Multiple sequence alignment - TraesCS2D01G066500

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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 TraesCS2D01G066500 chr2D 100.000 3618 0 0 1 3618 27966896 27963279 0.000000e+00 6682
1 TraesCS2D01G066500 chr2D 93.878 1911 81 24 1033 2924 27993783 27991890 0.000000e+00 2848
2 TraesCS2D01G066500 chr2D 88.331 1714 184 8 1034 2732 27980484 27978772 0.000000e+00 2043
3 TraesCS2D01G066500 chr2D 88.841 1631 140 19 1034 2650 27933797 27932195 0.000000e+00 1965
4 TraesCS2D01G066500 chr2D 88.749 1591 163 9 1035 2610 27951610 27950021 0.000000e+00 1932
5 TraesCS2D01G066500 chr2D 97.104 1036 30 0 1 1036 27994952 27993917 0.000000e+00 1748
6 TraesCS2D01G066500 chr2D 89.768 1036 106 0 1 1036 27952775 27951740 0.000000e+00 1327
7 TraesCS2D01G066500 chr2D 89.114 1038 109 3 1 1036 27934967 27933932 0.000000e+00 1288
8 TraesCS2D01G066500 chr2A 83.617 2527 330 41 1034 3520 30169116 30166634 0.000000e+00 2296
9 TraesCS2D01G066500 chr2A 89.315 1591 153 11 1035 2610 30177364 30175776 0.000000e+00 1980
10 TraesCS2D01G066500 chr2A 88.361 1031 120 0 6 1036 30178530 30177500 0.000000e+00 1240
11 TraesCS2D01G066500 chr2A 87.452 1036 130 0 1 1036 30157633 30156598 0.000000e+00 1194
12 TraesCS2D01G066500 chr2B 90.457 1729 140 15 1030 2737 45551723 45553447 0.000000e+00 2255
13 TraesCS2D01G066500 chr2B 86.476 1856 206 31 1034 2869 45674274 45676104 0.000000e+00 1995
14 TraesCS2D01G066500 chr2B 89.114 1580 165 5 1034 2610 44744212 44742637 0.000000e+00 1958
15 TraesCS2D01G066500 chr2B 86.970 1627 183 16 1034 2651 45680160 45681766 0.000000e+00 1803
16 TraesCS2D01G066500 chr2B 95.560 1036 46 0 1 1036 45550557 45551592 0.000000e+00 1659
17 TraesCS2D01G066500 chr2B 91.409 1036 89 0 1 1036 45673104 45674139 0.000000e+00 1421
18 TraesCS2D01G066500 chr2B 91.120 1036 92 0 1 1036 44745382 44744347 0.000000e+00 1404
19 TraesCS2D01G066500 chr2B 89.038 1040 106 7 1 1036 44434602 44433567 0.000000e+00 1282
20 TraesCS2D01G066500 chr2B 89.344 488 28 7 2650 3133 45683870 45684337 3.110000e-165 592
21 TraesCS2D01G066500 chr2B 86.893 412 45 6 3115 3519 45684372 45684781 1.530000e-123 453


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 TraesCS2D01G066500 chr2D 27963279 27966896 3617 True 6682.000000 6682 100.000000 1 3618 1 chr2D.!!$R1 3617
1 TraesCS2D01G066500 chr2D 27991890 27994952 3062 True 2298.000000 2848 95.491000 1 2924 2 chr2D.!!$R5 2923
2 TraesCS2D01G066500 chr2D 27978772 27980484 1712 True 2043.000000 2043 88.331000 1034 2732 1 chr2D.!!$R2 1698
3 TraesCS2D01G066500 chr2D 27950021 27952775 2754 True 1629.500000 1932 89.258500 1 2610 2 chr2D.!!$R4 2609
4 TraesCS2D01G066500 chr2D 27932195 27934967 2772 True 1626.500000 1965 88.977500 1 2650 2 chr2D.!!$R3 2649
5 TraesCS2D01G066500 chr2A 30166634 30169116 2482 True 2296.000000 2296 83.617000 1034 3520 1 chr2A.!!$R2 2486
