Multiple sequence alignment - TraesCS6B01G374300

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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 TraesCS6B01G374300 chr6B 100.000 2294 0 0 1 2294 647501495 647503788 0.000000e+00 4237.0
1 TraesCS6B01G374300 chr6B 90.484 578 48 3 782 1359 647595219 647595789 0.000000e+00 756.0
2 TraesCS6B01G374300 chr6B 89.851 404 30 4 1869 2271 647596303 647596696 2.030000e-140 508.0
3 TraesCS6B01G374300 chr6B 85.393 89 12 1 408 496 687532048 687531961 8.730000e-15 91.6
4 TraesCS6B01G374300 chr6B 84.615 65 9 1 375 438 42233926 42233862 1.900000e-06 63.9
5 TraesCS6B01G374300 chr6D 91.779 669 47 4 705 1368 429658281 429658946 0.000000e+00 924.0
6 TraesCS6B01G374300 chr6D 89.074 421 29 6 1858 2277 429659185 429659589 7.310000e-140 507.0
7 TraesCS6B01G374300 chr6D 78.901 564 72 27 165 710 429657687 429658221 2.820000e-89 339.0
8 TraesCS6B01G374300 chr6A 90.264 719 43 16 8 710 574817668 574818375 0.000000e+00 915.0
9 TraesCS6B01G374300 chr6A 89.549 421 38 3 1858 2277 574819457 574819872 1.560000e-146 529.0
10 TraesCS6B01G374300 chr6A 89.303 402 34 2 973 1368 574818805 574819203 1.580000e-136 496.0
11 TraesCS6B01G374300 chr6A 91.667 168 7 5 1673 1833 23679477 23679310 2.290000e-55 226.0
12 TraesCS6B01G374300 chr6A 98.361 61 0 1 1568 1627 566634978 566634918 3.120000e-19 106.0
13 TraesCS6B01G374300 chr6A 100.000 29 0 0 1632 1660 395255923 395255895 1.000000e-03 54.7
14 TraesCS6B01G374300 chr7B 79.104 402 39 18 986 1342 526854752 526854351 3.810000e-58 235.0
15 TraesCS6B01G374300 chr1D 90.805 174 15 1 1661 1833 229311004 229310831 4.930000e-57 231.0
16 TraesCS6B01G374300 chr3D 90.805 174 13 3 1661 1832 22917929 22917757 1.770000e-56 230.0
17 TraesCS6B01G374300 chr3D 90.751 173 11 4 1664 1831 56445138 56444966 2.290000e-55 226.0
18 TraesCS6B01G374300 chr2D 90.395 177 12 4 1661 1832 360552165 360552341 6.380000e-56 228.0
19 TraesCS6B01G374300 chr5D 89.189 185 13 5 1661 1844 560280990 560280812 8.250000e-55 224.0
20 TraesCS6B01G374300 chr5D 88.350 103 6 4 1564 1660 374387056 374386954 4.000000e-23 119.0
21 TraesCS6B01G374300 chr5D 100.000 29 0 0 1632 1660 276547673 276547645 1.000000e-03 54.7
22 TraesCS6B01G374300 chr5D 100.000 29 0 0 1632 1660 371069897 371069869 1.000000e-03 54.7
23 TraesCS6B01G374300 chr7A 82.657 271 26 7 1093 1342 564269726 564269456 1.070000e-53 220.0
24 TraesCS6B01G374300 chr7A 96.923 65 1 1 1564 1627 639289962 639290026 8.670000e-20 108.0
25 TraesCS6B01G374300 chr3A 89.655 174 15 2 1661 1831 77922308 77922135 3.840000e-53 219.0
26 TraesCS6B01G374300 chr3A 95.312 64 2 1 1565 1627 701344598 701344661 1.450000e-17 100.0
27 TraesCS6B01G374300 chr3A 81.111 90 16 1 405 493 472786068 472786157 1.140000e-08 71.3
28 TraesCS6B01G374300 chr1A 87.640 178 14 5 1661 1833 398112551 398112725 1.390000e-47 200.0
29 TraesCS6B01G374300 chr1A 96.923 65 1 1 1564 1627 202093107 202093043 8.670000e-20 108.0
30 TraesCS6B01G374300 chr1A 96.875 64 1 1 1565 1627 483658652 483658715 3.120000e-19 106.0
31 TraesCS6B01G374300 chr1A 100.000 29 0 0 1632 1660 542370099 542370127 1.000000e-03 54.7
32 TraesCS6B01G374300 chr5A 85.417 192 17 8 1662 1842 19220590 19220781 3.010000e-44 189.0
33 TraesCS6B01G374300 chr7D 80.505 277 24 12 1093 1342 498490700 498490427 3.890000e-43 185.0
34 TraesCS6B01G374300 chrUn 96.875 64 1 1 1565 1627 74039523 74039460 3.120000e-19 106.0
35 TraesCS6B01G374300 chr4D 96.875 64 1 1 1565 1627 416425167 416425230 3.120000e-19 106.0
36 TraesCS6B01G374300 chr2A 93.151 73 2 2 1565 1634 729352756 729352828 1.120000e-18 104.0
37 TraesCS6B01G374300 chr5B 100.000 29 0 0 1632 1660 255548415 255548443 1.000000e-03 54.7
38 TraesCS6B01G374300 chr5B 100.000 29 0 0 1632 1660 693568836 693568808 1.000000e-03 54.7
39 TraesCS6B01G374300 chr5B 100.000 29 0 0 1632 1660 693710045 693710073 1.000000e-03 54.7
40 TraesCS6B01G374300 chr4A 100.000 29 0 0 1632 1660 468752037 468752065 1.000000e-03 54.7


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 TraesCS6B01G374300 chr6B 647501495 647503788 2293 False 4237.000000 4237 100.000000 1 2294 1 chr6B.!!$F1 2293
1 TraesCS6B01G374300 chr6B 647595219 647596696 1477 False 632.000000 756 90.167500 782 2271 2 chr6B.!!$F2 1489
2 TraesCS6B01G374300 chr6D 429657687 429659589 1902 False 590.000000 924 86.584667 165 2277 3 chr6D.!!$F1 2112
3 TraesCS6B01G374300 chr6A 574817668 574819872 2204 False 646.666667 915 89.705333 8 2277 3 chr6A.!!$F1 2269

