Multiple sequence alignment - TraesCS2A01G165600

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 TraesCS2A01G165600 chr2A 100.000 2552 0 0 1 2552 118223516 118220965 0.000000e+00 4713.0
1 TraesCS2A01G165600 chr2A 84.890 953 106 18 1265 2183 118214169 118213221 0.000000e+00 928.0
2 TraesCS2A01G165600 chr2A 100.000 331 0 0 2892 3222 118220625 118220295 2.120000e-171 612.0
3 TraesCS2A01G165600 chr2A 82.687 670 95 13 1463 2116 118228479 118227815 2.790000e-160 575.0
4 TraesCS2A01G165600 chr2A 83.425 543 61 14 845 1367 118214486 118213953 8.090000e-131 477.0
5 TraesCS2A01G165600 chr2A 86.207 319 42 2 1455 1772 117850602 117850285 8.560000e-91 344.0
6 TraesCS2A01G165600 chr2A 79.913 458 58 20 7 452 118232302 118231867 4.040000e-79 305.0
7 TraesCS2A01G165600 chr2A 81.769 373 49 7 1077 1430 118228809 118228437 8.740000e-76 294.0
8 TraesCS2A01G165600 chr2A 83.784 148 11 6 286 432 118240691 118240556 9.380000e-26 128.0
9 TraesCS2A01G165600 chr2A 90.909 66 3 1 234 299 118246914 118246852 5.730000e-13 86.1
10 TraesCS2A01G165600 chr2D 92.141 1107 37 14 1463 2544 116776856 116775775 0.000000e+00 1517.0
11 TraesCS2A01G165600 chr2D 91.582 784 62 1 1463 2246 116620260 116619481 0.000000e+00 1079.0
12 TraesCS2A01G165600 chr2D 89.601 702 33 14 737 1428 116777487 116776816 0.000000e+00 856.0
13 TraesCS2A01G165600 chr2D 88.462 598 54 10 837 1425 116645894 116645303 0.000000e+00 708.0
14 TraesCS2A01G165600 chr2D 84.548 686 88 14 1442 2116 116800674 116799996 0.000000e+00 664.0
15 TraesCS2A01G165600 chr2D 90.867 427 22 8 1 427 116649459 116649050 1.010000e-154 556.0
16 TraesCS2A01G165600 chr2D 84.710 569 72 10 1469 2028 116597128 116596566 3.630000e-154 555.0
17 TraesCS2A01G165600 chr2D 94.578 332 17 1 2892 3222 116775716 116775385 2.220000e-141 512.0
18 TraesCS2A01G165600 chr2D 81.774 620 73 22 845 1430 116620831 116620218 1.740000e-132 483.0
19 TraesCS2A01G165600 chr2D 85.466 461 25 17 2 460 116778305 116777885 2.950000e-120 442.0
20 TraesCS2A01G165600 chr2D 82.927 246 16 12 845 1067 116621423 116621181 7.050000e-47 198.0
21 TraesCS2A01G165600 chr2D 85.484 186 24 2 1183 1365 116620360 116620175 1.180000e-44 191.0
22 TraesCS2A01G165600 chr2D 82.609 207 16 3 1463 1669 116645340 116645154 7.150000e-37 165.0
23 TraesCS2A01G165600 chr2D 80.702 228 26 13 7 223 116812681 116812461 9.250000e-36 161.0
24 TraesCS2A01G165600 chr2D 83.626 171 12 11 286 454 116808657 116808501 2.590000e-31 147.0
25 TraesCS2A01G165600 chrUn 92.245 490 38 0 1463 1952 460200229 460200718 0.000000e+00 695.0
26 TraesCS2A01G165600 chrUn 91.925 483 16 4 957 1430 460199803 460200271 0.000000e+00 654.0
27 TraesCS2A01G165600 chrUn 82.774 685 103 12 1463 2138 17426566 17427244 5.950000e-167 597.0
28 TraesCS2A01G165600 chrUn 85.776 464 33 16 1 460 17453601 17453167 8.140000e-126 460.0
29 TraesCS2A01G165600 chrUn 93.750 144 5 4 737 880 17453022 17452883 2.520000e-51 213.0
