Multiple sequence alignment - TraesCS2D01G142300

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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 TraesCS2D01G142300 chr2D 100.000 4674 0 0 1 4674 83838571 83843244 0.000000e+00 8632.0
1 TraesCS2D01G142300 chr2D 88.893 2485 254 17 1418 3892 85685738 85683266 0.000000e+00 3040.0
2 TraesCS2D01G142300 chr2D 87.678 1891 218 8 1531 3408 84927179 84925291 0.000000e+00 2187.0
3 TraesCS2D01G142300 chr2D 79.743 622 74 26 907 1490 84769671 84769064 2.030000e-108 403.0
4 TraesCS2D01G142300 chr2D 83.480 454 48 12 915 1349 85394908 85394463 9.420000e-107 398.0
5 TraesCS2D01G142300 chr2D 82.135 459 54 16 925 1368 85686304 85685859 7.390000e-98 368.0
6 TraesCS2D01G142300 chr2D 81.818 187 26 7 340 523 7217155 7216974 2.910000e-32 150.0
7 TraesCS2D01G142300 chr2B 90.843 4554 269 70 1 4467 135706585 135711077 0.000000e+00 5963.0
8 TraesCS2D01G142300 chr2B 85.090 2401 276 47 1377 3754 136627720 136625379 0.000000e+00 2375.0
9 TraesCS2D01G142300 chr2B 82.159 2158 312 43 1039 3152 167494074 167496202 0.000000e+00 1784.0
10 TraesCS2D01G142300 chr2B 80.665 1805 316 23 1363 3152 136633939 136632153 0.000000e+00 1369.0
11 TraesCS2D01G142300 chr2B 79.577 284 41 15 62 337 536623579 536623305 2.220000e-43 187.0
12 TraesCS2D01G142300 chr2A 95.395 3409 144 10 807 4211 84606566 84609965 0.000000e+00 5413.0
13 TraesCS2D01G142300 chr2A 87.342 2378 271 21 1655 4014 85805502 85803137 0.000000e+00 2697.0
14 TraesCS2D01G142300 chr2A 87.042 2377 278 21 1655 4014 85921409 85919046 0.000000e+00 2656.0
15 TraesCS2D01G142300 chr2A 87.522 2244 249 22 1791 4014 86052253 86050021 0.000000e+00 2564.0
16 TraesCS2D01G142300 chr2A 84.961 2294 294 30 1537 3813 85603695 85601436 0.000000e+00 2278.0
17 TraesCS2D01G142300 chr2A 83.878 1805 253 29 1371 3152 118477230 118479019 0.000000e+00 1687.0
18 TraesCS2D01G142300 chr2A 78.771 2115 391 39 1363 3451 85608413 85606331 0.000000e+00 1365.0
19 TraesCS2D01G142300 chr2A 93.856 472 23 4 4204 4674 84610591 84611057 0.000000e+00 706.0
20 TraesCS2D01G142300 chr2A 78.478 381 65 12 1035 1410 118476828 118477196 2.810000e-57 233.0
21 TraesCS2D01G142300 chr2A 89.844 128 10 2 1 126 84606429 84606555 1.350000e-35 161.0
22 TraesCS2D01G142300 chr2A 88.525 122 13 1 4487 4607 543307218 543307097 3.770000e-31 147.0
23 TraesCS2D01G142300 chr2A 86.555 119 12 2 895 1013 83989446 83989560 1.370000e-25 128.0
24 TraesCS2D01G142300 chr2A 80.423 189 17 6 4488 4674 751527258 751527428 4.910000e-25 126.0
25 TraesCS2D01G142300 chr2A 83.333 120 19 1 1226 1345 83989572 83989690 4.940000e-20 110.0
26 TraesCS2D01G142300 chr4A 87.342 2378 271 21 1655 4014 349801028 349798663 0.000000e+00 2697.0
27 TraesCS2D01G142300 chr4A 86.598 97 10 3 62 158 649548207 649548114 2.300000e-18 104.0
28 TraesCS2D01G142300 chr7A 79.049 1556 280 33 1198 2737 571323417 571321892 0.000000e+00 1026.0
29 TraesCS2D01G142300 chr7A 85.507 207 25 3 1144 1349 571279949 571279747 1.320000e-50 211.0
30 TraesCS2D01G142300 chr7A 86.264 182 22 2 4489 4669 637981503 637981324 1.330000e-45 195.0
