Multiple sequence alignment - TraesCS6A01G299300

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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 TraesCS6A01G299300 chr6A 100.000 7822 0 0 1 7822 532647147 532639326 0.000000e+00 14445.0
1 TraesCS6A01G299300 chr6A 82.216 686 91 13 7157 7821 532436378 532435703 5.300000e-156 562.0
2 TraesCS6A01G299300 chr6A 85.287 401 34 10 5459 5857 532633383 532633006 2.650000e-104 390.0
3 TraesCS6A01G299300 chr6A 87.296 307 34 3 7218 7520 532534323 532534018 5.810000e-91 346.0
4 TraesCS6A01G299300 chr6A 88.561 271 22 5 79 341 532646810 532646541 3.520000e-83 320.0
5 TraesCS6A01G299300 chr6A 88.561 271 22 5 338 607 532647069 532646807 3.520000e-83 320.0
6 TraesCS6A01G299300 chr6A 83.846 130 19 1 5851 5980 532632974 532632847 1.070000e-23 122.0
7 TraesCS6A01G299300 chr6B 92.531 7966 344 80 1 7821 578513497 578505638 0.000000e+00 11182.0
8 TraesCS6A01G299300 chr6B 91.429 245 11 1 97 341 578513157 578512923 2.100000e-85 327.0
9 TraesCS6A01G299300 chr6B 87.500 280 24 5 336 613 578513421 578513151 5.890000e-81 313.0
10 TraesCS6A01G299300 chr6D 94.341 7068 249 66 4 7002 387640126 387633141 0.000000e+00 10696.0
11 TraesCS6A01G299300 chr6D 91.899 716 34 6 7122 7822 387631518 387630812 0.000000e+00 979.0
12 TraesCS6A01G299300 chr6D 84.000 675 45 21 7172 7821 387405684 387405048 2.430000e-164 590.0
13 TraesCS6A01G299300 chr6D 82.287 621 80 11 7218 7821 387401018 387400411 1.950000e-140 510.0
14 TraesCS6A01G299300 chr6D 82.137 627 69 18 7218 7821 387627190 387626584 1.520000e-136 497.0
15 TraesCS6A01G299300 chr6D 91.353 266 16 4 79 341 387639788 387639527 2.680000e-94 357.0
16 TraesCS6A01G299300 chr6D 89.744 273 21 5 337 607 387640052 387639785 7.520000e-90 342.0
17 TraesCS6A01G299300 chr6D 87.603 242 27 2 6305 6546 387628411 387628173 2.150000e-70 278.0
18 TraesCS6A01G299300 chr6D 85.606 264 20 3 5594 5857 387629339 387629094 2.160000e-65 261.0
19 TraesCS6A01G299300 chr6D 78.802 217 34 3 5851 6057 387629062 387628848 1.370000e-27 135.0
20 TraesCS6A01G299300 chr6D 100.000 30 0 0 6742 6771 387106604 387106575 1.000000e-03 56.5
21 TraesCS6A01G299300 chr3D 82.667 150 26 0 3645 3794 250068360 250068509 4.920000e-27 134.0
22 TraesCS6A01G299300 chr3D 80.117 171 27 4 3674 3838 290717918 290717749 3.830000e-23 121.0
23 TraesCS6A01G299300 chr3D 80.117 171 27 4 3674 3838 511936680 511936511 3.830000e-23 121.0
24 TraesCS6A01G299300 chr3D 79.882 169 27 4 3676 3838 532139131 532138964 4.960000e-22 117.0
25 TraesCS6A01G299300 chr3D 81.452 124 14 5 4240 4355 250068835 250068957 8.360000e-15 93.5
26 TraesCS6A01G299300 chr7D 81.333 150 28 0 3645 3794 411628110 411628259 1.070000e-23 122.0
27 TraesCS6A01G299300 chr7D 80.117 171 27 4 3674 3838 328320064 328319895 3.830000e-23 121.0
28 TraesCS6A01G299300 chr7D 82.474 97 12 1 4228 4319 411887470 411887566 6.510000e-11 80.5
29 TraesCS6A01G299300 chr7D 96.970 33 1 0 303 335 467438503 467438535 1.000000e-03 56.5
30 TraesCS6A01G299300 chr3A 78.363 171 30 4 3674 3838 451494275 451494444 3.860000e-18 104.0
31 TraesCS6A01G299300 chr3A 81.513 119 14 5 4240 4351 334005202 334005085 3.010000e-14 91.6
32 TraesCS6A01G299300 chr3A 81.513 119 14 5 4240 4351 334008249 334008132 3.010000e-14 91.6
33 TraesCS6A01G299300 chr3A 86.585 82 5 2 4244 4319 333958948 333958867 1.400000e-12 86.1
34 TraesCS6A01G299300 chrUn 91.176 68 2 1 1 68 96732199 96732136 1.080000e-13 89.8


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 TraesCS6A01G299300 chr6A 532639326 532647147 7821 True 5028.333333 14445 92.374000 1 7822 3 chr6A.!!$R4 7821
1 TraesCS6A01G299300 chr6A 532435703 532436378 675 True 562.000000 562 82.216000 7157 7821 1 chr6A.!!$R1 664
2 TraesCS6A01G299300 chr6A 532632847 532633383 536 True 256.000000 390 84.566500 5459 5980 2 chr6A.!!$R3 521
3 TraesCS6A01G299300 chr6B 578505638 578513497 7859 True 3940.666667 11182 90.486667 1 7821 3 chr6B.!!$R1 7820
4 TraesCS6A01G299300 chr6D 387626584 387640126 13542 True 1693.125000 10696 87.685625 4 7822 8 chr6D.!!$R4 7818
