Multiple sequence alignment - TraesCS3A01G293100

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 TraesCS3A01G293100 chr3A 100.000 4170 0 0 1 4170 523734640 523730471 0.000000e+00 7701
1 TraesCS3A01G293100 chr3A 98.925 93 1 0 3200 3292 30456413 30456505 2.580000e-37 167
2 TraesCS3A01G293100 chr3D 95.345 2621 102 9 577 3196 402781491 402778890 0.000000e+00 4146
3 TraesCS3A01G293100 chr3D 95.490 887 27 5 3297 4170 402778865 402777979 0.000000e+00 1404
4 TraesCS3A01G293100 chr3D 85.799 507 60 12 16 518 533680836 533680338 1.030000e-145 527
5 TraesCS3A01G293100 chr3D 96.040 101 1 3 3185 3284 153849602 153849504 1.200000e-35 161
6 TraesCS3A01G293100 chr3B 94.515 2607 112 7 589 3195 528502994 528500419 0.000000e+00 3993
7 TraesCS3A01G293100 chr3B 97.082 891 22 3 3283 4170 528500414 528499525 0.000000e+00 1498
8 TraesCS3A01G293100 chr3B 86.111 504 56 13 21 519 735808820 735809314 7.940000e-147 531
9 TraesCS3A01G293100 chr6D 86.186 485 58 8 36 517 420967432 420966954 2.220000e-142 516
10 TraesCS3A01G293100 chr6D 85.323 511 60 13 14 518 324813526 324814027 7.990000e-142 514
11 TraesCS3A01G293100 chr1D 85.487 503 61 11 17 516 18984081 18983588 7.990000e-142 514
12 TraesCS3A01G293100 chr1D 85.458 502 63 10 19 517 365089126 365088632 7.990000e-142 514
13 TraesCS3A01G293100 chr4D 85.039 508 66 9 16 519 435967702 435967201 3.720000e-140 508
14 TraesCS3A01G293100 chr4D 84.902 510 63 13 16 519 361884982 361884481 1.730000e-138 503
15 TraesCS3A01G293100 chr2B 84.736 511 64 11 20 526 9867217 9867717 2.240000e-137 499
16 TraesCS3A01G293100 chr4A 98.925 93 1 0 3199 3291 452252059 452252151 2.580000e-37 167
17 TraesCS3A01G293100 chr4A 93.269 104 4 3 3182 3284 142348509 142348610 2.600000e-32 150
18 TraesCS3A01G293100 chr2D 96.907 97 1 2 3188 3284 555221196 555221102 1.200000e-35 161
19 TraesCS3A01G293100 chr6A 94.231 104 4 2 3192 3294 610209056 610209158 1.550000e-34 158
20 TraesCS3A01G293100 chr5A 94.231 104 4 2 3182 3285 673726849 673726950 1.550000e-34 158
21 TraesCS3A01G293100 chr6B 93.458 107 3 4 3199 3302 711374667 711374772 5.580000e-34 156
22 TraesCS3A01G293100 chr1B 90.435 115 8 2 3191 3305 47517439 47517328 9.340000e-32 148


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 TraesCS3A01G293100 chr3A 523730471 523734640 4169 True 7701.0 7701 100.0000 1 4170 1 chr3A.!!$R1 4169
1 TraesCS3A01G293100 chr3D 402777979 402781491 3512 True 2775.0 4146 95.4175 577 4170 2 chr3D.!!$R3 3593
2 TraesCS3A01G293100 chr3B 528499525 528502994 3469 True 2745.5 3993 95.7985 589 4170 2 chr3B.!!$R1 3581
3 TraesCS3A01G293100 chr6D 324813526 324814027 501 False 514.0 514 85.3230 14 518 1 chr6D.!!$F1 504
