Multiple sequence alignment - TraesCS5D01G385600

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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 TraesCS5D01G385600 chr5D 100.000 5068 0 0 949 6016 454808203 454813270 0.000000e+00 9359
1 TraesCS5D01G385600 chr5D 95.060 1761 41 8 3487 5239 455608053 455609775 0.000000e+00 2728
2 TraesCS5D01G385600 chr5D 99.891 915 1 0 2327 3241 454837350 454838264 0.000000e+00 1685
3 TraesCS5D01G385600 chr5D 94.124 902 31 7 2606 3489 455607033 455607930 0.000000e+00 1352
4 TraesCS5D01G385600 chr5D 94.052 891 25 10 4235 5114 454838679 454839552 0.000000e+00 1327
5 TraesCS5D01G385600 chr5D 100.000 521 0 0 1 521 454807255 454807775 0.000000e+00 963
6 TraesCS5D01G385600 chr5D 92.072 555 44 0 5312 5866 455596828 455597382 0.000000e+00 782
7 TraesCS5D01G385600 chr5D 97.403 385 7 2 3812 4194 454838300 454838683 0.000000e+00 652
8 TraesCS5D01G385600 chr5D 95.425 153 6 1 5865 6016 455597521 455597673 6.020000e-60 243
9 TraesCS5D01G385600 chr5D 100.000 53 0 0 2327 2379 455606984 455607036 1.380000e-16 99
10 TraesCS5D01G385600 chr5B 93.840 3052 82 30 2238 5229 556958964 556961969 0.000000e+00 4497
11 TraesCS5D01G385600 chr5B 98.220 618 10 1 1625 2241 556958188 556958805 0.000000e+00 1079
12 TraesCS5D01G385600 chr5B 94.006 684 18 8 957 1622 556954477 556955155 0.000000e+00 1014
13 TraesCS5D01G385600 chr5B 86.004 493 33 15 1 468 556953564 556954045 4.190000e-136 496
14 TraesCS5D01G385600 chrUn 93.993 1931 56 18 3329 5239 63664047 63665937 0.000000e+00 2868
15 TraesCS5D01G385600 chrUn 91.259 1716 96 30 1625 3301 63662348 63664048 0.000000e+00 2289
16 TraesCS5D01G385600 chrUn 96.232 690 9 4 949 1622 63659536 63660224 0.000000e+00 1114
17 TraesCS5D01G385600 chrUn 80.000 250 29 13 2119 2352 115037077 115037321 1.340000e-36 165
18 TraesCS5D01G385600 chrUn 94.521 73 4 0 5243 5315 305213228 305213156 4.930000e-21 113
19 TraesCS5D01G385600 chr5A 87.152 1401 83 37 2327 3661 572350283 572351652 0.000000e+00 1500
20 TraesCS5D01G385600 chr5A 94.530 969 38 12 4152 5114 572351691 572352650 0.000000e+00 1482
21 TraesCS5D01G385600 chr5A 94.553 257 10 3 214 468 573764328 573764582 1.570000e-105 394
22 TraesCS5D01G385600 chr5A 79.668 241 26 15 3 222 573762637 573762875 1.040000e-32 152
23 TraesCS5D01G385600 chr2D 90.288 556 53 1 5312 5866 365464995 365464440 0.000000e+00 726
24 TraesCS5D01G385600 chr2D 89.568 556 57 1 5312 5866 136410686 136410131 0.000000e+00 704
25 TraesCS5D01G385600 chr2D 89.550 555 57 1 5312 5866 264610660 264611213 0.000000e+00 702
26 TraesCS5D01G385600 chr2D 89.369 555 59 0 5312 5866 352352227 352351673 0.000000e+00 699
27 TraesCS5D01G385600 chr1D 89.730 555 57 0 5312 5866 450835384 450835938 0.000000e+00 710
28 TraesCS5D01G385600 chr1D 89.550 555 58 0 5312 5866 198595519 198594965 0.000000e+00 704
29 TraesCS5D01G385600 chr1D 89.550 555 56 1 5312 5866 405673222 405672670 0.000000e+00 702
30 TraesCS5D01G385600 chr1D 89.630 270 26 2 1625 1893 473026389 473026121 5.770000e-90 342
