Multiple sequence alignment - TraesCS5A01G112600

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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 TraesCS5A01G112600 chr5A 100.000 3718 0 0 1 3718 219697755 219694038 0.000000e+00 6866.0
1 TraesCS5A01G112600 chr5A 91.579 95 5 3 1 95 467574635 467574726 1.080000e-25 128.0
2 TraesCS5A01G112600 chr5D 92.729 1389 63 15 71 1439 203060668 203059298 0.000000e+00 1971.0
3 TraesCS5A01G112600 chr5D 92.734 1335 50 19 1610 2912 203059211 203057892 0.000000e+00 1884.0
4 TraesCS5A01G112600 chr5D 84.795 171 26 0 2191 2361 353795667 353795837 4.940000e-39 172.0
5 TraesCS5A01G112600 chr5D 83.448 145 22 2 2178 2321 412960775 412960918 2.330000e-27 134.0
6 TraesCS5A01G112600 chr5B 92.287 1115 50 14 333 1439 208700853 208701939 0.000000e+00 1550.0
7 TraesCS5A01G112600 chr5B 95.455 528 16 4 2385 2912 208702895 208703414 0.000000e+00 835.0
8 TraesCS5A01G112600 chr5B 94.533 439 21 2 1998 2435 208702467 208702903 0.000000e+00 675.0
9 TraesCS5A01G112600 chr5B 84.687 431 20 19 1610 2005 208702012 208702431 4.500000e-104 388.0
10 TraesCS5A01G112600 chr5B 83.448 145 22 2 2178 2321 497504680 497504823 2.330000e-27 134.0
11 TraesCS5A01G112600 chr6A 91.021 813 38 13 2912 3718 589324572 589325355 0.000000e+00 1064.0
12 TraesCS5A01G112600 chr6A 82.249 169 30 0 2195 2363 554855927 554856095 2.990000e-31 147.0
13 TraesCS5A01G112600 chr7B 87.450 502 53 9 3222 3717 720548667 720548170 1.500000e-158 569.0
14 TraesCS5A01G112600 chr7B 80.147 136 14 7 2900 3033 384097802 384097926 5.110000e-14 89.8
15 TraesCS5A01G112600 chr1A 86.604 321 27 9 308 623 570925343 570925034 1.280000e-89 340.0
16 TraesCS5A01G112600 chr1A 98.718 78 1 0 1 78 227722630 227722553 5.010000e-29 139.0
17 TraesCS5A01G112600 chr1A 100.000 75 0 0 1 75 269242451 269242525 5.010000e-29 139.0
18 TraesCS5A01G112600 chr1A 97.531 81 1 1 1 81 225655736 225655815 1.800000e-28 137.0
19 TraesCS5A01G112600 chr6D 81.609 174 32 0 2190 2363 409584513 409584686 1.080000e-30 145.0
20 TraesCS5A01G112600 chr6D 80.571 175 30 3 2190 2362 409516651 409516823 8.380000e-27 132.0
21 TraesCS5A01G112600 chr6B 81.548 168 31 0 2190 2357 615275789 615275956 5.010000e-29 139.0
22 TraesCS5A01G112600 chr4A 93.684 95 3 3 1 95 73657308 73657217 5.010000e-29 139.0
23 TraesCS5A01G112600 chr4A 92.553 94 3 4 1 94 438285301 438285390 8.380000e-27 132.0
24 TraesCS5A01G112600 chr3A 97.531 81 2 0 1 81 420792437 420792357 5.010000e-29 139.0
25 TraesCS5A01G112600 chr2A 97.561 82 1 1 1 82 569480246 569480326 5.010000e-29 139.0
26 TraesCS5A01G112600 chr2A 93.548 93 0 4 1 88 345787808 345787899 2.330000e-27 134.0


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 TraesCS5A01G112600 chr5A 219694038 219697755 3717 True 6866.0 6866 100.0000 1 3718 1 chr5A.!!$R1 3717
1 TraesCS5A01G112600 chr5D 203057892 203060668 2776 True 1927.5 1971 92.7315 71 2912 2 chr5D.!!$R1 2841
2 TraesCS5A01G112600 chr5B 208700853 208703414 2561 False 862.0 1550 91.7405 333 2912 4 chr5B.!!$F2 2579
3 TraesCS5A01G112600 chr6A 589324572 589325355 783 False 1064.0 1064 91.0210 2912 3718 1 chr6A.!!$F2 806

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
69 70 0.108992 GTCGCATCGAGGGTGTTACA 60.109 55.0 0.00 0.0 36.23 2.41 F
96 97 0.110056 CATGCCACACTTTCTCACGC 60.110 55.0 0.00 0.0 0.00 5.34 F
2078 2184 0.038618 ACTCGCGTGCAGATTACACA 60.039 50.0 5.77 0.0 37.93 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2008 0.514691 CTTGCTCTGTTTCGCTGGAC 59.485 55.000 0.00 0.0 0.0 4.02 R
2090 2196 4.569023 TGCGGCGAGTAGGATGCG 62.569 66.667 12.98 0.0 0.0 4.73 R
3104 3253 0.318107 GCGTTGTTCTGCTTGCATGT 60.318 50.000 1.14 0.0 0.0 3.21 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
24 25 7.706281 CTTCAATGCGATTATGTCTCTAAGT 57.294 36.000 0.00 0.00 0.00 2.24
25 26 7.700322 TTCAATGCGATTATGTCTCTAAGTC 57.300 36.000 0.00 0.00 0.00 3.01
26 27 5.915196 TCAATGCGATTATGTCTCTAAGTCG 59.085 40.000 0.00 0.00 0.00 4.18
27 28 4.895224 TGCGATTATGTCTCTAAGTCGT 57.105 40.909 0.00 0.00 0.00 4.34
28 29 4.598062 TGCGATTATGTCTCTAAGTCGTG 58.402 43.478 0.00 0.00 0.00 4.35