5 TraesCS6A01G299300 chr6D 387405048 387405684 636 True 590.000000 590 84.000000 7172 7821 1 chr6D.!!$R3 649
6 TraesCS6A01G299300 chr6D 387400411 387401018 607 True 510.000000 510 82.287000 7218 7821 1 chr6D.!!$R2 603

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
637 642 0.319469 TGCTCGAACTGCGACATGAA 60.319 50.000 0.00 0.0 45.59 2.57 F
1363 1391 0.037303 AGGTCGTCCGTCTCAACCTA 59.963 55.000 0.00 0.0 38.56 3.08 F
1708 1754 0.530211 TTGCTTTGCGTGCTTGCATT 60.530 45.000 4.30 0.0 45.78 3.56 F
1734 1781 0.657312 CGCTTGTGTCTTGTGCTTGA 59.343 50.000 0.00 0.0 0.00 3.02 F
1838 1885 1.883926 TCACTTGCTGTACTGTAGCGA 59.116 47.619 1.46 0.0 44.01 4.93 F
3558 3610 1.287425 CATCGTTCTTTAGGGACCGC 58.713 55.000 0.00 0.0 0.00 5.68 F
4489 4567 0.963355 TTCGGTTGGCAAGGGCATAC 60.963 55.000 0.00 0.0 43.71 2.39 F
5755 5837 0.243907 TCACCTTCTAGCACGCAGTC 59.756 55.000 0.00 0.0 41.61 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1673 0.396435 ACAGTCTCATTCCGCCAACA 59.604 50.000 0.0 0.00 0.00 3.33 R
2708 2758 2.642311 TCTTGAAGGGTGGTAGCATTCA 59.358 45.455 0.0 1.35 43.31 2.57 R
3526 3578 0.107017 AACGATGCAGAATCCTGGGG 60.107 55.000 0.0 0.00 40.72 4.96 R
3558 3610 0.673022 GAGAAGCAGCACCCAGACTG 60.673 60.000 0.0 0.00 36.96 3.51 R
3682 3734 2.071540 TGAGAAAGAGCATCAACAGCG 58.928 47.619 0.0 0.00 37.82 5.18 R
4917 4996 3.131396 CCCAGTGTGTTGTACTCAAGAC 58.869 50.000 0.0 2.12 44.61 3.01 R
6341 6465 0.750546 CTCGGTCCATACAGGGTCGA 60.751 60.000 0.0 0.00 38.92 4.20 R
7102 8730 0.039798 TGCTTCGTGACGGACACTAC 60.040 55.000 4.7 0.00 46.24 2.73 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
33 34 1.305201 GTTTGTCCTCCTGCGAACAA 58.695 50.000 0.00 0.00 0.00 2.83
77 78 3.820467 CTGATACAAACACCAAAGCTGGA 59.180 43.478 0.00 0.00 46.92 3.86
80 81 6.186957 TGATACAAACACCAAAGCTGGATAT 58.813 36.000 0.00 0.00 46.92 1.63
84 85 5.047802 ACAAACACCAAAGCTGGATATCAAG 60.048 40.000 2.35 2.35 46.92 3.02
304 309 1.402852 GCCTTTCCCTTGCGATTTGTC 60.403 52.381 0.00 0.00 0.00 3.18
330 335 2.438730 TTGCAGGGCAAAATCAGCA 58.561 47.368 0.41 0.00 45.96 4.41
372 377 0.527565 CCCAACCTCCAATTTCTGCG 59.472 55.000 0.00 0.00 0.00 5.18
478 483 7.653713 CCAGAGGTTCACACAATCATATACTAC 59.346 40.741 0.00 0.00 0.00 2.73
479 484 8.417106 CAGAGGTTCACACAATCATATACTACT 58.583 37.037 0.00 0.00 0.00 2.57
480 485 9.642343 AGAGGTTCACACAATCATATACTACTA 57.358 33.333 0.00 0.00 0.00 1.82
486 491 8.523658 TCACACAATCATATACTACTAGCATCC 58.476 37.037 0.00 0.00 0.00 3.51
497 502 1.342076 ACTAGCATCCGGTCAGAAGGA 60.342 52.381 0.00 0.00 41.30 3.36
533 538 5.712152 GGGGGCAGATAAAATGTAGAATG 57.288 43.478 0.00 0.00 0.00 2.67
613 618 1.658717 CGCGTTGCTATCCTCCTCG 60.659 63.158 0.00 0.00 0.00 4.63
633 638 1.737735 CCATGCTCGAACTGCGACA 60.738 57.895 0.00 0.00 45.59 4.35
637 642 0.319469 TGCTCGAACTGCGACATGAA 60.319 50.000 0.00 0.00 45.59 2.57
835 848 2.125350 GCCAACGGAGGAGAGCAG 60.125 66.667 0.00 0.00 0.00 4.24
838 851 1.447489 CAACGGAGGAGAGCAGCAG 60.447 63.158 0.00 0.00 0.00 4.24
1254 1281 3.666883 TCGCCGTGCTTATTTTATGTG 57.333 42.857 0.00 0.00 0.00 3.21
1280 1307 2.065906 GAGTCCAGTCGAGGCGATCC 62.066 65.000 0.00 0.00 38.42 3.36
1363 1391 0.037303 AGGTCGTCCGTCTCAACCTA 59.963 55.000 0.00 0.00 38.56 3.08
1401 1429 3.512724 GTGGACCTTGTTGGCTACTAGTA 59.487 47.826 1.89 1.89 40.22 1.82
1427 1457 4.647654 CTTTGGCAAGCTGCTGTG 57.352 55.556 1.35 5.22 44.28 3.66
1428 1458 1.663702 CTTTGGCAAGCTGCTGTGC 60.664 57.895 20.90 20.90 44.28 4.57
1507 1537 5.163571 TGCTGCTATCTCAGTTCTAGAAGTG 60.164 44.000 27.68 27.68 41.79 3.16
1508 1538 5.163561 GCTGCTATCTCAGTTCTAGAAGTGT 60.164 44.000 30.44 18.98 41.32 3.55
1513 1543 5.537300 TCTCAGTTCTAGAAGTGTTGCTT 57.463 39.130 30.44 0.09 41.32 3.91
1515 1545 5.755375 TCTCAGTTCTAGAAGTGTTGCTTTG 59.245 40.000 30.44 16.87 41.32 2.77
1516 1546 5.670485 TCAGTTCTAGAAGTGTTGCTTTGA 58.330 37.500 30.44 13.10 41.32 2.69
1523 1553 4.904241 AGAAGTGTTGCTTTGAGCTAGAT 58.096 39.130 0.00 0.00 42.97 1.98
1526 1556 7.108847 AGAAGTGTTGCTTTGAGCTAGATTAT 58.891 34.615 0.00 0.00 42.97 1.28
1533 1563 9.405587 GTTGCTTTGAGCTAGATTATACTAGAG 57.594 37.037 0.00 0.00 42.97 2.43
1552 1590 2.228822 GAGCCACACCACATTTGTAAGG 59.771 50.000 0.00 0.00 0.00 2.69
