Multiple sequence alignment - TraesCS3A01G283700

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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 TraesCS3A01G283700 chr3A 100.000 3413 0 0 1 3413 512302416 512305828 0.000000e+00 6303
1 TraesCS3A01G283700 chr3B 88.880 2608 134 61 1 2570 511065403 511067892 0.000000e+00 3066
2 TraesCS3A01G283700 chr3B 88.038 744 34 17 2678 3413 511068007 511068703 0.000000e+00 830
3 TraesCS3A01G283700 chr3B 89.076 119 10 1 1 119 511063687 511063802 9.870000e-31 145
4 TraesCS3A01G283700 chr3D 88.020 1586 88 41 1 1533 392040185 392041721 0.000000e+00 1783
5 TraesCS3A01G283700 chr3D 91.896 691 32 8 2732 3413 392042778 392043453 0.000000e+00 944
6 TraesCS3A01G283700 chr3D 84.161 947 61 41 1598 2512 392041738 392042627 0.000000e+00 835


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 TraesCS3A01G283700 chr3A 512302416 512305828 3412 False 6303.000000 6303 100.000000 1 3413 1 chr3A.!!$F1 3412
1 TraesCS3A01G283700 chr3B 511063687 511068703 5016 False 1347.000000 3066 88.664667 1 3413 3 chr3B.!!$F1 3412
2 TraesCS3A01G283700 chr3D 392040185 392043453 3268 False 1187.333333 1783 88.025667 1 3413 3 chr3D.!!$F1 3412

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
223 1955 0.029834 GATCGAACACCATGCATGCC 59.970 55.0 21.69 6.23 0.00 4.40 F
422 2178 0.168128 GCCAATCAAGAAACGGTCCG 59.832 55.0 10.48 10.48 0.00 4.79 F
1719 3536 0.177836 CACCGGCATCTATGTGGACA 59.822 55.0 0.00 0.00 32.25 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 4017 0.186630 TCTTCCCGGGGATGTCGATA 59.813 55.0 23.50 5.15 0.0 2.92 R
2281 4129 0.745845 AAGACATGGCTGCCGATCAC 60.746 55.0 14.98 4.50 0.0 3.06 R
2997 4904 0.179200 ATCGGAAATGTTCAACGCGC 60.179 50.0 5.73 0.00 0.0 6.86 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
54 1771 2.128507 CCTAGCCCTCTGGACGTCC 61.129 68.421 28.17 28.17 0.00 4.79
62 1779 1.616187 CCTCTGGACGTCCACTTCCTA 60.616 57.143 33.23 10.87 42.01 2.94
70 1787 2.158914 ACGTCCACTTCCTAACCGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
87 1804 1.246649 TTTCCGTTGCATGTGAGCAT 58.753 45.000 0.00 0.00 45.19 3.79
88 1805 0.804364 TTCCGTTGCATGTGAGCATC 59.196 50.000 0.00 0.00 45.19 3.91
89 1806 4.657077 CGTTGCATGTGAGCATCG 57.343 55.556 5.22 5.22 46.78 3.84
92 1809 0.097674 GTTGCATGTGAGCATCGTCC 59.902 55.000 0.00 0.00 45.19 4.79
106 1823 1.112113 TCGTCCTCCTAACTGATGCC 58.888 55.000 0.00 0.00 0.00 4.40
119 1836 0.958382 TGATGCCACCGTACCAAAGC 60.958 55.000 0.00 0.00 0.00 3.51
122 1839 1.240641 TGCCACCGTACCAAAGCATG 61.241 55.000 0.00 0.00 0.00 4.06
143 1875 2.606725 GGCAGTGAGTGAAGATCAATCG 59.393 50.000 0.00 0.00 43.69 3.34
180 1912 4.037208 CCCTTTTGATGTTGGCTATGCTAG 59.963 45.833 0.00 0.00 0.00 3.42
183 1915 4.486125 TTGATGTTGGCTATGCTAGACA 57.514 40.909 0.00 0.00 43.47 3.41
197 1929 1.675483 CTAGACACATCGCTCAGAGCT 59.325 52.381 20.39 0.00 39.60 4.09
198 1930 0.455410 AGACACATCGCTCAGAGCTC 59.545 55.000 20.39 5.27 39.60 4.09
199 1931 0.455410 GACACATCGCTCAGAGCTCT 59.545 55.000 20.39 11.45 39.60 4.09
222 1954 0.316442 CGATCGAACACCATGCATGC 60.316 55.000 21.69 11.82 0.00 4.06
223 1955 0.029834 GATCGAACACCATGCATGCC 59.970 55.000 21.69 6.23 0.00 4.40
341 2097 2.030274 GTGTTATCCACAAAGGTGCACC 60.030 50.000 29.22 29.22 43.88 5.01
