Multiple sequence alignment - TraesCS7D01G006600

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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 TraesCS7D01G006600 chr7D 100.000 3560 0 0 1 3560 3248279 3244720 0.000000e+00 6575.0
1 TraesCS7D01G006600 chr7D 89.578 1564 124 22 1 1538 3365557 3367107 0.000000e+00 1949.0
2 TraesCS7D01G006600 chr7D 93.070 938 61 4 1597 2531 3367107 3368043 0.000000e+00 1369.0
3 TraesCS7D01G006600 chr7D 99.611 514 2 0 3047 3560 3232537 3232024 0.000000e+00 939.0
4 TraesCS7D01G006600 chr7D 89.825 570 54 2 2528 3096 2500581 2500015 0.000000e+00 728.0
5 TraesCS7D01G006600 chr7D 80.835 934 142 26 1617 2526 621812356 621813276 0.000000e+00 699.0
6 TraesCS7D01G006600 chr7D 90.167 539 42 8 2530 3061 3784159 3783625 0.000000e+00 691.0
7 TraesCS7D01G006600 chr7D 89.552 536 53 3 2528 3061 2354891 2354357 0.000000e+00 676.0
8 TraesCS7D01G006600 chr7D 89.464 541 45 9 2530 3061 3630361 3629824 0.000000e+00 673.0
9 TraesCS7D01G006600 chr7D 89.366 536 52 3 2530 3061 2607093 2606559 0.000000e+00 669.0
10 TraesCS7D01G006600 chr7D 80.171 933 148 27 1611 2526 621867820 621868732 0.000000e+00 664.0
11 TraesCS7D01G006600 chr7D 83.578 341 21 9 3231 3536 2499827 2499487 1.620000e-73 287.0
12 TraesCS7D01G006600 chr7D 79.348 276 53 4 998 1272 621615608 621615880 1.300000e-44 191.0
13 TraesCS7D01G006600 chr7D 79.137 278 47 8 946 1219 621867270 621867540 7.850000e-42 182.0
14 TraesCS7D01G006600 chrUn 99.611 514 2 0 3047 3560 328676832 328676319 0.000000e+00 939.0
15 TraesCS7D01G006600 chrUn 99.611 514 2 0 3047 3560 347564489 347563976 0.000000e+00 939.0
16 TraesCS7D01G006600 chrUn 79.348 276 53 4 998 1272 314008291 314008563 1.300000e-44 191.0
17 TraesCS7D01G006600 chr7B 83.278 903 121 25 1640 2529 719431000 719431885 0.000000e+00 804.0
18 TraesCS7D01G006600 chr7B 81.828 930 138 20 1617 2529 718099630 718098715 0.000000e+00 752.0
19 TraesCS7D01G006600 chr7B 80.856 935 144 24 1617 2529 717894105 717893184 0.000000e+00 702.0
20 TraesCS7D01G006600 chr7B 80.426 940 146 30 1611 2529 717787339 717788261 0.000000e+00 682.0
21 TraesCS7D01G006600 chr7B 80.522 919 146 24 1621 2520 719626958 719627862 0.000000e+00 675.0
22 TraesCS7D01G006600 chr7B 78.526 950 150 39 1611 2529 717814791 717815717 3.080000e-160 575.0
23 TraesCS7D01G006600 chr7B 82.759 348 51 6 1621 1967 717632917 717632578 5.780000e-78 302.0
24 TraesCS7D01G006600 chr7B 81.429 350 54 9 1611 1957 717810868 717811209 3.500000e-70 276.0
25 TraesCS7D01G006600 chr7B 80.309 259 48 3 1699 1956 719106668 719106412 3.630000e-45 193.0
26 TraesCS7D01G006600 chr7B 81.532 222 37 3 930 1148 717633453 717633233 2.820000e-41 180.0
27 TraesCS7D01G006600 chr7B 82.796 186 31 1 954 1138 717542437 717542252 7.910000e-37 165.0
28 TraesCS7D01G006600 chr7A 82.623 915 128 21 1633 2526 717582595 717583499 0.000000e+00 780.0
29 TraesCS7D01G006600 chr7A 82.127 912 134 24 1631 2526 717253644 717254542 0.000000e+00 754.0
30 TraesCS7D01G006600 chr7A 89.033 538 51 5 2536 3067 2114742 2114207 0.000000e+00 660.0
31 TraesCS7D01G006600 chr7A 82.082 586 84 13 1954 2526 717439932 717440509 6.910000e-132 481.0