1553 1591 1.272212 GCCACACCACATTTGTAAGGG 59.728 52.381 0.00 0.00 0.00 3.95
1554 1592 1.892474 CCACACCACATTTGTAAGGGG 59.108 52.381 0.00 0.00 0.00 4.79
1563 1601 3.381272 ACATTTGTAAGGGGAATGCATCG 59.619 43.478 0.00 0.00 34.86 3.84
1566 1604 1.557371 TGTAAGGGGAATGCATCGTGA 59.443 47.619 0.00 0.00 0.00 4.35
1568 1606 3.389656 TGTAAGGGGAATGCATCGTGATA 59.610 43.478 0.00 0.00 0.00 2.15
1579 1624 4.180817 TGCATCGTGATACCTTACAACTG 58.819 43.478 0.00 0.00 0.00 3.16
1581 1626 3.945981 TCGTGATACCTTACAACTGCA 57.054 42.857 0.00 0.00 0.00 4.41
1584 1629 4.449743 TCGTGATACCTTACAACTGCAAAC 59.550 41.667 0.00 0.00 0.00 2.93
1589 1634 6.482641 TGATACCTTACAACTGCAAACGTTTA 59.517 34.615 14.20 0.00 0.00 2.01
1595 1640 7.062488 CCTTACAACTGCAAACGTTTAAGTTTT 59.938 33.333 26.53 23.85 41.84 2.43
1597 1642 5.119434 ACAACTGCAAACGTTTAAGTTTTGG 59.881 36.000 26.53 20.71 41.84 3.28
1598 1643 4.811908 ACTGCAAACGTTTAAGTTTTGGT 58.188 34.783 14.20 2.10 41.84 3.67
1599 1644 4.860352 ACTGCAAACGTTTAAGTTTTGGTC 59.140 37.500 14.20 0.00 41.84 4.02
1607 1652 7.090953 ACGTTTAAGTTTTGGTCTGAATTGA 57.909 32.000 0.00 0.00 0.00 2.57
1609 1654 7.700656 ACGTTTAAGTTTTGGTCTGAATTGAAG 59.299 33.333 0.00 0.00 0.00 3.02
1610 1655 7.167468 CGTTTAAGTTTTGGTCTGAATTGAAGG 59.833 37.037 0.00 0.00 0.00 3.46
1613 1658 5.200483 AGTTTTGGTCTGAATTGAAGGTCA 58.800 37.500 0.00 0.00 0.00 4.02
1615 1660 5.710513 TTTGGTCTGAATTGAAGGTCATG 57.289 39.130 0.00 0.00 0.00 3.07
1622 1667 5.884232 TCTGAATTGAAGGTCATGATTCTGG 59.116 40.000 0.00 0.00 30.33 3.86
1623 1668 4.951715 TGAATTGAAGGTCATGATTCTGGG 59.048 41.667 0.00 0.00 29.48 4.45
1625 1670 3.634397 TGAAGGTCATGATTCTGGGAC 57.366 47.619 0.00 0.00 0.00 4.46
1628 1673 2.555664 AGGTCATGATTCTGGGACTGT 58.444 47.619 0.00 0.00 0.00 3.55
1644 1689 0.798776 CTGTGTTGGCGGAATGAGAC 59.201 55.000 0.00 0.00 0.00 3.36
1658 1703 4.697352 GGAATGAGACTGTGTGCTGTTATT 59.303 41.667 0.00 0.00 0.00 1.40
1696 1741 8.349983 AGTTACAAAACTAGTATGGTTGCTTTG 58.650 33.333 11.91 10.78 44.26 2.77
1697 1742 5.528870 ACAAAACTAGTATGGTTGCTTTGC 58.471 37.500 10.76 0.00 39.61 3.68
1698 1743 4.419522 AAACTAGTATGGTTGCTTTGCG 57.580 40.909 0.00 0.00 39.61 4.85
1708 1754 0.530211 TTGCTTTGCGTGCTTGCATT 60.530 45.000 4.30 0.00 45.78 3.56
1709 1755 1.216298 TGCTTTGCGTGCTTGCATTG 61.216 50.000 4.30 2.60 45.78 2.82
1715 1761 1.592081 TGCGTGCTTGCATTGTTTTTC 59.408 42.857 0.00 0.00 40.62 2.29
1719 1766 2.284952 GTGCTTGCATTGTTTTTCGCTT 59.715 40.909 0.00 0.00 0.00 4.68
1725 1772 3.115554 GCATTGTTTTTCGCTTGTGTCT 58.884 40.909 0.00 0.00 0.00 3.41
1734 1781 0.657312 CGCTTGTGTCTTGTGCTTGA 59.343 50.000 0.00 0.00 0.00 3.02
1762 1809 6.015180 AGCTTGGAGATAGATTTGCAAAACAA 60.015 34.615 17.19 4.57 36.13 2.83
1766 1813 7.092079 TGGAGATAGATTTGCAAAACAATGTG 58.908 34.615 17.19 0.00 38.31 3.21
1768 1815 7.977853 GGAGATAGATTTGCAAAACAATGTGAT 59.022 33.333 17.19 0.00 38.31 3.06
1787 1834 6.577103 TGTGATAAGTTCTGGCTTCTCTATG 58.423 40.000 0.00 0.00 0.00 2.23
1794 1841 2.961741 TCTGGCTTCTCTATGGCTAGTG 59.038 50.000 0.00 0.00 36.28 2.74
1795 1842 2.036992 CTGGCTTCTCTATGGCTAGTGG 59.963 54.545 0.00 0.00 31.50 4.00
1808 1855 4.261801 TGGCTAGTGGCTCTGTTAAATTC 58.738 43.478 0.00 0.00 41.46 2.17
1825 1872 7.920682 TGTTAAATTCTTTTTCTCCTCACTTGC 59.079 33.333 0.00 0.00 0.00 4.01
1837 1884 2.254459 CTCACTTGCTGTACTGTAGCG 58.746 52.381 1.46 0.00 44.01 4.26
1838 1885 1.883926 TCACTTGCTGTACTGTAGCGA 59.116 47.619 1.46 0.00 44.01 4.93
1877 1924 6.095440 GCCTTTATGTTTTTCTAGGAGATGCA 59.905 38.462 0.00 0.00 0.00 3.96
1883 1930 3.717400 TTTCTAGGAGATGCAGCTACG 57.283 47.619 8.90 0.00 0.00 3.51
2043 2090 9.685276 TTATAGAATGGATTTGATGTTCTGTGT 57.315 29.630 0.00 0.00 32.02 3.72
2104 2151 6.382869 AATTGGTTCTCAGTGTCTCTTTTG 57.617 37.500 0.00 0.00 0.00 2.44
2462 2511 2.715749 TGTGCAGGGTATCCAATGAG 57.284 50.000 0.00 0.00 34.83 2.90
2616 2665 7.342769 TGTTCTGTTTCTGACTGTAGAGTTA 57.657 36.000 0.00 0.00 30.16 2.24
2708 2758 9.138596 TCCTGCTGTAAGTTTTAGGTTTTATTT 57.861 29.630 0.00 0.00 35.30 1.40
2734 2784 3.649023 TGCTACCACCCTTCAAGAGTTTA 59.351 43.478 0.00 0.00 0.00 2.01
