Multiple sequence alignment - TraesCS1B01G136500

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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 TraesCS1B01G136500 chr1B 100.000 4143 0 0 1 4143 174602718 174598576 0.000000e+00 7651
1 TraesCS1B01G136500 chr1B 100.000 695 0 0 4410 5104 174598309 174597615 0.000000e+00 1284
2 TraesCS1B01G136500 chr1D 92.581 2588 125 27 3 2569 114009544 114007003 0.000000e+00 3653
3 TraesCS1B01G136500 chr1D 93.750 672 27 2 3477 4143 114005052 114004391 0.000000e+00 994
4 TraesCS1B01G136500 chr1D 93.958 480 21 6 2895 3372 114005525 114005052 0.000000e+00 719
5 TraesCS1B01G136500 chr1D 96.209 422 11 3 4686 5104 114004120 114003701 0.000000e+00 686
6 TraesCS1B01G136500 chr1D 93.611 360 16 4 2564 2916 114006683 114006324 9.730000e-147 531
7 TraesCS1B01G136500 chr1D 98.404 188 3 0 4410 4597 114004309 114004122 1.060000e-86 331
8 TraesCS1B01G136500 chr1A 93.427 2069 87 21 3 2047 123553529 123551486 0.000000e+00 3022
9 TraesCS1B01G136500 chr1A 92.519 1350 68 17 2038 3372 123551341 123550010 0.000000e+00 1903
10 TraesCS1B01G136500 chr1A 95.299 702 21 6 4410 5104 123549258 123548562 0.000000e+00 1103
11 TraesCS1B01G136500 chr1A 94.792 672 30 1 3477 4143 123550010 123549339 0.000000e+00 1042
12 TraesCS1B01G136500 chr2D 93.636 110 7 0 3370 3479 71386572 71386463 1.140000e-36 165
13 TraesCS1B01G136500 chr2D 90.826 109 10 0 3372 3480 131283187 131283295 4.120000e-31 147
14 TraesCS1B01G136500 chr2D 90.654 107 10 0 3370 3476 568236111 568236217 5.330000e-30 143
15 TraesCS1B01G136500 chr6D 94.340 106 6 0 3371 3476 418956987 418957092 4.090000e-36 163
16 TraesCS1B01G136500 chr6A 94.949 99 5 0 3378 3476 562528393 562528491 6.840000e-34 156
17 TraesCS1B01G136500 chr7D 91.071 112 8 2 3366 3476 26540157 26540267 3.180000e-32 150
18 TraesCS1B01G136500 chr5B 90.826 109 10 0 3371 3479 459491710 459491602 4.120000e-31 147
19 TraesCS1B01G136500 chr4D 91.509 106 9 0 3368 3473 465124235 465124130 4.120000e-31 147
20 TraesCS1B01G136500 chr4B 90.654 107 10 0 3370 3476 525268175 525268281 5.330000e-30 143


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 TraesCS1B01G136500 chr1B 174597615 174602718 5103 True 4467.500000 7651 100.000000 1 5104 2 chr1B.!!$R1 5103
1 TraesCS1B01G136500 chr1D 114003701 114009544 5843 True 1152.333333 3653 94.752167 3 5104 6 chr1D.!!$R1 5101
2 TraesCS1B01G136500 chr1A 123548562 123553529 4967 True 1767.500000 3022 94.009250 3 5104 4 chr1A.!!$R1 5101

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
433 439 0.033504 GACTGTTTCTCACGCAGGGA 59.966 55.0 0.00 0.0 34.79 4.20 F
638 649 0.102481 ACACGGGTACATGAGATCGC 59.898 55.0 0.00 0.0 0.00 4.58 F
1624 1645 0.178068 ATTGCGGTGGCGAGTAAGAT 59.822 50.0 0.00 0.0 44.10 2.40 F
3417 4771 0.385751 CCCGCGCTTCTCAAGATCTA 59.614 55.0 5.56 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1256 0.101219 TGCTCCACGTCTGATCATCG 59.899 55.0 15.55 15.55 0.0 3.84 R
1730 1751 1.561769 TACCACCAGCCCCATGACTG 61.562 60.0 0.00 0.00 0.0 3.51 R
3434 4788 0.038892 GCAGTCCGTCTCGTTGGTTA 60.039 55.0 0.00 0.00 0.0 2.85 R
4810 6176 1.739067 AGAAAACTATCCTGCCGCAC 58.261 50.0 0.00 0.00 0.0 5.34 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
41 42 7.874940 TGAAGGAAACAGAGAATAACACATTG 58.125 34.615 0.00 0.00 0.00 2.82
46 47 8.243426 GGAAACAGAGAATAACACATTGCATAA 58.757 33.333 0.00 0.00 0.00 1.90
58 59 5.163205 ACACATTGCATAACTATCCTAGGCA 60.163 40.000 2.96 0.00 34.50 4.75
75 76 9.629878 ATCCTAGGCATATATACTACACTACAC 57.370 37.037 2.96 0.00 0.00 2.90
