Multiple sequence alignment - TraesCS3B01G427200

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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 TraesCS3B01G427200 chr3B 100.000 8799 0 0 1 8799 666004274 665995476 0.000000e+00 16249
1 TraesCS3B01G427200 chr3D 94.954 6342 209 36 1906 8185 504309225 504302933 0.000000e+00 9836
2 TraesCS3B01G427200 chr3D 94.114 1750 76 19 123 1863 504310952 504309221 0.000000e+00 2636
3 TraesCS3B01G427200 chr3D 86.278 583 26 22 8243 8781 504302937 504302365 1.270000e-162 584
4 TraesCS3B01G427200 chr3D 89.571 163 16 1 7702 7864 504303910 504303749 1.160000e-48 206
5 TraesCS3B01G427200 chr3D 90.667 150 13 1 7206 7354 504303411 504303262 1.940000e-46 198
6 TraesCS3B01G427200 chr3D 76.829 328 51 14 6860 7172 504303732 504303415 2.540000e-35 161
7 TraesCS3B01G427200 chr3A 96.088 3093 99 13 4731 7816 642713580 642710503 0.000000e+00 5022
8 TraesCS3B01G427200 chr3A 96.091 2251 73 10 2342 4587 642715817 642713577 0.000000e+00 3655
9 TraesCS3B01G427200 chr3A 92.314 2355 128 24 12 2345 642718261 642715939 0.000000e+00 3297
10 TraesCS3B01G427200 chr3A 87.525 1010 64 19 7802 8781 642710484 642709507 0.000000e+00 1110
11 TraesCS3B01G427200 chr3A 89.571 163 16 1 7702 7864 642711120 642710959 1.160000e-48 206
12 TraesCS3B01G427200 chr3A 78.078 333 42 16 6860 7172 642710942 642710621 1.950000e-41 182
13 TraesCS3B01G427200 chr3A 93.043 115 7 1 7206 7319 642710617 642710503 5.460000e-37 167
14 TraesCS3B01G427200 chr4D 96.503 143 5 0 2230 2372 481068903 481068761 4.110000e-58 237
15 TraesCS3B01G427200 chr5D 81.437 167 25 5 3 166 549604198 549604035 1.990000e-26 132
16 TraesCS3B01G427200 chr2A 82.927 82 14 0 5318 5399 585819470 585819389 3.410000e-09 75


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 TraesCS3B01G427200 chr3B 665995476 666004274 8798 True 16249.000000 16249 100.000000 1 8799 1 chr3B.!!$R1 8798
1 TraesCS3B01G427200 chr3D 504302365 504309225 6860 True 5210.000000 9836 90.616000 1906 8781 2 chr3D.!!$R2 6875
2 TraesCS3B01G427200 chr3D 504309221 504310952 1731 True 2636.000000 2636 94.114000 123 1863 1 chr3D.!!$R1 1740
3 TraesCS3B01G427200 chr3A 642709507 642718261 8754 True 1948.428571 5022 90.387143 12 8781 7 chr3A.!!$R1 8769

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
295 296 0.248289 GGTTTTCCTCACCGGATCGA 59.752 55.000 9.46 0.00 42.70 3.59 F
1657 1676 0.911769 TGATCTTGTTGGATCCGGCT 59.088 50.000 7.39 0.00 40.80 5.52 F
2233 2258 0.040499 GGGCAAGGTTTGGGATGGTA 59.960 55.000 0.00 0.00 0.00 3.25 F
2923 3074 0.179048 TGGCTTATCGTGCATCTGGG 60.179 55.000 0.00 0.00 0.00 4.45 F
2996 3147 1.148310 AAGCACGGTTCTGTTCGATG 58.852 50.000 0.00 0.00 0.00 3.84 F
3618 3770 2.145397 TACTTGATCGAGGCCTCAGT 57.855 50.000 31.67 26.41 0.00 3.41 F
4652 4811 0.461961 CTCCACCACTAGTAGGCTGC 59.538 60.000 0.00 0.00 0.00 5.25 F
5171 5349 1.129998 GCACAGTGCAATACAGCAGAG 59.870 52.381 21.22 0.00 46.69 3.35 F
5579 5783 0.104120 GCCAAAAACCCAGACCACAC 59.896 55.000 0.00 0.00 0.00 3.82 F
5626 5830 0.601576 ATTGTTGGCAGCGTCGTGTA 60.602 50.000 0.00 0.00 0.00 2.90 F
7415 7649 1.134401 TGTTCCTTGATCATCTCCCGC 60.134 52.381 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 1794 0.105194 TCCACTCCCACAGGTCTGAA 60.105 55.000 4.84 0.00 0.00 3.02 R
3601 3753 0.179089 CCACTGAGGCCTCGATCAAG 60.179 60.000 27.43 20.24 0.00 3.02 R
4095 4254 0.380378 GCCTCACGTTTTGTCTGCAA 59.620 50.000 0.00 0.00 0.00 4.08 R
4389 4548 0.319405 ATCCAACCAGCAAAAGCAGC 59.681 50.000 0.00 0.00 0.00 5.25 R
4488 4647 1.150827 CCGAACCCGTACAGGAAAAC 58.849 55.000 0.99 0.00 45.00 2.43 R
5562 5766 0.248866 GCGTGTGGTCTGGGTTTTTG 60.249 55.000 0.00 0.00 0.00 2.44 R
5563 5767 0.681564 TGCGTGTGGTCTGGGTTTTT 60.682 50.000 0.00 0.00 0.00 1.94 R
6527 6757 0.729116 CATCATCCAGAACACCACGC 59.271 55.000 0.00 0.00 0.00 5.34 R
6544 6774 1.366319 AGGTTCTCCAGAAGGTGCAT 58.634 50.000 0.00 0.00 34.27 3.96 R
7542 7777 1.467734 GGTGAAGCTCTGCACTCATTG 59.532 52.381 7.85 0.00 35.43 2.82 R
8561 8862 1.474478 GTGGATGAGAGTGAGCGAGAA 59.526 52.381 0.00 0.00 0.00 2.87 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
64 65 5.370880 ACATGGATAAGATCAACCCTTAGCT 59.629 40.000 0.00 0.00 34.14 3.32
66 67 6.672266 TGGATAAGATCAACCCTTAGCTAG 57.328 41.667 0.00 0.00 34.14 3.42