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
249 250 0.034896 GGGTCGTGAGTTGGATGTGT 59.965 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1675 0.041663 AAAACACACATTCGCGGTCG 60.042 50.0 6.13 0.0 0.0 4.79 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 1.746239 CATGCATGTGCCTCGGTCA 60.746 57.895 18.91 0.00 41.18 4.02
37 38 1.542492 GGTCAGTTCTGTCCTCCGTA 58.458 55.000 8.41 0.00 0.00 4.02
43 44 4.282449 TCAGTTCTGTCCTCCGTATTGAAA 59.718 41.667 0.00 0.00 0.00 2.69
58 59 5.163953 CGTATTGAAATGGTGTGTGTCTCTC 60.164 44.000 0.00 0.00 0.00 3.20
84 85 8.833231 TCTTTCTTTACTTCAGGTTGATACTG 57.167 34.615 0.00 0.00 37.30 2.74
132 133 9.385902 CATTGAATTGTGTAGTAACTTTGACAG 57.614 33.333 0.00 0.00 0.00 3.51
175 176 5.469760 TCACATGTCAACCTGTCTTATGTTG 59.530 40.000 0.00 0.00 40.48 3.33
184 185 2.884012 CTGTCTTATGTTGCCACAACCA 59.116 45.455 7.91 0.00 36.16 3.67
249 250 0.034896 GGGTCGTGAGTTGGATGTGT 59.965 55.000 0.00 0.00 0.00 3.72
257 258 1.474077 GAGTTGGATGTGTCATTGGCC 59.526 52.381 0.00 0.00 0.00 5.36
334 335 5.125739 AGTGGTTGAACGGTAAAAATGTCAA 59.874 36.000 0.00 0.00 0.00 3.18
352 353 8.810652 AATGTCAATAATGTTGTTTGGTGTAC 57.189 30.769 0.00 0.00 0.00 2.90
453 455 0.645355 AATTACGTGTCGCGAGCATG 59.355 50.000 10.24 18.01 44.77 4.06
457 459 3.857854 GTGTCGCGAGCATGGCAG 61.858 66.667 10.24 0.00 41.24 4.85
526 567 7.275888 ACTTGTGAAGATGCTGAAACATTTA 57.724 32.000 0.00 0.00 0.00 1.40
576 617 2.102588 AGATTTGTAGCGCGGTCCTAAT 59.897 45.455 16.92 12.69 0.00 1.73
739 866 2.630592 GATCCCAGGACCGCTCGTTC 62.631 65.000 0.00 0.00 0.00 3.95
743 870 1.084370 CCAGGACCGCTCGTTCATTC 61.084 60.000 0.00 0.00 0.00 2.67
755 882 4.452455 GCTCGTTCATTCTTCCTTGAGAAA 59.548 41.667 0.00 0.00 38.98 2.52
762 889 6.449698 TCATTCTTCCTTGAGAAAAACATGC 58.550 36.000 0.00 0.00 38.98 4.06
800 927 2.043992 TGGAAAGAAAGGGACTCGTGA 58.956 47.619 0.00 0.00 38.49 4.35
812 939 1.918609 GACTCGTGATTTGCGGACTAC 59.081 52.381 0.00 0.00 0.00 2.73
954 1082 0.099082 CTACAGTTCTCGCGTCTCCC 59.901 60.000 5.77 0.00 0.00 4.30
1263 1496 3.507009 GACCCCGACGAGTCCGAG 61.507 72.222 0.00 0.00 39.50 4.63
1306 1539 0.661552 CCACTGATACGATCGACCGT 59.338 55.000 24.34 10.96 45.54 4.83
1310 1543 1.206072 GATACGATCGACCGTCCGG 59.794 63.158 24.34 3.76 43.20 5.14
1311 1544 2.776954 GATACGATCGACCGTCCGGC 62.777 65.000 24.34 0.00 43.20 6.13
1383 1617 4.314740 TTTTTGAACACCGCTTAGCATT 57.685 36.364 4.70 0.00 0.00 3.56
1384 1618 5.440234 TTTTTGAACACCGCTTAGCATTA 57.560 34.783 4.70 0.00 0.00 1.90
1385 1619 4.413495 TTTGAACACCGCTTAGCATTAC 57.587 40.909 4.70 0.00 0.00 1.89
1386 1620 3.046968 TGAACACCGCTTAGCATTACA 57.953 42.857 4.70 0.00 0.00 2.41
1387 1621 3.605634 TGAACACCGCTTAGCATTACAT 58.394 40.909 4.70 0.00 0.00 2.29
1388 1622 4.006989 TGAACACCGCTTAGCATTACATT 58.993 39.130 4.70 0.00 0.00 2.71
1389 1623 4.457603 TGAACACCGCTTAGCATTACATTT 59.542 37.500 4.70 0.00 0.00 2.32
1390 1624 4.355543 ACACCGCTTAGCATTACATTTG 57.644 40.909 4.70 0.00 0.00 2.32
1391 1625 3.756434 ACACCGCTTAGCATTACATTTGT 59.244 39.130 4.70 0.00 0.00 2.83
1392 1626 4.217550 ACACCGCTTAGCATTACATTTGTT 59.782 37.500 4.70 0.00 0.00 2.83
1393 1627 5.413213 ACACCGCTTAGCATTACATTTGTTA 59.587 36.000 4.70 0.00 0.00 2.41
1394 1628 6.094881 ACACCGCTTAGCATTACATTTGTTAT 59.905 34.615 4.70 0.00 0.00 1.89
1433 1668 2.579207 TGGTGCGTCAAGTAGATAGC 57.421 50.000 0.00 0.00 34.61 2.97
1440 1675 2.110226 GTCAAGTAGATAGCGTGCGTC 58.890 52.381 0.00 0.00 0.00 5.19
1461 1696 1.263217 GACCGCGAATGTGTGTTTTCT 59.737 47.619 8.23 0.00 0.00 2.52
1462 1697 2.477375 GACCGCGAATGTGTGTTTTCTA 59.523 45.455 8.23 0.00 0.00 2.10
1463 1698 2.873472 ACCGCGAATGTGTGTTTTCTAA 59.127 40.909 8.23 0.00 0.00 2.10
1467 1702 5.732647 CCGCGAATGTGTGTTTTCTAATAAG 59.267 40.000 8.23 0.00 0.00 1.73
1469 1704 6.608610 GCGAATGTGTGTTTTCTAATAAGGT 58.391 36.000 0.00 0.00 0.00 3.50
1498 1994 6.933514 AAGGGATTTGAACATTTGGTATGT 57.066 33.333 0.00 0.00 0.00 2.29
1499 1995 6.284891 AGGGATTTGAACATTTGGTATGTG 57.715 37.500 0.00 0.00 31.80 3.21
1500 1996 5.779771 AGGGATTTGAACATTTGGTATGTGT 59.220 36.000 0.00 0.00 31.80 3.72
1501 1997 5.868801 GGGATTTGAACATTTGGTATGTGTG 59.131 40.000 0.00 0.00 31.80 3.82
1502 1998 6.295011 GGGATTTGAACATTTGGTATGTGTGA 60.295 38.462 0.00 0.00 31.80 3.58
1503 1999 7.322664 GGATTTGAACATTTGGTATGTGTGAT 58.677 34.615 0.00 0.00 31.80 3.06
1504 2000 7.489113 GGATTTGAACATTTGGTATGTGTGATC 59.511 37.037 0.00 0.00 31.80 2.92
