Multiple sequence alignment - TraesCS2D01G233300

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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 TraesCS2D01G233300 chr2D 100.000 3928 0 0 1 3928 207278059 207274132 0.000000e+00 7254.0
1 TraesCS2D01G233300 chr2B 95.884 1142 33 6 2118 3259 260606096 260607223 0.000000e+00 1836.0
2 TraesCS2D01G233300 chr2B 90.826 654 37 7 745 1389 260605443 260606082 0.000000e+00 854.0
3 TraesCS2D01G233300 chr2B 89.599 673 42 11 3257 3926 260607307 260607954 0.000000e+00 830.0
4 TraesCS2D01G233300 chr2B 82.243 749 113 15 1 739 11465387 11464649 2.580000e-176 628.0
5 TraesCS2D01G233300 chr2B 90.698 43 4 0 3790 3832 694245186 694245228 1.520000e-04 58.4
6 TraesCS2D01G233300 chr2A 94.185 963 44 9 746 1700 257780181 257781139 0.000000e+00 1458.0
7 TraesCS2D01G233300 chr2A 94.980 737 27 5 2501 3235 257781660 257782388 0.000000e+00 1147.0
8 TraesCS2D01G233300 chr2A 97.619 336 8 0 2117 2452 257781323 257781658 9.460000e-161 577.0
9 TraesCS2D01G233300 chr2A 90.840 262 16 2 3372 3633 257782441 257782694 1.040000e-90 344.0
10 TraesCS2D01G233300 chr2A 96.512 172 6 0 1960 2131 257781136 257781307 6.420000e-73 285.0
11 TraesCS2D01G233300 chr2A 96.341 164 5 1 3766 3928 257782726 257782889 6.470000e-68 268.0
12 TraesCS2D01G233300 chr2A 82.443 131 21 2 3774 3902 715383334 715383464 3.210000e-21 113.0
13 TraesCS2D01G233300 chr5A 85.901 1227 113 32 2016 3205 700596316 700597519 0.000000e+00 1253.0
14 TraesCS2D01G233300 chr5A 81.907 514 56 23 994 1477 700595794 700596300 2.200000e-107 399.0
15 TraesCS2D01G233300 chrUn 88.706 974 79 13 2139 3095 110648694 110649653 0.000000e+00 1160.0
16 TraesCS2D01G233300 chr4B 87.541 907 76 18 2074 2950 660653092 660653991 0.000000e+00 1014.0
17 TraesCS2D01G233300 chr4B 86.486 259 18 10 994 1235 660652551 660652809 6.470000e-68 268.0
18 TraesCS2D01G233300 chr4B 93.023 43 3 0 691 733 671680836 671680878 3.280000e-06 63.9
19 TraesCS2D01G233300 chr3D 85.606 132 17 1 3778 3907 595208336 595208205 1.900000e-28 137.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G233300 chr2D 207274132 207278059 3927 True 7254.000000 7254 100.0000 1 3928 1 chr2D.!!$R1 3927
1 TraesCS2D01G233300 chr2B 260605443 260607954 2511 False 1173.333333 1836 92.1030 745 3926 3 chr2B.!!$F2 3181
2 TraesCS2D01G233300 chr2B 11464649 11465387 738 True 628.000000 628 82.2430 1 739 1 chr2B.!!$R1 738
3 TraesCS2D01G233300 chr2A 257780181 257782889 2708 False 679.833333 1458 95.0795 746 3928 6 chr2A.!!$F2 3182
4 TraesCS2D01G233300 chr5A 700595794 700597519 1725 False 826.000000 1253 83.9040 994 3205 2 chr5A.!!$F1 2211
5 TraesCS2D01G233300 chrUn 110648694 110649653 959 False 1160.000000 1160 88.7060 2139 3095 1 chrUn.!!$F1 956
6 TraesCS2D01G233300 chr4B 660652551 660653991 1440 False 641.000000 1014 87.0135 994 2950 2 chr4B.!!$F2 1956

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
183 190 0.029567 TCGTCGCCGTTTTGCAAATT 59.970 45.0 13.65 0.0 35.01 1.82 F
1291 1353 0.105039 GGTGCCGATCTTCTCCGAAT 59.895 55.0 0.00 0.0 0.00 3.34 F
1956 2034 0.105408 AAAAAGGGCTTGCTGTGCTG 59.895 50.0 0.00 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1989 0.037303 TGAGAAGAGCCAAGCCCTTG 59.963 55.000 1.05 1.05 40.13 3.61 R
2169 2289 2.800985 CGATAGCTGTCCATGTCACTGG 60.801 54.545 4.73 0.00 37.66 4.00 R
3657 3921 0.107831 CTCCCTTCGTGGAACCACAA 59.892 55.000 21.41 13.93 46.47 3.33 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
25 26 3.253921 GGCCATGTTACGTAACCTTTTGT 59.746 43.478 30.20 10.70 35.37 2.83
38 39 7.227116 ACGTAACCTTTTGTAACAAAGCTCATA 59.773 33.333 0.00 0.00 0.00 2.15
41 42 8.816640 AACCTTTTGTAACAAAGCTCATATTG 57.183 30.769 0.00 0.00 0.00 1.90
45 46 6.816134 TTGTAACAAAGCTCATATTGCAGA 57.184 33.333 0.00 0.00 0.00 4.26
48 49 7.656412 TGTAACAAAGCTCATATTGCAGAAAA 58.344 30.769 0.00 0.00 0.00 2.29
49 50 8.140628 TGTAACAAAGCTCATATTGCAGAAAAA 58.859 29.630 0.00 0.00 0.00 1.94
65 66 9.606631 TTGCAGAAAAATATTTACAACAAAGGT 57.393 25.926 0.01 0.00 0.00 3.50
66 67 9.606631 TGCAGAAAAATATTTACAACAAAGGTT 57.393 25.926 0.01 0.00 37.87 3.50
76 77 3.229276 CAACAAAGGTTGTGTTGCAGA 57.771 42.857 4.52 0.00 46.63 4.26
115 122 2.492019 CAGCATGGATGATGTTGCAG 57.508 50.000 0.00 0.00 39.22 4.41
116 123 2.021457 CAGCATGGATGATGTTGCAGA 58.979 47.619 0.00 0.00 39.22 4.26
117 124 2.425668 CAGCATGGATGATGTTGCAGAA 59.574 45.455 0.00 0.00 39.22 3.02
118 125 3.068165 CAGCATGGATGATGTTGCAGAAT 59.932 43.478 0.00 0.00 39.22 2.40
157 164 2.745100 GCAGCAGCAGCACTAGCA 60.745 61.111 4.63 0.00 45.49 3.49
164 171 0.036952 AGCAGCACTAGCATCGTTGT 60.037 50.000 0.00 0.00 45.49 3.32
181 188 1.297745 GTCGTCGCCGTTTTGCAAA 60.298 52.632 8.05 8.05 35.01 3.68
183 190 0.029567 TCGTCGCCGTTTTGCAAATT 59.970 45.000 13.65 0.00 35.01 1.82
212 219 5.384063 TGTTGCAAATATTCATCGGTGTT 57.616 34.783 0.00 0.00 0.00 3.32
213 220 5.159925 TGTTGCAAATATTCATCGGTGTTG 58.840 37.500 0.00 0.00 0.00 3.33
214 221 3.768406 TGCAAATATTCATCGGTGTTGC 58.232 40.909 12.57 12.57 40.15 4.17
217 224 3.944422 AATATTCATCGGTGTTGCGAC 57.056 42.857 0.00 0.00 0.00 5.19
302 310 4.329545 TCCTGCACCCACTTCGCC 62.330 66.667 0.00 0.00 0.00 5.54
