Multiple sequence alignment - TraesCS1B01G115300

Loading Multiple Alignment...

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 TraesCS1B01G115300 chr1B 100.000 3404 0 0 1 3404 135828090 135824687 0.000000e+00 6287.0
1 TraesCS1B01G115300 chr1B 96.596 617 20 1 2788 3404 189691195 189691810 0.000000e+00 1022.0
2 TraesCS1B01G115300 chr1B 98.383 433 7 0 2787 3219 135820007 135819575 0.000000e+00 761.0
3 TraesCS1B01G115300 chr1B 94.808 443 13 2 2787 3219 189696717 189697159 0.000000e+00 682.0
4 TraesCS1B01G115300 chr1B 87.500 200 16 8 2345 2538 530659799 530659603 4.420000e-54 222.0
5 TraesCS1B01G115300 chr4D 95.667 2031 52 18 345 2352 329132887 329134904 0.000000e+00 3230.0
6 TraesCS1B01G115300 chr4D 80.284 634 100 23 2779 3397 214338362 214338985 4.000000e-124 455.0
7 TraesCS1B01G115300 chr4D 92.941 255 16 2 31 284 329132633 329132886 1.490000e-98 370.0
8 TraesCS1B01G115300 chr4D 96.396 222 6 1 2513 2734 329134902 329135121 6.940000e-97 364.0
9 TraesCS1B01G115300 chr4A 93.467 2097 51 29 337 2352 140984190 140982099 0.000000e+00 3035.0
10 TraesCS1B01G115300 chr4A 95.946 222 7 1 2513 2734 140982101 140981882 3.230000e-95 359.0
11 TraesCS1B01G115300 chr4A 92.814 167 10 1 2348 2514 743957166 743957330 1.220000e-59 241.0
12 TraesCS1B01G115300 chr4B 94.319 1866 60 17 505 2352 408975268 408977105 0.000000e+00 2817.0
13 TraesCS1B01G115300 chr4B 94.928 276 12 1 2513 2788 408977103 408977376 6.750000e-117 431.0
14 TraesCS1B01G115300 chr4B 91.133 203 15 2 1 203 408974079 408974278 4.330000e-69 272.0
15 TraesCS1B01G115300 chr4B 92.771 166 10 1 2349 2514 510313225 510313388 4.390000e-59 239.0
16 TraesCS1B01G115300 chr4B 95.536 112 5 0 337 448 408975047 408975158 2.700000e-41 180.0
17 TraesCS1B01G115300 chr4B 88.679 53 6 0 7 59 328107654 328107602 7.880000e-07 65.8
18 TraesCS1B01G115300 chr4B 84.127 63 8 2 7 68 73743575 73743514 3.670000e-05 60.2
19 TraesCS1B01G115300 chr3B 96.278 618 20 3 2788 3404 8869327 8868712 0.000000e+00 1011.0
20 TraesCS1B01G115300 chr3B 95.853 434 17 1 2787 3219 8863813 8863380 0.000000e+00 701.0
21 TraesCS1B01G115300 chr5A 87.167 639 55 17 2788 3404 10552330 10551697 0.000000e+00 701.0
22 TraesCS1B01G115300 chr5A 87.931 406 36 10 2820 3219 10546737 10546339 1.850000e-127 466.0
23 TraesCS1B01G115300 chr3A 85.226 643 63 16 2788 3404 737282162 737282798 1.720000e-177 632.0
24 TraesCS1B01G115300 chr6B 79.524 630 97 18 2791 3397 307187138 307187758 1.460000e-113 420.0
25 TraesCS1B01G115300 chr6B 90.385 52 5 0 7 58 699977666 699977615 6.100000e-08 69.4
26 TraesCS1B01G115300 chr2D 89.895 287 25 3 1 284 407120075 407119790 1.930000e-97 366.0
27 TraesCS1B01G115300 chr2D 94.737 57 3 0 345 401 407119789 407119733 4.680000e-14 89.8
28 TraesCS1B01G115300 chr2D 87.931 58 4 1 7 61 153181969 153181912 7.880000e-07 65.8
29 TraesCS1B01G115300 chr6D 91.813 171 12 1 2347 2517 447248791 447248959 1.580000e-58 237.0
30 TraesCS1B01G115300 chr2B 92.308 169 10 2 2350 2517 214378247 214378081 1.580000e-58 237.0
31 TraesCS1B01G115300 chr2B 91.860 172 11 2 2350 2521 418664087 418664255 1.580000e-58 237.0
32 TraesCS1B01G115300 chr2B 88.462 52 6 0 7 58 423908186 423908135 2.840000e-06 63.9
