Multiple sequence alignment - TraesCS1B01G378600

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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 TraesCS1B01G378600 chr1B 100.000 2560 0 0 1 2560 610964542 610967101 0.000000e+00 4728.0
1 TraesCS1B01G378600 chr1B 86.762 982 67 33 763 1689 608463185 608462212 0.000000e+00 1035.0
2 TraesCS1B01G378600 chr1B 90.818 697 36 15 759 1445 606839635 606840313 0.000000e+00 907.0
3 TraesCS1B01G378600 chr1B 89.888 712 43 15 748 1448 607429808 607429115 0.000000e+00 889.0
4 TraesCS1B01G378600 chr1B 86.788 772 63 17 758 1501 611131187 611131947 0.000000e+00 824.0
5 TraesCS1B01G378600 chr1B 83.853 706 64 21 1477 2168 606840398 606841067 6.010000e-176 627.0
6 TraesCS1B01G378600 chr1B 83.733 584 57 17 1480 2059 611131964 611132513 3.780000e-143 518.0
7 TraesCS1B01G378600 chr1B 100.000 28 0 0 660 687 606839606 606839633 5.000000e-03 52.8
8 TraesCS1B01G378600 chr1A 84.527 1299 122 37 749 1995 542358183 542359454 0.000000e+00 1212.0
9 TraesCS1B01G378600 chr1A 88.671 715 59 13 746 1449 541319046 541319749 0.000000e+00 852.0
10 TraesCS1B01G378600 chr1A 90.132 152 10 4 2019 2168 531920265 531920413 2.600000e-45 193.0
11 TraesCS1B01G378600 chr1A 94.030 67 4 0 2171 2237 510578866 510578800 4.510000e-18 102.0
12 TraesCS1B01G378600 chr1A 92.537 67 5 0 2171 2237 154791052 154790986 2.100000e-16 97.1
13 TraesCS1B01G378600 chr1A 92.537 67 5 0 2171 2237 552507265 552507331 2.100000e-16 97.1
14 TraesCS1B01G378600 chr1D 93.366 829 30 14 660 1464 446558087 446558914 0.000000e+00 1203.0
15 TraesCS1B01G378600 chr1D 90.222 767 45 16 746 1501 445317298 445318045 0.000000e+00 974.0
16 TraesCS1B01G378600 chr1D 87.795 721 68 10 763 1465 445387273 445386555 0.000000e+00 826.0
17 TraesCS1B01G378600 chr1D 82.070 937 82 39 1480 2387 445318062 445318941 0.000000e+00 721.0
18 TraesCS1B01G378600 chr1D 89.423 312 27 4 1480 1791 446558983 446559288 3.090000e-104 388.0
19 TraesCS1B01G378600 chr1D 84.091 176 26 2 1491 1666 445386481 445386308 4.380000e-38 169.0
20 TraesCS1B01G378600 chr1D 97.297 74 2 0 581 654 446557908 446557981 2.670000e-25 126.0
21 TraesCS1B01G378600 chr1D 91.837 49 3 1 660 708 445317254 445317301 1.640000e-07 67.6
22 TraesCS1B01G378600 chr3D 92.830 530 26 8 933 1452 114883213 114882686 0.000000e+00 758.0
23 TraesCS1B01G378600 chr3D 76.276 333 61 13 65 387 556841642 556841318 7.330000e-36 161.0
24 TraesCS1B01G378600 chr3A 91.150 565 33 12 947 1498 111106293 111105733 0.000000e+00 750.0
25 TraesCS1B01G378600 chr3A 80.512 508 57 25 1480 1982 722492431 722491961 4.050000e-93 351.0
26 TraesCS1B01G378600 chr3A 90.196 153 14 1 2019 2171 691427908 691427757 5.590000e-47 198.0
27 TraesCS1B01G378600 chr3A 88.889 153 15 2 2019 2171 722491961 722491811 1.210000e-43 187.0
28 TraesCS1B01G378600 chr3A 75.819 397 68 20 45 429 472576959 472576579 2.620000e-40 176.0
29 TraesCS1B01G378600 chr7D 82.213 506 43 25 1480 1982 16676196 16676657 2.390000e-105 392.0
30 TraesCS1B01G378600 chr7D 90.667 150 13 1 2019 2168 16676657 16676805 5.590000e-47 198.0
31 TraesCS1B01G378600 chr4D 80.874 549 53 21 1 539 48051341 48051847 4.000000e-103 385.0
32 TraesCS1B01G378600 chr4D 83.582 134 9 3 539 659 48051892 48052025 2.080000e-21 113.0
33 TraesCS1B01G378600 chr7B 80.079 507 56 24 1480 1982 425856877 425856412 4.080000e-88 335.0
34 TraesCS1B01G378600 chr7B 83.912 317 27 13 1759 2052 469017872 469018187 5.390000e-72 281.0
35 TraesCS1B01G378600 chr7B 89.091 220 17 5 1839 2052 603522167 603521949 1.510000e-67 267.0
36 TraesCS1B01G378600 chr7B 88.235 153 17 1 2019 2171 425856412 425856261 5.630000e-42 182.0
37 TraesCS1B01G378600 chr7B 92.537 67 5 0 2171 2237 688751828 688751894 2.100000e-16 97.1
38 TraesCS1B01G378600 chr7B 91.379 58 2 3 598 654 25670734 25670679 2.730000e-10 76.8
39 TraesCS1B01G378600 chr7B 91.379 58 2 3 598 654 104793554 104793499 2.730000e-10 76.8
40 TraesCS1B01G378600 chr7A 80.899 445 64 14 106 539 118216236 118215802 5.280000e-87 331.0
41 TraesCS1B01G378600 chr7A 77.716 359 54 21 94 435 728368426 728368775 2.010000e-46 196.0
42 TraesCS1B01G378600 chr7A 88.889 153 16 1 2019 2171 94865184 94865033 1.210000e-43 187.0
43 TraesCS1B01G378600 chr7A 92.537 67 5 0 2171 2237 94864950 94864884 2.100000e-16 97.1
44 TraesCS1B01G378600 chr5A 79.221 539 62 28 45 539 143328893 143329425 1.900000e-86 329.0
45 TraesCS1B01G378600 chr5A 85.489 317 22 14 1759 2052 131654357 131654672 2.470000e-80 309.0