371 2127 1.193203 CACGCAGACACACAGATCAAC 59.807 52.381 0.00 0.00 0.00 3.18
403 2159 0.952497 ATGCCAGACGAGCAACACAG 60.952 55.000 0.00 0.00 44.83 3.66
421 2177 1.200020 CAGCCAATCAAGAAACGGTCC 59.800 52.381 0.00 0.00 0.00 4.46
422 2178 0.168128 GCCAATCAAGAAACGGTCCG 59.832 55.000 10.48 10.48 0.00 4.79
441 2197 3.365535 CCGGTTGGCTTTCCTTGG 58.634 61.111 0.00 0.00 0.00 3.61
491 2247 1.813753 CGCGTCCGGGTTCATTCAT 60.814 57.895 0.00 0.00 0.00 2.57
533 2294 7.553760 TCGATCAGATCAAAATCAAAATCAGGA 59.446 33.333 11.12 0.00 34.07 3.86
534 2295 7.856398 CGATCAGATCAAAATCAAAATCAGGAG 59.144 37.037 11.12 0.00 34.07 3.69
535 2296 6.860080 TCAGATCAAAATCAAAATCAGGAGC 58.140 36.000 0.00 0.00 34.07 4.70
536 2297 6.662234 TCAGATCAAAATCAAAATCAGGAGCT 59.338 34.615 0.00 0.00 34.07 4.09
584 2345 2.124736 CCAACCGGCCACATCGAT 60.125 61.111 0.00 0.00 0.00 3.59
585 2346 2.180204 CCAACCGGCCACATCGATC 61.180 63.158 0.00 0.00 0.00 3.69
632 2393 2.747436 GTGAACGTACGGGGGAATATC 58.253 52.381 21.06 5.15 0.00 1.63
717 2478 1.372623 GGATCGCGGACGGGATTAC 60.373 63.158 22.17 15.51 45.73 1.89
923 2684 2.014554 CTGTCCGTCCGTCGTGTTG 61.015 63.158 0.00 0.00 37.94 3.33
942 2704 0.179205 GCACAAGCTCTCGTCATTGC 60.179 55.000 0.00 0.00 37.91 3.56
965 2727 2.478831 GCCTCATTCACAGCTAGCTAC 58.521 52.381 18.86 0.00 0.00 3.58
966 2728 2.102252 GCCTCATTCACAGCTAGCTACT 59.898 50.000 18.86 2.12 0.00 2.57
967 2729 3.431486 GCCTCATTCACAGCTAGCTACTT 60.431 47.826 18.86 1.41 0.00 2.24
968 2730 4.202161 GCCTCATTCACAGCTAGCTACTTA 60.202 45.833 18.86 4.03 0.00 2.24
969 2731 5.527951 CCTCATTCACAGCTAGCTACTTAG 58.472 45.833 18.86 7.23 0.00 2.18
1297 3066 0.316841 CTTCATCGAGAGCTAGCCCC 59.683 60.000 12.13 3.61 0.00 5.80
1342 3111 3.978723 CTGTCTCGCTCGTGGCCAG 62.979 68.421 5.11 0.00 37.74 4.85
1377 3177 1.202940 GCTCAAGGGTCTTCTTGGGTT 60.203 52.381 6.38 0.00 44.72 4.11
1390 3191 3.221771 TCTTGGGTTGATCCAGTTTGTG 58.778 45.455 0.00 0.00 38.17 3.33
1391 3192 2.746279 TGGGTTGATCCAGTTTGTGT 57.254 45.000 0.00 0.00 38.11 3.72
1392 3193 3.866703 TGGGTTGATCCAGTTTGTGTA 57.133 42.857 0.00 0.00 38.11 2.90
1478 3280 6.587608 GTCTCATTTGTGAATTGGTTGGAATC 59.412 38.462 0.00 0.00 0.00 2.52
1719 3536 0.177836 CACCGGCATCTATGTGGACA 59.822 55.000 0.00 0.00 32.25 4.02
1720 3537 0.178068 ACCGGCATCTATGTGGACAC 59.822 55.000 0.00 0.00 32.25 3.67
1721 3538 0.465705 CCGGCATCTATGTGGACACT 59.534 55.000 3.91 0.00 0.00 3.55
1722 3539 1.575244 CGGCATCTATGTGGACACTG 58.425 55.000 3.91 0.00 0.00 3.66
1723 3540 1.807755 CGGCATCTATGTGGACACTGG 60.808 57.143 3.91 0.00 0.00 4.00
1724 3541 1.486310 GGCATCTATGTGGACACTGGA 59.514 52.381 3.91 0.47 0.00 3.86
1725 3542 2.555199 GCATCTATGTGGACACTGGAC 58.445 52.381 3.91 0.00 0.00 4.02
1753 3570 4.067896 CAAACAACTACTGGATCAGCTGT 58.932 43.478 14.67 0.42 34.37 4.40
1754 3571 3.325293 ACAACTACTGGATCAGCTGTG 57.675 47.619 14.67 2.73 34.37 3.66
1755 3572 2.027745 ACAACTACTGGATCAGCTGTGG 60.028 50.000 14.67 0.00 34.37 4.17
1756 3573 1.198713 ACTACTGGATCAGCTGTGGG 58.801 55.000 14.67 3.74 34.37 4.61
1757 3574 1.273267 ACTACTGGATCAGCTGTGGGA 60.273 52.381 14.67 0.00 34.37 4.37
1758 3575 2.045524 CTACTGGATCAGCTGTGGGAT 58.954 52.381 14.67 0.00 34.37 3.85
1759 3576 1.293062 ACTGGATCAGCTGTGGGATT 58.707 50.000 14.67 0.00 34.37 3.01
