Multiple sequence alignment - TraesCS5A01G066900

Loading Multiple Alignment...

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 TraesCS5A01G066900 chr5A 100.000 4816 0 0 1 4816 74589212 74594027 0.000000e+00 8894.0
1 TraesCS5A01G066900 chr5A 85.935 2915 334 44 990 3865 74672098 74674975 0.000000e+00 3042.0
2 TraesCS5A01G066900 chr5A 89.139 1068 105 9 1615 2676 74496621 74497683 0.000000e+00 1319.0
3 TraesCS5A01G066900 chr5A 82.239 1599 195 44 2674 4205 74497802 74499378 0.000000e+00 1297.0
4 TraesCS5A01G066900 chr5A 89.716 457 46 1 1104 1560 74496165 74496620 2.500000e-162 582.0
5 TraesCS5A01G066900 chr5A 86.585 410 34 9 1 395 74671247 74671650 2.660000e-117 433.0
6 TraesCS5A01G066900 chr5B 95.820 2464 95 7 617 3076 87650095 87652554 0.000000e+00 3973.0
7 TraesCS5A01G066900 chr5B 86.292 2918 330 32 990 3871 87764680 87767563 0.000000e+00 3109.0
8 TraesCS5A01G066900 chr5B 90.790 1303 113 4 990 2288 87968506 87969805 0.000000e+00 1735.0
9 TraesCS5A01G066900 chr5B 83.261 1607 232 18 2290 3865 87969972 87971572 0.000000e+00 1443.0
10 TraesCS5A01G066900 chr5B 85.317 1260 151 16 2674 3913 87293945 87295190 0.000000e+00 1271.0
11 TraesCS5A01G066900 chr5B 93.846 845 45 3 3133 3970 87652583 87653427 0.000000e+00 1266.0
12 TraesCS5A01G066900 chr5B 90.111 900 80 7 1782 2677 87292932 87293826 0.000000e+00 1160.0
13 TraesCS5A01G066900 chr5B 85.824 522 63 8 475 991 87967964 87968479 1.180000e-150 544.0
14 TraesCS5A01G066900 chr5B 90.102 394 26 6 1 393 87967670 87968051 2.590000e-137 499.0
15 TraesCS5A01G066900 chr5B 85.222 406 42 9 1 395 87763809 87764207 7.510000e-108 401.0
16 TraesCS5A01G066900 chr5B 86.649 367 32 5 101 460 87649576 87649932 1.630000e-104 390.0
17 TraesCS5A01G066900 chr5B 83.590 390 46 3 438 827 87290502 87290873 2.760000e-92 350.0
18 TraesCS5A01G066900 chr5B 99.329 149 1 0 438 586 87649953 87650101 2.210000e-68 270.0
19 TraesCS5A01G066900 chr5B 87.742 155 13 4 4342 4493 87653697 87653848 4.950000e-40 176.0
20 TraesCS5A01G066900 chr5B 94.382 89 5 0 4253 4341 87653561 87653649 2.340000e-28 137.0
21 TraesCS5A01G066900 chr5B 88.571 70 8 0 4263 4332 87767893 87767962 8.590000e-13 86.1
22 TraesCS5A01G066900 chr5D 95.945 2170 77 7 912 3076 78010282 78012445 0.000000e+00 3509.0
23 TraesCS5A01G066900 chr5D 86.262 2919 324 35 990 3871 78052438 78055316 0.000000e+00 3097.0
24 TraesCS5A01G066900 chr5D 92.993 1213 71 6 3133 4341 78012474 78013676 0.000000e+00 1757.0
25 TraesCS5A01G066900 chr5D 90.084 1069 96 8 1615 2676 77737708 77738773 0.000000e+00 1378.0
26 TraesCS5A01G066900 chr5D 85.782 1259 130 28 2677 3913 77738895 77740126 0.000000e+00 1288.0
27 TraesCS5A01G066900 chr5D 91.859 909 48 10 4 897 78008993 78009890 0.000000e+00 1245.0
28 TraesCS5A01G066900 chr5D 86.015 522 63 7 475 991 78051895 78052411 7.040000e-153 551.0
29 TraesCS5A01G066900 chr5D 85.854 410 34 11 1 393 78051580 78051982 9.640000e-112 414.0
30 TraesCS5A01G066900 chr5D 94.142 239 13 1 4343 4581 78013768 78014005 3.540000e-96 363.0
31 TraesCS5A01G066900 chr5D 95.652 115 5 0 4699 4813 78014007 78014121 8.230000e-43 185.0
32 TraesCS5A01G066900 chr1D 89.274 317 32 2 990 1305 16107046 16106731 3.490000e-106 396.0


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 TraesCS5A01G066900 chr5A 74589212 74594027 4815 False 8894.000000 8894 100.000000 1 4816 1 chr5A.!!$F1 4815
