Multiple sequence alignment - TraesCS1D01G071900

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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 TraesCS1D01G071900 chr1D 100.000 3671 0 0 1 3671 52353934 52350264 0.000000e+00 6780.0
1 TraesCS1D01G071900 chr1D 76.642 685 132 15 1 663 299893175 299893853 1.620000e-93 353.0
2 TraesCS1D01G071900 chr1D 76.471 629 109 22 1 602 223536034 223535418 4.610000e-79 305.0
3 TraesCS1D01G071900 chr1A 93.361 1672 80 15 975 2634 52006714 52005062 0.000000e+00 2444.0
4 TraesCS1D01G071900 chr1A 91.598 726 52 8 1918 2634 51974042 51973317 0.000000e+00 994.0
5 TraesCS1D01G071900 chr1A 88.512 383 39 2 17 394 52052885 52052503 3.340000e-125 459.0
6 TraesCS1D01G071900 chr1A 83.742 326 52 1 405 729 52007673 52007348 1.280000e-79 307.0
7 TraesCS1D01G071900 chr1A 83.478 115 10 6 2660 2765 51973327 51973213 8.390000e-17 99.0
8 TraesCS1D01G071900 chr1A 95.833 48 2 0 1190 1237 51974097 51974050 1.090000e-10 78.7
9 TraesCS1D01G071900 chr1B 88.068 1936 147 33 730 2634 453811217 453813099 0.000000e+00 2218.0
10 TraesCS1D01G071900 chr1B 87.761 335 28 9 2099 2424 633706350 633706020 2.680000e-101 379.0
11 TraesCS1D01G071900 chr1B 73.118 279 64 10 451 725 668958884 668959155 5.050000e-14 89.8
12 TraesCS1D01G071900 chr6D 88.351 1468 136 21 972 2424 468559729 468561176 0.000000e+00 1731.0
13 TraesCS1D01G071900 chr2D 98.439 897 13 1 2776 3671 588496534 588495638 0.000000e+00 1578.0
14 TraesCS1D01G071900 chr2D 76.184 760 131 29 1 731 215849342 215850080 4.510000e-94 355.0
15 TraesCS1D01G071900 chr2D 76.131 641 119 22 49 663 333260433 333261065 4.610000e-79 305.0
16 TraesCS1D01G071900 chr4D 88.767 908 74 12 2778 3671 109805867 109806760 0.000000e+00 1086.0
17 TraesCS1D01G071900 chr4D 78.550 676 114 18 20 672 486934485 486935152 2.040000e-112 416.0
18 TraesCS1D01G071900 chr4D 77.863 524 96 8 21 525 356880342 356879820 1.280000e-79 307.0
19 TraesCS1D01G071900 chr7B 86.667 735 67 16 975 1705 357971831 357972538 0.000000e+00 785.0
20 TraesCS1D01G071900 chr7B 88.455 589 55 8 1846 2424 357977741 357978326 0.000000e+00 699.0
21 TraesCS1D01G071900 chr7B 87.280 511 38 14 2777 3275 327811104 327811599 3.200000e-155 558.0
22 TraesCS1D01G071900 chr7B 77.729 678 115 19 1 656 476883595 476884258 2.070000e-102 383.0
23 TraesCS1D01G071900 chr7B 84.667 300 25 5 3273 3568 327813199 327813481 2.790000e-71 279.0
24 TraesCS1D01G071900 chr7B 91.803 122 10 0 1727 1848 357972710 357972831 1.750000e-38 171.0
25 TraesCS1D01G071900 chr7B 92.593 108 8 0 3564 3671 327850012 327850119 4.910000e-34 156.0
26 TraesCS1D01G071900 chr4A 88.144 582 51 8 3102 3671 304415591 304416166 0.000000e+00 676.0
27 TraesCS1D01G071900 chr4A 86.186 333 30 9 2780 3103 304415231 304415556 2.710000e-91 346.0
28 TraesCS1D01G071900 chr4A 88.288 111 13 0 491 601 627622812 627622702 2.300000e-27 134.0
29 TraesCS1D01G071900 chr4A 87.069 116 15 0 491 606 627670200 627670085 8.270000e-27 132.0
