Multiple sequence alignment - TraesCS2D01G539400

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 TraesCS2D01G539400 chr2D 100.000 4308 0 0 1 4308 619731255 619735562 0.000000e+00 7956.0
1 TraesCS2D01G539400 chr2D 82.804 913 151 4 2387 3294 587166758 587165847 0.000000e+00 811.0
2 TraesCS2D01G539400 chr2D 75.841 327 52 14 867 1176 587168360 587168044 1.620000e-29 141.0
3 TraesCS2D01G539400 chr2A 93.362 3525 190 21 2 3509 751418821 751422318 0.000000e+00 5173.0
4 TraesCS2D01G539400 chr2A 86.712 888 81 21 3387 4264 751422265 751423125 0.000000e+00 952.0
5 TraesCS2D01G539400 chr2A 82.347 929 155 7 2385 3307 721989554 721988629 0.000000e+00 798.0
6 TraesCS2D01G539400 chr2B 92.236 3542 213 31 2 3509 759489690 759493203 0.000000e+00 4961.0
7 TraesCS2D01G539400 chr2B 82.024 929 159 6 2385 3307 708986913 708985987 0.000000e+00 784.0
8 TraesCS2D01G539400 chr2B 82.701 896 85 46 3387 4264 759493150 759493993 0.000000e+00 732.0
9 TraesCS2D01G539400 chr2B 76.324 321 57 10 884 1193 708988020 708987708 2.070000e-33 154.0
10 TraesCS2D01G539400 chr2B 94.340 53 3 0 3388 3440 759493224 759493276 9.930000e-12 82.4


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 TraesCS2D01G539400 chr2D 619731255 619735562 4307 False 7956.000000 7956 100.0000 1 4308 1 chr2D.!!$F1 4307
1 TraesCS2D01G539400 chr2D 587165847 587168360 2513 True 476.000000 811 79.3225 867 3294 2 chr2D.!!$R1 2427
2 TraesCS2D01G539400 chr2A 751418821 751423125 4304 False 3062.500000 5173 90.0370 2 4264 2 chr2A.!!$F1 4262
3 TraesCS2D01G539400 chr2A 721988629 721989554 925 True 798.000000 798 82.3470 2385 3307 1 chr2A.!!$R1 922
4 TraesCS2D01G539400 chr2B 759489690 759493993 4303 False 1925.133333 4961 89.7590 2 4264 3 chr2B.!!$F1 4262
5 TraesCS2D01G539400 chr2B 708985987 708988020 2033 True 469.000000 784 79.1740 884 3307 2 chr2B.!!$R1 2423

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
677 704 0.034896 TTGTCGGGCTCTTCCTGTTC 59.965 55.0 0.00 0.0 42.13 3.18 F
1290 1334 0.182299 TGTCCACAATGCTGACCACA 59.818 50.0 1.18 0.0 0.00 4.17 F
1300 1344 0.667792 GCTGACCACAGAAGACGACC 60.668 60.0 0.00 0.0 46.03 4.79 F
2598 3230 0.184451 CCATCCCCTGAGTGAATGGG 59.816 60.0 0.00 0.0 40.59 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2686 0.106519 ATATGCACAGAAGGCACCCC 60.107 55.000 0.00 0.0 45.23 4.95 R
2317 2929 0.898320 TAGAGACAGAGTGCCCAAGC 59.102 55.000 0.00 0.0 40.48 4.01 R
3169 3807 1.140589 ATTCACGAGCTCTCTGGCG 59.859 57.895 12.85 0.0 37.29 5.69 R
3820 4551 0.038310 CCCTCCCTTGGGTTTCTGTC 59.962 60.000 5.51 0.0 42.25 3.51 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
32 33 1.731098 CGTAAGCGGGGTGAAAATTGC 60.731 52.381 0.00 0.00 0.00 3.56
56 61 2.583593 GGACATGAGAGGCGTCGC 60.584 66.667 9.22 9.22 0.00 5.19
268 290 4.549458 CAGTTGCATAACAGGAACAAAGG 58.451 43.478 0.00 0.00 41.61 3.11
270 292 4.892934 AGTTGCATAACAGGAACAAAGGAA 59.107 37.500 0.00 0.00 41.61 3.36
271 293 5.362430 AGTTGCATAACAGGAACAAAGGAAA 59.638 36.000 0.00 0.00 41.61 3.13
272 294 5.452078 TGCATAACAGGAACAAAGGAAAG 57.548 39.130 0.00 0.00 0.00 2.62
