Multiple sequence alignment - TraesCS5A01G133000

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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 TraesCS5A01G133000 chr5A 100.000 5369 0 0 1 5369 299602571 299597203 0.000000e+00 9915.0
1 TraesCS5A01G133000 chr5A 100.000 81 0 0 2313 2393 299600215 299600135 3.350000e-32 150.0
2 TraesCS5A01G133000 chr5A 100.000 81 0 0 2357 2437 299600259 299600179 3.350000e-32 150.0
3 TraesCS5A01G133000 chr5A 81.250 128 19 5 5014 5140 603776988 603776865 1.230000e-16 99.0
4 TraesCS5A01G133000 chr5A 100.000 37 0 0 2313 2349 299600171 299600135 9.650000e-08 69.4
5 TraesCS5A01G133000 chr5A 100.000 37 0 0 2401 2437 299600259 299600223 9.650000e-08 69.4
6 TraesCS5A01G133000 chr5D 94.780 2414 96 17 1 2393 224951716 224949312 0.000000e+00 3733.0
7 TraesCS5A01G133000 chr5D 95.635 1810 50 10 3117 4910 224948450 224946654 0.000000e+00 2878.0
8 TraesCS5A01G133000 chr5D 90.593 776 36 11 2357 3116 224949392 224948638 0.000000e+00 994.0
9 TraesCS5A01G133000 chr5D 94.054 370 18 4 5002 5369 224946485 224946118 4.700000e-155 558.0
10 TraesCS5A01G133000 chr5D 95.420 131 6 0 4904 5034 224946615 224946485 5.450000e-50 209.0
11 TraesCS5A01G133000 chr5B 94.219 1851 64 15 552 2393 246136556 246138372 0.000000e+00 2785.0
12 TraesCS5A01G133000 chr5B 95.663 1176 25 8 3285 4446 246139716 246140879 0.000000e+00 1866.0
13 TraesCS5A01G133000 chr5B 96.879 769 21 2 2351 3116 246138286 246139054 0.000000e+00 1284.0
14 TraesCS5A01G133000 chr5B 94.000 550 30 3 10 558 246135851 246136398 0.000000e+00 830.0
15 TraesCS5A01G133000 chr5B 96.190 420 9 2 4492 4910 246140873 246141286 0.000000e+00 680.0
16 TraesCS5A01G133000 chr5B 95.918 343 9 4 4904 5245 246141324 246141662 7.860000e-153 551.0
17 TraesCS5A01G133000 chr5B 98.883 179 1 1 3115 3293 246139253 246139430 8.680000e-83 318.0
18 TraesCS5A01G133000 chr5B 93.023 43 3 0 2307 2349 246138330 246138372 4.490000e-06 63.9
19 TraesCS5A01G133000 chr3D 83.921 454 45 15 5 442 567901958 567901517 5.010000e-110 409.0
20 TraesCS5A01G133000 chr7A 88.545 323 33 4 5 324 642867071 642867392 6.520000e-104 388.0
21 TraesCS5A01G133000 chr1A 79.570 186 23 11 344 514 17440863 17440678 9.450000e-23 119.0
22 TraesCS5A01G133000 chr1A 78.378 185 20 11 346 513 510293868 510293687 9.510000e-18 102.0
23 TraesCS5A01G133000 chr7D 94.521 73 4 0 870 942 193192330 193192258 4.400000e-21 113.0
24 TraesCS5A01G133000 chr3A 87.500 96 12 0 340 435 731429649 731429554 1.580000e-20 111.0
25 TraesCS5A01G133000 chr2D 87.629 97 11 1 346 442 339700438 339700343 1.580000e-20 111.0
26 TraesCS5A01G133000 chr2A 86.275 102 13 1 332 433 365353021 365352921 5.690000e-20 110.0
27 TraesCS5A01G133000 chr4D 97.959 49 1 0 894 942 107698818 107698866 9.580000e-13 86.1


