Multiple sequence alignment - TraesCS1A01G113600

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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 TraesCS1A01G113600 chr1A 100.000 3880 0 0 1 3880 117194973 117191094 0.000000e+00 7166.0
1 TraesCS1A01G113600 chr1B 90.054 2242 112 29 694 2900 169644268 169642103 0.000000e+00 2802.0
2 TraesCS1A01G113600 chr1B 92.329 717 35 10 1 698 169662603 169661888 0.000000e+00 1002.0
3 TraesCS1A01G113600 chr1B 84.321 1046 117 28 1401 2411 2557232 2556199 0.000000e+00 979.0
4 TraesCS1A01G113600 chr1B 84.321 1046 117 28 1401 2411 2613967 2612934 0.000000e+00 979.0
5 TraesCS1A01G113600 chr1B 81.739 805 91 28 3108 3880 169579329 169578549 4.260000e-174 621.0
6 TraesCS1A01G113600 chr1B 88.646 229 19 5 2511 2732 2556130 2555902 4.940000e-69 272.0
7 TraesCS1A01G113600 chr1B 88.646 229 19 5 2511 2732 2612865 2612637 4.940000e-69 272.0
8 TraesCS1A01G113600 chr1B 93.421 76 5 0 2893 2968 451736560 451736485 3.170000e-21 113.0
9 TraesCS1A01G113600 chr1D 91.635 1052 58 12 1901 2936 111010393 111009356 0.000000e+00 1428.0
10 TraesCS1A01G113600 chr1D 89.694 1077 43 25 849 1906 111016208 111015181 0.000000e+00 1312.0
11 TraesCS1A01G113600 chr1D 91.335 854 40 7 1 820 111035837 111034984 0.000000e+00 1136.0
12 TraesCS1A01G113600 chr1D 84.447 958 91 33 2969 3880 111009138 111008193 0.000000e+00 891.0
13 TraesCS1A01G113600 chr1D 90.657 289 15 7 1619 1906 111011126 111010849 1.320000e-99 374.0
14 TraesCS1A01G113600 chr1D 94.737 76 4 0 2893 2968 335588901 335588826 6.810000e-23 119.0
15 TraesCS1A01G113600 chrUn 84.321 1046 117 28 1401 2411 297916728 297915695 0.000000e+00 979.0
16 TraesCS1A01G113600 chrUn 88.646 229 19 5 2511 2732 297915626 297915398 4.940000e-69 272.0
17 TraesCS1A01G113600 chr4B 90.909 330 30 0 1834 2163 121936848 121936519 9.890000e-121 444.0
18 TraesCS1A01G113600 chr4B 88.325 197 22 1 2450 2646 121936417 121936222 6.480000e-58 235.0
19 TraesCS1A01G113600 chr4B 93.878 49 1 1 2289 2335 121936531 121936483 5.380000e-09 73.1
20 TraesCS1A01G113600 chr2A 83.678 435 40 11 1043 1470 596358568 596358158 7.870000e-102 381.0
21 TraesCS1A01G113600 chr7D 91.398 279 20 4 1885 2163 326033835 326033561 2.830000e-101 379.0
22 TraesCS1A01G113600 chr7D 83.478 230 27 9 1551 1771 561875545 561875318 1.830000e-48 204.0
23 TraesCS1A01G113600 chr7D 93.750 48 2 1 2921 2968 531194558 531194604 1.930000e-08 71.3
24 TraesCS1A01G113600 chr6B 93.952 248 12 1 1831 2078 444302474 444302230 4.730000e-99 372.0
25 TraesCS1A01G113600 chr7A 88.235 306 35 1 1799 2104 134016149 134015845 7.920000e-97 364.0
26 TraesCS1A01G113600 chr7A 86.164 318 41 1 1399 1716 134016521 134016207 1.340000e-89 340.0
27 TraesCS1A01G113600 chr7A 88.312 77 7 2 2893 2968 459182969 459182894 1.480000e-14 91.6
28 TraesCS1A01G113600 chr2D 83.529 340 46 3 1137 1470 22816100 22815765 3.760000e-80 309.0
29 TraesCS1A01G113600 chr2D 87.149 249 25 3 1507 1755 22815765 22815524 3.820000e-70 276.0
30 TraesCS1A01G113600 chr2D 85.606 264 24 6 1212 1465 453570405 453570146 8.270000e-67 265.0
31 TraesCS1A01G113600 chr2D 78.908 403 50 16 1507 1898 453570141 453569763 1.390000e-59 241.0
32 TraesCS1A01G113600 chr2D 88.800 125 8 5 1043 1167 453570521 453570403 8.690000e-32 148.0
33 TraesCS1A01G113600 chr3B 77.698 278 53 7 2102 2379 73849873 73850141 1.120000e-35 161.0
34 TraesCS1A01G113600 chr3B 90.164 61 4 2 2921 2979 655635075 655635015 1.160000e-10 78.7
35 TraesCS1A01G113600 chr3A 76.868 281 59 4 2099 2379 59434846 59435120 1.870000e-33 154.0
36 TraesCS1A01G113600 chr7B 91.549 71 6 0 2898 2968 521567897 521567967 8.870000e-17 99.0
