Multiple sequence alignment - TraesCS3D01G099400

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 TraesCS3D01G099400 chr3D 100.000 3915 0 0 1 3915 51089218 51093132 0.000000e+00 7230.0
1 TraesCS3D01G099400 chr3D 97.744 133 3 0 3250 3382 210622553 210622421 3.040000e-56 230.0
2 TraesCS3D01G099400 chr3A 97.119 2534 64 4 556 3081 64015111 64017643 0.000000e+00 4266.0
3 TraesCS3D01G099400 chr3A 93.097 565 11 12 3379 3915 64018112 64018676 0.000000e+00 802.0
4 TraesCS3D01G099400 chr3A 87.327 505 29 15 43 535 64013908 64014389 2.660000e-151 545.0
5 TraesCS3D01G099400 chr3A 88.670 203 12 4 26 224 699289365 699289560 1.820000e-58 237.0
6 TraesCS3D01G099400 chr3A 94.366 71 4 0 3138 3208 64017957 64018027 4.140000e-20 110.0
7 TraesCS3D01G099400 chr3A 89.583 48 5 0 3209 3256 64018067 64018114 1.170000e-05 62.1
8 TraesCS3D01G099400 chr3B 96.012 1354 54 0 556 1909 82039787 82041140 0.000000e+00 2202.0
9 TraesCS3D01G099400 chr3B 97.034 1315 25 7 1895 3208 82042538 82043839 0.000000e+00 2200.0
10 TraesCS3D01G099400 chr3B 97.955 538 6 4 3379 3915 82043924 82044457 0.000000e+00 928.0
11 TraesCS3D01G099400 chr3B 98.425 127 2 0 3254 3380 383716491 383716617 1.420000e-54 224.0
12 TraesCS3D01G099400 chr2B 85.383 561 52 24 6 544 178858899 178858347 4.420000e-154 555.0
13 TraesCS3D01G099400 chr2B 85.383 561 52 24 6 544 178870454 178869902 4.420000e-154 555.0
14 TraesCS3D01G099400 chr2B 86.444 450 42 15 75 513 738135076 738135517 3.540000e-130 475.0
15 TraesCS3D01G099400 chr2B 96.454 141 2 2 3240 3380 662686295 662686158 3.040000e-56 230.0
16 TraesCS3D01G099400 chr2B 96.377 138 3 2 3243 3380 655599743 655599878 3.940000e-55 226.0
17 TraesCS3D01G099400 chrUn 83.759 548 56 21 1 536 29604462 29603936 4.550000e-134 488.0
18 TraesCS3D01G099400 chr6A 83.423 555 57 20 1 536 116795593 116796131 2.120000e-132 483.0
19 TraesCS3D01G099400 chr1D 85.331 484 48 17 6 472 339307896 339308373 2.740000e-131 479.0
20 TraesCS3D01G099400 chr1D 88.131 337 23 9 7 326 90621357 90621021 6.140000e-103 385.0
21 TraesCS3D01G099400 chr1D 98.425 127 2 0 3254 3380 38256717 38256843 1.420000e-54 224.0
22 TraesCS3D01G099400 chr5A 83.613 537 57 19 6 536 480553017 480553528 3.540000e-130 475.0
23 TraesCS3D01G099400 chr2D 85.232 474 52 14 75 539 606631496 606631960 4.580000e-129 472.0
24 TraesCS3D01G099400 chr2D 95.420 131 5 1 1 130 528393155 528393285 1.430000e-49 207.0
25 TraesCS3D01G099400 chr5D 86.567 402 29 11 1 388 380083867 380084257 1.680000e-113 420.0
26 TraesCS3D01G099400 chr5D 86.068 323 27 13 158 472 542578215 542578527 8.110000e-87 331.0
27 TraesCS3D01G099400 chr5D 95.862 145 5 1 3236 3380 211375766 211375623 2.350000e-57 233.0
28 TraesCS3D01G099400 chr4A 82.596 339 44 9 143 479 1533453 1533128 6.400000e-73 285.0
29 TraesCS3D01G099400 chr6D 97.810 137 2 1 3246 3381 335001268 335001132 6.540000e-58 235.0
30 TraesCS3D01G099400 chr5B 99.225 129 1 0 3254 3382 640272741 640272869 2.350000e-57 233.0
31 TraesCS3D01G099400 chr4B 97.794 136 2 1 3250 3385 180671292 180671158 2.350000e-57 233.0


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 TraesCS3D01G099400 chr3D 51089218 51093132 3914 False 7230.000000 7230 100.000000 1 3915 1 chr3D.!!$F1 3914
