Multiple sequence alignment - TraesCS5D01G067300

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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 TraesCS5D01G067300 chr5D 100.000 2624 0 0 1 2624 62509886 62512509 0.000000e+00 4846
1 TraesCS5D01G067300 chr5D 91.386 743 52 7 912 1647 62479036 62479773 0.000000e+00 1007
2 TraesCS5D01G067300 chr5D 91.328 738 44 10 49 767 62478157 62478893 0.000000e+00 990
3 TraesCS5D01G067300 chr5D 90.274 329 32 0 1217 1545 62475555 62475227 5.190000e-117 431
4 TraesCS5D01G067300 chr5D 85.455 110 12 4 1541 1646 62326861 62326752 7.680000e-21 111
5 TraesCS5D01G067300 chr5B 92.946 808 43 4 100 893 68195738 68194931 0.000000e+00 1164
6 TraesCS5D01G067300 chr5B 88.726 887 43 16 61 893 68049929 68049046 0.000000e+00 1031
7 TraesCS5D01G067300 chr5B 89.799 745 58 9 912 1647 68194870 68194135 0.000000e+00 939
8 TraesCS5D01G067300 chr5B 88.636 748 63 10 919 1647 68048982 68048238 0.000000e+00 891
9 TraesCS5D01G067300 chr5B 88.156 667 51 11 1739 2404 61659281 61658642 0.000000e+00 769
10 TraesCS5D01G067300 chr5B 86.438 671 57 19 1737 2404 523904721 523905360 0.000000e+00 704
11 TraesCS5D01G067300 chr5B 89.820 334 32 1 1214 1545 68052423 68052756 6.710000e-116 427
12 TraesCS5D01G067300 chr5B 86.486 111 11 4 1541 1647 68167497 68167607 4.590000e-23 119
13 TraesCS5D01G067300 chr5A 90.470 829 69 9 913 1733 52357490 52358316 0.000000e+00 1085
14 TraesCS5D01G067300 chr5A 91.385 650 43 6 85 721 52356636 52357285 0.000000e+00 878
15 TraesCS5D01G067300 chr5A 89.888 89 4 1 810 893 52357332 52357420 2.760000e-20 110
16 TraesCS5D01G067300 chrUn 91.888 678 46 7 1733 2404 36428791 36428117 0.000000e+00 939
17 TraesCS5D01G067300 chrUn 90.703 441 34 5 1739 2174 34107632 34108070 4.870000e-162 580
18 TraesCS5D01G067300 chrUn 90.703 441 34 5 1739 2174 234956153 234955715 4.870000e-162 580
19 TraesCS5D01G067300 chr3D 91.343 670 32 11 1739 2404 495303246 495302599 0.000000e+00 893
20 TraesCS5D01G067300 chr3D 90.452 199 8 7 2437 2624 409372788 409372986 4.340000e-63 252
21 TraesCS5D01G067300 chr7D 90.746 670 35 13 1739 2404 469644125 469643479 0.000000e+00 869
22 TraesCS5D01G067300 chr7D 90.405 667 42 8 1739 2404 148236032 148236677 0.000000e+00 857
23 TraesCS5D01G067300 chr7D 94.211 190 6 3 2440 2624 286010564 286010753 4.270000e-73 285
24 TraesCS5D01G067300 chr7D 91.579 190 8 3 2440 2624 512597451 512597265 3.350000e-64 255
25 TraesCS5D01G067300 chr3B 88.444 675 49 13 1736 2404 28798502 28799153 0.000000e+00 787
26 TraesCS5D01G067300 chr1B 88.393 672 49 13 1739 2404 547405257 547404609 0.000000e+00 782
27 TraesCS5D01G067300 chr1B 86.873 678 41 19 1731 2404 485307593 485306960 0.000000e+00 715
28 TraesCS5D01G067300 chr3A 86.161 672 44 17 1736 2404 25765228 25765853 0.000000e+00 680
29 TraesCS5D01G067300 chr6B 91.866 418 31 3 1989 2404 413933507 413933923 4.870000e-162 580
30 TraesCS5D01G067300 chr1D 93.651 189 6 3 2440 2624 22695347 22695533 7.150000e-71 278
31 TraesCS5D01G067300 chr1D 93.158 190 6 6 2440 2624 233159928 233160115 3.330000e-69 272
32 TraesCS5D01G067300 chr2D 92.784 194 7 5 2437 2624 501592298 501592490 9.250000e-70 274
33 TraesCS5D01G067300 chr2D 93.085 188 8 3 2440 2624 626527049 626526864 1.200000e-68 270
34 TraesCS5D01G067300 chr6D 92.063 189 9 5 2440 2624 217701647 217701833 7.200000e-66 261
35 TraesCS5D01G067300 chr6D 92.063 189 7 5 2440 2622 379254889 379254703 2.590000e-65 259


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 TraesCS5D01G067300 chr5D 62509886 62512509 2623 False 4846.0 4846 100.0000 1 2624 1 chr5D.!!$F1 2623
1 TraesCS5D01G067300 chr5D 62478157 62479773 1616 False 998.5 1007 91.3570 49 1647 2 chr5D.!!$F2 1598
2 TraesCS5D01G067300 chr5B 68194135 68195738 1603 True 1051.5 1164 91.3725 100 1647 2 chr5B.!!$R3 1547
3 TraesCS5D01G067300 chr5B 68048238 68049929 1691 True 961.0 1031 88.6810 61 1647 2 chr5B.!!$R2 1586
4 TraesCS5D01G067300 chr5B 61658642 61659281 639 True 769.0 769 88.1560 1739 2404 1 chr5B.!!$R1 665
5 TraesCS5D01G067300 chr5B 523904721 523905360 639 False 704.0 704 86.4380 1737 2404 1 chr5B.!!$F3 667
6 TraesCS5D01G067300 chr5A 52356636 52358316 1680 False 691.0 1085 90.5810 85 1733 3 chr5A.!!$F1 1648
7 TraesCS5D01G067300 chrUn 36428117 36428791 674 True 939.0 939 91.8880 1733 2404 1 chrUn.!!$R1 671
8 TraesCS5D01G067300 chr3D 495302599 495303246 647 True 893.0 893 91.3430 1739 2404 1 chr3D.!!$R1 665
9 TraesCS5D01G067300 chr7D 469643479 469644125 646 True 869.0 869 90.7460 1739 2404 1 chr7D.!!$R1 665
10 TraesCS5D01G067300 chr7D 148236032 148236677 645 False 857.0 857 90.4050 1739 2404 1 chr7D.!!$F1 665
11 TraesCS5D01G067300 chr3B 28798502 28799153 651 False 787.0 787 88.4440 1736 2404 1 chr3B.!!$F1 668