6 TraesCS2D01G066500 chr2A 30175776 30178530 2754 True 1610.000000 1980 88.838000 6 2610 2 chr2A.!!$R3 2604
7 TraesCS2D01G066500 chr2A 30156598 30157633 1035 True 1194.000000 1194 87.452000 1 1036 1 chr2A.!!$R1 1035
8 TraesCS2D01G066500 chr2B 45550557 45553447 2890 False 1957.000000 2255 93.008500 1 2737 2 chr2B.!!$F1 2736
9 TraesCS2D01G066500 chr2B 45673104 45676104 3000 False 1708.000000 1995 88.942500 1 2869 2 chr2B.!!$F2 2868
10 TraesCS2D01G066500 chr2B 44742637 44745382 2745 True 1681.000000 1958 90.117000 1 2610 2 chr2B.!!$R2 2609
11 TraesCS2D01G066500 chr2B 44433567 44434602 1035 True 1282.000000 1282 89.038000 1 1036 1 chr2B.!!$R1 1035
12 TraesCS2D01G066500 chr2B 45680160 45684781 4621 False 949.333333 1803 87.735667 1034 3519 3 chr2B.!!$F3 2485

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
695 696 1.956477 ACCAATTGCACTCAGTTGTCC 59.044 47.619 0.00 0.0 37.98 4.02 F
832 833 2.613133 CAGCTGAGATAGGAAAGCTTGC 59.387 50.000 8.42 0.0 43.33 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2562 2859 2.670905 CTGGCACAAACATCATGCATTG 59.329 45.455 0.00 0.0 41.27 2.82 R
2801 5232 1.979855 TTGGGCGCATACATAGCATT 58.020 45.000 10.83 0.0 0.00 3.56 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
51 52 4.537936 TCGTCACTCAGTGAGATAATCG 57.462 45.455 26.86 19.77 43.57 3.34
623 624 2.224314 GGCAAACTTGAGTGTACTGCTC 59.776 50.000 9.94 9.94 32.69 4.26
659 660 2.169789 CGAAGCTGATGACTGGGCG 61.170 63.158 0.00 0.00 0.00 6.13
694 695 2.618241 TGACCAATTGCACTCAGTTGTC 59.382 45.455 0.00 0.00 37.98 3.18
695 696 1.956477 ACCAATTGCACTCAGTTGTCC 59.044 47.619 0.00 0.00 37.98 4.02
824 825 4.345257 GGAAACATACCAGCTGAGATAGGA 59.655 45.833 17.39 0.00 0.00 2.94
832 833 2.613133 CAGCTGAGATAGGAAAGCTTGC 59.387 50.000 8.42 0.00 43.33 4.01
2536 2833 3.774766 TCAGTATTGGCCTGATGTGTACT 59.225 43.478 3.32 0.00 34.12 2.73
2562 2859 0.032130 TCGCCGAATGATAGACCAGC 59.968 55.000 0.00 0.00 0.00 4.85
2672 5080 7.481642 ACTAGATGTTAAAGACCATGTACGAG 58.518 38.462 0.00 0.00 0.00 4.18
2801 5232 5.776208 TGTACCTGATTAATATCCACCGCTA 59.224 40.000 0.00 0.00 0.00 4.26
2812 5243 4.826274 ATCCACCGCTAATGCTATGTAT 57.174 40.909 0.00 0.00 36.97 2.29
2844 5279 2.622436 AGCGGTGCAGATCTTACTTTC 58.378 47.619 0.00 0.00 0.00 2.62
2875 5312 7.487829 TCACATCAAAGTGAGTTTTTGCTTTAC 59.512 33.333 0.00 0.00 43.18 2.01
2898 5335 7.219484 ACCATCTAAAAGTGAATTGTGAAGG 57.781 36.000 0.00 0.00 0.00 3.46
2968 5407 4.261825 CCTGAGATGCTACTAGTTAGGCAC 60.262 50.000 16.27 11.76 37.52 5.01
3014 5453 2.888212 TGGTTCTTTCCTTGGATTGGG 58.112 47.619 0.00 0.00 0.00 4.12
3065 5504 3.067180 CAGGTATGTGCATTGGAACATCC 59.933 47.826 0.00 0.00 39.13 3.51
3066 5505 3.053395 AGGTATGTGCATTGGAACATCCT 60.053 43.478 0.00 0.00 39.13 3.24
3067 5506 3.067180 GGTATGTGCATTGGAACATCCTG 59.933 47.826 0.00 0.00 39.13 3.86