1 TraesCS3D01G099400 chr3A 64013908 64018676 4768 False 1157.020000 4266 92.298400 43 3915 5 chr3A.!!$F2 3872
2 TraesCS3D01G099400 chr3B 82039787 82044457 4670 False 1776.666667 2202 97.000333 556 3915 3 chr3B.!!$F2 3359
3 TraesCS3D01G099400 chr2B 178858347 178858899 552 True 555.000000 555 85.383000 6 544 1 chr2B.!!$R1 538
4 TraesCS3D01G099400 chr2B 178869902 178870454 552 True 555.000000 555 85.383000 6 544 1 chr2B.!!$R2 538
5 TraesCS3D01G099400 chrUn 29603936 29604462 526 True 488.000000 488 83.759000 1 536 1 chrUn.!!$R1 535
6 TraesCS3D01G099400 chr6A 116795593 116796131 538 False 483.000000 483 83.423000 1 536 1 chr6A.!!$F1 535
7 TraesCS3D01G099400 chr5A 480553017 480553528 511 False 475.000000 475 83.613000 6 536 1 chr5A.!!$F1 530

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
722 1464 0.108585 TCAGGGTCACCAACTTGAGC 59.891 55.000 0.00 0.00 42.24 4.26 F
723 1465 0.179020 CAGGGTCACCAACTTGAGCA 60.179 55.000 0.00 0.00 44.32 4.26 F
735 1477 0.453282 CTTGAGCATGAAACGCGTGG 60.453 55.000 14.98 1.17 33.98 4.94 F
1321 2069 1.066918 GACGTCGTGAACCAGGTGT 59.933 57.895 0.63 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 4417 0.039074 GTCGCACCTGATATCGAGGG 60.039 60.000 19.24 13.80 34.56 4.30 R
2710 4871 0.108898 CGCGGGCAAAAATGATTCCA 60.109 50.000 0.00 0.00 0.00 3.53 R
2770 4931 5.059833 CAGTCCATAGTCTTTCCTAATGCC 58.940 45.833 0.00 0.00 0.00 4.40 R
3139 5571 0.247655 CACGCGGCACATGTGATTAC 60.248 55.000 29.80 14.01 35.49 1.89 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
58 60 9.249053 TGGCAAGATTTACTATTTATTTGACCA 57.751 29.630 0.00 0.00 0.00 4.02
81 84 9.200817 ACCATTATTAACATGGCAGATTTTACT 57.799 29.630 13.36 0.00 44.69 2.24
140 147 5.941058 TGATTTTGGTTATGGCGTTTCTCTA 59.059 36.000 0.00 0.00 0.00 2.43
346 369 3.123157 TGTTCACCCATGGCAATTTTG 57.877 42.857 6.09 0.00 0.00 2.44
354 377 3.062763 CCATGGCAATTTTGTGCGTTTA 58.937 40.909 0.00 0.00 45.91 2.01
366 389 4.640789 TGTGCGTTTAAAAGTTGATGGT 57.359 36.364 3.09 0.00 0.00 3.55
465 491 6.385649 TTTCTTCTATTTTTCGTTGCTGGT 57.614 33.333 0.00 0.00 0.00 4.00
536 578 1.125093 TGGCTTTCTCCTCCCGAACA 61.125 55.000 0.00 0.00 0.00 3.18
550 993 0.248134 CGAACAAACGTTCCCGCAAA 60.248 50.000 0.00 0.00 39.77 3.68
551 994 1.598430 CGAACAAACGTTCCCGCAAAT 60.598 47.619 0.00 0.00 39.77 2.32
552 995 2.349627 CGAACAAACGTTCCCGCAAATA 60.350 45.455 0.00 0.00 39.77 1.40
553 996 3.668491 CGAACAAACGTTCCCGCAAATAT 60.668 43.478 0.00 0.00 39.77 1.28
554 997 3.481112 ACAAACGTTCCCGCAAATATC 57.519 42.857 0.00 0.00 37.70 1.63
722 1464 0.108585 TCAGGGTCACCAACTTGAGC 59.891 55.000 0.00 0.00 42.24 4.26
723 1465 0.179020 CAGGGTCACCAACTTGAGCA 60.179 55.000 0.00 0.00 44.32 4.26
735 1477 0.453282 CTTGAGCATGAAACGCGTGG 60.453 55.000 14.98 1.17 33.98 4.94
1302 2050 1.230635 ACATGGTGCAGCTGTTCGTC 61.231 55.000 18.08 0.00 0.00 4.20
1306 2054 2.729491 TGCAGCTGTTCGTCGACG 60.729 61.111 31.30 31.30 41.45 5.12
1321 2069 1.066918 GACGTCGTGAACCAGGTGT 59.933 57.895 0.63 0.00 0.00 4.16
1369 2117 3.315949 CGTCCTTCCGGTTCCCCA 61.316 66.667 0.00 0.00 0.00 4.96
1373 2121 3.728373 CTTCCGGTTCCCCAGGGG 61.728 72.222 20.55 20.55 46.11 4.79
1431 2179 5.407407 TCAACATAGTCTTCTTGTCCCTC 57.593 43.478 0.00 0.00 0.00 4.30
