Multiple sequence alignment - TraesCS7A01G458200

Loading Multiple Alignment...

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 TraesCS7A01G458200 chr7A 100.000 2688 0 0 1 2688 653015710 653013023 0.000000e+00 4964.0
1 TraesCS7A01G458200 chr7A 96.875 384 10 2 1507 1890 730872386 730872767 2.650000e-180 641.0
2 TraesCS7A01G458200 chr7A 98.684 304 4 0 2385 2688 55359266 55359569 9.930000e-150 540.0
3 TraesCS7A01G458200 chr7A 90.274 401 35 4 1488 1887 19077798 19078195 3.600000e-144 521.0
4 TraesCS7A01G458200 chr7A 100.000 73 0 0 3074 3146 653012637 653012565 5.470000e-28 135.0
5 TraesCS7A01G458200 chr7A 100.000 60 0 0 3087 3146 55360110 55360169 9.220000e-21 111.0
6 TraesCS7A01G458200 chr3A 96.940 1438 32 4 78 1507 80083603 80082170 0.000000e+00 2401.0
7 TraesCS7A01G458200 chr3A 97.639 466 10 1 1883 2347 80082177 80081712 0.000000e+00 798.0
8 TraesCS7A01G458200 chr3A 97.396 384 8 1 1507 1890 728396432 728396051 0.000000e+00 652.0
9 TraesCS7A01G458200 chr5A 96.801 1438 34 4 78 1507 666132483 666133916 0.000000e+00 2390.0
10 TraesCS7A01G458200 chr5A 95.885 1458 46 6 59 1507 496335826 496334374 0.000000e+00 2348.0
11 TraesCS7A01G458200 chr5A 96.827 914 27 2 54 966 664889334 664888422 0.000000e+00 1526.0
12 TraesCS7A01G458200 chr5A 97.425 466 11 1 1883 2347 496334381 496333916 0.000000e+00 793.0
13 TraesCS7A01G458200 chr5A 94.845 485 13 4 1031 1507 664888429 664887949 0.000000e+00 747.0
14 TraesCS7A01G458200 chr5A 100.000 272 0 0 2417 2688 43537084 43537355 1.300000e-138 503.0
15 TraesCS7A01G458200 chr5A 100.000 73 0 0 3074 3146 43537736 43537808 5.470000e-28 135.0
16 TraesCS7A01G458200 chr1D 94.963 1350 38 14 180 1500 404282251 404283599 0.000000e+00 2089.0
17 TraesCS7A01G458200 chr1D 95.354 452 15 1 1896 2347 404283622 404284067 0.000000e+00 713.0
18 TraesCS7A01G458200 chr1D 96.117 103 4 0 76 178 404281984 404282086 5.400000e-38 169.0
19 TraesCS7A01G458200 chr6A 97.938 388 6 2 1503 1890 590963998 590963613 0.000000e+00 671.0
20 TraesCS7A01G458200 chr6A 97.938 388 6 2 1503 1890 590989805 590989420 0.000000e+00 671.0
21 TraesCS7A01G458200 chr6A 91.429 385 27 5 1507 1890 423316143 423315764 1.000000e-144 523.0
22 TraesCS7A01G458200 chrUn 94.686 414 11 3 1037 1443 477751036 477751445 1.590000e-177 632.0
23 TraesCS7A01G458200 chrUn 95.866 387 16 0 1504 1890 1069543 1069929 7.410000e-176 627.0
24 TraesCS7A01G458200 chr5D 93.846 390 20 3 1505 1891 455823238 455823626 4.520000e-163 584.0
25 TraesCS7A01G458200 chr7B 99.342 304 2 0 2385 2688 477974307 477974004 4.590000e-153 551.0
26 TraesCS7A01G458200 chr7B 98.630 73 1 0 3074 3146 477973618 477973546 2.550000e-26 130.0
27 TraesCS7A01G458200 chr5B 92.308 390 27 3 1505 1891 557898310 557898699 4.590000e-153 551.0
28 TraesCS7A01G458200 chr5B 79.675 246 44 5 81 323 231110302 231110060 4.170000e-39 172.0
29 TraesCS7A01G458200 chr5B 100.000 73 0 0 3074 3146 692519216 692519288 5.470000e-28 135.0
30 TraesCS7A01G458200 chr5B 100.000 41 0 0 2648 2688 692519069 692519109 3.360000e-10 76.8
31 TraesCS7A01G458200 chr2B 98.684 304 4 0 2385 2688 677043421 677043724 9.930000e-150 540.0
32 TraesCS7A01G458200 chr2B 100.000 73 0 0 3074 3146 677043831 677043903 5.470000e-28 135.0
33 TraesCS7A01G458200 chr3B 97.368 304 8 0 2385 2688 415899672 415899975 4.650000e-143 518.0
34 TraesCS7A01G458200 chr3B 97.924 289 6 0 2385 2673 4304698 4304986 4.680000e-138 501.0
35 TraesCS7A01G458200 chr3B 100.000 73 0 0 3074 3146 4305511 4305583 5.470000e-28 135.0
36 TraesCS7A01G458200 chr3B 100.000 73 0 0 3074 3146 415900011 415900083 5.470000e-28 135.0
37 TraesCS7A01G458200 chr3B 98.182 55 1 0 3092 3146 685069898 685069844 2.580000e-16 97.1
38 TraesCS7A01G458200 chr1B 100.000 272 0 0 2417 2688 131779748 131780019 1.300000e-138 503.0
39 TraesCS7A01G458200 chr1B 98.842 259 3 0 2385 2643 131779218 131779476 2.210000e-126 462.0
40 TraesCS7A01G458200 chr1B 100.000 73 0 0 3074 3146 131780201 131780273 5.470000e-28 135.0
41 TraesCS7A01G458200 chr4D 96.578 263 9 0 2386 2648 95818427 95818165 1.340000e-118 436.0
42 TraesCS7A01G458200 chr4A 80.351 285 53 3 56 338 148888064 148888347 2.460000e-51 213.0
43 TraesCS7A01G458200 chr7D 85.024 207 28 3 51 256 111043333 111043129 1.140000e-49 207.0
44 TraesCS7A01G458200 chr3D 86.275 153 21 0 2191 2343 270460054 270460206 1.940000e-37 167.0


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 TraesCS7A01G458200 chr7A 653012565 653015710 3145 True 2549.500000 4964 100.0000 1 3146 2 chr7A.!!$R1 3145
1 TraesCS7A01G458200 chr7A 55359266 55360169 903 False 325.500000 540 99.3420 2385 3146 2 chr7A.!!$F3 761
2 TraesCS7A01G458200 chr3A 80081712 80083603 1891 True 1599.500000 2401 97.2895 78 2347 2 chr3A.!!$R2 2269
3 TraesCS7A01G458200 chr5A 666132483 666133916 1433 False 2390.000000 2390 96.8010 78 1507 1 chr5A.!!$F1 1429
4 TraesCS7A01G458200 chr5A 496333916 496335826 1910 True 1570.500000 2348 96.6550 59 2347 2 chr5A.!!$R1 2288
5 TraesCS7A01G458200 chr5A 664887949 664889334 1385 True 1136.500000 1526 95.8360 54 1507 2 chr5A.!!$R2 1453
