Multiple sequence alignment - TraesCS6B01G167300

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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 TraesCS6B01G167300 chr6B 100.000 2942 0 0 1 2942 176133676 176130735 0.000000e+00 5433.0
1 TraesCS6B01G167300 chr6B 97.117 1665 23 8 1 1661 176164851 176163208 0.000000e+00 2785.0
2 TraesCS6B01G167300 chr6B 97.057 1665 24 8 1 1661 176188728 176187085 0.000000e+00 2780.0
3 TraesCS6B01G167300 chr6B 96.212 1663 39 9 1 1661 176140639 176138999 0.000000e+00 2700.0
4 TraesCS6B01G167300 chr6B 96.450 676 24 0 986 1661 176249877 176249202 0.000000e+00 1116.0
5 TraesCS6B01G167300 chr6B 91.711 567 45 2 2378 2942 176115433 176114867 0.000000e+00 785.0
6 TraesCS6B01G167300 chr6B 81.009 337 39 17 542 868 176250296 176249975 8.140000e-61 244.0
7 TraesCS6B01G167300 chr6B 100.000 44 0 0 921 964 176132797 176132754 6.760000e-12 82.4
8 TraesCS6B01G167300 chrUn 97.057 1665 23 9 1 1661 78306612 78308254 0.000000e+00 2780.0
9 TraesCS6B01G167300 chrUn 96.877 1665 25 10 1 1661 78289794 78291435 0.000000e+00 2761.0
10 TraesCS6B01G167300 chrUn 97.035 1248 11 9 1 1244 356275318 356274093 0.000000e+00 2076.0
11 TraesCS6B01G167300 chrUn 97.035 1248 12 8 1 1244 379821465 379822691 0.000000e+00 2076.0
12 TraesCS6B01G167300 chrUn 99.546 441 1 1 1 441 274930895 274931334 0.000000e+00 802.0
13 TraesCS6B01G167300 chr6D 90.707 1302 82 20 367 1661 91821355 91820086 0.000000e+00 1698.0
14 TraesCS6B01G167300 chr6D 92.910 536 35 3 1660 2193 45411489 45410955 0.000000e+00 776.0
15 TraesCS6B01G167300 chr6D 93.095 391 27 0 992 1382 91830775 91830385 9.150000e-160 573.0
16 TraesCS6B01G167300 chr6D 96.774 124 3 1 2192 2315 91819960 91819838 3.840000e-49 206.0
17 TraesCS6B01G167300 chr6D 93.043 115 5 1 2204 2315 91829751 91829637 6.520000e-37 165.0
18 TraesCS6B01G167300 chr6A 89.308 982 68 18 682 1661 111449876 111448930 0.000000e+00 1197.0
19 TraesCS6B01G167300 chr6A 82.635 1169 120 41 542 1661 111531898 111530764 0.000000e+00 957.0
20 TraesCS6B01G167300 chr6A 90.106 566 53 3 2379 2942 540015593 540016157 0.000000e+00 732.0
21 TraesCS6B01G167300 chr6A 88.462 286 30 3 367 650 111450162 111449878 2.810000e-90 342.0
22 TraesCS6B01G167300 chr6A 95.000 40 2 0 2276 2315 111448563 111448524 2.450000e-06 63.9
23 TraesCS6B01G167300 chr1D 92.063 567 43 2 2378 2942 362052061 362051495 0.000000e+00 797.0
24 TraesCS6B01G167300 chr1D 92.523 535 33 5 1660 2193 136946291 136946819 0.000000e+00 760.0
25 TraesCS6B01G167300 chr7A 93.284 536 33 3 1660 2193 275967382 275967916 0.000000e+00 787.0
26 TraesCS6B01G167300 chr1B 92.818 543 35 4 1660 2198 105295073 105294531 0.000000e+00 784.0
27 TraesCS6B01G167300 chr1B 99.123 114 1 0 2 115 331291262 331291375 3.840000e-49 206.0
28 TraesCS6B01G167300 chr5B 92.910 536 33 5 1660 2193 461616537 461616005 0.000000e+00 774.0
29 TraesCS6B01G167300 chr5B 92.435 542 34 2 1660 2194 642599862 642599321 0.000000e+00 767.0
30 TraesCS6B01G167300 chr5B 89.860 572 50 7 2378 2942 264942918 264942348 0.000000e+00 728.0