1434 2182 1.183549 TAGTCTTCTTGTCCCTCGCC 58.816 55.000 0.00 0.00 0.00 5.54
1461 2209 3.144120 CTGCATCTACGAGGCGCCT 62.144 63.158 33.48 33.48 42.60 5.52
1491 2239 4.742201 CACGGGTGCCTGGACTCG 62.742 72.222 9.62 9.62 45.73 4.18
1510 2258 2.997315 TGAGGACCCAGCTGACCG 60.997 66.667 17.39 4.47 0.00 4.79
1512 2260 4.640690 AGGACCCAGCTGACCGGT 62.641 66.667 17.39 14.52 0.00 5.28
1560 2308 2.574212 GTCAAAATGCTCGGCGCG 60.574 61.111 0.00 0.00 43.27 6.86
1593 2341 1.662629 CAGTGGATGCAGACGATGAAC 59.337 52.381 0.00 0.00 0.00 3.18
1938 4098 5.407387 TCTTTGTCGCATTAACCACTTCTAC 59.593 40.000 0.00 0.00 0.00 2.59
2095 4255 3.133721 AGCAAGGCAACAACATGGTTTAA 59.866 39.130 0.00 0.00 41.41 1.52
2134 4294 1.078143 CTTAGCTGTGACTGGGCCC 60.078 63.158 17.59 17.59 0.00 5.80
2256 4417 6.396459 GTGAAGAACACTTACTGTAGCATC 57.604 41.667 0.00 0.00 45.13 3.91
2477 4638 2.202892 GCTCGTTCGATCCCCCAC 60.203 66.667 0.00 0.00 0.00 4.61
2710 4871 1.187567 GCCCATTCACAAAGCAGGGT 61.188 55.000 0.00 0.00 38.56 4.34
2770 4931 1.669115 CTGGAAGGTCTGTGGTGCG 60.669 63.158 0.00 0.00 0.00 5.34
3081 5243 4.067896 CGTGCCTCTTGGAGCAATATAAT 58.932 43.478 0.00 0.00 41.48 1.28
3097 5259 7.898946 GCAATATAATGCAAGTCCTTTTTGTC 58.101 34.615 7.93 0.00 45.70 3.18
3102 5264 6.667007 AATGCAAGTCCTTTTTGTCTTTTG 57.333 33.333 0.00 0.00 0.00 2.44
3104 5266 4.928615 TGCAAGTCCTTTTTGTCTTTTGTG 59.071 37.500 0.00 0.00 0.00 3.33
3106 5268 5.163963 GCAAGTCCTTTTTGTCTTTTGTGTG 60.164 40.000 0.00 0.00 0.00 3.82
3108 5270 5.469479 AGTCCTTTTTGTCTTTTGTGTGTG 58.531 37.500 0.00 0.00 0.00 3.82
3110 5272 5.118510 GTCCTTTTTGTCTTTTGTGTGTGTG 59.881 40.000 0.00 0.00 0.00 3.82
3113 5275 4.576216 TTTGTCTTTTGTGTGTGTGTGT 57.424 36.364 0.00 0.00 0.00 3.72
3154 5586 2.022764 TCTGGTAATCACATGTGCCG 57.977 50.000 21.38 11.93 0.00 5.69
3210 5681 7.608761 ACATTCCGTGTATGTACCACTTTAAAT 59.391 33.333 0.00 0.00 39.91 1.40
3215 5686 7.711772 CCGTGTATGTACCACTTTAAATATGGA 59.288 37.037 20.25 4.12 36.94 3.41
3216 5687 9.268268 CGTGTATGTACCACTTTAAATATGGAT 57.732 33.333 20.25 9.67 36.94 3.41
3262 5735 6.803366 TGGATAGTTTTTACTACTCCCTCC 57.197 41.667 0.00 0.00 0.00 4.30
3263 5736 5.361857 TGGATAGTTTTTACTACTCCCTCCG 59.638 44.000 0.00 0.00 0.00 4.63
3264 5737 5.362143 GGATAGTTTTTACTACTCCCTCCGT 59.638 44.000 0.00 0.00 0.00 4.69
3265 5738 4.797800 AGTTTTTACTACTCCCTCCGTC 57.202 45.455 0.00 0.00 0.00 4.79
3266 5739 3.513119 AGTTTTTACTACTCCCTCCGTCC 59.487 47.826 0.00 0.00 0.00 4.79
3267 5740 2.149973 TTTACTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
3268 5741 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3269 5742 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3270 5743 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3271 5744 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
3272 5745 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
