Multiple sequence alignment - TraesCS3D01G150800

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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 TraesCS3D01G150800 chr3D 100.000 3770 0 0 1 3770 115633487 115637256 0.000000e+00 6962.0
1 TraesCS3D01G150800 chr3D 93.282 387 16 1 2577 2953 115646786 115647172 2.540000e-156 562.0
2 TraesCS3D01G150800 chr3D 91.935 248 11 7 3063 3309 134818790 134818551 4.660000e-89 339.0
3 TraesCS3D01G150800 chr3B 94.072 3104 101 32 1 3066 169254409 169257467 0.000000e+00 4636.0
4 TraesCS3D01G150800 chr3B 88.780 410 37 7 3310 3711 169258559 169258967 9.410000e-136 494.0
5 TraesCS3D01G150800 chr3B 89.109 404 30 7 2562 2953 169272544 169272945 1.220000e-134 490.0
6 TraesCS3D01G150800 chr3A 93.499 2015 78 15 966 2953 111961726 111963714 0.000000e+00 2946.0
7 TraesCS3D01G150800 chr3A 81.944 648 55 29 330 959 111954804 111955407 3.380000e-135 492.0
8 TraesCS3D01G150800 chr3A 85.000 300 29 10 24 310 111952566 111952862 1.320000e-74 291.0
9 TraesCS3D01G150800 chr6A 79.021 1001 186 18 1214 2196 99968815 99967821 0.000000e+00 664.0
10 TraesCS3D01G150800 chr6A 92.369 249 10 5 3067 3314 471880970 471880730 2.790000e-91 346.0
11 TraesCS3D01G150800 chr6A 90.272 257 15 8 3063 3318 555116233 555115986 1.010000e-85 327.0
12 TraesCS3D01G150800 chr6A 96.667 60 2 0 3711 3770 63584348 63584407 2.400000e-17 100.0
13 TraesCS3D01G150800 chr6A 95.652 46 1 1 3666 3711 34240516 34240560 5.220000e-09 73.1
14 TraesCS3D01G150800 chr6A 95.652 46 1 1 3666 3711 338250553 338250509 5.220000e-09 73.1
15 TraesCS3D01G150800 chr5B 78.706 958 172 26 1213 2145 48860938 48859988 8.950000e-171 610.0
16 TraesCS3D01G150800 chr5B 91.045 67 5 1 3696 3761 458389705 458389771 5.190000e-14 89.8
17 TraesCS3D01G150800 chr6B 78.496 944 167 27 1213 2145 157864666 157863748 1.510000e-163 586.0
18 TraesCS3D01G150800 chr5D 76.180 953 201 22 1213 2145 46713280 46714226 2.630000e-131 479.0
19 TraesCS3D01G150800 chr5D 91.339 254 12 8 3063 3315 87803594 87803350 4.660000e-89 339.0
20 TraesCS3D01G150800 chr5D 91.667 72 5 1 3700 3770 28151591 28151520 8.620000e-17 99.0
21 TraesCS3D01G150800 chr5D 91.304 69 4 2 3702 3770 521487798 521487864 4.010000e-15 93.5
22 TraesCS3D01G150800 chr2A 91.600 250 12 7 3063 3311 585818905 585819146 1.680000e-88 337.0
23 TraesCS3D01G150800 chr2A 95.652 46 1 1 3666 3711 637191901 637191857 5.220000e-09 73.1
24 TraesCS3D01G150800 chr6D 91.016 256 10 8 3063 3313 328503640 328503393 2.170000e-87 333.0
25 TraesCS3D01G150800 chr6D 90.800 250 14 7 3063 3311 141388626 141388867 3.630000e-85 326.0
26 TraesCS3D01G150800 chr6D 95.000 60 3 0 3711 3770 453197173 453197232 1.110000e-15 95.3
27 TraesCS3D01G150800 chr6D 93.548 62 4 0 3709 3770 31964829 31964768 4.010000e-15 93.5
28 TraesCS3D01G150800 chr6D 98.113 53 1 0 3709 3761 377820329 377820381 4.010000e-15 93.5
29 TraesCS3D01G150800 chr7D 90.909 253 14 5 3063 3314 15027227 15026983 7.810000e-87 331.0
30 TraesCS3D01G150800 chr4D 91.803 244 11 6 3069 3311 47750942 47750707 7.810000e-87 331.0
31 TraesCS3D01G150800 chr4D 88.889 72 8 0 3699 3770 295434192 295434121 5.190000e-14 89.8