31 TraesCS6B01G167300 chr3D 92.477 545 36 5 1660 2202 516079592 516080133 0.000000e+00 774.0
32 TraesCS6B01G167300 chr3D 90.519 559 44 8 2391 2942 199126263 199126819 0.000000e+00 730.0
33 TraesCS6B01G167300 chr3D 92.647 68 1 3 2313 2377 380272302 380272368 8.680000e-16 95.3
34 TraesCS6B01G167300 chr2B 92.871 533 33 5 1660 2191 777138952 777139480 0.000000e+00 769.0
35 TraesCS6B01G167300 chr2B 91.667 72 3 2 2313 2382 30623447 30623517 2.410000e-16 97.1
36 TraesCS6B01G167300 chr7B 92.407 540 35 6 1660 2197 621543549 621544084 0.000000e+00 765.0
37 TraesCS6B01G167300 chr7B 89.375 160 13 4 223 378 303722542 303722383 6.430000e-47 198.0
38 TraesCS6B01G167300 chr7D 89.878 573 51 6 2377 2942 74856010 74855438 0.000000e+00 730.0
39 TraesCS6B01G167300 chr7D 89.649 570 52 6 2378 2940 69052046 69051477 0.000000e+00 719.0
40 TraesCS6B01G167300 chr2D 89.860 572 50 7 2378 2942 575691865 575692435 0.000000e+00 728.0
41 TraesCS6B01G167300 chr2D 89.510 572 54 5 2377 2942 572705676 572706247 0.000000e+00 719.0


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 TraesCS6B01G167300 chr6B 176130735 176133676 2941 True 2757.7 5433 100.000000 1 2942 2 chr6B.!!$R5 2941
1 TraesCS6B01G167300 chr6B 176163208 176164851 1643 True 2785.0 2785 97.117000 1 1661 1 chr6B.!!$R3 1660
2 TraesCS6B01G167300 chr6B 176187085 176188728 1643 True 2780.0 2780 97.057000 1 1661 1 chr6B.!!$R4 1660
3 TraesCS6B01G167300 chr6B 176138999 176140639 1640 True 2700.0 2700 96.212000 1 1661 1 chr6B.!!$R2 1660
4 TraesCS6B01G167300 chr6B 176114867 176115433 566 True 785.0 785 91.711000 2378 2942 1 chr6B.!!$R1 564
5 TraesCS6B01G167300 chr6B 176249202 176250296 1094 True 680.0 1116 88.729500 542 1661 2 chr6B.!!$R6 1119
6 TraesCS6B01G167300 chrUn 78306612 78308254 1642 False 2780.0 2780 97.057000 1 1661 1 chrUn.!!$F2 1660
7 TraesCS6B01G167300 chrUn 78289794 78291435 1641 False 2761.0 2761 96.877000 1 1661 1 chrUn.!!$F1 1660
8 TraesCS6B01G167300 chrUn 356274093 356275318 1225 True 2076.0 2076 97.035000 1 1244 1 chrUn.!!$R1 1243
9 TraesCS6B01G167300 chrUn 379821465 379822691 1226 False 2076.0 2076 97.035000 1 1244 1 chrUn.!!$F4 1243
10 TraesCS6B01G167300 chr6D 91819838 91821355 1517 True 952.0 1698 93.740500 367 2315 2 chr6D.!!$R2 1948
11 TraesCS6B01G167300 chr6D 45410955 45411489 534 True 776.0 776 92.910000 1660 2193 1 chr6D.!!$R1 533
12 TraesCS6B01G167300 chr6D 91829637 91830775 1138 True 369.0 573 93.069000 992 2315 2 chr6D.!!$R3 1323
13 TraesCS6B01G167300 chr6A 111530764 111531898 1134 True 957.0 957 82.635000 542 1661 1 chr6A.!!$R1 1119
14 TraesCS6B01G167300 chr6A 540015593 540016157 564 False 732.0 732 90.106000 2379 2942 1 chr6A.!!$F1 563
15 TraesCS6B01G167300 chr6A 111448524 111450162 1638 True 534.3 1197 90.923333 367 2315 3 chr6A.!!$R2 1948
16 TraesCS6B01G167300 chr1D 362051495 362052061 566 True 797.0 797 92.063000 2378 2942 1 chr1D.!!$R1 564
17 TraesCS6B01G167300 chr1D 136946291 136946819 528 False 760.0 760 92.523000 1660 2193 1 chr1D.!!$F1 533