1505 2001 7.523293 TTTGAACATTTGGTATGTGTGATCT 57.477 32.000 0.00 0.00 31.80 2.75
1506 2002 7.523293 TTGAACATTTGGTATGTGTGATCTT 57.477 32.000 0.00 0.00 31.80 2.40
1507 2003 8.628630 TTGAACATTTGGTATGTGTGATCTTA 57.371 30.769 0.00 0.00 31.80 2.10
1508 2004 8.039603 TGAACATTTGGTATGTGTGATCTTAC 57.960 34.615 0.00 0.00 31.80 2.34
1520 2016 6.025707 GTGTGATCTTACACGATTGATGAC 57.974 41.667 0.99 0.00 41.21 3.06
1523 2019 5.233050 GTGATCTTACACGATTGATGACCTG 59.767 44.000 0.00 0.00 0.00 4.00
1540 2036 2.769663 ACCTGGATTAATCTGCGGTACA 59.230 45.455 14.95 2.31 0.00 2.90
1560 2072 6.252655 GGTACACCGTTTTTGATTCAATATGC 59.747 38.462 0.00 0.00 0.00 3.14
1561 2073 6.024552 ACACCGTTTTTGATTCAATATGCT 57.975 33.333 0.00 0.00 0.00 3.79
1566 2078 9.950680 ACCGTTTTTGATTCAATATGCTAATAG 57.049 29.630 0.00 0.00 0.00 1.73
1583 2095 8.441311 TGCTAATAGGATCAATGATTAGGACT 57.559 34.615 0.00 0.00 34.05 3.85
1584 2096 8.884323 TGCTAATAGGATCAATGATTAGGACTT 58.116 33.333 0.00 0.00 34.05 3.01
1590 2102 8.503428 AGGATCAATGATTAGGACTTAGATGT 57.497 34.615 0.00 0.00 0.00 3.06
1591 2103 8.373981 AGGATCAATGATTAGGACTTAGATGTG 58.626 37.037 0.00 0.00 0.00 3.21
1592 2104 7.118971 GGATCAATGATTAGGACTTAGATGTGC 59.881 40.741 0.00 0.00 0.00 4.57
1593 2105 6.888105 TCAATGATTAGGACTTAGATGTGCA 58.112 36.000 0.00 0.00 0.00 4.57
1594 2106 7.337938 TCAATGATTAGGACTTAGATGTGCAA 58.662 34.615 0.00 0.00 0.00 4.08
1595 2107 7.994911 TCAATGATTAGGACTTAGATGTGCAAT 59.005 33.333 0.00 0.00 0.00 3.56
1596 2108 9.276590 CAATGATTAGGACTTAGATGTGCAATA 57.723 33.333 0.00 0.00 0.00 1.90
1597 2109 8.839310 ATGATTAGGACTTAGATGTGCAATAC 57.161 34.615 0.00 0.00 0.00 1.89
1598 2110 8.023021 TGATTAGGACTTAGATGTGCAATACT 57.977 34.615 0.00 0.00 0.00 2.12
1599 2111 8.486210 TGATTAGGACTTAGATGTGCAATACTT 58.514 33.333 0.00 0.00 0.00 2.24
1600 2112 9.982651 GATTAGGACTTAGATGTGCAATACTTA 57.017 33.333 0.00 0.00 0.00 2.24
1602 2114 9.764363 TTAGGACTTAGATGTGCAATACTTATG 57.236 33.333 0.00 0.00 0.00 1.90
1603 2115 7.220030 AGGACTTAGATGTGCAATACTTATGG 58.780 38.462 0.00 0.00 0.00 2.74
1604 2116 6.073003 GGACTTAGATGTGCAATACTTATGGC 60.073 42.308 0.00 0.00 33.16 4.40
1605 2117 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
1640 2152 5.768317 GCTTTAGCAATTGTTTAGGACACA 58.232 37.500 7.40 0.00 38.39 3.72
1641 2153 6.389906 GCTTTAGCAATTGTTTAGGACACAT 58.610 36.000 7.40 0.00 38.39 3.21
1642 2154 6.528072 GCTTTAGCAATTGTTTAGGACACATC 59.472 38.462 7.40 0.00 38.39 3.06
1643 2155 7.575720 GCTTTAGCAATTGTTTAGGACACATCT 60.576 37.037 7.40 0.00 38.39 2.90
1644 2156 8.856153 TTTAGCAATTGTTTAGGACACATCTA 57.144 30.769 7.40 0.00 38.18 1.98
1645 2157 6.992063 AGCAATTGTTTAGGACACATCTAG 57.008 37.500 7.40 0.00 38.18 2.43
1646 2158 6.711277 AGCAATTGTTTAGGACACATCTAGA 58.289 36.000 7.40 0.00 38.18 2.43
1647 2159 7.341805 AGCAATTGTTTAGGACACATCTAGAT 58.658 34.615 7.40 0.00 38.18 1.98
1648 2160 7.281774 AGCAATTGTTTAGGACACATCTAGATG 59.718 37.037 27.63 27.63 44.15 2.90
1672 2184 5.223225 GCTTTAGCAATTGTCTAGGACAC 57.777 43.478 7.40 0.00 40.67 3.67
1673 2185 4.695455 GCTTTAGCAATTGTCTAGGACACA 59.305 41.667 7.40 0.00 40.67 3.72
1674 2186 5.355350 GCTTTAGCAATTGTCTAGGACACAT 59.645 40.000 7.40 0.00 40.67 3.21
1675 2187 6.457528 GCTTTAGCAATTGTCTAGGACACATC 60.458 42.308 7.40 0.00 40.67 3.06
1676 2188 4.833478 AGCAATTGTCTAGGACACATCT 57.167 40.909 7.40 0.00 42.60 2.90
1677 2189 5.939764 AGCAATTGTCTAGGACACATCTA 57.060 39.130 7.40 0.00 42.60 1.98
1678 2190 5.911752 AGCAATTGTCTAGGACACATCTAG 58.088 41.667 7.40 0.00 42.60 2.43
1679 2191 5.658634 AGCAATTGTCTAGGACACATCTAGA 59.341 40.000 7.40 0.00 42.60 2.43
1680 2192 6.326064 AGCAATTGTCTAGGACACATCTAGAT 59.674 38.462 7.40 0.00 42.60 1.98
1681 2193 6.423302 GCAATTGTCTAGGACACATCTAGATG 59.577 42.308 27.63 27.63 42.60 2.90
1696 2208 7.126726 CATCTAGATGTGCCTTAGTTATTGC 57.873 40.000 22.42 0.00 34.23 3.56
1697 2209 6.233905 TCTAGATGTGCCTTAGTTATTGCA 57.766 37.500 0.00 0.00 0.00 4.08
1705 2217 6.925610 TGCCTTAGTTATTGCACATCTAAG 57.074 37.500 14.73 14.73 38.01 2.18
1706 2218 6.414732 TGCCTTAGTTATTGCACATCTAAGT 58.585 36.000 17.73 7.66 37.15 2.24
1707 2219 6.316140 TGCCTTAGTTATTGCACATCTAAGTG 59.684 38.462 17.73 13.14 42.37 3.16
1708 2220 6.538742 GCCTTAGTTATTGCACATCTAAGTGA 59.461 38.462 17.73 3.36 42.05 3.41
1709 2221 7.466050 GCCTTAGTTATTGCACATCTAAGTGAC 60.466 40.741 17.73 9.25 42.05 3.67
1710 2222 7.549134 CCTTAGTTATTGCACATCTAAGTGACA 59.451 37.037 17.73 0.00 42.05 3.58
1711 2223 6.727824 AGTTATTGCACATCTAAGTGACAC 57.272 37.500 0.00 0.00 42.05 3.67