6 TraesCS7A01G458200 chr5A 43537084 43537808 724 False 319.000000 503 100.0000 2417 3146 2 chr5A.!!$F2 729
7 TraesCS7A01G458200 chr1D 404281984 404284067 2083 False 990.333333 2089 95.4780 76 2347 3 chr1D.!!$F1 2271
8 TraesCS7A01G458200 chr7B 477973546 477974307 761 True 340.500000 551 98.9860 2385 3146 2 chr7B.!!$R1 761
9 TraesCS7A01G458200 chr3B 4304698 4305583 885 False 318.000000 501 98.9620 2385 3146 2 chr3B.!!$F1 761
10 TraesCS7A01G458200 chr1B 131779218 131780273 1055 False 366.666667 503 99.6140 2385 3146 3 chr1B.!!$F1 761

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
940 1117 1.963515 GGTTGCTTTCCATGTCTTGGT 59.036 47.619 4.76 0.0 46.52 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2564 0.305922 GATTTGGATCTTGCTCCGCG 59.694 55.0 0.0 0.0 38.21 6.46 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
22 23 5.452078 CTCTCTCTCTCTCTCTCTCTCTC 57.548 52.174 0.00 0.00 0.00 3.20
23 24 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
24 25 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
25 26 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
26 27 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
27 28 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
28 29 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
29 30 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
30 31 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
31 32 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
32 33 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
33 34 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
34 35 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
35 36 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
36 37 7.990055 TCTCTCTCTCTCTCTCTCTCTCTATA 58.010 42.308 0.00 0.00 0.00 1.31
37 38 8.619281 TCTCTCTCTCTCTCTCTCTCTCTATAT 58.381 40.741 0.00 0.00 0.00 0.86
38 39 9.913310 CTCTCTCTCTCTCTCTCTCTCTATATA 57.087 40.741 0.00 0.00 0.00 0.86
214 379 3.755155 GCATATACCAAAGGGGAAGCCAT 60.755 47.826 0.00 0.00 41.15 4.40
257 422 3.283751 CGGACCAAAATGGCAACCTATA 58.716 45.455 0.00 0.00 42.67 1.31
565 737 5.899120 TTACAGGCTAGACTTAGTGAGTG 57.101 43.478 0.00 0.00 39.19 3.51
598 770 4.586884 TGATGAGAGGTCGTTACAGTAGT 58.413 43.478 0.00 0.00 0.00 2.73
602 775 3.087781 AGAGGTCGTTACAGTAGTTCCC 58.912 50.000 0.00 0.00 0.00 3.97
650 823 3.006940 GGCAACACATTGTTCGGATCTA 58.993 45.455 0.00 0.00 38.77 1.98
940 1117 1.963515 GGTTGCTTTCCATGTCTTGGT 59.036 47.619 4.76 0.00 46.52 3.67
1076 1261 7.127405 TCCTATGTGGTAAGTGGTAACTGATA 58.873 38.462 0.00 0.00 35.23 2.15
1093 1278 6.272822 ACTGATATTGAAACTTGAAAGGCC 57.727 37.500 0.00 0.00 0.00 5.19
1111 1299 2.611518 GCCACTGCTGTCTTGTACTAG 58.388 52.381 0.00 0.00 33.53 2.57
1114 1302 4.734917 CCACTGCTGTCTTGTACTAGTAC 58.265 47.826 23.58 23.58 36.63 2.73
1115 1303 4.459685 CCACTGCTGTCTTGTACTAGTACT 59.540 45.833 28.56 0.00 37.00 2.73
1116 1304 5.646793 CCACTGCTGTCTTGTACTAGTACTA 59.353 44.000 28.56 21.90 37.00 1.82
1256 1448 2.977456 AACGGCAGCGCATCACAA 60.977 55.556 11.47 0.00 0.00 3.33
1324 1523 6.058183 GCATGTATTCCTACTCCTTGTCAAT 58.942 40.000 0.00 0.00 0.00 2.57
1373 1577 4.745620 GCGTTCTATAGAGGCTCGATTTTT 59.254 41.667 15.39 0.00 0.00 1.94
1490 1694 2.079158 CATCTCATGGCGTGTTCTTGT 58.921 47.619 6.60 0.00 0.00 3.16
1507 1716 7.116519 GTGTTCTTGTTGTCCTCTTAGTGATAC 59.883 40.741 0.00 0.00 0.00 2.24
1508 1717 7.015292 TGTTCTTGTTGTCCTCTTAGTGATACT 59.985 37.037 0.00 0.00 0.00 2.12
1509 1718 8.521176 GTTCTTGTTGTCCTCTTAGTGATACTA 58.479 37.037 0.00 0.00 0.00 1.82
1510 1719 8.282455 TCTTGTTGTCCTCTTAGTGATACTAG 57.718 38.462 0.00 0.00 31.47 2.57
1511 1720 8.107729 TCTTGTTGTCCTCTTAGTGATACTAGA 58.892 37.037 0.00 0.00 31.47 2.43
1512 1721 8.824756 TTGTTGTCCTCTTAGTGATACTAGAT 57.175 34.615 0.00 0.00 31.47 1.98
1513 1722 8.226819 TGTTGTCCTCTTAGTGATACTAGATG 57.773 38.462 0.00 0.00 31.47 2.90
1514 1723 8.053355 TGTTGTCCTCTTAGTGATACTAGATGA 58.947 37.037 0.00 0.00 31.47 2.92
1515 1724 9.073475 GTTGTCCTCTTAGTGATACTAGATGAT 57.927 37.037 0.00 0.00 31.47 2.45
1517 1726 9.727859 TGTCCTCTTAGTGATACTAGATGATAC 57.272 37.037 0.00 0.00 31.47 2.24
1518 1727 9.169592 GTCCTCTTAGTGATACTAGATGATACC 57.830 40.741 0.00 0.00 31.47 2.73
1519 1728 8.330247 TCCTCTTAGTGATACTAGATGATACCC 58.670 40.741 0.00 0.00 31.47 3.69
1520 1729 7.558444 CCTCTTAGTGATACTAGATGATACCCC 59.442 44.444 0.00 0.00 31.47 4.95
1521 1730 7.110810 TCTTAGTGATACTAGATGATACCCCG 58.889 42.308 0.00 0.00 31.47 5.73
1522 1731 4.017808 AGTGATACTAGATGATACCCCGC 58.982 47.826 0.00 0.00 0.00 6.13
1523 1732 3.762288 GTGATACTAGATGATACCCCGCA 59.238 47.826 0.00 0.00 0.00 5.69
1524 1733 3.762288 TGATACTAGATGATACCCCGCAC 59.238 47.826 0.00 0.00 0.00 5.34
1525 1734 0.959553 ACTAGATGATACCCCGCACG 59.040 55.000 0.00 0.00 0.00 5.34
1526 1735 0.959553 CTAGATGATACCCCGCACGT 59.040 55.000 0.00 0.00 0.00 4.49
1527 1736 1.340248 CTAGATGATACCCCGCACGTT 59.660 52.381 0.00 0.00 0.00 3.99
1528 1737 0.179084 AGATGATACCCCGCACGTTG 60.179 55.000 0.00 0.00 0.00 4.10
1529 1738 0.461339 GATGATACCCCGCACGTTGT 60.461 55.000 0.00 0.00 0.00 3.32
