Multiple sequence alignment - TraesCS5D01G110800

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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 TraesCS5D01G110800 chr5D 100.000 2621 0 0 1 2621 125779286 125776666 0.000000e+00 4841.0
1 TraesCS5D01G110800 chr5D 93.012 830 32 15 1 811 556930536 556931358 0.000000e+00 1188.0
2 TraesCS5D01G110800 chr5D 93.073 794 45 10 1 789 410249732 410248944 0.000000e+00 1153.0
3 TraesCS5D01G110800 chr5D 90.449 178 15 2 2441 2618 464579780 464579955 1.570000e-57 233.0
4 TraesCS5D01G110800 chr5D 90.449 178 14 3 2441 2618 59884882 59885056 5.640000e-57 231.0
5 TraesCS5D01G110800 chr5D 91.852 135 11 0 2442 2576 539050289 539050155 3.440000e-44 189.0
6 TraesCS5D01G110800 chr5B 90.871 1654 67 26 810 2440 138557768 138556176 0.000000e+00 2141.0
7 TraesCS5D01G110800 chr5B 90.909 627 34 7 1825 2440 138453697 138453083 0.000000e+00 821.0
8 TraesCS5D01G110800 chr5A 92.173 971 41 12 810 1763 139894140 139893188 0.000000e+00 1339.0
9 TraesCS5D01G110800 chr1D 95.889 827 16 8 1 810 463250727 463249902 0.000000e+00 1323.0
10 TraesCS5D01G110800 chr1D 94.194 155 8 1 2446 2600 468869247 468869400 4.360000e-58 235.0
11 TraesCS5D01G110800 chr1D 84.153 183 20 6 2441 2616 76428440 76428620 4.490000e-38 169.0
12 TraesCS5D01G110800 chr1D 87.121 132 16 1 2477 2608 9665767 9665637 5.840000e-32 148.0
13 TraesCS5D01G110800 chr7D 96.236 797 22 2 1 789 481609108 481609904 0.000000e+00 1299.0
14 TraesCS5D01G110800 chr7D 93.907 837 31 10 1 821 104758564 104757732 0.000000e+00 1245.0
15 TraesCS5D01G110800 chr7D 93.976 830 30 13 1 815 579573061 579572237 0.000000e+00 1238.0
16 TraesCS5D01G110800 chr7D 92.464 836 41 15 1 821 560574990 560575818 0.000000e+00 1175.0
17 TraesCS5D01G110800 chr7D 80.249 643 92 22 996 1625 549318822 549318202 3.980000e-123 451.0
18 TraesCS5D01G110800 chr7D 79.283 642 97 21 996 1625 549368932 549368315 1.450000e-112 416.0
19 TraesCS5D01G110800 chr7D 92.818 181 13 0 2441 2621 107860090 107859910 2.000000e-66 263.0
20 TraesCS5D01G110800 chr7D 89.888 178 15 3 2441 2618 134105481 134105307 2.620000e-55 226.0
21 TraesCS5D01G110800 chr7D 91.200 125 9 2 2477 2600 199845388 199845511 4.490000e-38 169.0
22 TraesCS5D01G110800 chr4D 96.241 798 20 5 1 789 364026074 364026870 0.000000e+00 1299.0
23 TraesCS5D01G110800 chr4D 95.175 829 21 8 1 812 35123888 35124714 0.000000e+00 1291.0
24 TraesCS5D01G110800 chr4D 86.982 169 21 1 2440 2608 131900843 131901010 3.440000e-44 189.0
25 TraesCS5D01G110800 chr4D 88.811 143 11 4 2479 2616 287567218 287567360 1.250000e-38 171.0
26 TraesCS5D01G110800 chr4D 86.792 106 12 2 2477 2582 83867541 83867438 1.650000e-22 117.0
27 TraesCS5D01G110800 chr6D 94.934 829 25 9 1 813 449815259 449814432 0.000000e+00 1282.0
28 TraesCS5D01G110800 chr6D 94.368 799 33 8 1 789 460655985 460656781 0.000000e+00 1216.0
29 TraesCS5D01G110800 chr6D 90.928 474 23 10 363 820 98077986 98077517 1.030000e-173 619.0
30 TraesCS5D01G110800 chr6D 81.269 662 98 18 999 1646 434604446 434605095 1.800000e-141 512.0