3069 5508 2.596346 TGTGCATTGGAACATCCTGTT 58.404 42.857 0.00 0.00 44.37 3.16
3071 5510 4.148079 TGTGCATTGGAACATCCTGTTAA 58.852 39.130 0.00 0.00 41.28 2.01
3073 5512 5.069648 TGTGCATTGGAACATCCTGTTAAAA 59.930 36.000 0.00 0.00 41.28 1.52
3074 5513 5.405269 GTGCATTGGAACATCCTGTTAAAAC 59.595 40.000 0.00 0.00 41.28 2.43
3146 5656 7.284919 TCCTTAAATTCAGGTTTGTTTCCTC 57.715 36.000 4.03 0.00 32.37 3.71
3154 5664 1.539712 GGTTTGTTTCCTCGACTCGGT 60.540 52.381 0.00 0.00 0.00 4.69
3176 5689 7.040271 TCGGTAAGTTAAGAATTTGGAAAAGGG 60.040 37.037 0.00 0.00 0.00 3.95
3180 5693 6.620429 AGTTAAGAATTTGGAAAAGGGAGGA 58.380 36.000 0.00 0.00 0.00 3.71
3197 5710 1.153765 GATGCGGCTTTGGCTTTCC 60.154 57.895 0.00 0.00 38.73 3.13
3199 5712 3.670377 GCGGCTTTGGCTTTCCGT 61.670 61.111 0.00 0.00 43.45 4.69
3200 5713 2.561373 CGGCTTTGGCTTTCCGTC 59.439 61.111 0.00 0.00 37.33 4.79
3206 5719 2.034685 GCTTTGGCTTTCCGTCTTTTCT 59.965 45.455 0.00 0.00 35.22 2.52
3224 5737 7.228706 GTCTTTTCTCAGGATTCAGGTTGTTTA 59.771 37.037 0.00 0.00 0.00 2.01
3233 5746 3.655276 TCAGGTTGTTTACTCGACTCC 57.345 47.619 0.00 0.00 0.00 3.85
3234 5747 2.960384 TCAGGTTGTTTACTCGACTCCA 59.040 45.455 0.00 0.00 0.00 3.86
3238 5751 3.872771 GGTTGTTTACTCGACTCCACAAA 59.127 43.478 0.00 0.00 0.00 2.83
3245 5758 4.884668 ACTCGACTCCACAAATTAGGAA 57.115 40.909 0.00 0.00 32.57 3.36
3246 5759 4.566987 ACTCGACTCCACAAATTAGGAAC 58.433 43.478 0.00 0.00 32.57 3.62
3248 5761 4.817517 TCGACTCCACAAATTAGGAACTC 58.182 43.478 0.00 0.00 41.75 3.01
3250 5763 4.562757 CGACTCCACAAATTAGGAACTCCA 60.563 45.833 0.00 0.00 41.75 3.86
3251 5764 4.652822 ACTCCACAAATTAGGAACTCCAC 58.347 43.478 0.00 0.00 41.75 4.02
3255 5768 5.894393 TCCACAAATTAGGAACTCCACAAAA 59.106 36.000 0.00 0.00 41.75 2.44
3256 5769 6.381420 TCCACAAATTAGGAACTCCACAAAAA 59.619 34.615 0.00 0.00 41.75 1.94
3258 5771 6.701400 CACAAATTAGGAACTCCACAAAAAGG 59.299 38.462 0.00 0.00 41.75 3.11
3259 5772 6.183360 ACAAATTAGGAACTCCACAAAAAGGG 60.183 38.462 0.00 0.00 41.75 3.95
3286 5799 2.095252 GCGAAGAAGCGACTCACCC 61.095 63.158 0.00 0.00 0.00 4.61
3303 5816 1.340405 ACCCTGGCTGAAATGCTACTG 60.340 52.381 0.00 0.00 0.00 2.74
3316 5829 1.272490 TGCTACTGGTCAGCTACACAC 59.728 52.381 0.00 0.00 39.83 3.82
3328 5841 3.066621 CAGCTACACACTTTTCAGGCAAA 59.933 43.478 0.00 0.00 0.00 3.68
3332 5845 3.784338 ACACACTTTTCAGGCAAACATG 58.216 40.909 0.00 0.00 0.00 3.21
3346 5859 3.670055 GCAAACATGGTCAGTTTTGATCG 59.330 43.478 8.05 0.00 37.24 3.69
3365 5880 1.135575 CGTCTTTGGAGCCAAGAATGC 60.136 52.381 1.79 0.00 37.24 3.56
3444 5960 0.550914 AACAGGAGCACCAGGAAACA 59.449 50.000 2.07 0.00 38.94 2.83
3452 5968 1.227853 ACCAGGAAACACAGCGTCC 60.228 57.895 0.00 0.00 0.00 4.79
3453 5969 1.227823 CCAGGAAACACAGCGTCCA 60.228 57.895 0.00 0.00 33.57 4.02
3505 6024 2.432874 TCAGGTTGTTTCCTCAAGTCGA 59.567 45.455 0.00 0.00 35.37 4.20
