Multiple sequence alignment - TraesCS2A01G585400

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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 TraesCS2A01G585400 chr2A 100.000 2964 0 0 1 2964 776173542 776176505 0.000000e+00 5474.0
1 TraesCS2A01G585400 chr2A 98.082 2242 34 3 1 2240 9951372 9953606 0.000000e+00 3893.0
2 TraesCS2A01G585400 chr2A 97.576 495 11 1 2470 2964 157497940 157497447 0.000000e+00 846.0
3 TraesCS2A01G585400 chr2A 95.226 398 8 2 2470 2857 753520077 753519681 1.170000e-173 619.0
4 TraesCS2A01G585400 chr2A 87.842 329 28 2 1950 2266 772969060 772969388 2.790000e-100 375.0
5 TraesCS2A01G585400 chr2A 98.214 112 2 0 2853 2964 753505826 753505715 2.330000e-46 196.0
6 TraesCS2A01G585400 chr5A 98.053 2260 32 5 1 2254 673237889 673240142 0.000000e+00 3919.0
7 TraesCS2A01G585400 chr5A 81.513 119 21 1 2310 2428 37614161 37614278 2.430000e-16 97.1
8 TraesCS2A01G585400 chr1A 95.963 2279 76 10 1 2266 532735325 532733050 0.000000e+00 3685.0
9 TraesCS2A01G585400 chr1A 93.156 1958 102 9 1 1952 584970309 584972240 0.000000e+00 2844.0
10 TraesCS2A01G585400 chr1A 96.677 1264 36 3 1 1262 12307856 12309115 0.000000e+00 2097.0
11 TraesCS2A01G585400 chr1A 93.528 958 41 5 1299 2254 12309363 12310301 0.000000e+00 1406.0
12 TraesCS2A01G585400 chr1A 96.349 493 17 1 2470 2962 66655482 66654991 0.000000e+00 809.0
13 TraesCS2A01G585400 chr1A 91.071 336 17 3 1946 2270 584972292 584972625 2.710000e-120 442.0
14 TraesCS2A01G585400 chr3A 94.967 2265 72 11 1 2254 698295937 698298170 0.000000e+00 3513.0
15 TraesCS2A01G585400 chr7B 93.654 1954 91 12 2 1952 706976366 706974443 0.000000e+00 2891.0
16 TraesCS2A01G585400 chr3B 92.748 1958 102 12 1 1952 772227374 772229297 0.000000e+00 2793.0
17 TraesCS2A01G585400 chr3B 90.675 311 26 3 1946 2254 772229349 772229658 7.650000e-111 411.0
18 TraesCS2A01G585400 chr3B 90.217 276 19 4 2470 2745 330581728 330581995 1.310000e-93 353.0
19 TraesCS2A01G585400 chr5B 92.323 1967 109 16 1 1952 26737096 26735157 0.000000e+00 2758.0
20 TraesCS2A01G585400 chr5B 91.935 310 22 3 1946 2254 26735105 26734798 5.870000e-117 431.0
21 TraesCS2A01G585400 chr5B 80.000 130 22 4 2310 2437 692367630 692367503 3.150000e-15 93.5
22 TraesCS2A01G585400 chrUn 94.280 944 44 5 1010 1952 117079696 117080630 0.000000e+00 1435.0
23 TraesCS2A01G585400 chrUn 92.988 927 58 4 1 925 117078747 117079668 0.000000e+00 1345.0
24 TraesCS2A01G585400 chrUn 90.196 306 29 1 1950 2254 290195665 290195970 5.950000e-107 398.0
25 TraesCS2A01G585400 chrUn 90.196 306 29 1 1950 2254 326178872 326179177 5.950000e-107 398.0
26 TraesCS2A01G585400 chrUn 75.648 193 23 16 2117 2292 112970068 112970253 1.140000e-09 75.0
27 TraesCS2A01G585400 chr4D 93.841 276 16 1 2470 2745 344881242 344881516 5.910000e-112 414.0
28 TraesCS2A01G585400 chr4D 86.017 236 13 1 2746 2961 344881608 344881843 4.940000e-58 235.0
29 TraesCS2A01G585400 chr4D 78.417 139 27 2 2307 2445 417470560 417470695 1.460000e-13 87.9
30 TraesCS2A01G585400 chr7D 88.953 172 18 1 2300 2471 544553998 544554168 8.320000e-51 211.0
31 TraesCS2A01G585400 chr7D 79.562 137 26 2 2303 2437 416257801 416257665 2.430000e-16 97.1
32 TraesCS2A01G585400 chr2B 78.249 354 44 16 1950 2280 33584403 33584060 2.330000e-46 196.0
33 TraesCS2A01G585400 chr6A 86.842 152 20 0 2320 2471 374410938 374410787 1.410000e-38 171.0
34 TraesCS2A01G585400 chr6A 94.872 39 2 0 2236 2274 15899948 15899910 8.870000e-06 62.1