30 TraesCS1D01G071900 chr2A 88.506 522 48 8 3156 3671 513831874 513831359 4.030000e-174 621.0
31 TraesCS1D01G071900 chr2A 77.339 684 127 16 1 661 160850018 160849340 2.680000e-101 379.0
32 TraesCS1D01G071900 chr2A 87.574 338 27 10 2836 3162 513832286 513831953 9.620000e-101 377.0
33 TraesCS1D01G071900 chr2A 83.390 295 40 5 1 288 16544667 16544375 7.820000e-67 265.0
34 TraesCS1D01G071900 chr2A 75.552 589 106 23 47 606 442500613 442501192 4.700000e-64 255.0
35 TraesCS1D01G071900 chr5A 85.565 478 55 10 3201 3671 83364120 83364590 4.260000e-134 488.0
36 TraesCS1D01G071900 chr5A 86.364 242 20 3 956 1197 483524452 483524680 6.090000e-63 252.0
37 TraesCS1D01G071900 chrUn 100.000 261 0 0 3411 3671 480927369 480927629 1.980000e-132 483.0
38 TraesCS1D01G071900 chr3D 81.004 558 79 17 48 583 153945771 153946323 5.670000e-113 418.0
39 TraesCS1D01G071900 chr3D 81.250 192 33 2 471 662 416409485 416409297 6.350000e-33 152.0
40 TraesCS1D01G071900 chr5D 78.049 697 120 20 3 675 212570064 212570751 3.410000e-110 409.0
41 TraesCS1D01G071900 chr5D 78.133 407 83 5 326 732 357081700 357081300 1.690000e-63 254.0
42 TraesCS1D01G071900 chr4B 76.618 757 146 20 1 732 178834830 178834080 4.450000e-104 388.0
43 TraesCS1D01G071900 chr2B 86.567 335 32 9 2099 2424 281935910 281935580 1.250000e-94 357.0
44 TraesCS1D01G071900 chr2B 77.323 538 107 11 1 527 443759922 443759389 1.660000e-78 303.0
45 TraesCS1D01G071900 chr2B 76.577 444 83 8 27 451 706292474 706292915 1.330000e-54 224.0
46 TraesCS1D01G071900 chr2B 77.869 366 63 7 21 368 776531530 776531165 1.030000e-50 211.0
47 TraesCS1D01G071900 chr7D 88.843 242 17 2 956 1197 400210228 400209997 4.640000e-74 289.0
48 TraesCS1D01G071900 chr7D 87.764 237 19 4 961 1197 116829660 116829434 6.040000e-68 268.0


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 TraesCS1D01G071900 chr1D 52350264 52353934 3670 True 6780.000000 6780 100.0000 1 3671 1 chr1D.!!$R1 3670
1 TraesCS1D01G071900 chr1D 299893175 299893853 678 False 353.000000 353 76.6420 1 663 1 chr1D.!!$F1 662
2 TraesCS1D01G071900 chr1D 223535418 223536034 616 True 305.000000 305 76.4710 1 602 1 chr1D.!!$R2 601
3 TraesCS1D01G071900 chr1A 52005062 52007673 2611 True 1375.500000 2444 88.5515 405 2634 2 chr1A.!!$R3 2229
4 TraesCS1D01G071900 chr1A 51973213 51974097 884 True 390.566667 994 90.3030 1190 2765 3 chr1A.!!$R2 1575
5 TraesCS1D01G071900 chr1B 453811217 453813099 1882 False 2218.000000 2218 88.0680 730 2634 1 chr1B.!!$F1 1904
6 TraesCS1D01G071900 chr6D 468559729 468561176 1447 False 1731.000000 1731 88.3510 972 2424 1 chr6D.!!$F1 1452
7 TraesCS1D01G071900 chr2D 588495638 588496534 896 True 1578.000000 1578 98.4390 2776 3671 1 chr2D.!!$R1 895
8 TraesCS1D01G071900 chr2D 215849342 215850080 738 False 355.000000 355 76.1840 1 731 1 chr2D.!!$F1 730
9 TraesCS1D01G071900 chr2D 333260433 333261065 632 False 305.000000 305 76.1310 49 663 1 chr2D.!!$F2 614
10 TraesCS1D01G071900 chr4D 109805867 109806760 893 False 1086.000000 1086 88.7670 2778 3671 1 chr4D.!!$F1 893
