Multiple sequence alignment - TraesCS6A01G020700

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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 TraesCS6A01G020700 chr6A 100.000 3394 0 0 1 3394 9655985 9652592 0.000000e+00 6268
1 TraesCS6A01G020700 chr6A 96.721 183 4 2 3213 3394 9642554 9642373 1.530000e-78 303
2 TraesCS6A01G020700 chr7A 98.946 3227 33 1 1 3226 60349347 60346121 0.000000e+00 5770
3 TraesCS6A01G020700 chr7B 98.822 3226 38 0 1 3226 716910712 716907487 0.000000e+00 5747
4 TraesCS6A01G020700 chr7B 98.760 3226 39 1 1 3226 716778895 716775671 0.000000e+00 5734
5 TraesCS6A01G020700 chr7B 98.760 3226 39 1 1 3226 742954451 742957675 0.000000e+00 5734
6 TraesCS6A01G020700 chr5A 98.822 3226 38 0 1 3226 16538869 16535644 0.000000e+00 5747
7 TraesCS6A01G020700 chr1B 98.543 3226 46 1 1 3226 583567261 583570485 0.000000e+00 5696
8 TraesCS6A01G020700 chr2B 98.513 3227 46 2 1 3226 391172731 391169506 0.000000e+00 5692
9 TraesCS6A01G020700 chr2B 96.721 183 4 2 3213 3394 570984434 570984615 1.530000e-78 303
10 TraesCS6A01G020700 chr4B 98.202 3226 57 1 1 3226 209224813 209221589 0.000000e+00 5635
11 TraesCS6A01G020700 chr4B 96.721 183 4 2 3213 3394 159468987 159469168 1.530000e-78 303
12 TraesCS6A01G020700 chr4B 96.721 183 4 2 3213 3394 243938846 243939027 1.530000e-78 303
13 TraesCS6A01G020700 chr4B 96.721 183 4 2 3213 3394 274027893 274027712 1.530000e-78 303
14 TraesCS6A01G020700 chr3B 97.770 3229 69 1 1 3226 39847343 39844115 0.000000e+00 5561
15 TraesCS6A01G020700 chr3A 97.268 183 3 2 3213 3394 563453113 563452932 3.290000e-80 309
16 TraesCS6A01G020700 chrUn 96.721 183 4 2 3213 3394 453789862 453789681 1.530000e-78 303
17 TraesCS6A01G020700 chr2A 96.721 183 4 2 3213 3394 389194675 389194494 1.530000e-78 303
18 TraesCS6A01G020700 chr1A 96.721 183 4 2 3213 3394 550285761 550285580 1.530000e-78 303


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 TraesCS6A01G020700 chr6A 9652592 9655985 3393 True 6268 6268 100.000 1 3394 1 chr6A.!!$R2 3393
1 TraesCS6A01G020700 chr7A 60346121 60349347 3226 True 5770 5770 98.946 1 3226 1 chr7A.!!$R1 3225
2 TraesCS6A01G020700 chr7B 716907487 716910712 3225 True 5747 5747 98.822 1 3226 1 chr7B.!!$R2 3225
3 TraesCS6A01G020700 chr7B 716775671 716778895 3224 True 5734 5734 98.760 1 3226 1 chr7B.!!$R1 3225
4 TraesCS6A01G020700 chr7B 742954451 742957675 3224 False 5734 5734 98.760 1 3226 1 chr7B.!!$F1 3225
5 TraesCS6A01G020700 chr5A 16535644 16538869 3225 True 5747 5747 98.822 1 3226 1 chr5A.!!$R1 3225
6 TraesCS6A01G020700 chr1B 583567261 583570485 3224 False 5696 5696 98.543 1 3226 1 chr1B.!!$F1 3225
7 TraesCS6A01G020700 chr2B 391169506 391172731 3225 True 5692 5692 98.513 1 3226 1 chr2B.!!$R1 3225