35 TraesCS2A01G585400 chr5D 76.506 332 58 10 1950 2270 523500196 523499874 2.360000e-36 163.0
36 TraesCS2A01G585400 chr4A 79.503 161 27 6 2279 2436 6019828 6019985 3.120000e-20 110.0
37 TraesCS2A01G585400 chr1B 79.720 143 24 5 2297 2437 342122252 342122113 6.760000e-17 99.0
38 TraesCS2A01G585400 chr4B 79.137 139 25 4 2304 2440 564627030 564626894 3.150000e-15 93.5


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 TraesCS2A01G585400 chr2A 776173542 776176505 2963 False 5474.0 5474 100.0000 1 2964 1 chr2A.!!$F3 2963
1 TraesCS2A01G585400 chr2A 9951372 9953606 2234 False 3893.0 3893 98.0820 1 2240 1 chr2A.!!$F1 2239
2 TraesCS2A01G585400 chr5A 673237889 673240142 2253 False 3919.0 3919 98.0530 1 2254 1 chr5A.!!$F2 2253
3 TraesCS2A01G585400 chr1A 532733050 532735325 2275 True 3685.0 3685 95.9630 1 2266 1 chr1A.!!$R2 2265
4 TraesCS2A01G585400 chr1A 12307856 12310301 2445 False 1751.5 2097 95.1025 1 2254 2 chr1A.!!$F1 2253
5 TraesCS2A01G585400 chr1A 584970309 584972625 2316 False 1643.0 2844 92.1135 1 2270 2 chr1A.!!$F2 2269
6 TraesCS2A01G585400 chr3A 698295937 698298170 2233 False 3513.0 3513 94.9670 1 2254 1 chr3A.!!$F1 2253
7 TraesCS2A01G585400 chr7B 706974443 706976366 1923 True 2891.0 2891 93.6540 2 1952 1 chr7B.!!$R1 1950
8 TraesCS2A01G585400 chr3B 772227374 772229658 2284 False 1602.0 2793 91.7115 1 2254 2 chr3B.!!$F2 2253
9 TraesCS2A01G585400 chr5B 26734798 26737096 2298 True 1594.5 2758 92.1290 1 2254 2 chr5B.!!$R2 2253
10 TraesCS2A01G585400 chrUn 117078747 117080630 1883 False 1390.0 1435 93.6340 1 1952 2 chrUn.!!$F4 1951
11 TraesCS2A01G585400 chr4D 344881242 344881843 601 False 324.5 414 89.9290 2470 2961 2 chr4D.!!$F2 491

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
915 966 1.594518 CCGCTCGCCGAATTGTTATTG 60.595 52.381 0.0 0.0 40.02 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2811 0.036765 GGACACAGCCGTCATTGGTA 60.037 55.0 1.5 0.0 37.66 3.25 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
97 106 2.772691 GCCCGATTCTCGACCGAGT 61.773 63.158 17.54 1.07 43.74 4.18
114 123 3.371063 TCGAGCCGAGTTTCGCCT 61.371 61.111 0.00 0.00 38.82 5.52
825 868 3.068881 CCGCTTGTCCCAGGAAGA 58.931 61.111 0.00 0.00 0.00 2.87
915 966 1.594518 CCGCTCGCCGAATTGTTATTG 60.595 52.381 0.00 0.00 40.02 1.90
1369 1639 4.162320 TCAAAGAGGTTCAGTCAGTCTGTT 59.838 41.667 0.00 0.00 43.97 3.16
1376 1646 4.184629 GTTCAGTCAGTCTGTTCAGTGTT 58.815 43.478 0.00 0.00 43.97 3.32
1502 1774 3.652274 TGCTGTTTTTGCTATCCAAAGC 58.348 40.909 0.00 0.00 43.77 3.51
1602 1874 8.137437 GCTCATGTATATGCTGTTTTTGGTATT 58.863 33.333 0.00 0.00 34.21 1.89
1847 2124 2.225491 GTCAAAGCGCCAAGTGTTATGA 59.775 45.455 2.29 0.00 0.00 2.15
2026 2362 9.762933 TTTTGCAATATAAAGTGCTTCTTTTCT 57.237 25.926 0.00 4.73 46.66 2.52
2070 2406 6.891388 TGTAGAAGGTCAAAACTGGTCTTTA 58.109 36.000 0.00 0.00 0.00 1.85
2220 2567 4.135153 GCCGAGCCGCTTGAGAGA 62.135 66.667 9.40 0.00 0.00 3.10
2257 2604 4.838486 CTCGGCTCGGCTCGTGTC 62.838 72.222 0.00 0.00 0.00 3.67
2260 2607 4.803426 GGCTCGGCTCGTGTCCAG 62.803 72.222 0.00 0.00 0.00 3.86
2266 2613 3.221222 GCTCGTGTCCAGCCCTAT 58.779 61.111 0.00 0.00 0.00 2.57
2267 2614 1.068250 GCTCGTGTCCAGCCCTATC 59.932 63.158 0.00 0.00 0.00 2.08
2268 2615 1.742768 CTCGTGTCCAGCCCTATCC 59.257 63.158 0.00 0.00 0.00 2.59
2269 2616 2.076622 CTCGTGTCCAGCCCTATCCG 62.077 65.000 0.00 0.00 0.00 4.18
2270 2617 2.109181 GTGTCCAGCCCTATCCGC 59.891 66.667 0.00 0.00 0.00 5.54
