Multiple sequence alignment - TraesCS7A01G187100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G187100 chr7A 100.000 6673 0 0 1 6673 142653851 142647179 0.000000e+00 12323.0
1 TraesCS7A01G187100 chr7A 84.295 312 33 10 2180 2485 142651379 142651078 2.350000e-74 291.0
2 TraesCS7A01G187100 chr7A 84.295 312 33 10 2473 2774 142651672 142651367 2.350000e-74 291.0
3 TraesCS7A01G187100 chr7B 94.652 4787 187 21 1477 6228 105839918 105835166 0.000000e+00 7358.0
4 TraesCS7A01G187100 chr7B 91.971 1121 40 19 541 1618 105840929 105839816 0.000000e+00 1526.0
5 TraesCS7A01G187100 chr7B 82.222 315 34 12 2473 2774 105839216 105838911 1.110000e-62 252.0
6 TraesCS7A01G187100 chr7B 95.726 117 4 1 6535 6651 105834878 105834763 3.180000e-43 187.0
7 TraesCS7A01G187100 chr7B 86.857 175 6 7 6263 6437 105835066 105834909 5.320000e-41 180.0
8 TraesCS7A01G187100 chr7D 95.296 2955 90 16 3701 6651 140770661 140767752 0.000000e+00 4641.0
9 TraesCS7A01G187100 chr7D 94.066 2174 80 18 1527 3671 140772815 140770662 0.000000e+00 3254.0
10 TraesCS7A01G187100 chr7D 93.351 1113 28 14 514 1581 140773833 140772722 0.000000e+00 1604.0
11 TraesCS7A01G187100 chr7D 83.175 315 35 10 2473 2774 140772162 140771853 8.530000e-69 272.0
12 TraesCS7A01G187100 chr1A 96.887 514 16 0 1 514 53320015 53320528 0.000000e+00 861.0
13 TraesCS7A01G187100 chr1A 86.486 296 36 3 78 370 377745980 377746274 8.350000e-84 322.0
14 TraesCS7A01G187100 chr1A 82.243 107 11 2 27 125 291678140 291678034 1.190000e-12 86.1
15 TraesCS7A01G187100 chr1A 100.000 28 0 0 1349 1376 23421493 23421520 1.200000e-02 52.8
16 TraesCS7A01G187100 chr6B 89.524 525 44 8 1 517 354950534 354950013 0.000000e+00 654.0
17 TraesCS7A01G187100 chr6B 89.443 521 44 6 1 514 356068991 356068475 0.000000e+00 647.0
18 TraesCS7A01G187100 chr6B 83.178 107 10 2 27 125 471315006 471314900 2.560000e-14 91.6
19 TraesCS7A01G187100 chr2A 92.683 410 24 2 1 405 331180826 331181234 2.680000e-163 586.0
20 TraesCS7A01G187100 chr2A 81.893 243 37 7 124 362 161631233 161631472 1.470000e-46 198.0
21 TraesCS7A01G187100 chr4A 89.818 275 22 5 237 511 648259118 648259386 1.380000e-91 348.0
22 TraesCS7A01G187100 chr4A 94.667 150 8 0 365 514 374620445 374620594 4.020000e-57 233.0
23 TraesCS7A01G187100 chr4A 82.979 141 16 4 5925 6063 60018917 60019051 3.270000e-23 121.0
24 TraesCS7A01G187100 chr4A 83.178 107 10 2 27 125 690238210 690238316 2.560000e-14 91.6
25 TraesCS7A01G187100 chr1B 79.921 254 42 9 124 371 323936129 323935879 1.910000e-40 178.0
26 TraesCS7A01G187100 chr4D 79.747 237 44 3 132 367 431198503 431198270 1.150000e-37 169.0
27 TraesCS7A01G187100 chr4D 85.000 140 16 5 5925 6063 402529387 402529522 3.250000e-28 137.0
28 TraesCS7A01G187100 chr4B 81.818 132 17 4 1 125 29295000 29294869 3.290000e-18 104.0
29 TraesCS7A01G187100 chr4B 90.909 44 2 2 476 517 475929004 475928961 2.600000e-04 58.4
30 TraesCS7A01G187100 chrUn 83.178 107 10 2 27 125 38661774 38661668 2.560000e-14 91.6
