Multiple sequence alignment - TraesCS5A01G240000

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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 TraesCS5A01G240000 chr5A 100.000 4295 0 0 1 4295 456475820 456471526 0.000000e+00 7932.0
1 TraesCS5A01G240000 chr5A 88.194 432 37 5 216 643 52340697 52340276 1.780000e-138 503.0
2 TraesCS5A01G240000 chr5A 84.173 278 22 9 3887 4164 52326317 52326062 2.560000e-62 250.0
3 TraesCS5A01G240000 chr5A 92.105 114 9 0 3016 3129 52340252 52340139 1.240000e-35 161.0
4 TraesCS5A01G240000 chr1B 93.905 1247 37 7 1773 2993 678413750 678414983 0.000000e+00 1845.0
5 TraesCS5A01G240000 chr1B 95.971 695 24 2 634 1326 678412800 678413492 0.000000e+00 1125.0
6 TraesCS5A01G240000 chr1B 97.770 269 3 1 1351 1619 678413490 678413755 1.090000e-125 460.0
7 TraesCS5A01G240000 chr1B 81.440 361 61 5 634 990 673788624 673788982 1.510000e-74 291.0
8 TraesCS5A01G240000 chr3A 96.114 875 26 3 2989 3862 20204172 20205039 0.000000e+00 1421.0
9 TraesCS5A01G240000 chr3A 97.012 502 11 1 134 635 20203678 20204175 0.000000e+00 841.0
10 TraesCS5A01G240000 chr3A 97.011 435 11 2 3861 4293 20205452 20205886 0.000000e+00 730.0
11 TraesCS5A01G240000 chr3A 90.909 143 5 5 1 136 20203475 20203616 7.330000e-43 185.0
12 TraesCS5A01G240000 chr3A 77.381 168 35 2 1934 2101 158168612 158168448 3.540000e-16 97.1
13 TraesCS5A01G240000 chr6A 95.528 872 31 3 2992 3862 22035924 22035060 0.000000e+00 1387.0
14 TraesCS5A01G240000 chr6A 96.813 502 12 1 134 635 77506710 77507207 0.000000e+00 835.0
15 TraesCS5A01G240000 chr6A 95.703 512 16 3 134 643 22036421 22035914 0.000000e+00 819.0
16 TraesCS5A01G240000 chr6A 97.241 435 10 2 3861 4293 77508743 77509177 0.000000e+00 736.0
17 TraesCS5A01G240000 chr6A 95.652 460 15 2 2989 3448 77507204 77507658 0.000000e+00 734.0
18 TraesCS5A01G240000 chr6A 95.172 435 19 2 3863 4295 22034645 22034211 0.000000e+00 686.0
19 TraesCS5A01G240000 chr6A 95.943 419 14 2 3445 3862 77507914 77508330 0.000000e+00 676.0
20 TraesCS5A01G240000 chr6A 81.954 737 82 25 3136 3853 65805605 65804901 1.040000e-160 577.0
21 TraesCS5A01G240000 chr6A 84.416 231 20 6 3129 3344 87757350 87757579 3.360000e-51 213.0
22 TraesCS5A01G240000 chr6A 92.308 143 4 4 1 136 77506506 77506648 3.390000e-46 196.0
23 TraesCS5A01G240000 chr6A 91.608 143 5 3 1 136 22036625 22036483 1.580000e-44 191.0
24 TraesCS5A01G240000 chr7B 88.586 990 97 11 634 1619 230383157 230384134 0.000000e+00 1188.0
25 TraesCS5A01G240000 chr7B 85.806 930 84 23 2106 2993 230580199 230581122 0.000000e+00 942.0
26 TraesCS5A01G240000 chr7B 86.335 322 25 13 1790 2108 230579582 230579887 2.480000e-87 333.0
27 TraesCS5A01G240000 chr7B 91.284 218 11 2 3971 4188 647786792 647786583 1.510000e-74 291.0
28 TraesCS5A01G240000 chr7B 92.208 154 10 1 492 643 647787128 647786975 2.600000e-52 217.0
29 TraesCS5A01G240000 chr7B 92.754 138 10 0 2992 3129 647786985 647786848 2.620000e-47 200.0
30 TraesCS5A01G240000 chr7B 90.741 108 10 0 142 249 478469141 478469248 1.240000e-30 145.0
31 TraesCS5A01G240000 chr2A 97.069 580 17 0 628 1207 17779143 17779722 0.000000e+00 977.0
32 TraesCS5A01G240000 chr2A 91.061 660 44 7 964 1622 335696374 335695729 0.000000e+00 878.0
33 TraesCS5A01G240000 chr2A 86.923 520 27 18 2142 2625 335695078 335694564 2.920000e-151 545.0
34 TraesCS5A01G240000 chr2A 91.940 335 18 6 1773 2106 335695737 335695411 1.090000e-125 460.0
35 TraesCS5A01G240000 chr2A 86.716 271 34 1 2618 2886 335689463 335689193 2.510000e-77 300.0
36 TraesCS5A01G240000 chr2A 93.243 74 5 0 2920 2993 335689195 335689122 4.540000e-20 110.0
37 TraesCS5A01G240000 chr7A 92.412 514 28 3 141 643 672031046 672030533 0.000000e+00 723.0
38 TraesCS5A01G240000 chr7A 80.088 452 67 11 633 1063 193662606 193662157 8.970000e-82 315.0
39 TraesCS5A01G240000 chr7A 85.942 313 20 13 3876 4188 672030382 672030094 3.220000e-81 313.0
40 TraesCS5A01G240000 chr7A 94.737 133 7 0 2992 3124 672030543 672030411 1.570000e-49 207.0
41 TraesCS5A01G240000 chr7A 91.837 147 12 0 1626 1772 116655490 116655636 5.630000e-49 206.0
42 TraesCS5A01G240000 chr7D 91.797 512 32 4 142 643 580548046 580547535 0.000000e+00 704.0
43 TraesCS5A01G240000 chr7D 83.439 314 18 6 3875 4188 580502374 580502095 1.180000e-65 261.0
44 TraesCS5A01G240000 chr7D 92.667 150 11 0 1625 1774 102903154 102903303 2.600000e-52 217.0
45 TraesCS5A01G240000 chr7D 92.517 147 11 0 1626 1772 141560454 141560600 1.210000e-50 211.0
46 TraesCS5A01G240000 chr7D 91.304 138 12 0 2992 3129 580547545 580547408 5.670000e-44 189.0
47 TraesCS5A01G240000 chr7D 85.185 135 16 2 1484 1617 45627340 45627209 7.490000e-28 135.0
48 TraesCS5A01G240000 chr7D 91.579 95 7 1 4188 4281 580502032 580501938 3.490000e-26 130.0
49 TraesCS5A01G240000 chr2D 90.784 510 38 5 3129 3637 543109533 543110034 0.000000e+00 673.0
