Multiple sequence alignment - TraesCS2D01G127000

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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 TraesCS2D01G127000 chr2D 100.000 2702 0 0 1 2702 73821088 73818387 0.000000e+00 4990
1 TraesCS2D01G127000 chr2D 88.241 1046 72 34 692 1709 73592448 73591426 0.000000e+00 1203
2 TraesCS2D01G127000 chr2D 86.515 1053 94 28 716 1749 323517318 323516295 0.000000e+00 1114
3 TraesCS2D01G127000 chr2D 88.624 712 70 7 996 1696 323561366 323562077 0.000000e+00 856
4 TraesCS2D01G127000 chr2D 91.234 559 46 3 1750 2306 610170399 610170956 0.000000e+00 758
5 TraesCS2D01G127000 chr2D 96.535 404 12 2 2300 2702 105192473 105192071 0.000000e+00 667
6 TraesCS2D01G127000 chr2D 90.418 407 30 4 2300 2697 610170982 610171388 6.630000e-146 527
7 TraesCS2D01G127000 chr2D 94.512 328 16 1 2373 2698 621218868 621219195 3.100000e-139 505
8 TraesCS2D01G127000 chr2B 92.018 1328 66 15 455 1748 111669969 111668648 0.000000e+00 1829
9 TraesCS2D01G127000 chr2B 83.407 452 53 17 2 441 111670396 111669955 1.510000e-107 399
10 TraesCS2D01G127000 chr2A 87.803 1033 87 28 692 1709 73180105 73179097 0.000000e+00 1173
11 TraesCS2D01G127000 chr2A 91.021 891 41 13 851 1716 73183544 73182668 0.000000e+00 1166
12 TraesCS2D01G127000 chr2A 85.409 1124 108 33 654 1749 406996612 406997707 0.000000e+00 1116
13 TraesCS2D01G127000 chr2A 85.320 1124 107 34 654 1749 407125111 407126204 0.000000e+00 1109
14 TraesCS2D01G127000 chr2A 88.359 713 70 7 996 1696 406964297 406963586 0.000000e+00 845
15 TraesCS2D01G127000 chr2A 92.021 564 39 6 1746 2306 55216297 55216857 0.000000e+00 787
16 TraesCS2D01G127000 chr2A 78.930 598 63 27 247 836 73184153 73183611 5.540000e-92 348
17 TraesCS2D01G127000 chr1A 86.633 980 99 21 1749 2700 103623599 103624574 0.000000e+00 1055
18 TraesCS2D01G127000 chr1A 80.732 410 66 7 1287 1691 511100169 511099768 9.400000e-80 307
19 TraesCS2D01G127000 chr4D 89.106 716 58 16 993 1696 354036691 354037398 0.000000e+00 872
20 TraesCS2D01G127000 chr5B 92.857 560 36 3 1750 2306 312010807 312011365 0.000000e+00 809
21 TraesCS2D01G127000 chr5B 94.789 403 18 2 2300 2700 312011401 312011802 2.280000e-175 625
22 TraesCS2D01G127000 chr5B 92.670 382 21 3 2321 2700 312014225 312013849 6.580000e-151 544
23 TraesCS2D01G127000 chr7D 92.143 560 41 3 1749 2306 33211635 33212193 0.000000e+00 787
24 TraesCS2D01G127000 chr7D 89.563 412 31 9 2300 2702 33212219 33212627 1.860000e-141 512
25 TraesCS2D01G127000 chr7D 88.742 302 23 9 2405 2699 4511729 4512026 2.560000e-95 359
26 TraesCS2D01G127000 chr6A 91.993 562 43 2 1746 2306 112394690 112395250 0.000000e+00 787
27 TraesCS2D01G127000 chr6A 88.509 409 36 7 2300 2702 607668446 607668043 4.040000e-133 484
28 TraesCS2D01G127000 chr6A 88.293 410 32 10 2300 2700 348027470 348027068 6.770000e-131 477
29 TraesCS2D01G127000 chr3A 91.771 559 43 3 1750 2306 53391773 53392330 0.000000e+00 774
