Multiple sequence alignment - TraesCS5A01G483500

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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 TraesCS5A01G483500 chr5A 100.000 5037 0 0 1 5037 654559490 654564526 0.000000e+00 9302.0
1 TraesCS5A01G483500 chr5A 82.220 1153 152 33 2605 3745 654408763 654409874 0.000000e+00 944.0
2 TraesCS5A01G483500 chr5A 83.281 640 56 22 4410 5020 654571381 654571998 4.440000e-150 542.0
3 TraesCS5A01G483500 chr5A 89.021 419 28 9 4573 4979 654611937 654612349 2.090000e-138 503.0
4 TraesCS5A01G483500 chr5A 90.000 80 8 0 3791 3870 654410170 654410249 2.480000e-18 104.0
5 TraesCS5A01G483500 chr5A 82.500 120 18 2 1451 1569 654407005 654407122 8.920000e-18 102.0
6 TraesCS5A01G483500 chr5D 94.035 2129 90 14 1914 4028 527431594 527433699 0.000000e+00 3193.0
7 TraesCS5A01G483500 chr5D 92.657 749 36 7 855 1600 527430650 527431382 0.000000e+00 1061.0
8 TraesCS5A01G483500 chr5D 91.904 667 38 9 4383 5037 527434118 527434780 0.000000e+00 918.0
9 TraesCS5A01G483500 chr5D 86.777 726 79 11 2605 3320 527198772 527199490 0.000000e+00 793.0
10 TraesCS5A01G483500 chr5D 94.529 329 10 5 4026 4351 527433726 527434049 7.530000e-138 501.0
11 TraesCS5A01G483500 chr5D 92.667 300 12 6 1028 1318 54191303 54191005 1.680000e-114 424.0
12 TraesCS5A01G483500 chr5D 81.802 555 46 23 4464 4979 527492515 527493053 1.010000e-111 414.0
13 TraesCS5A01G483500 chr5D 88.889 126 12 2 1599 1723 527431446 527431570 2.430000e-33 154.0
14 TraesCS5A01G483500 chr5D 86.441 118 16 0 3793 3910 527200120 527200237 4.090000e-26 130.0
15 TraesCS5A01G483500 chr5D 80.531 113 16 3 1457 1569 527197863 527197969 1.160000e-11 82.4
16 TraesCS5A01G483500 chr5B 92.932 1047 49 13 1599 2642 663796691 663797715 0.000000e+00 1500.0
17 TraesCS5A01G483500 chr5B 96.184 629 20 2 2605 3233 663797710 663798334 0.000000e+00 1026.0
18 TraesCS5A01G483500 chr5B 88.000 800 37 29 815 1600 663795875 663796629 0.000000e+00 891.0
19 TraesCS5A01G483500 chr5B 90.720 625 40 6 4411 5024 663800591 663801208 0.000000e+00 817.0
20 TraesCS5A01G483500 chr5B 89.442 663 37 9 4383 5024 663922715 663923365 0.000000e+00 806.0
21 TraesCS5A01G483500 chr5B 87.228 689 62 14 2605 3282 663521918 663522591 0.000000e+00 761.0
22 TraesCS5A01G483500 chr5B 85.889 574 52 16 4411 4968 663987709 663988269 7.270000e-163 584.0
23 TraesCS5A01G483500 chr5B 82.914 556 36 28 4464 4979 664016339 664016875 3.580000e-121 446.0
24 TraesCS5A01G483500 chr5B 94.158 291 15 1 3413 3703 663798355 663798643 4.630000e-120 442.0
25 TraesCS5A01G483500 chr5B 90.816 294 16 7 1028 1312 674913395 674913686 2.850000e-102 383.0
26 TraesCS5A01G483500 chr5B 93.860 114 7 0 3659 3772 663798632 663798745 6.700000e-39 172.0
27 TraesCS5A01G483500 chr5B 91.870 123 10 0 3787 3909 663798814 663798936 6.700000e-39 172.0
28 TraesCS5A01G483500 chr5B 83.333 132 18 4 1457 1586 663520742 663520871 8.860000e-23 119.0
