Multiple sequence alignment - TraesCS7D01G449300

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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 TraesCS7D01G449300 chr7D 100.000 6877 0 0 1 6877 568595319 568602195 0.000000e+00 12700.0
1 TraesCS7D01G449300 chr7D 88.602 465 38 8 332 784 637144806 637145267 1.010000e-152 551.0
2 TraesCS7D01G449300 chr7D 90.066 302 10 9 530 815 45625703 45625406 2.340000e-99 374.0
3 TraesCS7D01G449300 chr7A 91.992 5220 294 68 809 5944 657350812 657355991 0.000000e+00 7210.0
4 TraesCS7D01G449300 chr7A 86.986 584 50 21 6302 6877 65057691 65058256 9.730000e-178 634.0
5 TraesCS7D01G449300 chr7A 89.516 496 37 8 332 814 728029238 728029731 1.270000e-171 614.0
6 TraesCS7D01G449300 chr7A 80.357 840 136 17 1 816 54688694 54689528 1.640000e-170 610.0
7 TraesCS7D01G449300 chr7A 87.312 465 36 13 332 784 728663282 728662829 1.710000e-140 510.0
8 TraesCS7D01G449300 chr7A 89.565 345 36 0 373 717 728256268 728256612 8.190000e-119 438.0
9 TraesCS7D01G449300 chr7A 80.786 229 16 12 5938 6138 657356140 657356368 3.320000e-33 154.0
10 TraesCS7D01G449300 chr7A 95.349 43 1 1 6173 6214 657356440 657356482 4.450000e-07 67.6
11 TraesCS7D01G449300 chr7B 91.912 5131 282 68 809 5843 624348704 624353797 0.000000e+00 7053.0
12 TraesCS7D01G449300 chr7B 87.707 846 64 14 1 818 25957784 25958617 0.000000e+00 950.0
13 TraesCS7D01G449300 chr7B 80.453 839 134 18 4 817 44287691 44286858 1.270000e-171 614.0
14 TraesCS7D01G449300 chr7B 89.106 358 23 5 472 816 736624843 736624489 1.370000e-116 431.0
15 TraesCS7D01G449300 chr7B 95.652 46 1 1 5946 5990 624353981 624354026 9.570000e-09 73.1
16 TraesCS7D01G449300 chr5D 93.501 2862 163 19 2792 5641 534864655 534867505 0.000000e+00 4233.0
17 TraesCS7D01G449300 chr5D 91.245 2924 218 22 2789 5702 534856549 534859444 0.000000e+00 3947.0
18 TraesCS7D01G449300 chr5D 88.851 592 47 7 6304 6877 532649734 532649144 0.000000e+00 710.0
19 TraesCS7D01G449300 chr5D 86.971 591 50 14 6304 6877 44412141 44411561 2.090000e-179 640.0
20 TraesCS7D01G449300 chr5D 89.336 497 37 9 332 815 497168060 497167567 1.640000e-170 610.0
21 TraesCS7D01G449300 chr5D 83.243 185 10 12 960 1134 534854746 534854919 4.300000e-32 150.0
22 TraesCS7D01G449300 chr4A 93.009 2875 176 18 2786 5644 636680480 636677615 0.000000e+00 4172.0
23 TraesCS7D01G449300 chr4A 93.191 2614 158 15 3163 5761 636687186 636684578 0.000000e+00 3823.0
24 TraesCS7D01G449300 chr4A 88.256 843 67 12 1 818 648110762 648109927 0.000000e+00 979.0
25 TraesCS7D01G449300 chr4A 80.691 839 133 17 4 818 712836341 712835508 5.860000e-175 625.0
26 TraesCS7D01G449300 chr4A 79.643 280 42 10 2429 2697 636680861 636680586 3.270000e-43 187.0
27 TraesCS7D01G449300 chr5B 94.618 2527 135 1 3105 5631 675423326 675425851 0.000000e+00 3912.0
28 TraesCS7D01G449300 chr5B 94.584 2474 134 0 3174 5647 674892239 674894712 0.000000e+00 3827.0
29 TraesCS7D01G449300 chr5B 93.295 2595 158 13 3128 5709 675080163 675082754 0.000000e+00 3814.0
30 TraesCS7D01G449300 chr5B 80.142 282 37 11 2429 2697 675422799 675423074 7.040000e-45 193.0
31 TraesCS7D01G449300 chr3D 90.670 836 56 8 1 816 592544271 592545104 0.000000e+00 1092.0
32 TraesCS7D01G449300 chr3B 88.194 847 58 12 1 818 795035232 795034399 0.000000e+00 972.0
33 TraesCS7D01G449300 chr4D 88.870 593 46 9 6302 6877 351675990 351676579 0.000000e+00 712.0
34 TraesCS7D01G449300 chr4D 86.356 579 52 9 6320 6877 352572931 352572359 2.120000e-169 606.0
35 TraesCS7D01G449300 chrUn 91.749 509 30 8 6372 6874 111012143 111011641 0.000000e+00 697.0
36 TraesCS7D01G449300 chr2B 88.625 589 45 11 6308 6877 160749305 160749890 0.000000e+00 697.0
37 TraesCS7D01G449300 chr2B 75.466 322 44 21 6378 6693 152706577 152706285 2.600000e-24 124.0
38 TraesCS7D01G449300 chr2D 87.879 594 50 11 6302 6877 184848118 184847529 0.000000e+00 678.0
39 TraesCS7D01G449300 chr5A 89.354 526 32 12 6372 6877 631351323 631350802 2.090000e-179 640.0
40 TraesCS7D01G449300 chr1A 80.572 839 132 19 4 816 536887883 536887050 9.800000e-173 617.0
41 TraesCS7D01G449300 chr6B 80.406 837 135 17 4 816 12711003 12710172 1.640000e-170 610.0
42 TraesCS7D01G449300 chr6B 80.263 836 137 16 4 816 205956167 205955337 7.630000e-169 604.0
43 TraesCS7D01G449300 chr1D 87.356 261 33 0 332 592 17644037 17643777 4.030000e-77 300.0


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 TraesCS7D01G449300 chr7D 568595319 568602195 6876 False 12700.000000 12700 100.000000 1 6877 1 chr7D.!!$F1 6876
1 TraesCS7D01G449300 chr7A 657350812 657356482 5670 False 2477.200000 7210 89.375667 809 6214 3 chr7A.!!$F5 5405
2 TraesCS7D01G449300 chr7A 65057691 65058256 565 False 634.000000 634 86.986000 6302 6877 1 chr7A.!!$F2 575
3 TraesCS7D01G449300 chr7A 54688694 54689528 834 False 610.000000 610 80.357000 1 816 1 chr7A.!!$F1 815
4 TraesCS7D01G449300 chr7B 624348704 624354026 5322 False 3563.050000 7053 93.782000 809 5990 2 chr7B.!!$F2 5181
