Multiple sequence alignment - TraesCS1D01G197300

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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 TraesCS1D01G197300 chr1D 100.000 7970 0 0 1 7970 278111971 278104002 0.000000e+00 14718
1 TraesCS1D01G197300 chr1A 93.890 6874 215 66 516 7334 350401878 350395155 0.000000e+00 10178
2 TraesCS1D01G197300 chr1A 95.396 391 12 5 117 505 350402312 350401926 1.140000e-172 617
3 TraesCS1D01G197300 chr1A 84.810 632 71 16 7343 7970 350395103 350394493 5.290000e-171 612
4 TraesCS1D01G197300 chr1A 94.565 92 4 1 1 91 350410900 350410809 3.000000e-29 141
5 TraesCS1D01G197300 chr1B 93.060 5216 211 50 516 5649 377970808 377965662 0.000000e+00 7487
6 TraesCS1D01G197300 chr1B 95.557 1778 49 15 5726 7487 377965645 377963882 0.000000e+00 2819
7 TraesCS1D01G197300 chr1B 92.277 505 15 8 1 504 377971352 377970871 0.000000e+00 695
8 TraesCS1D01G197300 chr1B 86.059 538 37 12 7457 7970 377963860 377963337 1.960000e-150 544
9 TraesCS1D01G197300 chr3D 80.702 513 55 12 2867 3372 178587878 178587403 7.600000e-95 359
10 TraesCS1D01G197300 chr3B 81.585 429 53 9 2944 3372 228502180 228502582 1.660000e-86 331
11 TraesCS1D01G197300 chr5D 81.868 364 48 7 3010 3372 404857949 404858295 2.810000e-74 291
12 TraesCS1D01G197300 chr6D 88.618 123 14 0 2152 2274 413272373 413272251 4.980000e-32 150
13 TraesCS1D01G197300 chr6D 85.484 124 12 6 2154 2274 335068116 335067996 3.020000e-24 124
14 TraesCS1D01G197300 chr6A 88.618 123 14 0 2152 2274 558788606 558788484 4.980000e-32 150
15 TraesCS1D01G197300 chr6A 85.366 123 14 4 2154 2274 474333558 474333438 3.020000e-24 124
16 TraesCS1D01G197300 chr5A 93.137 102 3 2 7213 7310 34869439 34869338 6.450000e-31 147
17 TraesCS1D01G197300 chr6B 87.097 124 16 0 2151 2274 623084110 623083987 3.000000e-29 141
18 TraesCS1D01G197300 chr6B 84.615 130 14 6 2148 2274 485537656 485537782 3.020000e-24 124
19 TraesCS1D01G197300 chr7D 83.065 124 19 2 2152 2274 119568768 119568646 2.350000e-20 111
20 TraesCS1D01G197300 chr7A 92.754 69 5 0 2855 2923 76286057 76285989 5.090000e-17 100


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 TraesCS1D01G197300 chr1D 278104002 278111971 7969 True 14718.000000 14718 100.000000 1 7970 1 chr1D.!!$R1 7969
1 TraesCS1D01G197300 chr1A 350394493 350402312 7819 True 3802.333333 10178 91.365333 117 7970 3 chr1A.!!$R2 7853
2 TraesCS1D01G197300 chr1B 377963337 377971352 8015 True 2886.250000 7487 91.738250 1 7970 4 chr1B.!!$R1 7969

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
909 989 1.527380 GTTTCAACGGTGGGGCTGA 60.527 57.895 0.00 0.00 0.00 4.26 F
1711 1797 6.114767 TCATCTTGTCTGTTGCATATTAGCA 58.885 36.000 0.00 0.00 43.99 3.49 F
1927 2013 0.827925 ACGACAGAGACCAGAAGCCA 60.828 55.000 0.00 0.00 0.00 4.75 F
3728 3843 0.978667 AAGGCCCAATGCATGCATCA 60.979 50.000 32.25 6.09 43.89 3.07 F
3771 3886 0.315625 CATCGCGATGCATGTGTGAC 60.316 55.000 33.70 0.00 31.39 3.67 F
4048 4163 0.326264 ACGGCATGCCTTCTTCTCTT 59.674 50.000 33.07 4.22 0.00 2.85 F
