Multiple sequence alignment - TraesCS5D01G130200

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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 TraesCS5D01G130200 chr5D 100.000 4195 0 0 1 4195 205576430 205572236 0.000000e+00 7747
1 TraesCS5D01G130200 chr5D 100.000 4142 0 0 4526 8667 205571905 205567764 0.000000e+00 7649
2 TraesCS5D01G130200 chr5D 92.472 797 29 14 1 775 193125240 193124453 0.000000e+00 1110
3 TraesCS5D01G130200 chr5B 96.937 3950 96 7 4599 8526 206795837 206799783 0.000000e+00 6601
4 TraesCS5D01G130200 chr5B 95.279 1885 51 12 788 2650 206791635 206793503 0.000000e+00 2953
5 TraesCS5D01G130200 chr5B 91.524 1168 73 6 2953 4102 206793950 206795109 0.000000e+00 1585
6 TraesCS5D01G130200 chr5B 95.911 269 10 1 2643 2910 206793689 206793957 1.340000e-117 435
7 TraesCS5D01G130200 chr5B 97.244 254 7 0 1 254 448102732 448102479 1.730000e-116 431
8 TraesCS5D01G130200 chr5B 95.522 268 10 2 1 266 181824216 181824483 2.240000e-115 427
9 TraesCS5D01G130200 chr5B 93.793 145 8 1 8524 8667 206799943 206800087 5.270000e-52 217
10 TraesCS5D01G130200 chr5B 98.684 76 1 0 4526 4601 206795517 206795592 1.520000e-27 135
11 TraesCS5D01G130200 chr5A 95.917 4090 124 13 4607 8667 245441557 245437482 0.000000e+00 6588
12 TraesCS5D01G130200 chr5A 92.030 2133 104 32 783 2898 245445816 245443733 0.000000e+00 2937
13 TraesCS5D01G130200 chr5A 91.828 673 18 9 783 1448 245458371 245457729 0.000000e+00 904
14 TraesCS5D01G130200 chr7D 91.282 1147 87 7 3013 4153 555056454 555055315 0.000000e+00 1552
15 TraesCS5D01G130200 chr7D 91.360 787 38 13 1 775 587548924 587549692 0.000000e+00 1050
16 TraesCS5D01G130200 chr7D 92.565 538 18 11 252 779 94753452 94753977 0.000000e+00 752
17 TraesCS5D01G130200 chr2B 91.392 1092 89 3 3013 4102 45698149 45699237 0.000000e+00 1491
18 TraesCS5D01G130200 chr2B 90.629 811 28 17 1 775 133810947 133810149 0.000000e+00 1033
19 TraesCS5D01G130200 chr6B 90.376 1091 77 6 3010 4098 495809871 495810935 0.000000e+00 1408
20 TraesCS5D01G130200 chr2D 90.179 1059 89 10 3111 4164 400513902 400514950 0.000000e+00 1365
21 TraesCS5D01G130200 chr2D 94.264 523 21 5 259 779 205052163 205052678 0.000000e+00 791
22 TraesCS5D01G130200 chr2D 93.482 537 20 10 247 779 467054527 467055052 0.000000e+00 784
23 TraesCS5D01G130200 chr2D 93.446 534 25 5 255 782 534525094 534524565 0.000000e+00 784
24 TraesCS5D01G130200 chr2D 93.573 529 22 8 259 779 560744936 560745460 0.000000e+00 778
25 TraesCS5D01G130200 chr2D 97.244 254 7 0 1 254 111146096 111145843 1.730000e-116 431
26 TraesCS5D01G130200 chr2A 88.606 1062 104 14 3109 4164 684242808 684243858 0.000000e+00 1275
27 TraesCS5D01G130200 chr2A 88.324 1062 109 13 3109 4164 68252503 68253555 0.000000e+00 1260
28 TraesCS5D01G130200 chr2A 93.939 99 6 0 3014 3112 33014306 33014208 5.420000e-32 150
29 TraesCS5D01G130200 chr2A 92.308 104 6 1 3009 3112 684242666 684242767 7.010000e-31 147
30 TraesCS5D01G130200 chr4B 88.091 1058 112 12 3112 4164 299464333 299463285 0.000000e+00 1243
31 TraesCS5D01G130200 chr4B 71.473 1283 268 72 5594 6814 123451870 123453116 1.440000e-62 252
