Multiple sequence alignment - TraesCS3D01G009000

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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 TraesCS3D01G009000 chr3D 100.000 5157 0 0 1 5157 3076692 3071536 0.000000e+00 9524.0
1 TraesCS3D01G009000 chr3D 97.368 1216 25 6 1649 2860 416196704 416197916 0.000000e+00 2061.0
2 TraesCS3D01G009000 chr3D 85.884 1013 113 11 2911 3898 3084390 3083383 0.000000e+00 1051.0
3 TraesCS3D01G009000 chr3D 85.311 1028 105 17 2898 3898 3054184 3053176 0.000000e+00 1020.0
4 TraesCS3D01G009000 chr3D 80.448 803 70 37 429 1174 3055441 3054669 2.730000e-147 532.0
5 TraesCS3D01G009000 chr3D 81.791 681 81 22 4408 5074 3052555 3051904 9.830000e-147 531.0
6 TraesCS3D01G009000 chr3D 81.374 655 53 29 687 1289 3086120 3085483 2.170000e-128 470.0
7 TraesCS3D01G009000 chr3D 80.704 653 81 28 4510 5155 3046007 3045393 2.810000e-127 466.0
8 TraesCS3D01G009000 chr3D 83.730 504 51 18 3900 4377 3053140 3052642 1.020000e-121 448.0
9 TraesCS3D01G009000 chr3D 80.000 650 88 19 4510 5155 3049055 3048444 4.740000e-120 442.0
10 TraesCS3D01G009000 chr3D 85.285 333 42 5 4527 4859 3082200 3081875 2.300000e-88 337.0
11 TraesCS3D01G009000 chr3D 87.281 228 28 1 191 417 555147469 555147242 5.120000e-65 259.0
12 TraesCS3D01G009000 chr3D 89.130 184 15 3 3977 4155 3083289 3083106 1.870000e-54 224.0
13 TraesCS3D01G009000 chr3D 81.048 248 33 10 1042 1279 3154912 3154669 8.820000e-43 185.0
14 TraesCS3D01G009000 chr3D 83.957 187 22 6 1176 1358 3054601 3054419 6.870000e-39 172.0
15 TraesCS3D01G009000 chr3A 94.682 1429 70 5 3483 4908 130635 129210 0.000000e+00 2213.0
16 TraesCS3D01G009000 chr3A 91.957 1206 66 18 299 1489 132954 131765 0.000000e+00 1661.0
17 TraesCS3D01G009000 chr3A 85.933 981 97 10 2945 3898 126864 125898 0.000000e+00 1009.0
18 TraesCS3D01G009000 chr3A 96.465 594 18 3 2898 3489 131546 130954 0.000000e+00 977.0
19 TraesCS3D01G009000 chr3A 84.460 991 128 8 2898 3874 162422 161444 0.000000e+00 953.0
20 TraesCS3D01G009000 chr3A 85.000 760 85 14 4379 5117 105276 104525 0.000000e+00 745.0
21 TraesCS3D01G009000 chr3A 84.937 717 89 8 2901 3605 141616 140907 0.000000e+00 708.0
22 TraesCS3D01G009000 chr3A 79.920 996 106 52 423 1344 142921 141946 0.000000e+00 645.0
23 TraesCS3D01G009000 chr3A 82.575 769 79 24 4433 5155 125245 124486 1.220000e-175 627.0
24 TraesCS3D01G009000 chr3A 83.232 495 53 20 3905 4377 140436 139950 1.330000e-115 427.0
25 TraesCS3D01G009000 chr3A 80.285 492 53 20 707 1174 127870 127399 1.070000e-86 331.0
26 TraesCS3D01G009000 chr3A 80.676 414 51 19 1025 1416 163026 162620 1.400000e-75 294.0
27 TraesCS3D01G009000 chr3A 92.941 170 9 1 1486 1655 131704 131538 1.430000e-60 244.0
