Multiple sequence alignment - TraesCS2B01G136400

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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 TraesCS2B01G136400 chr2B 100.000 2324 0 0 1 2324 103758488 103756165 0.000000e+00 4292.0
1 TraesCS2B01G136400 chr2B 93.929 1400 69 8 1 1385 51008874 51010272 0.000000e+00 2100.0
2 TraesCS2B01G136400 chr2B 87.618 1583 101 28 749 2248 121619695 121618125 0.000000e+00 1749.0
3 TraesCS2B01G136400 chr2B 91.719 797 43 11 1473 2248 750617901 750618695 0.000000e+00 1085.0
4 TraesCS2B01G136400 chr2B 85.340 191 15 7 2090 2268 104861920 104861731 3.940000e-43 185.0
5 TraesCS2B01G136400 chr2B 98.684 76 1 0 2249 2324 559321056 559321131 4.030000e-28 135.0
6 TraesCS2B01G136400 chr6B 94.452 1478 70 2 1 1474 208208919 208210388 0.000000e+00 2265.0
7 TraesCS2B01G136400 chr6B 92.010 801 45 12 1459 2248 70652741 70653533 0.000000e+00 1107.0
8 TraesCS2B01G136400 chr6B 86.628 172 13 2 2090 2251 84141465 84141636 5.100000e-42 182.0
9 TraesCS2B01G136400 chr6B 87.143 140 7 2 2121 2250 152440249 152440111 5.170000e-32 148.0
10 TraesCS2B01G136400 chr5B 94.249 1478 71 5 1 1474 345189422 345187955 0.000000e+00 2246.0
11 TraesCS2B01G136400 chr5B 94.437 1402 62 7 1 1387 209176272 209174872 0.000000e+00 2143.0
12 TraesCS2B01G136400 chr5B 93.585 1403 74 7 1 1388 265537628 265536227 0.000000e+00 2078.0
13 TraesCS2B01G136400 chr5B 90.709 592 24 5 1 577 61819081 61819656 0.000000e+00 760.0
14 TraesCS2B01G136400 chr5B 88.931 524 26 15 958 1474 71855077 71855575 3.280000e-173 617.0
15 TraesCS2B01G136400 chr3B 94.722 1402 58 7 1 1387 228481161 228479761 0.000000e+00 2165.0
16 TraesCS2B01G136400 chr3B 91.922 817 45 7 1453 2249 787154878 787155693 0.000000e+00 1123.0
17 TraesCS2B01G136400 chr3B 90.452 796 54 9 1473 2248 766277138 766277931 0.000000e+00 1029.0
18 TraesCS2B01G136400 chr3B 87.076 913 73 24 1368 2248 29817661 29818560 0.000000e+00 990.0
19 TraesCS2B01G136400 chr3B 94.176 601 34 1 749 1349 632384554 632383955 0.000000e+00 915.0
20 TraesCS2B01G136400 chr3B 94.444 90 5 0 2235 2324 812161379 812161468 3.110000e-29 139.0
21 TraesCS2B01G136400 chr3B 85.612 139 9 2 2121 2249 286477817 286477954 4.030000e-28 135.0
22 TraesCS2B01G136400 chr3A 94.223 1402 66 1 1 1387 153244956 153243555 0.000000e+00 2126.0
23 TraesCS2B01G136400 chr5A 93.723 1402 73 7 1 1387 596914387 596915788 0.000000e+00 2087.0
24 TraesCS2B01G136400 chr5A 90.719 431 23 7 958 1385 168391363 168390947 2.020000e-155 558.0
25 TraesCS2B01G136400 chr1A 93.581 1402 72 9 1 1387 54871254 54869856 0.000000e+00 2074.0
26 TraesCS2B01G136400 chr1A 90.719 431 23 7 958 1385 443864323 443864739 2.020000e-155 558.0
