Multiple sequence alignment - TraesCS2A01G520000

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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 TraesCS2A01G520000 chr2A 100.000 2585 0 0 1 2585 743065153 743067737 0.000000e+00 4774
1 TraesCS2A01G520000 chr2A 88.068 352 36 4 2235 2584 58958443 58958096 1.850000e-111 412
2 TraesCS2A01G520000 chr2A 83.706 313 36 6 2236 2546 695344952 695345251 5.450000e-72 281
3 TraesCS2A01G520000 chr1D 92.688 1819 119 5 411 2220 250223363 250225176 0.000000e+00 2610
4 TraesCS2A01G520000 chr5A 92.588 1808 128 6 415 2220 536362165 536363968 0.000000e+00 2591
5 TraesCS2A01G520000 chr2D 92.486 1810 125 9 415 2220 7031493 7033295 0.000000e+00 2579
6 TraesCS2A01G520000 chr2D 92.749 1779 104 8 462 2220 596268284 596266511 0.000000e+00 2547
7 TraesCS2A01G520000 chr2D 91.556 1812 124 14 413 2220 346436077 346437863 0.000000e+00 2471
8 TraesCS2A01G520000 chr2D 91.478 1807 138 11 415 2220 500667212 500665421 0.000000e+00 2470
9 TraesCS2A01G520000 chr3D 92.240 1817 123 11 415 2220 553937352 553935543 0.000000e+00 2558
10 TraesCS2A01G520000 chr3D 92.871 1571 105 6 655 2220 540374905 540376473 0.000000e+00 2274
11 TraesCS2A01G520000 chr7B 91.667 1812 129 11 411 2220 619668173 619669964 0.000000e+00 2490
12 TraesCS2A01G520000 chr1A 90.579 1815 155 13 415 2220 119714781 119716588 0.000000e+00 2390
13 TraesCS2A01G520000 chr4B 89.615 1820 165 15 415 2220 425291630 425293439 0.000000e+00 2292
14 TraesCS2A01G520000 chr4B 87.630 1059 117 12 415 1466 3213141 3214192 0.000000e+00 1218
15 TraesCS2A01G520000 chr4B 89.916 357 34 2 2230 2585 480953019 480952664 2.340000e-125 459
16 TraesCS2A01G520000 chr4B 90.625 192 15 3 2236 2425 353378150 353377960 4.270000e-63 252
17 TraesCS2A01G520000 chr2B 94.780 613 31 1 1 613 745670500 745671111 0.000000e+00 953
18 TraesCS2A01G520000 chr2B 88.604 351 39 1 2236 2585 8318378 8318728 2.380000e-115 425
19 TraesCS2A01G520000 chr3A 90.341 352 30 4 2237 2585 65967409 65967759 2.340000e-125 459
20 TraesCS2A01G520000 chr3A 80.751 213 38 2 2373 2585 479147540 479147749 2.060000e-36 163
21 TraesCS2A01G520000 chr3B 89.831 354 34 2 2233 2585 714983238 714982886 1.090000e-123 453
22 TraesCS2A01G520000 chr4A 89.802 353 34 2 2234 2585 11710252 11709901 3.920000e-123 451
23 TraesCS2A01G520000 chr6B 89.415 359 34 4 2229 2585 126867795 126868151 1.410000e-122 449
24 TraesCS2A01G520000 chr6A 88.732 355 38 2 2232 2585 38726832 38727185 1.420000e-117 433
25 TraesCS2A01G520000 chr5B 86.158 354 30 9 2234 2585 15024691 15025027 5.260000e-97 364
26 TraesCS2A01G520000 chr5D 83.486 109 16 2 101 207 522604708 522604816 1.640000e-17 100


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 TraesCS2A01G520000 chr2A 743065153 743067737 2584 False 4774 4774 100.000 1 2585 1 chr2A.!!$F2 2584
1 TraesCS2A01G520000 chr1D 250223363 250225176 1813 False 2610 2610 92.688 411 2220 1 chr1D.!!$F1 1809
2 TraesCS2A01G520000 chr5A 536362165 536363968 1803 False 2591 2591 92.588 415 2220 1 chr5A.!!$F1 1805
3 TraesCS2A01G520000 chr2D 7031493 7033295 1802 False 2579 2579 92.486 415 2220 1 chr2D.!!$F1 1805
4 TraesCS2A01G520000 chr2D 596266511 596268284 1773 True 2547 2547 92.749 462 2220 1 chr2D.!!$R2 1758
5 TraesCS2A01G520000 chr2D 346436077 346437863 1786 False 2471 2471 91.556 413 2220 1 chr2D.!!$F2 1807
6 TraesCS2A01G520000 chr2D 500665421 500667212 1791 True 2470 2470 91.478 415 2220 1 chr2D.!!$R1 1805