30 TraesCS2D01G127000 chr3A 97.973 148 3 0 2554 2701 744606660 744606513 9.600000e-65 257
31 TraesCS2D01G127000 chr5D 91.590 547 42 3 1749 2292 313221997 313222542 0.000000e+00 752
32 TraesCS2D01G127000 chr1D 91.575 546 41 4 1750 2292 6670114 6669571 0.000000e+00 749
33 TraesCS2D01G127000 chr1D 80.929 409 67 9 1287 1691 414301649 414301248 2.020000e-81 313
34 TraesCS2D01G127000 chr6B 90.323 403 32 6 2300 2700 214323960 214323563 3.080000e-144 521
35 TraesCS2D01G127000 chr7A 89.024 410 33 6 2300 2702 667883175 667883579 5.200000e-137 497


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 TraesCS2D01G127000 chr2D 73818387 73821088 2701 True 4990.000000 4990 100.0000 1 2702 1 chr2D.!!$R2 2701
1 TraesCS2D01G127000 chr2D 73591426 73592448 1022 True 1203.000000 1203 88.2410 692 1709 1 chr2D.!!$R1 1017
2 TraesCS2D01G127000 chr2D 323516295 323517318 1023 True 1114.000000 1114 86.5150 716 1749 1 chr2D.!!$R4 1033
3 TraesCS2D01G127000 chr2D 323561366 323562077 711 False 856.000000 856 88.6240 996 1696 1 chr2D.!!$F1 700
4 TraesCS2D01G127000 chr2D 610170399 610171388 989 False 642.500000 758 90.8260 1750 2697 2 chr2D.!!$F3 947
5 TraesCS2D01G127000 chr2B 111668648 111670396 1748 True 1114.000000 1829 87.7125 2 1748 2 chr2B.!!$R1 1746
6 TraesCS2D01G127000 chr2A 406996612 406997707 1095 False 1116.000000 1116 85.4090 654 1749 1 chr2A.!!$F2 1095
7 TraesCS2D01G127000 chr2A 407125111 407126204 1093 False 1109.000000 1109 85.3200 654 1749 1 chr2A.!!$F3 1095
8 TraesCS2D01G127000 chr2A 73179097 73184153 5056 True 895.666667 1173 85.9180 247 1716 3 chr2A.!!$R2 1469
9 TraesCS2D01G127000 chr2A 406963586 406964297 711 True 845.000000 845 88.3590 996 1696 1 chr2A.!!$R1 700
10 TraesCS2D01G127000 chr2A 55216297 55216857 560 False 787.000000 787 92.0210 1746 2306 1 chr2A.!!$F1 560
11 TraesCS2D01G127000 chr1A 103623599 103624574 975 False 1055.000000 1055 86.6330 1749 2700 1 chr1A.!!$F1 951
12 TraesCS2D01G127000 chr4D 354036691 354037398 707 False 872.000000 872 89.1060 993 1696 1 chr4D.!!$F1 703
13 TraesCS2D01G127000 chr5B 312010807 312011802 995 False 717.000000 809 93.8230 1750 2700 2 chr5B.!!$F1 950
14 TraesCS2D01G127000 chr7D 33211635 33212627 992 False 649.500000 787 90.8530 1749 2702 2 chr7D.!!$F2 953
15 TraesCS2D01G127000 chr6A 112394690 112395250 560 False 787.000000 787 91.9930 1746 2306 1 chr6A.!!$F1 560
16 TraesCS2D01G127000 chr3A 53391773 53392330 557 False 774.000000 774 91.7710 1750 2306 1 chr3A.!!$F1 556
17 TraesCS2D01G127000 chr5D 313221997 313222542 545 False 752.000000 752 91.5900 1749 2292 1 chr5D.!!$F1 543
18 TraesCS2D01G127000 chr1D 6669571 6670114 543 True 749.000000 749 91.5750 1750 2292 1 chr1D.!!$R1 542

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
168 170 0.036294 AGCTAAAACTCAGCCGACCC 60.036 55.0 0.0 0.0 39.99 4.46 F
