Multiple sequence alignment - TraesCS2D01G480500

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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 TraesCS2D01G480500 chr2D 100.000 2509 0 0 1 2509 582495917 582493409 0.000000e+00 4634.0
1 TraesCS2D01G480500 chr2D 86.458 480 39 16 1430 1904 488229846 488230304 1.040000e-138 503.0
2 TraesCS2D01G480500 chr2D 80.512 703 64 31 698 1363 488228861 488229527 2.920000e-129 472.0
3 TraesCS2D01G480500 chr2D 90.972 144 10 2 2298 2440 580453881 580453740 9.160000e-45 191.0
4 TraesCS2D01G480500 chr2D 83.237 173 13 8 492 660 488228479 488228639 7.230000e-31 145.0
5 TraesCS2D01G480500 chr2D 74.636 343 47 26 1431 1757 488225728 488226046 5.670000e-22 115.0
6 TraesCS2D01G480500 chr2D 85.106 94 9 1 2410 2503 577601399 577601487 9.560000e-15 91.6
7 TraesCS2D01G480500 chr2D 97.297 37 0 1 698 734 488228823 488228858 7.490000e-06 62.1
8 TraesCS2D01G480500 chr2B 88.777 1096 43 26 847 1905 701491162 701490110 0.000000e+00 1269.0
9 TraesCS2D01G480500 chr2B 88.759 854 74 14 1 845 701493461 701492621 0.000000e+00 1026.0
10 TraesCS2D01G480500 chr2B 83.621 1044 87 43 888 1904 572586360 572587346 0.000000e+00 904.0
11 TraesCS2D01G480500 chr2B 91.218 501 27 12 2021 2508 701490113 701489617 0.000000e+00 665.0
12 TraesCS2D01G480500 chr2B 88.328 317 23 9 533 845 701492555 701492249 3.940000e-98 368.0
13 TraesCS2D01G480500 chr2B 85.492 193 11 4 698 888 572586133 572586310 4.260000e-43 185.0
14 TraesCS2D01G480500 chr2B 82.659 173 19 7 492 660 572585773 572585938 2.600000e-30 143.0
15 TraesCS2D01G480500 chr2B 86.170 94 8 1 2410 2503 694992240 694992152 2.050000e-16 97.1
16 TraesCS2D01G480500 chr5B 88.631 818 36 22 952 1758 448804033 448803262 0.000000e+00 942.0
17 TraesCS2D01G480500 chr5B 89.030 474 26 21 891 1346 441446522 441446057 4.690000e-157 564.0
18 TraesCS2D01G480500 chr5B 89.323 384 26 10 1525 1904 441442266 441441894 3.780000e-128 468.0
19 TraesCS2D01G480500 chr5B 92.126 127 6 1 1778 1904 448803267 448803145 2.560000e-40 176.0
20 TraesCS2D01G480500 chr5B 86.429 140 10 4 526 662 448808414 448808281 7.230000e-31 145.0
21 TraesCS2D01G480500 chr5B 93.103 58 4 0 1429 1486 441442337 441442280 4.450000e-13 86.1
22 TraesCS2D01G480500 chr5A 84.496 1032 76 44 892 1904 456485754 456484788 0.000000e+00 942.0
23 TraesCS2D01G480500 chr5A 83.153 1015 69 53 892 1877 474537712 474536771 0.000000e+00 833.0
24 TraesCS2D01G480500 chr5D 84.260 953 67 46 892 1822 371441020 371440129 0.000000e+00 852.0
25 TraesCS2D01G480500 chr2A 81.947 986 80 61 890 1818 632622381 632623325 0.000000e+00 745.0
26 TraesCS2D01G480500 chr2A 80.412 291 36 15 2166 2440 718263418 718263133 4.230000e-48 202.0
27 TraesCS2D01G480500 chr2A 87.135 171 11 3 698 866 632613449 632613610 1.530000e-42 183.0
28 TraesCS2D01G480500 chr2A 93.103 58 4 0 2446 2503 715814549 715814492 4.450000e-13 86.1
29 TraesCS2D01G480500 chr2A 100.000 31 0 0 630 660 632613316 632613346 9.690000e-05 58.4
30 TraesCS2D01G480500 chr6B 81.337 718 72 29 670 1360 674935111 674935793 6.150000e-146 527.0
31 TraesCS2D01G480500 chr6B 96.774 31 1 0 378 408 183301157 183301187 5.000000e-03 52.8
32 TraesCS2D01G480500 chr6D 80.993 705 76 21 670 1345 446488888 446489563 8.010000e-140 507.0
33 TraesCS2D01G480500 chr4A 82.869 467 50 18 908 1363 686385704 686385257 2.340000e-105 392.0
34 TraesCS2D01G480500 chr4A 80.556 360 39 16 548 888 641610152 641610499 5.360000e-62 248.0
35 TraesCS2D01G480500 chr4A 89.655 116 9 2 407 519 641611581 641611696 7.230000e-31 145.0
36 TraesCS2D01G480500 chr4A 90.000 80 8 0 406 485 641608418 641608497 1.230000e-18 104.0
37 TraesCS2D01G480500 chr4A 91.549 71 6 0 406 476 641603430 641603500 5.710000e-17 99.0
38 TraesCS2D01G480500 chr4A 92.453 53 4 0 670 722 686384242 686384190 2.680000e-10 76.8
39 TraesCS2D01G480500 chr1B 76.389 216 31 10 208 410 453137467 453137259 5.710000e-17 99.0
40 TraesCS2D01G480500 chr4B 92.157 51 4 0 1359 1409 426107968 426108018 3.460000e-09 73.1
41 TraesCS2D01G480500 chr4B 92.157 51 4 0 670 720 607286922 607286872 3.460000e-09 73.1
42 TraesCS2D01G480500 chr7B 100.000 29 0 0 381 409 614183921 614183893 1.000000e-03 54.7