7 TraesCS2A01G520000 chr3D 553935543 553937352 1809 True 2558 2558 92.240 415 2220 1 chr3D.!!$R1 1805
8 TraesCS2A01G520000 chr3D 540374905 540376473 1568 False 2274 2274 92.871 655 2220 1 chr3D.!!$F1 1565
9 TraesCS2A01G520000 chr7B 619668173 619669964 1791 False 2490 2490 91.667 411 2220 1 chr7B.!!$F1 1809
10 TraesCS2A01G520000 chr1A 119714781 119716588 1807 False 2390 2390 90.579 415 2220 1 chr1A.!!$F1 1805
11 TraesCS2A01G520000 chr4B 425291630 425293439 1809 False 2292 2292 89.615 415 2220 1 chr4B.!!$F2 1805
12 TraesCS2A01G520000 chr4B 3213141 3214192 1051 False 1218 1218 87.630 415 1466 1 chr4B.!!$F1 1051
13 TraesCS2A01G520000 chr2B 745670500 745671111 611 False 953 953 94.780 1 613 1 chr2B.!!$F2 612

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
856 906 0.314302 CGTCTGGTCGACCTTGTCTT 59.686 55.0 33.39 0.0 39.56 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2346 0.037232 GAAGGGGAGGTTGAGTCACG 60.037 60.0 0.0 0.0 0.0 4.35 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
59 60 2.124570 GTGCGGCTGATCCATGGT 60.125 61.111 12.58 0.00 34.01 3.55
111 112 6.558909 CAATTTCAGGAGATTAGAAGCCAAC 58.441 40.000 0.00 0.00 0.00 3.77
119 120 5.335976 GGAGATTAGAAGCCAACCAAACAAG 60.336 44.000 0.00 0.00 0.00 3.16
159 160 1.570813 TGAACAGTGCAGAAGACGTG 58.429 50.000 0.00 0.00 0.00 4.49
207 208 6.575162 ACTGATGTAAAGTGTTTCCCAATC 57.425 37.500 0.00 0.00 0.00 2.67
212 213 7.871973 TGATGTAAAGTGTTTCCCAATCATTTG 59.128 33.333 0.00 0.00 0.00 2.32
219 220 1.173043 TCCCAATCATTTGTGTCCGC 58.827 50.000 0.00 0.00 0.00 5.54
251 252 1.535462 AGCCGTCCAGATTTTTGTTCG 59.465 47.619 0.00 0.00 0.00 3.95
282 283 2.043450 CCAATTTAGCCGGCCCCA 60.043 61.111 26.15 7.26 0.00 4.96
385 386 3.243401 CCTTGACACCCAACTTTACAAGC 60.243 47.826 0.00 0.00 34.09 4.01
394 395 3.432252 CCAACTTTACAAGCTACGACCAG 59.568 47.826 0.00 0.00 0.00 4.00
401 402 0.388649 AAGCTACGACCAGTTGAGCG 60.389 55.000 0.00 0.00 38.20 5.03
450 451 1.675641 GCATCGAGCCCAAACAGGT 60.676 57.895 0.00 0.00 37.23 4.00
499 501 1.363807 GCCTGGTTTCACTGTTGGC 59.636 57.895 0.00 0.00 0.00 4.52
561 563 1.276421 ACTGGAAACACTCAGATCGGG 59.724 52.381 0.00 0.00 35.60 5.14
624 627 2.343758 GACTGCGACTCAAGGGCA 59.656 61.111 0.00 0.00 35.07 5.36
629 632 3.068881 CGACTCAAGGGCAAGGGA 58.931 61.111 0.00 0.00 0.00 4.20
637 640 3.743017 GGGCAAGGGAGGATGGCA 61.743 66.667 0.00 0.00 43.34 4.92
721 748 3.370527 GCTCACCCATAGCCACTTTCTTA 60.371 47.826 0.00 0.00 33.73 2.10
739 783 4.942944 TCTTACCTACTTCCTCACCATCA 58.057 43.478 0.00 0.00 0.00 3.07
745 789 2.526450 CTTCCTCACCATCAGCGGCA 62.526 60.000 1.45 0.00 0.00 5.69
828 878 2.551856 ATCTGGTGCTCCCCTGGCTA 62.552 60.000 1.59 0.00 0.00 3.93
856 906 0.314302 CGTCTGGTCGACCTTGTCTT 59.686 55.000 33.39 0.00 39.56 3.01
1044 1099 8.593156 CTGATAATTCAGGCAGCAACACTGATA 61.593 40.741 0.00 0.00 45.95 2.15
1095 1150 0.315251 CACCAGAGAGCTGTTCGTCA 59.685 55.000 0.00 0.00 40.63 4.35
1136 1191 5.056480 TCTGCTATGGTCCAATGTTTATCG 58.944 41.667 0.00 0.00 0.00 2.92
1179 1234 9.653287 CCAAAATCTGAACTACATCTACAACTA 57.347 33.333 0.00 0.00 0.00 2.24
1186 1241 9.809096 CTGAACTACATCTACAACTACAATGAT 57.191 33.333 0.00 0.00 0.00 2.45
1478 1536 1.275291 GACTCCACCCAAGATTCGTGA 59.725 52.381 0.82 0.00 0.00 4.35
1581 1640 3.762407 TTGAGCACTAACACAGGCTTA 57.238 42.857 0.00 0.00 36.59 3.09
