Multiple sequence alignment - TraesCS6B01G336100

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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 TraesCS6B01G336100 chr6B 100.000 3153 0 0 1 3153 591263113 591266265 0.000000e+00 5823.0
1 TraesCS6B01G336100 chr6B 96.610 118 3 1 2372 2488 599445611 599445728 8.920000e-46 195.0
2 TraesCS6B01G336100 chr6B 93.130 131 7 2 2359 2487 120355524 120355394 1.150000e-44 191.0
3 TraesCS6B01G336100 chr6B 92.683 123 8 1 2363 2484 15270335 15270457 3.230000e-40 176.0
4 TraesCS6B01G336100 chr6B 96.364 55 2 0 2871 2925 128888163 128888109 1.200000e-14 91.6
5 TraesCS6B01G336100 chr6B 96.364 55 2 0 2871 2925 388030264 388030318 1.200000e-14 91.6
6 TraesCS6B01G336100 chr6B 82.353 119 6 1 2926 3029 22426226 22426344 4.330000e-14 89.8
7 TraesCS6B01G336100 chr6B 81.633 98 14 3 131 228 43513003 43513096 9.380000e-11 78.7
8 TraesCS6B01G336100 chr6A 94.822 2414 90 20 1 2386 541594640 541597046 0.000000e+00 3733.0
9 TraesCS6B01G336100 chr6A 87.443 661 57 7 2510 3153 541597690 541598341 0.000000e+00 737.0
10 TraesCS6B01G336100 chr6D 94.157 2088 73 19 326 2379 395389898 395391970 0.000000e+00 3134.0
11 TraesCS6B01G336100 chr6D 85.196 689 50 10 2482 3153 395391975 395392628 0.000000e+00 660.0
12 TraesCS6B01G336100 chr6D 89.589 365 24 8 1 352 395388744 395389107 4.800000e-123 451.0
13 TraesCS6B01G336100 chr6D 92.708 96 6 1 342 437 395389677 395389771 1.530000e-28 137.0
14 TraesCS6B01G336100 chr2D 98.230 113 2 0 2372 2484 154110787 154110675 6.900000e-47 198.0
15 TraesCS6B01G336100 chr2D 96.364 55 2 0 2871 2925 291671309 291671363 1.200000e-14 91.6
16 TraesCS6B01G336100 chr4D 95.798 119 4 1 2375 2492 474591214 474591332 1.150000e-44 191.0
17 TraesCS6B01G336100 chr5B 95.041 121 4 2 2374 2494 531200072 531199954 4.150000e-44 189.0
18 TraesCS6B01G336100 chr5B 93.694 111 7 0 2378 2488 573045811 573045701 1.950000e-37 167.0
19 TraesCS6B01G336100 chr1D 95.041 121 5 1 2371 2491 220211117 220210998 4.150000e-44 189.0
20 TraesCS6B01G336100 chr5A 93.701 127 5 3 2362 2486 656477436 656477311 1.490000e-43 187.0
21 TraesCS6B01G336100 chr5A 82.500 120 4 9 2926 3029 267864221 267864103 4.330000e-14 89.8
22 TraesCS6B01G336100 chr7D 93.548 124 7 1 2377 2499 370063026 370062903 1.930000e-42 183.0
23 TraesCS6B01G336100 chr7A 94.215 121 5 2 2364 2484 689307100 689307218 1.930000e-42 183.0
24 TraesCS6B01G336100 chr3A 97.222 108 3 0 2378 2485 114429550 114429443 1.930000e-42 183.0
25 TraesCS6B01G336100 chr4A 93.443 122 6 2 2364 2484 467233848 467233728 2.500000e-41 180.0
26 TraesCS6B01G336100 chr7B 92.623 122 7 2 2364 2484 708501813 708501933 1.160000e-39 174.0
27 TraesCS6B01G336100 chr7B 81.667 120 6 2 2926 3029 125509515 125509634 5.600000e-13 86.1
28 TraesCS6B01G336100 chr7B 95.556 45 2 0 2985 3029 487350464 487350508 4.360000e-09 73.1
29 TraesCS6B01G336100 chr1B 91.339 127 10 1 2359 2484 533752014 533752140 4.180000e-39 172.0
30 TraesCS6B01G336100 chr1B 96.364 55 2 0 2871 2925 49783100 49783046 1.200000e-14 91.6
31 TraesCS6B01G336100 chr1B 96.364 55 2 0 2871 2925 49819667 49819721 1.200000e-14 91.6