1760 3577 2.481441 ACTGGATCAGCTGTGGGATTA 58.519 47.619 14.67 0.00 34.37 1.75
1761 3578 2.171448 ACTGGATCAGCTGTGGGATTAC 59.829 50.000 14.67 0.00 34.37 1.89
1762 3579 2.171237 CTGGATCAGCTGTGGGATTACA 59.829 50.000 14.67 2.95 0.00 2.41
1780 3597 7.419750 GGGATTACATACATGGGTAACTTCTGA 60.420 40.741 0.00 0.00 32.77 3.27
1792 3609 4.142160 GGTAACTTCTGAAAATCCCCATGC 60.142 45.833 0.00 0.00 0.00 4.06
1800 3617 6.138263 TCTGAAAATCCCCATGCAAGATAAT 58.862 36.000 0.00 0.00 0.00 1.28
1803 3620 7.068702 TGAAAATCCCCATGCAAGATAATACT 58.931 34.615 0.00 0.00 0.00 2.12
1804 3621 8.224025 TGAAAATCCCCATGCAAGATAATACTA 58.776 33.333 0.00 0.00 0.00 1.82
1806 3623 6.959606 ATCCCCATGCAAGATAATACTAGT 57.040 37.500 0.00 0.00 0.00 2.57
1807 3624 6.114187 TCCCCATGCAAGATAATACTAGTG 57.886 41.667 5.39 0.00 0.00 2.74
1808 3625 4.697352 CCCCATGCAAGATAATACTAGTGC 59.303 45.833 5.39 0.00 0.00 4.40
1809 3626 5.513788 CCCCATGCAAGATAATACTAGTGCT 60.514 44.000 5.39 0.00 33.19 4.40
1810 3627 6.295859 CCCCATGCAAGATAATACTAGTGCTA 60.296 42.308 5.39 0.00 33.19 3.49
1811 3628 6.815641 CCCATGCAAGATAATACTAGTGCTAG 59.184 42.308 5.39 4.80 39.04 3.42
1812 3629 6.312426 CCATGCAAGATAATACTAGTGCTAGC 59.688 42.308 8.10 8.10 36.66 3.42
1883 3700 6.928202 AGTCCTAGATATATACCCCATCCAG 58.072 44.000 0.00 0.00 0.00 3.86
1884 3701 6.078664 GTCCTAGATATATACCCCATCCAGG 58.921 48.000 0.00 0.00 31.22 4.45
1885 3702 4.841246 CCTAGATATATACCCCATCCAGGC 59.159 50.000 0.00 0.00 35.39 4.85
1886 3703 4.368240 AGATATATACCCCATCCAGGCA 57.632 45.455 0.00 0.00 35.39 4.75
1887 3704 4.912982 AGATATATACCCCATCCAGGCAT 58.087 43.478 0.00 0.00 35.39 4.40
1888 3705 4.910304 AGATATATACCCCATCCAGGCATC 59.090 45.833 0.00 0.00 35.39 3.91
1889 3706 1.668826 TATACCCCATCCAGGCATCC 58.331 55.000 0.00 0.00 35.39 3.51
1890 3707 0.403304 ATACCCCATCCAGGCATCCA 60.403 55.000 0.00 0.00 35.39 3.41
1895 3712 0.538977 CCATCCAGGCATCCACCATC 60.539 60.000 0.00 0.00 0.00 3.51
1901 3718 3.980022 TCCAGGCATCCACCATCTAATAA 59.020 43.478 0.00 0.00 0.00 1.40
1938 3763 8.710749 ATACGTACTTACCCTATCCAAATACA 57.289 34.615 0.00 0.00 0.00 2.29
1939 3764 6.809869 ACGTACTTACCCTATCCAAATACAC 58.190 40.000 0.00 0.00 0.00 2.90
1940 3765 6.380846 ACGTACTTACCCTATCCAAATACACA 59.619 38.462 0.00 0.00 0.00 3.72
1941 3766 6.698766 CGTACTTACCCTATCCAAATACACAC 59.301 42.308 0.00 0.00 0.00 3.82
1944 3769 4.938575 ACCCTATCCAAATACACACCAA 57.061 40.909 0.00 0.00 0.00 3.67
1961 3786 1.559682 CCAACAAAGCTAGCTAGGGGA 59.440 52.381 19.70 0.00 0.00 4.81
2003 3833 2.294078 AACGGGAAGAGCAGGAGGG 61.294 63.158 0.00 0.00 0.00 4.30
2040 3870 2.306341 CAGACATACTGTGGCCAGAG 57.694 55.000 27.52 27.52 41.50 3.35
2041 3871 0.539051 AGACATACTGTGGCCAGAGC 59.461 55.000 28.90 12.73 41.50 4.09
2101 3946 2.125512 ACGAAGGCCATGACGAGC 60.126 61.111 5.01 0.00 0.00 5.03
2102 3947 2.125552 CGAAGGCCATGACGAGCA 60.126 61.111 5.01 0.00 0.00 4.26
2103 3948 2.456119 CGAAGGCCATGACGAGCAC 61.456 63.158 5.01 0.00 0.00 4.40
2104 3949 1.078848 GAAGGCCATGACGAGCACT 60.079 57.895 5.01 0.00 0.00 4.40
2105 3950 1.078848 AAGGCCATGACGAGCACTC 60.079 57.895 5.01 0.00 0.00 3.51
2106 3951 2.512515 GGCCATGACGAGCACTCC 60.513 66.667 0.00 0.00 0.00 3.85
2107 3952 2.887568 GCCATGACGAGCACTCCG 60.888 66.667 0.00 0.00 0.00 4.63