1712 2224 6.230472 AGTTATTGCACATCTAAGTGACACA 58.770 36.000 8.59 0.00 42.05 3.72
1713 2225 6.710295 AGTTATTGCACATCTAAGTGACACAA 59.290 34.615 8.59 0.00 42.05 3.33
1714 2226 5.618056 ATTGCACATCTAAGTGACACAAG 57.382 39.130 8.59 5.04 42.05 3.16
1715 2227 2.807967 TGCACATCTAAGTGACACAAGC 59.192 45.455 8.59 0.70 42.05 4.01
1716 2228 2.807967 GCACATCTAAGTGACACAAGCA 59.192 45.455 8.59 0.00 42.05 3.91
1717 2229 3.250762 GCACATCTAAGTGACACAAGCAA 59.749 43.478 8.59 0.00 42.05 3.91
1718 2230 4.612259 GCACATCTAAGTGACACAAGCAAG 60.612 45.833 8.59 0.00 42.05 4.01
1719 2231 3.499918 ACATCTAAGTGACACAAGCAAGC 59.500 43.478 8.59 0.00 0.00 4.01
1720 2232 3.192541 TCTAAGTGACACAAGCAAGCA 57.807 42.857 8.59 0.00 0.00 3.91
1721 2233 3.743521 TCTAAGTGACACAAGCAAGCAT 58.256 40.909 8.59 0.00 0.00 3.79
1722 2234 4.893608 TCTAAGTGACACAAGCAAGCATA 58.106 39.130 8.59 0.00 0.00 3.14
1723 2235 4.931601 TCTAAGTGACACAAGCAAGCATAG 59.068 41.667 8.59 0.00 0.00 2.23
1724 2236 3.407424 AGTGACACAAGCAAGCATAGA 57.593 42.857 8.59 0.00 0.00 1.98
1725 2237 3.743521 AGTGACACAAGCAAGCATAGAA 58.256 40.909 8.59 0.00 0.00 2.10
1726 2238 4.136796 AGTGACACAAGCAAGCATAGAAA 58.863 39.130 8.59 0.00 0.00 2.52
1727 2239 4.214971 AGTGACACAAGCAAGCATAGAAAG 59.785 41.667 8.59 0.00 0.00 2.62
1728 2240 3.503363 TGACACAAGCAAGCATAGAAAGG 59.497 43.478 0.00 0.00 0.00 3.11
1729 2241 3.753272 GACACAAGCAAGCATAGAAAGGA 59.247 43.478 0.00 0.00 0.00 3.36
1730 2242 4.144297 ACACAAGCAAGCATAGAAAGGAA 58.856 39.130 0.00 0.00 0.00 3.36
1731 2243 4.584325 ACACAAGCAAGCATAGAAAGGAAA 59.416 37.500 0.00 0.00 0.00 3.13
1732 2244 5.068987 ACACAAGCAAGCATAGAAAGGAAAA 59.931 36.000 0.00 0.00 0.00 2.29
1733 2245 5.632347 CACAAGCAAGCATAGAAAGGAAAAG 59.368 40.000 0.00 0.00 0.00 2.27
1734 2246 5.166398 CAAGCAAGCATAGAAAGGAAAAGG 58.834 41.667 0.00 0.00 0.00 3.11
1735 2247 4.666512 AGCAAGCATAGAAAGGAAAAGGA 58.333 39.130 0.00 0.00 0.00 3.36
1736 2248 5.079643 AGCAAGCATAGAAAGGAAAAGGAA 58.920 37.500 0.00 0.00 0.00 3.36
1737 2249 5.539955 AGCAAGCATAGAAAGGAAAAGGAAA 59.460 36.000 0.00 0.00 0.00 3.13
1738 2250 6.041979 AGCAAGCATAGAAAGGAAAAGGAAAA 59.958 34.615 0.00 0.00 0.00 2.29
1739 2251 6.705825 GCAAGCATAGAAAGGAAAAGGAAAAA 59.294 34.615 0.00 0.00 0.00 1.94
1797 2309 9.314133 TGATATAGGACTTAGATGTGCAATACT 57.686 33.333 0.00 0.00 0.00 2.12
1801 2313 9.935241 ATAGGACTTAGATGTGCAATACTTATG 57.065 33.333 0.00 0.00 0.00 1.90
1802 2314 6.708054 AGGACTTAGATGTGCAATACTTATGC 59.292 38.462 0.00 0.00 44.08 3.14
1803 2315 6.073003 GGACTTAGATGTGCAATACTTATGCC 60.073 42.308 0.00 0.00 43.16 4.40
1804 2316 6.356556 ACTTAGATGTGCAATACTTATGCCA 58.643 36.000 0.00 0.00 43.16 4.92
1805 2317 6.260936 ACTTAGATGTGCAATACTTATGCCAC 59.739 38.462 0.00 0.00 43.16 5.01
1806 2318 4.525996 AGATGTGCAATACTTATGCCACA 58.474 39.130 0.00 0.00 43.16 4.17
1807 2319 5.135383 AGATGTGCAATACTTATGCCACAT 58.865 37.500 12.79 12.79 42.56 3.21
1808 2320 4.898829 TGTGCAATACTTATGCCACATC 57.101 40.909 0.00 0.00 43.16 3.06
1809 2321 4.525996 TGTGCAATACTTATGCCACATCT 58.474 39.130 0.00 0.00 43.16 2.90
1810 2322 5.679601 TGTGCAATACTTATGCCACATCTA 58.320 37.500 0.00 0.00 43.16 1.98
1811 2323 5.759763 TGTGCAATACTTATGCCACATCTAG 59.240 40.000 0.00 0.00 43.16 2.43
1812 2324 4.756642 TGCAATACTTATGCCACATCTAGC 59.243 41.667 0.00 0.00 43.16 3.42
1813 2325 4.999950 GCAATACTTATGCCACATCTAGCT 59.000 41.667 0.00 0.00 37.85 3.32
1814 2326 5.106791 GCAATACTTATGCCACATCTAGCTG 60.107 44.000 0.00 0.00 37.85 4.24
1815 2327 5.815233 ATACTTATGCCACATCTAGCTGT 57.185 39.130 0.00 0.00 0.00 4.40
1816 2328 3.801698 ACTTATGCCACATCTAGCTGTG 58.198 45.455 17.88 17.88 44.92 3.66
1817 2329 2.245159 TATGCCACATCTAGCTGTGC 57.755 50.000 19.12 14.94 44.16 4.57
1818 2330 0.545171 ATGCCACATCTAGCTGTGCT 59.455 50.000 19.12 5.30 44.16 4.40
1819 2331 0.325933 TGCCACATCTAGCTGTGCTT 59.674 50.000 19.12 0.00 44.16 3.91
1820 2332 1.271543 TGCCACATCTAGCTGTGCTTT 60.272 47.619 19.12 0.00 44.16 3.51
1821 2333 2.027285 TGCCACATCTAGCTGTGCTTTA 60.027 45.455 19.12 4.32 44.16 1.85
1822 2334 2.611292 GCCACATCTAGCTGTGCTTTAG 59.389 50.000 19.12 8.06 44.16 1.85
1823 2335 2.611292 CCACATCTAGCTGTGCTTTAGC 59.389 50.000 19.12 0.00 44.16 3.09
1944 2516 6.155737 ACCGACCTTGTATAAGTAAATGGAGT 59.844 38.462 0.00 0.00 31.80 3.85
2062 2636 1.961277 CGTGGTCTCACACAAGGCC 60.961 63.158 0.00 0.00 43.79 5.19
2064 2638 4.898607 GGTCTCACACAAGGCCAA 57.101 55.556 5.01 0.00 40.94 4.52
2103 2677 2.877097 TTCCTTTAGTGGCTGATGCA 57.123 45.000 0.00 0.00 41.91 3.96