32 TraesCS6B01G336100 chr4B 98.182 55 1 0 2871 2925 495535955 495535901 2.590000e-16 97.1
33 TraesCS6B01G336100 chr4B 96.364 55 2 0 2871 2925 310464645 310464591 1.200000e-14 91.6
34 TraesCS6B01G336100 chr3D 83.495 103 12 5 106 205 310685719 310685819 1.200000e-14 91.6
35 TraesCS6B01G336100 chr3D 90.000 60 6 0 2926 2985 555743386 555743445 9.380000e-11 78.7
36 TraesCS6B01G336100 chr1A 81.667 120 7 1 2926 3030 112775753 112775634 5.600000e-13 86.1
37 TraesCS6B01G336100 chr5D 85.185 81 12 0 131 211 289035889 289035809 2.020000e-12 84.2
38 TraesCS6B01G336100 chr2B 88.060 67 8 0 133 199 797419299 797419233 2.610000e-11 80.5
39 TraesCS6B01G336100 chr2B 80.000 105 14 4 131 228 754980171 754980275 1.570000e-08 71.3
40 TraesCS6B01G336100 chrUn 83.750 80 12 1 133 211 236181025 236181104 1.210000e-09 75.0


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 TraesCS6B01G336100 chr6B 591263113 591266265 3152 False 5823.0 5823 100.0000 1 3153 1 chr6B.!!$F5 3152
1 TraesCS6B01G336100 chr6A 541594640 541598341 3701 False 2235.0 3733 91.1325 1 3153 2 chr6A.!!$F1 3152
2 TraesCS6B01G336100 chr6D 395388744 395392628 3884 False 1095.5 3134 90.4125 1 3153 4 chr6D.!!$F1 3152

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
649 1485 0.179129 GCTGCCATTTCCAATCCACG 60.179 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 3344 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.3 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
69 70 6.265577 GTGATATTGGTGCATCCTAACAAAC 58.734 40.000 0.00 0.00 37.07 2.93
76 77 4.112716 TGCATCCTAACAAACATGCATG 57.887 40.909 25.09 25.09 45.19 4.06
103 105 9.086336 GTACAACCGTACAAGCACTTTTATATA 57.914 33.333 0.00 0.00 46.18 0.86
104 106 7.967178 ACAACCGTACAAGCACTTTTATATAC 58.033 34.615 0.00 0.00 0.00 1.47
105 107 7.064966 ACAACCGTACAAGCACTTTTATATACC 59.935 37.037 0.00 0.00 0.00 2.73
284 291 5.355071 GCAATTGCCCGATCATATCAGATAA 59.645 40.000 20.06 0.00 34.31 1.75
378 1210 7.703621 CGAGATTTTGCCAATAATGACAATTCT 59.296 33.333 0.00 0.00 28.60 2.40
382 1214 8.899427 TTTTGCCAATAATGACAATTCTCAAA 57.101 26.923 0.00 0.00 28.60 2.69
447 1279 0.301687 GCCACATCAATCTGTACGCG 59.698 55.000 3.53 3.53 0.00 6.01
482 1314 0.475044 TTACCGGTGCAAAAGGAGGT 59.525 50.000 19.93 5.94 35.91 3.85
599 1431 2.810164 TGTTCCCCTTTAAAATCCGGG 58.190 47.619 0.00 3.70 36.42 5.73
649 1485 0.179129 GCTGCCATTTCCAATCCACG 60.179 55.000 0.00 0.00 0.00 4.94
733 1572 5.176741 ACTTGAAGCTTCATGAAGAGGAT 57.823 39.130 35.85 18.24 40.79 3.24
855 1694 3.382227 TGCATCACAATCCTTGGCATAAG 59.618 43.478 0.00 0.00 34.12 1.73
863 1702 1.845791 TCCTTGGCATAAGCTCCATCA 59.154 47.619 0.00 0.00 41.70 3.07
864 1703 2.158711 TCCTTGGCATAAGCTCCATCAG 60.159 50.000 0.00 0.00 41.70 2.90
1013 1854 3.485394 TCTTTTGCATGTACCTGCTTCA 58.515 40.909 21.47 5.61 42.75 3.02
1115 1959 5.954153 ACTACTACTACCAGTCAGAGCTA 57.046 43.478 0.00 0.00 0.00 3.32
1345 2189 2.155194 CGCGGAGAAGAAGCACGAG 61.155 63.158 0.00 0.00 0.00 4.18
1411 2255 0.741221 GCACTAGCACCACTACTGCC 60.741 60.000 0.00 0.00 41.58 4.85
1476 2320 0.372679 GCATCATCATCGCGCATAGG 59.627 55.000 8.75 0.00 0.00 2.57
1495 2339 1.596220 GGAAGTTCGTTGGTTTCACGC 60.596 52.381 0.00 0.00 0.00 5.34
