Multiple sequence alignment - TraesCS3B01G246500

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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 TraesCS3B01G246500 chr3B 100.000 5203 0 0 1 5203 392293123 392298325 0.000000e+00 9609.0
1 TraesCS3B01G246500 chr3D 94.314 3957 131 34 878 4786 297491458 297495368 0.000000e+00 5975.0
2 TraesCS3B01G246500 chr3D 87.077 828 70 22 1 794 16121057 16121881 0.000000e+00 902.0
3 TraesCS3B01G246500 chr3D 86.506 830 71 24 1 793 468665341 468666166 0.000000e+00 874.0
4 TraesCS3B01G246500 chr3D 85.612 834 72 21 1 793 182085531 182084705 0.000000e+00 832.0
5 TraesCS3B01G246500 chr3D 96.471 425 10 1 4784 5203 297495413 297495837 0.000000e+00 697.0
6 TraesCS3B01G246500 chr3D 95.522 67 2 1 815 881 297491369 297491434 7.130000e-19 106.0
7 TraesCS3B01G246500 chr3A 93.745 2302 77 23 2946 5203 391474844 391472566 0.000000e+00 3391.0
8 TraesCS3B01G246500 chr3A 90.775 1496 61 34 893 2350 391476928 391475472 0.000000e+00 1927.0
9 TraesCS3B01G246500 chr3A 97.482 556 12 1 2350 2905 391475392 391474839 0.000000e+00 948.0
10 TraesCS3B01G246500 chr6D 87.273 825 71 21 1 793 100211631 100212453 0.000000e+00 911.0
11 TraesCS3B01G246500 chr5D 87.742 775 68 18 39 793 489756054 489755287 0.000000e+00 880.0
12 TraesCS3B01G246500 chr5D 87.047 772 71 17 39 793 525156318 525155559 0.000000e+00 845.0
13 TraesCS3B01G246500 chr5D 85.841 791 72 24 39 793 474543330 474542544 0.000000e+00 804.0
14 TraesCS3B01G246500 chr7D 86.445 841 62 32 1 793 154002285 154001449 0.000000e+00 874.0
15 TraesCS3B01G246500 chr7D 86.565 789 65 15 39 793 508795841 508795060 0.000000e+00 832.0
16 TraesCS3B01G246500 chr7D 85.612 834 72 21 1 793 574240750 574241576 0.000000e+00 832.0
17 TraesCS3B01G246500 chr2B 86.038 838 74 23 1 797 54453034 54453869 0.000000e+00 859.0
18 TraesCS3B01G246500 chr4A 85.663 837 66 32 1 793 693356029 693356855 0.000000e+00 832.0
19 TraesCS3B01G246500 chr4A 87.145 669 77 4 126 793 65493963 65494623 0.000000e+00 750.0
20 TraesCS3B01G246500 chr1D 85.714 791 73 24 39 793 481960845 481961631 0.000000e+00 798.0
21 TraesCS3B01G246500 chr1D 94.118 34 2 0 2997 3030 318118771 318118738 9.000000e-03 52.8
22 TraesCS3B01G246500 chr6B 84.184 784 84 27 40 793 609120130 609119357 0.000000e+00 725.0
23 TraesCS3B01G246500 chr6B 91.892 37 3 0 2961 2997 52988159 52988123 9.000000e-03 52.8
24 TraesCS3B01G246500 chr6A 78.873 284 40 11 4067 4334 52719441 52719720 1.930000e-39 174.0
25 TraesCS3B01G246500 chr5A 76.451 293 39 14 4067 4334 452925341 452925628 1.180000e-26 132.0
26 TraesCS3B01G246500 chr1B 100.000 28 0 0 2961 2988 129884873 129884846 9.000000e-03 52.8
27 TraesCS3B01G246500 chr1B 100.000 28 0 0 2961 2988 557130316 557130343 9.000000e-03 52.8


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 TraesCS3B01G246500 chr3B 392293123 392298325 5202 False 9609.000000 9609 100.000000 1 5203 1 chr3B.!!$F1 5202
1 TraesCS3B01G246500 chr3D 297491369 297495837 4468 False 2259.333333 5975 95.435667 815 5203 3 chr3D.!!$F3 4388
2 TraesCS3B01G246500 chr3D 16121057 16121881 824 False 902.000000 902 87.077000 1 794 1 chr3D.!!$F1 793