27 TraesCS2B01G136400 chr1A 90.330 424 24 7 958 1378 471034492 471034901 7.310000e-150 540.0
28 TraesCS2B01G136400 chr1A 89.858 424 26 7 958 1378 497983404 497983813 1.580000e-146 529.0
29 TraesCS2B01G136400 chr1A 98.649 74 1 0 2251 2324 315508458 315508385 5.210000e-27 132.0
30 TraesCS2B01G136400 chr7B 92.629 1438 74 6 1 1421 719311821 719310399 0.000000e+00 2039.0
31 TraesCS2B01G136400 chr7B 87.571 177 11 2 2090 2255 27650791 27650967 6.550000e-46 195.0
32 TraesCS2B01G136400 chr7B 100.000 74 0 0 2251 2324 536855630 536855557 1.120000e-28 137.0
33 TraesCS2B01G136400 chr7B 82.075 106 8 8 1476 1574 692777626 692777727 1.910000e-11 80.5
34 TraesCS2B01G136400 chr6A 93.325 794 33 5 1473 2248 136675497 136676288 0.000000e+00 1155.0
35 TraesCS2B01G136400 chr6A 93.182 792 38 7 1473 2248 436400175 436400966 0.000000e+00 1149.0
36 TraesCS2B01G136400 chr6A 91.183 431 21 7 958 1385 603924304 603924720 9.320000e-159 569.0
37 TraesCS2B01G136400 chr4A 93.266 787 37 4 1476 2248 29672652 29671868 0.000000e+00 1146.0
38 TraesCS2B01G136400 chr4A 92.579 795 40 9 1476 2252 549635648 549636441 0.000000e+00 1123.0
39 TraesCS2B01G136400 chr2A 92.794 791 39 7 1476 2248 55068114 55067324 0.000000e+00 1129.0
40 TraesCS2B01G136400 chr2A 91.955 808 40 12 1459 2248 538620506 538619706 0.000000e+00 1109.0
41 TraesCS2B01G136400 chr7A 92.462 796 40 8 1473 2248 493525540 493526335 0.000000e+00 1120.0
42 TraesCS2B01G136400 chr7A 89.857 631 29 12 1 605 153030919 153030298 0.000000e+00 778.0
43 TraesCS2B01G136400 chr7A 89.650 628 29 13 1 602 734442753 734443370 0.000000e+00 767.0
44 TraesCS2B01G136400 chrUn 89.223 631 33 13 1 605 38472744 38473365 0.000000e+00 756.0
45 TraesCS2B01G136400 chr1B 87.209 172 12 1 2090 2251 523583933 523583762 1.100000e-43 187.0
46 TraesCS2B01G136400 chr1B 85.549 173 15 1 2090 2252 663562564 663562392 3.070000e-39 172.0
47 TraesCS2B01G136400 chr4B 84.324 185 16 3 2090 2262 291448177 291447994 3.970000e-38 169.0
48 TraesCS2B01G136400 chr6D 98.649 74 1 0 2251 2324 67821639 67821566 5.210000e-27 132.0
49 TraesCS2B01G136400 chr6D 98.649 74 1 0 2251 2324 415701397 415701324 5.210000e-27 132.0
50 TraesCS2B01G136400 chr6D 98.649 74 1 0 2251 2324 416674220 416674147 5.210000e-27 132.0
51 TraesCS2B01G136400 chr4D 98.649 74 1 0 2251 2324 122908123 122908050 5.210000e-27 132.0
52 TraesCS2B01G136400 chr1D 98.649 74 1 0 2251 2324 272591282 272591209 5.210000e-27 132.0


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 TraesCS2B01G136400 chr2B 103756165 103758488 2323 True 4292 4292 100.000 1 2324 1 chr2B.!!$R1 2323
1 TraesCS2B01G136400 chr2B 51008874 51010272 1398 False 2100 2100 93.929 1 1385 1 chr2B.!!$F1 1384
