Multiple sequence alignment - TraesCS1B01G134000

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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 TraesCS1B01G134000 chr1B 100.000 5675 0 0 1 5675 169666820 169661146 0.000000e+00 10480.0
1 TraesCS1B01G134000 chr1B 99.090 659 5 1 5018 5675 685118928 685118270 0.000000e+00 1182.0
2 TraesCS1B01G134000 chr1B 100.000 61 0 0 1799 1859 169664961 169664901 4.650000e-21 113.0
3 TraesCS1B01G134000 chr1B 100.000 61 0 0 1860 1920 169665022 169664962 4.650000e-21 113.0
4 TraesCS1B01G134000 chr1A 95.101 3082 108 20 1860 4933 117197322 117194276 0.000000e+00 4815.0
5 TraesCS1B01G134000 chr1A 91.171 1008 46 16 882 1859 117198256 117197262 0.000000e+00 1328.0
6 TraesCS1B01G134000 chr1A 88.080 797 61 19 86 853 117199042 117198251 0.000000e+00 915.0
7 TraesCS1B01G134000 chr1D 93.963 1640 61 13 3322 4933 111036735 111035106 0.000000e+00 2446.0
8 TraesCS1B01G134000 chr1D 95.836 1369 42 5 1860 3219 111038098 111036736 0.000000e+00 2198.0
9 TraesCS1B01G134000 chr1D 91.667 996 42 17 882 1859 111039010 111038038 0.000000e+00 1341.0
10 TraesCS1B01G134000 chr1D 84.842 475 44 15 1 461 111040351 111039891 2.410000e-123 453.0
11 TraesCS1B01G134000 chr1D 84.500 400 24 17 462 853 111039374 111039005 1.500000e-95 361.0
12 TraesCS1B01G134000 chr2A 99.090 659 5 1 5018 5675 382804271 382804929 0.000000e+00 1182.0
13 TraesCS1B01G134000 chr7B 93.694 666 34 3 5018 5675 750333526 750334191 0.000000e+00 990.0
14 TraesCS1B01G134000 chr7B 91.538 650 41 5 5018 5655 220960664 220961311 0.000000e+00 883.0
15 TraesCS1B01G134000 chr7B 89.377 273 29 0 2438 2710 394213336 394213608 1.510000e-90 344.0
16 TraesCS1B01G134000 chr4B 91.602 643 41 5 5018 5649 665464054 665463414 0.000000e+00 876.0
17 TraesCS1B01G134000 chr4B 87.938 257 29 2 2457 2711 188515105 188515361 9.240000e-78 302.0
18 TraesCS1B01G134000 chr5A 89.590 634 42 13 5042 5675 129491623 129491014 0.000000e+00 784.0
19 TraesCS1B01G134000 chr5A 88.328 634 46 14 5042 5675 130006809 130006204 0.000000e+00 736.0
20 TraesCS1B01G134000 chr5B 89.246 623 61 6 5055 5675 321785386 321784768 0.000000e+00 774.0
21 TraesCS1B01G134000 chr2B 85.029 688 63 21 5019 5675 514789990 514789312 0.000000e+00 664.0
22 TraesCS1B01G134000 chr2B 86.842 266 31 4 2449 2711 790086982 790087246 1.550000e-75 294.0
23 TraesCS1B01G134000 chr7A 85.971 278 31 7 2441 2713 563154284 563154558 2.000000e-74 291.0
24 TraesCS1B01G134000 chr4A 87.050 139 15 3 2578 2713 464804050 464803912 2.740000e-33 154.0
25 TraesCS1B01G134000 chr3B 75.655 267 38 19 996 1253 73690082 73690330 2.160000e-19 108.0
26 TraesCS1B01G134000 chr3D 75.746 268 33 21 999 1253 47188801 47189049 7.780000e-19 106.0
27 TraesCS1B01G134000 chr3A 75.655 267 35 20 999 1253 58927247 58927495 7.780000e-19 106.0
28 TraesCS1B01G134000 chr6A 87.838 74 3 4 4934 5007 453898661 453898728 1.310000e-11 82.4
29 TraesCS1B01G134000 chr4D 100.000 28 0 0 2147 2174 136627842 136627869 1.000000e-02 52.8


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 TraesCS1B01G134000 chr1B 169661146 169666820 5674 True 3568.666667 10480 100.000000 1 5675 3 chr1B.!!$R2 5674
1 TraesCS1B01G134000 chr1B 685118270 685118928 658 True 1182.000000 1182 99.090000 5018 5675 1 chr1B.!!$R1 657
2 TraesCS1B01G134000 chr1A 117194276 117199042 4766 True 2352.666667 4815 91.450667 86 4933 3 chr1A.!!$R1 4847
3 TraesCS1B01G134000 chr1D 111035106 111040351 5245 True 1359.800000 2446 90.161600 1 4933 5 chr1D.!!$R1 4932
4 TraesCS1B01G134000 chr2A 382804271 382804929 658 False 1182.000000 1182 99.090000 5018 5675 1 chr2A.!!$F1 657
5 TraesCS1B01G134000 chr7B 750333526 750334191 665 False 990.000000 990 93.694000 5018 5675 1 chr7B.!!$F3 657
6 TraesCS1B01G134000 chr7B 220960664 220961311 647 False 883.000000 883 91.538000 5018 5655 1 chr7B.!!$F1 637
7 TraesCS1B01G134000 chr4B 665463414 665464054 640 True 876.000000 876 91.602000 5018 5649 1 chr4B.!!$R1 631
8 TraesCS1B01G134000 chr5A 129491014 129491623 609 True 784.000000 784 89.590000 5042 5675 1 chr5A.!!$R1 633
9 TraesCS1B01G134000 chr5A 130006204 130006809 605 True 736.000000 736 88.328000 5042 5675 1 chr5A.!!$R2 633
10 TraesCS1B01G134000 chr5B 321784768 321785386 618 True 774.000000 774 89.246000 5055 5675 1 chr5B.!!$R1 620
11 TraesCS1B01G134000 chr2B 514789312 514789990 678 True 664.000000 664 85.029000 5019 5675 1 chr2B.!!$R1 656

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
744 1298 0.038166 TGCCGATTTTCTTCTGGCCT 59.962 50.0 3.32 0.00 45.12 5.19 F
1006 1579 0.104120 AATCCCGATCGCGATGAACA 59.896 50.0 29.09 8.14 40.82 3.18 F
1873 2489 0.179192 CACATATTTGCGTGCGTGCT 60.179 50.0 1.52 0.00 35.36 4.40 F
3281 3913 0.106335 TTTGTTGCCCCTGTTGCATG 59.894 50.0 0.00 0.00 38.76 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 2491 0.110486 AAGTGCACGGGGAACATCTT 59.890 50.0 12.01 0.0 0.00 2.40 R
1877 2493 0.240945 CAAAGTGCACGGGGAACATC 59.759 55.0 12.01 0.0 0.00 3.06 R
3288 3920 0.371645 GACATGAAGCGCACTAGCAC 59.628 55.0 11.47 0.0 42.27 4.40 R
4979 5640 0.036483 TATGCCACGAAGCTCAAGCA 60.036 50.0 4.59 0.0 45.16 3.91 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
38 39 9.586150 CTTCATTCGTTGAATATAATTCCTTCG 57.414 33.333 4.46 1.16 43.30 3.79
47 48 2.638330 TAATTCCTTCGAGCCCGCCG 62.638 60.000 0.00 0.00 35.37 6.46
51 52 4.436998 CTTCGAGCCCGCCGAACT 62.437 66.667 8.33 0.00 40.56 3.01
