Multiple sequence alignment - TraesCS1D01G416700

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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 TraesCS1D01G416700 chr1D 100.000 2896 0 0 1815 4710 475432762 475429867 0.000000e+00 5349.0
1 TraesCS1D01G416700 chr1D 100.000 1214 0 0 1 1214 475434576 475433363 0.000000e+00 2242.0
2 TraesCS1D01G416700 chr1D 95.740 986 40 2 3348 4331 69688371 69687386 0.000000e+00 1587.0
3 TraesCS1D01G416700 chr7B 93.437 1417 84 4 3237 4652 68915801 68917209 0.000000e+00 2093.0
4 TraesCS1D01G416700 chr7B 94.197 517 28 2 2373 2887 597764645 597765161 0.000000e+00 787.0
5 TraesCS1D01G416700 chr7B 94.004 517 29 2 2373 2887 709578317 709577801 0.000000e+00 782.0
6 TraesCS1D01G416700 chr7B 96.154 234 9 0 2140 2373 673941499 673941266 2.660000e-102 383.0
7 TraesCS1D01G416700 chr7B 98.387 62 1 0 4649 4710 359366515 359366576 4.980000e-20 110.0
8 TraesCS1D01G416700 chr7B 100.000 42 0 0 4568 4609 24714432 24714473 1.410000e-10 78.7
9 TraesCS1D01G416700 chr7B 100.000 30 0 0 4681 4710 170959113 170959142 6.580000e-04 56.5
10 TraesCS1D01G416700 chr5D 94.113 1223 61 5 2911 4131 481667084 481665871 0.000000e+00 1849.0
11 TraesCS1D01G416700 chr5D 88.534 1160 89 18 1 1129 526726732 526725586 0.000000e+00 1365.0
12 TraesCS1D01G416700 chr5D 91.139 79 6 1 1877 1954 375987250 375987328 6.450000e-19 106.0
13 TraesCS1D01G416700 chr4B 92.729 1279 89 3 3237 4514 632834691 632833416 0.000000e+00 1844.0
14 TraesCS1D01G416700 chr4B 95.538 493 18 4 2911 3401 219273507 219273017 0.000000e+00 785.0
15 TraesCS1D01G416700 chr4B 93.642 519 29 4 2372 2887 515363184 515363701 0.000000e+00 773.0
16 TraesCS1D01G416700 chr5A 93.083 1200 80 3 3455 4652 380841503 380840305 0.000000e+00 1753.0
17 TraesCS1D01G416700 chr5A 92.994 1199 80 4 3455 4652 633520926 633522121 0.000000e+00 1746.0
18 TraesCS1D01G416700 chr5A 92.577 1199 86 3 3455 4652 533747082 533748278 0.000000e+00 1718.0
19 TraesCS1D01G416700 chr5A 93.088 868 58 2 1 866 98740690 98739823 0.000000e+00 1269.0
20 TraesCS1D01G416700 chr5A 95.037 544 27 0 2372 2915 566393107 566392564 0.000000e+00 856.0
21 TraesCS1D01G416700 chr5A 93.711 477 14 3 4234 4710 502849991 502850451 0.000000e+00 701.0
22 TraesCS1D01G416700 chr5A 91.633 490 35 4 2911 3399 699209234 699209718 0.000000e+00 673.0
23 TraesCS1D01G416700 chr5A 93.939 396 24 0 1977 2372 566393554 566393159 2.430000e-167 599.0
24 TraesCS1D01G416700 chr5A 88.559 236 17 1 886 1121 98739752 98739527 1.290000e-70 278.0
