Multiple sequence alignment - TraesCS6B01G133000

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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 TraesCS6B01G133000 chr6B 100.000 5167 0 0 1 5167 129852689 129857855 0.000000e+00 9542.0
1 TraesCS6B01G133000 chr6B 94.221 571 27 5 4600 5167 525553769 525553202 0.000000e+00 867.0
2 TraesCS6B01G133000 chr6D 92.965 3710 183 29 641 4333 57897517 57901165 0.000000e+00 5334.0
3 TraesCS6B01G133000 chr6D 93.621 580 26 4 1 569 57896939 57897518 0.000000e+00 856.0
4 TraesCS6B01G133000 chr6D 98.214 112 2 0 1707 1818 3196380 3196491 4.080000e-46 196.0
5 TraesCS6B01G133000 chr6D 92.727 55 4 0 4420 4474 78781821 78781767 4.290000e-11 80.5
6 TraesCS6B01G133000 chr6A 93.592 2341 132 11 1997 4333 73067880 73070206 0.000000e+00 3476.0
7 TraesCS6B01G133000 chr6A 93.676 1439 72 10 290 1712 73066105 73067540 0.000000e+00 2135.0
8 TraesCS6B01G133000 chr6A 96.169 261 10 0 1 261 73065849 73066109 1.330000e-115 427.0
9 TraesCS6B01G133000 chr6A 95.767 189 8 0 1812 2000 73067535 73067723 6.500000e-79 305.0
10 TraesCS6B01G133000 chr6A 85.635 181 15 1 4419 4599 73070356 73070525 4.110000e-41 180.0
11 TraesCS6B01G133000 chr3B 94.415 573 26 4 4600 5167 667721168 667720597 0.000000e+00 876.0
12 TraesCS6B01G133000 chr3B 92.366 131 6 4 1697 1824 749650697 749650826 3.180000e-42 183.0
13 TraesCS6B01G133000 chr7B 94.386 570 25 6 4602 5167 719494658 719494092 0.000000e+00 869.0
14 TraesCS6B01G133000 chr7B 94.077 574 29 5 4597 5167 588082424 588082995 0.000000e+00 867.0
15 TraesCS6B01G133000 chr5B 94.346 566 29 3 4604 5167 477185760 477185196 0.000000e+00 865.0
16 TraesCS6B01G133000 chr5B 93.520 571 28 5 4600 5167 693116761 693116197 0.000000e+00 841.0
17 TraesCS6B01G133000 chr2B 93.565 575 31 6 4597 5167 523765424 523765996 0.000000e+00 852.0
18 TraesCS6B01G133000 chr2B 92.995 571 37 3 4600 5167 672103437 672104007 0.000000e+00 830.0
19 TraesCS6B01G133000 chr2B 95.082 122 5 1 1708 1829 588685010 588684890 1.900000e-44 191.0
20 TraesCS6B01G133000 chr2B 94.262 122 7 0 1705 1826 715014872 715014993 2.460000e-43 187.0
21 TraesCS6B01G133000 chr4B 92.832 572 34 6 4600 5167 571337598 571338166 0.000000e+00 822.0
22 TraesCS6B01G133000 chr2D 91.971 137 7 4 1682 1816 139026183 139026049 6.830000e-44 189.0
23 TraesCS6B01G133000 chr1D 95.000 120 6 0 1696 1815 48024742 48024623 6.830000e-44 189.0
24 TraesCS6B01G133000 chr3A 93.651 126 7 1 1694 1819 405503651 405503775 2.460000e-43 187.0
25 TraesCS6B01G133000 chr3A 89.928 139 10 4 1685 1821 73900933 73901069 5.320000e-40 176.0
26 TraesCS6B01G133000 chr2A 91.111 135 8 3 1684 1817 748822334 748822465 4.110000e-41 180.0
27 TraesCS6B01G133000 chr7A 79.259 135 21 7 4419 4550 86071639 86071769 2.560000e-13 87.9
28 TraesCS6B01G133000 chr7D 92.727 55 4 0 4419 4473 467041238 467041184 4.290000e-11 80.5
29 TraesCS6B01G133000 chr3D 94.118 51 3 0 4420 4470 536512188 536512238 1.540000e-10 78.7


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 TraesCS6B01G133000 chr6B 129852689 129857855 5166 False 9542.0 9542 100.0000 1 5167 1 chr6B.!!$F1 5166
1 TraesCS6B01G133000 chr6B 525553202 525553769 567 True 867.0 867 94.2210 4600 5167 1 chr6B.!!$R1 567
2 TraesCS6B01G133000 chr6D 57896939 57901165 4226 False 3095.0 5334 93.2930 1 4333 2 chr6D.!!$F2 4332
3 TraesCS6B01G133000 chr6A 73065849 73070525 4676 False 1304.6 3476 92.9678 1 4599 5 chr6A.!!$F1 4598
4 TraesCS6B01G133000 chr3B 667720597 667721168 571 True 876.0 876 94.4150 4600 5167 1 chr3B.!!$R1 567
5 TraesCS6B01G133000 chr7B 719494092 719494658 566 True 869.0 869 94.3860 4602 5167 1 chr7B.!!$R1 565
6 TraesCS6B01G133000 chr7B 588082424 588082995 571 False 867.0 867 94.0770 4597 5167 1 chr7B.!!$F1 570
7 TraesCS6B01G133000 chr5B 477185196 477185760 564 True 865.0 865 94.3460 4604 5167 1 chr5B.!!$R1 563
8 TraesCS6B01G133000 chr5B 693116197 693116761 564 True 841.0 841 93.5200 4600 5167 1 chr5B.!!$R2 567
9 TraesCS6B01G133000 chr2B 523765424 523765996 572 False 852.0 852 93.5650 4597 5167 1 chr2B.!!$F1 570
10 TraesCS6B01G133000 chr2B 672103437 672104007 570 False 830.0 830 92.9950 4600 5167 1 chr2B.!!$F2 567
11 TraesCS6B01G133000 chr4B 571337598 571338166 568 False 822.0 822 92.8320 4600 5167 1 chr4B.!!$F1 567

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