31 TraesCS5D01G110800 chr6D 90.909 220 5 5 607 812 14164293 14164511 5.520000e-72 281.0
32 TraesCS5D01G110800 chr3D 95.000 820 25 5 1 806 22332194 22333011 0.000000e+00 1273.0
33 TraesCS5D01G110800 chr6A 81.497 708 100 18 999 1691 581965270 581965961 1.060000e-153 553.0
34 TraesCS5D01G110800 chr7A 79.563 641 97 18 996 1625 634930996 634930379 6.700000e-116 427.0
35 TraesCS5D01G110800 chr2B 92.265 181 14 0 2441 2621 31632792 31632972 9.310000e-65 257.0
36 TraesCS5D01G110800 chr7B 87.143 70 6 2 996 1062 593557587 593557518 2.800000e-10 76.8


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 TraesCS5D01G110800 chr5D 125776666 125779286 2620 True 4841 4841 100.000 1 2621 1 chr5D.!!$R1 2620
1 TraesCS5D01G110800 chr5D 556930536 556931358 822 False 1188 1188 93.012 1 811 1 chr5D.!!$F3 810
2 TraesCS5D01G110800 chr5D 410248944 410249732 788 True 1153 1153 93.073 1 789 1 chr5D.!!$R2 788
3 TraesCS5D01G110800 chr5B 138556176 138557768 1592 True 2141 2141 90.871 810 2440 1 chr5B.!!$R2 1630
4 TraesCS5D01G110800 chr5B 138453083 138453697 614 True 821 821 90.909 1825 2440 1 chr5B.!!$R1 615
5 TraesCS5D01G110800 chr5A 139893188 139894140 952 True 1339 1339 92.173 810 1763 1 chr5A.!!$R1 953
6 TraesCS5D01G110800 chr1D 463249902 463250727 825 True 1323 1323 95.889 1 810 1 chr1D.!!$R2 809
7 TraesCS5D01G110800 chr7D 481609108 481609904 796 False 1299 1299 96.236 1 789 1 chr7D.!!$F2 788
8 TraesCS5D01G110800 chr7D 104757732 104758564 832 True 1245 1245 93.907 1 821 1 chr7D.!!$R1 820
9 TraesCS5D01G110800 chr7D 579572237 579573061 824 True 1238 1238 93.976 1 815 1 chr7D.!!$R6 814
10 TraesCS5D01G110800 chr7D 560574990 560575818 828 False 1175 1175 92.464 1 821 1 chr7D.!!$F3 820
11 TraesCS5D01G110800 chr7D 549318202 549318822 620 True 451 451 80.249 996 1625 1 chr7D.!!$R4 629
12 TraesCS5D01G110800 chr7D 549368315 549368932 617 True 416 416 79.283 996 1625 1 chr7D.!!$R5 629
13 TraesCS5D01G110800 chr4D 364026074 364026870 796 False 1299 1299 96.241 1 789 1 chr4D.!!$F4 788
14 TraesCS5D01G110800 chr4D 35123888 35124714 826 False 1291 1291 95.175 1 812 1 chr4D.!!$F1 811
15 TraesCS5D01G110800 chr6D 449814432 449815259 827 True 1282 1282 94.934 1 813 1 chr6D.!!$R2 812
16 TraesCS5D01G110800 chr6D 460655985 460656781 796 False 1216 1216 94.368 1 789 1 chr6D.!!$F3 788
17 TraesCS5D01G110800 chr6D 434604446 434605095 649 False 512 512 81.269 999 1646 1 chr6D.!!$F2 647
18 TraesCS5D01G110800 chr3D 22332194 22333011 817 False 1273 1273 95.000 1 806 1 chr3D.!!$F1 805
19 TraesCS5D01G110800 chr6A 581965270 581965961 691 False 553 553 81.497 999 1691 1 chr6A.!!$F1 692
20 TraesCS5D01G110800 chr7A 634930379 634930996 617 True 427 427 79.563 996 1625 1 chr7A.!!$R1 629

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
866 899 0.386476 TACCACTCACACGGTCACAC 59.614 55.0 0.0 0.0 36.69 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 2587 0.107017 CGACCCATGGCCTCTCAAAT 60.107 55.0 6.09 0.0 0.0 2.32 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
