Multiple sequence alignment - TraesCS7D01G445400

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 TraesCS7D01G445400 chr7D 100.000 4949 0 0 1 4949 566199281 566204229 0.000000e+00 9140.0
1 TraesCS7D01G445400 chr7D 91.125 2783 198 18 1032 3780 566319892 566322659 0.000000e+00 3725.0
2 TraesCS7D01G445400 chr7D 88.503 461 51 1 3097 3555 566256712 566257172 1.560000e-154 556.0
3 TraesCS7D01G445400 chr7D 86.508 126 14 2 3562 3685 566262033 566262157 8.640000e-28 135.0
4 TraesCS7D01G445400 chr7D 96.875 32 0 1 3 34 421877828 421877858 9.000000e-03 52.8
5 TraesCS7D01G445400 chr7A 94.961 1905 83 6 2030 3922 652516457 652518360 0.000000e+00 2974.0
6 TraesCS7D01G445400 chr7A 94.428 664 22 2 1127 1790 652514957 652515605 0.000000e+00 1007.0
7 TraesCS7D01G445400 chr7A 84.121 1058 92 35 3918 4949 652518680 652519687 0.000000e+00 953.0
8 TraesCS7D01G445400 chr7A 80.028 711 74 43 346 1028 652513172 652513842 9.700000e-127 464.0
9 TraesCS7D01G445400 chr7A 88.563 341 19 12 1 325 652512761 652513097 3.590000e-106 396.0
10 TraesCS7D01G445400 chr7A 98.065 155 3 0 1788 1942 652516291 652516445 2.270000e-68 270.0
11 TraesCS7D01G445400 chr7A 97.500 120 2 1 1017 1135 652513894 652514013 2.340000e-48 204.0
12 TraesCS7D01G445400 chr7B 90.973 1562 105 17 2522 4056 617849836 617851388 0.000000e+00 2071.0
13 TraesCS7D01G445400 chr7B 85.367 1688 188 32 2075 3720 618334337 618336007 0.000000e+00 1694.0
14 TraesCS7D01G445400 chr7B 85.377 1696 178 37 2075 3726 618761026 618759357 0.000000e+00 1694.0
15 TraesCS7D01G445400 chr7B 85.308 1688 189 32 2075 3720 618850333 618848663 0.000000e+00 1688.0
16 TraesCS7D01G445400 chr7B 93.502 1108 66 4 1017 2123 617839504 617840606 0.000000e+00 1642.0
17 TraesCS7D01G445400 chr7B 83.072 1660 222 31 1855 3490 618428286 618429910 0.000000e+00 1454.0
18 TraesCS7D01G445400 chr7B 92.807 848 56 3 1026 1871 618851650 618850806 0.000000e+00 1223.0
19 TraesCS7D01G445400 chr7B 92.571 848 58 3 1026 1871 618762344 618761500 0.000000e+00 1212.0
20 TraesCS7D01G445400 chr7B 90.356 674 34 15 4280 4949 617851649 617852295 0.000000e+00 856.0
21 TraesCS7D01G445400 chr7B 86.723 708 50 14 334 1025 617838770 617839449 0.000000e+00 747.0
22 TraesCS7D01G445400 chr7B 97.375 419 11 0 2109 2527 617840672 617841090 0.000000e+00 713.0
23 TraesCS7D01G445400 chr7B 88.340 506 44 8 334 830 618105691 618106190 1.190000e-165 593.0
24 TraesCS7D01G445400 chr7B 88.340 506 41 9 334 830 618100025 618100521 4.270000e-165 592.0
25 TraesCS7D01G445400 chr7B 88.166 507 45 9 334 830 618082774 618083275 1.530000e-164 590.0
26 TraesCS7D01G445400 chr7B 88.142 506 45 10 334 830 617873968 617874467 5.520000e-164 588.0
27 TraesCS7D01G445400 chr7B 87.968 507 47 9 334 830 617877774 617878276 1.980000e-163 586.0
28 TraesCS7D01G445400 chr7B 87.791 516 40 11 334 830 618073726 618074237 2.570000e-162 582.0
29 TraesCS7D01G445400 chr7B 87.945 506 45 10 335 830 618109495 618109994 2.570000e-162 582.0
30 TraesCS7D01G445400 chr7B 87.723 505 48 7 334 830 617870169 617870667 1.190000e-160 577.0
31 TraesCS7D01G445400 chr7B 87.723 505 48 9 334 830 618024793 618025291 1.190000e-160 577.0
32 TraesCS7D01G445400 chr7B 81.739 345 27 19 687 1025 618333030 618333344 6.360000e-64 255.0
