Multiple sequence alignment - TraesCS4D01G109900

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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 TraesCS4D01G109900 chr4D 100.000 6510 0 0 1 6510 89426653 89433162 0.000000e+00 12022.0
1 TraesCS4D01G109900 chr4D 88.406 69 7 1 5725 5793 486932207 486932140 1.500000e-11 82.4
2 TraesCS4D01G109900 chr4A 98.177 2908 40 7 2922 5823 501969794 501972694 0.000000e+00 5064.0
3 TraesCS4D01G109900 chr4A 93.757 1682 60 18 73 1719 501966314 501967985 0.000000e+00 2483.0
4 TraesCS4D01G109900 chr4A 98.007 1204 20 4 1717 2918 501968534 501969735 0.000000e+00 2087.0
5 TraesCS4D01G109900 chr4A 87.166 561 23 16 5965 6510 501972837 501973363 5.620000e-165 592.0
6 TraesCS4D01G109900 chr4A 93.814 97 3 1 1 94 501966077 501966173 6.800000e-30 143.0
7 TraesCS4D01G109900 chr4B 95.842 2910 94 14 2921 5811 126333527 126336428 0.000000e+00 4678.0
8 TraesCS4D01G109900 chr4B 94.090 1726 59 13 18 1719 126327275 126328981 0.000000e+00 2582.0
9 TraesCS4D01G109900 chr4B 97.257 1203 26 6 1720 2921 126330379 126331575 0.000000e+00 2032.0
10 TraesCS4D01G109900 chr4B 79.677 310 15 19 6208 6510 126505463 126505731 5.190000e-41 180.0
11 TraesCS4D01G109900 chr5B 75.114 1318 271 45 3647 4935 221903919 221905208 1.230000e-156 564.0
12 TraesCS4D01G109900 chr5B 81.275 251 45 2 263 512 222367015 222367264 1.110000e-47 202.0
13 TraesCS4D01G109900 chr5B 83.886 211 31 3 2042 2251 221902012 221902220 1.430000e-46 198.0
14 TraesCS4D01G109900 chr5B 92.453 53 4 0 5725 5777 568404286 568404234 7.000000e-10 76.8
15 TraesCS4D01G109900 chr5D 74.639 1317 280 45 3647 4935 208510809 208512099 3.460000e-147 532.0
16 TraesCS4D01G109900 chr5D 85.000 200 28 2 2053 2251 208508991 208509189 1.110000e-47 202.0
17 TraesCS4D01G109900 chr5D 81.275 251 45 2 263 512 209309422 209309671 1.110000e-47 202.0
18 TraesCS4D01G109900 chr5D 79.592 98 17 3 5710 5807 255076534 255076440 4.210000e-07 67.6
19 TraesCS4D01G109900 chr5A 80.876 251 46 2 263 512 270177402 270177651 5.150000e-46 196.0
20 TraesCS4D01G109900 chr5A 83.495 206 33 1 2046 2251 269276275 269276479 2.400000e-44 191.0
21 TraesCS4D01G109900 chr5A 92.157 51 4 0 5725 5775 582384176 582384126 9.050000e-09 73.1
22 TraesCS4D01G109900 chr5A 79.592 98 17 3 5710 5807 338287883 338287789 4.210000e-07 67.6
23 TraesCS4D01G109900 chr1A 82.524 103 13 5 5706 5804 398461006 398460905 1.160000e-12 86.1
24 TraesCS4D01G109900 chr1D 81.553 103 13 6 5706 5804 317439610 317439510 5.410000e-11 80.5


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 TraesCS4D01G109900 chr4D 89426653 89433162 6509 False 12022.000000 12022 100.000000 1 6510 1 chr4D.!!$F1 6509
1 TraesCS4D01G109900 chr4A 501966077 501973363 7286 False 2073.800000 5064 94.184200 1 6510 5 chr4A.!!$F1 6509
2 TraesCS4D01G109900 chr4B 126327275 126336428 9153 False 3097.333333 4678 95.729667 18 5811 3 chr4B.!!$F2 5793
3 TraesCS4D01G109900 chr5B 221902012 221905208 3196 False 381.000000 564 79.500000 2042 4935 2 chr5B.!!$F2 2893
4 TraesCS4D01G109900 chr5D 208508991 208512099 3108 False 367.000000 532 79.819500 2053 4935 2 chr5D.!!$F2 2882

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
104 269 0.258774 ATCCCATAACACCCCACTGC 59.741 55.000 0.0 0.0 0.00 4.40 F
1151 1357 0.031178 GAATGGCGGCATGTGGATTC 59.969 55.000 26.5 14.8 0.00 2.52 F
1434 1641 0.462759 CCTCTTGGAGAACCATCCGC 60.463 60.000 0.0 0.0 46.34 5.54 F
1468 1676 0.670239 CCTTTTTCCCAACATGCGGC 60.670 55.000 0.0 0.0 0.00 6.53 F
1681 1889 0.966875 TTGCATGATCCTGTGTGGGC 60.967 55.000 0.0 0.0 36.20 5.36 F
