Multiple sequence alignment - TraesCS1B01G137200

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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 TraesCS1B01G137200 chr1B 100.000 2699 0 0 1 2699 175276995 175274297 0.000000e+00 4985.0
1 TraesCS1B01G137200 chr1B 89.051 548 33 8 2161 2682 268542550 268543096 0.000000e+00 654.0
2 TraesCS1B01G137200 chr1B 83.938 386 36 14 1127 1497 174763499 174763125 1.990000e-91 346.0
3 TraesCS1B01G137200 chr1B 85.714 287 20 7 1210 1475 174784173 174783887 1.580000e-72 283.0
4 TraesCS1B01G137200 chr1B 98.551 69 1 0 1960 2028 175274969 175274901 3.650000e-24 122.0
5 TraesCS1B01G137200 chr1B 97.500 40 1 0 1909 1948 268542413 268542452 4.820000e-08 69.4
6 TraesCS1B01G137200 chr1A 88.604 1913 115 51 1 1860 124788416 124786554 0.000000e+00 2230.0
7 TraesCS1B01G137200 chr1A 80.046 436 55 18 1089 1509 124181630 124181212 7.310000e-76 294.0
8 TraesCS1B01G137200 chr1A 79.612 412 31 26 1111 1474 124190179 124189773 2.080000e-61 246.0
9 TraesCS1B01G137200 chr1D 92.068 769 23 13 1107 1854 114313723 114312972 0.000000e+00 1048.0
10 TraesCS1B01G137200 chr1D 87.241 627 37 23 447 1035 114314376 114313755 0.000000e+00 675.0
11 TraesCS1B01G137200 chr1D 91.429 455 28 7 1 448 114316207 114315757 4.940000e-172 614.0
12 TraesCS1B01G137200 chr1D 83.028 436 45 15 1089 1509 114065186 114064765 4.250000e-98 368.0
13 TraesCS1B01G137200 chr1D 81.592 402 30 20 1112 1474 114083654 114083258 2.630000e-75 292.0
14 TraesCS1B01G137200 chr6B 91.630 681 23 14 2027 2678 188502868 188502193 0.000000e+00 911.0
15 TraesCS1B01G137200 chr6B 89.147 129 3 7 1909 2028 188502919 188502793 1.670000e-32 150.0
16 TraesCS1B01G137200 chrUn 91.189 681 27 14 2026 2677 67460517 67459841 0.000000e+00 894.0
17 TraesCS1B01G137200 chrUn 91.176 680 27 14 2027 2677 300660378 300659703 0.000000e+00 893.0
18 TraesCS1B01G137200 chrUn 91.176 680 27 14 2027 2677 300669726 300669051 0.000000e+00 893.0
19 TraesCS1B01G137200 chrUn 91.176 680 27 14 2027 2677 339772733 339772058 0.000000e+00 893.0
20 TraesCS1B01G137200 chrUn 88.372 129 4 7 1909 2028 339772784 339772658 7.790000e-31 145.0
21 TraesCS1B01G137200 chrUn 87.597 129 5 7 1909 2028 67460567 67460441 3.620000e-29 139.0
22 TraesCS1B01G137200 chr6A 89.118 680 38 12 2027 2673 524713342 524714018 0.000000e+00 813.0
23 TraesCS1B01G137200 chr6A 86.235 247 26 3 2442 2680 524713358 524713112 7.410000e-66 261.0
24 TraesCS1B01G137200 chr6A 92.593 81 5 1 1900 1979 524713857 524713777 6.110000e-22 115.0
25 TraesCS1B01G137200 chr7A 88.807 679 17 22 2027 2676 195277535 195278183 0.000000e+00 778.0
26 TraesCS1B01G137200 chr7A 84.181 177 5 4 1872 2028 195277437 195277610 1.670000e-32 150.0
27 TraesCS1B01G137200 chr6D 87.353 680 49 17 2027 2673 337506081 337506756 0.000000e+00 745.0
28 TraesCS1B01G137200 chr6D 80.791 177 10 13 1872 2028 337505984 337506156 1.700000e-22 117.0
29 TraesCS1B01G137200 chr6D 94.366 71 4 0 1909 1979 337506584 337506514 2.840000e-20 110.0
30 TraesCS1B01G137200 chr7B 82.085 307 24 8 2027 2304 742403325 742403629 1.620000e-57 233.0
31 TraesCS1B01G137200 chr7B 86.145 166 15 5 2034 2194 82706307 82706145 3.570000e-39 172.0
