Multiple sequence alignment - TraesCS1A01G351100

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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 TraesCS1A01G351100 chr1A 100.000 3326 0 0 1 3326 535484548 535487873 0.000000e+00 6143.0
1 TraesCS1A01G351100 chr1A 74.692 1462 280 53 965 2366 539741018 539742449 4.820000e-158 568.0
2 TraesCS1A01G351100 chr1A 80.449 624 84 18 965 1558 535703723 535704338 3.050000e-120 442.0
3 TraesCS1A01G351100 chr1A 80.095 633 83 25 965 1558 535705878 535706506 6.590000e-117 431.0
4 TraesCS1A01G351100 chr1A 84.866 337 43 6 2054 2386 535498088 535498420 1.910000e-87 333.0
5 TraesCS1A01G351100 chr1A 97.872 47 1 0 2396 2442 535486816 535486862 7.650000e-12 82.4
6 TraesCS1A01G351100 chr1B 89.922 2441 157 46 1 2386 603087859 603085453 0.000000e+00 3062.0
7 TraesCS1A01G351100 chr1B 84.760 1437 173 20 965 2369 602650506 602649084 0.000000e+00 1399.0
8 TraesCS1A01G351100 chr1B 97.952 537 11 0 2790 3326 680755073 680754537 0.000000e+00 931.0
9 TraesCS1A01G351100 chr1B 74.110 1460 279 54 965 2366 602735557 602734139 8.230000e-141 510.0
10 TraesCS1A01G351100 chr1B 85.075 335 40 6 2054 2381 603081681 603081350 1.910000e-87 333.0
11 TraesCS1A01G351100 chr1B 84.776 335 41 6 2054 2381 603019441 603019110 8.900000e-86 327.0
12 TraesCS1A01G351100 chr1B 84.179 335 42 7 2054 2381 603050533 603050203 6.930000e-82 315.0
13 TraesCS1A01G351100 chr1B 92.377 223 10 3 2438 2660 603023211 603022996 8.960000e-81 311.0
14 TraesCS1A01G351100 chr1B 92.377 223 10 2 2438 2660 603085450 603085235 8.960000e-81 311.0
15 TraesCS1A01G351100 chr1B 91.928 223 11 3 2438 2660 603054286 603054071 4.170000e-79 305.0
16 TraesCS1A01G351100 chr1B 93.750 96 6 0 2291 2386 603054384 603054289 9.620000e-31 145.0
17 TraesCS1A01G351100 chr1B 83.088 136 19 1 2446 2577 603019094 603018959 1.620000e-23 121.0
18 TraesCS1A01G351100 chr1B 83.088 136 19 1 2446 2577 603050187 603050052 1.620000e-23 121.0
19 TraesCS1A01G351100 chr1B 85.455 110 15 1 528 637 632635817 632635709 2.710000e-21 113.0
20 TraesCS1A01G351100 chr1B 100.000 36 0 0 2756 2791 603022924 603022889 2.140000e-07 67.6
21 TraesCS1A01G351100 chr1B 100.000 36 0 0 2756 2791 603053999 603053964 2.140000e-07 67.6
22 TraesCS1A01G351100 chr1B 100.000 36 0 0 2756 2791 603085163 603085128 2.140000e-07 67.6
23 TraesCS1A01G351100 chr1D 91.238 2157 112 38 301 2386 443379792 443377642 0.000000e+00 2865.0
24 TraesCS1A01G351100 chr1D 74.599 1370 265 50 973 2287 443219275 443217934 2.940000e-145 525.0
25 TraesCS1A01G351100 chr1D 80.168 595 82 20 997 1558 443200035 443199444 2.390000e-111 412.0
26 TraesCS1A01G351100 chr1D 83.188 345 44 7 2054 2386 443373917 443373575 1.500000e-78 303.0
27 TraesCS1A01G351100 chr1D 91.176 102 6 2 2559 2660 443377554 443377456 5.790000e-28 135.0
28 TraesCS1A01G351100 chr1D 82.031 128 19 1 2446 2569 443373564 443373437 4.540000e-19 106.0
29 TraesCS1A01G351100 chr1D 98.113 53 1 0 2739 2791 443377460 443377408 3.530000e-15 93.5
30 TraesCS1A01G351100 chr5B 98.696 537 7 0 2790 3326 664469981 664469445 0.000000e+00 953.0
