Multiple sequence alignment - TraesCS7B01G364000

Loading Multiple Alignment...

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 TraesCS7B01G364000 chr7B 100.000 5108 0 0 1 5108 626567634 626562527 0.000000e+00 9433
1 TraesCS7B01G364000 chr5D 87.534 4067 426 36 832 4858 474822353 474818328 0.000000e+00 4626
2 TraesCS7B01G364000 chr5D 87.790 2326 246 17 815 3121 464105959 464108265 0.000000e+00 2687
3 TraesCS7B01G364000 chr5D 85.757 2022 192 40 3110 5105 464108284 464110235 0.000000e+00 2050
4 TraesCS7B01G364000 chr5D 88.672 821 85 5 1 814 474823229 474822410 0.000000e+00 994
5 TraesCS7B01G364000 chr5D 87.028 848 79 17 1 830 464105104 464105938 0.000000e+00 928
6 TraesCS7B01G364000 chr5B 86.553 4291 444 63 815 5050 571201548 571205760 0.000000e+00 4604
7 TraesCS7B01G364000 chr5B 87.818 2003 209 17 3122 5108 582107200 582105217 0.000000e+00 2314
8 TraesCS7B01G364000 chr5B 86.322 1316 136 24 832 2119 582117017 582115718 0.000000e+00 1393
9 TraesCS7B01G364000 chr5B 85.811 1029 116 20 2116 3122 582108292 582107272 0.000000e+00 1064
10 TraesCS7B01G364000 chr5B 88.386 663 69 6 1 659 582117859 582117201 0.000000e+00 791
11 TraesCS7B01G364000 chr5B 79.823 565 91 13 3488 4038 57718718 57718163 1.720000e-104 390
12 TraesCS7B01G364000 chr7A 89.972 3221 249 21 1903 5108 660081004 660084165 0.000000e+00 4091
13 TraesCS7B01G364000 chr7A 93.072 1097 65 8 815 1907 660068976 660070065 0.000000e+00 1594
14 TraesCS7B01G364000 chr7A 90.146 822 69 6 1 814 660068125 660068942 0.000000e+00 1059
15 TraesCS7B01G364000 chr2A 79.980 3916 565 119 832 4675 692358493 692354725 0.000000e+00 2686
16 TraesCS7B01G364000 chr2A 81.152 2621 379 66 838 3427 692272545 692270009 0.000000e+00 1997
17 TraesCS7B01G364000 chr2A 80.823 1992 302 52 1464 3427 692328250 692326311 0.000000e+00 1489
18 TraesCS7B01G364000 chr2A 83.510 849 111 20 1 831 692359373 692358536 0.000000e+00 765
19 TraesCS7B01G364000 chr2A 83.195 845 110 20 1 831 692273420 692272594 0.000000e+00 745
20 TraesCS7B01G364000 chr2A 81.519 882 117 27 832 1696 715436664 715435812 0.000000e+00 684
21 TraesCS7B01G364000 chr2A 82.481 782 108 23 1 765 692345112 692344343 0.000000e+00 658
22 TraesCS7B01G364000 chr2A 80.690 290 39 7 4387 4673 692276283 692276008 5.180000e-50 209
23 TraesCS7B01G364000 chr2A 76.955 243 26 16 4820 5060 715427287 715427073 1.500000e-20 111
24 TraesCS7B01G364000 chr5A 86.476 2307 252 25 829 3124 584549018 584551275 0.000000e+00 2477
25 TraesCS7B01G364000 chr5A 84.800 2000 201 57 3136 5108 584551348 584553271 0.000000e+00 1914
26 TraesCS7B01G364000 chr5A 86.041 831 88 14 1 814 584548145 584548964 0.000000e+00 867
27 TraesCS7B01G364000 chr2D 84.355 2007 268 27 839 2830 551822696 551820721 0.000000e+00 1925
28 TraesCS7B01G364000 chr2D 84.000 850 105 20 1 831 551823583 551822746 0.000000e+00 787
29 TraesCS7B01G364000 chr2D 86.215 428 48 6 3477 3895 551808857 551808432 2.170000e-123 453
