Multiple sequence alignment - TraesCS2A01G032500

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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 TraesCS2A01G032500 chr2A 100.000 4785 0 0 985 5769 14808961 14813745 0.000000e+00 8837.0
1 TraesCS2A01G032500 chr2A 100.000 530 0 0 1 530 14807977 14808506 0.000000e+00 979.0
2 TraesCS2A01G032500 chr2A 82.422 256 26 10 212 455 14780032 14780280 7.580000e-49 206.0
3 TraesCS2A01G032500 chr2A 100.000 31 0 0 4340 4370 14812285 14812315 2.250000e-04 58.4
4 TraesCS2A01G032500 chr2A 100.000 31 0 0 4309 4339 14812316 14812346 2.250000e-04 58.4
5 TraesCS2A01G032500 chr2D 93.045 2516 114 29 1783 4292 12687230 12689690 0.000000e+00 3620.0
6 TraesCS2A01G032500 chr2D 89.682 1415 89 31 4378 5769 12689747 12691127 0.000000e+00 1751.0
7 TraesCS2A01G032500 chr2D 90.921 749 38 15 985 1719 12686489 12687221 0.000000e+00 979.0
8 TraesCS2A01G032500 chr2D 89.002 491 26 15 52 530 12685803 12686277 3.000000e-162 582.0
9 TraesCS2A01G032500 chr2D 89.706 68 6 1 1717 1784 592405545 592405611 1.030000e-12 86.1
10 TraesCS2A01G032500 chr2D 93.103 58 3 1 1729 1786 105501610 105501554 3.700000e-12 84.2
11 TraesCS2A01G032500 chr2B 91.146 1954 116 29 985 2908 23113986 23115912 0.000000e+00 2597.0
12 TraesCS2A01G032500 chr2B 95.765 1346 51 6 2997 4339 23115913 23117255 0.000000e+00 2165.0
13 TraesCS2A01G032500 chr2B 93.179 689 36 6 4416 5093 23117268 23117956 0.000000e+00 1002.0
14 TraesCS2A01G032500 chr2B 86.590 522 60 7 5254 5769 23117947 23118464 8.390000e-158 568.0
15 TraesCS2A01G032500 chr2B 84.182 373 29 13 172 530 23113411 23113767 9.260000e-88 335.0
16 TraesCS2A01G032500 chr2B 87.629 97 8 4 80 173 23113163 23113258 6.110000e-20 110.0
17 TraesCS2A01G032500 chr2B 97.826 46 1 0 4340 4385 23117225 23117270 4.790000e-11 80.5
18 TraesCS2A01G032500 chr4B 96.429 56 1 1 1729 1783 409585477 409585532 2.210000e-14 91.6
19 TraesCS2A01G032500 chr7B 94.643 56 2 1 1729 1783 81378728 81378673 1.030000e-12 86.1
20 TraesCS2A01G032500 chr6B 94.545 55 3 0 1729 1783 704956925 704956979 1.030000e-12 86.1
21 TraesCS2A01G032500 chrUn 87.143 70 6 2 1717 1785 255311831 255311898 6.200000e-10 76.8
22 TraesCS2A01G032500 chrUn 87.143 70 6 2 1717 1785 255322546 255322613 6.200000e-10 76.8
23 TraesCS2A01G032500 chrUn 87.143 70 6 2 1717 1785 307901542 307901475 6.200000e-10 76.8


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 TraesCS2A01G032500 chr2A 14807977 14813745 5768 False 2483.200000 8837 100.000000 1 5769 4 chr2A.!!$F2 5768
1 TraesCS2A01G032500 chr2D 12685803 12691127 5324 False 1733.000000 3620 90.662500 52 5769 4 chr2D.!!$F2 5717
2 TraesCS2A01G032500 chr2B 23113163 23118464 5301 False 979.642857 2597 90.902429 80 5769 7 chr2B.!!$F1 5689

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
343 504 0.031817 CCTTCAAATCCTGCCCCCAT 60.032 55.000 0.00 0.0 0.00 4.00 F
427 597 0.179094 CAACCCATGTCATGCCATGC 60.179 55.000 11.24 0.0 40.72 4.06 F
432 602 1.000612 ATGTCATGCCATGCCCACA 59.999 52.632 0.00 0.0 0.00 4.17 F
2063 2268 1.079819 ATCCTTGACGGTGCTGTCG 60.080 57.895 6.66 0.0 41.87 4.35 F
2975 3188 1.135286 TCTGTCTGTGACATGCTAGCG 60.135 52.381 10.77 0.0 41.94 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 2023 0.383860 GGGCGACGAAAAAGACAACG 60.384 55.000 0.00 0.0 0.00 4.10 R
2106 2311 1.255342 CACGAGGTCAAATACGCATCG 59.745 52.381 0.00 0.0 36.12 3.84 R
2159 2365 2.169144 TGATGACTGGTCACATAGGCAG 59.831 50.000 5.52 0.0 43.11 4.85 R
3546 3761 1.141881 AGCTGGTGTTATCGCCTCG 59.858 57.895 5.05 0.0 43.94 4.63 R
4800 5044 1.076777 CCATTCCTCACCGGCCAAT 60.077 57.895 0.00 0.0 0.00 3.16 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
22 23 3.912496 ACAAGGATCATCGTCCAATCA 57.088 42.857 0.00 0.00 40.90 2.57
23 24 4.220693 ACAAGGATCATCGTCCAATCAA 57.779 40.909 0.00 0.00 40.90 2.57
24 25 4.588899 ACAAGGATCATCGTCCAATCAAA 58.411 39.130 0.00 0.00 40.90 2.69
25 26 5.009631 ACAAGGATCATCGTCCAATCAAAA 58.990 37.500 0.00 0.00 40.90 2.44