72 73 2.266279 TCAACCCTTAGCTAGCAACCT 58.734 47.619 18.83 0.00 0.00 3.50
90 91 7.672983 GCAACCTGCTACATACATATTACAT 57.327 36.000 0.00 0.00 40.96 2.29
95 96 6.183360 CCTGCTACATACATATTACATGCACG 60.183 42.308 0.00 0.00 0.00 5.34
102 103 5.596268 ACATATTACATGCACGCACATAG 57.404 39.130 0.00 0.00 0.00 2.23
107 108 2.694213 ACATGCACGCACATAGTACAA 58.306 42.857 0.00 0.00 0.00 2.41
110 111 0.368907 GCACGCACATAGTACAACCG 59.631 55.000 0.00 0.00 0.00 4.44
150 151 4.394920 AGCACCAACCTATACAATTTCACG 59.605 41.667 0.00 0.00 0.00 4.35
166 167 4.585955 TTCACGAGCCTATCATCTAACC 57.414 45.455 0.00 0.00 0.00 2.85
251 252 2.649516 ACGTGAACAATTGCAATCGTG 58.350 42.857 17.52 13.57 0.00 4.35
295 296 0.248289 GGTTTTCCTCACCGGATCGA 59.752 55.000 9.46 0.00 42.70 3.59
297 298 2.000447 GTTTTCCTCACCGGATCGAAG 59.000 52.381 9.46 0.00 42.70 3.79
311 312 1.002250 TCGAAGAAGACGAGCGTTGC 61.002 55.000 0.00 0.00 34.85 4.17
433 435 1.665916 CTCCACACTCCACACTGCG 60.666 63.158 0.00 0.00 0.00 5.18
449 451 3.027170 GCGGTTGCTCGTCATGTGG 62.027 63.158 0.00 0.00 38.39 4.17
450 452 1.667830 CGGTTGCTCGTCATGTGGT 60.668 57.895 0.00 0.00 0.00 4.16
451 453 1.626654 CGGTTGCTCGTCATGTGGTC 61.627 60.000 0.00 0.00 0.00 4.02
531 533 3.611057 CGAGCGAACCATATACCAGTACC 60.611 52.174 0.00 0.00 0.00 3.34
538 542 2.370849 CCATATACCAGTACCACCACCC 59.629 54.545 0.00 0.00 0.00 4.61
584 595 4.752879 ACGCGGCGTGCCAACTAT 62.753 61.111 28.88 0.00 39.18 2.12
585 596 2.583868 CGCGGCGTGCCAACTATA 60.584 61.111 15.36 0.00 42.08 1.31
586 597 1.954146 CGCGGCGTGCCAACTATAT 60.954 57.895 15.36 0.00 42.08 0.86
721 736 6.676950 CACCACAGTGTCAATGCTAAAATAA 58.323 36.000 0.00 0.00 39.30 1.40
767 782 0.932585 GTATGAGAGCGCGCAGAGAC 60.933 60.000 35.10 18.48 0.00 3.36
824 839 1.228306 CCTACGCAAAACCCCACCA 60.228 57.895 0.00 0.00 0.00 4.17
827 842 1.997256 TACGCAAAACCCCACCACCT 61.997 55.000 0.00 0.00 0.00 4.00
834 849 3.569210 CCCCACCACCTGCTGACA 61.569 66.667 0.00 0.00 0.00 3.58
836 851 2.822637 CCCACCACCTGCTGACACT 61.823 63.158 0.00 0.00 0.00 3.55
837 852 1.480212 CCCACCACCTGCTGACACTA 61.480 60.000 0.00 0.00 0.00 2.74
1364 1381 3.758023 ACCAATCAATGCTGAAATCGTGA 59.242 39.130 0.00 0.00 34.49 4.35
1427 1444 8.026607 GCTGCTTTATTTGTAACTCAATGGTAA 58.973 33.333 0.00 0.00 35.84 2.85
1552 1571 6.926272 AGTTTGTCTCAACTCACTTAGCTAAG 59.074 38.462 28.16 28.16 39.18 2.18
1562 1581 5.000012 TCACTTAGCTAAGCTAGAACTGC 58.000 43.478 29.39 0.00 42.34 4.40
1573 1592 1.001293 CTAGAACTGCACTGCCACAGA 59.999 52.381 0.78 0.00 37.35 3.41
1580 1599 1.665916 CACTGCCACAGACCGACAG 60.666 63.158 0.78 0.00 35.18 3.51
1657 1676 0.911769 TGATCTTGTTGGATCCGGCT 59.088 50.000 7.39 0.00 40.80 5.52
1666 1685 4.464262 GATCCGGCTGGGTCAATC 57.536 61.111 20.64 7.60 45.47 2.67
1721 1740 6.128742 GGTTCATAGCTGAAATTTGCAACAAG 60.129 38.462 0.00 0.00 42.85 3.16
1775 1794 2.028130 TGTGGCGAAGAAATTGGTTGT 58.972 42.857 0.00 0.00 0.00 3.32
1778 1797 2.690497 TGGCGAAGAAATTGGTTGTTCA 59.310 40.909 0.00 0.00 39.02 3.18
1880 1899 2.001812 AGAACATGCTGACTACTGCG 57.998 50.000 0.00 0.00 42.50 5.18
1887 1906 2.814269 TGCTGACTACTGCGATCATTC 58.186 47.619 0.00 0.00 42.50 2.67
1888 1907 2.166254 TGCTGACTACTGCGATCATTCA 59.834 45.455 0.00 0.00 42.50 2.57
1894 1913 5.348724 TGACTACTGCGATCATTCACTTTTC 59.651 40.000 0.00 0.00 0.00 2.29
1901 1920 4.870426 GCGATCATTCACTTTTCCTCTGTA 59.130 41.667 0.00 0.00 0.00 2.74
1949 1968 5.525012 GTCCGTTAAATATCTTACCCACCAC 59.475 44.000 0.00 0.00 0.00 4.16
1954 1973 3.814005 ATATCTTACCCACCACGACAC 57.186 47.619 0.00 0.00 0.00 3.67
1970 1989 6.023435 CCACGACACAATGAAAGTGAATATG 58.977 40.000 0.00 0.00 40.16 1.78
1977 1996 9.618890 ACACAATGAAAGTGAATATGTAGCTAT 57.381 29.630 0.00 0.00 40.16 2.97
2055 2075 3.826157 TCATGGCACCACTTCCTTTAAAG 59.174 43.478 8.32 8.32 0.00 1.85
2097 2122 2.440539 ACTGCCTCGAAGTGTTAGTG 57.559 50.000 0.00 0.00 0.00 2.74
2107 2132 7.064253 GCCTCGAAGTGTTAGTGTTAATAACAT 59.936 37.037 9.22 1.91 43.10 2.71
2156 2181 8.388484 AGATGTTCCATAATAGCATTCTGAAC 57.612 34.615 0.00 0.00 33.32 3.18
2233 2258 0.040499 GGGCAAGGTTTGGGATGGTA 59.960 55.000 0.00 0.00 0.00 3.25
2337 2362 5.765182 AGGAGTGTTTTTCAGGTACATTCAG 59.235 40.000 0.00 0.00 32.21 3.02
2339 2364 6.431234 GGAGTGTTTTTCAGGTACATTCAGAT 59.569 38.462 0.00 0.00 32.21 2.90
