Multiple sequence alignment - TraesCS3A01G515500

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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 TraesCS3A01G515500 chr3A 100.000 4547 0 0 1 4547 733625392 733620846 0.000000e+00 8397.0
1 TraesCS3A01G515500 chr3A 91.275 1616 131 9 1387 2993 733043504 733045118 0.000000e+00 2194.0
2 TraesCS3A01G515500 chr3A 90.204 1419 115 13 2264 3664 733532477 733531065 0.000000e+00 1829.0
3 TraesCS3A01G515500 chr3A 90.808 631 56 2 3009 3637 733045351 733045981 0.000000e+00 843.0
4 TraesCS3A01G515500 chr3A 80.285 771 82 36 3706 4460 733046091 733046807 6.740000e-143 518.0
5 TraesCS3A01G515500 chr3A 85.207 507 70 5 1406 1907 733576222 733575716 2.430000e-142 516.0
6 TraesCS3A01G515500 chr3A 84.518 394 54 7 1496 1883 733570899 733570507 2.570000e-102 383.0
7 TraesCS3A01G515500 chr3A 86.574 216 20 4 3858 4064 733523104 733522889 3.540000e-56 230.0
8 TraesCS3A01G515500 chr3A 84.524 84 10 1 1588 1671 733606356 733606276 3.770000e-11 80.5
9 TraesCS3A01G515500 chr3B 92.855 3961 182 35 1 3878 811114665 811110723 0.000000e+00 5653.0
10 TraesCS3A01G515500 chr3B 90.737 2278 180 16 1387 3634 810952274 810954550 0.000000e+00 3009.0
11 TraesCS3A01G515500 chr3B 83.259 1571 234 17 1778 3326 811079574 811081137 0.000000e+00 1417.0
12 TraesCS3A01G515500 chr3B 80.988 1720 261 38 1614 3294 810948076 810949768 0.000000e+00 1304.0
13 TraesCS3A01G515500 chr3B 86.494 348 40 5 3958 4299 811110717 811110371 4.290000e-100 375.0
14 TraesCS3A01G515500 chr3D 92.980 3561 166 36 1 3493 604126071 604122527 0.000000e+00 5114.0
15 TraesCS3A01G515500 chr3D 90.758 2283 176 23 1387 3637 602799477 602797198 0.000000e+00 3014.0
16 TraesCS3A01G515500 chr3D 89.420 1569 136 15 1867 3416 604014845 604013288 0.000000e+00 1951.0
17 TraesCS3A01G515500 chr3D 83.116 1765 255 26 1591 3325 604137606 604135855 0.000000e+00 1568.0
18 TraesCS3A01G515500 chr3D 95.281 784 33 3 3656 4437 604032500 604031719 0.000000e+00 1240.0
19 TraesCS3A01G515500 chr3D 89.823 678 44 5 3412 4064 604009755 604009078 0.000000e+00 846.0
20 TraesCS3A01G515500 chr3D 93.143 175 9 2 3706 3878 602797088 602796915 2.100000e-63 254.0
21 TraesCS3A01G515500 chr3D 94.574 129 6 1 3491 3619 604036411 604036284 9.980000e-47 198.0
22 TraesCS3A01G515500 chr7D 83.333 312 44 5 68 372 555540589 555540899 9.630000e-72 281.0
23 TraesCS3A01G515500 chr7D 80.938 320 45 10 68 372 627617359 627617041 5.880000e-59 239.0
24 TraesCS3A01G515500 chr1D 82.692 312 46 5 68 372 339318087 339318397 2.080000e-68 270.0
25 TraesCS3A01G515500 chr2D 81.410 312 47 8 68 372 619632042 619631735 1.260000e-60 244.0
26 TraesCS3A01G515500 chr2B 82.857 280 40 5 465 739 728195128 728195404 1.260000e-60 244.0
27 TraesCS3A01G515500 chr6B 81.673 251 36 8 465 710 665537671 665537916 2.770000e-47 200.0
28 TraesCS3A01G515500 chr2A 86.000 100 12 2 801 899 578117512 578117610 6.220000e-19 106.0
29 TraesCS3A01G515500 chr4B 82.828 99 17 0 797 895 98453070 98453168 6.270000e-14 89.8


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 TraesCS3A01G515500 chr3A 733620846 733625392 4546 True 8397.0 8397 100.0000 1 4547 1 chr3A.!!$R6 4546
1 TraesCS3A01G515500 chr3A 733531065 733532477 1412 True 1829.0 1829 90.2040 2264 3664 1 chr3A.!!$R2 1400
