Multiple sequence alignment - TraesCS5D01G208500

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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 TraesCS5D01G208500 chr5D 100.000 1675 0 0 1 1675 314850811 314852485 0.000000e+00 3094.0
1 TraesCS5D01G208500 chr5D 100.000 627 0 0 1911 2537 314852721 314853347 0.000000e+00 1158.0
2 TraesCS5D01G208500 chr5B 95.341 880 14 6 2 858 362844953 362845828 0.000000e+00 1373.0
3 TraesCS5D01G208500 chr5B 82.648 778 113 12 917 1674 280996407 280995632 0.000000e+00 669.0
4 TraesCS5D01G208500 chr5A 93.205 883 36 8 1 863 408913832 408914710 0.000000e+00 1277.0
5 TraesCS5D01G208500 chr5A 86.081 819 91 10 879 1675 41449175 41448358 0.000000e+00 859.0
6 TraesCS5D01G208500 chr5A 84.512 820 101 13 879 1675 704956887 704956071 0.000000e+00 787.0
7 TraesCS5D01G208500 chr5A 87.879 396 45 2 1922 2315 41448312 41447918 1.780000e-126 462.0
8 TraesCS5D01G208500 chr5A 86.750 400 47 4 1919 2315 704956028 704955632 8.330000e-120 440.0
9 TraesCS5D01G208500 chr1D 92.164 587 39 3 1095 1675 463062340 463062925 0.000000e+00 822.0
10 TraesCS5D01G208500 chr1D 93.120 407 26 1 1911 2315 463062959 463063365 1.680000e-166 595.0
11 TraesCS5D01G208500 chr1D 96.537 231 7 1 2305 2534 95805265 95805495 5.120000e-102 381.0
12 TraesCS5D01G208500 chr6B 84.127 819 107 10 879 1675 497899978 497900795 0.000000e+00 771.0
13 TraesCS5D01G208500 chr6B 88.615 527 54 4 1153 1675 671754470 671754994 9.900000e-179 636.0
14 TraesCS5D01G208500 chr6B 89.976 409 38 3 1911 2317 671755028 671755435 2.240000e-145 525.0
15 TraesCS5D01G208500 chr6B 87.319 276 21 3 884 1146 671730423 671730697 1.140000e-78 303.0
16 TraesCS5D01G208500 chr6B 100.000 30 0 0 2080 2109 151651078 151651049 3.530000e-04 56.5
17 TraesCS5D01G208500 chr7D 92.566 417 31 0 1259 1675 132202769 132202353 1.300000e-167 599.0
18 TraesCS5D01G208500 chr7D 90.954 409 35 1 1911 2317 132202318 132201910 1.330000e-152 549.0
19 TraesCS5D01G208500 chr7D 88.953 344 20 6 864 1195 132203410 132203073 2.350000e-110 409.0
20 TraesCS5D01G208500 chr7D 95.708 233 9 1 2303 2534 146163657 146163889 8.570000e-100 374.0
21 TraesCS5D01G208500 chr7A 84.461 399 60 1 1919 2315 557653015 557652617 2.370000e-105 392.0
22 TraesCS5D01G208500 chr6D 97.309 223 6 0 2312 2534 436603390 436603612 1.840000e-101 379.0
23 TraesCS5D01G208500 chr4D 96.903 226 7 0 2312 2537 274479772 274479547 1.840000e-101 379.0
24 TraesCS5D01G208500 chr4D 95.763 236 7 2 2299 2534 17562403 17562635 6.630000e-101 377.0
25 TraesCS5D01G208500 chr4D 96.476 227 8 0 2308 2534 390219680 390219906 2.380000e-100 375.0
26 TraesCS5D01G208500 chr4D 95.726 234 7 3 2301 2532 380488924 380489156 8.570000e-100 374.0
27 TraesCS5D01G208500 chr4D 94.915 236 9 2 2296 2531 398935831 398936063 1.430000e-97 366.0
28 TraesCS5D01G208500 chr2D 94.979 239 9 3 2300 2537 240908614 240908378 3.080000e-99 372.0
29 TraesCS5D01G208500 chr3A 90.041 241 24 0 2069 2309 749244560 749244320 1.890000e-81 313.0