26 27 5.476599 ACAAGGATCATCGTCCAATCAAAAA 59.523 36.000 0.00 0.00 40.90 1.94
49 50 7.408132 AAATCACGACCTTGATAATATCACG 57.592 36.000 1.88 6.01 39.39 4.35
50 51 5.761165 TCACGACCTTGATAATATCACGA 57.239 39.130 14.92 0.00 39.39 4.35
56 57 6.342338 ACCTTGATAATATCACGACCTACC 57.658 41.667 8.14 0.00 39.39 3.18
69 70 2.671396 CGACCTACCGTCCAATCAAAAG 59.329 50.000 0.00 0.00 38.36 2.27
72 73 3.071892 ACCTACCGTCCAATCAAAAGTCA 59.928 43.478 0.00 0.00 0.00 3.41
79 80 3.189287 GTCCAATCAAAAGTCATGACGCT 59.811 43.478 19.85 8.84 36.20 5.07
82 83 4.153986 CAATCAAAAGTCATGACGCTCAC 58.846 43.478 19.85 0.00 36.20 3.51
85 86 1.139989 AAAGTCATGACGCTCACACG 58.860 50.000 19.85 0.00 39.50 4.49
95 99 3.556365 TGACGCTCACACGAACATTAAAA 59.444 39.130 0.00 0.00 36.70 1.52
157 161 2.828520 TCACAAACCAAACACACCATGT 59.171 40.909 0.00 0.00 46.42 3.21
237 395 8.715191 TTTGATATGCAATTACCCAAAACATC 57.285 30.769 0.00 0.00 36.15 3.06
341 502 2.060383 GCCTTCAAATCCTGCCCCC 61.060 63.158 0.00 0.00 0.00 5.40
342 503 1.387737 CCTTCAAATCCTGCCCCCA 59.612 57.895 0.00 0.00 0.00 4.96
343 504 0.031817 CCTTCAAATCCTGCCCCCAT 60.032 55.000 0.00 0.00 0.00 4.00
381 551 2.167487 ACATTTGGGGTCAACACAACAC 59.833 45.455 0.00 0.00 31.78 3.32
382 552 1.924731 TTTGGGGTCAACACAACACA 58.075 45.000 0.00 0.00 31.78 3.72
392 562 2.292103 ACACAACACAAACATGGTGC 57.708 45.000 0.00 0.00 41.28 5.01
399 569 1.107114 ACAAACATGGTGCGGTCAAA 58.893 45.000 0.00 0.00 0.00 2.69
424 594 0.335705 ATCCAACCCATGTCATGCCA 59.664 50.000 7.35 0.00 0.00 4.92
425 595 0.335705 TCCAACCCATGTCATGCCAT 59.664 50.000 7.35 0.00 0.00 4.40
426 596 0.462375 CCAACCCATGTCATGCCATG 59.538 55.000 9.77 9.77 41.52 3.66
427 597 0.179094 CAACCCATGTCATGCCATGC 60.179 55.000 11.24 0.00 40.72 4.06
429 599 2.504274 CCCATGTCATGCCATGCCC 61.504 63.158 11.24 0.00 40.72 5.36
430 600 1.758906 CCATGTCATGCCATGCCCA 60.759 57.895 11.24 0.00 40.72 5.36
431 601 1.440060 CATGTCATGCCATGCCCAC 59.560 57.895 3.43 0.00 36.15 4.61
432 602 1.000612 ATGTCATGCCATGCCCACA 59.999 52.632 0.00 0.00 0.00 4.17
433 603 1.324740 ATGTCATGCCATGCCCACAC 61.325 55.000 0.00 0.00 0.00 3.82
434 604 1.978080 GTCATGCCATGCCCACACA 60.978 57.895 0.00 0.00 0.00 3.72
455 625 8.993121 CACACAATATAAATACTCCACATCCTC 58.007 37.037 0.00 0.00 0.00 3.71
486 656 5.304101 ACCTCTGAGCCAATAGATTAGACAG 59.696 44.000 0.00 0.00 0.00 3.51
488 658 4.590647 TCTGAGCCAATAGATTAGACAGGG 59.409 45.833 0.00 0.00 0.00 4.45
489 659 4.556697 TGAGCCAATAGATTAGACAGGGA 58.443 43.478 0.00 0.00 0.00 4.20
490 660 4.968719 TGAGCCAATAGATTAGACAGGGAA 59.031 41.667 0.00 0.00 0.00 3.97
1062 1237 4.436998 CTGGTCGACCTCGTGGCC 62.437 72.222 33.39 6.83 40.80 5.36
1230 1405 2.533318 GTGCCTCCACTTCAACTCG 58.467 57.895 0.00 0.00 38.93 4.18
1431 1606 2.805099 CTCAGTTCCTTCTGCTGTTGTC 59.195 50.000 0.00 0.00 35.63 3.18
1474 1649 2.432444 CCATTTTTCACCCGTCTGCTA 58.568 47.619 0.00 0.00 0.00 3.49
1480 1655 1.557099 TCACCCGTCTGCTAGTTCAT 58.443 50.000 0.00 0.00 0.00 2.57
1523 1699 4.839796 TCTTGTTCGACCGAAAACATTTC 58.160 39.130 6.41 0.00 35.46 2.17
1524 1700 4.573201 TCTTGTTCGACCGAAAACATTTCT 59.427 37.500 6.41 0.00 35.46 2.52
1606 1787 3.814283 GGCTTGCAAATTGACAATTGGAA 59.186 39.130 17.88 14.87 0.00 3.53
1615 1806 7.432869 CAAATTGACAATTGGAAGAAGGTGTA 58.567 34.615 14.05 0.00 0.00 2.90
1675 1866 7.635423 TGTATTGACGATTTGATTTATTCCCG 58.365 34.615 0.00 0.00 0.00 5.14
1710 1901 1.678101 GTAGGATGCAATGTTGGCTCC 59.322 52.381 0.00 0.00 0.00 4.70
1726 1917 7.434492 TGTTGGCTCCACGAATTAAATTTAAA 58.566 30.769 14.35 0.00 0.00 1.52
1728 1919 6.626302 TGGCTCCACGAATTAAATTTAAAGG 58.374 36.000 14.35 11.08 0.00 3.11
1730 1921 6.750501 GGCTCCACGAATTAAATTTAAAGGTC 59.249 38.462 14.35 10.87 0.00 3.85
1769 1960 9.892130 AAAATACAGAGAGGACTTATAAACCAG 57.108 33.333 9.91 0.00 0.00 4.00
1773 1964 5.422331 CAGAGAGGACTTATAAACCAGGACA 59.578 44.000 0.00 0.00 0.00 4.02
1779 1970 5.659971 GGACTTATAAACCAGGACAGAGGTA 59.340 44.000 0.00 0.00 37.07 3.08
1789 1980 6.080009 ACCAGGACAGAGGTAGTACTTAAAA 58.920 40.000 0.00 0.00 36.07 1.52