32 TraesCS3D01G150800 chr4A 93.548 62 4 0 3709 3770 433726679 433726618 4.010000e-15 93.5


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 TraesCS3D01G150800 chr3D 115633487 115637256 3769 False 6962.0 6962 100.000 1 3770 1 chr3D.!!$F1 3769
1 TraesCS3D01G150800 chr3B 169254409 169258967 4558 False 2565.0 4636 91.426 1 3711 2 chr3B.!!$F2 3710
2 TraesCS3D01G150800 chr3A 111961726 111963714 1988 False 2946.0 2946 93.499 966 2953 1 chr3A.!!$F1 1987
3 TraesCS3D01G150800 chr3A 111952566 111955407 2841 False 391.5 492 83.472 24 959 2 chr3A.!!$F2 935
4 TraesCS3D01G150800 chr6A 99967821 99968815 994 True 664.0 664 79.021 1214 2196 1 chr6A.!!$R1 982
5 TraesCS3D01G150800 chr5B 48859988 48860938 950 True 610.0 610 78.706 1213 2145 1 chr5B.!!$R1 932
6 TraesCS3D01G150800 chr6B 157863748 157864666 918 True 586.0 586 78.496 1213 2145 1 chr6B.!!$R1 932
7 TraesCS3D01G150800 chr5D 46713280 46714226 946 False 479.0 479 76.180 1213 2145 1 chr5D.!!$F1 932

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
814 2765 0.174845 TAGTGGACAATTCGAGCCCG 59.825 55.0 0.0 0.0 37.07 6.13 F
1648 3644 0.175989 GCTTCACCTCTACTTCCGGG 59.824 60.0 0.0 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 3730 0.542333 TGTTCTGGACCACGAACCAA 59.458 50.0 23.02 10.99 38.93 3.67 R
2897 4913 0.456312 GACACGAGACGACCCATCAC 60.456 60.0 0.00 0.00 0.00 3.06 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
57 59 6.806668 AGATTGGGTCCTTTTTGAAAGAAA 57.193 33.333 2.15 0.00 0.00 2.52
58 60 6.820335 AGATTGGGTCCTTTTTGAAAGAAAG 58.180 36.000 2.15 0.00 34.63 2.62
105 120 5.705609 TTTGTGTTTTTAGATGGCTCTCC 57.294 39.130 0.00 0.00 32.66 3.71
106 121 3.334691 TGTGTTTTTAGATGGCTCTCCG 58.665 45.455 0.00 0.00 32.66 4.63
157 172 2.747855 CCTTGCTGCCGGGAGTTC 60.748 66.667 24.99 9.30 0.00 3.01
171 186 2.224209 GGGAGTTCAGACAGTTTTCGGA 60.224 50.000 0.00 0.00 0.00 4.55
182 197 7.444183 TCAGACAGTTTTCGGATTTAAGACAAT 59.556 33.333 0.00 0.00 0.00 2.71
196 211 9.769093 GATTTAAGACAATAACACGCAACTTAT 57.231 29.630 0.00 0.00 0.00 1.73
204 219 8.243426 ACAATAACACGCAACTTATTCATCAAT 58.757 29.630 0.00 0.00 0.00 2.57
212 227 6.906678 CGCAACTTATTCATCAATCGAATGAA 59.093 34.615 7.36 10.18 38.48 2.57
271 286 5.163457 GGAAGAGGGACAACAATTCAACAAA 60.163 40.000 0.00 0.00 0.00 2.83
310 325 3.406764 GGCAGGCCAACATAGAATCTAG 58.593 50.000 5.01 0.00 35.81 2.43
315 2240 6.164876 CAGGCCAACATAGAATCTAGATCTG 58.835 44.000 5.01 4.60 0.00 2.90
367 2305 5.067153 TCAAATTTATGAGCACAATACGGGG 59.933 40.000 0.00 0.00 0.00 5.73
420 2359 2.774234 CTCCTATGTGGGAGTTGATGGT 59.226 50.000 4.39 0.00 45.65 3.55
464 2403 6.775629 ACCTACATTTGTTTGTGATTAGGTGT 59.224 34.615 0.00 0.00 34.86 4.16
465 2404 7.040686 ACCTACATTTGTTTGTGATTAGGTGTC 60.041 37.037 0.00 0.00 34.86 3.67
512 2456 3.118454 CATCGCGCGTGGTCCTTT 61.118 61.111 30.98 2.69 0.00 3.11
538 2482 3.268103 ATGGAGCCGAGGCCGTTTT 62.268 57.895 10.95 0.00 43.17 2.43
566 2510 0.306533 AACTAACACGCAACCGCAAG 59.693 50.000 0.00 0.00 38.40 4.01
619 2564 7.014711 GGAGATCTTTGTTTCCTTTCTTTTCCT 59.985 37.037 0.00 0.00 0.00 3.36
620 2565 8.311395 AGATCTTTGTTTCCTTTCTTTTCCTT 57.689 30.769 0.00 0.00 0.00 3.36
621 2566 9.421399 AGATCTTTGTTTCCTTTCTTTTCCTTA 57.579 29.630 0.00 0.00 0.00 2.69