1619 2463 0.971447 AGGTACTGAAGGGCGAGGTC 60.971 60.000 0.00 0.00 37.18 3.85
1622 2466 2.776370 TACTGAAGGGCGAGGTCGGT 62.776 60.000 0.89 0.00 40.23 4.69
1693 2537 2.280797 GTTCCAGCAGGTGTCGCA 60.281 61.111 0.00 0.00 35.89 5.10
1857 2701 4.079253 TCAGGTGTTCTTGCTAATTTCCC 58.921 43.478 0.00 0.00 0.00 3.97
1860 2704 5.710099 CAGGTGTTCTTGCTAATTTCCCTAA 59.290 40.000 0.00 0.00 0.00 2.69
1931 2777 1.757682 TTTCTTCGCAAGTGGTTGGT 58.242 45.000 0.00 0.00 33.87 3.67
1932 2778 1.305201 TTCTTCGCAAGTGGTTGGTC 58.695 50.000 0.00 0.00 33.87 4.02
1935 2781 1.990160 TTCGCAAGTGGTTGGTCCCT 61.990 55.000 0.00 0.00 33.87 4.20
1936 2782 1.122632 TCGCAAGTGGTTGGTCCCTA 61.123 55.000 0.00 0.00 33.87 3.53
1937 2783 0.673644 CGCAAGTGGTTGGTCCCTAG 60.674 60.000 0.00 0.00 33.87 3.02
1939 2785 1.610886 GCAAGTGGTTGGTCCCTAGTC 60.611 57.143 0.00 0.00 33.87 2.59
2190 3068 4.385748 GCTTGTTCCATCGGAATTTTGTTC 59.614 41.667 0.00 0.00 44.04 3.18
2240 3118 3.242413 CGGGTATTTTGCAGTTCTGATCG 60.242 47.826 3.84 0.00 0.00 3.69
2251 3129 3.763897 CAGTTCTGATCGGGGGAATTTTT 59.236 43.478 0.62 0.00 0.00 1.94
2383 3261 7.683437 AGTTTTTGCTGTAAATACTACTCCC 57.317 36.000 11.30 0.00 38.33 4.30
2384 3262 7.459234 AGTTTTTGCTGTAAATACTACTCCCT 58.541 34.615 11.30 0.00 38.33 4.20
2385 3263 7.606839 AGTTTTTGCTGTAAATACTACTCCCTC 59.393 37.037 11.30 0.00 38.33 4.30
2386 3264 5.609533 TTGCTGTAAATACTACTCCCTCC 57.390 43.478 0.00 0.00 0.00 4.30
2387 3265 3.635373 TGCTGTAAATACTACTCCCTCCG 59.365 47.826 0.00 0.00 0.00 4.63
2388 3266 3.635836 GCTGTAAATACTACTCCCTCCGT 59.364 47.826 0.00 0.00 0.00 4.69
2389 3267 4.099113 GCTGTAAATACTACTCCCTCCGTT 59.901 45.833 0.00 0.00 0.00 4.44
2390 3268 5.735638 GCTGTAAATACTACTCCCTCCGTTC 60.736 48.000 0.00 0.00 0.00 3.95
2391 3269 4.336433 TGTAAATACTACTCCCTCCGTTCG 59.664 45.833 0.00 0.00 0.00 3.95
2392 3270 1.978454 ATACTACTCCCTCCGTTCGG 58.022 55.000 4.74 4.74 0.00 4.30
2393 3271 0.911769 TACTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2394 3272 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2395 3273 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
2396 3274 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
2397 3275 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2398 3276 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2399 3277 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2400 3278 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2401 3279 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2402 3280 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2403 3281 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2404 3282 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2405 3283 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2406 3284 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2407 3285 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2408 3286 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2409 3287 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2410 3288 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2411 3289 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2412 3290 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2413 3291 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