18 TraesCS6B01G167300 chr7A 275967382 275967916 534 False 787.0 787 93.284000 1660 2193 1 chr7A.!!$F1 533
19 TraesCS6B01G167300 chr1B 105294531 105295073 542 True 784.0 784 92.818000 1660 2198 1 chr1B.!!$R1 538
20 TraesCS6B01G167300 chr5B 461616005 461616537 532 True 774.0 774 92.910000 1660 2193 1 chr5B.!!$R2 533
21 TraesCS6B01G167300 chr5B 642599321 642599862 541 True 767.0 767 92.435000 1660 2194 1 chr5B.!!$R3 534
22 TraesCS6B01G167300 chr5B 264942348 264942918 570 True 728.0 728 89.860000 2378 2942 1 chr5B.!!$R1 564
23 TraesCS6B01G167300 chr3D 516079592 516080133 541 False 774.0 774 92.477000 1660 2202 1 chr3D.!!$F3 542
24 TraesCS6B01G167300 chr3D 199126263 199126819 556 False 730.0 730 90.519000 2391 2942 1 chr3D.!!$F1 551
25 TraesCS6B01G167300 chr2B 777138952 777139480 528 False 769.0 769 92.871000 1660 2191 1 chr2B.!!$F2 531
26 TraesCS6B01G167300 chr7B 621543549 621544084 535 False 765.0 765 92.407000 1660 2197 1 chr7B.!!$F1 537
27 TraesCS6B01G167300 chr7D 74855438 74856010 572 True 730.0 730 89.878000 2377 2942 1 chr7D.!!$R2 565
28 TraesCS6B01G167300 chr7D 69051477 69052046 569 True 719.0 719 89.649000 2378 2940 1 chr7D.!!$R1 562
29 TraesCS6B01G167300 chr2D 575691865 575692435 570 False 728.0 728 89.860000 2378 2942 1 chr2D.!!$F2 564
30 TraesCS6B01G167300 chr2D 572705676 572706247 571 False 719.0 719 89.510000 2377 2942 1 chr2D.!!$F1 565

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
914 950 1.312815 AGCACAAGCACAAGGTCTTC 58.687 50.0 0.0 0.0 45.49 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 2864 0.322975 TCAGGCAGAGAGAACAAGGC 59.677 55.0 0.0 0.0 0.0 4.35 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
640 644 4.488136 TTGCGCGATGGGAGGCAT 62.488 61.111 12.10 0.00 35.03 4.40
909 945 3.670055 CGAAAATAAGCACAAGCACAAGG 59.330 43.478 0.00 0.00 45.49 3.61
910 946 4.620982 GAAAATAAGCACAAGCACAAGGT 58.379 39.130 0.00 0.00 45.49 3.50
911 947 3.923017 AATAAGCACAAGCACAAGGTC 57.077 42.857 0.00 0.00 45.49 3.85
912 948 2.638480 TAAGCACAAGCACAAGGTCT 57.362 45.000 0.00 0.00 45.49 3.85
914 950 1.312815 AGCACAAGCACAAGGTCTTC 58.687 50.000 0.00 0.00 45.49 2.87
918 954 3.675775 GCACAAGCACAAGGTCTTCAAAA 60.676 43.478 0.00 0.00 41.58 2.44
919 955 3.859386 CACAAGCACAAGGTCTTCAAAAC 59.141 43.478 0.00 0.00 0.00 2.43
921 957 3.782889 AGCACAAGGTCTTCAAAACAC 57.217 42.857 0.00 0.00 0.00 3.32
922 958 3.088532 AGCACAAGGTCTTCAAAACACA 58.911 40.909 0.00 0.00 0.00 3.72
925 961 4.610945 CACAAGGTCTTCAAAACACATCC 58.389 43.478 0.00 0.00 0.00 3.51
926 962 4.097741 CACAAGGTCTTCAAAACACATCCA 59.902 41.667 0.00 0.00 0.00 3.41
929 965 3.753272 AGGTCTTCAAAACACATCCATCG 59.247 43.478 0.00 0.00 0.00 3.84
930 966 3.751175 GGTCTTCAAAACACATCCATCGA 59.249 43.478 0.00 0.00 0.00 3.59
931 967 4.215399 GGTCTTCAAAACACATCCATCGAA 59.785 41.667 0.00 0.00 0.00 3.71
932 968 5.278266 GGTCTTCAAAACACATCCATCGAAA 60.278 40.000 0.00 0.00 0.00 3.46
933 969 6.205784 GTCTTCAAAACACATCCATCGAAAA 58.794 36.000 0.00 0.00 0.00 2.29