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 TraesCS2D01G480500 chr2D 582493409 582495917 2508 True 4634.000000 4634 100.000000 1 2509 1 chr2D.!!$R2 2508
1 TraesCS2D01G480500 chr2D 488225728 488230304 4576 False 259.420000 503 84.428000 492 1904 5 chr2D.!!$F2 1412
2 TraesCS2D01G480500 chr2B 701489617 701493461 3844 True 832.000000 1269 89.270500 1 2508 4 chr2B.!!$R2 2507
3 TraesCS2D01G480500 chr2B 572585773 572587346 1573 False 410.666667 904 83.924000 492 1904 3 chr2B.!!$F1 1412
4 TraesCS2D01G480500 chr5B 448803145 448804033 888 True 559.000000 942 90.378500 952 1904 2 chr5B.!!$R3 952
5 TraesCS2D01G480500 chr5B 441441894 441446522 4628 True 372.700000 564 90.485333 891 1904 3 chr5B.!!$R2 1013
6 TraesCS2D01G480500 chr5A 456484788 456485754 966 True 942.000000 942 84.496000 892 1904 1 chr5A.!!$R1 1012
7 TraesCS2D01G480500 chr5A 474536771 474537712 941 True 833.000000 833 83.153000 892 1877 1 chr5A.!!$R2 985
8 TraesCS2D01G480500 chr5D 371440129 371441020 891 True 852.000000 852 84.260000 892 1822 1 chr5D.!!$R1 930
9 TraesCS2D01G480500 chr2A 632622381 632623325 944 False 745.000000 745 81.947000 890 1818 1 chr2A.!!$F1 928
10 TraesCS2D01G480500 chr6B 674935111 674935793 682 False 527.000000 527 81.337000 670 1360 1 chr6B.!!$F2 690
11 TraesCS2D01G480500 chr6D 446488888 446489563 675 False 507.000000 507 80.993000 670 1345 1 chr6D.!!$F1 675
12 TraesCS2D01G480500 chr4A 686384190 686385704 1514 True 234.400000 392 87.661000 670 1363 2 chr4A.!!$R1 693

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
247 253 0.388520 TTCGAGTCTGTCCATGCGTG 60.389 55.0 0.0 0.0 0.00 5.34 F
419 425 1.204146 TGCTCTAAGGTCATCCCCAC 58.796 55.0 0.0 0.0 0.00 4.61 F
892 4810 2.274920 CGGACTCGGTAGTTTTCCTC 57.725 55.0 0.0 0.0 35.56 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 5476 0.025898 GATGACGATGACGACGACGA 59.974 55.0 15.32 0.0 42.66 4.20 R
1356 5480 0.026414 AGACGATGACGATGACGACG 59.974 55.0 0.00 0.0 42.66 5.12 R
1925 10332 0.179045 CGATGCCGAAATCTCCCCTT 60.179 55.0 0.00 0.0 38.22 3.95 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
46 47 3.057806 ACCTTTGCATTTACGGTACAAGC 60.058 43.478 0.00 0.00 0.00 4.01
49 50 2.080693 TGCATTTACGGTACAAGCTGG 58.919 47.619 3.60 0.00 0.00 4.85
85 91 7.773224 CCCGAATATGTAAAATAGCATATCCCA 59.227 37.037 0.00 0.00 37.32 4.37
114 120 4.936685 ATTTCCAGGCTCCCCTATATTC 57.063 45.455 0.00 0.00 40.33 1.75
115 121 3.655972 TTCCAGGCTCCCCTATATTCT 57.344 47.619 0.00 0.00 40.33 2.40
185 191 1.311839 GTAAAGCCGTTTTTCGCGAC 58.688 50.000 9.15 0.00 38.35 5.19
189 195 4.003011 CCGTTTTTCGCGACGCCA 62.003 61.111 9.15 0.00 37.91 5.69
191 197 2.789723 GTTTTTCGCGACGCCACG 60.790 61.111 9.15 0.00 0.00 4.94
247 253 0.388520 TTCGAGTCTGTCCATGCGTG 60.389 55.000 0.00 0.00 0.00 5.34
251 257 2.432456 TCTGTCCATGCGTGCGTC 60.432 61.111 0.00 0.00 0.00 5.19
252 258 2.433145 CTGTCCATGCGTGCGTCT 60.433 61.111 0.00 0.00 0.00 4.18
253 259 2.432456 TGTCCATGCGTGCGTCTC 60.432 61.111 0.00 0.00 0.00 3.36
276 282 1.546476 GGAAGAAGAAGCGTGAGGAGA 59.454 52.381 0.00 0.00 0.00 3.71
319 325 3.068024 ACGCTACGGATTTACGGGATTTA 59.932 43.478 0.00 0.00 38.39 1.40
341 347 1.755395 CCCCCGATGTCTCACGGTA 60.755 63.158 0.00 0.00 46.53 4.02
386 392 3.472283 TTTACAGGTGGTGCTTTACGA 57.528 42.857 0.00 0.00 0.00 3.43
393 399 1.661112 GTGGTGCTTTACGAGATCTGC 59.339 52.381 0.00 0.00 0.00 4.26
411 417 4.141287 TCTGCTAGAGATGCTCTAAGGTC 58.859 47.826 5.75 0.00 41.74 3.85
419 425 1.204146 TGCTCTAAGGTCATCCCCAC 58.796 55.000 0.00 0.00 0.00 4.61
420 426 1.204146 GCTCTAAGGTCATCCCCACA 58.796 55.000 0.00 0.00 0.00 4.17
470 476 4.527509 ATCCTAACTACTCGCATCATGG 57.472 45.455 0.00 0.00 0.00 3.66
550 2818 2.413837 GTTCAACTAAGGAGCGCAGAA 58.586 47.619 11.47 0.00 0.00 3.02
590 2858 4.287552 TCAAGTACTACCAGGGGAGATTC 58.712 47.826 4.11 0.00 0.00 2.52
627 2895 7.218963 GCATCGATAAACTTTTTCAAGGTGATC 59.781 37.037 0.00 0.00 34.96 2.92
666 2935 4.220382 TGACGGGGAAAAAGAATCTACGTA 59.780 41.667 0.00 0.00 32.44 3.57
668 2937 3.549070 CGGGGAAAAAGAATCTACGTACG 59.451 47.826 15.01 15.01 0.00 3.67
740 3561 2.375509 GGAAGGAACAGGGAGAAAGGAA 59.624 50.000 0.00 0.00 0.00 3.36
763 3584 3.666253 CCCGTTCCCGTTTGCACC 61.666 66.667 0.00 0.00 0.00 5.01
823 3647 2.455674 TTCACTTGTGATCCAGTCCG 57.544 50.000 4.18 0.00 0.00 4.79