2108 3953 2.202797 CCATGACGAGCACTCCGG 60.203 66.667 0.00 0.00 0.00 5.14
2109 3954 2.887568 CATGACGAGCACTCCGGC 60.888 66.667 0.00 0.00 35.21 6.13
2110 3955 4.498520 ATGACGAGCACTCCGGCG 62.499 66.667 0.00 0.00 38.00 6.46
2112 3957 4.838486 GACGAGCACTCCGGCGAG 62.838 72.222 9.30 6.64 42.32 5.03
2169 4017 2.663196 CGGAAAGCGTCTTCCCCT 59.337 61.111 10.83 0.00 41.73 4.79
2184 4032 2.283529 CCCTATCGACATCCCCGGG 61.284 68.421 15.80 15.80 0.00 5.73
2211 4059 2.084546 GGTAAGGCTACTGGTGCAAAG 58.915 52.381 0.00 0.00 0.00 2.77
2235 4083 2.825836 GCTCATCAGGCCGGGTTG 60.826 66.667 2.18 2.64 0.00 3.77
2295 4143 2.191375 CTGGTGATCGGCAGCCAT 59.809 61.111 13.30 4.01 44.28 4.40
2409 4257 2.240500 GGCGATGGTGATGCTCGAC 61.241 63.158 0.00 0.00 34.41 4.20
2412 4260 1.536072 GCGATGGTGATGCTCGACTAA 60.536 52.381 0.00 0.00 34.41 2.24
2413 4261 2.864097 GCGATGGTGATGCTCGACTAAT 60.864 50.000 0.00 0.00 34.41 1.73
2522 4372 1.073768 GACGTGAAAGCGAGCTCCTC 61.074 60.000 8.47 0.00 35.59 3.71
2544 4394 3.621715 CCTACTGTTTACCTCGAAATGGC 59.378 47.826 0.00 0.00 0.00 4.40
2570 4420 3.361053 GCGAGTCATGTAATCCGAATACG 59.639 47.826 0.00 0.00 39.43 3.06
2572 4422 4.378910 CGAGTCATGTAATCCGAATACGTG 59.621 45.833 8.90 8.90 40.19 4.49
2585 4464 4.203828 CGAATACGTGTAGAAATGCATGC 58.796 43.478 11.82 11.82 34.56 4.06
2595 4474 3.540617 AGAAATGCATGCATACGTGGTA 58.459 40.909 32.36 1.82 35.31 3.25
2625 4511 4.698780 ACGTTTATTTGAAAGGGTAGCCTC 59.301 41.667 15.24 3.36 0.00 4.70
2630 4516 1.224870 GAAAGGGTAGCCTCCTGCC 59.775 63.158 15.24 0.00 42.54 4.85
2651 4537 1.076332 GCGCTTATCCGTTCACTGTT 58.924 50.000 0.00 0.00 0.00 3.16
2653 4539 2.669434 GCGCTTATCCGTTCACTGTTTA 59.331 45.455 0.00 0.00 0.00 2.01
2659 4545 6.561737 TTATCCGTTCACTGTTTATTTGCA 57.438 33.333 0.00 0.00 0.00 4.08
2660 4546 4.217754 TCCGTTCACTGTTTATTTGCAC 57.782 40.909 0.00 0.00 0.00 4.57
2661 4547 2.970609 CCGTTCACTGTTTATTTGCACG 59.029 45.455 0.00 0.00 0.00 5.34
2662 4548 2.400408 CGTTCACTGTTTATTTGCACGC 59.600 45.455 0.00 0.00 0.00 5.34
2665 4558 4.235939 TCACTGTTTATTTGCACGCATT 57.764 36.364 0.00 0.00 0.00 3.56
2673 4566 8.705239 TGTTTATTTGCACGCATTTTATTTTG 57.295 26.923 0.00 0.00 0.00 2.44
2678 4571 5.512573 TGCACGCATTTTATTTTGACATG 57.487 34.783 0.00 0.00 0.00 3.21
2760 4655 5.730550 TGTCAGACAGTCAATAATACCACC 58.269 41.667 0.00 0.00 0.00 4.61
2768 4663 9.841295 GACAGTCAATAATACCACCCTTAATAA 57.159 33.333 0.00 0.00 0.00 1.40
2825 4720 5.773239 ACACGTTATTAACTTGATCCACG 57.227 39.130 17.12 0.00 34.97 4.94
2857 4752 7.540474 AACACAGTATCTCTTACTTCCTGAA 57.460 36.000 0.00 0.00 39.19 3.02
2875 4770 4.493547 CTGAACAAGGAAAACTTTGTGCA 58.506 39.130 0.00 0.00 37.29 4.57
2876 4771 5.083533 TGAACAAGGAAAACTTTGTGCAT 57.916 34.783 0.00 0.00 37.29 3.96
2877 4772 4.869297 TGAACAAGGAAAACTTTGTGCATG 59.131 37.500 0.00 0.00 37.29 4.06
2878 4773 3.197265 ACAAGGAAAACTTTGTGCATGC 58.803 40.909 11.82 11.82 37.29 4.06
2879 4774 2.531522 AGGAAAACTTTGTGCATGCC 57.468 45.000 16.68 7.25 0.00 4.40
2880 4775 1.070601 AGGAAAACTTTGTGCATGCCC 59.929 47.619 16.68 3.59 0.00 5.36
2945 4852 1.376037 CCCACTCCCAGCGAGAAAC 60.376 63.158 0.00 0.00 41.63 2.78
2952 4859 4.003648 ACTCCCAGCGAGAAACAATTAAG 58.996 43.478 0.00 0.00 41.63 1.85