28 TraesCS3D01G009000 chr3A 79.058 382 51 16 3900 4267 161376 161010 8.630000e-58 235.0
29 TraesCS3D01G009000 chr3A 80.064 311 31 16 423 729 175569 175286 8.760000e-48 202.0
30 TraesCS3D01G009000 chr3A 86.740 181 21 3 4976 5155 159934 159756 1.130000e-46 198.0
31 TraesCS3D01G009000 chr3A 89.431 123 13 0 1 123 133455 133333 6.910000e-34 156.0
32 TraesCS3D01G009000 chr3A 87.313 134 15 2 3751 3884 140671 140540 8.940000e-33 152.0
33 TraesCS3D01G009000 chr3A 83.673 147 9 10 534 671 128014 127874 1.950000e-24 124.0
34 TraesCS3D01G009000 chr5D 97.590 1245 28 2 1656 2899 7471815 7473058 0.000000e+00 2132.0
35 TraesCS3D01G009000 chr5D 96.516 1263 34 5 1656 2909 178469432 178468171 0.000000e+00 2080.0
36 TraesCS3D01G009000 chr1D 97.224 1261 32 2 1650 2908 460759461 460760720 0.000000e+00 2132.0
37 TraesCS3D01G009000 chr1D 85.408 233 31 2 186 417 482827735 482827505 6.670000e-59 239.0
38 TraesCS3D01G009000 chr2D 97.586 1243 28 2 1656 2897 648155501 648154260 0.000000e+00 2128.0
39 TraesCS3D01G009000 chr2D 97.428 1244 29 1 1656 2896 15833558 15834801 0.000000e+00 2117.0
40 TraesCS3D01G009000 chr2D 90.123 81 8 0 2829 2909 531927393 531927473 7.060000e-19 106.0
41 TraesCS3D01G009000 chr7D 97.049 1254 29 6 1650 2898 77443245 77441995 0.000000e+00 2104.0
42 TraesCS3D01G009000 chr7D 95.794 1260 30 6 1656 2898 264074689 264075942 0.000000e+00 2012.0
43 TraesCS3D01G009000 chr7D 86.087 230 31 1 186 414 490884358 490884129 3.990000e-61 246.0
44 TraesCS3D01G009000 chr4D 96.785 1213 35 2 1652 2861 352521634 352520423 0.000000e+00 2021.0
45 TraesCS3D01G009000 chr4D 86.486 222 28 2 188 408 234655858 234656078 5.160000e-60 243.0
46 TraesCS3D01G009000 chr3B 90.741 1404 91 20 2898 4267 2109798 2108400 0.000000e+00 1836.0
47 TraesCS3D01G009000 chr3B 93.413 1002 61 3 2898 3898 2256635 2255638 0.000000e+00 1480.0
48 TraesCS3D01G009000 chr3B 91.206 887 58 10 4270 5155 2108301 2107434 0.000000e+00 1188.0
49 TraesCS3D01G009000 chr3B 85.855 1018 123 8 2898 3898 2344859 2345872 0.000000e+00 1062.0
50 TraesCS3D01G009000 chr3B 90.659 728 25 14 670 1358 2257701 2256978 0.000000e+00 928.0
51 TraesCS3D01G009000 chr3B 92.541 362 25 2 1 361 2258685 2258325 7.650000e-143 518.0
52 TraesCS3D01G009000 chr3B 79.747 790 97 31 426 1174 2111184 2110417 9.900000e-142 514.0
53 TraesCS3D01G009000 chr3B 81.073 671 82 20 4403 5059 2346497 2347136 1.290000e-135 494.0
54 TraesCS3D01G009000 chr3B 81.911 492 55 14 3914 4377 2345939 2346424 8.100000e-103 385.0
55 TraesCS3D01G009000 chr3B 81.780 472 53 21 4687 5155 2389087 2389528 1.060000e-96 364.0
56 TraesCS3D01G009000 chr3B 80.986 426 58 15 1011 1420 2268018 2267600 3.000000e-82 316.0
57 TraesCS3D01G009000 chr3B 86.477 281 34 4 4646 4923 2264447 2264168 6.490000e-79 305.0