30 TraesCS7B01G364000 chr2D 82.073 463 53 18 4216 4675 551826604 551826169 8.080000e-98 368
31 TraesCS7B01G364000 chr2D 77.888 606 89 22 2840 3428 551809447 551808870 8.190000e-88 335
32 TraesCS7B01G364000 chr7D 90.095 1474 115 17 3189 4646 570988178 570989636 0.000000e+00 1884
33 TraesCS7B01G364000 chr7D 88.653 1084 107 7 2118 3191 570978339 570979416 0.000000e+00 1306
34 TraesCS7B01G364000 chr7D 89.809 471 44 4 4641 5108 570992318 570992787 7.320000e-168 601
35 TraesCS7B01G364000 chr2B 82.971 875 123 19 832 1696 722379042 722378184 0.000000e+00 767
36 TraesCS7B01G364000 chr2B 83.477 696 87 22 1010 1696 694430486 694429810 1.560000e-174 623
37 TraesCS7B01G364000 chr2B 79.098 244 20 12 4820 5059 694477562 694477346 6.900000e-29 139
38 TraesCS7B01G364000 chr2B 78.776 245 20 13 4820 5059 694425902 694425685 8.920000e-28 135
39 TraesCS7B01G364000 chr2B 86.400 125 11 5 4940 5059 694446585 694446462 1.150000e-26 132


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 TraesCS7B01G364000 chr7B 626562527 626567634 5107 True 9433.000000 9433 100.000000 1 5108 1 chr7B.!!$R1 5107
1 TraesCS7B01G364000 chr5D 474818328 474823229 4901 True 2810.000000 4626 88.103000 1 4858 2 chr5D.!!$R1 4857
2 TraesCS7B01G364000 chr5D 464105104 464110235 5131 False 1888.333333 2687 86.858333 1 5105 3 chr5D.!!$F1 5104
3 TraesCS7B01G364000 chr5B 571201548 571205760 4212 False 4604.000000 4604 86.553000 815 5050 1 chr5B.!!$F1 4235
4 TraesCS7B01G364000 chr5B 582105217 582108292 3075 True 1689.000000 2314 86.814500 2116 5108 2 chr5B.!!$R2 2992
5 TraesCS7B01G364000 chr5B 582115718 582117859 2141 True 1092.000000 1393 87.354000 1 2119 2 chr5B.!!$R3 2118
6 TraesCS7B01G364000 chr5B 57718163 57718718 555 True 390.000000 390 79.823000 3488 4038 1 chr5B.!!$R1 550
7 TraesCS7B01G364000 chr7A 660081004 660084165 3161 False 4091.000000 4091 89.972000 1903 5108 1 chr7A.!!$F1 3205
8 TraesCS7B01G364000 chr7A 660068125 660070065 1940 False 1326.500000 1594 91.609000 1 1907 2 chr7A.!!$F2 1906
9 TraesCS7B01G364000 chr2A 692354725 692359373 4648 True 1725.500000 2686 81.745000 1 4675 2 chr2A.!!$R6 4674
10 TraesCS7B01G364000 chr2A 692326311 692328250 1939 True 1489.000000 1489 80.823000 1464 3427 1 chr2A.!!$R1 1963
11 TraesCS7B01G364000 chr2A 692270009 692276283 6274 True 983.666667 1997 81.679000 1 4673 3 chr2A.!!$R5 4672
12 TraesCS7B01G364000 chr2A 715435812 715436664 852 True 684.000000 684 81.519000 832 1696 1 chr2A.!!$R4 864
13 TraesCS7B01G364000 chr2A 692344343 692345112 769 True 658.000000 658 82.481000 1 765 1 chr2A.!!$R2 764
14 TraesCS7B01G364000 chr5A 584548145 584553271 5126 False 1752.666667 2477 85.772333 1 5108 3 chr5A.!!$F1 5107
15 TraesCS7B01G364000 chr2D 551820721 551826604 5883 True 1026.666667 1925 83.476000 1 4675 3 chr2D.!!$R2 4674
16 TraesCS7B01G364000 chr2D 551808432 551809447 1015 True 394.000000 453 82.051500 2840 3895 2 chr2D.!!$R1 1055