29 TraesCS5A01G483500 chr5B 96.610 59 2 0 4973 5031 663988301 663988359 1.150000e-16 99.0
30 TraesCS5A01G483500 chr5B 80.734 109 10 7 3931 4028 663799007 663799115 1.940000e-09 75.0
31 TraesCS5A01G483500 chr2A 96.898 806 24 1 1 806 532077868 532078672 0.000000e+00 1349.0
32 TraesCS5A01G483500 chr2A 95.676 370 16 0 218 587 749546570 749546939 3.360000e-166 595.0
33 TraesCS5A01G483500 chr2A 98.198 222 4 0 1 222 749526032 749526253 6.120000e-104 388.0
34 TraesCS5A01G483500 chr7A 91.677 805 52 4 1 792 715931137 715931939 0.000000e+00 1101.0
35 TraesCS5A01G483500 chr2B 88.303 778 83 7 3 778 727311596 727312367 0.000000e+00 926.0
36 TraesCS5A01G483500 chr2B 82.168 701 115 10 3 699 396417347 396416653 1.210000e-165 593.0
37 TraesCS5A01G483500 chr2B 88.667 300 22 7 1028 1318 23657083 23656787 6.200000e-94 355.0
38 TraesCS5A01G483500 chr3B 90.164 671 55 4 2 670 46100282 46100943 0.000000e+00 863.0
39 TraesCS5A01G483500 chr3B 89.667 300 20 5 1028 1318 417173245 417173542 6.160000e-99 372.0
40 TraesCS5A01G483500 chr3A 95.842 505 21 0 4 508 581627810 581627306 0.000000e+00 817.0
41 TraesCS5A01G483500 chr3A 92.070 227 4 3 555 767 581626977 581626751 1.760000e-79 307.0
42 TraesCS5A01G483500 chr7B 84.485 651 93 7 2 646 688599378 688600026 1.980000e-178 636.0
43 TraesCS5A01G483500 chr7B 89.333 300 21 6 1028 1318 540128978 540128681 2.870000e-97 366.0
44 TraesCS5A01G483500 chr6B 90.667 300 17 6 1028 1318 619067697 619067400 6.120000e-104 388.0
45 TraesCS5A01G483500 chr1B 90.333 300 19 3 1028 1318 102154524 102154822 7.910000e-103 385.0
46 TraesCS5A01G483500 chr4D 75.123 812 147 47 1 795 502029861 502029088 3.760000e-86 329.0
47 TraesCS5A01G483500 chrUn 78.571 350 48 21 448 793 396803960 396803634 6.610000e-49 206.0
48 TraesCS5A01G483500 chr3D 78.758 306 40 19 471 769 110311619 110311332 1.110000e-41 182.0
49 TraesCS5A01G483500 chr1D 85.629 167 17 5 629 792 235574122 235573960 8.670000e-38 169.0


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 TraesCS5A01G483500 chr5A 654559490 654564526 5036 False 9302.000000 9302 100.000000 1 5037 1 chr5A.!!$F1 5036
1 TraesCS5A01G483500 chr5A 654571381 654571998 617 False 542.000000 542 83.281000 4410 5020 1 chr5A.!!$F2 610
2 TraesCS5A01G483500 chr5A 654407005 654410249 3244 False 383.333333 944 84.906667 1451 3870 3 chr5A.!!$F4 2419
3 TraesCS5A01G483500 chr5D 527430650 527434780 4130 False 1165.400000 3193 92.402800 855 5037 5 chr5D.!!$F3 4182
4 TraesCS5A01G483500 chr5D 527492515 527493053 538 False 414.000000 414 81.802000 4464 4979 1 chr5D.!!$F1 515
5 TraesCS5A01G483500 chr5D 527197863 527200237 2374 False 335.133333 793 84.583000 1457 3910 3 chr5D.!!$F2 2453
6 TraesCS5A01G483500 chr5B 663922715 663923365 650 False 806.000000 806 89.442000 4383 5024 1 chr5B.!!$F1 641
7 TraesCS5A01G483500 chr5B 663795875 663801208 5333 False 636.875000 1500 91.057250 815 5024 8 chr5B.!!$F5 4209
8 TraesCS5A01G483500 chr5B 664016339 664016875 536 False 446.000000 446 82.914000 4464 4979 1 chr5B.!!$F2 515