2345 2370 9.612620 GTTTTTCAGGTACATTCAGATTTACTG 57.387 33.333 0.00 0.00 46.97 2.74
2480 2631 4.764823 TCATTTAGTTTGTTAGGTGCAGGG 59.235 41.667 0.00 0.00 0.00 4.45
2501 2652 4.262292 GGGTTTTGGGAATTCCTGTGTTAC 60.262 45.833 23.63 13.53 36.20 2.50
2645 2796 1.149174 CCAGTGTGCCACAGGTTCT 59.851 57.895 0.00 0.00 36.48 3.01
2652 2803 2.076863 GTGCCACAGGTTCTGATGTAC 58.923 52.381 1.59 0.00 35.18 2.90
2705 2856 1.216064 TTGCATGGAGGGCTCACTAT 58.784 50.000 0.00 0.00 0.00 2.12
2727 2878 1.341383 GGGAGGTGTTTGATCATGGCT 60.341 52.381 0.00 0.00 0.00 4.75
2775 2926 3.433513 GGGTGAAGTACTCGTATGTCC 57.566 52.381 0.00 0.00 0.00 4.02
2789 2940 2.359230 GTCCCTGGTGCTGAGTGC 60.359 66.667 0.00 0.00 43.25 4.40
2923 3074 0.179048 TGGCTTATCGTGCATCTGGG 60.179 55.000 0.00 0.00 0.00 4.45
2947 3098 2.103771 TGGTCATCTTGAGCTCATAGCC 59.896 50.000 19.04 13.95 44.58 3.93
2996 3147 1.148310 AAGCACGGTTCTGTTCGATG 58.852 50.000 0.00 0.00 0.00 3.84
3004 3155 3.074412 GGTTCTGTTCGATGTTGGTGAT 58.926 45.455 0.00 0.00 0.00 3.06
3010 3161 8.447833 GTTCTGTTCGATGTTGGTGATTAATTA 58.552 33.333 0.00 0.00 0.00 1.40
3152 3304 3.914312 TCCAAGATGTCGACAGTTCTTC 58.086 45.455 24.68 17.04 0.00 2.87
3276 3428 4.186077 TGGTCCCATTTCCAGTGTTTTA 57.814 40.909 0.00 0.00 0.00 1.52
3526 3678 5.404466 TTCTGCCATCTTTAACATTTGGG 57.596 39.130 0.00 0.00 0.00 4.12
3534 3686 6.813152 CCATCTTTAACATTTGGGTCATTCAC 59.187 38.462 0.00 0.00 0.00 3.18
3592 3744 4.161189 TCTTGAGGCCACAAAAACATCAAA 59.839 37.500 16.71 0.00 0.00 2.69
3601 3753 7.095816 GGCCACAAAAACATCAAATAGTGTTAC 60.096 37.037 0.00 0.00 37.56 2.50
3618 3770 2.145397 TACTTGATCGAGGCCTCAGT 57.855 50.000 31.67 26.41 0.00 3.41
3623 3775 3.625632 ATCGAGGCCTCAGTGGGGT 62.626 63.158 31.67 9.13 36.00 4.95
3832 3988 7.406799 AAGTTTGCAGGATAAACAAATTTCG 57.593 32.000 1.37 0.00 39.78 3.46
4347 4506 6.458342 CCCTTTTGAAATTAGGCTCGTATGTC 60.458 42.308 0.00 0.00 0.00 3.06
4356 4515 6.662414 TTAGGCTCGTATGTCAAAGAATTG 57.338 37.500 0.00 0.00 37.92 2.32
4471 4630 5.074515 ACCTTTTTCCTCTGGGTTATCAGAA 59.925 40.000 0.00 0.00 42.46 3.02
4488 4647 4.166523 TCAGAAGAGCATAAACTCGTTCG 58.833 43.478 0.00 0.00 41.77 3.95
4501 4660 1.717645 CTCGTTCGTTTTCCTGTACGG 59.282 52.381 0.00 0.00 38.26 4.02
4522 4681 2.289257 GGTTCGGTTGTTAGCAGTAGGT 60.289 50.000 0.00 0.00 0.00 3.08
4530 4689 1.463444 GTTAGCAGTAGGTGGCAAACG 59.537 52.381 0.00 0.00 0.00 3.60
4546 4705 4.512571 GGCAAACGGTACTCAAAGACTTAA 59.487 41.667 0.00 0.00 0.00 1.85
4576 4735 4.142381 ACTTTGTTCTGTTTGTCTTCTGGC 60.142 41.667 0.00 0.00 0.00 4.85
4601 4760 1.893137 GAGCCTGGGGTTTTTACCTTG 59.107 52.381 0.00 0.00 0.00 3.61
4652 4811 0.461961 CTCCACCACTAGTAGGCTGC 59.538 60.000 0.00 0.00 0.00 5.25
4689 4848 4.396478 GGAGGTTTTTCTCATTCACCTAGC 59.604 45.833 0.00 0.00 38.01 3.42
4697 4856 4.693283 TCTCATTCACCTAGCGTAAATGG 58.307 43.478 7.14 0.00 0.00 3.16
5127 5286 9.265901 GTAGATTTATCTTCTATGCACACACAT 57.734 33.333 0.00 0.00 38.32 3.21
5134 5293 5.185828 TCTTCTATGCACACACATACTCACT 59.814 40.000 0.00 0.00 0.00 3.41
5171 5349 1.129998 GCACAGTGCAATACAGCAGAG 59.870 52.381 21.22 0.00 46.69 3.35
5183 5361 2.280457 GCAGAGCCTCGTATGCCC 60.280 66.667 0.00 0.00 32.49 5.36
5306 5484 2.027192 TGGGTTCTTATCTTCGCTGCTT 60.027 45.455 0.00 0.00 0.00 3.91
5392 5570 5.989477 TGTAGCTGCACTTCTTGGTATTAT 58.011 37.500 0.00 0.00 0.00 1.28
5438 5616 8.601845 CATGGAATTTATGTCATGCATTTGAT 57.398 30.769 0.00 0.00 38.94 2.57
5439 5617 9.051679 CATGGAATTTATGTCATGCATTTGATT 57.948 29.630 0.00 6.52 38.94 2.57
5440 5618 9.621629 ATGGAATTTATGTCATGCATTTGATTT 57.378 25.926 0.00 0.00 38.94 2.17
5441 5619 8.884726 TGGAATTTATGTCATGCATTTGATTTG 58.115 29.630 0.00 0.00 38.94 2.32
5562 5766 7.580109 TGTAATGTACAAACCTAAGACTAGGCC 60.580 40.741 0.00 0.00 41.16 5.19
5570 5774 3.353557 CCTAAGACTAGGCCAAAAACCC 58.646 50.000 5.01 0.00 38.50 4.11
5571 5775 3.245122 CCTAAGACTAGGCCAAAAACCCA 60.245 47.826 5.01 0.00 38.50 4.51
5572 5776 2.586648 AGACTAGGCCAAAAACCCAG 57.413 50.000 5.01 0.00 0.00 4.45
5573 5777 2.062636 AGACTAGGCCAAAAACCCAGA 58.937 47.619 5.01 0.00 0.00 3.86
5574 5778 2.160205 GACTAGGCCAAAAACCCAGAC 58.840 52.381 5.01 0.00 0.00 3.51
5575 5779 1.203013 ACTAGGCCAAAAACCCAGACC 60.203 52.381 5.01 0.00 0.00 3.85