1919 3620 2.018515 GTTCAGTTTTGGTCGTTCCCA 58.981 47.619 0.0 0.0 34.77 4.37 F
4694 8486 1.344065 TCCTTCCAAACAGACCGCTA 58.656 50.000 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1296 1503 0.109597 CCAGCAGTGAAATTCCGCAC 60.110 55.000 0.00 0.0 35.30 5.34 R
3134 6879 1.097232 TCAGCGCCATCCAAATCTTG 58.903 50.000 2.29 0.0 0.00 3.02 R
3453 7228 2.364324 AGTGAAAGTTGGTCGCTCACTA 59.636 45.455 4.23 0.0 43.69 2.74 R
4000 7782 4.839121 AGTGTTTCACTTACAGTTCCACA 58.161 39.130 0.00 0.0 42.59 4.17 R
4694 8486 6.154877 TGAATGGAAATTGATTAGCCACATGT 59.845 34.615 0.00 0.0 30.45 3.21 R
5422 9230 4.063967 TGTGCAGCCCTACCGACG 62.064 66.667 0.00 0.0 0.00 5.12 R
5869 9677 0.031010 AAAGAGGGAGGGAGGCGTAT 60.031 55.000 0.00 0.0 0.00 3.06 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
104 269 0.258774 ATCCCATAACACCCCACTGC 59.741 55.000 0.00 0.00 0.00 4.40
105 270 1.136961 TCCCATAACACCCCACTGCA 61.137 55.000 0.00 0.00 0.00 4.41
120 287 2.877786 CACTGCACAACTACATCCAACA 59.122 45.455 0.00 0.00 0.00 3.33
125 292 4.019771 TGCACAACTACATCCAACATAGGA 60.020 41.667 0.00 0.00 43.01 2.94
129 296 5.721960 ACAACTACATCCAACATAGGAGACT 59.278 40.000 0.00 0.00 41.90 3.24
153 320 4.036262 AGCAGCATAAAAACAGACGAACAA 59.964 37.500 0.00 0.00 0.00 2.83
207 374 3.915437 AACATTCCCAATTCGTGTGAC 57.085 42.857 0.00 0.00 0.00 3.67
233 400 3.154827 ACCCAAACAATGACAGTAGGG 57.845 47.619 0.00 0.00 39.22 3.53
775 966 2.565391 TCTGGTGTTGAGCCGAAAGATA 59.435 45.455 0.00 0.00 0.00 1.98
776 967 2.932614 CTGGTGTTGAGCCGAAAGATAG 59.067 50.000 0.00 0.00 0.00 2.08
777 968 2.565391 TGGTGTTGAGCCGAAAGATAGA 59.435 45.455 0.00 0.00 0.00 1.98
778 969 2.930682 GGTGTTGAGCCGAAAGATAGAC 59.069 50.000 0.00 0.00 0.00 2.59
779 970 3.585862 GTGTTGAGCCGAAAGATAGACA 58.414 45.455 0.00 0.00 0.00 3.41
780 971 3.614616 GTGTTGAGCCGAAAGATAGACAG 59.385 47.826 0.00 0.00 0.00 3.51
781 972 3.509967 TGTTGAGCCGAAAGATAGACAGA 59.490 43.478 0.00 0.00 0.00 3.41
782 973 3.784701 TGAGCCGAAAGATAGACAGAC 57.215 47.619 0.00 0.00 0.00 3.51
783 974 3.089284 TGAGCCGAAAGATAGACAGACA 58.911 45.455 0.00 0.00 0.00 3.41
784 975 3.701542 TGAGCCGAAAGATAGACAGACAT 59.298 43.478 0.00 0.00 0.00 3.06
1095 1301 0.040058 AAGGGCCATGTGCATCTTCA 59.960 50.000 6.18 0.00 43.89 3.02
1109 1315 3.875369 GCATCTTCACTCCTTCCATTGGT 60.875 47.826 1.86 0.00 0.00 3.67
1151 1357 0.031178 GAATGGCGGCATGTGGATTC 59.969 55.000 26.50 14.80 0.00 2.52
1191 1397 5.393243 GGGTAGATAGAGATACGATTGGCAC 60.393 48.000 0.00 0.00 0.00 5.01
1242 1448 2.632377 CTGTGACCATTTCTATGCGGT 58.368 47.619 0.00 0.00 0.00 5.68
1271 1478 6.726258 TTTGGAGAATACATATAGCATGCG 57.274 37.500 13.01 0.00 0.00 4.73
1284 1491 7.384387 ACATATAGCATGCGCATCATCTATTAG 59.616 37.037 27.21 22.98 42.27 1.73
1296 1503 8.862074 CGCATCATCTATTAGAGAAGATTTCTG 58.138 37.037 0.00 0.00 39.11 3.02
1420 1627 2.909006 TGCTCTTCTGTCCATTCCTCTT 59.091 45.455 0.00 0.00 0.00 2.85
1434 1641 0.462759 CCTCTTGGAGAACCATCCGC 60.463 60.000 0.00 0.00 46.34 5.54
1468 1676 0.670239 CCTTTTTCCCAACATGCGGC 60.670 55.000 0.00 0.00 0.00 6.53
1494 1702 8.375465 CCGCTGTGAAATTTGATTATTTCTTTC 58.625 33.333 0.00 0.00 42.39 2.62
1609 1817 3.770933 AGGGTAGCACAATACGAAGGTTA 59.229 43.478 0.00 0.00 0.00 2.85
1681 1889 0.966875 TTGCATGATCCTGTGTGGGC 60.967 55.000 0.00 0.00 36.20 5.36
1705 1921 6.183360 GCGGAAGTAAATGTCTAAATTCGTGA 60.183 38.462 0.00 0.00 0.00 4.35
1919 3620 2.018515 GTTCAGTTTTGGTCGTTCCCA 58.981 47.619 0.00 0.00 34.77 4.37
2373 4081 9.733556 TTATGTTGAAGTTTGAGCTCCTATTTA 57.266 29.630 12.15 0.00 0.00 1.40
2443 4151 3.575256 TGGATCTTGTTTTGCATGCTCTT 59.425 39.130 20.33 0.00 0.00 2.85