1790 1981 6.210984 ACCAGGACAGAGGTAGTACTTAAAAG 59.789 42.308 0.00 0.00 36.07 2.27
1791 1982 6.436532 CCAGGACAGAGGTAGTACTTAAAAGA 59.563 42.308 0.00 0.00 0.00 2.52
1792 1983 7.314393 CAGGACAGAGGTAGTACTTAAAAGAC 58.686 42.308 0.00 0.00 0.00 3.01
1828 2023 1.683385 GCCAAAGAATATGGTGCCTCC 59.317 52.381 0.00 0.00 40.23 4.30
1875 2078 2.711009 ACTCTTGTCCTTCCATTGTGGA 59.289 45.455 0.00 0.00 46.61 4.02
1895 2098 8.213518 TGTGGAAGAATTTAGCATCTTATCAC 57.786 34.615 11.32 11.32 38.72 3.06
1898 2101 7.500227 TGGAAGAATTTAGCATCTTATCACTGG 59.500 37.037 0.00 0.00 36.08 4.00
2054 2259 2.020131 GATGCTGCCATCCTTGACG 58.980 57.895 0.00 0.00 41.62 4.35
2063 2268 1.079819 ATCCTTGACGGTGCTGTCG 60.080 57.895 6.66 0.00 41.87 4.35
2112 2317 2.025156 GGATTGCCTTGCGATGCG 59.975 61.111 0.00 0.00 31.59 4.73
2131 2337 2.281762 GCGTATTTGACCTCGTGCTTAG 59.718 50.000 0.00 0.00 0.00 2.18
2159 2365 3.026694 ACTTGATTTTAGCAGCCCCATC 58.973 45.455 0.00 0.00 0.00 3.51
2168 2374 1.842007 CAGCCCCATCTGCCTATGT 59.158 57.895 0.00 0.00 0.00 2.29
2179 2385 2.432146 TCTGCCTATGTGACCAGTCATC 59.568 50.000 3.41 0.00 42.18 2.92
2209 2415 8.166367 GCTACAGCATTTCTTTATTTTCACTG 57.834 34.615 0.00 0.00 41.59 3.66
2210 2416 7.809806 GCTACAGCATTTCTTTATTTTCACTGT 59.190 33.333 0.00 0.00 41.59 3.55
2211 2417 9.683069 CTACAGCATTTCTTTATTTTCACTGTT 57.317 29.630 0.00 0.00 36.22 3.16
2212 2418 8.947055 ACAGCATTTCTTTATTTTCACTGTTT 57.053 26.923 0.00 0.00 30.94 2.83
2213 2419 9.382275 ACAGCATTTCTTTATTTTCACTGTTTT 57.618 25.926 0.00 0.00 30.94 2.43
2214 2420 9.853921 CAGCATTTCTTTATTTTCACTGTTTTC 57.146 29.630 0.00 0.00 0.00 2.29
2215 2421 8.755018 AGCATTTCTTTATTTTCACTGTTTTCG 58.245 29.630 0.00 0.00 0.00 3.46
2216 2422 8.751335 GCATTTCTTTATTTTCACTGTTTTCGA 58.249 29.630 0.00 0.00 0.00 3.71
2219 2425 9.796120 TTTCTTTATTTTCACTGTTTTCGATGT 57.204 25.926 0.00 0.00 0.00 3.06
2220 2426 8.781067 TCTTTATTTTCACTGTTTTCGATGTG 57.219 30.769 0.00 0.00 0.00 3.21
2221 2427 8.616942 TCTTTATTTTCACTGTTTTCGATGTGA 58.383 29.630 0.00 0.00 37.62 3.58
2222 2428 8.555166 TTTATTTTCACTGTTTTCGATGTGAC 57.445 30.769 0.00 0.00 38.87 3.67
2223 2429 5.553290 TTTTCACTGTTTTCGATGTGACA 57.447 34.783 0.00 0.00 38.87 3.58
2224 2430 5.749596 TTTCACTGTTTTCGATGTGACAT 57.250 34.783 0.00 0.00 38.87 3.06
2225 2431 4.730600 TCACTGTTTTCGATGTGACATG 57.269 40.909 1.23 0.00 34.94 3.21
2226 2432 4.376146 TCACTGTTTTCGATGTGACATGA 58.624 39.130 1.23 0.00 34.94 3.07
2227 2433 4.996758 TCACTGTTTTCGATGTGACATGAT 59.003 37.500 1.23 0.00 34.94 2.45
2228 2434 5.084055 CACTGTTTTCGATGTGACATGATG 58.916 41.667 1.23 0.00 32.72 3.07
2229 2435 4.756642 ACTGTTTTCGATGTGACATGATGT 59.243 37.500 1.23 0.00 0.00 3.06
2230 2436 5.033326 TGTTTTCGATGTGACATGATGTG 57.967 39.130 1.23 0.00 0.00 3.21
2231 2437 4.514816 TGTTTTCGATGTGACATGATGTGT 59.485 37.500 1.23 0.00 45.83 3.72
2403 2610 2.816087 ACATGTGATGTTCTCCTTGTGC 59.184 45.455 0.00 0.00 41.63 4.57
2435 2642 5.084519 TGCCCTTCTCTTGAGTACTAAAGA 58.915 41.667 19.76 19.76 0.00 2.52
2450 2657 7.721402 AGTACTAAAGAATCCTATCAGCACTG 58.279 38.462 0.00 0.00 0.00 3.66
2455 2662 9.553064 CTAAAGAATCCTATCAGCACTGTTAAT 57.447 33.333 0.00 0.00 0.00 1.40
2473 2680 5.010516 TGTTAATTCACCCCATTGAACTGTG 59.989 40.000 0.00 0.00 38.31 3.66
2491 2698 7.766738 TGAACTGTGTTTGAACTATGTCTGTTA 59.233 33.333 0.00 0.00 0.00 2.41
2555 2762 3.861840 TGCAGTAGCTCTGAATTACCAC 58.138 45.455 14.86 0.00 46.27 4.16
2650 2862 3.008594 TGATGATTGACCAGTTACCGGTT 59.991 43.478 15.04 0.00 36.69 4.44
2665 2877 7.916450 CAGTTACCGGTTGTTTTTCTTGAATTA 59.084 33.333 15.04 0.00 0.00 1.40
2666 2878 8.132995 AGTTACCGGTTGTTTTTCTTGAATTAG 58.867 33.333 15.04 0.00 0.00 1.73
2694 2906 9.790344 ATTTTCACCAATTTGTATGGAATTTCA 57.210 25.926 0.00 0.00 40.56 2.69
2975 3188 1.135286 TCTGTCTGTGACATGCTAGCG 60.135 52.381 10.77 0.00 41.94 4.26
3019 3232 9.573133 CACCATCATAACCTTTTTGATTAACTC 57.427 33.333 0.00 0.00 0.00 3.01
3028 3241 7.716612 ACCTTTTTGATTAACTCCAAGTCTTG 58.283 34.615 5.53 5.53 0.00 3.02
3278 3493 7.933577 TCTGTCATGATTCACTTTAGAACAGTT 59.066 33.333 0.00 0.00 0.00 3.16