46 TraesCS1B01G378600 chr2A 84.591 318 24 14 1759 2052 484064620 484064936 2.490000e-75 292.0
47 TraesCS1B01G378600 chr2A 84.375 320 22 17 1759 2052 644823131 644823448 3.220000e-74 289.0
48 TraesCS1B01G378600 chr2A 88.889 153 16 1 2019 2171 630863420 630863269 1.210000e-43 187.0
49 TraesCS1B01G378600 chr2A 76.944 360 55 24 45 388 536691368 536691715 2.020000e-41 180.0
50 TraesCS1B01G378600 chr2A 95.833 48 2 0 607 654 118676660 118676613 7.590000e-11 78.7
51 TraesCS1B01G378600 chr5B 90.367 218 14 5 1841 2052 10091080 10090864 1.940000e-71 279.0
52 TraesCS1B01G378600 chr5B 91.549 71 5 1 2168 2237 667130617 667130547 2.100000e-16 97.1
53 TraesCS1B01G378600 chr5B 95.833 48 2 0 607 654 365409257 365409210 7.590000e-11 78.7
54 TraesCS1B01G378600 chr5B 95.833 48 2 0 607 654 365450356 365450309 7.590000e-11 78.7
55 TraesCS1B01G378600 chr3B 90.367 218 14 4 1841 2052 775129183 775128967 1.940000e-71 279.0
56 TraesCS1B01G378600 chr3B 92.537 67 5 0 2171 2237 729775531 729775465 2.100000e-16 97.1
57 TraesCS1B01G378600 chr2B 83.281 317 29 13 1759 2052 726406950 726407265 1.170000e-68 270.0
58 TraesCS1B01G378600 chr6A 85.532 235 13 12 1750 1982 595963761 595963976 2.560000e-55 226.0
59 TraesCS1B01G378600 chr6A 89.474 57 6 0 598 654 14985587 14985643 3.530000e-09 73.1
60 TraesCS1B01G378600 chr6A 89.474 57 6 0 598 654 15089080 15089136 3.530000e-09 73.1
61 TraesCS1B01G378600 chr5D 77.500 360 56 18 45 389 435218705 435218356 2.600000e-45 193.0
62 TraesCS1B01G378600 chr4B 92.537 67 5 0 2171 2237 317669057 317669123 2.100000e-16 97.1
63 TraesCS1B01G378600 chr4A 92.537 67 5 0 2171 2237 723878382 723878316 2.100000e-16 97.1


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 TraesCS1B01G378600 chr1B 610964542 610967101 2559 False 4728.000000 4728 100.0000 1 2560 1 chr1B.!!$F1 2559
1 TraesCS1B01G378600 chr1B 608462212 608463185 973 True 1035.000000 1035 86.7620 763 1689 1 chr1B.!!$R2 926
2 TraesCS1B01G378600 chr1B 607429115 607429808 693 True 889.000000 889 89.8880 748 1448 1 chr1B.!!$R1 700
3 TraesCS1B01G378600 chr1B 611131187 611132513 1326 False 671.000000 824 85.2605 758 2059 2 chr1B.!!$F3 1301
4 TraesCS1B01G378600 chr1B 606839606 606841067 1461 False 528.933333 907 91.5570 660 2168 3 chr1B.!!$F2 1508
5 TraesCS1B01G378600 chr1A 542358183 542359454 1271 False 1212.000000 1212 84.5270 749 1995 1 chr1A.!!$F3 1246
6 TraesCS1B01G378600 chr1A 541319046 541319749 703 False 852.000000 852 88.6710 746 1449 1 chr1A.!!$F2 703
7 TraesCS1B01G378600 chr1D 445317254 445318941 1687 False 587.533333 974 88.0430 660 2387 3 chr1D.!!$F1 1727
8 TraesCS1B01G378600 chr1D 446557908 446559288 1380 False 572.333333 1203 93.3620 581 1791 3 chr1D.!!$F2 1210
9 TraesCS1B01G378600 chr1D 445386308 445387273 965 True 497.500000 826 85.9430 763 1666 2 chr1D.!!$R1 903
10 TraesCS1B01G378600 chr3D 114882686 114883213 527 True 758.000000 758 92.8300 933 1452 1 chr3D.!!$R1 519
11 TraesCS1B01G378600 chr3A 111105733 111106293 560 True 750.000000 750 91.1500 947 1498 1 chr3A.!!$R1 551
12 TraesCS1B01G378600 chr3A 722491811 722492431 620 True 269.000000 351 84.7005 1480 2171 2 chr3A.!!$R4 691
13 TraesCS1B01G378600 chr7D 16676196 16676805 609 False 295.000000 392 86.4400 1480 2168 2 chr7D.!!$F1 688
14 TraesCS1B01G378600 chr4D 48051341 48052025 684 False 249.000000 385 82.2280 1 659 2 chr4D.!!$F1 658
15 TraesCS1B01G378600 chr7B 425856261 425856877 616 True 258.500000 335 84.1570 1480 2171 2 chr7B.!!$R4 691
16 TraesCS1B01G378600 chr5A 143328893 143329425 532 False 329.000000 329 79.2210 45 539 1 chr5A.!!$F2 494

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
717 957 0.837272 GCAGCACCAGTCCCCTAATA 59.163 55.0 0.0 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 2034 0.163788 GCACGATTTGGTCACTCACG 59.836 55.0 0.0 0.0 0.0 4.35 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
36 37 8.737168 TTCTCATCTTTCTTTGTTCTCTTCAA 57.263 30.769 0.00 0.00 0.00 2.69
39 40 7.365741 TCATCTTTCTTTGTTCTCTTCAATGC 58.634 34.615 0.00 0.00 0.00 3.56
41 42 5.296780 TCTTTCTTTGTTCTCTTCAATGCGT 59.703 36.000 0.00 0.00 0.00 5.24
157 187 3.435327 TCGATGAACTTTGTCAAATCCGG 59.565 43.478 0.00 0.00 0.00 5.14
162 192 3.982576 ACTTTGTCAAATCCGGTGAAC 57.017 42.857 0.00 0.00 0.00 3.18
163 193 3.551846 ACTTTGTCAAATCCGGTGAACT 58.448 40.909 0.00 0.00 0.00 3.01
257 292 5.912892 ACGGGATGAACACTTTTCAAAATT 58.087 33.333 0.00 0.00 31.55 1.82