2840 4548 3.914426 ACCATATGTCCGCTTTCTTCT 57.086 42.857 1.24 0.00 0.00 2.85
3128 6873 5.011738 AGGATCAGTAATGGTATTGGTACGG 59.988 44.000 0.00 0.00 0.00 4.02
3134 6879 2.973694 TGGTATTGGTACGGCTCTTC 57.026 50.000 0.00 0.00 0.00 2.87
4000 7782 6.966534 AATGAAGGTCAGTCTTTGTTGATT 57.033 33.333 0.00 0.00 0.00 2.57
4001 7783 5.756195 TGAAGGTCAGTCTTTGTTGATTG 57.244 39.130 0.00 0.00 0.00 2.67
4658 8449 4.720649 TCAGAAGTGCACTATCAGGTAC 57.279 45.455 22.01 4.68 0.00 3.34
4668 8460 5.482526 TGCACTATCAGGTACTTTCAACCTA 59.517 40.000 0.00 0.00 45.78 3.08
4694 8486 1.344065 TCCTTCCAAACAGACCGCTA 58.656 50.000 0.00 0.00 0.00 4.26
4936 8738 3.981071 ACAAGCTCTGCAAGGTACATA 57.019 42.857 0.00 0.00 33.60 2.29
5422 9230 0.246910 GACGGGACCTCAACTCCTTC 59.753 60.000 0.00 0.00 0.00 3.46
5523 9331 2.644299 TCCTGTGATGAATGAGGGTGTT 59.356 45.455 0.00 0.00 0.00 3.32
5701 9509 0.033642 GGGACGCTTGGGATACTAGC 59.966 60.000 0.00 0.00 39.69 3.42
5702 9510 1.041437 GGACGCTTGGGATACTAGCT 58.959 55.000 0.00 0.00 40.52 3.32
5703 9511 2.236766 GGACGCTTGGGATACTAGCTA 58.763 52.381 0.00 0.00 40.52 3.32
5704 9512 2.826725 GGACGCTTGGGATACTAGCTAT 59.173 50.000 0.00 0.00 40.52 2.97
5723 9531 9.756571 CTAGCTATCTAATACTCCCTCCTTTTA 57.243 37.037 0.00 0.00 0.00 1.52
5829 9637 7.611770 TCTGGGATATAACCTATGATGTTTCG 58.388 38.462 0.00 0.00 0.00 3.46
5830 9638 6.170506 TGGGATATAACCTATGATGTTTCGC 58.829 40.000 0.00 0.00 0.00 4.70
5831 9639 5.585047 GGGATATAACCTATGATGTTTCGCC 59.415 44.000 0.00 0.00 0.00 5.54
5832 9640 5.585047 GGATATAACCTATGATGTTTCGCCC 59.415 44.000 0.00 0.00 0.00 6.13
5833 9641 2.052782 AACCTATGATGTTTCGCCCC 57.947 50.000 0.00 0.00 0.00 5.80
5834 9642 1.213296 ACCTATGATGTTTCGCCCCT 58.787 50.000 0.00 0.00 0.00 4.79
5835 9643 1.564348 ACCTATGATGTTTCGCCCCTT 59.436 47.619 0.00 0.00 0.00 3.95
5836 9644 1.949525 CCTATGATGTTTCGCCCCTTG 59.050 52.381 0.00 0.00 0.00 3.61
5837 9645 1.949525 CTATGATGTTTCGCCCCTTGG 59.050 52.381 0.00 0.00 0.00 3.61
5838 9646 0.331278 ATGATGTTTCGCCCCTTGGA 59.669 50.000 0.00 0.00 0.00 3.53
5839 9647 0.322456 TGATGTTTCGCCCCTTGGAG 60.322 55.000 0.00 0.00 0.00 3.86
5840 9648 0.322546 GATGTTTCGCCCCTTGGAGT 60.323 55.000 0.00 0.00 32.47 3.85
5841 9649 0.322546 ATGTTTCGCCCCTTGGAGTC 60.323 55.000 0.00 0.00 32.47 3.36
5842 9650 1.072505 GTTTCGCCCCTTGGAGTCA 59.927 57.895 0.00 0.00 32.47 3.41
5843 9651 0.955919 GTTTCGCCCCTTGGAGTCAG 60.956 60.000 0.00 0.00 32.47 3.51
5844 9652 2.124507 TTTCGCCCCTTGGAGTCAGG 62.125 60.000 0.00 0.00 32.47 3.86
5845 9653 3.322466 CGCCCCTTGGAGTCAGGT 61.322 66.667 0.00 0.00 0.00 4.00
5846 9654 1.987855 CGCCCCTTGGAGTCAGGTA 60.988 63.158 0.00 0.00 0.00 3.08
5847 9655 1.908483 GCCCCTTGGAGTCAGGTAG 59.092 63.158 0.00 0.00 0.00 3.18
5848 9656 1.627297 GCCCCTTGGAGTCAGGTAGG 61.627 65.000 0.00 0.00 0.00 3.18
5849 9657 0.042731 CCCCTTGGAGTCAGGTAGGA 59.957 60.000 0.00 0.00 0.00 2.94
5850 9658 1.490574 CCCTTGGAGTCAGGTAGGAG 58.509 60.000 0.00 0.00 0.00 3.69
5851 9659 1.273324 CCCTTGGAGTCAGGTAGGAGT 60.273 57.143 0.00 0.00 0.00 3.85
5852 9660 2.024273 CCCTTGGAGTCAGGTAGGAGTA 60.024 54.545 0.00 0.00 0.00 2.59
5853 9661 3.292460 CCTTGGAGTCAGGTAGGAGTAG 58.708 54.545 0.00 0.00 0.00 2.57
5854 9662 3.309265 CCTTGGAGTCAGGTAGGAGTAGT 60.309 52.174 0.00 0.00 0.00 2.73
5855 9663 3.367646 TGGAGTCAGGTAGGAGTAGTG 57.632 52.381 0.00 0.00 0.00 2.74
5856 9664 2.025226 TGGAGTCAGGTAGGAGTAGTGG 60.025 54.545 0.00 0.00 0.00 4.00
5857 9665 2.657143 GAGTCAGGTAGGAGTAGTGGG 58.343 57.143 0.00 0.00 0.00 4.61
5858 9666 2.001558 AGTCAGGTAGGAGTAGTGGGT 58.998 52.381 0.00 0.00 0.00 4.51
