Multiple sequence alignment - TraesCS5D01G140100

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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 TraesCS5D01G140100 chr5D 100.000 7642 0 0 1 7642 223877902 223870261 0.000000e+00 14113.0
1 TraesCS5D01G140100 chr5D 84.457 4941 736 29 822 5744 277271966 277276892 0.000000e+00 4841.0
2 TraesCS5D01G140100 chr5D 98.125 800 8 3 1 793 223884943 223884144 0.000000e+00 1387.0
3 TraesCS5D01G140100 chr5D 97.011 803 16 6 1 796 223327310 223328111 0.000000e+00 1343.0
4 TraesCS5D01G140100 chr5D 76.853 1201 243 26 826 2006 348393119 348394304 0.000000e+00 645.0
5 TraesCS5D01G140100 chr5D 74.005 854 197 18 2566 3404 348394878 348395721 2.660000e-84 324.0
6 TraesCS5D01G140100 chr5D 84.942 259 33 5 7375 7629 480983626 480983882 2.740000e-64 257.0
7 TraesCS5D01G140100 chr5D 77.876 113 19 5 4325 4434 468685190 468685081 1.780000e-06 65.8
8 TraesCS5D01G140100 chr7D 92.155 6093 448 16 794 6883 498250602 498244537 0.000000e+00 8576.0
9 TraesCS5D01G140100 chr7D 86.274 4240 512 27 1808 6043 3207368 3203195 0.000000e+00 4542.0
10 TraesCS5D01G140100 chr3B 86.432 5874 723 54 983 6822 733088521 733082688 0.000000e+00 6364.0
11 TraesCS5D01G140100 chr3B 84.087 4204 627 30 2690 6881 54860873 54865046 0.000000e+00 4019.0
12 TraesCS5D01G140100 chr3B 87.433 2594 311 11 4099 6685 9911722 9909137 0.000000e+00 2970.0
13 TraesCS5D01G140100 chr3B 81.338 1854 319 25 819 2658 54859033 54860873 0.000000e+00 1482.0
14 TraesCS5D01G140100 chr1A 96.481 3240 107 7 3648 6883 471704888 471708124 0.000000e+00 5345.0
15 TraesCS5D01G140100 chr1A 88.556 2700 303 6 2501 5198 168563178 168565873 0.000000e+00 3269.0
16 TraesCS5D01G140100 chr1A 88.015 1602 182 8 5285 6883 168565871 168567465 0.000000e+00 1886.0
17 TraesCS5D01G140100 chr1A 89.011 1456 152 7 5431 6882 554076594 554078045 0.000000e+00 1796.0
18 TraesCS5D01G140100 chr1A 85.988 1670 213 12 806 2470 168561523 168563176 0.000000e+00 1768.0
19 TraesCS5D01G140100 chr1A 71.121 1347 365 22 4332 5666 3837010 3835676 2.070000e-80 311.0
20 TraesCS5D01G140100 chr2D 87.825 3885 432 29 3016 6889 417971875 417975729 0.000000e+00 4516.0
21 TraesCS5D01G140100 chr2D 86.094 1992 262 14 806 2789 417969897 417971881 0.000000e+00 2130.0
22 TraesCS5D01G140100 chr2D 85.057 261 34 4 7374 7631 400494418 400494676 2.120000e-65 261.0
23 TraesCS5D01G140100 chr1D 92.233 3180 226 12 3707 6883 486055671 486058832 0.000000e+00 4484.0
24 TraesCS5D01G140100 chr1D 91.356 2765 227 9 794 3558 486046200 486048952 0.000000e+00 3771.0
25 TraesCS5D01G140100 chr1D 97.250 800 14 7 1 793 402769086 402769884 0.000000e+00 1349.0
26 TraesCS5D01G140100 chr1D 97.132 802 14 5 1 793 416384018 416383217 0.000000e+00 1345.0
27 TraesCS5D01G140100 chr1D 97.132 802 11 10 1 793 354790838 354790040 0.000000e+00 1343.0
28 TraesCS5D01G140100 chr5A 87.003 2439 296 20 4455 6883 241748586 241746159 0.000000e+00 2728.0
29 TraesCS5D01G140100 chr6B 79.165 3043 603 28 3095 6122 677797738 677794712 0.000000e+00 2078.0
30 TraesCS5D01G140100 chr6B 75.979 2298 502 42 827 3099 678060533 678058261 0.000000e+00 1140.0
31 TraesCS5D01G140100 chr2B 78.762 3037 616 26 2344 5367 78406876 78409896 0.000000e+00 2008.0
32 TraesCS5D01G140100 chr2B 83.271 269 41 3 7367 7631 162862295 162862563 2.130000e-60 244.0
33 TraesCS5D01G140100 chrUn 97.132 802 11 10 1 793 396263637 396262839 0.000000e+00 1343.0
34 TraesCS5D01G140100 chr3D 97.132 802 11 10 1 793 403336161 403336959 0.000000e+00 1343.0
35 TraesCS5D01G140100 chr3D 97.011 803 14 6 1 793 482217611 482218413 0.000000e+00 1341.0
36 TraesCS5D01G140100 chr3D 82.900 269 42 3 7366 7631 402499937 402499670 9.910000e-59 239.0
37 TraesCS5D01G140100 chr4D 97.233 795 15 5 1 793 49534837 49535626 0.000000e+00 1339.0
38 TraesCS5D01G140100 chr4A 73.026 3737 891 102 2962 6642 620738331 620742006 0.000000e+00 1208.0
39 TraesCS5D01G140100 chr4A 84.701 268 30 10 7370 7631 537288269 537288531 2.740000e-64 257.0
40 TraesCS5D01G140100 chr5B 80.029 701 84 26 6876 7549 247667762 247668433 1.160000e-127 468.0
41 TraesCS5D01G140100 chr7B 86.719 256 33 1 7375 7629 581805326 581805071 4.510000e-72 283.0
42 TraesCS5D01G140100 chr1B 84.231 260 39 2 7374 7631 526618530 526618789 1.270000e-62 252.0
43 TraesCS5D01G140100 chr1B 81.720 93 17 0 6876 6968 65552535 65552627 2.290000e-10 78.7
44 TraesCS5D01G140100 chr6D 83.784 259 40 2 7371 7627 381542425 381542683 2.130000e-60 244.0
45 TraesCS5D01G140100 chr6A 83.209 268 41 3 7367 7631 414261019 414261285 7.660000e-60 243.0


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 TraesCS5D01G140100 chr5D 223870261 223877902 7641 True 14113.000000 14113 100.000000 1 7642 1 chr5D.!!$R1 7641
