Multiple sequence alignment - TraesCS2B01G278000

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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 TraesCS2B01G278000 chr2B 100.000 4084 0 0 1 4084 383929474 383925391 0.000000e+00 7542.0
1 TraesCS2B01G278000 chr2B 93.786 2108 95 10 1987 4084 687888474 687886393 0.000000e+00 3134.0
2 TraesCS2B01G278000 chr2B 92.038 1168 46 12 1895 3022 58402041 58400881 0.000000e+00 1598.0
3 TraesCS2B01G278000 chr2B 97.034 472 13 1 159 630 367443662 367444132 0.000000e+00 793.0
4 TraesCS2B01G278000 chr2B 88.697 522 54 5 3564 4084 20556009 20556526 2.070000e-177 632.0
5 TraesCS2B01G278000 chr2B 92.113 355 26 2 3219 3572 387354313 387353960 2.190000e-137 499.0
6 TraesCS2B01G278000 chr2B 94.969 159 6 2 1 157 380729445 380729603 8.770000e-62 248.0
7 TraesCS2B01G278000 chr2B 92.500 160 11 1 1633 1791 63478218 63478377 1.140000e-55 228.0
8 TraesCS2B01G278000 chr2B 91.083 157 14 0 1 157 367443282 367443438 3.200000e-51 213.0
9 TraesCS2B01G278000 chr2B 95.283 106 4 1 1529 1634 77856044 77856148 2.530000e-37 167.0
10 TraesCS2B01G278000 chr2B 97.059 34 1 0 1192 1225 383928344 383928311 1.590000e-04 58.4
11 TraesCS2B01G278000 chr5B 96.331 2453 86 2 1633 4084 675542509 675544958 0.000000e+00 4028.0
12 TraesCS2B01G278000 chr5B 93.926 1597 60 8 2498 4084 241067596 241066027 0.000000e+00 2377.0
13 TraesCS2B01G278000 chr5B 93.450 1374 49 7 1886 3219 314805276 314803904 0.000000e+00 2001.0
14 TraesCS2B01G278000 chr5B 97.251 1164 32 0 1 1164 675541021 675542184 0.000000e+00 1973.0
15 TraesCS2B01G278000 chr5B 95.604 364 15 1 1188 1550 675542147 675542510 2.120000e-162 582.0
16 TraesCS2B01G278000 chr5B 96.815 157 5 0 1 157 667408249 667408405 3.130000e-66 263.0
17 TraesCS2B01G278000 chr6B 96.060 2462 86 3 1633 4084 466777564 466775104 0.000000e+00 3999.0
18 TraesCS2B01G278000 chr6B 96.268 1554 53 3 1 1550 466779115 466777563 0.000000e+00 2543.0
19 TraesCS2B01G278000 chr6B 93.270 1367 54 14 1886 3216 418120418 418121782 0.000000e+00 1980.0
20 TraesCS2B01G278000 chr6B 96.010 802 25 3 1886 2680 644654000 644653199 0.000000e+00 1297.0
21 TraesCS2B01G278000 chr6B 93.889 540 33 0 2680 3219 644653168 644652629 0.000000e+00 815.0
22 TraesCS2B01G278000 chr6B 89.354 526 47 4 3564 4084 401422691 401423212 0.000000e+00 652.0
23 TraesCS2B01G278000 chr6B 89.527 296 27 2 1256 1550 381170013 381169721 4.990000e-99 372.0
24 TraesCS2B01G278000 chr6B 90.647 278 22 2 1256 1532 253547025 253547299 2.320000e-97 366.0
25 TraesCS2B01G278000 chr6B 94.340 159 9 0 1633 1791 178162905 178163063 1.130000e-60 244.0
26 TraesCS2B01G278000 chr6B 93.082 159 6 1 1633 1791 163449305 163449458 1.140000e-55 228.0
27 TraesCS2B01G278000 chr6B 91.975 162 10 1 1633 1791 142536928 142536767 1.480000e-54 224.0
28 TraesCS2B01G278000 chr6B 97.872 94 1 1 1541 1634 286726687 286726595 1.170000e-35 161.0
29 TraesCS2B01G278000 chr6B 92.381 105 6 2 1531 1635 173797197 173797095 9.150000e-32 148.0
30 TraesCS2B01G278000 chr6B 97.059 34 1 0 1131 1164 466777922 466777889 1.590000e-04 58.4
31 TraesCS2B01G278000 chr3B 94.397 2213 104 9 1886 4084 727195754 727193548 0.000000e+00 3382.0
32 TraesCS2B01G278000 chr3B 94.470 1103 56 3 159 1257 217776166 217777267 0.000000e+00 1694.0