273 295 5.136828 TGCATAACAGGAACAAAGGAAAGA 58.863 37.500 0.00 0.00 0.00 2.52
274 296 5.596361 TGCATAACAGGAACAAAGGAAAGAA 59.404 36.000 0.00 0.00 0.00 2.52
275 297 6.152379 GCATAACAGGAACAAAGGAAAGAAG 58.848 40.000 0.00 0.00 0.00 2.85
280 302 4.216472 CAGGAACAAAGGAAAGAAGTAGGC 59.784 45.833 0.00 0.00 0.00 3.93
359 382 4.614967 AGTTTCCAATGAGGGAATCCAT 57.385 40.909 0.09 0.00 45.90 3.41
416 439 3.803778 CCAGAAACATTGGCAGAAACAAC 59.196 43.478 0.00 0.00 0.00 3.32
425 448 1.268539 GGCAGAAACAACTTGTGTCCG 60.269 52.381 8.29 0.24 40.60 4.79
433 456 4.175787 ACAACTTGTGTCCGAGAGATAC 57.824 45.455 0.00 0.00 34.38 2.24
440 463 4.023980 TGTGTCCGAGAGATACCTTCATT 58.976 43.478 0.00 0.00 35.82 2.57
445 468 6.323996 TGTCCGAGAGATACCTTCATTATTGT 59.676 38.462 0.00 0.00 0.00 2.71
447 470 5.406780 CCGAGAGATACCTTCATTATTGTGC 59.593 44.000 0.00 0.00 0.00 4.57
477 500 2.496899 AACCAGTTGCATACCAGGAG 57.503 50.000 0.00 0.00 0.00 3.69
478 501 0.035056 ACCAGTTGCATACCAGGAGC 60.035 55.000 0.00 0.00 0.00 4.70
484 507 2.877097 TGCATACCAGGAGCAAGAAA 57.123 45.000 0.00 0.00 34.97 2.52
499 526 6.372937 GGAGCAAGAAATATATAGGCCAAGAC 59.627 42.308 5.01 0.00 0.00 3.01
501 528 6.712547 AGCAAGAAATATATAGGCCAAGACAC 59.287 38.462 5.01 0.00 0.00 3.67
529 556 8.567948 ACTTCATAATTGTGTCCTAAACAACAG 58.432 33.333 1.86 0.00 40.16 3.16
548 575 1.369091 GCCAGTTGCATACCAGGACG 61.369 60.000 0.00 0.00 40.77 4.79
558 585 0.752658 TACCAGGACGATGGAGCATG 59.247 55.000 11.97 0.00 43.57 4.06
586 613 1.841302 AAGAGCGAATGAGTGGCCCA 61.841 55.000 0.00 0.00 0.00 5.36
605 632 3.119101 CCCAGAGCGCGGTATTAAGATAT 60.119 47.826 12.41 0.00 0.00 1.63
677 704 0.034896 TTGTCGGGCTCTTCCTGTTC 59.965 55.000 0.00 0.00 42.13 3.18
707 734 3.458163 CCGCGTAGGAGCTTCCCA 61.458 66.667 4.92 0.00 45.00 4.37
709 736 1.461091 CCGCGTAGGAGCTTCCCATA 61.461 60.000 4.92 0.00 45.00 2.74
713 740 2.307768 CGTAGGAGCTTCCCATAGACA 58.692 52.381 0.00 0.00 37.19 3.41
720 747 5.848921 AGGAGCTTCCCATAGACAGATAATT 59.151 40.000 0.00 0.00 37.19 1.40
721 748 7.019388 AGGAGCTTCCCATAGACAGATAATTA 58.981 38.462 0.00 0.00 37.19 1.40
770 797 4.438131 CATGGACATGAATGGCTTGACCA 61.438 47.826 6.44 0.00 46.95 4.02
789 816 4.019174 ACCACTTATTTGGAATGAGCAGG 58.981 43.478 0.00 0.00 39.24 4.85
830 858 5.905331 AGGATCAGACCATGTAAGATACCAA 59.095 40.000 0.00 0.00 0.00 3.67
845 873 7.956328 AAGATACCAATACCGCTATATCTGA 57.044 36.000 0.00 0.00 31.41 3.27
850 878 5.105752 CCAATACCGCTATATCTGAAGAGC 58.894 45.833 0.23 0.23 0.00 4.09
953 988 8.816894 TCATCCTGTTTCTATTCTGAGTAAAGT 58.183 33.333 0.00 0.00 0.00 2.66
954 989 8.877779 CATCCTGTTTCTATTCTGAGTAAAGTG 58.122 37.037 0.00 0.00 0.00 3.16
957 992 8.307483 CCTGTTTCTATTCTGAGTAAAGTGAGA 58.693 37.037 0.00 0.00 0.00 3.27
958 993 9.868277 CTGTTTCTATTCTGAGTAAAGTGAGAT 57.132 33.333 0.00 0.00 0.00 2.75
963 998 8.625651 TCTATTCTGAGTAAAGTGAGATACTGC 58.374 37.037 0.00 0.00 40.26 4.40
964 999 6.590234 TTCTGAGTAAAGTGAGATACTGCA 57.410 37.500 0.00 0.00 40.26 4.41
1047 1085 2.430610 GGAGCAGCTCCCGTCTGAT 61.431 63.158 29.22 0.00 44.36 2.90
1101 1145 2.240667 CCTGGGTCATCTCAACCTTGAT 59.759 50.000 0.00 0.00 36.46 2.57