118 119 4.883585 GCTTCCATGTCATATCCTCACAAA 59.116 41.667 0.00 0.00 0.00 2.83
154 155 2.563471 GTGGTCTCACTGATACCGAC 57.437 55.000 8.63 5.28 40.58 4.79
186 189 6.626302 TGACACATACATCATGTAGTCGAAA 58.374 36.000 3.38 0.00 46.47 3.46
187 190 6.530181 TGACACATACATCATGTAGTCGAAAC 59.470 38.462 3.38 0.00 46.47 2.78
211 217 5.642686 GACAGCCTCCTAATACATATCGAC 58.357 45.833 0.00 0.00 0.00 4.20
273 279 5.221986 TGGCAATGCTCACCTATCATAGATT 60.222 40.000 4.82 0.00 0.00 2.40
275 281 6.538021 GGCAATGCTCACCTATCATAGATTAG 59.462 42.308 4.82 0.00 0.00 1.73
433 439 0.033504 GACTGTTTCTCACGCAGGGA 59.966 55.000 0.00 0.00 34.79 4.20
457 464 4.631813 CAGACAACCCTAGTCAGCAAATAC 59.368 45.833 0.00 0.00 38.46 1.89
563 574 3.965539 GAGCAGCATCAGCACCGGT 62.966 63.158 0.00 0.00 45.49 5.28
605 616 4.933064 CGCCTCGCTGACGGATCC 62.933 72.222 0.00 0.00 40.63 3.36
638 649 0.102481 ACACGGGTACATGAGATCGC 59.898 55.000 0.00 0.00 0.00 4.58
676 687 3.443037 GACTGGTGATGATCAAGAGACG 58.557 50.000 0.00 0.00 0.00 4.18
688 699 1.067495 CAAGAGACGGAGACTGGGAAC 60.067 57.143 0.00 0.00 29.49 3.62
691 702 2.915659 ACGGAGACTGGGAACGCA 60.916 61.111 0.00 0.00 0.00 5.24
695 706 3.959991 GAGACTGGGAACGCAGGGC 62.960 68.421 19.75 12.60 32.29 5.19
707 718 0.669318 CGCAGGGCACTTACTCGAAA 60.669 55.000 0.00 0.00 0.00 3.46
725 736 0.758685 AATGCGAGGAGGAGGAGGAG 60.759 60.000 0.00 0.00 0.00 3.69
726 737 2.520741 GCGAGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
727 738 3.063197 GCGAGGAGGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
740 751 2.498941 GGAGGACGCCATGATCGGA 61.499 63.158 11.07 0.00 0.00 4.55
826 838 1.598685 TTTTGGGAGTCCGCGGTTC 60.599 57.895 27.15 22.60 35.24 3.62
890 902 2.471749 GCATCGGTCACGTAAACGAAAG 60.472 50.000 1.36 0.00 43.02 2.62
891 903 2.490328 TCGGTCACGTAAACGAAAGT 57.510 45.000 9.86 0.00 44.49 2.66
892 904 2.118683 TCGGTCACGTAAACGAAAGTG 58.881 47.619 9.86 0.00 42.62 3.16
1051 1064 4.790962 TACTCCGCCTCGCCGACT 62.791 66.667 0.00 0.00 0.00 4.18
1149 1162 1.810030 CAAGGTAGGCGCTTCGGTC 60.810 63.158 7.64 0.00 0.00 4.79
1243 1256 1.529438 TCGGTTTTCTCGTGATGTTGC 59.471 47.619 0.00 0.00 0.00 4.17
1425 1446 3.936372 TTGGTCTAGTGCAGTACTGAC 57.064 47.619 27.08 19.45 40.65 3.51
1624 1645 0.178068 ATTGCGGTGGCGAGTAAGAT 59.822 50.000 0.00 0.00 44.10 2.40
1685 1706 1.774217 TTTGGAGTCCCCTGCTGGT 60.774 57.895 6.74 0.00 35.38 4.00
1728 1749 4.220413 CGTCTCCTCCGCTAGACA 57.780 61.111 0.00 0.00 41.83 3.41
1730 1751 1.731093 GTCTCCTCCGCTAGACAGC 59.269 63.158 0.00 0.00 44.90 4.40
1851 1872 3.520290 TGGTGCTGTACTGCTACATAC 57.480 47.619 23.07 13.35 32.21 2.39
1852 1873 2.829120 TGGTGCTGTACTGCTACATACA 59.171 45.455 23.07 11.27 32.21 2.29
1853 1874 3.450817 TGGTGCTGTACTGCTACATACAT 59.549 43.478 23.07 0.00 32.21 2.29
1854 1875 4.647399 TGGTGCTGTACTGCTACATACATA 59.353 41.667 23.07 5.58 32.21 2.29
1855 1876 5.304357 TGGTGCTGTACTGCTACATACATAT 59.696 40.000 23.07 0.00 32.21 1.78
1856 1877 5.635280 GGTGCTGTACTGCTACATACATATG 59.365 44.000 23.07 0.00 39.55 1.78
2064 2251 3.489738 GCCAGGTGCATAACATTCATGTC 60.490 47.826 0.00 0.00 39.09 3.06
2281 2468 2.238521 CTGAGCCAAGCCAGGTTTAAA 58.761 47.619 0.00 0.00 0.00 1.52
2327 2514 1.077265 CCACCTGGGACTGCCAAAT 59.923 57.895 0.00 0.00 40.01 2.32
2352 2539 8.870160 TTAAAACAAGTTGAAATGATGAGTGG 57.130 30.769 10.54 0.00 0.00 4.00
2367 2554 0.744281 AGTGGCACGTTTCCCTTTTG 59.256 50.000 12.71 0.00 0.00 2.44
2698 3220 3.733443 AAGAGGATGTGCCAACAAAAC 57.267 42.857 0.00 0.00 40.46 2.43