33 TraesCS7D01G445400 chr7B 81.481 351 29 19 687 1031 618852029 618851709 6.360000e-64 255.0
34 TraesCS7D01G445400 chr7B 81.429 350 27 21 687 1031 618762719 618762403 8.220000e-63 252.0
35 TraesCS7D01G445400 chr7B 98.198 111 2 0 1026 1136 618333409 618333519 1.410000e-45 195.0
36 TraesCS7D01G445400 chr5B 79.026 1540 261 46 2215 3719 598659266 598657754 0.000000e+00 998.0
37 TraesCS7D01G445400 chr5B 79.952 1252 201 35 2454 3680 599122966 599121740 0.000000e+00 876.0
38 TraesCS7D01G445400 chr5B 79.473 1291 214 38 2454 3718 598755472 598754207 0.000000e+00 869.0
39 TraesCS7D01G445400 chr5B 77.810 1023 182 33 2470 3482 79814007 79813020 1.530000e-164 590.0
40 TraesCS7D01G445400 chr5B 76.133 750 149 22 2466 3194 693033984 693033244 2.810000e-97 366.0
41 TraesCS7D01G445400 chr5A 78.609 1538 272 41 2215 3719 607578076 607576563 0.000000e+00 965.0
42 TraesCS7D01G445400 chr5A 84.127 63 4 6 3 61 691933443 691933503 6.920000e-04 56.5
43 TraesCS7D01G445400 chr5D 81.489 1048 160 27 2454 3481 487006111 487007144 0.000000e+00 830.0
44 TraesCS7D01G445400 chr5D 77.517 1023 184 32 2470 3481 72911133 72910146 1.550000e-159 573.0
45 TraesCS7D01G445400 chr5D 77.885 936 155 34 2817 3718 487173149 487172232 7.290000e-148 534.0
46 TraesCS7D01G445400 chr5D 94.595 37 2 0 1942 1978 486898580 486898544 1.920000e-04 58.4
47 TraesCS7D01G445400 chr4D 78.045 1248 239 30 2210 3436 21695478 21694245 0.000000e+00 754.0
48 TraesCS7D01G445400 chr4D 79.358 717 133 13 1073 1782 22572554 22573262 1.600000e-134 490.0
49 TraesCS7D01G445400 chr4D 78.638 749 137 18 1044 1781 21696511 21695775 4.480000e-130 475.0
50 TraesCS7D01G445400 chr4D 96.970 33 0 1 3 35 37831165 37831134 2.000000e-03 54.7
51 TraesCS7D01G445400 chr3D 82.066 881 146 12 2346 3219 45931952 45932827 0.000000e+00 741.0
52 TraesCS7D01G445400 chr3D 80.673 802 130 18 1045 1838 45930536 45931320 2.550000e-167 599.0
53 TraesCS7D01G445400 chr3D 74.920 941 197 30 2460 3375 63764546 63765472 1.290000e-105 394.0
54 TraesCS7D01G445400 chr3D 74.134 924 214 23 2465 3374 62073325 62072413 4.710000e-95 359.0
55 TraesCS7D01G445400 chr4B 77.447 1277 244 32 2190 3436 32971573 32972835 0.000000e+00 723.0
56 TraesCS7D01G445400 chr4B 78.905 749 135 18 1044 1781 32970562 32971298 2.070000e-133 486.0
57 TraesCS7D01G445400 chr1D 77.995 409 78 11 2206 2611 402136518 402136917 3.830000e-61 246.0
58 TraesCS7D01G445400 chr1D 84.507 71 7 4 3 70 469984996 469984927 3.200000e-07 67.6
59 TraesCS7D01G445400 chr6B 86.885 61 5 2 3 61 349466245 349466186 1.150000e-06 65.8
60 TraesCS7D01G445400 chr1A 80.460 87 16 1 3 88 563596376 563596290 1.150000e-06 65.8
61 TraesCS7D01G445400 chr2D 84.615 65 8 2 3 67 106638573 106638511 4.140000e-06 63.9
62 TraesCS7D01G445400 chr1B 92.500 40 1 2 3 40 5517085 5517046 6.920000e-04 56.5


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 TraesCS7D01G445400 chr7D 566199281 566204229 4948 False 9140.000000 9140 100.000000 1 4949 1 chr7D.!!$F2 4948
1 TraesCS7D01G445400 chr7D 566319892 566322659 2767 False 3725.000000 3725 91.125000 1032 3780 1 chr7D.!!$F5 2748
2 TraesCS7D01G445400 chr7A 652512761 652519687 6926 False 895.428571 2974 91.095143 1 4949 7 chr7A.!!$F1 4948