33 TraesCS1B01G115300 chrUn 91.765 170 12 1 2349 2518 129563469 129563636 5.680000e-58 235.0
34 TraesCS1B01G115300 chrUn 79.787 188 23 6 3225 3397 419038413 419038600 4.610000e-24 122.0
35 TraesCS1B01G115300 chr2A 91.329 173 13 1 2342 2514 753421736 753421566 5.680000e-58 235.0
36 TraesCS1B01G115300 chr7B 88.947 190 18 3 2347 2536 642071332 642071518 7.350000e-57 231.0
37 TraesCS1B01G115300 chr5D 84.106 151 21 2 2638 2788 69952041 69952188 3.540000e-30 143.0
38 TraesCS1B01G115300 chr5D 89.091 55 4 2 2 55 354707040 354706987 2.190000e-07 67.6
39 TraesCS1B01G115300 chr5D 100.000 31 0 0 1095 1125 218261284 218261254 1.320000e-04 58.4
40 TraesCS1B01G115300 chr7D 87.037 54 7 0 2 55 512434259 512434206 1.020000e-05 62.1


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 TraesCS1B01G115300 chr1B 135824687 135828090 3403 True 6287.000000 6287 100.000000 1 3404 1 chr1B.!!$R2 3403
1 TraesCS1B01G115300 chr1B 189691195 189691810 615 False 1022.000000 1022 96.596000 2788 3404 1 chr1B.!!$F1 616
2 TraesCS1B01G115300 chr4D 329132633 329135121 2488 False 1321.333333 3230 95.001333 31 2734 3 chr4D.!!$F2 2703
3 TraesCS1B01G115300 chr4D 214338362 214338985 623 False 455.000000 455 80.284000 2779 3397 1 chr4D.!!$F1 618
4 TraesCS1B01G115300 chr4A 140981882 140984190 2308 True 1697.000000 3035 94.706500 337 2734 2 chr4A.!!$R1 2397
5 TraesCS1B01G115300 chr4B 408974079 408977376 3297 False 925.000000 2817 93.979000 1 2788 4 chr4B.!!$F2 2787
6 TraesCS1B01G115300 chr3B 8868712 8869327 615 True 1011.000000 1011 96.278000 2788 3404 1 chr3B.!!$R2 616
7 TraesCS1B01G115300 chr5A 10551697 10552330 633 True 701.000000 701 87.167000 2788 3404 1 chr5A.!!$R2 616
8 TraesCS1B01G115300 chr3A 737282162 737282798 636 False 632.000000 632 85.226000 2788 3404 1 chr3A.!!$F1 616
9 TraesCS1B01G115300 chr6B 307187138 307187758 620 False 420.000000 420 79.524000 2791 3397 1 chr6B.!!$F1 606

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
735 1523 0.179092 GACCCGATTTCGATCCCGTT 60.179 55.0 0.67 0.0 43.02 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 3339 1.006758 TCATGTACTCCCTCCGTTCCT 59.993 52.381 0.0 0.0 0.0 3.36 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
24 25 6.102663 CGGTTGAAATTGGGCATAAAATACA 58.897 36.000 0.00 0.00 0.00 2.29
203 205 5.746307 AGTCTAACGTTGCAGTCGATATA 57.254 39.130 11.99 8.41 0.00 0.86
211 911 6.934210 ACGTTGCAGTCGATATAGAATTTTC 58.066 36.000 17.62 0.00 0.00 2.29
254 954 4.260620 CCATTGCTTTTATCCGTAACGAGG 60.261 45.833 0.00 0.00 0.00 4.63
257 957 3.121544 GCTTTTATCCGTAACGAGGAGG 58.878 50.000 0.00 0.00 41.66 4.30
277 977 7.942990 AGGAGGTACTTATCGAAGTAGAAATG 58.057 38.462 0.00 0.00 46.48 2.32
278 978 6.641723 GGAGGTACTTATCGAAGTAGAAATGC 59.358 42.308 0.00 0.00 46.48 3.56
279 979 6.207213 AGGTACTTATCGAAGTAGAAATGCG 58.793 40.000 0.00 0.00 46.48 4.73
280 980 5.975939 GGTACTTATCGAAGTAGAAATGCGT 59.024 40.000 0.00 0.00 46.48 5.24
281 981 6.474751 GGTACTTATCGAAGTAGAAATGCGTT 59.525 38.462 0.00 0.00 46.48 4.84
282 982 7.645340 GGTACTTATCGAAGTAGAAATGCGTTA 59.355 37.037 0.00 0.00 46.48 3.18
283 983 7.447243 ACTTATCGAAGTAGAAATGCGTTAC 57.553 36.000 0.00 0.00 44.36 2.50
284 984 6.474751 ACTTATCGAAGTAGAAATGCGTTACC 59.525 38.462 0.00 0.00 44.36 2.85