1 TraesCS5D01G140100 chr5D 277271966 277276892 4926 False 4841.000000 4841 84.457000 822 5744 1 chr5D.!!$F2 4922
2 TraesCS5D01G140100 chr5D 223884144 223884943 799 True 1387.000000 1387 98.125000 1 793 1 chr5D.!!$R2 792
3 TraesCS5D01G140100 chr5D 223327310 223328111 801 False 1343.000000 1343 97.011000 1 796 1 chr5D.!!$F1 795
4 TraesCS5D01G140100 chr5D 348393119 348395721 2602 False 484.500000 645 75.429000 826 3404 2 chr5D.!!$F4 2578
5 TraesCS5D01G140100 chr7D 498244537 498250602 6065 True 8576.000000 8576 92.155000 794 6883 1 chr7D.!!$R2 6089
6 TraesCS5D01G140100 chr7D 3203195 3207368 4173 True 4542.000000 4542 86.274000 1808 6043 1 chr7D.!!$R1 4235
7 TraesCS5D01G140100 chr3B 733082688 733088521 5833 True 6364.000000 6364 86.432000 983 6822 1 chr3B.!!$R2 5839
8 TraesCS5D01G140100 chr3B 9909137 9911722 2585 True 2970.000000 2970 87.433000 4099 6685 1 chr3B.!!$R1 2586
9 TraesCS5D01G140100 chr3B 54859033 54865046 6013 False 2750.500000 4019 82.712500 819 6881 2 chr3B.!!$F1 6062
10 TraesCS5D01G140100 chr1A 471704888 471708124 3236 False 5345.000000 5345 96.481000 3648 6883 1 chr1A.!!$F1 3235
11 TraesCS5D01G140100 chr1A 168561523 168567465 5942 False 2307.666667 3269 87.519667 806 6883 3 chr1A.!!$F3 6077
12 TraesCS5D01G140100 chr1A 554076594 554078045 1451 False 1796.000000 1796 89.011000 5431 6882 1 chr1A.!!$F2 1451
13 TraesCS5D01G140100 chr1A 3835676 3837010 1334 True 311.000000 311 71.121000 4332 5666 1 chr1A.!!$R1 1334
14 TraesCS5D01G140100 chr2D 417969897 417975729 5832 False 3323.000000 4516 86.959500 806 6889 2 chr2D.!!$F2 6083
15 TraesCS5D01G140100 chr1D 486055671 486058832 3161 False 4484.000000 4484 92.233000 3707 6883 1 chr1D.!!$F3 3176
16 TraesCS5D01G140100 chr1D 486046200 486048952 2752 False 3771.000000 3771 91.356000 794 3558 1 chr1D.!!$F2 2764
17 TraesCS5D01G140100 chr1D 402769086 402769884 798 False 1349.000000 1349 97.250000 1 793 1 chr1D.!!$F1 792
18 TraesCS5D01G140100 chr1D 416383217 416384018 801 True 1345.000000 1345 97.132000 1 793 1 chr1D.!!$R2 792
19 TraesCS5D01G140100 chr1D 354790040 354790838 798 True 1343.000000 1343 97.132000 1 793 1 chr1D.!!$R1 792
20 TraesCS5D01G140100 chr5A 241746159 241748586 2427 True 2728.000000 2728 87.003000 4455 6883 1 chr5A.!!$R1 2428
21 TraesCS5D01G140100 chr6B 677794712 677797738 3026 True 2078.000000 2078 79.165000 3095 6122 1 chr6B.!!$R1 3027
22 TraesCS5D01G140100 chr6B 678058261 678060533 2272 True 1140.000000 1140 75.979000 827 3099 1 chr6B.!!$R2 2272
23 TraesCS5D01G140100 chr2B 78406876 78409896 3020 False 2008.000000 2008 78.762000 2344 5367 1 chr2B.!!$F1 3023
24 TraesCS5D01G140100 chrUn 396262839 396263637 798 True 1343.000000 1343 97.132000 1 793 1 chrUn.!!$R1 792
25 TraesCS5D01G140100 chr3D 403336161 403336959 798 False 1343.000000 1343 97.132000 1 793 1 chr3D.!!$F1 792
26 TraesCS5D01G140100 chr3D 482217611 482218413 802 False 1341.000000 1341 97.011000 1 793 1 chr3D.!!$F2 792
27 TraesCS5D01G140100 chr4D 49534837 49535626 789 False 1339.000000 1339 97.233000 1 793 1 chr4D.!!$F1 792
28 TraesCS5D01G140100 chr4A 620738331 620742006 3675 False 1208.000000 1208 73.026000 2962 6642 1 chr4A.!!$F2 3680
29 TraesCS5D01G140100 chr5B 247667762 247668433 671 False 468.000000 468 80.029000 6876 7549 1 chr5B.!!$F1 673

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
804 820 1.131303 TCCCAACACTTCCATCCCGT 61.131 55.000 0.00 0.0 0.00 5.28 F
1341 1366 0.650512 ACAACGTGAACAACTGCTCG 59.349 50.000 0.00 0.0 0.00 5.03 F
2279 2334 1.216990 GGGGAGGAGTGTTCCATGAT 58.783 55.000 0.00 0.0 46.64 2.45 F
2619 2675 2.126882 ACTAGGCTGCATGGGAATGTA 58.873 47.619 0.50 0.0 0.00 2.29 F
3161 3236 2.902608 TCTGAGGGTTTCCTTAGAGCA 58.097 47.619 3.23 0.0 46.79 4.26 F
4517 4604 5.633830 TCAGACTCAATTTTGCCTTGATC 57.366 39.130 0.00 0.0 32.50 2.92 F
4966 5055 1.062505 AGGGGATCCTCACTCTCCTTC 60.063 57.143 15.83 0.0 40.95 3.46 F
5745 5958 2.525105 TCTATTGGGGAAAACCTGGC 57.475 50.000 0.00 0.0 40.03 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2518 2574 1.087501 GATCTTGCTTGGTCCGGAAC 58.912 55.000 14.24 14.24 0.00 3.62 R
2916 2972 1.604593 AGTGCCAACTGATGCCACC 60.605 57.895 0.00 0.00 34.48 4.61 R
3350 3429 0.606604 TCTTGAACTCACGGTAGGCC 59.393 55.000 0.00 0.00 0.00 5.19 R
4517 4604 1.616994 GGAGTTTTGGGGATGAGGGTG 60.617 57.143 0.00 0.00 0.00 4.61 R
4966 5055 2.886523 TCAGCCACCAAATTGAAGAGTG 59.113 45.455 0.00 0.00 0.00 3.51 R
6040 6253 0.985490 GGAGAGTCTGGGGCAATCCT 60.985 60.000 0.00 0.00 35.33 3.24 R
6236 6450 1.004044 CCACATGTCTCCTCTTGGCTT 59.996 52.381 0.00 0.00 0.00 4.35 R
7297 7546 0.041090 AGGAATTGGCGGGGAACAAT 59.959 50.000 0.00 0.00 38.85 2.71 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 97 1.529713 GGCCACCGGGAAAGTTTCA 60.530 57.895 17.16 0.00 35.59 2.69