3 TraesCS7D01G445400 chr7B 617849836 617852295 2459 False 1463.500000 2071 90.664500 2522 4949 2 chr7B.!!$F7 2427
4 TraesCS7D01G445400 chr7B 618428286 618429910 1624 False 1454.000000 1454 83.072000 1855 3490 1 chr7B.!!$F5 1635
5 TraesCS7D01G445400 chr7B 618848663 618852029 3366 True 1055.333333 1688 86.532000 687 3720 3 chr7B.!!$R2 3033
6 TraesCS7D01G445400 chr7B 618759357 618762719 3362 True 1052.666667 1694 86.459000 687 3726 3 chr7B.!!$R1 3039
7 TraesCS7D01G445400 chr7B 617838770 617841090 2320 False 1034.000000 1642 92.533333 334 2527 3 chr7B.!!$F6 2193
8 TraesCS7D01G445400 chr7B 618333030 618336007 2977 False 714.666667 1694 88.434667 687 3720 3 chr7B.!!$F10 3033
9 TraesCS7D01G445400 chr7B 618082774 618083275 501 False 590.000000 590 88.166000 334 830 1 chr7B.!!$F3 496
10 TraesCS7D01G445400 chr7B 618105691 618109994 4303 False 587.500000 593 88.142500 334 830 2 chr7B.!!$F9 496
11 TraesCS7D01G445400 chr7B 617870169 617878276 8107 False 583.666667 588 87.944333 334 830 3 chr7B.!!$F8 496
12 TraesCS7D01G445400 chr7B 618073726 618074237 511 False 582.000000 582 87.791000 334 830 1 chr7B.!!$F2 496
13 TraesCS7D01G445400 chr5B 598657754 598659266 1512 True 998.000000 998 79.026000 2215 3719 1 chr5B.!!$R2 1504
14 TraesCS7D01G445400 chr5B 599121740 599122966 1226 True 876.000000 876 79.952000 2454 3680 1 chr5B.!!$R4 1226
15 TraesCS7D01G445400 chr5B 598754207 598755472 1265 True 869.000000 869 79.473000 2454 3718 1 chr5B.!!$R3 1264
16 TraesCS7D01G445400 chr5B 79813020 79814007 987 True 590.000000 590 77.810000 2470 3482 1 chr5B.!!$R1 1012
17 TraesCS7D01G445400 chr5B 693033244 693033984 740 True 366.000000 366 76.133000 2466 3194 1 chr5B.!!$R5 728
18 TraesCS7D01G445400 chr5A 607576563 607578076 1513 True 965.000000 965 78.609000 2215 3719 1 chr5A.!!$R1 1504
19 TraesCS7D01G445400 chr5D 487006111 487007144 1033 False 830.000000 830 81.489000 2454 3481 1 chr5D.!!$F1 1027
20 TraesCS7D01G445400 chr5D 72910146 72911133 987 True 573.000000 573 77.517000 2470 3481 1 chr5D.!!$R1 1011
21 TraesCS7D01G445400 chr5D 487172232 487173149 917 True 534.000000 534 77.885000 2817 3718 1 chr5D.!!$R3 901
22 TraesCS7D01G445400 chr4D 21694245 21696511 2266 True 614.500000 754 78.341500 1044 3436 2 chr4D.!!$R2 2392
23 TraesCS7D01G445400 chr4D 22572554 22573262 708 False 490.000000 490 79.358000 1073 1782 1 chr4D.!!$F1 709
24 TraesCS7D01G445400 chr3D 45930536 45932827 2291 False 670.000000 741 81.369500 1045 3219 2 chr3D.!!$F2 2174
25 TraesCS7D01G445400 chr3D 63764546 63765472 926 False 394.000000 394 74.920000 2460 3375 1 chr3D.!!$F1 915
26 TraesCS7D01G445400 chr3D 62072413 62073325 912 True 359.000000 359 74.134000 2465 3374 1 chr3D.!!$R1 909
27 TraesCS7D01G445400 chr4B 32970562 32972835 2273 False 604.500000 723 78.176000 1044 3436 2 chr4B.!!$F1 2392

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
735 8472 1.209504 TCGCCCCTGTTAATCTTGGAG 59.790 52.381 0.00 0.0 0.00 3.86 F
1577 12244 1.001068 TGGGTGCGACGACTTTTGATA 59.999 47.619 0.00 0.0 0.00 2.15 F
2492 14888 0.478072 TTGTGAGCCAATGGACTGGT 59.522 50.000 2.05 0.0 38.86 4.00 F
3729 17367 1.135774 CGACGAAGGTGTCAGATTCGA 60.136 52.381 20.49 0.0 46.57 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 12295 1.166531 GCTCCTCAACGTGCACCTTT 61.167 55.000 12.15 1.41 0.00 3.11 R