29 30 3.422546 GCGATTATGTCTCTAAGTCGTGC 59.577 47.826 0.00 0.00 0.00 5.34
30 31 3.975670 CGATTATGTCTCTAAGTCGTGCC 59.024 47.826 0.00 0.00 0.00 5.01
31 32 4.261238 CGATTATGTCTCTAAGTCGTGCCT 60.261 45.833 0.00 0.00 0.00 4.75
32 33 4.634184 TTATGTCTCTAAGTCGTGCCTC 57.366 45.455 0.00 0.00 0.00 4.70
33 34 0.803117 TGTCTCTAAGTCGTGCCTCG 59.197 55.000 0.00 0.00 41.41 4.63
34 35 1.085091 GTCTCTAAGTCGTGCCTCGA 58.915 55.000 0.00 0.00 46.83 4.04
43 44 3.986006 GTGCCTCGACACGTGGGA 61.986 66.667 21.57 15.34 40.31 4.37
44 45 3.680786 TGCCTCGACACGTGGGAG 61.681 66.667 24.04 24.04 40.31 4.30
46 47 3.374402 CCTCGACACGTGGGAGCT 61.374 66.667 25.04 4.48 36.95 4.09
47 48 2.044555 CCTCGACACGTGGGAGCTA 61.045 63.158 25.04 4.72 36.95 3.32
48 49 1.384989 CCTCGACACGTGGGAGCTAT 61.385 60.000 25.04 3.08 36.95 2.97
49 50 1.306148 CTCGACACGTGGGAGCTATA 58.694 55.000 21.57 0.00 0.00 1.31
50 51 1.264557 CTCGACACGTGGGAGCTATAG 59.735 57.143 21.57 0.00 0.00 1.31
51 52 1.022735 CGACACGTGGGAGCTATAGT 58.977 55.000 21.57 0.00 0.00 2.12
52 53 1.002684 CGACACGTGGGAGCTATAGTC 60.003 57.143 21.57 2.91 0.00 2.59
53 54 1.002684 GACACGTGGGAGCTATAGTCG 60.003 57.143 21.57 0.00 0.00 4.18
54 55 0.317938 CACGTGGGAGCTATAGTCGC 60.318 60.000 7.95 6.96 0.00 5.19
55 56 0.750546 ACGTGGGAGCTATAGTCGCA 60.751 55.000 13.98 13.98 34.73 5.10
56 57 0.598562 CGTGGGAGCTATAGTCGCAT 59.401 55.000 18.16 0.00 38.90 4.73
57 58 1.401670 CGTGGGAGCTATAGTCGCATC 60.402 57.143 18.16 13.23 38.90 3.91
58 59 0.881796 TGGGAGCTATAGTCGCATCG 59.118 55.000 13.98 0.00 32.37 3.84
59 60 1.166129 GGGAGCTATAGTCGCATCGA 58.834 55.000 0.84 0.00 0.00 3.59
60 61 1.131504 GGGAGCTATAGTCGCATCGAG 59.868 57.143 0.84 0.00 36.23 4.04
61 62 1.131504 GGAGCTATAGTCGCATCGAGG 59.868 57.143 0.84 0.00 36.23 4.63
62 63 1.131504 GAGCTATAGTCGCATCGAGGG 59.868 57.143 0.00 0.00 36.23 4.30
63 64 0.882474 GCTATAGTCGCATCGAGGGT 59.118 55.000 0.00 0.00 36.23 4.34
64 65 1.401670 GCTATAGTCGCATCGAGGGTG 60.402 57.143 0.00 0.00 36.23 4.61
65 66 1.880675 CTATAGTCGCATCGAGGGTGT 59.119 52.381 0.00 0.00 36.23 4.16
66 67 1.112113 ATAGTCGCATCGAGGGTGTT 58.888 50.000 0.00 0.00 36.23 3.32
67 68 1.753930 TAGTCGCATCGAGGGTGTTA 58.246 50.000 0.00 0.00 36.23 2.41
68 69 0.172803 AGTCGCATCGAGGGTGTTAC 59.827 55.000 0.00 0.00 36.23 2.50
69 70 0.108992 GTCGCATCGAGGGTGTTACA 60.109 55.000 0.00 0.00 36.23 2.41
95 96 0.518636 CCATGCCACACTTTCTCACG 59.481 55.000 0.00 0.00 0.00 4.35
96 97 0.110056 CATGCCACACTTTCTCACGC 60.110 55.000 0.00 0.00 0.00 5.34
160 161 0.746659 GTCACAAGTTGGCAAGCCTT 59.253 50.000 12.96 0.00 36.94 4.35
167 168 4.161377 ACAAGTTGGCAAGCCTTAAGAAAA 59.839 37.500 12.96 0.00 36.94 2.29
168 169 5.115480 CAAGTTGGCAAGCCTTAAGAAAAA 58.885 37.500 12.96 0.00 36.94 1.94
173 174 5.679601 TGGCAAGCCTTAAGAAAAATTTGT 58.320 33.333 12.96 0.00 36.94 2.83
212 213 2.289631 TGCTATGTGGATCCCTAATGCG 60.290 50.000 9.90 0.00 0.00 4.73
216 217 0.886490 GTGGATCCCTAATGCGGCAG 60.886 60.000 9.90 0.00 0.00 4.85
219 220 1.230324 GATCCCTAATGCGGCAGAAC 58.770 55.000 9.25 0.00 0.00 3.01
235 237 6.511282 GCGGCAGAACATCTTACCTAAAATAC 60.511 42.308 0.00 0.00 0.00 1.89
236 238 6.761714 CGGCAGAACATCTTACCTAAAATACT 59.238 38.462 0.00 0.00 0.00 2.12
440 450 6.299922 AGGGGCTATCTTTAAGCTATGAAAC 58.700 40.000 0.00 0.00 39.97 2.78
490 504 3.569194 TGTCCCTGAAGCAAACTTGTA 57.431 42.857 0.00 0.00 35.82 2.41
624 638 4.409218 CACACACATGCGCCAGGC 62.409 66.667 4.18 0.00 43.96 4.85
641 655 2.092753 CAGGCCAGATACATTGTCACCT 60.093 50.000 5.01 0.00 0.00 4.00
642 656 3.134623 CAGGCCAGATACATTGTCACCTA 59.865 47.826 5.01 0.00 0.00 3.08
643 657 3.389329 AGGCCAGATACATTGTCACCTAG 59.611 47.826 5.01 0.00 0.00 3.02
672 686 4.970662 TCTAGATGAAACAAGCAATGCC 57.029 40.909 0.00 0.00 0.00 4.40
710 727 1.826720 GTATGTGGGTTCGTGGGTAGA 59.173 52.381 0.00 0.00 0.00 2.59
711 728 1.580059 ATGTGGGTTCGTGGGTAGAT 58.420 50.000 0.00 0.00 0.00 1.98
712 729 1.354101 TGTGGGTTCGTGGGTAGATT 58.646 50.000 0.00 0.00 0.00 2.40
713 730 2.538222 TGTGGGTTCGTGGGTAGATTA 58.462 47.619 0.00 0.00 0.00 1.75