804 820 1.131303 TCCCAACACTTCCATCCCGT 61.131 55.000 0.00 0.00 0.00 5.28
815 831 5.523916 CACTTCCATCCCGTAAAACTGATAG 59.476 44.000 0.00 0.00 0.00 2.08
817 833 2.800544 CCATCCCGTAAAACTGATAGCG 59.199 50.000 0.00 0.00 0.00 4.26
845 861 4.095483 CGGATTCCTTTGTTGGATTCAGAG 59.905 45.833 0.30 0.00 37.90 3.35
1089 1111 1.561769 CCCTGGGTGCTGGTGTATCA 61.562 60.000 3.97 0.00 0.00 2.15
1197 1222 7.065085 CAGGTTCAATCGTCTCAAGTTAATGAT 59.935 37.037 0.00 0.00 0.00 2.45
1266 1291 1.063070 TTAACTGTGGTGGCCCTGGA 61.063 55.000 0.00 0.00 0.00 3.86
1291 1316 7.630082 ACACTATGTGGGTAATTGTGTTAGAT 58.370 34.615 2.72 0.00 39.78 1.98
1294 1319 8.204836 ACTATGTGGGTAATTGTGTTAGATCTC 58.795 37.037 0.00 0.00 0.00 2.75
1326 1351 1.327303 TCTGCCAACAATCCCACAAC 58.673 50.000 0.00 0.00 0.00 3.32
1341 1366 0.650512 ACAACGTGAACAACTGCTCG 59.349 50.000 0.00 0.00 0.00 5.03
1371 1396 3.730761 GTTCAGCCCACTGCAGCG 61.731 66.667 15.27 3.57 44.10 5.18
1374 1399 2.358615 CAGCCCACTGCAGCGTTA 60.359 61.111 15.27 0.00 44.83 3.18
1419 1444 3.118261 TGGGCTTCTATCATGTTGAGGTC 60.118 47.826 0.00 0.00 0.00 3.85
1423 1448 4.345257 GCTTCTATCATGTTGAGGTCCCTA 59.655 45.833 0.00 0.00 0.00 3.53
1435 1460 3.217626 GAGGTCCCTATGGCAAATGAAG 58.782 50.000 0.00 0.00 0.00 3.02
1473 1498 4.735369 TCCAGAATTGTGGTGTGGTTAAT 58.265 39.130 20.27 0.00 38.88 1.40
1536 1561 4.818534 TCTGACTGCTACTTTTTGCAAG 57.181 40.909 0.00 0.00 38.81 4.01
1545 1570 1.683385 ACTTTTTGCAAGACCAGAGCC 59.317 47.619 0.00 0.00 0.00 4.70
1795 1820 3.072768 ACAAATTGCATCCATGTTTGGGT 59.927 39.130 7.39 0.00 43.81 4.51
1810 1835 2.363306 TGGGTTGCTCACTGATGTTT 57.637 45.000 0.00 0.00 0.00 2.83
1876 1902 3.648507 AGATTGCTTGCAGAGATCCTT 57.351 42.857 0.00 0.00 0.00 3.36
2074 2100 7.655521 ACCAAGAACAATGATGATGATGAAT 57.344 32.000 0.00 0.00 0.00 2.57
2238 2293 4.861102 ATGCCTCTCAAACAAAAGGAAG 57.139 40.909 0.00 0.00 0.00 3.46
2239 2294 3.631250 TGCCTCTCAAACAAAAGGAAGT 58.369 40.909 0.00 0.00 0.00 3.01
2267 2322 1.381867 AATGGTGTGAATGGGGAGGA 58.618 50.000 0.00 0.00 0.00 3.71
2279 2334 1.216990 GGGGAGGAGTGTTCCATGAT 58.783 55.000 0.00 0.00 46.64 2.45
2367 2422 6.118170 AGATGATGATGGTAACCAAAGTGAG 58.882 40.000 0.00 0.00 36.95 3.51
2494 2550 6.291377 ACAGTTCAGAAAATGCAAGAGTCTA 58.709 36.000 0.00 0.00 33.83 2.59
2518 2574 7.141100 AGTATAAAACGTTCATTGTTGGAGG 57.859 36.000 0.00 0.00 0.00 4.30
2619 2675 2.126882 ACTAGGCTGCATGGGAATGTA 58.873 47.619 0.50 0.00 0.00 2.29
2721 2777 5.011533 CCCTACCAATGATTCTACTCTCCTG 59.988 48.000 0.00 0.00 0.00 3.86
2746 2802 4.150897 AGTCAAGCTGTTCAAGTTGGTA 57.849 40.909 2.34 0.00 0.00 3.25
2750 2806 4.887071 TCAAGCTGTTCAAGTTGGTATTGT 59.113 37.500 2.34 0.00 0.00 2.71
2851 2907 8.469200 CCTTTGCTAATGATGAACCTGAAATAA 58.531 33.333 0.00 0.00 0.00 1.40
3040 3099 7.187824 TGATAGGGCTCATCTGGAATATTAC 57.812 40.000 0.00 0.00 0.00 1.89
3050 3109 9.160496 CTCATCTGGAATATTACAGGATTAAGC 57.840 37.037 24.54 0.00 39.66 3.09
3053 3112 9.866655 ATCTGGAATATTACAGGATTAAGCAAA 57.133 29.630 24.54 4.60 39.66 3.68
3161 3236 2.902608 TCTGAGGGTTTCCTTAGAGCA 58.097 47.619 3.23 0.00 46.79 4.26
3350 3429 5.751680 CATTTGGTCATAGTTTATGGCTCG 58.248 41.667 1.27 0.00 40.53 5.03
3405 3484 6.792326 TCTGAGCTGCATGATATTTTTGAAG 58.208 36.000 1.02 0.00 0.00 3.02
4517 4604 5.633830 TCAGACTCAATTTTGCCTTGATC 57.366 39.130 0.00 0.00 32.50 2.92
4646 4734 9.660180 AGAGTTTCTCCTTTATGTGATAAACTC 57.340 33.333 16.39 16.39 45.48 3.01
4966 5055 1.062505 AGGGGATCCTCACTCTCCTTC 60.063 57.143 15.83 0.00 40.95 3.46
4982 5071 5.065914 TCTCCTTCACTCTTCAATTTGGTG 58.934 41.667 0.00 0.00 0.00 4.17
5220 5406 5.618236 AGTGATCTCCATACCATCAATGTG 58.382 41.667 0.00 0.00 0.00 3.21
5224 5410 2.882761 CTCCATACCATCAATGTGCCTG 59.117 50.000 0.00 0.00 0.00 4.85
5265 5451 4.057406 TGCCCAAATTTTCTGTTGTCAG 57.943 40.909 0.00 0.00 42.54 3.51
5435 5625 4.019860 CCTCCTTACTACATGCATAGCCAT 60.020 45.833 0.00 0.00 0.00 4.40
5439 5629 6.440328 TCCTTACTACATGCATAGCCATCATA 59.560 38.462 0.00 0.00 0.00 2.15
5443 5633 5.721480 ACTACATGCATAGCCATCATACCTA 59.279 40.000 0.00 0.00 0.00 3.08
5745 5958 2.525105 TCTATTGGGGAAAACCTGGC 57.475 50.000 0.00 0.00 40.03 4.85
6013 6226 7.042523 GCATTATGGAAAAATGGTATGAGTTGC 60.043 37.037 0.00 0.00 35.34 4.17
6040 6253 9.413734 GTGAGATAGTTAGTAACTTTACCCCTA 57.586 37.037 20.28 0.78 42.81 3.53
6236 6450 9.755804 CAATAAGTGCTTGACTAGAGATAATCA 57.244 33.333 0.00 0.00 33.09 2.57
6410 6624 3.381272 TCCTTGTCTGCTTTGTGGAAAAG 59.619 43.478 0.00 0.00 0.00 2.27
6487 6703 1.922545 GGCTTCTGCGCAATGAATTTC 59.077 47.619 13.05 4.94 40.82 2.17
6661 6877 7.181665 TGCTTAGAATAGCTTGGGAGATATGAT 59.818 37.037 0.00 0.00 41.76 2.45
