Multiple sequence alignment - TraesCS4A01G420300

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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 TraesCS4A01G420300 chr4A 100.000 2683 0 0 1 2683 690984491 690981809 0.000000e+00 4955.0
1 TraesCS4A01G420300 chr4A 98.955 1722 17 1 57 1777 690993563 690991842 0.000000e+00 3079.0
2 TraesCS4A01G420300 chr4A 99.693 1305 3 1 1 1304 691009975 691008671 0.000000e+00 2386.0
3 TraesCS4A01G420300 chr4A 98.750 720 9 0 1195 1914 691017579 691016860 0.000000e+00 1280.0
4 TraesCS4A01G420300 chr4A 97.598 333 8 0 1582 1914 691008672 691008340 3.000000e-159 571.0
5 TraesCS4A01G420300 chr4A 93.050 259 14 1 703 957 691017836 691017578 2.520000e-100 375.0
6 TraesCS4A01G420300 chr4A 86.429 280 22 11 426 704 691018183 691017919 2.610000e-75 292.0
7 TraesCS4A01G420300 chr4A 90.210 143 12 2 1 142 691018323 691018182 4.560000e-43 185.0
8 TraesCS4A01G420300 chr4A 84.656 189 21 3 1009 1193 691050321 691050137 5.900000e-42 182.0
9 TraesCS4A01G420300 chr4A 84.656 189 21 3 1009 1193 691107248 691107064 5.900000e-42 182.0
10 TraesCS4A01G420300 chr4A 95.413 109 5 0 1806 1914 690991842 690991734 9.870000e-40 174.0
11 TraesCS4A01G420300 chr4A 98.361 61 1 0 4 64 691001444 691001384 1.020000e-19 108.0
12 TraesCS4A01G420300 chr4A 100.000 28 0 0 1906 1933 110093510 110093537 5.000000e-03 52.8
13 TraesCS4A01G420300 chrUn 90.027 742 60 8 1912 2642 235715665 235714927 0.000000e+00 948.0
14 TraesCS4A01G420300 chrUn 90.027 742 60 8 1912 2642 316935714 316936452 0.000000e+00 948.0
15 TraesCS4A01G420300 chr6D 86.538 780 68 20 1914 2683 439488393 439489145 0.000000e+00 824.0
16 TraesCS4A01G420300 chr3B 85.969 784 92 16 1914 2683 491147956 491147177 0.000000e+00 822.0
17 TraesCS4A01G420300 chr3B 86.154 780 85 14 1914 2683 109818460 109817694 0.000000e+00 821.0
18 TraesCS4A01G420300 chr3B 79.899 199 26 6 1064 1249 799773955 799773758 1.680000e-27 134.0
19 TraesCS4A01G420300 chr3B 85.870 92 10 3 1519 1608 799757328 799757238 7.910000e-16 95.3
20 TraesCS4A01G420300 chr2B 85.696 776 73 19 1923 2683 781117135 781116383 0.000000e+00 784.0
21 TraesCS4A01G420300 chr2B 85.223 785 82 12 1912 2683 157298688 157299451 0.000000e+00 776.0
22 TraesCS4A01G420300 chr2B 92.453 477 36 0 2207 2683 681945120 681944644 0.000000e+00 682.0
23 TraesCS4A01G420300 chr2B 88.136 531 58 5 2156 2683 1663277 1663805 6.310000e-176 627.0
24 TraesCS4A01G420300 chr5B 85.332 784 79 18 1914 2683 659760197 659760958 0.000000e+00 778.0
25 TraesCS4A01G420300 chr5B 84.487 780 64 29 1911 2683 548219907 548220636 0.000000e+00 717.0
26 TraesCS4A01G420300 chr5B 83.710 442 37 10 1912 2338 15587365 15586944 4.190000e-103 385.0
27 TraesCS4A01G420300 chr2D 87.216 704 61 16 1987 2683 92868397 92867716 0.000000e+00 774.0
28 TraesCS4A01G420300 chr3D 91.060 481 40 2 2204 2683 567547271 567547749 0.000000e+00 647.0
29 TraesCS4A01G420300 chr7D 80.645 372 60 5 1033 1392 34312174 34312545 7.320000e-71 278.0
30 TraesCS4A01G420300 chr7D 87.000 100 9 3 1520 1618 34331974 34332070 2.820000e-20 110.0
31 TraesCS4A01G420300 chr7D 79.310 145 26 3 502 644 34311858 34312000 6.110000e-17 99.0
32 TraesCS4A01G420300 chr4D 81.910 199 22 5 1064 1249 506283587 506283390 3.580000e-34 156.0
33 TraesCS4A01G420300 chr4D 85.870 92 10 2 1519 1608 506283164 506283074 7.910000e-16 95.3
34 TraesCS4A01G420300 chr7B 86.029 136 6 4 1911 2037 671280285 671280154 1.680000e-27 134.0
35 TraesCS4A01G420300 chr1B 92.683 82 6 0 1914 1995 15520218 15520299 4.690000e-23 119.0
36 TraesCS4A01G420300 chr6A 89.474 57 6 0 83 139 123504646 123504590 3.710000e-09 73.1
37 TraesCS4A01G420300 chr6B 84.848 66 10 0 206 271 288045015 288045080 1.720000e-07 67.6


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 TraesCS4A01G420300 chr4A 690981809 690984491 2682 True 4955.0 4955 100.00000 1 2683 1 chr4A.!!$R1 2682
1 TraesCS4A01G420300 chr4A 690991734 690993563 1829 True 1626.5 3079 97.18400 57 1914 2 chr4A.!!$R5 1857
2 TraesCS4A01G420300 chr4A 691008340 691009975 1635 True 1478.5 2386 98.64550 1 1914 2 chr4A.!!$R6 1913
3 TraesCS4A01G420300 chr4A 691016860 691018323 1463 True 533.0 1280 92.10975 1 1914 4 chr4A.!!$R7 1913
4 TraesCS4A01G420300 chrUn 235714927 235715665 738 True 948.0 948 90.02700 1912 2642 1 chrUn.!!$R1 730
5 TraesCS4A01G420300 chrUn 316935714 316936452 738 False 948.0 948 90.02700 1912 2642 1 chrUn.!!$F1 730
6 TraesCS4A01G420300 chr6D 439488393 439489145 752 False 824.0 824 86.53800 1914 2683 1 chr6D.!!$F1 769