622 2567 9.684448 GATCTTTGTTTCCTTTCTTTTCCTTAG 57.316 33.333 0.00 0.00 0.00 2.18
623 2568 8.817092 TCTTTGTTTCCTTTCTTTTCCTTAGA 57.183 30.769 0.00 0.00 0.00 2.10
650 2595 3.397482 AGAGAATGATTATCTGCGTGCC 58.603 45.455 0.90 0.00 0.00 5.01
664 2609 1.604593 GTGCCCCACTGTTGCTGAT 60.605 57.895 0.00 0.00 0.00 2.90
731 2682 2.583441 GCTGTTTTTGGCCCCTCCC 61.583 63.158 0.00 0.00 0.00 4.30
814 2765 0.174845 TAGTGGACAATTCGAGCCCG 59.825 55.000 0.00 0.00 37.07 6.13
835 2786 3.103742 GCCCAAAAGTCCCATAATTCCA 58.896 45.455 0.00 0.00 0.00 3.53
898 2849 8.180267 CACTCACAAAGCTGAATATTCCTTTAG 58.820 37.037 12.90 11.48 0.00 1.85
899 2850 8.103305 ACTCACAAAGCTGAATATTCCTTTAGA 58.897 33.333 12.90 13.66 0.00 2.10
926 2877 6.286648 CAAAGTGCATTTGTTTATACGACG 57.713 37.500 0.00 0.00 42.84 5.12
946 2897 8.599055 ACGACGAGATAGATATTGTTGTACTA 57.401 34.615 0.00 0.00 0.00 1.82
1648 3644 0.175989 GCTTCACCTCTACTTCCGGG 59.824 60.000 0.00 0.00 0.00 5.73
1671 3667 4.373116 GCCCAGCTGACGTCGGAA 62.373 66.667 28.38 0.56 0.00 4.30
1716 3712 2.776913 CCCCGTCTCGAGAAGCCTC 61.777 68.421 18.55 3.04 36.08 4.70
1734 3730 2.427245 CCCTCTCGACGATGGGCTT 61.427 63.158 18.94 0.00 32.49 4.35
2016 4018 1.648467 GCTCGTTCAATCTGCCCACC 61.648 60.000 0.00 0.00 0.00 4.61
2190 4192 3.950254 ATCTCCTACGACGCGCCG 61.950 66.667 14.75 14.75 0.00 6.46
2211 4213 2.981302 CTGTCGGGGAGCATCACA 59.019 61.111 0.00 0.00 43.69 3.58
2273 4275 4.427394 GAGCCGCAACATCTCGAT 57.573 55.556 0.00 0.00 0.00 3.59
2736 4738 0.865769 ACGTGCTTTTCGACCATGAC 59.134 50.000 0.00 0.00 0.00 3.06
2801 4803 4.564116 CGCCCGCCTACGTGGTAG 62.564 72.222 0.00 0.00 38.04 3.18
2802 4804 3.142838 GCCCGCCTACGTGGTAGA 61.143 66.667 0.00 0.00 38.29 2.59
2803 4805 2.496291 GCCCGCCTACGTGGTAGAT 61.496 63.158 0.00 0.00 38.29 1.98
2805 4807 1.362717 CCGCCTACGTGGTAGATGG 59.637 63.158 0.00 2.42 38.29 3.51
2806 4808 1.299926 CGCCTACGTGGTAGATGGC 60.300 63.158 0.00 0.00 38.29 4.40
2865 4875 2.539081 GGGAACAGAAGTGGGCCCT 61.539 63.158 25.70 1.15 37.87 5.19
2897 4913 6.481134 TCGTACTACTATAGTCTTTGCGTTG 58.519 40.000 9.12 0.00 40.14 4.10
2943 4959 5.729510 AGCTCTGAATAAGAAAGGAGTGAC 58.270 41.667 0.00 0.00 33.37 3.67
3032 5584 1.600912 GGCGTACAATTTGGTTTGCGT 60.601 47.619 0.78 0.00 0.00 5.24
3042 5594 0.460459 TGGTTTGCGTGTCTGTTCGA 60.460 50.000 0.00 0.00 0.00 3.71
3061 5613 6.788458 TGTTCGAATCAAAACGAATAGAAACG 59.212 34.615 0.00 0.00 46.97 3.60
3068 5620 1.538276 ACGAATAGAAACGTACGCCG 58.462 50.000 16.72 8.49 40.92 6.46
3069 5621 0.225489 CGAATAGAAACGTACGCCGC 59.775 55.000 16.72 4.36 41.42 6.53
3070 5622 1.270971 GAATAGAAACGTACGCCGCA 58.729 50.000 16.72 0.00 41.42 5.69
3071 5623 1.856597 GAATAGAAACGTACGCCGCAT 59.143 47.619 16.72 0.24 41.42 4.73
3072 5624 2.780065 ATAGAAACGTACGCCGCATA 57.220 45.000 16.72 2.72 41.42 3.14
3073 5625 2.780065 TAGAAACGTACGCCGCATAT 57.220 45.000 16.72 0.00 41.42 1.78
3074 5626 1.930567 AGAAACGTACGCCGCATATT 58.069 45.000 16.72 0.00 41.42 1.28
3075 5627 3.082698 AGAAACGTACGCCGCATATTA 57.917 42.857 16.72 0.00 41.42 0.98
3082 5634 2.882927 ACGCCGCATATTAGAGTTGA 57.117 45.000 0.00 0.00 0.00 3.18
3083 5635 2.470821 ACGCCGCATATTAGAGTTGAC 58.529 47.619 0.00 0.00 0.00 3.18