58 TraesCS3D01G009000 chr3B 86.667 225 29 1 191 414 26575431 26575207 1.110000e-61 248.0
59 TraesCS3D01G009000 chr3B 86.607 224 28 2 186 408 513938870 513939092 3.990000e-61 246.0
60 TraesCS3D01G009000 chr3B 92.941 170 9 1 1486 1655 2256793 2256627 1.430000e-60 244.0
61 TraesCS3D01G009000 chr3B 87.981 208 16 3 397 595 2258083 2257876 2.400000e-58 237.0
62 TraesCS3D01G009000 chr3B 81.270 315 37 19 634 934 2268466 2268160 8.630000e-58 235.0
63 TraesCS3D01G009000 chr3B 87.912 182 19 2 4976 5155 2347585 2347765 1.450000e-50 211.0
64 TraesCS3D01G009000 chr3B 78.986 276 48 7 4002 4267 2128532 2128257 4.100000e-41 180.0
65 TraesCS3D01G009000 chr3B 78.986 276 48 7 4002 4267 2324946 2325221 4.100000e-41 180.0
66 TraesCS3D01G009000 chr3B 84.940 166 25 0 193 358 403526134 403525969 8.880000e-38 169.0
67 TraesCS3D01G009000 chr3B 91.429 105 6 1 1551 1655 2109891 2109790 1.940000e-29 141.0
68 TraesCS3D01G009000 chr3B 78.077 260 30 12 438 673 2343661 2343917 6.960000e-29 139.0
69 TraesCS3D01G009000 chr3B 86.842 76 9 1 22 96 760601851 760601926 3.310000e-12 84.2
70 TraesCS3D01G009000 chr3B 81.818 99 17 1 314 412 7999028 7998931 1.190000e-11 82.4
71 TraesCS3D01G009000 chr6B 86.099 223 29 2 186 407 523207967 523208188 6.670000e-59 239.0
72 TraesCS3D01G009000 chr6D 97.143 70 2 0 2831 2900 14592306 14592237 9.070000e-23 119.0


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 TraesCS3D01G009000 chr3D 3071536 3076692 5156 True 9524.000000 9524 100.000000 1 5157 1 chr3D.!!$R1 5156
1 TraesCS3D01G009000 chr3D 416196704 416197916 1212 False 2061.000000 2061 97.368000 1649 2860 1 chr3D.!!$F1 1211
2 TraesCS3D01G009000 chr3D 3081875 3086120 4245 True 520.500000 1051 85.418250 687 4859 4 chr3D.!!$R5 4172
3 TraesCS3D01G009000 chr3D 3045393 3055441 10048 True 515.857143 1020 82.277286 429 5155 7 chr3D.!!$R4 4726
4 TraesCS3D01G009000 chr3A 124486 133455 8969 True 815.777778 2213 88.660222 1 5155 9 chr3A.!!$R3 5154
5 TraesCS3D01G009000 chr3A 104525 105276 751 True 745.000000 745 85.000000 4379 5117 1 chr3A.!!$R1 738
6 TraesCS3D01G009000 chr3A 139950 142921 2971 True 483.000000 708 83.850500 423 4377 4 chr3A.!!$R4 3954
7 TraesCS3D01G009000 chr3A 159756 163026 3270 True 420.000000 953 82.733500 1025 5155 4 chr3A.!!$R5 4130
8 TraesCS3D01G009000 chr5D 7471815 7473058 1243 False 2132.000000 2132 97.590000 1656 2899 1 chr5D.!!$F1 1243
9 TraesCS3D01G009000 chr5D 178468171 178469432 1261 True 2080.000000 2080 96.516000 1656 2909 1 chr5D.!!$R1 1253
10 TraesCS3D01G009000 chr1D 460759461 460760720 1259 False 2132.000000 2132 97.224000 1650 2908 1 chr1D.!!$F1 1258
11 TraesCS3D01G009000 chr2D 648154260 648155501 1241 True 2128.000000 2128 97.586000 1656 2897 1 chr2D.!!$R1 1241
