Multiple sequence alignment - TraesCS2A01G510800

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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 TraesCS2A01G510800 chr2A 100.000 4309 0 0 1 4309 735760447 735764755 0.000000e+00 7958.0
1 TraesCS2A01G510800 chr2A 90.138 1308 54 38 2041 3314 735601628 735600362 0.000000e+00 1631.0
2 TraesCS2A01G510800 chr2A 87.933 895 77 14 2689 3564 735701707 735700825 0.000000e+00 1026.0
3 TraesCS2A01G510800 chr2A 85.714 749 64 20 852 1590 735603023 735602308 0.000000e+00 750.0
4 TraesCS2A01G510800 chr2A 86.134 613 56 19 832 1417 735703622 735703012 6.080000e-178 634.0
5 TraesCS2A01G510800 chr2A 83.333 324 44 4 3988 4307 735696805 735696488 1.520000e-74 291.0
6 TraesCS2A01G510800 chr2A 78.525 461 57 20 13 442 735603960 735603511 9.190000e-67 265.0
7 TraesCS2A01G510800 chr2A 90.909 88 8 0 1 88 735716027 735715940 7.570000e-23 119.0
8 TraesCS2A01G510800 chr2D 90.087 1614 103 34 9 1594 603540120 603541704 0.000000e+00 2041.0
9 TraesCS2A01G510800 chr2D 89.550 1646 85 35 1968 3567 603542039 603543643 0.000000e+00 2006.0
10 TraesCS2A01G510800 chr2D 86.360 1371 100 37 1971 3313 603380078 603378767 0.000000e+00 1415.0
11 TraesCS2A01G510800 chr2D 84.638 1367 126 38 2689 3988 603501268 603499919 0.000000e+00 1284.0
12 TraesCS2A01G510800 chr2D 89.899 891 48 17 2440 3317 603401347 603400486 0.000000e+00 1109.0
13 TraesCS2A01G510800 chr2D 85.965 912 60 38 852 1743 603381181 603380318 0.000000e+00 913.0
14 TraesCS2A01G510800 chr2D 87.583 749 51 26 852 1590 603403096 603402380 0.000000e+00 830.0
15 TraesCS2A01G510800 chr2D 89.691 679 27 8 3637 4309 603543954 603544595 0.000000e+00 826.0
16 TraesCS2A01G510800 chr2D 93.510 416 27 0 986 1401 603502839 603502424 1.700000e-173 619.0
17 TraesCS2A01G510800 chr2D 79.771 524 66 20 30 535 603404151 603403650 1.150000e-90 344.0
18 TraesCS2A01G510800 chr2D 84.877 324 39 4 3988 4307 603399500 603399183 6.950000e-83 318.0
19 TraesCS2A01G510800 chr2D 96.639 119 4 0 1844 1962 603541843 603541961 9.450000e-47 198.0
20 TraesCS2A01G510800 chr2D 92.727 110 5 3 1646 1752 603541703 603541812 5.770000e-34 156.0
21 TraesCS2A01G510800 chr2D 90.526 95 6 3 1 95 603504733 603504642 5.850000e-24 122.0
22 TraesCS2A01G510800 chr2D 90.541 74 6 1 2356 2429 603401469 603401397 3.550000e-16 97.1
23 TraesCS2A01G510800 chr2D 95.000 60 3 0 3326 3385 603400450 603400391 1.280000e-15 95.3
24 TraesCS2A01G510800 chr2B 85.201 1365 105 41 2252 3578 733891130 733889825 0.000000e+00 1312.0
25 TraesCS2A01G510800 chr2B 92.440 873 56 5 2445 3317 733971645 733970783 0.000000e+00 1238.0
26 TraesCS2A01G510800 chr2B 90.513 917 53 12 2393 3309 733859942 733859060 0.000000e+00 1181.0
27 TraesCS2A01G510800 chr2B 84.978 912 79 31 852 1748 733973394 733972526 0.000000e+00 872.0
28 TraesCS2A01G510800 chr2B 84.159 928 70 37 852 1773 733862983 733862127 0.000000e+00 828.0
29 TraesCS2A01G510800 chr2B 88.404 664 52 11 927 1590 733892305 733891667 0.000000e+00 776.0
30 TraesCS2A01G510800 chr2B 87.719 570 43 17 857 1401 734051078 734050511 1.310000e-179 640.0
31 TraesCS2A01G510800 chr2B 87.328 363 42 4 3629 3989 733889535 733889175 3.100000e-111 412.0
32 TraesCS2A01G510800 chr2B 87.582 306 27 6 2044 2339 733861811 733861507 1.150000e-90 344.0
33 TraesCS2A01G510800 chr2B 84.639 332 37 7 13 334 733893062 733892735 6.950000e-83 318.0
34 TraesCS2A01G510800 chr2B 83.258 221 36 1 3768 3988 733968709 733968490 7.310000e-48 202.0