3084 5636 2.100916 ACGCCGCATATTAGAGTTGACT 59.899 45.455 0.00 0.00 0.00 3.41
3086 5638 3.717707 GCCGCATATTAGAGTTGACTGA 58.282 45.455 0.00 0.00 0.00 3.41
3088 5640 4.210120 GCCGCATATTAGAGTTGACTGAAG 59.790 45.833 0.00 0.00 0.00 3.02
3089 5641 5.352284 CCGCATATTAGAGTTGACTGAAGT 58.648 41.667 0.00 0.00 0.00 3.01
3090 5642 5.460419 CCGCATATTAGAGTTGACTGAAGTC 59.540 44.000 3.41 3.41 44.97 3.01
3173 5725 9.797642 AGCATAACAAATCTATATGATGTGGAA 57.202 29.630 9.00 0.56 43.15 3.53
3178 5730 9.857656 AACAAATCTATATGATGTGGAAGTCAT 57.142 29.630 9.00 0.00 43.15 3.06
3179 5731 9.857656 ACAAATCTATATGATGTGGAAGTCATT 57.142 29.630 9.00 0.00 43.15 2.57
3183 5735 8.893219 TCTATATGATGTGGAAGTCATTCAAC 57.107 34.615 0.00 0.00 39.49 3.18
3190 5742 4.578516 TGTGGAAGTCATTCAACAACGAAT 59.421 37.500 0.00 0.00 44.68 3.34
3191 5743 5.760743 TGTGGAAGTCATTCAACAACGAATA 59.239 36.000 0.00 0.00 44.68 1.75
3193 5745 7.604545 TGTGGAAGTCATTCAACAACGAATATA 59.395 33.333 0.00 0.00 44.68 0.86
3194 5746 8.447833 GTGGAAGTCATTCAACAACGAATATAA 58.552 33.333 0.00 0.00 38.96 0.98
3195 5747 9.173021 TGGAAGTCATTCAACAACGAATATAAT 57.827 29.630 0.00 0.00 37.15 1.28
3196 5748 9.438291 GGAAGTCATTCAACAACGAATATAATG 57.562 33.333 0.00 0.00 37.15 1.90
3197 5749 9.438291 GAAGTCATTCAACAACGAATATAATGG 57.562 33.333 0.00 0.00 33.82 3.16
3198 5750 8.506168 AGTCATTCAACAACGAATATAATGGT 57.494 30.769 0.00 0.00 33.82 3.55
3272 5824 6.036470 AAGTTTGTAAAGCTTGACTTTGAGC 58.964 36.000 15.19 1.67 45.94 4.26
3273 5825 6.350110 AAGTTTGTAAAGCTTGACTTTGAGCA 60.350 34.615 15.19 0.00 45.94 4.26
3274 5826 7.790707 AAGTTTGTAAAGCTTGACTTTGAGCAA 60.791 33.333 15.19 0.00 45.94 3.91
3279 5831 5.835113 AAGCTTGACTTTGAGCAAAACTA 57.165 34.783 0.00 0.00 41.31 2.24
3280 5832 5.835113 AGCTTGACTTTGAGCAAAACTAA 57.165 34.783 0.00 0.00 41.31 2.24
3282 5834 7.510549 AGCTTGACTTTGAGCAAAACTAATA 57.489 32.000 0.00 0.00 41.31 0.98
3283 5835 8.115490 AGCTTGACTTTGAGCAAAACTAATAT 57.885 30.769 0.00 0.00 41.31 1.28
3284 5836 8.025445 AGCTTGACTTTGAGCAAAACTAATATG 58.975 33.333 0.00 0.00 41.31 1.78
3286 5838 6.314018 TGACTTTGAGCAAAACTAATATGCG 58.686 36.000 0.00 0.00 44.60 4.73
3287 5839 6.148645 TGACTTTGAGCAAAACTAATATGCGA 59.851 34.615 0.00 0.00 44.60 5.10
3288 5840 6.908825 ACTTTGAGCAAAACTAATATGCGAA 58.091 32.000 0.00 0.00 44.60 4.70
3289 5841 7.023575 ACTTTGAGCAAAACTAATATGCGAAG 58.976 34.615 0.00 0.00 44.60 3.79
3290 5842 6.494893 TTGAGCAAAACTAATATGCGAAGT 57.505 33.333 0.00 0.00 44.60 3.01
3291 5843 7.603963 TTGAGCAAAACTAATATGCGAAGTA 57.396 32.000 0.00 0.00 44.60 2.24
3293 5845 8.035165 TGAGCAAAACTAATATGCGAAGTAAA 57.965 30.769 0.00 0.00 44.60 2.01
3294 5846 8.673711 TGAGCAAAACTAATATGCGAAGTAAAT 58.326 29.630 0.00 0.00 44.60 1.40
3302 5854 9.925268 ACTAATATGCGAAGTAAATAAAAACGG 57.075 29.630 0.00 0.00 0.00 4.44
3306 5858 4.154556 TGCGAAGTAAATAAAAACGGAGGG 59.845 41.667 0.00 0.00 0.00 4.30
3307 5859 4.392754 GCGAAGTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
3308 5860 5.446875 GCGAAGTAAATAAAAACGGAGGGAG 60.447 44.000 0.00 0.00 0.00 4.30
3315 6187 7.912056 AAATAAAAACGGAGGGAGTACTTAC 57.088 36.000 0.00 0.00 0.00 2.34
3354 6226 3.066203 GTCCGTCCAAACACATTTTCAGT 59.934 43.478 0.00 0.00 0.00 3.41
