Multiple sequence alignment - TraesCS5D01G320600

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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 TraesCS5D01G320600 chr5D 100.000 7511 0 0 1 7511 412745058 412737548 0.000000e+00 13871
1 TraesCS5D01G320600 chr5A 92.512 7292 296 118 1 7133 524913377 524906177 0.000000e+00 10211
2 TraesCS5D01G320600 chr5A 84.434 212 6 7 7300 7511 524905372 524905188 4.630000e-42 183
3 TraesCS5D01G320600 chr5B 92.587 5490 186 96 1 5346 497220542 497215130 0.000000e+00 7679
4 TraesCS5D01G320600 chr5B 92.857 1526 57 21 5581 7084 497214884 497213389 0.000000e+00 2167
5 TraesCS5D01G320600 chr5B 95.833 240 8 2 5330 5567 497215109 497214870 3.290000e-103 387
6 TraesCS5D01G320600 chr5B 87.500 256 17 8 7152 7399 497213116 497212868 1.600000e-71 281
7 TraesCS5D01G320600 chr5B 91.667 120 6 1 7396 7511 497212835 497212716 6.030000e-36 163
8 TraesCS5D01G320600 chr7B 90.776 1507 99 20 1018 2513 323761216 323762693 0.000000e+00 1977
9 TraesCS5D01G320600 chr7B 89.983 579 54 2 2506 3084 323817001 323817575 0.000000e+00 745
10 TraesCS5D01G320600 chr2A 91.398 1023 61 13 1018 2028 160935341 160936348 0.000000e+00 1376
11 TraesCS5D01G320600 chr2A 86.349 608 54 11 2177 2784 161051203 161051781 2.960000e-178 636
12 TraesCS5D01G320600 chr2A 91.582 297 22 1 2777 3073 161060538 161060831 2.520000e-109 407
13 TraesCS5D01G320600 chr2A 93.038 158 11 0 2025 2182 161031312 161031469 1.630000e-56 231
14 TraesCS5D01G320600 chr2A 90.110 91 2 4 5107 5197 756499553 756499636 2.220000e-20 111
15 TraesCS5D01G320600 chr6A 83.128 243 41 0 1885 2127 474333362 474333120 9.810000e-54 222
16 TraesCS5D01G320600 chr6A 91.892 74 6 0 1480 1553 474333727 474333654 3.710000e-18 104
17 TraesCS5D01G320600 chr6D 93.243 74 5 0 1480 1553 335068289 335068216 7.970000e-20 110
18 TraesCS5D01G320600 chr6B 87.629 97 8 4 1459 1553 485537472 485537566 7.970000e-20 110


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 TraesCS5D01G320600 chr5D 412737548 412745058 7510 True 13871.0 13871 100.0000 1 7511 1 chr5D.!!$R1 7510
1 TraesCS5D01G320600 chr5A 524905188 524913377 8189 True 5197.0 10211 88.4730 1 7511 2 chr5A.!!$R1 7510
2 TraesCS5D01G320600 chr5B 497212716 497220542 7826 True 2135.4 7679 92.0888 1 7511 5 chr5B.!!$R1 7510
3 TraesCS5D01G320600 chr7B 323761216 323762693 1477 False 1977.0 1977 90.7760 1018 2513 1 chr7B.!!$F1 1495
4 TraesCS5D01G320600 chr7B 323817001 323817575 574 False 745.0 745 89.9830 2506 3084 1 chr7B.!!$F2 578
5 TraesCS5D01G320600 chr2A 160935341 160936348 1007 False 1376.0 1376 91.3980 1018 2028 1 chr2A.!!$F1 1010
6 TraesCS5D01G320600 chr2A 161051203 161051781 578 False 636.0 636 86.3490 2177 2784 1 chr2A.!!$F3 607

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
679 703 0.037326 TCAGAGGCGCTGTTTGTAGG 60.037 55.0 17.85 0.00 45.14 3.18 F
1189 1216 0.247736 CCTCGGCCTGGTATGCTATC 59.752 60.0 0.00 0.00 0.00 2.08 F
2790 2841 0.106819 CTTGCTCTTGCCCAGCCTAT 60.107 55.0 0.00 0.00 38.71 2.57 F
3804 3997 0.165944 CTCGTGTTCGACCATTTGCC 59.834 55.0 0.00 0.00 41.35 4.52 F