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 TraesCS5A01G133000 chr5A 299597203 299602571 5368 True 2070.7600 9915 100.000000 1 5369 5 chr5A.!!$R2 5368
1 TraesCS5A01G133000 chr5D 224946118 224951716 5598 True 1674.4000 3733 94.096400 1 5369 5 chr5D.!!$R1 5368
2 TraesCS5A01G133000 chr5B 246135851 246141662 5811 False 1047.2375 2785 95.596875 10 5245 8 chr5B.!!$F1 5235

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
707 881 0.100503 GAATTTCGAATGGGCCGTGG 59.899 55.000 0.0 0.0 0.0 4.94 F
1302 1489 0.321564 TCGTGCTGTTTGGAGATGGG 60.322 55.000 0.0 0.0 0.0 4.00 F
2063 2264 0.394352 CCAAGAAGGTCCCAATCCCG 60.394 60.000 0.0 0.0 0.0 5.14 F
2683 2888 1.460497 TCCACCTGTGTACTGCCCA 60.460 57.895 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 1890 0.035820 CAGGCTTAAACCCTACGCCA 60.036 55.000 0.00 0.00 43.07 5.69 R
2118 2319 1.195448 GTGTCGTGCACCAGAAATCAG 59.805 52.381 12.15 0.00 42.10 2.90 R
3632 4346 1.202521 TGGTGCTCATAGGTGTATGCG 60.203 52.381 0.00 0.00 36.68 4.73 R
4456 5189 0.440371 GTGCTACGTGAAGCTTCAGC 59.560 55.000 29.13 26.23 43.19 4.26 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
319 321 8.713737 TCATTTCTGTTAGAGATGATTGTCTG 57.286 34.615 7.67 0.00 39.86 3.51
324 326 8.354711 TCTGTTAGAGATGATTGTCTGTAACT 57.645 34.615 18.55 0.00 46.73 2.24
424 427 7.452562 AGATTGGTTGGCTAAAATCACAATTT 58.547 30.769 9.17 0.00 36.64 1.82
426 429 7.872113 TTGGTTGGCTAAAATCACAATTTTT 57.128 28.000 1.85 0.00 41.27 1.94
445 448 9.439500 CAATTTTTCTTCATGTACATTCCCATT 57.561 29.630 5.37 0.00 0.00 3.16
449 452 6.575244 TCTTCATGTACATTCCCATTACCT 57.425 37.500 5.37 0.00 0.00 3.08
486 490 1.002792 GAGCGTGTGTTTTTCTCCCAC 60.003 52.381 0.00 0.00 0.00 4.61
528 532 4.592942 TGCTAGTAAACCTAACGAGAGGA 58.407 43.478 13.27 0.00 39.15 3.71
637 808 4.825085 TCAAACGGGTTAAGAATCAAAGCT 59.175 37.500 0.00 0.00 0.00 3.74
669 843 2.202349 GCTTGATTGGCACGTCGC 60.202 61.111 0.00 0.00 41.28 5.19
707 881 0.100503 GAATTTCGAATGGGCCGTGG 59.899 55.000 0.00 0.00 0.00 4.94
734 908 2.853290 GCTGGCAGCAGCAACAAGT 61.853 57.895 33.33 0.00 46.73 3.16
737 911 1.321805 TGGCAGCAGCAACAAGTGTT 61.322 50.000 2.65 0.00 44.61 3.32
773 959 1.352056 GCGCGAGGCCTTCAAATAC 59.648 57.895 12.10 0.00 34.80 1.89
965 1152 2.604686 TCCCAGTGCTCGCTCCTT 60.605 61.111 0.00 0.00 0.00 3.36
978 1165 1.134965 CGCTCCTTACACCTTCTCCTG 60.135 57.143 0.00 0.00 0.00 3.86
1117 1304 4.125695 GTACGTTCGCCGCCTCCT 62.126 66.667 0.00 0.00 41.42 3.69
1139 1326 1.668101 CCCTCTCCTCTCGAAACCCG 61.668 65.000 0.00 0.00 40.25 5.28
1302 1489 0.321564 TCGTGCTGTTTGGAGATGGG 60.322 55.000 0.00 0.00 0.00 4.00
1386 1573 1.061887 GTGTGCTCGTGTTGCGTTT 59.938 52.632 0.00 0.00 42.13 3.60
1415 1602 2.691409 TTCTCCCCTATTTCGTGCAG 57.309 50.000 0.00 0.00 0.00 4.41
1444 1632 1.117150 TAACTAGCGCCCTTGGTAGG 58.883 55.000 2.29 0.00 42.73 3.18
1496 1684 4.324267 CCACTTGATTTCTCTTTACCGGT 58.676 43.478 13.98 13.98 0.00 5.28