9 TraesCS5A01G483500 chr5B 663520742 663522591 1849 False 440.000000 761 85.280500 1457 3282 2 chr5B.!!$F4 1825
10 TraesCS5A01G483500 chr5B 663987709 663988359 650 False 341.500000 584 91.249500 4411 5031 2 chr5B.!!$F6 620
11 TraesCS5A01G483500 chr2A 532077868 532078672 804 False 1349.000000 1349 96.898000 1 806 1 chr2A.!!$F1 805
12 TraesCS5A01G483500 chr7A 715931137 715931939 802 False 1101.000000 1101 91.677000 1 792 1 chr7A.!!$F1 791
13 TraesCS5A01G483500 chr2B 727311596 727312367 771 False 926.000000 926 88.303000 3 778 1 chr2B.!!$F1 775
14 TraesCS5A01G483500 chr2B 396416653 396417347 694 True 593.000000 593 82.168000 3 699 1 chr2B.!!$R2 696
15 TraesCS5A01G483500 chr3B 46100282 46100943 661 False 863.000000 863 90.164000 2 670 1 chr3B.!!$F1 668
16 TraesCS5A01G483500 chr3A 581626751 581627810 1059 True 562.000000 817 93.956000 4 767 2 chr3A.!!$R1 763
17 TraesCS5A01G483500 chr7B 688599378 688600026 648 False 636.000000 636 84.485000 2 646 1 chr7B.!!$F1 644
18 TraesCS5A01G483500 chr4D 502029088 502029861 773 True 329.000000 329 75.123000 1 795 1 chr4D.!!$R1 794

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
853 1157 1.001974 CTCGTGGATGAAACACCTCCA 59.998 52.381 0.0 0.0 40.14 3.86 F
1026 1340 0.240945 AAAAATTCGGCACAGGAGCG 59.759 50.000 0.0 0.0 34.64 5.03 F
1029 1343 1.021390 AATTCGGCACAGGAGCGAAG 61.021 55.000 0.0 0.0 33.24 3.79 F
1588 1913 1.133513 AGTGGCAAATCACCAGGTTCA 60.134 47.619 0.0 0.0 38.04 3.18 F
1590 1915 1.686052 TGGCAAATCACCAGGTTCAAC 59.314 47.619 0.0 0.0 32.06 3.18 F
1802 2192 2.234414 CAGCCATACAAGCATTTTGGGT 59.766 45.455 0.0 0.0 38.65 4.51 F
1899 2290 2.241722 CGCACTTTCTTTTACGCATGG 58.758 47.619 0.0 0.0 0.00 3.66 F
2497 3614 2.363038 TCAGTACTTGCTGTTACGGTGT 59.637 45.455 0.0 0.0 37.70 4.16 F
3925 5595 1.749634 ACTAACTGGTAGCCTAGCACG 59.250 52.381 0.0 0.0 32.45 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2671 2.035961 TCGTTTCACCTCTCCTGAAGTG 59.964 50.000 0.00 0.00 36.31 3.16 R
2884 4296 0.906756 AGCAGCTGGAGTAGGAGCAA 60.907 55.000 17.12 0.00 37.70 3.91 R
2969 4384 2.618053 GTCGCATAGTAAGCAGGTGTT 58.382 47.619 0.00 0.00 0.00 3.32 R
3326 4741 1.002624 ACATCAACGGGCCGACATT 60.003 52.632 35.78 14.51 0.00 2.71 R
3495 4916 3.245990 ACGTACGAGGCAAAAGTACAAAC 59.754 43.478 24.41 0.00 40.32 2.93 R
3592 5013 2.203070 GCCTGGAGCGTACCCATG 60.203 66.667 0.00 0.00 32.49 3.66 R
3861 5527 0.663688 GCAGCAGCTGAATCCATCTG 59.336 55.000 27.39 14.06 39.01 2.90 R
3929 5599 0.248458 ACTTGCGCAAAACGGTCAAG 60.248 50.000 25.01 11.35 43.39 3.02 R
4905 7816 3.120408 CGTGCTTGATCCTCAGAAACTTG 60.120 47.826 0.00 0.00 0.00 3.16 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
394 399 3.458163 CTCCGTCCAAGCCCGCTA 61.458 66.667 0.00 0.00 0.00 4.26
457 462 2.125229 CAGCAGCCGCAGATCTGT 60.125 61.111 23.38 0.84 42.27 3.41
811 1114 3.900888 AAGAGTTCTTGGGGCCGA 58.099 55.556 0.00 0.00 34.38 5.54