1778 1837 1.605710 AGCGCATGATGCTAACATTCC 59.394 47.619 16.17 0.00 42.25 3.01
1798 1857 1.134877 CCAGTGACAGCATGAGTCGAT 60.135 52.381 12.29 3.11 39.69 3.59
1869 1928 3.127533 GCATGTCGGCCAGGTGTC 61.128 66.667 2.24 0.00 0.00 3.67
1923 1982 8.859090 CATCTCAATGAGTTCTCTAGTAGGAAT 58.141 37.037 10.36 0.00 34.61 3.01
2025 2084 8.643324 GCTCTGAAGAATAGGTTTAAGATCCTA 58.357 37.037 0.00 5.89 40.07 2.94
2040 2099 6.512514 AAGATCCTAGATCAGAAGCCATTT 57.487 37.500 7.30 0.00 0.00 2.32
2059 2118 2.919772 TCACCCATACTCCACTCAGA 57.080 50.000 0.00 0.00 0.00 3.27
2147 2206 1.040339 CCTGAGGAGGAAGAGGTCGG 61.040 65.000 0.00 0.00 42.93 4.79
2220 2279 5.531659 TGACGCTTGGAATAACAAAAGGTTA 59.468 36.000 0.00 0.00 45.55 2.85
2221 2280 5.765176 ACGCTTGGAATAACAAAAGGTTAC 58.235 37.500 0.00 0.00 44.36 2.50
2222 2281 5.533528 ACGCTTGGAATAACAAAAGGTTACT 59.466 36.000 0.00 0.00 44.36 2.24
2223 2282 6.084277 CGCTTGGAATAACAAAAGGTTACTC 58.916 40.000 0.00 0.00 44.36 2.59
2224 2283 6.293735 CGCTTGGAATAACAAAAGGTTACTCA 60.294 38.462 0.00 0.00 44.36 3.41
2225 2284 7.430441 GCTTGGAATAACAAAAGGTTACTCAA 58.570 34.615 0.00 0.00 44.36 3.02
2226 2285 8.088365 GCTTGGAATAACAAAAGGTTACTCAAT 58.912 33.333 0.00 0.00 44.36 2.57
2227 2286 9.626045 CTTGGAATAACAAAAGGTTACTCAATC 57.374 33.333 0.00 0.00 44.36 2.67
2228 2287 8.934023 TGGAATAACAAAAGGTTACTCAATCT 57.066 30.769 0.00 0.00 44.36 2.40
2229 2288 9.362151 TGGAATAACAAAAGGTTACTCAATCTT 57.638 29.630 0.00 0.00 44.36 2.40
2230 2289 9.841880 GGAATAACAAAAGGTTACTCAATCTTC 57.158 33.333 0.00 0.00 44.36 2.87
2231 2290 9.841880 GAATAACAAAAGGTTACTCAATCTTCC 57.158 33.333 0.00 0.00 44.36 3.46
2232 2291 6.650427 AACAAAAGGTTACTCAATCTTCCC 57.350 37.500 0.00 0.00 33.84 3.97
2233 2292 5.077564 ACAAAAGGTTACTCAATCTTCCCC 58.922 41.667 0.00 0.00 33.84 4.81
2234 2293 5.162980 ACAAAAGGTTACTCAATCTTCCCCT 60.163 40.000 0.00 0.00 33.84 4.79
2235 2294 4.846168 AAGGTTACTCAATCTTCCCCTC 57.154 45.455 0.00 0.00 28.43 4.30
2236 2295 3.116174 AGGTTACTCAATCTTCCCCTCC 58.884 50.000 0.00 0.00 0.00 4.30
2237 2296 2.172930 GGTTACTCAATCTTCCCCTCCC 59.827 54.545 0.00 0.00 0.00 4.30
2238 2297 2.172930 GTTACTCAATCTTCCCCTCCCC 59.827 54.545 0.00 0.00 0.00 4.81
2239 2298 0.423544 ACTCAATCTTCCCCTCCCCT 59.576 55.000 0.00 0.00 0.00 4.79
2240 2299 1.135960 CTCAATCTTCCCCTCCCCTC 58.864 60.000 0.00 0.00 0.00 4.30
2241 2300 0.327576 TCAATCTTCCCCTCCCCTCC 60.328 60.000 0.00 0.00 0.00 4.30
2242 2301 1.006227 AATCTTCCCCTCCCCTCCC 59.994 63.158 0.00 0.00 0.00 4.30
2243 2302 2.585523 AATCTTCCCCTCCCCTCCCC 62.586 65.000 0.00 0.00 0.00 4.81
2244 2303 3.711782 CTTCCCCTCCCCTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
2245 2304 3.707189 TTCCCCTCCCCTCCCCTC 61.707 72.222 0.00 0.00 0.00 4.30
2258 2317 3.382832 CCCTCCCGTGTCGCTCTT 61.383 66.667 0.00 0.00 0.00 2.85
2259 2318 2.125912 CCTCCCGTGTCGCTCTTG 60.126 66.667 0.00 0.00 0.00 3.02
2260 2319 2.811317 CTCCCGTGTCGCTCTTGC 60.811 66.667 0.00 0.00 0.00 4.01
2261 2320 3.573772 CTCCCGTGTCGCTCTTGCA 62.574 63.158 0.00 0.00 39.64 4.08
2262 2321 2.664851 CCCGTGTCGCTCTTGCAA 60.665 61.111 0.00 0.00 39.64 4.08
2263 2322 2.671177 CCCGTGTCGCTCTTGCAAG 61.671 63.158 20.81 20.81 39.64 4.01
2264 2323 2.171940 CGTGTCGCTCTTGCAAGC 59.828 61.111 21.99 11.13 39.64 4.01
2270 2329 3.793144 GCTCTTGCAAGCGACCGG 61.793 66.667 21.99 0.00 39.41 5.28
2271 2330 3.121030 CTCTTGCAAGCGACCGGG 61.121 66.667 21.99 0.00 0.00 5.73
2272 2331 4.697756 TCTTGCAAGCGACCGGGG 62.698 66.667 21.99 0.00 0.00 5.73