37 TraesCS1A01G113600 chr3D 97.778 45 1 0 2924 2968 443724264 443724220 1.160000e-10 78.7


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 TraesCS1A01G113600 chr1A 117191094 117194973 3879 True 7166.000000 7166 100.000000 1 3880 1 chr1A.!!$R1 3879
1 TraesCS1A01G113600 chr1B 169642103 169644268 2165 True 2802.000000 2802 90.054000 694 2900 1 chr1B.!!$R2 2206
2 TraesCS1A01G113600 chr1B 169661888 169662603 715 True 1002.000000 1002 92.329000 1 698 1 chr1B.!!$R3 697
3 TraesCS1A01G113600 chr1B 2555902 2557232 1330 True 625.500000 979 86.483500 1401 2732 2 chr1B.!!$R5 1331
4 TraesCS1A01G113600 chr1B 2612637 2613967 1330 True 625.500000 979 86.483500 1401 2732 2 chr1B.!!$R6 1331
5 TraesCS1A01G113600 chr1B 169578549 169579329 780 True 621.000000 621 81.739000 3108 3880 1 chr1B.!!$R1 772
6 TraesCS1A01G113600 chr1D 111015181 111016208 1027 True 1312.000000 1312 89.694000 849 1906 1 chr1D.!!$R1 1057
7 TraesCS1A01G113600 chr1D 111034984 111035837 853 True 1136.000000 1136 91.335000 1 820 1 chr1D.!!$R2 819
8 TraesCS1A01G113600 chr1D 111008193 111011126 2933 True 897.666667 1428 88.913000 1619 3880 3 chr1D.!!$R4 2261
9 TraesCS1A01G113600 chrUn 297915398 297916728 1330 True 625.500000 979 86.483500 1401 2732 2 chrUn.!!$R1 1331
10 TraesCS1A01G113600 chr4B 121936222 121936848 626 True 250.700000 444 91.037333 1834 2646 3 chr4B.!!$R1 812
11 TraesCS1A01G113600 chr7A 134015845 134016521 676 True 352.000000 364 87.199500 1399 2104 2 chr7A.!!$R2 705
12 TraesCS1A01G113600 chr2D 22815524 22816100 576 True 292.500000 309 85.339000 1137 1755 2 chr2D.!!$R1 618
13 TraesCS1A01G113600 chr2D 453569763 453570521 758 True 218.000000 265 84.438000 1043 1898 3 chr2D.!!$R2 855

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
307 311 0.253610 ACGTGGTGGACAAGGTTTCA 59.746 50.0 0.0 0.0 32.45 2.69 F
1350 1417 0.725117 CGCGATTGGGTAAGGTGTTC 59.275 55.0 0.0 0.0 0.00 3.18 F
2684 3275 0.461961 GTGCTCATAGACCGCCTCTT 59.538 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1870 1.152830 AATCACCCCACACCACACC 59.847 57.895 0.0 0.0 0.00 4.16 R
2782 3382 1.209504 GGGTGAGACCATCGAAATCCA 59.790 52.381 0.0 0.0 41.02 3.41 R
3717 4567 2.416836 CGAGCTAACCATCGACTTCCAA 60.417 50.000 0.0 0.0 41.40 3.53 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
51 52 3.000819 TCCACCACCGCCCTACAG 61.001 66.667 0.00 0.00 0.00 2.74
52 53 4.778143 CCACCACCGCCCTACAGC 62.778 72.222 0.00 0.00 0.00 4.40
97 98 1.679032 GGCGGTTTTCCTGAGCAGTAT 60.679 52.381 0.00 0.00 37.95 2.12
105 106 7.403346 GGTTTTCCTGAGCAGTATGGATACAG 61.403 46.154 0.00 0.00 44.19 2.74
126 130 2.567049 GTCTCCGTCTCACCGTGG 59.433 66.667 0.00 0.00 0.00 4.94
143 147 3.009723 CGTGGTAATGCTGGAATGAACT 58.990 45.455 0.00 0.00 0.00 3.01
247 251 4.756458 GCAGCGCCAGTGAGCTCT 62.756 66.667 16.19 0.89 45.08 4.09
248 252 2.814341 CAGCGCCAGTGAGCTCTG 60.814 66.667 16.19 5.58 45.08 3.35
250 254 4.756458 GCGCCAGTGAGCTCTGCT 62.756 66.667 16.19 10.29 43.88 4.24
307 311 0.253610 ACGTGGTGGACAAGGTTTCA 59.746 50.000 0.00 0.00 32.45 2.69
322 326 2.500229 GTTTCAACGATGGGGTTCTCA 58.500 47.619 0.00 0.00 0.00 3.27
414 418 1.388093 CGACAAGCTGATGAACGACAG 59.612 52.381 0.00 0.00 37.22 3.51
514 536 2.209838 CGATGAGCGAACACCTATGT 57.790 50.000 0.00 0.00 44.57 2.29
544 566 2.359900 GTGCATTCACGAGGGATTTCT 58.640 47.619 0.00 0.00 32.98 2.52
553 575 5.800296 TCACGAGGGATTTCTTATTTGTCA 58.200 37.500 0.00 0.00 0.00 3.58
555 577 5.065218 CACGAGGGATTTCTTATTTGTCAGG 59.935 44.000 0.00 0.00 0.00 3.86
566 588 6.954944 TCTTATTTGTCAGGTTTCTCGTTTG 58.045 36.000 0.00 0.00 0.00 2.93