285 985 3.514645 TCGAAGTAGAAATGCGTTACCC 58.485 45.455 0.00 0.00 0.00 3.69
286 986 2.606272 CGAAGTAGAAATGCGTTACCCC 59.394 50.000 0.00 0.00 0.00 4.95
287 987 2.304751 AGTAGAAATGCGTTACCCCG 57.695 50.000 0.00 0.00 0.00 5.73
434 1150 3.305813 CGCCAGGACAGAAACTTGTACTA 60.306 47.826 0.00 0.00 40.28 1.82
477 1227 3.494080 TTCCTTCCCCCACGTCCCT 62.494 63.158 0.00 0.00 0.00 4.20
521 1294 4.832266 ACCTAGCATCAAATCAAACCAACA 59.168 37.500 0.00 0.00 0.00 3.33
526 1299 4.269844 GCATCAAATCAAACCAACAAACGT 59.730 37.500 0.00 0.00 0.00 3.99
735 1523 0.179092 GACCCGATTTCGATCCCGTT 60.179 55.000 0.67 0.00 43.02 4.44
745 1533 2.901249 TCGATCCCGTTTCCAGATTTC 58.099 47.619 0.00 0.00 37.05 2.17
746 1534 1.940613 CGATCCCGTTTCCAGATTTCC 59.059 52.381 0.00 0.00 0.00 3.13
938 1759 1.570475 CGGCGTCGATCTAGACTCC 59.430 63.158 1.44 0.95 41.31 3.85
945 1769 1.577421 GATCTAGACTCCGAGGCGC 59.423 63.158 0.00 0.00 0.00 6.53
954 1778 3.443045 CCGAGGCGCCTGCATTTT 61.443 61.111 38.41 8.09 45.35 1.82
955 1779 2.202518 CGAGGCGCCTGCATTTTG 60.203 61.111 38.41 9.17 45.35 2.44
956 1780 2.507769 GAGGCGCCTGCATTTTGC 60.508 61.111 38.41 13.51 45.35 3.68
983 1814 0.250124 TGTTCGATTCGGCTTGGTGT 60.250 50.000 6.18 0.00 0.00 4.16
993 1824 1.359459 GGCTTGGTGTTCGATCCGAC 61.359 60.000 0.00 0.00 34.89 4.79
1680 2521 2.431771 TCCGACGCCATGTTCACG 60.432 61.111 0.00 0.00 0.00 4.35
1884 2725 1.066143 CCTGTTCGTATTGAGGCTGGT 60.066 52.381 0.00 0.00 0.00 4.00
1977 2818 4.504132 GCTACCCAGCGTGAGAAG 57.496 61.111 0.00 0.00 38.22 2.85
2163 3004 2.112898 GGATTACCCTGTCGAGCGA 58.887 57.895 0.00 0.00 0.00 4.93
2211 3052 2.949644 CAATTTCGGGGATAACCAGGTC 59.050 50.000 0.00 0.00 42.91 3.85
2266 3107 0.758123 GAGCAGGAGGATCAAGAGGG 59.242 60.000 0.00 0.00 36.25 4.30
2304 3145 4.407296 AGTGACCCTCTTGATATGAAGGAC 59.593 45.833 1.88 0.00 0.00 3.85
2349 3190 2.303311 GTTCAAGGCCCTCAAGACTACT 59.697 50.000 0.00 0.00 0.00 2.57
2350 3191 3.468071 TCAAGGCCCTCAAGACTACTA 57.532 47.619 0.00 0.00 0.00 1.82
2351 3192 3.097614 TCAAGGCCCTCAAGACTACTAC 58.902 50.000 0.00 0.00 0.00 2.73
2352 3193 3.100671 CAAGGCCCTCAAGACTACTACT 58.899 50.000 0.00 0.00 0.00 2.57
2353 3194 3.021177 AGGCCCTCAAGACTACTACTC 57.979 52.381 0.00 0.00 0.00 2.59
2354 3195 2.033372 GGCCCTCAAGACTACTACTCC 58.967 57.143 0.00 0.00 0.00 3.85
2355 3196 2.033372 GCCCTCAAGACTACTACTCCC 58.967 57.143 0.00 0.00 0.00 4.30
2356 3197 2.358405 GCCCTCAAGACTACTACTCCCT 60.358 54.545 0.00 0.00 0.00 4.20
2357 3198 3.558033 CCCTCAAGACTACTACTCCCTC 58.442 54.545 0.00 0.00 0.00 4.30
2358 3199 3.558033 CCTCAAGACTACTACTCCCTCC 58.442 54.545 0.00 0.00 0.00 4.30
2359 3200 3.207778 CTCAAGACTACTACTCCCTCCG 58.792 54.545 0.00 0.00 0.00 4.63
2360 3201 2.575279 TCAAGACTACTACTCCCTCCGT 59.425 50.000 0.00 0.00 0.00 4.69
2361 3202 2.683867 CAAGACTACTACTCCCTCCGTG 59.316 54.545 0.00 0.00 0.00 4.94
2362 3203 1.914798 AGACTACTACTCCCTCCGTGT 59.085 52.381 0.00 0.00 0.00 4.49
2363 3204 2.308275 AGACTACTACTCCCTCCGTGTT 59.692 50.000 0.00 0.00 0.00 3.32
2364 3205 2.682352 GACTACTACTCCCTCCGTGTTC 59.318 54.545 0.00 0.00 0.00 3.18
2365 3206 2.022934 CTACTACTCCCTCCGTGTTCC 58.977 57.143 0.00 0.00 0.00 3.62
2366 3207 0.408700 ACTACTCCCTCCGTGTTCCT 59.591 55.000 0.00 0.00 0.00 3.36