2752 3275 2.855180 CTGCAAAAATGTGTAGCCTCG 58.145 47.619 0.00 0.00 0.00 4.63
2773 3296 5.237815 TCGCATTTCTCTCTGTTACATGTT 58.762 37.500 2.30 0.00 0.00 2.71
2780 3303 9.739276 ATTTCTCTCTGTTACATGTTTCCATTA 57.261 29.630 2.30 0.00 0.00 1.90
2852 3379 5.036117 TCTAGTTGAATTATGGGCAGGTC 57.964 43.478 0.00 0.00 0.00 3.85
2864 3391 1.208293 GGGCAGGTCCACAAAAACAAA 59.792 47.619 0.00 0.00 36.21 2.83
2955 4305 5.428253 TGCCATACTAACTCTGGTTTCATC 58.572 41.667 0.00 0.00 36.92 2.92
2960 4310 9.667107 CCATACTAACTCTGGTTTCATCTTTTA 57.333 33.333 0.00 0.00 36.92 1.52
3062 4412 3.819368 TCAACAGAAAATGGCAGAGTCA 58.181 40.909 0.00 0.00 0.00 3.41
3160 4510 3.871006 TCTCAGTTTGTTACACAGTGCAG 59.129 43.478 0.00 1.86 0.00 4.41
3170 4520 6.517605 TGTTACACAGTGCAGAGTATGTTTA 58.482 36.000 0.00 0.00 0.00 2.01
3205 4558 6.183360 GCCATGCAAATTACCATTTACCTTTG 60.183 38.462 0.00 0.00 30.90 2.77
3264 4618 6.500684 TTCTAGAACTTCCATCAAATGTGC 57.499 37.500 0.00 0.00 0.00 4.57
3272 4626 4.354071 TCCATCAAATGTGCATGTAACG 57.646 40.909 0.00 0.00 0.00 3.18
3344 4698 3.544684 ACAGCAAGTGTGTCATTTCTCA 58.455 40.909 0.00 0.00 38.28 3.27
3361 4715 5.917541 TTCTCATTTTGTCCGTGTAAGTC 57.082 39.130 0.00 0.00 0.00 3.01
3366 4720 3.804786 TTTGTCCGTGTAAGTCTGTGA 57.195 42.857 0.00 0.00 0.00 3.58
3371 4725 5.845103 TGTCCGTGTAAGTCTGTGAAAATA 58.155 37.500 0.00 0.00 0.00 1.40
3372 4726 5.693104 TGTCCGTGTAAGTCTGTGAAAATAC 59.307 40.000 0.00 0.00 0.00 1.89
3373 4727 5.924825 GTCCGTGTAAGTCTGTGAAAATACT 59.075 40.000 0.00 0.00 0.00 2.12
3374 4728 6.089150 GTCCGTGTAAGTCTGTGAAAATACTC 59.911 42.308 0.00 0.00 0.00 2.59
3375 4729 5.060569 CCGTGTAAGTCTGTGAAAATACTCG 59.939 44.000 0.00 0.00 32.95 4.18
3376 4730 5.628193 CGTGTAAGTCTGTGAAAATACTCGT 59.372 40.000 0.00 0.00 0.00 4.18
3377 4731 6.143438 CGTGTAAGTCTGTGAAAATACTCGTT 59.857 38.462 0.00 0.00 0.00 3.85
3378 4732 7.499868 GTGTAAGTCTGTGAAAATACTCGTTC 58.500 38.462 0.00 0.00 0.00 3.95
3379 4733 6.643770 TGTAAGTCTGTGAAAATACTCGTTCC 59.356 38.462 0.00 0.00 0.00 3.62
3380 4734 5.209818 AGTCTGTGAAAATACTCGTTCCA 57.790 39.130 0.00 0.00 0.00 3.53
3381 4735 5.794894 AGTCTGTGAAAATACTCGTTCCAT 58.205 37.500 0.00 0.00 0.00 3.41
3382 4736 6.231211 AGTCTGTGAAAATACTCGTTCCATT 58.769 36.000 0.00 0.00 0.00 3.16
3383 4737 6.369065 AGTCTGTGAAAATACTCGTTCCATTC 59.631 38.462 0.00 0.00 0.00 2.67
3384 4738 5.642063 TCTGTGAAAATACTCGTTCCATTCC 59.358 40.000 0.00 0.00 0.00 3.01
3385 4739 5.309638 TGTGAAAATACTCGTTCCATTCCA 58.690 37.500 0.00 0.00 0.00 3.53
3386 4740 5.180492 TGTGAAAATACTCGTTCCATTCCAC 59.820 40.000 0.00 0.00 0.00 4.02
3387 4741 5.180492 GTGAAAATACTCGTTCCATTCCACA 59.820 40.000 0.00 0.00 0.00 4.17
3388 4742 5.765677 TGAAAATACTCGTTCCATTCCACAA 59.234 36.000 0.00 0.00 0.00 3.33
3389 4743 6.432783 TGAAAATACTCGTTCCATTCCACAAT 59.567 34.615 0.00 0.00 0.00 2.71
3390 4744 5.818136 AATACTCGTTCCATTCCACAATG 57.182 39.130 0.00 0.00 39.45 2.82
3391 4745 3.140325 ACTCGTTCCATTCCACAATGT 57.860 42.857 0.00 0.00 38.22 2.71
3392 4746 4.280436 ACTCGTTCCATTCCACAATGTA 57.720 40.909 0.00 0.00 38.22 2.29
3393 4747 4.253685 ACTCGTTCCATTCCACAATGTAG 58.746 43.478 0.00 0.00 38.22 2.74
3394 4748 4.253685 CTCGTTCCATTCCACAATGTAGT 58.746 43.478 0.00 0.00 38.22 2.73
3395 4749 4.000325 TCGTTCCATTCCACAATGTAGTG 59.000 43.478 0.00 0.00 38.22 2.74
3396 4750 3.426159 CGTTCCATTCCACAATGTAGTGC 60.426 47.826 0.00 0.00 38.22 4.40
3397 4751 2.355197 TCCATTCCACAATGTAGTGCG 58.645 47.619 0.00 0.00 38.22 5.34
3398 4752 1.202177 CCATTCCACAATGTAGTGCGC 60.202 52.381 0.00 0.00 38.22 6.09