31 TraesCS7A01G187100 chr3D 90.909 44 2 2 472 514 56449560 56449518 2.600000e-04 58.4
32 TraesCS7A01G187100 chr5D 89.130 46 4 1 470 514 316111414 316111369 1.000000e-03 56.5
33 TraesCS7A01G187100 chr3A 90.476 42 2 2 478 517 537496475 537496516 3.000000e-03 54.7


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 TraesCS7A01G187100 chr7A 142647179 142653851 6672 True 4301.666667 12323 89.5300 1 6673 3 chr7A.!!$R1 6672
1 TraesCS7A01G187100 chr7B 105834763 105840929 6166 True 1900.600000 7358 90.2856 541 6651 5 chr7B.!!$R1 6110
2 TraesCS7A01G187100 chr7D 140767752 140773833 6081 True 2442.750000 4641 91.4720 514 6651 4 chr7D.!!$R1 6137
3 TraesCS7A01G187100 chr1A 53320015 53320528 513 False 861.000000 861 96.8870 1 514 1 chr1A.!!$F2 513
4 TraesCS7A01G187100 chr6B 354950013 354950534 521 True 654.000000 654 89.5240 1 517 1 chr6B.!!$R1 516
5 TraesCS7A01G187100 chr6B 356068475 356068991 516 True 647.000000 647 89.4430 1 514 1 chr6B.!!$R2 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
676 696 1.004185 CATCAGCAGCGTGATAAGCAC 60.004 52.381 6.94 0.0 44.21 4.40 F
1571 1736 0.123266 AAGAAGGGGATGGGGAAGGA 59.877 55.000 0.00 0.0 0.00 3.36 F
1599 1764 0.179018 CGCAGGGGAATAAGAAGGGG 60.179 60.000 0.00 0.0 0.00 4.79 F
1618 1783 0.621862 GATGTGGAAGGAGGAGGGGT 60.622 60.000 0.00 0.0 0.00 4.95 F
2376 2544 1.131126 GCGGGCCATCATCGAATAATG 59.869 52.381 4.39 0.0 0.00 1.90 F
2377 2545 1.131126 CGGGCCATCATCGAATAATGC 59.869 52.381 4.39 0.0 0.00 3.56 F
4398 4616 1.417890 ACAAGTGAGTGTCCTTGGGAG 59.582 52.381 0.00 0.0 41.84 4.30 F
4898 5116 4.720902 CGGCATGTCCCACCAGCA 62.721 66.667 0.00 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1759 0.121197 TCCTCCTTCCACATCCCCTT 59.879 55.000 0.00 0.0 0.00 3.95 R
3541 3751 0.609131 AAGGATTCGTGCACAAGGGG 60.609 55.000 18.64 0.0 0.00 4.79 R
3697 3907 7.031975 CCATTTTTCAGAGGAATAAGAAGCAC 58.968 38.462 0.00 0.0 31.93 4.40 R
3796 4006 0.595053 ACATATCGCACGCCTCTTCG 60.595 55.000 0.00 0.0 0.00 3.79 R
3913 4130 3.754965 TCAAACAGATTGACCCTTGAGG 58.245 45.455 0.00 0.0 43.08 3.86 R
4542 4760 6.556495 AGATTACTCCTTGGAGCTGATTGATA 59.444 38.462 15.93 0.0 0.00 2.15 R
5207 5426 0.108756 GAACAGTGGTCCGGTAGAGC 60.109 60.000 0.00 0.0 43.62 4.09 R
6123 6344 0.247736 AAGGAGAGCACACGGATGTC 59.752 55.000 0.00 0.0 36.72 3.06 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
35 36 6.407202 ACAAGTTAGAGGAAAATAGCATCGT 58.593 36.000 0.00 0.00 0.00 3.73
187 196 5.983118 GGTTCACAGTTTGACCCTAAATTTG 59.017 40.000 0.00 0.00 33.87 2.32
525 535 6.369890 CAGGCCATGTGCTATAACTACAATAG 59.630 42.308 5.01 0.00 40.92 1.73
529 539 9.307121 GCCATGTGCTATAACTACAATAGATAG 57.693 37.037 0.00 0.00 36.87 2.08
650 669 2.984471 TCCAAGCGCGATATACGAAATC 59.016 45.455 12.10 0.00 45.77 2.17
676 696 1.004185 CATCAGCAGCGTGATAAGCAC 60.004 52.381 6.94 0.00 44.21 4.40
749 769 3.194005 TCAGTTTCAGTTCCACACTCC 57.806 47.619 0.00 0.00 30.92 3.85
1239 1320 0.471211 AACCGTCCACTCCTTCTGGA 60.471 55.000 0.00 0.00 40.69 3.86
