Multiple sequence alignment - TraesCS7A01G565100

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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 TraesCS7A01G565100 chr7A 100.000 2504 0 0 1 2504 734537589 734540092 0.000000e+00 4625.0
1 TraesCS7A01G565100 chr7A 87.097 62 8 0 643 704 19995989 19995928 1.240000e-08 71.3
2 TraesCS7A01G565100 chr7B 94.874 1034 43 5 570 1601 746098519 746097494 0.000000e+00 1607.0
3 TraesCS7A01G565100 chr7B 94.755 572 28 1 1 572 746102704 746102135 0.000000e+00 889.0
4 TraesCS7A01G565100 chr7B 87.280 739 63 14 1746 2472 746097274 746096555 0.000000e+00 815.0
5 TraesCS7A01G565100 chr7B 83.900 559 84 6 917 1471 121495946 121496502 1.710000e-146 529.0
6 TraesCS7A01G565100 chr7B 74.194 403 90 14 1074 1467 70825205 70825602 3.330000e-34 156.0
7 TraesCS7A01G565100 chr7D 83.900 559 84 6 917 1471 160534071 160534627 1.710000e-146 529.0
8 TraesCS7A01G565100 chr7D 90.566 53 5 0 630 682 19738088 19738036 1.240000e-08 71.3
9 TraesCS7A01G565100 chr2D 82.317 328 52 5 299 624 547154783 547154460 1.900000e-71 279.0
10 TraesCS7A01G565100 chr4A 79.038 291 55 5 295 584 477053504 477053219 7.070000e-46 195.0
11 TraesCS7A01G565100 chr1D 83.417 199 28 4 412 608 308448787 308448592 1.980000e-41 180.0
12 TraesCS7A01G565100 chr4D 78.707 263 49 6 295 552 98916874 98917134 4.280000e-38 169.0
13 TraesCS7A01G565100 chr1B 77.091 275 54 8 338 610 360602211 360601944 1.550000e-32 150.0
14 TraesCS7A01G565100 chr5D 73.508 419 95 11 1067 1471 496957017 496957433 7.220000e-31 145.0
15 TraesCS7A01G565100 chr5D 75.665 263 59 5 296 556 372453144 372453403 2.610000e-25 126.0
16 TraesCS7A01G565100 chr3D 78.475 223 42 6 335 555 504957204 504957422 9.340000e-30 141.0
17 TraesCS7A01G565100 chr5A 80.337 178 32 1 378 555 475595519 475595693 5.620000e-27 132.0


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 TraesCS7A01G565100 chr7A 734537589 734540092 2503 False 4625.000000 4625 100.000 1 2504 1 chr7A.!!$F1 2503
1 TraesCS7A01G565100 chr7B 746096555 746102704 6149 True 1103.666667 1607 92.303 1 2472 3 chr7B.!!$R1 2471
2 TraesCS7A01G565100 chr7B 121495946 121496502 556 False 529.000000 529 83.900 917 1471 1 chr7B.!!$F2 554
3 TraesCS7A01G565100 chr7D 160534071 160534627 556 False 529.000000 529 83.900 917 1471 1 chr7D.!!$F1 554

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
330 331 0.388294 TGATGCAGAGATCCTCGCAG 59.612 55.0 14.72 1.67 40.74 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 5756 0.250858 TCCATGTCCTTGGTGCTGTG 60.251 55.0 0.0 0.0 38.01 3.66 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
115 116 5.155643 TCAATGTTTCAATCTTGACATGCG 58.844 37.500 0.00 0.00 36.83 4.73
205 206 4.037089 ACTCCGTTTACCAATGGTCAAAAC 59.963 41.667 8.82 14.08 39.81 2.43
232 233 8.166422 GAAGGATTCAAAGAGAGTTTTTGGTA 57.834 34.615 0.00 0.00 46.62 3.25
255 256 3.655276 CTTCAGAAGCACTTTGGCATT 57.345 42.857 0.00 0.00 35.83 3.56
264 265 2.094752 GCACTTTGGCATTATTCGTGGT 60.095 45.455 0.00 0.00 0.00 4.16
287 288 2.695359 TGCCGAGTATTGAAACTCCAC 58.305 47.619 0.00 0.00 42.46 4.02
305 306 0.669077 ACGGTCCTAGATCACGATGC 59.331 55.000 0.00 0.00 0.00 3.91
315 316 4.547406 AGATCACGATGCAAACATGATG 57.453 40.909 9.78 0.00 36.35 3.07
327 328 2.816204 ACATGATGCAGAGATCCTCG 57.184 50.000 0.00 0.00 35.36 4.63
330 331 0.388294 TGATGCAGAGATCCTCGCAG 59.612 55.000 14.72 1.67 40.74 5.18