4 TraesCS3A01G293100 chr4D 435967201 435967702 501 True 508.0 508 85.0390 16 519 1 chr4D.!!$R2 503
5 TraesCS3A01G293100 chr4D 361884481 361884982 501 True 503.0 503 84.9020 16 519 1 chr4D.!!$R1 503
6 TraesCS3A01G293100 chr2B 9867217 9867717 500 False 499.0 499 84.7360 20 526 1 chr2B.!!$F1 506

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
58 60 0.036388 TTTTCTTCCGCGAGAGGCAT 60.036 50.000 8.23 0.0 43.84 4.40 F
474 487 0.109532 TTGTCGCAACATGGGGAGAA 59.890 50.000 0.00 0.0 34.73 2.87 F
907 934 0.110486 GAGAGGCCAACTTCCACCAA 59.890 55.000 5.01 0.0 0.00 3.67 F
1524 1551 0.667792 GCTCTCTCGTTGCGGTCTTT 60.668 55.000 0.00 0.0 0.00 2.52 F
2241 2268 1.203287 GGCTTTGTTTCTGATGCCCTC 59.797 52.381 0.00 0.0 34.81 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1093 1120 0.621082 GAGTTGAAGAGGGAAGGGGG 59.379 60.000 0.00 0.0 0.00 5.40 R
1524 1551 1.227527 CGGTGACACAAGTGCAGGA 60.228 57.895 8.08 0.0 0.00 3.86 R
2555 2582 1.004745 AGCACCCATAACTGGTCTTGG 59.995 52.381 0.00 0.0 41.37 3.61 R
2759 2786 1.228245 TCAGGTTTGACAGCAGCCC 60.228 57.895 0.00 0.0 0.00 5.19 R
3586 3623 2.147958 TGAAGGTAACAACATGGACGC 58.852 47.619 0.00 0.0 41.41 5.19 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 0.036388 TTTTCTTCCGCGAGAGGCAT 60.036 50.000 8.23 0.00 43.84 4.40
105 107 5.122869 CGGTTGTGATTTTCATGAGAGTCAT 59.877 40.000 13.47 0.00 37.65 3.06
141 145 4.996344 GGAAACGGGAAAACTGTGTTTTA 58.004 39.130 8.18 0.00 39.10 1.52
143 147 5.460748 GGAAACGGGAAAACTGTGTTTTATG 59.539 40.000 8.18 4.81 39.10 1.90
147 155 6.037726 ACGGGAAAACTGTGTTTTATGTTTC 58.962 36.000 8.18 0.00 37.28 2.78
167 175 2.244000 TTTTTGCTTCCGCGAGAGG 58.756 52.632 8.23 4.88 39.65 3.69
214 224 1.963515 AGGCGTGCCTCTTTTGAAAAT 59.036 42.857 7.79 0.00 44.43 1.82
300 312 6.317642 CGTCAAAAACCTATCAACATGGGATA 59.682 38.462 0.00 3.51 34.16 2.59
379 391 5.064325 GGACGCACGGTTTAAGAGATAAAAT 59.936 40.000 0.00 0.00 35.33 1.82
441 453 0.581529 ATTGTGACAAGTGACGCACG 59.418 50.000 3.74 0.00 39.64 5.34
474 487 0.109532 TTGTCGCAACATGGGGAGAA 59.890 50.000 0.00 0.00 34.73 2.87
489 502 2.573915 GGGAGAAGGGAGTGATCTTTGT 59.426 50.000 0.00 0.00 0.00 2.83
509 522 6.882610 TTGTAACGAGTACTCCTCAACTAA 57.117 37.500 17.23 2.06 40.48 2.24
519 532 7.484975 AGTACTCCTCAACTAATGATTTCGAG 58.515 38.462 0.00 0.00 37.44 4.04
520 533 6.287589 ACTCCTCAACTAATGATTTCGAGT 57.712 37.500 0.00 0.00 37.44 4.18
526 539 8.191446 CCTCAACTAATGATTTCGAGTTAGAGA 58.809 37.037 13.86 1.91 37.44 3.10
527 540 9.574458 CTCAACTAATGATTTCGAGTTAGAGAA 57.426 33.333 10.14 0.00 37.44 2.87
528 541 9.355215 TCAACTAATGATTTCGAGTTAGAGAAC 57.645 33.333 9.20 0.00 31.50 3.01