4141 4256 0.389391 AACCGATCGATCTCGCCATT 59.611 50.000 22.43 4.74 39.60 3.16 F
4750 4877 1.004918 AGCGCTGTCAGGTACCAAC 60.005 57.895 10.39 12.39 0.00 3.77 F
5976 6128 1.002624 GGTCACAATGAGCGGGGAA 60.003 57.895 0.00 0.00 35.04 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1896 0.037232 GGTCCAACTCCTCGTCCTTG 60.037 60.000 0.00 0.00 0.00 3.61 R
3433 3534 0.041400 CGCACGTTCATCAGCAAACA 60.041 50.000 0.00 0.00 0.00 2.83 R
3752 3867 0.315625 GTCACACATGCATCGCGATG 60.316 55.000 38.15 38.15 41.60 3.84 R
5414 5560 0.320771 CCTGAGCCTACACCACACAC 60.321 60.000 0.00 0.00 0.00 3.82 R
5423 5569 1.219393 GTGACCAGCCTGAGCCTAC 59.781 63.158 0.00 0.00 41.25 3.18 R
5429 5575 1.302752 GTGCATGTGACCAGCCTGA 60.303 57.895 0.00 0.00 0.00 3.86 R
5616 5768 2.632377 ACATGGAAAGGCAGTACATCG 58.368 47.619 0.00 0.00 0.00 3.84 R
6189 6341 0.806868 AGATGTGGCTGTTGATTGCG 59.193 50.000 0.00 0.00 0.00 4.85 R
7842 8140 0.031616 AGTGGGAGGGATGAGGACTC 60.032 60.000 0.00 0.00 0.00 3.36 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
91 92 7.754924 CACGCCAAAAGAAAATGTGTTATCTAT 59.245 33.333 0.00 0.00 0.00 1.98
92 93 8.952278 ACGCCAAAAGAAAATGTGTTATCTATA 58.048 29.630 0.00 0.00 0.00 1.31
93 94 9.438291 CGCCAAAAGAAAATGTGTTATCTATAG 57.562 33.333 0.00 0.00 0.00 1.31
94 95 9.237846 GCCAAAAGAAAATGTGTTATCTATAGC 57.762 33.333 0.00 0.00 0.00 2.97
553 606 2.224793 TGACCTCTCTCTCCGTCAGAAA 60.225 50.000 0.00 0.00 31.80 2.52
731 801 2.815503 GCCCGTAATTACCCGCATTAAT 59.184 45.455 10.01 0.00 0.00 1.40
909 989 1.527380 GTTTCAACGGTGGGGCTGA 60.527 57.895 0.00 0.00 0.00 4.26
1707 1793 6.183360 CGTCTTCATCTTGTCTGTTGCATATT 60.183 38.462 0.00 0.00 0.00 1.28
1708 1794 7.010460 CGTCTTCATCTTGTCTGTTGCATATTA 59.990 37.037 0.00 0.00 0.00 0.98
1709 1795 8.333908 GTCTTCATCTTGTCTGTTGCATATTAG 58.666 37.037 0.00 0.00 0.00 1.73
1710 1796 6.609237 TCATCTTGTCTGTTGCATATTAGC 57.391 37.500 0.00 0.00 0.00 3.09
1711 1797 6.114767 TCATCTTGTCTGTTGCATATTAGCA 58.885 36.000 0.00 0.00 43.99 3.49
1712 1798 6.769341 TCATCTTGTCTGTTGCATATTAGCAT 59.231 34.615 0.00 0.00 45.19 3.79
1713 1799 7.933033 TCATCTTGTCTGTTGCATATTAGCATA 59.067 33.333 0.00 0.00 45.19 3.14
1714 1800 8.727910 CATCTTGTCTGTTGCATATTAGCATAT 58.272 33.333 0.00 0.00 45.19 1.78
1715 1801 9.948964 ATCTTGTCTGTTGCATATTAGCATATA 57.051 29.630 0.00 0.00 45.19 0.86
1927 2013 0.827925 ACGACAGAGACCAGAAGCCA 60.828 55.000 0.00 0.00 0.00 4.75
2078 2164 3.875727 GGAGGCGTAAGAAATAAGAACCC 59.124 47.826 0.00 0.00 43.02 4.11
2079 2165 3.875727 GAGGCGTAAGAAATAAGAACCCC 59.124 47.826 0.00 0.00 43.02 4.95
2083 2169 3.943381 CGTAAGAAATAAGAACCCCACCC 59.057 47.826 0.00 0.00 43.02 4.61
2125 2211 9.620259 AAATCTTCCTGAATTAGTAATCTGACC 57.380 33.333 0.00 0.00 0.00 4.02
2531 2617 6.752351 CCTGCTAGTGTTACTGTAATGTACTG 59.248 42.308 17.63 11.98 0.00 2.74
2536 2622 6.697395 AGTGTTACTGTAATGTACTGCATCA 58.303 36.000 3.23 0.00 36.67 3.07
2588 2678 2.182614 CTTTTGCGCGTCGGATGGTT 62.183 55.000 8.43 0.00 0.00 3.67
2589 2679 2.450960 TTTTGCGCGTCGGATGGTTG 62.451 55.000 8.43 0.00 0.00 3.77
2598 2688 1.450134 CGGATGGTTGCTGCAGCTA 60.450 57.895 36.61 28.48 42.66 3.32