32 TraesCS5D01G130200 chr1B 87.747 1061 116 12 3109 4164 27292638 27293689 0.000000e+00 1227
33 TraesCS5D01G130200 chr3D 93.321 539 22 9 247 779 365118183 365118713 0.000000e+00 784
34 TraesCS5D01G130200 chr3D 92.379 538 29 9 247 782 50034417 50033890 0.000000e+00 756
35 TraesCS5D01G130200 chr3D 97.244 254 7 0 1 254 608917179 608916926 1.730000e-116 431
36 TraesCS5D01G130200 chr6D 93.097 536 18 8 255 782 58443642 58443118 0.000000e+00 767
37 TraesCS5D01G130200 chr6A 92.683 533 30 7 246 775 545538822 545538296 0.000000e+00 760
38 TraesCS5D01G130200 chr1D 98.008 251 5 0 1 251 411436195 411436445 3.720000e-118 436
39 TraesCS5D01G130200 chrUn 95.896 268 9 2 1 266 10305155 10305422 4.810000e-117 433
40 TraesCS5D01G130200 chr4D 71.641 1280 268 71 5594 6814 85880059 85881302 1.860000e-66 265
41 TraesCS5D01G130200 chr4A 74.156 681 121 40 5602 6244 500115855 500116518 1.880000e-56 231
42 TraesCS5D01G130200 chr3B 94.175 103 5 1 3010 3112 76506765 76506866 1.160000e-33 156
43 TraesCS5D01G130200 chr3B 93.204 103 7 0 3010 3112 131503571 131503673 1.510000e-32 152
44 TraesCS5D01G130200 chr3B 93.204 103 7 0 3010 3112 193400085 193400187 1.510000e-32 152


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 TraesCS5D01G130200 chr5D 205567764 205576430 8666 True 7698.000000 7747 100.000000 1 8667 2 chr5D.!!$R2 8666
1 TraesCS5D01G130200 chr5D 193124453 193125240 787 True 1110.000000 1110 92.472000 1 775 1 chr5D.!!$R1 774
2 TraesCS5D01G130200 chr5B 206791635 206800087 8452 False 1987.666667 6601 95.354667 788 8667 6 chr5B.!!$F2 7879
3 TraesCS5D01G130200 chr5A 245437482 245445816 8334 True 4762.500000 6588 93.973500 783 8667 2 chr5A.!!$R2 7884
4 TraesCS5D01G130200 chr5A 245457729 245458371 642 True 904.000000 904 91.828000 783 1448 1 chr5A.!!$R1 665
5 TraesCS5D01G130200 chr7D 555055315 555056454 1139 True 1552.000000 1552 91.282000 3013 4153 1 chr7D.!!$R1 1140
6 TraesCS5D01G130200 chr7D 587548924 587549692 768 False 1050.000000 1050 91.360000 1 775 1 chr7D.!!$F2 774
7 TraesCS5D01G130200 chr7D 94753452 94753977 525 False 752.000000 752 92.565000 252 779 1 chr7D.!!$F1 527
8 TraesCS5D01G130200 chr2B 45698149 45699237 1088 False 1491.000000 1491 91.392000 3013 4102 1 chr2B.!!$F1 1089
9 TraesCS5D01G130200 chr2B 133810149 133810947 798 True 1033.000000 1033 90.629000 1 775 1 chr2B.!!$R1 774
10 TraesCS5D01G130200 chr6B 495809871 495810935 1064 False 1408.000000 1408 90.376000 3010 4098 1 chr6B.!!$F1 1088
11 TraesCS5D01G130200 chr2D 400513902 400514950 1048 False 1365.000000 1365 90.179000 3111 4164 1 chr2D.!!$F2 1053
12 TraesCS5D01G130200 chr2D 205052163 205052678 515 False 791.000000 791 94.264000 259 779 1 chr2D.!!$F1 520
13 TraesCS5D01G130200 chr2D 467054527 467055052 525 False 784.000000 784 93.482000 247 779 1 chr2D.!!$F3 532
14 TraesCS5D01G130200 chr2D 534524565 534525094 529 True 784.000000 784 93.446000 255 782 1 chr2D.!!$R2 527
15 TraesCS5D01G130200 chr2D 560744936 560745460 524 False 778.000000 778 93.573000 259 779 1 chr2D.!!$F4 520