35 TraesCS2A01G510800 chr2B 88.199 161 12 1 2044 2197 733891302 733891142 7.360000e-43 185.0
36 TraesCS2A01G510800 chr2B 80.233 258 34 10 3337 3588 733969266 733969020 1.230000e-40 178.0
37 TraesCS2A01G510800 chr2B 91.597 119 10 0 1844 1962 733891515 733891397 9.590000e-37 165.0
38 TraesCS2A01G510800 chr2B 85.333 150 10 9 2041 2187 733972061 733971921 1.250000e-30 145.0
39 TraesCS2A01G510800 chr2B 75.931 349 39 13 129 463 733973978 733973661 2.090000e-28 137.0
40 TraesCS2A01G510800 chr2B 92.045 88 7 0 1 88 734052721 734052634 1.630000e-24 124.0
41 TraesCS2A01G510800 chr2B 81.818 143 12 7 2113 2242 734049798 734049657 1.640000e-19 108.0
42 TraesCS2A01G510800 chr2B 87.209 86 9 2 1876 1960 733972443 733972359 3.550000e-16 97.1
43 TraesCS2A01G510800 chr2B 93.182 44 3 0 2358 2401 733861469 733861426 1.000000e-06 65.8
44 TraesCS2A01G510800 chr3B 97.436 39 0 1 1807 1844 27165021 27164983 1.000000e-06 65.8
45 TraesCS2A01G510800 chr7A 88.679 53 1 5 3939 3989 146676789 146676740 4.650000e-05 60.2
46 TraesCS2A01G510800 chr6A 96.970 33 0 1 3955 3986 188420097 188420065 2.000000e-03 54.7
47 TraesCS2A01G510800 chr4D 94.444 36 0 2 3953 3986 214144903 214144938 2.000000e-03 54.7
48 TraesCS2A01G510800 chr4A 96.970 33 0 1 3955 3986 544383902 544383934 2.000000e-03 54.7
49 TraesCS2A01G510800 chr3A 88.000 50 1 5 3939 3986 170735979 170736025 2.000000e-03 54.7
50 TraesCS2A01G510800 chr3A 100.000 28 0 0 1621 1648 581381830 581381803 8.000000e-03 52.8
51 TraesCS2A01G510800 chr1A 96.875 32 1 0 3958 3989 23697430 23697399 2.000000e-03 54.7
52 TraesCS2A01G510800 chr1A 100.000 29 0 0 1615 1643 27289563 27289591 2.000000e-03 54.7
53 TraesCS2A01G510800 chr7B 100.000 28 0 0 1616 1643 610839106 610839133 8.000000e-03 52.8


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 TraesCS2A01G510800 chr2A 735760447 735764755 4308 False 7958.000000 7958 100.000000 1 4309 1 chr2A.!!$F1 4308
1 TraesCS2A01G510800 chr2A 735600362 735603960 3598 True 882.000000 1631 84.792333 13 3314 3 chr2A.!!$R3 3301
2 TraesCS2A01G510800 chr2A 735700825 735703622 2797 True 830.000000 1026 87.033500 832 3564 2 chr2A.!!$R4 2732
3 TraesCS2A01G510800 chr2D 603378767 603381181 2414 True 1164.000000 1415 86.162500 852 3313 2 chr2D.!!$R1 2461
4 TraesCS2A01G510800 chr2D 603540120 603544595 4475 False 1045.400000 2041 91.738800 9 4309 5 chr2D.!!$F1 4300
5 TraesCS2A01G510800 chr2D 603499919 603504733 4814 True 675.000000 1284 89.558000 1 3988 3 chr2D.!!$R3 3987
6 TraesCS2A01G510800 chr2D 603399183 603404151 4968 True 465.566667 1109 87.945167 30 4307 6 chr2D.!!$R2 4277
7 TraesCS2A01G510800 chr2B 733859060 733862983 3923 True 604.700000 1181 88.859000 852 3309 4 chr2B.!!$R1 2457
8 TraesCS2A01G510800 chr2B 733889175 733893062 3887 True 528.000000 1312 87.561333 13 3989 6 chr2B.!!$R2 3976
9 TraesCS2A01G510800 chr2B 733968490 733973978 5488 True 409.871429 1238 84.197429 129 3988 7 chr2B.!!$R3 3859
10 TraesCS2A01G510800 chr2B 734049657 734052721 3064 True 290.666667 640 87.194000 1 2242 3 chr2B.!!$R4 2241

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
779 2968 0.109179 TCGTATGTGGTGCCGTGTAC 60.109 55.0 0.0 0.0 0.0 2.90 F
1515 3962 0.179048 TGGGTGCATGGCGATCTAAG 60.179 55.0 0.0 0.0 0.0 2.18 F
2225 5402 0.383590 CGATTTTGTGTGTGTGGCCA 59.616 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 4450 0.249398 AATTGGAACGGAGGGAGTCG 59.751 55.0 0.00 0.0 0.0 4.18 R