1626 1814 5.232414 GTCTGTAGAATCCTTTCGAATTCGG 59.768 44.000 26.47 11.39 40.29 4.30
1627 1815 3.869246 TGTAGAATCCTTTCGAATTCGGC 59.131 43.478 26.47 7.24 40.29 5.54
1702 1890 1.814211 CGCGTTTTCGTCCACTTCGT 61.814 55.000 0.00 0.00 46.03 3.85
1917 2106 4.339247 CCATGAATTTGAATCCTAAGCCGT 59.661 41.667 0.00 0.00 0.00 5.68
1918 2107 5.530915 CCATGAATTTGAATCCTAAGCCGTA 59.469 40.000 0.00 0.00 0.00 4.02
1919 2108 6.039270 CCATGAATTTGAATCCTAAGCCGTAA 59.961 38.462 0.00 0.00 0.00 3.18
1920 2109 6.431198 TGAATTTGAATCCTAAGCCGTAAC 57.569 37.500 0.00 0.00 0.00 2.50
1921 2110 5.355910 TGAATTTGAATCCTAAGCCGTAACC 59.644 40.000 0.00 0.00 0.00 2.85
1922 2111 4.563140 TTTGAATCCTAAGCCGTAACCT 57.437 40.909 0.00 0.00 0.00 3.50
1923 2112 4.563140 TTGAATCCTAAGCCGTAACCTT 57.437 40.909 0.00 0.00 0.00 3.50
1924 2113 4.133013 TGAATCCTAAGCCGTAACCTTC 57.867 45.455 0.00 0.00 0.00 3.46
1925 2114 3.118519 TGAATCCTAAGCCGTAACCTTCC 60.119 47.826 0.00 0.00 0.00 3.46
1926 2115 2.242882 TCCTAAGCCGTAACCTTCCT 57.757 50.000 0.00 0.00 0.00 3.36
1927 2116 2.543635 TCCTAAGCCGTAACCTTCCTT 58.456 47.619 0.00 0.00 0.00 3.36
1928 2117 2.908351 TCCTAAGCCGTAACCTTCCTTT 59.092 45.455 0.00 0.00 0.00 3.11
1942 2143 4.514066 ACCTTCCTTTTAACGCTGTAACTG 59.486 41.667 0.00 0.00 0.00 3.16
2063 2264 0.394352 CCAAGAAGGTCCCAATCCCG 60.394 60.000 0.00 0.00 0.00 5.14
2071 2272 1.612146 TCCCAATCCCGTCAGAGCA 60.612 57.895 0.00 0.00 0.00 4.26
2118 2319 3.641437 TTTGTGGTTGCATACTGAAGC 57.359 42.857 0.00 0.00 0.00 3.86
2201 2402 7.362662 ACACATGATTGATGTTGTTTCAGTAC 58.637 34.615 0.00 0.00 43.20 2.73
2334 2535 7.315142 TCATCTTTGCATTGATTCTGGTTTAC 58.685 34.615 0.00 0.00 0.00 2.01
2375 2576 6.600882 ATTCTCTTTGCATTGATTCTGGTT 57.399 33.333 0.00 0.00 0.00 3.67
2376 2577 6.409524 TTCTCTTTGCATTGATTCTGGTTT 57.590 33.333 0.00 0.00 0.00 3.27
2377 2578 7.523293 TTCTCTTTGCATTGATTCTGGTTTA 57.477 32.000 0.00 0.00 0.00 2.01
2378 2579 6.913170 TCTCTTTGCATTGATTCTGGTTTAC 58.087 36.000 0.00 0.00 0.00 2.01
2379 2580 6.489700 TCTCTTTGCATTGATTCTGGTTTACA 59.510 34.615 0.00 0.00 0.00 2.41
2380 2581 7.014134 TCTCTTTGCATTGATTCTGGTTTACAA 59.986 33.333 0.00 0.00 0.00 2.41
2381 2582 6.922957 TCTTTGCATTGATTCTGGTTTACAAC 59.077 34.615 0.00 0.00 0.00 3.32
2382 2583 6.403866 TTGCATTGATTCTGGTTTACAACT 57.596 33.333 0.00 0.00 0.00 3.16
2383 2584 6.403866 TGCATTGATTCTGGTTTACAACTT 57.596 33.333 0.00 0.00 0.00 2.66
2384 2585 6.446318 TGCATTGATTCTGGTTTACAACTTC 58.554 36.000 0.00 0.00 0.00 3.01
2385 2586 6.265196 TGCATTGATTCTGGTTTACAACTTCT 59.735 34.615 0.00 0.00 0.00 2.85
2386 2587 6.583806 GCATTGATTCTGGTTTACAACTTCTG 59.416 38.462 0.00 0.00 0.00 3.02
2387 2588 7.651808 CATTGATTCTGGTTTACAACTTCTGT 58.348 34.615 0.00 0.00 42.47 3.41
2388 2589 6.618287 TGATTCTGGTTTACAACTTCTGTG 57.382 37.500 0.00 0.00 39.20 3.66
2389 2590 4.893424 TTCTGGTTTACAACTTCTGTGC 57.107 40.909 0.00 0.00 39.20 4.57
