Multiple sequence alignment - TraesCS5B01G538500

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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 TraesCS5B01G538500 chr5B 100.000 3397 0 0 1 3397 693994295 693997691 0.000000e+00 6274.0
1 TraesCS5B01G538500 chr5B 82.915 398 51 6 18 414 522054279 522054660 3.250000e-90 342.0
2 TraesCS5B01G538500 chr5B 89.529 191 14 2 349 536 519188957 519188770 1.580000e-58 237.0
3 TraesCS5B01G538500 chr5B 88.268 179 13 4 226 404 55950587 55950417 1.240000e-49 207.0
4 TraesCS5B01G538500 chr5B 85.000 80 10 1 2625 2704 690974424 690974501 2.810000e-11 80.5
5 TraesCS5B01G538500 chr5D 91.374 1194 58 16 47 1235 559729594 559730747 0.000000e+00 1592.0
6 TraesCS5B01G538500 chr5D 89.124 947 49 18 2022 2948 559731551 559732463 0.000000e+00 1129.0
7 TraesCS5B01G538500 chr5D 90.667 375 25 2 1869 2235 339383306 339383678 1.100000e-134 490.0
8 TraesCS5B01G538500 chr5D 89.450 218 15 6 3180 3391 559732830 559733045 5.590000e-68 268.0
9 TraesCS5B01G538500 chr5D 94.400 125 6 1 3053 3176 559732668 559732792 1.240000e-44 191.0
10 TraesCS5B01G538500 chr5D 95.455 110 5 0 2948 3057 559732525 559732634 3.480000e-40 176.0
11 TraesCS5B01G538500 chr5D 93.023 43 3 0 2890 2932 559832649 559832691 2.830000e-06 63.9
12 TraesCS5B01G538500 chr6B 82.993 882 88 34 1394 2238 651365423 651364567 0.000000e+00 741.0
13 TraesCS5B01G538500 chr6B 80.304 1051 115 48 1248 2237 671658695 671659714 0.000000e+00 710.0
14 TraesCS5B01G538500 chr6B 82.293 881 96 32 1394 2238 76226571 76225715 0.000000e+00 708.0
15 TraesCS5B01G538500 chr6B 89.811 265 26 1 1812 2076 687274153 687273890 4.200000e-89 339.0
16 TraesCS5B01G538500 chr6B 93.478 92 6 0 1154 1245 46305749 46305840 1.640000e-28 137.0
17 TraesCS5B01G538500 chr6B 84.524 84 8 2 2626 2704 51734977 51735060 1.010000e-10 78.7
18 TraesCS5B01G538500 chr4A 86.039 659 58 16 1969 2610 613325171 613325812 0.000000e+00 676.0
19 TraesCS5B01G538500 chr4A 85.817 416 41 10 129 536 613321591 613321996 3.130000e-115 425.0
20 TraesCS5B01G538500 chr4A 83.071 508 30 24 737 1238 613322178 613322635 8.770000e-111 411.0
21 TraesCS5B01G538500 chr4A 83.929 392 41 13 3011 3392 613326224 613326603 4.170000e-94 355.0
22 TraesCS5B01G538500 chr4A 94.545 55 2 1 2813 2867 613325992 613326045 2.170000e-12 84.2
23 TraesCS5B01G538500 chr4A 83.333 84 10 2 2625 2704 80859928 80860011 1.310000e-09 75.0
24 TraesCS5B01G538500 chr3B 81.612 881 93 35 1394 2238 748486735 748487582 0.000000e+00 665.0
25 TraesCS5B01G538500 chr3B 84.399 641 56 26 1232 1844 745606 746230 1.050000e-164 590.0
26 TraesCS5B01G538500 chr3B 84.112 642 56 28 1232 1844 817687523 817688147 2.270000e-161 579.0
27 TraesCS5B01G538500 chr3B 84.119 636 55 28 1238 1844 817710684 817711302 1.060000e-159 573.0
28 TraesCS5B01G538500 chr3B 98.810 84 1 0 1152 1235 817687415 817687498 2.110000e-32 150.0
29 TraesCS5B01G538500 chr3B 97.619 84 2 0 1152 1235 745498 745581 9.820000e-31 145.0
30 TraesCS5B01G538500 chr3B 91.139 79 7 0 454 532 761144114 761144036 1.290000e-19 108.0
31 TraesCS5B01G538500 chr3B 88.608 79 9 0 454 532 761168479 761168401 2.790000e-16 97.1
32 TraesCS5B01G538500 chr3B 81.720 93 8 2 2620 2704 596858945 596859036 6.080000e-08 69.4
33 TraesCS5B01G538500 chr1A 85.179 641 51 27 1232 1844 236392191 236392815 4.820000e-173 617.0
34 TraesCS5B01G538500 chr6A 85.197 635 50 28 1238 1844 307921463 307920845 2.240000e-171 612.0
35 TraesCS5B01G538500 chr6A 97.619 84 2 0 1152 1235 307921577 307921494 9.820000e-31 145.0
36 TraesCS5B01G538500 chr6A 84.783 92 5 2 2621 2704 508000856 508000946 2.170000e-12 84.2
37 TraesCS5B01G538500 chr6A 83.696 92 6 2 2621 2704 349779822 349779912 1.010000e-10 78.7
38 TraesCS5B01G538500 chr7A 84.555 641 55 27 1232 1844 395514703 395515327 2.260000e-166 595.0
39 TraesCS5B01G538500 chr7A 81.232 714 88 29 1389 2076 125840706 125840013 4.990000e-148 534.0
40 TraesCS5B01G538500 chr7A 90.037 271 26 1 1806 2076 689071962 689072231 1.940000e-92 350.0
41 TraesCS5B01G538500 chr7A 88.930 271 29 1 1806 2076 721273802 721274071 1.950000e-87 333.0
42 TraesCS5B01G538500 chr7A 90.576 191 12 3 349 536 487486142 487485955 7.280000e-62 248.0
43 TraesCS5B01G538500 chr5A 84.399 641 56 27 1232 1844 213047937 213048561 1.050000e-164 590.0
44 TraesCS5B01G538500 chr5A 83.780 635 59 23 1238 1844 631068809 631068191 2.290000e-156 562.0
45 TraesCS5B01G538500 chr5A 88.889 171 12 1 244 414 168349739 168349576 1.600000e-48 204.0