3273 8141 0.833287 ACCTCCATGAATCCGTCCTG 59.167 55.0 0.00 0.0 0.0 3.86 R
4130 11105 0.172578 CGACACGGTGATAGAAGGCA 59.827 55.0 16.29 0.0 0.0 4.75 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
43 44 2.238521 GGTTTGGCTTGTCTGGATTCA 58.761 47.619 0.00 0.00 0.00 2.57
184 993 5.094134 CGCTGTTTGTTCTAGGACTAGTAC 58.906 45.833 2.07 0.00 35.06 2.73
217 1027 4.379082 GCGTGTTTTGTGGGACTTATTAGG 60.379 45.833 0.00 0.00 0.00 2.69
226 1036 7.427989 TGTGGGACTTATTAGGGTACTTTAG 57.572 40.000 0.00 0.00 0.00 1.85
228 1038 5.367644 TGGGACTTATTAGGGTACTTTAGGC 59.632 44.000 0.00 0.00 0.00 3.93
230 1040 6.286758 GGACTTATTAGGGTACTTTAGGCAC 58.713 44.000 0.00 0.00 0.00 5.01
231 1041 6.126968 GGACTTATTAGGGTACTTTAGGCACA 60.127 42.308 0.00 0.00 0.00 4.57
232 1042 6.885922 ACTTATTAGGGTACTTTAGGCACAG 58.114 40.000 0.00 0.00 0.00 3.66
233 1043 3.622166 TTAGGGTACTTTAGGCACAGC 57.378 47.619 0.00 0.00 0.00 4.40
265 1323 7.201857 GGAATAATTTGGCACTAGAAGAATGCT 60.202 37.037 0.00 0.00 39.38 3.79
280 1339 6.857964 AGAAGAATGCTGTCAACAATTTAACG 59.142 34.615 0.00 0.00 0.00 3.18
306 1368 1.080230 CGGTGTCACTGCTCTGGAG 60.080 63.158 2.35 0.00 0.00 3.86
348 1410 2.346099 CGGAATCAACCGCACAAAAT 57.654 45.000 0.00 0.00 46.20 1.82
350 1412 3.827625 CGGAATCAACCGCACAAAATAA 58.172 40.909 0.00 0.00 46.20 1.40
353 1415 5.347364 CGGAATCAACCGCACAAAATAAAAT 59.653 36.000 0.00 0.00 46.20 1.82
419 2052 7.881142 TGTATTCACTTTTACCATGAAGTTGG 58.119 34.615 0.00 0.00 42.82 3.77
427 2060 0.529378 CCATGAAGTTGGCTTGCTCC 59.471 55.000 0.00 0.00 34.61 4.70
437 2071 0.600057 GGCTTGCTCCTTTTGTCCTG 59.400 55.000 0.00 0.00 0.00 3.86
463 2097 1.603802 GACATCATGCCATACCGTTGG 59.396 52.381 0.00 0.00 39.94 3.77
535 2192 2.877691 GTGCTGAATCCAACCGGC 59.122 61.111 0.00 0.00 35.34 6.13
582 2535 1.706287 GCTGCCGGATCCGTTTCTTC 61.706 60.000 31.22 13.61 37.81 2.87
604 2557 6.387041 TCATCGTTTGTATAGTACTGGAGG 57.613 41.667 5.39 0.00 0.00 4.30
623 2805 1.648467 GAAGGAACATGCAGGACCGC 61.648 60.000 4.84 2.84 0.00 5.68
659 2848 6.388435 TCCCTAGCGAAAGAATTAGTACTC 57.612 41.667 0.00 0.00 0.00 2.59
667 2856 6.539103 GCGAAAGAATTAGTACTCCCTTCATT 59.461 38.462 0.00 0.64 0.00 2.57
715 2904 8.668510 ACAGACTCCAACATGAATTACATATC 57.331 34.615 0.00 0.00 37.46 1.63
770 2959 8.809468 ATATGTCTATCTACATCGTATGTGGT 57.191 34.615 9.77 2.99 44.60 4.16
771 2960 6.313744 TGTCTATCTACATCGTATGTGGTG 57.686 41.667 9.77 4.34 44.60 4.17
772 2961 5.154932 GTCTATCTACATCGTATGTGGTGC 58.845 45.833 9.77 0.00 44.60 5.01
773 2962 2.882927 TCTACATCGTATGTGGTGCC 57.117 50.000 9.77 0.00 44.60 5.01
774 2963 1.066454 TCTACATCGTATGTGGTGCCG 59.934 52.381 9.77 0.00 44.60 5.69
775 2964 0.818938 TACATCGTATGTGGTGCCGT 59.181 50.000 9.77 0.00 44.60 5.68
776 2965 0.739462 ACATCGTATGTGGTGCCGTG 60.739 55.000 0.56 0.00 43.01 4.94
777 2966 0.739462 CATCGTATGTGGTGCCGTGT 60.739 55.000 0.00 0.00 0.00 4.49
778 2967 0.818938 ATCGTATGTGGTGCCGTGTA 59.181 50.000 0.00 0.00 0.00 2.90
779 2968 0.109179 TCGTATGTGGTGCCGTGTAC 60.109 55.000 0.00 0.00 0.00 2.90
780 2969 1.079875 CGTATGTGGTGCCGTGTACC 61.080 60.000 4.60 4.60 38.78 3.34
781 2970 1.079875 GTATGTGGTGCCGTGTACCG 61.080 60.000 6.66 0.00 41.19 4.02
855 3156 3.332783 CCCTTCCCCTATAAATACCCCAC 59.667 52.174 0.00 0.00 0.00 4.61
1194 3561 1.201429 AGACGGACCCCTGCTTCAAT 61.201 55.000 0.00 0.00 0.00 2.57
1314 3681 1.031235 CCACCGTTAAAAACCCCGTT 58.969 50.000 0.00 0.00 0.00 4.44
1476 3918 3.683365 AAAAATGCACCCCACTCAATC 57.317 42.857 0.00 0.00 0.00 2.67