2123 2697 5.862811 TGCACTTTTGTTGTTGTTAAATGC 58.137 33.333 0.00 0.00 0.00 3.56
2134 2708 6.785488 TGTTGTTAAATGCTGTCTCTAGTG 57.215 37.500 0.00 0.00 0.00 2.74
2219 2793 5.101628 TGCAAATGAAAGTGTGTTGTTCTC 58.898 37.500 0.00 0.00 0.00 2.87
2231 2805 7.707104 AGTGTGTTGTTCTCTAAGGAAAATTG 58.293 34.615 0.00 0.00 0.00 2.32
2234 2808 7.122055 TGTGTTGTTCTCTAAGGAAAATTGTGT 59.878 33.333 0.00 0.00 0.00 3.72
2239 2813 6.899393 TCTCTAAGGAAAATTGTGTGCAAT 57.101 33.333 0.00 0.00 46.38 3.56
2277 2851 8.404000 CAAATGATTTTGGACCTCTATGAAGAG 58.596 37.037 0.00 0.00 42.09 2.85
2278 2852 6.627087 TGATTTTGGACCTCTATGAAGAGT 57.373 37.500 2.02 0.00 46.80 3.24
2279 2853 6.644347 TGATTTTGGACCTCTATGAAGAGTC 58.356 40.000 2.02 0.00 46.80 3.36
2280 2854 5.422214 TTTTGGACCTCTATGAAGAGTCC 57.578 43.478 12.96 12.96 46.80 3.85
2281 2855 3.757947 TGGACCTCTATGAAGAGTCCA 57.242 47.619 16.19 16.19 46.80 4.02
2282 2856 4.271807 TGGACCTCTATGAAGAGTCCAT 57.728 45.455 16.19 0.00 46.80 3.41
2283 2857 4.219115 TGGACCTCTATGAAGAGTCCATC 58.781 47.826 16.19 4.67 46.80 3.51
2284 2858 4.078922 TGGACCTCTATGAAGAGTCCATCT 60.079 45.833 16.19 0.00 46.80 2.90
2285 2859 5.134509 TGGACCTCTATGAAGAGTCCATCTA 59.865 44.000 16.19 1.46 46.80 1.98
2286 2860 6.071984 GGACCTCTATGAAGAGTCCATCTAA 58.928 44.000 14.11 0.00 46.80 2.10
2287 2861 6.208599 GGACCTCTATGAAGAGTCCATCTAAG 59.791 46.154 14.11 0.00 46.80 2.18
2288 2862 6.678547 ACCTCTATGAAGAGTCCATCTAAGT 58.321 40.000 2.02 0.00 46.80 2.24
2289 2863 6.549364 ACCTCTATGAAGAGTCCATCTAAGTG 59.451 42.308 2.02 0.00 46.80 3.16
2290 2864 6.549364 CCTCTATGAAGAGTCCATCTAAGTGT 59.451 42.308 2.02 0.00 46.80 3.55
2291 2865 7.255451 CCTCTATGAAGAGTCCATCTAAGTGTC 60.255 44.444 2.02 0.00 46.80 3.67
2292 2866 4.703645 TGAAGAGTCCATCTAAGTGTCG 57.296 45.455 0.00 0.00 37.23 4.35
2293 2867 4.332828 TGAAGAGTCCATCTAAGTGTCGA 58.667 43.478 0.00 0.00 37.23 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.096967 CCGAGGCACATGCATGCTTA 61.097 55.000 26.53 0.00 45.38 3.09
1 2 2.412323 CCGAGGCACATGCATGCTT 61.412 57.895 26.53 11.92 45.38 3.91
2 3 2.827190 CCGAGGCACATGCATGCT 60.827 61.111 26.53 15.41 45.38 3.79
3 4 3.117175 GACCGAGGCACATGCATGC 62.117 63.158 26.53 15.36 45.34 4.06
4 5 1.712018 CTGACCGAGGCACATGCATG 61.712 60.000 25.09 25.09 44.36 4.06
5 6 1.450848 CTGACCGAGGCACATGCAT 60.451 57.895 6.15 0.00 44.36 3.96
6 7 2.046988 CTGACCGAGGCACATGCA 60.047 61.111 6.15 0.00 44.36 3.96
22 23 4.884668 TTTCAATACGGAGGACAGAACT 57.115 40.909 0.00 0.00 0.00 3.01
37 38 4.978099 AGAGAGACACACACCATTTCAAT 58.022 39.130 0.00 0.00 0.00 2.57
43 44 3.900601 AGAAAGAGAGAGACACACACCAT 59.099 43.478 0.00 0.00 0.00 3.55
58 59 8.930760 CAGTATCAACCTGAAGTAAAGAAAGAG 58.069 37.037 0.00 0.00 31.38 2.85
92 93 9.260002 ACACAATTCAATGATAAACAAAGGAAC 57.740 29.630 0.00 0.00 0.00 3.62
113 114 6.278363 GGAGACTGTCAAAGTTACTACACAA 58.722 40.000 10.88 0.00 40.07 3.33
175 176 1.810151 ACGTAATCATGTGGTTGTGGC 59.190 47.619 0.00 0.00 0.00 5.01
184 185 7.302350 TCGAATTTCAATCACGTAATCATGT 57.698 32.000 0.00 0.00 0.00 3.21
257 258 4.395519 TCCAAGCCGGACATTGTG 57.604 55.556 5.05 1.45 39.64 3.33
278 279 1.134560 ACCTCGTTATCGTTGCCTCTC 59.865 52.381 0.00 0.00 38.33 3.20
334 335 6.945435 TCCTCATGTACACCAAACAACATTAT 59.055 34.615 0.00 0.00 30.32 1.28
352 353 7.854557 TTTCTGTATCTTTGTGATCCTCATG 57.145 36.000 0.00 0.00 36.65 3.07
427 429 1.810197 GCGACACGTAATTTGCCATC 58.190 50.000 0.00 0.00 0.00 3.51
453 455 0.038801 GCTTGCTGAAGGAAACTGCC 60.039 55.000 0.00 0.00 42.68 4.85
455 457 2.352421 CCATGCTTGCTGAAGGAAACTG 60.352 50.000 0.00 0.00 42.68 3.16
457 459 1.670967 GCCATGCTTGCTGAAGGAAAC 60.671 52.381 0.00 0.00 32.62 2.78
495 497 6.942532 TCAGCATCTTCACAAGTTAAGTTT 57.057 33.333 0.00 0.00 0.00 2.66
496 498 6.942532 TTCAGCATCTTCACAAGTTAAGTT 57.057 33.333 0.00 0.00 0.00 2.66
497 499 6.318648 TGTTTCAGCATCTTCACAAGTTAAGT 59.681 34.615 0.00 0.00 0.00 2.24
526 567 7.033185 GTCCGATTTTTAACACATGGCTAATT 58.967 34.615 0.00 0.00 0.00 1.40
548 589 1.258982 CGCGCTACAAATCTGATGTCC 59.741 52.381 5.56 0.00 32.27 4.02
603 644 8.863872 ATGGGGTATAGTTATTCAATTAGTGC 57.136 34.615 0.00 0.00 0.00 4.40
623 664 2.483288 GCGTGCGTTGTAATGGGG 59.517 61.111 0.00 0.00 0.00 4.96
725 852 0.108615 AGAATGAACGAGCGGTCCTG 60.109 55.000 9.39 0.00 0.00 3.86
739 866 5.344128 CGCATGTTTTTCTCAAGGAAGAATG 59.656 40.000 0.00 0.00 35.30 2.67
743 870 3.976942 CACGCATGTTTTTCTCAAGGAAG 59.023 43.478 0.00 0.00 35.16 3.46