1530 1739 0.035820 ATGATACCCCGCACGTTGTT 60.036 50.000 0.00 0.00 0.00 2.83
1531 1740 0.951525 TGATACCCCGCACGTTGTTG 60.952 55.000 0.00 0.00 0.00 3.33
1532 1741 2.248274 GATACCCCGCACGTTGTTGC 62.248 60.000 0.00 0.00 39.28 4.17
1538 1747 2.642700 GCACGTTGTTGCGGGAAT 59.357 55.556 0.00 0.00 37.48 3.01
1539 1748 1.870383 GCACGTTGTTGCGGGAATA 59.130 52.632 0.00 0.00 37.48 1.75
1540 1749 0.450184 GCACGTTGTTGCGGGAATAT 59.550 50.000 0.00 0.00 37.48 1.28
1541 1750 1.135517 GCACGTTGTTGCGGGAATATT 60.136 47.619 0.00 0.00 37.48 1.28
1542 1751 2.669950 GCACGTTGTTGCGGGAATATTT 60.670 45.455 0.00 0.00 37.48 1.40
1543 1752 3.426426 GCACGTTGTTGCGGGAATATTTA 60.426 43.478 0.00 0.00 37.48 1.40
1544 1753 4.339429 CACGTTGTTGCGGGAATATTTAG 58.661 43.478 0.00 0.00 37.48 1.85
1545 1754 3.181504 ACGTTGTTGCGGGAATATTTAGC 60.182 43.478 0.00 0.00 35.98 3.09
1546 1755 3.181505 CGTTGTTGCGGGAATATTTAGCA 60.182 43.478 8.66 8.66 35.90 3.49
1547 1756 4.673061 CGTTGTTGCGGGAATATTTAGCAA 60.673 41.667 16.75 16.75 44.24 3.91
1552 1761 6.892658 TTGCGGGAATATTTAGCAACATAT 57.107 33.333 16.75 0.00 42.02 1.78
1553 1762 6.892658 TGCGGGAATATTTAGCAACATATT 57.107 33.333 9.86 0.00 34.66 1.28
1554 1763 7.283625 TGCGGGAATATTTAGCAACATATTT 57.716 32.000 9.86 0.00 34.66 1.40
1555 1764 8.397575 TGCGGGAATATTTAGCAACATATTTA 57.602 30.769 9.86 0.00 34.66 1.40
1556 1765 8.851145 TGCGGGAATATTTAGCAACATATTTAA 58.149 29.630 9.86 0.00 34.66 1.52
1557 1766 9.685828 GCGGGAATATTTAGCAACATATTTAAA 57.314 29.630 0.00 0.00 0.00 1.52
1570 1779 9.928236 GCAACATATTTAAATGTGTTTTGTTGT 57.072 25.926 29.79 13.13 44.80 3.32
1577 1786 8.649973 TTTAAATGTGTTTTGTTGTATGACCC 57.350 30.769 0.00 0.00 0.00 4.46
1578 1787 5.860941 AATGTGTTTTGTTGTATGACCCA 57.139 34.783 0.00 0.00 0.00 4.51
1579 1788 6.418057 AATGTGTTTTGTTGTATGACCCAT 57.582 33.333 0.00 0.00 0.00 4.00
1580 1789 5.193663 TGTGTTTTGTTGTATGACCCATG 57.806 39.130 0.00 0.00 0.00 3.66
1581 1790 4.889995 TGTGTTTTGTTGTATGACCCATGA 59.110 37.500 0.00 0.00 0.00 3.07
1582 1791 5.360999 TGTGTTTTGTTGTATGACCCATGAA 59.639 36.000 0.00 0.00 0.00 2.57
1583 1792 6.041409 TGTGTTTTGTTGTATGACCCATGAAT 59.959 34.615 0.00 0.00 0.00 2.57
1584 1793 7.231519 TGTGTTTTGTTGTATGACCCATGAATA 59.768 33.333 0.00 0.00 0.00 1.75
1585 1794 8.250332 GTGTTTTGTTGTATGACCCATGAATAT 58.750 33.333 0.00 0.00 0.00 1.28
1586 1795 8.811017 TGTTTTGTTGTATGACCCATGAATATT 58.189 29.630 0.00 0.00 0.00 1.28
1587 1796 9.651913 GTTTTGTTGTATGACCCATGAATATTT 57.348 29.630 0.00 0.00 0.00 1.40
1588 1797 9.650539 TTTTGTTGTATGACCCATGAATATTTG 57.349 29.630 0.00 0.00 0.00 2.32
1589 1798 8.586879 TTGTTGTATGACCCATGAATATTTGA 57.413 30.769 0.00 0.00 0.00 2.69
1590 1799 8.586879 TGTTGTATGACCCATGAATATTTGAA 57.413 30.769 0.00 0.00 0.00 2.69
1591 1800 8.685427 TGTTGTATGACCCATGAATATTTGAAG 58.315 33.333 0.00 0.00 0.00 3.02
1592 1801 8.686334 GTTGTATGACCCATGAATATTTGAAGT 58.314 33.333 0.00 0.00 0.00 3.01
1593 1802 9.913310 TTGTATGACCCATGAATATTTGAAGTA 57.087 29.630 0.00 0.00 0.00 2.24
1594 1803 9.913310 TGTATGACCCATGAATATTTGAAGTAA 57.087 29.630 0.00 0.00 0.00 2.24
1714 1923 7.705325 AGAATGAAAATTCTCATGTATGCTTGC 59.295 33.333 0.00 0.00 36.20 4.01
1715 1924 6.270156 TGAAAATTCTCATGTATGCTTGCA 57.730 33.333 0.00 0.00 0.00 4.08
1716 1925 6.869695 TGAAAATTCTCATGTATGCTTGCAT 58.130 32.000 12.88 12.88 0.00 3.96
1717 1926 6.754675 TGAAAATTCTCATGTATGCTTGCATG 59.245 34.615 20.18 20.18 44.56 4.06
1718 1927 5.847111 AATTCTCATGTATGCTTGCATGT 57.153 34.783 23.51 7.77 43.87 3.21
1719 1928 5.847111 ATTCTCATGTATGCTTGCATGTT 57.153 34.783 23.51 9.90 43.87 2.71
1720 1929 4.625972 TCTCATGTATGCTTGCATGTTG 57.374 40.909 23.51 18.51 43.87 3.33
1721 1930 4.263435 TCTCATGTATGCTTGCATGTTGA 58.737 39.130 23.51 19.89 43.87 3.18
1722 1931 4.334481 TCTCATGTATGCTTGCATGTTGAG 59.666 41.667 23.51 23.12 43.87 3.02
1723 1932 4.263435 TCATGTATGCTTGCATGTTGAGA 58.737 39.130 23.51 7.47 43.87 3.27
1724 1933 4.885325 TCATGTATGCTTGCATGTTGAGAT 59.115 37.500 23.51 0.00 43.87 2.75
1725 1934 4.625972 TGTATGCTTGCATGTTGAGATG 57.374 40.909 17.26 0.00 0.00 2.90
1726 1935 4.263435 TGTATGCTTGCATGTTGAGATGA 58.737 39.130 17.26 0.00 0.00 2.92
1727 1936 4.334481 TGTATGCTTGCATGTTGAGATGAG 59.666 41.667 17.26 0.00 0.00 2.90
1728 1937 2.786777 TGCTTGCATGTTGAGATGAGT 58.213 42.857 1.14 0.00 0.00 3.41
1729 1938 2.745821 TGCTTGCATGTTGAGATGAGTC 59.254 45.455 1.14 0.00 0.00 3.36
1730 1939 3.008330 GCTTGCATGTTGAGATGAGTCT 58.992 45.455 1.14 0.00 37.42 3.24
1731 1940 3.439476 GCTTGCATGTTGAGATGAGTCTT 59.561 43.478 1.14 0.00 33.97 3.01
1732 1941 4.082895 GCTTGCATGTTGAGATGAGTCTTT 60.083 41.667 1.14 0.00 33.97 2.52
1733 1942 5.564259 GCTTGCATGTTGAGATGAGTCTTTT 60.564 40.000 1.14 0.00 33.97 2.27
1734 1943 6.395426 TTGCATGTTGAGATGAGTCTTTTT 57.605 33.333 0.00 0.00 33.97 1.94
1760 1969 4.707030 TGATGTTTCATGATGAAGTGGC 57.293 40.909 8.01 1.39 37.70 5.01
1761 1970 4.080687 TGATGTTTCATGATGAAGTGGCA 58.919 39.130 8.01 7.03 37.70 4.92
1762 1971 4.707934 TGATGTTTCATGATGAAGTGGCAT 59.292 37.500 8.01 10.92 37.70 4.40