32 TraesCS7D01G006600 chr7A 79.420 379 65 10 1611 1983 717389309 717389680 4.560000e-64 255.0
33 TraesCS7D01G006600 chr7A 84.946 186 27 1 954 1138 717388776 717388961 1.690000e-43 187.0
34 TraesCS7D01G006600 chr7A 79.630 162 28 5 399 558 470594923 470595081 1.040000e-20 111.0
35 TraesCS7D01G006600 chr7A 87.273 55 3 4 656 709 717581206 717581257 3.840000e-05 60.2
36 TraesCS7D01G006600 chr4A 89.346 535 54 3 2528 3060 740016259 740015726 0.000000e+00 669.0
37 TraesCS7D01G006600 chr4A 88.848 538 56 2 2528 3061 740581895 740582432 0.000000e+00 658.0
38 TraesCS7D01G006600 chr4A 88.091 571 46 9 2532 3096 740940498 740941052 0.000000e+00 658.0
39 TraesCS7D01G006600 chr4A 82.883 222 30 5 453 671 514082338 514082554 3.630000e-45 193.0
40 TraesCS7D01G006600 chr4A 77.987 318 46 15 3171 3465 740941224 740941540 1.020000e-40 178.0
41 TraesCS7D01G006600 chr4A 83.417 199 22 3 475 666 105245551 105245357 1.310000e-39 174.0
42 TraesCS7D01G006600 chr3B 79.257 323 49 16 355 671 577495719 577496029 3.600000e-50 209.0
43 TraesCS7D01G006600 chr3B 82.081 173 27 4 401 571 753746268 753746098 1.030000e-30 145.0
44 TraesCS7D01G006600 chr3D 78.997 319 54 12 339 653 579597461 579597152 4.660000e-49 206.0
45 TraesCS7D01G006600 chr1A 81.707 164 21 4 508 671 577200900 577200746 1.040000e-25 128.0
46 TraesCS7D01G006600 chr1A 80.488 164 23 3 508 671 577150605 577150451 2.250000e-22 117.0
47 TraesCS7D01G006600 chr6D 79.096 177 31 3 495 671 428754409 428754579 2.250000e-22 117.0
48 TraesCS7D01G006600 chr2D 88.525 61 2 3 613 670 328464497 328464555 6.380000e-08 69.4


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 TraesCS7D01G006600 chr7D 3244720 3248279 3559 True 6575.0 6575 100.0000 1 3560 1 chr7D.!!$R4 3559
1 TraesCS7D01G006600 chr7D 3365557 3368043 2486 False 1659.0 1949 91.3240 1 2531 2 chr7D.!!$F3 2530
2 TraesCS7D01G006600 chr7D 3232024 3232537 513 True 939.0 939 99.6110 3047 3560 1 chr7D.!!$R3 513
3 TraesCS7D01G006600 chr7D 621812356 621813276 920 False 699.0 699 80.8350 1617 2526 1 chr7D.!!$F2 909
4 TraesCS7D01G006600 chr7D 3783625 3784159 534 True 691.0 691 90.1670 2530 3061 1 chr7D.!!$R6 531
5 TraesCS7D01G006600 chr7D 2354357 2354891 534 True 676.0 676 89.5520 2528 3061 1 chr7D.!!$R1 533
6 TraesCS7D01G006600 chr7D 3629824 3630361 537 True 673.0 673 89.4640 2530 3061 1 chr7D.!!$R5 531
7 TraesCS7D01G006600 chr7D 2606559 2607093 534 True 669.0 669 89.3660 2530 3061 1 chr7D.!!$R2 531
8 TraesCS7D01G006600 chr7D 2499487 2500581 1094 True 507.5 728 86.7015 2528 3536 2 chr7D.!!$R7 1008
9 TraesCS7D01G006600 chr7D 621867270 621868732 1462 False 423.0 664 79.6540 946 2526 2 chr7D.!!$F4 1580
10 TraesCS7D01G006600 chrUn 328676319 328676832 513 True 939.0 939 99.6110 3047 3560 1 chrUn.!!$R1 513
11 TraesCS7D01G006600 chrUn 347563976 347564489 513 True 939.0 939 99.6110 3047 3560 1 chrUn.!!$R2 513
12 TraesCS7D01G006600 chr7B 719431000 719431885 885 False 804.0 804 83.2780 1640 2529 1 chr7B.!!$F2 889
13 TraesCS7D01G006600 chr7B 718098715 718099630 915 True 752.0 752 81.8280 1617 2529 1 chr7B.!!$R3 912
14 TraesCS7D01G006600 chr7B 717893184 717894105 921 True 702.0 702 80.8560 1617 2529 1 chr7B.!!$R2 912