77 78 2.093394 TCGTGTGACTTGGTTGAAGGAA 60.093 45.455 0.00 0.00 35.78 3.36
82 83 1.423921 GACTTGGTTGAAGGAAGGGGA 59.576 52.381 0.00 0.00 35.78 4.81
125 137 1.580059 ACCACAATCCGGTACCATCT 58.420 50.000 13.54 0.00 34.02 2.90
127 139 1.484653 CCACAATCCGGTACCATCTGA 59.515 52.381 13.54 2.76 0.00 3.27
133 145 2.462723 TCCGGTACCATCTGATGACAA 58.537 47.619 18.92 1.22 0.00 3.18
134 146 2.835156 TCCGGTACCATCTGATGACAAA 59.165 45.455 18.92 0.00 0.00 2.83
172 186 4.574674 AGGCATCAATGAGAAGTGGTAA 57.425 40.909 0.00 0.00 0.00 2.85
175 189 5.183904 AGGCATCAATGAGAAGTGGTAAAAC 59.816 40.000 0.00 0.00 0.00 2.43
187 201 7.412063 AGAAGTGGTAAAACGAAAATGTACAC 58.588 34.615 0.00 0.00 0.00 2.90
215 229 5.250200 TCATTGTTTATAAGCTGTCCCGTT 58.750 37.500 0.83 0.00 0.00 4.44
283 299 0.396811 ACTTCAGGTGCTTAGGCGTT 59.603 50.000 0.00 0.00 42.25 4.84
312 328 1.508632 TGAAAGTGGTTAGTGCTCGC 58.491 50.000 0.00 0.00 0.00 5.03
327 343 1.067495 GCTCGCCTTAGATCGCCTTAT 60.067 52.381 0.00 0.00 0.00 1.73
343 359 7.542534 TCGCCTTATCACGTTATAAACAATT 57.457 32.000 3.92 0.00 0.00 2.32
501 1045 1.066422 GAGTCCGCTGCGATCATGA 59.934 57.895 25.45 8.85 0.00 3.07
502 1046 1.211818 GAGTCCGCTGCGATCATGAC 61.212 60.000 25.45 20.33 0.00 3.06
503 1047 1.227089 GTCCGCTGCGATCATGACT 60.227 57.895 25.45 0.00 0.00 3.41
504 1048 0.807667 GTCCGCTGCGATCATGACTT 60.808 55.000 25.45 0.00 0.00 3.01
505 1049 0.528466 TCCGCTGCGATCATGACTTC 60.528 55.000 25.45 0.00 0.00 3.01
506 1050 0.807275 CCGCTGCGATCATGACTTCA 60.807 55.000 25.45 0.00 0.00 3.02
507 1051 1.215244 CGCTGCGATCATGACTTCAT 58.785 50.000 18.66 0.00 36.96 2.57
678 1231 1.736645 CGTCGAGCCGTTTCACCAT 60.737 57.895 0.00 0.00 0.00 3.55
679 1232 1.683790 CGTCGAGCCGTTTCACCATC 61.684 60.000 0.00 0.00 0.00 3.51
733 1287 3.009723 CTCCACACACTTATGCCGATTT 58.990 45.455 0.00 0.00 0.00 2.17
734 1288 3.417101 TCCACACACTTATGCCGATTTT 58.583 40.909 0.00 0.00 0.00 1.82
744 1298 0.038166 TGCCGATTTTCTTCTGGCCT 59.962 50.000 3.32 0.00 45.12 5.19
762 1316 1.666209 CTGCAATTAACCTGGGCCGG 61.666 60.000 5.01 5.01 0.00 6.13
767 1321 1.502527 ATTAACCTGGGCCGGGAACA 61.503 55.000 37.99 19.82 33.36 3.18
771 1325 2.677228 CTGGGCCGGGAACAGAAT 59.323 61.111 3.77 0.00 34.21 2.40
779 1333 1.006832 CGGGAACAGAATTACGGCTG 58.993 55.000 0.00 0.00 38.10 4.85
853 1417 1.400759 GGACTTCGTCGTTTACTCGCT 60.401 52.381 0.00 0.00 32.65 4.93
855 1419 1.002033 ACTTCGTCGTTTACTCGCTGT 60.002 47.619 0.00 0.00 0.00 4.40
856 1420 2.224079 ACTTCGTCGTTTACTCGCTGTA 59.776 45.455 0.00 0.00 0.00 2.74
857 1421 2.232239 TCGTCGTTTACTCGCTGTAC 57.768 50.000 0.00 0.00 0.00 2.90
858 1422 1.800586 TCGTCGTTTACTCGCTGTACT 59.199 47.619 0.00 0.00 0.00 2.73
859 1423 1.903139 CGTCGTTTACTCGCTGTACTG 59.097 52.381 0.00 0.00 0.00 2.74
860 1424 2.411935 CGTCGTTTACTCGCTGTACTGA 60.412 50.000 3.61 0.00 0.00 3.41
861 1425 3.727079 CGTCGTTTACTCGCTGTACTGAT 60.727 47.826 3.61 0.00 0.00 2.90
862 1426 3.542704 GTCGTTTACTCGCTGTACTGATG 59.457 47.826 3.61 0.00 0.00 3.07
863 1427 2.279136 CGTTTACTCGCTGTACTGATGC 59.721 50.000 3.61 0.00 0.00 3.91
864 1428 3.512680 GTTTACTCGCTGTACTGATGCT 58.487 45.455 3.61 0.00 0.00 3.79
865 1429 3.422417 TTACTCGCTGTACTGATGCTC 57.578 47.619 3.61 0.00 0.00 4.26
866 1430 1.177401 ACTCGCTGTACTGATGCTCA 58.823 50.000 3.61 0.00 0.00 4.26
867 1431 1.546029 ACTCGCTGTACTGATGCTCAA 59.454 47.619 3.61 0.00 0.00 3.02
868 1432 2.029020 ACTCGCTGTACTGATGCTCAAA 60.029 45.455 3.61 0.00 0.00 2.69
869 1433 2.995939 CTCGCTGTACTGATGCTCAAAA 59.004 45.455 3.61 0.00 0.00 2.44
870 1434 3.398406 TCGCTGTACTGATGCTCAAAAA 58.602 40.909 3.61 0.00 0.00 1.94
1006 1579 0.104120 AATCCCGATCGCGATGAACA 59.896 50.000 29.09 8.14 40.82 3.18
1330 1906 3.053896 CCGCGTCCCCCAAACTTC 61.054 66.667 4.92 0.00 0.00 3.01
1356 1932 5.889289 GGTAATAATACTTGGCCACCTTCAA 59.111 40.000 3.88 0.00 32.36 2.69
1385 1961 5.173664 CACTGCTGTTCATAGATCTGTTCA 58.826 41.667 5.18 0.00 0.00 3.18
1388 1964 5.363101 TGCTGTTCATAGATCTGTTCATCC 58.637 41.667 5.18 0.00 0.00 3.51
1469 2045 0.742281 ATCGAATCGCTGTGCTTGCT 60.742 50.000 0.00 0.00 0.00 3.91
1508 2086 7.094205 TGTGATTCAGATAGAAAAGGGAAAAGC 60.094 37.037 0.00 0.00 40.22 3.51
1524 2102 4.323257 GGAAAAGCAGGCCTAGTAGTTGTA 60.323 45.833 3.98 0.00 0.00 2.41
1537 2115 2.632987 AGTTGTAGTTCCGGTGCTTT 57.367 45.000 0.00 0.00 0.00 3.51
1560 2140 4.466827 TGAAAGCTGATGCATATCCATGT 58.533 39.130 0.00 0.00 42.74 3.21
1561 2141 5.623169 TGAAAGCTGATGCATATCCATGTA 58.377 37.500 0.00 0.00 42.74 2.29
1562 2142 5.704053 TGAAAGCTGATGCATATCCATGTAG 59.296 40.000 0.00 0.00 42.74 2.74
1563 2143 4.904895 AGCTGATGCATATCCATGTAGT 57.095 40.909 0.00 0.00 42.74 2.73
1575 2183 9.555727 GCATATCCATGTAGTTACTTTTAGGAA 57.444 33.333 0.00 0.00 34.40 3.36
1658 2266 5.466728 GCTGATTTATGCTCTTTATGGTCGA 59.533 40.000 0.00 0.00 0.00 4.20
1671 2279 2.502142 TGGTCGACTGCTTACTCCTA 57.498 50.000 16.46 0.00 0.00 2.94
1672 2280 3.014304 TGGTCGACTGCTTACTCCTAT 57.986 47.619 16.46 0.00 0.00 2.57
1673 2281 2.950309 TGGTCGACTGCTTACTCCTATC 59.050 50.000 16.46 0.00 0.00 2.08
1674 2282 3.215975 GGTCGACTGCTTACTCCTATCT 58.784 50.000 16.46 0.00 0.00 1.98
1675 2283 3.251487 GGTCGACTGCTTACTCCTATCTC 59.749 52.174 16.46 0.00 0.00 2.75
1676 2284 3.878103 GTCGACTGCTTACTCCTATCTCA 59.122 47.826 8.70 0.00 0.00 3.27
1677 2285 4.517453 GTCGACTGCTTACTCCTATCTCAT 59.483 45.833 8.70 0.00 0.00 2.90
1678 2286 5.701750 GTCGACTGCTTACTCCTATCTCATA 59.298 44.000 8.70 0.00 0.00 2.15