31 TraesCS1A01G351100 chr5B 82.051 78 12 2 250 327 586817281 586817206 7.700000e-07 65.8
32 TraesCS1A01G351100 chr3B 98.324 537 9 0 2790 3326 11936243 11935707 0.000000e+00 942.0
33 TraesCS1A01G351100 chr3B 97.579 537 13 0 2790 3326 4510114 4510650 0.000000e+00 920.0
34 TraesCS1A01G351100 chr7B 96.756 524 15 1 2805 3326 322189717 322190240 0.000000e+00 872.0
35 TraesCS1A01G351100 chr7B 90.824 534 43 4 2791 3320 594017621 594017090 0.000000e+00 710.0
36 TraesCS1A01G351100 chr2B 93.284 536 36 0 2791 3326 25749676 25750211 0.000000e+00 791.0
37 TraesCS1A01G351100 chr2B 98.601 143 2 0 3184 3326 682190903 682190761 1.530000e-63 254.0
38 TraesCS1A01G351100 chr2B 98.864 88 1 0 2656 2743 542546503 542546590 1.240000e-34 158.0
39 TraesCS1A01G351100 chr7A 95.238 105 2 3 2636 2740 668551986 668552087 2.660000e-36 163.0
40 TraesCS1A01G351100 chr7A 82.432 74 12 1 253 326 136849103 136849175 2.770000e-06 63.9
41 TraesCS1A01G351100 chr4A 100.000 88 0 0 2653 2740 640896775 640896688 2.660000e-36 163.0
42 TraesCS1A01G351100 chr4A 98.889 90 1 0 2656 2745 295974345 295974256 9.550000e-36 161.0
43 TraesCS1A01G351100 chr6A 98.889 90 1 0 2656 2745 382867444 382867355 9.550000e-36 161.0
44 TraesCS1A01G351100 chr6A 95.918 98 4 0 2656 2753 99043463 99043366 3.430000e-35 159.0
45 TraesCS1A01G351100 chr4B 100.000 86 0 0 2656 2741 658907727 658907812 3.430000e-35 159.0
46 TraesCS1A01G351100 chr3A 98.876 89 1 0 2656 2744 70694538 70694450 3.430000e-35 159.0
47 TraesCS1A01G351100 chr5D 95.833 96 3 1 2646 2740 385037334 385037239 1.600000e-33 154.0
48 TraesCS1A01G351100 chr6B 90.385 52 4 1 469 520 81731950 81732000 2.140000e-07 67.6


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 TraesCS1A01G351100 chr1A 535484548 535487873 3325 False 3112.70 6143 98.93600 1 3326 2 chr1A.!!$F3 3325
1 TraesCS1A01G351100 chr1A 539741018 539742449 1431 False 568.00 568 74.69200 965 2366 1 chr1A.!!$F2 1401
2 TraesCS1A01G351100 chr1A 535703723 535706506 2783 False 436.50 442 80.27200 965 1558 2 chr1A.!!$F4 593
3 TraesCS1A01G351100 chr1B 602649084 602650506 1422 True 1399.00 1399 84.76000 965 2369 1 chr1B.!!$R1 1404
4 TraesCS1A01G351100 chr1B 603081350 603087859 6509 True 943.40 3062 91.84350 1 2791 4 chr1B.!!$R7 2790
5 TraesCS1A01G351100 chr1B 680754537 680755073 536 True 931.00 931 97.95200 2790 3326 1 chr1B.!!$R4 536
6 TraesCS1A01G351100 chr1B 602734139 602735557 1418 True 510.00 510 74.11000 965 2366 1 chr1B.!!$R2 1401
7 TraesCS1A01G351100 chr1B 603018959 603023211 4252 True 206.65 327 90.06025 2054 2791 4 chr1B.!!$R5 737
8 TraesCS1A01G351100 chr1D 443373437 443379792 6355 True 700.50 2865 89.14920 301 2791 5 chr1D.!!$R3 2490
9 TraesCS1A01G351100 chr1D 443217934 443219275 1341 True 525.00 525 74.59900 973 2287 1 chr1D.!!$R2 1314
10 TraesCS1A01G351100 chr1D 443199444 443200035 591 True 412.00 412 80.16800 997 1558 1 chr1D.!!$R1 561
11 TraesCS1A01G351100 chr5B 664469445 664469981 536 True 953.00 953 98.69600 2790 3326 1 chr5B.!!$R2 536