755 882 0.179032 TCTGGTGGTCACGCATGTTT 60.179 50.000 0.00 0.00 0.00 2.83
762 889 1.806542 CCATTTCTTCTGGTGGTCACG 59.193 52.381 0.00 0.00 0.00 4.35
843 970 1.246056 TTGCATGGTGGAGCTTCAGC 61.246 55.000 17.64 17.64 42.49 4.26
846 973 0.743097 GGATTGCATGGTGGAGCTTC 59.257 55.000 0.00 0.00 0.00 3.86
898 1025 4.508124 CGATCAAGAGGAAGGTTAAATCGG 59.492 45.833 0.00 0.00 32.19 4.18
1362 1596 4.314740 AATGCTAAGCGGTGTTCAAAAA 57.685 36.364 0.00 0.00 0.00 1.94
1363 1597 4.276183 TGTAATGCTAAGCGGTGTTCAAAA 59.724 37.500 0.00 0.00 0.00 2.44
1364 1598 3.815962 TGTAATGCTAAGCGGTGTTCAAA 59.184 39.130 0.00 0.00 0.00 2.69
1365 1599 3.403968 TGTAATGCTAAGCGGTGTTCAA 58.596 40.909 0.00 0.00 0.00 2.69
1366 1600 3.046968 TGTAATGCTAAGCGGTGTTCA 57.953 42.857 0.00 0.00 0.00 3.18
1367 1601 4.616181 AATGTAATGCTAAGCGGTGTTC 57.384 40.909 0.00 0.00 0.00 3.18
1368 1602 4.217550 ACAAATGTAATGCTAAGCGGTGTT 59.782 37.500 0.00 0.00 0.00 3.32
1369 1603 3.756434 ACAAATGTAATGCTAAGCGGTGT 59.244 39.130 0.00 0.00 0.00 4.16
1370 1604 4.355543 ACAAATGTAATGCTAAGCGGTG 57.644 40.909 0.00 0.00 0.00 4.94
1371 1605 6.693315 ATAACAAATGTAATGCTAAGCGGT 57.307 33.333 0.00 0.00 0.00 5.68
1372 1606 7.985634 AAATAACAAATGTAATGCTAAGCGG 57.014 32.000 0.00 0.00 0.00 5.52
1407 1641 3.745975 TCTACTTGACGCACCAAAAGATG 59.254 43.478 0.00 0.00 0.00 2.90
1410 1644 4.201724 GCTATCTACTTGACGCACCAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
1415 1649 1.202268 ACGCTATCTACTTGACGCACC 60.202 52.381 0.00 0.00 0.00 5.01
1417 1651 1.797713 GCACGCTATCTACTTGACGCA 60.798 52.381 0.00 0.00 0.00 5.24
1418 1652 0.847035 GCACGCTATCTACTTGACGC 59.153 55.000 0.00 0.00 0.00 5.19
1419 1653 1.113253 CGCACGCTATCTACTTGACG 58.887 55.000 0.00 0.00 0.00 4.35
1420 1654 2.110226 GACGCACGCTATCTACTTGAC 58.890 52.381 0.00 0.00 0.00 3.18
1421 1655 1.267882 CGACGCACGCTATCTACTTGA 60.268 52.381 0.00 0.00 34.51 3.02
1422 1656 1.113253 CGACGCACGCTATCTACTTG 58.887 55.000 0.00 0.00 34.51 3.16
1440 1675 0.041663 AAAACACACATTCGCGGTCG 60.042 50.000 6.13 0.00 0.00 4.79
1467 1702 9.161629 CCAAATGTTCAAATCCCTTAATAAACC 57.838 33.333 0.00 0.00 0.00 3.27
1474 1970 7.453126 ACACATACCAAATGTTCAAATCCCTTA 59.547 33.333 0.00 0.00 0.00 2.69
1485 1981 7.816640 GTGTAAGATCACACATACCAAATGTT 58.183 34.615 10.59 0.00 46.55 2.71
1497 1993 5.005779 GGTCATCAATCGTGTAAGATCACAC 59.994 44.000 6.30 6.30 44.37 3.82
1498 1994 5.105351 AGGTCATCAATCGTGTAAGATCACA 60.105 40.000 0.00 0.00 38.12 3.58
1499 1995 5.233050 CAGGTCATCAATCGTGTAAGATCAC 59.767 44.000 0.00 0.00 35.28 3.06
1500 1996 5.351458 CAGGTCATCAATCGTGTAAGATCA 58.649 41.667 0.00 0.00 0.00 2.92
1501 1997 4.747108 CCAGGTCATCAATCGTGTAAGATC 59.253 45.833 0.00 0.00 0.00 2.75
1502 1998 4.405680 TCCAGGTCATCAATCGTGTAAGAT 59.594 41.667 0.00 0.00 0.00 2.40
1503 1999 3.767131 TCCAGGTCATCAATCGTGTAAGA 59.233 43.478 0.00 0.00 0.00 2.10
1504 2000 4.123497 TCCAGGTCATCAATCGTGTAAG 57.877 45.455 0.00 0.00 0.00 2.34
1505 2001 4.753516 ATCCAGGTCATCAATCGTGTAA 57.246 40.909 0.00 0.00 0.00 2.41
1506 2002 4.753516 AATCCAGGTCATCAATCGTGTA 57.246 40.909 0.00 0.00 0.00 2.90
1507 2003 3.634397 AATCCAGGTCATCAATCGTGT 57.366 42.857 0.00 0.00 0.00 4.49
1508 2004 5.994054 AGATTAATCCAGGTCATCAATCGTG 59.006 40.000 11.92 0.00 0.00 4.35
1510 2006 5.106791 GCAGATTAATCCAGGTCATCAATCG 60.107 44.000 11.92 0.00 0.00 3.34
1511 2007 5.106791 CGCAGATTAATCCAGGTCATCAATC 60.107 44.000 11.92 0.00 0.00 2.67
1512 2008 4.758674 CGCAGATTAATCCAGGTCATCAAT 59.241 41.667 11.92 0.00 0.00 2.57
1513 2009 4.129380 CGCAGATTAATCCAGGTCATCAA 58.871 43.478 11.92 0.00 0.00 2.57
1514 2010 3.494924 CCGCAGATTAATCCAGGTCATCA 60.495 47.826 11.92 0.00 0.00 3.07
1515 2011 3.070018 CCGCAGATTAATCCAGGTCATC 58.930 50.000 11.92 0.00 0.00 2.92
1516 2012 2.439507 ACCGCAGATTAATCCAGGTCAT 59.560 45.455 16.70 1.25 0.00 3.06
1517 2013 1.837439 ACCGCAGATTAATCCAGGTCA 59.163 47.619 16.70 0.00 0.00 4.02
1518 2014 2.622064 ACCGCAGATTAATCCAGGTC 57.378 50.000 16.70 2.19 0.00 3.85
1519 2015 2.769663 TGTACCGCAGATTAATCCAGGT 59.230 45.455 22.47 22.47 34.36 4.00
1520 2016 3.131396 GTGTACCGCAGATTAATCCAGG 58.869 50.000 11.92 14.19 0.00 4.45
1540 2036 9.950680 CTATTAGCATATTGAATCAAAAACGGT 57.049 29.630 0.00 0.00 0.00 4.83
1566 2078 7.118971 GCACATCTAAGTCCTAATCATTGATCC 59.881 40.741 0.00 0.00 0.00 3.36
1570 2082 7.558161 TTGCACATCTAAGTCCTAATCATTG 57.442 36.000 0.00 0.00 0.00 2.82
1571 2083 9.277783 GTATTGCACATCTAAGTCCTAATCATT 57.722 33.333 0.00 0.00 0.00 2.57
