Multiple sequence alignment - TraesCS6B01G265200

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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 TraesCS6B01G265200 chr6B 100.000 4620 0 0 1 4620 476840042 476844661 0.000000e+00 8532.0
1 TraesCS6B01G265200 chr6B 87.356 87 11 0 2764 2850 32333634 32333548 2.940000e-17 100.0
2 TraesCS6B01G265200 chr6A 88.299 4179 242 112 84 4108 446090839 446094924 0.000000e+00 4780.0
3 TraesCS6B01G265200 chr6A 87.961 515 54 5 4109 4617 544215082 544215594 6.610000e-168 601.0
4 TraesCS6B01G265200 chr6A 87.356 87 11 0 2764 2850 18703454 18703540 2.940000e-17 100.0
5 TraesCS6B01G265200 chr6A 96.078 51 2 0 1 51 446090789 446090839 2.960000e-12 84.2
6 TraesCS6B01G265200 chr6D 92.981 2892 113 30 848 3667 309341214 309344087 0.000000e+00 4133.0
7 TraesCS6B01G265200 chr6D 91.057 738 38 10 1 732 309340305 309341020 0.000000e+00 972.0
8 TraesCS6B01G265200 chr6D 88.378 370 30 8 3660 4016 309345079 309345448 2.550000e-117 433.0
9 TraesCS6B01G265200 chr7D 88.610 518 54 2 4107 4620 199029782 199029266 3.920000e-175 625.0
10 TraesCS6B01G265200 chr7D 88.386 508 52 5 4109 4611 202758645 202759150 5.110000e-169 604.0
11 TraesCS6B01G265200 chr3D 88.247 519 56 2 4107 4620 314696723 314696205 2.360000e-172 616.0
12 TraesCS6B01G265200 chr1B 89.463 484 49 2 4107 4589 312027396 312027878 1.100000e-170 610.0
13 TraesCS6B01G265200 chr5D 87.914 513 58 1 4109 4617 240519466 240519978 6.610000e-168 601.0
14 TraesCS6B01G265200 chr1D 87.645 518 59 2 4107 4620 115958312 115957796 8.560000e-167 597.0
15 TraesCS6B01G265200 chr3A 88.797 482 52 2 4109 4589 678729031 678729511 1.430000e-164 590.0
16 TraesCS6B01G265200 chr4D 87.283 519 60 3 4107 4620 310570821 310570304 5.150000e-164 588.0
17 TraesCS6B01G265200 chr2A 90.850 153 13 1 1520 1671 613274642 613274490 2.180000e-48 204.0
18 TraesCS6B01G265200 chr2A 83.660 153 22 3 1114 1265 613038804 613038654 1.730000e-29 141.0
19 TraesCS6B01G265200 chr2A 83.803 142 21 2 1125 1265 613175773 613175633 2.900000e-27 134.0
20 TraesCS6B01G265200 chr2B 90.196 153 14 1 1520 1671 550997444 550997292 1.010000e-46 198.0
21 TraesCS6B01G265200 chr2B 89.542 153 15 1 1520 1671 550720280 550720128 4.720000e-45 193.0
22 TraesCS6B01G265200 chr2B 88.811 143 16 0 1520 1662 550512067 550511925 4.750000e-40 176.0
23 TraesCS6B01G265200 chr2B 84.507 142 20 2 1125 1265 550512562 550512422 6.230000e-29 139.0
24 TraesCS6B01G265200 chr2B 83.916 143 19 4 1125 1265 550859182 550859042 2.900000e-27 134.0
25 TraesCS6B01G265200 chr2B 83.099 142 22 2 1125 1265 550720730 550720590 1.350000e-25 128.0
26 TraesCS6B01G265200 chr2D 89.542 153 15 1 1520 1671 471373147 471372995 4.720000e-45 193.0
27 TraesCS6B01G265200 chr2D 89.610 154 13 3 1520 1671 471450877 471450725 4.720000e-45 193.0
28 TraesCS6B01G265200 chr2D 89.542 153 14 2 1520 1671 471896657 471896506 4.720000e-45 193.0
29 TraesCS6B01G265200 chr2D 83.660 153 22 3 1114 1265 471373638 471373488 1.730000e-29 141.0
30 TraesCS6B01G265200 chr2D 82.353 153 24 3 1114 1265 471451339 471451189 3.750000e-26 130.0
31 TraesCS6B01G265200 chr2D 84.536 97 15 0 2762 2858 471896132 471896036 3.800000e-16 97.1


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 TraesCS6B01G265200 chr6B 476840042 476844661 4619 False 8532.0 8532 100.000000 1 4620 1 chr6B.!!$F1 4619
1 TraesCS6B01G265200 chr6A 446090789 446094924 4135 False 2432.1 4780 92.188500 1 4108 2 chr6A.!!$F3 4107
2 TraesCS6B01G265200 chr6A 544215082 544215594 512 False 601.0 601 87.961000 4109 4617 1 chr6A.!!$F2 508