323 331 0.323629 CCAGCAACGGAAACCTCCTA 59.676 55.000 0.00 0.00 39.93 2.94
324 332 1.065418 CCAGCAACGGAAACCTCCTAT 60.065 52.381 0.00 0.00 39.93 2.57
331 339 0.837940 GGAAACCTCCTATCGGGCTT 59.162 55.000 0.00 0.00 38.88 4.35
332 340 1.475213 GGAAACCTCCTATCGGGCTTG 60.475 57.143 0.00 0.00 38.88 4.01
362 370 4.883354 GGCGGCCAAGGGGATGAG 62.883 72.222 15.62 0.00 35.59 2.90
364 372 4.113815 CGGCCAAGGGGATGAGCA 62.114 66.667 2.24 0.00 35.59 4.26
365 373 2.440980 GGCCAAGGGGATGAGCAC 60.441 66.667 0.00 0.00 35.59 4.40
375 383 1.141881 GATGAGCACCGTCCGACAT 59.858 57.895 0.00 0.00 0.00 3.06
385 393 4.128580 TCCGACATGGAAGGCTGA 57.871 55.556 0.00 0.00 46.38 4.26
386 394 1.900351 TCCGACATGGAAGGCTGAG 59.100 57.895 0.00 0.00 46.38 3.35
397 405 3.470567 GGCTGAGTCGTTGTCGCG 61.471 66.667 0.00 0.00 36.96 5.87
401 409 2.254651 GAGTCGTTGTCGCGGTCT 59.745 61.111 6.13 0.00 36.96 3.85
414 422 1.965219 CGGTCTCTCTTGGGTTCGT 59.035 57.895 0.00 0.00 0.00 3.85
424 432 0.256464 TTGGGTTCGTTGGACAAGGT 59.744 50.000 4.87 0.00 0.00 3.50
427 435 1.476291 GGGTTCGTTGGACAAGGTTCT 60.476 52.381 4.87 0.00 0.00 3.01
434 442 0.110486 TGGACAAGGTTCTTCCCTGC 59.890 55.000 0.00 0.00 34.19 4.85
436 444 0.110486 GACAAGGTTCTTCCCTGCCA 59.890 55.000 0.00 0.00 34.19 4.92
491 499 4.329545 GCCACCCTGTTCGCTCCA 62.330 66.667 0.00 0.00 0.00 3.86
492 500 2.671070 CCACCCTGTTCGCTCCAT 59.329 61.111 0.00 0.00 0.00 3.41
499 507 1.293924 CTGTTCGCTCCATCATGGTC 58.706 55.000 2.79 0.00 39.03 4.02
500 508 0.612744 TGTTCGCTCCATCATGGTCA 59.387 50.000 2.79 0.00 39.03 4.02
502 510 0.178767 TTCGCTCCATCATGGTCAGG 59.821 55.000 2.79 0.00 39.03 3.86
503 511 0.687427 TCGCTCCATCATGGTCAGGA 60.687 55.000 2.79 0.00 39.03 3.86
529 537 0.796927 GCGCCAACAGAAGTACCTTC 59.203 55.000 0.00 0.00 40.45 3.46
551 559 9.490379 CCTTCTAATTGGTCTATAACATACCAC 57.510 37.037 0.00 0.00 42.84 4.16
559 567 5.878116 GGTCTATAACATACCACTTGTTGCA 59.122 40.000 0.00 0.00 37.81 4.08
564 572 7.753309 ATAACATACCACTTGTTGCAGTTTA 57.247 32.000 0.00 0.00 37.81 2.01
565 573 5.432885 ACATACCACTTGTTGCAGTTTAC 57.567 39.130 0.00 0.00 0.00 2.01
569 577 5.400066 ACCACTTGTTGCAGTTTACTTTT 57.600 34.783 0.00 0.00 0.00 2.27
583 591 7.702348 GCAGTTTACTTTTTGAAACAGATGACT 59.298 33.333 0.00 0.00 37.89 3.41
596 604 7.819415 TGAAACAGATGACTAGTTACAGGAATG 59.181 37.037 0.00 0.00 0.00 2.67
602 610 5.834460 TGACTAGTTACAGGAATGGGAGTA 58.166 41.667 0.00 0.00 0.00 2.59
609 617 2.292918 ACAGGAATGGGAGTAGGCTACA 60.293 50.000 25.48 6.23 0.00 2.74
610 618 2.366916 CAGGAATGGGAGTAGGCTACAG 59.633 54.545 25.48 0.11 0.00 2.74
625 633 3.250040 GGCTACAGAAACACATTTGTCGT 59.750 43.478 0.00 0.00 33.55 4.34
628 636 6.071463 GCTACAGAAACACATTTGTCGTTAG 58.929 40.000 0.00 0.00 33.55 2.34
629 637 6.292703 GCTACAGAAACACATTTGTCGTTAGT 60.293 38.462 0.00 0.00 33.55 2.24
639 647 3.547054 TTGTCGTTAGTGTTTCAGGGT 57.453 42.857 0.00 0.00 0.00 4.34
642 650 3.890756 TGTCGTTAGTGTTTCAGGGTAGA 59.109 43.478 0.00 0.00 0.00 2.59
648 656 6.127535 CGTTAGTGTTTCAGGGTAGATAAGGA 60.128 42.308 0.00 0.00 0.00 3.36
649 657 5.678955 AGTGTTTCAGGGTAGATAAGGAC 57.321 43.478 0.00 0.00 0.00 3.85
653 661 5.246656 TGTTTCAGGGTAGATAAGGACGAAA 59.753 40.000 0.00 0.00 0.00 3.46
664 672 5.473846 AGATAAGGACGAAAGATAGATGCGA 59.526 40.000 0.00 0.00 0.00 5.10
674 682 1.771783 ATAGATGCGATGGGCTGGCA 61.772 55.000 2.88 0.00 43.16 4.92
696 704 2.094659 CGTGGCAAGCGTAGGACAG 61.095 63.158 0.00 0.00 0.00 3.51
715 723 1.067071 AGGGCGGACGTAAGAGAAAAG 60.067 52.381 0.00 0.00 43.62 2.27
725 734 2.011540 AAGAGAAAAGATCGGTCGGC 57.988 50.000 0.00 0.00 0.00 5.54
727 736 1.134965 AGAGAAAAGATCGGTCGGCTG 60.135 52.381 0.00 0.00 0.00 4.85
733 742 1.215647 GATCGGTCGGCTGAACACT 59.784 57.895 11.99 0.00 33.10 3.55
734 743 1.078759 GATCGGTCGGCTGAACACTG 61.079 60.000 11.99 0.00 33.10 3.66
739 748 1.301716 TCGGCTGAACACTGGCTTC 60.302 57.895 0.00 0.00 0.00 3.86
740 749 1.597854 CGGCTGAACACTGGCTTCA 60.598 57.895 0.00 0.00 0.00 3.02
741 750 1.165907 CGGCTGAACACTGGCTTCAA 61.166 55.000 0.00 0.00 0.00 2.69
742 751 0.312102 GGCTGAACACTGGCTTCAAC 59.688 55.000 0.00 0.00 0.00 3.18
743 752 0.312102 GCTGAACACTGGCTTCAACC 59.688 55.000 0.00 0.00 0.00 3.77
744 753 1.679139 CTGAACACTGGCTTCAACCA 58.321 50.000 0.00 0.00 38.29 3.67
751 760 3.012518 CACTGGCTTCAACCATAGAAGG 58.987 50.000 0.00 0.00 42.08 3.46
888 901 0.394625 GCCTATAAAACCCGGTGCCA 60.395 55.000 0.00 0.00 0.00 4.92
916 937 4.740822 GTTGGCCGCATCCACCCT 62.741 66.667 0.00 0.00 35.50 4.34
917 938 4.738998 TTGGCCGCATCCACCCTG 62.739 66.667 0.00 0.00 35.50 4.45
955 976 5.487131 ACCTGCTCCTTAATTCTCTCTTCTT 59.513 40.000 0.00 0.00 0.00 2.52
1098 1120 2.367202 CCACACCAGCGACCCCTAT 61.367 63.158 0.00 0.00 0.00 2.57
1126 1148 4.208686 GCTACGGCTCCCAGGTCG 62.209 72.222 0.00 0.00 35.22 4.79
1229 1286 1.988409 CCAACGACTCACGCATACG 59.012 57.895 0.00 0.00 46.94 3.06
1241 1298 1.748647 CGCATACGTAGGTTGTGGCG 61.749 60.000 9.23 7.53 37.82 5.69
1291 1353 0.105039 GGTGCCGATCTTCTCCGAAT 59.895 55.000 0.00 0.00 0.00 3.34
1307 1369 1.962547 CGAATTCGTTTTGTGCTCACG 59.037 47.619 19.67 0.00 35.18 4.35
1315 1377 3.546020 CGTTTTGTGCTCACGAGATGTTT 60.546 43.478 0.00 0.00 35.93 2.83
1436 1503 8.830201 TTATGAACAGGTTTTGAAATGATTGG 57.170 30.769 0.00 0.00 0.00 3.16