1270 1351 1.138247 GCATCTTTGAAGCCAGCCG 59.862 57.895 0.00 0.00 0.00 5.52
1304 1385 1.153086 CATCTGCTGCCCAGGTACC 60.153 63.158 2.73 2.73 42.05 3.34
1432 1519 1.404391 CTAGCGGTAGTAGTGGTGGTG 59.596 57.143 13.51 0.00 0.00 4.17
1520 1646 0.180406 GCGCAGGGGAATAAGAAGGA 59.820 55.000 0.30 0.00 0.00 3.36
1565 1730 1.429299 GGGGAATAAGAAGGGGATGGG 59.571 57.143 0.00 0.00 0.00 4.00
1566 1731 1.429299 GGGAATAAGAAGGGGATGGGG 59.571 57.143 0.00 0.00 0.00 4.96
1567 1732 2.428901 GGAATAAGAAGGGGATGGGGA 58.571 52.381 0.00 0.00 0.00 4.81
1568 1733 2.789399 GGAATAAGAAGGGGATGGGGAA 59.211 50.000 0.00 0.00 0.00 3.97
1569 1734 3.181428 GGAATAAGAAGGGGATGGGGAAG 60.181 52.174 0.00 0.00 0.00 3.46
1570 1735 1.907240 TAAGAAGGGGATGGGGAAGG 58.093 55.000 0.00 0.00 0.00 3.46
1571 1736 0.123266 AAGAAGGGGATGGGGAAGGA 59.877 55.000 0.00 0.00 0.00 3.36
1572 1737 0.327964 AGAAGGGGATGGGGAAGGAG 60.328 60.000 0.00 0.00 0.00 3.69
1573 1738 1.309102 AAGGGGATGGGGAAGGAGG 60.309 63.158 0.00 0.00 0.00 4.30
1574 1739 1.848835 AAGGGGATGGGGAAGGAGGA 61.849 60.000 0.00 0.00 0.00 3.71
1575 1740 1.772156 GGGGATGGGGAAGGAGGAG 60.772 68.421 0.00 0.00 0.00 3.69
1576 1741 1.772156 GGGATGGGGAAGGAGGAGG 60.772 68.421 0.00 0.00 0.00 4.30
1577 1742 1.772156 GGATGGGGAAGGAGGAGGG 60.772 68.421 0.00 0.00 0.00 4.30
1578 1743 1.772156 GATGGGGAAGGAGGAGGGG 60.772 68.421 0.00 0.00 0.00 4.79
1579 1744 3.369161 ATGGGGAAGGAGGAGGGGG 62.369 68.421 0.00 0.00 0.00 5.40
1591 1756 4.835456 AGGGGGCGCAGGGGAATA 62.835 66.667 10.83 0.00 0.00 1.75
1592 1757 3.816090 GGGGGCGCAGGGGAATAA 61.816 66.667 10.83 0.00 0.00 1.40
1593 1758 2.203351 GGGGCGCAGGGGAATAAG 60.203 66.667 10.83 0.00 0.00 1.73
1594 1759 2.752807 GGGGCGCAGGGGAATAAGA 61.753 63.158 10.83 0.00 0.00 2.10
1595 1760 1.226262 GGGCGCAGGGGAATAAGAA 59.774 57.895 10.83 0.00 0.00 2.52
1596 1761 0.819666 GGGCGCAGGGGAATAAGAAG 60.820 60.000 10.83 0.00 0.00 2.85
1597 1762 0.819666 GGCGCAGGGGAATAAGAAGG 60.820 60.000 10.83 0.00 0.00 3.46
1598 1763 0.819666 GCGCAGGGGAATAAGAAGGG 60.820 60.000 0.30 0.00 0.00 3.95
1599 1764 0.179018 CGCAGGGGAATAAGAAGGGG 60.179 60.000 0.00 0.00 0.00 4.79
1600 1765 1.222567 GCAGGGGAATAAGAAGGGGA 58.777 55.000 0.00 0.00 0.00 4.81
1601 1766 1.783365 GCAGGGGAATAAGAAGGGGAT 59.217 52.381 0.00 0.00 0.00 3.85
1602 1767 2.489802 GCAGGGGAATAAGAAGGGGATG 60.490 54.545 0.00 0.00 0.00 3.51
1603 1768 2.785857 CAGGGGAATAAGAAGGGGATGT 59.214 50.000 0.00 0.00 0.00 3.06
1618 1783 0.621862 GATGTGGAAGGAGGAGGGGT 60.622 60.000 0.00 0.00 0.00 4.95
1642 1807 1.355720 AGAAAGAAGGGGGTGGTGATG 59.644 52.381 0.00 0.00 0.00 3.07
1716 1881 2.184167 CCAGAACCGCGTGTTTGGT 61.184 57.895 20.21 5.85 41.20 3.67
1854 2019 4.706962 GGGATAAACCTTGTCAGAAATGCT 59.293 41.667 0.00 0.00 38.98 3.79
1972 2137 2.754552 TGCATTGTTCCTAAGGATGTGC 59.245 45.455 0.00 0.00 0.00 4.57
2053 2218 4.225942 TGAGTAGAAATCTTGCTGGGTCAT 59.774 41.667 0.00 0.00 0.00 3.06