332 333 2.657944 GCAGAGATCCTCGCAGCG 60.658 66.667 9.06 9.06 35.36 5.18
354 355 1.179152 TCGTAGCATGGAGAACCGAA 58.821 50.000 0.00 0.00 39.42 4.30
355 356 1.135199 TCGTAGCATGGAGAACCGAAC 60.135 52.381 0.00 0.00 39.42 3.95
426 427 3.346315 TCATGGCACTTCATAGTTGTGG 58.654 45.455 0.00 0.00 30.26 4.17
434 435 6.072175 GGCACTTCATAGTTGTGGTTTTATCA 60.072 38.462 0.00 0.00 30.26 2.15
450 451 8.296713 TGGTTTTATCATGCTCTTTACTTCAAC 58.703 33.333 0.00 0.00 0.00 3.18
641 4260 1.939980 ATAAGGGAGGGATCGGCTAC 58.060 55.000 0.00 0.00 0.00 3.58
651 4270 1.609580 GGATCGGCTACAAACCACACA 60.610 52.381 0.00 0.00 0.00 3.72
670 4289 9.802039 ACCACACATTTTTAGAGGAGTAAATAA 57.198 29.630 0.00 0.00 0.00 1.40
694 4313 4.224370 ACTCCTCTAAAATTTACTCGGCCA 59.776 41.667 2.24 0.00 0.00 5.36
802 4421 2.879002 ACCAGCATGTCTATGTCTCG 57.121 50.000 0.00 0.00 36.65 4.04
829 4448 6.927294 AATTGCATGGAAGTAACTAGCTAC 57.073 37.500 5.69 0.00 0.00 3.58
887 4506 1.863454 GGAGCTGCAAGTCATGATACG 59.137 52.381 0.00 0.00 35.30 3.06
952 4571 3.192001 ACGTCTCGAGGCTACAAATACAA 59.808 43.478 16.21 0.00 0.00 2.41
1072 4693 0.108804 CGTGGTAGCCAATGTCTCGT 60.109 55.000 0.00 0.00 34.18 4.18
1110 4731 3.009473 AGGACTACATCAACCTGCACAAT 59.991 43.478 0.00 0.00 0.00 2.71
1173 4794 2.515057 AACGTGGCCAAGTTCGCA 60.515 55.556 28.53 0.00 0.00 5.10
1368 4989 1.894756 GGTTTGCGGGCACTACACA 60.895 57.895 0.00 0.00 0.00 3.72
1422 5043 2.202932 GCCCGCGTGATCTGTGAT 60.203 61.111 4.92 0.00 0.00 3.06
1517 5138 3.302870 GCCAAGTAGTACGTGTGTTTGTG 60.303 47.826 14.03 0.05 0.00 3.33
1529 5150 3.611986 GTGTGTTTGTGTGTGATTTGTGG 59.388 43.478 0.00 0.00 0.00 4.17
1547 5168 2.030457 GTGGTATCGTGCTTATGTGTGC 59.970 50.000 0.00 0.00 0.00 4.57
1551 5172 0.598942 TCGTGCTTATGTGTGCGTGT 60.599 50.000 0.00 0.00 0.00 4.49
1554 5175 0.585838 TGCTTATGTGTGCGTGTGTG 59.414 50.000 0.00 0.00 0.00 3.82
1555 5176 0.586319 GCTTATGTGTGCGTGTGTGT 59.414 50.000 0.00 0.00 0.00 3.72
1556 5177 1.660052 GCTTATGTGTGCGTGTGTGTG 60.660 52.381 0.00 0.00 0.00 3.82
1557 5178 1.597195 CTTATGTGTGCGTGTGTGTGT 59.403 47.619 0.00 0.00 0.00 3.72
1558 5179 0.933796 TATGTGTGCGTGTGTGTGTG 59.066 50.000 0.00 0.00 0.00 3.82
1559 5180 1.024046 ATGTGTGCGTGTGTGTGTGT 61.024 50.000 0.00 0.00 0.00 3.72
1601 5222 8.390854 ACTGTAGTGTCTTTCGAATATTTACG 57.609 34.615 0.00 0.00 0.00 3.18
1602 5223 8.025445 ACTGTAGTGTCTTTCGAATATTTACGT 58.975 33.333 0.00 0.00 0.00 3.57
1604 5225 8.239314 TGTAGTGTCTTTCGAATATTTACGTCT 58.761 33.333 0.00 0.17 0.00 4.18
1605 5226 9.708222 GTAGTGTCTTTCGAATATTTACGTCTA 57.292 33.333 0.00 0.00 0.00 2.59
1607 5228 8.239314 AGTGTCTTTCGAATATTTACGTCTACA 58.761 33.333 0.00 0.00 0.00 2.74
1621 5242 9.681692 ATTTACGTCTACATATGTTATACGCAA 57.318 29.630 24.93 19.59 32.93 4.85
1622 5243 9.513727 TTTACGTCTACATATGTTATACGCAAA 57.486 29.630 24.93 22.52 32.93 3.68
1623 5244 9.681692 TTACGTCTACATATGTTATACGCAAAT 57.318 29.630 24.93 14.81 32.93 2.32
1625 5246 9.681692 ACGTCTACATATGTTATACGCAAATAA 57.318 29.630 24.93 2.71 32.93 1.40
1627 5248 9.953825 GTCTACATATGTTATACGCAAATAAGC 57.046 33.333 14.77 0.00 0.00 3.09
1628 5249 9.699703 TCTACATATGTTATACGCAAATAAGCA 57.300 29.630 14.77 0.00 0.00 3.91
1629 5250 9.741168 CTACATATGTTATACGCAAATAAGCAC 57.259 33.333 14.77 0.00 0.00 4.40
1630 5251 8.148807 ACATATGTTATACGCAAATAAGCACA 57.851 30.769 1.41 0.00 0.00 4.57
1631 5252 8.282592 ACATATGTTATACGCAAATAAGCACAG 58.717 33.333 1.41 0.00 0.00 3.66
