Multiple sequence alignment - TraesCS2D01G538000

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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 TraesCS2D01G538000 chr2D 100.000 2949 0 0 1 2949 619428185 619425237 0.000000e+00 5446.0
1 TraesCS2D01G538000 chr2D 89.775 1066 65 25 378 1427 619437966 619436929 0.000000e+00 1325.0
2 TraesCS2D01G538000 chr2D 90.649 663 45 9 1655 2309 619436589 619435936 0.000000e+00 865.0
3 TraesCS2D01G538000 chr2D 83.559 444 42 19 1655 2078 620614651 620615083 1.280000e-103 387.0
4 TraesCS2D01G538000 chr2D 81.646 474 55 19 1701 2173 585861003 585861445 6.010000e-97 364.0
5 TraesCS2D01G538000 chr2D 76.074 815 111 57 556 1319 585859978 585860759 6.050000e-92 348.0
6 TraesCS2D01G538000 chr2D 92.157 102 6 1 1543 1642 619436736 619436635 3.060000e-30 143.0
7 TraesCS2D01G538000 chr2A 86.497 1259 104 32 179 1424 750743815 750745020 0.000000e+00 1323.0
8 TraesCS2D01G538000 chr2A 86.313 1264 104 34 179 1427 750582745 750581536 0.000000e+00 1312.0
9 TraesCS2D01G538000 chr2A 90.663 664 44 9 1655 2309 750581299 750580645 0.000000e+00 867.0
10 TraesCS2D01G538000 chr2A 90.663 664 44 9 1655 2309 750617344 750616690 0.000000e+00 867.0
11 TraesCS2D01G538000 chr2A 89.717 671 44 11 1655 2309 750745260 750745921 0.000000e+00 833.0
12 TraesCS2D01G538000 chr2A 94.632 503 20 5 932 1427 750618083 750617581 0.000000e+00 773.0
13 TraesCS2D01G538000 chr2A 82.982 664 75 16 179 838 750621237 750620608 1.530000e-157 566.0
14 TraesCS2D01G538000 chr2A 89.623 106 10 1 1525 1629 750581502 750581397 1.840000e-27 134.0
15 TraesCS2D01G538000 chr2A 89.623 106 10 1 1525 1629 750617547 750617442 1.840000e-27 134.0
16 TraesCS2D01G538000 chr2A 90.291 103 9 1 1525 1626 750745057 750745159 1.840000e-27 134.0
17 TraesCS2D01G538000 chr2A 86.486 111 7 2 2106 2216 750615507 750615405 6.680000e-22 115.0
18 TraesCS2D01G538000 chr2A 85.586 111 8 5 2106 2216 750650131 750650029 3.110000e-20 110.0
19 TraesCS2D01G538000 chr2A 97.619 42 0 1 1 41 380709547 380709588 1.470000e-08 71.3
20 TraesCS2D01G538000 chr2B 92.298 792 46 12 426 1212 758374474 758373693 0.000000e+00 1110.0
21 TraesCS2D01G538000 chr2B 86.937 888 62 25 289 1162 758151221 758150374 0.000000e+00 948.0
22 TraesCS2D01G538000 chr2B 91.193 704 52 7 1608 2309 758373182 758372487 0.000000e+00 948.0
23 TraesCS2D01G538000 chr2B 93.171 615 29 8 1702 2308 758147513 758146904 0.000000e+00 891.0
24 TraesCS2D01G538000 chr2B 93.103 493 24 5 1702 2186 758389879 758389389 0.000000e+00 713.0
25 TraesCS2D01G538000 chr2B 91.881 505 28 4 702 1194 758390865 758390362 0.000000e+00 693.0
26 TraesCS2D01G538000 chr2B 86.861 411 35 6 305 711 758391434 758391039 2.700000e-120 442.0
27 TraesCS2D01G538000 chr2B 97.253 182 5 0 1246 1427 758373497 758373316 2.850000e-80 309.0
28 TraesCS2D01G538000 chr2B 88.780 205 7 8 1149 1337 758390374 758390170 1.370000e-58 237.0
29 TraesCS2D01G538000 chr2B 83.396 265 27 11 40 289 758151537 758151275 2.290000e-56 230.0
30 TraesCS2D01G538000 chr2B 91.156 147 4 4 1200 1337 758147949 758147803 1.080000e-44 191.0
31 TraesCS2D01G538000 chr2B 94.444 108 4 1 1522 1629 758147717 758147612 6.540000e-37 165.0
32 TraesCS2D01G538000 chr2B 94.444 108 4 1 1522 1629 758390083 758389978 6.540000e-37 165.0
33 TraesCS2D01G538000 chr2B 91.892 111 7 1 1522 1632 758373292 758373184 1.420000e-33 154.0
34 TraesCS2D01G538000 chr7D 97.670 558 9 4 2390 2947 421328060 421327507 0.000000e+00 955.0
35 TraesCS2D01G538000 chr7D 95.745 47 1 1 1 46 123870830 123870876 1.130000e-09 75.0