7 TraesCS4A01G420300 chr3B 491147177 491147956 779 True 822.0 822 85.96900 1914 2683 1 chr3B.!!$R2 769
8 TraesCS4A01G420300 chr3B 109817694 109818460 766 True 821.0 821 86.15400 1914 2683 1 chr3B.!!$R1 769
9 TraesCS4A01G420300 chr2B 781116383 781117135 752 True 784.0 784 85.69600 1923 2683 1 chr2B.!!$R2 760
10 TraesCS4A01G420300 chr2B 157298688 157299451 763 False 776.0 776 85.22300 1912 2683 1 chr2B.!!$F2 771
11 TraesCS4A01G420300 chr2B 1663277 1663805 528 False 627.0 627 88.13600 2156 2683 1 chr2B.!!$F1 527
12 TraesCS4A01G420300 chr5B 659760197 659760958 761 False 778.0 778 85.33200 1914 2683 1 chr5B.!!$F2 769
13 TraesCS4A01G420300 chr5B 548219907 548220636 729 False 717.0 717 84.48700 1911 2683 1 chr5B.!!$F1 772
14 TraesCS4A01G420300 chr2D 92867716 92868397 681 True 774.0 774 87.21600 1987 2683 1 chr2D.!!$R1 696

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
147 149 0.036306 CACACCCTACCCACTGAACC 59.964 60.0 0.0 0.0 0.0 3.62 F
1381 1772 0.108138 AACATGTGCGAGCCCTAGAC 60.108 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1926 0.038251 GACCAGTGATGCGTGACAGA 60.038 55.0 0.00 0.0 0.0 3.41 R
2364 2779 0.471617 CTTCTCCCCCAGCGATGAAT 59.528 55.0 0.06 0.0 0.0 2.57 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
147 149 0.036306 CACACCCTACCCACTGAACC 59.964 60.000 0.00 0.00 0.00 3.62
1109 1221 1.572085 GATCAATGGCAGGATCCGCG 61.572 60.000 18.18 0.00 35.07 6.46
1307 1698 4.821589 CCTTCAGGGCTCGGCGTC 62.822 72.222 6.85 0.00 0.00 5.19
1316 1707 2.805353 CTCGGCGTCGTGGACAAG 60.805 66.667 10.18 0.00 37.69 3.16
1317 1708 4.351938 TCGGCGTCGTGGACAAGG 62.352 66.667 10.18 0.00 37.69 3.61
1320 1711 4.681978 GCGTCGTGGACAAGGCCT 62.682 66.667 0.00 0.00 32.09 5.19
1321 1712 2.738521 CGTCGTGGACAAGGCCTG 60.739 66.667 5.69 2.82 32.09 4.85
1322 1713 3.050275 GTCGTGGACAAGGCCTGC 61.050 66.667 5.69 0.00 32.09 4.85
1323 1714 4.680237 TCGTGGACAAGGCCTGCG 62.680 66.667 5.69 2.72 0.00 5.18
1324 1715 4.988598 CGTGGACAAGGCCTGCGT 62.989 66.667 5.69 6.98 0.00 5.24
1325 1716 3.357079 GTGGACAAGGCCTGCGTG 61.357 66.667 5.69 2.95 0.00 5.34
1326 1717 4.641645 TGGACAAGGCCTGCGTGG 62.642 66.667 5.69 0.00 39.35 4.94
1327 1718 4.329545 GGACAAGGCCTGCGTGGA 62.330 66.667 5.69 0.00 38.35 4.02
1333 1724 2.676471 GGCCTGCGTGGACCATTT 60.676 61.111 0.00 0.00 38.13 2.32
1334 1725 2.700773 GGCCTGCGTGGACCATTTC 61.701 63.158 0.00 0.00 38.13 2.17
1335 1726 1.675641 GCCTGCGTGGACCATTTCT 60.676 57.895 0.00 0.00 38.35 2.52
1336 1727 1.244019 GCCTGCGTGGACCATTTCTT 61.244 55.000 0.00 0.00 38.35 2.52
1337 1728 0.804989 CCTGCGTGGACCATTTCTTC 59.195 55.000 0.00 0.00 38.35 2.87
1338 1729 1.522668 CTGCGTGGACCATTTCTTCA 58.477 50.000 0.00 0.00 0.00 3.02
1339 1730 1.197721 CTGCGTGGACCATTTCTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
1340 1731 1.234821 GCGTGGACCATTTCTTCACA 58.765 50.000 0.00 0.00 0.00 3.58
1341 1732 1.197721 GCGTGGACCATTTCTTCACAG 59.802 52.381 0.00 0.00 0.00 3.66
1342 1733 1.197721 CGTGGACCATTTCTTCACAGC 59.802 52.381 0.00 0.00 0.00 4.40
1343 1734 2.508526 GTGGACCATTTCTTCACAGCT 58.491 47.619 0.00 0.00 0.00 4.24
1344 1735 2.887152 GTGGACCATTTCTTCACAGCTT 59.113 45.455 0.00 0.00 0.00 3.74
1345 1736 2.886523 TGGACCATTTCTTCACAGCTTG 59.113 45.455 0.00 0.00 0.00 4.01
1346 1737 2.352127 GGACCATTTCTTCACAGCTTGC 60.352 50.000 0.00 0.00 0.00 4.01
1347 1738 2.294233 GACCATTTCTTCACAGCTTGCA 59.706 45.455 0.00 0.00 0.00 4.08
1348 1739 2.895404 ACCATTTCTTCACAGCTTGCAT 59.105 40.909 0.00 0.00 0.00 3.96
1349 1740 3.250744 CCATTTCTTCACAGCTTGCATG 58.749 45.455 0.00 0.00 0.00 4.06
1350 1741 3.250744 CATTTCTTCACAGCTTGCATGG 58.749 45.455 1.34 0.00 0.00 3.66
1351 1742 0.599558 TTCTTCACAGCTTGCATGGC 59.400 50.000 1.34 2.93 0.00 4.40
1352 1743 1.214589 CTTCACAGCTTGCATGGCC 59.785 57.895 0.00 0.00 0.00 5.36
1353 1744 1.529152 CTTCACAGCTTGCATGGCCA 61.529 55.000 8.56 8.56 0.00 5.36
1354 1745 0.901114 TTCACAGCTTGCATGGCCAT 60.901 50.000 14.09 14.09 0.00 4.40
1355 1746 1.141019 CACAGCTTGCATGGCCATC 59.859 57.895 17.61 11.64 0.00 3.51
1356 1747 1.000019 ACAGCTTGCATGGCCATCT 60.000 52.632 17.61 6.67 0.00 2.90
1357 1748 1.320344 ACAGCTTGCATGGCCATCTG 61.320 55.000 23.22 23.22 0.00 2.90
1358 1749 2.106332 GCTTGCATGGCCATCTGC 59.894 61.111 22.05 22.05 38.87 4.26
1359 1750 2.717044 GCTTGCATGGCCATCTGCA 61.717 57.895 26.47 26.47 46.08 4.41
1361 1752 3.610976 TGCATGGCCATCTGCAAG 58.389 55.556 27.69 12.33 44.87 4.01
1372 1763 3.304041 TCTGCAAGAACATGTGCGA 57.696 47.368 0.00 0.00 42.31 5.10
1373 1764 1.150827 TCTGCAAGAACATGTGCGAG 58.849 50.000 0.00 0.00 42.31 5.03