25 TraesCS1D01G416700 chr5A 91.139 79 6 1 1877 1954 476999900 476999978 6.450000e-19 106.0
26 TraesCS1D01G416700 chr5A 91.549 71 6 0 1815 1885 98738870 98738800 1.080000e-16 99.0
27 TraesCS1D01G416700 chr3D 94.165 1114 62 3 3221 4332 160281855 160280743 0.000000e+00 1694.0
28 TraesCS1D01G416700 chr6A 92.160 1199 89 4 3455 4652 97555165 97553971 0.000000e+00 1688.0
29 TraesCS1D01G416700 chr6A 91.470 1231 66 4 2911 4131 595722128 595723329 0.000000e+00 1655.0
30 TraesCS1D01G416700 chr6A 92.890 858 57 3 2 858 148688301 148689155 0.000000e+00 1243.0
31 TraesCS1D01G416700 chr6A 93.703 397 18 5 1979 2368 585485787 585486183 5.250000e-164 588.0
32 TraesCS1D01G416700 chr6A 88.732 71 8 0 1815 1885 148689939 148690009 2.330000e-13 87.9
33 TraesCS1D01G416700 chr7A 90.762 1234 70 9 2911 4131 61449129 61447927 0.000000e+00 1607.0
34 TraesCS1D01G416700 chr7A 89.196 1231 96 16 1 1214 309081589 309080379 0.000000e+00 1502.0
35 TraesCS1D01G416700 chr7A 93.541 867 55 1 1 866 655259290 655258424 0.000000e+00 1290.0
36 TraesCS1D01G416700 chr7A 93.945 545 16 2 4166 4710 61447927 61447400 0.000000e+00 808.0
37 TraesCS1D01G416700 chr7A 90.000 50 5 0 2873 2922 633535746 633535697 1.090000e-06 65.8
38 TraesCS1D01G416700 chr1B 90.016 1232 81 16 2911 4131 502574566 502575766 0.000000e+00 1555.0
39 TraesCS1D01G416700 chr1B 89.218 946 89 11 1 940 670003617 670004555 0.000000e+00 1170.0
40 TraesCS1D01G416700 chr1B 97.170 106 3 0 4605 4710 502584474 502584579 3.740000e-41 180.0
41 TraesCS1D01G416700 chr1B 98.387 62 1 0 4649 4710 126519644 126519705 4.980000e-20 110.0
42 TraesCS1D01G416700 chr5B 89.872 1175 85 15 1 1152 4881125 4882288 0.000000e+00 1480.0
43 TraesCS1D01G416700 chr5B 89.218 946 85 13 1 940 687968962 687968028 0.000000e+00 1166.0
44 TraesCS1D01G416700 chr5B 95.510 490 18 4 2911 3398 37322252 37322739 0.000000e+00 780.0
45 TraesCS1D01G416700 chr5B 93.254 252 15 2 2122 2373 655891761 655891512 2.070000e-98 370.0
46 TraesCS1D01G416700 chr5B 94.444 234 12 1 2140 2373 645505312 645505080 4.480000e-95 359.0
47 TraesCS1D01G416700 chr5B 90.244 82 4 3 1877 1954 448885370 448885451 2.320000e-18 104.0
48 TraesCS1D01G416700 chr3A 89.787 1175 91 15 1 1152 216929390 216930558 0.000000e+00 1478.0
49 TraesCS1D01G416700 chr3A 89.465 1177 93 16 1 1152 217005083 217006253 0.000000e+00 1458.0
50 TraesCS1D01G416700 chr3A 93.600 125 7 1 1977 2101 401131809 401131932 8.050000e-43 185.0
51 TraesCS1D01G416700 chr3A 92.920 113 8 0 1868 1980 216931207 216931319 1.050000e-36 165.0
