Multiple sequence alignment - TraesCS3A01G320600

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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 TraesCS3A01G320600 chr3A 100.000 2804 0 0 906 3709 563411305 563408502 0.000000e+00 5179.0
1 TraesCS3A01G320600 chr3A 87.986 874 94 9 948 1818 563402578 563401713 0.000000e+00 1022.0
2 TraesCS3A01G320600 chr3A 100.000 539 0 0 1 539 563412210 563411672 0.000000e+00 996.0
3 TraesCS3A01G320600 chr3A 88.018 217 12 6 2298 2504 563401351 563401139 1.030000e-60 244.0
4 TraesCS3A01G320600 chr3D 95.135 966 41 2 906 1868 425118904 425119866 0.000000e+00 1519.0
5 TraesCS3A01G320600 chr3D 88.380 852 83 8 1011 1851 425143920 425144766 0.000000e+00 1011.0
6 TraesCS3A01G320600 chr3D 85.531 781 55 21 1950 2710 425119948 425120690 0.000000e+00 763.0
7 TraesCS3A01G320600 chr3D 89.267 559 31 10 1 536 425118332 425118884 0.000000e+00 673.0
8 TraesCS3A01G320600 chr3D 90.722 194 10 2 2298 2483 425145124 425145317 6.150000e-63 252.0
9 TraesCS3A01G320600 chr3D 91.262 103 8 1 1 102 209493726 209493828 4.990000e-29 139.0
10 TraesCS3A01G320600 chr3D 88.288 111 13 0 1 111 105443859 105443749 2.320000e-27 134.0
11 TraesCS3A01G320600 chr3D 91.549 71 5 1 2751 2821 425121444 425121513 3.050000e-16 97.1
12 TraesCS3A01G320600 chr3B 90.719 765 44 8 1950 2714 555064053 555064790 0.000000e+00 994.0
13 TraesCS3A01G320600 chr3B 87.647 850 91 10 1011 1851 555109221 555110065 0.000000e+00 976.0
14 TraesCS3A01G320600 chr3B 94.000 550 32 1 906 1455 555063038 555063586 0.000000e+00 832.0
15 TraesCS3A01G320600 chr3B 92.840 419 27 1 1453 1868 555063551 555063969 4.100000e-169 604.0
16 TraesCS3A01G320600 chr3B 92.641 231 17 0 1 231 555061052 555061282 2.130000e-87 333.0
17 TraesCS3A01G320600 chr3B 89.524 210 12 6 221 421 555062721 555062929 1.320000e-64 257.0
18 TraesCS3A01G320600 chr3B 94.079 152 9 0 2306 2457 555110405 555110556 8.010000e-57 231.0
19 TraesCS3A01G320600 chr3B 90.179 112 9 2 1 111 186749124 186749014 1.070000e-30 145.0
20 TraesCS3A01G320600 chr3B 90.141 71 6 1 2751 2821 555095352 555095421 1.420000e-14 91.6
21 TraesCS3A01G320600 chr1D 89.309 767 38 8 2822 3568 11294595 11293853 0.000000e+00 922.0
22 TraesCS3A01G320600 chr1D 85.989 364 23 14 2822 3159 252510566 252510927 7.570000e-97 364.0
23 TraesCS3A01G320600 chr1B 87.662 770 61 18 2822 3565 20552329 20551568 0.000000e+00 865.0
24 TraesCS3A01G320600 chr2A 87.615 759 46 20 2822 3569 769152793 769153514 0.000000e+00 837.0
25 TraesCS3A01G320600 chr2A 86.800 250 32 1 1263 1511 46079988 46079739 1.010000e-70 278.0
26 TraesCS3A01G320600 chr4A 85.958 762 65 22 2822 3569 706556987 706556254 0.000000e+00 776.0
27 TraesCS3A01G320600 chr4A 88.393 112 11 2 1 111 412268890 412268780 2.320000e-27 134.0
28 TraesCS3A01G320600 chr4A 88.288 111 13 0 1 111 412274691 412274581 2.320000e-27 134.0
29 TraesCS3A01G320600 chr4A 88.288 111 13 0 1 111 412299035 412298925 2.320000e-27 134.0
30 TraesCS3A01G320600 chr7B 89.570 604 44 8 2893 3482 726733750 726733152 0.000000e+00 749.0
31 TraesCS3A01G320600 chr1A 88.441 372 23 4 2825 3176 376778096 376777725 7.360000e-117 431.0
32 TraesCS3A01G320600 chr1A 88.415 328 30 5 3240 3565 376777652 376777331 4.490000e-104 388.0
33 TraesCS3A01G320600 chr7D 89.427 227 21 2 1264 1490 63456918 63457141 2.180000e-72 283.0
34 TraesCS3A01G320600 chr7D 90.291 103 9 1 1 102 28072055 28071953 2.320000e-27 134.0
35 TraesCS3A01G320600 chr2D 84.615 260 39 1 1249 1508 43828809 43829067 1.320000e-64 257.0
36 TraesCS3A01G320600 chr2D 84.091 264 40 2 1249 1511 43657333 43657071 1.710000e-63 254.0
37 TraesCS3A01G320600 chr4B 81.250 208 27 8 994 1200 607672465 607672661 1.380000e-34 158.0
38 TraesCS3A01G320600 chr4B 80.769 208 28 9 994 1200 607660338 607660534 6.420000e-33 152.0
39 TraesCS3A01G320600 chr5A 88.182 110 12 1 2 111 473466030 473465922 3.010000e-26 130.0
40 TraesCS3A01G320600 chr2B 75.709 247 44 11 1175 1413 584873793 584874031 3.920000e-20 110.0
41 TraesCS3A01G320600 chr2B 97.222 36 0 1 3232 3266 578584558 578584593 4.000000e-05 60.2


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 TraesCS3A01G320600 chr3A 563408502 563412210 3708 True 3087.500 5179 100.0000 1 3709 2 chr3A.!!$R2 3708
1 TraesCS3A01G320600 chr3A 563401139 563402578 1439 True 633.000 1022 88.0020 948 2504 2 chr3A.!!$R1 1556
2 TraesCS3A01G320600 chr3D 425118332 425121513 3181 False 763.025 1519 90.3705 1 2821 4 chr3D.!!$F2 2820
3 TraesCS3A01G320600 chr3D 425143920 425145317 1397 False 631.500 1011 89.5510 1011 2483 2 chr3D.!!$F3 1472
4 TraesCS3A01G320600 chr3B 555061052 555064790 3738 False 604.000 994 91.9448 1 2714 5 chr3B.!!$F2 2713
5 TraesCS3A01G320600 chr3B 555109221 555110556 1335 False 603.500 976 90.8630 1011 2457 2 chr3B.!!$F3 1446
6 TraesCS3A01G320600 chr1D 11293853 11294595 742 True 922.000 922 89.3090 2822 3568 1 chr1D.!!$R1 746
7 TraesCS3A01G320600 chr1B 20551568 20552329 761 True 865.000 865 87.6620 2822 3565 1 chr1B.!!$R1 743
8 TraesCS3A01G320600 chr2A 769152793 769153514 721 False 837.000 837 87.6150 2822 3569 1 chr2A.!!$F1 747
9 TraesCS3A01G320600 chr4A 706556254 706556987 733 True 776.000 776 85.9580 2822 3569 1 chr4A.!!$R4 747