8 TraesCS6A01G020700 chr4B 209221589 209224813 3224 True 5635 5635 98.202 1 3226 1 chr4B.!!$R1 3225
9 TraesCS6A01G020700 chr3B 39844115 39847343 3228 True 5561 5561 97.770 1 3226 1 chr3B.!!$R1 3225

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
74 75 3.246203 TGACCCTATCCACCTCCTTTGTA 60.246 47.826 0.0 0.0 0.0 2.41 F
1629 1635 1.679032 GCATTTACCCTGAGTCGGCTT 60.679 52.381 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1727 1.126296 GCTCGAAAGCGTTAGTCAACC 59.874 52.381 0.00 0.0 39.1 3.77 R
3263 3269 0.036765 GTGGTGACGTGGCCTCATTA 60.037 55.000 3.32 0.0 0.0 1.90 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
74 75 3.246203 TGACCCTATCCACCTCCTTTGTA 60.246 47.826 0.00 0.00 0.00 2.41
102 103 6.244552 ACCAGATCAAGAGATGAATTAGCA 57.755 37.500 0.00 0.00 42.54 3.49
151 152 5.279556 GCCAGAACCTTCTTTAGTAGTGAGT 60.280 44.000 0.00 0.00 34.74 3.41
237 238 4.454504 GGGTACGAATGTCATGTTCAAAGT 59.545 41.667 0.00 0.00 0.00 2.66
392 393 9.432982 AGATTCTATATTCTCAAGGAAGTGAGT 57.567 33.333 2.38 0.00 44.56 3.41
534 535 8.801715 TCAAGTGATTCAGTAAAAATGAAAGC 57.198 30.769 0.00 0.00 39.92 3.51
559 560 9.970395 GCAATCTCACATAAAATTGGATTATCA 57.030 29.630 0.00 0.00 31.33 2.15
958 964 4.570079 CCCGCCCTATCTAGAGAAGGAATA 60.570 50.000 20.60 0.00 31.64 1.75
1629 1635 1.679032 GCATTTACCCTGAGTCGGCTT 60.679 52.381 0.00 0.00 0.00 4.35
1721 1727 3.817647 AGAAAAGCAAGGACAAGTAGCTG 59.182 43.478 0.00 0.00 35.42 4.24
2185 2191 3.756434 CGGATATGCCCGGTGAAAATTAT 59.244 43.478 0.00 0.00 45.43 1.28
2465 2471 3.259876 TGGTTAGCTGTTCACGGATTAGT 59.740 43.478 0.00 0.00 0.00 2.24
3038 3044 5.476599 CGGCCCTCATTATTGAATTTATCCA 59.523 40.000 0.00 0.00 0.00 3.41
3113 3119 9.147732 TCATTCCTATATCGGCATGTATTATCT 57.852 33.333 5.94 0.00 30.92 1.98
3226 3232 2.556622 CAATGTTTAGTGCGGGGAACTT 59.443 45.455 0.00 0.00 0.00 2.66
3227 3233 1.600023 TGTTTAGTGCGGGGAACTTG 58.400 50.000 0.00 0.00 0.00 3.16
3228 3234 1.134037 TGTTTAGTGCGGGGAACTTGT 60.134 47.619 0.00 0.00 0.00 3.16
3229 3235 1.265905 GTTTAGTGCGGGGAACTTGTG 59.734 52.381 0.00 0.00 0.00 3.33
3230 3236 0.759959 TTAGTGCGGGGAACTTGTGA 59.240 50.000 0.00 0.00 0.00 3.58
3231 3237 0.034337 TAGTGCGGGGAACTTGTGAC 59.966 55.000 0.00 0.00 0.00 3.67
3232 3238 2.280524 TGCGGGGAACTTGTGACG 60.281 61.111 0.00 0.00 0.00 4.35
3233 3239 3.723348 GCGGGGAACTTGTGACGC 61.723 66.667 0.00 0.00 40.19 5.19
3234 3240 3.047877 CGGGGAACTTGTGACGCC 61.048 66.667 0.00 0.00 0.00 5.68
3235 3241 2.671963 GGGGAACTTGTGACGCCC 60.672 66.667 0.00 0.00 38.08 6.13
3236 3242 3.047877 GGGAACTTGTGACGCCCG 61.048 66.667 0.00 0.00 0.00 6.13
3237 3243 3.047877 GGAACTTGTGACGCCCGG 61.048 66.667 0.00 0.00 0.00 5.73
3238 3244 2.029964 GAACTTGTGACGCCCGGA 59.970 61.111 0.73 0.00 0.00 5.14