934 970 6.863126 GTCTTCAAAACACATCCATCGAAAAT 59.137 34.615 0.00 0.00 0.00 1.82
935 971 8.020819 GTCTTCAAAACACATCCATCGAAAATA 58.979 33.333 0.00 0.00 0.00 1.40
936 972 8.572185 TCTTCAAAACACATCCATCGAAAATAA 58.428 29.630 0.00 0.00 0.00 1.40
937 973 8.741101 TTCAAAACACATCCATCGAAAATAAG 57.259 30.769 0.00 0.00 0.00 1.73
938 974 6.806249 TCAAAACACATCCATCGAAAATAAGC 59.194 34.615 0.00 0.00 0.00 3.09
939 975 5.895636 AACACATCCATCGAAAATAAGCA 57.104 34.783 0.00 0.00 0.00 3.91
940 976 5.235305 ACACATCCATCGAAAATAAGCAC 57.765 39.130 0.00 0.00 0.00 4.40
941 977 4.699735 ACACATCCATCGAAAATAAGCACA 59.300 37.500 0.00 0.00 0.00 4.57
942 978 5.182950 ACACATCCATCGAAAATAAGCACAA 59.817 36.000 0.00 0.00 0.00 3.33
943 979 5.740569 CACATCCATCGAAAATAAGCACAAG 59.259 40.000 0.00 0.00 0.00 3.16
944 980 4.355543 TCCATCGAAAATAAGCACAAGC 57.644 40.909 0.00 0.00 42.56 4.01
945 981 3.755905 TCCATCGAAAATAAGCACAAGCA 59.244 39.130 0.00 0.00 45.49 3.91
946 982 3.853671 CCATCGAAAATAAGCACAAGCAC 59.146 43.478 0.00 0.00 45.49 4.40
947 983 4.475028 CATCGAAAATAAGCACAAGCACA 58.525 39.130 0.00 0.00 45.49 4.57
948 984 4.560136 TCGAAAATAAGCACAAGCACAA 57.440 36.364 0.00 0.00 45.49 3.33
1477 1762 3.481559 AGACAGAGGAGGAGAAATCCA 57.518 47.619 0.00 0.00 39.47 3.41
1521 1806 1.066143 GCGGTGGAGATTCTTGAAGGA 60.066 52.381 0.00 0.00 0.00 3.36
1587 1872 2.167219 CGTAGGGCTCGTCGACGTA 61.167 63.158 34.40 21.01 40.80 3.57
1617 1902 1.565156 GCGTGCTGTCGTGGATGAAA 61.565 55.000 0.00 0.00 0.00 2.69
1653 1938 2.412089 GTCCGGTGACAAGATTTTCGAG 59.588 50.000 0.00 0.00 41.37 4.04
1665 1950 3.918253 TTTCGAGGCCGCCATTGCT 62.918 57.895 13.15 0.00 35.37 3.91
1751 2036 3.258372 TCCGAAACAGCTAGACACATTCT 59.742 43.478 0.00 0.00 38.51 2.40
1802 2087 6.401796 GCAATTTGGAACTGCAGAAATGATTC 60.402 38.462 23.35 12.25 36.09 2.52
1970 2256 2.940994 TCTTCAACCGGTTTGGATGA 57.059 45.000 19.55 16.82 46.81 2.92
2055 2347 2.479566 TGGCTTTTGTGTTTTTGGCA 57.520 40.000 0.00 0.00 0.00 4.92
2092 2385 3.443976 AGCTTGCCGTTACTTTTGTTTG 58.556 40.909 0.00 0.00 0.00 2.93
2108 2401 9.016438 ACTTTTGTTTGAAACTGTAAGACCTTA 57.984 29.630 17.52 0.00 37.43 2.69
2177 2549 4.787280 CAGAGGCCGGGGAGTCCT 62.787 72.222 9.58 0.00 0.00 3.85
2213 2585 1.000283 GTGAGCCGCTAGCACATATCT 60.000 52.381 16.45 1.43 44.23 1.98
2279 2817 7.148738 CGGCTGCTTGATGTAATAATGTAGTAG 60.149 40.741 0.00 0.00 0.00 2.57
2315 2853 7.554476 TCCATTTATTCGGTGTTGATTATGTCA 59.446 33.333 0.00 0.00 34.25 3.58
2316 2854 7.857389 CCATTTATTCGGTGTTGATTATGTCAG 59.143 37.037 0.00 0.00 38.29 3.51
2317 2855 4.882671 ATTCGGTGTTGATTATGTCAGC 57.117 40.909 0.00 0.00 38.29 4.26
2318 2856 3.610040 TCGGTGTTGATTATGTCAGCT 57.390 42.857 0.00 0.00 38.70 4.24
2319 2857 3.261580 TCGGTGTTGATTATGTCAGCTG 58.738 45.455 7.63 7.63 38.70 4.24
2320 2858 2.223112 CGGTGTTGATTATGTCAGCTGC 60.223 50.000 9.47 4.92 38.70 5.25
2321 2859 3.012518 GGTGTTGATTATGTCAGCTGCT 58.987 45.455 9.47 0.00 38.70 4.24
2322 2860 4.191544 GGTGTTGATTATGTCAGCTGCTA 58.808 43.478 9.47 0.00 38.70 3.49
2323 2861 4.272018 GGTGTTGATTATGTCAGCTGCTAG 59.728 45.833 9.47 0.00 38.70 3.42