52 TraesCS1D01G416700 chr3A 92.920 113 8 0 1868 1980 217006641 217006753 1.050000e-36 165.0
53 TraesCS1D01G416700 chrUn 89.185 1202 89 17 1 1176 40348870 40347684 0.000000e+00 1461.0
54 TraesCS1D01G416700 chr3B 87.803 1238 108 23 1 1212 767126848 767128068 0.000000e+00 1410.0
55 TraesCS1D01G416700 chr3B 92.816 696 44 5 2911 3605 816000272 816000962 0.000000e+00 1003.0
56 TraesCS1D01G416700 chr6B 87.399 1238 116 25 1 1212 78508989 78507766 0.000000e+00 1386.0
57 TraesCS1D01G416700 chr6B 92.228 386 20 4 1993 2368 661851457 661851842 5.360000e-149 538.0
58 TraesCS1D01G416700 chr4A 89.070 1107 87 13 1 1085 665579493 665578399 0.000000e+00 1343.0
59 TraesCS1D01G416700 chr4A 90.400 125 12 0 1977 2101 661010598 661010474 1.050000e-36 165.0
60 TraesCS1D01G416700 chr4A 92.958 71 5 0 1815 1885 665577783 665577713 2.320000e-18 104.0
61 TraesCS1D01G416700 chr1A 93.318 868 54 3 1 866 552054961 552054096 0.000000e+00 1279.0
62 TraesCS1D01G416700 chr1A 94.495 545 29 1 2372 2915 563485392 563485936 0.000000e+00 839.0
63 TraesCS1D01G416700 chr1A 93.023 129 8 1 1977 2105 421799763 421799890 2.240000e-43 187.0
64 TraesCS1D01G416700 chr2A 94.590 536 29 0 2380 2915 512512593 512512058 0.000000e+00 830.0
65 TraesCS1D01G416700 chr2A 92.172 396 30 1 1977 2372 512513047 512512653 4.120000e-155 558.0
66 TraesCS1D01G416700 chr2A 98.387 62 1 0 4649 4710 549725968 549725907 4.980000e-20 110.0
67 TraesCS1D01G416700 chr2A 91.463 82 3 3 1877 1954 718458845 718458926 4.980000e-20 110.0
68 TraesCS1D01G416700 chr2B 95.538 493 17 5 2911 3401 320514895 320514406 0.000000e+00 784.0
69 TraesCS1D01G416700 chr2B 93.064 519 32 4 2372 2887 63025329 63025846 0.000000e+00 756.0
70 TraesCS1D01G416700 chr2B 95.775 71 3 0 1815 1885 4967239 4967169 1.070000e-21 115.0
71 TraesCS1D01G416700 chr2B 92.958 71 5 0 1815 1885 759311813 759311883 2.320000e-18 104.0
72 TraesCS1D01G416700 chr4D 94.004 517 29 2 2373 2887 166138514 166139030 0.000000e+00 782.0
73 TraesCS1D01G416700 chr4D 93.810 517 30 2 2373 2887 150649509 150648993 0.000000e+00 776.0
74 TraesCS1D01G416700 chr4D 98.387 62 1 0 4649 4710 271102517 271102578 4.980000e-20 110.0
75 TraesCS1D01G416700 chr6D 92.051 390 23 6 1984 2365 437281615 437282004 4.150000e-150 542.0
76 TraesCS1D01G416700 chr2D 94.810 289 15 0 1977 2265 512459235 512459523 7.190000e-123 451.0
77 TraesCS1D01G416700 chr2D 95.708 233 10 0 2140 2372 58561938 58561706 4.450000e-100 375.0
78 TraesCS1D01G416700 chr2D 94.152 171 10 0 1815 1985 353923838 353924008 1.300000e-65 261.0