344 425 8.822652 ATGAACTCTTTTCAAATCAATGAACC 57.177 30.769 0.00 0.00 38.95 3.62
345 426 8.010733 TGAACTCTTTTCAAATCAATGAACCT 57.989 30.769 0.00 0.00 38.95 3.50
547 674 6.425417 GCTCTTATGGTTCTTATGGTTAGCTC 59.575 42.308 0.00 0.00 0.00 4.09
554 681 8.189119 TGGTTCTTATGGTTAGCTCAAAAATT 57.811 30.769 0.00 0.00 0.00 1.82
555 682 8.303876 TGGTTCTTATGGTTAGCTCAAAAATTC 58.696 33.333 0.00 0.00 0.00 2.17
561 688 3.057526 GGTTAGCTCAAAAATTCCGCTGT 60.058 43.478 0.00 0.00 32.49 4.40
717 957 0.837272 GCAGCACCAGTCCCCTAATA 59.163 55.000 0.00 0.00 0.00 0.98
719 959 2.158608 GCAGCACCAGTCCCCTAATAAT 60.159 50.000 0.00 0.00 0.00 1.28
720 960 3.688414 GCAGCACCAGTCCCCTAATAATT 60.688 47.826 0.00 0.00 0.00 1.40
721 961 4.536765 CAGCACCAGTCCCCTAATAATTT 58.463 43.478 0.00 0.00 0.00 1.82
722 962 4.956075 CAGCACCAGTCCCCTAATAATTTT 59.044 41.667 0.00 0.00 0.00 1.82
723 963 5.422012 CAGCACCAGTCCCCTAATAATTTTT 59.578 40.000 0.00 0.00 0.00 1.94
958 1224 2.177580 GCGCCGCCTATTTAGCACA 61.178 57.895 0.00 0.00 0.00 4.57
1544 1958 9.230122 TCTTGCTGTCATCAGTAATTTAAATGA 57.770 29.630 0.39 0.00 43.17 2.57
1620 2034 2.687700 ATGTGAGCCTGTCAGTGATC 57.312 50.000 0.00 0.00 35.13 2.92
1627 2041 1.988063 CCTGTCAGTGATCGTGAGTG 58.012 55.000 0.00 0.00 0.00 3.51
1691 2106 2.933492 GCCGGTTTATGCTACTGTGTCA 60.933 50.000 1.90 0.00 0.00 3.58
1721 2141 5.974751 TGCTTCAAGTTTTTAGCTTAAACGG 59.025 36.000 14.67 12.20 39.77 4.44
1727 2147 4.023450 AGTTTTTAGCTTAAACGGTGCCTC 60.023 41.667 14.67 0.00 39.77 4.70
1744 2164 2.232208 GCCTCTGGCTGCATTAAGTTTT 59.768 45.455 0.50 0.00 46.69 2.43
1753 2174 5.576774 GGCTGCATTAAGTTTTGTAATCACC 59.423 40.000 0.50 0.00 0.00 4.02
1801 2222 2.886523 CTGAATGAACAACCTTGGCTCA 59.113 45.455 0.00 0.00 0.00 4.26
1809 2230 3.299503 ACAACCTTGGCTCATTCAGTTT 58.700 40.909 0.00 0.00 0.00 2.66
1843 2290 6.012658 TCTGCTTTATGTTGTTTTAGCCTG 57.987 37.500 0.00 0.00 0.00 4.85
1875 2328 8.533569 TTATTCTGTATTTCCTTTTGATCCCC 57.466 34.615 0.00 0.00 0.00 4.81
1933 2389 7.859325 TGCTAACAACTGGTAAATTAGGATC 57.141 36.000 0.00 0.00 0.00 3.36
2027 2485 0.399075 TCGCATGCCATGATCCATCT 59.601 50.000 13.15 0.00 0.00 2.90
2171 2631 5.142061 TGTTCGCCTGTGTTAAGATCTTA 57.858 39.130 11.24 11.24 0.00 2.10
2172 2632 5.543714 TGTTCGCCTGTGTTAAGATCTTAA 58.456 37.500 21.46 21.46 33.10 1.85
2173 2633 6.170506 TGTTCGCCTGTGTTAAGATCTTAAT 58.829 36.000 26.46 0.82 37.37 1.40
2174 2634 6.092122 TGTTCGCCTGTGTTAAGATCTTAATG 59.908 38.462 26.46 17.37 37.37 1.90
2175 2635 4.570772 TCGCCTGTGTTAAGATCTTAATGC 59.429 41.667 26.46 21.48 37.37 3.56
2177 2637 5.065218 CGCCTGTGTTAAGATCTTAATGCTT 59.935 40.000 26.46 0.00 37.37 3.91
2178 2638 6.490534 GCCTGTGTTAAGATCTTAATGCTTC 58.509 40.000 26.46 15.73 37.37 3.86
2179 2639 6.458888 GCCTGTGTTAAGATCTTAATGCTTCC 60.459 42.308 26.46 15.13 37.37 3.46
2180 2640 6.038714 CCTGTGTTAAGATCTTAATGCTTCCC 59.961 42.308 26.46 14.53 37.37 3.97
2182 2642 6.599244 TGTGTTAAGATCTTAATGCTTCCCTG 59.401 38.462 26.46 0.00 37.37 4.45
2183 2643 5.590259 TGTTAAGATCTTAATGCTTCCCTGC 59.410 40.000 26.46 12.74 37.37 4.85
2185 2645 3.818180 AGATCTTAATGCTTCCCTGCAG 58.182 45.455 6.78 6.78 46.71 4.41
2186 2646 3.457380 AGATCTTAATGCTTCCCTGCAGA 59.543 43.478 17.39 0.00 46.71 4.26
2187 2647 3.272574 TCTTAATGCTTCCCTGCAGAG 57.727 47.619 17.39 0.39 46.71 3.35
2188 2648 1.674962 CTTAATGCTTCCCTGCAGAGC 59.325 52.381 17.39 17.04 46.71 4.09
2190 2650 2.838360 TGCTTCCCTGCAGAGCAA 59.162 55.556 22.32 9.25 42.89 3.91
2191 2651 1.151221 TGCTTCCCTGCAGAGCAAA 59.849 52.632 22.32 4.32 42.89 3.68
2192 2652 0.467844 TGCTTCCCTGCAGAGCAAAA 60.468 50.000 22.32 3.66 42.89 2.44
2193 2653 0.675633 GCTTCCCTGCAGAGCAAAAA 59.324 50.000 17.39 0.00 38.41 1.94
2194 2654 1.336609 GCTTCCCTGCAGAGCAAAAAG 60.337 52.381 17.39 9.81 38.41 2.27
2195 2655 1.271656 CTTCCCTGCAGAGCAAAAAGG 59.728 52.381 17.39 5.05 38.41 3.11
2196 2656 0.185901 TCCCTGCAGAGCAAAAAGGT 59.814 50.000 17.39 0.00 38.41 3.50
2197 2657 1.043022 CCCTGCAGAGCAAAAAGGTT 58.957 50.000 17.39 0.00 38.41 3.50
2198 2658 1.000171 CCCTGCAGAGCAAAAAGGTTC 60.000 52.381 17.39 0.00 38.41 3.62
2199 2659 1.335324 CCTGCAGAGCAAAAAGGTTCG 60.335 52.381 17.39 0.00 38.41 3.95
2237 2698 1.472376 GCTGAGGAGGTGTGATACTGC 60.472 57.143 0.00 0.00 0.00 4.40
2247 2708 4.584325 AGGTGTGATACTGCATGTTTTTGT 59.416 37.500 0.00 0.00 0.00 2.83
2283 2747 7.765360 TCCTCTGAACTTTAGAACGTGTTTTTA 59.235 33.333 0.00 0.00 0.00 1.52
2310 2774 8.341173 GCTCTAACATGTCTTAAGATCCATTTG 58.659 37.037 8.75 2.31 0.00 2.32
