Multiple sequence alignment - TraesCS1A01G066100

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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 TraesCS1A01G066100 chr1A 100.000 4486 0 0 1 4486 48770174 48774659 0.000000e+00 8285.0
1 TraesCS1A01G066100 chr1A 98.014 554 9 2 3934 4486 553953197 553953749 0.000000e+00 961.0
2 TraesCS1A01G066100 chr1A 97.112 554 13 3 3934 4486 577059797 577060348 0.000000e+00 931.0
3 TraesCS1A01G066100 chr1A 89.474 57 6 0 2606 2662 48772704 48772760 6.220000e-09 73.1
4 TraesCS1A01G066100 chr1A 89.474 57 6 0 2531 2587 48772779 48772835 6.220000e-09 73.1
5 TraesCS1A01G066100 chr1D 95.098 2183 73 14 1790 3940 48863142 48865322 0.000000e+00 3408.0
6 TraesCS1A01G066100 chr1D 94.052 1160 52 10 214 1367 48862002 48863150 0.000000e+00 1744.0
7 TraesCS1A01G066100 chr1D 93.474 567 36 1 3290 3855 48873169 48873735 0.000000e+00 841.0
8 TraesCS1A01G066100 chr1B 92.104 2191 127 15 1790 3940 68742214 68744398 0.000000e+00 3046.0
9 TraesCS1A01G066100 chr1B 94.922 1024 43 6 341 1364 68741205 68742219 0.000000e+00 1594.0
10 TraesCS1A01G066100 chr1B 96.029 554 20 2 3934 4486 51295128 51294576 0.000000e+00 900.0
11 TraesCS1A01G066100 chr1B 85.156 128 4 1 214 341 68740844 68740956 2.840000e-22 117.0
12 TraesCS1A01G066100 chr1B 88.136 59 7 0 2531 2589 68743061 68743119 2.240000e-08 71.3
13 TraesCS1A01G066100 chr3A 97.653 554 11 2 3934 4486 446536383 446536935 0.000000e+00 950.0
14 TraesCS1A01G066100 chr3A 96.390 554 18 2 3934 4486 146777040 146777592 0.000000e+00 911.0
15 TraesCS1A01G066100 chr3A 96.209 554 19 2 3934 4486 203838354 203838906 0.000000e+00 905.0
16 TraesCS1A01G066100 chr3A 98.578 422 5 1 1369 1789 93051412 93050991 0.000000e+00 745.0
17 TraesCS1A01G066100 chr3A 97.867 422 9 0 1368 1789 154987397 154986976 0.000000e+00 730.0
18 TraesCS1A01G066100 chr3A 96.020 201 8 0 1 201 522998133 522997933 1.200000e-85 327.0
19 TraesCS1A01G066100 chr2A 97.273 550 14 1 3938 4486 59993533 59992984 0.000000e+00 931.0
20 TraesCS1A01G066100 chr2A 99.052 422 3 1 1368 1789 614575137 614575557 0.000000e+00 756.0
21 TraesCS1A01G066100 chr2A 98.582 423 5 1 1368 1789 748798439 748798017 0.000000e+00 747.0
22 TraesCS1A01G066100 chr2A 98.578 422 5 1 1368 1789 8678936 8679356 0.000000e+00 745.0
23 TraesCS1A01G066100 chr3B 96.931 554 15 2 3934 4486 584198929 584199481 0.000000e+00 928.0
24 TraesCS1A01G066100 chr3B 89.231 195 19 1 1 193 19754179 19753985 4.480000e-60 243.0
25 TraesCS1A01G066100 chr3B 89.231 195 19 1 1 193 19782331 19782137 4.480000e-60 243.0
26 TraesCS1A01G066100 chr3B 95.690 116 5 0 78 193 19753608 19753493 2.130000e-43 187.0
27 TraesCS1A01G066100 chr4A 96.751 554 16 2 3934 4486 159499568 159499016 0.000000e+00 922.0
28 TraesCS1A01G066100 chr5A 98.815 422 5 0 1368 1789 350795715 350796136 0.000000e+00 752.0
29 TraesCS1A01G066100 chr5A 98.135 429 8 0 1361 1789 544219230 544219658 0.000000e+00 749.0
30 TraesCS1A01G066100 chr5A 98.353 425 7 0 1365 1789 595160273 595159849 0.000000e+00 747.0
31 TraesCS1A01G066100 chr2B 97.630 422 10 0 1368 1789 180052583 180052162 0.000000e+00 725.0
32 TraesCS1A01G066100 chr2B 90.000 200 18 1 1 198 314674133 314673934 1.600000e-64 257.0
33 TraesCS1A01G066100 chr6A 95.431 197 9 0 1 197 534925953 534925757 9.370000e-82 315.0
34 TraesCS1A01G066100 chrUn 89.231 195 19 1 1 193 304895926 304896120 4.480000e-60 243.0
35 TraesCS1A01G066100 chr3D 91.411 163 13 1 1 162 481879163 481879001 5.840000e-54 222.0
36 TraesCS1A01G066100 chr7D 87.662 154 17 1 21 172 400939414 400939261 1.280000e-40 178.0


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 TraesCS1A01G066100 chr1A 48770174 48774659 4485 False 2810.400 8285 92.982667 1 4486 3 chr1A.!!$F3 4485
1 TraesCS1A01G066100 chr1A 553953197 553953749 552 False 961.000 961 98.014000 3934 4486 1 chr1A.!!$F1 552
2 TraesCS1A01G066100 chr1A 577059797 577060348 551 False 931.000 931 97.112000 3934 4486 1 chr1A.!!$F2 552
3 TraesCS1A01G066100 chr1D 48862002 48865322 3320 False 2576.000 3408 94.575000 214 3940 2 chr1D.!!$F2 3726
4 TraesCS1A01G066100 chr1D 48873169 48873735 566 False 841.000 841 93.474000 3290 3855 1 chr1D.!!$F1 565
5 TraesCS1A01G066100 chr1B 68740844 68744398 3554 False 1207.075 3046 90.079500 214 3940 4 chr1B.!!$F1 3726
6 TraesCS1A01G066100 chr1B 51294576 51295128 552 True 900.000 900 96.029000 3934 4486 1 chr1B.!!$R1 552
7 TraesCS1A01G066100 chr3A 446536383 446536935 552 False 950.000 950 97.653000 3934 4486 1 chr3A.!!$F3 552
8 TraesCS1A01G066100 chr3A 146777040 146777592 552 False 911.000 911 96.390000 3934 4486 1 chr3A.!!$F1 552
9 TraesCS1A01G066100 chr3A 203838354 203838906 552 False 905.000 905 96.209000 3934 4486 1 chr3A.!!$F2 552
10 TraesCS1A01G066100 chr2A 59992984 59993533 549 True 931.000 931 97.273000 3938 4486 1 chr2A.!!$R1 548
11 TraesCS1A01G066100 chr3B 584198929 584199481 552 False 928.000 928 96.931000 3934 4486 1 chr3B.!!$F1 552
12 TraesCS1A01G066100 chr3B 19753493 19754179 686 True 215.000 243 92.460500 1 193 2 chr3B.!!$R2 192
13 TraesCS1A01G066100 chr4A 159499016 159499568 552 True 922.000 922 96.751000 3934 4486 1 chr4A.!!$R1 552