1632 5253 6.677781 ATGTTATACGCAAATAAGCACAGT 57.322 33.333 0.00 0.00 0.00 3.55
1633 5254 6.102006 TGTTATACGCAAATAAGCACAGTC 57.898 37.500 0.00 0.00 0.00 3.51
1634 5255 5.639931 TGTTATACGCAAATAAGCACAGTCA 59.360 36.000 0.00 0.00 0.00 3.41
1635 5256 2.969443 ACGCAAATAAGCACAGTCAC 57.031 45.000 0.00 0.00 0.00 3.67
1636 5257 1.535462 ACGCAAATAAGCACAGTCACC 59.465 47.619 0.00 0.00 0.00 4.02
1637 5258 1.464023 CGCAAATAAGCACAGTCACCG 60.464 52.381 0.00 0.00 0.00 4.94
1638 5259 1.135689 GCAAATAAGCACAGTCACCGG 60.136 52.381 0.00 0.00 0.00 5.28
1639 5260 1.135689 CAAATAAGCACAGTCACCGGC 60.136 52.381 0.00 0.00 0.00 6.13
1640 5261 0.676782 AATAAGCACAGTCACCGGCC 60.677 55.000 0.00 0.00 0.00 6.13
1641 5262 1.553690 ATAAGCACAGTCACCGGCCT 61.554 55.000 0.00 0.00 0.00 5.19
1642 5263 2.449031 TAAGCACAGTCACCGGCCTG 62.449 60.000 0.00 8.21 34.82 4.85
1652 5273 4.720902 CCGGCCTGCATGTGTCCA 62.721 66.667 0.00 0.00 0.00 4.02
1683 5304 4.201851 GCTCTGTGGTGCATGTAAATGTAG 60.202 45.833 0.00 0.00 32.83 2.74
1685 5306 4.935205 TCTGTGGTGCATGTAAATGTAGTC 59.065 41.667 0.00 0.00 0.00 2.59
1686 5307 3.682377 TGTGGTGCATGTAAATGTAGTCG 59.318 43.478 0.00 0.00 0.00 4.18
1687 5308 3.930229 GTGGTGCATGTAAATGTAGTCGA 59.070 43.478 0.00 0.00 0.00 4.20
1688 5309 3.930229 TGGTGCATGTAAATGTAGTCGAC 59.070 43.478 7.70 7.70 0.00 4.20
1689 5310 3.000078 GGTGCATGTAAATGTAGTCGACG 60.000 47.826 10.46 0.00 0.00 5.12
1690 5311 2.601314 TGCATGTAAATGTAGTCGACGC 59.399 45.455 10.46 8.05 0.00 5.19
1692 5313 2.282701 TGTAAATGTAGTCGACGCCC 57.717 50.000 10.46 2.52 0.00 6.13
1693 5314 1.194495 GTAAATGTAGTCGACGCCCG 58.806 55.000 10.46 0.00 40.25 6.13
1694 5315 0.101040 TAAATGTAGTCGACGCCCGG 59.899 55.000 10.46 0.00 39.14 5.73
1695 5316 3.711541 AATGTAGTCGACGCCCGGC 62.712 63.158 10.46 0.00 44.58 6.13
1803 5534 1.678101 ACTGCTGTGCTTTCCTTTCAC 59.322 47.619 0.00 0.00 0.00 3.18
1809 5540 0.605319 TGCTTTCCTTTCACGCGGAT 60.605 50.000 12.47 0.00 0.00 4.18
1811 5542 1.062148 GCTTTCCTTTCACGCGGATAC 59.938 52.381 12.47 0.00 0.00 2.24
1820 5551 5.236478 CCTTTCACGCGGATACATTATTCTT 59.764 40.000 12.47 0.00 0.00 2.52
1835 5566 2.181426 TTCTTGTTTTTGCGTCCACG 57.819 45.000 0.00 0.00 43.27 4.94
1841 5572 1.593933 GTTTTTGCGTCCACGTACTCA 59.406 47.619 0.36 0.00 42.22 3.41
1843 5574 2.157834 TTTGCGTCCACGTACTCATT 57.842 45.000 0.36 0.00 42.22 2.57
1844 5575 1.705256 TTGCGTCCACGTACTCATTC 58.295 50.000 0.36 0.00 42.22 2.67
1845 5576 0.455464 TGCGTCCACGTACTCATTCG 60.455 55.000 0.36 0.00 42.22 3.34
1846 5577 0.179181 GCGTCCACGTACTCATTCGA 60.179 55.000 0.36 0.00 42.22 3.71
1847 5578 1.811428 CGTCCACGTACTCATTCGAG 58.189 55.000 0.00 0.00 38.76 4.04
1848 5579 1.395954 CGTCCACGTACTCATTCGAGA 59.604 52.381 0.00 0.00 37.36 4.04
1849 5580 2.031807 CGTCCACGTACTCATTCGAGAT 59.968 50.000 0.00 0.00 37.36 2.75
1850 5581 3.487042 CGTCCACGTACTCATTCGAGATT 60.487 47.826 0.00 0.00 37.36 2.40
1869 5600 1.250328 TTCGAGGCGAGAGTTTGGTA 58.750 50.000 0.00 0.00 37.14 3.25
1871 5602 0.526662 CGAGGCGAGAGTTTGGTAGT 59.473 55.000 0.00 0.00 0.00 2.73
1872 5603 1.741706 CGAGGCGAGAGTTTGGTAGTA 59.258 52.381 0.00 0.00 0.00 1.82
1878 5609 4.804665 GGCGAGAGTTTGGTAGTATTTCTC 59.195 45.833 0.00 0.00 0.00 2.87
1879 5610 4.804665 GCGAGAGTTTGGTAGTATTTCTCC 59.195 45.833 0.00 0.00 0.00 3.71
1885 5616 5.936372 AGTTTGGTAGTATTTCTCCGTTTCC 59.064 40.000 0.00 0.00 0.00 3.13