3399 4753 1.094785 ATTCCACAATGTAGTGCGCC 58.905 50.000 4.18 0.00 38.18 6.53
3400 4754 0.958382 TTCCACAATGTAGTGCGCCC 60.958 55.000 4.18 0.00 38.18 6.13
3401 4755 2.749865 CCACAATGTAGTGCGCCCG 61.750 63.158 4.18 0.00 38.18 6.13
3402 4756 3.124921 ACAATGTAGTGCGCCCGC 61.125 61.111 4.18 5.60 42.35 6.13
3403 4757 4.222589 CAATGTAGTGCGCCCGCG 62.223 66.667 4.18 4.36 45.51 6.46
3414 4768 2.512515 GCCCGCGCTTCTCAAGAT 60.513 61.111 5.56 0.00 0.00 2.40
3415 4769 2.529619 GCCCGCGCTTCTCAAGATC 61.530 63.158 5.56 0.00 0.00 2.75
3416 4770 1.142748 CCCGCGCTTCTCAAGATCT 59.857 57.895 5.56 0.00 0.00 2.75
3417 4771 0.385751 CCCGCGCTTCTCAAGATCTA 59.614 55.000 5.56 0.00 0.00 1.98
3418 4772 1.202417 CCCGCGCTTCTCAAGATCTAA 60.202 52.381 5.56 0.00 0.00 2.10
3419 4773 2.123342 CCGCGCTTCTCAAGATCTAAG 58.877 52.381 5.56 0.00 0.00 2.18
3420 4774 2.480416 CCGCGCTTCTCAAGATCTAAGT 60.480 50.000 5.56 0.00 0.00 2.24
3421 4775 3.182967 CGCGCTTCTCAAGATCTAAGTT 58.817 45.455 5.56 0.00 0.00 2.66
3422 4776 3.614616 CGCGCTTCTCAAGATCTAAGTTT 59.385 43.478 5.56 0.00 0.00 2.66
3423 4777 4.491602 CGCGCTTCTCAAGATCTAAGTTTG 60.492 45.833 5.56 0.00 0.00 2.93
3424 4778 4.627467 GCGCTTCTCAAGATCTAAGTTTGA 59.373 41.667 0.00 0.00 0.00 2.69
3425 4779 5.220378 GCGCTTCTCAAGATCTAAGTTTGAG 60.220 44.000 13.13 13.13 45.70 3.02
3426 4780 5.220378 CGCTTCTCAAGATCTAAGTTTGAGC 60.220 44.000 14.14 12.35 44.59 4.26
3427 4781 5.641209 GCTTCTCAAGATCTAAGTTTGAGCA 59.359 40.000 14.14 5.34 44.59 4.26
3428 4782 6.315891 GCTTCTCAAGATCTAAGTTTGAGCAT 59.684 38.462 14.14 0.00 44.59 3.79
3429 4783 7.493971 GCTTCTCAAGATCTAAGTTTGAGCATA 59.506 37.037 14.14 4.43 44.59 3.14
3430 4784 9.376075 CTTCTCAAGATCTAAGTTTGAGCATAA 57.624 33.333 14.14 5.56 44.59 1.90
3431 4785 9.725019 TTCTCAAGATCTAAGTTTGAGCATAAA 57.275 29.630 14.14 3.77 44.59 1.40
3432 4786 9.896645 TCTCAAGATCTAAGTTTGAGCATAAAT 57.103 29.630 14.14 0.00 44.59 1.40
3442 4796 7.867445 AGTTTGAGCATAAATTTAACCAACG 57.133 32.000 1.21 0.00 0.00 4.10
3443 4797 7.653647 AGTTTGAGCATAAATTTAACCAACGA 58.346 30.769 1.21 0.00 0.00 3.85
3444 4798 7.807907 AGTTTGAGCATAAATTTAACCAACGAG 59.192 33.333 1.21 0.00 0.00 4.18
3445 4799 7.441890 TTGAGCATAAATTTAACCAACGAGA 57.558 32.000 1.21 0.00 0.00 4.04
3446 4800 6.837992 TGAGCATAAATTTAACCAACGAGAC 58.162 36.000 1.21 0.00 0.00 3.36
3447 4801 5.864986 AGCATAAATTTAACCAACGAGACG 58.135 37.500 1.21 0.00 0.00 4.18
3448 4802 5.025826 GCATAAATTTAACCAACGAGACGG 58.974 41.667 1.21 0.00 0.00 4.79
3449 4803 5.163834 GCATAAATTTAACCAACGAGACGGA 60.164 40.000 1.21 0.00 0.00 4.69
3450 4804 4.737353 AAATTTAACCAACGAGACGGAC 57.263 40.909 0.00 0.00 0.00 4.79
3451 4805 3.672767 ATTTAACCAACGAGACGGACT 57.327 42.857 0.00 0.00 0.00 3.85
3452 4806 2.427232 TTAACCAACGAGACGGACTG 57.573 50.000 0.00 0.00 0.00 3.51
3453 4807 0.038892 TAACCAACGAGACGGACTGC 60.039 55.000 0.00 0.00 0.00 4.40
3454 4808 2.805353 CCAACGAGACGGACTGCG 60.805 66.667 0.00 0.00 0.00 5.18
3455 4809 2.805353 CAACGAGACGGACTGCGG 60.805 66.667 0.00 0.00 0.00 5.69
3456 4810 4.719369 AACGAGACGGACTGCGGC 62.719 66.667 0.00 0.00 0.00 6.53
3506 4860 8.841444 ATATCGTTTGCAATGTTCATTACTTC 57.159 30.769 0.00 0.00 0.00 3.01
3575 4934 8.236586 TCATGTAGTCATTTTACATTCTTGCAC 58.763 33.333 0.00 0.00 39.16 4.57
3593 4952 2.875672 GCACCATGGTGTCTGCTAGAAA 60.876 50.000 38.41 0.00 46.90 2.52
3655 5014 8.094798 TGGTATGTAATTCTTTGGCGATAATC 57.905 34.615 0.00 0.00 0.00 1.75
3659 5018 6.494842 TGTAATTCTTTGGCGATAATCAAGC 58.505 36.000 0.00 0.00 0.00 4.01