812 1115 1.679898 AAGAGTTCTTGGGGCCGAG 59.320 57.895 0.00 0.00 34.38 4.63
813 1116 1.128188 AAGAGTTCTTGGGGCCGAGT 61.128 55.000 0.00 0.00 34.38 4.18
848 1152 1.225855 TGCACTCGTGGATGAAACAC 58.774 50.000 0.00 0.00 35.55 3.32
853 1157 1.001974 CTCGTGGATGAAACACCTCCA 59.998 52.381 0.00 0.00 40.14 3.86
857 1161 3.222603 GTGGATGAAACACCTCCAAGTT 58.777 45.455 0.00 0.00 43.02 2.66
886 1190 5.078411 TGAAACTCTGAATACTGCCTCTC 57.922 43.478 0.00 0.00 0.00 3.20
887 1191 3.791973 AACTCTGAATACTGCCTCTCG 57.208 47.619 0.00 0.00 0.00 4.04
888 1192 3.006112 ACTCTGAATACTGCCTCTCGA 57.994 47.619 0.00 0.00 0.00 4.04
889 1193 2.948979 ACTCTGAATACTGCCTCTCGAG 59.051 50.000 5.93 5.93 0.00 4.04
890 1194 2.948979 CTCTGAATACTGCCTCTCGAGT 59.051 50.000 13.13 0.00 0.00 4.18
891 1195 2.946329 TCTGAATACTGCCTCTCGAGTC 59.054 50.000 13.13 3.85 0.00 3.36
892 1196 2.948979 CTGAATACTGCCTCTCGAGTCT 59.051 50.000 13.13 0.00 0.00 3.24
957 1267 1.672356 GTCACCTGCGCTCACCAAT 60.672 57.895 9.73 0.00 0.00 3.16
966 1276 1.450312 GCTCACCAATCCCACTCCG 60.450 63.158 0.00 0.00 0.00 4.63
970 1280 2.190578 CCAATCCCACTCCGCTCC 59.809 66.667 0.00 0.00 0.00 4.70
971 1281 2.669133 CCAATCCCACTCCGCTCCA 61.669 63.158 0.00 0.00 0.00 3.86
972 1282 1.450312 CAATCCCACTCCGCTCCAC 60.450 63.158 0.00 0.00 0.00 4.02
973 1283 1.613630 AATCCCACTCCGCTCCACT 60.614 57.895 0.00 0.00 0.00 4.00
974 1284 1.617947 AATCCCACTCCGCTCCACTC 61.618 60.000 0.00 0.00 0.00 3.51
975 1285 3.775654 CCCACTCCGCTCCACTCC 61.776 72.222 0.00 0.00 0.00 3.85
976 1286 2.997315 CCACTCCGCTCCACTCCA 60.997 66.667 0.00 0.00 0.00 3.86
977 1287 2.362369 CCACTCCGCTCCACTCCAT 61.362 63.158 0.00 0.00 0.00 3.41
978 1288 1.599047 CACTCCGCTCCACTCCATT 59.401 57.895 0.00 0.00 0.00 3.16
982 1292 1.144936 CCGCTCCACTCCATTCCTC 59.855 63.158 0.00 0.00 0.00 3.71
1012 1326 4.037565 GGACGAACTCCACCAAAGAAAAAT 59.962 41.667 0.00 0.00 39.21 1.82
1026 1340 0.240945 AAAAATTCGGCACAGGAGCG 59.759 50.000 0.00 0.00 34.64 5.03
1029 1343 1.021390 AATTCGGCACAGGAGCGAAG 61.021 55.000 0.00 0.00 33.24 3.79
1431 1746 3.617531 CGTGCTCATAAGGTCTGGAGTTT 60.618 47.826 0.00 0.00 0.00 2.66
1495 1817 1.597663 CGCGTATGAATCTTTCCACCC 59.402 52.381 0.00 0.00 0.00 4.61
1517 1839 5.356470 CCCTAAAGAAAGAATGGAGCTTGAG 59.644 44.000 0.00 0.00 0.00 3.02
1525 1848 4.446371 AGAATGGAGCTTGAGGATTTACG 58.554 43.478 0.00 0.00 0.00 3.18
1530 1853 1.134371 AGCTTGAGGATTTACGGCTCC 60.134 52.381 0.00 0.00 0.00 4.70
1588 1913 1.133513 AGTGGCAAATCACCAGGTTCA 60.134 47.619 0.00 0.00 38.04 3.18
1590 1915 1.686052 TGGCAAATCACCAGGTTCAAC 59.314 47.619 0.00 0.00 32.06 3.18
1672 2062 4.870426 AGCCACTATCACAAGTTTACGATG 59.130 41.667 0.00 0.00 0.00 3.84
1753 2143 8.434733 GGGAGAACCTGAAATACATTAGTTAC 57.565 38.462 0.00 0.00 35.85 2.50
1754 2144 8.044908 GGGAGAACCTGAAATACATTAGTTACA 58.955 37.037 0.00 0.00 35.85 2.41
1755 2145 9.444600 GGAGAACCTGAAATACATTAGTTACAA 57.555 33.333 0.00 0.00 0.00 2.41
1801 2191 2.419021 CCAGCCATACAAGCATTTTGGG 60.419 50.000 0.00 0.00 0.00 4.12