1 TraesCS5A01G066900 chr5A 74671247 74674975 3728 False 1737.500000 3042 86.260000 1 3865 2 chr5A.!!$F3 3864
2 TraesCS5A01G066900 chr5A 74496165 74499378 3213 False 1066.000000 1319 87.031333 1104 4205 3 chr5A.!!$F2 3101
3 TraesCS5A01G066900 chr5B 87763809 87767962 4153 False 1198.700000 3109 86.695000 1 4332 3 chr5B.!!$F3 4331
4 TraesCS5A01G066900 chr5B 87967670 87971572 3902 False 1055.250000 1735 87.494250 1 3865 4 chr5B.!!$F4 3864
5 TraesCS5A01G066900 chr5B 87649576 87653848 4272 False 1035.333333 3973 92.961333 101 4493 6 chr5B.!!$F2 4392
6 TraesCS5A01G066900 chr5B 87290502 87295190 4688 False 927.000000 1271 86.339333 438 3913 3 chr5B.!!$F1 3475
7 TraesCS5A01G066900 chr5D 78008993 78014121 5128 False 1411.800000 3509 94.118200 4 4813 5 chr5D.!!$F2 4809
8 TraesCS5A01G066900 chr5D 78051580 78055316 3736 False 1354.000000 3097 86.043667 1 3871 3 chr5D.!!$F3 3870
9 TraesCS5A01G066900 chr5D 77737708 77740126 2418 False 1333.000000 1378 87.933000 1615 3913 2 chr5D.!!$F1 2298

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
688 783 0.179156 GCGCATCCATGTGAAGTTGG 60.179 55.0 0.30 0.0 40.61 3.77 F
2344 4297 0.107263 TGTGCAGCTGAAGGTGTCAA 60.107 50.0 20.43 0.0 44.70 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 4358 0.392461 GATTGCACCCCGTTGCTAGA 60.392 55.0 0.0 0.0 43.41 2.43 R
3825 5941 1.323412 AGGATACAGCTACGCAGGAG 58.677 55.0 0.0 0.0 41.41 3.69 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
59 70 9.305925 CATTGCTAAAAGTAGGAAAATGATTCC 57.694 33.333 0.00 0.00 40.58 3.01
94 105 4.057406 AGATTCCTTCTGCTCAGATTCG 57.943 45.455 0.00 0.00 37.29 3.34
145 158 6.592870 TGATTTCATCTGCATCTCTCTGAAT 58.407 36.000 0.00 0.00 0.00 2.57
175 188 9.640974 TTTTTAAACGAGACTCTATTTTCAACG 57.359 29.630 0.03 0.00 0.00 4.10
184 197 9.187455 GAGACTCTATTTTCAACGGAAGATATC 57.813 37.037 0.00 0.00 31.82 1.63
255 292 7.824289 GCATATATGTATACCCTTTTGCTCTGA 59.176 37.037 14.14 0.00 0.00 3.27
303 340 2.678190 GCTTCTCTGCCGAAGTATTGGT 60.678 50.000 8.63 0.00 41.84 3.67
304 341 2.672961 TCTCTGCCGAAGTATTGGTG 57.327 50.000 0.00 0.00 0.00 4.17
305 342 1.207089 TCTCTGCCGAAGTATTGGTGG 59.793 52.381 0.00 0.00 0.00 4.61
306 343 0.981183 TCTGCCGAAGTATTGGTGGT 59.019 50.000 0.00 0.00 0.00 4.16
428 472 5.651387 ATTTTAGGCTGCTCTTTTTCTCC 57.349 39.130 0.00 0.00 0.00 3.71
616 703 8.021396 GCTTACGTTCTATTTGTCCTGAAATTT 58.979 33.333 0.00 0.00 0.00 1.82
688 783 0.179156 GCGCATCCATGTGAAGTTGG 60.179 55.000 0.30 0.00 40.61 3.77
693 789 6.336521 CGCATCCATGTGAAGTTGGAACAA 62.337 45.833 0.00 0.00 41.87 2.83
854 968 4.439253 AGCTTACTTCCTGTTTGTCCTT 57.561 40.909 0.00 0.00 0.00 3.36
915 1406 8.483218 GGATTTATCTGACATCGAATATATGCG 58.517 37.037 6.78 6.78 0.00 4.73
964 1455 7.758076 TGCTCATAATAACACACACTACTACAC 59.242 37.037 0.00 0.00 0.00 2.90
1134 1682 7.872138 TGGATGATACCCAGAAGTATTTCTTT 58.128 34.615 0.00 0.00 41.71 2.52
1177 1725 3.181472 CCAAGATAAAATGGCAAGCCCTC 60.181 47.826 8.89 0.00 34.56 4.30
1249 1798 5.281376 CAGAATGATAACTTCGTTGTTTGCG 59.719 40.000 1.76 0.00 39.69 4.85
1460 2009 1.133884 GGTCTTTAGGTACATGGGGGC 60.134 57.143 0.00 0.00 0.00 5.80
1480 2029 3.251972 GGCTTCTCACTTCAAAGTTCTGG 59.748 47.826 0.00 0.00 37.08 3.86