36 TraesCS2D01G538000 chr7D 92.157 51 3 1 1 50 270998076 270998126 1.470000e-08 71.3
37 TraesCS2D01G538000 chr3A 97.496 559 10 2 2389 2947 735198660 735198106 0.000000e+00 952.0
38 TraesCS2D01G538000 chr3A 97.138 559 14 2 2390 2947 17670498 17671055 0.000000e+00 942.0
39 TraesCS2D01G538000 chr3A 96.780 559 17 1 2391 2949 17798573 17798016 0.000000e+00 931.0
40 TraesCS2D01G538000 chr5A 97.326 561 12 1 2387 2947 53371389 53371946 0.000000e+00 950.0
41 TraesCS2D01G538000 chr5A 96.953 558 15 2 2390 2947 53452442 53452997 0.000000e+00 935.0
42 TraesCS2D01G538000 chr5A 96.595 558 16 1 2390 2947 548683016 548683570 0.000000e+00 922.0
43 TraesCS2D01G538000 chr5A 100.000 31 0 0 1431 1461 673732876 673732906 1.140000e-04 58.4
44 TraesCS2D01G538000 chr7A 96.953 558 14 1 2390 2947 91932026 91931472 0.000000e+00 933.0
45 TraesCS2D01G538000 chr7A 96.774 558 14 2 2390 2947 695619717 695619164 0.000000e+00 928.0
46 TraesCS2D01G538000 chr7A 100.000 29 0 0 2361 2389 598236093 598236121 1.000000e-03 54.7
47 TraesCS2D01G538000 chr4D 84.615 260 25 6 381 635 465752833 465753082 8.160000e-61 244.0
48 TraesCS2D01G538000 chr4A 86.413 184 13 3 456 635 4824421 4824246 1.080000e-44 191.0
49 TraesCS2D01G538000 chr3B 95.652 46 0 2 1 44 29495491 29495446 4.080000e-09 73.1
50 TraesCS2D01G538000 chr3B 97.674 43 0 1 1 42 792683026 792683068 4.080000e-09 73.1
51 TraesCS2D01G538000 chr1D 97.674 43 0 1 1 42 442998099 442998141 4.080000e-09 73.1
52 TraesCS2D01G538000 chr6D 92.157 51 3 1 1 50 65247130 65247180 1.470000e-08 71.3
53 TraesCS2D01G538000 chr6D 95.556 45 1 1 1 44 172089858 172089814 1.470000e-08 71.3
54 TraesCS2D01G538000 chr1B 95.556 45 1 1 1 44 312143309 312143353 1.470000e-08 71.3


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 TraesCS2D01G538000 chr2D 619425237 619428185 2948 True 5446.000000 5446 100.000000 1 2949 1 chr2D.!!$R1 2948
1 TraesCS2D01G538000 chr2D 619435936 619437966 2030 True 777.666667 1325 90.860333 378 2309 3 chr2D.!!$R2 1931
2 TraesCS2D01G538000 chr2D 585859978 585861445 1467 False 356.000000 364 78.860000 556 2173 2 chr2D.!!$F2 1617
3 TraesCS2D01G538000 chr2A 750580645 750582745 2100 True 771.000000 1312 88.866333 179 2309 3 chr2A.!!$R2 2130
4 TraesCS2D01G538000 chr2A 750743815 750745921 2106 False 763.333333 1323 88.835000 179 2309 3 chr2A.!!$F2 2130
5 TraesCS2D01G538000 chr2A 750615405 750621237 5832 True 491.000000 867 88.877200 179 2309 5 chr2A.!!$R3 2130
6 TraesCS2D01G538000 chr2B 758372487 758374474 1987 True 630.250000 1110 93.159000 426 2309 4 chr2B.!!$R2 1883
7 TraesCS2D01G538000 chr2B 758146904 758151537 4633 True 485.000000 948 89.820800 40 2308 5 chr2B.!!$R1 2268
8 TraesCS2D01G538000 chr2B 758389389 758391434 2045 True 450.000000 713 91.013800 305 2186 5 chr2B.!!$R3 1881
9 TraesCS2D01G538000 chr7D 421327507 421328060 553 True 955.000000 955 97.670000 2390 2947 1 chr7D.!!$R1 557
10 TraesCS2D01G538000 chr3A 735198106 735198660 554 True 952.000000 952 97.496000 2389 2947 1 chr3A.!!$R2 558
11 TraesCS2D01G538000 chr3A 17670498 17671055 557 False 942.000000 942 97.138000 2390 2947 1 chr3A.!!$F1 557
12 TraesCS2D01G538000 chr3A 17798016 17798573 557 True 931.000000 931 96.780000 2391 2949 1 chr3A.!!$R1 558
13 TraesCS2D01G538000 chr5A 53371389 53371946 557 False 950.000000 950 97.326000 2387 2947 1 chr5A.!!$F1 560
14 TraesCS2D01G538000 chr5A 53452442 53452997 555 False 935.000000 935 96.953000 2390 2947 1 chr5A.!!$F2 557