2271 2618 3.161450 TGTCCAGCCCTATCCGCC 61.161 66.667 0.00 0.00 0.00 6.13
2272 2619 3.161450 GTCCAGCCCTATCCGCCA 61.161 66.667 0.00 0.00 0.00 5.69
2273 2620 3.161450 TCCAGCCCTATCCGCCAC 61.161 66.667 0.00 0.00 0.00 5.01
2274 2621 3.164269 CCAGCCCTATCCGCCACT 61.164 66.667 0.00 0.00 0.00 4.00
2275 2622 2.109799 CAGCCCTATCCGCCACTG 59.890 66.667 0.00 0.00 0.00 3.66
2276 2623 3.164269 AGCCCTATCCGCCACTGG 61.164 66.667 0.00 0.00 0.00 4.00
2277 2624 3.161450 GCCCTATCCGCCACTGGA 61.161 66.667 0.00 0.00 43.58 3.86
2279 2626 1.192146 GCCCTATCCGCCACTGGATA 61.192 60.000 0.00 2.75 46.95 2.59
2289 2636 6.465439 TCCGCCACTGGATATACTAATATG 57.535 41.667 0.00 0.00 31.53 1.78
2290 2637 6.192044 TCCGCCACTGGATATACTAATATGA 58.808 40.000 0.00 0.00 31.53 2.15
2291 2638 6.839134 TCCGCCACTGGATATACTAATATGAT 59.161 38.462 0.00 0.00 31.53 2.45
2292 2639 7.344612 TCCGCCACTGGATATACTAATATGATT 59.655 37.037 0.00 0.00 31.53 2.57
2293 2640 7.987458 CCGCCACTGGATATACTAATATGATTT 59.013 37.037 0.00 0.00 0.00 2.17
2294 2641 9.383519 CGCCACTGGATATACTAATATGATTTT 57.616 33.333 0.00 0.00 0.00 1.82
2345 2692 7.504922 TTAAACAAGCAAACATATTCATCGC 57.495 32.000 0.00 0.00 0.00 4.58
2346 2693 4.970662 ACAAGCAAACATATTCATCGCT 57.029 36.364 0.00 0.00 0.00 4.93
2347 2694 6.435430 AACAAGCAAACATATTCATCGCTA 57.565 33.333 0.00 0.00 0.00 4.26
2348 2695 6.435430 ACAAGCAAACATATTCATCGCTAA 57.565 33.333 0.00 0.00 0.00 3.09
2349 2696 6.851609 ACAAGCAAACATATTCATCGCTAAA 58.148 32.000 0.00 0.00 0.00 1.85
2350 2697 7.483307 ACAAGCAAACATATTCATCGCTAAAT 58.517 30.769 0.00 0.00 0.00 1.40
2351 2698 7.433131 ACAAGCAAACATATTCATCGCTAAATG 59.567 33.333 0.00 0.00 0.00 2.32
2352 2699 5.916883 AGCAAACATATTCATCGCTAAATGC 59.083 36.000 0.00 0.00 38.57 3.56
2353 2700 5.686841 GCAAACATATTCATCGCTAAATGCA 59.313 36.000 0.00 0.00 43.06 3.96
2354 2701 6.345250 GCAAACATATTCATCGCTAAATGCAC 60.345 38.462 0.00 0.00 43.06 4.57
2355 2702 6.375945 AACATATTCATCGCTAAATGCACA 57.624 33.333 0.00 0.00 43.06 4.57
2356 2703 5.751680 ACATATTCATCGCTAAATGCACAC 58.248 37.500 0.00 0.00 43.06 3.82
2357 2704 2.804421 TTCATCGCTAAATGCACACG 57.196 45.000 0.00 0.00 43.06 4.49
2358 2705 2.003196 TCATCGCTAAATGCACACGA 57.997 45.000 0.00 0.00 43.06 4.35
2359 2706 2.549926 TCATCGCTAAATGCACACGAT 58.450 42.857 0.00 0.00 43.70 3.73
2360 2707 2.539688 TCATCGCTAAATGCACACGATC 59.460 45.455 7.83 0.00 41.18 3.69
2361 2708 2.293677 TCGCTAAATGCACACGATCT 57.706 45.000 0.00 0.00 43.06 2.75
2362 2709 3.430333 TCGCTAAATGCACACGATCTA 57.570 42.857 0.00 0.00 43.06 1.98
2363 2710 3.776340 TCGCTAAATGCACACGATCTAA 58.224 40.909 0.00 0.00 43.06 2.10
2364 2711 3.550275 TCGCTAAATGCACACGATCTAAC 59.450 43.478 0.00 0.00 43.06 2.34
2365 2712 3.302480 CGCTAAATGCACACGATCTAACC 60.302 47.826 0.00 0.00 43.06 2.85
2366 2713 3.871594 GCTAAATGCACACGATCTAACCT 59.128 43.478 0.00 0.00 42.31 3.50
2367 2714 5.047847 GCTAAATGCACACGATCTAACCTA 58.952 41.667 0.00 0.00 42.31 3.08
2368 2715 5.696724 GCTAAATGCACACGATCTAACCTAT 59.303 40.000 0.00 0.00 42.31 2.57
2369 2716 6.866770 GCTAAATGCACACGATCTAACCTATA 59.133 38.462 0.00 0.00 42.31 1.31
2370 2717 7.148787 GCTAAATGCACACGATCTAACCTATAC 60.149 40.741 0.00 0.00 42.31 1.47
2371 2718 5.784578 ATGCACACGATCTAACCTATACA 57.215 39.130 0.00 0.00 0.00 2.29
2372 2719 5.784578 TGCACACGATCTAACCTATACAT 57.215 39.130 0.00 0.00 0.00 2.29
2373 2720 6.887626 TGCACACGATCTAACCTATACATA 57.112 37.500 0.00 0.00 0.00 2.29
2374 2721 7.279750 TGCACACGATCTAACCTATACATAA 57.720 36.000 0.00 0.00 0.00 1.90