32 TraesCS1B01G137200 chr3D 95.960 99 4 0 1364 1462 86237179 86237277 7.730000e-36 161.0
33 TraesCS1B01G137200 chr7D 87.313 134 7 7 2547 2672 614793535 614793666 7.790000e-31 145.0


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 TraesCS1B01G137200 chr1B 175274297 175276995 2698 True 2553.5 4985 99.2755 1 2699 2 chr1B.!!$R3 2698
1 TraesCS1B01G137200 chr1B 268542413 268543096 683 False 361.7 654 93.2755 1909 2682 2 chr1B.!!$F1 773
2 TraesCS1B01G137200 chr1A 124786554 124788416 1862 True 2230.0 2230 88.6040 1 1860 1 chr1A.!!$R3 1859
3 TraesCS1B01G137200 chr1D 114312972 114316207 3235 True 779.0 1048 90.2460 1 1854 3 chr1D.!!$R3 1853
4 TraesCS1B01G137200 chr6B 188502193 188502919 726 True 530.5 911 90.3885 1909 2678 2 chr6B.!!$R1 769
5 TraesCS1B01G137200 chrUn 300659703 300660378 675 True 893.0 893 91.1760 2027 2677 1 chrUn.!!$R1 650
6 TraesCS1B01G137200 chrUn 300669051 300669726 675 True 893.0 893 91.1760 2027 2677 1 chrUn.!!$R2 650
7 TraesCS1B01G137200 chrUn 339772058 339772784 726 True 519.0 893 89.7740 1909 2677 2 chrUn.!!$R4 768
8 TraesCS1B01G137200 chrUn 67459841 67460567 726 True 516.5 894 89.3930 1909 2677 2 chrUn.!!$R3 768
9 TraesCS1B01G137200 chr6A 524713342 524714018 676 False 813.0 813 89.1180 2027 2673 1 chr6A.!!$F1 646
10 TraesCS1B01G137200 chr7A 195277437 195278183 746 False 464.0 778 86.4940 1872 2676 2 chr7A.!!$F1 804
11 TraesCS1B01G137200 chr6D 337505984 337506756 772 False 431.0 745 84.0720 1872 2673 2 chr6D.!!$F1 801

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
450 465 0.81401 AGGGAACTGACGTGTGTTGC 60.814 55.0 11.5 11.5 41.13 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 3605 1.013596 GCATGCATTAGCCACGTACA 58.986 50.0 14.21 0.0 41.13 2.9 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
23 24 1.832998 TGCTCTCATGACAGGCATACA 59.167 47.619 0.00 0.00 34.82 2.29
24 25 2.436911 TGCTCTCATGACAGGCATACAT 59.563 45.455 0.00 0.00 34.82 2.29
25 26 3.065655 GCTCTCATGACAGGCATACATC 58.934 50.000 0.00 0.00 34.82 3.06
146 148 1.472662 GGGGCCATCTAGCGAGCTAA 61.473 60.000 4.39 0.00 0.00 3.09
194 196 5.813672 TGGAGACGGTAAAATACAGCAATAC 59.186 40.000 0.00 0.00 0.00 1.89
200 205 7.779073 ACGGTAAAATACAGCAATACTACTCT 58.221 34.615 0.00 0.00 0.00 3.24
206 211 8.480643 AAATACAGCAATACTACTCTTGTGTC 57.519 34.615 0.00 0.00 0.00 3.67
212 217 2.423926 ACTACTCTTGTGTCGTGCAG 57.576 50.000 0.00 0.00 0.00 4.41
275 280 8.400947 GTTGTATCTACCAGAAACATCTACGTA 58.599 37.037 0.00 0.00 0.00 3.57
332 337 4.566488 GGCAGGGATAAGGATGGAGTAATG 60.566 50.000 0.00 0.00 0.00 1.90
374 382 1.270094 GGCCACCTTTTGCCTTGTAAC 60.270 52.381 0.00 0.00 44.46 2.50
450 465 0.814010 AGGGAACTGACGTGTGTTGC 60.814 55.000 11.50 11.50 41.13 4.17
456 1848 0.924777 CTGACGTGTGTTGCGTTGTA 59.075 50.000 0.00 0.00 43.04 2.41
457 1849 1.325037 CTGACGTGTGTTGCGTTGTAA 59.675 47.619 0.00 0.00 43.04 2.41
459 1851 2.033577 TGACGTGTGTTGCGTTGTAATC 60.034 45.455 0.00 0.00 43.04 1.75
526 1922 3.908081 ACGCAGTCACCGTCCGTT 61.908 61.111 0.00 0.00 29.74 4.44
543 1939 5.389098 CGTCCGTTCATCGTTAGAAAATTGT 60.389 40.000 0.00 0.00 37.94 2.71