15 TraesCS2D01G538000 chr5A 548683016 548683570 554 False 922.000000 922 96.595000 2390 2947 1 chr5A.!!$F3 557
16 TraesCS2D01G538000 chr7A 91931472 91932026 554 True 933.000000 933 96.953000 2390 2947 1 chr7A.!!$R1 557
17 TraesCS2D01G538000 chr7A 695619164 695619717 553 True 928.000000 928 96.774000 2390 2947 1 chr7A.!!$R2 557

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
522 622 0.178967 TGGACCATTGCAGAAAGCCA 60.179 50.0 0.0 0.0 44.83 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 7982 0.035056 AAAATGGACCTAGCGCTGCT 60.035 50.0 22.9 0.69 43.41 4.24 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
28 29 8.988064 AATCTATAGCACTACATTATGGAACG 57.012 34.615 0.00 0.00 0.00 3.95
29 30 6.920817 TCTATAGCACTACATTATGGAACGG 58.079 40.000 0.00 0.00 0.00 4.44
30 31 5.801531 ATAGCACTACATTATGGAACGGA 57.198 39.130 0.00 0.00 0.00 4.69
31 32 4.060038 AGCACTACATTATGGAACGGAG 57.940 45.455 0.00 0.00 0.00 4.63
32 33 3.131396 GCACTACATTATGGAACGGAGG 58.869 50.000 0.00 0.00 0.00 4.30
33 34 3.728845 CACTACATTATGGAACGGAGGG 58.271 50.000 0.00 0.00 0.00 4.30
34 35 3.386726 CACTACATTATGGAACGGAGGGA 59.613 47.826 0.00 0.00 0.00 4.20
35 36 3.641906 ACTACATTATGGAACGGAGGGAG 59.358 47.826 0.00 0.00 0.00 4.30
36 37 2.478292 ACATTATGGAACGGAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
37 38 3.649843 ACATTATGGAACGGAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
38 39 3.641906 ACATTATGGAACGGAGGGAGTAG 59.358 47.826 0.00 0.00 0.00 2.57
39 40 3.393426 TTATGGAACGGAGGGAGTAGT 57.607 47.619 0.00 0.00 0.00 2.73
40 41 4.524802 TTATGGAACGGAGGGAGTAGTA 57.475 45.455 0.00 0.00 0.00 1.82
41 42 3.614568 ATGGAACGGAGGGAGTAGTAT 57.385 47.619 0.00 0.00 0.00 2.12
42 43 3.393426 TGGAACGGAGGGAGTAGTATT 57.607 47.619 0.00 0.00 0.00 1.89
43 44 3.716431 TGGAACGGAGGGAGTAGTATTT 58.284 45.455 0.00 0.00 0.00 1.40
49 50 7.232330 GGAACGGAGGGAGTAGTATTTACTAAT 59.768 40.741 0.00 0.00 40.20 1.73
69 70 7.203910 ACTAATATCTAGCAAAACCTCAGTCG 58.796 38.462 0.00 0.00 0.00 4.18
71 72 1.343142 TCTAGCAAAACCTCAGTCGCA 59.657 47.619 0.00 0.00 0.00 5.10
83 84 2.937519 TCAGTCGCATGAGAGATAGGT 58.062 47.619 0.00 0.00 0.00 3.08
88 90 1.875576 CGCATGAGAGATAGGTTGCCC 60.876 57.143 0.00 0.00 0.00 5.36
92 94 2.398588 TGAGAGATAGGTTGCCCGAAT 58.601 47.619 0.00 0.00 35.12 3.34
95 97 4.202223 TGAGAGATAGGTTGCCCGAATAAC 60.202 45.833 0.00 0.00 35.12 1.89
107 109 3.304293 GCCCGAATAACTGTAACGTGTAC 59.696 47.826 0.00 0.00 0.00 2.90
117 119 4.142227 ACTGTAACGTGTACTGGGATGATC 60.142 45.833 14.38 0.00 0.00 2.92
123 125 3.679917 CGTGTACTGGGATGATCAGCTTT 60.680 47.826 11.34 0.00 35.78 3.51
128 130 5.894298 ACTGGGATGATCAGCTTTATACA 57.106 39.130 11.34 0.71 35.78 2.29
130 132 4.645535 TGGGATGATCAGCTTTATACAGC 58.354 43.478 11.34 2.49 40.44 4.40
164 180 4.020543 GTTTGTATGGCCCTTGATGGTAA 58.979 43.478 0.00 0.00 0.00 2.85
217 233 0.326264 AGATCTGGTGGTGACTTGCC 59.674 55.000 0.00 0.00 0.00 4.52
259 275 5.543507 TTTTTGCATTCCAAGTACCACAT 57.456 34.783 0.00 0.00 34.34 3.21
263 279 2.445427 CATTCCAAGTACCACATGGCA 58.555 47.619 0.00 0.00 36.93 4.92
265 281 4.206375 CATTCCAAGTACCACATGGCATA 58.794 43.478 0.00 0.00 36.93 3.14
275 291 0.848735 ACATGGCATATGCTGACCCT 59.151 50.000 26.12 0.85 41.70 4.34
292 361 2.194271 CCCTTTAGCGCTAGTTTCTCG 58.806 52.381 17.98 2.42 0.00 4.04
303 372 3.308323 GCTAGTTTCTCGAGCCTTTCATG 59.692 47.826 7.81 0.00 38.54 3.07
368 448 9.733556 AACACTCCAATAGTTGTATTTGATGTA 57.266 29.630 0.00 0.00 35.76 2.29
369 449 9.162764 ACACTCCAATAGTTGTATTTGATGTAC 57.837 33.333 0.00 0.00 35.76 2.90
370 450 9.383519 CACTCCAATAGTTGTATTTGATGTACT 57.616 33.333 0.00 0.00 35.76 2.73