529 542 9.140286 CAACTAATGATTTCGAGTTAGAGAACA 57.860 33.333 9.20 0.00 38.10 3.18
530 543 9.877178 AACTAATGATTTCGAGTTAGAGAACAT 57.123 29.630 9.20 0.00 38.10 2.71
531 544 9.307121 ACTAATGATTTCGAGTTAGAGAACATG 57.693 33.333 0.00 0.00 38.10 3.21
532 545 9.521503 CTAATGATTTCGAGTTAGAGAACATGA 57.478 33.333 0.00 0.00 38.10 3.07
533 546 8.777865 AATGATTTCGAGTTAGAGAACATGAA 57.222 30.769 0.00 0.00 38.10 2.57
534 547 8.954950 ATGATTTCGAGTTAGAGAACATGAAT 57.045 30.769 0.00 0.00 38.10 2.57
535 548 8.777865 TGATTTCGAGTTAGAGAACATGAATT 57.222 30.769 0.00 0.00 38.10 2.17
536 549 9.219603 TGATTTCGAGTTAGAGAACATGAATTT 57.780 29.630 0.00 0.00 38.10 1.82
537 550 9.483062 GATTTCGAGTTAGAGAACATGAATTTG 57.517 33.333 0.00 0.00 38.10 2.32
538 551 8.601845 TTTCGAGTTAGAGAACATGAATTTGA 57.398 30.769 0.00 0.00 38.10 2.69
539 552 8.601845 TTCGAGTTAGAGAACATGAATTTGAA 57.398 30.769 0.00 0.00 38.10 2.69
540 553 8.244494 TCGAGTTAGAGAACATGAATTTGAAG 57.756 34.615 0.00 0.00 38.10 3.02
541 554 8.088365 TCGAGTTAGAGAACATGAATTTGAAGA 58.912 33.333 0.00 0.00 38.10 2.87
542 555 8.712363 CGAGTTAGAGAACATGAATTTGAAGAA 58.288 33.333 0.00 0.00 38.10 2.52
572 585 9.040939 AGTTCAAAATTTCGGAAAATGTTTAGG 57.959 29.630 7.33 1.51 35.27 2.69
573 586 9.036671 GTTCAAAATTTCGGAAAATGTTTAGGA 57.963 29.630 7.33 3.55 35.27 2.94
574 587 9.771534 TTCAAAATTTCGGAAAATGTTTAGGAT 57.228 25.926 7.33 0.00 35.27 3.24
575 588 9.771534 TCAAAATTTCGGAAAATGTTTAGGATT 57.228 25.926 7.33 0.00 35.27 3.01
693 719 7.867403 TGTTCATGAGATTTCCTTAAAAAGCAC 59.133 33.333 0.00 0.00 0.00 4.40
792 819 1.674057 GGCCCATAGCTCTGCGTAT 59.326 57.895 0.00 0.00 43.05 3.06
796 823 2.408050 CCCATAGCTCTGCGTATGAAC 58.592 52.381 0.00 0.00 0.00 3.18
812 839 2.436417 TGAACAGAGCTATGTTTGGCC 58.564 47.619 26.25 14.64 43.32 5.36
813 840 1.398390 GAACAGAGCTATGTTTGGCCG 59.602 52.381 26.25 0.00 43.32 6.13
817 844 0.378610 GAGCTATGTTTGGCCGCTTC 59.621 55.000 0.00 0.00 0.00 3.86
839 866 2.097466 AGCGTCAAATAGCATTTTCCGG 59.903 45.455 0.00 0.00 35.48 5.14
845 872 0.818040 ATAGCATTTTCCGGCGGTCC 60.818 55.000 27.32 8.79 34.54 4.46
848 875 1.078426 CATTTTCCGGCGGTCCTCT 60.078 57.895 27.32 5.37 0.00 3.69
849 876 0.676782 CATTTTCCGGCGGTCCTCTT 60.677 55.000 27.32 4.41 0.00 2.85
854 881 3.068691 CGGCGGTCCTCTTCTCCA 61.069 66.667 0.00 0.00 0.00 3.86
907 934 0.110486 GAGAGGCCAACTTCCACCAA 59.890 55.000 5.01 0.00 0.00 3.67
942 969 1.903404 CAGCCACAGTTGAACCCCC 60.903 63.158 0.00 0.00 0.00 5.40
1459 1486 3.311110 ATGTCCAGGACGCCGTGT 61.311 61.111 15.24 0.00 34.95 4.49
1524 1551 0.667792 GCTCTCTCGTTGCGGTCTTT 60.668 55.000 0.00 0.00 0.00 2.52
1629 1656 6.511121 CGTTGCTGAATTGTTACTGTACTTGT 60.511 38.462 0.00 0.00 0.00 3.16