2367 3208 1.637553 ACTACTCCCTCCGTGTTCCTA 59.362 52.381 0.00 0.00 0.00 2.94
2368 3209 2.042162 ACTACTCCCTCCGTGTTCCTAA 59.958 50.000 0.00 0.00 0.00 2.69
2369 3210 2.019807 ACTCCCTCCGTGTTCCTAAA 57.980 50.000 0.00 0.00 0.00 1.85
2370 3211 2.547990 ACTCCCTCCGTGTTCCTAAAT 58.452 47.619 0.00 0.00 0.00 1.40
2371 3212 3.716431 ACTCCCTCCGTGTTCCTAAATA 58.284 45.455 0.00 0.00 0.00 1.40
2372 3213 4.296056 ACTCCCTCCGTGTTCCTAAATAT 58.704 43.478 0.00 0.00 0.00 1.28
2373 3214 5.461327 ACTCCCTCCGTGTTCCTAAATATA 58.539 41.667 0.00 0.00 0.00 0.86
2374 3215 5.901276 ACTCCCTCCGTGTTCCTAAATATAA 59.099 40.000 0.00 0.00 0.00 0.98
2375 3216 6.041751 ACTCCCTCCGTGTTCCTAAATATAAG 59.958 42.308 0.00 0.00 0.00 1.73
2376 3217 5.901276 TCCCTCCGTGTTCCTAAATATAAGT 59.099 40.000 0.00 0.00 0.00 2.24
2377 3218 6.041296 TCCCTCCGTGTTCCTAAATATAAGTC 59.959 42.308 0.00 0.00 0.00 3.01
2378 3219 6.041751 CCCTCCGTGTTCCTAAATATAAGTCT 59.958 42.308 0.00 0.00 0.00 3.24
2379 3220 7.418712 CCCTCCGTGTTCCTAAATATAAGTCTT 60.419 40.741 0.00 0.00 0.00 3.01
2380 3221 7.985752 CCTCCGTGTTCCTAAATATAAGTCTTT 59.014 37.037 0.00 0.00 0.00 2.52
2381 3222 8.712285 TCCGTGTTCCTAAATATAAGTCTTTG 57.288 34.615 0.00 0.00 0.00 2.77
2382 3223 8.316214 TCCGTGTTCCTAAATATAAGTCTTTGT 58.684 33.333 0.00 0.00 0.00 2.83
2383 3224 9.590451 CCGTGTTCCTAAATATAAGTCTTTGTA 57.410 33.333 0.00 0.00 0.00 2.41
2432 3273 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
2444 3285 9.362539 AGATGCATTTTAAGTGTGAATTCATTC 57.637 29.630 12.12 7.96 37.31 2.67
2445 3286 9.142515 GATGCATTTTAAGTGTGAATTCATTCA 57.857 29.630 12.12 2.83 43.94 2.57
2459 3300 8.397215 TGAATTCATTCATTTTGCTTCGTATG 57.603 30.769 3.38 0.00 41.51 2.39
2460 3301 8.028354 TGAATTCATTCATTTTGCTTCGTATGT 58.972 29.630 3.38 0.00 41.51 2.29
2461 3302 9.502145 GAATTCATTCATTTTGCTTCGTATGTA 57.498 29.630 0.00 0.00 36.80 2.29
2462 3303 9.507280 AATTCATTCATTTTGCTTCGTATGTAG 57.493 29.630 0.00 0.00 0.00 2.74
2463 3304 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
2464 3305 7.684670 TCATTCATTTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
2465 3306 6.417191 TTCATTTTGCTTCGTATGTAGTCC 57.583 37.500 0.00 0.00 0.00 3.85
2466 3307 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
2467 3308 6.112734 TCATTTTGCTTCGTATGTAGTCCAT 58.887 36.000 0.00 0.00 37.58 3.41
2468 3309 6.257849 TCATTTTGCTTCGTATGTAGTCCATC 59.742 38.462 0.00 0.00 34.86 3.51
2469 3310 5.339008 TTTGCTTCGTATGTAGTCCATCT 57.661 39.130 0.00 0.00 34.86 2.90
2470 3311 6.459670 TTTGCTTCGTATGTAGTCCATCTA 57.540 37.500 0.00 0.00 34.86 1.98
2471 3312 5.690997 TGCTTCGTATGTAGTCCATCTAG 57.309 43.478 0.00 0.00 34.86 2.43
2472 3313 5.131067 TGCTTCGTATGTAGTCCATCTAGT 58.869 41.667 0.00 0.00 34.86 2.57
2473 3314 5.008712 TGCTTCGTATGTAGTCCATCTAGTG 59.991 44.000 0.00 0.00 34.86 2.74
2494 3335 5.055265 TGGAATTCCCACAAAGACTTACA 57.945 39.130 21.90 0.00 40.82 2.41
2495 3336 5.640147 TGGAATTCCCACAAAGACTTACAT 58.360 37.500 21.90 0.00 40.82 2.29
2496 3337 6.074648 TGGAATTCCCACAAAGACTTACATT 58.925 36.000 21.90 0.00 40.82 2.71
2497 3338 6.553100 TGGAATTCCCACAAAGACTTACATTT 59.447 34.615 21.90 0.00 40.82 2.32
2498 3339 7.726291 TGGAATTCCCACAAAGACTTACATTTA 59.274 33.333 21.90 0.00 40.82 1.40