46 TraesCS5B01G538500 chr5A 93.333 45 3 0 2663 2707 535020731 535020687 2.190000e-07 67.6
47 TraesCS5B01G538500 chr7B 84.399 641 55 28 1232 1844 681954202 681954825 3.780000e-164 588.0
48 TraesCS5B01G538500 chr7B 80.474 717 88 34 1389 2076 64580412 64579719 5.060000e-138 501.0
49 TraesCS5B01G538500 chr7B 90.052 191 13 2 349 536 336661919 336661732 3.390000e-60 243.0
50 TraesCS5B01G538500 chr7B 97.619 84 2 0 1152 1235 695575107 695575024 9.820000e-31 145.0
51 TraesCS5B01G538500 chr7B 91.139 79 6 1 454 532 644283911 644283834 4.640000e-19 106.0
52 TraesCS5B01G538500 chrUn 84.409 635 55 27 1238 1844 87514946 87514328 4.880000e-163 584.0
53 TraesCS5B01G538500 chrUn 85.948 427 36 14 1663 2076 306377660 306378075 5.210000e-118 435.0
54 TraesCS5B01G538500 chrUn 85.948 427 36 14 1663 2076 310664082 310663667 5.210000e-118 435.0
55 TraesCS5B01G538500 chr4B 84.385 634 55 27 1238 1843 636566355 636566972 1.760000e-162 582.0
56 TraesCS5B01G538500 chr4B 83.619 641 59 28 1232 1843 552797208 552797831 8.230000e-156 560.0
57 TraesCS5B01G538500 chr4B 97.619 84 2 0 1152 1235 552797100 552797183 9.820000e-31 145.0
58 TraesCS5B01G538500 chr4B 97.561 82 2 0 1152 1233 636566241 636566322 1.270000e-29 141.0
59 TraesCS5B01G538500 chr4B 88.889 99 5 4 295 387 16690006 16689908 2.140000e-22 117.0
60 TraesCS5B01G538500 chr7D 87.727 440 33 7 1806 2235 594651710 594652138 8.470000e-136 494.0
61 TraesCS5B01G538500 chr4D 87.528 441 33 10 1806 2235 332130507 332130936 1.100000e-134 490.0
62 TraesCS5B01G538500 chr4D 84.861 251 26 5 165 414 142309258 142309497 3.390000e-60 243.0
63 TraesCS5B01G538500 chr4D 93.617 47 0 2 2667 2713 101385920 101385963 2.190000e-07 67.6
64 TraesCS5B01G538500 chr6D 86.878 442 39 8 1806 2238 73253610 73253179 8.530000e-131 477.0
65 TraesCS5B01G538500 chr6D 80.208 96 11 1 2617 2704 65054555 65054650 7.870000e-07 65.8
66 TraesCS5B01G538500 chr2D 87.239 431 36 7 1806 2227 147702337 147702757 1.100000e-129 473.0
67 TraesCS5B01G538500 chr2A 90.683 322 19 7 1525 1845 290319798 290320109 5.240000e-113 418.0
68 TraesCS5B01G538500 chr2A 90.406 271 25 1 1806 2076 648543543 648543812 4.170000e-94 355.0
69 TraesCS5B01G538500 chr2A 89.811 265 26 1 1812 2076 539387641 539387378 4.200000e-89 339.0
70 TraesCS5B01G538500 chr2A 90.000 80 5 2 2625 2704 704774817 704774893 2.160000e-17 100.0
71 TraesCS5B01G538500 chr2A 84.783 92 6 3 2621 2704 235370960 235370869 6.040000e-13 86.1
72 TraesCS5B01G538500 chr1B 82.426 404 49 10 2 401 337425908 337426293 1.950000e-87 333.0
73 TraesCS5B01G538500 chr1B 80.542 406 60 8 2 404 600850170 600849781 9.220000e-76 294.0
74 TraesCS5B01G538500 chr1B 80.693 404 57 10 2 401 657829507 657829893 9.220000e-76 294.0
75 TraesCS5B01G538500 chr1B 95.349 43 2 0 2663 2705 374317171 374317213 6.080000e-08 69.4
76 TraesCS5B01G538500 chr1D 82.022 89 8 3 2625 2705 274943925 274944013 6.080000e-08 69.4


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 TraesCS5B01G538500 chr5B 693994295 693997691 3396 False 6274.00 6274 100.0000 1 3397 1 chr5B.!!$F3 3396
1 TraesCS5B01G538500 chr5D 559729594 559733045 3451 False 671.20 1592 91.9606 47 3391 5 chr5D.!!$F3 3344
2 TraesCS5B01G538500 chr6B 651364567 651365423 856 True 741.00 741 82.9930 1394 2238 1 chr6B.!!$R2 844
3 TraesCS5B01G538500 chr6B 671658695 671659714 1019 False 710.00 710 80.3040 1248 2237 1 chr6B.!!$F3 989
4 TraesCS5B01G538500 chr6B 76225715 76226571 856 True 708.00 708 82.2930 1394 2238 1 chr6B.!!$R1 844
5 TraesCS5B01G538500 chr4A 613321591 613326603 5012 False 390.24 676 86.6802 129 3392 5 chr4A.!!$F2 3263
6 TraesCS5B01G538500 chr3B 748486735 748487582 847 False 665.00 665 81.6120 1394 2238 1 chr3B.!!$F2 844
7 TraesCS5B01G538500 chr3B 817710684 817711302 618 False 573.00 573 84.1190 1238 1844 1 chr3B.!!$F3 606
8 TraesCS5B01G538500 chr3B 745498 746230 732 False 367.50 590 91.0090 1152 1844 2 chr3B.!!$F4 692
9 TraesCS5B01G538500 chr3B 817687415 817688147 732 False 364.50 579 91.4610 1152 1844 2 chr3B.!!$F5 692
10 TraesCS5B01G538500 chr1A 236392191 236392815 624 False 617.00 617 85.1790 1232 1844 1 chr1A.!!$F1 612
11 TraesCS5B01G538500 chr6A 307920845 307921577 732 True 378.50 612 91.4080 1152 1844 2 chr6A.!!$R1 692
12 TraesCS5B01G538500 chr7A 395514703 395515327 624 False 595.00 595 84.5550 1232 1844 1 chr7A.!!$F1 612
13 TraesCS5B01G538500 chr7A 125840013 125840706 693 True 534.00 534 81.2320 1389 2076 1 chr7A.!!$R1 687
14 TraesCS5B01G538500 chr5A 213047937 213048561 624 False 590.00 590 84.3990 1232 1844 1 chr5A.!!$F1 612