3356 6228 4.041723 CCGTCCAAACACATTTTCAGTTC 58.958 43.478 0.00 0.00 0.00 3.01
3370 6242 8.034215 ACATTTTCAGTTCAAATTTGTGTCAGA 58.966 29.630 17.47 8.18 0.00 3.27
3399 6271 1.226323 CGAGTCCGCTAGGTGTTCG 60.226 63.158 0.00 0.00 39.05 3.95
3408 6280 0.541863 CTAGGTGTTCGCCTTGGGAT 59.458 55.000 10.23 0.00 39.94 3.85
3427 6299 1.234821 TCGTGCTTTGACCATCCAAC 58.765 50.000 0.00 0.00 0.00 3.77
3445 6317 2.304751 ACGTGTTCGGATATGGGTTC 57.695 50.000 0.00 0.00 41.85 3.62
3456 6328 4.124238 GGATATGGGTTCGAAACGATGAA 58.876 43.478 19.59 2.14 35.23 2.57
3480 6353 4.494362 CGTTCAAACATGGACGTGTTAACA 60.494 41.667 3.59 3.59 41.22 2.41
3499 6372 3.037549 ACATGGGAAGGCTTGACAAAAA 58.962 40.909 3.46 0.00 0.00 1.94
3501 6374 3.025322 TGGGAAGGCTTGACAAAAAGA 57.975 42.857 3.46 0.00 0.00 2.52
3506 6379 5.294306 GGGAAGGCTTGACAAAAAGAAAAAG 59.706 40.000 3.46 0.00 0.00 2.27
3507 6380 5.220662 GGAAGGCTTGACAAAAAGAAAAAGC 60.221 40.000 3.46 0.00 39.38 3.51
3634 6511 7.719483 TCCGGAATCGTGTCTATTTTATACTT 58.281 34.615 0.00 0.00 33.95 2.24
3658 6536 6.978024 TTTTTACACGAATCCGAAATTGTG 57.022 33.333 0.00 4.23 39.50 3.33
3668 6546 8.388103 ACGAATCCGAAATTGTGTCTATTTTAG 58.612 33.333 0.00 0.00 39.50 1.85
3669 6547 8.600625 CGAATCCGAAATTGTGTCTATTTTAGA 58.399 33.333 0.00 0.00 38.22 2.10
3672 6550 8.251750 TCCGAAATTGTGTCTATTTTAGAGTG 57.748 34.615 0.00 0.00 35.04 3.51
3725 6605 9.296400 TGTTTTAGCAAACAGTTTGACTAATTC 57.704 29.630 27.16 22.45 46.06 2.17
3726 6606 9.296400 GTTTTAGCAAACAGTTTGACTAATTCA 57.704 29.630 27.16 15.43 43.26 2.57
3727 6607 8.850454 TTTAGCAAACAGTTTGACTAATTCAC 57.150 30.769 27.16 8.05 43.26 3.18
3728 6608 6.449635 AGCAAACAGTTTGACTAATTCACA 57.550 33.333 27.16 0.00 43.26 3.58
3729 6609 7.042797 AGCAAACAGTTTGACTAATTCACAT 57.957 32.000 27.16 0.22 43.26 3.21
3730 6610 7.141363 AGCAAACAGTTTGACTAATTCACATC 58.859 34.615 27.16 6.74 43.26 3.06
3731 6611 7.013655 AGCAAACAGTTTGACTAATTCACATCT 59.986 33.333 27.16 8.74 43.26 2.90
3732 6612 8.289618 GCAAACAGTTTGACTAATTCACATCTA 58.710 33.333 27.16 0.00 43.26 1.98
3733 6613 9.817365 CAAACAGTTTGACTAATTCACATCTAG 57.183 33.333 19.79 0.00 43.26 2.43
3734 6614 9.778741 AAACAGTTTGACTAATTCACATCTAGA 57.221 29.630 0.00 0.00 32.26 2.43
3735 6615 9.950496 AACAGTTTGACTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 32.26 1.98
3736 6616 9.376075 ACAGTTTGACTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.444388 AGGTACCCCTCCGTTTCTTTTT 59.556 45.455 8.74 0.00 35.62 1.94
10 11 3.920231 ATAAAGGTACCCCTCCGTTTC 57.080 47.619 8.74 0.00 41.56 2.78
37 39 6.613153 TTCTTTCTTTCAAAAAGGACCCAA 57.387 33.333 0.00 0.00 35.03 4.12
105 120 2.572191 TCGTAGTTATGAACCCTGCG 57.428 50.000 0.00 0.00 35.95 5.18
106 121 4.453136 TGTTTTCGTAGTTATGAACCCTGC 59.547 41.667 0.00 0.00 31.43 4.85
110 125 5.335113 GGGGTTGTTTTCGTAGTTATGAACC 60.335 44.000 0.00 0.00 31.43 3.62
157 172 6.539649 TGTCTTAAATCCGAAAACTGTCTG 57.460 37.500 0.00 0.00 0.00 3.51
182 197 6.311690 TCGATTGATGAATAAGTTGCGTGTTA 59.688 34.615 0.00 0.00 0.00 2.41
196 211 8.945057 TGTTGAGTTATTCATTCGATTGATGAA 58.055 29.630 12.18 12.18 38.48 2.57
204 219 6.878923 AGGTGATTGTTGAGTTATTCATTCGA 59.121 34.615 0.00 0.00 35.27 3.71