31 TraesCS2D01G142300 chr7A 83.810 105 12 4 61 163 24963408 24963509 1.380000e-15 95.3
32 TraesCS2D01G142300 chr5A 88.830 188 20 1 4488 4674 42098204 42098391 3.640000e-56 230.0
33 TraesCS2D01G142300 chr5A 87.634 186 22 1 4490 4674 138171119 138171304 1.020000e-51 215.0
34 TraesCS2D01G142300 chr5A 91.111 90 6 2 61 150 365962116 365962203 2.280000e-23 121.0
35 TraesCS2D01G142300 chr5A 79.042 167 28 5 344 509 540212380 540212220 1.780000e-19 108.0
36 TraesCS2D01G142300 chr6A 86.631 187 24 1 4489 4674 428691548 428691362 6.130000e-49 206.0
37 TraesCS2D01G142300 chr6A 85.106 188 26 2 4483 4669 597944274 597944088 1.720000e-44 191.0
38 TraesCS2D01G142300 chr6A 81.283 187 30 4 340 523 77427154 77427338 3.770000e-31 147.0
39 TraesCS2D01G142300 chr6A 89.583 96 10 0 4579 4674 97031202 97031107 6.350000e-24 122.0
40 TraesCS2D01G142300 chr3A 83.243 185 24 5 344 524 700743412 700743593 3.740000e-36 163.0
41 TraesCS2D01G142300 chr6B 84.800 125 19 0 4544 4668 221714288 221714412 4.910000e-25 126.0
42 TraesCS2D01G142300 chr6B 87.778 90 8 3 62 151 277804384 277804298 8.270000e-18 102.0
43 TraesCS2D01G142300 chr1A 85.833 120 12 4 340 456 589958995 589959112 6.350000e-24 122.0
44 TraesCS2D01G142300 chr1A 100.000 32 0 0 564 595 277640583 277640552 5.050000e-05 60.2
45 TraesCS2D01G142300 chr5D 85.593 118 12 3 64 181 221861129 221861017 8.220000e-23 119.0
46 TraesCS2D01G142300 chr5D 77.348 181 33 7 344 523 425983115 425982942 2.980000e-17 100.0
47 TraesCS2D01G142300 chr3B 78.378 185 37 3 340 523 12822911 12823093 2.950000e-22 117.0
48 TraesCS2D01G142300 chr3D 78.571 140 14 12 67 204 436039320 436039445 1.390000e-10 78.7
49 TraesCS2D01G142300 chr3D 95.652 46 2 0 353 398 156701179 156701134 1.800000e-09 75.0
50 TraesCS2D01G142300 chr1D 100.000 32 0 0 564 595 216726406 216726375 5.050000e-05 60.2
51 TraesCS2D01G142300 chr1B 100.000 32 0 0 564 595 310366831 310366800 5.050000e-05 60.2


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 TraesCS2D01G142300 chr2D 83838571 83843244 4673 False 8632.000000 8632 100.000000 1 4674 1 chr2D.!!$F1 4673
1 TraesCS2D01G142300 chr2D 84925291 84927179 1888 True 2187.000000 2187 87.678000 1531 3408 1 chr2D.!!$R3 1877
2 TraesCS2D01G142300 chr2D 85683266 85686304 3038 True 1704.000000 3040 85.514000 925 3892 2 chr2D.!!$R5 2967
3 TraesCS2D01G142300 chr2D 84769064 84769671 607 True 403.000000 403 79.743000 907 1490 1 chr2D.!!$R2 583
4 TraesCS2D01G142300 chr2B 135706585 135711077 4492 False 5963.000000 5963 90.843000 1 4467 1 chr2B.!!$F1 4466
5 TraesCS2D01G142300 chr2B 136625379 136627720 2341 True 2375.000000 2375 85.090000 1377 3754 1 chr2B.!!$R1 2377
6 TraesCS2D01G142300 chr2B 167494074 167496202 2128 False 1784.000000 1784 82.159000 1039 3152 1 chr2B.!!$F2 2113
7 TraesCS2D01G142300 chr2B 136632153 136633939 1786 True 1369.000000 1369 80.665000 1363 3152 1 chr2B.!!$R2 1789
8 TraesCS2D01G142300 chr2A 85803137 85805502 2365 True 2697.000000 2697 87.342000 1655 4014 1 chr2A.!!$R1 2359
9 TraesCS2D01G142300 chr2A 85919046 85921409 2363 True 2656.000000 2656 87.042000 1655 4014 1 chr2A.!!$R2 2359