12 TraesCS1A01G351100 chr3B 11935707 11936243 536 True 942.00 942 98.32400 2790 3326 1 chr3B.!!$R1 536
13 TraesCS1A01G351100 chr3B 4510114 4510650 536 False 920.00 920 97.57900 2790 3326 1 chr3B.!!$F1 536
14 TraesCS1A01G351100 chr7B 322189717 322190240 523 False 872.00 872 96.75600 2805 3326 1 chr7B.!!$F1 521
15 TraesCS1A01G351100 chr7B 594017090 594017621 531 True 710.00 710 90.82400 2791 3320 1 chr7B.!!$R1 529
16 TraesCS1A01G351100 chr2B 25749676 25750211 535 False 791.00 791 93.28400 2791 3326 1 chr2B.!!$F1 535

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
68 69 0.320374 TGCGTCTCTCGACCCAAAAT 59.680 50.0 0.0 0.0 42.86 1.82 F
464 514 0.393267 CTCTCGGTCGTCCTTCTCCT 60.393 60.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2200 0.606604 GCCAACCGTACTCTCCTTGA 59.393 55.0 0.0 0.0 0.00 3.02 R
2454 5119 0.320771 CCTTGCCTAGACGTTGCACT 60.321 55.0 0.0 0.0 34.16 4.40 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
48 49 5.106277 CGCTCAATACGAGATATACCTTCCA 60.106 44.000 0.00 0.00 45.45 3.53
68 69 0.320374 TGCGTCTCTCGACCCAAAAT 59.680 50.000 0.00 0.00 42.86 1.82
74 75 2.159282 TCTCTCGACCCAAAATAGCGTC 60.159 50.000 0.00 0.00 0.00 5.19
75 76 1.822990 TCTCGACCCAAAATAGCGTCT 59.177 47.619 0.00 0.00 0.00 4.18
102 103 7.310858 GGAAGAAGAATACACTACCCCAAACTA 60.311 40.741 0.00 0.00 0.00 2.24
198 199 6.617289 GACGCTTGTCATTTTAAGGATTTG 57.383 37.500 0.00 0.00 42.41 2.32
297 298 9.822185 AACCAAATGCATCTATAGGAAATTTTC 57.178 29.630 0.00 0.24 0.00 2.29
303 304 8.370493 TGCATCTATAGGAAATTTTCTTCTCG 57.630 34.615 3.81 0.00 0.00 4.04
304 305 8.204160 TGCATCTATAGGAAATTTTCTTCTCGA 58.796 33.333 3.81 0.00 0.00 4.04
316 319 6.935741 TTTTCTTCTCGAATTCCTTGTTCA 57.064 33.333 0.00 0.00 0.00 3.18
321 324 7.331026 TCTTCTCGAATTCCTTGTTCATATGT 58.669 34.615 1.90 0.00 0.00 2.29
340 343 9.537192 TCATATGTTTTTCGTACGAATATCCTT 57.463 29.630 29.56 17.34 33.79 3.36
345 348 9.368674 TGTTTTTCGTACGAATATCCTTGAATA 57.631 29.630 29.56 8.88 33.79 1.75
397 400 4.977393 GCCCAAGGCCTCGAATTA 57.023 55.556 5.23 0.00 44.06 1.40
464 514 0.393267 CTCTCGGTCGTCCTTCTCCT 60.393 60.000 0.00 0.00 0.00 3.69
671 768 4.373116 TCGCCGTCCAGCCACTTC 62.373 66.667 0.00 0.00 0.00 3.01
703 800 3.075005 CCCCATCGACCGTCACCT 61.075 66.667 0.00 0.00 0.00 4.00
824 949 1.192146 CGTCCTCCTGTTTCCTCCCA 61.192 60.000 0.00 0.00 0.00 4.37
845 970 2.192861 CCAGCGCCTCCAAACAACA 61.193 57.895 2.29 0.00 0.00 3.33
848 973 1.008538 GCGCCTCCAAACAACACAG 60.009 57.895 0.00 0.00 0.00 3.66
869 994 2.887151 AAAGGTAGCAGCTTCCACAT 57.113 45.000 19.55 3.35 34.42 3.21
893 1018 3.192922 AGCGCGCACGATTAACCC 61.193 61.111 35.10 0.00 43.93 4.11
943 1072 6.294286 CCTCAGATCGAGACCTAATTAACCTC 60.294 46.154 13.82 0.00 45.45 3.85
1110 1259 1.825281 GATGGCGCCTCCTCATAGCT 61.825 60.000 29.70 0.00 35.26 3.32
1482 1661 0.912486 AAGGATGCGCCCTTCTAACT 59.088 50.000 11.69 0.00 42.62 2.24
1979 2200 7.341805 ACCAAGATGATTGAGCTAATACAACT 58.658 34.615 0.00 0.00 0.00 3.16
2386 5051 0.458260 ATCACGTGTACCTGCGCATA 59.542 50.000 12.24 0.00 0.00 3.14
2387 5052 0.458260 TCACGTGTACCTGCGCATAT 59.542 50.000 12.24 4.33 0.00 1.78