30 TraesCS2A01G165600 chrUn 85.022 227 12 12 234 454 17442574 17442364 9.060000e-51 211.0
31 TraesCS2A01G165600 chrUn 85.149 101 15 0 1463 1563 17426449 17426549 1.580000e-18 104.0
32 TraesCS2A01G165600 chr2B 84.022 557 80 9 1469 2019 166813476 166814029 7.920000e-146 527.0
33 TraesCS2A01G165600 chr2B 85.111 450 34 15 15 460 166879371 166878951 2.300000e-116 429.0
34 TraesCS2A01G165600 chr2B 89.735 302 31 0 1815 2116 166892773 166892472 1.400000e-103 387.0
35 TraesCS2A01G165600 chr2B 80.112 538 65 27 845 1366 166861206 166860695 2.360000e-96 363.0
36 TraesCS2A01G165600 chr2B 84.241 349 46 7 1088 1430 166898626 166898281 6.660000e-87 331.0
37 TraesCS2A01G165600 chr2B 93.750 144 5 4 737 880 166878806 166878667 2.520000e-51 213.0


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 TraesCS2A01G165600 chr2A 118220295 118223516 3221 True 2662.500000 4713 100.000000 1 3222 2 chr2A.!!$R5 3221
1 TraesCS2A01G165600 chr2A 118213221 118214486 1265 True 702.500000 928 84.157500 845 2183 2 chr2A.!!$R4 1338
2 TraesCS2A01G165600 chr2A 118227815 118232302 4487 True 391.333333 575 81.456333 7 2116 3 chr2A.!!$R6 2109
3 TraesCS2A01G165600 chr2D 116775385 116778305 2920 True 831.750000 1517 90.446500 2 3222 4 chr2D.!!$R5 3220
4 TraesCS2A01G165600 chr2D 116799996 116800674 678 True 664.000000 664 84.548000 1442 2116 1 chr2D.!!$R2 674
5 TraesCS2A01G165600 chr2D 116596566 116597128 562 True 555.000000 555 84.710000 1469 2028 1 chr2D.!!$R1 559
6 TraesCS2A01G165600 chr2D 116619481 116621423 1942 True 487.750000 1079 85.441750 845 2246 4 chr2D.!!$R3 1401
7 TraesCS2A01G165600 chr2D 116645154 116649459 4305 True 476.333333 708 87.312667 1 1669 3 chr2D.!!$R4 1668
8 TraesCS2A01G165600 chrUn 460199803 460200718 915 False 674.500000 695 92.085000 957 1952 2 chrUn.!!$F2 995
9 TraesCS2A01G165600 chrUn 17426449 17427244 795 False 350.500000 597 83.961500 1463 2138 2 chrUn.!!$F1 675
10 TraesCS2A01G165600 chrUn 17452883 17453601 718 True 336.500000 460 89.763000 1 880 2 chrUn.!!$R2 879
11 TraesCS2A01G165600 chr2B 166813476 166814029 553 False 527.000000 527 84.022000 1469 2019 1 chr2B.!!$F1 550
12 TraesCS2A01G165600 chr2B 166860695 166861206 511 True 363.000000 363 80.112000 845 1366 1 chr2B.!!$R1 521
13 TraesCS2A01G165600 chr2B 166878667 166879371 704 True 321.000000 429 89.430500 15 880 2 chr2B.!!$R4 865

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
410 435 0.038166 CCACCACCATGTACCTGCTT 59.962 55.0 0.00 0.0 0.00 3.91 F
638 3636 0.250081 TCGTGTGCACTATTGTGGCA 60.250 50.0 19.41 5.1 43.97 4.92 F
1678 7143 0.181587 TGTTCTGCCCCGAAGACAAA 59.818 50.0 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 6881 0.249238 CACAGGCTCCTCGTCTATGC 60.249 60.0 0.0 0.0 0.0 3.14 R
1778 7243 0.878523 CAGTCGAACGCCTGGAACAA 60.879 55.0 0.0 0.0 38.7 2.83 R
3080 8581 0.944386 CAACAACGTGAAGGTCCTGG 59.056 55.0 0.0 0.0 0.0 4.45 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