10 TraesCS2D01G142300 chr2A 86050021 86052253 2232 True 2564.000000 2564 87.522000 1791 4014 1 chr2A.!!$R3 2223
11 TraesCS2D01G142300 chr2A 84606429 84611057 4628 False 2093.333333 5413 93.031667 1 4674 3 chr2A.!!$F3 4673
12 TraesCS2D01G142300 chr2A 85601436 85608413 6977 True 1821.500000 2278 81.866000 1363 3813 2 chr2A.!!$R5 2450
13 TraesCS2D01G142300 chr2A 118476828 118479019 2191 False 960.000000 1687 81.178000 1035 3152 2 chr2A.!!$F4 2117
14 TraesCS2D01G142300 chr4A 349798663 349801028 2365 True 2697.000000 2697 87.342000 1655 4014 1 chr4A.!!$R1 2359
15 TraesCS2D01G142300 chr7A 571321892 571323417 1525 True 1026.000000 1026 79.049000 1198 2737 1 chr7A.!!$R2 1539

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
834 852 0.036010 ATTTCTCTGTGGCGGTCTGG 60.036 55.000 0.00 0.00 0.00 3.86 F
1351 1409 0.472352 TTTCACTGTACCCGTCCCCT 60.472 55.000 0.00 0.00 0.00 4.79 F
1495 4801 1.376037 GTTTCTCAGCGTGGAGGGG 60.376 63.158 5.78 0.00 35.58 4.79 F
2701 6032 1.419762 ACTTCCACATATATGGCGGCA 59.580 47.619 16.34 16.34 39.85 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 5543 1.068434 ACTGTCCAAATGCCCAAAACG 59.932 47.619 0.00 0.00 0.00 3.60 R
2908 6242 0.918258 TGCCATACCTTGCTCCATCA 59.082 50.000 0.00 0.00 0.00 3.07 R
2971 6305 2.731572 AGGCATGTGATCCCTTTCAAG 58.268 47.619 0.00 0.00 0.00 3.02 R
3821 7173 0.892755 CCAGTGCAACATGGAAGCAT 59.107 50.000 11.29 0.67 41.43 3.79 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
185 188 2.947890 GCGCGCTATGTGATCAGGC 61.948 63.158 26.67 0.00 0.00 4.85
224 227 1.198759 ACTGTACCTGGCCGGACATT 61.199 55.000 12.52 2.84 36.31 2.71
225 228 0.462047 CTGTACCTGGCCGGACATTC 60.462 60.000 12.52 1.85 36.31 2.67
226 229 1.520787 GTACCTGGCCGGACATTCG 60.521 63.158 12.52 3.52 36.31 3.34
227 230 1.683025 TACCTGGCCGGACATTCGA 60.683 57.895 12.52 0.00 36.31 3.71
228 231 1.672854 TACCTGGCCGGACATTCGAG 61.673 60.000 12.52 0.00 36.31 4.04
229 232 2.202932 CTGGCCGGACATTCGAGG 60.203 66.667 12.52 0.00 0.00 4.63
231 234 3.467226 GGCCGGACATTCGAGGGA 61.467 66.667 5.05 0.00 0.00 4.20
234 237 0.391597 GCCGGACATTCGAGGGATAA 59.608 55.000 5.05 0.00 0.00 1.75
235 238 1.872653 GCCGGACATTCGAGGGATAAC 60.873 57.143 5.05 0.00 0.00 1.89
237 240 2.889045 CCGGACATTCGAGGGATAACTA 59.111 50.000 0.00 0.00 0.00 2.24
240 243 4.618460 CGGACATTCGAGGGATAACTATGG 60.618 50.000 0.00 0.00 0.00 2.74
242 245 5.187967 GGACATTCGAGGGATAACTATGGAT 59.812 44.000 0.00 0.00 0.00 3.41
243 246 6.042638 ACATTCGAGGGATAACTATGGATG 57.957 41.667 0.00 0.00 0.00 3.51
244 247 5.046304 ACATTCGAGGGATAACTATGGATGG 60.046 44.000 0.00 0.00 0.00 3.51
246 249 2.093447 CGAGGGATAACTATGGATGGCC 60.093 54.545 0.00 0.00 0.00 5.36
258 261 0.326264 GGATGGCCGGCTCTCATATT 59.674 55.000 28.56 0.30 0.00 1.28
263 266 1.344763 GGCCGGCTCTCATATTAGTGT 59.655 52.381 28.56 0.00 0.00 3.55
264 267 2.408050 GCCGGCTCTCATATTAGTGTG 58.592 52.381 22.15 0.00 0.00 3.82
276 279 3.863142 ATTAGTGTGTGTAGACGGTCC 57.137 47.619 4.14 0.00 0.00 4.46
348 351 2.024176 TGCCCTAATCTCGTTTGCTC 57.976 50.000 0.00 0.00 0.00 4.26
394 397 1.133761 TCTAGGGGAGGAGTGATGACG 60.134 57.143 0.00 0.00 0.00 4.35