839 3665 2.582498 CGACCCAGAATCCGCGTC 60.582 66.667 4.92 0.00 0.00 5.19
892 4810 2.274920 CGGACTCGGTAGTTTTCCTC 57.725 55.000 0.00 0.00 35.56 3.71
894 4812 3.012518 CGGACTCGGTAGTTTTCCTCTA 58.987 50.000 0.00 0.00 35.56 2.43
1347 5471 3.187432 TCGAGTCGCAGTAGATCATCATC 59.813 47.826 7.92 0.00 0.00 2.92
1348 5472 3.058639 CGAGTCGCAGTAGATCATCATCA 60.059 47.826 0.00 0.00 0.00 3.07
1349 5473 4.225984 GAGTCGCAGTAGATCATCATCAC 58.774 47.826 0.00 0.00 0.00 3.06
1350 5474 3.005261 AGTCGCAGTAGATCATCATCACC 59.995 47.826 0.00 0.00 0.00 4.02
1351 5475 2.958355 TCGCAGTAGATCATCATCACCA 59.042 45.455 0.00 0.00 0.00 4.17
1352 5476 3.575687 TCGCAGTAGATCATCATCACCAT 59.424 43.478 0.00 0.00 0.00 3.55
1353 5477 3.925299 CGCAGTAGATCATCATCACCATC 59.075 47.826 0.00 0.00 0.00 3.51
1354 5478 3.925299 GCAGTAGATCATCATCACCATCG 59.075 47.826 0.00 0.00 0.00 3.84
1355 5479 4.560311 GCAGTAGATCATCATCACCATCGT 60.560 45.833 0.00 0.00 0.00 3.73
1356 5480 5.159925 CAGTAGATCATCATCACCATCGTC 58.840 45.833 0.00 0.00 0.00 4.20
1357 5481 3.294816 AGATCATCATCACCATCGTCG 57.705 47.619 0.00 0.00 0.00 5.12
1358 5482 2.625314 AGATCATCATCACCATCGTCGT 59.375 45.455 0.00 0.00 0.00 4.34
1359 5483 2.492019 TCATCATCACCATCGTCGTC 57.508 50.000 0.00 0.00 0.00 4.20
1360 5484 1.123655 CATCATCACCATCGTCGTCG 58.876 55.000 0.00 0.00 38.55 5.12
1361 5485 0.738975 ATCATCACCATCGTCGTCGT 59.261 50.000 1.33 0.00 38.33 4.34
1369 5493 0.247537 CATCGTCGTCGTCATCGTCA 60.248 55.000 1.33 0.00 38.33 4.35
1393 5545 6.170846 TCGTCTAGATGGCCTATATATCGA 57.829 41.667 12.06 4.64 0.00 3.59
1590 9750 7.346751 ACCCATAGCAATTTCGTATGATTTT 57.653 32.000 0.00 0.00 0.00 1.82
1591 9751 7.425606 ACCCATAGCAATTTCGTATGATTTTC 58.574 34.615 0.00 0.00 0.00 2.29
1592 9752 7.285401 ACCCATAGCAATTTCGTATGATTTTCT 59.715 33.333 0.00 0.00 0.00 2.52
1593 9753 8.137437 CCCATAGCAATTTCGTATGATTTTCTT 58.863 33.333 0.00 0.00 0.00 2.52
1594 9754 9.520204 CCATAGCAATTTCGTATGATTTTCTTT 57.480 29.630 0.00 0.00 0.00 2.52
1661 9895 6.494835 AGGGCTCAGTTCAAAGAAATTTACAT 59.505 34.615 0.00 0.00 0.00 2.29
1738 10142 4.961438 ATAAAATTGCCATCCATCCACC 57.039 40.909 0.00 0.00 0.00 4.61
1739 10143 1.499368 AAATTGCCATCCATCCACCC 58.501 50.000 0.00 0.00 0.00 4.61
1740 10144 0.339162 AATTGCCATCCATCCACCCA 59.661 50.000 0.00 0.00 0.00 4.51
1742 10146 0.115944 TTGCCATCCATCCACCCAAA 59.884 50.000 0.00 0.00 0.00 3.28
1743 10147 0.339162 TGCCATCCATCCACCCAAAT 59.661 50.000 0.00 0.00 0.00 2.32
1744 10148 1.043022 GCCATCCATCCACCCAAATC 58.957 55.000 0.00 0.00 0.00 2.17
1745 10149 1.412074 GCCATCCATCCACCCAAATCT 60.412 52.381 0.00 0.00 0.00 2.40
1746 10150 2.590821 CCATCCATCCACCCAAATCTC 58.409 52.381 0.00 0.00 0.00 2.75
1747 10151 2.176364 CCATCCATCCACCCAAATCTCT 59.824 50.000 0.00 0.00 0.00 3.10
1785 10191 5.239306 TGTTTTCCTGTGCTGTCAAATCTAG 59.761 40.000 0.00 0.00 0.00 2.43
1834 10240 0.696501 TCCCACAGGGTTAAAGAGGC 59.303 55.000 1.36 0.00 44.74 4.70
1835 10241 0.323451 CCCACAGGGTTAAAGAGGCC 60.323 60.000 0.00 0.00 38.25 5.19
1836 10242 0.676782 CCACAGGGTTAAAGAGGCCG 60.677 60.000 0.00 0.00 0.00 6.13
1837 10243 0.676782 CACAGGGTTAAAGAGGCCGG 60.677 60.000 0.00 0.00 0.00 6.13
1884 10291 5.479306 TGTTTTTCCTATTCGAGTCCTGAG 58.521 41.667 0.00 0.00 0.00 3.35
1944 10351 0.179045 AAGGGGAGATTTCGGCATCG 60.179 55.000 0.00 0.00 37.82 3.84
1950 10357 0.530650 AGATTTCGGCATCGTCGCAT 60.531 50.000 1.52 0.00 37.69 4.73
1951 10358 0.304705 GATTTCGGCATCGTCGCATT 59.695 50.000 1.52 0.00 37.69 3.56
1952 10359 0.027979 ATTTCGGCATCGTCGCATTG 59.972 50.000 1.52 0.00 37.69 2.82
1953 10360 1.016653 TTTCGGCATCGTCGCATTGA 61.017 50.000 1.52 0.00 37.69 2.57
1954 10361 0.809636 TTCGGCATCGTCGCATTGAT 60.810 50.000 1.52 0.00 37.69 2.57
1955 10362 0.031449 TCGGCATCGTCGCATTGATA 59.969 50.000 1.52 0.00 37.69 2.15
1956 10363 0.858583 CGGCATCGTCGCATTGATAA 59.141 50.000 1.52 0.00 0.00 1.75
1957 10364 1.460743 CGGCATCGTCGCATTGATAAT 59.539 47.619 1.52 0.00 0.00 1.28
1958 10365 2.666022 CGGCATCGTCGCATTGATAATA 59.334 45.455 1.52 0.00 0.00 0.98
1959 10366 3.122780 CGGCATCGTCGCATTGATAATAA 59.877 43.478 1.52 0.00 0.00 1.40
1960 10367 4.376920 CGGCATCGTCGCATTGATAATAAA 60.377 41.667 1.52 0.00 0.00 1.40
1961 10368 4.846137 GGCATCGTCGCATTGATAATAAAC 59.154 41.667 1.52 0.00 0.00 2.01