567 589 3.414549 TTTGTCAGGTTTCTCGTTTGC 57.585 42.857 0.00 0.00 0.00 3.68
568 590 2.325583 TGTCAGGTTTCTCGTTTGCT 57.674 45.000 0.00 0.00 0.00 3.91
569 591 1.939934 TGTCAGGTTTCTCGTTTGCTG 59.060 47.619 0.00 0.00 0.00 4.41
570 592 0.944386 TCAGGTTTCTCGTTTGCTGC 59.056 50.000 0.00 0.00 0.00 5.25
571 593 0.947244 CAGGTTTCTCGTTTGCTGCT 59.053 50.000 0.00 0.00 0.00 4.24
598 625 6.128902 CCGTACAGTTAGTGTTAGCTCTTTTG 60.129 42.308 0.00 0.00 40.94 2.44
601 628 9.252962 GTACAGTTAGTGTTAGCTCTTTTGTTA 57.747 33.333 0.00 0.00 40.94 2.41
610 641 6.204108 TGTTAGCTCTTTTGTTAACTAGTGCC 59.796 38.462 17.89 9.68 0.00 5.01
629 660 3.395607 TGCCCTAGTGATTGCTATCCATT 59.604 43.478 5.67 0.00 0.00 3.16
633 664 5.455183 CCCTAGTGATTGCTATCCATTGTCA 60.455 44.000 5.67 0.00 0.00 3.58
636 667 5.503927 AGTGATTGCTATCCATTGTCAGTT 58.496 37.500 5.67 0.00 0.00 3.16
753 788 1.744522 GACGGTGACCTCTCTAACCTC 59.255 57.143 0.00 0.00 0.00 3.85
758 793 3.083293 GTGACCTCTCTAACCTCTTCGT 58.917 50.000 0.00 0.00 0.00 3.85
763 798 1.544691 TCTCTAACCTCTTCGTGTGGC 59.455 52.381 0.00 0.00 32.83 5.01
770 805 3.414700 CTTCGTGTGGCTGGCGAC 61.415 66.667 0.88 0.88 34.21 5.19
826 861 4.205996 CAGAGACAAATCGTTAGATCGCTG 59.794 45.833 0.00 0.00 35.74 5.18
1034 1091 2.669133 CCCACCGAGGATCAGCCAA 61.669 63.158 0.00 0.00 41.22 4.52
1185 1245 2.124320 GCCCGCAGCCCAAGATAA 60.124 61.111 0.00 0.00 34.35 1.75
1314 1374 2.355837 TCGAGCTGTGCGTGTTCC 60.356 61.111 0.00 0.00 0.00 3.62
1318 1378 2.356553 GCTGTGCGTGTTCCCGTA 60.357 61.111 0.00 0.00 0.00 4.02
1319 1379 1.957186 GCTGTGCGTGTTCCCGTAA 60.957 57.895 0.00 0.00 0.00 3.18
1327 1389 2.222574 GCGTGTTCCCGTAACGTATTTC 60.223 50.000 0.00 0.00 41.30 2.17
1350 1417 0.725117 CGCGATTGGGTAAGGTGTTC 59.275 55.000 0.00 0.00 0.00 3.18
1353 1420 2.354805 GCGATTGGGTAAGGTGTTCTCT 60.355 50.000 0.00 0.00 0.00 3.10
1374 1445 3.281751 CTGACAACGTGCTTCGCCG 62.282 63.158 0.00 0.00 44.19 6.46
1716 1791 0.892814 GGCGCCCTACTACTCGGTAT 60.893 60.000 18.11 0.00 0.00 2.73
1721 1796 4.321527 GCGCCCTACTACTCGGTATTTAAT 60.322 45.833 0.00 0.00 0.00 1.40
1722 1797 5.397326 CGCCCTACTACTCGGTATTTAATC 58.603 45.833 0.00 0.00 0.00 1.75
1760 1868 6.585702 TCCAAGTGCAAATTCAATTACATTCG 59.414 34.615 0.00 0.00 0.00 3.34
1761 1869 6.365789 CCAAGTGCAAATTCAATTACATTCGT 59.634 34.615 0.00 0.00 0.00 3.85
1762 1870 6.932901 AGTGCAAATTCAATTACATTCGTG 57.067 33.333 0.00 0.00 0.00 4.35
2000 2587 2.420568 GGCGATCCACGACCTGGTA 61.421 63.158 0.00 0.00 45.37 3.25
2243 2832 3.885521 GCCTACGGACCCGACGAG 61.886 72.222 16.07 8.77 42.83 4.18
2282 2871 3.891834 CTCTTCGACTTCGCGCGC 61.892 66.667 27.95 23.91 39.60 6.86
2429 3018 8.362639 CCCGGTACTGTACATTAAACATATACT 58.637 37.037 18.79 0.00 0.00 2.12
2430 3019 9.188588 CCGGTACTGTACATTAAACATATACTG 57.811 37.037 18.79 0.00 31.11 2.74
2472 3061 1.867233 CGAATTCCGCCATTACTCCAG 59.133 52.381 0.00 0.00 0.00 3.86
2477 3066 1.349688 TCCGCCATTACTCCAGTTTGT 59.650 47.619 0.00 0.00 0.00 2.83
2493 3084 5.008712 CCAGTTTGTTTAGTTCTTCTCACCC 59.991 44.000 0.00 0.00 0.00 4.61
2568 3159 2.507324 GACTGCGCCGAGTTCCTC 60.507 66.667 4.18 0.00 0.00 3.71
2674 3265 1.649171 GTGTGTTCGACGTGCTCATAG 59.351 52.381 0.00 0.00 0.00 2.23
2684 3275 0.461961 GTGCTCATAGACCGCCTCTT 59.538 55.000 0.00 0.00 0.00 2.85
2702 3293 5.703130 GCCTCTTCTCCATAACATGATTACC 59.297 44.000 0.00 0.00 0.00 2.85
2782 3382 4.625972 ACAAAACGAAAACGAATGGAGT 57.374 36.364 0.00 0.00 0.00 3.85
2810 3411 2.035449 CGATGGTCTCACCCGCTTATAA 59.965 50.000 0.00 0.00 37.50 0.98
2878 3482 2.344093 TCCTTGAGGCTTAACTCCCT 57.656 50.000 0.00 0.00 36.66 4.20