15 TraesCS5B01G538500 chr5A 631068191 631068809 618 True 562.00 562 83.7800 1238 1844 1 chr5A.!!$R3 606
16 TraesCS5B01G538500 chr7B 681954202 681954825 623 False 588.00 588 84.3990 1232 1844 1 chr7B.!!$F1 612
17 TraesCS5B01G538500 chr7B 64579719 64580412 693 True 501.00 501 80.4740 1389 2076 1 chr7B.!!$R1 687
18 TraesCS5B01G538500 chrUn 87514328 87514946 618 True 584.00 584 84.4090 1238 1844 1 chrUn.!!$R1 606
19 TraesCS5B01G538500 chr4B 636566241 636566972 731 False 361.50 582 90.9730 1152 1843 2 chr4B.!!$F2 691
20 TraesCS5B01G538500 chr4B 552797100 552797831 731 False 352.50 560 90.6190 1152 1843 2 chr4B.!!$F1 691

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
934 986 0.244994 CACTCACTCCTCGTCTTGGG 59.755 60.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 4852 0.256177 ATCCTCCTTTCCGGCCTTTC 59.744 55.0 0.0 0.0 0.0 2.62 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
20 21 3.584406 CAGAACTGACACTCTACAGGG 57.416 52.381 0.00 0.00 38.30 4.45
21 22 3.157881 CAGAACTGACACTCTACAGGGA 58.842 50.000 0.00 0.00 38.30 4.20
22 23 3.057174 CAGAACTGACACTCTACAGGGAC 60.057 52.174 0.00 0.00 38.30 4.46
23 24 2.982339 ACTGACACTCTACAGGGACT 57.018 50.000 0.00 0.00 43.88 3.85
24 25 4.043059 AGAACTGACACTCTACAGGGACTA 59.957 45.833 0.00 0.00 36.02 2.59
25 26 4.383931 ACTGACACTCTACAGGGACTAA 57.616 45.455 0.00 0.00 36.02 2.24
26 27 4.936802 ACTGACACTCTACAGGGACTAAT 58.063 43.478 0.00 0.00 36.02 1.73
27 28 6.075949 ACTGACACTCTACAGGGACTAATA 57.924 41.667 0.00 0.00 36.02 0.98
28 29 6.123651 ACTGACACTCTACAGGGACTAATAG 58.876 44.000 0.00 0.00 36.02 1.73
29 30 6.075949 TGACACTCTACAGGGACTAATAGT 57.924 41.667 0.00 0.00 36.02 2.12
30 31 6.120905 TGACACTCTACAGGGACTAATAGTC 58.879 44.000 11.79 11.79 44.32 2.59
31 32 6.075949 ACACTCTACAGGGACTAATAGTCA 57.924 41.667 20.57 0.51 46.79 3.41
32 33 6.123651 ACACTCTACAGGGACTAATAGTCAG 58.876 44.000 20.57 12.47 46.79 3.51
33 34 5.009210 CACTCTACAGGGACTAATAGTCAGC 59.991 48.000 20.57 5.58 46.79 4.26
34 35 5.125367 TCTACAGGGACTAATAGTCAGCA 57.875 43.478 20.57 2.03 46.79 4.41
35 36 5.133941 TCTACAGGGACTAATAGTCAGCAG 58.866 45.833 20.57 10.50 46.79 4.24
36 37 3.714144 ACAGGGACTAATAGTCAGCAGT 58.286 45.455 20.57 10.86 46.79 4.40
37 38 4.868268 ACAGGGACTAATAGTCAGCAGTA 58.132 43.478 20.57 0.00 46.79 2.74
38 39 5.459505 ACAGGGACTAATAGTCAGCAGTAT 58.540 41.667 20.57 0.00 46.79 2.12
39 40 5.900123 ACAGGGACTAATAGTCAGCAGTATT 59.100 40.000 20.57 0.00 46.79 1.89
40 41 6.384305 ACAGGGACTAATAGTCAGCAGTATTT 59.616 38.462 20.57 0.00 46.79 1.40
41 42 7.563924 ACAGGGACTAATAGTCAGCAGTATTTA 59.436 37.037 20.57 0.00 46.79 1.40
42 43 7.868415 CAGGGACTAATAGTCAGCAGTATTTAC 59.132 40.741 20.57 0.48 46.79 2.01
43 44 7.563924 AGGGACTAATAGTCAGCAGTATTTACA 59.436 37.037 20.57 0.00 46.79 2.41
44 45 7.652507 GGGACTAATAGTCAGCAGTATTTACAC 59.347 40.741 20.57 0.00 46.79 2.90
45 46 8.195436 GGACTAATAGTCAGCAGTATTTACACA 58.805 37.037 20.57 0.00 46.79 3.72
46 47 9.582431 GACTAATAGTCAGCAGTATTTACACAA 57.418 33.333 15.01 0.00 44.45 3.33
47 48 9.367444 ACTAATAGTCAGCAGTATTTACACAAC 57.633 33.333 0.00 0.00 31.59 3.32
48 49 9.366216 CTAATAGTCAGCAGTATTTACACAACA 57.634 33.333 0.00 0.00 31.59 3.33
85 86 7.538678 GCAGTATCTGATTCGAACAAACAAATT 59.461 33.333 0.00 0.00 32.44 1.82
89 90 5.914635 TCTGATTCGAACAAACAAATTGCTC 59.085 36.000 0.00 0.00 43.13 4.26
114 115 4.067896 ACAATCTCCAGTCACACATGTTC 58.932 43.478 0.00 0.00 0.00 3.18
172 174 3.329929 ACGGAAACCTGACTGAATACC 57.670 47.619 0.00 0.00 0.00 2.73
235 237 0.305313 TCGCACAAAAACGTGTAGGC 59.695 50.000 0.00 0.00 39.19 3.93
557 562 4.377708 ATCCGCGCTGCAGACACA 62.378 61.111 20.43 0.00 0.00 3.72
570 575 2.341257 CAGACACAGGATTCGACCAAG 58.659 52.381 0.00 0.00 0.00 3.61
641 689 1.320512 GTATTGAGGGGGAGGGGGA 59.679 63.158 0.00 0.00 0.00 4.81
642 690 0.768609 GTATTGAGGGGGAGGGGGAG 60.769 65.000 0.00 0.00 0.00 4.30
643 691 0.939443 TATTGAGGGGGAGGGGGAGA 60.939 60.000 0.00 0.00 0.00 3.71
644 692 2.277126 ATTGAGGGGGAGGGGGAGAG 62.277 65.000 0.00 0.00 0.00 3.20
645 693 4.179599 GAGGGGGAGGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
648 696 4.179599 GGGGAGGGGGAGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
649 697 3.036959 GGGAGGGGGAGAGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
650 698 2.612251 GGAGGGGGAGAGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
651 699 2.612251 GAGGGGGAGAGGGAGAGG 59.388 72.222 0.00 0.00 0.00 3.69
652 700 2.204705 AGGGGGAGAGGGAGAGGT 60.205 66.667 0.00 0.00 0.00 3.85