79 TraesCS1D01G416700 chr2D 100.000 62 0 0 4649 4710 92066293 92066354 1.070000e-21 115.0
80 TraesCS1D01G416700 chr2D 86.364 88 2 6 1877 1954 584264446 584264533 2.330000e-13 87.9
81 TraesCS1D01G416700 chr7D 92.308 169 13 0 1817 1985 54645034 54645202 1.690000e-59 241.0
82 TraesCS1D01G416700 chr7D 94.366 71 4 0 1815 1885 11836143 11836213 4.980000e-20 110.0


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 TraesCS1D01G416700 chr1D 475429867 475434576 4709 True 3795.500000 5349 100.000000 1 4710 2 chr1D.!!$R2 4709
1 TraesCS1D01G416700 chr1D 69687386 69688371 985 True 1587.000000 1587 95.740000 3348 4331 1 chr1D.!!$R1 983
2 TraesCS1D01G416700 chr7B 68915801 68917209 1408 False 2093.000000 2093 93.437000 3237 4652 1 chr7B.!!$F2 1415
3 TraesCS1D01G416700 chr7B 597764645 597765161 516 False 787.000000 787 94.197000 2373 2887 1 chr7B.!!$F5 514
4 TraesCS1D01G416700 chr7B 709577801 709578317 516 True 782.000000 782 94.004000 2373 2887 1 chr7B.!!$R2 514
5 TraesCS1D01G416700 chr5D 481665871 481667084 1213 True 1849.000000 1849 94.113000 2911 4131 1 chr5D.!!$R1 1220
6 TraesCS1D01G416700 chr5D 526725586 526726732 1146 True 1365.000000 1365 88.534000 1 1129 1 chr5D.!!$R2 1128
7 TraesCS1D01G416700 chr4B 632833416 632834691 1275 True 1844.000000 1844 92.729000 3237 4514 1 chr4B.!!$R2 1277
8 TraesCS1D01G416700 chr4B 515363184 515363701 517 False 773.000000 773 93.642000 2372 2887 1 chr4B.!!$F1 515
9 TraesCS1D01G416700 chr5A 380840305 380841503 1198 True 1753.000000 1753 93.083000 3455 4652 1 chr5A.!!$R1 1197
10 TraesCS1D01G416700 chr5A 633520926 633522121 1195 False 1746.000000 1746 92.994000 3455 4652 1 chr5A.!!$F4 1197
11 TraesCS1D01G416700 chr5A 533747082 533748278 1196 False 1718.000000 1718 92.577000 3455 4652 1 chr5A.!!$F3 1197
12 TraesCS1D01G416700 chr5A 566392564 566393554 990 True 727.500000 856 94.488000 1977 2915 2 chr5A.!!$R3 938
13 TraesCS1D01G416700 chr5A 98738800 98740690 1890 True 548.666667 1269 91.065333 1 1885 3 chr5A.!!$R2 1884
14 TraesCS1D01G416700 chr3D 160280743 160281855 1112 True 1694.000000 1694 94.165000 3221 4332 1 chr3D.!!$R1 1111
15 TraesCS1D01G416700 chr6A 97553971 97555165 1194 True 1688.000000 1688 92.160000 3455 4652 1 chr6A.!!$R1 1197
16 TraesCS1D01G416700 chr6A 595722128 595723329 1201 False 1655.000000 1655 91.470000 2911 4131 1 chr6A.!!$F2 1220
17 TraesCS1D01G416700 chr6A 148688301 148690009 1708 False 665.450000 1243 90.811000 2 1885 2 chr6A.!!$F3 1883
18 TraesCS1D01G416700 chr7A 309080379 309081589 1210 True 1502.000000 1502 89.196000 1 1214 1 chr7A.!!$R1 1213