12 TraesCS5D01G067300 chr1B 547404609 547405257 648 True 782.0 782 88.3930 1739 2404 1 chr1B.!!$R2 665
13 TraesCS5D01G067300 chr1B 485306960 485307593 633 True 715.0 715 86.8730 1731 2404 1 chr1B.!!$R1 673
14 TraesCS5D01G067300 chr3A 25765228 25765853 625 False 680.0 680 86.1610 1736 2404 1 chr3A.!!$F1 668

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
363 370 0.033601 TCCGCCTTGGCAATAACCAT 60.034 50.0 12.45 0.0 40.13 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1896 0.036671 CCCGGCTCTAAACGTTTCCT 60.037 55.0 18.42 0.0 0.0 3.36 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
17 18 2.191908 ACACCAACCAGCAGCGAA 59.808 55.556 0.00 0.00 0.00 4.70
18 19 1.453015 ACACCAACCAGCAGCGAAA 60.453 52.632 0.00 0.00 0.00 3.46
19 20 1.034838 ACACCAACCAGCAGCGAAAA 61.035 50.000 0.00 0.00 0.00 2.29
20 21 0.318107 CACCAACCAGCAGCGAAAAG 60.318 55.000 0.00 0.00 0.00 2.27
32 33 3.845625 CGAAAAGCGCCCATAATCC 57.154 52.632 2.29 0.00 0.00 3.01
33 34 0.041312 CGAAAAGCGCCCATAATCCG 60.041 55.000 2.29 0.00 0.00 4.18
34 35 1.021968 GAAAAGCGCCCATAATCCGT 58.978 50.000 2.29 0.00 0.00 4.69
35 36 1.404035 GAAAAGCGCCCATAATCCGTT 59.596 47.619 2.29 0.00 0.00 4.44
36 37 1.470051 AAAGCGCCCATAATCCGTTT 58.530 45.000 2.29 0.00 0.00 3.60
37 38 2.335316 AAGCGCCCATAATCCGTTTA 57.665 45.000 2.29 0.00 0.00 2.01
38 39 1.878953 AGCGCCCATAATCCGTTTAG 58.121 50.000 2.29 0.00 0.00 1.85
39 40 1.414919 AGCGCCCATAATCCGTTTAGA 59.585 47.619 2.29 0.00 0.00 2.10
40 41 2.158871 AGCGCCCATAATCCGTTTAGAA 60.159 45.455 2.29 0.00 0.00 2.10
41 42 2.614983 GCGCCCATAATCCGTTTAGAAA 59.385 45.455 0.00 0.00 0.00 2.52
42 43 3.252458 GCGCCCATAATCCGTTTAGAAAT 59.748 43.478 0.00 0.00 0.00 2.17
43 44 4.453136 GCGCCCATAATCCGTTTAGAAATA 59.547 41.667 0.00 0.00 0.00 1.40
44 45 5.123344 GCGCCCATAATCCGTTTAGAAATAT 59.877 40.000 0.00 0.00 0.00 1.28
45 46 6.314400 GCGCCCATAATCCGTTTAGAAATATA 59.686 38.462 0.00 0.00 0.00 0.86
46 47 7.148373 GCGCCCATAATCCGTTTAGAAATATAA 60.148 37.037 0.00 0.00 0.00 0.98
47 48 8.173130 CGCCCATAATCCGTTTAGAAATATAAC 58.827 37.037 0.00 0.00 0.00 1.89
48 49 9.227777 GCCCATAATCCGTTTAGAAATATAACT 57.772 33.333 0.00 0.00 0.00 2.24
78 79 4.048970 TGAACTCCTAGGCTAACTCACT 57.951 45.455 2.96 0.00 0.00 3.41
79 80 5.188988 TGAACTCCTAGGCTAACTCACTA 57.811 43.478 2.96 0.00 0.00 2.74
81 82 6.907961 TGAACTCCTAGGCTAACTCACTATA 58.092 40.000 2.96 0.00 0.00 1.31
98 99 7.176865 ACTCACTATACATACATGATACCGCTT 59.823 37.037 0.00 0.00 0.00 4.68
193 200 2.050836 AACGCACCCACATCCAGTCA 62.051 55.000 0.00 0.00 0.00 3.41
224 231 1.229209 ACCTCCACATCCACTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
363 370 0.033601 TCCGCCTTGGCAATAACCAT 60.034 50.000 12.45 0.00 40.13 3.55
460 467 1.372499 GGCGTGCAGAGTGACGTTA 60.372 57.895 0.00 0.00 37.89 3.18
467 474 2.121786 GCAGAGTGACGTTAAACGACA 58.878 47.619 0.00 0.00 46.05 4.35
528 547 2.437413 GGGTTCCATGGAGAACTTGAC 58.563 52.381 15.53 8.24 44.56 3.18
550 569 2.132996 CCCAACAAACTGCAGGCCA 61.133 57.895 19.93 0.00 0.00 5.36
605 624 0.034896 GGCGAGGAAGGTGAACAAGA 59.965 55.000 0.00 0.00 0.00 3.02
610 629 1.344763 AGGAAGGTGAACAAGACGAGG 59.655 52.381 0.00 0.00 0.00 4.63
711 736 4.243008 TTGCGACGAGGCCAACCA 62.243 61.111 5.01 0.00 39.06 3.67
811 872 4.820716 GTCTCCGTGTAGTCCTGTGTATAT 59.179 45.833 0.00 0.00 0.00 0.86
812 873 5.994054 GTCTCCGTGTAGTCCTGTGTATATA 59.006 44.000 0.00 0.00 0.00 0.86
893 961 3.632333 TGAACACCGGAGATAGTCATCT 58.368 45.455 9.46 0.00 44.51 2.90
894 962 3.381590 TGAACACCGGAGATAGTCATCTG 59.618 47.826 9.46 0.00 41.78 2.90
895 963 3.298686 ACACCGGAGATAGTCATCTGA 57.701 47.619 9.46 0.00 41.78 3.27
897 965 4.219115 ACACCGGAGATAGTCATCTGATT 58.781 43.478 9.46 0.00 41.78 2.57
900 1018 3.119673 CCGGAGATAGTCATCTGATTCCG 60.120 52.174 14.61 14.61 41.78 4.30
907 1025 9.352784 GAGATAGTCATCTGATTCCGAATAAAG 57.647 37.037 0.00 0.00 41.78 1.85
909 1027 9.134734 GATAGTCATCTGATTCCGAATAAAGAC 57.865 37.037 7.74 6.08 0.00 3.01
1008 1160 2.658285 CGTACGTACATCATGGTAGGC 58.342 52.381 24.50 0.00 33.58 3.93
1014 1166 1.414158 ACATCATGGTAGGCGCTAGT 58.586 50.000 7.64 0.00 0.00 2.57
1050 1202 0.590230 CGACGATGAGGAGAAGCGAC 60.590 60.000 0.00 0.00 0.00 5.19
1086 1238 2.047655 TTCATGGCCGTCACCGTC 60.048 61.111 0.00 0.00 0.00 4.79
1155 1307 1.149148 GTTTCTCCGTCAAGCTCACC 58.851 55.000 0.00 0.00 0.00 4.02
1313 1465 4.802051 CGTGGTGCTGGGATGGGG 62.802 72.222 0.00 0.00 0.00 4.96
1422 1574 4.477975 CGACGTCGCCTGGACTCC 62.478 72.222 26.59 0.00 43.79 3.85
1434 1586 2.202544 GACTCCGAGCTGCTCACG 60.203 66.667 27.46 17.16 0.00 4.35
1598 1752 1.091771 ACACGCAGATGTATGCAGCC 61.092 55.000 0.00 0.00 46.87 4.85
1600 1754 1.524393 CGCAGATGTATGCAGCCCA 60.524 57.895 0.00 0.00 46.87 5.36
1616 1771 2.849880 CCCAATAAGGCATGTGTTCG 57.150 50.000 0.00 0.00 35.39 3.95
1628 1783 0.528017 TGTGTTCGGCTCTAGCTCTG 59.472 55.000 1.39 0.00 41.70 3.35