545 1941 5.086058 CCGTTCATCGTTAGAAAATTGTGG 58.914 41.667 0.00 0.00 37.94 4.17
546 1942 5.106869 CCGTTCATCGTTAGAAAATTGTGGA 60.107 40.000 0.00 0.00 37.94 4.02
547 1943 6.403200 CCGTTCATCGTTAGAAAATTGTGGAT 60.403 38.462 0.00 0.00 37.94 3.41
548 1944 6.682863 CGTTCATCGTTAGAAAATTGTGGATC 59.317 38.462 0.00 0.00 34.52 3.36
549 1945 6.677781 TCATCGTTAGAAAATTGTGGATCC 57.322 37.500 4.20 4.20 0.00 3.36
560 1963 2.204136 TGGATCCAGCTGGTGGGT 60.204 61.111 31.58 19.06 45.49 4.51
594 1997 3.041940 GTGTGAGGCGTGAACGGG 61.042 66.667 4.84 0.00 40.23 5.28
652 2055 6.905076 CACGGATTATGTTTGTTACTGTATGC 59.095 38.462 0.00 0.00 0.00 3.14
653 2056 6.821665 ACGGATTATGTTTGTTACTGTATGCT 59.178 34.615 0.00 0.00 0.00 3.79
654 2057 7.335924 ACGGATTATGTTTGTTACTGTATGCTT 59.664 33.333 0.00 0.00 0.00 3.91
655 2058 8.181573 CGGATTATGTTTGTTACTGTATGCTTT 58.818 33.333 0.00 0.00 0.00 3.51
656 2059 9.855021 GGATTATGTTTGTTACTGTATGCTTTT 57.145 29.630 0.00 0.00 0.00 2.27
658 2061 9.638239 ATTATGTTTGTTACTGTATGCTTTTGG 57.362 29.630 0.00 0.00 0.00 3.28
659 2062 6.701145 TGTTTGTTACTGTATGCTTTTGGA 57.299 33.333 0.00 0.00 0.00 3.53
660 2063 6.734137 TGTTTGTTACTGTATGCTTTTGGAG 58.266 36.000 0.00 0.00 0.00 3.86
731 2136 3.457234 TCATCCAAGATCCGAAACATCG 58.543 45.455 0.00 0.00 0.00 3.84
821 2240 3.700831 AACGGTTTCACGGCCACCA 62.701 57.895 2.24 0.00 38.39 4.17
1035 2477 0.439985 CACCGTCTCGCATTTCACAG 59.560 55.000 0.00 0.00 0.00 3.66
1036 2478 1.291877 ACCGTCTCGCATTTCACAGC 61.292 55.000 0.00 0.00 0.00 4.40
1038 2480 0.792640 CGTCTCGCATTTCACAGCTT 59.207 50.000 0.00 0.00 0.00 3.74
1039 2481 1.201855 CGTCTCGCATTTCACAGCTTC 60.202 52.381 0.00 0.00 0.00 3.86
1040 2482 1.800586 GTCTCGCATTTCACAGCTTCA 59.199 47.619 0.00 0.00 0.00 3.02
1041 2483 2.417933 GTCTCGCATTTCACAGCTTCAT 59.582 45.455 0.00 0.00 0.00 2.57
1043 2485 3.503363 TCTCGCATTTCACAGCTTCATTT 59.497 39.130 0.00 0.00 0.00 2.32
1045 2487 4.722194 TCGCATTTCACAGCTTCATTTAC 58.278 39.130 0.00 0.00 0.00 2.01
1046 2488 4.215185 TCGCATTTCACAGCTTCATTTACA 59.785 37.500 0.00 0.00 0.00 2.41
1047 2489 4.916831 CGCATTTCACAGCTTCATTTACAA 59.083 37.500 0.00 0.00 0.00 2.41
1048 2490 5.060077 CGCATTTCACAGCTTCATTTACAAG 59.940 40.000 0.00 0.00 0.00 3.16
1049 2491 5.922544 GCATTTCACAGCTTCATTTACAAGT 59.077 36.000 0.00 0.00 0.00 3.16
1050 2492 6.088616 GCATTTCACAGCTTCATTTACAAGTC 59.911 38.462 0.00 0.00 0.00 3.01
1054 2496 3.433615 ACAGCTTCATTTACAAGTCTCGC 59.566 43.478 0.00 0.00 0.00 5.03
1061 2503 1.241165 TTACAAGTCTCGCCGTCTCA 58.759 50.000 0.00 0.00 0.00 3.27
1062 2504 1.460504 TACAAGTCTCGCCGTCTCAT 58.539 50.000 0.00 0.00 0.00 2.90
1063 2505 0.171455 ACAAGTCTCGCCGTCTCATC 59.829 55.000 0.00 0.00 0.00 2.92
1066 2508 2.122167 GTCTCGCCGTCTCATCCCT 61.122 63.158 0.00 0.00 0.00 4.20
1067 2509 1.824329 TCTCGCCGTCTCATCCCTC 60.824 63.158 0.00 0.00 0.00 4.30
1069 2511 2.105128 CGCCGTCTCATCCCTCAC 59.895 66.667 0.00 0.00 0.00 3.51
1071 2513 3.095347 GCCGTCTCATCCCTCACCC 62.095 68.421 0.00 0.00 0.00 4.61
1080 2522 1.919600 ATCCCTCACCCAAGCAGAGC 61.920 60.000 0.00 0.00 0.00 4.09
1086 2528 2.360852 CCCAAGCAGAGCACCCAG 60.361 66.667 0.00 0.00 0.00 4.45
1312 2766 4.570663 ACTACATCGAGGCCGCGC 62.571 66.667 25.23 0.00 35.37 6.86