2054 2219 4.521146 AGTAGAAATCTTGCTGGGTCATG 58.479 43.478 0.00 0.00 0.00 3.07
2119 2284 4.378459 GCCATGGATTACAGTAATTAGCGC 60.378 45.833 18.40 0.00 0.00 5.92
2161 2326 5.218885 TCAATTGTGCATTTGTTCGTAAGG 58.781 37.500 5.13 0.00 38.47 2.69
2174 2339 2.563702 TCGTAAGGGTTCACAAACACC 58.436 47.619 0.00 0.00 39.81 4.16
2269 2437 5.125257 TGTTTGTTGGATAGTATGTGCATGG 59.875 40.000 0.00 0.00 0.00 3.66
2311 2479 8.855804 AGGGTTCCTTAGTTTCATATCTTCTA 57.144 34.615 0.00 0.00 0.00 2.10
2358 2526 4.153117 GCTAGGTGGATCATGATTTTAGCG 59.847 45.833 10.14 0.00 0.00 4.26
2361 2529 2.030805 GTGGATCATGATTTTAGCGGGC 60.031 50.000 10.14 0.00 0.00 6.13
2369 2537 1.197721 GATTTTAGCGGGCCATCATCG 59.802 52.381 4.39 0.00 0.00 3.84
2376 2544 1.131126 GCGGGCCATCATCGAATAATG 59.869 52.381 4.39 0.00 0.00 1.90
2377 2545 1.131126 CGGGCCATCATCGAATAATGC 59.869 52.381 4.39 0.00 0.00 3.56
2571 2740 3.565063 TGCATGTGTCCATATATGTGCAC 59.435 43.478 17.67 19.34 33.84 4.57
2627 2796 8.728596 AGTTATTATGGAAGATGTAGCTAGGT 57.271 34.615 0.00 0.00 0.00 3.08
2691 2860 8.210946 TCCGTTCTCCAATTATAATTGAGATGT 58.789 33.333 31.05 0.00 46.72 3.06
2720 2889 7.611467 TCCTACATAGCATATAAAAATGGCCAG 59.389 37.037 13.05 0.00 0.00 4.85
2840 3010 6.098982 TCCCTTTTGGTGCTTGATTTTTCTTA 59.901 34.615 0.00 0.00 38.10 2.10
2845 3015 6.040209 TGGTGCTTGATTTTTCTTATGCAT 57.960 33.333 3.79 3.79 0.00 3.96
3091 3280 5.545658 AGTGTAAATTTATGTGTCAGCCG 57.454 39.130 0.31 0.00 0.00 5.52
3343 3548 7.109259 CGTCTAAAAAGTTTACAACGTTAGCAC 59.891 37.037 0.00 0.00 32.79 4.40
3474 3680 3.117851 GCTATCCTCTAAGTTGGCCCTTT 60.118 47.826 0.00 0.00 0.00 3.11
3475 3681 4.628959 GCTATCCTCTAAGTTGGCCCTTTT 60.629 45.833 0.00 0.00 0.00 2.27
3476 3682 3.895704 TCCTCTAAGTTGGCCCTTTTT 57.104 42.857 0.00 0.00 0.00 1.94
3541 3751 4.201920 GGCAAAAGCATAAGTACCTAGCAC 60.202 45.833 0.00 0.00 0.00 4.40
3543 3753 3.840124 AAGCATAAGTACCTAGCACCC 57.160 47.619 0.00 0.00 0.00 4.61
3697 3907 5.248870 GGCAACAACCATATAAGAAGTGG 57.751 43.478 0.00 0.00 38.96 4.00
3796 4006 4.536065 TGACACTTGATGAATGCGAAAAC 58.464 39.130 0.00 0.00 0.00 2.43
3843 4053 6.318900 GTGGTCCCTGGAAATTTCATAGTTAG 59.681 42.308 19.49 7.44 0.00 2.34
3875 4092 9.929180 TTGATGCTATCTACCATAGTTGTATTC 57.071 33.333 0.00 0.00 0.00 1.75
3898 4115 5.582269 TCTGTATGCACATCTAGTTTTGCTC 59.418 40.000 12.01 5.10 35.91 4.26
3913 4130 7.125536 AGTTTTGCTCGTAGTTGTATTTACC 57.874 36.000 0.00 0.00 0.00 2.85
4170 4387 2.162681 GGGTGAAGGATTCCACACAAG 58.837 52.381 24.07 0.00 46.93 3.16
4220 4438 6.071840 GCCAGAGAAGTTAGTACTGAAGAAGA 60.072 42.308 5.39 0.00 34.01 2.87
4398 4616 1.417890 ACAAGTGAGTGTCCTTGGGAG 59.582 52.381 0.00 0.00 41.84 4.30
4542 4760 6.696411 GCTCTATTCAAGCCTATCACTGTAT 58.304 40.000 0.00 0.00 33.53 2.29
4560 4778 5.604231 ACTGTATATCAATCAGCTCCAAGGA 59.396 40.000 0.00 0.00 33.12 3.36
4563 4781 6.782494 TGTATATCAATCAGCTCCAAGGAGTA 59.218 38.462 16.94 4.50 43.70 2.59
4760 4978 6.588719 TTTTTGGTTAATGTCCAGGATGAG 57.411 37.500 0.00 0.00 39.69 2.90