17 TraesCS7B01G364000 chr7D 570978339 570979416 1077 False 1306.000000 1306 88.653000 2118 3191 1 chr7D.!!$F1 1073
18 TraesCS7B01G364000 chr7D 570988178 570992787 4609 False 1242.500000 1884 89.952000 3189 5108 2 chr7D.!!$F2 1919
19 TraesCS7B01G364000 chr2B 722378184 722379042 858 True 767.000000 767 82.971000 832 1696 1 chr2B.!!$R3 864
20 TraesCS7B01G364000 chr2B 694425685 694430486 4801 True 379.000000 623 81.126500 1010 5059 2 chr2B.!!$R4 4049

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
161 3212 0.535335 CGCTGGGTTGCTAGTTAGGA 59.465 55.0 0.00 0.00 0.00 2.94 F
1756 4958 0.602638 TGGGTTGTGCTCGACATGTC 60.603 55.0 16.21 16.21 33.40 3.06 F
3655 8740 0.035056 CAAATCCGACAGGCCCTTCT 60.035 55.0 0.00 0.00 37.47 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 5284 0.396435 TCTTCATCACTGGCCACGTT 59.604 50.000 0.00 0.00 0.00 3.99 R
3671 8756 0.657840 GGCATAGACATCGTTGTGCC 59.342 55.000 3.34 6.95 35.79 5.01 R
4932 12901 2.225491 TGAAACTTGCACATACGGCTTC 59.775 45.455 0.00 0.00 0.00 3.86 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
161 3212 0.535335 CGCTGGGTTGCTAGTTAGGA 59.465 55.000 0.00 0.00 0.00 2.94
200 3259 4.932799 TCAACACAAGGATGGTAATACACG 59.067 41.667 0.00 0.00 0.00 4.49
231 3290 6.657117 TGTGCATGCTTCTTGGTTTACTAATA 59.343 34.615 20.33 0.00 0.00 0.98
335 3395 1.139853 GGGGAGCACATGAAGGTCTAG 59.860 57.143 17.06 0.00 34.14 2.43
376 3436 4.536765 AGGTATCAAAATCGGATTGCCTT 58.463 39.130 3.59 0.00 30.08 4.35
381 3442 5.713792 TCAAAATCGGATTGCCTTGTTAA 57.286 34.783 3.59 0.00 0.00 2.01
409 3470 8.839343 TGAATATATAGAAATGTGCAAGTGTGG 58.161 33.333 0.00 0.00 0.00 4.17
447 3513 7.806680 TTCCATGTGGCCACTCTATATATAA 57.193 36.000 34.75 12.51 34.44 0.98
659 3741 7.488322 TGAATAGTCAGAACAAAAACCCAAAG 58.512 34.615 0.00 0.00 0.00 2.77
661 3743 8.528044 AATAGTCAGAACAAAAACCCAAAGTA 57.472 30.769 0.00 0.00 0.00 2.24
677 3759 5.357032 CCCAAAGTAGGAAAGCGTTTCATAT 59.643 40.000 10.99 2.18 41.43 1.78
678 3760 6.258160 CCAAAGTAGGAAAGCGTTTCATATG 58.742 40.000 0.00 0.00 41.43 1.78
689 3771 6.604735 AGCGTTTCATATGTAGATTCAACC 57.395 37.500 1.90 0.00 0.00 3.77
735 3847 9.982291 GTATTATATGCCATTGTTACCATTACG 57.018 33.333 0.00 0.00 0.00 3.18
781 3899 9.539825 CCATATATCTCCTATTGTATTGCAGAC 57.460 37.037 0.00 0.00 0.00 3.51
788 3906 7.070447 TCTCCTATTGTATTGCAGACAGAGAAT 59.930 37.037 13.55 5.21 0.00 2.40
919 4079 6.546428 TGAAGGTGATAAGAAAGTAGAGGG 57.454 41.667 0.00 0.00 0.00 4.30
931 4091 7.603180 AGAAAGTAGAGGGAAAGCAAAATTT 57.397 32.000 0.00 0.00 0.00 1.82
953 4113 9.699703 AATTTATCGAAGAGGAAGATAGCTAAC 57.300 33.333 0.00 0.00 43.63 2.34
964 4124 5.338463 GGAAGATAGCTAACAACAAGGAGGT 60.338 44.000 0.00 0.00 0.00 3.85
965 4125 5.346181 AGATAGCTAACAACAAGGAGGTC 57.654 43.478 0.00 0.00 0.00 3.85
1070 4239 6.295916 GGAAGAAGGAGAACTCACATAAGGAA 60.296 42.308 4.23 0.00 0.00 3.36
1071 4240 6.688073 AGAAGGAGAACTCACATAAGGAAA 57.312 37.500 4.23 0.00 0.00 3.13
1072 4241 7.079451 AGAAGGAGAACTCACATAAGGAAAA 57.921 36.000 4.23 0.00 0.00 2.29