1633 1660 5.126779 TGAATTGTTACTGTACTTGTGGCA 58.873 37.500 0.00 0.00 0.00 4.92
1660 1687 1.852942 CGCGGCAGAGAAGCTATTTA 58.147 50.000 0.00 0.00 34.17 1.40
1665 1692 4.130118 CGGCAGAGAAGCTATTTAATGGT 58.870 43.478 0.00 0.00 34.17 3.55
1682 1709 8.408043 TTTAATGGTTTGATGTTCAGAGATGT 57.592 30.769 0.00 0.00 0.00 3.06
1686 1713 4.520492 GGTTTGATGTTCAGAGATGTGGTT 59.480 41.667 0.00 0.00 0.00 3.67
1765 1792 1.669779 AGCTTTTCTCAGCGATGCATC 59.330 47.619 17.10 17.10 45.24 3.91
1766 1793 1.399440 GCTTTTCTCAGCGATGCATCA 59.601 47.619 25.70 5.90 0.00 3.07
1884 1911 7.420800 CCAAATCTATCAAGCATAACCTCAAC 58.579 38.462 0.00 0.00 0.00 3.18
1936 1963 8.687242 TGGTTGATTTCTACAACAAATGTGTTA 58.313 29.630 0.00 0.00 46.47 2.41
1963 1990 3.428532 AGGGACGCTCTTAAAGTACTCA 58.571 45.455 0.00 0.00 0.00 3.41
2156 2183 4.579340 GCATCAGATTCACTCATTGGTCAT 59.421 41.667 0.00 0.00 0.00 3.06
2241 2268 1.203287 GGCTTTGTTTCTGATGCCCTC 59.797 52.381 0.00 0.00 34.81 4.30
2331 2358 3.883830 AGAGCTCACATGTACCAAGAG 57.116 47.619 17.77 1.51 0.00 2.85
2354 2381 3.707102 ACCAAGGAGCTACTCTTACATCC 59.293 47.826 0.00 0.00 0.00 3.51
2356 2383 3.579534 AGGAGCTACTCTTACATCCGA 57.420 47.619 0.00 0.00 31.97 4.55
2361 2388 4.421948 AGCTACTCTTACATCCGAAAACG 58.578 43.478 0.00 0.00 0.00 3.60
2435 2462 4.766373 TGATTATGCTGAAGCTTTTGGACA 59.234 37.500 0.00 0.00 42.66 4.02
2555 2582 1.392589 CTGGTGCATGGGGTAATCAC 58.607 55.000 0.00 0.00 0.00 3.06
2759 2786 4.202151 GGCATGGTTTAAAGCTATGGAAGG 60.202 45.833 17.61 0.35 0.00 3.46
2833 2860 1.002430 GACATGGAGGACTTGTGCAGA 59.998 52.381 0.00 0.00 37.56 4.26
3004 3031 5.820423 AGTACTATTATTTGGCGCACATTCA 59.180 36.000 10.83 0.00 0.00 2.57
3136 3163 9.093970 GGTTGTTGCCAAATTAATATTTAGACC 57.906 33.333 0.00 0.00 32.75 3.85
3204 3231 8.943909 ATTGTTACAGTAATGTAAGCTACTCC 57.056 34.615 15.59 3.76 35.25 3.85
3205 3232 6.870769 TGTTACAGTAATGTAAGCTACTCCC 58.129 40.000 15.59 3.10 35.25 4.30
3206 3233 6.666546 TGTTACAGTAATGTAAGCTACTCCCT 59.333 38.462 15.59 0.00 35.25 4.20
3207 3234 5.855740 ACAGTAATGTAAGCTACTCCCTC 57.144 43.478 0.00 0.00 0.00 4.30
3208 3235 4.650131 ACAGTAATGTAAGCTACTCCCTCC 59.350 45.833 0.00 0.00 0.00 4.30
3209 3236 3.890147 AGTAATGTAAGCTACTCCCTCCG 59.110 47.826 0.00 0.00 0.00 4.63
3210 3237 2.456073 ATGTAAGCTACTCCCTCCGT 57.544 50.000 0.00 0.00 0.00 4.69
3211 3238 3.589951 ATGTAAGCTACTCCCTCCGTA 57.410 47.619 0.00 0.00 0.00 4.02
3212 3239 3.370840 TGTAAGCTACTCCCTCCGTAA 57.629 47.619 0.00 0.00 0.00 3.18
3213 3240 3.700538 TGTAAGCTACTCCCTCCGTAAA 58.299 45.455 0.00 0.00 0.00 2.01
3214 3241 3.445096 TGTAAGCTACTCCCTCCGTAAAC 59.555 47.826 0.00 0.00 0.00 2.01