1632 1787 1.749634 GTTCGGCTCTAGCTCTGGTTA 59.250 52.381 1.39 0.00 41.70 2.85
1651 1810 9.807649 TCTGGTTATTTTTAGGTCTTATCGTAC 57.192 33.333 0.00 0.00 0.00 3.67
1655 1814 9.254133 GTTATTTTTAGGTCTTATCGTACTCCC 57.746 37.037 0.00 0.00 0.00 4.30
1657 1816 7.486407 TTTTTAGGTCTTATCGTACTCCCTT 57.514 36.000 0.00 0.00 0.00 3.95
1658 1817 6.705863 TTTAGGTCTTATCGTACTCCCTTC 57.294 41.667 0.00 0.00 0.00 3.46
1686 1845 8.491605 TTTAAAATGTAAGACGGCTTTTTACG 57.508 30.769 9.87 0.00 35.56 3.18
1692 1851 6.442952 TGTAAGACGGCTTTTTACGTTAGTA 58.557 36.000 9.87 0.00 44.24 1.82
1695 1854 9.072294 GTAAGACGGCTTTTTACGTTAGTATAA 57.928 33.333 9.87 0.00 44.24 0.98
1697 1856 8.123445 AGACGGCTTTTTACGTTAGTATAATG 57.877 34.615 0.00 0.00 44.24 1.90
1699 1858 8.255394 ACGGCTTTTTACGTTAGTATAATGTT 57.745 30.769 0.00 0.00 40.99 2.71
1727 1886 3.299340 TTGAGACGGAGAAAGTAGCAC 57.701 47.619 0.00 0.00 0.00 4.40
1730 1889 4.014406 TGAGACGGAGAAAGTAGCACATA 58.986 43.478 0.00 0.00 0.00 2.29
1732 1891 5.127194 TGAGACGGAGAAAGTAGCACATAAT 59.873 40.000 0.00 0.00 0.00 1.28
1734 1893 6.407202 AGACGGAGAAAGTAGCACATAATTT 58.593 36.000 0.00 0.00 34.50 1.82
1735 1894 6.879458 AGACGGAGAAAGTAGCACATAATTTT 59.121 34.615 0.00 0.00 32.07 1.82
1736 1895 8.038944 AGACGGAGAAAGTAGCACATAATTTTA 58.961 33.333 0.00 0.00 32.07 1.52
1737 1896 8.556213 ACGGAGAAAGTAGCACATAATTTTAA 57.444 30.769 0.00 0.00 32.07 1.52
1832 1991 0.972983 CAGGAGGGACACGTCATCCT 60.973 60.000 14.33 14.33 43.71 3.24
1928 2092 0.114954 TTTTTCCCTGCTCTGCCCAT 59.885 50.000 0.00 0.00 0.00 4.00
1930 2094 1.792757 TTTCCCTGCTCTGCCCATGT 61.793 55.000 0.00 0.00 0.00 3.21
1951 2115 1.067669 CGCTGCTTCTGCCTATCTACA 59.932 52.381 0.00 0.00 38.71 2.74
1970 2134 3.411446 ACATTTTCTCAGACGCCATTGA 58.589 40.909 0.00 0.00 0.00 2.57
1979 2143 2.862536 CAGACGCCATTGATGTAGAGTG 59.137 50.000 0.00 0.00 0.00 3.51
1980 2144 1.594862 GACGCCATTGATGTAGAGTGC 59.405 52.381 0.00 0.00 0.00 4.40
1982 2146 1.596260 CGCCATTGATGTAGAGTGCTG 59.404 52.381 0.00 0.00 0.00 4.41
1989 2156 0.686441 ATGTAGAGTGCTGCGGGGTA 60.686 55.000 0.00 0.00 0.00 3.69
2060 2230 2.203308 AGTTGCTGCTGCTGCACT 60.203 55.556 29.84 24.88 45.31 4.40
2133 2304 2.024305 CACCGGCGCTACTACGAG 59.976 66.667 7.64 0.00 34.06 4.18
2134 2305 3.207669 ACCGGCGCTACTACGAGG 61.208 66.667 7.64 0.88 38.04 4.63
2203 2375 3.733988 CGAGCTCGAGGCATGTTACTTAA 60.734 47.826 32.06 0.00 44.79 1.85
2209 2381 5.790593 TCGAGGCATGTTACTTAAAACTCT 58.209 37.500 0.00 0.00 0.00 3.24
2404 2580 7.112984 GTCGTTTGTTACATCCTTTTTCATGAC 59.887 37.037 0.00 0.00 0.00 3.06
2405 2581 6.915300 CGTTTGTTACATCCTTTTTCATGACA 59.085 34.615 0.00 0.00 0.00 3.58
2406 2582 7.096640 CGTTTGTTACATCCTTTTTCATGACAC 60.097 37.037 0.00 0.00 0.00 3.67
2407 2583 7.581213 TTGTTACATCCTTTTTCATGACACT 57.419 32.000 0.00 0.00 0.00 3.55
2408 2584 8.684386 TTGTTACATCCTTTTTCATGACACTA 57.316 30.769 0.00 0.00 0.00 2.74
2409 2585 8.862325 TGTTACATCCTTTTTCATGACACTAT 57.138 30.769 0.00 0.00 0.00 2.12
2410 2586 9.295825 TGTTACATCCTTTTTCATGACACTATT 57.704 29.630 0.00 0.00 0.00 1.73
2413 2589 8.511604 ACATCCTTTTTCATGACACTATTAGG 57.488 34.615 0.00 0.00 0.00 2.69
2414 2590 8.328758 ACATCCTTTTTCATGACACTATTAGGA 58.671 33.333 0.00 1.85 33.07 2.94
2415 2591 9.177608 CATCCTTTTTCATGACACTATTAGGAA 57.822 33.333 0.00 0.00 32.36 3.36
2416 2592 9.753674 ATCCTTTTTCATGACACTATTAGGAAA 57.246 29.630 0.00 0.00 32.36 3.13
2417 2593 9.581289 TCCTTTTTCATGACACTATTAGGAAAA 57.419 29.630 0.00 0.00 32.74 2.29
2418 2594 9.846248 CCTTTTTCATGACACTATTAGGAAAAG 57.154 33.333 12.04 12.04 35.15 2.27
2419 2595 9.846248 CTTTTTCATGACACTATTAGGAAAAGG 57.154 33.333 11.48 0.00 35.15 3.11
2420 2596 7.938140 TTTCATGACACTATTAGGAAAAGGG 57.062 36.000 0.00 0.00 0.00 3.95
2421 2597 5.437060 TCATGACACTATTAGGAAAAGGGC 58.563 41.667 0.00 0.00 0.00 5.19
2422 2598 5.191722 TCATGACACTATTAGGAAAAGGGCT 59.808 40.000 0.00 0.00 0.00 5.19
2423 2599 6.385759 TCATGACACTATTAGGAAAAGGGCTA 59.614 38.462 0.00 0.00 0.00 3.93
2424 2600 6.824958 TGACACTATTAGGAAAAGGGCTAT 57.175 37.500 0.00 0.00 0.00 2.97
2425 2601 7.924358 TGACACTATTAGGAAAAGGGCTATA 57.076 36.000 0.00 0.00 0.00 1.31
2426 2602 7.963532 TGACACTATTAGGAAAAGGGCTATAG 58.036 38.462 0.00 0.00 0.00 1.31
2427 2603 7.567622 TGACACTATTAGGAAAAGGGCTATAGT 59.432 37.037 0.84 0.00 0.00 2.12
2428 2604 9.086758 GACACTATTAGGAAAAGGGCTATAGTA 57.913 37.037 0.84 0.00 0.00 1.82
2429 2605 9.443365 ACACTATTAGGAAAAGGGCTATAGTAA 57.557 33.333 0.84 0.00 0.00 2.24
2432 2608 9.892130 CTATTAGGAAAAGGGCTATAGTAATGG 57.108 37.037 0.84 0.00 0.00 3.16
2433 2609 4.986783 AGGAAAAGGGCTATAGTAATGGC 58.013 43.478 0.84 0.00 38.79 4.40
2434 2610 3.751698 GGAAAAGGGCTATAGTAATGGCG 59.248 47.826 0.84 0.00 40.33 5.69
2438 2614 2.457366 GGCTATAGTAATGGCGCACT 57.543 50.000 10.83 6.53 40.33 4.40