33 TraesCS2B01G278000 chr3B 94.444 540 30 0 2680 3219 771941327 771940788 0.000000e+00 832.0
34 TraesCS2B01G278000 chr3B 87.856 527 54 8 3563 4084 603289095 603288574 9.710000e-171 610.0
35 TraesCS2B01G278000 chr3B 87.500 296 33 2 1256 1550 531498410 531498118 5.060000e-89 339.0
36 TraesCS2B01G278000 chr3B 95.541 157 7 0 1 157 366840702 366840858 6.780000e-63 252.0
37 TraesCS2B01G278000 chr3B 94.904 157 7 1 1 157 334282657 334282812 1.130000e-60 244.0
38 TraesCS2B01G278000 chr3B 96.939 98 1 2 1545 1642 567473512 567473607 3.270000e-36 163.0
39 TraesCS2B01G278000 chr3B 93.519 108 5 2 1529 1634 469635023 469635130 4.230000e-35 159.0
40 TraesCS2B01G278000 chr3B 92.453 106 6 2 1531 1634 487780561 487780666 2.540000e-32 150.0
41 TraesCS2B01G278000 chr3B 91.509 106 6 3 1530 1634 585415193 585415296 4.260000e-30 143.0
42 TraesCS2B01G278000 chr1B 93.727 1371 49 7 1886 3219 232233066 232231696 0.000000e+00 2021.0
43 TraesCS2B01G278000 chr1B 96.910 356 10 1 334 689 346285338 346285692 2.720000e-166 595.0
44 TraesCS2B01G278000 chr1B 92.394 355 24 3 3219 3572 233718500 233718852 1.690000e-138 503.0
45 TraesCS2B01G278000 chr1B 94.969 159 8 0 1633 1791 434006543 434006701 2.440000e-62 250.0
46 TraesCS2B01G278000 chr1B 94.937 158 7 1 1 157 372998611 372998454 3.150000e-61 246.0
47 TraesCS2B01G278000 chr1B 93.252 163 6 3 1633 1791 521345565 521345726 6.820000e-58 235.0
48 TraesCS2B01G278000 chr7D 96.007 1102 41 1 159 1257 343754542 343753441 0.000000e+00 1788.0
49 TraesCS2B01G278000 chr7D 96.136 647 25 0 326 972 557290508 557289862 0.000000e+00 1057.0
50 TraesCS2B01G278000 chr7D 95.906 171 5 2 1087 1257 557289864 557289696 4.020000e-70 276.0
51 TraesCS2B01G278000 chr7D 91.176 170 11 1 159 328 557303031 557302866 1.140000e-55 228.0
52 TraesCS2B01G278000 chr7D 93.836 146 8 1 12 157 557303399 557303255 6.870000e-53 219.0
53 TraesCS2B01G278000 chr7D 96.040 101 4 0 1541 1641 271541867 271541767 9.080000e-37 165.0
54 TraesCS2B01G278000 chr7D 98.851 87 1 0 1549 1635 169446011 169445925 5.470000e-34 156.0
55 TraesCS2B01G278000 chr7D 94.737 38 2 0 1188 1225 557289826 557289789 4.410000e-05 60.2
56 TraesCS2B01G278000 chr7D 97.059 34 1 0 1131 1164 343753506 343753473 1.590000e-04 58.4
57 TraesCS2B01G278000 chr7D 97.059 34 1 0 1131 1164 557289761 557289728 1.590000e-04 58.4
58 TraesCS2B01G278000 chr1A 90.342 1170 61 10 1895 3022 64329664 64330823 0.000000e+00 1487.0
59 TraesCS2B01G278000 chr2D 95.352 796 25 6 1895 2681 205892918 205892126 0.000000e+00 1254.0
60 TraesCS2B01G278000 chr2D 93.521 355 20 3 3219 3572 455240112 455239760 3.620000e-145 525.0
61 TraesCS2B01G278000 chr6D 90.673 847 65 8 419 1257 232427250 232426410 0.000000e+00 1114.0
62 TraesCS2B01G278000 chr6D 92.308 260 20 0 159 418 232427546 232427287 1.790000e-98 370.0
63 TraesCS2B01G278000 chr6D 94.737 38 2 0 1188 1225 232426542 232426505 4.410000e-05 60.2
64 TraesCS2B01G278000 chr7B 89.714 525 47 4 3567 4084 652637718 652637194 0.000000e+00 664.0
65 TraesCS2B01G278000 chr7B 92.373 354 25 2 3220 3572 43121423 43121071 1.690000e-138 503.0
66 TraesCS2B01G278000 chr5A 88.514 296 30 2 1256 1550 296724947 296724655 5.020000e-94 355.0
67 TraesCS2B01G278000 chrUn 89.928 278 23 3 1256 1532 261371572 261371845 1.810000e-93 353.0