3 TraesCS3B01G246500 chr3D 468665341 468666166 825 False 874.000000 874 86.506000 1 793 1 chr3D.!!$F2 792
4 TraesCS3B01G246500 chr3D 182084705 182085531 826 True 832.000000 832 85.612000 1 793 1 chr3D.!!$R1 792
5 TraesCS3B01G246500 chr3A 391472566 391476928 4362 True 2088.666667 3391 94.000667 893 5203 3 chr3A.!!$R1 4310
6 TraesCS3B01G246500 chr6D 100211631 100212453 822 False 911.000000 911 87.273000 1 793 1 chr6D.!!$F1 792
7 TraesCS3B01G246500 chr5D 489755287 489756054 767 True 880.000000 880 87.742000 39 793 1 chr5D.!!$R2 754
8 TraesCS3B01G246500 chr5D 525155559 525156318 759 True 845.000000 845 87.047000 39 793 1 chr5D.!!$R3 754
9 TraesCS3B01G246500 chr5D 474542544 474543330 786 True 804.000000 804 85.841000 39 793 1 chr5D.!!$R1 754
10 TraesCS3B01G246500 chr7D 154001449 154002285 836 True 874.000000 874 86.445000 1 793 1 chr7D.!!$R1 792
11 TraesCS3B01G246500 chr7D 508795060 508795841 781 True 832.000000 832 86.565000 39 793 1 chr7D.!!$R2 754
12 TraesCS3B01G246500 chr7D 574240750 574241576 826 False 832.000000 832 85.612000 1 793 1 chr7D.!!$F1 792
13 TraesCS3B01G246500 chr2B 54453034 54453869 835 False 859.000000 859 86.038000 1 797 1 chr2B.!!$F1 796
14 TraesCS3B01G246500 chr4A 693356029 693356855 826 False 832.000000 832 85.663000 1 793 1 chr4A.!!$F2 792
15 TraesCS3B01G246500 chr4A 65493963 65494623 660 False 750.000000 750 87.145000 126 793 1 chr4A.!!$F1 667
16 TraesCS3B01G246500 chr1D 481960845 481961631 786 False 798.000000 798 85.714000 39 793 1 chr1D.!!$F1 754
17 TraesCS3B01G246500 chr6B 609119357 609120130 773 True 725.000000 725 84.184000 40 793 1 chr6B.!!$R2 753

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
523 596 0.099791 GAGTAGCGTGGAGAGTGAGC 59.900 60.0 0.00 0.00 0.00 4.26 F
661 750 0.325933 TGGACCTGCCATGTCAGAAG 59.674 55.0 5.06 0.00 43.33 2.85 F
1805 1946 0.323178 AAGGGCAACAGCATCTCAGG 60.323 55.0 0.00 0.00 39.74 3.86 F
2020 2176 0.687354 GGGTCCAAGACTTGAGCTCA 59.313 55.0 13.74 13.74 32.47 4.26 F
3482 3718 1.774110 TGGCTTGCAAAAGTTCCTGA 58.226 45.0 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1857 0.739813 GTAGCTTCCCGTCACGCAAT 60.740 55.0 0.00 0.00 0.00 3.56 R
2046 2202 0.847373 TAGGCGGCCATTATTTCCCA 59.153 50.0 23.09 0.00 0.00 4.37 R
3069 3305 1.453155 GTGTTGCCGATTCCTGTGAT 58.547 50.0 0.00 0.00 0.00 3.06 R
3815 4060 0.036483 TGCTTTCTCTATGTGCGCCA 60.036 50.0 4.18 2.31 0.00 5.69 R
4943 5266 1.362224 CCTTCTGGGACTTTGGAGGA 58.638 55.0 0.00 0.00 37.23 3.71 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
31 32 1.511850 TGTGCAGACAGTCCAAATCG 58.488 50.000 0.00 0.00 0.00 3.34
55 56 8.286800 TCGTGTTTCATTAACTGAATTTACTGG 58.713 33.333 2.52 0.00 43.30 4.00
107 126 5.887754 ACACAAACCCTAGTTGGATAACAT 58.112 37.500 0.00 0.00 39.30 2.71
120 139 7.121382 AGTTGGATAACATTGACATGAGGAAT 58.879 34.615 0.00 0.00 39.30 3.01
130 149 4.441792 TGACATGAGGAATAACACATCCG 58.558 43.478 0.00 0.00 40.78 4.18
145 164 0.105607 ATCCGTAGAACCTCCTCCCC 60.106 60.000 0.00 0.00 0.00 4.81
252 279 4.125703 CAGAAGGATGCATCTTAGTGGTC 58.874 47.826 25.28 12.29 0.00 4.02
346 375 4.937201 AATTGAAGAACACTTGAACCCC 57.063 40.909 0.00 0.00 0.00 4.95