50 TraesCS5A01G240000 chr2D 80.859 512 48 18 2106 2575 412125533 412125030 1.470000e-94 357.0
51 TraesCS5A01G240000 chr2D 79.474 380 43 20 2629 3001 412125020 412124669 2.000000e-58 237.0
52 TraesCS5A01G240000 chr2D 88.205 195 19 3 142 333 211557262 211557455 3.340000e-56 230.0
53 TraesCS5A01G240000 chr2D 93.919 148 9 0 1625 1772 28918685 28918832 1.550000e-54 224.0
54 TraesCS5A01G240000 chr6B 83.696 736 89 13 3136 3853 122298242 122297520 0.000000e+00 665.0
55 TraesCS5A01G240000 chr6B 92.517 147 11 0 1626 1772 684989604 684989750 1.210000e-50 211.0
56 TraesCS5A01G240000 chr6B 83.983 231 21 6 3129 3344 144962156 144962385 1.570000e-49 207.0
57 TraesCS5A01G240000 chr5D 80.538 930 87 44 2124 2993 137088797 137087902 2.820000e-176 628.0
58 TraesCS5A01G240000 chr5D 88.631 431 30 5 207 635 62297450 62297037 1.380000e-139 507.0
59 TraesCS5A01G240000 chr5D 83.136 338 31 15 1773 2106 137089445 137089130 7.030000e-73 285.0
60 TraesCS5A01G240000 chr1A 88.694 513 35 8 3129 3639 513429184 513428693 4.750000e-169 604.0
61 TraesCS5A01G240000 chr6D 81.894 718 79 25 3151 3850 48855107 48855791 3.750000e-155 558.0
62 TraesCS5A01G240000 chr6D 78.923 427 60 14 634 1050 440680259 440680665 3.290000e-66 263.0
63 TraesCS5A01G240000 chr6D 83.983 231 21 6 3129 3344 69943934 69944163 1.570000e-49 207.0
64 TraesCS5A01G240000 chr3D 90.307 423 30 6 3217 3638 455704986 455704574 1.050000e-150 544.0
65 TraesCS5A01G240000 chr3D 90.307 423 30 6 3217 3638 455714615 455714203 1.050000e-150 544.0
66 TraesCS5A01G240000 chr3D 84.000 75 8 4 628 699 306493344 306493271 7.710000e-08 69.4
67 TraesCS5A01G240000 chr3B 79.730 666 99 19 632 1291 31184379 31185014 2.360000e-122 449.0
68 TraesCS5A01G240000 chr3B 81.799 467 46 15 2192 2634 31186359 31186810 5.280000e-94 355.0
69 TraesCS5A01G240000 chr3B 84.302 344 34 14 1773 2106 31185495 31185828 6.930000e-83 318.0
70 TraesCS5A01G240000 chr1D 79.607 662 66 22 637 1294 300130185 300130781 1.110000e-110 411.0
71 TraesCS5A01G240000 chr1D 80.594 572 61 17 2106 2639 300131917 300132476 3.110000e-106 396.0
72 TraesCS5A01G240000 chr1D 89.474 304 24 4 1316 1619 300130974 300131269 1.130000e-100 377.0
73 TraesCS5A01G240000 chr1D 83.815 346 35 10 1773 2106 300131264 300131600 4.170000e-80 309.0
74 TraesCS5A01G240000 chr5B 83.220 441 58 12 634 1071 136115044 136115471 1.450000e-104 390.0
75 TraesCS5A01G240000 chr5B 92.568 148 11 0 1626 1773 45842292 45842145 3.360000e-51 213.0
76 TraesCS5A01G240000 chr5B 90.291 103 9 1 1637 1738 26029139 26029037 2.690000e-27 134.0
77 TraesCS5A01G240000 chr4A 88.718 195 18 3 142 333 519162013 519161820 7.180000e-58 235.0
78 TraesCS5A01G240000 chr4D 91.275 149 13 0 1625 1773 293660296 293660444 2.020000e-48 204.0
79 TraesCS5A01G240000 chrUn 91.275 149 12 1 1626 1773 269914922 269914774 7.280000e-48 202.0


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 TraesCS5A01G240000 chr5A 456471526 456475820 4294 True 7932.000000 7932 100.000000 1 4295 1 chr5A.!!$R2 4294
1 TraesCS5A01G240000 chr5A 52340139 52340697 558 True 332.000000 503 90.149500 216 3129 2 chr5A.!!$R3 2913
2 TraesCS5A01G240000 chr1B 678412800 678414983 2183 False 1143.333333 1845 95.882000 634 2993 3 chr1B.!!$F2 2359
3 TraesCS5A01G240000 chr3A 20203475 20205886 2411 False 794.250000 1421 95.261500 1 4293 4 chr3A.!!$F1 4292
4 TraesCS5A01G240000 chr6A 22034211 22036625 2414 True 770.750000 1387 94.502750 1 4295 4 chr6A.!!$R2 4294
5 TraesCS5A01G240000 chr6A 77506506 77509177 2671 False 635.400000 835 95.591400 1 4293 5 chr6A.!!$F2 4292
6 TraesCS5A01G240000 chr6A 65804901 65805605 704 True 577.000000 577 81.954000 3136 3853 1 chr6A.!!$R1 717
7 TraesCS5A01G240000 chr7B 230383157 230384134 977 False 1188.000000 1188 88.586000 634 1619 1 chr7B.!!$F1 985
8 TraesCS5A01G240000 chr7B 230579582 230581122 1540 False 637.500000 942 86.070500 1790 2993 2 chr7B.!!$F3 1203
9 TraesCS5A01G240000 chr7B 647786583 647787128 545 True 236.000000 291 92.082000 492 4188 3 chr7B.!!$R1 3696
10 TraesCS5A01G240000 chr2A 17779143 17779722 579 False 977.000000 977 97.069000 628 1207 1 chr2A.!!$F1 579
11 TraesCS5A01G240000 chr2A 335694564 335696374 1810 True 627.666667 878 89.974667 964 2625 3 chr2A.!!$R2 1661
12 TraesCS5A01G240000 chr7A 672030094 672031046 952 True 414.333333 723 91.030333 141 4188 3 chr7A.!!$R2 4047
13 TraesCS5A01G240000 chr7D 580547408 580548046 638 True 446.500000 704 91.550500 142 3129 2 chr7D.!!$R3 2987
14 TraesCS5A01G240000 chr2D 543109533 543110034 501 False 673.000000 673 90.784000 3129 3637 1 chr2D.!!$F3 508
15 TraesCS5A01G240000 chr2D 412124669 412125533 864 True 297.000000 357 80.166500 2106 3001 2 chr2D.!!$R1 895
16 TraesCS5A01G240000 chr6B 122297520 122298242 722 True 665.000000 665 83.696000 3136 3853 1 chr6B.!!$R1 717