4239 4466 0.600255 ACTGCTGACGCTGTTGTACC 60.600 55.0 0.00 0.00 44.58 3.34 F
5517 5791 1.243902 TCTTTGTAAAGCGGCTTGGG 58.756 50.0 17.16 3.64 35.99 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 2582 1.360931 CGACGCTGTTGATGATGGCA 61.361 55.000 0.00 0.0 0.00 4.92 R
2810 2899 2.286563 TGCACACAACATAACGTCAGTG 59.713 45.455 0.00 0.0 38.70 3.66 R
4703 4930 0.179145 CGTCGCGGAGGTAGTCAAAT 60.179 55.000 6.13 0.0 0.00 2.32 R
4706 4933 1.672030 TTCGTCGCGGAGGTAGTCA 60.672 57.895 6.13 0.0 0.00 3.41 R
6055 6339 1.064979 TCAGTGACATGCATCAGCCAT 60.065 47.619 0.00 0.0 41.13 4.40 R
7404 8437 0.532573 TCGATCTGTTGCTGTCCTCC 59.467 55.000 0.00 0.0 0.00 4.30 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
73 74 8.834004 ATCTCAAGGTAAATACTACCAGTACA 57.166 34.615 3.88 0.00 39.99 2.90
74 75 8.059798 TCTCAAGGTAAATACTACCAGTACAC 57.940 38.462 3.88 0.00 39.99 2.90
75 76 7.670979 TCTCAAGGTAAATACTACCAGTACACA 59.329 37.037 3.88 0.00 39.99 3.72
139 141 4.101448 GCCCAGATCCGTGCCTGT 62.101 66.667 0.00 0.00 0.00 4.00
320 322 5.416326 CCATTTTCTTCCACGGGTTTACATA 59.584 40.000 0.00 0.00 0.00 2.29
333 335 2.858344 GTTTACATAGCGCACTCACGAT 59.142 45.455 11.47 0.00 34.99 3.73
409 423 2.281070 ACCAACGCTGTCTGCCTG 60.281 61.111 0.00 0.00 38.78 4.85
410 424 3.730761 CCAACGCTGTCTGCCTGC 61.731 66.667 0.00 0.00 38.78 4.85
531 554 2.297597 CACGAGTTCCTTCTCCTTGACT 59.702 50.000 0.00 0.00 0.00 3.41
564 587 4.615912 GCCGTTTGTTGCTATTCAGTTGAT 60.616 41.667 0.00 0.00 0.00 2.57
569 592 5.940192 TGTTGCTATTCAGTTGATTTCGT 57.060 34.783 0.00 0.00 0.00 3.85
579 602 3.667261 CAGTTGATTTCGTAGTCGTTCGT 59.333 43.478 0.00 0.00 38.33 3.85
581 604 4.741676 AGTTGATTTCGTAGTCGTTCGTTT 59.258 37.500 0.00 0.00 38.33 3.60
624 647 3.151022 CGAGGGAGGGAGACTGGC 61.151 72.222 0.00 0.00 0.00 4.85
654 677 4.735599 GGGGTCGGGGAGGAAGGT 62.736 72.222 0.00 0.00 0.00 3.50
655 678 2.609921 GGGTCGGGGAGGAAGGTT 60.610 66.667 0.00 0.00 0.00 3.50
679 703 0.037326 TCAGAGGCGCTGTTTGTAGG 60.037 55.000 17.85 0.00 45.14 3.18
703 727 1.996786 TAGGGATTCCACGTCGCGAC 61.997 60.000 28.96 28.96 34.14 5.19
743 767 2.546494 CGCCATGATTCCCTTCCGC 61.546 63.158 0.00 0.00 0.00 5.54
774 798 0.321564 TCATGCCATGTATAGCCCGC 60.322 55.000 4.31 0.00 0.00 6.13
805 829 0.401738 TAATGCATGCCTAGCCCTCC 59.598 55.000 16.68 0.00 0.00 4.30
806 830 1.358830 AATGCATGCCTAGCCCTCCT 61.359 55.000 16.68 0.00 0.00 3.69
807 831 1.776975 ATGCATGCCTAGCCCTCCTC 61.777 60.000 16.68 0.00 0.00 3.71
941 965 4.411327 GAGAGATTTCAGTCAGTCGTCAG 58.589 47.826 0.00 0.00 0.00 3.51
942 966 3.823873 AGAGATTTCAGTCAGTCGTCAGT 59.176 43.478 0.00 0.00 0.00 3.41
943 967 4.083003 AGAGATTTCAGTCAGTCGTCAGTC 60.083 45.833 0.00 0.00 0.00 3.51
985 1012 0.320771 CCGGGGAGTCTTTGTCTGTG 60.321 60.000 0.00 0.00 0.00 3.66
991 1018 2.033424 GGAGTCTTTGTCTGTGGTTTGC 59.967 50.000 0.00 0.00 0.00 3.68
1189 1216 0.247736 CCTCGGCCTGGTATGCTATC 59.752 60.000 0.00 0.00 0.00 2.08
1199 1228 5.892119 GCCTGGTATGCTATCCTATACTACA 59.108 44.000 0.00 0.00 31.92 2.74
1569 1602 1.621107 AAGCAATTGCAATTCTCGCG 58.379 45.000 30.89 11.40 45.16 5.87
1588 1621 2.696506 CGGGTTCTTGGTCTACTTTCC 58.303 52.381 0.00 0.00 0.00 3.13