1487 2941 1.974343 CCTAGGAGAGATCCGGCCG 60.974 68.421 21.04 21.04 34.28 6.13
1639 3096 3.952323 GGGGATCTAGTTTTAGGGTTTGC 59.048 47.826 0.00 0.00 0.00 3.68
1681 3138 3.224324 GCGATGCTCCCCGGTCTA 61.224 66.667 0.00 0.00 0.00 2.59
1732 3189 5.311265 ACAAGCTCAGAATCAGATGTTTCA 58.689 37.500 6.45 0.00 0.00 2.69
1733 3190 5.411977 ACAAGCTCAGAATCAGATGTTTCAG 59.588 40.000 6.45 0.00 0.00 3.02
1734 3191 5.417754 AGCTCAGAATCAGATGTTTCAGA 57.582 39.130 6.45 3.45 0.00 3.27
1735 3192 5.802465 AGCTCAGAATCAGATGTTTCAGAA 58.198 37.500 6.45 0.00 0.00 3.02
1736 3193 6.416415 AGCTCAGAATCAGATGTTTCAGAAT 58.584 36.000 6.45 0.00 0.00 2.40
1737 3194 6.539464 AGCTCAGAATCAGATGTTTCAGAATC 59.461 38.462 6.45 0.00 0.00 2.52
1738 3195 6.315642 GCTCAGAATCAGATGTTTCAGAATCA 59.684 38.462 6.45 0.00 0.00 2.57
1739 3196 7.466185 GCTCAGAATCAGATGTTTCAGAATCAG 60.466 40.741 6.45 0.00 0.00 2.90
1740 3197 7.618137 TCAGAATCAGATGTTTCAGAATCAGA 58.382 34.615 6.45 0.00 0.00 3.27
1741 3198 8.265764 TCAGAATCAGATGTTTCAGAATCAGAT 58.734 33.333 6.45 0.00 32.31 2.90
1742 3199 8.338986 CAGAATCAGATGTTTCAGAATCAGATG 58.661 37.037 6.45 2.28 31.64 2.90
1743 3200 8.047911 AGAATCAGATGTTTCAGAATCAGATGT 58.952 33.333 6.45 0.00 31.64 3.06
1744 3201 8.577048 AATCAGATGTTTCAGAATCAGATGTT 57.423 30.769 0.58 0.00 31.64 2.71
1745 3202 7.991084 TCAGATGTTTCAGAATCAGATGTTT 57.009 32.000 0.58 0.00 0.00 2.83
1746 3203 8.037382 TCAGATGTTTCAGAATCAGATGTTTC 57.963 34.615 0.58 0.00 0.00 2.78
1752 3209 7.388776 TGTTTCAGAATCAGATGTTTCGATTCT 59.611 33.333 7.82 7.82 44.12 2.40
1753 3210 8.873830 GTTTCAGAATCAGATGTTTCGATTCTA 58.126 33.333 12.19 0.00 42.96 2.10
1826 3288 3.187700 GCCGTCGTACATCTGAATTTCT 58.812 45.455 0.00 0.00 0.00 2.52
1830 3292 5.444613 CCGTCGTACATCTGAATTTCTGTTG 60.445 44.000 10.90 10.90 0.00 3.33
1843 3305 3.423539 TTCTGTTGGTTCTGGATCTGG 57.576 47.619 0.00 0.00 0.00 3.86
1854 3316 6.268617 TGGTTCTGGATCTGGATATCAGTTAG 59.731 42.308 4.83 0.00 43.76 2.34
1855 3317 5.991933 TCTGGATCTGGATATCAGTTAGC 57.008 43.478 4.83 0.00 43.76 3.09
1860 3322 5.714333 GGATCTGGATATCAGTTAGCTCTGA 59.286 44.000 7.51 7.51 46.39 3.27
1861 3323 6.210385 GGATCTGGATATCAGTTAGCTCTGAA 59.790 42.308 9.01 0.82 45.65 3.02
1862 3324 6.398234 TCTGGATATCAGTTAGCTCTGAAC 57.602 41.667 9.01 0.00 45.65 3.18
1863 3325 5.303078 TCTGGATATCAGTTAGCTCTGAACC 59.697 44.000 9.01 12.18 45.65 3.62
1864 3326 5.211973 TGGATATCAGTTAGCTCTGAACCT 58.788 41.667 9.01 0.00 45.65 3.50
1865 3327 6.373759 TGGATATCAGTTAGCTCTGAACCTA 58.626 40.000 9.01 0.00 45.65 3.08
1866 3328 7.013220 TGGATATCAGTTAGCTCTGAACCTAT 58.987 38.462 9.01 3.64 45.65 2.57
1867 3329 7.177568 TGGATATCAGTTAGCTCTGAACCTATC 59.822 40.741 9.01 10.92 45.65 2.08
1868 3330 5.799827 ATCAGTTAGCTCTGAACCTATCC 57.200 43.478 9.01 0.00 45.65 2.59
1869 3331 4.610333 TCAGTTAGCTCTGAACCTATCCA 58.390 43.478 2.73 0.00 40.82 3.41
1870 3332 5.023452 TCAGTTAGCTCTGAACCTATCCAA 58.977 41.667 2.73 0.00 40.82 3.53
1871 3333 5.127845 TCAGTTAGCTCTGAACCTATCCAAG 59.872 44.000 2.73 0.00 40.82 3.61
1872 3334 2.998316 AGCTCTGAACCTATCCAAGC 57.002 50.000 0.00 0.00 35.75 4.01