2324 2862 5.111989 GTGTTGATTATGTCAGCTGCTAGA 58.888 41.667 9.47 0.00 38.70 2.43
2325 2863 5.582269 GTGTTGATTATGTCAGCTGCTAGAA 59.418 40.000 9.47 4.17 38.70 2.10
2326 2864 5.814188 TGTTGATTATGTCAGCTGCTAGAAG 59.186 40.000 9.47 0.00 38.70 2.85
2327 2865 4.375272 TGATTATGTCAGCTGCTAGAAGC 58.625 43.478 15.63 15.63 43.88 3.86
2328 2866 2.898729 TATGTCAGCTGCTAGAAGCC 57.101 50.000 19.77 4.76 44.68 4.35
2329 2867 1.202330 ATGTCAGCTGCTAGAAGCCT 58.798 50.000 19.77 3.95 44.68 4.58
2330 2868 0.979665 TGTCAGCTGCTAGAAGCCTT 59.020 50.000 19.77 0.00 44.68 4.35
2331 2869 1.338484 TGTCAGCTGCTAGAAGCCTTG 60.338 52.381 19.77 12.17 44.68 3.61
2332 2870 0.979665 TCAGCTGCTAGAAGCCTTGT 59.020 50.000 19.77 0.00 44.68 3.16
2333 2871 1.349026 TCAGCTGCTAGAAGCCTTGTT 59.651 47.619 19.77 0.00 44.68 2.83
2334 2872 1.736681 CAGCTGCTAGAAGCCTTGTTC 59.263 52.381 19.77 0.00 44.68 3.18
2335 2873 1.627834 AGCTGCTAGAAGCCTTGTTCT 59.372 47.619 19.77 0.00 44.68 3.01
2336 2874 2.006169 GCTGCTAGAAGCCTTGTTCTC 58.994 52.381 12.21 0.00 41.51 2.87
2337 2875 2.354604 GCTGCTAGAAGCCTTGTTCTCT 60.355 50.000 12.21 0.00 41.51 3.10
2338 2876 3.520569 CTGCTAGAAGCCTTGTTCTCTC 58.479 50.000 0.00 0.00 41.51 3.20
2339 2877 3.169099 TGCTAGAAGCCTTGTTCTCTCT 58.831 45.455 0.00 0.00 41.51 3.10
2340 2878 3.056250 TGCTAGAAGCCTTGTTCTCTCTG 60.056 47.826 0.00 0.00 41.51 3.35
2341 2879 2.470983 AGAAGCCTTGTTCTCTCTGC 57.529 50.000 0.00 0.00 30.55 4.26
2342 2880 1.003003 AGAAGCCTTGTTCTCTCTGCC 59.997 52.381 0.00 0.00 30.55 4.85
2343 2881 1.003003 GAAGCCTTGTTCTCTCTGCCT 59.997 52.381 0.00 0.00 0.00 4.75
2344 2882 0.324285 AGCCTTGTTCTCTCTGCCTG 59.676 55.000 0.00 0.00 0.00 4.85
2345 2883 0.322975 GCCTTGTTCTCTCTGCCTGA 59.677 55.000 0.00 0.00 0.00 3.86
2346 2884 1.271054 GCCTTGTTCTCTCTGCCTGAA 60.271 52.381 0.00 0.00 0.00 3.02
2347 2885 2.697654 CCTTGTTCTCTCTGCCTGAAG 58.302 52.381 0.00 0.00 0.00 3.02
2348 2886 2.301296 CCTTGTTCTCTCTGCCTGAAGA 59.699 50.000 0.00 0.00 0.00 2.87
2349 2887 3.055240 CCTTGTTCTCTCTGCCTGAAGAT 60.055 47.826 0.00 0.00 0.00 2.40
2350 2888 3.606595 TGTTCTCTCTGCCTGAAGATG 57.393 47.619 0.00 0.00 0.00 2.90
2351 2889 3.168292 TGTTCTCTCTGCCTGAAGATGA 58.832 45.455 0.00 0.00 0.00 2.92
2352 2890 3.580022 TGTTCTCTCTGCCTGAAGATGAA 59.420 43.478 0.00 0.00 0.00 2.57
2353 2891 4.040829 TGTTCTCTCTGCCTGAAGATGAAA 59.959 41.667 0.00 0.00 0.00 2.69
2354 2892 4.897509 TCTCTCTGCCTGAAGATGAAAA 57.102 40.909 0.00 0.00 0.00 2.29
2355 2893 4.829968 TCTCTCTGCCTGAAGATGAAAAG 58.170 43.478 0.00 0.00 0.00 2.27
2356 2894 4.285517 TCTCTCTGCCTGAAGATGAAAAGT 59.714 41.667 0.00 0.00 0.00 2.66
2357 2895 4.978099 TCTCTGCCTGAAGATGAAAAGTT 58.022 39.130 0.00 0.00 0.00 2.66
2358 2896 6.014242 TCTCTCTGCCTGAAGATGAAAAGTTA 60.014 38.462 0.00 0.00 0.00 2.24
2359 2897 6.169094 TCTCTGCCTGAAGATGAAAAGTTAG 58.831 40.000 0.00 0.00 0.00 2.34
2360 2898 5.869579 TCTGCCTGAAGATGAAAAGTTAGT 58.130 37.500 0.00 0.00 0.00 2.24
2361 2899 5.702670 TCTGCCTGAAGATGAAAAGTTAGTG 59.297 40.000 0.00 0.00 0.00 2.74