2 TraesCS3A01G515500 chr3A 733043504 733046807 3303 False 1185.0 2194 87.4560 1387 4460 3 chr3A.!!$F1 3073
3 TraesCS3A01G515500 chr3A 733575716 733576222 506 True 516.0 516 85.2070 1406 1907 1 chr3A.!!$R4 501
4 TraesCS3A01G515500 chr3B 811110371 811114665 4294 True 3014.0 5653 89.6745 1 4299 2 chr3B.!!$R1 4298
5 TraesCS3A01G515500 chr3B 810948076 810954550 6474 False 2156.5 3009 85.8625 1387 3634 2 chr3B.!!$F2 2247
6 TraesCS3A01G515500 chr3B 811079574 811081137 1563 False 1417.0 1417 83.2590 1778 3326 1 chr3B.!!$F1 1548
7 TraesCS3A01G515500 chr3D 604122527 604126071 3544 True 5114.0 5114 92.9800 1 3493 1 chr3D.!!$R1 3492
8 TraesCS3A01G515500 chr3D 602796915 602799477 2562 True 1634.0 3014 91.9505 1387 3878 2 chr3D.!!$R3 2491
9 TraesCS3A01G515500 chr3D 604135855 604137606 1751 True 1568.0 1568 83.1160 1591 3325 1 chr3D.!!$R2 1734
10 TraesCS3A01G515500 chr3D 604009078 604014845 5767 True 1398.5 1951 89.6215 1867 4064 2 chr3D.!!$R4 2197
11 TraesCS3A01G515500 chr3D 604031719 604036411 4692 True 719.0 1240 94.9275 3491 4437 2 chr3D.!!$R5 946

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
653 665 0.465460 GATATTTGCCCGCTGGACCA 60.465 55.0 0.00 0.0 0.00 4.02 F
753 768 0.737715 GCGAGTGATCGAAACCAGCT 60.738 55.0 1.17 0.0 34.64 4.24 F
1184 1214 0.754217 CCGTCTCCTCCCGTTATCCA 60.754 60.0 0.00 0.0 0.00 3.41 F
2755 5591 0.321346 GTGTTGCCATTTCCCCCTTG 59.679 55.0 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 4909 2.224066 GCTAGCACCATATCGACCAACT 60.224 50.000 10.63 0.0 0.00 3.16 R
2328 5159 5.407407 TCAGGTAAGTTAGGCTCTTGAAG 57.593 43.478 0.00 0.0 0.00 3.02 R
3023 6105 1.352017 TGACACTGATCCCATGTGCTT 59.648 47.619 0.00 0.0 35.33 3.91 R
4464 15022 0.106719 CCCAACAGTTGACACCACCT 60.107 55.000 15.36 0.0 0.00 4.00 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
148 154 6.882610 TGCATTTGAATGTTCTAGTTGAGT 57.117 33.333 5.68 0.00 38.65 3.41
264 270 5.179452 AGAAAAGCAGCAAGGTAATAGGA 57.821 39.130 0.00 0.00 0.00 2.94
312 318 3.334583 GGCGATTGGCTGGAGATATAA 57.665 47.619 0.00 0.00 42.94 0.98
328 335 6.462487 GGAGATATAACAAAGGGACGATGACA 60.462 42.308 0.00 0.00 0.00 3.58
329 336 6.884832 AGATATAACAAAGGGACGATGACAA 58.115 36.000 0.00 0.00 0.00 3.18
356 363 3.127533 GGAAGCGGCAATGCGACT 61.128 61.111 1.45 0.00 40.67 4.18
378 385 4.776435 TGGAGATCATTACATTCCTGCA 57.224 40.909 0.00 0.00 0.00 4.41
541 551 1.257750 CCTCCCACACCTCATCGACA 61.258 60.000 0.00 0.00 0.00 4.35
597 607 5.729176 GCAAAACAGGAAAAACCGAAAATGG 60.729 40.000 0.00 0.00 44.74 3.16
653 665 0.465460 GATATTTGCCCGCTGGACCA 60.465 55.000 0.00 0.00 0.00 4.02
710 722 2.030562 ACTGACAAAGACGGCCCG 59.969 61.111 0.00 0.00 0.00 6.13
740 752 1.742880 CCCCACATGTCAGCGAGTG 60.743 63.158 0.00 0.00 0.00 3.51
753 768 0.737715 GCGAGTGATCGAAACCAGCT 60.738 55.000 1.17 0.00 34.64 4.24
827 842 3.838271 GCAGATCGTCCGGGAGCA 61.838 66.667 0.00 0.00 0.00 4.26
834 849 2.771639 CGTCCGGGAGCAAGATCGA 61.772 63.158 0.00 0.00 0.00 3.59
902 917 3.135942 GCTCTGAGAGCGCTTTTCT 57.864 52.632 19.71 3.78 45.85 2.52
903 918 1.437625 GCTCTGAGAGCGCTTTTCTT 58.562 50.000 19.71 0.00 45.85 2.52
905 920 1.128321 CTCTGAGAGCGCTTTTCTTGC 59.872 52.381 13.26 0.00 0.00 4.01
906 921 0.870393 CTGAGAGCGCTTTTCTTGCA 59.130 50.000 13.26 0.00 0.00 4.08
907 922 1.265095 CTGAGAGCGCTTTTCTTGCAA 59.735 47.619 13.26 0.00 0.00 4.08