5859 9667 3.196300 AGTCAGGTAGGAGTAGTGGGTA 58.804 50.000 0.00 0.00 0.00 3.69
5860 9668 3.595138 AGTCAGGTAGGAGTAGTGGGTAA 59.405 47.826 0.00 0.00 0.00 2.85
5861 9669 4.045079 AGTCAGGTAGGAGTAGTGGGTAAA 59.955 45.833 0.00 0.00 0.00 2.01
5862 9670 4.774200 GTCAGGTAGGAGTAGTGGGTAAAA 59.226 45.833 0.00 0.00 0.00 1.52
5863 9671 5.246883 GTCAGGTAGGAGTAGTGGGTAAAAA 59.753 44.000 0.00 0.00 0.00 1.94
5883 9691 4.838904 AAATTATATACGCCTCCCTCCC 57.161 45.455 0.00 0.00 0.00 4.30
5884 9692 3.778622 ATTATATACGCCTCCCTCCCT 57.221 47.619 0.00 0.00 0.00 4.20
5885 9693 2.822707 TATATACGCCTCCCTCCCTC 57.177 55.000 0.00 0.00 0.00 4.30
5886 9694 1.085715 ATATACGCCTCCCTCCCTCT 58.914 55.000 0.00 0.00 0.00 3.69
5887 9695 0.858369 TATACGCCTCCCTCCCTCTT 59.142 55.000 0.00 0.00 0.00 2.85
5888 9696 0.031010 ATACGCCTCCCTCCCTCTTT 60.031 55.000 0.00 0.00 0.00 2.52
5889 9697 0.632835 TACGCCTCCCTCCCTCTTTA 59.367 55.000 0.00 0.00 0.00 1.85
5890 9698 0.252558 ACGCCTCCCTCCCTCTTTAA 60.253 55.000 0.00 0.00 0.00 1.52
5891 9699 1.132500 CGCCTCCCTCCCTCTTTAAT 58.868 55.000 0.00 0.00 0.00 1.40
5892 9700 1.202698 CGCCTCCCTCCCTCTTTAATG 60.203 57.143 0.00 0.00 0.00 1.90
5893 9701 2.127708 GCCTCCCTCCCTCTTTAATGA 58.872 52.381 0.00 0.00 0.00 2.57
5894 9702 2.105649 GCCTCCCTCCCTCTTTAATGAG 59.894 54.545 10.66 10.66 0.00 2.90
5895 9703 3.658725 CCTCCCTCCCTCTTTAATGAGA 58.341 50.000 17.60 0.00 36.23 3.27
5896 9704 3.645687 CCTCCCTCCCTCTTTAATGAGAG 59.354 52.174 17.60 8.30 42.26 3.20
5897 9705 4.551671 CTCCCTCCCTCTTTAATGAGAGA 58.448 47.826 17.60 10.38 44.78 3.10
5898 9706 5.154418 CTCCCTCCCTCTTTAATGAGAGAT 58.846 45.833 17.60 0.00 44.78 2.75
5899 9707 4.904251 TCCCTCCCTCTTTAATGAGAGATG 59.096 45.833 17.60 8.52 44.78 2.90
5900 9708 4.657969 CCCTCCCTCTTTAATGAGAGATGT 59.342 45.833 17.60 0.00 44.78 3.06
5901 9709 5.454471 CCCTCCCTCTTTAATGAGAGATGTG 60.454 48.000 17.60 4.38 44.78 3.21
5902 9710 5.454471 CCTCCCTCTTTAATGAGAGATGTGG 60.454 48.000 17.60 10.18 44.78 4.17
5903 9711 5.280499 TCCCTCTTTAATGAGAGATGTGGA 58.720 41.667 17.60 11.95 44.78 4.02
5904 9712 5.726308 TCCCTCTTTAATGAGAGATGTGGAA 59.274 40.000 17.60 0.85 44.78 3.53
5905 9713 6.215431 TCCCTCTTTAATGAGAGATGTGGAAA 59.785 38.462 17.60 0.00 44.78 3.13
5906 9714 6.886459 CCCTCTTTAATGAGAGATGTGGAAAA 59.114 38.462 17.60 0.00 44.78 2.29
5907 9715 7.394359 CCCTCTTTAATGAGAGATGTGGAAAAA 59.606 37.037 17.60 0.00 44.78 1.94
5945 9784 4.082125 CCCTATGGGTATCTGATTTTGCC 58.918 47.826 0.00 0.00 38.25 4.52
5946 9785 4.082125 CCTATGGGTATCTGATTTTGCCC 58.918 47.826 0.00 4.16 36.73 5.36
5947 9786 2.452600 TGGGTATCTGATTTTGCCCC 57.547 50.000 13.13 8.49 35.39 5.80
5948 9787 1.063266 TGGGTATCTGATTTTGCCCCC 60.063 52.381 13.13 0.00 35.39 5.40
5949 9788 1.217942 GGGTATCTGATTTTGCCCCCT 59.782 52.381 0.00 0.00 0.00 4.79
5950 9789 2.359249 GGGTATCTGATTTTGCCCCCTT 60.359 50.000 0.00 0.00 0.00 3.95
5951 9790 3.374764 GGTATCTGATTTTGCCCCCTTT 58.625 45.455 0.00 0.00 0.00 3.11
5952 9791 3.774766 GGTATCTGATTTTGCCCCCTTTT 59.225 43.478 0.00 0.00 0.00 2.27
5953 9792 4.225042 GGTATCTGATTTTGCCCCCTTTTT 59.775 41.667 0.00 0.00 0.00 1.94
6044 9883 4.402474 ACCCTTGTTCAGTTTTCCAAAGAG 59.598 41.667 0.00 0.00 0.00 2.85
6140 9992 4.660938 GTCCAGCCCGGCCTGTTT 62.661 66.667 12.10 0.00 33.14 2.83
6199 10053 1.177401 GCCTGTGTTTGATTCCCTCC 58.823 55.000 0.00 0.00 0.00 4.30
6272 10126 3.767230 CGCCTGAGTGACGCAACG 61.767 66.667 0.00 0.00 0.00 4.10
6319 10173 4.314440 GGCCACCGTCACAGCTCA 62.314 66.667 0.00 0.00 0.00 4.26
6328 10182 1.802508 CGTCACAGCTCACTCACACAA 60.803 52.381 0.00 0.00 0.00 3.33
6338 10192 0.392863 ACTCACACAACAGCACAGCA 60.393 50.000 0.00 0.00 0.00 4.41