10 TraesCS3A01G320600 chr7B 726733152 726733750 598 True 749.000 749 89.5700 2893 3482 1 chr7B.!!$R1 589
11 TraesCS3A01G320600 chr1A 376777331 376778096 765 True 409.500 431 88.4280 2825 3565 2 chr1A.!!$R1 740

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
428 1909 0.174389 ACAGCGCTACAGGTCATCAG 59.826 55.0 10.99 0.0 0.0 2.90 F
1939 3556 0.037419 ATGCAATGTTTGGTTCCGGC 60.037 50.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 3570 0.101399 TGAAATGCCAAACGTTGCGT 59.899 45.0 0.00 0.00 43.97 5.24 R
3590 6129 0.108804 ATACAGCGACCGTCCTGTTG 60.109 55.0 20.72 7.91 42.02 3.33 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
58 59 9.127277 GTAGTCTAGGATTTGTAATCTGTCTCT 57.873 37.037 0.00 0.00 0.00 3.10
107 108 3.769844 ACCATCCAAGTCTGTACACCTAG 59.230 47.826 0.00 0.00 0.00 3.02
155 178 7.236640 GTCAATCCCTCTCTATTCCCTTCTAAT 59.763 40.741 0.00 0.00 0.00 1.73
195 218 5.083533 TGCTTTATTAATGTTTGGCCCAG 57.916 39.130 0.00 0.00 0.00 4.45
198 221 5.163457 GCTTTATTAATGTTTGGCCCAGCTA 60.163 40.000 0.00 0.00 0.00 3.32
342 1823 7.861630 TCACATTACACTTGCTCTAAAAAGAC 58.138 34.615 0.00 0.00 0.00 3.01
346 1827 4.694339 ACACTTGCTCTAAAAAGACGACT 58.306 39.130 0.00 0.00 0.00 4.18
354 1835 5.234543 GCTCTAAAAAGACGACTGAAGTTGT 59.765 40.000 2.89 2.89 44.88 3.32
385 1866 3.745799 TCTGTGGGTAATTCGCAAAGAA 58.254 40.909 10.39 0.00 45.98 2.52
395 1876 2.031258 TCGCAAAGAAACACACCTCA 57.969 45.000 0.00 0.00 0.00 3.86
406 1887 6.299141 AGAAACACACCTCACATTTCAGTAT 58.701 36.000 0.00 0.00 32.78 2.12
412 1893 5.702670 ACACCTCACATTTCAGTATCAACAG 59.297 40.000 0.00 0.00 0.00 3.16
421 1902 2.159240 TCAGTATCAACAGCGCTACAGG 60.159 50.000 10.99 0.00 0.00 4.00
422 1903 1.825474 AGTATCAACAGCGCTACAGGT 59.175 47.619 10.99 0.00 0.00 4.00
423 1904 2.159226 AGTATCAACAGCGCTACAGGTC 60.159 50.000 10.99 0.00 0.00 3.85
424 1905 0.608130 ATCAACAGCGCTACAGGTCA 59.392 50.000 10.99 0.00 0.00 4.02
425 1906 0.608130 TCAACAGCGCTACAGGTCAT 59.392 50.000 10.99 0.00 0.00 3.06
426 1907 1.002366 CAACAGCGCTACAGGTCATC 58.998 55.000 10.99 0.00 0.00 2.92
427 1908 0.608130 AACAGCGCTACAGGTCATCA 59.392 50.000 10.99 0.00 0.00 3.07
428 1909 0.174389 ACAGCGCTACAGGTCATCAG 59.826 55.000 10.99 0.00 0.00 2.90
429 1910 0.457443 CAGCGCTACAGGTCATCAGA 59.543 55.000 10.99 0.00 0.00 3.27
430 1911 0.743688 AGCGCTACAGGTCATCAGAG 59.256 55.000 8.99 0.00 0.00 3.35
431 1912 0.873743 GCGCTACAGGTCATCAGAGC 60.874 60.000 0.00 0.00 42.53 4.09
432 1913 0.249238 CGCTACAGGTCATCAGAGCC 60.249 60.000 0.00 0.00 43.21 4.70
433 1914 0.249238 GCTACAGGTCATCAGAGCCG 60.249 60.000 0.00 0.00 43.21 5.52
434 1915 1.393603 CTACAGGTCATCAGAGCCGA 58.606 55.000 0.00 0.00 43.21 5.54
435 1916 1.959985 CTACAGGTCATCAGAGCCGAT 59.040 52.381 0.00 0.00 43.21 4.18
436 1917 1.198713 ACAGGTCATCAGAGCCGATT 58.801 50.000 0.00 0.00 43.21 3.34
437 1918 1.556911 ACAGGTCATCAGAGCCGATTT 59.443 47.619 0.00 0.00 43.21 2.17
438 1919 2.208431 CAGGTCATCAGAGCCGATTTC 58.792 52.381 0.00 0.00 43.21 2.17
439 1920 1.833630 AGGTCATCAGAGCCGATTTCA 59.166 47.619 0.00 0.00 43.21 2.69
440 1921 2.158986 AGGTCATCAGAGCCGATTTCAG 60.159 50.000 0.00 0.00 43.21 3.02
441 1922 1.596727 GTCATCAGAGCCGATTTCAGC 59.403 52.381 0.00 0.00 0.00 4.26
442 1923 1.483827 TCATCAGAGCCGATTTCAGCT 59.516 47.619 0.00 0.00 43.55 4.24
443 1924 2.695147 TCATCAGAGCCGATTTCAGCTA 59.305 45.455 0.00 0.00 40.11 3.32
444 1925 3.323115 TCATCAGAGCCGATTTCAGCTAT 59.677 43.478 0.00 0.00 40.11 2.97
445 1926 3.377346 TCAGAGCCGATTTCAGCTATC 57.623 47.619 0.00 0.00 40.11 2.08
446 1927 2.057316 CAGAGCCGATTTCAGCTATCG 58.943 52.381 9.88 9.88 43.32 2.92
447 1928 1.957177 AGAGCCGATTTCAGCTATCGA 59.043 47.619 16.98 0.00 45.79 3.59
536 2044 4.699522 GCGAGCCCGAACCCAAGT 62.700 66.667 0.00 0.00 38.22 3.16
537 2045 2.742372 CGAGCCCGAACCCAAGTG 60.742 66.667 0.00 0.00 38.22 3.16
1424 2935 3.522731 CTCCTCTCCGCACGAGGG 61.523 72.222 11.65 2.38 46.43 4.30
1466 2977 3.584052 CGGCGAGGAGGTCTACCG 61.584 72.222 0.00 0.00 42.08 4.02
1470 2981 4.253257 GAGGAGGTCTACCGCGCG 62.253 72.222 25.67 25.67 42.08 6.86
1523 3034 0.759959 TACCCCAACTGCTTCGACAA 59.240 50.000 0.00 0.00 0.00 3.18
1791 3302 1.372997 CGTGCTCGGCTACAACTGT 60.373 57.895 0.00 0.00 0.00 3.55
1899 3516 9.829507 TGATAAAGAGAAAGCAAAATTTGGAAA 57.170 25.926 7.89 0.00 0.00 3.13
1903 3520 7.500720 AGAGAAAGCAAAATTTGGAAATTGG 57.499 32.000 7.89 0.00 38.53 3.16
1904 3521 7.281841 AGAGAAAGCAAAATTTGGAAATTGGA 58.718 30.769 7.89 0.00 38.53 3.53
1905 3522 7.774625 AGAGAAAGCAAAATTTGGAAATTGGAA 59.225 29.630 7.89 0.00 38.53 3.53
1906 3523 8.467963 AGAAAGCAAAATTTGGAAATTGGAAT 57.532 26.923 7.89 0.00 38.53 3.01
1907 3524 8.354426 AGAAAGCAAAATTTGGAAATTGGAATG 58.646 29.630 7.89 0.00 38.53 2.67
1908 3525 7.820578 AAGCAAAATTTGGAAATTGGAATGA 57.179 28.000 7.89 0.00 38.53 2.57
1909 3526 7.820578 AGCAAAATTTGGAAATTGGAATGAA 57.179 28.000 7.89 0.00 38.53 2.57
1910 3527 7.650890 AGCAAAATTTGGAAATTGGAATGAAC 58.349 30.769 7.89 0.00 38.53 3.18
1911 3528 6.578172 GCAAAATTTGGAAATTGGAATGAACG 59.422 34.615 7.89 0.00 38.53 3.95
1933 3550 3.666274 CACCATGAATGCAATGTTTGGT 58.334 40.909 0.00 0.00 34.05 3.67
1934 3551 4.066490 CACCATGAATGCAATGTTTGGTT 58.934 39.130 8.47 0.00 32.18 3.67
1935 3552 4.152759 CACCATGAATGCAATGTTTGGTTC 59.847 41.667 8.47 0.00 32.18 3.62
1936 3553 3.685756 CCATGAATGCAATGTTTGGTTCC 59.314 43.478 0.00 0.00 0.00 3.62