1873 3335 1.488393 AGCTCTGAACCTATCCAAGCC 59.512 52.381 0.00 0.00 35.99 4.35
1874 3336 1.808133 GCTCTGAACCTATCCAAGCCG 60.808 57.143 0.00 0.00 31.65 5.52
1875 3337 1.757118 CTCTGAACCTATCCAAGCCGA 59.243 52.381 0.00 0.00 0.00 5.54
1876 3338 2.168521 CTCTGAACCTATCCAAGCCGAA 59.831 50.000 0.00 0.00 0.00 4.30
1886 3348 2.244695 TCCAAGCCGAAAGTAGACTCA 58.755 47.619 0.00 0.00 0.00 3.41
1942 3415 0.823356 TTTTCGGCTTTGCTCTGGCT 60.823 50.000 0.00 0.00 39.59 4.75
1996 3469 3.845259 GCCTGGCCGGTGATCGTA 61.845 66.667 11.58 0.00 37.11 3.43
1997 3470 2.417516 CCTGGCCGGTGATCGTAG 59.582 66.667 11.58 0.00 37.11 3.51
1998 3471 2.279517 CTGGCCGGTGATCGTAGC 60.280 66.667 2.29 0.00 37.11 3.58
1999 3472 4.201679 TGGCCGGTGATCGTAGCG 62.202 66.667 1.90 0.00 40.91 4.26
2000 3473 4.203076 GGCCGGTGATCGTAGCGT 62.203 66.667 1.90 0.00 39.71 5.07
2001 3474 2.717485 GCCGGTGATCGTAGCGTA 59.283 61.111 1.90 0.00 39.71 4.42
2002 3475 1.656569 GCCGGTGATCGTAGCGTAC 60.657 63.158 1.90 0.00 39.71 3.67
2003 3476 1.723273 CCGGTGATCGTAGCGTACA 59.277 57.895 0.00 0.00 39.71 2.90
2004 3477 0.309922 CCGGTGATCGTAGCGTACAT 59.690 55.000 0.00 0.00 39.71 2.29
2005 3478 1.532437 CCGGTGATCGTAGCGTACATA 59.468 52.381 0.00 0.00 39.71 2.29
2006 3479 2.161012 CCGGTGATCGTAGCGTACATAT 59.839 50.000 0.00 0.00 39.71 1.78
2007 3480 3.161306 CGGTGATCGTAGCGTACATATG 58.839 50.000 0.00 0.00 36.85 1.78
2008 3481 3.120442 CGGTGATCGTAGCGTACATATGA 60.120 47.826 10.38 0.00 36.85 2.15
2009 3482 4.436986 CGGTGATCGTAGCGTACATATGAT 60.437 45.833 10.38 8.75 36.85 2.45
2010 3483 4.793731 GGTGATCGTAGCGTACATATGATG 59.206 45.833 10.38 0.00 30.71 3.07
2011 3484 4.263209 GTGATCGTAGCGTACATATGATGC 59.737 45.833 10.38 9.84 30.71 3.91
2012 3485 3.907894 TCGTAGCGTACATATGATGCA 57.092 42.857 10.38 0.00 0.00 3.96
2013 3486 4.434713 TCGTAGCGTACATATGATGCAT 57.565 40.909 10.38 0.00 0.00 3.96
2014 3487 4.805219 TCGTAGCGTACATATGATGCATT 58.195 39.130 10.38 0.00 0.00 3.56
2015 3488 5.945155 TCGTAGCGTACATATGATGCATTA 58.055 37.500 10.38 0.00 0.00 1.90
2016 3489 6.027749 TCGTAGCGTACATATGATGCATTAG 58.972 40.000 10.38 4.05 0.00 1.73
2017 3490 6.027749 CGTAGCGTACATATGATGCATTAGA 58.972 40.000 10.38 0.00 0.00 2.10
2018 3491 6.021390 CGTAGCGTACATATGATGCATTAGAC 60.021 42.308 10.38 4.36 0.00 2.59
2019 3492 6.030548 AGCGTACATATGATGCATTAGACT 57.969 37.500 10.38 0.00 0.00 3.24
2020 3493 7.158099 AGCGTACATATGATGCATTAGACTA 57.842 36.000 10.38 0.00 0.00 2.59
2021 3494 7.602753 AGCGTACATATGATGCATTAGACTAA 58.397 34.615 10.38 0.00 0.00 2.24
2022 3495 8.253810 AGCGTACATATGATGCATTAGACTAAT 58.746 33.333 10.38 1.63 0.00 1.73
2023 3496 8.323854 GCGTACATATGATGCATTAGACTAATG 58.676 37.037 24.94 24.94 46.37 1.90
2066 3548 3.071837 TGGCCGGTGATCGTAGCA 61.072 61.111 1.90 0.00 37.11 3.49
2123 3605 1.333619 GATCGGTATTGCATGCGGTTT 59.666 47.619 14.09 0.00 0.00 3.27
2136 3618 1.081094 GCGGTTTGTACGTGGCTAAT 58.919 50.000 0.00 0.00 0.00 1.73
2152 3634 1.534163 CTAATGCATGCATCAGGACCG 59.466 52.381 32.25 12.27 35.31 4.79
2258 3770 4.335874 AGAAGTACTGGCATACGAGTACAG 59.664 45.833 17.48 5.35 44.74 2.74
2268 3780 5.177511 GGCATACGAGTACAGTATACGTACA 59.822 44.000 25.65 14.18 41.40 2.90
