GATCGACGTGTGTCATCCTTT 58.393 47.619 0.00 0.00 45.80 3.11
114 115 1.467543 CGATCGACGTGTGTCATCCTT 60.468 52.381 10.26 0.00 45.80 3.36
158 159 7.229306 TCCCAAAAATAAGCACATATCTAGCTG 59.771 37.037 0.00 0.00 38.86 4.24
159 160 7.290061 TCCCAAAAATAAGCACATATCTAGCT 58.710 34.615 0.00 0.00 41.03 3.32
166 167 7.038729 TGGTTTCATCCCAAAAATAAGCACATA 60.039 33.333 0.00 0.00 0.00 2.29
190 191 5.360714 AGTGAGTACAATTTATTGCCCATGG 59.639 40.000 4.14 4.14 41.38 3.66
193 194 4.634004 CGAGTGAGTACAATTTATTGCCCA 59.366 41.667 2.46 0.00 41.38 5.36
221 222 3.575256 ACCTTTATGCCGACGATGGTATA 59.425 43.478 0.00 0.00 35.77 1.47
225 226 1.663695 AACCTTTATGCCGACGATGG 58.336 50.000 0.00 0.00 0.00 3.51
227 228 1.400494 GCAAACCTTTATGCCGACGAT 59.600 47.619 0.00 0.00 36.56 3.73
230 231 2.163412 TCATGCAAACCTTTATGCCGAC 59.837 45.455 0.00 0.00 41.87 4.79
232 233 2.801063 CTCATGCAAACCTTTATGCCG 58.199 47.619 0.00 0.00 41.87 5.69
237 238 2.095263 GCTTCGCTCATGCAAACCTTTA 60.095 45.455 0.00 0.00 39.64 1.85
238 239 1.336240 GCTTCGCTCATGCAAACCTTT 60.336 47.619 0.00 0.00 39.64 3.11
251 252 4.357918 AAGGGAATATGTATGCTTCGCT 57.642 40.909 0.00 0.00 42.03 4.93
252 253 5.438761 AAAAGGGAATATGTATGCTTCGC 57.561 39.130 0.00 0.00 33.45 4.70
303 304 2.094854 GGTATACAATAGGAGTCGCCCG 60.095 54.545 5.01 0.00 37.37 6.13
308 309 5.979288 ATGGACGGTATACAATAGGAGTC 57.021 43.478 5.01 2.65 0.00 3.36
321 322 4.549668 AGGACATAAACCTATGGACGGTA 58.450 43.478 0.00 0.00 39.49 4.02
332 333 2.941064 GCGTAAGGGAAGGACATAAACC 59.059 50.000 0.00 0.00 38.28 3.27
342 343 1.868498 TGTCGTTTTGCGTAAGGGAAG 59.132 47.619 0.00 0.00 42.13 3.46
345 346 0.938713 TGTGTCGTTTTGCGTAAGGG 59.061 50.000 0.00 0.00 42.13 3.95
346 347 1.595794 ACTGTGTCGTTTTGCGTAAGG 59.404 47.619 0.00 0.00 42.13 2.69
372 373 1.872237 CGGTTTGCAGACTCCTCGAAA 60.872 52.381 7.38 0.00 0.00 3.46
376 377 0.670854 GGACGGTTTGCAGACTCCTC 60.671 60.000 7.38 0.00 0.00 3.71
387 388 2.496871 TGTATACATGGACGGACGGTTT 59.503 45.455 0.08 0.00 0.00 3.27
415 416 2.726633 CAACTTTTCGCACCAAACGAT 58.273 42.857 0.00 0.00 39.65 3.73
438 439 1.452145 GGGCTTTGGACGAGTTTGCA 61.452 55.000 0.00 0.00 0.00 4.08
441 442 1.061546 TAGGGGCTTTGGACGAGTTT 58.938 50.000 0.00 0.00 0.00 2.66
444 445 2.040178 ACTATAGGGGCTTTGGACGAG 58.960 52.381 4.43 0.00 0.00 4.18