1374 1765 0.453950 CTGCAAGAACATGTGCGAGC 60.454 55.000 14.49 14.49 43.93 5.03
1375 1766 1.154150 GCAAGAACATGTGCGAGCC 60.154 57.895 11.28 0.00 0.00 4.70
1376 1767 1.503542 CAAGAACATGTGCGAGCCC 59.496 57.895 0.00 0.00 0.00 5.19
1377 1768 0.957395 CAAGAACATGTGCGAGCCCT 60.957 55.000 0.00 0.00 0.00 5.19
1378 1769 0.613260 AAGAACATGTGCGAGCCCTA 59.387 50.000 0.00 0.00 0.00 3.53
1379 1770 0.176680 AGAACATGTGCGAGCCCTAG 59.823 55.000 0.00 0.00 0.00 3.02
1380 1771 0.175760 GAACATGTGCGAGCCCTAGA 59.824 55.000 0.00 0.00 0.00 2.43
1381 1772 0.108138 AACATGTGCGAGCCCTAGAC 60.108 55.000 0.00 0.00 0.00 2.59
1382 1773 0.972983 ACATGTGCGAGCCCTAGACT 60.973 55.000 0.00 0.00 0.00 3.24
1383 1774 0.249238 CATGTGCGAGCCCTAGACTC 60.249 60.000 0.00 0.00 0.00 3.36
1384 1775 1.395826 ATGTGCGAGCCCTAGACTCC 61.396 60.000 7.04 2.38 0.00 3.85
1385 1776 2.442272 TGCGAGCCCTAGACTCCC 60.442 66.667 7.04 0.34 0.00 4.30
1386 1777 2.123640 GCGAGCCCTAGACTCCCT 60.124 66.667 7.04 0.00 0.00 4.20
1387 1778 2.494530 GCGAGCCCTAGACTCCCTG 61.495 68.421 7.04 0.00 0.00 4.45
1388 1779 1.227664 CGAGCCCTAGACTCCCTGA 59.772 63.158 7.04 0.00 0.00 3.86
1389 1780 0.178975 CGAGCCCTAGACTCCCTGAT 60.179 60.000 7.04 0.00 0.00 2.90
1390 1781 1.627864 GAGCCCTAGACTCCCTGATC 58.372 60.000 0.00 0.00 0.00 2.92
1391 1782 0.178975 AGCCCTAGACTCCCTGATCG 60.179 60.000 0.00 0.00 0.00 3.69
1392 1783 1.182385 GCCCTAGACTCCCTGATCGG 61.182 65.000 0.00 0.00 0.00 4.18
1393 1784 1.182385 CCCTAGACTCCCTGATCGGC 61.182 65.000 0.00 0.00 0.00 5.54
1394 1785 1.519751 CCTAGACTCCCTGATCGGCG 61.520 65.000 0.00 0.00 0.00 6.46
1395 1786 2.136196 CTAGACTCCCTGATCGGCGC 62.136 65.000 0.00 0.00 0.00 6.53
1396 1787 4.593864 GACTCCCTGATCGGCGCC 62.594 72.222 19.07 19.07 0.00 6.53
1415 1806 4.722700 GGTGACTGCCACGGCCAT 62.723 66.667 2.24 0.00 46.62 4.40
1416 1807 3.434319 GTGACTGCCACGGCCATG 61.434 66.667 2.24 0.00 41.09 3.66
1419 1810 4.746309 ACTGCCACGGCCATGCAT 62.746 61.111 10.85 0.00 41.09 3.96
1420 1811 4.201679 CTGCCACGGCCATGCATG 62.202 66.667 20.19 20.19 41.09 4.06
1423 1814 3.761140 CCACGGCCATGCATGCAA 61.761 61.111 26.68 8.49 0.00 4.08
1424 1815 2.507547 CACGGCCATGCATGCAAC 60.508 61.111 26.68 16.80 0.00 4.17
1425 1816 2.677524 ACGGCCATGCATGCAACT 60.678 55.556 26.68 6.15 0.00 3.16
1426 1817 2.277591 ACGGCCATGCATGCAACTT 61.278 52.632 26.68 5.25 0.00 2.66
1427 1818 1.517694 CGGCCATGCATGCAACTTC 60.518 57.895 26.68 13.64 0.00 3.01
1428 1819 1.592743 GGCCATGCATGCAACTTCA 59.407 52.632 26.68 0.00 0.00 3.02
1429 1820 0.459585 GGCCATGCATGCAACTTCAG 60.460 55.000 26.68 10.69 0.00 3.02
1430 1821 0.528924 GCCATGCATGCAACTTCAGA 59.471 50.000 26.68 0.00 0.00 3.27
1431 1822 1.469251 GCCATGCATGCAACTTCAGAG 60.469 52.381 26.68 8.22 0.00 3.35
1432 1823 2.089201 CCATGCATGCAACTTCAGAGA 58.911 47.619 26.68 0.00 0.00 3.10
1433 1824 2.688446 CCATGCATGCAACTTCAGAGAT 59.312 45.455 26.68 0.00 0.00 2.75
1434 1825 3.130516 CCATGCATGCAACTTCAGAGATT 59.869 43.478 26.68 0.00 0.00 2.40
1435 1826 4.381612 CCATGCATGCAACTTCAGAGATTT 60.382 41.667 26.68 0.00 0.00 2.17
1436 1827 4.430137 TGCATGCAACTTCAGAGATTTC 57.570 40.909 20.30 0.00 0.00 2.17
1437 1828 4.077108 TGCATGCAACTTCAGAGATTTCT 58.923 39.130 20.30 0.00 0.00 2.52
1438 1829 4.521639 TGCATGCAACTTCAGAGATTTCTT 59.478 37.500 20.30 0.00 0.00 2.52
1439 1830 5.706833 TGCATGCAACTTCAGAGATTTCTTA 59.293 36.000 20.30 0.00 0.00 2.10
1440 1831 6.026513 GCATGCAACTTCAGAGATTTCTTAC 58.973 40.000 14.21 0.00 0.00 2.34
1441 1832 6.549952 CATGCAACTTCAGAGATTTCTTACC 58.450 40.000 0.00 0.00 0.00 2.85
1442 1833 5.620206 TGCAACTTCAGAGATTTCTTACCA 58.380 37.500 0.00 0.00 0.00 3.25
1443 1834 6.240894 TGCAACTTCAGAGATTTCTTACCAT 58.759 36.000 0.00 0.00 0.00 3.55
1444 1835 6.372659 TGCAACTTCAGAGATTTCTTACCATC 59.627 38.462 0.00 0.00 0.00 3.51
1445 1836 6.456181 GCAACTTCAGAGATTTCTTACCATCG 60.456 42.308 0.00 0.00 0.00 3.84
1446 1837 5.112686 ACTTCAGAGATTTCTTACCATCGC 58.887 41.667 0.00 0.00 0.00 4.58
1447 1838 3.706698 TCAGAGATTTCTTACCATCGCG 58.293 45.455 0.00 0.00 0.00 5.87
1448 1839 2.219674 CAGAGATTTCTTACCATCGCGC 59.780 50.000 0.00 0.00 0.00 6.86
1449 1840 1.190323 GAGATTTCTTACCATCGCGCG 59.810 52.381 26.76 26.76 0.00 6.86
1450 1841 0.232303 GATTTCTTACCATCGCGCGG 59.768 55.000 31.69 16.94 0.00 6.46
1451 1842 0.461339 ATTTCTTACCATCGCGCGGT 60.461 50.000 31.69 23.12 40.73 5.68
1452 1843 1.355796 TTTCTTACCATCGCGCGGTG 61.356 55.000 35.04 35.04 37.33 4.94
1453 1844 2.202690 CTTACCATCGCGCGGTGA 60.203 61.111 42.16 22.76 37.33 4.02
1454 1845 1.807981 CTTACCATCGCGCGGTGAA 60.808 57.895 42.16 27.93 37.33 3.18