1518 2067 4.127171 GTTGCTGTGAGAAGGAAGTGTTA 58.873 43.478 0.00 0.00 0.00 2.41
1830 3613 8.941127 TTTGCTAATTGTTTTGTTGTTTGTTC 57.059 26.923 0.00 0.00 0.00 3.18
1831 3614 7.066374 TGCTAATTGTTTTGTTGTTTGTTCC 57.934 32.000 0.00 0.00 0.00 3.62
2149 3934 2.277969 CGGGCATATCTCATGATCAGC 58.722 52.381 0.09 0.00 34.32 4.26
2191 3979 1.726791 GTCACTGCGAATCACGTGATT 59.273 47.619 37.09 37.09 46.54 2.57
2293 4246 7.654568 CACGTATATTCTCATTGGTACCTGTA 58.345 38.462 14.36 0.00 0.00 2.74
2322 4275 4.478206 AACTGATGTCTTGATGATCGGT 57.522 40.909 0.00 0.00 37.31 4.69
2344 4297 0.107263 TGTGCAGCTGAAGGTGTCAA 60.107 50.000 20.43 0.00 44.70 3.18
2405 4358 0.392998 CCACCAAGCCTCGCTATGTT 60.393 55.000 0.00 0.00 38.25 2.71
2486 4439 2.622064 AAGTTAGGCCTGCTATTCCG 57.378 50.000 17.99 0.00 0.00 4.30
2497 4450 4.095782 GCCTGCTATTCCGTTTTACATCAA 59.904 41.667 0.00 0.00 0.00 2.57
2506 4459 4.155826 TCCGTTTTACATCAAAGCCATGAG 59.844 41.667 0.00 0.00 31.76 2.90
2519 4472 3.959573 GCCATGAGCAAGACAAGTATC 57.040 47.619 0.00 0.00 42.97 2.24
2543 4496 2.571202 TGGATCTCTGGTATGTGTGCAA 59.429 45.455 0.00 0.00 0.00 4.08
2548 4501 5.876651 TCTCTGGTATGTGTGCAATATCT 57.123 39.130 0.00 0.00 0.00 1.98
2583 4536 4.276926 AGTGAGACTCCTGCAAAATTTGTC 59.723 41.667 7.60 0.88 0.00 3.18
2699 4782 3.560105 TGATGATCCAGTCGTCTCTCAT 58.440 45.455 0.00 0.00 42.32 2.90
2845 4928 0.183492 TGCTTTCTGTTGGCTGGTCT 59.817 50.000 0.00 0.00 0.00 3.85
2901 4984 6.765036 AGTGACATCTGCCTATTTGAAGTATG 59.235 38.462 0.00 0.00 0.00 2.39
2917 5000 1.392510 GTATGGAAAAGCGACGGTGAC 59.607 52.381 0.00 0.00 0.00 3.67
2941 5024 5.615544 CGTGACAATGGTTGTTCATTCTCTC 60.616 44.000 0.00 0.00 45.52 3.20
2990 5074 5.620206 AGTATGAAACACATTGACACCTGA 58.380 37.500 0.00 0.00 40.07 3.86
3004 5088 8.843262 CATTGACACCTGAACATATGACATTAT 58.157 33.333 10.38 0.00 0.00 1.28
3087 5173 8.919777 ATAGATACCTTTTTGTTATGTAGCCC 57.080 34.615 0.00 0.00 0.00 5.19
3089 5175 4.023726 ACCTTTTTGTTATGTAGCCCGA 57.976 40.909 0.00 0.00 0.00 5.14
3090 5176 4.400120 ACCTTTTTGTTATGTAGCCCGAA 58.600 39.130 0.00 0.00 0.00 4.30
3100 5186 1.539388 TGTAGCCCGAAAATGCACAAG 59.461 47.619 0.00 0.00 0.00 3.16
3135 5223 2.480416 GGAATGGAGTGAGCTAGTGTCG 60.480 54.545 0.00 0.00 0.00 4.35
3164 5257 4.675976 TGATCATTTTGGATGCCCATTC 57.324 40.909 0.00 0.00 43.12 2.67
3196 5289 1.474143 GGGAAAGAGCCCGAATCTCAG 60.474 57.143 0.00 0.00 38.58 3.35
3289 5388 4.461781 TCCAACTACTACTACTCAAGGCAC 59.538 45.833 0.00 0.00 0.00 5.01
3515 5615 1.466167 CTGCCACGAAGATTTCTGTGG 59.534 52.381 19.22 19.22 46.91 4.17
3563 5673 2.949177 TCCCTAGAAAGTTTGCAGCA 57.051 45.000 0.00 0.00 0.00 4.41
3652 5762 4.025061 CGTGAGGTACTACTACCATTCGAG 60.025 50.000 1.95 0.00 44.75 4.04
3746 5862 2.275318 GTCTTCGAGCTGATCAAAGGG 58.725 52.381 0.00 0.00 0.00 3.95
3938 6072 3.242739 GCAAGTGCACTAATATGGTTCCG 60.243 47.826 22.01 0.00 41.59 4.30
4051 6227 2.493278 GCACCATGCCAACAAATCTAGT 59.507 45.455 0.00 0.00 37.42 2.57
4158 6381 2.231716 TACTGAGGGCTGCTACTCAA 57.768 50.000 21.38 10.42 42.62 3.02
4209 6432 9.462174 CATGTAACTTGTGTGTTCATGTTTAAT 57.538 29.630 0.00 0.00 37.11 1.40
4238 6461 2.943449 GGAGGTTCTCCTACTGTTCG 57.057 55.000 6.70 0.00 46.41 3.95
4246 6469 0.971386 TCCTACTGTTCGGGGTTCAC 59.029 55.000 0.00 0.00 0.00 3.18
4437 6767 2.232941 CAGCATGCATGTTTTCCCTCTT 59.767 45.455 26.79 0.00 0.00 2.85