136 140 0.806868 CAGTTGCCATGTCGCTGAAT 59.193 50.000 0.00 0.00 0.00 2.57
186 190 1.542915 GTCATGGTTGCTCAACTGCAT 59.457 47.619 11.91 5.87 42.96 3.96
274 280 1.813513 ACACTAGCAGTTGCCATGTC 58.186 50.000 0.00 0.00 43.38 3.06
639 654 0.534203 CTAAACGCCCACACACCAGT 60.534 55.000 0.00 0.00 0.00 4.00
694 719 2.659428 GGATGAATGCCCAGCTTAGTT 58.341 47.619 0.00 0.00 0.00 2.24
725 750 3.000177 CACACAAAAACTGCTAAAACGCC 60.000 43.478 0.00 0.00 0.00 5.68
859 892 4.166523 CTGATTGTACTACCACTCACACG 58.833 47.826 0.00 0.00 0.00 4.49
860 893 3.057104 TGATTGTACTACCACTCACACGG 60.057 47.826 0.00 0.00 0.00 4.94
861 894 1.985473 TGTACTACCACTCACACGGT 58.015 50.000 0.00 0.00 39.41 4.83
862 895 1.881973 TGTACTACCACTCACACGGTC 59.118 52.381 0.00 0.00 36.69 4.79
863 896 1.881973 GTACTACCACTCACACGGTCA 59.118 52.381 0.00 0.00 36.69 4.02
864 897 0.672342 ACTACCACTCACACGGTCAC 59.328 55.000 0.00 0.00 36.69 3.67
865 898 0.671796 CTACCACTCACACGGTCACA 59.328 55.000 0.00 0.00 36.69 3.58
866 899 0.386476 TACCACTCACACGGTCACAC 59.614 55.000 0.00 0.00 36.69 3.82
867 900 1.594293 CCACTCACACGGTCACACC 60.594 63.158 0.00 0.00 34.05 4.16
881 914 3.009143 GGTCACACCCCTTAAATCTCAGT 59.991 47.826 0.00 0.00 30.04 3.41
883 916 4.020128 GTCACACCCCTTAAATCTCAGTCT 60.020 45.833 0.00 0.00 0.00 3.24
884 917 4.597507 TCACACCCCTTAAATCTCAGTCTT 59.402 41.667 0.00 0.00 0.00 3.01
885 918 5.073144 TCACACCCCTTAAATCTCAGTCTTT 59.927 40.000 0.00 0.00 0.00 2.52
886 919 5.412904 CACACCCCTTAAATCTCAGTCTTTC 59.587 44.000 0.00 0.00 0.00 2.62
887 920 4.631813 CACCCCTTAAATCTCAGTCTTTCG 59.368 45.833 0.00 0.00 0.00 3.46
888 921 4.286291 ACCCCTTAAATCTCAGTCTTTCGT 59.714 41.667 0.00 0.00 0.00 3.85
889 922 5.221864 ACCCCTTAAATCTCAGTCTTTCGTT 60.222 40.000 0.00 0.00 0.00 3.85
890 923 5.122396 CCCCTTAAATCTCAGTCTTTCGTTG 59.878 44.000 0.00 0.00 0.00 4.10
891 924 5.122396 CCCTTAAATCTCAGTCTTTCGTTGG 59.878 44.000 0.00 0.00 0.00 3.77
938 971 0.527385 CTCTGCTCTCTTGCGCTACC 60.527 60.000 9.73 0.00 35.36 3.18
944 977 1.135139 CTCTCTTGCGCTACCAGCTAA 59.865 52.381 9.73 0.00 39.60 3.09
949 982 0.744874 TGCGCTACCAGCTAACTAGG 59.255 55.000 9.73 0.00 39.60 3.02
1281 1335 4.279043 GCACACAACCCCAACGCC 62.279 66.667 0.00 0.00 0.00 5.68
1911 1984 4.093743 TGGACTAGCATTAGTGGTTGAGA 58.906 43.478 5.93 0.00 40.21 3.27
1929 2002 1.005097 AGACCCACCCCCGTTAAATTC 59.995 52.381 0.00 0.00 0.00 2.17
2005 2078 5.258841 AGATTGAATTCATGCAGGAGTTGA 58.741 37.500 14.09 2.41 0.00 3.18
2033 2107 3.462199 GAGACCTACATGCCGGCCC 62.462 68.421 26.77 0.00 0.00 5.80
2074 2148 3.048337 TCAACTTGCTAGTAAACCCGG 57.952 47.619 0.00 0.00 33.17 5.73
2075 2149 2.633967 TCAACTTGCTAGTAAACCCGGA 59.366 45.455 0.73 0.00 33.17 5.14
2076 2150 3.000727 CAACTTGCTAGTAAACCCGGAG 58.999 50.000 0.73 0.00 33.17 4.63
2077 2151 1.066358 ACTTGCTAGTAAACCCGGAGC 60.066 52.381 0.73 1.68 31.21 4.70
2078 2152 0.108520 TTGCTAGTAAACCCGGAGCG 60.109 55.000 0.73 0.00 35.88 5.03
2137 2211 0.096976 GATGATGTGGTTTCGTGCCG 59.903 55.000 0.00 0.00 0.00 5.69
2207 2281 6.213677 CGATATACTTGGTCGAATGAAAGGA 58.786 40.000 0.00 0.00 37.55 3.36