3 TraesCS6B01G265200 chr6D 309340305 309345448 5143 False 1846.0 4133 90.805333 1 4016 3 chr6D.!!$F1 4015
4 TraesCS6B01G265200 chr7D 199029266 199029782 516 True 625.0 625 88.610000 4107 4620 1 chr7D.!!$R1 513
5 TraesCS6B01G265200 chr7D 202758645 202759150 505 False 604.0 604 88.386000 4109 4611 1 chr7D.!!$F1 502
6 TraesCS6B01G265200 chr3D 314696205 314696723 518 True 616.0 616 88.247000 4107 4620 1 chr3D.!!$R1 513
7 TraesCS6B01G265200 chr5D 240519466 240519978 512 False 601.0 601 87.914000 4109 4617 1 chr5D.!!$F1 508
8 TraesCS6B01G265200 chr1D 115957796 115958312 516 True 597.0 597 87.645000 4107 4620 1 chr1D.!!$R1 513
9 TraesCS6B01G265200 chr4D 310570304 310570821 517 True 588.0 588 87.283000 4107 4620 1 chr4D.!!$R1 513

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
200 204 0.179240 CGCGTCTGTGTTGAATGCTC 60.179 55.000 0.00 0.00 0.00 4.26 F
363 393 0.252193 CCAAGCAAGGGGGAAATCCA 60.252 55.000 1.22 0.00 37.91 3.41 F
659 691 1.006102 ACGCTTCGTGGTCTCTTGG 60.006 57.895 0.00 0.00 39.18 3.61 F
1024 1148 1.144936 CCAGAACGCTCCTCCATCC 59.855 63.158 0.00 0.00 0.00 3.51 F
2391 2607 0.106769 TGGAAACAGCTGCCTTGACA 60.107 50.000 15.27 6.35 35.01 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1026 1150 0.106419 TTCGGGTTCAAGCCTTGGTT 60.106 50.0 4.30 0.0 32.48 3.67 R
1469 1618 0.248289 GCCAGCCAATGTGCATTTCT 59.752 50.0 0.00 0.0 0.00 2.52 R
1508 1658 0.250513 GGAGTCCTGTGCGGAGAATT 59.749 55.0 0.41 0.0 44.20 2.17 R
2796 3053 0.031585 TCACTTCGTTGTCGGTCCTG 59.968 55.0 0.00 0.0 37.69 3.86 R
4003 5294 0.391793 GAGGACGAGGGGAAAGCTTG 60.392 60.0 0.00 0.0 0.00 4.01 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
78 79 3.554934 GACAGGCAATATGATGGTTCCA 58.445 45.455 0.00 0.00 0.00 3.53
148 152 3.684788 GCGTTGATTGTATATAGCAGGGG 59.315 47.826 0.00 0.00 0.00 4.79
198 202 1.793613 GCGCGTCTGTGTTGAATGC 60.794 57.895 8.43 0.00 0.00 3.56
200 204 0.179240 CGCGTCTGTGTTGAATGCTC 60.179 55.000 0.00 0.00 0.00 4.26
209 213 6.983307 GTCTGTGTTGAATGCTCATAGATAGT 59.017 38.462 0.00 0.00 33.45 2.12
210 214 6.982724 TCTGTGTTGAATGCTCATAGATAGTG 59.017 38.462 0.00 0.00 0.00 2.74
211 215 5.525012 TGTGTTGAATGCTCATAGATAGTGC 59.475 40.000 0.00 0.00 0.00 4.40
212 216 5.049818 GTGTTGAATGCTCATAGATAGTGCC 60.050 44.000 0.00 0.00 0.00 5.01
213 217 5.163269 TGTTGAATGCTCATAGATAGTGCCT 60.163 40.000 0.00 0.00 0.00 4.75
214 218 4.891260 TGAATGCTCATAGATAGTGCCTG 58.109 43.478 0.00 0.00 0.00 4.85
215 219 2.827800 TGCTCATAGATAGTGCCTGC 57.172 50.000 0.00 0.00 0.00 4.85
216 220 2.323599 TGCTCATAGATAGTGCCTGCT 58.676 47.619 0.00 0.00 0.00 4.24
269 296 4.905429 TGGCTTCTATTACAAGCAAGTCA 58.095 39.130 6.74 0.00 46.94 3.41
281 308 2.765122 AGCAAGTCACTCTCTTTCTGC 58.235 47.619 0.00 0.00 0.00 4.26
350 380 1.608590 GCTGCACTTTAGAACCAAGCA 59.391 47.619 0.00 0.00 0.00 3.91
351 381 2.034558 GCTGCACTTTAGAACCAAGCAA 59.965 45.455 0.00 0.00 0.00 3.91
352 382 3.854784 GCTGCACTTTAGAACCAAGCAAG 60.855 47.826 0.00 0.00 0.00 4.01
353 383 2.622942 TGCACTTTAGAACCAAGCAAGG 59.377 45.455 0.00 0.00 0.00 3.61
354 384 2.029918 GCACTTTAGAACCAAGCAAGGG 60.030 50.000 0.00 0.00 0.00 3.95
355 385 2.558359 CACTTTAGAACCAAGCAAGGGG 59.442 50.000 0.00 0.00 0.00 4.79
356 386 2.171003 CTTTAGAACCAAGCAAGGGGG 58.829 52.381 0.00 0.00 0.00 5.40
357 387 1.451449 TTAGAACCAAGCAAGGGGGA 58.549 50.000 0.00 0.00 0.00 4.81
358 388 1.451449 TAGAACCAAGCAAGGGGGAA 58.549 50.000 0.00 0.00 0.00 3.97
359 389 0.560688 AGAACCAAGCAAGGGGGAAA 59.439 50.000 0.00 0.00 0.00 3.13
360 390 1.149923 AGAACCAAGCAAGGGGGAAAT 59.850 47.619 0.00 0.00 0.00 2.17
361 391 1.550524 GAACCAAGCAAGGGGGAAATC 59.449 52.381 0.00 0.00 0.00 2.17