1096 1126 3.382832 AACGTCCTCGCCCCTCTG 61.383 66.667 0.00 0.00 41.18 3.35
1180 1210 3.136123 CGCCGTCTCCTCCCGTTA 61.136 66.667 0.00 0.00 0.00 3.18
1184 1214 0.754217 CCGTCTCCTCCCGTTATCCA 60.754 60.000 0.00 0.00 0.00 3.41
1237 1267 1.600023 GACCCACATCGAACACCAAA 58.400 50.000 0.00 0.00 0.00 3.28
1242 1272 2.223688 CCACATCGAACACCAAAAAGCA 60.224 45.455 0.00 0.00 0.00 3.91
1265 1295 6.151144 GCAACATAGGAGTAAGTTGATTTGGT 59.849 38.462 8.19 0.00 39.27 3.67
1335 1372 3.278574 GCCCAAACATGTGCTACATCTA 58.721 45.455 0.00 0.00 36.53 1.98
1374 1411 3.631686 ACTGCTTGTTCACATGCTTGTTA 59.368 39.130 16.27 0.00 44.41 2.41
1393 1430 9.584839 GCTTGTTAAGATTTGTTGCTTAAATTG 57.415 29.630 0.00 0.00 38.06 2.32
1477 4291 8.986477 AGCATGTTGATTTGGTAAGAAAATAC 57.014 30.769 0.00 0.00 0.00 1.89
1556 4370 7.033791 TGATCAAATTAGGACAGTCGTAACTC 58.966 38.462 16.19 9.70 31.71 3.01
1709 4524 8.746052 TTGTTTCCTAAAACTCTCATCTTTCA 57.254 30.769 3.06 0.00 44.23 2.69
1772 4588 8.739039 ACTATGCAGTGCACAATTTAATTTCTA 58.261 29.630 22.44 2.93 43.04 2.10
1831 4659 2.514803 CTCCCCGTCTTTTGGAAATGT 58.485 47.619 0.00 0.00 0.00 2.71
2046 4877 7.548780 ACAAATATGCCAAAAATATCTTTGCGT 59.451 29.630 0.00 0.00 35.38 5.24
2078 4909 1.666054 ACGCGAACCAGGTTTGTTAA 58.334 45.000 15.93 0.00 30.22 2.01
2415 5246 1.568504 TCTCATTCTGCCCCGTACTT 58.431 50.000 0.00 0.00 0.00 2.24
2466 5297 4.923281 GGCATCAACCAACTAAACATTCAC 59.077 41.667 0.00 0.00 0.00 3.18
2550 5381 1.302907 ATCTGAAGGTGGCCATCCTT 58.697 50.000 28.90 28.90 46.44 3.36
2595 5426 5.361571 AGCATATCAATCTGTTCCAATTGCA 59.638 36.000 0.00 0.00 33.76 4.08
2755 5591 0.321346 GTGTTGCCATTTCCCCCTTG 59.679 55.000 0.00 0.00 0.00 3.61
2757 5593 1.055849 GTTGCCATTTCCCCCTTGTT 58.944 50.000 0.00 0.00 0.00 2.83
2808 5664 4.141574 ACAAAGCTCCCTACTGTGTTTACA 60.142 41.667 0.00 0.00 31.32 2.41
2973 5838 2.289274 CACGCACTCCATGTTTGTTGTA 59.711 45.455 0.00 0.00 0.00 2.41
3214 6296 0.250901 AAGGGCGAAACAGACTGCAT 60.251 50.000 1.25 0.00 0.00 3.96
3276 6372 1.341080 CAGGGCCAAGGTCATTGTTT 58.659 50.000 6.18 0.00 37.17 2.83
3309 6405 0.040058 ATGCTGCCCCATCACTTTGA 59.960 50.000 0.00 0.00 0.00 2.69
3352 6448 2.498078 TCATGCGAATGTACCACCTACA 59.502 45.455 2.58 0.00 39.78 2.74
3400 6496 6.488006 GCATCTAATACAAATCATCAGGTGGT 59.512 38.462 0.00 0.00 0.00 4.16
3465 10098 1.069049 GCCACCAGCATGTGTTTTTCT 59.931 47.619 0.00 0.00 42.97 2.52
3523 10172 0.537143 TCCGCTTGTGGTCTTGCAAT 60.537 50.000 0.00 0.00 0.00 3.56
3558 10208 1.184431 TACCAATGCAATGCTGTGGG 58.816 50.000 24.33 15.11 37.45 4.61
3737 14190 6.879458 ACATCTGGTTGTTCTATTTACAGTCC 59.121 38.462 0.00 0.00 0.00 3.85
3888 14357 4.265073 GAAGGAATTATGGTGAGCACTGT 58.735 43.478 0.16 0.00 0.00 3.55
4044 14542 0.636647 TGGCTGACAGGGAGGATCTA 59.363 55.000 4.26 0.00 33.73 1.98
4048 14547 2.656002 CTGACAGGGAGGATCTAACGA 58.344 52.381 0.00 0.00 33.73 3.85
4135 14647 1.230635 ACATGCACAAGCTCGACCAC 61.231 55.000 0.00 0.00 42.74 4.16
4167 14679 1.771255 AGTAGGTGGAATCATGGGCTC 59.229 52.381 0.00 0.00 0.00 4.70
4180 14692 3.973305 TCATGGGCTCTATCCACAACATA 59.027 43.478 0.00 0.00 37.08 2.29
4220 14734 2.125106 AATTGTCCGCGGGCTCTC 60.125 61.111 32.34 13.89 0.00 3.20
4221 14735 2.579684 GAATTGTCCGCGGGCTCTCT 62.580 60.000 32.34 12.77 0.00 3.10
4326 14884 1.142936 AGTGGGATGATGCAGCCATA 58.857 50.000 0.00 0.00 42.36 2.74