4499 6829 7.657354 TCCAGTTCATAATCATATCTGGTTTCG 59.343 37.037 0.00 0.00 40.91 3.46
4500 6830 7.095060 CCAGTTCATAATCATATCTGGTTTCGG 60.095 40.741 0.00 0.00 37.00 4.30
4532 6862 5.664294 AATATGTGAAGCAAATTGGCAGA 57.336 34.783 7.75 0.00 35.83 4.26
4574 6904 3.347216 ACAGCAAGAATCAAGCGGTAAT 58.653 40.909 1.62 0.00 35.01 1.89
4575 6905 3.758554 ACAGCAAGAATCAAGCGGTAATT 59.241 39.130 1.62 0.00 35.01 1.40
4581 6911 7.067494 AGCAAGAATCAAGCGGTAATTTATTCT 59.933 33.333 0.00 0.00 34.55 2.40
4582 6912 7.166473 GCAAGAATCAAGCGGTAATTTATTCTG 59.834 37.037 9.23 6.54 33.67 3.02
4583 6913 7.865706 AGAATCAAGCGGTAATTTATTCTGT 57.134 32.000 0.00 0.00 32.51 3.41
4584 6914 8.281212 AGAATCAAGCGGTAATTTATTCTGTT 57.719 30.769 0.00 0.00 32.51 3.16
4585 6915 8.739972 AGAATCAAGCGGTAATTTATTCTGTTT 58.260 29.630 0.00 0.00 32.51 2.83
4586 6916 9.997482 GAATCAAGCGGTAATTTATTCTGTTTA 57.003 29.630 0.00 0.00 0.00 2.01
4588 6918 9.950680 ATCAAGCGGTAATTTATTCTGTTTATG 57.049 29.630 0.00 0.00 0.00 1.90
4589 6919 9.168451 TCAAGCGGTAATTTATTCTGTTTATGA 57.832 29.630 0.00 0.00 0.00 2.15
4590 6920 9.438291 CAAGCGGTAATTTATTCTGTTTATGAG 57.562 33.333 0.00 0.00 0.00 2.90
4591 6921 8.958119 AGCGGTAATTTATTCTGTTTATGAGA 57.042 30.769 0.00 0.00 0.00 3.27
4592 6922 9.561069 AGCGGTAATTTATTCTGTTTATGAGAT 57.439 29.630 0.00 0.00 0.00 2.75
4602 6932 8.815141 ATTCTGTTTATGAGATTGAGATCGAG 57.185 34.615 0.00 0.00 37.37 4.04
4603 6933 6.743110 TCTGTTTATGAGATTGAGATCGAGG 58.257 40.000 0.00 0.00 37.37 4.63
4604 6934 5.847304 TGTTTATGAGATTGAGATCGAGGG 58.153 41.667 0.00 0.00 37.37 4.30
4605 6935 5.221521 TGTTTATGAGATTGAGATCGAGGGG 60.222 44.000 0.00 0.00 37.37 4.79
4606 6936 1.709578 TGAGATTGAGATCGAGGGGG 58.290 55.000 0.00 0.00 37.37 5.40
4624 6954 4.684484 GGGGGATGAGTACTTACGAATT 57.316 45.455 0.00 0.00 0.00 2.17
4625 6955 4.377897 GGGGGATGAGTACTTACGAATTG 58.622 47.826 0.00 0.00 0.00 2.32
4626 6956 4.100498 GGGGGATGAGTACTTACGAATTGA 59.900 45.833 0.00 0.00 0.00 2.57
4627 6957 5.221661 GGGGGATGAGTACTTACGAATTGAT 60.222 44.000 0.00 0.00 0.00 2.57
4628 6958 6.014840 GGGGGATGAGTACTTACGAATTGATA 60.015 42.308 0.00 0.00 0.00 2.15
4629 6959 7.310485 GGGGGATGAGTACTTACGAATTGATAT 60.310 40.741 0.00 0.00 0.00 1.63
4630 6960 8.746530 GGGGATGAGTACTTACGAATTGATATA 58.253 37.037 0.00 0.00 0.00 0.86
4631 6961 9.570488 GGGATGAGTACTTACGAATTGATATAC 57.430 37.037 0.00 0.00 0.00 1.47
4635 6965 9.128404 TGAGTACTTACGAATTGATATACAGGT 57.872 33.333 0.00 0.00 0.00 4.00
4636 6966 9.395707 GAGTACTTACGAATTGATATACAGGTG 57.604 37.037 0.00 0.00 0.00 4.00
4637 6967 7.866393 AGTACTTACGAATTGATATACAGGTGC 59.134 37.037 0.00 0.00 0.00 5.01
4638 6968 6.817184 ACTTACGAATTGATATACAGGTGCT 58.183 36.000 0.00 0.00 0.00 4.40
4639 6969 7.948357 ACTTACGAATTGATATACAGGTGCTA 58.052 34.615 0.00 0.00 0.00 3.49
4640 6970 8.082852 ACTTACGAATTGATATACAGGTGCTAG 58.917 37.037 0.00 0.00 0.00 3.42
4641 6971 6.650427 ACGAATTGATATACAGGTGCTAGA 57.350 37.500 0.00 0.00 0.00 2.43
4642 6972 7.233389 ACGAATTGATATACAGGTGCTAGAT 57.767 36.000 0.00 0.00 0.00 1.98
4643 6973 7.093354 ACGAATTGATATACAGGTGCTAGATG 58.907 38.462 0.00 0.00 0.00 2.90
4644 6974 7.039714 ACGAATTGATATACAGGTGCTAGATGA 60.040 37.037 0.00 0.00 0.00 2.92
4645 6975 7.487509 CGAATTGATATACAGGTGCTAGATGAG 59.512 40.741 0.00 0.00 0.00 2.90