3273 5746 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3274 5747 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3275 5748 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3276 5749 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3277 5750 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3278 5751 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3279 5752 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3280 5753 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3281 5754 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3282 5755 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3283 5756 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3284 5757 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3285 5758 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3286 5759 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3287 5760 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3288 5761 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3289 5762 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3290 5763 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3291 5764 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3312 5785 9.863845 TTGTCTAAATACGAATGTATCAAGTCA 57.136 29.630 0.00 0.00 40.42 3.41
3313 5786 9.297586 TGTCTAAATACGAATGTATCAAGTCAC 57.702 33.333 0.00 0.00 40.42 3.67
3314 5787 8.469902 GTCTAAATACGAATGTATCAAGTCACG 58.530 37.037 0.00 0.00 40.42 4.35
3315 5788 8.186163 TCTAAATACGAATGTATCAAGTCACGT 58.814 33.333 0.00 0.00 40.42 4.49
3316 5789 7.591006 AAATACGAATGTATCAAGTCACGTT 57.409 32.000 0.00 0.00 40.42 3.99
3317 5790 7.591006 AATACGAATGTATCAAGTCACGTTT 57.409 32.000 0.00 0.00 40.42 3.60
3318 5791 5.917541 ACGAATGTATCAAGTCACGTTTT 57.082 34.783 0.00 0.00 0.00 2.43
3319 5792 8.692110 ATACGAATGTATCAAGTCACGTTTTA 57.308 30.769 0.00 0.00 36.56 1.52
3320 5793 7.045725 ACGAATGTATCAAGTCACGTTTTAG 57.954 36.000 0.00 0.00 0.00 1.85
3321 5794 6.643770 ACGAATGTATCAAGTCACGTTTTAGT 59.356 34.615 0.00 0.00 0.00 2.24
3322 5795 7.809331 ACGAATGTATCAAGTCACGTTTTAGTA 59.191 33.333 0.00 0.00 0.00 1.82
3323 5796 8.804743 CGAATGTATCAAGTCACGTTTTAGTAT 58.195 33.333 0.00 0.00 0.00 2.12
3327 5800 9.577110 TGTATCAAGTCACGTTTTAGTATTAGG 57.423 33.333 0.00 0.00 0.00 2.69
3328 5801 9.578439 GTATCAAGTCACGTTTTAGTATTAGGT 57.422 33.333 0.00 0.00 0.00 3.08
3330 5803 8.970691 TCAAGTCACGTTTTAGTATTAGGTAC 57.029 34.615 0.00 0.00 0.00 3.34
3331 5804 8.575589 TCAAGTCACGTTTTAGTATTAGGTACA 58.424 33.333 0.00 0.00 35.67 2.90
3332 5805 9.362539 CAAGTCACGTTTTAGTATTAGGTACAT 57.637 33.333 0.00 0.00 35.67 2.29
3333 5806 9.578439 AAGTCACGTTTTAGTATTAGGTACATC 57.422 33.333 0.00 0.00 35.67 3.06
3334 5807 8.193438 AGTCACGTTTTAGTATTAGGTACATCC 58.807 37.037 0.00 0.00 35.67 3.51
3335 5808 7.166473 GTCACGTTTTAGTATTAGGTACATCCG 59.834 40.741 0.00 0.00 41.99 4.18
3336 5809 6.974622 CACGTTTTAGTATTAGGTACATCCGT 59.025 38.462 0.00 0.00 41.99 4.69
3337 5810 8.128582 CACGTTTTAGTATTAGGTACATCCGTA 58.871 37.037 0.00 0.00 41.99 4.02
3338 5811 8.850156 ACGTTTTAGTATTAGGTACATCCGTAT 58.150 33.333 0.00 0.00 41.99 3.06
3339 5812 9.334693 CGTTTTAGTATTAGGTACATCCGTATC 57.665 37.037 0.00 0.00 41.99 2.24
3345 5818 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
3346 5819 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
3347 5820 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
3348 5821 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
3349 5822 7.216973 AGGTACATCCGTATCTAGACAAATC 57.783 40.000 0.00 0.00 37.29 2.17