362 392 0.252239 ACCAAGCAAGGGGGAAATCC 60.252 55.000 0.00 0.00 0.00 3.01
363 393 0.252193 CCAAGCAAGGGGGAAATCCA 60.252 55.000 1.22 0.00 37.91 3.41
364 394 1.643310 CAAGCAAGGGGGAAATCCAA 58.357 50.000 1.22 0.00 37.91 3.53
365 395 1.977129 CAAGCAAGGGGGAAATCCAAA 59.023 47.619 1.22 0.00 37.91 3.28
366 396 2.371510 CAAGCAAGGGGGAAATCCAAAA 59.628 45.455 1.22 0.00 37.91 2.44
367 397 2.259917 AGCAAGGGGGAAATCCAAAAG 58.740 47.619 1.22 0.00 37.91 2.27
368 398 1.339055 GCAAGGGGGAAATCCAAAAGC 60.339 52.381 1.22 0.00 37.91 3.51
369 399 1.066929 CAAGGGGGAAATCCAAAAGCG 60.067 52.381 1.22 0.00 37.91 4.68
373 403 2.361119 GGGGGAAATCCAAAAGCGATAC 59.639 50.000 1.22 0.00 37.91 2.24
389 419 7.948278 AAGCGATACTAATCAATCCAAGTAC 57.052 36.000 0.00 0.00 31.93 2.73
415 445 8.873830 CATCAAATACGTCTTACTGATGTCTTT 58.126 33.333 15.18 0.00 43.30 2.52
463 493 4.578928 GGTATTTGCCAATTACGACCTGAT 59.421 41.667 0.00 0.00 0.00 2.90
506 536 6.151985 ACAGTTTGAAAAACATACACCAGACA 59.848 34.615 5.72 0.00 33.91 3.41
539 569 2.730183 TTTGAAAAGCTGTCACGTCG 57.270 45.000 0.00 0.00 0.00 5.12
659 691 1.006102 ACGCTTCGTGGTCTCTTGG 60.006 57.895 0.00 0.00 39.18 3.61
732 766 8.883789 ATAATGTTCGTAACAAATGTAAACCG 57.116 30.769 4.87 0.00 45.86 4.44
770 858 3.095922 GCATTAGCCGCCCTTAAGT 57.904 52.632 0.97 0.00 33.58 2.24
779 870 4.833390 AGCCGCCCTTAAGTCATTATATC 58.167 43.478 0.97 0.00 0.00 1.63
786 877 9.383519 CGCCCTTAAGTCATTATATCACAATAT 57.616 33.333 0.97 0.00 32.72 1.28
809 900 4.481112 CTCGGGCGGCAATTGCAC 62.481 66.667 30.32 21.20 44.36 4.57
822 913 6.183360 GCGGCAATTGCACTAGATTATGATAT 60.183 38.462 30.32 0.00 44.36 1.63
823 914 7.011389 GCGGCAATTGCACTAGATTATGATATA 59.989 37.037 30.32 0.00 44.36 0.86
824 915 8.546244 CGGCAATTGCACTAGATTATGATATAG 58.454 37.037 30.32 0.00 44.36 1.31
825 916 9.388506 GGCAATTGCACTAGATTATGATATAGT 57.611 33.333 30.32 0.00 40.09 2.12
923 1046 4.738740 GCTAGTGGTGATGATAACACGTAC 59.261 45.833 0.00 0.00 38.78 3.67
925 1048 6.238566 GCTAGTGGTGATGATAACACGTACTA 60.239 42.308 0.00 0.00 37.45 1.82
926 1049 6.519679 AGTGGTGATGATAACACGTACTAA 57.480 37.500 0.00 0.00 38.78 2.24
929 1052 8.038944 AGTGGTGATGATAACACGTACTAATTT 58.961 33.333 0.00 0.00 38.78 1.82
1024 1148 1.144936 CCAGAACGCTCCTCCATCC 59.855 63.158 0.00 0.00 0.00 3.51
1026 1150 1.306141 AGAACGCTCCTCCATCCCA 60.306 57.895 0.00 0.00 0.00 4.37
1055 1181 3.249189 AACCCGAAGCCTCTGCCA 61.249 61.111 0.00 0.00 38.69 4.92
1335 1483 1.656652 ATTGAGGAGAATTCGGTGCG 58.343 50.000 0.00 0.00 0.00 5.34
1345 1494 2.515996 ATTCGGTGCGTTGGGTCGAT 62.516 55.000 0.00 0.00 0.00 3.59
1383 1532 4.963428 GTAATCGGCGCCCCTCGG 62.963 72.222 23.46 6.36 38.94 4.63
1398 1547 1.394917 CCTCGGCTGAATTTCGTTCTG 59.605 52.381 0.00 0.00 37.72 3.02
1446 1595 2.787723 CGATTTGTTCGTGGCAGTAG 57.212 50.000 0.00 0.00 43.01 2.57
1454 1603 4.444536 TGTTCGTGGCAGTAGTTAGTTTT 58.555 39.130 0.00 0.00 0.00 2.43
1463 1612 5.519206 GGCAGTAGTTAGTTTTATCTGTCCG 59.481 44.000 0.00 0.00 0.00 4.79
1464 1613 6.327934 GCAGTAGTTAGTTTTATCTGTCCGA 58.672 40.000 0.00 0.00 0.00 4.55
1469 1618 9.415544 GTAGTTAGTTTTATCTGTCCGAAAAGA 57.584 33.333 0.00 0.00 0.00 2.52
1499 1648 2.360475 GGCTGGCTGGTTCTGACC 60.360 66.667 0.00 0.00 46.71 4.02
1508 1658 3.927555 GGTTCTGACCATGACCGAA 57.072 52.632 0.00 0.00 45.77 4.30
1513 1663 3.981071 TCTGACCATGACCGAAATTCT 57.019 42.857 0.00 0.00 0.00 2.40
1514 1678 3.861840 TCTGACCATGACCGAAATTCTC 58.138 45.455 0.00 0.00 0.00 2.87
1518 1682 1.368641 CATGACCGAAATTCTCCGCA 58.631 50.000 0.00 0.00 0.00 5.69
1679 1848 2.305927 AGCCCAGCACACACTATTTACT 59.694 45.455 0.00 0.00 0.00 2.24
1867 2056 4.986054 AAGGTACCAGTGTAATTGTCCA 57.014 40.909 15.94 0.00 0.00 4.02