2890 3495 7.441836 AGGCTTAACTCCCTAAAAATGTTTTG 58.558 34.615 0.00 0.00 0.00 2.44
2908 3513 0.259065 TGCTACTCCCTCCGTCTGAT 59.741 55.000 0.00 0.00 0.00 2.90
2912 3517 4.202535 TGCTACTCCCTCCGTCTGATATTA 60.203 45.833 0.00 0.00 0.00 0.98
2915 3520 4.805744 ACTCCCTCCGTCTGATATTAACT 58.194 43.478 0.00 0.00 0.00 2.24
2916 3521 4.585162 ACTCCCTCCGTCTGATATTAACTG 59.415 45.833 0.00 0.00 0.00 3.16
2918 3523 4.960469 TCCCTCCGTCTGATATTAACTGTT 59.040 41.667 0.00 0.00 0.00 3.16
2922 3529 6.459670 TCCGTCTGATATTAACTGTTGCTA 57.540 37.500 2.69 0.00 0.00 3.49
2936 3543 7.986085 AACTGTTGCTAAAATGAGTGTATCT 57.014 32.000 0.00 0.00 0.00 1.98
2938 3545 8.480643 ACTGTTGCTAAAATGAGTGTATCTAC 57.519 34.615 0.00 0.00 0.00 2.59
2939 3546 8.094548 ACTGTTGCTAAAATGAGTGTATCTACA 58.905 33.333 0.00 0.00 0.00 2.74
2952 3559 5.190992 TGTATCTACACACTGAAACACGT 57.809 39.130 0.00 0.00 0.00 4.49
2953 3560 5.217393 TGTATCTACACACTGAAACACGTC 58.783 41.667 0.00 0.00 0.00 4.34
2954 3561 4.585955 ATCTACACACTGAAACACGTCT 57.414 40.909 0.00 0.00 0.00 4.18
2955 3562 5.700722 ATCTACACACTGAAACACGTCTA 57.299 39.130 0.00 0.00 0.00 2.59
2956 3563 5.104562 TCTACACACTGAAACACGTCTAG 57.895 43.478 0.00 0.00 0.00 2.43
2957 3564 4.818005 TCTACACACTGAAACACGTCTAGA 59.182 41.667 0.00 0.00 0.00 2.43
2958 3565 4.585955 ACACACTGAAACACGTCTAGAT 57.414 40.909 0.00 0.00 0.00 1.98
2959 3566 5.700722 ACACACTGAAACACGTCTAGATA 57.299 39.130 0.00 0.00 0.00 1.98
2961 3568 5.009310 ACACACTGAAACACGTCTAGATACA 59.991 40.000 0.00 0.00 0.00 2.29
2962 3569 5.342525 CACACTGAAACACGTCTAGATACAC 59.657 44.000 0.00 0.00 0.00 2.90
2963 3570 5.241064 ACACTGAAACACGTCTAGATACACT 59.759 40.000 0.00 0.00 0.00 3.55
2964 3571 5.795939 CACTGAAACACGTCTAGATACACTC 59.204 44.000 0.00 0.00 0.00 3.51
2965 3572 5.472478 ACTGAAACACGTCTAGATACACTCA 59.528 40.000 0.00 0.00 0.00 3.41
2967 3574 6.920817 TGAAACACGTCTAGATACACTCATT 58.079 36.000 0.00 0.00 0.00 2.57
2991 3783 8.718102 TTAAGAATAAGCTCGCATTCTAACTT 57.282 30.769 14.93 6.00 39.91 2.66
2992 3784 6.595772 AGAATAAGCTCGCATTCTAACTTG 57.404 37.500 13.62 0.00 39.22 3.16
2998 3790 3.742640 GCTCGCATTCTAACTTGATCCCT 60.743 47.826 0.00 0.00 0.00 4.20
3004 3796 7.556275 TCGCATTCTAACTTGATCCCTAAAATT 59.444 33.333 0.00 0.00 0.00 1.82
3032 3824 8.747538 ACTACTTTTCTTCATTAACTGGTTGT 57.252 30.769 0.00 0.00 0.00 3.32
3033 3825 9.841295 ACTACTTTTCTTCATTAACTGGTTGTA 57.159 29.630 0.00 0.00 0.00 2.41
3035 3827 8.974060 ACTTTTCTTCATTAACTGGTTGTAGA 57.026 30.769 0.00 0.00 0.00 2.59
3039 3831 7.496346 TCTTCATTAACTGGTTGTAGATCCT 57.504 36.000 0.00 0.00 0.00 3.24
3040 3832 7.556844 TCTTCATTAACTGGTTGTAGATCCTC 58.443 38.462 0.00 0.00 0.00 3.71
3041 3833 6.867519 TCATTAACTGGTTGTAGATCCTCA 57.132 37.500 0.00 0.00 0.00 3.86
3042 3834 7.437713 TCATTAACTGGTTGTAGATCCTCAT 57.562 36.000 0.00 0.00 0.00 2.90
3053 3845 4.635765 TGTAGATCCTCATTTCCTTTTGCG 59.364 41.667 0.00 0.00 0.00 4.85
3063 3855 6.801575 TCATTTCCTTTTGCGAACTTAAACT 58.198 32.000 0.00 0.00 0.00 2.66
3066 3858 4.457466 TCCTTTTGCGAACTTAAACTCCT 58.543 39.130 0.00 0.00 0.00 3.69
3077 3869 9.888878 GCGAACTTAAACTCCTTTTAAACTATT 57.111 29.630 0.00 0.00 38.84 1.73
3103 3898 9.798885 TTTTTGACATTAAAGTTCAAACGTTTG 57.201 25.926 30.63 30.63 39.48 2.93
3105 3900 5.517054 TGACATTAAAGTTCAAACGTTTGCC 59.483 36.000 31.42 23.83 38.05 4.52
3106 3901 4.501198 ACATTAAAGTTCAAACGTTTGCCG 59.499 37.500 31.42 12.74 44.03 5.69
3179 3977 7.675962 TTAGAAAATACGTACCAAGCACAAT 57.324 32.000 0.00 0.00 0.00 2.71
3209 4007 8.974060 AGACCAAATGAAACAAGTAGTCTAAA 57.026 30.769 0.00 0.00 30.65 1.85
3249 4055 3.653835 AAGAGTTATTCCCCAGAAGGC 57.346 47.619 0.00 0.00 34.86 4.35