1455 1846 2.020836 CTTACCATCGCGCGGTGAAC 62.021 60.000 42.16 0.00 37.33 3.18
1467 1858 2.501650 GTGAACGCGGCGTACGTA 60.502 61.111 29.63 12.28 44.30 3.57
1468 1859 1.869132 GTGAACGCGGCGTACGTAT 60.869 57.895 29.63 12.92 44.30 3.06
1469 1860 1.868692 TGAACGCGGCGTACGTATG 60.869 57.895 29.63 10.54 44.30 2.39
1470 1861 1.869132 GAACGCGGCGTACGTATGT 60.869 57.895 29.63 11.24 44.30 2.29
1471 1862 1.405469 GAACGCGGCGTACGTATGTT 61.405 55.000 29.63 10.40 44.30 2.71
1472 1863 1.676438 AACGCGGCGTACGTATGTTG 61.676 55.000 29.63 9.77 44.30 3.33
1473 1864 2.852087 CGCGGCGTACGTATGTTGG 61.852 63.158 17.90 7.00 46.52 3.77
1474 1865 3.000266 CGGCGTACGTATGTTGGC 59.000 61.111 17.90 9.49 37.93 4.52
1475 1866 1.806351 CGGCGTACGTATGTTGGCA 60.806 57.895 17.90 0.00 37.93 4.92
1476 1867 1.352882 CGGCGTACGTATGTTGGCAA 61.353 55.000 17.90 0.00 37.93 4.52
1477 1868 1.011333 GGCGTACGTATGTTGGCAAT 58.989 50.000 17.90 0.00 0.00 3.56
1478 1869 2.203401 GGCGTACGTATGTTGGCAATA 58.797 47.619 17.90 0.00 0.00 1.90
1479 1870 2.220133 GGCGTACGTATGTTGGCAATAG 59.780 50.000 17.90 0.00 0.00 1.73
1480 1871 2.348218 GCGTACGTATGTTGGCAATAGC 60.348 50.000 17.90 0.00 41.10 2.97
1494 1885 4.708726 GCAATAGCCAACTCTTTGATGT 57.291 40.909 0.00 0.00 34.24 3.06
1495 1886 5.064441 GCAATAGCCAACTCTTTGATGTT 57.936 39.130 0.00 0.00 34.24 2.71
1496 1887 5.473039 GCAATAGCCAACTCTTTGATGTTT 58.527 37.500 0.00 0.00 34.24 2.83
1497 1888 5.574443 GCAATAGCCAACTCTTTGATGTTTC 59.426 40.000 0.00 0.00 34.24 2.78
1498 1889 5.904362 ATAGCCAACTCTTTGATGTTTCC 57.096 39.130 0.00 0.00 34.24 3.13
1499 1890 3.837355 AGCCAACTCTTTGATGTTTCCT 58.163 40.909 0.00 0.00 34.24 3.36
1500 1891 4.218312 AGCCAACTCTTTGATGTTTCCTT 58.782 39.130 0.00 0.00 34.24 3.36
1501 1892 4.279420 AGCCAACTCTTTGATGTTTCCTTC 59.721 41.667 0.00 0.00 34.24 3.46
1502 1893 4.559502 GCCAACTCTTTGATGTTTCCTTCC 60.560 45.833 0.00 0.00 34.24 3.46
1503 1894 4.829492 CCAACTCTTTGATGTTTCCTTCCT 59.171 41.667 0.00 0.00 34.24 3.36
1504 1895 5.048434 CCAACTCTTTGATGTTTCCTTCCTC 60.048 44.000 0.00 0.00 34.24 3.71
1505 1896 5.310409 ACTCTTTGATGTTTCCTTCCTCA 57.690 39.130 0.00 0.00 0.00 3.86
1506 1897 5.694995 ACTCTTTGATGTTTCCTTCCTCAA 58.305 37.500 0.00 0.00 0.00 3.02
1507 1898 6.310149 ACTCTTTGATGTTTCCTTCCTCAAT 58.690 36.000 0.00 0.00 0.00 2.57
1508 1899 6.779539 ACTCTTTGATGTTTCCTTCCTCAATT 59.220 34.615 0.00 0.00 0.00 2.32
1509 1900 7.288621 ACTCTTTGATGTTTCCTTCCTCAATTT 59.711 33.333 0.00 0.00 0.00 1.82
1510 1901 8.021898 TCTTTGATGTTTCCTTCCTCAATTTT 57.978 30.769 0.00 0.00 0.00 1.82
1511 1902 8.485392 TCTTTGATGTTTCCTTCCTCAATTTTT 58.515 29.630 0.00 0.00 0.00 1.94
1531 1922 5.523438 TTTTTACACTTCCTTCCGCAATT 57.477 34.783 0.00 0.00 0.00 2.32
1532 1923 6.636562 TTTTTACACTTCCTTCCGCAATTA 57.363 33.333 0.00 0.00 0.00 1.40
1533 1924 6.827586 TTTTACACTTCCTTCCGCAATTAT 57.172 33.333 0.00 0.00 0.00 1.28
1534 1925 6.827586 TTTACACTTCCTTCCGCAATTATT 57.172 33.333 0.00 0.00 0.00 1.40
1535 1926 6.827586 TTACACTTCCTTCCGCAATTATTT 57.172 33.333 0.00 0.00 0.00 1.40
1536 1927 5.310720 ACACTTCCTTCCGCAATTATTTC 57.689 39.130 0.00 0.00 0.00 2.17
1537 1928 5.010282 ACACTTCCTTCCGCAATTATTTCT 58.990 37.500 0.00 0.00 0.00 2.52
1538 1929 5.106157 ACACTTCCTTCCGCAATTATTTCTG 60.106 40.000 0.00 0.00 0.00 3.02
1539 1930 5.010282 ACTTCCTTCCGCAATTATTTCTGT 58.990 37.500 0.00 0.00 0.00 3.41
1540 1931 5.123979 ACTTCCTTCCGCAATTATTTCTGTC 59.876 40.000 0.00 0.00 0.00 3.51
1541 1932 4.584874 TCCTTCCGCAATTATTTCTGTCA 58.415 39.130 0.00 0.00 0.00 3.58
1542 1933 4.394920 TCCTTCCGCAATTATTTCTGTCAC 59.605 41.667 0.00 0.00 0.00 3.67
1543 1934 4.334443 CTTCCGCAATTATTTCTGTCACG 58.666 43.478 0.00 0.00 0.00 4.35
1544 1935 2.095213 TCCGCAATTATTTCTGTCACGC 59.905 45.455 0.00 0.00 0.00 5.34
1545 1936 2.159585 CCGCAATTATTTCTGTCACGCA 60.160 45.455 0.00 0.00 0.00 5.24
1546 1937 3.487376 CCGCAATTATTTCTGTCACGCAT 60.487 43.478 0.00 0.00 0.00 4.73
1547 1938 3.720818 CGCAATTATTTCTGTCACGCATC 59.279 43.478 0.00 0.00 0.00 3.91
1548 1939 4.661125 GCAATTATTTCTGTCACGCATCA 58.339 39.130 0.00 0.00 0.00 3.07
1549 1940 4.496895 GCAATTATTTCTGTCACGCATCAC 59.503 41.667 0.00 0.00 0.00 3.06
1550 1941 5.674569 GCAATTATTTCTGTCACGCATCACT 60.675 40.000 0.00 0.00 0.00 3.41
1551 1942 4.926860 TTATTTCTGTCACGCATCACTG 57.073 40.909 0.00 0.00 0.00 3.66
1552 1943 1.511850 TTTCTGTCACGCATCACTGG 58.488 50.000 0.00 0.00 0.00 4.00
1553 1944 0.392706 TTCTGTCACGCATCACTGGT 59.607 50.000 0.00 0.00 0.00 4.00
1554 1945 0.038251 TCTGTCACGCATCACTGGTC 60.038 55.000 0.00 0.00 0.00 4.02