19 TraesCS1D01G416700 chr7A 655258424 655259290 866 True 1290.000000 1290 93.541000 1 866 1 chr7A.!!$R3 865
20 TraesCS1D01G416700 chr7A 61447400 61449129 1729 True 1207.500000 1607 92.353500 2911 4710 2 chr7A.!!$R4 1799
21 TraesCS1D01G416700 chr1B 502574566 502575766 1200 False 1555.000000 1555 90.016000 2911 4131 1 chr1B.!!$F2 1220
22 TraesCS1D01G416700 chr1B 670003617 670004555 938 False 1170.000000 1170 89.218000 1 940 1 chr1B.!!$F4 939
23 TraesCS1D01G416700 chr5B 4881125 4882288 1163 False 1480.000000 1480 89.872000 1 1152 1 chr5B.!!$F1 1151
24 TraesCS1D01G416700 chr5B 687968028 687968962 934 True 1166.000000 1166 89.218000 1 940 1 chr5B.!!$R3 939
25 TraesCS1D01G416700 chr3A 216929390 216931319 1929 False 821.500000 1478 91.353500 1 1980 2 chr3A.!!$F2 1979
26 TraesCS1D01G416700 chr3A 217005083 217006753 1670 False 811.500000 1458 91.192500 1 1980 2 chr3A.!!$F3 1979
27 TraesCS1D01G416700 chrUn 40347684 40348870 1186 True 1461.000000 1461 89.185000 1 1176 1 chrUn.!!$R1 1175
28 TraesCS1D01G416700 chr3B 767126848 767128068 1220 False 1410.000000 1410 87.803000 1 1212 1 chr3B.!!$F1 1211
29 TraesCS1D01G416700 chr3B 816000272 816000962 690 False 1003.000000 1003 92.816000 2911 3605 1 chr3B.!!$F2 694
30 TraesCS1D01G416700 chr6B 78507766 78508989 1223 True 1386.000000 1386 87.399000 1 1212 1 chr6B.!!$R1 1211
31 TraesCS1D01G416700 chr4A 665577713 665579493 1780 True 723.500000 1343 91.014000 1 1885 2 chr4A.!!$R2 1884
32 TraesCS1D01G416700 chr1A 552054096 552054961 865 True 1279.000000 1279 93.318000 1 866 1 chr1A.!!$R1 865
33 TraesCS1D01G416700 chr1A 563485392 563485936 544 False 839.000000 839 94.495000 2372 2915 1 chr1A.!!$F2 543
34 TraesCS1D01G416700 chr2A 512512058 512513047 989 True 694.000000 830 93.381000 1977 2915 2 chr2A.!!$R2 938
35 TraesCS1D01G416700 chr2B 63025329 63025846 517 False 756.000000 756 93.064000 2372 2887 1 chr2B.!!$F1 515
36 TraesCS1D01G416700 chr4D 166138514 166139030 516 False 782.000000 782 94.004000 2373 2887 1 chr4D.!!$F1 514
37 TraesCS1D01G416700 chr4D 150648993 150649509 516 True 776.000000 776 93.810000 2373 2887 1 chr4D.!!$R1 514

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
944 1041 0.037326 CTCTTGTGCGAACCCTAGCA 60.037 55.0 0.0 0.0 41.55 3.49 F
1896 2403 0.748367 CGATGTCCTCGTCCTCCTCA 60.748 60.0 0.0 0.0 42.56 3.86 F
2722 3336 0.463620 TTTTGGGCAGCGAGCTTTTT 59.536 45.0 0.0 0.0 44.79 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 3001 2.063015 AACAGATCGGGTGTTGGCCA 62.063 55.000 0.00 0.0 36.76 5.36 R