2 TraesCS2B01G136400 chr2B 121618125 121619695 1570 True 1749 1749 87.618 749 2248 1 chr2B.!!$R3 1499
3 TraesCS2B01G136400 chr2B 750617901 750618695 794 False 1085 1085 91.719 1473 2248 1 chr2B.!!$F3 775
4 TraesCS2B01G136400 chr6B 208208919 208210388 1469 False 2265 2265 94.452 1 1474 1 chr6B.!!$F3 1473
5 TraesCS2B01G136400 chr6B 70652741 70653533 792 False 1107 1107 92.010 1459 2248 1 chr6B.!!$F1 789
6 TraesCS2B01G136400 chr5B 345187955 345189422 1467 True 2246 2246 94.249 1 1474 1 chr5B.!!$R3 1473
7 TraesCS2B01G136400 chr5B 209174872 209176272 1400 True 2143 2143 94.437 1 1387 1 chr5B.!!$R1 1386
8 TraesCS2B01G136400 chr5B 265536227 265537628 1401 True 2078 2078 93.585 1 1388 1 chr5B.!!$R2 1387
9 TraesCS2B01G136400 chr5B 61819081 61819656 575 False 760 760 90.709 1 577 1 chr5B.!!$F1 576
10 TraesCS2B01G136400 chr3B 228479761 228481161 1400 True 2165 2165 94.722 1 1387 1 chr3B.!!$R1 1386
11 TraesCS2B01G136400 chr3B 787154878 787155693 815 False 1123 1123 91.922 1453 2249 1 chr3B.!!$F4 796
12 TraesCS2B01G136400 chr3B 766277138 766277931 793 False 1029 1029 90.452 1473 2248 1 chr3B.!!$F3 775
13 TraesCS2B01G136400 chr3B 29817661 29818560 899 False 990 990 87.076 1368 2248 1 chr3B.!!$F1 880
14 TraesCS2B01G136400 chr3B 632383955 632384554 599 True 915 915 94.176 749 1349 1 chr3B.!!$R2 600
15 TraesCS2B01G136400 chr3A 153243555 153244956 1401 True 2126 2126 94.223 1 1387 1 chr3A.!!$R1 1386
16 TraesCS2B01G136400 chr5A 596914387 596915788 1401 False 2087 2087 93.723 1 1387 1 chr5A.!!$F1 1386
17 TraesCS2B01G136400 chr1A 54869856 54871254 1398 True 2074 2074 93.581 1 1387 1 chr1A.!!$R1 1386
18 TraesCS2B01G136400 chr7B 719310399 719311821 1422 True 2039 2039 92.629 1 1421 1 chr7B.!!$R2 1420
19 TraesCS2B01G136400 chr6A 136675497 136676288 791 False 1155 1155 93.325 1473 2248 1 chr6A.!!$F1 775
20 TraesCS2B01G136400 chr6A 436400175 436400966 791 False 1149 1149 93.182 1473 2248 1 chr6A.!!$F2 775
21 TraesCS2B01G136400 chr4A 29671868 29672652 784 True 1146 1146 93.266 1476 2248 1 chr4A.!!$R1 772
22 TraesCS2B01G136400 chr4A 549635648 549636441 793 False 1123 1123 92.579 1476 2252 1 chr4A.!!$F1 776
23 TraesCS2B01G136400 chr2A 55067324 55068114 790 True 1129 1129 92.794 1476 2248 1 chr2A.!!$R1 772
24 TraesCS2B01G136400 chr2A 538619706 538620506 800 True 1109 1109 91.955 1459 2248 1 chr2A.!!$R2 789
25 TraesCS2B01G136400 chr7A 493525540 493526335 795 False 1120 1120 92.462 1473 2248 1 chr7A.!!$F1 775
26 TraesCS2B01G136400 chr7A 153030298 153030919 621 True 778 778 89.857 1 605 1 chr7A.!!$R1 604
27 TraesCS2B01G136400 chr7A 734442753 734443370 617 False 767 767 89.650 1 602 1 chr7A.!!$F2 601