2390 2591 3.211045 TCTGGTTTACAACTTCTGTGCC 58.789 45.455 0.00 0.00 39.20 5.01
2391 2592 2.948979 CTGGTTTACAACTTCTGTGCCA 59.051 45.455 0.00 0.00 39.20 4.92
2392 2593 3.561143 TGGTTTACAACTTCTGTGCCAT 58.439 40.909 0.00 0.00 39.20 4.40
2393 2594 4.720046 TGGTTTACAACTTCTGTGCCATA 58.280 39.130 0.00 0.00 39.20 2.74
2394 2595 5.321102 TGGTTTACAACTTCTGTGCCATAT 58.679 37.500 0.00 0.00 39.20 1.78
2395 2596 5.772672 TGGTTTACAACTTCTGTGCCATATT 59.227 36.000 0.00 0.00 39.20 1.28
2396 2597 6.943146 TGGTTTACAACTTCTGTGCCATATTA 59.057 34.615 0.00 0.00 39.20 0.98
2397 2598 7.613801 TGGTTTACAACTTCTGTGCCATATTAT 59.386 33.333 0.00 0.00 39.20 1.28
2398 2599 8.466798 GGTTTACAACTTCTGTGCCATATTATT 58.533 33.333 0.00 0.00 39.20 1.40
2399 2600 9.503427 GTTTACAACTTCTGTGCCATATTATTC 57.497 33.333 0.00 0.00 39.20 1.75
2400 2601 9.461312 TTTACAACTTCTGTGCCATATTATTCT 57.539 29.630 0.00 0.00 39.20 2.40
2401 2602 7.559590 ACAACTTCTGTGCCATATTATTCTC 57.440 36.000 0.00 0.00 36.69 2.87
2402 2603 7.341805 ACAACTTCTGTGCCATATTATTCTCT 58.658 34.615 0.00 0.00 36.69 3.10
2403 2604 7.831193 ACAACTTCTGTGCCATATTATTCTCTT 59.169 33.333 0.00 0.00 36.69 2.85
2404 2605 8.680903 CAACTTCTGTGCCATATTATTCTCTTT 58.319 33.333 0.00 0.00 0.00 2.52
2405 2606 8.218338 ACTTCTGTGCCATATTATTCTCTTTG 57.782 34.615 0.00 0.00 0.00 2.77
2406 2607 6.624352 TCTGTGCCATATTATTCTCTTTGC 57.376 37.500 0.00 0.00 0.00 3.68
2407 2608 6.121590 TCTGTGCCATATTATTCTCTTTGCA 58.878 36.000 0.00 0.00 0.00 4.08
2408 2609 6.774170 TCTGTGCCATATTATTCTCTTTGCAT 59.226 34.615 0.00 0.00 0.00 3.96
2409 2610 7.286087 TCTGTGCCATATTATTCTCTTTGCATT 59.714 33.333 0.00 0.00 0.00 3.56
2410 2611 7.204604 TGTGCCATATTATTCTCTTTGCATTG 58.795 34.615 0.00 0.00 0.00 2.82
2411 2612 7.068470 TGTGCCATATTATTCTCTTTGCATTGA 59.932 33.333 0.00 0.00 0.00 2.57
2412 2613 8.086522 GTGCCATATTATTCTCTTTGCATTGAT 58.913 33.333 0.00 0.00 0.00 2.57
2413 2614 8.644216 TGCCATATTATTCTCTTTGCATTGATT 58.356 29.630 0.00 0.00 0.00 2.57
2414 2615 9.136952 GCCATATTATTCTCTTTGCATTGATTC 57.863 33.333 0.00 0.00 0.00 2.52
2418 2619 7.707624 TTATTCTCTTTGCATTGATTCTGGT 57.292 32.000 0.00 0.00 0.00 4.00
2564 2765 3.512033 AAGCTACTGATGAAGGACGAC 57.488 47.619 0.00 0.00 0.00 4.34
2683 2888 1.460497 TCCACCTGTGTACTGCCCA 60.460 57.895 0.00 0.00 0.00 5.36
2702 2907 6.410540 TGCCCAGTTGTTTGATTTACTTTTT 58.589 32.000 0.00 0.00 0.00 1.94
2786 2991 2.544267 GCTTGGAGGTAACATATGTCGC 59.456 50.000 9.23 5.00 41.41 5.19
2829 3034 8.677148 TTATTTCTGATGTTATGCTCTAACCC 57.323 34.615 7.12 1.90 0.00 4.11
2916 3121 3.071892 AGTTCCGGTCAGTAAATGTTCCA 59.928 43.478 0.00 0.00 0.00 3.53
2965 3175 1.475213 GCAGGGAGCGCCTATTAGTTT 60.475 52.381 2.29 0.00 0.00 2.66
2998 3208 9.964303 TGTTATGTATGATTTGTGCCATATTTC 57.036 29.630 0.00 0.00 0.00 2.17
3011 3221 5.119279 GTGCCATATTTCGCAGTAGATGTAG 59.881 44.000 0.00 0.00 35.20 2.74