409 412 1.869774 TGACGATGGCATCTATGTGC 58.130 50.000 23.97 10.01 44.31 4.57
422 425 0.108186 TATGTGCTGTCTTGGCGAGG 60.108 55.000 0.97 0.00 0.00 4.63
456 459 6.402875 GGAATGGTGTACGTGAGGTTTTTATC 60.403 42.308 0.00 0.00 0.00 1.75
480 483 1.406341 GCCACTCAGCCGGTTGTTATA 60.406 52.381 18.51 0.00 0.00 0.98
516 519 9.932207 TGATTTTTCATAATCAACTGAGCAATT 57.068 25.926 0.00 0.00 40.55 2.32
526 529 4.889409 TCAACTGAGCAATTTGAGTTCCTT 59.111 37.500 0.00 0.00 0.00 3.36
533 536 6.980397 TGAGCAATTTGAGTTCCTTTTTCTTC 59.020 34.615 0.00 0.00 0.00 2.87
553 556 9.850628 TTTCTTCTTAATGAATGCAGAATTCTG 57.149 29.630 27.82 27.82 44.42 3.02
556 559 7.926674 TCTTAATGAATGCAGAATTCTGTCA 57.073 32.000 30.88 27.53 44.42 3.58
557 560 8.515695 TCTTAATGAATGCAGAATTCTGTCAT 57.484 30.769 30.88 28.26 44.42 3.06
586 595 8.454106 AGAAAAATGTTGAGAACCTGAATATCG 58.546 33.333 0.00 0.00 0.00 2.92
604 613 2.441410 TCGCAATTGTATGGAAGGCAA 58.559 42.857 7.40 0.00 0.00 4.52
605 614 3.023119 TCGCAATTGTATGGAAGGCAAT 58.977 40.909 7.40 0.00 34.69 3.56
606 615 3.117794 CGCAATTGTATGGAAGGCAATG 58.882 45.455 7.40 0.00 33.68 2.82
653 662 3.751893 GCTTCAGGGGTAATATGGCATGT 60.752 47.826 10.98 0.00 0.00 3.21
699 712 7.147689 TGCCACTATATTCATTGCTGGATTTTT 60.148 33.333 0.00 0.00 0.00 1.94
753 769 8.672815 TGATTTGGAACTTGAATTTGTTTTTCC 58.327 29.630 0.00 0.00 33.10 3.13
759 777 8.726068 GGAACTTGAATTTGTTTTTCCTTTTCA 58.274 29.630 0.00 0.00 0.00 2.69
770 788 2.038863 TCCTTTTCAGGGGTCTGCTA 57.961 50.000 0.00 0.00 41.25 3.49
778 796 7.559897 CCTTTTCAGGGGTCTGCTATTTTATTA 59.440 37.037 0.00 0.00 40.69 0.98
783 801 7.347222 TCAGGGGTCTGCTATTTTATTAAGAGA 59.653 37.037 0.00 0.00 40.69 3.10
784 802 7.659390 CAGGGGTCTGCTATTTTATTAAGAGAG 59.341 40.741 0.00 0.00 33.86 3.20
786 804 7.993758 GGGGTCTGCTATTTTATTAAGAGAGTT 59.006 37.037 0.00 0.00 0.00 3.01
822 840 6.540551 GGAGAGCGGATTTCTTTTATTTCTCT 59.459 38.462 0.00 0.00 0.00 3.10
830 848 4.015872 TCTTTTATTTCTCTGTGGCGGT 57.984 40.909 0.00 0.00 0.00 5.68
832 850 3.695830 TTTATTTCTCTGTGGCGGTCT 57.304 42.857 0.00 0.00 0.00 3.85
833 851 2.672961 TATTTCTCTGTGGCGGTCTG 57.327 50.000 0.00 0.00 0.00 3.51
834 852 0.036010 ATTTCTCTGTGGCGGTCTGG 60.036 55.000 0.00 0.00 0.00 3.86
835 853 2.731691 TTTCTCTGTGGCGGTCTGGC 62.732 60.000 0.00 0.00 45.12 4.85
907 927 2.366916 CCTTCCTACAGCCCAGATACAG 59.633 54.545 0.00 0.00 0.00 2.74
909 929 1.062886 TCCTACAGCCCAGATACAGCT 60.063 52.381 0.00 0.00 37.32 4.24
1285 1335 3.168528 GGAAGGCCCCGGCTATGA 61.169 66.667 0.00 0.00 37.50 2.15
1351 1409 0.472352 TTTCACTGTACCCGTCCCCT 60.472 55.000 0.00 0.00 0.00 4.79
1356 1417 2.226149 CTGTACCCGTCCCCTCTCCT 62.226 65.000 0.00 0.00 0.00 3.69
1405 4637 2.222976 CGTCTGATTCTGTTGCATCTGC 60.223 50.000 0.00 0.00 42.50 4.26
1495 4801 1.376037 GTTTCTCAGCGTGGAGGGG 60.376 63.158 5.78 0.00 35.58 4.79
1506 4812 2.222027 CGTGGAGGGGAATGATTTAGC 58.778 52.381 0.00 0.00 0.00 3.09
2206 5532 4.215613 GCAGGGTGTAAAGATTTTCGAGTT 59.784 41.667 0.00 0.00 0.00 3.01
2214 5540 2.771089 AGATTTTCGAGTTCTGCAGCA 58.229 42.857 9.47 0.00 0.00 4.41
2217 5543 4.331168 AGATTTTCGAGTTCTGCAGCATAC 59.669 41.667 9.47 7.08 0.00 2.39
2533 5864 1.425412 GTGAACGACAGTGGCGTAAT 58.575 50.000 27.06 10.58 41.75 1.89