146 147 4.870426 AGACGTGGATTAATTGTAGCTGTG 59.130 41.667 0.00 0.00 0.00 3.66
150 151 4.700213 GTGGATTAATTGTAGCTGTGGTGT 59.300 41.667 0.00 0.00 0.00 4.16
158 159 3.758425 TGTAGCTGTGGTGTACTAGTGA 58.242 45.455 5.39 0.00 0.00 3.41
179 183 5.907391 GTGATTGAAGTAAAAGGTGTGAACG 59.093 40.000 0.00 0.00 0.00 3.95
334 358 2.669569 GACCTTGGCAGCAGCGAA 60.670 61.111 0.00 0.00 43.41 4.70
335 359 2.034687 ACCTTGGCAGCAGCGAAT 59.965 55.556 0.00 0.00 43.41 3.34
354 378 2.981859 TAAACGCCCTCCTCATCTTC 57.018 50.000 0.00 0.00 0.00 2.87
410 435 0.038166 CCACCACCATGTACCTGCTT 59.962 55.000 0.00 0.00 0.00 3.91
430 455 2.108362 GTGTTATCTCCCGGCCGG 59.892 66.667 37.99 37.99 0.00 6.13
447 1624 2.466867 GGGACGTCGCATTCAACAT 58.533 52.632 25.93 0.00 0.00 2.71
462 1639 5.376854 TTCAACATAGCTTTTCTGCTTCC 57.623 39.130 0.00 0.00 43.74 3.46
512 2471 2.198827 TCCAAATGTTCTCCATGCGT 57.801 45.000 0.00 0.00 32.82 5.24
519 2478 4.819761 TCTCCATGCGTCGCTGGC 62.820 66.667 22.99 0.00 32.30 4.85
543 2503 5.509272 CACGCACATCTCATTTCATTTACAC 59.491 40.000 0.00 0.00 0.00 2.90
553 2513 8.999431 TCTCATTTCATTTACACTTTACAGGTC 58.001 33.333 0.00 0.00 0.00 3.85
580 2540 0.451383 TCCATGCACGCATTGTTAGC 59.549 50.000 0.72 0.00 33.90 3.09
589 2549 0.577269 GCATTGTTAGCGCTCCTACG 59.423 55.000 16.34 0.00 0.00 3.51
590 2550 1.922570 CATTGTTAGCGCTCCTACGT 58.077 50.000 16.34 0.00 34.88 3.57
593 2553 2.028420 TGTTAGCGCTCCTACGTAGA 57.972 50.000 24.15 9.09 34.88 2.59
595 2555 1.263752 GTTAGCGCTCCTACGTAGAGG 59.736 57.143 24.15 11.31 38.03 3.69
600 2560 0.315568 GCTCCTACGTAGAGGGCATG 59.684 60.000 24.15 5.33 37.20 4.06
638 3636 0.250081 TCGTGTGCACTATTGTGGCA 60.250 50.000 19.41 5.10 43.97 4.92
644 3654 2.009051 TGCACTATTGTGGCAATCGAG 58.991 47.619 9.35 0.00 43.97 4.04
661 3676 1.171308 GAGGCATCACAATGTGCTGT 58.829 50.000 17.03 0.04 41.04 4.40
693 3756 8.776376 TTAATTAGGAAGGAATAACGTCGTTT 57.224 30.769 16.98 0.00 0.00 3.60
703 3766 2.618442 AACGTCGTTTCCTAAACCCA 57.382 45.000 4.40 0.00 38.14 4.51
709 3772 2.617774 TCGTTTCCTAAACCCAAAACCG 59.382 45.455 0.00 0.00 38.14 4.44
710 3773 2.617774 CGTTTCCTAAACCCAAAACCGA 59.382 45.455 0.00 0.00 38.14 4.69
711 3774 3.066481 CGTTTCCTAAACCCAAAACCGAA 59.934 43.478 0.00 0.00 38.14 4.30
713 3776 5.417811 GTTTCCTAAACCCAAAACCGAAAA 58.582 37.500 0.00 0.00 35.35 2.29
714 3777 4.652421 TCCTAAACCCAAAACCGAAAAC 57.348 40.909 0.00 0.00 0.00 2.43
715 3778 3.384146 TCCTAAACCCAAAACCGAAAACC 59.616 43.478 0.00 0.00 0.00 3.27
719 3782 3.029483 ACCCAAAACCGAAAACCCTAA 57.971 42.857 0.00 0.00 0.00 2.69
729 3796 4.823442 ACCGAAAACCCTAAAGTAACCTTG 59.177 41.667 0.00 0.00 0.00 3.61
840 4168 0.871057 GCCTTGCTCGCTTCCATATC 59.129 55.000 0.00 0.00 0.00 1.63
872 4231 0.870393 GGGCGATCGACACGTATAGA 59.130 55.000 24.83 0.00 0.00 1.98
873 4232 1.136029 GGGCGATCGACACGTATAGAG 60.136 57.143 24.83 0.00 0.00 2.43
880 4239 1.307097 GACACGTATAGAGCCCTCGT 58.693 55.000 0.00 0.00 35.12 4.18