2414 3292 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
2415 3293 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
2416 3294 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
2417 3295 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
2418 3296 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
2419 3297 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
2420 3298 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
2421 3299 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
2422 3300 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
2423 3301 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
2424 3302 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
2425 3303 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
2426 3304 4.618912 CGCAGAAATGGATGTATCTAGACG 59.381 45.833 0.00 0.00 0.00 4.18
2427 3305 5.533482 GCAGAAATGGATGTATCTAGACGT 58.467 41.667 0.00 0.00 0.00 4.34
2428 3306 6.567891 CGCAGAAATGGATGTATCTAGACGTA 60.568 42.308 0.00 0.00 0.00 3.57
2429 3307 7.316640 GCAGAAATGGATGTATCTAGACGTAT 58.683 38.462 0.00 0.00 0.00 3.06
2430 3308 7.815068 GCAGAAATGGATGTATCTAGACGTATT 59.185 37.037 0.00 0.00 0.00 1.89
2431 3309 9.698309 CAGAAATGGATGTATCTAGACGTATTT 57.302 33.333 0.00 0.00 0.00 1.40
2457 3335 7.166628 AGTTCTAGATACATTCATTTTCGCG 57.833 36.000 0.00 0.00 0.00 5.87
2458 3336 6.978659 AGTTCTAGATACATTCATTTTCGCGA 59.021 34.615 3.71 3.71 0.00 5.87
2459 3337 6.749216 TCTAGATACATTCATTTTCGCGAC 57.251 37.500 9.15 0.00 0.00 5.19
2460 3338 6.270064 TCTAGATACATTCATTTTCGCGACA 58.730 36.000 9.15 0.00 0.00 4.35
2461 3339 5.794687 AGATACATTCATTTTCGCGACAA 57.205 34.783 9.15 9.93 0.00 3.18
2462 3340 5.799960 AGATACATTCATTTTCGCGACAAG 58.200 37.500 9.15 3.14 0.00 3.16
2463 3341 3.896648 ACATTCATTTTCGCGACAAGT 57.103 38.095 9.15 0.00 0.00 3.16
2464 3342 6.533723 AGATACATTCATTTTCGCGACAAGTA 59.466 34.615 9.15 7.41 0.00 2.24
2465 3343 5.351233 ACATTCATTTTCGCGACAAGTAA 57.649 34.783 9.15 7.80 0.00 2.24
2466 3344 5.938322 ACATTCATTTTCGCGACAAGTAAT 58.062 33.333 9.15 9.89 0.00 1.89
2467 3345 6.378582 ACATTCATTTTCGCGACAAGTAATT 58.621 32.000 9.15 0.00 0.00 1.40
2468 3346 6.523201 ACATTCATTTTCGCGACAAGTAATTC 59.477 34.615 9.15 0.00 0.00 2.17
2469 3347 4.965062 TCATTTTCGCGACAAGTAATTCC 58.035 39.130 9.15 0.00 0.00 3.01
2470 3348 3.443054 TTTTCGCGACAAGTAATTCCG 57.557 42.857 9.15 0.00 0.00 4.30
2471 3349 2.350899 TTCGCGACAAGTAATTCCGA 57.649 45.000 9.15 0.00 0.00 4.55
2472 3350 2.350899 TCGCGACAAGTAATTCCGAA 57.649 45.000 3.71 0.00 0.00 4.30
2473 3351 1.987770 TCGCGACAAGTAATTCCGAAC 59.012 47.619 3.71 0.00 0.00 3.95
2474 3352 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
2475 3353 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2476 3354 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2477 3355 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2478 3356 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2479 3357 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2480 3358 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2487 3365 1.020437 CCGAACGGAGGGAGTACTAC 58.980 60.000 7.53 0.00 37.50 2.73