2668 2758 3.282745 ATGTCGTCGGCTTCAGCGT 62.283 57.895 0.00 0.00 43.26 5.07
3014 3113 4.148825 GGACGCCGAGGAGCATGT 62.149 66.667 0.00 0.00 0.00 3.21
3138 3237 2.408271 ACAGCATCACATTGGTCGAT 57.592 45.000 0.00 0.00 0.00 3.59
3211 3311 8.445493 CAAATTACTTCATTTTCTTCCATTGCC 58.555 33.333 0.00 0.00 0.00 4.52
3244 3344 3.452627 AGATTAACTTGAGATCACCCGCT 59.547 43.478 0.00 0.00 0.00 5.52
3433 3534 4.916870 TCGATCGATGTCGTAGTTGATTT 58.083 39.130 15.15 0.00 42.07 2.17
3450 3551 4.289342 TGATTTGTTTGCTGATGAACGTG 58.711 39.130 0.00 0.00 0.00 4.49
3728 3843 0.978667 AAGGCCCAATGCATGCATCA 60.979 50.000 32.25 6.09 43.89 3.07
3749 3864 1.154169 CATGTGTGACGTGGCATGC 60.154 57.895 9.90 9.90 33.45 4.06
3750 3865 2.334946 ATGTGTGACGTGGCATGCC 61.335 57.895 30.54 30.54 0.00 4.40
3751 3866 2.977456 GTGTGACGTGGCATGCCA 60.977 61.111 35.59 35.59 45.02 4.92
3759 3874 4.774503 TGGCATGCCACATCGCGA 62.775 61.111 35.59 13.09 41.89 5.87
3760 3875 3.282157 GGCATGCCACATCGCGAT 61.282 61.111 32.08 17.62 35.81 4.58
3761 3876 2.051614 GCATGCCACATCGCGATG 60.052 61.111 39.76 39.76 44.15 3.84
3762 3877 2.051614 CATGCCACATCGCGATGC 60.052 61.111 40.92 30.21 42.39 3.91
3763 3878 2.514360 ATGCCACATCGCGATGCA 60.514 55.556 40.92 34.11 42.39 3.96
3764 3879 1.895231 ATGCCACATCGCGATGCAT 60.895 52.632 40.92 34.62 42.39 3.96
3765 3880 2.051614 GCCACATCGCGATGCATG 60.052 61.111 40.92 32.40 42.39 4.06
3766 3881 2.827051 GCCACATCGCGATGCATGT 61.827 57.895 40.92 25.66 42.39 3.21
3767 3882 1.010462 CCACATCGCGATGCATGTG 60.010 57.895 40.92 33.06 42.13 3.21
3768 3883 1.708193 CCACATCGCGATGCATGTGT 61.708 55.000 40.92 24.57 41.57 3.72
3769 3884 0.587985 CACATCGCGATGCATGTGTG 60.588 55.000 40.92 30.24 42.39 3.82
3770 3885 0.740516 ACATCGCGATGCATGTGTGA 60.741 50.000 40.92 9.20 42.39 3.58
3771 3886 0.315625 CATCGCGATGCATGTGTGAC 60.316 55.000 33.70 0.00 31.39 3.67
3772 3887 1.755405 ATCGCGATGCATGTGTGACG 61.755 55.000 23.04 0.48 0.00 4.35
3773 3888 2.729675 CGCGATGCATGTGTGACGT 61.730 57.895 2.46 0.00 0.00 4.34
3774 3889 1.225827 GCGATGCATGTGTGACGTG 60.226 57.895 2.46 0.00 38.13 4.49
3780 3895 1.503091 CATGTGTGACGTGGCATGG 59.497 57.895 12.05 0.00 36.15 3.66
4045 4160 4.308526 CACGGCATGCCTTCTTCT 57.691 55.556 33.07 6.62 0.00 2.85
4048 4163 0.326264 ACGGCATGCCTTCTTCTCTT 59.674 50.000 33.07 4.22 0.00 2.85
4070 4185 5.963176 TTGCTGCTTACATTTCATCTGAA 57.037 34.783 0.00 0.00 0.00 3.02
4095 4210 2.751259 TGCTCATCCTGCTTGTGAATTC 59.249 45.455 0.00 0.00 0.00 2.17
4141 4256 0.389391 AACCGATCGATCTCGCCATT 59.611 50.000 22.43 4.74 39.60 3.16
4164 4285 8.768955 CATTTATCTCTATGCTTGTTCTGTACC 58.231 37.037 0.00 0.00 0.00 3.34
4170 4291 3.738830 TGCTTGTTCTGTACCGTAGTT 57.261 42.857 0.00 0.00 0.00 2.24
4194 4315 2.437359 GCCTGCTCGCCTGTCAAT 60.437 61.111 0.00 0.00 0.00 2.57
4218 4339 2.666317 TCGACATTATGCCTCAGAGGA 58.334 47.619 21.89 5.86 37.67 3.71
4310 4434 7.759886 AGATCGTACCAATATATGTGTACATGC 59.240 37.037 18.14 10.24 36.38 4.06
4396 4523 8.161425 ACTGGTTGTACTTACCACTTTTATCAT 58.839 33.333 14.12 0.00 40.65 2.45