1962 10369 5.334105 GGCATCGTCGCATTGATAATAAACT 60.334 40.000 1.52 0.00 0.00 2.66
1963 10370 6.136071 GCATCGTCGCATTGATAATAAACTT 58.864 36.000 0.00 0.00 0.00 2.66
1964 10371 6.085458 GCATCGTCGCATTGATAATAAACTTG 59.915 38.462 0.00 0.00 0.00 3.16
1965 10372 5.498159 TCGTCGCATTGATAATAAACTTGC 58.502 37.500 0.00 0.00 0.00 4.01
1966 10373 5.293324 TCGTCGCATTGATAATAAACTTGCT 59.707 36.000 0.00 0.00 0.00 3.91
1967 10374 5.393452 CGTCGCATTGATAATAAACTTGCTG 59.607 40.000 0.00 0.00 0.00 4.41
1968 10375 6.486248 GTCGCATTGATAATAAACTTGCTGA 58.514 36.000 0.00 0.00 0.00 4.26
1969 10376 6.412072 GTCGCATTGATAATAAACTTGCTGAC 59.588 38.462 0.00 0.00 0.00 3.51
1970 10377 6.316140 TCGCATTGATAATAAACTTGCTGACT 59.684 34.615 0.00 0.00 0.00 3.41
1971 10378 7.494298 TCGCATTGATAATAAACTTGCTGACTA 59.506 33.333 0.00 0.00 0.00 2.59
1972 10379 7.584123 CGCATTGATAATAAACTTGCTGACTAC 59.416 37.037 0.00 0.00 0.00 2.73
1973 10380 8.616076 GCATTGATAATAAACTTGCTGACTACT 58.384 33.333 0.00 0.00 0.00 2.57
1974 10381 9.926751 CATTGATAATAAACTTGCTGACTACTG 57.073 33.333 0.00 0.00 0.00 2.74
1975 10382 8.492673 TTGATAATAAACTTGCTGACTACTGG 57.507 34.615 0.00 0.00 0.00 4.00
1976 10383 7.620880 TGATAATAAACTTGCTGACTACTGGT 58.379 34.615 0.00 0.00 0.00 4.00
1977 10384 8.755028 TGATAATAAACTTGCTGACTACTGGTA 58.245 33.333 0.00 0.00 0.00 3.25
1978 10385 9.765795 GATAATAAACTTGCTGACTACTGGTAT 57.234 33.333 0.00 0.00 0.00 2.73
1980 10387 7.849804 ATAAACTTGCTGACTACTGGTATTG 57.150 36.000 0.00 0.00 0.00 1.90
1981 10388 4.891992 ACTTGCTGACTACTGGTATTGT 57.108 40.909 0.00 0.00 0.00 2.71
1982 10389 4.569943 ACTTGCTGACTACTGGTATTGTG 58.430 43.478 0.00 0.00 0.00 3.33
1983 10390 4.040461 ACTTGCTGACTACTGGTATTGTGT 59.960 41.667 0.00 0.00 0.00 3.72
1984 10391 4.617253 TGCTGACTACTGGTATTGTGTT 57.383 40.909 0.00 0.00 0.00 3.32
1985 10392 4.314961 TGCTGACTACTGGTATTGTGTTG 58.685 43.478 0.00 0.00 0.00 3.33
1986 10393 4.039852 TGCTGACTACTGGTATTGTGTTGA 59.960 41.667 0.00 0.00 0.00 3.18
1987 10394 4.389077 GCTGACTACTGGTATTGTGTTGAC 59.611 45.833 0.00 0.00 0.00 3.18
1988 10395 5.784177 CTGACTACTGGTATTGTGTTGACT 58.216 41.667 0.00 0.00 0.00 3.41
1989 10396 5.538118 TGACTACTGGTATTGTGTTGACTG 58.462 41.667 0.00 0.00 0.00 3.51
1990 10397 5.303333 TGACTACTGGTATTGTGTTGACTGA 59.697 40.000 0.00 0.00 0.00 3.41
1991 10398 5.784177 ACTACTGGTATTGTGTTGACTGAG 58.216 41.667 0.00 0.00 0.00 3.35
1992 10399 4.955811 ACTGGTATTGTGTTGACTGAGA 57.044 40.909 0.00 0.00 0.00 3.27
1993 10400 4.887748 ACTGGTATTGTGTTGACTGAGAG 58.112 43.478 0.00 0.00 0.00 3.20
1994 10401 4.588951 ACTGGTATTGTGTTGACTGAGAGA 59.411 41.667 0.00 0.00 0.00 3.10
1995 10402 5.070446 ACTGGTATTGTGTTGACTGAGAGAA 59.930 40.000 0.00 0.00 0.00 2.87
1996 10403 6.114187 TGGTATTGTGTTGACTGAGAGAAT 57.886 37.500 0.00 0.00 0.00 2.40
1997 10404 7.039011 ACTGGTATTGTGTTGACTGAGAGAATA 60.039 37.037 0.00 0.00 0.00 1.75
1998 10405 7.676004 TGGTATTGTGTTGACTGAGAGAATAA 58.324 34.615 0.00 0.00 0.00 1.40
1999 10406 7.819415 TGGTATTGTGTTGACTGAGAGAATAAG 59.181 37.037 0.00 0.00 0.00 1.73
2000 10407 7.278868 GGTATTGTGTTGACTGAGAGAATAAGG 59.721 40.741 0.00 0.00 0.00 2.69
2001 10408 5.808366 TGTGTTGACTGAGAGAATAAGGT 57.192 39.130 0.00 0.00 0.00 3.50
2002 10409 5.541845 TGTGTTGACTGAGAGAATAAGGTG 58.458 41.667 0.00 0.00 0.00 4.00
2003 10410 5.070446 TGTGTTGACTGAGAGAATAAGGTGT 59.930 40.000 0.00 0.00 0.00 4.16
2004 10411 5.992217 GTGTTGACTGAGAGAATAAGGTGTT 59.008 40.000 0.00 0.00 0.00 3.32
2005 10412 5.991606 TGTTGACTGAGAGAATAAGGTGTTG 59.008 40.000 0.00 0.00 0.00 3.33
2006 10413 6.183360 TGTTGACTGAGAGAATAAGGTGTTGA 60.183 38.462 0.00 0.00 0.00 3.18
2007 10414 6.419484 TGACTGAGAGAATAAGGTGTTGAA 57.581 37.500 0.00 0.00 0.00 2.69
2008 10415 6.826668 TGACTGAGAGAATAAGGTGTTGAAA 58.173 36.000 0.00 0.00 0.00 2.69
2009 10416 7.279615 TGACTGAGAGAATAAGGTGTTGAAAA 58.720 34.615 0.00 0.00 0.00 2.29
2010 10417 7.773224 TGACTGAGAGAATAAGGTGTTGAAAAA 59.227 33.333 0.00 0.00 0.00 1.94
2011 10418 7.931275 ACTGAGAGAATAAGGTGTTGAAAAAC 58.069 34.615 0.00 0.00 0.00 2.43
2012 10419 7.013369 ACTGAGAGAATAAGGTGTTGAAAAACC 59.987 37.037 0.00 0.00 36.66 3.27
2014 10421 8.215050 TGAGAGAATAAGGTGTTGAAAAACCTA 58.785 33.333 5.32 0.00 46.29 3.08
2015 10422 8.392372 AGAGAATAAGGTGTTGAAAAACCTAC 57.608 34.615 5.32 0.00 46.29 3.18