3258 3876 2.038952 TGTGTAGCACAAGCAAGAGGAT 59.961 45.455 0.00 0.0 41.69 3.24 R
4080 4713 1.006220 CAGCTGACAGTACGCCACA 60.006 57.895 8.42 0.0 0.00 4.17 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
212 215 4.282195 ACAATGCGAAGGTTTCCCAATTTA 59.718 37.500 0.00 0.00 0.00 1.40
445 456 4.602957 CGGCGAAAATTTGTCTTTTTCACG 60.603 41.667 0.00 8.36 41.15 4.35
466 477 4.887655 ACGAGAGGTGGATCAAAACTTTTT 59.112 37.500 0.00 0.00 0.00 1.94
469 480 6.313744 AGAGGTGGATCAAAACTTTTTACG 57.686 37.500 0.00 0.00 0.00 3.18
514 525 9.800572 TGTGCATTAAATATGGCCTAGTATTTA 57.199 29.630 17.23 17.23 33.75 1.40
543 554 6.563222 AATGATTTGGTCCAATTTTGCAAG 57.437 33.333 4.80 0.00 0.00 4.01
552 563 9.956640 TTGGTCCAATTTTGCAAGAAATATATT 57.043 25.926 0.00 0.00 0.00 1.28
685 701 4.655027 CACACATGTGCACACTATTGATC 58.345 43.478 24.37 0.00 39.39 2.92
734 751 9.445786 GTAATATGTTGAATGTTACCCGAAATG 57.554 33.333 0.00 0.00 0.00 2.32
739 756 5.160607 TGAATGTTACCCGAAATGAGAGT 57.839 39.130 0.00 0.00 0.00 3.24
853 873 1.502231 CGAACATCCGTCCATCCATC 58.498 55.000 0.00 0.00 0.00 3.51
858 878 1.627329 CATCCGTCCATCCATCCATCT 59.373 52.381 0.00 0.00 0.00 2.90
859 879 1.051008 TCCGTCCATCCATCCATCTG 58.949 55.000 0.00 0.00 0.00 2.90
878 943 1.230116 TCCATCCATCCCACCACCA 60.230 57.895 0.00 0.00 0.00 4.17
924 1020 1.811025 AAACCCCACCCAATCCCTCC 61.811 60.000 0.00 0.00 0.00 4.30
944 1041 0.037326 CTCTTGTGCGAACCCTAGCA 60.037 55.000 0.00 0.00 41.55 3.49
981 1078 2.283809 CCTCCAGACCCCGATCCT 59.716 66.667 0.00 0.00 0.00 3.24
1189 1696 2.203998 CCTCCACCACACCTCCCT 60.204 66.667 0.00 0.00 0.00 4.20
1896 2403 0.748367 CGATGTCCTCGTCCTCCTCA 60.748 60.000 0.00 0.00 42.56 3.86
1960 2467 1.954362 CTCTTCCTCGCCCCACTCTG 61.954 65.000 0.00 0.00 0.00 3.35
2021 2528 4.570663 CACCTCCGTCGGATCGCC 62.571 72.222 15.81 0.00 0.00 5.54
2046 2553 2.992689 TGAGCCTAACGCCGGTCA 60.993 61.111 1.90 0.00 38.78 4.02
2135 2642 3.805891 GAGAGCATCGGGGAGCTGC 62.806 68.421 0.00 0.00 42.04 5.25
2168 2675 2.201022 ACCGACTGCAAGGACTCGT 61.201 57.895 9.22 0.00 39.30 4.18
2224 2731 3.336568 TCCGTCGGGGACTCCTCT 61.337 66.667 12.29 0.00 40.94 3.69
2359 2866 1.153978 GGATGTGTGGTTGCGCATG 60.154 57.895 12.75 0.00 39.39 4.06
2377 2988 2.571757 CGTTCTGCTACTCGGGCA 59.428 61.111 0.00 0.00 38.10 5.36
2410 3021 0.893727 GGCCAACACCCGATCTGTTT 60.894 55.000 0.00 0.00 29.02 2.83
2426 3039 4.632153 TCTGTTTTCTCTACTCCTTGTGC 58.368 43.478 0.00 0.00 0.00 4.57
2505 3118 1.473434 CGGGGCTGATTAGTTGGACTC 60.473 57.143 0.00 0.00 0.00 3.36