68 TraesCS2B01G278000 chrUn 94.304 158 9 0 1634 1791 67174009 67173852 4.080000e-60 243.0
69 TraesCS2B01G278000 chr2A 87.162 296 34 2 1256 1550 331192290 331191998 2.350000e-87 333.0
70 TraesCS2B01G278000 chr2A 96.552 87 3 0 1548 1634 101846909 101846823 1.180000e-30 145.0
71 TraesCS2B01G278000 chr6A 86.824 296 35 2 1256 1550 533017692 533017400 1.090000e-85 327.0
72 TraesCS2B01G278000 chr5D 98.947 95 1 0 1547 1641 491871584 491871678 1.950000e-38 171.0
73 TraesCS2B01G278000 chr7A 98.925 93 1 0 1542 1634 416496840 416496932 2.530000e-37 167.0
74 TraesCS2B01G278000 chr1D 96.939 98 3 0 1541 1638 407351086 407351183 9.080000e-37 165.0
75 TraesCS2B01G278000 chr1D 91.429 105 8 1 1531 1634 194453188 194453084 4.260000e-30 143.0
76 TraesCS2B01G278000 chr4B 96.040 101 1 3 1544 1642 631442106 631442205 1.170000e-35 161.0
77 TraesCS2B01G278000 chr4B 90.517 116 5 3 1895 2005 578569915 578570029 9.150000e-32 148.0
78 TraesCS2B01G278000 chr3A 91.964 112 2 6 1527 1635 65704227 65704334 2.540000e-32 150.0


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 TraesCS2B01G278000 chr2B 383925391 383929474 4083 True 3800.200000 7542 98.529500 1 4084 2 chr2B.!!$R4 4083
1 TraesCS2B01G278000 chr2B 687886393 687888474 2081 True 3134.000000 3134 93.786000 1987 4084 1 chr2B.!!$R3 2097
2 TraesCS2B01G278000 chr2B 58400881 58402041 1160 True 1598.000000 1598 92.038000 1895 3022 1 chr2B.!!$R1 1127
3 TraesCS2B01G278000 chr2B 20556009 20556526 517 False 632.000000 632 88.697000 3564 4084 1 chr2B.!!$F1 520
4 TraesCS2B01G278000 chr2B 367443282 367444132 850 False 503.000000 793 94.058500 1 630 2 chr2B.!!$F5 629
5 TraesCS2B01G278000 chr5B 241066027 241067596 1569 True 2377.000000 2377 93.926000 2498 4084 1 chr5B.!!$R1 1586
6 TraesCS2B01G278000 chr5B 675541021 675544958 3937 False 2194.333333 4028 96.395333 1 4084 3 chr5B.!!$F2 4083
7 TraesCS2B01G278000 chr5B 314803904 314805276 1372 True 2001.000000 2001 93.450000 1886 3219 1 chr5B.!!$R2 1333
8 TraesCS2B01G278000 chr6B 466775104 466779115 4011 True 2200.133333 3999 96.462333 1 4084 3 chr6B.!!$R5 4083
9 TraesCS2B01G278000 chr6B 418120418 418121782 1364 False 1980.000000 1980 93.270000 1886 3216 1 chr6B.!!$F5 1330
10 TraesCS2B01G278000 chr6B 644652629 644654000 1371 True 1056.000000 1297 94.949500 1886 3219 2 chr6B.!!$R6 1333
11 TraesCS2B01G278000 chr6B 401422691 401423212 521 False 652.000000 652 89.354000 3564 4084 1 chr6B.!!$F4 520
12 TraesCS2B01G278000 chr3B 727193548 727195754 2206 True 3382.000000 3382 94.397000 1886 4084 1 chr3B.!!$R3 2198
13 TraesCS2B01G278000 chr3B 217776166 217777267 1101 False 1694.000000 1694 94.470000 159 1257 1 chr3B.!!$F1 1098
14 TraesCS2B01G278000 chr3B 771940788 771941327 539 True 832.000000 832 94.444000 2680 3219 1 chr3B.!!$R4 539
15 TraesCS2B01G278000 chr3B 603288574 603289095 521 True 610.000000 610 87.856000 3563 4084 1 chr3B.!!$R2 521
16 TraesCS2B01G278000 chr1B 232231696 232233066 1370 True 2021.000000 2021 93.727000 1886 3219 1 chr1B.!!$R1 1333
17 TraesCS2B01G278000 chr7D 343753441 343754542 1101 True 923.200000 1788 96.533000 159 1257 2 chr7D.!!$R3 1098
18 TraesCS2B01G278000 chr7D 557289696 557290508 812 True 362.900000 1057 95.959500 326 1257 4 chr7D.!!$R4 931