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
66 67 0.023354 GTCGCGAGTTCGAATTTCCG 59.977 55.0 10.24 4.41 43.02 4.30 F
193 196 0.105408 TAAGGCGCCGAATAGGGTTC 59.895 55.0 23.20 0.00 41.48 3.62 F
1028 1331 0.249911 ACTGGTTTCGCTTCGCTCTT 60.250 50.0 0.00 0.00 0.00 2.85 F
1787 2198 0.250597 GGTCACCAAAACGCCCTACT 60.251 55.0 0.00 0.00 0.00 2.57 F
3313 3760 0.108615 AGTCACATCGCGGGAAAGAG 60.109 55.0 6.13 1.34 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2184 0.034477 ATGGGAGTAGGGCGTTTTGG 60.034 55.000 0.0 0.0 0.0 3.28 R
1777 2188 0.988832 TGAAATGGGAGTAGGGCGTT 59.011 50.000 0.0 0.0 0.0 4.84 R
2529 2946 0.597568 TGTTTTGCCTGAGATTGCCG 59.402 50.000 0.0 0.0 0.0 5.69 R
3398 3845 0.263172 CTCCCAGCTCCTCTTCCCTA 59.737 60.000 0.0 0.0 0.0 3.53 R
4263 4715 1.482182 CTGTTCGGGTCTCATCCATCA 59.518 52.381 0.0 0.0 0.0 3.07 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
38 39 3.041946 CAGCTTAGGTAGTTGGAGGGAT 58.958 50.000 0.00 0.00 31.96 3.85
41 42 3.200165 GCTTAGGTAGTTGGAGGGATGTT 59.800 47.826 0.00 0.00 0.00 2.71
43 44 2.915869 AGGTAGTTGGAGGGATGTTGA 58.084 47.619 0.00 0.00 0.00 3.18
44 45 3.464828 AGGTAGTTGGAGGGATGTTGAT 58.535 45.455 0.00 0.00 0.00 2.57
60 61 1.089112 TGATAGGTCGCGAGTTCGAA 58.911 50.000 10.24 0.00 43.02 3.71
66 67 0.023354 GTCGCGAGTTCGAATTTCCG 59.977 55.000 10.24 4.41 43.02 4.30
74 75 4.868900 CGAATTTCCGCGGCGCAG 62.869 66.667 32.61 21.98 0.00 5.18
75 76 4.536687 GAATTTCCGCGGCGCAGG 62.537 66.667 32.61 30.12 0.00 4.85
163 166 4.026226 GTTTGCCAAAACGCCTGG 57.974 55.556 0.00 0.00 36.60 4.45
193 196 0.105408 TAAGGCGCCGAATAGGGTTC 59.895 55.000 23.20 0.00 41.48 3.62
202 205 2.908916 CGAATAGGGTTCGGCCTTAAA 58.091 47.619 0.00 0.00 38.19 1.52
203 206 3.473625 CGAATAGGGTTCGGCCTTAAAT 58.526 45.455 0.00 0.00 38.19 1.40
204 207 4.634199 CGAATAGGGTTCGGCCTTAAATA 58.366 43.478 0.00 0.00 38.19 1.40
205 208 4.689345 CGAATAGGGTTCGGCCTTAAATAG 59.311 45.833 0.00 0.00 38.19 1.73
207 210 1.493446 AGGGTTCGGCCTTAAATAGGG 59.507 52.381 0.00 0.00 44.91 3.53
216 219 3.149981 GCCTTAAATAGGGCACTCCATC 58.850 50.000 8.56 0.00 46.63 3.51
315 349 5.485353 TGGAGATGCCTCTTCTCTCTTAAAA 59.515 40.000 0.00 0.00 39.65 1.52
341 375 6.255670 GGGAACAAAACAAGTGTGAATCTTTC 59.744 38.462 0.00 0.00 0.00 2.62
344 378 5.422012 ACAAAACAAGTGTGAATCTTTCCCT 59.578 36.000 0.00 0.00 0.00 4.20
380 662 4.887071 TGATTAGTTTGCTCCAACAAGTGT 59.113 37.500 0.00 0.00 0.00 3.55
445 727 5.508280 TCCAGATGGATAATGCATCATCA 57.492 39.130 21.56 10.36 46.03 3.07
452 734 6.584185 TGGATAATGCATCATCATGGAAAG 57.416 37.500 12.00 0.00 33.45 2.62
455 737 4.322080 AATGCATCATCATGGAAAGCTG 57.678 40.909 0.00 0.00 33.45 4.24
461 743 4.877378 TCATCATGGAAAGCTGCTTTTT 57.123 36.364 26.64 13.31 33.49 1.94
565 850 4.609947 TCATCATCACACAAGTGCAAAAC 58.390 39.130 0.00 0.00 45.49 2.43
578 863 7.814107 CACAAGTGCAAAACTATCCAAATGTAT 59.186 33.333 0.00 0.00 38.56 2.29
677 962 8.812972 AGACAGAAGTTGGTACAGATATGTTTA 58.187 33.333 0.00 0.00 42.39 2.01
999 1302 2.564947 TCTCTCTCCTCTTCAAACAGCC 59.435 50.000 0.00 0.00 0.00 4.85
1028 1331 0.249911 ACTGGTTTCGCTTCGCTCTT 60.250 50.000 0.00 0.00 0.00 2.85
1149 1560 6.155221 TCAGAGAGTGTACATTCAATAGGCTT 59.845 38.462 19.24 0.00 0.00 4.35
1197 1608 1.072159 GTCACAAGCAGGCCTGACT 59.928 57.895 37.21 27.51 31.99 3.41
1234 1645 4.984161 AGGAAAATGAGCAATTTCGTTGTG 59.016 37.500 5.28 0.00 37.51 3.33
1254 1665 1.064060 GCTGGTGTATTTGTCATCCGC 59.936 52.381 0.00 0.00 0.00 5.54
1287 1698 4.354893 ACCTCGTGGTTATTTGTTACCA 57.645 40.909 2.61 0.00 46.05 3.25
1305 1716 2.066262 CCACGATACCACAACACTCAC 58.934 52.381 0.00 0.00 0.00 3.51
1376 1787 5.650543 AGTTACCATTTCATCGAAAATGCC 58.349 37.500 14.46 5.07 42.63 4.40
1377 1788 5.418840 AGTTACCATTTCATCGAAAATGCCT 59.581 36.000 14.46 6.62 42.63 4.75
1378 1789 4.806640 ACCATTTCATCGAAAATGCCTT 57.193 36.364 14.46 2.03 42.63 4.35
1379 1790 5.151297 ACCATTTCATCGAAAATGCCTTT 57.849 34.783 14.46 0.11 42.63 3.11
1380 1791 5.550290 ACCATTTCATCGAAAATGCCTTTT 58.450 33.333 14.46 0.00 42.63 2.27
1381 1792 5.409214 ACCATTTCATCGAAAATGCCTTTTG 59.591 36.000 14.46 5.37 42.63 2.44
1382 1793 5.163834 CCATTTCATCGAAAATGCCTTTTGG 60.164 40.000 14.46 3.80 42.63 3.28
1383 1794 4.862902 TTCATCGAAAATGCCTTTTGGA 57.137 36.364 12.74 12.74 41.40 3.53
1384 1795 4.439305 TCATCGAAAATGCCTTTTGGAG 57.561 40.909 14.92 8.98 40.78 3.86
1385 1796 2.723124 TCGAAAATGCCTTTTGGAGC 57.277 45.000 4.31 0.00 44.07 4.70
1386 1797 2.238521 TCGAAAATGCCTTTTGGAGCT 58.761 42.857 4.31 0.00 44.07 4.09
1387 1798 2.228822 TCGAAAATGCCTTTTGGAGCTC 59.771 45.455 4.71 4.71 44.07 4.09
1388 1799 2.599659 GAAAATGCCTTTTGGAGCTCG 58.400 47.619 7.83 0.00 44.07 5.03
1389 1800 0.890683 AAATGCCTTTTGGAGCTCGG 59.109 50.000 7.83 3.78 44.07 4.63
1390 1801 1.598701 AATGCCTTTTGGAGCTCGGC 61.599 55.000 19.32 19.32 44.07 5.54
1391 1802 3.443925 GCCTTTTGGAGCTCGGCC 61.444 66.667 16.31 0.00 44.07 6.13
1392 1803 2.352805 CCTTTTGGAGCTCGGCCT 59.647 61.111 7.83 0.00 44.07 5.19
1393 1804 1.746991 CCTTTTGGAGCTCGGCCTC 60.747 63.158 7.83 0.00 44.07 4.70
1399 1810 3.157252 GAGCTCGGCCTCCATGGA 61.157 66.667 15.27 15.27 38.35 3.41
1400 1811 3.160047 AGCTCGGCCTCCATGGAG 61.160 66.667 31.69 31.69 41.63 3.86