3800 5159 0.835941 AGGCGAGCATTCCTGAAGAT 59.164 50.000 0.00 0.00 0.00 2.40
3897 5256 7.360361 AGCTTCAAATTGTAAACCTTCTTACG 58.640 34.615 0.00 0.00 35.00 3.18
3911 5270 4.324022 CCTTCTTACGGGGTAATGTTTCCT 60.324 45.833 0.00 0.00 0.00 3.36
3935 5294 5.812286 TCCCCTTTAGACATTCAGTAAACC 58.188 41.667 0.00 0.00 0.00 3.27
4774 6133 3.381590 GGAGATTGTGTCAATTAAGGCCC 59.618 47.826 0.00 0.00 0.00 5.80
4879 6245 2.281761 CACGAGCCTGGCAACCTT 60.282 61.111 22.65 0.00 0.00 3.50
4921 6287 2.277949 CGACGTCGATCGCACCAT 60.278 61.111 33.35 0.00 44.19 3.55
4942 6308 1.145156 CATACCCCATGGCGACGAA 59.855 57.895 6.09 0.00 33.59 3.85
4957 6323 0.608130 ACGAAGAGCACCAGCACATA 59.392 50.000 0.00 0.00 45.49 2.29
4958 6324 1.001974 ACGAAGAGCACCAGCACATAA 59.998 47.619 0.00 0.00 45.49 1.90
5091 6457 1.753073 GATTTGGCTGAAGATGGTGGG 59.247 52.381 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.858935 TCCTTCAATATAAAATGCTGCGC 58.141 39.130 0.00 0.00 0.00 6.09
1 2 6.751425 TGTTTCCTTCAATATAAAATGCTGCG 59.249 34.615 0.00 0.00 0.00 5.18
24 25 7.928307 AGTTATGCAATGTGTTATTCTCTGT 57.072 32.000 0.00 0.00 0.00 3.41
75 76 4.370620 GCTATTATAGCGTTCAACCACG 57.629 45.455 8.56 0.00 42.62 4.94
93 94 4.901250 TGTGAGGATATGACATGGAAGCTA 59.099 41.667 0.00 0.00 0.00 3.32
118 119 3.707102 GACCACTAGGAGAGGCTGTAATT 59.293 47.826 0.00 0.00 38.69 1.40
145 146 4.142049 TGTGTCAATGCATAGTCGGTATCA 60.142 41.667 0.00 0.00 0.00 2.15
151 152 5.463061 TGATGTATGTGTCAATGCATAGTCG 59.537 40.000 0.00 0.00 33.63 4.18
186 189 4.156190 CGATATGTATTAGGAGGCTGTCGT 59.844 45.833 0.00 0.00 0.00 4.34
187 190 4.395231 TCGATATGTATTAGGAGGCTGTCG 59.605 45.833 0.00 0.00 0.00 4.35
211 217 6.456718 GCTCTCTTGCTGATTTTGTTAGCTAG 60.457 42.308 0.00 0.00 41.40 3.42
224 230 2.696506 CAGTGATTGCTCTCTTGCTGA 58.303 47.619 0.00 0.00 0.00 4.26
254 260 9.314133 TGTTACTAATCTATGATAGGTGAGCAT 57.686 33.333 0.00 0.00 37.99 3.79
273 279 7.870954 CACTTGTCCTAACTGTGATTGTTACTA 59.129 37.037 0.00 0.00 34.67 1.82
275 281 6.704493 TCACTTGTCCTAACTGTGATTGTTAC 59.296 38.462 0.00 0.00 35.91 2.50
279 285 6.808008 ATTCACTTGTCCTAACTGTGATTG 57.192 37.500 0.00 0.00 38.42 2.67
288 294 7.037438 GTCCGTGTATTATTCACTTGTCCTAA 58.963 38.462 0.87 0.00 34.14 2.69
433 439 1.717032 TGCTGACTAGGGTTGTCTGT 58.283 50.000 0.00 0.00 36.30 3.41
448 455 2.190161 TCGTTCGGATCGTATTTGCTG 58.810 47.619 8.18 0.00 0.00 4.41
457 464 2.041966 CGTAATTCCTCGTTCGGATCG 58.958 52.381 2.13 2.13 32.02 3.69
605 616 2.179517 GTGTCGTCTCGGAGCAGG 59.820 66.667 0.00 0.00 0.00 4.85
676 687 2.266055 CCTGCGTTCCCAGTCTCC 59.734 66.667 0.00 0.00 0.00 3.71
688 699 0.669318 TTTCGAGTAAGTGCCCTGCG 60.669 55.000 0.00 0.00 0.00 5.18
691 702 1.739067 GCATTTCGAGTAAGTGCCCT 58.261 50.000 0.00 0.00 43.14 5.19
707 718 1.152567 CTCCTCCTCCTCCTCGCAT 60.153 63.158 0.00 0.00 0.00 4.73
725 736 2.029666 CCTCCGATCATGGCGTCC 59.970 66.667 7.84 0.00 0.00 4.79
726 737 1.300233 GTCCTCCGATCATGGCGTC 60.300 63.158 7.84 0.00 0.00 5.19
727 738 2.815308 GTCCTCCGATCATGGCGT 59.185 61.111 7.84 0.00 0.00 5.68
740 751 1.957877 GATTCGATCCTTCTCCGTCCT 59.042 52.381 0.00 0.00 0.00 3.85
890 902 0.110823 CGCAGCTGGAAAACGTACAC 60.111 55.000 17.12 0.00 0.00 2.90
891 903 0.531090 ACGCAGCTGGAAAACGTACA 60.531 50.000 17.12 0.00 34.79 2.90
892 904 0.584876 AACGCAGCTGGAAAACGTAC 59.415 50.000 17.12 0.00 35.64 3.67
916 929 2.162921 CTGTGCACGACCGCTTGAAG 62.163 60.000 13.13 0.00 0.00 3.02
1170 1183 1.764054 CAGGGAGTAGCAGAGGGGG 60.764 68.421 0.00 0.00 0.00 5.40
1171 1184 2.439104 GCAGGGAGTAGCAGAGGGG 61.439 68.421 0.00 0.00 0.00 4.79