4441 4568 7.601886 CGATATTTATCCATCTTCACAAGAGCT 59.398 37.037 0.00 0.00 41.61 4.09
4712 4839 2.361757 CAGCCATCAACAGGTGTTTGAA 59.638 45.455 0.00 0.00 35.83 2.69
4746 4873 1.901650 GCAACAGCGCTGTCAGGTAC 61.902 60.000 40.60 22.45 44.13 3.34
4750 4877 1.004918 AGCGCTGTCAGGTACCAAC 60.005 57.895 10.39 12.39 0.00 3.77
5047 5180 2.303175 GTACACCAAGAGGCCACAAAA 58.697 47.619 5.01 0.00 39.06 2.44
5052 5187 1.613836 CAAGAGGCCACAAAAGCTCT 58.386 50.000 5.01 0.00 0.00 4.09
5127 5262 6.512253 CGTGTACTTAGTATCTATGCCGAACA 60.512 42.308 0.00 0.00 0.00 3.18
5128 5263 7.368833 GTGTACTTAGTATCTATGCCGAACAT 58.631 38.462 0.00 0.00 43.18 2.71
5144 5279 6.971756 TGCCGAACATGTATAATCACAATTTG 59.028 34.615 0.00 0.00 30.84 2.32
5265 5411 5.789521 TGCTACTGAATTACTGCAGTAACA 58.210 37.500 35.31 27.84 44.36 2.41
5272 5418 7.607991 ACTGAATTACTGCAGTAACAGCTATTT 59.392 33.333 34.78 26.46 43.10 1.40
5391 5537 6.345096 ACAATAAATTAACACTGGCTGCTT 57.655 33.333 0.00 0.00 0.00 3.91
5419 5565 8.052748 AGGTACCACATTAAATGATATGTGTGT 58.947 33.333 15.94 11.86 46.40 3.72
5423 5569 6.974048 CCACATTAAATGATATGTGTGTGGTG 59.026 38.462 11.86 0.00 46.40 4.17
5429 5575 2.837591 TGATATGTGTGTGGTGTAGGCT 59.162 45.455 0.00 0.00 0.00 4.58
5447 5593 1.302752 TCAGGCTGGTCACATGCAC 60.303 57.895 15.73 0.00 0.00 4.57
5492 5641 5.228012 GCTTTTAGATTCGTTTATGTGCTGC 59.772 40.000 0.00 0.00 0.00 5.25
5510 5659 3.416277 CTGCCATTACGTTCACAATTCG 58.584 45.455 0.00 0.00 0.00 3.34
5550 5699 9.631452 AAGAGCTTTTAGATGCAAAGAAAATAC 57.369 29.630 0.00 0.00 33.69 1.89
5616 5768 8.046294 TGTCTAGTGAGTTCTAAATCAGTCTC 57.954 38.462 3.94 0.00 37.74 3.36
5697 5849 5.014858 GGTCGGTAGATATGGAACTATGGA 58.985 45.833 0.00 0.00 0.00 3.41
5768 5920 9.930693 ACTCCTTGTAAGATCAACTAAGTTTAG 57.069 33.333 0.00 0.00 36.82 1.85
5976 6128 1.002624 GGTCACAATGAGCGGGGAA 60.003 57.895 0.00 0.00 35.04 3.97
6039 6191 3.970410 CCAGCCACCAGCCCTTCA 61.970 66.667 0.00 0.00 45.47 3.02
6189 6341 0.033504 TCAACCTCTCAAGCGTCACC 59.966 55.000 0.00 0.00 0.00 4.02
6322 6474 4.675303 TGGGTGGGAGTGGAGGGG 62.675 72.222 0.00 0.00 0.00 4.79
6345 6497 3.367743 ACGCCGCAGACCGAAGTA 61.368 61.111 0.00 0.00 40.02 2.24
6366 6518 3.929094 ACAATTATTTTGCCACCTGCTG 58.071 40.909 0.00 0.00 42.00 4.41
6384 6536 3.031736 GCTGACACCTCAAGTATCCCTA 58.968 50.000 0.00 0.00 0.00 3.53
6397 6549 4.093011 AGTATCCCTATTAGCAGCTCAGG 58.907 47.826 0.00 4.30 0.00 3.86
6737 6896 3.658351 AATTAGTTTGAGCGTGCGATC 57.342 42.857 2.69 2.69 0.00 3.69
6741 6900 1.666553 TTTGAGCGTGCGATCCGTT 60.667 52.632 7.38 0.00 0.00 4.44
6969 7131 8.580657 GGTACTTCTTACATTGCAATCTGCGG 62.581 46.154 9.53 0.04 38.17 5.69
7192 7356 5.070847 AGGACCAATTTCATTTTTGAGCTGT 59.929 36.000 0.00 0.00 0.00 4.40
7286 7450 0.539051 GCTACACAGGGAGATGCTGT 59.461 55.000 0.00 0.00 0.00 4.40
7296 7460 1.597742 GAGATGCTGTGTGTGGTTGT 58.402 50.000 0.00 0.00 0.00 3.32
7324 7488 4.202461 TGGGGAGATGCCTCACATAAATAC 60.202 45.833 0.00 0.00 44.19 1.89
7366 7571 4.430441 AGAGGAAAGGCTCTTCTTCCTTA 58.570 43.478 17.10 0.00 41.54 2.69
7429 7639 3.650942 TCTATTTATACCACCCCTGCCTG 59.349 47.826 0.00 0.00 0.00 4.85