1654 1687 2.317609 CGTGTTCAAGGAGTGCCCG 61.318 63.158 0.00 0.00 40.87 6.13
1776 1809 0.962489 CGGACTGTCAGTCAGAACCT 59.038 55.000 29.50 0.00 46.79 3.50
1786 1819 5.172205 GTCAGTCAGAACCTAGAACAATCC 58.828 45.833 0.00 0.00 0.00 3.01
1788 1821 4.932200 CAGTCAGAACCTAGAACAATCCAC 59.068 45.833 0.00 0.00 0.00 4.02
1789 1822 4.841246 AGTCAGAACCTAGAACAATCCACT 59.159 41.667 0.00 0.00 0.00 4.00
1790 1823 6.017192 AGTCAGAACCTAGAACAATCCACTA 58.983 40.000 0.00 0.00 0.00 2.74
1804 1841 7.200434 ACAATCCACTATCTATCTTTGGTGT 57.800 36.000 0.00 0.00 0.00 4.16
2144 2195 4.959596 GCCATCTCCTCGCCGCTC 62.960 72.222 0.00 0.00 0.00 5.03
2582 2633 1.811266 CCTCATGAACGAGGTGCGG 60.811 63.158 0.00 0.00 46.48 5.69
2636 2687 4.214119 TCATGCAGAAACACAAGAGCTAAC 59.786 41.667 0.00 0.00 0.00 2.34
2778 2829 1.376424 CATGCACCGTCCTTGCTCT 60.376 57.895 0.00 0.00 40.86 4.09
2787 2838 3.066814 CCTTGCTCTTGCCCAGCC 61.067 66.667 0.00 0.00 38.71 4.85
2790 2841 0.106819 CTTGCTCTTGCCCAGCCTAT 60.107 55.000 0.00 0.00 38.71 2.57
2892 2981 0.406750 TCAGGGAGGTGACGTTCCTA 59.593 55.000 4.54 0.00 35.20 2.94
3188 3295 4.511246 CCACCGCCAGCCCATGAT 62.511 66.667 0.00 0.00 0.00 2.45
3190 3297 3.410628 ACCGCCAGCCCATGATCA 61.411 61.111 0.00 0.00 0.00 2.92
3191 3298 2.593725 CCGCCAGCCCATGATCAG 60.594 66.667 0.09 0.00 0.00 2.90
3192 3299 2.507452 CGCCAGCCCATGATCAGA 59.493 61.111 0.09 0.00 0.00 3.27
3193 3300 1.890979 CGCCAGCCCATGATCAGAC 60.891 63.158 0.09 0.00 0.00 3.51
3194 3301 1.527844 GCCAGCCCATGATCAGACC 60.528 63.158 0.09 0.00 0.00 3.85
3196 3303 0.549950 CCAGCCCATGATCAGACCTT 59.450 55.000 0.09 0.00 0.00 3.50
3197 3304 1.476471 CCAGCCCATGATCAGACCTTC 60.476 57.143 0.09 0.00 0.00 3.46
3198 3305 1.489649 CAGCCCATGATCAGACCTTCT 59.510 52.381 0.09 0.00 0.00 2.85
3199 3306 1.489649 AGCCCATGATCAGACCTTCTG 59.510 52.381 0.09 0.00 45.59 3.02
3203 3310 2.702478 CCATGATCAGACCTTCTGCCTA 59.298 50.000 0.09 0.00 43.95 3.93
3340 3470 1.177401 GAAGGTGAATCCAAGGCCAC 58.823 55.000 5.01 0.00 39.02 5.01
3402 3544 2.069273 GGGACGTGCATGCATAGATAC 58.931 52.381 25.64 8.75 0.00 2.24
3415 3557 5.670485 TGCATAGATACGATCAGTTGGTTT 58.330 37.500 0.00 0.00 0.00 3.27
3564 3721 3.378427 GGTTCCTTGGCTGCTTATACAAG 59.622 47.826 0.00 4.17 39.88 3.16
3567 3724 5.023533 TCCTTGGCTGCTTATACAAGTAG 57.976 43.478 12.42 0.00 44.69 2.57
3571 3728 4.303086 GGCTGCTTATACAAGTAGACGA 57.697 45.455 2.73 0.00 44.68 4.20
3572 3729 4.291783 GGCTGCTTATACAAGTAGACGAG 58.708 47.826 2.73 0.00 44.68 4.18
3573 3730 4.202030 GGCTGCTTATACAAGTAGACGAGT 60.202 45.833 2.73 0.00 44.68 4.18
3576 3749 6.238429 GCTGCTTATACAAGTAGACGAGTACT 60.238 42.308 2.73 0.00 44.68 2.73
3681 3866 0.250295 CTGTTGACACCCCACGTGAT 60.250 55.000 19.30 0.00 46.20 3.06
3772 3957 2.419198 GATCTGATCGCCAGCCGT 59.581 61.111 1.26 0.00 42.62 5.68
3804 3997 0.165944 CTCGTGTTCGACCATTTGCC 59.834 55.000 0.00 0.00 41.35 4.52
3807 4000 0.951558 GTGTTCGACCATTTGCCTGT 59.048 50.000 0.00 0.00 0.00 4.00
3808 4001 2.147958 GTGTTCGACCATTTGCCTGTA 58.852 47.619 0.00 0.00 0.00 2.74
3809 4002 2.550606 GTGTTCGACCATTTGCCTGTAA 59.449 45.455 0.00 0.00 0.00 2.41