2375 2722 7.143340 TGCACACGATCTAACCTATACATAAC 58.857 38.462 0.00 0.00 0.00 1.89
2376 2723 7.143340 GCACACGATCTAACCTATACATAACA 58.857 38.462 0.00 0.00 0.00 2.41
2377 2724 7.650504 GCACACGATCTAACCTATACATAACAA 59.349 37.037 0.00 0.00 0.00 2.83
2378 2725 8.965172 CACACGATCTAACCTATACATAACAAC 58.035 37.037 0.00 0.00 0.00 3.32
2379 2726 8.689061 ACACGATCTAACCTATACATAACAACA 58.311 33.333 0.00 0.00 0.00 3.33
2380 2727 8.965172 CACGATCTAACCTATACATAACAACAC 58.035 37.037 0.00 0.00 0.00 3.32
2381 2728 8.689061 ACGATCTAACCTATACATAACAACACA 58.311 33.333 0.00 0.00 0.00 3.72
2382 2729 9.524106 CGATCTAACCTATACATAACAACACAA 57.476 33.333 0.00 0.00 0.00 3.33
2394 2741 8.574196 ACATAACAACACAAAACAATTAGAGC 57.426 30.769 0.00 0.00 0.00 4.09
2395 2742 7.651704 ACATAACAACACAAAACAATTAGAGCC 59.348 33.333 0.00 0.00 0.00 4.70
2396 2743 4.944048 ACAACACAAAACAATTAGAGCCC 58.056 39.130 0.00 0.00 0.00 5.19
2397 2744 4.649218 ACAACACAAAACAATTAGAGCCCT 59.351 37.500 0.00 0.00 0.00 5.19
2398 2745 5.830991 ACAACACAAAACAATTAGAGCCCTA 59.169 36.000 0.00 0.00 0.00 3.53
2399 2746 5.959618 ACACAAAACAATTAGAGCCCTAC 57.040 39.130 0.00 0.00 0.00 3.18
2400 2747 4.454504 ACACAAAACAATTAGAGCCCTACG 59.545 41.667 0.00 0.00 0.00 3.51
2401 2748 4.693566 CACAAAACAATTAGAGCCCTACGA 59.306 41.667 0.00 0.00 0.00 3.43
2402 2749 5.354234 CACAAAACAATTAGAGCCCTACGAT 59.646 40.000 0.00 0.00 0.00 3.73
2403 2750 5.585047 ACAAAACAATTAGAGCCCTACGATC 59.415 40.000 0.00 0.00 0.00 3.69
2404 2751 5.353394 AAACAATTAGAGCCCTACGATCA 57.647 39.130 0.00 0.00 0.00 2.92
2405 2752 5.353394 AACAATTAGAGCCCTACGATCAA 57.647 39.130 0.00 0.00 0.00 2.57
2406 2753 4.950050 ACAATTAGAGCCCTACGATCAAG 58.050 43.478 0.00 0.00 0.00 3.02
2407 2754 3.669251 ATTAGAGCCCTACGATCAAGC 57.331 47.619 0.00 0.00 0.00 4.01
2408 2755 1.329256 TAGAGCCCTACGATCAAGCC 58.671 55.000 0.00 0.00 0.00 4.35
2409 2756 1.069935 GAGCCCTACGATCAAGCCC 59.930 63.158 0.00 0.00 0.00 5.19
2410 2757 1.686325 GAGCCCTACGATCAAGCCCA 61.686 60.000 0.00 0.00 0.00 5.36
2411 2758 1.523938 GCCCTACGATCAAGCCCAC 60.524 63.158 0.00 0.00 0.00 4.61
2412 2759 1.972660 GCCCTACGATCAAGCCCACT 61.973 60.000 0.00 0.00 0.00 4.00
2413 2760 0.105039 CCCTACGATCAAGCCCACTC 59.895 60.000 0.00 0.00 0.00 3.51
2414 2761 0.105039 CCTACGATCAAGCCCACTCC 59.895 60.000 0.00 0.00 0.00 3.85
2415 2762 1.115467 CTACGATCAAGCCCACTCCT 58.885 55.000 0.00 0.00 0.00 3.69
2416 2763 1.482593 CTACGATCAAGCCCACTCCTT 59.517 52.381 0.00 0.00 0.00 3.36
2417 2764 0.693049 ACGATCAAGCCCACTCCTTT 59.307 50.000 0.00 0.00 0.00 3.11
2418 2765 1.906574 ACGATCAAGCCCACTCCTTTA 59.093 47.619 0.00 0.00 0.00 1.85
2419 2766 2.093447 ACGATCAAGCCCACTCCTTTAG 60.093 50.000 0.00 0.00 0.00 1.85
2420 2767 2.168521 CGATCAAGCCCACTCCTTTAGA 59.831 50.000 0.00 0.00 0.00 2.10
2421 2768 3.181461 CGATCAAGCCCACTCCTTTAGAT 60.181 47.826 0.00 0.00 0.00 1.98
2422 2769 3.914426 TCAAGCCCACTCCTTTAGATC 57.086 47.619 0.00 0.00 0.00 2.75
2423 2770 3.454858 TCAAGCCCACTCCTTTAGATCT 58.545 45.455 0.00 0.00 0.00 2.75
2424 2771 4.620723 TCAAGCCCACTCCTTTAGATCTA 58.379 43.478 0.00 0.00 0.00 1.98
2425 2772 5.030147 TCAAGCCCACTCCTTTAGATCTAA 58.970 41.667 11.24 11.24 0.00 2.10
2426 2773 5.104900 TCAAGCCCACTCCTTTAGATCTAAC 60.105 44.000 14.85 0.69 0.00 2.34
2427 2774 3.712218 AGCCCACTCCTTTAGATCTAACC 59.288 47.826 14.85 0.00 0.00 2.85
2428 2775 3.454812 GCCCACTCCTTTAGATCTAACCA 59.545 47.826 14.85 0.76 0.00 3.67