5 TraesCS7D01G449300 chr7B 25957784 25958617 833 False 950.000000 950 87.707000 1 818 1 chr7B.!!$F1 817
6 TraesCS7D01G449300 chr7B 44286858 44287691 833 True 614.000000 614 80.453000 4 817 1 chr7B.!!$R1 813
7 TraesCS7D01G449300 chr5D 534864655 534867505 2850 False 4233.000000 4233 93.501000 2792 5641 1 chr5D.!!$F1 2849
8 TraesCS7D01G449300 chr5D 534854746 534859444 4698 False 2048.500000 3947 87.244000 960 5702 2 chr5D.!!$F2 4742
9 TraesCS7D01G449300 chr5D 532649144 532649734 590 True 710.000000 710 88.851000 6304 6877 1 chr5D.!!$R3 573
10 TraesCS7D01G449300 chr5D 44411561 44412141 580 True 640.000000 640 86.971000 6304 6877 1 chr5D.!!$R1 573
11 TraesCS7D01G449300 chr4A 636677615 636687186 9571 True 2727.333333 4172 88.614333 2429 5761 3 chr4A.!!$R3 3332
12 TraesCS7D01G449300 chr4A 648109927 648110762 835 True 979.000000 979 88.256000 1 818 1 chr4A.!!$R1 817
13 TraesCS7D01G449300 chr4A 712835508 712836341 833 True 625.000000 625 80.691000 4 818 1 chr4A.!!$R2 814
14 TraesCS7D01G449300 chr5B 674892239 674894712 2473 False 3827.000000 3827 94.584000 3174 5647 1 chr5B.!!$F1 2473
15 TraesCS7D01G449300 chr5B 675080163 675082754 2591 False 3814.000000 3814 93.295000 3128 5709 1 chr5B.!!$F2 2581
16 TraesCS7D01G449300 chr5B 675422799 675425851 3052 False 2052.500000 3912 87.380000 2429 5631 2 chr5B.!!$F3 3202
17 TraesCS7D01G449300 chr3D 592544271 592545104 833 False 1092.000000 1092 90.670000 1 816 1 chr3D.!!$F1 815
18 TraesCS7D01G449300 chr3B 795034399 795035232 833 True 972.000000 972 88.194000 1 818 1 chr3B.!!$R1 817
19 TraesCS7D01G449300 chr4D 351675990 351676579 589 False 712.000000 712 88.870000 6302 6877 1 chr4D.!!$F1 575
20 TraesCS7D01G449300 chr4D 352572359 352572931 572 True 606.000000 606 86.356000 6320 6877 1 chr4D.!!$R1 557
21 TraesCS7D01G449300 chrUn 111011641 111012143 502 True 697.000000 697 91.749000 6372 6874 1 chrUn.!!$R1 502
22 TraesCS7D01G449300 chr2B 160749305 160749890 585 False 697.000000 697 88.625000 6308 6877 1 chr2B.!!$F1 569
23 TraesCS7D01G449300 chr2D 184847529 184848118 589 True 678.000000 678 87.879000 6302 6877 1 chr2D.!!$R1 575
24 TraesCS7D01G449300 chr5A 631350802 631351323 521 True 640.000000 640 89.354000 6372 6877 1 chr5A.!!$R1 505
25 TraesCS7D01G449300 chr1A 536887050 536887883 833 True 617.000000 617 80.572000 4 816 1 chr1A.!!$R1 812
26 TraesCS7D01G449300 chr6B 12710172 12711003 831 True 610.000000 610 80.406000 4 816 1 chr6B.!!$R1 812
27 TraesCS7D01G449300 chr6B 205955337 205956167 830 True 604.000000 604 80.263000 4 816 1 chr6B.!!$R2 812

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
422 450 0.182775 ACCGGCTCAGTTGTTTCCTT 59.817 50.000 0.00 0.0 0.0 3.36 F
919 977 1.007038 GGGCCGTAATCGCGTGATA 60.007 57.895 12.67 0.0 33.4 2.15 F
1877 2067 1.005450 TCCCATTTACCCAAGTCCAGC 59.995 52.381 0.00 0.0 0.0 4.85 F
2860 6812 0.043183 TCCCAGGGCTCAGAATCTCA 59.957 55.000 0.00 0.0 0.0 3.27 F
3261 7250 1.197721 GAAGTTGCTGGTGATGTTCGG 59.802 52.381 0.00 0.0 0.0 4.30 F
3438 7427 2.221055 CCACGTTGACTTTTCTTCGGAG 59.779 50.000 0.00 0.0 0.0 4.63 F
5097 9086 1.056700 AGGACTCTGTTGTGGCTGGT 61.057 55.000 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1819 0.246635 CGAAATGGTCCGGTCAGAGT 59.753 55.000 0.00 0.0 0.00 3.24 R
2244 2471 2.227865 CACTTCAACCAACAATACCCGG 59.772 50.000 0.00 0.0 0.00 5.73 R
3438 7427 0.243907 TACGAAGAGCAGCTGTGACC 59.756 55.000 16.64 0.0 0.00 4.02 R
4020 8009 0.250234 TGCCCATCAAGTCCTTCTCG 59.750 55.000 0.00 0.0 0.00 4.04 R
5097 9086 0.821711 CCTTTGACGCCCACTGGAAA 60.822 55.000 0.00 0.0 0.00 3.13 R
5427 9416 2.519013 GTGCTTGAGAACCCAAAGGAT 58.481 47.619 0.00 0.0 36.73 3.24 R
6281 10522 0.409092 TCCACCACCATGATGGCTTT 59.591 50.000 12.25 0.0 44.33 3.51 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
96 98 3.942829 TCTGGAGACATGCGAGAAAAAT 58.057 40.909 0.00 0.00 41.51 1.82
121 123 3.634504 TCTTGGTACTATGGCGTTCCTA 58.365 45.455 0.00 0.00 0.00 2.94
122 124 4.025360 TCTTGGTACTATGGCGTTCCTAA 58.975 43.478 0.00 0.00 0.00 2.69
200 213 8.163408 TCAGTCCTTTTCCTGAAGAATTATTGA 58.837 33.333 0.00 0.00 34.88 2.57
299 312 4.206375 TGACCACTGCTGAGAAAATGAAA 58.794 39.130 0.00 0.00 0.00 2.69
419 447 1.282875 GCACCGGCTCAGTTGTTTC 59.717 57.895 0.00 0.00 36.96 2.78
422 450 0.182775 ACCGGCTCAGTTGTTTCCTT 59.817 50.000 0.00 0.00 0.00 3.36
477 512 1.604278 GAGGAAGTTGAAGCAAACGCT 59.396 47.619 0.00 0.00 43.25 5.07
560 595 1.138671 GTGCTGTTGTTGTTGCGGT 59.861 52.632 0.00 0.00 0.00 5.68
566 601 1.135546 TGTTGTTGTTGCGGTTGTGAG 60.136 47.619 0.00 0.00 0.00 3.51
649 684 1.608025 GGGAGTTCAGTTCGTGCATGA 60.608 52.381 3.97 3.97 0.00 3.07
836 888 4.311520 AAGTTATCCCTTGGGGTGTTAC 57.688 45.455 5.78 0.00 44.74 2.50
888 946 1.374758 GCTTGTCTGACTCCACCCG 60.375 63.158 9.51 0.00 0.00 5.28
919 977 1.007038 GGGCCGTAATCGCGTGATA 60.007 57.895 12.67 0.00 33.40 2.15
958 1019 1.945354 ATCTGGCCCGTCACAGTACG 61.945 60.000 0.00 0.00 42.49 3.67
1001 1063 3.172106 GCCCTAGCCTTCCTCCCC 61.172 72.222 0.00 0.00 0.00 4.81