447 448 6.379417 ACGTATATACTATAGGGGCTTTGGAC 59.621 42.308 11.05 0.00 0.00 4.02
448 449 6.496743 ACGTATATACTATAGGGGCTTTGGA 58.503 40.000 11.05 0.00 0.00 3.53
449 450 6.786967 ACGTATATACTATAGGGGCTTTGG 57.213 41.667 11.05 0.00 0.00 3.28
452 453 9.140874 GGATTAACGTATATACTATAGGGGCTT 57.859 37.037 11.05 0.00 0.00 4.35
453 454 8.509441 AGGATTAACGTATATACTATAGGGGCT 58.491 37.037 11.05 0.00 0.00 5.19
454 455 8.703378 AGGATTAACGTATATACTATAGGGGC 57.297 38.462 11.05 0.00 0.00 5.80
472 473 3.054655 AGCGCCTCCAAAGTTAGGATTAA 60.055 43.478 2.29 0.00 34.58 1.40
477 478 1.084370 CGAGCGCCTCCAAAGTTAGG 61.084 60.000 2.29 0.00 35.86 2.69
511 512 0.461548 TCATAGAGCACCCTCGCAAG 59.538 55.000 0.00 0.00 43.05 4.01
521 522 7.067372 CCTCATGGTAAAATGTTTCATAGAGCA 59.933 37.037 0.00 0.00 0.00 4.26
539 540 6.546034 CCGGTTTCTTATTATTTCCTCATGGT 59.454 38.462 0.00 0.00 34.23 3.55
540 541 6.515035 GCCGGTTTCTTATTATTTCCTCATGG 60.515 42.308 1.90 0.00 0.00 3.66
541 542 6.263168 AGCCGGTTTCTTATTATTTCCTCATG 59.737 38.462 1.90 0.00 0.00 3.07
542 543 6.365520 AGCCGGTTTCTTATTATTTCCTCAT 58.634 36.000 1.90 0.00 0.00 2.90
543 544 5.751586 AGCCGGTTTCTTATTATTTCCTCA 58.248 37.500 1.90 0.00 0.00 3.86
581 593 9.684448 CCAATAAAACACACACACATAAATACA 57.316 29.630 0.00 0.00 0.00 2.29
582 594 9.900710 TCCAATAAAACACACACACATAAATAC 57.099 29.630 0.00 0.00 0.00 1.89
584 596 9.474920 CTTCCAATAAAACACACACACATAAAT 57.525 29.630 0.00 0.00 0.00 1.40
585 597 7.923344 CCTTCCAATAAAACACACACACATAAA 59.077 33.333 0.00 0.00 0.00 1.40
590 602 5.278604 GTCCTTCCAATAAAACACACACAC 58.721 41.667 0.00 0.00 0.00 3.82
592 604 4.533222 CGTCCTTCCAATAAAACACACAC 58.467 43.478 0.00 0.00 0.00 3.82
594 606 3.057806 CCCGTCCTTCCAATAAAACACAC 60.058 47.826 0.00 0.00 0.00 3.82
595 607 3.150767 CCCGTCCTTCCAATAAAACACA 58.849 45.455 0.00 0.00 0.00 3.72
600 612 2.555670 CCAACCCCGTCCTTCCAATAAA 60.556 50.000 0.00 0.00 0.00 1.40
603 615 1.382629 CCAACCCCGTCCTTCCAAT 59.617 57.895 0.00 0.00 0.00 3.16
605 617 3.961414 GCCAACCCCGTCCTTCCA 61.961 66.667 0.00 0.00 0.00 3.53
619 631 9.716531 TGTATACATTTTGAAATTTTGATGCCA 57.283 25.926 0.08 0.00 0.00 4.92
632 649 3.537580 GACCGGGCTGTATACATTTTGA 58.462 45.455 6.32 0.00 0.00 2.69
633 650 2.286833 CGACCGGGCTGTATACATTTTG 59.713 50.000 5.33 0.00 0.00 2.44
638 655 1.386525 GGACGACCGGGCTGTATACA 61.387 60.000 5.33 5.25 0.00 2.29