1876 2065 0.304705 GTAATTGTCCATGCTCGGCG 59.695 55.000 0.00 0.00 0.00 6.46
1877 2066 0.813610 TAATTGTCCATGCTCGGCGG 60.814 55.000 7.21 0.00 0.00 6.13
1926 2115 7.310664 TCTAGAACACGTTAATTCGAGTGAAT 58.689 34.615 7.17 0.00 46.75 2.57
1983 2176 3.410541 GGTGATGGTAGCCACCCA 58.589 61.111 8.66 0.00 45.30 4.51
2026 2219 2.182791 CTGACGCTCACGCTCCAT 59.817 61.111 0.00 0.00 45.53 3.41
2065 2258 3.618507 CGAGATTTTTCCCTCTGTCTGCT 60.619 47.826 0.00 0.00 0.00 4.24
2066 2259 3.683802 AGATTTTTCCCTCTGTCTGCTG 58.316 45.455 0.00 0.00 0.00 4.41
2086 2279 2.231721 TGGGTGCACATTGTGATGATTG 59.768 45.455 20.77 0.00 35.23 2.67
2089 2282 3.318886 GTGCACATTGTGATGATTGCAA 58.681 40.909 20.77 0.00 42.97 4.08
2142 2339 9.127277 GTTAGTATAAAATATTGTGGGCTTGGA 57.873 33.333 0.00 0.00 0.00 3.53
2143 2340 7.582667 AGTATAAAATATTGTGGGCTTGGAC 57.417 36.000 0.00 0.00 0.00 4.02
2169 2366 3.724374 GGACGCTAAATGGCATACAGTA 58.276 45.455 0.00 0.00 0.00 2.74
2391 2607 0.106769 TGGAAACAGCTGCCTTGACA 60.107 50.000 15.27 6.35 35.01 3.58
2811 3068 2.029964 GGCAGGACCGACAACGAA 59.970 61.111 0.00 0.00 42.66 3.85
2856 3113 0.114560 TCAAGAAGAGGGTCGAGGGT 59.885 55.000 0.00 0.00 0.00 4.34
2935 3192 3.005539 GGTCCCAGAGCCAGAGCA 61.006 66.667 0.00 0.00 43.56 4.26
2947 3204 1.079543 CAGAGCACAGGGGAAGTCG 60.080 63.158 0.00 0.00 0.00 4.18
2991 3248 3.744719 CCGTCGAACTCCGGCTCA 61.745 66.667 0.00 0.00 41.49 4.26
3297 3554 2.116125 GGCACCTGCTGGGAGTTT 59.884 61.111 14.82 0.00 41.70 2.66
3309 3566 1.202806 TGGGAGTTTCTGGAGCAGTTG 60.203 52.381 0.00 0.00 32.61 3.16
3333 3590 2.244946 CATGGATCAGATGCAGGCG 58.755 57.895 10.71 0.00 32.88 5.52
3361 3618 2.994671 TTCTGCGACCTGCTCTCCG 61.995 63.158 0.00 0.00 46.63 4.63
3603 3878 3.262420 CACCGACAGTAAGATGGAAAGG 58.738 50.000 0.00 0.00 0.00 3.11
3708 4985 1.722034 AGAGCACTGTGAAGGGAAGA 58.278 50.000 12.86 0.00 0.00 2.87
3710 4987 1.346068 GAGCACTGTGAAGGGAAGAGT 59.654 52.381 12.86 0.00 0.00 3.24
3776 5053 5.502153 TTTCACGTTTTGGCTTTAAGCTA 57.498 34.783 16.89 8.04 41.99 3.32
3833 5111 2.287368 CGGCCCAACTTGTTGTAAGAAC 60.287 50.000 11.82 0.00 0.00 3.01
3845 5123 4.994217 TGTTGTAAGAACTTCATGCATCGA 59.006 37.500 0.00 0.00 0.00 3.59
3864 5142 2.159627 CGACTTTCCTCCGAAAACCATG 59.840 50.000 0.00 0.00 37.53 3.66
3869 5147 1.281867 TCCTCCGAAAACCATGCATCT 59.718 47.619 0.00 0.00 0.00 2.90
3895 5173 9.448438 TTGTTTGTGAGCTGTGACTATTTATAT 57.552 29.630 0.00 0.00 0.00 0.86
3920 5198 2.755650 CTAATGATTCCTTCCGGTCGG 58.244 52.381 0.00 2.52 0.00 4.79
3921 5199 0.909623 AATGATTCCTTCCGGTCGGT 59.090 50.000 9.36 0.00 36.47 4.69
3932 5210 4.699522 GGTCGGTCGGCCAAAGCT 62.700 66.667 6.96 0.00 40.19 3.74
3933 5211 2.668550 GTCGGTCGGCCAAAGCTT 60.669 61.111 6.96 0.00 39.73 3.74
3935 5213 3.788766 CGGTCGGCCAAAGCTTCG 61.789 66.667 6.96 0.00 39.73 3.79
3936 5214 3.431725 GGTCGGCCAAAGCTTCGG 61.432 66.667 0.00 0.00 39.73 4.30
3937 5215 2.668550 GTCGGCCAAAGCTTCGGT 60.669 61.111 5.10 0.00 39.73 4.69
3953 5244 4.760840 GTCTCGCTCGCTCGTGCA 62.761 66.667 10.43 0.00 39.64 4.57
3969 5260 0.972983 TGCAGCTCTCTCCCCTACAC 60.973 60.000 0.00 0.00 0.00 2.90
3976 5267 0.250513 CTCTCCCCTACACAAGCCAC 59.749 60.000 0.00 0.00 0.00 5.01
3997 5288 2.713877 GTGTTTTATCGGGCCCACTTA 58.286 47.619 24.92 6.93 0.00 2.24
3998 5289 3.284617 GTGTTTTATCGGGCCCACTTAT 58.715 45.455 24.92 11.78 0.00 1.73
3999 5290 3.697542 GTGTTTTATCGGGCCCACTTATT 59.302 43.478 24.92 1.17 0.00 1.40
4003 5294 0.179018 ATCGGGCCCACTTATTGCTC 60.179 55.000 24.92 0.00 0.00 4.26
4016 5307 1.844687 ATTGCTCAAGCTTTCCCCTC 58.155 50.000 0.00 0.00 42.66 4.30