1439 1506 6.760770 TGAACAGGTTTTGAAATGATTGGTTC 59.239 34.615 0.00 0.00 0.00 3.62
1445 1512 6.183359 GGTTTTGAAATGATTGGTTCGAATCG 60.183 38.462 0.00 0.00 35.43 3.34
1546 1623 5.237344 AGCATGTTGAACTGAACTACTGAAC 59.763 40.000 0.00 0.00 0.00 3.18
1613 1690 3.763097 TCGTGATGGAAATGTGAATGC 57.237 42.857 0.00 0.00 0.00 3.56
1661 1739 8.488668 AGAGTACAAAACCTAAAAGTTCACCTA 58.511 33.333 0.00 0.00 0.00 3.08
1662 1740 9.112725 GAGTACAAAACCTAAAAGTTCACCTAA 57.887 33.333 0.00 0.00 0.00 2.69
1700 1778 9.673454 CATGATGTTATGTCCATTTAGTTGATG 57.327 33.333 0.00 0.00 0.00 3.07
1701 1779 9.631257 ATGATGTTATGTCCATTTAGTTGATGA 57.369 29.630 0.00 0.00 0.00 2.92
1702 1780 9.631257 TGATGTTATGTCCATTTAGTTGATGAT 57.369 29.630 0.00 0.00 0.00 2.45
1703 1781 9.888878 GATGTTATGTCCATTTAGTTGATGATG 57.111 33.333 0.00 0.00 0.00 3.07
1704 1782 9.631257 ATGTTATGTCCATTTAGTTGATGATGA 57.369 29.630 0.00 0.00 0.00 2.92
1705 1783 9.460019 TGTTATGTCCATTTAGTTGATGATGAA 57.540 29.630 0.00 0.00 0.00 2.57
1710 1788 9.685276 TGTCCATTTAGTTGATGATGAATTAGT 57.315 29.630 0.00 0.00 0.00 2.24
1719 1797 9.319143 AGTTGATGATGAATTAGTACAGTAAGC 57.681 33.333 0.00 0.00 0.00 3.09
1720 1798 7.930513 TGATGATGAATTAGTACAGTAAGCG 57.069 36.000 0.00 0.00 0.00 4.68
1721 1799 6.923508 TGATGATGAATTAGTACAGTAAGCGG 59.076 38.462 0.00 0.00 0.00 5.52
1722 1800 5.047847 TGATGAATTAGTACAGTAAGCGGC 58.952 41.667 0.00 0.00 0.00 6.53
1723 1801 3.788937 TGAATTAGTACAGTAAGCGGCC 58.211 45.455 0.00 0.00 0.00 6.13
1724 1802 3.449737 TGAATTAGTACAGTAAGCGGCCT 59.550 43.478 0.00 0.00 0.00 5.19
1725 1803 4.081309 TGAATTAGTACAGTAAGCGGCCTT 60.081 41.667 0.00 0.00 35.05 4.35
1726 1804 3.967332 TTAGTACAGTAAGCGGCCTTT 57.033 42.857 0.00 0.00 32.47 3.11
1727 1805 2.094762 AGTACAGTAAGCGGCCTTTG 57.905 50.000 0.00 0.00 32.47 2.77
1728 1806 1.084289 GTACAGTAAGCGGCCTTTGG 58.916 55.000 0.00 0.00 32.47 3.28
1729 1807 0.978151 TACAGTAAGCGGCCTTTGGA 59.022 50.000 0.00 0.00 32.47 3.53
1730 1808 0.328258 ACAGTAAGCGGCCTTTGGAT 59.672 50.000 0.00 0.00 32.47 3.41
1731 1809 0.734889 CAGTAAGCGGCCTTTGGATG 59.265 55.000 0.00 0.00 32.47 3.51
1732 1810 0.618458 AGTAAGCGGCCTTTGGATGA 59.382 50.000 0.00 0.00 32.47 2.92
1733 1811 1.212935 AGTAAGCGGCCTTTGGATGAT 59.787 47.619 0.00 0.00 32.47 2.45
1734 1812 2.024414 GTAAGCGGCCTTTGGATGATT 58.976 47.619 0.00 0.00 32.47 2.57
1735 1813 1.106285 AAGCGGCCTTTGGATGATTC 58.894 50.000 0.00 0.00 0.00 2.52
1736 1814 0.753111 AGCGGCCTTTGGATGATTCC 60.753 55.000 0.00 0.00 42.94 3.01
1737 1815 1.738346 GCGGCCTTTGGATGATTCCC 61.738 60.000 0.00 0.00 41.83 3.97
1738 1816 0.395586 CGGCCTTTGGATGATTCCCA 60.396 55.000 0.00 0.00 41.83 4.37
1739 1817 1.114627 GGCCTTTGGATGATTCCCAC 58.885 55.000 0.00 0.00 41.83 4.61
1740 1818 1.619432 GGCCTTTGGATGATTCCCACA 60.619 52.381 0.00 0.00 41.83 4.17
1741 1819 1.478105 GCCTTTGGATGATTCCCACAC 59.522 52.381 0.00 0.00 41.83 3.82
1742 1820 2.885554 GCCTTTGGATGATTCCCACACT 60.886 50.000 0.00 0.00 41.83 3.55
1743 1821 2.756760 CCTTTGGATGATTCCCACACTG 59.243 50.000 0.00 0.00 41.83 3.66
1744 1822 3.561960 CCTTTGGATGATTCCCACACTGA 60.562 47.826 0.00 0.00 41.83 3.41
1745 1823 4.275810 CTTTGGATGATTCCCACACTGAT 58.724 43.478 0.00 0.00 41.83 2.90
1746 1824 5.439721 CTTTGGATGATTCCCACACTGATA 58.560 41.667 0.00 0.00 41.83 2.15
1747 1825 4.694760 TGGATGATTCCCACACTGATAG 57.305 45.455 0.00 0.00 41.83 2.08
1748 1826 3.392285 TGGATGATTCCCACACTGATAGG 59.608 47.826 0.00 0.00 41.83 2.57
1749 1827 3.406764 GATGATTCCCACACTGATAGGC 58.593 50.000 0.00 0.00 0.00 3.93
1750 1828 2.481441 TGATTCCCACACTGATAGGCT 58.519 47.619 0.00 0.00 0.00 4.58
1751 1829 3.653164 TGATTCCCACACTGATAGGCTA 58.347 45.455 0.00 0.00 0.00 3.93
1752 1830 4.037222 TGATTCCCACACTGATAGGCTAA 58.963 43.478 0.00 0.00 0.00 3.09
1753 1831 4.660303 TGATTCCCACACTGATAGGCTAAT 59.340 41.667 0.00 0.00 0.00 1.73
1754 1832 4.689612 TTCCCACACTGATAGGCTAATC 57.310 45.455 0.00 0.00 0.00 1.75
1755 1833 3.653164 TCCCACACTGATAGGCTAATCA 58.347 45.455 0.00 2.63 34.72 2.57
1756 1834 4.037222 TCCCACACTGATAGGCTAATCAA 58.963 43.478 0.00 0.00 35.51 2.57
1757 1835 4.473196 TCCCACACTGATAGGCTAATCAAA 59.527 41.667 0.00 0.00 35.51 2.69
1758 1836 5.045213 TCCCACACTGATAGGCTAATCAAAA 60.045 40.000 0.00 0.00 35.51 2.44
1759 1837 5.829924 CCCACACTGATAGGCTAATCAAAAT 59.170 40.000 0.00 0.00 35.51 1.82
1760 1838 6.238842 CCCACACTGATAGGCTAATCAAAATG 60.239 42.308 0.00 5.10 35.51 2.32
1761 1839 6.238842 CCACACTGATAGGCTAATCAAAATGG 60.239 42.308 0.00 6.89 35.51 3.16
1762 1840 6.319658 CACACTGATAGGCTAATCAAAATGGT 59.680 38.462 0.00 0.00 35.51 3.55
1763 1841 7.498900 CACACTGATAGGCTAATCAAAATGGTA 59.501 37.037 0.00 0.00 35.51 3.25
1764 1842 8.220559 ACACTGATAGGCTAATCAAAATGGTAT 58.779 33.333 0.00 0.00 35.51 2.73
1765 1843 9.725019 CACTGATAGGCTAATCAAAATGGTATA 57.275 33.333 0.00 0.00 35.51 1.47
1771 1849 8.498054 AGGCTAATCAAAATGGTATATCATCG 57.502 34.615 0.00 0.00 0.00 3.84
1772 1850 7.554118 AGGCTAATCAAAATGGTATATCATCGG 59.446 37.037 0.00 0.00 0.00 4.18
1773 1851 7.336931 GGCTAATCAAAATGGTATATCATCGGT 59.663 37.037 0.00 0.00 0.00 4.69
1774 1852 8.730680 GCTAATCAAAATGGTATATCATCGGTT 58.269 33.333 0.00 0.00 0.00 4.44