1679 2287 5.935206 TCGACTGCTTACTCCTATCTCATAG 59.065 44.000 0.00 0.00 0.00 2.23
1680 2288 5.703592 CGACTGCTTACTCCTATCTCATAGT 59.296 44.000 0.00 0.00 0.00 2.12
1683 2299 7.294584 ACTGCTTACTCCTATCTCATAGTCTT 58.705 38.462 0.00 0.00 0.00 3.01
1706 2322 9.706691 TCTTATATTGATGAACCTAAATCGGTC 57.293 33.333 0.00 0.00 35.89 4.79
1746 2362 1.271926 ACATCACTTTAGTGGGGGTGC 60.272 52.381 9.82 0.00 45.65 5.01
1836 2452 1.178534 ATGTTCCCCGTGCACTTTGG 61.179 55.000 16.19 12.19 0.00 3.28
1837 2453 1.527380 GTTCCCCGTGCACTTTGGA 60.527 57.895 16.19 14.35 0.00 3.53
1838 2454 1.104577 GTTCCCCGTGCACTTTGGAA 61.105 55.000 20.91 20.91 32.87 3.53
1839 2455 0.821711 TTCCCCGTGCACTTTGGAAG 60.822 55.000 20.91 9.21 31.69 3.46
1840 2456 1.228124 CCCCGTGCACTTTGGAAGA 60.228 57.895 16.19 0.00 0.00 2.87
1841 2457 0.821711 CCCCGTGCACTTTGGAAGAA 60.822 55.000 16.19 0.00 0.00 2.52
1842 2458 1.028905 CCCGTGCACTTTGGAAGAAA 58.971 50.000 16.19 0.00 0.00 2.52
1843 2459 1.407258 CCCGTGCACTTTGGAAGAAAA 59.593 47.619 16.19 0.00 0.00 2.29
1844 2460 2.159170 CCCGTGCACTTTGGAAGAAAAA 60.159 45.455 16.19 0.00 0.00 1.94
1845 2461 3.492482 CCCGTGCACTTTGGAAGAAAAAT 60.492 43.478 16.19 0.00 0.00 1.82
1846 2462 3.490526 CCGTGCACTTTGGAAGAAAAATG 59.509 43.478 16.19 0.00 0.00 2.32
1847 2463 3.490526 CGTGCACTTTGGAAGAAAAATGG 59.509 43.478 16.19 0.00 0.00 3.16
1848 2464 4.441792 GTGCACTTTGGAAGAAAAATGGT 58.558 39.130 10.32 0.00 0.00 3.55
1849 2465 5.596845 GTGCACTTTGGAAGAAAAATGGTA 58.403 37.500 10.32 0.00 0.00 3.25
1850 2466 5.691754 GTGCACTTTGGAAGAAAAATGGTAG 59.308 40.000 10.32 0.00 0.00 3.18
1851 2467 5.362430 TGCACTTTGGAAGAAAAATGGTAGT 59.638 36.000 0.00 0.00 0.00 2.73
1852 2468 5.691754 GCACTTTGGAAGAAAAATGGTAGTG 59.308 40.000 0.00 0.00 0.00 2.74
1853 2469 6.215845 CACTTTGGAAGAAAAATGGTAGTGG 58.784 40.000 0.00 0.00 0.00 4.00
1854 2470 4.864704 TTGGAAGAAAAATGGTAGTGGC 57.135 40.909 0.00 0.00 0.00 5.01
1855 2471 3.838565 TGGAAGAAAAATGGTAGTGGCA 58.161 40.909 0.00 0.00 0.00 4.92
1856 2472 3.572255 TGGAAGAAAAATGGTAGTGGCAC 59.428 43.478 10.29 10.29 0.00 5.01
1857 2473 3.572255 GGAAGAAAAATGGTAGTGGCACA 59.428 43.478 21.41 2.83 0.00 4.57
1858 2474 4.220602 GGAAGAAAAATGGTAGTGGCACAT 59.779 41.667 21.41 7.59 44.52 3.21
1859 2475 5.417580 GGAAGAAAAATGGTAGTGGCACATA 59.582 40.000 21.41 6.56 44.52 2.29
1860 2476 6.096846 GGAAGAAAAATGGTAGTGGCACATAT 59.903 38.462 21.41 1.16 44.52 1.78
1861 2477 7.363793 GGAAGAAAAATGGTAGTGGCACATATT 60.364 37.037 21.41 11.02 44.52 1.28
1862 2478 7.480760 AGAAAAATGGTAGTGGCACATATTT 57.519 32.000 21.41 15.83 44.52 1.40
1863 2479 7.322664 AGAAAAATGGTAGTGGCACATATTTG 58.677 34.615 21.41 0.00 44.52 2.32
1864 2480 4.654091 AATGGTAGTGGCACATATTTGC 57.346 40.909 21.41 5.23 44.52 3.68
1865 2481 2.013400 TGGTAGTGGCACATATTTGCG 58.987 47.619 21.41 0.00 44.52 4.85
1866 2482 2.014128 GGTAGTGGCACATATTTGCGT 58.986 47.619 21.41 0.00 44.52 5.24
1867 2483 2.223249 GGTAGTGGCACATATTTGCGTG 60.223 50.000 21.41 0.00 44.52 5.34
1872 2488 2.268229 CACATATTTGCGTGCGTGC 58.732 52.632 0.00 0.00 0.00 5.34
1873 2489 0.179192 CACATATTTGCGTGCGTGCT 60.179 50.000 1.52 0.00 35.36 4.40
1874 2490 0.521291 ACATATTTGCGTGCGTGCTT 59.479 45.000 1.52 0.00 35.36 3.91
1875 2491 1.735018 ACATATTTGCGTGCGTGCTTA 59.265 42.857 1.52 0.00 35.36 3.09
1876 2492 2.160615 ACATATTTGCGTGCGTGCTTAA 59.839 40.909 1.52 0.00 35.36 1.85
1877 2493 2.519002 TATTTGCGTGCGTGCTTAAG 57.481 45.000 0.00 0.00 35.36 1.85
1878 2494 0.871722 ATTTGCGTGCGTGCTTAAGA 59.128 45.000 6.67 0.00 35.36 2.10
1879 2495 0.871722 TTTGCGTGCGTGCTTAAGAT 59.128 45.000 6.67 0.00 35.36 2.40
1880 2496 0.165727 TTGCGTGCGTGCTTAAGATG 59.834 50.000 6.67 0.00 35.36 2.90
1881 2497 0.948623 TGCGTGCGTGCTTAAGATGT 60.949 50.000 6.67 0.00 35.36 3.06
1882 2498 0.165944 GCGTGCGTGCTTAAGATGTT 59.834 50.000 6.67 0.00 0.00 2.71
1883 2499 1.786928 GCGTGCGTGCTTAAGATGTTC 60.787 52.381 6.67 0.00 0.00 3.18
1884 2500 1.201921 CGTGCGTGCTTAAGATGTTCC 60.202 52.381 6.67 0.00 0.00 3.62
1885 2501 1.130561 GTGCGTGCTTAAGATGTTCCC 59.869 52.381 6.67 0.00 0.00 3.97
1886 2502 0.733150 GCGTGCTTAAGATGTTCCCC 59.267 55.000 6.67 0.00 0.00 4.81
1887 2503 1.006832 CGTGCTTAAGATGTTCCCCG 58.993 55.000 6.67 0.00 0.00 5.73
1888 2504 1.674817 CGTGCTTAAGATGTTCCCCGT 60.675 52.381 6.67 0.00 0.00 5.28
1889 2505 1.737793 GTGCTTAAGATGTTCCCCGTG 59.262 52.381 6.67 0.00 0.00 4.94
1890 2506 0.733150 GCTTAAGATGTTCCCCGTGC 59.267 55.000 6.67 0.00 0.00 5.34
1891 2507 1.948611 GCTTAAGATGTTCCCCGTGCA 60.949 52.381 6.67 0.00 0.00 4.57
1892 2508 1.737793 CTTAAGATGTTCCCCGTGCAC 59.262 52.381 6.82 6.82 0.00 4.57
1893 2509 0.981183 TAAGATGTTCCCCGTGCACT 59.019 50.000 16.19 0.00 0.00 4.40
1894 2510 0.110486 AAGATGTTCCCCGTGCACTT 59.890 50.000 16.19 0.00 0.00 3.16
1895 2511 0.110486 AGATGTTCCCCGTGCACTTT 59.890 50.000 16.19 0.00 0.00 2.66
1896 2512 0.240945 GATGTTCCCCGTGCACTTTG 59.759 55.000 16.19 3.04 0.00 2.77
2063 2686 3.898123 GGTATCTCCAGAACTGCAGGATA 59.102 47.826 19.93 10.26 31.05 2.59
2069 2692 2.158986 CCAGAACTGCAGGATAGACCAG 60.159 54.545 19.93 0.00 42.04 4.00
2084 2707 0.188342 ACCAGTTGGCCATGTCCTTT 59.812 50.000 6.09 0.00 39.32 3.11
2126 2749 2.113433 CAGTCCAGCTCCAGCATGC 61.113 63.158 10.51 10.51 45.16 4.06
2141 2764 5.474532 TCCAGCATGCTCCATGTTATATTTC 59.525 40.000 19.68 0.00 43.10 2.17
2191 2814 4.679197 TCAACATTTTTCTTATGCGCACAC 59.321 37.500 14.90 0.00 0.00 3.82
2239 2862 9.330063 TGGCAACTGATTGAGTATAAGAATTAG 57.670 33.333 0.00 0.00 38.15 1.73