4646 6976 6.596309 TTGATATACAGGTGCTAGATGAGG 57.404 41.667 0.00 0.00 0.00 3.86
4647 6977 5.892348 TGATATACAGGTGCTAGATGAGGA 58.108 41.667 0.00 0.00 0.00 3.71
4648 6978 5.712446 TGATATACAGGTGCTAGATGAGGAC 59.288 44.000 0.00 0.00 45.47 3.85
4649 6979 2.541233 ACAGGTGCTAGATGAGGACT 57.459 50.000 0.00 0.00 45.50 3.85
4650 6980 2.826488 ACAGGTGCTAGATGAGGACTT 58.174 47.619 0.00 0.00 45.50 3.01
4651 6981 3.982516 ACAGGTGCTAGATGAGGACTTA 58.017 45.455 0.00 0.00 45.50 2.24
4652 6982 3.702045 ACAGGTGCTAGATGAGGACTTAC 59.298 47.826 0.00 0.00 45.50 2.34
4653 6983 3.701542 CAGGTGCTAGATGAGGACTTACA 59.298 47.826 0.00 0.00 45.50 2.41
4654 6984 4.160439 CAGGTGCTAGATGAGGACTTACAA 59.840 45.833 0.00 0.00 45.50 2.41
4655 6985 4.777896 AGGTGCTAGATGAGGACTTACAAA 59.222 41.667 0.00 0.00 45.50 2.83
4656 6986 5.426833 AGGTGCTAGATGAGGACTTACAAAT 59.573 40.000 0.00 0.00 45.50 2.32
4657 6987 6.069963 AGGTGCTAGATGAGGACTTACAAATT 60.070 38.462 0.00 0.00 45.50 1.82
4658 6988 6.037610 GGTGCTAGATGAGGACTTACAAATTG 59.962 42.308 0.00 0.00 45.50 2.32
4659 6989 6.818644 GTGCTAGATGAGGACTTACAAATTGA 59.181 38.462 0.00 0.00 42.99 2.57
4660 6990 7.497249 GTGCTAGATGAGGACTTACAAATTGAT 59.503 37.037 0.00 0.00 42.99 2.57
4661 6991 8.704668 TGCTAGATGAGGACTTACAAATTGATA 58.295 33.333 0.00 0.00 0.00 2.15
4662 6992 9.717942 GCTAGATGAGGACTTACAAATTGATAT 57.282 33.333 0.00 0.00 0.00 1.63
4667 6997 8.908786 TGAGGACTTACAAATTGATATGATCC 57.091 34.615 0.00 0.00 0.00 3.36
4668 6998 8.717717 TGAGGACTTACAAATTGATATGATCCT 58.282 33.333 0.00 4.20 34.40 3.24
4671 7001 8.940952 GGACTTACAAATTGATATGATCCTAGC 58.059 37.037 0.00 0.00 0.00 3.42
4672 7002 9.494271 GACTTACAAATTGATATGATCCTAGCA 57.506 33.333 0.00 0.00 0.00 3.49
4765 7095 2.428171 CGATTTGATTTGTGGATGGGCT 59.572 45.455 0.00 0.00 0.00 5.19
4767 7097 1.462616 TTGATTTGTGGATGGGCTCG 58.537 50.000 0.00 0.00 0.00 5.03
4773 7103 1.068250 GTGGATGGGCTCGTAGCTC 59.932 63.158 0.00 3.74 43.59 4.09
4796 7126 2.118732 TGTCGCCCCACTGACCTA 59.881 61.111 0.00 0.00 34.18 3.08
4803 7133 0.905357 CCCCACTGACCTAGGTTCAG 59.095 60.000 26.70 26.70 37.50 3.02
4813 7143 1.573108 CTAGGTTCAGCCCCTCTTCA 58.427 55.000 0.00 0.00 38.26 3.02
4814 7144 1.909302 CTAGGTTCAGCCCCTCTTCAA 59.091 52.381 0.00 0.00 38.26 2.69
4815 7145 0.695347 AGGTTCAGCCCCTCTTCAAG 59.305 55.000 0.00 0.00 38.26 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.584835 TTAGCAATGCCAAGGAGTGT 57.415 45.000 0.00 0.00 0.00 3.55
23 24 3.256631 ACTTTTAGCAATGCCAAGGAGTG 59.743 43.478 0.00 0.00 0.00 3.51
59 70 4.669206 AGGAATCTAGTGACATCTGCTG 57.331 45.455 0.00 0.00 0.00 4.41
94 105 5.048713 ACATGGTTCCAATCGAGAACTTTTC 60.049 40.000 13.69 1.24 42.63 2.29
175 188 7.389053 GTGGGTCTTGTTATCATGATATCTTCC 59.611 40.741 16.06 12.78 31.98 3.46
184 197 6.823182 TGATACTTGTGGGTCTTGTTATCATG 59.177 38.462 0.00 0.00 0.00 3.07
189 202 4.286032 AGCTGATACTTGTGGGTCTTGTTA 59.714 41.667 0.00 0.00 0.00 2.41
241 278 1.613836 CAAGCTCAGAGCAAAAGGGT 58.386 50.000 24.64 0.00 45.56 4.34
255 292 3.064324 GCCAACGATGCCCAAGCT 61.064 61.111 0.00 0.00 40.80 3.74
303 340 3.486383 CTCTTACCTTTGCCAAGAACCA 58.514 45.455 0.00 0.00 30.57 3.67
304 341 2.820197 CCTCTTACCTTTGCCAAGAACC 59.180 50.000 0.00 0.00 30.57 3.62
305 342 2.229062 GCCTCTTACCTTTGCCAAGAAC 59.771 50.000 0.00 0.00 30.57 3.01