17 TraesCS5A01G240000 chr5D 137087902 137089445 1543 True 456.500000 628 81.837000 1773 2993 2 chr5D.!!$R2 1220
18 TraesCS5A01G240000 chr6D 48855107 48855791 684 False 558.000000 558 81.894000 3151 3850 1 chr6D.!!$F1 699
19 TraesCS5A01G240000 chr3B 31184379 31186810 2431 False 374.000000 449 81.943667 632 2634 3 chr3B.!!$F1 2002
20 TraesCS5A01G240000 chr1D 300130185 300132476 2291 False 373.250000 411 83.372500 637 2639 4 chr1D.!!$F1 2002

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
799 890 2.342279 CCACCCGTTCGCTTCTCA 59.658 61.111 0.00 0.0 0.00 3.27 F
1180 1286 0.392461 GTAAGTCGCCTTCATGCCCA 60.392 55.000 0.00 0.0 31.89 5.36 F
1638 1953 0.037697 ATTCGGCGTTGCTACACAGA 60.038 50.000 6.85 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1934 0.037697 TCTGTGTAGCAACGCCGAAT 60.038 50.000 0.0 0.0 35.12 3.34 R
2588 3458 2.138320 CCGATGTGGCTGATATGTGAC 58.862 52.381 0.0 0.0 0.00 3.67 R
3308 4239 0.954452 CTGCACACCTTCCTTTGGAC 59.046 55.000 0.0 0.0 0.00 4.02 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
40 41 3.769739 TTAAGGCATGCGATCATACCT 57.230 42.857 12.44 0.00 46.10 3.08
41 42 4.882842 TTAAGGCATGCGATCATACCTA 57.117 40.909 12.44 0.00 43.95 3.08
42 43 3.988976 AAGGCATGCGATCATACCTAT 57.011 42.857 12.44 0.00 43.95 2.57
43 44 6.538945 TTAAGGCATGCGATCATACCTATA 57.461 37.500 12.44 0.00 43.95 1.31
44 45 4.392921 AGGCATGCGATCATACCTATAC 57.607 45.455 12.44 0.00 43.13 1.47
45 46 3.769300 AGGCATGCGATCATACCTATACA 59.231 43.478 12.44 0.00 43.13 2.29
46 47 4.406972 AGGCATGCGATCATACCTATACAT 59.593 41.667 12.44 0.00 43.13 2.29
47 48 5.598417 AGGCATGCGATCATACCTATACATA 59.402 40.000 12.44 0.00 43.13 2.29
110 118 6.593268 TGAAATCCTCAAATGCAGAATCAA 57.407 33.333 0.00 0.00 0.00 2.57
278 352 9.491675 TGCAATCAAAATCATGTGATAGTTTTT 57.508 25.926 0.00 0.00 33.31 1.94
664 751 5.373812 ACCTAAATAGTTGATCCCCACTG 57.626 43.478 0.00 0.00 0.00 3.66
799 890 2.342279 CCACCCGTTCGCTTCTCA 59.658 61.111 0.00 0.00 0.00 3.27
847 938 4.457466 GGTGGTTTTCTCCTACTGAAACA 58.543 43.478 0.00 0.00 33.77 2.83
960 1057 2.600729 AACTGAGCCCAGCCTCCTG 61.601 63.158 0.00 0.00 44.16 3.86
1050 1156 3.054139 TGGAAGACAATCAATCTGGAGGG 60.054 47.826 0.00 0.00 0.00 4.30
1180 1286 0.392461 GTAAGTCGCCTTCATGCCCA 60.392 55.000 0.00 0.00 31.89 5.36
1215 1321 2.746697 CCTAGCCTAGGCCGATTCA 58.253 57.895 30.42 7.78 43.17 2.57
1323 1611 1.831106 TCGCTCCAATCCTACATGTGT 59.169 47.619 9.11 0.00 0.00 3.72
1324 1612 1.935873 CGCTCCAATCCTACATGTGTG 59.064 52.381 9.11 0.87 0.00 3.82
1325 1613 2.677902 CGCTCCAATCCTACATGTGTGT 60.678 50.000 9.11 0.00 42.39 3.72
1326 1614 3.347216 GCTCCAATCCTACATGTGTGTT 58.653 45.455 9.11 0.00 39.77 3.32
1327 1615 4.513442 GCTCCAATCCTACATGTGTGTTA 58.487 43.478 9.11 0.00 39.77 2.41
1328 1616 5.126067 GCTCCAATCCTACATGTGTGTTAT 58.874 41.667 9.11 0.00 39.77 1.89
1329 1617 5.237344 GCTCCAATCCTACATGTGTGTTATC 59.763 44.000 9.11 0.00 39.77 1.75
1330 1618 6.560003 TCCAATCCTACATGTGTGTTATCT 57.440 37.500 9.11 0.00 39.77 1.98
1331 1619 6.957631 TCCAATCCTACATGTGTGTTATCTT 58.042 36.000 9.11 0.00 39.77 2.40
1332 1620 7.402054 TCCAATCCTACATGTGTGTTATCTTT 58.598 34.615 9.11 0.00 39.77 2.52
1333 1621 8.544622 TCCAATCCTACATGTGTGTTATCTTTA 58.455 33.333 9.11 0.00 39.77 1.85
1334 1622 8.612619 CCAATCCTACATGTGTGTTATCTTTAC 58.387 37.037 9.11 0.00 39.77 2.01
1335 1623 9.161629 CAATCCTACATGTGTGTTATCTTTACA 57.838 33.333 9.11 0.00 39.77 2.41
1336 1624 8.948631 ATCCTACATGTGTGTTATCTTTACAG 57.051 34.615 9.11 0.00 39.77 2.74
1337 1625 8.129496 TCCTACATGTGTGTTATCTTTACAGA 57.871 34.615 9.11 0.00 39.77 3.41
1338 1626 8.758829 TCCTACATGTGTGTTATCTTTACAGAT 58.241 33.333 9.11 0.00 40.17 2.90
1339 1627 9.383519 CCTACATGTGTGTTATCTTTACAGATT 57.616 33.333 9.11 0.00 38.96 2.40
1345 1633 9.817809 TGTGTGTTATCTTTACAGATTATCTCC 57.182 33.333 0.00 0.00 40.53 3.71
1613 1928 8.440771 CAAACCTTCCTATTAGGATTCCAGTAT 58.559 37.037 13.22 0.00 45.34 2.12
1614 1929 9.684702 AAACCTTCCTATTAGGATTCCAGTATA 57.315 33.333 13.22 0.00 45.34 1.47
1615 1930 8.903059 ACCTTCCTATTAGGATTCCAGTATAG 57.097 38.462 13.22 8.25 45.34 1.31
1616 1931 8.465971 ACCTTCCTATTAGGATTCCAGTATAGT 58.534 37.037 13.22 0.00 45.34 2.12
1617 1932 9.992442 CCTTCCTATTAGGATTCCAGTATAGTA 57.008 37.037 13.22 0.00 45.34 1.82
1625 1940 7.349412 AGGATTCCAGTATAGTATATTCGGC 57.651 40.000 5.29 0.00 0.00 5.54
1626 1941 6.039493 AGGATTCCAGTATAGTATATTCGGCG 59.961 42.308 0.00 0.00 0.00 6.46
1627 1942 6.183360 GGATTCCAGTATAGTATATTCGGCGT 60.183 42.308 6.85 0.00 0.00 5.68
1628 1943 6.579666 TTCCAGTATAGTATATTCGGCGTT 57.420 37.500 6.85 0.00 0.00 4.84
1629 1944 5.946298 TCCAGTATAGTATATTCGGCGTTG 58.054 41.667 6.85 0.00 0.00 4.10
1630 1945 4.561606 CCAGTATAGTATATTCGGCGTTGC 59.438 45.833 6.85 0.00 0.00 4.17
1631 1946 5.399858 CAGTATAGTATATTCGGCGTTGCT 58.600 41.667 6.85 2.46 0.00 3.91
1632 1947 6.403964 CCAGTATAGTATATTCGGCGTTGCTA 60.404 42.308 6.85 4.66 0.00 3.49