1937 3554 3.023946 TGAATGCAATGTTTGGTTCCG 57.976 42.857 0.00 0.00 0.00 4.30
1938 3555 2.288702 TGAATGCAATGTTTGGTTCCGG 60.289 45.455 0.00 0.00 0.00 5.14
1939 3556 0.037419 ATGCAATGTTTGGTTCCGGC 60.037 50.000 0.00 0.00 0.00 6.13
1940 3557 1.365633 GCAATGTTTGGTTCCGGCA 59.634 52.632 0.00 0.00 0.00 5.69
1941 3558 0.249657 GCAATGTTTGGTTCCGGCAA 60.250 50.000 0.00 0.00 0.00 4.52
1942 3559 1.808133 GCAATGTTTGGTTCCGGCAAA 60.808 47.619 0.00 0.00 0.00 3.68
1943 3560 2.765122 CAATGTTTGGTTCCGGCAAAT 58.235 42.857 8.66 0.00 0.00 2.32
1944 3561 3.862642 GCAATGTTTGGTTCCGGCAAATA 60.863 43.478 8.66 6.90 0.00 1.40
1945 3562 4.310769 CAATGTTTGGTTCCGGCAAATAA 58.689 39.130 8.66 2.53 0.00 1.40
1946 3563 4.608948 ATGTTTGGTTCCGGCAAATAAA 57.391 36.364 8.66 0.00 0.00 1.40
1947 3564 4.402056 TGTTTGGTTCCGGCAAATAAAA 57.598 36.364 8.66 0.00 0.00 1.52
1948 3565 4.766375 TGTTTGGTTCCGGCAAATAAAAA 58.234 34.783 8.66 0.00 0.00 1.94
1984 3601 4.659111 TGGCATTTCATGGAGCATTTAG 57.341 40.909 0.00 0.00 0.00 1.85
1990 3607 6.514048 GCATTTCATGGAGCATTTAGGTAGTC 60.514 42.308 0.00 0.00 0.00 2.59
2006 3623 0.321919 AGTCAATGCCATCTGTGCGT 60.322 50.000 0.00 0.00 0.00 5.24
2047 3664 0.897621 TGGACTCATCGAGCATGTGT 59.102 50.000 0.00 0.00 41.08 3.72
2048 3665 1.284657 GGACTCATCGAGCATGTGTG 58.715 55.000 0.00 0.00 38.96 3.82
2049 3666 1.284657 GACTCATCGAGCATGTGTGG 58.715 55.000 0.00 0.00 38.96 4.17
2050 3667 0.610174 ACTCATCGAGCATGTGTGGT 59.390 50.000 0.00 0.00 37.73 4.16
2051 3668 1.004595 CTCATCGAGCATGTGTGGTG 58.995 55.000 0.00 0.00 35.91 4.17
2059 3676 0.171007 GCATGTGTGGTGTGGTATGC 59.829 55.000 0.00 0.00 34.86 3.14
2103 3724 1.284982 GCGTCTCATCAACGTGCAGT 61.285 55.000 0.00 0.00 42.02 4.40
2293 3982 9.241317 CAAAATTAATCTGGAGTACATTCATGC 57.759 33.333 0.00 0.00 0.00 4.06
2494 4219 1.006805 GTGCGGAGATGGAGATCGG 60.007 63.158 0.00 0.00 33.34 4.18
2562 4287 3.944055 AGTAGCTGAACTAGTGGTGTG 57.056 47.619 0.00 0.00 33.01 3.82
2563 4288 2.563179 AGTAGCTGAACTAGTGGTGTGG 59.437 50.000 0.00 0.00 33.01 4.17
2588 4313 2.753043 CAGGAATTGGCCGCTGCT 60.753 61.111 0.00 0.00 37.74 4.24
2662 4387 8.035394 TGTCAACTTTATGTCCTAGATCAGTTC 58.965 37.037 0.00 0.00 0.00 3.01
2666 4391 5.537300 TTATGTCCTAGATCAGTTCCAGC 57.463 43.478 0.00 0.00 0.00 4.85
2694 4423 1.276705 TGTGTGCCTATGCGTTCCTTA 59.723 47.619 0.00 0.00 41.78 2.69
2695 4424 2.289756 TGTGTGCCTATGCGTTCCTTAA 60.290 45.455 0.00 0.00 41.78 1.85
2697 4426 3.189702 GTGTGCCTATGCGTTCCTTAAAA 59.810 43.478 0.00 0.00 41.78 1.52
2710 4439 1.464997 CCTTAAAACTGCAGGCGAGAC 59.535 52.381 19.93 0.00 0.00 3.36
2714 4443 1.797025 AAACTGCAGGCGAGACTTAC 58.203 50.000 19.93 0.00 0.00 2.34
2716 4445 0.244994 ACTGCAGGCGAGACTTACTG 59.755 55.000 19.93 0.00 0.00 2.74
2718 4447 0.243907 TGCAGGCGAGACTTACTGTC 59.756 55.000 0.00 0.00 45.67 3.51
2756 4856 3.557185 TGCAGCGTGATTGTTGATATCTC 59.443 43.478 3.98 0.00 0.00 2.75
2757 4857 3.557185 GCAGCGTGATTGTTGATATCTCA 59.443 43.478 3.98 0.94 0.00 3.27
2759 4859 5.447683 GCAGCGTGATTGTTGATATCTCAAA 60.448 40.000 14.34 3.49 42.85 2.69
2760 4860 6.722301 CAGCGTGATTGTTGATATCTCAAAT 58.278 36.000 14.34 7.27 42.85 2.32
2761 4861 7.518848 GCAGCGTGATTGTTGATATCTCAAATA 60.519 37.037 14.34 7.07 42.85 1.40
2762 4862 8.337532 CAGCGTGATTGTTGATATCTCAAATAA 58.662 33.333 14.34 3.07 42.85 1.40
2763 4863 8.892723 AGCGTGATTGTTGATATCTCAAATAAA 58.107 29.630 14.34 0.00 42.85 1.40
2764 4864 9.162793 GCGTGATTGTTGATATCTCAAATAAAG 57.837 33.333 14.34 5.12 42.85 1.85
2840 5281 2.439701 CGGCGAGTCTACCAGGGA 60.440 66.667 0.00 0.00 0.00 4.20
2853 5295 1.001641 CAGGGAGGCTTCAACAGGG 60.002 63.158 0.00 0.00 0.00 4.45
2877 5319 2.062636 AGCCTACCCTCCAGAAAAACA 58.937 47.619 0.00 0.00 0.00 2.83
2885 5327 8.425703 CCTACCCTCCAGAAAAACAAAATTTTA 58.574 33.333 2.44 0.00 32.85 1.52
3047 5519 4.028490 CAACCCTAGTGCCGCCCA 62.028 66.667 0.00 0.00 0.00 5.36
3360 5887 4.535781 TCCCAGCTTGTGCATATGTAATT 58.464 39.130 4.29 0.00 42.74 1.40
3477 6016 6.570764 GCTTATTTGAACCACGGGTTTATGAA 60.571 38.462 9.31 0.20 46.95 2.57
3489 6028 4.805192 CGGGTTTATGAAGCAATGATTTGG 59.195 41.667 1.64 0.00 34.98 3.28
3539 6078 1.816183 CGTTAACTTTGAGCCCACCCA 60.816 52.381 3.71 0.00 0.00 4.51
3550 6089 0.472044 GCCCACCCACCATTTTGTTT 59.528 50.000 0.00 0.00 0.00 2.83
3551 6090 1.133945 GCCCACCCACCATTTTGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
3565 6104 6.423604 CCATTTTGTTTTTAGATTCGCCACTT 59.576 34.615 0.00 0.00 0.00 3.16
3568 6107 3.568007 TGTTTTTAGATTCGCCACTTGCT 59.432 39.130 0.00 0.00 38.05 3.91
3569 6108 3.829886 TTTTAGATTCGCCACTTGCTG 57.170 42.857 0.00 0.00 38.05 4.41
3570 6109 2.760634 TTAGATTCGCCACTTGCTGA 57.239 45.000 0.00 0.00 38.05 4.26
3571 6110 2.760634 TAGATTCGCCACTTGCTGAA 57.239 45.000 0.00 0.00 38.05 3.02
3572 6111 1.160137 AGATTCGCCACTTGCTGAAC 58.840 50.000 0.00 0.00 36.07 3.18
3573 6112 0.169009 GATTCGCCACTTGCTGAACC 59.831 55.000 0.00 0.00 36.07 3.62
3574 6113 1.577328 ATTCGCCACTTGCTGAACCG 61.577 55.000 0.00 0.00 36.07 4.44
3575 6114 2.652382 TTCGCCACTTGCTGAACCGA 62.652 55.000 0.00 0.00 38.05 4.69
3576 6115 2.034879 CGCCACTTGCTGAACCGAT 61.035 57.895 0.00 0.00 38.05 4.18
3577 6116 1.503542 GCCACTTGCTGAACCGATG 59.496 57.895 0.00 0.00 36.87 3.84
3578 6117 1.237285 GCCACTTGCTGAACCGATGT 61.237 55.000 0.00 0.00 36.87 3.06