19 TraesCS2B01G278000 chr7D 557302866 557303399 533 True 223.500000 228 92.506000 12 328 2 chr7D.!!$R5 316
20 TraesCS2B01G278000 chr1A 64329664 64330823 1159 False 1487.000000 1487 90.342000 1895 3022 1 chr1A.!!$F1 1127
21 TraesCS2B01G278000 chr2D 205892126 205892918 792 True 1254.000000 1254 95.352000 1895 2681 1 chr2D.!!$R1 786
22 TraesCS2B01G278000 chr6D 232426410 232427546 1136 True 514.733333 1114 92.572667 159 1257 3 chr6D.!!$R1 1098
23 TraesCS2B01G278000 chr7B 652637194 652637718 524 True 664.000000 664 89.714000 3567 4084 1 chr7B.!!$R2 517

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
869 1132 0.677731 CTTGCCACCGTCATGGACAT 60.678 55.000 0.00 0.0 43.02 3.06 F
1449 1780 1.675310 CATGGGCGCTCTTGGACAA 60.675 57.895 15.12 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2762 3170 6.974932 TGAATAAGAACAGAGCATCAAGAC 57.025 37.5 0.0 0.0 37.82 3.01 R
3216 3626 0.176680 CGGCTCTACTCCTGTTGCAT 59.823 55.0 0.0 0.0 0.00 3.96 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
165 388 5.880054 TTGCTAGCTCGCTTTTTCTTAAT 57.120 34.783 17.23 0.00 0.00 1.40
413 637 8.922931 TTGTTGTATGGTGATGCTAATCATAT 57.077 30.769 0.00 0.00 44.54 1.78
548 809 3.381272 CCATTACACTTTTCATGCCCGAT 59.619 43.478 0.00 0.00 0.00 4.18
555 816 4.336433 CACTTTTCATGCCCGATAGTTCAT 59.664 41.667 0.00 0.00 0.00 2.57
869 1132 0.677731 CTTGCCACCGTCATGGACAT 60.678 55.000 0.00 0.00 43.02 3.06
953 1216 2.986413 ACTGCTGGCTCGTCGTCT 60.986 61.111 0.00 0.00 0.00 4.18
1175 1503 7.807977 ACTGAACTTGTGTGATAATTCAACT 57.192 32.000 0.00 0.00 32.48 3.16
1177 1505 8.131100 ACTGAACTTGTGTGATAATTCAACTTG 58.869 33.333 0.00 0.00 32.48 3.16
1410 1741 5.757808 ACTTTTGTGTATGAAAAATGGTGCC 59.242 36.000 0.00 0.00 0.00 5.01
1421 1752 5.541868 TGAAAAATGGTGCCAGGAAATTCTA 59.458 36.000 0.00 0.00 0.00 2.10
1433 1764 7.294017 CCAGGAAATTCTAAATACATGGCAT 57.706 36.000 0.00 0.00 0.00 4.40
1449 1780 1.675310 CATGGGCGCTCTTGGACAA 60.675 57.895 15.12 0.00 0.00 3.18
1557 1888 9.750783 TTTGTATCAGTATATACTACTCCCTCC 57.249 37.037 15.03 0.23 34.13 4.30
1558 1889 7.563020 TGTATCAGTATATACTACTCCCTCCG 58.437 42.308 15.03 0.43 34.13 4.63
1559 1890 6.639590 ATCAGTATATACTACTCCCTCCGT 57.360 41.667 15.03 0.00 34.13 4.69
1560 1891 6.445451 TCAGTATATACTACTCCCTCCGTT 57.555 41.667 15.03 0.00 34.13 4.44
1561 1892 6.471146 TCAGTATATACTACTCCCTCCGTTC 58.529 44.000 15.03 0.00 34.13 3.95
1562 1893 5.647225 CAGTATATACTACTCCCTCCGTTCC 59.353 48.000 15.03 0.00 34.13 3.62
1563 1894 4.736611 ATATACTACTCCCTCCGTTCCA 57.263 45.455 0.00 0.00 0.00 3.53
1564 1895 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
1565 1896 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1566 1897 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1567 1898 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1568 1899 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1569 1900 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1570 1901 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1571 1902 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1572 1903 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1573 1904 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1574 1905 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1575 