306 343 2.108250 AGCCTCTTACCTTTGCCAAGAA 59.892 45.455 0.00 0.00 30.57 2.52
364 408 1.741706 TGATCTTAAGCTGCAGCAAGC 59.258 47.619 38.24 21.19 45.16 4.01
688 783 6.554334 TGAGTTATTACCAGCAGTTTGTTC 57.446 37.500 0.00 0.00 0.00 3.18
739 849 3.245087 TGCCAACAGCCAATACCTCTTTA 60.245 43.478 0.00 0.00 42.71 1.85
745 855 1.892474 TCTTTGCCAACAGCCAATACC 59.108 47.619 0.00 0.00 42.71 2.73
915 1406 3.251004 GTCTGTTCCAACCTCACATTGAC 59.749 47.826 0.00 0.00 0.00 3.18
964 1455 6.939163 AGATACAGCAGCCTAAAATATGAAGG 59.061 38.462 0.00 0.00 0.00 3.46
1134 1682 3.306641 GGAAATTGCCAACCATGCACTTA 60.307 43.478 0.00 0.00 38.72 2.24
1236 1785 2.166741 TGAACACGCAAACAACGAAG 57.833 45.000 0.00 0.00 0.00 3.79
1249 1798 2.420022 GTGGTATGGTCTGCATGAACAC 59.580 50.000 6.11 0.00 46.28 3.32
1460 2009 7.736447 AATACCAGAACTTTGAAGTGAGAAG 57.264 36.000 0.00 0.00 39.66 2.85
1811 3594 5.471456 TGCAGGAACAAACAACAAAACAATT 59.529 32.000 0.00 0.00 0.00 2.32
1830 3613 5.543507 ATTTCTCTGGTATACTCTGCAGG 57.456 43.478 15.13 7.28 0.00 4.85
1831 3614 6.820656 ACAAATTTCTCTGGTATACTCTGCAG 59.179 38.462 7.63 7.63 0.00 4.41
1954 3739 2.707791 CTGCCCATCCAGATCTAAGGAA 59.292 50.000 5.92 0.00 37.48 3.36
2149 3934 3.612479 CGCCTTGTTTCTTTGAGGAATGG 60.612 47.826 0.00 0.00 0.00 3.16
2293 4246 7.692460 TCATCAAGACATCAGTTAGCAATTT 57.308 32.000 0.00 0.00 0.00 1.82
2322 4275 0.394216 ACACCTTCAGCTGCACAACA 60.394 50.000 9.47 0.00 0.00 3.33
2344 4297 1.079490 TCAGGGTGTCCTCTGGAGATT 59.921 52.381 0.00 0.00 42.67 2.40
2405 4358 0.392461 GATTGCACCCCGTTGCTAGA 60.392 55.000 0.00 0.00 43.41 2.43
2486 4439 4.808558 TGCTCATGGCTTTGATGTAAAAC 58.191 39.130 7.54 0.00 42.39 2.43
2497 4450 2.283145 ACTTGTCTTGCTCATGGCTT 57.717 45.000 7.54 0.00 42.39 4.35
2506 4459 5.068987 AGAGATCCAGAGATACTTGTCTTGC 59.931 44.000 0.00 0.00 30.90 4.01
2519 4472 3.492309 GCACACATACCAGAGATCCAGAG 60.492 52.174 0.00 0.00 0.00 3.35
2543 4496 8.995027 AGTCTCACTGAATCTGTAGAAGATAT 57.005 34.615 0.00 0.00 45.37 1.63
2548 4501 5.417266 CAGGAGTCTCACTGAATCTGTAGAA 59.583 44.000 11.05 0.00 39.49 2.10
2667 4628 4.607239 ACTGGATCATCAGGCTTTGAAAT 58.393 39.130 0.00 0.00 39.77 2.17
2699 4782 3.492656 GCGTAATCCTTGCAGATGACCTA 60.493 47.826 0.00 0.00 0.00 3.08
2901 4984 1.952635 ACGTCACCGTCGCTTTTCC 60.953 57.895 0.00 0.00 46.28 3.13
2917 5000 4.214119 AGAGAATGAACAACCATTGTCACG 59.786 41.667 13.64 0.00 44.48 4.35
2973 5056 6.489700 TCATATGTTCAGGTGTCAATGTGTTT 59.510 34.615 1.90 0.00 0.00 2.83
3004 5088 4.713553 TGGCGATCCTGAGCATTATTTTA 58.286 39.130 0.00 0.00 34.54 1.52
3068 5154 4.023726 TCGGGCTACATAACAAAAAGGT 57.976 40.909 0.00 0.00 0.00 3.50
3076 5162 3.127895 TGTGCATTTTCGGGCTACATAAC 59.872 43.478 0.00 0.00 0.00 1.89
3087 5173 2.053627 GTTCAGGCTTGTGCATTTTCG 58.946 47.619 0.00 0.00 41.91 3.46
3089 5175 1.761784 TGGTTCAGGCTTGTGCATTTT 59.238 42.857 0.00 0.00 41.91 1.82
3090 5176 1.342174 CTGGTTCAGGCTTGTGCATTT 59.658 47.619 0.00 0.00 41.91 2.32
3100 5186 2.092429 TCCATTCCATACTGGTTCAGGC 60.092 50.000 0.00 0.00 39.03 4.85
3119 5205 0.528470 AAGCGACACTAGCTCACTCC 59.472 55.000 0.00 0.00 45.31 3.85
3135 5223 5.521372 GGCATCCAAAATGATCAAGTAAAGC 59.479 40.000 0.00 0.00 0.00 3.51
3164 5257 3.304458 GGCTCTTTCCCTGTAAAAACACG 60.304 47.826 0.00 0.00 0.00 4.49
3196 5289 7.518529 GCCTTAACTGGATATCTACGCTTTTTC 60.519 40.741 2.05 0.00 0.00 2.29