11 TraesCS1D01G071900 chr4D 486934485 486935152 667 False 416.000000 416 78.5500 20 672 1 chr4D.!!$F2 652
12 TraesCS1D01G071900 chr4D 356879820 356880342 522 True 307.000000 307 77.8630 21 525 1 chr4D.!!$R1 504
13 TraesCS1D01G071900 chr7B 357977741 357978326 585 False 699.000000 699 88.4550 1846 2424 1 chr7B.!!$F2 578
14 TraesCS1D01G071900 chr7B 357971831 357972831 1000 False 478.000000 785 89.2350 975 1848 2 chr7B.!!$F5 873
15 TraesCS1D01G071900 chr7B 327811104 327813481 2377 False 418.500000 558 85.9735 2777 3568 2 chr7B.!!$F4 791
16 TraesCS1D01G071900 chr7B 476883595 476884258 663 False 383.000000 383 77.7290 1 656 1 chr7B.!!$F3 655
17 TraesCS1D01G071900 chr4A 304415231 304416166 935 False 511.000000 676 87.1650 2780 3671 2 chr4A.!!$F1 891
18 TraesCS1D01G071900 chr2A 513831359 513832286 927 True 499.000000 621 88.0400 2836 3671 2 chr2A.!!$R3 835
19 TraesCS1D01G071900 chr2A 160849340 160850018 678 True 379.000000 379 77.3390 1 661 1 chr2A.!!$R2 660
20 TraesCS1D01G071900 chr2A 442500613 442501192 579 False 255.000000 255 75.5520 47 606 1 chr2A.!!$F1 559
21 TraesCS1D01G071900 chr3D 153945771 153946323 552 False 418.000000 418 81.0040 48 583 1 chr3D.!!$F1 535
22 TraesCS1D01G071900 chr5D 212570064 212570751 687 False 409.000000 409 78.0490 3 675 1 chr5D.!!$F1 672
23 TraesCS1D01G071900 chr4B 178834080 178834830 750 True 388.000000 388 76.6180 1 732 1 chr4B.!!$R1 731
24 TraesCS1D01G071900 chr2B 443759389 443759922 533 True 303.000000 303 77.3230 1 527 1 chr2B.!!$R2 526

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
379 416 0.686789 CGGCATACAGATGGATGGGA 59.313 55.0 7.15 0.00 33.26 4.37 F
1543 1997 0.391395 TCCGAGTCTGAGTCCGAGTC 60.391 60.0 8.86 8.86 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2446 1.082117 GGGTCGCACACATAGAACCG 61.082 60.000 0.0 0.0 31.51 4.44 R
2994 3637 1.280710 TGCGGGAGTAATGGACAACAT 59.719 47.619 0.0 0.0 43.07 2.71 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
19 20 2.973899 CACAGGAGACGTGGGAGG 59.026 66.667 0.00 0.00 33.29 4.30
40 41 4.980805 GGCGGTGTCGTTGGAGCA 62.981 66.667 0.00 0.00 38.89 4.26
68 69 0.884259 TCGTGGTGTCGTCCTCGTTA 60.884 55.000 13.99 0.20 42.59 3.18
166 168 1.278637 CGGCCACTTCGTGTTTCAC 59.721 57.895 2.24 0.00 0.00 3.18
169 171 1.541670 GGCCACTTCGTGTTTCACCTA 60.542 52.381 0.00 0.00 0.00 3.08
302 327 7.445945 CATCTTTAAATAGAGGATTCCGGTCT 58.554 38.462 0.00 0.00 0.00 3.85
309 344 2.511600 GATTCCGGTCTGGTGCGG 60.512 66.667 0.00 0.00 39.52 5.69
379 416 0.686789 CGGCATACAGATGGATGGGA 59.313 55.000 7.15 0.00 33.26 4.37
649 690 2.033448 GTGGGTGCGGATGGTCAA 59.967 61.111 0.00 0.00 0.00 3.18
677 718 1.406341 CGTGGGTGGTGTCCGAATATT 60.406 52.381 0.00 0.00 0.00 1.28
690 737 1.796459 CGAATATTCGTAAAGCCCCCG 59.204 52.381 26.11 0.44 45.09 5.73
720 768 0.989890 CGGTTCGCGGAAGAAAGTAG 59.010 55.000 6.13 0.00 0.00 2.57
742 790 4.436332 GGTCCGAACCGTATTAAATGACT 58.564 43.478 0.00 0.00 35.36 3.41
744 792 5.352293 GGTCCGAACCGTATTAAATGACTTT 59.648 40.000 0.00 0.00 35.36 2.66