2722 3336 0.463620 TTTTGGGCAGCGAGCTTTTT 59.536 45.000 0.00 0.00 44.79 1.94
2730 3344 3.366374 GGCAGCGAGCTTTTTACTGAAAT 60.366 43.478 0.00 0.00 44.79 2.17
2757 3371 8.677300 ACGAGTTTGTTATGCTCATAATTTCAT 58.323 29.630 5.71 0.00 35.90 2.57
2908 3522 7.768120 AGTTTGTAAAAGCAACCAATTCATGAA 59.232 29.630 11.26 11.26 0.00 2.57
3050 3667 9.965824 AGTTAAAATGTTTGTTCAGACAATAGG 57.034 29.630 0.61 0.00 44.71 2.57
3060 3677 5.647658 TGTTCAGACAATAGGGTTTATGCTG 59.352 40.000 0.00 0.00 31.49 4.41
3136 3753 4.367039 AGTTTACCTCTTTGGCTTGCTA 57.633 40.909 0.00 0.00 40.22 3.49
3181 3798 4.164981 ACATCGGCCCTAGAATAATACCA 58.835 43.478 0.00 0.00 0.00 3.25
3234 3852 3.737663 GCTCTCACTCTTGCCATCTACTG 60.738 52.174 0.00 0.00 0.00 2.74
3258 3876 6.666113 TGTGTGTAATTAGGAGTAGGACATGA 59.334 38.462 0.00 0.00 0.00 3.07
3475 4103 6.069905 TGGGTTGAGGCTTAGTGTAATTGATA 60.070 38.462 0.00 0.00 0.00 2.15
3494 4122 4.405680 TGATATACTAGTGCACTGCTTGGT 59.594 41.667 29.57 19.38 0.00 3.67
3781 4412 4.954680 GCGCGTGCGTGCTTTGAA 62.955 61.111 20.75 0.00 46.85 2.69
3978 4609 2.132300 GAGGAGATCCAGGGCTCAC 58.868 63.158 11.10 3.14 38.89 3.51
4050 4683 3.888930 TCTTCCTCCAGTTGCGAATTTTT 59.111 39.130 0.00 0.00 0.00 1.94
4080 4713 0.109132 GCTGTTTATTTGGCTGCGCT 60.109 50.000 9.73 0.00 0.00 5.92
4131 4764 8.035984 GCTTCTGTATTTTCTACTCCAGTACTT 58.964 37.037 0.00 0.00 0.00 2.24
4232 4865 0.554305 TTCATGATGCTGGCTGGGAT 59.446 50.000 0.00 0.00 0.00 3.85
4420 5055 4.129317 AGGTAGTAAGAGTGTGAAGGGT 57.871 45.455 0.00 0.00 0.00 4.34
4439 5074 2.354403 GGTAGGTTATCAAGTGCACGGT 60.354 50.000 12.01 0.00 0.00 4.83
4517 5152 9.959721 GGATTTTAAGCATGGTTCCTATAGATA 57.040 33.333 14.50 0.00 0.00 1.98
4647 5282 6.000891 TGTAGTTTCAGAAACACATGCATC 57.999 37.500 24.85 8.56 43.79 3.91
4662 5297 6.379133 ACACATGCATCTATCCATTTCTTTGT 59.621 34.615 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
381 392 6.273071 GTCAAATTTGAACTGTAGTTGCCTT 58.727 36.000 22.07 0.00 39.21 4.35
445 456 6.371389 CGTAAAAAGTTTTGATCCACCTCTC 58.629 40.000 0.61 0.00 0.00 3.20
575 587 4.524714 TCCATTTTTCGAGTGCCCAAAATA 59.475 37.500 3.59 0.00 29.64 1.40
612 628 4.640364 TGGAGGTTTTCATTTTCATTGCC 58.360 39.130 0.00 0.00 0.00 4.52
651 667 3.584834 CACATGTGTGTATCTTCGGACA 58.415 45.455 18.03 0.00 40.96 4.02
853 873 1.142936 TGGGATGGATGGACAGATGG 58.857 55.000 0.00 0.00 0.00 3.51
858 878 1.570857 GGTGGTGGGATGGATGGACA 61.571 60.000 0.00 0.00 0.00 4.02
859 879 1.227383 GGTGGTGGGATGGATGGAC 59.773 63.158 0.00 0.00 0.00 4.02
878 943 1.384643 GGGGAGAGGGGTATGCTGT 60.385 63.158 0.00 0.00 0.00 4.40