2429 2776 4.103311 GCCCACTCCTTTAGATCTAACCAT 59.897 45.833 14.85 0.00 0.00 3.55
2430 2777 5.398012 GCCCACTCCTTTAGATCTAACCATT 60.398 44.000 14.85 0.00 0.00 3.16
2431 2778 6.183361 GCCCACTCCTTTAGATCTAACCATTA 60.183 42.308 14.85 0.00 0.00 1.90
2432 2779 7.637301 GCCCACTCCTTTAGATCTAACCATTAA 60.637 40.741 14.85 0.00 0.00 1.40
2433 2780 8.272173 CCCACTCCTTTAGATCTAACCATTAAA 58.728 37.037 14.85 0.00 0.00 1.52
2434 2781 9.681062 CCACTCCTTTAGATCTAACCATTAAAA 57.319 33.333 14.85 0.00 0.00 1.52
2448 2795 9.777575 CTAACCATTAAAATAACAAGTAACCCG 57.222 33.333 0.00 0.00 0.00 5.28
2449 2796 7.999450 ACCATTAAAATAACAAGTAACCCGA 57.001 32.000 0.00 0.00 0.00 5.14
2450 2797 8.406730 ACCATTAAAATAACAAGTAACCCGAA 57.593 30.769 0.00 0.00 0.00 4.30
2451 2798 8.858094 ACCATTAAAATAACAAGTAACCCGAAA 58.142 29.630 0.00 0.00 0.00 3.46
2452 2799 9.863845 CCATTAAAATAACAAGTAACCCGAAAT 57.136 29.630 0.00 0.00 0.00 2.17
2468 2815 8.810990 AACCCGAAATAAAAATACATCTACCA 57.189 30.769 0.00 0.00 0.00 3.25
2469 2816 8.810990 ACCCGAAATAAAAATACATCTACCAA 57.189 30.769 0.00 0.00 0.00 3.67
2470 2817 9.416284 ACCCGAAATAAAAATACATCTACCAAT 57.584 29.630 0.00 0.00 0.00 3.16
2471 2818 9.677567 CCCGAAATAAAAATACATCTACCAATG 57.322 33.333 0.00 0.00 0.00 2.82
2482 2829 1.067142 TCTACCAATGACGGCTGTGTC 60.067 52.381 0.80 0.00 39.37 3.67
2498 2845 1.888512 GTGTCCTGGCACACAAATCAT 59.111 47.619 18.41 0.00 45.25 2.45
2513 2860 9.926751 CACACAAATCATCAATTAGTACAGATC 57.073 33.333 0.00 0.00 0.00 2.75
2541 2888 7.508687 AGCACAGTATGAACAACATATATGGA 58.491 34.615 16.96 0.00 42.42 3.41
2542 2889 7.992608 AGCACAGTATGAACAACATATATGGAA 59.007 33.333 16.96 0.00 42.42 3.53
2543 2890 8.620416 GCACAGTATGAACAACATATATGGAAA 58.380 33.333 16.96 0.00 42.42 3.13
2574 2921 3.958798 TCTACAGGGTGGTGATTAGCTAC 59.041 47.826 0.00 0.00 0.00 3.58
2580 2927 3.134804 GGGTGGTGATTAGCTACACAGAT 59.865 47.826 14.43 0.00 38.57 2.90
2582 2929 5.012148 GGGTGGTGATTAGCTACACAGATAT 59.988 44.000 14.43 0.00 38.57 1.63
2585 2932 6.015010 GTGGTGATTAGCTACACAGATATCCT 60.015 42.308 14.43 0.00 38.57 3.24
2627 2974 3.824414 ATTTTTAGGCGACAAACTCCG 57.176 42.857 0.00 0.00 0.00 4.63
2647 2994 0.392193 AAATCGTGCAGCAGAGGAGG 60.392 55.000 0.00 0.00 0.00 4.30
2692 3039 1.667236 TCTTCAATAGCATGGTGGCG 58.333 50.000 7.89 0.00 39.27 5.69
2741 3088 0.863956 AGGAGAGGAATCGGGAGGAT 59.136 55.000 0.00 0.00 36.78 3.24
2767 3205 2.289756 GCGAGGAGAGGAAGGAAAAGTT 60.290 50.000 0.00 0.00 0.00 2.66
2831 3269 0.106669 ATCCAGGTCATCCTCGTCGA 60.107 55.000 0.00 0.00 43.07 4.20
2857 3295 1.821332 CGCATCAAGCTCCCCTTCC 60.821 63.158 0.00 0.00 42.61 3.46
2897 3355 0.970937 CTCTCTTGGGCGTGGTCCTA 60.971 60.000 0.00 0.00 0.00 2.94
2902 3360 4.091939 GGGCGTGGTCCTACACCC 62.092 72.222 2.85 2.85 46.18 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
825 868 1.699752 CCATGCCCTTCCCCTTCTT 59.300 57.895 0.00 0.00 0.00 2.52
1502 1774 6.127810 AGCTTGCACACACATATATTTGAG 57.872 37.500 5.88 0.62 0.00 3.02
1572 1844 5.762825 AAACAGCATATACATGAGCTTGG 57.237 39.130 0.00 0.00 34.61 3.61
2143 2480 1.144969 CTCGGCTCGTTTTTGCTACA 58.855 50.000 0.00 0.00 0.00 2.74
2240 2587 4.838486 GACACGAGCCGAGCCGAG 62.838 72.222 11.42 7.65 0.00 4.63
2243 2590 4.803426 CTGGACACGAGCCGAGCC 62.803 72.222 1.50 1.42 0.00 4.70
2245 2592 4.803426 GGCTGGACACGAGCCGAG 62.803 72.222 8.81 0.00 46.47 4.63
2250 2597 1.742768 GGATAGGGCTGGACACGAG 59.257 63.158 0.00 0.00 0.00 4.18
2251 2598 2.125326 CGGATAGGGCTGGACACGA 61.125 63.158 0.00 0.00 0.00 4.35