886 4245 3.814283 ACGTATAGAGCCCTCGTCTTTAG 59.186 47.826 0.00 0.00 34.09 1.85
905 4264 2.052690 TCCTTCCTTCCTCGCTCCG 61.053 63.158 0.00 0.00 0.00 4.63
949 4313 0.886490 CGCCATTCCTATGCCTGACC 60.886 60.000 0.00 0.00 0.00 4.02
1032 4430 1.071385 CTACCAGCCATAGCCAGAAGG 59.929 57.143 0.00 0.00 41.25 3.46
1067 5165 4.521062 CCCTCGCGCTCTCTTGGG 62.521 72.222 5.56 3.83 0.00 4.12
1068 5166 3.452786 CCTCGCGCTCTCTTGGGA 61.453 66.667 5.56 0.00 0.00 4.37
1069 5167 2.103934 CTCGCGCTCTCTTGGGAG 59.896 66.667 5.56 0.00 40.73 4.30
1070 5168 2.361230 TCGCGCTCTCTTGGGAGA 60.361 61.111 5.56 0.00 45.30 3.71
1071 5169 1.938657 CTCGCGCTCTCTTGGGAGAA 61.939 60.000 5.56 0.00 46.50 2.87
1072 5170 1.079819 CGCGCTCTCTTGGGAGAAA 60.080 57.895 5.56 0.00 46.50 2.52
1073 5171 1.080995 CGCGCTCTCTTGGGAGAAAG 61.081 60.000 5.56 0.00 46.50 2.62
1074 5172 0.742635 GCGCTCTCTTGGGAGAAAGG 60.743 60.000 0.00 0.00 46.50 3.11
1075 5173 0.610687 CGCTCTCTTGGGAGAAAGGT 59.389 55.000 1.07 0.00 46.50 3.50
1076 5174 1.674221 CGCTCTCTTGGGAGAAAGGTG 60.674 57.143 1.07 0.00 46.50 4.00
1077 5175 1.349357 GCTCTCTTGGGAGAAAGGTGT 59.651 52.381 1.07 0.00 46.50 4.16
1078 5176 2.873649 GCTCTCTTGGGAGAAAGGTGTG 60.874 54.545 1.07 0.00 46.50 3.82
1083 6536 1.973812 GGGAGAAAGGTGTGGCAGC 60.974 63.158 0.00 0.00 0.00 5.25
1252 6705 2.202932 CCGGAGTTCATGCCCGAG 60.203 66.667 14.28 4.47 45.58 4.63
1431 6884 4.592192 CATCGACGGCTCGGGCAT 62.592 66.667 10.74 0.00 40.58 4.40
1432 6885 2.910479 ATCGACGGCTCGGGCATA 60.910 61.111 10.74 0.00 40.58 3.14
1433 6886 2.920645 ATCGACGGCTCGGGCATAG 61.921 63.158 10.74 1.59 40.58 2.23
1434 6887 3.592814 CGACGGCTCGGGCATAGA 61.593 66.667 10.74 0.00 40.87 1.98
1435 6888 2.027751 GACGGCTCGGGCATAGAC 59.972 66.667 10.74 0.00 40.87 2.59
1441 6894 4.159266 TCGGGCATAGACGAGGAG 57.841 61.111 0.00 0.00 34.67 3.69
1442 6895 2.194212 TCGGGCATAGACGAGGAGC 61.194 63.158 0.00 0.00 34.67 4.70
1443 6896 2.737830 GGGCATAGACGAGGAGCC 59.262 66.667 0.00 0.00 44.48 4.70
1444 6897 1.834822 GGGCATAGACGAGGAGCCT 60.835 63.158 0.00 0.00 44.60 4.58
1445 6898 1.365633 GGCATAGACGAGGAGCCTG 59.634 63.158 0.00 0.00 42.01 4.85
1446 6899 1.395826 GGCATAGACGAGGAGCCTGT 61.396 60.000 0.00 0.00 42.01 4.00
1447 6900 0.249238 GCATAGACGAGGAGCCTGTG 60.249 60.000 0.00 0.00 0.00 3.66
1448 6901 0.249238 CATAGACGAGGAGCCTGTGC 60.249 60.000 0.00 0.00 37.95 4.57
1458 6911 2.265739 GCCTGTGCTCATGGACGA 59.734 61.111 8.01 0.00 37.34 4.20
1459 6912 2.103042 GCCTGTGCTCATGGACGAC 61.103 63.158 8.01 0.00 37.34 4.34
1460 6913 1.807165 CCTGTGCTCATGGACGACG 60.807 63.158 0.00 0.00 37.34 5.12
1461 6914 1.212751 CTGTGCTCATGGACGACGA 59.787 57.895 0.00 0.00 37.34 4.20
1462 6915 1.073216 CTGTGCTCATGGACGACGAC 61.073 60.000 0.00 0.00 37.34 4.34
1463 6916 2.152699 GTGCTCATGGACGACGACG 61.153 63.158 5.58 5.58 45.75 5.12
1464 6917 2.329614 TGCTCATGGACGACGACGA 61.330 57.895 15.32 0.00 42.66 4.20
1465 6918 1.154093 GCTCATGGACGACGACGAA 60.154 57.895 15.32 0.00 42.66 3.85