31 TraesCS5D01G385600 chr1D 92.810 153 10 1 5865 6016 448530564 448530412 2.820000e-53 220
32 TraesCS5D01G385600 chr1D 90.805 87 6 2 5230 5315 279100965 279100880 1.370000e-21 115
33 TraesCS5D01G385600 chr7D 89.369 555 59 0 5312 5866 204133949 204134503 0.000000e+00 699
34 TraesCS5D01G385600 chr7D 92.763 152 10 1 5865 6015 273121914 273121763 1.020000e-52 219
35 TraesCS5D01G385600 chr7D 92.308 156 8 2 5865 6016 311566555 311566400 1.020000e-52 219
36 TraesCS5D01G385600 chr7D 92.771 83 6 0 5233 5315 60439586 60439668 2.940000e-23 121
37 TraesCS5D01G385600 chr3B 87.871 371 42 3 1078 1448 342532429 342532062 3.330000e-117 433
38 TraesCS5D01G385600 chr3B 87.770 139 17 0 1222 1360 533559004 533558866 4.820000e-36 163
39 TraesCS5D01G385600 chr3B 91.566 83 6 1 5233 5315 714106395 714106476 4.930000e-21 113
40 TraesCS5D01G385600 chr6D 84.536 388 43 14 1116 1493 195978309 195978689 9.530000e-98 368
41 TraesCS5D01G385600 chr6D 95.890 73 3 0 5243 5315 309588606 309588534 1.060000e-22 119
42 TraesCS5D01G385600 chr3A 88.889 270 27 3 1625 1893 696369739 696370006 4.500000e-86 329
43 TraesCS5D01G385600 chr3A 89.231 195 18 3 1700 1893 696370101 696370293 2.170000e-59 241
44 TraesCS5D01G385600 chr6A 95.082 183 8 1 1440 1621 153910531 153910349 2.740000e-73 287
45 TraesCS5D01G385600 chr6A 79.600 250 30 13 2119 2352 49993867 49993623 6.240000e-35 159
46 TraesCS5D01G385600 chr7B 92.763 152 11 0 5865 6016 356902556 356902707 2.820000e-53 220
47 TraesCS5D01G385600 chr4D 92.763 152 11 0 5865 6016 226159677 226159828 2.820000e-53 220
48 TraesCS5D01G385600 chr4D 92.715 151 9 2 5865 6013 177162969 177162819 3.650000e-52 217
49 TraesCS5D01G385600 chr4D 91.613 155 10 2 5865 6016 267374722 267374876 1.700000e-50 211
50 TraesCS5D01G385600 chr4D 92.593 81 4 1 5235 5315 122272732 122272810 1.370000e-21 115
51 TraesCS5D01G385600 chr3D 92.258 155 9 2 5865 6016 162832125 162831971 3.650000e-52 217
52 TraesCS5D01G385600 chr3D 95.890 73 3 0 5243 5315 382104927 382104855 1.060000e-22 119
53 TraesCS5D01G385600 chr6B 79.116 249 33 13 2119 2352 89436472 89436228 2.900000e-33 154
54 TraesCS5D01G385600 chr7A 92.593 81 6 0 5235 5315 663553649 663553569 3.810000e-22 117
55 TraesCS5D01G385600 chr2B 91.566 83 6 1 5233 5315 440223872 440223791 4.930000e-21 113


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 TraesCS5D01G385600 chr5D 454807255 454813270 6015 False 5161.000000 9359 100.000000 1 6016 2 chr5D.!!$F1 6015
1 TraesCS5D01G385600 chr5D 455606984 455609775 2791 False 1393.000000 2728 96.394667 2327 5239 3 chr5D.!!$F4 2912
2 TraesCS5D01G385600 chr5D 454837350 454839552 2202 False 1221.333333 1685 97.115333 2327 5114 3 chr5D.!!$F2 2787
3 TraesCS5D01G385600 chr5D 455596828 455597673 845 False 512.500000 782 93.748500 5312 6016 2 chr5D.!!$F3 704
4 TraesCS5D01G385600 chr5B 556953564 556961969 8405 False 1771.500000 4497 93.017500 1 5229 4 chr5B.!!$F1 5228