3273 4079 0.833287 ATTGGTGCTCGCTGAGGTAT 59.167 50.000 7.50 0.00 0.00 2.73
3275 4081 0.108186 TGGTGCTCGCTGAGGTATTG 60.108 55.000 7.50 0.00 0.00 1.90
3276 4082 0.175760 GGTGCTCGCTGAGGTATTGA 59.824 55.000 7.50 0.00 0.00 2.57
3277 4083 1.202580 GGTGCTCGCTGAGGTATTGAT 60.203 52.381 7.50 0.00 0.00 2.57
3278 4084 2.555199 GTGCTCGCTGAGGTATTGATT 58.445 47.619 7.50 0.00 0.00 2.57
3279 4085 2.286294 GTGCTCGCTGAGGTATTGATTG 59.714 50.000 7.50 0.00 0.00 2.67
3294 4100 7.229306 AGGTATTGATTGTATAGTTGCACATGG 59.771 37.037 0.00 0.00 0.00 3.66
3298 4104 2.642427 TGTATAGTTGCACATGGGCTG 58.358 47.619 22.81 0.00 34.04 4.85
3299 4105 1.334869 GTATAGTTGCACATGGGCTGC 59.665 52.381 22.81 13.64 35.03 5.25
3341 4163 8.766994 AACCTATGGATTGTATTGTTATTGCT 57.233 30.769 0.00 0.00 0.00 3.91
3388 4210 3.511146 GGCCTCAAAATCCAAGTTCATCA 59.489 43.478 0.00 0.00 0.00 3.07
3434 4266 7.719778 TCTATATGATCATGTTGTGCAAGAC 57.280 36.000 18.72 0.00 0.00 3.01
3445 4294 3.768873 TTGTGCAAGACCACACAGTGTG 61.769 50.000 24.73 24.73 46.65 3.82
3453 4302 1.211703 ACCACACAGTGTGTTCCATGA 59.788 47.619 28.18 0.00 45.08 3.07
3460 4309 5.769662 ACACAGTGTGTTCCATGAATAATGT 59.230 36.000 23.27 0.00 45.08 2.71
3474 4323 6.088016 TGAATAATGTGAAAGCAAGCTTGT 57.912 33.333 26.55 11.54 36.26 3.16
3485 4334 2.287915 AGCAAGCTTGTAACACAACGAG 59.712 45.455 26.55 0.00 33.96 4.18
3509 4358 8.911918 AGAAGCTCTCTCGATATAGTTTCTTA 57.088 34.615 8.67 0.00 36.50 2.10
3527 4376 2.011741 TATGGATTCGTGAGCCGCGT 62.012 55.000 4.92 0.00 38.57 6.01
3552 4401 2.105477 AGTGAGCTTTCTTCTTGCCTCA 59.895 45.455 0.00 0.00 0.00 3.86
3554 4403 3.505293 GTGAGCTTTCTTCTTGCCTCAAT 59.495 43.478 0.00 0.00 0.00 2.57
3561 4410 4.478206 TCTTCTTGCCTCAATGGTCTAG 57.522 45.455 0.00 0.00 38.35 2.43
3585 4434 5.957842 TTGTCTTCACAAATATGGACCAC 57.042 39.130 0.00 0.00 39.69 4.16
3602 4451 2.091499 ACCACGAGGGGTAGATGTCATA 60.091 50.000 3.29 0.00 40.07 2.15
3604 4453 4.202641 ACCACGAGGGGTAGATGTCATATA 60.203 45.833 3.29 0.00 40.07 0.86
3613 4462 6.351117 GGGGTAGATGTCATATACAAGGTAGC 60.351 46.154 17.19 0.97 42.70 3.58
3629 4478 6.607198 ACAAGGTAGCTTTAATATGCAATGGT 59.393 34.615 3.96 0.00 0.00 3.55
3646 4495 3.202829 TGGTTTGTCTTTCCGCTACTT 57.797 42.857 0.00 0.00 0.00 2.24
3684 4533 6.604735 ACAAGAGACACAAGTTTACATGTC 57.395 37.500 0.00 0.00 41.47 3.06
3685 4534 6.112734 ACAAGAGACACAAGTTTACATGTCA 58.887 36.000 0.00 0.00 43.19 3.58
3686 4535 6.767902 ACAAGAGACACAAGTTTACATGTCAT 59.232 34.615 0.00 0.00 43.19 3.06
3726 4576 7.063544 GCTATGCCTACTAATATTTGGAAGTCG 59.936 40.741 0.00 0.00 0.00 4.18
3750 4600 7.040892 TCGATGGTTAGCTCGTAATAATAGTGT 60.041 37.037 0.00 0.00 36.33 3.55
3751 4601 7.270793 CGATGGTTAGCTCGTAATAATAGTGTC 59.729 40.741 0.00 0.00 0.00 3.67
3752 4602 7.337480 TGGTTAGCTCGTAATAATAGTGTCA 57.663 36.000 0.00 0.00 0.00 3.58
3753 4603 7.948357 TGGTTAGCTCGTAATAATAGTGTCAT 58.052 34.615 0.00 0.00 0.00 3.06
3754 4604 9.070179 TGGTTAGCTCGTAATAATAGTGTCATA 57.930 33.333 0.00 0.00 0.00 2.15
3755 4605 9.557338 GGTTAGCTCGTAATAATAGTGTCATAG 57.443 37.037 0.00 0.00 0.00 2.23
3824 4674 4.732672 AGTATTACGGAAACCCTCTCAC 57.267 45.455 0.00 0.00 0.00 3.51
3835 4685 0.318441 CCCTCTCACAGTTTGCTCGA 59.682 55.000 0.00 0.00 0.00 4.04
3839 4689 3.312421 CCTCTCACAGTTTGCTCGAAAAA 59.688 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.711924 GCTGCTTGTATCCAGCGC 59.288 61.111 0.00 0.00 44.12 5.92
122 126 3.009723 AGTTCATTCCAGCATTACCACG 58.990 45.455 0.00 0.00 0.00 4.94
126 130 2.032178 GGCGAGTTCATTCCAGCATTAC 59.968 50.000 0.00 0.00 0.00 1.89
143 147 2.282180 GGCAAAGGGTGAAGGCGA 60.282 61.111 0.00 0.00 0.00 5.54
