Multiple sequence alignment - TraesCS7B01G302500

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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 TraesCS7B01G302500 chr7B 100.000 4514 0 0 935 5448 539236629 539232116 0.000000e+00 8336.0
1 TraesCS7B01G302500 chr7B 100.000 690 0 0 1 690 539237563 539236874 0.000000e+00 1275.0
2 TraesCS7B01G302500 chr7A 90.575 3565 204 41 981 4460 581436537 581433020 0.000000e+00 4601.0
3 TraesCS7B01G302500 chr7A 94.205 742 34 5 4709 5448 581432778 581432044 0.000000e+00 1123.0
4 TraesCS7B01G302500 chr7A 88.780 713 34 14 1 677 581437394 581436692 0.000000e+00 832.0
5 TraesCS7B01G302500 chr7A 93.750 128 4 3 4580 4707 581432938 581432815 7.200000e-44 189.0
6 TraesCS7B01G302500 chr7D 86.475 2610 200 67 1382 3914 510711030 510708497 0.000000e+00 2723.0
7 TraesCS7B01G302500 chr7D 95.822 742 26 4 4709 5448 510707686 510706948 0.000000e+00 1194.0
8 TraesCS7B01G302500 chr7D 91.635 789 28 9 3945 4706 510708502 510707725 0.000000e+00 1057.0
9 TraesCS7B01G302500 chr7D 85.153 687 75 21 1 675 510712230 510711559 0.000000e+00 678.0
10 TraesCS7B01G302500 chr7D 84.352 409 43 10 935 1334 510711430 510711034 1.110000e-101 381.0
11 TraesCS7B01G302500 chr5D 92.963 270 16 3 4722 4990 390710146 390709879 1.840000e-104 390.0
12 TraesCS7B01G302500 chr5B 89.437 284 16 5 4707 4989 471138153 471137883 4.040000e-91 346.0
13 TraesCS7B01G302500 chr6B 76.124 356 72 10 5098 5448 229204889 229205236 2.020000e-39 174.0
14 TraesCS7B01G302500 chr6A 97.917 48 1 0 4213 4260 39607505 39607552 3.500000e-12 84.2
15 TraesCS7B01G302500 chr6A 96.000 50 1 1 4213 4261 39566019 39566068 4.520000e-11 80.5
16 TraesCS7B01G302500 chr4B 97.917 48 1 0 4213 4260 260433313 260433360 3.500000e-12 84.2
17 TraesCS7B01G302500 chr4B 96.000 50 1 1 4213 4261 171195808 171195857 4.520000e-11 80.5
18 TraesCS7B01G302500 chr1A 96.000 50 1 1 4213 4261 30447936 30447985 4.520000e-11 80.5
19 TraesCS7B01G302500 chr1A 96.000 50 1 1 4213 4261 501900651 501900602 4.520000e-11 80.5
20 TraesCS7B01G302500 chr1A 96.000 50 1 1 4213 4261 585668931 585668980 4.520000e-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 TraesCS7B01G302500 chr7B 539232116 539237563 5447 True 4805.50 8336 100.0000 1 5448 2 chr7B.!!$R1 5447
1 TraesCS7B01G302500 chr7A 581432044 581437394 5350 True 1686.25 4601 91.8275 1 5448 4 chr7A.!!$R1 5447
2 TraesCS7B01G302500 chr7D 510706948 510712230 5282 True 1206.60 2723 88.6874 1 5448 5 chr7D.!!$R1 5447

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
122 131 0.251653 TCCTCTACACCACCGAGCTT 60.252 55.0 0.0 0.0 0.00 3.74 F
1067 1125 0.179124 GTCATCTCGCAGGTGGAGAC 60.179 60.0 0.0 0.0 42.87 3.36 F
1643 1729 0.532573 GCCTCGTTGAGATGGTCTGA 59.467 55.0 0.0 0.0 0.00 3.27 F
1844 1941 0.827368 CCAGTAGAAGGAGGACTGCC 59.173 60.0 0.0 0.0 39.42 4.85 F
3637 3805 0.106967 GGAGGGGGAAGAACTGATGC 60.107 60.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1960 0.035534 ACACACACCTGTTCAGTGCA 60.036 50.000 0.00 0.00 38.87 4.57 R
3010 3147 2.821378 CACATTCATTTCCACTCTGCCA 59.179 45.455 0.00 0.00 0.00 4.92 R
3232 3370 0.115547 TGGGTAGTACCTGCCAGTCA 59.884 55.000 18.85 3.83 38.00 3.41 R
3721 3889 1.001641 GTGCAGGCATCTCCACCTT 60.002 57.895 0.00 0.00 37.29 3.50 R