3908 4112 3.315470 GGTCAACTGGGTTTCTTCTGAAC 59.685 47.826 0.00 0.00 31.02 3.18
4239 4466 0.600255 ACTGCTGACGCTGTTGTACC 60.600 55.000 0.00 0.00 44.58 3.34
4240 4467 1.291877 CTGCTGACGCTGTTGTACCC 61.292 60.000 0.00 0.00 36.97 3.69
4502 4729 3.423154 GACAACTTCTGCGCCGGG 61.423 66.667 4.18 0.00 0.00 5.73
4889 5123 3.198635 TCTCATTTCCTCTCCACACATCC 59.801 47.826 0.00 0.00 0.00 3.51
4916 5150 6.836007 AGTTCCTTCTGAATTTTTCTGTTCCT 59.164 34.615 0.00 0.00 34.90 3.36
4917 5151 6.884280 TCCTTCTGAATTTTTCTGTTCCTC 57.116 37.500 0.00 0.00 0.00 3.71
4918 5152 5.470098 TCCTTCTGAATTTTTCTGTTCCTCG 59.530 40.000 0.00 0.00 0.00 4.63
4919 5153 4.749245 TCTGAATTTTTCTGTTCCTCGC 57.251 40.909 0.00 0.00 0.00 5.03
4927 5161 5.801350 TTTTCTGTTCCTCGCTCATAATG 57.199 39.130 0.00 0.00 0.00 1.90
5002 5236 7.492524 TCTGTGCATCTAACATTAACTAGGAG 58.507 38.462 0.00 0.00 0.00 3.69
5052 5287 4.574674 AACTCCTGCAACCAGATCAATA 57.425 40.909 0.00 0.00 41.77 1.90
5313 5551 6.374417 AGTAGGGTTGACATTTGTGATAGT 57.626 37.500 0.00 0.00 0.00 2.12
5315 5553 7.556844 AGTAGGGTTGACATTTGTGATAGTAG 58.443 38.462 0.00 0.00 0.00 2.57
5316 5554 6.620877 AGGGTTGACATTTGTGATAGTAGA 57.379 37.500 0.00 0.00 0.00 2.59
5317 5555 7.016153 AGGGTTGACATTTGTGATAGTAGAA 57.984 36.000 0.00 0.00 0.00 2.10
5318 5556 7.458397 AGGGTTGACATTTGTGATAGTAGAAA 58.542 34.615 0.00 0.00 0.00 2.52
5319 5557 7.607991 AGGGTTGACATTTGTGATAGTAGAAAG 59.392 37.037 0.00 0.00 0.00 2.62
5320 5558 7.244192 GGTTGACATTTGTGATAGTAGAAAGC 58.756 38.462 0.00 0.00 0.00 3.51
5478 5752 6.078202 TCAAAGATCCATGACGAGTATCTC 57.922 41.667 0.00 0.00 0.00 2.75
5483 5757 6.068010 AGATCCATGACGAGTATCTCTTTCT 58.932 40.000 0.00 0.00 0.00 2.52
5517 5791 1.243902 TCTTTGTAAAGCGGCTTGGG 58.756 50.000 17.16 3.64 35.99 4.12
5531 5805 2.222027 GCTTGGGAATATCCTGGTTCG 58.778 52.381 0.00 0.00 36.57 3.95
5567 5841 2.301870 TGACACCAAGTACACCAGGATC 59.698 50.000 0.00 0.00 0.00 3.36
5600 5876 4.710375 TCTCAAGTACACCAGGATTCTACC 59.290 45.833 0.00 0.00 0.00 3.18
5626 5902 5.695816 GCATGATTGGCTAAAGAAAAACACA 59.304 36.000 0.00 0.00 0.00 3.72
5653 5929 9.444600 TTGAATTTACAGAAGTACCATCCTAAC 57.555 33.333 0.00 0.00 0.00 2.34
5654 5930 8.598916 TGAATTTACAGAAGTACCATCCTAACA 58.401 33.333 0.00 0.00 0.00 2.41
5699 5976 6.183360 GCACAGTTTTTCAGTTTTCTCCAAAG 60.183 38.462 0.00 0.00 0.00 2.77
5705 5982 5.659440 TTCAGTTTTCTCCAAAGTTGCTT 57.341 34.783 0.00 0.00 0.00 3.91
5714 5991 7.849804 TTCTCCAAAGTTGCTTATACAGATC 57.150 36.000 0.00 0.00 0.00 2.75
5782 6060 5.345202 CCTCCGTGCAATAATATAAGACGTC 59.655 44.000 7.70 7.70 0.00 4.34
6031 6313 1.808945 CTTGCAAGGACTGTCCACATC 59.191 52.381 27.48 13.92 39.61 3.06
6567 6857 2.125713 CACACCGATACAGCGCCA 60.126 61.111 2.29 0.00 0.00 5.69
6618 6908 1.845266 CGATCAGGTCGTGGAAGATG 58.155 55.000 0.00 0.00 45.19 2.90
6661 6962 4.249661 AGAAGAAGATTTCAGGCGAGAAC 58.750 43.478 0.00 0.00 0.00 3.01
6664 6965 3.259374 AGAAGATTTCAGGCGAGAACTCA 59.741 43.478 12.78 0.00 31.73 3.41
6676 6977 4.022416 GGCGAGAACTCAGATCATCATAGT 60.022 45.833 0.00 0.00 0.00 2.12
6905 7211 6.121776 CCCCTAGGGCTTTGTTTTATTTTT 57.878 37.500 23.84 0.00 35.35 1.94
6944 7256 7.599630 AGTGCTTTGGTTTTATTAATGCATG 57.400 32.000 0.00 0.00 37.01 4.06