178 180 0.320374 CAGCCGACCCAGACTTAACA 59.680 55.0 0.0 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 5380 0.984995 GAAGTACTTCCCCTGGTGCT 59.015 55.000 22.74 0.0 33.64 4.40 R
1833 5570 1.484653 CCACCACCATGGAGATCGTTA 59.515 52.381 21.47 0.0 43.02 3.18 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
41 43 0.977395 CTCCCCGTGTTTCTCTCCTT 59.023 55.000 0.00 0.00 0.00 3.36
49 51 3.206150 GTGTTTCTCTCCTTGTTCAGCA 58.794 45.455 0.00 0.00 0.00 4.41
58 60 0.595095 CTTGTTCAGCAGCAAGGGAC 59.405 55.000 0.00 0.00 38.61 4.46
61 63 0.957888 GTTCAGCAGCAAGGGACTCC 60.958 60.000 0.00 0.00 38.49 3.85
63 65 1.673665 CAGCAGCAAGGGACTCCAC 60.674 63.158 0.00 0.00 38.49 4.02
79 81 3.612681 ACACCCACGACCTCACCG 61.613 66.667 0.00 0.00 0.00 4.94
89 91 0.611340 GACCTCACCGTGTAGGGACT 60.611 60.000 16.61 2.02 46.96 3.85
90 92 0.898789 ACCTCACCGTGTAGGGACTG 60.899 60.000 16.61 0.00 46.96 3.51
91 93 0.611062 CCTCACCGTGTAGGGACTGA 60.611 60.000 0.00 0.00 46.96 3.41
93 95 1.825474 CTCACCGTGTAGGGACTGATT 59.175 52.381 0.00 0.00 46.96 2.57
94 96 1.548719 TCACCGTGTAGGGACTGATTG 59.451 52.381 0.00 0.00 46.96 2.67
95 97 1.548719 CACCGTGTAGGGACTGATTGA 59.451 52.381 0.00 0.00 46.96 2.57
97 99 1.825474 CCGTGTAGGGACTGATTGAGT 59.175 52.381 0.00 0.00 41.52 3.41
101 103 1.486726 GTAGGGACTGATTGAGTGGGG 59.513 57.143 0.00 0.00 41.52 4.96
107 109 0.460987 CTGATTGAGTGGGGCGAGAC 60.461 60.000 0.00 0.00 0.00 3.36
108 110 1.153349 GATTGAGTGGGGCGAGACC 60.153 63.158 0.00 0.00 37.93 3.85
122 124 2.277084 CGAGACCCCCTAACGATTTTG 58.723 52.381 0.00 0.00 0.00 2.44
124 126 3.682696 GAGACCCCCTAACGATTTTGTT 58.317 45.455 0.00 0.00 35.86 2.83
133 135 7.771826 CCCCCTAACGATTTTGTTCTTAATAGA 59.228 37.037 0.00 0.00 33.32 1.98
134 136 9.338622 CCCCTAACGATTTTGTTCTTAATAGAT 57.661 33.333 0.00 0.00 33.32 1.98
147 149 9.507329 TGTTCTTAATAGATATTCAGGATTGCC 57.493 33.333 0.00 0.00 0.00 4.52
151 153 9.323985 CTTAATAGATATTCAGGATTGCCTAGC 57.676 37.037 0.00 0.00 44.80 3.42
152 154 7.507797 AATAGATATTCAGGATTGCCTAGCT 57.492 36.000 0.00 0.00 44.80 3.32
153 155 8.615360 AATAGATATTCAGGATTGCCTAGCTA 57.385 34.615 0.00 0.00 44.80 3.32
154 156 6.942163 AGATATTCAGGATTGCCTAGCTAA 57.058 37.500 0.00 0.00 44.80 3.09
156 158 7.749666 AGATATTCAGGATTGCCTAGCTAAAA 58.250 34.615 0.00 0.00 44.80 1.52
157 159 7.663493 AGATATTCAGGATTGCCTAGCTAAAAC 59.337 37.037 0.00 0.00 44.80 2.43
158 160 4.844349 TCAGGATTGCCTAGCTAAAACT 57.156 40.909 0.00 0.00 44.80 2.66
159 161 4.770795 TCAGGATTGCCTAGCTAAAACTC 58.229 43.478 0.00 0.00 44.80 3.01
161 163 4.574013 CAGGATTGCCTAGCTAAAACTCAG 59.426 45.833 0.00 0.00 44.80 3.35
162 164 3.313803 GGATTGCCTAGCTAAAACTCAGC 59.686 47.826 0.00 0.00 39.41 4.26
163 165 2.403252 TGCCTAGCTAAAACTCAGCC 57.597 50.000 0.00 0.00 39.99 4.85
164 166 1.291132 GCCTAGCTAAAACTCAGCCG 58.709 55.000 0.00 0.00 39.99 5.52
165 167 1.134788 GCCTAGCTAAAACTCAGCCGA 60.135 52.381 0.00 0.00 39.99 5.54