745 793 6.128200 GGTCCGAACCGTATTAAATGACTTTT 60.128 38.462 0.00 0.00 35.36 2.27
780 841 1.476488 GTGGTGGTTTGGATGTATGCC 59.524 52.381 0.00 0.00 0.00 4.40
792 853 0.958382 TGTATGCCGGTGGTTTGAGC 60.958 55.000 1.90 0.00 0.00 4.26
802 863 2.051345 GTTTGAGCGTGGCGTTGG 60.051 61.111 0.00 0.00 0.00 3.77
813 874 4.445699 GCGTTGGAGATGCCCTAG 57.554 61.111 0.00 0.00 34.03 3.02
829 892 2.310647 CCCTAGGCCTAAGTTTCCCAAA 59.689 50.000 14.85 0.00 0.00 3.28
857 920 3.199880 AGTTGTTGACTCTTCTGTGGG 57.800 47.619 0.00 0.00 31.20 4.61
858 921 2.505819 AGTTGTTGACTCTTCTGTGGGT 59.494 45.455 0.00 0.00 31.20 4.51
859 922 2.872858 GTTGTTGACTCTTCTGTGGGTC 59.127 50.000 0.00 0.00 0.00 4.46
860 923 2.398588 TGTTGACTCTTCTGTGGGTCT 58.601 47.619 0.00 0.00 0.00 3.85
861 924 2.103094 TGTTGACTCTTCTGTGGGTCTG 59.897 50.000 0.00 0.00 0.00 3.51
863 926 1.133167 TGACTCTTCTGTGGGTCTGGA 60.133 52.381 0.00 0.00 0.00 3.86
864 927 1.548269 GACTCTTCTGTGGGTCTGGAG 59.452 57.143 0.00 0.00 0.00 3.86
885 1262 1.500512 TTGACTTAACCCGCACGCAC 61.501 55.000 0.00 0.00 0.00 5.34
903 1280 4.854784 GCACGCTCGCGAGATCCA 62.855 66.667 38.74 0.50 42.83 3.41
904 1281 2.026734 CACGCTCGCGAGATCCAT 59.973 61.111 38.74 15.50 42.83 3.41
935 1337 4.202264 TGAAATTAAAACACAACGCCCCAT 60.202 37.500 0.00 0.00 0.00 4.00
1011 1458 1.956159 GCCCGGCCCAATTACAAGTTA 60.956 52.381 0.00 0.00 0.00 2.24
1020 1467 5.007724 GCCCAATTACAAGTTAGATTCCGAG 59.992 44.000 0.00 0.00 0.00 4.63
1542 1996 0.674269 GTCCGAGTCTGAGTCCGAGT 60.674 60.000 6.91 0.00 0.00 4.18
1543 1997 0.391395 TCCGAGTCTGAGTCCGAGTC 60.391 60.000 8.86 8.86 0.00 3.36
1544 1998 1.370587 CCGAGTCTGAGTCCGAGTCC 61.371 65.000 12.29 0.00 0.00 3.85
1545 1999 1.697772 CGAGTCTGAGTCCGAGTCCG 61.698 65.000 12.29 5.67 0.00 4.79
1546 2000 0.391395 GAGTCTGAGTCCGAGTCCGA 60.391 60.000 7.91 0.00 38.22 4.55
1547 2001 0.391927 AGTCTGAGTCCGAGTCCGAG 60.392 60.000 0.62 0.00 38.22 4.63
1733 2346 3.716006 CCGGCGTCACAAGTGCAG 61.716 66.667 6.01 0.00 0.00 4.41
1902 2515 0.321210 ATCAACAATCGCACCGGACA 60.321 50.000 9.46 0.00 0.00 4.02
1956 2569 4.953868 CGTCCACCGGCAACACGA 62.954 66.667 0.00 0.00 35.47 4.35
1964 2577 1.416049 CGGCAACACGATCTTCACG 59.584 57.895 0.00 0.00 35.47 4.35
2290 2903 2.305826 TTCGACATCCGCGACGAGAG 62.306 60.000 8.23 0.00 37.52 3.20
2350 2968 2.125147 CGGCGTGTGGGTGATGAT 60.125 61.111 0.00 0.00 0.00 2.45
2353 2971 1.078497 GCGTGTGGGTGATGATGGA 60.078 57.895 0.00 0.00 0.00 3.41
2354 2972 1.091771 GCGTGTGGGTGATGATGGAG 61.092 60.000 0.00 0.00 0.00 3.86
2356 2974 0.107017 GTGTGGGTGATGATGGAGGG 60.107 60.000 0.00 0.00 0.00 4.30
2357 2975 1.152881 GTGGGTGATGATGGAGGGC 60.153 63.158 0.00 0.00 0.00 5.19
2358 2976 2.111878 GGGTGATGATGGAGGGCG 59.888 66.667 0.00 0.00 0.00 6.13
2359 2977 2.746375 GGGTGATGATGGAGGGCGT 61.746 63.158 0.00 0.00 0.00 5.68
2360 2978 1.524621 GGTGATGATGGAGGGCGTG 60.525 63.158 0.00 0.00 0.00 5.34
2361 2979 2.182842 GTGATGATGGAGGGCGTGC 61.183 63.158 0.00 0.00 0.00 5.34