357 387 1.146152 CTTGAACCCCAACCCTAACCA 59.854 52.381 0.00 0.00 0.00 3.67
416 446 1.142748 CCATGTCGACCAGCTCCTC 59.857 63.158 14.12 0.00 0.00 3.71
417 447 1.142748 CATGTCGACCAGCTCCTCC 59.857 63.158 14.12 0.00 0.00 4.30
418 448 1.000993 ATGTCGACCAGCTCCTCCT 59.999 57.895 14.12 0.00 0.00 3.69
510 574 0.686112 AGGGGACAGAGCAGAGTAGC 60.686 60.000 0.00 0.00 0.00 3.58
519 592 0.322997 AGCAGAGTAGCGTGGAGAGT 60.323 55.000 0.00 0.00 40.15 3.24
523 596 0.099791 GAGTAGCGTGGAGAGTGAGC 59.900 60.000 0.00 0.00 0.00 4.26
527 600 2.983930 GCGTGGAGAGTGAGCGAGT 61.984 63.158 0.00 0.00 0.00 4.18
551 630 2.574955 GGAGTGGAGTGTGAGCGGT 61.575 63.158 0.00 0.00 0.00 5.68
577 663 2.108250 AGTGGTGGGCTCTGTTTTGTAT 59.892 45.455 0.00 0.00 0.00 2.29
607 693 2.042404 TAACGGCCGTCAACCCAGTT 62.042 55.000 34.29 15.38 0.00 3.16
609 695 2.203294 GGCCGTCAACCCAGTTGT 60.203 61.111 7.30 0.00 43.23 3.32
661 750 0.325933 TGGACCTGCCATGTCAGAAG 59.674 55.000 5.06 0.00 43.33 2.85
707 796 9.757227 ACGGTCATTTGATTTTATTGAGAAAAA 57.243 25.926 0.00 0.00 32.29 1.94
783 872 4.430137 GATGCTTGAGCTTCAAATGTGA 57.570 40.909 12.42 0.00 42.61 3.58
819 908 5.880054 TTTTGCAATTCAGTCTAGTAGGC 57.120 39.130 0.00 0.00 0.00 3.93
820 909 4.551702 TTGCAATTCAGTCTAGTAGGCA 57.448 40.909 4.25 0.00 0.00 4.75
821 910 3.861840 TGCAATTCAGTCTAGTAGGCAC 58.138 45.455 4.25 0.00 0.00 5.01
822 911 2.860735 GCAATTCAGTCTAGTAGGCACG 59.139 50.000 4.25 0.00 0.00 5.34
823 912 3.676324 GCAATTCAGTCTAGTAGGCACGT 60.676 47.826 4.25 0.00 0.00 4.49
850 939 4.827087 AGATGCAGCGAGCCCACG 62.827 66.667 0.00 0.00 44.83 4.94
919 1035 3.123620 GAGTTGCTGCCGCTGGAG 61.124 66.667 0.70 0.00 36.97 3.86
949 1074 2.290705 GCCAGGGTGTAATGTAACCACT 60.291 50.000 0.00 0.00 38.27 4.00
968 1093 1.477295 CTCCGTCCTTCCACTTACTCC 59.523 57.143 0.00 0.00 0.00 3.85
1079 1204 4.131581 CTCGTCGTCGTCGTCGCT 62.132 66.667 15.28 0.00 44.86 4.93
1124 1249 1.559149 GCCGCTGAAAACCGTACGAA 61.559 55.000 18.76 0.00 0.00 3.85
1126 1251 0.854062 CGCTGAAAACCGTACGAACA 59.146 50.000 18.76 8.06 0.00 3.18
1149 1274 2.175931 TCCCCTTGCTTTGGTTTCTACA 59.824 45.455 0.00 0.00 0.00 2.74
1150 1275 2.296190 CCCCTTGCTTTGGTTTCTACAC 59.704 50.000 0.00 0.00 0.00 2.90
1151 1276 2.955660 CCCTTGCTTTGGTTTCTACACA 59.044 45.455 0.00 0.00 0.00 3.72
1152 1277 3.573967 CCCTTGCTTTGGTTTCTACACAT 59.426 43.478 0.00 0.00 0.00 3.21
1153 1278 4.764823 CCCTTGCTTTGGTTTCTACACATA 59.235 41.667 0.00 0.00 0.00 2.29
1154 1279 5.335661 CCCTTGCTTTGGTTTCTACACATAC 60.336 44.000 0.00 0.00 0.00 2.39
1155 1280 5.240623 CCTTGCTTTGGTTTCTACACATACA 59.759 40.000 0.00 0.00 0.00 2.29
1159 1284 6.937465 TGCTTTGGTTTCTACACATACATACA 59.063 34.615 0.00 0.00 0.00 2.29
1181 1306 0.825010 CTGCAGTTTCCTTGCCCACT 60.825 55.000 5.25 0.00 40.81 4.00
1223 1348 1.004440 GCGCCTCCTGACTTGACTT 60.004 57.895 0.00 0.00 0.00 3.01
1236 1361 2.034558 ACTTGACTTGATGGGTTTTGCG 59.965 45.455 0.00 0.00 0.00 4.85
1258 1383 0.534877 TGCTTGCAGCCCATATACCG 60.535 55.000 5.82 0.00 41.51 4.02
1259 1384 1.237285 GCTTGCAGCCCATATACCGG 61.237 60.000 0.00 0.00 34.48 5.28
1408 1533 7.066284 GGATACAAGTGCAAACAAGATATCAGT 59.934 37.037 5.32 0.02 0.00 3.41