3513 6032 5.421277 TGTTTCCTCAAGTCGACAAGTTAA 58.579 37.500 19.50 6.05 0.00 2.01
3520 6039 6.647067 CCTCAAGTCGACAAGTTAAGAATTCT 59.353 38.462 19.50 0.88 0.00 2.40
3521 6040 7.359598 CCTCAAGTCGACAAGTTAAGAATTCTG 60.360 40.741 19.50 0.00 0.00 3.02
3522 6041 7.207383 TCAAGTCGACAAGTTAAGAATTCTGA 58.793 34.615 19.50 0.00 0.00 3.27
3523 6042 7.709182 TCAAGTCGACAAGTTAAGAATTCTGAA 59.291 33.333 19.50 4.69 0.00 3.02
3524 6043 8.335356 CAAGTCGACAAGTTAAGAATTCTGAAA 58.665 33.333 19.50 4.08 0.00 2.69
3525 6044 8.433421 AGTCGACAAGTTAAGAATTCTGAAAA 57.567 30.769 19.50 1.46 0.00 2.29
3526 6045 8.552034 AGTCGACAAGTTAAGAATTCTGAAAAG 58.448 33.333 19.50 3.92 0.00 2.27
3527 6046 7.798982 GTCGACAAGTTAAGAATTCTGAAAAGG 59.201 37.037 11.55 3.21 0.00 3.11
3528 6047 7.713507 TCGACAAGTTAAGAATTCTGAAAAGGA 59.286 33.333 9.17 0.00 0.00 3.36
3529 6048 8.342634 CGACAAGTTAAGAATTCTGAAAAGGAA 58.657 33.333 9.17 0.00 0.00 3.36
3530 6049 9.670719 GACAAGTTAAGAATTCTGAAAAGGAAG 57.329 33.333 9.17 0.00 0.00 3.46
3531 6050 8.633561 ACAAGTTAAGAATTCTGAAAAGGAAGG 58.366 33.333 9.17 0.00 0.00 3.46
3532 6051 8.850156 CAAGTTAAGAATTCTGAAAAGGAAGGA 58.150 33.333 9.17 0.00 0.00 3.36
3533 6052 9.593565 AAGTTAAGAATTCTGAAAAGGAAGGAT 57.406 29.630 9.17 0.00 0.00 3.24
3534 6053 9.018582 AGTTAAGAATTCTGAAAAGGAAGGATG 57.981 33.333 9.17 0.00 0.00 3.51
3535 6054 8.797438 GTTAAGAATTCTGAAAAGGAAGGATGT 58.203 33.333 9.17 0.00 0.00 3.06
3536 6055 6.830873 AGAATTCTGAAAAGGAAGGATGTG 57.169 37.500 7.30 0.00 0.00 3.21
3537 6056 5.713861 AGAATTCTGAAAAGGAAGGATGTGG 59.286 40.000 7.30 0.00 0.00 4.17
3538 6057 4.722526 TTCTGAAAAGGAAGGATGTGGA 57.277 40.909 0.00 0.00 0.00 4.02
3539 6058 4.934797 TCTGAAAAGGAAGGATGTGGAT 57.065 40.909 0.00 0.00 0.00 3.41
3540 6059 5.261040 TCTGAAAAGGAAGGATGTGGATT 57.739 39.130 0.00 0.00 0.00 3.01
3541 6060 5.644188 TCTGAAAAGGAAGGATGTGGATTT 58.356 37.500 0.00 0.00 0.00 2.17
3542 6061 5.477984 TCTGAAAAGGAAGGATGTGGATTTG 59.522 40.000 0.00 0.00 0.00 2.32
3543 6062 4.527816 TGAAAAGGAAGGATGTGGATTTGG 59.472 41.667 0.00 0.00 0.00 3.28
3544 6063 2.149973 AGGAAGGATGTGGATTTGGC 57.850 50.000 0.00 0.00 0.00 4.52
3545 6064 1.642762 AGGAAGGATGTGGATTTGGCT 59.357 47.619 0.00 0.00 0.00 4.75
3546 6065 2.043526 AGGAAGGATGTGGATTTGGCTT 59.956 45.455 0.00 0.00 0.00 4.35
3547 6066 2.833943 GGAAGGATGTGGATTTGGCTTT 59.166 45.455 0.00 0.00 0.00 3.51
3548 6067 3.118992 GGAAGGATGTGGATTTGGCTTTC 60.119 47.826 0.00 0.00 0.00 2.62
3549 6068 3.463048 AGGATGTGGATTTGGCTTTCT 57.537 42.857 0.00 0.00 0.00 2.52
3550 6069 4.591321 AGGATGTGGATTTGGCTTTCTA 57.409 40.909 0.00 0.00 0.00 2.10
3551 6070 4.530875 AGGATGTGGATTTGGCTTTCTAG 58.469 43.478 0.00 0.00 0.00 2.43
3552 6071 4.018050 AGGATGTGGATTTGGCTTTCTAGT 60.018 41.667 0.00 0.00 0.00 2.57
3553 6072 4.706962 GGATGTGGATTTGGCTTTCTAGTT 59.293 41.667 0.00 0.00 0.00 2.24
3554 6073 5.885912 GGATGTGGATTTGGCTTTCTAGTTA 59.114 40.000 0.00 0.00 0.00 2.24