1633 1948 6.468319 CAGTATAGTATATTCGGCGTTGCTAC 59.532 42.308 6.85 5.63 0.00 3.58
1634 1949 3.720949 AGTATATTCGGCGTTGCTACA 57.279 42.857 6.85 0.00 0.00 2.74
1635 1950 3.378339 AGTATATTCGGCGTTGCTACAC 58.622 45.455 6.85 0.00 0.00 2.90
1636 1951 2.303163 ATATTCGGCGTTGCTACACA 57.697 45.000 6.85 0.00 0.00 3.72
1637 1952 1.635844 TATTCGGCGTTGCTACACAG 58.364 50.000 6.85 0.00 0.00 3.66
1638 1953 0.037697 ATTCGGCGTTGCTACACAGA 60.038 50.000 6.85 0.00 0.00 3.41
1639 1954 0.942410 TTCGGCGTTGCTACACAGAC 60.942 55.000 6.85 0.00 0.00 3.51
1640 1955 2.716828 CGGCGTTGCTACACAGACG 61.717 63.158 0.00 0.00 36.50 4.18
1641 1956 1.372499 GGCGTTGCTACACAGACGA 60.372 57.895 0.00 0.00 35.90 4.20
1642 1957 1.615107 GGCGTTGCTACACAGACGAC 61.615 60.000 0.00 0.00 35.90 4.34
1643 1958 0.937699 GCGTTGCTACACAGACGACA 60.938 55.000 0.00 0.00 35.90 4.35
1644 1959 1.483316 CGTTGCTACACAGACGACAA 58.517 50.000 0.00 0.00 35.90 3.18
1645 1960 1.189446 CGTTGCTACACAGACGACAAC 59.811 52.381 0.00 0.00 35.90 3.32
1646 1961 1.189446 GTTGCTACACAGACGACAACG 59.811 52.381 0.00 0.00 45.75 4.10
1647 1962 0.937699 TGCTACACAGACGACAACGC 60.938 55.000 0.00 0.00 43.96 4.84
1648 1963 0.663568 GCTACACAGACGACAACGCT 60.664 55.000 0.00 0.00 43.96 5.07
1649 1964 1.053048 CTACACAGACGACAACGCTG 58.947 55.000 0.00 0.00 43.49 5.18
1650 1965 0.318360 TACACAGACGACAACGCTGG 60.318 55.000 0.00 0.00 42.81 4.85
1651 1966 1.299850 CACAGACGACAACGCTGGA 60.300 57.895 0.00 0.00 42.81 3.86
1652 1967 1.299926 ACAGACGACAACGCTGGAC 60.300 57.895 0.00 0.00 42.81 4.02
1665 1980 2.961522 GCTGGACGATTTTCAAACGA 57.038 45.000 0.00 0.00 0.00 3.85
1666 1981 3.471495 GCTGGACGATTTTCAAACGAT 57.529 42.857 0.00 0.00 0.00 3.73
1667 1982 3.163594 GCTGGACGATTTTCAAACGATG 58.836 45.455 0.00 0.00 0.00 3.84
1668 1983 3.364964 GCTGGACGATTTTCAAACGATGT 60.365 43.478 0.00 0.00 0.00 3.06
1669 1984 4.142988 GCTGGACGATTTTCAAACGATGTA 60.143 41.667 0.00 0.00 0.00 2.29
1670 1985 5.615984 GCTGGACGATTTTCAAACGATGTAA 60.616 40.000 0.00 0.00 0.00 2.41
1671 1986 5.681880 TGGACGATTTTCAAACGATGTAAC 58.318 37.500 0.00 0.00 0.00 2.50
1672 1987 5.236695 TGGACGATTTTCAAACGATGTAACA 59.763 36.000 0.00 0.00 0.00 2.41
1673 1988 5.562623 GGACGATTTTCAAACGATGTAACAC 59.437 40.000 0.00 0.00 0.00 3.32
1674 1989 6.050454 ACGATTTTCAAACGATGTAACACA 57.950 33.333 0.00 0.00 0.00 3.72
1675 1990 6.664515 ACGATTTTCAAACGATGTAACACAT 58.335 32.000 0.00 0.00 42.43 3.21
1684 1999 2.489938 ATGTAACACATCAGGCCGTT 57.510 45.000 0.00 0.00 32.38 4.44
1685 2000 1.803334 TGTAACACATCAGGCCGTTC 58.197 50.000 0.00 0.00 0.00 3.95
1686 2001 1.070914 TGTAACACATCAGGCCGTTCA 59.929 47.619 0.00 0.00 0.00 3.18
1687 2002 1.463444 GTAACACATCAGGCCGTTCAC 59.537 52.381 0.00 0.00 0.00 3.18
1688 2003 1.227999 AACACATCAGGCCGTTCACG 61.228 55.000 0.00 0.00 39.44 4.35
1689 2004 1.374125 CACATCAGGCCGTTCACGA 60.374 57.895 0.00 0.00 43.02 4.35
1690 2005 1.079819 ACATCAGGCCGTTCACGAG 60.080 57.895 0.00 0.00 43.02 4.18
1691 2006 1.811266 CATCAGGCCGTTCACGAGG 60.811 63.158 0.00 0.00 43.02 4.63
1692 2007 1.982395 ATCAGGCCGTTCACGAGGA 60.982 57.895 0.00 0.00 43.02 3.71
1693 2008 1.949847 ATCAGGCCGTTCACGAGGAG 61.950 60.000 0.00 0.00 43.02 3.69
1694 2009 2.282958 AGGCCGTTCACGAGGAGA 60.283 61.111 0.00 0.00 43.02 3.71
1695 2010 2.182030 GGCCGTTCACGAGGAGAG 59.818 66.667 0.00 0.00 43.02 3.20
1696 2011 2.507324 GCCGTTCACGAGGAGAGC 60.507 66.667 0.00 0.00 43.02 4.09
1697 2012 2.995872 GCCGTTCACGAGGAGAGCT 61.996 63.158 0.00 0.00 43.02 4.09
1698 2013 1.654954 GCCGTTCACGAGGAGAGCTA 61.655 60.000 0.00 0.00 43.02 3.32
1699 2014 0.809385 CCGTTCACGAGGAGAGCTAA 59.191 55.000 0.00 0.00 43.02 3.09
1700 2015 1.201647 CCGTTCACGAGGAGAGCTAAA 59.798 52.381 0.00 0.00 43.02 1.85
1701 2016 2.251893 CGTTCACGAGGAGAGCTAAAC 58.748 52.381 0.00 0.00 43.02 2.01
1702 2017 2.095161 CGTTCACGAGGAGAGCTAAACT 60.095 50.000 0.00 0.00 43.02 2.66
1703 2018 3.126514 CGTTCACGAGGAGAGCTAAACTA 59.873 47.826 0.00 0.00 43.02 2.24
1704 2019 4.379186 CGTTCACGAGGAGAGCTAAACTAA 60.379 45.833 0.00 0.00 43.02 2.24
1705 2020 5.467705 GTTCACGAGGAGAGCTAAACTAAA 58.532 41.667 0.00 0.00 0.00 1.85
1706 2021 5.056894 TCACGAGGAGAGCTAAACTAAAC 57.943 43.478 0.00 0.00 0.00 2.01
1707 2022 4.521639 TCACGAGGAGAGCTAAACTAAACA 59.478 41.667 0.00 0.00 0.00 2.83
1708 2023 5.010314 TCACGAGGAGAGCTAAACTAAACAA 59.990 40.000 0.00 0.00 0.00 2.83
1709 2024 5.118817 CACGAGGAGAGCTAAACTAAACAAC 59.881 44.000 0.00 0.00 0.00 3.32
1710 2025 4.323868 CGAGGAGAGCTAAACTAAACAACG 59.676 45.833 0.00 0.00 0.00 4.10
1711 2026 3.995048 AGGAGAGCTAAACTAAACAACGC 59.005 43.478 0.00 0.00 0.00 4.84
1712 2027 3.124806 GGAGAGCTAAACTAAACAACGCC 59.875 47.826 0.00 0.00 0.00 5.68
1713 2028 2.735134 AGAGCTAAACTAAACAACGCCG 59.265 45.455 0.00 0.00 0.00 6.46
1714 2029 2.477754 GAGCTAAACTAAACAACGCCGT 59.522 45.455 0.00 0.00 0.00 5.68
1715 2030 2.874086 AGCTAAACTAAACAACGCCGTT 59.126 40.909 0.00 0.00 0.00 4.44