2388 5053 1.134936 TCACGTGTACCTGCGCATATT 60.135 47.619 12.24 0.00 0.00 1.28
2389 5054 1.663643 CACGTGTACCTGCGCATATTT 59.336 47.619 12.24 0.00 0.00 1.40
2390 5055 1.663643 ACGTGTACCTGCGCATATTTG 59.336 47.619 12.24 0.00 0.00 2.32
2391 5056 1.003972 CGTGTACCTGCGCATATTTGG 60.004 52.381 12.24 11.38 0.00 3.28
2392 5057 1.333619 GTGTACCTGCGCATATTTGGG 59.666 52.381 12.24 10.51 38.75 4.12
2393 5058 1.065053 TGTACCTGCGCATATTTGGGT 60.065 47.619 19.12 19.12 38.05 4.51
2394 5059 2.021457 GTACCTGCGCATATTTGGGTT 58.979 47.619 20.15 6.72 38.05 4.11
2395 5060 2.428544 ACCTGCGCATATTTGGGTTA 57.571 45.000 12.24 0.00 38.05 2.85
2396 5061 2.729194 ACCTGCGCATATTTGGGTTAA 58.271 42.857 12.24 0.00 38.05 2.01
2397 5062 3.295973 ACCTGCGCATATTTGGGTTAAT 58.704 40.909 12.24 0.00 38.05 1.40
2398 5063 3.704061 ACCTGCGCATATTTGGGTTAATT 59.296 39.130 12.24 0.00 38.05 1.40
2399 5064 4.890581 ACCTGCGCATATTTGGGTTAATTA 59.109 37.500 12.24 0.00 38.05 1.40
2400 5065 5.538433 ACCTGCGCATATTTGGGTTAATTAT 59.462 36.000 12.24 0.00 38.05 1.28
2401 5066 6.092748 CCTGCGCATATTTGGGTTAATTATC 58.907 40.000 12.24 0.00 38.05 1.75
2402 5067 6.071952 CCTGCGCATATTTGGGTTAATTATCT 60.072 38.462 12.24 0.00 38.05 1.98
2403 5068 7.283625 TGCGCATATTTGGGTTAATTATCTT 57.716 32.000 5.66 0.00 38.05 2.40
2404 5069 7.721402 TGCGCATATTTGGGTTAATTATCTTT 58.279 30.769 5.66 0.00 38.05 2.52
2405 5070 7.651304 TGCGCATATTTGGGTTAATTATCTTTG 59.349 33.333 5.66 0.00 38.05 2.77
2406 5071 7.116233 GCGCATATTTGGGTTAATTATCTTTGG 59.884 37.037 0.30 0.00 38.05 3.28
2407 5072 7.598493 CGCATATTTGGGTTAATTATCTTTGGG 59.402 37.037 0.00 0.00 0.00 4.12
2408 5073 8.428852 GCATATTTGGGTTAATTATCTTTGGGT 58.571 33.333 0.00 0.00 0.00 4.51
2412 5077 8.959676 TTTGGGTTAATTATCTTTGGGTTAGT 57.040 30.769 0.00 0.00 0.00 2.24
2413 5078 8.959676 TTGGGTTAATTATCTTTGGGTTAGTT 57.040 30.769 0.00 0.00 0.00 2.24
2414 5079 8.356000 TGGGTTAATTATCTTTGGGTTAGTTG 57.644 34.615 0.00 0.00 0.00 3.16
2415 5080 7.951245 TGGGTTAATTATCTTTGGGTTAGTTGT 59.049 33.333 0.00 0.00 0.00 3.32
2416 5081 8.809066 GGGTTAATTATCTTTGGGTTAGTTGTT 58.191 33.333 0.00 0.00 0.00 2.83
2422 5087 9.975218 ATTATCTTTGGGTTAGTTGTTATGAGT 57.025 29.630 0.00 0.00 0.00 3.41
2423 5088 7.923414 ATCTTTGGGTTAGTTGTTATGAGTC 57.077 36.000 0.00 0.00 0.00 3.36
2424 5089 7.074653 TCTTTGGGTTAGTTGTTATGAGTCT 57.925 36.000 0.00 0.00 0.00 3.24
2425 5090 6.934645 TCTTTGGGTTAGTTGTTATGAGTCTG 59.065 38.462 0.00 0.00 0.00 3.51
2426 5091 5.160607 TGGGTTAGTTGTTATGAGTCTGG 57.839 43.478 0.00 0.00 0.00 3.86
2427 5092 4.841813 TGGGTTAGTTGTTATGAGTCTGGA 59.158 41.667 0.00 0.00 0.00 3.86
2428 5093 5.487488 TGGGTTAGTTGTTATGAGTCTGGAT 59.513 40.000 0.00 0.00 0.00 3.41
2429 5094 6.049790 GGGTTAGTTGTTATGAGTCTGGATC 58.950 44.000 0.00 0.00 0.00 3.36
2430 5095 6.351881 GGGTTAGTTGTTATGAGTCTGGATCA 60.352 42.308 0.00 0.00 0.00 2.92
2431 5096 7.275920 GGTTAGTTGTTATGAGTCTGGATCAT 58.724 38.462 0.00 0.00 40.45 2.45
2432 5097 7.225538 GGTTAGTTGTTATGAGTCTGGATCATG 59.774 40.741 0.00 0.00 37.91 3.07
2433 5098 6.550938 AGTTGTTATGAGTCTGGATCATGA 57.449 37.500 0.00 0.00 37.91 3.07