3555 6074 6.547510 GGATGTGGATTTGGCTTTCTAGTTAT 59.452 38.462 0.00 0.00 0.00 1.89
3556 6075 7.068716 GGATGTGGATTTGGCTTTCTAGTTATT 59.931 37.037 0.00 0.00 0.00 1.40
3557 6076 7.391148 TGTGGATTTGGCTTTCTAGTTATTC 57.609 36.000 0.00 0.00 0.00 1.75
3558 6077 6.945435 TGTGGATTTGGCTTTCTAGTTATTCA 59.055 34.615 0.00 0.00 0.00 2.57
3559 6078 7.615365 TGTGGATTTGGCTTTCTAGTTATTCAT 59.385 33.333 0.00 0.00 0.00 2.57
3560 6079 8.131731 GTGGATTTGGCTTTCTAGTTATTCATC 58.868 37.037 0.00 0.00 0.00 2.92
3561 6080 7.285401 TGGATTTGGCTTTCTAGTTATTCATCC 59.715 37.037 0.00 0.00 0.00 3.51
3562 6081 7.503902 GGATTTGGCTTTCTAGTTATTCATCCT 59.496 37.037 0.00 0.00 0.00 3.24
3563 6082 7.630242 TTTGGCTTTCTAGTTATTCATCCTG 57.370 36.000 0.00 0.00 0.00 3.86
3564 6083 6.560003 TGGCTTTCTAGTTATTCATCCTGA 57.440 37.500 0.00 0.00 0.00 3.86
3565 6084 6.957631 TGGCTTTCTAGTTATTCATCCTGAA 58.042 36.000 0.00 0.00 41.09 3.02
3566 6085 7.050377 TGGCTTTCTAGTTATTCATCCTGAAG 58.950 38.462 0.00 0.00 40.05 3.02
3567 6086 6.017523 GGCTTTCTAGTTATTCATCCTGAAGC 60.018 42.308 0.00 0.00 40.05 3.86
3568 6087 6.540189 GCTTTCTAGTTATTCATCCTGAAGCA 59.460 38.462 0.00 0.00 40.05 3.91
3569 6088 7.228308 GCTTTCTAGTTATTCATCCTGAAGCAT 59.772 37.037 0.00 0.00 40.05 3.79
3570 6089 8.442632 TTTCTAGTTATTCATCCTGAAGCATG 57.557 34.615 0.00 0.00 40.05 4.06
3571 6090 6.528321 TCTAGTTATTCATCCTGAAGCATGG 58.472 40.000 0.00 0.00 40.05 3.66
3572 6091 5.378230 AGTTATTCATCCTGAAGCATGGA 57.622 39.130 0.00 0.00 40.05 3.41
3573 6092 5.374921 AGTTATTCATCCTGAAGCATGGAG 58.625 41.667 0.00 0.00 40.05 3.86
3574 6093 3.947612 ATTCATCCTGAAGCATGGAGT 57.052 42.857 0.00 0.00 40.05 3.85
3575 6094 2.704464 TCATCCTGAAGCATGGAGTG 57.296 50.000 0.00 0.00 35.63 3.51
3595 6114 4.360405 GGCCGGCAAAGAGGGGAA 62.360 66.667 30.85 0.00 0.00 3.97
3596 6115 2.282887 GCCGGCAAAGAGGGGAAA 60.283 61.111 24.80 0.00 0.00 3.13
3597 6116 1.906333 GCCGGCAAAGAGGGGAAAA 60.906 57.895 24.80 0.00 0.00 2.29
3598 6117 1.877576 GCCGGCAAAGAGGGGAAAAG 61.878 60.000 24.80 0.00 0.00 2.27
3599 6118 0.251165 CCGGCAAAGAGGGGAAAAGA 60.251 55.000 0.00 0.00 0.00 2.52
3600 6119 1.168714 CGGCAAAGAGGGGAAAAGAG 58.831 55.000 0.00 0.00 0.00 2.85
3601 6120 1.550327 GGCAAAGAGGGGAAAAGAGG 58.450 55.000 0.00 0.00 0.00 3.69
3602 6121 1.075536 GGCAAAGAGGGGAAAAGAGGA 59.924 52.381 0.00 0.00 0.00 3.71
3603 6122 2.441410 GCAAAGAGGGGAAAAGAGGAG 58.559 52.381 0.00 0.00 0.00 3.69
3604 6123 2.881816 GCAAAGAGGGGAAAAGAGGAGG 60.882 54.545 0.00 0.00 0.00 4.30
3605 6124 2.644798 CAAAGAGGGGAAAAGAGGAGGA 59.355 50.000 0.00 0.00 0.00 3.71
3606 6125 2.980699 AGAGGGGAAAAGAGGAGGAT 57.019 50.000 0.00 0.00 0.00 3.24
3607 6126 2.770447 AGAGGGGAAAAGAGGAGGATC 58.230 52.381 0.00 0.00 0.00 3.36
3608 6127 2.046447 AGAGGGGAAAAGAGGAGGATCA 59.954 50.000 0.00 0.00 36.25 2.92
3609 6128 2.846827 GAGGGGAAAAGAGGAGGATCAA 59.153 50.000 0.00 0.00 36.25 2.57