2362 2980 2.592861 GATGATGGAGGGCGTGCC 60.593 66.667 1.16 1.16 0.00 5.01
2540 3173 4.029809 AGCGGCCACAAGGTACCC 62.030 66.667 8.74 0.00 37.19 3.69
2558 3191 1.395826 CCCTCTTCAGCCTCTACCGG 61.396 65.000 0.00 0.00 0.00 5.28
2634 3267 3.343617 CGCTGAAATTAAGGACCCTTCA 58.656 45.455 4.31 0.00 37.47 3.02
2635 3268 3.127030 CGCTGAAATTAAGGACCCTTCAC 59.873 47.826 4.31 0.00 37.47 3.18
2636 3269 4.336280 GCTGAAATTAAGGACCCTTCACT 58.664 43.478 4.31 0.00 37.47 3.41
2637 3270 4.396478 GCTGAAATTAAGGACCCTTCACTC 59.604 45.833 4.31 0.00 37.47 3.51
2638 3271 5.804771 GCTGAAATTAAGGACCCTTCACTCT 60.805 44.000 4.31 0.00 37.47 3.24
2639 3272 6.200878 TGAAATTAAGGACCCTTCACTCTT 57.799 37.500 4.31 0.00 37.47 2.85
2640 3273 6.610830 TGAAATTAAGGACCCTTCACTCTTT 58.389 36.000 4.31 0.34 37.47 2.52
2641 3274 7.066781 TGAAATTAAGGACCCTTCACTCTTTT 58.933 34.615 4.31 0.00 37.47 2.27
2642 3275 7.563556 TGAAATTAAGGACCCTTCACTCTTTTT 59.436 33.333 4.31 0.00 37.47 1.94
2666 3299 6.538945 TTTGGCAGAATAAATTAAGGACCC 57.461 37.500 0.00 0.00 0.00 4.46
2667 3300 5.466127 TGGCAGAATAAATTAAGGACCCT 57.534 39.130 0.00 0.00 0.00 4.34
2668 3301 5.837829 TGGCAGAATAAATTAAGGACCCTT 58.162 37.500 6.54 6.54 39.83 3.95
2669 3302 5.891551 TGGCAGAATAAATTAAGGACCCTTC 59.108 40.000 4.31 0.00 37.47 3.46
2672 3305 7.778382 GGCAGAATAAATTAAGGACCCTTCTTA 59.222 37.037 4.31 3.13 37.47 2.10
2686 3319 7.553044 AGGACCCTTCTTAATTAGTTCGATTTG 59.447 37.037 0.00 0.00 0.00 2.32
2687 3320 7.201705 GGACCCTTCTTAATTAGTTCGATTTGG 60.202 40.741 0.00 0.00 0.00 3.28
2688 3321 7.173032 ACCCTTCTTAATTAGTTCGATTTGGT 58.827 34.615 0.00 0.00 0.00 3.67
2691 3324 8.512138 CCTTCTTAATTAGTTCGATTTGGTGTT 58.488 33.333 0.00 0.00 0.00 3.32
2702 3341 6.403333 TCGATTTGGTGTTTAATTCGAGAG 57.597 37.500 0.00 0.00 35.97 3.20
2705 3344 7.977293 TCGATTTGGTGTTTAATTCGAGAGATA 59.023 33.333 0.00 0.00 41.60 1.98
2707 3346 9.704098 GATTTGGTGTTTAATTCGAGAGATAAC 57.296 33.333 0.00 0.00 41.60 1.89
2712 3351 8.596380 GGTGTTTAATTCGAGAGATAACTTCAG 58.404 37.037 0.00 0.00 41.60 3.02
2720 3359 7.683437 TCGAGAGATAACTTCAGTACTTGAA 57.317 36.000 0.00 0.10 38.24 2.69
2721 3360 8.107399 TCGAGAGATAACTTCAGTACTTGAAA 57.893 34.615 0.00 0.00 39.38 2.69
2722 3361 8.021973 TCGAGAGATAACTTCAGTACTTGAAAC 58.978 37.037 0.00 0.00 39.38 2.78
2729 3368 7.681939 AACTTCAGTACTTGAAACAAACAGA 57.318 32.000 0.00 0.00 44.84 3.41
2730 3369 7.073342 ACTTCAGTACTTGAAACAAACAGAC 57.927 36.000 0.00 0.00 44.84 3.51
2731 3370 6.093633 ACTTCAGTACTTGAAACAAACAGACC 59.906 38.462 0.00 0.00 44.84 3.85
2765 3407 2.363306 ATGTTCCTGTGACTTTGCCA 57.637 45.000 0.00 0.00 0.00 4.92
2766 3408 2.136298 TGTTCCTGTGACTTTGCCAA 57.864 45.000 0.00 0.00 0.00 4.52
2767 3409 2.451490 TGTTCCTGTGACTTTGCCAAA 58.549 42.857 0.00 0.00 0.00 3.28
2768 3410 3.030291 TGTTCCTGTGACTTTGCCAAAT 58.970 40.909 0.00 0.00 0.00 2.32
2769 3411 4.211125 TGTTCCTGTGACTTTGCCAAATA 58.789 39.130 0.00 0.00 0.00 1.40
2770 3412 4.646945 TGTTCCTGTGACTTTGCCAAATAA 59.353 37.500 0.00 0.00 0.00 1.40
2771 3413 5.304101 TGTTCCTGTGACTTTGCCAAATAAT 59.696 36.000 0.00 0.00 0.00 1.28