28 TraesCS2B01G136400 chrUn 38472744 38473365 621 False 756 756 89.223 1 605 1 chrUn.!!$F1 604

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
254 283 0.670546 CTGGTTCCAGGCACTACACG 60.671 60.0 10.71 0.0 36.02 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1701 0.106015 AGGTTCAAACAGCAAGGCCT 60.106 50.0 0.0 0.0 0.0 5.19 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
43 44 7.530010 GCAAATAAAGTCAGCATTAAGTCTCA 58.470 34.615 0.00 0.00 0.00 3.27
136 137 4.388485 TGTCTCTGCTTTGTTTGATGCTA 58.612 39.130 0.00 0.00 0.00 3.49
215 231 6.010074 GTCGAACAAGATGAATCGAGAAAAC 58.990 40.000 11.21 1.01 38.84 2.43
218 234 5.924475 ACAAGATGAATCGAGAAAACGTT 57.076 34.783 0.00 0.00 34.70 3.99
254 283 0.670546 CTGGTTCCAGGCACTACACG 60.671 60.000 10.71 0.00 36.02 4.49
350 379 9.985730 TTCTGATTCTTGCTGAATAACATTTTT 57.014 25.926 5.70 0.00 44.70 1.94
378 407 9.890352 TTTTTGTTGAAAAACATTTCAGAAAGG 57.110 25.926 6.00 6.00 41.38 3.11
569 598 6.809689 TGATGATTTGATGCTGTTTGATTCAC 59.190 34.615 0.00 0.00 0.00 3.18
615 644 7.555914 TGCTGTTTGATAGTTCCATGCTTATAA 59.444 33.333 0.00 0.00 0.00 0.98
759 788 5.997746 AGAACTTGCTGTAGCTATTTGTTGA 59.002 36.000 5.38 0.00 42.66 3.18
830 860 6.599638 GCCATCTTATATAGAACCACCATTCC 59.400 42.308 0.00 0.00 36.22 3.01
1023 1053 2.336341 AAAAATGAAGGACGCGCCA 58.664 47.368 19.30 5.45 40.02 5.69
1078 1108 4.126437 TGAAATTGTCGAAGAAGTGCTGA 58.874 39.130 0.00 0.00 39.69 4.26
1087 1117 7.320399 TGTCGAAGAAGTGCTGATAAAATCTA 58.680 34.615 0.00 0.00 39.69 1.98
1269 1299 4.848357 TCAAGATGAAGGTGGAAGAATCC 58.152 43.478 0.00 0.00 46.76 3.01
1327 1357 5.814705 CGCAAGAAGTCTCAAGAATAGGAAT 59.185 40.000 0.00 0.00 43.02 3.01
1428 1486 3.281727 TGTCTTTGAGCTGTGAACCTT 57.718 42.857 0.00 0.00 0.00 3.50
1431 1489 3.627577 GTCTTTGAGCTGTGAACCTTGAA 59.372 43.478 0.00 0.00 0.00 2.69
1488 1581 5.221803 CCTGGGAGCTATGAAGTTATGTGAT 60.222 44.000 0.00 0.00 0.00 3.06
1560 1701 1.696884 TGTGGATCACTTGTGCACCTA 59.303 47.619 15.69 1.01 37.14 3.08
1693 1834 7.505923 ACAAGAATTAGACTAAAAAGGCTTGGT 59.494 33.333 18.99 0.00 34.82 3.67
1848 1995 2.899256 CAGAAAAAGGCTCCATTCCCAA 59.101 45.455 0.00 0.00 0.00 4.12
2130 2289 3.557054 CGTCCATTCCAGAAGAAAGGTCA 60.557 47.826 0.00 0.00 42.78 4.02
2148 2307 5.710984 AGGTCACTAATGTCAGTTTACGAG 58.289 41.667 0.00 0.00 0.00 4.18
2162 2321 0.398696 TACGAGGGCCAGCTTTTGAA 59.601 50.000 6.18 0.00 0.00 2.69
2252 2421 9.046296 AGTTGACATACTTCTTGTAGTGAAAAG 57.954 33.333 0.00 0.00 34.24 2.27
2253 2422 7.421530 TGACATACTTCTTGTAGTGAAAAGC 57.578 36.000 0.00 0.00 34.24 3.51
2254 2423 6.989759 TGACATACTTCTTGTAGTGAAAAGCA 59.010 34.615 0.00 0.00 34.24 3.91
2255 2424 7.661437 TGACATACTTCTTGTAGTGAAAAGCAT 59.339 33.333 0.00 0.00 34.24 3.79