2439 2615 3.587797 GGCTATAGTAATGGCGCACTA 57.412 47.619 10.83 8.93 40.33 2.74
2440 2616 4.124851 GGCTATAGTAATGGCGCACTAT 57.875 45.455 18.60 18.60 40.33 2.12
2441 2617 5.258456 GGCTATAGTAATGGCGCACTATA 57.742 43.478 18.79 18.79 40.33 1.31
2442 2618 5.041940 GGCTATAGTAATGGCGCACTATAC 58.958 45.833 16.96 14.13 40.33 1.47
2443 2619 5.393787 GGCTATAGTAATGGCGCACTATACA 60.394 44.000 16.96 3.13 40.33 2.29
2444 2620 5.515626 GCTATAGTAATGGCGCACTATACAC 59.484 44.000 16.96 10.93 38.57 2.90
2445 2621 3.812156 AGTAATGGCGCACTATACACA 57.188 42.857 10.83 0.00 0.00 3.72
2446 2622 4.336889 AGTAATGGCGCACTATACACAT 57.663 40.909 10.83 0.00 0.00 3.21
2447 2623 5.462530 AGTAATGGCGCACTATACACATA 57.537 39.130 10.83 0.00 0.00 2.29
2448 2624 5.470368 AGTAATGGCGCACTATACACATAG 58.530 41.667 10.83 0.00 40.14 2.23
2449 2625 4.336889 AATGGCGCACTATACACATAGT 57.663 40.909 10.83 0.00 46.80 2.12
2450 2626 5.462530 AATGGCGCACTATACACATAGTA 57.537 39.130 10.83 0.00 44.55 1.82
2451 2627 4.922471 TGGCGCACTATACACATAGTAA 57.078 40.909 10.83 0.00 44.55 2.24
2452 2628 5.462530 TGGCGCACTATACACATAGTAAT 57.537 39.130 10.83 0.00 44.55 1.89
2453 2629 5.227152 TGGCGCACTATACACATAGTAATG 58.773 41.667 10.83 0.00 44.55 1.90
2454 2630 4.625742 GGCGCACTATACACATAGTAATGG 59.374 45.833 10.83 0.00 44.55 3.16
2455 2631 5.227908 GCGCACTATACACATAGTAATGGT 58.772 41.667 0.30 0.00 44.55 3.55
2456 2632 5.118664 GCGCACTATACACATAGTAATGGTG 59.881 44.000 0.30 0.00 44.55 4.17
2457 2633 5.118664 CGCACTATACACATAGTAATGGTGC 59.881 44.000 16.27 16.27 44.55 5.01
2458 2634 5.989168 GCACTATACACATAGTAATGGTGCA 59.011 40.000 19.04 0.00 44.55 4.57
2459 2635 6.073765 GCACTATACACATAGTAATGGTGCAC 60.074 42.308 8.80 8.80 44.55 4.57
2460 2636 7.210174 CACTATACACATAGTAATGGTGCACT 58.790 38.462 17.98 0.00 44.55 4.40
2461 2637 7.710907 CACTATACACATAGTAATGGTGCACTT 59.289 37.037 17.98 6.69 44.55 3.16
2462 2638 8.265055 ACTATACACATAGTAATGGTGCACTTT 58.735 33.333 17.98 13.17 44.53 2.66
2463 2639 5.627499 ACACATAGTAATGGTGCACTTTG 57.373 39.130 17.98 3.71 37.43 2.77
2464 2640 5.070001 ACACATAGTAATGGTGCACTTTGT 58.930 37.500 17.98 4.36 37.41 2.83
2465 2641 6.234920 ACACATAGTAATGGTGCACTTTGTA 58.765 36.000 17.98 7.83 35.59 2.41
2466 2642 6.148811 ACACATAGTAATGGTGCACTTTGTAC 59.851 38.462 17.98 13.34 35.59 2.90
2467 2643 6.148645 CACATAGTAATGGTGCACTTTGTACA 59.851 38.462 17.98 5.15 35.59 2.90
2468 2644 6.371548 ACATAGTAATGGTGCACTTTGTACAG 59.628 38.462 17.98 10.14 35.88 2.74
2469 2645 4.072131 AGTAATGGTGCACTTTGTACAGG 58.928 43.478 17.98 0.00 34.53 4.00
2470 2646 2.656947 ATGGTGCACTTTGTACAGGT 57.343 45.000 17.98 0.00 34.53 4.00
2471 2647 1.674359 TGGTGCACTTTGTACAGGTG 58.326 50.000 17.98 19.91 34.53 4.00
2474 2650 1.082104 GCACTTTGTACAGGTGCGC 60.082 57.895 27.61 14.74 44.91 6.09
2475 2651 1.574428 CACTTTGTACAGGTGCGCC 59.426 57.895 8.71 8.71 0.00 6.53
2476 2652 1.147376 ACTTTGTACAGGTGCGCCA 59.853 52.632 20.59 0.00 37.19 5.69
2477 2653 0.250727 ACTTTGTACAGGTGCGCCAT 60.251 50.000 20.59 8.81 37.19 4.40
2478 2654 0.881118 CTTTGTACAGGTGCGCCATT 59.119 50.000 20.59 7.01 37.19 3.16
2479 2655 2.080693 CTTTGTACAGGTGCGCCATTA 58.919 47.619 20.59 5.89 37.19 1.90
2480 2656 1.444836 TTGTACAGGTGCGCCATTAC 58.555 50.000 20.59 18.19 37.19 1.89
2481 2657 0.611200 TGTACAGGTGCGCCATTACT 59.389 50.000 20.59 0.00 37.19 2.24
2482 2658 1.826096 TGTACAGGTGCGCCATTACTA 59.174 47.619 20.59 7.12 37.19 1.82
2483 2659 2.432874 TGTACAGGTGCGCCATTACTAT 59.567 45.455 20.59 0.00 37.19 2.12
2484 2660 1.953559 ACAGGTGCGCCATTACTATG 58.046 50.000 20.59 8.54 37.19 2.23
2485 2661 1.209504 ACAGGTGCGCCATTACTATGT 59.790 47.619 20.59 9.25 37.19 2.29
2486 2662 1.867233 CAGGTGCGCCATTACTATGTC 59.133 52.381 20.59 0.00 37.19 3.06
2487 2663 1.484653 AGGTGCGCCATTACTATGTCA 59.515 47.619 20.59 0.00 37.19 3.58
2488 2664 2.093181 AGGTGCGCCATTACTATGTCAA 60.093 45.455 20.59 0.00 37.19 3.18
2489 2665 2.031683 GGTGCGCCATTACTATGTCAAC 59.968 50.000 12.58 0.00 34.09 3.18
2490 2666 2.936498 GTGCGCCATTACTATGTCAACT 59.064 45.455 4.18 0.00 0.00 3.16
2491 2667 4.116961 GTGCGCCATTACTATGTCAACTA 58.883 43.478 4.18 0.00 0.00 2.24
2492 2668 4.209288 GTGCGCCATTACTATGTCAACTAG 59.791 45.833 4.18 0.00 0.00 2.57
2493 2669 4.142026 TGCGCCATTACTATGTCAACTAGT 60.142 41.667 4.18 0.00 34.01 2.57
2494 2670 5.068067 TGCGCCATTACTATGTCAACTAGTA 59.932 40.000 4.18 0.00 31.96 1.82
2495 2671 5.981315 GCGCCATTACTATGTCAACTAGTAA 59.019 40.000 0.00 8.01 42.67 2.24
2496 2672 6.645415 GCGCCATTACTATGTCAACTAGTAAT 59.355 38.462 10.95 10.95 46.13 1.89
2501 2677 4.369182 ACTATGTCAACTAGTAATGGCGC 58.631 43.478 0.00 0.00 0.00 6.53
2502 2678 2.753055 TGTCAACTAGTAATGGCGCA 57.247 45.000 10.83 0.00 0.00 6.09
2503 2679 2.343101 TGTCAACTAGTAATGGCGCAC 58.657 47.619 10.83 0.00 0.00 5.34
2504 2680 2.028476 TGTCAACTAGTAATGGCGCACT 60.028 45.455 10.83 6.53 0.00 4.40