3409 17001 1.661509 CGGCATCGCTCGCAGATAA 60.662 57.895 0.00 0.00 33.89 1.75 R
3751 17397 0.321387 TACGGAGTCTCGCAGTCACT 60.321 55.000 0.00 0.00 43.93 3.41 R
4619 18701 0.605589 AGGCTGAGACGAGAGGTTTG 59.394 55.000 0.00 0.00 0.00 2.93 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
83 84 6.155691 TGTATACGTCACGAACATTTTTCC 57.844 37.500 2.91 0.00 0.00 3.13
89 90 7.000575 ACGTCACGAACATTTTTCCTATATG 57.999 36.000 2.91 0.00 0.00 1.78
322 335 9.889128 AAATGTGAAAAATGGAAGAAGAAGAAA 57.111 25.926 0.00 0.00 0.00 2.52
325 338 9.369904 TGTGAAAAATGGAAGAAGAAGAAAAAG 57.630 29.630 0.00 0.00 0.00 2.27
326 339 8.331022 GTGAAAAATGGAAGAAGAAGAAAAAGC 58.669 33.333 0.00 0.00 0.00 3.51
327 340 8.260114 TGAAAAATGGAAGAAGAAGAAAAAGCT 58.740 29.630 0.00 0.00 0.00 3.74
328 341 8.654230 AAAAATGGAAGAAGAAGAAAAAGCTC 57.346 30.769 0.00 0.00 0.00 4.09
330 343 3.815401 TGGAAGAAGAAGAAAAAGCTCCG 59.185 43.478 0.00 0.00 0.00 4.63
331 344 3.365465 GGAAGAAGAAGAAAAAGCTCCGC 60.365 47.826 0.00 0.00 0.00 5.54
332 345 2.851195 AGAAGAAGAAAAAGCTCCGCA 58.149 42.857 0.00 0.00 0.00 5.69
492 2469 1.218316 GGTAAGGCACCTGACCTCG 59.782 63.158 15.27 0.00 42.97 4.63
502 2479 4.671590 TGACCTCGCCGGACCAGA 62.672 66.667 5.05 0.00 36.31 3.86
592 6402 3.625897 CGGTGGGCACTGAGGACA 61.626 66.667 0.00 0.00 40.06 4.02
661 8390 3.309410 CCCTCAAATCCCAATGTTCCTCT 60.309 47.826 0.00 0.00 0.00 3.69
669 8398 2.554032 CCCAATGTTCCTCTTGTCACAC 59.446 50.000 0.00 0.00 0.00 3.82
685 8414 5.688823 TGTCACACTTTTGCTGATTAATCG 58.311 37.500 10.80 6.90 0.00 3.34
722 8459 6.988580 GTGTAAGTTAATATAAGTTCGCCCCT 59.011 38.462 0.00 0.00 0.00 4.79
735 8472 1.209504 TCGCCCCTGTTAATCTTGGAG 59.790 52.381 0.00 0.00 0.00 3.86
882 10532 6.902771 AGTCCGATACTTCTGCAATATACT 57.097 37.500 0.00 0.00 33.35 2.12
883 10533 7.997773 AGTCCGATACTTCTGCAATATACTA 57.002 36.000 0.00 0.00 33.35 1.82
946 10597 4.579869 TGCTCAGGTTAGGTCTTTTCATC 58.420 43.478 0.00 0.00 0.00 2.92
947 10598 4.041567 TGCTCAGGTTAGGTCTTTTCATCA 59.958 41.667 0.00 0.00 0.00 3.07
948 10599 4.393371 GCTCAGGTTAGGTCTTTTCATCAC 59.607 45.833 0.00 0.00 0.00 3.06
949 10600 4.906618 TCAGGTTAGGTCTTTTCATCACC 58.093 43.478 0.00 0.00 0.00 4.02
950 10601 4.349636 TCAGGTTAGGTCTTTTCATCACCA 59.650 41.667 0.00 0.00 31.99 4.17
951 10602 5.014123 TCAGGTTAGGTCTTTTCATCACCAT 59.986 40.000 0.00 0.00 31.99 3.55
952 10603 5.355350 CAGGTTAGGTCTTTTCATCACCATC 59.645 44.000 0.00 0.00 31.99 3.51
953 10604 5.014123 AGGTTAGGTCTTTTCATCACCATCA 59.986 40.000 0.00 0.00 31.99 3.07
954 10605 5.123979 GGTTAGGTCTTTTCATCACCATCAC 59.876 44.000 0.00 0.00 31.99 3.06
955 10606 3.690460 AGGTCTTTTCATCACCATCACC 58.310 45.455 0.00 0.00 31.99 4.02
956 10607 3.074390 AGGTCTTTTCATCACCATCACCA 59.926 43.478 0.00 0.00 31.99 4.17
957 10608 3.826157 GGTCTTTTCATCACCATCACCAA 59.174 43.478 0.00 0.00 0.00 3.67
958 10609 4.463891 GGTCTTTTCATCACCATCACCAAT 59.536 41.667 0.00 0.00 0.00 3.16
970 10621 2.214376 TCACCAATTCACCATCACCC 57.786 50.000 0.00 0.00 0.00 4.61
975 10626 3.527253 ACCAATTCACCATCACCCTATGA 59.473 43.478 0.00 0.00 43.13 2.15
1071 10786 1.578206 GGAGCAGCCTTCGGTTTGTC 61.578 60.000 0.00 0.00 0.00 3.18