695 743 0.955919 GGAAGGGGCAAGTTCGTCAG 60.956 60.000 0.00 0.00 0.00 3.51
696 744 0.955919 GAAGGGGCAAGTTCGTCAGG 60.956 60.000 0.00 0.00 0.00 3.86
697 745 3.056328 GGGGCAAGTTCGTCAGGC 61.056 66.667 0.00 0.00 0.00 4.85
698 746 3.423154 GGGCAAGTTCGTCAGGCG 61.423 66.667 0.00 0.00 43.01 5.52
699 747 3.423154 GGCAAGTTCGTCAGGCGG 61.423 66.667 0.00 0.00 41.72 6.13
700 748 4.090057 GCAAGTTCGTCAGGCGGC 62.090 66.667 0.00 0.00 41.72 6.53
785 833 1.823899 GGATGGATGGTTGGTCGGC 60.824 63.158 0.00 0.00 0.00 5.54
814 862 2.636412 CGCCGAGACAGTGAAGGGA 61.636 63.158 0.00 0.00 0.00 4.20
860 908 4.755123 GGACGGACCCAAATGTAATATCTG 59.245 45.833 0.00 0.00 0.00 2.90
862 910 5.123227 ACGGACCCAAATGTAATATCTGTG 58.877 41.667 0.00 0.00 0.00 3.66
863 911 4.515191 CGGACCCAAATGTAATATCTGTGG 59.485 45.833 0.00 0.00 0.00 4.17
865 913 4.215109 ACCCAAATGTAATATCTGTGGGC 58.785 43.478 5.74 0.00 46.86 5.36
866 914 3.573967 CCCAAATGTAATATCTGTGGGCC 59.426 47.826 0.00 0.00 37.97 5.80
867 915 4.214310 CCAAATGTAATATCTGTGGGCCA 58.786 43.478 0.00 0.00 0.00 5.36
868 916 4.279169 CCAAATGTAATATCTGTGGGCCAG 59.721 45.833 6.40 0.00 42.97 4.85
882 930 2.047844 CCAGACCGCCAGAGTGTG 60.048 66.667 0.00 0.00 0.00 3.82
883 931 2.737180 CAGACCGCCAGAGTGTGT 59.263 61.111 0.00 0.00 0.00 3.72
934 986 0.244994 CACTCACTCCTCGTCTTGGG 59.755 60.000 0.00 0.00 0.00 4.12
935 987 1.216710 CTCACTCCTCGTCTTGGGC 59.783 63.158 0.00 0.00 0.00 5.36
936 988 1.228894 TCACTCCTCGTCTTGGGCT 60.229 57.895 0.00 0.00 0.00 5.19
937 989 0.832135 TCACTCCTCGTCTTGGGCTT 60.832 55.000 0.00 0.00 0.00 4.35
945 997 0.391793 CGTCTTGGGCTTCTTCTCCC 60.392 60.000 0.00 0.00 42.93 4.30
969 1021 4.468689 CTCTCGGCCGAAACCCCC 62.469 72.222 30.53 0.00 0.00 5.40
1073 1130 2.351276 GTCAATGGCGTGGGAGGT 59.649 61.111 0.00 0.00 0.00 3.85
1077 1134 1.603455 AATGGCGTGGGAGGTGTTG 60.603 57.895 0.00 0.00 0.00 3.33
1314 1460 2.186903 CGGCCAGTAGATGCGGTT 59.813 61.111 2.24 0.00 0.00 4.44
1315 1461 2.173669 CGGCCAGTAGATGCGGTTG 61.174 63.158 2.24 0.00 0.00 3.77
1316 1462 1.078426 GGCCAGTAGATGCGGTTGT 60.078 57.895 0.00 0.00 0.00 3.32
1317 1463 0.177141 GGCCAGTAGATGCGGTTGTA 59.823 55.000 0.00 0.00 0.00 2.41
1318 1464 1.287425 GCCAGTAGATGCGGTTGTAC 58.713 55.000 0.00 0.00 0.00 2.90
1453 1624 1.909302 CCCTCTTTCTAGTGCCTTGGA 59.091 52.381 0.00 0.00 0.00 3.53
1465 1637 4.410099 AGTGCCTTGGATTCTTGAATTGA 58.590 39.130 0.00 0.00 0.00 2.57
1467 1639 4.460382 GTGCCTTGGATTCTTGAATTGAGA 59.540 41.667 0.00 0.00 0.00 3.27
1469 1641 5.047802 TGCCTTGGATTCTTGAATTGAGAAC 60.048 40.000 3.64 0.28 36.08 3.01
1477 1676 9.927668 GGATTCTTGAATTGAGAACCAAAAATA 57.072 29.630 3.64 0.00 38.43 1.40
1484 1683 9.010029 TGAATTGAGAACCAAAAATACTACTCC 57.990 33.333 0.00 0.00 38.43 3.85
1493 1692 5.163088 CCAAAAATACTACTCCCCTAGCCAT 60.163 44.000 0.00 0.00 0.00 4.40
1494 1693 6.365520 CAAAAATACTACTCCCCTAGCCATT 58.634 40.000 0.00 0.00 0.00 3.16
1495 1694 5.827326 AAATACTACTCCCCTAGCCATTC 57.173 43.478 0.00 0.00 0.00 2.67
1503 1702 3.576550 CTCCCCTAGCCATTCTACTCTTC 59.423 52.174 0.00 0.00 0.00 2.87
1508 1707 6.378848 CCCCTAGCCATTCTACTCTTCTATAC 59.621 46.154 0.00 0.00 0.00 1.47
1513 1712 7.675062 AGCCATTCTACTCTTCTATACCAATG 58.325 38.462 0.00 0.00 0.00 2.82
1515 1714 7.675062 CCATTCTACTCTTCTATACCAATGCT 58.325 38.462 0.00 0.00 0.00 3.79
1516 1715 7.601886 CCATTCTACTCTTCTATACCAATGCTG 59.398 40.741 0.00 0.00 0.00 4.41
1517 1716 7.661536 TTCTACTCTTCTATACCAATGCTGT 57.338 36.000 0.00 0.00 0.00 4.40
1541 1800 7.229907 TGTGTAGCCGTATCTTGTGATTAGATA 59.770 37.037 0.00 0.00 34.35 1.98
1578 1837 5.470098 TGTTCAACTCAGTGATTTTAGCCTC 59.530 40.000 0.00 0.00 0.00 4.70
1598 1866 4.406003 CCTCAGTATTTGGGTGCTAGTAGT 59.594 45.833 0.00 0.00 0.00 2.73
1599 1867 5.597182 CCTCAGTATTTGGGTGCTAGTAGTA 59.403 44.000 0.00 0.00 0.00 1.82
1600 1868 6.267928 CCTCAGTATTTGGGTGCTAGTAGTAT 59.732 42.308 0.00 0.00 0.00 2.12
1603 1871 7.509318 TCAGTATTTGGGTGCTAGTAGTATGAT 59.491 37.037 0.00 0.00 0.00 2.45
1612 1880 6.814146 GGTGCTAGTAGTATGATATTTCTGCC 59.186 42.308 0.00 0.00 0.00 4.85
1642 1911 6.029346 AGGTTTGTAATCAGGCATCTTTTG 57.971 37.500 0.00 0.00 0.00 2.44
1683 1955 6.555812 AAGCTGAATGTGTATGCTATGATG 57.444 37.500 0.00 0.00 33.28 3.07
1708 1985 2.227194 CCTGGTGGTGAGGTAAACAAC 58.773 52.381 0.00 0.00 0.00 3.32
1716 1993 5.179555 GTGGTGAGGTAAACAACTGATTCTC 59.820 44.000 0.00 0.00 0.00 2.87
1741 2019 6.092122 CGTTCATGCCACTTCTGTTTTAGATA 59.908 38.462 0.00 0.00 34.80 1.98
1742 2020 7.467623 GTTCATGCCACTTCTGTTTTAGATAG 58.532 38.462 0.00 0.00 34.80 2.08