640 657 0.683828 TTGGACGACCGGGCTGTATA 60.684 55.000 5.33 0.00 39.42 1.47
650 667 1.874872 TCATTTTTCGGTTGGACGACC 59.125 47.619 0.00 0.00 43.37 4.79
661 678 3.361644 CGTTTCCAGCACATCATTTTTCG 59.638 43.478 0.00 0.00 0.00 3.46
662 679 3.674753 CCGTTTCCAGCACATCATTTTTC 59.325 43.478 0.00 0.00 0.00 2.29
710 733 2.091885 AGATCTGACCTCACTCCTCCTC 60.092 54.545 0.00 0.00 0.00 3.71
713 736 3.892284 TGTAGATCTGACCTCACTCCTC 58.108 50.000 5.18 0.00 0.00 3.71
763 786 2.775890 AGCATGGCTGTATCTGTATGC 58.224 47.619 0.00 0.00 37.57 3.14
912 939 4.890306 GAGGGAGGGAGGGAGGGC 62.890 77.778 0.00 0.00 0.00 5.19
913 940 3.039526 AGAGGGAGGGAGGGAGGG 61.040 72.222 0.00 0.00 0.00 4.30
914 941 2.285180 CAGAGGGAGGGAGGGAGG 59.715 72.222 0.00 0.00 0.00 4.30
915 942 2.445654 GCAGAGGGAGGGAGGGAG 60.446 72.222 0.00 0.00 0.00 4.30
916 943 4.095400 GGCAGAGGGAGGGAGGGA 62.095 72.222 0.00 0.00 0.00 4.20
917 944 3.649652 AAGGCAGAGGGAGGGAGGG 62.650 68.421 0.00 0.00 0.00 4.30
918 945 2.041928 AAGGCAGAGGGAGGGAGG 59.958 66.667 0.00 0.00 0.00 4.30
983 1016 4.706962 CCTCCATGGTAAAAAGGGAAGAAG 59.293 45.833 12.58 0.00 0.00 2.85
988 1021 1.713647 TGCCTCCATGGTAAAAAGGGA 59.286 47.619 12.58 9.18 38.35 4.20
1410 1443 2.110967 CGGGAAGTCCAGCATGCTG 61.111 63.158 35.88 35.88 43.26 4.41
1648 1681 0.177373 CAGAGCAGAGCATACCAGCA 59.823 55.000 0.00 0.00 36.85 4.41
1649 1682 1.159098 GCAGAGCAGAGCATACCAGC 61.159 60.000 0.00 0.00 0.00 4.85
1650 1683 0.464870 AGCAGAGCAGAGCATACCAG 59.535 55.000 0.00 0.00 0.00 4.00
1656 1689 2.228389 GAGCAGAGCAGAGCAGAGCA 62.228 60.000 0.00 0.00 0.00 4.26
1657 1690 1.519898 GAGCAGAGCAGAGCAGAGC 60.520 63.158 0.00 0.00 0.00 4.09
1658 1691 0.458889 GTGAGCAGAGCAGAGCAGAG 60.459 60.000 0.00 0.00 0.00 3.35
1659 1692 1.590665 GTGAGCAGAGCAGAGCAGA 59.409 57.895 0.00 0.00 0.00 4.26
1660 1693 1.448189 GGTGAGCAGAGCAGAGCAG 60.448 63.158 0.00 0.00 0.00 4.24
1661 1694 2.661399 GGTGAGCAGAGCAGAGCA 59.339 61.111 0.00 0.00 0.00 4.26
1662 1695 2.125188 GGGTGAGCAGAGCAGAGC 60.125 66.667 0.00 0.00 0.00 4.09
1663 1696 2.183811 CGGGTGAGCAGAGCAGAG 59.816 66.667 0.00 0.00 0.00 3.35
1664 1697 3.385384 CCGGGTGAGCAGAGCAGA 61.385 66.667 0.00 0.00 0.00 4.26
1665 1698 3.655810 GACCGGGTGAGCAGAGCAG 62.656 68.421 3.30 0.00 0.00 4.24
1679 1716 1.258982 CTAGCATTTTAGCAGCGACCG 59.741 52.381 0.00 0.00 36.85 4.79