1891 5622 0.676782 ATTTCTCCGTTTCCGCCCAG 60.677 55.000 0.00 0.00 0.00 4.45
1899 5630 0.738975 GTTTCCGCCCAGATTTAGGC 59.261 55.000 0.00 0.00 46.17 3.93
1932 5663 1.254026 GGGTTTTCCTTTCCTTCCCG 58.746 55.000 0.00 0.00 40.46 5.14
1933 5664 1.202964 GGGTTTTCCTTTCCTTCCCGA 60.203 52.381 0.00 0.00 40.46 5.14
1934 5665 2.160205 GGTTTTCCTTTCCTTCCCGAG 58.840 52.381 0.00 0.00 36.94 4.63
1939 5670 2.335933 TCCTTTCCTTCCCGAGAGTTT 58.664 47.619 0.00 0.00 0.00 2.66
1954 5685 5.334414 CCGAGAGTTTGGTTGATTTCTTCAG 60.334 44.000 0.00 0.00 35.27 3.02
1965 5696 3.190535 TGATTTCTTCAGCCCTTTAACGC 59.809 43.478 0.00 0.00 0.00 4.84
1985 5716 2.879646 GCACCACTCGTACTAGCTAGAT 59.120 50.000 27.45 13.50 0.00 1.98
2004 5735 1.153628 GCTGGAGTCGTTATGCGGT 60.154 57.895 0.00 0.00 41.72 5.68
2009 5740 0.989890 GAGTCGTTATGCGGTGACAC 59.010 55.000 0.00 0.00 41.72 3.67
2024 5755 0.806884 GACACGGTGTTGGTTGTCGA 60.807 55.000 15.94 0.00 0.00 4.20
2025 5756 1.085501 ACACGGTGTTGGTTGTCGAC 61.086 55.000 9.11 9.11 0.00 4.20
2044 5775 0.250858 CACAGCACCAAGGACATGGA 60.251 55.000 0.00 0.00 43.54 3.41
2045 5776 0.700564 ACAGCACCAAGGACATGGAT 59.299 50.000 0.00 0.00 43.54 3.41
2046 5777 1.340405 ACAGCACCAAGGACATGGATC 60.340 52.381 0.00 0.00 43.54 3.36
2047 5778 0.107508 AGCACCAAGGACATGGATCG 60.108 55.000 0.00 0.00 43.54 3.69
2048 5779 0.107703 GCACCAAGGACATGGATCGA 60.108 55.000 0.00 0.00 43.54 3.59
2049 5780 1.656652 CACCAAGGACATGGATCGAC 58.343 55.000 0.00 0.00 43.54 4.20
2050 5781 0.541863 ACCAAGGACATGGATCGACC 59.458 55.000 0.00 0.00 43.54 4.79
2051 5782 0.179045 CCAAGGACATGGATCGACCC 60.179 60.000 0.00 0.00 43.54 4.46
2052 5783 0.530650 CAAGGACATGGATCGACCCG 60.531 60.000 0.00 0.00 38.00 5.28
2053 5784 1.686325 AAGGACATGGATCGACCCGG 61.686 60.000 0.00 0.00 38.00 5.73
2054 5785 2.131709 GGACATGGATCGACCCGGA 61.132 63.158 0.73 0.00 38.00 5.14
2069 5800 2.737376 GGAACTCCACCGTGTCGC 60.737 66.667 0.00 0.00 35.64 5.19
2073 5804 2.738521 CTCCACCGTGTCGCCAAG 60.739 66.667 0.00 0.00 0.00 3.61
2086 5817 1.966451 GCCAAGGACCCGTCAACTG 60.966 63.158 0.00 0.00 0.00 3.16
2087 5818 1.450211 CCAAGGACCCGTCAACTGT 59.550 57.895 0.00 0.00 0.00 3.55
2098 5829 3.357079 CAACTGTGAGGCCGCCAC 61.357 66.667 20.09 20.09 35.23 5.01
2125 5856 3.041701 CACAGCGGTGGCAATGTT 58.958 55.556 20.20 0.00 43.41 2.71
2133 5864 1.733389 CGGTGGCAATGTTGAGAATGC 60.733 52.381 0.00 0.00 38.06 3.56
2188 5919 1.138247 GGATTCGCGGTCTACACGT 59.862 57.895 6.13 0.00 0.00 4.49
2191 5922 2.107178 GATTCGCGGTCTACACGTTAG 58.893 52.381 6.13 0.00 0.00 2.34
2228 5959 1.754803 TCGAGTTCACCAAGTCACAGT 59.245 47.619 0.00 0.00 32.06 3.55
2231 5962 3.531538 GAGTTCACCAAGTCACAGTTGA 58.468 45.455 0.00 0.00 32.74 3.18
2232 5963 3.535561 AGTTCACCAAGTCACAGTTGAG 58.464 45.455 0.00 0.00 30.18 3.02
2233 5964 3.055094 AGTTCACCAAGTCACAGTTGAGT 60.055 43.478 0.00 0.00 36.94 3.41
2254 5986 2.832931 CAAGTCGTGCTCTGGAAGG 58.167 57.895 0.00 0.00 0.00 3.46
2272 6004 0.391263 GGTGGAGAAGGGTACAAGCG 60.391 60.000 0.00 0.00 0.00 4.68
2301 6033 0.834687 TTCTGGCAGGAAGTACCGGT 60.835 55.000 13.98 13.98 44.74 5.28
2303 6035 2.267961 GGCAGGAAGTACCGGTGG 59.732 66.667 19.93 0.00 44.74 4.61
2351 6090 1.677217 GCTGGCTAGACAGGGTTGAAG 60.677 57.143 26.99 0.00 38.90 3.02
2367 6106 5.123344 GGGTTGAAGCACGTAAAGTATTCAT 59.877 40.000 0.00 0.00 37.48 2.57
2389 6128 1.961394 CATGCCTGCATGCTTTATCCT 59.039 47.619 20.33 0.00 45.71 3.24