1408 1819 2.677228 CTCCATGGAGGCCGGTTT 59.323 61.111 31.14 0.00 38.51 3.27
1409 1820 1.000896 CTCCATGGAGGCCGGTTTT 60.001 57.895 31.14 0.00 38.51 2.43
1410 1821 0.611896 CTCCATGGAGGCCGGTTTTT 60.612 55.000 31.14 0.00 38.51 1.94
1411 1822 0.897863 TCCATGGAGGCCGGTTTTTG 60.898 55.000 11.44 0.00 37.29 2.44
1412 1823 0.897863 CCATGGAGGCCGGTTTTTGA 60.898 55.000 5.56 0.00 0.00 2.69
1413 1824 0.965439 CATGGAGGCCGGTTTTTGAA 59.035 50.000 1.90 0.00 0.00 2.69
1414 1825 1.342819 CATGGAGGCCGGTTTTTGAAA 59.657 47.619 1.90 0.00 0.00 2.69
1415 1826 1.486211 TGGAGGCCGGTTTTTGAAAA 58.514 45.000 1.90 0.00 0.00 2.29
1416 1827 1.831736 TGGAGGCCGGTTTTTGAAAAA 59.168 42.857 1.90 0.00 0.00 1.94
1417 1828 2.436173 TGGAGGCCGGTTTTTGAAAAAT 59.564 40.909 6.35 0.00 0.00 1.82
1418 1829 3.641906 TGGAGGCCGGTTTTTGAAAAATA 59.358 39.130 6.35 0.00 0.00 1.40
1419 1830 3.991773 GGAGGCCGGTTTTTGAAAAATAC 59.008 43.478 6.35 2.66 0.00 1.89
1420 1831 4.501743 GGAGGCCGGTTTTTGAAAAATACA 60.502 41.667 6.35 0.00 0.00 2.29
1421 1832 5.024785 AGGCCGGTTTTTGAAAAATACAA 57.975 34.783 6.35 0.00 0.00 2.41
1422 1833 5.429130 AGGCCGGTTTTTGAAAAATACAAA 58.571 33.333 6.35 0.00 35.81 2.83
1423 1834 5.880887 AGGCCGGTTTTTGAAAAATACAAAA 59.119 32.000 6.35 0.00 42.72 2.44
1490 1901 8.995027 AAAAATTACAGATATACATGGAGGCA 57.005 30.769 0.00 0.00 0.00 4.75
1491 1902 9.592196 AAAAATTACAGATATACATGGAGGCAT 57.408 29.630 0.00 0.00 0.00 4.40
1494 1905 9.672673 AATTACAGATATACATGGAGGCATAAC 57.327 33.333 0.00 0.00 0.00 1.89
1495 1906 6.686484 ACAGATATACATGGAGGCATAACA 57.314 37.500 0.00 0.00 0.00 2.41
1496 1907 6.467677 ACAGATATACATGGAGGCATAACAC 58.532 40.000 0.00 0.00 0.00 3.32
1497 1908 6.043127 ACAGATATACATGGAGGCATAACACA 59.957 38.462 0.00 0.00 0.00 3.72
1498 1909 6.369890 CAGATATACATGGAGGCATAACACAC 59.630 42.308 0.00 0.00 0.00 3.82
1499 1910 2.877097 ACATGGAGGCATAACACACA 57.123 45.000 0.00 0.00 0.00 3.72
1500 1911 3.370840 ACATGGAGGCATAACACACAT 57.629 42.857 0.00 0.00 0.00 3.21
1501 1912 3.018856 ACATGGAGGCATAACACACATG 58.981 45.455 0.00 0.00 39.88 3.21
1502 1913 2.877097 TGGAGGCATAACACACATGT 57.123 45.000 0.00 0.00 42.46 3.21
1520 1931 7.547285 CACATGTGTGTAAATTTTTAGGACG 57.453 36.000 18.03 0.00 40.96 4.79
1521 1932 7.356540 CACATGTGTGTAAATTTTTAGGACGA 58.643 34.615 18.03 0.00 40.96 4.20
1522 1933 7.858382 CACATGTGTGTAAATTTTTAGGACGAA 59.142 33.333 18.03 0.00 40.96 3.85
1523 1934 8.407064 ACATGTGTGTAAATTTTTAGGACGAAA 58.593 29.630 0.00 0.00 36.63 3.46
1524 1935 9.405587 CATGTGTGTAAATTTTTAGGACGAAAT 57.594 29.630 0.00 0.00 0.00 2.17
1526 1937 9.881529 TGTGTGTAAATTTTTAGGACGAAATAC 57.118 29.630 0.00 0.00 0.00 1.89
1541 1952 4.969816 CGAAATACGTTGAAATGAAGGCT 58.030 39.130 0.00 0.00 37.22 4.58
1542 1953 4.788100 CGAAATACGTTGAAATGAAGGCTG 59.212 41.667 0.00 0.00 37.22 4.85
1543 1954 5.616866 CGAAATACGTTGAAATGAAGGCTGT 60.617 40.000 0.00 0.00 37.22 4.40
1544 1955 4.685169 ATACGTTGAAATGAAGGCTGTG 57.315 40.909 0.00 0.00 0.00 3.66
1545 1956 1.001378 ACGTTGAAATGAAGGCTGTGC 60.001 47.619 0.00 0.00 0.00 4.57
1546 1957 1.001487 CGTTGAAATGAAGGCTGTGCA 60.001 47.619 0.00 0.00 0.00 4.57
1547 1958 2.543445 CGTTGAAATGAAGGCTGTGCAA 60.543 45.455 0.00 0.00 0.00 4.08
1548 1959 3.456280 GTTGAAATGAAGGCTGTGCAAA 58.544 40.909 0.00 0.00 0.00 3.68
1549 1960 3.815856 TGAAATGAAGGCTGTGCAAAA 57.184 38.095 0.00 0.00 0.00 2.44
1550 1961 4.134379 TGAAATGAAGGCTGTGCAAAAA 57.866 36.364 0.00 0.00 0.00 1.94
1573 1984 8.662781 AAAAGAAAAATCTGAGGCCTTTTAAC 57.337 30.769 6.77 1.56 32.63 2.01
1574 1985 6.976934 AGAAAAATCTGAGGCCTTTTAACA 57.023 33.333 6.77 0.00 0.00 2.41
1575 1986 6.749139 AGAAAAATCTGAGGCCTTTTAACAC 58.251 36.000 6.77 0.00 0.00 3.32
1576 1987 6.323739 AGAAAAATCTGAGGCCTTTTAACACA 59.676 34.615 6.77 0.00 0.00 3.72
1577 1988 6.670695 AAAATCTGAGGCCTTTTAACACAT 57.329 33.333 6.77 0.00 0.00 3.21
1578 1989 5.649782 AATCTGAGGCCTTTTAACACATG 57.350 39.130 6.77 0.00 0.00 3.21
1579 1990 4.098914 TCTGAGGCCTTTTAACACATGT 57.901 40.909 6.77 0.00 0.00 3.21
1580 1991 4.469657 TCTGAGGCCTTTTAACACATGTT 58.530 39.130 6.77 2.32 41.73 2.71
1581 1992 5.626142 TCTGAGGCCTTTTAACACATGTTA 58.374 37.500 6.77 0.22 39.31 2.41
1582 1993 5.472137 TCTGAGGCCTTTTAACACATGTTAC 59.528 40.000 6.77 0.00 39.92 2.50
1583 1994 5.381757 TGAGGCCTTTTAACACATGTTACT 58.618 37.500 6.77 0.00 39.92 2.24
1584 1995 6.535540 TGAGGCCTTTTAACACATGTTACTA 58.464 36.000 6.77 0.00 39.92 1.82
1585 1996 7.172342 TGAGGCCTTTTAACACATGTTACTAT 58.828 34.615 6.77 0.00 39.92 2.12
1586 1997 7.668052 TGAGGCCTTTTAACACATGTTACTATT 59.332 33.333 6.77 0.00 39.92 1.73
1587 1998 8.051901 AGGCCTTTTAACACATGTTACTATTC 57.948 34.615 0.00 0.00 39.92 1.75
1588 1999 7.668052 AGGCCTTTTAACACATGTTACTATTCA 59.332 33.333 0.00 0.00 39.92 2.57
1589 2000 8.466798 GGCCTTTTAACACATGTTACTATTCAT 58.533 33.333 3.95 0.00 39.92 2.57
1590 2001 9.503427 GCCTTTTAACACATGTTACTATTCATC 57.497 33.333 3.95 0.00 39.92 2.92
1594 2005 9.952030 TTTAACACATGTTACTATTCATCCTCA 57.048 29.630 3.95 0.00 39.92 3.86
1595 2006 9.952030 TTAACACATGTTACTATTCATCCTCAA 57.048 29.630 3.95 0.00 39.92 3.02
1596 2007 8.862325 AACACATGTTACTATTCATCCTCAAA 57.138 30.769 0.00 0.00 36.32 2.69
1597 2008 8.498054 ACACATGTTACTATTCATCCTCAAAG 57.502 34.615 0.00 0.00 0.00 2.77