2772 3414 6.183360 TGTTCCTGTGACTTTGCCAAATAATT 60.183 34.615 0.00 0.00 0.00 1.40
2773 3415 6.418057 TCCTGTGACTTTGCCAAATAATTT 57.582 33.333 0.00 0.00 0.00 1.82
2774 3416 6.454795 TCCTGTGACTTTGCCAAATAATTTC 58.545 36.000 0.00 0.00 0.00 2.17
2994 3637 8.706322 TCTACATAGATTAGCACTGACCATTA 57.294 34.615 0.00 0.00 0.00 1.90
3018 3668 3.916359 TGTCCATTACTCCCGCAAATA 57.084 42.857 0.00 0.00 0.00 1.40
3088 3740 2.870411 AGTCCGTGCTGTAAAGTGTTTC 59.130 45.455 0.00 0.00 0.00 2.78
3094 3747 4.207635 CGTGCTGTAAAGTGTTTCTTCGTA 59.792 41.667 0.00 0.00 35.02 3.43
3241 4015 1.700955 GGACGCTAGAAGGATGGGTA 58.299 55.000 0.00 0.00 0.00 3.69
3271 4046 7.747155 ACTGCATACACTCTACGTATAAGAT 57.253 36.000 11.01 3.27 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.585006 GACACCACGATGGAGACGT 59.415 57.895 10.46 0.00 40.96 4.34
68 69 2.363795 TCGCCCGAGGTCTCCAAT 60.364 61.111 0.00 0.00 0.00 3.16
166 168 1.210722 GGGAGAGCCTTTCCACTTAGG 59.789 57.143 3.40 0.00 36.40 2.69
169 171 1.679898 CGGGAGAGCCTTTCCACTT 59.320 57.895 3.40 0.00 36.40 3.16
193 195 1.005037 ATGACTGCAGGCGACGAAA 60.005 52.632 19.93 0.00 0.00 3.46
243 251 0.678366 ACTCCACGCCACAACACAAA 60.678 50.000 0.00 0.00 0.00 2.83
279 291 6.183360 CCAGACCGGAATCCTCTATTTAAAGA 60.183 42.308 9.46 0.00 36.56 2.52
309 344 1.021390 ACTCTAGTGCGGTGCATTGC 61.021 55.000 0.46 0.46 41.91 3.56
318 353 1.732732 CGAGAAACCCACTCTAGTGCG 60.733 57.143 4.53 0.00 44.34 5.34
379 416 6.481313 CAGATATCTTCATGTCCGTTGAATGT 59.519 38.462 1.33 0.00 32.94 2.71
508 547 1.337071 GTGAACACGACCTCTCACTGA 59.663 52.381 0.00 0.00 36.18 3.41
627 668 2.751436 CATCCGCACCCACCCAAG 60.751 66.667 0.00 0.00 0.00 3.61
638 679 2.485122 CCGCTTTTGACCATCCGC 59.515 61.111 0.00 0.00 0.00 5.54
639 680 3.051392 GCCCGCTTTTGACCATCCG 62.051 63.158 0.00 0.00 0.00 4.18
677 718 1.271488 ACAAATTCGGGGGCTTTACGA 60.271 47.619 0.00 0.00 34.47 3.43
679 720 3.671008 AAACAAATTCGGGGGCTTTAC 57.329 42.857 0.00 0.00 0.00 2.01
690 737 1.711824 CCGCGAACCGAAAACAAATTC 59.288 47.619 8.23 0.00 40.02 2.17
706 754 0.801067 CGGACCTACTTTCTTCCGCG 60.801 60.000 0.00 0.00 44.16 6.46
720 768 4.436332 AGTCATTTAATACGGTTCGGACC 58.564 43.478 1.39 1.39 42.87 4.46
740 788 4.876107 CCACGTTATCCAGATAGCAAAAGT 59.124 41.667 0.00 0.00 0.00 2.66
742 790 4.634004 CACCACGTTATCCAGATAGCAAAA 59.366 41.667 0.00 0.00 0.00 2.44
744 792 3.431626 CCACCACGTTATCCAGATAGCAA 60.432 47.826 0.00 0.00 0.00 3.91
745 793 2.102420 CCACCACGTTATCCAGATAGCA 59.898 50.000 0.00 0.00 0.00 3.49
780 841 4.025401 GCCACGCTCAAACCACCG 62.025 66.667 0.00 0.00 0.00 4.94
792 853 3.499737 GGCATCTCCAACGCCACG 61.500 66.667 0.00 0.00 45.52 4.94
813 874 4.409718 TTTGTTTTGGGAAACTTAGGCC 57.590 40.909 0.00 0.00 44.33 5.19
817 880 7.672240 ACAACTCTTTTGTTTTGGGAAACTTA 58.328 30.769 3.98 0.00 44.33 2.24
854 917 3.181448 GGTTAAGTCAAACTCCAGACCCA 60.181 47.826 0.00 0.00 35.38 4.51
855 918 3.409570 GGTTAAGTCAAACTCCAGACCC 58.590 50.000 0.00 0.00 35.38 4.46