1716 2031 3.059393 AGCTAAACTAAACAACGCCGTTC 60.059 43.478 0.00 0.00 0.00 3.95
1717 2032 3.303263 GCTAAACTAAACAACGCCGTTCA 60.303 43.478 0.00 0.00 0.00 3.18
1718 2033 3.761311 AAACTAAACAACGCCGTTCAA 57.239 38.095 0.00 0.00 0.00 2.69
1719 2034 3.974871 AACTAAACAACGCCGTTCAAT 57.025 38.095 0.00 0.00 0.00 2.57
1720 2035 3.531262 ACTAAACAACGCCGTTCAATC 57.469 42.857 0.00 0.00 0.00 2.67
1721 2036 2.224784 ACTAAACAACGCCGTTCAATCC 59.775 45.455 0.00 0.00 0.00 3.01
1722 2037 1.025812 AAACAACGCCGTTCAATCCA 58.974 45.000 0.00 0.00 0.00 3.41
1723 2038 1.025812 AACAACGCCGTTCAATCCAA 58.974 45.000 0.00 0.00 0.00 3.53
1724 2039 0.309612 ACAACGCCGTTCAATCCAAC 59.690 50.000 0.00 0.00 0.00 3.77
1725 2040 0.309302 CAACGCCGTTCAATCCAACA 59.691 50.000 0.00 0.00 0.00 3.33
1726 2041 1.068610 CAACGCCGTTCAATCCAACAT 60.069 47.619 0.00 0.00 0.00 2.71
1727 2042 0.802494 ACGCCGTTCAATCCAACATC 59.198 50.000 0.00 0.00 0.00 3.06
1728 2043 0.247655 CGCCGTTCAATCCAACATCG 60.248 55.000 0.00 0.00 0.00 3.84
1729 2044 0.802494 GCCGTTCAATCCAACATCGT 59.198 50.000 0.00 0.00 0.00 3.73
1730 2045 1.202031 GCCGTTCAATCCAACATCGTC 60.202 52.381 0.00 0.00 0.00 4.20
1731 2046 1.396996 CCGTTCAATCCAACATCGTCC 59.603 52.381 0.00 0.00 0.00 4.79
1732 2047 2.073056 CGTTCAATCCAACATCGTCCA 58.927 47.619 0.00 0.00 0.00 4.02
1733 2048 2.159707 CGTTCAATCCAACATCGTCCAC 60.160 50.000 0.00 0.00 0.00 4.02
1734 2049 2.107950 TCAATCCAACATCGTCCACC 57.892 50.000 0.00 0.00 0.00 4.61
1735 2050 1.094785 CAATCCAACATCGTCCACCC 58.905 55.000 0.00 0.00 0.00 4.61
1736 2051 0.991920 AATCCAACATCGTCCACCCT 59.008 50.000 0.00 0.00 0.00 4.34
1737 2052 0.991920 ATCCAACATCGTCCACCCTT 59.008 50.000 0.00 0.00 0.00 3.95
1738 2053 0.323629 TCCAACATCGTCCACCCTTC 59.676 55.000 0.00 0.00 0.00 3.46
1739 2054 1.019278 CCAACATCGTCCACCCTTCG 61.019 60.000 0.00 0.00 0.00 3.79
1740 2055 1.019278 CAACATCGTCCACCCTTCGG 61.019 60.000 0.00 0.00 0.00 4.30
1741 2056 1.189524 AACATCGTCCACCCTTCGGA 61.190 55.000 0.00 0.00 0.00 4.55
1745 2060 4.078516 GTCCACCCTTCGGACGGG 62.079 72.222 17.45 17.45 43.36 5.28
1746 2061 4.304413 TCCACCCTTCGGACGGGA 62.304 66.667 24.99 0.86 44.90 5.14
1747 2062 3.081409 CCACCCTTCGGACGGGAT 61.081 66.667 24.99 7.58 44.90 3.85
1748 2063 2.186903 CACCCTTCGGACGGGATG 59.813 66.667 24.99 15.06 44.90 3.51
1749 2064 3.782443 ACCCTTCGGACGGGATGC 61.782 66.667 24.99 0.00 44.90 3.91
1750 2065 3.470888 CCCTTCGGACGGGATGCT 61.471 66.667 14.17 0.00 44.90 3.79
1751 2066 2.202932 CCTTCGGACGGGATGCTG 60.203 66.667 0.00 0.00 0.00 4.41
1752 2067 2.579201 CTTCGGACGGGATGCTGT 59.421 61.111 0.00 0.00 0.00 4.40
1753 2068 1.519455 CTTCGGACGGGATGCTGTC 60.519 63.158 17.32 17.32 0.00 3.51
1754 2069 3.350909 TTCGGACGGGATGCTGTCG 62.351 63.158 18.68 14.06 35.95 4.35
1755 2070 4.129737 CGGACGGGATGCTGTCGT 62.130 66.667 18.68 3.36 39.99 4.34
1757 2072 2.885861 GACGGGATGCTGTCGTCT 59.114 61.111 10.69 0.00 46.49 4.18
1758 2073 1.517257 GACGGGATGCTGTCGTCTG 60.517 63.158 10.69 0.00 46.49 3.51
1759 2074 2.887568 CGGGATGCTGTCGTCTGC 60.888 66.667 4.67 4.67 38.66 4.26
1767 2082 3.801114 TGCTGTCGTCTGCATAGTAAT 57.199 42.857 9.90 0.00 42.06 1.89
1768 2083 4.123497 TGCTGTCGTCTGCATAGTAATT 57.877 40.909 9.90 0.00 42.06 1.40
1769 2084 4.503910 TGCTGTCGTCTGCATAGTAATTT 58.496 39.130 9.90 0.00 42.06 1.82
1770 2085 4.566759 TGCTGTCGTCTGCATAGTAATTTC 59.433 41.667 9.90 0.00 42.06 2.17
1771 2086 4.317418 GCTGTCGTCTGCATAGTAATTTCG 60.317 45.833 6.65 0.00 38.20 3.46
1965 2297 5.030295 CAGGCTTTTCATTTGTGCTATACG 58.970 41.667 0.00 0.00 0.00 3.06
1975 2307 3.868757 TGTGCTATACGGCTATCCATC 57.131 47.619 0.00 0.00 0.00 3.51
2034 2368 4.756642 TGAGACTTTTGCAGGTTAGTGATG 59.243 41.667 0.00 0.00 0.00 3.07
2588 3458 5.735285 TGGAGCTAGAAGATATGGACATG 57.265 43.478 0.00 0.00 0.00 3.21
2671 3544 6.062095 AGAGCCTGCTTTACTAAGTTTTTCA 58.938 36.000 0.00 0.00 33.74 2.69
2704 3577 7.116805 CCAAATTGTTAGACAAAGATTTCTGGC 59.883 37.037 0.00 0.00 41.96 4.85
2845 3744 5.463392 TCTCAACTTTCTTGACTCAACATCG 59.537 40.000 0.00 0.00 0.00 3.84
2877 3781 5.652994 AAAAGGTCTTTTTGTGCACAGTA 57.347 34.783 20.59 9.64 39.52 2.74
3085 4001 7.999679 TGATTCATACCTAGCAAAAATTCCTG 58.000 34.615 0.00 0.00 0.00 3.86
3180 4096 5.061853 CAGAAGGAAATCGTGGATCATGAT 58.938 41.667 8.25 8.25 41.25 2.45
3308 4239 4.639310 CCATCAATGACAAGAAAGAGGAGG 59.361 45.833 0.00 0.00 0.00 4.30
3429 4361 5.996513 TCAATTTGGTTGAAACATGGAATGG 59.003 36.000 0.00 0.00 45.82 3.16
3430 4362 5.335035 CAATTTGGTTGAAACATGGAATGGC 60.335 40.000 0.00 0.00 44.29 4.40
3431 4363 7.682611 CAATTTGGTTGAAACATGGAATGGCA 61.683 38.462 0.00 0.00 44.29 4.92
3432 4364 8.918431 CAATTTGGTTGAAACATGGAATGGCAT 61.918 37.037 0.00 0.00 44.29 4.40
3734 4927 3.856900 TCCATACCTAGAGCCAAGCATA 58.143 45.455 0.00 0.00 0.00 3.14
3735 4928 4.429505 TCCATACCTAGAGCCAAGCATAT 58.570 43.478 0.00 0.00 0.00 1.78