3610 6129 3.461458 GAGGGGAAAAGAGGAGGATCAAT 59.539 47.826 0.00 0.00 36.25 2.57
3611 6130 3.203934 AGGGGAAAAGAGGAGGATCAATG 59.796 47.826 0.00 0.00 36.25 2.82
3612 6131 3.203040 GGGGAAAAGAGGAGGATCAATGA 59.797 47.826 0.00 0.00 36.25 2.57
3613 6132 4.141065 GGGGAAAAGAGGAGGATCAATGAT 60.141 45.833 0.00 0.00 36.25 2.45
3614 6133 4.826183 GGGAAAAGAGGAGGATCAATGATG 59.174 45.833 0.00 0.00 36.25 3.07
3615 6134 4.826183 GGAAAAGAGGAGGATCAATGATGG 59.174 45.833 0.00 0.00 36.25 3.51
3616 6135 5.398353 GGAAAAGAGGAGGATCAATGATGGA 60.398 44.000 0.00 0.00 36.25 3.41
3617 6136 4.978438 AAGAGGAGGATCAATGATGGAG 57.022 45.455 0.00 0.00 36.25 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 6.157211 CCCCAGATATGTTATTACGTGAGAC 58.843 44.000 0.00 0.00 0.00 3.36
623 624 7.040340 TCAGCTTCGAGTTTATTATCTCCTAGG 60.040 40.741 0.82 0.82 0.00 3.02
659 660 4.828072 ATTGGTCAGAGAGGTAAGGAAC 57.172 45.455 0.00 0.00 0.00 3.62
824 825 0.871057 GAGCGAGACTTGCAAGCTTT 59.129 50.000 26.27 11.81 38.39 3.51
832 833 1.066914 GTCAAGCAGAGCGAGACTTG 58.933 55.000 8.78 6.33 40.66 3.16
2536 2833 4.381612 GGTCTATCATTCGGCGATTCCATA 60.382 45.833 11.76 5.26 34.01 2.74
2562 2859 2.670905 CTGGCACAAACATCATGCATTG 59.329 45.455 0.00 0.00 41.27 2.82
2672 5080 5.638783 AGTGTAGTAACTGTGCTATCGAAC 58.361 41.667 0.00 0.00 0.00 3.95
2801 5232 1.979855 TTGGGCGCATACATAGCATT 58.020 45.000 10.83 0.00 0.00 3.56
2869 5306 8.296713 TCACAATTCACTTTTAGATGGTAAAGC 58.703 33.333 0.00 0.00 35.31 3.51
2875 5312 7.175641 AGACCTTCACAATTCACTTTTAGATGG 59.824 37.037 0.00 0.00 0.00 3.51
2898 5335 9.914923 ATTCAGCGAAACAAAATTTAAAAAGAC 57.085 25.926 0.00 0.00 0.00 3.01
2950 5388 6.036191 GTGAAAAGTGCCTAACTAGTAGCATC 59.964 42.308 15.67 10.80 38.56 3.91
2968 5407 3.133691 TGACAGCAGCTAGTGTGAAAAG 58.866 45.455 4.89 0.00 0.00 2.27
3032 5471 4.331108 TGCACATACCTGCAATACTTGAA 58.669 39.130 0.00 0.00 44.28 2.69
3066 5505 7.414436 GTTTACTGATGCTCTGTGTTTTAACA 58.586 34.615 0.00 0.00 36.38 2.41
3067 5506 6.856426 GGTTTACTGATGCTCTGTGTTTTAAC 59.144 38.462 6.13 0.00 31.00 2.01
3069 5508 5.472137 GGGTTTACTGATGCTCTGTGTTTTA 59.528 40.000 6.13 0.00 31.00 1.52
3071 5510 3.821033 GGGTTTACTGATGCTCTGTGTTT 59.179 43.478 6.13 0.00 31.00 2.83
3073 5512 2.612972 CGGGTTTACTGATGCTCTGTGT 60.613 50.000 6.13 0.00 31.00 3.72
3074 5513 2.002586 CGGGTTTACTGATGCTCTGTG 58.997 52.381 6.13 0.00 31.00 3.66
3146 5656 5.865552 TCCAAATTCTTAACTTACCGAGTCG 59.134 40.000 5.29 5.29 37.72 4.18
3154 5664 8.228905 TCCTCCCTTTTCCAAATTCTTAACTTA 58.771 33.333 0.00 0.00 0.00 2.24
3176 5689 1.598701 AAAGCCAAAGCCGCATCCTC 61.599 55.000 0.00 0.00 41.25 3.71
3180 5693 2.973082 GGAAAGCCAAAGCCGCAT 59.027 55.556 0.00 0.00 41.25 4.73
3197 5710 3.931578 ACCTGAATCCTGAGAAAAGACG 58.068 45.455 0.00 0.00 0.00 4.18
3199 5712 5.310409 ACAACCTGAATCCTGAGAAAAGA 57.690 39.130 0.00 0.00 0.00 2.52