2953 4860 4.003648 CTCCCAGCGAGAAACAATTAAGT 58.996 43.478 0.00 0.00 41.63 2.24
2954 4861 5.155278 TCCCAGCGAGAAACAATTAAGTA 57.845 39.130 0.00 0.00 0.00 2.24
2982 4889 6.944862 AGAGTGCAAACTTATCCTTCAAGAAT 59.055 34.615 0.00 0.00 0.00 2.40
3014 4921 0.454285 ATGCGCGTTGAACATTTCCG 60.454 50.000 8.43 0.00 0.00 4.30
3036 4943 4.443034 CGATTAAACCTAACCTCTCCCCAG 60.443 50.000 0.00 0.00 0.00 4.45
3096 5003 3.300711 GCAACGGCGAACCCTATAT 57.699 52.632 16.62 0.00 0.00 0.86
3097 5004 2.443887 GCAACGGCGAACCCTATATA 57.556 50.000 16.62 0.00 0.00 0.86
3107 5014 6.201044 CGGCGAACCCTATATATCATTTCATC 59.799 42.308 0.00 0.00 0.00 2.92
3115 5022 7.507277 CCCTATATATCATTTCATCTCCTCCGA 59.493 40.741 0.00 0.00 0.00 4.55
3116 5023 9.087871 CCTATATATCATTTCATCTCCTCCGAT 57.912 37.037 0.00 0.00 0.00 4.18
3118 5025 4.550076 ATCATTTCATCTCCTCCGATCC 57.450 45.455 0.00 0.00 0.00 3.36
3119 5026 2.297315 TCATTTCATCTCCTCCGATCCG 59.703 50.000 0.00 0.00 0.00 4.18
3120 5027 2.067365 TTTCATCTCCTCCGATCCGA 57.933 50.000 0.00 0.00 0.00 4.55
3174 5083 6.040842 CCTTATCTTCTTCTTCCTCCTCTCTG 59.959 46.154 0.00 0.00 0.00 3.35
3220 5129 0.533032 AAGCAACCTCTCCTACTCGC 59.467 55.000 0.00 0.00 0.00 5.03
3260 5169 1.153706 GGTGTCTGCATGCCATTGC 60.154 57.895 16.68 2.61 43.07 3.56
3332 5249 1.808531 GCTGTGGCCACTTGCATGAA 61.809 55.000 33.61 16.21 43.89 2.57
3333 5250 0.675083 CTGTGGCCACTTGCATGAAA 59.325 50.000 34.75 11.86 43.89 2.69
3334 5251 1.274167 CTGTGGCCACTTGCATGAAAT 59.726 47.619 34.75 0.00 43.89 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.927477 GTGAACGGCTCGTCAAATGATA 59.073 45.455 0.69 0.00 39.99 2.15
54 1771 2.874086 AACGGAAAACGGTTAGGAAGTG 59.126 45.455 0.00 0.00 41.94 3.16
62 1779 0.741915 ACATGCAACGGAAAACGGTT 59.258 45.000 0.00 0.00 41.94 4.44
70 1787 2.470156 GATGCTCACATGCAACGGA 58.530 52.632 0.00 0.00 46.61 4.69
87 1804 1.112113 GGCATCAGTTAGGAGGACGA 58.888 55.000 0.00 0.00 0.00 4.20
88 1805 0.824109 TGGCATCAGTTAGGAGGACG 59.176 55.000 0.00 0.00 26.40 4.79
89 1806 1.134371 GGTGGCATCAGTTAGGAGGAC 60.134 57.143 0.00 0.00 0.00 3.85
92 1809 0.537188 ACGGTGGCATCAGTTAGGAG 59.463 55.000 0.00 0.00 0.00 3.69
119 1836 2.981898 TGATCTTCACTCACTGCCATG 58.018 47.619 0.00 0.00 0.00 3.66
122 1839 2.606725 CGATTGATCTTCACTCACTGCC 59.393 50.000 0.00 0.00 0.00 4.85
157 1889 2.762327 AGCATAGCCAACATCAAAAGGG 59.238 45.455 0.00 0.00 0.00 3.95
197 1929 0.817654 ATGGTGTTCGATCGCTCAGA 59.182 50.000 11.09 2.39 0.00 3.27
198 1930 0.926155 CATGGTGTTCGATCGCTCAG 59.074 55.000 11.09 0.00 0.00 3.35
199 1931 1.083806 GCATGGTGTTCGATCGCTCA 61.084 55.000 11.09 9.05 0.00 4.26
223 1955 3.620300 CTTGGCAGTGGCACATGCG 62.620 63.158 20.46 14.31 44.52 4.73
349 2105 1.949015 GATCTGTGTGTCTGCGTGCG 61.949 60.000 0.00 0.00 0.00 5.34
371 2127 1.302913 TGGCATACCCCACGTGTTG 60.303 57.895 15.65 7.42 33.59 3.33
403 2159 0.168128 CGGACCGTTTCTTGATTGGC 59.832 55.000 5.48 0.00 0.00 4.52
437 2193 2.010817 GTTTTGTCGCAGCGCCAAG 61.011 57.895 11.57 0.00 0.00 3.61
439 2195 4.306471 CGTTTTGTCGCAGCGCCA 62.306 61.111 10.87 0.41 0.00 5.69
474 2230 0.742990 TGATGAATGAACCCGGACGC 60.743 55.000 0.73 0.00 0.00 5.19
491 2247 1.872388 TCGATCGTTTTGGTGCTTGA 58.128 45.000 15.94 0.00 0.00 3.02
533 2294 0.681564 CTCGACCACTCCACCTAGCT 60.682 60.000 0.00 0.00 0.00 3.32
