Multiple sequence alignment - TraesCS5A01G325600

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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 TraesCS5A01G325600 chr5A 100.000 6231 0 0 1 6231 536260634 536266864 0.000000e+00 11507.0
1 TraesCS5A01G325600 chr5A 91.369 869 75 0 1 869 634468350 634469218 0.000000e+00 1190.0
2 TraesCS5A01G325600 chr5A 91.119 867 73 4 1 864 584709800 584710665 0.000000e+00 1171.0
3 TraesCS5A01G325600 chr5A 88.945 199 20 1 1302 1500 131303516 131303320 1.740000e-60 244.0
4 TraesCS5A01G325600 chr5A 87.931 174 15 1 1960 2127 131302950 131302777 3.810000e-47 200.0
5 TraesCS5A01G325600 chr5A 92.063 126 6 2 1699 1821 131303074 131302950 2.310000e-39 174.0
6 TraesCS5A01G325600 chr5A 87.919 149 14 2 1676 1821 486468771 486468624 8.300000e-39 172.0
7 TraesCS5A01G325600 chr5A 97.802 91 2 0 1502 1592 131303190 131303100 2.330000e-34 158.0
8 TraesCS5A01G325600 chr5D 92.902 2719 126 25 2803 5498 422758697 422761371 0.000000e+00 3890.0
9 TraesCS5A01G325600 chr5D 95.552 1686 46 8 1145 2815 422756696 422758367 0.000000e+00 2671.0
10 TraesCS5A01G325600 chr5D 91.116 878 72 4 1 877 493830161 493829289 0.000000e+00 1184.0
11 TraesCS5A01G325600 chr5D 88.545 550 32 8 5691 6231 422761579 422762106 6.810000e-179 638.0
12 TraesCS5A01G325600 chr5D 90.000 100 8 2 5549 5646 206590158 206590059 1.820000e-25 128.0
13 TraesCS5A01G325600 chr5B 95.236 2036 85 7 3288 5317 510376306 510378335 0.000000e+00 3212.0
14 TraesCS5A01G325600 chr5B 89.578 1564 100 23 1749 3279 510374526 510376059 0.000000e+00 1927.0
15 TraesCS5A01G325600 chr5B 94.032 754 30 9 908 1655 510373592 510374336 0.000000e+00 1129.0
16 TraesCS5A01G325600 chr5B 87.352 593 52 14 5643 6231 510378598 510379171 0.000000e+00 658.0
17 TraesCS5A01G325600 chr5B 96.894 161 5 0 5349 5509 510378438 510378598 2.860000e-68 270.0
18 TraesCS5A01G325600 chr5B 97.802 91 2 0 1502 1592 641053708 641053618 2.330000e-34 158.0
19 TraesCS5A01G325600 chr5B 90.265 113 6 3 1699 1808 641053592 641053482 6.510000e-30 143.0
20 TraesCS5A01G325600 chr2D 91.344 878 70 5 1 878 201455745 201456616 0.000000e+00 1195.0
21 TraesCS5A01G325600 chr2D 91.264 870 75 1 1 869 511531495 511532364 0.000000e+00 1184.0
22 TraesCS5A01G325600 chr2D 90.000 100 8 2 5549 5646 245235730 245235829 1.820000e-25 128.0
23 TraesCS5A01G325600 chr2A 91.494 870 71 3 1 869 689163616 689164483 0.000000e+00 1194.0
24 TraesCS5A01G325600 chr2A 90.992 877 74 4 1 877 559107173 559108044 0.000000e+00 1177.0
25 TraesCS5A01G325600 chr2A 87.919 149 14 2 1676 1821 60668891 60668744 8.300000e-39 172.0
26 TraesCS5A01G325600 chr2A 96.703 91 3 0 1502 1592 60668984 60668894 1.080000e-32 152.0
27 TraesCS5A01G325600 chr2A 90.000 100 8 2 5549 5646 2922066 2921967 1.820000e-25 128.0
28 TraesCS5A01G325600 chr7D 91.106 877 72 5 2 877 159701566 159702437 0.000000e+00 1182.0
29 TraesCS5A01G325600 chr4A 90.878 877 79 1 1 877 11807048 11807923 0.000000e+00 1175.0
30 TraesCS5A01G325600 chr4A 91.000 200 16 1 1301 1500 666458985 666459182 1.030000e-67 268.0
31 TraesCS5A01G325600 chr4A 91.000 200 16 1 1301 1500 666461527 666461724 1.030000e-67 268.0
32 TraesCS5A01G325600 chr4A 91.000 200 16 1 1301 1500 666465838 666466035 1.030000e-67 268.0
33 TraesCS5A01G325600 chr4A 89.000 200 20 2 1301 1500 724894335 724894138 4.820000e-61 246.0
34 TraesCS5A01G325600 chr4A 96.703 91 3 0 1502 1592 666459312 666459402 1.080000e-32 152.0
35 TraesCS5A01G325600 chr4A 96.703 91 3 0 1502 1592 666461854 666461944 1.080000e-32 152.0
36 TraesCS5A01G325600 chr4A 96.703 91 3 0 1502 1592 666466165 666466255 1.080000e-32 152.0
37 TraesCS5A01G325600 chr4A 88.496 113 8 3 1699 1808 666459428 666459538 1.410000e-26 132.0
38 TraesCS5A01G325600 chr4A 88.496 113 8 3 1699 1808 666461970 666462080 1.410000e-26 132.0
39 TraesCS5A01G325600 chr6A 88.937 461 37 5 1676 2127 217308900 217309355 1.960000e-154 556.0
40 TraesCS5A01G325600 chr6A 91.096 292 23 2 1301 1592 217308609 217308897 5.860000e-105 392.0
41 TraesCS5A01G325600 chr1A 90.452 199 17 1 1302 1500 119395997 119396193 1.720000e-65 261.0
42 TraesCS5A01G325600 chr1A 88.506 174 14 1 1960 2127 119396563 119396736 8.190000e-49 206.0