1230 11897 2.292267 CAAGACCAAGAACTGTGCTGT 58.708 47.619 0.00 0.00 0.00 4.40
1235 11902 1.302366 CAAGAACTGTGCTGTGCTGA 58.698 50.000 0.00 0.00 0.00 4.26
1374 12041 2.427506 GATGGTTTCTGGGACTGTGTC 58.572 52.381 0.00 0.00 0.00 3.67
1577 12244 1.001068 TGGGTGCGACGACTTTTGATA 59.999 47.619 0.00 0.00 0.00 2.15
1771 12438 1.148157 CTCGCTGCCCGTTACATCAG 61.148 60.000 0.00 0.00 38.35 2.90
1882 13245 2.291217 ACATGAAGGGAAGAAAGAGGGC 60.291 50.000 0.00 0.00 0.00 5.19
1943 13381 5.916661 TCTTGTTAAGGTCCACTAGCTAG 57.083 43.478 19.44 19.44 33.87 3.42
1944 13382 4.159879 TCTTGTTAAGGTCCACTAGCTAGC 59.840 45.833 20.91 6.62 33.87 3.42
2219 14612 8.258708 GGAGTTAATTGATGTCTACTGTAGGTT 58.741 37.037 14.47 0.54 0.00 3.50
2492 14888 0.478072 TTGTGAGCCAATGGACTGGT 59.522 50.000 2.05 0.00 38.86 4.00
2907 15369 7.833285 TGGCTTTATTTGTTCCTTCTTAAGT 57.167 32.000 1.63 0.00 0.00 2.24
2989 15456 6.430925 CAGTGTTATCCTTTTTGATGAGGTGA 59.569 38.462 0.00 0.00 34.57 4.02
2990 15457 6.656693 AGTGTTATCCTTTTTGATGAGGTGAG 59.343 38.462 0.00 0.00 34.57 3.51
2995 15462 3.192212 CCTTTTTGATGAGGTGAGGAAGC 59.808 47.826 0.00 0.00 0.00 3.86
3221 15815 1.789464 GAGACTGCTGTTGTGAAGTCG 59.211 52.381 0.00 0.00 43.06 4.18
3409 17001 2.785357 AGCTAGCAGGGGTATCTCTT 57.215 50.000 18.83 0.00 0.00 2.85
3446 17044 1.725066 CGCTGGACGTGGTTTTGTT 59.275 52.632 0.00 0.00 36.87 2.83
3503 17108 5.437060 TCAAACCTGAGGCAATATTAGTCC 58.563 41.667 0.00 0.00 0.00 3.85
3729 17367 1.135774 CGACGAAGGTGTCAGATTCGA 60.136 52.381 20.49 0.00 46.57 3.71
3751 17397 0.893270 CGCAACAATCCAACTCCCCA 60.893 55.000 0.00 0.00 0.00 4.96
3766 17412 1.214062 CCCAGTGACTGCGAGACTC 59.786 63.158 7.16 0.00 0.00 3.36
3767 17413 1.214062 CCAGTGACTGCGAGACTCC 59.786 63.158 7.16 0.00 0.00 3.85
3788 17434 2.474526 CGTAGCTTTCTTTGGCATGACG 60.475 50.000 0.00 0.00 0.00 4.35
3789 17435 0.883833 AGCTTTCTTTGGCATGACGG 59.116 50.000 0.00 0.00 0.00 4.79
3792 17438 1.270550 CTTTCTTTGGCATGACGGCTT 59.729 47.619 0.00 0.00 41.89 4.35
3805 17469 2.290896 TGACGGCTTGGGATTTCTGAAT 60.291 45.455 0.00 0.00 0.00 2.57
3806 17470 2.356069 GACGGCTTGGGATTTCTGAATC 59.644 50.000 0.00 0.00 40.78 2.52
3815 17480 5.540911 TGGGATTTCTGAATCTTTTTGTGC 58.459 37.500 0.00 0.00 41.18 4.57
3817 17482 6.493115 TGGGATTTCTGAATCTTTTTGTGCTA 59.507 34.615 0.00 0.00 41.18 3.49
3825 17490 1.810151 TCTTTTTGTGCTATGGCGGAC 59.190 47.619 0.00 0.00 42.25 4.79
3848 17513 2.143122 GTTTCTCGTTCATCAGTGGCA 58.857 47.619 0.00 0.00 0.00 4.92
3852 17517 1.395954 CTCGTTCATCAGTGGCATGTG 59.604 52.381 0.00 0.00 0.00 3.21
3882 17549 3.303495 CGTACGTGATGATTCAACAGGTC 59.697 47.826 20.82 13.57 36.80 3.85
3884 17551 1.660607 CGTGATGATTCAACAGGTCGG 59.339 52.381 8.07 0.00 32.48 4.79
3910 17577 7.358830 CCTCGTAGTTTATAGCAGTAACTACC 58.641 42.308 17.73 7.46 45.71 3.18
3927 17920 9.765795 AGTAACTACCTAAATGCTAATGCTAAG 57.234 33.333 0.00 0.00 40.48 2.18
4034 18030 2.084546 GTCACTACACCCAATCCAAGC 58.915 52.381 0.00 0.00 0.00 4.01
4051 18047 9.227777 CAATCCAAGCATAGATCATTGAATCTA 57.772 33.333 0.00 0.02 41.31 1.98
4144 18208 3.834732 CGCACTTGGGCTACTAACT 57.165 52.632 0.00 0.00 0.00 2.24
4174 18252 3.137176 ACCATGAGAACATCCCGATTCAT 59.863 43.478 0.00 0.00 34.15 2.57
4197 18275 9.346005 TCATCAGTACTTATATACGAAGGTTCA 57.654 33.333 0.00 0.00 0.00 3.18