16 TraesCS5D01G130200 chr2A 68252503 68253555 1052 False 1260.000000 1260 88.324000 3109 4164 1 chr2A.!!$F1 1055
17 TraesCS5D01G130200 chr2A 684242666 684243858 1192 False 711.000000 1275 90.457000 3009 4164 2 chr2A.!!$F2 1155
18 TraesCS5D01G130200 chr4B 299463285 299464333 1048 True 1243.000000 1243 88.091000 3112 4164 1 chr4B.!!$R1 1052
19 TraesCS5D01G130200 chr4B 123451870 123453116 1246 False 252.000000 252 71.473000 5594 6814 1 chr4B.!!$F1 1220
20 TraesCS5D01G130200 chr1B 27292638 27293689 1051 False 1227.000000 1227 87.747000 3109 4164 1 chr1B.!!$F1 1055
21 TraesCS5D01G130200 chr3D 365118183 365118713 530 False 784.000000 784 93.321000 247 779 1 chr3D.!!$F1 532
22 TraesCS5D01G130200 chr3D 50033890 50034417 527 True 756.000000 756 92.379000 247 782 1 chr3D.!!$R1 535
23 TraesCS5D01G130200 chr6D 58443118 58443642 524 True 767.000000 767 93.097000 255 782 1 chr6D.!!$R1 527
24 TraesCS5D01G130200 chr6A 545538296 545538822 526 True 760.000000 760 92.683000 246 775 1 chr6A.!!$R1 529
25 TraesCS5D01G130200 chr4D 85880059 85881302 1243 False 265.000000 265 71.641000 5594 6814 1 chr4D.!!$F1 1220
26 TraesCS5D01G130200 chr4A 500115855 500116518 663 False 231.000000 231 74.156000 5602 6244 1 chr4A.!!$F1 642

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
882 982 0.174845 CCACACGCTATCGAAGGGAA 59.825 55.000 15.09 0.00 40.56 3.97 F
884 984 0.460311 ACACGCTATCGAAGGGAAGG 59.540 55.000 15.09 8.69 40.56 3.46 F
906 1006 1.077858 GGAGGAGGGCAGCAGAAAG 60.078 63.158 0.00 0.00 0.00 2.62 F
1629 1748 1.484653 GTTTGCTTGGTTGGTTTCCCT 59.515 47.619 0.00 0.00 0.00 4.20 F
3037 3381 0.956633 ACACACATACACGACCGTCT 59.043 50.000 0.00 0.00 0.00 4.18 F
3047 3391 1.006102 CGACCGTCTTCACCAAGCT 60.006 57.895 0.00 0.00 0.00 3.74 F
4043 4438 1.078528 ACACCATCTCGACCTCCCA 59.921 57.895 0.00 0.00 0.00 4.37 F
5425 7971 0.249398 ATGGGAGTTGACGCTGGTAC 59.751 55.000 0.00 0.00 0.00 3.34 F
6786 9421 0.577269 GACGCGTGCATAGATTCACC 59.423 55.000 20.70 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1811 3.343617 TCTTTTCCCCATCGATCAACAC 58.656 45.455 0.00 0.0 0.00 3.32 R
1996 2119 4.336889 ACAGTACAAAGCAGAACTAGCA 57.663 40.909 0.00 0.0 0.00 3.49 R
2500 2625 6.969993 AGTATGATACTCAGGAAAGAGTCC 57.030 41.667 0.00 0.0 45.35 3.85 R
3366 3755 1.334869 CTCTTGAAGGCGTTGCTTTGT 59.665 47.619 0.00 0.0 0.00 2.83 R
4015 4410 0.602638 GAGATGGTGTGGAACGTGCA 60.603 55.000 0.00 0.0 42.39 4.57 R
4715 7261 0.956633 ACAGCAACTCAGCAACATGG 59.043 50.000 0.00 0.0 36.85 3.66 R
5508 8071 1.140052 ACAAGTGTGACGACCCAATCA 59.860 47.619 0.00 0.0 0.00 2.57 R
7098 9733 0.674895 AGGCGGTGATTTCAGCACTC 60.675 55.000 10.09 0.0 44.00 3.51 R
7685 10328 1.276989 TGAGACGCGGGTTTAGGAAAT 59.723 47.619 12.47 0.0 0.00 2.17 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
149 150 8.190122 CGGATGATAATCAATCTCCAAACAAAA 58.810 33.333 0.00 0.00 34.26 2.44
257 281 2.655685 GATTCTCGAGGACGGCGC 60.656 66.667 13.56 0.00 40.21 6.53
330 391 3.580319 GGCCCTGGGAGTTGGTGT 61.580 66.667 19.27 0.00 0.00 4.16
519 580 6.972328 CAGTTGTGGTGGCAAATATAATACAC 59.028 38.462 0.00 0.00 0.00 2.90
605 690 5.188948 CCCGTACCCAATAAGATGGATATGA 59.811 44.000 0.00 0.00 43.54 2.15