2256 2425 7.810658 ACATACTTCTTGTAGTGAAAAGCATG 58.189 34.615 0.00 0.00 34.24 4.06
2257 2426 7.661437 ACATACTTCTTGTAGTGAAAAGCATGA 59.339 33.333 0.00 0.00 34.24 3.07
2258 2427 6.942532 ACTTCTTGTAGTGAAAAGCATGAA 57.057 33.333 0.00 0.00 0.00 2.57
2259 2428 6.729187 ACTTCTTGTAGTGAAAAGCATGAAC 58.271 36.000 0.00 0.00 0.00 3.18
2260 2429 6.318648 ACTTCTTGTAGTGAAAAGCATGAACA 59.681 34.615 0.00 0.00 0.00 3.18
2261 2430 6.882610 TCTTGTAGTGAAAAGCATGAACAT 57.117 33.333 0.00 0.00 0.00 2.71
2262 2431 7.275888 TCTTGTAGTGAAAAGCATGAACATT 57.724 32.000 0.00 0.00 0.00 2.71
2263 2432 8.389779 TCTTGTAGTGAAAAGCATGAACATTA 57.610 30.769 0.00 0.00 0.00 1.90
2264 2433 8.289618 TCTTGTAGTGAAAAGCATGAACATTAC 58.710 33.333 0.00 0.00 0.00 1.89
2265 2434 6.598525 TGTAGTGAAAAGCATGAACATTACG 58.401 36.000 0.00 0.00 0.00 3.18
2266 2435 4.475944 AGTGAAAAGCATGAACATTACGC 58.524 39.130 0.00 0.00 0.00 4.42
2267 2436 3.608073 GTGAAAAGCATGAACATTACGCC 59.392 43.478 0.00 0.00 0.00 5.68
2268 2437 2.939460 AAAGCATGAACATTACGCCC 57.061 45.000 0.00 0.00 0.00 6.13
2269 2438 1.832883 AAGCATGAACATTACGCCCA 58.167 45.000 0.00 0.00 0.00 5.36
2270 2439 1.832883 AGCATGAACATTACGCCCAA 58.167 45.000 0.00 0.00 0.00 4.12
2271 2440 2.378038 AGCATGAACATTACGCCCAAT 58.622 42.857 0.00 0.00 0.00 3.16
2272 2441 2.358898 AGCATGAACATTACGCCCAATC 59.641 45.455 0.00 0.00 0.00 2.67
2273 2442 2.358898 GCATGAACATTACGCCCAATCT 59.641 45.455 0.00 0.00 0.00 2.40
2274 2443 3.793129 GCATGAACATTACGCCCAATCTG 60.793 47.826 0.00 0.00 0.00 2.90
2275 2444 3.342377 TGAACATTACGCCCAATCTGA 57.658 42.857 0.00 0.00 0.00 3.27
2276 2445 3.270027 TGAACATTACGCCCAATCTGAG 58.730 45.455 0.00 0.00 0.00 3.35
2277 2446 3.270877 GAACATTACGCCCAATCTGAGT 58.729 45.455 0.00 0.00 0.00 3.41
2278 2447 4.081365 TGAACATTACGCCCAATCTGAGTA 60.081 41.667 0.00 0.00 0.00 2.59
2279 2448 4.689612 ACATTACGCCCAATCTGAGTAT 57.310 40.909 0.00 0.00 0.00 2.12
2280 2449 4.380531 ACATTACGCCCAATCTGAGTATG 58.619 43.478 0.00 0.00 0.00 2.39
2281 2450 4.100963 ACATTACGCCCAATCTGAGTATGA 59.899 41.667 0.00 0.00 0.00 2.15
2282 2451 4.746535 TTACGCCCAATCTGAGTATGAA 57.253 40.909 0.00 0.00 0.00 2.57
2283 2452 3.185246 ACGCCCAATCTGAGTATGAAG 57.815 47.619 0.00 0.00 0.00 3.02
2284 2453 2.766263 ACGCCCAATCTGAGTATGAAGA 59.234 45.455 0.00 0.00 0.00 2.87
2285 2454 3.126831 CGCCCAATCTGAGTATGAAGAC 58.873 50.000 0.00 0.00 0.00 3.01
2286 2455 3.430790 CGCCCAATCTGAGTATGAAGACA 60.431 47.826 0.00 0.00 0.00 3.41
2287 2456 4.517285 GCCCAATCTGAGTATGAAGACAA 58.483 43.478 0.00 0.00 0.00 3.18
2288 2457 5.128919 GCCCAATCTGAGTATGAAGACAAT 58.871 41.667 0.00 0.00 0.00 2.71
2289 2458 5.591877 GCCCAATCTGAGTATGAAGACAATT 59.408 40.000 0.00 0.00 0.00 2.32