12 TraesCS3D01G009000 chr2D 15833558 15834801 1243 False 2117.000000 2117 97.428000 1656 2896 1 chr2D.!!$F1 1240
13 TraesCS3D01G009000 chr7D 77441995 77443245 1250 True 2104.000000 2104 97.049000 1650 2898 1 chr7D.!!$R1 1248
14 TraesCS3D01G009000 chr7D 264074689 264075942 1253 False 2012.000000 2012 95.794000 1656 2898 1 chr7D.!!$F1 1242
15 TraesCS3D01G009000 chr4D 352520423 352521634 1211 True 2021.000000 2021 96.785000 1652 2861 1 chr4D.!!$R1 1209
16 TraesCS3D01G009000 chr3B 2107434 2111184 3750 True 919.750000 1836 88.280750 426 5155 4 chr3B.!!$R5 4729
17 TraesCS3D01G009000 chr3B 2255638 2258685 3047 True 681.400000 1480 91.507000 1 3898 5 chr3B.!!$R6 3897
18 TraesCS3D01G009000 chr3B 2343661 2347765 4104 False 458.200000 1062 82.965600 438 5155 5 chr3B.!!$F5 4717
19 TraesCS3D01G009000 chr3B 2264168 2268466 4298 True 285.333333 316 82.911000 634 4923 3 chr3B.!!$R7 4289

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
472 921 0.458669 CCACTTGCATCCAATCCTGC 59.541 55.000 0.00 0.00 38.87 4.85 F
1019 1708 0.625683 ATGGAGATGAAGGCCAGGGT 60.626 55.000 5.01 0.00 34.74 4.34 F
1668 3024 0.107897 AATAATGGACGTGGCTCGCA 60.108 50.000 9.11 0.16 44.19 5.10 F
1724 3080 0.678048 CCCAGAAAAGGAAGGAGCCG 60.678 60.000 0.00 0.00 0.00 5.52 F
3240 5243 1.209504 GCCCACTATCACTGCTACCAA 59.790 52.381 0.00 0.00 0.00 3.67 F
3524 5854 0.248661 CGCACACGAGTCCTAGGATG 60.249 60.000 16.27 11.69 43.93 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 2387 0.036732 TGCCCAGCAAACACTCCTAG 59.963 55.0 0.00 0.00 34.76 3.02 R
2482 3847 4.522789 ACCACTTAGAAATCACGGCAAATT 59.477 37.5 0.00 0.00 0.00 1.82 R
3111 5114 0.514255 CTTGATGTATGATGCCGCCG 59.486 55.0 0.00 0.00 0.00 6.46 R
3487 5814 1.326576 CGCATTACGTTTTGCAGTGG 58.673 50.0 18.67 3.01 38.80 4.00 R
4142 7108 0.461163 TACGATCACACCAATGCCCG 60.461 55.0 0.00 0.00 0.00 6.13 R
4655 9618 0.758310 TGGTGGTGAAATTGCAGCCA 60.758 50.0 13.10 8.21 35.50 4.75 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
101 102 8.648557 TGACATGACAACTTCATATAACTAGC 57.351 34.615 0.00 0.00 43.68 3.42
103 104 9.967346 GACATGACAACTTCATATAACTAGCTA 57.033 33.333 0.00 0.00 43.68 3.32
104 105 9.751542 ACATGACAACTTCATATAACTAGCTAC 57.248 33.333 0.00 0.00 43.68 3.58
111 112 4.747583 TCATATAACTAGCTACTGGCCCA 58.252 43.478 0.00 0.00 43.05 5.36
147 387 1.991230 CAACCCCTACAGGTCCCAG 59.009 63.158 0.00 0.00 40.05 4.45
156 396 3.009033 CCTACAGGTCCCAGAAAACATCA 59.991 47.826 0.00 0.00 0.00 3.07
157 397 3.814504 ACAGGTCCCAGAAAACATCAT 57.185 42.857 0.00 0.00 0.00 2.45
218 458 2.964925 GGCACGTGCACGAAGACA 60.965 61.111 42.94 0.00 44.36 3.41
220 460 1.569493 GCACGTGCACGAAGACATT 59.431 52.632 42.94 18.38 43.02 2.71
272 512 2.289694 ACAGTATGGGAGCAGTGACAAC 60.290 50.000 0.00 0.00 43.62 3.32