3281 3496 6.655003 TCATGATTCACTTTAGAACAGTTCCC 59.345 38.462 9.85 0.00 0.00 3.97
3301 3516 3.440522 CCCTCTTAAGTGGCTTTAACTGC 59.559 47.826 16.65 0.00 0.00 4.40
3414 3629 6.079424 TGTCCTTTGTGGTATTACTTTTGC 57.921 37.500 0.00 0.00 37.07 3.68
3431 3646 3.306917 TTGCGTCCAATTCTAACGAGA 57.693 42.857 7.70 0.00 38.65 4.04
3522 3737 1.256812 CAAGAACATGGGGGACAACC 58.743 55.000 0.00 0.00 39.11 3.77
3546 3761 2.822764 CCTGGCTTACCTTATGTCGAC 58.177 52.381 9.11 9.11 36.63 4.20
3582 3797 1.304381 TGGGAACTGGCTGATTGGC 60.304 57.895 0.00 0.00 42.18 4.52
3588 3803 2.359850 TGGCTGATTGGCGGTGAC 60.360 61.111 0.00 0.00 45.14 3.67
3609 3824 0.539438 TGGAGGTGTTGCAACCCATC 60.539 55.000 28.02 23.31 41.54 3.51
3612 3827 1.686052 GAGGTGTTGCAACCCATCAAA 59.314 47.619 28.02 9.12 41.54 2.69
3766 3981 1.174783 TGACACTAGAAGGCGTCTCC 58.825 55.000 6.13 0.00 37.84 3.71
3858 4073 2.636830 CCACTGCCTGTTAGAATGGAG 58.363 52.381 0.00 0.00 0.00 3.86
3876 4092 2.162408 GGAGCAACACAGCAAGGTAATC 59.838 50.000 0.00 0.00 36.85 1.75
3882 4098 6.015519 AGCAACACAGCAAGGTAATCATTTTA 60.016 34.615 0.00 0.00 36.85 1.52
3987 4203 2.840651 CCTTGACCCTGAGACCACTATT 59.159 50.000 0.00 0.00 0.00 1.73
3999 4215 8.085296 CCTGAGACCACTATTGTGTCTATATTC 58.915 40.741 6.55 0.08 42.34 1.75
4080 4296 7.524717 AATTAATGCCGGTGCTAATTTCTAT 57.475 32.000 1.90 0.00 38.71 1.98
4173 4389 1.589414 AGAAGGTCCTAAGCATGGCT 58.411 50.000 0.00 0.00 42.56 4.75
4228 4444 4.156556 TCAAGGTATTTGATGCACAGAAGC 59.843 41.667 0.00 0.00 40.82 3.86
4231 4447 4.080356 AGGTATTTGATGCACAGAAGCCTA 60.080 41.667 0.00 0.00 0.00 3.93
4271 4487 8.871686 AATATTGTCAAAGTTGTCCTGTTTTC 57.128 30.769 0.00 0.00 0.00 2.29
4286 4502 6.264518 GTCCTGTTTTCCTTTAGTTGGATCAA 59.735 38.462 0.00 0.00 33.09 2.57
4299 4515 1.888512 TGGATCAACTTCAAGGCTTGC 59.111 47.619 22.31 5.57 0.00 4.01
4309 4525 8.147058 TCAACTTCAAGGCTTGCAATTTATTAA 58.853 29.630 22.31 7.15 0.00 1.40
4310 4526 8.772705 CAACTTCAAGGCTTGCAATTTATTAAA 58.227 29.630 22.31 6.45 0.00 1.52
4311 4527 8.900983 ACTTCAAGGCTTGCAATTTATTAAAA 57.099 26.923 22.31 5.96 0.00 1.52
4312 4528 9.506018 ACTTCAAGGCTTGCAATTTATTAAAAT 57.494 25.926 22.31 0.00 36.87 1.82
4338 4554 7.382898 TGTTTCCACCTTTTAATTCTAATGCC 58.617 34.615 0.00 0.00 0.00 4.40
4339 4555 7.015682 TGTTTCCACCTTTTAATTCTAATGCCA 59.984 33.333 0.00 0.00 0.00 4.92
4387 4621 2.375174 TGCCCTTAACACATCTCTTGGT 59.625 45.455 0.00 0.00 0.00 3.67
4391 4625 5.556915 CCCTTAACACATCTCTTGGTTGTA 58.443 41.667 0.00 0.00 0.00 2.41
4401 4635 8.950210 CACATCTCTTGGTTGTATTACTCATTT 58.050 33.333 0.00 0.00 0.00 2.32
4409 4643 8.958119 TGGTTGTATTACTCATTTGTATCTCC 57.042 34.615 0.00 0.00 0.00 3.71
4410 4644 8.544622 TGGTTGTATTACTCATTTGTATCTCCA 58.455 33.333 0.00 0.00 0.00 3.86
4418 4652 4.264253 TCATTTGTATCTCCAGCCACTTG 58.736 43.478 0.00 0.00 0.00 3.16
4555 4790 6.349860 GGAACCAAGGTAAGCGTTTCATTTAT 60.350 38.462 0.00 0.00 0.00 1.40
4562 4797 8.106247 AGGTAAGCGTTTCATTTATTTTCAGA 57.894 30.769 0.00 0.00 0.00 3.27
4574 4809 8.587608 TCATTTATTTTCAGAGGACAAATGCTT 58.412 29.630 0.00 0.00 33.84 3.91
4623 4867 1.993370 GCTGCTAACAACTGACCTACG 59.007 52.381 0.00 0.00 0.00 3.51
4732 4976 5.642063 TGACTACTACAATAGCTTGCAAACC 59.358 40.000 0.00 0.00 35.69 3.27
4799 5043 3.706698 CTGCATGGCTTTGAGATCATTG 58.293 45.455 0.00 0.00 0.00 2.82
4800 5044 3.358118 TGCATGGCTTTGAGATCATTGA 58.642 40.909 0.00 0.00 0.00 2.57
4803 5047 4.745125 GCATGGCTTTGAGATCATTGATTG 59.255 41.667 0.00 0.00 0.00 2.67
4809 5053 1.212688 TGAGATCATTGATTGGCCGGT 59.787 47.619 1.90 0.00 0.00 5.28
4810 5054 1.605710 GAGATCATTGATTGGCCGGTG 59.394 52.381 1.90 0.00 0.00 4.94
4813 5057 0.394216 TCATTGATTGGCCGGTGAGG 60.394 55.000 1.90 0.00 44.97 3.86
4906 5161 6.654161 GCTAGTTTATTGATGCCATCAGATCT 59.346 38.462 7.55 6.39 40.94 2.75
4912 5167 3.548770 TGATGCCATCAGATCTTCCAAC 58.451 45.455 2.53 0.00 33.59 3.77
4920 5175 5.651139 CCATCAGATCTTCCAACTGTTCAAT 59.349 40.000 0.00 0.00 33.93 2.57
5001 5257 0.647410 CAGATTGAGCTGTAACCGCG 59.353 55.000 0.00 0.00 0.00 6.46