1172 1185 2.790791 CGCAGGGAGTAGCAGAGGG 61.791 68.421 0.00 0.00 0.00 4.30
1173 1186 1.754621 TCGCAGGGAGTAGCAGAGG 60.755 63.158 0.00 0.00 0.00 3.69
1174 1187 1.034838 AGTCGCAGGGAGTAGCAGAG 61.035 60.000 0.00 0.00 0.00 3.35
1175 1188 1.000771 AGTCGCAGGGAGTAGCAGA 60.001 57.895 0.00 0.00 0.00 4.26
1176 1189 1.140589 CAGTCGCAGGGAGTAGCAG 59.859 63.158 0.00 0.00 0.00 4.24
1243 1256 0.101219 TGCTCCACGTCTGATCATCG 59.899 55.000 15.55 15.55 0.00 3.84
1425 1446 0.757188 AGTACCCCCTGCTCATCTCG 60.757 60.000 0.00 0.00 0.00 4.04
1476 1497 4.183223 AGATGCCATTTATACCTTGCCA 57.817 40.909 0.00 0.00 0.00 4.92
1529 1550 3.135895 ACCAACAGTTACTGCTTACTGGT 59.864 43.478 12.80 13.52 44.68 4.00
1530 1551 3.498397 CACCAACAGTTACTGCTTACTGG 59.502 47.826 12.80 12.94 44.68 4.00
1531 1552 4.377021 TCACCAACAGTTACTGCTTACTG 58.623 43.478 12.80 0.00 45.61 2.74
1624 1645 1.688735 CAGCGACCTCTGGGATAATGA 59.311 52.381 0.00 0.00 36.25 2.57
1685 1706 1.647545 GCGGCAGTTGCAATGCTCTA 61.648 55.000 23.69 0.00 43.35 2.43
1728 1749 2.937689 ACCAGCCCCATGACTGCT 60.938 61.111 0.00 0.00 35.25 4.24
1730 1751 1.561769 TACCACCAGCCCCATGACTG 61.562 60.000 0.00 0.00 0.00 3.51
2027 2055 4.125703 CACCTGGCATCATTTACTCTCTC 58.874 47.826 0.00 0.00 0.00 3.20
2029 2057 2.615912 GCACCTGGCATCATTTACTCTC 59.384 50.000 0.00 0.00 43.97 3.20
2064 2251 7.137490 TCTAATTTGCATCTGACAAGTGAAG 57.863 36.000 0.00 0.00 0.00 3.02
2140 2327 7.230510 AGACACAGAACATTGCTTAATTGGTTA 59.769 33.333 0.00 0.00 0.00 2.85
2141 2328 6.040842 AGACACAGAACATTGCTTAATTGGTT 59.959 34.615 0.00 0.00 0.00 3.67
2142 2329 5.536161 AGACACAGAACATTGCTTAATTGGT 59.464 36.000 0.00 0.00 0.00 3.67
2153 2340 4.940046 CCATAAGCAGAGACACAGAACATT 59.060 41.667 0.00 0.00 0.00 2.71
2159 2346 4.153117 GTCAAACCATAAGCAGAGACACAG 59.847 45.833 0.00 0.00 0.00 3.66
2161 2348 3.123621 CGTCAAACCATAAGCAGAGACAC 59.876 47.826 0.00 0.00 0.00 3.67
2281 2468 5.045797 GGAGTTACACCCTTTCTGGATAAGT 60.046 44.000 0.00 0.00 38.35 2.24
2327 2514 7.437862 GCCACTCATCATTTCAACTTGTTTTAA 59.562 33.333 0.00 0.00 0.00 1.52
2352 2539 1.598601 TCGTACAAAAGGGAAACGTGC 59.401 47.619 0.00 0.00 35.21 5.34
2367 2554 5.291128 CCAAGAAACATGACCATAGTCGTAC 59.709 44.000 0.00 0.00 46.74 3.67
2569 3091 2.722094 TGGTGTGATTTCCATACTGCC 58.278 47.619 0.00 0.00 37.11 4.85
2618 3140 1.987770 GCAAGACAAATGGATGCAACG 59.012 47.619 0.00 0.00 37.00 4.10
2698 3220 1.745087 GACCATGCACATAACAGTGGG 59.255 52.381 3.90 0.00 39.87 4.61
2752 3275 6.072508 TGGAAACATGTAACAGAGAGAAATGC 60.073 38.462 0.00 0.00 33.40 3.56
2780 3303 8.855110 TGTGAACTTGACATGGTAATTTGTAAT 58.145 29.630 0.00 0.00 0.00 1.89
2830 3357 4.141482 GGACCTGCCCATAATTCAACTAGA 60.141 45.833 0.00 0.00 0.00 2.43
2941 4290 8.695456 ACAATGTTAAAAGATGAAACCAGAGTT 58.305 29.630 0.00 0.00 38.03 3.01
2960 4310 7.776969 AGAGCATATATCCAAGTTGACAATGTT 59.223 33.333 3.87 0.00 0.00 2.71
3062 4412 5.189180 GCATCAAGAAAAGGTAGACTCCAT 58.811 41.667 0.00 0.00 0.00 3.41
3101 4451 6.535508 AGAATACCTCATACGCTTCAACTTTC 59.464 38.462 0.00 0.00 0.00 2.62
3160 4510 7.805071 GCATGGCTTTACATCATAAACATACTC 59.195 37.037 0.00 0.00 0.00 2.59
3170 4520 6.127111 TGGTAATTTGCATGGCTTTACATCAT 60.127 34.615 0.00 0.00 0.00 2.45
3205 4558 5.587844 AGCACCATCTCATGTAGATTGAAAC 59.412 40.000 10.92 3.58 42.62 2.78
3242 4596 5.559770 TGCACATTTGATGGAAGTTCTAGA 58.440 37.500 2.25 0.00 33.60 2.43
3264 4618 4.406069 CTCAATTCACAAGGCGTTACATG 58.594 43.478 0.00 0.00 0.00 3.21
3272 4626 2.704725 TTTCGCTCAATTCACAAGGC 57.295 45.000 0.00 0.00 0.00 4.35