1457 1554 3.607987 GCGCGGATCTGTCGTTCG 61.608 66.667 8.83 7.07 0.00 3.95
1647 1819 4.951715 AGTTCAGCCATTCTGCATGAATTA 59.048 37.500 0.00 0.00 43.00 1.40
1696 1884 7.581213 ATGAGTATTTTCTGTGTGTTTTCCA 57.419 32.000 0.00 0.00 0.00 3.53
1697 1885 7.397892 TGAGTATTTTCTGTGTGTTTTCCAA 57.602 32.000 0.00 0.00 0.00 3.53
1702 1890 5.713792 TTTCTGTGTGTTTTCCAAAGTCA 57.286 34.783 0.00 0.00 0.00 3.41
1806 1995 8.404765 TGTTGGTAATTACATGATATTGCAGTG 58.595 33.333 17.16 0.00 0.00 3.66
1841 2030 6.523201 GCATAAAACTGTCATTCCGTTACAAG 59.477 38.462 0.00 0.00 0.00 3.16
1877 2067 1.005450 TCCCATTTACCCAAGTCCAGC 59.995 52.381 0.00 0.00 0.00 4.85
1886 2076 1.208293 CCCAAGTCCAGCCTTAGTCTC 59.792 57.143 0.00 0.00 0.00 3.36
1952 2144 5.895928 TCTGGTGAAGTTTCTCTATGATCG 58.104 41.667 0.00 0.00 0.00 3.69
1962 2154 7.662897 AGTTTCTCTATGATCGATCCCTTTAC 58.337 38.462 22.31 10.04 0.00 2.01
1979 2171 2.902705 TACAAGTTTCGCAGTCCTGT 57.097 45.000 0.00 0.00 0.00 4.00
2086 2279 7.627939 GCTTTTGCATCTACACTTCTCATGATT 60.628 37.037 0.00 0.00 46.58 2.57
2137 2364 4.573201 GGTCGTATTGCTTTGTGGCTATTA 59.427 41.667 0.00 0.00 0.00 0.98
2138 2365 5.499047 GTCGTATTGCTTTGTGGCTATTAC 58.501 41.667 0.00 0.00 0.00 1.89
2149 2376 2.103263 GTGGCTATTACCCTCTGGACAG 59.897 54.545 0.00 0.00 34.81 3.51
2153 2380 4.407945 GGCTATTACCCTCTGGACAGTTAA 59.592 45.833 0.00 0.00 34.81 2.01
2154 2381 5.104652 GGCTATTACCCTCTGGACAGTTAAA 60.105 44.000 0.00 0.00 34.81 1.52
2155 2382 6.412214 GCTATTACCCTCTGGACAGTTAAAA 58.588 40.000 0.00 0.00 34.81 1.52
2162 2389 5.183904 CCCTCTGGACAGTTAAAATTTCAGG 59.816 44.000 0.00 0.00 0.00 3.86
2170 2397 7.360113 ACAGTTAAAATTTCAGGTCATGGTT 57.640 32.000 0.00 0.00 0.00 3.67
2176 2403 5.867903 AATTTCAGGTCATGGTTTGTTGA 57.132 34.783 0.00 0.00 0.00 3.18
2191 2418 5.334879 GGTTTGTTGATGCTAGTGTTAGGTG 60.335 44.000 0.00 0.00 0.00 4.00
2269 2496 4.098807 GGGTATTGTTGGTTGAAGTGTTGT 59.901 41.667 0.00 0.00 0.00 3.32
2302 2529 4.844349 AGGTGGCAGTGTATATGACTTT 57.156 40.909 0.00 0.00 0.00 2.66
2311 2538 7.717875 GGCAGTGTATATGACTTTTGGGTATAA 59.282 37.037 0.00 0.00 0.00 0.98
2355 2582 9.856162 TTTTGAGTATTACTTAGACTTTTGGGT 57.144 29.630 0.00 0.00 0.00 4.51
2401 2653 8.816144 GTGTCAGATCTATTCACTTGATTCTTC 58.184 37.037 13.36 0.00 0.00 2.87
2530 6428 8.812513 AATCATGGACAAGAAGAACAATATCA 57.187 30.769 0.00 0.00 0.00 2.15
2532 6430 7.623630 TCATGGACAAGAAGAACAATATCAGA 58.376 34.615 0.00 0.00 0.00 3.27
2550 6448 5.627499 TCAGAAACATGTCTGTTATTGCC 57.373 39.130 12.77 0.00 44.83 4.52
2559 6457 4.343231 TGTCTGTTATTGCCCATGTTGAT 58.657 39.130 0.00 0.00 0.00 2.57
2585 6494 1.597742 ATGTGCCTGAACAGTGACAC 58.402 50.000 0.00 0.00 32.52 3.67
2589 6498 2.996621 GTGCCTGAACAGTGACACTATC 59.003 50.000 8.02 10.33 0.00 2.08
2621 6531 8.900781 CATTCAGTAGGATCTTGTTGATTGATT 58.099 33.333 0.00 0.00 35.14 2.57
2650 6560 4.399004 AGCCTGCTCATTCTACTGTAAG 57.601 45.455 0.00 0.00 42.29 2.34
2744 6654 9.116067 TGAAATAATAACTAGTTTTCATCCCGG 57.884 33.333 14.49 0.00 32.88 5.73
2754 6664 2.500392 TTCATCCCGGAAAACCGATT 57.500 45.000 0.73 0.00 34.88 3.34
2755 6665 1.745232 TCATCCCGGAAAACCGATTG 58.255 50.000 0.73 5.01 34.88 2.67
2772 6688 7.316393 ACCGATTGATCCTATTCTTGGAATA 57.684 36.000 0.00 0.00 37.13 1.75
2860 6812 0.043183 TCCCAGGGCTCAGAATCTCA 59.957 55.000 0.00 0.00 0.00 3.27
2889 6841 2.489329 GGTGCATGCTCATGTTAGTTGT 59.511 45.455 20.33 0.00 40.80 3.32
2893 6845 4.460034 TGCATGCTCATGTTAGTTGTTGAT 59.540 37.500 20.33 0.00 40.80 2.57
2945 6919 6.225318 TCATGCGGTTGTACTTAGTTACTTT 58.775 36.000 0.00 0.00 0.00 2.66
3033 7007 6.423182 ACTAAATAGCTGGTTTGCCTTATGA 58.577 36.000 0.00 0.00 35.27 2.15
3034 7008 5.582689 AAATAGCTGGTTTGCCTTATGAC 57.417 39.130 0.00 0.00 35.27 3.06
3035 7009 1.839424 AGCTGGTTTGCCTTATGACC 58.161 50.000 0.00 0.00 35.27 4.02
3036 7010 1.355720 AGCTGGTTTGCCTTATGACCT 59.644 47.619 0.00 0.00 35.27 3.85
3061 7041 9.815936 CTTTTTATTTCTGGATTGTTTGAATGC 57.184 29.630 0.00 0.00 0.00 3.56
3085 7065 5.462398 CACTGTACTGTTGTGTTCTACTTCC 59.538 44.000 2.16 0.00 0.00 3.46
3091 7071 4.761975 TGTTGTGTTCTACTTCCGTCTTT 58.238 39.130 0.00 0.00 0.00 2.52
3098 7078 7.223387 TGTGTTCTACTTCCGTCTTTTAAGTTC 59.777 37.037 0.00 0.00 35.23 3.01
3101 7081 7.884816 TCTACTTCCGTCTTTTAAGTTCATG 57.115 36.000 0.00 0.00 35.23 3.07
3103 7083 6.300354 ACTTCCGTCTTTTAAGTTCATGTG 57.700 37.500 0.00 0.00 29.25 3.21
3106 7086 6.055231 TCCGTCTTTTAAGTTCATGTGTTG 57.945 37.500 0.00 0.00 0.00 3.33
3145 7134 5.743398 CGATTGTGTTCAACTGTCAAACAAT 59.257 36.000 8.85 2.22 38.95 2.71
3198 7187 3.947834 ACATATTTGCAGGCAAGTCTACC 59.052 43.478 5.24 0.00 37.24 3.18
3261 7250 1.197721 GAAGTTGCTGGTGATGTTCGG 59.802 52.381 0.00 0.00 0.00 4.30
3438 7427 2.221055 CCACGTTGACTTTTCTTCGGAG 59.779 50.000 0.00 0.00 0.00 4.63
3645 7634 3.128938 AGACTTTCTCCCGTGTTATCGAG 59.871 47.826 0.00 0.00 0.00 4.04
4020 8009 3.942829 TGGAGTGACCATGAAGAATGAC 58.057 45.455 0.00 0.00 44.64 3.06
5097 9086 1.056700 AGGACTCTGTTGTGGCTGGT 61.057 55.000 0.00 0.00 0.00 4.00