1515 3962 0.179048 TGGGTGCATGGCGATCTAAG 60.179 55.000 0.00 0.00 0.00 2.18
1528 3975 4.058124 GCGATCTAAGCACCACATATTGA 58.942 43.478 0.00 0.00 34.19 2.57
1532 3979 7.065085 GCGATCTAAGCACCACATATTGATATT 59.935 37.037 0.00 0.00 34.19 1.28
1534 3981 7.984422 TCTAAGCACCACATATTGATATTGG 57.016 36.000 0.00 9.03 32.28 3.16
1535 3982 7.517320 TCTAAGCACCACATATTGATATTGGT 58.483 34.615 9.86 9.86 35.99 3.67
1536 3983 8.655901 TCTAAGCACCACATATTGATATTGGTA 58.344 33.333 12.97 3.64 34.94 3.25
1537 3984 9.453572 CTAAGCACCACATATTGATATTGGTAT 57.546 33.333 12.97 8.46 34.94 2.73
1539 3986 9.453572 AAGCACCACATATTGATATTGGTATAG 57.546 33.333 12.97 6.92 34.94 1.31
1541 3988 9.884636 GCACCACATATTGATATTGGTATAGTA 57.115 33.333 12.97 0.00 34.94 1.82
1615 4120 3.753846 TCATGGAAAGGGTCCTTGGAAAC 60.754 47.826 2.65 0.00 46.84 2.78
1616 4121 2.375014 GGAAAGGGTCCTTGGAAACA 57.625 50.000 2.65 0.00 43.98 2.83
1622 4127 1.982958 GGGTCCTTGGAAACAGAGGTA 59.017 52.381 0.00 0.00 44.54 3.08
1624 4129 2.638363 GGTCCTTGGAAACAGAGGTACT 59.362 50.000 0.00 0.00 44.54 2.73
1635 4140 4.781264 AGGTACTCCCTCCGTTCC 57.219 61.111 0.00 0.00 40.71 3.62
1636 4141 1.379576 AGGTACTCCCTCCGTTCCG 60.380 63.158 0.00 0.00 40.71 4.30
1637 4142 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
1638 4143 0.967380 GGTACTCCCTCCGTTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
1639 4144 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
1640 4145 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
1641 4146 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1642 4147 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1643 4148 0.457035 TCCCTCCGTTCCGAATTACG 59.543 55.000 0.00 0.00 42.18 3.18
1644 4149 0.457035 CCCTCCGTTCCGAATTACGA 59.543 55.000 0.10 0.00 45.77 3.43
1647 4152 2.355756 CCTCCGTTCCGAATTACGAGTA 59.644 50.000 0.10 0.00 45.77 2.59
1688 4194 1.302511 GATGACGTGTGGGGCACTT 60.303 57.895 0.00 0.00 45.57 3.16
1773 4421 4.392921 TCCAGAGACGGATCTTCATTTC 57.607 45.455 0.00 0.00 34.34 2.17
1774 4422 3.769300 TCCAGAGACGGATCTTCATTTCA 59.231 43.478 0.00 0.00 34.34 2.69
1787 4435 3.657398 TCATTTCACATCCAGCTCCAT 57.343 42.857 0.00 0.00 0.00 3.41
1796 4444 5.072736 TCACATCCAGCTCCATTCTTATGAT 59.927 40.000 0.00 0.00 33.37 2.45
1797 4445 5.411977 CACATCCAGCTCCATTCTTATGATC 59.588 44.000 0.00 0.00 33.37 2.92
1798 4446 5.310068 ACATCCAGCTCCATTCTTATGATCT 59.690 40.000 0.00 0.00 33.37 2.75
1802 4450 7.619050 TCCAGCTCCATTCTTATGATCTTATC 58.381 38.462 0.00 0.00 33.37 1.75
1803 4451 6.534436 CCAGCTCCATTCTTATGATCTTATCG 59.466 42.308 0.00 0.00 33.37 2.92
1805 4453 7.275341 CAGCTCCATTCTTATGATCTTATCGAC 59.725 40.741 0.00 0.00 33.37 4.20
1807 4455 7.487829 GCTCCATTCTTATGATCTTATCGACTC 59.512 40.741 0.00 0.00 33.37 3.36
1809 4457 7.038659 CCATTCTTATGATCTTATCGACTCCC 58.961 42.308 0.00 0.00 33.37 4.30
1812 4460 5.946972 TCTTATGATCTTATCGACTCCCTCC 59.053 44.000 0.00 0.00 0.00 4.30
1813 4461 2.505405 TGATCTTATCGACTCCCTCCG 58.495 52.381 0.00 0.00 0.00 4.63
1820 4468 0.613853 TCGACTCCCTCCGTTCCAAT 60.614 55.000 0.00 0.00 0.00 3.16
1824 4472 3.268330 GACTCCCTCCGTTCCAATTTAC 58.732 50.000 0.00 0.00 0.00 2.01
1829 4477 3.439129 CCCTCCGTTCCAATTTACTTGTC 59.561 47.826 0.00 0.00 32.61 3.18
1830 4478 3.124636 CCTCCGTTCCAATTTACTTGTCG 59.875 47.826 0.00 0.00 32.61 4.35
1831 4479 3.731089 TCCGTTCCAATTTACTTGTCGT 58.269 40.909 0.00 0.00 32.61 4.34
