Multiple sequence alignment - TraesCS5B01G047100

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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 TraesCS5B01G047100 chr5B 100.000 6086 0 0 1 6086 53019093 53025178 0.000000e+00 11239.0
1 TraesCS5B01G047100 chr5B 94.444 126 5 1 4506 4629 53023517 53023642 6.230000e-45 193.0
2 TraesCS5B01G047100 chr5B 94.444 126 5 1 4425 4550 53023598 53023721 6.230000e-45 193.0
3 TraesCS5B01G047100 chr5B 93.478 46 3 0 4584 4629 53023516 53023561 1.090000e-07 69.4
4 TraesCS5B01G047100 chr5B 93.478 46 3 0 4424 4469 53023676 53023721 1.090000e-07 69.4
5 TraesCS5B01G047100 chr5D 95.874 1721 46 5 2847 4550 50321209 50322921 0.000000e+00 2761.0
6 TraesCS5B01G047100 chr5D 94.232 1335 55 10 1493 2812 50319881 50321208 0.000000e+00 2019.0
7 TraesCS5B01G047100 chr5D 94.399 1232 44 13 4506 5725 50322798 50324016 0.000000e+00 1869.0
8 TraesCS5B01G047100 chr5D 88.168 1572 95 47 17 1521 50318309 50319856 0.000000e+00 1788.0
9 TraesCS5B01G047100 chr5D 95.635 252 10 1 5750 6000 50324123 50324374 2.640000e-108 403.0
10 TraesCS5B01G047100 chr5D 95.652 46 2 0 4424 4469 50322876 50322921 2.350000e-09 75.0
11 TraesCS5B01G047100 chr5D 93.478 46 3 0 4584 4629 50322797 50322842 1.090000e-07 69.4
12 TraesCS5B01G047100 chr5D 100.000 28 0 0 6045 6072 50324380 50324407 1.100000e-02 52.8
13 TraesCS5B01G047100 chr5A 92.970 1522 63 17 1495 2993 39733797 39735297 0.000000e+00 2178.0
14 TraesCS5B01G047100 chr5A 91.098 1539 81 21 17 1521 39732254 39733770 0.000000e+00 2032.0
15 TraesCS5B01G047100 chr5A 92.502 1307 51 16 3222 4506 39735873 39737154 0.000000e+00 1827.0
16 TraesCS5B01G047100 chr5A 92.100 1076 59 18 4633 5699 39737177 39738235 0.000000e+00 1493.0
17 TraesCS5B01G047100 chr5A 92.045 352 18 6 5724 6072 39738391 39738735 2.550000e-133 486.0
18 TraesCS5B01G047100 chr5A 94.608 204 10 1 3027 3229 39735484 39735687 1.270000e-81 315.0
19 TraesCS5B01G047100 chr5A 82.707 133 19 4 2792 2923 397334986 397334857 1.390000e-21 115.0
20 TraesCS5B01G047100 chr4A 89.083 458 40 5 1066 1521 590664661 590664212 1.480000e-155 560.0
21 TraesCS5B01G047100 chr4A 81.188 404 45 16 1502 1904 590664182 590663809 4.610000e-76 296.0
22 TraesCS5B01G047100 chr4A 83.843 229 28 6 2802 3023 488250300 488250526 6.180000e-50 209.0
23 TraesCS5B01G047100 chr4A 81.784 269 24 15 1077 1335 67175040 67175293 1.030000e-47 202.0
24 TraesCS5B01G047100 chr4D 88.412 466 44 5 1058 1521 11858481 11858938 2.480000e-153 553.0
25 TraesCS5B01G047100 chr4D 81.188 404 46 15 1502 1904 11858968 11859342 1.280000e-76 298.0
26 TraesCS5B01G047100 chr4D 81.661 289 26 17 1058 1335 385739444 385739716 1.330000e-51 215.0
27 TraesCS5B01G047100 chr4B 87.660 470 46 5 1061 1521 21941082 21940616 2.500000e-148 536.0
28 TraesCS5B01G047100 chr4B 85.542 249 33 2 1666 1911 21939899 21939651 2.180000e-64 257.0