5 TraesCS5D01G385600 chrUn 63659536 63665937 6401 False 2090.333333 2868 93.828000 949 5239 3 chrUn.!!$F2 4290
6 TraesCS5D01G385600 chr5A 572350283 572352650 2367 False 1491.000000 1500 90.841000 2327 5114 2 chr5A.!!$F1 2787
7 TraesCS5D01G385600 chr5A 573762637 573764582 1945 False 273.000000 394 87.110500 3 468 2 chr5A.!!$F2 465
8 TraesCS5D01G385600 chr2D 365464440 365464995 555 True 726.000000 726 90.288000 5312 5866 1 chr2D.!!$R3 554
9 TraesCS5D01G385600 chr2D 136410131 136410686 555 True 704.000000 704 89.568000 5312 5866 1 chr2D.!!$R1 554
10 TraesCS5D01G385600 chr2D 264610660 264611213 553 False 702.000000 702 89.550000 5312 5866 1 chr2D.!!$F1 554
11 TraesCS5D01G385600 chr2D 352351673 352352227 554 True 699.000000 699 89.369000 5312 5866 1 chr2D.!!$R2 554
12 TraesCS5D01G385600 chr1D 450835384 450835938 554 False 710.000000 710 89.730000 5312 5866 1 chr1D.!!$F1 554
13 TraesCS5D01G385600 chr1D 198594965 198595519 554 True 704.000000 704 89.550000 5312 5866 1 chr1D.!!$R1 554
14 TraesCS5D01G385600 chr1D 405672670 405673222 552 True 702.000000 702 89.550000 5312 5866 1 chr1D.!!$R3 554
15 TraesCS5D01G385600 chr7D 204133949 204134503 554 False 699.000000 699 89.369000 5312 5866 1 chr7D.!!$F2 554
16 TraesCS5D01G385600 chr3A 696369739 696370293 554 False 285.000000 329 89.060000 1625 1893 2 chr3A.!!$F1 268

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
421 467 0.099791 GCTCGAGACCTCTCTTTCGG 59.900 60.000 18.75 0.00 40.75 4.30 F
424 470 0.099791 CGAGACCTCTCTTTCGGCTC 59.900 60.000 0.93 0.00 40.75 4.70 F
1364 1414 0.531974 GCATCCGGCAAGGTTCGATA 60.532 55.000 0.00 0.00 43.97 2.92 F
1623 1693 1.202782 TCCTCTAGCTAGGCGTACTGG 60.203 57.143 20.58 11.00 36.51 4.00 F
1766 5434 1.289109 GCTTTCTTGTCACGCGCCTA 61.289 55.000 5.73 0.00 0.00 3.93 F
3265 7164 3.500331 CACAGAATGCAGGGCCATA 57.500 52.632 6.18 0.00 42.53 2.74 F
4070 8212 2.592102 ATTTATCCGGCTGCATGGAT 57.408 45.000 23.44 23.44 46.52 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1664 2.111384 CTAGCTAGAGGAACAGGCCAA 58.889 52.381 16.15 0.0 0.00 4.52 R
1634 5301 7.924947 GCGTTAATCTACTAGGGTACTTCAATT 59.075 37.037 0.00 0.0 0.00 2.32 R
3248 7144 2.530460 TTTATGGCCCTGCATTCTGT 57.470 45.000 0.00 0.0 0.00 3.41 R
3339 7239 4.857130 ACAGACCCCCTTATTTTCCTAC 57.143 45.455 0.00 0.0 0.00 3.18 R
3677 7724 1.377333 GGCTTGGTAGGTGCAGGAC 60.377 63.158 0.00 0.0 0.00 3.85 R
4702 8910 2.052782 ACTTTGAAAGCTGGACGGTT 57.947 45.000 4.57 0.0 34.13 4.44 R
5426 9816 0.394488 TGTGGGAAACAACTGCCGAA 60.394 50.000 0.00 0.0 35.24 4.30 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
35 36 3.777478 TCGTGACAAGTAATTCCGGATC 58.223 45.455 4.15 0.00 0.00 3.36
36 37 2.534349 CGTGACAAGTAATTCCGGATCG 59.466 50.000 4.15 0.00 0.00 3.69
43 44 0.966920 TAATTCCGGATCGAGGGAGC 59.033 55.000 4.15 0.00 33.01 4.70
138 144 1.973281 CCCGCCAGCTCACATTTGT 60.973 57.895 0.00 0.00 0.00 2.83
165 192 5.404968 TCAATTGCTGCCTTAATTGAAAACG 59.595 36.000 18.57 0.00 45.27 3.60
233 275 2.990066 AGAACTTATTGCTCCCTCCG 57.010 50.000 0.00 0.00 0.00 4.63