2275 2898 4.104102 GGGATCTTATGTACCCATTCACCA 59.896 45.833 0.00 0.00 41.72 4.17
2291 2914 7.039011 CCCATTCACCATATACTTCTGTAGCTA 60.039 40.741 0.00 0.00 31.51 3.32
2324 2948 7.703058 ATTAGTAACCAATCCAAGAGGTTTG 57.297 36.000 1.03 0.00 42.72 2.93
2383 3008 6.166279 TCACTTCATATCACCTCACTGTTTC 58.834 40.000 0.00 0.00 0.00 2.78
2714 3341 2.223782 GGCAATTTGAGAACACACTGCA 60.224 45.455 0.00 0.00 0.00 4.41
3221 3851 3.340814 TGAGTTTCCTTCAGCTCCATC 57.659 47.619 0.00 0.00 0.00 3.51
3240 3870 1.448893 CAAGGGCACAATGGCATGC 60.449 57.895 9.90 9.90 45.76 4.06
3254 3884 1.133790 GGCATGCTGACAAGTGGAATC 59.866 52.381 18.92 0.00 0.00 2.52
3281 3913 0.106335 TTTGTTGCCCCTGTTGCATG 59.894 50.000 0.00 0.00 38.76 4.06
3328 3960 4.092675 GTCTTTCTTCTGCCTTCTTCATCG 59.907 45.833 0.00 0.00 0.00 3.84
3613 4248 0.178992 TGAGGCCCAGGTTCAACTTG 60.179 55.000 0.00 0.00 0.00 3.16
3755 4390 1.971695 CTCCTTCCCAACCAACGGC 60.972 63.158 0.00 0.00 0.00 5.68
3850 4485 2.354821 GGTCATTTACCGCATCCTCAAC 59.645 50.000 0.00 0.00 38.88 3.18
3882 4517 2.226315 ACCTGCTCCATCTGTGCCA 61.226 57.895 0.00 0.00 32.45 4.92
3963 4598 1.406539 CAATATCAAGCACCACCAGCC 59.593 52.381 0.00 0.00 0.00 4.85
4002 4637 0.454957 CAGCAGCACCGCAACATTAC 60.455 55.000 0.00 0.00 0.00 1.89
4041 4676 3.387962 TGCTCCATATTCTCAACCTCCT 58.612 45.455 0.00 0.00 0.00 3.69
4044 4679 3.969976 CTCCATATTCTCAACCTCCTCCA 59.030 47.826 0.00 0.00 0.00 3.86
4069 4704 2.626266 GGAAGTGTTAACCCCCAAACTG 59.374 50.000 2.48 0.00 0.00 3.16
4074 4709 0.187361 TTAACCCCCAAACTGCAGCT 59.813 50.000 15.27 0.00 0.00 4.24
4248 4883 0.107945 CAGCAGTCAGGCCTAACTCC 60.108 60.000 5.23 0.00 0.00 3.85
4291 4926 3.393472 GGATACAAGCAGCAGGGAG 57.607 57.895 0.00 0.00 0.00 4.30
4299 4934 2.366167 CAGCAGGGAGGAGGAGGA 59.634 66.667 0.00 0.00 0.00 3.71
4368 5006 0.749454 ATGCTGGAATGAACTCGCCC 60.749 55.000 0.00 0.00 0.00 6.13
4566 5204 1.185618 AGCAAGTGAGGGCGACTGTA 61.186 55.000 0.00 0.00 34.54 2.74
4668 5306 3.700109 CAGAGAGGCTGGTTCGGA 58.300 61.111 0.00 0.00 41.07 4.55
4669 5307 1.975327 CAGAGAGGCTGGTTCGGAA 59.025 57.895 0.00 0.00 41.07 4.30
4740 5397 1.668419 GCGAACAGCTATGGAACCAT 58.332 50.000 11.20 11.20 44.04 3.55
4743 5400 3.119495 GCGAACAGCTATGGAACCATTTT 60.119 43.478 11.68 0.00 44.04 1.82
4745 5402 3.874392 ACAGCTATGGAACCATTTTGC 57.126 42.857 11.68 12.95 37.82 3.68
4753 5410 2.028294 TGGAACCATTTTGCGCATTCAT 60.028 40.909 12.75 0.00 0.00 2.57
4792 5449 1.808945 CAGATTTCTCGTTTGGCTGCT 59.191 47.619 0.00 0.00 0.00 4.24
4798 5455 0.392193 CTCGTTTGGCTGCTGGAGAT 60.392 55.000 0.00 0.00 0.00 2.75
4835 5492 6.037830 TGTTAGCTCTTTTGTTCACCTGTTAC 59.962 38.462 0.00 0.00 0.00 2.50
4836 5493 4.781934 AGCTCTTTTGTTCACCTGTTACT 58.218 39.130 0.00 0.00 0.00 2.24
4837 5494 5.193679 AGCTCTTTTGTTCACCTGTTACTT 58.806 37.500 0.00 0.00 0.00 2.24
4873 5530 2.099921 GCTATCCATCGTCAGTGTGACT 59.900 50.000 5.57 0.00 44.85 3.41
4874 5531 2.949451 ATCCATCGTCAGTGTGACTC 57.051 50.000 5.57 0.00 44.85 3.36
4875 5532 0.521735 TCCATCGTCAGTGTGACTCG 59.478 55.000 5.57 0.00 44.85 4.18
4933 5594 6.772716 ACTATTGTTGATGACCTGTGAAACTT 59.227 34.615 0.00 0.00 38.04 2.66
4934 5595 4.898829 TGTTGATGACCTGTGAAACTTG 57.101 40.909 0.00 0.00 38.04 3.16
4935 5596 4.269183 TGTTGATGACCTGTGAAACTTGT 58.731 39.130 0.00 0.00 38.04 3.16
4936 5597 4.704540 TGTTGATGACCTGTGAAACTTGTT 59.295 37.500 0.00 0.00 38.04 2.83
4937 5598 5.883115 TGTTGATGACCTGTGAAACTTGTTA 59.117 36.000 0.00 0.00 38.04 2.41
4938 5599 6.038161 TGTTGATGACCTGTGAAACTTGTTAG 59.962 38.462 0.00 0.00 38.04 2.34
4939 5600 5.924356 TGATGACCTGTGAAACTTGTTAGA 58.076 37.500 0.00 0.00 38.04 2.10
4940 5601 6.353323 TGATGACCTGTGAAACTTGTTAGAA 58.647 36.000 0.00 0.00 38.04 2.10
4941 5602 6.483307 TGATGACCTGTGAAACTTGTTAGAAG 59.517 38.462 0.00 0.00 38.04 2.85
4942 5603 5.123227 TGACCTGTGAAACTTGTTAGAAGG 58.877 41.667 0.00 0.00 38.04 3.46
4943 5604 4.461198 ACCTGTGAAACTTGTTAGAAGGG 58.539 43.478 0.00 0.00 38.04 3.95
4944 5605 4.165372 ACCTGTGAAACTTGTTAGAAGGGA 59.835 41.667 0.00 0.00 38.04 4.20
4945 5606 4.757149 CCTGTGAAACTTGTTAGAAGGGAG 59.243 45.833 0.00 0.00 38.04 4.30
4946 5607 4.714632 TGTGAAACTTGTTAGAAGGGAGG 58.285 43.478 0.00 0.00 38.04 4.30
4947 5608 4.072839 GTGAAACTTGTTAGAAGGGAGGG 58.927 47.826 0.00 0.00 0.00 4.30
4948 5609 3.977999 TGAAACTTGTTAGAAGGGAGGGA 59.022 43.478 0.00 0.00 0.00 4.20
4949 5610 4.041691 TGAAACTTGTTAGAAGGGAGGGAG 59.958 45.833 0.00 0.00 0.00 4.30
4950 5611 2.552367 ACTTGTTAGAAGGGAGGGAGG 58.448 52.381 0.00 0.00 0.00 4.30
4951 5612 1.840635 CTTGTTAGAAGGGAGGGAGGG 59.159 57.143 0.00 0.00 0.00 4.30
4952 5613 1.098589 TGTTAGAAGGGAGGGAGGGA 58.901 55.000 0.00 0.00 0.00 4.20
4953 5614 1.657162 TGTTAGAAGGGAGGGAGGGAT 59.343 52.381 0.00 0.00 0.00 3.85
4954 5615 2.047296 TGTTAGAAGGGAGGGAGGGATT 59.953 50.000 0.00 0.00 0.00 3.01
4955 5616 2.439880 GTTAGAAGGGAGGGAGGGATTG 59.560 54.545 0.00 0.00 0.00 2.67
4956 5617 0.327964 AGAAGGGAGGGAGGGATTGG 60.328 60.000 0.00 0.00 0.00 3.16
4957 5618 0.624795 GAAGGGAGGGAGGGATTGGT 60.625 60.000 0.00 0.00 0.00 3.67
4958 5619 0.921256 AAGGGAGGGAGGGATTGGTG 60.921 60.000 0.00 0.00 0.00 4.17
4959 5620 2.386935 GGGAGGGAGGGATTGGTGG 61.387 68.421 0.00 0.00 0.00 4.61
4960 5621 1.307866 GGAGGGAGGGATTGGTGGA 60.308 63.158 0.00 0.00 0.00 4.02
4961 5622 0.919289 GGAGGGAGGGATTGGTGGAA 60.919 60.000 0.00 0.00 0.00 3.53
4962 5623 1.226311 GAGGGAGGGATTGGTGGAAT 58.774 55.000 0.00 0.00 0.00 3.01