1743 2021 6.946340 TCATGCCACTTCTGTTTTAGATAGA 58.054 36.000 0.00 0.00 34.80 1.98
1744 2022 7.568349 TCATGCCACTTCTGTTTTAGATAGAT 58.432 34.615 0.00 0.00 34.80 1.98
1761 2594 6.520272 AGATAGATGCTCAATGTGGTTACTC 58.480 40.000 0.00 0.00 0.00 2.59
1781 2614 8.552034 GTTACTCCATGACTTTGTTATGCTATC 58.448 37.037 0.00 0.00 29.81 2.08
1854 2856 4.808414 TCTGTCTTAGCAGCTAACATGT 57.192 40.909 11.07 0.00 36.49 3.21
1859 2861 4.803088 GTCTTAGCAGCTAACATGTCTCAG 59.197 45.833 11.07 0.00 0.00 3.35
1867 2869 1.742761 AACATGTCTCAGCATTCCGG 58.257 50.000 0.00 0.00 0.00 5.14
1886 2937 2.699954 GGCTAACTGCTTGCTCACTTA 58.300 47.619 0.00 0.00 42.39 2.24
1929 2981 9.690913 TTCATGTTCTCTTTTATCCATTCTCAT 57.309 29.630 0.00 0.00 0.00 2.90
1943 3965 6.233434 TCCATTCTCATATTCTGGCATGTAC 58.767 40.000 0.00 0.00 0.00 2.90
2020 4059 5.024785 ACTTAAGCTCAGGCAATACTACC 57.975 43.478 1.29 0.00 41.70 3.18
2029 4068 6.649557 GCTCAGGCAATACTACCGTTTATATT 59.350 38.462 0.00 0.00 38.54 1.28
2130 4180 3.566742 TGCGCTGATGCAAAATATCTGAT 59.433 39.130 9.73 0.00 43.02 2.90
2137 4187 5.536916 TGATGCAAAATATCTGATGATGGCA 59.463 36.000 0.00 4.60 34.32 4.92
2428 4484 3.566130 GCTGTGAGCATCCCTTTCT 57.434 52.632 0.00 0.00 41.89 2.52
2440 4496 0.602562 CCCTTTCTGGCATTTTCGCA 59.397 50.000 0.00 0.00 0.00 5.10
2507 4565 5.596268 TTTCTCGTCATCTGTTTGACATG 57.404 39.130 11.82 0.00 45.08 3.21
2533 4595 4.223477 AGGATTTTGTGATGGACCATTTGG 59.777 41.667 8.78 0.00 42.17 3.28
2544 4606 2.262292 CATTTGGGGTTGGCGCAG 59.738 61.111 10.83 0.00 0.00 5.18
2607 4675 5.536538 AGACTCGCTGGTAGAATAATGATGA 59.463 40.000 0.00 0.00 0.00 2.92
2608 4676 5.533482 ACTCGCTGGTAGAATAATGATGAC 58.467 41.667 0.00 0.00 0.00 3.06
2609 4677 5.069119 ACTCGCTGGTAGAATAATGATGACA 59.931 40.000 0.00 0.00 0.00 3.58
2610 4678 6.101650 TCGCTGGTAGAATAATGATGACAT 57.898 37.500 0.00 0.00 38.50 3.06
2611 4679 6.159293 TCGCTGGTAGAATAATGATGACATC 58.841 40.000 8.59 8.59 35.50 3.06
2612 4680 5.928264 CGCTGGTAGAATAATGATGACATCA 59.072 40.000 20.09 20.09 44.55 3.07
2637 4705 6.864421 ACATGATAATCTAGTACTCCCTCCA 58.136 40.000 0.00 0.00 0.00 3.86
2690 4761 9.678260 AGTGATCTAAATGCTCTTACATTTCTT 57.322 29.630 5.81 0.00 44.89 2.52
2775 4847 1.335132 GGCTGGGATAACCGAGGTGA 61.335 60.000 3.25 0.00 44.64 4.02
2776 4848 0.105039 GCTGGGATAACCGAGGTGAG 59.895 60.000 3.25 0.00 44.64 3.51
2777 4849 0.105039 CTGGGATAACCGAGGTGAGC 59.895 60.000 0.00 0.00 44.64 4.26
2778 4850 1.335132 TGGGATAACCGAGGTGAGCC 61.335 60.000 5.33 5.33 44.64 4.70
2779 4851 1.335132 GGGATAACCGAGGTGAGCCA 61.335 60.000 15.31 0.00 36.77 4.75
2780 4852 0.105039 GGATAACCGAGGTGAGCCAG 59.895 60.000 9.01 0.00 35.19 4.85
2781 4853 1.112113 GATAACCGAGGTGAGCCAGA 58.888 55.000 0.00 0.00 37.19 3.86
2782 4854 1.480954 GATAACCGAGGTGAGCCAGAA 59.519 52.381 0.00 0.00 37.19 3.02
2875 4970 5.519722 TCCGTTTGCTTCTCTTTCAATTTC 58.480 37.500 0.00 0.00 0.00 2.17
3007 5195 5.771469 TCAACATTTGACAATTGTGGCTAG 58.229 37.500 17.58 5.64 34.08 3.42
3081 5307 7.009815 GCTAATTTATTAGGGTTGCCGAAAAAC 59.990 37.037 10.59 0.00 40.01 2.43
3098 5324 3.473923 AAACATGCCTCCAAACCAAAG 57.526 42.857 0.00 0.00 0.00 2.77
3155 5381 2.252747 CATGGCGTGTGTGCAAATTAG 58.747 47.619 0.00 0.00 36.28 1.73
3173 5399 0.180406 AGGAGTGTCACGGCTTGTTT 59.820 50.000 0.00 0.00 0.00 2.83
3175 5401 1.268539 GGAGTGTCACGGCTTGTTTTG 60.269 52.381 0.00 0.00 0.00 2.44
3177 5403 0.736053 GTGTCACGGCTTGTTTTGGA 59.264 50.000 0.00 0.00 0.00 3.53
3178 5404 1.336755 GTGTCACGGCTTGTTTTGGAT 59.663 47.619 0.00 0.00 0.00 3.41
3207 5468 3.647590 CGGGGGTAAAATAGCTAGGGTTA 59.352 47.826 0.00 0.00 0.00 2.85
3221 5482 7.750947 AGCTAGGGTTATCTTCTTCCTTTTA 57.249 36.000 0.00 0.00 0.00 1.52
3235 5496 5.820947 TCTTCCTTTTAACGAGCAAGAGTTT 59.179 36.000 0.00 0.00 0.00 2.66
3251 5512 6.198687 CAAGAGTTTTACAAGCACGAATTCA 58.801 36.000 6.22 0.00 0.00 2.57
3258 5519 2.226437 ACAAGCACGAATTCATCACACC 59.774 45.455 6.22 0.00 0.00 4.16
3293 5554 5.622346 TTGGTTTGGAGCTAAAATTTGGT 57.378 34.783 0.00 0.00 0.00 3.67
3306 5567 8.860088 AGCTAAAATTTGGTAAAACTCTGACAT 58.140 29.630 0.00 0.00 0.00 3.06
3307 5568 8.915654 GCTAAAATTTGGTAAAACTCTGACATG 58.084 33.333 0.00 0.00 0.00 3.21
3349 5613 6.048509 ACAATTTTGGCTAGTGTTTTTGAGG 58.951 36.000 0.00 0.00 0.00 3.86
3383 5648 8.503458 ACATTTGACAATTTTGGACAAATTGA 57.497 26.923 21.28 4.89 45.59 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.057174 GTCCCTGTAGAGTGTCAGTTCTG 60.057 52.174 0.00 0.00 0.00 3.02
1 2 3.158676 GTCCCTGTAGAGTGTCAGTTCT 58.841 50.000 0.00 0.00 0.00 3.01