3215 3242 2.528673 AGCTACTCCCTCCGTAAACT 57.471 50.000 0.00 0.00 0.00 2.66
3216 3243 3.659183 AGCTACTCCCTCCGTAAACTA 57.341 47.619 0.00 0.00 0.00 2.24
3217 3244 3.973425 AGCTACTCCCTCCGTAAACTAA 58.027 45.455 0.00 0.00 0.00 2.24
3218 3245 4.544683 AGCTACTCCCTCCGTAAACTAAT 58.455 43.478 0.00 0.00 0.00 1.73
3219 3246 5.699143 AGCTACTCCCTCCGTAAACTAATA 58.301 41.667 0.00 0.00 0.00 0.98
3220 3247 6.313324 AGCTACTCCCTCCGTAAACTAATAT 58.687 40.000 0.00 0.00 0.00 1.28
3221 3248 7.465116 AGCTACTCCCTCCGTAAACTAATATA 58.535 38.462 0.00 0.00 0.00 0.86
3222 3249 7.946776 AGCTACTCCCTCCGTAAACTAATATAA 59.053 37.037 0.00 0.00 0.00 0.98
3223 3250 8.242739 GCTACTCCCTCCGTAAACTAATATAAG 58.757 40.741 0.00 0.00 0.00 1.73
3224 3251 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
3225 3252 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3226 3253 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3227 3254 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3228 3255 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3229 3256 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3230 3257 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3231 3258 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3232 3259 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3233 3260 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3247 3274 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
3248 3275 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
3249 3276 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
3250 3277 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
3251 3278 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
3257 3284 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
3258 3285 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
3259 3286 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
3260 3287 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
3261 3288 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
3262 3289 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
3263 3290 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
3278 3305 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
3279 3306 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
3280 3307 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
3281 3308 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
3562 3599 1.884579 CTTGCTCTTTCTGCATGGTGT 59.115 47.619 0.00 0.00 40.34 4.16
3586 3623 2.457366 AACTAGCAAGAGGTGTTCCG 57.543 50.000 0.00 0.00 39.05 4.30
3588 3625 1.078759 CTAGCAAGAGGTGTTCCGCG 61.079 60.000 0.00 0.00 38.56 6.46