4217 18295 2.163010 CACACAAGATGGCTTCATGGAC 59.837 50.000 9.90 0.00 30.14 4.02
4218 18296 2.224843 ACACAAGATGGCTTCATGGACA 60.225 45.455 9.90 0.00 30.14 4.02
4226 18304 1.363744 GCTTCATGGACAGTCCTTCG 58.636 55.000 20.82 8.90 37.46 3.79
4246 18324 4.940463 TCGACCTTCCCATAATTTACTCG 58.060 43.478 0.00 0.00 0.00 4.18
4250 18328 6.309389 ACCTTCCCATAATTTACTCGAACT 57.691 37.500 0.00 0.00 0.00 3.01
4274 18352 9.884814 ACTACCCTATATCTAATCTTCACACTT 57.115 33.333 0.00 0.00 0.00 3.16
4312 18391 0.320374 TGCTACTTCTTCCACCCACG 59.680 55.000 0.00 0.00 0.00 4.94
4361 18440 7.825331 ATATATGCCACGTGATATACTAGCT 57.175 36.000 19.30 0.00 0.00 3.32
4362 18441 8.919777 ATATATGCCACGTGATATACTAGCTA 57.080 34.615 19.30 4.77 0.00 3.32
4363 18442 4.761235 TGCCACGTGATATACTAGCTAC 57.239 45.455 19.30 0.00 0.00 3.58
4565 18644 2.102757 GCTACCTTTCCTACTACAGCCC 59.897 54.545 0.00 0.00 0.00 5.19
4598 18680 0.543277 TGCCCAGCTTCACATAGAGG 59.457 55.000 0.00 0.00 0.00 3.69
4619 18701 2.863809 CAAGCCAAGTATGATACCCCC 58.136 52.381 0.00 0.00 0.00 5.40
4638 18720 0.605589 CAAACCTCTCGTCTCAGCCT 59.394 55.000 0.00 0.00 0.00 4.58
4712 18796 7.324935 TCTTGGTGTGCGTAAGATTCTAATTA 58.675 34.615 0.00 0.00 43.02 1.40
4861 18959 2.271800 CAGAGTTTGTCCGCCAGATAC 58.728 52.381 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 7.229228 TCATATAGGAAAAATGTTCGTGACG 57.771 36.000 0.00 0.00 0.00 4.35
68 69 9.173021 ACATTCATATAGGAAAAATGTTCGTGA 57.827 29.630 3.62 0.00 37.28 4.35
292 305 9.889128 TTCTTCTTCCATTTTTCACATTTTTCT 57.111 25.926 0.00 0.00 0.00 2.52
308 321 3.815401 CGGAGCTTTTTCTTCTTCTTCCA 59.185 43.478 0.00 0.00 0.00 3.53
326 339 0.605319 TGGCCTTTTGTACTGCGGAG 60.605 55.000 3.32 0.85 0.00 4.63
327 340 0.037590 ATGGCCTTTTGTACTGCGGA 59.962 50.000 3.32 0.00 0.00 5.54
328 341 0.451783 GATGGCCTTTTGTACTGCGG 59.548 55.000 3.32 0.00 0.00 5.69
330 343 0.451783 CCGATGGCCTTTTGTACTGC 59.548 55.000 3.32 0.00 0.00 4.40
331 344 1.094785 CCCGATGGCCTTTTGTACTG 58.905 55.000 3.32 0.00 0.00 2.74
332 345 0.696501 ACCCGATGGCCTTTTGTACT 59.303 50.000 3.32 0.00 33.59 2.73
378 446 1.071228 TCTACCGCGGTCAGCTAGATA 59.929 52.381 38.01 13.37 45.59 1.98
435 2403 4.704103 TCGAGTCCCAGCCAGCCT 62.704 66.667 0.00 0.00 0.00 4.58
492 2469 4.593864 GCCTCGATCTGGTCCGGC 62.594 72.222 0.00 0.81 34.17 6.13
661 8390 6.017523 TCGATTAATCAGCAAAAGTGTGACAA 60.018 34.615 15.57 0.00 0.00 3.18
669 8398 6.857777 ATCCTCTCGATTAATCAGCAAAAG 57.142 37.500 15.57 3.92 0.00 2.27
710 8447 4.258543 CAAGATTAACAGGGGCGAACTTA 58.741 43.478 0.00 0.00 0.00 2.24
711 8448 3.081804 CAAGATTAACAGGGGCGAACTT 58.918 45.455 0.00 0.00 0.00 2.66
712 8449 2.618045 CCAAGATTAACAGGGGCGAACT 60.618 50.000 0.00 0.00 0.00 3.01
722 8459 2.912956 AGGCAGGACTCCAAGATTAACA 59.087 45.455 0.00 0.00 0.00 2.41
757 10397 6.607004 TGGTTTTTAGGGACTGTTCAAAAA 57.393 33.333 0.00 0.00 41.52 1.94
767 10407 7.713073 TGTGATCAAAATTTGGTTTTTAGGGAC 59.287 33.333 5.83 0.00 37.93 4.46
897 10548 9.748708 ACGAAAATGCACTGCAATAATAATAAT 57.251 25.926 8.03 0.00 43.62 1.28
898 10549 9.579768 AACGAAAATGCACTGCAATAATAATAA 57.420 25.926 8.03 0.00 43.62 1.40
899 10550 9.018716 CAACGAAAATGCACTGCAATAATAATA 57.981 29.630 8.03 0.00 43.62 0.98