1555 1946 1.347097 CTGTCACGCATCACTGGTCG 61.347 60.000 0.00 0.00 0.00 4.79
1556 1947 1.372997 GTCACGCATCACTGGTCGT 60.373 57.895 0.00 0.00 35.35 4.34
1557 1948 1.080772 TCACGCATCACTGGTCGTC 60.081 57.895 0.00 0.00 32.38 4.20
1558 1949 1.080501 CACGCATCACTGGTCGTCT 60.081 57.895 0.00 0.00 32.38 4.18
1559 1950 0.170339 CACGCATCACTGGTCGTCTA 59.830 55.000 0.00 0.00 32.38 2.59
1560 1951 1.103803 ACGCATCACTGGTCGTCTAT 58.896 50.000 0.00 0.00 0.00 1.98
1561 1952 1.065701 ACGCATCACTGGTCGTCTATC 59.934 52.381 0.00 0.00 0.00 2.08
1562 1953 1.600663 CGCATCACTGGTCGTCTATCC 60.601 57.143 0.00 0.00 0.00 2.59
1563 1954 1.409064 GCATCACTGGTCGTCTATCCA 59.591 52.381 0.00 0.00 0.00 3.41
1564 1955 2.036475 GCATCACTGGTCGTCTATCCAT 59.964 50.000 0.00 0.00 33.01 3.41
1565 1956 3.493350 GCATCACTGGTCGTCTATCCATT 60.493 47.826 0.00 0.00 33.01 3.16
1566 1957 4.302455 CATCACTGGTCGTCTATCCATTC 58.698 47.826 0.00 0.00 33.01 2.67
1567 1958 3.361786 TCACTGGTCGTCTATCCATTCA 58.638 45.455 0.00 0.00 33.01 2.57
1568 1959 3.960755 TCACTGGTCGTCTATCCATTCAT 59.039 43.478 0.00 0.00 33.01 2.57
1569 1960 4.053983 CACTGGTCGTCTATCCATTCATG 58.946 47.826 0.00 0.00 33.01 3.07
1891 2282 1.237285 TTTTGGCTCTCTTCGGCTGC 61.237 55.000 0.00 0.00 0.00 5.25
1935 2326 3.706373 ATCTCCAACAGGCGCCGT 61.706 61.111 23.20 19.32 0.00 5.68
1976 2367 1.735198 CTTTACGGCGCGTCCTTCA 60.735 57.895 6.90 0.00 41.54 3.02
2057 2461 1.226773 GCTGGCGCTAAAATGCAGG 60.227 57.895 7.64 0.00 0.00 4.85
2069 2475 1.252904 AATGCAGGGCACGCTCATTT 61.253 50.000 4.52 0.00 43.04 2.32
2072 2478 0.740737 GCAGGGCACGCTCATTTTAT 59.259 50.000 0.00 0.00 0.00 1.40
2076 2482 4.499696 GCAGGGCACGCTCATTTTATAAAT 60.500 41.667 0.00 0.00 0.00 1.40
2192 2606 9.621629 AAAGGATACAATGGTATTTTACATCGA 57.378 29.630 0.00 0.00 40.28 3.59
2281 2696 2.066262 CGGTGCAACGAGACAAACTAT 58.934 47.619 22.23 0.00 38.12 2.12
2292 2707 2.233922 AGACAAACTATGGTGACTCCCG 59.766 50.000 0.00 0.00 34.77 5.14
2364 2779 0.405198 AGCCACATGTCATCCCAACA 59.595 50.000 0.00 0.00 0.00 3.33
2372 2787 2.016318 TGTCATCCCAACATTCATCGC 58.984 47.619 0.00 0.00 0.00 4.58
2392 2807 2.499827 GGGGGAGAAGATCGACCGG 61.500 68.421 0.00 0.00 0.00 5.28
2404 2819 4.162690 GACCGGCCGCCATTCTCT 62.163 66.667 22.85 0.00 0.00 3.10
2420 2835 2.218603 TCTCTACGATATCGCACTGCA 58.781 47.619 24.59 2.24 44.43 4.41
2599 3014 1.376424 CTGCTGCCGAACATGGTCT 60.376 57.895 9.52 0.00 0.00 3.85
2666 3082 2.259818 CCTGCTCGCGAGTGAAGT 59.740 61.111 34.46 0.00 0.00 3.01
2668 3084 1.081175 CTGCTCGCGAGTGAAGTCA 60.081 57.895 34.46 21.96 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 193 0.977395 GTCCTAGAGTTGCCACTGGT 59.023 55.000 0.00 0.00 31.22 4.00
1109 1221 2.517875 ATGGCCGCCATCTTGAGC 60.518 61.111 19.79 0.00 40.74 4.26
1304 1695 2.738521 CAGGCCTTGTCCACGACG 60.739 66.667 0.00 0.00 34.95 5.12
1305 1696 3.050275 GCAGGCCTTGTCCACGAC 61.050 66.667 0.00 0.00 0.00 4.34
1306 1697 4.680237 CGCAGGCCTTGTCCACGA 62.680 66.667 0.00 0.00 32.02 4.35
1307 1698 4.988598 ACGCAGGCCTTGTCCACG 62.989 66.667 0.00 2.74 35.12 4.94
1308 1699 3.357079 CACGCAGGCCTTGTCCAC 61.357 66.667 0.00 0.00 0.00 4.02
1309 1700 4.641645 CCACGCAGGCCTTGTCCA 62.642 66.667 0.00 0.00 0.00 4.02
1310 1701 4.329545 TCCACGCAGGCCTTGTCC 62.330 66.667 0.00 0.00 37.29 4.02
1311 1702 3.050275 GTCCACGCAGGCCTTGTC 61.050 66.667 0.00 0.00 37.29 3.18
1312 1703 4.643387 GGTCCACGCAGGCCTTGT 62.643 66.667 0.00 0.76 37.29 3.16
1313 1704 3.925630 ATGGTCCACGCAGGCCTTG 62.926 63.158 0.00 0.00 37.29 3.61
1314 1705 2.713531 AAATGGTCCACGCAGGCCTT 62.714 55.000 0.00 0.00 37.29 4.35
1315 1706 3.210012 AAATGGTCCACGCAGGCCT 62.210 57.895 0.00 0.00 37.29 5.19
1316 1707 2.676471 AAATGGTCCACGCAGGCC 60.676 61.111 0.00 0.00 37.29 5.19
1317 1708 1.244019 AAGAAATGGTCCACGCAGGC 61.244 55.000 0.00 0.00 37.29 4.85
1318 1709 0.804989 GAAGAAATGGTCCACGCAGG 59.195 55.000 0.00 0.00 39.47 4.85
1319 1710 1.197721 GTGAAGAAATGGTCCACGCAG 59.802 52.381 0.00 0.00 0.00 5.18
1320 1711 1.234821 GTGAAGAAATGGTCCACGCA 58.765 50.000 0.00 0.00 0.00 5.24
1321 1712 1.197721 CTGTGAAGAAATGGTCCACGC 59.802 52.381 0.00 0.00 0.00 5.34
1322 1713 1.197721 GCTGTGAAGAAATGGTCCACG 59.802 52.381 0.00 0.00 0.00 4.94
1323 1714 2.508526 AGCTGTGAAGAAATGGTCCAC 58.491 47.619 0.00 0.00 0.00 4.02
1324 1715 2.886523 CAAGCTGTGAAGAAATGGTCCA 59.113 45.455 0.00 0.00 0.00 4.02
1325 1716 2.352127 GCAAGCTGTGAAGAAATGGTCC 60.352 50.000 0.00 0.00 0.00 4.46
1326 1717 2.294233 TGCAAGCTGTGAAGAAATGGTC 59.706 45.455 0.00 0.00 0.00 4.02
1327 1718 2.309613 TGCAAGCTGTGAAGAAATGGT 58.690 42.857 0.00 0.00 0.00 3.55