907 920 1.002430 TCCATCACACAGCCACTCTTC 59.998 52.381 0.00 0.00 0.00 2.87 F
1041 1056 0.107361 TGCAGATGTGGATGCTCCTG 60.107 55.000 0.00 0.00 42.98 3.86 F
2814 3000 0.325933 CATTGTGGGGAGCACTCTGA 59.674 55.000 0.00 0.00 0.00 3.27 F
3561 3747 1.078759 CGGAGCATGTCCTTGTCGAC 61.079 60.000 9.11 9.11 44.35 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 2845 0.033601 TGTTTGTCAGGGTTGGCAGT 60.034 50.000 0.00 0.00 40.59 4.40 R
3026 3212 1.273606 GGGCGCTCTGCAAGATAGATA 59.726 52.381 7.64 0.00 45.62 1.98 R
4128 4314 0.034896 CCAAGTTGGTACTCTGCCGT 59.965 55.000 14.21 0.00 31.99 5.68 R
4362 4596 0.113190 ATAGCTTGCTATTGGGGCCC 59.887 55.000 18.17 18.17 0.00 5.80 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
42 43 4.539726 CCTTTGATGAAATGGAGGATGGA 58.460 43.478 0.00 0.00 35.52 3.41
71 72 4.162131 TGGTGCTGAGAAATATGCTCACTA 59.838 41.667 4.82 0.00 37.46 2.74
196 197 7.608308 AGCTGAATTTGTTGAACTCTATCTC 57.392 36.000 0.00 0.00 0.00 2.75
197 198 6.597280 AGCTGAATTTGTTGAACTCTATCTCC 59.403 38.462 0.00 0.00 0.00 3.71
223 224 7.715265 ATGAGAGTTGTACTGTACTTTTGTG 57.285 36.000 17.98 0.00 0.00 3.33
224 225 6.636705 TGAGAGTTGTACTGTACTTTTGTGT 58.363 36.000 17.98 0.00 0.00 3.72
262 263 5.924356 TGTCTGTTTATCCTTGTTCAGTCA 58.076 37.500 0.00 0.00 0.00 3.41
272 273 4.104102 TCCTTGTTCAGTCATTAACCTGGT 59.896 41.667 0.00 0.00 0.00 4.00
394 400 2.486203 TCAGTGTGCGAGTGTTTTGTTT 59.514 40.909 0.00 0.00 0.00 2.83
424 430 3.117491 TCAGAGTCAGGAAAGCAACAG 57.883 47.619 0.00 0.00 0.00 3.16
441 452 4.705492 CAACAGTGATCATGTTCAAGTCG 58.295 43.478 15.99 0.00 38.80 4.18
465 476 5.616204 GCATTTTGATTTTTGAGGCTTCTGC 60.616 40.000 0.00 0.00 38.76 4.26
509 521 7.795047 TCTTGCTTCATCCTATAACATTCAGA 58.205 34.615 0.00 0.00 0.00 3.27
536 548 2.826128 TCATCTTGTAAGCGAGACACCT 59.174 45.455 0.00 0.00 37.92 4.00
540 552 3.570975 TCTTGTAAGCGAGACACCTTACA 59.429 43.478 8.64 8.64 46.83 2.41
547 559 2.673368 GCGAGACACCTTACATTTCCTG 59.327 50.000 0.00 0.00 0.00 3.86
555 567 4.399303 CACCTTACATTTCCTGGTTGATCC 59.601 45.833 0.00 0.00 0.00 3.36
567 579 1.956477 GGTTGATCCCACACATATGCC 59.044 52.381 1.58 0.00 0.00 4.40
574 586 2.109774 CCCACACATATGCCCATTGTT 58.890 47.619 1.58 0.00 0.00 2.83
575 587 2.159071 CCCACACATATGCCCATTGTTG 60.159 50.000 1.58 0.00 0.00 3.33
577 589 3.698539 CCACACATATGCCCATTGTTGTA 59.301 43.478 1.58 0.00 0.00 2.41
584 596 6.661377 ACATATGCCCATTGTTGTAGTGTTTA 59.339 34.615 1.58 0.00 0.00 2.01
585 597 7.341769 ACATATGCCCATTGTTGTAGTGTTTAT 59.658 33.333 1.58 0.00 0.00 1.40
588 600 4.321601 GCCCATTGTTGTAGTGTTTATGCA 60.322 41.667 0.00 0.00 0.00 3.96
590 602 5.401550 CCATTGTTGTAGTGTTTATGCAGG 58.598 41.667 0.00 0.00 0.00 4.85
612 624 4.389687 GGACATGCTTTTTAATGGTTGCTG 59.610 41.667 0.00 0.00 0.00 4.41
624 636 8.531622 TTTAATGGTTGCTGTCATGTTTATTG 57.468 30.769 0.00 0.00 0.00 1.90
662 674 3.209410 CTCTTATCCAGTTGGGCATGTC 58.791 50.000 0.00 0.00 36.21 3.06
677 690 4.479619 GGCATGTCTTTGATTGAGAACAC 58.520 43.478 0.00 0.00 0.00 3.32
684 697 8.731275 TGTCTTTGATTGAGAACACTTTTCTA 57.269 30.769 0.00 0.00 0.00 2.10
765 778 3.273434 GGATAACTTGCAGAGCATGTCA 58.727 45.455 10.35 0.00 44.18 3.58
777 790 1.002468 AGCATGTCACAAGAAACGCAC 60.002 47.619 0.00 0.00 0.00 5.34
797 810 1.812571 CGAAAAGGAGTGACCCATTGG 59.187 52.381 0.00 0.00 40.05 3.16
907 920 1.002430 TCCATCACACAGCCACTCTTC 59.998 52.381 0.00 0.00 0.00 2.87
1041 1056 0.107361 TGCAGATGTGGATGCTCCTG 60.107 55.000 0.00 0.00 42.98 3.86
1150 1165 2.663826 AGACGGTGAGAAGAATCTGC 57.336 50.000 0.00 0.00 35.54 4.26
1367 1392 5.767816 ACCGAAATGTTAGCTGTTCTTTT 57.232 34.783 0.00 0.00 0.00 2.27
1377 1402 9.732130 ATGTTAGCTGTTCTTTTAGAATCTCTT 57.268 29.630 0.00 0.00 36.50 2.85
1400 1425 1.063649 CATGCCGAGCTTCATGCAC 59.936 57.895 10.29 0.00 45.94 4.57
1403 1428 0.460811 TGCCGAGCTTCATGCACTAG 60.461 55.000 0.00 0.00 45.94 2.57
1431 1457 7.903995 ATCACAGAAAAGCTTTTTGTTGAAA 57.096 28.000 24.58 15.48 0.00 2.69
1441 1467 4.266265 GCTTTTTGTTGAAACTGACAGAGC 59.734 41.667 10.08 0.00 0.00 4.09
1453 1479 1.905922 GACAGAGCACTCAAAGGCGC 61.906 60.000 0.00 0.00 34.54 6.53
1670 1696 2.234414 GGCAATGCTCAAATCCCTTTCA 59.766 45.455 4.82 0.00 0.00 2.69
1720 1746 5.134725 TCCTAATTAGTACTCCCTCCGTT 57.865 43.478 11.50 0.00 0.00 4.44
1722 1748 4.023365 CCTAATTAGTACTCCCTCCGTTCG 60.023 50.000 11.50 0.00 0.00 3.95