2499 3340 8.244113 GGAATTCCCACAAAGACTTACATTTAG 58.756 37.037 14.03 0.00 34.14 1.85
2500 3341 7.703058 ATTCCCACAAAGACTTACATTTAGG 57.297 36.000 0.00 0.00 0.00 2.69
2501 3342 6.442541 TCCCACAAAGACTTACATTTAGGA 57.557 37.500 0.00 0.00 0.00 2.94
2502 3343 6.843752 TCCCACAAAGACTTACATTTAGGAA 58.156 36.000 0.00 0.00 0.00 3.36
2503 3344 6.713450 TCCCACAAAGACTTACATTTAGGAAC 59.287 38.462 0.00 0.00 0.00 3.62
2504 3345 6.348213 CCCACAAAGACTTACATTTAGGAACG 60.348 42.308 0.00 0.00 0.00 3.95
2505 3346 6.348213 CCACAAAGACTTACATTTAGGAACGG 60.348 42.308 0.00 0.00 0.00 4.44
2506 3347 6.425721 CACAAAGACTTACATTTAGGAACGGA 59.574 38.462 0.00 0.00 0.00 4.69
2507 3348 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
2508 3349 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2509 3350 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2510 3351 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2511 3352 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2572 3413 4.730657 TGTTCGTTCGTTCTAGATTCTCC 58.269 43.478 0.00 0.00 0.00 3.71
2743 3584 7.337184 TCTGCTTCTAGAAATCGAGTTAGAGAA 59.663 37.037 16.32 16.32 0.00 2.87
2744 3585 7.251994 TGCTTCTAGAAATCGAGTTAGAGAAC 58.748 38.462 14.31 12.31 35.64 3.01
2748 3589 4.734917 AGAAATCGAGTTAGAGAACGGTG 58.265 43.478 0.00 0.00 40.76 4.94
2779 3620 6.934048 AACTGCTCATTTCTAAATAGCTCC 57.066 37.500 0.00 0.00 34.28 4.70
2784 3625 5.767168 GCTCATTTCTAAATAGCTCCATGGT 59.233 40.000 12.58 0.00 0.00 3.55
2936 3779 0.471191 TCGCAGATGCTCCATCCAAT 59.529 50.000 2.95 0.00 41.36 3.16
2958 3801 1.202580 GCTATCATCGCCCTGAGTGTT 60.203 52.381 0.00 0.00 0.00 3.32
3119 3966 1.523758 CGTGCTTTGCTACTTTCCCT 58.476 50.000 0.00 0.00 0.00 4.20
3148 3996 5.125417 TGAGCAATACAAACCCTAGCAAATC 59.875 40.000 0.00 0.00 0.00 2.17
3252 4104 1.614241 CCCAATCGGTTCTCGGAGGT 61.614 60.000 4.96 0.00 39.77 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.449041 TCCTGGTTTATTAGTCCCCTTTGTAT 59.551 38.462 0.00 0.00 0.00 2.29
24 25 4.324022 CGTCCTGGTTTATTAGTCCCCTTT 60.324 45.833 0.00 0.00 0.00 3.11
84 85 5.934935 TGAAAAGTCCGTTGGAGATTAAC 57.065 39.130 0.00 0.00 29.39 2.01
125 127 7.133133 TGTCACCCTCCTAAATTTACTATCC 57.867 40.000 0.00 0.00 0.00 2.59
129 131 6.012858 TCACATGTCACCCTCCTAAATTTACT 60.013 38.462 0.00 0.00 0.00 2.24
235 935 3.429822 CCTCCTCGTTACGGATAAAAGCA 60.430 47.826 4.53 0.00 0.00 3.91
254 954 6.360148 CGCATTTCTACTTCGATAAGTACCTC 59.640 42.308 0.00 0.00 44.26 3.85
257 957 7.447243 AACGCATTTCTACTTCGATAAGTAC 57.553 36.000 0.00 0.00 44.26 2.73
290 990 6.966021 TGCTAACGCATTTCTACTTCTTTTT 58.034 32.000 0.00 0.00 42.25 1.94
291 991 6.204882 ACTGCTAACGCATTTCTACTTCTTTT 59.795 34.615 0.00 0.00 46.74 2.27
292 992 5.701290 ACTGCTAACGCATTTCTACTTCTTT 59.299 36.000 0.00 0.00 46.74 2.52
293 993 5.120830 CACTGCTAACGCATTTCTACTTCTT 59.879 40.000 0.00 0.00 46.74 2.52
294 994 4.627467 CACTGCTAACGCATTTCTACTTCT 59.373 41.667 0.00 0.00 46.74 2.85
295 995 4.389077 ACACTGCTAACGCATTTCTACTTC 59.611 41.667 0.00 0.00 46.74 3.01
296 996 4.152402 CACACTGCTAACGCATTTCTACTT 59.848 41.667 0.00 0.00 46.74 2.24
297 997 3.679980 CACACTGCTAACGCATTTCTACT 59.320 43.478 0.00 0.00 46.74 2.57
298 998 3.432252 ACACACTGCTAACGCATTTCTAC 59.568 43.478 0.00 0.00 46.74 2.59