2244 2318 5.298026 TCGAAAAGATTGACCACATGTTCAA 59.702 36.000 13.84 13.84 0.00 2.69
2247 2321 6.409524 AAAGATTGACCACATGTTCAACAT 57.590 33.333 13.77 0.00 39.91 2.71
2319 2393 2.737180 AGTGTCAGACCACTGCCG 59.263 61.111 0.00 0.00 43.86 5.69
2320 2394 1.832608 AGTGTCAGACCACTGCCGA 60.833 57.895 0.00 0.00 43.86 5.54
2324 2398 0.946221 GTCAGACCACTGCCGACTTG 60.946 60.000 0.00 0.00 43.17 3.16
2325 2399 1.112916 TCAGACCACTGCCGACTTGA 61.113 55.000 0.00 0.00 43.17 3.02
2326 2400 0.249868 CAGACCACTGCCGACTTGAA 60.250 55.000 0.00 0.00 37.33 2.69
2327 2401 0.249911 AGACCACTGCCGACTTGAAC 60.250 55.000 0.00 0.00 0.00 3.18
2328 2402 1.557443 GACCACTGCCGACTTGAACG 61.557 60.000 0.00 0.00 0.00 3.95
2329 2403 2.551270 CACTGCCGACTTGAACGC 59.449 61.111 0.00 0.00 0.00 4.84
2358 2442 0.255890 TCATGGGGCAGAGGTTTAGC 59.744 55.000 0.00 0.00 0.00 3.09
2367 2451 1.205893 CAGAGGTTTAGCTTCGAGGCT 59.794 52.381 26.07 26.07 45.29 4.58
2423 2507 1.384502 AGGAGGCATGGGAATCGGA 60.385 57.895 0.00 0.00 0.00 4.55
2440 2524 1.132500 GGACCCTAGTTATGGCAGCT 58.868 55.000 0.00 0.00 0.00 4.24
2441 2525 1.070914 GGACCCTAGTTATGGCAGCTC 59.929 57.143 0.00 0.00 0.00 4.09
2442 2526 1.762957 GACCCTAGTTATGGCAGCTCA 59.237 52.381 0.00 0.00 0.00 4.26
2443 2527 1.765314 ACCCTAGTTATGGCAGCTCAG 59.235 52.381 0.00 0.00 0.00 3.35
2444 2528 1.071385 CCCTAGTTATGGCAGCTCAGG 59.929 57.143 0.00 0.00 0.00 3.86
2445 2529 2.042464 CCTAGTTATGGCAGCTCAGGA 58.958 52.381 0.00 0.00 0.00 3.86
2446 2530 2.636893 CCTAGTTATGGCAGCTCAGGAT 59.363 50.000 0.00 0.00 0.00 3.24
2447 2531 2.634815 AGTTATGGCAGCTCAGGATG 57.365 50.000 0.00 0.00 37.54 3.51
2448 2532 1.142465 AGTTATGGCAGCTCAGGATGG 59.858 52.381 0.00 0.00 36.16 3.51
2449 2533 0.475475 TTATGGCAGCTCAGGATGGG 59.525 55.000 0.00 0.00 42.01 4.00
2450 2534 0.400381 TATGGCAGCTCAGGATGGGA 60.400 55.000 0.00 0.00 41.11 4.37
2451 2535 1.284111 ATGGCAGCTCAGGATGGGAA 61.284 55.000 0.00 0.00 41.11 3.97
2452 2536 1.452833 GGCAGCTCAGGATGGGAAC 60.453 63.158 0.00 0.00 41.11 3.62
2453 2537 1.817099 GCAGCTCAGGATGGGAACG 60.817 63.158 0.00 0.00 41.11 3.95
2454 2538 1.153289 CAGCTCAGGATGGGAACGG 60.153 63.158 0.00 0.00 41.11 4.44
2455 2539 2.190578 GCTCAGGATGGGAACGGG 59.809 66.667 0.00 0.00 41.11 5.28
2456 2540 2.190578 CTCAGGATGGGAACGGGC 59.809 66.667 0.00 0.00 41.11 6.13
2457 2541 3.406595 CTCAGGATGGGAACGGGCC 62.407 68.421 0.00 0.00 41.11 5.80
2458 2542 4.856801 CAGGATGGGAACGGGCCG 62.857 72.222 27.06 27.06 0.00 6.13
2460 2544 4.851179 GGATGGGAACGGGCCGAC 62.851 72.222 35.78 24.35 0.00 4.79
2461 2545 4.851179 GATGGGAACGGGCCGACC 62.851 72.222 35.78 31.06 0.00 4.79
2481 2565 3.373565 GCCTTTGCCTTGGACCCG 61.374 66.667 0.00 0.00 0.00 5.28
2482 2566 2.676471 CCTTTGCCTTGGACCCGG 60.676 66.667 0.00 0.00 0.00 5.73
2483 2567 3.373565 CTTTGCCTTGGACCCGGC 61.374 66.667 13.57 13.57 46.46 6.13
2484 2568 4.986708 TTTGCCTTGGACCCGGCC 62.987 66.667 16.78 0.00 45.71 6.13
2510 2594 3.379617 CCCCAAGGCCAATTTGAGA 57.620 52.632 5.01 0.00 0.00 3.27
2511 2595 1.188863 CCCCAAGGCCAATTTGAGAG 58.811 55.000 5.01 0.00 0.00 3.20