371 451 9.601217 ACTCCAATAGTTGTATTTGATGTACTC 57.399 33.333 0.00 0.00 33.35 2.59
372 452 8.958119 TCCAATAGTTGTATTTGATGTACTCC 57.042 34.615 0.00 0.00 0.00 3.85
373 453 8.544622 TCCAATAGTTGTATTTGATGTACTCCA 58.455 33.333 0.00 0.00 0.00 3.86
374 454 9.173021 CCAATAGTTGTATTTGATGTACTCCAA 57.827 33.333 0.00 0.00 0.00 3.53
378 458 8.964476 AGTTGTATTTGATGTACTCCAATAGG 57.036 34.615 0.00 0.00 0.00 2.57
379 459 8.768397 AGTTGTATTTGATGTACTCCAATAGGA 58.232 33.333 0.00 0.00 43.21 2.94
443 527 4.513692 CACGGTAGGTTCAGATTTTGTCAA 59.486 41.667 0.00 0.00 0.00 3.18
520 620 2.097825 AGATGGACCATTGCAGAAAGC 58.902 47.619 8.78 0.00 45.96 3.51
521 621 1.135721 GATGGACCATTGCAGAAAGCC 59.864 52.381 8.78 0.00 44.83 4.35
522 622 0.178967 TGGACCATTGCAGAAAGCCA 60.179 50.000 0.00 0.00 44.83 4.75
523 623 0.529378 GGACCATTGCAGAAAGCCAG 59.471 55.000 0.00 0.00 44.83 4.85
524 624 1.538047 GACCATTGCAGAAAGCCAGA 58.462 50.000 0.00 0.00 44.83 3.86
525 625 1.888512 GACCATTGCAGAAAGCCAGAA 59.111 47.619 0.00 0.00 44.83 3.02
526 626 2.297033 GACCATTGCAGAAAGCCAGAAA 59.703 45.455 0.00 0.00 44.83 2.52
527 627 2.298163 ACCATTGCAGAAAGCCAGAAAG 59.702 45.455 0.00 0.00 44.83 2.62
540 640 5.441718 AGCCAGAAAGTTATCAGATTCCA 57.558 39.130 0.00 0.00 0.00 3.53
549 652 9.442047 GAAAGTTATCAGATTCCAAGAAGAAGA 57.558 33.333 0.00 0.00 0.00 2.87
551 654 8.144862 AGTTATCAGATTCCAAGAAGAAGACT 57.855 34.615 0.00 0.00 0.00 3.24
646 749 0.389817 CAGCCGTCCGATCAGAAACA 60.390 55.000 0.00 0.00 0.00 2.83
715 1023 6.491383 ACAGTCCAGTATCTTTCAGGTACTA 58.509 40.000 0.00 0.00 36.02 1.82
728 1036 8.275758 TCTTTCAGGTACTAGTGATCAGTCTAT 58.724 37.037 6.25 0.00 36.02 1.98
734 1042 8.221251 AGGTACTAGTGATCAGTCTATGATTGA 58.779 37.037 6.25 0.00 43.69 2.57
747 1055 6.373774 AGTCTATGATTGAAGAAAAGGCACAG 59.626 38.462 0.00 0.00 0.00 3.66
777 1085 1.813513 ATCTTTTGAGCCGTGGTCAG 58.186 50.000 6.03 0.00 41.12 3.51
794 1102 3.470567 GACTGAGAACGCGTGCGG 61.471 66.667 14.98 13.40 44.69 5.69
830 1138 3.006537 GGACGCCTATAAATAGCAGGACA 59.993 47.826 0.00 0.00 0.00 4.02
865 3629 2.644992 CACCCCAAGCTTTCACGC 59.355 61.111 0.00 0.00 0.00 5.34
1165 4027 3.067601 GTCTCCATGCATGCATCATTTGA 59.932 43.478 30.07 19.11 33.90 2.69
1320 6718 1.016627 CTCCATTGGTACGTGCATGG 58.983 55.000 14.43 14.43 38.04 3.66
1590 7088 2.545952 GGCTACATACAGGATGGTGACG 60.546 54.545 0.00 0.00 43.62 4.35
1700 7340 4.988540 GGAACCATTACTCAAACTTTTGCC 59.011 41.667 0.00 0.00 38.05 4.52
1973 7620 1.302752 CAAGCTGGCTGGCACTACA 60.303 57.895 0.00 0.00 34.17 2.74
1982 7629 2.460918 GCTGGCACTACATAGTACGTG 58.539 52.381 0.00 0.50 34.13 4.49
2028 7680 8.714179 TCCAAACGTGTCACACTAAATAAATAG 58.286 33.333 6.33 0.00 31.34 1.73
2034 7686 9.901724 CGTGTCACACTAAATAAATAGATGAAC 57.098 33.333 6.33 0.00 31.34 3.18
2053 7708 9.325198 AGATGAACGAATAAATATGTGTAAGCA 57.675 29.630 0.00 0.00 0.00 3.91
2161 7822 7.214381 GGAATATACTGTGTACTTGGTGCATA 58.786 38.462 0.00 0.00 30.01 3.14
2162 7823 7.878127 GGAATATACTGTGTACTTGGTGCATAT 59.122 37.037 0.00 0.00 30.01 1.78
2229 7890 8.146412 GGCAAATGAATAATGCTTCCTCTATTT 58.854 33.333 0.00 0.00 39.94 1.40
2279 7952 0.690192 TTGGTCCCTCGCAAATGAGA 59.310 50.000 0.00 0.00 38.28 3.27
2280 7953 0.911769 TGGTCCCTCGCAAATGAGAT 59.088 50.000 0.00 0.00 38.28 2.75
2281 7954 1.134401 TGGTCCCTCGCAAATGAGATC 60.134 52.381 0.00 0.00 38.28 2.75
2309 7982 1.843421 CCAAACTGGGGGTGTGAGA 59.157 57.895 0.00 0.00 35.21 3.27
2311 7984 0.890996 CAAACTGGGGGTGTGAGAGC 60.891 60.000 0.00 0.00 35.21 4.09
2312 7985 1.352622 AAACTGGGGGTGTGAGAGCA 61.353 55.000 0.00 0.00 0.00 4.26