4343 14901 3.560025 GCCATATCTGGGGAATCAACGAT 60.560 47.826 0.00 0.00 43.36 3.73
4388 14946 0.107703 TCCACTTTATGCCGAGGCTG 60.108 55.000 15.75 3.86 42.51 4.85
4389 14947 0.392998 CCACTTTATGCCGAGGCTGT 60.393 55.000 15.75 6.74 42.51 4.40
4441 14999 3.233355 ACTCATTGAGTTGGCGACC 57.767 52.632 13.61 0.00 40.28 4.79
4446 15004 2.107041 ATTGAGTTGGCGACCGACCA 62.107 55.000 11.31 7.58 38.65 4.02
4447 15005 2.432628 GAGTTGGCGACCGACCAG 60.433 66.667 11.31 0.00 38.65 4.00
4460 15018 1.481056 CGACCAGGAGGGGAAACAGT 61.481 60.000 0.00 0.00 42.91 3.55
4461 15019 0.771755 GACCAGGAGGGGAAACAGTT 59.228 55.000 0.00 0.00 42.91 3.16
4462 15020 0.478507 ACCAGGAGGGGAAACAGTTG 59.521 55.000 0.00 0.00 42.91 3.16
4463 15021 0.771127 CCAGGAGGGGAAACAGTTGA 59.229 55.000 0.00 0.00 0.00 3.18
4464 15022 1.144913 CCAGGAGGGGAAACAGTTGAA 59.855 52.381 0.00 0.00 0.00 2.69
4465 15023 2.508526 CAGGAGGGGAAACAGTTGAAG 58.491 52.381 0.00 0.00 0.00 3.02
4466 15024 1.425448 AGGAGGGGAAACAGTTGAAGG 59.575 52.381 0.00 0.00 0.00 3.46
4467 15025 1.145119 GGAGGGGAAACAGTTGAAGGT 59.855 52.381 0.00 0.00 0.00 3.50
4468 15026 2.230660 GAGGGGAAACAGTTGAAGGTG 58.769 52.381 0.00 0.00 0.00 4.00
4469 15027 1.133482 AGGGGAAACAGTTGAAGGTGG 60.133 52.381 0.00 0.00 0.00 4.61
4470 15028 1.411074 GGGGAAACAGTTGAAGGTGGT 60.411 52.381 0.00 0.00 0.00 4.16
4471 15029 1.681264 GGGAAACAGTTGAAGGTGGTG 59.319 52.381 0.00 0.00 0.00 4.17
4472 15030 2.375146 GGAAACAGTTGAAGGTGGTGT 58.625 47.619 0.00 0.00 0.00 4.16
4473 15031 2.357952 GGAAACAGTTGAAGGTGGTGTC 59.642 50.000 0.00 0.00 0.00 3.67
4474 15032 2.799126 AACAGTTGAAGGTGGTGTCA 57.201 45.000 0.00 0.00 0.00 3.58
4475 15033 2.799126 ACAGTTGAAGGTGGTGTCAA 57.201 45.000 0.00 0.00 0.00 3.18
4479 15037 2.365582 GTTGAAGGTGGTGTCAACTGT 58.634 47.619 8.83 0.00 46.57 3.55
4480 15038 2.752903 GTTGAAGGTGGTGTCAACTGTT 59.247 45.455 8.83 0.00 46.57 3.16
4481 15039 2.364632 TGAAGGTGGTGTCAACTGTTG 58.635 47.619 14.24 14.24 40.66 3.33
4482 15040 1.676006 GAAGGTGGTGTCAACTGTTGG 59.324 52.381 19.55 2.55 40.66 3.77
4483 15041 0.106719 AGGTGGTGTCAACTGTTGGG 60.107 55.000 19.55 0.00 39.91 4.12
4484 15042 0.395173 GGTGGTGTCAACTGTTGGGT 60.395 55.000 19.55 0.00 0.00 4.51
4485 15043 1.134037 GGTGGTGTCAACTGTTGGGTA 60.134 52.381 19.55 4.71 0.00 3.69
4486 15044 1.944709 GTGGTGTCAACTGTTGGGTAC 59.055 52.381 19.55 14.86 0.00 3.34
4487 15045 1.223187 GGTGTCAACTGTTGGGTACG 58.777 55.000 19.55 0.00 0.00 3.67
4488 15046 1.223187 GTGTCAACTGTTGGGTACGG 58.777 55.000 19.55 0.00 39.17 4.02
4489 15047 1.121378 TGTCAACTGTTGGGTACGGA 58.879 50.000 19.55 0.00 36.57 4.69
4490 15048 1.069513 TGTCAACTGTTGGGTACGGAG 59.930 52.381 19.55 0.00 36.57 4.63
4491 15049 0.682852 TCAACTGTTGGGTACGGAGG 59.317 55.000 19.55 0.00 36.57 4.30
4492 15050 0.953960 CAACTGTTGGGTACGGAGGC 60.954 60.000 12.66 0.00 36.57 4.70
4493 15051 1.125711 AACTGTTGGGTACGGAGGCT 61.126 55.000 0.00 0.00 36.57 4.58
4494 15052 1.125711 ACTGTTGGGTACGGAGGCTT 61.126 55.000 0.00 0.00 36.57 4.35
4495 15053 0.391263 CTGTTGGGTACGGAGGCTTC 60.391 60.000 0.00 0.00 34.90 3.86
4496 15054 1.122632 TGTTGGGTACGGAGGCTTCA 61.123 55.000 0.00 0.00 0.00 3.02
4497 15055 0.391263 GTTGGGTACGGAGGCTTCAG 60.391 60.000 0.00 0.00 0.00 3.02
4498 15056 2.180159 TTGGGTACGGAGGCTTCAGC 62.180 60.000 0.00 0.00 41.14 4.26