7477 7741 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
7613 7900 6.019318 GTCCTTGCATGCATGTTTTAATCATC 60.019 38.462 26.79 7.53 0.00 2.92
7655 7942 1.347707 CTACTGAGGGCAACTCCAACA 59.652 52.381 5.35 0.00 46.01 3.33
7674 7961 0.468029 ATGGATCATCAAACCGCCCC 60.468 55.000 0.00 0.00 0.00 5.80
7679 7966 0.470080 TCATCAAACCGCCCCCAAAA 60.470 50.000 0.00 0.00 0.00 2.44
7680 7967 0.394565 CATCAAACCGCCCCCAAAAA 59.605 50.000 0.00 0.00 0.00 1.94
7689 7976 0.033894 GCCCCCAAAAATCCCGACTA 60.034 55.000 0.00 0.00 0.00 2.59
7705 7992 3.744426 CCGACTAAACGGTCTTTGTCATT 59.256 43.478 0.00 0.00 46.70 2.57
7708 7995 5.120208 CGACTAAACGGTCTTTGTCATTCAT 59.880 40.000 13.25 0.00 32.64 2.57
7712 7999 1.062587 CGGTCTTTGTCATTCATCGGC 59.937 52.381 0.00 0.00 0.00 5.54
7725 8012 0.525761 CATCGGCGGTCACCAAAAAT 59.474 50.000 7.21 0.00 0.00 1.82
7726 8013 0.525761 ATCGGCGGTCACCAAAAATG 59.474 50.000 7.21 0.00 0.00 2.32
7727 8014 0.820074 TCGGCGGTCACCAAAAATGT 60.820 50.000 7.21 0.00 0.00 2.71
7728 8015 0.386731 CGGCGGTCACCAAAAATGTC 60.387 55.000 0.00 0.00 0.00 3.06
7729 8016 0.038618 GGCGGTCACCAAAAATGTCC 60.039 55.000 0.00 0.00 0.00 4.02
7730 8017 3.765349 CGGTCACCAAAAATGTCCG 57.235 52.632 0.00 0.00 41.19 4.79
7731 8018 0.239879 CGGTCACCAAAAATGTCCGG 59.760 55.000 0.00 0.00 42.63 5.14
7732 8019 1.611519 GGTCACCAAAAATGTCCGGA 58.388 50.000 0.00 0.00 0.00 5.14
7733 8020 1.268625 GGTCACCAAAAATGTCCGGAC 59.731 52.381 28.17 28.17 0.00 4.79
7734 8021 1.268625 GTCACCAAAAATGTCCGGACC 59.731 52.381 31.19 14.15 0.00 4.46
7829 8127 1.221840 GACACTCCCGCACATCCAT 59.778 57.895 0.00 0.00 0.00 3.41
7839 8137 1.767759 GCACATCCATAAAGCCCACT 58.232 50.000 0.00 0.00 0.00 4.00
7842 8140 1.134098 ACATCCATAAAGCCCACTCGG 60.134 52.381 0.00 0.00 0.00 4.63
7850 8148 2.680352 GCCCACTCGGAGTCCTCA 60.680 66.667 7.89 0.00 0.00 3.86
7870 8168 0.840722 TCCCTCCCACTTTGTCCCTC 60.841 60.000 0.00 0.00 0.00 4.30
7872 8170 1.685820 CTCCCACTTTGTCCCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
7873 8171 0.842467 CTCCCACTTTGTCCCTCCCT 60.842 60.000 0.00 0.00 0.00 4.20
7878 8176 3.112263 CCACTTTGTCCCTCCCTATGTA 58.888 50.000 0.00 0.00 0.00 2.29
7898 8196 2.745100 CTCCCTCGACGACCGACA 60.745 66.667 0.00 0.00 43.23 4.35
7918 8216 3.712907 CCCACTGTACCACCCCGG 61.713 72.222 0.00 0.00 42.50 5.73
7936 8234 3.777556 CCACCACCTTGGCCTTTC 58.222 61.111 3.32 0.00 42.67 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 9.017509 TGGTCTCGTTTCTTTAGTTCTCTAATA 57.982 33.333 0.00 0.00 36.25 0.98
114 115 7.893658 TGGTCTCGTTTCTTTAGTTCTCTAAT 58.106 34.615 0.00 0.00 36.25 1.73
115 116 7.281040 TGGTCTCGTTTCTTTAGTTCTCTAA 57.719 36.000 0.00 0.00 34.76 2.10
288 289 0.110867 TTTTGCATGCGTTCTCGTCG 60.111 50.000 14.09 0.00 39.49 5.12
462 464 3.546543 GGATCCGTCCATGGGCGA 61.547 66.667 39.13 24.65 44.42 5.54
508 511 1.110518 GTCTCCTCCCCGCTTCTAGG 61.111 65.000 0.00 0.00 0.00 3.02
509 512 1.448922 CGTCTCCTCCCCGCTTCTAG 61.449 65.000 0.00 0.00 0.00 2.43
510 513 1.453379 CGTCTCCTCCCCGCTTCTA 60.453 63.158 0.00 0.00 0.00 2.10
511 514 2.756283 CGTCTCCTCCCCGCTTCT 60.756 66.667 0.00 0.00 0.00 2.85