2313 7986 1.772819 AACTGGGGGTGTGAGAGCAG 61.773 60.000 0.00 0.00 0.00 4.24
2314 7987 3.618780 CTGGGGGTGTGAGAGCAGC 62.619 68.421 0.00 0.00 36.26 5.25
2315 7988 4.767255 GGGGGTGTGAGAGCAGCG 62.767 72.222 0.00 0.00 37.71 5.18
2317 7990 4.385405 GGGTGTGAGAGCAGCGCT 62.385 66.667 2.64 2.64 43.88 5.92
2320 7993 1.518133 GTGTGAGAGCAGCGCTAGG 60.518 63.158 10.99 0.00 39.88 3.02
2321 7994 1.979155 TGTGAGAGCAGCGCTAGGT 60.979 57.895 10.99 10.72 39.88 3.08
2322 7995 1.226831 GTGAGAGCAGCGCTAGGTC 60.227 63.158 22.86 22.86 39.88 3.85
2323 7996 2.415426 GAGAGCAGCGCTAGGTCC 59.585 66.667 25.09 17.05 39.88 4.46
2324 7997 2.363018 AGAGCAGCGCTAGGTCCA 60.363 61.111 25.09 0.00 39.88 4.02
2325 7998 1.743321 GAGAGCAGCGCTAGGTCCAT 61.743 60.000 25.09 14.30 39.88 3.41
2326 7999 1.144936 GAGCAGCGCTAGGTCCATT 59.855 57.895 10.99 0.00 39.88 3.16
2327 8000 0.462759 GAGCAGCGCTAGGTCCATTT 60.463 55.000 10.99 0.00 39.88 2.32
2328 8001 0.035056 AGCAGCGCTAGGTCCATTTT 60.035 50.000 10.99 0.00 36.99 1.82
2329 8002 1.209504 AGCAGCGCTAGGTCCATTTTA 59.790 47.619 10.99 0.00 36.99 1.52
2330 8003 2.158755 AGCAGCGCTAGGTCCATTTTAT 60.159 45.455 10.99 0.00 36.99 1.40
2331 8004 3.071023 AGCAGCGCTAGGTCCATTTTATA 59.929 43.478 10.99 0.00 36.99 0.98
2332 8005 3.433615 GCAGCGCTAGGTCCATTTTATAG 59.566 47.826 10.99 0.00 0.00 1.31
2333 8006 4.632153 CAGCGCTAGGTCCATTTTATAGT 58.368 43.478 10.99 0.00 0.00 2.12
2334 8007 5.779922 CAGCGCTAGGTCCATTTTATAGTA 58.220 41.667 10.99 0.00 0.00 1.82
2335 8008 6.398918 CAGCGCTAGGTCCATTTTATAGTAT 58.601 40.000 10.99 0.00 0.00 2.12
2336 8009 6.531948 CAGCGCTAGGTCCATTTTATAGTATC 59.468 42.308 10.99 0.00 0.00 2.24
2337 8010 5.811100 GCGCTAGGTCCATTTTATAGTATCC 59.189 44.000 0.00 0.00 0.00 2.59
2338 8011 6.573680 GCGCTAGGTCCATTTTATAGTATCCA 60.574 42.308 0.00 0.00 0.00 3.41
2339 8012 7.556844 CGCTAGGTCCATTTTATAGTATCCAT 58.443 38.462 0.00 0.00 0.00 3.41
2340 8013 7.707035 CGCTAGGTCCATTTTATAGTATCCATC 59.293 40.741 0.00 0.00 0.00 3.51
2341 8014 7.988028 GCTAGGTCCATTTTATAGTATCCATCC 59.012 40.741 0.00 0.00 0.00 3.51
2342 8015 9.273137 CTAGGTCCATTTTATAGTATCCATCCT 57.727 37.037 0.00 0.00 0.00 3.24
2343 8016 8.525729 AGGTCCATTTTATAGTATCCATCCTT 57.474 34.615 0.00 0.00 0.00 3.36
2344 8017 8.606830 AGGTCCATTTTATAGTATCCATCCTTC 58.393 37.037 0.00 0.00 0.00 3.46
2345 8018 8.383175 GGTCCATTTTATAGTATCCATCCTTCA 58.617 37.037 0.00 0.00 0.00 3.02
2346 8019 9.793259 GTCCATTTTATAGTATCCATCCTTCAA 57.207 33.333 0.00 0.00 0.00 2.69
2348 8021 8.734386 CCATTTTATAGTATCCATCCTTCAAGC 58.266 37.037 0.00 0.00 0.00 4.01
2349 8022 8.734386 CATTTTATAGTATCCATCCTTCAAGCC 58.266 37.037 0.00 0.00 0.00 4.35
2350 8023 4.917906 ATAGTATCCATCCTTCAAGCCC 57.082 45.455 0.00 0.00 0.00 5.19
2351 8024 1.777272 AGTATCCATCCTTCAAGCCCC 59.223 52.381 0.00 0.00 0.00 5.80
2352 8025 1.149101 TATCCATCCTTCAAGCCCCC 58.851 55.000 0.00 0.00 0.00 5.40
2353 8026 1.999634 ATCCATCCTTCAAGCCCCCG 62.000 60.000 0.00 0.00 0.00 5.73
2354 8027 2.830370 CATCCTTCAAGCCCCCGC 60.830 66.667 0.00 0.00 0.00 6.13
2355 8028 4.489771 ATCCTTCAAGCCCCCGCG 62.490 66.667 0.00 0.00 41.18 6.46
2384 8057 3.541713 GCTAGGGAGGCTCGGGTG 61.542 72.222 8.69 0.26 0.00 4.61
2385 8058 2.840102 CTAGGGAGGCTCGGGTGG 60.840 72.222 8.69 0.00 0.00 4.61
2395 8068 1.450211 CTCGGGTGGAAACAGTGGT 59.550 57.895 0.00 0.00 44.46 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.424319 CGTTCCATAATGTAGTGCTATAGATTT 57.576 33.333 3.21 0.00 0.00 2.17
3 4 8.035394 CCGTTCCATAATGTAGTGCTATAGATT 58.965 37.037 3.21 0.00 0.00 2.40