2016 10423 8.218488 AGAGAATAAGGTGTTGAAAAACCTACT 58.782 33.333 5.32 3.87 46.29 2.57
2017 10424 8.166422 AGAATAAGGTGTTGAAAAACCTACTG 57.834 34.615 5.32 0.00 46.29 2.74
2018 10425 6.894339 ATAAGGTGTTGAAAAACCTACTGG 57.106 37.500 5.32 0.00 46.29 4.00
2019 10426 4.513406 AGGTGTTGAAAAACCTACTGGA 57.487 40.909 2.89 0.00 45.15 3.86
2020 10427 4.862371 AGGTGTTGAAAAACCTACTGGAA 58.138 39.130 2.89 0.00 45.15 3.53
2021 10428 5.265989 AGGTGTTGAAAAACCTACTGGAAA 58.734 37.500 2.89 0.00 45.15 3.13
2022 10429 5.897250 AGGTGTTGAAAAACCTACTGGAAAT 59.103 36.000 2.89 0.00 45.15 2.17
2027 10434 6.569179 TGAAAAACCTACTGGAAATAGTGC 57.431 37.500 0.00 0.00 37.04 4.40
2051 10458 6.278861 CGCTTAATAAAACTTTTGACAACGC 58.721 36.000 0.00 0.00 0.00 4.84
2099 10506 3.151022 CCTGCCCCTCTCGGACTC 61.151 72.222 0.00 0.00 0.00 3.36
2101 10508 3.670629 CTGCCCCTCTCGGACTCCT 62.671 68.421 0.00 0.00 0.00 3.69
2162 10573 8.693625 AGTTTAATAGATAGATATGGTACGGCC 58.306 37.037 0.00 0.00 37.90 6.13
2175 10586 2.352388 GTACGGCCAAGCTGTTTGATA 58.648 47.619 6.34 0.00 46.97 2.15
2182 10593 4.823989 GGCCAAGCTGTTTGATAGATATGT 59.176 41.667 5.77 0.00 39.21 2.29
2209 10620 0.318445 GTGCTGTTACCTCGTCGTGT 60.318 55.000 0.00 0.00 0.00 4.49
2236 10647 6.680810 TGTTTTCATTGTGATGGAGCTAAAG 58.319 36.000 0.00 0.00 33.93 1.85
2238 10649 7.177216 TGTTTTCATTGTGATGGAGCTAAAGAT 59.823 33.333 0.00 0.00 33.93 2.40
2261 10672 4.883006 TGCAAGACATCTGCTTTGCATATA 59.117 37.500 14.29 0.00 38.13 0.86
2293 10704 0.239347 ACTACGTACTGGTGTCGTGC 59.761 55.000 12.80 0.00 38.27 5.34
2299 10710 2.137425 TACTGGTGTCGTGCACTCCG 62.137 60.000 16.19 1.41 46.86 4.63
2305 10716 1.154073 GTCGTGCACTCCGGTACTC 60.154 63.158 16.19 0.00 0.00 2.59
2390 10802 0.765510 GTCAAAGGTCCAGTCCAGGT 59.234 55.000 0.00 0.00 0.00 4.00
2399 10811 1.691976 TCCAGTCCAGGTTGTACACAG 59.308 52.381 0.00 0.00 0.00 3.66
2400 10812 1.691976 CCAGTCCAGGTTGTACACAGA 59.308 52.381 0.00 0.00 0.00 3.41
2444 10860 1.364626 CTCACCGGCAGATCAAGCAC 61.365 60.000 0.00 1.80 0.00 4.40
2466 10882 5.812642 CACGAGGACATAAACTAATTCTGCT 59.187 40.000 0.00 0.00 0.00 4.24
2467 10883 6.978659 CACGAGGACATAAACTAATTCTGCTA 59.021 38.462 0.00 0.00 0.00 3.49
2484 10900 3.802866 TGCTATGAACACTGACACACAA 58.197 40.909 0.00 0.00 0.00 3.33
2492 10908 4.685169 ACACTGACACACAAAAGACTTG 57.315 40.909 0.00 0.00 0.00 3.16
2493 10909 3.440173 ACACTGACACACAAAAGACTTGG 59.560 43.478 0.00 0.00 0.00 3.61
2503 10919 4.741676 CACAAAAGACTTGGATTCAGCAAC 59.258 41.667 0.00 0.00 0.00 4.17
2508 10924 2.146342 ACTTGGATTCAGCAACGACAG 58.854 47.619 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 91 3.774766 GGGGAGCCTGGAAATTGTTTTAT 59.225 43.478 0.00 0.00 0.00 1.40
90 96 1.681229 TAGGGGAGCCTGGAAATTGT 58.319 50.000 0.00 0.00 0.00 2.71
97 103 2.769095 GCTAGAATATAGGGGAGCCTGG 59.231 54.545 0.00 0.00 0.00 4.45
114 120 5.842874 TCCATATATGATGGATGGGAGCTAG 59.157 44.000 14.54 0.00 42.81 3.42
115 121 5.791749 TCCATATATGATGGATGGGAGCTA 58.208 41.667 14.54 0.00 42.81 3.32
149 155 5.095490 GCTTTACATGATCCTCCAAAAACG 58.905 41.667 0.00 0.00 0.00 3.60
211 217 0.250513 GAACTCCGTCTGGCCAGAAT 59.749 55.000 36.66 18.01 39.48 2.40
220 226 1.158434 GACAGACTCGAACTCCGTCT 58.842 55.000 0.00 0.00 38.47 4.18
247 253 2.003196 CTTCTTCTTCCCTGAGACGC 57.997 55.000 0.00 0.00 0.00 5.19
251 257 1.273606 TCACGCTTCTTCTTCCCTGAG 59.726 52.381 0.00 0.00 0.00 3.35
252 258 1.273606 CTCACGCTTCTTCTTCCCTGA 59.726 52.381 0.00 0.00 0.00 3.86
253 259 1.674221 CCTCACGCTTCTTCTTCCCTG 60.674 57.143 0.00 0.00 0.00 4.45
294 300 2.033299 TCCCGTAAATCCGTAGCGTAAG 59.967 50.000 0.00 0.00 43.44 2.34
300 306 6.716898 GGAATAAATCCCGTAAATCCGTAG 57.283 41.667 0.00 0.00 43.00 3.51
379 385 5.048782 AGCATCTCTAGCAGATCTCGTAAAG 60.049 44.000 0.00 0.00 40.20 1.85
382 388 4.000325 GAGCATCTCTAGCAGATCTCGTA 59.000 47.826 0.00 0.00 40.20 3.43
393 399 4.462483 GGGATGACCTTAGAGCATCTCTAG 59.538 50.000 11.76 0.00 42.92 2.43
411 417 2.299582 TGAAGCAACATTTGTGGGGATG 59.700 45.455 0.00 0.00 0.00 3.51
419 425 4.930963 TGTTGTAGGTGAAGCAACATTTG 58.069 39.130 5.39 0.00 44.82 2.32
441 447 5.310451 TGCGAGTAGTTAGGATTTGGTTTT 58.690 37.500 0.00 0.00 0.00 2.43
572 2840 1.962100 CGGAATCTCCCCTGGTAGTAC 59.038 57.143 0.00 0.00 31.13 2.73
576 2844 1.764854 GCCGGAATCTCCCCTGGTA 60.765 63.158 5.05 0.00 31.13 3.25