3350 5823 7.005296 AGGTACATCCGTATCTAGACAAATCT 58.995 38.462 0.00 0.00 37.29 2.40
3351 5824 8.162085 AGGTACATCCGTATCTAGACAAATCTA 58.838 37.037 0.00 0.00 37.29 1.98
3352 5825 8.790718 GGTACATCCGTATCTAGACAAATCTAA 58.209 37.037 0.00 0.00 36.98 2.10
3353 5826 9.828852 GTACATCCGTATCTAGACAAATCTAAG 57.171 37.037 0.00 0.00 36.98 2.18
3354 5827 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3355 5828 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3356 5829 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3357 5830 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3358 5831 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3359 5832 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3367 5840 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3368 5841 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3369 5842 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3370 5843 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3371 5844 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3372 5845 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3373 5846 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3374 5847 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3375 5848 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3376 5849 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3377 5850 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3903 6404 1.279271 GGTGAATGTGCTCCTACACCT 59.721 52.381 0.00 0.00 42.73 4.00
3904 6405 2.350522 GTGAATGTGCTCCTACACCTG 58.649 52.381 0.00 0.00 39.93 4.00
3905 6406 1.977854 TGAATGTGCTCCTACACCTGT 59.022 47.619 0.00 0.00 39.93 4.00
3906 6407 3.056107 GTGAATGTGCTCCTACACCTGTA 60.056 47.826 0.00 0.00 39.93 2.74
3907 6408 3.195610 TGAATGTGCTCCTACACCTGTAG 59.804 47.826 5.60 5.60 45.68 2.74
3908 6409 0.895530 TGTGCTCCTACACCTGTAGC 59.104 55.000 6.92 0.05 44.97 3.58
3909 6410 0.895530 GTGCTCCTACACCTGTAGCA 59.104 55.000 6.92 2.60 44.97 3.49
3911 6412 1.272480 TGCTCCTACACCTGTAGCAGA 60.272 52.381 7.48 0.74 44.97 4.26
3912 6413 1.407258 GCTCCTACACCTGTAGCAGAG 59.593 57.143 7.48 9.85 44.97 3.35
3913 6414 2.946341 GCTCCTACACCTGTAGCAGAGA 60.946 54.545 16.74 6.16 44.97 3.10
3914 6415 3.561143 CTCCTACACCTGTAGCAGAGAT 58.439 50.000 6.92 0.00 44.97 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.038492 GCAATAAAAGTTAAAATTGCCATGGA 57.962 30.769 18.40 0.00 45.31 3.41
346 369 7.631915 AAATACCATCAACTTTTAAACGCAC 57.368 32.000 0.00 0.00 0.00 5.34
408 433 9.387257 AGATTTTTCTTTTCTTTTGCTGTGATT 57.613 25.926 0.00 0.00 0.00 2.57
456 482 3.730715 GTGAATCAAAAAGACCAGCAACG 59.269 43.478 0.00 0.00 0.00 4.10
460 486 4.590850 AAGGTGAATCAAAAAGACCAGC 57.409 40.909 0.00 0.00 33.46 4.85
463 489 6.573434 ACTCAAAAGGTGAATCAAAAAGACC 58.427 36.000 0.00 0.00 35.22 3.85
465 491 7.610865 ACAACTCAAAAGGTGAATCAAAAAGA 58.389 30.769 0.00 0.00 43.38 2.52
552 995 9.918630 CATTTATCCTTCTCTTTGTGTTTTGAT 57.081 29.630 0.00 0.00 0.00 2.57
553 996 8.359642 CCATTTATCCTTCTCTTTGTGTTTTGA 58.640 33.333 0.00 0.00 0.00 2.69
554 997 7.116805 GCCATTTATCCTTCTCTTTGTGTTTTG 59.883 37.037 0.00 0.00 0.00 2.44
722 1464 7.341024 TGTTATATATACCACGCGTTTCATG 57.659 36.000 10.22 0.00 0.00 3.07
723 1465 6.090358 GCTGTTATATATACCACGCGTTTCAT 59.910 38.462 10.22 5.13 0.00 2.57