4499 15057 2.656069 GGGTACGGAGGCTTCAGCA 61.656 63.158 0.30 0.00 44.36 4.41
4500 15058 1.295423 GGTACGGAGGCTTCAGCAA 59.705 57.895 0.30 0.00 44.36 3.91
4501 15059 0.741221 GGTACGGAGGCTTCAGCAAG 60.741 60.000 0.30 0.00 44.36 4.01
4502 15060 0.246635 GTACGGAGGCTTCAGCAAGA 59.753 55.000 0.30 0.00 44.36 3.02
4503 15061 0.246635 TACGGAGGCTTCAGCAAGAC 59.753 55.000 0.30 0.00 44.36 3.01
4504 15062 1.004560 CGGAGGCTTCAGCAAGACA 60.005 57.895 0.30 0.00 40.68 3.41
4505 15063 1.018226 CGGAGGCTTCAGCAAGACAG 61.018 60.000 0.30 0.00 40.68 3.51
4506 15064 0.676151 GGAGGCTTCAGCAAGACAGG 60.676 60.000 0.30 0.00 40.68 4.00
4507 15065 1.303155 AGGCTTCAGCAAGACAGGC 60.303 57.895 0.30 1.02 40.68 4.85
4508 15066 1.601759 GGCTTCAGCAAGACAGGCA 60.602 57.895 0.30 0.00 44.36 4.75
4509 15067 1.578423 GCTTCAGCAAGACAGGCAC 59.422 57.895 0.00 0.00 41.59 5.01
4510 15068 0.888285 GCTTCAGCAAGACAGGCACT 60.888 55.000 0.00 0.00 41.59 4.40
4511 15069 1.602311 CTTCAGCAAGACAGGCACTT 58.398 50.000 0.00 0.00 34.60 3.16
4512 15070 1.266175 CTTCAGCAAGACAGGCACTTG 59.734 52.381 12.37 12.37 44.92 3.16
4515 15073 2.949106 CAAGACAGGCACTTGCGG 59.051 61.111 0.00 0.00 43.26 5.69
4516 15074 2.980233 AAGACAGGCACTTGCGGC 60.980 61.111 0.00 0.00 43.26 6.53
4523 15081 2.582436 GCACTTGCGGCCTAGGTA 59.418 61.111 11.31 0.00 0.00 3.08
4524 15082 1.146263 GCACTTGCGGCCTAGGTAT 59.854 57.895 11.31 0.00 0.00 2.73
4525 15083 0.391597 GCACTTGCGGCCTAGGTATA 59.608 55.000 11.31 0.00 0.00 1.47
4526 15084 1.872653 GCACTTGCGGCCTAGGTATAC 60.873 57.143 11.31 0.00 0.00 1.47
4527 15085 1.411246 CACTTGCGGCCTAGGTATACA 59.589 52.381 11.31 1.13 0.00 2.29
4528 15086 1.687123 ACTTGCGGCCTAGGTATACAG 59.313 52.381 11.31 4.37 0.00 2.74
4529 15087 1.961394 CTTGCGGCCTAGGTATACAGA 59.039 52.381 11.31 0.00 0.00 3.41
4530 15088 2.076207 TGCGGCCTAGGTATACAGAA 57.924 50.000 11.31 0.00 0.00 3.02
4531 15089 2.390696 TGCGGCCTAGGTATACAGAAA 58.609 47.619 11.31 0.00 0.00 2.52
4532 15090 2.101917 TGCGGCCTAGGTATACAGAAAC 59.898 50.000 11.31 0.00 0.00 2.78
4533 15091 2.547430 GCGGCCTAGGTATACAGAAACC 60.547 54.545 11.31 0.00 35.91 3.27
4535 15093 3.387050 CGGCCTAGGTATACAGAAACCTT 59.613 47.826 11.31 0.00 43.77 3.50
4536 15094 4.586001 CGGCCTAGGTATACAGAAACCTTA 59.414 45.833 11.31 0.00 43.77 2.69
4537 15095 5.069516 CGGCCTAGGTATACAGAAACCTTAA 59.930 44.000 11.31 0.00 43.77 1.85
4538 15096 6.407299 CGGCCTAGGTATACAGAAACCTTAAA 60.407 42.308 11.31 0.00 43.77 1.52
4539 15097 6.990939 GGCCTAGGTATACAGAAACCTTAAAG 59.009 42.308 11.31 0.00 43.77 1.85
4540 15098 6.990939 GCCTAGGTATACAGAAACCTTAAAGG 59.009 42.308 11.31 2.32 43.77 3.11
4541 15099 7.506971 CCTAGGTATACAGAAACCTTAAAGGG 58.493 42.308 5.01 0.00 43.77 3.95
4542 15100 5.752650 AGGTATACAGAAACCTTAAAGGGC 58.247 41.667 5.01 0.00 43.77 5.19
4543 15101 5.252164 AGGTATACAGAAACCTTAAAGGGCA 59.748 40.000 5.01 0.00 43.77 5.36
4544 15102 5.947566 GGTATACAGAAACCTTAAAGGGCAA 59.052 40.000 5.01 0.00 40.58 4.52
4545 15103 6.434965 GGTATACAGAAACCTTAAAGGGCAAA 59.565 38.462 5.01 0.00 40.58 3.68
4546 15104 7.123697 GGTATACAGAAACCTTAAAGGGCAAAT 59.876 37.037 5.01 0.00 40.58 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 114 6.530887 TCAAATGCATTGGAAATATTCACGTG 59.469 34.615 14.35 9.94 39.62 4.49
173 179 4.637771 CCCTTTGGGCTACTTCCG 57.362 61.111 0.00 0.00 35.35 4.30