1466 6919 1.134530 GCTCATGGACGACGACGAAG 61.135 60.000 15.32 0.00 42.66 3.79
1467 6920 1.134530 CTCATGGACGACGACGAAGC 61.135 60.000 15.32 2.81 42.66 3.86
1468 6921 2.202440 ATGGACGACGACGAAGCG 60.202 61.111 15.32 4.89 42.66 4.68
1678 7143 0.181587 TGTTCTGCCCCGAAGACAAA 59.818 50.000 0.00 0.00 0.00 2.83
1957 7433 4.516195 GAAGCTCCCCTCGCCGTC 62.516 72.222 0.00 0.00 0.00 4.79
2146 7622 0.404040 TGGCCGGGTTTCTTCTTCAT 59.596 50.000 2.18 0.00 0.00 2.57
2155 7631 4.142513 GGGTTTCTTCTTCATGATGCAGTC 60.143 45.833 0.00 0.00 0.00 3.51
2166 7642 2.884827 TGATGCAGTCGACAAGATGAG 58.115 47.619 19.50 0.00 0.00 2.90
2248 7724 7.335924 GCTCTAGAATTATGGTTGTGGTGTTTA 59.664 37.037 0.00 0.00 0.00 2.01
2249 7725 8.786826 TCTAGAATTATGGTTGTGGTGTTTAG 57.213 34.615 0.00 0.00 0.00 1.85
2250 7726 6.267496 AGAATTATGGTTGTGGTGTTTAGC 57.733 37.500 0.00 0.00 0.00 3.09
2251 7727 6.010219 AGAATTATGGTTGTGGTGTTTAGCT 58.990 36.000 0.00 0.00 0.00 3.32
2252 7728 5.897377 ATTATGGTTGTGGTGTTTAGCTC 57.103 39.130 0.00 0.00 0.00 4.09
2253 7729 2.719531 TGGTTGTGGTGTTTAGCTCA 57.280 45.000 0.00 0.00 0.00 4.26
2254 7730 2.571212 TGGTTGTGGTGTTTAGCTCAG 58.429 47.619 0.00 0.00 0.00 3.35
2255 7731 1.266989 GGTTGTGGTGTTTAGCTCAGC 59.733 52.381 0.00 0.00 0.00 4.26
2256 7732 1.946768 GTTGTGGTGTTTAGCTCAGCA 59.053 47.619 0.00 1.95 40.25 4.41
2257 7733 2.554032 GTTGTGGTGTTTAGCTCAGCAT 59.446 45.455 8.77 0.00 43.40 3.79
2258 7734 3.694043 TGTGGTGTTTAGCTCAGCATA 57.306 42.857 8.77 4.10 43.40 3.14
2259 7735 4.220693 TGTGGTGTTTAGCTCAGCATAT 57.779 40.909 8.77 0.00 43.40 1.78
2292 7768 3.767256 CTGAAAGCATGTCGATCGATC 57.233 47.619 22.50 15.68 0.00 3.69
2317 7793 3.486263 GTGGCATGGCACGTACTC 58.514 61.111 33.16 12.76 0.00 2.59
2323 7799 1.002366 CATGGCACGTACTCTTCTGC 58.998 55.000 0.00 0.00 0.00 4.26
2333 7809 3.731264 CGTACTCTTCTGCCGGAGTTAAG 60.731 52.174 5.05 2.47 42.06 1.85
2334 7810 2.249139 ACTCTTCTGCCGGAGTTAAGT 58.751 47.619 5.05 0.00 39.44 2.24
2335 7811 3.428532 ACTCTTCTGCCGGAGTTAAGTA 58.571 45.455 5.05 0.00 39.44 2.24
2336 7812 3.193056 ACTCTTCTGCCGGAGTTAAGTAC 59.807 47.826 5.05 0.00 39.44 2.73
2345 7821 3.304928 CCGGAGTTAAGTACGTGTGAGTT 60.305 47.826 13.76 0.00 0.00 3.01
2357 7833 2.365582 GTGTGAGTTCCTGTGTTTGGT 58.634 47.619 0.00 0.00 0.00 3.67
2384 7860 4.092821 TGTGCTACAGCTTAATTTGCGTAG 59.907 41.667 18.56 18.56 42.66 3.51
2492 7985 1.334869 GAGAACCAGTGCACCAAACTG 59.665 52.381 14.63 4.47 43.84 3.16
2506 7999 3.807622 ACCAAACTGTGACAATACACTCG 59.192 43.478 0.00 0.00 40.87 4.18
2509 8002 3.299340 ACTGTGACAATACACTCGGTC 57.701 47.619 0.00 0.00 40.87 4.79
2529 8030 3.859386 GTCACGGATCCAAATTTGAATGC 59.141 43.478 19.86 9.37 0.00 3.56
2549 8050 1.962807 CACAAATGCAAGTCCCCTCAA 59.037 47.619 0.00 0.00 0.00 3.02
2550 8051 2.564062 CACAAATGCAAGTCCCCTCAAT 59.436 45.455 0.00 0.00 0.00 2.57
2984 8485 7.687941 ACCTCCAAAACACATGAAATACTAG 57.312 36.000 0.00 0.00 0.00 2.57