2396 6135 4.325119 CTGCATGCTTTATCCTGCTAGAT 58.675 43.478 20.33 0.00 35.66 1.98
2417 6156 0.526211 GGGTTGGGCAAATCGACTTC 59.474 55.000 0.00 0.00 0.00 3.01
2427 6166 4.800471 GGCAAATCGACTTCCATCATTTTC 59.200 41.667 0.00 0.00 0.00 2.29
2428 6167 5.393461 GGCAAATCGACTTCCATCATTTTCT 60.393 40.000 0.00 0.00 0.00 2.52
2430 6169 6.252228 GCAAATCGACTTCCATCATTTTCTTC 59.748 38.462 0.00 0.00 0.00 2.87
2432 6171 4.905429 TCGACTTCCATCATTTTCTTCCA 58.095 39.130 0.00 0.00 0.00 3.53
2434 6173 5.355071 TCGACTTCCATCATTTTCTTCCATG 59.645 40.000 0.00 0.00 0.00 3.66
2439 6181 7.234166 ACTTCCATCATTTTCTTCCATGTTCTT 59.766 33.333 0.00 0.00 0.00 2.52
2442 6184 8.108999 TCCATCATTTTCTTCCATGTTCTTCTA 58.891 33.333 0.00 0.00 0.00 2.10
2451 6193 8.029642 TCTTCCATGTTCTTCTAAAAATCGAC 57.970 34.615 0.00 0.00 0.00 4.20
2475 6217 3.475494 TGGATACATGCCCGCGGT 61.475 61.111 26.12 7.53 46.17 5.68
2476 6218 2.665185 GGATACATGCCCGCGGTC 60.665 66.667 26.12 13.25 0.00 4.79
2477 6219 2.665185 GATACATGCCCGCGGTCC 60.665 66.667 26.12 15.34 0.00 4.46
2478 6220 3.161450 ATACATGCCCGCGGTCCT 61.161 61.111 26.12 0.00 0.00 3.85
2479 6221 3.165160 ATACATGCCCGCGGTCCTC 62.165 63.158 26.12 10.61 0.00 3.71
2484 6226 3.547513 GCCCGCGGTCCTCCTTAT 61.548 66.667 26.12 0.00 0.00 1.73
2485 6227 2.421739 CCCGCGGTCCTCCTTATG 59.578 66.667 26.12 0.00 0.00 1.90
2486 6228 2.432300 CCCGCGGTCCTCCTTATGT 61.432 63.158 26.12 0.00 0.00 2.29
2487 6229 1.111116 CCCGCGGTCCTCCTTATGTA 61.111 60.000 26.12 0.00 0.00 2.29
2488 6230 0.314302 CCGCGGTCCTCCTTATGTAG 59.686 60.000 19.50 0.00 0.00 2.74
2489 6231 0.318784 CGCGGTCCTCCTTATGTAGC 60.319 60.000 0.00 0.00 0.00 3.58
2490 6232 0.033642 GCGGTCCTCCTTATGTAGCC 59.966 60.000 0.00 0.00 0.00 3.93
2491 6233 1.410004 CGGTCCTCCTTATGTAGCCA 58.590 55.000 0.00 0.00 0.00 4.75
2492 6234 1.971357 CGGTCCTCCTTATGTAGCCAT 59.029 52.381 0.00 0.00 34.97 4.40
2493 6235 2.028930 CGGTCCTCCTTATGTAGCCATC 60.029 54.545 0.00 0.00 32.29 3.51
2494 6236 3.243724 GGTCCTCCTTATGTAGCCATCT 58.756 50.000 0.00 0.00 32.29 2.90
2495 6237 4.417437 GGTCCTCCTTATGTAGCCATCTA 58.583 47.826 0.00 0.00 32.29 1.98
2496 6238 5.026790 GGTCCTCCTTATGTAGCCATCTAT 58.973 45.833 0.00 0.00 32.29 1.98
2497 6239 5.485708 GGTCCTCCTTATGTAGCCATCTATT 59.514 44.000 0.00 0.00 32.29 1.73
2498 6240 6.013293 GGTCCTCCTTATGTAGCCATCTATTT 60.013 42.308 0.00 0.00 32.29 1.40
2499 6241 7.100409 GTCCTCCTTATGTAGCCATCTATTTC 58.900 42.308 0.00 0.00 32.29 2.17
2500 6242 7.019388 TCCTCCTTATGTAGCCATCTATTTCT 58.981 38.462 0.00 0.00 32.29 2.52
2501 6243 7.038729 TCCTCCTTATGTAGCCATCTATTTCTG 60.039 40.741 0.00 0.00 32.29 3.02
2502 6244 6.467677 TCCTTATGTAGCCATCTATTTCTGC 58.532 40.000 0.00 0.00 32.29 4.26
2503 6245 6.043127 TCCTTATGTAGCCATCTATTTCTGCA 59.957 38.462 0.00 0.00 32.29 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.148705 CGCATGTCAAGATTGAAACATTGATTT 60.149 33.333 0.00 0.00 39.21 2.17
91 92 5.803461 CGCATGTCAAGATTGAAACATTGAT 59.197 36.000 0.00 0.00 39.21 2.57
115 116 4.253685 ACCACTACTTGCATCACACATAC 58.746 43.478 0.00 0.00 0.00 2.39
183 184 4.542735 GTTTTGACCATTGGTAAACGGAG 58.457 43.478 8.70 0.00 35.25 4.63
184 185 3.003482 CGTTTTGACCATTGGTAAACGGA 59.997 43.478 31.07 9.37 45.74 4.69
197 198 4.277423 TCTTTGAATCCTTCCGTTTTGACC 59.723 41.667 0.00 0.00 0.00 4.02
205 206 5.948992 AAAACTCTCTTTGAATCCTTCCG 57.051 39.130 0.00 0.00 0.00 4.30
255 256 0.892755 ACTCGGCAAGACCACGAATA 59.107 50.000 0.00 0.00 39.03 1.75