15 TraesCS7D01G006600 chr7B 717787339 717788261 922 False 682.0 682 80.4260 1611 2529 1 chr7B.!!$F1 918
16 TraesCS7D01G006600 chr7B 719626958 719627862 904 False 675.0 675 80.5220 1621 2520 1 chr7B.!!$F3 899
17 TraesCS7D01G006600 chr7B 717810868 717815717 4849 False 425.5 575 79.9775 1611 2529 2 chr7B.!!$F4 918
18 TraesCS7D01G006600 chr7B 717632578 717633453 875 True 241.0 302 82.1455 930 1967 2 chr7B.!!$R5 1037
19 TraesCS7D01G006600 chr7A 717253644 717254542 898 False 754.0 754 82.1270 1631 2526 1 chr7A.!!$F2 895
20 TraesCS7D01G006600 chr7A 2114207 2114742 535 True 660.0 660 89.0330 2536 3067 1 chr7A.!!$R1 531
21 TraesCS7D01G006600 chr7A 717439932 717440509 577 False 481.0 481 82.0820 1954 2526 1 chr7A.!!$F3 572
22 TraesCS7D01G006600 chr7A 717581206 717583499 2293 False 420.1 780 84.9480 656 2526 2 chr7A.!!$F5 1870
23 TraesCS7D01G006600 chr7A 717388776 717389680 904 False 221.0 255 82.1830 954 1983 2 chr7A.!!$F4 1029
24 TraesCS7D01G006600 chr4A 740015726 740016259 533 True 669.0 669 89.3460 2528 3060 1 chr4A.!!$R2 532
25 TraesCS7D01G006600 chr4A 740581895 740582432 537 False 658.0 658 88.8480 2528 3061 1 chr4A.!!$F2 533
26 TraesCS7D01G006600 chr4A 740940498 740941540 1042 False 418.0 658 83.0390 2532 3465 2 chr4A.!!$F3 933

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
351 364 0.449786 CGTGCATTGCCGTGGAATTA 59.55 50.0 6.12 0.0 0.0 1.40 F
1482 2015 0.250295 TGTGGTGGAGCAAGTGTAGC 60.25 55.0 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 2121 0.179020 CCACTCAGCCAACCAGTCAA 60.179 55.0 0.0 0.0 0.0 3.18 R
2635 7169 0.821517 ACCGCATGTCAATACCTCGA 59.178 50.0 0.0 0.0 0.0 4.04 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
27 28 5.030295 CAGCGGTGTTATGATGTCAATTTC 58.970 41.667 6.41 0.00 0.00 2.17
47 48 9.844790 CAATTTCACAAGCATTATCTTCTTACA 57.155 29.630 0.00 0.00 0.00 2.41
135 138 4.287067 ACATCACTGGAGTACTGGACATTT 59.713 41.667 0.00 0.00 0.00 2.32
143 146 3.585862 AGTACTGGACATTTGTGTAGCG 58.414 45.455 0.00 0.00 0.00 4.26
148 151 2.224426 TGGACATTTGTGTAGCGGTTCT 60.224 45.455 0.00 0.00 0.00 3.01
155 158 1.616865 TGTGTAGCGGTTCTAGCTTGT 59.383 47.619 0.00 0.00 43.24 3.16
156 159 1.993370 GTGTAGCGGTTCTAGCTTGTG 59.007 52.381 0.00 0.00 43.24 3.33
157 160 1.890489 TGTAGCGGTTCTAGCTTGTGA 59.110 47.619 0.00 0.00 43.24 3.58
161 164 3.003480 AGCGGTTCTAGCTTGTGATTTC 58.997 45.455 0.00 0.00 43.24 2.17
169 172 4.991056 TCTAGCTTGTGATTTCTGACACAC 59.009 41.667 0.00 0.00 44.81 3.82
184 187 5.011635 TCTGACACACTAAGTTGCCAATAGA 59.988 40.000 0.00 0.00 0.00 1.98
186 189 5.874810 TGACACACTAAGTTGCCAATAGATC 59.125 40.000 0.00 0.00 0.00 2.75
281 293 9.696917 GTTTATTTTGAGACAGTGGATTTGAAT 57.303 29.630 0.00 0.00 0.00 2.57
300 312 4.337274 TGAATATGCAAGATCAGGTGCTTG 59.663 41.667 14.68 0.00 43.26 4.01
333 345 7.062605 GGATTTACATATACAACACGATACCCG 59.937 40.741 0.00 0.00 45.44 5.28
344 357 1.817941 GATACCCGTGCATTGCCGT 60.818 57.895 6.12 0.00 0.00 5.68
351 364 0.449786 CGTGCATTGCCGTGGAATTA 59.550 50.000 6.12 0.00 0.00 1.40
363 376 6.694447 TGCCGTGGAATTAGGTATATAGTTC 58.306 40.000 0.00 0.00 0.00 3.01
395 408 7.681939 TGTGTAAAATGGTAATTCAGTCCTC 57.318 36.000 0.00 0.00 0.00 3.71
396 409 6.657541 TGTGTAAAATGGTAATTCAGTCCTCC 59.342 38.462 0.00 0.00 0.00 4.30