2505 2681 3.193903 TGTCAACTAGTAATGGCGCACTA 59.806 43.478 10.83 7.49 0.00 2.74
2506 2682 4.142026 TGTCAACTAGTAATGGCGCACTAT 60.142 41.667 10.83 0.00 0.00 2.12
2507 2683 5.068067 TGTCAACTAGTAATGGCGCACTATA 59.932 40.000 10.83 0.00 0.00 1.31
2508 2684 5.401674 GTCAACTAGTAATGGCGCACTATAC 59.598 44.000 10.83 6.75 0.00 1.47
2509 2685 4.516365 ACTAGTAATGGCGCACTATACC 57.484 45.455 10.83 0.00 0.00 2.73
2510 2686 2.833631 AGTAATGGCGCACTATACCC 57.166 50.000 10.83 0.00 0.00 3.69
2511 2687 2.326428 AGTAATGGCGCACTATACCCT 58.674 47.619 10.83 0.00 0.00 4.34
2512 2688 2.037251 AGTAATGGCGCACTATACCCTG 59.963 50.000 10.83 0.00 0.00 4.45
2513 2689 0.108585 AATGGCGCACTATACCCTGG 59.891 55.000 10.83 0.00 0.00 4.45
2514 2690 1.054406 ATGGCGCACTATACCCTGGT 61.054 55.000 10.83 0.00 0.00 4.00
2515 2691 1.227556 GGCGCACTATACCCTGGTG 60.228 63.158 10.83 0.00 39.24 4.17
2518 2694 4.438346 CACTATACCCTGGTGCGC 57.562 61.111 0.00 0.00 28.87 6.09
2519 2695 1.227556 CACTATACCCTGGTGCGCC 60.228 63.158 10.11 10.11 28.87 6.53
2520 2696 1.687840 ACTATACCCTGGTGCGCCA 60.688 57.895 19.93 19.93 43.73 5.69
2521 2697 1.227556 CTATACCCTGGTGCGCCAC 60.228 63.158 16.89 2.79 40.46 5.01
2522 2698 1.686325 CTATACCCTGGTGCGCCACT 61.686 60.000 16.89 3.10 40.46 4.00
2523 2699 1.966901 TATACCCTGGTGCGCCACTG 61.967 60.000 16.89 11.85 40.46 3.66
2526 2702 4.393155 CCTGGTGCGCCACTGCTA 62.393 66.667 16.89 0.00 40.46 3.49
2527 2703 2.358615 CTGGTGCGCCACTGCTAA 60.359 61.111 16.89 0.00 40.46 3.09
2528 2704 2.668212 TGGTGCGCCACTGCTAAC 60.668 61.111 16.89 0.00 40.46 2.34
2529 2705 2.668212 GGTGCGCCACTGCTAACA 60.668 61.111 12.58 0.00 34.40 2.41
2530 2706 2.258013 GGTGCGCCACTGCTAACAA 61.258 57.895 12.58 0.00 34.40 2.83
2531 2707 1.082104 GTGCGCCACTGCTAACAAC 60.082 57.895 4.18 0.00 35.36 3.32
2532 2708 1.227823 TGCGCCACTGCTAACAACT 60.228 52.632 4.18 0.00 35.36 3.16
2533 2709 1.227999 TGCGCCACTGCTAACAACTC 61.228 55.000 4.18 0.00 35.36 3.01
2534 2710 1.227999 GCGCCACTGCTAACAACTCA 61.228 55.000 0.00 0.00 34.43 3.41
2535 2711 1.442769 CGCCACTGCTAACAACTCAT 58.557 50.000 0.00 0.00 34.43 2.90
2536 2712 2.616960 CGCCACTGCTAACAACTCATA 58.383 47.619 0.00 0.00 34.43 2.15
2537 2713 3.000041 CGCCACTGCTAACAACTCATAA 59.000 45.455 0.00 0.00 34.43 1.90
2538 2714 3.181520 CGCCACTGCTAACAACTCATAAC 60.182 47.826 0.00 0.00 34.43 1.89
2539 2715 3.127030 GCCACTGCTAACAACTCATAACC 59.873 47.826 0.00 0.00 33.53 2.85
2540 2716 4.323417 CCACTGCTAACAACTCATAACCA 58.677 43.478 0.00 0.00 0.00 3.67
2541 2717 4.759693 CCACTGCTAACAACTCATAACCAA 59.240 41.667 0.00 0.00 0.00 3.67
2542 2718 5.240623 CCACTGCTAACAACTCATAACCAAA 59.759 40.000 0.00 0.00 0.00 3.28
2543 2719 6.071952 CCACTGCTAACAACTCATAACCAAAT 60.072 38.462 0.00 0.00 0.00 2.32
2544 2720 6.803320 CACTGCTAACAACTCATAACCAAATG 59.197 38.462 0.00 0.00 0.00 2.32
2545 2721 5.708948 TGCTAACAACTCATAACCAAATGC 58.291 37.500 0.00 0.00 0.00 3.56
2546 2722 5.242615 TGCTAACAACTCATAACCAAATGCA 59.757 36.000 0.00 0.00 0.00 3.96
2547 2723 5.572896 GCTAACAACTCATAACCAAATGCAC 59.427 40.000 0.00 0.00 0.00 4.57
2548 2724 4.519540 ACAACTCATAACCAAATGCACC 57.480 40.909 0.00 0.00 0.00 5.01
2549 2725 3.258123 ACAACTCATAACCAAATGCACCC 59.742 43.478 0.00 0.00 0.00 4.61
2550 2726 2.456577 ACTCATAACCAAATGCACCCC 58.543 47.619 0.00 0.00 0.00 4.95
2551 2727 1.756538 CTCATAACCAAATGCACCCCC 59.243 52.381 0.00 0.00 0.00 5.40
2569 2745 4.029809 CCTCCCCGACCGCCTTTT 62.030 66.667 0.00 0.00 0.00 2.27
2570 2746 2.436115 CTCCCCGACCGCCTTTTC 60.436 66.667 0.00 0.00 0.00 2.29
2571 2747 3.243053 TCCCCGACCGCCTTTTCA 61.243 61.111 0.00 0.00 0.00 2.69
2572 2748 2.746277 CCCCGACCGCCTTTTCAG 60.746 66.667 0.00 0.00 0.00 3.02
2573 2749 2.032071 CCCGACCGCCTTTTCAGT 59.968 61.111 0.00 0.00 0.00 3.41
2574 2750 1.599797 CCCGACCGCCTTTTCAGTT 60.600 57.895 0.00 0.00 0.00 3.16
2575 2751 1.170290 CCCGACCGCCTTTTCAGTTT 61.170 55.000 0.00 0.00 0.00 2.66
2576 2752 1.515081 CCGACCGCCTTTTCAGTTTA 58.485 50.000 0.00 0.00 0.00 2.01
2577 2753 1.874872 CCGACCGCCTTTTCAGTTTAA 59.125 47.619 0.00 0.00 0.00 1.52
2578 2754 2.291190 CCGACCGCCTTTTCAGTTTAAA 59.709 45.455 0.00 0.00 0.00 1.52
2579 2755 3.243134 CCGACCGCCTTTTCAGTTTAAAA 60.243 43.478 0.00 0.00 0.00 1.52
2580 2756 4.352887 CGACCGCCTTTTCAGTTTAAAAA 58.647 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.318107 CTTTTCGCTGCTGGTTGGTG 60.318 55.000 0.00 0.00 0.00 4.17
5 6 2.639286 CGCTTTTCGCTGCTGGTT 59.361 55.556 0.00 0.00 36.13 3.67
14 15 0.041312 CGGATTATGGGCGCTTTTCG 60.041 55.000 7.64 0.00 42.12 3.46
15 16 1.021968 ACGGATTATGGGCGCTTTTC 58.978 50.000 7.64 0.00 0.00 2.29
16 17 1.470051 AACGGATTATGGGCGCTTTT 58.530 45.000 7.64 0.00 0.00 2.27
17 18 1.470051 AAACGGATTATGGGCGCTTT 58.530 45.000 7.64 0.00 0.00 3.51
18 19 2.158871 TCTAAACGGATTATGGGCGCTT 60.159 45.455 7.64 0.00 0.00 4.68