3059 3276 8.547967 TTTAGTTGGTAAACTCTGATAAGCTG 57.452 34.615 0.00 0.00 43.34 4.24
3107 3324 6.172136 AGTCTTCCAGAGGTATTGATGATG 57.828 41.667 0.00 0.00 0.00 3.07
3119 3531 6.657966 AGGTATTGATGATGGTGCATATTCAG 59.342 38.462 0.00 0.00 0.00 3.02
3234 3651 3.785887 AGGTCCATTTCCTGCCTTGTATA 59.214 43.478 0.00 0.00 33.62 1.47
3431 4143 9.642327 TTCAATGAATTCATTTACATTCCTGTG 57.358 29.630 27.30 14.48 43.48 3.66
3432 4144 7.760794 TCAATGAATTCATTTACATTCCTGTGC 59.239 33.333 27.30 0.00 43.48 4.57
3444 4156 5.730550 ACATTCCTGTGCTTATCGAAACTA 58.269 37.500 0.00 0.00 33.22 2.24
3454 4166 7.825270 TGTGCTTATCGAAACTATTCCCTTAAA 59.175 33.333 0.00 0.00 31.52 1.52
3632 4346 5.856986 TCTGTTTTAGATCATATACGCTCGC 59.143 40.000 0.00 0.00 0.00 5.03
3736 4450 3.725895 CGCATGACTTTGCTGACATGTAC 60.726 47.826 0.00 0.00 40.39 2.90
3738 4452 4.631377 GCATGACTTTGCTGACATGTACTA 59.369 41.667 0.00 0.00 40.39 1.82
3740 4454 6.510799 GCATGACTTTGCTGACATGTACTATC 60.511 42.308 0.00 0.00 40.39 2.08
4203 4921 2.915137 GACCCCAAAAAGCCGGCA 60.915 61.111 31.54 0.00 0.00 5.69
4255 4973 1.073125 TCCGGTTGATGCTGAGGAAAA 59.927 47.619 0.00 0.00 0.00 2.29
4438 5171 7.452880 TGCACAGCTTTATGATTTAGTTCTT 57.547 32.000 0.00 0.00 0.00 2.52
4456 5189 7.803279 AGTTCTTAGTTGTTAACCTCCTTTG 57.197 36.000 2.48 0.00 0.00 2.77
4484 5217 3.120338 GCTTCACGTAGCACAAATTAGCA 60.120 43.478 5.44 0.00 40.89 3.49
4486 5219 5.621197 TTCACGTAGCACAAATTAGCAAT 57.379 34.783 0.00 0.00 0.00 3.56
4601 5334 0.250513 AGGGCGCTTCCTGTCTTAAG 59.749 55.000 7.64 0.00 35.47 1.85
4708 5443 6.621394 ACCTCTATGCTGTTTATACCTCCTA 58.379 40.000 0.00 0.00 0.00 2.94
4731 5466 4.002906 TGGGTGTTCTGTAAGCTTGTAG 57.997 45.455 9.86 7.33 0.00 2.74
4732 5467 3.389983 TGGGTGTTCTGTAAGCTTGTAGT 59.610 43.478 9.86 0.00 0.00 2.73
4733 5468 4.589798 TGGGTGTTCTGTAAGCTTGTAGTA 59.410 41.667 9.86 0.00 0.00 1.82
4734 5469 5.169295 GGGTGTTCTGTAAGCTTGTAGTAG 58.831 45.833 9.86 0.30 0.00 2.57
4735 5470 5.279356 GGGTGTTCTGTAAGCTTGTAGTAGT 60.279 44.000 9.86 0.00 0.00 2.73
4736 5471 6.071728 GGGTGTTCTGTAAGCTTGTAGTAGTA 60.072 42.308 9.86 0.00 0.00 1.82
4755 5490 7.630082 AGTAGTAATGCCTTAAGGATTTGTGA 58.370 34.615 26.21 1.86 37.39 3.58
4844 5579 5.009610 GGTTAACATGTTCTTTGCTTCAGGA 59.990 40.000 15.85 0.00 0.00 3.86
4955 5735 6.302269 ACACAAAGTGATCTTCCATTCTCTT 58.698 36.000 3.88 0.00 36.96 2.85
4970 5750 9.658799 TTCCATTCTCTTTCTGTATGAGTAAAG 57.341 33.333 0.00 0.00 31.64 1.85
4979 5759 5.580998 TCTGTATGAGTAAAGGTGGACTCT 58.419 41.667 3.90 0.00 42.21 3.24
5010 5790 4.991056 TGCATGGATCGAGCTCTAAATAAC 59.009 41.667 12.85 0.99 0.00 1.89
5095 5907 9.733219 CATTTTGCAGTTTTTCCATGTTTTTAT 57.267 25.926 0.00 0.00 0.00 1.40
5139 5951 7.990314 GTGCCACAAATTACCCCATTTAATATT 59.010 33.333 0.00 0.00 0.00 1.28
5140 5952 9.213777 TGCCACAAATTACCCCATTTAATATTA 57.786 29.630 0.00 0.00 0.00 0.98