1832 4480 3.495377 TCCGTTCCAATTTACTTGTCGTG 59.505 43.478 0.00 0.00 32.61 4.35
1833 4481 3.364565 CCGTTCCAATTTACTTGTCGTGG 60.365 47.826 0.00 0.00 32.61 4.94
1834 4482 3.249080 CGTTCCAATTTACTTGTCGTGGT 59.751 43.478 0.00 0.00 32.61 4.16
1835 4483 4.260866 CGTTCCAATTTACTTGTCGTGGTT 60.261 41.667 0.00 0.00 32.61 3.67
1836 4484 5.584442 GTTCCAATTTACTTGTCGTGGTTT 58.416 37.500 0.00 0.00 32.61 3.27
1837 4485 6.511444 CGTTCCAATTTACTTGTCGTGGTTTA 60.511 38.462 0.00 0.00 32.61 2.01
1838 4486 6.548441 TCCAATTTACTTGTCGTGGTTTAG 57.452 37.500 0.00 0.00 32.61 1.85
1839 4487 6.056884 TCCAATTTACTTGTCGTGGTTTAGT 58.943 36.000 0.00 0.00 32.61 2.24
1840 4488 6.543100 TCCAATTTACTTGTCGTGGTTTAGTT 59.457 34.615 0.00 0.00 32.61 2.24
1841 4489 6.854381 CCAATTTACTTGTCGTGGTTTAGTTC 59.146 38.462 0.00 0.00 32.61 3.01
1962 4687 5.063204 TGGTCTTTGGAGAAATGTGTGTAG 58.937 41.667 0.00 0.00 32.66 2.74
2099 5219 7.495055 TGTCCTCTCCTACGTATTAAAATTCC 58.505 38.462 0.00 0.00 0.00 3.01
2225 5402 0.383590 CGATTTTGTGTGTGTGGCCA 59.616 50.000 0.00 0.00 0.00 5.36
2244 5421 4.176271 GCCAGCACCATTTTTCATTACTC 58.824 43.478 0.00 0.00 0.00 2.59
2246 5423 5.404946 CCAGCACCATTTTTCATTACTCTG 58.595 41.667 0.00 0.00 0.00 3.35
2295 5498 4.900684 TGTAAACAGTGCAAGGCTATACA 58.099 39.130 0.00 0.00 0.00 2.29
2339 5557 1.140052 TGTCGTGCCGGATCCATTAAT 59.860 47.619 13.41 0.00 0.00 1.40
2340 5558 2.218603 GTCGTGCCGGATCCATTAATT 58.781 47.619 13.41 0.00 0.00 1.40
2344 5562 4.273969 TCGTGCCGGATCCATTAATTTAAC 59.726 41.667 13.41 0.00 0.00 2.01
2345 5563 4.555906 CGTGCCGGATCCATTAATTTAACC 60.556 45.833 13.41 0.00 0.00 2.85
2347 5565 5.766174 GTGCCGGATCCATTAATTTAACCTA 59.234 40.000 13.41 0.00 0.00 3.08
2349 5567 5.414765 GCCGGATCCATTAATTTAACCTAGG 59.585 44.000 13.41 7.41 0.00 3.02
2350 5568 6.746043 GCCGGATCCATTAATTTAACCTAGGA 60.746 42.308 17.98 0.00 0.00 2.94
2351 5569 6.879458 CCGGATCCATTAATTTAACCTAGGAG 59.121 42.308 17.98 0.00 0.00 3.69
3413 9997 5.079689 TCGTTACTTCATAACCATGAGCA 57.920 39.130 0.00 0.00 42.11 4.26
3427 10011 4.578928 ACCATGAGCAACCGGATAATAAAC 59.421 41.667 9.46 0.00 0.00 2.01
3605 10248 1.815421 CAGCCGAGGCATAAACGCT 60.815 57.895 17.18 0.00 44.88 5.07
3613 10256 1.433471 GCATAAACGCTTGCCTCCC 59.567 57.895 0.00 0.00 32.66 4.30
3661 10491 4.988598 CCGTGCTGGTTGTCGCCT 62.989 66.667 0.00 0.00 0.00 5.52
3786 10669 3.718210 GAGGTCCGCCGTGGCTAAG 62.718 68.421 9.55 0.00 40.50 2.18
3800 10683 3.252458 GTGGCTAAGAAAATGACCAACGT 59.748 43.478 0.00 0.00 0.00 3.99
3956 10851 7.234187 GTTATTGAACGAGTGCATCATCTTA 57.766 36.000 0.00 0.00 0.00 2.10
4000 10962 8.272545 TGCATTAGAATAATGGCATATCAGAC 57.727 34.615 0.00 0.00 0.00 3.51
4011 10973 6.994421 TGGCATATCAGACTGTTCCTATTA 57.006 37.500 1.59 0.00 0.00 0.98
4012 10974 7.373617 TGGCATATCAGACTGTTCCTATTAA 57.626 36.000 1.59 0.00 0.00 1.40
4057 11019 5.467035 TTTTTGCCCTTAATGAGAACCTG 57.533 39.130 0.00 0.00 0.00 4.00
4129 11104 7.775053 AGATTTGTTTAATAGGTTGCCTGAA 57.225 32.000 0.00 0.00 34.61 3.02
4130 11105 8.366359 AGATTTGTTTAATAGGTTGCCTGAAT 57.634 30.769 0.00 0.00 34.61 2.57
4131 11106 8.253113 AGATTTGTTTAATAGGTTGCCTGAATG 58.747 33.333 0.00 0.00 34.61 2.67
4132 11107 5.323371 TGTTTAATAGGTTGCCTGAATGC 57.677 39.130 0.00 0.00 34.61 3.56
4133 11108 4.159506 TGTTTAATAGGTTGCCTGAATGCC 59.840 41.667 0.00 0.00 34.61 4.40
4134 11109 2.834638 AATAGGTTGCCTGAATGCCT 57.165 45.000 0.00 0.00 34.61 4.75
4135 11110 2.834638 ATAGGTTGCCTGAATGCCTT 57.165 45.000 0.00 0.00 34.61 4.35