5022 5278 3.900116 CGCCGCAAATTCTGTTATTATCG 59.100 43.478 0.00 0.00 0.00 2.92
5107 5363 6.932356 TCCAAGATCAGACTGCAATTAATC 57.068 37.500 0.00 0.00 0.00 1.75
5116 5372 8.387190 TCAGACTGCAATTAATCTCCATATTG 57.613 34.615 0.00 0.00 0.00 1.90
5183 5439 6.580788 AGATGATGACAGTCCAACTTATCAG 58.419 40.000 0.00 0.00 29.73 2.90
5216 5472 8.856153 TTTGTACTATATTCAACAAAGCCTCA 57.144 30.769 0.00 0.00 37.02 3.86
5238 5494 7.094805 CCTCACGATTCAGGATTTAAACAAAGA 60.095 37.037 0.00 0.00 30.32 2.52
5318 5574 4.261489 GCATCAGGCCATTATCAGAAAGTG 60.261 45.833 5.01 0.00 36.11 3.16
5340 5596 2.140717 GTTGGAGTGTAACCAAGGACG 58.859 52.381 0.00 0.00 46.12 4.79
5346 5602 3.399330 AGTGTAACCAAGGACGATGTTG 58.601 45.455 0.00 0.00 37.80 3.33
5398 5656 3.626028 ATCAAAGTGCGGAAAAGTGTC 57.374 42.857 0.00 0.00 0.00 3.67
5436 5694 4.081406 TCATAGCATGCCACACTTTCTTT 58.919 39.130 15.66 0.00 0.00 2.52
5456 5714 0.736325 AGTCACATACGCCGCTTGTC 60.736 55.000 0.00 0.00 0.00 3.18
5463 5721 0.812549 TACGCCGCTTGTCATAGACA 59.187 50.000 0.00 0.00 41.09 3.41
5487 5745 1.904287 TGCTAACCAACTTTCGCCAT 58.096 45.000 0.00 0.00 0.00 4.40
5538 5796 4.514816 GGCATAAAAAGTGTGGCAAAATGT 59.485 37.500 0.00 0.00 38.21 2.71
5578 5837 0.534877 TGACACTGGCGCTTGTTCAT 60.535 50.000 7.64 0.00 0.00 2.57
5604 5863 1.152860 ACATGTTGGGTTGTGCCGA 60.153 52.632 0.00 0.00 38.44 5.54
5611 5870 0.457851 TGGGTTGTGCCGACAAAAAG 59.542 50.000 0.00 0.00 43.77 2.27
5612 5871 0.249280 GGGTTGTGCCGACAAAAAGG 60.249 55.000 0.00 0.00 43.77 3.11
5616 5878 1.104577 TGTGCCGACAAAAAGGGTCC 61.105 55.000 0.00 0.00 31.55 4.46
5620 5882 2.951458 GACAAAAAGGGTCCGCGG 59.049 61.111 22.12 22.12 0.00 6.46
5631 5893 4.094830 AGGGTCCGCGGAAAATATTATT 57.905 40.909 32.93 5.13 0.00 1.40
5648 5910 7.891498 ATATTATTTTGCGGTTTACTCCCTT 57.109 32.000 0.00 0.00 0.00 3.95
5649 5911 5.632244 TTATTTTGCGGTTTACTCCCTTC 57.368 39.130 0.00 0.00 0.00 3.46
5685 5947 3.060473 CGACGTTTTGGAGACTTGAAGTC 60.060 47.826 17.22 17.22 45.38 3.01
5708 5970 7.235812 AGTCTACATAGGAAGTCCTTTTGAAGT 59.764 37.037 4.91 0.00 46.09 3.01
5739 6001 6.870439 CACAAGAAAAAGGGAGAAAATGGATC 59.130 38.462 0.00 0.00 0.00 3.36
5743 6005 2.604046 AGGGAGAAAATGGATCGTCG 57.396 50.000 0.00 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.220693 TGATTGGACGATGATCCTTGTT 57.779 40.909 0.00 0.00 39.75 2.83
3 4 5.565592 TTTTGATTGGACGATGATCCTTG 57.434 39.130 0.00 0.00 39.75 3.61
23 24 8.335356 CGTGATATTATCAAGGTCGTGATTTTT 58.665 33.333 7.93 0.00 41.69 1.94
24 25 7.709182 TCGTGATATTATCAAGGTCGTGATTTT 59.291 33.333 16.34 0.00 41.69 1.82
25 26 7.169308 GTCGTGATATTATCAAGGTCGTGATTT 59.831 37.037 16.34 0.00 41.69 2.17
26 27 6.641314 GTCGTGATATTATCAAGGTCGTGATT 59.359 38.462 16.34 0.00 41.69 2.57
27 28 6.150318 GTCGTGATATTATCAAGGTCGTGAT 58.850 40.000 16.34 4.93 41.69 3.06
28 29 5.506815 GGTCGTGATATTATCAAGGTCGTGA 60.507 44.000 16.34 2.57 41.69 4.35
29 30 4.680110 GGTCGTGATATTATCAAGGTCGTG 59.320 45.833 16.34 0.72 41.69 4.35
30 31 4.583489 AGGTCGTGATATTATCAAGGTCGT 59.417 41.667 16.34 10.38 41.69 4.34
31 32 5.122512 AGGTCGTGATATTATCAAGGTCG 57.877 43.478 16.34 11.94 41.69 4.79
32 33 6.388278 GGTAGGTCGTGATATTATCAAGGTC 58.612 44.000 16.34 11.14 41.69 3.85
33 34 5.048224 CGGTAGGTCGTGATATTATCAAGGT 60.048 44.000 16.34 7.24 41.69 3.50
34 35 5.048224 ACGGTAGGTCGTGATATTATCAAGG 60.048 44.000 16.34 8.91 41.69 3.61
35 36 6.010294 ACGGTAGGTCGTGATATTATCAAG 57.990 41.667 7.93 10.14 41.69 3.02
36 37 6.005583 GACGGTAGGTCGTGATATTATCAA 57.994 41.667 7.93 0.00 43.96 2.57
37 38 5.618056 GACGGTAGGTCGTGATATTATCA 57.382 43.478 2.14 2.14 43.96 2.15
49 50 3.671716 ACTTTTGATTGGACGGTAGGTC 58.328 45.455 0.00 0.00 45.31 3.85
50 51 3.071892 TGACTTTTGATTGGACGGTAGGT 59.928 43.478 0.00 0.00 0.00 3.08
56 57 3.736213 CGTCATGACTTTTGATTGGACG 58.264 45.455 22.95 2.41 40.45 4.79
69 70 0.435008 GTTCGTGTGAGCGTCATGAC 59.565 55.000 16.21 16.21 31.71 3.06
72 73 1.795768 AATGTTCGTGTGAGCGTCAT 58.204 45.000 0.00 0.00 32.82 3.06