2993 8494 6.779860 ACACATGAAATACTAGAAACAGGGT 58.220 36.000 0.00 0.00 0.00 4.34
3004 8505 0.476771 AAACAGGGTCGTGGAATGGT 59.523 50.000 0.00 0.00 0.00 3.55
3023 8524 3.127548 TGGTTAGGTTACTTAGACGCTCG 59.872 47.826 0.00 0.00 0.00 5.03
3066 8567 2.643551 GCTCAAGTGCTAGCCCATTTA 58.356 47.619 13.29 0.00 32.40 1.40
3111 8612 0.314302 CGTTGTTGGTCTCCTCTCGT 59.686 55.000 0.00 0.00 0.00 4.18
3112 8613 1.666311 CGTTGTTGGTCTCCTCTCGTC 60.666 57.143 0.00 0.00 0.00 4.20
3132 8633 4.223953 GTCCCTGATACAAGGACCTATCA 58.776 47.826 7.96 0.00 43.60 2.15
3164 8665 2.088423 TCCAAAATGAATCGGGGTTCG 58.912 47.619 0.00 0.00 40.90 3.95
3198 8699 3.585862 ACGATCACATCACACAACTACC 58.414 45.455 0.00 0.00 0.00 3.18
3200 8701 3.859961 CGATCACATCACACAACTACCTC 59.140 47.826 0.00 0.00 0.00 3.85
3204 8706 0.108804 ATCACACAACTACCTCGGCG 60.109 55.000 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 7.876582 ACCTTTTACTTCAATCACTAGTACACC 59.123 37.037 0.00 0.00 0.00 4.16
150 151 8.644216 TCACACCTTTTACTTCAATCACTAGTA 58.356 33.333 0.00 0.00 0.00 1.82
158 159 5.820947 ACTCGTTCACACCTTTTACTTCAAT 59.179 36.000 0.00 0.00 0.00 2.57
179 183 1.450312 CCGATGCCTCCAACCACTC 60.450 63.158 0.00 0.00 0.00 3.51
282 295 0.372679 GCGTGCTCACATGATCACAG 59.627 55.000 14.35 9.01 40.18 3.66
334 358 2.104963 GGAAGATGAGGAGGGCGTTTAT 59.895 50.000 0.00 0.00 0.00 1.40
335 359 1.485066 GGAAGATGAGGAGGGCGTTTA 59.515 52.381 0.00 0.00 0.00 2.01
397 422 0.036388 ACACGGAAGCAGGTACATGG 60.036 55.000 9.91 0.00 0.00 3.66
430 455 1.004927 GCTATGTTGAATGCGACGTCC 60.005 52.381 10.58 3.43 0.00 4.79
447 1624 2.561478 AACCGGAAGCAGAAAAGCTA 57.439 45.000 9.46 0.00 45.89 3.32
462 1639 1.352156 GCTTCTCACAGGCGTAACCG 61.352 60.000 0.00 0.00 46.52 4.44
487 1682 3.940209 TGGAGAACATTTGGATGCAAC 57.060 42.857 0.00 0.00 36.72 4.17
512 2471 4.377708 AGATGTGCGTGCCAGCGA 62.378 61.111 0.00 0.00 40.67 4.93
519 2478 5.509272 GTGTAAATGAAATGAGATGTGCGTG 59.491 40.000 0.00 0.00 0.00 5.34
543 2503 3.411446 TGGACTGCATTGACCTGTAAAG 58.589 45.455 0.00 0.00 0.00 1.85
580 2540 1.173444 ATGCCCTCTACGTAGGAGCG 61.173 60.000 22.01 11.35 39.15 5.03
586 2546 2.154567 ACTTCCATGCCCTCTACGTA 57.845 50.000 0.00 0.00 0.00 3.57
587 2547 2.154567 TACTTCCATGCCCTCTACGT 57.845 50.000 0.00 0.00 0.00 3.57
588 2548 2.167693 TGTTACTTCCATGCCCTCTACG 59.832 50.000 0.00 0.00 0.00 3.51
589 2549 3.906720 TGTTACTTCCATGCCCTCTAC 57.093 47.619 0.00 0.00 0.00 2.59
590 2550 5.192927 CAAATGTTACTTCCATGCCCTCTA 58.807 41.667 0.00 0.00 0.00 2.43
593 2553 3.511146 CACAAATGTTACTTCCATGCCCT 59.489 43.478 0.00 0.00 0.00 5.19
595 2555 4.782019 TCACAAATGTTACTTCCATGCC 57.218 40.909 0.00 0.00 0.00 4.40
600 2560 5.049680 ACACGACATCACAAATGTTACTTCC 60.050 40.000 0.00 0.00 31.52 3.46
638 3636 1.402968 GCACATTGTGATGCCTCGATT 59.597 47.619 20.77 0.00 36.72 3.34
661 3676 9.472361 CGTTATTCCTTCCTAATTAAGATCGAA 57.528 33.333 0.00 0.00 0.00 3.71
685 3708 2.618442 TTGGGTTTAGGAAACGACGT 57.382 45.000 0.00 0.00 42.29 4.34