577 2845 3.090532 GCCGGAATCTCCCCTGGT 61.091 66.667 5.05 0.00 31.13 4.00
578 2846 2.403132 GATGCCGGAATCTCCCCTGG 62.403 65.000 15.91 0.00 31.13 4.45
579 2847 1.072159 GATGCCGGAATCTCCCCTG 59.928 63.158 15.91 0.00 31.13 4.45
580 2848 0.769776 ATGATGCCGGAATCTCCCCT 60.770 55.000 23.35 0.48 31.13 4.79
581 2849 0.322008 GATGATGCCGGAATCTCCCC 60.322 60.000 23.35 6.13 31.13 4.81
590 2858 0.458370 TATCGATGCGATGATGCCGG 60.458 55.000 8.54 0.00 46.43 6.13
627 2895 3.618594 CCCGTCAGTTCAGTGATGTATTG 59.381 47.826 0.00 0.00 32.36 1.90
666 2935 0.801251 GTGCAGTCTAGGACGTACGT 59.199 55.000 23.04 23.04 37.67 3.57
668 2937 2.415625 CCAAGTGCAGTCTAGGACGTAC 60.416 54.545 0.00 0.00 37.67 3.67
672 2941 3.145228 GCCAAGTGCAGTCTAGGAC 57.855 57.895 10.79 0.00 40.77 3.85
763 3584 4.001652 CCGATGAGATGATGATTTCCCAG 58.998 47.826 0.00 0.00 0.00 4.45
823 3647 0.248949 GTAGACGCGGATTCTGGGTC 60.249 60.000 26.86 26.86 46.28 4.46
839 3665 8.272545 TCATCATCATGGAAGAAAACAAGTAG 57.727 34.615 0.00 0.00 0.00 2.57
889 4807 2.413765 GCGGGCTTCGAGTAGAGG 59.586 66.667 4.34 0.00 42.43 3.69
890 4808 2.024871 CGCGGGCTTCGAGTAGAG 59.975 66.667 0.00 0.00 42.43 2.43
892 4810 2.278013 GTCGCGGGCTTCGAGTAG 60.278 66.667 6.13 0.00 42.43 2.57
1103 5158 4.168291 CCTGCGCCTCCTTCTCCC 62.168 72.222 4.18 0.00 0.00 4.30
1347 5471 1.194280 CGATGACGACGACGATGGTG 61.194 60.000 15.32 0.00 42.66 4.17
1348 5472 1.062047 CGATGACGACGACGATGGT 59.938 57.895 15.32 0.00 42.66 3.55
1349 5473 0.924363 GACGATGACGACGACGATGG 60.924 60.000 15.32 1.95 42.66 3.51
1350 5474 0.247537 TGACGATGACGACGACGATG 60.248 55.000 15.32 0.00 42.66 3.84
1351 5475 0.656259 ATGACGATGACGACGACGAT 59.344 50.000 15.32 0.00 42.66 3.73
1352 5476 0.025898 GATGACGATGACGACGACGA 59.974 55.000 15.32 0.00 42.66 4.20
1353 5477 1.247261 CGATGACGATGACGACGACG 61.247 60.000 5.58 5.58 42.66 5.12
1354 5478 0.247576 ACGATGACGATGACGACGAC 60.248 55.000 0.00 0.00 42.66 4.34
1355 5479 0.025898 GACGATGACGATGACGACGA 59.974 55.000 0.00 0.00 42.66 4.20
1356 5480 0.026414 AGACGATGACGATGACGACG 59.974 55.000 0.00 0.00 42.66 5.12
1357 5481 2.538861 TCTAGACGATGACGATGACGAC 59.461 50.000 0.00 0.00 42.66 4.34
1358 5482 2.817901 TCTAGACGATGACGATGACGA 58.182 47.619 0.00 0.00 42.66 4.20
1359 5483 3.797348 ATCTAGACGATGACGATGACG 57.203 47.619 0.00 0.00 42.66 4.35
1369 5493 6.770542 TCGATATATAGGCCATCTAGACGAT 58.229 40.000 5.01 0.00 0.00 3.73
1409 8883 9.477484 CTCAACTTTCACAACTAGTACTAACAT 57.523 33.333 3.76 0.00 0.00 2.71
1411 8885 7.924947 ACCTCAACTTTCACAACTAGTACTAAC 59.075 37.037 3.76 0.00 0.00 2.34
1414 8888 6.324254 AGACCTCAACTTTCACAACTAGTACT 59.676 38.462 0.00 0.00 0.00 2.73
1415 8889 6.514063 AGACCTCAACTTTCACAACTAGTAC 58.486 40.000 0.00 0.00 0.00 2.73
1433 9263 4.159879 TCCTCGAGTTTAATCCAAGACCTC 59.840 45.833 12.31 0.00 0.00 3.85
1503 9412 5.470437 AGAGCTCGTCTTCGATATAATCACA 59.530 40.000 8.37 0.00 45.21 3.58
1512 9667 2.088423 ACAAGAGAGCTCGTCTTCGAT 58.912 47.619 19.37 9.92 45.21 3.59
1526 9681 7.267857 AGGGAACATGAAAAGAAAAACAAGAG 58.732 34.615 0.00 0.00 0.00 2.85
1528 9684 7.848223 AAGGGAACATGAAAAGAAAAACAAG 57.152 32.000 0.00 0.00 0.00 3.16
1531 9687 9.764363 AGAATAAGGGAACATGAAAAGAAAAAC 57.236 29.630 0.00 0.00 0.00 2.43
1718 10115 3.037549 GGGTGGATGGATGGCAATTTTA 58.962 45.455 0.00 0.00 0.00 1.52
1733 10136 6.780031 TGATTTGTAAAAGAGATTTGGGTGGA 59.220 34.615 0.00 0.00 32.27 4.02
1785 10191 8.237267 CACTAGGATTACAAAACCACAGAAATC 58.763 37.037 0.00 0.00 0.00 2.17
1834 10240 3.273434 CATTGGAGTGATATATGGCCGG 58.727 50.000 0.00 0.00 0.00 6.13
1835 10241 2.679837 GCATTGGAGTGATATATGGCCG 59.320 50.000 0.00 0.00 0.00 6.13
1836 10242 3.960571 AGCATTGGAGTGATATATGGCC 58.039 45.455 0.00 0.00 0.00 5.36
1837 10243 7.121759 ACAATTAGCATTGGAGTGATATATGGC 59.878 37.037 0.00 0.00 43.82 4.40
1904 10311 7.364762 CCCCTTAGTTGAGTGATGTATGTAGTT 60.365 40.741 0.00 0.00 0.00 2.24
1905 10312 6.098409 CCCCTTAGTTGAGTGATGTATGTAGT 59.902 42.308 0.00 0.00 0.00 2.73
1906 10313 6.323996 TCCCCTTAGTTGAGTGATGTATGTAG 59.676 42.308 0.00 0.00 0.00 2.74
1909 10316 5.363868 TCTCCCCTTAGTTGAGTGATGTATG 59.636 44.000 0.00 0.00 0.00 2.39
1916 10323 4.184629 CGAAATCTCCCCTTAGTTGAGTG 58.815 47.826 0.00 0.00 0.00 3.51
1925 10332 0.179045 CGATGCCGAAATCTCCCCTT 60.179 55.000 0.00 0.00 38.22 3.95