2 3 3.158676 AGTCCCTGTAGAGTGTCAGTTC 58.841 50.000 0.00 0.00 0.00 3.01
3 4 3.246416 AGTCCCTGTAGAGTGTCAGTT 57.754 47.619 0.00 0.00 0.00 3.16
4 5 2.982339 AGTCCCTGTAGAGTGTCAGT 57.018 50.000 0.00 0.00 0.00 3.41
5 6 6.123651 ACTATTAGTCCCTGTAGAGTGTCAG 58.876 44.000 0.00 0.00 0.00 3.51
6 7 6.075949 ACTATTAGTCCCTGTAGAGTGTCA 57.924 41.667 0.00 0.00 0.00 3.58
7 8 6.120905 TGACTATTAGTCCCTGTAGAGTGTC 58.879 44.000 18.81 0.00 44.44 3.67
8 9 6.075949 TGACTATTAGTCCCTGTAGAGTGT 57.924 41.667 18.81 0.00 44.44 3.55
9 10 5.009210 GCTGACTATTAGTCCCTGTAGAGTG 59.991 48.000 18.81 1.33 44.44 3.51
10 11 5.134661 GCTGACTATTAGTCCCTGTAGAGT 58.865 45.833 18.81 0.00 44.44 3.24
11 12 5.133941 TGCTGACTATTAGTCCCTGTAGAG 58.866 45.833 18.81 10.04 44.44 2.43
12 13 5.125367 TGCTGACTATTAGTCCCTGTAGA 57.875 43.478 18.81 0.53 44.44 2.59
13 14 4.890581 ACTGCTGACTATTAGTCCCTGTAG 59.109 45.833 18.81 17.62 44.44 2.74
14 15 4.868268 ACTGCTGACTATTAGTCCCTGTA 58.132 43.478 18.81 9.29 44.44 2.74
15 16 3.714144 ACTGCTGACTATTAGTCCCTGT 58.286 45.455 18.81 15.70 44.44 4.00
16 17 6.412362 AATACTGCTGACTATTAGTCCCTG 57.588 41.667 18.81 15.21 44.44 4.45
17 18 7.563924 TGTAAATACTGCTGACTATTAGTCCCT 59.436 37.037 18.81 2.43 44.44 4.20
18 19 7.652507 GTGTAAATACTGCTGACTATTAGTCCC 59.347 40.741 18.81 11.50 44.44 4.46
19 20 8.195436 TGTGTAAATACTGCTGACTATTAGTCC 58.805 37.037 18.81 7.14 44.44 3.85
20 21 9.582431 TTGTGTAAATACTGCTGACTATTAGTC 57.418 33.333 15.57 15.57 45.26 2.59
21 22 9.367444 GTTGTGTAAATACTGCTGACTATTAGT 57.633 33.333 0.00 0.00 0.00 2.24
22 23 9.366216 TGTTGTGTAAATACTGCTGACTATTAG 57.634 33.333 0.00 0.00 0.00 1.73
23 24 9.146984 GTGTTGTGTAAATACTGCTGACTATTA 57.853 33.333 0.00 0.00 0.00 0.98
24 25 7.119262 GGTGTTGTGTAAATACTGCTGACTATT 59.881 37.037 0.00 0.00 0.00 1.73
25 26 6.594159 GGTGTTGTGTAAATACTGCTGACTAT 59.406 38.462 0.00 0.00 0.00 2.12
26 27 5.929992 GGTGTTGTGTAAATACTGCTGACTA 59.070 40.000 0.00 0.00 0.00 2.59
27 28 4.755123 GGTGTTGTGTAAATACTGCTGACT 59.245 41.667 0.00 0.00 0.00 3.41
28 29 4.755123 AGGTGTTGTGTAAATACTGCTGAC 59.245 41.667 0.00 0.00 0.00 3.51
29 30 4.968259 AGGTGTTGTGTAAATACTGCTGA 58.032 39.130 0.00 0.00 0.00 4.26
30 31 6.795098 TTAGGTGTTGTGTAAATACTGCTG 57.205 37.500 0.00 0.00 0.00 4.41
31 32 6.073440 CGTTTAGGTGTTGTGTAAATACTGCT 60.073 38.462 0.00 0.00 0.00 4.24
32 33 6.075280 CGTTTAGGTGTTGTGTAAATACTGC 58.925 40.000 0.00 0.00 0.00 4.40
33 34 6.075280 GCGTTTAGGTGTTGTGTAAATACTG 58.925 40.000 0.00 0.00 0.00 2.74
34 35 5.179929 GGCGTTTAGGTGTTGTGTAAATACT 59.820 40.000 0.00 0.00 0.00 2.12
35 36 5.384787 GGCGTTTAGGTGTTGTGTAAATAC 58.615 41.667 0.00 0.00 0.00 1.89
36 37 4.152045 CGGCGTTTAGGTGTTGTGTAAATA 59.848 41.667 0.00 0.00 0.00 1.40
37 38 3.058777 CGGCGTTTAGGTGTTGTGTAAAT 60.059 43.478 0.00 0.00 0.00 1.40
38 39 2.287373 CGGCGTTTAGGTGTTGTGTAAA 59.713 45.455 0.00 0.00 0.00 2.01
39 40 1.865970 CGGCGTTTAGGTGTTGTGTAA 59.134 47.619 0.00 0.00 0.00 2.41
40 41 1.500108 CGGCGTTTAGGTGTTGTGTA 58.500 50.000 0.00 0.00 0.00 2.90
41 42 1.778027 GCGGCGTTTAGGTGTTGTGT 61.778 55.000 9.37 0.00 0.00 3.72
42 43 1.082366 GCGGCGTTTAGGTGTTGTG 60.082 57.895 9.37 0.00 0.00 3.33
43 44 1.503818 CTGCGGCGTTTAGGTGTTGT 61.504 55.000 9.37 0.00 0.00 3.32
44 45 1.206578 CTGCGGCGTTTAGGTGTTG 59.793 57.895 9.37 0.00 0.00 3.33
45 46 0.033781 TACTGCGGCGTTTAGGTGTT 59.966 50.000 9.37 0.00 0.00 3.32
46 47 0.248289 ATACTGCGGCGTTTAGGTGT 59.752 50.000 9.37 0.07 0.00 4.16
47 48 0.928229 GATACTGCGGCGTTTAGGTG 59.072 55.000 9.37 0.00 0.00 4.00
48 49 0.822164 AGATACTGCGGCGTTTAGGT 59.178 50.000 9.37 3.32 0.00 3.08
85 86 3.578282 TGTGACTGGAGATTGTTAGAGCA 59.422 43.478 0.00 0.00 0.00 4.26
89 90 5.240891 ACATGTGTGACTGGAGATTGTTAG 58.759 41.667 0.00 0.00 0.00 2.34
114 115 6.662414 TGTTCAGTGTTGTGTTTTCTAGAG 57.338 37.500 0.00 0.00 0.00 2.43
172 174 2.930040 AGGTCGTTTGATGAGTATTGCG 59.070 45.455 0.00 0.00 0.00 4.85
489 494 4.069232 TGCAAGGGAGCCGTCGAG 62.069 66.667 0.00 0.00 0.00 4.04
491 496 4.680237 TGTGCAAGGGAGCCGTCG 62.680 66.667 0.00 0.00 0.00 5.12
552 557 2.743636 TCTTGGTCGAATCCTGTGTC 57.256 50.000 0.00 0.00 0.00 3.67
557 562 4.467795 TCTGAGATTTCTTGGTCGAATCCT 59.532 41.667 0.00 0.00 0.00 3.24
641 689 0.930726 CACCTCCTACCTCTCCCTCT 59.069 60.000 0.00 0.00 0.00 3.69
642 690 0.757561 GCACCTCCTACCTCTCCCTC 60.758 65.000 0.00 0.00 0.00 4.30
643 691 1.311747 GCACCTCCTACCTCTCCCT 59.688 63.158 0.00 0.00 0.00 4.20
644 692 1.001760 TGCACCTCCTACCTCTCCC 59.998 63.158 0.00 0.00 0.00 4.30
645 693 1.045911 CCTGCACCTCCTACCTCTCC 61.046 65.000 0.00 0.00 0.00 3.71