2556 4061 1.178534 AGTTGGGACGTGCCAAATGG 61.179 55.000 38.49 0.00 38.95 3.16
2572 4077 4.096382 CCAAATGGAAAGTACATCTTCGGG 59.904 45.833 0.00 0.00 37.39 5.14
2585 4090 1.810151 TCTTCGGGCATTACTTGTTGC 59.190 47.619 0.00 0.00 38.14 4.17
2599 4104 1.635810 GTTGCGCCAACAAAAGTGC 59.364 52.632 4.18 0.00 43.09 4.40
2628 4133 8.450578 TCTTGTGAAATTTCATAACAGTCACT 57.549 30.769 23.05 0.00 39.73 3.41
2629 4134 9.554395 TCTTGTGAAATTTCATAACAGTCACTA 57.446 29.630 23.05 4.90 39.73 2.74
2680 4185 1.885388 TGCTCCGTCGTTGGTGTTG 60.885 57.895 0.00 0.00 0.00 3.33
2681 4186 2.604174 GCTCCGTCGTTGGTGTTGG 61.604 63.158 0.00 0.00 0.00 3.77
2682 4187 1.227438 CTCCGTCGTTGGTGTTGGT 60.227 57.895 0.00 0.00 0.00 3.67
2683 4188 0.812412 CTCCGTCGTTGGTGTTGGTT 60.812 55.000 0.00 0.00 0.00 3.67
2684 4189 1.090625 TCCGTCGTTGGTGTTGGTTG 61.091 55.000 0.00 0.00 0.00 3.77
2754 4259 1.943340 GGCCATCGAAAGGTCTTCATC 59.057 52.381 0.00 0.00 0.00 2.92
2762 4267 5.130350 TCGAAAGGTCTTCATCAAGGTTTT 58.870 37.500 0.00 0.00 0.00 2.43
2766 4271 7.423844 AAAGGTCTTCATCAAGGTTTTTCTT 57.576 32.000 0.00 0.00 0.00 2.52
2768 4273 8.533569 AAGGTCTTCATCAAGGTTTTTCTTTA 57.466 30.769 0.00 0.00 0.00 1.85
2773 4278 8.966868 TCTTCATCAAGGTTTTTCTTTACAAGT 58.033 29.630 0.00 0.00 0.00 3.16
2781 4286 4.904253 TTTTCTTTACAAGTTCCGGTGG 57.096 40.909 0.00 0.00 0.00 4.61
2807 4312 1.116308 ACCCTCCAAAAACAAACCGG 58.884 50.000 0.00 0.00 0.00 5.28
2813 4318 0.176910 CAAAAACAAACCGGCCCAGT 59.823 50.000 0.00 0.00 0.00 4.00
2821 4326 1.612676 AACCGGCCCAGTAAGAAAAC 58.387 50.000 0.00 0.00 0.00 2.43
2824 4329 0.521735 CGGCCCAGTAAGAAAACTGC 59.478 55.000 0.00 0.00 44.56 4.40
2834 4339 1.453155 AGAAAACTGCATGCGTAGGG 58.547 50.000 14.09 3.21 0.00 3.53
2849 4354 0.178873 TAGGGCCCCTCAACTCAACT 60.179 55.000 21.43 0.00 34.61 3.16
2886 4392 4.973168 ACTTGGTGCTTTCATAGAAGTGA 58.027 39.130 0.00 0.00 0.00 3.41
3058 4580 3.262420 GTGAGATGCAAACTATGGACGT 58.738 45.455 0.00 0.00 29.34 4.34
3059 4581 3.307242 GTGAGATGCAAACTATGGACGTC 59.693 47.826 7.13 7.13 29.34 4.34
3060 4582 3.195610 TGAGATGCAAACTATGGACGTCT 59.804 43.478 16.46 0.00 29.34 4.18
3073 4595 1.005037 ACGTCTCGGCTTGATGCAA 60.005 52.632 0.00 0.00 45.15 4.08
3094 4616 0.106708 GGGATGGTTGAGCAGCGATA 59.893 55.000 0.00 0.00 0.00 2.92
3108 4630 1.299089 CGATAGCGGTCGCACATCA 60.299 57.895 17.71 0.00 44.88 3.07
3130 4652 2.683968 GTGTAACTGCTGGAATCACGA 58.316 47.619 0.00 0.00 0.00 4.35
3137 4659 4.385825 ACTGCTGGAATCACGAAAAAGTA 58.614 39.130 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.599558 TTGCTTGCATTGCTCAGTCC 59.400 50.000 10.49 0.00 0.00 3.85
128 131 9.023962 TCCACTTGATGCTATATTTTGAGTTTT 57.976 29.630 0.00 0.00 0.00 2.43
129 132 8.579850 TCCACTTGATGCTATATTTTGAGTTT 57.420 30.769 0.00 0.00 0.00 2.66
140 146 5.379187 TGCATTGTATCCACTTGATGCTAT 58.621 37.500 7.52 0.00 37.04 2.97
151 157 2.212652 GCTCGTCATGCATTGTATCCA 58.787 47.619 0.00 0.00 0.00 3.41
160 166 1.965930 GGGTGTTGCTCGTCATGCA 60.966 57.895 0.00 0.00 38.80 3.96
167 173 0.803768 CAGAGATCGGGTGTTGCTCG 60.804 60.000 0.00 0.00 43.78 5.03
284 291 4.405680 TGTCCTTTGACGTCATCCATATCT 59.594 41.667 20.80 0.00 44.86 1.98