5371 5633 1.600916 GCTGGCCATCCGGGATAAC 60.601 63.158 5.51 4.57 40.01 1.89 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
52 53 2.311701 CCGCAGCGGTAAAACACGA 61.312 57.895 26.69 0.00 42.73 4.35
110 119 3.834799 CCCGTGCCCGTCCTCTAC 61.835 72.222 0.00 0.00 0.00 2.59
115 124 2.280552 TGCCCGTCCTCTACACCAC 61.281 63.158 0.00 0.00 0.00 4.16
122 131 0.251653 TCCTCTACACCACCGAGCTT 60.252 55.000 0.00 0.00 0.00 3.74
136 145 0.534427 GAGCTTAACCCGCCCCATAC 60.534 60.000 0.00 0.00 0.00 2.39
243 252 1.724654 CGCGACTCAAATTTTCACCGG 60.725 52.381 0.00 0.00 0.00 5.28
432 448 1.353022 TGGTTCGGCTTCAAATACCCT 59.647 47.619 0.00 0.00 0.00 4.34
433 449 2.014857 GGTTCGGCTTCAAATACCCTC 58.985 52.381 0.00 0.00 0.00 4.30
434 450 2.617021 GGTTCGGCTTCAAATACCCTCA 60.617 50.000 0.00 0.00 0.00 3.86
435 451 3.078837 GTTCGGCTTCAAATACCCTCAA 58.921 45.455 0.00 0.00 0.00 3.02
436 452 3.426787 TCGGCTTCAAATACCCTCAAA 57.573 42.857 0.00 0.00 0.00 2.69
437 453 3.963129 TCGGCTTCAAATACCCTCAAAT 58.037 40.909 0.00 0.00 0.00 2.32
438 454 5.105567 TCGGCTTCAAATACCCTCAAATA 57.894 39.130 0.00 0.00 0.00 1.40
439 455 4.879545 TCGGCTTCAAATACCCTCAAATAC 59.120 41.667 0.00 0.00 0.00 1.89
440 456 4.036380 CGGCTTCAAATACCCTCAAATACC 59.964 45.833 0.00 0.00 0.00 2.73
441 457 4.341235 GGCTTCAAATACCCTCAAATACCC 59.659 45.833 0.00 0.00 0.00 3.69
472 488 0.984995 CTTCTCCGGTTCCTTCCCTT 59.015 55.000 0.00 0.00 0.00 3.95
507 523 2.488153 CACTCCCGAAATCCTCAAAACC 59.512 50.000 0.00 0.00 0.00 3.27
1067 1125 0.179124 GTCATCTCGCAGGTGGAGAC 60.179 60.000 0.00 0.00 42.87 3.36
1077 1135 2.665603 GTGGAGACCCTGCACCTC 59.334 66.667 7.27 0.00 44.99 3.85
1184 1242 7.430441 GTTAGGTGAAGTTTCATGCCTTTTTA 58.570 34.615 8.72 0.00 39.73 1.52
1186 1244 6.458210 AGGTGAAGTTTCATGCCTTTTTATG 58.542 36.000 0.00 0.00 39.73 1.90
1212 1276 2.507854 CGTGTGTGGGGTCTCCTGT 61.508 63.158 0.00 0.00 36.20 4.00
1215 1279 1.002087 GTGTGTGGGGTCTCCTGTTAG 59.998 57.143 0.00 0.00 36.20 2.34
1222 1286 2.224793 GGGGTCTCCTGTTAGCAAAACT 60.225 50.000 3.94 0.00 0.00 2.66
1226 1291 4.127171 GTCTCCTGTTAGCAAAACTGTGA 58.873 43.478 3.94 2.31 0.00 3.58
1263 1328 1.694150 TGCTACTCTGTGTTTGCTCCT 59.306 47.619 8.27 0.00 0.00 3.69
1276 1348 4.168760 GTTTGCTCCTGTGATAAACATGC 58.831 43.478 0.00 0.00 38.39 4.06
1344 1416 6.989437 TCGACAACGCAGAAGAAAATAATAG 58.011 36.000 0.00 0.00 39.58 1.73
1397 1469 4.202212 TGCTCTGTTACTACTCTGTTGCAA 60.202 41.667 0.00 0.00 0.00 4.08
1454 1540 2.241160 TCAATTGTGCCTTCATGCTGT 58.759 42.857 5.13 0.00 0.00 4.40
1597 1683 1.956477 CACTCCTCAACAAGTTTGGGG 59.044 52.381 0.00 0.00 41.43 4.96
1598 1684 1.569072 ACTCCTCAACAAGTTTGGGGT 59.431 47.619 2.86 2.51 40.88 4.95
1643 1729 0.532573 GCCTCGTTGAGATGGTCTGA 59.467 55.000 0.00 0.00 0.00 3.27
1709 1795 2.746142 GCTGCACCATGTAAGGCATCTA 60.746 50.000 0.00 0.00 35.19 1.98
1712 1798 5.303259 TGCACCATGTAAGGCATCTAATA 57.697 39.130 0.00 0.00 35.19 0.98
1713 1799 5.879763 TGCACCATGTAAGGCATCTAATAT 58.120 37.500 0.00 0.00 35.19 1.28
1756 1853 8.177119 TGCCTTACAAATTTCAACTGACTAAT 57.823 30.769 0.00 0.00 0.00 1.73
1828 1925 2.007049 GCCACGGAGAACACATACCAG 61.007 57.143 0.00 0.00 0.00 4.00
1834 1931 4.158025 ACGGAGAACACATACCAGTAGAAG 59.842 45.833 0.00 0.00 0.00 2.85
1844 1941 0.827368 CCAGTAGAAGGAGGACTGCC 59.173 60.000 0.00 0.00 39.42 4.85
1863 1960 2.746472 GCCAGGCCGAGTAGAAATGATT 60.746 50.000 0.00 0.00 0.00 2.57