4898 5116 4.720902 CGGCATGTCCCACCAGCA 62.721 66.667 0.00 0.00 0.00 4.41
4991 5209 5.731263 GCGGTAAGTTCAAATTCGTATGTTC 59.269 40.000 0.00 0.00 0.00 3.18
5001 5219 7.693952 TCAAATTCGTATGTTCTGCTAATTCC 58.306 34.615 0.00 0.00 0.00 3.01
5030 5248 6.072112 ACAGTTGAACACATTGTGGTTATC 57.928 37.500 20.33 10.16 37.94 1.75
5049 5267 9.764363 TGGTTATCACAATACTATCATGTCTTC 57.236 33.333 0.00 0.00 0.00 2.87
5322 5541 1.064832 GCCCAGGAGAGATTGCTTCTT 60.065 52.381 0.00 0.00 33.74 2.52
5623 5842 4.265056 GGCCAACGGACCAGGTGT 62.265 66.667 0.00 0.00 0.00 4.16
5624 5843 2.978010 GCCAACGGACCAGGTGTG 60.978 66.667 0.00 0.00 0.00 3.82
5651 5870 2.032620 TCCTCACTCTATTCCTTCGCC 58.967 52.381 0.00 0.00 0.00 5.54
5673 5892 2.759783 GCGCCAGCATATCGATGAT 58.240 52.632 8.54 0.00 44.35 2.45
5682 5901 6.513884 GCCAGCATATCGATGATTTTTCTCAA 60.514 38.462 8.54 0.00 34.73 3.02
5695 5914 8.309163 TGATTTTTCTCAACATTTAACATGCC 57.691 30.769 0.00 0.00 0.00 4.40
5696 5915 7.930325 TGATTTTTCTCAACATTTAACATGCCA 59.070 29.630 0.00 0.00 0.00 4.92
5788 6008 3.815401 CTGTGAGAAGTCGGGATGTTTTT 59.185 43.478 0.00 0.00 0.00 1.94
5789 6009 3.813166 TGTGAGAAGTCGGGATGTTTTTC 59.187 43.478 0.00 0.00 0.00 2.29
5884 6104 6.092092 TGTTGCTGTGTTGATGTTATTATGC 58.908 36.000 0.00 0.00 0.00 3.14
5890 6110 8.961092 GCTGTGTTGATGTTATTATGCTTTATG 58.039 33.333 0.00 0.00 0.00 1.90
5923 6143 0.395173 GGTGGTTGGTGACTTGGTGT 60.395 55.000 0.00 0.00 0.00 4.16
5940 6160 2.633488 GTGTCCTCTATCTGGGTTTGC 58.367 52.381 0.00 0.00 0.00 3.68
5986 6206 3.006940 TCGTCAAATTGGCTAGCGAAAT 58.993 40.909 16.45 11.85 0.00 2.17
6040 6261 6.633500 TGGATTCTTCGTTGAATGAAGTTT 57.367 33.333 22.41 13.38 40.99 2.66
6065 6286 4.593597 AACATATACTTTTCGTGGCGTG 57.406 40.909 0.00 0.00 0.00 5.34
6069 6290 1.823260 TACTTTTCGTGGCGTGCACG 61.823 55.000 34.01 34.01 46.21 5.34
6129 6350 5.814705 AGTCAAATTGAAGATCGAGACATCC 59.185 40.000 0.00 0.00 0.00 3.51
6160 6381 2.831526 CCTTACAAACCAAATGGAGGGG 59.168 50.000 6.42 0.00 38.94 4.79
6170 6391 0.626574 AATGGAGGGGGTAGGGGTTC 60.627 60.000 0.00 0.00 0.00 3.62
6213 6434 1.201414 TGCAACATCTGAGCATGCTTG 59.799 47.619 23.61 18.24 37.86 4.01
6321 6607 4.048470 GGAGTTGGGGGAGGTGCC 62.048 72.222 0.00 0.00 0.00 5.01
6391 6679 2.275380 GGTTGTTCCGGCTGGCATT 61.275 57.895 6.73 0.00 34.14 3.56
6475 6763 1.449601 CGGGCGTGGCTTGTAGATT 60.450 57.895 0.00 0.00 0.00 2.40
6514 6802 1.771746 GGGGGATGAGGCTGGATGA 60.772 63.158 0.00 0.00 0.00 2.92
6605 6893 0.613572 TGAGCCTCGTGGTGGTATGA 60.614 55.000 5.26 0.00 35.27 2.15
6610 6898 1.536072 CCTCGTGGTGGTATGATGTCG 60.536 57.143 0.00 0.00 0.00 4.35
6652 6940 2.926250 GCATATGCAGGGGTGGGA 59.074 61.111 22.84 0.00 41.59 4.37
6653 6941 1.462035 GCATATGCAGGGGTGGGAT 59.538 57.895 22.84 0.00 41.59 3.85
6654 6942 0.896940 GCATATGCAGGGGTGGGATG 60.897 60.000 22.84 0.00 41.59 3.51
6655 6943 0.251474 CATATGCAGGGGTGGGATGG 60.251 60.000 0.00 0.00 0.00 3.51
6656 6944 0.403304 ATATGCAGGGGTGGGATGGA 60.403 55.000 0.00 0.00 0.00 3.41