3239 3245 1.375523 GAACTTGTGACGCCCGGAT 60.376 57.895 0.73 0.00 0.00 4.18
3240 3246 0.108520 GAACTTGTGACGCCCGGATA 60.109 55.000 0.73 0.00 0.00 2.59
3241 3247 0.322322 AACTTGTGACGCCCGGATAA 59.678 50.000 0.73 0.00 0.00 1.75
3242 3248 0.539986 ACTTGTGACGCCCGGATAAT 59.460 50.000 0.73 0.00 0.00 1.28
3243 3249 1.217882 CTTGTGACGCCCGGATAATC 58.782 55.000 0.73 0.00 0.00 1.75
3244 3250 0.537653 TTGTGACGCCCGGATAATCA 59.462 50.000 0.73 0.00 0.00 2.57
3245 3251 0.537653 TGTGACGCCCGGATAATCAA 59.462 50.000 0.73 0.00 0.00 2.57
3246 3252 1.217882 GTGACGCCCGGATAATCAAG 58.782 55.000 0.73 0.00 0.00 3.02
3247 3253 0.531974 TGACGCCCGGATAATCAAGC 60.532 55.000 0.73 0.00 0.00 4.01
3248 3254 0.249911 GACGCCCGGATAATCAAGCT 60.250 55.000 0.73 0.00 0.00 3.74
3249 3255 1.000506 GACGCCCGGATAATCAAGCTA 59.999 52.381 0.73 0.00 0.00 3.32
3250 3256 1.270147 ACGCCCGGATAATCAAGCTAC 60.270 52.381 0.73 0.00 0.00 3.58
3251 3257 1.270094 CGCCCGGATAATCAAGCTACA 60.270 52.381 0.73 0.00 0.00 2.74
3252 3258 2.417719 GCCCGGATAATCAAGCTACAG 58.582 52.381 0.73 0.00 0.00 2.74
3253 3259 2.224305 GCCCGGATAATCAAGCTACAGT 60.224 50.000 0.73 0.00 0.00 3.55
3254 3260 3.393800 CCCGGATAATCAAGCTACAGTG 58.606 50.000 0.73 0.00 0.00 3.66
3255 3261 3.069586 CCCGGATAATCAAGCTACAGTGA 59.930 47.826 0.73 0.00 0.00 3.41
3256 3262 4.051922 CCGGATAATCAAGCTACAGTGAC 58.948 47.826 0.00 0.00 0.00 3.67
3257 3263 4.051922 CGGATAATCAAGCTACAGTGACC 58.948 47.826 0.00 0.00 0.00 4.02
3258 3264 4.202161 CGGATAATCAAGCTACAGTGACCT 60.202 45.833 0.00 0.00 0.00 3.85
3259 3265 5.293560 GGATAATCAAGCTACAGTGACCTC 58.706 45.833 0.00 0.00 0.00 3.85
3260 3266 5.069781 GGATAATCAAGCTACAGTGACCTCT 59.930 44.000 0.00 0.00 0.00 3.69
3261 3267 3.883830 ATCAAGCTACAGTGACCTCTG 57.116 47.619 0.00 0.00 40.80 3.35
3262 3268 1.273606 TCAAGCTACAGTGACCTCTGC 59.726 52.381 0.00 0.00 38.84 4.26
3263 3269 1.274728 CAAGCTACAGTGACCTCTGCT 59.725 52.381 0.00 0.00 38.84 4.24
3264 3270 2.493675 CAAGCTACAGTGACCTCTGCTA 59.506 50.000 0.00 0.00 38.84 3.49
3265 3271 2.808919 AGCTACAGTGACCTCTGCTAA 58.191 47.619 0.00 0.00 38.84 3.09
3266 3272 3.370104 AGCTACAGTGACCTCTGCTAAT 58.630 45.455 0.00 0.00 38.84 1.73
3267 3273 3.131933 AGCTACAGTGACCTCTGCTAATG 59.868 47.826 0.00 0.00 38.84 1.90
3268 3274 3.131223 GCTACAGTGACCTCTGCTAATGA 59.869 47.826 0.00 0.00 38.84 2.57
3269 3275 3.883830 ACAGTGACCTCTGCTAATGAG 57.116 47.619 0.00 0.00 38.84 2.90
3274 3280 3.393472 CCTCTGCTAATGAGGCCAC 57.607 57.895 5.01 0.00 43.67 5.01
3275 3281 0.531532 CCTCTGCTAATGAGGCCACG 60.532 60.000 5.01 0.00 43.67 4.94
3276 3282 0.176680 CTCTGCTAATGAGGCCACGT 59.823 55.000 5.01 0.00 0.00 4.49
3277 3283 0.175760 TCTGCTAATGAGGCCACGTC 59.824 55.000 5.01 0.00 0.00 4.34
3278 3284 0.108186 CTGCTAATGAGGCCACGTCA 60.108 55.000 5.01 0.00 32.83 4.35