1108 4288 1.145738 AGAAAGAAGAGCAGGGGCAAA 59.854 47.619 0.00 0.00 44.61 3.68
1160 4352 6.998968 ACAAAAGGAGATAAATGAGCAGAG 57.001 37.500 0.00 0.00 0.00 3.35
1188 4380 4.719273 AGGAAGGAGAATGGTAAAGAGGAG 59.281 45.833 0.00 0.00 0.00 3.69
1189 4381 4.471747 GGAAGGAGAATGGTAAAGAGGAGT 59.528 45.833 0.00 0.00 0.00 3.85
1199 4391 6.978674 TGGTAAAGAGGAGTATGATTCGAT 57.021 37.500 0.00 0.00 0.00 3.59
1254 4448 3.825908 AATTGCCCCCACTTCTTTAGA 57.174 42.857 0.00 0.00 0.00 2.10
1258 4452 0.902531 CCCCCACTTCTTTAGAGCGA 59.097 55.000 0.00 0.00 0.00 4.93
1419 4614 6.015519 CCATTGTGGTTCACTTTTAGGAATGA 60.016 38.462 0.00 0.00 35.11 2.57
1434 4629 8.455903 TTTAGGAATGATGCTCTCTAATTTGG 57.544 34.615 0.00 0.00 0.00 3.28
1756 4958 0.602638 TGGGTTGTGCTCGACATGTC 60.603 55.000 16.21 16.21 33.40 3.06
1759 4961 1.195448 GGTTGTGCTCGACATGTCTTG 59.805 52.381 22.95 15.67 33.40 3.02
1769 4971 3.056179 TCGACATGTCTTGAGCCATTACA 60.056 43.478 22.95 0.00 0.00 2.41
1824 5026 5.016173 CCATTCCAGTAGGATTCCACAAAA 58.984 41.667 5.29 0.00 45.26 2.44
1845 5047 8.641541 ACAAAAACTTGGAAGATTGTACATCAT 58.358 29.630 0.00 0.00 33.06 2.45
2082 5284 1.514678 GCCGCAACACAAGGACATCA 61.515 55.000 0.00 0.00 0.00 3.07
2093 5295 4.379174 GACATCAACGTGGCCAGT 57.621 55.556 5.11 3.37 0.00 4.00
2096 5298 0.036732 ACATCAACGTGGCCAGTGAT 59.963 50.000 5.11 13.32 0.00 3.06
2169 5375 0.385751 AGACACTCACACTGACACCG 59.614 55.000 0.00 0.00 0.00 4.94
2172 5378 0.671796 CACTCACACTGACACCGGTA 59.328 55.000 6.87 0.00 0.00 4.02
2206 5412 8.908786 ACACTACAAAATGAATCTTCAGAAGA 57.091 30.769 15.44 15.44 41.08 2.87
2238 5462 9.852091 AAAATTCTTTAGAAGATGAAGATGCAC 57.148 29.630 0.00 0.00 37.38 4.57
2240 5464 8.749026 ATTCTTTAGAAGATGAAGATGCACAT 57.251 30.769 0.00 0.00 37.38 3.21
2243 5467 7.991460 TCTTTAGAAGATGAAGATGCACATGAT 59.009 33.333 0.00 0.00 29.08 2.45
2279 5503 8.943085 ACATTATCAGAAACTCTAGGGAATGAT 58.057 33.333 0.00 2.95 0.00 2.45
2303 5527 1.221466 ACTGTGAACGTCGCATGTGG 61.221 55.000 6.39 0.00 36.18 4.17
2359 5583 1.143305 GATGATCGATGCAAGACCGG 58.857 55.000 0.54 0.00 0.00 5.28
2370 5594 1.444836 CAAGACCGGCGATGGTTTTA 58.555 50.000 9.30 0.00 44.01 1.52
2466 5690 2.367567 ACTGCGGAGTGGAAAAACTCTA 59.632 45.455 9.49 0.00 44.98 2.43
2467 5691 2.737252 CTGCGGAGTGGAAAAACTCTAC 59.263 50.000 0.00 0.00 44.98 2.59
2483 5707 2.762887 CTCTACAGCTCCATCTGGTGAA 59.237 50.000 2.54 0.00 38.36 3.18
2537 5762 6.431234 ACAGTTTGGCAGGTAATTAAGAAGAG 59.569 38.462 0.00 0.00 0.00 2.85
2549 5774 7.875554 GGTAATTAAGAAGAGCCCTCTAATCAG 59.124 40.741 0.00 0.00 39.39 2.90
2661 5907 5.652518 ACTCTTGTTATCGAGCTAACCTTC 58.347 41.667 6.49 0.00 31.83 3.46
2662 5908 4.669318 TCTTGTTATCGAGCTAACCTTCG 58.331 43.478 6.49 0.00 31.83 3.79
2761 6007 3.118112 CCATCTGGTGGTTCTGCTTCTAT 60.118 47.826 0.00 0.00 43.44 1.98
2803 6049 6.400568 ACAATTTGGCAGGTAATTCAGAATG 58.599 36.000 0.00 0.00 37.54 2.67
2873 6119 8.615211 GCTAAATGTTGTCACATGATTCATAGA 58.385 33.333 0.00 0.00 43.34 1.98