1763 1972 4.443913 TGTTTCATGATGAAGTGGCATG 57.556 40.909 8.01 0.00 37.70 4.06
1764 1973 3.184541 GTTTCATGATGAAGTGGCATGC 58.815 45.455 9.90 9.90 37.70 4.06
1765 1974 2.430248 TCATGATGAAGTGGCATGCT 57.570 45.000 18.92 0.00 39.30 3.79
1766 1975 2.730382 TCATGATGAAGTGGCATGCTT 58.270 42.857 18.92 3.65 39.30 3.91
1767 1976 2.425668 TCATGATGAAGTGGCATGCTTG 59.574 45.455 18.92 0.00 39.30 4.01
1768 1977 6.697653 TTCATGATGAAGTGGCATGCTTGC 62.698 45.833 18.92 15.87 38.74 4.01
1782 1991 5.690997 CATGCTTGCATGTTGAGAGATAT 57.309 39.130 23.00 0.00 0.00 1.63
1783 1992 6.796705 CATGCTTGCATGTTGAGAGATATA 57.203 37.500 23.00 0.00 0.00 0.86
1784 1993 7.379098 CATGCTTGCATGTTGAGAGATATAT 57.621 36.000 23.00 0.00 0.00 0.86
1785 1994 6.796705 TGCTTGCATGTTGAGAGATATATG 57.203 37.500 1.14 0.00 0.00 1.78
1786 1995 6.527423 TGCTTGCATGTTGAGAGATATATGA 58.473 36.000 1.14 0.00 0.00 2.15
1787 1996 7.166167 TGCTTGCATGTTGAGAGATATATGAT 58.834 34.615 1.14 0.00 0.00 2.45
1788 1997 8.316214 TGCTTGCATGTTGAGAGATATATGATA 58.684 33.333 1.14 0.00 0.00 2.15
1789 1998 9.159364 GCTTGCATGTTGAGAGATATATGATAA 57.841 33.333 1.14 0.00 0.00 1.75
1792 2001 9.609346 TGCATGTTGAGAGATATATGATAATGG 57.391 33.333 0.00 0.00 0.00 3.16
1793 2002 9.828039 GCATGTTGAGAGATATATGATAATGGA 57.172 33.333 0.00 0.00 0.00 3.41
1796 2005 9.552695 TGTTGAGAGATATATGATAATGGAGGT 57.447 33.333 0.00 0.00 0.00 3.85
1797 2006 9.814899 GTTGAGAGATATATGATAATGGAGGTG 57.185 37.037 0.00 0.00 0.00 4.00
1798 2007 8.544687 TGAGAGATATATGATAATGGAGGTGG 57.455 38.462 0.00 0.00 0.00 4.61
1799 2008 7.566509 TGAGAGATATATGATAATGGAGGTGGG 59.433 40.741 0.00 0.00 0.00 4.61
1800 2009 6.328672 AGAGATATATGATAATGGAGGTGGGC 59.671 42.308 0.00 0.00 0.00 5.36
1801 2010 5.370880 AGATATATGATAATGGAGGTGGGCC 59.629 44.000 0.00 0.00 0.00 5.80
1811 2020 3.056213 AGGTGGGCCTTTTGTCATG 57.944 52.632 4.53 0.00 44.18 3.07
1812 2021 1.187567 AGGTGGGCCTTTTGTCATGC 61.188 55.000 4.53 0.00 44.18 4.06
1813 2022 1.470996 GGTGGGCCTTTTGTCATGCA 61.471 55.000 4.53 0.00 0.00 3.96
1814 2023 0.609662 GTGGGCCTTTTGTCATGCAT 59.390 50.000 4.53 0.00 0.00 3.96
1815 2024 0.609151 TGGGCCTTTTGTCATGCATG 59.391 50.000 21.07 21.07 0.00 4.06
1816 2025 0.609662 GGGCCTTTTGTCATGCATGT 59.390 50.000 25.43 0.00 0.00 3.21
1817 2026 1.002315 GGGCCTTTTGTCATGCATGTT 59.998 47.619 25.43 0.00 0.00 2.71
1818 2027 2.070783 GGCCTTTTGTCATGCATGTTG 58.929 47.619 25.43 2.63 0.00 3.33
1819 2028 2.548493 GGCCTTTTGTCATGCATGTTGT 60.548 45.455 25.43 0.00 0.00 3.32
1820 2029 2.477375 GCCTTTTGTCATGCATGTTGTG 59.523 45.455 25.43 12.02 0.00 3.33
1821 2030 3.719924 CCTTTTGTCATGCATGTTGTGT 58.280 40.909 25.43 0.00 0.00 3.72
1822 2031 3.491639 CCTTTTGTCATGCATGTTGTGTG 59.508 43.478 25.43 12.95 0.00 3.82
1823 2032 4.361420 CTTTTGTCATGCATGTTGTGTGA 58.639 39.130 25.43 2.95 0.00 3.58
1824 2033 4.587584 TTTGTCATGCATGTTGTGTGAT 57.412 36.364 25.43 0.00 0.00 3.06
1825 2034 3.562567 TGTCATGCATGTTGTGTGATG 57.437 42.857 25.43 0.00 0.00 3.07
1826 2035 3.147629 TGTCATGCATGTTGTGTGATGA 58.852 40.909 25.43 0.54 30.85 2.92
1827 2036 3.759618 TGTCATGCATGTTGTGTGATGAT 59.240 39.130 25.43 0.00 33.91 2.45
1828 2037 4.102649 GTCATGCATGTTGTGTGATGATG 58.897 43.478 25.43 0.00 33.91 3.07
1829 2038 3.759618 TCATGCATGTTGTGTGATGATGT 59.240 39.130 25.43 0.00 29.35 3.06
1830 2039 3.562567 TGCATGTTGTGTGATGATGTG 57.437 42.857 0.00 0.00 0.00 3.21
1831 2040 2.229302 TGCATGTTGTGTGATGATGTGG 59.771 45.455 0.00 0.00 0.00 4.17
1832 2041 2.871133 CATGTTGTGTGATGATGTGGC 58.129 47.619 0.00 0.00 0.00 5.01
1833 2042 1.978454 TGTTGTGTGATGATGTGGCA 58.022 45.000 0.00 0.00 0.00 4.92
1834 2043 2.516906 TGTTGTGTGATGATGTGGCAT 58.483 42.857 0.00 0.00 0.00 4.40
1835 2044 3.683802 TGTTGTGTGATGATGTGGCATA 58.316 40.909 0.00 0.00 0.00 3.14
1836 2045 3.439825 TGTTGTGTGATGATGTGGCATAC 59.560 43.478 0.00 0.00 0.00 2.39
1837 2046 3.632643 TGTGTGATGATGTGGCATACT 57.367 42.857 0.00 0.00 0.00 2.12
1838 2047 3.954200 TGTGTGATGATGTGGCATACTT 58.046 40.909 0.00 0.00 0.00 2.24
1839 2048 3.690628 TGTGTGATGATGTGGCATACTTG 59.309 43.478 0.00 0.00 0.00 3.16
1857 2066 8.206325 CATACTTGCATGTTGAGAGAAATAGT 57.794 34.615 10.85 0.00 0.00 2.12
1858 2067 8.671921 CATACTTGCATGTTGAGAGAAATAGTT 58.328 33.333 10.85 0.00 0.00 2.24
1859 2068 9.890629 ATACTTGCATGTTGAGAGAAATAGTTA 57.109 29.630 10.85 0.00 0.00 2.24
1860 2069 8.261492 ACTTGCATGTTGAGAGAAATAGTTAG 57.739 34.615 0.00 0.00 0.00 2.34
1861 2070 7.880195 ACTTGCATGTTGAGAGAAATAGTTAGT 59.120 33.333 0.00 0.00 0.00 2.24
1862 2071 7.601073 TGCATGTTGAGAGAAATAGTTAGTG 57.399 36.000 0.00 0.00 0.00 2.74
1863 2072 6.595326 TGCATGTTGAGAGAAATAGTTAGTGG 59.405 38.462 0.00 0.00 0.00 4.00
1864 2073 6.037610 GCATGTTGAGAGAAATAGTTAGTGGG 59.962 42.308 0.00 0.00 0.00 4.61
1865 2074 6.049955 TGTTGAGAGAAATAGTTAGTGGGG 57.950 41.667 0.00 0.00 0.00 4.96
1866 2075 5.045869 TGTTGAGAGAAATAGTTAGTGGGGG 60.046 44.000 0.00 0.00 0.00 5.40
1867 2076 3.454812 TGAGAGAAATAGTTAGTGGGGGC 59.545 47.826 0.00 0.00 0.00 5.80
1868 2077 3.712218 GAGAGAAATAGTTAGTGGGGGCT 59.288 47.826 0.00 0.00 0.00 5.19
1869 2078 4.892198 AGAGAAATAGTTAGTGGGGGCTA 58.108 43.478 0.00 0.00 0.00 3.93