2252 2599 2.417516 CGGATAGGGCTGGACACG 59.582 66.667 0.00 0.00 0.00 4.49
2253 2600 2.109181 GCGGATAGGGCTGGACAC 59.891 66.667 0.00 0.00 0.00 3.67
2254 2601 3.161450 GGCGGATAGGGCTGGACA 61.161 66.667 0.00 0.00 0.00 4.02
2255 2602 3.161450 TGGCGGATAGGGCTGGAC 61.161 66.667 0.00 0.00 0.00 4.02
2256 2603 3.161450 GTGGCGGATAGGGCTGGA 61.161 66.667 0.00 0.00 0.00 3.86
2257 2604 3.164269 AGTGGCGGATAGGGCTGG 61.164 66.667 0.00 0.00 0.00 4.85
2258 2605 2.109799 CAGTGGCGGATAGGGCTG 59.890 66.667 0.00 0.00 0.00 4.85
2259 2606 2.972589 ATCCAGTGGCGGATAGGGCT 62.973 60.000 3.51 0.00 44.26 5.19
2260 2607 1.192146 TATCCAGTGGCGGATAGGGC 61.192 60.000 3.51 0.00 44.26 5.19
2261 2608 3.067011 TATCCAGTGGCGGATAGGG 57.933 57.895 3.51 0.00 44.26 3.53
2266 2613 6.192044 TCATATTAGTATATCCAGTGGCGGA 58.808 40.000 3.51 0.00 40.07 5.54
2267 2614 6.465439 TCATATTAGTATATCCAGTGGCGG 57.535 41.667 3.51 0.00 0.00 6.13
2268 2615 8.948631 AAATCATATTAGTATATCCAGTGGCG 57.051 34.615 3.51 0.00 0.00 5.69
2319 2666 9.232082 GCGATGAATATGTTTGCTTGTTTAATA 57.768 29.630 0.00 0.00 0.00 0.98
2320 2667 7.975616 AGCGATGAATATGTTTGCTTGTTTAAT 59.024 29.630 0.00 0.00 0.00 1.40
2321 2668 7.312154 AGCGATGAATATGTTTGCTTGTTTAA 58.688 30.769 0.00 0.00 0.00 1.52
2322 2669 6.851609 AGCGATGAATATGTTTGCTTGTTTA 58.148 32.000 0.00 0.00 0.00 2.01
2323 2670 5.713025 AGCGATGAATATGTTTGCTTGTTT 58.287 33.333 0.00 0.00 0.00 2.83
2324 2671 5.314923 AGCGATGAATATGTTTGCTTGTT 57.685 34.783 0.00 0.00 0.00 2.83
2325 2672 4.970662 AGCGATGAATATGTTTGCTTGT 57.029 36.364 0.00 0.00 0.00 3.16
2326 2673 7.566328 GCATTTAGCGATGAATATGTTTGCTTG 60.566 37.037 0.00 0.00 32.72 4.01
2327 2674 6.418819 GCATTTAGCGATGAATATGTTTGCTT 59.581 34.615 0.00 0.00 32.72 3.91
2328 2675 5.916883 GCATTTAGCGATGAATATGTTTGCT 59.083 36.000 0.00 0.00 35.12 3.91
2329 2676 6.132353 GCATTTAGCGATGAATATGTTTGC 57.868 37.500 0.00 0.00 0.00 3.68
2344 2691 3.871594 AGGTTAGATCGTGTGCATTTAGC 59.128 43.478 0.00 0.00 45.96 3.09
2345 2692 7.865889 TGTATAGGTTAGATCGTGTGCATTTAG 59.134 37.037 0.00 0.00 0.00 1.85
2346 2693 7.718525 TGTATAGGTTAGATCGTGTGCATTTA 58.281 34.615 0.00 0.00 0.00 1.40
2347 2694 6.578944 TGTATAGGTTAGATCGTGTGCATTT 58.421 36.000 0.00 0.00 0.00 2.32
2348 2695 6.156748 TGTATAGGTTAGATCGTGTGCATT 57.843 37.500 0.00 0.00 0.00 3.56
2349 2696 5.784578 TGTATAGGTTAGATCGTGTGCAT 57.215 39.130 0.00 0.00 0.00 3.96
2350 2697 5.784578 ATGTATAGGTTAGATCGTGTGCA 57.215 39.130 0.00 0.00 0.00 4.57
2351 2698 7.143340 TGTTATGTATAGGTTAGATCGTGTGC 58.857 38.462 0.00 0.00 0.00 4.57
2352 2699 8.965172 GTTGTTATGTATAGGTTAGATCGTGTG 58.035 37.037 0.00 0.00 0.00 3.82
2353 2700 8.689061 TGTTGTTATGTATAGGTTAGATCGTGT 58.311 33.333 0.00 0.00 0.00 4.49
2354 2701 8.965172 GTGTTGTTATGTATAGGTTAGATCGTG 58.035 37.037 0.00 0.00 0.00 4.35
2355 2702 8.689061 TGTGTTGTTATGTATAGGTTAGATCGT 58.311 33.333 0.00 0.00 0.00 3.73
2356 2703 9.524106 TTGTGTTGTTATGTATAGGTTAGATCG 57.476 33.333 0.00 0.00 0.00 3.69
2368 2715 9.672086 GCTCTAATTGTTTTGTGTTGTTATGTA 57.328 29.630 0.00 0.00 0.00 2.29
2369 2716 7.651704 GGCTCTAATTGTTTTGTGTTGTTATGT 59.348 33.333 0.00 0.00 0.00 2.29
2370 2717 7.116233 GGGCTCTAATTGTTTTGTGTTGTTATG 59.884 37.037 0.00 0.00 0.00 1.90
2371 2718 7.015195 AGGGCTCTAATTGTTTTGTGTTGTTAT 59.985 33.333 0.00 0.00 0.00 1.89
2372 2719 6.322712 AGGGCTCTAATTGTTTTGTGTTGTTA 59.677 34.615 0.00 0.00 0.00 2.41
2373 2720 5.128663 AGGGCTCTAATTGTTTTGTGTTGTT 59.871 36.000 0.00 0.00 0.00 2.83