512 515 3.069318 ACGTCTCCTCCCCGCTTC 61.069 66.667 0.00 0.00 0.00 3.86
513 516 3.382832 CACGTCTCCTCCCCGCTT 61.383 66.667 0.00 0.00 0.00 4.68
553 606 3.501548 GCGCTCTCCTCGTCGTCT 61.502 66.667 0.00 0.00 0.00 4.18
731 801 3.323775 AGGAAAGCCGAATATAGGGGAA 58.676 45.455 0.00 0.00 39.96 3.97
882 962 2.720750 CGTTGAAACCGCGTGCAC 60.721 61.111 6.82 6.82 0.00 4.57
883 963 3.943034 CCGTTGAAACCGCGTGCA 61.943 61.111 4.92 0.00 0.00 4.57
884 964 3.944233 ACCGTTGAAACCGCGTGC 61.944 61.111 4.92 0.00 0.00 5.34
941 1022 1.647346 AAGAACAAACGCAGTGACGA 58.353 45.000 12.77 0.00 45.00 4.20
1810 1896 0.037232 GGTCCAACTCCTCGTCCTTG 60.037 60.000 0.00 0.00 0.00 3.61
1915 2001 1.072159 GTGCTGTGGCTTCTGGTCT 59.928 57.895 0.00 0.00 39.59 3.85
2078 2164 1.411246 TCGTCATTAAGATCGGGGTGG 59.589 52.381 0.00 0.00 0.00 4.61
2079 2165 2.882927 TCGTCATTAAGATCGGGGTG 57.117 50.000 0.00 0.00 0.00 4.61
2083 2169 6.480320 AGGAAGATTTTCGTCATTAAGATCGG 59.520 38.462 0.00 0.00 33.98 4.18
2125 2211 3.105782 ATCCATACGCGCGCATCG 61.106 61.111 32.58 16.48 42.12 3.84
2531 2617 3.291585 CGTGTGAAGAACAACTTGATGC 58.708 45.455 0.00 0.00 41.57 3.91
2536 2622 1.021968 GCCCGTGTGAAGAACAACTT 58.978 50.000 0.00 0.00 41.57 2.66
2668 2758 3.120385 CGCCGACATGCAGCTCAA 61.120 61.111 0.00 0.00 0.00 3.02
3211 3311 4.478699 TCAAGTTAATCTGACGTACGTGG 58.521 43.478 28.16 17.77 0.00 4.94
3244 3344 0.587768 CACTTGTTCTGCACGCATGA 59.412 50.000 0.00 0.00 0.00 3.07
3420 3521 5.090652 TCAGCAAACAAATCAACTACGAC 57.909 39.130 0.00 0.00 0.00 4.34
3422 3523 5.688823 TCATCAGCAAACAAATCAACTACG 58.311 37.500 0.00 0.00 0.00 3.51
3433 3534 0.041400 CGCACGTTCATCAGCAAACA 60.041 50.000 0.00 0.00 0.00 2.83
3684 3797 4.382320 GCGGTGCGTACCCTGGAA 62.382 66.667 17.62 0.00 44.53 3.53
3728 3843 0.961857 ATGCCACGTCACACATGCAT 60.962 50.000 0.00 0.00 34.81 3.96
3749 3864 1.010462 CACATGCATCGCGATGTGG 60.010 57.895 40.22 31.82 40.60 4.17
3750 3865 0.587985 CACACATGCATCGCGATGTG 60.588 55.000 40.22 34.57 44.81 3.21
3751 3866 0.740516 TCACACATGCATCGCGATGT 60.741 50.000 40.22 25.81 40.80 3.06
3752 3867 0.315625 GTCACACATGCATCGCGATG 60.316 55.000 38.15 38.15 41.60 3.84
3753 3868 1.755405 CGTCACACATGCATCGCGAT 61.755 55.000 17.62 17.62 0.00 4.58
3754 3869 2.443811 CGTCACACATGCATCGCGA 61.444 57.895 13.09 13.09 0.00 5.87
3755 3870 2.020423 CGTCACACATGCATCGCG 59.980 61.111 0.00 0.00 0.00 5.87
3756 3871 1.225827 CACGTCACACATGCATCGC 60.226 57.895 0.00 0.00 0.00 4.58
3757 3872 1.421093 CCACGTCACACATGCATCG 59.579 57.895 0.00 0.00 0.00 3.84
3758 3873 1.135315 GCCACGTCACACATGCATC 59.865 57.895 0.00 0.00 0.00 3.91
3759 3874 0.961857 ATGCCACGTCACACATGCAT 60.962 50.000 0.00 0.00 34.81 3.96
3760 3875 1.600356 ATGCCACGTCACACATGCA 60.600 52.632 0.00 0.00 0.00 3.96
3761 3876 1.154169 CATGCCACGTCACACATGC 60.154 57.895 0.00 0.00 34.11 4.06
3762 3877 1.503091 CCATGCCACGTCACACATG 59.497 57.895 8.80 8.80 39.65 3.21
3763 3878 2.334946 GCCATGCCACGTCACACAT 61.335 57.895 0.00 0.00 0.00 3.21
3764 3879 2.977456 GCCATGCCACGTCACACA 60.977 61.111 0.00 0.00 0.00 3.72