19 20 1.414919 TCTAAACGGATTATGGGCGCT 59.585 47.619 7.64 0.00 0.00 5.92
20 21 1.873698 TCTAAACGGATTATGGGCGC 58.126 50.000 0.00 0.00 0.00 6.53
21 22 6.737254 ATATTTCTAAACGGATTATGGGCG 57.263 37.500 0.00 0.00 0.00 6.13
22 23 9.227777 AGTTATATTTCTAAACGGATTATGGGC 57.772 33.333 0.00 0.00 0.00 5.36
44 45 9.435570 AGCCTAGGAGTTCATTATTCTTAGTTA 57.564 33.333 14.75 0.00 0.00 2.24
45 46 8.325477 AGCCTAGGAGTTCATTATTCTTAGTT 57.675 34.615 14.75 0.00 0.00 2.24
46 47 7.922699 AGCCTAGGAGTTCATTATTCTTAGT 57.077 36.000 14.75 0.00 0.00 2.24
47 48 9.699703 GTTAGCCTAGGAGTTCATTATTCTTAG 57.300 37.037 14.75 0.00 0.00 2.18
48 49 9.435570 AGTTAGCCTAGGAGTTCATTATTCTTA 57.564 33.333 14.75 0.00 0.00 2.10
49 50 8.325477 AGTTAGCCTAGGAGTTCATTATTCTT 57.675 34.615 14.75 0.00 0.00 2.52
50 51 7.565398 TGAGTTAGCCTAGGAGTTCATTATTCT 59.435 37.037 14.75 0.00 0.00 2.40
51 52 7.654116 GTGAGTTAGCCTAGGAGTTCATTATTC 59.346 40.741 14.75 0.00 0.00 1.75
52 53 7.345914 AGTGAGTTAGCCTAGGAGTTCATTATT 59.654 37.037 14.75 0.00 0.00 1.40
53 54 6.841755 AGTGAGTTAGCCTAGGAGTTCATTAT 59.158 38.462 14.75 0.00 0.00 1.28
54 55 6.195700 AGTGAGTTAGCCTAGGAGTTCATTA 58.804 40.000 14.75 0.00 0.00 1.90
55 56 5.026790 AGTGAGTTAGCCTAGGAGTTCATT 58.973 41.667 14.75 2.44 0.00 2.57
56 57 4.615513 AGTGAGTTAGCCTAGGAGTTCAT 58.384 43.478 14.75 0.00 0.00 2.57
59 60 6.670617 TGTATAGTGAGTTAGCCTAGGAGTT 58.329 40.000 14.75 0.00 0.00 3.01
78 79 9.016438 TGAGTTAAGCGGTATCATGTATGTATA 57.984 33.333 0.00 0.00 0.00 1.47
79 80 7.813148 GTGAGTTAAGCGGTATCATGTATGTAT 59.187 37.037 0.00 0.00 0.00 2.29
81 82 5.983720 GTGAGTTAAGCGGTATCATGTATGT 59.016 40.000 0.00 0.00 0.00 2.29
98 99 6.833041 TCAGTTTTATTCCACCAGTGAGTTA 58.167 36.000 0.00 0.00 0.00 2.24
297 304 4.077184 GGGACACCGTGATCGCCA 62.077 66.667 5.28 0.00 35.54 5.69
343 350 0.033601 TGGTTATTGCCAAGGCGGAT 60.034 50.000 6.60 5.87 45.51 4.18
367 374 1.258445 CCGTGGAAGTGGCCTACTCT 61.258 60.000 3.32 0.00 39.18 3.24
460 467 4.307908 GCAACGCCGCTGTCGTTT 62.308 61.111 7.39 0.00 46.47 3.60
528 547 1.181098 CCTGCAGTTTGTTGGGAGGG 61.181 60.000 13.81 0.00 36.59 4.30
550 569 0.816825 CCGGTTGCATGCTAGCTCAT 60.817 55.000 24.74 0.00 34.99 2.90
605 624 1.202582 CGACAACTGGAAGATCCTCGT 59.797 52.381 0.00 0.00 37.46 4.18
610 629 3.369451 GCTTCTTCGACAACTGGAAGATC 59.631 47.826 4.52 0.00 45.69 2.75
811 872 2.507484 TCGGACTCTTTCCTCGTTGTA 58.493 47.619 0.00 0.00 43.25 2.41
812 873 1.325355 TCGGACTCTTTCCTCGTTGT 58.675 50.000 0.00 0.00 43.25 3.32
868 931 3.280295 GACTATCTCCGGTGTTCAGAGA 58.720 50.000 0.00 0.00 40.73 3.10
900 1018 3.973657 TCGCTGGTATCCGTCTTTATTC 58.026 45.455 0.00 0.00 0.00 1.75
907 1025 0.110147 CTCGATCGCTGGTATCCGTC 60.110 60.000 11.09 0.00 0.00 4.79
909 1027 1.442857 GCTCGATCGCTGGTATCCG 60.443 63.158 11.09 0.00 0.00 4.18
962 1111 2.555782 GCGCGCAATCAGACAACA 59.444 55.556 29.10 0.00 0.00 3.33
1086 1238 0.670546 ACCCGCAGACAATGAGAACG 60.671 55.000 0.00 0.00 0.00 3.95
1248 1400 1.194781 TCTCCCTGCAGGTCTTGACC 61.195 60.000 30.63 11.59 36.75 4.02
1493 1646 2.930562 AGTCCTGGCACTCCCACC 60.931 66.667 0.00 0.00 39.18 4.61
1494 1647 2.348998 CAGTCCTGGCACTCCCAC 59.651 66.667 0.00 0.00 39.18 4.61
1520 1673 2.281070 ACACTGCCAAGCACTCCG 60.281 61.111 0.00 0.00 33.79 4.63
1577 1730 1.933181 GCTGCATACATCTGCGTGTTA 59.067 47.619 0.00 0.00 45.30 2.41
1598 1752 1.202290 GCCGAACACATGCCTTATTGG 60.202 52.381 0.00 0.00 39.35 3.16
1600 1754 2.017049 GAGCCGAACACATGCCTTATT 58.983 47.619 0.00 0.00 0.00 1.40
1615 1770 3.460857 AAATAACCAGAGCTAGAGCCG 57.539 47.619 0.00 0.00 43.38 5.52
1616 1771 5.760743 CCTAAAAATAACCAGAGCTAGAGCC 59.239 44.000 0.00 0.00 43.38 4.70
1628 1783 9.254133 GGAGTACGATAAGACCTAAAAATAACC 57.746 37.037 0.00 0.00 0.00 2.85
1632 1787 7.672122 AGGGAGTACGATAAGACCTAAAAAT 57.328 36.000 0.00 0.00 0.00 1.82
1651 1810 7.013529 CGTCTTACATTTTAAAACGAAGGGAG 58.986 38.462 1.97 0.00 0.00 4.30
1655 1814 6.368213 AGCCGTCTTACATTTTAAAACGAAG 58.632 36.000 1.97 7.27 0.00 3.79
1657 1816 5.927954 AGCCGTCTTACATTTTAAAACGA 57.072 34.783 1.97 0.00 0.00 3.85
1658 1817 6.979701 AAAGCCGTCTTACATTTTAAAACG 57.020 33.333 1.97 0.00 31.02 3.60
1724 1883 9.615295 TCTAAACGTTTCCTTAAAATTATGTGC 57.385 29.630 18.42 0.00 0.00 4.57
1727 1886 9.285770 GGCTCTAAACGTTTCCTTAAAATTATG 57.714 33.333 18.42 0.00 0.00 1.90
1730 1889 6.376177 CGGCTCTAAACGTTTCCTTAAAATT 58.624 36.000 18.42 0.00 0.00 1.82
1732 1891 4.213906 CCGGCTCTAAACGTTTCCTTAAAA 59.786 41.667 18.42 0.00 0.00 1.52
1734 1893 3.328505 CCGGCTCTAAACGTTTCCTTAA 58.671 45.455 18.42 0.00 0.00 1.85
1735 1894 2.354003 CCCGGCTCTAAACGTTTCCTTA 60.354 50.000 18.42 0.00 0.00 2.69
1736 1895 1.609841 CCCGGCTCTAAACGTTTCCTT 60.610 52.381 18.42 0.00 0.00 3.36
1737 1896 0.036671 CCCGGCTCTAAACGTTTCCT 60.037 55.000 18.42 0.00 0.00 3.36
1883 2043 1.202758 GGAGATGTGGTGTGTGGACAA 60.203 52.381 0.00 0.00 32.49 3.18