30 TraesCS5D01G208500 chr3B 81.127 355 46 9 917 1251 381972497 381972144 5.380000e-67 265.0
31 TraesCS5D01G208500 chr6A 80.000 105 19 2 1418 1521 454209302 454209199 2.710000e-10 76.8
32 TraesCS5D01G208500 chr2A 92.157 51 2 2 1418 1467 546680689 546680640 1.260000e-08 71.3
33 TraesCS5D01G208500 chr2B 76.522 115 21 4 1997 2108 239827994 239827883 9.800000e-05 58.4


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 TraesCS5D01G208500 chr5D 314850811 314853347 2536 False 2126.0 3094 100.000000 1 2537 2 chr5D.!!$F1 2536
1 TraesCS5D01G208500 chr5B 362844953 362845828 875 False 1373.0 1373 95.341000 2 858 1 chr5B.!!$F1 856
2 TraesCS5D01G208500 chr5B 280995632 280996407 775 True 669.0 669 82.648000 917 1674 1 chr5B.!!$R1 757
3 TraesCS5D01G208500 chr5A 408913832 408914710 878 False 1277.0 1277 93.205000 1 863 1 chr5A.!!$F1 862
4 TraesCS5D01G208500 chr5A 41447918 41449175 1257 True 660.5 859 86.980000 879 2315 2 chr5A.!!$R1 1436
5 TraesCS5D01G208500 chr5A 704955632 704956887 1255 True 613.5 787 85.631000 879 2315 2 chr5A.!!$R2 1436
6 TraesCS5D01G208500 chr1D 463062340 463063365 1025 False 708.5 822 92.642000 1095 2315 2 chr1D.!!$F2 1220
7 TraesCS5D01G208500 chr6B 497899978 497900795 817 False 771.0 771 84.127000 879 1675 1 chr6B.!!$F1 796
8 TraesCS5D01G208500 chr6B 671754470 671755435 965 False 580.5 636 89.295500 1153 2317 2 chr6B.!!$F3 1164
9 TraesCS5D01G208500 chr7D 132201910 132203410 1500 True 519.0 599 90.824333 864 2317 3 chr7D.!!$R1 1453

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
437 439 1.079612 CTGCTGACATGAGACGGCA 60.08 57.895 18.5 18.5 46.73 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 2722 0.250338 GCTGGGCCTCCGGTTAATAG 60.25 60.0 4.53 0.0 41.53 1.73 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
47 49 7.678947 AAGTGTTATTCTTCTCTGTTCATGG 57.321 36.000 0.00 0.00 0.00 3.66
208 210 5.249852 TGTGTTACTAAATTACCCTCTGCCT 59.750 40.000 0.00 0.00 0.00 4.75
354 356 4.703575 AGCTACCAGAGTACAACACGATAA 59.296 41.667 0.00 0.00 0.00 1.75
437 439 1.079612 CTGCTGACATGAGACGGCA 60.080 57.895 18.50 18.50 46.73 5.69
508 518 9.244799 CAAACTACGCTGTATATAGATGTTTGA 57.755 33.333 19.43 0.59 41.36 2.69
640 650 4.290969 TGCTCGCATAGATAGAACTTTCG 58.709 43.478 0.00 0.00 0.00 3.46
650 660 6.222038 AGATAGAACTTTCGAACCATAGCA 57.778 37.500 0.00 0.00 0.00 3.49
657 671 5.699839 ACTTTCGAACCATAGCATGAAAAC 58.300 37.500 0.00 0.00 0.00 2.43
782 811 1.958288 TTCAGAGGCTAGGGCTTTCT 58.042 50.000 0.00 0.00 38.98 2.52
859 888 7.757941 TTCCTATTGTGTTCATGATTTGTGA 57.242 32.000 0.00 0.00 0.00 3.58
1149 1192 0.607620 TCAGTGACATGGTGATCGCA 59.392 50.000 8.82 0.00 0.00 5.10
1161 1210 4.814294 ATCGCACCGGAAGACGCC 62.814 66.667 9.46 0.00 42.52 5.68
1211 1260 0.877649 CCGCCACCGATCATCAAGAG 60.878 60.000 0.00 0.00 36.29 2.85
1218 1267 1.418334 CGATCATCAAGAGTCCCCCT 58.582 55.000 0.00 0.00 0.00 4.79
1244 1296 1.694150 CAAGTCTCCACCCAAGTCTCA 59.306 52.381 0.00 0.00 0.00 3.27
1251 1303 0.397941 CACCCAAGTCTCAGGCAAGA 59.602 55.000 0.00 0.00 0.00 3.02