6339 10193 0.306840 CTCACACAACAGCACAGCAG 59.693 55.000 0.00 0.00 0.00 4.24
6340 10194 1.298863 CACACAACAGCACAGCAGC 60.299 57.895 0.00 0.00 0.00 5.25
6341 10195 1.750018 ACACAACAGCACAGCAGCA 60.750 52.632 0.00 0.00 36.85 4.41
6342 10196 1.008881 CACAACAGCACAGCAGCAG 60.009 57.895 0.00 0.00 36.85 4.24
6379 10233 1.594021 AGCACGCATCGTTCACACA 60.594 52.632 0.00 0.00 38.32 3.72
6386 10240 1.594518 GCATCGTTCACACACACACAC 60.595 52.381 0.00 0.00 0.00 3.82
6387 10241 1.663135 CATCGTTCACACACACACACA 59.337 47.619 0.00 0.00 0.00 3.72
6388 10242 1.072391 TCGTTCACACACACACACAC 58.928 50.000 0.00 0.00 0.00 3.82
6389 10243 0.793250 CGTTCACACACACACACACA 59.207 50.000 0.00 0.00 0.00 3.72
6390 10244 1.463363 CGTTCACACACACACACACAC 60.463 52.381 0.00 0.00 0.00 3.82
6391 10245 1.533299 GTTCACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
6392 10246 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
6393 10247 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6394 10248 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6395 10249 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6396 10250 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6397 10251 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6398 10252 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6399 10253 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6400 10254 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6401 10255 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6402 10256 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6403 10257 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6404 10258 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6405 10259 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6406 10260 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6407 10261 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
6408 10262 1.136000 CACACACACACACACACACTG 60.136 52.381 0.00 0.00 0.00 3.66
6409 10263 0.179192 CACACACACACACACACTGC 60.179 55.000 0.00 0.00 0.00 4.40
6426 10280 2.688666 CCTGCACAGGGCCTCCTA 60.689 66.667 0.95 0.00 44.87 2.94
6427 10281 2.586792 CTGCACAGGGCCTCCTAC 59.413 66.667 0.95 0.00 42.67 3.18
6428 10282 1.992277 CTGCACAGGGCCTCCTACT 60.992 63.158 0.95 0.00 42.67 2.57
6430 10284 2.736826 GCACAGGGCCTCCTACTCC 61.737 68.421 0.95 0.00 42.67 3.85
6431 10285 1.002274 CACAGGGCCTCCTACTCCT 59.998 63.158 0.95 0.00 42.67 3.69
6432 10286 0.261991 CACAGGGCCTCCTACTCCTA 59.738 60.000 0.95 0.00 42.67 2.94
6433 10287 0.558712 ACAGGGCCTCCTACTCCTAG 59.441 60.000 0.95 0.00 42.67 3.02
6434 10288 0.558712 CAGGGCCTCCTACTCCTAGT 59.441 60.000 0.95 0.00 42.67 2.57
6435 10289 1.781529 CAGGGCCTCCTACTCCTAGTA 59.218 57.143 0.95 0.00 42.67 1.82
6436 10290 1.782140 AGGGCCTCCTACTCCTAGTAC 59.218 57.143 0.00 0.00 42.75 2.73
6437 10291 1.782140 GGGCCTCCTACTCCTAGTACT 59.218 57.143 0.84 0.00 0.00 2.73
6438 10292 2.985311 GGGCCTCCTACTCCTAGTACTA 59.015 54.545 0.84 1.89 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.561184 ATGATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
68 73 5.815233 TGGGATTGGAAATTTGCTACAAA 57.185 34.783 11.22 0.00 0.00 2.83
104 269 5.812642 GTCTCCTATGTTGGATGTAGTTGTG 59.187 44.000 0.00 0.00 35.30 3.33
105 270 5.721960 AGTCTCCTATGTTGGATGTAGTTGT 59.278 40.000 0.00 0.00 35.30 3.32
120 287 6.889198 TGTTTTTATGCTGCTAGTCTCCTAT 58.111 36.000 0.00 0.00 0.00 2.57
125 292 4.627467 CGTCTGTTTTTATGCTGCTAGTCT 59.373 41.667 0.00 0.00 0.00 3.24
129 296 4.752604 TGTTCGTCTGTTTTTATGCTGCTA 59.247 37.500 0.00 0.00 0.00 3.49