240 286 1.717032 ATTGCTCCCTCCGTATAGCA 58.283 50.000 0.00 0.00 42.91 3.49
244 290 2.236766 GCTCCCTCCGTATAGCAGTAA 58.763 52.381 0.00 0.00 35.05 2.24
296 342 0.107456 CACTGCTCACACCTTCCACT 59.893 55.000 0.00 0.00 0.00 4.00
314 360 0.392193 CTCTGGCTGACATGTGGGTC 60.392 60.000 1.15 0.00 38.29 4.46
315 361 1.377725 CTGGCTGACATGTGGGTCC 60.378 63.158 1.15 0.00 36.97 4.46
316 362 2.128290 CTGGCTGACATGTGGGTCCA 62.128 60.000 1.15 4.32 36.97 4.02
317 363 1.074775 GGCTGACATGTGGGTCCAA 59.925 57.895 1.15 0.00 36.97 3.53
318 364 1.244019 GGCTGACATGTGGGTCCAAC 61.244 60.000 1.15 0.00 36.97 3.77
319 365 1.577328 GCTGACATGTGGGTCCAACG 61.577 60.000 1.15 0.00 36.97 4.10
320 366 1.577328 CTGACATGTGGGTCCAACGC 61.577 60.000 1.15 0.00 36.97 4.84
321 367 2.282180 ACATGTGGGTCCAACGCC 60.282 61.111 0.00 0.00 0.00 5.68
322 368 2.034066 CATGTGGGTCCAACGCCT 59.966 61.111 0.00 0.00 0.00 5.52
363 409 2.439156 GGCCTCCGCTGAAGCAAT 60.439 61.111 0.00 0.00 42.21 3.56
401 447 3.377798 GTGTAAACCCCTTCGTTTTGACA 59.622 43.478 0.00 0.00 37.20 3.58
417 463 1.271652 TGACAGCTCGAGACCTCTCTT 60.272 52.381 18.75 0.00 40.75 2.85
418 464 1.816224 GACAGCTCGAGACCTCTCTTT 59.184 52.381 18.75 0.00 40.75 2.52
419 465 1.816224 ACAGCTCGAGACCTCTCTTTC 59.184 52.381 18.75 0.00 40.75 2.62
420 466 1.091537 AGCTCGAGACCTCTCTTTCG 58.908 55.000 18.75 0.00 40.75 3.46
421 467 0.099791 GCTCGAGACCTCTCTTTCGG 59.900 60.000 18.75 0.00 40.75 4.30
423 469 0.322636 TCGAGACCTCTCTTTCGGCT 60.323 55.000 0.93 0.00 40.75 5.52
424 470 0.099791 CGAGACCTCTCTTTCGGCTC 59.900 60.000 0.93 0.00 40.75 4.70
425 471 1.470051 GAGACCTCTCTTTCGGCTCT 58.530 55.000 0.00 0.00 39.81 4.09
493 539 2.778899 CCCCCACAGTTTCTCCTCT 58.221 57.895 0.00 0.00 0.00 3.69
494 540 0.615850 CCCCCACAGTTTCTCCTCTC 59.384 60.000 0.00 0.00 0.00 3.20
495 541 1.650528 CCCCACAGTTTCTCCTCTCT 58.349 55.000 0.00 0.00 0.00 3.10
496 542 1.552792 CCCCACAGTTTCTCCTCTCTC 59.447 57.143 0.00 0.00 0.00 3.20
497 543 1.552792 CCCACAGTTTCTCCTCTCTCC 59.447 57.143 0.00 0.00 0.00 3.71
498 544 2.534990 CCACAGTTTCTCCTCTCTCCT 58.465 52.381 0.00 0.00 0.00 3.69
499 545 2.495669 CCACAGTTTCTCCTCTCTCCTC 59.504 54.545 0.00 0.00 0.00 3.71
1364 1414 0.531974 GCATCCGGCAAGGTTCGATA 60.532 55.000 0.00 0.00 43.97 2.92
1376 1426 3.055080 TTCGATACTTCGCGCCCGT 62.055 57.895 0.00 0.00 45.10 5.28
1594 1664 2.700540 GGAGGAGGGAGGGGATTTATGT 60.701 54.545 0.00 0.00 0.00 2.29
1622 1692 2.257691 TCCTCTAGCTAGGCGTACTG 57.742 55.000 20.58 2.50 36.51 2.74
1623 1693 1.202782 TCCTCTAGCTAGGCGTACTGG 60.203 57.143 20.58 11.00 36.51 4.00
1633 5300 4.381292 GCTAGGCGTACTGGAACTTCTTTA 60.381 45.833 0.00 0.00 0.00 1.85
1634 5301 4.612264 AGGCGTACTGGAACTTCTTTAA 57.388 40.909 0.00 0.00 0.00 1.52
1766 5434 1.289109 GCTTTCTTGTCACGCGCCTA 61.289 55.000 5.73 0.00 0.00 3.93
2669 6518 5.451520 GGCTCATGATCCTTTTTCCATTCAG 60.452 44.000 8.39 0.00 0.00 3.02
3265 7164 3.500331 CACAGAATGCAGGGCCATA 57.500 52.632 6.18 0.00 42.53 2.74