378 1210 5.034852 TCTTGTCACCTCTTGTCATTTGA 57.965 39.130 0.00 0.00 0.00 2.69
382 1214 4.040829 TCACATCTTGTCACCTCTTGTCAT 59.959 41.667 0.00 0.00 0.00 3.06
447 1279 2.540361 CGGTAAATCTTGCATGCAGAGC 60.540 50.000 21.50 11.24 0.00 4.09
482 1314 0.896923 GGAAAGTGGCCAATGATGCA 59.103 50.000 7.24 0.00 0.00 3.96
547 1379 0.596082 AAATGCGCGCTTTGGTAACT 59.404 45.000 33.29 12.90 37.61 2.24
599 1431 2.910994 GGCCTGCTGATGATGCCC 60.911 66.667 0.00 0.00 36.07 5.36
733 1572 3.063510 CTGAAATCCAGGAAGCAGTGA 57.936 47.619 0.00 0.00 39.23 3.41
863 1702 5.221244 GCAAACAAGAAAACCAGTATCCACT 60.221 40.000 0.00 0.00 34.42 4.00
864 1703 4.982295 GCAAACAAGAAAACCAGTATCCAC 59.018 41.667 0.00 0.00 0.00 4.02
1013 1854 6.838382 AGTAGGTACTCAAAACTCCATTGTT 58.162 36.000 0.00 0.00 41.75 2.83
1345 2189 3.378399 GAGTGCTTCCTCCGAGCCC 62.378 68.421 0.00 0.00 39.38 5.19
1476 2320 1.329599 AGCGTGAAACCAACGAACTTC 59.670 47.619 0.00 0.00 43.68 3.01
1495 2339 6.459066 TGGTCTACATTGACAGAAGAAAGAG 58.541 40.000 0.00 0.00 38.61 2.85
1797 2641 2.975489 TCTCCAGGCTCTTCAACTTTCT 59.025 45.455 0.00 0.00 0.00 2.52
1857 2701 5.472137 TGGAAATTCCAGACGAAAAGGTTAG 59.528 40.000 11.23 0.00 42.67 2.34
1860 2704 3.827722 TGGAAATTCCAGACGAAAAGGT 58.172 40.909 11.23 0.00 42.67 3.50
1899 2745 3.181501 TGCGAAGAAATGGGCTAAAATCG 60.182 43.478 0.00 0.00 0.00 3.34
1965 2813 2.292845 TGCAGCACATGAACAATTTCGA 59.707 40.909 0.00 0.00 34.04 3.71
2006 2868 1.467734 CTGCAGCATCTCCACTTCAAC 59.532 52.381 0.00 0.00 0.00 3.18
2178 3056 1.604755 TCACCCACGAACAAAATTCCG 59.395 47.619 0.00 0.00 0.00 4.30
2190 3068 4.752879 ACCCGCGAATCACCCACG 62.753 66.667 8.23 0.00 0.00 4.94
2240 3118 6.818142 CACATTTGATCAGTAAAAATTCCCCC 59.182 38.462 0.00 0.00 0.00 5.40
2251 3129 5.084818 ACGGATGACACATTTGATCAGTA 57.915 39.130 0.00 0.00 0.00 2.74
2379 3257 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2381 3259 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2383 3261 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2384 3262 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2385 3263 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2386 3264 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2387 3265 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
2388 3266 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
2389 3267 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
2390 3268 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
2391 3269 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
2392 3270 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
2393 3271 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
2394 3272 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
2395 3273 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
2396 3274 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
2397 3275 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
2398 3276 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
2399 3277 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
2400 3278 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2401 3279 5.631512 GTCTAGATACATCCATTTCTGCGAC 59.368 44.000 0.00 0.00 0.00 5.19