2288 2347 4.315941 GGGGAATCCTAGCCGCCG 62.316 72.222 0.00 0.00 0.00 6.46
2289 2348 3.547513 GGGAATCCTAGCCGCCGT 61.548 66.667 0.00 0.00 0.00 5.68
2290 2349 2.280186 GGAATCCTAGCCGCCGTG 60.280 66.667 0.00 0.00 0.00 4.94
2291 2350 2.792947 GGAATCCTAGCCGCCGTGA 61.793 63.158 0.00 0.00 0.00 4.35
2292 2351 1.591863 GAATCCTAGCCGCCGTGAC 60.592 63.158 0.00 0.00 0.00 3.67
2293 2352 2.017559 GAATCCTAGCCGCCGTGACT 62.018 60.000 0.00 0.00 0.00 3.41
2294 2353 2.017559 AATCCTAGCCGCCGTGACTC 62.018 60.000 0.00 0.00 0.00 3.36
2295 2354 3.449227 CCTAGCCGCCGTGACTCA 61.449 66.667 0.00 0.00 0.00 3.41
2296 2355 2.571757 CTAGCCGCCGTGACTCAA 59.428 61.111 0.00 0.00 0.00 3.02
2297 2356 1.805945 CTAGCCGCCGTGACTCAAC 60.806 63.158 0.00 0.00 0.00 3.18
2298 2357 3.291101 TAGCCGCCGTGACTCAACC 62.291 63.158 0.00 0.00 0.00 3.77
2299 2358 4.681978 GCCGCCGTGACTCAACCT 62.682 66.667 0.00 0.00 0.00 3.50
2300 2359 2.432628 CCGCCGTGACTCAACCTC 60.433 66.667 0.00 0.00 0.00 3.85
2301 2360 2.432628 CGCCGTGACTCAACCTCC 60.433 66.667 0.00 0.00 0.00 4.30
2302 2361 2.047179 GCCGTGACTCAACCTCCC 60.047 66.667 0.00 0.00 0.00 4.30
2303 2362 2.663196 CCGTGACTCAACCTCCCC 59.337 66.667 0.00 0.00 0.00 4.81
2304 2363 1.913762 CCGTGACTCAACCTCCCCT 60.914 63.158 0.00 0.00 0.00 4.79
2305 2364 1.481056 CCGTGACTCAACCTCCCCTT 61.481 60.000 0.00 0.00 0.00 3.95
2306 2365 0.037232 CGTGACTCAACCTCCCCTTC 60.037 60.000 0.00 0.00 0.00 3.46
2307 2366 0.325272 GTGACTCAACCTCCCCTTCC 59.675 60.000 0.00 0.00 0.00 3.46
2308 2367 0.193574 TGACTCAACCTCCCCTTCCT 59.806 55.000 0.00 0.00 0.00 3.36
2309 2368 0.906066 GACTCAACCTCCCCTTCCTC 59.094 60.000 0.00 0.00 0.00 3.71
2310 2369 0.494095 ACTCAACCTCCCCTTCCTCT 59.506 55.000 0.00 0.00 0.00 3.69
2311 2370 0.908198 CTCAACCTCCCCTTCCTCTG 59.092 60.000 0.00 0.00 0.00 3.35
2312 2371 1.201429 TCAACCTCCCCTTCCTCTGC 61.201 60.000 0.00 0.00 0.00 4.26
2313 2372 1.162085 AACCTCCCCTTCCTCTGCT 59.838 57.895 0.00 0.00 0.00 4.24
2314 2373 0.912006 AACCTCCCCTTCCTCTGCTC 60.912 60.000 0.00 0.00 0.00 4.26
2315 2374 1.002792 CCTCCCCTTCCTCTGCTCT 59.997 63.158 0.00 0.00 0.00 4.09
2316 2375 1.048160 CCTCCCCTTCCTCTGCTCTC 61.048 65.000 0.00 0.00 0.00 3.20
2317 2376 1.002274 TCCCCTTCCTCTGCTCTCC 59.998 63.158 0.00 0.00 0.00 3.71
2318 2377 1.002792 CCCCTTCCTCTGCTCTCCT 59.997 63.158 0.00 0.00 0.00 3.69
2319 2378 0.620121 CCCCTTCCTCTGCTCTCCTT 60.620 60.000 0.00 0.00 0.00 3.36
2320 2379 0.829990 CCCTTCCTCTGCTCTCCTTC 59.170 60.000 0.00 0.00 0.00 3.46
2321 2380 0.829990 CCTTCCTCTGCTCTCCTTCC 59.170 60.000 0.00 0.00 0.00 3.46
2322 2381 1.622173 CCTTCCTCTGCTCTCCTTCCT 60.622 57.143 0.00 0.00 0.00 3.36
2323 2382 1.756538 CTTCCTCTGCTCTCCTTCCTC 59.243 57.143 0.00 0.00 0.00 3.71
2324 2383 0.395036 TCCTCTGCTCTCCTTCCTCG 60.395 60.000 0.00 0.00 0.00 4.63
2325 2384 1.437160 CTCTGCTCTCCTTCCTCGC 59.563 63.158 0.00 0.00 0.00 5.03
2326 2385 2.015227 CTCTGCTCTCCTTCCTCGCC 62.015 65.000 0.00 0.00 0.00 5.54
2327 2386 3.423162 CTGCTCTCCTTCCTCGCCG 62.423 68.421 0.00 0.00 0.00 6.46
2328 2387 4.882396 GCTCTCCTTCCTCGCCGC 62.882 72.222 0.00 0.00 0.00 6.53
2329 2388 4.214327 CTCTCCTTCCTCGCCGCC 62.214 72.222 0.00 0.00 0.00 6.13
2354 2413 2.877691 GACACCATCGGGCAAAGC 59.122 61.111 0.00 0.00 37.90 3.51
2389 2448 4.491409 GGCGGGGCCTCTTCTTCC 62.491 72.222 0.00 0.00 46.69 3.46
2390 2449 3.403558 GCGGGGCCTCTTCTTCCT 61.404 66.667 0.00 0.00 0.00 3.36