372 612 6.938030 TGTTTGAGGTGATTTATACTTTCGGT 59.062 34.615 0.00 0.00 0.00 4.69
373 613 6.978343 TTGAGGTGATTTATACTTTCGGTG 57.022 37.500 0.00 0.00 0.00 4.94
387 627 6.633500 ACTTTCGGTGAATCTTTTTCATGA 57.367 33.333 0.00 0.00 0.00 3.07
462 911 2.036256 GCCCACTCCCACTTGCAT 59.964 61.111 0.00 0.00 0.00 3.96
469 918 1.341383 ACTCCCACTTGCATCCAATCC 60.341 52.381 0.00 0.00 0.00 3.01
470 919 1.002069 TCCCACTTGCATCCAATCCT 58.998 50.000 0.00 0.00 0.00 3.24
471 920 1.108776 CCCACTTGCATCCAATCCTG 58.891 55.000 0.00 0.00 0.00 3.86
472 921 0.458669 CCACTTGCATCCAATCCTGC 59.541 55.000 0.00 0.00 38.87 4.85
553 1025 3.504520 ACGTGTTTAACCAATGGATCCAC 59.495 43.478 18.99 0.90 0.00 4.02
559 1031 0.677731 ACCAATGGATCCACGCACAG 60.678 55.000 18.99 5.56 0.00 3.66
570 1042 3.420606 CGCACAGGCTGCTGTCAG 61.421 66.667 15.89 0.00 44.64 3.51
633 1111 3.249091 CGCTCCTGCTAGCATATAACAG 58.751 50.000 19.72 4.24 42.91 3.16
831 1470 3.801997 AGATCCGGCCAGCCCTTG 61.802 66.667 2.24 0.00 0.00 3.61
909 1559 2.492012 CATGAACCTAGCATCTGCCTC 58.508 52.381 0.00 0.00 43.38 4.70
1019 1708 0.625683 ATGGAGATGAAGGCCAGGGT 60.626 55.000 5.01 0.00 34.74 4.34
1251 2308 9.123902 TCTCCAATTCTCCATGTTTATTATGTG 57.876 33.333 0.00 0.00 0.00 3.21
1270 2334 2.690497 GTGATGATCTCGTCCTCTCCAA 59.310 50.000 0.00 0.00 0.00 3.53
1413 2666 5.164954 TGGAAAACAAGTGCAAAGTACAAC 58.835 37.500 0.00 0.00 0.00 3.32
1449 2702 1.448985 TTCGAAAAGGAGGATTGCCG 58.551 50.000 0.00 0.00 39.96 5.69
1452 2705 1.002624 AAAAGGAGGATTGCCGCGA 60.003 52.632 8.23 0.00 39.96 5.87
1474 2728 3.117246 ACCTCTGCATCAATTGATCCCAT 60.117 43.478 18.16 0.00 31.21 4.00
1549 2899 3.975670 GCTAACTAGTGCTATAGCGTGTG 59.024 47.826 19.55 12.05 45.83 3.82
1572 2922 3.965379 TTGGTGGTAATCGACTTAGCA 57.035 42.857 12.41 12.41 43.65 3.49
1573 2923 4.481368 TTGGTGGTAATCGACTTAGCAT 57.519 40.909 16.74 0.00 46.38 3.79
1574 2924 3.792401 TGGTGGTAATCGACTTAGCATG 58.208 45.455 16.74 0.00 46.38 4.06
1668 3024 0.107897 AATAATGGACGTGGCTCGCA 60.108 50.000 9.11 0.16 44.19 5.10
1724 3080 0.678048 CCCAGAAAAGGAAGGAGCCG 60.678 60.000 0.00 0.00 0.00 5.52
1816 3172 1.222387 CCCCCGCGTGATTAGGAAA 59.778 57.895 4.92 0.00 0.00 3.13
1858 3214 4.792702 TCGCATGCATTAATTTGAGTTTCG 59.207 37.500 19.57 0.00 0.00 3.46
2159 3518 3.188667 GTCCTAGTAAACCAAGCAACTGC 59.811 47.826 0.00 0.00 42.49 4.40
2248 3607 4.097892 CCTAACAAAACCAAGCAACTGTCT 59.902 41.667 0.00 0.00 0.00 3.41
2482 3847 7.940137 AGTTGCCCATATACGGTCAAAAATATA 59.060 33.333 0.00 0.00 0.00 0.86
2757 4125 6.877611 ATGAAACGGAATAAAGAGTGTGTT 57.122 33.333 0.00 0.00 0.00 3.32
2899 4281 3.182967 GCACGAGTCAGACTTTAGGATG 58.817 50.000 4.05 0.00 0.00 3.51
2902 4284 5.655488 CACGAGTCAGACTTTAGGATGAAT 58.345 41.667 4.05 0.00 0.00 2.57