1440 1565 4.564821 CGAGAGGGACAAGGTAAATCCAAA 60.565 45.833 0.00 0.00 39.02 3.28
1443 1568 4.270008 AGGGACAAGGTAAATCCAAATCG 58.730 43.478 0.00 0.00 39.02 3.34
1454 1593 0.889994 TCCAAATCGCATTGCTGCTT 59.110 45.000 7.12 0.00 46.65 3.91
1475 1614 3.887741 TCATTGTGAACACGCTTTCATG 58.112 40.909 2.87 0.00 37.80 3.07
1485 1626 3.058914 ACACGCTTTCATGCTTGTACTTC 60.059 43.478 0.00 0.00 42.32 3.01
1500 1641 5.339008 TGTACTTCGTGGCAGAGAATAAT 57.661 39.130 5.89 0.00 0.00 1.28
1504 1645 3.610040 TCGTGGCAGAGAATAATGTGT 57.390 42.857 0.00 0.00 0.00 3.72
1505 1646 3.261580 TCGTGGCAGAGAATAATGTGTG 58.738 45.455 0.00 0.00 0.00 3.82
1511 1652 4.572389 GGCAGAGAATAATGTGTGTCGATT 59.428 41.667 0.00 0.00 0.00 3.34
1512 1653 5.496387 GCAGAGAATAATGTGTGTCGATTG 58.504 41.667 0.00 0.00 0.00 2.67
1513 1654 5.063944 GCAGAGAATAATGTGTGTCGATTGT 59.936 40.000 0.00 0.00 0.00 2.71
1514 1655 6.472680 CAGAGAATAATGTGTGTCGATTGTG 58.527 40.000 0.00 0.00 0.00 3.33
1519 1660 2.017138 TGTGTGTCGATTGTGTGTGT 57.983 45.000 0.00 0.00 0.00 3.72
1644 1785 2.249743 AGGGAGGTCTGAGGAGATCATT 59.750 50.000 0.00 0.00 37.28 2.57
1716 1857 2.494059 CGTGGCCTTTTCTCTTTCTCA 58.506 47.619 3.32 0.00 0.00 3.27
1734 1875 0.739462 CATTGCGTGACGGGAAGCTA 60.739 55.000 7.25 0.00 0.00 3.32
1805 1946 0.323178 AAGGGCAACAGCATCTCAGG 60.323 55.000 0.00 0.00 39.74 3.86
1848 1989 2.198827 TTGTTGATCAATGCGAGGGT 57.801 45.000 12.12 0.00 0.00 4.34
1863 2004 4.049869 GCGAGGGTACTCTTTATGTAAGC 58.950 47.826 0.00 0.00 41.71 3.09
1879 2020 3.332485 TGTAAGCCCTTATTTCACTGGGT 59.668 43.478 0.00 0.00 41.59 4.51
1881 2022 3.646736 AGCCCTTATTTCACTGGGTAC 57.353 47.619 0.00 0.00 41.59 3.34
1955 2111 5.858381 TGACTGAGCAGATATCAAATACCC 58.142 41.667 5.32 0.00 0.00 3.69
1972 2128 0.842635 CCCAAGGCCAGCTCTATTCT 59.157 55.000 5.01 0.00 0.00 2.40
1989 2145 8.253810 GCTCTATTCTATGTACATTCATAGCCA 58.746 37.037 14.77 2.80 43.84 4.75
2020 2176 0.687354 GGGTCCAAGACTTGAGCTCA 59.313 55.000 13.74 13.74 32.47 4.26
2046 2202 2.682856 ACAAAGTCGTGACAATTGCACT 59.317 40.909 22.12 9.10 35.30 4.40
2080 2236 2.550208 CCGCCTATACATTGTCCTTCCC 60.550 54.545 0.00 0.00 0.00 3.97
2161 2317 5.548406 AGTGTTGGTCCACTTAGTAATGAC 58.452 41.667 0.00 0.00 42.99 3.06
2339 2495 7.652300 TCGTATACCAACATCTATTTGCATC 57.348 36.000 0.00 0.00 0.00 3.91
2438 2674 6.749139 TCGTTAGATGGGATCTTGTATTCAG 58.251 40.000 0.00 0.00 40.76 3.02
2505 2741 5.352569 CACCTAACTCAGTGATCCATTCAAC 59.647 44.000 0.00 0.00 35.70 3.18
2698 2934 4.364415 TCCTGGTTTGTTTCGTTCTTTG 57.636 40.909 0.00 0.00 0.00 2.77
2699 2935 3.129638 TCCTGGTTTGTTTCGTTCTTTGG 59.870 43.478 0.00 0.00 0.00 3.28
2971 3207 7.519347 AATTGGTAAAGTTATACTCCCTCCA 57.481 36.000 0.00 0.00 0.00 3.86
2994 3230 3.181497 CCCCAAAATAAGTGTCGCTGATG 60.181 47.826 0.00 0.00 0.00 3.07
3069 3305 6.259550 GCTTTGAGCTCCTGAAATTTCTTA 57.740 37.500 18.64 4.03 38.45 2.10
3124 3360 5.107453 ACACGAGAAGTATGCTTTCTTTTCG 60.107 40.000 21.46 21.46 46.30 3.46
3482 3718 1.774110 TGGCTTGCAAAAGTTCCTGA 58.226 45.000 0.00 0.00 0.00 3.86
3815 4060 4.649692 AGCACAAGAGTCACTCATTTCAT 58.350 39.130 7.77 0.00 32.06 2.57
3953 4198 4.522022 AGCTTTGAAGAAATGGAACTGGAG 59.478 41.667 0.00 0.00 0.00 3.86