1598 2009 8.103305 ACACATGTTACTATTCATCCTCAAAGT 58.897 33.333 0.00 0.00 0.00 2.66
1599 2010 8.607459 CACATGTTACTATTCATCCTCAAAGTC 58.393 37.037 0.00 0.00 0.00 3.01
1600 2011 7.770897 ACATGTTACTATTCATCCTCAAAGTCC 59.229 37.037 0.00 0.00 0.00 3.85
1601 2012 7.252612 TGTTACTATTCATCCTCAAAGTCCA 57.747 36.000 0.00 0.00 0.00 4.02
1602 2013 7.331026 TGTTACTATTCATCCTCAAAGTCCAG 58.669 38.462 0.00 0.00 0.00 3.86
1603 2014 7.180229 TGTTACTATTCATCCTCAAAGTCCAGA 59.820 37.037 0.00 0.00 0.00 3.86
1604 2015 6.627087 ACTATTCATCCTCAAAGTCCAGAA 57.373 37.500 0.00 0.00 0.00 3.02
1605 2016 7.020827 ACTATTCATCCTCAAAGTCCAGAAA 57.979 36.000 0.00 0.00 0.00 2.52
1606 2017 7.637511 ACTATTCATCCTCAAAGTCCAGAAAT 58.362 34.615 0.00 0.00 0.00 2.17
1607 2018 8.112183 ACTATTCATCCTCAAAGTCCAGAAATT 58.888 33.333 0.00 0.00 0.00 1.82
1608 2019 7.787623 ATTCATCCTCAAAGTCCAGAAATTT 57.212 32.000 0.00 0.00 0.00 1.82
1609 2020 6.579666 TCATCCTCAAAGTCCAGAAATTTG 57.420 37.500 0.00 0.00 35.68 2.32
1610 2021 6.070656 TCATCCTCAAAGTCCAGAAATTTGT 58.929 36.000 0.00 0.00 35.80 2.83
1611 2022 6.207417 TCATCCTCAAAGTCCAGAAATTTGTC 59.793 38.462 0.00 0.00 35.80 3.18
1612 2023 5.694995 TCCTCAAAGTCCAGAAATTTGTCT 58.305 37.500 0.00 0.00 35.80 3.41
1613 2024 6.129179 TCCTCAAAGTCCAGAAATTTGTCTT 58.871 36.000 0.00 0.00 35.80 3.01
1614 2025 6.607198 TCCTCAAAGTCCAGAAATTTGTCTTT 59.393 34.615 0.00 0.00 35.80 2.52
1615 2026 7.124147 TCCTCAAAGTCCAGAAATTTGTCTTTT 59.876 33.333 0.00 0.00 35.80 2.27
1616 2027 7.765819 CCTCAAAGTCCAGAAATTTGTCTTTTT 59.234 33.333 0.00 0.00 35.80 1.94
1648 2059 6.662414 TCGCATTTCGAAGTATTTCATCTT 57.338 33.333 0.00 0.00 45.36 2.40
1649 2060 6.477742 TCGCATTTCGAAGTATTTCATCTTG 58.522 36.000 0.00 0.00 45.36 3.02
1650 2061 6.312672 TCGCATTTCGAAGTATTTCATCTTGA 59.687 34.615 0.00 0.00 45.36 3.02
1651 2062 6.960992 CGCATTTCGAAGTATTTCATCTTGAA 59.039 34.615 0.00 0.00 41.67 2.69
1652 2063 7.641411 CGCATTTCGAAGTATTTCATCTTGAAT 59.359 33.333 0.00 0.00 41.67 2.57
1653 2064 9.294030 GCATTTCGAAGTATTTCATCTTGAATT 57.706 29.630 0.00 0.00 36.11 2.17
1665 2076 9.814899 ATTTCATCTTGAATTTTTACACACACA 57.185 25.926 0.00 0.00 36.11 3.72
1666 2077 9.814899 TTTCATCTTGAATTTTTACACACACAT 57.185 25.926 0.00 0.00 36.11 3.21
1667 2078 8.800231 TCATCTTGAATTTTTACACACACATG 57.200 30.769 0.00 0.00 0.00 3.21
1668 2079 7.381948 TCATCTTGAATTTTTACACACACATGC 59.618 33.333 0.00 0.00 0.00 4.06
1669 2080 6.567959 TCTTGAATTTTTACACACACATGCA 58.432 32.000 0.00 0.00 0.00 3.96
1670 2081 7.208777 TCTTGAATTTTTACACACACATGCAT 58.791 30.769 0.00 0.00 0.00 3.96
1671 2082 7.710044 TCTTGAATTTTTACACACACATGCATT 59.290 29.630 0.00 0.00 0.00 3.56
1672 2083 7.783090 TGAATTTTTACACACACATGCATTT 57.217 28.000 0.00 0.00 0.00 2.32
1673 2084 7.849496 TGAATTTTTACACACACATGCATTTC 58.151 30.769 0.00 0.00 0.00 2.17
1674 2085 7.493645 TGAATTTTTACACACACATGCATTTCA 59.506 29.630 0.00 0.00 0.00 2.69
1675 2086 7.966246 ATTTTTACACACACATGCATTTCAT 57.034 28.000 0.00 0.00 35.31 2.57
1676 2087 7.405469 TTTTTACACACACATGCATTTCATC 57.595 32.000 0.00 0.00 31.79 2.92
1677 2088 3.581024 ACACACACATGCATTTCATCC 57.419 42.857 0.00 0.00 31.79 3.51
1678 2089 2.095110 ACACACACATGCATTTCATCCG 60.095 45.455 0.00 0.00 31.79 4.18
1679 2090 2.095110 CACACACATGCATTTCATCCGT 60.095 45.455 0.00 0.00 31.79 4.69
1680 2091 2.095110 ACACACATGCATTTCATCCGTG 60.095 45.455 0.00 2.72 38.97 4.94
1681 2092 2.095110 CACACATGCATTTCATCCGTGT 60.095 45.455 10.07 10.07 40.70 4.49
1682 2093 3.126686 CACACATGCATTTCATCCGTGTA 59.873 43.478 14.20 0.00 39.10 2.90
1683 2094 3.947196 ACACATGCATTTCATCCGTGTAT 59.053 39.130 13.29 0.00 39.25 2.29
1684 2095 5.007528 CACACATGCATTTCATCCGTGTATA 59.992 40.000 14.20 0.00 39.10 1.47
1685 2096 5.237127 ACACATGCATTTCATCCGTGTATAG 59.763 40.000 13.29 0.00 39.25 1.31
1686 2097 5.237127 CACATGCATTTCATCCGTGTATAGT 59.763 40.000 0.00 0.00 31.79 2.12
1687 2098 5.822519 ACATGCATTTCATCCGTGTATAGTT 59.177 36.000 0.00 0.00 31.79 2.24
1688 2099 6.989759 ACATGCATTTCATCCGTGTATAGTTA 59.010 34.615 0.00 0.00 31.79 2.24
1689 2100 6.838198 TGCATTTCATCCGTGTATAGTTAC 57.162 37.500 0.00 0.00 0.00 2.50
1690 2101 6.342111 TGCATTTCATCCGTGTATAGTTACA 58.658 36.000 0.00 0.00 35.97 2.41
1691 2102 6.989759 TGCATTTCATCCGTGTATAGTTACAT 59.010 34.615 0.00 0.00 40.35 2.29
1692 2103 8.145122 TGCATTTCATCCGTGTATAGTTACATA 58.855 33.333 0.00 0.00 40.35 2.29
1693 2104 9.151471 GCATTTCATCCGTGTATAGTTACATAT 57.849 33.333 0.00 0.00 40.35 1.78
1758 2169 8.389779 TGAATTTTTCAAAAATAAAGGGCTCC 57.610 30.769 8.55 0.00 36.59 4.70
1759 2170 7.995488 TGAATTTTTCAAAAATAAAGGGCTCCA 59.005 29.630 8.55 0.00 36.59 3.86
1760 2171 8.938801 AATTTTTCAAAAATAAAGGGCTCCAT 57.061 26.923 8.55 0.00 0.00 3.41
1761 2172 7.742556 TTTTTCAAAAATAAAGGGCTCCATG 57.257 32.000 0.00 0.00 0.00 3.66
1762 2173 5.419239 TTCAAAAATAAAGGGCTCCATGG 57.581 39.130 4.97 4.97 0.00 3.66
1763 2174 4.682563 TCAAAAATAAAGGGCTCCATGGA 58.317 39.130 15.27 15.27 0.00 3.41
1764 2175 4.711355 TCAAAAATAAAGGGCTCCATGGAG 59.289 41.667 33.73 33.73 44.56 3.86
1772 2183 3.621225 CTCCATGGAGCTCGGTCA 58.379 61.111 28.45 0.00 35.31 4.02
1773 2184 1.142748 CTCCATGGAGCTCGGTCAC 59.857 63.158 28.45 0.00 35.31 3.67
1774 2185 2.187946 CCATGGAGCTCGGTCACC 59.812 66.667 5.56 0.00 0.00 4.02