2317 2781 8.573885 CATGTCTTAAGATCCATTTGCACATAT 58.426 33.333 8.75 0.00 0.00 1.78
2335 2799 6.483307 GCACATATTTCTGTTGGCATCTAGTA 59.517 38.462 0.00 0.00 0.00 1.82
2336 2800 7.307632 GCACATATTTCTGTTGGCATCTAGTAG 60.308 40.741 0.00 0.00 0.00 2.57
2337 2801 7.712639 CACATATTTCTGTTGGCATCTAGTAGT 59.287 37.037 0.00 0.00 0.00 2.73
2341 2805 7.900782 TTTCTGTTGGCATCTAGTAGTTTAC 57.099 36.000 0.00 0.00 0.00 2.01
2342 2806 6.599356 TCTGTTGGCATCTAGTAGTTTACA 57.401 37.500 0.00 0.00 0.00 2.41
2343 2807 6.999950 TCTGTTGGCATCTAGTAGTTTACAA 58.000 36.000 0.00 0.00 0.00 2.41
2352 2816 9.651718 GCATCTAGTAGTTTACAATTTACATGC 57.348 33.333 0.00 0.00 0.00 4.06
2358 2822 8.677300 AGTAGTTTACAATTTACATGCATCCAG 58.323 33.333 0.00 0.00 0.00 3.86
2364 2828 3.836365 TTTACATGCATCCAGATCCGA 57.164 42.857 0.00 0.00 0.00 4.55
2368 2832 2.902486 ACATGCATCCAGATCCGATAGT 59.098 45.455 0.00 0.00 0.00 2.12
2371 2835 3.168292 TGCATCCAGATCCGATAGTGAT 58.832 45.455 0.00 0.00 0.00 3.06
2372 2836 3.056322 TGCATCCAGATCCGATAGTGATG 60.056 47.826 8.25 8.25 33.13 3.07
2374 2838 4.141981 GCATCCAGATCCGATAGTGATGAT 60.142 45.833 13.66 0.00 31.98 2.45
2387 2851 7.366513 CGATAGTGATGATGAAGCTCTAAAGA 58.633 38.462 0.00 0.00 0.00 2.52
2388 2852 7.864882 CGATAGTGATGATGAAGCTCTAAAGAA 59.135 37.037 0.00 0.00 0.00 2.52
2389 2853 9.709495 GATAGTGATGATGAAGCTCTAAAGAAT 57.291 33.333 0.00 0.00 0.00 2.40
2390 2854 7.789273 AGTGATGATGAAGCTCTAAAGAATG 57.211 36.000 0.00 0.00 0.00 2.67
2391 2855 6.766944 AGTGATGATGAAGCTCTAAAGAATGG 59.233 38.462 0.00 0.00 0.00 3.16
2392 2856 6.765036 GTGATGATGAAGCTCTAAAGAATGGA 59.235 38.462 0.00 0.00 0.00 3.41
2393 2857 7.444792 GTGATGATGAAGCTCTAAAGAATGGAT 59.555 37.037 0.00 0.00 0.00 3.41
2394 2858 7.997223 TGATGATGAAGCTCTAAAGAATGGATT 59.003 33.333 0.00 0.00 0.00 3.01
2395 2859 7.563888 TGATGAAGCTCTAAAGAATGGATTG 57.436 36.000 0.00 0.00 0.00 2.67
2396 2860 5.824904 TGAAGCTCTAAAGAATGGATTGC 57.175 39.130 0.00 0.00 0.00 3.56
2397 2861 5.503927 TGAAGCTCTAAAGAATGGATTGCT 58.496 37.500 0.00 0.00 0.00 3.91
2398 2862 5.948162 TGAAGCTCTAAAGAATGGATTGCTT 59.052 36.000 0.00 0.00 40.31 3.91
2399 2863 7.112122 TGAAGCTCTAAAGAATGGATTGCTTA 58.888 34.615 0.00 0.00 38.18 3.09
2400 2864 6.934048 AGCTCTAAAGAATGGATTGCTTAC 57.066 37.500 0.00 0.00 0.00 2.34
2401 2865 6.418101 AGCTCTAAAGAATGGATTGCTTACA 58.582 36.000 0.00 0.00 0.00 2.41
2402 2866 6.886459 AGCTCTAAAGAATGGATTGCTTACAA 59.114 34.615 0.00 0.00 40.87 2.41
2403 2867 7.394359 AGCTCTAAAGAATGGATTGCTTACAAA 59.606 33.333 0.00 0.00 39.77 2.83
2404 2868 8.028938 GCTCTAAAGAATGGATTGCTTACAAAA 58.971 33.333 0.00 0.00 39.77 2.44
2405 2869 9.912634 CTCTAAAGAATGGATTGCTTACAAAAA 57.087 29.630 0.00 0.00 39.77 1.94
2427 2891 8.722480 AAAAAGTATCACATGATCGATGAAGA 57.278 30.769 0.54 0.00 35.80 2.87
2428 2892 8.899427 AAAAGTATCACATGATCGATGAAGAT 57.101 30.769 0.54 2.90 35.80 2.40
2429 2893 7.886405 AAGTATCACATGATCGATGAAGATG 57.114 36.000 0.54 2.26 35.80 2.90
2430 2894 7.224522 AGTATCACATGATCGATGAAGATGA 57.775 36.000 0.54 0.22 35.80 2.92
2431 2895 7.664758 AGTATCACATGATCGATGAAGATGAA 58.335 34.615 0.54 0.00 35.80 2.57
2432 2896 6.782298 ATCACATGATCGATGAAGATGAAC 57.218 37.500 0.54 0.00 35.80 3.18
2433 2897 5.052481 TCACATGATCGATGAAGATGAACC 58.948 41.667 0.54 0.00 35.80 3.62
2434 2898 4.812626 CACATGATCGATGAAGATGAACCA 59.187 41.667 0.54 0.00 35.80 3.67
2435 2899 5.050295 CACATGATCGATGAAGATGAACCAG 60.050 44.000 0.54 0.00 35.80 4.00
2436 2900 4.743057 TGATCGATGAAGATGAACCAGT 57.257 40.909 0.54 0.00 0.00 4.00
2437 2901 5.852282 TGATCGATGAAGATGAACCAGTA 57.148 39.130 0.54 0.00 0.00 2.74
2438 2902 5.592054 TGATCGATGAAGATGAACCAGTAC 58.408 41.667 0.54 0.00 0.00 2.73
2439 2903 5.360999 TGATCGATGAAGATGAACCAGTACT 59.639 40.000 0.54 0.00 0.00 2.73
2440 2904 6.546034 TGATCGATGAAGATGAACCAGTACTA 59.454 38.462 0.54 0.00 0.00 1.82
2441 2905 6.378710 TCGATGAAGATGAACCAGTACTAG 57.621 41.667 0.00 0.00 0.00 2.57
2442 2906 6.120220 TCGATGAAGATGAACCAGTACTAGA 58.880 40.000 0.00 0.00 0.00 2.43
2443 2907 6.261158 TCGATGAAGATGAACCAGTACTAGAG 59.739 42.308 0.00 0.00 0.00 2.43
2444 2908 6.261158 CGATGAAGATGAACCAGTACTAGAGA 59.739 42.308 0.00 0.00 0.00 3.10
2445 2909 7.201741 CGATGAAGATGAACCAGTACTAGAGAA 60.202 40.741 0.00 0.00 0.00 2.87
2446 2910 7.776618 TGAAGATGAACCAGTACTAGAGAAA 57.223 36.000 0.00 0.00 0.00 2.52
2447 2911 7.831753 TGAAGATGAACCAGTACTAGAGAAAG 58.168 38.462 0.00 0.00 0.00 2.62
2448 2912 6.215495 AGATGAACCAGTACTAGAGAAAGC 57.785 41.667 0.00 0.00 0.00 3.51