1723 1749 1.755179 TTAGTACTCCCTCCGTTCGG 58.245 55.000 0.00 4.74 0.00 4.30
1726 1752 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
1729 1755 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1730 1756 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1735 1761 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
1738 1764 2.091588 CGTTCGGAATTACTTGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
1739 1765 3.319755 GTTCGGAATTACTTGTCGTGGA 58.680 45.455 0.00 0.00 0.00 4.02
1740 1766 3.663995 TCGGAATTACTTGTCGTGGAA 57.336 42.857 0.00 0.00 0.00 3.53
1741 1767 3.992643 TCGGAATTACTTGTCGTGGAAA 58.007 40.909 0.00 0.00 0.00 3.13
1743 1769 4.390603 TCGGAATTACTTGTCGTGGAAATG 59.609 41.667 0.00 0.00 0.00 2.32
1745 1771 4.698304 GGAATTACTTGTCGTGGAAATGGA 59.302 41.667 0.00 0.00 0.00 3.41
1746 1772 5.357032 GGAATTACTTGTCGTGGAAATGGAT 59.643 40.000 0.00 0.00 0.00 3.41
1747 1773 5.818136 ATTACTTGTCGTGGAAATGGATG 57.182 39.130 0.00 0.00 0.00 3.51
1748 1774 3.140325 ACTTGTCGTGGAAATGGATGT 57.860 42.857 0.00 0.00 0.00 3.06
1750 1776 4.843728 ACTTGTCGTGGAAATGGATGTAT 58.156 39.130 0.00 0.00 0.00 2.29
1751 1777 4.876107 ACTTGTCGTGGAAATGGATGTATC 59.124 41.667 0.00 0.00 0.00 2.24
1753 1779 5.862678 TGTCGTGGAAATGGATGTATCTA 57.137 39.130 0.00 0.00 0.00 1.98
1754 1780 5.842907 TGTCGTGGAAATGGATGTATCTAG 58.157 41.667 0.00 0.00 0.00 2.43
1755 1781 5.596772 TGTCGTGGAAATGGATGTATCTAGA 59.403 40.000 0.00 0.00 0.00 2.43
1756 1782 5.921408 GTCGTGGAAATGGATGTATCTAGAC 59.079 44.000 0.00 0.00 0.00 2.59
1757 1783 4.917998 CGTGGAAATGGATGTATCTAGACG 59.082 45.833 0.00 0.00 0.00 4.18
1760 1786 7.575155 CGTGGAAATGGATGTATCTAGACGTAT 60.575 40.741 0.00 0.00 0.00 3.06
1761 1787 8.088981 GTGGAAATGGATGTATCTAGACGTATT 58.911 37.037 0.00 0.00 0.00 1.89
1762 1788 8.647796 TGGAAATGGATGTATCTAGACGTATTT 58.352 33.333 0.00 0.00 0.00 1.40
1763 1789 9.490379 GGAAATGGATGTATCTAGACGTATTTT 57.510 33.333 0.00 0.00 0.00 1.82
1792 1818 8.007405 TCTAGATACATTCATTTCCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
1793 1819 8.138074 TCTAGATACATTCATTTCCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
1796 1822 8.258007 AGATACATTCATTTCCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
1799 1825 7.752695 ACATTCATTTCCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
1800 1826 6.737254 TTCATTTCCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
1802 1828 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
1808 1834 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
1832 1858 5.536916 GGGAGTACTATGCAGTGATACTCTT 59.463 44.000 20.62 0.00 37.75 2.85
1907 1934 0.665369 GGCATGTGCAGAACAACAGC 60.665 55.000 7.36 0.00 43.61 4.40
1913 1940 2.222027 GTGCAGAACAACAGCCTAACT 58.778 47.619 0.00 0.00 0.00 2.24
1969 1996 6.303839 TGAAAGACCTGTAATTGCTTTACCT 58.696 36.000 7.40 0.00 39.63 3.08
2008 2035 7.291182 ACCTCCTTAGCTCATACTGTGAAATAT 59.709 37.037 0.00 0.00 36.14 1.28
2009 2036 7.601886 CCTCCTTAGCTCATACTGTGAAATATG 59.398 40.741 0.00 0.00 36.14 1.78
2010 2037 8.250143 TCCTTAGCTCATACTGTGAAATATGA 57.750 34.615 0.00 0.00 36.14 2.15
2011 2038 8.874156 TCCTTAGCTCATACTGTGAAATATGAT 58.126 33.333 0.00 0.00 37.23 2.45
2012 2039 8.933807 CCTTAGCTCATACTGTGAAATATGATG 58.066 37.037 0.00 0.00 37.23 3.07
2018 2203 9.708092 CTCATACTGTGAAATATGATGATCACT 57.292 33.333 0.00 0.00 42.03 3.41
2107 2292 2.887152 ACAAAGGTCTGACTGCATTTCC 59.113 45.455 7.85 0.00 0.00 3.13
2134 2319 5.128033 TGCCCATTCCTGAATCTTGATTA 57.872 39.130 0.00 0.00 0.00 1.75
2140 2325 7.255381 CCCATTCCTGAATCTTGATTATGTGAC 60.255 40.741 0.00 0.00 0.00 3.67
2198 2383 3.555527 TCAATCCCAGAGAAGATGCTG 57.444 47.619 0.00 0.00 0.00 4.41
2272 2457 3.565905 CCAAAAGAGCTTGGCTAACTG 57.434 47.619 0.00 0.00 39.88 3.16
2419 2604 6.823182 CACATCCTCACATTACTGTAATTCCA 59.177 38.462 10.25 0.00 33.14 3.53
2454 2639 2.358247 CACTACACACGGTGGGGC 60.358 66.667 15.88 0.00 37.94 5.80
2457 2642 3.310860 CTACACACGGTGGGGCTCC 62.311 68.421 15.88 0.00 37.94 4.70
2458 2643 3.839046 TACACACGGTGGGGCTCCT 62.839 63.158 15.88 0.00 37.94 3.69
2512 2697 0.942962 CTGCCGGATTCAGCATTCTC 59.057 55.000 5.05 0.00 38.56 2.87
2527 2712 3.688272 CATTCTCGCTGCCAGTTTATTG 58.312 45.455 0.00 0.00 0.00 1.90
2545 2730 2.535012 TGACCATTGCTGTCGTTGTA 57.465 45.000 0.00 0.00 35.46 2.41