29 TraesCS5B01G047100 chr4B 80.233 172 21 6 2878 3042 132055150 132054985 3.850000e-22 117.0
30 TraesCS5B01G047100 chr6B 82.025 484 46 22 1048 1521 382771899 382771447 2.070000e-99 374.0
31 TraesCS5B01G047100 chr6D 82.258 434 48 16 1045 1466 223941567 223941983 1.260000e-91 348.0
32 TraesCS5B01G047100 chr6D 84.034 119 13 3 1531 1646 223942117 223942232 6.450000e-20 110.0
33 TraesCS5B01G047100 chr7A 88.350 103 12 0 2809 2911 316018578 316018680 2.300000e-24 124.0
34 TraesCS5B01G047100 chr2D 75.781 256 50 10 2796 3043 622362969 622363220 1.070000e-22 119.0
35 TraesCS5B01G047100 chr6A 83.333 120 14 3 1531 1647 277279103 277279219 8.340000e-19 106.0
36 TraesCS5B01G047100 chr1D 76.630 184 28 9 2835 3007 492612962 492613141 3.020000e-13 87.9
37 TraesCS5B01G047100 chr3A 82.178 101 17 1 2800 2900 583703473 583703572 1.090000e-12 86.1
38 TraesCS5B01G047100 chr2B 80.899 89 16 1 2800 2887 662897041 662897129 1.090000e-07 69.4
39 TraesCS5B01G047100 chr2B 100.000 28 0 0 2803 2830 640841319 640841346 1.100000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G047100 chr5B 53019093 53025178 6085 False 2352.76 11239 95.168800 1 6086 5 chr5B.!!$F1 6085
1 TraesCS5B01G047100 chr5D 50318309 50324407 6098 False 1129.65 2761 94.679750 17 6072 8 chr5D.!!$F1 6055
2 TraesCS5B01G047100 chr5A 39732254 39738735 6481 False 1388.50 2178 92.553833 17 6072 6 chr5A.!!$F1 6055
3 TraesCS5B01G047100 chr4A 590663809 590664661 852 True 428.00 560 85.135500 1066 1904 2 chr4A.!!$R1 838
4 TraesCS5B01G047100 chr4D 11858481 11859342 861 False 425.50 553 84.800000 1058 1904 2 chr4D.!!$F2 846
5 TraesCS5B01G047100 chr4B 21939651 21941082 1431 True 396.50 536 86.601000 1061 1911 2 chr4B.!!$R2 850
6 TraesCS5B01G047100 chr6D 223941567 223942232 665 False 229.00 348 83.146000 1045 1646 2 chr6D.!!$F1 601

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
574 632 0.099436 GTCTGCGGTGGATTGATTGC 59.901 55.0 0.0 0.0 0.00 3.56 F
1109 1203 0.185658 TACGGGGACATGGGATACGA 59.814 55.0 0.0 0.0 37.60 3.43 F
1835 2575 0.350541 ACCAAGGGATACTGGGGGAT 59.649 55.0 0.0 0.0 45.50 3.85 F
3020 3783 0.101219 GCCATGAGCAAATCCCGAAC 59.899 55.0 0.0 0.0 42.97 3.95 F
3363 4473 0.461548 CGCTACCTCTTCTGCATCCA 59.538 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 2575 1.070134 GGACACGCTGGGATAAGCATA 59.930 52.381 0.00 0.0 43.73 3.14 R
2948 3711 1.399791 GCAAGAGATGGCAAGTGTAGC 59.600 52.381 0.00 0.0 0.00 3.58 R
3620 4734 0.535780 TTGACCCTGCTGAGCACAAG 60.536 55.000 1.40 0.0 33.79 3.16 R
4554 5685 0.981183 TGGGTTGCCTTCTACGACAT 59.019 50.000 0.00 0.0 0.00 3.06 R
5308 6442 0.818296 CCCGGAACACAAAAACCACA 59.182 50.000 0.73 0.0 0.00 4.17 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
24 25 5.675684 AACAAAAACCTTGATGACCACTT 57.324 34.783 0.00 0.00 0.00 3.16
27 28 6.805713 ACAAAAACCTTGATGACCACTTAAG 58.194 36.000 0.00 0.00 0.00 1.85