1775 2186 2.659063 CCATGGAGCTCGGTCACCA 61.659 63.158 5.56 0.00 36.83 4.17
1776 2187 1.296392 CATGGAGCTCGGTCACCAA 59.704 57.895 7.83 0.00 36.00 3.67
1777 2188 0.321564 CATGGAGCTCGGTCACCAAA 60.322 55.000 7.83 0.00 36.00 3.28
1778 2189 0.400213 ATGGAGCTCGGTCACCAAAA 59.600 50.000 7.83 0.00 36.00 2.44
1779 2190 0.534203 TGGAGCTCGGTCACCAAAAC 60.534 55.000 7.83 0.00 0.00 2.43
1780 2191 1.566018 GGAGCTCGGTCACCAAAACG 61.566 60.000 7.83 0.00 0.00 3.60
1781 2192 2.171489 GAGCTCGGTCACCAAAACGC 62.171 60.000 0.00 0.00 0.00 4.84
1782 2193 2.943653 CTCGGTCACCAAAACGCC 59.056 61.111 0.00 0.00 0.00 5.68
1783 2194 2.592287 TCGGTCACCAAAACGCCC 60.592 61.111 0.00 0.00 0.00 6.13
1784 2195 2.593436 CGGTCACCAAAACGCCCT 60.593 61.111 0.00 0.00 0.00 5.19
1785 2196 1.301874 CGGTCACCAAAACGCCCTA 60.302 57.895 0.00 0.00 0.00 3.53
1786 2197 1.571215 CGGTCACCAAAACGCCCTAC 61.571 60.000 0.00 0.00 0.00 3.18
1787 2198 0.250597 GGTCACCAAAACGCCCTACT 60.251 55.000 0.00 0.00 0.00 2.57
1788 2199 1.154197 GTCACCAAAACGCCCTACTC 58.846 55.000 0.00 0.00 0.00 2.59
1945 2356 2.517959 TGCCCAGAGACATTCCAAAAG 58.482 47.619 0.00 0.00 0.00 2.27
2324 2735 2.803492 CGCTGGCAACTATAGGAGTTCC 60.803 54.545 4.43 0.00 45.81 3.62
2489 2906 5.184096 TCTGAAGCCTGTTTTTACACAACAA 59.816 36.000 0.00 0.00 33.74 2.83
2758 3205 1.037493 TATCCGGGATGTCAACCTCG 58.963 55.000 19.82 1.66 0.00 4.63
3244 3691 7.701539 ATGTTATTATGAAGAAGGCACAACA 57.298 32.000 0.00 0.00 0.00 3.33
3305 3752 0.930310 CCATGGTTAGTCACATCGCG 59.070 55.000 2.57 0.00 0.00 5.87
3313 3760 0.108615 AGTCACATCGCGGGAAAGAG 60.109 55.000 6.13 1.34 0.00 2.85
3398 3845 3.944087 AGCTCGAAGCCTCAAATTTAGT 58.056 40.909 0.00 0.00 43.77 2.24
3457 3904 9.606631 ATTCAGTCAAAGTATCTTCCATAGTTC 57.393 33.333 0.00 0.00 0.00 3.01
3463 3910 8.915036 TCAAAGTATCTTCCATAGTTCTCCTAC 58.085 37.037 0.00 0.00 0.00 3.18
3621 4068 7.826690 AGGTCCATTGTGTTTCATATGTTTAC 58.173 34.615 1.90 0.69 0.00 2.01
3653 4104 6.628461 GGAAATTTCATGAACTTTGTTTTGCG 59.372 34.615 23.69 0.00 0.00 4.85
3730 4181 8.687292 TGTACTACTATTCTATGTGGTAGTGG 57.313 38.462 12.44 0.00 41.72 4.00
3733 4184 8.235359 ACTACTATTCTATGTGGTAGTGGTTC 57.765 38.462 0.00 0.00 40.67 3.62
3751 4202 3.060895 GGTTCTCGTTTCTCATTGTAGCG 59.939 47.826 0.00 0.00 0.00 4.26
3815 4266 6.141560 TCATTTGTGTTTGCACTGACATAA 57.858 33.333 0.00 0.00 45.44 1.90
3818 4269 4.972514 TGTGTTTGCACTGACATAAACA 57.027 36.364 0.00 0.00 45.44 2.83
3934 4385 5.577945 CACTTGTGTTGTCTTCTGCAAAAAT 59.422 36.000 0.00 0.00 0.00 1.82
3995 4446 5.601729 AGACCTCTATCTGAGCATGAAATCA 59.398 40.000 0.00 0.00 41.35 2.57
4296 4748 1.536922 CCGAACAGATGACATCCCTCG 60.537 57.143 11.92 15.61 0.00 4.63
4432 4885 6.292596 CGCTAAGTTCTATCAGAAATTCTGGC 60.293 42.308 21.35 11.99 41.02 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.479323 CCAACTACCTAAGCTGCGGTA 59.521 52.381 12.39 12.39 34.76 4.02
15 16 1.471676 CCTCCAACTACCTAAGCTGCG 60.472 57.143 0.00 0.00 0.00 5.18
19 20 2.772515 ACATCCCTCCAACTACCTAAGC 59.227 50.000 0.00 0.00 0.00 3.09
25 26 4.409247 ACCTATCAACATCCCTCCAACTAC 59.591 45.833 0.00 0.00 0.00 2.73
30 31 2.039418 CGACCTATCAACATCCCTCCA 58.961 52.381 0.00 0.00 0.00 3.86
38 39 1.466866 CGAACTCGCGACCTATCAACA 60.467 52.381 3.71 0.00 0.00 3.33
41 42 1.089112 TTCGAACTCGCGACCTATCA 58.911 50.000 3.71 0.00 40.42 2.15
43 44 2.865343 AATTCGAACTCGCGACCTAT 57.135 45.000 3.71 0.00 40.42 2.57
44 45 2.523015 GAAATTCGAACTCGCGACCTA 58.477 47.619 3.71 0.00 40.42 3.08
74 75 3.520569 TCTGTTTCAAACTGCAAAAGCC 58.479 40.909 1.10 0.00 0.00 4.35
75 76 5.529014 TTTCTGTTTCAAACTGCAAAAGC 57.471 34.783 1.10 0.00 0.00 3.51
126 129 2.109181 GCGCATACCCTCCCTGTC 59.891 66.667 0.30 0.00 0.00 3.51
127 130 3.480133 GGCGCATACCCTCCCTGT 61.480 66.667 10.83 0.00 0.00 4.00
162 165 3.506096 GCCTTAAGCGCCCGTTCC 61.506 66.667 2.29 0.00 0.00 3.62
197 200 4.818546 CACTGATGGAGTGCCCTATTTAAG 59.181 45.833 0.00 0.00 45.72 1.85
198 201 4.780815 CACTGATGGAGTGCCCTATTTAA 58.219 43.478 0.00 0.00 45.72 1.52
199 202 4.422073 CACTGATGGAGTGCCCTATTTA 57.578 45.455 0.00 0.00 45.72 1.40
200 203 3.287867 CACTGATGGAGTGCCCTATTT 57.712 47.619 0.00 0.00 45.72 1.40
209 212 5.248640 CCAACATTTCTACACTGATGGAGT 58.751 41.667 0.00 0.00 38.08 3.85
210 213 4.637534 CCCAACATTTCTACACTGATGGAG 59.362 45.833 0.00 0.00 38.27 3.86
211 214 4.042809 ACCCAACATTTCTACACTGATGGA 59.957 41.667 0.00 0.00 35.50 3.41
212 215 4.335416 ACCCAACATTTCTACACTGATGG 58.665 43.478 0.00 0.00 33.84 3.51
213 216 5.003160 TGACCCAACATTTCTACACTGATG 58.997 41.667 0.00 0.00 0.00 3.07
216 219 5.108385 GTTGACCCAACATTTCTACACTG 57.892 43.478 5.08 0.00 43.09 3.66
315 349 4.956075 AGATTCACACTTGTTTTGTTCCCT 59.044 37.500 0.00 0.00 0.00 4.20
461 743 9.976511 CACTTAATACGTATCAGGATAAGGAAA 57.023 33.333 20.23 0.00 0.00 3.13
515 800 4.178540 TGCTTCGCCAAAGTAGTGTATAC 58.821 43.478 0.00 0.00 37.31 1.47
578 863 6.384258 TCACTTTAGTTGCTGCATAACAAA 57.616 33.333 1.84 11.28 0.00 2.83
677 962 9.550811 CTTTTTCACGTAACTTACAAACTTCTT 57.449 29.630 0.00 0.00 0.00 2.52
999 1302 1.588082 GAAACCAGTGGCTGCCATG 59.412 57.895 26.22 21.36 35.28 3.66
1149 1560 2.299013 ACGAAGTGGTGTAGATGCTTGA 59.701 45.455 0.00 0.00 42.51 3.02