408 421 9.886132 GTAATTCAGTCCTCCAGATTTAAACTA 57.114 33.333 0.00 0.00 0.00 2.24
412 425 6.058183 CAGTCCTCCAGATTTAAACTATGGG 58.942 44.000 12.74 6.21 0.00 4.00
434 447 6.207417 TGGGAGAAAGTTCTGCATAAGAAAAG 59.793 38.462 13.64 0.00 46.51 2.27
436 449 7.040409 GGGAGAAAGTTCTGCATAAGAAAAGAA 60.040 37.037 13.64 0.00 46.51 2.52
437 450 8.352942 GGAGAAAGTTCTGCATAAGAAAAGAAA 58.647 33.333 7.60 0.00 46.51 2.52
438 451 9.736023 GAGAAAGTTCTGCATAAGAAAAGAAAA 57.264 29.630 0.00 0.00 46.51 2.29
469 482 6.825284 TGAAAAGTTGTGCATGTTACAATG 57.175 33.333 16.86 0.00 39.88 2.82
483 496 7.360185 GCATGTTACAATGAAATGCAATGTGAA 60.360 33.333 0.00 0.00 40.69 3.18
484 497 8.496751 CATGTTACAATGAAATGCAATGTGAAA 58.503 29.630 0.00 0.00 40.69 2.69
538 551 5.820404 TGCATGATAGAGGATTCTCATGT 57.180 39.130 3.21 0.00 42.34 3.21
560 573 6.447162 TGTATAGATTGGACGAATGCTAGTG 58.553 40.000 0.00 0.00 0.00 2.74
561 574 2.555199 AGATTGGACGAATGCTAGTGC 58.445 47.619 0.00 0.00 40.20 4.40
577 590 2.966050 AGTGCAGCAAGCTAGTAACTC 58.034 47.619 0.00 0.00 45.94 3.01
584 597 5.582665 GCAGCAAGCTAGTAACTCTAACAAT 59.417 40.000 0.00 0.00 41.15 2.71
587 600 8.812329 CAGCAAGCTAGTAACTCTAACAATTAG 58.188 37.037 0.00 0.00 34.52 1.73
663 676 5.135533 TGTGGGGATCACTCTCTTAGGTATA 59.864 44.000 0.00 0.00 46.20 1.47
872 1272 3.059166 GGTTGGTGTGCAAATGCTTTAG 58.941 45.455 6.97 0.00 42.66 1.85
921 1342 7.377766 ACACAAATGTTGTCATATGGTAGTC 57.622 36.000 2.13 0.00 43.23 2.59
978 1409 4.972514 TGTGTTGAAAGTGCATTGTGTA 57.027 36.364 0.00 0.00 0.00 2.90
983 1414 7.976175 TGTGTTGAAAGTGCATTGTGTAAAATA 59.024 29.630 0.00 0.00 0.00 1.40
1045 1481 5.180117 CGTATAATTGATGGAAGGCAGAAGG 59.820 44.000 0.00 0.00 0.00 3.46
1048 1484 1.821332 GATGGAAGGCAGAAGGCGG 60.821 63.158 0.00 0.00 46.16 6.13
1089 1525 7.867403 GCACTTTTGAAGGATATCACAGAAAAA 59.133 33.333 4.83 4.23 0.00 1.94
1095 1531 9.927668 TTGAAGGATATCACAGAAAAATTTTCC 57.072 29.630 14.17 0.00 0.00 3.13
1134 1570 1.131126 CATGGTGGATTCGCAACAGTC 59.869 52.381 0.00 0.00 0.00 3.51
1145 1581 2.691526 TCGCAACAGTCTATCGGGTAAT 59.308 45.455 0.00 0.00 0.00 1.89
1149 1585 5.163794 CGCAACAGTCTATCGGGTAATTTTT 60.164 40.000 0.00 0.00 0.00 1.94
1248 1690 7.332430 CCTCGTGTTGTCCAACTATGTTAATAA 59.668 37.037 11.14 0.00 41.67 1.40
1250 1692 9.221933 TCGTGTTGTCCAACTATGTTAATAATT 57.778 29.630 11.14 0.00 41.67 1.40
1259 1701 8.181573 CCAACTATGTTAATAATTGACGTTGCT 58.818 33.333 0.00 0.00 28.89 3.91
1329 1771 7.342799 ACTCGAAGGTACCATATAGTTTTGGTA 59.657 37.037 15.94 0.00 44.36 3.25
1377 1853 5.886960 AAATCAGGCAAAGTCTATGTGTC 57.113 39.130 0.00 0.00 0.00 3.67
1378 1854 4.558226 ATCAGGCAAAGTCTATGTGTCA 57.442 40.909 0.00 0.00 0.00 3.58
1379 1855 3.664107 TCAGGCAAAGTCTATGTGTCAC 58.336 45.455 0.00 0.00 0.00 3.67
1380 1856 2.413112 CAGGCAAAGTCTATGTGTCACG 59.587 50.000 0.00 0.00 0.00 4.35
1396 1928 0.376152 CACGAGAATGTGCTCATGCC 59.624 55.000 1.29 0.00 38.71 4.40
1411 1943 3.631250 TCATGCCTTGATAGGGAAAACC 58.369 45.455 0.00 0.00 45.84 3.27
1482 2015 0.250295 TGTGGTGGAGCAAGTGTAGC 60.250 55.000 0.00 0.00 0.00 3.58
1500 2034 5.233689 GTGTAGCGTATTTCCATTAGGTGTC 59.766 44.000 0.00 0.00 35.89 3.67
1504 2038 4.034048 GCGTATTTCCATTAGGTGTCTGTG 59.966 45.833 0.00 0.00 35.89 3.66