534 2295 1.810532 CTCGACCACTCCACCTAGC 59.189 63.158 0.00 0.00 0.00 3.42
535 2296 1.668101 GGCTCGACCACTCCACCTAG 61.668 65.000 0.00 0.00 38.86 3.02
536 2297 1.681327 GGCTCGACCACTCCACCTA 60.681 63.158 0.00 0.00 38.86 3.08
580 2341 5.505819 CGTTGCTCAATTAGTAGGAGATCGA 60.506 44.000 0.00 0.00 0.00 3.59
584 2345 3.733988 CGCGTTGCTCAATTAGTAGGAGA 60.734 47.826 0.00 0.00 0.00 3.71
585 2346 2.535984 CGCGTTGCTCAATTAGTAGGAG 59.464 50.000 0.00 0.00 0.00 3.69
887 2648 0.878416 AGACAGCTCGCCGAGATATC 59.122 55.000 20.05 11.06 0.00 1.63
923 2684 0.179205 GCAATGACGAGAGCTTGTGC 60.179 55.000 0.00 0.00 40.05 4.57
942 2704 1.850377 CTAGCTGTGAATGAGGCGAG 58.150 55.000 0.00 0.00 0.00 5.03
1363 3132 1.354368 TGGATCAACCCAAGAAGACCC 59.646 52.381 0.00 0.00 38.00 4.46
1377 3177 7.770366 TTACTCTACTACACAAACTGGATCA 57.230 36.000 0.00 0.00 0.00 2.92
1392 3193 9.439500 CTCCGTAGCTATCTTATTTACTCTACT 57.561 37.037 0.00 0.00 0.00 2.57
1478 3280 5.718649 TTAAATTTCATCTCGCTCTTCCG 57.281 39.130 0.00 0.00 0.00 4.30
1711 3528 2.639347 TGAATGAGTCCAGTGTCCACAT 59.361 45.455 0.00 0.00 0.00 3.21
1719 3536 5.760253 CAGTAGTTGTTTGAATGAGTCCAGT 59.240 40.000 0.00 0.00 0.00 4.00
1720 3537 5.180117 CCAGTAGTTGTTTGAATGAGTCCAG 59.820 44.000 0.00 0.00 0.00 3.86
1721 3538 5.063204 CCAGTAGTTGTTTGAATGAGTCCA 58.937 41.667 0.00 0.00 0.00 4.02
1722 3539 5.305585 TCCAGTAGTTGTTTGAATGAGTCC 58.694 41.667 0.00 0.00 0.00 3.85
1723 3540 6.650807 TGATCCAGTAGTTGTTTGAATGAGTC 59.349 38.462 0.00 0.00 0.00 3.36
1724 3541 6.533730 TGATCCAGTAGTTGTTTGAATGAGT 58.466 36.000 0.00 0.00 0.00 3.41
1725 3542 6.402983 GCTGATCCAGTAGTTGTTTGAATGAG 60.403 42.308 0.00 0.00 33.43 2.90
1753 3570 6.388689 AGAAGTTACCCATGTATGTAATCCCA 59.611 38.462 0.00 0.00 30.35 4.37
1754 3571 6.710744 CAGAAGTTACCCATGTATGTAATCCC 59.289 42.308 0.00 0.00 30.35 3.85
1755 3572 7.506114 TCAGAAGTTACCCATGTATGTAATCC 58.494 38.462 0.00 0.00 30.35 3.01
1756 3573 8.958119 TTCAGAAGTTACCCATGTATGTAATC 57.042 34.615 0.00 0.00 30.35 1.75
1757 3574 9.747898 TTTTCAGAAGTTACCCATGTATGTAAT 57.252 29.630 0.00 0.00 30.35 1.89
1758 3575 9.747898 ATTTTCAGAAGTTACCCATGTATGTAA 57.252 29.630 0.00 0.00 0.00 2.41
1759 3576 9.391006 GATTTTCAGAAGTTACCCATGTATGTA 57.609 33.333 0.00 0.00 0.00 2.29
1760 3577 7.339466 GGATTTTCAGAAGTTACCCATGTATGT 59.661 37.037 0.00 0.00 0.00 2.29
1761 3578 7.201821 GGGATTTTCAGAAGTTACCCATGTATG 60.202 40.741 0.00 0.00 36.47 2.39
1762 3579 6.833933 GGGATTTTCAGAAGTTACCCATGTAT 59.166 38.462 0.00 0.00 36.47 2.29
1780 3597 8.227507 ACTAGTATTATCTTGCATGGGGATTTT 58.772 33.333 0.00 0.00 0.00 1.82
1792 3609 8.961634 TCCTATGCTAGCACTAGTATTATCTTG 58.038 37.037 22.07 0.19 38.93 3.02
1800 3617 6.785337 TTTTGTCCTATGCTAGCACTAGTA 57.215 37.500 22.07 7.62 35.65 1.82
1803 3620 5.822519 CCATTTTTGTCCTATGCTAGCACTA 59.177 40.000 22.07 12.46 0.00 2.74
1804 3621 4.641989 CCATTTTTGTCCTATGCTAGCACT 59.358 41.667 22.07 11.96 0.00 4.40
1806 3623 3.381272 GCCATTTTTGTCCTATGCTAGCA 59.619 43.478 21.85 21.85 0.00 3.49
1807 3624 3.633986 AGCCATTTTTGTCCTATGCTAGC 59.366 43.478 8.10 8.10 0.00 3.42
1808 3625 4.037208 CCAGCCATTTTTGTCCTATGCTAG 59.963 45.833 0.00 0.00 0.00 3.42
1809 3626 3.953612 CCAGCCATTTTTGTCCTATGCTA 59.046 43.478 0.00 0.00 0.00 3.49
1810 3627 2.762327 CCAGCCATTTTTGTCCTATGCT 59.238 45.455 0.00 0.00 0.00 3.79