2449 2913 4.803098 TGAACCAGTACTAGAGAAAGCC 57.197 45.455 0.00 0.00 0.00 4.35
2450 2914 4.157246 TGAACCAGTACTAGAGAAAGCCA 58.843 43.478 0.00 0.00 0.00 4.75
2451 2915 4.777896 TGAACCAGTACTAGAGAAAGCCAT 59.222 41.667 0.00 0.00 0.00 4.40
2452 2916 5.248477 TGAACCAGTACTAGAGAAAGCCATT 59.752 40.000 0.00 0.00 0.00 3.16
2453 2917 6.439375 TGAACCAGTACTAGAGAAAGCCATTA 59.561 38.462 0.00 0.00 0.00 1.90
2454 2918 6.472686 ACCAGTACTAGAGAAAGCCATTAG 57.527 41.667 0.00 0.00 0.00 1.73
2455 2919 5.364157 ACCAGTACTAGAGAAAGCCATTAGG 59.636 44.000 0.00 0.00 38.23 2.69
2456 2920 5.364157 CCAGTACTAGAGAAAGCCATTAGGT 59.636 44.000 0.00 0.00 37.19 3.08
2457 2921 6.550108 CCAGTACTAGAGAAAGCCATTAGGTA 59.450 42.308 0.00 0.00 37.19 3.08
2458 2922 7.069578 CCAGTACTAGAGAAAGCCATTAGGTAA 59.930 40.741 0.00 0.00 37.19 2.85
2459 2923 8.643324 CAGTACTAGAGAAAGCCATTAGGTAAT 58.357 37.037 0.00 0.00 37.19 1.89
2460 2924 9.214962 AGTACTAGAGAAAGCCATTAGGTAATT 57.785 33.333 0.00 0.00 37.19 1.40
2461 2925 9.833917 GTACTAGAGAAAGCCATTAGGTAATTT 57.166 33.333 0.00 0.00 37.19 1.82
2480 2944 9.023967 GGTAATTTATCATTTGAACTCACATGC 57.976 33.333 0.00 0.00 34.85 4.06
2481 2945 9.793252 GTAATTTATCATTTGAACTCACATGCT 57.207 29.630 0.00 0.00 34.85 3.79
2482 2946 8.922058 AATTTATCATTTGAACTCACATGCTC 57.078 30.769 0.00 0.00 34.85 4.26
2483 2947 7.692460 TTTATCATTTGAACTCACATGCTCT 57.308 32.000 0.00 0.00 34.85 4.09
2484 2948 8.791327 TTTATCATTTGAACTCACATGCTCTA 57.209 30.769 0.00 0.00 34.85 2.43
2485 2949 8.969260 TTATCATTTGAACTCACATGCTCTAT 57.031 30.769 0.00 0.00 34.85 1.98
2486 2950 7.876936 ATCATTTGAACTCACATGCTCTATT 57.123 32.000 0.00 0.00 34.85 1.73
2487 2951 7.692460 TCATTTGAACTCACATGCTCTATTT 57.308 32.000 0.00 0.00 34.85 1.40
2488 2952 7.532571 TCATTTGAACTCACATGCTCTATTTG 58.467 34.615 0.00 0.00 34.85 2.32
2489 2953 6.882610 TTTGAACTCACATGCTCTATTTGT 57.117 33.333 0.00 0.00 0.00 2.83
2490 2954 7.977789 TTTGAACTCACATGCTCTATTTGTA 57.022 32.000 0.00 0.00 0.00 2.41
2491 2955 8.565896 TTTGAACTCACATGCTCTATTTGTAT 57.434 30.769 0.00 0.00 0.00 2.29
2492 2956 8.565896 TTGAACTCACATGCTCTATTTGTATT 57.434 30.769 0.00 0.00 0.00 1.89
2493 2957 9.665719 TTGAACTCACATGCTCTATTTGTATTA 57.334 29.630 0.00 0.00 0.00 0.98
2494 2958 9.836864 TGAACTCACATGCTCTATTTGTATTAT 57.163 29.630 0.00 0.00 0.00 1.28
2504 2968 9.474313 TGCTCTATTTGTATTATTTTTCCCACT 57.526 29.630 0.00 0.00 0.00 4.00
2528 2992 4.930463 TTTTTCTGTTTTGGCGGTTTTC 57.070 36.364 0.00 0.00 0.00 2.29
2529 2993 2.588027 TTCTGTTTTGGCGGTTTTCC 57.412 45.000 0.00 0.00 0.00 3.13
2530 2994 1.475403 TCTGTTTTGGCGGTTTTCCA 58.525 45.000 0.00 0.00 40.70 3.53
2531 2995 1.407258 TCTGTTTTGGCGGTTTTCCAG 59.593 47.619 0.00 0.00 40.70 3.86
2532 2996 1.136110 CTGTTTTGGCGGTTTTCCAGT 59.864 47.619 0.00 0.00 40.70 4.00
2533 2997 2.359531 CTGTTTTGGCGGTTTTCCAGTA 59.640 45.455 0.00 0.00 40.70 2.74
2534 2998 2.099427 TGTTTTGGCGGTTTTCCAGTAC 59.901 45.455 0.00 0.00 40.70 2.73
2535 2999 2.351706 TTTGGCGGTTTTCCAGTACT 57.648 45.000 0.00 0.00 40.70 2.73
2536 3000 1.600023 TTGGCGGTTTTCCAGTACTG 58.400 50.000 16.34 16.34 40.70 2.74
2537 3001 0.759959 TGGCGGTTTTCCAGTACTGA 59.240 50.000 24.68 7.64 40.70 3.41
2538 3002 1.141254 TGGCGGTTTTCCAGTACTGAA 59.859 47.619 24.68 13.16 40.70 3.02
2539 3003 2.223745 GGCGGTTTTCCAGTACTGAAA 58.776 47.619 24.68 17.81 40.70 2.69
2540 3004 2.817844 GGCGGTTTTCCAGTACTGAAAT 59.182 45.455 24.68 0.00 40.70 2.17
2541 3005 3.254903 GGCGGTTTTCCAGTACTGAAATT 59.745 43.478 24.68 0.00 40.70 1.82
2542 3006 4.456566 GGCGGTTTTCCAGTACTGAAATTA 59.543 41.667 24.68 6.33 40.70 1.40
2543 3007 5.124936 GGCGGTTTTCCAGTACTGAAATTAT 59.875 40.000 24.68 0.00 40.70 1.28
2544 3008 6.255950 GCGGTTTTCCAGTACTGAAATTATC 58.744 40.000 24.68 8.12 40.70 1.75
2545 3009 6.677187 GCGGTTTTCCAGTACTGAAATTATCC 60.677 42.308 24.68 12.70 40.70 2.59
2546 3010 6.598064 CGGTTTTCCAGTACTGAAATTATCCT 59.402 38.462 24.68 0.00 40.70 3.24
2547 3011 7.120726 CGGTTTTCCAGTACTGAAATTATCCTT 59.879 37.037 24.68 0.00 40.70 3.36
2548 3012 8.244113 GGTTTTCCAGTACTGAAATTATCCTTG 58.756 37.037 24.68 2.83 40.31 3.61
2549 3013 7.938140 TTTCCAGTACTGAAATTATCCTTGG 57.062 36.000 24.68 3.51 0.00 3.61
2550 3014 6.884472 TCCAGTACTGAAATTATCCTTGGA 57.116 37.500 24.68 6.00 0.00 3.53
2551 3015 7.265599 TCCAGTACTGAAATTATCCTTGGAA 57.734 36.000 24.68 0.00 0.00 3.53
2552 3016 7.338710 TCCAGTACTGAAATTATCCTTGGAAG 58.661 38.462 24.68 1.15 0.00 3.46