3801 3848 5.535753 AGGTCCACAAAGAAAAATGGAAG 57.464 39.130 0.00 0.00 42.79 3.46
3906 3953 7.608376 AGAAATGAAGATGATCTCATGGCATAG 59.392 37.037 0.00 0.00 36.57 2.23
4013 4061 5.309638 AGAGTAAAAGGAGAAAGGCTGTTC 58.690 41.667 0.00 0.00 0.00 3.18
4015 4063 5.696030 AGTAAAAGGAGAAAGGCTGTTCTT 58.304 37.500 11.47 0.00 37.98 2.52
4016 4064 4.926140 AAAAGGAGAAAGGCTGTTCTTG 57.074 40.909 11.47 0.00 37.98 3.02
4060 4108 4.081406 ACTTGCAGCCTATGAAAATGTGA 58.919 39.130 0.00 0.00 0.00 3.58
4069 4117 7.599621 CAGCCTATGAAAATGTGAAAAATGACA 59.400 33.333 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 2.040544 AAAACCATGCCTCTCGCGG 61.041 57.895 6.13 0.00 42.08 6.46
96 98 2.265739 GCACGGCCATGACTCTCA 59.734 61.111 1.12 0.00 0.00 3.27
283 295 8.723365 TCAAAACTATATCCCATGTTGATAGGT 58.277 33.333 7.86 6.67 0.00 3.08
300 312 3.791887 CGCGTCGAGATCTTCAAAACTAT 59.208 43.478 0.00 0.00 0.00 2.12
422 434 0.581529 CGTGCGTCACTTGTCACAAT 59.418 50.000 0.00 0.00 31.34 2.71
426 438 2.521771 GCACGTGCGTCACTTGTCA 61.522 57.895 26.77 0.00 36.27 3.58
465 477 1.296523 AGATCACTCCCTTCTCCCCAT 59.703 52.381 0.00 0.00 0.00 4.00
474 487 3.833070 ACTCGTTACAAAGATCACTCCCT 59.167 43.478 0.00 0.00 0.00 4.20
509 522 8.954950 ATTCATGTTCTCTAACTCGAAATCAT 57.045 30.769 0.00 0.00 36.51 2.45
546 559 9.040939 CCTAAACATTTTCCGAAATTTTGAACT 57.959 29.630 7.02 0.00 33.25 3.01
547 560 9.036671 TCCTAAACATTTTCCGAAATTTTGAAC 57.963 29.630 7.02 0.00 33.25 3.18
548 561 9.771534 ATCCTAAACATTTTCCGAAATTTTGAA 57.228 25.926 7.02 3.75 33.25 2.69
549 562 9.771534 AATCCTAAACATTTTCCGAAATTTTGA 57.228 25.926 7.02 0.00 33.25 2.69
553 566 9.996554 AGAAAATCCTAAACATTTTCCGAAATT 57.003 25.926 12.21 0.00 45.52 1.82
554 567 9.996554 AAGAAAATCCTAAACATTTTCCGAAAT 57.003 25.926 12.21 0.00 45.52 2.17
555 568 9.255304 CAAGAAAATCCTAAACATTTTCCGAAA 57.745 29.630 12.21 0.00 45.52 3.46
556 569 8.634444 TCAAGAAAATCCTAAACATTTTCCGAA 58.366 29.630 12.21 0.00 45.52 4.30
557 570 8.172352 TCAAGAAAATCCTAAACATTTTCCGA 57.828 30.769 12.21 8.17 45.52 4.55
558 571 8.810652 TTCAAGAAAATCCTAAACATTTTCCG 57.189 30.769 12.21 6.48 45.52 4.30
665 678 9.428097 GCTTTTTAAGGAAATCTCATGAACATT 57.572 29.630 0.00 0.00 0.00 2.71
666 679 8.587608 TGCTTTTTAAGGAAATCTCATGAACAT 58.412 29.630 0.00 0.00 0.00 2.71
668 681 7.061094 CGTGCTTTTTAAGGAAATCTCATGAAC 59.939 37.037 0.00 0.00 0.00 3.18
712 738 7.770366 TCCTGTTCCTTATTTTACTTTTCCC 57.230 36.000 0.00 0.00 0.00 3.97
754 781 4.449743 GGCCGGTTTTGTTCTTTTTATTCC 59.550 41.667 1.90 0.00 0.00 3.01
792 819 2.436417 GGCCAAACATAGCTCTGTTCA 58.564 47.619 16.84 0.00 38.38 3.18
796 823 0.745845 AGCGGCCAAACATAGCTCTG 60.746 55.000 2.24 0.00 31.94 3.35