1866 1963 2.092968 AGGCCGAGTAGAAATGATTGCA 60.093 45.455 0.00 0.00 0.00 4.08
1890 1987 5.221722 ACTGAACAGGTGTGTGTATCATCTT 60.222 40.000 6.76 0.00 36.84 2.40
1901 2006 6.316140 TGTGTGTATCATCTTGATGCTAAACC 59.684 38.462 10.48 5.17 39.71 3.27
1935 2040 4.928615 TGTTTTCTGTTTGGTGCTTGAAAG 59.071 37.500 0.00 0.00 0.00 2.62
2131 2247 5.071653 AGTGTTATTTGGGCATGTTTCCTTT 59.928 36.000 0.00 0.00 0.00 3.11
2200 2324 5.648092 AGTGTAATTGCTACTGGTTTCCATC 59.352 40.000 0.00 0.00 30.82 3.51
2229 2353 2.558359 GCAAGTGGCAGGTTCATACTTT 59.442 45.455 0.00 0.00 43.97 2.66
2356 2484 7.095060 GCACTTGTTGATCTTTTGTGATAGAGA 60.095 37.037 0.00 0.00 0.00 3.10
2524 2652 6.532657 GGCCATCTTCATTTTGTATTCTGTTG 59.467 38.462 0.00 0.00 0.00 3.33
2592 2729 6.471233 TTGTTCTGCTATAGCTGTATCACT 57.529 37.500 24.61 0.00 42.66 3.41
2593 2730 5.836347 TGTTCTGCTATAGCTGTATCACTG 58.164 41.667 24.61 5.02 42.66 3.66
2642 2779 4.695396 AGCTCATCTAACTGAATCTGCTG 58.305 43.478 0.00 0.00 0.00 4.41
2643 2780 4.161942 AGCTCATCTAACTGAATCTGCTGT 59.838 41.667 0.00 0.00 0.00 4.40
2650 2787 2.255406 ACTGAATCTGCTGTCTGGTCT 58.745 47.619 0.00 0.00 0.00 3.85
2651 2788 3.435275 ACTGAATCTGCTGTCTGGTCTA 58.565 45.455 0.00 0.00 0.00 2.59
2767 2904 9.247126 TCAGTTTGTGATTGTCATTTTGTATTG 57.753 29.630 0.00 0.00 0.00 1.90
2789 2926 5.078949 TGTGTCATCCCATGATCAGTTTTT 58.921 37.500 0.09 0.00 42.04 1.94
2800 2937 6.816640 CCATGATCAGTTTTTGCAAGATCAAT 59.183 34.615 23.90 14.09 45.51 2.57
2801 2938 7.201522 CCATGATCAGTTTTTGCAAGATCAATG 60.202 37.037 23.90 20.72 45.51 2.82
2835 2972 8.220559 ACATGTTGACCTATTCTGCCTTATTAT 58.779 33.333 0.00 0.00 0.00 1.28
2836 2973 9.071276 CATGTTGACCTATTCTGCCTTATTATT 57.929 33.333 0.00 0.00 0.00 1.40
2989 3126 3.350219 ACGGTGGAGAACATATTTGCT 57.650 42.857 0.00 0.00 0.00 3.91
3010 3147 8.635765 TTGCTTTGTCATTCCTAGTTAAAGAT 57.364 30.769 0.00 0.00 0.00 2.40
3064 3201 3.584848 GCCATCATATCCTCTGTAAGGGT 59.415 47.826 0.00 0.00 46.23 4.34
3095 3233 5.523552 GCTTTATTGCTCTTTTGTTGGTGTT 59.476 36.000 0.00 0.00 0.00 3.32
3098 3236 3.951775 TGCTCTTTTGTTGGTGTTGTT 57.048 38.095 0.00 0.00 0.00 2.83
3204 3342 4.187694 GCCTCAGGAGAAGTGAAATACAG 58.812 47.826 0.00 0.00 0.00 2.74
3248 3386 6.018994 CGATTTTAATGACTGGCAGGTACTAC 60.019 42.308 20.34 3.60 36.02 2.73
3301 3439 4.248859 AGTGCTGATCATGTACTGTTCAC 58.751 43.478 12.57 4.22 31.73 3.18
3304 3442 5.812127 GTGCTGATCATGTACTGTTCACATA 59.188 40.000 0.00 0.00 34.88 2.29
3321 3459 6.834168 TCACATAATCTTTTTGGGAGGTTC 57.166 37.500 0.00 0.00 0.00 3.62
3347 3485 5.517770 GCAAGATAATGCAGTTTTCACCATC 59.482 40.000 0.00 0.00 45.70 3.51
3415 3553 4.595762 TCAAACACACTAGACCAGTACC 57.404 45.455 0.00 0.00 34.98 3.34
3425 3563 3.391506 AGACCAGTACCGTAAACCAAC 57.608 47.619 0.00 0.00 0.00 3.77
3436 3574 3.497640 CCGTAAACCAACCGTATGACAAA 59.502 43.478 0.00 0.00 0.00 2.83
3490 3658 6.718912 TCATGGATTATCACTCAAACCAAACA 59.281 34.615 0.00 0.00 0.00 2.83
3506 3674 9.398170 CAAACCAAACATATTCTTCTGTACTTG 57.602 33.333 0.00 0.00 0.00 3.16
3526 3694 0.967380 GGGTGAATGCTGGGAAGGTG 60.967 60.000 0.00 0.00 0.00 4.00
3557 3725 3.395607 TGGCTAATCCATCTACTTGCCAT 59.604 43.478 0.00 0.00 43.29 4.40
3558 3726 3.755378 GGCTAATCCATCTACTTGCCATG 59.245 47.826 0.00 0.00 38.99 3.66
3637 3805 0.106967 GGAGGGGGAAGAACTGATGC 60.107 60.000 0.00 0.00 0.00 3.91