3279 3285 0.391130 TGCTAATGAGGCCACGTCAC 60.391 55.000 5.01 0.00 31.07 3.67
3280 3286 1.090052 GCTAATGAGGCCACGTCACC 61.090 60.000 5.01 0.00 31.07 4.02
3281 3287 0.249120 CTAATGAGGCCACGTCACCA 59.751 55.000 5.01 0.00 31.07 4.17
3282 3288 0.036765 TAATGAGGCCACGTCACCAC 60.037 55.000 5.01 0.45 31.07 4.16
3283 3289 1.768684 AATGAGGCCACGTCACCACT 61.769 55.000 5.01 0.00 31.07 4.00
3284 3290 2.048127 GAGGCCACGTCACCACTC 60.048 66.667 5.01 0.00 0.00 3.51
3285 3291 2.524394 AGGCCACGTCACCACTCT 60.524 61.111 5.01 0.00 0.00 3.24
3286 3292 2.100879 GAGGCCACGTCACCACTCTT 62.101 60.000 5.01 0.00 0.00 2.85
3287 3293 0.830444 AGGCCACGTCACCACTCTTA 60.830 55.000 5.01 0.00 0.00 2.10
3288 3294 0.669625 GGCCACGTCACCACTCTTAC 60.670 60.000 0.00 0.00 0.00 2.34
3289 3295 0.317479 GCCACGTCACCACTCTTACT 59.683 55.000 0.00 0.00 0.00 2.24
3290 3296 1.935300 GCCACGTCACCACTCTTACTG 60.935 57.143 0.00 0.00 0.00 2.74
3291 3297 1.340248 CCACGTCACCACTCTTACTGT 59.660 52.381 0.00 0.00 0.00 3.55
3292 3298 2.223971 CCACGTCACCACTCTTACTGTT 60.224 50.000 0.00 0.00 0.00 3.16
3293 3299 2.794910 CACGTCACCACTCTTACTGTTG 59.205 50.000 0.00 0.00 0.00 3.33
3294 3300 2.429610 ACGTCACCACTCTTACTGTTGT 59.570 45.455 0.00 0.00 0.00 3.32
3295 3301 3.633525 ACGTCACCACTCTTACTGTTGTA 59.366 43.478 0.00 0.00 0.00 2.41
3296 3302 4.098349 ACGTCACCACTCTTACTGTTGTAA 59.902 41.667 0.00 0.00 37.16 2.41
3297 3303 5.045215 CGTCACCACTCTTACTGTTGTAAA 58.955 41.667 0.00 0.00 38.09 2.01
3298 3304 5.694910 CGTCACCACTCTTACTGTTGTAAAT 59.305 40.000 0.00 0.00 38.09 1.40
3299 3305 6.128902 CGTCACCACTCTTACTGTTGTAAATC 60.129 42.308 0.00 0.00 38.09 2.17
3300 3306 6.929606 GTCACCACTCTTACTGTTGTAAATCT 59.070 38.462 0.00 0.00 38.09 2.40
3301 3307 7.116519 GTCACCACTCTTACTGTTGTAAATCTC 59.883 40.741 0.00 0.00 38.09 2.75
3302 3308 6.929049 CACCACTCTTACTGTTGTAAATCTCA 59.071 38.462 0.00 0.00 38.09 3.27
3303 3309 6.929606 ACCACTCTTACTGTTGTAAATCTCAC 59.070 38.462 0.00 0.00 38.09 3.51
3304 3310 6.089551 CCACTCTTACTGTTGTAAATCTCACG 59.910 42.308 0.00 0.00 38.09 4.35
3305 3311 6.861572 CACTCTTACTGTTGTAAATCTCACGA 59.138 38.462 0.00 0.00 38.09 4.35
3306 3312 7.542477 CACTCTTACTGTTGTAAATCTCACGAT 59.458 37.037 0.00 0.00 38.09 3.73
3307 3313 7.542477 ACTCTTACTGTTGTAAATCTCACGATG 59.458 37.037 0.00 0.00 38.09 3.84
3308 3314 7.599171 TCTTACTGTTGTAAATCTCACGATGA 58.401 34.615 0.00 0.00 38.09 2.92
3309 3315 8.251026 TCTTACTGTTGTAAATCTCACGATGAT 58.749 33.333 0.00 0.00 38.09 2.45
3310 3316 8.771920 TTACTGTTGTAAATCTCACGATGATT 57.228 30.769 0.00 0.00 35.90 2.57
3311 3317 7.295952 ACTGTTGTAAATCTCACGATGATTC 57.704 36.000 0.00 0.00 33.54 2.52
3312 3318 6.873605 ACTGTTGTAAATCTCACGATGATTCA 59.126 34.615 0.00 0.00 33.54 2.57
3313 3319 7.387673 ACTGTTGTAAATCTCACGATGATTCAA 59.612 33.333 0.00 0.00 33.54 2.69