813 840 3.411415 AATGCTATTTGACGCTGAAGC 57.589 42.857 0.00 0.00 37.78 3.86
817 844 3.100817 CGGAAAATGCTATTTGACGCTG 58.899 45.455 0.00 0.00 0.00 5.18
839 866 2.185608 GCTGGAGAAGAGGACCGC 59.814 66.667 0.00 0.00 0.00 5.68
845 872 0.179113 GGAAGAGCGCTGGAGAAGAG 60.179 60.000 18.48 0.00 0.00 2.85
848 875 1.194781 AAGGGAAGAGCGCTGGAGAA 61.195 55.000 18.48 0.00 40.06 2.87
849 876 1.610673 AAGGGAAGAGCGCTGGAGA 60.611 57.895 18.48 0.00 40.06 3.71
854 881 4.416738 GGGCAAGGGAAGAGCGCT 62.417 66.667 11.27 11.27 42.29 5.92
907 934 2.397413 CTGGCCGGAGTGGAACAAGT 62.397 60.000 5.28 0.00 44.16 3.16
942 969 2.281070 AGCTGTGTTGGCGTGGAG 60.281 61.111 0.00 0.00 34.52 3.86
1092 1119 1.000771 GTTGAAGAGGGAAGGGGGC 60.001 63.158 0.00 0.00 0.00 5.80
1093 1120 0.621082 GAGTTGAAGAGGGAAGGGGG 59.379 60.000 0.00 0.00 0.00 5.40
1098 1125 2.415983 TGAGGGAGTTGAAGAGGGAA 57.584 50.000 0.00 0.00 0.00 3.97
1319 1346 2.359107 CGAAGAAGCCCAGCAGCA 60.359 61.111 0.00 0.00 34.23 4.41
1377 1404 3.864686 CTCCGTGCGGGCATTTCG 61.865 66.667 10.94 0.00 34.94 3.46
1459 1486 2.092861 TCACGAGTTCCCTGAACCAAAA 60.093 45.455 3.47 0.00 42.85 2.44
1524 1551 1.227527 CGGTGACACAAGTGCAGGA 60.228 57.895 8.08 0.00 0.00 3.86
1633 1660 3.349006 CTCTGCCGCGCAAACTGT 61.349 61.111 8.75 0.00 38.41 3.55
1660 1687 5.184479 CCACATCTCTGAACATCAAACCATT 59.816 40.000 0.00 0.00 0.00 3.16
1665 1692 5.049474 CGAAACCACATCTCTGAACATCAAA 60.049 40.000 0.00 0.00 0.00 2.69
1682 1709 5.123186 GTGATCATTGTATTCCACGAAACCA 59.877 40.000 0.00 0.00 0.00 3.67
1686 1713 4.332543 GCAGTGATCATTGTATTCCACGAA 59.667 41.667 18.28 0.00 0.00 3.85
1765 1792 3.276857 CATCTGGAGAAACACCCTGATG 58.723 50.000 11.84 11.84 45.63 3.07
1766 1793 3.184628 TCATCTGGAGAAACACCCTGAT 58.815 45.455 0.00 0.00 40.35 2.90
1816 1843 2.358898 CCTGTGCATTTATACTGGTGCC 59.641 50.000 0.00 0.00 36.79 5.01
1884 1911 5.918576 TGAAGTACTCACAAATACTGTCGTG 59.081 40.000 0.00 0.00 35.47 4.35
1936 1963 2.822707 TTAAGAGCGTCCCTCCTACT 57.177 50.000 0.00 0.00 41.74 2.57
1963 1990 4.534103 AGTGCTCTTATGAGGAACCTCTTT 59.466 41.667 19.61 10.97 42.22 2.52
2156 2183 6.594937 GTCATTACCGTCATAACCCAGTTTTA 59.405 38.462 0.00 0.00 0.00 1.52
2241 2268 4.452455 GGATCCAATGTAACTCCATAAGCG 59.548 45.833 6.95 0.00 0.00 4.68
2331 2358 4.202172 GGATGTAAGAGTAGCTCCTTGGTC 60.202 50.000 0.00 0.00 0.00 4.02
2354 2381 7.222031 TCCATGAAATAGTATCACTCGTTTTCG 59.778 37.037 0.00 0.00 45.64 3.46
2356 2383 7.011482 GCTCCATGAAATAGTATCACTCGTTTT 59.989 37.037 0.00 0.00 0.00 2.43
2361 2388 8.310382 AGTATGCTCCATGAAATAGTATCACTC 58.690 37.037 0.00 0.00 0.00 3.51
2404 2431 3.887716 GCTTCAGCATAATCACCATTCCT 59.112 43.478 0.00 0.00 41.59 3.36