1109 1153 1.833630 TCTCAACCTTGATCCAGCGAT 59.166 47.619 0.00 0.00 36.46 4.58
1117 1161 1.032794 TGATCCAGCGATACGAGCTT 58.967 50.000 0.00 0.00 44.06 3.74
1181 1225 6.726764 GGATACTTCCAGGTATACTCCTTGAT 59.273 42.308 2.25 0.00 42.12 2.57
1185 1229 6.326843 ACTTCCAGGTATACTCCTTGATAACC 59.673 42.308 2.25 0.00 35.37 2.85
1193 1237 2.009774 CTCCTTGATAACCTTGCCACG 58.990 52.381 0.00 0.00 0.00 4.94
1244 1288 3.195396 GCCTTGGCATGTATCTTTTCCAA 59.805 43.478 6.79 0.00 33.18 3.53
1260 1304 4.433186 TTCCAAACTGCAATGGATAACG 57.567 40.909 14.33 0.00 44.83 3.18
1289 1333 0.593128 GTGTCCACAATGCTGACCAC 59.407 55.000 1.18 0.00 0.00 4.16
1290 1334 0.182299 TGTCCACAATGCTGACCACA 59.818 50.000 1.18 0.00 0.00 4.17
1300 1344 0.667792 GCTGACCACAGAAGACGACC 60.668 60.000 0.00 0.00 46.03 4.79
1301 1345 0.673985 CTGACCACAGAAGACGACCA 59.326 55.000 0.00 0.00 46.03 4.02
1307 1351 2.417379 CCACAGAAGACGACCATACAGG 60.417 54.545 0.00 0.00 45.67 4.00
1310 1354 1.478510 AGAAGACGACCATACAGGCAG 59.521 52.381 0.00 0.00 43.14 4.85
1317 1361 3.196901 ACGACCATACAGGCAGATAAACA 59.803 43.478 0.00 0.00 43.14 2.83
1332 1376 7.430441 GCAGATAAACAAGGAAACCAAACTAA 58.570 34.615 0.00 0.00 0.00 2.24
1405 1450 2.311124 ATGACGACCTTCGAAATCCC 57.689 50.000 0.00 0.00 43.74 3.85
1420 1465 4.227134 CCCGCGGCTAGCTGTGAT 62.227 66.667 33.61 0.00 45.59 3.06
1452 1498 3.125146 TGTTAGTACTAGTACACGCACCG 59.875 47.826 29.87 0.00 38.48 4.94
1455 1501 2.932614 AGTACTAGTACACGCACCGTAG 59.067 50.000 29.87 0.00 38.32 3.51
1515 1561 1.283029 TGAGCTCCATCCTCCTTTTGG 59.717 52.381 12.15 0.00 42.21 3.28
1551 1597 5.715070 AGAGTATGAGCTGTGTAAACAGTC 58.285 41.667 14.60 10.82 39.76 3.51
1580 1626 4.720649 AGTATGCTAGAACACATCACGT 57.279 40.909 0.00 0.00 0.00 4.49
1595 1641 1.616374 TCACGTGACTGTATGAGGCAA 59.384 47.619 15.76 0.00 43.39 4.52
1602 1648 1.556911 ACTGTATGAGGCAACAGGGAG 59.443 52.381 7.33 0.00 45.94 4.30
1624 1670 2.158058 TGGCAAAAACTGTACGATACGC 59.842 45.455 0.00 0.00 0.00 4.42
1625 1671 2.158058 GGCAAAAACTGTACGATACGCA 59.842 45.455 0.00 0.00 0.00 5.24
1684 1730 7.446931 TGGAAACTGACAAATAACATGAAGCTA 59.553 33.333 0.00 0.00 0.00 3.32
1686 1732 9.846248 GAAACTGACAAATAACATGAAGCTAAT 57.154 29.630 0.00 0.00 0.00 1.73
1764 1821 6.265196 ACATTGAAGGTCATTTTAGCACTTGA 59.735 34.615 0.00 0.00 0.00 3.02
1784 1842 5.272283 TGACGGTTGTAGATAATCCCTTC 57.728 43.478 0.00 0.00 0.00 3.46
1997 2058 4.865365 GCCTACTCGATATAAATGTCTGGC 59.135 45.833 0.00 0.00 0.00 4.85
2017 2078 1.003580 CTTTAGAGCAACAGGGAGCCA 59.996 52.381 0.00 0.00 0.00 4.75
2051 2118 9.482627 CTTAAATGGCTGGTTTTAACAACATTA 57.517 29.630 0.00 0.00 0.00 1.90
2053 2120 7.903995 AATGGCTGGTTTTAACAACATTATG 57.096 32.000 0.00 0.00 0.00 1.90
2064 2586 9.469097 TTTTAACAACATTATGCTATGGGTACT 57.531 29.630 0.00 0.00 0.00 2.73
2317 2929 1.856629 ATGGCCTTTCATGAACCCTG 58.143 50.000 7.89 0.00 0.00 4.45
2441 3073 2.012673 GTCATGGATGGAGCTGTTGAC 58.987 52.381 0.00 0.00 0.00 3.18
2598 3230 0.184451 CCATCCCCTGAGTGAATGGG 59.816 60.000 0.00 0.00 40.59 4.00
2600 3232 2.126882 CATCCCCTGAGTGAATGGGTA 58.873 52.381 0.00 0.00 39.31 3.69