6959 7271 1.538512 TGCATGCTTCTGTGAAGCTTC 59.461 47.619 25.92 19.89 43.38 3.86
7062 7382 7.523293 TTCTAGCTTGAAAATGTTGGAATGA 57.477 32.000 8.20 0.00 0.00 2.57
7069 7389 7.359765 GCTTGAAAATGTTGGAATGAGTTCATG 60.360 37.037 0.00 0.00 36.56 3.07
7081 7401 7.549134 TGGAATGAGTTCATGTACACTATGTTC 59.451 37.037 0.00 5.70 36.56 3.18
7084 7404 6.398095 TGAGTTCATGTACACTATGTTCTGG 58.602 40.000 0.00 0.00 0.00 3.86
7086 7406 6.769512 AGTTCATGTACACTATGTTCTGGTT 58.230 36.000 0.00 0.00 0.00 3.67
7088 7408 8.372459 AGTTCATGTACACTATGTTCTGGTTTA 58.628 33.333 0.00 0.00 0.00 2.01
7089 7409 8.656849 GTTCATGTACACTATGTTCTGGTTTAG 58.343 37.037 0.00 0.00 0.00 1.85
7092 7412 6.384224 TGTACACTATGTTCTGGTTTAGTCG 58.616 40.000 0.00 0.00 0.00 4.18
7111 7450 5.542779 AGTCGTGCTTACTCAAGAAAGATT 58.457 37.500 0.00 0.00 31.44 2.40
7138 7477 9.635520 TTTTGAAAACCAAAATACGTCAAGTTA 57.364 25.926 0.00 0.00 46.48 2.24
7139 7478 9.804758 TTTGAAAACCAAAATACGTCAAGTTAT 57.195 25.926 0.00 0.00 41.43 1.89
7140 7479 9.804758 TTGAAAACCAAAATACGTCAAGTTATT 57.195 25.926 0.00 0.00 0.00 1.40
7141 7480 9.239002 TGAAAACCAAAATACGTCAAGTTATTG 57.761 29.630 0.00 0.00 37.80 1.90
7219 7930 8.789762 GGCTTAGAACTTCTTTATTTGGTGTTA 58.210 33.333 0.00 0.00 0.00 2.41
7249 7960 1.314534 TTCCCAGTTGATGCATGGCG 61.315 55.000 2.46 0.00 32.46 5.69
7289 8000 4.536090 TGTGACCAATCTTATCCCTCTTGT 59.464 41.667 0.00 0.00 0.00 3.16
7351 8348 7.918076 TGTGAAACCTAAGGTCTTGAAGATAT 58.082 34.615 0.00 0.00 33.12 1.63
7352 8349 9.042450 TGTGAAACCTAAGGTCTTGAAGATATA 57.958 33.333 0.00 0.00 33.12 0.86
7353 8350 9.315525 GTGAAACCTAAGGTCTTGAAGATATAC 57.684 37.037 0.00 0.00 33.12 1.47
7354 8351 9.042450 TGAAACCTAAGGTCTTGAAGATATACA 57.958 33.333 0.00 0.00 33.12 2.29
7375 8372 2.898705 TGCTTGCCAATGTTCGTTTTT 58.101 38.095 0.00 0.00 0.00 1.94
7404 8437 3.902261 TCTGTGCAGCAAATACTTGTG 57.098 42.857 0.00 0.00 34.79 3.33
7424 8457 1.470632 GGAGGACAGCAACAGATCGAG 60.471 57.143 0.00 0.00 0.00 4.04
7425 8458 1.474478 GAGGACAGCAACAGATCGAGA 59.526 52.381 0.00 0.00 0.00 4.04
7439 8476 1.227205 CGAGAGTCTGCAGGGCATC 60.227 63.158 15.13 7.05 38.13 3.91
7483 8520 2.281498 CACGTACACACTGACACTGTTG 59.719 50.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.485463 TGAGATTAATTACCCGGCTGG 57.515 47.619 3.88 3.88 41.37 4.85
73 74 0.679002 TAGCGAGGAGTTAGCGGTGT 60.679 55.000 0.00 0.00 37.02 4.16
74 75 0.454600 TTAGCGAGGAGTTAGCGGTG 59.545 55.000 0.00 0.00 37.02 4.94
75 76 1.180029 TTTAGCGAGGAGTTAGCGGT 58.820 50.000 0.00 0.00 39.26 5.68
320 322 2.507992 GCTCATCGTGAGTGCGCT 60.508 61.111 9.73 0.00 45.94 5.92
333 335 3.305403 CGGTTGTGTTAAGAGAGAGCTCA 60.305 47.826 17.77 0.00 43.81 4.26
336 338 3.027974 ACGGTTGTGTTAAGAGAGAGC 57.972 47.619 0.00 0.00 0.00 4.09
337 339 5.986004 AAAACGGTTGTGTTAAGAGAGAG 57.014 39.130 0.00 0.00 0.00 3.20
338 340 7.384115 CAGATAAAACGGTTGTGTTAAGAGAGA 59.616 37.037 0.00 0.00 31.66 3.10
415 429 0.394352 ATAACGAAGCCAAGCCAGGG 60.394 55.000 0.00 0.00 0.00 4.45
416 430 2.325583 TATAACGAAGCCAAGCCAGG 57.674 50.000 0.00 0.00 0.00 4.45
417 431 2.808543 GGATATAACGAAGCCAAGCCAG 59.191 50.000 0.00 0.00 0.00 4.85