264 265 3.007506 TGGAGTTTCAATACTCGGCAAGA 59.992 43.478 0.00 0.00 44.38 3.02
287 288 0.668535 TGCATCGTGATCTAGGACCG 59.331 55.000 0.00 0.00 0.00 4.79
305 306 3.247886 CGAGGATCTCTGCATCATGTTTG 59.752 47.826 0.00 0.00 0.00 2.93
315 316 2.619840 TTCGCTGCGAGGATCTCTGC 62.620 60.000 24.61 0.00 40.71 4.26
327 328 0.875908 TCCATGCTACGATTCGCTGC 60.876 55.000 5.86 11.04 0.00 5.25
330 331 1.523095 GTTCTCCATGCTACGATTCGC 59.477 52.381 5.86 0.00 0.00 4.70
332 333 2.128035 CGGTTCTCCATGCTACGATTC 58.872 52.381 0.00 0.00 0.00 2.52
354 355 3.194968 CCAAGAGTACGGGTATGAACTGT 59.805 47.826 0.00 0.00 0.00 3.55
355 356 3.446161 TCCAAGAGTACGGGTATGAACTG 59.554 47.826 0.00 0.00 0.00 3.16
426 427 9.334693 CAGTTGAAGTAAAGAGCATGATAAAAC 57.665 33.333 0.00 0.00 0.00 2.43
434 435 4.762251 GGGTTCAGTTGAAGTAAAGAGCAT 59.238 41.667 0.00 0.00 34.27 3.79
450 451 3.278574 TCAAACACACAGAAGGGTTCAG 58.721 45.455 0.00 0.00 0.00 3.02
622 4241 1.149288 TGTAGCCGATCCCTCCCTTAT 59.851 52.381 0.00 0.00 0.00 1.73
641 4260 6.391227 ACTCCTCTAAAAATGTGTGGTTTG 57.609 37.500 0.00 0.00 0.00 2.93
670 4289 5.183969 GGCCGAGTAAATTTTAGAGGAGTT 58.816 41.667 0.00 0.00 0.00 3.01
760 4379 0.474273 TTAGGTCGGGGAGTTGGGTT 60.474 55.000 0.00 0.00 0.00 4.11
761 4380 0.253020 ATTAGGTCGGGGAGTTGGGT 60.253 55.000 0.00 0.00 0.00 4.51
802 4421 5.450550 GCTAGTTACTTCCATGCAATTTCCC 60.451 44.000 0.00 0.00 0.00 3.97
829 4448 6.901887 GCAACATTCATACGTATGACAAGAAG 59.098 38.462 32.50 21.92 42.00 2.85
952 4571 1.734465 GTAGAGCGCTGCAATTTGACT 59.266 47.619 18.48 4.37 0.00 3.41
1072 4693 4.680237 CTGCGGGGTGTTCTGCGA 62.680 66.667 0.00 0.00 41.67 5.10
1096 4717 1.796151 CGCGATTGTGCAGGTTGAT 59.204 52.632 0.00 0.00 34.15 2.57
1236 4857 1.763545 GACCCCCAGTAGATGTTCTCC 59.236 57.143 0.00 0.00 0.00 3.71
1368 4989 4.935495 CTGCGCCACACCACCTGT 62.935 66.667 4.18 0.00 0.00 4.00
1422 5043 2.284112 AAGACGCCCCGGTTCCTA 60.284 61.111 0.00 0.00 0.00 2.94
1517 5138 2.742053 AGCACGATACCACAAATCACAC 59.258 45.455 0.00 0.00 0.00 3.82
1529 5150 1.924524 ACGCACACATAAGCACGATAC 59.075 47.619 0.00 0.00 0.00 2.24
1547 5168 4.374538 CGCTTTATAAAACACACACACACG 59.625 41.667 0.00 0.00 0.00 4.49
1601 5222 9.953825 GCTTATTTGCGTATAACATATGTAGAC 57.046 33.333 9.21 6.70 0.00 2.59
1602 5223 9.699703 TGCTTATTTGCGTATAACATATGTAGA 57.300 29.630 9.21 0.44 35.36 2.59
1604 5225 9.262358 TGTGCTTATTTGCGTATAACATATGTA 57.738 29.630 9.21 0.00 35.36 2.29
1605 5226 8.148807 TGTGCTTATTTGCGTATAACATATGT 57.851 30.769 1.41 1.41 35.36 2.29
1607 5228 8.378172 ACTGTGCTTATTTGCGTATAACATAT 57.622 30.769 0.00 0.00 35.36 1.78
1609 5230 6.315144 TGACTGTGCTTATTTGCGTATAACAT 59.685 34.615 0.00 0.00 35.36 2.71
1610 5231 5.639931 TGACTGTGCTTATTTGCGTATAACA 59.360 36.000 0.00 0.00 35.36 2.41
1611 5232 5.957796 GTGACTGTGCTTATTTGCGTATAAC 59.042 40.000 0.00 0.00 35.36 1.89
1612 5233 5.064198 GGTGACTGTGCTTATTTGCGTATAA 59.936 40.000 0.00 0.00 35.36 0.98
1613 5234 4.569162 GGTGACTGTGCTTATTTGCGTATA 59.431 41.667 0.00 0.00 35.36 1.47
1614 5235 3.374058 GGTGACTGTGCTTATTTGCGTAT 59.626 43.478 0.00 0.00 35.36 3.06
1615 5236 2.739913 GGTGACTGTGCTTATTTGCGTA 59.260 45.455 0.00 0.00 35.36 4.42
1616 5237 1.535462 GGTGACTGTGCTTATTTGCGT 59.465 47.619 0.00 0.00 35.36 5.24
1617 5238 1.464023 CGGTGACTGTGCTTATTTGCG 60.464 52.381 0.00 0.00 35.36 4.85
1618 5239 1.135689 CCGGTGACTGTGCTTATTTGC 60.136 52.381 0.00 0.00 0.00 3.68