1927 10334 0.880718 GACGATGCCGAAATCTCCCC 60.881 60.000 0.00 0.00 39.50 4.81
1944 10351 6.412072 GTCAGCAAGTTTATTATCAATGCGAC 59.588 38.462 0.00 0.00 37.40 5.19
1950 10357 8.100791 ACCAGTAGTCAGCAAGTTTATTATCAA 58.899 33.333 0.00 0.00 0.00 2.57
1951 10358 7.620880 ACCAGTAGTCAGCAAGTTTATTATCA 58.379 34.615 0.00 0.00 0.00 2.15
1952 10359 9.765795 ATACCAGTAGTCAGCAAGTTTATTATC 57.234 33.333 0.00 0.00 0.00 1.75
1954 10361 9.378551 CAATACCAGTAGTCAGCAAGTTTATTA 57.621 33.333 0.00 0.00 0.00 0.98
1955 10362 7.883311 ACAATACCAGTAGTCAGCAAGTTTATT 59.117 33.333 0.00 0.00 0.00 1.40
1956 10363 7.334421 CACAATACCAGTAGTCAGCAAGTTTAT 59.666 37.037 0.00 0.00 0.00 1.40
1957 10364 6.649141 CACAATACCAGTAGTCAGCAAGTTTA 59.351 38.462 0.00 0.00 0.00 2.01
1958 10365 5.470098 CACAATACCAGTAGTCAGCAAGTTT 59.530 40.000 0.00 0.00 0.00 2.66
1959 10366 4.997395 CACAATACCAGTAGTCAGCAAGTT 59.003 41.667 0.00 0.00 0.00 2.66
1960 10367 4.040461 ACACAATACCAGTAGTCAGCAAGT 59.960 41.667 0.00 0.00 0.00 3.16
1961 10368 4.569943 ACACAATACCAGTAGTCAGCAAG 58.430 43.478 0.00 0.00 0.00 4.01
1962 10369 4.617253 ACACAATACCAGTAGTCAGCAA 57.383 40.909 0.00 0.00 0.00 3.91
1963 10370 4.039852 TCAACACAATACCAGTAGTCAGCA 59.960 41.667 0.00 0.00 0.00 4.41
1964 10371 4.389077 GTCAACACAATACCAGTAGTCAGC 59.611 45.833 0.00 0.00 0.00 4.26
1965 10372 5.635280 CAGTCAACACAATACCAGTAGTCAG 59.365 44.000 0.00 0.00 0.00 3.51
1966 10373 5.303333 TCAGTCAACACAATACCAGTAGTCA 59.697 40.000 0.00 0.00 0.00 3.41
1967 10374 5.779922 TCAGTCAACACAATACCAGTAGTC 58.220 41.667 0.00 0.00 0.00 2.59
1968 10375 5.538813 TCTCAGTCAACACAATACCAGTAGT 59.461 40.000 0.00 0.00 0.00 2.73
1969 10376 6.025749 TCTCAGTCAACACAATACCAGTAG 57.974 41.667 0.00 0.00 0.00 2.57
1970 10377 5.773176 TCTCTCAGTCAACACAATACCAGTA 59.227 40.000 0.00 0.00 0.00 2.74
1971 10378 4.588951 TCTCTCAGTCAACACAATACCAGT 59.411 41.667 0.00 0.00 0.00 4.00
1972 10379 5.139435 TCTCTCAGTCAACACAATACCAG 57.861 43.478 0.00 0.00 0.00 4.00
1973 10380 5.545063 TTCTCTCAGTCAACACAATACCA 57.455 39.130 0.00 0.00 0.00 3.25
1974 10381 7.278868 CCTTATTCTCTCAGTCAACACAATACC 59.721 40.741 0.00 0.00 0.00 2.73
1975 10382 7.819900 ACCTTATTCTCTCAGTCAACACAATAC 59.180 37.037 0.00 0.00 0.00 1.89
1976 10383 7.819415 CACCTTATTCTCTCAGTCAACACAATA 59.181 37.037 0.00 0.00 0.00 1.90
1977 10384 6.652481 CACCTTATTCTCTCAGTCAACACAAT 59.348 38.462 0.00 0.00 0.00 2.71
1978 10385 5.991606 CACCTTATTCTCTCAGTCAACACAA 59.008 40.000 0.00 0.00 0.00 3.33
1979 10386 5.070446 ACACCTTATTCTCTCAGTCAACACA 59.930 40.000 0.00 0.00 0.00 3.72
1980 10387 5.542779 ACACCTTATTCTCTCAGTCAACAC 58.457 41.667 0.00 0.00 0.00 3.32
1981 10388 5.808366 ACACCTTATTCTCTCAGTCAACA 57.192 39.130 0.00 0.00 0.00 3.33
1982 10389 6.223852 TCAACACCTTATTCTCTCAGTCAAC 58.776 40.000 0.00 0.00 0.00 3.18
1983 10390 6.419484 TCAACACCTTATTCTCTCAGTCAA 57.581 37.500 0.00 0.00 0.00 3.18
1984 10391 6.419484 TTCAACACCTTATTCTCTCAGTCA 57.581 37.500 0.00 0.00 0.00 3.41
1985 10392 7.730364 TTTTCAACACCTTATTCTCTCAGTC 57.270 36.000 0.00 0.00 0.00 3.51
1986 10393 7.013369 GGTTTTTCAACACCTTATTCTCTCAGT 59.987 37.037 0.00 0.00 34.15 3.41
1987 10394 7.229506 AGGTTTTTCAACACCTTATTCTCTCAG 59.770 37.037 0.00 0.00 40.85 3.35
1988 10395 7.060421 AGGTTTTTCAACACCTTATTCTCTCA 58.940 34.615 0.00 0.00 40.85 3.27
1989 10396 7.511959 AGGTTTTTCAACACCTTATTCTCTC 57.488 36.000 0.00 0.00 40.85 3.20
1990 10397 8.218488 AGTAGGTTTTTCAACACCTTATTCTCT 58.782 33.333 2.73 0.00 40.85 3.10
1991 10398 8.290325 CAGTAGGTTTTTCAACACCTTATTCTC 58.710 37.037 2.73 0.00 40.85 2.87
1992 10399 7.230712 CCAGTAGGTTTTTCAACACCTTATTCT 59.769 37.037 2.73 0.00 40.85 2.40
1993 10400 7.229907 TCCAGTAGGTTTTTCAACACCTTATTC 59.770 37.037 2.73 0.00 40.85 1.75
1994 10401 7.064229 TCCAGTAGGTTTTTCAACACCTTATT 58.936 34.615 2.73 0.00 40.85 1.40
1995 10402 6.607019 TCCAGTAGGTTTTTCAACACCTTAT 58.393 36.000 2.73 0.00 40.85 1.73
1996 10403 6.003859 TCCAGTAGGTTTTTCAACACCTTA 57.996 37.500 2.73 0.00 40.85 2.69
1997 10404 4.862371 TCCAGTAGGTTTTTCAACACCTT 58.138 39.130 2.73 0.00 40.85 3.50
1998 10405 4.513406 TCCAGTAGGTTTTTCAACACCT 57.487 40.909 2.97 2.97 45.85 4.00
1999 10406 5.585820 TTTCCAGTAGGTTTTTCAACACC 57.414 39.130 0.00 0.00 34.15 4.16