2932 4909 7.609760 AGTTTCAAATCCAAAAGGTTTGTTC 57.390 32.000 0.00 0.00 35.09 3.18
2933 4910 6.597672 AGTTTCAAATCCAAAAGGTTTGTTCC 59.402 34.615 0.00 0.00 35.09 3.62
3111 5114 2.594013 GCTAGGCAGCCTGGATGC 60.594 66.667 28.44 27.86 44.80 3.91
3240 5243 1.209504 GCCCACTATCACTGCTACCAA 59.790 52.381 0.00 0.00 0.00 3.67
3428 5431 3.250040 GGCCGTCATCATTAACGCTAATT 59.750 43.478 0.00 0.00 37.56 1.40
3439 5442 7.585867 TCATTAACGCTAATTACTTTGTTGCA 58.414 30.769 0.00 0.00 0.00 4.08
3440 5443 8.240682 TCATTAACGCTAATTACTTTGTTGCAT 58.759 29.630 0.00 0.00 0.00 3.96
3487 5814 2.227388 CTCCCGGGTACGTACATACATC 59.773 54.545 26.02 8.31 38.78 3.06
3524 5854 0.248661 CGCACACGAGTCCTAGGATG 60.249 60.000 16.27 11.69 43.93 3.51
3722 6252 6.400568 TGACGGGTAATGTTAGTTTCTAAGG 58.599 40.000 0.00 0.00 0.00 2.69
3811 6676 1.196808 GTGCGTATGTGAAACTGTGGG 59.803 52.381 0.00 0.00 38.04 4.61
3821 6686 4.141711 TGTGAAACTGTGGGGCTATAGATC 60.142 45.833 3.21 0.00 38.04 2.75
3865 6734 6.879400 AGGCTGTAGAACGATAGAAAGAAAT 58.121 36.000 0.00 0.00 41.38 2.17
3898 6770 2.959465 AAGCTGGCCTAGAAGTTTGT 57.041 45.000 3.32 0.00 0.00 2.83
3930 6890 4.522022 CCATCTTTGTTTGCCTCTCTCTTT 59.478 41.667 0.00 0.00 0.00 2.52
3937 6897 0.250901 TGCCTCTCTCTTTTGGCCAC 60.251 55.000 3.88 0.00 44.32 5.01
3975 6935 5.801350 TTCAATTAGATGACGCTTCCAAG 57.199 39.130 0.00 0.00 0.00 3.61
4093 7058 3.008375 TCTCTCTTGTTATTGTGCAGGCT 59.992 43.478 0.00 0.00 0.00 4.58
4142 7108 4.078363 TCAAGAATTTCCGAACGAATGC 57.922 40.909 0.00 0.00 0.00 3.56
4158 7124 1.386525 ATGCGGGCATTGGTGTGATC 61.387 55.000 0.00 0.00 31.82 2.92
4242 7225 3.179048 TGATGTCTGCTCATTAACGACG 58.821 45.455 0.00 0.00 0.00 5.12
4400 7800 5.696270 TCCATTGATATTTCTCGATCGTTGG 59.304 40.000 15.94 7.05 32.20 3.77
4427 7828 3.969976 AGCCTCTCAACCAATAGCATCTA 59.030 43.478 0.00 0.00 0.00 1.98
4630 8956 1.583054 GGACGAAAAGAGCAGTGTGT 58.417 50.000 0.00 0.00 0.00 3.72
4746 14142 1.878953 ATTCAACCTCGTGGACACAC 58.121 50.000 11.17 0.00 44.23 3.82
4760 14156 1.673920 GACACACGAGGCCTTTTTCAA 59.326 47.619 6.77 0.00 0.00 2.69
4800 17005 3.684103 TGCACGTCGAGAACAAATTTT 57.316 38.095 0.00 0.00 0.00 1.82
4853 17058 2.107204 AGACTTTGGCCTGACATTGACT 59.893 45.455 3.32 0.00 0.00 3.41
4937 17165 6.645003 TGTACGAAATATATGTGGATGTCAGC 59.355 38.462 0.00 0.00 0.00 4.26
4985 17213 7.769044 AGTAAAGTATGAATCGTGCCTAACAAT 59.231 33.333 0.00 0.00 0.00 2.71
5079 20369 2.973983 AAGGTAGAGCTAGGCCGATA 57.026 50.000 0.00 0.00 0.00 2.92
5081 20371 2.729194 AGGTAGAGCTAGGCCGATATG 58.271 52.381 0.00 0.00 0.00 1.78
5082 20372 1.751924 GGTAGAGCTAGGCCGATATGG 59.248 57.143 0.00 0.00 42.50 2.74
5119 20409 2.569059 CCGAATGAAGATGTGATGGCT 58.431 47.619 0.00 0.00 0.00 4.75
5155 20445 2.352421 CCACTTCGCTTTCTTCCTCGTA 60.352 50.000 0.00 0.00 0.00 3.43