3579 6118 1.943968 GCCACTTGCTGAACCGATGTA 60.944 52.381 0.00 0.00 36.87 2.29
3580 6119 2.632377 CCACTTGCTGAACCGATGTAT 58.368 47.619 0.00 0.00 0.00 2.29
3581 6120 2.609459 CCACTTGCTGAACCGATGTATC 59.391 50.000 0.00 0.00 0.00 2.24
3582 6121 3.525537 CACTTGCTGAACCGATGTATCT 58.474 45.455 0.00 0.00 0.00 1.98
3583 6122 3.935203 CACTTGCTGAACCGATGTATCTT 59.065 43.478 0.00 0.00 0.00 2.40
3584 6123 4.033358 CACTTGCTGAACCGATGTATCTTC 59.967 45.833 0.00 0.00 0.00 2.87
3585 6124 3.885724 TGCTGAACCGATGTATCTTCA 57.114 42.857 0.00 0.00 0.00 3.02
3586 6125 4.406648 TGCTGAACCGATGTATCTTCAT 57.593 40.909 0.00 0.00 0.00 2.57
3587 6126 4.122046 TGCTGAACCGATGTATCTTCATG 58.878 43.478 0.00 0.00 0.00 3.07
3588 6127 4.141959 TGCTGAACCGATGTATCTTCATGA 60.142 41.667 0.00 0.00 0.00 3.07
3589 6128 4.811024 GCTGAACCGATGTATCTTCATGAA 59.189 41.667 8.12 8.12 0.00 2.57
3590 6129 5.277058 GCTGAACCGATGTATCTTCATGAAC 60.277 44.000 3.38 0.00 0.00 3.18
3591 6130 5.729510 TGAACCGATGTATCTTCATGAACA 58.270 37.500 3.38 1.82 0.00 3.18
3592 6131 6.169800 TGAACCGATGTATCTTCATGAACAA 58.830 36.000 3.38 0.00 0.00 2.83
3593 6132 6.092122 TGAACCGATGTATCTTCATGAACAAC 59.908 38.462 3.38 3.78 0.00 3.32
3594 6133 5.487433 ACCGATGTATCTTCATGAACAACA 58.513 37.500 3.38 9.33 0.00 3.33
3595 6134 5.582269 ACCGATGTATCTTCATGAACAACAG 59.418 40.000 3.38 0.00 0.00 3.16
3596 6135 5.007039 CCGATGTATCTTCATGAACAACAGG 59.993 44.000 3.38 3.78 0.00 4.00
3597 6136 5.812127 CGATGTATCTTCATGAACAACAGGA 59.188 40.000 3.38 0.00 37.53 3.86
3598 6137 6.237942 CGATGTATCTTCATGAACAACAGGAC 60.238 42.308 3.38 4.91 39.05 3.85
3599 6138 4.929211 TGTATCTTCATGAACAACAGGACG 59.071 41.667 3.38 0.00 39.05 4.79
3600 6139 2.766313 TCTTCATGAACAACAGGACGG 58.234 47.619 3.38 0.00 39.05 4.79
3601 6140 2.104111 TCTTCATGAACAACAGGACGGT 59.896 45.455 3.38 0.00 39.05 4.83
3602 6141 2.163818 TCATGAACAACAGGACGGTC 57.836 50.000 0.00 0.00 34.30 4.79
3603 6142 0.790207 CATGAACAACAGGACGGTCG 59.210 55.000 1.43 0.00 31.40 4.79
3604 6143 0.949105 ATGAACAACAGGACGGTCGC 60.949 55.000 1.43 0.00 0.00 5.19
3605 6144 1.300697 GAACAACAGGACGGTCGCT 60.301 57.895 1.43 0.00 0.00 4.93
3606 6145 1.557443 GAACAACAGGACGGTCGCTG 61.557 60.000 18.85 18.85 0.00 5.18
3607 6146 2.029073 CAACAGGACGGTCGCTGT 59.971 61.111 19.83 19.83 32.06 4.40
3608 6147 1.287815 CAACAGGACGGTCGCTGTA 59.712 57.895 23.39 0.00 31.07 2.74
3609 6148 0.108804 CAACAGGACGGTCGCTGTAT 60.109 55.000 23.39 14.98 31.07 2.29
3610 6149 0.606604 AACAGGACGGTCGCTGTATT 59.393 50.000 23.39 12.44 31.07 1.89
3611 6150 1.466856 ACAGGACGGTCGCTGTATTA 58.533 50.000 22.44 0.00 30.03 0.98
3612 6151 1.820519 ACAGGACGGTCGCTGTATTAA 59.179 47.619 22.44 0.00 30.03 1.40
3613 6152 2.231964 ACAGGACGGTCGCTGTATTAAA 59.768 45.455 22.44 0.00 30.03 1.52
3614 6153 2.601763 CAGGACGGTCGCTGTATTAAAC 59.398 50.000 14.65 0.00 0.00 2.01
3615 6154 2.231964 AGGACGGTCGCTGTATTAAACA 59.768 45.455 1.43 0.00 36.42 2.83
3616 6155 3.118884 AGGACGGTCGCTGTATTAAACAT 60.119 43.478 1.43 0.00 37.50 2.71
3617 6156 3.619929 GGACGGTCGCTGTATTAAACATT 59.380 43.478 1.43 0.00 37.50 2.71
3618 6157 4.805192 GGACGGTCGCTGTATTAAACATTA 59.195 41.667 1.43 0.00 37.50 1.90
3619 6158 5.464389 GGACGGTCGCTGTATTAAACATTAT 59.536 40.000 1.43 0.00 37.50 1.28
3620 6159 6.346359 GGACGGTCGCTGTATTAAACATTATC 60.346 42.308 1.43 0.00 37.50 1.75
3621 6160 6.278363 ACGGTCGCTGTATTAAACATTATCT 58.722 36.000 0.00 0.00 37.50 1.98
3622 6161 6.200286 ACGGTCGCTGTATTAAACATTATCTG 59.800 38.462 0.00 0.00 37.50 2.90
3623 6162 6.419710 CGGTCGCTGTATTAAACATTATCTGA 59.580 38.462 0.00 0.00 37.50 3.27
3624 6163 7.042992 CGGTCGCTGTATTAAACATTATCTGAA 60.043 37.037 0.00 0.00 37.50 3.02
3625 6164 8.062448 GGTCGCTGTATTAAACATTATCTGAAC 58.938 37.037 0.00 0.00 37.50 3.18
3626 6165 8.818057 GTCGCTGTATTAAACATTATCTGAACT 58.182 33.333 0.00 0.00 37.50 3.01
3627 6166 9.378551 TCGCTGTATTAAACATTATCTGAACTT 57.621 29.630 0.00 0.00 37.50 2.66
3628 6167 9.425893 CGCTGTATTAAACATTATCTGAACTTG 57.574 33.333 0.00 0.00 37.50 3.16
3629 6168 9.226345 GCTGTATTAAACATTATCTGAACTTGC 57.774 33.333 0.00 0.00 37.50 4.01
3630 6169 9.722056 CTGTATTAAACATTATCTGAACTTGCC 57.278 33.333 0.00 0.00 37.50 4.52
3631 6170 9.237187 TGTATTAAACATTATCTGAACTTGCCA 57.763 29.630 0.00 0.00 31.43 4.92
3632 6171 9.722056 GTATTAAACATTATCTGAACTTGCCAG 57.278 33.333 0.00 0.00 0.00 4.85
3633 6172 7.994425 TTAAACATTATCTGAACTTGCCAGA 57.006 32.000 0.00 0.00 43.84 3.86
3634 6173 5.886960 AACATTATCTGAACTTGCCAGAC 57.113 39.130 0.00 0.00 42.68 3.51
3635 6174 3.935203 ACATTATCTGAACTTGCCAGACG 59.065 43.478 0.00 0.00 42.68 4.18
3636 6175 2.010145 TATCTGAACTTGCCAGACGC 57.990 50.000 0.00 0.00 42.68 5.19
3637 6176 0.322975 ATCTGAACTTGCCAGACGCT 59.677 50.000 0.00 0.00 42.68 5.07
3638 6177 0.319900 TCTGAACTTGCCAGACGCTC 60.320 55.000 0.00 0.00 35.89 5.03
3639 6178 0.601046 CTGAACTTGCCAGACGCTCA 60.601 55.000 0.00 0.00 38.78 4.26
3640 6179 0.179059 TGAACTTGCCAGACGCTCAA 60.179 50.000 0.00 0.00 38.78 3.02
3641 6180 0.235926 GAACTTGCCAGACGCTCAAC 59.764 55.000 0.00 0.00 38.78 3.18
3656 6195 4.768659 GCTCAACGAGTATCTGAACATG 57.231 45.455 0.00 0.00 31.39 3.21
3657 6196 3.000724 GCTCAACGAGTATCTGAACATGC 59.999 47.826 0.00 0.00 31.39 4.06
3658 6197 4.176271 CTCAACGAGTATCTGAACATGCA 58.824 43.478 0.00 0.00 0.00 3.96