2391 2450 2.904131 CGGGGCCTCTTCTTCCTC 59.096 66.667 0.00 0.00 0.00 3.71
2392 2451 2.736826 CGGGGCCTCTTCTTCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
2393 2452 2.379459 GGGGCCTCTTCTTCCTCCC 61.379 68.421 0.84 0.00 0.00 4.30
2394 2453 2.379459 GGGCCTCTTCTTCCTCCCC 61.379 68.421 0.84 0.00 0.00 4.81
2395 2454 2.379459 GGCCTCTTCTTCCTCCCCC 61.379 68.421 0.00 0.00 0.00 5.40
2396 2455 1.307430 GCCTCTTCTTCCTCCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
2397 2456 1.341913 GCCTCTTCTTCCTCCCCCTC 61.342 65.000 0.00 0.00 0.00 4.30
2398 2457 1.045911 CCTCTTCTTCCTCCCCCTCG 61.046 65.000 0.00 0.00 0.00 4.63
2399 2458 0.324830 CTCTTCTTCCTCCCCCTCGT 60.325 60.000 0.00 0.00 0.00 4.18
2400 2459 0.614979 TCTTCTTCCTCCCCCTCGTG 60.615 60.000 0.00 0.00 0.00 4.35
2401 2460 2.245438 CTTCTTCCTCCCCCTCGTGC 62.245 65.000 0.00 0.00 0.00 5.34
2402 2461 2.685380 CTTCCTCCCCCTCGTGCT 60.685 66.667 0.00 0.00 0.00 4.40
2403 2462 2.683933 TTCCTCCCCCTCGTGCTC 60.684 66.667 0.00 0.00 0.00 4.26
2404 2463 4.779733 TCCTCCCCCTCGTGCTCC 62.780 72.222 0.00 0.00 0.00 4.70
2435 2494 4.436998 GACAGCCGGTCGAGTGGG 62.437 72.222 1.90 0.00 36.65 4.61
2503 2562 4.796495 GCGGCGGGGTTTCCTGAT 62.796 66.667 9.78 0.00 42.08 2.90
2504 2563 2.824041 CGGCGGGGTTTCCTGATG 60.824 66.667 0.00 0.00 42.08 3.07
2505 2564 2.440247 GGCGGGGTTTCCTGATGG 60.440 66.667 0.00 0.00 42.08 3.51
2506 2565 2.440247 GCGGGGTTTCCTGATGGG 60.440 66.667 0.00 0.00 42.08 4.00
2507 2566 2.978946 GCGGGGTTTCCTGATGGGA 61.979 63.158 0.00 0.00 42.08 4.37
2514 2573 2.577059 TCCTGATGGGAACGCGAC 59.423 61.111 15.93 6.28 41.91 5.19
2515 2574 2.264480 CCTGATGGGAACGCGACA 59.736 61.111 15.93 6.56 37.23 4.35
2516 2575 1.153369 CCTGATGGGAACGCGACAT 60.153 57.895 15.93 11.65 37.23 3.06
2517 2576 1.154205 CCTGATGGGAACGCGACATC 61.154 60.000 15.93 19.82 40.96 3.06
2518 2577 1.482621 CTGATGGGAACGCGACATCG 61.483 60.000 15.93 12.55 42.91 3.84
2519 2578 1.226859 GATGGGAACGCGACATCGA 60.227 57.895 15.93 0.00 43.02 3.59
2520 2579 1.209275 GATGGGAACGCGACATCGAG 61.209 60.000 15.93 4.24 44.60 4.04
2521 2580 3.255379 GGGAACGCGACATCGAGC 61.255 66.667 15.93 0.00 42.87 5.03
2547 2606 4.659874 CGTTTGTGGCGTGGCGAC 62.660 66.667 0.00 0.00 37.76 5.19
2548 2607 4.322385 GTTTGTGGCGTGGCGACC 62.322 66.667 0.37 0.00 36.46 4.79
2577 2636 4.552365 CGATCTGGGCGGTGGCAT 62.552 66.667 0.00 0.00 42.47 4.40
2578 2637 2.903855 GATCTGGGCGGTGGCATG 60.904 66.667 0.00 0.00 42.47 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.215201 CGTACATCGTCTCTCATCATGTC 58.785 47.826 0.00 0.00 34.52 3.06
59 60 2.161855 CTGCAGTAATGTTGCTTGGGA 58.838 47.619 5.25 0.00 42.02 4.37
111 112 2.613474 CCACATCCAATGGCTTGTTTGG 60.613 50.000 5.18 2.33 43.10 3.28
119 120 1.134521 TCTCGTACCACATCCAATGGC 60.135 52.381 0.00 0.00 41.31 4.40
207 208 3.722295 ACGCGGCGGACACAAATG 61.722 61.111 27.37 0.00 0.00 2.32
228 229 1.000274 ACAAAAATCTGGACGGCTTGC 60.000 47.619 0.00 0.00 0.00 4.01
231 232 1.535462 CGAACAAAAATCTGGACGGCT 59.465 47.619 0.00 0.00 0.00 5.52
282 283 1.607467 GGCTGAGTTGGGCCACAAT 60.607 57.895 5.23 0.00 46.84 2.71
385 386 0.803117 TCTCGCTCAACTGGTCGTAG 59.197 55.000 0.00 0.00 0.00 3.51
394 395 3.125316 CCCAAAGTGTATTCTCGCTCAAC 59.875 47.826 0.00 0.00 0.00 3.18
450 451 1.626356 CCTCTTCCTTCCCATGCGGA 61.626 60.000 0.00 0.00 39.68 5.54
499 501 1.970917 GAGAAACGTGCGATGCAGGG 61.971 60.000 14.92 2.81 46.80 4.45