3200 5713 6.396829 AAACAACCTGAATCCTGAGAAAAG 57.603 37.500 0.00 0.00 0.00 2.27
3206 5719 4.282449 TCGAGTAAACAACCTGAATCCTGA 59.718 41.667 0.00 0.00 0.00 3.86
3224 5737 4.283722 AGTTCCTAATTTGTGGAGTCGAGT 59.716 41.667 0.00 0.00 33.46 4.18
3233 5746 6.701400 CCTTTTTGTGGAGTTCCTAATTTGTG 59.299 38.462 0.00 0.00 36.82 3.33
3234 5747 6.183360 CCCTTTTTGTGGAGTTCCTAATTTGT 60.183 38.462 0.00 0.00 36.82 2.83
3238 5751 5.333566 TCCCTTTTTGTGGAGTTCCTAAT 57.666 39.130 0.00 0.00 36.82 1.73
3245 5758 1.704641 GCCTTCCCTTTTTGTGGAGT 58.295 50.000 0.00 0.00 30.91 3.85
3246 5759 0.598065 CGCCTTCCCTTTTTGTGGAG 59.402 55.000 0.00 0.00 30.91 3.86
3248 5761 1.067635 CATCGCCTTCCCTTTTTGTGG 60.068 52.381 0.00 0.00 0.00 4.17
3250 5763 0.603065 GCATCGCCTTCCCTTTTTGT 59.397 50.000 0.00 0.00 0.00 2.83
3251 5764 0.456653 CGCATCGCCTTCCCTTTTTG 60.457 55.000 0.00 0.00 0.00 2.44
3255 5768 1.450312 CTTCGCATCGCCTTCCCTT 60.450 57.895 0.00 0.00 0.00 3.95
3256 5769 1.899437 TTCTTCGCATCGCCTTCCCT 61.899 55.000 0.00 0.00 0.00 4.20
3258 5771 2.009888 CTTCTTCGCATCGCCTTCC 58.990 57.895 0.00 0.00 0.00 3.46
3259 5772 1.349973 GCTTCTTCGCATCGCCTTC 59.650 57.895 0.00 0.00 0.00 3.46
3286 5799 2.012673 GACCAGTAGCATTTCAGCCAG 58.987 52.381 0.00 0.00 34.23 4.85
3303 5816 2.808543 CCTGAAAAGTGTGTAGCTGACC 59.191 50.000 0.00 0.00 0.00 4.02
3309 5822 4.630894 TGTTTGCCTGAAAAGTGTGTAG 57.369 40.909 0.00 0.00 0.00 2.74
3316 5829 3.068590 ACTGACCATGTTTGCCTGAAAAG 59.931 43.478 0.00 0.00 0.00 2.27
3328 5841 4.008074 AGACGATCAAAACTGACCATGT 57.992 40.909 0.00 0.00 0.00 3.21
3332 5845 3.813166 TCCAAAGACGATCAAAACTGACC 59.187 43.478 0.00 0.00 0.00 4.02
3346 5859 1.203287 GGCATTCTTGGCTCCAAAGAC 59.797 52.381 2.69 0.00 44.68 3.01
3365 5880 6.857777 TTTGAATACCTGCAAAACATTTGG 57.142 33.333 5.12 0.00 31.64 3.28
3398 5914 6.090088 CGAGTTCTCAATGGTTACAGAGAAAG 59.910 42.308 5.41 0.00 45.49 2.62
3410 5926 3.664107 TCCTGTTTCGAGTTCTCAATGG 58.336 45.455 0.79 0.00 0.00 3.16
3444 5960 2.665185 GAAAGCCGTGGACGCTGT 60.665 61.111 0.00 0.00 38.18 4.40
3452 5968 1.082366 CGGAAAACCGAAAGCCGTG 60.082 57.895 2.30 0.00 37.35 4.94
3453 5969 2.255881 CCGGAAAACCGAAAGCCGT 61.256 57.895 10.28 0.00 40.33 5.68
3463 5979 6.419710 CCTGAATTTAAGACAAACCGGAAAAC 59.580 38.462 9.46 0.00 0.00 2.43
3475 5991 7.272037 TGAGGAAACAACCTGAATTTAAGAC 57.728 36.000 0.00 0.00 40.73 3.01
3505 6024 8.633561 CCTTCCTTTTCAGAATTCTTAACTTGT 58.366 33.333 4.86 0.00 0.00 3.16
3513 6032 5.713861 CCACATCCTTCCTTTTCAGAATTCT 59.286 40.000 0.88 0.88 0.00 2.40
3520 6039 4.527816 CCAAATCCACATCCTTCCTTTTCA 59.472 41.667 0.00 0.00 0.00 2.69
3521 6040 4.621510 GCCAAATCCACATCCTTCCTTTTC 60.622 45.833 0.00 0.00 0.00 2.29
3522 6041 3.261643 GCCAAATCCACATCCTTCCTTTT 59.738 43.478 0.00 0.00 0.00 2.27
3523 6042 2.833943 GCCAAATCCACATCCTTCCTTT 59.166 45.455 0.00 0.00 0.00 3.11
3524 6043 2.043526 AGCCAAATCCACATCCTTCCTT 59.956 45.455 0.00 0.00 0.00 3.36