299 999 3.659786 ACACACTGCTAACGCATTTCTA 58.340 40.909 0.00 0.00 46.74 2.10
300 1000 2.494059 ACACACTGCTAACGCATTTCT 58.506 42.857 0.00 0.00 46.74 2.52
301 1001 2.969443 ACACACTGCTAACGCATTTC 57.031 45.000 0.00 0.00 46.74 2.17
302 1002 4.822036 TTAACACACTGCTAACGCATTT 57.178 36.364 0.00 0.00 46.74 2.32
303 1003 4.822036 TTTAACACACTGCTAACGCATT 57.178 36.364 0.00 0.00 46.74 3.56
304 1004 4.822036 TTTTAACACACTGCTAACGCAT 57.178 36.364 0.00 0.00 46.74 4.73
305 1005 4.617808 TTTTTAACACACTGCTAACGCA 57.382 36.364 0.00 0.00 45.60 5.24
328 1028 8.594687 CGTTGCTGCTAATGCTTTTATTTTTAT 58.405 29.630 0.00 0.00 40.48 1.40
329 1029 7.062839 CCGTTGCTGCTAATGCTTTTATTTTTA 59.937 33.333 0.00 0.00 40.48 1.52
330 1030 6.128580 CCGTTGCTGCTAATGCTTTTATTTTT 60.129 34.615 0.00 0.00 40.48 1.94
331 1031 5.348451 CCGTTGCTGCTAATGCTTTTATTTT 59.652 36.000 0.00 0.00 40.48 1.82
332 1032 4.864247 CCGTTGCTGCTAATGCTTTTATTT 59.136 37.500 0.00 0.00 40.48 1.40
333 1033 4.423732 CCGTTGCTGCTAATGCTTTTATT 58.576 39.130 0.00 0.00 40.48 1.40
334 1034 3.181487 CCCGTTGCTGCTAATGCTTTTAT 60.181 43.478 0.00 0.00 40.48 1.40
335 1035 2.163412 CCCGTTGCTGCTAATGCTTTTA 59.837 45.455 0.00 0.00 40.48 1.52
336 1036 1.067635 CCCGTTGCTGCTAATGCTTTT 60.068 47.619 0.00 0.00 40.48 2.27
337 1037 0.527565 CCCGTTGCTGCTAATGCTTT 59.472 50.000 0.00 0.00 40.48 3.51
338 1038 1.937546 GCCCGTTGCTGCTAATGCTT 61.938 55.000 0.00 0.00 40.48 3.91
339 1039 2.409870 GCCCGTTGCTGCTAATGCT 61.410 57.895 0.00 0.00 40.48 3.79
434 1150 1.636988 GCCGTTGTTCGTATGCTAGT 58.363 50.000 0.00 0.00 37.94 2.57
477 1227 0.620410 AATGACGGATGGGTCCTGGA 60.620 55.000 0.00 0.00 42.73 3.86
559 1333 3.632189 GCCCGGTAAGTAATACAGTACG 58.368 50.000 0.00 0.00 36.14 3.67
560 1334 3.315191 TCGCCCGGTAAGTAATACAGTAC 59.685 47.826 0.00 0.00 36.14 2.73
561 1335 3.550820 TCGCCCGGTAAGTAATACAGTA 58.449 45.455 0.00 0.00 36.14 2.74
562 1336 2.360165 CTCGCCCGGTAAGTAATACAGT 59.640 50.000 0.00 0.00 36.14 3.55
563 1337 2.288030 CCTCGCCCGGTAAGTAATACAG 60.288 54.545 0.00 0.00 36.14 2.74
735 1523 0.999712 GGTGGAGGGGAAATCTGGAA 59.000 55.000 0.00 0.00 0.00 3.53
745 1533 2.122729 TGTCTGGAGGTGGAGGGG 59.877 66.667 0.00 0.00 0.00 4.79
746 1534 2.294078 GGTGTCTGGAGGTGGAGGG 61.294 68.421 0.00 0.00 0.00 4.30
938 1759 2.202518 CAAAATGCAGGCGCCTCG 60.203 61.111 30.29 22.86 37.32 4.63
945 1769 2.287788 ACAAGAAGACGCAAAATGCAGG 60.288 45.455 2.99 0.00 45.36 4.85
954 1778 1.719246 CGAATCGAACAAGAAGACGCA 59.281 47.619 0.00 0.00 0.00 5.24
955 1779 1.059264 CCGAATCGAACAAGAAGACGC 59.941 52.381 3.36 0.00 0.00 5.19
956 1780 1.059264 GCCGAATCGAACAAGAAGACG 59.941 52.381 3.36 0.00 0.00 4.18
959 1783 2.159653 CCAAGCCGAATCGAACAAGAAG 60.160 50.000 3.36 0.00 0.00 2.85
962 1786 1.135972 CACCAAGCCGAATCGAACAAG 60.136 52.381 3.36 0.00 0.00 3.16
964 1788 0.250124 ACACCAAGCCGAATCGAACA 60.250 50.000 3.36 0.00 0.00 3.18
983 1814 3.435327 CCACATTTTCTTGTCGGATCGAA 59.565 43.478 0.00 0.00 37.72 3.71
993 1824 0.038343 CCGCCACCCACATTTTCTTG 60.038 55.000 0.00 0.00 0.00 3.02
1680 2521 1.817099 CAGCTCGAAGGCCATGTCC 60.817 63.158 5.01 0.00 0.00 4.02
1857 2698 1.094785 CAATACGAACAGGGCCCTTG 58.905 55.000 26.10 20.38 0.00 3.61
1884 2725 2.565834 GAGGTACTTGGTGAGCACCTTA 59.434 50.000 19.47 7.80 46.93 2.69