646 694 0.324830 ACCTGCACCTCCTACCTCTC 60.325 60.000 0.00 0.00 0.00 3.20
647 695 0.616111 CACCTGCACCTCCTACCTCT 60.616 60.000 0.00 0.00 0.00 3.69
648 696 1.617947 CCACCTGCACCTCCTACCTC 61.618 65.000 0.00 0.00 0.00 3.85
649 697 1.613630 CCACCTGCACCTCCTACCT 60.614 63.158 0.00 0.00 0.00 3.08
650 698 0.983378 ATCCACCTGCACCTCCTACC 60.983 60.000 0.00 0.00 0.00 3.18
651 699 0.912486 AATCCACCTGCACCTCCTAC 59.088 55.000 0.00 0.00 0.00 3.18
652 700 2.116238 GTAATCCACCTGCACCTCCTA 58.884 52.381 0.00 0.00 0.00 2.94
679 727 2.750350 CCTGACGAACTTGCCCCT 59.250 61.111 0.00 0.00 0.00 4.79
794 842 2.125912 CTTCACTGTCTCGGCGGG 60.126 66.667 7.21 2.41 0.00 6.13
814 862 1.973812 GCTTGGCCCGCTTCTCTTT 60.974 57.895 0.00 0.00 0.00 2.52
864 912 4.008933 ACACTCTGGCGGTCTGGC 62.009 66.667 0.00 0.00 45.12 4.85
865 913 1.532604 TACACACTCTGGCGGTCTGG 61.533 60.000 0.00 0.00 0.00 3.86
866 914 0.317160 TTACACACTCTGGCGGTCTG 59.683 55.000 0.00 0.00 0.00 3.51
867 915 0.317479 GTTACACACTCTGGCGGTCT 59.683 55.000 0.00 0.00 0.00 3.85
868 916 0.317479 AGTTACACACTCTGGCGGTC 59.683 55.000 0.00 0.00 0.00 4.79
869 917 1.271656 GTAGTTACACACTCTGGCGGT 59.728 52.381 0.00 0.00 36.88 5.68
870 918 1.271379 TGTAGTTACACACTCTGGCGG 59.729 52.381 0.00 0.00 36.88 6.13
871 919 2.717580 TGTAGTTACACACTCTGGCG 57.282 50.000 0.00 0.00 36.88 5.69
882 930 5.508657 CGGGAAGCCCTAGTAATGTAGTTAC 60.509 48.000 0.38 0.00 42.67 2.50
883 931 4.586001 CGGGAAGCCCTAGTAATGTAGTTA 59.414 45.833 0.38 0.00 42.67 2.24
934 986 0.617935 AGAAGCAGGGGAGAAGAAGC 59.382 55.000 0.00 0.00 0.00 3.86
935 987 2.168313 GAGAGAAGCAGGGGAGAAGAAG 59.832 54.545 0.00 0.00 0.00 2.85
936 988 2.183679 GAGAGAAGCAGGGGAGAAGAA 58.816 52.381 0.00 0.00 0.00 2.52
937 989 1.859302 GAGAGAAGCAGGGGAGAAGA 58.141 55.000 0.00 0.00 0.00 2.87
945 997 2.507110 TTTCGGCCGAGAGAAGCAGG 62.507 60.000 29.20 0.00 0.00 4.85
1059 1116 1.603455 CAACACCTCCCACGCCATT 60.603 57.895 0.00 0.00 0.00 3.16
1061 1118 3.164977 TCAACACCTCCCACGCCA 61.165 61.111 0.00 0.00 0.00 5.69
1073 1130 1.945819 GCGAGAAATGCCTCCTCAACA 60.946 52.381 0.00 0.00 0.00 3.33
1077 1134 1.884926 CCGCGAGAAATGCCTCCTC 60.885 63.158 8.23 0.00 0.00 3.71
1197 1254 3.712881 GTGTTGCCGACGGTGAGC 61.713 66.667 16.73 5.38 0.00 4.26
1240 1378 1.475280 TCAATCGGTAGAGGTCGTTGG 59.525 52.381 0.00 0.00 0.00 3.77
1253 1391 2.156504 GCAATACATCGAGCTCAATCGG 59.843 50.000 15.40 0.00 42.93 4.18
1314 1460 8.630917 GTTCCATCAGCTCTTAATACTAGTACA 58.369 37.037 4.31 0.00 0.00 2.90
1315 1461 8.852135 AGTTCCATCAGCTCTTAATACTAGTAC 58.148 37.037 4.31 0.00 0.00 2.73
1316 1462 8.851145 CAGTTCCATCAGCTCTTAATACTAGTA 58.149 37.037 4.77 4.77 0.00 1.82
1317 1463 7.561722 TCAGTTCCATCAGCTCTTAATACTAGT 59.438 37.037 0.00 0.00 0.00 2.57
1318 1464 7.946207 TCAGTTCCATCAGCTCTTAATACTAG 58.054 38.462 0.00 0.00 0.00 2.57
1465 1637 6.352823 GCTAGGGGAGTAGTATTTTTGGTTCT 60.353 42.308 0.00 0.00 0.00 3.01
1467 1639 5.339778 GGCTAGGGGAGTAGTATTTTTGGTT 60.340 44.000 0.00 0.00 0.00 3.67
1469 1641 4.165372 TGGCTAGGGGAGTAGTATTTTTGG 59.835 45.833 0.00 0.00 0.00 3.28
1477 1676 3.467863 AGTAGAATGGCTAGGGGAGTAGT 59.532 47.826 0.00 0.00 0.00 2.73
1480 1679 2.520549 AGAGTAGAATGGCTAGGGGAGT 59.479 50.000 0.00 0.00 0.00 3.85
1482 1681 3.207777 AGAAGAGTAGAATGGCTAGGGGA 59.792 47.826 0.00 0.00 0.00 4.81
1484 1683 6.378848 GGTATAGAAGAGTAGAATGGCTAGGG 59.621 46.154 0.00 0.00 0.00 3.53
1493 1692 7.124298 ACACAGCATTGGTATAGAAGAGTAGAA 59.876 37.037 0.00 0.00 0.00 2.10
1494 1693 6.607600 ACACAGCATTGGTATAGAAGAGTAGA 59.392 38.462 0.00 0.00 0.00 2.59
1495 1694 6.810911 ACACAGCATTGGTATAGAAGAGTAG 58.189 40.000 0.00 0.00 0.00 2.57
1513 1712 3.738281 ATCACAAGATACGGCTACACAGC 60.738 47.826 0.00 0.00 38.83 4.40
1515 1714 4.465632 AATCACAAGATACGGCTACACA 57.534 40.909 0.00 0.00 33.08 3.72
1516 1715 5.828747 TCTAATCACAAGATACGGCTACAC 58.171 41.667 0.00 0.00 33.08 2.90
1517 1716 6.650427 ATCTAATCACAAGATACGGCTACA 57.350 37.500 0.00 0.00 31.88 2.74
1541 1800 7.119699 CACTGAGTTGAACATACACCATATTGT 59.880 37.037 0.00 0.00 0.00 2.71
1578 1837 7.050970 TCATACTACTAGCACCCAAATACTG 57.949 40.000 0.00 0.00 0.00 2.74
1600 1868 9.420118 ACAAACCTAATAATGGCAGAAATATCA 57.580 29.630 0.00 0.00 0.00 2.15
1612 1880 9.071276 AGATGCCTGATTACAAACCTAATAATG 57.929 33.333 0.00 0.00 0.00 1.90
1617 1885 7.309744 CCAAAAGATGCCTGATTACAAACCTAA 60.310 37.037 0.00 0.00 0.00 2.69
1618 1886 6.152661 CCAAAAGATGCCTGATTACAAACCTA 59.847 38.462 0.00 0.00 0.00 3.08
1619 1887 5.047092 CCAAAAGATGCCTGATTACAAACCT 60.047 40.000 0.00 0.00 0.00 3.50