833 854 4.757149 GTGGGCATATCTTACTGCTTAAGG 59.243 45.833 4.29 0.00 38.24 2.69
835 856 5.104109 TGGGCATATCTTACTGCTTAAGGTT 60.104 40.000 4.29 0.00 38.24 3.50
836 857 5.828328 GGGCATATCTTACTGCTTAAGGTTT 59.172 40.000 4.29 0.00 38.24 3.27
837 858 6.996282 GGGCATATCTTACTGCTTAAGGTTTA 59.004 38.462 4.29 0.00 38.24 2.01
838 859 7.173390 GGGCATATCTTACTGCTTAAGGTTTAG 59.827 40.741 4.29 0.00 38.24 1.85
839 860 7.173390 GGCATATCTTACTGCTTAAGGTTTAGG 59.827 40.741 4.29 1.41 38.24 2.69
840 861 7.308049 GCATATCTTACTGCTTAAGGTTTAGGC 60.308 40.741 4.29 0.00 38.24 3.93
866 887 0.882927 GCCAGCACGTACACCTGAAA 60.883 55.000 6.11 0.00 0.00 2.69
869 890 2.210116 CAGCACGTACACCTGAAACTT 58.790 47.619 0.00 0.00 0.00 2.66
870 891 2.221055 CAGCACGTACACCTGAAACTTC 59.779 50.000 0.00 0.00 0.00 3.01
871 892 1.529865 GCACGTACACCTGAAACTTCC 59.470 52.381 0.00 0.00 0.00 3.46
882 904 3.566775 CCTGAAACTTCCCCCTCTCTCTA 60.567 52.174 0.00 0.00 0.00 2.43
903 925 7.440556 TCTCTATATATATAGTTGTCCGTCGCC 59.559 40.741 23.23 0.00 37.51 5.54
1097 1121 3.005539 ACGGGAGGAGCATGCACT 61.006 61.111 21.98 17.51 0.00 4.40
1098 1122 1.676678 GACGGGAGGAGCATGCACTA 61.677 60.000 21.98 0.00 0.00 2.74
1099 1123 1.227380 CGGGAGGAGCATGCACTAC 60.227 63.158 21.98 17.64 0.00 2.73
1182 1206 2.105128 GTGTCGGCGCTAGCTCAT 59.895 61.111 13.93 0.00 44.37 2.90
1215 1239 3.211963 GTGGGCGATGGTGGCATC 61.212 66.667 0.00 0.00 35.84 3.91
1428 1454 8.741101 AACGACACGTAACAATAGTATTGTTA 57.259 30.769 31.23 31.23 39.99 2.41
1429 1455 8.385789 ACGACACGTAACAATAGTATTGTTAG 57.614 34.615 33.75 28.72 43.14 2.34
1430 1456 7.008628 ACGACACGTAACAATAGTATTGTTAGC 59.991 37.037 33.75 27.40 43.14 3.09
1431 1457 7.514125 CGACACGTAACAATAGTATTGTTAGCC 60.514 40.741 33.75 25.51 43.14 3.93
1432 1458 7.325694 ACACGTAACAATAGTATTGTTAGCCT 58.674 34.615 33.75 21.92 43.14 4.58
1433 1459 7.820872 ACACGTAACAATAGTATTGTTAGCCTT 59.179 33.333 33.75 21.84 43.14 4.35
1434 1460 9.304731 CACGTAACAATAGTATTGTTAGCCTTA 57.695 33.333 33.75 19.80 43.14 2.69
1435 1461 9.874205 ACGTAACAATAGTATTGTTAGCCTTAA 57.126 29.630 33.75 19.25 43.14 1.85
1441 1467 9.450807 CAATAGTATTGTTAGCCTTAAACATGC 57.549 33.333 13.80 0.00 36.75 4.06
1442 1468 8.980481 ATAGTATTGTTAGCCTTAAACATGCT 57.020 30.769 0.00 0.00 36.75 3.79
1443 1469 7.703058 AGTATTGTTAGCCTTAAACATGCTT 57.297 32.000 0.00 0.00 36.75 3.91
1444 1470 8.122472 AGTATTGTTAGCCTTAAACATGCTTT 57.878 30.769 0.00 0.00 36.75 3.51
1445 1471 8.585018 AGTATTGTTAGCCTTAAACATGCTTTT 58.415 29.630 0.00 0.00 36.75 2.27
1446 1472 9.203421 GTATTGTTAGCCTTAAACATGCTTTTT 57.797 29.630 0.00 0.00 36.75 1.94
1528 1555 6.091718 GGAGTTCATCAATCCCTAGTACTC 57.908 45.833 0.00 0.00 0.00 2.59
1529 1556 5.836358 GGAGTTCATCAATCCCTAGTACTCT 59.164 44.000 0.00 0.00 32.30 3.24
1530 1557 6.325286 GGAGTTCATCAATCCCTAGTACTCTT 59.675 42.308 0.00 0.00 32.30 2.85
1532 1559 8.152023 AGTTCATCAATCCCTAGTACTCTTTT 57.848 34.615 0.00 0.00 0.00 2.27
1533 1560 8.261522 AGTTCATCAATCCCTAGTACTCTTTTC 58.738 37.037 0.00 0.00 0.00 2.29
1534 1561 6.806751 TCATCAATCCCTAGTACTCTTTTCG 58.193 40.000 0.00 0.00 0.00 3.46
1536 1563 6.600882 TCAATCCCTAGTACTCTTTTCGTT 57.399 37.500 0.00 0.00 0.00 3.85
1537 1564 7.001099 TCAATCCCTAGTACTCTTTTCGTTT 57.999 36.000 0.00 0.00 0.00 3.60
1542 1569 7.447594 TCCCTAGTACTCTTTTCGTTTCAAAT 58.552 34.615 0.00 0.00 0.00 2.32
1543 1570 7.935210 TCCCTAGTACTCTTTTCGTTTCAAATT 59.065 33.333 0.00 0.00 0.00 1.82
1548 1575 8.485591 AGTACTCTTTTCGTTTCAAATTACTCG 58.514 33.333 0.00 0.00 0.00 4.18
1549 1576 7.242914 ACTCTTTTCGTTTCAAATTACTCGT 57.757 32.000 0.00 0.00 0.00 4.18
1550 1577 8.356533 ACTCTTTTCGTTTCAAATTACTCGTA 57.643 30.769 0.00 0.00 0.00 3.43
1551 1578 8.819974 ACTCTTTTCGTTTCAAATTACTCGTAA 58.180 29.630 0.00 0.00 0.00 3.18
1552 1579 9.640974 CTCTTTTCGTTTCAAATTACTCGTAAA 57.359 29.630 0.00 0.00 0.00 2.01
1613 1640 8.361139 CGAGTAATTTAGAATGGATGGAGTACT 58.639 37.037 0.00 0.00 0.00 2.73
1621 1648 7.979786 AGAATGGATGGAGTACTTCTTAGAA 57.020 36.000 2.07 0.00 0.00 2.10
1674 1702 9.953697 AAACTAGAGTACTATCATGAACGATTC 57.046 33.333 0.00 0.00 0.00 2.52
1723 1751 0.663568 CGTCAGACACGTGTTCCTCC 60.664 60.000 24.26 9.56 44.07 4.30