1802 2192 2.234414 CAGCCATACAAGCATTTTGGGT 59.766 45.455 0.00 0.00 38.65 4.51
1886 2277 2.472816 CAATGAACTTTGCCGCACTTT 58.527 42.857 0.00 0.00 0.00 2.66
1899 2290 2.241722 CGCACTTTCTTTTACGCATGG 58.758 47.619 0.00 0.00 0.00 3.66
1901 2292 2.979813 GCACTTTCTTTTACGCATGGTG 59.020 45.455 0.00 0.00 0.00 4.17
2055 2459 4.885907 ACATCCAGCAATCAACTTCATAGG 59.114 41.667 0.00 0.00 0.00 2.57
2108 2512 6.910536 AACTGAGTGTTTAGTGTTCTTCTG 57.089 37.500 0.00 0.00 34.84 3.02
2109 2513 4.811557 ACTGAGTGTTTAGTGTTCTTCTGC 59.188 41.667 0.00 0.00 0.00 4.26
2111 2515 4.811024 TGAGTGTTTAGTGTTCTTCTGCTG 59.189 41.667 0.00 0.00 0.00 4.41
2401 3491 7.134815 GCTTATGTATGGTCTTTTGCATACAG 58.865 38.462 2.55 0.00 38.13 2.74
2494 3611 3.650139 ACTTCAGTACTTGCTGTTACGG 58.350 45.455 0.00 0.00 37.70 4.02
2495 3612 3.069158 ACTTCAGTACTTGCTGTTACGGT 59.931 43.478 0.00 0.00 37.70 4.83
2496 3613 3.021269 TCAGTACTTGCTGTTACGGTG 57.979 47.619 0.00 0.00 37.70 4.94
2497 3614 2.363038 TCAGTACTTGCTGTTACGGTGT 59.637 45.455 0.00 0.00 37.70 4.16
2498 3615 3.569277 TCAGTACTTGCTGTTACGGTGTA 59.431 43.478 0.00 0.00 37.70 2.90
2499 3616 4.037803 TCAGTACTTGCTGTTACGGTGTAA 59.962 41.667 0.00 0.00 37.70 2.41
2500 3617 4.746115 CAGTACTTGCTGTTACGGTGTAAA 59.254 41.667 0.00 0.00 0.00 2.01
2534 3656 5.330455 TGTAGAAGCAAGTCGAGATTGAT 57.670 39.130 13.16 5.04 0.00 2.57
2691 4097 5.695816 GCATTTACCTGCACTGAATTTTCAA 59.304 36.000 0.00 0.00 41.87 2.69
2884 4296 3.130264 TGCATCACCCAAGCACTTT 57.870 47.368 0.00 0.00 32.55 2.66
2969 4384 2.632512 TCCTGTGACTGCTCAATACACA 59.367 45.455 0.00 0.00 38.78 3.72
3088 4503 4.320788 GCCTCCTTTGCAATATCACTATGC 60.321 45.833 0.00 0.00 0.00 3.14
3271 4686 6.321945 GGTCCTAGTACTTTCCTCTTTCCTAG 59.678 46.154 0.00 0.00 0.00 3.02
3286 4701 4.505313 TTCCTAGTATCTGCTACATGCG 57.495 45.455 0.00 0.00 46.63 4.73
3290 4705 4.216472 CCTAGTATCTGCTACATGCGAAGA 59.784 45.833 0.00 0.00 46.63 2.87
3295 4710 3.860641 TCTGCTACATGCGAAGAAATCA 58.139 40.909 0.00 0.00 46.63 2.57
3300 4715 7.065683 TCTGCTACATGCGAAGAAATCATTTTA 59.934 33.333 0.00 0.00 46.63 1.52
3326 4741 7.389330 ACAAAACAATCTGTATACATCCGTCAA 59.611 33.333 5.91 0.00 0.00 3.18
3410 4827 2.783135 ACTACTTGCAGGGACAATGTG 58.217 47.619 0.00 0.00 0.00 3.21
3495 4916 5.693104 GCTACATGCACAAATAATTGATGGG 59.307 40.000 0.00 0.00 42.31 4.00
3592 5013 4.687215 TGCAGCTCGTCAGGCACC 62.687 66.667 0.00 0.00 0.00 5.01
3641 5062 4.760047 CGGAGGAACCCCACAGCG 62.760 72.222 0.00 0.00 34.64 5.18
3861 5527 5.353956 TGCTGATGTGTTTGGTATGATGTAC 59.646 40.000 0.00 0.00 0.00 2.90
3899 5569 4.569943 CTGCTCTTTGGTTTGCTAGACTA 58.430 43.478 0.00 0.00 0.00 2.59
3925 5595 1.749634 ACTAACTGGTAGCCTAGCACG 59.250 52.381 0.00 0.00 32.45 5.34
3929 5599 0.315568 CTGGTAGCCTAGCACGATCC 59.684 60.000 0.00 0.00 32.06 3.36
3979 5709 1.754226 GGTCATTGTGTTTGTGGGTGT 59.246 47.619 0.00 0.00 0.00 4.16
3983 5713 4.693095 GTCATTGTGTTTGTGGGTGTTTTT 59.307 37.500 0.00 0.00 0.00 1.94