609 696 5.564550 ACCCAATAAGATGGATATGAGTGC 58.435 41.667 0.00 0.00 43.54 4.40
665 759 0.930726 GGAAGAGGGAGGGAGAGAGA 59.069 60.000 0.00 0.00 0.00 3.10
666 760 1.133482 GGAAGAGGGAGGGAGAGAGAG 60.133 61.905 0.00 0.00 0.00 3.20
727 821 9.112725 CCAATGTCACTTGATATGTATGAGAAA 57.887 33.333 0.00 0.00 0.00 2.52
880 980 1.227263 CCCACACGCTATCGAAGGG 60.227 63.158 0.00 0.00 43.65 3.95
881 981 1.672854 CCCACACGCTATCGAAGGGA 61.673 60.000 15.09 0.00 42.53 4.20
882 982 0.174845 CCACACGCTATCGAAGGGAA 59.825 55.000 15.09 0.00 40.56 3.97
883 983 1.560923 CACACGCTATCGAAGGGAAG 58.439 55.000 15.09 10.61 40.56 3.46
884 984 0.460311 ACACGCTATCGAAGGGAAGG 59.540 55.000 15.09 8.69 40.56 3.46
902 1002 3.847602 CGAGGAGGAGGGCAGCAG 61.848 72.222 0.00 0.00 0.00 4.24
903 1003 2.364842 GAGGAGGAGGGCAGCAGA 60.365 66.667 0.00 0.00 0.00 4.26
904 1004 1.992277 GAGGAGGAGGGCAGCAGAA 60.992 63.158 0.00 0.00 0.00 3.02
905 1005 1.539869 AGGAGGAGGGCAGCAGAAA 60.540 57.895 0.00 0.00 0.00 2.52
906 1006 1.077858 GGAGGAGGGCAGCAGAAAG 60.078 63.158 0.00 0.00 0.00 2.62
907 1007 1.748500 GAGGAGGGCAGCAGAAAGC 60.749 63.158 0.00 0.00 46.19 3.51
1219 1337 5.960811 AGATTGGATTCTCTGACTGAGGTTA 59.039 40.000 9.24 0.00 42.86 2.85
1449 1568 4.245660 GTGTGCTTTCATAGTAGCTGTGA 58.754 43.478 0.00 0.00 38.22 3.58
1491 1610 5.883180 AGCTACGAGGAATCTAGGATAGTT 58.117 41.667 0.00 0.00 40.38 2.24
1629 1748 1.484653 GTTTGCTTGGTTGGTTTCCCT 59.515 47.619 0.00 0.00 0.00 4.20
1635 1754 1.989706 TGGTTGGTTTCCCTTAGTGC 58.010 50.000 0.00 0.00 0.00 4.40
1668 1787 8.417780 TTTTTGTGACCATTGAATTTGTACAG 57.582 30.769 0.00 0.00 0.00 2.74
1677 1796 8.469200 ACCATTGAATTTGTACAGATATTGGTG 58.531 33.333 15.59 6.66 30.51 4.17
1692 1811 6.599244 AGATATTGGTGTGTTGTGTGATTAGG 59.401 38.462 0.00 0.00 0.00 2.69
1713 1833 3.343617 GTGTTGATCGATGGGGAAAAGA 58.656 45.455 0.54 0.00 0.00 2.52
1847 1970 2.944129 TGGAAGTTTGGCTTACTGCTT 58.056 42.857 0.00 0.00 38.85 3.91
1875 1998 5.047021 GCTTTCTTTTGCCCTTTCTTATCCT 60.047 40.000 0.00 0.00 0.00 3.24
2334 2457 4.889409 TCATTCCCATTATTCTGCCACTTC 59.111 41.667 0.00 0.00 0.00 3.01
2409 2532 8.723311 CCTATACTTGTAATTTTCACCGAACAA 58.277 33.333 0.00 0.00 0.00 2.83
2462 2585 9.712305 TTTGAGTAATTTTCAGTTTTTCACCAA 57.288 25.926 0.00 0.00 0.00 3.67
2590 2718 3.569701 ACCTAACTGTGAAAACTGCCATG 59.430 43.478 0.00 0.00 0.00 3.66
2591 2719 3.569701 CCTAACTGTGAAAACTGCCATGT 59.430 43.478 0.00 0.00 0.00 3.21
2628 2758 8.548433 GTTTCACTGAAACTTTGATACAAGAC 57.452 34.615 22.37 0.00 45.65 3.01
2699 3022 6.839124 TGAAGAAAATCCACTTATGTGCAT 57.161 33.333 3.24 0.00 42.54 3.96
2745 3068 2.030371 CTAGTGAGCCTCTCTGCATGA 58.970 52.381 6.56 0.00 0.00 3.07
2838 3162 8.966868 TCAACTTTGACCAAGTCTTTAGAAAAT 58.033 29.630 0.00 0.00 45.77 1.82
3005 3329 2.519377 TTCGAGAAAACGCAAGAGGA 57.481 45.000 0.00 0.00 43.62 3.71
3006 3330 2.519377 TCGAGAAAACGCAAGAGGAA 57.481 45.000 0.00 0.00 43.62 3.36
3007 3331 3.040147 TCGAGAAAACGCAAGAGGAAT 57.960 42.857 0.00 0.00 43.62 3.01
3011 3351 2.821969 AGAAAACGCAAGAGGAATGCAT 59.178 40.909 0.00 0.00 44.01 3.96