3718 3886 1.078143 AGCACGCCTGGAGGAAATC 60.078 57.895 0.00 0.00 37.39 2.17
3730 3898 1.916181 GAGGAAATCCCAAGGTGGAGA 59.084 52.381 0.00 0.00 40.96 3.71
3735 3903 0.625683 ATCCCAAGGTGGAGATGCCT 60.626 55.000 0.00 0.00 40.96 4.75
3742 3910 3.159615 TGGAGATGCCTGCACACA 58.840 55.556 0.00 0.00 35.75 3.72
3768 3936 2.066999 GGGAGGCAACGAGGATCCT 61.067 63.158 16.13 16.13 46.39 3.24
3774 3942 1.215382 CAACGAGGATCCTGCGACA 59.785 57.895 28.76 0.00 0.00 4.35
3797 3965 4.504596 GCATGGCATGTCCGGGGA 62.505 66.667 26.94 0.00 37.80 4.81
3906 4074 3.909662 GCGACAGCCATGGACAAT 58.090 55.556 18.40 0.00 37.42 2.71
3907 4075 3.079131 GCGACAGCCATGGACAATA 57.921 52.632 18.40 0.00 37.42 1.90
3908 4076 0.657840 GCGACAGCCATGGACAATAC 59.342 55.000 18.40 0.00 37.42 1.89
3909 4077 0.930310 CGACAGCCATGGACAATACG 59.070 55.000 18.40 8.89 0.00 3.06
3910 4078 0.657840 GACAGCCATGGACAATACGC 59.342 55.000 18.40 0.00 0.00 4.42
3911 4079 0.035534 ACAGCCATGGACAATACGCA 60.036 50.000 18.40 0.00 0.00 5.24
3912 4080 0.659427 CAGCCATGGACAATACGCAG 59.341 55.000 18.40 0.00 0.00 5.18
3913 4081 0.464373 AGCCATGGACAATACGCAGG 60.464 55.000 18.40 0.00 0.00 4.85
3914 4082 1.447317 GCCATGGACAATACGCAGGG 61.447 60.000 18.40 0.00 0.00 4.45
3915 4083 0.180171 CCATGGACAATACGCAGGGA 59.820 55.000 5.56 0.00 0.00 4.20
3916 4084 1.586422 CATGGACAATACGCAGGGAG 58.414 55.000 0.00 0.00 0.00 4.30
3917 4085 0.179045 ATGGACAATACGCAGGGAGC 60.179 55.000 0.00 0.00 40.87 4.70
3918 4086 1.523938 GGACAATACGCAGGGAGCC 60.524 63.158 0.00 0.00 41.38 4.70
3919 4087 1.220749 GACAATACGCAGGGAGCCA 59.779 57.895 0.00 0.00 41.38 4.75
3920 4088 0.179045 GACAATACGCAGGGAGCCAT 60.179 55.000 0.00 0.00 41.38 4.40
3932 4100 0.767375 GGAGCCATGGAGGATAAGCA 59.233 55.000 18.40 0.00 41.22 3.91
3937 4105 1.544982 CCATGGAGGATAAGCAGCAGG 60.545 57.143 5.56 0.00 41.22 4.85
3995 4163 1.762522 CGGGAGGACATGGAGATGGG 61.763 65.000 0.00 0.00 33.39 4.00
4086 4254 2.500369 CGTGCACATGCGTCTTGC 60.500 61.111 18.64 2.55 45.83 4.01
4195 4375 2.352805 GGGTGGGCAAGTCCAGAG 59.647 66.667 0.00 0.00 37.50 3.35
4227 4413 4.184629 GGATGCTGTGTAAAGTAGTCTGG 58.815 47.826 0.00 0.00 0.00 3.86
4285 4473 3.490526 GTGTTGGTTTACTGCTGCATTTG 59.509 43.478 1.31 0.00 0.00 2.32
4325 4516 1.409427 ACCTGGCTCGTTATACAGCTC 59.591 52.381 0.00 0.00 35.82 4.09
4349 4540 3.837213 TGCTTTCAGCTGCTTGATTAC 57.163 42.857 9.47 0.00 42.97 1.89
4350 4541 3.415212 TGCTTTCAGCTGCTTGATTACT 58.585 40.909 9.47 0.00 42.97 2.24
4432 4639 2.863740 CAAGCGGCAATTATCACTCGTA 59.136 45.455 1.45 0.00 0.00 3.43
4492 4699 4.039124 CCAATTGGGTTCAGCAACTTACTT 59.961 41.667 17.36 0.00 32.50 2.24
4499 4706 3.207265 TCAGCAACTTACTTTCTGGCA 57.793 42.857 0.00 0.00 0.00 4.92
4524 4734 2.342648 GTTCGGGTGAGGCGAACT 59.657 61.111 1.57 0.00 38.93 3.01
4568 4778 3.279434 CTGGCAACTGTTAGGGTTATCC 58.721 50.000 0.00 0.00 37.61 2.59
4570 4780 3.014623 GGCAACTGTTAGGGTTATCCAC 58.985 50.000 0.00 0.00 38.24 4.02
4579 4789 6.843752 TGTTAGGGTTATCCACTCTTTTGAA 58.156 36.000 0.00 0.00 37.43 2.69
4580 4790 7.291566 TGTTAGGGTTATCCACTCTTTTGAAA 58.708 34.615 0.00 0.00 37.43 2.69
4581 4791 7.447238 TGTTAGGGTTATCCACTCTTTTGAAAG 59.553 37.037 0.00 0.00 37.43 2.62
4582 4792 5.953571 AGGGTTATCCACTCTTTTGAAAGT 58.046 37.500 3.63 0.00 27.89 2.66