2512 2596 1.188863 CCCAAGGCCAATTTGAGAGG 58.811 55.000 5.01 0.00 0.00 3.69
2518 2602 0.462789 GCCAATTTGAGAGGCCATGG 59.537 55.000 7.63 7.63 42.58 3.66
2519 2603 1.117150 CCAATTTGAGAGGCCATGGG 58.883 55.000 15.13 0.00 0.00 4.00
2520 2604 1.620524 CCAATTTGAGAGGCCATGGGT 60.621 52.381 15.13 0.00 0.00 4.51
2521 2605 1.753073 CAATTTGAGAGGCCATGGGTC 59.247 52.381 15.13 0.00 0.00 4.46
2522 2606 0.107017 ATTTGAGAGGCCATGGGTCG 60.107 55.000 15.13 0.00 29.39 4.79
2523 2607 1.198094 TTTGAGAGGCCATGGGTCGA 61.198 55.000 15.13 0.00 29.39 4.20
2524 2608 1.899437 TTGAGAGGCCATGGGTCGAC 61.899 60.000 15.13 7.13 29.39 4.20
2525 2609 3.083997 AGAGGCCATGGGTCGACC 61.084 66.667 27.04 27.04 40.81 4.79
2542 2626 6.091437 GGTCGACCCATATAAAGAATAGTCG 58.909 44.000 24.75 0.00 45.25 4.18
2544 2628 7.698506 TCGACCCATATAAAGAATAGTCGAT 57.301 36.000 7.73 0.00 46.81 3.59
2545 2629 7.535997 TCGACCCATATAAAGAATAGTCGATG 58.464 38.462 7.73 0.00 46.81 3.84
2546 2630 6.752351 CGACCCATATAAAGAATAGTCGATGG 59.248 42.308 3.30 0.00 46.41 3.51
2547 2631 6.407202 ACCCATATAAAGAATAGTCGATGGC 58.593 40.000 0.00 0.00 0.00 4.40
2548 2632 5.817816 CCCATATAAAGAATAGTCGATGGCC 59.182 44.000 0.00 0.00 0.00 5.36
2549 2633 6.352222 CCCATATAAAGAATAGTCGATGGCCT 60.352 42.308 3.32 0.00 0.00 5.19
2550 2634 6.758886 CCATATAAAGAATAGTCGATGGCCTC 59.241 42.308 3.32 0.00 0.00 4.70
2565 2649 4.096003 CTCGTTGGCCCGATGGGT 62.096 66.667 0.00 0.00 46.51 4.51
2566 2650 2.684294 TCGTTGGCCCGATGGGTA 60.684 61.111 0.00 0.00 46.51 3.69
2567 2651 2.040009 CTCGTTGGCCCGATGGGTAT 62.040 60.000 0.00 0.00 46.51 2.73
2568 2652 1.153046 CGTTGGCCCGATGGGTATT 60.153 57.895 0.00 0.00 46.51 1.89
2569 2653 0.750182 CGTTGGCCCGATGGGTATTT 60.750 55.000 0.00 0.00 46.51 1.40
2570 2654 1.480789 GTTGGCCCGATGGGTATTTT 58.519 50.000 0.00 0.00 46.51 1.82
2571 2655 1.136110 GTTGGCCCGATGGGTATTTTG 59.864 52.381 0.00 0.00 46.51 2.44
2572 2656 0.396417 TGGCCCGATGGGTATTTTGG 60.396 55.000 0.00 0.00 46.51 3.28
2573 2657 1.112916 GGCCCGATGGGTATTTTGGG 61.113 60.000 3.40 0.00 46.51 4.12
2574 2658 0.396556 GCCCGATGGGTATTTTGGGT 60.397 55.000 3.40 0.00 46.51 4.51
2575 2659 1.687563 CCCGATGGGTATTTTGGGTC 58.312 55.000 0.00 0.00 38.25 4.46
2576 2660 1.305201 CCGATGGGTATTTTGGGTCG 58.695 55.000 0.00 0.00 0.00 4.79
2577 2661 1.134340 CCGATGGGTATTTTGGGTCGA 60.134 52.381 0.00 0.00 0.00 4.20
2578 2662 1.937899 CGATGGGTATTTTGGGTCGAC 59.062 52.381 7.13 7.13 0.00 4.20
2579 2663 2.419574 CGATGGGTATTTTGGGTCGACT 60.420 50.000 16.46 0.00 0.00 4.18
2580 2664 2.773993 TGGGTATTTTGGGTCGACTC 57.226 50.000 16.46 12.99 0.00 3.36
2581 2665 1.979308 TGGGTATTTTGGGTCGACTCA 59.021 47.619 15.77 15.77 0.00 3.41
2582 2666 2.027561 TGGGTATTTTGGGTCGACTCAG 60.028 50.000 19.17 0.00 0.00 3.35
2583 2667 2.027469 GGGTATTTTGGGTCGACTCAGT 60.027 50.000 19.17 11.34 0.00 3.41
2584 2668 3.558533 GGGTATTTTGGGTCGACTCAGTT 60.559 47.826 19.17 9.90 0.00 3.16
2585 2669 4.070009 GGTATTTTGGGTCGACTCAGTTT 58.930 43.478 19.17 9.54 0.00 2.66
2586 2670 4.517832 GGTATTTTGGGTCGACTCAGTTTT 59.482 41.667 19.17 7.75 0.00 2.43