43 TraesCS5A01G325600 chr1A 91.270 126 7 2 1699 1821 119396439 119396563 1.070000e-37 169.0
44 TraesCS5A01G325600 chr4B 93.333 90 6 0 5558 5647 628078751 628078662 3.920000e-27 134.0
45 TraesCS5A01G325600 chr4B 90.000 100 7 3 5549 5646 166701524 166701426 6.560000e-25 126.0
46 TraesCS5A01G325600 chr4B 96.552 58 2 0 5505 5562 548143378 548143435 5.140000e-16 97.1
47 TraesCS5A01G325600 chr6B 90.099 101 8 2 5549 5647 39312868 39312968 5.070000e-26 130.0
48 TraesCS5A01G325600 chr6B 85.897 78 9 2 5486 5562 431707946 431707870 1.440000e-11 82.4
49 TraesCS5A01G325600 chr1D 89.109 101 9 2 5549 5647 11354715 11354615 2.360000e-24 124.0
50 TraesCS5A01G325600 chr1D 89.109 101 9 2 5549 5647 243460749 243460849 2.360000e-24 124.0
51 TraesCS5A01G325600 chr1D 89.109 101 9 2 5549 5647 420065340 420065240 2.360000e-24 124.0
52 TraesCS5A01G325600 chr1D 96.491 57 2 0 5506 5562 298168121 298168065 1.850000e-15 95.3
53 TraesCS5A01G325600 chr7B 82.609 138 20 3 5508 5641 623571307 623571170 1.100000e-22 119.0
54 TraesCS5A01G325600 chr7B 98.246 57 1 0 5506 5562 300702956 300702900 3.970000e-17 100.0
55 TraesCS5A01G325600 chr3D 96.491 57 2 0 5506 5562 93914195 93914139 1.850000e-15 95.3
56 TraesCS5A01G325600 chr3D 96.491 57 2 0 5506 5562 119035599 119035655 1.850000e-15 95.3
57 TraesCS5A01G325600 chr3D 96.491 57 2 0 5506 5562 395959608 395959664 1.850000e-15 95.3
58 TraesCS5A01G325600 chr3D 96.491 57 2 0 5506 5562 432438899 432438955 1.850000e-15 95.3


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 TraesCS5A01G325600 chr5A 536260634 536266864 6230 False 11507.000000 11507 100.0000 1 6231 1 chr5A.!!$F1 6230
1 TraesCS5A01G325600 chr5A 634468350 634469218 868 False 1190.000000 1190 91.3690 1 869 1 chr5A.!!$F3 868
2 TraesCS5A01G325600 chr5A 584709800 584710665 865 False 1171.000000 1171 91.1190 1 864 1 chr5A.!!$F2 863
3 TraesCS5A01G325600 chr5D 422756696 422762106 5410 False 2399.666667 3890 92.3330 1145 6231 3 chr5D.!!$F1 5086
4 TraesCS5A01G325600 chr5D 493829289 493830161 872 True 1184.000000 1184 91.1160 1 877 1 chr5D.!!$R2 876
5 TraesCS5A01G325600 chr5B 510373592 510379171 5579 False 1439.200000 3212 92.6184 908 6231 5 chr5B.!!$F1 5323
6 TraesCS5A01G325600 chr2D 201455745 201456616 871 False 1195.000000 1195 91.3440 1 878 1 chr2D.!!$F1 877
7 TraesCS5A01G325600 chr2D 511531495 511532364 869 False 1184.000000 1184 91.2640 1 869 1 chr2D.!!$F3 868
8 TraesCS5A01G325600 chr2A 689163616 689164483 867 False 1194.000000 1194 91.4940 1 869 1 chr2A.!!$F2 868
9 TraesCS5A01G325600 chr2A 559107173 559108044 871 False 1177.000000 1177 90.9920 1 877 1 chr2A.!!$F1 876
10 TraesCS5A01G325600 chr7D 159701566 159702437 871 False 1182.000000 1182 91.1060 2 877 1 chr7D.!!$F1 875
11 TraesCS5A01G325600 chr4A 11807048 11807923 875 False 1175.000000 1175 90.8780 1 877 1 chr4A.!!$F1 876
12 TraesCS5A01G325600 chr6A 217308609 217309355 746 False 474.000000 556 90.0165 1301 2127 2 chr6A.!!$F1 826
13 TraesCS5A01G325600 chr1A 119395997 119396736 739 False 212.000000 261 90.0760 1302 2127 3 chr1A.!!$F1 825

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
870 877 0.108945 GGTCGGTCCGTTGGAGTTAG 60.109 60.000 11.88 0.0 29.39 2.34 F
872 879 1.000171 GTCGGTCCGTTGGAGTTAGTT 60.000 52.381 11.88 0.0 29.39 2.24 F
1682 1946 0.108585 ACAGTGTTGGTCGATGCCTT 59.891 50.000 0.00 0.0 0.00 4.35 F
2711 3002 2.028112 TCCTTTGTATGCGTTGCTCTCT 60.028 45.455 0.00 0.0 0.00 3.10 F
4133 5037 0.172578 GTTCCCCAATAAGTTGCGCC 59.827 55.000 4.18 0.0 33.90 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1946 0.036164 ACCAGCCGAACAATACTGCA 59.964 50.000 0.00 0.0 0.00 4.41 R
2701 2992 2.473816 TGTGAACAGAAGAGAGCAACG 58.526 47.619 0.00 0.0 0.00 4.10 R
3093 3752 1.613925 AGAAGTACGTGCAGCTGAAGA 59.386 47.619 20.43 0.0 0.00 2.87 R
4500 5413 2.708051 ACATTGCAGTCTCACCATCAG 58.292 47.619 0.00 0.0 0.00 2.90 R
5817 6830 0.390340 GCTGCGTTCAGTCAGATGGA 60.390 55.000 0.00 0.0 42.29 3.41 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
141 142 4.168291 GCAAGGAGGAGGAGCGGG 62.168 72.222 0.00 0.00 0.00 6.13
296 297 2.115911 CGAGCGCTACTCCTGGACT 61.116 63.158 11.50 0.00 43.01 3.85