2683 6014 2.500392 AGGAGCTAGACGAGTTGACT 57.500 50.000 0.00 0.00 0.00 3.41
2700 6031 2.076863 GACTTCCACATATATGGCGGC 58.923 52.381 16.96 0.00 39.85 6.53
2701 6032 1.419762 ACTTCCACATATATGGCGGCA 59.580 47.619 16.34 16.34 39.85 5.69
2720 6051 4.634004 CGGCAAAAGAACATGATGGTAGTA 59.366 41.667 0.00 0.00 0.00 1.82
2770 6101 2.749441 GTGGCAGAGCTTGAGGCC 60.749 66.667 10.78 10.78 46.58 5.19
2772 6103 3.726144 GGCAGAGCTTGAGGCCCT 61.726 66.667 0.00 0.00 43.05 5.19
2816 6150 2.507471 GTGGAGGATGTGAAGGAAGGAT 59.493 50.000 0.00 0.00 0.00 3.24
2827 6161 3.390967 TGAAGGAAGGATATCATGCCGAA 59.609 43.478 8.78 0.00 0.00 4.30
2858 6192 7.800847 GCAACAGAAAGATAACAAAGTTCTCTC 59.199 37.037 0.00 0.00 0.00 3.20
2946 6280 2.747467 GCATCATGGGCAGTGATACAGT 60.747 50.000 0.00 0.00 34.68 3.55
2969 6303 7.814587 CAGTTGATGCATATAAGAACGATCCTA 59.185 37.037 0.00 0.00 0.00 2.94
2971 6305 8.812329 GTTGATGCATATAAGAACGATCCTATC 58.188 37.037 0.00 0.00 0.00 2.08
3172 6506 6.308041 CGCATAGATTTATGTACACATACGCT 59.692 38.462 0.00 3.25 38.44 5.07
3259 6594 3.179443 GTGACTGTTCACCTGAAGACA 57.821 47.619 0.00 0.00 45.77 3.41
3518 6866 5.395657 CCACACTGCTTCAGAGGTATCATAA 60.396 44.000 0.29 0.00 35.18 1.90
3675 7026 3.314635 GCAGGCAATCATGAAACCTAGAG 59.685 47.826 12.66 4.54 0.00 2.43
3730 7081 8.945481 ATTCTAATCTCATCTGTCAAACTCTG 57.055 34.615 0.00 0.00 0.00 3.35
3771 7122 3.234596 GCTTAGTATGCGTTTTAGCCG 57.765 47.619 0.00 0.00 36.02 5.52
3772 7123 2.861935 GCTTAGTATGCGTTTTAGCCGA 59.138 45.455 0.00 0.00 36.02 5.54
3773 7124 3.493503 GCTTAGTATGCGTTTTAGCCGAT 59.506 43.478 0.00 0.00 36.02 4.18
3774 7125 4.608445 GCTTAGTATGCGTTTTAGCCGATG 60.608 45.833 0.00 0.00 36.02 3.84
3776 7127 3.527533 AGTATGCGTTTTAGCCGATGAA 58.472 40.909 0.00 0.00 36.02 2.57
3777 7128 3.555956 AGTATGCGTTTTAGCCGATGAAG 59.444 43.478 0.00 0.00 36.02 3.02
3779 7130 2.147958 TGCGTTTTAGCCGATGAAGTT 58.852 42.857 0.00 0.00 36.02 2.66
3820 7172 5.041287 TCTGAACCTCTGTTATTATTCGCG 58.959 41.667 0.00 0.00 33.97 5.87
3821 7173 5.001237 TGAACCTCTGTTATTATTCGCGA 57.999 39.130 3.71 3.71 33.97 5.87
3849 7201 0.736053 TGTTGCACTGGAAACCGAAC 59.264 50.000 0.00 0.00 30.86 3.95
3859 7211 6.759827 GCACTGGAAACCGAACTTCTTATATA 59.240 38.462 0.00 0.00 0.00 0.86
3995 7347 4.441792 TGATAGTGTGACATGCATACCAC 58.558 43.478 18.46 18.46 39.21 4.16
4030 7382 5.931441 AATTGTCAGTAGAAGCACTTGAC 57.069 39.130 8.05 8.05 32.18 3.18
4071 7423 9.899661 TTAGTATATCAAGCAACCATTTACTGT 57.100 29.630 0.00 0.00 0.00 3.55
4121 7473 5.237815 CACTGCTCAGGATTACAAACTACA 58.762 41.667 1.66 0.00 0.00 2.74
4487 8515 8.938801 ATTTAAAATTTGCCCCTCAATTCTTT 57.061 26.923 0.00 0.00 34.12 2.52
4528 8556 7.911130 AAGAGATTCTCATTACTCATGGAGA 57.089 36.000 15.83 0.00 33.07 3.71
4534 8562 6.707440 TCTCATTACTCATGGAGACTTCTC 57.293 41.667 0.00 0.00 42.14 2.87
4535 8563 5.298026 TCTCATTACTCATGGAGACTTCTCG 59.702 44.000 0.00 0.00 43.76 4.04
4537 8565 2.223803 ACTCATGGAGACTTCTCGGT 57.776 50.000 0.00 0.00 43.76 4.69
4542 8570 4.278310 TCATGGAGACTTCTCGGTCATTA 58.722 43.478 0.13 0.00 43.76 1.90
4552 8580 7.760340 AGACTTCTCGGTCATTATCAAGTTTAC 59.240 37.037 0.00 0.00 38.57 2.01