1870 2079 4.902448 AGAGAAATAGTTAGTGGGGGCTAG 59.098 45.833 0.00 0.00 0.00 3.42
1871 2080 3.391626 AGAAATAGTTAGTGGGGGCTAGC 59.608 47.826 6.04 6.04 0.00 3.42
1872 2081 2.797285 ATAGTTAGTGGGGGCTAGCT 57.203 50.000 15.72 0.00 36.65 3.32
1873 2082 3.917324 ATAGTTAGTGGGGGCTAGCTA 57.083 47.619 15.72 0.00 38.49 3.32
1874 2083 2.797285 AGTTAGTGGGGGCTAGCTAT 57.203 50.000 15.72 0.00 32.08 2.97
1875 2084 3.061909 AGTTAGTGGGGGCTAGCTATT 57.938 47.619 15.72 0.00 32.08 1.73
1876 2085 3.394645 AGTTAGTGGGGGCTAGCTATTT 58.605 45.455 15.72 0.00 32.08 1.40
1877 2086 4.563782 AGTTAGTGGGGGCTAGCTATTTA 58.436 43.478 15.72 0.00 32.08 1.40
1878 2087 4.593634 AGTTAGTGGGGGCTAGCTATTTAG 59.406 45.833 15.72 0.00 32.08 1.85
1879 2088 3.346146 AGTGGGGGCTAGCTATTTAGA 57.654 47.619 15.72 0.00 0.00 2.10
1880 2089 3.875571 AGTGGGGGCTAGCTATTTAGAT 58.124 45.455 15.72 0.00 0.00 1.98
1881 2090 5.024803 AGTGGGGGCTAGCTATTTAGATA 57.975 43.478 15.72 0.00 0.00 1.98
1882 2091 5.604752 AGTGGGGGCTAGCTATTTAGATAT 58.395 41.667 15.72 0.00 0.00 1.63
1883 2092 6.753134 AGTGGGGGCTAGCTATTTAGATATA 58.247 40.000 15.72 0.00 0.00 0.86
1884 2093 6.841755 AGTGGGGGCTAGCTATTTAGATATAG 59.158 42.308 15.72 0.00 0.00 1.31
1885 2094 6.612049 GTGGGGGCTAGCTATTTAGATATAGT 59.388 42.308 15.72 0.00 31.96 2.12
1886 2095 7.783596 GTGGGGGCTAGCTATTTAGATATAGTA 59.216 40.741 15.72 0.00 31.96 1.82
1887 2096 8.005388 TGGGGGCTAGCTATTTAGATATAGTAG 58.995 40.741 15.72 0.00 31.96 2.57
1888 2097 8.226112 GGGGGCTAGCTATTTAGATATAGTAGA 58.774 40.741 15.72 0.00 31.96 2.59
1968 2181 6.406370 TGATGAAACATCTTCCTATCGTTGT 58.594 36.000 11.98 0.00 0.00 3.32
1977 2190 1.275010 TCCTATCGTTGTTGCTGCTCA 59.725 47.619 0.00 0.00 0.00 4.26
2057 2270 1.620822 AGCAATGGAAGCGGAAGTTT 58.379 45.000 0.00 0.00 37.19 2.66
2229 2442 7.493320 AGTGTACATTTGTTCGTTGTTCTCTTA 59.507 33.333 0.00 0.00 0.00 2.10
2261 2474 1.737236 TGATTGTTACACCTCGCATGC 59.263 47.619 7.91 7.91 0.00 4.06
2281 2494 2.978010 CGCAACCGAGCCAAAGGT 60.978 61.111 0.00 0.00 43.68 3.50
2347 2560 4.502950 GGTTCATCCCATGTTGAAGCAAAA 60.503 41.667 19.32 0.00 43.36 2.44
2348 2561 4.524316 TCATCCCATGTTGAAGCAAAAG 57.476 40.909 0.00 0.00 0.00 2.27
2349 2562 3.258872 TCATCCCATGTTGAAGCAAAAGG 59.741 43.478 0.00 0.00 0.00 3.11
2350 2563 1.969923 TCCCATGTTGAAGCAAAAGGG 59.030 47.619 0.00 0.00 32.87 3.95
2351 2564 1.608801 CCCATGTTGAAGCAAAAGGGC 60.609 52.381 0.00 0.00 31.85 5.19
2352 2565 1.421382 CATGTTGAAGCAAAAGGGCG 58.579 50.000 0.00 0.00 39.27 6.13
2353 2566 0.319813 ATGTTGAAGCAAAAGGGCGC 60.320 50.000 0.00 0.00 39.27 6.53
2354 2567 2.016165 GTTGAAGCAAAAGGGCGCG 61.016 57.895 0.00 0.00 39.27 6.86
2355 2568 3.206211 TTGAAGCAAAAGGGCGCGG 62.206 57.895 8.83 0.00 39.27 6.46
2356 2569 3.361977 GAAGCAAAAGGGCGCGGA 61.362 61.111 8.83 0.00 39.27 5.54
2357 2570 3.328288 GAAGCAAAAGGGCGCGGAG 62.328 63.158 8.83 0.00 39.27 4.63
2372 2585 2.042686 CGGAGCAAGATCCAAATCCA 57.957 50.000 5.11 0.00 39.53 3.41
2373 2586 2.368439 CGGAGCAAGATCCAAATCCAA 58.632 47.619 5.11 0.00 39.53 3.53
2374 2587 2.754552 CGGAGCAAGATCCAAATCCAAA 59.245 45.455 5.11 0.00 39.53 3.28
2375 2588 3.193267 CGGAGCAAGATCCAAATCCAAAA 59.807 43.478 5.11 0.00 39.53 2.44
2376 2589 4.321899 CGGAGCAAGATCCAAATCCAAAAA 60.322 41.667 5.11 0.00 39.53 1.94
2377 2590 5.625197 CGGAGCAAGATCCAAATCCAAAAAT 60.625 40.000 5.11 0.00 39.53 1.82
2378 2591 5.814188 GGAGCAAGATCCAAATCCAAAAATC 59.186 40.000 0.00 0.00 39.34 2.17
2379 2592 5.737860 AGCAAGATCCAAATCCAAAAATCC 58.262 37.500 0.00 0.00 31.78 3.01
2380 2593 5.486419 AGCAAGATCCAAATCCAAAAATCCT 59.514 36.000 0.00 0.00 31.78 3.24
2381 2594 5.814188 GCAAGATCCAAATCCAAAAATCCTC 59.186 40.000 0.00 0.00 31.78 3.71
2382 2595 6.574859 GCAAGATCCAAATCCAAAAATCCTCA 60.575 38.462 0.00 0.00 31.78 3.86
2383 2596 7.388437 CAAGATCCAAATCCAAAAATCCTCAA 58.612 34.615 0.00 0.00 31.78 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2 3 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4 5 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5 6 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
6 7 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
7 8 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
8 9 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9 10 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
10 11 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
11 12 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
12 13 8.821686 ATATAGAGAGAGAGAGAGAGAGAGAG 57.178 42.308 0.00 0.00 0.00 3.20
73 74 9.364653 AGTGTAGATAGGAAAACCGTTCTATAT 57.635 33.333 0.00 0.00 0.00 0.86
74 75 8.757982 AGTGTAGATAGGAAAACCGTTCTATA 57.242 34.615 0.00 0.00 0.00 1.31
76 78 7.201767 GCTAGTGTAGATAGGAAAACCGTTCTA 60.202 40.741 0.00 0.00 0.00 2.10
84 86 5.656859 TCTGCTGCTAGTGTAGATAGGAAAA 59.343 40.000 0.00 0.00 0.00 2.29
214 379 3.751479 TGCTCTCTAAAGTTCAGCACA 57.249 42.857 0.00 0.00 35.17 4.57
565 737 2.699846 ACCTCTCATCAATGCCTCTCTC 59.300 50.000 0.00 0.00 0.00 3.20
598 770 2.331893 CGAATTGCAGTGCCGGGAA 61.332 57.895 13.72 0.00 0.00 3.97