297 298 0.814410 CGAGCGCTACTCCTGGACTA 60.814 60.000 11.50 0.00 43.01 2.59
360 361 2.701780 GCGACGGAGAAGCAGGAGA 61.702 63.158 0.00 0.00 34.28 3.71
557 558 0.168348 CGACGTTGATCGACCTCACT 59.832 55.000 7.54 0.00 45.13 3.41
620 622 3.550561 CAGCGCGTCATCTTGTTTTTAA 58.449 40.909 8.43 0.00 0.00 1.52
659 661 0.109532 TGGACTTTCACCGGCATTCA 59.890 50.000 0.00 0.00 0.00 2.57
780 786 0.447801 GCTCGCACCGATTCAAACAT 59.552 50.000 0.00 0.00 34.61 2.71
869 876 1.535204 GGGTCGGTCCGTTGGAGTTA 61.535 60.000 11.88 0.00 37.00 2.24
870 877 0.108945 GGTCGGTCCGTTGGAGTTAG 60.109 60.000 11.88 0.00 29.39 2.34
872 879 1.000171 GTCGGTCCGTTGGAGTTAGTT 60.000 52.381 11.88 0.00 29.39 2.24
873 880 1.270550 TCGGTCCGTTGGAGTTAGTTC 59.729 52.381 11.88 0.00 29.39 3.01
875 882 2.288640 CGGTCCGTTGGAGTTAGTTCTT 60.289 50.000 2.08 0.00 29.39 2.52
876 883 3.057315 CGGTCCGTTGGAGTTAGTTCTTA 60.057 47.826 2.08 0.00 29.39 2.10
877 884 4.492611 GGTCCGTTGGAGTTAGTTCTTAG 58.507 47.826 0.00 0.00 29.39 2.18
878 885 4.492611 GTCCGTTGGAGTTAGTTCTTAGG 58.507 47.826 0.00 0.00 29.39 2.69
879 886 3.056322 TCCGTTGGAGTTAGTTCTTAGGC 60.056 47.826 0.00 0.00 0.00 3.93
880 887 3.056035 CCGTTGGAGTTAGTTCTTAGGCT 60.056 47.826 0.00 0.00 0.00 4.58
881 888 4.159135 CCGTTGGAGTTAGTTCTTAGGCTA 59.841 45.833 0.00 0.00 0.00 3.93
882 889 5.337009 CCGTTGGAGTTAGTTCTTAGGCTAA 60.337 44.000 6.80 6.80 0.00 3.09
883 890 5.575995 CGTTGGAGTTAGTTCTTAGGCTAAC 59.424 44.000 2.04 14.72 44.26 2.34
884 891 5.320549 TGGAGTTAGTTCTTAGGCTAACG 57.679 43.478 2.04 0.38 46.80 3.18
885 892 4.159135 TGGAGTTAGTTCTTAGGCTAACGG 59.841 45.833 2.04 0.00 46.80 4.44
886 893 4.441217 GGAGTTAGTTCTTAGGCTAACGGG 60.441 50.000 2.04 0.00 46.80 5.28
887 894 4.347607 AGTTAGTTCTTAGGCTAACGGGA 58.652 43.478 2.04 0.00 46.80 5.14
888 895 4.401837 AGTTAGTTCTTAGGCTAACGGGAG 59.598 45.833 2.04 0.00 46.80 4.30
889 896 3.097342 AGTTCTTAGGCTAACGGGAGA 57.903 47.619 2.04 0.00 0.00 3.71
890 897 3.025262 AGTTCTTAGGCTAACGGGAGAG 58.975 50.000 2.04 0.00 0.00 3.20
891 898 3.022406 GTTCTTAGGCTAACGGGAGAGA 58.978 50.000 2.04 0.00 0.00 3.10
892 899 3.377253 TCTTAGGCTAACGGGAGAGAA 57.623 47.619 2.04 0.00 0.00 2.87
893 900 3.705051 TCTTAGGCTAACGGGAGAGAAA 58.295 45.455 2.04 0.00 0.00 2.52
894 901 3.700038 TCTTAGGCTAACGGGAGAGAAAG 59.300 47.826 2.04 0.00 0.00 2.62
895 902 2.233305 AGGCTAACGGGAGAGAAAGA 57.767 50.000 0.00 0.00 0.00 2.52
896 903 2.104170 AGGCTAACGGGAGAGAAAGAG 58.896 52.381 0.00 0.00 0.00 2.85
897 904 1.826096 GGCTAACGGGAGAGAAAGAGT 59.174 52.381 0.00 0.00 0.00 3.24
898 905 2.234168 GGCTAACGGGAGAGAAAGAGTT 59.766 50.000 0.00 0.00 0.00 3.01
899 906 3.306849 GGCTAACGGGAGAGAAAGAGTTT 60.307 47.826 0.00 0.00 0.00 2.66
900 907 4.316645 GCTAACGGGAGAGAAAGAGTTTT 58.683 43.478 0.00 0.00 0.00 2.43
901 908 4.152580 GCTAACGGGAGAGAAAGAGTTTTG 59.847 45.833 0.00 0.00 0.00 2.44
902 909 3.840124 ACGGGAGAGAAAGAGTTTTGT 57.160 42.857 0.00 0.00 0.00 2.83
903 910 3.729966 ACGGGAGAGAAAGAGTTTTGTC 58.270 45.455 0.00 0.00 36.97 3.18
904 911 3.134081 ACGGGAGAGAAAGAGTTTTGTCA 59.866 43.478 0.00 0.00 38.63 3.58
905 912 4.202367 ACGGGAGAGAAAGAGTTTTGTCAT 60.202 41.667 0.00 0.00 38.63 3.06
906 913 4.390297 CGGGAGAGAAAGAGTTTTGTCATC 59.610 45.833 0.96 0.00 38.63 2.92
954 961 2.445845 TAGATCGGGTGGCCCTGG 60.446 66.667 0.00 0.00 42.67 4.45
997 1004 1.323412 CAGTAGGCGAGGCATAGACT 58.677 55.000 0.00 0.00 0.00 3.24
1003 1010 2.543802 CGAGGCATAGACTCCGCGA 61.544 63.158 8.23 0.00 46.23 5.87
1004 1011 1.857318 CGAGGCATAGACTCCGCGAT 61.857 60.000 8.23 0.00 46.23 4.58
1011 1018 4.632458 GACTCCGCGATCGAGGCC 62.632 72.222 30.37 18.32 38.10 5.19
1036 1043 1.070134 CGAAATCGCCCTATTCCTCCA 59.930 52.381 0.00 0.00 0.00 3.86
1405 1412 4.788521 GCGACCAAATCTTCGTCTGTTTTT 60.789 41.667 0.00 0.00 37.56 1.94
1406 1413 4.670621 CGACCAAATCTTCGTCTGTTTTTG 59.329 41.667 0.00 0.00 0.00 2.44
1514 1649 5.730550 TGAGTAGGTAATTGCTCGATTTGT 58.269 37.500 0.00 0.00 0.00 2.83
1601 1738 6.986904 AGTTAGCTTTACTTGGATAACTGC 57.013 37.500 0.00 0.00 41.21 4.40
1602 1739 6.472887 AGTTAGCTTTACTTGGATAACTGCA 58.527 36.000 0.00 0.00 41.21 4.41
1603 1740 6.371825 AGTTAGCTTTACTTGGATAACTGCAC 59.628 38.462 0.00 0.00 41.21 4.57