946 10597 3.090790 TGATGGTGAATTGGTGATGGTG 58.909 45.455 0.00 0.00 0.00 4.17
947 10598 3.091545 GTGATGGTGAATTGGTGATGGT 58.908 45.455 0.00 0.00 0.00 3.55
948 10599 2.428171 GGTGATGGTGAATTGGTGATGG 59.572 50.000 0.00 0.00 0.00 3.51
949 10600 2.428171 GGGTGATGGTGAATTGGTGATG 59.572 50.000 0.00 0.00 0.00 3.07
950 10601 2.312741 AGGGTGATGGTGAATTGGTGAT 59.687 45.455 0.00 0.00 0.00 3.06
951 10602 1.710244 AGGGTGATGGTGAATTGGTGA 59.290 47.619 0.00 0.00 0.00 4.02
952 10603 2.220653 AGGGTGATGGTGAATTGGTG 57.779 50.000 0.00 0.00 0.00 4.17
953 10604 3.527253 TCATAGGGTGATGGTGAATTGGT 59.473 43.478 0.00 0.00 0.00 3.67
954 10605 4.169059 TCATAGGGTGATGGTGAATTGG 57.831 45.455 0.00 0.00 0.00 3.16
955 10606 4.581824 CCTTCATAGGGTGATGGTGAATTG 59.418 45.833 2.72 0.00 43.67 2.32
956 10607 4.796606 CCTTCATAGGGTGATGGTGAATT 58.203 43.478 2.72 0.00 43.67 2.17
957 10608 4.443978 CCTTCATAGGGTGATGGTGAAT 57.556 45.455 2.72 0.00 43.67 2.57
958 10609 3.931907 CCTTCATAGGGTGATGGTGAA 57.068 47.619 2.72 0.00 43.67 3.18
970 10621 2.831333 AGATTGCAGTCGCCTTCATAG 58.169 47.619 3.29 0.00 37.32 2.23
975 10626 0.530744 TCGTAGATTGCAGTCGCCTT 59.469 50.000 3.29 0.00 37.32 4.35
1071 10786 2.300967 TACCTCCAAGCTGCCCAGG 61.301 63.158 0.00 0.00 0.00 4.45
1230 11897 2.435410 CTGCAGCACCGATCAGCA 60.435 61.111 0.00 0.00 0.00 4.41
1235 11902 2.581354 GACTCCTGCAGCACCGAT 59.419 61.111 8.66 0.00 0.00 4.18
1374 12041 2.796483 TTCCTCGAACATGCCACGGG 62.796 60.000 0.00 0.00 0.00 5.28
1577 12244 7.844009 TCCTTCTCAATGTACTTACGGTAATT 58.156 34.615 0.29 0.00 31.56 1.40
1628 12295 1.166531 GCTCCTCAACGTGCACCTTT 61.167 55.000 12.15 1.41 0.00 3.11
1943 13381 7.041508 AGCAGATAGTTTAATTAGCATGTGAGC 60.042 37.037 0.00 0.00 0.00 4.26
1944 13382 8.375608 AGCAGATAGTTTAATTAGCATGTGAG 57.624 34.615 0.00 0.00 0.00 3.51
2096 13615 8.615211 GCATCTGACACTATCATGAATTTGTTA 58.385 33.333 0.00 0.00 36.48 2.41
2219 14612 4.314522 TTGCCTTATCAGGAAATGGACA 57.685 40.909 0.00 0.00 44.19 4.02
2492 14888 3.557054 GGTCAAGCACAGTGACAGGAATA 60.557 47.826 4.15 0.00 45.94 1.75
2717 15114 3.193479 TCTTCTCGCTGTCAAATAGCTGA 59.807 43.478 0.00 0.00 39.00 4.26
2829 15249 9.715121 ATGAGAAAGTAATGCAATGTTCAAAAT 57.285 25.926 0.00 0.00 0.00 1.82
2906 15368 5.010012 CCACCATCTTCATGCCCTTTATAAC 59.990 44.000 0.00 0.00 0.00 1.89
2907 15369 5.103728 TCCACCATCTTCATGCCCTTTATAA 60.104 40.000 0.00 0.00 0.00 0.98
2916 15379 3.444742 TCAATTGTCCACCATCTTCATGC 59.555 43.478 5.13 0.00 0.00 4.06
2989 15456 2.511452 CCGATGGATCCGGCTTCCT 61.511 63.158 20.08 9.02 40.54 3.36
2990 15457 2.031163 CCGATGGATCCGGCTTCC 59.969 66.667 14.53 14.53 40.54 3.46
3221 15815 3.242870 GCATTAAGCATGTGTCTACTGGC 60.243 47.826 0.00 0.00 44.79 4.85
3402 16994 4.727475 CATCGCTCGCAGATAAAGAGATA 58.273 43.478 0.00 0.00 33.89 1.98
3409 17001 1.661509 CGGCATCGCTCGCAGATAA 60.662 57.895 0.00 0.00 33.89 1.75
3503 17108 8.455682 ACATAAACATCGTTACCTTAAACATGG 58.544 33.333 0.00 0.00 0.00 3.66
3729 17367 1.523758 GGAGTTGGATTGTTGCGTCT 58.476 50.000 0.00 0.00 0.00 4.18
3751 17397 0.321387 TACGGAGTCTCGCAGTCACT 60.321 55.000 0.00 0.00 43.93 3.41
3766 17412 2.083774 TCATGCCAAAGAAAGCTACGG 58.916 47.619 0.00 0.00 0.00 4.02
3767 17413 2.474526 CGTCATGCCAAAGAAAGCTACG 60.475 50.000 0.00 0.00 0.00 3.51