1524 2058 2.373169 TGCTCTGTGTTCTCCCAGAAAT 59.627 45.455 0.00 0.00 35.75 2.17
1538 2072 7.103641 TCTCCCAGAAATATTTGTGTGTACTC 58.896 38.462 20.35 0.00 30.21 2.59
1540 2074 5.447279 CCCAGAAATATTTGTGTGTACTCGC 60.447 44.000 20.35 1.55 30.21 5.03
1541 2075 5.121611 CCAGAAATATTTGTGTGTACTCGCA 59.878 40.000 20.35 7.07 30.21 5.10
1542 2076 6.348132 CCAGAAATATTTGTGTGTACTCGCAA 60.348 38.462 20.35 17.45 35.78 4.85
1543 2077 7.075121 CAGAAATATTTGTGTGTACTCGCAAA 58.925 34.615 28.61 28.61 46.66 3.68
1544 2078 7.589587 CAGAAATATTTGTGTGTACTCGCAAAA 59.410 33.333 29.57 21.55 46.07 2.44
1545 2079 8.296713 AGAAATATTTGTGTGTACTCGCAAAAT 58.703 29.630 29.57 22.39 46.07 1.82
1546 2080 9.549509 GAAATATTTGTGTGTACTCGCAAAATA 57.450 29.630 29.57 22.93 46.07 1.40
1547 2081 9.900710 AAATATTTGTGTGTACTCGCAAAATAA 57.099 25.926 29.57 21.28 46.07 1.40
1548 2082 9.900710 AATATTTGTGTGTACTCGCAAAATAAA 57.099 25.926 29.57 19.53 46.07 1.40
1549 2083 9.900710 ATATTTGTGTGTACTCGCAAAATAAAA 57.099 25.926 29.57 17.81 46.07 1.52
1550 2084 8.810652 ATTTGTGTGTACTCGCAAAATAAAAT 57.189 26.923 29.57 16.04 46.07 1.82
1551 2085 9.900710 ATTTGTGTGTACTCGCAAAATAAAATA 57.099 25.926 29.57 13.10 46.07 1.40
1552 2086 9.731819 TTTGTGTGTACTCGCAAAATAAAATAA 57.268 25.926 26.00 7.87 42.29 1.40
1553 2087 9.731819 TTGTGTGTACTCGCAAAATAAAATAAA 57.268 25.926 18.69 0.00 35.36 1.40
1554 2088 9.731819 TGTGTGTACTCGCAAAATAAAATAAAA 57.268 25.926 8.64 0.00 35.78 1.52
1571 2105 7.945033 AAATAAAATTTGTGTGTACTGGCTG 57.055 32.000 0.00 0.00 0.00 4.85
1572 2106 6.892658 ATAAAATTTGTGTGTACTGGCTGA 57.107 33.333 0.00 0.00 0.00 4.26
1573 2107 4.836125 AAATTTGTGTGTACTGGCTGAG 57.164 40.909 0.00 0.00 0.00 3.35
1574 2108 3.492102 ATTTGTGTGTACTGGCTGAGT 57.508 42.857 0.00 0.00 38.88 3.41
1575 2109 2.238942 TTGTGTGTACTGGCTGAGTG 57.761 50.000 0.00 0.00 35.96 3.51
1576 2110 0.392706 TGTGTGTACTGGCTGAGTGG 59.607 55.000 0.00 0.00 35.96 4.00
1577 2111 0.320771 GTGTGTACTGGCTGAGTGGG 60.321 60.000 0.00 0.00 35.96 4.61
1578 2112 0.762842 TGTGTACTGGCTGAGTGGGT 60.763 55.000 0.00 0.00 35.96 4.51
1579 2113 0.320771 GTGTACTGGCTGAGTGGGTG 60.321 60.000 0.00 0.00 35.96 4.61
1580 2114 0.762842 TGTACTGGCTGAGTGGGTGT 60.763 55.000 0.00 0.00 35.96 4.16
1581 2115 0.396811 GTACTGGCTGAGTGGGTGTT 59.603 55.000 0.00 0.00 35.96 3.32
1582 2116 1.136828 TACTGGCTGAGTGGGTGTTT 58.863 50.000 0.00 0.00 35.96 2.83
1583 2117 0.258774 ACTGGCTGAGTGGGTGTTTT 59.741 50.000 0.00 0.00 31.75 2.43
1584 2118 1.341976 ACTGGCTGAGTGGGTGTTTTT 60.342 47.619 0.00 0.00 31.75 1.94
1647 2209 9.482627 ACCTTCTAATCAGCTAAATATTCTTCG 57.517 33.333 0.00 0.00 0.00 3.79
1705 6191 0.958822 ACGGGAAAACCATTGCTGTC 59.041 50.000 0.00 0.00 40.22 3.51
1748 6234 9.811995 ACCATTCAATCAATGAGACATTATTTG 57.188 29.630 0.00 0.00 44.40 2.32
1873 6361 2.953466 AAGAGCATACTTACGCCGAA 57.047 45.000 0.00 0.00 0.00 4.30
1889 6377 3.927142 CGCCGAAGTAAGAGAAAGATTGT 59.073 43.478 0.00 0.00 0.00 2.71
2020 6529 5.939883 TCTGACATGTTTTATCTGGTCAAGG 59.060 40.000 0.00 0.00 35.15 3.61
2121 6639 2.622064 ATTCTTCGCTCCATGGTACC 57.378 50.000 12.58 4.43 0.00 3.34
2407 6939 7.806690 TCTTGAGATTTGGACTAACATTTTCG 58.193 34.615 0.00 0.00 0.00 3.46