1604 1741 4.911390 AGCTTTACTTGGATAACTGCACT 58.089 39.130 0.00 0.00 0.00 4.40
1682 1946 0.108585 ACAGTGTTGGTCGATGCCTT 59.891 50.000 0.00 0.00 0.00 4.35
1695 1959 2.537529 CGATGCCTTGCAGTATTGTTCG 60.538 50.000 0.00 0.00 43.65 3.95
1926 2193 6.127619 GGATTATAGAGGTTTTTGCAAGTGCT 60.128 38.462 0.00 0.00 42.66 4.40
2098 2377 5.431179 TGTACCTTTCCTTGTCTATTCCC 57.569 43.478 0.00 0.00 0.00 3.97
2256 2535 7.672983 TGGCTGAATCAGAAACTTACTTTAG 57.327 36.000 15.38 0.00 32.44 1.85
2425 2704 4.935808 AGTTTGAGAACCGTATGATGTTCC 59.064 41.667 0.00 0.00 41.36 3.62
2550 2830 7.781324 ACCTTTCATATTGACTGTGGATTTT 57.219 32.000 0.00 0.00 0.00 1.82
2552 2832 7.671398 ACCTTTCATATTGACTGTGGATTTTCT 59.329 33.333 0.00 0.00 0.00 2.52
2594 2874 4.977963 ACTTTTGTGATCAAGATTGTTGCG 59.022 37.500 0.00 0.00 34.88 4.85
2701 2992 8.383318 AGTACATATGTCATTCCTTTGTATGC 57.617 34.615 12.68 0.00 0.00 3.14
2711 3002 2.028112 TCCTTTGTATGCGTTGCTCTCT 60.028 45.455 0.00 0.00 0.00 3.10
2716 3007 2.029020 TGTATGCGTTGCTCTCTTCTGT 60.029 45.455 0.00 0.00 0.00 3.41
2772 3063 6.780706 TTAGACCAGTCATTCTTTCGTTTC 57.219 37.500 0.00 0.00 0.00 2.78
2969 3627 5.710409 ACCTGGTATGGTAATGCTTACTT 57.290 39.130 0.00 0.00 38.79 2.24
2996 3654 4.874970 AGTGAAAATGTGCACTGATTTCC 58.125 39.130 25.54 19.97 43.26 3.13
3006 3664 2.553028 GCACTGATTTCCCTTGACCTCA 60.553 50.000 0.00 0.00 0.00 3.86
3071 3729 4.782019 TGCGAATCTGCAAGGTTTTAAT 57.218 36.364 0.00 0.00 37.45 1.40
3310 4207 0.535335 GTCGGTTCCTGGTGATAGCA 59.465 55.000 0.00 0.00 0.00 3.49
3364 4261 3.124297 GTCTCACTGTTTGTGCTCATAGC 59.876 47.826 0.00 0.00 45.81 2.97
3407 4304 4.273480 CCTATCGGCACTGTTTCTTTATGG 59.727 45.833 0.00 0.00 0.00 2.74
3884 4787 5.128919 AGAGCTATCCAGGTGCATTTTTAG 58.871 41.667 0.00 0.00 30.99 1.85
4133 5037 0.172578 GTTCCCCAATAAGTTGCGCC 59.827 55.000 4.18 0.00 33.90 6.53
4259 5165 0.252197 AAGAGTGGACCGGTAATGCC 59.748 55.000 7.34 4.75 0.00 4.40
4295 5201 6.208988 ACCACTGTTTTCTTTTCTTTCCTC 57.791 37.500 0.00 0.00 0.00 3.71
4494 5407 8.141909 TGTCTCAATATAGTTTAGCGCACTTAT 58.858 33.333 11.47 2.73 0.00 1.73
4500 5413 4.278678 AGTTTAGCGCACTTATGAATGC 57.721 40.909 11.47 0.00 38.52 3.56
4516 5429 0.616891 ATGCTGATGGTGAGACTGCA 59.383 50.000 0.00 0.00 41.12 4.41
4629 5542 5.109903 AGTTGAGGTATTAATCACTGACGC 58.890 41.667 0.00 0.00 0.00 5.19
4718 5631 4.550076 AAAGAGAAGGATGAGGTGACTG 57.450 45.455 0.00 0.00 44.43 3.51
4742 5655 6.071952 TGACCAATCTCTTCTATTTTTGGTGC 60.072 38.462 9.67 3.41 45.00 5.01
4763 5676 0.179156 CACATGCGGCATTCCAGAAC 60.179 55.000 13.81 0.00 0.00 3.01
4767 5680 2.409870 GCGGCATTCCAGAACCCAG 61.410 63.158 0.00 0.00 0.00 4.45
4780 5693 8.561536 TTCCAGAACCCAGATGTCTAATAATA 57.438 34.615 0.00 0.00 0.00 0.98
4910 5823 7.538678 CGACCCTTTTATCTTTTCATTCACTTG 59.461 37.037 0.00 0.00 0.00 3.16
4944 5857 1.259316 GCATTGTCGGCAAATTCGTC 58.741 50.000 6.51 0.00 38.21 4.20
5074 5991 6.411652 GTTTGAGAACTGAAGTGTTTCTACG 58.588 40.000 0.00 0.00 34.31 3.51
5177 6094 9.152595 GATTTCCCTTACTGAACTGTAGTAAAG 57.847 37.037 5.09 0.30 39.40 1.85
5211 6128 4.853924 ATGCTCCTGAAAATTTTCGTGT 57.146 36.364 22.51 5.11 40.01 4.49
5240 6157 2.222027 GGTGCACTTGGATATGGTAGC 58.778 52.381 17.98 0.00 0.00 3.58
5241 6158 2.222027 GTGCACTTGGATATGGTAGCC 58.778 52.381 10.32 0.00 34.02 3.93
5271 6188 2.242047 TTTTCGACGACCATGTTCCA 57.758 45.000 0.00 0.00 0.00 3.53
5398 6386 4.210832 TCGTGTAGTATCATGCTTCTCG 57.789 45.455 0.00 0.00 0.00 4.04
5462 6450 0.251922 ACTCACGCCTGGGTAGGTTA 60.252 55.000 0.00 0.00 46.41 2.85
5499 6487 5.171339 ACCATCTGCTGATTGAAAGTAGT 57.829 39.130 11.03 0.00 0.00 2.73
5515 6503 8.946797 TGAAAGTAGTAGTTTAGTACTCCCTT 57.053 34.615 0.00 3.17 42.53 3.95
5518 6506 6.716284 AGTAGTAGTTTAGTACTCCCTTCGT 58.284 40.000 0.00 0.00 40.04 3.85
5519 6507 7.171653 AGTAGTAGTTTAGTACTCCCTTCGTT 58.828 38.462 0.00 0.00 40.04 3.85
5520 6508 6.507958 AGTAGTTTAGTACTCCCTTCGTTC 57.492 41.667 0.00 0.00 38.33 3.95
5522 6510 4.414677 AGTTTAGTACTCCCTTCGTTCCT 58.585 43.478 0.00 0.00 28.23 3.36
5523 6511 5.574188 AGTTTAGTACTCCCTTCGTTCCTA 58.426 41.667 0.00 0.00 28.23 2.94
5525 6513 6.494835 AGTTTAGTACTCCCTTCGTTCCTAAA 59.505 38.462 0.00 0.00 28.23 1.85
5528 6516 8.773033 TTAGTACTCCCTTCGTTCCTAAATAT 57.227 34.615 0.00 0.00 0.00 1.28