1771 1828 4.313277 TCTTCTTCCATGTGCTCGATAG 57.687 45.455 0.00 0.00 0.00 2.08
1832 1890 4.662145 GCCAACAGTATGAAAGGAAATCG 58.338 43.478 0.00 0.00 39.69 3.34
1868 1926 4.119862 CCCACTGTTCCATTCATACTACG 58.880 47.826 0.00 0.00 0.00 3.51
1869 1927 4.382685 CCCACTGTTCCATTCATACTACGT 60.383 45.833 0.00 0.00 0.00 3.57
1870 1928 5.163488 CCCACTGTTCCATTCATACTACGTA 60.163 44.000 0.00 0.00 0.00 3.57
1871 1929 5.747197 CCACTGTTCCATTCATACTACGTAC 59.253 44.000 0.00 0.00 0.00 3.67
1934 1997 4.754372 GCTGATTCATTTCGGCATCATA 57.246 40.909 0.54 0.00 45.51 2.15
1936 1999 4.720090 CTGATTCATTTCGGCATCATAGC 58.280 43.478 0.00 0.00 0.00 2.97
1942 2005 1.215014 TTCGGCATCATAGCTTCGCG 61.215 55.000 0.00 0.00 34.17 5.87
1945 2008 1.484659 GCATCATAGCTTCGCGTCG 59.515 57.895 5.77 0.00 0.00 5.12
1977 2040 0.538287 GAGCAAGTGGGCAGGAAAGT 60.538 55.000 0.00 0.00 35.83 2.66
1982 2045 2.031495 AGTGGGCAGGAAAGTAGAGT 57.969 50.000 0.00 0.00 0.00 3.24
2041 2146 5.006386 ACTTGTCATGACATTCTTTCCCTC 58.994 41.667 28.32 0.00 41.52 4.30
2057 2163 5.941555 TTCCCTCTCTCCTCTGTTTATTC 57.058 43.478 0.00 0.00 0.00 1.75
2078 2184 0.038618 ACTCGCGTGCAGATTACACA 60.039 50.000 5.77 0.00 37.93 3.72
2283 2389 3.379445 GGCTCGGGACCTTCGACA 61.379 66.667 0.00 0.00 32.86 4.35
2357 2463 2.639286 CGCGCCAAGCTCAACTTT 59.361 55.556 0.00 0.00 45.59 2.66
2360 2466 1.207593 CGCCAAGCTCAACTTTCCG 59.792 57.895 0.00 0.00 36.04 4.30
2366 2472 0.321996 AGCTCAACTTTCCGGAGTCC 59.678 55.000 3.34 0.00 0.00 3.85
2783 2931 3.430929 CGGATACTGACAAGGAAGGAAGG 60.431 52.174 0.00 0.00 0.00 3.46
2784 2932 3.775316 GGATACTGACAAGGAAGGAAGGA 59.225 47.826 0.00 0.00 0.00 3.36
2785 2933 4.225267 GGATACTGACAAGGAAGGAAGGAA 59.775 45.833 0.00 0.00 0.00 3.36
2786 2934 3.778954 ACTGACAAGGAAGGAAGGAAG 57.221 47.619 0.00 0.00 0.00 3.46
2983 3132 1.425412 GCATAGGACGACACGTGTTT 58.575 50.000 24.26 13.23 41.37 2.83
2997 3146 1.525077 TGTTTCAGTGGGTCCGTGC 60.525 57.895 0.00 0.00 0.00 5.34
3006 3155 4.980805 GGTCCGTGCACCGCTTCA 62.981 66.667 12.15 0.00 34.38 3.02
3022 3171 4.049186 CGCTTCACGTGCTACCTTATTAT 58.951 43.478 11.67 0.00 36.87 1.28
3023 3172 4.148348 CGCTTCACGTGCTACCTTATTATC 59.852 45.833 11.67 0.00 36.87 1.75
3024 3173 5.290386 GCTTCACGTGCTACCTTATTATCT 58.710 41.667 11.67 0.00 0.00 1.98
3025 3174 5.402867 GCTTCACGTGCTACCTTATTATCTC 59.597 44.000 11.67 0.00 0.00 2.75
3026 3175 5.104562 TCACGTGCTACCTTATTATCTCG 57.895 43.478 11.67 0.00 0.00 4.04
3027 3176 4.577693 TCACGTGCTACCTTATTATCTCGT 59.422 41.667 11.67 0.00 0.00 4.18
3028 3177 5.066893 TCACGTGCTACCTTATTATCTCGTT 59.933 40.000 11.67 0.00 0.00 3.85
3029 3178 5.747197 CACGTGCTACCTTATTATCTCGTTT 59.253 40.000 0.82 0.00 0.00 3.60
3030 3179 5.747197 ACGTGCTACCTTATTATCTCGTTTG 59.253 40.000 0.00 0.00 0.00 2.93
3031 3180 5.975344 CGTGCTACCTTATTATCTCGTTTGA 59.025 40.000 0.00 0.00 0.00 2.69
3032 3181 6.641314 CGTGCTACCTTATTATCTCGTTTGAT 59.359 38.462 0.00 0.00 0.00 2.57
3033 3182 7.169308 CGTGCTACCTTATTATCTCGTTTGATT 59.831 37.037 0.00 0.00 0.00 2.57
3034 3183 8.276325 GTGCTACCTTATTATCTCGTTTGATTG 58.724 37.037 0.00 0.00 0.00 2.67
3035 3184 7.042051 TGCTACCTTATTATCTCGTTTGATTGC 60.042 37.037 0.00 0.00 0.00 3.56
3036 3185 7.171678 GCTACCTTATTATCTCGTTTGATTGCT 59.828 37.037 0.00 0.00 0.00 3.91
3037 3186 7.484035 ACCTTATTATCTCGTTTGATTGCTC 57.516 36.000 0.00 0.00 0.00 4.26
3038 3187 7.047891 ACCTTATTATCTCGTTTGATTGCTCA 58.952 34.615 0.00 0.00 0.00 4.26
3039 3188 7.552687 ACCTTATTATCTCGTTTGATTGCTCAA 59.447 33.333 0.00 0.00 39.62 3.02
3040 3189 8.066595 CCTTATTATCTCGTTTGATTGCTCAAG 58.933 37.037 0.00 0.00 42.19 3.02
3041 3190 3.754188 ATCTCGTTTGATTGCTCAAGC 57.246 42.857 0.00 0.00 42.19 4.01
3042 3191 1.806542 TCTCGTTTGATTGCTCAAGCC 59.193 47.619 0.00 0.00 42.19 4.35
3043 3192 1.536766 CTCGTTTGATTGCTCAAGCCA 59.463 47.619 0.00 0.00 42.19 4.75
3044 3193 2.161855 TCGTTTGATTGCTCAAGCCAT 58.838 42.857 0.00 0.00 42.19 4.40
3045 3194 3.342719 TCGTTTGATTGCTCAAGCCATA 58.657 40.909 0.00 0.00 42.19 2.74
3046 3195 3.947196 TCGTTTGATTGCTCAAGCCATAT 59.053 39.130 0.00 0.00 42.19 1.78