212 227 3.010584 AGGCCAGGTGATTGTTGAGTTAT 59.989 43.478 5.01 0.00 0.00 1.89
271 286 1.377725 CCATGCTTGAGCCGGTCTT 60.378 57.895 1.90 0.00 41.18 3.01
310 325 7.919091 TGGTACGTGTGTATTTAGATTCAGATC 59.081 37.037 0.00 0.00 32.11 2.75
315 2240 6.021153 GTCGTGGTACGTGTGTATTTAGATTC 60.021 42.308 0.00 0.00 43.14 2.52
420 2359 0.612744 TGGAATCCAGACGCACATCA 59.387 50.000 0.00 0.00 0.00 3.07
465 2404 2.572095 TTATCAGCACTGTCGGCCGG 62.572 60.000 27.83 12.37 0.00 6.13
538 2482 5.521544 GGTTGCGTGTTAGTTTATTGGAAA 58.478 37.500 0.00 0.00 0.00 3.13
566 2510 7.336931 ACAGATAACTTGTGGTGGATGAATAAC 59.663 37.037 0.00 0.00 0.00 1.89
621 2566 8.584157 ACGCAGATAATCATTCTCTTCTAATCT 58.416 33.333 0.00 0.00 0.00 2.40
622 2567 8.646356 CACGCAGATAATCATTCTCTTCTAATC 58.354 37.037 0.00 0.00 0.00 1.75
623 2568 7.117523 GCACGCAGATAATCATTCTCTTCTAAT 59.882 37.037 0.00 0.00 0.00 1.73
650 2595 2.559668 ACAATGAATCAGCAACAGTGGG 59.440 45.455 0.00 0.00 34.63 4.61
664 2609 4.610605 TCCACTAGAACGGAACAATGAA 57.389 40.909 0.00 0.00 0.00 2.57
692 2637 0.606673 GGAAACACACCTCTCCAGCC 60.607 60.000 0.00 0.00 0.00 4.85
731 2682 2.576053 CGACGATCACACGACCCG 60.576 66.667 0.00 0.00 37.03 5.28
752 2703 8.002984 ACAATAATAACCCGGAAAAATACAGG 57.997 34.615 0.73 0.00 0.00 4.00
814 2765 3.103742 TGGAATTATGGGACTTTTGGGC 58.896 45.455 0.00 0.00 0.00 5.36
835 2786 1.549170 CAAAGTGGCGAGTAGGTAGGT 59.451 52.381 0.00 0.00 0.00 3.08
905 2856 5.636121 TCTCGTCGTATAAACAAATGCACTT 59.364 36.000 0.00 0.00 0.00 3.16
907 2858 5.444586 TCTCGTCGTATAAACAAATGCAC 57.555 39.130 0.00 0.00 0.00 4.57
909 2860 7.618964 TCTATCTCGTCGTATAAACAAATGC 57.381 36.000 0.00 0.00 0.00 3.56
1734 3730 0.542333 TGTTCTGGACCACGAACCAA 59.458 50.000 23.02 10.99 38.93 3.67
2016 4018 3.135306 CGTGAGCTCGATGTCGTAG 57.865 57.895 9.64 0.74 40.80 3.51
2190 4192 1.522580 GATGCTCCCCGACAGCTTC 60.523 63.158 0.00 2.26 37.79 3.86
2272 4274 1.615424 AGCTTACCCACCCCGTGAT 60.615 57.895 0.00 0.00 35.23 3.06
2273 4275 2.203877 AGCTTACCCACCCCGTGA 60.204 61.111 0.00 0.00 35.23 4.35
2577 4579 4.680237 TCCGCCACCTGCTCGTTG 62.680 66.667 0.00 0.00 38.05 4.10
2799 4801 2.358039 CCGTTATCCCGGCCATCTA 58.642 57.895 2.24 0.00 41.78 1.98
2800 4802 3.148084 CCGTTATCCCGGCCATCT 58.852 61.111 2.24 0.00 41.78 2.90
2897 4913 0.456312 GACACGAGACGACCCATCAC 60.456 60.000 0.00 0.00 0.00 3.06
2967 5000 3.062909 GCGCATAACCATGTTCGTCTTTA 59.937 43.478 0.30 0.00 34.40 1.85
2972 5005 1.378531 ATGCGCATAACCATGTTCGT 58.621 45.000 24.02 0.00 34.40 3.85
3032 5584 5.666969 ATTCGTTTTGATTCGAACAGACA 57.333 34.783 0.00 0.00 46.11 3.41
3042 5594 6.011277 GCGTACGTTTCTATTCGTTTTGATT 58.989 36.000 17.90 0.00 40.70 2.57
3061 5613 3.424529 GTCAACTCTAATATGCGGCGTAC 59.575 47.826 9.37 0.00 0.00 3.67
3152 5704 9.857656 ATGACTTCCACATCATATAGATTTGTT 57.142 29.630 0.00 0.00 33.49 2.83
3153 5705 9.857656 AATGACTTCCACATCATATAGATTTGT 57.142 29.630 0.00 0.00 34.41 2.83
3158 5710 8.485392 TGTTGAATGACTTCCACATCATATAGA 58.515 33.333 0.00 0.00 33.44 1.98
3159 5711 8.667076 TGTTGAATGACTTCCACATCATATAG 57.333 34.615 0.00 0.00 33.44 1.31
3162 5714 6.128309 CGTTGTTGAATGACTTCCACATCATA 60.128 38.462 0.00 0.00 37.02 2.15
3163 5715 5.335113 CGTTGTTGAATGACTTCCACATCAT 60.335 40.000 0.00 0.00 37.02 2.45