6657 6945 0.625980 TATGCAGGGGTGGGATGGAA 60.626 55.000 0.00 0.00 0.00 3.53
6658 6946 1.941403 ATGCAGGGGTGGGATGGAAG 61.941 60.000 0.00 0.00 0.00 3.46
6659 6947 2.308722 GCAGGGGTGGGATGGAAGA 61.309 63.158 0.00 0.00 0.00 2.87
6660 6948 1.863155 GCAGGGGTGGGATGGAAGAA 61.863 60.000 0.00 0.00 0.00 2.52
6661 6949 0.704076 CAGGGGTGGGATGGAAGAAA 59.296 55.000 0.00 0.00 0.00 2.52
6662 6950 1.288932 CAGGGGTGGGATGGAAGAAAT 59.711 52.381 0.00 0.00 0.00 2.17
6663 6951 1.570979 AGGGGTGGGATGGAAGAAATC 59.429 52.381 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
501 511 4.771114 TTGTAGTTATAGCACATGGCCT 57.229 40.909 3.32 0.00 46.50 5.19
650 669 0.179163 TCACGCTGCTGATGTCGTAG 60.179 55.000 0.00 0.00 33.51 3.51
749 769 4.856607 GCGAAGACGGCGAGAGGG 62.857 72.222 16.62 0.16 40.15 4.30
1270 1351 1.342819 AGATGATCCTTCAGCTACGGC 59.657 52.381 0.00 0.00 46.45 5.68
1392 1479 1.854979 ACCCACCCCATTGCTGGTA 60.855 57.895 0.00 0.00 41.37 3.25
1406 1493 0.033796 ACTACTACCGCTAGCACCCA 60.034 55.000 16.45 0.00 0.00 4.51
1432 1519 2.441410 CCCCTTCTTCTTCTTCTTGCC 58.559 52.381 0.00 0.00 0.00 4.52
1520 1646 0.267356 CCCCTCCTCCTTCCTCATCT 59.733 60.000 0.00 0.00 0.00 2.90
1574 1739 4.835456 TATTCCCCTGCGCCCCCT 62.835 66.667 4.18 0.00 0.00 4.79
1575 1740 3.792185 CTTATTCCCCTGCGCCCCC 62.792 68.421 4.18 0.00 0.00 5.40
1576 1741 2.203351 CTTATTCCCCTGCGCCCC 60.203 66.667 4.18 0.00 0.00 5.80
1577 1742 0.819666 CTTCTTATTCCCCTGCGCCC 60.820 60.000 4.18 0.00 0.00 6.13
1578 1743 0.819666 CCTTCTTATTCCCCTGCGCC 60.820 60.000 4.18 0.00 0.00 6.53
1579 1744 0.819666 CCCTTCTTATTCCCCTGCGC 60.820 60.000 0.00 0.00 0.00 6.09
1580 1745 0.179018 CCCCTTCTTATTCCCCTGCG 60.179 60.000 0.00 0.00 0.00 5.18
1581 1746 1.222567 TCCCCTTCTTATTCCCCTGC 58.777 55.000 0.00 0.00 0.00 4.85
1582 1747 2.785857 ACATCCCCTTCTTATTCCCCTG 59.214 50.000 0.00 0.00 0.00 4.45
1583 1748 2.785857 CACATCCCCTTCTTATTCCCCT 59.214 50.000 0.00 0.00 0.00 4.79
1584 1749 2.158460 CCACATCCCCTTCTTATTCCCC 60.158 54.545 0.00 0.00 0.00 4.81
1585 1750 2.783510 TCCACATCCCCTTCTTATTCCC 59.216 50.000 0.00 0.00 0.00 3.97
1586 1751 4.464947 CTTCCACATCCCCTTCTTATTCC 58.535 47.826 0.00 0.00 0.00 3.01
1587 1752 4.166144 TCCTTCCACATCCCCTTCTTATTC 59.834 45.833 0.00 0.00 0.00 1.75
1588 1753 4.119155 TCCTTCCACATCCCCTTCTTATT 58.881 43.478 0.00 0.00 0.00 1.40
1589 1754 3.718956 CTCCTTCCACATCCCCTTCTTAT 59.281 47.826 0.00 0.00 0.00 1.73
1590 1755 3.115390 CTCCTTCCACATCCCCTTCTTA 58.885 50.000 0.00 0.00 0.00 2.10
1591 1756 1.918957 CTCCTTCCACATCCCCTTCTT 59.081 52.381 0.00 0.00 0.00 2.52
1592 1757 1.589414 CTCCTTCCACATCCCCTTCT 58.411 55.000 0.00 0.00 0.00 2.85
1593 1758 0.548510 CCTCCTTCCACATCCCCTTC 59.451 60.000 0.00 0.00 0.00 3.46
1594 1759 0.121197 TCCTCCTTCCACATCCCCTT 59.879 55.000 0.00 0.00 0.00 3.95
1595 1760 0.327000 CTCCTCCTTCCACATCCCCT 60.327 60.000 0.00 0.00 0.00 4.79
1596 1761 1.348775 CCTCCTCCTTCCACATCCCC 61.349 65.000 0.00 0.00 0.00 4.81
1597 1762 1.348775 CCCTCCTCCTTCCACATCCC 61.349 65.000 0.00 0.00 0.00 3.85