4583 4793 6.004574 AGGGTTATCCACTCTTTTGAAAGTC 58.995 40.000 3.63 0.00 27.89 3.01
4584 4794 6.004574 GGGTTATCCACTCTTTTGAAAGTCT 58.995 40.000 3.63 0.00 35.02 3.24
4585 4795 6.490381 GGGTTATCCACTCTTTTGAAAGTCTT 59.510 38.462 3.63 0.00 35.02 3.01
4586 4796 7.308649 GGGTTATCCACTCTTTTGAAAGTCTTC 60.309 40.741 3.63 0.00 35.02 2.87
4670 4890 8.428186 TCTTATTGTATCCAAACCGAATGTAC 57.572 34.615 0.00 0.00 33.44 2.90
4674 4894 5.353938 TGTATCCAAACCGAATGTACTAGC 58.646 41.667 0.00 0.00 0.00 3.42
4675 4895 4.755266 ATCCAAACCGAATGTACTAGCT 57.245 40.909 0.00 0.00 0.00 3.32
4676 4896 4.119442 TCCAAACCGAATGTACTAGCTC 57.881 45.455 0.00 0.00 0.00 4.09
4677 4897 3.767673 TCCAAACCGAATGTACTAGCTCT 59.232 43.478 0.00 0.00 0.00 4.09
4749 5009 2.341257 CCAGACTGACCAAGAACATCG 58.659 52.381 3.32 0.00 0.00 3.84
4752 5012 2.027745 AGACTGACCAAGAACATCGCAT 60.028 45.455 0.00 0.00 0.00 4.73
4769 5029 6.372659 ACATCGCATGAAAGATACTCAAGTTT 59.627 34.615 0.00 0.00 0.00 2.66
4787 5048 8.251750 TCAAGTTTGGTTGATTCTATAACTCG 57.748 34.615 0.00 0.00 31.31 4.18
4789 5050 6.407202 AGTTTGGTTGATTCTATAACTCGCT 58.593 36.000 0.00 0.00 0.00 4.93
4790 5051 6.313905 AGTTTGGTTGATTCTATAACTCGCTG 59.686 38.462 0.00 0.00 0.00 5.18
4802 5063 8.178313 TCTATAACTCGCTGGAAATAGAATCA 57.822 34.615 0.00 0.00 0.00 2.57
4872 5133 3.032017 CGGAGCAGAGAGACAAAAAGA 57.968 47.619 0.00 0.00 0.00 2.52
4873 5134 2.734079 CGGAGCAGAGAGACAAAAAGAC 59.266 50.000 0.00 0.00 0.00 3.01
4874 5135 3.733337 GGAGCAGAGAGACAAAAAGACA 58.267 45.455 0.00 0.00 0.00 3.41
4888 5149 7.284489 AGACAAAAAGACAGGCAATACACTAAA 59.716 33.333 0.00 0.00 0.00 1.85
4965 5226 0.392863 TGATCACACCGAAGCCATGG 60.393 55.000 7.63 7.63 0.00 3.66
5010 5271 2.554032 ACAGGCTTATGCAACTCAACAC 59.446 45.455 2.72 0.00 41.91 3.32
5081 5342 7.864686 TCACTATTAATCATGAAAAGCGATGG 58.135 34.615 0.00 0.00 0.00 3.51
5177 5439 2.409975 CAAATGTGCAAGAGCCTTTGG 58.590 47.619 0.00 0.00 41.13 3.28
5269 5531 1.485294 TTGCTTGAGGAGGGGCGTTA 61.485 55.000 0.00 0.00 0.00 3.18
5308 5570 2.295349 CAGCTCTTTCACCATTGCACTT 59.705 45.455 0.00 0.00 0.00 3.16
5338 5600 0.613260 CCTGATCAAACGACCCCTCA 59.387 55.000 0.00 0.00 0.00 3.86
5371 5633 1.622607 TATGGTTGGGGTCTGCCTCG 61.623 60.000 0.00 0.00 38.38 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.533222 CTTTTTCATCGTGTTTTACCGCT 58.467 39.130 0.00 0.00 0.00 5.52
52 53 1.644509 GGGGTTCTGGGCTTTTTCAT 58.355 50.000 0.00 0.00 0.00 2.57
54 55 1.532604 CCGGGGTTCTGGGCTTTTTC 61.533 60.000 0.00 0.00 35.76 2.29
55 56 1.533033 CCGGGGTTCTGGGCTTTTT 60.533 57.895 0.00 0.00 35.76 1.94
96 98 2.280552 TGGTGTAGAGGACGGGCAC 61.281 63.158 0.00 0.00 0.00 5.01
109 118 1.373812 GGGTTAAGCTCGGTGGTGT 59.626 57.895 4.41 0.00 0.00 4.16
110 119 1.740296 CGGGTTAAGCTCGGTGGTG 60.740 63.158 4.41 0.00 37.44 4.17
115 124 4.851179 GGGGCGGGTTAAGCTCGG 62.851 72.222 14.41 3.12 42.38 4.63
122 131 0.989212 ATGGTGTATGGGGCGGGTTA 60.989 55.000 0.00 0.00 0.00 2.85
136 145 2.815211 CGGCTCGTGGACATGGTG 60.815 66.667 0.00 0.00 0.00 4.17
243 252 2.818274 GTGGGGGTGAATCGCGTC 60.818 66.667 5.77 0.00 0.00 5.19
349 359 3.766691 CTGCATGTGGGGCTTGGC 61.767 66.667 0.00 0.00 0.00 4.52
409 425 2.084546 GTATTTGAAGCCGAACCAGCT 58.915 47.619 0.00 0.00 44.19 4.24
432 448 2.844348 GGAGGAGAGGTTGGGTATTTGA 59.156 50.000 0.00 0.00 0.00 2.69