2374 2721 4.649218 AGGGCTCTAATTGTTTTGTGTTGT 59.351 37.500 0.00 0.00 0.00 3.32
2375 2722 5.200368 AGGGCTCTAATTGTTTTGTGTTG 57.800 39.130 0.00 0.00 0.00 3.33
2376 2723 5.048991 CGTAGGGCTCTAATTGTTTTGTGTT 60.049 40.000 0.00 0.00 0.00 3.32
2377 2724 4.454504 CGTAGGGCTCTAATTGTTTTGTGT 59.545 41.667 0.00 0.00 0.00 3.72
2378 2725 4.693566 TCGTAGGGCTCTAATTGTTTTGTG 59.306 41.667 0.00 0.00 0.00 3.33
2379 2726 4.901868 TCGTAGGGCTCTAATTGTTTTGT 58.098 39.130 0.00 0.00 0.00 2.83
2380 2727 5.584649 TGATCGTAGGGCTCTAATTGTTTTG 59.415 40.000 0.00 0.00 0.00 2.44
2381 2728 5.741011 TGATCGTAGGGCTCTAATTGTTTT 58.259 37.500 0.00 0.00 0.00 2.43
2382 2729 5.353394 TGATCGTAGGGCTCTAATTGTTT 57.647 39.130 0.00 0.00 0.00 2.83
2383 2730 5.353394 TTGATCGTAGGGCTCTAATTGTT 57.647 39.130 0.00 0.00 0.00 2.83
2384 2731 4.740934 GCTTGATCGTAGGGCTCTAATTGT 60.741 45.833 0.00 0.00 0.00 2.71
2385 2732 3.743396 GCTTGATCGTAGGGCTCTAATTG 59.257 47.826 0.00 0.00 0.00 2.32
2386 2733 3.244249 GGCTTGATCGTAGGGCTCTAATT 60.244 47.826 0.00 0.00 0.00 1.40
2387 2734 2.300437 GGCTTGATCGTAGGGCTCTAAT 59.700 50.000 0.00 0.00 0.00 1.73
2388 2735 1.687123 GGCTTGATCGTAGGGCTCTAA 59.313 52.381 0.00 0.00 0.00 2.10
2389 2736 1.329256 GGCTTGATCGTAGGGCTCTA 58.671 55.000 0.00 0.00 0.00 2.43
2390 2737 1.403687 GGGCTTGATCGTAGGGCTCT 61.404 60.000 0.00 0.00 0.00 4.09
2391 2738 1.069935 GGGCTTGATCGTAGGGCTC 59.930 63.158 0.00 0.00 0.00 4.70
2392 2739 1.689233 TGGGCTTGATCGTAGGGCT 60.689 57.895 0.00 0.00 0.00 5.19
2393 2740 1.523938 GTGGGCTTGATCGTAGGGC 60.524 63.158 0.00 0.00 0.00 5.19
2394 2741 0.105039 GAGTGGGCTTGATCGTAGGG 59.895 60.000 0.00 0.00 0.00 3.53
2395 2742 0.105039 GGAGTGGGCTTGATCGTAGG 59.895 60.000 0.00 0.00 0.00 3.18
2396 2743 1.115467 AGGAGTGGGCTTGATCGTAG 58.885 55.000 0.00 0.00 0.00 3.51
2397 2744 1.568504 AAGGAGTGGGCTTGATCGTA 58.431 50.000 0.00 0.00 0.00 3.43
2398 2745 0.693049 AAAGGAGTGGGCTTGATCGT 59.307 50.000 0.00 0.00 0.00 3.73
2399 2746 2.168521 TCTAAAGGAGTGGGCTTGATCG 59.831 50.000 0.00 0.00 0.00 3.69
2400 2747 3.914426 TCTAAAGGAGTGGGCTTGATC 57.086 47.619 0.00 0.00 0.00 2.92
2401 2748 4.043596 AGATCTAAAGGAGTGGGCTTGAT 58.956 43.478 0.00 0.00 0.00 2.57
2402 2749 3.454858 AGATCTAAAGGAGTGGGCTTGA 58.545 45.455 0.00 0.00 0.00 3.02
2403 2750 3.922171 AGATCTAAAGGAGTGGGCTTG 57.078 47.619 0.00 0.00 0.00 4.01
2404 2751 4.164413 GGTTAGATCTAAAGGAGTGGGCTT 59.836 45.833 16.73 0.00 0.00 4.35
2405 2752 3.712218 GGTTAGATCTAAAGGAGTGGGCT 59.288 47.826 16.73 0.00 0.00 5.19
2406 2753 3.454812 TGGTTAGATCTAAAGGAGTGGGC 59.545 47.826 16.73 1.53 0.00 5.36
2407 2754 5.896073 ATGGTTAGATCTAAAGGAGTGGG 57.104 43.478 16.73 0.00 0.00 4.61
2408 2755 9.681062 TTTTAATGGTTAGATCTAAAGGAGTGG 57.319 33.333 16.73 0.00 0.00 4.00
2422 2769 9.777575 CGGGTTACTTGTTATTTTAATGGTTAG 57.222 33.333 0.00 0.00 0.00 2.34
2423 2770 9.512588 TCGGGTTACTTGTTATTTTAATGGTTA 57.487 29.630 0.00 0.00 0.00 2.85
2424 2771 8.406730 TCGGGTTACTTGTTATTTTAATGGTT 57.593 30.769 0.00 0.00 0.00 3.67
2425 2772 7.999450 TCGGGTTACTTGTTATTTTAATGGT 57.001 32.000 0.00 0.00 0.00 3.55
2426 2773 9.863845 ATTTCGGGTTACTTGTTATTTTAATGG 57.136 29.630 0.00 0.00 0.00 3.16
2442 2789 9.902684 TGGTAGATGTATTTTTATTTCGGGTTA 57.097 29.630 0.00 0.00 0.00 2.85
2443 2790 8.810990 TGGTAGATGTATTTTTATTTCGGGTT 57.189 30.769 0.00 0.00 0.00 4.11
2444 2791 8.810990 TTGGTAGATGTATTTTTATTTCGGGT 57.189 30.769 0.00 0.00 0.00 5.28
2445 2792 9.677567 CATTGGTAGATGTATTTTTATTTCGGG 57.322 33.333 0.00 0.00 0.00 5.14