4963 5624 2.418669 GAGGGAGGGATTGGTGGAATA 58.581 52.381 0.00 0.00 0.00 1.75
4964 5625 2.373502 GAGGGAGGGATTGGTGGAATAG 59.626 54.545 0.00 0.00 0.00 1.73
4965 5626 2.136026 GGGAGGGATTGGTGGAATAGT 58.864 52.381 0.00 0.00 0.00 2.12
4966 5627 2.514160 GGGAGGGATTGGTGGAATAGTT 59.486 50.000 0.00 0.00 0.00 2.24
4967 5628 3.052869 GGGAGGGATTGGTGGAATAGTTT 60.053 47.826 0.00 0.00 0.00 2.66
4968 5629 3.954258 GGAGGGATTGGTGGAATAGTTTG 59.046 47.826 0.00 0.00 0.00 2.93
4969 5630 4.325030 GGAGGGATTGGTGGAATAGTTTGA 60.325 45.833 0.00 0.00 0.00 2.69
4970 5631 5.449553 GAGGGATTGGTGGAATAGTTTGAT 58.550 41.667 0.00 0.00 0.00 2.57
4971 5632 5.842339 AGGGATTGGTGGAATAGTTTGATT 58.158 37.500 0.00 0.00 0.00 2.57
4972 5633 5.658190 AGGGATTGGTGGAATAGTTTGATTG 59.342 40.000 0.00 0.00 0.00 2.67
4973 5634 5.422012 GGGATTGGTGGAATAGTTTGATTGT 59.578 40.000 0.00 0.00 0.00 2.71
4974 5635 6.070824 GGGATTGGTGGAATAGTTTGATTGTT 60.071 38.462 0.00 0.00 0.00 2.83
4975 5636 7.386059 GGATTGGTGGAATAGTTTGATTGTTT 58.614 34.615 0.00 0.00 0.00 2.83
4976 5637 7.877612 GGATTGGTGGAATAGTTTGATTGTTTT 59.122 33.333 0.00 0.00 0.00 2.43
4977 5638 9.921637 GATTGGTGGAATAGTTTGATTGTTTTA 57.078 29.630 0.00 0.00 0.00 1.52
4980 5641 9.703892 TGGTGGAATAGTTTGATTGTTTTATTG 57.296 29.630 0.00 0.00 0.00 1.90
4981 5642 8.655970 GGTGGAATAGTTTGATTGTTTTATTGC 58.344 33.333 0.00 0.00 0.00 3.56
4982 5643 9.423061 GTGGAATAGTTTGATTGTTTTATTGCT 57.577 29.630 0.00 0.00 0.00 3.91
4983 5644 9.995003 TGGAATAGTTTGATTGTTTTATTGCTT 57.005 25.926 0.00 0.00 0.00 3.91
4987 5648 7.412137 AGTTTGATTGTTTTATTGCTTGAGC 57.588 32.000 0.00 0.00 42.50 4.26
4988 5649 7.212274 AGTTTGATTGTTTTATTGCTTGAGCT 58.788 30.769 4.44 0.00 42.66 4.09
4989 5650 7.712205 AGTTTGATTGTTTTATTGCTTGAGCTT 59.288 29.630 4.44 0.00 42.66 3.74
4990 5651 7.642071 TTGATTGTTTTATTGCTTGAGCTTC 57.358 32.000 4.44 0.00 42.66 3.86
4991 5652 5.858049 TGATTGTTTTATTGCTTGAGCTTCG 59.142 36.000 4.44 0.00 42.66 3.79
4992 5653 4.829064 TGTTTTATTGCTTGAGCTTCGT 57.171 36.364 4.44 0.00 42.66 3.85
4993 5654 4.536065 TGTTTTATTGCTTGAGCTTCGTG 58.464 39.130 4.44 0.00 42.66 4.35
4994 5655 3.829886 TTTATTGCTTGAGCTTCGTGG 57.170 42.857 4.44 0.00 42.66 4.94
4995 5656 1.086696 TATTGCTTGAGCTTCGTGGC 58.913 50.000 4.44 0.00 42.66 5.01
4996 5657 0.890542 ATTGCTTGAGCTTCGTGGCA 60.891 50.000 4.44 0.00 42.66 4.92
4997 5658 0.890542 TTGCTTGAGCTTCGTGGCAT 60.891 50.000 4.44 0.00 42.66 4.40
4998 5659 0.036483 TGCTTGAGCTTCGTGGCATA 60.036 50.000 4.44 0.00 42.66 3.14
4999 5660 1.303309 GCTTGAGCTTCGTGGCATAT 58.697 50.000 0.00 0.00 38.21 1.78
5000 5661 2.158971 TGCTTGAGCTTCGTGGCATATA 60.159 45.455 4.44 0.00 42.66 0.86
5001 5662 3.070018 GCTTGAGCTTCGTGGCATATAT 58.930 45.455 0.00 0.00 38.21 0.86
5002 5663 4.245660 GCTTGAGCTTCGTGGCATATATA 58.754 43.478 0.00 0.00 38.21 0.86
5003 5664 4.872691 GCTTGAGCTTCGTGGCATATATAT 59.127 41.667 0.00 0.00 38.21 0.86
5004 5665 6.042777 GCTTGAGCTTCGTGGCATATATATA 58.957 40.000 0.00 0.00 38.21 0.86
5005 5666 6.703607 GCTTGAGCTTCGTGGCATATATATAT 59.296 38.462 0.00 0.00 38.21 0.86
5006 5667 7.867909 GCTTGAGCTTCGTGGCATATATATATA 59.132 37.037 4.90 4.92 38.21 0.86
5007 5668 9.920133 CTTGAGCTTCGTGGCATATATATATAT 57.080 33.333 9.12 9.12 34.17 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.202188 GGCTCGAAGGAATTATATTCAACGAA 59.798 38.462 0.00 0.00 0.00 3.85
19 20 5.107065 GGGCTCGAAGGAATTATATTCAACG 60.107 44.000 2.24 0.00 0.00 4.10
47 48 1.789464 CAAGTCACACGAGAGCAGTTC 59.211 52.381 0.00 0.00 0.00 3.01
51 52 0.464036 AACCAAGTCACACGAGAGCA 59.536 50.000 0.00 0.00 0.00 4.26
77 78 2.288525 AGGCCTATGTTTCTTTCCCCT 58.711 47.619 1.29 0.00 0.00 4.79
82 83 5.256806 AGTACCAAGGCCTATGTTTCTTT 57.743 39.130 5.16 0.00 0.00 2.52
115 127 4.875536 TGATTTTGTCATCAGATGGTACCG 59.124 41.667 10.67 0.00 0.00 4.02
133 145 8.076910 TGATGCCTTTAATGTTACCATGATTT 57.923 30.769 0.00 0.00 0.00 2.17
134 146 7.658525 TGATGCCTTTAATGTTACCATGATT 57.341 32.000 0.00 0.00 0.00 2.57
146 158 5.954150 ACCACTTCTCATTGATGCCTTTAAT 59.046 36.000 0.00 0.00 0.00 1.40
153 166 5.088739 CGTTTTACCACTTCTCATTGATGC 58.911 41.667 0.00 0.00 0.00 3.91
172 186 9.959749 ACAATGATTTAGTGTACATTTTCGTTT 57.040 25.926 0.00 0.00 35.52 3.60
187 201 8.070171 CGGGACAGCTTATAAACAATGATTTAG 58.930 37.037 0.00 0.00 0.00 1.85
197 211 3.602483 TCCAACGGGACAGCTTATAAAC 58.398 45.455 0.00 0.00 38.64 2.01
215 229 2.601067 TGGCCGTCTAACCGTCCA 60.601 61.111 0.00 0.00 0.00 4.02
263 279 1.263356 ACGCCTAAGCACCTGAAGTA 58.737 50.000 0.00 0.00 39.83 2.24
264 280 0.396811 AACGCCTAAGCACCTGAAGT 59.603 50.000 0.00 0.00 39.83 3.01
268 284 1.237285 AAGCAACGCCTAAGCACCTG 61.237 55.000 0.00 0.00 39.83 4.00
294 310 0.796927 GGCGAGCACTAACCACTTTC 59.203 55.000 0.00 0.00 0.00 2.62
296 312 0.396811 AAGGCGAGCACTAACCACTT 59.603 50.000 0.00 0.00 0.00 3.16
312 328 3.644884 ACGTGATAAGGCGATCTAAGG 57.355 47.619 0.00 0.00 0.00 2.69
506 1050 2.828520 ACCTGTCGTCTCATGAAGTCAT 59.171 45.455 0.00 0.00 36.96 3.06
507 1051 2.239400 ACCTGTCGTCTCATGAAGTCA 58.761 47.619 0.00 0.00 0.00 3.41
508 1052 3.732471 GCTACCTGTCGTCTCATGAAGTC 60.732 52.174 0.00 0.00 0.00 3.01
515 1059 1.595993 GGCTGCTACCTGTCGTCTCA 61.596 60.000 0.00 0.00 0.00 3.27
617 1170 2.871216 TTTGGTGACGTCGGCCAACA 62.871 55.000 31.14 22.58 41.39 3.33
678 1231 1.408961 CCAGCCTAACGGAGAGAGAGA 60.409 57.143 0.00 0.00 0.00 3.10
679 1232 1.028905 CCAGCCTAACGGAGAGAGAG 58.971 60.000 0.00 0.00 0.00 3.20