1572 2084 8.654997 AGTATTGCACATCTAAGTCCTAATCAT 58.345 33.333 0.00 0.00 0.00 2.45
1573 2085 8.023021 AGTATTGCACATCTAAGTCCTAATCA 57.977 34.615 0.00 0.00 0.00 2.57
1574 2086 8.894768 AAGTATTGCACATCTAAGTCCTAATC 57.105 34.615 0.00 0.00 0.00 1.75
1576 2088 9.764363 CATAAGTATTGCACATCTAAGTCCTAA 57.236 33.333 0.00 0.00 0.00 2.69
1577 2089 8.367911 CCATAAGTATTGCACATCTAAGTCCTA 58.632 37.037 0.00 0.00 0.00 2.94
1578 2090 7.220030 CCATAAGTATTGCACATCTAAGTCCT 58.780 38.462 0.00 0.00 0.00 3.85
1579 2091 6.073003 GCCATAAGTATTGCACATCTAAGTCC 60.073 42.308 0.00 0.00 0.00 3.85
1580 2092 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
1581 2093 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
1582 2094 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
1590 2102 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
1591 2103 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
1612 2124 7.787795 TGTCCTAAACAATTGCTAAAGCACATC 60.788 37.037 5.05 0.00 42.56 3.06
1613 2125 6.015519 TGTCCTAAACAATTGCTAAAGCACAT 60.016 34.615 5.05 0.00 42.56 3.21
1614 2126 5.300539 TGTCCTAAACAATTGCTAAAGCACA 59.699 36.000 5.05 0.00 42.56 4.57
1615 2127 5.629435 GTGTCCTAAACAATTGCTAAAGCAC 59.371 40.000 5.05 3.86 45.26 4.40
1616 2128 5.300539 TGTGTCCTAAACAATTGCTAAAGCA 59.699 36.000 5.05 0.00 44.45 3.91
1617 2129 5.768317 TGTGTCCTAAACAATTGCTAAAGC 58.232 37.500 5.05 0.00 40.31 3.51
1618 2130 7.820648 AGATGTGTCCTAAACAATTGCTAAAG 58.179 34.615 5.05 0.00 40.31 1.85
1619 2131 7.759489 AGATGTGTCCTAAACAATTGCTAAA 57.241 32.000 5.05 0.00 40.31 1.85
1620 2132 8.318412 TCTAGATGTGTCCTAAACAATTGCTAA 58.682 33.333 5.05 0.00 40.31 3.09
1621 2133 7.847096 TCTAGATGTGTCCTAAACAATTGCTA 58.153 34.615 5.05 0.00 40.31 3.49
1622 2134 6.711277 TCTAGATGTGTCCTAAACAATTGCT 58.289 36.000 5.05 0.00 40.31 3.91
1623 2135 6.985188 TCTAGATGTGTCCTAAACAATTGC 57.015 37.500 5.05 0.00 40.31 3.56
1644 2156 8.540076 GTCCTAGACAATTGCTAAAGCACATCT 61.540 40.741 5.05 7.71 40.67 2.90
1645 2157 6.457528 GTCCTAGACAATTGCTAAAGCACATC 60.458 42.308 5.05 0.53 40.67 3.06
1646 2158 5.355350 GTCCTAGACAATTGCTAAAGCACAT 59.645 40.000 5.05 0.00 40.67 3.21
1647 2159 4.695455 GTCCTAGACAATTGCTAAAGCACA 59.305 41.667 5.05 0.00 40.67 4.57
1648 2160 4.695455 TGTCCTAGACAATTGCTAAAGCAC 59.305 41.667 5.05 0.00 44.54 4.40
1649 2161 4.695455 GTGTCCTAGACAATTGCTAAAGCA 59.305 41.667 5.05 0.00 46.20 3.91
1650 2162 4.695455 TGTGTCCTAGACAATTGCTAAAGC 59.305 41.667 5.05 0.00 44.49 3.51
1651 2163 6.820656 AGATGTGTCCTAGACAATTGCTAAAG 59.179 38.462 5.05 3.49 44.49 1.85
1652 2164 6.711277 AGATGTGTCCTAGACAATTGCTAAA 58.289 36.000 5.05 0.00 44.49 1.85
1653 2165 6.299805 AGATGTGTCCTAGACAATTGCTAA 57.700 37.500 5.05 0.00 44.49 3.09
1654 2166 5.939764 AGATGTGTCCTAGACAATTGCTA 57.060 39.130 5.05 7.32 44.49 3.49
1655 2167 4.833478 AGATGTGTCCTAGACAATTGCT 57.167 40.909 5.05 6.49 44.49 3.91
1656 2168 5.907207 TCTAGATGTGTCCTAGACAATTGC 58.093 41.667 5.05 0.00 44.49 3.56
1657 2169 7.943413 CATCTAGATGTGTCCTAGACAATTG 57.057 40.000 22.42 3.24 44.49 2.32
1672 2184 6.707608 TGCAATAACTAAGGCACATCTAGATG 59.292 38.462 27.63 27.63 44.15 2.90
1673 2185 6.830912 TGCAATAACTAAGGCACATCTAGAT 58.169 36.000 0.00 0.00 0.00 1.98
1674 2186 6.233905 TGCAATAACTAAGGCACATCTAGA 57.766 37.500 0.00 0.00 0.00 2.43
1682 2194 6.316140 CACTTAGATGTGCAATAACTAAGGCA 59.684 38.462 22.21 2.55 42.10 4.75
1683 2195 6.538742 TCACTTAGATGTGCAATAACTAAGGC 59.461 38.462 22.21 0.00 42.10 4.35
1684 2196 7.549134 TGTCACTTAGATGTGCAATAACTAAGG 59.451 37.037 22.21 15.42 42.10 2.69
1685 2197 8.383619 GTGTCACTTAGATGTGCAATAACTAAG 58.616 37.037 19.21 19.21 42.89 2.18
1686 2198 7.875554 TGTGTCACTTAGATGTGCAATAACTAA 59.124 33.333 4.27 0.00 37.81 2.24
1687 2199 7.382898 TGTGTCACTTAGATGTGCAATAACTA 58.617 34.615 4.27 0.00 37.81 2.24
1688 2200 6.230472 TGTGTCACTTAGATGTGCAATAACT 58.770 36.000 4.27 0.00 37.81 2.24
1689 2201 6.480524 TGTGTCACTTAGATGTGCAATAAC 57.519 37.500 4.27 0.00 37.81 1.89
1690 2202 6.348458 GCTTGTGTCACTTAGATGTGCAATAA 60.348 38.462 4.27 0.00 37.81 1.40
1691 2203 5.122239 GCTTGTGTCACTTAGATGTGCAATA 59.878 40.000 4.27 0.00 37.81 1.90
1692 2204 4.083110 GCTTGTGTCACTTAGATGTGCAAT 60.083 41.667 4.27 0.00 37.81 3.56
1693 2205 3.250762 GCTTGTGTCACTTAGATGTGCAA 59.749 43.478 4.27 0.00 37.81 4.08
1694 2206 2.807967 GCTTGTGTCACTTAGATGTGCA 59.192 45.455 4.27 0.00 37.81 4.57
1695 2207 2.807967 TGCTTGTGTCACTTAGATGTGC 59.192 45.455 4.27 0.00 37.81 4.57
1696 2208 4.612259 GCTTGCTTGTGTCACTTAGATGTG 60.612 45.833 4.27 0.00 39.15 3.21