5193 9182 4.128925 TGTTCTCCACACTGATGCTATC 57.871 45.455 0.00 0.00 0.00 2.08
5424 9413 2.070650 GGCCTACCTCCCCGTCATT 61.071 63.158 0.00 0.00 0.00 2.57
5427 9416 1.200519 CCTACCTCCCCGTCATTGAA 58.799 55.000 0.00 0.00 0.00 2.69
5532 9521 1.004745 GCTTCTGATCCTTTGGACCCA 59.995 52.381 0.00 0.00 32.98 4.51
5562 9551 4.831307 GCGACGCTCGTCACGGAT 62.831 66.667 20.35 0.00 44.77 4.18
5703 9701 7.041721 TGCACTATTTTGTATCGATGAGTCTT 58.958 34.615 8.54 0.00 0.00 3.01
5704 9702 7.010460 TGCACTATTTTGTATCGATGAGTCTTG 59.990 37.037 8.54 0.00 0.00 3.02
5707 9705 5.784750 TTTTGTATCGATGAGTCTTGCTG 57.215 39.130 8.54 0.00 0.00 4.41
5709 9707 4.456280 TGTATCGATGAGTCTTGCTGTT 57.544 40.909 8.54 0.00 0.00 3.16
5710 9708 5.576447 TGTATCGATGAGTCTTGCTGTTA 57.424 39.130 8.54 0.00 0.00 2.41
5718 9729 5.073311 TGAGTCTTGCTGTTATGACCTAC 57.927 43.478 0.00 0.00 0.00 3.18
5845 9858 9.685276 TTGATCTTTAGATTTGCCTGATTCTTA 57.315 29.630 0.00 0.00 34.37 2.10
5850 9863 4.446371 AGATTTGCCTGATTCTTAGTCGG 58.554 43.478 0.00 0.00 0.00 4.79
5881 9894 4.043750 TGCTTTCTCATGAAAAAGTTGCG 58.956 39.130 19.98 0.00 41.09 4.85
5884 9897 4.891627 TTCTCATGAAAAAGTTGCGTCA 57.108 36.364 0.00 0.00 0.00 4.35
5885 9898 4.209452 TCTCATGAAAAAGTTGCGTCAC 57.791 40.909 0.00 0.00 0.00 3.67
5886 9899 3.625313 TCTCATGAAAAAGTTGCGTCACA 59.375 39.130 0.00 0.00 0.00 3.58
5888 9901 4.930963 TCATGAAAAAGTTGCGTCACATT 58.069 34.783 0.00 0.00 0.00 2.71
5889 9902 4.975502 TCATGAAAAAGTTGCGTCACATTC 59.024 37.500 0.00 0.00 0.00 2.67
5914 9931 3.297461 GTCACTATTCTCGTTCGTTGACG 59.703 47.826 0.00 0.00 44.06 4.35
5990 10165 1.482593 CCTCTAGGATTGGCGTTCTGT 59.517 52.381 0.00 0.00 37.39 3.41
5992 10167 2.166459 CTCTAGGATTGGCGTTCTGTCA 59.834 50.000 0.00 0.00 0.00 3.58
6009 10196 2.203788 ACCTTGCGAGTCCCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
6010 10197 1.613630 ACCTTGCGAGTCCCTCCAT 60.614 57.895 0.00 0.00 0.00 3.41
6011 10198 1.144936 CCTTGCGAGTCCCTCCATC 59.855 63.158 0.00 0.00 0.00 3.51
6012 10199 1.144936 CTTGCGAGTCCCTCCATCC 59.855 63.158 0.00 0.00 0.00 3.51
6013 10200 1.306141 TTGCGAGTCCCTCCATCCT 60.306 57.895 0.00 0.00 0.00 3.24
6014 10201 1.330655 TTGCGAGTCCCTCCATCCTC 61.331 60.000 0.00 0.00 0.00 3.71
6015 10202 2.503382 GCGAGTCCCTCCATCCTCC 61.503 68.421 0.00 0.00 0.00 4.30
6016 10203 1.834822 CGAGTCCCTCCATCCTCCC 60.835 68.421 0.00 0.00 0.00 4.30
6018 10205 1.949449 AGTCCCTCCATCCTCCCCT 60.949 63.158 0.00 0.00 0.00 4.79
6021 10208 1.238896 TCCCTCCATCCTCCCCTTCT 61.239 60.000 0.00 0.00 0.00 2.85
6022 10209 0.766288 CCCTCCATCCTCCCCTTCTC 60.766 65.000 0.00 0.00 0.00 2.87
6023 10210 1.118356 CCTCCATCCTCCCCTTCTCG 61.118 65.000 0.00 0.00 0.00 4.04
6036 10238 1.364626 CTTCTCGCAGCCATGGTGTC 61.365 60.000 14.67 1.36 33.19 3.67
6037 10239 1.830587 TTCTCGCAGCCATGGTGTCT 61.831 55.000 14.67 0.00 33.19 3.41
6049 10251 2.251642 GGTGTCTGTGTTCGGTGGC 61.252 63.158 0.00 0.00 0.00 5.01
6056 10258 2.282110 TGTTCGGTGGCATGGTGG 60.282 61.111 0.00 0.00 0.00 4.61
6061 10263 2.929903 CGGTGGCATGGTGGTTTGG 61.930 63.158 0.00 0.00 0.00 3.28
6086 10289 0.591659 GGTGAAGTTTTCTCCACGGC 59.408 55.000 5.33 0.00 41.71 5.68
6089 10292 0.875059 GAAGTTTTCTCCACGGCCAG 59.125 55.000 2.24 0.00 0.00 4.85
6097 10300 2.046314 CCACGGCCAGTAAGGTGG 60.046 66.667 10.37 10.37 43.41 4.61
6149 10365 1.002134 CTTCTTCCATGCCGGTGGT 60.002 57.895 10.70 0.00 40.27 4.16
6163 10379 1.134965 CGGTGGTAAAGAGGCTGAGAG 60.135 57.143 0.00 0.00 0.00 3.20
6166 10382 3.368948 GGTGGTAAAGAGGCTGAGAGAAG 60.369 52.174 0.00 0.00 0.00 2.85
6174 10390 1.909986 AGGCTGAGAGAAGGTTTACCC 59.090 52.381 0.00 0.00 36.42 3.69
6177 10393 2.266279 CTGAGAGAAGGTTTACCCCCA 58.734 52.381 0.00 0.00 36.42 4.96
6214 10455 3.528597 AGCTTAGACCCGTCTGATTTC 57.471 47.619 7.63 0.00 40.71 2.17
6215 10456 2.832129 AGCTTAGACCCGTCTGATTTCA 59.168 45.455 7.63 0.00 40.71 2.69
6216 10457 2.930682 GCTTAGACCCGTCTGATTTCAC 59.069 50.000 7.63 0.00 40.71 3.18
6217 10458 3.368531 GCTTAGACCCGTCTGATTTCACT 60.369 47.826 7.63 0.00 40.71 3.41
6218 10459 4.425520 CTTAGACCCGTCTGATTTCACTC 58.574 47.826 7.63 0.00 40.71 3.51
6219 10460 1.550976 AGACCCGTCTGATTTCACTCC 59.449 52.381 0.00 0.00 38.75 3.85
6220 10461 0.613777 ACCCGTCTGATTTCACTCCC 59.386 55.000 0.00 0.00 0.00 4.30
6221 10462 0.107654 CCCGTCTGATTTCACTCCCC 60.108 60.000 0.00 0.00 0.00 4.81
6222 10463 0.107654 CCGTCTGATTTCACTCCCCC 60.108 60.000 0.00 0.00 0.00 5.40
6237 10478 4.413074 CCCCCTTCCTAATCCCGT 57.587 61.111 0.00 0.00 0.00 5.28
6238 10479 2.143129 CCCCCTTCCTAATCCCGTC 58.857 63.158 0.00 0.00 0.00 4.79
6239 10480 1.746517 CCCCTTCCTAATCCCGTCG 59.253 63.158 0.00 0.00 0.00 5.12
6240 10481 0.757935 CCCCTTCCTAATCCCGTCGA 60.758 60.000 0.00 0.00 0.00 4.20
6241 10482 1.339097 CCCTTCCTAATCCCGTCGAT 58.661 55.000 0.00 0.00 0.00 3.59
6242 10483 1.692519 CCCTTCCTAATCCCGTCGATT 59.307 52.381 0.00 1.20 43.79 3.34
6243 10484 2.548067 CCCTTCCTAATCCCGTCGATTG 60.548 54.545 0.00 0.00 41.47 2.67