3047 3196 5.122519 TCGTTTGATTGCTCAAGCCATATA 58.877 37.500 0.00 0.00 42.19 0.86
3048 3197 5.588246 TCGTTTGATTGCTCAAGCCATATAA 59.412 36.000 0.00 0.00 42.19 0.98
3049 3198 6.094742 TCGTTTGATTGCTCAAGCCATATAAA 59.905 34.615 0.00 0.00 42.19 1.40
3050 3199 6.919662 CGTTTGATTGCTCAAGCCATATAAAT 59.080 34.615 0.00 0.00 42.19 1.40
3104 3253 3.181473 GCCATTCAGCCTTTTGCATCATA 60.181 43.478 0.00 0.00 44.83 2.15
3126 3275 1.286880 GCAAGCAGAACAACGCCAT 59.713 52.632 0.00 0.00 0.00 4.40
3156 3305 0.179100 CCGGCCTGTGAGTAGACATG 60.179 60.000 0.00 0.00 0.00 3.21
3199 3348 3.256960 ACAACCCGGCCATGTCCT 61.257 61.111 2.24 0.00 0.00 3.85
3202 3351 2.231380 AACCCGGCCATGTCCTTCT 61.231 57.895 2.24 0.00 0.00 2.85
3216 3365 2.838202 GTCCTTCTCCAACCCAGTCATA 59.162 50.000 0.00 0.00 0.00 2.15
3220 3369 3.769189 TCTCCAACCCAGTCATAGGTA 57.231 47.619 0.00 0.00 34.45 3.08
3284 3433 2.012673 GTCCATGAAGGTAGCTTGCAG 58.987 52.381 12.82 1.07 39.02 4.41
3313 3466 1.001378 GGGTACAAACAGCAAGCACTG 60.001 52.381 0.00 0.37 43.59 3.66
3333 3486 3.671716 TGATGGAGTATCATGCATGCTC 58.328 45.455 22.25 20.35 40.82 4.26
3377 3530 1.614317 GGGATTGACAGTTGGAGGTGG 60.614 57.143 0.00 0.00 0.00 4.61
3423 3576 1.358725 GGCGAACAACAGCGATGCTA 61.359 55.000 0.00 0.00 36.40 3.49
3428 3581 2.680312 ACAACAGCGATGCTATCAGT 57.320 45.000 0.00 0.00 36.40 3.41
3429 3582 2.274437 ACAACAGCGATGCTATCAGTG 58.726 47.619 0.00 0.00 36.40 3.66
3532 3687 2.289195 ACACCCATGCTGCAGAAAAATG 60.289 45.455 20.43 14.09 0.00 2.32
3536 3691 3.259064 CCATGCTGCAGAAAAATGAAGG 58.741 45.455 20.43 1.29 0.00 3.46
3582 3737 1.464734 TGTTGCAAAAGTCCGTTCCA 58.535 45.000 0.00 0.00 0.00 3.53
3589 3744 3.736740 GCAAAAGTCCGTTCCACAACAAT 60.737 43.478 0.00 0.00 32.14 2.71
3596 3751 3.944650 TCCGTTCCACAACAATATCCATG 59.055 43.478 0.00 0.00 32.14 3.66
3660 3815 3.701241 TCCGTGTTGCAAAAGTTGATTC 58.299 40.909 0.00 0.00 0.00 2.52
3662 3817 3.443037 CGTGTTGCAAAAGTTGATTCCA 58.557 40.909 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.357941 CGACTTAGAGACATAATCGCATTGAAG 60.358 40.741 0.00 0.00 0.00 3.02
1 2 6.417930 CGACTTAGAGACATAATCGCATTGAA 59.582 38.462 0.00 0.00 0.00 2.69
2 3 5.915196 CGACTTAGAGACATAATCGCATTGA 59.085 40.000 0.00 0.00 0.00 2.57
3 4 5.687730 ACGACTTAGAGACATAATCGCATTG 59.312 40.000 0.00 0.00 0.00 2.82
4 5 5.687730 CACGACTTAGAGACATAATCGCATT 59.312 40.000 0.00 0.00 0.00 3.56
5 6 5.215903 CACGACTTAGAGACATAATCGCAT 58.784 41.667 0.00 0.00 0.00 4.73
6 7 4.598062 CACGACTTAGAGACATAATCGCA 58.402 43.478 0.00 0.00 0.00 5.10
7 8 3.422546 GCACGACTTAGAGACATAATCGC 59.577 47.826 0.00 0.00 0.00 4.58
8 9 3.975670 GGCACGACTTAGAGACATAATCG 59.024 47.826 0.00 0.00 0.00 3.34
9 10 5.189659 AGGCACGACTTAGAGACATAATC 57.810 43.478 0.00 0.00 0.00 1.75
10 11 4.261238 CGAGGCACGACTTAGAGACATAAT 60.261 45.833 0.00 0.00 45.77 1.28
11 12 3.064958 CGAGGCACGACTTAGAGACATAA 59.935 47.826 0.00 0.00 45.77 1.90
12 13 2.612672 CGAGGCACGACTTAGAGACATA 59.387 50.000 0.00 0.00 45.77 2.29
13 14 1.402259 CGAGGCACGACTTAGAGACAT 59.598 52.381 0.00 0.00 45.77 3.06
14 15 0.803117 CGAGGCACGACTTAGAGACA 59.197 55.000 0.00 0.00 45.77 3.41
15 16 1.085091 TCGAGGCACGACTTAGAGAC 58.915 55.000 2.07 0.00 46.45 3.36
16 17 3.545724 TCGAGGCACGACTTAGAGA 57.454 52.632 2.07 0.00 46.45 3.10
26 27 3.916392 CTCCCACGTGTCGAGGCAC 62.916 68.421 15.65 0.00 36.35 5.01
27 28 3.680786 CTCCCACGTGTCGAGGCA 61.681 66.667 15.65 0.00 36.35 4.75
29 30 1.384989 ATAGCTCCCACGTGTCGAGG 61.385 60.000 23.66 14.89 37.35 4.63
30 31 1.264557 CTATAGCTCCCACGTGTCGAG 59.735 57.143 20.16 20.16 0.00 4.04
31 32 1.306148 CTATAGCTCCCACGTGTCGA 58.694 55.000 15.65 8.55 0.00 4.20
32 33 1.002684 GACTATAGCTCCCACGTGTCG 60.003 57.143 15.65 4.04 0.00 4.35
33 34 1.002684 CGACTATAGCTCCCACGTGTC 60.003 57.143 15.65 0.00 0.00 3.67
34 35 1.022735 CGACTATAGCTCCCACGTGT 58.977 55.000 15.65 0.00 0.00 4.49
35 36 0.317938 GCGACTATAGCTCCCACGTG 60.318 60.000 9.08 9.08 0.00 4.49
36 37 0.750546 TGCGACTATAGCTCCCACGT 60.751 55.000 0.00 0.00 35.28 4.49
37 38 0.598562 ATGCGACTATAGCTCCCACG 59.401 55.000 0.00 0.00 35.28 4.94