4017 5308 0.606401 TTGCTCAAGCTTTCCCCTCG 60.606 55.000 0.00 0.00 42.66 4.63
4020 5311 0.391793 CTCAAGCTTTCCCCTCGTCC 60.392 60.000 0.00 0.00 0.00 4.79
4021 5312 0.836400 TCAAGCTTTCCCCTCGTCCT 60.836 55.000 0.00 0.00 0.00 3.85
4022 5313 0.391793 CAAGCTTTCCCCTCGTCCTC 60.392 60.000 0.00 0.00 0.00 3.71
4023 5314 1.554583 AAGCTTTCCCCTCGTCCTCC 61.555 60.000 0.00 0.00 0.00 4.30
4024 5315 3.032667 GCTTTCCCCTCGTCCTCCC 62.033 68.421 0.00 0.00 0.00 4.30
4025 5316 1.612442 CTTTCCCCTCGTCCTCCCA 60.612 63.158 0.00 0.00 0.00 4.37
4042 5333 4.065281 ACGCGCCTGACACCTACC 62.065 66.667 5.73 0.00 0.00 3.18
4060 5351 1.353103 CGCCGCTCATTTCACATCC 59.647 57.895 0.00 0.00 0.00 3.51
4081 5372 3.687321 TTCCTCTGCTGCCGCATCC 62.687 63.158 2.34 0.00 46.74 3.51
4098 5389 1.753848 CCCATCGCCCAGCATTTGA 60.754 57.895 0.00 0.00 0.00 2.69
4102 5393 2.215451 ATCGCCCAGCATTTGACCCT 62.215 55.000 0.00 0.00 0.00 4.34
4112 5403 2.160417 GCATTTGACCCTGTCGAAGAAG 59.840 50.000 3.54 0.00 39.02 2.85
4124 5415 3.488310 TGTCGAAGAAGTAGAAACGCAAC 59.512 43.478 0.00 0.00 39.69 4.17
4126 5417 2.722629 CGAAGAAGTAGAAACGCAACGA 59.277 45.455 0.00 0.00 0.00 3.85
4147 5438 8.708742 CAACGAAAACTAAGTCATCACAGAATA 58.291 33.333 0.00 0.00 0.00 1.75
4161 5453 9.176460 TCATCACAGAATAAGAATACATGCAAA 57.824 29.630 0.00 0.00 0.00 3.68
4164 5456 8.959548 TCACAGAATAAGAATACATGCAAACAT 58.040 29.630 0.00 0.00 36.79 2.71
4234 5526 9.674824 CATGAAGAATATGAACTAAGGAAATGC 57.325 33.333 0.00 0.00 0.00 3.56
4257 5549 7.592938 TGCAAGATAACGTGATGAAATTCTTT 58.407 30.769 0.00 0.00 0.00 2.52
4291 5583 8.437360 TTCGTCATAGCATAGATCACAAATTT 57.563 30.769 0.00 0.00 0.00 1.82
4329 5621 5.622346 ATGTAAGAGAGGGTTGAGGAATC 57.378 43.478 0.00 0.00 0.00 2.52
4332 5624 3.197927 AGAGAGGGTTGAGGAATCTGT 57.802 47.619 0.00 0.00 0.00 3.41
4366 5658 4.321230 GCTCGGTGAAGACAATGGAATTTT 60.321 41.667 0.00 0.00 31.22 1.82
4374 5666 8.352942 GTGAAGACAATGGAATTTTGTAGACTT 58.647 33.333 0.00 0.00 37.43 3.01
4502 5795 1.066430 GCCCAATCACTCGTGGTAAGA 60.066 52.381 0.00 0.00 32.60 2.10
4560 5853 2.625823 CCGGCACACCACAATGACC 61.626 63.158 0.00 0.00 34.57 4.02
4569 5862 0.961019 CCACAATGACCCTTGGTGTG 59.039 55.000 0.00 0.00 35.25 3.82
4583 5876 1.209261 TGGTGTGCTCAGAACTTGACA 59.791 47.619 0.00 0.00 0.00 3.58
4590 5883 4.757149 GTGCTCAGAACTTGACACCTAATT 59.243 41.667 0.00 0.00 34.53 1.40
4593 5886 7.119846 GTGCTCAGAACTTGACACCTAATTATT 59.880 37.037 0.00 0.00 34.53 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.550914 ATTTAGCGCCCCTCCATCAA 59.449 50.000 2.29 0.00 0.00 2.57
62 63 3.820467 TCGGAATGGAACCATCATATTGC 59.180 43.478 6.81 0.00 35.31 3.56
78 79 2.368875 ACTTGACTGTTGGTCTCGGAAT 59.631 45.455 0.00 0.00 44.74 3.01
148 152 2.789491 AAGAAGAAACAAGCTGCAGC 57.211 45.000 31.53 31.53 42.49 5.25
198 202 3.614630 GCAGAGCAGGCACTATCTATGAG 60.615 52.174 0.00 0.00 36.02 2.90
200 204 2.299582 AGCAGAGCAGGCACTATCTATG 59.700 50.000 0.00 0.00 36.02 2.23
209 213 3.312285 GAGCAGAGCAGAGCAGGCA 62.312 63.158 0.00 0.00 0.00 4.75
210 214 2.512057 GAGCAGAGCAGAGCAGGC 60.512 66.667 0.00 0.00 0.00 4.85
211 215 1.153529 CAGAGCAGAGCAGAGCAGG 60.154 63.158 0.00 0.00 0.00 4.85
212 216 1.812093 GCAGAGCAGAGCAGAGCAG 60.812 63.158 0.00 0.00 0.00 4.24
213 217 2.265109 GCAGAGCAGAGCAGAGCA 59.735 61.111 0.00 0.00 0.00 4.26
214 218 2.512057 GGCAGAGCAGAGCAGAGC 60.512 66.667 0.00 0.00 0.00 4.09
215 219 2.187424 GGGCAGAGCAGAGCAGAG 59.813 66.667 0.00 0.00 0.00 3.35
216 220 3.397439 GGGGCAGAGCAGAGCAGA 61.397 66.667 0.00 0.00 0.00 4.26
269 296 4.696479 TCCTTTGAAGCAGAAAGAGAGT 57.304 40.909 0.00 0.00 33.01 3.24
281 308 2.297315 GACTGGCCCTTTTCCTTTGAAG 59.703 50.000 0.00 0.00 0.00 3.02