5156 20446 3.314553 CACTTCGCTTTCTTCCTCGTAA 58.685 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 3.498774 AGCATATTTCTGGGCCAGTAG 57.501 47.619 31.60 16.80 32.61 2.57
103 104 4.459852 AATAGCATATTTCTGGGCCAGT 57.540 40.909 31.60 16.48 32.61 4.00
104 105 5.809001 TCTAATAGCATATTTCTGGGCCAG 58.191 41.667 28.01 28.01 0.00 4.85
189 429 0.250553 CACGTGCCCCTAAAGACCAA 60.251 55.000 0.82 0.00 0.00 3.67
195 435 2.661840 TTCGTGCACGTGCCCCTAAA 62.662 55.000 35.72 19.03 41.18 1.85
218 458 2.346803 CTTGTCGATGACAACCGGAAT 58.653 47.619 9.46 0.00 45.88 3.01
220 460 0.037697 CCTTGTCGATGACAACCGGA 60.038 55.000 9.46 0.00 45.88 5.14
362 602 8.335532 TCATGAAAAAGATTCACCGAAAGTAT 57.664 30.769 0.00 0.00 0.00 2.12
381 621 5.725325 TGCCAAAATGTCAGATTCATGAA 57.275 34.783 11.26 11.26 0.00 2.57
570 1042 0.028902 GTGTGTTCCGGTGACAAAGC 59.971 55.000 13.56 4.53 0.00 3.51
616 1088 4.024556 GTGTTGCTGTTATATGCTAGCAGG 60.025 45.833 23.89 7.78 45.69 4.85
831 1470 1.172812 AGGAAAAAGGAGTGCGTGGC 61.173 55.000 0.00 0.00 0.00 5.01
909 1559 2.362717 GGAGAAGAAGATACCGAGGTGG 59.637 54.545 4.80 0.00 46.41 4.61
1196 2245 6.983307 ACAACTAGCTAGCTATCAATCAACTG 59.017 38.462 24.36 11.20 0.00 3.16
1251 2308 4.392921 TTTTGGAGAGGACGAGATCATC 57.607 45.455 0.00 0.00 38.47 2.92
1316 2387 0.036732 TGCCCAGCAAACACTCCTAG 59.963 55.000 0.00 0.00 34.76 3.02
1368 2614 0.460109 CGACCTCGACATGCCATGAA 60.460 55.000 12.53 0.00 43.02 2.57
1428 2681 2.159517 CGGCAATCCTCCTTTTCGAAAG 60.160 50.000 10.98 5.63 0.00 2.62
1430 2683 1.448985 CGGCAATCCTCCTTTTCGAA 58.551 50.000 0.00 0.00 0.00 3.71
1431 2684 1.024579 GCGGCAATCCTCCTTTTCGA 61.025 55.000 0.00 0.00 0.00 3.71
1432 2685 1.429423 GCGGCAATCCTCCTTTTCG 59.571 57.895 0.00 0.00 0.00 3.46
1433 2686 1.024579 TCGCGGCAATCCTCCTTTTC 61.025 55.000 6.13 0.00 0.00 2.29
1434 2687 1.002624 TCGCGGCAATCCTCCTTTT 60.003 52.632 6.13 0.00 0.00 2.27
1435 2688 1.745489 GTCGCGGCAATCCTCCTTT 60.745 57.895 5.47 0.00 0.00 3.11
1439 2692 2.586357 GAGGTCGCGGCAATCCTC 60.586 66.667 14.93 14.93 39.41 3.71
1446 2699 4.819761 TGATGCAGAGGTCGCGGC 62.820 66.667 6.13 3.04 0.00 6.53
1449 2702 1.372582 TCAATTGATGCAGAGGTCGC 58.627 50.000 3.38 0.00 0.00 5.19
1452 2705 2.242965 TGGGATCAATTGATGCAGAGGT 59.757 45.455 32.61 7.84 43.56 3.85
1549 2899 4.873827 TGCTAAGTCGATTACCACCAATTC 59.126 41.667 0.00 0.00 0.00 2.17
1572 2922 2.811873 GCGTTTAGAGGGGCATCATCAT 60.812 50.000 0.00 0.00 0.00 2.45
1573 2923 1.475034 GCGTTTAGAGGGGCATCATCA 60.475 52.381 0.00 0.00 0.00 3.07
1574 2924 1.202698 AGCGTTTAGAGGGGCATCATC 60.203 52.381 0.00 0.00 0.00 2.92
1689 3045 2.442272 GGAGAGTGCTCGGGGCTA 60.442 66.667 0.00 0.00 42.25 3.93
1700 3056 2.909662 CTCCTTCCTTTTCTGGGAGAGT 59.090 50.000 0.00 0.00 44.37 3.24
1816 3172 0.250467 AACTGACGTGGCAGAGCATT 60.250 50.000 10.26 0.00 39.20 3.56