5533 6521 6.822170 ACTCCCTTCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
5534 6522 6.954232 TCCCTTCGTTCCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
5535 6523 7.399634 TCCCTTCGTTCCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
5537 6525 9.169592 CCCTTCGTTCCTAAATATTTGTCTTTA 57.830 33.333 11.05 0.00 0.00 1.85
5581 6569 9.988350 GACTACACTTTAAAATATGTCCACATG 57.012 33.333 2.26 0.00 37.15 3.21
5582 6570 8.458843 ACTACACTTTAAAATATGTCCACATGC 58.541 33.333 2.26 0.00 37.15 4.06
5583 6571 7.225784 ACACTTTAAAATATGTCCACATGCA 57.774 32.000 2.26 0.00 37.15 3.96
5585 6573 7.975616 ACACTTTAAAATATGTCCACATGCATC 59.024 33.333 0.00 0.00 37.15 3.91
5586 6574 7.436080 CACTTTAAAATATGTCCACATGCATCC 59.564 37.037 0.00 0.00 37.15 3.51
5587 6575 4.572985 AAAATATGTCCACATGCATCCG 57.427 40.909 0.00 0.00 37.15 4.18
5588 6576 3.490439 AATATGTCCACATGCATCCGA 57.510 42.857 0.00 0.00 37.15 4.55
5589 6577 2.998316 TATGTCCACATGCATCCGAA 57.002 45.000 0.00 0.00 37.15 4.30
5590 6578 2.353357 ATGTCCACATGCATCCGAAT 57.647 45.000 0.00 0.00 34.83 3.34
5591 6579 1.381522 TGTCCACATGCATCCGAATG 58.618 50.000 0.00 0.00 35.87 2.67
5592 6580 1.339920 TGTCCACATGCATCCGAATGT 60.340 47.619 0.00 0.00 37.50 2.71
5594 6582 3.930400 CACATGCATCCGAATGTGG 57.070 52.632 7.79 0.00 46.43 4.17
5596 6584 2.287769 CACATGCATCCGAATGTGGTA 58.712 47.619 7.79 0.00 46.43 3.25
5597 6585 2.288729 CACATGCATCCGAATGTGGTAG 59.711 50.000 7.79 0.00 46.43 3.18
5598 6586 2.092968 ACATGCATCCGAATGTGGTAGT 60.093 45.455 0.00 0.00 35.71 2.73
5600 6588 2.627945 TGCATCCGAATGTGGTAGTTC 58.372 47.619 0.00 0.00 35.18 3.01
5602 6590 3.206150 GCATCCGAATGTGGTAGTTCAT 58.794 45.455 0.00 0.00 35.18 2.57
5603 6591 3.627577 GCATCCGAATGTGGTAGTTCATT 59.372 43.478 0.00 0.00 37.04 2.57
5604 6592 4.096382 GCATCCGAATGTGGTAGTTCATTT 59.904 41.667 0.00 0.00 34.92 2.32
5605 6593 5.572211 CATCCGAATGTGGTAGTTCATTTG 58.428 41.667 0.00 0.00 34.92 2.32
5606 6594 4.900684 TCCGAATGTGGTAGTTCATTTGA 58.099 39.130 0.00 0.00 37.53 2.69
5607 6595 5.309638 TCCGAATGTGGTAGTTCATTTGAA 58.690 37.500 0.00 0.00 37.53 2.69
5611 6624 7.362056 CCGAATGTGGTAGTTCATTTGAAATCT 60.362 37.037 0.00 0.00 37.53 2.40
5693 6706 7.066163 GTCAATCCAGTGATGACACATCATAAA 59.934 37.037 15.71 5.14 46.01 1.40
5708 6721 9.751542 ACACATCATAAAACTACTAGCTGTATC 57.248 33.333 0.00 0.00 0.00 2.24
5720 6733 6.299805 ACTAGCTGTATCCTGAATTGTTCA 57.700 37.500 0.00 0.00 38.17 3.18
5773 6786 3.567478 GGTTAGAGACCTCCAATGCAT 57.433 47.619 0.00 0.00 45.55 3.96
5868 6881 4.608269 TGAAATCATATCCCAAACAGCCA 58.392 39.130 0.00 0.00 0.00 4.75
5902 6915 1.364626 GCTCTCCACTCCATGCAACG 61.365 60.000 0.00 0.00 0.00 4.10
5923 6936 2.093606 GCACACCTTTCTCCTACTACCC 60.094 54.545 0.00 0.00 0.00 3.69
5924 6937 2.500504 CACACCTTTCTCCTACTACCCC 59.499 54.545 0.00 0.00 0.00 4.95
5925 6938 2.113052 ACACCTTTCTCCTACTACCCCA 59.887 50.000 0.00 0.00 0.00 4.96
5926 6939 2.500504 CACCTTTCTCCTACTACCCCAC 59.499 54.545 0.00 0.00 0.00 4.61
5927 6940 2.386113 ACCTTTCTCCTACTACCCCACT 59.614 50.000 0.00 0.00 0.00 4.00
5928 6941 3.599698 ACCTTTCTCCTACTACCCCACTA 59.400 47.826 0.00 0.00 0.00 2.74
5929 6942 3.959449 CCTTTCTCCTACTACCCCACTAC 59.041 52.174 0.00 0.00 0.00 2.73
5930 6943 4.571362 CCTTTCTCCTACTACCCCACTACA 60.571 50.000 0.00 0.00 0.00 2.74
5931 6944 3.659183 TCTCCTACTACCCCACTACAC 57.341 52.381 0.00 0.00 0.00 2.90
5932 6945 2.921612 TCTCCTACTACCCCACTACACA 59.078 50.000 0.00 0.00 0.00 3.72
5933 6946 3.022406 CTCCTACTACCCCACTACACAC 58.978 54.545 0.00 0.00 0.00 3.82
5934 6947 2.651334 TCCTACTACCCCACTACACACT 59.349 50.000 0.00 0.00 0.00 3.55
5935 6948 2.758979 CCTACTACCCCACTACACACTG 59.241 54.545 0.00 0.00 0.00 3.66
5936 6949 1.640917 ACTACCCCACTACACACTGG 58.359 55.000 0.00 0.00 0.00 4.00
5937 6950 1.148446 ACTACCCCACTACACACTGGA 59.852 52.381 0.00 0.00 0.00 3.86
5938 6951 1.825474 CTACCCCACTACACACTGGAG 59.175 57.143 0.00 0.00 33.50 3.86
5939 6952 0.105142 ACCCCACTACACACTGGAGT 60.105 55.000 0.00 0.00 43.76 3.85
5940 6953 1.056660 CCCCACTACACACTGGAGTT 58.943 55.000 0.00 0.00 38.73 3.01
5941 6954 1.270839 CCCCACTACACACTGGAGTTG 60.271 57.143 0.00 0.00 38.73 3.16