350 380 1.203125 TCGCTTTTGGATTTCCCCCTT 60.203 47.619 0.00 0.00 34.29 3.95
351 381 0.407918 TCGCTTTTGGATTTCCCCCT 59.592 50.000 0.00 0.00 34.29 4.79
352 382 1.485124 ATCGCTTTTGGATTTCCCCC 58.515 50.000 0.00 0.00 34.29 5.40
353 383 3.288092 AGTATCGCTTTTGGATTTCCCC 58.712 45.455 0.00 0.00 34.29 4.81
354 384 6.262273 TGATTAGTATCGCTTTTGGATTTCCC 59.738 38.462 0.00 0.00 33.23 3.97
355 385 7.259290 TGATTAGTATCGCTTTTGGATTTCC 57.741 36.000 0.00 0.00 33.23 3.13
356 386 9.387123 GATTGATTAGTATCGCTTTTGGATTTC 57.613 33.333 0.00 0.00 33.23 2.17
357 387 8.352942 GGATTGATTAGTATCGCTTTTGGATTT 58.647 33.333 0.00 0.00 33.23 2.17
358 388 7.502226 TGGATTGATTAGTATCGCTTTTGGATT 59.498 33.333 0.00 0.00 33.23 3.01
359 389 6.998074 TGGATTGATTAGTATCGCTTTTGGAT 59.002 34.615 0.00 0.00 33.23 3.41
360 390 6.353323 TGGATTGATTAGTATCGCTTTTGGA 58.647 36.000 0.00 0.00 33.23 3.53
361 391 6.618287 TGGATTGATTAGTATCGCTTTTGG 57.382 37.500 0.00 0.00 33.23 3.28
362 392 7.697691 ACTTGGATTGATTAGTATCGCTTTTG 58.302 34.615 0.00 0.00 33.23 2.44
363 393 7.865706 ACTTGGATTGATTAGTATCGCTTTT 57.134 32.000 0.00 0.00 33.23 2.27
364 394 7.985184 TGTACTTGGATTGATTAGTATCGCTTT 59.015 33.333 0.00 0.00 33.23 3.51
365 395 7.497595 TGTACTTGGATTGATTAGTATCGCTT 58.502 34.615 0.00 0.00 33.23 4.68
366 396 7.050970 TGTACTTGGATTGATTAGTATCGCT 57.949 36.000 0.00 0.00 33.23 4.93
367 397 7.598869 TGATGTACTTGGATTGATTAGTATCGC 59.401 37.037 0.00 0.00 33.23 4.58
368 398 9.476202 TTGATGTACTTGGATTGATTAGTATCG 57.524 33.333 0.00 0.00 33.23 2.92
389 419 7.993821 AGACATCAGTAAGACGTATTTGATG 57.006 36.000 25.18 25.18 44.47 3.07
398 428 5.377358 CAGCAAAAAGACATCAGTAAGACG 58.623 41.667 0.00 0.00 0.00 4.18
415 445 1.672682 TAACATCCGCGCCAGCAAA 60.673 52.632 0.00 0.00 45.49 3.68
441 471 5.295787 TCATCAGGTCGTAATTGGCAAATAC 59.704 40.000 14.14 14.14 0.00 1.89
451 481 1.112113 ACGCCTCATCAGGTCGTAAT 58.888 50.000 3.49 0.00 45.17 1.89
506 536 5.418524 AGCTTTTCAAAAACCCATTGCTTTT 59.581 32.000 0.00 0.00 0.00 2.27
522 552 1.205657 GACGACGTGACAGCTTTTCA 58.794 50.000 4.58 0.00 0.00 2.69
528 558 3.461982 CTGCGACGACGTGACAGC 61.462 66.667 4.58 6.31 41.98 4.40
656 688 3.949113 AGTGAGGTTTTAAAGAACGCCAA 59.051 39.130 0.00 0.00 0.00 4.52
659 691 4.750598 AGAGAGTGAGGTTTTAAAGAACGC 59.249 41.667 0.00 0.00 0.00 4.84
714 746 6.542574 AATCACGGTTTACATTTGTTACGA 57.457 33.333 0.00 0.00 0.00 3.43
717 749 7.378995 CCGAAAAATCACGGTTTACATTTGTTA 59.621 33.333 0.00 0.00 43.53 2.41
732 766 4.000988 TGCCTTCTACTCCGAAAAATCAC 58.999 43.478 0.00 0.00 0.00 3.06
794 885 3.112126 CTAGTGCAATTGCCGCCCG 62.112 63.158 26.94 8.49 41.18 6.13
795 886 1.103398 ATCTAGTGCAATTGCCGCCC 61.103 55.000 26.94 12.37 41.18 6.13
865 988 8.648097 GCGATTACTGGTATTAATGTACTGATG 58.352 37.037 0.00 0.00 0.00 3.07
866 989 8.364894 TGCGATTACTGGTATTAATGTACTGAT 58.635 33.333 0.00 0.00 0.00 2.90
929 1052 6.872020 TGTTTTGTGTCGTTTGGGAAATAAAA 59.128 30.769 0.00 0.00 0.00 1.52
1024 1148 1.805428 CGGGTTCAAGCCTTGGTTGG 61.805 60.000 4.30 0.00 40.81 3.77
1026 1150 0.106419 TTCGGGTTCAAGCCTTGGTT 60.106 50.000 4.30 0.00 32.48 3.67
1066 1192 3.261250 TCGGAGAGGTGTACAGGAC 57.739 57.895 0.00 0.00 0.00 3.85
1282 1429 2.739292 GTGCTCGTAGAAATGCGGATA 58.261 47.619 0.00 0.00 34.09 2.59
1335 1483 0.810031 CACCCGATCATCGACCCAAC 60.810 60.000 9.16 0.00 43.74 3.77
1383 1532 2.092838 CGGAGACAGAACGAAATTCAGC 59.907 50.000 0.00 0.00 40.09 4.26
1398 1547 4.500116 GACGAGCTGGCCGGAGAC 62.500 72.222 18.31 4.29 0.00 3.36
1441 1590 8.752766 TTTCGGACAGATAAAACTAACTACTG 57.247 34.615 0.00 0.00 0.00 2.74
1445 1594 8.365647 TCTCTTTTCGGACAGATAAAACTAACT 58.634 33.333 0.00 0.00 0.00 2.24