6765 6986 2.501261 GGGTAGTTCGCTTTGTCCTTT 58.499 47.619 0.00 0.00 0.00 3.11
6933 7156 6.015688 GTCATTCTGGGCATCATATTTGACAT 60.016 38.462 0.00 0.00 33.85 3.06
6947 7170 9.806203 TCATATTTGACATGCTTAAAAATCCAG 57.194 29.630 0.00 0.00 0.00 3.86
6948 7171 9.590451 CATATTTGACATGCTTAAAAATCCAGT 57.410 29.630 0.00 0.00 0.00 4.00
6952 7175 5.534278 TGACATGCTTAAAAATCCAGTGTCA 59.466 36.000 0.00 0.00 40.51 3.58
6953 7176 6.040278 TGACATGCTTAAAAATCCAGTGTCAA 59.960 34.615 0.00 0.00 40.03 3.18
6989 7213 7.893658 TCCCGATAGAAATTAGAGGTCATTAC 58.106 38.462 0.00 0.00 39.76 1.89
6992 7216 7.038941 CCGATAGAAATTAGAGGTCATTACCCT 60.039 40.741 0.00 0.00 43.42 4.34
7027 7254 1.375853 GCATGTTCATGCGGCACCTA 61.376 55.000 19.50 0.00 37.84 3.08
7031 7258 1.957177 TGTTCATGCGGCACCTAAAAA 59.043 42.857 4.03 0.00 0.00 1.94
7054 7281 7.972832 AAAATCAGTGTTAACCGTTAGATGA 57.027 32.000 2.48 0.00 0.00 2.92
7055 7282 6.963049 AATCAGTGTTAACCGTTAGATGAC 57.037 37.500 2.48 0.00 0.00 3.06
7056 7283 4.813027 TCAGTGTTAACCGTTAGATGACC 58.187 43.478 2.48 0.00 0.00 4.02
7057 7284 4.281435 TCAGTGTTAACCGTTAGATGACCA 59.719 41.667 2.48 0.00 0.00 4.02
7058 7285 5.046878 TCAGTGTTAACCGTTAGATGACCAT 60.047 40.000 2.48 0.00 0.00 3.55
7059 7286 6.153170 TCAGTGTTAACCGTTAGATGACCATA 59.847 38.462 2.48 0.00 0.00 2.74
7085 7312 1.069906 GTCAAGATCGTGTGTGCAACC 60.070 52.381 8.54 0.00 34.36 3.77
7096 7323 1.197721 GTGTGCAACCATTCCTCTTCG 59.802 52.381 0.00 0.00 34.36 3.79
7163 7391 1.689582 CTCCCTTAGCCTTCCCCGT 60.690 63.158 0.00 0.00 0.00 5.28
7164 7392 0.398098 CTCCCTTAGCCTTCCCCGTA 60.398 60.000 0.00 0.00 0.00 4.02
7168 7396 1.192428 CTTAGCCTTCCCCGTAGTGT 58.808 55.000 0.00 0.00 0.00 3.55
7181 7430 1.402984 CGTAGTGTTGCCTCAGGTCTC 60.403 57.143 0.00 0.00 0.00 3.36
7242 7491 1.681780 CGCACCCTGGACCATTAACAT 60.682 52.381 0.00 0.00 0.00 2.71
7260 7509 0.842030 ATCTGACTTGCCTCCACCCA 60.842 55.000 0.00 0.00 0.00 4.51
7294 7543 2.560981 GAGCTCCCTTATCTCTGGCTAC 59.439 54.545 0.87 0.00 0.00 3.58
7295 7544 2.091055 AGCTCCCTTATCTCTGGCTACA 60.091 50.000 0.00 0.00 0.00 2.74
7297 7546 3.134804 GCTCCCTTATCTCTGGCTACAAA 59.865 47.826 0.00 0.00 0.00 2.83
7299 7548 5.688766 GCTCCCTTATCTCTGGCTACAAATT 60.689 44.000 0.00 0.00 0.00 1.82
7307 7556 1.472480 CTGGCTACAAATTGTTCCCCG 59.528 52.381 3.17 0.00 0.00 5.73
7312 7561 1.347062 ACAAATTGTTCCCCGCCAAT 58.653 45.000 0.00 0.00 32.83 3.16
7313 7562 1.696884 ACAAATTGTTCCCCGCCAATT 59.303 42.857 0.00 0.00 41.69 2.32
7320 7569 3.420482 CCCCGCCAATTCCTCCCT 61.420 66.667 0.00 0.00 0.00 4.20
7321 7570 2.124151 CCCGCCAATTCCTCCCTG 60.124 66.667 0.00 0.00 0.00 4.45
7322 7571 2.124151 CCGCCAATTCCTCCCTGG 60.124 66.667 0.00 0.00 37.10 4.45
7328 7577 1.616994 CCAATTCCTCCCTGGTGTTCC 60.617 57.143 0.00 0.00 37.07 3.62
7329 7578 0.704664 AATTCCTCCCTGGTGTTCCC 59.295 55.000 0.00 0.00 37.07 3.97
7331 7580 3.717294 CCTCCCTGGTGTTCCCGG 61.717 72.222 0.00 0.00 39.59 5.73
7341 7590 4.525949 GTTCCCGGGCCTCGCTAC 62.526 72.222 18.49 0.79 37.59 3.58
7352 7601 1.719425 CTCGCTACGCTCGATCACG 60.719 63.158 0.00 1.61 41.26 4.35
7359 7608 0.782384 ACGCTCGATCACGTTTTCAC 59.218 50.000 2.82 0.00 40.09 3.18
7378 7627 1.674611 CGTGTCTAGAGCGCGTTTGG 61.675 60.000 8.43 0.00 35.44 3.28
7381 7630 0.438830 GTCTAGAGCGCGTTTGGTTG 59.561 55.000 8.43 0.00 0.00 3.77
7399 7648 3.486383 GTTGACATCTCTGTTTTGGGGA 58.514 45.455 0.00 0.00 35.14 4.81
7405 7654 5.857268 ACATCTCTGTTTTGGGGAATTTTG 58.143 37.500 0.00 0.00 28.70 2.44
7414 7663 5.559148 TTTGGGGAATTTTGCATACTTGT 57.441 34.783 0.00 0.00 0.00 3.16
7418 7667 3.513515 GGGAATTTTGCATACTTGTCCCA 59.486 43.478 13.14 0.00 42.63 4.37
7434 7683 2.819477 CCAGTTGGGCCTGTTTGAA 58.181 52.632 4.53 0.00 0.00 2.69
7439 7688 3.383185 CAGTTGGGCCTGTTTGAACTAAA 59.617 43.478 4.53 0.00 0.00 1.85
7441 7690 3.306472 TGGGCCTGTTTGAACTAAAGT 57.694 42.857 4.53 0.00 0.00 2.66
7442 7691 3.219281 TGGGCCTGTTTGAACTAAAGTC 58.781 45.455 4.53 0.00 0.00 3.01
7443 7692 2.225727 GGGCCTGTTTGAACTAAAGTCG 59.774 50.000 0.84 0.00 0.00 4.18
7445 7694 2.350484 GCCTGTTTGAACTAAAGTCGGC 60.350 50.000 0.00 0.00 32.47 5.54
7451 7700 7.086230 TGTTTGAACTAAAGTCGGCTAAAAA 57.914 32.000 0.00 0.00 0.00 1.94
7455 7704 5.589452 TGAACTAAAGTCGGCTAAAAACCAA 59.411 36.000 0.00 0.00 0.00 3.67
7456 7705 5.428496 ACTAAAGTCGGCTAAAAACCAAC 57.572 39.130 0.00 0.00 0.00 3.77
7457 7706 4.883006 ACTAAAGTCGGCTAAAAACCAACA 59.117 37.500 0.00 0.00 0.00 3.33
7458 7707 4.929819 AAAGTCGGCTAAAAACCAACAT 57.070 36.364 0.00 0.00 0.00 2.71
7459 7708 4.499037 AAGTCGGCTAAAAACCAACATC 57.501 40.909 0.00 0.00 0.00 3.06
7460 7709 3.751518 AGTCGGCTAAAAACCAACATCT 58.248 40.909 0.00 0.00 0.00 2.90
7461 7710 4.901868 AGTCGGCTAAAAACCAACATCTA 58.098 39.130 0.00 0.00 0.00 1.98