2835 2887 3.961480 ACCCCTTTAATGCAAAAGCTC 57.039 42.857 5.50 0.00 35.53 4.09
2864 2916 5.127194 TGTGCTTCCAGTATACCTCTGTTAG 59.873 44.000 0.00 0.00 0.00 2.34
3094 3146 6.321945 ACAATGGATATCAAGCAAATGTAGCA 59.678 34.615 4.83 0.00 0.00 3.49
3120 3172 3.500448 TGACCTTGTTATGCAGGTTCA 57.500 42.857 0.00 0.00 34.38 3.18
3558 3610 1.287425 CATCGTTCTTTAGGGACCGC 58.713 55.000 0.00 0.00 0.00 5.68
3682 3734 2.417787 GGGATTGATTGCTTTGCTCACC 60.418 50.000 0.00 0.00 0.00 4.02
4060 4126 3.146104 ACAAGAACTGGATGAAGGTGG 57.854 47.619 0.00 0.00 0.00 4.61
4407 4485 9.903682 ATCTTTCTGTTATTTCACAATTGTCTG 57.096 29.630 8.48 0.00 0.00 3.51
4489 4567 0.963355 TTCGGTTGGCAAGGGCATAC 60.963 55.000 0.00 0.00 43.71 2.39
4532 4610 1.885887 TGCACATGCTTCAAGGGTAAC 59.114 47.619 5.31 0.00 42.66 2.50
4589 4667 7.841282 ATATTGCTAGGTAGTATGGCGATAT 57.159 36.000 0.00 0.00 36.04 1.63
4611 4690 3.660970 TTTAGCTCACCATATTGGCCA 57.339 42.857 0.00 0.00 42.67 5.36
4690 4769 4.399303 GGTTTTCTAGATTCATGGTGGTGG 59.601 45.833 0.00 0.00 0.00 4.61
4716 4795 8.493547 GTGTAGTGGTAAAAACTCATCTTGTAC 58.506 37.037 0.00 0.00 0.00 2.90
4773 4852 1.971357 GATACATGAGATCCGTGGGGT 59.029 52.381 0.00 0.00 36.10 4.95
4917 4996 7.095910 AGAGATCTGTCAGAGTAATTGTTGTG 58.904 38.462 8.82 0.00 0.00 3.33
4997 5076 6.126185 TGGGGTTTTATTTTTGAATTTGGGGA 60.126 34.615 0.00 0.00 0.00 4.81
5281 5362 7.482169 TCCTTGCTATTCTCTTTGAAGACTA 57.518 36.000 0.00 0.00 38.18 2.59
5315 5396 2.226330 TGTTTTCTGTTGACCCATCCG 58.774 47.619 0.00 0.00 0.00 4.18
5440 5521 3.554934 TCATAGATGTGGCCATTTGTCC 58.445 45.455 9.72 0.00 0.00 4.02
5467 5548 9.226606 CACCAAAGGTAGTTATGAATCTGTAAA 57.773 33.333 0.00 0.00 32.11 2.01
5755 5837 0.243907 TCACCTTCTAGCACGCAGTC 59.756 55.000 0.00 0.00 41.61 3.51
5760 5842 2.017782 CTTCTAGCACGCAGTCTCCTA 58.982 52.381 0.00 0.00 41.61 2.94
5761 5843 2.350057 TCTAGCACGCAGTCTCCTAT 57.650 50.000 0.00 0.00 41.61 2.57
5816 5898 3.118261 ACTTCTTGGCAGACAGAACTTCA 60.118 43.478 0.00 0.00 0.00 3.02
5827 5909 3.356290 ACAGAACTTCAACTTTGGCAGT 58.644 40.909 0.00 0.00 37.30 4.40
5833 5915 0.380378 TCAACTTTGGCAGTCAACGC 59.620 50.000 0.00 0.00 32.94 4.84
5905 6025 3.507143 AAGTGGAGGGTGGAGGCCT 62.507 63.158 3.86 3.86 0.00 5.19
6099 6219 2.125673 GCTCGGCTGCTACGGAAA 60.126 61.111 0.00 0.00 0.00 3.13
6107 6227 1.666023 GCTGCTACGGAAAAACAAGCC 60.666 52.381 0.00 0.00 32.14 4.35
6115 6235 3.119990 ACGGAAAAACAAGCCATGATACG 60.120 43.478 0.00 0.00 0.00 3.06
6143 6263 8.621532 ATTACTCTCATTTTACTTGCTTGTGA 57.378 30.769 0.00 0.00 0.00 3.58
6148 6268 8.256611 TCTCATTTTACTTGCTTGTGATAGTC 57.743 34.615 0.00 0.00 0.00 2.59
6154 6274 5.016051 ACTTGCTTGTGATAGTCATCGAT 57.984 39.130 0.00 0.00 33.51 3.59
6158 6278 3.666334 GCTTGTGATAGTCATCGATCGTC 59.334 47.826 15.94 3.78 33.51 4.20
6193 6317 8.960591 ACCTTATGTCATTCTTATTTGGTCAAG 58.039 33.333 0.00 0.00 0.00 3.02
6202 6326 6.783708 TCTTATTTGGTCAAGGTGTTGTTT 57.216 33.333 0.00 0.00 34.98 2.83
6203 6327 6.801575 TCTTATTTGGTCAAGGTGTTGTTTC 58.198 36.000 0.00 0.00 34.98 2.78
6204 6328 3.878160 TTTGGTCAAGGTGTTGTTTCC 57.122 42.857 0.00 0.00 34.98 3.13
6205 6329 2.818751 TGGTCAAGGTGTTGTTTCCT 57.181 45.000 0.00 0.00 34.98 3.36
6206 6330 3.094484 TGGTCAAGGTGTTGTTTCCTT 57.906 42.857 0.00 0.00 43.79 3.36
6207 6331 3.436243 TGGTCAAGGTGTTGTTTCCTTT 58.564 40.909 0.00 0.00 41.44 3.11
6208 6332 3.835395 TGGTCAAGGTGTTGTTTCCTTTT 59.165 39.130 0.00 0.00 41.44 2.27
6209 6333 4.284746 TGGTCAAGGTGTTGTTTCCTTTTT 59.715 37.500 0.00 0.00 41.44 1.94
6210 6334 4.629634 GGTCAAGGTGTTGTTTCCTTTTTG 59.370 41.667 0.00 0.00 41.44 2.44
6211 6335 5.234752 GTCAAGGTGTTGTTTCCTTTTTGT 58.765 37.500 0.00 0.00 41.44 2.83
6212 6336 5.699001 GTCAAGGTGTTGTTTCCTTTTTGTT 59.301 36.000 0.00 0.00 41.44 2.83
6379 6503 1.478510 AGAGCTACTGGAACACCATCG 59.521 52.381 0.00 0.00 32.90 3.84
6432 6556 0.539051 CCGACAGGCTCATCCTTCTT 59.461 55.000 0.00 0.00 44.75 2.52
6435 6559 0.694771 ACAGGCTCATCCTTCTTGCA 59.305 50.000 0.00 0.00 44.75 4.08
6441 6565 0.700564 TCATCCTTCTTGCAGGGCTT 59.299 50.000 0.00 0.00 34.24 4.35
6472 6596 2.747460 CGTCGTACCTCGGGGTGA 60.747 66.667 20.02 3.13 46.75 4.02
6486 6610 2.951745 GTGATCGTCGGCAGAGCG 60.952 66.667 0.00 0.00 0.00 5.03