2304 3816 2.066262 GGCAAGCACGCGTATGTATAT 58.934 47.619 13.44 0.00 0.00 0.86
2376 3896 0.249120 TCGGCATCAAATCTCGGTGT 59.751 50.000 0.00 0.00 0.00 4.16
2617 4159 6.377146 AGGCCGACAGATTTTACAAATAACAT 59.623 34.615 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 148 1.447317 CTTGTCACCTTTGCGCTGGT 61.447 55.000 9.73 11.78 36.96 4.00
152 154 0.307760 CACGTCCTTGTCACCTTTGC 59.692 55.000 0.00 0.00 0.00 3.68
182 184 6.752351 CGACACAAGAGTAGTATTGCTGTATT 59.248 38.462 4.83 0.00 0.00 1.89
194 196 2.320367 GTCTGCACGACACAAGAGTAG 58.680 52.381 10.30 0.00 42.37 2.57
206 211 5.139077 AGTGAATACTAACACGTCTGCACG 61.139 45.833 0.00 0.00 43.11 5.34
212 217 6.323266 AGATCACAGTGAATACTAACACGTC 58.677 40.000 7.50 0.00 41.22 4.34
275 280 2.039462 GGGCTGCCCAGGGAATTT 59.961 61.111 32.46 0.00 44.65 1.82
432 447 1.647084 GCAACACACGTCAGTTCCC 59.353 57.895 0.00 0.00 0.00 3.97
450 465 7.494625 TCCAAGCCTAGATTTAAGATTACAACG 59.505 37.037 0.00 0.00 0.00 4.10
456 1848 7.200434 TCACTCCAAGCCTAGATTTAAGATT 57.800 36.000 0.00 0.00 0.00 2.40
457 1849 6.814954 TCACTCCAAGCCTAGATTTAAGAT 57.185 37.500 0.00 0.00 0.00 2.40
459 1851 7.872113 ATTTCACTCCAAGCCTAGATTTAAG 57.128 36.000 0.00 0.00 0.00 1.85
526 1922 6.176896 TGGATCCACAATTTTCTAACGATGA 58.823 36.000 11.44 0.00 0.00 2.92
543 1939 1.852157 AACCCACCAGCTGGATCCA 60.852 57.895 39.19 15.27 43.95 3.41
545 1941 2.048603 GCAACCCACCAGCTGGATC 61.049 63.158 39.19 14.46 43.95 3.36
546 1942 2.036256 GCAACCCACCAGCTGGAT 59.964 61.111 39.19 20.19 43.95 3.41
547 1943 3.067084 TTGCAACCCACCAGCTGGA 62.067 57.895 39.19 11.44 43.95 3.86
548 1944 2.521465 TTGCAACCCACCAGCTGG 60.521 61.111 31.60 31.60 40.26 4.85
549 1945 1.394266 AAGTTGCAACCCACCAGCTG 61.394 55.000 25.62 6.78 0.00 4.24
560 1963 0.457851 CACGGGGACAAAAGTTGCAA 59.542 50.000 0.00 0.00 0.00 4.08
652 2055 1.017387 GTAGGATGCCGCTCCAAAAG 58.983 55.000 10.36 0.00 37.81 2.27
653 2056 0.326595 TGTAGGATGCCGCTCCAAAA 59.673 50.000 10.36 0.00 37.81 2.44
654 2057 0.546122 ATGTAGGATGCCGCTCCAAA 59.454 50.000 10.36 0.00 37.81 3.28
655 2058 0.546122 AATGTAGGATGCCGCTCCAA 59.454 50.000 10.36 0.00 37.81 3.53
656 2059 0.179048 CAATGTAGGATGCCGCTCCA 60.179 55.000 10.36 0.00 37.81 3.86
657 2060 1.510480 GCAATGTAGGATGCCGCTCC 61.510 60.000 0.00 0.00 36.56 4.70
658 2061 0.533755 AGCAATGTAGGATGCCGCTC 60.534 55.000 0.00 0.00 43.57 5.03
659 2062 0.816825 CAGCAATGTAGGATGCCGCT 60.817 55.000 0.00 0.00 43.57 5.52
660 2063 1.650912 CAGCAATGTAGGATGCCGC 59.349 57.895 0.00 0.00 43.57 6.53
661 2064 1.096967 TGCAGCAATGTAGGATGCCG 61.097 55.000 0.00 0.00 46.47 5.69
664 2067 3.853831 TTGTTGCAGCAATGTAGGATG 57.146 42.857 12.36 0.00 0.00 3.51
665 2068 4.081406 TCTTTGTTGCAGCAATGTAGGAT 58.919 39.130 22.54 0.00 0.00 3.24
821 2240 0.322322 TTTTACTGCCGGACGGTGAT 59.678 50.000 5.05 0.63 38.72 3.06
1035 2477 2.222819 CGGCGAGACTTGTAAATGAAGC 60.223 50.000 0.00 0.00 0.00 3.86
1036 2478 2.993899 ACGGCGAGACTTGTAAATGAAG 59.006 45.455 16.62 0.00 0.00 3.02
1038 2480 2.230508 AGACGGCGAGACTTGTAAATGA 59.769 45.455 16.62 0.00 0.00 2.57
1039 2481 2.599082 GAGACGGCGAGACTTGTAAATG 59.401 50.000 16.62 0.00 0.00 2.32
1040 2482 2.230508 TGAGACGGCGAGACTTGTAAAT 59.769 45.455 16.62 0.00 0.00 1.40