3659 6198 4.176271 TCAACGAGTATCTGAACATGCAG 58.824 43.478 0.00 0.00 37.24 4.41
3660 6199 3.170791 ACGAGTATCTGAACATGCAGG 57.829 47.619 0.00 0.00 36.55 4.85
3661 6200 2.760650 ACGAGTATCTGAACATGCAGGA 59.239 45.455 4.84 0.00 36.55 3.86
3662 6201 3.195610 ACGAGTATCTGAACATGCAGGAA 59.804 43.478 4.84 0.00 36.55 3.36
3663 6202 3.553511 CGAGTATCTGAACATGCAGGAAC 59.446 47.826 4.84 0.00 36.55 3.62
3664 6203 4.679106 CGAGTATCTGAACATGCAGGAACT 60.679 45.833 4.84 0.89 43.88 3.01
3665 6204 5.171339 AGTATCTGAACATGCAGGAACTT 57.829 39.130 4.84 0.00 34.60 2.66
3666 6205 4.940046 AGTATCTGAACATGCAGGAACTTG 59.060 41.667 4.84 0.00 34.60 3.16
3667 6206 3.490439 TCTGAACATGCAGGAACTTGA 57.510 42.857 4.84 0.00 34.60 3.02
3668 6207 3.405831 TCTGAACATGCAGGAACTTGAG 58.594 45.455 4.84 0.00 34.60 3.02
3669 6208 1.881973 TGAACATGCAGGAACTTGAGC 59.118 47.619 4.84 0.00 34.60 4.26
3670 6209 1.881973 GAACATGCAGGAACTTGAGCA 59.118 47.619 4.84 0.00 39.18 4.26
3671 6210 2.211250 ACATGCAGGAACTTGAGCAT 57.789 45.000 4.84 0.00 44.68 3.79
3672 6211 3.354948 ACATGCAGGAACTTGAGCATA 57.645 42.857 4.84 0.00 42.48 3.14
3673 6212 3.276857 ACATGCAGGAACTTGAGCATAG 58.723 45.455 4.84 0.00 42.48 2.23
3674 6213 1.742761 TGCAGGAACTTGAGCATAGC 58.257 50.000 0.00 0.00 34.60 2.97
3675 6214 1.003464 TGCAGGAACTTGAGCATAGCA 59.997 47.619 0.00 0.00 34.60 3.49
3676 6215 1.669779 GCAGGAACTTGAGCATAGCAG 59.330 52.381 0.00 0.00 34.60 4.24
3677 6216 2.286872 CAGGAACTTGAGCATAGCAGG 58.713 52.381 0.00 0.00 34.60 4.85
3678 6217 1.211457 AGGAACTTGAGCATAGCAGGG 59.789 52.381 0.00 0.00 27.25 4.45
3679 6218 1.210478 GGAACTTGAGCATAGCAGGGA 59.790 52.381 0.00 0.00 0.00 4.20
3680 6219 2.284190 GAACTTGAGCATAGCAGGGAC 58.716 52.381 0.00 0.00 0.00 4.46
3681 6220 1.279496 ACTTGAGCATAGCAGGGACA 58.721 50.000 0.00 0.00 0.00 4.02
3682 6221 1.065854 ACTTGAGCATAGCAGGGACAC 60.066 52.381 0.00 0.00 0.00 3.67
3683 6222 1.209019 CTTGAGCATAGCAGGGACACT 59.791 52.381 0.00 0.00 0.00 3.55
3684 6223 0.826715 TGAGCATAGCAGGGACACTC 59.173 55.000 0.00 0.00 0.00 3.51
3685 6224 0.249238 GAGCATAGCAGGGACACTCG 60.249 60.000 0.00 0.00 0.00 4.18
3686 6225 1.227380 GCATAGCAGGGACACTCGG 60.227 63.158 0.00 0.00 0.00 4.63
3687 6226 1.676678 GCATAGCAGGGACACTCGGA 61.677 60.000 0.00 0.00 0.00 4.55
3688 6227 0.824109 CATAGCAGGGACACTCGGAA 59.176 55.000 0.00 0.00 0.00 4.30
3689 6228 0.824759 ATAGCAGGGACACTCGGAAC 59.175 55.000 0.00 0.00 0.00 3.62
3690 6229 0.251653 TAGCAGGGACACTCGGAACT 60.252 55.000 0.00 0.00 0.00 3.01
3691 6230 0.251653 AGCAGGGACACTCGGAACTA 60.252 55.000 0.00 0.00 0.00 2.24
3692 6231 0.606604 GCAGGGACACTCGGAACTAA 59.393 55.000 0.00 0.00 0.00 2.24
3693 6232 1.001633 GCAGGGACACTCGGAACTAAA 59.998 52.381 0.00 0.00 0.00 1.85
3694 6233 2.685100 CAGGGACACTCGGAACTAAAC 58.315 52.381 0.00 0.00 0.00 2.01
3695 6234 2.299297 CAGGGACACTCGGAACTAAACT 59.701 50.000 0.00 0.00 0.00 2.66
3696 6235 2.299297 AGGGACACTCGGAACTAAACTG 59.701 50.000 0.00 0.00 0.00 3.16
3697 6236 2.298163 GGGACACTCGGAACTAAACTGA 59.702 50.000 0.00 0.00 0.00 3.41
3698 6237 3.243975 GGGACACTCGGAACTAAACTGAA 60.244 47.826 0.00 0.00 0.00 3.02
3699 6238 3.988517 GGACACTCGGAACTAAACTGAAG 59.011 47.826 0.00 0.00 0.00 3.02
3700 6239 4.261909 GGACACTCGGAACTAAACTGAAGA 60.262 45.833 0.00 0.00 0.00 2.87
3701 6240 5.470047 ACACTCGGAACTAAACTGAAGAT 57.530 39.130 0.00 0.00 0.00 2.40
3702 6241 5.230942 ACACTCGGAACTAAACTGAAGATG 58.769 41.667 0.00 0.00 0.00 2.90
3703 6242 5.221461 ACACTCGGAACTAAACTGAAGATGT 60.221 40.000 0.00 0.00 0.00 3.06
3704 6243 5.346281 CACTCGGAACTAAACTGAAGATGTC 59.654 44.000 0.00 0.00 0.00 3.06
3705 6244 4.817517 TCGGAACTAAACTGAAGATGTCC 58.182 43.478 0.00 0.00 0.00 4.02
3706 6245 4.282449 TCGGAACTAAACTGAAGATGTCCA 59.718 41.667 0.00 0.00 0.00 4.02
3707 6246 4.994852 CGGAACTAAACTGAAGATGTCCAA 59.005 41.667 0.00 0.00 0.00 3.53
3708 6247 5.643777 CGGAACTAAACTGAAGATGTCCAAT 59.356 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.156256 TCCTAGACTACCAAATACATGCAACT 59.844 38.462 0.00 0.00 0.00 3.16
52 53 8.994500 TCTCTCCTAGAGATAAGTTAAGAGACA 58.006 37.037 2.50 0.00 45.77 3.41
78 79 5.542635 TGTACAGACTTGGATGGTAAGAAGT 59.457 40.000 0.00 0.00 0.00 3.01
88 89 6.432581 TGTATCTAGGTGTACAGACTTGGAT 58.567 40.000 0.00 8.00 0.00 3.41
155 178 2.963101 AGCAACGACATATAGCCTGGTA 59.037 45.455 0.00 0.00 0.00 3.25
287 1759 7.205297 GTGATGTAAGCATGCCATAAAGATTT 58.795 34.615 15.66 0.78 30.84 2.17
342 1823 3.099267 ACTTCCTCACAACTTCAGTCG 57.901 47.619 0.00 0.00 0.00 4.18
346 1827 4.635765 CACAGAAACTTCCTCACAACTTCA 59.364 41.667 0.00 0.00 0.00 3.02
354 1835 4.993705 ATTACCCACAGAAACTTCCTCA 57.006 40.909 0.00 0.00 0.00 3.86
385 1866 5.620206 TGATACTGAAATGTGAGGTGTGTT 58.380 37.500 0.00 0.00 0.00 3.32
395 1876 3.338249 AGCGCTGTTGATACTGAAATGT 58.662 40.909 10.39 0.00 0.00 2.71
406 1887 0.608130 ATGACCTGTAGCGCTGTTGA 59.392 50.000 22.90 0.00 0.00 3.18
412 1893 0.873743 GCTCTGATGACCTGTAGCGC 60.874 60.000 0.00 0.00 0.00 5.92
421 1902 1.596727 GCTGAAATCGGCTCTGATGAC 59.403 52.381 6.98 0.00 44.58 3.06
422 1903 1.945387 GCTGAAATCGGCTCTGATGA 58.055 50.000 6.98 0.00 44.58 2.92
430 1911 1.996191 GGATCGATAGCTGAAATCGGC 59.004 52.381 15.44 6.10 44.88 5.54
431 1912 3.303881 TGGATCGATAGCTGAAATCGG 57.696 47.619 15.44 0.49 44.88 4.18