178 182 1.298859 CGTAGTTGCCACTTCCAGCC 61.299 60.000 0.00 0.00 34.06 4.85
283 287 2.014554 CTTGTCCACCACGTCGTCG 61.015 63.158 0.00 0.00 43.34 5.12
307 311 1.702957 TCCTTTGAGAACCCCATCGTT 59.297 47.619 0.00 0.00 0.00 3.85
322 326 1.302832 CGCCCTCACTTGCTCCTTT 60.303 57.895 0.00 0.00 0.00 3.11
508 530 5.065859 TGAATGCACGAATTGGTTACATAGG 59.934 40.000 6.37 0.00 0.00 2.57
544 566 5.298276 AGCAAACGAGAAACCTGACAAATAA 59.702 36.000 0.00 0.00 0.00 1.40
553 575 2.143925 GTAGCAGCAAACGAGAAACCT 58.856 47.619 0.00 0.00 0.00 3.50
555 577 1.136336 CGGTAGCAGCAAACGAGAAAC 60.136 52.381 0.00 0.00 0.00 2.78
566 588 2.094854 ACACTAACTGTACGGTAGCAGC 60.095 50.000 8.00 0.00 36.26 5.25
567 589 3.844577 ACACTAACTGTACGGTAGCAG 57.155 47.619 8.00 8.42 38.58 4.24
568 590 4.379813 GCTAACACTAACTGTACGGTAGCA 60.380 45.833 8.00 0.00 30.51 3.49
569 591 4.101235 GCTAACACTAACTGTACGGTAGC 58.899 47.826 8.00 7.73 30.51 3.58
570 592 5.353678 AGAGCTAACACTAACTGTACGGTAG 59.646 44.000 8.00 7.90 30.51 3.18
571 593 5.248640 AGAGCTAACACTAACTGTACGGTA 58.751 41.667 8.00 0.00 30.51 4.02
610 641 5.614308 TGACAATGGATAGCAATCACTAGG 58.386 41.667 0.00 0.00 33.41 3.02
633 664 3.819564 TGCAGACACACTAGTCAAACT 57.180 42.857 0.00 0.00 40.98 2.66
636 667 3.118775 ACACTTGCAGACACACTAGTCAA 60.119 43.478 0.00 0.00 40.98 3.18
643 674 4.527564 GACAATAACACTTGCAGACACAC 58.472 43.478 0.00 0.00 0.00 3.82
753 788 3.414700 GTCGCCAGCCACACGAAG 61.415 66.667 0.00 0.00 37.60 3.79
763 798 3.463505 GTGATCACACGTCGCCAG 58.536 61.111 21.07 0.00 37.28 4.85
968 1016 2.378858 GCAGCTCACGCAGACAGAC 61.379 63.158 0.00 0.00 39.10 3.51
969 1017 2.048784 GCAGCTCACGCAGACAGA 60.049 61.111 0.00 0.00 39.10 3.41
970 1018 2.048409 AGCAGCTCACGCAGACAG 60.048 61.111 0.00 0.00 39.10 3.51
971 1019 2.356673 CAGCAGCTCACGCAGACA 60.357 61.111 0.00 0.00 39.10 3.41
1034 1091 4.505742 GGGATGAGAAGAGGTGTTTTCTGT 60.506 45.833 0.00 0.00 33.97 3.41
1168 1228 2.124320 TTATCTTGGGCTGCGGGC 60.124 61.111 11.40 11.40 40.90 6.13
1171 1231 4.147701 CCCTTATCTTGGGCTGCG 57.852 61.111 0.00 0.00 37.99 5.18
1327 1389 2.701006 CTTACCCAATCGCGCACG 59.299 61.111 8.75 0.00 42.01 5.34
1338 1404 4.710375 TGTCAGATAGAGAACACCTTACCC 59.290 45.833 0.00 0.00 0.00 3.69
1339 1405 5.916661 TGTCAGATAGAGAACACCTTACC 57.083 43.478 0.00 0.00 0.00 2.85
1350 1417 2.848887 CGAAGCACGTTGTCAGATAGAG 59.151 50.000 0.00 0.00 37.22 2.43
1374 1445 1.299850 GAACCAAAACCGGCAGTGC 60.300 57.895 6.55 6.55 0.00 4.40
1760 1868 2.351924 ATCACCCCACACCACACCAC 62.352 60.000 0.00 0.00 0.00 4.16
1761 1869 1.650242 AATCACCCCACACCACACCA 61.650 55.000 0.00 0.00 0.00 4.17
1762 1870 1.152830 AATCACCCCACACCACACC 59.847 57.895 0.00 0.00 0.00 4.16
2239 2828 3.735029 GCGTGTCGTCCTCCTCGT 61.735 66.667 0.00 0.00 0.00 4.18
2241 2830 4.477975 CCGCGTGTCGTCCTCCTC 62.478 72.222 4.92 0.00 36.19 3.71
2264 2853 3.891834 CGCGCGAAGTCGAAGAGC 61.892 66.667 28.94 3.24 43.02 4.09
2383 2972 2.265182 TAAGCTGCCACGGTTTGCC 61.265 57.895 0.00 0.00 0.00 4.52
2429 3018 6.652900 TCGTGTTCATGGATTAAGAATGTTCA 59.347 34.615 0.00 0.00 0.00 3.18
2430 3019 7.072177 TCGTGTTCATGGATTAAGAATGTTC 57.928 36.000 0.00 0.00 0.00 3.18
2472 3061 4.024302 CCGGGTGAGAAGAACTAAACAAAC 60.024 45.833 0.00 0.00 0.00 2.93
2477 3066 1.975680 AGCCGGGTGAGAAGAACTAAA 59.024 47.619 4.72 0.00 0.00 1.85
2493 3084 4.005472 GCATCCGATTGCGAGCCG 62.005 66.667 0.00 0.00 40.82 5.52
2674 3265 1.480954 TGTTATGGAGAAGAGGCGGTC 59.519 52.381 0.00 0.00 0.00 4.79
2702 3293 1.676529 CTCTGGCTTTGCATCCTCATG 59.323 52.381 0.00 0.00 0.00 3.07
2782 3382 1.209504 GGGTGAGACCATCGAAATCCA 59.790 52.381 0.00 0.00 41.02 3.41