2000 10407 7.860872 CACTATTTCCAGTAGGTTTTTCAACAC 59.139 37.037 0.00 0.00 34.15 3.32
2001 10408 7.469456 GCACTATTTCCAGTAGGTTTTTCAACA 60.469 37.037 0.00 0.00 34.15 3.33
2002 10409 6.861572 GCACTATTTCCAGTAGGTTTTTCAAC 59.138 38.462 0.00 0.00 35.89 3.18
2003 10410 6.293735 CGCACTATTTCCAGTAGGTTTTTCAA 60.294 38.462 0.00 0.00 35.89 2.69
2004 10411 5.180492 CGCACTATTTCCAGTAGGTTTTTCA 59.820 40.000 0.00 0.00 35.89 2.69
2005 10412 5.628134 CGCACTATTTCCAGTAGGTTTTTC 58.372 41.667 0.00 0.00 35.89 2.29
2006 10413 4.082949 GCGCACTATTTCCAGTAGGTTTTT 60.083 41.667 0.30 0.00 35.89 1.94
2007 10414 3.439129 GCGCACTATTTCCAGTAGGTTTT 59.561 43.478 0.30 0.00 35.89 2.43
2008 10415 3.007635 GCGCACTATTTCCAGTAGGTTT 58.992 45.455 0.30 0.00 35.89 3.27
2009 10416 2.236395 AGCGCACTATTTCCAGTAGGTT 59.764 45.455 11.47 0.00 35.89 3.50
2010 10417 1.831736 AGCGCACTATTTCCAGTAGGT 59.168 47.619 11.47 0.00 35.89 3.08
2011 10418 2.604046 AGCGCACTATTTCCAGTAGG 57.396 50.000 11.47 0.00 0.00 3.18
2012 10419 7.709269 TTATTAAGCGCACTATTTCCAGTAG 57.291 36.000 11.47 0.00 0.00 2.57
2013 10420 8.392612 GTTTTATTAAGCGCACTATTTCCAGTA 58.607 33.333 11.47 0.00 0.00 2.74
2014 10421 6.995511 TTTATTAAGCGCACTATTTCCAGT 57.004 33.333 11.47 0.00 0.00 4.00
2015 10422 7.472543 AGTTTTATTAAGCGCACTATTTCCAG 58.527 34.615 11.47 0.00 0.00 3.86
2016 10423 7.385778 AGTTTTATTAAGCGCACTATTTCCA 57.614 32.000 11.47 0.00 0.00 3.53
2017 10424 8.683550 AAAGTTTTATTAAGCGCACTATTTCC 57.316 30.769 11.47 0.00 0.00 3.13
2018 10425 9.937577 CAAAAGTTTTATTAAGCGCACTATTTC 57.062 29.630 11.47 0.00 0.00 2.17
2019 10426 9.685828 TCAAAAGTTTTATTAAGCGCACTATTT 57.314 25.926 11.47 0.00 0.00 1.40
2020 10427 9.124807 GTCAAAAGTTTTATTAAGCGCACTATT 57.875 29.630 11.47 0.00 0.00 1.73
2021 10428 8.293867 TGTCAAAAGTTTTATTAAGCGCACTAT 58.706 29.630 11.47 1.31 0.00 2.12
2022 10429 7.640852 TGTCAAAAGTTTTATTAAGCGCACTA 58.359 30.769 11.47 0.00 0.00 2.74
2027 10434 6.141685 AGCGTTGTCAAAAGTTTTATTAAGCG 59.858 34.615 0.00 3.10 0.00 4.68
2154 10565 0.887387 TCAAACAGCTTGGCCGTACC 60.887 55.000 0.00 0.00 35.56 3.34
2155 10566 1.165270 ATCAAACAGCTTGGCCGTAC 58.835 50.000 0.00 0.00 35.56 3.67
2156 10567 2.235155 TCTATCAAACAGCTTGGCCGTA 59.765 45.455 0.00 0.00 35.56 4.02
2157 10568 1.003118 TCTATCAAACAGCTTGGCCGT 59.997 47.619 0.00 0.00 35.56 5.68
2158 10569 1.737838 TCTATCAAACAGCTTGGCCG 58.262 50.000 0.00 0.00 35.56 6.13
2159 10570 4.823989 ACATATCTATCAAACAGCTTGGCC 59.176 41.667 0.00 0.00 35.56 5.36
2160 10571 6.382869 AACATATCTATCAAACAGCTTGGC 57.617 37.500 0.00 0.00 35.56 4.52
2162 10573 7.972277 AGCAAAACATATCTATCAAACAGCTTG 59.028 33.333 0.00 0.00 36.25 4.01
2164 10575 7.415989 CCAGCAAAACATATCTATCAAACAGCT 60.416 37.037 0.00 0.00 0.00 4.24
2165 10576 6.694411 CCAGCAAAACATATCTATCAAACAGC 59.306 38.462 0.00 0.00 0.00 4.40
2166 10577 7.699391 CACCAGCAAAACATATCTATCAAACAG 59.301 37.037 0.00 0.00 0.00 3.16
2168 10579 6.473455 GCACCAGCAAAACATATCTATCAAAC 59.527 38.462 0.00 0.00 41.58 2.93
2175 10586 3.424703 ACAGCACCAGCAAAACATATCT 58.575 40.909 0.00 0.00 45.49 1.98
2182 10593 1.953686 GAGGTAACAGCACCAGCAAAA 59.046 47.619 0.00 0.00 45.49 2.44
2209 10620 4.341806 AGCTCCATCACAATGAAAACAACA 59.658 37.500 0.00 0.00 34.61 3.33
2238 10649 1.320507 TGCAAAGCAGATGTCTTGCA 58.679 45.000 15.30 15.30 33.32 4.08
2293 10704 2.833631 AGGTTTTGAGTACCGGAGTG 57.166 50.000 9.46 0.00 40.69 3.51
2299 10710 4.515567 CCTGAACTGAAGGTTTTGAGTACC 59.484 45.833 0.00 0.00 38.41 3.34
2305 10716 2.294512 GGCTCCTGAACTGAAGGTTTTG 59.705 50.000 0.00 0.00 38.41 2.44
2339 10750 2.292569 GCATCTGTAGGTGCATGAATGG 59.707 50.000 12.04 0.00 40.94 3.16
2342 10753 3.452264 AGTAGCATCTGTAGGTGCATGAA 59.548 43.478 18.43 0.00 43.63 2.57
2390 10802 1.346395 ACGGCTGGAATCTGTGTACAA 59.654 47.619 0.00 0.00 0.00 2.41
2399 10811 1.803289 GGCAAAGACGGCTGGAATC 59.197 57.895 0.00 0.00 0.00 2.52
2400 10812 2.040544 CGGCAAAGACGGCTGGAAT 61.041 57.895 0.00 0.00 33.98 3.01
2444 10860 7.867909 TCATAGCAGAATTAGTTTATGTCCTCG 59.132 37.037 0.00 0.00 0.00 4.63
2466 10882 6.112734 AGTCTTTTGTGTGTCAGTGTTCATA 58.887 36.000 0.00 0.00 0.00 2.15
2467 10883 4.943705 AGTCTTTTGTGTGTCAGTGTTCAT 59.056 37.500 0.00 0.00 0.00 2.57
2484 10900 3.251004 GTCGTTGCTGAATCCAAGTCTTT 59.749 43.478 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.