3765 3880 2.334946 ATGCCATGCCACGTCACAC 61.335 57.895 0.00 0.00 0.00 3.82
3766 3881 2.033911 ATGCCATGCCACGTCACA 59.966 55.556 0.00 0.00 0.00 3.58
3767 3882 2.486504 CATGCCATGCCACGTCAC 59.513 61.111 0.00 0.00 0.00 3.67
3780 3895 0.464013 AGAGCTCAGTCCATGCATGC 60.464 55.000 21.69 11.82 0.00 4.06
4043 4158 5.942236 AGATGAAATGTAAGCAGCAAAGAGA 59.058 36.000 0.00 0.00 0.00 3.10
4044 4159 6.028368 CAGATGAAATGTAAGCAGCAAAGAG 58.972 40.000 0.00 0.00 0.00 2.85
4045 4160 5.706833 TCAGATGAAATGTAAGCAGCAAAGA 59.293 36.000 0.00 0.00 0.00 2.52
4048 4163 5.963176 TTCAGATGAAATGTAAGCAGCAA 57.037 34.783 0.00 0.00 0.00 3.91
4095 4210 7.551585 AGGTAATAATCTAGATTCAGCATCGG 58.448 38.462 21.17 0.00 36.93 4.18
4141 4256 6.096423 ACGGTACAGAACAAGCATAGAGATAA 59.904 38.462 0.00 0.00 0.00 1.75
4164 4285 1.461127 GAGCAGGCAAGAACAACTACG 59.539 52.381 0.00 0.00 0.00 3.51
4170 4291 2.669569 GGCGAGCAGGCAAGAACA 60.670 61.111 0.00 0.00 45.92 3.18
4194 4315 4.183865 CTCTGAGGCATAATGTCGAACAA 58.816 43.478 0.00 0.00 0.00 2.83
4218 4339 6.648879 TTAAAGAAGCAACTAAGCATTGGT 57.351 33.333 0.00 0.00 43.71 3.67
4310 4434 7.461156 GCACTCGAGTATAAACAAGTAAACGAG 60.461 40.741 19.57 0.00 45.36 4.18
4396 4523 3.745799 TCGATAAAACCCAGCACAGAAA 58.254 40.909 0.00 0.00 0.00 2.52
4465 4592 1.308998 GGTGCGGATAACTGGGATTG 58.691 55.000 0.00 0.00 0.00 2.67
4580 4707 6.037720 CAGTGTCGTCTGTAGAATCAGATAGT 59.962 42.308 0.00 0.00 44.59 2.12
4598 4725 3.649073 TGTTGTAATCCTGACAGTGTCG 58.351 45.455 18.17 12.43 34.95 4.35
4604 4731 5.560722 TCTTCCTTGTTGTAATCCTGACA 57.439 39.130 0.00 0.00 0.00 3.58
4824 4957 4.389992 CACGCATCACAGAACTGATAAAGT 59.610 41.667 8.87 0.00 42.60 2.66
4825 4958 4.389992 ACACGCATCACAGAACTGATAAAG 59.610 41.667 8.87 0.00 29.28 1.85
4837 4970 1.237533 AAAGCATGACACGCATCACA 58.762 45.000 0.00 0.00 34.15 3.58
5047 5180 1.004440 GAGTGTGCCCGAAAGAGCT 60.004 57.895 0.00 0.00 0.00 4.09
5052 5187 7.051623 AGTTATATTATTGAGTGTGCCCGAAA 58.948 34.615 0.00 0.00 0.00 3.46
5127 5262 9.466497 AGGAAGTGACAAATTGTGATTATACAT 57.534 29.630 2.20 0.00 0.00 2.29
5128 5263 8.862325 AGGAAGTGACAAATTGTGATTATACA 57.138 30.769 2.20 0.00 0.00 2.29
5144 5279 6.698380 TGGTCAGTAAGATTTAGGAAGTGAC 58.302 40.000 0.00 0.00 38.97 3.67
5149 5284 8.603898 TCTACATGGTCAGTAAGATTTAGGAA 57.396 34.615 0.00 0.00 0.00 3.36
5296 5442 9.969001 AATGTTGGTATTGGTAGTAAACAGTAT 57.031 29.630 0.00 0.00 30.39 2.12
5414 5560 0.320771 CCTGAGCCTACACCACACAC 60.321 60.000 0.00 0.00 0.00 3.82
5419 5565 2.293318 CCAGCCTGAGCCTACACCA 61.293 63.158 0.00 0.00 41.25 4.17
5423 5569 1.219393 GTGACCAGCCTGAGCCTAC 59.781 63.158 0.00 0.00 41.25 3.18
5429 5575 1.302752 GTGCATGTGACCAGCCTGA 60.303 57.895 0.00 0.00 0.00 3.86
5492 5641 4.921470 AGACGAATTGTGAACGTAATGG 57.079 40.909 0.00 0.00 40.29 3.16
5550 5699 8.673626 ACGCAACATGTATTTCTAAAATTGAG 57.326 30.769 0.00 0.00 0.00 3.02
5614 5766 2.672961 TGGAAAGGCAGTACATCGAG 57.327 50.000 0.00 0.00 0.00 4.04
5616 5768 2.632377 ACATGGAAAGGCAGTACATCG 58.368 47.619 0.00 0.00 0.00 3.84
5770 5922 9.509956 AGCATGTTATTAACTGTAAACTGGTAA 57.490 29.630 7.99 0.75 32.77 2.85