1041 2483 1.610038 TGAGACGGCGAGACTTGTAAA 59.390 47.619 16.62 0.00 0.00 2.01
1043 2485 1.400846 GATGAGACGGCGAGACTTGTA 59.599 52.381 16.62 1.83 0.00 2.41
1045 2487 0.526524 GGATGAGACGGCGAGACTTG 60.527 60.000 16.62 0.00 0.00 3.16
1046 2488 1.668101 GGGATGAGACGGCGAGACTT 61.668 60.000 16.62 1.92 0.00 3.01
1047 2489 2.122167 GGGATGAGACGGCGAGACT 61.122 63.158 16.62 9.95 0.00 3.24
1048 2490 2.065906 GAGGGATGAGACGGCGAGAC 62.066 65.000 16.62 4.50 0.00 3.36
1049 2491 1.824329 GAGGGATGAGACGGCGAGA 60.824 63.158 16.62 0.00 0.00 4.04
1050 2492 2.121538 TGAGGGATGAGACGGCGAG 61.122 63.158 16.62 0.00 0.00 5.03
1054 2496 1.264749 TTGGGTGAGGGATGAGACGG 61.265 60.000 0.00 0.00 0.00 4.79
1061 2503 1.919600 GCTCTGCTTGGGTGAGGGAT 61.920 60.000 0.00 0.00 0.00 3.85
1062 2504 2.596851 GCTCTGCTTGGGTGAGGGA 61.597 63.158 0.00 0.00 0.00 4.20
1063 2505 2.045536 GCTCTGCTTGGGTGAGGG 60.046 66.667 0.00 0.00 0.00 4.30
1066 2508 2.431683 GGTGCTCTGCTTGGGTGA 59.568 61.111 0.00 0.00 0.00 4.02
1067 2509 2.674380 GGGTGCTCTGCTTGGGTG 60.674 66.667 0.00 0.00 0.00 4.61
1069 2511 2.360852 CTGGGTGCTCTGCTTGGG 60.361 66.667 0.00 0.00 0.00 4.12
1071 2513 2.281970 TGCTGGGTGCTCTGCTTG 60.282 61.111 2.80 0.00 43.37 4.01
1080 2522 3.496309 TTCTGCTGGGTGCTGGGTG 62.496 63.158 0.00 0.00 43.37 4.61
1094 2536 0.094387 GCTTCGCTCGAAAGCTTCTG 59.906 55.000 12.09 0.00 46.91 3.02
1487 2941 2.700773 GGCGAGATGGTTGGTTGGC 61.701 63.158 0.00 0.00 0.00 4.52
1639 3096 3.459063 GGAGACGACGGGAAGGGG 61.459 72.222 0.00 0.00 0.00 4.79
1733 3190 7.169982 ACGGAATAGAATCGAAACATCTGATTC 59.830 37.037 6.15 6.15 45.23 2.52
1734 3191 6.986817 ACGGAATAGAATCGAAACATCTGATT 59.013 34.615 0.00 0.00 35.16 2.57
1735 3192 6.516718 ACGGAATAGAATCGAAACATCTGAT 58.483 36.000 0.00 0.00 0.00 2.90
1736 3193 5.902681 ACGGAATAGAATCGAAACATCTGA 58.097 37.500 0.00 0.00 0.00 3.27
1737 3194 5.980116 AGACGGAATAGAATCGAAACATCTG 59.020 40.000 0.00 0.00 0.00 2.90
1738 3195 6.039941 AGAGACGGAATAGAATCGAAACATCT 59.960 38.462 0.00 0.00 0.00 2.90
1739 3196 6.210078 AGAGACGGAATAGAATCGAAACATC 58.790 40.000 0.00 0.00 0.00 3.06
1740 3197 6.150396 AGAGACGGAATAGAATCGAAACAT 57.850 37.500 0.00 0.00 0.00 2.71
1741 3198 5.578005 AGAGACGGAATAGAATCGAAACA 57.422 39.130 0.00 0.00 0.00 2.83
1742 3199 5.805994 ACAAGAGACGGAATAGAATCGAAAC 59.194 40.000 0.00 0.00 0.00 2.78
1743 3200 5.962433 ACAAGAGACGGAATAGAATCGAAA 58.038 37.500 0.00 0.00 0.00 3.46
1744 3201 5.578005 ACAAGAGACGGAATAGAATCGAA 57.422 39.130 0.00 0.00 0.00 3.71
1745 3202 5.340803 CAACAAGAGACGGAATAGAATCGA 58.659 41.667 0.00 0.00 0.00 3.59
1746 3203 4.026475 GCAACAAGAGACGGAATAGAATCG 60.026 45.833 0.00 0.00 0.00 3.34
1826 3288 4.721274 TGATATCCAGATCCAGAACCAACA 59.279 41.667 0.00 0.00 0.00 3.33
1830 3292 5.559148 AACTGATATCCAGATCCAGAACC 57.441 43.478 13.59 0.00 45.78 3.62
1843 3305 7.177568 TGGATAGGTTCAGAGCTAACTGATATC 59.822 40.741 5.99 9.77 44.67 1.63
1854 3316 1.808133 CGGCTTGGATAGGTTCAGAGC 60.808 57.143 0.00 0.00 34.69 4.09
1855 3317 1.757118 TCGGCTTGGATAGGTTCAGAG 59.243 52.381 0.00 0.00 0.00 3.35
1860 3322 3.773119 TCTACTTTCGGCTTGGATAGGTT 59.227 43.478 0.00 0.00 0.00 3.50