2676 3312 3.338249 TCTTGCAATCCTGAACTACAGC 58.662 45.455 0.00 0.00 44.52 4.40
2718 3356 9.725019 TCTGACATAACTCTTTTGTTCATGTAT 57.275 29.630 0.00 0.00 0.00 2.29
3169 3807 0.251354 TGCATGAGAAGGTCTCCAGC 59.749 55.000 0.00 10.41 42.73 4.85
3210 3848 4.997395 TGAGCAGAATCCTGAAAAGTACAC 59.003 41.667 0.00 0.00 43.02 2.90
3325 3964 4.157472 GCGTAGTAGGGTATAATCTCCACC 59.843 50.000 0.00 0.00 0.00 4.61
3338 3977 1.202879 TCTCCACCCGAAGCACAAAAT 60.203 47.619 0.00 0.00 0.00 1.82
3346 3985 3.181497 CCCGAAGCACAAAATGATACCTG 60.181 47.826 0.00 0.00 0.00 4.00
3627 4354 7.575720 GCTGTTAGTTAGCCATTTGACTTCAAT 60.576 37.037 0.00 0.00 33.99 2.57
3717 4444 4.216257 AGGTTGGACATATAATGCGCAATC 59.784 41.667 17.11 3.48 0.00 2.67
3723 4452 6.035975 TGGACATATAATGCGCAATCTAATCG 59.964 38.462 17.11 1.48 0.00 3.34
3730 4459 3.381045 TGCGCAATCTAATCGGTAAGAG 58.619 45.455 8.16 0.00 0.00 2.85
3735 4464 4.212214 GCAATCTAATCGGTAAGAGCAAGG 59.788 45.833 0.00 0.00 0.00 3.61
3737 4466 4.650754 TCTAATCGGTAAGAGCAAGGTC 57.349 45.455 0.00 0.00 0.00 3.85
3754 4484 2.045340 CGGATTGCGGGGTTCCTT 60.045 61.111 0.00 0.00 0.00 3.36
3766 4496 1.766496 GGGTTCCTTCGTGGATGGATA 59.234 52.381 1.62 0.00 45.68 2.59
3776 4507 3.967326 TCGTGGATGGATAGTCTGGAAAT 59.033 43.478 0.00 0.00 0.00 2.17
3820 4551 2.829023 TGGGGAGGAAACTACTACCAG 58.171 52.381 0.00 0.00 42.84 4.00
3831 4562 3.853207 ACTACTACCAGACAGAAACCCA 58.147 45.455 0.00 0.00 0.00 4.51
3835 4566 0.478507 ACCAGACAGAAACCCAAGGG 59.521 55.000 2.91 2.91 42.03 3.95
4193 4938 2.607282 CGTCCTACGCTCAAGTCAAAGT 60.607 50.000 0.00 0.00 33.65 2.66
4196 4941 2.476619 CCTACGCTCAAGTCAAAGTGTG 59.523 50.000 0.00 0.00 36.90 3.82
4200 4945 1.679139 CTCAAGTCAAAGTGTGGCCA 58.321 50.000 0.00 0.00 29.16 5.36
4205 4950 2.047061 AGTCAAAGTGTGGCCAGAGTA 58.953 47.619 11.24 0.00 29.16 2.59
4213 4958 3.136626 AGTGTGGCCAGAGTAAAAGAAGT 59.863 43.478 5.11 0.00 0.00 3.01
4242 4987 2.687935 TGCTTGGAGAAAATAATCGGCC 59.312 45.455 0.00 0.00 0.00 6.13
4244 4989 3.243201 GCTTGGAGAAAATAATCGGCCAG 60.243 47.826 2.24 0.00 32.73 4.85
4251 4996 6.262273 GGAGAAAATAATCGGCCAGAAATACA 59.738 38.462 2.24 0.00 0.00 2.29
4264 5009 5.010617 GCCAGAAATACACCTTCCTTTGAAA 59.989 40.000 0.00 0.00 0.00 2.69
4265 5010 6.681777 CCAGAAATACACCTTCCTTTGAAAG 58.318 40.000 0.00 0.00 0.00 2.62
4266 5011 6.152379 CAGAAATACACCTTCCTTTGAAAGC 58.848 40.000 0.00 0.00 0.00 3.51
4267 5012 5.243954 AGAAATACACCTTCCTTTGAAAGCC 59.756 40.000 0.00 0.00 0.00 4.35
4268 5013 2.755952 ACACCTTCCTTTGAAAGCCT 57.244 45.000 0.00 0.00 0.00 4.58
4269 5014 3.032265 ACACCTTCCTTTGAAAGCCTT 57.968 42.857 0.00 0.00 0.00 4.35
4270 5015 3.374764 ACACCTTCCTTTGAAAGCCTTT 58.625 40.909 0.00 0.00 0.00 3.11
4271 5016 3.774766 ACACCTTCCTTTGAAAGCCTTTT 59.225 39.130 0.00 0.00 0.00 2.27
4272 5017 4.959839 ACACCTTCCTTTGAAAGCCTTTTA 59.040 37.500 0.00 0.00 0.00 1.52
4273 5018 5.069119 ACACCTTCCTTTGAAAGCCTTTTAG 59.931 40.000 0.00 0.00 0.00 1.85
4274 5019 5.069119 CACCTTCCTTTGAAAGCCTTTTAGT 59.931 40.000 0.00 0.00 0.00 2.24
4275 5020 5.069119 ACCTTCCTTTGAAAGCCTTTTAGTG 59.931 40.000 0.00 0.00 0.00 2.74