4 5 7.396339 TCCGTTCCATAATGTAGTGCTATAGAT 59.604 37.037 3.21 0.00 0.00 1.98
5 6 6.717997 TCCGTTCCATAATGTAGTGCTATAGA 59.282 38.462 3.21 0.00 0.00 1.98
6 7 6.920817 TCCGTTCCATAATGTAGTGCTATAG 58.079 40.000 0.00 0.00 0.00 1.31
7 8 6.071560 CCTCCGTTCCATAATGTAGTGCTATA 60.072 42.308 0.00 0.00 0.00 1.31
8 9 5.279506 CCTCCGTTCCATAATGTAGTGCTAT 60.280 44.000 0.00 0.00 0.00 2.97
9 10 4.038763 CCTCCGTTCCATAATGTAGTGCTA 59.961 45.833 0.00 0.00 0.00 3.49
10 11 3.181465 CCTCCGTTCCATAATGTAGTGCT 60.181 47.826 0.00 0.00 0.00 4.40
11 12 3.131396 CCTCCGTTCCATAATGTAGTGC 58.869 50.000 0.00 0.00 0.00 4.40
12 13 3.386726 TCCCTCCGTTCCATAATGTAGTG 59.613 47.826 0.00 0.00 0.00 2.74
13 14 3.641906 CTCCCTCCGTTCCATAATGTAGT 59.358 47.826 0.00 0.00 0.00 2.73
14 15 3.641906 ACTCCCTCCGTTCCATAATGTAG 59.358 47.826 0.00 0.00 0.00 2.74
15 16 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
16 17 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
17 18 3.641906 ACTACTCCCTCCGTTCCATAATG 59.358 47.826 0.00 0.00 0.00 1.90
18 19 3.924922 ACTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
19 20 3.393426 ACTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
20 21 4.736611 ATACTACTCCCTCCGTTCCATA 57.263 45.455 0.00 0.00 0.00 2.74
21 22 3.614568 ATACTACTCCCTCCGTTCCAT 57.385 47.619 0.00 0.00 0.00 3.41
22 23 3.393426 AATACTACTCCCTCCGTTCCA 57.607 47.619 0.00 0.00 0.00 3.53
23 24 4.892345 AGTAAATACTACTCCCTCCGTTCC 59.108 45.833 0.00 0.00 34.13 3.62
24 25 7.573968 TTAGTAAATACTACTCCCTCCGTTC 57.426 40.000 0.00 0.00 38.43 3.95
25 26 9.819754 ATATTAGTAAATACTACTCCCTCCGTT 57.180 33.333 0.00 0.00 38.43 4.44
26 27 9.460019 GATATTAGTAAATACTACTCCCTCCGT 57.540 37.037 0.00 0.00 38.43 4.69
27 28 9.683870 AGATATTAGTAAATACTACTCCCTCCG 57.316 37.037 0.00 0.00 38.43 4.63
43 44 8.350722 CGACTGAGGTTTTGCTAGATATTAGTA 58.649 37.037 0.00 0.00 0.00 1.82
49 50 3.194755 TGCGACTGAGGTTTTGCTAGATA 59.805 43.478 0.00 0.00 0.00 1.98
61 62 2.228582 CCTATCTCTCATGCGACTGAGG 59.771 54.545 12.89 6.05 42.42 3.86
83 84 2.737783 CACGTTACAGTTATTCGGGCAA 59.262 45.455 0.00 0.00 0.00 4.52
88 90 4.560035 CCCAGTACACGTTACAGTTATTCG 59.440 45.833 0.00 0.00 0.00 3.34
92 94 4.766373 TCATCCCAGTACACGTTACAGTTA 59.234 41.667 0.00 0.00 0.00 2.24
95 97 3.861276 TCATCCCAGTACACGTTACAG 57.139 47.619 0.00 3.26 0.00 2.74
107 109 4.694509 GCTGTATAAAGCTGATCATCCCAG 59.305 45.833 7.72 0.00 40.20 4.45
117 119 5.461526 TCTATGCTACGCTGTATAAAGCTG 58.538 41.667 13.08 8.88 41.24 4.24
123 125 5.301045 ACAAACCTCTATGCTACGCTGTATA 59.699 40.000 0.00 0.00 0.00 1.47
128 130 4.501571 CCATACAAACCTCTATGCTACGCT 60.502 45.833 0.00 0.00 0.00 5.07
130 132 3.741344 GCCATACAAACCTCTATGCTACG 59.259 47.826 0.00 0.00 0.00 3.51
138 140 1.992557 TCAAGGGCCATACAAACCTCT 59.007 47.619 6.18 0.00 31.69 3.69
145 147 4.079500 TCAATTACCATCAAGGGCCATACA 60.080 41.667 6.18 0.00 43.89 2.29
149 151 3.686227 ATCAATTACCATCAAGGGCCA 57.314 42.857 6.18 0.00 43.89 5.36
150 152 3.321968 GGAATCAATTACCATCAAGGGCC 59.678 47.826 0.00 0.00 43.89 5.80
151 153 4.218312 AGGAATCAATTACCATCAAGGGC 58.782 43.478 0.00 0.00 43.89 5.19
217 233 7.201350 GCAAAAATAACGCTAGGATTTTGACTG 60.201 37.037 11.65 0.00 39.08 3.51
226 242 4.702612 TGGAATGCAAAAATAACGCTAGGA 59.297 37.500 0.00 0.00 0.00 2.94
231 247 5.061684 GGTACTTGGAATGCAAAAATAACGC 59.938 40.000 0.00 0.00 0.00 4.84
259 275 2.749466 GCTAAAGGGTCAGCATATGCCA 60.749 50.000 23.96 8.49 43.38 4.92
263 279 1.417890 AGCGCTAAAGGGTCAGCATAT 59.582 47.619 8.99 0.00 37.66 1.78
265 281 0.830648 TAGCGCTAAAGGGTCAGCAT 59.169 50.000 16.33 0.00 37.66 3.79