2971 6222 3.370953 GGATGAGGGAAAAAGCTCTGCTA 60.371 47.826 0.00 0.00 38.25 3.49
3024 6275 4.940654 GCTTCAGCATCTAAAAGAGTTCCT 59.059 41.667 0.00 0.00 41.59 3.36
3054 6305 5.859205 AAGCTTTGGAAGAAACAACATCT 57.141 34.783 0.00 0.00 0.00 2.90
3077 6355 4.151883 AGTGACAATTTGGCAGGTAACAT 58.848 39.130 4.84 0.00 35.04 2.71
3150 6561 4.937620 TGGTTGAGATGTCTTAGATGTTGC 59.062 41.667 0.00 0.00 0.00 4.17
3279 6699 9.778741 CCACATATAGTTCATACAGGTGTATTT 57.221 33.333 0.00 0.00 39.06 1.40
3296 6716 1.573829 TTTGCGCCAGAATCCGTGTC 61.574 55.000 4.18 0.00 0.00 3.67
3298 6718 2.579201 CGCCAGAATCCGTGTCCT 59.421 61.111 0.00 0.00 0.00 3.85
3304 6724 1.067846 CAGAATCCGTGTCCTCGAACA 60.068 52.381 0.00 0.00 0.00 3.18
3316 6736 1.067425 CCTCGAACATAACCACGTGGA 60.067 52.381 40.21 20.46 40.31 4.02
3329 6749 3.697045 ACCACGTGGAACAAATCTTTTGA 59.303 39.130 40.21 0.00 44.16 2.69
3400 6820 1.754226 GTGAAAACCAACCTGGCAGAA 59.246 47.619 17.94 0.00 42.67 3.02
3416 6856 7.106239 CCTGGCAGAAGTAAATCTCTTTCTTA 58.894 38.462 17.94 0.00 0.00 2.10
3417 6857 7.065204 CCTGGCAGAAGTAAATCTCTTTCTTAC 59.935 40.741 17.94 0.00 0.00 2.34
3418 6858 7.680730 TGGCAGAAGTAAATCTCTTTCTTACT 58.319 34.615 0.00 0.00 37.45 2.24
3419 6859 8.157476 TGGCAGAAGTAAATCTCTTTCTTACTT 58.843 33.333 6.23 6.23 44.54 2.24
3430 6870 9.549984 AATCTCTTTCTTACTTCCTTACTACCT 57.450 33.333 0.00 0.00 0.00 3.08
3431 6871 8.953223 TCTCTTTCTTACTTCCTTACTACCTT 57.047 34.615 0.00 0.00 0.00 3.50
3444 6896 5.962641 CCTTACTACCTTCCTTCCTTCCTTA 59.037 44.000 0.00 0.00 0.00 2.69
3454 6906 7.311360 CCTTCCTTCCTTCCTTACTTCTTGTAT 60.311 40.741 0.00 0.00 0.00 2.29
3522 6984 9.126151 CTTGAAGTGAACTATCCTCATAGTCTA 57.874 37.037 0.00 0.00 43.94 2.59
3564 8649 5.178096 TCATCAAAGTTATGAGAAGGCCA 57.822 39.130 5.01 0.00 31.76 5.36
3645 8730 1.464997 GCACTGAGGTTCAAATCCGAC 59.535 52.381 0.00 0.00 0.00 4.79
3655 8740 0.035056 CAAATCCGACAGGCCCTTCT 60.035 55.000 0.00 0.00 37.47 2.85
3656 8741 1.209504 CAAATCCGACAGGCCCTTCTA 59.790 52.381 0.00 0.00 37.47 2.10
3671 8756 3.881688 CCCTTCTACATCAAGGCAATGAG 59.118 47.826 2.16 0.00 39.43 2.90
3775 8933 2.093816 GCTCACTGACTGGTCATGATCA 60.094 50.000 8.71 8.71 39.13 2.92
3846 9005 3.269178 CAAAGAGAGCAGGAAGATGACC 58.731 50.000 0.00 0.00 0.00 4.02
3892 9051 1.135575 GGAAGGTGTGGTACGAGTACG 60.136 57.143 7.24 0.00 45.75 3.67
4071 9241 0.664166 CACCAAAACCTCGCACATGC 60.664 55.000 0.00 0.00 37.78 4.06
4157 9327 6.540438 TTCTATCCTGTCGTTATCAAACCT 57.460 37.500 0.00 0.00 31.46 3.50
4171 9341 9.655769 CGTTATCAAACCTCAATATTCAGAATG 57.344 33.333 5.85 0.00 31.73 2.67
4197 9370 2.878406 TGTGTTTCTTGCTGAGGCTAAC 59.122 45.455 0.00 0.00 39.59 2.34
4252 9439 5.304871 AGTTCGTACTTTCCTTTCTTCTCCT 59.695 40.000 0.00 0.00 0.00 3.69
4258 9445 4.166144 ACTTTCCTTTCTTCTCCTTGTCCA 59.834 41.667 0.00 0.00 0.00 4.02
4294 9482 0.693622 TAGGGTTTCCATCGTTGCCA 59.306 50.000 0.00 0.00 34.83 4.92
4408 9678 3.254903 TGTCCTCTCGTTTGAATCGAAGA 59.745 43.478 0.00 0.25 45.75 2.87