6244 10485 2.135933 CTTCCTAATCCCGTCGATTGC 58.864 52.381 0.00 0.00 41.47 3.56
6245 10486 1.410004 TCCTAATCCCGTCGATTGCT 58.590 50.000 0.00 0.00 41.47 3.91
6246 10487 1.760613 TCCTAATCCCGTCGATTGCTT 59.239 47.619 0.00 0.00 41.47 3.91
6247 10488 1.867233 CCTAATCCCGTCGATTGCTTG 59.133 52.381 0.00 0.00 41.47 4.01
6248 10489 2.550978 CTAATCCCGTCGATTGCTTGT 58.449 47.619 0.00 0.00 41.47 3.16
6249 10490 2.684001 AATCCCGTCGATTGCTTGTA 57.316 45.000 0.00 0.00 39.84 2.41
6250 10491 1.935933 ATCCCGTCGATTGCTTGTAC 58.064 50.000 0.00 0.00 0.00 2.90
6251 10492 0.604073 TCCCGTCGATTGCTTGTACA 59.396 50.000 0.00 0.00 0.00 2.90
6252 10493 1.001068 TCCCGTCGATTGCTTGTACAA 59.999 47.619 8.28 8.28 0.00 2.41
6253 10494 1.393539 CCCGTCGATTGCTTGTACAAG 59.606 52.381 27.85 27.85 41.24 3.16
6254 10495 2.333926 CCGTCGATTGCTTGTACAAGA 58.666 47.619 34.43 18.10 40.79 3.02
6255 10496 2.345641 CCGTCGATTGCTTGTACAAGAG 59.654 50.000 34.43 19.78 40.79 2.85
6256 10497 2.345641 CGTCGATTGCTTGTACAAGAGG 59.654 50.000 34.43 18.67 40.79 3.69
6257 10498 3.585862 GTCGATTGCTTGTACAAGAGGA 58.414 45.455 34.43 20.40 40.79 3.71
6258 10499 3.368236 GTCGATTGCTTGTACAAGAGGAC 59.632 47.826 34.43 25.49 40.79 3.85
6259 10500 2.673368 CGATTGCTTGTACAAGAGGACC 59.327 50.000 34.43 18.79 40.79 4.46
6260 10501 2.561478 TTGCTTGTACAAGAGGACCC 57.439 50.000 34.43 18.14 40.79 4.46
6261 10502 1.729586 TGCTTGTACAAGAGGACCCT 58.270 50.000 34.43 0.00 40.79 4.34
6262 10503 1.623811 TGCTTGTACAAGAGGACCCTC 59.376 52.381 34.43 16.85 40.79 4.30
6271 10512 2.909140 GAGGACCCTCTGCTTAGCT 58.091 57.895 5.60 0.00 39.80 3.32
6272 10513 0.750249 GAGGACCCTCTGCTTAGCTC 59.250 60.000 5.60 0.00 39.80 4.09
6273 10514 0.689412 AGGACCCTCTGCTTAGCTCC 60.689 60.000 5.60 2.63 0.00 4.70
6274 10515 0.689412 GGACCCTCTGCTTAGCTCCT 60.689 60.000 5.60 0.00 0.00 3.69
6275 10516 1.411787 GGACCCTCTGCTTAGCTCCTA 60.412 57.143 5.60 0.00 0.00 2.94
6276 10517 1.684450 GACCCTCTGCTTAGCTCCTAC 59.316 57.143 5.60 0.00 0.00 3.18
6277 10518 1.289530 ACCCTCTGCTTAGCTCCTACT 59.710 52.381 5.60 0.00 0.00 2.57
6278 10519 2.292587 ACCCTCTGCTTAGCTCCTACTT 60.293 50.000 5.60 0.00 0.00 2.24
6279 10520 2.364002 CCCTCTGCTTAGCTCCTACTTC 59.636 54.545 5.60 0.00 0.00 3.01
6280 10521 3.027412 CCTCTGCTTAGCTCCTACTTCA 58.973 50.000 5.60 0.00 0.00 3.02
6281 10522 3.449018 CCTCTGCTTAGCTCCTACTTCAA 59.551 47.826 5.60 0.00 0.00 2.69
6282 10523 4.081420 CCTCTGCTTAGCTCCTACTTCAAA 60.081 45.833 5.60 0.00 0.00 2.69
6283 10524 5.482908 CTCTGCTTAGCTCCTACTTCAAAA 58.517 41.667 5.60 0.00 0.00 2.44
6284 10525 5.482908 TCTGCTTAGCTCCTACTTCAAAAG 58.517 41.667 5.60 0.00 0.00 2.27
6285 10526 4.003648 TGCTTAGCTCCTACTTCAAAAGC 58.996 43.478 5.60 0.00 38.78 3.51
6286 10527 3.375610 GCTTAGCTCCTACTTCAAAAGCC 59.624 47.826 0.00 0.00 33.66 4.35
6287 10528 4.579869 CTTAGCTCCTACTTCAAAAGCCA 58.420 43.478 0.00 0.00 33.43 4.75
6288 10529 3.728385 AGCTCCTACTTCAAAAGCCAT 57.272 42.857 0.00 0.00 33.43 4.40
6289 10530 3.615155 AGCTCCTACTTCAAAAGCCATC 58.385 45.455 0.00 0.00 33.43 3.51
6290 10531 3.009473 AGCTCCTACTTCAAAAGCCATCA 59.991 43.478 0.00 0.00 33.43 3.07
6291 10532 3.950395 GCTCCTACTTCAAAAGCCATCAT 59.050 43.478 0.00 0.00 0.00 2.45
6292 10533 4.201990 GCTCCTACTTCAAAAGCCATCATG 60.202 45.833 0.00 0.00 0.00 3.07
6293 10534 4.272489 TCCTACTTCAAAAGCCATCATGG 58.728 43.478 0.00 0.00 41.55 3.66
6294 10535 4.019174 CCTACTTCAAAAGCCATCATGGT 58.981 43.478 5.31 0.00 40.46 3.55
6295 10536 3.947910 ACTTCAAAAGCCATCATGGTG 57.052 42.857 5.31 0.00 40.46 4.17
6296 10537 2.564062 ACTTCAAAAGCCATCATGGTGG 59.436 45.455 21.48 21.48 40.46 4.61
6297 10538 2.307496 TCAAAAGCCATCATGGTGGT 57.693 45.000 25.82 10.33 40.46 4.16
6298 10539 1.894466 TCAAAAGCCATCATGGTGGTG 59.106 47.619 25.82 15.98 40.46 4.17
6359 10600 3.314080 TGCTAAAAACTACTTTGCAGCGT 59.686 39.130 0.00 0.00 38.13 5.07
6463 10733 4.899687 GCGCACGACTCGCCGATA 62.900 66.667 0.30 0.00 46.18 2.92
6575 10853 6.601613 AGTTGATGACTAAAAGTGTCCACAAA 59.398 34.615 0.00 0.00 36.65 2.83
6619 10897 5.867903 TCATCCAACCAAGTTCAAAATGT 57.132 34.783 0.00 0.00 0.00 2.71
6624 10902 7.176589 TCCAACCAAGTTCAAAATGTAAACT 57.823 32.000 0.00 0.00 34.81 2.66
6727 11012 2.826725 ACTCCTCCGAAGACGATTCTTT 59.173 45.455 0.00 0.00 42.53 2.52
6731 11016 3.129638 CCTCCGAAGACGATTCTTTCTCT 59.870 47.826 0.00 0.00 42.53 3.10
6801 11095 0.169009 GGCAAGATCTTCAACGGCAC 59.831 55.000 4.57 0.00 0.00 5.01
6837 11131 2.432628 GAGGCACACCGGAAGACG 60.433 66.667 9.46 0.00 42.76 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.104487 TCACGGGTAACAAGCGACAA 59.896 50.000 0.00 0.00 39.74 3.18
22 23 0.598158 GTCACGGGTAACAAGCGACA 60.598 55.000 0.00 0.00 39.74 4.35
96 98 1.553248 ACGCCATAGTACCAAGAGCAA 59.447 47.619 0.00 0.00 0.00 3.91
200 213 7.169158 TGGATTGTTTGAGTTCAAAGTTTCT 57.831 32.000 7.51 0.00 45.36 2.52
220 233 5.242393 CCTTTCACATCACTTTCACTTGGAT 59.758 40.000 0.00 0.00 0.00 3.41
419 447 1.804748 GAAAGTGACGGCCTACAAAGG 59.195 52.381 0.00 0.00 46.76 3.11
422 450 2.851263 ATGAAAGTGACGGCCTACAA 57.149 45.000 0.00 0.00 0.00 2.41