602 775 2.176546 CACCGAATTGCAGTGCCG 59.823 61.111 13.72 8.63 0.00 5.69
759 932 4.605968 CACAAATCCGTGATGAAAACACA 58.394 39.130 0.00 0.00 39.94 3.72
1076 1261 3.493176 GCAGTGGCCTTTCAAGTTTCAAT 60.493 43.478 3.32 0.00 0.00 2.57
1093 1278 5.630661 AGTACTAGTACAAGACAGCAGTG 57.369 43.478 29.87 0.00 38.48 3.66
1137 1325 3.275143 TCAAAAACACGCTTCTTCCTCA 58.725 40.909 0.00 0.00 0.00 3.86
1256 1448 2.049433 CGTCTCCGCGTGGTCTTT 60.049 61.111 16.01 0.00 36.30 2.52
1324 1523 7.554118 CAGCTCTAAATCCAGAATAGGACAAAA 59.446 37.037 0.00 0.00 41.30 2.44
1507 1716 0.959553 ACGTGCGGGGTATCATCTAG 59.040 55.000 0.00 0.00 0.00 2.43
1508 1717 1.067974 CAACGTGCGGGGTATCATCTA 59.932 52.381 0.00 0.00 0.00 1.98
1509 1718 0.179084 CAACGTGCGGGGTATCATCT 60.179 55.000 0.00 0.00 0.00 2.90
1510 1719 0.461339 ACAACGTGCGGGGTATCATC 60.461 55.000 0.00 0.00 0.00 2.92
1511 1720 0.035820 AACAACGTGCGGGGTATCAT 60.036 50.000 0.00 0.00 0.00 2.45
1512 1721 0.951525 CAACAACGTGCGGGGTATCA 60.952 55.000 0.00 0.00 0.00 2.15
1513 1722 1.791662 CAACAACGTGCGGGGTATC 59.208 57.895 0.00 0.00 0.00 2.24
1514 1723 2.329614 GCAACAACGTGCGGGGTAT 61.330 57.895 0.00 0.00 34.21 2.73
1515 1724 2.973600 GCAACAACGTGCGGGGTA 60.974 61.111 0.00 0.00 34.21 3.69
1521 1730 0.450184 ATATTCCCGCAACAACGTGC 59.550 50.000 0.00 0.00 41.32 5.34
1522 1731 2.911819 AATATTCCCGCAACAACGTG 57.088 45.000 0.00 0.00 0.00 4.49
1523 1732 3.181504 GCTAAATATTCCCGCAACAACGT 60.182 43.478 0.00 0.00 0.00 3.99
1524 1733 3.181505 TGCTAAATATTCCCGCAACAACG 60.182 43.478 4.41 0.00 0.00 4.10
1525 1734 4.364415 TGCTAAATATTCCCGCAACAAC 57.636 40.909 4.41 0.00 0.00 3.32
1529 1738 6.892658 ATATGTTGCTAAATATTCCCGCAA 57.107 33.333 12.29 12.29 38.16 4.85
1530 1739 6.892658 AATATGTTGCTAAATATTCCCGCA 57.107 33.333 0.00 3.11 0.00 5.69
1531 1740 9.685828 TTTAAATATGTTGCTAAATATTCCCGC 57.314 29.630 4.34 0.00 30.44 6.13
1544 1753 9.928236 ACAACAAAACACATTTAAATATGTTGC 57.072 25.926 22.08 0.00 41.25 4.17
1551 1760 9.267084 GGGTCATACAACAAAACACATTTAAAT 57.733 29.630 0.00 0.00 0.00 1.40
1552 1761 8.258007 TGGGTCATACAACAAAACACATTTAAA 58.742 29.630 0.00 0.00 0.00 1.52
1553 1762 7.782049 TGGGTCATACAACAAAACACATTTAA 58.218 30.769 0.00 0.00 0.00 1.52
1554 1763 7.348080 TGGGTCATACAACAAAACACATTTA 57.652 32.000 0.00 0.00 0.00 1.40
1555 1764 6.227298 TGGGTCATACAACAAAACACATTT 57.773 33.333 0.00 0.00 0.00 2.32
1556 1765 5.860941 TGGGTCATACAACAAAACACATT 57.139 34.783 0.00 0.00 0.00 2.71
1557 1766 5.538053 TCATGGGTCATACAACAAAACACAT 59.462 36.000 0.00 0.00 34.40 3.21
1558 1767 4.889995 TCATGGGTCATACAACAAAACACA 59.110 37.500 0.00 0.00 0.00 3.72
1559 1768 5.446143 TCATGGGTCATACAACAAAACAC 57.554 39.130 0.00 0.00 0.00 3.32
1560 1769 6.662865 ATTCATGGGTCATACAACAAAACA 57.337 33.333 0.00 0.00 0.00 2.83
1561 1770 9.651913 AAATATTCATGGGTCATACAACAAAAC 57.348 29.630 0.00 0.00 0.00 2.43
1562 1771 9.650539 CAAATATTCATGGGTCATACAACAAAA 57.349 29.630 0.00 0.00 0.00 2.44
1563 1772 9.029368 TCAAATATTCATGGGTCATACAACAAA 57.971 29.630 0.00 0.00 0.00 2.83
1564 1773 8.586879 TCAAATATTCATGGGTCATACAACAA 57.413 30.769 0.00 0.00 0.00 2.83
1565 1774 8.586879 TTCAAATATTCATGGGTCATACAACA 57.413 30.769 0.00 0.00 0.00 3.33
1566 1775 8.686334 ACTTCAAATATTCATGGGTCATACAAC 58.314 33.333 0.00 0.00 0.00 3.32
1567 1776 8.821686 ACTTCAAATATTCATGGGTCATACAA 57.178 30.769 0.00 0.00 0.00 2.41
1568 1777 9.913310 TTACTTCAAATATTCATGGGTCATACA 57.087 29.630 0.00 0.00 0.00 2.29
1689 1898 7.490079 TGCAAGCATACATGAGAATTTTCATTC 59.510 33.333 8.69 0.00 39.45 2.67
1690 1899 7.324935 TGCAAGCATACATGAGAATTTTCATT 58.675 30.769 8.69 4.38 35.67 2.57
1691 1900 6.869695 TGCAAGCATACATGAGAATTTTCAT 58.130 32.000 5.67 5.67 38.30 2.57
1692 1901 6.270156 TGCAAGCATACATGAGAATTTTCA 57.730 33.333 0.00 0.54 0.00 2.69
1693 1902 6.755141 ACATGCAAGCATACATGAGAATTTTC 59.245 34.615 16.70 0.00 45.23 2.29
1694 1903 6.636705 ACATGCAAGCATACATGAGAATTTT 58.363 32.000 16.70 0.00 45.23 1.82
1695 1904 6.216801 ACATGCAAGCATACATGAGAATTT 57.783 33.333 16.70 0.00 45.23 1.82
1696 1905 5.847111 ACATGCAAGCATACATGAGAATT 57.153 34.783 16.70 0.00 45.23 2.17
1697 1906 5.358725 TCAACATGCAAGCATACATGAGAAT 59.641 36.000 16.70 0.00 45.23 2.40
1698 1907 4.701171 TCAACATGCAAGCATACATGAGAA 59.299 37.500 16.70 2.40 45.23 2.87
1699 1908 4.263435 TCAACATGCAAGCATACATGAGA 58.737 39.130 16.70 11.77 45.23 3.27
1700 1909 4.334481 TCTCAACATGCAAGCATACATGAG 59.666 41.667 23.66 23.66 45.23 2.90
1701 1910 4.263435 TCTCAACATGCAAGCATACATGA 58.737 39.130 16.70 10.79 45.23 3.07
1703 1912 4.885325 TCATCTCAACATGCAAGCATACAT 59.115 37.500 7.29 0.00 34.91 2.29
1704 1913 4.263435 TCATCTCAACATGCAAGCATACA 58.737 39.130 7.29 0.00 34.91 2.29
1705 1914 4.334759 ACTCATCTCAACATGCAAGCATAC 59.665 41.667 7.29 0.00 34.91 2.39
1706 1915 4.520179 ACTCATCTCAACATGCAAGCATA 58.480 39.130 7.29 0.00 34.91 3.14
1707 1916 3.353557 ACTCATCTCAACATGCAAGCAT 58.646 40.909 0.86 0.86 37.08 3.79
1708 1917 2.745821 GACTCATCTCAACATGCAAGCA 59.254 45.455 0.00 0.00 0.00 3.91
1709 1918 3.008330 AGACTCATCTCAACATGCAAGC 58.992 45.455 0.00 0.00 0.00 4.01
1710 1919 5.624344 AAAGACTCATCTCAACATGCAAG 57.376 39.130 0.00 0.00 32.34 4.01