3314 3320 8.267620 TGTTGTAAATCTCACGATGATTCAAT 57.732 30.769 0.00 0.00 33.54 2.57
3315 3321 8.390354 TGTTGTAAATCTCACGATGATTCAATC 58.610 33.333 0.00 0.00 33.54 2.67
3316 3322 7.482654 TGTAAATCTCACGATGATTCAATCC 57.517 36.000 0.00 0.00 33.54 3.01
3317 3323 6.483307 TGTAAATCTCACGATGATTCAATCCC 59.517 38.462 0.00 0.00 33.54 3.85
3318 3324 3.097877 TCTCACGATGATTCAATCCCG 57.902 47.619 7.49 7.49 0.00 5.14
3319 3325 2.430694 TCTCACGATGATTCAATCCCGT 59.569 45.455 8.58 8.58 37.81 5.28
3320 3326 3.118775 TCTCACGATGATTCAATCCCGTT 60.119 43.478 10.98 0.00 36.11 4.44
3321 3327 3.194861 TCACGATGATTCAATCCCGTTC 58.805 45.455 10.98 0.00 36.11 3.95
3322 3328 2.033747 CACGATGATTCAATCCCGTTCG 60.034 50.000 10.98 9.02 36.11 3.95
3323 3329 2.159156 ACGATGATTCAATCCCGTTCGA 60.159 45.455 13.06 0.00 35.20 3.71
3324 3330 2.863740 CGATGATTCAATCCCGTTCGAA 59.136 45.455 0.00 0.00 0.00 3.71
3325 3331 3.494626 CGATGATTCAATCCCGTTCGAAT 59.505 43.478 0.00 0.00 0.00 3.34
3326 3332 4.024893 CGATGATTCAATCCCGTTCGAATT 60.025 41.667 0.00 0.00 0.00 2.17
3327 3333 4.875544 TGATTCAATCCCGTTCGAATTC 57.124 40.909 0.00 0.00 0.00 2.17
3328 3334 4.257731 TGATTCAATCCCGTTCGAATTCA 58.742 39.130 0.00 0.00 0.00 2.57
3329 3335 4.697828 TGATTCAATCCCGTTCGAATTCAA 59.302 37.500 0.00 0.00 0.00 2.69
3330 3336 5.182190 TGATTCAATCCCGTTCGAATTCAAA 59.818 36.000 0.00 0.00 0.00 2.69
3331 3337 5.440234 TTCAATCCCGTTCGAATTCAAAA 57.560 34.783 0.00 0.00 0.00 2.44
3332 3338 5.637006 TCAATCCCGTTCGAATTCAAAAT 57.363 34.783 0.00 0.00 0.00 1.82
3333 3339 6.019779 TCAATCCCGTTCGAATTCAAAATT 57.980 33.333 0.00 0.00 0.00 1.82
3334 3340 6.451393 TCAATCCCGTTCGAATTCAAAATTT 58.549 32.000 0.00 0.00 0.00 1.82
3335 3341 7.594714 TCAATCCCGTTCGAATTCAAAATTTA 58.405 30.769 0.00 0.00 0.00 1.40
3336 3342 8.082852 TCAATCCCGTTCGAATTCAAAATTTAA 58.917 29.630 0.00 0.00 0.00 1.52
3337 3343 8.704234 CAATCCCGTTCGAATTCAAAATTTAAA 58.296 29.630 0.00 0.00 0.00 1.52
3338 3344 8.819643 ATCCCGTTCGAATTCAAAATTTAAAA 57.180 26.923 0.00 0.00 0.00 1.52
3339 3345 8.819643 TCCCGTTCGAATTCAAAATTTAAAAT 57.180 26.923 0.00 0.00 0.00 1.82
3340 3346 8.917655 TCCCGTTCGAATTCAAAATTTAAAATC 58.082 29.630 0.00 0.00 0.00 2.17
3341 3347 8.704234 CCCGTTCGAATTCAAAATTTAAAATCA 58.296 29.630 0.00 0.00 0.00 2.57
3352 3358 9.372369 TCAAAATTTAAAATCAAGTCAAACGGT 57.628 25.926 0.00 0.00 0.00 4.83
3358 3364 9.857957 TTTAAAATCAAGTCAAACGGTAAAGTT 57.142 25.926 0.00 0.00 35.59 2.66
3359 3365 9.857957 TTAAAATCAAGTCAAACGGTAAAGTTT 57.142 25.926 0.00 0.00 44.27 2.66
3360 3366 8.766000 AAAATCAAGTCAAACGGTAAAGTTTT 57.234 26.923 0.00 0.00 41.84 2.43
3361 3367 7.980742 AATCAAGTCAAACGGTAAAGTTTTC 57.019 32.000 0.00 0.00 41.84 2.29
3362 3368 6.497785 TCAAGTCAAACGGTAAAGTTTTCA 57.502 33.333 0.00 0.00 41.84 2.69