2547 2732 3.407698 TGACCATTGCTGTCGTTGTAAT 58.592 40.909 0.00 0.00 35.46 1.89
2549 2734 2.415168 ACCATTGCTGTCGTTGTAATCG 59.585 45.455 0.00 0.00 0.00 3.34
2562 2747 2.485903 TGTAATCGTGTTCGCAACCTT 58.514 42.857 0.00 0.00 36.96 3.50
2567 2752 0.934496 CGTGTTCGCAACCTTGAGAA 59.066 50.000 0.59 0.59 43.13 2.87
2613 2798 2.505557 GCACCTGAGCGCAATTGC 60.506 61.111 20.76 20.76 37.78 3.56
2660 2845 0.541863 GCCTCCTAAGCTAGGTGCAA 59.458 55.000 0.00 0.00 46.32 4.08
2666 2851 0.690192 TAAGCTAGGTGCAACTGCCA 59.310 50.000 16.44 4.40 45.94 4.92
2783 2969 7.652909 TCCATTGTTGTTTTGATCATTGAAGTC 59.347 33.333 0.00 0.00 0.00 3.01
2814 3000 0.325933 CATTGTGGGGAGCACTCTGA 59.674 55.000 0.00 0.00 0.00 3.27
2832 3018 3.144506 CTGAGAGATTGCACAAAGGTGT 58.855 45.455 0.00 0.00 46.95 4.16
2874 3060 2.935201 CCTCTCAAGAACTACAGCATGC 59.065 50.000 10.51 10.51 42.53 4.06
2904 3090 7.008992 GCATTGTTTCAGATAAGAATGTTCAGC 59.991 37.037 12.55 0.00 39.59 4.26
2962 3148 5.239306 CCTTCAAGTTCTTCACTGTTGCATA 59.761 40.000 0.00 0.00 35.12 3.14
3026 3212 1.439679 GAGAAACTCGGTTCGGCAAT 58.560 50.000 0.00 0.00 32.50 3.56
3035 3221 4.281182 ACTCGGTTCGGCAATATCTATCTT 59.719 41.667 0.00 0.00 0.00 2.40
3129 3315 8.684520 TCAGTTTCTTTATAGTAGCAGAGTACC 58.315 37.037 0.00 0.00 0.00 3.34
3248 3434 2.677003 CGAAAATGGCGGCTGACGT 61.677 57.895 11.43 0.00 46.52 4.34
3352 3538 1.276421 AGAGGCTGCTCGTGTACAAAT 59.724 47.619 0.00 0.00 0.00 2.32
3492 3678 1.681793 CTCGAATACCTCCATGACGGT 59.318 52.381 10.20 10.20 37.31 4.83
3561 3747 1.078759 CGGAGCATGTCCTTGTCGAC 61.079 60.000 9.11 9.11 44.35 4.20
3628 3814 2.338620 CACCGTCAGCGTCAGGAA 59.661 61.111 0.00 0.00 36.15 3.36
3645 3831 1.547372 GGAACTACTACGGACTGGCAA 59.453 52.381 0.00 0.00 0.00 4.52
3669 3855 2.567049 GCACTGAGCTACGTCGGT 59.433 61.111 0.00 0.00 41.15 4.69
3897 4083 2.682494 GTGCCGGTCAGGTCCCTA 60.682 66.667 1.90 0.00 43.70 3.53
3956 4142 5.718146 GGTAACTAAAGCTCGTCCTTACTT 58.282 41.667 0.00 0.00 0.00 2.24
3970 4156 5.220719 CGTCCTTACTTTGGTTTCTCGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
3992 4178 4.077188 GGCTGCTGCGTTGTCGTC 62.077 66.667 9.65 0.00 40.82 4.20
3993 4179 4.415501 GCTGCTGCGTTGTCGTCG 62.416 66.667 0.00 0.00 39.49 5.12
3994 4180 3.030308 CTGCTGCGTTGTCGTCGT 61.030 61.111 0.00 0.00 39.49 4.34
4010 4196 2.601763 CGTCGTAATGGAGTTTGCCTAC 59.398 50.000 0.00 0.00 0.00 3.18
4097 4283 1.153647 CACGGAAGAGGCGCACATA 60.154 57.895 10.83 0.00 0.00 2.29
4128 4314 2.194212 GGAGAGCTATCGCCGGTGA 61.194 63.158 22.04 22.04 35.55 4.02
4146 4332 1.270094 TGACGGCAGAGTACCAACTTG 60.270 52.381 0.00 0.00 35.56 3.16
4211 4426 3.106827 TGTCCTCACCATCAGCATAGAA 58.893 45.455 0.00 0.00 0.00 2.10
4212 4427 3.713248 TGTCCTCACCATCAGCATAGAAT 59.287 43.478 0.00 0.00 0.00 2.40
4213 4428 4.063689 GTCCTCACCATCAGCATAGAATG 58.936 47.826 0.00 0.00 0.00 2.67
4234 4449 7.655328 AGAATGCATCTATTGTACTCACTAAGC 59.345 37.037 0.00 0.00 36.32 3.09
4235 4450 5.601662 TGCATCTATTGTACTCACTAAGCC 58.398 41.667 0.00 0.00 0.00 4.35
4236 4451 5.128663 TGCATCTATTGTACTCACTAAGCCA 59.871 40.000 0.00 0.00 0.00 4.75
4302 4517 9.341078 ACTGTTTCAAGCAAATTATTTTTCCAT 57.659 25.926 0.00 0.00 0.00 3.41
4309 4524 9.001542 CAAGCAAATTATTTTTCCATCAAAGGA 57.998 29.630 0.00 0.00 35.41 3.36
4324 4539 6.239686 CCATCAAAGGAGAATTCTTGGGTTTT 60.240 38.462 9.87 4.03 0.00 2.43
4333 4548 8.590204 GGAGAATTCTTGGGTTTTATTTGGTTA 58.410 33.333 9.87 0.00 0.00 2.85
4362 4596 1.153823 CGCCCGGACTACACTTGAG 60.154 63.158 0.73 0.00 0.00 3.02
4364 4598 1.898154 CCCGGACTACACTTGAGGG 59.102 63.158 0.73 0.00 0.00 4.30
4377 4611 0.033208 TTGAGGGCCCCAATAGCAAG 60.033 55.000 21.43 0.00 0.00 4.01
4383 4617 1.889170 GGCCCCAATAGCAAGCTATTC 59.111 52.381 21.06 11.86 44.61 1.75
4386 4620 3.748668 GCCCCAATAGCAAGCTATTCTGA 60.749 47.826 21.06 0.00 44.61 3.27
4395 4629 3.737850 CAAGCTATTCTGATGGACCCTC 58.262 50.000 0.00 0.00 0.00 4.30
4398 4632 2.983296 CTATTCTGATGGACCCTCCCT 58.017 52.381 0.00 0.00 35.03 4.20
4399 4633 1.516110 ATTCTGATGGACCCTCCCTG 58.484 55.000 0.00 0.00 35.03 4.45
4400 4634 0.417437 TTCTGATGGACCCTCCCTGA 59.583 55.000 0.00 0.00 35.03 3.86
4403 4665 0.909610 TGATGGACCCTCCCTGACAC 60.910 60.000 0.00 0.00 35.03 3.67
4406 4668 0.490017 TGGACCCTCCCTGACACTTA 59.510 55.000 0.00 0.00 35.03 2.24
4429 4708 5.371526 AGCCCACATATCAAACAGATACTG 58.628 41.667 0.00 0.00 41.81 2.74