3804 4997 7.068962 TGTCATACCAGGTCGAATATAAGACAA 59.931 37.037 0.00 0.00 39.01 3.18
3831 5024 7.786178 TTGCATAGTTGTGGTGTAATCTATC 57.214 36.000 0.00 0.00 0.00 2.08
3894 5502 6.784031 AGCCACAAATCTATTAAGGGATAGG 58.216 40.000 0.00 0.00 31.83 2.57
4048 5656 6.487828 TCTGTTACTGCCTTACTCCTTACTA 58.512 40.000 0.00 0.00 0.00 1.82
4142 5750 6.430925 ACTGCACTGCTCAAAGTAAATTGATA 59.569 34.615 1.98 0.00 38.55 2.15
4214 5822 2.420022 CAGTTGGAAAAGGTAGGATGCG 59.580 50.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.248380 TCTGAGGAGCTCTGCTATGTATA 57.752 43.478 14.64 0.00 39.88 1.47
41 42 4.081406 CTCTGAGGAGCTCTGCTATGTAT 58.919 47.826 14.64 0.00 39.88 2.29
42 43 3.485394 CTCTGAGGAGCTCTGCTATGTA 58.515 50.000 14.64 0.00 39.88 2.29
43 44 2.309613 CTCTGAGGAGCTCTGCTATGT 58.690 52.381 14.64 0.00 39.88 2.29
664 751 0.034670 ACAGGGCAGAGAAATCAGGC 60.035 55.000 0.00 0.00 0.00 4.85
695 782 4.881850 ACGGCCGAAAAGAATTAAGATGAT 59.118 37.500 35.90 0.00 0.00 2.45
799 890 0.678048 GCTTCTGCGGGTCAAGGAAT 60.678 55.000 0.00 0.00 0.00 3.01
960 1057 0.676782 ATGGCAGACGCAAACCCTAC 60.677 55.000 0.00 0.00 41.24 3.18
1050 1156 2.744202 CTCTGCATAAAGTCCCACACAC 59.256 50.000 0.00 0.00 0.00 3.82
1215 1321 1.492176 AGATCAGCACCGGATTGGATT 59.508 47.619 9.46 0.00 42.00 3.01
1306 1413 6.586344 AGATAACACACATGTAGGATTGGAG 58.414 40.000 0.00 0.00 38.45 3.86
1331 1619 9.599866 CACACACAAATAGGAGATAATCTGTAA 57.400 33.333 0.00 0.00 0.00 2.41
1332 1620 8.758829 ACACACACAAATAGGAGATAATCTGTA 58.241 33.333 0.00 0.00 0.00 2.74
1333 1621 7.550551 CACACACACAAATAGGAGATAATCTGT 59.449 37.037 0.00 0.00 0.00 3.41
1334 1622 7.550551 ACACACACACAAATAGGAGATAATCTG 59.449 37.037 0.00 0.00 0.00 2.90
1335 1623 7.550551 CACACACACACAAATAGGAGATAATCT 59.449 37.037 0.00 0.00 0.00 2.40
1336 1624 7.334421 ACACACACACACAAATAGGAGATAATC 59.666 37.037 0.00 0.00 0.00 1.75
1337 1625 7.168219 ACACACACACACAAATAGGAGATAAT 58.832 34.615 0.00 0.00 0.00 1.28
1338 1626 6.530120 ACACACACACACAAATAGGAGATAA 58.470 36.000 0.00 0.00 0.00 1.75
1339 1627 6.109156 ACACACACACACAAATAGGAGATA 57.891 37.500 0.00 0.00 0.00 1.98
1340 1628 4.973168 ACACACACACACAAATAGGAGAT 58.027 39.130 0.00 0.00 0.00 2.75
1341 1629 4.415881 ACACACACACACAAATAGGAGA 57.584 40.909 0.00 0.00 0.00 3.71
1342 1630 5.273170 CAAACACACACACACAAATAGGAG 58.727 41.667 0.00 0.00 0.00 3.69
1343 1631 4.439426 GCAAACACACACACACAAATAGGA 60.439 41.667 0.00 0.00 0.00 2.94
1344 1632 3.796178 GCAAACACACACACACAAATAGG 59.204 43.478 0.00 0.00 0.00 2.57
1345 1633 3.796178 GGCAAACACACACACACAAATAG 59.204 43.478 0.00 0.00 0.00 1.73
1346 1634 3.732169 CGGCAAACACACACACACAAATA 60.732 43.478 0.00 0.00 0.00 1.40
1347 1635 2.615869 GGCAAACACACACACACAAAT 58.384 42.857 0.00 0.00 0.00 2.32
1348 1636 1.667177 CGGCAAACACACACACACAAA 60.667 47.619 0.00 0.00 0.00 2.83
1349 1637 0.109551 CGGCAAACACACACACACAA 60.110 50.000 0.00 0.00 0.00 3.33
1613 1928 4.036616 TGTGTAGCAACGCCGAATATACTA 59.963 41.667 0.00 0.00 35.12 1.82
1614 1929 3.181484 TGTGTAGCAACGCCGAATATACT 60.181 43.478 0.00 0.00 35.12 2.12
1615 1930 3.117794 TGTGTAGCAACGCCGAATATAC 58.882 45.455 0.00 0.00 35.12 1.47
1616 1931 3.067040 TCTGTGTAGCAACGCCGAATATA 59.933 43.478 0.00 0.00 35.12 0.86
1617 1932 2.159156 TCTGTGTAGCAACGCCGAATAT 60.159 45.455 0.00 0.00 35.12 1.28
1618 1933 1.202817 TCTGTGTAGCAACGCCGAATA 59.797 47.619 0.00 0.00 35.12 1.75
1619 1934 0.037697 TCTGTGTAGCAACGCCGAAT 60.038 50.000 0.00 0.00 35.12 3.34
1620 1935 0.942410 GTCTGTGTAGCAACGCCGAA 60.942 55.000 0.00 0.00 35.12 4.30
1621 1936 1.372499 GTCTGTGTAGCAACGCCGA 60.372 57.895 0.00 0.00 35.12 5.54
1622 1937 2.716828 CGTCTGTGTAGCAACGCCG 61.717 63.158 0.00 0.00 35.12 6.46
1623 1938 1.372499 TCGTCTGTGTAGCAACGCC 60.372 57.895 0.00 0.00 35.12 5.68
1624 1939 0.937699 TGTCGTCTGTGTAGCAACGC 60.938 55.000 0.00 0.00 34.25 4.84
1625 1940 1.189446 GTTGTCGTCTGTGTAGCAACG 59.811 52.381 0.00 0.00 34.96 4.10
1626 1941 1.189446 CGTTGTCGTCTGTGTAGCAAC 59.811 52.381 0.00 0.00 34.61 4.17
1627 1942 1.483316 CGTTGTCGTCTGTGTAGCAA 58.517 50.000 0.00 0.00 0.00 3.91
1628 1943 0.937699 GCGTTGTCGTCTGTGTAGCA 60.938 55.000 0.00 0.00 39.49 3.49
1629 1944 0.663568 AGCGTTGTCGTCTGTGTAGC 60.664 55.000 0.00 0.00 39.49 3.58
1630 1945 1.053048 CAGCGTTGTCGTCTGTGTAG 58.947 55.000 0.00 0.00 36.89 2.74
1631 1946 0.318360 CCAGCGTTGTCGTCTGTGTA 60.318 55.000 0.00 0.00 38.50 2.90
1632 1947 1.591594 CCAGCGTTGTCGTCTGTGT 60.592 57.895 0.00 0.00 38.50 3.72
1633 1948 1.299850 TCCAGCGTTGTCGTCTGTG 60.300 57.895 0.00 0.00 38.50 3.66
1634 1949 1.299926 GTCCAGCGTTGTCGTCTGT 60.300 57.895 0.00 0.00 38.50 3.41
1635 1950 2.365068 CGTCCAGCGTTGTCGTCTG 61.365 63.158 0.00 0.00 39.22 3.51
1636 1951 1.863662 ATCGTCCAGCGTTGTCGTCT 61.864 55.000 11.94 1.98 42.13 4.18
1637 1952 1.007336 AATCGTCCAGCGTTGTCGTC 61.007 55.000 11.94 0.00 42.13 4.20
1638 1953 0.599204 AAATCGTCCAGCGTTGTCGT 60.599 50.000 11.94 0.95 42.13 4.34