68 71 1.230635 CGAGCAGGTGTCAGTTTGGG 61.231 60.000 0.00 0.00 0.00 4.12
90 93 1.523154 GGTTCGGTTCAATGGCTGCA 61.523 55.000 0.50 0.00 0.00 4.41
126 139 0.802494 CTTCCGTTGGTTTCCATCCG 59.198 55.000 0.00 0.00 31.53 4.18
170 186 2.294979 ACGAAAACACCCCTGAGAAAC 58.705 47.619 0.00 0.00 0.00 2.78
171 187 1.607148 CGAAAACACCCCTGAGAAACC 59.393 52.381 0.00 0.00 0.00 3.27
280 322 2.892425 CTAAGCGCGCCAGGGAAG 60.892 66.667 30.33 12.32 0.00 3.46
281 323 4.467084 TAAGCGCGCCAGGGAAGG 62.467 66.667 30.33 0.00 0.00 3.46
295 337 0.179043 GGAAGGAATTCTCTCGCCCC 60.179 60.000 5.23 0.00 0.00 5.80
378 422 2.362632 CCCGAACTCGACCCCTCT 60.363 66.667 0.00 0.00 43.02 3.69
448 492 3.287867 AATATCATCGCCCCATCATCC 57.712 47.619 0.00 0.00 0.00 3.51
525 572 3.258722 ACAATTGGGGGTTCAACTGAT 57.741 42.857 10.83 0.00 29.72 2.90
541 599 2.037208 ATTGAACCCTTGCCCCCG 59.963 61.111 0.00 0.00 0.00 5.73
574 632 0.099436 GTCTGCGGTGGATTGATTGC 59.901 55.000 0.00 0.00 0.00 3.56
595 653 2.192608 CTCTTTGCTGGCTGCGGAAC 62.193 60.000 11.85 0.00 46.63 3.62
732 825 5.531122 TGTATACATAGGTCTGCCTTGTC 57.469 43.478 0.08 0.00 44.18 3.18
748 841 3.611674 TCGCCGTGGCTTCAGTGA 61.612 61.111 9.55 0.00 39.32 3.41
782 875 5.538849 AAGAAACTTTTATTTTGCGGGGA 57.461 34.783 0.00 0.00 0.00 4.81
819 912 1.377333 GCTGTAGTGGGGTCTTGCC 60.377 63.158 0.00 0.00 0.00 4.52
867 961 2.294074 CTGTTTCCCGTTTCAGGACAA 58.706 47.619 0.00 0.00 31.50 3.18
868 962 2.685897 CTGTTTCCCGTTTCAGGACAAA 59.314 45.455 0.00 0.00 31.50 2.83
872 966 0.537371 CCCGTTTCAGGACAAAGCCT 60.537 55.000 0.00 0.00 39.37 4.58
877 971 0.667993 TTCAGGACAAAGCCTTTGCG 59.332 50.000 16.89 3.94 44.39 4.85
979 1073 0.381801 CTTGACACTGGTTGCGCTTT 59.618 50.000 9.73 0.00 0.00 3.51
1040 1134 4.575885 GGTGTTTCAGGTATGCTTCTGTA 58.424 43.478 0.00 0.00 33.13 2.74
1043 1137 6.821665 GGTGTTTCAGGTATGCTTCTGTATTA 59.178 38.462 0.00 0.00 33.13 0.98
1068 1162 1.068474 GCACGCATACGGATATGGAC 58.932 55.000 0.00 0.00 46.04 4.02
1083 1177 3.118454 GACACACGGACATGGCGG 61.118 66.667 4.24 4.24 0.00 6.13
1100 1194 1.744014 GGTACGCATACGGGGACAT 59.256 57.895 0.00 0.00 46.04 3.06
1109 1203 0.185658 TACGGGGACATGGGATACGA 59.814 55.000 0.00 0.00 37.60 3.43
1140 1234 0.773644 AAGCTGCCATTCGGGGATAT 59.226 50.000 0.00 0.00 35.87 1.63
1193 1293 7.716998 ACATGCCCTGTAATATAGAGTGAAAAG 59.283 37.037 0.00 0.00 35.91 2.27
1328 1442 7.816945 ACTTGCAAAATACATCAAATGCTAC 57.183 32.000 0.00 0.00 34.97 3.58
1479 1593 1.528161 GCAACAATCAAAACAGCAGCC 59.472 47.619 0.00 0.00 0.00 4.85
1535 1701 5.266733 ACAGCAAGAAATCAAGCAAAGAA 57.733 34.783 0.00 0.00 0.00 2.52
1574 1777 0.469917 GCTGCTGGGGTTATCTGCTA 59.530 55.000 0.00 0.00 0.00 3.49
1575 1778 1.542108 GCTGCTGGGGTTATCTGCTAG 60.542 57.143 0.00 0.00 0.00 3.42
1576 1779 1.765314 CTGCTGGGGTTATCTGCTAGT 59.235 52.381 0.00 0.00 0.00 2.57