4444 4723 4.749099 CAGATACTGCACTTGATCTTAGCC 59.251 45.833 0.00 0.00 0.00 3.93
4450 4729 3.507233 TGCACTTGATCTTAGCCAAAAGG 59.493 43.478 0.00 0.00 0.00 3.11
4452 4731 4.379918 GCACTTGATCTTAGCCAAAAGGTC 60.380 45.833 0.00 0.00 37.17 3.85
4460 4739 2.930826 AGCCAAAAGGTCGAGAAAGA 57.069 45.000 0.00 0.00 0.00 2.52
4478 4757 9.831737 CGAGAAAGATATGATTTGAAACTTTGT 57.168 29.630 0.00 0.00 0.00 2.83
4504 4783 3.950395 CCCTCTCCTTTTATGGCTTCTTG 59.050 47.826 0.00 0.00 0.00 3.02
4516 4795 1.527433 GCTTCTTGGGCCAACTCCAC 61.527 60.000 16.66 0.05 33.43 4.02
4517 4796 0.895559 CTTCTTGGGCCAACTCCACC 60.896 60.000 16.66 0.00 33.43 4.61
4518 4797 1.650242 TTCTTGGGCCAACTCCACCA 61.650 55.000 16.66 0.00 33.43 4.17
4557 4836 6.294731 GGTGGGACTAAACGAAACTAAGAGTA 60.295 42.308 0.00 0.00 0.00 2.59
4558 4837 7.147976 GTGGGACTAAACGAAACTAAGAGTAA 58.852 38.462 0.00 0.00 0.00 2.24
4559 4838 7.653311 GTGGGACTAAACGAAACTAAGAGTAAA 59.347 37.037 0.00 0.00 0.00 2.01
4560 4839 7.653311 TGGGACTAAACGAAACTAAGAGTAAAC 59.347 37.037 0.00 0.00 0.00 2.01
4561 4840 7.869937 GGGACTAAACGAAACTAAGAGTAAACT 59.130 37.037 0.00 0.00 0.00 2.66
4562 4841 9.899226 GGACTAAACGAAACTAAGAGTAAACTA 57.101 33.333 0.00 0.00 0.00 2.24
4587 4866 7.986085 AGAGTTGCAGTGAGTATTAACAAAT 57.014 32.000 0.00 0.00 0.00 2.32
4588 4867 8.396272 AGAGTTGCAGTGAGTATTAACAAATT 57.604 30.769 0.00 0.00 0.00 1.82
4593 4872 9.672086 TTGCAGTGAGTATTAACAAATTTGTAC 57.328 29.630 23.53 17.21 41.31 2.90
4689 4968 9.056005 GCCCATTTCTTCTTTTTCTGTTAAAAT 57.944 29.630 0.00 0.00 0.00 1.82
4802 5082 3.931285 GCTGTTTGCAAACCTCTTTTG 57.069 42.857 33.33 17.59 46.57 2.44
4818 5098 7.564793 ACCTCTTTTGCCTCTTTTATTGTTTT 58.435 30.769 0.00 0.00 0.00 2.43
5107 5400 7.589587 CGATGAACAATTTTTAACTACACAGCA 59.410 33.333 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.277672 GCATATTTCTCAGCACCATCATGT 59.722 41.667 0.00 0.00 0.00 3.21
71 72 3.713764 ACCAAGGCTTGAGTGCTATATCT 59.286 43.478 28.18 0.00 0.00 1.98
196 197 7.226720 ACAAAAGTACAGTACAACTCTCATTGG 59.773 37.037 13.37 0.00 33.63 3.16
197 198 8.064222 CACAAAAGTACAGTACAACTCTCATTG 58.936 37.037 13.37 7.92 35.59 2.82
204 205 6.174760 TCCAACACAAAAGTACAGTACAACT 58.825 36.000 13.37 0.00 0.00 3.16
223 224 3.254166 ACAGACAATGTCATGCTTCCAAC 59.746 43.478 16.38 0.00 37.75 3.77
224 225 3.489355 ACAGACAATGTCATGCTTCCAA 58.511 40.909 16.38 0.00 37.75 3.53
262 263 3.056607 GCTGCAAACATGACCAGGTTAAT 60.057 43.478 0.00 0.00 33.87 1.40
272 273 1.618487 TGATGTGGCTGCAAACATGA 58.382 45.000 20.53 12.32 37.15 3.07
343 345 4.107127 TGGGCAACAATAACCTGTAACT 57.893 40.909 0.00 0.00 39.74 2.24
380 382 0.920664 GCACCAAACAAAACACTCGC 59.079 50.000 0.00 0.00 0.00 5.03
394 400 1.202806 CCTGACTCTGAAAAGGCACCA 60.203 52.381 0.00 0.00 29.06 4.17
424 430 4.346734 AATGCGACTTGAACATGATCAC 57.653 40.909 4.98 0.00 0.00 3.06
441 452 5.616204 GCAGAAGCCTCAAAAATCAAAATGC 60.616 40.000 0.00 0.00 33.58 3.56
509 521 5.536538 TGTCTCGCTTACAAGATGAGGATAT 59.463 40.000 10.10 0.00 33.50 1.63
536 548 4.202620 TGTGGGATCAACCAGGAAATGTAA 60.203 41.667 0.00 0.00 42.20 2.41
540 552 2.109834 TGTGTGGGATCAACCAGGAAAT 59.890 45.455 0.00 0.00 42.20 2.17
547 559 1.956477 GGCATATGTGTGGGATCAACC 59.044 52.381 4.29 0.00 38.08 3.77
555 567 2.496871 ACAACAATGGGCATATGTGTGG 59.503 45.455 4.29 0.59 0.00 4.17
567 579 5.182950 TCCTGCATAAACACTACAACAATGG 59.817 40.000 0.00 0.00 0.00 3.16
588 600 4.284234 AGCAACCATTAAAAAGCATGTCCT 59.716 37.500 0.00 0.00 0.00 3.85
590 602 4.990426 ACAGCAACCATTAAAAAGCATGTC 59.010 37.500 0.00 0.00 0.00 3.06
612 624 7.698130 GGAGTATTTGCAGTCAATAAACATGAC 59.302 37.037 0.00 0.00 45.94 3.06
624 636 3.618690 AGAGGTGGAGTATTTGCAGTC 57.381 47.619 0.00 0.00 0.00 3.51
765 778 2.011222 TCCTTTTCGTGCGTTTCTTGT 58.989 42.857 0.00 0.00 0.00 3.16
777 790 1.812571 CCAATGGGTCACTCCTTTTCG 59.187 52.381 0.00 0.00 36.25 3.46
907 920 5.678583 AGCCAGGCAAGCATATATACATAG 58.321 41.667 15.80 0.00 0.00 2.23
1150 1165 5.514204 CACTGCAAGACTCAGAAAAGTTTTG 59.486 40.000 5.36 3.66 41.74 2.44
1400 1425 5.382618 AAAGCTTTTCTGTGATTGGCTAG 57.617 39.130 5.69 0.00 0.00 3.42
1403 1428 4.571984 ACAAAAAGCTTTTCTGTGATTGGC 59.428 37.500 24.04 0.00 0.00 4.52
1431 1457 1.542108 GCCTTTGAGTGCTCTGTCAGT 60.542 52.381 0.00 0.00 0.00 3.41
1441 1467 2.501223 TAGACCCGCGCCTTTGAGTG 62.501 60.000 0.00 0.00 0.00 3.51