95 99 5.766150 TCTGTCATTTGGTCGTGATTTTT 57.234 34.783 0.00 0.00 0.00 1.94
173 177 1.063266 TGACTCCCCTTGGCACTTTTT 60.063 47.619 0.00 0.00 0.00 1.94
177 181 0.779997 ATTTGACTCCCCTTGGCACT 59.220 50.000 0.00 0.00 0.00 4.40
178 182 1.177401 GATTTGACTCCCCTTGGCAC 58.823 55.000 0.00 0.00 0.00 5.01
237 395 5.750067 GGTTTATGGCAATAAAGTGAGCATG 59.250 40.000 6.52 0.00 38.60 4.06
381 551 2.215907 TTTTGACCGCACCATGTTTG 57.784 45.000 0.00 0.00 0.00 2.93
382 552 2.363680 TGATTTTGACCGCACCATGTTT 59.636 40.909 0.00 0.00 0.00 2.83
392 562 3.006323 TGGGTTGGATTTGATTTTGACCG 59.994 43.478 0.00 0.00 0.00 4.79
399 569 4.383335 GCATGACATGGGTTGGATTTGATT 60.383 41.667 17.03 0.00 0.00 2.57
424 594 6.490040 GTGGAGTATTTATATTGTGTGGGCAT 59.510 38.462 0.00 0.00 0.00 4.40
425 595 5.825679 GTGGAGTATTTATATTGTGTGGGCA 59.174 40.000 0.00 0.00 0.00 5.36
426 596 5.825679 TGTGGAGTATTTATATTGTGTGGGC 59.174 40.000 0.00 0.00 0.00 5.36
427 597 7.174946 GGATGTGGAGTATTTATATTGTGTGGG 59.825 40.741 0.00 0.00 0.00 4.61
429 599 8.908786 AGGATGTGGAGTATTTATATTGTGTG 57.091 34.615 0.00 0.00 0.00 3.82
430 600 8.157476 GGAGGATGTGGAGTATTTATATTGTGT 58.843 37.037 0.00 0.00 0.00 3.72
431 601 7.607991 GGGAGGATGTGGAGTATTTATATTGTG 59.392 40.741 0.00 0.00 0.00 3.33
432 602 7.294720 TGGGAGGATGTGGAGTATTTATATTGT 59.705 37.037 0.00 0.00 0.00 2.71
433 603 7.607991 GTGGGAGGATGTGGAGTATTTATATTG 59.392 40.741 0.00 0.00 0.00 1.90
434 604 7.294720 TGTGGGAGGATGTGGAGTATTTATATT 59.705 37.037 0.00 0.00 0.00 1.28
455 625 0.178992 TTGGCTCAGAGGTTTGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
1383 1558 3.765257 ATGAGAGGAGGAGGGGGCG 62.765 68.421 0.00 0.00 0.00 6.13
1474 1649 1.308069 AAATGGAGCGCGCATGAACT 61.308 50.000 35.10 11.72 0.00 3.01
1480 1655 1.137194 CATGAAAATGGAGCGCGCA 59.863 52.632 35.10 13.97 0.00 6.09
1506 1681 3.065510 TGCAAGAAATGTTTTCGGTCGAA 59.934 39.130 1.33 1.33 0.00 3.71
1606 1787 4.332828 GGCCACAAAAGTATACACCTTCT 58.667 43.478 5.50 0.00 0.00 2.85
1615 1806 3.366052 CCTACAGGGCCACAAAAGTAT 57.634 47.619 6.18 0.00 0.00 2.12
1638 1829 9.225201 CAAATCGTCAATACATATCAAAACTGG 57.775 33.333 0.00 0.00 0.00 4.00
1675 1866 8.589335 TTGCATCCTACGTTCTCTAAATTATC 57.411 34.615 0.00 0.00 0.00 1.75
1726 1917 6.352516 TGTATTTTGTGCCAAATTTTGACCT 58.647 32.000 10.72 0.00 0.00 3.85
1728 1919 7.437862 TCTCTGTATTTTGTGCCAAATTTTGAC 59.562 33.333 10.72 0.00 0.00 3.18
1730 1921 7.095523 CCTCTCTGTATTTTGTGCCAAATTTTG 60.096 37.037 1.99 1.99 0.00 2.44
1751 1942 5.657302 TCTGTCCTGGTTTATAAGTCCTCTC 59.343 44.000 0.00 1.56 0.00 3.20
1753 1944 5.163395 CCTCTGTCCTGGTTTATAAGTCCTC 60.163 48.000 0.00 1.57 0.00 3.71
1755 1946 4.470304 ACCTCTGTCCTGGTTTATAAGTCC 59.530 45.833 0.00 2.91 31.62 3.85
1769 1960 7.465353 AGTCTTTTAAGTACTACCTCTGTCC 57.535 40.000 0.00 0.00 0.00 4.02
1773 1964 9.750783 TGTGATAGTCTTTTAAGTACTACCTCT 57.249 33.333 0.00 0.00 0.00 3.69
1789 1980 2.237392 GGCCCTGAACTTGTGATAGTCT 59.763 50.000 0.00 0.00 0.00 3.24
1790 1981 2.027192 TGGCCCTGAACTTGTGATAGTC 60.027 50.000 0.00 0.00 0.00 2.59
1791 1982 1.985159 TGGCCCTGAACTTGTGATAGT 59.015 47.619 0.00 0.00 0.00 2.12
1792 1983 2.787473 TGGCCCTGAACTTGTGATAG 57.213 50.000 0.00 0.00 0.00 2.08
1806 2001 0.752658 GGCACCATATTCTTTGGCCC 59.247 55.000 0.00 0.00 37.81 5.80
1828 2023 0.383860 GGGCGACGAAAAAGACAACG 60.384 55.000 0.00 0.00 0.00 4.10
1875 2078 6.774656 CCCCAGTGATAAGATGCTAAATTCTT 59.225 38.462 0.00 0.00 36.26 2.52
1895 2098 3.831911 TGCTTCACTAAATTTTCCCCCAG 59.168 43.478 0.00 0.00 0.00 4.45
1898 2101 5.921962 AGATGCTTCACTAAATTTTCCCC 57.078 39.130 0.00 0.00 0.00 4.81
2106 2311 1.255342 CACGAGGTCAAATACGCATCG 59.745 52.381 0.00 0.00 36.12 3.84
2112 2317 6.366877 TGTTAACTAAGCACGAGGTCAAATAC 59.633 38.462 7.22 0.00 0.00 1.89
2131 2337 5.633601 GGGCTGCTAAAATCAAGTTGTTAAC 59.366 40.000 2.11 0.00 0.00 2.01
2159 2365 2.169144 TGATGACTGGTCACATAGGCAG 59.831 50.000 5.52 0.00 43.11 4.85
2168 2374 4.256110 CTGTAGCAATTGATGACTGGTCA 58.744 43.478 10.34 5.87 44.59 4.02
2202 2408 5.295540 TCATGTCACATCGAAAACAGTGAAA 59.704 36.000 0.00 5.52 42.03 2.69