1639 1954 0.511221 AAAATCGTCCAGCGTTGTCG 59.489 50.000 0.00 3.27 42.13 4.35
1640 1955 1.529438 TGAAAATCGTCCAGCGTTGTC 59.471 47.619 0.00 0.00 42.13 3.18
1641 1956 1.588674 TGAAAATCGTCCAGCGTTGT 58.411 45.000 0.00 0.00 42.13 3.32
1642 1957 2.679355 TTGAAAATCGTCCAGCGTTG 57.321 45.000 0.00 0.00 42.13 4.10
1643 1958 2.601266 CGTTTGAAAATCGTCCAGCGTT 60.601 45.455 0.00 0.00 42.13 4.84
1644 1959 1.070175 CGTTTGAAAATCGTCCAGCGT 60.070 47.619 0.00 0.00 42.13 5.07
1645 1960 1.193650 TCGTTTGAAAATCGTCCAGCG 59.806 47.619 0.00 0.00 39.81 5.18
1646 1961 2.961522 TCGTTTGAAAATCGTCCAGC 57.038 45.000 0.00 0.00 39.81 4.85
1647 1962 4.404507 ACATCGTTTGAAAATCGTCCAG 57.595 40.909 0.00 0.00 39.81 3.86
1648 1963 5.236695 TGTTACATCGTTTGAAAATCGTCCA 59.763 36.000 0.00 0.00 39.81 4.02
1649 1964 5.562623 GTGTTACATCGTTTGAAAATCGTCC 59.437 40.000 0.00 0.00 39.81 4.79
1650 1965 6.130723 TGTGTTACATCGTTTGAAAATCGTC 58.869 36.000 0.00 0.00 39.81 4.20
1651 1966 6.050454 TGTGTTACATCGTTTGAAAATCGT 57.950 33.333 0.00 0.00 39.81 3.73
1652 1967 7.180737 GATGTGTTACATCGTTTGAAAATCG 57.819 36.000 6.23 0.00 44.55 3.34
1665 1980 2.290008 TGAACGGCCTGATGTGTTACAT 60.290 45.455 0.00 0.00 42.43 2.29
1666 1981 1.070914 TGAACGGCCTGATGTGTTACA 59.929 47.619 0.00 0.00 0.00 2.41
1667 1982 1.463444 GTGAACGGCCTGATGTGTTAC 59.537 52.381 0.00 0.00 0.00 2.50
1668 1983 1.803334 GTGAACGGCCTGATGTGTTA 58.197 50.000 0.00 0.00 0.00 2.41
1669 1984 1.227999 CGTGAACGGCCTGATGTGTT 61.228 55.000 0.00 0.00 35.37 3.32
1670 1985 1.667830 CGTGAACGGCCTGATGTGT 60.668 57.895 0.00 0.00 35.37 3.72
1671 1986 1.354337 CTCGTGAACGGCCTGATGTG 61.354 60.000 0.00 0.00 40.29 3.21
1672 1987 1.079819 CTCGTGAACGGCCTGATGT 60.080 57.895 0.00 0.00 40.29 3.06
1673 1988 1.811266 CCTCGTGAACGGCCTGATG 60.811 63.158 0.00 0.00 40.29 3.07
1674 1989 1.949847 CTCCTCGTGAACGGCCTGAT 61.950 60.000 0.00 0.00 40.29 2.90
1675 1990 2.599281 TCCTCGTGAACGGCCTGA 60.599 61.111 0.00 0.00 40.29 3.86
1676 1991 2.125912 CTCCTCGTGAACGGCCTG 60.126 66.667 0.00 0.00 40.29 4.85
1677 1992 2.282958 TCTCCTCGTGAACGGCCT 60.283 61.111 0.00 0.00 40.29 5.19
1678 1993 2.182030 CTCTCCTCGTGAACGGCC 59.818 66.667 2.59 0.00 40.29 6.13
1679 1994 1.654954 TAGCTCTCCTCGTGAACGGC 61.655 60.000 2.59 0.00 40.29 5.68
1680 1995 0.809385 TTAGCTCTCCTCGTGAACGG 59.191 55.000 2.59 0.00 40.29 4.44
1681 1996 2.095161 AGTTTAGCTCTCCTCGTGAACG 60.095 50.000 0.00 0.00 41.45 3.95
1682 1997 3.579335 AGTTTAGCTCTCCTCGTGAAC 57.421 47.619 0.00 0.00 0.00 3.18
1683 1998 5.010314 TGTTTAGTTTAGCTCTCCTCGTGAA 59.990 40.000 0.00 0.00 0.00 3.18
1684 1999 4.521639 TGTTTAGTTTAGCTCTCCTCGTGA 59.478 41.667 0.00 0.00 0.00 4.35
1685 2000 4.806330 TGTTTAGTTTAGCTCTCCTCGTG 58.194 43.478 0.00 0.00 0.00 4.35
1686 2001 5.228665 GTTGTTTAGTTTAGCTCTCCTCGT 58.771 41.667 0.00 0.00 0.00 4.18
1687 2002 4.323868 CGTTGTTTAGTTTAGCTCTCCTCG 59.676 45.833 0.00 0.00 0.00 4.63
1688 2003 4.091655 GCGTTGTTTAGTTTAGCTCTCCTC 59.908 45.833 0.00 0.00 0.00 3.71
1689 2004 3.995048 GCGTTGTTTAGTTTAGCTCTCCT 59.005 43.478 0.00 0.00 0.00 3.69
1690 2005 3.124806 GGCGTTGTTTAGTTTAGCTCTCC 59.875 47.826 0.00 0.00 0.00 3.71
1691 2006 3.181533 CGGCGTTGTTTAGTTTAGCTCTC 60.182 47.826 0.00 0.00 0.00 3.20
1692 2007 2.735134 CGGCGTTGTTTAGTTTAGCTCT 59.265 45.455 0.00 0.00 0.00 4.09
1693 2008 2.477754 ACGGCGTTGTTTAGTTTAGCTC 59.522 45.455 6.77 0.00 0.00 4.09
1694 2009 2.486918 ACGGCGTTGTTTAGTTTAGCT 58.513 42.857 6.77 0.00 0.00 3.32
1695 2010 2.955607 ACGGCGTTGTTTAGTTTAGC 57.044 45.000 6.77 0.00 0.00 3.09
1696 2011 4.455917 TGAACGGCGTTGTTTAGTTTAG 57.544 40.909 31.90 0.00 30.75 1.85
1697 2012 4.871993 TTGAACGGCGTTGTTTAGTTTA 57.128 36.364 31.90 0.00 30.75 2.01
1698 2013 3.761311 TTGAACGGCGTTGTTTAGTTT 57.239 38.095 31.90 1.43 30.75 2.66
1699 2014 3.304190 GGATTGAACGGCGTTGTTTAGTT 60.304 43.478 31.90 2.35 30.75 2.24
1700 2015 2.224784 GGATTGAACGGCGTTGTTTAGT 59.775 45.455 31.90 10.08 30.75 2.24
1701 2016 2.224549 TGGATTGAACGGCGTTGTTTAG 59.775 45.455 31.90 0.00 30.75 1.85
1702 2017 2.219458 TGGATTGAACGGCGTTGTTTA 58.781 42.857 31.90 12.28 30.75 2.01
1703 2018 1.025812 TGGATTGAACGGCGTTGTTT 58.974 45.000 31.90 13.74 30.75 2.83
1704 2019 1.025812 TTGGATTGAACGGCGTTGTT 58.974 45.000 31.90 14.13 34.02 2.83
1705 2020 0.309612 GTTGGATTGAACGGCGTTGT 59.690 50.000 31.90 15.62 0.00 3.32
1706 2021 0.309302 TGTTGGATTGAACGGCGTTG 59.691 50.000 31.90 0.00 0.00 4.10
1707 2022 1.199097 GATGTTGGATTGAACGGCGTT 59.801 47.619 27.15 27.15 0.00 4.84
1708 2023 0.802494 GATGTTGGATTGAACGGCGT 59.198 50.000 6.77 6.77 0.00 5.68
1709 2024 0.247655 CGATGTTGGATTGAACGGCG 60.248 55.000 4.80 4.80 0.00 6.46
1710 2025 0.802494 ACGATGTTGGATTGAACGGC 59.198 50.000 0.00 0.00 0.00 5.68
1711 2026 1.396996 GGACGATGTTGGATTGAACGG 59.603 52.381 0.00 0.00 0.00 4.44
1712 2027 2.073056 TGGACGATGTTGGATTGAACG 58.927 47.619 0.00 0.00 0.00 3.95