7462 7711 4.694037 AGTCGGCTAAAAACCAACATCTAC 59.306 41.667 0.00 0.00 0.00 2.59
7463 7712 4.453136 GTCGGCTAAAAACCAACATCTACA 59.547 41.667 0.00 0.00 0.00 2.74
7464 7713 5.123344 GTCGGCTAAAAACCAACATCTACAT 59.877 40.000 0.00 0.00 0.00 2.29
7465 7714 5.123186 TCGGCTAAAAACCAACATCTACATG 59.877 40.000 0.00 0.00 35.92 3.21
7473 7722 8.458573 AAAACCAACATCTACATGTAGTTTGA 57.541 30.769 28.99 16.31 42.86 2.69
7478 7727 6.683974 ACATCTACATGTAGTTTGATTGCC 57.316 37.500 28.99 0.00 41.81 4.52
7517 7767 4.439289 GCATCAAGGAAGCAATTCTACCAC 60.439 45.833 0.00 0.00 0.00 4.16
7519 7769 3.074412 CAAGGAAGCAATTCTACCACGT 58.926 45.455 0.00 0.00 0.00 4.49
7525 7775 4.223320 AGCAATTCTACCACGTTGTTTG 57.777 40.909 0.00 0.00 0.00 2.93
7539 7789 2.515057 TTTGGTTGCCTGCGTCGT 60.515 55.556 0.00 0.00 0.00 4.34
7549 7799 1.493772 CCTGCGTCGTTGTTGTTAGA 58.506 50.000 0.00 0.00 0.00 2.10
7550 7800 2.066262 CCTGCGTCGTTGTTGTTAGAT 58.934 47.619 0.00 0.00 0.00 1.98
7551 7801 3.247442 CCTGCGTCGTTGTTGTTAGATA 58.753 45.455 0.00 0.00 0.00 1.98
7552 7802 3.676172 CCTGCGTCGTTGTTGTTAGATAA 59.324 43.478 0.00 0.00 0.00 1.75
7553 7803 4.150980 CCTGCGTCGTTGTTGTTAGATAAA 59.849 41.667 0.00 0.00 0.00 1.40
7554 7804 5.009048 TGCGTCGTTGTTGTTAGATAAAC 57.991 39.130 0.00 0.00 38.67 2.01
7555 7805 4.507021 TGCGTCGTTGTTGTTAGATAAACA 59.493 37.500 0.00 0.00 46.41 2.83
7575 7825 4.675190 CAACACATTGTTTGGTTGCAAA 57.325 36.364 0.00 0.00 38.77 3.68
7576 7826 4.401714 CAACACATTGTTTGGTTGCAAAC 58.598 39.130 7.78 7.78 42.04 2.93
7577 7827 3.124297 AACACATTGTTTGGTTGCAAACG 59.876 39.130 10.47 0.00 42.63 3.60
7578 7828 5.911013 AACACATTGTTTGGTTGCAAACGG 61.911 41.667 10.47 0.00 42.63 4.44
7591 7841 3.775661 GCAAACGGCATAAGGTGTTAT 57.224 42.857 0.00 0.00 43.97 1.89
7592 7842 3.691498 GCAAACGGCATAAGGTGTTATC 58.309 45.455 0.00 0.00 43.97 1.75
7593 7843 3.127895 GCAAACGGCATAAGGTGTTATCA 59.872 43.478 0.00 0.00 43.97 2.15
7594 7844 4.202010 GCAAACGGCATAAGGTGTTATCAT 60.202 41.667 0.00 0.00 43.97 2.45
7595 7845 5.510671 CAAACGGCATAAGGTGTTATCATC 58.489 41.667 0.00 0.00 0.00 2.92
7596 7846 4.415881 ACGGCATAAGGTGTTATCATCA 57.584 40.909 0.00 0.00 0.00 3.07
7597 7847 4.127171 ACGGCATAAGGTGTTATCATCAC 58.873 43.478 0.00 0.00 35.36 3.06
7598 7848 4.141711 ACGGCATAAGGTGTTATCATCACT 60.142 41.667 0.00 0.00 36.25 3.41
7599 7849 4.816385 CGGCATAAGGTGTTATCATCACTT 59.184 41.667 0.00 0.00 36.25 3.16
7600 7850 5.296780 CGGCATAAGGTGTTATCATCACTTT 59.703 40.000 0.00 0.00 38.35 2.66
7601 7851 6.183360 CGGCATAAGGTGTTATCATCACTTTT 60.183 38.462 0.00 0.00 36.69 2.27
7602 7852 7.196331 GGCATAAGGTGTTATCATCACTTTTC 58.804 38.462 0.00 0.00 36.69 2.29
7603 7853 7.148086 GGCATAAGGTGTTATCATCACTTTTCA 60.148 37.037 0.00 0.00 36.69 2.69
7604 7854 7.698130 GCATAAGGTGTTATCATCACTTTTCAC 59.302 37.037 0.00 0.00 36.69 3.18
7605 7855 8.950210 CATAAGGTGTTATCATCACTTTTCACT 58.050 33.333 0.00 0.00 36.69 3.41
7607 7857 7.907214 AGGTGTTATCATCACTTTTCACTAC 57.093 36.000 0.00 0.00 36.25 2.73
7608 7858 7.680730 AGGTGTTATCATCACTTTTCACTACT 58.319 34.615 0.00 0.00 36.25 2.57
7609 7859 7.604164 AGGTGTTATCATCACTTTTCACTACTG 59.396 37.037 0.00 0.00 36.25 2.74
7610 7860 7.148407 GGTGTTATCATCACTTTTCACTACTGG 60.148 40.741 0.00 0.00 36.25 4.00
7611 7861 7.387948 GTGTTATCATCACTTTTCACTACTGGT 59.612 37.037 0.00 0.00 33.59 4.00
7612 7862 7.387673 TGTTATCATCACTTTTCACTACTGGTG 59.612 37.037 0.00 0.00 46.60 4.17
7622 7872 0.893447 ACTACTGGTGACCTTACCGC 59.107 55.000 2.11 0.00 43.87 5.68
7623 7873 0.892755 CTACTGGTGACCTTACCGCA 59.107 55.000 2.11 0.00 43.87 5.69
7624 7874 0.604578 TACTGGTGACCTTACCGCAC 59.395 55.000 2.11 0.00 43.87 5.34
7625 7875 1.369692 CTGGTGACCTTACCGCACA 59.630 57.895 2.11 0.00 43.87 4.57
7626 7876 0.949105 CTGGTGACCTTACCGCACAC 60.949 60.000 2.11 0.00 43.87 3.82
7627 7877 1.070105 GGTGACCTTACCGCACACA 59.930 57.895 0.00 0.00 34.33 3.72
7628 7878 1.226030 GGTGACCTTACCGCACACAC 61.226 60.000 0.00 0.00 34.33 3.82
7629 7879 0.249741 GTGACCTTACCGCACACACT 60.250 55.000 0.00 0.00 32.96 3.55
7630 7880 0.249699 TGACCTTACCGCACACACTG 60.250 55.000 0.00 0.00 0.00 3.66
7631 7881 0.949105 GACCTTACCGCACACACTGG 60.949 60.000 0.00 0.00 0.00 4.00
7632 7882 1.070786 CCTTACCGCACACACTGGT 59.929 57.895 0.00 0.00 39.80 4.00
7633 7883 0.534203 CCTTACCGCACACACTGGTT 60.534 55.000 0.00 0.00 37.20 3.67
7634 7884 0.586319 CTTACCGCACACACTGGTTG 59.414 55.000 0.00 0.00 37.20 3.77
7635 7885 0.178301 TTACCGCACACACTGGTTGA 59.822 50.000 0.00 0.00 37.20 3.18
7636 7886 0.178301 TACCGCACACACTGGTTGAA 59.822 50.000 0.00 0.00 37.20 2.69
7637 7887 1.355210 CCGCACACACTGGTTGAAC 59.645 57.895 0.00 0.00 0.00 3.18
7638 7888 1.372838 CCGCACACACTGGTTGAACA 61.373 55.000 0.00 0.00 0.00 3.18