4078 5840 3.868757 TCCAGTACAAGATTCTCACCG 57.131 47.619 0.00 0.00 0.00 4.94
4079 5841 3.162666 TCCAGTACAAGATTCTCACCGT 58.837 45.455 0.00 0.00 0.00 4.83
4278 6043 6.154203 TGATGATAAGTCACATGAGAGTCC 57.846 41.667 0.00 0.00 37.14 3.85
4330 6095 8.737175 TGTATCTCAAATAAGTCGAGTAGTTGT 58.263 33.333 13.08 1.75 30.57 3.32
4351 6802 6.271488 TGTCCAATGATGAATTTGGAAGAC 57.729 37.500 5.99 0.00 31.45 3.01
4372 6834 0.892755 TTCATAGTCTGAACCGCGGT 59.107 50.000 28.70 28.70 38.97 5.68
4375 6837 0.172803 ATAGTCTGAACCGCGGTGTC 59.827 55.000 34.95 28.37 0.00 3.67
4378 6840 2.256158 CTGAACCGCGGTGTCGTA 59.744 61.111 34.95 15.29 38.89 3.43
4379 6841 1.800315 CTGAACCGCGGTGTCGTAG 60.800 63.158 34.95 20.61 38.89 3.51
4380 6842 2.256461 GAACCGCGGTGTCGTAGT 59.744 61.111 34.95 15.03 38.89 2.73
4381 6843 1.799121 GAACCGCGGTGTCGTAGTC 60.799 63.158 34.95 20.16 38.89 2.59
4441 7302 3.815569 CTCTGCGCCGGTCGATCTC 62.816 68.421 20.06 4.92 41.67 2.75
4486 7353 4.374584 CCCCGCAACCCCATTGGA 62.375 66.667 3.62 0.00 38.88 3.53
4562 7438 4.056125 CGGCTCACGTCTGCTCCA 62.056 66.667 8.85 0.00 37.93 3.86
4611 7499 3.902086 GCTCCGGCTCCGTCTACC 61.902 72.222 7.59 0.00 37.81 3.18
4702 7596 4.814294 CCCGTACGAGGTGCTGGC 62.814 72.222 18.76 0.00 0.00 4.85
4905 7816 3.207669 CAGGCGAATGCTCAGGCC 61.208 66.667 0.00 0.00 45.91 5.19
4946 7857 1.002366 GCCTACAACACGCTGATGAG 58.998 55.000 3.13 0.00 0.00 2.90
5013 7951 0.386113 GGCTCGGTACTGACATCTCC 59.614 60.000 0.00 0.00 0.00 3.71
5033 7971 2.830923 CCTCTCTTCTCTTCTGCTCCAA 59.169 50.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 218 4.961511 TGCGCGGTGTGGTGAGTC 62.962 66.667 8.83 0.00 0.00 3.36
394 399 1.136329 AACATGGAGTCTGGCAGGGT 61.136 55.000 15.73 1.40 0.00 4.34
457 462 3.379445 GGCGGGACTCGTCTTGGA 61.379 66.667 0.00 0.00 40.86 3.53
605 895 1.686587 TCTTCTTCACTCAAGACGGCA 59.313 47.619 0.00 0.00 41.13 5.69
806 1109 0.321298 TAACTTGCTGGAACTCGGCC 60.321 55.000 0.00 0.00 46.96 6.13
807 1110 6.201064 CAAGATAACTTGCTGGAACTCGGC 62.201 50.000 0.00 0.00 45.19 5.54
808 1111 3.252974 AGATAACTTGCTGGAACTCGG 57.747 47.619 0.00 0.00 0.00 4.63
809 1112 4.590400 CAAGATAACTTGCTGGAACTCG 57.410 45.455 0.00 0.00 45.19 4.18
848 1152 6.150140 CAGAGTTTCAAAGGATAACTTGGAGG 59.850 42.308 0.00 0.00 40.20 4.30
857 1161 6.823689 GGCAGTATTCAGAGTTTCAAAGGATA 59.176 38.462 0.00 0.00 0.00 2.59
886 1190 4.727725 CGTGTCACTCGAGACTCG 57.272 61.111 21.68 18.91 45.14 4.18
887 1191 1.510204 CGCGTGTCACTCGAGACTC 60.510 63.158 21.68 8.07 39.27 3.36
888 1192 2.172719 GACGCGTGTCACTCGAGACT 62.173 60.000 20.70 0.00 44.82 3.24
889 1193 1.792834 GACGCGTGTCACTCGAGAC 60.793 63.158 20.70 8.79 44.82 3.36
890 1194 2.554775 GACGCGTGTCACTCGAGA 59.445 61.111 20.70 0.00 44.82 4.04
951 1261 1.450312 GAGCGGAGTGGGATTGGTG 60.450 63.158 0.00 0.00 0.00 4.17
954 1264 1.450312 GTGGAGCGGAGTGGGATTG 60.450 63.158 0.00 0.00 0.00 2.67
957 1267 2.680352 GAGTGGAGCGGAGTGGGA 60.680 66.667 0.00 0.00 0.00 4.37
966 1276 0.467804 GAGGAGGAATGGAGTGGAGC 59.532 60.000 0.00 0.00 0.00 4.70