3955 4200 5.335504 GCTTTGAAGAAATGGAACTGGAGAG 60.336 44.000 0.00 0.00 0.00 3.20
4034 4279 5.827797 TCAAGACAAATTGCCAGTAGAAGTT 59.172 36.000 0.00 0.00 0.00 2.66
4043 4288 3.054875 TGCCAGTAGAAGTTGCATCATCT 60.055 43.478 7.59 7.59 0.00 2.90
4049 4294 7.496920 CCAGTAGAAGTTGCATCATCTTATCAA 59.503 37.037 7.75 0.00 0.00 2.57
4061 4306 9.687210 GCATCATCTTATCAAGCATTTATGAAA 57.313 29.630 0.00 0.00 0.00 2.69
4102 4347 2.185004 AGCAGTAGCAAATCACCGTT 57.815 45.000 0.00 0.00 45.49 4.44
4139 4384 1.890979 GATGGAGACCATGCGGCAG 60.891 63.158 9.25 0.00 45.26 4.85
4212 4457 7.936847 TGTCCTCAACAAACTGATATGTAACTT 59.063 33.333 0.00 0.00 34.03 2.66
4254 4499 2.703416 AGCTTGCTTGATTGTCGATGA 58.297 42.857 0.00 0.00 0.00 2.92
4388 4633 7.974243 TTCATTTTGATTCAGATTGCATACG 57.026 32.000 0.00 0.00 0.00 3.06
4392 4637 6.741992 TTTGATTCAGATTGCATACGAACT 57.258 33.333 0.00 0.00 0.00 3.01
4393 4638 6.741992 TTGATTCAGATTGCATACGAACTT 57.258 33.333 0.00 0.00 0.00 2.66
4394 4639 6.741992 TGATTCAGATTGCATACGAACTTT 57.258 33.333 0.00 0.00 0.00 2.66
4396 4641 8.437360 TGATTCAGATTGCATACGAACTTTAT 57.563 30.769 0.00 0.00 0.00 1.40
4401 4646 7.017645 CAGATTGCATACGAACTTTATATGCC 58.982 38.462 11.74 0.00 46.99 4.40
4402 4647 6.936900 AGATTGCATACGAACTTTATATGCCT 59.063 34.615 11.74 1.34 46.99 4.75
4403 4648 6.935741 TTGCATACGAACTTTATATGCCTT 57.064 33.333 11.74 0.00 46.99 4.35
4404 4649 6.299023 TGCATACGAACTTTATATGCCTTG 57.701 37.500 11.74 0.00 46.99 3.61
4406 4651 6.540551 TGCATACGAACTTTATATGCCTTGAA 59.459 34.615 11.74 0.00 46.99 2.69
4407 4652 6.851330 GCATACGAACTTTATATGCCTTGAAC 59.149 38.462 4.47 0.00 43.50 3.18
4408 4653 7.466725 GCATACGAACTTTATATGCCTTGAACA 60.467 37.037 4.47 0.00 43.50 3.18
4409 4654 6.811253 ACGAACTTTATATGCCTTGAACAA 57.189 33.333 0.00 0.00 0.00 2.83
4410 4655 7.209471 ACGAACTTTATATGCCTTGAACAAA 57.791 32.000 0.00 0.00 0.00 2.83
4433 4692 6.566197 ACTTGTCATTTTGTTTTGCCAAAA 57.434 29.167 0.00 0.00 45.43 2.44
4446 4705 6.541641 TGTTTTGCCAAAATAGAGCAACATTT 59.458 30.769 5.81 0.00 45.57 2.32
4450 4709 6.620678 TGCCAAAATAGAGCAACATTTAGAC 58.379 36.000 0.00 0.00 32.56 2.59
4478 4737 1.532868 GTGTAACAGCTGCTCCAGTTG 59.467 52.381 15.27 7.40 45.77 3.16
4519 4778 4.850680 TCCCCTGACCAAATATTGTACAC 58.149 43.478 0.00 0.00 0.00 2.90
4617 4880 8.625786 TCAATCAACAGAATACATGGATATGG 57.374 34.615 7.72 0.00 38.66 2.74
4676 4941 9.030452 AGTAAGATATGAACATGTCTATCCTCC 57.970 37.037 12.87 0.00 38.15 4.30
4747 5018 0.603065 AATCCCGGCTGAAACAAAGC 59.397 50.000 0.00 0.00 40.06 3.51
4811 5129 8.743085 ATTTATATGCTGCCCATATAGAACTG 57.257 34.615 11.64 0.00 45.42 3.16
4812 5130 2.936919 TGCTGCCCATATAGAACTGG 57.063 50.000 0.00 0.00 0.00 4.00
4943 5266 2.158549 AGCAAGAACTGAAGGGCTTTCT 60.159 45.455 10.86 0.00 36.71 2.52
5006 5329 2.280592 GACGTGAACCGGTGGCTT 60.281 61.111 8.52 0.00 42.24 4.35
5153 5476 1.676384 GTCCCTCTGCTTGAGCTGT 59.324 57.895 4.44 0.00 41.35 4.40
5190 5513 3.018423 TCATCTTCTCCATCTCGGACA 57.982 47.619 0.00 0.00 39.64 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.195448 CACGATTTGGACTGTCTGCAC 59.805 52.381 7.85 0.00 0.00 4.57
107 126 4.875536 CGGATGTGTTATTCCTCATGTCAA 59.124 41.667 0.00 0.00 0.00 3.18