3164 5716 4.024133 CGTTGTTGAATGACTTCCACATCA 60.024 41.667 0.00 0.00 37.02 3.07
3165 5717 4.213270 TCGTTGTTGAATGACTTCCACATC 59.787 41.667 0.00 0.00 37.02 3.06
3166 5718 4.133820 TCGTTGTTGAATGACTTCCACAT 58.866 39.130 0.00 0.00 37.02 3.21
3167 5719 3.536570 TCGTTGTTGAATGACTTCCACA 58.463 40.909 0.00 0.00 35.78 4.17
3168 5720 4.545823 TTCGTTGTTGAATGACTTCCAC 57.454 40.909 0.00 0.00 0.00 4.02
3169 5721 8.554835 TTATATTCGTTGTTGAATGACTTCCA 57.445 30.769 0.00 0.00 38.92 3.53
3170 5722 9.438291 CATTATATTCGTTGTTGAATGACTTCC 57.562 33.333 0.00 0.00 38.92 3.46
3171 5723 9.438291 CCATTATATTCGTTGTTGAATGACTTC 57.562 33.333 0.00 0.00 38.92 3.01
3173 5725 8.506168 ACCATTATATTCGTTGTTGAATGACT 57.494 30.769 0.00 0.00 38.92 3.41
3240 5792 9.353999 AGTCAAGCTTTACAAACTTTAACAAAG 57.646 29.630 13.07 0.00 44.10 2.77
3242 5794 9.699703 AAAGTCAAGCTTTACAAACTTTAACAA 57.300 25.926 13.07 0.00 44.90 2.83
3243 5795 9.134734 CAAAGTCAAGCTTTACAAACTTTAACA 57.865 29.630 13.07 0.00 44.95 2.41
3244 5796 9.349145 TCAAAGTCAAGCTTTACAAACTTTAAC 57.651 29.630 13.07 0.00 44.95 2.01
3245 5797 9.567848 CTCAAAGTCAAGCTTTACAAACTTTAA 57.432 29.630 13.07 3.15 44.95 1.52
3246 5798 7.700656 GCTCAAAGTCAAGCTTTACAAACTTTA 59.299 33.333 13.07 5.79 44.95 1.85
3248 5800 6.036470 GCTCAAAGTCAAGCTTTACAAACTT 58.964 36.000 13.07 7.60 44.95 2.66
3250 5802 5.339990 TGCTCAAAGTCAAGCTTTACAAAC 58.660 37.500 13.07 0.00 44.95 2.93
3251 5803 5.574891 TGCTCAAAGTCAAGCTTTACAAA 57.425 34.783 13.07 0.00 44.95 2.83
3253 5805 5.574891 TTTGCTCAAAGTCAAGCTTTACA 57.425 34.783 13.07 0.00 44.95 2.41
3257 5809 4.725790 AGTTTTGCTCAAAGTCAAGCTT 57.274 36.364 0.00 0.00 39.31 3.74
3258 5810 5.835113 TTAGTTTTGCTCAAAGTCAAGCT 57.165 34.783 0.00 0.00 39.31 3.74
3259 5811 7.201384 GCATATTAGTTTTGCTCAAAGTCAAGC 60.201 37.037 0.00 0.00 39.02 4.01
3263 5815 6.542852 TCGCATATTAGTTTTGCTCAAAGTC 58.457 36.000 0.00 0.00 34.23 3.01
3265 5817 7.023575 ACTTCGCATATTAGTTTTGCTCAAAG 58.976 34.615 0.00 0.00 34.23 2.77
3266 5818 6.908825 ACTTCGCATATTAGTTTTGCTCAAA 58.091 32.000 0.00 0.00 34.23 2.69
3276 5828 9.925268 CCGTTTTTATTTACTTCGCATATTAGT 57.075 29.630 0.00 0.00 0.00 2.24
3279 5831 8.126700 CCTCCGTTTTTATTTACTTCGCATATT 58.873 33.333 0.00 0.00 0.00 1.28
3280 5832 7.255001 CCCTCCGTTTTTATTTACTTCGCATAT 60.255 37.037 0.00 0.00 0.00 1.78
3282 5834 5.163693 CCCTCCGTTTTTATTTACTTCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
3283 5835 4.154556 CCCTCCGTTTTTATTTACTTCGCA 59.845 41.667 0.00 0.00 0.00 5.10
3284 5836 4.392754 TCCCTCCGTTTTTATTTACTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
3286 5838 7.821359 AGTACTCCCTCCGTTTTTATTTACTTC 59.179 37.037 0.00 0.00 0.00 3.01
3287 5839 7.683578 AGTACTCCCTCCGTTTTTATTTACTT 58.316 34.615 0.00 0.00 0.00 2.24
3288 5840 7.250032 AGTACTCCCTCCGTTTTTATTTACT 57.750 36.000 0.00 0.00 0.00 2.24
3289 5841 7.912056 AAGTACTCCCTCCGTTTTTATTTAC 57.088 36.000 0.00 0.00 0.00 2.01
3290 5842 8.592809 TGTAAGTACTCCCTCCGTTTTTATTTA 58.407 33.333 0.00 0.00 0.00 1.40
3291 5843 7.452562 TGTAAGTACTCCCTCCGTTTTTATTT 58.547 34.615 0.00 0.00 0.00 1.40
3293 5845 6.610075 TGTAAGTACTCCCTCCGTTTTTAT 57.390 37.500 0.00 0.00 0.00 1.40