3788 17434 5.411831 AAAAGATTCAGAAATCCCAAGCC 57.588 39.130 0.00 0.00 41.97 4.35
3789 17435 6.146673 CACAAAAAGATTCAGAAATCCCAAGC 59.853 38.462 0.00 0.00 41.97 4.01
3792 17438 5.305128 AGCACAAAAAGATTCAGAAATCCCA 59.695 36.000 0.00 0.00 41.97 4.37
3805 17469 1.810151 GTCCGCCATAGCACAAAAAGA 59.190 47.619 0.00 0.00 39.83 2.52
3806 17470 1.465689 CGTCCGCCATAGCACAAAAAG 60.466 52.381 0.00 0.00 39.83 2.27
3815 17480 1.841450 GAGAAACTCGTCCGCCATAG 58.159 55.000 0.00 0.00 0.00 2.23
3817 17482 4.913126 GAGAAACTCGTCCGCCAT 57.087 55.556 0.00 0.00 0.00 4.40
3852 17517 7.852454 TGTTGAATCATCACGTACGTAGTATAC 59.148 37.037 22.34 10.51 39.59 1.47
3882 17549 2.034305 ACTGCTATAAACTACGAGGCCG 59.966 50.000 0.00 0.00 42.50 6.13
3884 17551 5.829829 AGTTACTGCTATAAACTACGAGGC 58.170 41.667 0.00 0.00 31.84 4.70
3920 17913 6.633325 ACAGCCTGATATATTCCTTAGCAT 57.367 37.500 0.00 0.00 0.00 3.79
3927 17920 5.482908 CTGTGGTACAGCCTGATATATTCC 58.517 45.833 0.00 0.00 41.80 3.01
3953 17946 9.669353 CCATTTGCATGTCTACACTATAATTTC 57.331 33.333 0.00 0.00 0.00 2.17
3959 17953 6.239217 TCTCCATTTGCATGTCTACACTAT 57.761 37.500 0.00 0.00 0.00 2.12
4123 18187 0.391130 TTAGTAGCCCAAGTGCGCTG 60.391 55.000 9.73 0.00 36.53 5.18
4140 18204 5.968254 TGTTCTCATGGTGCGTTATAGTTA 58.032 37.500 0.00 0.00 0.00 2.24
4141 18205 4.827692 TGTTCTCATGGTGCGTTATAGTT 58.172 39.130 0.00 0.00 0.00 2.24
4142 18206 4.465632 TGTTCTCATGGTGCGTTATAGT 57.534 40.909 0.00 0.00 0.00 2.12
4143 18207 4.449068 GGATGTTCTCATGGTGCGTTATAG 59.551 45.833 0.00 0.00 34.06 1.31
4144 18208 4.377021 GGATGTTCTCATGGTGCGTTATA 58.623 43.478 0.00 0.00 34.06 0.98
4174 18252 8.400947 GTGTGAACCTTCGTATATAAGTACTGA 58.599 37.037 0.00 0.00 0.00 3.41
4197 18275 2.224843 TGTCCATGAAGCCATCTTGTGT 60.225 45.455 0.00 0.00 32.65 3.72
4217 18295 0.905357 ATGGGAAGGTCGAAGGACTG 59.095 55.000 0.00 0.00 42.97 3.51
4218 18296 2.544844 TATGGGAAGGTCGAAGGACT 57.455 50.000 0.00 0.00 42.97 3.85
4226 18304 6.346896 AGTTCGAGTAAATTATGGGAAGGTC 58.653 40.000 0.00 0.00 0.00 3.85
4355 18434 4.430908 GCCTCAACGTTATTGTAGCTAGT 58.569 43.478 0.00 0.00 0.00 2.57
4358 18437 2.236395 AGGCCTCAACGTTATTGTAGCT 59.764 45.455 0.00 0.00 0.00 3.32
4361 18440 3.965379 TCAGGCCTCAACGTTATTGTA 57.035 42.857 0.00 0.00 0.00 2.41
4362 18441 2.851263 TCAGGCCTCAACGTTATTGT 57.149 45.000 0.00 0.00 0.00 2.71
4363 18442 3.941483 AGATTCAGGCCTCAACGTTATTG 59.059 43.478 0.00 0.00 0.00 1.90
4443 18522 5.227908 ACAAACTAGTGAGTATTGGACGTG 58.772 41.667 0.00 0.00 33.58 4.49
4513 18592 2.094957 GTCGGGTCTGAAGAGAAGTCAG 60.095 54.545 0.00 0.00 43.28 3.51
4598 18680 2.230660 GGGGTATCATACTTGGCTTGC 58.769 52.381 0.00 0.00 0.00 4.01
4603 18685 3.204382 AGGTTTGGGGGTATCATACTTGG 59.796 47.826 0.00 0.00 0.00 3.61
4619 18701 0.605589 AGGCTGAGACGAGAGGTTTG 59.394 55.000 0.00 0.00 0.00 2.93
4638 18720 4.759693 ACATGACCTAGCGACATTTTTCAA 59.240 37.500 0.00 0.00 0.00 2.69
4712 18796 7.290948 TCACATGGAGGTACAGATCAATAAGAT 59.709 37.037 0.00 0.00 40.48 2.40
4861 18959 8.538701 GGATAGAGCTATATTGGATCCATATGG 58.461 40.741 17.06 16.25 33.12 2.74
4897 18999 6.017523 GTCCCAAACCATGTTTTATTTGTTGG 60.018 38.462 0.00 0.00 31.48 3.77
4907 19009 4.772100 CCTATGAAGTCCCAAACCATGTTT 59.228 41.667 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.