3363 3369 6.910995 TCAAGTCAAACGGTAAAGTTTTCAA 58.089 32.000 0.00 0.00 41.84 2.69
3364 3370 7.368833 TCAAGTCAAACGGTAAAGTTTTCAAA 58.631 30.769 0.00 0.00 41.84 2.69
3365 3371 7.326547 TCAAGTCAAACGGTAAAGTTTTCAAAC 59.673 33.333 0.00 0.00 41.84 2.93
3366 3372 6.679843 AGTCAAACGGTAAAGTTTTCAAACA 58.320 32.000 5.26 0.00 41.84 2.83
3367 3373 7.317390 AGTCAAACGGTAAAGTTTTCAAACAT 58.683 30.769 5.26 0.00 41.84 2.71
3368 3374 7.815549 AGTCAAACGGTAAAGTTTTCAAACATT 59.184 29.630 5.26 2.11 41.84 2.71
3369 3375 9.074443 GTCAAACGGTAAAGTTTTCAAACATTA 57.926 29.630 5.26 1.19 41.84 1.90
3370 3376 9.635520 TCAAACGGTAAAGTTTTCAAACATTAA 57.364 25.926 5.26 0.00 41.84 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 2.145397 TCGACTTAGCCCTGTGATCT 57.855 50.000 0.00 0.00 0.00 2.75
324 325 5.698741 TGTTGACCCATATGATCTCAGTT 57.301 39.130 3.65 0.00 0.00 3.16
325 326 5.698741 TTGTTGACCCATATGATCTCAGT 57.301 39.130 3.65 0.00 0.00 3.41
392 393 0.898320 GCTAGGCTGAGGTTGAGTGA 59.102 55.000 0.00 0.00 0.00 3.41
958 964 9.467796 TTTTTGTACATTCAAAAAGGGGAATTT 57.532 25.926 11.53 0.00 45.82 1.82
1090 1096 2.223249 CGAATAACCAACCCGCAATGAG 60.223 50.000 0.00 0.00 0.00 2.90
1721 1727 1.126296 GCTCGAAAGCGTTAGTCAACC 59.874 52.381 0.00 0.00 39.10 3.77
2090 2096 3.507233 TCGCTTCTTTCCATTGCTTCAAT 59.493 39.130 0.00 0.00 34.04 2.57
2185 2191 4.657814 AATCCTTCCTCAGCCTTGTTTA 57.342 40.909 0.00 0.00 0.00 2.01
2465 2471 7.164803 TCATATGTGTTGTCATTCCAGTACAA 58.835 34.615 1.90 0.00 0.00 2.41
2829 2835 3.558829 CGCAGTAGTAGATGACGTTCCTA 59.441 47.826 0.00 0.00 0.00 2.94
3038 3044 2.890311 TGAATTTGGTTGCATCGAAGGT 59.110 40.909 0.00 0.00 0.00 3.50
3113 3119 1.419381 TGTCTCACAACCAGCCTACA 58.581 50.000 0.00 0.00 0.00 2.74
3226 3232 0.537653 TTGATTATCCGGGCGTCACA 59.462 50.000 0.00 0.00 0.00 3.58
3227 3233 1.217882 CTTGATTATCCGGGCGTCAC 58.782 55.000 0.00 0.00 0.00 3.67
3228 3234 0.531974 GCTTGATTATCCGGGCGTCA 60.532 55.000 0.00 0.00 0.00 4.35
3229 3235 0.249911 AGCTTGATTATCCGGGCGTC 60.250 55.000 0.00 0.00 0.00 5.19
3230 3236 1.045407 TAGCTTGATTATCCGGGCGT 58.955 50.000 0.00 0.00 0.00 5.68
3231 3237 1.270094 TGTAGCTTGATTATCCGGGCG 60.270 52.381 0.00 0.00 0.00 6.13
3232 3238 2.224305 ACTGTAGCTTGATTATCCGGGC 60.224 50.000 0.00 0.00 0.00 6.13
3233 3239 3.069586 TCACTGTAGCTTGATTATCCGGG 59.930 47.826 0.00 0.00 0.00 5.73
3234 3240 4.051922 GTCACTGTAGCTTGATTATCCGG 58.948 47.826 0.00 0.00 0.00 5.14
3235 3241 4.051922 GGTCACTGTAGCTTGATTATCCG 58.948 47.826 0.00 0.00 0.00 4.18
3236 3242 5.069781 AGAGGTCACTGTAGCTTGATTATCC 59.930 44.000 0.00 0.00 0.00 2.59
3237 3243 5.982516 CAGAGGTCACTGTAGCTTGATTATC 59.017 44.000 0.00 0.00 33.73 1.75
3238 3244 5.683509 GCAGAGGTCACTGTAGCTTGATTAT 60.684 44.000 0.00 0.00 39.73 1.28