2553 3017 6.038714 CCAGTACTGAAATTATCCTTGGAAGC 59.961 42.308 24.68 0.00 0.00 3.86
2554 3018 5.817816 AGTACTGAAATTATCCTTGGAAGCG 59.182 40.000 0.00 0.00 0.00 4.68
2555 3019 3.378427 ACTGAAATTATCCTTGGAAGCGC 59.622 43.478 0.00 0.00 0.00 5.92
2556 3020 3.620488 TGAAATTATCCTTGGAAGCGCT 58.380 40.909 2.64 2.64 0.00 5.92
2557 3021 4.016444 TGAAATTATCCTTGGAAGCGCTT 58.984 39.130 25.35 25.35 0.00 4.68
2558 3022 4.142403 TGAAATTATCCTTGGAAGCGCTTG 60.142 41.667 30.47 13.11 0.00 4.01
2559 3023 1.750193 TTATCCTTGGAAGCGCTTGG 58.250 50.000 30.47 22.20 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 270 5.982516 TCAATTTTGAAAAGTGTTCATCCCG 59.017 36.000 16.28 0.00 33.55 5.14
315 392 8.301720 TCATTGATTTGAAAAGAGTTCATCCTG 58.698 33.333 0.00 0.00 0.00 3.86
316 393 8.413309 TCATTGATTTGAAAAGAGTTCATCCT 57.587 30.769 0.00 0.00 0.00 3.24
463 545 9.705290 ACTTTATAACTTGGATTTGCGAATTTT 57.295 25.926 0.00 0.00 0.00 1.82
500 582 3.486708 CCGCGCTATTTATTGCACAGAAA 60.487 43.478 5.56 0.00 0.00 2.52
561 688 1.875514 ACTAGAACACACGACGCTACA 59.124 47.619 0.00 0.00 0.00 2.74
568 695 1.888215 ACGAGGACTAGAACACACGA 58.112 50.000 0.00 0.00 0.00 4.35
572 699 3.755378 TGGTAGAACGAGGACTAGAACAC 59.245 47.826 0.00 0.00 0.00 3.32
573 700 4.008330 CTGGTAGAACGAGGACTAGAACA 58.992 47.826 0.00 0.00 0.00 3.18
654 794 2.224523 TGTTGGCCCGAGATGGATATTC 60.225 50.000 0.00 0.00 42.00 1.75
722 962 2.030007 GTGCTGGTGCTGCTGATAAAAA 60.030 45.455 0.00 0.00 40.48 1.94
723 963 1.541147 GTGCTGGTGCTGCTGATAAAA 59.459 47.619 0.00 0.00 40.48 1.52
725 965 0.325933 AGTGCTGGTGCTGCTGATAA 59.674 50.000 0.00 0.00 40.48 1.75
726 966 0.107993 GAGTGCTGGTGCTGCTGATA 60.108 55.000 0.00 0.00 40.48 2.15
776 1017 1.278238 GATTGGTTCGCTACGAGTGG 58.722 55.000 0.00 0.00 37.14 4.00
958 1224 4.467107 GACGGAGGGGAGGGAGCT 62.467 72.222 0.00 0.00 0.00 4.09
1544 1958 8.635765 TCTTAGAACAGATAGCCAACATTTTT 57.364 30.769 0.00 0.00 0.00 1.94
1620 2034 0.163788 GCACGATTTGGTCACTCACG 59.836 55.000 0.00 0.00 0.00 4.35
1627 2041 6.348540 GGGATAATAGAATGCACGATTTGGTC 60.349 42.308 0.00 0.00 0.00 4.02
1727 2147 6.308766 GTGATTACAAAACTTAATGCAGCCAG 59.691 38.462 0.00 0.00 0.00 4.85
1753 2174 6.680810 TCAGAGGCAATCAACAAAATTACTG 58.319 36.000 0.00 0.00 0.00 2.74
1801 2222 4.261741 GCAGATGGACACACAAAACTGAAT 60.262 41.667 0.00 0.00 0.00 2.57
1809 2230 4.397420 ACATAAAGCAGATGGACACACAA 58.603 39.130 0.00 0.00 0.00 3.33
1843 2290 8.925700 CAAAAGGAAATACAGAATAAAACAGCC 58.074 33.333 0.00 0.00 0.00 4.85
1875 2328 0.870393 AGTTGATTGCAGCAGTCACG 59.130 50.000 19.55 0.00 30.16 4.35
1933 2389 8.939929 TGCAAAATAGAAACATCTCTTGTCTAG 58.060 33.333 0.00 0.00 37.68 2.43
1990 2446 6.128849 GCATGCGACACAAAATTTGATAGTTT 60.129 34.615 13.19 0.00 0.00 2.66
2027 2485 2.231964 GCAGGTGCAAGAAATCCATCAA 59.768 45.455 0.00 0.00 41.59 2.57
2053 2511 1.948834 TGACAACACCATGAAGCTGTG 59.051 47.619 0.00 0.00 36.11 3.66
2078 2538 1.000955 ACACCTTCTGCCTCAACTACG 59.999 52.381 0.00 0.00 0.00 3.51
2080 2540 3.007614 GGTTACACCTTCTGCCTCAACTA 59.992 47.826 0.00 0.00 34.73 2.24
2081 2541 2.224548 GGTTACACCTTCTGCCTCAACT 60.225 50.000 0.00 0.00 34.73 3.16
2171 2631 0.251474 TTGCTCTGCAGGGAAGCATT 60.251 50.000 24.32 0.00 44.68 3.56
2172 2632 0.251474 TTTGCTCTGCAGGGAAGCAT 60.251 50.000 24.32 0.00 44.68 3.79
2173 2633 0.467844 TTTTGCTCTGCAGGGAAGCA 60.468 50.000 20.53 20.88 40.61 3.91
2174 2634 0.675633 TTTTTGCTCTGCAGGGAAGC 59.324 50.000 20.53 18.29 40.61 3.86
2175 2635 1.271656 CCTTTTTGCTCTGCAGGGAAG 59.728 52.381 20.53 11.85 40.61 3.46
2177 2637 0.185901 ACCTTTTTGCTCTGCAGGGA 59.814 50.000 20.53 4.87 40.61 4.20
2178 2638 1.000171 GAACCTTTTTGCTCTGCAGGG 60.000 52.381 15.13 12.70 40.61 4.45
2179 2639 1.335324 CGAACCTTTTTGCTCTGCAGG 60.335 52.381 15.13 5.82 40.61 4.85
2180 2640 1.603802 TCGAACCTTTTTGCTCTGCAG 59.396 47.619 7.63 7.63 40.61 4.41
2182 2642 1.333619 TGTCGAACCTTTTTGCTCTGC 59.666 47.619 0.00 0.00 0.00 4.26
2183 2643 3.363178 GTTGTCGAACCTTTTTGCTCTG 58.637 45.455 0.00 0.00 0.00 3.35
2195 2655 3.252974 AGGATCTCATGGTTGTCGAAC 57.747 47.619 0.00 0.00 0.00 3.95
2196 2656 3.181475 GCTAGGATCTCATGGTTGTCGAA 60.181 47.826 0.00 0.00 0.00 3.71
2197 2657 2.362397 GCTAGGATCTCATGGTTGTCGA 59.638 50.000 0.00 0.00 0.00 4.20
2198 2658 2.363680 AGCTAGGATCTCATGGTTGTCG 59.636 50.000 0.00 0.00 0.00 4.35
2199 2659 3.386078 TCAGCTAGGATCTCATGGTTGTC 59.614 47.826 0.00 0.00 0.00 3.18
2224 2684 4.584325 ACAAAAACATGCAGTATCACACCT 59.416 37.500 0.00 0.00 0.00 4.00