3294 5846 6.610075 ATGTAAGTACTCCCTCCGTTTTTA 57.390 37.500 0.00 0.00 0.00 1.52
3295 5847 4.961438 TGTAAGTACTCCCTCCGTTTTT 57.039 40.909 0.00 0.00 0.00 1.94
3296 5848 5.243207 CAATGTAAGTACTCCCTCCGTTTT 58.757 41.667 0.00 0.00 0.00 2.43
3297 5849 4.828829 CAATGTAAGTACTCCCTCCGTTT 58.171 43.478 0.00 0.00 0.00 3.60
3298 5850 3.369157 GCAATGTAAGTACTCCCTCCGTT 60.369 47.826 0.00 0.00 0.00 4.44
3299 5851 2.167900 GCAATGTAAGTACTCCCTCCGT 59.832 50.000 0.00 0.00 0.00 4.69
3300 5852 2.798499 CGCAATGTAAGTACTCCCTCCG 60.798 54.545 0.00 0.00 0.00 4.63
3301 5853 2.167900 ACGCAATGTAAGTACTCCCTCC 59.832 50.000 0.00 0.00 0.00 4.30
3302 5854 3.521947 ACGCAATGTAAGTACTCCCTC 57.478 47.619 0.00 0.00 0.00 4.30
3303 5855 3.975168 AACGCAATGTAAGTACTCCCT 57.025 42.857 0.00 0.00 0.00 4.20
3304 5856 4.251268 AGAAACGCAATGTAAGTACTCCC 58.749 43.478 0.00 0.00 0.00 4.30
3306 5858 6.077838 CCAAAGAAACGCAATGTAAGTACTC 58.922 40.000 0.00 0.00 0.00 2.59
3307 5859 5.529800 ACCAAAGAAACGCAATGTAAGTACT 59.470 36.000 0.00 0.00 0.00 2.73
3308 5860 5.623673 CACCAAAGAAACGCAATGTAAGTAC 59.376 40.000 0.00 0.00 0.00 2.73
3315 6187 2.393764 GGACACCAAAGAAACGCAATG 58.606 47.619 0.00 0.00 0.00 2.82
3354 6226 5.347342 ACGCAAATCTGACACAAATTTGAA 58.653 33.333 24.64 6.36 40.97 2.69
3356 6228 4.148696 GGACGCAAATCTGACACAAATTTG 59.851 41.667 16.67 16.67 41.26 2.32
3370 6242 1.736645 CGGACTCGTGGACGCAAAT 60.737 57.895 0.00 0.00 39.60 2.32
3399 6271 0.960364 TCAAAGCACGATCCCAAGGC 60.960 55.000 0.00 0.00 0.00 4.35
3408 6280 1.234821 GTTGGATGGTCAAAGCACGA 58.765 50.000 0.00 0.00 0.00 4.35
3427 6299 1.202325 TCGAACCCATATCCGAACACG 60.202 52.381 0.00 0.00 0.00 4.49
3462 6334 3.254657 CCCATGTTAACACGTCCATGTTT 59.745 43.478 11.22 0.00 39.86 2.83
3465 6337 2.705730 TCCCATGTTAACACGTCCATG 58.294 47.619 11.22 4.02 35.56 3.66
3466 6338 3.343617 CTTCCCATGTTAACACGTCCAT 58.656 45.455 11.22 0.00 0.00 3.41
3480 6353 3.575805 TCTTTTTGTCAAGCCTTCCCAT 58.424 40.909 0.00 0.00 0.00 4.00
3499 6372 2.359975 CCCCGCTCCGCTTTTTCT 60.360 61.111 0.00 0.00 0.00 2.52
3501 6374 2.114411 TTCCCCGCTCCGCTTTTT 59.886 55.556 0.00 0.00 0.00 1.94
3546 6421 8.962884 AAAGAGCTATGGTTGTTTTCAAAATT 57.037 26.923 0.00 0.00 41.76 1.82
3582 6457 7.339466 TGCAATCTTCTCTCCTATATATGCGTA 59.661 37.037 0.00 0.00 0.00 4.42
3585 6460 7.656948 GGATGCAATCTTCTCTCCTATATATGC 59.343 40.741 0.00 0.00 44.71 3.14
3586 6461 7.866898 CGGATGCAATCTTCTCTCCTATATATG 59.133 40.741 0.00 0.00 44.71 1.78
3602 6479 1.261619 GACACGATTCCGGATGCAATC 59.738 52.381 4.15 4.10 44.55 2.67
3640 6517 3.399330 AGACACAATTTCGGATTCGTGT 58.601 40.909 14.09 14.09 40.11 4.49
3641 6518 5.718649 ATAGACACAATTTCGGATTCGTG 57.281 39.130 0.00 0.00 37.69 4.35
3642 6519 6.737254 AAATAGACACAATTTCGGATTCGT 57.263 33.333 0.00 0.00 37.69 3.85
3643 6520 8.600625 TCTAAAATAGACACAATTTCGGATTCG 58.399 33.333 0.00 0.00 37.82 3.34
3645 6522 9.449719 ACTCTAAAATAGACACAATTTCGGATT 57.550 29.630 0.00 0.00 0.00 3.01
3647 6524 7.876068 ACACTCTAAAATAGACACAATTTCGGA 59.124 33.333 0.00 0.00 0.00 4.55
3701 6581 9.296400 GTGAATTAGTCAAACTGTTTGCTAAAA 57.704 29.630 30.49 22.94 39.84 1.52


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

AutoCloner maintained by Alex Coulton.