2587 2671 5.009310 GGTATTTTGGGTCGACTCAGTTTTT 59.991 40.000 19.17 6.00 0.00 1.94
2607 2691 5.731599 TTTTTGCTTTACATTGCCTTGTG 57.268 34.783 0.00 0.00 0.00 3.33
2608 2692 4.399004 TTTGCTTTACATTGCCTTGTGT 57.601 36.364 0.00 0.00 0.00 3.72
2609 2693 3.367992 TGCTTTACATTGCCTTGTGTG 57.632 42.857 0.00 0.00 0.00 3.82
2610 2694 2.035704 TGCTTTACATTGCCTTGTGTGG 59.964 45.455 0.00 0.00 0.00 4.17
2611 2695 2.295909 GCTTTACATTGCCTTGTGTGGA 59.704 45.455 0.00 0.00 0.00 4.02
2612 2696 3.056607 GCTTTACATTGCCTTGTGTGGAT 60.057 43.478 0.00 0.00 0.00 3.41
2613 2697 4.157656 GCTTTACATTGCCTTGTGTGGATA 59.842 41.667 0.00 0.00 0.00 2.59
2614 2698 5.336372 GCTTTACATTGCCTTGTGTGGATAA 60.336 40.000 0.00 0.00 0.00 1.75
2615 2699 6.656632 TTTACATTGCCTTGTGTGGATAAA 57.343 33.333 0.00 0.00 0.00 1.40
2616 2700 6.849085 TTACATTGCCTTGTGTGGATAAAT 57.151 33.333 0.00 0.00 0.00 1.40
2617 2701 7.946381 TTACATTGCCTTGTGTGGATAAATA 57.054 32.000 0.00 0.00 0.00 1.40
2618 2702 6.455360 ACATTGCCTTGTGTGGATAAATAG 57.545 37.500 0.00 0.00 0.00 1.73
2619 2703 5.360714 ACATTGCCTTGTGTGGATAAATAGG 59.639 40.000 0.00 0.00 0.00 2.57
2620 2704 4.584638 TGCCTTGTGTGGATAAATAGGT 57.415 40.909 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 140 1.071642 TCCGACATGGCAACCGAAA 59.928 52.632 0.00 0.00 37.80 3.46
274 280 0.729116 CCATGCCTTCTTGTAGTGCG 59.271 55.000 0.00 0.00 0.00 5.34
571 584 2.450502 AGAGGGGGCTGGTGTGTT 60.451 61.111 0.00 0.00 0.00 3.32
694 719 2.353269 CAGTTTTTGTGTGCCACGTAGA 59.647 45.455 0.00 0.00 37.14 2.59
725 750 2.159338 CCAATTCTGCACGAATCTTGGG 60.159 50.000 15.97 10.68 41.42 4.12
829 860 8.105197 TGAGTGGTAGTACAATCAGTCTAAGTA 58.895 37.037 2.06 0.00 40.12 2.24
835 866 5.162075 GTGTGAGTGGTAGTACAATCAGTC 58.838 45.833 2.06 4.56 44.81 3.51
859 892 3.009143 ACTGAGATTTAAGGGGTGTGACC 59.991 47.826 0.00 0.00 37.60 4.02
860 893 4.020128 AGACTGAGATTTAAGGGGTGTGAC 60.020 45.833 0.00 0.00 0.00 3.67
861 894 4.168101 AGACTGAGATTTAAGGGGTGTGA 58.832 43.478 0.00 0.00 0.00 3.58
862 895 4.559862 AGACTGAGATTTAAGGGGTGTG 57.440 45.455 0.00 0.00 0.00 3.82
863 896 5.561679 GAAAGACTGAGATTTAAGGGGTGT 58.438 41.667 0.00 0.00 0.00 4.16
864 897 4.631813 CGAAAGACTGAGATTTAAGGGGTG 59.368 45.833 0.00 0.00 0.00 4.61
865 898 4.286291 ACGAAAGACTGAGATTTAAGGGGT 59.714 41.667 0.00 0.00 0.00 4.95
866 899 4.833390 ACGAAAGACTGAGATTTAAGGGG 58.167 43.478 0.00 0.00 0.00 4.79
867 900 5.122396 CCAACGAAAGACTGAGATTTAAGGG 59.878 44.000 0.00 0.00 0.00 3.95
881 914 1.686587 TCTGTCTGAGCCAACGAAAGA 59.313 47.619 0.00 0.00 0.00 2.52
883 916 1.540363 GGTCTGTCTGAGCCAACGAAA 60.540 52.381 0.00 0.00 37.22 3.46
884 917 0.033504 GGTCTGTCTGAGCCAACGAA 59.966 55.000 0.00 0.00 37.22 3.85
885 918 1.666011 GGTCTGTCTGAGCCAACGA 59.334 57.895 0.00 0.00 37.22 3.85
886 919 4.268687 GGTCTGTCTGAGCCAACG 57.731 61.111 0.00 0.00 37.22 4.10
891 924 2.363172 GGGGAGGGTCTGTCTGAGC 61.363 68.421 0.56 0.56 42.07 4.26
938 971 0.462759 GCTGCCCACCTAGTTAGCTG 60.463 60.000 0.00 0.00 0.00 4.24
944 977 2.664081 GCTGAGCTGCCCACCTAGT 61.664 63.158 0.00 0.00 0.00 2.57