1328 1719 3.250744 CATGCAAGCTGTGAAGAAATGG 58.749 45.455 0.00 0.00 0.00 3.16
1329 1720 3.250744 CCATGCAAGCTGTGAAGAAATG 58.749 45.455 0.00 0.00 0.00 2.32
1330 1721 2.353406 GCCATGCAAGCTGTGAAGAAAT 60.353 45.455 4.90 0.00 0.00 2.17
1331 1722 1.000060 GCCATGCAAGCTGTGAAGAAA 60.000 47.619 4.90 0.00 0.00 2.52
1332 1723 0.599558 GCCATGCAAGCTGTGAAGAA 59.400 50.000 4.90 0.00 0.00 2.52
1333 1724 1.246056 GGCCATGCAAGCTGTGAAGA 61.246 55.000 11.41 0.00 0.00 2.87
1334 1725 1.214589 GGCCATGCAAGCTGTGAAG 59.785 57.895 11.41 0.00 0.00 3.02
1335 1726 0.901114 ATGGCCATGCAAGCTGTGAA 60.901 50.000 20.04 0.00 0.00 3.18
1336 1727 1.304630 ATGGCCATGCAAGCTGTGA 60.305 52.632 20.04 0.00 0.00 3.58
1337 1728 1.141019 GATGGCCATGCAAGCTGTG 59.859 57.895 26.56 0.00 0.00 3.66
1338 1729 1.000019 AGATGGCCATGCAAGCTGT 60.000 52.632 26.56 0.00 21.82 4.40
1339 1730 1.437573 CAGATGGCCATGCAAGCTG 59.562 57.895 26.56 19.50 39.65 4.24
1340 1731 2.423898 GCAGATGGCCATGCAAGCT 61.424 57.895 26.56 10.91 42.11 3.74
1341 1732 2.106332 GCAGATGGCCATGCAAGC 59.894 61.111 26.56 17.11 42.11 4.01
1345 1736 0.179119 GTTCTTGCAGATGGCCATGC 60.179 55.000 26.56 23.92 43.89 4.06
1346 1737 1.179152 TGTTCTTGCAGATGGCCATG 58.821 50.000 26.56 13.27 43.89 3.66
1347 1738 1.754803 CATGTTCTTGCAGATGGCCAT 59.245 47.619 20.96 20.96 43.89 4.40
1348 1739 1.179152 CATGTTCTTGCAGATGGCCA 58.821 50.000 8.56 8.56 43.89 5.36
1349 1740 1.135199 CACATGTTCTTGCAGATGGCC 60.135 52.381 0.00 0.00 43.89 5.36
1350 1741 1.734707 GCACATGTTCTTGCAGATGGC 60.735 52.381 0.00 0.00 45.13 4.40
1351 1742 1.466866 CGCACATGTTCTTGCAGATGG 60.467 52.381 0.00 0.00 38.76 3.51
1352 1743 1.465777 TCGCACATGTTCTTGCAGATG 59.534 47.619 0.00 0.00 38.76 2.90
1353 1744 1.736126 CTCGCACATGTTCTTGCAGAT 59.264 47.619 0.00 0.00 38.76 2.90
1354 1745 1.150827 CTCGCACATGTTCTTGCAGA 58.849 50.000 0.00 0.00 38.76 4.26
1355 1746 0.453950 GCTCGCACATGTTCTTGCAG 60.454 55.000 0.00 0.00 38.76 4.41
1356 1747 1.575922 GCTCGCACATGTTCTTGCA 59.424 52.632 0.00 0.00 38.76 4.08
1357 1748 1.154150 GGCTCGCACATGTTCTTGC 60.154 57.895 0.00 0.00 35.26 4.01
1358 1749 0.957395 AGGGCTCGCACATGTTCTTG 60.957 55.000 0.00 0.00 0.00 3.02
1359 1750 0.613260 TAGGGCTCGCACATGTTCTT 59.387 50.000 0.00 0.00 0.00 2.52
1360 1751 0.176680 CTAGGGCTCGCACATGTTCT 59.823 55.000 0.00 0.00 0.00 3.01
1361 1752 0.175760 TCTAGGGCTCGCACATGTTC 59.824 55.000 0.00 0.00 0.00 3.18
1362 1753 0.108138 GTCTAGGGCTCGCACATGTT 60.108 55.000 0.00 0.00 0.00 2.71
1363 1754 0.972983 AGTCTAGGGCTCGCACATGT 60.973 55.000 0.00 0.00 0.00 3.21
1364 1755 0.249238 GAGTCTAGGGCTCGCACATG 60.249 60.000 0.00 0.00 0.00 3.21
1365 1756 1.395826 GGAGTCTAGGGCTCGCACAT 61.396 60.000 0.00 0.00 34.00 3.21
1366 1757 2.052690 GGAGTCTAGGGCTCGCACA 61.053 63.158 0.00 0.00 34.00 4.57
1367 1758 2.787567 GGGAGTCTAGGGCTCGCAC 61.788 68.421 19.52 7.14 42.93 5.34
1368 1759 2.442272 GGGAGTCTAGGGCTCGCA 60.442 66.667 19.52 0.00 42.93 5.10
1369 1760 2.123640 AGGGAGTCTAGGGCTCGC 60.124 66.667 17.90 17.90 43.49 5.03
1370 1761 0.178975 ATCAGGGAGTCTAGGGCTCG 60.179 60.000 8.45 0.00 34.00 5.03
1371 1762 1.627864 GATCAGGGAGTCTAGGGCTC 58.372 60.000 6.67 6.67 0.00 4.70
1372 1763 0.178975 CGATCAGGGAGTCTAGGGCT 60.179 60.000 0.00 0.00 0.00 5.19
1373 1764 1.182385 CCGATCAGGGAGTCTAGGGC 61.182 65.000 0.00 0.00 35.97 5.19
1374 1765 1.182385 GCCGATCAGGGAGTCTAGGG 61.182 65.000 5.87 0.00 41.48 3.53
1375 1766 1.519751 CGCCGATCAGGGAGTCTAGG 61.520 65.000 5.87 0.00 41.48 3.02
1376 1767 1.953017 CGCCGATCAGGGAGTCTAG 59.047 63.158 5.87 0.00 41.48 2.43
1377 1768 2.194212 GCGCCGATCAGGGAGTCTA 61.194 63.158 0.00 0.00 41.48 2.59
1378 1769 3.532155 GCGCCGATCAGGGAGTCT 61.532 66.667 0.00 0.00 41.48 3.24
1379 1770 4.593864 GGCGCCGATCAGGGAGTC 62.594 72.222 12.58 0.00 41.48 3.36
1398 1789 4.722700 ATGGCCGTGGCAGTCACC 62.723 66.667 13.76 0.00 42.43 4.02
1399 1790 3.434319 CATGGCCGTGGCAGTCAC 61.434 66.667 17.90 0.00 42.43 3.67
1402 1793 4.746309 ATGCATGGCCGTGGCAGT 62.746 61.111 26.22 11.32 42.43 4.40
1403 1794 4.201679 CATGCATGGCCGTGGCAG 62.202 66.667 26.22 13.42 42.43 4.85
1406 1797 3.761140 TTGCATGCATGGCCGTGG 61.761 61.111 27.34 11.02 0.00 4.94
1407 1798 2.495366 AAGTTGCATGCATGGCCGTG 62.495 55.000 27.34 21.33 0.00 4.94
1408 1799 2.216750 GAAGTTGCATGCATGGCCGT 62.217 55.000 27.34 8.19 0.00 5.68
1409 1800 1.517694 GAAGTTGCATGCATGGCCG 60.518 57.895 27.34 2.89 0.00 6.13
1410 1801 0.459585 CTGAAGTTGCATGCATGGCC 60.460 55.000 27.34 12.69 0.00 5.36
1411 1802 0.528924 TCTGAAGTTGCATGCATGGC 59.471 50.000 27.34 19.18 0.00 4.40
1412 1803 2.089201 TCTCTGAAGTTGCATGCATGG 58.911 47.619 27.34 10.03 0.00 3.66