1711 1920 6.395426 AAAAAGACTCATCTCAACATGCAA 57.605 33.333 0.00 0.00 32.34 4.08
1737 1946 5.041287 GCCACTTCATCATGAAACATCATG 58.959 41.667 11.61 11.61 46.41 3.07
1738 1947 4.707934 TGCCACTTCATCATGAAACATCAT 59.292 37.500 0.00 0.00 35.73 2.45
1739 1948 4.080687 TGCCACTTCATCATGAAACATCA 58.919 39.130 0.00 0.00 35.73 3.07
1740 1949 4.707030 TGCCACTTCATCATGAAACATC 57.293 40.909 0.00 0.00 35.73 3.06
1741 1950 4.679639 GCATGCCACTTCATCATGAAACAT 60.680 41.667 6.36 0.92 39.80 2.71
1742 1951 3.367600 GCATGCCACTTCATCATGAAACA 60.368 43.478 6.36 0.00 39.80 2.83
1743 1952 3.119245 AGCATGCCACTTCATCATGAAAC 60.119 43.478 15.66 0.00 39.80 2.78
1744 1953 3.093814 AGCATGCCACTTCATCATGAAA 58.906 40.909 15.66 0.00 39.80 2.69
1745 1954 2.730382 AGCATGCCACTTCATCATGAA 58.270 42.857 15.66 0.00 39.80 2.57
1746 1955 2.425668 CAAGCATGCCACTTCATCATGA 59.574 45.455 15.66 0.00 39.80 3.07
1747 1956 2.809446 CAAGCATGCCACTTCATCATG 58.191 47.619 15.66 0.00 40.23 3.07
1761 1970 7.166167 TCATATATCTCTCAACATGCAAGCAT 58.834 34.615 0.86 0.86 37.08 3.79
1762 1971 6.527423 TCATATATCTCTCAACATGCAAGCA 58.473 36.000 0.00 0.00 0.00 3.91
1763 1972 7.612668 ATCATATATCTCTCAACATGCAAGC 57.387 36.000 0.00 0.00 0.00 4.01
1766 1975 9.609346 CCATTATCATATATCTCTCAACATGCA 57.391 33.333 0.00 0.00 0.00 3.96
1767 1976 9.828039 TCCATTATCATATATCTCTCAACATGC 57.172 33.333 0.00 0.00 0.00 4.06
1770 1979 9.552695 ACCTCCATTATCATATATCTCTCAACA 57.447 33.333 0.00 0.00 0.00 3.33
1771 1980 9.814899 CACCTCCATTATCATATATCTCTCAAC 57.185 37.037 0.00 0.00 0.00 3.18
1772 1981 8.985922 CCACCTCCATTATCATATATCTCTCAA 58.014 37.037 0.00 0.00 0.00 3.02
1773 1982 7.566509 CCCACCTCCATTATCATATATCTCTCA 59.433 40.741 0.00 0.00 0.00 3.27
1774 1983 7.472663 GCCCACCTCCATTATCATATATCTCTC 60.473 44.444 0.00 0.00 0.00 3.20
1775 1984 6.328672 GCCCACCTCCATTATCATATATCTCT 59.671 42.308 0.00 0.00 0.00 3.10
1776 1985 6.465035 GGCCCACCTCCATTATCATATATCTC 60.465 46.154 0.00 0.00 0.00 2.75
1777 1986 5.370880 GGCCCACCTCCATTATCATATATCT 59.629 44.000 0.00 0.00 0.00 1.98
1778 1987 5.370880 AGGCCCACCTCCATTATCATATATC 59.629 44.000 0.00 0.00 46.34 1.63
1779 1988 5.300304 AGGCCCACCTCCATTATCATATAT 58.700 41.667 0.00 0.00 46.34 0.86
1780 1989 4.709944 AGGCCCACCTCCATTATCATATA 58.290 43.478 0.00 0.00 46.34 0.86
1781 1990 3.545779 AGGCCCACCTCCATTATCATAT 58.454 45.455 0.00 0.00 46.34 1.78
1782 1991 3.004126 AGGCCCACCTCCATTATCATA 57.996 47.619 0.00 0.00 46.34 2.15
1783 1992 1.838611 AGGCCCACCTCCATTATCAT 58.161 50.000 0.00 0.00 46.34 2.45
1784 1993 3.357874 AGGCCCACCTCCATTATCA 57.642 52.632 0.00 0.00 46.34 2.15
1794 2003 1.293179 GCATGACAAAAGGCCCACC 59.707 57.895 0.00 0.00 0.00 4.61
1795 2004 0.609662 ATGCATGACAAAAGGCCCAC 59.390 50.000 0.00 0.00 0.00 4.61
1796 2005 0.609151 CATGCATGACAAAAGGCCCA 59.391 50.000 22.59 0.00 0.00 5.36
1797 2006 0.609662 ACATGCATGACAAAAGGCCC 59.390 50.000 32.75 0.00 0.00 5.80
1798 2007 2.070783 CAACATGCATGACAAAAGGCC 58.929 47.619 32.75 0.00 0.00 5.19
1799 2008 2.477375 CACAACATGCATGACAAAAGGC 59.523 45.455 32.75 0.00 0.00 4.35
1800 2009 3.491639 CACACAACATGCATGACAAAAGG 59.508 43.478 32.75 16.03 0.00 3.11
1801 2010 4.361420 TCACACAACATGCATGACAAAAG 58.639 39.130 32.75 17.73 0.00 2.27
1802 2011 4.382345 TCACACAACATGCATGACAAAA 57.618 36.364 32.75 8.98 0.00 2.44
1803 2012 4.037684 TCATCACACAACATGCATGACAAA 59.962 37.500 32.75 11.26 29.69 2.83
1804 2013 3.568853 TCATCACACAACATGCATGACAA 59.431 39.130 32.75 10.74 29.69 3.18
1805 2014 3.147629 TCATCACACAACATGCATGACA 58.852 40.909 32.75 8.31 29.69 3.58
1806 2015 3.835378 TCATCACACAACATGCATGAC 57.165 42.857 32.75 0.00 29.69 3.06
1807 2016 3.759618 ACATCATCACACAACATGCATGA 59.240 39.130 32.75 10.20 36.06 3.07
1808 2017 3.857093 CACATCATCACACAACATGCATG 59.143 43.478 25.09 25.09 0.00 4.06
1809 2018 3.119280 CCACATCATCACACAACATGCAT 60.119 43.478 0.00 0.00 0.00 3.96
1810 2019 2.229302 CCACATCATCACACAACATGCA 59.771 45.455 0.00 0.00 0.00 3.96
1811 2020 2.871133 CCACATCATCACACAACATGC 58.129 47.619 0.00 0.00 0.00 4.06
1812 2021 2.229302 TGCCACATCATCACACAACATG 59.771 45.455 0.00 0.00 0.00 3.21
1813 2022 2.516906 TGCCACATCATCACACAACAT 58.483 42.857 0.00 0.00 0.00 2.71
1814 2023 1.978454 TGCCACATCATCACACAACA 58.022 45.000 0.00 0.00 0.00 3.33
1815 2024 3.691118 AGTATGCCACATCATCACACAAC 59.309 43.478 0.00 0.00 0.00 3.32
1816 2025 3.954200 AGTATGCCACATCATCACACAA 58.046 40.909 0.00 0.00 0.00 3.33
1817 2026 3.632643 AGTATGCCACATCATCACACA 57.367 42.857 0.00 0.00 0.00 3.72
1818 2027 4.282950 CAAGTATGCCACATCATCACAC 57.717 45.455 0.00 0.00 0.00 3.82
1832 2041 8.206325 ACTATTTCTCTCAACATGCAAGTATG 57.794 34.615 0.00 0.00 0.00 2.39
1833 2042 8.798859 AACTATTTCTCTCAACATGCAAGTAT 57.201 30.769 0.00 0.00 0.00 2.12
1834 2043 9.371136 CTAACTATTTCTCTCAACATGCAAGTA 57.629 33.333 0.00 0.00 0.00 2.24
1835 2044 7.880195 ACTAACTATTTCTCTCAACATGCAAGT 59.120 33.333 0.00 0.00 0.00 3.16
1836 2045 8.173775 CACTAACTATTTCTCTCAACATGCAAG 58.826 37.037 0.00 0.00 0.00 4.01
1837 2046 7.119699 CCACTAACTATTTCTCTCAACATGCAA 59.880 37.037 0.00 0.00 0.00 4.08