949 982 1.153469 GACTAGCTGAGCTGCCCAC 60.153 63.158 18.79 0.31 40.10 4.61
974 1007 1.059006 ATCAGAGATGGAGTGCCCCC 61.059 60.000 0.00 0.00 0.00 5.40
1398 1452 4.851214 GCCGAGGAGAGGGAGGCT 62.851 72.222 0.00 0.00 44.06 4.58
1650 1721 6.803320 ACAAAGTAATTCAATTGACTGATGCG 59.197 34.615 7.89 0.00 0.00 4.73
1911 1984 0.778720 TGAATTTAACGGGGGTGGGT 59.221 50.000 0.00 0.00 0.00 4.51
1929 2002 2.552093 TTAACCCTCTCTCCTCCCTG 57.448 55.000 0.00 0.00 0.00 4.45
1974 2047 6.011476 TGCATGAATTCAATCTTGTCGAAA 57.989 33.333 13.09 0.00 0.00 3.46
2005 2078 5.760253 CGGCATGTAGGTCTCTAATTTCAAT 59.240 40.000 0.00 0.00 0.00 2.57
2033 2107 1.202604 AGTCACCAACTACAACCCACG 60.203 52.381 0.00 0.00 36.07 4.94
2074 2148 1.005394 TTTTGTCCTCCGTCCGCTC 60.005 57.895 0.00 0.00 0.00 5.03
2075 2149 1.004918 CTTTTGTCCTCCGTCCGCT 60.005 57.895 0.00 0.00 0.00 5.52
2076 2150 2.677979 GCTTTTGTCCTCCGTCCGC 61.678 63.158 0.00 0.00 0.00 5.54
2077 2151 0.882927 TTGCTTTTGTCCTCCGTCCG 60.883 55.000 0.00 0.00 0.00 4.79
2078 2152 1.200020 CATTGCTTTTGTCCTCCGTCC 59.800 52.381 0.00 0.00 0.00 4.79
2079 2153 1.401539 GCATTGCTTTTGTCCTCCGTC 60.402 52.381 0.16 0.00 0.00 4.79
2080 2154 0.598065 GCATTGCTTTTGTCCTCCGT 59.402 50.000 0.16 0.00 0.00 4.69
2207 2281 0.313043 TTTTCGAGAGTCGCTTCCGT 59.687 50.000 0.00 0.00 40.21 4.69
2244 2318 0.534412 CTCCTCCGAGCAAGACATGT 59.466 55.000 0.00 0.00 0.00 3.21
2319 2393 3.003275 TGACCAAATCAAGCGTTCAAGTC 59.997 43.478 0.00 0.00 33.02 3.01
2320 2394 2.948979 TGACCAAATCAAGCGTTCAAGT 59.051 40.909 0.00 0.00 33.02 3.16
2324 2398 2.415893 CCCATGACCAAATCAAGCGTTC 60.416 50.000 0.00 0.00 41.93 3.95
2325 2399 1.545582 CCCATGACCAAATCAAGCGTT 59.454 47.619 0.00 0.00 41.93 4.84
2326 2400 1.176527 CCCATGACCAAATCAAGCGT 58.823 50.000 0.00 0.00 41.93 5.07
2327 2401 0.457035 CCCCATGACCAAATCAAGCG 59.543 55.000 0.00 0.00 41.93 4.68
2328 2402 0.176449 GCCCCATGACCAAATCAAGC 59.824 55.000 0.00 0.00 41.93 4.01
2329 2403 1.479323 CTGCCCCATGACCAAATCAAG 59.521 52.381 0.00 0.00 41.93 3.02
2367 2451 1.544724 CCTCCATCTTCGGCCAAAAA 58.455 50.000 2.24 0.00 0.00 1.94
2423 2507 1.765314 CTGAGCTGCCATAACTAGGGT 59.235 52.381 0.00 0.00 0.00 4.34
2440 2524 3.407967 GGCCCGTTCCCATCCTGA 61.408 66.667 0.00 0.00 0.00 3.86
2441 2525 4.856801 CGGCCCGTTCCCATCCTG 62.857 72.222 0.00 0.00 0.00 3.86
2443 2527 4.851179 GTCGGCCCGTTCCCATCC 62.851 72.222 1.63 0.00 0.00 3.51
2444 2528 4.851179 GGTCGGCCCGTTCCCATC 62.851 72.222 1.63 0.00 0.00 3.51
2464 2548 3.373565 CGGGTCCAAGGCAAAGGC 61.374 66.667 0.00 0.00 40.13 4.35
2465 2549 2.676471 CCGGGTCCAAGGCAAAGG 60.676 66.667 0.00 0.00 0.00 3.11
2492 2576 1.188863 CTCTCAAATTGGCCTTGGGG 58.811 55.000 3.32 0.00 0.00 4.96
2493 2577 1.188863 CCTCTCAAATTGGCCTTGGG 58.811 55.000 3.32 0.00 0.00 4.12
2494 2578 0.533951 GCCTCTCAAATTGGCCTTGG 59.466 55.000 3.32 0.00 40.71 3.61
2499 2583 0.462789 CCATGGCCTCTCAAATTGGC 59.537 55.000 3.32 0.00 45.42 4.52
2500 2584 1.117150 CCCATGGCCTCTCAAATTGG 58.883 55.000 6.09 0.00 0.00 3.16
2501 2585 1.753073 GACCCATGGCCTCTCAAATTG 59.247 52.381 6.09 0.00 0.00 2.32