1468 1757 3.123620 CCAAGCTCACTCGCCTGC 61.124 66.667 0.00 0.00 0.00 4.85
1541 1832 4.376340 CCATTGATGGCCAGTAGTTTTC 57.624 45.455 13.05 1.79 41.75 2.29
1552 1846 6.014070 TGGCCAGTAGTTTTCTATGTTAGTCA 60.014 38.462 0.00 0.00 34.69 3.41
1615 1909 9.181061 GTCAGTTAGAGTTAGGATCTAGTTTCT 57.819 37.037 0.00 0.00 31.17 2.52
1646 1940 7.273320 TGCTCTATAATCGTAGCTGTAGTTT 57.727 36.000 0.00 0.00 35.95 2.66
1967 2263 4.828829 TCAGTAAACCTTTCGGAGATTCC 58.171 43.478 0.00 0.00 35.04 3.01
1988 2284 3.696051 CCGGTGTCCTCATGATTGAAAAT 59.304 43.478 0.00 0.00 0.00 1.82
2073 2369 1.613437 CTGAAATTGCCGTTTCCCACT 59.387 47.619 8.03 0.00 37.31 4.00
2171 2467 4.744570 CCAAACTCAGAGATTGCGTAGTA 58.255 43.478 13.72 0.00 28.02 1.82
2279 2575 2.069273 GCGATAACTGCACAAGTCAGT 58.931 47.619 0.00 0.00 45.83 3.41
2317 2613 5.470098 GCAAATCTTTCTGGTTGACTACTGA 59.530 40.000 0.00 0.00 0.00 3.41
2318 2614 6.150140 GCAAATCTTTCTGGTTGACTACTGAT 59.850 38.462 0.00 0.00 0.00 2.90
2319 2615 7.334421 GCAAATCTTTCTGGTTGACTACTGATA 59.666 37.037 0.00 0.00 0.00 2.15
2320 2616 8.660373 CAAATCTTTCTGGTTGACTACTGATAC 58.340 37.037 0.00 0.00 0.00 2.24
2321 2617 5.950883 TCTTTCTGGTTGACTACTGATACG 58.049 41.667 0.00 0.00 0.00 3.06
2322 2618 5.475909 TCTTTCTGGTTGACTACTGATACGT 59.524 40.000 0.00 0.00 0.00 3.57
2323 2619 4.959596 TCTGGTTGACTACTGATACGTC 57.040 45.455 0.00 0.00 0.00 4.34
2324 2620 4.586884 TCTGGTTGACTACTGATACGTCT 58.413 43.478 0.00 0.00 0.00 4.18
2325 2621 4.634883 TCTGGTTGACTACTGATACGTCTC 59.365 45.833 0.00 0.00 0.00 3.36
2326 2622 3.693085 TGGTTGACTACTGATACGTCTCC 59.307 47.826 0.00 0.00 0.00 3.71
2327 2623 3.693085 GGTTGACTACTGATACGTCTCCA 59.307 47.826 0.00 0.00 0.00 3.86
2328 2624 4.157289 GGTTGACTACTGATACGTCTCCAA 59.843 45.833 0.00 0.00 0.00 3.53
2329 2625 4.959596 TGACTACTGATACGTCTCCAAC 57.040 45.455 0.00 0.00 0.00 3.77
2389 2685 8.947055 ATATTCTGTTTTGAACATTATTGGGC 57.053 30.769 0.00 0.00 41.26 5.36
2390 2686 6.418057 TTCTGTTTTGAACATTATTGGGCT 57.582 33.333 0.00 0.00 41.26 5.19
2391 2687 6.418057 TCTGTTTTGAACATTATTGGGCTT 57.582 33.333 0.00 0.00 41.26 4.35
2392 2688 6.825610 TCTGTTTTGAACATTATTGGGCTTT 58.174 32.000 0.00 0.00 41.26 3.51
2393 2689 7.957002 TCTGTTTTGAACATTATTGGGCTTTA 58.043 30.769 0.00 0.00 41.26 1.85
2394 2690 8.592809 TCTGTTTTGAACATTATTGGGCTTTAT 58.407 29.630 0.00 0.00 41.26 1.40
2395 2691 9.218440 CTGTTTTGAACATTATTGGGCTTTATT 57.782 29.630 0.00 0.00 41.26 1.40
2396 2692 9.566432 TGTTTTGAACATTATTGGGCTTTATTT 57.434 25.926 0.00 0.00 36.25 1.40
2400 2696 9.784531 TTGAACATTATTGGGCTTTATTTTTCA 57.215 25.926 0.00 0.00 0.00 2.69
2401 2697 9.213799 TGAACATTATTGGGCTTTATTTTTCAC 57.786 29.630 0.00 0.00 0.00 3.18
2402 2698 9.213799 GAACATTATTGGGCTTTATTTTTCACA 57.786 29.630 0.00 0.00 0.00 3.58
2403 2699 9.737844 AACATTATTGGGCTTTATTTTTCACAT 57.262 25.926 0.00 0.00 0.00 3.21
2404 2700 9.737844 ACATTATTGGGCTTTATTTTTCACATT 57.262 25.926 0.00 0.00 0.00 2.71
2435 2731 7.634671 ATTTTTGGGACTAACCTATTAACCG 57.365 36.000 0.00 0.00 38.98 4.44