120 139 3.698040 GAGGAGGTTCTACGGATGTGTTA 59.302 47.826 0.00 0.00 0.00 2.41
130 149 0.614134 ACACGGGGAGGAGGTTCTAC 60.614 60.000 0.00 0.00 0.00 2.59
145 164 2.293122 TGCATTTGAAGGAAAGGACACG 59.707 45.455 0.00 0.00 0.00 4.49
357 387 4.500499 AAGAGATCTGCTTTGCACCTAT 57.500 40.909 0.00 0.00 33.79 2.57
403 433 2.043852 GGAGGAGGAGCTGGTCGA 60.044 66.667 0.00 0.00 0.00 4.20
416 446 2.441901 AGGAGAGCAGCGAGGAGG 60.442 66.667 0.00 0.00 0.00 4.30
417 447 1.447317 GAGAGGAGAGCAGCGAGGAG 61.447 65.000 0.00 0.00 0.00 3.69
418 448 1.453015 GAGAGGAGAGCAGCGAGGA 60.453 63.158 0.00 0.00 0.00 3.71
487 551 0.689623 CTCTGCTCTGTCCCCTGTTT 59.310 55.000 0.00 0.00 0.00 2.83
510 574 1.154131 CACTCGCTCACTCTCCACG 60.154 63.158 0.00 0.00 0.00 4.94
519 592 1.228583 ACTCCACTCCACTCGCTCA 60.229 57.895 0.00 0.00 0.00 4.26
523 596 0.896019 ACTCCACTCCACTCCACTCG 60.896 60.000 0.00 0.00 0.00 4.18
527 600 0.105709 TCACACTCCACTCCACTCCA 60.106 55.000 0.00 0.00 0.00 3.86
645 734 0.036952 CGACTTCTGACATGGCAGGT 60.037 55.000 28.28 18.90 36.55 4.00
661 750 0.308376 TTTGCCGCAACTAAACCGAC 59.692 50.000 4.98 0.00 0.00 4.79
707 796 9.054922 CAAGAATCCACCATTTTTGTTGTAAAT 57.945 29.630 0.00 0.00 33.66 1.40
720 809 0.394352 GCGTCCCAAGAATCCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
730 819 0.652592 CATTTCTAGCGCGTCCCAAG 59.347 55.000 8.43 0.00 0.00 3.61
797 886 5.181245 GTGCCTACTAGACTGAATTGCAAAA 59.819 40.000 1.71 0.00 0.00 2.44
798 887 4.695455 GTGCCTACTAGACTGAATTGCAAA 59.305 41.667 1.71 0.00 0.00 3.68
799 888 4.253685 GTGCCTACTAGACTGAATTGCAA 58.746 43.478 0.00 0.00 0.00 4.08
800 889 3.676049 CGTGCCTACTAGACTGAATTGCA 60.676 47.826 0.00 0.00 0.00 4.08
801 890 2.860735 CGTGCCTACTAGACTGAATTGC 59.139 50.000 0.00 0.00 0.00 3.56
802 891 4.111375 ACGTGCCTACTAGACTGAATTG 57.889 45.455 0.00 0.00 0.00 2.32
803 892 4.803098 AACGTGCCTACTAGACTGAATT 57.197 40.909 0.00 0.00 0.00 2.17
804 893 4.703575 TGTAACGTGCCTACTAGACTGAAT 59.296 41.667 0.00 0.00 0.00 2.57
805 894 4.074259 TGTAACGTGCCTACTAGACTGAA 58.926 43.478 0.00 0.00 0.00 3.02
806 895 3.438087 GTGTAACGTGCCTACTAGACTGA 59.562 47.826 0.00 0.00 0.00 3.41
807 896 3.756069 GTGTAACGTGCCTACTAGACTG 58.244 50.000 0.00 0.00 0.00 3.51
845 934 1.011968 TTTCTCGCAATCGTCGTGGG 61.012 55.000 0.00 0.00 36.96 4.61
850 939 2.537730 GCAGGAATTTCTCGCAATCGTC 60.538 50.000 3.99 0.00 36.96 4.20
949 1074 1.203087 TGGAGTAAGTGGAAGGACGGA 60.203 52.381 0.00 0.00 0.00 4.69
968 1093 4.261363 GGTTGCAGAGAGGAAGAGTTTTTG 60.261 45.833 0.00 0.00 0.00 2.44
1079 1204 2.189191 ATTGAGCCTCTGAAGCGCCA 62.189 55.000 2.29 0.00 34.64 5.69
1124 1249 2.101640 AACCAAAGCAAGGGGATTGT 57.898 45.000 0.00 0.00 41.29 2.71
1126 1251 2.976440 AGAAACCAAAGCAAGGGGATT 58.024 42.857 0.00 0.00 0.00 3.01
1149 1274 5.046304 AGGAAACTGCAGACTGTATGTATGT 60.046 40.000 23.35 0.00 39.83 2.29
1150 1275 5.423015 AGGAAACTGCAGACTGTATGTATG 58.577 41.667 23.35 0.00 41.13 2.39
1151 1276 5.683876 AGGAAACTGCAGACTGTATGTAT 57.316 39.130 23.35 0.00 41.13 2.29
1152 1277 5.237815 CAAGGAAACTGCAGACTGTATGTA 58.762 41.667 23.35 0.00 42.68 2.29
1153 1278 4.067896 CAAGGAAACTGCAGACTGTATGT 58.932 43.478 23.35 0.00 42.68 2.29