2810 3411 5.475220 CCAGTCGTTCCATATACAGAGAGAT 59.525 44.000 0.00 0.00 0.00 2.75
2864 3468 6.835819 AACATTTTTAGGGAGTTAAGCCTC 57.164 37.500 0.00 0.00 0.00 4.70
2878 3482 5.182380 CGGAGGGAGTAGCAAAACATTTTTA 59.818 40.000 0.00 0.00 0.00 1.52
2890 3495 2.273538 TATCAGACGGAGGGAGTAGC 57.726 55.000 0.00 0.00 0.00 3.58
2912 3517 7.986085 AGATACACTCATTTTAGCAACAGTT 57.014 32.000 0.00 0.00 0.00 3.16
2936 3543 5.700722 ATCTAGACGTGTTTCAGTGTGTA 57.299 39.130 0.00 0.00 0.00 2.90
2937 3544 4.585955 ATCTAGACGTGTTTCAGTGTGT 57.414 40.909 0.00 0.00 0.00 3.72
2938 3545 5.342525 GTGTATCTAGACGTGTTTCAGTGTG 59.657 44.000 0.00 0.00 0.00 3.82
2939 3546 5.241064 AGTGTATCTAGACGTGTTTCAGTGT 59.759 40.000 0.00 0.00 0.00 3.55
2940 3547 5.700846 AGTGTATCTAGACGTGTTTCAGTG 58.299 41.667 0.00 0.00 0.00 3.66
2941 3548 5.472478 TGAGTGTATCTAGACGTGTTTCAGT 59.528 40.000 0.00 0.00 0.00 3.41
2942 3549 5.939457 TGAGTGTATCTAGACGTGTTTCAG 58.061 41.667 0.00 0.00 0.00 3.02
2943 3550 5.952526 TGAGTGTATCTAGACGTGTTTCA 57.047 39.130 0.00 0.00 0.00 2.69
2944 3551 8.906636 TTAATGAGTGTATCTAGACGTGTTTC 57.093 34.615 0.00 0.00 0.00 2.78
2945 3552 8.737175 TCTTAATGAGTGTATCTAGACGTGTTT 58.263 33.333 0.00 0.00 0.00 2.83
2955 3562 7.596995 GCGAGCTTATTCTTAATGAGTGTATCT 59.403 37.037 0.00 0.00 0.00 1.98
2956 3563 7.382488 TGCGAGCTTATTCTTAATGAGTGTATC 59.618 37.037 0.00 0.00 0.00 2.24
2957 3564 7.210174 TGCGAGCTTATTCTTAATGAGTGTAT 58.790 34.615 0.00 0.00 0.00 2.29
2958 3565 6.569780 TGCGAGCTTATTCTTAATGAGTGTA 58.430 36.000 0.00 0.00 0.00 2.90
2959 3566 5.419542 TGCGAGCTTATTCTTAATGAGTGT 58.580 37.500 0.00 0.00 0.00 3.55
2961 3568 6.989169 AGAATGCGAGCTTATTCTTAATGAGT 59.011 34.615 13.08 0.00 39.86 3.41
2962 3569 7.418840 AGAATGCGAGCTTATTCTTAATGAG 57.581 36.000 13.08 0.00 39.86 2.90
2963 3570 8.765219 GTTAGAATGCGAGCTTATTCTTAATGA 58.235 33.333 20.00 6.11 42.12 2.57
2964 3571 8.768955 AGTTAGAATGCGAGCTTATTCTTAATG 58.231 33.333 20.00 0.00 42.12 1.90
2965 3572 8.894768 AGTTAGAATGCGAGCTTATTCTTAAT 57.105 30.769 20.00 11.96 42.12 1.40
2967 3574 7.979537 TCAAGTTAGAATGCGAGCTTATTCTTA 59.020 33.333 20.00 12.52 42.12 2.10
2979 3771 6.677781 TTTTAGGGATCAAGTTAGAATGCG 57.322 37.500 0.00 0.00 0.00 4.73
3028 3820 6.325596 GCAAAAGGAAATGAGGATCTACAAC 58.674 40.000 0.00 0.00 34.92 3.32
3030 3822 4.635765 CGCAAAAGGAAATGAGGATCTACA 59.364 41.667 0.00 0.00 34.92 2.74
3031 3823 4.876107 TCGCAAAAGGAAATGAGGATCTAC 59.124 41.667 0.00 0.00 34.92 2.59
3032 3824 5.097742 TCGCAAAAGGAAATGAGGATCTA 57.902 39.130 0.00 0.00 34.92 1.98
3033 3825 3.955471 TCGCAAAAGGAAATGAGGATCT 58.045 40.909 0.00 0.00 34.92 2.75
3034 3826 4.156739 AGTTCGCAAAAGGAAATGAGGATC 59.843 41.667 0.00 0.00 0.00 3.36
3035 3827 4.082125 AGTTCGCAAAAGGAAATGAGGAT 58.918 39.130 0.00 0.00 0.00 3.24
3039 3831 6.801575 AGTTTAAGTTCGCAAAAGGAAATGA 58.198 32.000 0.00 0.00 0.00 2.57
3040 3832 6.143919 GGAGTTTAAGTTCGCAAAAGGAAATG 59.856 38.462 0.00 0.00 0.00 2.32
3041 3833 6.040504 AGGAGTTTAAGTTCGCAAAAGGAAAT 59.959 34.615 0.00 0.00 0.00 2.17
3042 3834 5.358725 AGGAGTTTAAGTTCGCAAAAGGAAA 59.641 36.000 0.00 0.00 0.00 3.13
3077 3869 9.798885 CAAACGTTTGAACTTTAATGTCAAAAA 57.201 25.926 32.36 6.47 40.55 1.94
3081 3873 5.517054 GGCAAACGTTTGAACTTTAATGTCA 59.483 36.000 38.04 0.00 40.55 3.58
3102 3897 1.300481 TGTTTTCATCGTTGACGGCA 58.700 45.000 3.48 0.00 40.29 5.69
3103 3898 2.611974 ATGTTTTCATCGTTGACGGC 57.388 45.000 3.48 0.00 40.29 5.68
3105 3900 8.874745 AGTATTAAATGTTTTCATCGTTGACG 57.125 30.769 0.00 0.00 39.94 4.35
3173 3971 7.761409 TGTTTCATTTGGTCTATCTATTGTGC 58.239 34.615 0.00 0.00 0.00 4.57
3179 3977 9.871238 GACTACTTGTTTCATTTGGTCTATCTA 57.129 33.333 0.00 0.00 0.00 1.98