733 1287 2.825532 GGTTAATTGCAGGCCAGAAGAA 59.174 45.455 5.01 0.00 0.00 2.52
734 1288 2.041620 AGGTTAATTGCAGGCCAGAAGA 59.958 45.455 5.01 0.00 0.00 2.87
744 1298 1.680651 CCGGCCCAGGTTAATTGCA 60.681 57.895 0.00 0.00 0.00 4.08
762 1316 2.007608 GGTCAGCCGTAATTCTGTTCC 58.992 52.381 0.00 0.00 0.00 3.62
767 1321 0.613260 TGCAGGTCAGCCGTAATTCT 59.387 50.000 0.00 0.00 40.50 2.40
779 1333 1.832167 TTTTGGTGGGCTGCAGGTC 60.832 57.895 17.12 0.00 0.00 3.85
877 1441 1.279840 GCGACTGCTGCGAGTTTTT 59.720 52.632 10.56 0.00 38.39 1.94
878 1442 1.835483 CTGCGACTGCTGCGAGTTTT 61.835 55.000 10.56 0.00 43.34 2.43
879 1443 2.280119 TGCGACTGCTGCGAGTTT 60.280 55.556 10.56 0.00 43.34 2.66
880 1444 2.736236 CTGCGACTGCTGCGAGTT 60.736 61.111 10.56 0.00 43.34 3.01
881 1445 3.905705 GACTGCGACTGCTGCGAGT 62.906 63.158 10.56 4.76 43.22 4.18
882 1446 3.177920 GACTGCGACTGCTGCGAG 61.178 66.667 10.56 0.00 43.22 5.03
883 1447 3.212906 AAGACTGCGACTGCTGCGA 62.213 57.895 10.56 0.00 43.22 5.10
884 1448 2.724708 GAAGACTGCGACTGCTGCG 61.725 63.158 0.00 0.00 43.22 5.18
885 1449 1.350706 GAGAAGACTGCGACTGCTGC 61.351 60.000 0.00 0.00 43.22 5.25
886 1450 0.735632 GGAGAAGACTGCGACTGCTG 60.736 60.000 0.00 0.00 44.78 4.41
887 1451 1.181741 TGGAGAAGACTGCGACTGCT 61.182 55.000 0.00 0.00 43.34 4.24
888 1452 0.108424 ATGGAGAAGACTGCGACTGC 60.108 55.000 0.00 0.00 43.20 4.40
889 1453 1.470632 GGATGGAGAAGACTGCGACTG 60.471 57.143 0.00 0.00 37.28 3.51
1006 1579 0.249699 TTGTCCATGAACTGCGACGT 60.250 50.000 0.00 0.00 31.45 4.34
1330 1906 5.048846 AGGTGGCCAAGTATTATTACCTG 57.951 43.478 7.24 0.00 36.06 4.00
1356 1932 2.760650 TCTATGAACAGCAGTGTCGGAT 59.239 45.455 0.00 0.00 35.08 4.18
1385 1961 5.878406 AGCTAGCAAATACTAGTGTGGAT 57.122 39.130 18.83 0.00 41.49 3.41
1469 2045 5.559770 TCTGAATCACATAGTGCCAAAAGA 58.440 37.500 0.00 0.00 32.98 2.52
1508 2086 3.181489 CGGAACTACAACTACTAGGCCTG 60.181 52.174 17.99 8.18 0.00 4.85
1537 2115 4.891168 ACATGGATATGCATCAGCTTTCAA 59.109 37.500 6.76 0.00 42.74 2.69
1575 2183 5.805751 GCATCTGCAACCATCCTATCCTAAT 60.806 44.000 0.00 0.00 41.59 1.73
1576 2184 4.505566 GCATCTGCAACCATCCTATCCTAA 60.506 45.833 0.00 0.00 41.59 2.69
1577 2185 3.008375 GCATCTGCAACCATCCTATCCTA 59.992 47.826 0.00 0.00 41.59 2.94
1578 2186 2.224719 GCATCTGCAACCATCCTATCCT 60.225 50.000 0.00 0.00 41.59 3.24
1579 2187 2.157738 GCATCTGCAACCATCCTATCC 58.842 52.381 0.00 0.00 41.59 2.59
1580 2188 2.812591 CAGCATCTGCAACCATCCTATC 59.187 50.000 4.79 0.00 45.16 2.08
1581 2189 2.860009 CAGCATCTGCAACCATCCTAT 58.140 47.619 4.79 0.00 45.16 2.57
1582 2190 2.336945 CAGCATCTGCAACCATCCTA 57.663 50.000 4.79 0.00 45.16 2.94
1583 2191 3.186345 CAGCATCTGCAACCATCCT 57.814 52.632 4.79 0.00 45.16 3.24
1658 2266 6.848069 AGACTATGAGATAGGAGTAAGCAGT 58.152 40.000 0.00 0.00 37.18 4.40
1678 2286 9.712305 CCGATTTAGGTTCATCAATATAAGACT 57.288 33.333 0.00 0.00 0.00 3.24
1679 2287 9.490379 ACCGATTTAGGTTCATCAATATAAGAC 57.510 33.333 0.00 0.00 43.00 3.01
1680 2288 9.706691 GACCGATTTAGGTTCATCAATATAAGA 57.293 33.333 0.00 0.00 46.09 2.10
1683 2299 7.888424 TCGACCGATTTAGGTTCATCAATATA 58.112 34.615 0.00 0.00 46.09 0.86
1693 2309 4.196626 TGAACATCGACCGATTTAGGTT 57.803 40.909 1.72 4.16 46.09 3.50
1706 2322 5.012655 TGTTGTGTATTCGTTGAACATCG 57.987 39.130 0.00 0.00 0.00 3.84
1746 2362 9.793252 GGCAGACCATATTTAATTTGCTATATG 57.207 33.333 0.00 0.00 35.26 1.78
1836 2452 4.846779 TGTGCCACTACCATTTTTCTTC 57.153 40.909 0.00 0.00 0.00 2.87
1837 2453 7.480760 AATATGTGCCACTACCATTTTTCTT 57.519 32.000 0.00 0.00 0.00 2.52
1838 2454 7.322664 CAAATATGTGCCACTACCATTTTTCT 58.677 34.615 0.00 0.00 0.00 2.52
1839 2455 6.035975 GCAAATATGTGCCACTACCATTTTTC 59.964 38.462 6.61 0.00 38.66 2.29
1840 2456 5.874261 GCAAATATGTGCCACTACCATTTTT 59.126 36.000 6.61 0.00 38.66 1.94
1841 2457 5.418676 GCAAATATGTGCCACTACCATTTT 58.581 37.500 6.61 0.00 38.66 1.82
1842 2458 4.439974 CGCAAATATGTGCCACTACCATTT 60.440 41.667 12.38 0.00 41.73 2.32
1843 2459 3.066621 CGCAAATATGTGCCACTACCATT 59.933 43.478 12.38 0.00 41.73 3.16
1844 2460 2.618241 CGCAAATATGTGCCACTACCAT 59.382 45.455 12.38 0.00 41.73 3.55
1845 2461 2.013400 CGCAAATATGTGCCACTACCA 58.987 47.619 12.38 0.00 41.73 3.25
1846 2462 2.014128 ACGCAAATATGTGCCACTACC 58.986 47.619 12.38 0.00 41.73 3.18
1847 2463 3.051606 CACGCAAATATGTGCCACTAC 57.948 47.619 12.38 0.00 41.73 2.73
1854 2470 0.179192 AGCACGCACGCAAATATGTG 60.179 50.000 0.00 0.00 42.84 3.21
1855 2471 0.521291 AAGCACGCACGCAAATATGT 59.479 45.000 0.00 0.00 0.00 2.29
1856 2472 2.450365 TAAGCACGCACGCAAATATG 57.550 45.000 0.00 0.00 0.00 1.78
1857 2473 2.675844 TCTTAAGCACGCACGCAAATAT 59.324 40.909 0.00 0.00 0.00 1.28
1858 2474 2.070028 TCTTAAGCACGCACGCAAATA 58.930 42.857 0.00 0.00 0.00 1.40
1859 2475 0.871722 TCTTAAGCACGCACGCAAAT 59.128 45.000 0.00 0.00 0.00 2.32
1860 2476 0.871722 ATCTTAAGCACGCACGCAAA 59.128 45.000 0.00 0.00 0.00 3.68
1861 2477 0.165727 CATCTTAAGCACGCACGCAA 59.834 50.000 0.00 0.00 0.00 4.85
1862 2478 0.948623 ACATCTTAAGCACGCACGCA 60.949 50.000 0.00 0.00 0.00 5.24
1863 2479 0.165944 AACATCTTAAGCACGCACGC 59.834 50.000 0.00 0.00 0.00 5.34
1864 2480 1.201921 GGAACATCTTAAGCACGCACG 60.202 52.381 0.00 0.00 0.00 5.34
1865 2481 1.130561 GGGAACATCTTAAGCACGCAC 59.869 52.381 0.00 0.00 0.00 5.34
1866 2482 1.448985 GGGAACATCTTAAGCACGCA 58.551 50.000 0.00 0.00 0.00 5.24
1867 2483 0.733150 GGGGAACATCTTAAGCACGC 59.267 55.000 0.00 0.00 0.00 5.34