4136 11111 2.128771 TAGGTTGCCTGAATGCCTTC 57.871 50.000 0.00 0.00 34.61 3.46
4137 11112 0.407139 AGGTTGCCTGAATGCCTTCT 59.593 50.000 3.32 0.00 29.57 2.85
4138 11113 1.635487 AGGTTGCCTGAATGCCTTCTA 59.365 47.619 3.32 0.00 29.57 2.10
4139 11114 2.243221 AGGTTGCCTGAATGCCTTCTAT 59.757 45.455 3.32 0.00 29.57 1.98
4140 11115 2.620585 GGTTGCCTGAATGCCTTCTATC 59.379 50.000 3.32 0.00 32.29 2.08
4141 11116 3.282021 GTTGCCTGAATGCCTTCTATCA 58.718 45.455 3.32 0.00 32.29 2.15
4286 11265 1.749665 CTTACACACCGGACCCACA 59.250 57.895 9.46 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.299976 GACGGGCTGATTCCCTGTT 59.700 57.895 0.00 0.00 44.30 3.16
184 993 1.269206 ACAAAACACGCATTCAGGCAG 60.269 47.619 0.00 0.00 0.00 4.85
228 1038 4.497300 CCAAATTATTCCAACAGGCTGTG 58.503 43.478 22.83 14.75 0.00 3.66
230 1040 3.055963 TGCCAAATTATTCCAACAGGCTG 60.056 43.478 14.16 14.16 41.33 4.85
231 1041 3.055891 GTGCCAAATTATTCCAACAGGCT 60.056 43.478 0.00 0.00 41.33 4.58
232 1042 3.055891 AGTGCCAAATTATTCCAACAGGC 60.056 43.478 0.00 0.00 41.15 4.85
233 1043 4.806640 AGTGCCAAATTATTCCAACAGG 57.193 40.909 0.00 0.00 0.00 4.00
234 1044 6.757897 TCTAGTGCCAAATTATTCCAACAG 57.242 37.500 0.00 0.00 0.00 3.16
236 1046 7.391148 TCTTCTAGTGCCAAATTATTCCAAC 57.609 36.000 0.00 0.00 0.00 3.77
237 1047 8.469200 CATTCTTCTAGTGCCAAATTATTCCAA 58.531 33.333 0.00 0.00 0.00 3.53
265 1323 5.960683 CGACAAGAACGTTAAATTGTTGACA 59.039 36.000 23.61 0.00 38.70 3.58
280 1339 0.582005 GCAGTGACACCGACAAGAAC 59.418 55.000 0.84 0.00 0.00 3.01
306 1368 4.215613 GGTGAATTTACTCAACCTCCACAC 59.784 45.833 0.00 0.00 0.00 3.82
419 2052 0.600057 CCAGGACAAAAGGAGCAAGC 59.400 55.000 0.00 0.00 0.00 4.01
427 2060 3.008375 TGATGTCTCTCCCAGGACAAAAG 59.992 47.826 0.00 0.00 44.10 2.27
437 2071 2.289945 GGTATGGCATGATGTCTCTCCC 60.290 54.545 10.98 0.00 0.00 4.30
463 2097 5.594926 CCAATTACCTGGCATCAGATTTTC 58.405 41.667 0.00 0.00 43.49 2.29
535 2192 0.179000 AGAGGCCGTGCAATTAGAGG 59.821 55.000 0.00 0.00 0.00 3.69
582 2535 6.387041 TCCTCCAGTACTATACAAACGATG 57.613 41.667 0.00 0.00 0.00 3.84
604 2557 1.648467 GCGGTCCTGCATGTTCCTTC 61.648 60.000 0.00 0.00 34.15 3.46
623 2805 1.245732 CTAGGGAACGGATCGGTAGG 58.754 60.000 6.32 0.00 0.00 3.18
630 2819 1.481871 TCTTTCGCTAGGGAACGGAT 58.518 50.000 20.79 0.00 0.00 4.18
679 2868 8.154203 TCATGTTGGAGTCTGTAAAATGACTTA 58.846 33.333 0.00 0.00 42.79 2.24
682 2871 6.801539 TCATGTTGGAGTCTGTAAAATGAC 57.198 37.500 0.00 0.00 0.00 3.06
697 2886 9.949174 TTTTCATCGATATGTAATTCATGTTGG 57.051 29.630 0.00 0.00 37.91 3.77
746 2935 7.361799 GCACCACATACGATGTAGATAGACATA 60.362 40.741 0.00 0.00 42.70 2.29
755 2944 1.202371 ACGGCACCACATACGATGTAG 60.202 52.381 0.00 0.00 42.70 2.74
758 2947 0.739462 ACACGGCACCACATACGATG 60.739 55.000 0.00 0.00 0.00 3.84
760 2949 0.109179 GTACACGGCACCACATACGA 60.109 55.000 0.00 0.00 0.00 3.43
762 2951 1.079875 CGGTACACGGCACCACATAC 61.080 60.000 0.00 0.00 39.42 2.39
763 2952 1.215912 CGGTACACGGCACCACATA 59.784 57.895 0.00 0.00 39.42 2.29
764 2953 2.047655 CGGTACACGGCACCACAT 60.048 61.111 0.00 0.00 39.42 3.21
773 2962 1.099879 CCTACTCCCTCCGGTACACG 61.100 65.000 0.00 0.00 43.80 4.49
774 2963 0.257039 TCCTACTCCCTCCGGTACAC 59.743 60.000 0.00 0.00 0.00 2.90
775 2964 0.257039 GTCCTACTCCCTCCGGTACA 59.743 60.000 0.00 0.00 0.00 2.90
776 2965 0.817229 CGTCCTACTCCCTCCGGTAC 60.817 65.000 0.00 0.00 0.00 3.34
777 2966 1.528824 CGTCCTACTCCCTCCGGTA 59.471 63.158 0.00 0.00 0.00 4.02