2225 2685 4.870363 ACAAAAACATGCAGTATCACACC 58.130 39.130 0.00 0.00 0.00 4.16
2229 2689 7.503521 TCTGTTACAAAAACATGCAGTATCA 57.496 32.000 0.00 0.00 0.00 2.15
2232 2693 6.320164 ACCTTCTGTTACAAAAACATGCAGTA 59.680 34.615 0.00 0.00 0.00 2.74
2237 2698 6.263168 AGAGGACCTTCTGTTACAAAAACATG 59.737 38.462 0.00 0.00 0.00 3.21
2247 2708 5.888982 AAAGTTCAGAGGACCTTCTGTTA 57.111 39.130 16.04 7.27 43.96 2.41
2268 2732 8.492748 CATGTTAGAGCTAAAAACACGTTCTAA 58.507 33.333 9.45 0.00 36.06 2.10
2270 2734 6.482308 ACATGTTAGAGCTAAAAACACGTTCT 59.518 34.615 9.45 0.00 36.06 3.01
2283 2747 6.798427 TGGATCTTAAGACATGTTAGAGCT 57.202 37.500 7.48 0.00 0.00 4.09
2310 2774 4.644103 AGATGCCAACAGAAATATGTGC 57.356 40.909 0.00 0.00 32.52 4.57
2317 2781 7.446769 TGTAAACTACTAGATGCCAACAGAAA 58.553 34.615 0.00 0.00 0.00 2.52
2335 2799 7.701539 TCTGGATGCATGTAAATTGTAAACT 57.298 32.000 2.46 0.00 0.00 2.66
2336 2800 7.649306 GGATCTGGATGCATGTAAATTGTAAAC 59.351 37.037 2.46 0.00 0.00 2.01
2337 2801 7.468494 CGGATCTGGATGCATGTAAATTGTAAA 60.468 37.037 2.46 0.00 0.00 2.01
2340 2804 4.276678 CGGATCTGGATGCATGTAAATTGT 59.723 41.667 2.46 0.00 0.00 2.71
2341 2805 4.516321 TCGGATCTGGATGCATGTAAATTG 59.484 41.667 2.46 0.00 0.00 2.32
2342 2806 4.717877 TCGGATCTGGATGCATGTAAATT 58.282 39.130 2.46 0.00 0.00 1.82
2343 2807 4.356405 TCGGATCTGGATGCATGTAAAT 57.644 40.909 2.46 0.00 0.00 1.40
2352 2816 5.126707 TCATCATCACTATCGGATCTGGATG 59.873 44.000 14.54 14.54 33.71 3.51
2354 2818 4.666512 TCATCATCACTATCGGATCTGGA 58.333 43.478 0.62 0.00 0.00 3.86
2358 2822 5.070770 AGCTTCATCATCACTATCGGATC 57.929 43.478 0.00 0.00 0.00 3.36
2364 2828 9.491675 CATTCTTTAGAGCTTCATCATCACTAT 57.508 33.333 0.00 0.00 0.00 2.12
2368 2832 6.892485 TCCATTCTTTAGAGCTTCATCATCA 58.108 36.000 0.00 0.00 0.00 3.07
2371 2835 6.039047 GCAATCCATTCTTTAGAGCTTCATCA 59.961 38.462 0.00 0.00 0.00 3.07
2372 2836 6.262720 AGCAATCCATTCTTTAGAGCTTCATC 59.737 38.462 0.00 0.00 0.00 2.92
2374 2838 5.503927 AGCAATCCATTCTTTAGAGCTTCA 58.496 37.500 0.00 0.00 0.00 3.02
2402 2866 8.722480 TCTTCATCGATCATGTGATACTTTTT 57.278 30.769 0.00 0.00 34.37 1.94
2403 2867 8.771766 CATCTTCATCGATCATGTGATACTTTT 58.228 33.333 0.00 0.00 34.37 2.27
2404 2868 8.146412 TCATCTTCATCGATCATGTGATACTTT 58.854 33.333 0.00 0.00 34.37 2.66
2405 2869 7.664758 TCATCTTCATCGATCATGTGATACTT 58.335 34.615 0.00 0.00 34.37 2.24
2406 2870 7.224522 TCATCTTCATCGATCATGTGATACT 57.775 36.000 0.00 0.00 34.37 2.12
2407 2871 7.148672 GGTTCATCTTCATCGATCATGTGATAC 60.149 40.741 0.00 0.00 34.37 2.24
2408 2872 6.870439 GGTTCATCTTCATCGATCATGTGATA 59.130 38.462 0.00 0.00 34.37 2.15
2409 2873 5.699915 GGTTCATCTTCATCGATCATGTGAT 59.300 40.000 0.00 0.00 37.51 3.06
2410 2874 5.052481 GGTTCATCTTCATCGATCATGTGA 58.948 41.667 0.00 0.00 33.66 3.58
2411 2875 4.812626 TGGTTCATCTTCATCGATCATGTG 59.187 41.667 0.00 0.00 33.66 3.21
2412 2876 5.027293 TGGTTCATCTTCATCGATCATGT 57.973 39.130 0.00 0.00 33.66 3.21
2413 2877 5.055144 ACTGGTTCATCTTCATCGATCATG 58.945 41.667 0.00 0.00 0.00 3.07
2414 2878 5.287674 ACTGGTTCATCTTCATCGATCAT 57.712 39.130 0.00 0.00 0.00 2.45
2415 2879 4.743057 ACTGGTTCATCTTCATCGATCA 57.257 40.909 0.00 0.00 0.00 2.92
2416 2880 5.837437 AGTACTGGTTCATCTTCATCGATC 58.163 41.667 0.00 0.00 0.00 3.69
2417 2881 5.860941 AGTACTGGTTCATCTTCATCGAT 57.139 39.130 0.00 0.00 0.00 3.59
2418 2882 6.120220 TCTAGTACTGGTTCATCTTCATCGA 58.880 40.000 5.39 0.00 0.00 3.59
2419 2883 6.261158 TCTCTAGTACTGGTTCATCTTCATCG 59.739 42.308 5.39 0.00 0.00 3.84
2420 2884 7.575414 TCTCTAGTACTGGTTCATCTTCATC 57.425 40.000 5.39 0.00 0.00 2.92
2421 2885 7.962995 TTCTCTAGTACTGGTTCATCTTCAT 57.037 36.000 5.39 0.00 0.00 2.57
2422 2886 7.577807 GCTTTCTCTAGTACTGGTTCATCTTCA 60.578 40.741 5.39 0.00 0.00 3.02
2423 2887 6.754675 GCTTTCTCTAGTACTGGTTCATCTTC 59.245 42.308 5.39 0.00 0.00 2.87
2424 2888 6.351456 GGCTTTCTCTAGTACTGGTTCATCTT 60.351 42.308 5.39 0.00 0.00 2.40
2425 2889 5.128008 GGCTTTCTCTAGTACTGGTTCATCT 59.872 44.000 5.39 0.00 0.00 2.90
2426 2890 5.105310 TGGCTTTCTCTAGTACTGGTTCATC 60.105 44.000 5.39 0.00 0.00 2.92
2427 2891 4.777896 TGGCTTTCTCTAGTACTGGTTCAT 59.222 41.667 5.39 0.00 0.00 2.57
2428 2892 4.157246 TGGCTTTCTCTAGTACTGGTTCA 58.843 43.478 5.39 0.00 0.00 3.18
2429 2893 4.803098 TGGCTTTCTCTAGTACTGGTTC 57.197 45.455 5.39 0.00 0.00 3.62
2430 2894 5.763876 AATGGCTTTCTCTAGTACTGGTT 57.236 39.130 5.39 0.00 0.00 3.67
2431 2895 5.364157 CCTAATGGCTTTCTCTAGTACTGGT 59.636 44.000 5.39 0.00 0.00 4.00