513 515 1.069049 GCTTTGGGCTGCTTTGAGAAA 59.931 47.619 0.00 0.00 38.06 2.52
561 563 1.807573 CCTGGCTCGCGAGAAACTC 60.808 63.158 38.74 20.30 41.32 3.01
608 611 1.302033 CTTGCCCTTGAGTCGCAGT 60.302 57.895 0.00 0.00 33.30 4.40
616 619 1.574526 CCATCCTCCCTTGCCCTTGA 61.575 60.000 0.00 0.00 0.00 3.02
624 627 0.029267 ATCTCCTGCCATCCTCCCTT 60.029 55.000 0.00 0.00 0.00 3.95
629 632 0.327867 TTCCCATCTCCTGCCATCCT 60.328 55.000 0.00 0.00 0.00 3.24
637 640 1.213926 GTGCCAGATTTCCCATCTCCT 59.786 52.381 0.00 0.00 0.00 3.69
668 671 0.255890 GGGTGAGGCTAGATTTGGCA 59.744 55.000 0.00 0.00 31.41 4.92
721 748 1.834263 GCTGATGGTGAGGAAGTAGGT 59.166 52.381 0.00 0.00 0.00 3.08
745 789 1.797046 CGCATATCTGAAATCGCAGCT 59.203 47.619 0.00 0.00 35.86 4.24
805 855 1.727062 CAGGGGAGCACCAGATCTAT 58.273 55.000 1.58 0.00 42.91 1.98
856 906 2.286808 TAGGGGGAGCCATGGCAA 60.287 61.111 37.18 11.29 44.88 4.52
1044 1099 2.173519 CCCATGCCTGAATCACACTTT 58.826 47.619 0.00 0.00 0.00 2.66
1095 1150 2.092538 CAGATCAAAGGTCTCCCAGCAT 60.093 50.000 0.00 0.00 0.00 3.79
1136 1191 0.326618 TGGATCCTCTCCTGTTCCCC 60.327 60.000 14.23 0.00 45.21 4.81
1179 1234 1.552337 ACAGAGCCTCGACATCATTGT 59.448 47.619 0.00 0.00 39.32 2.71
1186 1241 1.893062 CATCCACAGAGCCTCGACA 59.107 57.895 0.00 0.00 0.00 4.35
1250 1306 1.208293 CTTGTAGCAGTCCCTTCTCCC 59.792 57.143 0.00 0.00 0.00 4.30
1260 1317 5.643777 GGTGTTGATGTTATCTTGTAGCAGT 59.356 40.000 0.00 0.00 0.00 4.40
1478 1536 3.979501 ATGGATACCATCTTGGGCTTT 57.020 42.857 0.00 0.00 40.74 3.51
1581 1640 3.452990 TGCAATCCTGAAAATGGCATCAT 59.547 39.130 0.00 0.00 27.98 2.45
1778 1837 0.244721 TCGACTCATGCTGTCACTGG 59.755 55.000 15.47 3.54 34.37 4.00
1819 1878 1.418637 TCCAAGGTAGAACTTGCCGTT 59.581 47.619 1.54 0.00 44.98 4.44
1869 1928 2.239400 GTTTTCCTGAAGGGTGGAAGG 58.761 52.381 0.00 0.00 42.46 3.46
1923 1982 3.300388 CTCCTGTGCAGTCCTAGGATAA 58.700 50.000 16.27 0.00 38.56 1.75
2025 2084 2.309755 TGGGTGAAATGGCTTCTGATCT 59.690 45.455 0.00 0.00 34.86 2.75
2040 2099 2.919772 TCTGAGTGGAGTATGGGTGA 57.080 50.000 0.00 0.00 0.00 4.02
2059 2118 7.038154 TGCAACAAGTAAGAACAAGCTTAAT 57.962 32.000 0.00 0.00 32.58 1.40
2147 2206 2.162408 GAGCTAACAACATTGTCAGGCC 59.838 50.000 0.00 0.00 41.31 5.19
2155 2214 0.037590 TGGCCGGAGCTAACAACATT 59.962 50.000 5.05 0.00 39.73 2.71
2191 2250 5.446143 TTGTTATTCCAAGCGTCATTGTT 57.554 34.783 0.00 0.00 0.00 2.83
2220 2279 0.423544 AGGGGAGGGGAAGATTGAGT 59.576 55.000 0.00 0.00 0.00 3.41
2221 2280 1.135960 GAGGGGAGGGGAAGATTGAG 58.864 60.000 0.00 0.00 0.00 3.02
2222 2281 0.327576 GGAGGGGAGGGGAAGATTGA 60.328 60.000 0.00 0.00 0.00 2.57
2223 2282 1.356494 GGGAGGGGAGGGGAAGATTG 61.356 65.000 0.00 0.00 0.00 2.67
2224 2283 1.006227 GGGAGGGGAGGGGAAGATT 59.994 63.158 0.00 0.00 0.00 2.40
2225 2284 2.712746 GGGAGGGGAGGGGAAGAT 59.287 66.667 0.00 0.00 0.00 2.40
2226 2285 3.707189 GGGGAGGGGAGGGGAAGA 61.707 72.222 0.00 0.00 0.00 2.87
2227 2286 3.711782 AGGGGAGGGGAGGGGAAG 61.712 72.222 0.00 0.00 0.00 3.46
2228 2287 3.707189 GAGGGGAGGGGAGGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
2241 2300 3.382832 AAGAGCGACACGGGAGGG 61.383 66.667 0.00 0.00 40.95 4.30
2242 2301 2.125912 CAAGAGCGACACGGGAGG 60.126 66.667 0.00 0.00 0.00 4.30
2243 2302 2.811317 GCAAGAGCGACACGGGAG 60.811 66.667 0.00 0.00 0.00 4.30
2244 2303 3.158537 TTGCAAGAGCGACACGGGA 62.159 57.895 0.00 0.00 46.23 5.14
2245 2304 2.664851 TTGCAAGAGCGACACGGG 60.665 61.111 0.00 0.00 46.23 5.28