1713 2028 2.161609 GGTGGACGATGTTGGATTGAAC 59.838 50.000 0.00 0.00 0.00 3.18
1714 2029 2.432444 GGTGGACGATGTTGGATTGAA 58.568 47.619 0.00 0.00 0.00 2.69
1715 2030 1.339631 GGGTGGACGATGTTGGATTGA 60.340 52.381 0.00 0.00 0.00 2.57
1716 2031 1.094785 GGGTGGACGATGTTGGATTG 58.905 55.000 0.00 0.00 0.00 2.67
1717 2032 0.991920 AGGGTGGACGATGTTGGATT 59.008 50.000 0.00 0.00 0.00 3.01
1718 2033 0.991920 AAGGGTGGACGATGTTGGAT 59.008 50.000 0.00 0.00 0.00 3.41
1719 2034 0.323629 GAAGGGTGGACGATGTTGGA 59.676 55.000 0.00 0.00 0.00 3.53
1720 2035 1.019278 CGAAGGGTGGACGATGTTGG 61.019 60.000 0.00 0.00 0.00 3.77
1721 2036 2.456000 CGAAGGGTGGACGATGTTG 58.544 57.895 0.00 0.00 0.00 3.33
1735 2050 1.519455 GACAGCATCCCGTCCGAAG 60.519 63.158 0.00 0.00 0.00 3.79
1736 2051 2.577059 GACAGCATCCCGTCCGAA 59.423 61.111 0.00 0.00 0.00 4.30
1737 2052 3.822192 CGACAGCATCCCGTCCGA 61.822 66.667 0.00 0.00 0.00 4.55
1738 2053 4.129737 ACGACAGCATCCCGTCCG 62.130 66.667 0.00 0.00 29.82 4.79
1739 2054 2.202756 GACGACAGCATCCCGTCC 60.203 66.667 0.00 0.00 44.67 4.79
1741 2056 2.573869 CAGACGACAGCATCCCGT 59.426 61.111 0.00 0.00 39.41 5.28
1742 2057 2.887568 GCAGACGACAGCATCCCG 60.888 66.667 0.00 0.00 0.00 5.14
1743 2058 0.104855 TATGCAGACGACAGCATCCC 59.895 55.000 19.51 0.00 43.83 3.85
1744 2059 1.202463 ACTATGCAGACGACAGCATCC 60.202 52.381 19.51 0.00 43.83 3.51
1745 2060 2.215907 ACTATGCAGACGACAGCATC 57.784 50.000 19.51 0.00 43.83 3.91
1747 2062 3.801114 ATTACTATGCAGACGACAGCA 57.199 42.857 7.46 7.46 42.25 4.41
1748 2063 4.317418 CGAAATTACTATGCAGACGACAGC 60.317 45.833 0.00 0.00 0.00 4.40
1749 2064 4.798907 ACGAAATTACTATGCAGACGACAG 59.201 41.667 0.00 0.00 0.00 3.51
1750 2065 4.740268 ACGAAATTACTATGCAGACGACA 58.260 39.130 0.00 0.00 0.00 4.35
1751 2066 5.970023 ACTACGAAATTACTATGCAGACGAC 59.030 40.000 0.00 0.00 0.00 4.34
1752 2067 6.127810 ACTACGAAATTACTATGCAGACGA 57.872 37.500 0.00 0.00 0.00 4.20
1753 2068 8.016229 AGATACTACGAAATTACTATGCAGACG 58.984 37.037 0.00 0.00 0.00 4.18
1754 2069 9.680315 AAGATACTACGAAATTACTATGCAGAC 57.320 33.333 0.00 0.00 0.00 3.51
1863 2183 8.442632 AAGTAAACTGACCTAAACACCTAAAC 57.557 34.615 0.00 0.00 0.00 2.01
1864 2184 9.546428 GTAAGTAAACTGACCTAAACACCTAAA 57.454 33.333 0.00 0.00 0.00 1.85
1865 2185 7.867403 CGTAAGTAAACTGACCTAAACACCTAA 59.133 37.037 0.00 0.00 0.00 2.69
1866 2186 7.370383 CGTAAGTAAACTGACCTAAACACCTA 58.630 38.462 0.00 0.00 0.00 3.08
1867 2187 6.218746 CGTAAGTAAACTGACCTAAACACCT 58.781 40.000 0.00 0.00 0.00 4.00
1868 2188 5.107337 GCGTAAGTAAACTGACCTAAACACC 60.107 44.000 0.00 0.00 41.68 4.16
1869 2189 5.693555 AGCGTAAGTAAACTGACCTAAACAC 59.306 40.000 0.00 0.00 41.68 3.32
1870 2190 5.846203 AGCGTAAGTAAACTGACCTAAACA 58.154 37.500 0.00 0.00 41.68 2.83
1965 2297 4.881019 AGATGTGTACTGATGGATAGCC 57.119 45.455 0.00 0.00 0.00 3.93
2034 2368 2.164422 GACAAATGTAGGAAAGCCAGCC 59.836 50.000 0.00 0.00 36.29 4.85
2588 3458 2.138320 CCGATGTGGCTGATATGTGAC 58.862 52.381 0.00 0.00 0.00 3.67
2671 3544 6.772716 TCTTTGTCTAACAATTTGGAAGAGCT 59.227 34.615 0.78 0.00 38.00 4.09
2704 3577 8.864024 CAGAACTACTGTCATTGTATTACTGTG 58.136 37.037 0.00 0.00 41.30 3.66
2793 3666 9.912634 AGGAATGTTAAAAGTTGTATTGATGTG 57.087 29.630 0.00 0.00 0.00 3.21
2877 3781 8.964772 CCTGGAATTTTGAGTCAATAAAGAGAT 58.035 33.333 6.36 0.00 0.00 2.75
3024 3940 7.582352 CATTTAGATATGTGAGCAACCATCTG 58.418 38.462 11.14 0.00 0.00 2.90
3085 4001 6.377146 TGTTCCTGGTTCTAGAAAATATTGCC 59.623 38.462 6.78 2.92 0.00 4.52
3180 4096 1.519246 CTCCATCTGCTCCGCAAGA 59.481 57.895 0.00 0.00 38.41 3.02
3308 4239 0.954452 CTGCACACCTTCCTTTGGAC 59.046 55.000 0.00 0.00 0.00 4.02
3425 4357 7.966339 ATTACTAATCATATGCCATGCCATT 57.034 32.000 0.00 0.00 0.00 3.16
3429 4361 8.960591 ACCTAAATTACTAATCATATGCCATGC 58.039 33.333 0.00 0.00 0.00 4.06
3485 4677 5.247110 TGAAGCAGAGATTCAAGTAGACCTT 59.753 40.000 0.00 0.00 34.96 3.50
3499 4691 2.301296 AGTTTAGCAGCTGAAGCAGAGA 59.699 45.455 20.43 0.00 45.16 3.10
3734 4927 6.098838 TCAGAAACTCATAGACCATGTAGCAT 59.901 38.462 0.00 0.00 35.96 3.79
3735 4928 5.422012 TCAGAAACTCATAGACCATGTAGCA 59.578 40.000 0.00 0.00 35.96 3.49
3804 4997 6.003950 AGATTACACCACAACTATGCAAAGT 58.996 36.000 0.00 0.00 0.00 2.66
3831 5024 2.336088 CCAAACGCACAAGGCTGG 59.664 61.111 0.00 0.00 41.67 4.85
3856 5049 2.423446 GGCTAGCCACCTGATCGG 59.577 66.667 29.33 0.00 39.35 4.18
3872 5479 6.485171 CCCCTATCCCTTAATAGATTTGTGG 58.515 44.000 0.00 0.00 31.98 4.17
3894 5502 3.567478 ACTGATTCATGTCTTAGCCCC 57.433 47.619 0.00 0.00 0.00 5.80
4048 5656 6.035368 TGCATATTTTGTTGTAATGGCTGT 57.965 33.333 0.00 0.00 0.00 4.40
4142 5750 1.852309 TGCCCATGGAGGTTCATATGT 59.148 47.619 15.22 0.00 34.66 2.29
4214 5822 0.381089 CAGATCCGACCAGGTACGAC 59.619 60.000 11.67 4.86 41.99 4.34


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

AutoCloner maintained by Alex Coulton.