2450 2797 8.349983 GCCGTCATTGGTAGATGTATTTTTATT 58.650 33.333 0.00 0.00 0.00 1.40
2451 2798 7.719633 AGCCGTCATTGGTAGATGTATTTTTAT 59.280 33.333 0.00 0.00 0.00 1.40
2452 2799 7.011950 CAGCCGTCATTGGTAGATGTATTTTTA 59.988 37.037 0.00 0.00 0.00 1.52
2453 2800 5.885912 AGCCGTCATTGGTAGATGTATTTTT 59.114 36.000 0.00 0.00 0.00 1.94
2454 2801 5.296780 CAGCCGTCATTGGTAGATGTATTTT 59.703 40.000 0.00 0.00 0.00 1.82
2455 2802 4.816385 CAGCCGTCATTGGTAGATGTATTT 59.184 41.667 0.00 0.00 0.00 1.40
2456 2803 4.141711 ACAGCCGTCATTGGTAGATGTATT 60.142 41.667 0.00 0.00 0.00 1.89
2457 2804 3.388024 ACAGCCGTCATTGGTAGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2458 2805 2.764010 ACAGCCGTCATTGGTAGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
2459 2806 1.555075 ACAGCCGTCATTGGTAGATGT 59.445 47.619 0.00 0.00 0.00 3.06
2460 2807 1.935873 CACAGCCGTCATTGGTAGATG 59.064 52.381 0.00 0.00 0.00 2.90
2461 2808 1.555075 ACACAGCCGTCATTGGTAGAT 59.445 47.619 0.00 0.00 0.00 1.98
2462 2809 0.973632 ACACAGCCGTCATTGGTAGA 59.026 50.000 0.00 0.00 0.00 2.59
2463 2810 1.359848 GACACAGCCGTCATTGGTAG 58.640 55.000 0.00 0.00 35.88 3.18
2464 2811 0.036765 GGACACAGCCGTCATTGGTA 60.037 55.000 1.50 0.00 37.66 3.25
2465 2812 1.302511 GGACACAGCCGTCATTGGT 60.303 57.895 1.50 0.00 37.66 3.67
2466 2813 1.003355 AGGACACAGCCGTCATTGG 60.003 57.895 1.50 0.00 37.66 3.16
2467 2814 1.300971 CCAGGACACAGCCGTCATTG 61.301 60.000 1.50 0.00 37.66 2.82
2468 2815 1.003355 CCAGGACACAGCCGTCATT 60.003 57.895 1.50 0.00 37.66 2.57
2469 2816 2.665000 CCAGGACACAGCCGTCAT 59.335 61.111 1.50 0.00 37.66 3.06
2470 2817 4.314440 GCCAGGACACAGCCGTCA 62.314 66.667 0.00 0.00 37.66 4.35
2471 2818 4.314440 TGCCAGGACACAGCCGTC 62.314 66.667 0.00 0.00 35.03 4.79
2472 2819 4.626081 GTGCCAGGACACAGCCGT 62.626 66.667 8.64 0.00 40.40 5.68
2482 2829 3.880047 ATTGATGATTTGTGTGCCAGG 57.120 42.857 0.00 0.00 0.00 4.45
2498 2845 6.095021 ACTGTGCTACGATCTGTACTAATTGA 59.905 38.462 0.00 0.00 0.00 2.57
2513 2860 6.828502 ATATGTTGTTCATACTGTGCTACG 57.171 37.500 0.00 0.00 41.13 3.51
2542 2889 4.827284 CACCACCCTGTAGATGTTCTTTTT 59.173 41.667 0.00 0.00 0.00 1.94
2543 2890 4.104102 TCACCACCCTGTAGATGTTCTTTT 59.896 41.667 0.00 0.00 0.00 2.27
2547 2894 3.914426 ATCACCACCCTGTAGATGTTC 57.086 47.619 0.00 0.00 0.00 3.18
2563 2910 9.184523 AGATAGGATATCTGTGTAGCTAATCAC 57.815 37.037 7.39 7.39 35.43 3.06
2574 2921 6.070938 TGCTCCAATCAGATAGGATATCTGTG 60.071 42.308 20.62 14.59 44.30 3.66
2580 2927 6.021672 AGTGATGCTCCAATCAGATAGGATA 58.978 40.000 0.00 0.00 37.24 2.59
2582 2929 4.229639 AGTGATGCTCCAATCAGATAGGA 58.770 43.478 0.00 0.00 37.24 2.94
2585 2932 8.985315 AAATTTAGTGATGCTCCAATCAGATA 57.015 30.769 0.00 0.00 37.24 1.98
2627 2974 1.005340 CTCCTCTGCTGCACGATTTC 58.995 55.000 0.00 0.00 0.00 2.17
2692 3039 3.003480 CGAGGGTGGATCTTTCTGTTTC 58.997 50.000 0.00 0.00 0.00 2.78
2721 3068 0.186386 TCCTCCCGATTCCTCTCCTC 59.814 60.000 0.00 0.00 0.00 3.71
2741 3088 0.967887 CCTTCCTCTCCTCGCACAGA 60.968 60.000 0.00 0.00 0.00 3.41
2772 3210 4.770874 TTAGGAGGGCGCGTTGGC 62.771 66.667 8.43 0.00 43.88 4.52
2773 3211 1.436983 GATTTAGGAGGGCGCGTTGG 61.437 60.000 8.43 0.00 0.00 3.77
2807 3245 2.592861 GGATGACCTGGATGCGGC 60.593 66.667 0.00 0.00 0.00 6.53
2831 3269 2.437359 GCTTGATGCGAGGCCAGT 60.437 61.111 5.01 0.00 0.00 4.00
2891 3349 0.177373 GTGGAATCGGGTGTAGGACC 59.823 60.000 0.00 0.00 45.28 4.46


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

AutoCloner maintained by Alex Coulton.