432 1913 4.051237 TGTTGGATCGATAGCTGAAATCG 58.949 43.478 10.48 10.48 45.88 3.34
433 1914 4.212214 GGTGTTGGATCGATAGCTGAAATC 59.788 45.833 0.00 0.00 0.00 2.17
434 1915 4.130118 GGTGTTGGATCGATAGCTGAAAT 58.870 43.478 0.00 0.00 0.00 2.17
435 1916 3.197766 AGGTGTTGGATCGATAGCTGAAA 59.802 43.478 0.00 0.00 0.00 2.69
436 1917 2.766263 AGGTGTTGGATCGATAGCTGAA 59.234 45.455 0.00 0.00 0.00 3.02
437 1918 2.362397 GAGGTGTTGGATCGATAGCTGA 59.638 50.000 0.00 0.00 0.00 4.26
438 1919 2.101415 TGAGGTGTTGGATCGATAGCTG 59.899 50.000 0.00 0.00 0.00 4.24
439 1920 2.101582 GTGAGGTGTTGGATCGATAGCT 59.898 50.000 0.00 0.00 0.00 3.32
440 1921 2.474816 GTGAGGTGTTGGATCGATAGC 58.525 52.381 0.00 0.00 0.00 2.97
441 1922 2.357952 TCGTGAGGTGTTGGATCGATAG 59.642 50.000 0.00 0.00 0.00 2.08
442 1923 2.357952 CTCGTGAGGTGTTGGATCGATA 59.642 50.000 0.00 0.00 0.00 2.92
443 1924 1.135139 CTCGTGAGGTGTTGGATCGAT 59.865 52.381 0.00 0.00 0.00 3.59
444 1925 0.526211 CTCGTGAGGTGTTGGATCGA 59.474 55.000 0.00 0.00 0.00 3.59
445 1926 0.458543 CCTCGTGAGGTGTTGGATCG 60.459 60.000 7.79 0.00 43.61 3.69
446 1927 3.442996 CCTCGTGAGGTGTTGGATC 57.557 57.895 7.79 0.00 43.61 3.36
476 1983 3.438360 GTTCCTTTTCTGTGCAACACTG 58.562 45.455 0.00 0.00 45.67 3.66
908 2416 1.003866 GTGGAACAAGTGAACGACTGC 60.004 52.381 0.00 0.00 44.16 4.40
986 2494 2.976490 GCCATGGACCTGACAGCCT 61.976 63.158 18.40 0.00 0.00 4.58
992 2500 3.770040 CGGACGCCATGGACCTGA 61.770 66.667 18.40 0.00 0.00 3.86
1282 2793 3.443925 CAGGCAGTCTCTCGGCGA 61.444 66.667 10.14 10.14 38.10 5.54
1470 2981 3.031660 GTCGTTGACGGAGATGACC 57.968 57.895 3.48 0.00 40.29 4.02
1899 3516 2.445427 TCATGGTGCGTTCATTCCAAT 58.555 42.857 0.00 0.00 33.55 3.16
1900 3517 1.902938 TCATGGTGCGTTCATTCCAA 58.097 45.000 0.00 0.00 33.55 3.53
1901 3518 1.902938 TTCATGGTGCGTTCATTCCA 58.097 45.000 0.00 0.00 0.00 3.53
1902 3519 2.801063 CATTCATGGTGCGTTCATTCC 58.199 47.619 0.00 0.00 0.00 3.01
1903 3520 2.187707 GCATTCATGGTGCGTTCATTC 58.812 47.619 7.98 0.00 32.29 2.67
1904 3521 1.545136 TGCATTCATGGTGCGTTCATT 59.455 42.857 15.85 0.00 45.37 2.57
1905 3522 1.175654 TGCATTCATGGTGCGTTCAT 58.824 45.000 15.85 0.00 45.37 2.57
1906 3523 0.957362 TTGCATTCATGGTGCGTTCA 59.043 45.000 15.85 0.34 45.37 3.18
1907 3524 1.921887 CATTGCATTCATGGTGCGTTC 59.078 47.619 15.85 0.00 45.37 3.95
1908 3525 1.273048 ACATTGCATTCATGGTGCGTT 59.727 42.857 15.85 6.24 45.37 4.84
1909 3526 0.889994 ACATTGCATTCATGGTGCGT 59.110 45.000 15.85 7.85 45.37 5.24
1910 3527 1.999048 AACATTGCATTCATGGTGCG 58.001 45.000 15.85 7.36 45.37 5.34
1911 3528 2.417239 CCAAACATTGCATTCATGGTGC 59.583 45.455 14.59 14.59 42.81 5.01
1951 3568 6.618222 CATGAAATGCCAAACGTTGCGTTC 62.618 45.833 15.83 15.20 43.30 3.95
1952 3569 4.880031 CATGAAATGCCAAACGTTGCGTT 61.880 43.478 11.18 11.18 44.99 4.84
1953 3570 0.101399 TGAAATGCCAAACGTTGCGT 59.899 45.000 0.00 0.00 43.97 5.24
1954 3571 1.124658 CATGAAATGCCAAACGTTGCG 59.875 47.619 0.00 0.00 37.62 4.85
1955 3572 1.460359 CCATGAAATGCCAAACGTTGC 59.540 47.619 0.00 1.95 44.97 4.17
1956 3573 2.988493 CTCCATGAAATGCCAAACGTTG 59.012 45.455 0.00 0.00 44.97 4.10
1957 3574 2.610232 GCTCCATGAAATGCCAAACGTT 60.610 45.455 0.00 0.00 44.97 3.99
1958 3575 1.067635 GCTCCATGAAATGCCAAACGT 60.068 47.619 0.00 0.00 44.97 3.99
1959 3576 1.067706 TGCTCCATGAAATGCCAAACG 60.068 47.619 0.00 0.00 44.97 3.60
1960 3577 2.747396 TGCTCCATGAAATGCCAAAC 57.253 45.000 0.00 0.00 44.97 2.93
1961 3578 3.985019 AATGCTCCATGAAATGCCAAA 57.015 38.095 0.00 0.00 44.97 3.28
1962 3579 3.985019 AAATGCTCCATGAAATGCCAA 57.015 38.095 0.00 0.00 44.97 4.52
1963 3580 3.385433 CCTAAATGCTCCATGAAATGCCA 59.615 43.478 0.00 0.00 44.97 4.92
1964 3581 3.385755 ACCTAAATGCTCCATGAAATGCC 59.614 43.478 0.00 0.00 44.97 4.40
1965 3582 4.660789 ACCTAAATGCTCCATGAAATGC 57.339 40.909 0.00 0.00 44.97 3.56
1984 3601 1.672881 GCACAGATGGCATTGACTACC 59.327 52.381 0.00 0.00 0.00 3.18
1990 3607 2.009051 TCTTACGCACAGATGGCATTG 58.991 47.619 0.00 4.82 0.00 2.82
2006 3623 3.690475 ATCTGCATGCCGATCATCTTA 57.310 42.857 17.82 0.00 31.79 2.10
2047 3664 1.345089 AGTACAACGCATACCACACCA 59.655 47.619 0.00 0.00 0.00 4.17
2048 3665 1.997606 GAGTACAACGCATACCACACC 59.002 52.381 0.00 0.00 0.00 4.16
2049 3666 1.997606 GGAGTACAACGCATACCACAC 59.002 52.381 0.00 0.00 0.00 3.82
2050 3667 1.619332 TGGAGTACAACGCATACCACA 59.381 47.619 0.00 0.00 0.00 4.17
2051 3668 2.268298 CTGGAGTACAACGCATACCAC 58.732 52.381 0.00 0.00 0.00 4.16
2059 3676 6.089551 CACTTGATTAGAACTGGAGTACAACG 59.910 42.308 0.00 0.00 0.00 4.10
2103 3724 1.519719 GCCAAAACCACTGGTTGCA 59.480 52.632 14.46 0.00 46.20 4.08
2228 3911 1.005630 AGACAGAAGACGCACCTGC 60.006 57.895 0.00 0.00 37.78 4.85
2293 3982 4.572909 TGACATTCTGATTGACAGTCAGG 58.427 43.478 23.26 12.71 45.86 3.86
2393 4101 0.250467 TCTCCCTCAGTTTGCAGCAC 60.250 55.000 0.00 0.00 0.00 4.40
2512 4237 3.278668 AGCATGGATCTCAAACCAGAG 57.721 47.619 0.00 0.00 39.62 3.35
2557 4282 4.974721 CCTGGCCACACCCACACC 62.975 72.222 0.00 0.00 37.83 4.16
2558 4283 2.713531 ATTCCTGGCCACACCCACAC 62.714 60.000 0.00 0.00 37.83 3.82
2559 4284 2.017668 AATTCCTGGCCACACCCACA 62.018 55.000 0.00 0.00 37.83 4.17
2560 4285 1.228862 AATTCCTGGCCACACCCAC 60.229 57.895 0.00 0.00 37.83 4.61
2561 4286 1.228831 CAATTCCTGGCCACACCCA 60.229 57.895 0.00 0.00 37.83 4.51