6515 6639 2.030579 CGAAGATCACGAAGCGAGACTA 59.969 50.000 6.49 0.00 0.00 2.59
6527 6651 5.333035 CGAAGCGAGACTAAAAACATGACAA 60.333 40.000 0.00 0.00 0.00 3.18
6549 6673 7.201145 ACAACGTGTATCATATAGAACTGACC 58.799 38.462 0.00 0.00 0.00 4.02
6597 6721 5.300752 AGTATGGATGTAATTCTTGAGCGG 58.699 41.667 0.00 0.00 0.00 5.52
6683 6808 4.877378 TGTTGTTGGTAGGTACTGTAGG 57.123 45.455 0.00 0.00 41.52 3.18
6702 6827 3.761897 AGGTGCTTTGGTAATGTGCTTA 58.238 40.909 0.00 0.00 0.00 3.09
6723 6848 0.389391 AGCAGACTACTTGCGTGTGT 59.611 50.000 0.00 0.00 0.00 3.72
6727 6852 3.546670 GCAGACTACTTGCGTGTGTATAC 59.453 47.826 0.00 0.00 0.00 1.47
6763 6900 0.736053 TTTGTTGTGCACGTCTTCCC 59.264 50.000 13.13 0.00 0.00 3.97
6795 6932 4.219288 AGACTTTGCCCAATCATTGTCTTC 59.781 41.667 0.00 0.00 30.42 2.87
6846 6995 1.502231 CCTCGTGTGTGGAGTTCTTG 58.498 55.000 0.00 0.00 0.00 3.02
6887 7036 3.662153 CCATGTGCGTGCAGTGCA 61.662 61.111 15.37 15.37 40.70 4.57
6933 7082 7.331791 GGTTGGTTAAGACTTGAGAGTGATAT 58.668 38.462 0.00 0.00 35.88 1.63
6973 7122 1.876156 CTTTTAGATGATGGCGAGCCC 59.124 52.381 12.05 0.00 34.56 5.19
7021 8619 3.114616 CAGCGAGGTGAGCCGTTG 61.115 66.667 0.00 0.00 40.50 4.10
7022 8620 4.379243 AGCGAGGTGAGCCGTTGG 62.379 66.667 0.00 0.00 40.50 3.77
7067 8695 1.069358 CTCGGGATAACCAAGCTCTCC 59.931 57.143 0.00 0.00 40.22 3.71
7079 8707 3.133014 CTCTCCATCCGGCGTGAT 58.867 61.111 6.01 5.55 0.00 3.06
7099 8727 2.590073 TGCGTTCACAACAAACAAGTG 58.410 42.857 0.00 0.00 34.67 3.16
7100 8728 1.917303 GCGTTCACAACAAACAAGTGG 59.083 47.619 0.00 0.00 34.17 4.00
7101 8729 2.414824 GCGTTCACAACAAACAAGTGGA 60.415 45.455 0.00 0.00 34.17 4.02
7102 8730 3.425404 CGTTCACAACAAACAAGTGGAG 58.575 45.455 0.00 0.00 34.17 3.86
7103 8731 3.119990 CGTTCACAACAAACAAGTGGAGT 60.120 43.478 0.00 0.00 34.17 3.85
7107 8735 4.634004 TCACAACAAACAAGTGGAGTAGTG 59.366 41.667 0.00 0.00 34.17 2.74
7127 8755 0.934496 TCCGTCACGAAGCAAGTTTG 59.066 50.000 0.00 0.00 0.00 2.93
7619 9358 4.856607 GCGCTCGGTCTTCTCCCG 62.857 72.222 0.00 0.00 46.83 5.14
7681 9420 2.754658 TCGAAGACCTCCCTCCGC 60.755 66.667 0.00 0.00 0.00 5.54
7686 9425 1.831652 AAGACCTCCCTCCGCAGTTG 61.832 60.000 0.00 0.00 0.00 3.16
7810 13778 0.097674 GCATGCCTACTTCTTGCACG 59.902 55.000 6.36 0.00 37.92 5.34
7821 13789 3.007398 ACTTCTTGCACGATCCTTTCTCT 59.993 43.478 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.194640 GCATATATTGATGCCGGTCTGAT 58.805 43.478 1.90 0.00 45.41 2.90
77 78 5.728741 AGGTTGGGACTTCTTCTCTTGATAT 59.271 40.000 0.00 0.00 0.00 1.63
80 81 3.318313 AGGTTGGGACTTCTTCTCTTGA 58.682 45.455 0.00 0.00 0.00 3.02
84 85 1.978580 TGGAGGTTGGGACTTCTTCTC 59.021 52.381 0.00 0.00 32.81 2.87
304 309 1.075482 TTGCCCTGCAAGAGGAAGG 59.925 57.895 0.00 0.00 46.33 3.46
349 354 3.084786 CAGAAATTGGAGGTTGGGACTC 58.915 50.000 0.00 0.00 0.00 3.36
450 455 3.126001 TGATTGTGTGAACCTCTGGTC 57.874 47.619 0.00 0.00 33.12 4.02
452 457 6.586344 AGTATATGATTGTGTGAACCTCTGG 58.414 40.000 0.00 0.00 0.00 3.86
478 483 1.403814 TCCTTCTGACCGGATGCTAG 58.596 55.000 9.46 0.00 0.00 3.42
479 484 1.860641 TTCCTTCTGACCGGATGCTA 58.139 50.000 9.46 0.00 0.00 3.49
480 485 0.984230 TTTCCTTCTGACCGGATGCT 59.016 50.000 9.46 0.00 0.00 3.79
486 491 2.548480 GTCTTGGTTTTCCTTCTGACCG 59.452 50.000 0.00 0.00 41.38 4.79
497 502 4.591038 CCCCCGTGTCTTGGTTTT 57.409 55.556 0.00 0.00 0.00 2.43
527 532 7.073215 AGGCAAGGTAATAATGGGTACATTCTA 59.927 37.037 0.00 0.00 43.67 2.10
529 534 6.068670 AGGCAAGGTAATAATGGGTACATTC 58.931 40.000 0.00 0.00 43.67 2.67
531 536 5.663158 AGGCAAGGTAATAATGGGTACAT 57.337 39.130 0.00 0.00 39.54 2.29
532 537 5.459982 AAGGCAAGGTAATAATGGGTACA 57.540 39.130 0.00 0.00 0.00 2.90
533 538 5.301045 GGAAAGGCAAGGTAATAATGGGTAC 59.699 44.000 0.00 0.00 0.00 3.34
613 618 1.446099 TCGCAGTTCGAGCATGGAC 60.446 57.895 1.01 0.00 43.16 4.02
633 638 3.578688 GCGGTTTCTGATGCTTTTTCAT 58.421 40.909 0.00 0.00 0.00 2.57
637 642 0.240945 CCGCGGTTTCTGATGCTTTT 59.759 50.000 19.50 0.00 0.00 2.27
780 793 4.220163 TCGCCCCTCTCGGCCTAT 62.220 66.667 0.00 0.00 46.98 2.57
919 937 3.509967 CCCTTATGGCCGTTTTCTTCTTT 59.490 43.478 0.77 0.00 0.00 2.52