2434 5099 6.950842 AGTTGTTATGAGTCTGGATCATGAA 58.049 36.000 0.00 0.00 37.91 2.57
2435 5100 7.046652 AGTTGTTATGAGTCTGGATCATGAAG 58.953 38.462 0.00 0.00 37.91 3.02
2436 5101 6.796785 TGTTATGAGTCTGGATCATGAAGA 57.203 37.500 0.00 0.00 37.91 2.87
2454 5119 6.884280 TGAAGAGCTACGAGATTGATCATA 57.116 37.500 0.00 0.00 0.00 2.15
2460 5125 4.984785 GCTACGAGATTGATCATAGTGCAA 59.015 41.667 0.00 0.00 0.00 4.08
2465 5130 5.016051 AGATTGATCATAGTGCAACGTCT 57.984 39.130 0.00 0.00 45.86 4.18
2489 5154 2.294233 GCAAGGAACAGATGTTGCAAGA 59.706 45.455 17.76 0.00 46.84 3.02
2520 5185 7.986320 CCCTGCTAAATCAGATCAATAGGATAG 59.014 40.741 0.00 0.00 36.00 2.08
2528 5193 6.080682 TCAGATCAATAGGATAGAACTGCCT 58.919 40.000 0.00 0.00 36.00 4.75
2572 5237 3.134804 GTGGTGTAGAATATGGCCTCTGT 59.865 47.826 3.32 0.00 0.00 3.41
2573 5238 3.134623 TGGTGTAGAATATGGCCTCTGTG 59.865 47.826 3.32 0.00 0.00 3.66
2581 5246 7.961326 AGAATATGGCCTCTGTGTTTTATTT 57.039 32.000 3.32 0.00 0.00 1.40
2582 5247 8.000780 AGAATATGGCCTCTGTGTTTTATTTC 57.999 34.615 3.32 0.00 0.00 2.17
2665 5330 5.475719 TCTGTTGAACAAATACTACCTCCG 58.524 41.667 0.00 0.00 0.00 4.63
2666 5331 5.011329 TCTGTTGAACAAATACTACCTCCGT 59.989 40.000 0.00 0.00 0.00 4.69
2667 5332 6.209192 TCTGTTGAACAAATACTACCTCCGTA 59.791 38.462 0.00 0.00 0.00 4.02
2668 5333 6.757237 TGTTGAACAAATACTACCTCCGTAA 58.243 36.000 0.00 0.00 0.00 3.18
2669 5334 7.215789 TGTTGAACAAATACTACCTCCGTAAA 58.784 34.615 0.00 0.00 0.00 2.01
2670 5335 7.171337 TGTTGAACAAATACTACCTCCGTAAAC 59.829 37.037 0.00 0.00 0.00 2.01
2671 5336 6.996509 TGAACAAATACTACCTCCGTAAACT 58.003 36.000 0.00 0.00 0.00 2.66
2672 5337 8.121305 TGAACAAATACTACCTCCGTAAACTA 57.879 34.615 0.00 0.00 0.00 2.24
2673 5338 8.584157 TGAACAAATACTACCTCCGTAAACTAA 58.416 33.333 0.00 0.00 0.00 2.24
2674 5339 9.591792 GAACAAATACTACCTCCGTAAACTAAT 57.408 33.333 0.00 0.00 0.00 1.73
2682 5347 8.791675 ACTACCTCCGTAAACTAATATAAGAGC 58.208 37.037 0.00 0.00 0.00 4.09
2683 5348 6.675987 ACCTCCGTAAACTAATATAAGAGCG 58.324 40.000 0.00 0.00 0.00 5.03
2684 5349 6.264067 ACCTCCGTAAACTAATATAAGAGCGT 59.736 38.462 0.00 0.00 0.00 5.07
2685 5350 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2686 5351 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2687 5352 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2688 5353 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2689 5354 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2736 5401 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2738 5403 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
3161 6941 6.053632 TCCATTAGACATGCTTTCTTCTGA 57.946 37.500 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.020720 GCGAGACAGAAGGATCTCTCA 58.979 52.381 7.83 0.00 39.43 3.27
38 39 2.552743 CGAGAGACGCATGGAAGGTATA 59.447 50.000 0.00 0.00 34.51 1.47
42 43 1.809869 TCGAGAGACGCATGGAAGG 59.190 57.895 0.00 0.00 42.26 3.46
68 69 4.705507 AGTGTATTCTTCTTCCAGACGCTA 59.294 41.667 0.00 0.00 0.00 4.26
74 75 4.469945 TGGGGTAGTGTATTCTTCTTCCAG 59.530 45.833 0.00 0.00 0.00 3.86