1598 1763 1.348775 CCCCTCCTCCTTCCACATCC 61.349 65.000 0.00 0.00 0.00 3.51
1599 1764 0.621862 ACCCCTCCTCCTTCCACATC 60.622 60.000 0.00 0.00 0.00 3.06
1600 1765 0.621862 GACCCCTCCTCCTTCCACAT 60.622 60.000 0.00 0.00 0.00 3.21
1601 1766 1.229529 GACCCCTCCTCCTTCCACA 60.230 63.158 0.00 0.00 0.00 4.17
1602 1767 1.996187 GGACCCCTCCTCCTTCCAC 60.996 68.421 0.00 0.00 33.07 4.02
1603 1768 2.056099 TTGGACCCCTCCTCCTTCCA 62.056 60.000 0.00 0.00 37.48 3.53
1618 1783 0.777446 CCACCCCCTTCTTTCTTGGA 59.223 55.000 0.00 0.00 0.00 3.53
1649 1814 3.474600 CACATGAAGATAAGCCCTCCTG 58.525 50.000 0.00 0.00 0.00 3.86
1716 1881 0.852842 CCTTCTTCCCCATGGGCATA 59.147 55.000 26.87 10.04 43.94 3.14
2119 2284 9.630098 ACAATTGAAGTTACAATGCAAGATTAG 57.370 29.630 13.59 0.00 39.88 1.73
2161 2326 4.023193 CCTCATTACTGGTGTTTGTGAACC 60.023 45.833 0.00 0.00 34.80 3.62
2174 2339 4.630644 AGGGCATACATCCTCATTACTG 57.369 45.455 0.00 0.00 0.00 2.74
2269 2437 2.639839 ACCCTCTGCACATATATGGACC 59.360 50.000 16.96 5.33 0.00 4.46
2311 2479 6.998673 GCTACATCTTCCATAATAACTTGGGT 59.001 38.462 0.00 0.00 33.62 4.51
2358 2526 2.440409 AGCATTATTCGATGATGGCCC 58.560 47.619 0.00 0.00 0.00 5.80
2529 2698 3.190079 CACATACTGTCCAACAGGATCG 58.810 50.000 11.48 6.23 46.52 3.69
2571 2740 7.168905 AGAAGATACAAAACTAAGGAACCCTG 58.831 38.462 0.00 0.00 32.13 4.45
2627 2796 3.225104 GGCCAGCTAAATTCATGATCCA 58.775 45.455 0.00 0.00 0.00 3.41
2720 2889 5.859495 AGATAACTGGTAGAGGCATTAAGC 58.141 41.667 0.00 0.00 44.65 3.09
2853 3023 8.012809 CGTTTCTTGTGTGTTGCAATAACTATA 58.987 33.333 0.59 0.00 0.00 1.31
2857 3027 4.796312 ACGTTTCTTGTGTGTTGCAATAAC 59.204 37.500 0.59 5.29 0.00 1.89
2915 3086 5.079643 ACCATGAAGAAACCATGCTTTAGT 58.920 37.500 0.00 0.00 39.89 2.24
3224 3428 6.302535 TGATTTCTTCATACGAGGGGTTAA 57.697 37.500 0.00 0.00 0.00 2.01
3271 3475 2.571653 TGGAGTGGTTAGATTGGGTCAG 59.428 50.000 0.00 0.00 0.00 3.51
3411 3616 8.097662 GCTTCATAGATAAAGTTGTATAGGGCT 58.902 37.037 0.00 0.00 0.00 5.19
3423 3629 7.396540 AACAAGTTGGGCTTCATAGATAAAG 57.603 36.000 7.96 0.00 34.69 1.85
3474 3680 4.225042 TCACTTGCTAGCCTTCATCCTAAA 59.775 41.667 13.29 0.00 0.00 1.85
3475 3681 3.774766 TCACTTGCTAGCCTTCATCCTAA 59.225 43.478 13.29 0.00 0.00 2.69
3476 3682 3.374764 TCACTTGCTAGCCTTCATCCTA 58.625 45.455 13.29 0.00 0.00 2.94
3531 3741 3.855159 CACAAGGGGTGCTAGGTAC 57.145 57.895 0.00 0.00 41.36 3.34
3541 3751 0.609131 AAGGATTCGTGCACAAGGGG 60.609 55.000 18.64 0.00 0.00 4.79
3697 3907 7.031975 CCATTTTTCAGAGGAATAAGAAGCAC 58.968 38.462 0.00 0.00 31.93 4.40
3796 4006 0.595053 ACATATCGCACGCCTCTTCG 60.595 55.000 0.00 0.00 0.00 3.79
3843 4053 9.664332 AACTATGGTAGATAGCATCAATCATTC 57.336 33.333 7.76 0.00 42.77 2.67
3875 4092 5.501413 CGAGCAAAACTAGATGTGCATACAG 60.501 44.000 16.67 0.65 40.79 2.74
3913 4130 3.754965 TCAAACAGATTGACCCTTGAGG 58.245 45.455 0.00 0.00 43.08 3.86
4170 4387 7.063426 GCATAAGGTCCAGTTTTAATCAAAAGC 59.937 37.037 0.00 0.00 34.34 3.51