2502 2586 1.683011 CGACCCATGGCCTCTCAAATT 60.683 52.381 6.09 0.00 0.00 1.82
2503 2587 0.107017 CGACCCATGGCCTCTCAAAT 60.107 55.000 6.09 0.00 0.00 2.32
2504 2588 1.198094 TCGACCCATGGCCTCTCAAA 61.198 55.000 6.09 0.00 0.00 2.69
2505 2589 1.612146 TCGACCCATGGCCTCTCAA 60.612 57.895 6.09 0.00 0.00 3.02
2506 2590 2.038813 TCGACCCATGGCCTCTCA 59.961 61.111 6.09 0.00 0.00 3.27
2507 2591 2.501610 GTCGACCCATGGCCTCTC 59.498 66.667 6.09 0.00 0.00 3.20
2508 2592 3.083997 GGTCGACCCATGGCCTCT 61.084 66.667 24.75 0.00 0.00 3.69
2518 2602 6.072286 TCGACTATTCTTTATATGGGTCGACC 60.072 42.308 27.04 27.04 45.50 4.79
2519 2603 6.906659 TCGACTATTCTTTATATGGGTCGAC 58.093 40.000 7.13 7.13 45.50 4.20
2521 2605 6.752351 CCATCGACTATTCTTTATATGGGTCG 59.248 42.308 0.00 0.00 44.04 4.79
2522 2606 6.535508 GCCATCGACTATTCTTTATATGGGTC 59.464 42.308 0.00 0.00 0.00 4.46
2523 2607 6.407202 GCCATCGACTATTCTTTATATGGGT 58.593 40.000 0.00 0.00 0.00 4.51
2524 2608 5.817816 GGCCATCGACTATTCTTTATATGGG 59.182 44.000 0.00 0.00 0.00 4.00
2525 2609 6.644347 AGGCCATCGACTATTCTTTATATGG 58.356 40.000 5.01 0.00 0.00 2.74
2526 2610 7.763172 GAGGCCATCGACTATTCTTTATATG 57.237 40.000 5.01 0.00 0.00 1.78
2557 2641 1.134340 TCGACCCAAAATACCCATCGG 60.134 52.381 0.00 0.00 0.00 4.18
2558 2642 1.937899 GTCGACCCAAAATACCCATCG 59.062 52.381 3.51 0.00 0.00 3.84
2559 2643 3.203716 GAGTCGACCCAAAATACCCATC 58.796 50.000 13.01 0.00 0.00 3.51
2560 2644 2.574369 TGAGTCGACCCAAAATACCCAT 59.426 45.455 13.01 0.00 0.00 4.00
2561 2645 1.979308 TGAGTCGACCCAAAATACCCA 59.021 47.619 13.01 0.00 0.00 4.51
2562 2646 2.027469 ACTGAGTCGACCCAAAATACCC 60.027 50.000 13.01 0.00 0.00 3.69
2563 2647 3.329929 ACTGAGTCGACCCAAAATACC 57.670 47.619 13.01 0.00 0.00 2.73
2564 2648 5.684550 AAAACTGAGTCGACCCAAAATAC 57.315 39.130 13.01 0.00 0.00 1.89
2585 2669 5.064452 CACACAAGGCAATGTAAAGCAAAAA 59.936 36.000 0.00 0.00 30.84 1.94
2586 2670 4.569966 CACACAAGGCAATGTAAAGCAAAA 59.430 37.500 0.00 0.00 30.84 2.44
2587 2671 4.118410 CACACAAGGCAATGTAAAGCAAA 58.882 39.130 0.00 0.00 30.84 3.68
2588 2672 3.492309 CCACACAAGGCAATGTAAAGCAA 60.492 43.478 0.00 0.00 30.84 3.91
2589 2673 2.035704 CCACACAAGGCAATGTAAAGCA 59.964 45.455 0.00 0.00 30.84 3.91
2590 2674 2.295909 TCCACACAAGGCAATGTAAAGC 59.704 45.455 0.00 0.00 30.84 3.51
2591 2675 4.789012 ATCCACACAAGGCAATGTAAAG 57.211 40.909 0.00 0.00 30.84 1.85
2592 2676 6.656632 TTTATCCACACAAGGCAATGTAAA 57.343 33.333 0.00 0.00 30.84 2.01
2593 2677 6.849085 ATTTATCCACACAAGGCAATGTAA 57.151 33.333 0.00 0.00 30.84 2.41
2594 2678 6.545666 CCTATTTATCCACACAAGGCAATGTA 59.454 38.462 0.00 0.00 30.84 2.29
2595 2679 5.360714 CCTATTTATCCACACAAGGCAATGT 59.639 40.000 0.00 0.00 0.00 2.71
2596 2680 5.360714 ACCTATTTATCCACACAAGGCAATG 59.639 40.000 0.00 0.00 0.00 2.82
2597 2681 5.518865 ACCTATTTATCCACACAAGGCAAT 58.481 37.500 0.00 0.00 0.00 3.56
2598 2682 4.929479 ACCTATTTATCCACACAAGGCAA 58.071 39.130 0.00 0.00 0.00 4.52
2599 2683 4.584638 ACCTATTTATCCACACAAGGCA 57.415 40.909 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.