1619 5240 1.135689 GCCGGTGACTGTGCTTATTTG 60.136 52.381 1.90 0.00 0.00 2.32
1620 5241 1.165270 GCCGGTGACTGTGCTTATTT 58.835 50.000 1.90 0.00 0.00 1.40
1621 5242 0.676782 GGCCGGTGACTGTGCTTATT 60.677 55.000 1.90 0.00 0.00 1.40
1622 5243 1.078426 GGCCGGTGACTGTGCTTAT 60.078 57.895 1.90 0.00 0.00 1.73
1623 5244 2.214216 AGGCCGGTGACTGTGCTTA 61.214 57.895 1.90 0.00 0.00 3.09
1624 5245 3.560251 AGGCCGGTGACTGTGCTT 61.560 61.111 1.90 0.00 0.00 3.91
1625 5246 4.320456 CAGGCCGGTGACTGTGCT 62.320 66.667 1.90 0.00 0.00 4.40
1627 5248 3.907260 ATGCAGGCCGGTGACTGTG 62.907 63.158 19.30 0.00 37.07 3.66
1628 5249 3.640407 ATGCAGGCCGGTGACTGT 61.640 61.111 19.30 3.47 37.07 3.55
1629 5250 3.129502 CATGCAGGCCGGTGACTG 61.130 66.667 15.65 15.65 37.76 3.51
1630 5251 3.640407 ACATGCAGGCCGGTGACT 61.640 61.111 1.90 0.00 0.00 3.41
1631 5252 3.434319 CACATGCAGGCCGGTGAC 61.434 66.667 1.90 0.00 33.16 3.67
1632 5253 3.899981 GACACATGCAGGCCGGTGA 62.900 63.158 17.27 1.10 35.33 4.02
1633 5254 3.434319 GACACATGCAGGCCGGTG 61.434 66.667 1.90 8.68 37.29 4.94
1634 5255 4.722700 GGACACATGCAGGCCGGT 62.723 66.667 1.90 0.00 0.00 5.28
1635 5256 4.720902 TGGACACATGCAGGCCGG 62.721 66.667 0.00 0.00 0.00 6.13
1636 5257 2.438975 ATGGACACATGCAGGCCG 60.439 61.111 0.00 0.00 35.57 6.13
1658 5279 0.673333 TTACATGCACCACAGAGCCG 60.673 55.000 0.00 0.00 0.00 5.52
1695 5316 8.447833 ACAAAATATATAAATGGACGCATACGG 58.552 33.333 0.00 0.00 46.04 4.02
1731 5352 7.391833 GTGTTGGATCTTTCCTAACTTCAAGAT 59.608 37.037 0.00 0.00 43.07 2.40
1744 5365 4.022068 TCATTTGCCTGTGTTGGATCTTTC 60.022 41.667 0.00 0.00 0.00 2.62
1784 5515 1.334419 CGTGAAAGGAAAGCACAGCAG 60.334 52.381 0.00 0.00 32.96 4.24
1803 5534 6.291060 GCAAAAACAAGAATAATGTATCCGCG 60.291 38.462 0.00 0.00 0.00 6.46
1809 5540 6.858993 GTGGACGCAAAAACAAGAATAATGTA 59.141 34.615 0.00 0.00 0.00 2.29
1811 5542 5.164196 CGTGGACGCAAAAACAAGAATAATG 60.164 40.000 0.00 0.00 0.00 1.90
1820 5551 1.593933 GAGTACGTGGACGCAAAAACA 59.406 47.619 0.00 0.00 44.43 2.83
1844 5575 0.378962 ACTCTCGCCTCGAAATCTCG 59.621 55.000 0.00 0.00 46.87 4.04
1845 5576 2.570442 AACTCTCGCCTCGAAATCTC 57.430 50.000 0.00 0.00 34.74 2.75
1846 5577 2.611518 CAAACTCTCGCCTCGAAATCT 58.388 47.619 0.00 0.00 34.74 2.40
1847 5578 1.661112 CCAAACTCTCGCCTCGAAATC 59.339 52.381 0.00 0.00 34.74 2.17
1848 5579 1.002087 ACCAAACTCTCGCCTCGAAAT 59.998 47.619 0.00 0.00 34.74 2.17
1849 5580 0.391597 ACCAAACTCTCGCCTCGAAA 59.608 50.000 0.00 0.00 34.74 3.46
1850 5581 1.201647 CTACCAAACTCTCGCCTCGAA 59.798 52.381 0.00 0.00 34.74 3.71
1926 5657 2.543777 TCAACCAAACTCTCGGGAAG 57.456 50.000 0.00 0.00 0.00 3.46
1932 5663 5.456265 GCTGAAGAAATCAACCAAACTCTC 58.544 41.667 0.00 0.00 37.67 3.20
1933 5664 4.279420 GGCTGAAGAAATCAACCAAACTCT 59.721 41.667 0.00 0.00 42.79 3.24
1934 5665 4.550422 GGCTGAAGAAATCAACCAAACTC 58.450 43.478 0.00 0.00 42.79 3.01
1939 5670 2.978156 AGGGCTGAAGAAATCAACCA 57.022 45.000 0.85 0.00 44.69 3.67
1954 5685 1.873863 GAGTGGTGCGTTAAAGGGC 59.126 57.895 0.00 0.00 0.00 5.19
1965 5696 3.304123 GCATCTAGCTAGTACGAGTGGTG 60.304 52.174 20.10 1.09 41.15 4.17
1995 5726 0.947180 ACACCGTGTCACCGCATAAC 60.947 55.000 0.00 0.00 0.00 1.89
2004 5735 1.084935 CGACAACCAACACCGTGTCA 61.085 55.000 4.23 0.00 40.32 3.58
2009 5740 1.084935 TGTGTCGACAACCAACACCG 61.085 55.000 21.95 0.00 42.01 4.94
2024 5755 0.538057 CCATGTCCTTGGTGCTGTGT 60.538 55.000 0.00 0.00 31.74 3.72