924 1020 0.741221 GCTAGGGTTCGCACAAGAGG 60.741 60.000 0.00 0.00 0.00 3.69
971 1068 0.397254 CTAGTCACCAGGATCGGGGT 60.397 60.000 0.00 4.25 38.10 4.95
1189 1696 1.198094 TTCTGCATCGAGGTGGGGAA 61.198 55.000 0.00 0.00 0.00 3.97
1840 2347 4.446413 GGTCGTGGGGTGTAGGCG 62.446 72.222 0.00 0.00 0.00 5.52
1910 2417 3.378399 GAGCTCCTTGGCCGTCTCC 62.378 68.421 0.87 0.00 0.00 3.71
2060 2567 3.458163 GTCCCGATGCACCTCCGA 61.458 66.667 0.00 0.00 0.00 4.55
2150 2657 2.201022 ACGAGTCCTTGCAGTCGGT 61.201 57.895 4.31 0.00 42.52 4.69
2359 2866 2.886124 GCCCGAGTAGCAGAACGC 60.886 66.667 0.00 0.00 42.91 4.84
2390 3001 2.063015 AACAGATCGGGTGTTGGCCA 62.063 55.000 0.00 0.00 36.76 5.36
2410 3021 8.135382 ACTAAAATAGCACAAGGAGTAGAGAA 57.865 34.615 0.00 0.00 0.00 2.87
2451 3064 2.457598 CTACAGGGACTAGGTTGCTCA 58.542 52.381 0.00 0.00 36.02 4.26
2505 3118 2.482864 GGCAAAACAATCCACACCAAG 58.517 47.619 0.00 0.00 0.00 3.61
2722 3336 7.815549 TGAGCATAACAAACTCGTATTTCAGTA 59.184 33.333 0.00 0.00 32.98 2.74
2730 3344 9.157104 TGAAATTATGAGCATAACAAACTCGTA 57.843 29.630 5.15 0.00 36.24 3.43
2757 3371 4.225042 ACAACTCATATGTAGAGGCCAACA 59.775 41.667 5.01 6.81 37.43 3.33
2908 3522 4.220602 AGCCAAACTTCACACTGAGTTTTT 59.779 37.500 0.00 0.00 30.82 1.94
2976 3593 8.423349 TGACATTTTGGATCAATCAGAAAAAGT 58.577 29.630 0.00 6.88 30.86 2.66
3084 3701 7.510001 TCCCATTACAGAATGCAAATTCCATAT 59.490 33.333 0.00 0.00 42.53 1.78
3136 3753 2.121948 TCATCTCTAGGGCACAGCAAT 58.878 47.619 0.00 0.00 0.00 3.56
3181 3798 3.439857 TGGAAGTGCAATAAAGAGGCT 57.560 42.857 0.00 0.00 0.00 4.58
3234 3852 7.108841 TCATGTCCTACTCCTAATTACACAC 57.891 40.000 0.00 0.00 0.00 3.82
3258 3876 2.038952 TGTGTAGCACAAGCAAGAGGAT 59.961 45.455 0.00 0.00 41.69 3.24
3475 4103 2.303022 ACACCAAGCAGTGCACTAGTAT 59.697 45.455 21.20 3.27 41.67 2.12
3577 4206 2.305928 TGCTGCAACTTTAAGCCAAGA 58.694 42.857 0.00 0.00 36.05 3.02
3631 4260 5.045215 ACATCGCCAATAAATTGCAGATTG 58.955 37.500 7.80 0.00 36.48 2.67
3838 4469 2.804167 CAGCATCTCGTCGCCTCT 59.196 61.111 0.00 0.00 0.00 3.69
4080 4713 1.006220 CAGCTGACAGTACGCCACA 60.006 57.895 8.42 0.00 0.00 4.17
4415 5050 3.618997 CGTGCACTTGATAACCTACCCTT 60.619 47.826 16.19 0.00 0.00 3.95
4420 5055 3.331150 CAACCGTGCACTTGATAACCTA 58.669 45.455 16.19 0.00 0.00 3.08
4531 5166 3.918591 CAGACAAAGATGAGTTGCAATGC 59.081 43.478 0.59 0.00 0.00 3.56
4543 5178 7.149202 TGGCCTTATAATACCAGACAAAGAT 57.851 36.000 3.32 0.00 0.00 2.40
4647 5282 6.373774 ACAAGAGCAGACAAAGAAATGGATAG 59.626 38.462 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.