275 291 2.527100 GCTCGAGAAACTAGCGCTAAA 58.473 47.619 19.37 0.00 0.00 1.85
303 372 3.201290 CTCCAGTACATCATCTTGTGGC 58.799 50.000 0.00 0.00 0.00 5.01
370 450 7.515586 TCTTCTTACGAGATACTCCTATTGGA 58.484 38.462 0.00 0.00 40.69 3.53
371 451 7.747155 TCTTCTTACGAGATACTCCTATTGG 57.253 40.000 0.00 0.00 0.00 3.16
372 452 9.672086 CTTTCTTCTTACGAGATACTCCTATTG 57.328 37.037 0.00 0.00 0.00 1.90
373 453 9.629878 TCTTTCTTCTTACGAGATACTCCTATT 57.370 33.333 0.00 0.00 0.00 1.73
374 454 9.629878 TTCTTTCTTCTTACGAGATACTCCTAT 57.370 33.333 0.00 0.00 0.00 2.57
375 455 9.111613 CTTCTTTCTTCTTACGAGATACTCCTA 57.888 37.037 0.00 0.00 0.00 2.94
376 456 7.830201 TCTTCTTTCTTCTTACGAGATACTCCT 59.170 37.037 0.00 0.00 0.00 3.69
377 457 7.987649 TCTTCTTTCTTCTTACGAGATACTCC 58.012 38.462 0.00 0.00 0.00 3.85
378 458 8.671028 ACTCTTCTTTCTTCTTACGAGATACTC 58.329 37.037 0.00 0.00 0.00 2.59
379 459 8.570068 ACTCTTCTTTCTTCTTACGAGATACT 57.430 34.615 0.00 0.00 0.00 2.12
380 460 9.628746 AAACTCTTCTTTCTTCTTACGAGATAC 57.371 33.333 0.00 0.00 0.00 2.24
443 527 6.128007 CCGTTTGGAGTTATAATCTGCAACTT 60.128 38.462 15.97 0.00 41.44 2.66
520 620 7.826252 TCTTCTTGGAATCTGATAACTTTCTGG 59.174 37.037 0.00 0.00 0.00 3.86
521 621 8.783833 TCTTCTTGGAATCTGATAACTTTCTG 57.216 34.615 0.00 0.00 0.00 3.02
522 622 9.447157 CTTCTTCTTGGAATCTGATAACTTTCT 57.553 33.333 0.00 0.00 0.00 2.52
523 623 9.442047 TCTTCTTCTTGGAATCTGATAACTTTC 57.558 33.333 0.00 0.00 0.00 2.62
524 624 9.225436 GTCTTCTTCTTGGAATCTGATAACTTT 57.775 33.333 0.00 0.00 0.00 2.66
525 625 8.601546 AGTCTTCTTCTTGGAATCTGATAACTT 58.398 33.333 0.00 0.00 0.00 2.66
526 626 8.144862 AGTCTTCTTCTTGGAATCTGATAACT 57.855 34.615 0.00 0.00 0.00 2.24
527 627 8.257306 AGAGTCTTCTTCTTGGAATCTGATAAC 58.743 37.037 0.00 0.00 33.98 1.89
540 640 7.123547 CACCAAGTAGGATAGAGTCTTCTTCTT 59.876 40.741 0.00 1.50 41.22 2.52
549 652 3.116096 TGGCACCAAGTAGGATAGAGT 57.884 47.619 0.00 0.00 41.22 3.24
578 681 3.512680 ACGATCTGACGACTGAAAATCC 58.487 45.455 0.00 0.00 37.03 3.01
715 1023 9.381033 CTTTTCTTCAATCATAGACTGATCACT 57.619 33.333 0.00 0.00 44.03 3.41
728 1036 2.957680 TGCTGTGCCTTTTCTTCAATCA 59.042 40.909 0.00 0.00 0.00 2.57
734 1042 0.746659 GGTGTGCTGTGCCTTTTCTT 59.253 50.000 0.00 0.00 0.00 2.52
735 1043 0.106519 AGGTGTGCTGTGCCTTTTCT 60.107 50.000 0.00 0.00 0.00 2.52
747 1055 2.094417 GCTCAAAAGATACGAGGTGTGC 59.906 50.000 0.00 0.00 0.00 4.57
777 1085 3.470567 CCGCACGCGTTCTCAGTC 61.471 66.667 10.22 0.00 37.81 3.51
794 1102 2.346365 GTCCCGGTGAAGTCCCAC 59.654 66.667 0.00 0.00 36.37 4.61
865 3629 0.539051 AGCTAGCCAGTACTGCCTTG 59.461 55.000 17.86 13.75 0.00 3.61
1320 6718 5.238868 GGGTAAAGCTAGCTAAATTAGGCAC 59.761 44.000 19.70 3.87 0.00 5.01
1590 7088 0.460311 CACCTCCGTCTGGTATGTCC 59.540 60.000 0.00 0.00 35.80 4.02
1687 7326 2.195922 GCACACAGGCAAAAGTTTGAG 58.804 47.619 7.96 0.00 40.55 3.02
1973 7620 2.514013 GCGCGCTTGCACGTACTAT 61.514 57.895 26.67 0.00 39.07 2.12
2028 7680 9.929722 TTGCTTACACATATTTATTCGTTCATC 57.070 29.630 0.00 0.00 0.00 2.92
2053 7708 7.151308 GTGTATCTGAAGCAGCTACATATCTT 58.849 38.462 12.48 0.00 42.38 2.40
2189 7850 3.869832 TCATTTGCCAACAACAACACATG 59.130 39.130 0.00 0.00 34.87 3.21
2191 7852 3.599730 TCATTTGCCAACAACAACACA 57.400 38.095 0.00 0.00 34.87 3.72
2279 7952 0.957395 CAGTTTGGCGAGGTGCTGAT 60.957 55.000 0.00 0.00 45.43 2.90
2280 7953 1.597854 CAGTTTGGCGAGGTGCTGA 60.598 57.895 0.00 0.00 45.43 4.26
2281 7954 2.620112 CCAGTTTGGCGAGGTGCTG 61.620 63.158 0.00 0.00 45.43 4.41
2309 7982 0.035056 AAAATGGACCTAGCGCTGCT 60.035 50.000 22.90 0.69 43.41 4.24