1197 1608 7.394077 TGCTCATTTTCCTCATCAAAATACTCA 59.606 33.333 0.00 0.00 32.74 3.41
1234 1645 1.064060 GCGGATGACAAATACACCAGC 59.936 52.381 0.00 0.00 0.00 4.85
1254 1665 1.265568 CACGAGGTTCGATTACACGG 58.734 55.000 5.38 0.00 43.74 4.94
1287 1698 1.336517 CCGTGAGTGTTGTGGTATCGT 60.337 52.381 0.00 0.00 0.00 3.73
1305 1716 5.011125 ACCTTGGATGATGTAGACTAATCCG 59.989 44.000 6.48 0.00 39.79 4.18
1358 1769 5.163834 CCAAAAGGCATTTTCGATGAAATGG 60.164 40.000 19.22 0.00 43.75 3.16
1359 1770 5.638657 TCCAAAAGGCATTTTCGATGAAATG 59.361 36.000 15.26 15.26 45.42 2.32
1360 1771 5.792741 TCCAAAAGGCATTTTCGATGAAAT 58.207 33.333 6.03 0.00 36.47 2.17
1361 1772 5.207110 TCCAAAAGGCATTTTCGATGAAA 57.793 34.783 6.03 0.00 36.47 2.69
1362 1773 4.808558 CTCCAAAAGGCATTTTCGATGAA 58.191 39.130 6.03 0.00 36.47 2.57
1363 1774 3.367292 GCTCCAAAAGGCATTTTCGATGA 60.367 43.478 6.03 0.95 36.47 2.92
1364 1775 2.925563 GCTCCAAAAGGCATTTTCGATG 59.074 45.455 6.03 0.00 36.47 3.84
1365 1776 2.827921 AGCTCCAAAAGGCATTTTCGAT 59.172 40.909 6.03 0.00 36.47 3.59
1366 1777 2.228822 GAGCTCCAAAAGGCATTTTCGA 59.771 45.455 6.03 4.86 36.47 3.71
1367 1778 2.599659 GAGCTCCAAAAGGCATTTTCG 58.400 47.619 6.03 0.00 36.47 3.46
1368 1779 2.599659 CGAGCTCCAAAAGGCATTTTC 58.400 47.619 6.03 0.00 36.47 2.29
1369 1780 1.273327 CCGAGCTCCAAAAGGCATTTT 59.727 47.619 8.47 2.67 39.22 1.82
1370 1781 0.890683 CCGAGCTCCAAAAGGCATTT 59.109 50.000 8.47 0.00 0.00 2.32
1371 1782 1.598701 GCCGAGCTCCAAAAGGCATT 61.599 55.000 20.71 0.00 46.48 3.56
1372 1783 2.048603 GCCGAGCTCCAAAAGGCAT 61.049 57.895 20.71 0.00 46.48 4.40
1373 1784 2.672996 GCCGAGCTCCAAAAGGCA 60.673 61.111 20.71 0.00 46.48 4.75
1374 1785 3.443925 GGCCGAGCTCCAAAAGGC 61.444 66.667 18.28 18.28 46.51 4.35
1375 1786 1.746991 GAGGCCGAGCTCCAAAAGG 60.747 63.158 8.47 4.02 0.00 3.11
1376 1787 1.746991 GGAGGCCGAGCTCCAAAAG 60.747 63.158 8.47 0.00 39.45 2.27
1377 1788 2.351276 GGAGGCCGAGCTCCAAAA 59.649 61.111 8.47 0.00 39.45 2.44
1378 1789 2.927856 TGGAGGCCGAGCTCCAAA 60.928 61.111 8.96 0.00 45.68 3.28
1381 1792 4.247380 CCATGGAGGCCGAGCTCC 62.247 72.222 5.56 0.00 40.05 4.70
1382 1793 3.157252 TCCATGGAGGCCGAGCTC 61.157 66.667 11.44 2.73 37.29 4.09
1383 1794 3.160047 CTCCATGGAGGCCGAGCT 61.160 66.667 31.14 0.00 38.51 4.09
1391 1802 0.611896 AAAAACCGGCCTCCATGGAG 60.612 55.000 31.69 31.69 41.63 3.86
1392 1803 0.897863 CAAAAACCGGCCTCCATGGA 60.898 55.000 15.27 15.27 38.35 3.41
1393 1804 0.897863 TCAAAAACCGGCCTCCATGG 60.898 55.000 4.97 4.97 39.35 3.66
1394 1805 0.965439 TTCAAAAACCGGCCTCCATG 59.035 50.000 0.00 0.00 0.00 3.66
1395 1806 1.710816 TTTCAAAAACCGGCCTCCAT 58.289 45.000 0.00 0.00 0.00 3.41
1396 1807 1.486211 TTTTCAAAAACCGGCCTCCA 58.514 45.000 0.00 0.00 0.00 3.86
1397 1808 2.605837 TTTTTCAAAAACCGGCCTCC 57.394 45.000 0.00 0.00 0.00 4.30
1398 1809 4.623002 TGTATTTTTCAAAAACCGGCCTC 58.377 39.130 0.00 0.00 0.00 4.70
1399 1810 4.674281 TGTATTTTTCAAAAACCGGCCT 57.326 36.364 0.00 0.00 0.00 5.19
1400 1811 5.736486 TTTGTATTTTTCAAAAACCGGCC 57.264 34.783 0.00 0.00 32.86 6.13
1470 1881 8.094548 GTGTTATGCCTCCATGTATATCTGTAA 58.905 37.037 0.00 0.00 32.85 2.41
1471 1882 7.234577 TGTGTTATGCCTCCATGTATATCTGTA 59.765 37.037 0.00 0.00 32.85 2.74
1473 1884 6.369890 GTGTGTTATGCCTCCATGTATATCTG 59.630 42.308 0.00 0.00 32.85 2.90
1476 1887 6.186420 TGTGTGTTATGCCTCCATGTATAT 57.814 37.500 0.00 0.00 32.85 0.86
1481 1892 3.018856 ACATGTGTGTTATGCCTCCATG 58.981 45.455 0.00 0.00 34.01 3.66
1497 1908 7.499321 TCGTCCTAAAAATTTACACACATGT 57.501 32.000 0.00 0.00 43.30 3.21
1498 1909 8.789881 TTTCGTCCTAAAAATTTACACACATG 57.210 30.769 0.00 0.00 0.00 3.21
1500 1911 9.881529 GTATTTCGTCCTAAAAATTTACACACA 57.118 29.630 0.00 0.00 0.00 3.72
1501 1912 9.043678 CGTATTTCGTCCTAAAAATTTACACAC 57.956 33.333 0.00 0.00 34.52 3.82
1519 1930 4.788100 CAGCCTTCATTTCAACGTATTTCG 59.212 41.667 0.00 0.00 46.00 3.46
1520 1931 5.569059 CACAGCCTTCATTTCAACGTATTTC 59.431 40.000 0.00 0.00 0.00 2.17
1521 1932 5.460646 CACAGCCTTCATTTCAACGTATTT 58.539 37.500 0.00 0.00 0.00 1.40
1522 1933 4.615912 GCACAGCCTTCATTTCAACGTATT 60.616 41.667 0.00 0.00 0.00 1.89
1523 1934 3.119849 GCACAGCCTTCATTTCAACGTAT 60.120 43.478 0.00 0.00 0.00 3.06
1524 1935 2.225491 GCACAGCCTTCATTTCAACGTA 59.775 45.455 0.00 0.00 0.00 3.57
1525 1936 1.001378 GCACAGCCTTCATTTCAACGT 60.001 47.619 0.00 0.00 0.00 3.99
1526 1937 1.001487 TGCACAGCCTTCATTTCAACG 60.001 47.619 0.00 0.00 0.00 4.10
1527 1938 2.798976 TGCACAGCCTTCATTTCAAC 57.201 45.000 0.00 0.00 0.00 3.18
1528 1939 3.815856 TTTGCACAGCCTTCATTTCAA 57.184 38.095 0.00 0.00 0.00 2.69
1529 1940 3.815856 TTTTGCACAGCCTTCATTTCA 57.184 38.095 0.00 0.00 0.00 2.69
1547 1958 9.109393 GTTAAAAGGCCTCAGATTTTTCTTTTT 57.891 29.630 5.23 0.00 35.48 1.94
1548 1959 8.264347 TGTTAAAAGGCCTCAGATTTTTCTTTT 58.736 29.630 5.23 0.13 37.00 2.27
1549 1960 7.710907 GTGTTAAAAGGCCTCAGATTTTTCTTT 59.289 33.333 5.23 0.72 0.00 2.52
1550 1961 7.147742 TGTGTTAAAAGGCCTCAGATTTTTCTT 60.148 33.333 5.23 0.00 0.00 2.52
1551 1962 6.323739 TGTGTTAAAAGGCCTCAGATTTTTCT 59.676 34.615 5.23 0.00 0.00 2.52
1552 1963 6.512297 TGTGTTAAAAGGCCTCAGATTTTTC 58.488 36.000 5.23 0.63 0.00 2.29
1553 1964 6.478512 TGTGTTAAAAGGCCTCAGATTTTT 57.521 33.333 5.23 4.11 0.00 1.94