2436 2732 4.758773 TTGGGACTAACCTATTAACCGG 57.241 45.455 0.00 0.00 38.98 5.28
2437 2733 3.992999 TGGGACTAACCTATTAACCGGA 58.007 45.455 9.46 0.00 38.98 5.14
2438 2734 3.962718 TGGGACTAACCTATTAACCGGAG 59.037 47.826 9.46 0.00 38.98 4.63
2439 2735 4.597404 GGACTAACCTATTAACCGGAGG 57.403 50.000 9.46 6.51 45.59 4.30
2440 2736 3.244009 GGACTAACCTATTAACCGGAGGC 60.244 52.174 9.46 0.00 44.44 4.70
2441 2737 6.309757 GGACTAACCTATTAACCGGAGGCC 62.310 54.167 9.46 0.00 44.44 5.19
2455 2751 3.464494 GGCCCAGCCCAGAATTGC 61.464 66.667 0.00 0.00 44.06 3.56
2456 2752 2.363406 GCCCAGCCCAGAATTGCT 60.363 61.111 0.00 0.00 38.67 3.91
2467 2763 3.116079 CAGAATTGCTGGTTTTTGCCT 57.884 42.857 0.00 0.00 41.07 4.75
2468 2764 4.255833 CAGAATTGCTGGTTTTTGCCTA 57.744 40.909 0.00 0.00 41.07 3.93
2469 2765 4.824289 CAGAATTGCTGGTTTTTGCCTAT 58.176 39.130 0.00 0.00 41.07 2.57
2470 2766 5.240121 CAGAATTGCTGGTTTTTGCCTATT 58.760 37.500 0.00 0.00 41.07 1.73
2471 2767 5.702209 CAGAATTGCTGGTTTTTGCCTATTT 59.298 36.000 0.00 0.00 41.07 1.40
2472 2768 5.934043 AGAATTGCTGGTTTTTGCCTATTTC 59.066 36.000 0.00 0.00 0.00 2.17
2473 2769 4.679373 TTGCTGGTTTTTGCCTATTTCA 57.321 36.364 0.00 0.00 0.00 2.69
2474 2770 4.255833 TGCTGGTTTTTGCCTATTTCAG 57.744 40.909 0.00 0.00 0.00 3.02
2475 2771 3.894427 TGCTGGTTTTTGCCTATTTCAGA 59.106 39.130 0.00 0.00 0.00 3.27
2476 2772 4.022068 TGCTGGTTTTTGCCTATTTCAGAG 60.022 41.667 0.00 0.00 0.00 3.35
2477 2773 4.021981 GCTGGTTTTTGCCTATTTCAGAGT 60.022 41.667 0.00 0.00 0.00 3.24
2478 2774 5.509670 GCTGGTTTTTGCCTATTTCAGAGTT 60.510 40.000 0.00 0.00 0.00 3.01
2479 2775 6.478512 TGGTTTTTGCCTATTTCAGAGTTT 57.521 33.333 0.00 0.00 0.00 2.66
2480 2776 6.512297 TGGTTTTTGCCTATTTCAGAGTTTC 58.488 36.000 0.00 0.00 0.00 2.78
2481 2777 5.629435 GGTTTTTGCCTATTTCAGAGTTTCG 59.371 40.000 0.00 0.00 0.00 3.46
2482 2778 4.419522 TTTGCCTATTTCAGAGTTTCGC 57.580 40.909 0.00 0.00 0.00 4.70
2483 2779 3.052455 TGCCTATTTCAGAGTTTCGCA 57.948 42.857 0.00 0.00 0.00 5.10
2484 2780 3.002791 TGCCTATTTCAGAGTTTCGCAG 58.997 45.455 0.00 0.00 0.00 5.18
2485 2781 3.262420 GCCTATTTCAGAGTTTCGCAGA 58.738 45.455 0.00 0.00 0.00 4.26
2486 2782 3.684788 GCCTATTTCAGAGTTTCGCAGAA 59.315 43.478 0.00 0.00 45.90 3.02
2487 2783 4.154195 GCCTATTTCAGAGTTTCGCAGAAA 59.846 41.667 0.00 0.00 45.90 2.52
2488 2784 5.334879 GCCTATTTCAGAGTTTCGCAGAAAA 60.335 40.000 5.51 0.00 45.90 2.29
2489 2785 6.668323 CCTATTTCAGAGTTTCGCAGAAAAA 58.332 36.000 5.51 0.00 45.90 1.94
2490 2786 6.798959 CCTATTTCAGAGTTTCGCAGAAAAAG 59.201 38.462 5.51 0.00 45.90 2.27
2491 2787 5.811399 TTTCAGAGTTTCGCAGAAAAAGA 57.189 34.783 5.51 0.89 45.90 2.52
2492 2788 5.811399 TTCAGAGTTTCGCAGAAAAAGAA 57.189 34.783 5.51 5.50 45.90 2.52
2493 2789 6.377327 TTCAGAGTTTCGCAGAAAAAGAAT 57.623 33.333 5.51 0.00 45.90 2.40
2494 2790 7.490962 TTCAGAGTTTCGCAGAAAAAGAATA 57.509 32.000 5.51 0.00 45.90 1.75
2495 2791 7.672983 TCAGAGTTTCGCAGAAAAAGAATAT 57.327 32.000 5.51 0.00 45.90 1.28