3239 3245 4.382040 GCAGAGGTCACTGTAGCTTGATTA 60.382 45.833 0.00 0.00 39.73 1.75
3240 3246 3.618507 GCAGAGGTCACTGTAGCTTGATT 60.619 47.826 0.00 0.00 39.73 2.57
3241 3247 2.093764 GCAGAGGTCACTGTAGCTTGAT 60.094 50.000 0.00 0.00 39.73 2.57
3242 3248 1.273606 GCAGAGGTCACTGTAGCTTGA 59.726 52.381 0.00 0.00 39.73 3.02
3243 3249 1.274728 AGCAGAGGTCACTGTAGCTTG 59.725 52.381 0.00 0.00 39.73 4.01
3244 3250 1.638529 AGCAGAGGTCACTGTAGCTT 58.361 50.000 0.00 0.00 39.73 3.74
3245 3251 2.516227 TAGCAGAGGTCACTGTAGCT 57.484 50.000 0.00 0.00 39.73 3.32
3246 3252 3.131223 TCATTAGCAGAGGTCACTGTAGC 59.869 47.826 0.00 0.00 39.73 3.58
3247 3253 4.202101 CCTCATTAGCAGAGGTCACTGTAG 60.202 50.000 0.00 0.00 46.07 2.74
3248 3254 3.701542 CCTCATTAGCAGAGGTCACTGTA 59.298 47.826 0.00 0.00 46.07 2.74
3249 3255 2.499289 CCTCATTAGCAGAGGTCACTGT 59.501 50.000 0.00 0.00 46.07 3.55
3250 3256 3.176552 CCTCATTAGCAGAGGTCACTG 57.823 52.381 0.00 0.00 46.07 3.66
3257 3263 0.176680 ACGTGGCCTCATTAGCAGAG 59.823 55.000 3.32 0.00 0.00 3.35
3258 3264 0.175760 GACGTGGCCTCATTAGCAGA 59.824 55.000 3.32 0.00 0.00 4.26
3259 3265 0.108186 TGACGTGGCCTCATTAGCAG 60.108 55.000 3.32 0.00 0.00 4.24
3260 3266 0.391130 GTGACGTGGCCTCATTAGCA 60.391 55.000 3.32 0.00 0.00 3.49
3261 3267 1.090052 GGTGACGTGGCCTCATTAGC 61.090 60.000 3.32 0.00 0.00 3.09
3262 3268 0.249120 TGGTGACGTGGCCTCATTAG 59.751 55.000 3.32 0.00 0.00 1.73
3263 3269 0.036765 GTGGTGACGTGGCCTCATTA 60.037 55.000 3.32 0.00 0.00 1.90
3264 3270 1.302511 GTGGTGACGTGGCCTCATT 60.303 57.895 3.32 0.00 0.00 2.57
3265 3271 2.172483 GAGTGGTGACGTGGCCTCAT 62.172 60.000 3.32 0.00 0.00 2.90
3266 3272 2.842462 AGTGGTGACGTGGCCTCA 60.842 61.111 3.32 0.00 0.00 3.86
3267 3273 2.048127 GAGTGGTGACGTGGCCTC 60.048 66.667 3.32 0.00 0.00 4.70
3268 3274 0.830444 TAAGAGTGGTGACGTGGCCT 60.830 55.000 3.32 0.00 0.00 5.19
3269 3275 0.669625 GTAAGAGTGGTGACGTGGCC 60.670 60.000 0.00 0.00 0.00 5.36
3270 3276 0.317479 AGTAAGAGTGGTGACGTGGC 59.683 55.000 0.00 0.00 0.00 5.01
3271 3277 1.340248 ACAGTAAGAGTGGTGACGTGG 59.660 52.381 0.00 0.00 0.00 4.94
3272 3278 2.794910 CAACAGTAAGAGTGGTGACGTG 59.205 50.000 0.00 0.00 38.50 4.49
3273 3279 2.429610 ACAACAGTAAGAGTGGTGACGT 59.570 45.455 6.35 0.00 38.50 4.34
3274 3280 3.093717 ACAACAGTAAGAGTGGTGACG 57.906 47.619 6.35 0.00 38.50 4.35
3275 3281 6.929606 AGATTTACAACAGTAAGAGTGGTGAC 59.070 38.462 6.35 0.00 38.50 3.67
3276 3282 7.062749 AGATTTACAACAGTAAGAGTGGTGA 57.937 36.000 6.35 0.00 38.50 4.02
3277 3283 6.929049 TGAGATTTACAACAGTAAGAGTGGTG 59.071 38.462 0.00 0.00 41.88 4.17
3278 3284 6.929606 GTGAGATTTACAACAGTAAGAGTGGT 59.070 38.462 0.00 0.00 0.00 4.16
3279 3285 6.089551 CGTGAGATTTACAACAGTAAGAGTGG 59.910 42.308 0.00 0.00 0.00 4.00