1453 1479 0.461961 CAGCTTCCCTTCTAGACCCG 59.538 60.000 0.00 0.00 0.00 5.28
1592 1618 2.559785 CAGGTCCCTGCATGAACAC 58.440 57.895 0.00 0.00 37.24 3.32
1641 1667 3.581024 TTTGAGCATTGCCATTGACTC 57.419 42.857 4.70 0.00 0.00 3.36
1670 1696 0.833834 ACTCAGCTACCCACAGTGCT 60.834 55.000 0.00 0.00 34.47 4.40
1720 1746 3.663995 TTCCACGACAAGTAATTCCGA 57.336 42.857 0.00 0.00 0.00 4.55
1722 1748 4.698304 TCCATTTCCACGACAAGTAATTCC 59.302 41.667 0.00 0.00 0.00 3.01
1723 1749 5.873179 TCCATTTCCACGACAAGTAATTC 57.127 39.130 0.00 0.00 0.00 2.17
1726 1752 4.647611 ACATCCATTTCCACGACAAGTAA 58.352 39.130 0.00 0.00 0.00 2.24
1729 1755 5.118990 AGATACATCCATTTCCACGACAAG 58.881 41.667 0.00 0.00 0.00 3.16
1730 1756 5.097742 AGATACATCCATTTCCACGACAA 57.902 39.130 0.00 0.00 0.00 3.18
1735 1761 5.844004 ACGTCTAGATACATCCATTTCCAC 58.156 41.667 0.00 0.00 0.00 4.02
1762 1788 9.967346 CTCGGAAATGAATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
1763 1789 9.350951 TCTCGGAAATGAATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
1764 1790 8.138712 GTCTCGGAAATGAATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
1765 1791 7.921214 TGTCTCGGAAATGAATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
1766 1792 8.007405 TGTCTCGGAAATGAATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
1768 1794 7.923344 ACTTGTCTCGGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
1769 1795 7.782049 ACTTGTCTCGGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
1771 1797 6.910536 ACTTGTCTCGGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
1773 1799 8.786826 AATTACTTGTCTCGGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
1774 1800 7.148239 GGAATTACTTGTCTCGGAAATGAATGT 60.148 37.037 0.00 0.00 0.00 2.71
1775 1801 7.189512 GGAATTACTTGTCTCGGAAATGAATG 58.810 38.462 0.00 0.00 0.00 2.67
1776 1802 6.037172 CGGAATTACTTGTCTCGGAAATGAAT 59.963 38.462 0.00 0.00 0.00 2.57
1777 1803 5.350365 CGGAATTACTTGTCTCGGAAATGAA 59.650 40.000 0.00 0.00 0.00 2.57
1778 1804 4.868171 CGGAATTACTTGTCTCGGAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1779 1805 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
1780 1806 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
1781 1807 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
1782 1808 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
1783 1809 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
1784 1810 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
1785 1811 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
1792 1818 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1793 1819 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1796 1822 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
1799 1825 1.607628 CATAGTACTCCCTCCGTTCGG 59.392 57.143 0.00 4.74 0.00 4.30
1800 1826 1.001597 GCATAGTACTCCCTCCGTTCG 60.002 57.143 0.00 0.00 0.00 3.95
1802 1828 2.032620 CTGCATAGTACTCCCTCCGTT 58.967 52.381 0.00 0.00 0.00 4.44
1808 1834 5.074115 AGAGTATCACTGCATAGTACTCCC 58.926 45.833 17.73 0.00 39.34 4.30
1832 1858 6.461788 GCATTTAACCACAAACTACCAGGAAA 60.462 38.462 0.00 0.00 0.00 3.13
1907 1934 1.825474 ACATCGAGTGTCCCAGTTAGG 59.175 52.381 0.00 0.00 35.77 2.69
1969 1996 7.783119 TGAGCTAAGGAGGTATCTGTGTAAATA 59.217 37.037 0.00 0.00 32.11 1.40
2008 2035 4.336713 CGTCAAGGAGTAGAGTGATCATCA 59.663 45.833 0.00 0.00 0.00 3.07
2009 2036 4.576873 TCGTCAAGGAGTAGAGTGATCATC 59.423 45.833 0.00 0.00 0.00 2.92
2010 2037 4.527944 TCGTCAAGGAGTAGAGTGATCAT 58.472 43.478 0.00 0.00 0.00 2.45
2011 2038 3.942115 CTCGTCAAGGAGTAGAGTGATCA 59.058 47.826 0.00 0.00 0.00 2.92
2012 2039 4.193090 TCTCGTCAAGGAGTAGAGTGATC 58.807 47.826 0.16 0.00 35.52 2.92
2018 2203 4.331992 CACGTTATCTCGTCAAGGAGTAGA 59.668 45.833 0.00 0.00 42.27 2.59
2107 2292 1.111116 ATTCAGGAATGGGCATGCGG 61.111 55.000 12.44 0.00 0.00 5.69
2134 2319 3.751175 CACATTCCTGTAAACGGTCACAT 59.249 43.478 0.00 0.00 33.14 3.21
2140 2325 3.328382 TCTCCACATTCCTGTAAACGG 57.672 47.619 0.00 0.00 33.14 4.44
2198 2383 8.360390 AGTTCTTACAGAAATTTTGGGATGTTC 58.640 33.333 0.00 0.00 35.75 3.18
2272 2457 1.176527 TGATTTGTTAGGCAGGCAGC 58.823 50.000 0.00 0.00 44.65 5.25
2323 2508 1.622811 GGAATGGTGAAATGGTTGCCA 59.377 47.619 0.00 0.00 38.19 4.92
2371 2556 0.448593 CTGGAGAAGGAGACGACGTC 59.551 60.000 20.25 20.25 0.00 4.34