5196 6010 4.390909 CGTCGGCTGGTTTATTTTACTCTT 59.609 41.667 0.00 0.00 0.00 2.85
5197 6011 5.106830 CGTCGGCTGGTTTATTTTACTCTTT 60.107 40.000 0.00 0.00 0.00 2.52
5198 6012 6.084277 GTCGGCTGGTTTATTTTACTCTTTG 58.916 40.000 0.00 0.00 0.00 2.77
5199 6013 5.766174 TCGGCTGGTTTATTTTACTCTTTGT 59.234 36.000 0.00 0.00 0.00 2.83
5250 6064 2.248686 AGGGGATGAGTCCTACATGTCT 59.751 50.000 0.00 0.00 44.44 3.41
5309 6124 0.179029 AGTGTGTTTGGGGTTCGGAG 60.179 55.000 0.00 0.00 0.00 4.63
5311 6126 0.179040 TGTGTTTGGGGTTCGGAGAC 60.179 55.000 0.00 0.00 34.32 3.36
5348 6163 2.221299 AACCCTGCCTCCGCAACTA 61.221 57.895 0.00 0.00 46.66 2.24
5350 6165 1.745489 CCCTGCCTCCGCAACTAAC 60.745 63.158 0.00 0.00 46.66 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
333 336 7.392418 GGTTAGGTTAAAGACAATCACCTACT 58.608 38.462 0.00 0.00 39.37 2.57
424 427 7.410174 AGGTAATGGGAATGTACATGAAGAAA 58.590 34.615 9.63 0.00 0.00 2.52
426 429 6.575244 AGGTAATGGGAATGTACATGAAGA 57.425 37.500 9.63 0.00 0.00 2.87
445 448 5.690865 CTCCTAAACCCAATATGCAAGGTA 58.309 41.667 0.00 0.00 30.63 3.08
449 452 2.948979 CGCTCCTAAACCCAATATGCAA 59.051 45.455 0.00 0.00 0.00 4.08
637 808 6.349280 GCCAATCAAGCAATCTAGTAACAACA 60.349 38.462 0.00 0.00 0.00 3.33
707 881 1.375098 CTGCTGCCAGCTAAGCCTTC 61.375 60.000 18.96 0.28 42.97 3.46
731 905 2.576615 GAACTTGAGAGCCCAACACTT 58.423 47.619 0.00 0.00 0.00 3.16
734 908 1.072331 GAGGAACTTGAGAGCCCAACA 59.928 52.381 0.00 0.00 41.55 3.33
737 911 1.975327 CGAGGAACTTGAGAGCCCA 59.025 57.895 0.00 0.00 44.22 5.36
744 930 2.126463 CTCGCGCGAGGAACTTGA 60.126 61.111 43.86 16.54 44.22 3.02
892 1079 1.025647 AGGACGAGACCTGTACGAGC 61.026 60.000 0.00 0.00 39.01 5.03
965 1152 0.601558 GCGTCACAGGAGAAGGTGTA 59.398 55.000 0.00 0.00 36.43 2.90
1117 1304 1.341778 GGTTTCGAGAGGAGAGGGGTA 60.342 57.143 0.00 0.00 0.00 3.69
1199 1386 4.343323 CCCCCACATGCCGACACA 62.343 66.667 0.00 0.00 0.00 3.72
1208 1395 2.996330 GCAGGCCTAACCCCCACAT 61.996 63.158 3.98 0.00 40.58 3.21
1209 1396 3.657350 GCAGGCCTAACCCCCACA 61.657 66.667 3.98 0.00 40.58 4.17
1386 1573 6.492087 ACGAAATAGGGGAGAAAATCAAAACA 59.508 34.615 0.00 0.00 0.00 2.83
1415 1602 1.540580 GGCGCTAGTTAATCCCCAGAC 60.541 57.143 7.64 0.00 0.00 3.51
1626 1814 3.180584 CGCGATTGAACTGTATCTAGTGC 59.819 47.826 0.00 0.00 0.00 4.40
1627 1815 4.205181 CACGCGATTGAACTGTATCTAGTG 59.795 45.833 15.93 0.00 0.00 2.74
1702 1890 0.035820 CAGGCTTAAACCCTACGCCA 60.036 55.000 0.00 0.00 43.07 5.69
1711 1900 4.633565 CAGATGAGGAAGACAGGCTTAAAC 59.366 45.833 0.00 0.00 36.83 2.01
1825 2014 1.032794 AAGCGCGGATCACATCTAGA 58.967 50.000 8.83 0.00 0.00 2.43
1917 2106 6.203338 CAGTTACAGCGTTAAAAGGAAGGTTA 59.797 38.462 0.00 0.00 0.00 2.85
1918 2107 5.008316 CAGTTACAGCGTTAAAAGGAAGGTT 59.992 40.000 0.00 0.00 0.00 3.50
1919 2108 4.514066 CAGTTACAGCGTTAAAAGGAAGGT 59.486 41.667 0.00 0.00 0.00 3.50