4276 5021 4.584327 TCCTTTGAAAGCCTTTTAGTGC 57.416 40.909 0.00 0.00 0.00 4.40
4277 5022 4.215109 TCCTTTGAAAGCCTTTTAGTGCT 58.785 39.130 0.00 0.00 40.17 4.40
4278 5023 4.037923 TCCTTTGAAAGCCTTTTAGTGCTG 59.962 41.667 0.00 0.00 38.00 4.41
4279 5024 3.369546 TTGAAAGCCTTTTAGTGCTGC 57.630 42.857 0.00 0.00 38.00 5.25
4280 5025 2.305928 TGAAAGCCTTTTAGTGCTGCA 58.694 42.857 0.00 0.00 38.00 4.41
4281 5026 2.294233 TGAAAGCCTTTTAGTGCTGCAG 59.706 45.455 10.11 10.11 38.00 4.41
4282 5027 2.276732 AAGCCTTTTAGTGCTGCAGA 57.723 45.000 20.43 0.00 38.00 4.26
4283 5028 2.503895 AGCCTTTTAGTGCTGCAGAT 57.496 45.000 20.43 4.69 36.23 2.90
4284 5029 2.800250 AGCCTTTTAGTGCTGCAGATT 58.200 42.857 20.43 3.94 36.23 2.40
4285 5030 2.490903 AGCCTTTTAGTGCTGCAGATTG 59.509 45.455 20.43 0.00 36.23 2.67
4286 5031 2.872370 CCTTTTAGTGCTGCAGATTGC 58.128 47.619 20.43 2.64 45.29 3.56
4287 5032 2.490903 CCTTTTAGTGCTGCAGATTGCT 59.509 45.455 20.43 11.12 45.31 3.91
4288 5033 3.427233 CCTTTTAGTGCTGCAGATTGCTC 60.427 47.826 20.43 3.51 45.31 4.26
4289 5034 1.362768 TTAGTGCTGCAGATTGCTCG 58.637 50.000 20.43 0.00 45.31 5.03
4290 5035 1.086067 TAGTGCTGCAGATTGCTCGC 61.086 55.000 20.43 4.95 45.31 5.03
4291 5036 2.358984 TGCTGCAGATTGCTCGCA 60.359 55.556 20.43 2.84 45.31 5.10
4292 5037 1.967494 TGCTGCAGATTGCTCGCAA 60.967 52.632 20.43 6.80 45.31 4.85
4293 5038 1.210931 GCTGCAGATTGCTCGCAAA 59.789 52.632 20.43 0.00 45.31 3.68
4294 5039 0.179145 GCTGCAGATTGCTCGCAAAT 60.179 50.000 20.43 0.00 45.31 2.32
4295 5040 1.545759 CTGCAGATTGCTCGCAAATG 58.454 50.000 8.42 11.22 45.31 2.32
4296 5041 0.457166 TGCAGATTGCTCGCAAATGC 60.457 50.000 25.58 25.58 45.31 3.56
4306 5051 2.126888 GCAAATGCGTGGACCGTG 60.127 61.111 0.00 0.00 39.32 4.94
4307 5052 2.560861 CAAATGCGTGGACCGTGG 59.439 61.111 0.00 0.00 39.32 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.032799 TGTCCTGTCACGCAATTTTCAC 59.967 45.455 0.00 0.00 0.00 3.18
30 31 0.244721 CTCTCATGTCCTGTCACGCA 59.755 55.000 0.00 0.00 0.00 5.24
32 33 0.459237 GCCTCTCATGTCCTGTCACG 60.459 60.000 0.00 0.00 0.00 4.35
56 61 0.466555 TTTTGTCGGTTCCCACAGGG 60.467 55.000 0.00 0.00 46.11 4.45
132 151 1.297968 TCATGAAGGCTGGAATCCCA 58.702 50.000 0.00 0.00 40.95 4.37
268 290 1.017387 CCATGCCGCCTACTTCTTTC 58.983 55.000 0.00 0.00 0.00 2.62
270 292 0.618458 TTCCATGCCGCCTACTTCTT 59.382 50.000 0.00 0.00 0.00 2.52
271 293 0.107654 GTTCCATGCCGCCTACTTCT 60.108 55.000 0.00 0.00 0.00 2.85
272 294 1.429148 CGTTCCATGCCGCCTACTTC 61.429 60.000 0.00 0.00 0.00 3.01
273 295 1.449601 CGTTCCATGCCGCCTACTT 60.450 57.895 0.00 0.00 0.00 2.24
274 296 1.324740 TACGTTCCATGCCGCCTACT 61.325 55.000 0.00 0.00 0.00 2.57
275 297 0.874607 CTACGTTCCATGCCGCCTAC 60.875 60.000 0.00 0.00 0.00 3.18
280 302 2.519377 TAATCCTACGTTCCATGCCG 57.481 50.000 0.00 0.00 0.00 5.69
359 382 1.910722 GCTTCATGGAGAGGCTGGA 59.089 57.895 4.75 0.00 45.20 3.86
364 387 1.457346 GGTGTTGCTTCATGGAGAGG 58.543 55.000 4.75 0.00 0.00 3.69
365 388 1.004044 AGGGTGTTGCTTCATGGAGAG 59.996 52.381 4.75 0.00 0.00 3.20
416 439 3.444034 TGAAGGTATCTCTCGGACACAAG 59.556 47.826 0.00 0.00 0.00 3.16