3037 3381 0.956633 ACACACATACACGACCGTCT 59.043 50.000 0.00 0.00 0.00 4.18
3047 3391 1.006102 CGACCGTCTTCACCAAGCT 60.006 57.895 0.00 0.00 0.00 3.74
3739 4131 2.031616 GAGCAGGTGACAGCAGCA 59.968 61.111 21.83 0.00 46.80 4.41
3860 4255 3.706373 CACCCAGCGGCTACCACT 61.706 66.667 0.26 0.00 0.00 4.00
4043 4438 1.078528 ACACCATCTCGACCTCCCA 59.921 57.895 0.00 0.00 0.00 4.37
4060 4455 3.285215 ACGAGTGCAGACGACCGT 61.285 61.111 17.25 0.00 0.00 4.83
4129 4524 2.510238 GCGAGCAGCTCACGGAAT 60.510 61.111 22.49 0.00 44.04 3.01
4180 4575 4.548513 CGAGGGGAGGGAGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
4181 4576 4.179599 GAGGGGAGGGAGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
4182 4577 4.761304 AGGGGAGGGAGGGGAGGA 62.761 72.222 0.00 0.00 0.00 3.71
4183 4578 4.179599 GGGGAGGGAGGGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
4184 4579 4.179599 GGGAGGGAGGGGAGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
4185 4580 4.179599 GGAGGGAGGGGAGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
4186 4581 4.890306 GAGGGAGGGGAGGAGGGC 62.890 77.778 0.00 0.00 0.00 5.19
4190 4585 4.814041 GAGGGGAGGAGGGCAGCT 62.814 72.222 0.00 0.00 0.00 4.24
4191 4586 4.361429 AGGGGAGGAGGGCAGCTT 62.361 66.667 0.00 0.00 0.00 3.74
4192 4587 2.366972 GGGGAGGAGGGCAGCTTA 60.367 66.667 0.00 0.00 0.00 3.09
4193 4588 2.447714 GGGGAGGAGGGCAGCTTAG 61.448 68.421 0.00 0.00 0.00 2.18
4194 4589 2.447714 GGGAGGAGGGCAGCTTAGG 61.448 68.421 0.00 0.00 0.00 2.69
4631 7177 9.616634 AATATGATGTTTGATTTCATATCACGC 57.383 29.630 5.41 0.00 40.45 5.34
4651 7197 2.032204 GCGATCATTGATGAGCCACTTC 60.032 50.000 3.32 0.00 39.91 3.01
4715 7261 8.854979 AAAAACATGGCTTTATTTTTCTTTGC 57.145 26.923 0.00 0.00 30.39 3.68
4780 7326 2.158475 ACATACATATGTGGGGGCTTGG 60.158 50.000 18.81 0.35 44.66 3.61
4991 7537 0.250640 CAGCTGAACAAGGGAGTGCT 60.251 55.000 8.42 0.00 0.00 4.40
5107 7653 2.700897 CCCCTGAAGTAGTACCCTGATG 59.299 54.545 0.00 0.00 0.00 3.07
5116 7662 6.720112 AGTAGTACCCTGATGCGTAAAATA 57.280 37.500 0.00 0.00 0.00 1.40
5425 7971 0.249398 ATGGGAGTTGACGCTGGTAC 59.751 55.000 0.00 0.00 0.00 3.34
5507 8070 2.617308 GACGTGTGATCTCGATTCCCTA 59.383 50.000 0.00 0.00 35.08 3.53
5508 8071 3.223435 ACGTGTGATCTCGATTCCCTAT 58.777 45.455 11.10 0.00 35.08 2.57
5723 8286 3.748048 TCTGCTCTGACAATTTCCTTTCG 59.252 43.478 0.00 0.00 0.00 3.46
5760 8325 4.703093 TGTTCGGATAGTGAGTGTGATGTA 59.297 41.667 0.00 0.00 0.00 2.29
6048 8641 4.995487 CCTTAGTAGAAAAGGTTTCTGCGT 59.005 41.667 12.43 5.26 38.98 5.24
6076 8669 5.273944 GCGACACTTGTCTTTCTTCAAATT 58.726 37.500 7.74 0.00 42.66 1.82
6262 8855 6.846505 AGAGGTATGACCCAATTCTTATCTCA 59.153 38.462 8.29 0.00 39.75 3.27
6314 8907 3.208594 TGATGCTTCATCTGGTACATGC 58.791 45.455 8.11 0.00 41.06 4.06
6316 8909 3.286329 TGCTTCATCTGGTACATGCAT 57.714 42.857 0.00 0.00 38.20 3.96
6351 8972 1.017701 GCCAAATTGCTGCTTGCCTC 61.018 55.000 0.00 0.00 42.00 4.70
6449 9070 9.975218 TCTGCTAAAGTTTCCTATCCTAATTTT 57.025 29.630 0.00 0.00 0.00 1.82
6786 9421 0.577269 GACGCGTGCATAGATTCACC 59.423 55.000 20.70 0.00 0.00 4.02
6840 9475 6.991531 ACAAATATGTTGAACCTTGTTGCATT 59.008 30.769 0.00 0.00 35.91 3.56