1413 1804 4.371855 AATCTCTGAAGTTGCATGCATG 57.628 40.909 23.37 22.70 0.00 4.06
1414 1805 4.705507 AGAAATCTCTGAAGTTGCATGCAT 59.294 37.500 23.37 6.60 0.00 3.96
1415 1806 4.077108 AGAAATCTCTGAAGTTGCATGCA 58.923 39.130 18.46 18.46 0.00 3.96
1416 1807 4.698583 AGAAATCTCTGAAGTTGCATGC 57.301 40.909 11.82 11.82 0.00 4.06
1417 1808 6.149973 TGGTAAGAAATCTCTGAAGTTGCATG 59.850 38.462 0.00 0.00 30.03 4.06
1418 1809 6.240894 TGGTAAGAAATCTCTGAAGTTGCAT 58.759 36.000 0.00 0.00 30.03 3.96
1419 1810 5.620206 TGGTAAGAAATCTCTGAAGTTGCA 58.380 37.500 0.00 0.00 30.03 4.08
1420 1811 6.456181 CGATGGTAAGAAATCTCTGAAGTTGC 60.456 42.308 0.00 0.00 30.03 4.17
1421 1812 6.456181 GCGATGGTAAGAAATCTCTGAAGTTG 60.456 42.308 0.00 0.00 30.03 3.16
1422 1813 5.582665 GCGATGGTAAGAAATCTCTGAAGTT 59.417 40.000 0.00 0.00 30.03 2.66
1423 1814 5.112686 GCGATGGTAAGAAATCTCTGAAGT 58.887 41.667 0.00 0.00 30.03 3.01
1424 1815 4.208047 CGCGATGGTAAGAAATCTCTGAAG 59.792 45.833 0.00 0.00 30.03 3.02
1425 1816 4.112634 CGCGATGGTAAGAAATCTCTGAA 58.887 43.478 0.00 0.00 30.03 3.02
1426 1817 3.706698 CGCGATGGTAAGAAATCTCTGA 58.293 45.455 0.00 0.00 30.03 3.27
1427 1818 2.219674 GCGCGATGGTAAGAAATCTCTG 59.780 50.000 12.10 0.00 30.03 3.35
1428 1819 2.474816 GCGCGATGGTAAGAAATCTCT 58.525 47.619 12.10 0.00 0.00 3.10
1429 1820 1.190323 CGCGCGATGGTAAGAAATCTC 59.810 52.381 28.94 0.00 0.00 2.75
1430 1821 1.209128 CGCGCGATGGTAAGAAATCT 58.791 50.000 28.94 0.00 0.00 2.40
1431 1822 0.232303 CCGCGCGATGGTAAGAAATC 59.768 55.000 34.63 0.00 0.00 2.17
1432 1823 0.461339 ACCGCGCGATGGTAAGAAAT 60.461 50.000 34.63 0.00 38.15 2.17
1433 1824 1.079681 ACCGCGCGATGGTAAGAAA 60.080 52.632 34.63 0.00 38.15 2.52
1434 1825 1.807981 CACCGCGCGATGGTAAGAA 60.808 57.895 34.63 0.00 37.72 2.52
1435 1826 2.202690 CACCGCGCGATGGTAAGA 60.203 61.111 34.63 0.00 37.72 2.10
1436 1827 1.807981 TTCACCGCGCGATGGTAAG 60.808 57.895 34.63 15.43 37.72 2.34
1437 1828 2.095847 GTTCACCGCGCGATGGTAA 61.096 57.895 34.63 13.67 37.72 2.85
1438 1829 2.507547 GTTCACCGCGCGATGGTA 60.508 61.111 34.63 14.19 37.72 3.25
1449 1840 3.944526 TACGTACGCCGCGTTCACC 62.945 63.158 25.47 8.91 42.85 4.02
1450 1841 1.869132 ATACGTACGCCGCGTTCAC 60.869 57.895 25.47 15.97 42.85 3.18
1451 1842 1.868692 CATACGTACGCCGCGTTCA 60.869 57.895 25.47 3.55 42.85 3.18
1452 1843 1.405469 AACATACGTACGCCGCGTTC 61.405 55.000 25.47 18.19 42.85 3.95
1453 1844 1.444212 AACATACGTACGCCGCGTT 60.444 52.632 25.47 8.92 42.85 4.84
1454 1845 2.153945 CAACATACGTACGCCGCGT 61.154 57.895 23.72 23.72 45.11 6.01
1455 1846 2.611365 CAACATACGTACGCCGCG 59.389 61.111 16.72 12.14 41.42 6.46
1456 1847 3.000266 CCAACATACGTACGCCGC 59.000 61.111 16.72 0.00 41.42 6.53
1457 1848 1.352882 TTGCCAACATACGTACGCCG 61.353 55.000 16.72 6.39 44.03 6.46
1458 1849 1.011333 ATTGCCAACATACGTACGCC 58.989 50.000 16.72 0.00 0.00 5.68
1459 1850 2.348218 GCTATTGCCAACATACGTACGC 60.348 50.000 16.72 0.00 0.00 4.42
1460 1851 3.499072 GCTATTGCCAACATACGTACG 57.501 47.619 15.01 15.01 0.00 3.67
1473 1864 4.708726 ACATCAAAGAGTTGGCTATTGC 57.291 40.909 0.00 0.00 35.29 3.56
1474 1865 6.071728 AGGAAACATCAAAGAGTTGGCTATTG 60.072 38.462 0.00 0.00 35.29 1.90
1475 1866 6.012745 AGGAAACATCAAAGAGTTGGCTATT 58.987 36.000 0.00 0.00 35.29 1.73
1476 1867 5.574188 AGGAAACATCAAAGAGTTGGCTAT 58.426 37.500 0.00 0.00 35.29 2.97
1477 1868 4.985538 AGGAAACATCAAAGAGTTGGCTA 58.014 39.130 0.00 0.00 35.29 3.93
1478 1869 3.837355 AGGAAACATCAAAGAGTTGGCT 58.163 40.909 0.00 0.00 35.29 4.75
1479 1870 4.550422 GAAGGAAACATCAAAGAGTTGGC 58.450 43.478 0.00 0.00 35.29 4.52
1480 1871 4.829492 AGGAAGGAAACATCAAAGAGTTGG 59.171 41.667 0.00 0.00 35.29 3.77
1481 1872 5.532406 TGAGGAAGGAAACATCAAAGAGTTG 59.468 40.000 0.00 0.00 35.95 3.16
1482 1873 5.694995 TGAGGAAGGAAACATCAAAGAGTT 58.305 37.500 0.00 0.00 0.00 3.01
1483 1874 5.310409 TGAGGAAGGAAACATCAAAGAGT 57.690 39.130 0.00 0.00 0.00 3.24
1484 1875 6.830873 ATTGAGGAAGGAAACATCAAAGAG 57.169 37.500 0.00 0.00 40.41 2.85
1485 1876 7.601705 AAATTGAGGAAGGAAACATCAAAGA 57.398 32.000 0.00 0.00 40.41 2.52
1486 1877 8.667076 AAAAATTGAGGAAGGAAACATCAAAG 57.333 30.769 0.00 0.00 40.41 2.77
1519 1910 4.394920 GTGACAGAAATAATTGCGGAAGGA 59.605 41.667 0.00 0.00 0.00 3.36
1520 1911 4.662145 GTGACAGAAATAATTGCGGAAGG 58.338 43.478 0.00 0.00 0.00 3.46
1521 1912 4.334443 CGTGACAGAAATAATTGCGGAAG 58.666 43.478 0.00 0.00 0.00 3.46
1522 1913 3.425625 GCGTGACAGAAATAATTGCGGAA 60.426 43.478 0.00 0.00 0.00 4.30
1523 1914 2.095213 GCGTGACAGAAATAATTGCGGA 59.905 45.455 0.00 0.00 0.00 5.54