1780 1858 9.624697 CAAAATGGTATATCATCGGTTAAATGG 57.375 33.333 0.00 0.00 0.00 3.16
1781 1859 8.934023 AAATGGTATATCATCGGTTAAATGGT 57.066 30.769 0.00 0.00 0.00 3.55
1782 1860 8.561738 AATGGTATATCATCGGTTAAATGGTC 57.438 34.615 0.00 0.00 0.00 4.02
1783 1861 7.068686 TGGTATATCATCGGTTAAATGGTCA 57.931 36.000 0.00 0.00 0.00 4.02
1784 1862 7.158697 TGGTATATCATCGGTTAAATGGTCAG 58.841 38.462 0.00 0.00 0.00 3.51
1785 1863 6.092259 GGTATATCATCGGTTAAATGGTCAGC 59.908 42.308 0.00 0.00 0.00 4.26
1786 1864 3.627395 TCATCGGTTAAATGGTCAGCT 57.373 42.857 0.00 0.00 0.00 4.24
1787 1865 3.950397 TCATCGGTTAAATGGTCAGCTT 58.050 40.909 0.00 0.00 0.00 3.74
1788 1866 4.331968 TCATCGGTTAAATGGTCAGCTTT 58.668 39.130 0.00 0.00 0.00 3.51
1789 1867 4.764823 TCATCGGTTAAATGGTCAGCTTTT 59.235 37.500 0.00 0.00 0.00 2.27
1790 1868 5.242838 TCATCGGTTAAATGGTCAGCTTTTT 59.757 36.000 0.00 0.00 0.00 1.94
1813 1891 7.759489 TTTTTAGATTGGTCAGCTAACATGT 57.241 32.000 0.00 0.00 0.00 3.21
1814 1892 7.759489 TTTTAGATTGGTCAGCTAACATGTT 57.241 32.000 16.68 16.68 0.00 2.71
1815 1893 6.985188 TTAGATTGGTCAGCTAACATGTTC 57.015 37.500 15.85 1.24 0.00 3.18
1816 1894 5.171339 AGATTGGTCAGCTAACATGTTCT 57.829 39.130 15.85 3.96 0.00 3.01
1817 1895 6.299805 AGATTGGTCAGCTAACATGTTCTA 57.700 37.500 15.85 0.00 0.00 2.10
1818 1896 6.344500 AGATTGGTCAGCTAACATGTTCTAG 58.656 40.000 15.85 9.23 0.00 2.43
1819 1897 5.738619 TTGGTCAGCTAACATGTTCTAGA 57.261 39.130 15.85 6.60 0.00 2.43
1820 1898 5.939764 TGGTCAGCTAACATGTTCTAGAT 57.060 39.130 15.85 3.56 0.00 1.98
1821 1899 6.299805 TGGTCAGCTAACATGTTCTAGATT 57.700 37.500 15.85 0.00 0.00 2.40
1822 1900 6.108687 TGGTCAGCTAACATGTTCTAGATTG 58.891 40.000 15.85 9.98 0.00 2.67
1823 1901 5.007136 GGTCAGCTAACATGTTCTAGATTGC 59.993 44.000 15.85 9.07 0.00 3.56
1824 1902 5.814705 GTCAGCTAACATGTTCTAGATTGCT 59.185 40.000 15.85 11.02 0.00 3.91
1825 1903 6.980978 GTCAGCTAACATGTTCTAGATTGCTA 59.019 38.462 15.85 0.00 0.00 3.49
1826 1904 7.655328 GTCAGCTAACATGTTCTAGATTGCTAT 59.345 37.037 15.85 0.00 0.00 2.97
1827 1905 8.206867 TCAGCTAACATGTTCTAGATTGCTATT 58.793 33.333 15.85 0.00 0.00 1.73
1828 1906 8.834465 CAGCTAACATGTTCTAGATTGCTATTT 58.166 33.333 15.85 0.00 0.00 1.40
1829 1907 9.401058 AGCTAACATGTTCTAGATTGCTATTTT 57.599 29.630 15.85 0.00 0.00 1.82
1830 1908 9.443283 GCTAACATGTTCTAGATTGCTATTTTG 57.557 33.333 15.85 0.00 0.00 2.44
1844 1922 9.956720 GATTGCTATTTTGTTATTCATAGCTGT 57.043 29.630 10.50 0.00 38.17 4.40
1845 1923 9.956720 ATTGCTATTTTGTTATTCATAGCTGTC 57.043 29.630 10.50 0.00 38.17 3.51
1846 1924 8.504812 TGCTATTTTGTTATTCATAGCTGTCA 57.495 30.769 10.50 0.00 38.17 3.58
1847 1925 8.955388 TGCTATTTTGTTATTCATAGCTGTCAA 58.045 29.630 10.50 0.00 38.17 3.18
1848 1926 9.956720 GCTATTTTGTTATTCATAGCTGTCAAT 57.043 29.630 0.00 0.00 35.45 2.57
1865 1943 9.678260 AGCTGTCAATTTCTAAGATAAATCACT 57.322 29.630 0.00 0.00 0.00 3.41
1866 1944 9.713740 GCTGTCAATTTCTAAGATAAATCACTG 57.286 33.333 0.00 0.00 0.00 3.66
1920 1998 3.791973 TTGTGTGTTAACAAGGGCTTG 57.208 42.857 10.51 0.00 45.58 4.01
1921 1999 2.028130 TGTGTGTTAACAAGGGCTTGG 58.972 47.619 10.51 0.00 44.45 3.61
1922 2000 1.036707 TGTGTTAACAAGGGCTTGGC 58.963 50.000 10.51 0.00 44.45 4.52
1923 2001 1.328279 GTGTTAACAAGGGCTTGGCT 58.672 50.000 10.51 0.00 44.45 4.75
1924 2002 1.269723 GTGTTAACAAGGGCTTGGCTC 59.730 52.381 10.51 0.00 44.45 4.70
1925 2003 1.144913 TGTTAACAAGGGCTTGGCTCT 59.855 47.619 5.64 0.00 43.58 4.09
1930 2008 4.239991 AGGGCTTGGCTCTTCTCA 57.760 55.556 0.00 0.00 34.72 3.27
1931 2009 2.468015 AGGGCTTGGCTCTTCTCAA 58.532 52.632 0.00 0.00 34.72 3.02
1932 2010 0.773644 AGGGCTTGGCTCTTCTCAAA 59.226 50.000 0.00 0.00 34.72 2.69
1933 2011 1.357079 AGGGCTTGGCTCTTCTCAAAT 59.643 47.619 0.00 0.00 34.72 2.32
1934 2012 2.578021 AGGGCTTGGCTCTTCTCAAATA 59.422 45.455 0.00 0.00 34.72 1.40
1935 2013 2.948315 GGGCTTGGCTCTTCTCAAATAG 59.052 50.000 0.00 0.00 0.00 1.73
1936 2014 3.370953 GGGCTTGGCTCTTCTCAAATAGA 60.371 47.826 0.00 0.00 0.00 1.98
1937 2015 4.265073 GGCTTGGCTCTTCTCAAATAGAA 58.735 43.478 0.00 0.00 42.07 2.10
1938 2016 4.702131 GGCTTGGCTCTTCTCAAATAGAAA 59.298 41.667 0.00 0.00 43.66 2.52
1939 2017 5.183904 GGCTTGGCTCTTCTCAAATAGAAAA 59.816 40.000 0.00 0.00 43.66 2.29
1940 2018 6.294731 GGCTTGGCTCTTCTCAAATAGAAAAA 60.295 38.462 0.00 0.00 43.66 1.94
1955 2033 2.519937 AAAAAGGGCTTGCTGTGCT 58.480 47.368 0.00 0.00 0.00 4.40
1956 2034 0.105408 AAAAAGGGCTTGCTGTGCTG 59.895 50.000 0.00 0.00 0.00 4.41
1957 2035 2.373434 AAAAGGGCTTGCTGTGCTGC 62.373 55.000 0.00 0.00 0.00 5.25
1958 2036 4.591399 AGGGCTTGCTGTGCTGCA 62.591 61.111 0.00 0.00 41.65 4.41
1959 2037 3.379445 GGGCTTGCTGTGCTGCAT 61.379 61.111 5.27 0.00 42.96 3.96
1960 2038 2.126071 GGCTTGCTGTGCTGCATG 60.126 61.111 5.27 3.28 42.96 4.06
1961 2039 2.632544 GGCTTGCTGTGCTGCATGA 61.633 57.895 5.27 0.00 42.96 3.07
1962 2040 1.511305 GCTTGCTGTGCTGCATGAT 59.489 52.632 5.27 0.00 42.96 2.45
2086 2168 8.255394 AGTTGGTTGAATGCTATAAATTTTGC 57.745 30.769 0.00 0.00 0.00 3.68
2169 2289 7.656137 TGTAATTTCTACAGTTGACTTCAGGTC 59.344 37.037 0.00 0.00 44.70 3.85
2399 2540 9.482627 AGTTTCTTCATCAAGTAAACTCTACTG 57.517 33.333 0.00 0.00 36.39 2.74
2540 2693 8.078596 AGAATTTTCTTCTGTGCTGAAACATAC 58.921 33.333 0.00 0.00 32.55 2.39