5576 5780 0.854218 TAGGCCAAAAACCCAGACCA 59.146 50.000 5.01 0.00 0.00 4.02
5577 5781 0.759060 AGGCCAAAAACCCAGACCAC 60.759 55.000 5.01 0.00 0.00 4.16
5578 5782 1.045911 GGCCAAAAACCCAGACCACA 61.046 55.000 0.00 0.00 0.00 4.17
5579 5783 0.104120 GCCAAAAACCCAGACCACAC 59.896 55.000 0.00 0.00 0.00 3.82
5626 5830 0.601576 ATTGTTGGCAGCGTCGTGTA 60.602 50.000 0.00 0.00 0.00 2.90
5627 5831 0.601576 TTGTTGGCAGCGTCGTGTAT 60.602 50.000 0.00 0.00 0.00 2.29
5761 5965 2.156098 GCCGAACTATTTTGGGTGTCA 58.844 47.619 1.52 0.00 36.81 3.58
5771 5975 6.777580 ACTATTTTGGGTGTCACTCTTTTCAT 59.222 34.615 4.09 0.00 0.00 2.57
5808 6012 2.624838 CCCATGAGGCACCAAATCATAC 59.375 50.000 0.00 0.00 32.51 2.39
5998 6228 2.486982 AGATGCATGCTCACAGTTTGTC 59.513 45.455 20.33 1.92 0.00 3.18
6140 6370 3.435327 TCCACAACGATGAATTTTCCTCG 59.565 43.478 13.93 13.93 46.24 4.63
6407 6637 2.297701 GTGTTCCTCTTTGGTCAAGCA 58.702 47.619 0.00 0.00 37.07 3.91
6431 6661 7.875971 CAATATCTTGCTTGGTAAATACTCCC 58.124 38.462 0.00 0.00 0.00 4.30
6527 6757 4.207019 GGTGAAAAATTGACTGTTGCTTCG 59.793 41.667 0.00 0.00 0.00 3.79
6544 6774 1.374125 CGCGTGGTGTTCTGGATGA 60.374 57.895 0.00 0.00 0.00 2.92
6567 6797 2.303311 GCACCTTCTGGAGAACCTAGTT 59.697 50.000 0.00 0.00 37.04 2.24
6591 6821 8.454106 GTTATGCATACAGAGATGACAAGTTTT 58.546 33.333 5.74 0.00 0.00 2.43
6594 6824 6.073058 TGCATACAGAGATGACAAGTTTTCAC 60.073 38.462 0.00 0.00 0.00 3.18
6651 6881 8.333235 ACAGGTTACCTCATTCAAATAATGGTA 58.667 33.333 0.00 0.00 0.00 3.25
6838 7068 1.726791 AGCATTTATAGCGAATCGGCG 59.273 47.619 4.35 0.00 38.18 6.46
6919 7149 8.017418 AGGTATATCCTCAGAAACTCTCTTTG 57.983 38.462 0.00 0.00 44.42 2.77
7021 7255 2.231964 TCCAACTTGGAATGAATGCTGC 59.768 45.455 8.15 0.00 45.00 5.25
7022 7256 2.232941 CCAACTTGGAATGAATGCTGCT 59.767 45.455 0.92 0.00 40.96 4.24
7023 7257 3.250744 CAACTTGGAATGAATGCTGCTG 58.749 45.455 0.00 0.00 0.00 4.41
7171 7405 4.655963 AGATAACCACAGCATTGTTCACT 58.344 39.130 0.00 0.00 34.62 3.41
7222 7456 2.256117 ACTGCTTTGTAGGTGTCACC 57.744 50.000 14.68 14.68 38.99 4.02
7309 7543 7.068839 GTGGAGAGGATTCTGTCTAACTGAATA 59.931 40.741 10.85 0.00 43.66 1.75
7320 7554 6.049149 TGTCTAACTGAATATGTTAGGCTGC 58.951 40.000 15.89 0.00 46.64 5.25
7415 7649 1.134401 TGTTCCTTGATCATCTCCCGC 60.134 52.381 0.00 0.00 0.00 6.13
7507 7742 5.256474 ACTCATGTGGAAAGTTCATTAGGG 58.744 41.667 0.00 0.00 0.00 3.53
7559 7794 2.810274 TGAACAATGAGTGCAGAGCTTC 59.190 45.455 0.00 0.00 30.20 3.86
7688 7935 3.611113 CCGTGACAAGGATAACTACAACG 59.389 47.826 0.36 0.00 0.00 4.10
7689 7936 4.232221 CGTGACAAGGATAACTACAACGT 58.768 43.478 0.00 0.00 0.00 3.99
7746 7993 5.184864 CCATGCAAAGGGTTATAGAAACACA 59.815 40.000 0.00 0.00 0.00 3.72
7758 8005 1.937899 AGAAACACAGAAACGGAACCG 59.062 47.619 11.83 11.83 46.03 4.44
7822 8102 2.853235 AACCTGTTAGGCTGGTACAC 57.147 50.000 0.00 0.00 46.85 2.90
7831 8111 3.543680 AGGCTGGTACACATGTATCAC 57.456 47.619 0.00 0.00 36.77 3.06
7845 8125 4.760530 TGTATCACTATTCAGCTTGCCT 57.239 40.909 0.00 0.00 0.00 4.75
7847 8127 5.118990 TGTATCACTATTCAGCTTGCCTTC 58.881 41.667 0.00 0.00 0.00 3.46
7848 8128 3.988976 TCACTATTCAGCTTGCCTTCT 57.011 42.857 0.00 0.00 0.00 2.85
7849 8129 4.292186 TCACTATTCAGCTTGCCTTCTT 57.708 40.909 0.00 0.00 0.00 2.52
7850 8130 4.256920 TCACTATTCAGCTTGCCTTCTTC 58.743 43.478 0.00 0.00 0.00 2.87
7868 8148 7.224949 GCCTTCTTCCTTCTGTACATATACAAC 59.775 40.741 0.00 0.00 40.84 3.32
7933 8213 1.981495 AGCTGTAGAAGAAGCAAGGGT 59.019 47.619 0.00 0.00 42.06 4.34
7961 8241 0.846427 AGCCTTGGGTCCATCCTGAA 60.846 55.000 0.00 0.00 36.25 3.02
8034 8314 1.135774 CGCGCCGCTCTTAGATATACA 60.136 52.381 7.78 0.00 0.00 2.29
8037 8317 3.927142 GCGCCGCTCTTAGATATACAATT 59.073 43.478 0.00 0.00 0.00 2.32
8131 8412 1.194772 GCTTCGAGCAGTGTTGTAACC 59.805 52.381 0.00 0.00 41.89 2.85
8182 8463 6.127535 CCTGTAAAATCTGAACTGCCATGAAT 60.128 38.462 0.00 0.00 0.00 2.57
8186 8467 3.581024 TCTGAACTGCCATGAATTTGC 57.419 42.857 0.00 0.00 0.00 3.68
8202 8483 6.506147 TGAATTTGCGGATGGAAAATGATAG 58.494 36.000 0.00 0.00 38.97 2.08
8203 8484 6.320926 TGAATTTGCGGATGGAAAATGATAGA 59.679 34.615 0.00 0.00 38.97 1.98
8204 8485 6.713762 ATTTGCGGATGGAAAATGATAGAA 57.286 33.333 0.00 0.00 38.97 2.10
8277 8558 0.679505 TGTGTCAGCTGGGTCTACAC 59.320 55.000 22.28 22.28 40.61 2.90