6906 9541 9.928236 CCAAAAATTAAACTTGTATGTTGTTGG 57.072 29.630 0.00 0.00 0.00 3.77
7098 9733 1.301677 GGTCAAGCTTTCCCTCTGCG 61.302 60.000 0.00 0.00 0.00 5.18
7159 9794 8.432359 TGAAAGCGTTTCTTATATGCATATACG 58.568 33.333 24.62 24.62 40.32 3.06
7186 9821 1.479323 CATTGGCTGTTCCTCATTGGG 59.521 52.381 0.00 0.00 36.20 4.12
7402 10037 6.478129 TCCGGTTTGAAGGTATTCTGTATTT 58.522 36.000 0.00 0.00 36.33 1.40
7406 10041 8.079809 CGGTTTGAAGGTATTCTGTATTTTTGT 58.920 33.333 0.00 0.00 36.33 2.83
7481 10124 6.331369 TCTCATGAAAGTGAAAATTCCACC 57.669 37.500 0.00 0.00 35.23 4.61
7563 10206 2.231716 TTACAGGAGCTAGCACCTCA 57.768 50.000 28.52 17.42 34.83 3.86
7578 10221 1.310933 CCTCACAGCAGGAATGGTGC 61.311 60.000 7.31 0.00 40.59 5.01
7594 10237 4.742438 TGGTGCGTCTTCTGTTAAAATC 57.258 40.909 0.00 0.00 0.00 2.17
7685 10328 7.502226 GGGTGTGATTACCAGATGAATCAATAA 59.498 37.037 0.00 0.00 42.23 1.40
7700 10343 4.886247 TCAATAATTTCCTAAACCCGCG 57.114 40.909 0.00 0.00 0.00 6.46
7822 10465 5.935945 TCCAGTCTGTCAGGTAATTGAAAA 58.064 37.500 0.00 0.00 0.00 2.29
8005 10649 6.509418 TTTGGAGCATAACATTAAGTGGAC 57.491 37.500 0.00 0.00 0.00 4.02
8234 10878 0.178975 GGATTGGGTTGGTGTGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
8345 10991 2.666317 TGAGTGGAATGGAGCGATCTA 58.334 47.619 0.00 0.00 0.00 1.98
8366 11012 2.428890 AGTGCTCCTCTTCCAACTATCG 59.571 50.000 0.00 0.00 0.00 2.92
8469 11115 3.070018 GCCATGTGTATATCTGTCTGCC 58.930 50.000 0.00 0.00 0.00 4.85
8529 11337 8.980481 ATCAACTGGGGTTAGATACTAAAATG 57.020 34.615 0.00 0.00 33.88 2.32
8654 11463 7.944061 AGTACCGTAAGTTTGGCTTTAAAAAT 58.056 30.769 0.00 0.00 38.57 1.82
8656 11466 9.117145 GTACCGTAAGTTTGGCTTTAAAAATAC 57.883 33.333 0.00 0.00 38.57 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.374333 TGTGATTGAGTGATTTAAGGTAAGGC 59.626 38.462 0.00 0.00 0.00 4.35
149 150 3.197766 TGCTCCCTCGATGTATTGTTTCT 59.802 43.478 0.00 0.00 0.00 2.52
216 217 2.687805 CGCTCGACAACGGAGAGGA 61.688 63.158 0.00 0.00 40.21 3.71
330 391 2.594303 CAAGTGCCGCTTCCACCA 60.594 61.111 0.00 0.00 34.69 4.17
519 580 8.400947 GCTAGTGCATAACAATATGGATTATGG 58.599 37.037 12.39 2.14 41.20 2.74
605 690 2.088423 CCTCTCTCTCTAACACGCACT 58.912 52.381 0.00 0.00 0.00 4.40
609 696 3.202906 CTCTCCCTCTCTCTCTAACACG 58.797 54.545 0.00 0.00 0.00 4.49
665 759 3.558931 TCAAATCCTCACACACACACT 57.441 42.857 0.00 0.00 0.00 3.55
666 760 3.058016 CCATCAAATCCTCACACACACAC 60.058 47.826 0.00 0.00 0.00 3.82
779 873 3.717707 TCGAAGTGGACTTTTGACTGAG 58.282 45.455 0.00 0.00 36.11 3.35
786 880 8.410141 TGACATTATTTTTCGAAGTGGACTTTT 58.590 29.630 0.00 0.00 36.11 2.27
880 980 3.855853 GCCCTCCTCCTCGCCTTC 61.856 72.222 0.00 0.00 0.00 3.46
881 981 4.722535 TGCCCTCCTCCTCGCCTT 62.723 66.667 0.00 0.00 0.00 4.35
900 1000 3.318839 TGAATGGTGTTTCTGGCTTTCTG 59.681 43.478 0.00 0.00 0.00 3.02
901 1001 3.565307 TGAATGGTGTTTCTGGCTTTCT 58.435 40.909 0.00 0.00 0.00 2.52
902 1002 4.320608 TTGAATGGTGTTTCTGGCTTTC 57.679 40.909 0.00 0.00 0.00 2.62
903 1003 4.590222 AGATTGAATGGTGTTTCTGGCTTT 59.410 37.500 0.00 0.00 0.00 3.51
904 1004 4.021719 CAGATTGAATGGTGTTTCTGGCTT 60.022 41.667 0.00 0.00 0.00 4.35