735 1477 8.570096 TGAACGTGAACTGCTGTTATATATAC 57.430 34.615 9.14 0.00 36.39 1.47
902 1650 4.211374 AGAACTTCGGTTTATCGCATATGC 59.789 41.667 18.08 18.08 38.41 3.14
1302 2050 2.014554 CACCTGGTTCACGACGTCG 61.015 63.158 34.58 34.58 46.33 5.12
1306 2054 1.647084 GCAACACCTGGTTCACGAC 59.353 57.895 0.00 0.00 37.72 4.34
1321 2069 4.382320 GTCTGGCCCGTACCGCAA 62.382 66.667 0.00 0.00 0.00 4.85
1335 2083 2.256591 CGGCTTGCTGCTGTTGTCT 61.257 57.895 0.00 0.00 42.87 3.41
1369 2117 2.943265 ATGGAGTTGCTGCCCCCT 60.943 61.111 0.00 0.00 0.00 4.79
1373 2121 3.818787 CGCCATGGAGTTGCTGCC 61.819 66.667 18.40 0.00 0.00 4.85
1380 2128 3.984193 GAAGCTGCCGCCATGGAGT 62.984 63.158 18.40 0.00 42.00 3.85
1406 2154 4.695928 GGGACAAGAAGACTATGTTGAACC 59.304 45.833 0.00 0.00 0.00 3.62
1431 2179 1.817099 GATGCAGACCAGGAAGGCG 60.817 63.158 0.00 0.00 43.14 5.52
1434 2182 1.751351 TCGTAGATGCAGACCAGGAAG 59.249 52.381 0.00 0.00 0.00 3.46
1510 2258 2.328099 CGCCTCTGCACTTTGGACC 61.328 63.158 0.00 0.00 37.32 4.46
1512 2260 2.669569 GCGCCTCTGCACTTTGGA 60.670 61.111 0.00 0.00 37.32 3.53
1560 2308 0.898789 TCCACTGGTCCTCGAGGTTC 60.899 60.000 30.17 22.53 36.34 3.62
2095 4255 7.383300 GCTAAGATCAACAAGCATTTGAACTTT 59.617 33.333 16.91 7.77 40.98 2.66
2256 4417 0.039074 GTCGCACCTGATATCGAGGG 60.039 60.000 19.24 13.80 34.56 4.30
2477 4638 1.815003 GGCCTTGAGACCAAATGAGTG 59.185 52.381 0.00 0.00 0.00 3.51
2710 4871 0.108898 CGCGGGCAAAAATGATTCCA 60.109 50.000 0.00 0.00 0.00 3.53
2770 4931 5.059833 CAGTCCATAGTCTTTCCTAATGCC 58.940 45.833 0.00 0.00 0.00 4.40
3012 5173 9.922305 CTCTTAAATGTATAGCAAAACTACAGC 57.078 33.333 0.00 0.00 32.32 4.40
3081 5243 4.928615 CACAAAAGACAAAAAGGACTTGCA 59.071 37.500 0.00 0.00 0.00 4.08
3097 5259 1.135141 CCCCACACACACACACAAAAG 60.135 52.381 0.00 0.00 0.00 2.27
3101 5263 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
3124 5556 5.741011 TGTGATTACCAGATTACCAACTCC 58.259 41.667 0.00 0.00 0.00 3.85
3125 5557 6.823689 ACATGTGATTACCAGATTACCAACTC 59.176 38.462 0.00 0.00 0.00 3.01
3126 5558 6.599244 CACATGTGATTACCAGATTACCAACT 59.401 38.462 21.64 0.00 0.00 3.16
3127 5559 6.677920 GCACATGTGATTACCAGATTACCAAC 60.678 42.308 29.80 0.87 0.00 3.77
3128 5560 5.356751 GCACATGTGATTACCAGATTACCAA 59.643 40.000 29.80 0.00 0.00 3.67
3129 5561 4.881273 GCACATGTGATTACCAGATTACCA 59.119 41.667 29.80 0.00 0.00 3.25
3130 5562 4.275936 GGCACATGTGATTACCAGATTACC 59.724 45.833 29.80 11.84 0.00 2.85
3131 5563 4.024893 CGGCACATGTGATTACCAGATTAC 60.025 45.833 29.80 6.38 0.00 1.89
3132 5564 4.126437 CGGCACATGTGATTACCAGATTA 58.874 43.478 29.80 0.00 0.00 1.75
3133 5565 2.945008 CGGCACATGTGATTACCAGATT 59.055 45.455 29.80 0.00 0.00 2.40
3134 5566 2.564771 CGGCACATGTGATTACCAGAT 58.435 47.619 29.80 0.00 0.00 2.90
3135 5567 2.011548 GCGGCACATGTGATTACCAGA 61.012 52.381 29.80 0.00 0.00 3.86
3136 5568 0.378257 GCGGCACATGTGATTACCAG 59.622 55.000 29.80 16.04 0.00 4.00
3139 5571 0.247655 CACGCGGCACATGTGATTAC 60.248 55.000 29.80 14.01 35.49 1.89
3154 5586 4.349663 TTGTTGCATTATAGTTCCACGC 57.650 40.909 0.00 0.00 0.00 5.34