2496 2792 7.743104 TCAGAGTTTCGCAGAAAAAGAATATC 58.257 34.615 5.51 0.00 45.90 1.63
2497 2793 7.387673 TCAGAGTTTCGCAGAAAAAGAATATCA 59.612 33.333 5.51 0.00 45.90 2.15
2498 2794 8.017373 CAGAGTTTCGCAGAAAAAGAATATCAA 58.983 33.333 5.51 0.00 45.90 2.57
2499 2795 8.567948 AGAGTTTCGCAGAAAAAGAATATCAAA 58.432 29.630 5.51 0.00 45.90 2.69
2500 2796 8.507470 AGTTTCGCAGAAAAAGAATATCAAAC 57.493 30.769 5.51 0.00 45.90 2.93
2501 2797 7.323656 AGTTTCGCAGAAAAAGAATATCAAACG 59.676 33.333 5.51 0.00 45.90 3.60
2502 2798 5.627172 TCGCAGAAAAAGAATATCAAACGG 58.373 37.500 0.00 0.00 0.00 4.44
2503 2799 5.410132 TCGCAGAAAAAGAATATCAAACGGA 59.590 36.000 0.00 0.00 0.00 4.69
2504 2800 5.734498 CGCAGAAAAAGAATATCAAACGGAG 59.266 40.000 0.00 0.00 0.00 4.63
2506 2802 6.743172 GCAGAAAAAGAATATCAAACGGAGTC 59.257 38.462 0.00 0.00 45.00 3.36
2507 2803 7.244192 CAGAAAAAGAATATCAAACGGAGTCC 58.756 38.462 0.00 0.00 45.00 3.85
2508 2804 6.940298 AGAAAAAGAATATCAAACGGAGTCCA 59.060 34.615 10.49 0.00 45.00 4.02
2509 2805 7.447238 AGAAAAAGAATATCAAACGGAGTCCAA 59.553 33.333 10.49 0.00 45.00 3.53
2510 2806 7.519032 AAAAGAATATCAAACGGAGTCCAAA 57.481 32.000 10.49 0.00 45.00 3.28
2511 2807 6.496338 AAGAATATCAAACGGAGTCCAAAC 57.504 37.500 10.49 0.00 45.00 2.93
2512 2808 4.630069 AGAATATCAAACGGAGTCCAAACG 59.370 41.667 10.49 0.00 45.00 3.60
2513 2809 1.519408 ATCAAACGGAGTCCAAACGG 58.481 50.000 10.49 0.00 45.00 4.44
2514 2810 0.464870 TCAAACGGAGTCCAAACGGA 59.535 50.000 10.49 0.00 45.00 4.69
2515 2811 1.134461 TCAAACGGAGTCCAAACGGAA 60.134 47.619 10.49 0.00 45.00 4.30
2516 2812 1.877443 CAAACGGAGTCCAAACGGAAT 59.123 47.619 10.49 0.00 45.00 3.01
2517 2813 1.519408 AACGGAGTCCAAACGGAATG 58.481 50.000 10.49 0.00 45.00 2.67
2518 2814 0.682852 ACGGAGTCCAAACGGAATGA 59.317 50.000 10.49 0.00 29.74 2.57
2519 2815 1.071071 ACGGAGTCCAAACGGAATGAA 59.929 47.619 10.49 0.00 29.74 2.57
2520 2816 2.147958 CGGAGTCCAAACGGAATGAAA 58.852 47.619 10.49 0.00 33.16 2.69
2521 2817 2.095919 CGGAGTCCAAACGGAATGAAAC 60.096 50.000 10.49 0.00 33.16 2.78
2522 2818 2.228103 GGAGTCCAAACGGAATGAAACC 59.772 50.000 3.60 0.00 33.16 3.27
2523 2819 3.146847 GAGTCCAAACGGAATGAAACCT 58.853 45.455 0.00 0.00 33.16 3.50
2524 2820 3.562182 AGTCCAAACGGAATGAAACCTT 58.438 40.909 0.00 0.00 33.16 3.50
2525 2821 3.568430 AGTCCAAACGGAATGAAACCTTC 59.432 43.478 0.00 0.00 33.16 3.46
2526 2822 2.550606 TCCAAACGGAATGAAACCTTCG 59.449 45.455 0.00 0.00 0.00 3.79
2527 2823 2.351350 CCAAACGGAATGAAACCTTCGG 60.351 50.000 0.00 0.00 0.00 4.30
2528 2824 1.530323 AACGGAATGAAACCTTCGGG 58.470 50.000 0.00 0.00 41.87 5.14
2529 2825 0.688487 ACGGAATGAAACCTTCGGGA 59.312 50.000 0.00 0.00 38.77 5.14
2530 2826 1.072648 ACGGAATGAAACCTTCGGGAA 59.927 47.619 0.00 0.00 38.77 3.97
2531 2827 1.467342 CGGAATGAAACCTTCGGGAAC 59.533 52.381 0.00 0.00 38.77 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 6.913132 TCGAAATCGTCTCAGATGTAGAAATC 59.087 38.462 2.41 0.00 40.80 2.17
208 210 1.919240 ATATGCGTCCCGTATCTGGA 58.081 50.000 0.00 0.00 33.75 3.86