233 239 6.481643 ACCTTGCTGCTTTTCTTACCTATAA 58.518 36.000 0.00 0.00 0.00 0.98
264 270 1.032014 ACTGCGCCTTTCATGTTTGT 58.968 45.000 4.18 0.00 0.00 2.83
302 308 5.600898 TCATCGTCCCTTTGTTATATCTCCA 59.399 40.000 0.00 0.00 0.00 3.86
308 314 4.865925 CGTTGTCATCGTCCCTTTGTTATA 59.134 41.667 0.00 0.00 0.00 0.98
312 318 1.069513 TCGTTGTCATCGTCCCTTTGT 59.930 47.619 3.38 0.00 0.00 2.83
328 335 1.961277 CCGCTTCCTGCTTGTCGTT 60.961 57.895 0.00 0.00 40.11 3.85
329 336 2.357517 CCGCTTCCTGCTTGTCGT 60.358 61.111 0.00 0.00 40.11 4.34
350 357 3.885724 TGTAATGATCTCCAAGTCGCA 57.114 42.857 0.00 0.00 0.00 5.10
356 363 4.883585 GTGCAGGAATGTAATGATCTCCAA 59.116 41.667 0.00 0.00 0.00 3.53
571 581 1.137282 TCGGTTTTTCCTGTTTTGCCC 59.863 47.619 0.00 0.00 0.00 5.36
710 722 3.574780 GTGGGGTAACTCGCTTGC 58.425 61.111 0.00 0.00 46.92 4.01
740 752 2.266554 CTCACTCAGCTGGTTTCGATC 58.733 52.381 15.13 0.00 0.00 3.69
753 768 4.381398 GCTCACTCTATTCTTGCTCACTCA 60.381 45.833 0.00 0.00 0.00 3.41
811 826 1.227089 CTTGCTCCCGGACGATCTG 60.227 63.158 0.73 0.00 0.00 2.90
814 829 1.742768 GATCTTGCTCCCGGACGAT 59.257 57.895 0.73 0.00 0.00 3.73
840 855 2.158971 TCGATTCCTTGATGCGATTCCA 60.159 45.455 0.00 0.00 0.00 3.53
901 916 2.821969 GGGCCATGTATCCTATTGCAAG 59.178 50.000 4.39 0.00 0.00 4.01
902 917 2.176581 TGGGCCATGTATCCTATTGCAA 59.823 45.455 0.00 0.00 0.00 4.08
903 918 1.779700 TGGGCCATGTATCCTATTGCA 59.220 47.619 0.00 0.00 0.00 4.08
905 920 3.795688 ACTGGGCCATGTATCCTATTG 57.204 47.619 6.72 0.00 0.00 1.90
906 921 3.264450 GCTACTGGGCCATGTATCCTATT 59.736 47.826 6.72 0.00 0.00 1.73
907 922 2.840651 GCTACTGGGCCATGTATCCTAT 59.159 50.000 6.72 0.00 0.00 2.57
999 1029 1.282738 TGGTTAGGGTTCGGATTTCCC 59.717 52.381 5.61 5.61 41.36 3.97
1096 1126 2.948720 AAGACAGGGCGCTGAGGAC 61.949 63.158 34.63 21.12 0.00 3.85
1220 1250 2.862140 GCTTTTTGGTGTTCGATGTGGG 60.862 50.000 0.00 0.00 0.00 4.61
1237 1267 8.299570 CAAATCAACTTACTCCTATGTTGCTTT 58.700 33.333 0.00 0.00 37.10 3.51
1242 1272 8.706322 AAACCAAATCAACTTACTCCTATGTT 57.294 30.769 0.00 0.00 0.00 2.71
1265 1295 7.979444 AATTGTTCGACTCTGAAATAGGAAA 57.021 32.000 0.00 0.00 0.00 3.13
1347 1384 3.003689 AGCATGTGAACAAGCAGTACAAC 59.996 43.478 12.61 0.00 42.43 3.32
1428 4242 9.765795 GCTAGCTAGGAAAAGATTTATTCTACA 57.234 33.333 22.10 0.00 33.05 2.74
1436 4250 6.886459 TCAACATGCTAGCTAGGAAAAGATTT 59.114 34.615 19.55 0.00 0.00 2.17
1476 4290 7.287810 ACTAAGGTCCAACTGACAATTAAAGT 58.712 34.615 0.00 0.00 46.38 2.66
1477 4291 7.745620 ACTAAGGTCCAACTGACAATTAAAG 57.254 36.000 0.00 0.00 46.38 1.85
1556 4370 9.325198 TGCAATAACTTATAGTCATGGTTACTG 57.675 33.333 0.00 0.00 0.00 2.74
1633 4447 2.953648 TGAACTCGACTACTGGTGTTGA 59.046 45.455 0.00 0.00 0.00 3.18
1709 4524 5.234972 GCAAAACAAAGAATAAGCAACAGCT 59.765 36.000 0.00 0.00 41.23 4.24
1772 4588 7.290014 TGGATTCTACCACATATCACTACATGT 59.710 37.037 2.69 2.69 35.79 3.21
1831 4659 9.567776 TTCAGAATCCAGATTAAACTGTTGTAA 57.432 29.630 11.34 0.00 36.30 2.41
1929 4760 4.467438 AGGATGTTGCCTTTTATCTTTGGG 59.533 41.667 0.00 0.00 33.46 4.12
2046 4877 5.064198 CCTGGTTCGCGTAAAATTTCTATCA 59.936 40.000 5.77 0.00 0.00 2.15
2078 4909 2.224066 GCTAGCACCATATCGACCAACT 60.224 50.000 10.63 0.00 0.00 3.16
2328 5159 5.407407 TCAGGTAAGTTAGGCTCTTGAAG 57.593 43.478 0.00 0.00 0.00 3.02