131 298 3.884169 TGTTCGTCTGTTTTTATGCTGC 58.116 40.909 0.00 0.00 0.00 5.25
153 320 2.100916 GCCTCAGAATGCATTGCAGAAT 59.899 45.455 18.59 5.81 43.65 2.40
207 374 5.009854 ACTGTCATTGTTTGGGTTTTCTG 57.990 39.130 0.00 0.00 0.00 3.02
233 400 2.369394 CAGCCACCATTTCCTTACTCC 58.631 52.381 0.00 0.00 0.00 3.85
775 966 1.701847 ACTTTGAGCCCATGTCTGTCT 59.298 47.619 0.00 0.00 0.00 3.41
776 967 1.808945 CACTTTGAGCCCATGTCTGTC 59.191 52.381 0.00 0.00 0.00 3.51
777 968 1.546323 CCACTTTGAGCCCATGTCTGT 60.546 52.381 0.00 0.00 0.00 3.41
778 969 1.171308 CCACTTTGAGCCCATGTCTG 58.829 55.000 0.00 0.00 0.00 3.51
779 970 0.610232 GCCACTTTGAGCCCATGTCT 60.610 55.000 0.00 0.00 0.00 3.41
780 971 1.598701 GGCCACTTTGAGCCCATGTC 61.599 60.000 0.00 0.00 43.76 3.06
781 972 1.607467 GGCCACTTTGAGCCCATGT 60.607 57.895 0.00 0.00 43.76 3.21
782 973 3.291611 GGCCACTTTGAGCCCATG 58.708 61.111 0.00 0.00 43.76 3.66
1095 1301 0.329596 GGAGCACCAATGGAAGGAGT 59.670 55.000 6.16 0.00 35.97 3.85
1109 1315 6.064060 TCAAGAATCAAGAAAAGAAGGAGCA 58.936 36.000 0.00 0.00 0.00 4.26
1151 1357 2.422231 CCCGACAGAGGCTCAGGAG 61.422 68.421 18.26 7.07 0.00 3.69
1191 1397 4.201851 ACATTCATCTGAAGGAAAATCGCG 60.202 41.667 11.17 0.00 37.99 5.87
1251 1458 4.183865 TGCGCATGCTATATGTATTCTCC 58.816 43.478 17.13 0.00 43.34 3.71
1271 1478 9.709495 ACAGAAATCTTCTCTAATAGATGATGC 57.291 33.333 4.69 2.05 44.34 3.91
1284 1491 4.954092 AATTCCGCACAGAAATCTTCTC 57.046 40.909 0.00 0.00 38.11 2.87
1296 1503 0.109597 CCAGCAGTGAAATTCCGCAC 60.110 55.000 0.00 0.00 35.30 5.34
1401 1608 3.517100 TCCAAGAGGAATGGACAGAAGAG 59.483 47.826 0.00 0.00 41.98 2.85
1434 1641 1.463553 AAAGGGGCGGAAGTTTGCAG 61.464 55.000 3.82 0.00 0.00 4.41
1468 1676 7.816945 AAGAAATAATCAAATTTCACAGCGG 57.183 32.000 10.86 0.00 44.70 5.52
1494 1702 3.418619 CACGCAGACACAAGAAAATTTCG 59.581 43.478 0.00 0.00 34.02 3.46
1502 1710 1.441311 TCTGCACGCAGACACAAGA 59.559 52.632 17.54 0.00 46.80 3.02
1586 1794 2.570302 ACCTTCGTATTGTGCTACCCTT 59.430 45.455 0.00 0.00 0.00 3.95
1609 1817 1.410004 CAAGCCATGGGAGATGCAAT 58.590 50.000 15.13 0.00 0.00 3.56
1681 1889 7.285783 TCACGAATTTAGACATTTACTTCCG 57.714 36.000 0.00 0.00 0.00 4.30
1919 3620 1.341852 TCATTGCAGCACAACAAGCAT 59.658 42.857 0.00 0.00 42.27 3.79
2443 4151 4.644234 ACTCCACAATGAACAAACATGTCA 59.356 37.500 0.00 0.00 0.00 3.58
3128 6873 2.223433 CGCCATCCAAATCTTGAAGAGC 60.223 50.000 0.00 0.00 0.00 4.09
3134 6879 1.097232 TCAGCGCCATCCAAATCTTG 58.903 50.000 2.29 0.00 0.00 3.02
3453 7228 2.364324 AGTGAAAGTTGGTCGCTCACTA 59.636 45.455 4.23 0.00 43.69 2.74
4000 7782 4.839121 AGTGTTTCACTTACAGTTCCACA 58.161 39.130 0.00 0.00 42.59 4.17
4694 8486 6.154877 TGAATGGAAATTGATTAGCCACATGT 59.845 34.615 0.00 0.00 30.45 3.21
5422 9230 4.063967 TGTGCAGCCCTACCGACG 62.064 66.667 0.00 0.00 0.00 5.12
5523 9331 1.077930 CTCGTCCCCAGTCTACGGA 60.078 63.158 0.00 0.00 37.24 4.69
5699 9507 9.448587 TTTAAAAGGAGGGAGTATTAGATAGCT 57.551 33.333 0.00 0.00 0.00 3.32
5817 9625 1.949525 CCAAGGGGCGAAACATCATAG 59.050 52.381 0.00 0.00 0.00 2.23
5823 9631 1.072505 GACTCCAAGGGGCGAAACA 59.927 57.895 0.00 0.00 0.00 2.83
5824 9632 0.955919 CTGACTCCAAGGGGCGAAAC 60.956 60.000 0.00 0.00 0.00 2.78
5825 9633 1.374947 CTGACTCCAAGGGGCGAAA 59.625 57.895 0.00 0.00 0.00 3.46
5826 9634 2.592993 CCTGACTCCAAGGGGCGAA 61.593 63.158 0.00 0.00 0.00 4.70
5827 9635 2.449967 TACCTGACTCCAAGGGGCGA 62.450 60.000 0.00 0.00 0.00 5.54
5828 9636 1.961180 CTACCTGACTCCAAGGGGCG 61.961 65.000 0.00 0.00 0.00 6.13
5829 9637 1.627297 CCTACCTGACTCCAAGGGGC 61.627 65.000 0.00 0.00 0.00 5.80