75 76 4.431378 TGGGGTAGTGTATTCTTCTTCCA 58.569 43.478 0.00 0.00 0.00 3.53
102 103 2.227194 CCAAACGAGCCCTACAAAGTT 58.773 47.619 0.00 0.00 0.00 2.66
140 141 6.582636 TCATGTACAACTCCTTATGCCTAAG 58.417 40.000 0.00 2.01 35.15 2.18
198 199 2.187163 GTAGGGACGAGGCAAGGC 59.813 66.667 0.00 0.00 0.00 4.35
289 290 8.803201 AACAAGGAATTCGAGAAGAAAATTTC 57.197 30.769 0.00 0.00 42.91 2.17
297 298 7.545362 ACATATGAACAAGGAATTCGAGAAG 57.455 36.000 10.38 0.00 0.00 2.85
300 301 8.970691 AAAAACATATGAACAAGGAATTCGAG 57.029 30.769 10.38 0.00 0.00 4.04
302 303 7.537306 ACGAAAAACATATGAACAAGGAATTCG 59.463 33.333 10.38 12.77 39.24 3.34
303 304 8.742554 ACGAAAAACATATGAACAAGGAATTC 57.257 30.769 10.38 0.00 0.00 2.17
304 305 9.620660 GTACGAAAAACATATGAACAAGGAATT 57.379 29.630 10.38 0.00 0.00 2.17
316 319 9.537192 TCAAGGATATTCGTACGAAAAACATAT 57.463 29.630 32.12 23.60 37.69 1.78
340 343 3.536956 CCGTCACTAAGGCCTTATTCA 57.463 47.619 25.37 3.66 0.00 2.57
397 400 0.893727 GACGTTGGGCCCATCAACTT 60.894 55.000 29.23 15.26 41.47 2.66
464 514 1.705002 ATCGCGGGGATTGGGATGAA 61.705 55.000 6.13 0.00 37.58 2.57
556 611 4.200283 GAGACGGCGCTGGAGGAG 62.200 72.222 22.44 0.00 0.00 3.69
582 637 4.778415 CGAGTGGCTGGACGACGG 62.778 72.222 0.00 0.00 31.20 4.79
703 800 2.488771 TAGCCCTGGAACGACGAGGA 62.489 60.000 0.00 0.00 45.50 3.71
824 949 2.032681 GTTTGGAGGCGCTGGACT 59.967 61.111 7.64 0.00 0.00 3.85
845 970 2.106511 TGGAAGCTGCTACCTTTTCTGT 59.893 45.455 0.90 0.00 0.00 3.41
848 973 2.504367 TGTGGAAGCTGCTACCTTTTC 58.496 47.619 5.63 0.00 0.00 2.29
869 994 1.565156 AATCGTGCGCGCTGAAGAAA 61.565 50.000 33.29 6.82 38.14 2.52
893 1018 3.135056 GAACCCGAGTCGATCCCCG 62.135 68.421 15.64 0.00 40.25 5.73
987 1133 2.544694 CGTCTCCATCGATCTTCCTTGG 60.545 54.545 0.00 0.00 0.00 3.61
989 1135 1.067821 GCGTCTCCATCGATCTTCCTT 59.932 52.381 0.00 0.00 0.00 3.36
1110 1259 2.939261 GCGGAGGAAAGACGGGTCA 61.939 63.158 1.17 0.00 0.00 4.02
1267 1437 1.374190 GCTGATCAGGGATGGCGAT 59.626 57.895 23.89 0.00 0.00 4.58
1499 1678 4.323477 CCCCTCGCCGTTTGGTCA 62.323 66.667 0.00 0.00 37.67 4.02
1979 2200 0.606604 GCCAACCGTACTCTCCTTGA 59.393 55.000 0.00 0.00 0.00 3.02
1984 2205 1.218316 CCAGGCCAACCGTACTCTC 59.782 63.158 5.01 0.00 42.76 3.20
1995 2216 4.972733 ACGCATTGCACCAGGCCA 62.973 61.111 5.01 0.00 43.89 5.36
2066 3818 5.520288 CCAGTTTGGAGATCTACAATGTACG 59.480 44.000 21.14 11.86 40.96 3.67
2386 5051 9.555411 ACTAACCCAAAGATAATTAACCCAAAT 57.445 29.630 0.00 0.00 0.00 2.32
2387 5052 8.959676 ACTAACCCAAAGATAATTAACCCAAA 57.040 30.769 0.00 0.00 0.00 3.28
2388 5053 8.808092 CAACTAACCCAAAGATAATTAACCCAA 58.192 33.333 0.00 0.00 0.00 4.12
2389 5054 7.951245 ACAACTAACCCAAAGATAATTAACCCA 59.049 33.333 0.00 0.00 0.00 4.51
2390 5055 8.357290 ACAACTAACCCAAAGATAATTAACCC 57.643 34.615 0.00 0.00 0.00 4.11
2396 5061 9.975218 ACTCATAACAACTAACCCAAAGATAAT 57.025 29.630 0.00 0.00 0.00 1.28
2397 5062 9.444600 GACTCATAACAACTAACCCAAAGATAA 57.555 33.333 0.00 0.00 0.00 1.75
2398 5063 8.822805 AGACTCATAACAACTAACCCAAAGATA 58.177 33.333 0.00 0.00 0.00 1.98
2399 5064 7.607991 CAGACTCATAACAACTAACCCAAAGAT 59.392 37.037 0.00 0.00 0.00 2.40