2311 7984 4.632153 ACTATAAAATGGACCTAGCGCTG 58.368 43.478 22.90 6.70 0.00 5.18
2312 7985 4.957684 ACTATAAAATGGACCTAGCGCT 57.042 40.909 17.26 17.26 0.00 5.92
2313 7986 5.811100 GGATACTATAAAATGGACCTAGCGC 59.189 44.000 0.00 0.00 0.00 5.92
2314 7987 6.931838 TGGATACTATAAAATGGACCTAGCG 58.068 40.000 0.00 0.00 37.61 4.26
2315 7988 7.988028 GGATGGATACTATAAAATGGACCTAGC 59.012 40.741 0.00 0.00 37.61 3.42
2317 7990 9.629649 AAGGATGGATACTATAAAATGGACCTA 57.370 33.333 0.00 0.00 37.61 3.08
2320 7993 9.793259 TTGAAGGATGGATACTATAAAATGGAC 57.207 33.333 0.00 0.00 37.61 4.02
2322 7995 8.734386 GCTTGAAGGATGGATACTATAAAATGG 58.266 37.037 0.00 0.00 37.61 3.16
2323 7996 8.734386 GGCTTGAAGGATGGATACTATAAAATG 58.266 37.037 0.00 0.00 37.61 2.32
2324 7997 7.890655 GGGCTTGAAGGATGGATACTATAAAAT 59.109 37.037 0.00 0.00 37.61 1.82
2325 7998 7.231467 GGGCTTGAAGGATGGATACTATAAAA 58.769 38.462 0.00 0.00 37.61 1.52
2326 7999 6.240176 GGGGCTTGAAGGATGGATACTATAAA 60.240 42.308 0.00 0.00 37.61 1.40
2327 8000 5.250774 GGGGCTTGAAGGATGGATACTATAA 59.749 44.000 0.00 0.00 37.61 0.98
2328 8001 4.783227 GGGGCTTGAAGGATGGATACTATA 59.217 45.833 0.00 0.00 37.61 1.31
2329 8002 3.589288 GGGGCTTGAAGGATGGATACTAT 59.411 47.826 0.00 0.00 37.61 2.12
2330 8003 2.979678 GGGGCTTGAAGGATGGATACTA 59.020 50.000 0.00 0.00 37.61 1.82
2331 8004 1.777272 GGGGCTTGAAGGATGGATACT 59.223 52.381 0.00 0.00 37.61 2.12
2332 8005 1.202940 GGGGGCTTGAAGGATGGATAC 60.203 57.143 0.00 0.00 0.00 2.24
2333 8006 1.149101 GGGGGCTTGAAGGATGGATA 58.851 55.000 0.00 0.00 0.00 2.59
2334 8007 1.933629 GGGGGCTTGAAGGATGGAT 59.066 57.895 0.00 0.00 0.00 3.41
2335 8008 2.679342 CGGGGGCTTGAAGGATGGA 61.679 63.158 0.00 0.00 0.00 3.41
2336 8009 2.124151 CGGGGGCTTGAAGGATGG 60.124 66.667 0.00 0.00 0.00 3.51
2337 8010 2.830370 GCGGGGGCTTGAAGGATG 60.830 66.667 0.00 0.00 0.00 3.51
2338 8011 4.489771 CGCGGGGGCTTGAAGGAT 62.490 66.667 0.00 0.00 0.00 3.24
2367 8040 3.541713 CACCCGAGCCTCCCTAGC 61.542 72.222 0.00 0.00 0.00 3.42
2368 8041 2.840102 CCACCCGAGCCTCCCTAG 60.840 72.222 0.00 0.00 0.00 3.02
2369 8042 2.465010 TTTCCACCCGAGCCTCCCTA 62.465 60.000 0.00 0.00 0.00 3.53
2370 8043 3.864983 TTTCCACCCGAGCCTCCCT 62.865 63.158 0.00 0.00 0.00 4.20
2371 8044 3.327404 TTTCCACCCGAGCCTCCC 61.327 66.667 0.00 0.00 0.00 4.30
2372 8045 2.046217 GTTTCCACCCGAGCCTCC 60.046 66.667 0.00 0.00 0.00 4.30
2373 8046 1.376037 CTGTTTCCACCCGAGCCTC 60.376 63.158 0.00 0.00 0.00 4.70
2374 8047 2.147387 ACTGTTTCCACCCGAGCCT 61.147 57.895 0.00 0.00 0.00 4.58
2375 8048 1.966451 CACTGTTTCCACCCGAGCC 60.966 63.158 0.00 0.00 0.00 4.70
2376 8049 1.966451 CCACTGTTTCCACCCGAGC 60.966 63.158 0.00 0.00 0.00 5.03
2377 8050 0.884704 CACCACTGTTTCCACCCGAG 60.885 60.000 0.00 0.00 0.00 4.63
2378 8051 1.147376 CACCACTGTTTCCACCCGA 59.853 57.895 0.00 0.00 0.00 5.14
2379 8052 1.896660 CCACCACTGTTTCCACCCG 60.897 63.158 0.00 0.00 0.00 5.28
2380 8053 2.200337 GCCACCACTGTTTCCACCC 61.200 63.158 0.00 0.00 0.00 4.61
2381 8054 2.551912 CGCCACCACTGTTTCCACC 61.552 63.158 0.00 0.00 0.00 4.61
2382 8055 3.030652 CGCCACCACTGTTTCCAC 58.969 61.111 0.00 0.00 0.00 4.02
2383 8056 2.904866 GCGCCACCACTGTTTCCA 60.905 61.111 0.00 0.00 0.00 3.53
2384 8057 3.670377 GGCGCCACCACTGTTTCC 61.670 66.667 24.80 0.00 38.86 3.13
2385 8058 2.904866 TGGCGCCACCACTGTTTC 60.905 61.111 29.03 0.00 46.36 2.78
2395 8068 1.678635 CCTTCATTTCCTGGCGCCA 60.679 57.895 30.59 30.59 0.00 5.69


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

AutoCloner maintained by Alex Coulton.