3332 4686 4.911610 CACGGACAAAATGAGAAATGACAC 59.088 41.667 0.00 0.00 0.00 3.67
3344 4698 4.699637 TCACAGACTTACACGGACAAAAT 58.300 39.130 0.00 0.00 0.00 1.82
3361 4715 5.411361 TGGAATGGAACGAGTATTTTCACAG 59.589 40.000 0.00 0.00 0.00 3.66
3366 4720 6.208599 ACATTGTGGAATGGAACGAGTATTTT 59.791 34.615 0.00 0.00 43.00 1.82
3371 4725 3.140325 ACATTGTGGAATGGAACGAGT 57.860 42.857 0.00 0.00 43.00 4.18
3372 4726 4.093408 CACTACATTGTGGAATGGAACGAG 59.907 45.833 7.20 0.00 43.00 4.18
3373 4727 4.000325 CACTACATTGTGGAATGGAACGA 59.000 43.478 7.20 0.00 43.00 3.85
3374 4728 3.426159 GCACTACATTGTGGAATGGAACG 60.426 47.826 7.20 0.00 43.00 3.95
3375 4729 3.426159 CGCACTACATTGTGGAATGGAAC 60.426 47.826 7.20 0.00 43.00 3.62
3376 4730 2.746904 CGCACTACATTGTGGAATGGAA 59.253 45.455 7.20 0.00 43.00 3.53
3377 4731 2.355197 CGCACTACATTGTGGAATGGA 58.645 47.619 7.20 0.00 43.00 3.41
3378 4732 1.202177 GCGCACTACATTGTGGAATGG 60.202 52.381 0.30 0.00 43.00 3.16
3379 4733 1.202177 GGCGCACTACATTGTGGAATG 60.202 52.381 10.83 0.00 44.11 2.67
3380 4734 1.094785 GGCGCACTACATTGTGGAAT 58.905 50.000 10.83 0.00 38.31 3.01
3381 4735 0.958382 GGGCGCACTACATTGTGGAA 60.958 55.000 10.83 0.00 38.31 3.53
3382 4736 1.376683 GGGCGCACTACATTGTGGA 60.377 57.895 10.83 0.00 38.31 4.02
3383 4737 2.749865 CGGGCGCACTACATTGTGG 61.750 63.158 8.62 0.00 38.31 4.17
3384 4738 2.784596 CGGGCGCACTACATTGTG 59.215 61.111 8.62 0.00 40.62 3.33
3385 4739 3.124921 GCGGGCGCACTACATTGT 61.125 61.111 8.62 0.00 41.49 2.71
3386 4740 4.222589 CGCGGGCGCACTACATTG 62.223 66.667 8.62 0.00 42.06 2.82
3397 4751 2.512515 ATCTTGAGAAGCGCGGGC 60.513 61.111 17.92 17.92 40.37 6.13
3398 4752 0.385751 TAGATCTTGAGAAGCGCGGG 59.614 55.000 8.83 0.00 0.00 6.13
3399 4753 2.123342 CTTAGATCTTGAGAAGCGCGG 58.877 52.381 8.83 0.00 0.00 6.46
3400 4754 2.803451 ACTTAGATCTTGAGAAGCGCG 58.197 47.619 0.00 0.00 0.00 6.86
3401 4755 4.627467 TCAAACTTAGATCTTGAGAAGCGC 59.373 41.667 0.00 0.00 0.00 5.92
3402 4756 5.220378 GCTCAAACTTAGATCTTGAGAAGCG 60.220 44.000 20.64 4.22 45.86 4.68
3403 4757 5.641209 TGCTCAAACTTAGATCTTGAGAAGC 59.359 40.000 20.64 16.38 45.86 3.86
3404 4758 7.846644 ATGCTCAAACTTAGATCTTGAGAAG 57.153 36.000 20.64 12.13 45.86 2.85
3405 4759 9.725019 TTTATGCTCAAACTTAGATCTTGAGAA 57.275 29.630 20.64 13.33 45.86 2.87
3406 4760 9.896645 ATTTATGCTCAAACTTAGATCTTGAGA 57.103 29.630 20.64 9.51 45.86 3.27
3416 4770 9.400638 CGTTGGTTAAATTTATGCTCAAACTTA 57.599 29.630 0.00 0.00 0.00 2.24
3417 4771 8.138712 TCGTTGGTTAAATTTATGCTCAAACTT 58.861 29.630 0.00 0.00 0.00 2.66
3418 4772 7.653647 TCGTTGGTTAAATTTATGCTCAAACT 58.346 30.769 0.00 0.00 0.00 2.66
3419 4773 7.806014 TCTCGTTGGTTAAATTTATGCTCAAAC 59.194 33.333 0.00 0.00 0.00 2.93
3420 4774 7.806014 GTCTCGTTGGTTAAATTTATGCTCAAA 59.194 33.333 0.00 0.00 0.00 2.69
3421 4775 7.302524 GTCTCGTTGGTTAAATTTATGCTCAA 58.697 34.615 0.00 0.00 0.00 3.02
3422 4776 6.401688 CGTCTCGTTGGTTAAATTTATGCTCA 60.402 38.462 0.00 0.00 0.00 4.26
3423 4777 5.957796 CGTCTCGTTGGTTAAATTTATGCTC 59.042 40.000 0.00 0.00 0.00 4.26
3424 4778 5.163794 CCGTCTCGTTGGTTAAATTTATGCT 60.164 40.000 0.00 0.00 0.00 3.79
3425 4779 5.025826 CCGTCTCGTTGGTTAAATTTATGC 58.974 41.667 0.00 0.00 0.00 3.14
3426 4780 6.091713 AGTCCGTCTCGTTGGTTAAATTTATG 59.908 38.462 0.00 0.00 0.00 1.90
3427 4781 6.091713 CAGTCCGTCTCGTTGGTTAAATTTAT 59.908 38.462 0.00 0.00 0.00 1.40
3428 4782 5.406175 CAGTCCGTCTCGTTGGTTAAATTTA 59.594 40.000 0.00 0.00 0.00 1.40
3429 4783 4.212636 CAGTCCGTCTCGTTGGTTAAATTT 59.787 41.667 0.00 0.00 0.00 1.82