8323 8604 4.836825 ACTGAATATGTGGAGAAGTGGTG 58.163 43.478 0.00 0.00 0.00 4.17
8480 8780 1.484444 AAGGTGACCTCTGGACCAGC 61.484 60.000 17.33 3.19 30.89 4.85
8512 8813 1.808411 TGATTGAAGCTCAACGTCCC 58.192 50.000 0.00 0.00 39.45 4.46
8541 8842 4.398319 ACAAATATTATGGGAAGCTCCGG 58.602 43.478 0.00 0.00 37.43 5.14
8561 8862 3.195825 CGGGTGAATCAGTAGAAAGGTCT 59.804 47.826 0.00 0.00 37.95 3.85
8566 8867 5.802956 GTGAATCAGTAGAAAGGTCTTCTCG 59.197 44.000 0.00 0.00 35.12 4.04
8570 8891 3.191581 CAGTAGAAAGGTCTTCTCGCTCA 59.808 47.826 0.00 0.00 35.12 4.26
8625 8946 1.981256 AAGTGTTGTCCTTGGCGATT 58.019 45.000 0.00 0.00 0.00 3.34
8743 9067 1.819229 CCAGAGGGTGACGAGGATG 59.181 63.158 0.00 0.00 0.00 3.51
8750 9074 3.002583 TGACGAGGATGCAGCCCA 61.003 61.111 19.48 5.32 0.00 5.36
8752 9076 1.153086 GACGAGGATGCAGCCCAAT 60.153 57.895 19.48 2.08 0.00 3.16
8753 9077 1.442526 GACGAGGATGCAGCCCAATG 61.443 60.000 19.48 7.63 0.00 2.82
8754 9078 1.153107 CGAGGATGCAGCCCAATGA 60.153 57.895 19.48 0.00 0.00 2.57
8755 9079 1.164662 CGAGGATGCAGCCCAATGAG 61.165 60.000 19.48 0.00 0.00 2.90
8756 9080 0.106819 GAGGATGCAGCCCAATGAGT 60.107 55.000 19.48 0.00 0.00 3.41
8757 9081 0.333993 AGGATGCAGCCCAATGAGTT 59.666 50.000 19.48 0.00 0.00 3.01
8758 9082 0.458669 GGATGCAGCCCAATGAGTTG 59.541 55.000 10.76 0.00 35.05 3.16
8781 9105 9.710900 GTTGGAATTGGAATAGACAAAGATTTT 57.289 29.630 0.00 0.00 0.00 1.82
8788 9112 9.973661 TTGGAATAGACAAAGATTTTAGATGGA 57.026 29.630 0.00 0.00 0.00 3.41
8792 9116 6.610741 AGACAAAGATTTTAGATGGATCGC 57.389 37.500 0.00 0.00 0.00 4.58
8793 9117 5.529060 AGACAAAGATTTTAGATGGATCGCC 59.471 40.000 0.00 0.00 0.00 5.54
8794 9118 5.440610 ACAAAGATTTTAGATGGATCGCCT 58.559 37.500 0.00 0.00 34.31 5.52
8795 9119 5.888161 ACAAAGATTTTAGATGGATCGCCTT 59.112 36.000 0.00 0.00 34.31 4.35
8796 9120 6.038714 ACAAAGATTTTAGATGGATCGCCTTC 59.961 38.462 0.00 0.00 38.34 3.46
8797 9121 5.296151 AGATTTTAGATGGATCGCCTTCA 57.704 39.130 0.00 0.00 40.02 3.02
8798 9122 5.303971 AGATTTTAGATGGATCGCCTTCAG 58.696 41.667 0.00 0.00 40.02 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.738370 CAAAGCCTAGTAATAACATGCGTC 58.262 41.667 0.00 0.00 0.00 5.19
6 7 7.417570 GGAGTAGAGCAAAGCCTAGTAATAACA 60.418 40.741 0.00 0.00 0.00 2.41
7 8 6.924612 GGAGTAGAGCAAAGCCTAGTAATAAC 59.075 42.308 0.00 0.00 0.00 1.89
8 9 6.610020 TGGAGTAGAGCAAAGCCTAGTAATAA 59.390 38.462 0.00 0.00 0.00 1.40
9 10 6.134055 TGGAGTAGAGCAAAGCCTAGTAATA 58.866 40.000 0.00 0.00 0.00 0.98
10 11 4.962995 TGGAGTAGAGCAAAGCCTAGTAAT 59.037 41.667 0.00 0.00 0.00 1.89
66 67 7.521529 CATGTAATATGTATGTAGCAGGTTGC 58.478 38.462 0.00 0.00 45.46 4.17
72 73 5.120053 GCGTGCATGTAATATGTATGTAGCA 59.880 40.000 7.93 0.00 0.00 3.49
90 91 1.434555 GGTTGTACTATGTGCGTGCA 58.565 50.000 0.00 0.00 0.00 4.57
95 96 2.679450 TGTCACGGTTGTACTATGTGC 58.321 47.619 0.00 0.00 0.00 4.57
102 103 3.515071 GACATGTTGTCACGGTTGTAC 57.485 47.619 0.00 0.00 46.22 2.90
125 126 6.456449 CGTGAAATTGTATAGGTTGGTGCTAC 60.456 42.308 0.00 0.00 0.00 3.58
127 128 4.394920 CGTGAAATTGTATAGGTTGGTGCT 59.605 41.667 0.00 0.00 0.00 4.40
150 151 2.610727 GGCACGGTTAGATGATAGGCTC 60.611 54.545 0.00 0.00 0.00 4.70
251 252 1.792006 AATCTTGCTTGCTTGCTTGC 58.208 45.000 3.47 0.00 0.00 4.01
252 253 3.386486 TCAAATCTTGCTTGCTTGCTTG 58.614 40.909 3.47 0.28 0.00 4.01
253 254 3.738830 TCAAATCTTGCTTGCTTGCTT 57.261 38.095 3.47 0.00 0.00 3.91
254 255 3.585862 CATCAAATCTTGCTTGCTTGCT 58.414 40.909 3.47 0.00 0.00 3.91
295 296 0.946221 CCAGCAACGCTCGTCTTCTT 60.946 55.000 0.00 0.00 36.40 2.52
297 298 0.944311 TTCCAGCAACGCTCGTCTTC 60.944 55.000 0.00 0.00 36.40 2.87
311 312 5.300286 ACCACAAGATGTTTCTTTCTTCCAG 59.700 40.000 0.00 0.00 40.28 3.86
402 404 4.468153 GGAGTGTGGAGAGGAAAGTAGATT 59.532 45.833 0.00 0.00 0.00 2.40
433 435 1.626654 CGACCACATGACGAGCAACC 61.627 60.000 0.00 0.00 0.00 3.77
449 451 2.181021 CGGGTCCACTGCTACGAC 59.819 66.667 0.00 0.00 0.00 4.34
450 452 2.034532 TCGGGTCCACTGCTACGA 59.965 61.111 0.00 0.00 0.00 3.43
451 453 2.181021 GTCGGGTCCACTGCTACG 59.819 66.667 0.00 0.00 0.00 3.51
531 533 0.391263 GCTTCTAGAACGGGGTGGTG 60.391 60.000 0.00 0.00 0.00 4.17
584 595 7.653503 TGATGGAAAATAGGTTGGGGTTTATA 58.346 34.615 0.00 0.00 0.00 0.98