425 448 5.703130 GGGCACAATAATGAAGGTATCTCTC 59.297 44.000 0.00 0.00 0.00 3.20
433 456 5.913137 TGTTTAGGGCACAATAATGAAGG 57.087 39.130 0.00 0.00 0.00 3.46
440 463 5.364157 ACTGGTTTTTGTTTAGGGCACAATA 59.636 36.000 0.00 0.00 34.13 1.90
445 468 3.680196 GCAACTGGTTTTTGTTTAGGGCA 60.680 43.478 0.00 0.00 0.00 5.36
447 470 4.130286 TGCAACTGGTTTTTGTTTAGGG 57.870 40.909 0.00 0.00 0.00 3.53
477 500 6.486657 TGTGTCTTGGCCTATATATTTCTTGC 59.513 38.462 3.32 0.00 0.00 4.01
478 501 8.345565 GTTGTGTCTTGGCCTATATATTTCTTG 58.654 37.037 3.32 0.00 0.00 3.02
484 507 7.136822 TGAAGTTGTGTCTTGGCCTATATAT 57.863 36.000 3.32 0.00 0.00 0.86
501 528 9.180678 GTTGTTTAGGACACAATTATGAAGTTG 57.819 33.333 0.00 0.00 38.18 3.16
529 556 1.369091 CGTCCTGGTATGCAACTGGC 61.369 60.000 0.00 0.00 45.13 4.85
548 575 1.725641 TTCGTCACACATGCTCCATC 58.274 50.000 0.00 0.00 0.00 3.51
558 585 2.058798 TCATTCGCTCTTTCGTCACAC 58.941 47.619 0.00 0.00 0.00 3.82
586 613 4.381718 GGGAATATCTTAATACCGCGCTCT 60.382 45.833 5.56 0.00 0.00 4.09
605 632 0.459489 GCCGCATAGCAAATTGGGAA 59.541 50.000 0.00 0.00 0.00 3.97
746 773 0.742505 AAGCCATTCATGTCCATGCG 59.257 50.000 2.33 0.00 38.65 4.73
770 797 3.445096 GTGCCTGCTCATTCCAAATAAGT 59.555 43.478 0.00 0.00 0.00 2.24
845 873 1.808945 CCACTCTTTTGCATCGCTCTT 59.191 47.619 0.00 0.00 0.00 2.85
850 878 3.976942 CAGAAAACCACTCTTTTGCATCG 59.023 43.478 0.00 0.00 0.00 3.84
953 988 4.383444 CCAGAGTCCAATTGCAGTATCTCA 60.383 45.833 0.00 0.00 0.00 3.27
954 989 4.125703 CCAGAGTCCAATTGCAGTATCTC 58.874 47.826 0.00 1.60 0.00 2.75
957 992 3.614092 CACCAGAGTCCAATTGCAGTAT 58.386 45.455 0.00 0.00 0.00 2.12
958 993 2.875672 GCACCAGAGTCCAATTGCAGTA 60.876 50.000 0.00 0.00 0.00 2.74
960 995 0.524862 GCACCAGAGTCCAATTGCAG 59.475 55.000 0.00 0.00 0.00 4.41
961 996 0.111061 AGCACCAGAGTCCAATTGCA 59.889 50.000 0.00 0.00 32.24 4.08
962 997 1.068055 CAAGCACCAGAGTCCAATTGC 60.068 52.381 0.00 0.00 0.00 3.56
963 998 2.233271 ACAAGCACCAGAGTCCAATTG 58.767 47.619 0.00 0.00 0.00 2.32
964 999 2.664402 ACAAGCACCAGAGTCCAATT 57.336 45.000 0.00 0.00 0.00 2.32
1071 1115 2.503356 GAGATGACCCAGGTTGATCACT 59.497 50.000 0.00 0.00 0.00 3.41
1101 1145 1.226974 GCAAGCTCGTATCGCTGGA 60.227 57.895 0.00 0.00 37.87 3.86
1109 1153 0.249531 TTCAACCACGCAAGCTCGTA 60.250 50.000 0.00 0.00 41.21 3.43
1117 1161 2.027653 TGGTGATATCTTCAACCACGCA 60.028 45.455 8.24 0.00 41.74 5.24
1181 1225 1.669760 CGAAGGCGTGGCAAGGTTA 60.670 57.895 1.91 0.00 0.00 2.85
1193 1237 4.735338 CAGAAAAGAAAAAGACACGAAGGC 59.265 41.667 0.00 0.00 0.00 4.35
1232 1276 6.024552 TCCATTGCAGTTTGGAAAAGATAC 57.975 37.500 11.45 0.00 39.05 2.24
1244 1288 3.216147 GCAACGTTATCCATTGCAGTT 57.784 42.857 0.00 0.00 46.37 3.16
1260 1304 0.814457 TTGTGGACACAAGTGGCAAC 59.186 50.000 13.42 6.63 45.42 4.17
1282 1326 0.673985 TGGTCGTCTTCTGTGGTCAG 59.326 55.000 0.00 0.00 42.54 3.51
1289 1333 1.204704 TGCCTGTATGGTCGTCTTCTG 59.795 52.381 0.00 0.00 38.35 3.02
1290 1334 1.478510 CTGCCTGTATGGTCGTCTTCT 59.521 52.381 0.00 0.00 38.35 2.85
1300 1344 6.404734 GGTTTCCTTGTTTATCTGCCTGTATG 60.405 42.308 0.00 0.00 0.00 2.39