1868 2484 1.006832 CGGGGAACATCTTAAGCACG 58.993 55.000 0.00 0.00 0.00 5.34
1869 2485 1.737793 CACGGGGAACATCTTAAGCAC 59.262 52.381 0.00 0.00 0.00 4.40
1870 2486 1.948611 GCACGGGGAACATCTTAAGCA 60.949 52.381 0.00 0.00 0.00 3.91
1871 2487 0.733150 GCACGGGGAACATCTTAAGC 59.267 55.000 0.00 0.00 0.00 3.09
1872 2488 1.737793 GTGCACGGGGAACATCTTAAG 59.262 52.381 0.00 0.00 0.00 1.85
1873 2489 1.349688 AGTGCACGGGGAACATCTTAA 59.650 47.619 12.01 0.00 0.00 1.85
1874 2490 0.981183 AGTGCACGGGGAACATCTTA 59.019 50.000 12.01 0.00 0.00 2.10
1875 2491 0.110486 AAGTGCACGGGGAACATCTT 59.890 50.000 12.01 0.00 0.00 2.40
1876 2492 0.110486 AAAGTGCACGGGGAACATCT 59.890 50.000 12.01 0.00 0.00 2.90
1877 2493 0.240945 CAAAGTGCACGGGGAACATC 59.759 55.000 12.01 0.00 0.00 3.06
1878 2494 1.178534 CCAAAGTGCACGGGGAACAT 61.179 55.000 12.01 0.00 0.00 2.71
1879 2495 1.826054 CCAAAGTGCACGGGGAACA 60.826 57.895 12.01 0.00 0.00 3.18
1880 2496 1.104577 TTCCAAAGTGCACGGGGAAC 61.105 55.000 25.87 0.00 32.95 3.62
1881 2497 0.821711 CTTCCAAAGTGCACGGGGAA 60.822 55.000 26.98 26.98 36.31 3.97
1882 2498 1.228124 CTTCCAAAGTGCACGGGGA 60.228 57.895 19.07 19.07 0.00 4.81
1883 2499 0.821711 TTCTTCCAAAGTGCACGGGG 60.822 55.000 20.31 18.05 0.00 5.73
1884 2500 1.028905 TTTCTTCCAAAGTGCACGGG 58.971 50.000 12.01 14.55 0.00 5.28
1885 2501 2.861462 TTTTCTTCCAAAGTGCACGG 57.139 45.000 12.01 7.09 0.00 4.94
1886 2502 3.490526 CCATTTTTCTTCCAAAGTGCACG 59.509 43.478 12.01 0.00 0.00 5.34
1887 2503 4.441792 ACCATTTTTCTTCCAAAGTGCAC 58.558 39.130 9.40 9.40 0.00 4.57
1888 2504 4.751767 ACCATTTTTCTTCCAAAGTGCA 57.248 36.364 0.00 0.00 0.00 4.57
1889 2505 5.691754 CACTACCATTTTTCTTCCAAAGTGC 59.308 40.000 0.00 0.00 0.00 4.40
1890 2506 6.215845 CCACTACCATTTTTCTTCCAAAGTG 58.784 40.000 0.00 0.00 0.00 3.16
1891 2507 5.221441 GCCACTACCATTTTTCTTCCAAAGT 60.221 40.000 0.00 0.00 0.00 2.66
1892 2508 5.221422 TGCCACTACCATTTTTCTTCCAAAG 60.221 40.000 0.00 0.00 0.00 2.77
1893 2509 4.651503 TGCCACTACCATTTTTCTTCCAAA 59.348 37.500 0.00 0.00 0.00 3.28
1894 2510 4.038642 GTGCCACTACCATTTTTCTTCCAA 59.961 41.667 0.00 0.00 0.00 3.53
1895 2511 3.572255 GTGCCACTACCATTTTTCTTCCA 59.428 43.478 0.00 0.00 0.00 3.53
1896 2512 3.572255 TGTGCCACTACCATTTTTCTTCC 59.428 43.478 0.00 0.00 0.00 3.46
2063 2686 1.136329 AGGACATGGCCAACTGGTCT 61.136 55.000 22.78 3.64 41.34 3.85
2069 2692 5.362430 TGGAATAATAAAGGACATGGCCAAC 59.638 40.000 22.78 4.22 0.00 3.77
2126 2749 6.321848 TGCATGCAGAAATATAACATGGAG 57.678 37.500 18.46 0.00 38.79 3.86
2141 2764 8.915871 AAACATAGTAATAACTTTGCATGCAG 57.084 30.769 21.50 13.01 37.98 4.41
2191 2814 5.241506 CCAATTGTATTGCATACCCTACCAG 59.758 44.000 4.43 0.00 34.86 4.00
2239 2862 2.034687 ATCCCTGTGTGCCTGTGC 59.965 61.111 0.00 0.00 38.26 4.57
2275 2898 7.883391 ACCGCATATAGCTACAGAAGTATAT 57.117 36.000 0.00 0.00 42.61 0.86
2291 2914 7.011499 TGGATTGGTTACTAATACCGCATAT 57.989 36.000 1.21 0.00 38.55 1.78
2298 2921 8.674607 CAAACCTCTTGGATTGGTTACTAATAC 58.325 37.037 0.00 0.00 42.53 1.89
2304 2927 6.887626 TTACAAACCTCTTGGATTGGTTAC 57.112 37.500 9.30 0.00 46.45 2.50
2324 2948 8.795786 TGCATCACAACAACTAAAGAATTTAC 57.204 30.769 0.00 0.00 40.09 2.01
2435 3062 4.741837 GCTCCATCATAGCAGCACTCTTTA 60.742 45.833 0.00 0.00 39.83 1.85
2714 3341 5.339282 GGAGTTGGAATAAAGCTTACCTCCT 60.339 44.000 17.09 10.59 0.00 3.69
3173 3803 9.574516 AAGTGAAAACTAATGATGAAACCTAGT 57.425 29.630 0.00 0.00 0.00 2.57
3177 3807 9.528018 TCAAAAGTGAAAACTAATGATGAAACC 57.472 29.630 0.00 0.00 0.00 3.27
3221 3851 1.219664 CATGCCATTGTGCCCTTGG 59.780 57.895 0.00 0.00 0.00 3.61
3254 3884 5.294060 GCAACAGGGGCAACAAATATTAATG 59.706 40.000 0.00 0.00 39.74 1.90
3267 3899 1.457267 ACAACATGCAACAGGGGCA 60.457 52.632 0.00 0.00 46.66 5.36
3281 3913 2.170985 CGCACTAGCACGCACAAC 59.829 61.111 0.00 0.00 42.27 3.32
3288 3920 0.371645 GACATGAAGCGCACTAGCAC 59.628 55.000 11.47 0.00 42.27 4.40
3328 3960 3.057526 GGTGAAGGCATGTAAAACCACTC 60.058 47.826 0.00 0.00 0.00 3.51
3364 3996 9.396022 AGGTACGAAACATTCTTCATGATTAAT 57.604 29.630 0.00 0.00 36.24 1.40
3546 4181 1.103398 GCACACCTGCTTGAACCTGT 61.103 55.000 0.00 0.00 40.63 4.00
3574 4209 3.698539 TCAACAATTTCCTGCTTGTCACA 59.301 39.130 0.00 0.00 34.61 3.58
3613 4248 3.665585 GCTTTAGACACTTGAAGCTTCGC 60.666 47.826 21.11 9.96 40.87 4.70
3755 4390 2.360852 CAGGAAGGGCAGGCAGTG 60.361 66.667 0.00 0.00 0.00 3.66
3850 4485 1.792301 CAGGTGCGACTGATTGCAG 59.208 57.895 1.49 0.00 46.32 4.41
3882 4517 3.904339 AGTAGGATTCCTGCGATATGGTT 59.096 43.478 15.80 0.00 41.15 3.67
3963 4598 2.180131 GAGGTGCTTGTTGCTGCGAG 62.180 60.000 0.00 0.00 43.37 5.03
3971 4606 1.900498 GCTGCTGGAGGTGCTTGTT 60.900 57.895 0.00 0.00 0.00 2.83
3993 4628 1.506262 CGGGTGCTGGTAATGTTGC 59.494 57.895 0.00 0.00 0.00 4.17
4002 4637 2.735772 ATACTGAGGCGGGTGCTGG 61.736 63.158 0.00 0.00 42.25 4.85
4041 4676 1.422402 GGGTTAACACTTCCAGGTGGA 59.578 52.381 8.10 0.00 43.73 4.02
4044 4679 0.775542 GGGGGTTAACACTTCCAGGT 59.224 55.000 7.98 0.00 0.00 4.00
4215 4850 0.176680 CTGCTGGAGGCTCGTACATT 59.823 55.000 8.69 0.00 42.39 2.71
4299 4934 2.912956 TCCATACTGCTCAGGAAAACCT 59.087 45.455 1.66 0.00 0.00 3.50
4335 4973 1.338674 CCAGCATTACCACGGTGAGAA 60.339 52.381 10.28 3.43 32.37 2.87
4368 5006 2.283173 GTGGGGGCAAAGGGTGAG 60.283 66.667 0.00 0.00 0.00 3.51
4401 5039 2.388232 GCCGTAGTTGCCACTTCCG 61.388 63.158 0.00 0.00 34.06 4.30
4566 5204 1.005630 GTTCTCTGTCAGCCTGCGT 60.006 57.895 0.00 0.00 0.00 5.24