354 356 3.057876 TCATTCATTTTTGCGTACGGCTT 60.058 39.130 18.39 0.00 44.05 4.35
508 518 3.764434 CCCGTGGATACTGCTATCTGTAT 59.236 47.826 0.00 0.00 39.20 2.29
640 650 6.446318 TCAACAAGTTTTCATGCTATGGTTC 58.554 36.000 0.00 0.00 0.00 3.62
650 660 8.033038 CCAAGATCATCATCAACAAGTTTTCAT 58.967 33.333 0.00 0.00 0.00 2.57
657 671 5.124936 TGAAGCCAAGATCATCATCAACAAG 59.875 40.000 0.00 0.00 0.00 3.16
782 811 3.068560 CCGGACACATAACCTCGAAAAA 58.931 45.455 0.00 0.00 0.00 1.94
948 977 1.805428 GCTTGGCCTTGGCGAAGAAA 61.805 55.000 31.00 10.16 0.00 2.52
1070 1113 1.028868 GGAAGAAGGCTGCGCTTGAT 61.029 55.000 9.73 0.00 0.00 2.57
1218 1267 4.373116 GGTGGAGACTTGCGCGGA 62.373 66.667 8.83 0.00 0.00 5.54
1251 1303 4.345286 ACAGGAGCAGAGGGGGCT 62.345 66.667 0.00 0.00 46.07 5.19
1289 1578 1.134699 GGACCGAGCAGTTCATCATCA 60.135 52.381 0.00 0.00 0.00 3.07
1552 1846 5.045724 ACCCTCGGAGACTAATACTATCGAT 60.046 44.000 6.58 2.16 0.00 3.59
1615 1909 7.031975 CAGCTACGATTATAGAGCATCATCAA 58.968 38.462 0.00 0.00 37.82 2.57
1646 1940 2.740826 GGCGCCAGCTAAACGACA 60.741 61.111 24.80 0.00 44.37 4.35
1967 2263 4.637534 AGATTTTCAATCATGAGGACACCG 59.362 41.667 0.09 0.00 36.78 4.94
1988 2284 3.010472 TCCATGAAAGAATTGGGCAGAGA 59.990 43.478 0.00 0.00 0.00 3.10
2073 2369 2.873245 GCAGACAGAGAATGCCAAGACA 60.873 50.000 0.00 0.00 33.81 3.41
2261 2557 4.560128 TGAGACTGACTTGTGCAGTTATC 58.440 43.478 0.00 0.00 45.94 1.75
2279 2575 1.745087 GATTTGCCCGATGCTTTGAGA 59.255 47.619 0.00 0.00 42.00 3.27
2364 2660 8.761689 AGCCCAATAATGTTCAAAACAGAATAT 58.238 29.630 0.00 0.00 45.95 1.28
2365 2661 8.133024 AGCCCAATAATGTTCAAAACAGAATA 57.867 30.769 0.00 0.00 45.95 1.75
2366 2662 7.008021 AGCCCAATAATGTTCAAAACAGAAT 57.992 32.000 0.00 0.00 45.95 2.40
2367 2663 6.418057 AGCCCAATAATGTTCAAAACAGAA 57.582 33.333 0.00 0.00 45.95 3.02
2368 2664 6.418057 AAGCCCAATAATGTTCAAAACAGA 57.582 33.333 0.00 0.00 45.95 3.41
2369 2665 8.776376 ATAAAGCCCAATAATGTTCAAAACAG 57.224 30.769 0.00 0.00 45.95 3.16
2370 2666 9.566432 AAATAAAGCCCAATAATGTTCAAAACA 57.434 25.926 0.00 0.00 46.94 2.83
2374 2670 9.784531 TGAAAAATAAAGCCCAATAATGTTCAA 57.215 25.926 0.00 0.00 0.00 2.69
2375 2671 9.213799 GTGAAAAATAAAGCCCAATAATGTTCA 57.786 29.630 0.00 0.00 0.00 3.18
2376 2672 9.213799 TGTGAAAAATAAAGCCCAATAATGTTC 57.786 29.630 0.00 0.00 0.00 3.18
2377 2673 9.737844 ATGTGAAAAATAAAGCCCAATAATGTT 57.262 25.926 0.00 0.00 0.00 2.71
2378 2674 9.737844 AATGTGAAAAATAAAGCCCAATAATGT 57.262 25.926 0.00 0.00 0.00 2.71
2409 2705 9.176460 CGGTTAATAGGTTAGTCCCAAAAATAA 57.824 33.333 0.00 0.00 36.75 1.40
2410 2706 7.774625 CCGGTTAATAGGTTAGTCCCAAAAATA 59.225 37.037 0.00 0.00 36.75 1.40
2411 2707 6.604396 CCGGTTAATAGGTTAGTCCCAAAAAT 59.396 38.462 0.00 0.00 36.75 1.82
2412 2708 5.945191 CCGGTTAATAGGTTAGTCCCAAAAA 59.055 40.000 0.00 0.00 36.75 1.94
2413 2709 5.250313 TCCGGTTAATAGGTTAGTCCCAAAA 59.750 40.000 0.00 0.00 36.75 2.44
2414 2710 4.782156 TCCGGTTAATAGGTTAGTCCCAAA 59.218 41.667 0.00 0.00 36.75 3.28
2415 2711 4.360889 TCCGGTTAATAGGTTAGTCCCAA 58.639 43.478 0.00 0.00 36.75 4.12