778 2967 2.274760 CGTCCTACTCCCTCCGGT 59.725 66.667 0.00 0.00 0.00 5.28
779 2968 2.518825 CCGTCCTACTCCCTCCGG 60.519 72.222 0.00 0.00 0.00 5.14
780 2969 3.217743 GCCGTCCTACTCCCTCCG 61.218 72.222 0.00 0.00 0.00 4.63
781 2970 3.217743 CGCCGTCCTACTCCCTCC 61.218 72.222 0.00 0.00 0.00 4.30
782 2971 2.439883 ACGCCGTCCTACTCCCTC 60.440 66.667 0.00 0.00 0.00 4.30
783 2972 2.754658 CACGCCGTCCTACTCCCT 60.755 66.667 0.00 0.00 0.00 4.20
784 2973 2.753043 TCACGCCGTCCTACTCCC 60.753 66.667 0.00 0.00 0.00 4.30
785 2974 2.045131 ACTCACGCCGTCCTACTCC 61.045 63.158 0.00 0.00 0.00 3.85
786 2975 1.136984 CACTCACGCCGTCCTACTC 59.863 63.158 0.00 0.00 0.00 2.59
787 2976 2.991076 GCACTCACGCCGTCCTACT 61.991 63.158 0.00 0.00 0.00 2.57
788 2977 2.506438 GCACTCACGCCGTCCTAC 60.506 66.667 0.00 0.00 0.00 3.18
830 3115 4.453272 GGGGTATTTATAGGGGAAGGGAGA 60.453 50.000 0.00 0.00 0.00 3.71
855 3156 1.613437 GGTGTGTGTTGGAATGAAGGG 59.387 52.381 0.00 0.00 0.00 3.95
984 3348 1.664016 GCCATGCGTGCTTATGTATGC 60.664 52.381 0.00 4.26 40.48 3.14
1347 3714 1.142097 GAAGGCGAGGTAGGAGTGC 59.858 63.158 0.00 0.00 0.00 4.40
1476 3918 9.313118 GCACCCAGTTTATATTTTTCCTTATTG 57.687 33.333 0.00 0.00 0.00 1.90
1515 3962 8.792830 ACTATACCAATATCAATATGTGGTGC 57.207 34.615 17.73 0.00 0.00 5.01
1631 4136 7.634522 ACTGTATACTACTCGTAATTCGGAAC 58.365 38.462 4.17 0.00 40.32 3.62
1632 4137 7.792374 ACTGTATACTACTCGTAATTCGGAA 57.208 36.000 4.17 0.00 40.32 4.30
1633 4138 8.144478 AGTACTGTATACTACTCGTAATTCGGA 58.856 37.037 4.17 0.00 40.32 4.55
1634 4139 8.304202 AGTACTGTATACTACTCGTAATTCGG 57.696 38.462 4.17 0.00 40.32 4.30
1635 4140 9.578306 CAAGTACTGTATACTACTCGTAATTCG 57.422 37.037 4.17 0.00 41.41 3.34
1636 4141 9.379811 GCAAGTACTGTATACTACTCGTAATTC 57.620 37.037 4.17 0.00 28.89 2.17
1637 4142 8.896744 TGCAAGTACTGTATACTACTCGTAATT 58.103 33.333 4.17 1.77 30.23 1.40
1638 4143 8.341173 GTGCAAGTACTGTATACTACTCGTAAT 58.659 37.037 4.17 0.00 0.00 1.89
1639 4144 7.464577 CGTGCAAGTACTGTATACTACTCGTAA 60.465 40.741 4.17 0.00 0.00 3.18
1640 4145 6.019559 CGTGCAAGTACTGTATACTACTCGTA 60.020 42.308 4.17 0.00 0.00 3.43
1641 4146 5.220548 CGTGCAAGTACTGTATACTACTCGT 60.221 44.000 4.17 0.00 0.00 4.18
1642 4147 5.196102 CGTGCAAGTACTGTATACTACTCG 58.804 45.833 4.17 1.59 0.00 4.18
1643 4148 5.964168 CACGTGCAAGTACTGTATACTACTC 59.036 44.000 4.57 0.00 0.00 2.59
1644 4149 5.413833 ACACGTGCAAGTACTGTATACTACT 59.586 40.000 17.22 1.88 0.00 2.57
1647 4152 4.482386 CACACGTGCAAGTACTGTATACT 58.518 43.478 17.22 0.00 0.00 2.12
1773 4421 4.711399 TCATAAGAATGGAGCTGGATGTG 58.289 43.478 0.00 0.00 33.61 3.21
1774 4422 5.310068 AGATCATAAGAATGGAGCTGGATGT 59.690 40.000 0.00 0.00 33.61 3.06
1787 4435 6.434652 GGAGGGAGTCGATAAGATCATAAGAA 59.565 42.308 0.00 0.00 0.00 2.52
1796 4444 2.295885 GAACGGAGGGAGTCGATAAGA 58.704 52.381 0.00 0.00 0.00 2.10
1797 4445 1.337387 GGAACGGAGGGAGTCGATAAG 59.663 57.143 0.00 0.00 0.00 1.73
1798 4446 1.341285 TGGAACGGAGGGAGTCGATAA 60.341 52.381 0.00 0.00 0.00 1.75
1802 4450 0.249398 AATTGGAACGGAGGGAGTCG 59.751 55.000 0.00 0.00 0.00 4.18
1803 4451 2.491675 AAATTGGAACGGAGGGAGTC 57.508 50.000 0.00 0.00 0.00 3.36
1805 4453 3.629142 AGTAAATTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1807 4455 3.418047 ACAAGTAAATTGGAACGGAGGG 58.582 45.455 0.00 0.00 43.68 4.30
1809 4457 3.744426 ACGACAAGTAAATTGGAACGGAG 59.256 43.478 0.00 0.00 43.68 4.63
1812 4460 3.249080 ACCACGACAAGTAAATTGGAACG 59.751 43.478 0.00 0.00 43.68 3.95