4687 5326 0.108662 CACATGCTGCTCCACGACTA 60.109 55.000 0.00 0.00 0.00 2.59
4740 5397 1.543607 TCCCTCATGAATGCGCAAAA 58.456 45.000 17.11 2.69 0.00 2.44
4743 5400 1.677576 GAAATCCCTCATGAATGCGCA 59.322 47.619 14.96 14.96 0.00 6.09
4745 5402 1.942657 ACGAAATCCCTCATGAATGCG 59.057 47.619 0.00 0.00 0.00 4.73
4753 5410 5.414789 TCTGACAAATACGAAATCCCTCA 57.585 39.130 0.00 0.00 0.00 3.86
4792 5449 5.163683 GCTAACACTAACTGTACGATCTCCA 60.164 44.000 0.00 0.00 30.51 3.86
4798 5455 5.954296 AAGAGCTAACACTAACTGTACGA 57.046 39.130 0.00 0.00 30.51 3.43
4873 5530 1.407618 ACACTTGCAGACACAGTACGA 59.592 47.619 0.00 0.00 0.00 3.43
4874 5531 1.852942 ACACTTGCAGACACAGTACG 58.147 50.000 0.00 0.00 0.00 3.67
4875 5532 5.236478 ACAATAACACTTGCAGACACAGTAC 59.764 40.000 0.00 0.00 0.00 2.73
4933 5594 1.098589 TCCCTCCCTCCCTTCTAACA 58.901 55.000 0.00 0.00 0.00 2.41
4934 5595 2.439880 CAATCCCTCCCTCCCTTCTAAC 59.560 54.545 0.00 0.00 0.00 2.34
4935 5596 2.632360 CCAATCCCTCCCTCCCTTCTAA 60.632 54.545 0.00 0.00 0.00 2.10
4936 5597 1.061346 CCAATCCCTCCCTCCCTTCTA 60.061 57.143 0.00 0.00 0.00 2.10
4937 5598 0.327964 CCAATCCCTCCCTCCCTTCT 60.328 60.000 0.00 0.00 0.00 2.85
4938 5599 0.624795 ACCAATCCCTCCCTCCCTTC 60.625 60.000 0.00 0.00 0.00 3.46
4939 5600 0.921256 CACCAATCCCTCCCTCCCTT 60.921 60.000 0.00 0.00 0.00 3.95
4940 5601 1.308216 CACCAATCCCTCCCTCCCT 60.308 63.158 0.00 0.00 0.00 4.20
4941 5602 2.386935 CCACCAATCCCTCCCTCCC 61.387 68.421 0.00 0.00 0.00 4.30
4942 5603 0.919289 TTCCACCAATCCCTCCCTCC 60.919 60.000 0.00 0.00 0.00 4.30
4943 5604 1.226311 ATTCCACCAATCCCTCCCTC 58.774 55.000 0.00 0.00 0.00 4.30
4944 5605 2.294536 ACTATTCCACCAATCCCTCCCT 60.295 50.000 0.00 0.00 0.00 4.20
4945 5606 2.136026 ACTATTCCACCAATCCCTCCC 58.864 52.381 0.00 0.00 0.00 4.30
4946 5607 3.953542 AACTATTCCACCAATCCCTCC 57.046 47.619 0.00 0.00 0.00 4.30
4947 5608 4.855340 TCAAACTATTCCACCAATCCCTC 58.145 43.478 0.00 0.00 0.00 4.30
4948 5609 4.946160 TCAAACTATTCCACCAATCCCT 57.054 40.909 0.00 0.00 0.00 4.20
4949 5610 5.422012 ACAATCAAACTATTCCACCAATCCC 59.578 40.000 0.00 0.00 0.00 3.85
4950 5611 6.530019 ACAATCAAACTATTCCACCAATCC 57.470 37.500 0.00 0.00 0.00 3.01
4951 5612 8.831715 AAAACAATCAAACTATTCCACCAATC 57.168 30.769 0.00 0.00 0.00 2.67
4954 5615 9.703892 CAATAAAACAATCAAACTATTCCACCA 57.296 29.630 0.00 0.00 0.00 4.17
4955 5616 8.655970 GCAATAAAACAATCAAACTATTCCACC 58.344 33.333 0.00 0.00 0.00 4.61
4956 5617 9.423061 AGCAATAAAACAATCAAACTATTCCAC 57.577 29.630 0.00 0.00 0.00 4.02
4957 5618 9.995003 AAGCAATAAAACAATCAAACTATTCCA 57.005 25.926 0.00 0.00 0.00 3.53
4961 5622 9.143631 GCTCAAGCAATAAAACAATCAAACTAT 57.856 29.630 0.00 0.00 41.59 2.12
4962 5623 8.359642 AGCTCAAGCAATAAAACAATCAAACTA 58.640 29.630 4.59 0.00 45.16 2.24
4963 5624 7.212274 AGCTCAAGCAATAAAACAATCAAACT 58.788 30.769 4.59 0.00 45.16 2.66
4964 5625 7.412137 AGCTCAAGCAATAAAACAATCAAAC 57.588 32.000 4.59 0.00 45.16 2.93
4965 5626 7.096106 CGAAGCTCAAGCAATAAAACAATCAAA 60.096 33.333 4.59 0.00 45.16 2.69
4966 5627 6.363088 CGAAGCTCAAGCAATAAAACAATCAA 59.637 34.615 4.59 0.00 45.16 2.57
4967 5628 5.858049 CGAAGCTCAAGCAATAAAACAATCA 59.142 36.000 4.59 0.00 45.16 2.57
4968 5629 5.858581 ACGAAGCTCAAGCAATAAAACAATC 59.141 36.000 4.59 0.00 45.16 2.67
4969 5630 5.630680 CACGAAGCTCAAGCAATAAAACAAT 59.369 36.000 4.59 0.00 45.16 2.71
4970 5631 4.975502 CACGAAGCTCAAGCAATAAAACAA 59.024 37.500 4.59 0.00 45.16 2.83
4971 5632 4.536065 CACGAAGCTCAAGCAATAAAACA 58.464 39.130 4.59 0.00 45.16 2.83
4972 5633 3.914364 CCACGAAGCTCAAGCAATAAAAC 59.086 43.478 4.59 0.00 45.16 2.43
4973 5634 3.611530 GCCACGAAGCTCAAGCAATAAAA 60.612 43.478 4.59 0.00 45.16 1.52
4974 5635 2.095263 GCCACGAAGCTCAAGCAATAAA 60.095 45.455 4.59 0.00 45.16 1.40
4975 5636 1.468520 GCCACGAAGCTCAAGCAATAA 59.531 47.619 4.59 0.00 45.16 1.40
4976 5637 1.086696 GCCACGAAGCTCAAGCAATA 58.913 50.000 4.59 0.00 45.16 1.90
4977 5638 0.890542 TGCCACGAAGCTCAAGCAAT 60.891 50.000 4.59 0.00 45.16 3.56
4978 5639 0.890542 ATGCCACGAAGCTCAAGCAA 60.891 50.000 4.59 0.00 45.16 3.91
4979 5640 0.036483 TATGCCACGAAGCTCAAGCA 60.036 50.000 4.59 0.00 45.16 3.91
4980 5641 1.303309 ATATGCCACGAAGCTCAAGC 58.697 50.000 0.00 0.00 42.49 4.01
4981 5642 9.920133 ATATATATATATGCCACGAAGCTCAAG 57.080 33.333 13.42 0.00 0.00 3.02
5005 5666 9.601810 CTCCAACCACTGCCCTATATATATATA 57.398 37.037 11.21 11.21 0.00 0.86
5006 5667 8.296906 TCTCCAACCACTGCCCTATATATATAT 58.703 37.037 10.10 10.10 0.00 0.86
5007 5668 7.658260 TCTCCAACCACTGCCCTATATATATA 58.342 38.462 2.49 2.49 0.00 0.86
5008 5669 6.512120 TCTCCAACCACTGCCCTATATATAT 58.488 40.000 0.00 0.00 0.00 0.86
5009 5670 5.910931 TCTCCAACCACTGCCCTATATATA 58.089 41.667 0.00 0.00 0.00 0.86
5010 5671 4.763355 TCTCCAACCACTGCCCTATATAT 58.237 43.478 0.00 0.00 0.00 0.86
5011 5672 4.207698 TCTCCAACCACTGCCCTATATA 57.792 45.455 0.00 0.00 0.00 0.86
5012 5673 3.060479 TCTCCAACCACTGCCCTATAT 57.940 47.619 0.00 0.00 0.00 0.86
5013 5674 2.561209 TCTCCAACCACTGCCCTATA 57.439 50.000 0.00 0.00 0.00 1.31
5014 5675 1.898863 ATCTCCAACCACTGCCCTAT 58.101 50.000 0.00 0.00 0.00 2.57
5015 5676 2.023404 TCTATCTCCAACCACTGCCCTA 60.023 50.000 0.00 0.00 0.00 3.53
5016 5677 1.207791 CTATCTCCAACCACTGCCCT 58.792 55.000 0.00 0.00 0.00 5.19
5255 5922 9.653067 CGAAGTGTACAACATTTTTATTGTGTA 57.347 29.630 0.00 0.00 39.36 2.90


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

AutoCloner maintained by Alex Coulton.