4542 4760 6.556495 AGATTACTCCTTGGAGCTGATTGATA 59.444 38.462 15.93 0.00 0.00 2.15
4560 4778 4.523558 GCGGTACCTTCCATCTAGATTACT 59.476 45.833 10.90 0.00 0.00 2.24
4563 4781 2.296471 CGCGGTACCTTCCATCTAGATT 59.704 50.000 10.90 0.00 0.00 2.40
4760 4978 5.297776 AGGTGCTTGTTGATAATATCTGTGC 59.702 40.000 1.66 0.90 0.00 4.57
5030 5248 8.707938 TTCAGTGAAGACATGATAGTATTGTG 57.292 34.615 0.08 0.00 0.00 3.33
5065 5283 8.958119 ATAACTTCAGTAAAGACAAGAACACA 57.042 30.769 0.00 0.00 38.44 3.72
5207 5426 0.108756 GAACAGTGGTCCGGTAGAGC 60.109 60.000 0.00 0.00 43.62 4.09
5623 5842 1.568504 ATAGAGTGAGGAAACCGGCA 58.431 50.000 0.00 0.00 0.00 5.69
5624 5843 2.552031 GAATAGAGTGAGGAAACCGGC 58.448 52.381 0.00 0.00 0.00 6.13
5651 5870 2.825726 ATCGATATGCTGGCGCTCCG 62.826 60.000 7.64 0.00 36.97 4.63
5673 5892 7.307870 GCATGGCATGTTAAATGTTGAGAAAAA 60.308 33.333 26.94 0.00 0.00 1.94
5682 5901 3.369681 CCAAGGCATGGCATGTTAAATGT 60.370 43.478 26.94 4.97 43.80 2.71
5695 5914 0.322098 TACAACCGACCCAAGGCATG 60.322 55.000 0.00 0.00 0.00 4.06
5696 5915 0.322187 GTACAACCGACCCAAGGCAT 60.322 55.000 0.00 0.00 0.00 4.40
5788 6008 6.798427 AACAGGCATACAAGATAAGAGAGA 57.202 37.500 0.00 0.00 0.00 3.10
5789 6009 8.821894 GTTTAACAGGCATACAAGATAAGAGAG 58.178 37.037 0.00 0.00 0.00 3.20
5884 6104 2.415893 CCGGCACAGGAAAAGCATAAAG 60.416 50.000 0.00 0.00 0.00 1.85
5890 6110 2.644992 CACCGGCACAGGAAAAGC 59.355 61.111 0.00 0.00 34.73 3.51
5923 6143 2.239654 CCTTGCAAACCCAGATAGAGGA 59.760 50.000 0.00 0.00 0.00 3.71
6040 6261 6.035220 CACGCCACGAAAAGTATATGTTTAGA 59.965 38.462 0.00 0.00 0.00 2.10
6065 6286 4.513000 TTTCAACAAAGAAAATGCGTGC 57.487 36.364 0.00 0.00 34.77 5.34
6069 6290 6.901357 GTGACACATTTCAACAAAGAAAATGC 59.099 34.615 0.00 0.00 40.54 3.56
6123 6344 0.247736 AAGGAGAGCACACGGATGTC 59.752 55.000 0.00 0.00 36.72 3.06
6129 6350 1.798813 GGTTTGTAAGGAGAGCACACG 59.201 52.381 0.00 0.00 0.00 4.49
6213 6434 1.374758 CACCTCAGCCACGAAGACC 60.375 63.158 0.00 0.00 0.00 3.85
6348 6634 1.624813 CCCAACCATCTTGCCACAATT 59.375 47.619 0.00 0.00 0.00 2.32
6457 6745 1.024579 AAATCTACAAGCCACGCCCG 61.025 55.000 0.00 0.00 0.00 6.13
6495 6783 2.851102 ATCCAGCCTCATCCCCCG 60.851 66.667 0.00 0.00 0.00 5.73
6496 6784 1.138863 ATCATCCAGCCTCATCCCCC 61.139 60.000 0.00 0.00 0.00 5.40
6497 6785 0.327591 GATCATCCAGCCTCATCCCC 59.672 60.000 0.00 0.00 0.00 4.81
6498 6786 1.003349 CAGATCATCCAGCCTCATCCC 59.997 57.143 0.00 0.00 0.00 3.85
6499 6787 1.003349 CCAGATCATCCAGCCTCATCC 59.997 57.143 0.00 0.00 0.00 3.51
6500 6788 1.003349 CCCAGATCATCCAGCCTCATC 59.997 57.143 0.00 0.00 0.00 2.92
6501 6789 1.065647 CCCAGATCATCCAGCCTCAT 58.934 55.000 0.00 0.00 0.00 2.90
6502 6790 1.703014 GCCCAGATCATCCAGCCTCA 61.703 60.000 0.00 0.00 0.00 3.86
6503 6791 1.072852 GCCCAGATCATCCAGCCTC 59.927 63.158 0.00 0.00 0.00 4.70
6504 6792 2.459086 GGCCCAGATCATCCAGCCT 61.459 63.158 0.00 0.00 37.42 4.58
6505 6793 2.114838 GGCCCAGATCATCCAGCC 59.885 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.