433 449 2.846827 AGGAGGAGAGGTTGGGTATTTG 59.153 50.000 0.00 0.00 0.00 2.32
434 450 3.222394 AGGAGGAGAGGTTGGGTATTT 57.778 47.619 0.00 0.00 0.00 1.40
435 451 2.972153 AGGAGGAGAGGTTGGGTATT 57.028 50.000 0.00 0.00 0.00 1.89
436 452 2.319438 AGAAGGAGGAGAGGTTGGGTAT 59.681 50.000 0.00 0.00 0.00 2.73
437 453 1.722851 AGAAGGAGGAGAGGTTGGGTA 59.277 52.381 0.00 0.00 0.00 3.69
438 454 0.494095 AGAAGGAGGAGAGGTTGGGT 59.506 55.000 0.00 0.00 0.00 4.51
439 455 1.199615 GAGAAGGAGGAGAGGTTGGG 58.800 60.000 0.00 0.00 0.00 4.12
440 456 1.199615 GGAGAAGGAGGAGAGGTTGG 58.800 60.000 0.00 0.00 0.00 3.77
441 457 0.820871 CGGAGAAGGAGGAGAGGTTG 59.179 60.000 0.00 0.00 0.00 3.77
472 488 1.414919 GGGAGTGGTGTTGTGAGTACA 59.585 52.381 0.00 0.00 34.31 2.90
1077 1135 0.601046 AGCGATCGTGCATACCATGG 60.601 55.000 17.81 11.19 37.31 3.66
1132 1190 0.319211 TACGCCTCGTCCAAACTGTG 60.319 55.000 0.00 0.00 41.54 3.66
1133 1191 0.390124 TTACGCCTCGTCCAAACTGT 59.610 50.000 0.00 0.00 41.54 3.55
1134 1192 1.393539 CATTACGCCTCGTCCAAACTG 59.606 52.381 0.00 0.00 41.54 3.16
1184 1242 1.243902 CCCACACACGGCTAAAACAT 58.756 50.000 0.00 0.00 0.00 2.71
1186 1244 0.820482 ACCCCACACACGGCTAAAAC 60.820 55.000 0.00 0.00 0.00 2.43
1212 1276 4.520111 ACAGATGCATCACAGTTTTGCTAA 59.480 37.500 27.81 0.00 37.28 3.09
1215 1279 2.984471 CACAGATGCATCACAGTTTTGC 59.016 45.455 27.81 0.00 36.91 3.68
1263 1328 4.870123 AGGCAAAAGCATGTTTATCACA 57.130 36.364 0.00 0.00 40.71 3.58
1344 1416 8.976471 GGCGGAGAAGAAAATATTAAGTACTAC 58.024 37.037 0.00 0.00 0.00 2.73
1351 1423 7.816640 GCATATGGCGGAGAAGAAAATATTAA 58.183 34.615 4.56 0.00 0.00 1.40
1397 1469 1.001181 AGCATTCGCCAACAGCAAAAT 59.999 42.857 0.00 0.00 44.04 1.82
1407 1479 7.119992 TCAGTTTTTAGTAAATAGCATTCGCCA 59.880 33.333 0.00 0.00 39.83 5.69
1454 1540 1.559682 GCTCCCTGGGATTGTGAACTA 59.440 52.381 17.51 0.00 0.00 2.24
1521 1607 1.218316 CTGGGACCTTACAGACGCC 59.782 63.158 0.00 0.00 36.86 5.68
1524 1610 1.066787 GCTGACTGGGACCTTACAGAC 60.067 57.143 3.51 0.00 38.09 3.51
1597 1683 2.124151 ATCGGCATCCCCTTGCAC 60.124 61.111 0.00 0.00 44.59 4.57
1598 1684 2.124193 CATCGGCATCCCCTTGCA 60.124 61.111 0.00 0.00 44.59 4.08
1643 1729 2.598394 ACGCAGCAAGCCCAACAT 60.598 55.556 0.00 0.00 41.38 2.71
1756 1853 7.509318 ACCTGTCAGAATAGTAGCCATACATAA 59.491 37.037 0.00 0.00 34.07 1.90
1828 1925 0.827368 CCTGGCAGTCCTCCTTCTAC 59.173 60.000 14.43 0.00 0.00 2.59
1844 1941 2.289002 GCAATCATTTCTACTCGGCCTG 59.711 50.000 0.00 0.00 0.00 4.85
1863 1960 0.035534 ACACACACCTGTTCAGTGCA 60.036 50.000 0.00 0.00 38.87 4.57
1866 1963 4.284490 AGATGATACACACACCTGTTCAGT 59.716 41.667 0.00 0.00 0.00 3.41
1890 1987 5.069119 ACATAGATGACTCGGTTTAGCATCA 59.931 40.000 0.00 0.00 38.19 3.07
1901 2006 6.147821 ACCAAACAGAAAACATAGATGACTCG 59.852 38.462 0.00 0.00 0.00 4.18
1935 2040 7.816513 TCAATATCAACTGCTATAGAGTGCATC 59.183 37.037 3.21 0.00 38.59 3.91
2075 2189 6.974048 TGCAATTCACTTATACATCAATGTGC 59.026 34.615 5.89 0.00 41.89 4.57
2109 2225 5.559148 AAAGGAAACATGCCCAAATAACA 57.441 34.783 0.00 0.00 0.00 2.41
2229 2353 9.959721 GATTAACTAGGGAATGAATAGCCAATA 57.040 33.333 0.00 0.00 0.00 1.90
2272 2396 4.948847 TGACTGCTAGGCTATGTAACATG 58.051 43.478 0.00 0.00 0.00 3.21
2356 2484 4.158394 GTGACATTAAGATGCAACCACCAT 59.842 41.667 0.00 0.00 36.72 3.55
2483 2611 5.025453 AGATGGCCAAACATCCATTTTACT 58.975 37.500 10.96 0.00 46.56 2.24