2432 2896 5.364157 ACCTAATGGCTTTCTCTAGTACTGG 59.636 44.000 5.39 1.87 36.63 4.00
2433 2897 6.472686 ACCTAATGGCTTTCTCTAGTACTG 57.527 41.667 5.39 0.00 36.63 2.74
2434 2898 8.785184 ATTACCTAATGGCTTTCTCTAGTACT 57.215 34.615 0.00 0.00 36.63 2.73
2435 2899 9.833917 AAATTACCTAATGGCTTTCTCTAGTAC 57.166 33.333 0.00 0.00 36.63 2.73
2454 2918 9.023967 GCATGTGAGTTCAAATGATAAATTACC 57.976 33.333 14.93 0.00 42.78 2.85
2455 2919 9.793252 AGCATGTGAGTTCAAATGATAAATTAC 57.207 29.630 14.93 0.00 42.78 1.89
2457 2921 8.746530 AGAGCATGTGAGTTCAAATGATAAATT 58.253 29.630 14.93 0.00 40.02 1.82
2458 2922 8.289939 AGAGCATGTGAGTTCAAATGATAAAT 57.710 30.769 14.93 0.00 40.02 1.40
2459 2923 7.692460 AGAGCATGTGAGTTCAAATGATAAA 57.308 32.000 14.93 0.00 40.02 1.40
2460 2924 8.969260 ATAGAGCATGTGAGTTCAAATGATAA 57.031 30.769 14.93 2.85 40.02 1.75
2461 2925 8.969260 AATAGAGCATGTGAGTTCAAATGATA 57.031 30.769 14.93 5.87 40.02 2.15
2462 2926 7.876936 AATAGAGCATGTGAGTTCAAATGAT 57.123 32.000 14.93 9.33 42.37 2.45
2463 2927 7.175467 ACAAATAGAGCATGTGAGTTCAAATGA 59.825 33.333 14.93 0.00 42.78 2.57
2464 2928 7.310664 ACAAATAGAGCATGTGAGTTCAAATG 58.689 34.615 7.75 7.75 42.96 2.32
2465 2929 7.458409 ACAAATAGAGCATGTGAGTTCAAAT 57.542 32.000 0.00 0.00 0.00 2.32
2466 2930 6.882610 ACAAATAGAGCATGTGAGTTCAAA 57.117 33.333 0.00 0.00 0.00 2.69
2467 2931 8.565896 AATACAAATAGAGCATGTGAGTTCAA 57.434 30.769 0.00 0.00 0.00 2.69
2468 2932 9.836864 ATAATACAAATAGAGCATGTGAGTTCA 57.163 29.630 0.00 0.00 0.00 3.18
2478 2942 9.474313 AGTGGGAAAAATAATACAAATAGAGCA 57.526 29.630 0.00 0.00 0.00 4.26
2507 2971 3.685272 GGAAAACCGCCAAAACAGAAAAA 59.315 39.130 0.00 0.00 0.00 1.94
2508 2972 3.263261 GGAAAACCGCCAAAACAGAAAA 58.737 40.909 0.00 0.00 0.00 2.29
2509 2973 2.233922 TGGAAAACCGCCAAAACAGAAA 59.766 40.909 0.00 0.00 31.13 2.52
2510 2974 1.825474 TGGAAAACCGCCAAAACAGAA 59.175 42.857 0.00 0.00 31.13 3.02
2511 2975 1.407258 CTGGAAAACCGCCAAAACAGA 59.593 47.619 0.00 0.00 34.44 3.41
2512 2976 1.136110 ACTGGAAAACCGCCAAAACAG 59.864 47.619 0.00 0.00 34.44 3.16
2513 2977 1.187087 ACTGGAAAACCGCCAAAACA 58.813 45.000 0.00 0.00 34.44 2.83
2514 2978 2.359848 AGTACTGGAAAACCGCCAAAAC 59.640 45.455 0.00 0.00 34.44 2.43
2515 2979 2.359531 CAGTACTGGAAAACCGCCAAAA 59.640 45.455 15.49 0.00 34.44 2.44
2516 2980 1.950909 CAGTACTGGAAAACCGCCAAA 59.049 47.619 15.49 0.00 34.44 3.28
2517 2981 1.141254 TCAGTACTGGAAAACCGCCAA 59.859 47.619 22.48 0.00 34.44 4.52
2518 2982 0.759959 TCAGTACTGGAAAACCGCCA 59.240 50.000 22.48 0.00 0.00 5.69
2519 2983 1.886886 TTCAGTACTGGAAAACCGCC 58.113 50.000 22.48 0.00 0.00 6.13
2520 2984 4.499037 AATTTCAGTACTGGAAAACCGC 57.501 40.909 20.42 0.00 37.74 5.68
2521 2985 6.598064 AGGATAATTTCAGTACTGGAAAACCG 59.402 38.462 20.42 0.00 37.74 4.44
2522 2986 7.939784 AGGATAATTTCAGTACTGGAAAACC 57.060 36.000 20.42 18.32 37.74 3.27
2523 2987 8.244113 CCAAGGATAATTTCAGTACTGGAAAAC 58.756 37.037 20.42 11.35 37.74 2.43
2524 2988 8.167392 TCCAAGGATAATTTCAGTACTGGAAAA 58.833 33.333 20.42 15.21 37.74 2.29
2525 2989 7.695055 TCCAAGGATAATTTCAGTACTGGAAA 58.305 34.615 20.42 18.48 38.49 3.13
2526 2990 7.265599 TCCAAGGATAATTTCAGTACTGGAA 57.734 36.000 18.94 18.94 31.71 3.53
2527 2991 6.884472 TCCAAGGATAATTTCAGTACTGGA 57.116 37.500 22.48 11.97 0.00 3.86
2528 2992 6.038714 GCTTCCAAGGATAATTTCAGTACTGG 59.961 42.308 22.48 4.59 0.00 4.00
2529 2993 6.238211 CGCTTCCAAGGATAATTTCAGTACTG 60.238 42.308 17.17 17.17 0.00 2.74
2530 2994 5.817816 CGCTTCCAAGGATAATTTCAGTACT 59.182 40.000 0.00 0.00 0.00 2.73
2531 2995 5.504173 GCGCTTCCAAGGATAATTTCAGTAC 60.504 44.000 0.00 0.00 0.00 2.73
2532 2996 4.574828 GCGCTTCCAAGGATAATTTCAGTA 59.425 41.667 0.00 0.00 0.00 2.74
2533 2997 3.378427 GCGCTTCCAAGGATAATTTCAGT 59.622 43.478 0.00 0.00 0.00 3.41
2534 2998 3.629398 AGCGCTTCCAAGGATAATTTCAG 59.371 43.478 2.64 0.00 0.00 3.02
2535 2999 3.620488 AGCGCTTCCAAGGATAATTTCA 58.380 40.909 2.64 0.00 0.00 2.69
2536 3000 4.354587 CAAGCGCTTCCAAGGATAATTTC 58.645 43.478 22.21 0.00 0.00 2.17
2537 3001 3.131046 CCAAGCGCTTCCAAGGATAATTT 59.869 43.478 22.21 0.00 0.00 1.82
2538 3002 2.689983 CCAAGCGCTTCCAAGGATAATT 59.310 45.455 22.21 0.00 0.00 1.40
2539 3003 2.301346 CCAAGCGCTTCCAAGGATAAT 58.699 47.619 22.21 0.00 0.00 1.28
2540 3004 1.750193 CCAAGCGCTTCCAAGGATAA 58.250 50.000 22.21 0.00 0.00 1.75
2541 3005 3.476740 CCAAGCGCTTCCAAGGATA 57.523 52.632 22.21 0.00 0.00 2.59
2542 3006 4.326255 CCAAGCGCTTCCAAGGAT 57.674 55.556 22.21 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.