1301 1345 5.652452 GGTTTCCTTGTTTATCTGCCTGTAT 59.348 40.000 0.00 0.00 0.00 2.29
1307 1351 5.842907 AGTTTGGTTTCCTTGTTTATCTGC 58.157 37.500 0.00 0.00 0.00 4.26
1332 1376 5.359576 TGCAGTGGTTCTTCAACTACAAATT 59.640 36.000 4.46 0.00 44.46 1.82
1405 1450 4.235065 CTATCACAGCTAGCCGCG 57.765 61.111 12.13 0.00 45.59 6.46
1425 1470 7.243487 GTGCGTGTACTAGTACTAACATACAA 58.757 38.462 28.56 7.13 37.00 2.41
1426 1471 6.183360 GGTGCGTGTACTAGTACTAACATACA 60.183 42.308 28.56 16.32 37.00 2.29
1428 1473 5.006649 CGGTGCGTGTACTAGTACTAACATA 59.993 44.000 28.56 9.13 37.00 2.29
1438 1484 0.731417 AGCTACGGTGCGTGTACTAG 59.269 55.000 0.00 0.00 41.39 2.57
1455 1501 4.921337 AGCATAGTCAGTTTGCTCCTAAGC 60.921 45.833 0.00 0.00 42.88 3.09
1471 1517 8.206867 TCATCAAACTATTTAGCTGAGCATAGT 58.793 33.333 7.39 8.62 34.54 2.12
1474 1520 7.493743 CTCATCAAACTATTTAGCTGAGCAT 57.506 36.000 7.39 0.00 0.00 3.79
1475 1521 6.915544 CTCATCAAACTATTTAGCTGAGCA 57.084 37.500 7.39 0.00 0.00 4.26
1476 1522 5.746539 GCTCATCAAACTATTTAGCTGAGC 58.253 41.667 0.00 0.00 45.01 4.26
1515 1561 3.631250 TCATACTCTTCATTTTGGGGGC 58.369 45.455 0.00 0.00 0.00 5.80
1580 1626 1.278985 CCCTGTTGCCTCATACAGTCA 59.721 52.381 0.00 0.00 40.06 3.41
1595 1641 1.341976 ACAGTTTTTGCCACTCCCTGT 60.342 47.619 0.00 0.00 0.00 4.00
1602 1648 3.728600 CGTATCGTACAGTTTTTGCCAC 58.271 45.455 0.00 0.00 0.00 5.01
1607 1653 3.924686 CCTCTGCGTATCGTACAGTTTTT 59.075 43.478 0.00 0.00 33.12 1.94
1624 1670 3.679389 ACAAAATGTAGCTGGTCCTCTG 58.321 45.455 0.00 0.00 0.00 3.35
1625 1671 3.327757 TGACAAAATGTAGCTGGTCCTCT 59.672 43.478 0.00 0.00 0.00 3.69
1684 1730 4.918588 ACGAAATGGGGACTGAACTTATT 58.081 39.130 0.00 0.00 0.00 1.40
1686 1732 3.307199 GGACGAAATGGGGACTGAACTTA 60.307 47.826 0.00 0.00 0.00 2.24
1764 1821 4.344390 GGAGAAGGGATTATCTACAACCGT 59.656 45.833 0.00 0.00 0.00 4.83
1910 1970 6.094603 GGAAACTGAGATGCTTGAACATACAT 59.905 38.462 0.00 0.00 0.00 2.29
1997 2058 1.003580 TGGCTCCCTGTTGCTCTAAAG 59.996 52.381 0.00 0.00 0.00 1.85
2017 2078 0.394352 CAGCCATTTAAGCCGACCCT 60.394 55.000 0.00 0.00 0.00 4.34
2051 2118 2.843730 TGTCCACAAGTACCCATAGCAT 59.156 45.455 0.00 0.00 0.00 3.79
2053 2120 3.560636 ATGTCCACAAGTACCCATAGC 57.439 47.619 0.00 0.00 0.00 2.97
2064 2586 1.825090 CTGCCTTGCTATGTCCACAA 58.175 50.000 0.00 0.00 0.00 3.33
2140 2663 5.830991 GCACCCCCTGTATAAATGATTTGTA 59.169 40.000 0.00 0.00 0.00 2.41
2158 2686 0.106519 ATATGCACAGAAGGCACCCC 60.107 55.000 0.00 0.00 45.23 4.95
2159 2687 2.638480 TATATGCACAGAAGGCACCC 57.362 50.000 0.00 0.00 45.23 4.61
2215 2743 2.982488 AGTGGTCCTTGAGAACCTTGAT 59.018 45.455 0.00 0.00 0.00 2.57
2317 2929 0.898320 TAGAGACAGAGTGCCCAAGC 59.102 55.000 0.00 0.00 40.48 4.01
2441 3073 3.818961 TTGAAGAAATCTGAAGCTGCG 57.181 42.857 0.00 0.00 0.00 5.18
2598 3230 4.426416 GGTTTTTCCGGCCAATATTGTAC 58.574 43.478 14.25 6.00 0.00 2.90
2600 3232 2.235155 GGGTTTTTCCGGCCAATATTGT 59.765 45.455 14.25 0.00 37.00 2.71
2676 3312 9.973246 GTTATGTCAGACATTACACAATTAGTG 57.027 33.333 21.30 6.51 45.37 2.74
2718 3356 9.777008 AATTTCCCATATACTCCCTGTTTTTAA 57.223 29.630 0.00 0.00 0.00 1.52