4472 9747 5.142061 TCTCAATTGGTTGACTACGCTTA 57.858 39.130 5.42 0.00 39.36 3.09
4532 9808 5.581874 CGCAATTGAATCTTTAGCCCATTTT 59.418 36.000 10.34 0.00 0.00 1.82
4543 9819 6.894654 TCTTTAGCCCATTTTCACCATTATGA 59.105 34.615 0.00 0.00 0.00 2.15
4654 12617 6.126883 TGTTCCTAGTTCTTTCTTCCTGAACA 60.127 38.462 0.00 0.00 41.56 3.18
4712 12677 6.076981 ACTAGAGGTTTCAAAATGTTGCAG 57.923 37.500 0.00 0.00 34.50 4.41
4755 12720 1.737838 TTTGCGGGCATCTTAGACTG 58.262 50.000 0.00 0.00 0.00 3.51
4830 12795 8.220755 TGGTGATTATTGTAATGCTACCTTTC 57.779 34.615 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 3212 5.680619 TGTGTTGAGACAAGAAAGGTATGT 58.319 37.500 0.00 0.00 37.57 2.29
294 3354 6.099845 TCCCCATGTTTATCCTTCTAGAGAAC 59.900 42.308 0.00 0.00 0.00 3.01
335 3395 9.570468 TGATACCTTATCCGATATATCCACTAC 57.430 37.037 7.15 0.00 34.26 2.73
409 3470 2.880890 ACATGGAAATATTCTGGCGAGC 59.119 45.455 0.00 0.00 0.00 5.03
417 3478 4.210331 AGAGTGGCCACATGGAAATATTC 58.790 43.478 36.39 20.60 37.39 1.75
424 3485 7.071196 GGATTATATATAGAGTGGCCACATGGA 59.929 40.741 36.39 19.17 37.39 3.41
447 3513 4.694037 CACATCATACATGAATGCTCGGAT 59.306 41.667 0.00 0.00 40.69 4.18
653 3735 2.882137 TGAAACGCTTTCCTACTTTGGG 59.118 45.455 7.64 0.00 38.90 4.12
659 3741 7.948278 ATCTACATATGAAACGCTTTCCTAC 57.052 36.000 10.38 0.00 38.90 3.18
661 3743 7.047891 TGAATCTACATATGAAACGCTTTCCT 58.952 34.615 10.38 2.35 38.90 3.36
677 3759 2.496070 CCACTCGAGGGTTGAATCTACA 59.504 50.000 18.41 0.00 0.00 2.74
678 3760 2.758979 TCCACTCGAGGGTTGAATCTAC 59.241 50.000 18.41 0.00 0.00 2.59
689 3771 1.337260 CCACTCAAGTTCCACTCGAGG 60.337 57.143 18.41 5.65 0.00 4.63
781 3899 4.148128 ACTGATGGCAGGTAATTCTCTG 57.852 45.455 0.00 4.20 46.60 3.35
788 3906 2.116238 GGACCTACTGATGGCAGGTAA 58.884 52.381 0.00 0.00 46.60 2.85
919 4079 8.237267 TCTTCCTCTTCGATAAATTTTGCTTTC 58.763 33.333 0.00 0.00 0.00 2.62
931 4091 7.284716 TGTTGTTAGCTATCTTCCTCTTCGATA 59.715 37.037 0.00 0.00 0.00 2.92
953 4113 4.708177 TCTTCTCTTTGACCTCCTTGTTG 58.292 43.478 0.00 0.00 0.00 3.33
964 4124 8.400947 CAACAACTCTCATTTTCTTCTCTTTGA 58.599 33.333 0.00 0.00 0.00 2.69
965 4125 8.400947 TCAACAACTCTCATTTTCTTCTCTTTG 58.599 33.333 0.00 0.00 0.00 2.77
1072 4241 7.521669 TCTTCTTTCTCATTCTCCTCCTTTTT 58.478 34.615 0.00 0.00 0.00 1.94
1160 4352 1.299939 ACCATTCTCCTTCCTTCCCC 58.700 55.000 0.00 0.00 0.00 4.81
1188 4380 5.551233 TCATCCCTTTCCATCGAATCATAC 58.449 41.667 0.00 0.00 0.00 2.39
1189 4381 5.543790 TCTCATCCCTTTCCATCGAATCATA 59.456 40.000 0.00 0.00 0.00 2.15
1199 4391 1.916181 GGTCCTTCTCATCCCTTTCCA 59.084 52.381 0.00 0.00 0.00 3.53
1230 4424 6.078664 TCTAAAGAAGTGGGGGCAATTTTTA 58.921 36.000 0.00 0.00 0.00 1.52
1254 4448 8.708378 TCCATAAATGAATAGGATATGATCGCT 58.292 33.333 0.00 0.00 0.00 4.93
1356 4551 6.442112 TCACAACAATCATGCAAAAATACGA 58.558 32.000 0.00 0.00 0.00 3.43
1419 4614 9.959721 TTTTAACTCTACCAAATTAGAGAGCAT 57.040 29.630 12.96 1.81 45.64 3.79
1727 4929 1.417145 AGCACAACCCAAACATGCATT 59.583 42.857 0.00 0.00 38.79 3.56