3506 5606 7.604164 CAGAACATAAGTCACTACCACAGAAAT 59.396 37.037 0.00 0.00 0.00 2.17
3652 5762 1.960689 TGTTGCTGAAACCCCTTAAGC 59.039 47.619 0.00 0.00 38.06 3.09
3746 5862 2.202703 ATCGTCGCCTTACGCACC 60.203 61.111 0.00 0.00 42.56 5.01
3825 5941 1.323412 AGGATACAGCTACGCAGGAG 58.677 55.000 0.00 0.00 41.41 3.69
3848 5964 8.977505 AGGTTTCAATTATTCAACGACAAATTG 58.022 29.630 0.00 0.00 38.36 2.32
3938 6072 4.267349 TGGCTCAACAACTAGTTCTACC 57.733 45.455 4.77 2.73 38.74 3.18
4051 6227 3.071457 TGAGAATTTCAGTGGAGTGAGCA 59.929 43.478 0.00 0.00 0.00 4.26
4158 6381 3.188048 ACAACTTCTCGTCGTCGATTAGT 59.812 43.478 5.00 8.96 45.21 2.24
4209 6432 1.549170 GGAGAACCTCCTACTGCGAAA 59.451 52.381 5.78 0.00 46.41 3.46
4396 6723 6.820335 TGCTGCTCACTGAACTTATGTATAT 58.180 36.000 0.00 0.00 0.00 0.86
4411 6741 1.990563 GAAAACATGCATGCTGCTCAC 59.009 47.619 26.53 8.11 45.31 3.51
4465 6795 9.342308 GATATGATTATGAACTGGAAAGAACCA 57.658 33.333 0.00 0.00 38.33 3.67
4499 6829 7.903995 TTGCTTCACATATTTCCAAATTTCC 57.096 32.000 0.00 0.00 0.00 3.13
4506 6836 5.177326 GCCAATTTGCTTCACATATTTCCA 58.823 37.500 0.00 0.00 28.66 3.53
4507 6837 5.177326 TGCCAATTTGCTTCACATATTTCC 58.823 37.500 2.90 0.00 28.66 3.13
4532 6862 4.277174 TGTTTATGTTGTGATCGGCAACTT 59.723 37.500 24.00 21.08 44.54 2.66
4581 6911 5.221521 CCCCTCGATCTCAATCTCATAAACA 60.222 44.000 0.00 0.00 0.00 2.83
4582 6912 5.233988 CCCCTCGATCTCAATCTCATAAAC 58.766 45.833 0.00 0.00 0.00 2.01
4583 6913 4.284490 CCCCCTCGATCTCAATCTCATAAA 59.716 45.833 0.00 0.00 0.00 1.40
4584 6914 3.834813 CCCCCTCGATCTCAATCTCATAA 59.165 47.826 0.00 0.00 0.00 1.90
4585 6915 3.435275 CCCCCTCGATCTCAATCTCATA 58.565 50.000 0.00 0.00 0.00 2.15
4586 6916 2.255406 CCCCCTCGATCTCAATCTCAT 58.745 52.381 0.00 0.00 0.00 2.90
4587 6917 1.709578 CCCCCTCGATCTCAATCTCA 58.290 55.000 0.00 0.00 0.00 3.27
4603 6933 4.100498 TCAATTCGTAAGTACTCATCCCCC 59.900 45.833 0.00 0.00 39.48 5.40
4604 6934 5.272283 TCAATTCGTAAGTACTCATCCCC 57.728 43.478 0.00 0.00 39.48 4.81
4605 6935 9.570488 GTATATCAATTCGTAAGTACTCATCCC 57.430 37.037 0.00 0.00 39.48 3.85
4609 6939 9.128404 ACCTGTATATCAATTCGTAAGTACTCA 57.872 33.333 0.00 0.00 39.48 3.41
4610 6940 9.395707 CACCTGTATATCAATTCGTAAGTACTC 57.604 37.037 0.00 0.00 39.48 2.59
4611 6941 7.866393 GCACCTGTATATCAATTCGTAAGTACT 59.134 37.037 0.00 0.00 39.48 2.73
4612 6942 7.866393 AGCACCTGTATATCAATTCGTAAGTAC 59.134 37.037 0.00 0.00 39.48 2.73
4613 6943 7.948357 AGCACCTGTATATCAATTCGTAAGTA 58.052 34.615 0.00 0.00 39.48 2.24
4614 6944 6.817184 AGCACCTGTATATCAATTCGTAAGT 58.183 36.000 0.00 0.00 39.48 2.24
4615 6945 8.297426 TCTAGCACCTGTATATCAATTCGTAAG 58.703 37.037 0.00 0.00 0.00 2.34
4616 6946 8.173542 TCTAGCACCTGTATATCAATTCGTAA 57.826 34.615 0.00 0.00 0.00 3.18
4617 6947 7.754851 TCTAGCACCTGTATATCAATTCGTA 57.245 36.000 0.00 0.00 0.00 3.43
4618 6948 6.650427 TCTAGCACCTGTATATCAATTCGT 57.350 37.500 0.00 0.00 0.00 3.85
4619 6949 7.315890 TCATCTAGCACCTGTATATCAATTCG 58.684 38.462 0.00 0.00 0.00 3.34
4620 6950 7.763528 CCTCATCTAGCACCTGTATATCAATTC 59.236 40.741 0.00 0.00 0.00 2.17
4621 6951 7.455953 TCCTCATCTAGCACCTGTATATCAATT 59.544 37.037 0.00 0.00 0.00 2.32
4622 6952 6.956435 TCCTCATCTAGCACCTGTATATCAAT 59.044 38.462 0.00 0.00 0.00 2.57
4623 6953 6.209589 GTCCTCATCTAGCACCTGTATATCAA 59.790 42.308 0.00 0.00 0.00 2.57