585 596 6.507568 TGATGGAAAATAGGTTGGGGTTTAT 58.492 36.000 0.00 0.00 0.00 1.40
586 597 5.905088 TGATGGAAAATAGGTTGGGGTTTA 58.095 37.500 0.00 0.00 0.00 2.01
604 615 0.758734 TCGGAGGGCTACATTGATGG 59.241 55.000 0.00 0.00 0.00 3.51
721 736 1.735571 GTTCCGTGTACGAAATGGCAT 59.264 47.619 5.91 0.00 43.02 4.40
767 782 0.739112 GCTGACCCGCTTTCTCTCTG 60.739 60.000 0.00 0.00 0.00 3.35
824 839 2.294078 GGGCCTAGTGTCAGCAGGT 61.294 63.158 0.84 0.00 0.00 4.00
827 842 2.203922 TGGGGCCTAGTGTCAGCA 60.204 61.111 0.84 0.00 0.00 4.41
928 945 2.286826 CAGCACTACTAGGTGGGCA 58.713 57.895 12.81 0.00 37.65 5.36
1270 1287 1.739338 CTTACCCGCGAGAGATGCCT 61.739 60.000 8.23 0.00 0.00 4.75
1374 1391 9.278011 TCCCAAAATCCATTTTTCCATAATAGT 57.722 29.630 0.00 0.00 37.86 2.12
1375 1392 9.768662 CTCCCAAAATCCATTTTTCCATAATAG 57.231 33.333 0.00 0.00 37.86 1.73
1427 1444 7.360861 CCGTGAACATGACATTGTTACTGTTAT 60.361 37.037 0.00 0.00 39.85 1.89
1437 1454 0.880441 TGGCCGTGAACATGACATTG 59.120 50.000 0.00 0.00 0.00 2.82
1468 1486 1.876156 CTTGCCTTTTCGAGAAGCACT 59.124 47.619 10.12 0.00 0.00 4.40
1496 1514 9.088987 AGGTAATTCTATTTCCTGCAAAGAAAA 57.911 29.630 13.77 1.29 36.83 2.29
1500 1518 7.630242 TCAGGTAATTCTATTTCCTGCAAAG 57.370 36.000 16.00 0.00 43.49 2.77
1552 1571 0.603707 TGTGGCAGTGCAGTTCTAGC 60.604 55.000 18.61 0.00 0.00 3.42
1562 1581 1.665916 CTGTCGGTCTGTGGCAGTG 60.666 63.158 0.00 0.00 32.61 3.66
1580 1599 8.543774 GCTACATATTGTGACAGTTTCTCATAC 58.456 37.037 0.00 0.00 0.00 2.39
1666 1685 2.536323 AAATGTTAAAGCCGGCCGCG 62.536 55.000 26.15 14.87 44.76 6.46
1721 1740 5.346011 GCTTTGCCATAGTTTAGCAGAAAAC 59.654 40.000 0.00 2.19 37.89 2.43
1751 1770 3.652274 ACCAATTTCTTCGCCACATTTG 58.348 40.909 0.00 0.00 0.00 2.32
1775 1794 0.105194 TCCACTCCCACAGGTCTGAA 60.105 55.000 4.84 0.00 0.00 3.02
1778 1797 0.399949 TGTTCCACTCCCACAGGTCT 60.400 55.000 0.00 0.00 0.00 3.85
1880 1899 7.604164 TGTTCTACAGAGGAAAAGTGAATGATC 59.396 37.037 0.00 0.00 0.00 2.92
1887 1906 9.522804 GATACTATGTTCTACAGAGGAAAAGTG 57.477 37.037 6.43 0.00 41.44 3.16
1888 1907 9.256228 TGATACTATGTTCTACAGAGGAAAAGT 57.744 33.333 6.43 0.00 41.44 2.66
1894 1913 5.915758 GCGTTGATACTATGTTCTACAGAGG 59.084 44.000 6.43 0.00 41.44 3.69
1901 1920 4.827692 TGGTTGCGTTGATACTATGTTCT 58.172 39.130 0.00 0.00 0.00 3.01
1949 1968 6.901887 GCTACATATTCACTTTCATTGTGTCG 59.098 38.462 0.00 0.00 36.83 4.35
2055 2075 5.824904 AGCCATCAACAATACATCACTTC 57.175 39.130 0.00 0.00 0.00 3.01
2059 2079 4.576053 GCAGTAGCCATCAACAATACATCA 59.424 41.667 0.00 0.00 33.58 3.07
2107 2132 8.988060 TCTACAAACCAAGTAGGATATGAATCA 58.012 33.333 0.00 0.00 41.22 2.57
2233 2258 4.281688 AGCACAAATTGGAGCACTGTAATT 59.718 37.500 13.50 0.00 0.00 1.40
2345 2370 9.439537 GAAGTTCTTTGTACTTCAGACAAATTC 57.560 33.333 10.05 0.00 46.78 2.17
2480 2631 5.523438 TGTAACACAGGAATTCCCAAAAC 57.477 39.130 21.22 12.08 37.41 2.43
2645 2796 5.144159 AGGACCTCCATCTTAGTACATCA 57.856 43.478 0.00 0.00 38.89 3.07
2652 2803 5.684704 TGCATAAAAGGACCTCCATCTTAG 58.315 41.667 0.00 0.00 38.89 2.18
2705 2856 2.092429 GCCATGATCAAACACCTCCCTA 60.092 50.000 0.00 0.00 0.00 3.53
2727 2878 6.425721 CCTAGACAACATAAAACCTCACGAAA 59.574 38.462 0.00 0.00 0.00 3.46
2923 3074 3.540314 ATGAGCTCAAGATGACCAGTC 57.460 47.619 22.50 0.00 0.00 3.51
2947 3098 6.428771 TGAGAAGGTAAATAGAAAACCAACCG 59.571 38.462 0.00 0.00 35.64 4.44
3010 3161 4.515191 ACGTCAAAGCACAGATAAACACAT 59.485 37.500 0.00 0.00 0.00 3.21
3105 3256 2.768527 TGCAACAATGAAAACCCTGGAA 59.231 40.909 0.00 0.00 0.00 3.53
3106 3257 2.364970 CTGCAACAATGAAAACCCTGGA 59.635 45.455 0.00 0.00 0.00 3.86
3107 3258 2.364970 TCTGCAACAATGAAAACCCTGG 59.635 45.455 0.00 0.00 0.00 4.45
3152 3304 1.163554 GCTTCCACTTGCTCTCTTGG 58.836 55.000 0.00 0.00 0.00 3.61
3427 3579 8.204160 ACAATGATCTGATGATTGATTGCAAAT 58.796 29.630 28.53 7.82 36.88 2.32
3526 3678 0.671781 ACTGAGCAGGCGTGAATGAC 60.672 55.000 11.29 0.00 0.00 3.06
3534 3686 0.320771 AGTACCAAACTGAGCAGGCG 60.321 55.000 2.20 0.00 36.93 5.52
3592 3744 3.961408 AGGCCTCGATCAAGTAACACTAT 59.039 43.478 0.00 0.00 0.00 2.12
3601 3753 0.179089 CCACTGAGGCCTCGATCAAG 60.179 60.000 27.43 20.24 0.00 3.02
3618 3770 1.002659 CACCAACTCGTATGAACCCCA 59.997 52.381 0.00 0.00 0.00 4.96
3623 3775 5.703592 ACTAAAATGCACCAACTCGTATGAA 59.296 36.000 0.00 0.00 0.00 2.57