2409 6941 6.001460 TGAGATTTGGACTAACATTTTCGGT 58.999 36.000 0.00 0.00 0.00 4.69
2534 7068 9.472361 TTTAGGAGTTATAATTATCGAGCACAC 57.528 33.333 0.00 0.00 0.00 3.82
2613 7147 3.003394 TGGATGGCAAGTTCTATGTGG 57.997 47.619 0.00 0.00 0.00 4.17
2635 7169 0.613777 GGTGGTGTTAGCAGTAGCCT 59.386 55.000 0.00 0.00 43.56 4.58
2766 7300 4.924305 ATTGCAGTTGTGAACAATGAGT 57.076 36.364 0.00 0.00 38.24 3.41
2784 7318 3.308595 TGAGTTTTATGCCGCTGATTACG 59.691 43.478 0.00 0.00 0.00 3.18
2811 7345 9.875675 GTGAGAATAATGATTTGAAGCAGTATC 57.124 33.333 2.95 0.00 34.94 2.24
2948 7485 7.411486 TCCAAACAATTCTACTGGTGAAAAA 57.589 32.000 0.00 0.00 0.00 1.94
2952 7489 7.639113 AACAATTCTACTGGTGAAAAAGTGA 57.361 32.000 0.00 0.00 0.00 3.41
3155 7771 2.932614 CCTGATACTGCTCTTTTCCACG 59.067 50.000 0.00 0.00 0.00 4.94
3519 8207 6.537355 AGACATGAATGAGTTTTGAGGAAGA 58.463 36.000 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.692710 AGATAATGCTTGTGAAATTGACATCAT 58.307 29.630 0.00 0.00 0.00 2.45
19 20 8.976986 AAGAAGATAATGCTTGTGAAATTGAC 57.023 30.769 0.00 0.00 0.00 3.18
135 138 1.616865 ACAAGCTAGAACCGCTACACA 59.383 47.619 0.00 0.00 36.56 3.72
143 146 4.997395 TGTCAGAAATCACAAGCTAGAACC 59.003 41.667 0.00 0.00 0.00 3.62
148 151 4.960938 AGTGTGTCAGAAATCACAAGCTA 58.039 39.130 0.00 0.00 44.37 3.32
155 158 4.515191 GGCAACTTAGTGTGTCAGAAATCA 59.485 41.667 0.00 0.00 0.00 2.57
156 159 4.515191 TGGCAACTTAGTGTGTCAGAAATC 59.485 41.667 0.00 0.00 37.61 2.17
157 160 4.460263 TGGCAACTTAGTGTGTCAGAAAT 58.540 39.130 0.00 0.00 37.61 2.17
161 164 5.237815 TCTATTGGCAACTTAGTGTGTCAG 58.762 41.667 0.00 0.00 37.61 3.51
268 280 7.034685 TGATCTTGCATATTCAAATCCACTG 57.965 36.000 0.00 0.00 0.00 3.66
281 293 3.538591 CTCAAGCACCTGATCTTGCATA 58.461 45.455 14.40 2.17 41.48 3.14
282 294 2.366533 CTCAAGCACCTGATCTTGCAT 58.633 47.619 14.40 2.81 41.48 3.96
300 312 8.700644 CGTGTTGTATATGTAAATCCTAAGCTC 58.299 37.037 0.00 0.00 0.00 4.09
333 345 1.202290 CCTAATTCCACGGCAATGCAC 60.202 52.381 7.79 0.00 0.00 4.57
370 383 7.175990 GGAGGACTGAATTACCATTTTACACAA 59.824 37.037 0.00 0.00 0.00 3.33
374 387 7.110155 TCTGGAGGACTGAATTACCATTTTAC 58.890 38.462 0.00 0.00 0.00 2.01
381 394 7.829706 AGTTTAAATCTGGAGGACTGAATTACC 59.170 37.037 0.00 0.00 0.00 2.85
395 408 8.581253 AACTTTCTCCCATAGTTTAAATCTGG 57.419 34.615 0.00 0.00 0.00 3.86
396 409 9.454859 AGAACTTTCTCCCATAGTTTAAATCTG 57.545 33.333 0.00 0.00 32.58 2.90
408 421 5.441718 TCTTATGCAGAACTTTCTCCCAT 57.558 39.130 0.00 6.79 34.74 4.00
412 425 9.736023 TTTTCTTTTCTTATGCAGAACTTTCTC 57.264 29.630 0.00 0.00 41.56 2.87
434 447 7.904094 TGCACAACTTTTCATGTTACATTTTC 58.096 30.769 0.00 0.00 0.00 2.29
436 449 7.495279 ACATGCACAACTTTTCATGTTACATTT 59.505 29.630 0.00 0.00 44.83 2.32
437 450 6.985645 ACATGCACAACTTTTCATGTTACATT 59.014 30.769 0.00 0.00 44.83 2.71
438 451 6.514947 ACATGCACAACTTTTCATGTTACAT 58.485 32.000 0.00 0.00 44.83 2.29
439 452 5.900425 ACATGCACAACTTTTCATGTTACA 58.100 33.333 0.00 0.00 44.83 2.41
538 551 5.470368 GCACTAGCATTCGTCCAATCTATA 58.530 41.667 0.00 0.00 41.58 1.31
560 573 4.495422 TGTTAGAGTTACTAGCTTGCTGC 58.505 43.478 5.26 0.00 43.29 5.25
561 574 7.602517 AATTGTTAGAGTTACTAGCTTGCTG 57.397 36.000 5.26 0.00 34.22 4.41
563 576 7.492994 AGCTAATTGTTAGAGTTACTAGCTTGC 59.507 37.037 0.00 0.00 35.20 4.01