3280 3286 6.861572 TCGTGAGATTTACAACAGTAAGAGTG 59.138 38.462 0.00 0.00 33.31 3.51
3281 3287 6.978338 TCGTGAGATTTACAACAGTAAGAGT 58.022 36.000 0.00 0.00 33.31 3.24
3299 3305 2.826428 ACGGGATTGAATCATCGTGAG 58.174 47.619 19.41 2.14 38.55 3.51
3300 3306 2.979814 ACGGGATTGAATCATCGTGA 57.020 45.000 19.41 0.00 38.55 4.35
3301 3307 2.033747 CGAACGGGATTGAATCATCGTG 60.034 50.000 20.33 9.86 39.40 4.35
3302 3308 2.159156 TCGAACGGGATTGAATCATCGT 60.159 45.455 16.12 16.12 40.51 3.73
3303 3309 2.469826 TCGAACGGGATTGAATCATCG 58.530 47.619 15.10 15.10 34.96 3.84
3304 3310 5.007626 TGAATTCGAACGGGATTGAATCATC 59.992 40.000 7.56 0.00 31.06 2.92
3305 3311 4.881273 TGAATTCGAACGGGATTGAATCAT 59.119 37.500 7.56 0.00 31.06 2.45
3306 3312 4.257731 TGAATTCGAACGGGATTGAATCA 58.742 39.130 7.56 0.00 31.06 2.57
3307 3313 4.875544 TGAATTCGAACGGGATTGAATC 57.124 40.909 0.00 0.00 31.06 2.52
3308 3314 5.637006 TTTGAATTCGAACGGGATTGAAT 57.363 34.783 0.00 0.00 32.69 2.57
3309 3315 5.440234 TTTTGAATTCGAACGGGATTGAA 57.560 34.783 7.67 0.00 0.00 2.69
3310 3316 5.637006 ATTTTGAATTCGAACGGGATTGA 57.363 34.783 7.67 0.00 0.00 2.57
3311 3317 6.704512 AAATTTTGAATTCGAACGGGATTG 57.295 33.333 7.67 0.00 0.00 2.67
3312 3318 8.819643 TTTAAATTTTGAATTCGAACGGGATT 57.180 26.923 7.67 2.88 0.00 3.01
3313 3319 8.819643 TTTTAAATTTTGAATTCGAACGGGAT 57.180 26.923 7.67 0.00 0.00 3.85
3314 3320 8.819643 ATTTTAAATTTTGAATTCGAACGGGA 57.180 26.923 7.67 0.00 0.00 5.14
3315 3321 8.704234 TGATTTTAAATTTTGAATTCGAACGGG 58.296 29.630 7.67 0.00 0.00 5.28
3326 3332 9.372369 ACCGTTTGACTTGATTTTAAATTTTGA 57.628 25.926 0.00 0.00 0.00 2.69
3332 3338 9.857957 AACTTTACCGTTTGACTTGATTTTAAA 57.142 25.926 0.00 0.00 0.00 1.52
3333 3339 9.857957 AAACTTTACCGTTTGACTTGATTTTAA 57.142 25.926 0.00 0.00 35.88 1.52
3334 3340 9.857957 AAAACTTTACCGTTTGACTTGATTTTA 57.142 25.926 0.00 0.00 37.20 1.52
3335 3341 8.766000 AAAACTTTACCGTTTGACTTGATTTT 57.234 26.923 0.00 0.00 37.20 1.82
3336 3342 8.030106 TGAAAACTTTACCGTTTGACTTGATTT 58.970 29.630 0.00 0.00 37.20 2.17
3337 3343 7.540299 TGAAAACTTTACCGTTTGACTTGATT 58.460 30.769 0.00 0.00 37.20 2.57
3338 3344 7.090953 TGAAAACTTTACCGTTTGACTTGAT 57.909 32.000 0.00 0.00 37.20 2.57
3339 3345 6.497785 TGAAAACTTTACCGTTTGACTTGA 57.502 33.333 0.00 0.00 37.20 3.02
3340 3346 7.115095 TGTTTGAAAACTTTACCGTTTGACTTG 59.885 33.333 7.39 0.00 39.59 3.16
3341 3347 7.146648 TGTTTGAAAACTTTACCGTTTGACTT 58.853 30.769 7.39 0.00 39.59 3.01
3342 3348 6.679843 TGTTTGAAAACTTTACCGTTTGACT 58.320 32.000 7.39 0.00 39.59 3.41
3343 3349 6.931243 TGTTTGAAAACTTTACCGTTTGAC 57.069 33.333 7.39 0.00 39.59 3.18
3344 3350 9.635520 TTAATGTTTGAAAACTTTACCGTTTGA 57.364 25.926 11.62 0.00 37.88 2.69


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

AutoCloner maintained by Alex Coulton.