970 1280 1.690219 CGGGGAGGAGGAATGGAGTG 61.690 65.000 0.00 0.00 0.00 3.51
971 1281 1.383248 CGGGGAGGAGGAATGGAGT 60.383 63.158 0.00 0.00 0.00 3.85
972 1282 2.143419 CCGGGGAGGAGGAATGGAG 61.143 68.421 0.00 0.00 45.00 3.86
973 1283 2.040884 CCGGGGAGGAGGAATGGA 60.041 66.667 0.00 0.00 45.00 3.41
974 1284 2.040884 TCCGGGGAGGAGGAATGG 60.041 66.667 0.00 0.00 45.98 3.16
982 1292 3.459063 GGAGTTCGTCCGGGGAGG 61.459 72.222 0.00 1.00 42.97 4.30
1012 1326 2.048222 CTTCGCTCCTGTGCCGAA 60.048 61.111 0.00 0.00 0.00 4.30
1272 1587 0.607217 TGGCGTGGAAGTCGTAGAGA 60.607 55.000 0.00 0.00 36.95 3.10
1395 1710 2.511600 CACGAATCGCCAGGGGAC 60.512 66.667 8.73 0.00 0.00 4.46
1402 1717 0.861837 CCTTATGAGCACGAATCGCC 59.138 55.000 1.15 0.00 0.00 5.54
1431 1746 3.389983 GCATACTCCACCCACTAATACCA 59.610 47.826 0.00 0.00 0.00 3.25
1495 1817 6.176183 TCCTCAAGCTCCATTCTTTCTTTAG 58.824 40.000 0.00 0.00 0.00 1.85
1517 1839 1.940613 GACACATGGAGCCGTAAATCC 59.059 52.381 0.00 0.00 36.05 3.01
1525 1848 1.896220 TTTCAGTGACACATGGAGCC 58.104 50.000 8.59 0.00 0.00 4.70
1530 1853 2.886523 ACCCACATTTCAGTGACACATG 59.113 45.455 8.59 5.28 42.05 3.21
1672 2062 4.107622 CCCAACTTTTCATCAATCATCGC 58.892 43.478 0.00 0.00 0.00 4.58
1755 2145 9.220767 GGAGAATGAAACATTACTGTTCTAACT 57.779 33.333 0.00 0.00 44.83 2.24
1756 2146 8.999431 TGGAGAATGAAACATTACTGTTCTAAC 58.001 33.333 0.00 0.00 44.83 2.34
1757 2147 9.219603 CTGGAGAATGAAACATTACTGTTCTAA 57.780 33.333 0.00 0.00 44.83 2.10
1758 2148 7.334421 GCTGGAGAATGAAACATTACTGTTCTA 59.666 37.037 0.00 0.00 44.83 2.10
1759 2149 6.150140 GCTGGAGAATGAAACATTACTGTTCT 59.850 38.462 0.00 0.00 44.83 3.01
1766 2156 6.422333 TGTATGGCTGGAGAATGAAACATTA 58.578 36.000 0.00 0.00 0.00 1.90
1801 2191 4.736896 GGACCGACAGTGGGCGAC 62.737 72.222 0.51 0.00 38.23 5.19
1816 2206 7.707624 TTAGTTTACGACTGATTAAGAGGGA 57.292 36.000 0.00 0.00 39.48 4.20
1857 2248 2.836262 CAAAGTTCATTGCCAAAGCCA 58.164 42.857 0.00 0.00 38.69 4.75
1886 2277 4.576873 TGAGTTTTCACCATGCGTAAAAGA 59.423 37.500 0.00 0.00 0.00 2.52
1899 2290 4.574599 AGCACTGGAAATGAGTTTTCAC 57.425 40.909 1.05 0.00 44.67 3.18
1901 2292 9.294030 CATTAATAGCACTGGAAATGAGTTTTC 57.706 33.333 0.00 0.00 42.57 2.29
1991 2393 7.173032 AGCATAATATGAGCCAAGATGAATCA 58.827 34.615 4.14 0.00 0.00 2.57
2096 2500 2.483876 GCACACAGCAGAAGAACACTA 58.516 47.619 0.00 0.00 44.79 2.74
2108 2512 2.129607 CAAATTTGACCTGCACACAGC 58.870 47.619 13.08 0.00 43.02 4.40
2109 2513 3.117794 CACAAATTTGACCTGCACACAG 58.882 45.455 24.64 0.00 44.05 3.66
2111 2515 3.435105 TCACAAATTTGACCTGCACAC 57.565 42.857 24.64 0.00 0.00 3.82
2267 2671 2.035961 TCGTTTCACCTCTCCTGAAGTG 59.964 50.000 0.00 0.00 36.31 3.16
2272 2676 2.224066 ACAGTTCGTTTCACCTCTCCTG 60.224 50.000 0.00 0.00 0.00 3.86
2401 3491 9.624697 TGTGAATTGACTAATTTGATACTTTGC 57.375 29.630 0.00 0.00 36.66 3.68
2494 3611 7.797123 GCTTCTACATGTGTTTACACTTTACAC 59.203 37.037 9.11 0.00 46.55 2.90