1690 1727 0.181350 CTCCGGGAGCCTAGCATTTT 59.819 55.000 11.83 0.00 0.00 1.82
1705 1742 4.554363 AATCGACCTCGCGCTCCG 62.554 66.667 5.56 2.13 39.60 4.63
1710 1747 0.994241 CAGATCGAATCGACCTCGCG 60.994 60.000 7.77 0.00 39.18 5.87
1845 1882 0.250338 AGACAAAGAACACTCGGGCC 60.250 55.000 0.00 0.00 0.00 5.80
1849 1886 5.047847 TGGTAAAGAGACAAAGAACACTCG 58.952 41.667 0.00 0.00 34.98 4.18
1899 1936 6.461788 GCCAAGCTAAATCTACTACTACTGCT 60.462 42.308 0.00 0.00 0.00 4.24
1900 1937 5.692654 GCCAAGCTAAATCTACTACTACTGC 59.307 44.000 0.00 0.00 0.00 4.40
1901 1938 6.806751 TGCCAAGCTAAATCTACTACTACTG 58.193 40.000 0.00 0.00 0.00 2.74
1938 1975 1.593006 ACAAGACAAGTTCACGAAGCG 59.407 47.619 0.00 0.00 0.00 4.68
1948 1985 9.436957 CCAAACTAGTAATATGACAAGACAAGT 57.563 33.333 0.00 0.00 0.00 3.16
1976 2013 7.382218 ACAGCTTTAATGTACAAGATTTGCAAC 59.618 33.333 0.00 0.00 0.00 4.17
2017 2054 2.765969 CCACTTGCCTCCCATGGT 59.234 61.111 11.73 0.00 0.00 3.55
2018 2055 2.043652 CCCACTTGCCTCCCATGG 60.044 66.667 4.14 4.14 0.00 3.66
2035 2072 1.197721 CAAGATGTCAACTTGGGCGTC 59.802 52.381 13.59 0.00 40.39 5.19
2036 2073 1.238439 CAAGATGTCAACTTGGGCGT 58.762 50.000 13.59 0.00 40.39 5.68
2037 2074 0.109597 GCAAGATGTCAACTTGGGCG 60.110 55.000 20.60 0.40 43.12 6.13
2083 2123 1.889545 AGCAAGGCTCAGTTCAAGTC 58.110 50.000 0.00 0.00 30.62 3.01
2100 2140 4.400961 AGCCCGTCCTGAGCAAGC 62.401 66.667 0.00 0.00 0.00 4.01
2104 2144 1.078143 AAATCAGCCCGTCCTGAGC 60.078 57.895 8.05 0.00 44.37 4.26
2107 2147 1.757118 TCTAGAAATCAGCCCGTCCTG 59.243 52.381 0.00 0.00 0.00 3.86
2113 2153 1.069358 CCGTCCTCTAGAAATCAGCCC 59.931 57.143 0.00 0.00 0.00 5.19
2153 2209 7.965107 CCATACTTTGAATTTGCACTAACTCTC 59.035 37.037 0.00 0.00 0.00 3.20
2202 2260 1.484240 ACTGTAATGCCTGAGAGGAGC 59.516 52.381 0.00 0.00 37.67 4.70
2219 2283 8.642908 TGATGACACGGAATAATAACTTACTG 57.357 34.615 0.00 0.00 0.00 2.74
2235 2306 3.968096 GTGTGTGACAAAATGATGACACG 59.032 43.478 0.00 0.00 45.01 4.49
2270 2341 7.875554 AGATCAGGTTTCTTCTTCTTAACTGAC 59.124 37.037 0.00 0.00 0.00 3.51
2290 2361 3.136750 CCCCTCCGCTCAGATCAG 58.863 66.667 0.00 0.00 0.00 2.90
2301 2372 4.741239 TGAGACAGGGGCCCCTCC 62.741 72.222 42.42 32.78 46.28 4.30
2307 2378 1.376553 GCTGAAGTGAGACAGGGGC 60.377 63.158 0.00 0.00 35.05 5.80
2334 2405 1.163554 CTTTGAGCTGCCACTTCCTC 58.836 55.000 0.00 0.00 0.00 3.71