3253 5726 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3254 5727 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3255 5728 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3256 5729 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3257 5730 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3258 5731 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3259 5732 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3260 5733 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3261 5734 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3262 5735 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3263 5736 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3264 5737 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3265 5738 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3286 5759 9.863845 TGACTTGATACATTCGTATTTAGACAA 57.136 29.630 0.00 0.00 38.48 3.18
3287 5760 9.297586 GTGACTTGATACATTCGTATTTAGACA 57.702 33.333 0.00 0.00 38.48 3.41
3288 5761 8.469902 CGTGACTTGATACATTCGTATTTAGAC 58.530 37.037 0.00 0.00 38.48 2.59
3289 5762 8.186163 ACGTGACTTGATACATTCGTATTTAGA 58.814 33.333 0.00 0.00 38.48 2.10
3290 5763 8.336498 ACGTGACTTGATACATTCGTATTTAG 57.664 34.615 0.00 0.00 38.48 1.85
3291 5764 8.692110 AACGTGACTTGATACATTCGTATTTA 57.308 30.769 0.00 0.00 38.48 1.40
3292 5765 7.591006 AACGTGACTTGATACATTCGTATTT 57.409 32.000 0.00 0.00 38.48 1.40
3293 5766 7.591006 AAACGTGACTTGATACATTCGTATT 57.409 32.000 0.00 0.00 38.48 1.89
3294 5767 7.591006 AAAACGTGACTTGATACATTCGTAT 57.409 32.000 0.00 0.00 41.16 3.06
3295 5768 7.809331 ACTAAAACGTGACTTGATACATTCGTA 59.191 33.333 0.00 0.00 0.00 3.43
3296 5769 5.917541 AAAACGTGACTTGATACATTCGT 57.082 34.783 0.00 0.00 0.00 3.85
3297 5770 7.045725 ACTAAAACGTGACTTGATACATTCG 57.954 36.000 0.00 0.00 0.00 3.34
3301 5774 9.577110 CCTAATACTAAAACGTGACTTGATACA 57.423 33.333 0.00 0.00 0.00 2.29
3302 5775 9.578439 ACCTAATACTAAAACGTGACTTGATAC 57.422 33.333 0.00 0.00 0.00 2.24
3304 5777 9.578439 GTACCTAATACTAAAACGTGACTTGAT 57.422 33.333 0.00 0.00 0.00 2.57
3305 5778 8.575589 TGTACCTAATACTAAAACGTGACTTGA 58.424 33.333 0.00 0.00 34.56 3.02
3306 5779 8.746922 TGTACCTAATACTAAAACGTGACTTG 57.253 34.615 0.00 0.00 34.56 3.16
3307 5780 9.578439 GATGTACCTAATACTAAAACGTGACTT 57.422 33.333 0.00 0.00 34.56 3.01
3308 5781 8.193438 GGATGTACCTAATACTAAAACGTGACT 58.807 37.037 0.00 0.00 34.56 3.41
3309 5782 7.166473 CGGATGTACCTAATACTAAAACGTGAC 59.834 40.741 0.00 0.00 34.56 3.67
3310 5783 7.148086 ACGGATGTACCTAATACTAAAACGTGA 60.148 37.037 0.00 0.00 34.56 4.35
3311 5784 6.974622 ACGGATGTACCTAATACTAAAACGTG 59.025 38.462 0.00 0.00 34.56 4.49
3312 5785 7.100458 ACGGATGTACCTAATACTAAAACGT 57.900 36.000 0.00 0.00 34.56 3.99
3313 5786 9.334693 GATACGGATGTACCTAATACTAAAACG 57.665 37.037 0.00 0.00 34.56 3.60
3319 5792 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
3320 5793 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
3321 5794 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
3322 5795 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
3323 5796 8.701908 ATTTGTCTAGATACGGATGTACCTAA 57.298 34.615 0.00 0.00 36.31 2.69
3324 5797 8.162085 AGATTTGTCTAGATACGGATGTACCTA 58.838 37.037 0.00 0.00 36.31 3.08
3325 5798 7.005296 AGATTTGTCTAGATACGGATGTACCT 58.995 38.462 0.00 0.00 36.31 3.08