7639 7889 0.662619 CGCACACACTGGTTGAACAT 59.337 50.000 0.00 0.00 0.00 2.71
7640 7890 1.334059 CGCACACACTGGTTGAACATC 60.334 52.381 0.00 0.00 0.00 3.06
7641 7891 1.334059 GCACACACTGGTTGAACATCG 60.334 52.381 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.118679 GGTACAATACCGGTAACCCCT 58.881 52.381 20.22 0.00 39.39 4.79
392 403 0.825010 CCCAAGGCTGTCTGTTGCTT 60.825 55.000 0.00 0.00 0.00 3.91
804 820 1.647346 CGGTGGCGCTATCAGTTTTA 58.353 50.000 7.64 0.00 0.00 1.52
815 831 2.750237 AAAGGAATCCGGTGGCGC 60.750 61.111 0.00 0.00 0.00 6.53
817 833 0.243636 CAACAAAGGAATCCGGTGGC 59.756 55.000 0.00 0.00 0.00 5.01
845 861 5.860941 TGACCTATTCTCCACAAGATCTC 57.139 43.478 0.00 0.00 32.82 2.75
904 920 2.022718 TTTGGGGTGGGATCAAAAGG 57.977 50.000 0.00 0.00 0.00 3.11
1085 1107 6.096423 ACCAGTAGTATTCGTCTGCTTTGATA 59.904 38.462 0.00 0.00 0.00 2.15
1089 1111 4.803098 ACCAGTAGTATTCGTCTGCTTT 57.197 40.909 0.00 0.00 0.00 3.51
1197 1222 1.143684 AGAGGCTGCTCTTTTTCCACA 59.856 47.619 0.00 0.00 0.00 4.17
1266 1291 7.011499 TCTAACACAATTACCCACATAGTGT 57.989 36.000 0.00 0.00 40.10 3.55
1291 1316 4.397420 TGGCAGATAAAACAAGCTTGAGA 58.603 39.130 32.50 14.11 0.00 3.27
1294 1319 4.619973 TGTTGGCAGATAAAACAAGCTTG 58.380 39.130 24.84 24.84 31.16 4.01
1326 1351 1.498865 AAGCCGAGCAGTTGTTCACG 61.499 55.000 0.00 0.00 0.00 4.35
1341 1366 0.393132 GCTGAACCCTAGTCCAAGCC 60.393 60.000 0.00 0.00 0.00 4.35
1371 1396 3.689649 CACTAGCACCACTCCCAAATAAC 59.310 47.826 0.00 0.00 0.00 1.89
1374 1399 1.004745 CCACTAGCACCACTCCCAAAT 59.995 52.381 0.00 0.00 0.00 2.32
1473 1498 3.911260 TGTCCACTTCACCCTTGGTAATA 59.089 43.478 0.00 0.00 32.11 0.98
1545 1570 0.466922 CCCTAATCTGCCAAGGCCAG 60.467 60.000 5.01 6.43 41.09 4.85
1677 1702 3.307379 GTCACAAGACCCAGTCCAC 57.693 57.895 0.00 0.00 38.89 4.02
1698 1723 4.846779 TGCCTCAATAAGTTCACCAAAC 57.153 40.909 0.00 0.00 38.21 2.93
1795 1820 6.350361 CCATTCCAATAAACATCAGTGAGCAA 60.350 38.462 0.00 0.00 0.00 3.91
2074 2100 6.377712 TCAATGGCAGTGTCATAATCAATGAA 59.622 34.615 11.35 0.00 46.17 2.57
2083 2109 5.300411 AGATCATCAATGGCAGTGTCATA 57.700 39.130 11.35 0.00 0.00 2.15
2136 2162 5.514274 TTTTCCCAACAGAAGAACATGTC 57.486 39.130 0.00 0.00 0.00 3.06
2238 2293 4.511082 CCATTCACACCATTTTCACCAAAC 59.489 41.667 0.00 0.00 0.00 2.93
2239 2294 4.444022 CCCATTCACACCATTTTCACCAAA 60.444 41.667 0.00 0.00 0.00 3.28
2243 2298 2.896685 TCCCCATTCACACCATTTTCAC 59.103 45.455 0.00 0.00 0.00 3.18
2247 2302 1.715931 TCCTCCCCATTCACACCATTT 59.284 47.619 0.00 0.00 0.00 2.32
2267 2322 4.079958 GGGTACCCTTAATCATGGAACACT 60.080 45.833 24.75 0.00 44.52 3.55
2319 2374 6.062095 TCTCTTTAACCAAGTCTTTTCAGGG 58.938 40.000 0.00 0.00 33.66 4.45
2367 2422 5.725362 AGGTTCAAACAGTAGCTCATACTC 58.275 41.667 0.00 0.00 43.13 2.59
2424 2479 4.226846 TCCTCCTCTTCAGCATTTTCATCT 59.773 41.667 0.00 0.00 0.00 2.90
2494 2550 6.713450 ACCTCCAACAATGAACGTTTTATACT 59.287 34.615 0.46 0.00 0.00 2.12
2518 2574 1.087501 GATCTTGCTTGGTCCGGAAC 58.912 55.000 14.24 14.24 0.00 3.62
2619 2675 7.349598 ACTGGGCATCTTTCTTAATTATGTCT 58.650 34.615 0.00 0.00 0.00 3.41
2636 2692 6.753913 TCTTCTTCATCTTATACTGGGCAT 57.246 37.500 0.00 0.00 0.00 4.40
2817 2873 3.957591 TCATTAGCAAAGGCAATGCAA 57.042 38.095 7.79 8.81 46.22 4.08
2851 2907 9.686683 AGTTAGATCAATATTAACAGGCAAAGT 57.313 29.630 0.00 0.00 31.38 2.66
2916 2972 1.604593 AGTGCCAACTGATGCCACC 60.605 57.895 0.00 0.00 34.48 4.61
3040 3099 5.476945 ACTTTACCAGGTTTGCTTAATCCTG 59.523 40.000 0.00 9.22 44.74 3.86
3050 3109 3.243401 GGCACTGAACTTTACCAGGTTTG 60.243 47.826 0.00 0.00 34.85 2.93
3053 3112 1.774856 AGGCACTGAACTTTACCAGGT 59.225 47.619 0.00 0.00 37.18 4.00
3161 3236 4.373156 AAACAGCTTCTTACCATCCAGT 57.627 40.909 0.00 0.00 0.00 4.00
3350 3429 0.606604 TCTTGAACTCACGGTAGGCC 59.393 55.000 0.00 0.00 0.00 5.19
3405 3484 6.759497 AATCAAAACAGGATAAGTACTGGC 57.241 37.500 0.00 0.00 40.89 4.85
3970 4054 5.783111 CAAAATCACTAGGGGAAAGGTTTG 58.217 41.667 0.00 0.00 0.00 2.93
4517 4604 1.616994 GGAGTTTTGGGGATGAGGGTG 60.617 57.143 0.00 0.00 0.00 4.61
4646 4734 5.033589 AGGCAGTCTGATTAGAGGAAATG 57.966 43.478 3.32 0.00 32.48 2.32
4892 4980 5.360714 TGGCCCATTAGTTTCATTGATTCTC 59.639 40.000 0.00 0.00 0.00 2.87
4966 5055 2.886523 TCAGCCACCAAATTGAAGAGTG 59.113 45.455 0.00 0.00 0.00 3.51
4982 5071 3.679502 GCATTTTGGTAAACACATCAGCC 59.320 43.478 0.00 0.00 0.00 4.85
5098 5188 7.630242 TCCATAGAGTCTTGCAAAAATAAGG 57.370 36.000 0.00 0.00 0.00 2.69
5435 5625 6.432581 ACAGACATCAGGTAAGTAGGTATGA 58.567 40.000 0.00 0.00 0.00 2.15
5439 5629 6.895756 TCATAACAGACATCAGGTAAGTAGGT 59.104 38.462 0.00 0.00 0.00 3.08
5443 5633 9.167311 GAATTTCATAACAGACATCAGGTAAGT 57.833 33.333 0.00 0.00 0.00 2.24
5913 6126 4.342427 GCAATGGTGGCATCCTGA 57.658 55.556 0.00 0.00 0.00 3.86