4556 8584 7.156000 TCTCGGTCATTATCAAGTTTACAACA 58.844 34.615 0.00 0.00 0.00 3.33
4569 8597 8.293867 TCAAGTTTACAACAAAATCTATTCCCG 58.706 33.333 0.00 0.00 0.00 5.14
4590 8618 2.332063 ATGTGGCCATACTGCAGTAC 57.668 50.000 28.28 17.51 32.72 2.73
4599 8627 1.601419 TACTGCAGTACGGGGAGTGC 61.601 60.000 22.67 3.70 44.60 4.40
4602 8630 1.141234 GCAGTACGGGGAGTGCTAC 59.859 63.158 3.42 0.00 44.09 3.58
4610 8638 2.103736 GGAGTGCTACGGCCGTAC 59.896 66.667 33.45 26.17 37.74 3.67
4645 8673 5.142061 TGACTAACTTTATTCTGCGACCA 57.858 39.130 0.00 0.00 0.00 4.02
4659 8687 3.271729 TGCGACCAACAACAAAGAGTAA 58.728 40.909 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.332819 GGTCACAAAAGAATATCAGTCCGG 59.667 45.833 0.00 0.00 0.00 5.14
78 79 4.032900 CGGTCACAAAAGAATATCAGTCCG 59.967 45.833 0.00 0.00 0.00 4.79
134 137 3.071892 ACAGTACCCGATCAGAACCAAAA 59.928 43.478 0.00 0.00 0.00 2.44
135 138 2.635915 ACAGTACCCGATCAGAACCAAA 59.364 45.455 0.00 0.00 0.00 3.28
145 148 2.623889 GCTAGATCACACAGTACCCGAT 59.376 50.000 0.00 0.00 0.00 4.18
185 188 9.993881 GTACAGTCAATTCGAAATTCAAATTTG 57.006 29.630 12.15 12.15 38.64 2.32
224 227 2.832129 GCCATCCATAGTTATCCCTCGA 59.168 50.000 0.00 0.00 0.00 4.04
225 228 2.093447 GGCCATCCATAGTTATCCCTCG 60.093 54.545 0.00 0.00 0.00 4.63
226 229 2.093447 CGGCCATCCATAGTTATCCCTC 60.093 54.545 2.24 0.00 0.00 4.30
227 230 1.909302 CGGCCATCCATAGTTATCCCT 59.091 52.381 2.24 0.00 0.00 4.20
228 231 1.065418 CCGGCCATCCATAGTTATCCC 60.065 57.143 2.24 0.00 0.00 3.85
229 232 1.679032 GCCGGCCATCCATAGTTATCC 60.679 57.143 18.11 0.00 0.00 2.59
231 234 1.279271 GAGCCGGCCATCCATAGTTAT 59.721 52.381 26.15 0.00 0.00 1.89
234 237 1.460305 AGAGCCGGCCATCCATAGT 60.460 57.895 26.15 0.00 0.00 2.12
235 238 1.294780 GAGAGCCGGCCATCCATAG 59.705 63.158 26.15 0.00 0.00 2.23
237 240 0.837691 TATGAGAGCCGGCCATCCAT 60.838 55.000 26.15 22.24 0.00 3.41
240 243 2.234908 ACTAATATGAGAGCCGGCCATC 59.765 50.000 26.15 21.97 0.00 3.51
242 245 1.344438 CACTAATATGAGAGCCGGCCA 59.656 52.381 26.15 15.43 0.00 5.36
243 246 1.344763 ACACTAATATGAGAGCCGGCC 59.655 52.381 26.15 15.34 0.00 6.13
244 247 2.224066 ACACACTAATATGAGAGCCGGC 60.224 50.000 21.89 21.89 0.00 6.13
246 249 4.046938 ACACACACTAATATGAGAGCCG 57.953 45.455 0.00 0.00 0.00 5.52
258 261 1.538047 GGGACCGTCTACACACACTA 58.462 55.000 0.00 0.00 0.00 2.74
276 279 4.373116 CGTCTGTGGACCGGTGGG 62.373 72.222 14.63 0.00 39.15 4.61
348 351 4.778213 TCATTCCCATCCCTAAACTCTG 57.222 45.455 0.00 0.00 0.00 3.35
422 425 2.092323 GTACACCATTCCAAAGAGGGC 58.908 52.381 0.00 0.00 38.24 5.19
456 459 3.832237 AACCGGCTGAGTGGCACAG 62.832 63.158 21.41 10.63 41.80 3.66
480 483 7.601856 TGATTATGAAAAATCAGGCGAAAACT 58.398 30.769 0.00 0.00 40.17 2.66
560 563 8.454106 CGATATTCAGGTTCTCAACATTTTTCT 58.546 33.333 0.00 0.00 0.00 2.52
561 564 7.218963 GCGATATTCAGGTTCTCAACATTTTTC 59.781 37.037 0.00 0.00 0.00 2.29
579 588 5.048782 TGCCTTCCATACAATTGCGATATTC 60.049 40.000 5.05 0.00 0.00 1.75
586 595 2.867975 GCATTGCCTTCCATACAATTGC 59.132 45.455 5.05 0.00 31.82 3.56
604 613 3.719268 TTGGAGGTAACATCACTGCAT 57.281 42.857 0.00 0.00 41.41 3.96