2541 2694 6.691754 TTTTCTTCTGTGCTGAAACATACA 57.308 33.333 0.00 0.00 30.66 2.29
2542 2695 5.929697 TTCTTCTGTGCTGAAACATACAG 57.070 39.130 0.00 0.00 41.34 2.74
2543 2696 4.960938 TCTTCTGTGCTGAAACATACAGT 58.039 39.130 0.00 0.00 40.91 3.55
2544 2697 6.096673 TCTTCTGTGCTGAAACATACAGTA 57.903 37.500 0.00 0.00 40.91 2.74
2710 2870 4.326548 GGCTGAGTTCAACGTAACTGATAC 59.673 45.833 8.42 1.79 39.78 2.24
2997 3163 2.053747 ATGGGTTCCTGTTCCTGGTA 57.946 50.000 0.00 0.00 0.00 3.25
3054 3221 2.212652 CAGTGTATGTGCTGTGTGTGT 58.787 47.619 0.00 0.00 0.00 3.72
3104 3273 6.204108 GCACTGTATTTGTAGTACTGTGGTTT 59.796 38.462 18.41 0.00 44.90 3.27
3119 3288 4.241681 TGTGGTTTTGAAGTTTGTGCTTC 58.758 39.130 0.00 0.00 43.68 3.86
3203 3378 6.041979 ACAGCTTAAATTGAAAGATTGGTGGT 59.958 34.615 5.25 0.00 0.00 4.16
3204 3379 7.232534 ACAGCTTAAATTGAAAGATTGGTGGTA 59.767 33.333 5.25 0.00 0.00 3.25
3205 3380 7.542130 CAGCTTAAATTGAAAGATTGGTGGTAC 59.458 37.037 5.25 0.00 0.00 3.34
3285 3546 0.250989 GGGATCGGGTGTTTGGTTCA 60.251 55.000 0.00 0.00 0.00 3.18
3300 3561 6.038825 TGTTTGGTTCAACTGAATACATCGTT 59.961 34.615 0.00 0.00 36.33 3.85
3328 3589 1.388547 TCGCAGAGCAACCAAAAACT 58.611 45.000 0.00 0.00 0.00 2.66
3343 3604 8.560374 CAACCAAAAACTAAGAACAACCAAAAA 58.440 29.630 0.00 0.00 0.00 1.94
3354 3615 4.717188 ACAACCAAAAACAACACAAACG 57.283 36.364 0.00 0.00 0.00 3.60
3467 3730 2.435805 GGAGCAACCCATCTCATACTCA 59.564 50.000 0.00 0.00 0.00 3.41
3560 3823 4.209538 TCTATACCATTGCTGCAAATGCT 58.790 39.130 20.06 8.18 42.66 3.79
3587 3851 0.950555 GTTGTGAGCTGGTGCGATGA 60.951 55.000 0.00 0.00 45.42 2.92
3589 3853 0.036105 TGTGAGCTGGTGCGATGAAT 60.036 50.000 0.00 0.00 45.42 2.57
3593 3857 3.113745 CTGGTGCGATGAATGGCC 58.886 61.111 0.00 0.00 0.00 5.36
3622 3886 0.904865 TGAGGATGTTCTGAGGGCGT 60.905 55.000 0.00 0.00 0.00 5.68
3627 3891 0.687354 ATGTTCTGAGGGCGTTGAGT 59.313 50.000 0.00 0.00 0.00 3.41
3658 3922 3.036084 CGGACAGCGACGTTGCTT 61.036 61.111 27.81 18.23 44.46 3.91
3664 3928 1.817941 AGCGACGTTGCTTGTGGTT 60.818 52.632 24.88 0.50 44.46 3.67
3669 3933 1.010125 CGTTGCTTGTGGTTCCACG 60.010 57.895 15.82 5.25 39.60 4.94
3676 3940 0.107831 TTGTGGTTCCACGAAGGGAG 59.892 55.000 15.82 0.00 38.42 4.30
3687 3951 3.003173 AAGGGAGCGCCTAGTGCA 61.003 61.111 2.29 0.00 42.00 4.57
3703 3967 3.957586 CAGGAGGTGCTGGTGCCA 61.958 66.667 0.00 0.00 38.71 4.92
3705 3969 2.753043 GGAGGTGCTGGTGCCATG 60.753 66.667 0.00 0.00 38.71 3.66
3710 3974 4.746309 TGCTGGTGCCATGAGCCC 62.746 66.667 0.00 0.91 42.71 5.19
3801 4065 2.334946 GGATGTTGCGAGCTTGCCA 61.335 57.895 23.34 14.89 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.354792 TGAGCTTTGTTACAAAAGGTTACGT 59.645 36.000 11.80 0.00 45.34 3.57
15 16 9.906660 CAATATGAGCTTTGTTACAAAAGGTTA 57.093 29.630 11.80 8.60 45.34 2.85
41 42 9.862585 CAACCTTTGTTGTAAATATTTTTCTGC 57.137 29.630 5.91 0.00 45.51 4.26
58 59 4.470334 AAATCTGCAACACAACCTTTGT 57.530 36.364 0.00 0.00 46.75 2.83
83 84 2.109128 TCCATGCTGTAAAAGTTGGGGA 59.891 45.455 0.00 0.00 34.07 4.81
84 85 2.524306 TCCATGCTGTAAAAGTTGGGG 58.476 47.619 0.00 0.00 34.07 4.96
87 94 5.957798 ACATCATCCATGCTGTAAAAGTTG 58.042 37.500 0.00 0.00 35.59 3.16
89 96 5.622914 GCAACATCATCCATGCTGTAAAAGT 60.623 40.000 0.00 0.00 36.25 2.66
95 102 1.749063 CTGCAACATCATCCATGCTGT 59.251 47.619 0.00 0.00 38.64 4.40
98 105 3.728076 ATTCTGCAACATCATCCATGC 57.272 42.857 0.00 0.00 35.65 4.06
99 106 6.978343 AAAAATTCTGCAACATCATCCATG 57.022 33.333 0.00 0.00 38.64 3.66
142 149 1.521010 CGATGCTAGTGCTGCTGCT 60.521 57.895 17.00 1.80 40.48 4.24
181 188 2.999507 TATTTGCAACAACGGCGAAT 57.000 40.000 16.62 2.26 45.08 3.34
183 190 2.226674 TGAATATTTGCAACAACGGCGA 59.773 40.909 16.62 0.00 0.00 5.54
283 290 2.358737 CGAAGTGGGTGCAGGACC 60.359 66.667 1.45 1.45 45.28 4.46
294 302 4.389576 GTTGCTGGCGGCGAAGTG 62.390 66.667 12.98 0.00 45.43 3.16
302 310 2.966309 GAGGTTTCCGTTGCTGGCG 61.966 63.158 0.00 0.00 0.00 5.69
323 331 2.198287 GCCATGATGCAAGCCCGAT 61.198 57.895 0.00 0.00 0.00 4.18
324 332 2.829914 GCCATGATGCAAGCCCGA 60.830 61.111 0.00 0.00 0.00 5.14
349 357 2.440980 GGTGCTCATCCCCTTGGC 60.441 66.667 0.00 0.00 0.00 4.52
351 359 1.450312 GACGGTGCTCATCCCCTTG 60.450 63.158 0.00 0.00 0.00 3.61
353 361 3.083997 GGACGGTGCTCATCCCCT 61.084 66.667 0.00 0.00 0.00 4.79
356 364 2.202756 GTCGGACGGTGCTCATCC 60.203 66.667 0.00 0.00 0.00 3.51
361 369 2.507110 CTTCCATGTCGGACGGTGCT 62.507 60.000 3.34 0.00 46.36 4.40
362 370 2.047655 TTCCATGTCGGACGGTGC 60.048 61.111 3.34 0.00 46.36 5.01
364 372 2.978824 CCTTCCATGTCGGACGGT 59.021 61.111 3.34 0.00 46.20 4.83
367 375 0.460987 CTCAGCCTTCCATGTCGGAC 60.461 60.000 0.00 0.00 46.36 4.79
372 380 0.687354 AACGACTCAGCCTTCCATGT 59.313 50.000 0.00 0.00 0.00 3.21
375 383 0.033504 GACAACGACTCAGCCTTCCA 59.966 55.000 0.00 0.00 0.00 3.53
385 393 2.185103 GAGAGACCGCGACAACGACT 62.185 60.000 8.23 0.00 42.66 4.18
386 394 1.796749 GAGAGACCGCGACAACGAC 60.797 63.158 8.23 0.00 42.66 4.34
397 405 1.608283 CCAACGAACCCAAGAGAGACC 60.608 57.143 0.00 0.00 0.00 3.85
401 409 1.124780 TGTCCAACGAACCCAAGAGA 58.875 50.000 0.00 0.00 0.00 3.10
414 422 1.478654 GCAGGGAAGAACCTTGTCCAA 60.479 52.381 0.00 0.00 45.86 3.53