2362 2900 5.376625 TGCCTGAAGATGAAAAGTTAGTGT 58.623 37.500 0.00 0.00 0.00 3.55
2363 2901 6.530120 TGCCTGAAGATGAAAAGTTAGTGTA 58.470 36.000 0.00 0.00 0.00 2.90
2364 2902 7.168219 TGCCTGAAGATGAAAAGTTAGTGTAT 58.832 34.615 0.00 0.00 0.00 2.29
2365 2903 7.665559 TGCCTGAAGATGAAAAGTTAGTGTATT 59.334 33.333 0.00 0.00 0.00 1.89
2366 2904 8.515414 GCCTGAAGATGAAAAGTTAGTGTATTT 58.485 33.333 0.00 0.00 0.00 1.40
2367 2905 9.831737 CCTGAAGATGAAAAGTTAGTGTATTTG 57.168 33.333 0.00 0.00 0.00 2.32
2368 2906 9.334693 CTGAAGATGAAAAGTTAGTGTATTTGC 57.665 33.333 0.00 0.00 0.00 3.68
2369 2907 9.066892 TGAAGATGAAAAGTTAGTGTATTTGCT 57.933 29.630 0.00 0.00 0.00 3.91
2370 2908 9.899226 GAAGATGAAAAGTTAGTGTATTTGCTT 57.101 29.630 0.00 0.00 0.00 3.91
2517 3056 9.486497 AGCATCTTCATATATGAACTGTAACTG 57.514 33.333 21.67 11.20 41.51 3.16
2616 3155 1.222113 GAACTGTAGCAGGGCCTCC 59.778 63.158 0.95 0.00 35.51 4.30
2650 3189 3.695830 AGAACATGTACGGGACAACAT 57.304 42.857 0.00 0.00 42.78 2.71
2653 3192 3.410631 ACATGTACGGGACAACATCAA 57.589 42.857 0.00 0.00 42.78 2.57
2681 3220 1.295423 CGGACTTGGGGTCGACATT 59.705 57.895 18.91 0.00 45.35 2.71
2699 3238 0.816018 TTGTCGCCAACCATGTCGTT 60.816 50.000 0.00 0.00 0.00 3.85
2854 3394 2.158957 ACTCAAAGAGGTGCAGTTTCGA 60.159 45.455 0.00 0.00 33.35 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
909 945 5.356882 TTCGATGGATGTGTTTTGAAGAC 57.643 39.130 0.00 0.00 0.00 3.01
910 946 6.384258 TTTTCGATGGATGTGTTTTGAAGA 57.616 33.333 0.00 0.00 0.00 2.87
911 947 8.741101 TTATTTTCGATGGATGTGTTTTGAAG 57.259 30.769 0.00 0.00 0.00 3.02
912 948 7.328249 GCTTATTTTCGATGGATGTGTTTTGAA 59.672 33.333 0.00 0.00 0.00 2.69
914 950 6.585702 TGCTTATTTTCGATGGATGTGTTTTG 59.414 34.615 0.00 0.00 0.00 2.44
918 954 4.699735 TGTGCTTATTTTCGATGGATGTGT 59.300 37.500 0.00 0.00 0.00 3.72
919 955 5.233957 TGTGCTTATTTTCGATGGATGTG 57.766 39.130 0.00 0.00 0.00 3.21
921 957 4.736793 GCTTGTGCTTATTTTCGATGGATG 59.263 41.667 0.00 0.00 36.03 3.51
922 958 4.398988 TGCTTGTGCTTATTTTCGATGGAT 59.601 37.500 0.00 0.00 40.48 3.41
925 961 4.475028 TGTGCTTGTGCTTATTTTCGATG 58.525 39.130 0.00 0.00 40.48 3.84
926 962 4.764679 TGTGCTTGTGCTTATTTTCGAT 57.235 36.364 0.00 0.00 40.48 3.59
929 965 4.620982 ACCTTGTGCTTGTGCTTATTTTC 58.379 39.130 0.00 0.00 40.48 2.29
930 966 4.342092 AGACCTTGTGCTTGTGCTTATTTT 59.658 37.500 0.00 0.00 40.48 1.82
931 967 3.891366 AGACCTTGTGCTTGTGCTTATTT 59.109 39.130 0.00 0.00 40.48 1.40
932 968 3.490348 AGACCTTGTGCTTGTGCTTATT 58.510 40.909 0.00 0.00 40.48 1.40
933 969 3.146104 AGACCTTGTGCTTGTGCTTAT 57.854 42.857 0.00 0.00 40.48 1.73
934 970 2.638480 AGACCTTGTGCTTGTGCTTA 57.362 45.000 0.00 0.00 40.48 3.09
935 971 1.678101 GAAGACCTTGTGCTTGTGCTT 59.322 47.619 0.00 0.00 40.48 3.91
936 972 1.312815 GAAGACCTTGTGCTTGTGCT 58.687 50.000 0.00 0.00 40.48 4.40
937 973 1.024271 TGAAGACCTTGTGCTTGTGC 58.976 50.000 0.00 0.00 40.20 4.57
938 974 3.781079 TTTGAAGACCTTGTGCTTGTG 57.219 42.857 0.00 0.00 0.00 3.33
939 975 3.509575 TGTTTTGAAGACCTTGTGCTTGT 59.490 39.130 0.00 0.00 0.00 3.16