1920 2109 4.753107 TCAGTTACAGCGTTAAAAGGAAGG 59.247 41.667 0.00 0.00 0.00 3.46
1921 2110 5.917541 TCAGTTACAGCGTTAAAAGGAAG 57.082 39.130 0.00 0.00 0.00 3.46
1922 2111 5.992829 TGATCAGTTACAGCGTTAAAAGGAA 59.007 36.000 0.00 0.00 0.00 3.36
1923 2112 5.407387 GTGATCAGTTACAGCGTTAAAAGGA 59.593 40.000 0.00 0.00 0.00 3.36
1924 2113 5.408604 AGTGATCAGTTACAGCGTTAAAAGG 59.591 40.000 0.00 0.00 0.00 3.11
1925 2114 6.467723 AGTGATCAGTTACAGCGTTAAAAG 57.532 37.500 0.00 0.00 0.00 2.27
1926 2115 5.118050 CGAGTGATCAGTTACAGCGTTAAAA 59.882 40.000 4.13 0.00 0.00 1.52
1927 2116 4.619760 CGAGTGATCAGTTACAGCGTTAAA 59.380 41.667 4.13 0.00 0.00 1.52
1928 2117 4.163552 CGAGTGATCAGTTACAGCGTTAA 58.836 43.478 4.13 0.00 0.00 2.01
1942 2143 3.026630 TCACTGTTTGGACGAGTGATC 57.973 47.619 0.00 0.00 38.16 2.92
2055 2256 2.620251 TTATGCTCTGACGGGATTGG 57.380 50.000 0.00 0.00 0.00 3.16
2056 2257 4.212847 CAGATTTATGCTCTGACGGGATTG 59.787 45.833 0.00 0.00 42.22 2.67
2063 2264 2.286067 GCGTGCAGATTTATGCTCTGAC 60.286 50.000 4.21 0.04 46.63 3.51
2071 2272 2.880890 GGGAGAATGCGTGCAGATTTAT 59.119 45.455 0.00 0.00 0.00 1.40
2118 2319 1.195448 GTGTCGTGCACCAGAAATCAG 59.805 52.381 12.15 0.00 42.10 2.90
2201 2402 5.533528 TCTGCAAGATGAATCCATACATTGG 59.466 40.000 0.00 0.00 42.69 3.16
2386 2587 7.428020 TCAATGCAAAGAGAATAATATGGCAC 58.572 34.615 0.00 0.00 0.00 5.01
2387 2588 7.585579 TCAATGCAAAGAGAATAATATGGCA 57.414 32.000 0.00 0.00 0.00 4.92
2388 2589 9.136952 GAATCAATGCAAAGAGAATAATATGGC 57.863 33.333 0.00 0.00 0.00 4.40
2392 2593 9.412460 ACCAGAATCAATGCAAAGAGAATAATA 57.588 29.630 0.00 0.00 0.00 0.98
2393 2594 8.302515 ACCAGAATCAATGCAAAGAGAATAAT 57.697 30.769 0.00 0.00 0.00 1.28
2394 2595 7.707624 ACCAGAATCAATGCAAAGAGAATAA 57.292 32.000 0.00 0.00 0.00 1.40
2395 2596 7.707624 AACCAGAATCAATGCAAAGAGAATA 57.292 32.000 0.00 0.00 0.00 1.75
2396 2597 6.600882 AACCAGAATCAATGCAAAGAGAAT 57.399 33.333 0.00 0.00 0.00 2.40
2397 2598 6.409524 AAACCAGAATCAATGCAAAGAGAA 57.590 33.333 0.00 0.00 0.00 2.87
2398 2599 6.489700 TGTAAACCAGAATCAATGCAAAGAGA 59.510 34.615 0.00 0.00 0.00 3.10
2399 2600 6.680810 TGTAAACCAGAATCAATGCAAAGAG 58.319 36.000 0.00 0.00 0.00 2.85
2400 2601 6.647334 TGTAAACCAGAATCAATGCAAAGA 57.353 33.333 0.00 0.00 0.00 2.52
2401 2602 7.109006 GTTGTAAACCAGAATCAATGCAAAG 57.891 36.000 0.00 0.00 42.21 2.77
2602 2803 8.798748 ATTACAGTAAGTTTAGCATAGTAGCG 57.201 34.615 0.00 0.00 40.15 4.26
2702 2907 5.647589 ACAGACTTTCGCTTCAATATACGA 58.352 37.500 0.00 0.00 0.00 3.43
2786 2991 8.404000 CAGAAATAATCAGAACAGAATCAAGGG 58.596 37.037 0.00 0.00 0.00 3.95
2965 3175 9.056005 GGCACAAATCATACATAACAGAGATAA 57.944 33.333 0.00 0.00 0.00 1.75
2998 3208 7.005062 ACTAAAAATTGCTACATCTACTGCG 57.995 36.000 0.00 0.00 0.00 5.18
3059 3276 2.030451 CAGCAGAAAAGGAGGTGAAAGC 60.030 50.000 0.00 0.00 32.85 3.51