1920 2084 3.258228 AAGCAGCGACATGGGCAGA 62.258 57.895 12.69 0.00 0.00 4.26
1928 2092 0.179100 GATAGGCAGAAGCAGCGACA 60.179 55.000 0.00 0.00 44.61 4.35
1930 2094 1.338337 GTAGATAGGCAGAAGCAGCGA 59.662 52.381 0.00 0.00 44.61 4.93
1951 2115 4.012374 ACATCAATGGCGTCTGAGAAAAT 58.988 39.130 0.00 0.00 0.00 1.82
1970 2134 0.686441 TACCCCGCAGCACTCTACAT 60.686 55.000 0.00 0.00 0.00 2.29
2039 2208 2.281970 CAGCAGCAGCAACTCCCA 60.282 61.111 3.17 0.00 45.49 4.37
2060 2230 2.203379 CCATGGCGATGGCATCCA 60.203 61.111 21.20 15.50 45.69 3.41
2145 2317 2.435586 GCATGTGAGCTCGCAGGT 60.436 61.111 34.31 18.74 39.94 4.00
2203 2375 7.014615 ACAAACATGGAAGCAAATCTAGAGTTT 59.985 33.333 1.94 0.00 0.00 2.66
2249 2422 5.055812 ACGAAGACGGTGGTAACAAATTAA 58.944 37.500 0.00 0.00 46.47 1.40
2289 2462 4.339872 AAGACATGGCAGCAAAATTTGA 57.660 36.364 10.26 0.00 0.00 2.69
2406 2582 9.892130 CCATTACTATAGCCCTTTTCCTAATAG 57.108 37.037 0.00 0.00 0.00 1.73
2407 2583 8.326529 GCCATTACTATAGCCCTTTTCCTAATA 58.673 37.037 0.00 0.00 0.00 0.98
2408 2584 7.175797 GCCATTACTATAGCCCTTTTCCTAAT 58.824 38.462 0.00 0.00 0.00 1.73
2409 2585 6.540083 GCCATTACTATAGCCCTTTTCCTAA 58.460 40.000 0.00 0.00 0.00 2.69
2410 2586 5.279809 CGCCATTACTATAGCCCTTTTCCTA 60.280 44.000 0.00 0.00 0.00 2.94
2411 2587 4.505039 CGCCATTACTATAGCCCTTTTCCT 60.505 45.833 0.00 0.00 0.00 3.36
2412 2588 3.751698 CGCCATTACTATAGCCCTTTTCC 59.248 47.826 0.00 0.00 0.00 3.13
2413 2589 3.188667 GCGCCATTACTATAGCCCTTTTC 59.811 47.826 0.00 0.00 0.00 2.29
2414 2590 3.146847 GCGCCATTACTATAGCCCTTTT 58.853 45.455 0.00 0.00 0.00 2.27
2415 2591 2.105821 TGCGCCATTACTATAGCCCTTT 59.894 45.455 4.18 0.00 0.00 3.11
2416 2592 1.697432 TGCGCCATTACTATAGCCCTT 59.303 47.619 4.18 0.00 0.00 3.95
2417 2593 1.002087 GTGCGCCATTACTATAGCCCT 59.998 52.381 4.18 0.00 0.00 5.19
2418 2594 1.002087 AGTGCGCCATTACTATAGCCC 59.998 52.381 4.18 0.00 0.00 5.19
2419 2595 2.457366 AGTGCGCCATTACTATAGCC 57.543 50.000 4.18 0.00 0.00 3.93
2420 2596 5.515626 GTGTATAGTGCGCCATTACTATAGC 59.484 44.000 19.86 15.82 40.88 2.97
2421 2597 6.617879 TGTGTATAGTGCGCCATTACTATAG 58.382 40.000 19.86 0.00 40.88 1.31
2422 2598 6.578163 TGTGTATAGTGCGCCATTACTATA 57.422 37.500 16.96 16.96 39.89 1.31
2423 2599 5.462530 TGTGTATAGTGCGCCATTACTAT 57.537 39.130 18.60 18.60 41.57 2.12
2424 2600 4.922471 TGTGTATAGTGCGCCATTACTA 57.078 40.909 4.18 6.34 34.23 1.82
2425 2601 3.812156 TGTGTATAGTGCGCCATTACT 57.188 42.857 4.18 3.74 0.00 2.24
2426 2602 5.227908 ACTATGTGTATAGTGCGCCATTAC 58.772 41.667 4.18 2.35 45.93 1.89
2427 2603 5.462530 ACTATGTGTATAGTGCGCCATTA 57.537 39.130 4.18 0.00 45.93 1.90
2428 2604 4.336889 ACTATGTGTATAGTGCGCCATT 57.663 40.909 4.18 0.00 45.93 3.16
2429 2605 5.462530 TTACTATGTGTATAGTGCGCCAT 57.537 39.130 4.18 0.19 46.80 4.40
2430 2606 4.922471 TTACTATGTGTATAGTGCGCCA 57.078 40.909 4.18 0.00 46.80 5.69
2431 2607 4.625742 CCATTACTATGTGTATAGTGCGCC 59.374 45.833 4.18 0.00 46.80 6.53
2432 2608 5.118664 CACCATTACTATGTGTATAGTGCGC 59.881 44.000 0.00 0.00 46.80 6.09
2433 2609 5.118664 GCACCATTACTATGTGTATAGTGCG 59.881 44.000 9.56 0.00 46.80 5.34
2434 2610 5.989168 TGCACCATTACTATGTGTATAGTGC 59.011 40.000 9.56 0.00 46.80 4.40
2435 2611 7.210174 AGTGCACCATTACTATGTGTATAGTG 58.790 38.462 14.63 0.00 46.80 2.74
2437 2613 8.551205 CAAAGTGCACCATTACTATGTGTATAG 58.449 37.037 14.63 0.00 41.68 1.31
2438 2614 8.044309 ACAAAGTGCACCATTACTATGTGTATA 58.956 33.333 14.63 0.00 0.00 1.47
2439 2615 6.884295 ACAAAGTGCACCATTACTATGTGTAT 59.116 34.615 14.63 0.00 0.00 2.29
2440 2616 6.234920 ACAAAGTGCACCATTACTATGTGTA 58.765 36.000 14.63 0.00 0.00 2.90
2441 2617 5.070001 ACAAAGTGCACCATTACTATGTGT 58.930 37.500 14.63 0.38 0.00 3.72
2442 2618 5.627499 ACAAAGTGCACCATTACTATGTG 57.373 39.130 14.63 0.00 0.00 3.21
2443 2619 6.234920 TGTACAAAGTGCACCATTACTATGT 58.765 36.000 14.63 9.49 0.00 2.29
2444 2620 6.183360 CCTGTACAAAGTGCACCATTACTATG 60.183 42.308 14.63 3.93 0.00 2.23
2445 2621 5.880332 CCTGTACAAAGTGCACCATTACTAT 59.120 40.000 14.63 0.00 0.00 2.12
2446 2622 5.221762 ACCTGTACAAAGTGCACCATTACTA 60.222 40.000 14.63 0.00 0.00 1.82
2447 2623 4.072131 CCTGTACAAAGTGCACCATTACT 58.928 43.478 14.63 0.91 0.00 2.24
2448 2624 3.818773 ACCTGTACAAAGTGCACCATTAC 59.181 43.478 14.63 10.49 0.00 1.89
2449 2625 3.818210 CACCTGTACAAAGTGCACCATTA 59.182 43.478 14.63 0.00 0.00 1.90
2450 2626 2.622942 CACCTGTACAAAGTGCACCATT 59.377 45.455 14.63 6.43 0.00 3.16
2451 2627 2.229792 CACCTGTACAAAGTGCACCAT 58.770 47.619 14.63 0.00 0.00 3.55
2452 2628 1.674359 CACCTGTACAAAGTGCACCA 58.326 50.000 14.63 1.78 0.00 4.17
2457 2633 1.163420 TGGCGCACCTGTACAAAGTG 61.163 55.000 10.83 17.42 36.63 3.16
2458 2634 0.250727 ATGGCGCACCTGTACAAAGT 60.251 50.000 10.83 0.00 36.63 2.66
2459 2635 0.881118 AATGGCGCACCTGTACAAAG 59.119 50.000 10.83 0.00 36.63 2.77