2402 3280 5.562890 CGTCTAGATACATCCATTTCTGCGA 60.563 44.000 0.00 0.00 0.00 5.10
2403 3281 4.618912 CGTCTAGATACATCCATTTCTGCG 59.381 45.833 0.00 0.00 0.00 5.18
2404 3282 5.533482 ACGTCTAGATACATCCATTTCTGC 58.467 41.667 0.00 0.00 0.00 4.26
2405 3283 9.698309 AAATACGTCTAGATACATCCATTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
2431 3309 8.752254 CGCGAAAATGAATGTATCTAGAACTAA 58.248 33.333 0.00 0.00 0.00 2.24
2432 3310 8.132995 TCGCGAAAATGAATGTATCTAGAACTA 58.867 33.333 6.20 0.00 0.00 2.24
2433 3311 6.978659 TCGCGAAAATGAATGTATCTAGAACT 59.021 34.615 6.20 0.00 0.00 3.01
2434 3312 7.058005 GTCGCGAAAATGAATGTATCTAGAAC 58.942 38.462 12.06 0.00 0.00 3.01
2435 3313 6.754675 TGTCGCGAAAATGAATGTATCTAGAA 59.245 34.615 12.06 0.00 0.00 2.10
2436 3314 6.270064 TGTCGCGAAAATGAATGTATCTAGA 58.730 36.000 12.06 0.00 0.00 2.43
2437 3315 6.510746 TGTCGCGAAAATGAATGTATCTAG 57.489 37.500 12.06 0.00 0.00 2.43
2438 3316 6.533723 ACTTGTCGCGAAAATGAATGTATCTA 59.466 34.615 13.05 0.00 0.00 1.98
2439 3317 5.351465 ACTTGTCGCGAAAATGAATGTATCT 59.649 36.000 13.05 0.00 0.00 1.98
2440 3318 5.560148 ACTTGTCGCGAAAATGAATGTATC 58.440 37.500 13.05 0.00 0.00 2.24
2441 3319 5.545658 ACTTGTCGCGAAAATGAATGTAT 57.454 34.783 13.05 0.00 0.00 2.29
2442 3320 6.469139 TTACTTGTCGCGAAAATGAATGTA 57.531 33.333 13.05 8.01 0.00 2.29
2443 3321 3.896648 ACTTGTCGCGAAAATGAATGT 57.103 38.095 13.05 3.46 0.00 2.71
2444 3322 6.021468 GGAATTACTTGTCGCGAAAATGAATG 60.021 38.462 13.05 2.76 0.00 2.67
2445 3323 6.027749 GGAATTACTTGTCGCGAAAATGAAT 58.972 36.000 13.05 11.81 0.00 2.57
2446 3324 5.387279 GGAATTACTTGTCGCGAAAATGAA 58.613 37.500 13.05 9.97 0.00 2.57
2447 3325 4.434989 CGGAATTACTTGTCGCGAAAATGA 60.435 41.667 13.05 0.13 0.00 2.57
2448 3326 3.778718 CGGAATTACTTGTCGCGAAAATG 59.221 43.478 13.05 9.32 0.00 2.32
2449 3327 3.680937 TCGGAATTACTTGTCGCGAAAAT 59.319 39.130 13.05 5.74 0.00 1.82
2450 3328 3.058450 TCGGAATTACTTGTCGCGAAAA 58.942 40.909 12.06 12.01 0.00 2.29
2451 3329 2.674954 TCGGAATTACTTGTCGCGAAA 58.325 42.857 12.06 0.54 0.00 3.46
2452 3330 2.350899 TCGGAATTACTTGTCGCGAA 57.649 45.000 12.06 0.00 0.00 4.70
2453 3331 1.987770 GTTCGGAATTACTTGTCGCGA 59.012 47.619 3.71 3.71 0.00 5.87
2454 3332 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
2455 3333 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2456 3334 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2457 3335 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2458 3336 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2459 3337 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2460 3338 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2461 3339 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2462 3340 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2463 3341 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2464 3342 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2465 3343 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2466 3344 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2467 3345 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2468 3346 1.020437 GTAGTACTCCCTCCGTTCGG 58.980 60.000 0.00 4.74 0.00 4.30