2366 2437 4.462483 GGCAATTATTGAAGGGTGTTCAGA 59.538 41.667 9.36 0.00 0.00 3.27
2373 2444 1.651235 AGGGGGCAATTATTGAAGGGT 59.349 47.619 9.36 0.00 0.00 4.34
2422 2493 4.973663 GTGTGTGTTCCCAGATTTTTAACG 59.026 41.667 0.00 0.00 0.00 3.18
2430 2501 1.768275 TCAGTGTGTGTGTTCCCAGAT 59.232 47.619 0.00 0.00 0.00 2.90
2434 2505 2.146342 CAGATCAGTGTGTGTGTTCCC 58.854 52.381 0.00 0.00 0.00 3.97
2443 2519 1.132453 CCAATGCAGCAGATCAGTGTG 59.868 52.381 0.00 0.00 0.00 3.82
2444 2520 1.003928 TCCAATGCAGCAGATCAGTGT 59.996 47.619 0.00 0.00 0.00 3.55
2445 2521 1.671328 CTCCAATGCAGCAGATCAGTG 59.329 52.381 0.00 0.00 0.00 3.66
2447 2523 1.134189 TCCTCCAATGCAGCAGATCAG 60.134 52.381 0.00 0.00 0.00 2.90
2448 2524 0.913924 TCCTCCAATGCAGCAGATCA 59.086 50.000 0.00 0.00 0.00 2.92
2449 2525 1.140452 TCTCCTCCAATGCAGCAGATC 59.860 52.381 0.00 0.00 0.00 2.75
2450 2526 1.141254 CTCTCCTCCAATGCAGCAGAT 59.859 52.381 0.00 0.00 0.00 2.90
2451 2527 0.540454 CTCTCCTCCAATGCAGCAGA 59.460 55.000 0.00 0.00 0.00 4.26
2452 2528 0.464013 CCTCTCCTCCAATGCAGCAG 60.464 60.000 0.00 0.00 0.00 4.24
2453 2529 1.605992 CCTCTCCTCCAATGCAGCA 59.394 57.895 0.00 0.00 0.00 4.41
2454 2530 1.823041 GCCTCTCCTCCAATGCAGC 60.823 63.158 0.00 0.00 0.00 5.25
2480 2556 4.414677 AGATGCAGACAGAGATGGCTATA 58.585 43.478 0.00 0.00 0.00 1.31
2481 2557 3.241156 AGATGCAGACAGAGATGGCTAT 58.759 45.455 0.00 0.00 0.00 2.97
2518 2594 2.200373 AGTTCCCCAGGACGAATTTG 57.800 50.000 0.00 0.00 0.00 2.32
2520 2596 2.547990 AGTAGTTCCCCAGGACGAATT 58.452 47.619 0.00 0.00 0.00 2.17
2521 2597 2.249309 AGTAGTTCCCCAGGACGAAT 57.751 50.000 0.00 0.00 0.00 3.34
2522 2598 2.042162 AGTAGTAGTTCCCCAGGACGAA 59.958 50.000 0.00 0.00 0.00 3.85
2525 2602 1.481363 GCAGTAGTAGTTCCCCAGGAC 59.519 57.143 0.00 0.00 0.00 3.85
2535 2612 3.090037 CACCACCAGTAGCAGTAGTAGT 58.910 50.000 0.00 0.00 0.00 2.73
2538 2615 2.304221 TCACCACCAGTAGCAGTAGT 57.696 50.000 0.00 0.00 0.00 2.73
2585 2664 4.400529 TTGTTTTCTTCCCTGCCTTTTC 57.599 40.909 0.00 0.00 0.00 2.29
2594 2673 6.322969 ACCGGGATTATTATTGTTTTCTTCCC 59.677 38.462 6.32 0.00 37.51 3.97
2595 2674 7.342769 ACCGGGATTATTATTGTTTTCTTCC 57.657 36.000 6.32 0.00 0.00 3.46
2596 2675 7.130269 CGACCGGGATTATTATTGTTTTCTTC 58.870 38.462 6.32 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.