2524 2652 3.497262 GGTGCAACAACTAGTCTTGGTAC 59.503 47.826 0.00 6.39 39.98 3.34
2592 2729 9.884636 AACATAGACTACTTGCATTTACATACA 57.115 29.630 0.00 0.00 0.00 2.29
2631 2768 4.669206 ATAGACCAGACAGCAGATTCAG 57.331 45.455 0.00 0.00 0.00 3.02
2767 2904 5.404946 CAAAAACTGATCATGGGATGACAC 58.595 41.667 0.00 0.00 43.01 3.67
2789 2926 8.510243 ACATGTTATTAGACATTGATCTTGCA 57.490 30.769 0.00 0.00 38.15 4.08
2800 2937 9.599866 CAGAATAGGTCAACATGTTATTAGACA 57.400 33.333 21.52 8.44 0.00 3.41
2801 2938 8.552034 GCAGAATAGGTCAACATGTTATTAGAC 58.448 37.037 11.53 13.74 0.00 2.59
2848 2985 2.894126 AGTCGTTGTTGTCTCTGGATCT 59.106 45.455 0.00 0.00 0.00 2.75
2989 3126 6.945435 TGCCATCTTTAACTAGGAATGACAAA 59.055 34.615 0.00 0.00 0.00 2.83
3010 3147 2.821378 CACATTCATTTCCACTCTGCCA 59.179 45.455 0.00 0.00 0.00 4.92
3064 3201 7.608308 ACAAAAGAGCAATAAAGCAACAAAA 57.392 28.000 0.00 0.00 36.85 2.44
3204 3342 5.741388 ATCGTATCTGAAGACAAAATGGC 57.259 39.130 0.00 0.00 0.00 4.40
3232 3370 0.115547 TGGGTAGTACCTGCCAGTCA 59.884 55.000 18.85 3.83 38.00 3.41
3248 3386 3.830744 AATGGCAATCAATGATGTGGG 57.169 42.857 0.00 0.00 0.00 4.61
3301 3439 5.185635 TGCAGAACCTCCCAAAAAGATTATG 59.814 40.000 0.00 0.00 0.00 1.90
3304 3442 3.575805 TGCAGAACCTCCCAAAAAGATT 58.424 40.909 0.00 0.00 0.00 2.40
3384 3522 8.205512 TGGTCTAGTGTGTTTGATAAACTGTAA 58.794 33.333 6.07 0.00 41.90 2.41
3404 3542 3.258123 GGTTGGTTTACGGTACTGGTCTA 59.742 47.826 6.65 0.00 0.00 2.59
3415 3553 4.728917 TTTGTCATACGGTTGGTTTACG 57.271 40.909 0.00 0.00 0.00 3.18
3425 3563 4.757799 TTCACACCATTTTGTCATACGG 57.242 40.909 0.00 0.00 0.00 4.02
3479 3647 8.918202 AGTACAGAAGAATATGTTTGGTTTGA 57.082 30.769 0.00 0.00 0.00 2.69
3490 3658 6.636454 TTCACCCCAAGTACAGAAGAATAT 57.364 37.500 0.00 0.00 0.00 1.28
3506 3674 1.380380 CCTTCCCAGCATTCACCCC 60.380 63.158 0.00 0.00 0.00 4.95
3547 3715 1.825090 TTGGAGTGCATGGCAAGTAG 58.175 50.000 0.00 0.00 41.47 2.57
3557 3725 5.748402 ACAGATTGATTAGATTGGAGTGCA 58.252 37.500 0.00 0.00 0.00 4.57
3558 3726 6.690194 AACAGATTGATTAGATTGGAGTGC 57.310 37.500 0.00 0.00 0.00 4.40
3637 3805 4.711949 AGAAGGCGGCCTGTGCAG 62.712 66.667 24.63 0.00 40.13 4.41
3718 3886 1.077212 CAGGCATCTCCACCTTGGG 60.077 63.158 0.00 0.00 38.32 4.12
3719 3887 1.751927 GCAGGCATCTCCACCTTGG 60.752 63.158 0.00 0.00 39.43 3.61
3721 3889 1.001641 GTGCAGGCATCTCCACCTT 60.002 57.895 0.00 0.00 37.29 3.50
3725 3893 1.002990 CTGTGTGCAGGCATCTCCA 60.003 57.895 0.00 0.00 39.01 3.86
3750 3918 2.066999 AGGATCCTCGTTGCCTCCC 61.067 63.158 9.02 0.00 0.00 4.30
3797 3965 1.537202 GCATCTCAGGCTCGTTGTTTT 59.463 47.619 0.00 0.00 0.00 2.43
3889 4057 0.657840 GTATTGTCCATGGCTGTCGC 59.342 55.000 6.96 0.00 0.00 5.19
3905 4073 1.762522 CTCCATGGCTCCCTGCGTAT 61.763 60.000 6.96 0.00 44.05 3.06
3906 4074 2.364973 TCCATGGCTCCCTGCGTA 60.365 61.111 6.96 0.00 44.05 4.42
3907 4075 3.790437 CTCCATGGCTCCCTGCGT 61.790 66.667 6.96 0.00 44.05 5.24
3908 4076 4.559063 CCTCCATGGCTCCCTGCG 62.559 72.222 6.96 0.00 44.05 5.18
3909 4077 1.130054 TATCCTCCATGGCTCCCTGC 61.130 60.000 6.96 0.00 41.94 4.85
3910 4078 1.350351 CTTATCCTCCATGGCTCCCTG 59.650 57.143 6.96 0.00 35.26 4.45
3911 4079 1.739750 CTTATCCTCCATGGCTCCCT 58.260 55.000 6.96 0.00 35.26 4.20
3912 4080 0.037447 GCTTATCCTCCATGGCTCCC 59.963 60.000 6.96 0.00 35.26 4.30