6013 6226 7.067981 AGGGGTAAAGTTACTAACTATCTCACG 59.932 40.741 1.74 0.00 41.91 4.35
6040 6253 0.985490 GGAGAGTCTGGGGCAATCCT 60.985 60.000 0.00 0.00 35.33 3.24
6236 6450 1.004044 CCACATGTCTCCTCTTGGCTT 59.996 52.381 0.00 0.00 0.00 4.35
6313 6527 4.359434 TTTGACTGGCTACCACACAATA 57.641 40.909 0.00 0.00 0.00 1.90
6487 6703 1.067635 CCATTTTCGCCCCTGAAACAG 60.068 52.381 0.00 0.00 37.57 3.16
6661 6877 5.808366 AAGTTCTGGTAGTTCAGATCACA 57.192 39.130 0.00 0.00 42.57 3.58
6765 6986 3.616219 ACAACCAAAGTAGCTGTCACAA 58.384 40.909 0.00 0.00 0.00 3.33
6884 7107 6.838883 ACAAATTATGTTGTCACGAGCATGAC 60.839 38.462 0.00 8.41 40.06 3.06
6886 7109 5.393124 ACAAATTATGTTGTCACGAGCATG 58.607 37.500 0.00 0.00 40.06 4.06
6914 7137 3.572682 AGCATGTCAAATATGATGCCCAG 59.427 43.478 0.00 0.00 40.76 4.45
6915 7138 3.568443 AGCATGTCAAATATGATGCCCA 58.432 40.909 0.00 0.00 40.76 5.36
6933 7156 8.729805 AAAATTTGACACTGGATTTTTAAGCA 57.270 26.923 0.00 0.00 29.97 3.91
6944 7167 7.767261 TCGGGAATATTAAAATTTGACACTGG 58.233 34.615 0.00 0.00 0.00 4.00
6967 7191 7.897864 AGGGTAATGACCTCTAATTTCTATCG 58.102 38.462 0.00 0.00 46.09 2.92
7010 7237 1.832883 TTTAGGTGCCGCATGAACAT 58.167 45.000 0.00 0.00 0.00 2.71
7012 7239 2.715737 TTTTTAGGTGCCGCATGAAC 57.284 45.000 0.00 0.00 0.00 3.18
7031 7258 6.370718 GGTCATCTAACGGTTAACACTGATTT 59.629 38.462 8.10 0.00 32.93 2.17
7034 7261 4.281435 TGGTCATCTAACGGTTAACACTGA 59.719 41.667 8.10 0.00 32.93 3.41
7035 7262 4.562082 TGGTCATCTAACGGTTAACACTG 58.438 43.478 8.10 0.00 35.09 3.66
7037 7264 8.758715 GTTATATGGTCATCTAACGGTTAACAC 58.241 37.037 8.10 0.00 0.00 3.32
7038 7265 7.648908 CGTTATATGGTCATCTAACGGTTAACA 59.351 37.037 22.58 0.00 43.73 2.41
7054 7281 4.098960 ACACGATCTTGACCGTTATATGGT 59.901 41.667 6.16 0.00 40.99 3.55
7055 7282 4.444388 CACACGATCTTGACCGTTATATGG 59.556 45.833 6.16 0.00 0.00 2.74
7056 7283 5.041287 ACACACGATCTTGACCGTTATATG 58.959 41.667 6.16 0.00 0.00 1.78
7057 7284 5.041287 CACACACGATCTTGACCGTTATAT 58.959 41.667 6.16 0.00 0.00 0.86
7058 7285 4.417506 CACACACGATCTTGACCGTTATA 58.582 43.478 6.16 0.00 0.00 0.98
7059 7286 3.250744 CACACACGATCTTGACCGTTAT 58.749 45.455 6.16 0.00 0.00 1.89
7065 7292 1.069906 GGTTGCACACACGATCTTGAC 60.070 52.381 6.16 0.00 0.00 3.18
7066 7293 1.225855 GGTTGCACACACGATCTTGA 58.774 50.000 6.16 0.00 0.00 3.02
7074 7301 1.609208 AGAGGAATGGTTGCACACAC 58.391 50.000 0.00 0.00 0.00 3.82
7077 7304 1.071542 TCGAAGAGGAATGGTTGCACA 59.928 47.619 0.00 0.00 0.00 4.57
7085 7312 3.193263 CATGTGGAGTCGAAGAGGAATG 58.807 50.000 0.00 0.00 36.95 2.67
7096 7323 2.821366 CCGGCTGCATGTGGAGTC 60.821 66.667 0.50 0.00 35.78 3.36
7163 7391 0.888619 CGAGACCTGAGGCAACACTA 59.111 55.000 0.00 0.00 41.41 2.74
7164 7392 0.827925 TCGAGACCTGAGGCAACACT 60.828 55.000 0.00 0.00 41.41 3.55
7168 7396 1.471829 TTGCTCGAGACCTGAGGCAA 61.472 55.000 18.75 8.57 33.99 4.52
7220 7469 3.673956 TAATGGTCCAGGGTGCGCG 62.674 63.158 0.00 0.00 0.00 6.86
7221 7470 1.377987 TTAATGGTCCAGGGTGCGC 60.378 57.895 0.00 0.00 0.00 6.09
7231 7480 4.265073 AGGCAAGTCAGATGTTAATGGTC 58.735 43.478 0.00 0.00 0.00 4.02
7242 7491 1.059584 TTGGGTGGAGGCAAGTCAGA 61.060 55.000 0.00 0.00 0.00 3.27
7260 7509 3.308014 GAGCTCCCTGCAGCGTCTT 62.308 63.158 8.66 0.00 44.82 3.01
7282 7531 5.437060 GGGAACAATTTGTAGCCAGAGATA 58.563 41.667 17.89 0.00 29.61 1.98
7294 7543 2.345876 GAATTGGCGGGGAACAATTTG 58.654 47.619 0.00 0.00 44.68 2.32
7295 7544 1.277842 GGAATTGGCGGGGAACAATTT 59.722 47.619 0.00 0.00 44.68 1.82
7297 7546 0.041090 AGGAATTGGCGGGGAACAAT 59.959 50.000 0.00 0.00 38.85 2.71
7299 7548 1.001393 GAGGAATTGGCGGGGAACA 60.001 57.895 0.00 0.00 0.00 3.18
7307 7556 0.251787 AACACCAGGGAGGAATTGGC 60.252 55.000 0.00 0.00 41.22 4.52
7312 7561 2.221299 CGGGAACACCAGGGAGGAA 61.221 63.158 0.00 0.00 41.22 3.36
7313 7562 2.606519 CGGGAACACCAGGGAGGA 60.607 66.667 0.00 0.00 41.22 3.71
7341 7590 0.246374 CGTGAAAACGTGATCGAGCG 60.246 55.000 0.00 0.44 40.62 5.03
7352 7601 1.124477 GCGCTCTAGACACGTGAAAAC 59.876 52.381 25.01 10.33 0.00 2.43
7359 7608 1.674611 CCAAACGCGCTCTAGACACG 61.675 60.000 5.73 6.13 0.00 4.49
7362 7611 0.438830 CAACCAAACGCGCTCTAGAC 59.561 55.000 5.73 0.00 0.00 2.59
7363 7612 0.315886 TCAACCAAACGCGCTCTAGA 59.684 50.000 5.73 0.00 0.00 2.43
7368 7617 0.884704 AGATGTCAACCAAACGCGCT 60.885 50.000 5.73 0.00 0.00 5.92
7378 7627 3.486383 TCCCCAAAACAGAGATGTCAAC 58.514 45.455 0.00 0.00 0.00 3.18
7381 7630 5.728637 AAATTCCCCAAAACAGAGATGTC 57.271 39.130 0.00 0.00 0.00 3.06
7399 7648 5.511202 CCAACTGGGACAAGTATGCAAAATT 60.511 40.000 0.00 0.00 38.70 1.82
7418 7667 3.306472 TTAGTTCAAACAGGCCCAACT 57.694 42.857 0.00 1.03 0.00 3.16
7425 7674 3.139077 AGCCGACTTTAGTTCAAACAGG 58.861 45.455 0.00 0.00 0.00 4.00