3525 6044 1.642762 AGCCAAATCCACATCCTTCCT 59.357 47.619 0.00 0.00 0.00 3.36
3526 6045 2.149973 AGCCAAATCCACATCCTTCC 57.850 50.000 0.00 0.00 0.00 3.46
3527 6046 3.766051 AGAAAGCCAAATCCACATCCTTC 59.234 43.478 0.00 0.00 0.00 3.46
3528 6047 3.782992 AGAAAGCCAAATCCACATCCTT 58.217 40.909 0.00 0.00 0.00 3.36
3529 6048 3.463048 AGAAAGCCAAATCCACATCCT 57.537 42.857 0.00 0.00 0.00 3.24
3530 6049 4.273318 ACTAGAAAGCCAAATCCACATCC 58.727 43.478 0.00 0.00 0.00 3.51
3531 6050 5.904362 AACTAGAAAGCCAAATCCACATC 57.096 39.130 0.00 0.00 0.00 3.06
3532 6051 7.615365 TGAATAACTAGAAAGCCAAATCCACAT 59.385 33.333 0.00 0.00 0.00 3.21
3533 6052 6.945435 TGAATAACTAGAAAGCCAAATCCACA 59.055 34.615 0.00 0.00 0.00 4.17
3534 6053 7.391148 TGAATAACTAGAAAGCCAAATCCAC 57.609 36.000 0.00 0.00 0.00 4.02
3535 6054 7.285401 GGATGAATAACTAGAAAGCCAAATCCA 59.715 37.037 0.00 0.00 0.00 3.41
3536 6055 7.503902 AGGATGAATAACTAGAAAGCCAAATCC 59.496 37.037 0.00 0.00 0.00 3.01
3537 6056 8.348507 CAGGATGAATAACTAGAAAGCCAAATC 58.651 37.037 0.00 0.00 39.69 2.17
3538 6057 8.055181 TCAGGATGAATAACTAGAAAGCCAAAT 58.945 33.333 0.00 0.00 45.97 2.32
3539 6058 7.402054 TCAGGATGAATAACTAGAAAGCCAAA 58.598 34.615 0.00 0.00 45.97 3.28
3540 6059 6.957631 TCAGGATGAATAACTAGAAAGCCAA 58.042 36.000 0.00 0.00 45.97 4.52
3541 6060 6.560003 TCAGGATGAATAACTAGAAAGCCA 57.440 37.500 0.00 0.00 45.97 4.75
3578 6097 3.879180 TTTCCCCTCTTTGCCGGCC 62.879 63.158 26.77 6.44 0.00 6.13
3579 6098 1.877576 CTTTTCCCCTCTTTGCCGGC 61.878 60.000 22.73 22.73 0.00 6.13
3580 6099 0.251165 TCTTTTCCCCTCTTTGCCGG 60.251 55.000 0.00 0.00 0.00 6.13
3581 6100 1.168714 CTCTTTTCCCCTCTTTGCCG 58.831 55.000 0.00 0.00 0.00 5.69
3582 6101 1.075536 TCCTCTTTTCCCCTCTTTGCC 59.924 52.381 0.00 0.00 0.00 4.52
3583 6102 2.441410 CTCCTCTTTTCCCCTCTTTGC 58.559 52.381 0.00 0.00 0.00 3.68
3584 6103 2.644798 TCCTCCTCTTTTCCCCTCTTTG 59.355 50.000 0.00 0.00 0.00 2.77
3585 6104 3.005529 TCCTCCTCTTTTCCCCTCTTT 57.994 47.619 0.00 0.00 0.00 2.52
3586 6105 2.743131 TCCTCCTCTTTTCCCCTCTT 57.257 50.000 0.00 0.00 0.00 2.85
3587 6106 2.046447 TGATCCTCCTCTTTTCCCCTCT 59.954 50.000 0.00 0.00 0.00 3.69
3588 6107 2.482494 TGATCCTCCTCTTTTCCCCTC 58.518 52.381 0.00 0.00 0.00 4.30
3589 6108 2.668850 TGATCCTCCTCTTTTCCCCT 57.331 50.000 0.00 0.00 0.00 4.79
3590 6109 3.203040 TCATTGATCCTCCTCTTTTCCCC 59.797 47.826 0.00 0.00 0.00 4.81
3591 6110 4.510167 TCATTGATCCTCCTCTTTTCCC 57.490 45.455 0.00 0.00 0.00 3.97
3592 6111 4.826183 CCATCATTGATCCTCCTCTTTTCC 59.174 45.833 0.00 0.00 0.00 3.13
3593 6112 5.688807 TCCATCATTGATCCTCCTCTTTTC 58.311 41.667 0.00 0.00 0.00 2.29
3594 6113 5.692928 CTCCATCATTGATCCTCCTCTTTT 58.307 41.667 0.00 0.00 0.00 2.27
3595 6114 5.307544 CTCCATCATTGATCCTCCTCTTT 57.692 43.478 0.00 0.00 0.00 2.52
3596 6115 4.978438 CTCCATCATTGATCCTCCTCTT 57.022 45.455 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.