2400 5065 6.934645 CAGACTCATAACAACTAACCCAAAGA 59.065 38.462 0.00 0.00 0.00 2.52
2401 5066 6.149474 CCAGACTCATAACAACTAACCCAAAG 59.851 42.308 0.00 0.00 0.00 2.77
2402 5067 6.001460 CCAGACTCATAACAACTAACCCAAA 58.999 40.000 0.00 0.00 0.00 3.28
2403 5068 5.308497 TCCAGACTCATAACAACTAACCCAA 59.692 40.000 0.00 0.00 0.00 4.12
2404 5069 4.841813 TCCAGACTCATAACAACTAACCCA 59.158 41.667 0.00 0.00 0.00 4.51
2405 5070 5.416271 TCCAGACTCATAACAACTAACCC 57.584 43.478 0.00 0.00 0.00 4.11
2406 5071 6.640518 TGATCCAGACTCATAACAACTAACC 58.359 40.000 0.00 0.00 0.00 2.85
2407 5072 7.981789 TCATGATCCAGACTCATAACAACTAAC 59.018 37.037 0.00 0.00 32.18 2.34
2408 5073 8.078060 TCATGATCCAGACTCATAACAACTAA 57.922 34.615 0.00 0.00 32.18 2.24
2409 5074 7.660030 TCATGATCCAGACTCATAACAACTA 57.340 36.000 0.00 0.00 32.18 2.24
2410 5075 6.550938 TCATGATCCAGACTCATAACAACT 57.449 37.500 0.00 0.00 32.18 3.16
2411 5076 7.044181 TCTTCATGATCCAGACTCATAACAAC 58.956 38.462 0.00 0.00 32.18 3.32
2412 5077 7.186570 TCTTCATGATCCAGACTCATAACAA 57.813 36.000 0.00 0.00 32.18 2.83
2413 5078 6.684865 GCTCTTCATGATCCAGACTCATAACA 60.685 42.308 0.00 0.00 32.18 2.41
2414 5079 5.695816 GCTCTTCATGATCCAGACTCATAAC 59.304 44.000 0.00 0.00 32.18 1.89
2415 5080 5.601729 AGCTCTTCATGATCCAGACTCATAA 59.398 40.000 0.00 0.00 32.18 1.90
2416 5081 5.146298 AGCTCTTCATGATCCAGACTCATA 58.854 41.667 0.00 0.00 32.18 2.15
2417 5082 3.968649 AGCTCTTCATGATCCAGACTCAT 59.031 43.478 0.00 0.00 33.65 2.90
2418 5083 3.372897 AGCTCTTCATGATCCAGACTCA 58.627 45.455 0.00 0.00 0.00 3.41
2419 5084 4.556501 CGTAGCTCTTCATGATCCAGACTC 60.557 50.000 0.00 0.00 0.00 3.36
2420 5085 3.317711 CGTAGCTCTTCATGATCCAGACT 59.682 47.826 0.00 0.53 0.00 3.24
2421 5086 3.316588 TCGTAGCTCTTCATGATCCAGAC 59.683 47.826 0.00 0.00 0.00 3.51
2422 5087 3.555966 TCGTAGCTCTTCATGATCCAGA 58.444 45.455 0.00 0.00 0.00 3.86
2423 5088 3.567585 TCTCGTAGCTCTTCATGATCCAG 59.432 47.826 0.00 0.00 0.00 3.86
2424 5089 3.555966 TCTCGTAGCTCTTCATGATCCA 58.444 45.455 0.00 0.00 0.00 3.41
2425 5090 4.782019 ATCTCGTAGCTCTTCATGATCC 57.218 45.455 0.00 0.00 0.00 3.36
2426 5091 5.767269 TCAATCTCGTAGCTCTTCATGATC 58.233 41.667 0.00 0.00 0.00 2.92
2427 5092 5.781210 TCAATCTCGTAGCTCTTCATGAT 57.219 39.130 0.00 0.00 0.00 2.45
2428 5093 5.300286 TGATCAATCTCGTAGCTCTTCATGA 59.700 40.000 0.00 0.00 0.00 3.07
2429 5094 5.527033 TGATCAATCTCGTAGCTCTTCATG 58.473 41.667 0.00 0.00 0.00 3.07
2430 5095 5.781210 TGATCAATCTCGTAGCTCTTCAT 57.219 39.130 0.00 0.00 0.00 2.57
2431 5096 5.781210 ATGATCAATCTCGTAGCTCTTCA 57.219 39.130 0.00 0.00 0.00 3.02
2432 5097 6.801377 CACTATGATCAATCTCGTAGCTCTTC 59.199 42.308 0.00 0.00 37.99 2.87
2433 5098 6.676950 CACTATGATCAATCTCGTAGCTCTT 58.323 40.000 0.00 0.00 37.99 2.85
2434 5099 5.335583 GCACTATGATCAATCTCGTAGCTCT 60.336 44.000 0.00 0.00 37.99 4.09
2435 5100 4.856487 GCACTATGATCAATCTCGTAGCTC 59.144 45.833 0.00 0.00 37.99 4.09
2436 5101 4.279420 TGCACTATGATCAATCTCGTAGCT 59.721 41.667 0.00 0.00 37.99 3.32
2454 5119 0.320771 CCTTGCCTAGACGTTGCACT 60.321 55.000 0.00 0.00 34.16 4.40