752 1152 2.030946 GCAATCGTGAGTGCCTATGTTC 59.969 50.000 10.95 0.00 45.58 3.18
816 1216 7.060421 GGAAGGGAAATTCCATGTATTCTACA 58.940 38.462 14.68 0.00 46.77 2.74
834 1234 5.955355 CACCAACCAATATTTAAGGAAGGGA 59.045 40.000 0.00 0.00 0.00 4.20
836 1236 6.630071 CACACCAACCAATATTTAAGGAAGG 58.370 40.000 0.00 2.09 0.00 3.46
837 1237 6.099341 GCACACCAACCAATATTTAAGGAAG 58.901 40.000 0.00 0.00 0.00 3.46
957 1388 3.865011 ACACAATGCACTTTCAACACA 57.135 38.095 0.00 0.00 0.00 3.72
978 1409 6.205464 CCATGTATCTGCGTGGAATCTATTTT 59.795 38.462 0.61 0.00 45.87 1.82
983 1414 3.117491 CCATGTATCTGCGTGGAATCT 57.883 47.619 0.61 0.00 45.87 2.40
1045 1481 0.308993 GCAAATGGTAGATCTGCCGC 59.691 55.000 22.95 16.56 38.25 6.53
1048 1484 4.708726 AAAGTGCAAATGGTAGATCTGC 57.291 40.909 5.18 3.29 0.00 4.26
1089 1525 5.007724 GCCAATTTCTCTATCGTCGGAAAAT 59.992 40.000 0.00 0.00 32.60 1.82
1095 1531 2.821546 TGGCCAATTTCTCTATCGTCG 58.178 47.619 0.61 0.00 0.00 5.12
1367 1811 3.304559 GCACATTCTCGTGACACATAGAC 59.695 47.826 6.37 0.00 39.34 2.59
1371 1815 2.289010 TGAGCACATTCTCGTGACACAT 60.289 45.455 6.37 0.00 39.34 3.21
1378 1854 0.251354 AGGCATGAGCACATTCTCGT 59.749 50.000 0.00 0.00 44.61 4.18
1379 1855 1.063616 CAAGGCATGAGCACATTCTCG 59.936 52.381 0.00 0.00 44.61 4.04
1380 1856 2.362736 TCAAGGCATGAGCACATTCTC 58.637 47.619 0.00 0.00 44.61 2.87
1396 1928 4.379499 GCGACAAAGGTTTTCCCTATCAAG 60.379 45.833 0.00 0.00 45.47 3.02
1411 1943 2.331809 GCCAACTTAAGGCGACAAAG 57.668 50.000 7.53 0.00 43.15 2.77
1482 2015 4.034048 GCACAGACACCTAATGGAAATACG 59.966 45.833 0.00 0.00 37.04 3.06
1500 2034 0.394192 TGGGAGAACACAGAGCACAG 59.606 55.000 0.00 0.00 0.00 3.66
1524 2058 9.900710 ATTTTATTTTGCGAGTACACACAAATA 57.099 25.926 7.21 6.90 32.50 1.40
1545 2079 9.469807 CAGCCAGTACACACAAATTTTATTTTA 57.530 29.630 0.00 0.00 0.00 1.52
1546 2080 8.200792 TCAGCCAGTACACACAAATTTTATTTT 58.799 29.630 0.00 0.00 0.00 1.82
1547 2081 7.721402 TCAGCCAGTACACACAAATTTTATTT 58.279 30.769 0.00 0.00 0.00 1.40
1548 2082 7.014230 ACTCAGCCAGTACACACAAATTTTATT 59.986 33.333 0.00 0.00 31.37 1.40
1549 2083 6.490040 ACTCAGCCAGTACACACAAATTTTAT 59.510 34.615 0.00 0.00 31.37 1.40
1550 2084 5.825679 ACTCAGCCAGTACACACAAATTTTA 59.174 36.000 0.00 0.00 31.37 1.52
1551 2085 4.644685 ACTCAGCCAGTACACACAAATTTT 59.355 37.500 0.00 0.00 31.37 1.82
1552 2086 4.036734 CACTCAGCCAGTACACACAAATTT 59.963 41.667 0.00 0.00 32.21 1.82
1553 2087 3.565482 CACTCAGCCAGTACACACAAATT 59.435 43.478 0.00 0.00 32.21 1.82
1554 2088 3.141398 CACTCAGCCAGTACACACAAAT 58.859 45.455 0.00 0.00 32.21 2.32
1555 2089 2.560504 CACTCAGCCAGTACACACAAA 58.439 47.619 0.00 0.00 32.21 2.83
1556 2090 1.202639 CCACTCAGCCAGTACACACAA 60.203 52.381 0.00 0.00 32.21 3.33
1557 2091 0.392706 CCACTCAGCCAGTACACACA 59.607 55.000 0.00 0.00 32.21 3.72
1558 2092 0.320771 CCCACTCAGCCAGTACACAC 60.321 60.000 0.00 0.00 32.21 3.82
1559 2093 0.762842 ACCCACTCAGCCAGTACACA 60.763 55.000 0.00 0.00 32.21 3.72
1560 2094 0.320771 CACCCACTCAGCCAGTACAC 60.321 60.000 0.00 0.00 32.21 2.90
1561 2095 0.762842 ACACCCACTCAGCCAGTACA 60.763 55.000 0.00 0.00 32.21 2.90
1562 2096 0.396811 AACACCCACTCAGCCAGTAC 59.603 55.000 0.00 0.00 32.21 2.73