2469 3347 1.020437 GGTAGTACTCCCTCCGTTCG 58.980 60.000 0.00 0.00 0.00 3.95
2470 3348 1.747924 GTGGTAGTACTCCCTCCGTTC 59.252 57.143 6.02 0.00 0.00 3.95
2471 3349 1.357079 AGTGGTAGTACTCCCTCCGTT 59.643 52.381 6.02 0.00 0.00 4.44
2472 3350 0.998145 AGTGGTAGTACTCCCTCCGT 59.002 55.000 6.02 0.00 0.00 4.69
2473 3351 1.064906 TGAGTGGTAGTACTCCCTCCG 60.065 57.143 6.02 0.00 45.07 4.63
2474 3352 2.822707 TGAGTGGTAGTACTCCCTCC 57.177 55.000 6.02 3.17 45.07 4.30
2475 3353 3.117436 AGGATGAGTGGTAGTACTCCCTC 60.117 52.174 6.02 12.12 45.07 4.30
2476 3354 2.860041 AGGATGAGTGGTAGTACTCCCT 59.140 50.000 6.02 4.57 45.07 4.20
2477 3355 3.117436 AGAGGATGAGTGGTAGTACTCCC 60.117 52.174 0.00 0.00 45.07 4.30
2478 3356 3.886505 CAGAGGATGAGTGGTAGTACTCC 59.113 52.174 0.00 1.20 45.07 3.85
2479 3357 3.886505 CCAGAGGATGAGTGGTAGTACTC 59.113 52.174 0.00 0.00 45.71 2.59
2480 3358 3.904717 CCAGAGGATGAGTGGTAGTACT 58.095 50.000 0.00 0.00 0.00 2.73
2487 3365 2.607499 AGATAGCCAGAGGATGAGTGG 58.393 52.381 0.00 0.00 0.00 4.00
2556 4061 5.116882 AGTAATGCCCGAAGATGTACTTTC 58.883 41.667 0.00 0.00 39.13 2.62
2572 4077 1.059942 GTTGGCGCAACAAGTAATGC 58.940 50.000 10.83 0.00 43.09 3.56
2585 4090 2.539476 AGAAAAGCACTTTTGTTGGCG 58.461 42.857 12.85 0.00 42.26 5.69
2628 4133 4.703575 AGCAACGAAGGAGTATGTGTACTA 59.296 41.667 0.00 0.00 41.19 1.82
2629 4134 3.510360 AGCAACGAAGGAGTATGTGTACT 59.490 43.478 0.00 0.00 43.76 2.73
2731 4236 0.400213 AAGACCTTTCGATGGCCACA 59.600 50.000 8.16 0.00 0.00 4.17
2766 4271 3.181453 TGATCAACCACCGGAACTTGTAA 60.181 43.478 9.46 0.00 0.00 2.41
2768 4273 1.142060 TGATCAACCACCGGAACTTGT 59.858 47.619 9.46 0.00 0.00 3.16
2781 4286 4.664150 TTGTTTTTGGAGGGTGATCAAC 57.336 40.909 0.73 0.73 0.00 3.18
2792 4297 0.976073 TGGGCCGGTTTGTTTTTGGA 60.976 50.000 1.90 0.00 0.00 3.53
2794 4299 0.176910 ACTGGGCCGGTTTGTTTTTG 59.823 50.000 13.59 0.00 0.00 2.44
2807 4312 2.672195 GCATGCAGTTTTCTTACTGGGC 60.672 50.000 14.21 0.00 44.50 5.36
2813 4318 3.006940 CCCTACGCATGCAGTTTTCTTA 58.993 45.455 19.57 0.01 0.00 2.10
2824 4329 3.042733 TTGAGGGGCCCTACGCATG 62.043 63.158 28.92 0.00 40.31 4.06
2834 4339 1.239347 GTCAAGTTGAGTTGAGGGGC 58.761 55.000 5.62 0.00 37.12 5.80
2849 4354 1.862201 CCAAGTTTGCGTACTCGTCAA 59.138 47.619 0.00 0.00 39.49 3.18
2886 4392 0.611062 TCAGAGTGGATTCGGACCGT 60.611 55.000 14.79 0.00 0.00 4.83
2947 4454 4.401925 CTCCTCATCTTCCAAAACAACCT 58.598 43.478 0.00 0.00 0.00 3.50
3058 4580 0.677731 CCCTTTGCATCAAGCCGAGA 60.678 55.000 0.00 0.00 44.83 4.04
3059 4581 0.677731 TCCCTTTGCATCAAGCCGAG 60.678 55.000 0.00 0.00 44.83 4.63
3060 4582 0.034186 ATCCCTTTGCATCAAGCCGA 60.034 50.000 0.00 0.00 44.83 5.54
3073 4595 1.377725 CGCTGCTCAACCATCCCTT 60.378 57.895 0.00 0.00 0.00 3.95
3094 4616 4.357947 ACGTGATGTGCGACCGCT 62.358 61.111 15.61 0.00 42.51 5.52
3108 4630 2.413837 GTGATTCCAGCAGTTACACGT 58.586 47.619 0.00 0.00 0.00 4.49
3115 4637 3.214328 ACTTTTTCGTGATTCCAGCAGT 58.786 40.909 0.00 0.00 0.00 4.40
3130 4652 3.011119 TGTGTTGTCGCCACTACTTTTT 58.989 40.909 0.00 0.00 33.92 1.94


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

AutoCloner maintained by Alex Coulton.