2562 4287 1.984026 CCAATTCCTGGCCACACCC 60.984 63.158 0.00 0.00 38.76 4.61
2563 4288 3.698765 CCAATTCCTGGCCACACC 58.301 61.111 0.00 0.00 38.76 4.16
2583 4308 1.905922 GACGACAGAGCCAAAGCAGC 61.906 60.000 0.00 0.00 43.56 5.25
2588 4313 1.371183 CCAGGACGACAGAGCCAAA 59.629 57.895 0.00 0.00 0.00 3.28
2662 4387 2.959372 CACACACATGGCTGCTGG 59.041 61.111 0.00 0.00 0.00 4.85
2694 4423 2.143925 GTAAGTCTCGCCTGCAGTTTT 58.856 47.619 13.81 0.00 0.00 2.43
2695 4424 1.344763 AGTAAGTCTCGCCTGCAGTTT 59.655 47.619 13.81 0.00 0.00 2.66
2697 4426 0.244994 CAGTAAGTCTCGCCTGCAGT 59.755 55.000 13.81 0.00 0.00 4.40
2710 4439 4.857588 AGTCTAAATTGCGACGACAGTAAG 59.142 41.667 0.00 0.00 35.38 2.34
2714 4443 3.722082 GCAAGTCTAAATTGCGACGACAG 60.722 47.826 0.00 0.00 43.15 3.51
2716 4445 2.759038 GCAAGTCTAAATTGCGACGAC 58.241 47.619 0.00 0.00 43.15 4.34
2726 4826 3.138304 ACAATCACGCTGCAAGTCTAAA 58.862 40.909 0.00 0.00 35.30 1.85
2737 4837 6.932356 ATTTGAGATATCAACAATCACGCT 57.068 33.333 1.37 0.00 0.00 5.07
2776 5217 3.989817 GCCCTGCTAAAATTGTTGTTCTG 59.010 43.478 0.00 0.00 0.00 3.02
2778 5219 3.989817 CAGCCCTGCTAAAATTGTTGTTC 59.010 43.478 0.00 0.00 36.40 3.18
2840 5281 3.733709 CTTCACCCTGTTGAAGCCT 57.266 52.632 0.16 0.00 44.53 4.58
2853 5295 1.276622 TTCTGGAGGGTAGGCTTCAC 58.723 55.000 0.00 0.00 0.00 3.18
3069 5541 2.472029 CTCTACCACAACCATCTCCCT 58.528 52.381 0.00 0.00 0.00 4.20
3279 5803 8.166422 ACTCGTATGTTTTCTCCTCAATTTTT 57.834 30.769 0.00 0.00 0.00 1.94
3280 5804 7.745620 ACTCGTATGTTTTCTCCTCAATTTT 57.254 32.000 0.00 0.00 0.00 1.82
3447 5982 3.443681 CCCGTGGTTCAAATAAGCTTCAT 59.556 43.478 0.00 0.00 0.00 2.57
3477 6016 9.729281 ATCATTTTAAAGAACCAAATCATTGCT 57.271 25.926 0.00 0.00 35.10 3.91
3539 6078 5.694458 GTGGCGAATCTAAAAACAAAATGGT 59.306 36.000 0.00 0.00 0.00 3.55
3565 6104 3.885724 TGAAGATACATCGGTTCAGCA 57.114 42.857 0.00 0.00 0.00 4.41
3568 6107 5.729510 TGTTCATGAAGATACATCGGTTCA 58.270 37.500 8.80 0.00 33.61 3.18
3569 6108 6.092122 TGTTGTTCATGAAGATACATCGGTTC 59.908 38.462 8.80 0.00 0.00 3.62
3570 6109 5.937540 TGTTGTTCATGAAGATACATCGGTT 59.062 36.000 8.80 0.00 0.00 4.44
3571 6110 5.487433 TGTTGTTCATGAAGATACATCGGT 58.513 37.500 8.80 0.00 0.00 4.69
3572 6111 5.007039 CCTGTTGTTCATGAAGATACATCGG 59.993 44.000 8.80 8.07 0.00 4.18
3573 6112 5.812127 TCCTGTTGTTCATGAAGATACATCG 59.188 40.000 8.80 8.07 0.00 3.84
3574 6113 6.237942 CGTCCTGTTGTTCATGAAGATACATC 60.238 42.308 8.80 4.04 0.00 3.06
3575 6114 5.582269 CGTCCTGTTGTTCATGAAGATACAT 59.418 40.000 8.80 0.00 0.00 2.29
3576 6115 4.929211 CGTCCTGTTGTTCATGAAGATACA 59.071 41.667 8.80 12.93 0.00 2.29
3577 6116 4.330074 CCGTCCTGTTGTTCATGAAGATAC 59.670 45.833 8.80 9.24 0.00 2.24
3578 6117 4.020573 ACCGTCCTGTTGTTCATGAAGATA 60.021 41.667 8.80 0.00 0.00 1.98
3579 6118 3.244561 ACCGTCCTGTTGTTCATGAAGAT 60.245 43.478 8.80 0.00 0.00 2.40
3580 6119 2.104111 ACCGTCCTGTTGTTCATGAAGA 59.896 45.455 8.80 4.42 0.00 2.87
3581 6120 2.480419 GACCGTCCTGTTGTTCATGAAG 59.520 50.000 8.80 0.00 0.00 3.02
3582 6121 2.489971 GACCGTCCTGTTGTTCATGAA 58.510 47.619 3.38 3.38 0.00 2.57
3583 6122 1.604438 CGACCGTCCTGTTGTTCATGA 60.604 52.381 0.00 0.00 0.00 3.07
3584 6123 0.790207 CGACCGTCCTGTTGTTCATG 59.210 55.000 0.00 0.00 0.00 3.07
3585 6124 0.949105 GCGACCGTCCTGTTGTTCAT 60.949 55.000 0.00 0.00 0.00 2.57
3586 6125 1.593209 GCGACCGTCCTGTTGTTCA 60.593 57.895 0.00 0.00 0.00 3.18
3587 6126 1.300697 AGCGACCGTCCTGTTGTTC 60.301 57.895 0.00 0.00 0.00 3.18
3588 6127 1.594293 CAGCGACCGTCCTGTTGTT 60.594 57.895 8.21 0.00 0.00 2.83
3589 6128 1.457823 TACAGCGACCGTCCTGTTGT 61.458 55.000 20.72 12.22 42.02 3.32
3590 6129 0.108804 ATACAGCGACCGTCCTGTTG 60.109 55.000 20.72 7.91 42.02 3.33
3591 6130 0.606604 AATACAGCGACCGTCCTGTT 59.393 50.000 20.72 10.85 42.02 3.16
3592 6131 1.466856 TAATACAGCGACCGTCCTGT 58.533 50.000 19.90 19.90 44.02 4.00
3593 6132 2.572191 TTAATACAGCGACCGTCCTG 57.428 50.000 12.76 12.76 35.26 3.86
3594 6133 2.231964 TGTTTAATACAGCGACCGTCCT 59.768 45.455 0.00 0.00 31.68 3.85
3595 6134 2.609350 TGTTTAATACAGCGACCGTCC 58.391 47.619 0.00 0.00 31.68 4.79
3596 6135 4.852609 AATGTTTAATACAGCGACCGTC 57.147 40.909 0.00 0.00 40.83 4.79
3597 6136 6.200286 CAGATAATGTTTAATACAGCGACCGT 59.800 38.462 0.00 0.00 40.83 4.83
3598 6137 6.419710 TCAGATAATGTTTAATACAGCGACCG 59.580 38.462 0.00 0.00 40.83 4.79
3599 6138 7.709269 TCAGATAATGTTTAATACAGCGACC 57.291 36.000 0.00 0.00 40.83 4.79
3600 6139 8.818057 AGTTCAGATAATGTTTAATACAGCGAC 58.182 33.333 0.00 0.00 40.83 5.19
3601 6140 8.942338 AGTTCAGATAATGTTTAATACAGCGA 57.058 30.769 0.00 0.00 40.83 4.93
3602 6141 9.425893 CAAGTTCAGATAATGTTTAATACAGCG 57.574 33.333 0.00 0.00 40.83 5.18
3603 6142 9.226345 GCAAGTTCAGATAATGTTTAATACAGC 57.774 33.333 0.00 0.00 40.83 4.40
3604 6143 9.722056 GGCAAGTTCAGATAATGTTTAATACAG 57.278 33.333 0.00 0.00 40.83 2.74
3605 6144 9.237187 TGGCAAGTTCAGATAATGTTTAATACA 57.763 29.630 0.00 0.00 41.97 2.29
3606 6145 9.722056 CTGGCAAGTTCAGATAATGTTTAATAC 57.278 33.333 0.00 0.00 34.36 1.89
3607 6146 9.679661 TCTGGCAAGTTCAGATAATGTTTAATA 57.320 29.630 0.00 0.00 36.46 0.98
3608 6147 8.462016 GTCTGGCAAGTTCAGATAATGTTTAAT 58.538 33.333 0.00 0.00 42.36 1.40
3609 6148 7.360861 CGTCTGGCAAGTTCAGATAATGTTTAA 60.361 37.037 0.00 0.00 42.36 1.52