2419 2604 1.344763 GTGTCCTGTGGAGTAACTGCT 59.655 52.381 0.00 0.00 29.39 4.24
2457 2642 4.680237 TGTTGGCGTGCCTCCGAG 62.680 66.667 12.84 0.00 36.94 4.63
2458 2643 4.243008 TTGTTGGCGTGCCTCCGA 62.243 61.111 12.84 0.00 36.94 4.55
2512 2697 1.164411 TGGTCAATAAACTGGCAGCG 58.836 50.000 15.89 0.00 0.00 5.18
2527 2712 3.483574 CGATTACAACGACAGCAATGGTC 60.484 47.826 0.00 0.00 0.00 4.02
2545 2730 1.531149 CTCAAGGTTGCGAACACGATT 59.469 47.619 0.00 0.00 0.00 3.34
2547 2732 0.103390 TCTCAAGGTTGCGAACACGA 59.897 50.000 0.00 0.00 0.00 4.35
2549 2734 1.264288 CCTTCTCAAGGTTGCGAACAC 59.736 52.381 0.00 0.00 43.95 3.32
2562 2747 1.687146 ATCTCCTGCCGCCTTCTCA 60.687 57.895 0.00 0.00 0.00 3.27
2567 2752 3.474570 GGACATCTCCTGCCGCCT 61.475 66.667 0.00 0.00 33.07 5.52
2613 2798 2.169789 CAGATTGCCACGCTCCTCG 61.170 63.158 0.00 0.00 45.38 4.63
2660 2845 0.033601 TGTTTGTCAGGGTTGGCAGT 60.034 50.000 0.00 0.00 40.59 4.40
2666 2851 2.802719 ACTGTGTTGTTTGTCAGGGTT 58.197 42.857 0.00 0.00 32.92 4.11
2757 2943 7.499292 ACTTCAATGATCAAAACAACAATGGA 58.501 30.769 0.00 0.00 0.00 3.41
2783 2969 1.342555 CCACAATGTCATTTGCAGCG 58.657 50.000 0.00 0.00 0.00 5.18
2814 3000 2.146342 CGACACCTTTGTGCAATCTCT 58.854 47.619 0.00 0.00 46.86 3.10
2832 3018 1.481363 TGTATGTGCCGATAAACCCGA 59.519 47.619 0.00 0.00 0.00 5.14
2874 3060 7.318141 ACATTCTTATCTGAAACAATGCTTGG 58.682 34.615 0.00 0.00 34.12 3.61
2904 3090 2.124507 TTGCCTTCTTCTGACCCCCG 62.125 60.000 0.00 0.00 0.00 5.73
2992 3178 5.604010 AGTTTCTCGCAGAAAATTCTCAG 57.396 39.130 11.33 0.00 44.84 3.35
3026 3212 1.273606 GGGCGCTCTGCAAGATAGATA 59.726 52.381 7.64 0.00 45.62 1.98
3121 3307 5.799213 ACAGGAAAAAGAGATGGTACTCTG 58.201 41.667 0.00 0.00 45.08 3.35
3248 3434 3.399330 GTCCGAACATTCTCCAGAAACA 58.601 45.455 0.00 0.00 37.61 2.83
3352 3538 4.068599 TCCAATGTGTGTTCGCTGAAATA 58.931 39.130 0.00 0.00 0.00 1.40
3628 3814 1.817447 GTCTTGCCAGTCCGTAGTAGT 59.183 52.381 0.00 0.00 0.00 2.73
3897 4083 1.518572 GATGTCCGCGAACCGTGAT 60.519 57.895 8.23 0.00 39.94 3.06
3940 4126 3.487120 ACCAAAGTAAGGACGAGCTTT 57.513 42.857 0.00 0.00 0.00 3.51
3948 4134 6.117488 AGAAAACGAGAAACCAAAGTAAGGA 58.883 36.000 0.00 0.00 0.00 3.36
3949 4135 6.373186 AGAAAACGAGAAACCAAAGTAAGG 57.627 37.500 0.00 0.00 0.00 2.69
3951 4137 6.404954 CCCAAGAAAACGAGAAACCAAAGTAA 60.405 38.462 0.00 0.00 0.00 2.24
3953 4139 4.142249 CCCAAGAAAACGAGAAACCAAAGT 60.142 41.667 0.00 0.00 0.00 2.66
3956 4142 2.100087 GCCCAAGAAAACGAGAAACCAA 59.900 45.455 0.00 0.00 0.00 3.67
3970 4156 2.979676 CAACGCAGCAGCCCAAGA 60.980 61.111 0.00 0.00 37.52 3.02
3992 4178 2.347452 CACGTAGGCAAACTCCATTACG 59.653 50.000 0.00 0.88 36.74 3.18
3993 4179 2.095372 GCACGTAGGCAAACTCCATTAC 59.905 50.000 0.00 0.00 0.00 1.89
3994 4180 2.289756 TGCACGTAGGCAAACTCCATTA 60.290 45.455 0.00 0.00 41.65 1.90
4078 4264 2.572095 TATGTGCGCCTCTTCCGTGG 62.572 60.000 4.18 0.00 0.00 4.94
4079 4265 1.148157 CTATGTGCGCCTCTTCCGTG 61.148 60.000 4.18 0.00 0.00 4.94
4080 4266 1.141881 CTATGTGCGCCTCTTCCGT 59.858 57.895 4.18 0.00 0.00 4.69
4093 4279 1.516386 CCGCAGTCGTTCGCTATGT 60.516 57.895 0.00 0.00 0.00 2.29
4097 4283 3.329688 CTCTCCGCAGTCGTTCGCT 62.330 63.158 0.00 0.00 0.00 4.93
4101 4287 0.382515 GATAGCTCTCCGCAGTCGTT 59.617 55.000 0.00 0.00 42.61 3.85
4128 4314 0.034896 CCAAGTTGGTACTCTGCCGT 59.965 55.000 14.21 0.00 31.99 5.68
4146 4332 1.005630 AGAGCGAGCAGTTCACACC 60.006 57.895 0.00 0.00 31.99 4.16
4211 4426 6.183361 TGGCTTAGTGAGTACAATAGATGCAT 60.183 38.462 0.00 0.00 0.00 3.96
4212 4427 5.128663 TGGCTTAGTGAGTACAATAGATGCA 59.871 40.000 0.00 0.00 0.00 3.96
4213 4428 5.601662 TGGCTTAGTGAGTACAATAGATGC 58.398 41.667 0.00 0.00 0.00 3.91
4214 4429 8.668510 AAATGGCTTAGTGAGTACAATAGATG 57.331 34.615 0.00 0.00 0.00 2.90
4215 4430 9.765795 GTAAATGGCTTAGTGAGTACAATAGAT 57.234 33.333 0.00 0.00 0.00 1.98
4216 4431 8.978472 AGTAAATGGCTTAGTGAGTACAATAGA 58.022 33.333 0.00 0.00 0.00 1.98
4219 4434 9.547753 CATAGTAAATGGCTTAGTGAGTACAAT 57.452 33.333 0.00 0.00 0.00 2.71
4220 4435 7.494625 GCATAGTAAATGGCTTAGTGAGTACAA 59.505 37.037 0.00 0.00 0.00 2.41
4221 4436 6.984474 GCATAGTAAATGGCTTAGTGAGTACA 59.016 38.462 0.00 0.00 0.00 2.90
4222 4437 7.169982 CAGCATAGTAAATGGCTTAGTGAGTAC 59.830 40.741 0.00 0.00 33.60 2.73
4223 4438 7.210174 CAGCATAGTAAATGGCTTAGTGAGTA 58.790 38.462 0.00 0.00 33.60 2.59