477 512 0.468226 ACTTGAGTCCCAAACGCAGA 59.532 50.000 0.00 0.00 38.97 4.26
489 524 2.851263 TATCCCGCAAACACTTGAGT 57.149 45.000 0.00 0.00 34.14 3.41
560 595 4.699735 TGTTTCTTTCTTCTGCACTCACAA 59.300 37.500 0.00 0.00 0.00 3.33
566 601 8.560374 ACTTAGTATTGTTTCTTTCTTCTGCAC 58.440 33.333 0.00 0.00 0.00 4.57
649 684 6.240894 TGCACTCTCTTCCAATTTTACTCAT 58.759 36.000 0.00 0.00 0.00 2.90
730 766 7.307694 TCAATTACATGAAAGACATTCTGCAC 58.692 34.615 0.00 0.00 38.92 4.57
767 815 7.431668 GCTCTTTCATTCATTCATAGCAAGTTC 59.568 37.037 0.00 0.00 0.00 3.01
847 905 1.207791 CTGGCCCAAGGTATGACTCT 58.792 55.000 0.00 0.00 0.00 3.24
848 906 0.181350 CCTGGCCCAAGGTATGACTC 59.819 60.000 0.00 0.00 32.17 3.36
849 907 1.926426 GCCTGGCCCAAGGTATGACT 61.926 60.000 7.66 0.00 39.75 3.41
958 1019 4.627611 TCGCTTGCCGGTATATATAGTC 57.372 45.455 1.90 0.00 37.59 2.59
1001 1063 1.127343 GAGAGAATGGGAGGGGTGAG 58.873 60.000 0.00 0.00 0.00 3.51
1174 1270 3.558411 GACGCGCAGGCTAAGCAG 61.558 66.667 5.73 8.31 36.88 4.24
1201 1298 1.403323 GTAGCGGCTTAGTACGGACTT 59.597 52.381 5.12 0.00 37.10 3.01
1457 1554 1.266178 AATAGCCAAAACCAGCACCC 58.734 50.000 0.00 0.00 0.00 4.61
1549 1661 0.312102 GCAGCTGAACAAACCTGACC 59.688 55.000 20.43 0.00 0.00 4.02
1647 1819 0.246635 CGAAATGGTCCGGTCAGAGT 59.753 55.000 0.00 0.00 0.00 3.24
1692 1880 5.891198 CCATATATGGGGATGACTTTGGAA 58.109 41.667 22.31 0.00 44.31 3.53
1841 2030 2.238521 TGGGATGGAGCAAAAGTTGAC 58.761 47.619 0.00 0.00 0.00 3.18
1877 2067 8.952278 AGCGTATAAGATGATTAGAGACTAAGG 58.048 37.037 0.00 0.00 0.00 2.69
1886 2076 7.630026 TGCAAAACAGCGTATAAGATGATTAG 58.370 34.615 10.93 0.05 37.31 1.73
1962 2154 3.131396 ACTTACAGGACTGCGAAACTTG 58.869 45.455 0.00 0.00 0.00 3.16
2015 2207 5.154222 GCTACACAACTATGAAGCAAAACC 58.846 41.667 0.00 0.00 33.55 3.27
2103 2296 5.968528 AGCAATACGACCAACCAAAATTA 57.031 34.783 0.00 0.00 0.00 1.40
2137 2364 5.701224 TGAAATTTTAACTGTCCAGAGGGT 58.299 37.500 0.40 0.00 34.93 4.34
2138 2365 5.183904 CCTGAAATTTTAACTGTCCAGAGGG 59.816 44.000 0.40 0.00 0.00 4.30
2149 2376 8.334632 CAACAAACCATGACCTGAAATTTTAAC 58.665 33.333 0.00 0.00 0.00 2.01
2153 2380 6.232581 TCAACAAACCATGACCTGAAATTT 57.767 33.333 0.00 0.00 0.00 1.82
2154 2381 5.867903 TCAACAAACCATGACCTGAAATT 57.132 34.783 0.00 0.00 0.00 1.82
2155 2382 5.786311 CATCAACAAACCATGACCTGAAAT 58.214 37.500 0.00 0.00 0.00 2.17
2162 2389 4.216257 ACACTAGCATCAACAAACCATGAC 59.784 41.667 0.00 0.00 0.00 3.06
2170 2397 5.222079 TCACCTAACACTAGCATCAACAA 57.778 39.130 0.00 0.00 0.00 2.83
2176 2403 8.730680 CAAAAATACTTCACCTAACACTAGCAT 58.269 33.333 0.00 0.00 0.00 3.79
2231 2458 6.837471 ACAATACCCGGTAAAGCAAAATAA 57.163 33.333 0.16 0.00 0.00 1.40
2244 2471 2.227865 CACTTCAACCAACAATACCCGG 59.772 50.000 0.00 0.00 0.00 5.73
2250 2477 7.875554 ACTTTAAACAACACTTCAACCAACAAT 59.124 29.630 0.00 0.00 0.00 2.71
2449 6347 2.611751 TGACTGTGTTTGAATGTCACGG 59.388 45.455 0.00 0.00 42.16 4.94
2585 6494 7.447374 AGATCCTACTGAATGAACTCGATAG 57.553 40.000 0.00 0.00 0.00 2.08
2589 6498 5.655488 ACAAGATCCTACTGAATGAACTCG 58.345 41.667 0.00 0.00 0.00 4.18
2621 6531 6.763135 CAGTAGAATGAGCAGGCTACAAAATA 59.237 38.462 0.00 0.00 36.55 1.40
2622 6532 5.587844 CAGTAGAATGAGCAGGCTACAAAAT 59.412 40.000 0.00 0.00 36.55 1.82
2743 6653 6.238759 CCAAGAATAGGATCAATCGGTTTTCC 60.239 42.308 0.00 0.00 0.00 3.13
2744 6654 6.542370 TCCAAGAATAGGATCAATCGGTTTTC 59.458 38.462 0.00 0.00 0.00 2.29
2782 6698 9.807649 AAGCAGAAATCAATCATACAATAAACC 57.192 29.630 0.00 0.00 0.00 3.27
2914 6888 4.685169 AGTACAACCGCATGAATTCAAG 57.315 40.909 13.09 9.46 0.00 3.02
2916 6890 5.242434 ACTAAGTACAACCGCATGAATTCA 58.758 37.500 11.26 11.26 0.00 2.57
2917 6891 5.796350 ACTAAGTACAACCGCATGAATTC 57.204 39.130 0.00 0.00 0.00 2.17
2919 6893 6.403878 AGTAACTAAGTACAACCGCATGAAT 58.596 36.000 0.00 0.00 0.00 2.57
2955 6929 4.039004 TGCAAACAACACAAATATCAGGCT 59.961 37.500 0.00 0.00 0.00 4.58
2956 6930 4.305769 TGCAAACAACACAAATATCAGGC 58.694 39.130 0.00 0.00 0.00 4.85
3035 7009 9.815936 GCATTCAAACAATCCAGAAATAAAAAG 57.184 29.630 0.00 0.00 0.00 2.27
3036 7010 9.334947 TGCATTCAAACAATCCAGAAATAAAAA 57.665 25.926 0.00 0.00 0.00 1.94
3061 7041 5.462398 GGAAGTAGAACACAACAGTACAGTG 59.538 44.000 0.00 0.97 39.12 3.66
3085 7065 8.471457 CAAATCAACACATGAACTTAAAAGACG 58.529 33.333 0.00 0.00 42.54 4.18
3121 7110 4.657055 TGTTTGACAGTTGAACACAATCG 58.343 39.130 0.00 0.00 0.00 3.34
3145 7134 2.223144 GTGAGAACAGTGCGCAAACATA 59.777 45.455 14.00 0.00 0.00 2.29
3153 7142 5.536554 AAATAATCTGTGAGAACAGTGCG 57.463 39.130 5.82 0.00 38.75 5.34
3261 7250 0.597637 CTGCACGGGTATCGGTCATC 60.598 60.000 0.00 0.00 44.45 2.92
3438 7427 0.243907 TACGAAGAGCAGCTGTGACC 59.756 55.000 16.64 0.00 0.00 4.02
3645 7634 2.101750 TGCCATGATGACATTGGCATTC 59.898 45.455 23.97 1.03 45.71 2.67
4020 8009 0.250234 TGCCCATCAAGTCCTTCTCG 59.750 55.000 0.00 0.00 0.00 4.04
4638 8627 5.144159 TGGTACAGAGAACCATAGGATCT 57.856 43.478 0.00 0.00 42.10 2.75