2246 2305 2.856032 CTTGCAAGAGCGACACGG 59.144 61.111 22.31 0.00 46.23 4.94
2247 2306 2.171940 GCTTGCAAGAGCGACACG 59.828 61.111 30.39 1.03 46.23 4.49
2253 2312 3.793144 CCGGTCGCTTGCAAGAGC 61.793 66.667 30.39 20.51 42.57 4.09
2254 2313 3.121030 CCCGGTCGCTTGCAAGAG 61.121 66.667 30.39 26.38 0.00 2.85
2255 2314 4.697756 CCCCGGTCGCTTGCAAGA 62.698 66.667 30.39 7.54 0.00 3.02
2270 2329 3.955044 GGCGGCTAGGATTCCCCC 61.955 72.222 0.00 0.00 34.66 5.40
2271 2330 4.315941 CGGCGGCTAGGATTCCCC 62.316 72.222 7.61 0.00 0.00 4.81
2272 2331 3.547513 ACGGCGGCTAGGATTCCC 61.548 66.667 13.24 0.00 0.00 3.97
2273 2332 2.280186 CACGGCGGCTAGGATTCC 60.280 66.667 13.24 0.00 0.00 3.01
2274 2333 1.591863 GTCACGGCGGCTAGGATTC 60.592 63.158 13.24 0.00 0.00 2.52
2275 2334 2.017559 GAGTCACGGCGGCTAGGATT 62.018 60.000 13.24 0.00 0.00 3.01
2276 2335 2.442272 AGTCACGGCGGCTAGGAT 60.442 61.111 13.24 0.00 0.00 3.24
2277 2336 3.138798 GAGTCACGGCGGCTAGGA 61.139 66.667 13.24 0.00 0.00 2.94
2278 2337 3.001902 TTGAGTCACGGCGGCTAGG 62.002 63.158 13.24 0.00 0.00 3.02
2279 2338 1.805945 GTTGAGTCACGGCGGCTAG 60.806 63.158 13.24 0.00 0.00 3.42
2280 2339 2.260434 GTTGAGTCACGGCGGCTA 59.740 61.111 13.24 0.00 0.00 3.93
2281 2340 4.681978 GGTTGAGTCACGGCGGCT 62.682 66.667 13.24 6.19 0.00 5.52
2282 2341 4.681978 AGGTTGAGTCACGGCGGC 62.682 66.667 13.24 0.00 0.00 6.53
2283 2342 2.432628 GAGGTTGAGTCACGGCGG 60.433 66.667 13.24 0.00 0.00 6.13
2284 2343 2.432628 GGAGGTTGAGTCACGGCG 60.433 66.667 4.80 4.80 0.00 6.46
2285 2344 2.047179 GGGAGGTTGAGTCACGGC 60.047 66.667 0.00 0.00 0.00 5.68
2286 2345 1.481056 AAGGGGAGGTTGAGTCACGG 61.481 60.000 0.00 0.00 0.00 4.94
2287 2346 0.037232 GAAGGGGAGGTTGAGTCACG 60.037 60.000 0.00 0.00 0.00 4.35
2288 2347 0.325272 GGAAGGGGAGGTTGAGTCAC 59.675 60.000 0.00 0.00 0.00 3.67
2289 2348 0.193574 AGGAAGGGGAGGTTGAGTCA 59.806 55.000 0.00 0.00 0.00 3.41
2290 2349 0.906066 GAGGAAGGGGAGGTTGAGTC 59.094 60.000 0.00 0.00 0.00 3.36
2291 2350 0.494095 AGAGGAAGGGGAGGTTGAGT 59.506 55.000 0.00 0.00 0.00 3.41
2292 2351 0.908198 CAGAGGAAGGGGAGGTTGAG 59.092 60.000 0.00 0.00 0.00 3.02
2293 2352 1.201429 GCAGAGGAAGGGGAGGTTGA 61.201 60.000 0.00 0.00 0.00 3.18
2294 2353 1.204113 AGCAGAGGAAGGGGAGGTTG 61.204 60.000 0.00 0.00 0.00 3.77
2295 2354 0.912006 GAGCAGAGGAAGGGGAGGTT 60.912 60.000 0.00 0.00 0.00 3.50
2296 2355 1.306568 GAGCAGAGGAAGGGGAGGT 60.307 63.158 0.00 0.00 0.00 3.85
2297 2356 1.002792 AGAGCAGAGGAAGGGGAGG 59.997 63.158 0.00 0.00 0.00 4.30
2298 2357 1.048160 GGAGAGCAGAGGAAGGGGAG 61.048 65.000 0.00 0.00 0.00 4.30
2299 2358 1.002274 GGAGAGCAGAGGAAGGGGA 59.998 63.158 0.00 0.00 0.00 4.81
2300 2359 0.620121 AAGGAGAGCAGAGGAAGGGG 60.620 60.000 0.00 0.00 0.00 4.79
2301 2360 0.829990 GAAGGAGAGCAGAGGAAGGG 59.170 60.000 0.00 0.00 0.00 3.95
2302 2361 0.829990 GGAAGGAGAGCAGAGGAAGG 59.170 60.000 0.00 0.00 0.00 3.46
2303 2362 1.756538 GAGGAAGGAGAGCAGAGGAAG 59.243 57.143 0.00 0.00 0.00 3.46
2304 2363 1.859302 GAGGAAGGAGAGCAGAGGAA 58.141 55.000 0.00 0.00 0.00 3.36
2305 2364 0.395036 CGAGGAAGGAGAGCAGAGGA 60.395 60.000 0.00 0.00 0.00 3.71
2306 2365 2.015227 GCGAGGAAGGAGAGCAGAGG 62.015 65.000 0.00 0.00 0.00 3.69
2307 2366 1.437160 GCGAGGAAGGAGAGCAGAG 59.563 63.158 0.00 0.00 0.00 3.35
2308 2367 2.055042 GGCGAGGAAGGAGAGCAGA 61.055 63.158 0.00 0.00 0.00 4.26
2309 2368 2.498726 GGCGAGGAAGGAGAGCAG 59.501 66.667 0.00 0.00 0.00 4.24