4224 4439 6.051717 CAGCATAGTAAATGGCTTAGTGAGT 58.948 40.000 0.00 0.00 33.60 3.41
4225 4440 5.049818 GCAGCATAGTAAATGGCTTAGTGAG 60.050 44.000 0.00 0.00 33.60 3.51
4226 4441 4.816385 GCAGCATAGTAAATGGCTTAGTGA 59.184 41.667 0.00 0.00 33.60 3.41
4227 4442 4.576053 TGCAGCATAGTAAATGGCTTAGTG 59.424 41.667 0.00 0.00 33.60 2.74
4228 4443 4.780815 TGCAGCATAGTAAATGGCTTAGT 58.219 39.130 0.00 0.00 33.60 2.24
4229 4444 5.954296 ATGCAGCATAGTAAATGGCTTAG 57.046 39.130 5.94 0.00 33.60 2.18
4230 4445 5.507817 GCAATGCAGCATAGTAAATGGCTTA 60.508 40.000 8.75 0.00 33.60 3.09
4231 4446 4.738541 GCAATGCAGCATAGTAAATGGCTT 60.739 41.667 8.75 0.00 33.60 4.35
4232 4447 3.243636 GCAATGCAGCATAGTAAATGGCT 60.244 43.478 8.75 0.00 36.99 4.75
4233 4448 3.054878 GCAATGCAGCATAGTAAATGGC 58.945 45.455 8.75 0.00 0.00 4.40
4234 4449 3.319972 AGGCAATGCAGCATAGTAAATGG 59.680 43.478 8.75 0.00 35.83 3.16
4235 4450 4.579454 AGGCAATGCAGCATAGTAAATG 57.421 40.909 8.75 3.05 35.83 2.32
4236 4451 5.127519 TCAAAGGCAATGCAGCATAGTAAAT 59.872 36.000 8.75 0.00 35.83 1.40
4243 4458 2.100916 GAGATCAAAGGCAATGCAGCAT 59.899 45.455 7.79 0.52 35.83 3.79
4302 4517 8.491045 AATAAAACCCAAGAATTCTCCTTTGA 57.509 30.769 8.78 0.00 0.00 2.69
4324 4539 3.628487 GCGTTGCACCCTATAACCAAATA 59.372 43.478 0.00 0.00 0.00 1.40
4333 4548 4.483243 CCGGGCGTTGCACCCTAT 62.483 66.667 9.08 0.00 46.04 2.57
4337 4552 4.382320 TAGTCCGGGCGTTGCACC 62.382 66.667 0.00 0.00 0.00 5.01
4353 4587 1.843851 CTATTGGGGCCCTCAAGTGTA 59.156 52.381 25.93 12.16 0.00 2.90
4362 4596 0.113190 ATAGCTTGCTATTGGGGCCC 59.887 55.000 18.17 18.17 0.00 5.80
4364 4598 2.555757 CAGAATAGCTTGCTATTGGGGC 59.444 50.000 26.41 14.97 30.47 5.80
4377 4611 1.349357 GGGAGGGTCCATCAGAATAGC 59.651 57.143 5.78 0.00 38.64 2.97
4383 4617 0.618680 TGTCAGGGAGGGTCCATCAG 60.619 60.000 5.78 0.00 38.64 2.90
4386 4620 0.178861 AAGTGTCAGGGAGGGTCCAT 60.179 55.000 0.00 0.00 38.64 3.41
4395 4629 0.620556 ATGTGGGCTAAGTGTCAGGG 59.379 55.000 0.00 0.00 0.00 4.45
4398 4632 4.835284 TTGATATGTGGGCTAAGTGTCA 57.165 40.909 0.00 0.00 0.00 3.58
4399 4633 4.941263 TGTTTGATATGTGGGCTAAGTGTC 59.059 41.667 0.00 0.00 0.00 3.67
4400 4634 4.917385 TGTTTGATATGTGGGCTAAGTGT 58.083 39.130 0.00 0.00 0.00 3.55
4403 4665 7.172190 CAGTATCTGTTTGATATGTGGGCTAAG 59.828 40.741 0.00 0.00 39.56 2.18
4406 4668 5.371526 CAGTATCTGTTTGATATGTGGGCT 58.628 41.667 0.00 0.00 39.56 5.19
4429 4708 3.507622 ACCTTTTGGCTAAGATCAAGTGC 59.492 43.478 0.00 0.00 45.59 4.40
4444 4723 8.668353 TCAAATCATATCTTTCTCGACCTTTTG 58.332 33.333 0.00 0.00 0.00 2.44
4452 4731 9.831737 ACAAAGTTTCAAATCATATCTTTCTCG 57.168 29.630 0.00 0.00 0.00 4.04
4460 4739 7.184862 AGGGAGGACAAAGTTTCAAATCATAT 58.815 34.615 0.00 0.00 0.00 1.78
4478 4757 2.127708 GCCATAAAAGGAGAGGGAGGA 58.872 52.381 0.00 0.00 0.00 3.71
4482 4761 3.941704 AGAAGCCATAAAAGGAGAGGG 57.058 47.619 0.00 0.00 0.00 4.30
4504 4783 4.265056 ACGTGGTGGAGTTGGCCC 62.265 66.667 0.00 0.00 0.00 5.80
4529 4808 2.064014 GTTTCGTTTAGTCCCACCTCG 58.936 52.381 0.00 0.00 0.00 4.63
4557 4836 8.989980 GTTAATACTCACTGCAACTCTTAGTTT 58.010 33.333 0.00 0.00 36.03 2.66
4558 4837 8.148351 TGTTAATACTCACTGCAACTCTTAGTT 58.852 33.333 0.00 0.00 39.39 2.24
4559 4838 7.667557 TGTTAATACTCACTGCAACTCTTAGT 58.332 34.615 0.00 0.00 0.00 2.24
4560 4839 8.534333 TTGTTAATACTCACTGCAACTCTTAG 57.466 34.615 0.00 0.00 0.00 2.18
4561 4840 8.896320 TTTGTTAATACTCACTGCAACTCTTA 57.104 30.769 0.00 0.00 0.00 2.10
4562 4841 7.801716 TTTGTTAATACTCACTGCAACTCTT 57.198 32.000 0.00 0.00 0.00 2.85
4563 4842 7.986085 ATTTGTTAATACTCACTGCAACTCT 57.014 32.000 0.00 0.00 0.00 3.24
4564 4843 8.905702 CAAATTTGTTAATACTCACTGCAACTC 58.094 33.333 10.15 0.00 0.00 3.01
4565 4844 8.413229 ACAAATTTGTTAATACTCACTGCAACT 58.587 29.630 18.13 0.00 38.47 3.16
4566 4845 8.574196 ACAAATTTGTTAATACTCACTGCAAC 57.426 30.769 18.13 0.00 38.47 4.17
4567 4846 9.672086 GTACAAATTTGTTAATACTCACTGCAA 57.328 29.630 27.66 2.33 42.35 4.08
4587 4866 1.228306 CAACGGGGGCAGGTACAAA 60.228 57.895 0.00 0.00 0.00 2.83
4588 4867 2.432563 CAACGGGGGCAGGTACAA 59.567 61.111 0.00 0.00 0.00 2.41
4802 5082 5.853936 ACCTGGAAAAACAATAAAAGAGGC 58.146 37.500 0.00 0.00 0.00 4.70
4818 5098 2.178912 AAAAATCTCGCGACCTGGAA 57.821 45.000 3.71 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.