3680 3836 3.815856 TTAGCTTCAGATCCAGAGCAG 57.184 47.619 12.55 0.00 0.00 4.24
3899 4055 5.862860 GGTCGTCTAAGGAAGTAAAGTTCTG 59.137 44.000 0.00 0.00 0.00 3.02
4094 4253 1.597937 GCCTCACGTTTTGTCTGCAAG 60.598 52.381 0.00 0.00 35.82 4.01
4095 4254 0.380378 GCCTCACGTTTTGTCTGCAA 59.620 50.000 0.00 0.00 0.00 4.08
4096 4255 0.463654 AGCCTCACGTTTTGTCTGCA 60.464 50.000 0.00 0.00 0.00 4.41
4152 4311 3.558931 TCCACGAATGGCAATGACTAT 57.441 42.857 0.00 0.00 46.80 2.12
4347 4506 9.063615 TGATGATATGGATCAGACAATTCTTTG 57.936 33.333 0.00 0.00 45.29 2.77
4378 4537 5.335897 CCAGCAAAAGCAGCTATTCAGTAAA 60.336 40.000 0.00 0.00 41.14 2.01
4389 4548 0.319405 ATCCAACCAGCAAAAGCAGC 59.681 50.000 0.00 0.00 0.00 5.25
4471 4630 4.151867 GGAAAACGAACGAGTTTATGCTCT 59.848 41.667 0.14 0.00 42.81 4.09
4488 4647 1.150827 CCGAACCCGTACAGGAAAAC 58.849 55.000 0.99 0.00 45.00 2.43
4501 4660 2.289257 ACCTACTGCTAACAACCGAACC 60.289 50.000 0.00 0.00 0.00 3.62
4522 4681 2.158871 AGTCTTTGAGTACCGTTTGCCA 60.159 45.455 0.00 0.00 0.00 4.92
4530 4689 7.894708 AGTTCCTACTTAAGTCTTTGAGTACC 58.105 38.462 12.39 0.00 35.13 3.34
4546 4705 6.415573 AGACAAACAGAACAAAGTTCCTACT 58.584 36.000 6.29 0.00 35.68 2.57
4576 4735 2.586648 AAAAACCCCAGGCTCTACTG 57.413 50.000 0.00 0.00 38.21 2.74
4680 4839 6.046593 CAGATAACCATTTACGCTAGGTGAA 58.953 40.000 0.00 0.00 33.93 3.18
4750 4909 6.071334 CCAGACTCTATTACCAGAAGACAACA 60.071 42.308 0.00 0.00 0.00 3.33
5127 5286 7.013942 TGCTAGTTTCTAAGAACACAGTGAGTA 59.986 37.037 7.81 0.00 31.94 2.59
5134 5293 5.753438 CACTGTGCTAGTTTCTAAGAACACA 59.247 40.000 0.00 0.00 37.60 3.72
5144 5303 4.670221 GCTGTATTGCACTGTGCTAGTTTC 60.670 45.833 30.43 16.85 45.31 2.78
5171 5349 2.846193 TCTTTTATGGGCATACGAGGC 58.154 47.619 0.00 0.00 0.00 4.70
5183 5361 7.305993 GCGGTTGAAGTGTTCTTTTCTTTTATG 60.306 37.037 0.00 0.00 33.64 1.90
5306 5484 0.322648 CACACTCACATCCAGCTCCA 59.677 55.000 0.00 0.00 0.00 3.86
5392 5570 7.996066 TCCATGCAAATATAAGCTAACTTACCA 59.004 33.333 0.00 0.00 41.12 3.25
5425 5603 7.577979 ACAAATCAACAAATCAAATGCATGAC 58.422 30.769 0.00 0.00 30.82 3.06
5435 5613 9.681692 CTGACTGAATAACAAATCAACAAATCA 57.318 29.630 0.00 0.00 0.00 2.57
5436 5614 9.897744 TCTGACTGAATAACAAATCAACAAATC 57.102 29.630 0.00 0.00 0.00 2.17
5437 5615 9.903682 CTCTGACTGAATAACAAATCAACAAAT 57.096 29.630 0.00 0.00 0.00 2.32
5438 5616 7.862372 GCTCTGACTGAATAACAAATCAACAAA 59.138 33.333 0.00 0.00 0.00 2.83
5439 5617 7.229306 AGCTCTGACTGAATAACAAATCAACAA 59.771 33.333 0.00 0.00 0.00 2.83
5440 5618 6.712095 AGCTCTGACTGAATAACAAATCAACA 59.288 34.615 0.00 0.00 0.00 3.33
5441 5619 7.138692 AGCTCTGACTGAATAACAAATCAAC 57.861 36.000 0.00 0.00 0.00 3.18
5562 5766 0.248866 GCGTGTGGTCTGGGTTTTTG 60.249 55.000 0.00 0.00 0.00 2.44
5563 5767 0.681564 TGCGTGTGGTCTGGGTTTTT 60.682 50.000 0.00 0.00 0.00 1.94
5564 5768 1.077357 TGCGTGTGGTCTGGGTTTT 60.077 52.632 0.00 0.00 0.00 2.43
5565 5769 1.822186 GTGCGTGTGGTCTGGGTTT 60.822 57.895 0.00 0.00 0.00 3.27
5566 5770 2.203153 GTGCGTGTGGTCTGGGTT 60.203 61.111 0.00 0.00 0.00 4.11
5567 5771 4.602259 CGTGCGTGTGGTCTGGGT 62.602 66.667 0.00 0.00 0.00 4.51
5568 5772 4.293648 TCGTGCGTGTGGTCTGGG 62.294 66.667 0.00 0.00 0.00 4.45
5569 5773 2.734723 CTCGTGCGTGTGGTCTGG 60.735 66.667 0.00 0.00 0.00 3.86
5570 5774 2.016704 GTCTCGTGCGTGTGGTCTG 61.017 63.158 0.00 0.00 0.00 3.51
5571 5775 2.194212 AGTCTCGTGCGTGTGGTCT 61.194 57.895 0.00 0.00 0.00 3.85
5572 5776 2.016704 CAGTCTCGTGCGTGTGGTC 61.017 63.158 0.00 0.00 0.00 4.02
5573 5777 2.027605 CAGTCTCGTGCGTGTGGT 59.972 61.111 0.00 0.00 0.00 4.16
5574 5778 2.027605 ACAGTCTCGTGCGTGTGG 59.972 61.111 0.00 0.00 0.00 4.17
5575 5779 3.224806 CACAGTCTCGTGCGTGTG 58.775 61.111 5.14 5.14 34.77 3.82
5626 5830 1.825474 CGTCTGGTGAGACTGGGTTAT 59.175 52.381 0.00 0.00 45.80 1.89
5627 5831 1.202964 TCGTCTGGTGAGACTGGGTTA 60.203 52.381 0.00 0.00 45.80 2.85
5646 5850 2.105960 GATGCGCGTATGTGGGCTTC 62.106 60.000 16.28 0.00 46.86 3.86
5702 5906 3.841255 ACTTGTGTTTTTGAGGGGGAAAA 59.159 39.130 0.00 0.00 0.00 2.29
5761 5965 7.362920 GCATGTACCCACATTTATGAAAAGAGT 60.363 37.037 0.00 0.00 42.98 3.24
5808 6012 6.017400 ACAATTGCAAGAACATAGAAGTGG 57.983 37.500 4.94 0.00 0.00 4.00
5998 6228 5.163519 ACAGAAATTTGAAGTTCACCTGGTG 60.164 40.000 20.86 20.86 35.60 4.17