3339 7239 4.012374 AGTGCATGGATAACTTCACCTTG 58.988 43.478 0.00 0.00 33.77 3.61
3552 7599 7.277098 TCTGTTAGTGGCTTAACACGATATTTC 59.723 37.037 9.92 0.00 45.80 2.17
3677 7724 6.037786 TCTCCTAATTTGGGATATGCGTAG 57.962 41.667 6.08 0.00 31.89 3.51
4066 8208 4.655963 ACAATCTATTTATCCGGCTGCAT 58.344 39.130 0.50 0.00 0.00 3.96
4068 8210 3.057969 TCTATTTATCCGGCTGCATGG 57.942 47.619 0.50 2.51 0.00 3.66
4070 8212 2.592102 ATTTATCCGGCTGCATGGAT 57.408 45.000 23.44 23.44 46.52 3.41
4277 8482 5.914085 TGGTTTTGTTTCTGTTGTTTGTG 57.086 34.783 0.00 0.00 0.00 3.33
4287 8492 8.920665 TGTTTCTGTTGTTTGTGTAAAGAAATG 58.079 29.630 0.00 0.00 31.80 2.32
4702 8910 5.014202 GGTTTGGGATCTAAGCAGGTAAAA 58.986 41.667 0.00 0.00 0.00 1.52
5239 9537 5.954150 GTCCTGGGGATTATACCGTTAGATA 59.046 44.000 0.00 0.00 32.73 1.98
5240 9538 6.610425 GTCCTGGGGATTATACCGTTAGATAT 59.390 42.308 0.00 0.00 32.73 1.63
5241 9539 7.125356 GTCCTGGGGATTATACCGTTAGATATT 59.875 40.741 0.00 0.00 32.73 1.28
5242 9540 7.681168 TCCTGGGGATTATACCGTTAGATATTT 59.319 37.037 0.00 0.00 0.00 1.40
5243 9541 8.984855 CCTGGGGATTATACCGTTAGATATTTA 58.015 37.037 0.00 0.00 0.00 1.40
5244 9542 9.813446 CTGGGGATTATACCGTTAGATATTTAC 57.187 37.037 0.00 0.00 0.00 2.01
5245 9543 8.761689 TGGGGATTATACCGTTAGATATTTACC 58.238 37.037 0.00 0.00 0.00 2.85
5246 9544 8.206867 GGGGATTATACCGTTAGATATTTACCC 58.793 40.741 0.00 0.00 0.00 3.69
5247 9545 8.206867 GGGATTATACCGTTAGATATTTACCCC 58.793 40.741 0.00 0.00 0.00 4.95
5248 9546 8.206867 GGATTATACCGTTAGATATTTACCCCC 58.793 40.741 0.00 0.00 0.00 5.40
5249 9547 8.922229 ATTATACCGTTAGATATTTACCCCCT 57.078 34.615 0.00 0.00 0.00 4.79
5250 9548 6.864151 ATACCGTTAGATATTTACCCCCTC 57.136 41.667 0.00 0.00 0.00 4.30
5251 9549 3.906218 ACCGTTAGATATTTACCCCCTCC 59.094 47.826 0.00 0.00 0.00 4.30
5252 9550 3.056322 CCGTTAGATATTTACCCCCTCCG 60.056 52.174 0.00 0.00 0.00 4.63
5253 9551 3.575687 CGTTAGATATTTACCCCCTCCGT 59.424 47.826 0.00 0.00 0.00 4.69
5254 9552 4.039609 CGTTAGATATTTACCCCCTCCGTT 59.960 45.833 0.00 0.00 0.00 4.44
5255 9553 5.453762 CGTTAGATATTTACCCCCTCCGTTT 60.454 44.000 0.00 0.00 0.00 3.60
5256 9554 4.701651 AGATATTTACCCCCTCCGTTTC 57.298 45.455 0.00 0.00 0.00 2.78
5257 9555 4.042174 AGATATTTACCCCCTCCGTTTCA 58.958 43.478 0.00 0.00 0.00 2.69
5258 9556 4.475747 AGATATTTACCCCCTCCGTTTCAA 59.524 41.667 0.00 0.00 0.00 2.69
5259 9557 3.529216 ATTTACCCCCTCCGTTTCAAA 57.471 42.857 0.00 0.00 0.00 2.69
5260 9558 3.309600 TTTACCCCCTCCGTTTCAAAA 57.690 42.857 0.00 0.00 0.00 2.44
5261 9559 3.529216 TTACCCCCTCCGTTTCAAAAT 57.471 42.857 0.00 0.00 0.00 1.82
5262 9560 4.654389 TTACCCCCTCCGTTTCAAAATA 57.346 40.909 0.00 0.00 0.00 1.40
5263 9561 3.081710 ACCCCCTCCGTTTCAAAATAG 57.918 47.619 0.00 0.00 0.00 1.73
5264 9562 2.645797 ACCCCCTCCGTTTCAAAATAGA 59.354 45.455 0.00 0.00 0.00 1.98
5265 9563 3.268595 ACCCCCTCCGTTTCAAAATAGAT 59.731 43.478 0.00 0.00 0.00 1.98
5266 9564 3.632145 CCCCCTCCGTTTCAAAATAGATG 59.368 47.826 0.00 0.00 0.00 2.90
5267 9565 4.523083 CCCCTCCGTTTCAAAATAGATGA 58.477 43.478 0.00 0.00 0.00 2.92