2310 2369 3.452786 CGGCGAGGAAGGAGAGCA 61.453 66.667 0.00 0.00 0.00 4.26
2311 2370 4.882396 GCGGCGAGGAAGGAGAGC 62.882 72.222 12.98 0.00 0.00 4.09
2312 2371 4.214327 GGCGGCGAGGAAGGAGAG 62.214 72.222 12.98 0.00 0.00 3.20
2337 2396 2.700773 GGCTTTGCCCGATGGTGTC 61.701 63.158 0.00 0.00 44.06 3.67
2338 2397 2.676471 GGCTTTGCCCGATGGTGT 60.676 61.111 0.00 0.00 44.06 4.16
2373 2432 3.393149 GAGGAAGAAGAGGCCCCGC 62.393 68.421 0.00 0.00 0.00 6.13
2374 2433 2.736826 GGAGGAAGAAGAGGCCCCG 61.737 68.421 0.00 0.00 0.00 5.73
2375 2434 2.379459 GGGAGGAAGAAGAGGCCCC 61.379 68.421 0.00 0.00 0.00 5.80
2376 2435 2.379459 GGGGAGGAAGAAGAGGCCC 61.379 68.421 0.00 0.00 34.79 5.80
2377 2436 2.379459 GGGGGAGGAAGAAGAGGCC 61.379 68.421 0.00 0.00 0.00 5.19
2378 2437 1.307430 AGGGGGAGGAAGAAGAGGC 60.307 63.158 0.00 0.00 0.00 4.70
2379 2438 1.045911 CGAGGGGGAGGAAGAAGAGG 61.046 65.000 0.00 0.00 0.00 3.69
2380 2439 0.324830 ACGAGGGGGAGGAAGAAGAG 60.325 60.000 0.00 0.00 0.00 2.85
2381 2440 0.614979 CACGAGGGGGAGGAAGAAGA 60.615 60.000 0.00 0.00 0.00 2.87
2382 2441 1.901085 CACGAGGGGGAGGAAGAAG 59.099 63.158 0.00 0.00 0.00 2.85
2383 2442 2.291043 GCACGAGGGGGAGGAAGAA 61.291 63.158 0.00 0.00 0.00 2.52
2384 2443 2.683933 GCACGAGGGGGAGGAAGA 60.684 66.667 0.00 0.00 0.00 2.87
2385 2444 2.685380 AGCACGAGGGGGAGGAAG 60.685 66.667 0.00 0.00 0.00 3.46
2386 2445 2.683933 GAGCACGAGGGGGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
2387 2446 4.779733 GGAGCACGAGGGGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
2414 2473 4.838486 CTCGACCGGCTGTCTCGC 62.838 72.222 0.00 0.00 42.13 5.03
2415 2474 3.432588 ACTCGACCGGCTGTCTCG 61.433 66.667 0.00 2.49 42.13 4.04
2416 2475 2.179517 CACTCGACCGGCTGTCTC 59.820 66.667 0.00 0.00 42.13 3.36
2417 2476 3.374402 CCACTCGACCGGCTGTCT 61.374 66.667 0.00 0.00 42.13 3.41
2418 2477 4.436998 CCCACTCGACCGGCTGTC 62.437 72.222 0.00 0.00 40.81 3.51
2431 2490 4.280019 AAAGACCGGTGCCCCCAC 62.280 66.667 14.63 0.00 41.32 4.61
2432 2491 4.278513 CAAAGACCGGTGCCCCCA 62.279 66.667 14.63 0.00 0.00 4.96
2486 2545 4.796495 ATCAGGAAACCCCGCCGC 62.796 66.667 0.00 0.00 40.87 6.53
2487 2546 2.824041 CATCAGGAAACCCCGCCG 60.824 66.667 0.00 0.00 40.87 6.46
2488 2547 2.440247 CCATCAGGAAACCCCGCC 60.440 66.667 0.00 0.00 40.87 6.13
2489 2548 2.440247 CCCATCAGGAAACCCCGC 60.440 66.667 0.00 0.00 40.87 6.13
2490 2549 3.410541 TCCCATCAGGAAACCCCG 58.589 61.111 0.00 0.00 43.78 5.73
2497 2556 1.613317 ATGTCGCGTTCCCATCAGGA 61.613 55.000 5.77 0.00 45.68 3.86
2498 2557 1.153369 ATGTCGCGTTCCCATCAGG 60.153 57.895 5.77 0.00 0.00 3.86
2499 2558 1.482621 CGATGTCGCGTTCCCATCAG 61.483 60.000 21.19 14.16 35.76 2.90
2500 2559 1.518352 CGATGTCGCGTTCCCATCA 60.518 57.895 21.19 7.93 35.76 3.07
2501 2560 1.209275 CTCGATGTCGCGTTCCCATC 61.209 60.000 5.77 12.50 39.60 3.51
2502 2561 1.226974 CTCGATGTCGCGTTCCCAT 60.227 57.895 5.77 4.47 39.60 4.00
2503 2562 2.180769 CTCGATGTCGCGTTCCCA 59.819 61.111 5.77 0.00 39.60 4.37
2504 2563 3.255379 GCTCGATGTCGCGTTCCC 61.255 66.667 5.77 0.00 39.60 3.97
2505 2564 3.607987 CGCTCGATGTCGCGTTCC 61.608 66.667 5.77 0.00 44.01 3.62
2530 2589 4.659874 GTCGCCACGCCACAAACG 62.660 66.667 0.00 0.00 0.00 3.60
2531 2590 4.322385 GGTCGCCACGCCACAAAC 62.322 66.667 0.00 0.00 0.00 2.93
2560 2619 4.552365 ATGCCACCGCCCAGATCG 62.552 66.667 0.00 0.00 0.00 3.69
2561 2620 2.903855 CATGCCACCGCCCAGATC 60.904 66.667 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.