857 920 3.064931 CGGGTTAAGTCAAACTCCAGAC 58.935 50.000 0.00 0.00 35.02 3.51
858 921 2.549349 GCGGGTTAAGTCAAACTCCAGA 60.549 50.000 0.00 0.00 0.00 3.86
859 922 1.804748 GCGGGTTAAGTCAAACTCCAG 59.195 52.381 0.00 0.00 0.00 3.86
860 923 1.141254 TGCGGGTTAAGTCAAACTCCA 59.859 47.619 0.00 0.00 0.00 3.86
861 924 1.534163 GTGCGGGTTAAGTCAAACTCC 59.466 52.381 0.00 0.00 0.00 3.85
863 926 1.223187 CGTGCGGGTTAAGTCAAACT 58.777 50.000 0.00 0.00 0.00 2.66
864 927 0.385098 GCGTGCGGGTTAAGTCAAAC 60.385 55.000 0.00 0.00 0.00 2.93
888 1265 2.333225 GATGGATCTCGCGAGCGT 59.667 61.111 30.97 21.24 40.74 5.07
892 1269 3.978491 GGCCGATGGATCTCGCGA 61.978 66.667 9.26 9.26 37.33 5.87
896 1273 0.179084 TTCAACGGCCGATGGATCTC 60.179 55.000 35.90 0.00 0.00 2.75
897 1274 0.251916 TTTCAACGGCCGATGGATCT 59.748 50.000 35.90 3.57 0.00 2.75
898 1275 1.308998 ATTTCAACGGCCGATGGATC 58.691 50.000 35.90 0.00 0.00 3.36
899 1276 1.762708 AATTTCAACGGCCGATGGAT 58.237 45.000 35.90 23.43 0.00 3.41
901 1278 3.495670 TTTAATTTCAACGGCCGATGG 57.504 42.857 35.90 20.27 0.00 3.51
902 1279 4.089351 GTGTTTTAATTTCAACGGCCGATG 59.911 41.667 35.90 31.47 0.00 3.84
903 1280 4.231439 GTGTTTTAATTTCAACGGCCGAT 58.769 39.130 35.90 19.90 0.00 4.18
904 1281 3.066342 TGTGTTTTAATTTCAACGGCCGA 59.934 39.130 35.90 9.64 0.00 5.54
931 1333 3.669824 CGACCTCGTATGATCGTTATGGG 60.670 52.174 0.00 0.00 34.11 4.00
935 1337 1.265095 GCCGACCTCGTATGATCGTTA 59.735 52.381 7.08 0.00 37.74 3.18
1011 1458 1.215647 GCACGTGGACTCGGAATCT 59.784 57.895 18.88 0.00 34.94 2.40
1020 1467 1.366111 AACGCCATATGCACGTGGAC 61.366 55.000 18.88 11.66 40.44 4.02
1297 1744 3.360867 AGAGTGAGGTGTGAGTATCCTG 58.639 50.000 0.00 0.00 0.00 3.86
1298 1745 3.626930 GAGAGTGAGGTGTGAGTATCCT 58.373 50.000 0.00 0.00 0.00 3.24
1369 1816 1.605712 GCAGGCGATCCATGTACCTAC 60.606 57.143 0.00 0.00 33.74 3.18
1544 1998 3.610791 TTCAGCAGCGACGTCCTCG 62.611 63.158 10.58 0.00 45.97 4.63
1545 1999 1.803519 CTTCAGCAGCGACGTCCTC 60.804 63.158 10.58 1.88 0.00 3.71
1546 2000 2.259818 CTTCAGCAGCGACGTCCT 59.740 61.111 10.58 5.32 0.00 3.85
1547 2001 3.482783 GCTTCAGCAGCGACGTCC 61.483 66.667 10.58 2.76 39.29 4.79
1683 2143 2.033141 ATGCTCCAAGCGCACAGT 59.967 55.556 11.47 0.00 46.26 3.55
1833 2446 1.082117 GGGTCGCACACATAGAACCG 61.082 60.000 0.00 0.00 31.51 4.44
1837 2450 1.897423 CCTGGGTCGCACACATAGA 59.103 57.895 0.00 0.00 26.99 1.98
1889 2502 1.374252 GTCACTGTCCGGTGCGATT 60.374 57.895 0.00 0.00 37.16 3.34
1956 2569 1.550976 GAGAAGGACCACCGTGAAGAT 59.449 52.381 0.00 0.00 41.83 2.40
1964 2577 3.300013 CGGAGGAGAAGGACCACC 58.700 66.667 0.00 0.00 35.37 4.61
2290 2903 4.593864 GGAGCATCGAGTCGCCCC 62.594 72.222 7.92 0.38 34.37 5.80
2519 3152 3.583276 TACCTTGTGGCCGCTGTCG 62.583 63.158 18.96 4.82 36.63 4.35
2540 3173 1.395826 CCCGGTAGAGGCTGAAGAGG 61.396 65.000 0.00 0.00 0.00 3.69
2641 3274 7.236640 AGGGTCCTTAATTTATTCTGCCAAAAA 59.763 33.333 0.00 0.00 0.00 1.94
2642 3275 6.728632 AGGGTCCTTAATTTATTCTGCCAAAA 59.271 34.615 0.00 0.00 0.00 2.44
2643 3276 6.260663 AGGGTCCTTAATTTATTCTGCCAAA 58.739 36.000 0.00 0.00 0.00 3.28