552 575 7.507672 AACGACTACGAAATCAACTGAATAG 57.492 36.000 0.00 0.00 42.66 1.73
564 587 3.061928 CGAACAAACGAACGACTACGAAA 60.062 43.478 0.14 0.00 37.97 3.46
569 592 2.036217 CGACGAACAAACGAACGACTA 58.964 47.619 0.14 0.00 38.11 2.59
579 602 2.673114 GGCGATGGCGACGAACAAA 61.673 57.895 0.00 0.00 41.24 2.83
654 677 0.106708 AACAGCGCCTCTGACTTGAA 59.893 50.000 2.29 0.00 45.72 2.69
655 678 0.106708 AAACAGCGCCTCTGACTTGA 59.893 50.000 2.29 0.00 45.72 3.02
679 703 1.001597 CGACGTGGAATCCCTAGTAGC 60.002 57.143 0.00 0.00 0.00 3.58
703 727 1.001378 CCGGTGCAAACAAGGAAAGAG 60.001 52.381 0.00 0.00 0.00 2.85
774 798 4.280174 AGGCATGCATTAAAATAGCAGGAG 59.720 41.667 21.36 5.22 42.08 3.69
805 829 6.603095 CGTTGTTTTTATGAGGAAAGAGGAG 58.397 40.000 0.00 0.00 0.00 3.69
806 830 5.048991 GCGTTGTTTTTATGAGGAAAGAGGA 60.049 40.000 0.00 0.00 0.00 3.71
807 831 5.154222 GCGTTGTTTTTATGAGGAAAGAGG 58.846 41.667 0.00 0.00 0.00 3.69
892 916 1.139654 TCCCGAGAATTGATCCTGCTG 59.860 52.381 0.00 0.00 0.00 4.41
941 965 4.812626 TGTGGTTTTCTTTTCTAGGACGAC 59.187 41.667 0.00 0.00 0.00 4.34
942 966 5.026038 TGTGGTTTTCTTTTCTAGGACGA 57.974 39.130 0.00 0.00 0.00 4.20
943 967 4.319549 GCTGTGGTTTTCTTTTCTAGGACG 60.320 45.833 0.00 0.00 0.00 4.79
985 1012 1.278238 CTCATCTACGACCGCAAACC 58.722 55.000 0.00 0.00 0.00 3.27
991 1018 0.317103 CCGAAGCTCATCTACGACCG 60.317 60.000 0.00 0.00 0.00 4.79
1189 1216 0.316204 CGGCCGGGTTGTAGTATAGG 59.684 60.000 20.10 0.00 0.00 2.57
1569 1602 3.782656 TGGAAAGTAGACCAAGAACCC 57.217 47.619 0.00 0.00 32.93 4.11
1588 1621 5.049129 GCAAGCTGTAATTTAGGGCTAGATG 60.049 44.000 0.00 2.06 32.64 2.90
1654 1687 4.373116 TGCTTCTCGTCGGGGTGC 62.373 66.667 0.00 0.00 0.00 5.01
1776 1809 9.213777 ACCAAAGATAGATAGTGGATTGTTCTA 57.786 33.333 0.00 0.00 33.39 2.10
1786 1819 7.033791 ACACGTTACACCAAAGATAGATAGTG 58.966 38.462 0.00 0.00 0.00 2.74
1788 1821 6.414109 CGACACGTTACACCAAAGATAGATAG 59.586 42.308 0.00 0.00 0.00 2.08
1789 1822 6.260377 CGACACGTTACACCAAAGATAGATA 58.740 40.000 0.00 0.00 0.00 1.98
1790 1823 5.100259 CGACACGTTACACCAAAGATAGAT 58.900 41.667 0.00 0.00 0.00 1.98
1804 1841 2.223758 TGTCACATCAACCGACACGTTA 60.224 45.455 0.00 0.00 34.83 3.18
2531 2582 1.360931 CGACGCTGTTGATGATGGCA 61.361 55.000 0.00 0.00 0.00 4.92
2582 2633 3.206150 AGTATCCATGTTGACGGCAATC 58.794 45.455 7.13 1.24 36.22 2.67
2589 2640 3.123804 CACCGCTAGTATCCATGTTGAC 58.876 50.000 0.00 0.00 0.00 3.18
2808 2897 2.869801 CACACAACATAACGTCAGTGGT 59.130 45.455 0.00 0.00 37.68 4.16
2809 2898 2.349438 GCACACAACATAACGTCAGTGG 60.349 50.000 0.00 0.00 37.68 4.00
2810 2899 2.286563 TGCACACAACATAACGTCAGTG 59.713 45.455 0.00 0.00 38.70 3.66
3340 3470 3.190878 GCATTGACTTGCGGGAGG 58.809 61.111 0.00 0.00 32.06 4.30
3391 3533 5.474578 ACCAACTGATCGTATCTATGCAT 57.525 39.130 3.79 3.79 0.00 3.96
3395 3537 5.068723 ACGGAAACCAACTGATCGTATCTAT 59.931 40.000 0.00 0.00 0.00 1.98
3397 3539 3.194968 ACGGAAACCAACTGATCGTATCT 59.805 43.478 0.00 0.00 0.00 1.98
3398 3540 3.306166 CACGGAAACCAACTGATCGTATC 59.694 47.826 0.00 0.00 0.00 2.24
3402 3544 0.165944 GCACGGAAACCAACTGATCG 59.834 55.000 0.00 0.00 0.00 3.69