2290 2459 6.238593 GCCCAATCTGAGTATGAAGACAATTC 60.239 42.308 0.00 0.00 0.00 2.17
2291 2460 7.052873 CCCAATCTGAGTATGAAGACAATTCT 58.947 38.462 0.00 0.00 0.00 2.40
2292 2461 7.012138 CCCAATCTGAGTATGAAGACAATTCTG 59.988 40.741 0.00 0.00 29.98 3.02
2293 2462 7.408123 CAATCTGAGTATGAAGACAATTCTGC 58.592 38.462 0.00 0.00 29.98 4.26
2294 2463 6.041423 TCTGAGTATGAAGACAATTCTGCA 57.959 37.500 0.00 0.00 42.11 4.41
2295 2464 5.871524 TCTGAGTATGAAGACAATTCTGCAC 59.128 40.000 0.00 0.00 40.55 4.57
2296 2465 5.550290 TGAGTATGAAGACAATTCTGCACA 58.450 37.500 0.00 0.00 40.55 4.57
2297 2466 5.409520 TGAGTATGAAGACAATTCTGCACAC 59.590 40.000 0.00 0.00 40.55 3.82
2298 2467 5.308014 AGTATGAAGACAATTCTGCACACA 58.692 37.500 0.00 0.00 40.55 3.72
2299 2468 4.761235 ATGAAGACAATTCTGCACACAG 57.239 40.909 0.00 0.00 40.55 3.66
2300 2469 2.291465 TGAAGACAATTCTGCACACAGC 59.709 45.455 0.00 0.00 44.10 4.40
2310 2479 2.460330 GCACACAGCGCTGATAAGT 58.540 52.632 42.03 28.46 0.00 2.24
2311 2480 0.371645 GCACACAGCGCTGATAAGTC 59.628 55.000 42.03 20.91 0.00 3.01
2312 2481 0.642291 CACACAGCGCTGATAAGTCG 59.358 55.000 42.03 21.46 0.00 4.18
2316 2485 3.313750 GCGCTGATAAGTCGCCTG 58.686 61.111 0.00 0.00 42.71 4.85
2317 2486 2.240500 GCGCTGATAAGTCGCCTGG 61.241 63.158 0.00 0.00 42.71 4.45
2318 2487 1.592669 CGCTGATAAGTCGCCTGGG 60.593 63.158 0.00 0.00 0.00 4.45
2319 2488 1.889573 GCTGATAAGTCGCCTGGGC 60.890 63.158 0.82 0.82 37.85 5.36
2320 2489 1.522092 CTGATAAGTCGCCTGGGCA 59.478 57.895 12.34 0.00 42.06 5.36
2321 2490 0.811616 CTGATAAGTCGCCTGGGCAC 60.812 60.000 12.34 8.83 42.06 5.01
2322 2491 1.264749 TGATAAGTCGCCTGGGCACT 61.265 55.000 12.34 10.78 42.06 4.40
2323 2492 0.530870 GATAAGTCGCCTGGGCACTC 60.531 60.000 12.34 1.57 42.06 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.485480 CATCTGTCAGATCAGGCACCT 59.515 52.381 12.62 0.00 31.32 4.00
82 83 1.866015 TGGGGTAGACCACATCTCTG 58.134 55.000 0.00 0.00 46.28 3.35
136 137 5.048713 CAGCATGATCATGTGCAGAACATAT 60.049 40.000 31.09 3.97 43.69 1.78
215 231 5.694910 ACCAGTTCTCTAATTGTACACAACG 59.305 40.000 0.00 0.00 38.86 4.10
218 234 6.183361 TGGAACCAGTTCTCTAATTGTACACA 60.183 38.462 10.19 0.00 39.45 3.72
378 407 0.741915 CTCCTCACCCTTACGCTCTC 59.258 60.000 0.00 0.00 0.00 3.20
569 598 1.165907 TCAAAGCACGGAACTGGCTG 61.166 55.000 0.00 0.00 35.65 4.85
615 644 5.945310 TCTTCATTAAGCCTAGCATGGAAT 58.055 37.500 0.00 0.00 32.36 3.01
907 937 2.948979 TGAAGTAACCAAACCAGCACAG 59.051 45.455 0.00 0.00 0.00 3.66
1023 1053 1.903183 GGCTCTTCACCTTCTGGTACT 59.097 52.381 0.00 0.00 46.60 2.73
1078 1108 9.525409 GAATGTGCTTTGCTTGATAGATTTTAT 57.475 29.630 0.00 0.00 0.00 1.40