3130 3768 4.358851 GCATTGCGAAACCATTAATGCTA 58.641 39.130 10.11 0.00 46.03 3.49
3169 3807 1.140589 ATTCACGAGCTCTCTGGCG 59.859 57.895 12.85 0.00 37.29 5.69
3210 3848 1.732259 AGTCATTAAAACTGCTCGCGG 59.268 47.619 6.13 0.00 0.00 6.46
3325 3964 3.731867 GCAGGTATCATTTTGTGCTTCGG 60.732 47.826 0.00 0.00 0.00 4.30
3338 3977 2.683968 GACAAACTGTCGCAGGTATCA 58.316 47.619 10.80 0.00 37.67 2.15
3466 4178 2.376808 ACTTCAGTGCCTTCAGATCG 57.623 50.000 0.00 0.00 0.00 3.69
3470 4182 2.684881 ACAACAACTTCAGTGCCTTCAG 59.315 45.455 0.00 0.00 0.00 3.02
3587 4314 9.915629 GCTAACTAACAGCATACAGTATCTTAT 57.084 33.333 0.00 0.00 38.93 1.73
3588 4315 8.358148 GGCTAACTAACAGCATACAGTATCTTA 58.642 37.037 0.00 0.00 40.95 2.10
3589 4316 7.147724 TGGCTAACTAACAGCATACAGTATCTT 60.148 37.037 0.00 0.00 40.95 2.40
3590 4317 6.323996 TGGCTAACTAACAGCATACAGTATCT 59.676 38.462 0.00 0.00 40.95 1.98
3591 4318 6.513180 TGGCTAACTAACAGCATACAGTATC 58.487 40.000 0.00 0.00 40.95 2.24
3592 4319 6.479972 TGGCTAACTAACAGCATACAGTAT 57.520 37.500 0.00 0.00 40.95 2.12
3627 4354 1.448119 TTCATGCGCACCGTGGAAAA 61.448 50.000 14.90 0.00 0.00 2.29
3717 4444 3.372954 CGACCTTGCTCTTACCGATTAG 58.627 50.000 0.00 0.00 0.00 1.73
3723 4452 2.280628 CAATCCGACCTTGCTCTTACC 58.719 52.381 0.00 0.00 0.00 2.85
3730 4459 3.508840 CCCGCAATCCGACCTTGC 61.509 66.667 6.51 6.51 44.32 4.01
3735 4464 2.814913 AAGGAACCCCGCAATCCGAC 62.815 60.000 0.00 0.00 40.02 4.79
3737 4466 2.045340 AAGGAACCCCGCAATCCG 60.045 61.111 0.00 0.00 38.31 4.18
3754 4484 2.748209 TCCAGACTATCCATCCACGA 57.252 50.000 0.00 0.00 0.00 4.35
3766 4496 7.067494 CCTCCATTTCGATTTTATTTCCAGACT 59.933 37.037 0.00 0.00 0.00 3.24
3776 4507 3.537580 CCCGTCCTCCATTTCGATTTTA 58.462 45.455 0.00 0.00 0.00 1.52
3820 4551 0.038310 CCCTCCCTTGGGTTTCTGTC 59.962 60.000 5.51 0.00 42.25 3.51
4005 4742 3.607661 GGCGAGATCCCCGGAGAC 61.608 72.222 0.73 0.00 0.00 3.36
4029 4767 2.185350 CGAAGGCAGGCTCACGAT 59.815 61.111 15.18 0.00 0.00 3.73
4030 4768 4.069232 CCGAAGGCAGGCTCACGA 62.069 66.667 19.82 0.00 46.14 4.35
4193 4938 3.857157 ACTTCTTTTACTCTGGCCACA 57.143 42.857 0.00 0.00 0.00 4.17
4196 4941 3.751518 TCCAACTTCTTTTACTCTGGCC 58.248 45.455 0.00 0.00 0.00 5.36
4200 4945 7.588497 AGCATTTTCCAACTTCTTTTACTCT 57.412 32.000 0.00 0.00 0.00 3.24
4205 4950 5.988287 TCCAAGCATTTTCCAACTTCTTTT 58.012 33.333 0.00 0.00 0.00 2.27
4213 4958 7.545265 CGATTATTTTCTCCAAGCATTTTCCAA 59.455 33.333 0.00 0.00 0.00 3.53
4242 4987 6.152379 GCTTTCAAAGGAAGGTGTATTTCTG 58.848 40.000 0.00 0.00 33.01 3.02
4244 4989 5.243954 AGGCTTTCAAAGGAAGGTGTATTTC 59.756 40.000 0.00 0.00 33.01 2.17
4251 4996 5.069119 CACTAAAAGGCTTTCAAAGGAAGGT 59.931 40.000 13.76 0.00 33.01 3.50
4264 5009 2.490903 CAATCTGCAGCACTAAAAGGCT 59.509 45.455 9.47 0.00 42.06 4.58
4265 5010 2.872370 CAATCTGCAGCACTAAAAGGC 58.128 47.619 9.47 0.00 0.00 4.35
4266 5011 2.872370 GCAATCTGCAGCACTAAAAGG 58.128 47.619 9.47 0.00 44.26 3.11
4278 5023 2.285154 GCATTTGCGAGCAATCTGC 58.715 52.632 21.45 21.45 45.46 4.26


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

AutoCloner maintained by Alex Coulton.