3610 6149 6.092122 CGTCTGGCAAGTTCAGATAATGTTTA 59.908 38.462 0.00 0.00 42.36 2.01
3611 6150 5.106555 CGTCTGGCAAGTTCAGATAATGTTT 60.107 40.000 0.00 0.00 42.36 2.83
3612 6151 4.393062 CGTCTGGCAAGTTCAGATAATGTT 59.607 41.667 0.00 0.00 42.36 2.71
3613 6152 3.935203 CGTCTGGCAAGTTCAGATAATGT 59.065 43.478 0.00 0.00 42.36 2.71
3614 6153 3.242543 GCGTCTGGCAAGTTCAGATAATG 60.243 47.826 0.00 0.00 42.36 1.90
3615 6154 2.939103 GCGTCTGGCAAGTTCAGATAAT 59.061 45.455 0.00 0.00 42.36 1.28
3616 6155 2.346803 GCGTCTGGCAAGTTCAGATAA 58.653 47.619 0.00 0.00 42.36 1.75
3617 6156 2.010145 GCGTCTGGCAAGTTCAGATA 57.990 50.000 0.00 0.00 42.36 1.98
3618 6157 2.846371 GCGTCTGGCAAGTTCAGAT 58.154 52.632 0.00 0.00 42.36 2.90
3619 6158 4.361253 GCGTCTGGCAAGTTCAGA 57.639 55.556 0.00 0.00 42.87 3.27
3628 6167 0.179134 ATACTCGTTGAGCGTCTGGC 60.179 55.000 0.00 0.00 42.13 4.85
3629 6168 1.402259 AGATACTCGTTGAGCGTCTGG 59.598 52.381 0.00 0.00 42.13 3.86
3630 6169 2.096013 TCAGATACTCGTTGAGCGTCTG 59.904 50.000 16.64 16.64 41.52 3.51
3631 6170 2.357075 TCAGATACTCGTTGAGCGTCT 58.643 47.619 0.00 0.00 42.13 4.18
3632 6171 2.826979 TCAGATACTCGTTGAGCGTC 57.173 50.000 0.00 0.00 42.13 5.19
3633 6172 2.228103 TGTTCAGATACTCGTTGAGCGT 59.772 45.455 0.00 0.00 42.13 5.07
3634 6173 2.863739 TGTTCAGATACTCGTTGAGCG 58.136 47.619 0.00 0.00 43.01 5.03
3635 6174 3.000724 GCATGTTCAGATACTCGTTGAGC 59.999 47.826 0.00 0.00 32.04 4.26
3636 6175 4.176271 TGCATGTTCAGATACTCGTTGAG 58.824 43.478 0.00 0.00 35.52 3.02
3637 6176 4.176271 CTGCATGTTCAGATACTCGTTGA 58.824 43.478 0.00 0.00 36.19 3.18
3638 6177 3.308053 CCTGCATGTTCAGATACTCGTTG 59.692 47.826 2.22 0.00 36.19 4.10
3639 6178 3.195610 TCCTGCATGTTCAGATACTCGTT 59.804 43.478 2.22 0.00 36.19 3.85
3640 6179 2.760650 TCCTGCATGTTCAGATACTCGT 59.239 45.455 2.22 0.00 36.19 4.18
3641 6180 3.443099 TCCTGCATGTTCAGATACTCG 57.557 47.619 2.22 0.00 36.19 4.18
3642 6181 4.764172 AGTTCCTGCATGTTCAGATACTC 58.236 43.478 2.22 0.00 36.19 2.59
3643 6182 4.833478 AGTTCCTGCATGTTCAGATACT 57.167 40.909 2.22 2.86 36.19 2.12
3644 6183 4.937620 TCAAGTTCCTGCATGTTCAGATAC 59.062 41.667 2.22 0.94 36.19 2.24
3645 6184 5.164620 TCAAGTTCCTGCATGTTCAGATA 57.835 39.130 2.22 0.00 36.19 1.98
3646 6185 4.008330 CTCAAGTTCCTGCATGTTCAGAT 58.992 43.478 2.22 0.00 36.19 2.90
3647 6186 3.405831 CTCAAGTTCCTGCATGTTCAGA 58.594 45.455 2.22 0.00 36.19 3.27
3648 6187 2.095364 GCTCAAGTTCCTGCATGTTCAG 60.095 50.000 0.00 0.00 0.00 3.02
3649 6188 1.881973 GCTCAAGTTCCTGCATGTTCA 59.118 47.619 0.00 0.00 0.00 3.18
3650 6189 1.881973 TGCTCAAGTTCCTGCATGTTC 59.118 47.619 0.00 0.00 0.00 3.18
3651 6190 1.985473 TGCTCAAGTTCCTGCATGTT 58.015 45.000 0.00 0.00 0.00 2.71
3652 6191 2.211250 ATGCTCAAGTTCCTGCATGT 57.789 45.000 0.00 0.00 43.41 3.21
3653 6192 2.033049 GCTATGCTCAAGTTCCTGCATG 59.967 50.000 13.72 0.00 44.52 4.06
3654 6193 2.295885 GCTATGCTCAAGTTCCTGCAT 58.704 47.619 10.37 10.37 46.22 3.96
3655 6194 1.003464 TGCTATGCTCAAGTTCCTGCA 59.997 47.619 0.00 0.00 39.83 4.41
3656 6195 1.669779 CTGCTATGCTCAAGTTCCTGC 59.330 52.381 0.00 0.00 0.00 4.85
3657 6196 2.286872 CCTGCTATGCTCAAGTTCCTG 58.713 52.381 0.00 0.00 0.00 3.86
3658 6197 1.211457 CCCTGCTATGCTCAAGTTCCT 59.789 52.381 0.00 0.00 0.00 3.36
3659 6198 1.210478 TCCCTGCTATGCTCAAGTTCC 59.790 52.381 0.00 0.00 0.00 3.62
3660 6199 2.284190 GTCCCTGCTATGCTCAAGTTC 58.716 52.381 0.00 0.00 0.00 3.01
3661 6200 1.630369 TGTCCCTGCTATGCTCAAGTT 59.370 47.619 0.00 0.00 0.00 2.66
3662 6201 1.065854 GTGTCCCTGCTATGCTCAAGT 60.066 52.381 0.00 0.00 0.00 3.16
3663 6202 1.209019 AGTGTCCCTGCTATGCTCAAG 59.791 52.381 0.00 0.00 0.00 3.02
3664 6203 1.208052 GAGTGTCCCTGCTATGCTCAA 59.792 52.381 0.00 0.00 0.00 3.02
3665 6204 0.826715 GAGTGTCCCTGCTATGCTCA 59.173 55.000 0.00 0.00 0.00 4.26
3666 6205 0.249238 CGAGTGTCCCTGCTATGCTC 60.249 60.000 0.00 0.00 0.00 4.26
3667 6206 1.680522 CCGAGTGTCCCTGCTATGCT 61.681 60.000 0.00 0.00 0.00 3.79
3668 6207 1.227380 CCGAGTGTCCCTGCTATGC 60.227 63.158 0.00 0.00 0.00 3.14
3669 6208 0.824109 TTCCGAGTGTCCCTGCTATG 59.176 55.000 0.00 0.00 0.00 2.23
3670 6209 0.824759 GTTCCGAGTGTCCCTGCTAT 59.175 55.000 0.00 0.00 0.00 2.97
3671 6210 0.251653 AGTTCCGAGTGTCCCTGCTA 60.252 55.000 0.00 0.00 0.00 3.49
3672 6211 0.251653 TAGTTCCGAGTGTCCCTGCT 60.252 55.000 0.00 0.00 0.00 4.24
3673 6212 0.606604 TTAGTTCCGAGTGTCCCTGC 59.393 55.000 0.00 0.00 0.00 4.85
3674 6213 2.299297 AGTTTAGTTCCGAGTGTCCCTG 59.701 50.000 0.00 0.00 0.00 4.45
3675 6214 2.299297 CAGTTTAGTTCCGAGTGTCCCT 59.701 50.000 0.00 0.00 0.00 4.20
3676 6215 2.298163 TCAGTTTAGTTCCGAGTGTCCC 59.702 50.000 0.00 0.00 0.00 4.46
3677 6216 3.655276 TCAGTTTAGTTCCGAGTGTCC 57.345 47.619 0.00 0.00 0.00 4.02
3678 6217 4.868067 TCTTCAGTTTAGTTCCGAGTGTC 58.132 43.478 0.00 0.00 0.00 3.67
3679 6218 4.931661 TCTTCAGTTTAGTTCCGAGTGT 57.068 40.909 0.00 0.00 0.00 3.55
3680 6219 5.230942 ACATCTTCAGTTTAGTTCCGAGTG 58.769 41.667 0.00 0.00 0.00 3.51
3681 6220 5.470047 ACATCTTCAGTTTAGTTCCGAGT 57.530 39.130 0.00 0.00 0.00 4.18
3682 6221 4.865365 GGACATCTTCAGTTTAGTTCCGAG 59.135 45.833 0.00 0.00 0.00 4.63
3683 6222 4.282449 TGGACATCTTCAGTTTAGTTCCGA 59.718 41.667 0.00 0.00 0.00 4.55
3684 6223 4.566004 TGGACATCTTCAGTTTAGTTCCG 58.434 43.478 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.