1087 1117 3.057033 GTGAGGAATGTGCTTTGCTTGAT 60.057 43.478 0.00 0.00 0.00 2.57
1269 1299 3.620187 CTTGTCGCGTGCAGCTTCG 62.620 63.158 5.77 0.00 45.59 3.79
1327 1357 4.487714 CCATCAAGTGGGCTAACTTCTA 57.512 45.455 3.59 0.00 44.79 2.10
1349 1379 6.213600 TCAAACTACCTTAGCTCCAAAGAGAT 59.786 38.462 0.00 0.00 43.39 2.75
1428 1486 9.290988 TCAAAATGCAATAACTACCTTAGTTCA 57.709 29.630 1.85 0.00 45.38 3.18
1431 1489 8.520351 GGTTCAAAATGCAATAACTACCTTAGT 58.480 33.333 0.00 0.00 41.73 2.24
1443 1501 4.101430 AGGTTCACAGGTTCAAAATGCAAT 59.899 37.500 0.00 0.00 0.00 3.56
1488 1581 5.934043 CACAAGATCACATAACTTCACAGGA 59.066 40.000 0.00 0.00 0.00 3.86
1560 1701 0.106015 AGGTTCAAACAGCAAGGCCT 60.106 50.000 0.00 0.00 0.00 5.19
1939 2096 1.202533 CGGTCCATTTCAGCCGTCTAT 60.203 52.381 0.00 0.00 39.41 1.98
2110 2269 3.652869 AGTGACCTTTCTTCTGGAATGGA 59.347 43.478 14.37 0.00 46.24 3.41
2130 2289 3.369157 GGCCCTCGTAAACTGACATTAGT 60.369 47.826 0.00 0.00 0.00 2.24
2148 2307 2.562738 ACATAAGTTCAAAAGCTGGCCC 59.437 45.455 0.00 0.00 0.00 5.80
2174 2333 5.406649 GTCACTGTTTTCCATTTTGTGACA 58.593 37.500 15.51 0.00 46.68 3.58
2236 2405 6.728200 TGTTCATGCTTTTCACTACAAGAAG 58.272 36.000 0.00 0.00 0.00 2.85
2252 2421 2.358898 AGATTGGGCGTAATGTTCATGC 59.641 45.455 0.00 0.00 0.00 4.06
2253 2422 3.627123 TCAGATTGGGCGTAATGTTCATG 59.373 43.478 0.00 0.00 0.00 3.07
2254 2423 3.879295 CTCAGATTGGGCGTAATGTTCAT 59.121 43.478 0.00 0.00 0.00 2.57
2255 2424 3.270027 CTCAGATTGGGCGTAATGTTCA 58.730 45.455 0.00 0.00 0.00 3.18
2256 2425 3.270877 ACTCAGATTGGGCGTAATGTTC 58.729 45.455 0.00 0.00 0.00 3.18
2257 2426 3.350219 ACTCAGATTGGGCGTAATGTT 57.650 42.857 0.00 0.00 0.00 2.71
2258 2427 4.100963 TCATACTCAGATTGGGCGTAATGT 59.899 41.667 0.00 0.00 0.00 2.71
2259 2428 4.631131 TCATACTCAGATTGGGCGTAATG 58.369 43.478 0.00 0.00 0.00 1.90
2260 2429 4.955811 TCATACTCAGATTGGGCGTAAT 57.044 40.909 0.00 0.00 0.00 1.89
2261 2430 4.404394 TCTTCATACTCAGATTGGGCGTAA 59.596 41.667 0.00 0.00 0.00 3.18
2262 2431 3.958147 TCTTCATACTCAGATTGGGCGTA 59.042 43.478 0.00 0.00 0.00 4.42
2263 2432 2.766263 TCTTCATACTCAGATTGGGCGT 59.234 45.455 0.00 0.00 0.00 5.68
2264 2433 3.126831 GTCTTCATACTCAGATTGGGCG 58.873 50.000 0.00 0.00 0.00 6.13
2265 2434 4.142609 TGTCTTCATACTCAGATTGGGC 57.857 45.455 0.00 0.00 0.00 5.36
2266 2435 7.012138 CAGAATTGTCTTCATACTCAGATTGGG 59.988 40.741 0.00 0.00 28.78 4.12
2267 2436 7.466996 GCAGAATTGTCTTCATACTCAGATTGG 60.467 40.741 0.00 0.00 28.78 3.16
2268 2437 7.065443 TGCAGAATTGTCTTCATACTCAGATTG 59.935 37.037 0.00 0.00 28.78 2.67
2269 2438 7.065563 GTGCAGAATTGTCTTCATACTCAGATT 59.934 37.037 0.00 0.00 29.42 2.40
2270 2439 6.538021 GTGCAGAATTGTCTTCATACTCAGAT 59.462 38.462 0.00 0.00 29.42 2.90