1697 2209 3.499918 GCTTGCTTGTGTCACTTAGATGT 59.500 43.478 4.27 0.00 0.00 3.06
1698 2210 3.499537 TGCTTGCTTGTGTCACTTAGATG 59.500 43.478 4.27 0.00 0.00 2.90
1699 2211 3.743521 TGCTTGCTTGTGTCACTTAGAT 58.256 40.909 4.27 0.00 0.00 1.98
1700 2212 3.192541 TGCTTGCTTGTGTCACTTAGA 57.807 42.857 4.27 0.00 0.00 2.10
1701 2213 4.931601 TCTATGCTTGCTTGTGTCACTTAG 59.068 41.667 4.27 3.19 0.00 2.18
1702 2214 4.893608 TCTATGCTTGCTTGTGTCACTTA 58.106 39.130 4.27 0.00 0.00 2.24
1703 2215 3.743521 TCTATGCTTGCTTGTGTCACTT 58.256 40.909 4.27 0.00 0.00 3.16
1704 2216 3.407424 TCTATGCTTGCTTGTGTCACT 57.593 42.857 4.27 0.00 0.00 3.41
1705 2217 4.470462 CTTTCTATGCTTGCTTGTGTCAC 58.530 43.478 0.00 0.00 0.00 3.67
1706 2218 3.503363 CCTTTCTATGCTTGCTTGTGTCA 59.497 43.478 0.00 0.00 0.00 3.58
1707 2219 3.753272 TCCTTTCTATGCTTGCTTGTGTC 59.247 43.478 0.00 0.00 0.00 3.67
1708 2220 3.754965 TCCTTTCTATGCTTGCTTGTGT 58.245 40.909 0.00 0.00 0.00 3.72
1709 2221 4.771590 TTCCTTTCTATGCTTGCTTGTG 57.228 40.909 0.00 0.00 0.00 3.33
1710 2222 5.279156 CCTTTTCCTTTCTATGCTTGCTTGT 60.279 40.000 0.00 0.00 0.00 3.16
1711 2223 5.047802 TCCTTTTCCTTTCTATGCTTGCTTG 60.048 40.000 0.00 0.00 0.00 4.01
1712 2224 5.079643 TCCTTTTCCTTTCTATGCTTGCTT 58.920 37.500 0.00 0.00 0.00 3.91
1713 2225 4.666512 TCCTTTTCCTTTCTATGCTTGCT 58.333 39.130 0.00 0.00 0.00 3.91
1714 2226 5.391312 TTCCTTTTCCTTTCTATGCTTGC 57.609 39.130 0.00 0.00 0.00 4.01
1771 2283 9.314133 AGTATTGCACATCTAAGTCCTATATCA 57.686 33.333 0.00 0.00 0.00 2.15
1775 2287 9.935241 CATAAGTATTGCACATCTAAGTCCTAT 57.065 33.333 0.00 0.00 0.00 2.57
1776 2288 7.872993 GCATAAGTATTGCACATCTAAGTCCTA 59.127 37.037 0.00 0.00 39.90 2.94
1777 2289 6.708054 GCATAAGTATTGCACATCTAAGTCCT 59.292 38.462 0.00 0.00 39.90 3.85
1778 2290 6.073003 GGCATAAGTATTGCACATCTAAGTCC 60.073 42.308 0.00 0.00 41.95 3.85
1779 2291 6.483307 TGGCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 41.95 3.01
1780 2292 6.260936 GTGGCATAAGTATTGCACATCTAAGT 59.739 38.462 0.00 0.00 41.95 2.24
1781 2293 6.260714 TGTGGCATAAGTATTGCACATCTAAG 59.739 38.462 0.00 0.00 41.95 2.18
1782 2294 6.118852 TGTGGCATAAGTATTGCACATCTAA 58.881 36.000 0.00 0.00 41.95 2.10
1783 2295 5.679601 TGTGGCATAAGTATTGCACATCTA 58.320 37.500 0.00 0.00 41.95 1.98
1784 2296 4.525996 TGTGGCATAAGTATTGCACATCT 58.474 39.130 0.00 0.00 41.95 2.90
1785 2297 4.898829 TGTGGCATAAGTATTGCACATC 57.101 40.909 0.00 0.00 41.95 3.06
1786 2298 5.135383 AGATGTGGCATAAGTATTGCACAT 58.865 37.500 0.00 0.00 41.95 3.21
1787 2299 4.525996 AGATGTGGCATAAGTATTGCACA 58.474 39.130 0.00 0.00 41.95 4.57
1788 2300 5.334414 GCTAGATGTGGCATAAGTATTGCAC 60.334 44.000 0.00 0.00 41.95 4.57
1789 2301 4.756642 GCTAGATGTGGCATAAGTATTGCA 59.243 41.667 0.00 0.00 41.95 4.08
1790 2302 4.999950 AGCTAGATGTGGCATAAGTATTGC 59.000 41.667 0.00 0.00 39.41 3.56
1791 2303 5.994054 ACAGCTAGATGTGGCATAAGTATTG 59.006 40.000 13.91 0.00 30.99 1.90
1792 2304 5.994054 CACAGCTAGATGTGGCATAAGTATT 59.006 40.000 29.28 0.00 45.53 1.89
1793 2305 5.545588 CACAGCTAGATGTGGCATAAGTAT 58.454 41.667 29.28 0.00 45.53 2.12
1794 2306 4.948847 CACAGCTAGATGTGGCATAAGTA 58.051 43.478 29.28 0.00 45.53 2.24
1795 2307 3.801698 CACAGCTAGATGTGGCATAAGT 58.198 45.455 29.28 0.00 45.53 2.24
1816 2328 8.023128 TGTATCTTTGATCAGTTTTGCTAAAGC 58.977 33.333 0.00 0.00 42.50 3.51
1922 2494 8.788325 AACACTCCATTTACTTATACAAGGTC 57.212 34.615 0.00 0.00 35.97 3.85
1923 2495 9.227777 GAAACACTCCATTTACTTATACAAGGT 57.772 33.333 0.00 0.00 35.97 3.50
1924 2496 9.449719 AGAAACACTCCATTTACTTATACAAGG 57.550 33.333 0.00 0.00 35.97 3.61
1944 2516 2.380064 ATCCAAACTGGCCAGAAACA 57.620 45.000 39.19 17.99 37.47 2.83
1991 2563 4.890088 TCAGCCACACGAAGTATTTTACT 58.110 39.130 0.00 0.00 41.61 2.24
2003 2575 1.626654 GACGACCATTCAGCCACACG 61.627 60.000 0.00 0.00 0.00 4.49
2042 2615 1.301716 CCTTGTGTGAGACCACGGG 60.302 63.158 0.00 0.00 46.06 5.28
2062 2636 6.416750 GGAAATAAACACGGAGACAAAAGTTG 59.583 38.462 0.00 0.00 0.00 3.16
2064 2638 5.826208 AGGAAATAAACACGGAGACAAAAGT 59.174 36.000 0.00 0.00 0.00 2.66
2103 2677 7.096551 AGACAGCATTTAACAACAACAAAAGT 58.903 30.769 0.00 0.00 0.00 2.66
2123 2697 0.820871 GCCACCTCCACTAGAGACAG 59.179 60.000 0.00 0.00 46.50 3.51
2134 2708 2.149973 AAATCTTGGATGCCACCTCC 57.850 50.000 0.00 0.00 30.78 4.30
2231 2805 9.713740 TCATTTGAATAAACAAAAATTGCACAC 57.286 25.926 0.00 0.00 41.88 3.82


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

AutoCloner maintained by Alex Coulton.