2460 5125 1.629043 TCTGTTCCTTGCCTAGACGT 58.371 50.000 0.00 0.00 0.00 4.34
2465 5130 2.224744 TGCAACATCTGTTCCTTGCCTA 60.225 45.455 0.00 0.00 35.83 3.93
2489 5154 3.054139 TGATCTGATTTAGCAGGGCAACT 60.054 43.478 0.00 0.00 36.55 3.16
2528 5193 6.150976 CCACTAGACCAAATTATTCTGCACAA 59.849 38.462 0.00 0.00 0.00 3.33
2572 5237 8.821894 GCACATGTTAAAACTGGAAATAAAACA 58.178 29.630 0.00 0.00 0.00 2.83
2573 5238 8.279800 GGCACATGTTAAAACTGGAAATAAAAC 58.720 33.333 0.00 0.00 0.00 2.43
2581 5246 3.561143 ACAGGCACATGTTAAAACTGGA 58.439 40.909 0.00 0.00 0.00 3.86
2582 5247 4.320608 AACAGGCACATGTTAAAACTGG 57.679 40.909 0.00 0.00 41.53 4.00
2657 5322 7.961827 CGCTCTTATATTAGTTTACGGAGGTAG 59.038 40.741 0.00 0.00 0.00 3.18
2658 5323 7.445402 ACGCTCTTATATTAGTTTACGGAGGTA 59.555 37.037 0.00 0.00 0.00 3.08
2659 5324 6.264067 ACGCTCTTATATTAGTTTACGGAGGT 59.736 38.462 0.00 0.00 0.00 3.85
2660 5325 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2661 5326 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2662 5327 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2663 5328 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2710 5375 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2712 5377 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2720 5385 9.710818 TCATTACTACTCCCTCTGTAAACTAAT 57.289 33.333 0.00 0.00 0.00 1.73
2721 5386 9.186837 CTCATTACTACTCCCTCTGTAAACTAA 57.813 37.037 0.00 0.00 0.00 2.24
2722 5387 7.778853 CCTCATTACTACTCCCTCTGTAAACTA 59.221 40.741 0.00 0.00 0.00 2.24
2723 5388 6.608002 CCTCATTACTACTCCCTCTGTAAACT 59.392 42.308 0.00 0.00 0.00 2.66
2724 5389 6.380560 ACCTCATTACTACTCCCTCTGTAAAC 59.619 42.308 0.00 0.00 0.00 2.01
2725 5390 6.380274 CACCTCATTACTACTCCCTCTGTAAA 59.620 42.308 0.00 0.00 0.00 2.01
2726 5391 5.892119 CACCTCATTACTACTCCCTCTGTAA 59.108 44.000 0.00 0.00 0.00 2.41
2727 5392 5.446860 CACCTCATTACTACTCCCTCTGTA 58.553 45.833 0.00 0.00 0.00 2.74
2728 5393 4.282496 CACCTCATTACTACTCCCTCTGT 58.718 47.826 0.00 0.00 0.00 3.41
2729 5394 3.068873 GCACCTCATTACTACTCCCTCTG 59.931 52.174 0.00 0.00 0.00 3.35
2730 5395 3.052490 AGCACCTCATTACTACTCCCTCT 60.052 47.826 0.00 0.00 0.00 3.69
2731 5396 3.068873 CAGCACCTCATTACTACTCCCTC 59.931 52.174 0.00 0.00 0.00 4.30
2732 5397 3.034635 CAGCACCTCATTACTACTCCCT 58.965 50.000 0.00 0.00 0.00 4.20
2733 5398 3.031736 TCAGCACCTCATTACTACTCCC 58.968 50.000 0.00 0.00 0.00 4.30
2734 5399 3.702045 ACTCAGCACCTCATTACTACTCC 59.298 47.826 0.00 0.00 0.00 3.85
2735 5400 4.993029 ACTCAGCACCTCATTACTACTC 57.007 45.455 0.00 0.00 0.00 2.59
2736 5401 5.511363 ACTACTCAGCACCTCATTACTACT 58.489 41.667 0.00 0.00 0.00 2.57
2737 5402 5.504337 CGACTACTCAGCACCTCATTACTAC 60.504 48.000 0.00 0.00 0.00 2.73
2738 5403 4.575236 CGACTACTCAGCACCTCATTACTA 59.425 45.833 0.00 0.00 0.00 1.82
2739 5404 3.378742 CGACTACTCAGCACCTCATTACT 59.621 47.826 0.00 0.00 0.00 2.24
2998 6626 4.502431 CCCGCCAACCTGTTAAGAATTTTT 60.502 41.667 0.00 0.00 0.00 1.94
3161 6941 3.812053 CAGTACAAGTTTCTTCTGCAGCT 59.188 43.478 9.47 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.