1824 5026 6.721208 ACCAATGATGTACAATCTTCCAAGTT 59.279 34.615 0.00 0.00 0.00 2.66
2082 5284 0.396435 TCTTCATCACTGGCCACGTT 59.604 50.000 0.00 0.00 0.00 3.99
2093 5295 2.783135 GTGAGCCCTTTGTCTTCATCA 58.217 47.619 0.00 0.00 0.00 3.07
2096 5298 0.756294 TCGTGAGCCCTTTGTCTTCA 59.244 50.000 0.00 0.00 0.00 3.02
2169 5375 9.826574 TTCATTTTGTAGTGTACCATCTATACC 57.173 33.333 0.00 0.00 0.00 2.73
2214 5432 8.571461 TGTGCATCTTCATCTTCTAAAGAATT 57.429 30.769 0.00 0.00 41.63 2.17
2238 5462 8.205131 TCTGATAATGTGTCTTCAACATCATG 57.795 34.615 0.00 0.00 40.80 3.07
2240 5464 8.506437 GTTTCTGATAATGTGTCTTCAACATCA 58.494 33.333 0.00 0.00 40.80 3.07
2243 5467 7.933577 AGAGTTTCTGATAATGTGTCTTCAACA 59.066 33.333 0.00 0.00 34.78 3.33
2279 5503 0.101579 TGCGACGTTCACAGTCTTCA 59.898 50.000 0.00 0.00 36.53 3.02
2359 5583 4.879545 TCTTCCTAACCATAAAACCATCGC 59.120 41.667 0.00 0.00 0.00 4.58
2370 5594 2.021936 ACCTAGCCCTCTTCCTAACCAT 60.022 50.000 0.00 0.00 0.00 3.55
2466 5690 0.326264 GGTTCACCAGATGGAGCTGT 59.674 55.000 5.72 0.00 38.94 4.40
2467 5691 0.325933 TGGTTCACCAGATGGAGCTG 59.674 55.000 5.72 0.00 42.01 4.24
2483 5707 1.774217 TGCTCCCCCAGAAGTTGGT 60.774 57.895 0.00 0.00 46.25 3.67
2537 5762 3.735237 TCGATCAACTGATTAGAGGGC 57.265 47.619 0.00 0.00 34.37 5.19
2662 5908 3.837213 ACAGTTTGATGTGCACATAGC 57.163 42.857 31.45 20.35 45.96 2.97
2711 5957 2.550277 TCTCCTCAGCCTTGGACATA 57.450 50.000 0.00 0.00 0.00 2.29
2761 6007 4.335400 TTGTCACTTGATACTGCTGACA 57.665 40.909 0.00 0.00 39.51 3.58
2770 6016 4.406456 ACCTGCCAAATTGTCACTTGATA 58.594 39.130 0.00 0.00 0.00 2.15
2873 6119 8.634444 CACATAGGTTAGCTAGATAACAAGAGT 58.366 37.037 27.16 18.19 37.38 3.24
2971 6222 8.612145 AGACCTGGTATAAACAATTAAAGGAGT 58.388 33.333 0.00 0.00 0.00 3.85
3054 6305 4.720046 TGTTACCTGCCAAATTGTCACTA 58.280 39.130 0.00 0.00 0.00 2.74
3108 6415 7.162082 TCAACCAATATATGTGTGTGTGTGTA 58.838 34.615 0.00 0.00 0.00 2.90
3150 6561 4.419280 AGCATATTGATAGCTCGATGACG 58.581 43.478 0.00 0.00 41.26 4.35
3224 6644 5.188555 AGTTCATTAGCTCCATGACAAGAGA 59.811 40.000 7.82 0.00 30.09 3.10
3279 6699 2.434185 GACACGGATTCTGGCGCA 60.434 61.111 10.83 0.00 0.00 6.09
3296 6716 1.067425 TCCACGTGGTTATGTTCGAGG 60.067 52.381 32.74 3.78 35.92 4.63
3298 6718 2.223994 TGTTCCACGTGGTTATGTTCGA 60.224 45.455 32.74 8.68 36.34 3.71
3304 6724 6.039941 TCAAAAGATTTGTTCCACGTGGTTAT 59.960 34.615 32.74 18.99 36.34 1.89
3416 6856 5.026093 AGGAAGGAAGGTAGTAAGGAAGT 57.974 43.478 0.00 0.00 0.00 3.01
3417 6857 5.104859 GGAAGGAAGGAAGGTAGTAAGGAAG 60.105 48.000 0.00 0.00 0.00 3.46
3418 6858 4.781621 GGAAGGAAGGAAGGTAGTAAGGAA 59.218 45.833 0.00 0.00 0.00 3.36
3419 6859 4.046876 AGGAAGGAAGGAAGGTAGTAAGGA 59.953 45.833 0.00 0.00 0.00 3.36
3420 6860 4.363573 AGGAAGGAAGGAAGGTAGTAAGG 58.636 47.826 0.00 0.00 0.00 2.69
3421 6861 6.668718 AGTAAGGAAGGAAGGAAGGTAGTAAG 59.331 42.308 0.00 0.00 0.00 2.34
3422 6862 6.568795 AGTAAGGAAGGAAGGAAGGTAGTAA 58.431 40.000 0.00 0.00 0.00 2.24