7434 7683 4.883006 TGTTGGTTTTTAGCCGACTTTAGT 59.117 37.500 0.00 0.00 40.29 2.24
7439 7688 3.751518 AGATGTTGGTTTTTAGCCGACT 58.248 40.909 0.00 0.00 40.29 4.18
7441 7690 4.643463 TGTAGATGTTGGTTTTTAGCCGA 58.357 39.130 0.00 0.00 0.00 5.54
7442 7691 5.106317 ACATGTAGATGTTGGTTTTTAGCCG 60.106 40.000 0.00 0.00 40.05 5.52
7443 7692 6.267496 ACATGTAGATGTTGGTTTTTAGCC 57.733 37.500 0.00 0.00 40.05 3.93
7451 7700 7.362056 GCAATCAAACTACATGTAGATGTTGGT 60.362 37.037 34.16 25.64 40.05 3.67
7455 7704 6.317140 CAGGCAATCAAACTACATGTAGATGT 59.683 38.462 34.16 18.21 45.24 3.06
7456 7705 6.722301 CAGGCAATCAAACTACATGTAGATG 58.278 40.000 34.16 28.70 36.97 2.90
7457 7706 5.297776 GCAGGCAATCAAACTACATGTAGAT 59.702 40.000 34.16 22.81 36.97 1.98
7458 7707 4.635765 GCAGGCAATCAAACTACATGTAGA 59.364 41.667 34.16 16.08 36.97 2.59
7459 7708 4.395854 TGCAGGCAATCAAACTACATGTAG 59.604 41.667 27.66 27.66 39.04 2.74
7460 7709 4.331108 TGCAGGCAATCAAACTACATGTA 58.669 39.130 5.25 5.25 0.00 2.29
7461 7710 3.156293 TGCAGGCAATCAAACTACATGT 58.844 40.909 2.69 2.69 0.00 3.21
7462 7711 3.853831 TGCAGGCAATCAAACTACATG 57.146 42.857 0.00 0.00 0.00 3.21
7463 7712 5.068198 CCTAATGCAGGCAATCAAACTACAT 59.932 40.000 0.00 0.00 37.70 2.29
7464 7713 4.398988 CCTAATGCAGGCAATCAAACTACA 59.601 41.667 0.00 0.00 37.70 2.74
7465 7714 4.925068 CCTAATGCAGGCAATCAAACTAC 58.075 43.478 0.00 0.00 37.70 2.73
7478 7727 1.225426 TGCAGGGAGCCTAATGCAG 59.775 57.895 9.44 0.00 43.34 4.41
7490 7739 1.481871 ATTGCTTCCTTGATGCAGGG 58.518 50.000 0.00 0.00 42.14 4.45
7517 7767 1.943693 CGCAGGCAACCAAACAACG 60.944 57.895 0.00 0.00 37.17 4.10
7519 7769 1.435515 GACGCAGGCAACCAAACAA 59.564 52.632 0.00 0.00 37.17 2.83
7525 7775 2.830285 AACAACGACGCAGGCAACC 61.830 57.895 0.00 0.00 37.17 3.77
7554 7804 4.675190 TTTGCAACCAAACAATGTGTTG 57.325 36.364 0.00 9.77 40.14 3.33
7571 7821 3.127895 TGATAACACCTTATGCCGTTTGC 59.872 43.478 0.00 0.00 41.77 3.68
7572 7822 4.955925 TGATAACACCTTATGCCGTTTG 57.044 40.909 0.00 0.00 0.00 2.93
7573 7823 5.065988 GTGATGATAACACCTTATGCCGTTT 59.934 40.000 0.00 0.00 32.84 3.60
7574 7824 4.574828 GTGATGATAACACCTTATGCCGTT 59.425 41.667 0.00 0.00 32.84 4.44
7575 7825 4.127171 GTGATGATAACACCTTATGCCGT 58.873 43.478 0.00 0.00 32.84 5.68
7576 7826 4.380531 AGTGATGATAACACCTTATGCCG 58.619 43.478 0.00 0.00 38.82 5.69
7577 7827 6.699575 AAAGTGATGATAACACCTTATGCC 57.300 37.500 0.00 0.00 38.82 4.40
7578 7828 7.698130 GTGAAAAGTGATGATAACACCTTATGC 59.302 37.037 0.00 0.00 38.82 3.14
7579 7829 8.950210 AGTGAAAAGTGATGATAACACCTTATG 58.050 33.333 0.00 0.00 38.82 1.90
7581 7831 9.431887 GTAGTGAAAAGTGATGATAACACCTTA 57.568 33.333 0.00 0.00 38.82 2.69
7582 7832 8.157476 AGTAGTGAAAAGTGATGATAACACCTT 58.843 33.333 0.00 0.00 38.82 3.50
7583 7833 7.604164 CAGTAGTGAAAAGTGATGATAACACCT 59.396 37.037 0.00 0.00 38.82 4.00
7584 7834 7.148407 CCAGTAGTGAAAAGTGATGATAACACC 60.148 40.741 0.00 0.00 38.82 4.16
7585 7835 7.387948 ACCAGTAGTGAAAAGTGATGATAACAC 59.612 37.037 0.00 0.00 38.38 3.32
7586 7836 7.450074 ACCAGTAGTGAAAAGTGATGATAACA 58.550 34.615 0.00 0.00 0.00 2.41
7587 7837 7.907214 ACCAGTAGTGAAAAGTGATGATAAC 57.093 36.000 0.00 0.00 0.00 1.89
7603 7853 0.893447 GCGGTAAGGTCACCAGTAGT 59.107 55.000 0.00 0.00 38.61 2.73
7604 7854 0.892755 TGCGGTAAGGTCACCAGTAG 59.107 55.000 0.00 0.00 38.61 2.57
7605 7855 0.604578 GTGCGGTAAGGTCACCAGTA 59.395 55.000 0.00 0.00 38.61 2.74
7606 7856 1.370064 GTGCGGTAAGGTCACCAGT 59.630 57.895 0.00 0.00 38.61 4.00
7607 7857 0.949105 GTGTGCGGTAAGGTCACCAG 60.949 60.000 0.00 0.00 38.61 4.00
7608 7858 1.070105 GTGTGCGGTAAGGTCACCA 59.930 57.895 0.00 0.00 38.61 4.17
7609 7859 1.070105 TGTGTGCGGTAAGGTCACC 59.930 57.895 0.00 0.00 35.04 4.02
7610 7860 0.249741 AGTGTGTGCGGTAAGGTCAC 60.250 55.000 0.00 0.00 0.00 3.67
7611 7861 0.249699 CAGTGTGTGCGGTAAGGTCA 60.250 55.000 0.00 0.00 0.00 4.02
7612 7862 0.949105 CCAGTGTGTGCGGTAAGGTC 60.949 60.000 0.00 0.00 0.00 3.85
7613 7863 1.070786 CCAGTGTGTGCGGTAAGGT 59.929 57.895 0.00 0.00 0.00 3.50
7614 7864 0.534203 AACCAGTGTGTGCGGTAAGG 60.534 55.000 0.00 0.00 31.12 2.69
7615 7865 0.586319 CAACCAGTGTGTGCGGTAAG 59.414 55.000 0.00 0.00 31.12 2.34
7616 7866 0.178301 TCAACCAGTGTGTGCGGTAA 59.822 50.000 0.00 0.00 31.12 2.85
7617 7867 0.178301 TTCAACCAGTGTGTGCGGTA 59.822 50.000 0.00 0.00 31.12 4.02
7618 7868 1.078072 TTCAACCAGTGTGTGCGGT 60.078 52.632 0.00 0.00 33.32 5.68
7619 7869 1.355210 GTTCAACCAGTGTGTGCGG 59.645 57.895 0.00 0.00 0.00 5.69
7620 7870 0.662619 ATGTTCAACCAGTGTGTGCG 59.337 50.000 0.00 0.00 0.00 5.34
7621 7871 1.334059 CGATGTTCAACCAGTGTGTGC 60.334 52.381 0.00 0.00 0.00 4.57
7622 7872 2.668617 CGATGTTCAACCAGTGTGTG 57.331 50.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.