1811 3628 2.760092 TCCAGCCATTTTTGTCCTATGC 59.240 45.455 0.00 0.00 0.00 3.14
1812 3629 4.202182 CCATCCAGCCATTTTTGTCCTATG 60.202 45.833 0.00 0.00 0.00 2.23
1883 3700 7.852263 AGTAGTATTATTAGATGGTGGATGCC 58.148 38.462 0.00 0.00 0.00 4.40
1935 3760 3.485463 AGCTAGCTTTGTTGGTGTGTA 57.515 42.857 12.68 0.00 0.00 2.90
1936 3761 2.348411 AGCTAGCTTTGTTGGTGTGT 57.652 45.000 12.68 0.00 0.00 3.72
1937 3762 2.744202 CCTAGCTAGCTTTGTTGGTGTG 59.256 50.000 24.88 0.00 0.00 3.82
1938 3763 2.290323 CCCTAGCTAGCTTTGTTGGTGT 60.290 50.000 24.88 0.00 0.00 4.16
1939 3764 2.359900 CCCTAGCTAGCTTTGTTGGTG 58.640 52.381 24.88 8.11 0.00 4.17
1940 3765 1.282157 CCCCTAGCTAGCTTTGTTGGT 59.718 52.381 24.88 0.00 0.00 3.67
1941 3766 1.559682 TCCCCTAGCTAGCTTTGTTGG 59.440 52.381 24.88 16.00 0.00 3.77
1944 3769 2.764269 TGATCCCCTAGCTAGCTTTGT 58.236 47.619 24.88 0.00 0.00 2.83
1961 3786 3.126001 TCGTCCTTTGCTTGACTTGAT 57.874 42.857 0.00 0.00 0.00 2.57
2040 3870 3.432445 ATCCTGGGCTGCATCTGGC 62.432 63.158 0.50 0.00 45.13 4.85
2041 3871 1.228184 GATCCTGGGCTGCATCTGG 60.228 63.158 0.50 6.88 0.00 3.86
2042 3872 1.228184 GGATCCTGGGCTGCATCTG 60.228 63.158 3.84 0.00 0.00 2.90
2043 3873 2.815945 CGGATCCTGGGCTGCATCT 61.816 63.158 10.75 0.00 0.00 2.90
2044 3874 2.281345 CGGATCCTGGGCTGCATC 60.281 66.667 10.75 0.00 0.00 3.91
2045 3875 3.882326 CCGGATCCTGGGCTGCAT 61.882 66.667 10.75 0.00 0.00 3.96
2153 4001 1.538419 CGATAGGGGAAGACGCTTTCC 60.538 57.143 9.45 9.45 44.82 3.13
2169 4017 0.186630 TCTTCCCGGGGATGTCGATA 59.813 55.000 23.50 5.15 0.00 2.92
2184 4032 1.136500 CCAGTAGCCTTACCGGTCTTC 59.864 57.143 12.40 0.00 34.25 2.87
2195 4043 1.303643 GCCTTTGCACCAGTAGCCT 60.304 57.895 0.00 0.00 37.47 4.58
2223 4071 3.551496 CTTGCTCAACCCGGCCTGA 62.551 63.158 0.00 0.00 0.00 3.86
2235 4083 3.843240 CTCGCGCCGAACTTGCTC 61.843 66.667 0.00 0.00 34.74 4.26
2278 4126 2.184830 CATGGCTGCCGATCACCAG 61.185 63.158 14.98 5.47 35.20 4.00
2281 4129 0.745845 AAGACATGGCTGCCGATCAC 60.746 55.000 14.98 4.50 0.00 3.06
2490 4340 5.228220 CGCTTTCACGTCAATTACACAAAAA 59.772 36.000 0.00 0.00 0.00 1.94
2522 4372 3.621715 GCCATTTCGAGGTAAACAGTAGG 59.378 47.826 0.00 0.00 0.00 3.18
2544 4394 1.854743 CGGATTACATGACTCGCTGTG 59.145 52.381 0.00 0.00 0.00 3.66
2570 4420 4.274069 CACGTATGCATGCATTTCTACAC 58.726 43.478 36.23 24.95 37.82 2.90
2572 4422 3.312421 ACCACGTATGCATGCATTTCTAC 59.688 43.478 36.23 25.97 37.82 2.59
2595 4474 5.296531 ACCCTTTCAAATAAACGTACGTGTT 59.703 36.000 23.57 18.94 0.00 3.32
2600 4479 5.645067 AGGCTACCCTTTCAAATAAACGTAC 59.355 40.000 0.00 0.00 38.74 3.67
2633 4519 5.464965 AATAAACAGTGAACGGATAAGCG 57.535 39.130 0.00 0.00 0.00 4.68
2651 4537 8.076714 TGTCAAAATAAAATGCGTGCAAATAA 57.923 26.923 0.00 0.00 0.00 1.40
2653 4539 6.536731 TGTCAAAATAAAATGCGTGCAAAT 57.463 29.167 0.00 0.00 0.00 2.32
2661 4547 5.307368 CACACGCATGTCAAAATAAAATGC 58.693 37.500 0.00 0.00 36.72 3.56
2662 4548 5.163972 CCCACACGCATGTCAAAATAAAATG 60.164 40.000 0.00 0.00 36.72 2.32
2665 4558 3.858877 GCCCACACGCATGTCAAAATAAA 60.859 43.478 0.00 0.00 36.72 1.40
2673 4566 1.915614 CTTCTGCCCACACGCATGTC 61.916 60.000 0.00 0.00 36.72 3.06
2678 4571 0.674895 ATCTTCTTCTGCCCACACGC 60.675 55.000 0.00 0.00 0.00 5.34