1563 2097 1.136828 AAACACCCACTCAGCCAGTA 58.863 50.000 0.00 0.00 32.21 2.74
1564 2098 0.258774 AAAACACCCACTCAGCCAGT 59.741 50.000 0.00 0.00 34.67 4.00
1565 2099 1.402787 AAAAACACCCACTCAGCCAG 58.597 50.000 0.00 0.00 0.00 4.85
1566 2100 3.605946 AAAAACACCCACTCAGCCA 57.394 47.368 0.00 0.00 0.00 4.75
1584 2118 2.426738 CACTCAGCCAACCAGTCAAAAA 59.573 45.455 0.00 0.00 0.00 1.94
1585 2119 2.023673 CACTCAGCCAACCAGTCAAAA 58.976 47.619 0.00 0.00 0.00 2.44
1586 2120 1.679139 CACTCAGCCAACCAGTCAAA 58.321 50.000 0.00 0.00 0.00 2.69
1587 2121 0.179020 CCACTCAGCCAACCAGTCAA 60.179 55.000 0.00 0.00 0.00 3.18
1588 2122 1.451504 CCACTCAGCCAACCAGTCA 59.548 57.895 0.00 0.00 0.00 3.41
1589 2123 1.302832 CCCACTCAGCCAACCAGTC 60.303 63.158 0.00 0.00 0.00 3.51
1590 2124 2.078665 ACCCACTCAGCCAACCAGT 61.079 57.895 0.00 0.00 0.00 4.00
1591 2125 1.601759 CACCCACTCAGCCAACCAG 60.602 63.158 0.00 0.00 0.00 4.00
1592 2126 1.932156 AACACCCACTCAGCCAACCA 61.932 55.000 0.00 0.00 0.00 3.67
1593 2127 1.152756 AACACCCACTCAGCCAACC 60.153 57.895 0.00 0.00 0.00 3.77
1594 2128 2.032981 CAACACCCACTCAGCCAAC 58.967 57.895 0.00 0.00 0.00 3.77
1595 2129 1.827789 GCAACACCCACTCAGCCAA 60.828 57.895 0.00 0.00 0.00 4.52
1596 2130 2.203337 GCAACACCCACTCAGCCA 60.203 61.111 0.00 0.00 0.00 4.75
1597 2131 0.322456 TATGCAACACCCACTCAGCC 60.322 55.000 0.00 0.00 0.00 4.85
1598 2132 0.804989 GTATGCAACACCCACTCAGC 59.195 55.000 0.00 0.00 0.00 4.26
1599 2133 2.183478 TGTATGCAACACCCACTCAG 57.817 50.000 0.00 0.00 31.43 3.35
1647 2209 7.076842 TGTTTAGCTTATCTTGTGAGCATTC 57.923 36.000 0.00 0.00 41.64 2.67
1705 6191 5.185635 TGAATGGTTGCTCCTTATCCTTTTG 59.814 40.000 0.80 0.00 37.07 2.44
1748 6234 2.258726 GGGTGTCAACTTCACGGCC 61.259 63.158 0.00 0.00 36.76 6.13
1863 6349 4.730657 TCTTTCTCTTACTTCGGCGTAAG 58.269 43.478 6.85 11.83 44.81 2.34
1889 6377 9.625747 TCCATTGCTGATATACTCAAAACATAA 57.374 29.630 0.00 0.00 32.14 1.90
2020 6529 8.988064 TTATTGTGTTTCTGTCTATCTCACTC 57.012 34.615 0.00 0.00 0.00 3.51
2147 6666 2.158813 ACGTGTGTTCCATTCAAGTCCT 60.159 45.455 0.00 0.00 0.00 3.85
2180 6699 3.706086 ACAAACCTTCACAAATGCCTCTT 59.294 39.130 0.00 0.00 0.00 2.85
2407 6939 6.428159 CCAGTACTCCAATGCATTATAGAACC 59.572 42.308 21.09 11.21 0.00 3.62
2409 6941 5.997746 GCCAGTACTCCAATGCATTATAGAA 59.002 40.000 21.09 3.70 0.00 2.10
2534 7068 1.074951 GGGAAGGGGTGTCCAAGTG 59.925 63.158 0.00 0.00 36.83 3.16
2613 7147 1.992170 CTACTGCTAACACCACCGAC 58.008 55.000 0.00 0.00 0.00 4.79
2635 7169 0.821517 ACCGCATGTCAATACCTCGA 59.178 50.000 0.00 0.00 0.00 4.04
2784 7318 7.093322 ACTGCTTCAAATCATTATTCTCACC 57.907 36.000 0.00 0.00 0.00 4.02
2811 7345 3.411446 TCCACTTGTTGTCCAGCTTATG 58.589 45.455 0.00 0.00 0.00 1.90
2906 7443 2.310538 GGAGGCCCAATAACAATCAGG 58.689 52.381 0.00 0.00 0.00 3.86
2948 7485 4.851843 TCCATGAATGAAGCTCAATCACT 58.148 39.130 0.00 0.00 38.91 3.41
2952 7489 4.150359 GGGATCCATGAATGAAGCTCAAT 58.850 43.478 15.23 0.00 0.00 2.57
3032 7572 1.066908 CCCATCACCGCGCATTTAATT 59.933 47.619 8.75 0.00 0.00 1.40
3155 7771 6.503524 TGCCTTTGTTTCAGTGAAAAGATAC 58.496 36.000 19.63 8.62 33.14 2.24


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

AutoCloner maintained by Alex Coulton.