166 168 2.541556 CCTAGCTAAAACTCAGCCGAC 58.458 52.381 0.00 0.00 39.99 4.79
167 169 2.541556 CTAGCTAAAACTCAGCCGACC 58.458 52.381 0.00 0.00 39.99 4.79
168 170 0.036294 AGCTAAAACTCAGCCGACCC 60.036 55.000 0.00 0.00 39.99 4.46
178 180 0.320374 CAGCCGACCCAGACTTAACA 59.680 55.000 0.00 0.00 0.00 2.41
202 204 7.223582 ACAAAGTCTCAATCACTGCTATATTCG 59.776 37.037 0.00 0.00 0.00 3.34
205 207 5.980116 GTCTCAATCACTGCTATATTCGTGT 59.020 40.000 0.00 0.00 0.00 4.49
206 208 7.013369 AGTCTCAATCACTGCTATATTCGTGTA 59.987 37.037 0.00 0.00 0.00 2.90
209 211 8.520835 TCAATCACTGCTATATTCGTGTAATC 57.479 34.615 0.00 0.00 0.00 1.75
213 215 9.627395 ATCACTGCTATATTCGTGTAATCTTAC 57.373 33.333 0.00 0.00 0.00 2.34
214 216 8.626526 TCACTGCTATATTCGTGTAATCTTACA 58.373 33.333 0.00 0.00 41.06 2.41
235 237 6.817765 ACATGAAGATCCGTGTAATGTTTT 57.182 33.333 0.00 0.00 34.76 2.43
236 238 6.842163 ACATGAAGATCCGTGTAATGTTTTC 58.158 36.000 0.00 0.00 34.76 2.29
242 244 9.887406 GAAGATCCGTGTAATGTTTTCTTTAAA 57.113 29.630 0.00 0.00 0.00 1.52
284 290 6.374053 TGTTTTGTCACTTGATTGAGACTTCA 59.626 34.615 0.00 0.00 32.41 3.02
290 296 7.095060 TGTCACTTGATTGAGACTTCATTAAGC 60.095 37.037 0.00 0.00 36.05 3.09
302 308 4.705507 ACTTCATTAAGCCTCAGTCGACTA 59.294 41.667 19.57 6.17 36.05 2.59
304 310 5.654603 TCATTAAGCCTCAGTCGACTAAA 57.345 39.130 19.57 8.71 0.00 1.85
306 312 6.640518 TCATTAAGCCTCAGTCGACTAAAAT 58.359 36.000 19.57 7.42 0.00 1.82
319 325 3.195661 GACTAAAATCTAGCCACACCCG 58.804 50.000 0.00 0.00 0.00 5.28
324 330 0.686441 ATCTAGCCACACCCGTAGCA 60.686 55.000 0.00 0.00 31.42 3.49
400 409 3.181445 ACATGCACAGGTGAAGGTTTAGA 60.181 43.478 3.10 0.00 26.62 2.10
405 414 4.518970 GCACAGGTGAAGGTTTAGAATTGA 59.481 41.667 3.10 0.00 0.00 2.57
428 437 9.953697 TTGAAAATAAGTACAATACACCACAAC 57.046 29.630 0.00 0.00 0.00 3.32
429 438 8.569641 TGAAAATAAGTACAATACACCACAACC 58.430 33.333 0.00 0.00 0.00 3.77
430 439 7.457024 AAATAAGTACAATACACCACAACCC 57.543 36.000 0.00 0.00 0.00 4.11
431 440 3.428413 AGTACAATACACCACAACCCC 57.572 47.619 0.00 0.00 0.00 4.95
432 441 2.983898 AGTACAATACACCACAACCCCT 59.016 45.455 0.00 0.00 0.00 4.79
433 442 4.169666 AGTACAATACACCACAACCCCTA 58.830 43.478 0.00 0.00 0.00 3.53
434 443 4.598373 AGTACAATACACCACAACCCCTAA 59.402 41.667 0.00 0.00 0.00 2.69
435 444 4.456662 ACAATACACCACAACCCCTAAA 57.543 40.909 0.00 0.00 0.00 1.85
436 445 4.805744 ACAATACACCACAACCCCTAAAA 58.194 39.130 0.00 0.00 0.00 1.52
437 446 4.585581 ACAATACACCACAACCCCTAAAAC 59.414 41.667 0.00 0.00 0.00 2.43
438 447 4.734843 ATACACCACAACCCCTAAAACT 57.265 40.909 0.00 0.00 0.00 2.66
439 448 5.846528 ATACACCACAACCCCTAAAACTA 57.153 39.130 0.00 0.00 0.00 2.24
440 449 4.734843 ACACCACAACCCCTAAAACTAT 57.265 40.909 0.00 0.00 0.00 2.12
441 450 5.069518 ACACCACAACCCCTAAAACTATT 57.930 39.130 0.00 0.00 0.00 1.73
442 451 5.460416 ACACCACAACCCCTAAAACTATTT 58.540 37.500 0.00 0.00 0.00 1.40
443 452 5.900699 ACACCACAACCCCTAAAACTATTTT 59.099 36.000 0.00 0.00 36.67 1.82