2416 2712 3.962718 CTCCGGTTAATAGGTTAGTCCCA 59.037 47.826 0.00 0.00 36.75 4.37
2417 2713 3.323115 CCTCCGGTTAATAGGTTAGTCCC 59.677 52.174 0.00 0.00 36.75 4.46
2418 2714 3.244009 GCCTCCGGTTAATAGGTTAGTCC 60.244 52.174 0.00 0.00 32.67 3.85
2419 2715 3.244009 GGCCTCCGGTTAATAGGTTAGTC 60.244 52.174 0.00 0.00 32.67 2.59
2420 2716 2.702478 GGCCTCCGGTTAATAGGTTAGT 59.298 50.000 0.00 0.00 32.67 2.24
2421 2717 2.038164 GGGCCTCCGGTTAATAGGTTAG 59.962 54.545 0.84 0.00 32.67 2.34
2422 2718 2.049372 GGGCCTCCGGTTAATAGGTTA 58.951 52.381 0.84 0.00 32.67 2.85
2423 2719 0.841961 GGGCCTCCGGTTAATAGGTT 59.158 55.000 0.84 0.00 32.67 3.50
2424 2720 0.326808 TGGGCCTCCGGTTAATAGGT 60.327 55.000 4.53 0.00 35.24 3.08
2425 2721 0.396811 CTGGGCCTCCGGTTAATAGG 59.603 60.000 4.53 0.51 34.69 2.57
2426 2722 0.250338 GCTGGGCCTCCGGTTAATAG 60.250 60.000 4.53 0.00 41.53 1.73
2427 2723 1.702022 GGCTGGGCCTCCGGTTAATA 61.702 60.000 4.53 0.00 46.69 0.98
2428 2724 2.595655 GCTGGGCCTCCGGTTAAT 59.404 61.111 4.53 0.00 41.53 1.40
2429 2725 3.723922 GGCTGGGCCTCCGGTTAA 61.724 66.667 4.53 0.00 46.69 2.01
2439 2735 2.363406 AGCAATTCTGGGCTGGGC 60.363 61.111 0.00 0.00 39.30 5.36
2447 2743 3.116079 AGGCAAAAACCAGCAATTCTG 57.884 42.857 0.00 0.00 42.49 3.02
2448 2744 5.488262 AATAGGCAAAAACCAGCAATTCT 57.512 34.783 0.00 0.00 0.00 2.40
2449 2745 5.700373 TGAAATAGGCAAAAACCAGCAATTC 59.300 36.000 0.00 0.00 0.00 2.17
2450 2746 5.619220 TGAAATAGGCAAAAACCAGCAATT 58.381 33.333 0.00 0.00 0.00 2.32
2451 2747 5.011943 TCTGAAATAGGCAAAAACCAGCAAT 59.988 36.000 0.00 0.00 0.00 3.56
2452 2748 4.343526 TCTGAAATAGGCAAAAACCAGCAA 59.656 37.500 0.00 0.00 0.00 3.91
2453 2749 3.894427 TCTGAAATAGGCAAAAACCAGCA 59.106 39.130 0.00 0.00 0.00 4.41
2454 2750 4.021981 ACTCTGAAATAGGCAAAAACCAGC 60.022 41.667 0.00 0.00 0.00 4.85
2455 2751 5.712152 ACTCTGAAATAGGCAAAAACCAG 57.288 39.130 0.00 0.00 0.00 4.00
2456 2752 6.478512 AAACTCTGAAATAGGCAAAAACCA 57.521 33.333 0.00 0.00 0.00 3.67
2457 2753 5.629435 CGAAACTCTGAAATAGGCAAAAACC 59.371 40.000 0.00 0.00 0.00 3.27
2458 2754 5.117135 GCGAAACTCTGAAATAGGCAAAAAC 59.883 40.000 0.00 0.00 0.00 2.43
2459 2755 5.219633 GCGAAACTCTGAAATAGGCAAAAA 58.780 37.500 0.00 0.00 0.00 1.94
2460 2756 4.277174 TGCGAAACTCTGAAATAGGCAAAA 59.723 37.500 0.00 0.00 0.00 2.44
2461 2757 3.818210 TGCGAAACTCTGAAATAGGCAAA 59.182 39.130 0.00 0.00 0.00 3.68
2462 2758 3.407698 TGCGAAACTCTGAAATAGGCAA 58.592 40.909 0.00 0.00 0.00 4.52
2463 2759 3.002791 CTGCGAAACTCTGAAATAGGCA 58.997 45.455 0.00 0.00 0.00 4.75
2464 2760 3.262420 TCTGCGAAACTCTGAAATAGGC 58.738 45.455 0.00 0.00 0.00 3.93
2465 2761 5.862924 TTTCTGCGAAACTCTGAAATAGG 57.137 39.130 0.00 0.00 0.00 2.57
2466 2762 7.576236 TCTTTTTCTGCGAAACTCTGAAATAG 58.424 34.615 3.71 0.00 34.78 1.73
2467 2763 7.490962 TCTTTTTCTGCGAAACTCTGAAATA 57.509 32.000 3.71 0.00 33.51 1.40
2468 2764 6.377327 TCTTTTTCTGCGAAACTCTGAAAT 57.623 33.333 3.71 0.00 33.51 2.17
2469 2765 5.811399 TCTTTTTCTGCGAAACTCTGAAA 57.189 34.783 3.71 0.00 32.22 2.69