1524 1915 2.159585 TGCGTGACAGAAATAATTGCGG 60.160 45.455 0.00 0.00 0.00 5.69
1525 1916 3.116063 TGCGTGACAGAAATAATTGCG 57.884 42.857 0.00 0.00 0.00 4.85
1526 1917 4.496895 GTGATGCGTGACAGAAATAATTGC 59.503 41.667 0.00 0.00 0.00 3.56
1527 1918 5.735892 CAGTGATGCGTGACAGAAATAATTG 59.264 40.000 0.00 0.00 0.00 2.32
1528 1919 5.163723 CCAGTGATGCGTGACAGAAATAATT 60.164 40.000 0.00 0.00 0.00 1.40
1529 1920 4.333649 CCAGTGATGCGTGACAGAAATAAT 59.666 41.667 0.00 0.00 0.00 1.28
1530 1921 3.684305 CCAGTGATGCGTGACAGAAATAA 59.316 43.478 0.00 0.00 0.00 1.40
1531 1922 3.261580 CCAGTGATGCGTGACAGAAATA 58.738 45.455 0.00 0.00 0.00 1.40
1532 1923 2.079158 CCAGTGATGCGTGACAGAAAT 58.921 47.619 0.00 0.00 0.00 2.17
1533 1924 1.202639 ACCAGTGATGCGTGACAGAAA 60.203 47.619 0.00 0.00 0.00 2.52
1534 1925 0.392706 ACCAGTGATGCGTGACAGAA 59.607 50.000 0.00 0.00 0.00 3.02
1535 1926 0.038251 GACCAGTGATGCGTGACAGA 60.038 55.000 0.00 0.00 0.00 3.41
1536 1927 1.347097 CGACCAGTGATGCGTGACAG 61.347 60.000 0.00 0.00 0.00 3.51
1537 1928 1.372872 CGACCAGTGATGCGTGACA 60.373 57.895 0.00 0.00 0.00 3.58
1538 1929 1.344942 GACGACCAGTGATGCGTGAC 61.345 60.000 9.09 0.00 37.07 3.67
1539 1930 1.080772 GACGACCAGTGATGCGTGA 60.081 57.895 9.09 0.00 37.07 4.35
1540 1931 0.170339 TAGACGACCAGTGATGCGTG 59.830 55.000 9.09 0.00 37.07 5.34
1541 1932 1.065701 GATAGACGACCAGTGATGCGT 59.934 52.381 4.90 4.90 39.99 5.24
1542 1933 1.600663 GGATAGACGACCAGTGATGCG 60.601 57.143 0.00 0.00 0.00 4.73
1543 1934 1.409064 TGGATAGACGACCAGTGATGC 59.591 52.381 0.00 0.00 0.00 3.91
1544 1935 4.202151 TGAATGGATAGACGACCAGTGATG 60.202 45.833 0.00 0.00 39.62 3.07
1545 1936 3.960755 TGAATGGATAGACGACCAGTGAT 59.039 43.478 0.00 0.00 39.62 3.06
1546 1937 3.361786 TGAATGGATAGACGACCAGTGA 58.638 45.455 0.00 0.00 39.62 3.41
1547 1938 3.801114 TGAATGGATAGACGACCAGTG 57.199 47.619 0.00 0.00 39.62 3.66
1548 1939 4.327982 CATGAATGGATAGACGACCAGT 57.672 45.455 0.00 0.00 39.62 4.00
1562 1953 3.497262 CACCATCTGTCGATCCATGAATG 59.503 47.826 0.00 0.00 0.00 2.67
1563 1954 3.495629 CCACCATCTGTCGATCCATGAAT 60.496 47.826 0.00 0.00 0.00 2.57
1564 1955 2.158914 CCACCATCTGTCGATCCATGAA 60.159 50.000 0.00 0.00 0.00 2.57
1565 1956 1.413812 CCACCATCTGTCGATCCATGA 59.586 52.381 0.00 0.00 0.00 3.07
1566 1957 1.139654 ACCACCATCTGTCGATCCATG 59.860 52.381 0.00 0.00 0.00 3.66
1567 1958 1.139654 CACCACCATCTGTCGATCCAT 59.860 52.381 0.00 0.00 0.00 3.41
1568 1959 0.536724 CACCACCATCTGTCGATCCA 59.463 55.000 0.00 0.00 0.00 3.41
1569 1960 0.537188 ACACCACCATCTGTCGATCC 59.463 55.000 0.00 0.00 0.00 3.36
1570 1961 2.093973 AGAACACCACCATCTGTCGATC 60.094 50.000 0.00 0.00 0.00 3.69
1571 1962 1.902508 AGAACACCACCATCTGTCGAT 59.097 47.619 0.00 0.00 0.00 3.59
1572 1963 1.000843 CAGAACACCACCATCTGTCGA 59.999 52.381 0.00 0.00 36.64 4.20
1573 1964 1.432514 CAGAACACCACCATCTGTCG 58.567 55.000 0.00 0.00 36.64 4.35
1576 1967 3.127548 GCATAACAGAACACCACCATCTG 59.872 47.826 0.00 0.00 44.77 2.90
1577 1968 3.009473 AGCATAACAGAACACCACCATCT 59.991 43.478 0.00 0.00 0.00 2.90
1578 1969 3.347216 AGCATAACAGAACACCACCATC 58.653 45.455 0.00 0.00 0.00 3.51
1579 1970 3.439857 AGCATAACAGAACACCACCAT 57.560 42.857 0.00 0.00 0.00 3.55
1580 1971 2.949177 AGCATAACAGAACACCACCA 57.051 45.000 0.00 0.00 0.00 4.17
1581 1972 3.007635 GGTAGCATAACAGAACACCACC 58.992 50.000 0.00 0.00 0.00 4.61
1582 1973 2.671396 CGGTAGCATAACAGAACACCAC 59.329 50.000 0.00 0.00 0.00 4.16
1901 2292 3.295973 GAGATGCTCTAAGAGGGAGTGT 58.704 50.000 0.00 0.00 33.73 3.55
2041 2443 2.709883 GCCCTGCATTTTAGCGCCA 61.710 57.895 2.29 0.00 37.31 5.69
2177 2591 7.269316 TCTAGTTGCATCGATGTAAAATACCA 58.731 34.615 27.16 11.55 34.26 3.25
2192 2606 7.596995 GCTTTCGAACTATCTATCTAGTTGCAT 59.403 37.037 0.00 0.00 41.00 3.96
2230 2644 5.909621 TCTATCTAGTTGCACCGTAGTTT 57.090 39.130 0.00 0.00 0.00 2.66
2292 2707 2.263741 GGTGATGATGATGGCGGCC 61.264 63.158 13.32 13.32 0.00 6.13
2364 2779 0.471617 CTTCTCCCCCAGCGATGAAT 59.528 55.000 0.06 0.00 0.00 2.57
2372 2787 1.739338 CGGTCGATCTTCTCCCCCAG 61.739 65.000 0.00 0.00 0.00 4.45
2392 2807 2.531206 GATATCGTAGAGAATGGCGGC 58.469 52.381 0.00 0.00 43.63 6.53
2398 2813 3.253432 TGCAGTGCGATATCGTAGAGAAT 59.747 43.478 24.99 3.43 43.63 2.40
2549 2964 4.821589 CGCCGAGGAGGACAAGCC 62.822 72.222 0.00 0.00 45.00 4.35
2553 2968 2.044352 TCATCGCCGAGGAGGACA 60.044 61.111 0.00 0.00 45.00 4.02
2647 3063 3.921767 CTTCACTCGCGAGCAGGCA 62.922 63.158 34.83 14.77 0.00 4.75
2659 3075 1.645710 ACTTCCGGGATGACTTCACT 58.354 50.000 16.10 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.