2550 5381 7.124573 TGCTTTAGCTTGGTGATCTAGATAA 57.875 36.000 4.89 0.00 42.66 1.75
2595 5426 6.947733 TCTTGATATGGTTTTCCTTGTCATGT 59.052 34.615 0.00 0.00 41.89 3.21
2755 5591 5.116882 ACGCCCTTTTGATAGATACTGAAC 58.883 41.667 0.00 0.00 0.00 3.18
2757 5593 6.665992 ATACGCCCTTTTGATAGATACTGA 57.334 37.500 0.00 0.00 0.00 3.41
2973 5838 3.255642 ACAACTCATTAGGCGTTGCAAAT 59.744 39.130 0.00 0.00 41.15 2.32
3023 6105 1.352017 TGACACTGATCCCATGTGCTT 59.648 47.619 0.00 0.00 35.33 3.91
3214 6296 2.877097 TAGCTTGGCAAGAACCATGA 57.123 45.000 30.45 3.97 40.13 3.07
3309 6405 3.338249 ACTCAGCAGCAAATTACATCGT 58.662 40.909 0.00 0.00 0.00 3.73
3352 6448 5.428253 CACACATATAACCACCAGCTAGTT 58.572 41.667 0.00 0.00 0.00 2.24
3400 6496 1.067974 CCTCGACAACACACACTACCA 59.932 52.381 0.00 0.00 0.00 3.25
3465 10098 6.204108 GGAAAACTTCCTCGAGTGTTTCATAA 59.796 38.462 20.67 1.66 46.57 1.90
3523 10172 6.435591 TGCATTGGTAAACATGGAAATACTGA 59.564 34.615 0.00 0.00 0.00 3.41
4044 14542 2.571653 TCCATTCCTTGGTCTGATCGTT 59.428 45.455 0.00 0.00 46.52 3.85
4048 14547 1.849039 CCCTCCATTCCTTGGTCTGAT 59.151 52.381 0.00 0.00 46.52 2.90
4135 14647 1.269621 CCACCTACTTTATCCGGCTCG 60.270 57.143 0.00 0.00 0.00 5.03
4167 14679 7.207383 TCACCTTACGATTATGTTGTGGATAG 58.793 38.462 0.00 0.00 0.00 2.08
4211 14724 0.883814 CATGATTCCAGAGAGCCCGC 60.884 60.000 0.00 0.00 0.00 6.13
4220 14734 3.836146 TGGATAAAGCCCATGATTCCAG 58.164 45.455 0.00 0.00 0.00 3.86
4221 14735 3.969466 TGGATAAAGCCCATGATTCCA 57.031 42.857 0.00 0.00 0.00 3.53
4247 14761 5.414454 CCAATTCTTTTCACCTTACCGATGA 59.586 40.000 0.00 0.00 0.00 2.92
4326 14884 3.458118 TGGTTATCGTTGATTCCCCAGAT 59.542 43.478 0.00 0.00 0.00 2.90
4343 14901 2.380941 TCGATCGAGGGTCAATGGTTA 58.619 47.619 15.15 0.00 0.00 2.85
4388 14946 4.641989 AGCATCAATACCCACAAGATCAAC 59.358 41.667 0.00 0.00 0.00 3.18
4389 14947 4.858850 AGCATCAATACCCACAAGATCAA 58.141 39.130 0.00 0.00 0.00 2.57
4437 14995 4.753662 TCCCCTCCTGGTCGGTCG 62.754 72.222 0.00 0.00 0.00 4.79
4439 14997 2.206036 TTTCCCCTCCTGGTCGGT 59.794 61.111 0.00 0.00 0.00 4.69
4441 14999 1.296715 CTGTTTCCCCTCCTGGTCG 59.703 63.158 0.00 0.00 0.00 4.79
4446 15004 1.425448 CCTTCAACTGTTTCCCCTCCT 59.575 52.381 0.00 0.00 0.00 3.69
4447 15005 1.145119 ACCTTCAACTGTTTCCCCTCC 59.855 52.381 0.00 0.00 0.00 4.30
4452 15010 2.357952 GACACCACCTTCAACTGTTTCC 59.642 50.000 0.00 0.00 0.00 3.13
4460 15018 2.752354 CAACAGTTGACACCACCTTCAA 59.248 45.455 7.61 0.00 0.00 2.69
4461 15019 2.364632 CAACAGTTGACACCACCTTCA 58.635 47.619 7.61 0.00 0.00 3.02
4462 15020 1.676006 CCAACAGTTGACACCACCTTC 59.324 52.381 15.36 0.00 0.00 3.46
4463 15021 1.684869 CCCAACAGTTGACACCACCTT 60.685 52.381 15.36 0.00 0.00 3.50
4464 15022 0.106719 CCCAACAGTTGACACCACCT 60.107 55.000 15.36 0.00 0.00 4.00
4465 15023 0.395173 ACCCAACAGTTGACACCACC 60.395 55.000 15.36 0.00 0.00 4.61
4466 15024 1.944709 GTACCCAACAGTTGACACCAC 59.055 52.381 15.36 1.90 0.00 4.16
4467 15025 1.473610 CGTACCCAACAGTTGACACCA 60.474 52.381 15.36 0.00 0.00 4.17
4468 15026 1.223187 CGTACCCAACAGTTGACACC 58.777 55.000 15.36 0.00 0.00 4.16
4469 15027 1.202557 TCCGTACCCAACAGTTGACAC 60.203 52.381 15.36 8.09 0.00 3.67
4470 15028 1.069513 CTCCGTACCCAACAGTTGACA 59.930 52.381 15.36 0.00 0.00 3.58
4471 15029 1.607251 CCTCCGTACCCAACAGTTGAC 60.607 57.143 15.36 4.28 0.00 3.18