5771 5923 8.941977 CAGCATGTTATTAACTGTAAACTGGTA 58.058 33.333 7.99 0.00 0.00 3.25
5772 5924 7.663905 TCAGCATGTTATTAACTGTAAACTGGT 59.336 33.333 7.99 0.00 37.40 4.00
5976 6128 4.672650 AGTAGAGGGATGTAGGAAGGATCT 59.327 45.833 0.00 0.00 0.00 2.75
6189 6341 0.806868 AGATGTGGCTGTTGATTGCG 59.193 50.000 0.00 0.00 0.00 4.85
6340 6492 5.576774 GCAGGTGGCAAAATAATTGTACTTC 59.423 40.000 0.00 0.00 43.97 3.01
6345 6497 8.891141 GTGTCAGCAGGTGGCAAAATAATTGT 62.891 42.308 8.85 0.00 44.30 2.71
6366 6518 5.304614 TGCTAATAGGGATACTTGAGGTGTC 59.695 44.000 0.00 0.00 35.67 3.67
6384 6536 1.681166 CCTTGCACCTGAGCTGCTAAT 60.681 52.381 0.15 0.00 35.53 1.73
6397 6549 3.569701 TCTTGTCAAATCCTTCCTTGCAC 59.430 43.478 0.00 0.00 0.00 4.57
6405 6557 2.978156 TGGGCTCTTGTCAAATCCTT 57.022 45.000 0.00 0.00 0.00 3.36
6969 7131 5.833131 ACAACCAGAGGAGAGATAAGAGATC 59.167 44.000 0.00 0.00 0.00 2.75
7286 7450 1.380515 CCCACCCAACAACCACACA 60.381 57.895 0.00 0.00 0.00 3.72
7296 7460 2.204291 AGGCATCTCCCCACCCAA 60.204 61.111 0.00 0.00 34.51 4.12
7412 7617 2.121129 GTACAGGCAGGGGTGGTATAA 58.879 52.381 0.00 0.00 0.00 0.98
7429 7639 6.363357 GTCAAAGCATCAAACAAATCCAGTAC 59.637 38.462 0.00 0.00 0.00 2.73
7655 7942 0.468029 GGGGCGGTTTGATGATCCAT 60.468 55.000 0.00 0.00 0.00 3.41
7663 7950 0.682292 GATTTTTGGGGGCGGTTTGA 59.318 50.000 0.00 0.00 0.00 2.69
7674 7961 3.481112 CCGTTTAGTCGGGATTTTTGG 57.519 47.619 0.00 0.00 45.88 3.28
7689 7976 3.188460 CCGATGAATGACAAAGACCGTTT 59.812 43.478 0.00 0.00 0.00 3.60
7705 7992 0.535328 TTTTTGGTGACCGCCGATGA 60.535 50.000 0.00 0.00 0.00 2.92
7708 7995 0.820074 ACATTTTTGGTGACCGCCGA 60.820 50.000 0.00 0.00 0.00 5.54
7712 7999 3.765349 CGGACATTTTTGGTGACCG 57.235 52.632 0.00 3.04 45.21 4.79
7730 8017 1.450312 CAGGCATTCGGACAGGTCC 60.450 63.158 8.44 8.44 46.18 4.46
7731 8018 0.036388 TTCAGGCATTCGGACAGGTC 60.036 55.000 0.00 0.00 0.00 3.85
7732 8019 0.400213 TTTCAGGCATTCGGACAGGT 59.600 50.000 0.00 0.00 0.00 4.00
7733 8020 1.672881 GATTTCAGGCATTCGGACAGG 59.327 52.381 0.00 0.00 0.00 4.00
7734 8021 1.672881 GGATTTCAGGCATTCGGACAG 59.327 52.381 0.00 0.00 0.00 3.51
7803 8101 2.276116 GCGGGAGTGTCTGAGTCCA 61.276 63.158 0.00 0.00 45.32 4.02
7829 8127 0.252103 AGGACTCCGAGTGGGCTTTA 60.252 55.000 5.57 0.00 35.24 1.85
7839 8137 1.230497 GGAGGGATGAGGACTCCGA 59.770 63.158 0.00 0.00 41.15 4.55
7842 8140 0.031616 AGTGGGAGGGATGAGGACTC 60.032 60.000 0.00 0.00 0.00 3.36
7850 8148 0.178831 AGGGACAAAGTGGGAGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
7870 8168 1.546476 GTCGAGGGAGCATACATAGGG 59.454 57.143 0.00 0.00 0.00 3.53
7872 8170 2.095668 GTCGTCGAGGGAGCATACATAG 60.096 54.545 5.12 0.00 0.00 2.23
7873 8171 1.878088 GTCGTCGAGGGAGCATACATA 59.122 52.381 5.12 0.00 0.00 2.29
7878 8176 3.518998 CGGTCGTCGAGGGAGCAT 61.519 66.667 13.91 0.00 42.43 3.79
7898 8196 2.530916 GGGTGGTACAGTGGGGGT 60.531 66.667 0.00 0.00 41.80 4.95
7904 8202 4.966274 TGGCCGGGGTGGTACAGT 62.966 66.667 2.18 0.00 41.80 3.55


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

AutoCloner maintained by Alex Coulton.