2271 2440 5.871524 GTGCAGAATTGTCTTCATACTCAGA 59.128 40.000 0.00 0.00 29.42 3.27
2272 2441 5.640783 TGTGCAGAATTGTCTTCATACTCAG 59.359 40.000 0.00 0.00 29.42 3.35
2273 2442 5.409520 GTGTGCAGAATTGTCTTCATACTCA 59.590 40.000 0.00 0.00 36.61 3.41
2274 2443 5.409520 TGTGTGCAGAATTGTCTTCATACTC 59.590 40.000 0.00 0.00 39.02 2.59
2275 2444 5.308014 TGTGTGCAGAATTGTCTTCATACT 58.692 37.500 0.00 0.00 39.02 2.12
2276 2445 5.611796 TGTGTGCAGAATTGTCTTCATAC 57.388 39.130 0.00 0.00 38.83 2.39
2277 2446 4.154737 GCTGTGTGCAGAATTGTCTTCATA 59.845 41.667 0.00 0.00 45.28 2.15
2278 2447 3.057736 GCTGTGTGCAGAATTGTCTTCAT 60.058 43.478 0.00 0.00 45.28 2.57
2279 2448 2.291465 GCTGTGTGCAGAATTGTCTTCA 59.709 45.455 0.00 0.00 45.28 3.02
2280 2449 2.663879 CGCTGTGTGCAGAATTGTCTTC 60.664 50.000 0.00 0.00 45.28 2.87
2281 2450 1.265095 CGCTGTGTGCAGAATTGTCTT 59.735 47.619 0.00 0.00 45.28 3.01
2282 2451 0.870393 CGCTGTGTGCAGAATTGTCT 59.130 50.000 0.00 0.00 45.28 3.41
2283 2452 0.727122 GCGCTGTGTGCAGAATTGTC 60.727 55.000 0.00 0.00 45.28 3.18
2284 2453 1.168407 AGCGCTGTGTGCAGAATTGT 61.168 50.000 10.39 0.00 45.28 2.71
2285 2454 0.728129 CAGCGCTGTGTGCAGAATTG 60.728 55.000 29.24 0.00 45.28 2.32
2286 2455 0.886043 TCAGCGCTGTGTGCAGAATT 60.886 50.000 34.70 0.00 45.28 2.17
2287 2456 0.675837 ATCAGCGCTGTGTGCAGAAT 60.676 50.000 34.70 16.92 45.28 2.40
2288 2457 0.037419 TATCAGCGCTGTGTGCAGAA 60.037 50.000 34.70 15.28 45.28 3.02
2289 2458 0.037419 TTATCAGCGCTGTGTGCAGA 60.037 50.000 34.70 16.06 45.28 4.26
2290 2459 0.372679 CTTATCAGCGCTGTGTGCAG 59.627 55.000 34.70 20.37 42.00 4.41
2291 2460 0.320683 ACTTATCAGCGCTGTGTGCA 60.321 50.000 34.70 17.61 42.00 4.57
2292 2461 0.371645 GACTTATCAGCGCTGTGTGC 59.628 55.000 34.70 17.42 39.59 4.57
2293 2462 0.642291 CGACTTATCAGCGCTGTGTG 59.358 55.000 34.70 23.99 0.00 3.82
2294 2463 1.078759 GCGACTTATCAGCGCTGTGT 61.079 55.000 34.70 26.61 46.53 3.72
2295 2464 1.633171 GCGACTTATCAGCGCTGTG 59.367 57.895 34.70 23.99 46.53 3.66
2296 2465 4.094684 GCGACTTATCAGCGCTGT 57.905 55.556 34.70 24.05 46.53 4.40
2300 2469 1.592669 CCCAGGCGACTTATCAGCG 60.593 63.158 0.00 0.00 40.21 5.18
2301 2470 1.889573 GCCCAGGCGACTTATCAGC 60.890 63.158 0.00 0.00 40.21 4.26
2302 2471 0.811616 GTGCCCAGGCGACTTATCAG 60.812 60.000 3.83 0.00 45.51 2.90
2303 2472 1.220749 GTGCCCAGGCGACTTATCA 59.779 57.895 3.83 0.00 45.51 2.15
2304 2473 0.530870 GAGTGCCCAGGCGACTTATC 60.531 60.000 12.86 1.28 45.51 1.75
2305 2474 1.522569 GAGTGCCCAGGCGACTTAT 59.477 57.895 12.86 0.00 45.51 1.73
2306 2475 2.978824 GAGTGCCCAGGCGACTTA 59.021 61.111 12.86 0.00 45.51 2.24


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

AutoCloner maintained by Alex Coulton.