4472 15030 0.682852 CCTCCGTACCCAACAGTTGA 59.317 55.000 15.36 0.00 0.00 3.18
4473 15031 0.953960 GCCTCCGTACCCAACAGTTG 60.954 60.000 6.28 6.28 0.00 3.16
4474 15032 1.125711 AGCCTCCGTACCCAACAGTT 61.126 55.000 0.00 0.00 0.00 3.16
4475 15033 1.125711 AAGCCTCCGTACCCAACAGT 61.126 55.000 0.00 0.00 0.00 3.55
4476 15034 0.391263 GAAGCCTCCGTACCCAACAG 60.391 60.000 0.00 0.00 0.00 3.16
4477 15035 1.122632 TGAAGCCTCCGTACCCAACA 61.123 55.000 0.00 0.00 0.00 3.33
4478 15036 0.391263 CTGAAGCCTCCGTACCCAAC 60.391 60.000 0.00 0.00 0.00 3.77
4479 15037 1.980052 CTGAAGCCTCCGTACCCAA 59.020 57.895 0.00 0.00 0.00 4.12
4480 15038 2.656069 GCTGAAGCCTCCGTACCCA 61.656 63.158 0.00 0.00 34.31 4.51
4481 15039 2.180159 TTGCTGAAGCCTCCGTACCC 62.180 60.000 0.00 0.00 41.18 3.69
4482 15040 0.741221 CTTGCTGAAGCCTCCGTACC 60.741 60.000 0.00 0.00 41.18 3.34
4483 15041 0.246635 TCTTGCTGAAGCCTCCGTAC 59.753 55.000 0.00 0.00 41.18 3.67
4484 15042 0.246635 GTCTTGCTGAAGCCTCCGTA 59.753 55.000 0.00 0.00 41.18 4.02
4485 15043 1.004440 GTCTTGCTGAAGCCTCCGT 60.004 57.895 0.00 0.00 41.18 4.69
4486 15044 1.004560 TGTCTTGCTGAAGCCTCCG 60.005 57.895 0.00 0.00 41.18 4.63
4487 15045 0.676151 CCTGTCTTGCTGAAGCCTCC 60.676 60.000 0.00 0.00 41.18 4.30
4488 15046 1.304509 GCCTGTCTTGCTGAAGCCTC 61.305 60.000 0.00 0.00 41.18 4.70
4489 15047 1.303155 GCCTGTCTTGCTGAAGCCT 60.303 57.895 0.00 0.00 41.18 4.58
4490 15048 1.601759 TGCCTGTCTTGCTGAAGCC 60.602 57.895 0.00 0.00 41.18 4.35
4491 15049 0.888285 AGTGCCTGTCTTGCTGAAGC 60.888 55.000 0.00 0.00 42.50 3.86
4492 15050 1.266175 CAAGTGCCTGTCTTGCTGAAG 59.734 52.381 0.00 0.00 36.38 3.02
4493 15051 1.311859 CAAGTGCCTGTCTTGCTGAA 58.688 50.000 0.00 0.00 36.38 3.02
4494 15052 3.011085 CAAGTGCCTGTCTTGCTGA 57.989 52.632 0.00 0.00 36.38 4.26
4498 15056 2.949106 CCGCAAGTGCCTGTCTTG 59.051 61.111 0.00 0.00 43.31 3.02
4499 15057 2.980233 GCCGCAAGTGCCTGTCTT 60.980 61.111 0.00 0.00 37.91 3.01
4506 15064 0.391597 TATACCTAGGCCGCAAGTGC 59.608 55.000 9.30 0.00 37.78 4.40
4507 15065 1.411246 TGTATACCTAGGCCGCAAGTG 59.589 52.381 9.30 0.00 0.00 3.16
4508 15066 1.687123 CTGTATACCTAGGCCGCAAGT 59.313 52.381 9.30 0.00 0.00 3.16
4509 15067 1.961394 TCTGTATACCTAGGCCGCAAG 59.039 52.381 9.30 1.68 0.00 4.01
4510 15068 2.076207 TCTGTATACCTAGGCCGCAA 57.924 50.000 9.30 0.00 0.00 4.85
4511 15069 2.076207 TTCTGTATACCTAGGCCGCA 57.924 50.000 9.30 2.19 0.00 5.69
4512 15070 2.547430 GGTTTCTGTATACCTAGGCCGC 60.547 54.545 9.30 0.00 0.00 6.53
4513 15071 2.963782 AGGTTTCTGTATACCTAGGCCG 59.036 50.000 9.30 0.00 42.87 6.13
4514 15072 6.490241 TTAAGGTTTCTGTATACCTAGGCC 57.510 41.667 9.30 0.00 43.88 5.19
4515 15073 6.990939 CCTTTAAGGTTTCTGTATACCTAGGC 59.009 42.308 9.30 0.00 43.88 3.93
4516 15074 7.506971 CCCTTTAAGGTTTCTGTATACCTAGG 58.493 42.308 7.41 7.41 43.88 3.02
4517 15075 6.990939 GCCCTTTAAGGTTTCTGTATACCTAG 59.009 42.308 10.40 0.00 43.88 3.02
4518 15076 6.444493 TGCCCTTTAAGGTTTCTGTATACCTA 59.556 38.462 10.40 0.00 43.88 3.08
4519 15077 5.252164 TGCCCTTTAAGGTTTCTGTATACCT 59.748 40.000 10.40 0.00 46.58 3.08
4520 15078 5.503002 TGCCCTTTAAGGTTTCTGTATACC 58.497 41.667 10.40 0.00 31.93 2.73
4521 15079 7.457024 TTTGCCCTTTAAGGTTTCTGTATAC 57.543 36.000 10.40 0.00 31.93 1.47


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

AutoCloner maintained by Alex Coulton.