940 976 3.859386 GTGTTTTGAAGACCTTGTGCTTG 59.141 43.478 0.00 0.00 0.00 4.01
941 977 3.509575 TGTGTTTTGAAGACCTTGTGCTT 59.490 39.130 0.00 0.00 0.00 3.91
942 978 3.088532 TGTGTTTTGAAGACCTTGTGCT 58.911 40.909 0.00 0.00 0.00 4.40
943 979 3.179048 GTGTGTTTTGAAGACCTTGTGC 58.821 45.455 0.00 0.00 0.00 4.57
944 980 4.165779 GTGTGTGTTTTGAAGACCTTGTG 58.834 43.478 0.00 0.00 0.00 3.33
945 981 3.823873 TGTGTGTGTTTTGAAGACCTTGT 59.176 39.130 0.00 0.00 0.00 3.16
946 982 4.165779 GTGTGTGTGTTTTGAAGACCTTG 58.834 43.478 0.00 0.00 0.00 3.61
947 983 3.823873 TGTGTGTGTGTTTTGAAGACCTT 59.176 39.130 0.00 0.00 0.00 3.50
948 984 3.190535 GTGTGTGTGTGTTTTGAAGACCT 59.809 43.478 0.00 0.00 0.00 3.85
1477 1762 0.178990 AACGCCTGCTTCTTTCCCTT 60.179 50.000 0.00 0.00 0.00 3.95
1521 1806 2.381941 GGAGCATTCCCTCAGGGCT 61.382 63.158 4.08 0.00 43.94 5.19
1572 1857 3.507009 GCTACGTCGACGAGCCCT 61.507 66.667 41.52 22.75 43.02 5.19
1617 1902 2.574955 GGACAGCACCTCGGTCACT 61.575 63.158 0.00 0.00 40.93 3.41
1713 1998 3.095912 TCGGACTCTATCCCAACAAGA 57.904 47.619 0.00 0.00 46.04 3.02
1774 2059 0.971386 CTGCAGTTCCAAATTGCCCT 59.029 50.000 5.25 0.00 42.75 5.19
1901 2186 2.029290 AGATCCAGTAACAAACGCTCGT 60.029 45.455 0.00 0.00 0.00 4.18
1902 2187 2.607187 AGATCCAGTAACAAACGCTCG 58.393 47.619 0.00 0.00 0.00 5.03
1970 2256 3.192844 CGCCTATCCTATTACATGACCGT 59.807 47.826 0.00 0.00 0.00 4.83
2092 2385 8.392372 AGGTTCAAATAAGGTCTTACAGTTTC 57.608 34.615 0.00 0.00 0.00 2.78
2234 2609 6.410038 CAGCCGAACAAACAACATTTAAAAG 58.590 36.000 0.00 0.00 0.00 2.27
2279 2817 3.059597 CCGAATAAATGGACGACATCAGC 60.060 47.826 0.00 0.00 39.40 4.26
2315 2853 1.627834 AGAACAAGGCTTCTAGCAGCT 59.372 47.619 14.16 0.00 44.75 4.24
2316 2854 2.006169 GAGAACAAGGCTTCTAGCAGC 58.994 52.381 5.74 5.74 44.75 5.25
2317 2855 3.195396 AGAGAGAACAAGGCTTCTAGCAG 59.805 47.826 0.00 0.00 44.75 4.24
2318 2856 3.056250 CAGAGAGAACAAGGCTTCTAGCA 60.056 47.826 0.00 0.00 44.75 3.49
2319 2857 3.520569 CAGAGAGAACAAGGCTTCTAGC 58.479 50.000 0.00 0.00 41.46 3.42
2320 2858 3.520569 GCAGAGAGAACAAGGCTTCTAG 58.479 50.000 0.00 0.00 30.21 2.43
2321 2859 2.234908 GGCAGAGAGAACAAGGCTTCTA 59.765 50.000 0.00 0.00 30.21 2.10
2322 2860 1.003003 GGCAGAGAGAACAAGGCTTCT 59.997 52.381 0.00 0.00 32.91 2.85
2323 2861 1.003003 AGGCAGAGAGAACAAGGCTTC 59.997 52.381 0.00 0.00 0.00 3.86
2324 2862 1.063183 AGGCAGAGAGAACAAGGCTT 58.937 50.000 0.00 0.00 0.00 4.35
2325 2863 0.324285 CAGGCAGAGAGAACAAGGCT 59.676 55.000 0.00 0.00 35.30 4.58
2326 2864 0.322975 TCAGGCAGAGAGAACAAGGC 59.677 55.000 0.00 0.00 0.00 4.35
2327 2865 2.301296 TCTTCAGGCAGAGAGAACAAGG 59.699 50.000 0.00 0.00 0.00 3.61
2328 2866 3.674528 TCTTCAGGCAGAGAGAACAAG 57.325 47.619 0.00 0.00 0.00 3.16
2329 2867 3.580022 TCATCTTCAGGCAGAGAGAACAA 59.420 43.478 0.00 0.00 0.00 2.83
2330 2868 3.168292 TCATCTTCAGGCAGAGAGAACA 58.832 45.455 0.00 0.00 0.00 3.18
2331 2869 3.883830 TCATCTTCAGGCAGAGAGAAC 57.116 47.619 0.00 0.00 0.00 3.01
2332 2870 4.897509 TTTCATCTTCAGGCAGAGAGAA 57.102 40.909 0.00 0.00 0.00 2.87