1906 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1576 1907 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1577 1908 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1578 1909 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1579 1910 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1580 1911 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1581 1912 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1582 1913 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1583 1914 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1584 1915 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1585 1916 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1586 1917 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1587 1918 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1620 1951 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1621 1952 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1622 1953 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1623 1954 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1624 1955 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1625 1956 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1626 1957 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1627 1958 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1628 1959 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1629 1960 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1630 1961 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1631 1962 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1632 1963 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1633 1964 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1658 1989 5.931724 TGTTGCTTCTTCGATTTCTGTATGA 59.068 36.000 0.00 0.00 0.00 2.15
1701 2032 4.019174 CCTGCCTATTTTGGTTGATGTCT 58.981 43.478 0.00 0.00 0.00 3.41
2215 2549 7.152645 CCAAAAGTACAACTCTTGCTACTCTA 58.847 38.462 0.00 0.00 31.66 2.43
2506 2849 5.161943 ACTTTGTAGGTTCAGATGGGTAC 57.838 43.478 0.00 0.00 0.00 3.34
2800 3208 9.426534 TGTTCTTATTCATCTAGAGATTCCTCA 57.573 33.333 0.00 0.00 41.87 3.86
3042 3450 0.392998 AGCTGGCCTTCACATAACGG 60.393 55.000 3.32 0.00 0.00 4.44
3138 3548 1.640428 CACGCGTACATCCACTTCAT 58.360 50.000 13.44 0.00 0.00 2.57
3163 3573 8.785329 TGTGTTAGTCAATAGAATTGTGCATA 57.215 30.769 0.00 0.00 0.00 3.14
3253 3663 2.416747 CCGTTTGAGATGCTCTGTTCA 58.583 47.619 0.00 0.00 0.00 3.18
3344 3754 2.373938 CGGAGCACGGACAAAGATC 58.626 57.895 0.00 0.00 39.42 2.75
3361 3771 9.713740 GACAAAGATCATGTCATTATGAACTTC 57.286 33.333 20.57 0.00 44.40 3.01
3375 3785 3.659786 TGAACTTCGGTTGTGATGGTAG 58.340 45.455 0.00 0.00 38.41 3.18
3468 3878 4.225042 TGTGCTCCCTATTATGAACTGTGT 59.775 41.667 0.00 0.00 0.00 3.72
3484 3894 8.572828 TGAACTGTGTTATAAAAATGCACTTG 57.427 30.769 0.00 2.07 0.00 3.16
3555 3965 3.307199 GGAGGTAAAAGTGAACCATCCGA 60.307 47.826 0.00 0.00 38.30 4.55
3607 4018 6.839124 AAGACTACATGCAATTCAAATGGA 57.161 33.333 0.00 0.00 0.00 3.41
3657 4068 8.504005 AGAAGTCCATAACATCGTTGTAAAAAG 58.496 33.333 0.00 0.00 34.06 2.27
3987 4410 7.333672 GTCTCACCGTAATCCAAATTACTCTTT 59.666 37.037 6.71 0.00 43.37 2.52
3993 4416 8.349983 CCGTAATCCAAATTACTCTTTAATGGG 58.650 37.037 6.71 0.00 43.37 4.00