2026 3385 8.677148 TTAGACAAACAAGAAGAGTTGCTTAT 57.323 30.769 0.00 0.00 36.83 1.73
2482 3847 4.522789 ACCACTTAGAAATCACGGCAAATT 59.477 37.500 0.00 0.00 0.00 1.82
2994 4973 5.513233 ACATGATTTCCTTGGCTGATAGTT 58.487 37.500 0.00 0.00 0.00 2.24
3111 5114 0.514255 CTTGATGTATGATGCCGCCG 59.486 55.000 0.00 0.00 0.00 6.46
3383 5386 4.006319 CCTTCTTCCTCAAGAATGGTGAC 58.994 47.826 0.00 0.00 45.70 3.67
3428 5431 5.940192 ATTCTGTCGAATGCAACAAAGTA 57.060 34.783 0.00 0.00 38.41 2.24
3487 5814 1.326576 CGCATTACGTTTTGCAGTGG 58.673 50.000 18.67 3.01 38.80 4.00
3811 6676 4.357325 TGATTGGAGAGGGATCTATAGCC 58.643 47.826 0.00 0.00 0.00 3.93
3821 6686 4.582240 GCCTAAGAAAATGATTGGAGAGGG 59.418 45.833 0.00 0.00 0.00 4.30
3865 6734 1.203050 CCAGCTTTCCCCCTTCTTTCA 60.203 52.381 0.00 0.00 0.00 2.69
3898 6770 7.178983 AGAGGCAAACAAAGATGGAAATCAATA 59.821 33.333 0.00 0.00 0.00 1.90
3930 6890 2.512692 AGCTCATACATTGTGGCCAA 57.487 45.000 7.24 0.00 34.45 4.52
3966 6926 5.577945 ACAATATGCAATTTTCTTGGAAGCG 59.422 36.000 0.00 0.00 0.00 4.68
3975 6935 6.808829 TCCTCCATCACAATATGCAATTTTC 58.191 36.000 0.00 0.00 0.00 2.29
4093 7058 1.702182 TGCCAATTCTGGTGCTGAAA 58.298 45.000 0.00 0.00 45.53 2.69
4142 7108 0.461163 TACGATCACACCAATGCCCG 60.461 55.000 0.00 0.00 0.00 6.13
4185 7158 9.961264 TGTGGGATGTTTATTTATACAGTTACA 57.039 29.630 0.00 0.00 0.00 2.41
4242 7225 7.255277 GCTAAGGTGTTTTCATCCCTAATCATC 60.255 40.741 0.00 0.00 0.00 2.92
4301 7571 6.487689 AGATCGAAGGTTGATCAACTTTTC 57.512 37.500 29.73 28.63 43.73 2.29
4400 7800 1.760192 ATTGGTTGAGAGGCTGCATC 58.240 50.000 6.12 6.12 0.00 3.91
4529 8245 3.637998 GCATCTCCACCATGCAATTAG 57.362 47.619 0.00 0.00 45.19 1.73
4615 8331 5.734855 TGTTAAGACACACTGCTCTTTTC 57.265 39.130 0.00 0.00 0.00 2.29
4655 9618 0.758310 TGGTGGTGAAATTGCAGCCA 60.758 50.000 13.10 8.21 35.50 4.75
4659 9622 6.596309 TTTATATGTGGTGGTGAAATTGCA 57.404 33.333 0.00 0.00 0.00 4.08
4746 14142 4.766404 ATGTAGTTTGAAAAAGGCCTCG 57.234 40.909 5.23 0.00 0.00 4.63
4800 17005 3.892588 AGGTATTTGTTCCTTTCGCCAAA 59.107 39.130 0.00 0.00 0.00 3.28
4909 17117 9.384764 TGACATCCACATATATTTCGTACAAAA 57.615 29.630 0.00 0.00 0.00 2.44
4937 17165 5.747197 ACTAAATCTTTCTACCATACGCACG 59.253 40.000 0.00 0.00 0.00 5.34
5026 20307 8.190784 TCACTTCTCTTTTTCTTTTGGAACATC 58.809 33.333 0.00 0.00 39.30 3.06
5079 20369 1.469595 GCACGTTTACATGCATGCCAT 60.470 47.619 26.53 10.06 41.65 4.40
5081 20371 0.801836 GGCACGTTTACATGCATGCC 60.802 55.000 26.53 16.93 45.26 4.40
5082 20372 2.652548 GGCACGTTTACATGCATGC 58.347 52.632 26.53 11.82 43.93 4.06
5119 20409 1.912763 GTGGAGCATGGGCCCAAAA 60.913 57.895 32.58 5.36 40.51 2.44


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

AutoCloner maintained by Alex Coulton.