2333 2871 4.285517 ACTTTTCATCTTCAGGCAGAGAGA 59.714 41.667 0.00 0.00 0.00 3.10
2334 2872 4.577875 ACTTTTCATCTTCAGGCAGAGAG 58.422 43.478 0.00 0.00 0.00 3.20
2335 2873 4.630644 ACTTTTCATCTTCAGGCAGAGA 57.369 40.909 0.00 0.00 0.00 3.10
2336 2874 5.936956 ACTAACTTTTCATCTTCAGGCAGAG 59.063 40.000 0.00 0.00 0.00 3.35
2337 2875 5.702670 CACTAACTTTTCATCTTCAGGCAGA 59.297 40.000 0.00 0.00 0.00 4.26
2338 2876 5.471456 ACACTAACTTTTCATCTTCAGGCAG 59.529 40.000 0.00 0.00 0.00 4.85
2339 2877 5.376625 ACACTAACTTTTCATCTTCAGGCA 58.623 37.500 0.00 0.00 0.00 4.75
2340 2878 5.948992 ACACTAACTTTTCATCTTCAGGC 57.051 39.130 0.00 0.00 0.00 4.85
2341 2879 9.831737 CAAATACACTAACTTTTCATCTTCAGG 57.168 33.333 0.00 0.00 0.00 3.86
2342 2880 9.334693 GCAAATACACTAACTTTTCATCTTCAG 57.665 33.333 0.00 0.00 0.00 3.02
2343 2881 9.066892 AGCAAATACACTAACTTTTCATCTTCA 57.933 29.630 0.00 0.00 0.00 3.02
2344 2882 9.899226 AAGCAAATACACTAACTTTTCATCTTC 57.101 29.630 0.00 0.00 0.00 2.87
2353 2891 9.720769 ACACATAGTAAGCAAATACACTAACTT 57.279 29.630 0.00 0.00 0.00 2.66
2354 2892 9.720769 AACACATAGTAAGCAAATACACTAACT 57.279 29.630 0.00 0.00 0.00 2.24
2355 2893 9.755064 CAACACATAGTAAGCAAATACACTAAC 57.245 33.333 0.00 0.00 0.00 2.34
2356 2894 8.941977 CCAACACATAGTAAGCAAATACACTAA 58.058 33.333 0.00 0.00 0.00 2.24
2357 2895 8.315482 TCCAACACATAGTAAGCAAATACACTA 58.685 33.333 0.00 0.00 0.00 2.74
2358 2896 7.165485 TCCAACACATAGTAAGCAAATACACT 58.835 34.615 0.00 0.00 0.00 3.55
2359 2897 7.372451 TCCAACACATAGTAAGCAAATACAC 57.628 36.000 0.00 0.00 0.00 2.90
2360 2898 7.987750 TTCCAACACATAGTAAGCAAATACA 57.012 32.000 0.00 0.00 0.00 2.29
2364 2902 9.237187 TCATATTTCCAACACATAGTAAGCAAA 57.763 29.630 0.00 0.00 0.00 3.68
2365 2903 8.800370 TCATATTTCCAACACATAGTAAGCAA 57.200 30.769 0.00 0.00 0.00 3.91
2366 2904 7.012327 GCTCATATTTCCAACACATAGTAAGCA 59.988 37.037 0.00 0.00 0.00 3.91
2367 2905 7.012327 TGCTCATATTTCCAACACATAGTAAGC 59.988 37.037 0.00 0.00 0.00 3.09
2368 2906 8.437360 TGCTCATATTTCCAACACATAGTAAG 57.563 34.615 0.00 0.00 0.00 2.34
2369 2907 8.800370 TTGCTCATATTTCCAACACATAGTAA 57.200 30.769 0.00 0.00 0.00 2.24
2370 2908 8.978874 ATTGCTCATATTTCCAACACATAGTA 57.021 30.769 0.00 0.00 0.00 1.82
2371 2909 7.886629 ATTGCTCATATTTCCAACACATAGT 57.113 32.000 0.00 0.00 0.00 2.12
2374 2912 7.981225 GGTAAATTGCTCATATTTCCAACACAT 59.019 33.333 0.00 0.00 0.00 3.21
2375 2913 7.319646 GGTAAATTGCTCATATTTCCAACACA 58.680 34.615 0.00 0.00 0.00 3.72
2460 2999 5.947228 TCTCTTTGTCAAATCACATGACC 57.053 39.130 0.00 0.00 45.19 4.02
2517 3056 8.181573 GCTATACTGTCTGCTCTAGATATGTTC 58.818 40.741 0.00 0.00 37.83 3.18
2616 3155 7.176075 CGTACATGTTCTTGCTCTTTCTATTG 58.824 38.462 2.30 0.00 0.00 1.90
2650 3189 0.468226 AAGTCCGGTGCTTCTGTTGA 59.532 50.000 0.00 0.00 0.00 3.18
2653 3192 1.071471 CCAAGTCCGGTGCTTCTGT 59.929 57.895 0.00 0.00 0.00 3.41
2699 3238 1.001974 CCAACATCGACAACCTCCTCA 59.998 52.381 0.00 0.00 0.00 3.86
2854 3394 0.971447 GAGTCGGGACAGTAGGCCTT 60.971 60.000 12.58 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.