444 453 6.384595 ACACCACAACCCCTAAAACTATTTTT 59.615 34.615 0.00 0.00 38.51 1.94
489 498 3.672767 TCGAGGGGTTTGAAGTTAGTC 57.327 47.619 0.00 0.00 0.00 2.59
490 499 2.301009 TCGAGGGGTTTGAAGTTAGTCC 59.699 50.000 0.00 0.00 0.00 3.85
512 521 7.040340 AGTCCTAATACTATGACAATCCTCGTG 60.040 40.741 0.00 0.00 0.00 4.35
515 537 2.893637 ACTATGACAATCCTCGTGTGC 58.106 47.619 0.00 0.00 0.00 4.57
550 572 9.414295 CCCAACGTGTATTTTCGATTCTATATA 57.586 33.333 0.00 0.00 0.00 0.86
603 626 3.488778 AGCTTCCTCTATGGCTTCATG 57.511 47.619 0.00 0.00 35.26 3.07
616 639 0.673644 CTTCATGGCCGTTCTTCCGT 60.674 55.000 0.00 0.00 0.00 4.69
624 647 1.600485 GCCGTTCTTCCGTGAGAAAAA 59.400 47.619 0.00 0.00 37.40 1.94
631 654 4.065088 TCTTCCGTGAGAAAAACATCCAG 58.935 43.478 0.00 0.00 32.88 3.86
634 657 4.312443 TCCGTGAGAAAAACATCCAGTAC 58.688 43.478 0.00 0.00 0.00 2.73
638 661 3.244422 TGAGAAAAACATCCAGTACGGCT 60.244 43.478 0.00 0.00 33.14 5.52
639 662 3.074412 AGAAAAACATCCAGTACGGCTG 58.926 45.455 0.00 0.00 44.63 4.85
790 843 3.498397 TCAGATCAGCGTCTTTTTCCAAC 59.502 43.478 0.00 0.00 0.00 3.77
813 868 8.495148 CAACAACCCTTTAAAATATTCTGCAAC 58.505 33.333 0.00 0.00 0.00 4.17
1773 5508 2.815211 CATATGCCCGCGCGCTAT 60.815 61.111 30.48 19.40 38.08 2.97
1780 5515 2.048597 CCGCGCGCTATAATGGGA 60.049 61.111 30.48 0.00 0.00 4.37
1799 5534 8.866970 AATGGGAAGATAATTGTTTTTGCAAT 57.133 26.923 0.00 0.00 40.43 3.56
1825 5560 5.047377 AGCGGTGGAAAATGTAATTGATGTT 60.047 36.000 0.00 0.00 36.10 2.71
1845 5582 9.559732 TGATGTTTTCATAATAACGATCTCCAT 57.440 29.630 0.00 0.00 41.05 3.41
1897 5634 2.441375 TCTTCCCACTGGTCATGTTTGA 59.559 45.455 0.00 0.00 0.00 2.69
1915 5652 4.659111 TTGACCCGCGAGATCTTAATAA 57.341 40.909 8.23 0.00 0.00 1.40
1939 5676 4.789075 GGCTAGTCAACGCGGCGA 62.789 66.667 30.94 3.21 0.00 5.54
1958 5695 2.227388 CGACGACCACCTAACTTGTACT 59.773 50.000 0.00 0.00 0.00 2.73
1986 5728 3.060615 CGGGTCGACCTCCGTCTT 61.061 66.667 32.52 0.00 41.23 3.01
2007 5749 2.779506 GGAATTGTGGTTCCGTCTTCT 58.220 47.619 0.00 0.00 38.41 2.85
2158 5900 1.007479 ACCAGGCATGAATGTCCCATT 59.993 47.619 0.00 0.00 31.37 3.16
2333 6130 5.580691 TCGTTCTGCTCATAATTGTCGAAAT 59.419 36.000 0.00 0.00 0.00 2.17
2336 6133 7.370836 CGTTCTGCTCATAATTGTCGAAATAAC 59.629 37.037 0.00 0.00 0.00 1.89
2337 6134 7.246674 TCTGCTCATAATTGTCGAAATAACC 57.753 36.000 0.00 0.00 0.00 2.85
2338 6135 7.047891 TCTGCTCATAATTGTCGAAATAACCT 58.952 34.615 0.00 0.00 0.00 3.50
2339 6136 7.224753 TCTGCTCATAATTGTCGAAATAACCTC 59.775 37.037 0.00 0.00 0.00 3.85
2340 6137 6.260050 TGCTCATAATTGTCGAAATAACCTCC 59.740 38.462 0.00 0.00 0.00 4.30
2341 6138 6.483640 GCTCATAATTGTCGAAATAACCTCCT 59.516 38.462 0.00 0.00 0.00 3.69
2342 6139 7.012421 GCTCATAATTGTCGAAATAACCTCCTT 59.988 37.037 0.00 0.00 0.00 3.36
2343 6140 9.542462 CTCATAATTGTCGAAATAACCTCCTTA 57.458 33.333 0.00 0.00 0.00 2.69