605 614 3.500448 TTTGGAGGTAACATCACTGCA 57.500 42.857 0.00 0.00 41.41 4.41
606 615 5.186198 ACTATTTGGAGGTAACATCACTGC 58.814 41.667 0.00 0.00 41.41 4.40
703 716 8.654997 TCAAAATCATTTGGGAGGTATGAAAAA 58.345 29.630 1.86 0.00 44.88 1.94
742 758 5.428457 AGACCCCTGAAAAGGAAAAACAAAT 59.572 36.000 0.00 0.00 0.00 2.32
746 762 3.492656 GCAGACCCCTGAAAAGGAAAAAC 60.493 47.826 0.00 0.00 43.02 2.43
749 765 1.499007 AGCAGACCCCTGAAAAGGAAA 59.501 47.619 0.00 0.00 43.02 3.13
750 766 1.149101 AGCAGACCCCTGAAAAGGAA 58.851 50.000 0.00 0.00 43.02 3.36
752 768 3.372440 AATAGCAGACCCCTGAAAAGG 57.628 47.619 0.00 0.00 43.02 3.11
753 769 7.410120 AATAAAATAGCAGACCCCTGAAAAG 57.590 36.000 0.00 0.00 43.02 2.27
759 777 7.348537 ACTCTCTTAATAAAATAGCAGACCCCT 59.651 37.037 0.00 0.00 0.00 4.79
778 796 7.095017 CGCTCTCCTGAAAAATAAAACTCTCTT 60.095 37.037 0.00 0.00 0.00 2.85
783 801 5.313712 TCCGCTCTCCTGAAAAATAAAACT 58.686 37.500 0.00 0.00 0.00 2.66
784 802 5.622770 TCCGCTCTCCTGAAAAATAAAAC 57.377 39.130 0.00 0.00 0.00 2.43
786 804 6.659242 AGAAATCCGCTCTCCTGAAAAATAAA 59.341 34.615 0.00 0.00 0.00 1.40
788 806 5.745227 AGAAATCCGCTCTCCTGAAAAATA 58.255 37.500 0.00 0.00 0.00 1.40
790 808 4.021102 AGAAATCCGCTCTCCTGAAAAA 57.979 40.909 0.00 0.00 0.00 1.94
796 814 6.418946 AGAAATAAAAGAAATCCGCTCTCCT 58.581 36.000 0.00 0.00 0.00 3.69
834 852 1.523154 TTGTTGTTGGGCTCATCCGC 61.523 55.000 0.00 0.00 34.94 5.54
835 853 0.958091 TTTGTTGTTGGGCTCATCCG 59.042 50.000 0.00 0.00 34.94 4.18
836 854 2.354003 CCATTTGTTGTTGGGCTCATCC 60.354 50.000 0.00 0.00 0.00 3.51
837 855 2.562298 TCCATTTGTTGTTGGGCTCATC 59.438 45.455 0.00 0.00 33.62 2.92
838 856 2.607499 TCCATTTGTTGTTGGGCTCAT 58.393 42.857 0.00 0.00 33.62 2.90
839 857 2.079170 TCCATTTGTTGTTGGGCTCA 57.921 45.000 0.00 0.00 33.62 4.26
1185 1234 3.781307 TGGCGGAGAACCCATCGG 61.781 66.667 0.00 0.00 34.14 4.18
1351 1409 2.768527 CAACCTAGATTGCAGGAGGAGA 59.231 50.000 11.06 0.00 36.61 3.71
1356 1417 3.450904 ACTACCAACCTAGATTGCAGGA 58.549 45.455 0.00 0.00 36.61 3.86
1405 4637 1.207390 CCACCAAACAATGCACAACG 58.793 50.000 0.00 0.00 0.00 4.10
1495 4801 7.012138 TCTGAGCAATCTTCAGCTAAATCATTC 59.988 37.037 0.00 0.00 42.04 2.67
1506 4812 5.009410 ACAAAAAGGTCTGAGCAATCTTCAG 59.991 40.000 9.78 0.00 0.00 3.02
2206 5532 1.164411 CCCAAAACGTATGCTGCAGA 58.836 50.000 20.43 0.00 0.00 4.26
2214 5540 2.894126 TGTCCAAATGCCCAAAACGTAT 59.106 40.909 0.00 0.00 0.00 3.06
2217 5543 1.068434 ACTGTCCAAATGCCCAAAACG 59.932 47.619 0.00 0.00 0.00 3.60
2533 5864 2.334946 GCACCATCGGCTTTCTGCA 61.335 57.895 0.00 0.00 45.15 4.41
2683 6014 2.647683 TTGCCGCCATATATGTGGAA 57.352 45.000 21.73 10.56 42.02 3.53
2700 6031 7.921786 TTCCTACTACCATCATGTTCTTTTG 57.078 36.000 0.00 0.00 0.00 2.44
2701 6032 8.934023 TTTTCCTACTACCATCATGTTCTTTT 57.066 30.769 0.00 0.00 0.00 2.27
2720 6051 2.758979 CTGATTCCTGCTGCATTTTCCT 59.241 45.455 1.31 0.00 0.00 3.36
2816 6150 2.169561 TGTTGCTACCTTCGGCATGATA 59.830 45.455 0.00 0.00 38.30 2.15
2827 6161 6.998673 ACTTTGTTATCTTTCTGTTGCTACCT 59.001 34.615 0.00 0.00 0.00 3.08
2829 6163 8.560374 AGAACTTTGTTATCTTTCTGTTGCTAC 58.440 33.333 0.00 0.00 0.00 3.58