1554 1965 6.041979 ACATGTGTTAAAAGGCCTCAGATTTT 59.958 34.615 5.23 4.97 0.00 1.82
1555 1966 5.539955 ACATGTGTTAAAAGGCCTCAGATTT 59.460 36.000 5.23 5.41 0.00 2.17
1556 1967 5.079643 ACATGTGTTAAAAGGCCTCAGATT 58.920 37.500 5.23 1.64 0.00 2.40
1557 1968 4.666512 ACATGTGTTAAAAGGCCTCAGAT 58.333 39.130 5.23 0.00 0.00 2.90
1558 1969 4.098914 ACATGTGTTAAAAGGCCTCAGA 57.901 40.909 5.23 0.00 0.00 3.27
1559 1970 4.853924 AACATGTGTTAAAAGGCCTCAG 57.146 40.909 5.23 0.00 36.32 3.35
1560 1971 5.381757 AGTAACATGTGTTAAAAGGCCTCA 58.618 37.500 5.23 0.00 41.58 3.86
1561 1972 5.959618 AGTAACATGTGTTAAAAGGCCTC 57.040 39.130 5.23 0.00 41.58 4.70
1562 1973 7.668052 TGAATAGTAACATGTGTTAAAAGGCCT 59.332 33.333 0.00 0.00 41.58 5.19
1563 1974 7.822658 TGAATAGTAACATGTGTTAAAAGGCC 58.177 34.615 0.00 0.00 41.58 5.19
1564 1975 9.503427 GATGAATAGTAACATGTGTTAAAAGGC 57.497 33.333 0.00 0.00 41.58 4.35
1568 1979 9.952030 TGAGGATGAATAGTAACATGTGTTAAA 57.048 29.630 0.00 0.47 41.58 1.52
1569 1980 9.952030 TTGAGGATGAATAGTAACATGTGTTAA 57.048 29.630 0.00 0.00 41.58 2.01
1570 1981 9.952030 TTTGAGGATGAATAGTAACATGTGTTA 57.048 29.630 0.00 1.62 39.31 2.41
1571 1982 8.862325 TTTGAGGATGAATAGTAACATGTGTT 57.138 30.769 0.00 3.64 41.73 3.32
1572 1983 8.103305 ACTTTGAGGATGAATAGTAACATGTGT 58.897 33.333 0.00 0.00 0.00 3.72
1573 1984 8.498054 ACTTTGAGGATGAATAGTAACATGTG 57.502 34.615 0.00 0.00 0.00 3.21
1574 1985 7.770897 GGACTTTGAGGATGAATAGTAACATGT 59.229 37.037 0.00 0.00 0.00 3.21
1575 1986 7.770433 TGGACTTTGAGGATGAATAGTAACATG 59.230 37.037 0.00 0.00 0.00 3.21
1576 1987 7.861629 TGGACTTTGAGGATGAATAGTAACAT 58.138 34.615 0.00 0.00 0.00 2.71
1577 1988 7.180229 TCTGGACTTTGAGGATGAATAGTAACA 59.820 37.037 0.00 0.00 0.00 2.41
1578 1989 7.556844 TCTGGACTTTGAGGATGAATAGTAAC 58.443 38.462 0.00 0.00 0.00 2.50
1579 1990 7.733773 TCTGGACTTTGAGGATGAATAGTAA 57.266 36.000 0.00 0.00 0.00 2.24
1580 1991 7.733773 TTCTGGACTTTGAGGATGAATAGTA 57.266 36.000 0.00 0.00 0.00 1.82
1581 1992 6.627087 TTCTGGACTTTGAGGATGAATAGT 57.373 37.500 0.00 0.00 0.00 2.12
1582 1993 8.517062 AATTTCTGGACTTTGAGGATGAATAG 57.483 34.615 0.00 0.00 0.00 1.73
1583 1994 8.742777 CAAATTTCTGGACTTTGAGGATGAATA 58.257 33.333 0.00 0.00 32.83 1.75
1584 1995 7.234166 ACAAATTTCTGGACTTTGAGGATGAAT 59.766 33.333 5.85 0.00 34.69 2.57
1585 1996 6.550854 ACAAATTTCTGGACTTTGAGGATGAA 59.449 34.615 5.85 0.00 34.69 2.57
1586 1997 6.070656 ACAAATTTCTGGACTTTGAGGATGA 58.929 36.000 5.85 0.00 34.69 2.92
1587 1998 6.208204 AGACAAATTTCTGGACTTTGAGGATG 59.792 38.462 5.85 0.00 34.69 3.51
1588 1999 6.310149 AGACAAATTTCTGGACTTTGAGGAT 58.690 36.000 5.85 0.00 34.69 3.24
1589 2000 5.694995 AGACAAATTTCTGGACTTTGAGGA 58.305 37.500 5.85 0.00 34.69 3.71
1590 2001 6.396829 AAGACAAATTTCTGGACTTTGAGG 57.603 37.500 5.85 0.00 34.69 3.86
1591 2002 8.707938 AAAAAGACAAATTTCTGGACTTTGAG 57.292 30.769 5.85 0.00 34.69 3.02
1625 2036 7.148490 TTCAAGATGAAATACTTCGAAATGCGA 60.148 33.333 0.00 0.00 39.38 5.10
1626 2037 6.477742 TCAAGATGAAATACTTCGAAATGCG 58.522 36.000 0.00 0.00 42.69 4.73
1627 2038 8.847444 ATTCAAGATGAAATACTTCGAAATGC 57.153 30.769 0.00 0.00 40.12 3.56
1639 2050 9.814899 TGTGTGTGTAAAAATTCAAGATGAAAT 57.185 25.926 0.00 0.00 40.12 2.17
1640 2051 9.814899 ATGTGTGTGTAAAAATTCAAGATGAAA 57.185 25.926 0.00 0.00 40.12 2.69
1641 2052 9.247126 CATGTGTGTGTAAAAATTCAAGATGAA 57.753 29.630 0.00 0.00 41.09 2.57
1642 2053 7.381948 GCATGTGTGTGTAAAAATTCAAGATGA 59.618 33.333 0.00 0.00 0.00 2.92
1643 2054 7.169476 TGCATGTGTGTGTAAAAATTCAAGATG 59.831 33.333 0.00 0.00 0.00 2.90
1644 2055 7.208777 TGCATGTGTGTGTAAAAATTCAAGAT 58.791 30.769 0.00 0.00 0.00 2.40
1645 2056 6.567959 TGCATGTGTGTGTAAAAATTCAAGA 58.432 32.000 0.00 0.00 0.00 3.02
1646 2057 6.825284 TGCATGTGTGTGTAAAAATTCAAG 57.175 33.333 0.00 0.00 0.00 3.02
1647 2058 7.783090 AATGCATGTGTGTGTAAAAATTCAA 57.217 28.000 0.00 0.00 0.00 2.69
1648 2059 7.493645 TGAAATGCATGTGTGTGTAAAAATTCA 59.506 29.630 0.00 0.00 0.00 2.57
1649 2060 7.849496 TGAAATGCATGTGTGTGTAAAAATTC 58.151 30.769 0.00 0.00 0.00 2.17
1650 2061 7.783090 TGAAATGCATGTGTGTGTAAAAATT 57.217 28.000 0.00 0.00 0.00 1.82
1651 2062 7.118101 GGATGAAATGCATGTGTGTGTAAAAAT 59.882 33.333 0.00 0.00 37.34 1.82
1652 2063 6.423302 GGATGAAATGCATGTGTGTGTAAAAA 59.577 34.615 0.00 0.00 37.34 1.94
1653 2064 5.925397 GGATGAAATGCATGTGTGTGTAAAA 59.075 36.000 0.00 0.00 37.34 1.52
1654 2065 5.468592 GGATGAAATGCATGTGTGTGTAAA 58.531 37.500 0.00 0.00 37.34 2.01
1655 2066 4.379290 CGGATGAAATGCATGTGTGTGTAA 60.379 41.667 0.00 0.00 37.34 2.41
1656 2067 3.126686 CGGATGAAATGCATGTGTGTGTA 59.873 43.478 0.00 0.00 37.34 2.90
1657 2068 2.095110 CGGATGAAATGCATGTGTGTGT 60.095 45.455 0.00 0.00 37.34 3.72
1658 2069 2.095110 ACGGATGAAATGCATGTGTGTG 60.095 45.455 0.00 0.00 37.34 3.82
1659 2070 2.095110 CACGGATGAAATGCATGTGTGT 60.095 45.455 0.00 0.00 37.34 3.72
1660 2071 2.095110 ACACGGATGAAATGCATGTGTG 60.095 45.455 13.94 8.81 40.54 3.82
1661 2072 2.161855 ACACGGATGAAATGCATGTGT 58.838 42.857 10.07 10.07 38.54 3.72
1662 2073 2.925578 ACACGGATGAAATGCATGTG 57.074 45.000 0.00 4.64 37.34 3.21
1663 2074 5.368145 ACTATACACGGATGAAATGCATGT 58.632 37.500 0.00 0.00 37.34 3.21