2348 6145 9.543783 AATTGTCGAAATAACCTCCTTATACTC 57.456 33.333 0.00 0.00 0.00 2.59
2349 6146 7.649533 TGTCGAAATAACCTCCTTATACTCA 57.350 36.000 0.00 0.00 0.00 3.41
2350 6147 7.486647 TGTCGAAATAACCTCCTTATACTCAC 58.513 38.462 0.00 0.00 0.00 3.51
2351 6148 7.123098 TGTCGAAATAACCTCCTTATACTCACA 59.877 37.037 0.00 0.00 0.00 3.58
2352 6149 8.142551 GTCGAAATAACCTCCTTATACTCACAT 58.857 37.037 0.00 0.00 0.00 3.21
2353 6150 9.358406 TCGAAATAACCTCCTTATACTCACATA 57.642 33.333 0.00 0.00 0.00 2.29
2354 6151 9.976511 CGAAATAACCTCCTTATACTCACATAA 57.023 33.333 0.00 0.00 0.00 1.90
2459 6275 4.493220 CGTAATTGCAAGCTAGCTGAGTTC 60.493 45.833 20.16 6.51 34.99 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.805345 CTTGCTGCTGAACAAGGAGAG 59.195 52.381 0.00 0.00 46.96 3.20
41 43 0.250467 GAGTCCCTTGCTGCTGAACA 60.250 55.000 0.00 0.00 0.00 3.18
49 51 2.529744 GGGTGTGGAGTCCCTTGCT 61.530 63.158 6.74 0.00 40.48 3.91
58 60 2.207229 TGAGGTCGTGGGTGTGGAG 61.207 63.158 0.00 0.00 0.00 3.86
61 63 2.030562 GGTGAGGTCGTGGGTGTG 59.969 66.667 0.00 0.00 0.00 3.82
63 65 3.612681 ACGGTGAGGTCGTGGGTG 61.613 66.667 0.00 0.00 39.55 4.61
79 81 2.093447 CCCACTCAATCAGTCCCTACAC 60.093 54.545 0.00 0.00 30.26 2.90
89 91 1.596934 GTCTCGCCCCACTCAATCA 59.403 57.895 0.00 0.00 0.00 2.57
90 92 1.153349 GGTCTCGCCCCACTCAATC 60.153 63.158 0.00 0.00 0.00 2.67
91 93 2.990479 GGTCTCGCCCCACTCAAT 59.010 61.111 0.00 0.00 0.00 2.57
101 103 0.177373 AAATCGTTAGGGGGTCTCGC 59.823 55.000 0.00 0.00 0.00 5.03
107 109 6.769134 ATTAAGAACAAAATCGTTAGGGGG 57.231 37.500 0.00 0.00 0.00 5.40
108 110 8.726870 TCTATTAAGAACAAAATCGTTAGGGG 57.273 34.615 0.00 0.00 0.00 4.79
122 124 9.732130 AGGCAATCCTGAATATCTATTAAGAAC 57.268 33.333 0.00 0.00 42.34 3.01
133 135 7.521669 AGTTTTAGCTAGGCAATCCTGAATAT 58.478 34.615 0.00 0.00 44.08 1.28
134 136 6.900194 AGTTTTAGCTAGGCAATCCTGAATA 58.100 36.000 0.00 0.00 44.08 1.75
147 149 2.541556 GGTCGGCTGAGTTTTAGCTAG 58.458 52.381 0.00 0.00 40.92 3.42
148 150 1.206371 GGGTCGGCTGAGTTTTAGCTA 59.794 52.381 0.00 0.00 40.92 3.32
149 151 0.036294 GGGTCGGCTGAGTTTTAGCT 60.036 55.000 0.00 0.00 40.92 3.32
150 152 0.321298 TGGGTCGGCTGAGTTTTAGC 60.321 55.000 0.00 0.00 40.41 3.09
151 153 1.275291 TCTGGGTCGGCTGAGTTTTAG 59.725 52.381 0.00 0.00 0.00 1.85
152 154 1.001633 GTCTGGGTCGGCTGAGTTTTA 59.998 52.381 0.00 0.00 0.00 1.52
153 155 0.250338 GTCTGGGTCGGCTGAGTTTT 60.250 55.000 0.00 0.00 0.00 2.43
154 156 1.122019 AGTCTGGGTCGGCTGAGTTT 61.122 55.000 0.00 0.00 0.00 2.66
156 158 0.251653 TAAGTCTGGGTCGGCTGAGT 60.252 55.000 0.00 0.00 0.00 3.41
157 159 0.895530 TTAAGTCTGGGTCGGCTGAG 59.104 55.000 0.00 0.00 0.00 3.35
158 160 0.606604 GTTAAGTCTGGGTCGGCTGA 59.393 55.000 0.00 0.00 0.00 4.26
159 161 0.320374 TGTTAAGTCTGGGTCGGCTG 59.680 55.000 0.00 0.00 0.00 4.85
161 163 1.804748 CTTTGTTAAGTCTGGGTCGGC 59.195 52.381 0.00 0.00 0.00 5.54
162 164 3.121738 ACTTTGTTAAGTCTGGGTCGG 57.878 47.619 0.00 0.00 40.60 4.79