2722 4617 3.182572 GTCTGACAGATGACGTGTTCAAC 59.817 47.826 8.73 0.00 37.92 3.18
2760 4655 8.671384 TCATGAAGGTTAATCGGTTATTAAGG 57.329 34.615 0.00 0.00 40.02 2.69
2799 4694 7.697710 CGTGGATCAAGTTAATAACGTGTAGTA 59.302 37.037 16.27 0.93 40.92 1.82
2803 4698 4.092383 GCGTGGATCAAGTTAATAACGTGT 59.908 41.667 16.27 6.46 40.92 4.49
2804 4699 4.092237 TGCGTGGATCAAGTTAATAACGTG 59.908 41.667 11.86 11.86 41.38 4.49
2805 4700 4.247258 TGCGTGGATCAAGTTAATAACGT 58.753 39.130 0.00 0.00 36.23 3.99
2825 4720 8.535690 AGTAAGAGATACTGTGTTAAACTTGC 57.464 34.615 0.00 0.00 43.33 4.01
2857 4752 3.197265 GCATGCACAAAGTTTTCCTTGT 58.803 40.909 14.21 0.00 32.32 3.16
2879 4774 4.475444 TACTGCTCCTCCCCGGGG 62.475 72.222 35.80 35.80 35.81 5.73
2880 4775 3.155167 GTACTGCTCCTCCCCGGG 61.155 72.222 15.80 15.80 0.00 5.73
2952 4859 7.321153 TGAAGGATAAGTTTGCACTCTACTAC 58.679 38.462 0.00 0.00 30.45 2.73
2953 4860 7.476540 TGAAGGATAAGTTTGCACTCTACTA 57.523 36.000 0.00 0.00 30.45 1.82
2954 4861 6.360370 TGAAGGATAAGTTTGCACTCTACT 57.640 37.500 0.00 0.00 30.45 2.57
2982 4889 4.081917 TCAACGCGCATATATATTCCTCCA 60.082 41.667 5.73 0.00 0.00 3.86
2995 4902 0.454285 CGGAAATGTTCAACGCGCAT 60.454 50.000 5.73 0.00 0.00 4.73
2997 4904 0.179200 ATCGGAAATGTTCAACGCGC 60.179 50.000 5.73 0.00 0.00 6.86
2998 4905 2.241259 AATCGGAAATGTTCAACGCG 57.759 45.000 3.53 3.53 0.00 6.01
3014 4921 4.141459 CCTGGGGAGAGGTTAGGTTTAATC 60.141 50.000 0.00 0.00 0.00 1.75
3036 4943 2.369394 CCCTCCAACAGCTGTAAATCC 58.631 52.381 22.01 0.00 0.00 3.01
3096 5003 4.158579 CGGATCGGAGGAGATGAAATGATA 59.841 45.833 0.00 0.00 0.00 2.15
3097 5004 3.056250 CGGATCGGAGGAGATGAAATGAT 60.056 47.826 0.00 0.00 0.00 2.45
3107 5014 1.068194 GTATGCTTCGGATCGGAGGAG 60.068 57.143 15.38 7.03 36.04 3.69
3115 5022 3.627577 GTGTCCAATTGTATGCTTCGGAT 59.372 43.478 4.43 0.00 0.00 4.18
3116 5023 3.006940 GTGTCCAATTGTATGCTTCGGA 58.993 45.455 4.43 0.00 0.00 4.55
3117 5024 2.223021 CGTGTCCAATTGTATGCTTCGG 60.223 50.000 4.43 0.00 0.00 4.30
3118 5025 2.415168 ACGTGTCCAATTGTATGCTTCG 59.585 45.455 4.43 2.97 0.00 3.79
3119 5026 3.483574 CGACGTGTCCAATTGTATGCTTC 60.484 47.826 4.43 0.00 0.00 3.86
3120 5027 2.415168 CGACGTGTCCAATTGTATGCTT 59.585 45.455 4.43 0.00 0.00 3.91
3174 5083 2.697431 TTTGCACACGTAATCAAGGC 57.303 45.000 0.00 0.00 0.00 4.35
3220 5129 2.220615 TACTGACGTGCACATCCGGG 62.221 60.000 18.64 6.86 0.00 5.73
3319 5228 3.513680 TCATCATTTCATGCAAGTGGC 57.486 42.857 0.00 0.00 45.13 5.01
3332 5249 6.094603 GCCACAGAATAGTGTCTTTCATCATT 59.905 38.462 0.00 0.00 37.82 2.57
3333 5250 5.587844 GCCACAGAATAGTGTCTTTCATCAT 59.412 40.000 0.00 0.00 37.82 2.45
3334 5251 4.937620 GCCACAGAATAGTGTCTTTCATCA 59.062 41.667 0.00 0.00 37.82 3.07
3335 5252 5.064452 CAGCCACAGAATAGTGTCTTTCATC 59.936 44.000 0.00 0.00 37.82 2.92
3336 5253 4.940046 CAGCCACAGAATAGTGTCTTTCAT 59.060 41.667 0.00 0.00 37.82 2.57
3337 5254 4.040339 TCAGCCACAGAATAGTGTCTTTCA 59.960 41.667 0.00 0.00 37.82 2.69
3338 5255 4.390297 GTCAGCCACAGAATAGTGTCTTTC 59.610 45.833 0.00 0.00 37.82 2.62
3339 5256 4.319177 GTCAGCCACAGAATAGTGTCTTT 58.681 43.478 0.00 0.00 37.82 2.52
3371 5288 1.848388 TCACATCTCCATTGGCCAGAT 59.152 47.619 5.11 1.33 0.00 2.90


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

AutoCloner maintained by Alex Coulton.