1446 1595 8.530269 TCTCTTTTCGGACAGATAAAACTAAC 57.470 34.615 0.00 0.00 0.00 2.34
1454 1603 5.351465 GTGCATTTCTCTTTTCGGACAGATA 59.649 40.000 0.00 0.00 0.00 1.98
1463 1612 4.387862 CAGCCAATGTGCATTTCTCTTTTC 59.612 41.667 0.00 0.00 0.00 2.29
1464 1613 4.312443 CAGCCAATGTGCATTTCTCTTTT 58.688 39.130 0.00 0.00 0.00 2.27
1469 1618 0.248289 GCCAGCCAATGTGCATTTCT 59.752 50.000 0.00 0.00 0.00 2.52
1499 1648 1.062587 GTGCGGAGAATTTCGGTCATG 59.937 52.381 0.00 0.00 0.00 3.07
1500 1649 1.338674 TGTGCGGAGAATTTCGGTCAT 60.339 47.619 0.00 0.00 0.00 3.06
1506 1656 2.003301 GAGTCCTGTGCGGAGAATTTC 58.997 52.381 0.00 0.00 44.20 2.17
1507 1657 1.339151 GGAGTCCTGTGCGGAGAATTT 60.339 52.381 0.41 0.00 44.20 1.82
1508 1658 0.250513 GGAGTCCTGTGCGGAGAATT 59.749 55.000 0.41 0.00 44.20 2.17
1513 1663 3.695606 GCTGGAGTCCTGTGCGGA 61.696 66.667 16.61 0.00 40.30 5.54
1518 1682 2.932234 CGTTCCGCTGGAGTCCTGT 61.932 63.158 16.61 0.00 31.21 4.00
1523 1687 3.883744 CTTGCCGTTCCGCTGGAGT 62.884 63.158 0.00 0.00 31.21 3.85
1679 1848 9.429359 GTACAGTACAGTACAGAGAGTAAGTAA 57.571 37.037 20.17 0.00 42.97 2.24
1693 1862 6.391537 TCAATCATTTGCGTACAGTACAGTA 58.608 36.000 11.37 0.00 32.61 2.74
1841 2030 5.067954 ACAATTACACTGGTACCTTTCACC 58.932 41.667 14.36 0.00 36.54 4.02
1879 2068 3.885521 GATTGCCGCCAGCTCAGC 61.886 66.667 0.00 0.00 44.23 4.26
1880 2069 3.207669 GGATTGCCGCCAGCTCAG 61.208 66.667 0.00 0.00 44.23 3.35
1881 2070 4.802051 GGGATTGCCGCCAGCTCA 62.802 66.667 0.00 0.00 44.23 4.26
1885 2074 2.587322 TAGAACGGGATTGCCGCCAG 62.587 60.000 17.19 0.00 33.83 4.85
1926 2115 4.415512 TCCCTCTTTTCTTTCCTTCCTTCA 59.584 41.667 0.00 0.00 0.00 3.02
1974 2167 0.696501 GGAAAAGGTCTGGGTGGCTA 59.303 55.000 0.00 0.00 0.00 3.93
1982 2175 2.299297 ACTCCACTACGGAAAAGGTCTG 59.701 50.000 0.00 0.00 45.75 3.51
1983 2176 2.606378 ACTCCACTACGGAAAAGGTCT 58.394 47.619 0.00 0.00 45.75 3.85
2026 2219 1.375396 CGTGGATTTGGAGCGTCCA 60.375 57.895 3.02 3.02 46.61 4.02
2052 2245 1.915266 CACCCAGCAGACAGAGGGA 60.915 63.158 2.90 0.00 44.30 4.20
2065 2258 2.219080 ATCATCACAATGTGCACCCA 57.781 45.000 15.69 0.00 34.32 4.51
2066 2259 2.883574 CAATCATCACAATGTGCACCC 58.116 47.619 15.69 0.00 34.32 4.61
2142 2339 1.153706 CCATTTAGCGTCCGTCCGT 60.154 57.895 0.00 0.00 0.00 4.69
2143 2340 2.522638 GCCATTTAGCGTCCGTCCG 61.523 63.158 0.00 0.00 0.00 4.79
2246 2452 3.505386 ACTGCCAGAGGATATACCAGAG 58.495 50.000 0.00 0.00 42.04 3.35
2250 2456 2.370189 AGCAACTGCCAGAGGATATACC 59.630 50.000 0.00 0.00 43.38 2.73
2298 2504 3.675228 GCCGCTCTACTGTACAGCTAAAA 60.675 47.826 22.90 3.57 0.00 1.52
2391 2607 0.690762 ACTACGTGCCAGTTGGGATT 59.309 50.000 0.00 0.00 40.01 3.01
2567 2793 0.988832 TCCTTTTGTGGCTCGGGTAT 59.011 50.000 0.00 0.00 0.00 2.73
2569 2795 1.073199 CTCCTTTTGTGGCTCGGGT 59.927 57.895 0.00 0.00 0.00 5.28
2796 3053 0.031585 TCACTTCGTTGTCGGTCCTG 59.968 55.000 0.00 0.00 37.69 3.86
2811 3068 3.890147 ACGAGTTCCAGTAGTTCTTCACT 59.110 43.478 0.00 0.00 39.87 3.41
2930 3187 2.286523 CCGACTTCCCCTGTGCTCT 61.287 63.158 0.00 0.00 0.00 4.09
2935 3192 4.003788 CGCACCGACTTCCCCTGT 62.004 66.667 0.00 0.00 0.00 4.00
3297 3554 1.372683 GCTGTCCAACTGCTCCAGA 59.627 57.895 0.00 0.00 39.55 3.86
3309 3566 1.236628 GCATCTGATCCATGCTGTCC 58.763 55.000 16.10 0.00 42.95 4.02
3521 3786 4.437390 GCACCAGTATACATGCTGTCAAAC 60.437 45.833 15.65 0.00 38.62 2.93
3603 3878 1.909700 TGTGCATTCTTCCTGAACCC 58.090 50.000 0.00 0.00 37.52 4.11
3708 4985 5.163301 TGTTAAAGTGGAAGAGAGCTTGACT 60.163 40.000 0.00 0.00 33.61 3.41
3710 4987 5.290493 TGTTAAAGTGGAAGAGAGCTTGA 57.710 39.130 0.00 0.00 33.61 3.02