1642 1911 0.674269 TTATTCGGTGACAACGGGCC 60.674 55.000 13.91 0.00 0.00 5.80
1644 1913 0.725117 GCTTATTCGGTGACAACGGG 59.275 55.000 13.91 0.18 0.00 5.28
1708 1985 2.625737 AGTGGCATGAACGAGAATCAG 58.374 47.619 0.00 0.00 33.17 2.90
1716 1993 3.354089 AAAACAGAAGTGGCATGAACG 57.646 42.857 0.00 0.00 0.00 3.95
1741 2019 3.264193 TGGAGTAACCACATTGAGCATCT 59.736 43.478 0.00 0.00 44.64 2.90
1742 2020 3.609853 TGGAGTAACCACATTGAGCATC 58.390 45.455 0.00 0.00 44.64 3.91
1743 2021 3.719268 TGGAGTAACCACATTGAGCAT 57.281 42.857 0.00 0.00 44.64 3.79
1761 2594 9.276590 TGAATAGATAGCATAACAAAGTCATGG 57.723 33.333 0.00 0.00 0.00 3.66
1854 2856 1.134699 CAGTTAGCCGGAATGCTGAGA 60.135 52.381 5.05 0.00 42.77 3.27
1867 2869 4.437930 CCATTAAGTGAGCAAGCAGTTAGC 60.438 45.833 0.00 0.00 46.19 3.09
1886 2937 4.525487 ACATGAATGTTCTCAAGTGCCATT 59.475 37.500 0.00 0.00 37.90 3.16
1913 2965 8.400184 TGCCAGAATATGAGAATGGATAAAAG 57.600 34.615 0.00 0.00 32.55 2.27
1929 2981 6.040247 CGTTGAAGTAGTACATGCCAGAATA 58.960 40.000 2.52 0.00 0.00 1.75
1943 3965 4.169508 CCACTGTGAGATCGTTGAAGTAG 58.830 47.826 9.86 0.00 0.00 2.57
2002 4041 1.831736 ACGGTAGTATTGCCTGAGCTT 59.168 47.619 0.00 0.00 40.80 3.74
2130 4180 1.317431 GCAGCATCCTGTTGCCATCA 61.317 55.000 4.81 0.00 46.79 3.07
2137 4187 0.807667 GTCGATCGCAGCATCCTGTT 60.808 55.000 11.09 0.00 41.26 3.16
2327 4383 2.893489 CCCTTTCCACCCTTTCTTCTTG 59.107 50.000 0.00 0.00 0.00 3.02
2428 4484 1.286570 CAGCAGTGCGAAAATGCCA 59.713 52.632 10.00 0.00 40.89 4.92
2507 4565 5.665916 ATGGTCCATCACAAAATCCTTTC 57.334 39.130 0.00 0.00 0.00 2.62
2533 4595 3.098555 CGTAATCTGCGCCAACCC 58.901 61.111 4.18 0.00 0.00 4.11
2544 4606 3.272334 CGGCCTGCCAGCGTAATC 61.272 66.667 9.17 0.00 35.37 1.75
2563 4625 2.039405 CAACAGAGAGCCCAGCAGC 61.039 63.158 0.00 0.00 0.00 5.25
2564 4626 0.610174 TACAACAGAGAGCCCAGCAG 59.390 55.000 0.00 0.00 0.00 4.24
2569 4631 1.133407 CGAGTCTACAACAGAGAGCCC 59.867 57.143 0.00 0.00 32.51 5.19
2576 4638 2.747989 TCTACCAGCGAGTCTACAACAG 59.252 50.000 0.00 0.00 0.00 3.16
2607 4675 8.589338 GGGAGTACTAGATTATCATGTTGATGT 58.411 37.037 0.00 0.00 37.70 3.06
2608 4676 8.811017 AGGGAGTACTAGATTATCATGTTGATG 58.189 37.037 0.00 0.00 37.70 3.07
2609 4677 8.964533 AGGGAGTACTAGATTATCATGTTGAT 57.035 34.615 0.00 0.00 40.72 2.57
2610 4678 7.451877 GGAGGGAGTACTAGATTATCATGTTGA 59.548 40.741 0.00 0.00 0.00 3.18
2611 4679 7.233553 TGGAGGGAGTACTAGATTATCATGTTG 59.766 40.741 0.00 0.00 0.00 3.33
2612 4680 7.306013 TGGAGGGAGTACTAGATTATCATGTT 58.694 38.462 0.00 0.00 0.00 2.71
2705 4776 8.595421 ACAATGCATCTCAAGACTGATAGATAT 58.405 33.333 0.00 0.00 0.00 1.63
2777 4849 0.678048 CTCCTTTCCGGCCTTTCTGG 60.678 60.000 0.00 0.00 42.90 3.86
2778 4850 0.678048 CCTCCTTTCCGGCCTTTCTG 60.678 60.000 0.00 0.00 0.00 3.02
2779 4851 0.840722 TCCTCCTTTCCGGCCTTTCT 60.841 55.000 0.00 0.00 0.00 2.52
2780 4852 0.256177 ATCCTCCTTTCCGGCCTTTC 59.744 55.000 0.00 0.00 0.00 2.62
2781 4853 0.256177 GATCCTCCTTTCCGGCCTTT 59.744 55.000 0.00 0.00 0.00 3.11
2782 4854 1.915983 GATCCTCCTTTCCGGCCTT 59.084 57.895 0.00 0.00 0.00 4.35
2788 4860 1.538419 CGCTAACCGATCCTCCTTTCC 60.538 57.143 0.00 0.00 40.02 3.13
2823 4907 4.764050 TGTACACACAAAGAGGAAGGAA 57.236 40.909 0.00 0.00 0.00 3.36
2894 5020 5.105877 GCTTGTAATGGTAAAAGGAAGGGAC 60.106 44.000 0.00 0.00 0.00 4.46
2949 5137 6.091986 CAGTCAGAGAGAGCTTTACCAAATTC 59.908 42.308 0.00 0.00 0.00 2.17
2984 5172 4.669206 AGCCACAATTGTCAAATGTTGA 57.331 36.364 8.48 0.00 37.33 3.18
2997 5185 7.168219 TCTTCTAATCAAACACTAGCCACAAT 58.832 34.615 0.00 0.00 0.00 2.71
3007 5195 7.945033 TTTGGCAATTCTTCTAATCAAACAC 57.055 32.000 0.00 0.00 0.00 3.32
3081 5307 0.680618 TGCTTTGGTTTGGAGGCATG 59.319 50.000 0.00 0.00 0.00 4.06
3098 5324 0.676151 AGCACTTAGAGCCTGCTTGC 60.676 55.000 4.93 4.93 38.07 4.01
3155 5381 1.021968 AAAACAAGCCGTGACACTCC 58.978 50.000 3.68 0.00 0.00 3.85
3207 5468 6.231211 TCTTGCTCGTTAAAAGGAAGAAGAT 58.769 36.000 16.09 0.00 44.85 2.40
3221 5482 3.625764 TGCTTGTAAAACTCTTGCTCGTT 59.374 39.130 0.00 0.00 0.00 3.85
3235 5496 4.083537 GGTGTGATGAATTCGTGCTTGTAA 60.084 41.667 4.51 0.00 0.00 2.41
3251 5512 1.303317 GAACCCCTTGCGGTGTGAT 60.303 57.895 0.00 0.00 35.83 3.06
3258 5519 0.678950 AAACCAATGAACCCCTTGCG 59.321 50.000 0.00 0.00 0.00 4.85
3269 5530 5.997129 ACCAAATTTTAGCTCCAAACCAATG 59.003 36.000 0.00 0.00 0.00 2.82
3349 5613 3.683365 ATTGTCAAATGTTGGCTTCCC 57.317 42.857 0.00 0.00 35.94 3.97


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

AutoCloner maintained by Alex Coulton.