5830 9638 0.042731 TCCTACCTGACTCCAAGGGG 59.957 60.000 0.00 0.00 0.00 4.79
5831 9639 1.273324 ACTCCTACCTGACTCCAAGGG 60.273 57.143 0.00 0.00 0.00 3.95
5832 9640 2.239681 ACTCCTACCTGACTCCAAGG 57.760 55.000 0.00 0.00 0.00 3.61
5833 9641 3.697045 CACTACTCCTACCTGACTCCAAG 59.303 52.174 0.00 0.00 0.00 3.61
5834 9642 3.563697 CCACTACTCCTACCTGACTCCAA 60.564 52.174 0.00 0.00 0.00 3.53
5835 9643 2.025226 CCACTACTCCTACCTGACTCCA 60.025 54.545 0.00 0.00 0.00 3.86
5836 9644 2.657143 CCACTACTCCTACCTGACTCC 58.343 57.143 0.00 0.00 0.00 3.85
5837 9645 2.025131 ACCCACTACTCCTACCTGACTC 60.025 54.545 0.00 0.00 0.00 3.36
5838 9646 2.001558 ACCCACTACTCCTACCTGACT 58.998 52.381 0.00 0.00 0.00 3.41
5839 9647 2.528673 ACCCACTACTCCTACCTGAC 57.471 55.000 0.00 0.00 0.00 3.51
5840 9648 4.680278 TTTACCCACTACTCCTACCTGA 57.320 45.455 0.00 0.00 0.00 3.86
5841 9649 5.750352 TTTTTACCCACTACTCCTACCTG 57.250 43.478 0.00 0.00 0.00 4.00
5860 9668 5.312443 AGGGAGGGAGGCGTATATAATTTTT 59.688 40.000 0.00 0.00 0.00 1.94
5861 9669 4.850386 AGGGAGGGAGGCGTATATAATTTT 59.150 41.667 0.00 0.00 0.00 1.82
5862 9670 4.436079 AGGGAGGGAGGCGTATATAATTT 58.564 43.478 0.00 0.00 0.00 1.82
5863 9671 4.031611 GAGGGAGGGAGGCGTATATAATT 58.968 47.826 0.00 0.00 0.00 1.40
5864 9672 3.272551 AGAGGGAGGGAGGCGTATATAAT 59.727 47.826 0.00 0.00 0.00 1.28
5865 9673 2.653366 AGAGGGAGGGAGGCGTATATAA 59.347 50.000 0.00 0.00 0.00 0.98
5866 9674 2.285707 AGAGGGAGGGAGGCGTATATA 58.714 52.381 0.00 0.00 0.00 0.86
5867 9675 1.085715 AGAGGGAGGGAGGCGTATAT 58.914 55.000 0.00 0.00 0.00 0.86
5868 9676 0.858369 AAGAGGGAGGGAGGCGTATA 59.142 55.000 0.00 0.00 0.00 1.47
5869 9677 0.031010 AAAGAGGGAGGGAGGCGTAT 60.031 55.000 0.00 0.00 0.00 3.06
5870 9678 0.632835 TAAAGAGGGAGGGAGGCGTA 59.367 55.000 0.00 0.00 0.00 4.42
5871 9679 0.252558 TTAAAGAGGGAGGGAGGCGT 60.253 55.000 0.00 0.00 0.00 5.68
5872 9680 1.132500 ATTAAAGAGGGAGGGAGGCG 58.868 55.000 0.00 0.00 0.00 5.52
5873 9681 2.105649 CTCATTAAAGAGGGAGGGAGGC 59.894 54.545 0.00 0.00 31.94 4.70
5874 9682 3.645687 CTCTCATTAAAGAGGGAGGGAGG 59.354 52.174 1.12 0.00 38.43 4.30
5875 9683 4.551671 TCTCTCATTAAAGAGGGAGGGAG 58.448 47.826 6.18 0.00 40.14 4.30
5876 9684 4.626942 TCTCTCATTAAAGAGGGAGGGA 57.373 45.455 6.18 0.00 40.14 4.20
5881 9689 5.620738 TCCACATCTCTCATTAAAGAGGG 57.379 43.478 7.80 4.56 42.58 4.30
5882 9690 7.928307 TTTTCCACATCTCTCATTAAAGAGG 57.072 36.000 7.80 0.00 42.58 3.69
5951 9790 6.091986 GGGCAAAATCAGATTATTCGCAAAAA 59.908 34.615 0.00 0.00 0.00 1.94
5952 9791 5.580297 GGGCAAAATCAGATTATTCGCAAAA 59.420 36.000 0.00 0.00 0.00 2.44
5953 9792 5.108517 GGGCAAAATCAGATTATTCGCAAA 58.891 37.500 0.00 0.00 0.00 3.68
5954 9793 4.441356 GGGGCAAAATCAGATTATTCGCAA 60.441 41.667 0.00 0.00 0.00 4.85
5955 9794 3.068024 GGGGCAAAATCAGATTATTCGCA 59.932 43.478 0.00 0.00 0.00 5.10
5956 9795 3.319122 AGGGGCAAAATCAGATTATTCGC 59.681 43.478 0.00 0.00 0.00 4.70
5957 9796 5.284079 CAAGGGGCAAAATCAGATTATTCG 58.716 41.667 0.00 0.00 0.00 3.34
5958 9797 5.129320 ACCAAGGGGCAAAATCAGATTATTC 59.871 40.000 0.00 0.00 37.90 1.75
5959 9798 5.032170 ACCAAGGGGCAAAATCAGATTATT 58.968 37.500 0.00 0.00 37.90 1.40
5960 9799 4.623863 ACCAAGGGGCAAAATCAGATTAT 58.376 39.130 0.00 0.00 37.90 1.28
5961 9800 4.023291 GACCAAGGGGCAAAATCAGATTA 58.977 43.478 0.00 0.00 37.90 1.75
5962 9801 2.833943 GACCAAGGGGCAAAATCAGATT 59.166 45.455 0.00 0.00 37.90 2.40
5963 9802 2.043526 AGACCAAGGGGCAAAATCAGAT 59.956 45.455 0.00 0.00 37.90 2.90
5992 9831 7.966246 TGAATGGAATTTCCTTTTTGTCATG 57.034 32.000 16.25 0.00 36.07 3.07
5996 9835 8.839343 GTTCAATGAATGGAATTTCCTTTTTGT 58.161 29.630 16.25 4.56 36.07 2.83