2203 2409 4.813697 TCATGTCACATCGAAAACAGTGAA 59.186 37.500 0.00 3.03 42.03 3.18
2204 2410 4.376146 TCATGTCACATCGAAAACAGTGA 58.624 39.130 0.00 0.00 38.56 3.41
2206 2412 4.756642 ACATCATGTCACATCGAAAACAGT 59.243 37.500 0.00 0.00 0.00 3.55
2207 2413 5.084055 CACATCATGTCACATCGAAAACAG 58.916 41.667 0.00 0.00 0.00 3.16
2209 2415 5.034554 ACACATCATGTCACATCGAAAAC 57.965 39.130 0.00 0.00 36.54 2.43
2222 2428 3.021695 AGAATTGGCCAGACACATCATG 58.978 45.455 5.11 0.00 0.00 3.07
2223 2429 3.377253 AGAATTGGCCAGACACATCAT 57.623 42.857 5.11 0.00 0.00 2.45
2224 2430 2.885135 AGAATTGGCCAGACACATCA 57.115 45.000 5.11 0.00 0.00 3.07
2225 2431 3.350833 AGAAGAATTGGCCAGACACATC 58.649 45.455 5.11 1.82 0.00 3.06
2226 2432 3.446442 AGAAGAATTGGCCAGACACAT 57.554 42.857 5.11 0.00 0.00 3.21
2227 2433 2.957402 AGAAGAATTGGCCAGACACA 57.043 45.000 5.11 0.00 0.00 3.72
2228 2434 3.416156 AGAAGAAGAATTGGCCAGACAC 58.584 45.455 5.11 0.00 0.00 3.67
2229 2435 3.795688 AGAAGAAGAATTGGCCAGACA 57.204 42.857 5.11 0.00 0.00 3.41
2230 2436 5.459536 AAAAGAAGAAGAATTGGCCAGAC 57.540 39.130 5.11 1.23 0.00 3.51
2231 2437 7.781324 ATAAAAAGAAGAAGAATTGGCCAGA 57.219 32.000 5.11 0.00 0.00 3.86
2232 2438 9.927668 TTTATAAAAAGAAGAAGAATTGGCCAG 57.072 29.630 5.11 0.00 0.00 4.85
2279 2486 8.515414 AGCACAGATACCTTCAACTTTAAAATC 58.485 33.333 0.00 0.00 0.00 2.17
2357 2564 6.764085 TGTCAATTTCTACTTTTGAAGTCGGA 59.236 34.615 0.00 0.00 41.77 4.55
2435 2642 6.543831 GGTGAATTAACAGTGCTGATAGGATT 59.456 38.462 6.17 0.00 0.00 3.01
2450 2657 5.010617 ACACAGTTCAATGGGGTGAATTAAC 59.989 40.000 0.00 0.00 39.61 2.01
2455 2662 2.746279 ACACAGTTCAATGGGGTGAA 57.254 45.000 0.00 0.00 35.14 3.18
2491 2698 7.877097 GGATTCAGATATGCTTAGAATGTCTGT 59.123 37.037 21.32 7.96 41.47 3.41
2723 2935 7.411274 TGGTACAATTTTTGAAGTACTCAACG 58.589 34.615 0.00 0.00 38.75 4.10
3019 3232 9.345517 CAAAATATGTATGTGTTCAAGACTTGG 57.654 33.333 15.13 0.00 0.00 3.61
3028 3241 8.396272 AGATAGCCCAAAATATGTATGTGTTC 57.604 34.615 0.00 0.00 0.00 3.18
3278 3493 4.806286 GCAGTTAAAGCCACTTAAGAGGGA 60.806 45.833 19.08 0.00 0.00 4.20
3281 3496 5.062308 CGTAGCAGTTAAAGCCACTTAAGAG 59.938 44.000 10.09 0.27 0.00 2.85
3301 3516 4.380841 TGATTGGTTGCTACTACCGTAG 57.619 45.455 3.88 3.88 44.77 3.51
3414 3629 6.090898 AGTGAAAATCTCGTTAGAATTGGACG 59.909 38.462 0.00 0.00 34.73 4.79
3522 3737 1.227556 ATAAGGTAAGCCAGGCGCG 60.228 57.895 5.55 0.00 44.76 6.86
3546 3761 1.141881 AGCTGGTGTTATCGCCTCG 59.858 57.895 5.05 0.00 43.94 4.63
3588 3803 1.903404 GGGTTGCAACACCTCCAGG 60.903 63.158 29.55 0.00 36.97 4.45
3766 3981 4.081476 GGGATTCTTGAAACCCATTTCCAG 60.081 45.833 19.63 0.00 43.18 3.86
3858 4073 3.855689 ATGATTACCTTGCTGTGTTGC 57.144 42.857 0.00 0.00 0.00 4.17
3882 4098 8.966868 CCCAACTGGTAAATAATCTGTGTAAAT 58.033 33.333 0.00 0.00 0.00 1.40
3928 4144 3.195825 ACCTGTCATGCAGTAGGACTTAC 59.804 47.826 13.33 0.00 43.55 2.34
3987 4203 4.552883 TGGAGAGGGGAATATAGACACA 57.447 45.455 0.00 0.00 0.00 3.72
3999 4215 1.891150 GCATAATGCATTGGAGAGGGG 59.109 52.381 22.27 3.64 44.26 4.79
4080 4296 1.961394 GCTGGATCACGACCCACTATA 59.039 52.381 0.00 0.00 0.00 1.31
4173 4389 1.133363 TGAGTTTCTCCAAACCGGGA 58.867 50.000 6.32 0.00 42.72 5.14
4286 4502 8.900983 TTTTAATAAATTGCAAGCCTTGAAGT 57.099 26.923 9.04 0.00 0.00 3.01
4311 4527 9.435688 GCATTAGAATTAAAAGGTGGAAACAAT 57.564 29.630 0.00 0.00 46.06 2.71
4312 4528 7.875554 GGCATTAGAATTAAAAGGTGGAAACAA 59.124 33.333 0.00 0.00 46.06 2.83
4313 4529 7.015682 TGGCATTAGAATTAAAAGGTGGAAACA 59.984 33.333 0.00 0.00 38.70 2.83
4314 4530 7.382898 TGGCATTAGAATTAAAAGGTGGAAAC 58.617 34.615 0.00 0.00 0.00 2.78
4315 4531 7.546250 TGGCATTAGAATTAAAAGGTGGAAA 57.454 32.000 0.00 0.00 0.00 3.13
4316 4532 7.546250 TTGGCATTAGAATTAAAAGGTGGAA 57.454 32.000 0.00 0.00 0.00 3.53
4317 4533 7.546250 TTTGGCATTAGAATTAAAAGGTGGA 57.454 32.000 0.00 0.00 0.00 4.02
4318 4534 8.791327 ATTTTGGCATTAGAATTAAAAGGTGG 57.209 30.769 0.00 0.00 0.00 4.61
4320 4536 9.791801 ACAATTTTGGCATTAGAATTAAAAGGT 57.208 25.926 0.00 0.00 0.00 3.50