5268 9566 5.133221 CCCCTCCGTTTCAAAATAGATGAT 58.867 41.667 0.00 0.00 0.00 2.45
5269 9567 5.239525 CCCCTCCGTTTCAAAATAGATGATC 59.760 44.000 0.00 0.00 0.00 2.92
5270 9568 5.239525 CCCTCCGTTTCAAAATAGATGATCC 59.760 44.000 0.00 0.00 0.00 3.36
5271 9569 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
5272 9570 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
5273 9571 7.083875 TCCGTTTCAAAATAGATGATCCAAC 57.916 36.000 0.00 0.00 0.00 3.77
5274 9572 6.884295 TCCGTTTCAAAATAGATGATCCAACT 59.116 34.615 0.00 0.00 0.00 3.16
5275 9573 7.393234 TCCGTTTCAAAATAGATGATCCAACTT 59.607 33.333 0.00 0.00 0.00 2.66
5276 9574 8.028938 CCGTTTCAAAATAGATGATCCAACTTT 58.971 33.333 0.00 0.00 0.00 2.66
5407 9797 0.976073 CGAGGCCTAGGAAGGGAACA 60.976 60.000 14.75 0.00 43.87 3.18
5420 9810 1.070786 GGAACAACACGGAGCCAGA 59.929 57.895 0.00 0.00 0.00 3.86
5426 9816 1.066573 CAACACGGAGCCAGAGAAGAT 60.067 52.381 0.00 0.00 0.00 2.40
5507 9897 4.471904 CTGGAGAATAACAGCAGGTGTA 57.528 45.455 5.48 0.00 39.03 2.90
5607 10019 2.686835 GGAGGGAGCAGGCAGTCT 60.687 66.667 0.00 0.00 0.00 3.24
5643 10080 0.914644 AGCAGCTGGAGCAGGAATAA 59.085 50.000 17.12 0.00 45.16 1.40
5716 10358 5.666462 TGCTCTTGTGTGTTGACTAAGTTA 58.334 37.500 0.00 0.00 0.00 2.24
5836 10597 7.066142 ACATACAACCCATCTGCCATTATTTA 58.934 34.615 0.00 0.00 0.00 1.40
5866 10627 7.896383 ATTTACAGCCCATTTGCTAATTCTA 57.104 32.000 0.00 0.00 40.32 2.10
5998 10900 7.938563 TGATGTGTTTTAAAAATGTACAGCC 57.061 32.000 1.31 4.08 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.144359 CGGAATTACTTGTCACGAAAAAGG 58.856 41.667 0.00 0.00 0.00 3.11
10 11 4.815308 TCCGGAATTACTTGTCACGAAAAA 59.185 37.500 0.00 0.00 0.00 1.94
14 15 3.732774 CGATCCGGAATTACTTGTCACGA 60.733 47.826 9.01 0.00 0.00 4.35
15 16 2.534349 CGATCCGGAATTACTTGTCACG 59.466 50.000 9.01 0.00 0.00 4.35
35 36 2.690497 TCTCTTCTAACATGCTCCCTCG 59.310 50.000 0.00 0.00 0.00 4.63
36 37 3.069443 CCTCTCTTCTAACATGCTCCCTC 59.931 52.174 0.00 0.00 0.00 4.30
43 44 7.959651 CGACAAAAATTCCTCTCTTCTAACATG 59.040 37.037 0.00 0.00 0.00 3.21
89 92 4.828072 TTACCATTTTTATTGGGGTGGC 57.172 40.909 0.00 0.00 38.64 5.01
131 137 3.259876 AGGCAGCAATTGATGACAAATGT 59.740 39.130 29.95 7.38 43.08 2.71
138 144 5.918426 TCAATTAAGGCAGCAATTGATGA 57.082 34.783 27.03 6.18 43.00 2.92
261 307 2.159627 GCAGTGGAGTAAATGTGGAACG 59.840 50.000 0.00 0.00 42.39 3.95
296 342 1.679311 GACCCACATGTCAGCCAGA 59.321 57.895 0.00 0.00 35.29 3.86
315 361 3.423154 GAGGCGTTGGAGGCGTTG 61.423 66.667 0.00 0.00 41.99 4.10
318 364 4.124351 TACGAGGCGTTGGAGGCG 62.124 66.667 0.00 0.00 41.54 5.52
319 365 2.202756 CTACGAGGCGTTGGAGGC 60.203 66.667 0.00 0.00 41.54 4.70
320 366 2.202756 GCTACGAGGCGTTGGAGG 60.203 66.667 7.99 0.00 41.54 4.30
321 367 2.202756 GGCTACGAGGCGTTGGAG 60.203 66.667 1.10 1.10 41.54 3.86
356 402 1.203287 GAGTTTGGGCCTCATTGCTTC 59.797 52.381 4.53 0.00 0.00 3.86
363 409 3.936203 ACGCGAGTTTGGGCCTCA 61.936 61.111 15.93 0.00 46.40 3.86
417 463 5.875359 GGAAGAATAAAAAGAGAGAGCCGAA 59.125 40.000 0.00 0.00 0.00 4.30