6070 6300 7.330208 GCTAATCAGAAAATCAAATGCTGTTGT 59.670 33.333 0.00 0.00 0.00 3.32
6257 6487 4.793071 CGTGTTGTTCATCATGCCTTTTA 58.207 39.130 0.00 0.00 0.00 1.52
6407 6637 7.582719 TGGGAGTATTTACCAAGCAAGATATT 58.417 34.615 0.00 0.00 0.00 1.28
6431 6661 5.503031 CGCAGTGGAGCTAATTCTATGTTTG 60.503 44.000 0.00 0.00 0.00 2.93
6527 6757 0.729116 CATCATCCAGAACACCACGC 59.271 55.000 0.00 0.00 0.00 5.34
6544 6774 1.366319 AGGTTCTCCAGAAGGTGCAT 58.634 50.000 0.00 0.00 34.27 3.96
6567 6797 7.823799 TGAAAACTTGTCATCTCTGTATGCATA 59.176 33.333 1.16 1.16 0.00 3.14
6778 7008 2.044860 GACGAGTCACAAGTGTCTTCG 58.955 52.381 15.98 15.98 36.09 3.79
6838 7068 4.770010 TCACAACAAGGTCCATAAAATCCC 59.230 41.667 0.00 0.00 0.00 3.85
6950 7184 3.713826 ATGAACTTTCCACACGGGTAT 57.286 42.857 0.00 0.00 38.11 2.73
7021 7255 9.566432 AATTAATCTAGAATGGGTTAAGCTCAG 57.434 33.333 4.41 0.00 0.00 3.35
7022 7256 9.342308 CAATTAATCTAGAATGGGTTAAGCTCA 57.658 33.333 4.41 1.64 0.00 4.26
7023 7257 8.787852 CCAATTAATCTAGAATGGGTTAAGCTC 58.212 37.037 4.41 0.00 0.00 4.09
7063 7297 8.672823 AAACGTTTTTACTTTGATCTAGACCT 57.327 30.769 7.96 0.00 0.00 3.85
7157 7391 2.057137 ACACCAGTGAACAATGCTGT 57.943 45.000 4.48 0.00 37.39 4.40
7222 7456 3.890756 TCTATAACCCTTTGCATGGCATG 59.109 43.478 22.99 22.99 38.76 4.06
7309 7543 6.356556 TGATACATTTGTAGCAGCCTAACAT 58.643 36.000 4.65 0.00 41.36 2.71
7320 7554 8.509690 CCAAGCTGGATAATGATACATTTGTAG 58.490 37.037 2.40 0.00 40.96 2.74
7442 7676 9.702253 TGCCATAATAAAGTTTTATTCCCTGTA 57.298 29.630 11.89 0.00 41.17 2.74
7507 7742 9.657121 GAACAGCAATCAAATATAGCTCTTAAC 57.343 33.333 0.00 0.00 32.35 2.01
7542 7777 1.467734 GGTGAAGCTCTGCACTCATTG 59.532 52.381 7.85 0.00 35.43 2.82
7667 7914 4.232221 ACGTTGTAGTTATCCTTGTCACG 58.768 43.478 0.00 0.00 0.00 4.35
7688 7935 3.988819 TGCAAAGCAAATAGGGAACAAC 58.011 40.909 0.00 0.00 34.76 3.32
7689 7936 3.006752 CCTGCAAAGCAAATAGGGAACAA 59.993 43.478 0.00 0.00 38.41 2.83
7746 7993 2.420466 AATGGGCCGGTTCCGTTTCT 62.420 55.000 14.90 0.00 29.85 2.52
7758 8005 0.032540 GGATGAATTGCGAATGGGCC 59.967 55.000 0.00 0.00 0.00 5.80
7822 8102 5.061853 AGGCAAGCTGAATAGTGATACATG 58.938 41.667 0.00 0.00 0.00 3.21
7831 8111 3.883669 AGGAAGAAGGCAAGCTGAATAG 58.116 45.455 0.00 0.00 0.00 1.73
7847 8127 9.751542 CCTAAGTTGTATATGTACAGAAGGAAG 57.248 37.037 0.33 4.79 41.56 3.46
7848 8128 8.701895 CCCTAAGTTGTATATGTACAGAAGGAA 58.298 37.037 16.35 0.00 41.56 3.36
7849 8129 8.063153 TCCCTAAGTTGTATATGTACAGAAGGA 58.937 37.037 16.35 10.24 41.56 3.36
7850 8130 8.246430 TCCCTAAGTTGTATATGTACAGAAGG 57.754 38.462 0.33 8.05 41.56 3.46
7868 8148 3.519579 CGCATGATCATAGCTCCCTAAG 58.480 50.000 20.46 4.04 0.00 2.18
7961 8241 1.067495 GCTGAGGTCAAGTAGCGTTCT 60.067 52.381 0.00 0.00 0.00 3.01
8020 8300 7.095607 CCGTTGACCAATTGTATATCTAAGAGC 60.096 40.741 4.43 0.00 0.00 4.09
8084 8365 4.762251 AGTTGACACCAGAGGCTTTAATTC 59.238 41.667 0.00 0.00 0.00 2.17
8131 8412 3.076621 ACATACATGTGCTGGTGTCAAG 58.923 45.455 9.11 0.00 40.03 3.02
8182 8463 6.522625 TTTCTATCATTTTCCATCCGCAAA 57.477 33.333 0.00 0.00 0.00 3.68
8186 8467 6.882610 TGGATTTCTATCATTTTCCATCCG 57.117 37.500 0.00 0.00 32.98 4.18
8323 8604 5.066593 AGAGGAAATTCCACAGTTCAGAAC 58.933 41.667 15.21 5.00 39.61 3.01
8353 8640 2.224079 AGTGCAATACGAGCAACAACAG 59.776 45.455 0.00 0.00 44.64 3.16
8512 8813 3.750371 TCCCATAATATTTGTCAGCCGG 58.250 45.455 0.00 0.00 0.00 6.13
8541 8842 6.043854 AGAAGACCTTTCTACTGATTCACC 57.956 41.667 0.00 0.00 0.00 4.02
8561 8862 1.474478 GTGGATGAGAGTGAGCGAGAA 59.526 52.381 0.00 0.00 0.00 2.87
8566 8867 2.344950 CACAAGTGGATGAGAGTGAGC 58.655 52.381 0.00 0.00 0.00 4.26
8625 8946 3.054875 AGAGGATTGAATGTGTGCAGCTA 60.055 43.478 0.00 0.00 0.00 3.32
8634 8955 5.483231 TCTTCTGTCAGAGAGGATTGAATGT 59.517 40.000 2.12 0.00 31.99 2.71
8750 9074 8.421249 TTTGTCTATTCCAATTCCAACTCATT 57.579 30.769 0.00 0.00 0.00 2.57
8752 9076 7.230747 TCTTTGTCTATTCCAATTCCAACTCA 58.769 34.615 0.00 0.00 0.00 3.41
8753 9077 7.687941 TCTTTGTCTATTCCAATTCCAACTC 57.312 36.000 0.00 0.00 0.00 3.01
8754 9078 8.655935 AATCTTTGTCTATTCCAATTCCAACT 57.344 30.769 0.00 0.00 0.00 3.16
8755 9079 9.710900 AAAATCTTTGTCTATTCCAATTCCAAC 57.289 29.630 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.