693 3756 3.384146 GGTTTTCGGTTTTGGGTTTAGGA 59.616 43.478 0.00 0.00 0.00 2.94
703 3766 5.893255 AGGTTACTTTAGGGTTTTCGGTTTT 59.107 36.000 0.00 0.00 0.00 2.43
709 3772 8.625786 TGATACAAGGTTACTTTAGGGTTTTC 57.374 34.615 0.00 0.00 33.81 2.29
710 3773 8.999905 TTGATACAAGGTTACTTTAGGGTTTT 57.000 30.769 0.00 0.00 33.81 2.43
711 3774 8.442374 TCTTGATACAAGGTTACTTTAGGGTTT 58.558 33.333 10.84 0.00 33.81 3.27
713 3776 7.016858 TGTCTTGATACAAGGTTACTTTAGGGT 59.983 37.037 10.84 0.00 33.81 4.34
714 3777 7.333672 GTGTCTTGATACAAGGTTACTTTAGGG 59.666 40.741 10.84 0.00 33.81 3.53
715 3778 7.876068 TGTGTCTTGATACAAGGTTACTTTAGG 59.124 37.037 10.84 0.00 33.81 2.69
719 3782 5.995897 GGTGTGTCTTGATACAAGGTTACTT 59.004 40.000 10.84 0.00 37.43 2.24
729 3796 4.056050 ACTTTGTCGGTGTGTCTTGATAC 58.944 43.478 0.00 0.00 0.00 2.24
819 4147 0.462581 TATGGAAGCGAGCAAGGCAG 60.463 55.000 0.00 0.00 0.00 4.85
872 4231 1.826096 GAAGGACTAAAGACGAGGGCT 59.174 52.381 0.00 0.00 0.00 5.19
873 4232 1.134759 GGAAGGACTAAAGACGAGGGC 60.135 57.143 0.00 0.00 0.00 5.19
880 4239 2.496470 GCGAGGAAGGAAGGACTAAAGA 59.504 50.000 0.00 0.00 0.00 2.52
886 4245 1.518302 GGAGCGAGGAAGGAAGGAC 59.482 63.158 0.00 0.00 0.00 3.85
905 4264 1.153349 GAGCTCCATGGTCCGGAAC 60.153 63.158 14.24 14.24 37.22 3.62
949 4313 0.742505 TATACACGGTGAAGGAGGCG 59.257 55.000 16.29 0.00 0.00 5.52
1032 4430 1.376553 GAGGGGAGTTGCTGAGTGC 60.377 63.158 0.00 0.00 43.25 4.40
1067 5165 2.328099 CGGCTGCCACACCTTTCTC 61.328 63.158 20.29 0.00 0.00 2.87
1068 5166 2.281761 CGGCTGCCACACCTTTCT 60.282 61.111 20.29 0.00 0.00 2.52
1069 5167 4.043200 GCGGCTGCCACACCTTTC 62.043 66.667 20.29 0.00 33.98 2.62
1252 6705 1.868251 GTCGTCGTGCGTGGAGATC 60.868 63.158 0.00 0.00 42.13 2.75
1348 6801 3.499737 GCCATGAACACCGGCTCG 61.500 66.667 0.00 0.00 42.78 5.03
1403 6856 2.267961 GTCGATGCCCCGGAACTT 59.732 61.111 0.73 0.00 0.00 2.66
1425 6878 2.336809 GCTCCTCGTCTATGCCCG 59.663 66.667 0.00 0.00 0.00 6.13
1427 6880 1.365633 CAGGCTCCTCGTCTATGCC 59.634 63.158 0.00 0.00 43.52 4.40
1428 6881 0.249238 CACAGGCTCCTCGTCTATGC 60.249 60.000 0.00 0.00 0.00 3.14
1429 6882 0.249238 GCACAGGCTCCTCGTCTATG 60.249 60.000 0.00 0.00 36.96 2.23
1430 6883 2.119886 GCACAGGCTCCTCGTCTAT 58.880 57.895 0.00 0.00 36.96 1.98
1431 6884 3.604629 GCACAGGCTCCTCGTCTA 58.395 61.111 0.00 0.00 36.96 2.59
1441 6894 2.103042 GTCGTCCATGAGCACAGGC 61.103 63.158 0.00 0.00 41.61 4.85
1442 6895 1.807165 CGTCGTCCATGAGCACAGG 60.807 63.158 0.00 0.00 0.00 4.00
1443 6896 1.073216 GTCGTCGTCCATGAGCACAG 61.073 60.000 0.00 0.00 0.00 3.66
1444 6897 1.080772 GTCGTCGTCCATGAGCACA 60.081 57.895 0.00 0.00 0.00 4.57
1445 6898 2.152699 CGTCGTCGTCCATGAGCAC 61.153 63.158 0.00 0.00 0.00 4.40
1446 6899 1.858372 TTCGTCGTCGTCCATGAGCA 61.858 55.000 1.33 0.00 38.33 4.26
1447 6900 1.134530 CTTCGTCGTCGTCCATGAGC 61.135 60.000 1.33 0.00 38.33 4.26
1448 6901 1.134530 GCTTCGTCGTCGTCCATGAG 61.135 60.000 1.33 0.00 38.33 2.90