4017 4440 5.173131 GTGCGAATTTGAGAAAACGTTGAAT 59.827 36.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
292 516 9.444600 TCTAGTTTTTCGCTCATACCTAAAAAT 57.555 29.630 0.00 0.00 33.20 1.82
375 599 7.038659 CACCATACAACAAAAGGAAGAACAAA 58.961 34.615 0.00 0.00 0.00 2.83
413 637 3.935024 CTAGCCTCCACGCTGGTA 58.065 61.111 4.33 0.00 40.08 3.25
548 809 9.860650 ATAATGTTACCTATTTGCCATGAACTA 57.139 29.630 0.00 0.00 0.00 2.24
555 816 8.934697 AGTAGAGATAATGTTACCTATTTGCCA 58.065 33.333 0.00 0.00 0.00 4.92
689 950 1.878070 CTGAATTCAGCAGCGCCAA 59.122 52.632 21.96 0.00 37.15 4.52
890 1153 0.316204 GGAAGAACGACCACCGAGAA 59.684 55.000 0.00 0.00 41.76 2.87
953 1216 4.935578 TCAGTAGATGGAGAAGAAGGACA 58.064 43.478 0.00 0.00 0.00 4.02
984 1247 7.470289 TGTACACATGTTGCCAATTAAAAAC 57.530 32.000 0.00 0.00 0.00 2.43
1000 1263 1.446099 CCGTCGCTGCTGTACACAT 60.446 57.895 0.00 0.00 0.00 3.21
1175 1503 0.894141 AGCACACACAAGCAAACCAA 59.106 45.000 0.00 0.00 0.00 3.67
1177 1505 1.676006 AGTAGCACACACAAGCAAACC 59.324 47.619 0.00 0.00 0.00 3.27
1285 1615 6.578163 TTTCAATCAACTCATGCTCATCAA 57.422 33.333 0.00 0.00 0.00 2.57
1410 1741 7.149973 CCATGCCATGTATTTAGAATTTCCTG 58.850 38.462 3.63 0.00 0.00 3.86
1421 1752 0.756442 AGCGCCCATGCCATGTATTT 60.756 50.000 2.29 0.00 34.65 1.40
1433 1764 0.326595 TTATTGTCCAAGAGCGCCCA 59.673 50.000 2.29 0.00 0.00 5.36
1550 1881 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1551 1882 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1552 1883 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1553 1884 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1554 1885 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1555 1886 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1556 1887 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1557 1888 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1558 1889 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1559 1890 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1560 1891 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1561 1892 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1594 1925 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1595 1926 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1596 1927 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1597 1928 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1598 1929 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1599 1930 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1600 1931 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1601 1932 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1602 1933 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1603 1934 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1604 1935 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1605 1936 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1606 1937 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1607 1938 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1608 1939 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1609 1940 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1610 1941 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1611 1942 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1612 1943 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1613 1944 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