1154 1279 3.120060 GCAAGGAAACTGCAGACTGTATG 60.120 47.826 23.35 13.07 42.68 2.39
1155 1280 3.077359 GCAAGGAAACTGCAGACTGTAT 58.923 45.455 23.35 0.00 42.68 2.29
1159 1284 0.538287 GGGCAAGGAAACTGCAGACT 60.538 55.000 23.35 9.85 42.68 3.24
1198 1323 4.680237 TCAGGAGGCGCAACCGTG 62.680 66.667 10.83 9.40 46.52 4.94
1199 1324 4.681978 GTCAGGAGGCGCAACCGT 62.682 66.667 10.83 0.00 46.52 4.83
1223 1348 1.112315 AGCAACCGCAAAACCCATCA 61.112 50.000 0.00 0.00 42.27 3.07
1390 1515 5.772521 ACCAAACTGATATCTTGTTTGCAC 58.227 37.500 28.90 0.00 45.12 4.57
1393 1518 5.634859 GGCAACCAAACTGATATCTTGTTTG 59.365 40.000 28.15 28.15 45.68 2.93
1408 1533 1.072505 GTCCCTCTCGGCAACCAAA 59.927 57.895 0.00 0.00 0.00 3.28
1440 1565 1.475280 ACAATGAAGCAGCAATGCGAT 59.525 42.857 0.00 0.00 40.27 4.58
1443 1568 2.357327 TCACAATGAAGCAGCAATGC 57.643 45.000 0.00 0.00 0.00 3.56
1454 1593 3.852939 GCATGAAAGCGTGTTCACAATGA 60.853 43.478 0.00 0.00 40.22 2.57
1475 1614 1.071605 CTCTGCCACGAAGTACAAGC 58.928 55.000 0.00 0.00 41.61 4.01
1485 1626 3.002791 ACACACATTATTCTCTGCCACG 58.997 45.455 0.00 0.00 0.00 4.94
1500 1641 2.017138 ACACACACAATCGACACACA 57.983 45.000 0.00 0.00 0.00 3.72
1504 1645 7.329588 AGTATATCTACACACACAATCGACA 57.670 36.000 0.00 0.00 0.00 4.35
1505 1646 7.167635 CCAAGTATATCTACACACACAATCGAC 59.832 40.741 0.00 0.00 0.00 4.20
1511 1652 5.625886 GCCACCAAGTATATCTACACACACA 60.626 44.000 0.00 0.00 0.00 3.72
1512 1653 4.809426 GCCACCAAGTATATCTACACACAC 59.191 45.833 0.00 0.00 0.00 3.82
1513 1654 4.468153 TGCCACCAAGTATATCTACACACA 59.532 41.667 0.00 0.00 0.00 3.72
1514 1655 5.018539 TGCCACCAAGTATATCTACACAC 57.981 43.478 0.00 0.00 0.00 3.82
1519 1660 8.721133 TTATCTTCTGCCACCAAGTATATCTA 57.279 34.615 0.00 0.00 0.00 1.98
1644 1785 3.047807 GCTGCTGGTGGATAGGCCA 62.048 63.158 5.01 0.00 46.96 5.36
1716 1857 0.739813 GTAGCTTCCCGTCACGCAAT 60.740 55.000 0.00 0.00 0.00 3.56
1805 1946 5.762825 TGGAGATGAATTGAAATAGCAGC 57.237 39.130 0.00 0.00 0.00 5.25
1848 1989 9.609346 GTGAAATAAGGGCTTACATAAAGAGTA 57.391 33.333 0.00 0.00 37.38 2.59
1863 2004 4.569719 ACAGTACCCAGTGAAATAAGGG 57.430 45.455 0.00 0.00 46.96 3.95
1955 2111 4.348863 ACATAGAATAGAGCTGGCCTTG 57.651 45.455 3.32 0.00 0.00 3.61
1989 2145 5.721225 AGTCTTGGACCCATCTATACTGAT 58.279 41.667 0.00 0.00 32.18 2.90
2046 2202 0.847373 TAGGCGGCCATTATTTCCCA 59.153 50.000 23.09 0.00 0.00 4.37
2080 2236 2.816087 CCCCATCACAGTTGACTTTCTG 59.184 50.000 0.00 0.00 33.38 3.02
2161 2317 1.614903 TCCACAGCTGGCAAGATTTTG 59.385 47.619 19.93 3.32 37.49 2.44
2297 2453 7.114529 GGTATACGAATACGAATGTTGAAGAGG 59.885 40.741 0.00 0.00 39.16 3.69
2478 2714 3.506398 TGGATCACTGAGTTAGGTGTCA 58.494 45.455 0.00 0.00 35.26 3.58
2479 2715 4.744795 ATGGATCACTGAGTTAGGTGTC 57.255 45.455 0.00 0.00 35.26 3.67
2480 2716 4.532126 TGAATGGATCACTGAGTTAGGTGT 59.468 41.667 0.00 0.00 35.26 4.16
2698 2934 5.416952 AGGAACAAGAATGACACATTCATCC 59.583 40.000 21.15 19.85 44.86 3.51
2699 2935 6.404074 GGAGGAACAAGAATGACACATTCATC 60.404 42.308 21.15 14.45 44.86 2.92
2971 3207 2.159382 CAGCGACACTTATTTTGGGGT 58.841 47.619 0.00 0.00 0.00 4.95
2994 3230 7.523415 TCCCTCCATCCCAAAATAAGTATTAC 58.477 38.462 0.00 0.00 30.46 1.89