4665 8654 4.063689 CAATGATATGCTCACCAGACTCC 58.936 47.826 0.00 0.00 36.48 3.85
4731 8720 1.561076 CCACCCATGAAGTCATCCTGA 59.439 52.381 0.00 0.00 33.61 3.86
4911 8900 3.620419 ATCACGTGGGCCAATGCGA 62.620 57.895 20.23 10.63 38.85 5.10
5097 9086 0.821711 CCTTTGACGCCCACTGGAAA 60.822 55.000 0.00 0.00 0.00 3.13
5424 9413 3.157087 GCTTGAGAACCCAAAGGATTCA 58.843 45.455 0.00 0.00 36.73 2.57
5427 9416 2.519013 GTGCTTGAGAACCCAAAGGAT 58.481 47.619 0.00 0.00 36.73 3.24
5562 9551 1.696097 GGCCCTTCCTCTTGCGGATA 61.696 60.000 0.00 0.00 32.02 2.59
5703 9701 3.257375 ACGACAAGTAGGTCATAACAGCA 59.743 43.478 0.00 0.00 37.66 4.41
5704 9702 3.612860 CACGACAAGTAGGTCATAACAGC 59.387 47.826 0.00 0.00 37.66 4.40
5707 9705 6.691818 CAGTATCACGACAAGTAGGTCATAAC 59.308 42.308 0.00 0.00 37.66 1.89
5709 9707 5.298527 CCAGTATCACGACAAGTAGGTCATA 59.701 44.000 0.00 0.00 37.66 2.15
5710 9708 4.098044 CCAGTATCACGACAAGTAGGTCAT 59.902 45.833 0.00 0.00 37.66 3.06
5718 9729 3.594603 AGTTCCCAGTATCACGACAAG 57.405 47.619 0.00 0.00 0.00 3.16
5784 9797 4.543590 AGAACCAGTGGACAACAGATAG 57.456 45.455 18.40 0.00 0.00 2.08
5845 9858 6.222038 TGAGAAAGCAAGATTATACCGACT 57.778 37.500 0.00 0.00 0.00 4.18
5881 9894 4.800993 CGAGAATAGTGACCAGAATGTGAC 59.199 45.833 0.00 0.00 0.00 3.67
5884 9897 5.407407 AACGAGAATAGTGACCAGAATGT 57.593 39.130 0.00 0.00 0.00 2.71
5885 9898 4.500837 CGAACGAGAATAGTGACCAGAATG 59.499 45.833 0.00 0.00 0.00 2.67
5886 9899 4.158025 ACGAACGAGAATAGTGACCAGAAT 59.842 41.667 0.14 0.00 0.00 2.40
5888 9901 3.079578 ACGAACGAGAATAGTGACCAGA 58.920 45.455 0.14 0.00 0.00 3.86
5889 9902 3.489180 ACGAACGAGAATAGTGACCAG 57.511 47.619 0.14 0.00 0.00 4.00
5944 9964 0.669932 GCTGCATGCTCGGATAGAGG 60.670 60.000 20.33 0.00 46.91 3.69
6009 10196 2.439104 GCTGCGAGAAGGGGAGGAT 61.439 63.158 0.00 0.00 0.00 3.24
6010 10197 3.077556 GCTGCGAGAAGGGGAGGA 61.078 66.667 0.00 0.00 0.00 3.71
6011 10198 4.168291 GGCTGCGAGAAGGGGAGG 62.168 72.222 0.00 0.00 0.00 4.30
6012 10199 2.739996 ATGGCTGCGAGAAGGGGAG 61.740 63.158 0.00 0.00 0.00 4.30
6013 10200 2.688666 ATGGCTGCGAGAAGGGGA 60.689 61.111 0.00 0.00 0.00 4.81
6014 10201 2.515523 CATGGCTGCGAGAAGGGG 60.516 66.667 0.00 0.00 0.00 4.79
6015 10202 2.515523 CCATGGCTGCGAGAAGGG 60.516 66.667 0.00 0.00 0.00 3.95
6016 10203 2.110967 CACCATGGCTGCGAGAAGG 61.111 63.158 13.04 0.00 0.00 3.46
6018 10205 1.375908 GACACCATGGCTGCGAGAA 60.376 57.895 13.04 0.00 0.00 2.87
6036 10238 1.600636 ACCATGCCACCGAACACAG 60.601 57.895 0.00 0.00 0.00 3.66
6037 10239 1.896183 CACCATGCCACCGAACACA 60.896 57.895 0.00 0.00 0.00 3.72
6049 10251 4.085733 TCACCTAAATCCAAACCACCATG 58.914 43.478 0.00 0.00 0.00 3.66
6056 10258 7.145985 GGAGAAAACTTCACCTAAATCCAAAC 58.854 38.462 0.00 0.00 37.43 2.93
6061 10263 5.106673 CCGTGGAGAAAACTTCACCTAAATC 60.107 44.000 0.00 0.00 40.56 2.17
6086 10289 3.976701 CTGGGCGCCACCTTACTGG 62.977 68.421 30.85 3.19 42.93 4.00
6089 10292 1.523938 GATCTGGGCGCCACCTTAC 60.524 63.158 30.85 10.31 39.10 2.34
6118 10321 0.744771 GAAGAAGATGCCCCACCGAC 60.745 60.000 0.00 0.00 0.00 4.79
6143 10359 0.895530 TCTCAGCCTCTTTACCACCG 59.104 55.000 0.00 0.00 0.00 4.94
6149 10365 5.046520 GGTAAACCTTCTCTCAGCCTCTTTA 60.047 44.000 0.00 0.00 0.00 1.85
6157 10373 2.237392 CTGGGGGTAAACCTTCTCTCAG 59.763 54.545 0.00 0.00 40.03 3.35
6163 10379 1.378119 CGGCTGGGGGTAAACCTTC 60.378 63.158 0.00 0.00 40.03 3.46
6166 10382 3.214190 AACCGGCTGGGGGTAAACC 62.214 63.158 18.00 0.00 41.60 3.27
6177 10393 3.976701 CTTCGCCATGGAACCGGCT 62.977 63.158 18.40 0.00 42.85 5.52
6220 10461 1.755393 CGACGGGATTAGGAAGGGGG 61.755 65.000 0.00 0.00 0.00 5.40
6221 10462 0.757935 TCGACGGGATTAGGAAGGGG 60.758 60.000 0.00 0.00 0.00 4.79
6222 10463 1.339097 ATCGACGGGATTAGGAAGGG 58.661 55.000 0.00 0.00 28.32 3.95
6223 10464 2.755650 CAATCGACGGGATTAGGAAGG 58.244 52.381 4.00 0.00 43.52 3.46
6224 10465 2.135933 GCAATCGACGGGATTAGGAAG 58.864 52.381 4.00 0.00 43.52 3.46
6225 10466 1.760613 AGCAATCGACGGGATTAGGAA 59.239 47.619 4.00 0.00 43.52 3.36
6226 10467 1.410004 AGCAATCGACGGGATTAGGA 58.590 50.000 4.00 0.00 43.52 2.94
6227 10468 1.867233 CAAGCAATCGACGGGATTAGG 59.133 52.381 4.00 0.00 43.52 2.69
6228 10469 2.550978 ACAAGCAATCGACGGGATTAG 58.449 47.619 4.00 1.78 43.52 1.73
6229 10470 2.684001 ACAAGCAATCGACGGGATTA 57.316 45.000 4.00 0.00 43.52 1.75
6230 10471 2.277084 GTACAAGCAATCGACGGGATT 58.723 47.619 0.00 0.00 46.29 3.01
6231 10472 1.206132 TGTACAAGCAATCGACGGGAT 59.794 47.619 0.00 0.00 36.78 3.85
6232 10473 0.604073 TGTACAAGCAATCGACGGGA 59.396 50.000 0.00 0.00 0.00 5.14
6233 10474 1.393539 CTTGTACAAGCAATCGACGGG 59.606 52.381 22.03 0.00 0.00 5.28
6234 10475 2.333926 TCTTGTACAAGCAATCGACGG 58.666 47.619 27.49 4.46 38.28 4.79
6235 10476 2.345641 CCTCTTGTACAAGCAATCGACG 59.654 50.000 27.49 5.17 38.28 5.12
6236 10477 3.368236 GTCCTCTTGTACAAGCAATCGAC 59.632 47.826 27.49 21.14 38.28 4.20
6237 10478 3.585862 GTCCTCTTGTACAAGCAATCGA 58.414 45.455 27.49 15.43 38.28 3.59