424 432 1.284785 CCAGGTATTGGCAGGGAAGAA 59.715 52.381 0.00 0.00 40.87 2.52
427 435 2.006748 CCCAGGTATTGGCAGGGAA 58.993 57.895 1.04 0.00 46.32 3.97
434 442 1.898574 GATGCCGCCCAGGTATTGG 60.899 63.158 0.00 0.00 45.76 3.16
436 444 2.111043 CGATGCCGCCCAGGTATT 59.889 61.111 0.00 0.00 45.76 1.89
484 492 0.687427 TCCTGACCATGATGGAGCGA 60.687 55.000 20.11 4.91 40.96 4.93
491 499 0.549950 CTGGCCTTCCTGACCATGAT 59.450 55.000 3.32 0.00 33.56 2.45
492 500 1.993653 CTGGCCTTCCTGACCATGA 59.006 57.895 3.32 0.00 33.56 3.07
510 518 4.695560 AGGTACTTCTGTTGGCGC 57.304 55.556 0.00 0.00 27.25 6.53
538 546 6.985188 ACTGCAACAAGTGGTATGTTATAG 57.015 37.500 0.00 0.00 38.90 1.31
540 548 6.648879 AAACTGCAACAAGTGGTATGTTAT 57.351 33.333 0.00 0.00 38.90 1.89
541 549 6.768861 AGTAAACTGCAACAAGTGGTATGTTA 59.231 34.615 0.00 0.00 38.90 2.41
549 557 6.942886 TCAAAAAGTAAACTGCAACAAGTG 57.057 33.333 0.00 0.00 0.00 3.16
551 559 7.791949 TGTTTCAAAAAGTAAACTGCAACAAG 58.208 30.769 0.00 0.00 36.70 3.16
556 564 7.487829 GTCATCTGTTTCAAAAAGTAAACTGCA 59.512 33.333 0.00 0.00 36.70 4.41
564 572 9.391006 TGTAACTAGTCATCTGTTTCAAAAAGT 57.609 29.630 0.00 0.00 0.00 2.66
565 573 9.869844 CTGTAACTAGTCATCTGTTTCAAAAAG 57.130 33.333 0.00 0.00 0.00 2.27
569 577 7.297936 TCCTGTAACTAGTCATCTGTTTCAA 57.702 36.000 0.00 0.00 0.00 2.69
583 591 3.965347 GCCTACTCCCATTCCTGTAACTA 59.035 47.826 0.00 0.00 0.00 2.24
588 596 2.292918 TGTAGCCTACTCCCATTCCTGT 60.293 50.000 3.13 0.00 0.00 4.00
596 604 2.565834 TGTGTTTCTGTAGCCTACTCCC 59.434 50.000 3.13 0.00 0.00 4.30
602 610 3.498397 CGACAAATGTGTTTCTGTAGCCT 59.502 43.478 0.00 0.00 38.41 4.58
609 617 6.431198 AACACTAACGACAAATGTGTTTCT 57.569 33.333 0.00 0.00 45.72 2.52
625 633 6.127535 CGTCCTTATCTACCCTGAAACACTAA 60.128 42.308 0.00 0.00 0.00 2.24
628 636 4.159135 TCGTCCTTATCTACCCTGAAACAC 59.841 45.833 0.00 0.00 0.00 3.32
629 637 4.346730 TCGTCCTTATCTACCCTGAAACA 58.653 43.478 0.00 0.00 0.00 2.83
633 641 4.863548 TCTTTCGTCCTTATCTACCCTGA 58.136 43.478 0.00 0.00 0.00 3.86
639 647 6.653740 TCGCATCTATCTTTCGTCCTTATCTA 59.346 38.462 0.00 0.00 0.00 1.98
642 650 5.707242 TCGCATCTATCTTTCGTCCTTAT 57.293 39.130 0.00 0.00 0.00 1.73
648 656 2.868044 GCCCATCGCATCTATCTTTCGT 60.868 50.000 0.00 0.00 37.47 3.85
649 657 1.728971 GCCCATCGCATCTATCTTTCG 59.271 52.381 0.00 0.00 37.47 3.46
653 661 0.612229 CCAGCCCATCGCATCTATCT 59.388 55.000 0.00 0.00 41.38 1.98
677 685 3.488090 GTCCTACGCTTGCCACGC 61.488 66.667 0.00 0.00 0.00 5.34
696 704 1.067354 TCTTTTCTCTTACGTCCGCCC 60.067 52.381 0.00 0.00 0.00 6.13
715 723 1.078759 CAGTGTTCAGCCGACCGATC 61.079 60.000 0.00 0.00 0.00 3.69
725 734 1.679139 TGGTTGAAGCCAGTGTTCAG 58.321 50.000 0.00 0.00 35.39 3.02
727 736 3.674997 TCTATGGTTGAAGCCAGTGTTC 58.325 45.455 0.00 0.00 42.47 3.18
733 742 1.284785 CCCCTTCTATGGTTGAAGCCA 59.715 52.381 0.00 0.00 43.48 4.75
734 743 2.024306 GCCCCTTCTATGGTTGAAGCC 61.024 57.143 0.00 0.00 39.47 4.35
739 748 0.034186 TGCTGCCCCTTCTATGGTTG 60.034 55.000 0.00 0.00 0.00 3.77
740 749 0.257039 CTGCTGCCCCTTCTATGGTT 59.743 55.000 0.00 0.00 0.00 3.67
741 750 0.621571 TCTGCTGCCCCTTCTATGGT 60.622 55.000 0.00 0.00 0.00 3.55
742 751 0.548031 TTCTGCTGCCCCTTCTATGG 59.452 55.000 0.00 0.00 0.00 2.74
743 752 2.653234 ATTCTGCTGCCCCTTCTATG 57.347 50.000 0.00 0.00 0.00 2.23
744 753 2.486191 CGAATTCTGCTGCCCCTTCTAT 60.486 50.000 3.52 0.00 0.00 1.98
751 760 0.174162 AATTGCGAATTCTGCTGCCC 59.826 50.000 18.44 0.00 0.00 5.36
808 821 3.360867 TCGTGGACAATAATGGGCAATT 58.639 40.909 0.00 0.00 0.00 2.32
916 937 4.033776 GGTAGCTGGCTGGTGGCA 62.034 66.667 6.33 0.00 46.87 4.92
917 938 3.721706 AGGTAGCTGGCTGGTGGC 61.722 66.667 6.33 0.00 40.90 5.01
918 939 2.270205 CAGGTAGCTGGCTGGTGG 59.730 66.667 14.29 0.00 0.00 4.61
919 940 2.437359 GCAGGTAGCTGGCTGGTG 60.437 66.667 22.69 0.00 41.15 4.17
955 976 2.445845 CGGGATGGGAGTAGGGCA 60.446 66.667 0.00 0.00 0.00 5.36
1098 1120 2.697761 GCCGTAGCAGAGGACGACA 61.698 63.158 0.00 0.00 41.60 4.35
1126 1148 2.456443 GGAGAAGGGGATGAGGGCC 61.456 68.421 0.00 0.00 0.00 5.80
1229 1286 3.419759 CGTGCCGCCACAACCTAC 61.420 66.667 0.00 0.00 42.17 3.18
1291 1353 1.929230 TCTCGTGAGCACAAAACGAA 58.071 45.000 1.20 0.00 44.84 3.85
1315 1377 6.294564 GCTGGTCCGTACTTATTGATCTATCA 60.295 42.308 0.00 0.00 34.44 2.15
1380 1444 1.180029 GTGCCTCTCCGGTGTAACTA 58.820 55.000 0.00 0.00 36.74 2.24
1390 1457 2.633481 AGGTATTAATCGGTGCCTCTCC 59.367 50.000 0.00 0.00 0.00 3.71
1629 1706 8.324163 ACTTTTAGGTTTTGTACTCTGCTATG 57.676 34.615 0.00 0.00 0.00 2.23
1631 1708 7.988599 TGAACTTTTAGGTTTTGTACTCTGCTA 59.011 33.333 0.00 0.00 0.00 3.49
1662 1740 9.520204 GGACATAACATCATGATTTTTCGATTT 57.480 29.630 12.12 0.00 0.00 2.17
1700 1778 4.448060 GGCCGCTTACTGTACTAATTCATC 59.552 45.833 0.00 0.00 0.00 2.92
1701 1779 4.101119 AGGCCGCTTACTGTACTAATTCAT 59.899 41.667 0.00 0.00 0.00 2.57
1702 1780 3.449737 AGGCCGCTTACTGTACTAATTCA 59.550 43.478 0.00 0.00 0.00 2.57
1703 1781 4.056092 AGGCCGCTTACTGTACTAATTC 57.944 45.455 0.00 0.00 0.00 2.17
1704 1782 4.482952 AAGGCCGCTTACTGTACTAATT 57.517 40.909 0.00 0.00 0.00 1.40
1705 1783 4.189231 CAAAGGCCGCTTACTGTACTAAT 58.811 43.478 0.00 0.00 0.00 1.73
1706 1784 3.592059 CAAAGGCCGCTTACTGTACTAA 58.408 45.455 0.00 0.00 0.00 2.24