2495 3612 7.496263 TGCTTCTACATGTGTTTACACTTTACA 59.504 33.333 9.11 0.00 46.55 2.41
2496 3613 7.857569 TGCTTCTACATGTGTTTACACTTTAC 58.142 34.615 9.11 0.00 46.55 2.01
2497 3614 8.439993 TTGCTTCTACATGTGTTTACACTTTA 57.560 30.769 9.11 2.68 46.55 1.85
2498 3615 6.935741 TGCTTCTACATGTGTTTACACTTT 57.064 33.333 9.11 0.00 46.55 2.66
2499 3616 6.542370 ACTTGCTTCTACATGTGTTTACACTT 59.458 34.615 9.11 5.22 46.55 3.16
2500 3617 6.055588 ACTTGCTTCTACATGTGTTTACACT 58.944 36.000 9.11 0.00 46.55 3.55
2691 4097 8.245195 ACCTACAACAGAATTACCAAAAACAT 57.755 30.769 0.00 0.00 0.00 2.71
2884 4296 0.906756 AGCAGCTGGAGTAGGAGCAA 60.907 55.000 17.12 0.00 37.70 3.91
2969 4384 2.618053 GTCGCATAGTAAGCAGGTGTT 58.382 47.619 0.00 0.00 0.00 3.32
3088 4503 3.673484 CAGGGTGTTGGGCTTGCG 61.673 66.667 0.00 0.00 0.00 4.85
3271 4686 5.463392 TGATTTCTTCGCATGTAGCAGATAC 59.537 40.000 0.00 0.00 46.13 2.24
3300 4715 6.876789 TGACGGATGTATACAGATTGTTTTGT 59.123 34.615 11.91 0.03 0.00 2.83
3321 4736 2.322081 AACGGGCCGACATTTGACG 61.322 57.895 35.78 1.17 0.00 4.35
3326 4741 1.002624 ACATCAACGGGCCGACATT 60.003 52.632 35.78 14.51 0.00 2.71
3410 4827 8.648097 CAACACGCAAAGTATGTATCTATATCC 58.352 37.037 0.00 0.00 0.00 2.59
3495 4916 3.245990 ACGTACGAGGCAAAAGTACAAAC 59.754 43.478 24.41 0.00 40.32 2.93
3592 5013 2.203070 GCCTGGAGCGTACCCATG 60.203 66.667 0.00 0.00 32.49 3.66
3861 5527 0.663688 GCAGCAGCTGAATCCATCTG 59.336 55.000 27.39 14.06 39.01 2.90
3899 5569 3.469750 AGGCTACCAGTTAGTACCACT 57.530 47.619 0.00 0.00 0.00 4.00
3925 5595 0.454452 GCGCAAAACGGTCAAGGATC 60.454 55.000 0.30 0.00 43.93 3.36
3929 5599 0.248458 ACTTGCGCAAAACGGTCAAG 60.248 50.000 25.01 11.35 43.39 3.02
3983 5713 8.160521 TCGATAAGGAGTCAATTTTGTCAAAA 57.839 30.769 12.97 12.97 34.41 2.44
3984 5714 7.737972 TCGATAAGGAGTCAATTTTGTCAAA 57.262 32.000 0.00 0.00 0.00 2.69
4088 5850 7.946655 TTACGATTGCTATCTCGATTTGATT 57.053 32.000 6.58 0.00 38.24 2.57
4298 6063 9.268268 ACTCGACTTATTTGAGATACAACAAAA 57.732 29.630 0.00 0.00 37.93 2.44
4301 6066 8.737175 ACTACTCGACTTATTTGAGATACAACA 58.263 33.333 0.00 0.00 37.93 3.33
4320 6085 6.668541 AATTCATCATTGGACAACTACTCG 57.331 37.500 0.00 0.00 0.00 4.18
4372 6834 2.605837 TGTGCCAAAAGACTACGACA 57.394 45.000 0.00 0.00 0.00 4.35
4375 6837 1.862201 TCGTTGTGCCAAAAGACTACG 59.138 47.619 0.00 0.00 40.94 3.51
4378 6840 2.290641 GTGATCGTTGTGCCAAAAGACT 59.709 45.455 0.00 0.00 0.00 3.24
4379 6841 2.604614 GGTGATCGTTGTGCCAAAAGAC 60.605 50.000 0.00 0.00 0.00 3.01
4380 6842 1.606668 GGTGATCGTTGTGCCAAAAGA 59.393 47.619 0.00 0.00 0.00 2.52
4381 6843 1.336440 TGGTGATCGTTGTGCCAAAAG 59.664 47.619 0.00 0.00 0.00 2.27
4562 7438 2.362632 AGAGGAGGCGCCGTACTT 60.363 61.111 23.20 13.22 43.43 2.24
4669 7563 4.467107 GGGACTCCCTCCTCCGCT 62.467 72.222 6.90 0.00 41.34 5.52
4905 7816 3.120408 CGTGCTTGATCCTCAGAAACTTG 60.120 47.826 0.00 0.00 0.00 3.16
5013 7951 3.257873 TGTTGGAGCAGAAGAGAAGAGAG 59.742 47.826 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.