905 1005 3.508793 CAGATTGAATGGTGTTTCTGGCT 59.491 43.478 0.00 0.00 0.00 4.75
906 1006 3.841643 CAGATTGAATGGTGTTTCTGGC 58.158 45.455 0.00 0.00 0.00 4.85
907 1007 3.508793 AGCAGATTGAATGGTGTTTCTGG 59.491 43.478 0.00 0.00 33.02 3.86
1491 1610 5.366768 TCTCAAAAGAGAAGTGGGAAGAGAA 59.633 40.000 0.00 0.00 0.00 2.87
1527 1646 4.283212 TCCAAACCAAAGAATCCAATCCAC 59.717 41.667 0.00 0.00 0.00 4.02
1629 1748 5.504994 GGTCACAAAAATTGTCTCGCACTAA 60.505 40.000 0.00 0.00 43.23 2.24
1635 1754 5.518812 TCAATGGTCACAAAAATTGTCTCG 58.481 37.500 0.00 0.00 43.23 4.04
1668 1787 6.374333 ACCTAATCACACAACACACCAATATC 59.626 38.462 0.00 0.00 0.00 1.63
1677 1796 5.614668 CGATCAACACCTAATCACACAACAC 60.615 44.000 0.00 0.00 0.00 3.32
1692 1811 3.343617 TCTTTTCCCCATCGATCAACAC 58.656 45.455 0.00 0.00 0.00 3.32
1713 1833 6.488006 ACACATTTTCTTCAGCATAGTTCACT 59.512 34.615 0.00 0.00 0.00 3.41
1993 2116 5.588648 ACAGTACAAAGCAGAACTAGCAAAA 59.411 36.000 0.00 0.00 0.00 2.44
1996 2119 4.336889 ACAGTACAAAGCAGAACTAGCA 57.663 40.909 0.00 0.00 0.00 3.49
2068 2191 7.356089 TGTACCACTTGGGATAATACTAGTG 57.644 40.000 5.39 0.00 41.15 2.74
2069 2192 7.016268 CCATGTACCACTTGGGATAATACTAGT 59.984 40.741 0.00 0.00 39.11 2.57
2500 2625 6.969993 AGTATGATACTCAGGAAAGAGTCC 57.030 41.667 0.00 0.00 45.35 3.85
2622 2752 7.915397 CAGTTGTTGCAATTAAGTAAGTCTTGT 59.085 33.333 0.59 0.00 37.56 3.16
2745 3068 9.401058 AGAAGTCAATTAATAGTTAAGCATGCT 57.599 29.630 16.30 16.30 0.00 3.79
3005 3329 4.759183 TGTATGTGTGTGTGTGTATGCATT 59.241 37.500 3.54 0.00 0.00 3.56
3006 3330 4.154015 GTGTATGTGTGTGTGTGTATGCAT 59.846 41.667 3.79 3.79 0.00 3.96
3007 3331 3.496507 GTGTATGTGTGTGTGTGTATGCA 59.503 43.478 0.00 0.00 0.00 3.96
3011 3351 3.373849 GTCGTGTATGTGTGTGTGTGTA 58.626 45.455 0.00 0.00 0.00 2.90
3037 3381 4.836736 ACCTAGTTGTAGTAGCTTGGTGAA 59.163 41.667 0.00 0.00 42.31 3.18
3047 3391 4.952335 GCACCTCCTTACCTAGTTGTAGTA 59.048 45.833 0.00 0.00 0.00 1.82
3366 3755 1.334869 CTCTTGAAGGCGTTGCTTTGT 59.665 47.619 0.00 0.00 0.00 2.83
3374 3763 1.375326 GTTCCCCTCTTGAAGGCGT 59.625 57.895 0.00 0.00 44.71 5.68
3603 3993 1.801913 CTCCGACGTTCTTCGCCAG 60.802 63.158 0.00 0.00 44.19 4.85
4015 4410 0.602638 GAGATGGTGTGGAACGTGCA 60.603 55.000 0.00 0.00 42.39 4.57
4043 4438 3.251318 GACGGTCGTCTGCACTCGT 62.251 63.158 15.25 0.00 41.57 4.18
4121 4516 3.407967 GGGGCCCTCATTCCGTGA 61.408 66.667 24.38 0.00 35.05 4.35
4122 4517 4.856801 CGGGGCCCTCATTCCGTG 62.857 72.222 24.38 0.00 37.92 4.94
4164 4559 4.179599 CCTCCCCTCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
4165 4560 4.761304 TCCTCCCCTCCCTCCCCT 62.761 72.222 0.00 0.00 0.00 4.79
4166 4561 4.179599 CTCCTCCCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
4167 4562 4.179599 CCTCCTCCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
4168 4563 4.179599 CCCTCCTCCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
4169 4564 4.890306 GCCCTCCTCCCCTCCCTC 62.890 77.778 0.00 0.00 0.00 4.30
4173 4568 2.898472 TAAGCTGCCCTCCTCCCCTC 62.898 65.000 0.00 0.00 0.00 4.30
4174 4569 2.905676 CTAAGCTGCCCTCCTCCCCT 62.906 65.000 0.00 0.00 0.00 4.79