38 39 1.401670 CGATGCGACTATAGCTCCCAC 60.402 57.143 0.00 0.00 35.28 4.61
39 40 0.881796 CGATGCGACTATAGCTCCCA 59.118 55.000 0.00 0.00 35.28 4.37
40 41 1.131504 CTCGATGCGACTATAGCTCCC 59.868 57.143 0.00 0.00 35.28 4.30
41 42 1.131504 CCTCGATGCGACTATAGCTCC 59.868 57.143 0.00 0.00 35.28 4.70
42 43 1.131504 CCCTCGATGCGACTATAGCTC 59.868 57.143 0.00 0.00 35.28 4.09
43 44 1.169577 CCCTCGATGCGACTATAGCT 58.830 55.000 0.00 0.00 35.28 3.32
44 45 0.882474 ACCCTCGATGCGACTATAGC 59.118 55.000 0.00 0.00 0.00 2.97
45 46 1.880675 ACACCCTCGATGCGACTATAG 59.119 52.381 0.00 0.00 0.00 1.31
46 47 1.977056 ACACCCTCGATGCGACTATA 58.023 50.000 0.00 0.00 0.00 1.31
47 48 1.112113 AACACCCTCGATGCGACTAT 58.888 50.000 0.00 0.00 0.00 2.12
48 49 1.402968 GTAACACCCTCGATGCGACTA 59.597 52.381 0.00 0.00 0.00 2.59
49 50 0.172803 GTAACACCCTCGATGCGACT 59.827 55.000 0.00 0.00 0.00 4.18
50 51 0.108992 TGTAACACCCTCGATGCGAC 60.109 55.000 0.00 0.00 0.00 5.19
51 52 0.172578 CTGTAACACCCTCGATGCGA 59.827 55.000 0.00 0.00 0.00 5.10
52 53 1.421410 GCTGTAACACCCTCGATGCG 61.421 60.000 0.00 0.00 0.00 4.73
53 54 1.090052 GGCTGTAACACCCTCGATGC 61.090 60.000 0.00 0.00 0.00 3.91
54 55 0.537188 AGGCTGTAACACCCTCGATG 59.463 55.000 0.00 0.00 0.00 3.84
55 56 1.066143 CAAGGCTGTAACACCCTCGAT 60.066 52.381 0.00 0.00 0.00 3.59
56 57 0.320374 CAAGGCTGTAACACCCTCGA 59.680 55.000 0.00 0.00 0.00 4.04
57 58 1.298859 GCAAGGCTGTAACACCCTCG 61.299 60.000 0.00 0.00 0.00 4.63
58 59 0.960861 GGCAAGGCTGTAACACCCTC 60.961 60.000 0.00 0.00 0.00 4.30
59 60 1.074951 GGCAAGGCTGTAACACCCT 59.925 57.895 0.00 0.00 0.00 4.34
60 61 0.611896 ATGGCAAGGCTGTAACACCC 60.612 55.000 0.00 0.00 0.00 4.61
61 62 0.527565 CATGGCAAGGCTGTAACACC 59.472 55.000 0.00 0.00 0.00 4.16
62 63 0.109132 GCATGGCAAGGCTGTAACAC 60.109 55.000 7.20 0.00 0.00 3.32
63 64 1.250154 GGCATGGCAAGGCTGTAACA 61.250 55.000 15.47 0.00 32.40 2.41
64 65 1.250154 TGGCATGGCAAGGCTGTAAC 61.250 55.000 21.13 0.09 32.40 2.50
65 66 1.076370 TGGCATGGCAAGGCTGTAA 59.924 52.632 21.13 0.00 32.40 2.41
66 67 1.678635 GTGGCATGGCAAGGCTGTA 60.679 57.895 25.11 0.00 32.40 2.74
67 68 2.993264 GTGGCATGGCAAGGCTGT 60.993 61.111 25.11 0.00 32.40 4.40
68 69 2.992689 TGTGGCATGGCAAGGCTG 60.993 61.111 25.11 0.00 32.40 4.85
69 70 2.993264 GTGTGGCATGGCAAGGCT 60.993 61.111 25.11 0.00 32.40 4.58
104 105 7.825270 TGGAACTAACTTTAGACAACTTTGACA 59.175 33.333 2.95 0.00 34.84 3.58
105 106 8.205131 TGGAACTAACTTTAGACAACTTTGAC 57.795 34.615 2.95 0.00 34.84 3.18
106 107 8.974060 ATGGAACTAACTTTAGACAACTTTGA 57.026 30.769 2.95 0.00 34.84 2.69
120 121 9.349713 TGTGACTTTCATTTTATGGAACTAACT 57.650 29.630 0.00 0.00 0.00 2.24
140 141 0.106519 AGGCTTGCCAACTTGTGACT 60.107 50.000 14.54 0.00 0.00 3.41
145 146 4.320608 TTTCTTAAGGCTTGCCAACTTG 57.679 40.909 10.69 0.54 0.00 3.16
185 186 4.564782 AGGGATCCACATAGCATACATG 57.435 45.455 15.23 0.00 0.00 3.21
186 187 6.656902 CATTAGGGATCCACATAGCATACAT 58.343 40.000 15.23 0.00 0.00 2.29
190 191 3.620719 CGCATTAGGGATCCACATAGCAT 60.621 47.826 15.23 0.00 0.00 3.79
193 194 2.936993 GCCGCATTAGGGATCCACATAG 60.937 54.545 15.23 1.04 0.00 2.23
201 202 0.546122 TGTTCTGCCGCATTAGGGAT 59.454 50.000 0.00 0.00 0.00 3.85
212 213 7.988028 AGAGTATTTTAGGTAAGATGTTCTGCC 59.012 37.037 0.00 0.00 0.00 4.85
292 301 9.503427 GTTCATATACTATTGGTTGTTTGCTTC 57.497 33.333 0.00 0.00 0.00 3.86
322 331 7.040478 TGTTTGATCATGTTAAGCTAGTTTGCT 60.040 33.333 1.54 0.00 46.40 3.91
359 368 1.878953 AGTGTCCAAAGTACCTTGCG 58.121 50.000 0.00 0.00 0.00 4.85
468 482 2.689983 ACAAGTTTGCTTCAGGGACAAG 59.310 45.455 0.00 0.00 31.49 3.16
490 504 3.802948 ATTTACTCGCTTCATCTCGGT 57.197 42.857 0.00 0.00 0.00 4.69
624 638 6.716934 ACTACTAGGTGACAATGTATCTGG 57.283 41.667 0.00 0.00 0.00 3.86
641 655 9.628500 TGCTTGTTTCATCTAGATCTACTACTA 57.372 33.333 1.03 0.00 0.00 1.82
642 656 8.526667 TGCTTGTTTCATCTAGATCTACTACT 57.473 34.615 1.03 0.00 0.00 2.57
643 657 9.757227 ATTGCTTGTTTCATCTAGATCTACTAC 57.243 33.333 1.03 0.00 0.00 2.73
699 713 7.514784 TCGATCTAATTAATCTACCCACGAA 57.485 36.000 0.00 0.00 0.00 3.85
713 730 8.085296 GGAACAGTGATCTACATCGATCTAATT 58.915 37.037 0.00 0.00 40.32 1.40