4624 6954 5.712446 GTCCTCATCTAGCACCTGTATATCA 59.288 44.000 0.00 0.00 0.00 2.15
4625 6955 5.949354 AGTCCTCATCTAGCACCTGTATATC 59.051 44.000 0.00 0.00 0.00 1.63
4626 6956 5.898120 AGTCCTCATCTAGCACCTGTATAT 58.102 41.667 0.00 0.00 0.00 0.86
4627 6957 5.326283 AGTCCTCATCTAGCACCTGTATA 57.674 43.478 0.00 0.00 0.00 1.47
4628 6958 4.191804 AGTCCTCATCTAGCACCTGTAT 57.808 45.455 0.00 0.00 0.00 2.29
4629 6959 3.671740 AGTCCTCATCTAGCACCTGTA 57.328 47.619 0.00 0.00 0.00 2.74
4630 6960 2.541233 AGTCCTCATCTAGCACCTGT 57.459 50.000 0.00 0.00 0.00 4.00
4631 6961 3.701542 TGTAAGTCCTCATCTAGCACCTG 59.298 47.826 0.00 0.00 0.00 4.00
4632 6962 3.982516 TGTAAGTCCTCATCTAGCACCT 58.017 45.455 0.00 0.00 0.00 4.00
4633 6963 4.737855 TTGTAAGTCCTCATCTAGCACC 57.262 45.455 0.00 0.00 0.00 5.01
4634 6964 6.818644 TCAATTTGTAAGTCCTCATCTAGCAC 59.181 38.462 0.00 0.00 0.00 4.40
4635 6965 6.946340 TCAATTTGTAAGTCCTCATCTAGCA 58.054 36.000 0.00 0.00 0.00 3.49
4636 6966 9.717942 ATATCAATTTGTAAGTCCTCATCTAGC 57.282 33.333 0.00 0.00 0.00 3.42
4641 6971 9.512588 GGATCATATCAATTTGTAAGTCCTCAT 57.487 33.333 0.00 0.00 0.00 2.90
4642 6972 8.717717 AGGATCATATCAATTTGTAAGTCCTCA 58.282 33.333 0.00 0.00 0.00 3.86
4645 6975 8.940952 GCTAGGATCATATCAATTTGTAAGTCC 58.059 37.037 0.00 0.00 0.00 3.85
4646 6976 9.494271 TGCTAGGATCATATCAATTTGTAAGTC 57.506 33.333 0.00 0.00 0.00 3.01
4678 7008 9.093970 CCATCGACAATAAGAACAATAGTAACA 57.906 33.333 0.00 0.00 0.00 2.41
4679 7009 8.062448 GCCATCGACAATAAGAACAATAGTAAC 58.938 37.037 0.00 0.00 0.00 2.50
4680 7010 7.766738 TGCCATCGACAATAAGAACAATAGTAA 59.233 33.333 0.00 0.00 0.00 2.24
4681 7011 7.269316 TGCCATCGACAATAAGAACAATAGTA 58.731 34.615 0.00 0.00 0.00 1.82
4682 7012 6.112734 TGCCATCGACAATAAGAACAATAGT 58.887 36.000 0.00 0.00 0.00 2.12
4683 7013 6.603237 TGCCATCGACAATAAGAACAATAG 57.397 37.500 0.00 0.00 0.00 1.73
4684 7014 6.993786 TTGCCATCGACAATAAGAACAATA 57.006 33.333 0.00 0.00 0.00 1.90
4685 7015 5.895636 TTGCCATCGACAATAAGAACAAT 57.104 34.783 0.00 0.00 0.00 2.71
4686 7016 5.414144 TCATTGCCATCGACAATAAGAACAA 59.586 36.000 0.00 0.00 36.00 2.83
4687 7017 4.940654 TCATTGCCATCGACAATAAGAACA 59.059 37.500 0.00 0.00 36.00 3.18
4688 7018 5.484173 TCATTGCCATCGACAATAAGAAC 57.516 39.130 0.00 0.00 36.00 3.01
4689 7019 6.507958 TTTCATTGCCATCGACAATAAGAA 57.492 33.333 0.00 0.00 36.00 2.52
4690 7020 6.072230 TGTTTTCATTGCCATCGACAATAAGA 60.072 34.615 0.00 0.00 36.00 2.10
4691 7021 6.092092 TGTTTTCATTGCCATCGACAATAAG 58.908 36.000 0.00 0.00 36.00 1.73
4692 7022 6.018589 TGTTTTCATTGCCATCGACAATAA 57.981 33.333 0.00 0.00 36.00 1.40
4693 7023 5.635417 TGTTTTCATTGCCATCGACAATA 57.365 34.783 0.00 0.00 36.00 1.90
4694 7024 4.517952 TGTTTTCATTGCCATCGACAAT 57.482 36.364 0.00 0.00 38.25 2.71
4695 7025 3.998099 TGTTTTCATTGCCATCGACAA 57.002 38.095 0.00 0.00 0.00 3.18
4696 7026 3.998099 TTGTTTTCATTGCCATCGACA 57.002 38.095 0.00 0.00 0.00 4.35
4697 7027 5.844301 AATTTGTTTTCATTGCCATCGAC 57.156 34.783 0.00 0.00 0.00 4.20
4765 7095 1.873863 CGACACCACTGAGCTACGA 59.126 57.895 0.00 0.00 0.00 3.43
4767 7097 1.446272 GGCGACACCACTGAGCTAC 60.446 63.158 0.00 0.00 38.86 3.58
4796 7126 0.695347 CTTGAAGAGGGGCTGAACCT 59.305 55.000 0.00 0.00 42.18 3.50


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

AutoCloner maintained by Alex Coulton.