1838 2047 6.595326 CCACTAACTATTTCTCTCAACATGCA 59.405 38.462 0.00 0.00 0.00 3.96
1839 2048 6.037610 CCCACTAACTATTTCTCTCAACATGC 59.962 42.308 0.00 0.00 0.00 4.06
1840 2049 6.540189 CCCCACTAACTATTTCTCTCAACATG 59.460 42.308 0.00 0.00 0.00 3.21
1841 2050 6.353082 CCCCCACTAACTATTTCTCTCAACAT 60.353 42.308 0.00 0.00 0.00 2.71
1842 2051 5.045869 CCCCCACTAACTATTTCTCTCAACA 60.046 44.000 0.00 0.00 0.00 3.33
1843 2052 5.429130 CCCCCACTAACTATTTCTCTCAAC 58.571 45.833 0.00 0.00 0.00 3.18
1844 2053 4.080526 GCCCCCACTAACTATTTCTCTCAA 60.081 45.833 0.00 0.00 0.00 3.02
1845 2054 3.454812 GCCCCCACTAACTATTTCTCTCA 59.545 47.826 0.00 0.00 0.00 3.27
1846 2055 3.712218 AGCCCCCACTAACTATTTCTCTC 59.288 47.826 0.00 0.00 0.00 3.20
1847 2056 3.737263 AGCCCCCACTAACTATTTCTCT 58.263 45.455 0.00 0.00 0.00 3.10
1848 2057 4.503469 GCTAGCCCCCACTAACTATTTCTC 60.503 50.000 2.29 0.00 0.00 2.87
1849 2058 3.391626 GCTAGCCCCCACTAACTATTTCT 59.608 47.826 2.29 0.00 0.00 2.52
1850 2059 3.391626 AGCTAGCCCCCACTAACTATTTC 59.608 47.826 12.13 0.00 0.00 2.17
1851 2060 3.394645 AGCTAGCCCCCACTAACTATTT 58.605 45.455 12.13 0.00 0.00 1.40
1852 2061 3.061909 AGCTAGCCCCCACTAACTATT 57.938 47.619 12.13 0.00 0.00 1.73
1853 2062 2.797285 AGCTAGCCCCCACTAACTAT 57.203 50.000 12.13 0.00 0.00 2.12
1854 2063 3.917324 ATAGCTAGCCCCCACTAACTA 57.083 47.619 12.13 0.00 0.00 2.24
1855 2064 2.797285 ATAGCTAGCCCCCACTAACT 57.203 50.000 12.13 0.00 0.00 2.24
1856 2065 3.859061 AAATAGCTAGCCCCCACTAAC 57.141 47.619 12.13 0.00 0.00 2.34
1857 2066 4.823107 TCTAAATAGCTAGCCCCCACTAA 58.177 43.478 12.13 0.00 0.00 2.24
1858 2067 4.480777 TCTAAATAGCTAGCCCCCACTA 57.519 45.455 12.13 0.00 0.00 2.74
1859 2068 3.346146 TCTAAATAGCTAGCCCCCACT 57.654 47.619 12.13 0.00 0.00 4.00
1860 2069 5.959583 ATATCTAAATAGCTAGCCCCCAC 57.040 43.478 12.13 0.00 0.00 4.61
1861 2070 6.753134 ACTATATCTAAATAGCTAGCCCCCA 58.247 40.000 12.13 0.00 33.49 4.96
1862 2071 8.226112 TCTACTATATCTAAATAGCTAGCCCCC 58.774 40.741 12.13 0.00 33.49 5.40
1863 2072 9.816787 ATCTACTATATCTAAATAGCTAGCCCC 57.183 37.037 12.13 0.00 33.49 5.80
1977 2190 3.202595 AGGGCTGTAGTACTAGTAGCAGT 59.797 47.826 27.43 17.30 36.15 4.40
2057 2270 4.040829 CCCTAGCAATACTCATCATGGTCA 59.959 45.833 0.00 0.00 0.00 4.02
2229 2442 3.505680 TGTAACAATCAAGGCGCTGAAAT 59.494 39.130 7.64 0.00 0.00 2.17
2261 2474 2.668212 TTTGGCTCGGTTGCGGAG 60.668 61.111 0.00 0.00 34.58 4.63
2347 2560 4.537433 GATCTTGCTCCGCGCCCT 62.537 66.667 0.00 0.00 38.05 5.19
2349 2562 4.838152 TGGATCTTGCTCCGCGCC 62.838 66.667 0.00 0.00 38.21 6.53
2350 2563 1.718757 ATTTGGATCTTGCTCCGCGC 61.719 55.000 0.00 0.00 38.21 6.86
2351 2564 0.305922 GATTTGGATCTTGCTCCGCG 59.694 55.000 0.00 0.00 38.21 6.46
2352 2565 0.665298 GGATTTGGATCTTGCTCCGC 59.335 55.000 0.00 0.00 38.21 5.54
2353 2566 2.042686 TGGATTTGGATCTTGCTCCG 57.957 50.000 0.00 0.00 38.21 4.63
2354 2567 4.806640 TTTTGGATTTGGATCTTGCTCC 57.193 40.909 0.00 0.00 35.74 4.70
2355 2568 5.814188 GGATTTTTGGATTTGGATCTTGCTC 59.186 40.000 0.00 0.00 32.66 4.26
2356 2569 5.486419 AGGATTTTTGGATTTGGATCTTGCT 59.514 36.000 0.00 0.00 32.66 3.91
2357 2570 5.737860 AGGATTTTTGGATTTGGATCTTGC 58.262 37.500 0.00 0.00 32.66 4.01
2358 2571 6.938507 TGAGGATTTTTGGATTTGGATCTTG 58.061 36.000 0.00 0.00 32.66 3.02
2359 2572 7.016465 TGTTGAGGATTTTTGGATTTGGATCTT 59.984 33.333 0.00 0.00 32.66 2.40
2360 2573 6.497954 TGTTGAGGATTTTTGGATTTGGATCT 59.502 34.615 0.00 0.00 32.66 2.75
2361 2574 6.700352 TGTTGAGGATTTTTGGATTTGGATC 58.300 36.000 0.00 0.00 0.00 3.36
2362 2575 6.684897 TGTTGAGGATTTTTGGATTTGGAT 57.315 33.333 0.00 0.00 0.00 3.41
2363 2576 5.511202 GCTGTTGAGGATTTTTGGATTTGGA 60.511 40.000 0.00 0.00 0.00 3.53
2364 2577 4.692155 GCTGTTGAGGATTTTTGGATTTGG 59.308 41.667 0.00 0.00 0.00 3.28
2365 2578 4.692155 GGCTGTTGAGGATTTTTGGATTTG 59.308 41.667 0.00 0.00 0.00 2.32
2366 2579 4.263025 GGGCTGTTGAGGATTTTTGGATTT 60.263 41.667 0.00 0.00 0.00 2.17
2367 2580 3.261643 GGGCTGTTGAGGATTTTTGGATT 59.738 43.478 0.00 0.00 0.00 3.01
2368 2581 2.833943 GGGCTGTTGAGGATTTTTGGAT 59.166 45.455 0.00 0.00 0.00 3.41
2369 2582 2.158325 AGGGCTGTTGAGGATTTTTGGA 60.158 45.455 0.00 0.00 0.00 3.53
2370 2583 2.232208 GAGGGCTGTTGAGGATTTTTGG 59.768 50.000 0.00 0.00 0.00 3.28
2371 2584 2.095059 CGAGGGCTGTTGAGGATTTTTG 60.095 50.000 0.00 0.00 0.00 2.44
2372 2585 2.162681 CGAGGGCTGTTGAGGATTTTT 58.837 47.619 0.00 0.00 0.00 1.94
2373 2586 1.826385 CGAGGGCTGTTGAGGATTTT 58.174 50.000 0.00 0.00 0.00 1.82
2374 2587 0.678048 GCGAGGGCTGTTGAGGATTT 60.678 55.000 0.00 0.00 35.83 2.17
2375 2588 1.078143 GCGAGGGCTGTTGAGGATT 60.078 57.895 0.00 0.00 35.83 3.01
2376 2589 2.586792 GCGAGGGCTGTTGAGGAT 59.413 61.111 0.00 0.00 35.83 3.24
2377 2590 4.069232 CGCGAGGGCTGTTGAGGA 62.069 66.667 0.00 0.00 36.88 3.71
2378 2591 4.379243 ACGCGAGGGCTGTTGAGG 62.379 66.667 15.93 0.00 36.88 3.86
2379 2592 2.811317 GACGCGAGGGCTGTTGAG 60.811 66.667 15.93 0.00 36.88 3.02
2380 2593 4.717629 CGACGCGAGGGCTGTTGA 62.718 66.667 15.93 0.00 36.88 3.18


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

AutoCloner maintained by Alex Coulton.