813 834 6.944234 AAACCTTAAGCAGTAAGATATGCC 57.056 37.500 8.38 0.00 43.60 4.40
840 861 2.358615 TACGTGCTGGCTTGGCTG 60.359 61.111 0.00 0.00 0.00 4.85
866 887 9.767751 ACTATATATATAGAGAGAGGGGGAAGT 57.232 37.037 28.76 7.70 38.30 3.01
869 890 9.535801 ACAACTATATATATAGAGAGAGGGGGA 57.464 37.037 28.76 0.00 38.30 4.81
870 891 9.802039 GACAACTATATATATAGAGAGAGGGGG 57.198 40.741 28.76 13.04 38.30 5.40
871 892 9.802039 GGACAACTATATATATAGAGAGAGGGG 57.198 40.741 28.76 14.14 38.30 4.79
903 925 2.807967 TCACAAATGCTTCAACTCCTCG 59.192 45.455 0.00 0.00 0.00 4.63
1206 1230 2.434185 GAAGACGCGATGCCACCA 60.434 61.111 15.93 0.00 0.00 4.17
1287 1311 2.675423 CCGTCTCCGTCTCCACCA 60.675 66.667 0.00 0.00 0.00 4.17
1346 1370 0.598158 TGGTCGTTGTCAAGCGTACC 60.598 55.000 14.52 14.52 0.00 3.34
1443 1469 7.426606 AACTTGTTTAAGGCTTCCCTAAAAA 57.573 32.000 1.30 0.00 41.90 1.94
1444 1470 8.536340 TTAACTTGTTTAAGGCTTCCCTAAAA 57.464 30.769 1.30 0.00 41.90 1.52
1445 1471 8.173542 CTTAACTTGTTTAAGGCTTCCCTAAA 57.826 34.615 1.30 0.00 42.17 1.85
1446 1472 7.754851 CTTAACTTGTTTAAGGCTTCCCTAA 57.245 36.000 1.30 0.00 42.17 2.69
1475 1502 5.856126 AAAAATGATCGAGTCGTTAGCAA 57.144 34.783 13.12 0.00 34.99 3.91
1509 1536 7.093465 ACGAAAAGAGTACTAGGGATTGATGAA 60.093 37.037 0.00 0.00 0.00 2.57
1513 1540 6.600882 AACGAAAAGAGTACTAGGGATTGA 57.399 37.500 0.00 0.00 0.00 2.57
1517 1544 6.409524 TTGAAACGAAAAGAGTACTAGGGA 57.590 37.500 0.00 0.00 0.00 4.20
1522 1549 8.485591 CGAGTAATTTGAAACGAAAAGAGTACT 58.514 33.333 0.00 0.00 0.00 2.73
1525 1552 7.242914 ACGAGTAATTTGAAACGAAAAGAGT 57.757 32.000 0.00 0.00 0.00 3.24
1526 1553 9.640974 TTTACGAGTAATTTGAAACGAAAAGAG 57.359 29.630 0.00 0.00 0.00 2.85
1583 1610 9.542462 CTCCATCCATTCTAAATTACTCGTAAA 57.458 33.333 0.00 0.00 0.00 2.01
1584 1611 8.701895 ACTCCATCCATTCTAAATTACTCGTAA 58.298 33.333 0.00 0.00 0.00 3.18
1585 1612 8.246430 ACTCCATCCATTCTAAATTACTCGTA 57.754 34.615 0.00 0.00 0.00 3.43
1586 1613 7.125792 ACTCCATCCATTCTAAATTACTCGT 57.874 36.000 0.00 0.00 0.00 4.18
1587 1614 8.361139 AGTACTCCATCCATTCTAAATTACTCG 58.639 37.037 0.00 0.00 0.00 4.18
1594 1621 9.488762 TCTAAGAAGTACTCCATCCATTCTAAA 57.511 33.333 0.00 0.00 0.00 1.85
1595 1622 9.488762 TTCTAAGAAGTACTCCATCCATTCTAA 57.511 33.333 0.00 0.00 0.00 2.10
1596 1623 9.137459 CTTCTAAGAAGTACTCCATCCATTCTA 57.863 37.037 0.00 0.00 0.00 2.10
1597 1624 7.070571 CCTTCTAAGAAGTACTCCATCCATTCT 59.929 40.741 0.00 0.00 0.00 2.40
1598 1625 7.070074 TCCTTCTAAGAAGTACTCCATCCATTC 59.930 40.741 0.00 0.00 0.00 2.67
1599 1626 6.903534 TCCTTCTAAGAAGTACTCCATCCATT 59.096 38.462 0.00 0.00 0.00 3.16
1600 1627 6.444704 TCCTTCTAAGAAGTACTCCATCCAT 58.555 40.000 0.00 0.00 0.00 3.41
1601 1628 5.838955 TCCTTCTAAGAAGTACTCCATCCA 58.161 41.667 0.00 0.00 0.00 3.41
1602 1629 6.130569 TCTCCTTCTAAGAAGTACTCCATCC 58.869 44.000 0.00 0.00 0.00 3.51
1603 1630 7.057894 TCTCTCCTTCTAAGAAGTACTCCATC 58.942 42.308 0.00 0.00 0.00 3.51
1604 1631 6.975949 TCTCTCCTTCTAAGAAGTACTCCAT 58.024 40.000 0.00 0.00 0.00 3.41
1605 1632 6.215841 TCTCTCTCCTTCTAAGAAGTACTCCA 59.784 42.308 0.00 0.00 0.00 3.86
1606 1633 6.655930 TCTCTCTCCTTCTAAGAAGTACTCC 58.344 44.000 0.00 0.00 0.00 3.85
1607 1634 8.747538 ATTCTCTCTCCTTCTAAGAAGTACTC 57.252 38.462 0.00 0.00 30.16 2.59
1608 1635 8.333235 TGATTCTCTCTCCTTCTAAGAAGTACT 58.667 37.037 0.00 0.00 30.16 2.73
1654 1682 5.759963 ACCGAATCGTTCATGATAGTACTC 58.240 41.667 0.00 0.00 0.00 2.59
1655 1683 5.769484 ACCGAATCGTTCATGATAGTACT 57.231 39.130 0.00 0.00 0.00 2.73
1657 1685 7.174426 ACATCTACCGAATCGTTCATGATAGTA 59.826 37.037 0.82 0.00 0.00 1.82
1658 1686 6.016192 ACATCTACCGAATCGTTCATGATAGT 60.016 38.462 0.82 0.00 0.00 2.12
1667 1695 1.135199 ACGCACATCTACCGAATCGTT 60.135 47.619 0.82 0.00 0.00 3.85
1669 1697 2.041966 GTACGCACATCTACCGAATCG 58.958 52.381 0.00 0.00 0.00 3.34
1674 1702 0.928908 GCTCGTACGCACATCTACCG 60.929 60.000 11.24 0.00 0.00 4.02
1723 1751 0.680921 CATGCCCTGTTGTAGGTGGG 60.681 60.000 0.00 0.00 45.80 4.61
1741 1769 4.136796 CACATGGAAGAAGAAGACCAACA 58.863 43.478 0.00 0.00 36.00 3.33