1449 6902 1.154093 GCTTCGTCGTCGTCCATGA 60.154 57.895 1.33 0.00 38.33 3.07
1450 6903 2.497092 CGCTTCGTCGTCGTCCATG 61.497 63.158 1.33 0.00 38.33 3.66
1451 6904 2.202440 CGCTTCGTCGTCGTCCAT 60.202 61.111 1.33 0.00 38.33 3.41
1778 7243 0.878523 CAGTCGAACGCCTGGAACAA 60.879 55.000 0.00 0.00 38.70 2.83
1945 7421 4.415150 ACGTAGACGGCGAGGGGA 62.415 66.667 16.62 0.00 44.95 4.81
2146 7622 2.884827 CTCATCTTGTCGACTGCATCA 58.115 47.619 17.92 0.00 0.00 3.07
2155 7631 1.135859 GCCTTGTTGCTCATCTTGTCG 60.136 52.381 0.00 0.00 0.00 4.35
2166 7642 3.055891 ACCAGATAAATTGGCCTTGTTGC 60.056 43.478 3.32 0.00 39.39 4.17
2204 7680 8.982091 TCTAGAGCATTATTCACTACTAGTGT 57.018 34.615 14.63 0.00 46.03 3.55
2317 7793 2.094854 ACGTACTTAACTCCGGCAGAAG 60.095 50.000 0.00 0.00 0.00 2.85
2323 7799 2.227388 ACTCACACGTACTTAACTCCGG 59.773 50.000 0.00 0.00 0.00 5.14
2333 7809 2.503920 ACACAGGAACTCACACGTAC 57.496 50.000 0.00 0.00 34.60 3.67
2334 7810 3.191669 CAAACACAGGAACTCACACGTA 58.808 45.455 0.00 0.00 34.60 3.57
2335 7811 2.006888 CAAACACAGGAACTCACACGT 58.993 47.619 0.00 0.00 34.60 4.49
2336 7812 1.330521 CCAAACACAGGAACTCACACG 59.669 52.381 0.00 0.00 34.60 4.49
2345 7821 1.680735 GCACATGAACCAAACACAGGA 59.319 47.619 0.00 0.00 0.00 3.86
2357 7833 5.401550 GCAAATTAAGCTGTAGCACATGAA 58.598 37.500 0.00 0.00 45.16 2.57
2384 7860 4.734854 CGTAAATGCCACACTAAATCATGC 59.265 41.667 0.00 0.00 0.00 4.06
2506 7999 4.423732 CATTCAAATTTGGATCCGTGACC 58.576 43.478 17.90 0.00 0.00 4.02
2509 8002 3.613737 GTGCATTCAAATTTGGATCCGTG 59.386 43.478 17.90 5.93 0.00 4.94
2529 8030 1.619654 TGAGGGGACTTGCATTTGTG 58.380 50.000 0.00 0.00 44.43 3.33
2943 8444 8.746052 TTTGGAGGTTACATCATATAGGTTTG 57.254 34.615 0.00 0.00 0.00 2.93
2945 8446 8.333235 TGTTTTGGAGGTTACATCATATAGGTT 58.667 33.333 0.00 0.00 0.00 3.50
2952 8453 6.009589 TCATGTGTTTTGGAGGTTACATCAT 58.990 36.000 0.00 0.00 0.00 2.45
2984 8485 1.165270 CCATTCCACGACCCTGTTTC 58.835 55.000 0.00 0.00 0.00 2.78
2993 8494 4.895668 AAGTAACCTAACCATTCCACGA 57.104 40.909 0.00 0.00 0.00 4.35
3004 8505 5.449588 CCAATCGAGCGTCTAAGTAACCTAA 60.450 44.000 0.00 0.00 0.00 2.69
3023 8524 4.379499 CGAAAAACAACCTAGAGGCCAATC 60.379 45.833 5.01 0.00 39.32 2.67
3066 8567 2.235891 GTCCTGGAAAACCGTCCATTT 58.764 47.619 0.00 0.00 46.66 2.32
3071 8572 1.202722 TGAAGGTCCTGGAAAACCGTC 60.203 52.381 10.67 10.67 42.30 4.79
3080 8581 0.944386 CAACAACGTGAAGGTCCTGG 59.056 55.000 0.00 0.00 0.00 4.45
3111 8612 4.223953 GTGATAGGTCCTTGTATCAGGGA 58.776 47.826 0.00 0.00 37.29 4.20
3112 8613 3.325135 GGTGATAGGTCCTTGTATCAGGG 59.675 52.174 0.00 0.00 36.54 4.45
3132 8633 0.974383 ATTTTGGACGAGGAGACGGT 59.026 50.000 0.00 0.00 37.61 4.83
3164 8665 1.335132 TGATCGTTGAGCCCCTACCC 61.335 60.000 0.00 0.00 0.00 3.69
3204 8706 4.581093 GGGAAGGTATGGGCGGCC 62.581 72.222 23.42 23.42 0.00 6.13


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

AutoCloner maintained by Alex Coulton.