1977 2818 3.677976 CGAGATACACCTTGTTACCCCAC 60.678 52.174 0.00 0.00 0.00 4.61
2211 3052 3.674138 GCTCAAACCCATACATGTGCAAG 60.674 47.826 9.11 0.00 33.72 4.01
2266 3107 2.354203 GGTCACTGGTCTCATTCCTGAC 60.354 54.545 0.00 0.00 32.75 3.51
2304 3145 1.087771 GGTGGAGCAACCCGTAATCG 61.088 60.000 0.00 0.00 38.00 3.34
2349 3190 2.905415 TTAGGAACACGGAGGGAGTA 57.095 50.000 0.00 0.00 0.00 2.59
2350 3191 2.019807 TTTAGGAACACGGAGGGAGT 57.980 50.000 0.00 0.00 0.00 3.85
2351 3192 4.957684 ATATTTAGGAACACGGAGGGAG 57.042 45.455 0.00 0.00 0.00 4.30
2352 3193 5.901276 ACTTATATTTAGGAACACGGAGGGA 59.099 40.000 0.00 0.00 0.00 4.20
2353 3194 6.041751 AGACTTATATTTAGGAACACGGAGGG 59.958 42.308 0.00 0.00 0.00 4.30
2354 3195 7.052142 AGACTTATATTTAGGAACACGGAGG 57.948 40.000 0.00 0.00 0.00 4.30
2355 3196 8.818057 CAAAGACTTATATTTAGGAACACGGAG 58.182 37.037 0.00 0.00 0.00 4.63
2356 3197 8.316214 ACAAAGACTTATATTTAGGAACACGGA 58.684 33.333 0.00 0.00 0.00 4.69
2357 3198 8.488651 ACAAAGACTTATATTTAGGAACACGG 57.511 34.615 0.00 0.00 0.00 4.94
2406 3247 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
2418 3259 9.362539 GAATGAATTCACACTTAAAATGCATCT 57.637 29.630 11.07 0.00 36.80 2.90
2419 3260 9.142515 TGAATGAATTCACACTTAAAATGCATC 57.857 29.630 11.07 0.00 41.51 3.91
2435 3276 8.398491 ACATACGAAGCAAAATGAATGAATTC 57.602 30.769 0.00 0.00 37.31 2.17
2436 3277 9.507280 CTACATACGAAGCAAAATGAATGAATT 57.493 29.630 0.00 0.00 0.00 2.17
2437 3278 8.677300 ACTACATACGAAGCAAAATGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
2438 3279 8.039603 ACTACATACGAAGCAAAATGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
2439 3280 7.201609 GGACTACATACGAAGCAAAATGAATGA 60.202 37.037 0.00 0.00 0.00 2.57
2440 3281 6.907212 GGACTACATACGAAGCAAAATGAATG 59.093 38.462 0.00 0.00 0.00 2.67
2441 3282 6.597672 TGGACTACATACGAAGCAAAATGAAT 59.402 34.615 0.00 0.00 0.00 2.57
2442 3283 5.935206 TGGACTACATACGAAGCAAAATGAA 59.065 36.000 0.00 0.00 0.00 2.57
2443 3284 5.483811 TGGACTACATACGAAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
2444 3285 5.794687 TGGACTACATACGAAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
2445 3286 6.349300 AGATGGACTACATACGAAGCAAAAT 58.651 36.000 0.00 0.00 40.72 1.82
2446 3287 5.730550 AGATGGACTACATACGAAGCAAAA 58.269 37.500 0.00 0.00 40.72 2.44
2447 3288 5.339008 AGATGGACTACATACGAAGCAAA 57.661 39.130 0.00 0.00 40.72 3.68
2448 3289 5.593095 ACTAGATGGACTACATACGAAGCAA 59.407 40.000 0.00 0.00 40.72 3.91
2449 3290 5.008712 CACTAGATGGACTACATACGAAGCA 59.991 44.000 0.00 0.00 40.72 3.91
2450 3291 5.453648 CACTAGATGGACTACATACGAAGC 58.546 45.833 0.00 0.00 40.72 3.86
2472 3313 5.055265 TGTAAGTCTTTGTGGGAATTCCA 57.945 39.130 25.67 9.48 44.79 3.53
2473 3314 6.590234 AATGTAAGTCTTTGTGGGAATTCC 57.410 37.500 16.74 16.74 0.00 3.01
2474 3315 8.244113 CCTAAATGTAAGTCTTTGTGGGAATTC 58.756 37.037 0.00 0.00 0.00 2.17
2475 3316 7.947890 TCCTAAATGTAAGTCTTTGTGGGAATT 59.052 33.333 0.00 0.00 0.00 2.17
2476 3317 7.466804 TCCTAAATGTAAGTCTTTGTGGGAAT 58.533 34.615 0.00 0.00 0.00 3.01
2477 3318 6.843752 TCCTAAATGTAAGTCTTTGTGGGAA 58.156 36.000 0.00 0.00 0.00 3.97
2478 3319 6.442541 TCCTAAATGTAAGTCTTTGTGGGA 57.557 37.500 0.00 0.00 0.00 4.37
2479 3320 6.348213 CGTTCCTAAATGTAAGTCTTTGTGGG 60.348 42.308 0.00 0.00 0.00 4.61