3107 3324 5.183904 AGAAAGTTGGAACTGAATATGCACC 59.816 40.000 0.00 0.00 39.66 5.01
3119 3531 5.352643 TTTTAGCGCTAGAAAGTTGGAAC 57.647 39.130 17.24 0.00 0.00 3.62
3397 4109 9.905171 TGTAAATGAATTCATTGAACAAATCGA 57.095 25.926 29.48 16.14 45.06 3.59
3431 4143 7.713942 TCCTTTAAGGGAATAGTTTCGATAAGC 59.286 37.037 11.50 0.00 35.59 3.09
3432 4144 9.262358 CTCCTTTAAGGGAATAGTTTCGATAAG 57.738 37.037 11.50 0.00 35.59 1.73
3444 4156 5.687706 CGGCTGATAACTCCTTTAAGGGAAT 60.688 44.000 11.50 0.00 35.59 3.01
3454 4166 1.383248 AGGCCGGCTGATAACTCCT 60.383 57.895 28.56 8.48 0.00 3.69
3632 4346 1.202521 TGGTGCTCATAGGTGTATGCG 60.203 52.381 0.00 0.00 36.68 4.73
4255 4973 4.996434 ACGCTGCTCGCCTTTGCT 62.996 61.111 0.00 0.00 43.23 3.91
4438 5171 5.298989 TCAGCAAAGGAGGTTAACAACTA 57.701 39.130 8.10 0.00 0.00 2.24
4456 5189 0.440371 GTGCTACGTGAAGCTTCAGC 59.560 55.000 29.13 26.23 43.19 4.26
4484 5217 7.621428 AACAATTTCTCGACATCTGATCATT 57.379 32.000 0.00 0.00 0.00 2.57
4486 5219 6.092670 GGAAACAATTTCTCGACATCTGATCA 59.907 38.462 0.00 0.00 39.59 2.92
4601 5334 3.525537 TGCTAGCAGAACTATCAACAGC 58.474 45.455 14.93 0.00 0.00 4.40
4708 5443 3.832527 ACAAGCTTACAGAACACCCAAT 58.167 40.909 0.00 0.00 0.00 3.16
4731 5466 7.859325 TCACAAATCCTTAAGGCATTACTAC 57.141 36.000 17.32 0.00 34.44 2.73
4732 5467 8.271458 TCATCACAAATCCTTAAGGCATTACTA 58.729 33.333 17.32 0.00 34.44 1.82
4733 5468 7.118723 TCATCACAAATCCTTAAGGCATTACT 58.881 34.615 17.32 1.69 34.44 2.24
4734 5469 7.333528 TCATCACAAATCCTTAAGGCATTAC 57.666 36.000 17.32 0.00 34.44 1.89
4735 5470 6.547141 CCTCATCACAAATCCTTAAGGCATTA 59.453 38.462 17.32 0.00 34.44 1.90
4736 5471 5.361857 CCTCATCACAAATCCTTAAGGCATT 59.638 40.000 17.32 13.68 34.44 3.56
4755 5490 3.865745 CGCGAGATAACTTTTGTCCTCAT 59.134 43.478 0.00 0.00 0.00 2.90
4844 5579 6.126863 TCATATCCTTCAGTTTGGTGTCTT 57.873 37.500 0.00 0.00 0.00 3.01
4955 5735 6.017192 AGAGTCCACCTTTACTCATACAGAA 58.983 40.000 5.38 0.00 43.74 3.02
4970 5750 4.999950 CCATGCAAGATAATAGAGTCCACC 59.000 45.833 0.00 0.00 0.00 4.61
4979 5759 5.186603 AGAGCTCGATCCATGCAAGATAATA 59.813 40.000 8.37 0.00 0.00 0.98
5095 5907 4.202060 TGGCACAAGTTCGCTTAAAATTGA 60.202 37.500 9.49 0.00 36.57 2.57
5107 5919 3.554129 GGGGTAATTTGTGGCACAAGTTC 60.554 47.826 34.67 26.16 44.16 3.01
5250 6064 0.478072 TTCTTTCTCCCTTGCTGGCA 59.522 50.000 0.00 0.00 0.00 4.92
5296 6111 1.278127 GAGATGTCTCCGAACCCCAAA 59.722 52.381 0.00 0.00 37.02 3.28
5298 6113 0.252057 TGAGATGTCTCCGAACCCCA 60.252 55.000 7.51 0.00 42.20 4.96
5299 6114 1.123928 ATGAGATGTCTCCGAACCCC 58.876 55.000 7.51 0.00 42.20 4.95
5309 6124 4.046938 TGAGCGGACTAAATGAGATGTC 57.953 45.455 0.00 0.00 0.00 3.06
5311 6126 3.557595 GGTTGAGCGGACTAAATGAGATG 59.442 47.826 0.00 0.00 0.00 2.90
5350 6165 3.146783 TAGGGAACGCAATCAACCG 57.853 52.632 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.