3564 3721 5.174395 TGGACTAGTTGAGTACTCGTCTAC 58.826 45.833 17.85 12.42 44.70 2.59
3567 3724 4.002316 ACTGGACTAGTTGAGTACTCGTC 58.998 47.826 17.85 16.53 44.63 4.20
3641 3816 1.442769 CCGCAACTGTGTCATTAGCT 58.557 50.000 0.00 0.00 0.00 3.32
3643 3818 0.447801 GGCCGCAACTGTGTCATTAG 59.552 55.000 0.00 0.00 0.00 1.73
3772 3957 1.728074 CACGAGACGCGCAGTACAA 60.728 57.895 5.73 0.00 46.04 2.41
4200 4419 2.102070 TACACTTACCACGGGCATTG 57.898 50.000 0.00 0.00 0.00 2.82
4202 4421 1.626825 AGTTACACTTACCACGGGCAT 59.373 47.619 0.00 0.00 0.00 4.40
4234 4461 1.263356 GACCTGCACAGTAGGGTACA 58.737 55.000 6.12 0.00 39.71 2.90
4235 4462 1.067071 GTGACCTGCACAGTAGGGTAC 60.067 57.143 6.12 1.15 46.91 3.34
4484 4711 2.664851 CCGGCGCAGAAGTTGTCA 60.665 61.111 10.83 0.00 0.00 3.58
4700 4927 2.093890 TCGCGGAGGTAGTCAAATACA 58.906 47.619 6.13 0.00 0.00 2.29
4703 4930 0.179145 CGTCGCGGAGGTAGTCAAAT 60.179 55.000 6.13 0.00 0.00 2.32
4706 4933 1.672030 TTCGTCGCGGAGGTAGTCA 60.672 57.895 6.13 0.00 0.00 3.41
4736 4963 2.359169 GGCGAGGATGTCCCACTCA 61.359 63.158 0.00 0.00 37.41 3.41
4889 5123 6.396829 ACAGAAAAATTCAGAAGGAACTGG 57.603 37.500 0.00 0.00 40.86 4.00
4916 5150 5.068329 AGACACTGAGATTCATTATGAGCGA 59.932 40.000 0.00 0.00 0.00 4.93
4917 5151 5.288015 AGACACTGAGATTCATTATGAGCG 58.712 41.667 0.00 0.00 0.00 5.03
4918 5152 6.985645 AGAAGACACTGAGATTCATTATGAGC 59.014 38.462 0.00 0.00 0.00 4.26
4919 5153 8.196103 TCAGAAGACACTGAGATTCATTATGAG 58.804 37.037 0.00 0.00 41.21 2.90
5083 5320 3.676291 AGAGGAGTGCTTGACTTCTTC 57.324 47.619 0.00 0.00 41.12 2.87
5130 5367 4.998788 TGCTAGTTCATGCTAGTACAGTG 58.001 43.478 8.58 0.00 40.29 3.66
5259 5496 2.352805 CCCAGACCCCAGTTCTGC 59.647 66.667 0.00 0.00 0.00 4.26
5313 5551 6.653740 GGGAAAAGTTAACAGCTAGCTTTCTA 59.346 38.462 16.46 3.72 39.38 2.10
5315 5553 5.473846 AGGGAAAAGTTAACAGCTAGCTTTC 59.526 40.000 16.46 13.32 39.38 2.62
5316 5554 5.386060 AGGGAAAAGTTAACAGCTAGCTTT 58.614 37.500 16.46 14.88 41.34 3.51
5317 5555 4.986783 AGGGAAAAGTTAACAGCTAGCTT 58.013 39.130 16.46 3.98 32.84 3.74
5318 5556 4.565861 GGAGGGAAAAGTTAACAGCTAGCT 60.566 45.833 12.68 12.68 0.00 3.32
5319 5557 3.690139 GGAGGGAAAAGTTAACAGCTAGC 59.310 47.826 6.62 6.62 0.00 3.42
5320 5558 5.167303 AGGAGGGAAAAGTTAACAGCTAG 57.833 43.478 8.61 0.00 0.00 3.42
5478 5752 9.463443 ACAAAGAAATCAAATAACGGAAGAAAG 57.537 29.630 0.00 0.00 0.00 2.62
5483 5757 9.187455 GCTTTACAAAGAAATCAAATAACGGAA 57.813 29.630 5.89 0.00 38.28 4.30
5517 5791 5.272283 TGGTTCTACGAACCAGGATATTC 57.728 43.478 21.09 0.00 44.74 1.75
5567 5841 4.010349 GGTGTACTTGAGATCAAAAGGGG 58.990 47.826 10.96 0.00 35.15 4.79
5600 5876 5.927689 TGTTTTTCTTTAGCCAATCATGCTG 59.072 36.000 0.00 0.00 39.91 4.41
5699 5976 5.355350 AGTGGCAAAGATCTGTATAAGCAAC 59.645 40.000 0.00 0.00 0.00 4.17
5782 6060 5.522456 TGCAGCTCAAATTGAACTGTAAAG 58.478 37.500 22.51 3.08 41.34 1.85
5862 6141 5.806502 TCAATTGCTTTCTTTCACTGTGTTG 59.193 36.000 7.79 0.85 0.00 3.33
5976 6258 6.377996 TGTCAGCTTAATTAAGGTACGGAGTA 59.622 38.462 25.22 10.95 39.87 2.59
6054 6338 1.065551 CAGTGACATGCATCAGCCATG 59.934 52.381 0.00 0.00 41.13 3.66