3423 6863 6.163110 AGTAAGGAAGGAAGGAAGGTAGTA 57.837 41.667 0.00 0.00 0.00 1.82
3424 6864 5.026093 AGTAAGGAAGGAAGGAAGGTAGT 57.974 43.478 0.00 0.00 0.00 2.73
3425 6865 5.722441 AGAAGTAAGGAAGGAAGGAAGGTAG 59.278 44.000 0.00 0.00 0.00 3.18
3426 6866 5.662597 AGAAGTAAGGAAGGAAGGAAGGTA 58.337 41.667 0.00 0.00 0.00 3.08
3427 6867 4.504382 AGAAGTAAGGAAGGAAGGAAGGT 58.496 43.478 0.00 0.00 0.00 3.50
3428 6868 5.221945 ACAAGAAGTAAGGAAGGAAGGAAGG 60.222 44.000 0.00 0.00 0.00 3.46
3429 6869 5.870706 ACAAGAAGTAAGGAAGGAAGGAAG 58.129 41.667 0.00 0.00 0.00 3.46
3430 6870 5.906772 ACAAGAAGTAAGGAAGGAAGGAA 57.093 39.130 0.00 0.00 0.00 3.36
3431 6871 6.576442 GCATACAAGAAGTAAGGAAGGAAGGA 60.576 42.308 0.00 0.00 36.05 3.36
3444 6896 2.106683 GGGCGCGCATACAAGAAGT 61.107 57.895 34.42 0.00 0.00 3.01
3454 6906 2.546368 CAGTATAATAAAAGGGCGCGCA 59.454 45.455 34.42 11.89 0.00 6.09
3549 7014 5.975988 TTAATCCTGGCCTTCTCATAACT 57.024 39.130 3.32 0.00 0.00 2.24
3564 8649 2.501723 ACGCCTCTGTGACATTAATCCT 59.498 45.455 0.00 0.00 0.00 3.24
3629 8714 1.610624 GCCTGTCGGATTTGAACCTCA 60.611 52.381 0.00 0.00 0.00 3.86
3645 8730 1.748591 GCCTTGATGTAGAAGGGCCTG 60.749 57.143 6.92 0.00 40.47 4.85
3655 8740 2.290832 TGTGCCTCATTGCCTTGATGTA 60.291 45.455 0.00 0.00 0.00 2.29
3656 8741 1.180029 GTGCCTCATTGCCTTGATGT 58.820 50.000 0.00 0.00 0.00 3.06
3671 8756 0.657840 GGCATAGACATCGTTGTGCC 59.342 55.000 3.34 6.95 35.79 5.01
3892 9051 2.965716 AATGCCGCATGGGGACTAGC 62.966 60.000 31.50 15.97 39.90 3.42
4079 9249 4.458295 TCAAAACGTATTGGGGCGAATTAA 59.542 37.500 0.00 0.00 0.00 1.40
4171 9341 3.737774 GCCTCAGCAAGAAACACAAAATC 59.262 43.478 0.00 0.00 39.53 2.17
4174 9344 2.378038 AGCCTCAGCAAGAAACACAAA 58.622 42.857 0.00 0.00 43.56 2.83
4252 9439 4.045334 AGGTTATGAAGGGGATTTGGACAA 59.955 41.667 0.00 0.00 0.00 3.18
4472 9747 7.620880 TCTGATACACAAAATGTAGGCTTACT 58.379 34.615 7.57 0.00 47.00 2.24
4486 9762 5.703876 CGCTAGCATAGATCTGATACACAA 58.296 41.667 16.45 0.00 42.77 3.33
4532 9808 5.593909 AGCCGATTGAAAATCATAATGGTGA 59.406 36.000 1.30 0.00 0.00 4.02
4543 9819 7.881775 ATAGAAACCTAAGCCGATTGAAAAT 57.118 32.000 0.00 0.00 0.00 1.82
4624 9900 5.877564 GGAAGAAAGAACTAGGAACATGGAG 59.122 44.000 0.00 0.00 0.00 3.86
4681 12645 8.164070 ACATTTTGAAACCTCTAGTTACATCCT 58.836 33.333 0.00 0.00 37.88 3.24
4702 12666 6.212888 GGATAAGTCAATCCTGCAACATTT 57.787 37.500 0.00 0.00 41.99 2.32
4703 12667 5.841957 GGATAAGTCAATCCTGCAACATT 57.158 39.130 0.00 0.00 41.99 2.71
4804 12769 8.766994 AAAGGTAGCATTACAATAATCACCAT 57.233 30.769 0.00 0.00 0.00 3.55
4830 12795 3.375699 ACCCAAGGACTATCACTACAGG 58.624 50.000 0.00 0.00 0.00 4.00
4895 12864 2.549633 GGTGATTCAAATCTGCACCG 57.450 50.000 0.00 0.00 39.53 4.94
4925 12894 2.296190 TGCACATACGGCTTCGATATCT 59.704 45.455 0.34 0.00 37.63 1.98
4932 12901 2.225491 TGAAACTTGCACATACGGCTTC 59.775 45.455 0.00 0.00 0.00 3.86
5050 13021 2.284625 ATCTCCACGTGCTCCCCA 60.285 61.111 10.91 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.