996 1023 2.751913 CGTCTCGTCTCTGACCGGG 61.752 68.421 6.32 0.00 0.00 5.73
1121 1148 3.063084 GAGGAGCACGAGGACGGT 61.063 66.667 0.00 0.00 44.46 4.83
1182 1209 2.370519 TGAGAACGAGGGTTTTGGATGA 59.629 45.455 0.00 0.00 36.24 2.92
1254 1281 2.737039 GCCTCGACTGGACTCAATTCTC 60.737 54.545 0.00 0.00 0.00 2.87
1280 1307 2.747855 GGCTCCAAGGAAGCGTGG 60.748 66.667 0.00 0.00 36.13 4.94
1363 1391 3.518303 GGTCCACTACTTGGTTCACCTAT 59.482 47.826 0.00 0.00 46.97 2.57
1383 1411 4.591924 ACAACTACTAGTAGCCAACAAGGT 59.408 41.667 26.54 11.95 40.61 3.50
1391 1419 5.811100 CCAAAGCTTACAACTACTAGTAGCC 59.189 44.000 26.54 8.90 36.66 3.93
1443 1473 2.223340 CGAAGCAACTACCAATCCATGC 60.223 50.000 0.00 0.00 0.00 4.06
1444 1474 3.270027 TCGAAGCAACTACCAATCCATG 58.730 45.455 0.00 0.00 0.00 3.66
1487 1517 5.518487 GCAACACTTCTAGAACTGAGATAGC 59.482 44.000 16.25 9.60 0.00 2.97
1488 1518 6.862209 AGCAACACTTCTAGAACTGAGATAG 58.138 40.000 16.25 1.39 0.00 2.08
1489 1519 6.842437 AGCAACACTTCTAGAACTGAGATA 57.158 37.500 16.25 0.00 0.00 1.98
1507 1537 9.405587 CTCTAGTATAATCTAGCTCAAAGCAAC 57.594 37.037 0.00 0.00 45.56 4.17
1508 1538 8.085296 GCTCTAGTATAATCTAGCTCAAAGCAA 58.915 37.037 0.00 0.00 45.56 3.91
1513 1543 7.004691 TGTGGCTCTAGTATAATCTAGCTCAA 58.995 38.462 0.00 0.00 37.78 3.02
1515 1545 6.127842 GGTGTGGCTCTAGTATAATCTAGCTC 60.128 46.154 0.00 2.89 37.78 4.09
1516 1546 5.712917 GGTGTGGCTCTAGTATAATCTAGCT 59.287 44.000 0.00 0.00 37.78 3.32
1523 1553 5.950544 AATGTGGTGTGGCTCTAGTATAA 57.049 39.130 0.00 0.00 0.00 0.98
1526 1556 3.326588 ACAAATGTGGTGTGGCTCTAGTA 59.673 43.478 0.00 0.00 0.00 1.82
1533 1563 1.272212 CCCTTACAAATGTGGTGTGGC 59.728 52.381 0.00 0.00 0.00 5.01
1552 1590 2.550830 AGGTATCACGATGCATTCCC 57.449 50.000 0.00 0.00 0.00 3.97
1553 1591 4.377021 TGTAAGGTATCACGATGCATTCC 58.623 43.478 0.00 0.00 30.66 3.01
1554 1592 5.523916 AGTTGTAAGGTATCACGATGCATTC 59.476 40.000 0.00 0.00 30.66 2.67
1563 1601 4.212636 ACGTTTGCAGTTGTAAGGTATCAC 59.787 41.667 0.00 0.00 0.00 3.06
1566 1604 5.761165 AAACGTTTGCAGTTGTAAGGTAT 57.239 34.783 13.81 0.00 31.43 2.73
1568 1606 5.124297 ACTTAAACGTTTGCAGTTGTAAGGT 59.876 36.000 23.46 3.83 32.75 3.50
1579 1624 5.096849 TCAGACCAAAACTTAAACGTTTGC 58.903 37.500 23.46 1.36 37.20 3.68
1581 1626 8.030106 TCAATTCAGACCAAAACTTAAACGTTT 58.970 29.630 18.90 18.90 38.66 3.60
1584 1629 7.167468 CCTTCAATTCAGACCAAAACTTAAACG 59.833 37.037 0.00 0.00 0.00 3.60
1589 1634 5.656416 TGACCTTCAATTCAGACCAAAACTT 59.344 36.000 0.00 0.00 0.00 2.66
1595 1640 4.639078 TCATGACCTTCAATTCAGACCA 57.361 40.909 0.00 0.00 0.00 4.02
1597 1642 6.183360 CCAGAATCATGACCTTCAATTCAGAC 60.183 42.308 10.82 0.00 30.09 3.51
1598 1643 5.884232 CCAGAATCATGACCTTCAATTCAGA 59.116 40.000 10.82 0.00 30.09 3.27
1599 1644 5.067413 CCCAGAATCATGACCTTCAATTCAG 59.933 44.000 10.82 1.31 30.09 3.02
1607 1652 2.915604 ACAGTCCCAGAATCATGACCTT 59.084 45.455 0.00 0.00 0.00 3.50
1609 1654 2.026822 ACACAGTCCCAGAATCATGACC 60.027 50.000 0.00 0.00 0.00 4.02
1610 1655 3.340814 ACACAGTCCCAGAATCATGAC 57.659 47.619 0.00 0.00 0.00 3.06
1613 1658 2.881403 GCCAACACAGTCCCAGAATCAT 60.881 50.000 0.00 0.00 0.00 2.45
1615 1660 1.168714 GCCAACACAGTCCCAGAATC 58.831 55.000 0.00 0.00 0.00 2.52
1622 1667 0.605319 TCATTCCGCCAACACAGTCC 60.605 55.000 0.00 0.00 0.00 3.85
1623 1668 0.798776 CTCATTCCGCCAACACAGTC 59.201 55.000 0.00 0.00 0.00 3.51
1625 1670 0.798776 GTCTCATTCCGCCAACACAG 59.201 55.000 0.00 0.00 0.00 3.66
1628 1673 0.396435 ACAGTCTCATTCCGCCAACA 59.604 50.000 0.00 0.00 0.00 3.33
1658 1703 8.090214 ACTAGTTTTGTAACTAAATCGCCTGTA 58.910 33.333 0.00 0.00 44.14 2.74
1670 1715 8.349983 CAAAGCAACCATACTAGTTTTGTAACT 58.650 33.333 0.00 0.00 46.18 2.24
1696 1741 1.395820 CGAAAAACAATGCAAGCACGC 60.396 47.619 0.00 0.00 0.00 5.34
1697 1742 1.395820 GCGAAAAACAATGCAAGCACG 60.396 47.619 0.00 0.00 0.00 5.34
1698 1743 1.860326 AGCGAAAAACAATGCAAGCAC 59.140 42.857 0.00 0.00 0.00 4.40
1708 1754 3.497118 CACAAGACACAAGCGAAAAACA 58.503 40.909 0.00 0.00 0.00 2.83
1709 1755 2.278875 GCACAAGACACAAGCGAAAAAC 59.721 45.455 0.00 0.00 0.00 2.43
1715 1761 0.657312 TCAAGCACAAGACACAAGCG 59.343 50.000 0.00 0.00 0.00 4.68