3430 4784 3.744426 CAGTCCGTCTCGTTGGTTAAATT 59.256 43.478 0.00 0.00 0.00 1.82
3431 4785 3.323243 CAGTCCGTCTCGTTGGTTAAAT 58.677 45.455 0.00 0.00 0.00 1.40
3432 4786 2.746269 CAGTCCGTCTCGTTGGTTAAA 58.254 47.619 0.00 0.00 0.00 1.52
3433 4787 1.603678 GCAGTCCGTCTCGTTGGTTAA 60.604 52.381 0.00 0.00 0.00 2.01
3434 4788 0.038892 GCAGTCCGTCTCGTTGGTTA 60.039 55.000 0.00 0.00 0.00 2.85
3435 4789 1.300697 GCAGTCCGTCTCGTTGGTT 60.301 57.895 0.00 0.00 0.00 3.67
3436 4790 2.338984 GCAGTCCGTCTCGTTGGT 59.661 61.111 0.00 0.00 0.00 3.67
3437 4791 2.805353 CGCAGTCCGTCTCGTTGG 60.805 66.667 0.00 0.00 0.00 3.77
3438 4792 2.805353 CCGCAGTCCGTCTCGTTG 60.805 66.667 0.00 0.00 34.38 4.10
3439 4793 4.719369 GCCGCAGTCCGTCTCGTT 62.719 66.667 0.00 0.00 34.38 3.85
3449 4803 4.947147 TTTTGCTCCCGCCGCAGT 62.947 61.111 0.00 0.00 38.80 4.40
3450 4804 2.490993 AATTTTTGCTCCCGCCGCAG 62.491 55.000 0.00 0.00 38.80 5.18
3451 4805 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
3452 4806 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
3453 4807 2.287368 GGTATAATTTTTGCTCCCGCCG 60.287 50.000 0.00 0.00 34.43 6.46
3454 4808 2.691011 TGGTATAATTTTTGCTCCCGCC 59.309 45.455 0.00 0.00 34.43 6.13
3455 4809 4.379339 TTGGTATAATTTTTGCTCCCGC 57.621 40.909 0.00 0.00 0.00 6.13
3456 4810 5.901552 ACATTGGTATAATTTTTGCTCCCG 58.098 37.500 0.00 0.00 0.00 5.14
3470 4824 8.629158 ACATTGCAAACGATATAACATTGGTAT 58.371 29.630 1.71 0.00 0.00 2.73
3471 4825 7.990917 ACATTGCAAACGATATAACATTGGTA 58.009 30.769 1.71 0.00 0.00 3.25
3472 4826 6.862209 ACATTGCAAACGATATAACATTGGT 58.138 32.000 1.71 0.00 0.00 3.67
3473 4827 7.487509 TGAACATTGCAAACGATATAACATTGG 59.512 33.333 1.71 0.00 0.00 3.16
3474 4828 8.392124 TGAACATTGCAAACGATATAACATTG 57.608 30.769 1.71 0.00 0.00 2.82
3475 4829 9.585099 AATGAACATTGCAAACGATATAACATT 57.415 25.926 1.71 4.04 0.00 2.71
3575 4934 3.679389 AGTTTTCTAGCAGACACCATGG 58.321 45.455 11.19 11.19 0.00 3.66
3593 4952 5.116180 TCAAATGACGAGTCAAGACAAGTT 58.884 37.500 10.15 0.00 43.58 2.66
3636 4995 6.729187 AGCTTGATTATCGCCAAAGAATTAC 58.271 36.000 0.00 0.00 0.00 1.89
3659 5018 2.433604 TCAGCCCATCAGAAGCTCTTAG 59.566 50.000 0.00 0.00 33.70 2.18
3735 5094 6.470278 CCATGCATCTATAAATGAGACCTGA 58.530 40.000 0.00 0.00 0.00 3.86
3754 5113 3.004106 GGACTTGATGATAACAGCCATGC 59.996 47.826 0.00 0.00 0.00 4.06
3786 5145 3.715315 TCCTCATCATCTTCAGGAATGCT 59.285 43.478 0.00 0.00 31.78 3.79
3800 5159 3.199727 TGGATTGTCCGATTTCCTCATCA 59.800 43.478 0.00 0.00 40.17 3.07
3897 5256 2.154567 GGGGAAGGAAACATTACCCC 57.845 55.000 5.25 0.00 44.19 4.95
3911 5270 6.183361 TGGTTTACTGAATGTCTAAAGGGGAA 60.183 38.462 0.00 0.00 0.00 3.97
3935 5294 2.557920 AACCAGAACCTCTGCTTCTG 57.442 50.000 5.82 5.82 42.98 3.02
4105 5464 6.708502 GGCCAATGTTTAAGAAGGCTTTTAAA 59.291 34.615 16.38 16.38 41.71 1.52
4113 5472 6.818142 CCTAAAATGGCCAATGTTTAAGAAGG 59.182 38.462 10.96 10.30 0.00 3.46
4727 6086 9.507280 CCAACATACACATTTGATCATAACTTC 57.493 33.333 0.00 0.00 0.00 3.01
4733 6092 8.410912 CAATCTCCAACATACACATTTGATCAT 58.589 33.333 0.00 0.00 0.00 2.45
4774 6133 6.972328 CCCATAAATAACCAAGTTTGACGATG 59.028 38.462 0.00 0.00 0.00 3.84
4810 6176 1.739067 AGAAAACTATCCTGCCGCAC 58.261 50.000 0.00 0.00 0.00 5.34
4942 6308 4.220693 TGTTATTATGTGCTGGTGCTCT 57.779 40.909 0.00 0.00 40.48 4.09
4957 6323 4.100189 CGGTGGAGAAGAGGAGATGTTATT 59.900 45.833 0.00 0.00 0.00 1.40
4958 6324 3.639094 CGGTGGAGAAGAGGAGATGTTAT 59.361 47.826 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.