3326 5799 7.216973 AGATTTGTCTAGATACGGATGTACC 57.783 40.000 0.00 0.00 32.26 3.34
3327 5800 9.828852 CTTAGATTTGTCTAGATACGGATGTAC 57.171 37.037 0.00 0.00 32.26 2.90
3328 5801 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3329 5802 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3330 5803 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3331 5804 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3332 5805 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3333 5806 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3341 5814 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3342 5815 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3343 5816 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3344 5817 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3345 5818 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3346 5819 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3347 5820 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3348 5821 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3349 5822 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3350 5823 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3351 5824 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3352 5825 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3353 5826 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3354 5827 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3355 5828 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3356 5829 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3357 5830 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3358 5831 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3359 5832 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3360 5833 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3361 5834 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3362 5835 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3363 5836 0.901580 GTGTACTCCCTCCGTCCCAA 60.902 60.000 0.00 0.00 0.00 4.12
3364 5837 1.304713 GTGTACTCCCTCCGTCCCA 60.305 63.158 0.00 0.00 0.00 4.37
3365 5838 0.686769 ATGTGTACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
3366 5839 0.460311 CATGTGTACTCCCTCCGTCC 59.540 60.000 0.00 0.00 0.00 4.79
3367 5840 1.471119 TCATGTGTACTCCCTCCGTC 58.529 55.000 0.00 0.00 0.00 4.79
3368 5841 1.549170 GTTCATGTGTACTCCCTCCGT 59.451 52.381 0.00 0.00 0.00 4.69
3369 5842 1.825474 AGTTCATGTGTACTCCCTCCG 59.175 52.381 0.00 0.00 0.00 4.63
3370 5843 2.832129 TGAGTTCATGTGTACTCCCTCC 59.168 50.000 14.55 0.00 40.39 4.30
3371 5844 4.246458 GTTGAGTTCATGTGTACTCCCTC 58.754 47.826 14.55 4.64 40.39 4.30
3372 5845 3.646162 TGTTGAGTTCATGTGTACTCCCT 59.354 43.478 14.55 0.00 40.39 4.20
3373 5846 4.002906 TGTTGAGTTCATGTGTACTCCC 57.997 45.455 14.55 7.90 40.39 4.30
3374 5847 5.536554 CATGTTGAGTTCATGTGTACTCC 57.463 43.478 14.55 4.11 40.39 3.85
3517 5990 8.393259 ACATATATGGAATTTGATGGGCTTAGA 58.607 33.333 16.96 0.00 0.00 2.10
3586 6060 8.635877 AAGTTGTAGTTCTCGACATGATAATC 57.364 34.615 0.00 0.00 0.00 1.75
3605 6079 9.959721 AGTTACATATGATTACTCCAAAGTTGT 57.040 29.630 10.38 0.00 36.92 3.32


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

AutoCloner maintained by Alex Coulton.