1734 1781 7.886629 TTTGCAAATCTATCTCCAAGCTATT 57.113 32.000 8.05 0.00 0.00 1.73
1762 1809 5.690464 AGAGAAGCCAGAACTTATCACAT 57.310 39.130 2.23 0.00 39.75 3.21
1766 1813 4.994217 GCCATAGAGAAGCCAGAACTTATC 59.006 45.833 0.00 0.00 38.00 1.75
1768 1815 4.033709 AGCCATAGAGAAGCCAGAACTTA 58.966 43.478 0.00 0.00 0.00 2.24
1787 1834 4.518249 AGAATTTAACAGAGCCACTAGCC 58.482 43.478 0.00 0.00 45.47 3.93
1794 1841 7.040409 TGAGGAGAAAAAGAATTTAACAGAGCC 60.040 37.037 0.00 0.00 37.28 4.70
1795 1842 7.805542 GTGAGGAGAAAAAGAATTTAACAGAGC 59.194 37.037 0.00 0.00 37.28 4.09
1808 1855 5.049818 CAGTACAGCAAGTGAGGAGAAAAAG 60.050 44.000 0.00 0.00 0.00 2.27
1825 1872 3.190744 TGAACCTCTTCGCTACAGTACAG 59.809 47.826 0.00 0.00 0.00 2.74
1837 1884 5.183904 ACATAAAGGCAACATGAACCTCTTC 59.816 40.000 0.00 0.00 41.41 2.87
1838 1885 5.079643 ACATAAAGGCAACATGAACCTCTT 58.920 37.500 0.00 3.57 41.41 2.85
2043 2090 6.998074 ACAGACTTGTTGAAGATTGTTATGGA 59.002 34.615 0.00 0.00 32.28 3.41
2074 2121 6.692486 AGACACTGAGAACCAATTACACTAG 58.308 40.000 0.00 0.00 0.00 2.57
2075 2122 6.493802 AGAGACACTGAGAACCAATTACACTA 59.506 38.462 0.00 0.00 0.00 2.74
2104 2151 2.614057 CGTGCCCAGGATCTGATTAAAC 59.386 50.000 0.00 0.00 32.44 2.01
2371 2418 5.752892 ATGCAGCTATGAAAGACAATCAG 57.247 39.130 0.00 0.00 0.00 2.90
2616 2665 5.505780 TGTGGAAATTTTCTATCCGGTGAT 58.494 37.500 0.00 0.00 35.96 3.06
2708 2758 2.642311 TCTTGAAGGGTGGTAGCATTCA 59.358 45.455 0.00 1.35 43.31 2.57
2835 2887 6.703607 CAGAGGTATACTGGAAGCACAATAAG 59.296 42.308 2.25 0.00 37.60 1.73
3094 3146 5.079643 ACCTGCATAACAAGGTCAAATTCT 58.920 37.500 0.00 0.00 0.00 2.40
3435 3487 0.307760 CACTGCCCTTCAAACACGAC 59.692 55.000 0.00 0.00 0.00 4.34
3526 3578 0.107017 AACGATGCAGAATCCTGGGG 60.107 55.000 0.00 0.00 40.72 4.96
3558 3610 0.673022 GAGAAGCAGCACCCAGACTG 60.673 60.000 0.00 0.00 36.96 3.51
3572 3624 9.226606 CTCTACTACTTACTGATATGGGAGAAG 57.773 40.741 0.00 0.00 0.00 2.85
3682 3734 2.071540 TGAGAAAGAGCATCAACAGCG 58.928 47.619 0.00 0.00 37.82 5.18
4060 4126 5.953183 TGTTAATGCCATTCACAGAATCAC 58.047 37.500 0.37 0.00 0.00 3.06
4159 4225 7.520798 TGTCCCTAGGAAAACTCGTCTATATA 58.479 38.462 11.48 0.00 31.38 0.86
4335 4413 9.222916 GCACTCAAGAGACTTAAAAGTTAAAAC 57.777 33.333 3.73 0.00 39.88 2.43
4336 4414 9.174166 AGCACTCAAGAGACTTAAAAGTTAAAA 57.826 29.630 3.73 0.00 39.88 1.52
4337 4415 8.732746 AGCACTCAAGAGACTTAAAAGTTAAA 57.267 30.769 3.73 0.00 39.88 1.52
4338 4416 9.998106 ATAGCACTCAAGAGACTTAAAAGTTAA 57.002 29.630 3.73 0.00 39.88 2.01
4340 4418 9.425577 GTATAGCACTCAAGAGACTTAAAAGTT 57.574 33.333 3.73 0.00 39.88 2.66
4341 4419 8.808092 AGTATAGCACTCAAGAGACTTAAAAGT 58.192 33.333 3.73 0.00 35.48 2.66
4342 4420 9.081997 CAGTATAGCACTCAAGAGACTTAAAAG 57.918 37.037 3.73 0.00 34.26 2.27
4407 4485 8.925161 TGTTACAAAAATTAAGCATGATAGGC 57.075 30.769 0.00 0.00 0.00 3.93
4489 4567 6.968904 GCATAAAATAATGTATCTCCATGGCG 59.031 38.462 6.96 0.00 0.00 5.69
4494 4572 8.298854 GCATGTGCATAAAATAATGTATCTCCA 58.701 33.333 0.00 0.00 41.59 3.86
4532 4610 4.024438 GTCATGCGTGATTCAAAGAATCG 58.976 43.478 12.67 6.03 36.60 3.34
4589 4667 4.348486 TGGCCAATATGGTGAGCTAAAAA 58.652 39.130 0.61 0.00 40.46 1.94
4690 4769 7.492352 ACAAGATGAGTTTTTACCACTACAC 57.508 36.000 0.00 0.00 0.00 2.90
4773 4852 3.773860 AAAAAGTCATGCACAACGACA 57.226 38.095 9.31 0.00 31.92 4.35
4917 4996 3.131396 CCCAGTGTGTTGTACTCAAGAC 58.869 50.000 0.00 2.12 44.61 3.01
5257 5338 6.365970 AGTCTTCAAAGAGAATAGCAAGGA 57.634 37.500 0.00 0.00 35.32 3.36
5281 5362 7.498900 TCAACAGAAAACAGACTATGACACAAT 59.501 33.333 0.00 0.00 0.00 2.71
5315 5396 4.937620 TCCTGAAGTTGATGTATTCTGCAC 59.062 41.667 0.00 0.00 0.00 4.57
5440 5521 6.180472 ACAGATTCATAACTACCTTTGGTGG 58.820 40.000 0.00 0.00 40.15 4.61
5755 5837 7.178274 GGGAGGTATCATCTGCATATATAGGAG 59.822 44.444 0.00 0.00 0.00 3.69
5760 5842 5.798125 CGGGAGGTATCATCTGCATATAT 57.202 43.478 0.00 0.00 0.00 0.86
5816 5898 0.814457 TTGCGTTGACTGCCAAAGTT 59.186 45.000 0.00 0.00 40.07 2.66
5827 5909 2.135139 CAGTACAAGAGCTTGCGTTGA 58.865 47.619 9.99 0.81 44.03 3.18
5833 5915 3.070018 CACTTCCCAGTACAAGAGCTTG 58.930 50.000 8.60 8.60 45.58 4.01