2470 2766 5.811399 TTCTTTTTCTGCGAAACTCTGAA 57.189 34.783 3.71 4.31 0.00 3.02
2471 2767 7.387673 TGATATTCTTTTTCTGCGAAACTCTGA 59.612 33.333 3.71 0.00 0.00 3.27
2472 2768 7.521529 TGATATTCTTTTTCTGCGAAACTCTG 58.478 34.615 3.71 0.00 0.00 3.35
2473 2769 7.672983 TGATATTCTTTTTCTGCGAAACTCT 57.327 32.000 3.71 0.00 0.00 3.24
2474 2770 8.630840 GTTTGATATTCTTTTTCTGCGAAACTC 58.369 33.333 3.71 0.00 0.00 3.01
2475 2771 7.323656 CGTTTGATATTCTTTTTCTGCGAAACT 59.676 33.333 3.71 0.00 0.00 2.66
2476 2772 7.409343 CCGTTTGATATTCTTTTTCTGCGAAAC 60.409 37.037 3.71 0.00 0.00 2.78
2477 2773 6.580791 CCGTTTGATATTCTTTTTCTGCGAAA 59.419 34.615 0.00 0.55 0.00 3.46
2478 2774 6.072948 TCCGTTTGATATTCTTTTTCTGCGAA 60.073 34.615 0.00 0.00 0.00 4.70
2479 2775 5.410132 TCCGTTTGATATTCTTTTTCTGCGA 59.590 36.000 0.00 0.00 0.00 5.10
2480 2776 5.627172 TCCGTTTGATATTCTTTTTCTGCG 58.373 37.500 0.00 0.00 0.00 5.18
2481 2777 6.612306 ACTCCGTTTGATATTCTTTTTCTGC 58.388 36.000 0.00 0.00 0.00 4.26
2482 2778 7.094805 TGGACTCCGTTTGATATTCTTTTTCTG 60.095 37.037 0.00 0.00 0.00 3.02
2483 2779 6.940298 TGGACTCCGTTTGATATTCTTTTTCT 59.060 34.615 0.00 0.00 0.00 2.52
2484 2780 7.141100 TGGACTCCGTTTGATATTCTTTTTC 57.859 36.000 0.00 0.00 0.00 2.29
2485 2781 7.519032 TTGGACTCCGTTTGATATTCTTTTT 57.481 32.000 0.00 0.00 0.00 1.94
2486 2782 7.368059 GTTTGGACTCCGTTTGATATTCTTTT 58.632 34.615 0.00 0.00 0.00 2.27
2487 2783 6.348213 CGTTTGGACTCCGTTTGATATTCTTT 60.348 38.462 0.00 0.00 0.00 2.52
2488 2784 5.121768 CGTTTGGACTCCGTTTGATATTCTT 59.878 40.000 0.00 0.00 0.00 2.52
2489 2785 4.630069 CGTTTGGACTCCGTTTGATATTCT 59.370 41.667 0.00 0.00 0.00 2.40
2490 2786 4.201783 CCGTTTGGACTCCGTTTGATATTC 60.202 45.833 0.00 0.00 37.49 1.75
2491 2787 3.687698 CCGTTTGGACTCCGTTTGATATT 59.312 43.478 0.00 0.00 37.49 1.28
2492 2788 3.055675 TCCGTTTGGACTCCGTTTGATAT 60.056 43.478 0.00 0.00 40.17 1.63
2493 2789 2.299582 TCCGTTTGGACTCCGTTTGATA 59.700 45.455 0.00 0.00 40.17 2.15
2494 2790 1.071071 TCCGTTTGGACTCCGTTTGAT 59.929 47.619 0.00 0.00 40.17 2.57
2495 2791 0.464870 TCCGTTTGGACTCCGTTTGA 59.535 50.000 0.00 0.00 40.17 2.69
2496 2792 1.301423 TTCCGTTTGGACTCCGTTTG 58.699 50.000 0.00 0.00 46.45 2.93
2497 2793 1.877443 CATTCCGTTTGGACTCCGTTT 59.123 47.619 0.00 0.00 46.45 3.60
2498 2794 1.071071 TCATTCCGTTTGGACTCCGTT 59.929 47.619 0.00 0.00 46.45 4.44
2499 2795 0.682852 TCATTCCGTTTGGACTCCGT 59.317 50.000 0.00 0.00 46.45 4.69
2500 2796 1.803334 TTCATTCCGTTTGGACTCCG 58.197 50.000 0.00 0.00 46.45 4.63
2501 2797 2.228103 GGTTTCATTCCGTTTGGACTCC 59.772 50.000 0.00 0.00 46.45 3.85
2502 2798 3.146847 AGGTTTCATTCCGTTTGGACTC 58.853 45.455 0.00 0.00 46.45 3.36
2503 2799 3.223674 AGGTTTCATTCCGTTTGGACT 57.776 42.857 0.00 0.00 46.45 3.85
2504 2800 3.608474 CGAAGGTTTCATTCCGTTTGGAC 60.608 47.826 0.00 0.00 46.45 4.02
2505 2801 2.550606 CGAAGGTTTCATTCCGTTTGGA 59.449 45.455 0.00 0.00 44.61 3.53
2506 2802 2.928694 CGAAGGTTTCATTCCGTTTGG 58.071 47.619 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.