4325 4541 9.784531 TGGAAACAATTTTGGCATTAGAATTAA 57.215 25.926 0.00 0.00 37.44 1.40
4326 4542 9.213799 GTGGAAACAATTTTGGCATTAGAATTA 57.786 29.630 0.00 0.00 46.06 1.40
4327 4543 7.174772 GGTGGAAACAATTTTGGCATTAGAATT 59.825 33.333 0.00 0.00 46.06 2.17
4328 4544 6.654582 GGTGGAAACAATTTTGGCATTAGAAT 59.345 34.615 0.00 0.00 46.06 2.40
4329 4545 5.994668 GGTGGAAACAATTTTGGCATTAGAA 59.005 36.000 0.00 0.00 46.06 2.10
4330 4546 5.306678 AGGTGGAAACAATTTTGGCATTAGA 59.693 36.000 0.00 0.00 46.06 2.10
4331 4547 5.550290 AGGTGGAAACAATTTTGGCATTAG 58.450 37.500 0.00 0.00 46.06 1.73
4332 4548 5.559148 AGGTGGAAACAATTTTGGCATTA 57.441 34.783 0.00 0.00 46.06 1.90
4336 4552 6.685527 TTAAAAGGTGGAAACAATTTTGGC 57.314 33.333 0.00 0.00 46.06 4.52
4387 4621 7.715249 GGCTGGAGATACAAATGAGTAATACAA 59.285 37.037 0.00 0.00 0.00 2.41
4391 4625 6.058183 GTGGCTGGAGATACAAATGAGTAAT 58.942 40.000 0.00 0.00 0.00 1.89
4401 4635 4.093743 TCTAACAAGTGGCTGGAGATACA 58.906 43.478 0.00 0.00 0.00 2.29
4409 4643 6.932356 ATATGTGAATCTAACAAGTGGCTG 57.068 37.500 0.00 0.00 0.00 4.85
4410 4644 7.564793 TGTATATGTGAATCTAACAAGTGGCT 58.435 34.615 0.00 0.00 0.00 4.75
4555 4790 3.638160 AGCAAGCATTTGTCCTCTGAAAA 59.362 39.130 0.00 0.00 36.65 2.29
4562 4797 3.285484 CCATAGAGCAAGCATTTGTCCT 58.715 45.455 0.00 0.00 36.65 3.85
4623 4867 3.687572 AAGTGCGCATCTGATTGATTC 57.312 42.857 15.91 0.00 32.05 2.52
4799 5043 1.103398 CCATTCCTCACCGGCCAATC 61.103 60.000 0.00 0.00 0.00 2.67
4800 5044 1.076777 CCATTCCTCACCGGCCAAT 60.077 57.895 0.00 0.00 0.00 3.16
4803 5047 2.438434 CACCATTCCTCACCGGCC 60.438 66.667 0.00 0.00 0.00 6.13
4809 5053 1.341285 CCCTGCATTCACCATTCCTCA 60.341 52.381 0.00 0.00 0.00 3.86
4810 5054 1.396653 CCCTGCATTCACCATTCCTC 58.603 55.000 0.00 0.00 0.00 3.71
4813 5057 2.077687 ATCCCCTGCATTCACCATTC 57.922 50.000 0.00 0.00 0.00 2.67
5001 5257 4.670621 CACGATAATAACAGAATTTGCGGC 59.329 41.667 0.00 0.00 0.00 6.53
5107 5363 3.595173 TCCGTTGTGTCACAATATGGAG 58.405 45.455 20.86 8.83 40.59 3.86
5116 5372 1.498865 CTGCCACTCCGTTGTGTCAC 61.499 60.000 0.00 0.00 36.30 3.67
5146 5402 5.237815 TGTCATCATCTAATAATCCACCGC 58.762 41.667 0.00 0.00 0.00 5.68
5205 5461 2.154462 CCTGAATCGTGAGGCTTTGTT 58.846 47.619 0.00 0.00 0.00 2.83
5216 5472 9.981114 ATTTTCTTTGTTTAAATCCTGAATCGT 57.019 25.926 0.00 0.00 0.00 3.73
5274 5530 5.724328 TGCCATCACTTACTAAAGACTCAG 58.276 41.667 0.00 0.00 36.50 3.35
5311 5567 4.196971 GGTTACACTCCAACACACTTTCT 58.803 43.478 0.00 0.00 0.00 2.52
5318 5574 2.876550 GTCCTTGGTTACACTCCAACAC 59.123 50.000 0.00 0.00 39.62 3.32
5340 5596 1.077787 TGGATGCCGACCCAACATC 60.078 57.895 0.00 0.00 39.57 3.06
5436 5694 0.528924 ACAAGCGGCGTATGTGACTA 59.471 50.000 16.67 0.00 0.00 2.59
5456 5714 2.967362 TGGTTAGCAACGGTGTCTATG 58.033 47.619 0.66 0.00 0.00 2.23
5463 5721 1.600485 CGAAAGTTGGTTAGCAACGGT 59.400 47.619 19.42 12.39 37.60 4.83
5538 5796 2.158534 AGACATGTTTGGTTGCCCTACA 60.159 45.455 0.00 0.00 32.85 2.74
5578 5837 1.678627 CAACCCAACATGTCCGACAAA 59.321 47.619 5.07 0.00 0.00 2.83
5604 5863 0.752376 TTTCCGCGGACCCTTTTTGT 60.752 50.000 31.19 0.00 0.00 2.83
5611 5870 4.841443 AAATAATATTTTCCGCGGACCC 57.159 40.909 31.19 0.00 0.00 4.46
5612 5871 4.443063 GCAAAATAATATTTTCCGCGGACC 59.557 41.667 31.19 0.00 0.00 4.46
5616 5878 4.039032 ACCGCAAAATAATATTTTCCGCG 58.961 39.130 24.09 24.09 38.81 6.46
5620 5882 9.027129 GGGAGTAAACCGCAAAATAATATTTTC 57.973 33.333 7.92 3.75 0.00 2.29
5631 5893 1.202675 ACGAAGGGAGTAAACCGCAAA 60.203 47.619 0.00 0.00 0.00 3.68
5648 5910 9.295214 TCCAAAACGTCGTATATTAATTTACGA 57.705 29.630 26.84 26.84 45.58 3.43
5649 5911 9.558891 CTCCAAAACGTCGTATATTAATTTACG 57.441 33.333 24.06 24.06 41.85 3.18
5694 5956 6.235231 TGTGTAGAGACTTCAAAAGGACTT 57.765 37.500 0.00 0.00 0.00 3.01
5708 5970 6.494666 TTCTCCCTTTTTCTTGTGTAGAGA 57.505 37.500 0.00 0.00 33.51 3.10
5743 6005 4.754667 GGGAACGGCTGTCGGGTC 62.755 72.222 6.61 2.65 44.45 4.46


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

AutoCloner maintained by Alex Coulton.