1614 1945 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
1615 1946 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
1616 1947 2.262637 ACATACTCCCTCCGTTCCAAA 58.737 47.619 0.00 0.00 0.00 3.28
1617 1948 1.946984 ACATACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
1618 1949 1.553248 CAACATACTCCCTCCGTTCCA 59.447 52.381 0.00 0.00 0.00 3.53
1619 1950 1.742750 GCAACATACTCCCTCCGTTCC 60.743 57.143 0.00 0.00 0.00 3.62
1620 1951 1.207329 AGCAACATACTCCCTCCGTTC 59.793 52.381 0.00 0.00 0.00 3.95
1621 1952 1.276622 AGCAACATACTCCCTCCGTT 58.723 50.000 0.00 0.00 0.00 4.44
1622 1953 1.207329 GAAGCAACATACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
1623 1954 1.482593 AGAAGCAACATACTCCCTCCG 59.517 52.381 0.00 0.00 0.00 4.63
1624 1955 3.536570 GAAGAAGCAACATACTCCCTCC 58.463 50.000 0.00 0.00 0.00 4.30
1625 1956 3.119101 TCGAAGAAGCAACATACTCCCTC 60.119 47.826 0.00 0.00 0.00 4.30
1626 1957 2.832129 TCGAAGAAGCAACATACTCCCT 59.168 45.455 0.00 0.00 0.00 4.20
1627 1958 3.247006 TCGAAGAAGCAACATACTCCC 57.753 47.619 0.00 0.00 0.00 4.30
1628 1959 5.582665 AGAAATCGAAGAAGCAACATACTCC 59.417 40.000 0.00 0.00 43.58 3.85
1629 1960 6.091441 ACAGAAATCGAAGAAGCAACATACTC 59.909 38.462 0.00 0.00 43.58 2.59
1630 1961 5.934625 ACAGAAATCGAAGAAGCAACATACT 59.065 36.000 0.00 0.00 43.58 2.12
1631 1962 6.170675 ACAGAAATCGAAGAAGCAACATAC 57.829 37.500 0.00 0.00 43.58 2.39
1632 1963 7.763985 TCATACAGAAATCGAAGAAGCAACATA 59.236 33.333 0.00 0.00 43.58 2.29
1633 1964 6.595326 TCATACAGAAATCGAAGAAGCAACAT 59.405 34.615 0.00 0.00 43.58 2.71
1658 1989 4.530161 AGGAGAGAGCAGTCAGTACAAAAT 59.470 41.667 0.00 0.00 0.00 1.82
2215 2549 8.290325 GCTTAGAAAATAAGTGCAAGTACAAGT 58.710 33.333 0.00 0.00 0.00 3.16
2762 3170 6.974932 TGAATAAGAACAGAGCATCAAGAC 57.025 37.500 0.00 0.00 37.82 3.01
3034 3442 0.685097 ACTGCACCACTCCGTTATGT 59.315 50.000 0.00 0.00 0.00 2.29
3042 3450 2.880890 ACAAGATCAAACTGCACCACTC 59.119 45.455 0.00 0.00 0.00 3.51
3138 3548 7.686438 ATGCACAATTCTATTGACTAACACA 57.314 32.000 6.42 0.00 0.00 3.72
3163 3573 5.763876 AGAGTAGCAAAGGTACCAAGAAT 57.236 39.130 15.94 0.00 37.24 2.40
3195 3605 8.715191 TGCATAGAAAAGTGAACAACAAATTT 57.285 26.923 0.00 0.00 0.00 1.82
3197 3607 7.763528 TGTTGCATAGAAAAGTGAACAACAAAT 59.236 29.630 0.00 0.00 42.06 2.32
3216 3626 0.176680 CGGCTCTACTCCTGTTGCAT 59.823 55.000 0.00 0.00 0.00 3.96
3335 3745 9.713740 GAAGTTCATAATGACATGATCTTTGTC 57.286 33.333 17.41 17.41 41.62 3.18
3344 3754 6.023435 CACAACCGAAGTTCATAATGACATG 58.977 40.000 3.32 0.00 32.45 3.21
3361 3771 4.312443 AGTTTGTACTACCATCACAACCG 58.688 43.478 0.00 0.00 32.19 4.44
3468 3878 5.244851 TGGTGAGCCAAGTGCATTTTTATAA 59.755 36.000 0.00 0.00 42.83 0.98
3484 3894 5.154222 CGAACTAAAAGAAAATGGTGAGCC 58.846 41.667 0.00 0.00 0.00 4.70
3987 4410 5.465935 GTTTTCTCAAATTCGCACCCATTA 58.534 37.500 0.00 0.00 0.00 1.90
3993 4416 4.032355 TCAACGTTTTCTCAAATTCGCAC 58.968 39.130 0.00 0.00 0.00 5.34
4017 4440 9.701098 ATATCGAAAATACGAAACTTAGCCATA 57.299 29.630 0.00 0.00 45.16 2.74


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

AutoCloner maintained by Alex Coulton.