4175 4570 2.366972 TAAGCTGCCCTCCTCCCC 60.367 66.667 0.00 0.00 0.00 4.81
4176 4571 2.447714 CCTAAGCTGCCCTCCTCCC 61.448 68.421 0.00 0.00 0.00 4.30
4177 4572 3.235369 CCTAAGCTGCCCTCCTCC 58.765 66.667 0.00 0.00 0.00 4.30
4631 7177 2.547211 GGAAGTGGCTCATCAATGATCG 59.453 50.000 0.00 0.00 36.02 3.69
4704 7250 4.706035 TCAGCAACATGGCAAAGAAAAAT 58.294 34.783 0.00 0.00 35.83 1.82
4715 7261 0.956633 ACAGCAACTCAGCAACATGG 59.043 50.000 0.00 0.00 36.85 3.66
4780 7326 5.065218 TCTCTCTGCAAGAACAAGAAAACAC 59.935 40.000 0.00 0.00 46.34 3.32
4991 7537 2.242926 CCCTCTACTGCAGCTGCTATA 58.757 52.381 36.61 26.22 42.66 1.31
5107 7653 9.562583 TCACAAAATAGACCATTTATTTTACGC 57.437 29.630 3.48 0.00 38.17 4.42
5267 7813 2.436646 GGGGATGCAGGTGTGACG 60.437 66.667 0.00 0.00 0.00 4.35
5298 7844 1.672356 CCAGGCCACTTGAAGTCCG 60.672 63.158 5.01 0.00 0.00 4.79
5323 7869 2.292016 CACACTGAACCCAAACGCATAA 59.708 45.455 0.00 0.00 0.00 1.90
5425 7971 1.554160 AGCAGGTGGTGAGATTCAGAG 59.446 52.381 0.00 0.00 0.00 3.35
5507 8070 2.224523 ACAAGTGTGACGACCCAATCAT 60.225 45.455 0.00 0.00 0.00 2.45
5508 8071 1.140052 ACAAGTGTGACGACCCAATCA 59.860 47.619 0.00 0.00 0.00 2.57
5723 8286 3.585862 TCCGAACATCTTACTTGCAGTC 58.414 45.455 0.00 0.00 0.00 3.51
5760 8325 5.869649 AACAATTGCTACCCTGAAAGTTT 57.130 34.783 5.05 0.00 0.00 2.66
6116 8709 9.353999 GTCATCACCTTTATAAAATTCACAACC 57.646 33.333 0.00 0.00 0.00 3.77
6262 8855 3.262915 AGAGCTATTCACTTCACAGGCTT 59.737 43.478 0.00 0.00 0.00 4.35
6351 8972 1.338674 TGGGTAAGTTGCAGGACATCG 60.339 52.381 0.00 0.00 0.00 3.84
6771 9406 1.935873 CCACAGGTGAATCTATGCACG 59.064 52.381 0.00 0.00 35.91 5.34
7098 9733 0.674895 AGGCGGTGATTTCAGCACTC 60.675 55.000 10.09 0.00 44.00 3.51
7141 9776 9.984190 TGGTGTAACGTATATGCATATAAGAAA 57.016 29.630 32.86 21.80 38.12 2.52
7186 9821 6.652481 ACTCTTGCAATCCATATGTAGTATGC 59.348 38.462 0.00 5.75 39.10 3.14
7244 9879 4.441495 GGCAGTCCAGGCAAATATTTTACC 60.441 45.833 0.00 3.52 0.00 2.85
7402 10037 4.331443 ACTCGCAATATCGCAACATACAAA 59.669 37.500 0.00 0.00 0.00 2.83
7406 10041 3.303066 GCAACTCGCAATATCGCAACATA 60.303 43.478 0.00 0.00 41.79 2.29
7481 10124 1.581934 TGCAACTTGAGAACCTGACG 58.418 50.000 0.00 0.00 0.00 4.35
7563 10206 1.672356 GACGCACCATTCCTGCTGT 60.672 57.895 0.00 0.00 32.03 4.40
7578 10221 3.000727 AGCCCGATTTTAACAGAAGACG 58.999 45.455 0.00 0.00 0.00 4.18
7685 10328 1.276989 TGAGACGCGGGTTTAGGAAAT 59.723 47.619 12.47 0.00 0.00 2.17
7700 10343 2.462456 TGGATGTCAGCTGTTGAGAC 57.538 50.000 14.67 4.45 36.21 3.36
7822 10465 2.214181 CTACCGCCTGCTGTTCGACT 62.214 60.000 0.00 0.00 0.00 4.18
8005 10649 3.701542 TGTAGGACACTGGCAGAGAATAG 59.298 47.826 23.66 5.95 0.00 1.73
8052 10696 5.997746 AGTAGTATGTTTGACAGTGTGCATT 59.002 36.000 0.00 0.00 0.00 3.56
8234 10878 2.756760 CAGCCAGCAACCATAACTTGAT 59.243 45.455 0.00 0.00 0.00 2.57
8345 10991 2.428890 CGATAGTTGGAAGAGGAGCACT 59.571 50.000 0.00 0.00 0.00 4.40
8469 11115 2.299013 TGTGTGCCACTAGTACAGAAGG 59.701 50.000 0.00 0.00 42.19 3.46


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

AutoCloner maintained by Alex Coulton.