2644 3277 5.837829 AGGGTCCTTAATTTATTCTGCCAA 58.162 37.500 0.00 0.00 0.00 4.52
2645 3278 5.466127 AGGGTCCTTAATTTATTCTGCCA 57.534 39.130 0.00 0.00 0.00 4.92
2646 3279 6.129874 AGAAGGGTCCTTAATTTATTCTGCC 58.870 40.000 1.74 0.00 36.26 4.85
2647 3280 7.646548 AAGAAGGGTCCTTAATTTATTCTGC 57.353 36.000 1.74 0.00 36.26 4.26
2656 3289 8.765517 TCGAACTAATTAAGAAGGGTCCTTAAT 58.234 33.333 1.74 0.00 44.28 1.40
2657 3290 8.137745 TCGAACTAATTAAGAAGGGTCCTTAA 57.862 34.615 1.74 0.00 39.52 1.85
2658 3291 7.722949 TCGAACTAATTAAGAAGGGTCCTTA 57.277 36.000 1.74 0.00 36.26 2.69
2659 3292 6.616237 TCGAACTAATTAAGAAGGGTCCTT 57.384 37.500 1.27 1.27 39.23 3.36
2660 3293 6.809976 ATCGAACTAATTAAGAAGGGTCCT 57.190 37.500 0.00 0.00 0.00 3.85
2661 3294 7.201705 CCAAATCGAACTAATTAAGAAGGGTCC 60.202 40.741 0.00 0.00 0.00 4.46
2662 3295 7.336176 ACCAAATCGAACTAATTAAGAAGGGTC 59.664 37.037 0.00 0.00 0.00 4.46
2663 3296 7.120726 CACCAAATCGAACTAATTAAGAAGGGT 59.879 37.037 0.00 0.00 0.00 4.34
2664 3297 7.120726 ACACCAAATCGAACTAATTAAGAAGGG 59.879 37.037 0.00 0.00 0.00 3.95
2665 3298 8.040716 ACACCAAATCGAACTAATTAAGAAGG 57.959 34.615 0.00 0.00 0.00 3.46
2666 3299 9.893305 AAACACCAAATCGAACTAATTAAGAAG 57.107 29.630 0.00 0.00 0.00 2.85
2672 3305 9.337091 CGAATTAAACACCAAATCGAACTAATT 57.663 29.630 0.00 0.00 0.00 1.40
2686 3319 8.475331 TGAAGTTATCTCTCGAATTAAACACC 57.525 34.615 0.00 0.00 0.00 4.16
2687 3320 9.141400 ACTGAAGTTATCTCTCGAATTAAACAC 57.859 33.333 0.00 0.00 0.00 3.32
2697 3336 7.808381 TGTTTCAAGTACTGAAGTTATCTCTCG 59.192 37.037 0.00 0.00 44.84 4.04
2702 3341 9.651718 CTGTTTGTTTCAAGTACTGAAGTTATC 57.348 33.333 0.00 0.00 44.84 1.75
2705 3344 7.361799 GGTCTGTTTGTTTCAAGTACTGAAGTT 60.362 37.037 0.00 0.00 44.84 2.66
2707 3346 6.458342 GGGTCTGTTTGTTTCAAGTACTGAAG 60.458 42.308 0.00 0.00 44.84 3.02
2712 3351 5.570234 TTGGGTCTGTTTGTTTCAAGTAC 57.430 39.130 0.00 0.00 0.00 2.73
2720 3359 6.811954 ACGAAATTATTTGGGTCTGTTTGTT 58.188 32.000 4.83 0.00 0.00 2.83
2721 3360 6.399639 ACGAAATTATTTGGGTCTGTTTGT 57.600 33.333 4.83 0.00 0.00 2.83
2722 3361 8.859156 CATAACGAAATTATTTGGGTCTGTTTG 58.141 33.333 4.83 0.00 30.54 2.93
2729 3368 7.177744 ACAGGAACATAACGAAATTATTTGGGT 59.822 33.333 4.83 0.30 30.54 4.51
2730 3369 7.487829 CACAGGAACATAACGAAATTATTTGGG 59.512 37.037 4.83 0.00 30.54 4.12
2731 3370 8.240682 TCACAGGAACATAACGAAATTATTTGG 58.759 33.333 0.00 0.00 30.54 3.28
2994 3637 1.280710 TGCGGGAGTAATGGACAACAT 59.719 47.619 0.00 0.00 43.07 2.71
3018 3668 5.007921 GCCTTGATTGCATTGTGAACTTTTT 59.992 36.000 0.00 0.00 0.00 1.94
3088 3740 7.307396 CCAGCCAAACACTTATATCATACGAAG 60.307 40.741 0.00 0.00 0.00 3.79
3094 3747 3.891366 GGCCAGCCAAACACTTATATCAT 59.109 43.478 3.12 0.00 35.81 2.45
3241 4015 3.487042 CGTAGAGTGTATGCAGTAGCGTT 60.487 47.826 0.00 0.00 46.23 4.84
3271 4046 3.002144 GCGTCTGTTTTACAACCGGTTAA 59.998 43.478 21.79 9.22 31.02 2.01


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

AutoCloner maintained by Alex Coulton.