6055 6339 1.064979 TCAGTGACATGCATCAGCCAT 60.065 47.619 0.00 0.00 41.13 4.40
6567 6857 1.137479 CATTTGAAATGGCATCCGGCT 59.863 47.619 9.98 0.00 44.01 5.52
6612 6902 6.479660 CCTCTAGCTTTGTGATCTTCATCTTC 59.520 42.308 0.00 0.00 0.00 2.87
6613 6903 6.155910 TCCTCTAGCTTTGTGATCTTCATCTT 59.844 38.462 0.00 0.00 0.00 2.40
6614 6904 5.660417 TCCTCTAGCTTTGTGATCTTCATCT 59.340 40.000 0.00 0.00 0.00 2.90
6615 6905 5.911752 TCCTCTAGCTTTGTGATCTTCATC 58.088 41.667 0.00 0.00 0.00 2.92
6616 6906 5.946942 TCCTCTAGCTTTGTGATCTTCAT 57.053 39.130 0.00 0.00 0.00 2.57
6617 6907 5.481824 TCTTCCTCTAGCTTTGTGATCTTCA 59.518 40.000 0.00 0.00 0.00 3.02
6618 6908 5.971763 TCTTCCTCTAGCTTTGTGATCTTC 58.028 41.667 0.00 0.00 0.00 2.87
6661 6962 5.471556 AGAAGCCACTATGATGATCTGAG 57.528 43.478 0.00 0.00 0.00 3.35
6664 6965 4.202440 CCCAAGAAGCCACTATGATGATCT 60.202 45.833 0.00 0.00 0.00 2.75
6676 6977 7.732222 AATTTATTTGTATCCCAAGAAGCCA 57.268 32.000 0.00 0.00 33.75 4.75
6933 7244 5.591472 AGCTTCACAGAAGCATGCATTAATA 59.409 36.000 27.45 0.00 45.30 0.98
6944 7256 2.626840 CCTAGGAAGCTTCACAGAAGC 58.373 52.381 27.02 20.81 43.31 3.86
7025 7345 7.687941 TTCAAGCTAGAAAAGACATTTAGGG 57.312 36.000 0.00 0.00 0.00 3.53
7040 7360 6.917533 ACTCATTCCAACATTTTCAAGCTAG 58.082 36.000 0.00 0.00 0.00 3.42
7062 7382 6.360370 ACCAGAACATAGTGTACATGAACT 57.640 37.500 0.00 2.62 0.00 3.01
7069 7389 6.307318 CACGACTAAACCAGAACATAGTGTAC 59.693 42.308 0.00 0.00 0.00 2.90
7081 7401 3.909430 TGAGTAAGCACGACTAAACCAG 58.091 45.455 0.00 0.00 0.00 4.00
7084 7404 6.420008 TCTTTCTTGAGTAAGCACGACTAAAC 59.580 38.462 0.00 0.00 33.82 2.01
7086 7406 6.080648 TCTTTCTTGAGTAAGCACGACTAA 57.919 37.500 0.00 0.00 33.82 2.24
7088 7408 4.585955 TCTTTCTTGAGTAAGCACGACT 57.414 40.909 0.00 0.00 33.82 4.18
7089 7409 5.847670 AATCTTTCTTGAGTAAGCACGAC 57.152 39.130 0.00 0.00 33.82 4.34
7130 7469 5.705905 AGTCCAACCTAAGCAATAACTTGAC 59.294 40.000 0.00 0.00 34.04 3.18
7133 7472 7.597288 AAAAGTCCAACCTAAGCAATAACTT 57.403 32.000 0.00 0.00 0.00 2.66
7134 7473 7.597288 AAAAAGTCCAACCTAAGCAATAACT 57.403 32.000 0.00 0.00 0.00 2.24
7219 7930 5.739935 GCATCAACTGGGAATTGTTCAAGTT 60.740 40.000 0.00 4.94 38.11 2.66
7271 7982 4.080356 TGTGGACAAGAGGGATAAGATTGG 60.080 45.833 0.00 0.00 0.00 3.16
7289 8000 3.125829 CGACTACTACTTAAGCGTGTGGA 59.874 47.826 1.29 0.00 0.00 4.02
7351 8348 2.158559 ACGAACATTGGCAAGCATGTA 58.841 42.857 5.96 0.00 33.11 2.29
7352 8349 0.961019 ACGAACATTGGCAAGCATGT 59.039 45.000 5.96 2.25 35.00 3.21
7353 8350 2.068837 AACGAACATTGGCAAGCATG 57.931 45.000 5.96 1.53 0.00 4.06
7354 8351 2.818130 AAACGAACATTGGCAAGCAT 57.182 40.000 5.96 0.00 0.00 3.79
7404 8437 0.532573 TCGATCTGTTGCTGTCCTCC 59.467 55.000 0.00 0.00 0.00 4.30
7424 8457 2.894387 GCGATGCCCTGCAGACTC 60.894 66.667 17.39 4.01 43.65 3.36
7425 8458 1.689243 TATGCGATGCCCTGCAGACT 61.689 55.000 17.39 0.00 45.52 3.24
7439 8476 4.143242 GCACTAGCTATCAATGTGTATGCG 60.143 45.833 10.66 0.00 37.91 4.73
7483 8520 2.299867 AGGAATGAATGGCCAACAACAC 59.700 45.455 10.96 7.79 0.00 3.32


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

AutoCloner maintained by Alex Coulton.