2025 5756 0.250858 TCCATGTCCTTGGTGCTGTG 60.251 55.000 0.00 0.00 38.01 3.66
2044 5775 2.356780 GGTGGAGTTCCGGGTCGAT 61.357 63.158 0.00 0.00 39.43 3.59
2045 5776 2.993264 GGTGGAGTTCCGGGTCGA 60.993 66.667 0.00 0.00 39.43 4.20
2046 5777 4.430765 CGGTGGAGTTCCGGGTCG 62.431 72.222 0.00 0.00 43.68 4.79
2052 5783 2.737376 GCGACACGGTGGAGTTCC 60.737 66.667 13.48 0.00 0.00 3.62
2053 5784 2.737376 GGCGACACGGTGGAGTTC 60.737 66.667 13.48 0.00 0.00 3.01
2054 5785 2.989055 CTTGGCGACACGGTGGAGTT 62.989 60.000 13.48 0.00 42.67 3.01
2069 5800 0.884704 CACAGTTGACGGGTCCTTGG 60.885 60.000 0.00 0.00 0.00 3.61
2073 5804 1.004918 CCTCACAGTTGACGGGTCC 60.005 63.158 0.00 0.00 0.00 4.46
2086 5817 4.980805 TTGTCGTGGCGGCCTCAC 62.981 66.667 21.46 16.36 0.00 3.51
2087 5818 4.680237 CTTGTCGTGGCGGCCTCA 62.680 66.667 21.46 11.09 0.00 3.86
2098 5829 1.372997 ACCGCTGTGCTACTTGTCG 60.373 57.895 0.00 0.00 0.00 4.35
2133 5864 3.289834 AACGCTGTGCTTGGCCAG 61.290 61.111 5.11 1.08 32.70 4.85
2168 5899 1.138247 GTGTAGACCGCGAATCCGT 59.862 57.895 8.23 0.00 38.24 4.69
2169 5900 3.993103 GTGTAGACCGCGAATCCG 58.007 61.111 8.23 0.00 39.16 4.18
2188 5919 1.667830 GTGCCAGTCTGCGTGCTAA 60.668 57.895 0.00 0.00 0.00 3.09
2249 5981 1.652947 TGTACCCTTCTCCACCTTCC 58.347 55.000 0.00 0.00 0.00 3.46
2254 5986 0.391263 CCGCTTGTACCCTTCTCCAC 60.391 60.000 0.00 0.00 0.00 4.02
2272 6004 4.980805 TGCCAGAACGCCGTCACC 62.981 66.667 0.00 0.00 0.00 4.02
2310 6042 4.688419 CGCACAGCCGGCAAACAG 62.688 66.667 31.54 14.95 0.00 3.16
2351 6090 3.725740 GCATGCATGAATACTTTACGTGC 59.274 43.478 30.64 7.16 43.88 5.34
2382 6121 3.138283 CCAACCCCATCTAGCAGGATAAA 59.862 47.826 2.20 0.00 0.00 1.40
2386 6125 0.988145 CCCAACCCCATCTAGCAGGA 60.988 60.000 2.20 0.00 0.00 3.86
2389 6128 1.505151 TTGCCCAACCCCATCTAGCA 61.505 55.000 0.00 0.00 0.00 3.49
2396 6135 1.605165 GTCGATTTGCCCAACCCCA 60.605 57.895 0.00 0.00 0.00 4.96
2417 6156 7.166691 AGAAGAACATGGAAGAAAATGATGG 57.833 36.000 0.00 0.00 0.00 3.51
2427 6166 8.034058 AGTCGATTTTTAGAAGAACATGGAAG 57.966 34.615 0.00 0.00 0.00 3.46
2428 6167 7.979444 AGTCGATTTTTAGAAGAACATGGAA 57.021 32.000 0.00 0.00 0.00 3.53
2430 6169 7.402640 GCTAGTCGATTTTTAGAAGAACATGG 58.597 38.462 0.00 0.00 0.00 3.66
2432 6171 6.237861 GCGCTAGTCGATTTTTAGAAGAACAT 60.238 38.462 0.00 0.00 41.67 2.71
2434 6173 5.288952 AGCGCTAGTCGATTTTTAGAAGAAC 59.711 40.000 8.99 0.00 41.67 3.01
2439 6181 3.129813 TCCAGCGCTAGTCGATTTTTAGA 59.870 43.478 10.99 0.00 41.67 2.10
2442 6184 2.380084 TCCAGCGCTAGTCGATTTTT 57.620 45.000 10.99 0.00 41.67 1.94
2451 6193 0.671781 GGGCATGTATCCAGCGCTAG 60.672 60.000 10.99 1.56 38.09 3.42
2472 6214 1.410004 TGGCTACATAAGGAGGACCG 58.590 55.000 0.00 0.00 41.83 4.79
2473 6215 3.243724 AGATGGCTACATAAGGAGGACC 58.756 50.000 0.00 0.00 37.47 4.46
2474 6216 6.613153 AATAGATGGCTACATAAGGAGGAC 57.387 41.667 0.00 0.00 37.47 3.85
2475 6217 7.019388 AGAAATAGATGGCTACATAAGGAGGA 58.981 38.462 0.00 0.00 37.47 3.71
2476 6218 7.102346 CAGAAATAGATGGCTACATAAGGAGG 58.898 42.308 0.00 0.00 37.47 4.30
2477 6219 6.593382 GCAGAAATAGATGGCTACATAAGGAG 59.407 42.308 0.00 0.00 37.47 3.69
2478 6220 6.043127 TGCAGAAATAGATGGCTACATAAGGA 59.957 38.462 0.00 0.00 37.47 3.36
2479 6221 6.233434 TGCAGAAATAGATGGCTACATAAGG 58.767 40.000 0.00 0.00 37.47 2.69


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

AutoCloner maintained by Alex Coulton.