6009 7027 1.298340 CTACACCACCCATCGCCAA 59.702 57.895 0.00 0.00 0.00 4.52
6051 7077 0.328258 TGGCCTCTTCTTACCTTGCC 59.672 55.000 3.32 0.00 37.90 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.478371 TCGCCTCGCCTCCTCGTA 62.478 66.667 0.00 0.00 0.00 3.43
35 36 2.900273 GGCAGGCTGTGGTCGATA 59.100 61.111 17.16 0.00 0.00 2.92
36 37 4.457496 CGGCAGGCTGTGGTCGAT 62.457 66.667 17.16 0.00 0.00 3.59
109 110 0.034767 CTTGCTCTCCTTGATGGCCA 60.035 55.000 8.56 8.56 35.26 5.36
296 297 1.374343 CCCACTCGCGCACTACTCTA 61.374 60.000 8.75 0.00 0.00 2.43
297 298 2.701780 CCCACTCGCGCACTACTCT 61.702 63.158 8.75 0.00 0.00 3.24
360 361 3.066814 GTGGTCGAGGTAGGCCGT 61.067 66.667 0.00 0.00 39.14 5.68
402 403 3.710722 CTCGCCCTCCCAGTGCTT 61.711 66.667 0.00 0.00 0.00 3.91
481 482 1.448893 GCGGTGATGTCGGGCTTTA 60.449 57.895 0.00 0.00 0.00 1.85
575 576 1.136984 GGCGTTCTCATCGTCGACT 59.863 57.895 14.70 0.00 0.00 4.18
577 578 0.656259 CTAGGCGTTCTCATCGTCGA 59.344 55.000 0.00 0.00 37.99 4.20
659 661 5.351948 AATTAAACATAAAAGCCGGCCAT 57.648 34.783 26.15 10.27 0.00 4.40
767 773 4.454504 GTCTGGTGTTATGTTTGAATCGGT 59.545 41.667 0.00 0.00 0.00 4.69
780 786 4.941263 GGCTGATACAAATGTCTGGTGTTA 59.059 41.667 0.00 0.00 0.00 2.41
869 876 3.025262 CTCTCCCGTTAGCCTAAGAACT 58.975 50.000 0.00 0.00 0.00 3.01
870 877 3.022406 TCTCTCCCGTTAGCCTAAGAAC 58.978 50.000 0.00 0.00 0.00 3.01
872 879 3.377253 TTCTCTCCCGTTAGCCTAAGA 57.623 47.619 0.00 0.00 0.00 2.10
873 880 3.700038 TCTTTCTCTCCCGTTAGCCTAAG 59.300 47.826 0.00 0.00 0.00 2.18
875 882 3.288964 CTCTTTCTCTCCCGTTAGCCTA 58.711 50.000 0.00 0.00 0.00 3.93
876 883 2.104170 CTCTTTCTCTCCCGTTAGCCT 58.896 52.381 0.00 0.00 0.00 4.58
877 884 1.826096 ACTCTTTCTCTCCCGTTAGCC 59.174 52.381 0.00 0.00 0.00 3.93
878 885 3.596310 AACTCTTTCTCTCCCGTTAGC 57.404 47.619 0.00 0.00 0.00 3.09
879 886 5.298347 ACAAAACTCTTTCTCTCCCGTTAG 58.702 41.667 0.00 0.00 0.00 2.34
880 887 5.163385 TGACAAAACTCTTTCTCTCCCGTTA 60.163 40.000 0.00 0.00 0.00 3.18
881 888 4.127907 GACAAAACTCTTTCTCTCCCGTT 58.872 43.478 0.00 0.00 0.00 4.44
882 889 3.134081 TGACAAAACTCTTTCTCTCCCGT 59.866 43.478 0.00 0.00 0.00 5.28
883 890 3.728845 TGACAAAACTCTTTCTCTCCCG 58.271 45.455 0.00 0.00 0.00 5.14
884 891 5.555966 AGATGACAAAACTCTTTCTCTCCC 58.444 41.667 0.00 0.00 0.00 4.30
885 892 6.463360 AGAGATGACAAAACTCTTTCTCTCC 58.537 40.000 0.00 0.00 37.69 3.71
886 893 7.961325 AAGAGATGACAAAACTCTTTCTCTC 57.039 36.000 13.44 3.28 44.97 3.20
893 900 5.762218 CCAGACAAAGAGATGACAAAACTCT 59.238 40.000 0.00 0.00 41.86 3.24
894 901 5.760253 TCCAGACAAAGAGATGACAAAACTC 59.240 40.000 0.00 0.00 0.00 3.01
895 902 5.529060 GTCCAGACAAAGAGATGACAAAACT 59.471 40.000 0.00 0.00 0.00 2.66
896 903 5.278022 GGTCCAGACAAAGAGATGACAAAAC 60.278 44.000 0.00 0.00 0.00 2.43
897 904 4.821805 GGTCCAGACAAAGAGATGACAAAA 59.178 41.667 0.00 0.00 0.00 2.44
898 905 4.103153 AGGTCCAGACAAAGAGATGACAAA 59.897 41.667 0.00 0.00 0.00 2.83
899 906 3.648067 AGGTCCAGACAAAGAGATGACAA 59.352 43.478 0.00 0.00 0.00 3.18
900 907 3.242867 AGGTCCAGACAAAGAGATGACA 58.757 45.455 0.00 0.00 0.00 3.58
901 908 3.259374 TGAGGTCCAGACAAAGAGATGAC 59.741 47.826 0.00 0.00 0.00 3.06
902 909 3.510459 TGAGGTCCAGACAAAGAGATGA 58.490 45.455 0.00 0.00 0.00 2.92
903 910 3.969287 TGAGGTCCAGACAAAGAGATG 57.031 47.619 0.00 0.00 0.00 2.90
904 911 4.080638 GGATTGAGGTCCAGACAAAGAGAT 60.081 45.833 0.00 0.00 38.20 2.75
905 912 3.261897 GGATTGAGGTCCAGACAAAGAGA 59.738 47.826 0.00 0.00 38.20 3.10
906 913 3.604582 GGATTGAGGTCCAGACAAAGAG 58.395 50.000 0.00 0.00 38.20 2.85
954 961 0.388134 ATATACCACGCGATCGCCAC 60.388 55.000 32.63 7.86 39.84 5.01
964 971 2.921069 GCCTACTGCGACATATACCACG 60.921 54.545 0.00 0.00 0.00 4.94
990 997 0.167033 CCTCGATCGCGGAGTCTATG 59.833 60.000 19.37 0.00 38.28 2.23
997 1004 3.900892 GAAGGCCTCGATCGCGGA 61.901 66.667 27.60 1.05 38.28 5.54
1003 1010 0.106894 GATTTCGGGAAGGCCTCGAT 59.893 55.000 15.03 2.28 36.95 3.59
1004 1011 1.520666 GATTTCGGGAAGGCCTCGA 59.479 57.895 5.23 8.65 35.84 4.04
1011 1018 2.143925 GAATAGGGCGATTTCGGGAAG 58.856 52.381 1.75 0.00 40.23 3.46
1165 1172 0.764752 ACATCCTTCCTCCCCGGATC 60.765 60.000 0.73 0.00 42.70 3.36
1171 1178 2.444256 CCCCGACATCCTTCCTCCC 61.444 68.421 0.00 0.00 0.00 4.30