418 464 5.420409 GGAAGAATAAAAAGAGAGAGCCGA 58.580 41.667 0.00 0.00 0.00 5.54
419 465 4.572795 GGGAAGAATAAAAAGAGAGAGCCG 59.427 45.833 0.00 0.00 0.00 5.52
420 466 4.884744 GGGGAAGAATAAAAAGAGAGAGCC 59.115 45.833 0.00 0.00 0.00 4.70
421 467 4.884744 GGGGGAAGAATAAAAAGAGAGAGC 59.115 45.833 0.00 0.00 0.00 4.09
423 469 5.191921 GGAGGGGGAAGAATAAAAAGAGAGA 59.808 44.000 0.00 0.00 0.00 3.10
424 470 5.441500 GGAGGGGGAAGAATAAAAAGAGAG 58.558 45.833 0.00 0.00 0.00 3.20
425 471 4.080526 CGGAGGGGGAAGAATAAAAAGAGA 60.081 45.833 0.00 0.00 0.00 3.10
479 525 2.495669 GGAGGAGAGAGGAGAAACTGTG 59.504 54.545 0.00 0.00 0.00 3.66
480 526 2.558800 GGGAGGAGAGAGGAGAAACTGT 60.559 54.545 0.00 0.00 0.00 3.55
485 531 2.020137 GGGGGAGGAGAGAGGAGAA 58.980 63.158 0.00 0.00 0.00 2.87
1594 1664 2.111384 CTAGCTAGAGGAACAGGCCAA 58.889 52.381 16.15 0.00 0.00 4.52
1633 5300 9.813446 CGTTAATCTACTAGGGTACTTCAATTT 57.187 33.333 0.00 0.00 0.00 1.82
1634 5301 7.924947 GCGTTAATCTACTAGGGTACTTCAATT 59.075 37.037 0.00 0.00 0.00 2.32
3248 7144 2.530460 TTTATGGCCCTGCATTCTGT 57.470 45.000 0.00 0.00 0.00 3.41
3339 7239 4.857130 ACAGACCCCCTTATTTTCCTAC 57.143 45.455 0.00 0.00 0.00 3.18
3552 7599 8.026607 TGAAACTAAACAGAACAGAACCAAAAG 58.973 33.333 0.00 0.00 0.00 2.27
3677 7724 1.377333 GGCTTGGTAGGTGCAGGAC 60.377 63.158 0.00 0.00 0.00 3.85
4066 8208 5.420421 TGAGGTTTTCAAGTGAAACAATCCA 59.580 36.000 5.98 0.01 43.01 3.41
4068 8210 7.035612 AGTTGAGGTTTTCAAGTGAAACAATC 58.964 34.615 5.98 5.47 46.09 2.67
4070 8212 6.339587 AGTTGAGGTTTTCAAGTGAAACAA 57.660 33.333 5.98 5.04 46.09 2.83
4171 8331 7.264947 TCTGAATAGAAATCATGCACGAGTAA 58.735 34.615 0.00 0.00 0.00 2.24
4257 8462 8.756864 TCTTTACACAAACAACAGAAACAAAAC 58.243 29.630 0.00 0.00 0.00 2.43
4551 8756 9.438228 TTCAAGACCGATAATAACAAACATACA 57.562 29.630 0.00 0.00 0.00 2.29
4702 8910 2.052782 ACTTTGAAAGCTGGACGGTT 57.947 45.000 4.57 0.00 34.13 4.44
4729 8941 4.887655 AGTGAGGAAACGAAAAAGGAATGT 59.112 37.500 0.00 0.00 0.00 2.71
5037 9331 5.912149 AGGTATTATCTTGCCTCCATTCA 57.088 39.130 0.00 0.00 0.00 2.57
5176 9474 6.254281 ACAGGTAAATGCATCAACTACAAC 57.746 37.500 0.00 0.00 0.00 3.32
5239 9537 3.529216 TTTGAAACGGAGGGGGTAAAT 57.471 42.857 0.00 0.00 0.00 1.40
5240 9538 3.309600 TTTTGAAACGGAGGGGGTAAA 57.690 42.857 0.00 0.00 0.00 2.01
5241 9539 3.529216 ATTTTGAAACGGAGGGGGTAA 57.471 42.857 0.00 0.00 0.00 2.85
5242 9540 3.845398 TCTATTTTGAAACGGAGGGGGTA 59.155 43.478 0.00 0.00 0.00 3.69
5243 9541 2.645797 TCTATTTTGAAACGGAGGGGGT 59.354 45.455 0.00 0.00 0.00 4.95
5244 9542 3.359695 TCTATTTTGAAACGGAGGGGG 57.640 47.619 0.00 0.00 0.00 5.40
5245 9543 4.523083 TCATCTATTTTGAAACGGAGGGG 58.477 43.478 0.00 0.00 0.00 4.79
5246 9544 5.239525 GGATCATCTATTTTGAAACGGAGGG 59.760 44.000 0.00 0.00 0.00 4.30
5247 9545 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
5248 9546 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
5249 9547 6.884295 AGTTGGATCATCTATTTTGAAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