178 180 7.223582 CACGAATATAGCAGTGATTGAGACTTT 59.776 37.037 0.00 0.00 36.79 2.66
185 187 8.526218 AGATTACACGAATATAGCAGTGATTG 57.474 34.615 10.10 0.00 37.95 2.67
191 193 9.626045 TCATGTAAGATTACACGAATATAGCAG 57.374 33.333 7.55 0.00 45.47 4.24
209 211 7.539712 AACATTACACGGATCTTCATGTAAG 57.460 36.000 13.25 0.00 40.00 2.34
213 215 7.076842 AGAAAACATTACACGGATCTTCATG 57.923 36.000 0.00 0.00 0.00 3.07
214 216 7.687941 AAGAAAACATTACACGGATCTTCAT 57.312 32.000 0.00 0.00 0.00 2.57
269 275 6.998968 AGGCTTAATGAAGTCTCAATCAAG 57.001 37.500 0.00 0.00 44.60 3.02
284 290 6.879400 AGATTTTAGTCGACTGAGGCTTAAT 58.121 36.000 28.12 15.07 0.00 1.40
290 296 4.098044 TGGCTAGATTTTAGTCGACTGAGG 59.902 45.833 28.12 9.84 0.00 3.86
302 308 3.261981 CTACGGGTGTGGCTAGATTTT 57.738 47.619 0.00 0.00 0.00 1.82
319 325 7.031975 AGCATCTTTCTTTTGCTAATTGCTAC 58.968 34.615 0.00 0.00 44.51 3.58
376 382 0.473755 ACCTTCACCTGTGCATGTCA 59.526 50.000 0.00 0.00 0.00 3.58
405 414 7.039574 GGGGTTGTGGTGTATTGTACTTATTTT 60.040 37.037 0.00 0.00 0.00 1.82
415 424 4.830600 AGTTTTAGGGGTTGTGGTGTATTG 59.169 41.667 0.00 0.00 0.00 1.90
446 455 9.034800 TCGAATAGTTTTAGGAGTTTACCCTAA 57.965 33.333 0.00 0.00 42.68 2.69
447 456 8.593945 TCGAATAGTTTTAGGAGTTTACCCTA 57.406 34.615 0.00 0.00 35.30 3.53
448 457 7.364497 CCTCGAATAGTTTTAGGAGTTTACCCT 60.364 40.741 0.00 0.00 37.80 4.34
449 458 6.760298 CCTCGAATAGTTTTAGGAGTTTACCC 59.240 42.308 0.00 0.00 0.00 3.69
450 459 6.760298 CCCTCGAATAGTTTTAGGAGTTTACC 59.240 42.308 0.00 0.00 0.00 2.85
451 460 6.760298 CCCCTCGAATAGTTTTAGGAGTTTAC 59.240 42.308 0.00 0.00 0.00 2.01
452 461 6.441604 ACCCCTCGAATAGTTTTAGGAGTTTA 59.558 38.462 0.00 0.00 0.00 2.01
453 462 5.250082 ACCCCTCGAATAGTTTTAGGAGTTT 59.750 40.000 0.00 0.00 0.00 2.66
469 478 2.301009 GGACTAACTTCAAACCCCTCGA 59.699 50.000 0.00 0.00 0.00 4.04
470 479 2.302157 AGGACTAACTTCAAACCCCTCG 59.698 50.000 0.00 0.00 0.00 4.63
489 498 6.863645 CACACGAGGATTGTCATAGTATTAGG 59.136 42.308 0.00 0.00 0.00 2.69
490 499 6.363626 GCACACGAGGATTGTCATAGTATTAG 59.636 42.308 0.00 0.00 0.00 1.73
512 521 2.625823 CGTTGGGACATGGTGGCAC 61.626 63.158 9.70 9.70 39.30 5.01
515 537 0.035598 TACACGTTGGGACATGGTGG 59.964 55.000 0.00 0.00 43.23 4.61
550 572 7.661847 AGGTCGAAAGAAAAAGAATAGACACAT 59.338 33.333 0.00 0.00 45.01 3.21
551 573 6.990349 AGGTCGAAAGAAAAAGAATAGACACA 59.010 34.615 0.00 0.00 45.01 3.72
552 574 7.291567 CAGGTCGAAAGAAAAAGAATAGACAC 58.708 38.462 0.00 0.00 45.01 3.67
555 577 5.995282 TGCAGGTCGAAAGAAAAAGAATAGA 59.005 36.000 0.00 0.00 45.01 1.98
596 619 1.803289 GGAAGAACGGCCATGAAGC 59.197 57.895 2.24 0.00 0.00 3.86
599 622 1.375396 CACGGAAGAACGGCCATGA 60.375 57.895 2.24 0.00 38.39 3.07
603 626 0.601841 TTTCTCACGGAAGAACGGCC 60.602 55.000 0.00 0.00 35.06 6.13
616 639 3.071479 GCCGTACTGGATGTTTTTCTCA 58.929 45.455 7.77 0.00 42.00 3.27
631 654 5.163913 CGTAGGTAGATATGTACAGCCGTAC 60.164 48.000 11.75 3.14 46.94 3.67