6238 10479 2.673368 GGTCCTCTTGTACAAGCAATCG 59.327 50.000 27.49 13.68 38.28 3.34
6239 10480 3.010420 GGGTCCTCTTGTACAAGCAATC 58.990 50.000 27.49 15.91 38.28 2.67
6240 10481 2.644798 AGGGTCCTCTTGTACAAGCAAT 59.355 45.455 27.49 8.62 38.28 3.56
6241 10482 2.038557 GAGGGTCCTCTTGTACAAGCAA 59.961 50.000 27.49 12.92 39.80 3.91
6242 10483 1.623811 GAGGGTCCTCTTGTACAAGCA 59.376 52.381 27.49 16.45 39.80 3.91
6243 10484 2.388310 GAGGGTCCTCTTGTACAAGC 57.612 55.000 27.49 14.97 39.80 4.01
6253 10494 0.750249 GAGCTAAGCAGAGGGTCCTC 59.250 60.000 8.91 8.91 43.03 3.71
6254 10495 0.689412 GGAGCTAAGCAGAGGGTCCT 60.689 60.000 0.00 0.00 42.33 3.85
6255 10496 0.689412 AGGAGCTAAGCAGAGGGTCC 60.689 60.000 0.00 0.00 44.90 4.46
6256 10497 1.684450 GTAGGAGCTAAGCAGAGGGTC 59.316 57.143 0.00 0.00 0.00 4.46
6257 10498 1.289530 AGTAGGAGCTAAGCAGAGGGT 59.710 52.381 0.00 0.00 0.00 4.34
6258 10499 2.080654 AGTAGGAGCTAAGCAGAGGG 57.919 55.000 0.00 0.00 0.00 4.30
6259 10500 3.027412 TGAAGTAGGAGCTAAGCAGAGG 58.973 50.000 0.00 0.00 0.00 3.69
6260 10501 4.727507 TTGAAGTAGGAGCTAAGCAGAG 57.272 45.455 0.00 0.00 0.00 3.35
6261 10502 5.482908 CTTTTGAAGTAGGAGCTAAGCAGA 58.517 41.667 0.00 0.00 0.00 4.26
6262 10503 4.094146 GCTTTTGAAGTAGGAGCTAAGCAG 59.906 45.833 5.82 0.00 37.34 4.24
6263 10504 4.003648 GCTTTTGAAGTAGGAGCTAAGCA 58.996 43.478 5.82 0.00 37.34 3.91
6264 10505 3.375610 GGCTTTTGAAGTAGGAGCTAAGC 59.624 47.826 2.61 2.61 36.82 3.09
6265 10506 4.579869 TGGCTTTTGAAGTAGGAGCTAAG 58.420 43.478 0.00 0.00 33.96 2.18
6266 10507 4.634012 TGGCTTTTGAAGTAGGAGCTAA 57.366 40.909 0.00 0.00 33.96 3.09
6267 10508 4.225042 TGATGGCTTTTGAAGTAGGAGCTA 59.775 41.667 0.00 0.00 33.96 3.32
6268 10509 3.009473 TGATGGCTTTTGAAGTAGGAGCT 59.991 43.478 0.00 0.00 33.96 4.09
6269 10510 3.347216 TGATGGCTTTTGAAGTAGGAGC 58.653 45.455 0.00 0.00 0.00 4.70
6270 10511 4.337555 CCATGATGGCTTTTGAAGTAGGAG 59.662 45.833 0.00 0.00 0.00 3.69
6271 10512 4.263905 ACCATGATGGCTTTTGAAGTAGGA 60.264 41.667 12.25 0.00 42.67 2.94
6272 10513 4.019174 ACCATGATGGCTTTTGAAGTAGG 58.981 43.478 12.25 0.00 42.67 3.18
6273 10514 4.142315 CCACCATGATGGCTTTTGAAGTAG 60.142 45.833 12.25 0.00 42.67 2.57
6274 10515 3.763360 CCACCATGATGGCTTTTGAAGTA 59.237 43.478 12.25 0.00 42.67 2.24
6275 10516 2.564062 CCACCATGATGGCTTTTGAAGT 59.436 45.455 12.25 0.00 42.67 3.01
6276 10517 2.564062 ACCACCATGATGGCTTTTGAAG 59.436 45.455 12.25 0.00 44.33 3.02
6277 10518 2.299582 CACCACCATGATGGCTTTTGAA 59.700 45.455 12.25 0.00 44.33 2.69
6278 10519 1.894466 CACCACCATGATGGCTTTTGA 59.106 47.619 12.25 0.00 44.33 2.69
6279 10520 1.066716 CCACCACCATGATGGCTTTTG 60.067 52.381 12.25 1.83 44.33 2.44
6280 10521 1.203162 TCCACCACCATGATGGCTTTT 60.203 47.619 12.25 0.00 44.33 2.27
6281 10522 0.409092 TCCACCACCATGATGGCTTT 59.591 50.000 12.25 0.00 44.33 3.51
6282 10523 0.632835 ATCCACCACCATGATGGCTT 59.367 50.000 12.25 0.00 44.33 4.35
6283 10524 1.521764 TATCCACCACCATGATGGCT 58.478 50.000 12.25 0.00 44.33 4.75
6284 10525 2.158623 TCTTATCCACCACCATGATGGC 60.159 50.000 12.25 0.00 44.33 4.40
6285 10526 3.748083 CTCTTATCCACCACCATGATGG 58.252 50.000 10.53 10.53 46.10 3.51
6286 10527 3.144506 GCTCTTATCCACCACCATGATG 58.855 50.000 0.00 0.00 0.00 3.07
6287 10528 2.779430 TGCTCTTATCCACCACCATGAT 59.221 45.455 0.00 0.00 0.00 2.45
6288 10529 2.195727 TGCTCTTATCCACCACCATGA 58.804 47.619 0.00 0.00 0.00 3.07
6289 10530 2.715749 TGCTCTTATCCACCACCATG 57.284 50.000 0.00 0.00 0.00 3.66
6290 10531 3.051581 AGATGCTCTTATCCACCACCAT 58.948 45.455 0.00 0.00 0.00 3.55
6291 10532 2.435805 GAGATGCTCTTATCCACCACCA 59.564 50.000 0.00 0.00 0.00 4.17
6292 10533 2.224402 GGAGATGCTCTTATCCACCACC 60.224 54.545 0.00 0.00 0.00 4.61
6293 10534 2.435805 TGGAGATGCTCTTATCCACCAC 59.564 50.000 0.00 0.00 36.92 4.16
6294 10535 2.763039 TGGAGATGCTCTTATCCACCA 58.237 47.619 0.00 0.00 36.92 4.17
6295 10536 3.326006 TCATGGAGATGCTCTTATCCACC 59.674 47.826 1.90 0.00 44.28 4.61
6296 10537 4.567971 CTCATGGAGATGCTCTTATCCAC 58.432 47.826 1.90 0.00 44.28 4.02
6297 10538 3.007723 GCTCATGGAGATGCTCTTATCCA 59.992 47.826 0.00 2.30 45.48 3.41
6298 10539 3.598299 GCTCATGGAGATGCTCTTATCC 58.402 50.000 0.00 0.00 0.00 2.59
6299 10540 3.598299 GGCTCATGGAGATGCTCTTATC 58.402 50.000 0.00 0.00 0.00 1.75
6300 10541 2.028294 CGGCTCATGGAGATGCTCTTAT 60.028 50.000 0.00 0.00 0.00 1.73
6331 10572 3.891056 AAGTAGTTTTTAGCACGCCAC 57.109 42.857 0.00 0.00 0.00 5.01
6332 10573 3.549221 GCAAAGTAGTTTTTAGCACGCCA 60.549 43.478 0.00 0.00 0.00 5.69
6502 10772 7.018826 CCATGTTCATTGCATTTTGAATGTTC 58.981 34.615 9.58 0.55 34.60 3.18
6575 10853 5.188163 TGATCTTGTGGGCATGAATTTGAAT 59.812 36.000 0.00 0.00 33.40 2.57
6619 10897 7.773864 TCGTTTGTGTCATGAACTTAGTTTA 57.226 32.000 0.00 0.00 0.00 2.01
6624 10902 5.504994 GCCTTTCGTTTGTGTCATGAACTTA 60.505 40.000 0.00 0.00 0.00 2.24
6727 11012 4.952957 ACGAGAATGATGAAGAGGAAGAGA 59.047 41.667 0.00 0.00 0.00 3.10
6731 11016 3.525537 GCACGAGAATGATGAAGAGGAA 58.474 45.455 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.