6001 9840 5.786975 AGGGTTCAATGAATGGAATTTCCTT 59.213 36.000 16.25 7.47 36.07 3.36
6002 9841 5.344566 AGGGTTCAATGAATGGAATTTCCT 58.655 37.500 16.25 0.00 36.07 3.36
6079 9918 2.295909 GTGGTCTAGAGCAGCCTGATAG 59.704 54.545 24.43 0.00 39.74 2.08
6140 9992 2.653726 TCTTGTTCTTCCTTGCAGCAA 58.346 42.857 7.81 7.81 0.00 3.91
6156 10008 3.281341 TGTGCGCTGGTATTTTTCTTG 57.719 42.857 9.73 0.00 0.00 3.02
6182 10034 4.935352 TTTTGGAGGGAATCAAACACAG 57.065 40.909 0.00 0.00 33.29 3.66
6207 10061 0.601046 CCTGTCAGACACACGCACAT 60.601 55.000 0.00 0.00 0.00 3.21
6208 10062 1.227234 CCTGTCAGACACACGCACA 60.227 57.895 0.00 0.00 0.00 4.57
6209 10063 1.227263 ACCTGTCAGACACACGCAC 60.227 57.895 0.00 0.00 0.00 5.34
6210 10064 1.227234 CACCTGTCAGACACACGCA 60.227 57.895 0.00 0.00 0.00 5.24
6211 10065 1.956170 CCACCTGTCAGACACACGC 60.956 63.158 0.00 0.00 0.00 5.34
6213 10067 1.338200 GGATCCACCTGTCAGACACAC 60.338 57.143 6.95 0.00 35.41 3.82
6272 10126 1.824230 TGCATATTGCTGGGTTTCACC 59.176 47.619 0.75 0.00 45.31 4.02
6317 10171 1.655484 CTGTGCTGTTGTGTGAGTGA 58.345 50.000 0.00 0.00 0.00 3.41
6319 10173 0.392863 TGCTGTGCTGTTGTGTGAGT 60.393 50.000 0.00 0.00 0.00 3.41
6328 10182 2.668889 GCTCTGCTGCTGTGCTGT 60.669 61.111 21.21 0.00 34.27 4.40
6339 10193 3.677284 TAGCTGCTGCCTGCTCTGC 62.677 63.158 18.02 2.60 43.97 4.26
6340 10194 1.521906 CTAGCTGCTGCCTGCTCTG 60.522 63.158 18.02 10.45 43.97 3.35
6341 10195 2.901813 CTAGCTGCTGCCTGCTCT 59.098 61.111 18.02 2.05 43.97 4.09
6342 10196 2.896359 GCTAGCTGCTGCCTGCTC 60.896 66.667 18.02 4.59 43.97 4.26
6356 10210 1.809619 GAACGATGCGTGCTGGCTA 60.810 57.895 0.00 0.00 39.99 3.93
6365 10219 0.383002 GTGTGTGTGTGAACGATGCG 60.383 55.000 0.00 0.00 0.00 4.73
6366 10220 0.655208 TGTGTGTGTGTGAACGATGC 59.345 50.000 0.00 0.00 0.00 3.91
6371 10225 1.533299 TGTGTGTGTGTGTGTGTGAAC 59.467 47.619 0.00 0.00 0.00 3.18
6379 10233 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6386 10240 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6387 10241 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6388 10242 1.136000 CAGTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
6389 10243 1.155889 CAGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
6390 10244 0.179192 GCAGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
6391 10245 1.305219 GGCAGTGTGTGTGTGTGTGT 61.305 55.000 0.00 0.00 0.00 3.72
6392 10246 1.026182 AGGCAGTGTGTGTGTGTGTG 61.026 55.000 0.00 0.00 0.00 3.82
6393 10247 1.026182 CAGGCAGTGTGTGTGTGTGT 61.026 55.000 0.00 0.00 0.00 3.72
6394 10248 1.723273 CAGGCAGTGTGTGTGTGTG 59.277 57.895 0.00 0.00 0.00 3.82
6395 10249 2.114670 GCAGGCAGTGTGTGTGTGT 61.115 57.895 0.00 0.00 0.00 3.72
6396 10250 2.114051 TGCAGGCAGTGTGTGTGTG 61.114 57.895 0.00 0.00 0.00 3.82
6397 10251 2.114670 GTGCAGGCAGTGTGTGTGT 61.115 57.895 0.00 0.00 0.00 3.72
6398 10252 2.055310 CTGTGCAGGCAGTGTGTGTG 62.055 60.000 0.00 0.00 0.00 3.82
6399 10253 1.820906 CTGTGCAGGCAGTGTGTGT 60.821 57.895 0.00 0.00 0.00 3.72
6400 10254 2.549198 CCTGTGCAGGCAGTGTGTG 61.549 63.158 5.19 0.00 42.44 3.82
6401 10255 2.203252 CCTGTGCAGGCAGTGTGT 60.203 61.111 5.19 0.00 42.44 3.72
6434 10288 7.503549 TCATCATCGGTCAAGTACTAGTAGTA 58.496 38.462 10.68 5.90 0.00 1.82
6435 10289 6.354938 TCATCATCGGTCAAGTACTAGTAGT 58.645 40.000 8.14 8.14 0.00 2.73
6436 10290 6.862711 TCATCATCGGTCAAGTACTAGTAG 57.137 41.667 1.87 0.00 0.00 2.57
6437 10291 6.294010 GCATCATCATCGGTCAAGTACTAGTA 60.294 42.308 0.00 0.00 0.00 1.82
6438 10292 5.508153 GCATCATCATCGGTCAAGTACTAGT 60.508 44.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.