1861 3323 3.132467 GTCTACTTTCGGCTTGGATAGGT 59.868 47.826 0.00 0.00 0.00 3.08
1862 3324 3.385111 AGTCTACTTTCGGCTTGGATAGG 59.615 47.826 0.00 0.00 0.00 2.57
1863 3325 4.098044 TGAGTCTACTTTCGGCTTGGATAG 59.902 45.833 0.00 0.00 0.00 2.08
1864 3326 4.021229 TGAGTCTACTTTCGGCTTGGATA 58.979 43.478 0.00 0.00 0.00 2.59
1865 3327 2.832129 TGAGTCTACTTTCGGCTTGGAT 59.168 45.455 0.00 0.00 0.00 3.41
1866 3328 2.244695 TGAGTCTACTTTCGGCTTGGA 58.755 47.619 0.00 0.00 0.00 3.53
1867 3329 2.743636 TGAGTCTACTTTCGGCTTGG 57.256 50.000 0.00 0.00 0.00 3.61
1868 3330 2.854777 CGATGAGTCTACTTTCGGCTTG 59.145 50.000 7.95 0.00 32.12 4.01
1869 3331 2.159226 CCGATGAGTCTACTTTCGGCTT 60.159 50.000 17.17 0.00 41.61 4.35
1870 3332 1.405821 CCGATGAGTCTACTTTCGGCT 59.594 52.381 17.17 0.00 41.61 5.52
1871 3333 1.134560 ACCGATGAGTCTACTTTCGGC 59.865 52.381 24.02 0.00 46.73 5.54
1872 3334 2.683867 AGACCGATGAGTCTACTTTCGG 59.316 50.000 23.15 23.15 45.31 4.30
1886 3348 1.828660 CGGCCAGTAGGAGACCGAT 60.829 63.158 2.24 0.00 46.71 4.18
1995 3468 7.158099 AGTCTAATGCATCATATGTACGCTA 57.842 36.000 0.00 0.00 0.00 4.26
1996 3469 6.030548 AGTCTAATGCATCATATGTACGCT 57.969 37.500 0.00 0.00 0.00 5.07
1997 3470 7.812309 TTAGTCTAATGCATCATATGTACGC 57.188 36.000 0.00 4.87 0.00 4.42
2011 3484 7.594015 GCCAAAAGATGATGCATTAGTCTAATG 59.406 37.037 23.11 23.11 46.37 1.90
2012 3485 7.255730 GGCCAAAAGATGATGCATTAGTCTAAT 60.256 37.037 0.00 0.00 0.00 1.73
2013 3486 6.039717 GGCCAAAAGATGATGCATTAGTCTAA 59.960 38.462 0.00 0.00 0.00 2.10
2014 3487 5.532406 GGCCAAAAGATGATGCATTAGTCTA 59.468 40.000 0.00 0.00 0.00 2.59
2015 3488 4.340381 GGCCAAAAGATGATGCATTAGTCT 59.660 41.667 0.00 2.01 0.00 3.24
2016 3489 4.614946 GGCCAAAAGATGATGCATTAGTC 58.385 43.478 0.00 0.00 0.00 2.59
2017 3490 3.067180 CGGCCAAAAGATGATGCATTAGT 59.933 43.478 2.24 0.00 0.00 2.24
2018 3491 3.316029 TCGGCCAAAAGATGATGCATTAG 59.684 43.478 2.24 0.00 0.00 1.73
2019 3492 3.286353 TCGGCCAAAAGATGATGCATTA 58.714 40.909 2.24 0.00 0.00 1.90
2020 3493 2.101783 TCGGCCAAAAGATGATGCATT 58.898 42.857 2.24 0.00 0.00 3.56
2021 3494 1.766494 TCGGCCAAAAGATGATGCAT 58.234 45.000 2.24 0.00 0.00 3.96
2022 3495 1.473677 CTTCGGCCAAAAGATGATGCA 59.526 47.619 2.24 0.00 0.00 3.96
2023 3496 1.745087 TCTTCGGCCAAAAGATGATGC 59.255 47.619 12.42 0.00 0.00 3.91
2024 3497 2.223433 GCTCTTCGGCCAAAAGATGATG 60.223 50.000 15.86 7.48 32.56 3.07
2079 3561 4.040952 AGCCCTTCGATGCATTAGTCTAAT 59.959 41.667 0.00 0.00 0.00 1.73
2080 3562 3.388024 AGCCCTTCGATGCATTAGTCTAA 59.612 43.478 0.00 0.00 0.00 2.10
2123 3605 1.013596 GCATGCATTAGCCACGTACA 58.986 50.000 14.21 0.00 41.13 2.90
2136 3618 1.153309 CTCGGTCCTGATGCATGCA 60.153 57.895 25.04 25.04 0.00 3.96
2172 3680 2.968675 AGTACGTATGCACCAAGTTCC 58.031 47.619 0.00 0.00 0.00 3.62
2258 3770 7.416022 GGCTGGACTATATCATGTACGTATAC 58.584 42.308 0.00 0.00 0.00 1.47
2268 3780 1.644509 TGCCGGCTGGACTATATCAT 58.355 50.000 29.70 0.00 37.49 2.45
2304 3816 1.870402 CTGGTTGTGTGCACGTATTCA 59.130 47.619 13.13 7.06 0.00 2.57
2376 3896 3.725819 GTGCACACACGTTAGCCA 58.274 55.556 13.17 0.00 36.98 4.75


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

AutoCloner maintained by Alex Coulton.