2858 6192 1.726853 GGTTTCAGACCGATCCAGTG 58.273 55.000 0.00 0.00 39.00 3.66
2908 6242 0.918258 TGCCATACCTTGCTCCATCA 59.082 50.000 0.00 0.00 0.00 3.07
2946 6280 8.753133 AGATAGGATCGTTCTTATATGCATCAA 58.247 33.333 0.19 0.00 0.00 2.57
2969 6303 3.053095 AGGCATGTGATCCCTTTCAAGAT 60.053 43.478 0.00 0.00 0.00 2.40
2971 6305 2.731572 AGGCATGTGATCCCTTTCAAG 58.268 47.619 0.00 0.00 0.00 3.02
3172 6506 9.753674 ACCTTACCAAGATAATTCTTTTCATCA 57.246 29.630 0.00 0.00 40.28 3.07
3259 6594 8.053026 ACTTATTAATGCCGACGATATAGTCT 57.947 34.615 13.23 0.00 38.90 3.24
3675 7026 2.563179 TGGCTAGGTTCTTCTGAGTGTC 59.437 50.000 0.00 0.00 0.00 3.67
3730 7081 9.651718 CTAAGCGTCCAAAATATGAATAACTTC 57.348 33.333 0.00 0.00 0.00 3.01
3766 7117 4.408276 AGGATAGCTAACTTCATCGGCTA 58.592 43.478 0.00 0.00 39.35 3.93
3767 7118 3.235200 AGGATAGCTAACTTCATCGGCT 58.765 45.455 0.00 0.00 37.08 5.52
3768 7119 3.669251 AGGATAGCTAACTTCATCGGC 57.331 47.619 0.00 0.00 0.00 5.54
3770 7121 4.218635 TGCCTAGGATAGCTAACTTCATCG 59.781 45.833 14.75 0.00 37.37 3.84
3771 7122 5.730296 TGCCTAGGATAGCTAACTTCATC 57.270 43.478 14.75 0.00 37.37 2.92
3772 7123 6.100424 AGTTTGCCTAGGATAGCTAACTTCAT 59.900 38.462 14.75 0.00 37.43 2.57
3773 7124 5.425539 AGTTTGCCTAGGATAGCTAACTTCA 59.574 40.000 14.75 0.00 37.43 3.02
3774 7125 5.919755 AGTTTGCCTAGGATAGCTAACTTC 58.080 41.667 14.75 0.00 37.43 3.01
3776 7127 5.069781 CAGAGTTTGCCTAGGATAGCTAACT 59.930 44.000 14.75 14.71 40.32 2.24
3777 7128 5.069251 TCAGAGTTTGCCTAGGATAGCTAAC 59.931 44.000 14.75 10.15 37.37 2.34
3779 7130 4.804597 TCAGAGTTTGCCTAGGATAGCTA 58.195 43.478 14.75 0.00 37.37 3.32
3820 7172 1.135199 CCAGTGCAACATGGAAGCATC 60.135 52.381 11.29 6.54 41.43 3.91
3821 7173 0.892755 CCAGTGCAACATGGAAGCAT 59.107 50.000 11.29 0.67 41.43 3.79
3859 7211 5.422214 ACTGCAACCTAGTACTAGCAAAT 57.578 39.130 22.39 8.05 31.95 2.32
3867 7219 5.581085 CAGATACCAAACTGCAACCTAGTAC 59.419 44.000 0.00 0.00 0.00 2.73
3870 7222 4.832248 TCAGATACCAAACTGCAACCTAG 58.168 43.478 0.00 0.00 34.57 3.02
4071 7423 4.375272 CTCAGAGAAACTTGAACTGCTGA 58.625 43.478 0.00 0.00 0.00 4.26
4080 7432 1.070309 GTGCGTGCTCAGAGAAACTTG 60.070 52.381 0.00 0.00 0.00 3.16
4121 7473 8.548880 TGCCCTTACAGAATCTTACTACTTAT 57.451 34.615 0.00 0.00 0.00 1.73
4505 8533 7.068702 AGTCTCCATGAGTAATGAGAATCTCT 58.931 38.462 11.92 0.00 38.72 3.10
4523 8551 4.278310 TGATAATGACCGAGAAGTCTCCA 58.722 43.478 2.75 0.00 39.79 3.86
4528 8556 7.383687 TGTAAACTTGATAATGACCGAGAAGT 58.616 34.615 0.00 0.00 0.00 3.01
4552 8580 6.035843 CCACATTCGGGAATAGATTTTGTTG 58.964 40.000 0.00 0.00 0.00 3.33
4556 8584 3.636764 GGCCACATTCGGGAATAGATTTT 59.363 43.478 0.00 0.00 0.00 1.82
4566 8594 1.447317 GCAGTATGGCCACATTCGGG 61.447 60.000 8.16 0.00 38.53 5.14
4569 8597 1.755179 ACTGCAGTATGGCCACATTC 58.245 50.000 20.16 0.00 38.53 2.67
4599 8627 3.665825 TTGTCGCGTACGGCCGTAG 62.666 63.158 37.18 28.59 45.45 3.51
4610 8638 2.987149 AGTTAGTCATGAACTTGTCGCG 59.013 45.455 0.00 0.00 39.55 5.87
4614 8642 8.507249 GCAGAATAAAGTTAGTCATGAACTTGT 58.493 33.333 11.15 5.72 44.43 3.16


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

AutoCloner maintained by Alex Coulton.