3776 5053 9.632638 ATTGTAAGATAAACTAATCACTGGCAT 57.367 29.630 0.00 0.00 0.00 4.40
3813 5090 2.956333 AGTTCTTACAACAAGTTGGGCC 59.044 45.455 16.45 0.00 44.45 5.80
3833 5111 2.611292 GGAGGAAAGTCGATGCATGAAG 59.389 50.000 2.46 0.00 0.00 3.02
3845 5123 1.886542 GCATGGTTTTCGGAGGAAAGT 59.113 47.619 0.00 0.00 42.72 2.66
3864 5142 2.291465 TCACAGCTCACAAACAAGATGC 59.709 45.455 0.00 0.00 32.22 3.91
3869 5147 7.744087 ATAAATAGTCACAGCTCACAAACAA 57.256 32.000 0.00 0.00 0.00 2.83
3920 5198 2.668550 ACCGAAGCTTTGGCCGAC 60.669 61.111 29.64 0.64 39.73 4.79
3921 5199 2.358247 GACCGAAGCTTTGGCCGA 60.358 61.111 29.64 0.00 39.73 5.54
3931 5209 2.277628 GAGCGAGCGAGACCGAAG 60.278 66.667 0.00 0.00 38.22 3.79
3932 5210 4.161976 CGAGCGAGCGAGACCGAA 62.162 66.667 0.00 0.00 38.22 4.30
3936 5214 4.760840 TGCACGAGCGAGCGAGAC 62.761 66.667 7.70 0.00 46.23 3.36
3937 5215 4.467062 CTGCACGAGCGAGCGAGA 62.467 66.667 7.70 0.00 46.23 4.04
3950 5241 0.972983 GTGTAGGGGAGAGAGCTGCA 60.973 60.000 1.02 0.00 33.56 4.41
3952 5243 1.480137 CTTGTGTAGGGGAGAGAGCTG 59.520 57.143 0.00 0.00 0.00 4.24
3953 5244 1.859302 CTTGTGTAGGGGAGAGAGCT 58.141 55.000 0.00 0.00 0.00 4.09
3969 5260 1.135803 CCCGATAAAACACGTGGCTTG 60.136 52.381 21.57 2.58 0.00 4.01
3976 5267 0.675522 AGTGGGCCCGATAAAACACG 60.676 55.000 19.37 0.00 34.28 4.49
3997 5288 1.844687 GAGGGGAAAGCTTGAGCAAT 58.155 50.000 0.00 0.00 45.16 3.56
3998 5289 0.606401 CGAGGGGAAAGCTTGAGCAA 60.606 55.000 0.00 0.00 45.16 3.91
3999 5290 1.003355 CGAGGGGAAAGCTTGAGCA 60.003 57.895 0.00 0.00 45.16 4.26
4003 5294 0.391793 GAGGACGAGGGGAAAGCTTG 60.392 60.000 0.00 0.00 0.00 4.01
4023 5314 4.063967 TAGGTGTCAGGCGCGTGG 62.064 66.667 27.93 11.20 0.00 4.94
4024 5315 2.809601 GTAGGTGTCAGGCGCGTG 60.810 66.667 23.52 23.52 0.00 5.34
4025 5316 4.065281 GGTAGGTGTCAGGCGCGT 62.065 66.667 8.43 0.00 0.00 6.01
4034 5325 2.180159 AAATGAGCGGCGGTAGGTGT 62.180 55.000 13.22 0.00 0.00 4.16
4042 5333 1.091771 AGGATGTGAAATGAGCGGCG 61.092 55.000 0.51 0.51 0.00 6.46
4060 5351 2.873288 GCGGCAGCAGAGGAAAAG 59.127 61.111 3.18 0.00 44.35 2.27
4081 5372 1.434696 GTCAAATGCTGGGCGATGG 59.565 57.895 0.00 0.00 0.00 3.51
4086 5377 1.598701 GACAGGGTCAAATGCTGGGC 61.599 60.000 0.00 0.00 32.09 5.36
4098 5389 3.305199 CGTTTCTACTTCTTCGACAGGGT 60.305 47.826 0.00 0.00 0.00 4.34
4102 5393 3.358707 TGCGTTTCTACTTCTTCGACA 57.641 42.857 0.00 0.00 0.00 4.35
4112 5403 5.731278 ACTTAGTTTTCGTTGCGTTTCTAC 58.269 37.500 0.00 0.00 0.00 2.59
4124 5415 9.140286 TCTTATTCTGTGATGACTTAGTTTTCG 57.860 33.333 0.00 0.00 0.00 3.46
4164 5456 8.334263 TGCATGTTCTTCACTTTTACATATCA 57.666 30.769 0.00 0.00 0.00 2.15
4174 5466 6.822667 TGTATGATTGCATGTTCTTCACTT 57.177 33.333 0.00 0.00 35.94 3.16
4257 5549 9.411801 GATCTATGCTATGACGAATTTGAACTA 57.588 33.333 0.00 0.00 0.00 2.24
4273 5565 8.054152 TGCTGAAAAATTTGTGATCTATGCTA 57.946 30.769 0.00 0.00 0.00 3.49
4291 5583 6.593770 TCTCTTACATTATTTCGCTGCTGAAA 59.406 34.615 17.24 17.24 41.69 2.69
4329 5621 1.740296 CGAGCCAACCCGGTTACAG 60.740 63.158 1.43 0.00 36.97 2.74
4366 5658 3.625764 GCAACAACTGGAACAAGTCTACA 59.374 43.478 0.00 0.00 38.70 2.74
4374 5666 3.435105 GTTGATGCAACAACTGGAACA 57.565 42.857 27.07 0.00 43.09 3.18
4502 5795 6.424032 AGGTTTTGAAAGTCTACCTTGAAGT 58.576 36.000 0.00 0.00 35.77 3.01
4560 5853 1.605710 CAAGTTCTGAGCACACCAAGG 59.394 52.381 0.00 0.00 0.00 3.61
4569 5862 7.617041 AATAATTAGGTGTCAAGTTCTGAGC 57.383 36.000 0.00 0.00 33.60 4.26
4583 5876 8.794335 GAAGACTGTCTTCCAAATAATTAGGT 57.206 34.615 31.05 3.55 45.34 3.08


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

AutoCloner maintained by Alex Coulton.