1707 1785 2.093869 CCAAAGGCCGCTTACTGTACTA 60.094 50.000 0.00 0.00 0.00 1.82
1708 1786 1.338769 CCAAAGGCCGCTTACTGTACT 60.339 52.381 0.00 0.00 0.00 2.73
1709 1787 1.084289 CCAAAGGCCGCTTACTGTAC 58.916 55.000 0.00 0.00 0.00 2.90
1710 1788 0.978151 TCCAAAGGCCGCTTACTGTA 59.022 50.000 0.00 0.00 0.00 2.74
1711 1789 0.328258 ATCCAAAGGCCGCTTACTGT 59.672 50.000 0.00 0.00 0.00 3.55
1712 1790 0.734889 CATCCAAAGGCCGCTTACTG 59.265 55.000 0.00 0.00 0.00 2.74
1713 1791 0.618458 TCATCCAAAGGCCGCTTACT 59.382 50.000 0.00 0.00 0.00 2.24
1714 1792 1.680338 ATCATCCAAAGGCCGCTTAC 58.320 50.000 0.00 0.00 0.00 2.34
1715 1793 2.297701 GAATCATCCAAAGGCCGCTTA 58.702 47.619 0.00 0.00 0.00 3.09
1716 1794 1.106285 GAATCATCCAAAGGCCGCTT 58.894 50.000 0.00 0.00 0.00 4.68
1717 1795 0.753111 GGAATCATCCAAAGGCCGCT 60.753 55.000 0.00 0.00 45.79 5.52
1718 1796 1.735973 GGAATCATCCAAAGGCCGC 59.264 57.895 0.00 0.00 45.79 6.53
1727 1805 3.808618 GCCTATCAGTGTGGGAATCATCC 60.809 52.174 0.00 0.00 45.77 3.51
1728 1806 3.072184 AGCCTATCAGTGTGGGAATCATC 59.928 47.826 0.00 0.00 0.00 2.92
1729 1807 3.051581 AGCCTATCAGTGTGGGAATCAT 58.948 45.455 0.00 0.00 0.00 2.45
1730 1808 2.481441 AGCCTATCAGTGTGGGAATCA 58.519 47.619 0.00 0.00 0.00 2.57
1731 1809 4.689612 TTAGCCTATCAGTGTGGGAATC 57.310 45.455 0.00 0.00 0.00 2.52
1732 1810 4.660303 TGATTAGCCTATCAGTGTGGGAAT 59.340 41.667 0.00 0.00 31.19 3.01
1733 1811 4.037222 TGATTAGCCTATCAGTGTGGGAA 58.963 43.478 0.00 0.00 31.19 3.97
1734 1812 3.653164 TGATTAGCCTATCAGTGTGGGA 58.347 45.455 0.00 0.00 31.19 4.37
1735 1813 4.422073 TTGATTAGCCTATCAGTGTGGG 57.578 45.455 0.00 0.00 36.03 4.61
1736 1814 6.238842 CCATTTTGATTAGCCTATCAGTGTGG 60.239 42.308 0.00 5.26 36.03 4.17
1737 1815 6.319658 ACCATTTTGATTAGCCTATCAGTGTG 59.680 38.462 0.00 1.09 36.03 3.82
1738 1816 6.426587 ACCATTTTGATTAGCCTATCAGTGT 58.573 36.000 0.00 0.00 36.03 3.55
1739 1817 6.949352 ACCATTTTGATTAGCCTATCAGTG 57.051 37.500 0.00 0.00 36.03 3.66
1745 1823 9.599866 CGATGATATACCATTTTGATTAGCCTA 57.400 33.333 0.00 0.00 0.00 3.93
1746 1824 7.554118 CCGATGATATACCATTTTGATTAGCCT 59.446 37.037 0.00 0.00 0.00 4.58
1747 1825 7.336931 ACCGATGATATACCATTTTGATTAGCC 59.663 37.037 0.00 0.00 0.00 3.93
1748 1826 8.268850 ACCGATGATATACCATTTTGATTAGC 57.731 34.615 0.00 0.00 0.00 3.09
1754 1832 9.624697 CCATTTAACCGATGATATACCATTTTG 57.375 33.333 0.00 0.00 0.00 2.44
1755 1833 9.362151 ACCATTTAACCGATGATATACCATTTT 57.638 29.630 0.00 0.00 0.00 1.82
1756 1834 8.934023 ACCATTTAACCGATGATATACCATTT 57.066 30.769 0.00 0.00 0.00 2.32
1757 1835 8.160765 TGACCATTTAACCGATGATATACCATT 58.839 33.333 0.00 0.00 0.00 3.16
1758 1836 7.685481 TGACCATTTAACCGATGATATACCAT 58.315 34.615 0.00 0.00 0.00 3.55
1759 1837 7.068686 TGACCATTTAACCGATGATATACCA 57.931 36.000 0.00 0.00 0.00 3.25
1760 1838 6.092259 GCTGACCATTTAACCGATGATATACC 59.908 42.308 0.00 0.00 0.00 2.73
1761 1839 6.874134 AGCTGACCATTTAACCGATGATATAC 59.126 38.462 0.00 0.00 0.00 1.47
1762 1840 7.004555 AGCTGACCATTTAACCGATGATATA 57.995 36.000 0.00 0.00 0.00 0.86
1763 1841 5.869579 AGCTGACCATTTAACCGATGATAT 58.130 37.500 0.00 0.00 0.00 1.63
1764 1842 5.290493 AGCTGACCATTTAACCGATGATA 57.710 39.130 0.00 0.00 0.00 2.15
1765 1843 4.156455 AGCTGACCATTTAACCGATGAT 57.844 40.909 0.00 0.00 0.00 2.45
1766 1844 3.627395 AGCTGACCATTTAACCGATGA 57.373 42.857 0.00 0.00 0.00 2.92
1767 1845 4.701956 AAAGCTGACCATTTAACCGATG 57.298 40.909 0.00 0.00 0.00 3.84
1768 1846 5.722021 AAAAAGCTGACCATTTAACCGAT 57.278 34.783 0.00 0.00 0.00 4.18
1789 1867 7.759489 ACATGTTAGCTGACCAATCTAAAAA 57.241 32.000 6.13 0.00 0.00 1.94
1790 1868 7.665559 AGAACATGTTAGCTGACCAATCTAAAA 59.334 33.333 11.95 0.00 0.00 1.52
1791 1869 7.168219 AGAACATGTTAGCTGACCAATCTAAA 58.832 34.615 11.95 0.00 0.00 1.85
1792 1870 6.711277 AGAACATGTTAGCTGACCAATCTAA 58.289 36.000 11.95 0.00 0.00 2.10
1793 1871 6.299805 AGAACATGTTAGCTGACCAATCTA 57.700 37.500 11.95 0.00 0.00 1.98
1794 1872 5.171339 AGAACATGTTAGCTGACCAATCT 57.829 39.130 11.95 0.00 0.00 2.40
1795 1873 6.341316 TCTAGAACATGTTAGCTGACCAATC 58.659 40.000 11.95 0.00 0.00 2.67
1796 1874 6.299805 TCTAGAACATGTTAGCTGACCAAT 57.700 37.500 11.95 0.00 0.00 3.16
1797 1875 5.738619 TCTAGAACATGTTAGCTGACCAA 57.261 39.130 11.95 0.00 0.00 3.67
1798 1876 5.939764 ATCTAGAACATGTTAGCTGACCA 57.060 39.130 11.95 0.00 0.00 4.02
1799 1877 5.007136 GCAATCTAGAACATGTTAGCTGACC 59.993 44.000 11.95 0.00 0.00 4.02
1800 1878 5.814705 AGCAATCTAGAACATGTTAGCTGAC 59.185 40.000 11.95 0.78 0.00 3.51
1801 1879 5.982356 AGCAATCTAGAACATGTTAGCTGA 58.018 37.500 11.95 8.13 0.00 4.26
1802 1880 7.959689 ATAGCAATCTAGAACATGTTAGCTG 57.040 36.000 11.95 8.18 0.00 4.24
1803 1881 8.970859 AAATAGCAATCTAGAACATGTTAGCT 57.029 30.769 11.95 13.54 0.00 3.32
1804 1882 9.443283 CAAAATAGCAATCTAGAACATGTTAGC 57.557 33.333 11.95 7.28 0.00 3.09
1818 1896 9.956720 ACAGCTATGAATAACAAAATAGCAATC 57.043 29.630 14.08 0.00 46.44 2.67
1819 1897 9.956720 GACAGCTATGAATAACAAAATAGCAAT 57.043 29.630 14.08 3.59 46.44 3.56
1820 1898 8.955388 TGACAGCTATGAATAACAAAATAGCAA 58.045 29.630 14.08 0.00 46.44 3.91
1821 1899 8.504812 TGACAGCTATGAATAACAAAATAGCA 57.495 30.769 14.08 0.00 46.44 3.49