2480 3321 6.348213 CCGTTCCTAAATGTAAGTCTTTGTGG 60.348 42.308 0.00 0.00 0.00 4.17
2481 3322 6.425721 TCCGTTCCTAAATGTAAGTCTTTGTG 59.574 38.462 0.00 0.00 0.00 3.33
2482 3323 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
2483 3324 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
2484 3325 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2485 3326 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2486 3327 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2487 3328 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2488 3329 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2489 3330 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2490 3331 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2491 3332 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2492 3333 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2493 3334 3.449737 TGTACTCCCTCCGTTCCTAAATG 59.550 47.826 0.00 0.00 0.00 2.32
2494 3335 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2495 3336 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2496 3337 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2497 3338 2.242965 TCATGTACTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
2498 3339 1.006758 TCATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
2499 3340 1.481871 TCATGTACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
2500 3341 4.341520 AGTTATCATGTACTCCCTCCGTTC 59.658 45.833 0.00 0.00 0.00 3.95
2501 3342 4.287552 AGTTATCATGTACTCCCTCCGTT 58.712 43.478 0.00 0.00 0.00 4.44
2502 3343 3.912248 AGTTATCATGTACTCCCTCCGT 58.088 45.455 0.00 0.00 0.00 4.69
2503 3344 6.885376 ACTATAGTTATCATGTACTCCCTCCG 59.115 42.308 0.00 0.00 0.00 4.63
2504 3345 9.176460 GTACTATAGTTATCATGTACTCCCTCC 57.824 40.741 11.40 0.00 0.00 4.30
2505 3346 9.736414 TGTACTATAGTTATCATGTACTCCCTC 57.264 37.037 11.40 0.00 33.59 4.30
2506 3347 9.517868 GTGTACTATAGTTATCATGTACTCCCT 57.482 37.037 11.40 0.00 33.59 4.20
2507 3348 9.517868 AGTGTACTATAGTTATCATGTACTCCC 57.482 37.037 11.40 0.00 33.59 4.30
2610 3451 4.967084 AACCAAATTTCCTTGTTACCCC 57.033 40.909 0.00 0.00 0.00 4.95
2707 3548 9.853555 CGATTTCTAGAAGCAGAAGACATATAT 57.146 33.333 5.12 0.00 35.99 0.86
2708 3549 9.067986 TCGATTTCTAGAAGCAGAAGACATATA 57.932 33.333 5.12 0.00 35.99 0.86
2709 3550 7.946207 TCGATTTCTAGAAGCAGAAGACATAT 58.054 34.615 5.12 0.00 35.99 1.78
2743 3584 1.374758 GCAGTTAGCTGAGCACCGT 60.375 57.895 11.20 0.00 45.28 4.83
2744 3585 3.479370 GCAGTTAGCTGAGCACCG 58.521 61.111 11.20 0.00 45.28 4.94
2765 3606 7.450014 TGACAAAACCATGGAGCTATTTAGAAA 59.550 33.333 21.47 0.00 0.00 2.52
2770 3611 4.463891 CCTGACAAAACCATGGAGCTATTT 59.536 41.667 21.47 4.95 0.00 1.40
2779 3620 1.270550 GACTGGCCTGACAAAACCATG 59.729 52.381 17.64 0.00 0.00 3.66
2784 3625 1.340889 GCAATGACTGGCCTGACAAAA 59.659 47.619 17.64 0.00 0.00 2.44
2958 3801 2.434185 GTCGGGCGATGAACAGCA 60.434 61.111 0.00 0.00 34.54 4.41
3119 3966 5.183140 GCTAGGGTTTGTATTGCTCAGAAAA 59.817 40.000 0.00 0.00 0.00 2.29
3148 3996 4.727507 TTTCAGAGAGAGAATTCGAGGG 57.272 45.455 0.00 0.00 0.00 4.30
3252 4104 2.353704 CCTCTACACGCCAGATTCAACA 60.354 50.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.