1405 1412 1.668826 AGTAAGGGAATCCACCAGCA 58.331 50.000 0.09 0.00 34.83 4.41
1406 1413 2.485657 GCTAGTAAGGGAATCCACCAGC 60.486 54.545 0.09 0.00 34.83 4.85
1514 1649 1.064003 ACAACATACCACAGGGCTGA 58.936 50.000 0.00 0.00 37.90 4.26
1601 1738 9.243637 GCTATAAACTTACATCTTCTGAGAGTG 57.756 37.037 0.00 0.00 34.85 3.51
1602 1739 8.417884 GGCTATAAACTTACATCTTCTGAGAGT 58.582 37.037 0.00 0.00 34.85 3.24
1603 1740 8.637986 AGGCTATAAACTTACATCTTCTGAGAG 58.362 37.037 0.00 0.00 34.85 3.20
1604 1741 8.540507 AGGCTATAAACTTACATCTTCTGAGA 57.459 34.615 0.00 0.00 36.09 3.27
1682 1946 0.036164 ACCAGCCGAACAATACTGCA 59.964 50.000 0.00 0.00 0.00 4.41
1695 1959 2.871633 CAAATCCAACAAAACACCAGCC 59.128 45.455 0.00 0.00 0.00 4.85
1859 2126 7.890127 TCAAAGATCCAATGAAATAACTCCACT 59.110 33.333 0.00 0.00 0.00 4.00
1926 2193 4.160814 AGCTCCACGGTATACATTTACACA 59.839 41.667 5.01 0.00 0.00 3.72
2098 2377 5.047188 AGTGAACAAAATTTACTTTGCCCG 58.953 37.500 0.00 0.00 39.46 6.13
2550 2830 8.500753 AAAGTACATAAACAGTCAAACACAGA 57.499 30.769 0.00 0.00 0.00 3.41
2552 2832 8.516234 ACAAAAGTACATAAACAGTCAAACACA 58.484 29.630 0.00 0.00 0.00 3.72
2594 2874 9.455847 GAAAGAAATATGATATCCAAACTGCAC 57.544 33.333 0.00 0.00 0.00 4.57
2701 2992 2.473816 TGTGAACAGAAGAGAGCAACG 58.526 47.619 0.00 0.00 0.00 4.10
2711 3002 5.398603 ACAACACCAATTTGTGAACAGAA 57.601 34.783 16.01 0.00 39.57 3.02
2838 3493 9.253832 TCATACAAAAATTCCATCAGGTTGTAT 57.746 29.630 0.00 0.00 40.16 2.29
2969 3627 3.698539 TCAGTGCACATTTTCACTTCCAA 59.301 39.130 21.04 0.00 41.19 3.53
2996 3654 4.589216 TTGCAAAGAATTGAGGTCAAGG 57.411 40.909 0.00 0.00 39.47 3.61
3006 3664 4.518970 ACACCACGAGTATTGCAAAGAATT 59.481 37.500 1.71 0.00 0.00 2.17
3093 3752 1.613925 AGAAGTACGTGCAGCTGAAGA 59.386 47.619 20.43 0.00 0.00 2.87
3094 3753 2.071688 AGAAGTACGTGCAGCTGAAG 57.928 50.000 20.43 9.97 0.00 3.02
3364 4261 2.615493 GGTCAATACATATCCCAGGGCG 60.615 54.545 0.00 0.00 0.00 6.13
3549 4448 5.010282 ACCAACACTCCAAGGAATCATAAC 58.990 41.667 0.00 0.00 0.00 1.89
3794 4697 4.276926 GGTTCATCTGAAACAGGGATATGC 59.723 45.833 3.12 0.00 41.25 3.14
3884 4787 4.590850 AAGAGGAACAATTTTCCAGTGC 57.409 40.909 16.65 7.35 41.00 4.40
4259 5165 6.766467 AGAAAACAGTGGTAGTTAAGGAACAG 59.234 38.462 0.00 0.00 38.10 3.16
4429 5335 4.702831 TGCGCTTTGATGATAGGTGATAA 58.297 39.130 9.73 0.00 0.00 1.75
4494 5407 2.938314 GCAGTCTCACCATCAGCATTCA 60.938 50.000 0.00 0.00 0.00 2.57
4500 5413 2.708051 ACATTGCAGTCTCACCATCAG 58.292 47.619 0.00 0.00 0.00 2.90
4516 5429 9.607285 GTGTCACGTGATTTTCTTTTATACATT 57.393 29.630 23.12 0.00 0.00 2.71
4718 5631 6.325596 GCACCAAAAATAGAAGAGATTGGTC 58.674 40.000 5.09 0.00 45.39 4.02
4742 5655 2.755064 TGGAATGCCGCATGTGGG 60.755 61.111 26.23 13.53 36.79 4.61
4785 5698 3.340928 CATGAGACTGCAACCATCAAGA 58.659 45.455 0.00 0.00 0.00 3.02
4910 5823 3.806380 ACAATGCAGACAGATCATCCTC 58.194 45.455 0.00 0.00 0.00 3.71
5049 5966 5.819825 AGAAACACTTCAGTTCTCAAACC 57.180 39.130 0.00 0.00 35.92 3.27
5074 5991 6.487103 GTGCTAGTTGCTACATAAATCCAAC 58.513 40.000 0.13 0.00 43.37 3.77
5101 6018 5.069318 TCGGATATGGCATTAGCAAAATCA 58.931 37.500 4.78 0.00 44.61 2.57
5177 6094 1.482593 AGGAGCATACAGGTGTACAGC 59.517 52.381 17.29 17.29 36.03 4.40
5211 6128 6.040729 CCATATCCAAGTGCACCAAATGATTA 59.959 38.462 14.63 4.08 0.00 1.75
5240 6157 2.601314 TCGTCGAAAATAAGATGTGCGG 59.399 45.455 0.00 0.00 0.00 5.69
5241 6158 3.541516 GGTCGTCGAAAATAAGATGTGCG 60.542 47.826 0.00 0.00 0.00 5.34
5271 6188 4.058817 CAAAAGCACCGAGAAGACTAACT 58.941 43.478 0.00 0.00 0.00 2.24
5321 6238 1.043816 ATGTCCCTCACCATAGCGAG 58.956 55.000 0.00 0.00 0.00 5.03
5398 6386 3.313526 GTGTGTGAACCATATCTGCATCC 59.686 47.826 0.00 0.00 0.00 3.51
5462 6450 3.822735 CAGATGGTCAAACTGTTGGTGAT 59.177 43.478 0.00 0.00 35.29 3.06
5499 6487 5.574188 AGGAACGAAGGGAGTACTAAACTA 58.426 41.667 0.00 0.00 39.07 2.24
5555 6543 9.988350 CATGTGGACATATTTTAAAGTGTAGTC 57.012 33.333 0.00 0.00 34.26 2.59
5556 6544 8.458843 GCATGTGGACATATTTTAAAGTGTAGT 58.541 33.333 0.00 0.00 34.26 2.73
5557 6545 8.458052 TGCATGTGGACATATTTTAAAGTGTAG 58.542 33.333 0.00 0.00 34.26 2.74
5558 6546 8.341892 TGCATGTGGACATATTTTAAAGTGTA 57.658 30.769 0.00 0.00 34.26 2.90