3069 3305 1.453155 GTGTTGCCGATTCCTGTGAT 58.547 50.000 0.00 0.00 0.00 3.06
3124 3360 7.446625 AGGATGGAAAATCAACTAGATACATGC 59.553 37.037 0.00 0.00 35.39 4.06
3219 3455 7.657761 TGAACAAACTTTGGTTTTGCTTTTCTA 59.342 29.630 6.47 0.00 42.96 2.10
3451 3687 3.540314 TGCAAGCCATTGTTTTGAAGT 57.460 38.095 0.00 0.00 38.76 3.01
3482 3718 8.434392 TGTTTCTAGTACACATACCCTCTTTTT 58.566 33.333 0.00 0.00 30.88 1.94
3815 4060 0.036483 TGCTTTCTCTATGTGCGCCA 60.036 50.000 4.18 2.31 0.00 5.69
3953 4198 3.883830 TCTGCTGACTTGGATCTTCTC 57.116 47.619 0.00 0.00 0.00 2.87
3955 4200 4.183101 CTCTTCTGCTGACTTGGATCTTC 58.817 47.826 0.00 0.00 0.00 2.87
4034 4279 8.398878 TCATAAATGCTTGATAAGATGATGCA 57.601 30.769 0.00 0.00 31.87 3.96
4043 4288 7.598278 ACAACGGTTTCATAAATGCTTGATAA 58.402 30.769 0.00 0.00 0.00 1.75
4049 4294 6.321717 CACATACAACGGTTTCATAAATGCT 58.678 36.000 0.00 0.00 0.00 3.79
4061 4306 1.346395 TCTCCTTGCACATACAACGGT 59.654 47.619 0.00 0.00 0.00 4.83
4139 4384 1.815003 CTCTTGGTTGGTGCAAGATCC 59.185 52.381 0.00 0.00 34.87 3.36
4216 4461 8.743085 AGCAAGCTAAATCTTCATCTAATTCA 57.257 30.769 0.00 0.00 0.00 2.57
4275 4520 9.874205 AAATGAACCACAATAAATAACATCCTG 57.126 29.630 0.00 0.00 0.00 3.86
4388 4633 8.915654 CAAGTTTGTTCAAGGCATATAAAGTTC 58.084 33.333 0.00 0.00 0.00 3.01
4392 4637 7.946207 TGACAAGTTTGTTCAAGGCATATAAA 58.054 30.769 0.00 0.00 42.43 1.40
4393 4638 7.517614 TGACAAGTTTGTTCAAGGCATATAA 57.482 32.000 0.00 0.00 42.43 0.98
4394 4639 7.701539 ATGACAAGTTTGTTCAAGGCATATA 57.298 32.000 0.00 0.00 42.43 0.86
4396 4641 6.403866 AATGACAAGTTTGTTCAAGGCATA 57.596 33.333 0.00 0.00 42.43 3.14
4398 4643 4.734398 AATGACAAGTTTGTTCAAGGCA 57.266 36.364 0.00 0.00 42.43 4.75
4407 4652 5.936054 TGGCAAAACAAAATGACAAGTTTG 58.064 33.333 11.49 11.49 44.80 2.93
4408 4653 6.566197 TTGGCAAAACAAAATGACAAGTTT 57.434 29.167 0.00 0.00 39.57 2.66
4409 4654 6.566197 TTTGGCAAAACAAAATGACAAGTT 57.434 29.167 10.83 0.00 44.80 2.66
4410 4655 6.566197 TTTTGGCAAAACAAAATGACAAGT 57.434 29.167 20.81 0.00 44.80 3.16
4433 4692 7.697691 CATTTTCCGTCTAAATGTTGCTCTAT 58.302 34.615 0.00 0.00 37.90 1.98
4435 4694 5.942872 CATTTTCCGTCTAAATGTTGCTCT 58.057 37.500 0.00 0.00 37.90 4.09
4446 4705 4.688879 CAGCTGTTACACATTTTCCGTCTA 59.311 41.667 5.25 0.00 0.00 2.59
4450 4709 2.226437 AGCAGCTGTTACACATTTTCCG 59.774 45.455 16.64 0.00 0.00 4.30
4478 4737 6.015940 CAGGGGAGAGAACATTTATATTTGGC 60.016 42.308 0.00 0.00 0.00 4.52
4593 4856 8.400184 ACCATATCCATGTATTCTGTTGATTG 57.600 34.615 0.00 0.00 0.00 2.67
4609 4872 6.905736 TGCTAATTGGAGTTTACCATATCCA 58.094 36.000 0.00 0.00 40.04 3.41
4617 4880 6.538742 TGTCAGCTATGCTAATTGGAGTTTAC 59.461 38.462 0.00 0.00 36.40 2.01
4676 4941 1.857217 CTCAGGAGACGAATGAATGCG 59.143 52.381 0.00 0.00 0.00 4.73
4747 5018 1.819632 GGCCTCACCCTGCATTACG 60.820 63.158 0.00 0.00 0.00 3.18
4943 5266 1.362224 CCTTCTGGGACTTTGGAGGA 58.638 55.000 0.00 0.00 37.23 3.71
4984 5307 1.661480 CACCGGTTCACGTCACCTA 59.339 57.895 2.97 0.00 42.24 3.08
5153 5476 7.967908 AGAAGATGAAGAAGGAACACTTTCTA 58.032 34.615 0.00 0.00 40.21 2.10


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

AutoCloner maintained by Alex Coulton.