1822 1900 9.956720 ATTGACAGCTATGAATAACAAAATAGC 57.043 29.630 5.57 5.57 45.07 2.97
1839 1917 9.678260 AGTGATTTATCTTAGAAATTGACAGCT 57.322 29.630 0.00 0.00 0.00 4.24
1840 1918 9.713740 CAGTGATTTATCTTAGAAATTGACAGC 57.286 33.333 0.00 0.00 0.00 4.40
1900 1978 2.428890 CCAAGCCCTTGTTAACACACAA 59.571 45.455 8.07 0.00 38.85 3.33
1901 1979 2.028130 CCAAGCCCTTGTTAACACACA 58.972 47.619 8.07 0.00 38.85 3.72
1902 1980 1.269569 GCCAAGCCCTTGTTAACACAC 60.270 52.381 8.07 0.00 38.85 3.82
1903 1981 1.036707 GCCAAGCCCTTGTTAACACA 58.963 50.000 8.07 0.00 38.85 3.72
1904 1982 1.269723 GAGCCAAGCCCTTGTTAACAC 59.730 52.381 8.07 0.00 38.85 3.32
1905 1983 1.144913 AGAGCCAAGCCCTTGTTAACA 59.855 47.619 3.59 3.59 38.85 2.41
1906 1984 1.911057 AGAGCCAAGCCCTTGTTAAC 58.089 50.000 7.21 0.00 38.85 2.01
1907 1985 2.108250 AGAAGAGCCAAGCCCTTGTTAA 59.892 45.455 7.21 0.00 38.85 2.01
1908 1986 1.705186 AGAAGAGCCAAGCCCTTGTTA 59.295 47.619 7.21 0.00 38.85 2.41
1909 1987 0.480252 AGAAGAGCCAAGCCCTTGTT 59.520 50.000 7.21 0.00 38.85 2.83
1910 1988 0.037447 GAGAAGAGCCAAGCCCTTGT 59.963 55.000 7.21 0.00 38.85 3.16
1911 1989 0.037303 TGAGAAGAGCCAAGCCCTTG 59.963 55.000 1.05 1.05 40.13 3.61
1912 1990 0.773644 TTGAGAAGAGCCAAGCCCTT 59.226 50.000 0.00 0.00 0.00 3.95
1913 1991 0.773644 TTTGAGAAGAGCCAAGCCCT 59.226 50.000 0.00 0.00 0.00 5.19
1914 1992 1.844687 ATTTGAGAAGAGCCAAGCCC 58.155 50.000 0.00 0.00 0.00 5.19
1915 1993 3.878778 TCTATTTGAGAAGAGCCAAGCC 58.121 45.455 0.00 0.00 0.00 4.35
1916 1994 5.886960 TTTCTATTTGAGAAGAGCCAAGC 57.113 39.130 0.00 0.00 45.05 4.01
1937 2015 0.105408 CAGCACAGCAAGCCCTTTTT 59.895 50.000 0.00 0.00 0.00 1.94
1938 2016 1.744014 CAGCACAGCAAGCCCTTTT 59.256 52.632 0.00 0.00 0.00 2.27
1939 2017 2.864471 GCAGCACAGCAAGCCCTTT 61.864 57.895 0.00 0.00 0.00 3.11
1940 2018 3.300765 GCAGCACAGCAAGCCCTT 61.301 61.111 0.00 0.00 0.00 3.95
1941 2019 4.591399 TGCAGCACAGCAAGCCCT 62.591 61.111 0.00 0.00 42.46 5.19
1948 2026 1.386533 AGGTAATCATGCAGCACAGC 58.613 50.000 0.00 0.00 0.00 4.40
1949 2027 2.874701 GGTAGGTAATCATGCAGCACAG 59.125 50.000 0.00 0.00 0.00 3.66
1950 2028 2.421388 GGGTAGGTAATCATGCAGCACA 60.421 50.000 0.00 0.00 0.00 4.57
1951 2029 2.222027 GGGTAGGTAATCATGCAGCAC 58.778 52.381 0.00 0.00 0.00 4.40
1952 2030 1.843206 TGGGTAGGTAATCATGCAGCA 59.157 47.619 0.00 0.00 0.00 4.41
1953 2031 2.638480 TGGGTAGGTAATCATGCAGC 57.362 50.000 0.00 0.00 0.00 5.25
1954 2032 3.822735 CCATTGGGTAGGTAATCATGCAG 59.177 47.826 0.00 0.00 0.00 4.41
1955 2033 3.831323 CCATTGGGTAGGTAATCATGCA 58.169 45.455 0.00 0.00 0.00 3.96
2086 2168 2.103537 TCTGACATCATGCCACTGTG 57.896 50.000 0.00 0.00 0.00 3.66
2169 2289 2.800985 CGATAGCTGTCCATGTCACTGG 60.801 54.545 4.73 0.00 37.66 4.00
2540 2693 3.953542 AAGGCCCCCTATCTTTTACTG 57.046 47.619 0.00 0.00 31.13 2.74
2541 2694 4.967209 AAAAGGCCCCCTATCTTTTACT 57.033 40.909 0.00 0.00 38.47 2.24
2543 2696 5.512298 GTGTAAAAGGCCCCCTATCTTTTA 58.488 41.667 0.00 0.00 40.09 1.52
2544 2697 4.350245 GTGTAAAAGGCCCCCTATCTTTT 58.650 43.478 0.00 0.00 41.66 2.27
2997 3163 5.711506 TCCACAAATTGCTAACACATCTGAT 59.288 36.000 0.00 0.00 0.00 2.90
3054 3221 7.916977 GCATACATCAAGCTGAAATCAATAACA 59.083 33.333 0.00 0.00 0.00 2.41
3119 3288 5.615544 CGGTGTCTCTTATTTGTTCAGCTTG 60.616 44.000 0.00 0.00 0.00 4.01
3123 3292 5.924475 AACGGTGTCTCTTATTTGTTCAG 57.076 39.130 0.00 0.00 0.00 3.02
3255 3430 6.503560 AACACCCGATCCCTATAAAATACA 57.496 37.500 0.00 0.00 0.00 2.29
3285 3546 3.756434 CCCACCAAACGATGTATTCAGTT 59.244 43.478 0.00 0.00 0.00 3.16
3328 3589 7.306632 CGTTTGTGTTGTTTTTGGTTGTTCTTA 60.307 33.333 0.00 0.00 0.00 2.10
3343 3604 3.495434 TCCCTTATCCGTTTGTGTTGT 57.505 42.857 0.00 0.00 0.00 3.32
3354 3615 0.377203 CGCAAGCGTTTCCCTTATCC 59.623 55.000 6.25 0.00 34.35 2.59
3495 3758 1.447663 ATGTGTCGCATGCGCTACA 60.448 52.632 34.45 34.45 41.15 2.74
3507 3770 2.746277 GCACGGGGGACATGTGTC 60.746 66.667 1.15 4.58 44.04 3.67
3560 3823 1.379916 CAGCTCACAACATCCCCCA 59.620 57.895 0.00 0.00 0.00 4.96
3587 3851 2.186903 CACTCGTAGCCGGCCATT 59.813 61.111 26.15 7.52 33.95 3.16
3589 3853 3.449227 CTCACTCGTAGCCGGCCA 61.449 66.667 26.15 6.66 33.95 5.36
3593 3857 0.456221 AACATCCTCACTCGTAGCCG 59.544 55.000 0.00 0.00 0.00 5.52
3622 3886 1.032014 GGTTCAAAGCAGCCACTCAA 58.968 50.000 0.00 0.00 0.00 3.02
3627 3891 1.896660 GTCCGGTTCAAAGCAGCCA 60.897 57.895 0.00 0.00 0.00 4.75
3657 3921 0.107831 CTCCCTTCGTGGAACCACAA 59.892 55.000 21.41 13.93 46.47 3.33
3658 3922 1.752198 CTCCCTTCGTGGAACCACA 59.248 57.895 21.41 8.07 46.47 4.17
3664 3928 3.949885 TAGGCGCTCCCTTCGTGGA 62.950 63.158 7.64 0.00 43.06 4.02
3669 3933 2.202946 GCACTAGGCGCTCCCTTC 60.203 66.667 7.64 0.00 43.06 3.46
3687 3951 2.937689 ATGGCACCAGCACCTCCT 60.938 61.111 0.00 0.00 44.61 3.69
3710 3974 3.418913 TGACGTTGCAATCCGCCG 61.419 61.111 0.59 3.28 41.33 6.46
3712 3976 2.175811 GGTGACGTTGCAATCCGC 59.824 61.111 0.59 1.53 42.89 5.54
3731 3995 1.798223 CAGGCGATGTTTCAGAAACGA 59.202 47.619 19.08 10.19 44.28 3.85
3767 4031 1.227999 ATCCACACCTTCGCAACACG 61.228 55.000 0.00 0.00 45.62 4.49
3801 4065 4.320608 AATGACGGTGAAGTTGCAATTT 57.679 36.364 6.93 6.93 0.00 1.82


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

AutoCloner maintained by Alex Coulton.