5250 9548 7.088589 AGTTGGATCATCTATTTTGAAACGG 57.911 36.000 0.00 0.00 0.00 4.44
5251 9549 8.970691 AAAGTTGGATCATCTATTTTGAAACG 57.029 30.769 0.00 0.00 0.00 3.60
5287 9585 8.042515 ACTCAACTTTGTACCAACTTTAGTACA 58.957 33.333 0.00 0.00 45.29 2.90
5288 9586 8.429493 ACTCAACTTTGTACCAACTTTAGTAC 57.571 34.615 0.00 0.00 39.44 2.73
5289 9587 7.712205 GGACTCAACTTTGTACCAACTTTAGTA 59.288 37.037 0.00 0.00 0.00 1.82
5290 9588 6.541278 GGACTCAACTTTGTACCAACTTTAGT 59.459 38.462 0.00 0.00 0.00 2.24
5291 9589 6.540914 TGGACTCAACTTTGTACCAACTTTAG 59.459 38.462 0.00 0.00 0.00 1.85
5292 9590 6.316890 GTGGACTCAACTTTGTACCAACTTTA 59.683 38.462 0.00 0.00 31.99 1.85
5293 9591 5.124936 GTGGACTCAACTTTGTACCAACTTT 59.875 40.000 0.00 0.00 31.99 2.66
5294 9592 4.638865 GTGGACTCAACTTTGTACCAACTT 59.361 41.667 0.00 0.00 31.99 2.66
5295 9593 4.080526 AGTGGACTCAACTTTGTACCAACT 60.081 41.667 0.00 0.00 31.99 3.16
5296 9594 4.196971 AGTGGACTCAACTTTGTACCAAC 58.803 43.478 0.00 0.00 31.99 3.77
5297 9595 4.497291 AGTGGACTCAACTTTGTACCAA 57.503 40.909 0.00 0.00 31.99 3.67
5298 9596 4.448210 GAAGTGGACTCAACTTTGTACCA 58.552 43.478 0.08 0.00 0.00 3.25
5299 9597 3.813724 GGAAGTGGACTCAACTTTGTACC 59.186 47.826 0.08 0.00 0.00 3.34
5300 9598 3.493503 CGGAAGTGGACTCAACTTTGTAC 59.506 47.826 0.08 0.00 0.00 2.90
5301 9599 3.385433 TCGGAAGTGGACTCAACTTTGTA 59.615 43.478 0.08 0.00 0.00 2.41
5302 9600 2.169769 TCGGAAGTGGACTCAACTTTGT 59.830 45.455 0.08 0.00 0.00 2.83
5303 9601 2.833794 TCGGAAGTGGACTCAACTTTG 58.166 47.619 0.08 0.00 0.00 2.77
5304 9602 3.403038 CATCGGAAGTGGACTCAACTTT 58.597 45.455 0.08 0.00 0.00 2.66
5305 9603 2.289694 CCATCGGAAGTGGACTCAACTT 60.290 50.000 0.00 0.00 39.12 2.66
5306 9604 1.276421 CCATCGGAAGTGGACTCAACT 59.724 52.381 0.00 0.00 39.12 3.16
5307 9605 1.275291 TCCATCGGAAGTGGACTCAAC 59.725 52.381 0.00 0.00 40.72 3.18
5308 9606 1.639722 TCCATCGGAAGTGGACTCAA 58.360 50.000 0.00 0.00 40.72 3.02
5309 9607 3.374318 TCCATCGGAAGTGGACTCA 57.626 52.632 0.00 0.00 40.72 3.41
5376 9766 1.675641 GGCCTCGCTGTTGTCCAAT 60.676 57.895 0.00 0.00 0.00 3.16
5377 9767 1.476845 TAGGCCTCGCTGTTGTCCAA 61.477 55.000 9.68 0.00 0.00 3.53
5407 9797 1.270907 ATCTTCTCTGGCTCCGTGTT 58.729 50.000 0.00 0.00 0.00 3.32
5420 9810 2.814336 GGAAACAACTGCCGAATCTTCT 59.186 45.455 0.00 0.00 0.00 2.85
5426 9816 0.394488 TGTGGGAAACAACTGCCGAA 60.394 50.000 0.00 0.00 35.24 4.30
5507 9897 0.639392 AGCCATCCCTCTACTCACCT 59.361 55.000 0.00 0.00 0.00 4.00
5643 10080 5.655488 CCGTCATACTTCTTCAATCTCTGT 58.345 41.667 0.00 0.00 0.00 3.41
5680 10214 3.248602 CACAAGAGCAGTAACTGTTGGAC 59.751 47.826 2.69 0.00 43.33 4.02
5750 10511 1.280206 GGTTGACGCGTACGCTTTCT 61.280 55.000 34.69 16.31 45.53 2.52
5784 10545 1.808945 CCACACATTTGAGGCTGACTC 59.191 52.381 2.79 2.79 46.78 3.36
5956 10858 6.264518 ACACATCAAACCGGAAATTAGTTTCT 59.735 34.615 9.46 0.00 42.66 2.52
5967 10869 7.042335 ACATTTTTAAAACACATCAAACCGGA 58.958 30.769 9.46 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.