1664 2075 5.929697 ACTATACACGGATGAAATGCATG 57.070 39.130 0.00 0.00 37.34 4.06
1665 2076 6.989759 TGTAACTATACACGGATGAAATGCAT 59.010 34.615 0.00 0.00 37.11 3.96
1666 2077 6.342111 TGTAACTATACACGGATGAAATGCA 58.658 36.000 0.00 0.00 37.11 3.96
1667 2078 6.838198 TGTAACTATACACGGATGAAATGC 57.162 37.500 0.00 0.00 37.11 3.56
1733 2144 7.995488 TGGAGCCCTTTATTTTTGAAAAATTCA 59.005 29.630 19.57 6.12 38.04 2.57
1734 2145 8.389779 TGGAGCCCTTTATTTTTGAAAAATTC 57.610 30.769 19.57 9.97 0.00 2.17
1735 2146 8.795513 CATGGAGCCCTTTATTTTTGAAAAATT 58.204 29.630 19.57 1.63 0.00 1.82
1736 2147 7.394077 CCATGGAGCCCTTTATTTTTGAAAAAT 59.606 33.333 18.56 18.56 0.00 1.82
1737 2148 6.714356 CCATGGAGCCCTTTATTTTTGAAAAA 59.286 34.615 5.56 5.47 0.00 1.94
1738 2149 6.043706 TCCATGGAGCCCTTTATTTTTGAAAA 59.956 34.615 11.44 0.00 0.00 2.29
1739 2150 5.545723 TCCATGGAGCCCTTTATTTTTGAAA 59.454 36.000 11.44 0.00 0.00 2.69
1740 2151 5.090139 TCCATGGAGCCCTTTATTTTTGAA 58.910 37.500 11.44 0.00 0.00 2.69
1741 2152 4.682563 TCCATGGAGCCCTTTATTTTTGA 58.317 39.130 11.44 0.00 0.00 2.69
1742 2153 5.014808 CTCCATGGAGCCCTTTATTTTTG 57.985 43.478 28.45 0.93 35.31 2.44
1755 2166 1.142748 GTGACCGAGCTCCATGGAG 59.857 63.158 33.73 33.73 44.56 3.86
1756 2167 2.359169 GGTGACCGAGCTCCATGGA 61.359 63.158 15.27 15.27 0.00 3.41
1757 2168 2.184020 TTGGTGACCGAGCTCCATGG 62.184 60.000 4.97 4.97 32.09 3.66
1758 2169 0.321564 TTTGGTGACCGAGCTCCATG 60.322 55.000 8.47 0.00 32.09 3.66
1759 2170 0.400213 TTTTGGTGACCGAGCTCCAT 59.600 50.000 8.47 0.00 32.09 3.41
1760 2171 0.534203 GTTTTGGTGACCGAGCTCCA 60.534 55.000 8.47 0.00 0.00 3.86
1761 2172 1.566018 CGTTTTGGTGACCGAGCTCC 61.566 60.000 8.47 0.00 0.00 4.70
1762 2173 1.860078 CGTTTTGGTGACCGAGCTC 59.140 57.895 2.73 2.73 0.00 4.09
1763 2174 2.251642 GCGTTTTGGTGACCGAGCT 61.252 57.895 0.00 0.00 0.00 4.09
1764 2175 2.251371 GCGTTTTGGTGACCGAGC 59.749 61.111 0.00 0.00 0.00 5.03
1765 2176 2.613506 GGGCGTTTTGGTGACCGAG 61.614 63.158 0.00 0.00 0.00 4.63
1766 2177 1.756408 TAGGGCGTTTTGGTGACCGA 61.756 55.000 0.00 0.00 0.00 4.69
1767 2178 1.301874 TAGGGCGTTTTGGTGACCG 60.302 57.895 0.00 0.00 0.00 4.79
1768 2179 0.250597 AGTAGGGCGTTTTGGTGACC 60.251 55.000 0.00 0.00 0.00 4.02
1769 2180 1.154197 GAGTAGGGCGTTTTGGTGAC 58.846 55.000 0.00 0.00 0.00 3.67
1770 2181 0.035739 GGAGTAGGGCGTTTTGGTGA 59.964 55.000 0.00 0.00 0.00 4.02
1771 2182 0.958876 GGGAGTAGGGCGTTTTGGTG 60.959 60.000 0.00 0.00 0.00 4.17
1772 2183 1.377612 GGGAGTAGGGCGTTTTGGT 59.622 57.895 0.00 0.00 0.00 3.67
1773 2184 0.034477 ATGGGAGTAGGGCGTTTTGG 60.034 55.000 0.00 0.00 0.00 3.28
1774 2185 1.834188 AATGGGAGTAGGGCGTTTTG 58.166 50.000 0.00 0.00 0.00 2.44
1775 2186 2.224917 TGAAATGGGAGTAGGGCGTTTT 60.225 45.455 0.00 0.00 0.00 2.43
1776 2187 1.353022 TGAAATGGGAGTAGGGCGTTT 59.647 47.619 0.00 0.00 0.00 3.60
1777 2188 0.988832 TGAAATGGGAGTAGGGCGTT 59.011 50.000 0.00 0.00 0.00 4.84
1778 2189 1.213296 ATGAAATGGGAGTAGGGCGT 58.787 50.000 0.00 0.00 0.00 5.68
1779 2190 3.703001 ATATGAAATGGGAGTAGGGCG 57.297 47.619 0.00 0.00 0.00 6.13
1780 2191 6.128138 AGTAATATGAAATGGGAGTAGGGC 57.872 41.667 0.00 0.00 0.00 5.19
1876 2287 3.941483 CACTTCCTGGGTGACAACATATC 59.059 47.826 0.00 0.00 36.89 1.63
1945 2356 4.142838 GCTTGCCCATATTTTTGAAACTGC 60.143 41.667 0.00 0.00 0.00 4.40
2324 2735 6.867662 ATGTTTTGACTAGAGTGAAGTTGG 57.132 37.500 0.00 0.00 0.00 3.77
2489 2906 1.404843 GGTAGGATTCTGGCTCTCGT 58.595 55.000 0.00 0.00 0.00 4.18
2529 2946 0.597568 TGTTTTGCCTGAGATTGCCG 59.402 50.000 0.00 0.00 0.00 5.69
2701 3148 4.104383 TGTTCTTCTTGAGATTGCCCTT 57.896 40.909 0.00 0.00 33.49 3.95
2758 3205 1.317431 TGCATGAGATTGCCCTGCAC 61.317 55.000 0.00 0.00 42.06 4.57
3057 3504 3.818961 AATAATGGCATTCTGCGATCG 57.181 42.857 17.41 11.69 46.21 3.69
3225 3672 6.183360 CCATCATGTTGTGCCTTCTTCATAAT 60.183 38.462 3.19 0.00 0.00 1.28
3228 3675 3.446161 CCATCATGTTGTGCCTTCTTCAT 59.554 43.478 3.19 0.00 0.00 2.57
3244 3691 7.123098 TGAATTCAATGTACTTGCTTCCATCAT 59.877 33.333 5.45 0.00 34.66 2.45
3305 3752 1.474143 CCGAGGATTGAGCTCTTTCCC 60.474 57.143 23.71 15.75 0.00 3.97
3313 3760 4.537433 AGGCGCCGAGGATTGAGC 62.537 66.667 23.20 0.00 0.00 4.26
3398 3845 0.263172 CTCCCAGCTCCTCTTCCCTA 59.737 60.000 0.00 0.00 0.00 3.53
3457 3904 2.096248 ACTCTTCTTCGCTGGTAGGAG 58.904 52.381 0.00 0.00 0.00 3.69
3463 3910 2.957491 AGATGACTCTTCTTCGCTGG 57.043 50.000 0.00 0.00 32.34 4.85
3575 4022 9.396022 GGACCTTTGTTGATATCTTATTGAGAA 57.604 33.333 3.98 0.00 38.06 2.87
3621 4068 7.712205 ACAAAGTTCATGAAATTTCCAGAAAGG 59.288 33.333 26.25 16.61 36.60 3.11
3653 4104 2.813779 AGAATTCGCGAATGCAACTC 57.186 45.000 35.13 26.47 42.97 3.01
3730 4181 3.918591 TCGCTACAATGAGAAACGAGAAC 59.081 43.478 0.00 0.00 0.00 3.01
3733 4184 5.034797 TGTATCGCTACAATGAGAAACGAG 58.965 41.667 0.00 0.00 34.92 4.18
3995 4446 5.064452 GTGCATTCGACTGATTCTTGATCTT 59.936 40.000 6.99 0.00 35.69 2.40
4263 4715 1.482182 CTGTTCGGGTCTCATCCATCA 59.518 52.381 0.00 0.00 0.00 3.07
4296 4748 3.703001 TGTTTTCCTCATCAGAGACCC 57.297 47.619 0.00 0.00 44.98 4.46
4349 4801 5.163652 CCATTAGGAAAACCGCCTTTCTAAG 60.164 44.000 7.21 0.00 36.96 2.18
4432 4885 2.939103 GGAGATCCGGTTTGATGACTTG 59.061 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.