3913 4081 0.767375 TGCTTATCCTCCATGGCTCC 59.233 55.000 6.96 0.00 35.26 4.70
3914 4082 1.881498 GCTGCTTATCCTCCATGGCTC 60.881 57.143 6.96 0.00 35.26 4.70
3915 4083 0.110104 GCTGCTTATCCTCCATGGCT 59.890 55.000 6.96 0.00 35.26 4.75
3916 4084 0.179009 TGCTGCTTATCCTCCATGGC 60.179 55.000 6.96 0.00 35.26 4.40
3917 4085 1.544982 CCTGCTGCTTATCCTCCATGG 60.545 57.143 4.97 4.97 37.10 3.66
3918 4086 1.893544 CCTGCTGCTTATCCTCCATG 58.106 55.000 0.00 0.00 0.00 3.66
3919 4087 0.110104 GCCTGCTGCTTATCCTCCAT 59.890 55.000 0.00 0.00 36.87 3.41
3920 4088 1.528824 GCCTGCTGCTTATCCTCCA 59.471 57.895 0.00 0.00 36.87 3.86
3995 4163 3.036429 ATCTCCGGCCTGTCCTTGC 62.036 63.158 0.00 0.00 0.00 4.01
4007 4175 0.381089 GTACGTCTGGACCATCTCCG 59.619 60.000 0.00 0.00 43.03 4.63
4086 4254 0.033781 TACCGACACCAAAGGAACCG 59.966 55.000 0.00 0.00 0.00 4.44
4195 4375 6.095440 ACTTTACACAGCATCCAAATCATACC 59.905 38.462 0.00 0.00 0.00 2.73
4227 4413 7.440523 AACACTGATCAACATTTCTCTAACC 57.559 36.000 0.00 0.00 0.00 2.85
4285 4473 4.081917 AGGTAGCTCAAGAGAACTGCTTAC 60.082 45.833 0.32 0.00 35.47 2.34
4432 4639 4.219725 CGTAAATTGTTCCCCTTTGTCCAT 59.780 41.667 0.00 0.00 0.00 3.41
4548 4758 2.645297 TGGATAACCCTAACAGTTGCCA 59.355 45.455 0.00 0.00 33.39 4.92
4568 4778 8.388103 TCGTTTAAGAAGACTTTCAAAAGAGTG 58.612 33.333 9.39 0.00 39.31 3.51
4570 4780 8.818057 TCTCGTTTAAGAAGACTTTCAAAAGAG 58.182 33.333 17.24 17.24 39.31 2.85
4579 4789 6.595716 CCATCCAATCTCGTTTAAGAAGACTT 59.404 38.462 0.00 0.00 39.81 3.01
4580 4790 6.109359 CCATCCAATCTCGTTTAAGAAGACT 58.891 40.000 0.00 0.00 0.00 3.24
4581 4791 5.875359 ACCATCCAATCTCGTTTAAGAAGAC 59.125 40.000 0.00 0.00 0.00 3.01
4582 4792 5.874810 CACCATCCAATCTCGTTTAAGAAGA 59.125 40.000 0.00 0.00 0.00 2.87
4583 4793 5.874810 TCACCATCCAATCTCGTTTAAGAAG 59.125 40.000 0.00 0.00 0.00 2.85
4584 4794 5.642063 GTCACCATCCAATCTCGTTTAAGAA 59.358 40.000 0.00 0.00 0.00 2.52
4585 4795 5.046591 AGTCACCATCCAATCTCGTTTAAGA 60.047 40.000 0.00 0.00 0.00 2.10
4586 4796 5.063944 CAGTCACCATCCAATCTCGTTTAAG 59.936 44.000 0.00 0.00 0.00 1.85
4670 4890 8.807667 AATTTTTGACAATGAACAAGAGCTAG 57.192 30.769 0.00 0.00 0.00 3.42
4707 4932 4.014406 GGACCGAACATCCTTGGTATTTT 58.986 43.478 0.00 0.00 34.12 1.82
4749 5009 6.259550 ACCAAACTTGAGTATCTTTCATGC 57.740 37.500 0.00 0.00 34.92 4.06
4752 5012 8.463930 AATCAACCAAACTTGAGTATCTTTCA 57.536 30.769 0.00 0.00 33.65 2.69
4769 5029 4.404394 TCCAGCGAGTTATAGAATCAACCA 59.596 41.667 0.00 0.00 0.00 3.67
4787 5048 7.436376 GGCAAATTTAGTGATTCTATTTCCAGC 59.564 37.037 0.00 0.00 0.00 4.85
4789 5050 8.359875 TGGCAAATTTAGTGATTCTATTTCCA 57.640 30.769 0.00 0.00 0.00 3.53
4865 5126 6.640907 GGTTTAGTGTATTGCCTGTCTTTTTG 59.359 38.462 0.00 0.00 0.00 2.44
4871 5132 8.904099 ATTATAGGTTTAGTGTATTGCCTGTC 57.096 34.615 0.00 0.00 0.00 3.51
4965 5226 4.883585 TGTTGATTGATTGGGAGATACTGC 59.116 41.667 0.00 0.00 0.00 4.40
5010 5271 2.120909 GGCCATTCACCCATGGTCG 61.121 63.158 11.73 0.57 45.17 4.79
5308 5570 2.557924 GTTTGATCAGGTCAACCATGCA 59.442 45.455 0.00 0.00 46.14 3.96
5338 5600 5.512921 CCCCAACCATAAAAACATTGAGCTT 60.513 40.000 0.00 0.00 0.00 3.74
5371 5633 1.600916 GCTGGCCATCCGGGATAAC 60.601 63.158 5.51 4.57 40.01 1.89


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

AutoCloner maintained by Alex Coulton.