1813 4461 4.823790 ACCACGACAAGTAAATTGGAAC 57.176 40.909 0.00 0.00 43.68 3.62
1820 4468 6.457257 GCTTGAACTAAACCACGACAAGTAAA 60.457 38.462 0.00 0.00 36.61 2.01
1824 4472 3.560068 AGCTTGAACTAAACCACGACAAG 59.440 43.478 0.00 0.00 37.09 3.16
1829 4477 3.966218 CGAAAAGCTTGAACTAAACCACG 59.034 43.478 0.00 0.00 0.00 4.94
1830 4478 4.733405 CACGAAAAGCTTGAACTAAACCAC 59.267 41.667 0.00 0.00 0.00 4.16
1831 4479 4.732355 GCACGAAAAGCTTGAACTAAACCA 60.732 41.667 0.00 0.00 0.00 3.67
1832 4480 3.729217 GCACGAAAAGCTTGAACTAAACC 59.271 43.478 0.00 0.00 0.00 3.27
1833 4481 4.598062 AGCACGAAAAGCTTGAACTAAAC 58.402 39.130 0.00 0.00 39.87 2.01
1834 4482 4.893424 AGCACGAAAAGCTTGAACTAAA 57.107 36.364 0.00 0.00 39.87 1.85
1962 4687 1.398390 CAAGGCGGCTGTTATCTTCAC 59.602 52.381 14.21 0.00 0.00 3.18
2051 5165 2.214376 TTAAGTTGGAGTGGCATGGG 57.786 50.000 0.00 0.00 0.00 4.00
2213 5387 3.595758 GGTGCTGGCCACACACAC 61.596 66.667 28.16 21.10 46.50 3.82
2215 5389 1.747325 AAATGGTGCTGGCCACACAC 61.747 55.000 28.16 24.99 46.50 3.82
2225 5402 6.714810 TGTACAGAGTAATGAAAAATGGTGCT 59.285 34.615 0.00 0.00 0.00 4.40
2273 5476 4.693566 GTGTATAGCCTTGCACTGTTTACA 59.306 41.667 0.00 0.00 0.00 2.41
2295 5498 2.821969 CCTATTTGCCACTGCTTCTTGT 59.178 45.455 0.00 0.00 38.71 3.16
2349 5567 0.884514 GCCAAAAACAGAGGAGGCTC 59.115 55.000 5.78 5.78 39.02 4.70
2350 5568 0.890996 CGCCAAAAACAGAGGAGGCT 60.891 55.000 0.00 0.00 39.91 4.58
2351 5569 1.581447 CGCCAAAAACAGAGGAGGC 59.419 57.895 0.00 0.00 38.73 4.70
3273 8141 0.833287 ACCTCCATGAATCCGTCCTG 59.167 55.000 0.00 0.00 0.00 3.86
3413 9997 4.573201 CCGTCACATGTTTATTATCCGGTT 59.427 41.667 0.00 0.00 0.00 4.44
3427 10011 0.870393 GCATCATAGGCCGTCACATG 59.130 55.000 0.00 0.00 0.00 3.21
3567 10154 3.740397 CGGCGGGTACACGTGAGA 61.740 66.667 25.01 6.70 35.98 3.27
3597 10240 1.076995 GGGGGAGGCAAGCGTTTAT 60.077 57.895 0.00 0.00 0.00 1.40
3661 10491 1.264045 TGATGTGGCAGGGATGTCGA 61.264 55.000 0.00 0.00 0.00 4.20
3813 10696 3.616956 TGCTATTTCTCAGGTGTCTGG 57.383 47.619 0.00 0.00 41.23 3.86
3874 10757 7.819415 GCAATCCAACTTTTAAAGGAAGCTTAT 59.181 33.333 9.64 0.00 34.44 1.73
4017 10979 6.128309 GGCAAAAATGCGATTGTTCCTTAAAT 60.128 34.615 0.00 0.00 35.24 1.40
4025 10987 2.837532 AGGGCAAAAATGCGATTGTT 57.162 40.000 0.00 0.00 35.24 2.83
4057 11019 0.833287 TAAGAGCAGACCTCATGGGC 59.167 55.000 0.00 0.00 43.31 5.36
4129 11104 1.202417 CGACACGGTGATAGAAGGCAT 60.202 52.381 16.29 0.00 0.00 4.40
4130 11105 0.172578 CGACACGGTGATAGAAGGCA 59.827 55.000 16.29 0.00 0.00 4.75
4131 11106 0.172803 ACGACACGGTGATAGAAGGC 59.827 55.000 16.29 0.00 0.00 4.35
4132 11107 1.743958 AGACGACACGGTGATAGAAGG 59.256 52.381 16.29 0.00 0.00 3.46
4133 11108 2.478031 CCAGACGACACGGTGATAGAAG 60.478 54.545 16.29 0.61 0.00 2.85
4134 11109 1.471287 CCAGACGACACGGTGATAGAA 59.529 52.381 16.29 0.00 0.00 2.10
4135 11110 1.092348 CCAGACGACACGGTGATAGA 58.908 55.000 16.29 0.00 0.00 1.98
4136 11111 0.809385 ACCAGACGACACGGTGATAG 59.191 55.000 16.29 7.82 0.00 2.08
4137 11112 0.806868 GACCAGACGACACGGTGATA 59.193 55.000 16.29 0.00 31.63 2.15
4138 11113 1.176619 TGACCAGACGACACGGTGAT 61.177 55.000 16.29 0.00 31.63 3.06
4139 11114 1.385756 TTGACCAGACGACACGGTGA 61.386 55.000 16.29 0.00 31.63 4.02
4140 11115 0.528901 TTTGACCAGACGACACGGTG 60.529 55.000 6.58 6.58 31.63 4.94
4141 11116 0.249322 CTTTGACCAGACGACACGGT 60.249 55.000 0.00 0.00 35.12 4.83


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

AutoCloner maintained by Alex Coulton.