5559 6547 7.225784 TGCATGTGGACATATTTTAAAGTGT 57.774 32.000 0.00 3.53 34.26 3.55
5560 6548 7.436080 GGATGCATGTGGACATATTTTAAAGTG 59.564 37.037 2.46 0.00 34.26 3.16
5561 6549 7.491682 GGATGCATGTGGACATATTTTAAAGT 58.508 34.615 2.46 0.00 34.26 2.66
5562 6550 6.638063 CGGATGCATGTGGACATATTTTAAAG 59.362 38.462 2.46 0.00 34.26 1.85
5563 6551 6.319911 TCGGATGCATGTGGACATATTTTAAA 59.680 34.615 2.46 0.00 34.26 1.52
5565 6553 5.372373 TCGGATGCATGTGGACATATTTTA 58.628 37.500 2.46 0.00 34.26 1.52
5566 6554 4.206375 TCGGATGCATGTGGACATATTTT 58.794 39.130 2.46 0.00 34.26 1.82
5569 6557 3.490439 TTCGGATGCATGTGGACATAT 57.510 42.857 2.46 0.00 34.26 1.78
5571 6559 1.951602 CATTCGGATGCATGTGGACAT 59.048 47.619 2.46 0.00 36.96 3.06
5573 6561 1.064505 CACATTCGGATGCATGTGGAC 59.935 52.381 2.46 0.00 43.34 4.02
5575 6563 3.930400 CACATTCGGATGCATGTGG 57.070 52.632 2.46 0.00 43.34 4.17
5581 6569 2.627945 TGAACTACCACATTCGGATGC 58.372 47.619 2.75 0.00 36.72 3.91
5582 6570 5.353956 TCAAATGAACTACCACATTCGGATG 59.646 40.000 0.88 0.88 35.99 3.51
5583 6571 5.496556 TCAAATGAACTACCACATTCGGAT 58.503 37.500 0.00 0.00 35.99 4.18
5585 6573 5.621197 TTCAAATGAACTACCACATTCGG 57.379 39.130 0.00 0.00 35.99 4.30
5586 6574 7.530010 AGATTTCAAATGAACTACCACATTCG 58.470 34.615 0.00 0.00 35.99 3.34
5587 6575 9.696917 AAAGATTTCAAATGAACTACCACATTC 57.303 29.630 0.00 0.00 35.99 2.67
5616 6629 9.768215 TCCCTCCATTTCTAAATATTTGTCTTT 57.232 29.630 11.05 0.00 0.00 2.52
5620 6633 9.853177 CTACTCCCTCCATTTCTAAATATTTGT 57.147 33.333 11.05 0.00 0.00 2.83
5621 6634 9.289782 CCTACTCCCTCCATTTCTAAATATTTG 57.710 37.037 11.05 1.65 0.00 2.32
5622 6635 9.015146 ACCTACTCCCTCCATTTCTAAATATTT 57.985 33.333 5.89 5.89 0.00 1.40
5623 6636 8.582891 ACCTACTCCCTCCATTTCTAAATATT 57.417 34.615 0.00 0.00 0.00 1.28
5624 6637 8.582891 AACCTACTCCCTCCATTTCTAAATAT 57.417 34.615 0.00 0.00 0.00 1.28
5630 6643 4.175962 TGAAACCTACTCCCTCCATTTCT 58.824 43.478 0.00 0.00 0.00 2.52
5632 6645 4.325344 CCATGAAACCTACTCCCTCCATTT 60.325 45.833 0.00 0.00 0.00 2.32
5635 6648 2.196595 CCATGAAACCTACTCCCTCCA 58.803 52.381 0.00 0.00 0.00 3.86
5693 6706 7.425224 ACAATTCAGGATACAGCTAGTAGTT 57.575 36.000 0.00 0.00 35.85 2.24
5720 6733 9.462606 CCACCTCTCCTTAAAAATATTAACACT 57.537 33.333 0.00 0.00 0.00 3.55
5729 6742 3.092301 GCTGCCACCTCTCCTTAAAAAT 58.908 45.455 0.00 0.00 0.00 1.82
5733 6746 1.003580 CTTGCTGCCACCTCTCCTTAA 59.996 52.381 0.00 0.00 0.00 1.85
5734 6747 0.615331 CTTGCTGCCACCTCTCCTTA 59.385 55.000 0.00 0.00 0.00 2.69
5737 6750 2.045536 CCTTGCTGCCACCTCTCC 60.046 66.667 0.00 0.00 0.00 3.71
5773 6786 2.477245 TCCAACAGCTAGGGCATTAGA 58.523 47.619 0.00 0.00 41.70 2.10
5817 6830 0.390340 GCTGCGTTCAGTCAGATGGA 60.390 55.000 0.00 0.00 42.29 3.41
5828 6841 3.476295 TCAAATTGAGATGCTGCGTTC 57.524 42.857 0.00 0.00 0.00 3.95
5829 6842 3.921119 TTCAAATTGAGATGCTGCGTT 57.079 38.095 0.00 0.00 0.00 4.84
5831 6844 4.417506 TGATTTCAAATTGAGATGCTGCG 58.582 39.130 3.62 0.00 0.00 5.18
5832 6845 7.328737 GGATATGATTTCAAATTGAGATGCTGC 59.671 37.037 3.62 0.00 0.00 5.25
5835 6848 7.663827 TGGGATATGATTTCAAATTGAGATGC 58.336 34.615 3.62 0.00 0.00 3.91
5862 6875 3.679389 CATCTTAGTCCAGTTTGGCTGT 58.321 45.455 0.00 0.00 43.55 4.40
5902 6915 2.093606 GGGTAGTAGGAGAAAGGTGTGC 60.094 54.545 0.00 0.00 0.00 4.57
5923 6936 1.070758 AGCAACTCCAGTGTGTAGTGG 59.929 52.381 0.00 0.00 46.90 4.00
5924 6937 2.408050 GAGCAACTCCAGTGTGTAGTG 58.592 52.381 0.00 0.00 0.00 2.74
5925 6938 2.821991 GAGCAACTCCAGTGTGTAGT 57.178 50.000 0.00 0.00 0.00 2.73
5951 6964 0.396974 AGGGTTTGGTGCAAGCTCAA 60.397 50.000 0.00 0.00 33.76 3.02
5958 6971 0.467290 GTGGAAGAGGGTTTGGTGCA 60.467 55.000 0.00 0.00 0.00 4.57
6009 7027 0.463204 CGATGATGGTGTGAGGAGCT 59.537 55.000 0.00 0.00 0.00 4.09
6051 7077 3.715495 CAGCAAGAGTAGCACTAGGATG 58.285 50.000 0.00 0.00 0.00 3.51
6091 7117 2.831894 TAGCTGGAGAGGACGGCGAA 62.832 60.000 16.62 0.00 44.77 4.70
6100 7126 1.537776 CCTTGCGATGTAGCTGGAGAG 60.538 57.143 0.00 0.00 38.13 3.20
6101 7127 0.461548 CCTTGCGATGTAGCTGGAGA 59.538 55.000 0.00 0.00 38.13 3.71


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

AutoCloner maintained by Alex Coulton.