6099 6219 5.885912 AGTAATTCCGTATCATGGCTTGTTT 59.114 36.000 0.00 0.00 0.00 2.83
6115 6235 8.515414 ACAAGCAAGTAAAATGAGAGTAATTCC 58.485 33.333 0.00 0.00 0.00 3.01
6143 6263 6.862711 TGAAACTAGACGATCGATGACTAT 57.137 37.500 24.34 2.60 0.00 2.12
6148 6268 4.673441 AGGTTGAAACTAGACGATCGATG 58.327 43.478 24.34 10.61 0.00 3.84
6154 6274 6.335471 TGACATAAGGTTGAAACTAGACGA 57.665 37.500 0.00 0.00 0.00 4.20
6193 6317 4.454161 AGCAAACAAAAAGGAAACAACACC 59.546 37.500 0.00 0.00 0.00 4.16
6202 6326 5.398603 TTCAGACAAGCAAACAAAAAGGA 57.601 34.783 0.00 0.00 0.00 3.36
6203 6327 6.480285 CAATTCAGACAAGCAAACAAAAAGG 58.520 36.000 0.00 0.00 0.00 3.11
6204 6328 5.961263 GCAATTCAGACAAGCAAACAAAAAG 59.039 36.000 0.00 0.00 0.00 2.27
6205 6329 5.642919 AGCAATTCAGACAAGCAAACAAAAA 59.357 32.000 0.00 0.00 0.00 1.94
6206 6330 5.063691 CAGCAATTCAGACAAGCAAACAAAA 59.936 36.000 0.00 0.00 0.00 2.44
6207 6331 4.567558 CAGCAATTCAGACAAGCAAACAAA 59.432 37.500 0.00 0.00 0.00 2.83
6208 6332 4.114073 CAGCAATTCAGACAAGCAAACAA 58.886 39.130 0.00 0.00 0.00 2.83
6209 6333 3.130869 ACAGCAATTCAGACAAGCAAACA 59.869 39.130 0.00 0.00 0.00 2.83
6210 6334 3.709987 ACAGCAATTCAGACAAGCAAAC 58.290 40.909 0.00 0.00 0.00 2.93
6211 6335 4.580167 AGTACAGCAATTCAGACAAGCAAA 59.420 37.500 0.00 0.00 0.00 3.68
6212 6336 4.136796 AGTACAGCAATTCAGACAAGCAA 58.863 39.130 0.00 0.00 0.00 3.91
6341 6465 0.750546 CTCGGTCCATACAGGGTCGA 60.751 60.000 0.00 0.00 38.92 4.20
6342 6466 0.750546 TCTCGGTCCATACAGGGTCG 60.751 60.000 0.00 0.00 38.24 4.79
6348 6472 2.298610 CAGTAGCTCTCGGTCCATACA 58.701 52.381 0.00 0.00 0.00 2.29
6379 6503 4.208686 CGCGTAGACCCTCAGGCC 62.209 72.222 0.00 0.00 36.11 5.19
6472 6596 1.725557 ATGTACGCTCTGCCGACGAT 61.726 55.000 0.00 0.00 0.00 3.73
6486 6610 3.726730 GCTTCGTGATCTTCGAGATGTAC 59.273 47.826 11.76 0.00 34.53 2.90
6527 6651 6.016192 CCAGGTCAGTTCTATATGATACACGT 60.016 42.308 0.00 0.00 0.00 4.49
6549 6673 2.094675 CCATCCCTACAAAGTTGCCAG 58.905 52.381 0.00 0.00 0.00 4.85
6597 6721 1.086634 GGTGGAAGTCTGCATCGCTC 61.087 60.000 0.00 0.00 0.00 5.03
6633 6757 3.528217 AACCCACCCAGGCCACATG 62.528 63.158 5.01 0.00 35.39 3.21
6683 6808 4.672801 GCTCTAAGCACATTACCAAAGCAC 60.673 45.833 0.00 0.00 41.89 4.40
6723 6848 4.877378 AAACCACTTGTCGTCCAGTATA 57.123 40.909 0.00 0.00 0.00 1.47
6727 6852 2.422127 ACAAAAACCACTTGTCGTCCAG 59.578 45.455 0.00 0.00 31.29 3.86
6763 6900 1.079503 GGGCAAAGTCTTAGTCGCAG 58.920 55.000 0.00 0.00 0.00 5.18
6795 6932 2.864946 CAGCAAACCATCTCATCGAGAG 59.135 50.000 0.00 0.00 42.26 3.20
6857 7006 2.974698 CATGGCGAATCCGAGGGC 60.975 66.667 0.00 0.00 38.22 5.19
6904 7053 3.146847 CTCAAGTCTTAACCAACCCACC 58.853 50.000 0.00 0.00 0.00 4.61
6933 7082 0.312102 CAGCTCGACTCCGCATGATA 59.688 55.000 0.00 0.00 35.37 2.15
6973 7122 4.082571 CCAGGTTTGAATTTCTGGCTAGTG 60.083 45.833 0.00 0.00 40.04 2.74
7054 8682 0.830648 CCGGATGGAGAGCTTGGTTA 59.169 55.000 0.00 0.00 37.49 2.85
7079 8707 2.590073 CACTTGTTTGTTGTGAACGCA 58.410 42.857 0.00 0.00 33.95 5.24
7084 8712 4.634004 CACTACTCCACTTGTTTGTTGTGA 59.366 41.667 0.00 0.00 36.84 3.58
7099 8727 0.877071 TTCGTGACGGACACTACTCC 59.123 55.000 4.70 0.00 46.24 3.85
7100 8728 1.728502 GCTTCGTGACGGACACTACTC 60.729 57.143 4.70 0.00 46.24 2.59
7101 8729 0.240411 GCTTCGTGACGGACACTACT 59.760 55.000 4.70 0.00 46.24 2.57
7102 8730 0.039798 TGCTTCGTGACGGACACTAC 60.040 55.000 4.70 0.00 46.24 2.73
7103 8731 0.669619 TTGCTTCGTGACGGACACTA 59.330 50.000 4.70 0.00 46.24 2.74
7107 8735 0.935196 AAACTTGCTTCGTGACGGAC 59.065 50.000 4.70 0.00 0.00 4.79
7127 8755 1.512926 CGGGATTCATGGTCGGATTC 58.487 55.000 0.00 0.00 0.00 2.52
7167 8824 4.149598 GGGTAGGGCAAATAAATAGGGTG 58.850 47.826 0.00 0.00 0.00 4.61
7222 8889 5.334724 GCCATCTATCTATGCTGCTTGTTTC 60.335 44.000 0.00 0.00 0.00 2.78
7225 8892 3.072038 TGCCATCTATCTATGCTGCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
7543 9282 1.000506 CGGGGGTGACGATATTGGTAG 59.999 57.143 0.00 0.00 0.00 3.18
7681 9420 2.022129 GCCAGACGTCGGACAACTG 61.022 63.158 24.32 18.34 0.00 3.16


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

AutoCloner maintained by Alex Coulton.