2460 2636 1.807742 GTAATGGCGCACCTGTACAAA 59.192 47.619 10.83 0.00 36.63 2.83
2461 2637 1.002659 AGTAATGGCGCACCTGTACAA 59.997 47.619 10.83 0.00 36.63 2.41
2462 2638 0.611200 AGTAATGGCGCACCTGTACA 59.389 50.000 10.83 0.00 36.63 2.90
2463 2639 2.589798 TAGTAATGGCGCACCTGTAC 57.410 50.000 10.83 3.77 36.63 2.90
2464 2640 2.432874 ACATAGTAATGGCGCACCTGTA 59.567 45.455 10.83 0.00 37.43 2.74
2465 2641 1.209504 ACATAGTAATGGCGCACCTGT 59.790 47.619 10.83 2.70 37.43 4.00
2466 2642 1.867233 GACATAGTAATGGCGCACCTG 59.133 52.381 10.83 2.04 37.43 4.00
2467 2643 1.484653 TGACATAGTAATGGCGCACCT 59.515 47.619 10.83 0.00 44.94 4.00
2468 2644 1.948104 TGACATAGTAATGGCGCACC 58.052 50.000 10.83 0.00 44.94 5.01
2469 2645 2.936498 AGTTGACATAGTAATGGCGCAC 59.064 45.455 10.83 0.00 44.94 5.34
2470 2646 3.260475 AGTTGACATAGTAATGGCGCA 57.740 42.857 10.83 0.00 44.94 6.09
2471 2647 4.369182 ACTAGTTGACATAGTAATGGCGC 58.631 43.478 0.00 0.00 44.94 6.53
2477 2653 5.981315 GCGCCATTACTAGTTGACATAGTAA 59.019 40.000 0.00 9.89 45.16 2.24
2478 2654 5.068067 TGCGCCATTACTAGTTGACATAGTA 59.932 40.000 4.18 0.00 35.20 1.82
2479 2655 4.142026 TGCGCCATTACTAGTTGACATAGT 60.142 41.667 4.18 0.00 37.29 2.12
2480 2656 4.209288 GTGCGCCATTACTAGTTGACATAG 59.791 45.833 4.18 0.00 0.00 2.23
2481 2657 4.116961 GTGCGCCATTACTAGTTGACATA 58.883 43.478 4.18 0.00 0.00 2.29
2482 2658 2.936498 GTGCGCCATTACTAGTTGACAT 59.064 45.455 4.18 0.00 0.00 3.06
2483 2659 2.028476 AGTGCGCCATTACTAGTTGACA 60.028 45.455 4.18 0.00 0.00 3.58
2484 2660 2.618053 AGTGCGCCATTACTAGTTGAC 58.382 47.619 4.18 0.00 0.00 3.18
2485 2661 4.665833 ATAGTGCGCCATTACTAGTTGA 57.334 40.909 4.18 0.00 33.32 3.18
2486 2662 4.684703 GGTATAGTGCGCCATTACTAGTTG 59.315 45.833 4.18 0.00 33.32 3.16
2487 2663 4.262335 GGGTATAGTGCGCCATTACTAGTT 60.262 45.833 4.18 0.00 33.32 2.24
2488 2664 3.257624 GGGTATAGTGCGCCATTACTAGT 59.742 47.826 4.18 0.00 33.32 2.57
2489 2665 3.510360 AGGGTATAGTGCGCCATTACTAG 59.490 47.826 4.18 0.00 33.32 2.57
2490 2666 3.257375 CAGGGTATAGTGCGCCATTACTA 59.743 47.826 4.18 6.34 34.23 1.82
2491 2667 2.037251 CAGGGTATAGTGCGCCATTACT 59.963 50.000 4.18 3.74 0.00 2.24
2492 2668 2.413837 CAGGGTATAGTGCGCCATTAC 58.586 52.381 4.18 0.00 0.00 1.89
2493 2669 1.346395 CCAGGGTATAGTGCGCCATTA 59.654 52.381 4.18 0.00 0.00 1.90
2494 2670 0.108585 CCAGGGTATAGTGCGCCATT 59.891 55.000 4.18 0.00 0.00 3.16
2495 2671 1.054406 ACCAGGGTATAGTGCGCCAT 61.054 55.000 4.18 0.00 0.00 4.40
2496 2672 1.687840 ACCAGGGTATAGTGCGCCA 60.688 57.895 4.18 0.00 0.00 5.69
2497 2673 1.227556 CACCAGGGTATAGTGCGCC 60.228 63.158 4.18 0.00 0.00 6.53
2498 2674 1.887707 GCACCAGGGTATAGTGCGC 60.888 63.158 0.00 0.00 46.43 6.09
2499 2675 4.438346 GCACCAGGGTATAGTGCG 57.562 61.111 0.00 0.00 46.43 5.34
2501 2677 1.227556 GGCGCACCAGGGTATAGTG 60.228 63.158 10.83 0.00 35.26 2.74
2502 2678 1.687840 TGGCGCACCAGGGTATAGT 60.688 57.895 10.83 0.00 42.67 2.12
2503 2679 3.226242 TGGCGCACCAGGGTATAG 58.774 61.111 10.83 0.00 42.67 1.31
2517 2693 3.127030 GGTTATGAGTTGTTAGCAGTGGC 59.873 47.826 0.00 0.00 41.61 5.01
2518 2694 4.323417 TGGTTATGAGTTGTTAGCAGTGG 58.677 43.478 0.00 0.00 0.00 4.00
2519 2695 5.940192 TTGGTTATGAGTTGTTAGCAGTG 57.060 39.130 0.00 0.00 0.00 3.66
2520 2696 6.570378 GCATTTGGTTATGAGTTGTTAGCAGT 60.570 38.462 0.00 0.00 0.00 4.40
2521 2697 5.801947 GCATTTGGTTATGAGTTGTTAGCAG 59.198 40.000 0.00 0.00 0.00 4.24
2522 2698 5.242615 TGCATTTGGTTATGAGTTGTTAGCA 59.757 36.000 0.00 0.00 0.00 3.49
2523 2699 5.572896 GTGCATTTGGTTATGAGTTGTTAGC 59.427 40.000 0.00 0.00 0.00 3.09
2524 2700 6.092748 GGTGCATTTGGTTATGAGTTGTTAG 58.907 40.000 0.00 0.00 0.00 2.34
2525 2701 5.047660 GGGTGCATTTGGTTATGAGTTGTTA 60.048 40.000 0.00 0.00 0.00 2.41
2526 2702 4.262420 GGGTGCATTTGGTTATGAGTTGTT 60.262 41.667 0.00 0.00 0.00 2.83
2527 2703 3.258123 GGGTGCATTTGGTTATGAGTTGT 59.742 43.478 0.00 0.00 0.00 3.32
2528 2704 3.368323 GGGGTGCATTTGGTTATGAGTTG 60.368 47.826 0.00 0.00 0.00 3.16
2529 2705 2.831526 GGGGTGCATTTGGTTATGAGTT 59.168 45.455 0.00 0.00 0.00 3.01
2530 2706 2.456577 GGGGTGCATTTGGTTATGAGT 58.543 47.619 0.00 0.00 0.00 3.41
2531 2707 1.756538 GGGGGTGCATTTGGTTATGAG 59.243 52.381 0.00 0.00 0.00 2.90
2532 2708 1.859302 GGGGGTGCATTTGGTTATGA 58.141 50.000 0.00 0.00 0.00 2.15
2552 2728 3.971109 GAAAAGGCGGTCGGGGAGG 62.971 68.421 0.00 0.00 0.00 4.30
2553 2729 2.436115 GAAAAGGCGGTCGGGGAG 60.436 66.667 0.00 0.00 0.00 4.30
2554 2730 3.243053 TGAAAAGGCGGTCGGGGA 61.243 61.111 0.00 0.00 0.00 4.81
2555 2731 2.746277 CTGAAAAGGCGGTCGGGG 60.746 66.667 0.00 0.00 0.00 5.73
2556 2732 1.170290 AAACTGAAAAGGCGGTCGGG 61.170 55.000 0.00 0.00 0.00 5.14
2557 2733 1.515081 TAAACTGAAAAGGCGGTCGG 58.485 50.000 0.00 0.00 0.00 4.79
2558 2734 3.612472 TTTAAACTGAAAAGGCGGTCG 57.388 42.857 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.