634 657 3.750130 ACGTAGGTAGATATGTACAGCCG 59.250 47.826 11.75 11.14 0.00 5.52
638 661 7.543520 CGATACTGACGTAGGTAGATATGTACA 59.456 40.741 11.75 0.00 0.00 2.90
639 662 7.757173 TCGATACTGACGTAGGTAGATATGTAC 59.243 40.741 1.36 1.36 0.00 2.90
778 831 7.908827 TTTTAAAGGGTTGTTGGAAAAAGAC 57.091 32.000 0.00 0.00 0.00 3.01
790 843 8.600449 TTGTTGCAGAATATTTTAAAGGGTTG 57.400 30.769 0.00 0.00 0.00 3.77
901 1018 0.251341 ATGGGTGGCTGGTGAAGAAC 60.251 55.000 0.00 0.00 0.00 3.01
989 1117 4.908687 TCGCCATTGCCGATCGGG 62.909 66.667 33.98 18.62 39.58 5.14
1554 1716 4.020617 CTGCCGCCCTTGACCTCA 62.021 66.667 0.00 0.00 0.00 3.86
1646 5380 0.984995 GAAGTACTTCCCCTGGTGCT 59.015 55.000 22.74 0.00 33.64 4.40
1766 5501 5.351465 ACAATTATCTTCCCATTATAGCGCG 59.649 40.000 0.00 0.00 0.00 6.86
1773 5508 9.956640 ATTGCAAAAACAATTATCTTCCCATTA 57.043 25.926 1.71 0.00 36.91 1.90
1780 5515 7.602265 ACCGCTTATTGCAAAAACAATTATCTT 59.398 29.630 1.71 0.00 40.64 2.40
1799 5534 6.151985 ACATCAATTACATTTTCCACCGCTTA 59.848 34.615 0.00 0.00 0.00 3.09
1825 5560 6.710295 CCACCATGGAGATCGTTATTATGAAA 59.290 38.462 21.47 0.00 40.96 2.69
1833 5570 1.484653 CCACCACCATGGAGATCGTTA 59.515 52.381 21.47 0.00 43.02 3.18
1845 5582 2.818169 GCTCTGTCACCCACCACCA 61.818 63.158 0.00 0.00 0.00 4.17
1897 5634 3.323979 ACCATTATTAAGATCTCGCGGGT 59.676 43.478 5.57 0.00 0.00 5.28
1915 5652 1.602237 CGTTGACTAGCCCCACCAT 59.398 57.895 0.00 0.00 0.00 3.55
1939 5676 4.677673 AAAGTACAAGTTAGGTGGTCGT 57.322 40.909 0.00 0.00 0.00 4.34
2007 5749 3.922640 GCCGCCCAGCAACCAAAA 61.923 61.111 0.00 0.00 0.00 2.44
2333 6130 7.508296 GGAGGTTATGTGAGTATAAGGAGGTTA 59.492 40.741 0.00 0.00 0.00 2.85
2336 6133 6.078664 AGGAGGTTATGTGAGTATAAGGAGG 58.921 44.000 0.00 0.00 0.00 4.30
2337 6134 7.604657 AAGGAGGTTATGTGAGTATAAGGAG 57.395 40.000 0.00 0.00 0.00 3.69
2338 6135 9.670442 AATAAGGAGGTTATGTGAGTATAAGGA 57.330 33.333 0.00 0.00 31.22 3.36
2344 6141 9.931698 TCTAGAAATAAGGAGGTTATGTGAGTA 57.068 33.333 0.00 0.00 31.22 2.59
2345 6142 8.697292 GTCTAGAAATAAGGAGGTTATGTGAGT 58.303 37.037 0.00 0.00 31.22 3.41
2346 6143 8.696374 TGTCTAGAAATAAGGAGGTTATGTGAG 58.304 37.037 0.00 0.00 31.22 3.51
2347 6144 8.603898 TGTCTAGAAATAAGGAGGTTATGTGA 57.396 34.615 0.00 0.00 31.22 3.58
2348 6145 9.099454 GTTGTCTAGAAATAAGGAGGTTATGTG 57.901 37.037 0.00 0.00 31.22 3.21
2349 6146 9.047947 AGTTGTCTAGAAATAAGGAGGTTATGT 57.952 33.333 0.00 0.00 31.22 2.29
2350 6147 9.892130 AAGTTGTCTAGAAATAAGGAGGTTATG 57.108 33.333 0.00 0.00 31.22 1.90
2353 6150 9.892130 CATAAGTTGTCTAGAAATAAGGAGGTT 57.108 33.333 0.00 0.00 0.00 3.50
2354 6151 8.487028 CCATAAGTTGTCTAGAAATAAGGAGGT 58.513 37.037 0.00 0.00 0.00 3.85
2427 6243 4.770795 AGCTTGCAATTACGATAGGAACT 58.229 39.130 0.00 0.00 45.47 3.01
2459 6275 0.875728 TTGTGCCCACGGATAAAACG 59.124 50.000 0.00 0.00 37.36 3.60


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

AutoCloner maintained by Alex Coulton.