3216 4014 9.971922 GGGGAATAACTCTTTGATCATAATTTG 57.028 33.333 0.00 0.00 0.00 2.32
3218 4016 9.359653 CTGGGGAATAACTCTTTGATCATAATT 57.640 33.333 0.00 0.00 0.00 1.40
3220 4018 8.101309 TCTGGGGAATAACTCTTTGATCATAA 57.899 34.615 0.00 0.00 0.00 1.90
3221 4019 7.690454 TCTGGGGAATAACTCTTTGATCATA 57.310 36.000 0.00 0.00 0.00 2.15
3222 4020 6.581388 TCTGGGGAATAACTCTTTGATCAT 57.419 37.500 0.00 0.00 0.00 2.45
3223 4021 6.387192 TTCTGGGGAATAACTCTTTGATCA 57.613 37.500 0.00 0.00 0.00 2.92
3224 4022 5.825151 CCTTCTGGGGAATAACTCTTTGATC 59.175 44.000 0.00 0.00 0.00 2.92
3225 4023 5.760131 CCTTCTGGGGAATAACTCTTTGAT 58.240 41.667 0.00 0.00 0.00 2.57
3226 4024 4.567747 GCCTTCTGGGGAATAACTCTTTGA 60.568 45.833 0.00 0.00 35.12 2.69
3227 4025 3.696548 GCCTTCTGGGGAATAACTCTTTG 59.303 47.826 0.00 0.00 35.12 2.77
3249 4055 2.749044 AGCGAGCACCAATGGCAG 60.749 61.111 0.00 0.00 0.00 4.85
3273 4079 4.097741 GCCCATGTGCAACTATACAATCAA 59.902 41.667 0.00 0.00 38.04 2.57
3275 4081 3.885297 AGCCCATGTGCAACTATACAATC 59.115 43.478 2.19 0.00 38.04 2.67
3276 4082 3.633525 CAGCCCATGTGCAACTATACAAT 59.366 43.478 2.19 0.00 38.04 2.71
3277 4083 3.016031 CAGCCCATGTGCAACTATACAA 58.984 45.455 2.19 0.00 38.04 2.41
3278 4084 2.642427 CAGCCCATGTGCAACTATACA 58.358 47.619 2.19 0.00 38.04 2.29
3279 4085 1.334869 GCAGCCCATGTGCAACTATAC 59.665 52.381 2.19 0.00 40.86 1.47
3298 4104 2.802247 GGTTCTTTTGAAGTGCATTGGC 59.198 45.455 0.00 0.00 39.39 4.52
3299 4105 4.326504 AGGTTCTTTTGAAGTGCATTGG 57.673 40.909 0.00 0.00 39.39 3.16
3341 4163 5.097742 TGAAGAACTTGTCACTCCTCAAA 57.902 39.130 0.00 0.00 0.00 2.69
3445 4294 6.035327 GCTTGCTTTCACATTATTCATGGAAC 59.965 38.462 0.00 0.00 37.17 3.62
3446 4295 6.071221 AGCTTGCTTTCACATTATTCATGGAA 60.071 34.615 0.00 0.00 37.17 3.53
3453 4302 7.382218 GTGTTACAAGCTTGCTTTCACATTATT 59.618 33.333 26.27 4.53 0.00 1.40
3460 4309 4.420168 GTTGTGTTACAAGCTTGCTTTCA 58.580 39.130 26.27 16.37 39.00 2.69
3527 4376 3.316308 GGCAAGAAGAAAGCTCACTTTGA 59.684 43.478 6.77 0.00 46.20 2.69
3552 4401 9.911788 ATATTTGTGAAGACAATCTAGACCATT 57.088 29.630 0.00 0.00 41.77 3.16
3554 4403 7.770433 CCATATTTGTGAAGACAATCTAGACCA 59.230 37.037 0.00 0.00 41.77 4.02
3561 4410 6.555315 GTGGTCCATATTTGTGAAGACAATC 58.445 40.000 0.00 0.00 41.77 2.67
3585 4434 5.105716 CCTTGTATATGACATCTACCCCTCG 60.106 48.000 8.14 0.00 38.07 4.63
3602 4451 8.796475 CCATTGCATATTAAAGCTACCTTGTAT 58.204 33.333 0.00 0.00 0.00 2.29
3604 4453 6.607198 ACCATTGCATATTAAAGCTACCTTGT 59.393 34.615 0.00 0.00 0.00 3.16
3613 4462 8.872845 GGAAAGACAAACCATTGCATATTAAAG 58.127 33.333 0.00 0.00 40.34 1.85
3629 4478 2.806244 GCAGAAGTAGCGGAAAGACAAA 59.194 45.455 0.00 0.00 0.00 2.83
3646 4495 5.480422 TGTCTCTTGTATTCTGGTAAGCAGA 59.520 40.000 0.00 0.00 0.00 4.26
3684 4533 6.513180 AGGCATAGCTTTCAAAATGATGATG 58.487 36.000 0.00 0.00 0.00 3.07
3685 4534 6.726490 AGGCATAGCTTTCAAAATGATGAT 57.274 33.333 0.00 0.00 0.00 2.45
3686 4535 6.830324 AGTAGGCATAGCTTTCAAAATGATGA 59.170 34.615 0.00 0.00 0.00 2.92
3717 4567 2.416836 CGAGCTAACCATCGACTTCCAA 60.417 50.000 0.00 0.00 41.40 3.53
3726 4576 8.080417 TGACACTATTATTACGAGCTAACCATC 58.920 37.037 0.00 0.00 0.00 3.51
3750 4600 9.612066 TGCAAGATAAATACAATGACACTATGA 57.388 29.630 0.00 0.00 0.00 2.15
3789 4639 8.515695 TTCCGTAATACTATCAAGAGAGTGAA 57.484 34.615 7.56 0.00 34.36 3.18
3797 4647 7.052142 AGAGGGTTTCCGTAATACTATCAAG 57.948 40.000 0.00 0.00 38.33 3.02
3802 4652 5.263599 TGTGAGAGGGTTTCCGTAATACTA 58.736 41.667 0.00 0.00 38.33 1.82


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

AutoCloner maintained by Alex Coulton.