1742 1770 3.057946 GCACATGGAAGAAGAAGACCAAC 60.058 47.826 0.00 0.00 36.00 3.77
1743 1771 3.149196 GCACATGGAAGAAGAAGACCAA 58.851 45.455 0.00 0.00 36.00 3.67
1744 1772 2.373169 AGCACATGGAAGAAGAAGACCA 59.627 45.455 0.00 0.00 36.83 4.02
1746 1774 2.670414 CGAGCACATGGAAGAAGAAGAC 59.330 50.000 0.00 0.00 0.00 3.01
1771 1828 9.990360 TTCAAACCCTTTTTAATTGGACTTATC 57.010 29.630 0.00 0.00 0.00 1.75
1774 1831 9.337396 GATTTCAAACCCTTTTTAATTGGACTT 57.663 29.630 0.00 0.00 0.00 3.01
1775 1832 8.713971 AGATTTCAAACCCTTTTTAATTGGACT 58.286 29.630 0.00 0.00 0.00 3.85
1832 1890 2.752903 ACAGTGGGAAAACGATAATGCC 59.247 45.455 0.00 0.00 0.00 4.40
1868 1926 2.423538 CAGCCTAGGTTTGCCAATGTAC 59.576 50.000 11.31 0.00 37.19 2.90
1869 1927 2.307392 TCAGCCTAGGTTTGCCAATGTA 59.693 45.455 11.31 0.00 37.19 2.29
1870 1928 1.075374 TCAGCCTAGGTTTGCCAATGT 59.925 47.619 11.31 0.00 37.19 2.71
1871 1929 1.838112 TCAGCCTAGGTTTGCCAATG 58.162 50.000 11.31 0.00 37.19 2.82
1911 1974 1.677576 GATGCCGAAATGAATCAGCCA 59.322 47.619 0.00 0.00 0.00 4.75
1945 2008 0.514691 CTTGCTCTGTTTCGCTGGAC 59.485 55.000 0.00 0.00 0.00 4.02
2041 2146 4.593157 CGAGTCGAATAAACAGAGGAGAG 58.407 47.826 6.73 0.00 0.00 3.20
2090 2196 4.569023 TGCGGCGAGTAGGATGCG 62.569 66.667 12.98 0.00 0.00 4.73
2360 2466 4.176752 GGGATGGTGGCGGACTCC 62.177 72.222 0.00 0.00 0.00 3.85
2442 2590 3.596066 GAGCCTGCGACTCCAGCAA 62.596 63.158 0.00 0.00 44.67 3.91
2556 2704 1.281899 GCTCCGAAGCTGTACATCAC 58.718 55.000 0.00 0.00 45.55 3.06
2592 2740 3.079478 TCTGCTCTCCGGCTGCAT 61.079 61.111 14.33 0.00 36.07 3.96
2959 3108 1.807886 GTGTCGTCCTATGCGAGGT 59.192 57.895 4.50 0.00 46.76 3.85
2976 3125 1.227438 CGGACCCACTGAAACACGT 60.227 57.895 0.00 0.00 0.00 4.49
2983 3132 3.936203 GGTGCACGGACCCACTGA 61.936 66.667 11.45 0.00 32.68 3.41
2997 3146 2.380410 GGTAGCACGTGAAGCGGTG 61.380 63.158 22.23 0.00 46.52 4.94
3006 3155 5.511234 AACGAGATAATAAGGTAGCACGT 57.489 39.130 0.00 0.00 38.11 4.49
3008 3157 7.948278 ATCAAACGAGATAATAAGGTAGCAC 57.052 36.000 0.00 0.00 0.00 4.40
3022 3171 1.806542 GGCTTGAGCAATCAAACGAGA 59.193 47.619 5.24 0.00 44.36 4.04
3023 3172 1.536766 TGGCTTGAGCAATCAAACGAG 59.463 47.619 5.24 0.00 44.36 4.18
3024 3173 1.603456 TGGCTTGAGCAATCAAACGA 58.397 45.000 5.24 0.00 44.36 3.85
3025 3174 2.642139 ATGGCTTGAGCAATCAAACG 57.358 45.000 5.24 0.00 44.36 3.60
3026 3175 8.652810 AATTTATATGGCTTGAGCAATCAAAC 57.347 30.769 5.24 0.00 44.36 2.93
3027 3176 9.669887 AAAATTTATATGGCTTGAGCAATCAAA 57.330 25.926 5.24 4.36 44.36 2.69
3028 3177 9.669887 AAAAATTTATATGGCTTGAGCAATCAA 57.330 25.926 5.24 0.00 44.36 2.57
3082 3231 1.066716 TGATGCAAAAGGCTGAATGGC 60.067 47.619 0.00 0.00 45.15 4.40
3104 3253 0.318107 GCGTTGTTCTGCTTGCATGT 60.318 50.000 1.14 0.00 0.00 3.21
3149 3298 2.753452 GACTCTTCCGTGGACATGTCTA 59.247 50.000 24.50 17.03 0.00 2.59
3156 3305 1.079750 GCCAGACTCTTCCGTGGAC 60.080 63.158 0.00 0.00 31.04 4.02
3199 3348 2.915869 ACCTATGACTGGGTTGGAGAA 58.084 47.619 0.00 0.00 30.85 2.87
3202 3351 4.367166 TGAATACCTATGACTGGGTTGGA 58.633 43.478 0.00 0.00 37.44 3.53
3216 3365 3.244700 GCATGCTACCTCCATGAATACCT 60.245 47.826 11.37 0.00 41.97 3.08
3220 3369 3.220110 CTTGCATGCTACCTCCATGAAT 58.780 45.455 20.33 0.00 41.97 2.57
3257 3406 1.906105 TACCTTCATGGACGCCCACC 61.906 60.000 0.00 0.00 46.98 4.61
3284 3433 0.672401 TGTTTGTACCCGCTAGCTGC 60.672 55.000 13.93 0.00 38.57 5.25
3313 3466 2.671888 CGAGCATGCATGATACTCCATC 59.328 50.000 30.64 9.11 0.00 3.51
3423 3576 8.467598 AGTTACATAAACATAGACGTCACTGAT 58.532 33.333 19.50 6.34 40.83 2.90
3428 3581 9.647797 AATGAAGTTACATAAACATAGACGTCA 57.352 29.630 19.50 4.13 40.83 4.35
3504 3658 0.598158 GCAGCATGGGTGTTGTTGTG 60.598 55.000 0.00 0.00 38.64 3.33
3505 3659 1.042003 TGCAGCATGGGTGTTGTTGT 61.042 50.000 0.00 0.00 38.64 3.32
3546 3701 3.983344 GCAACATTGATGTGTTCCAGAAC 59.017 43.478 3.52 3.52 40.17 3.01
3589 3744 6.101332 GCTTCAATTTTCTGCAACATGGATA 58.899 36.000 0.00 0.00 0.00 2.59
3596 3751 2.061028 CCGGCTTCAATTTTCTGCAAC 58.939 47.619 0.00 0.00 0.00 4.17
3599 3754 2.723124 TTCCGGCTTCAATTTTCTGC 57.277 45.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.