2435 2462 6.154021 CCCCAAAATTCTCATCTGTCTGAAAT 59.846 38.462 0.00 0.00 0.00 2.17
2555 2582 1.004745 AGCACCCATAACTGGTCTTGG 59.995 52.381 0.00 0.00 41.37 3.61
2759 2786 1.228245 TCAGGTTTGACAGCAGCCC 60.228 57.895 0.00 0.00 0.00 5.19
2833 2860 5.755849 ACGTTTGAATATCTCCATTCCCTT 58.244 37.500 0.00 0.00 34.59 3.95
3004 3031 4.708421 GCCATATGTATTGCATCCTTGGAT 59.292 41.667 12.42 0.00 38.94 3.41
3196 3223 2.528673 AGTTTACGGAGGGAGTAGCT 57.471 50.000 0.00 0.00 0.00 3.32
3198 3225 9.512588 TCTTATATTAGTTTACGGAGGGAGTAG 57.487 37.037 0.00 0.00 0.00 2.57
3199 3226 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3200 3227 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3201 3228 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3202 3229 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3203 3230 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3204 3231 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3205 3232 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3206 3233 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
3207 3234 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3221 3248 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
3222 3249 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
3223 3250 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
3224 3251 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
3225 3252 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
3231 3258 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
3232 3259 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
3233 3260 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
3234 3261 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
3235 3262 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
3236 3263 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
3237 3264 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
3252 3279 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3253 3280 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
3254 3281 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
3255 3282 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
3256 3283 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3586 3623 2.147958 TGAAGGTAACAACATGGACGC 58.852 47.619 0.00 0.00 41.41 5.19
3906 3953 9.771534 AGTAGATTCCTAATGCTCAATAAACTC 57.228 33.333 0.00 0.00 0.00 3.01
4060 4108 4.398044 ACTGAACACGTTCCTGTCATTTTT 59.602 37.500 7.43 0.00 38.77 1.94
4069 4117 3.056035 GGGATCTTACTGAACACGTTCCT 60.056 47.826 7.43 0.00 38.77 3.36


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

AutoCloner maintained by Alex Coulton.