1594 1797 3.741830 TTGAGCGTGGTTGCCGTCA 62.742 57.895 0.00 0.00 34.65 4.35
1599 1802 2.741092 GTGGTTGCCGTCAGGAGA 59.259 61.111 0.00 0.00 41.02 3.71
1609 1815 1.313772 CGTCAGGAGATCGAGTCCAT 58.686 55.000 16.82 2.19 36.43 3.41
1817 2557 8.651391 TTTTTCCCTTTTCTTATTTCGGAAAC 57.349 30.769 5.12 0.00 37.57 2.78
1835 2575 0.350541 ACCAAGGGATACTGGGGGAT 59.649 55.000 0.00 0.00 45.50 3.85
1837 2577 2.186847 ACCAAGGGATACTGGGGGATAT 59.813 50.000 0.00 0.00 45.50 1.63
1866 2606 2.787249 CGTGTCCGGTCGTATCGT 59.213 61.111 0.00 0.00 0.00 3.73
1933 2673 3.795488 GCTTTGTAGCTTTTGTCACCCAC 60.795 47.826 0.00 0.00 44.27 4.61
1959 2699 4.412796 TTGCCATGTCAATTTTGAACCA 57.587 36.364 0.00 0.00 39.21 3.67
2063 2803 4.046286 TGGAATTGGAGCTTTGGTGTAT 57.954 40.909 0.00 0.00 0.00 2.29
2174 2914 8.492415 AATAGCTGGTAAGATTACTGGACATA 57.508 34.615 0.00 0.00 34.16 2.29
2200 2940 5.893255 TGGGATTTCATTCCTTATCTGTTGG 59.107 40.000 0.00 0.00 35.97 3.77
2201 2941 6.129179 GGGATTTCATTCCTTATCTGTTGGA 58.871 40.000 0.00 0.00 35.97 3.53
2202 2942 6.264067 GGGATTTCATTCCTTATCTGTTGGAG 59.736 42.308 0.00 0.00 35.97 3.86
2268 3010 9.853555 TTCCAAATGTTGACATGTTGATAATAC 57.146 29.630 0.00 0.00 36.56 1.89
2704 3458 2.253610 TCACTATGGGTTGGTCGTTCT 58.746 47.619 0.00 0.00 0.00 3.01
2735 3489 2.310779 TCTGCCTGACTACCTGTTCT 57.689 50.000 0.00 0.00 0.00 3.01
2755 3509 8.640063 TGTTCTGCATTATATTGATAGGCATT 57.360 30.769 0.00 0.00 32.50 3.56
2784 3547 6.418057 TTCCTGGTTGAAGCACATTAAATT 57.582 33.333 0.00 0.00 0.00 1.82
2790 3553 9.853555 CTGGTTGAAGCACATTAAATTAACATA 57.146 29.630 0.00 0.00 0.00 2.29
2823 3586 5.448089 CGGAAATGATAAATCCCGAACGTTT 60.448 40.000 0.46 0.00 39.31 3.60
2939 3702 4.465632 AAAAACAAACTGAGGGTGGAAC 57.534 40.909 0.00 0.00 0.00 3.62
2970 3733 1.136147 CACTTGCCATCTCTTGCGC 59.864 57.895 0.00 0.00 0.00 6.09
3007 3770 3.634568 AAAACGTTCGATTTGCCATGA 57.365 38.095 0.00 0.00 0.00 3.07
3020 3783 0.101219 GCCATGAGCAAATCCCGAAC 59.899 55.000 0.00 0.00 42.97 3.95
3024 3940 1.600023 TGAGCAAATCCCGAACGTTT 58.400 45.000 0.46 0.00 0.00 3.60
3025 3941 2.768698 TGAGCAAATCCCGAACGTTTA 58.231 42.857 0.46 0.00 0.00 2.01
3055 3971 9.639601 CTTATCAGCGTCCAATAATATTAGACA 57.360 33.333 11.06 0.00 0.00 3.41
3183 4100 8.990163 AGATTTTGTTCCTTTTAAGGTAGACA 57.010 30.769 8.31 8.98 46.54 3.41
3184 4101 8.847196 AGATTTTGTTCCTTTTAAGGTAGACAC 58.153 33.333 8.31 1.10 46.54 3.67
3229 4146 6.712095 AGACGTGCAATGTTGATTATATCCAT 59.288 34.615 0.00 0.00 35.18 3.41
3247 4357 2.877786 CCATTGCCACAGTTCGCATATA 59.122 45.455 0.00 0.00 34.35 0.86
3277 4387 2.300433 TGTCATACTGATTGCCCATGC 58.700 47.619 0.00 0.00 38.26 4.06
3286 4396 2.509931 ATTGCCCATGCCAGCTCACT 62.510 55.000 0.00 0.00 36.33 3.41
3363 4473 0.461548 CGCTACCTCTTCTGCATCCA 59.538 55.000 0.00 0.00 0.00 3.41
3491 4601 1.200020 AGCGCTGCCATTTGTTCTAAC 59.800 47.619 10.39 0.00 0.00 2.34
3525 4635 1.965414 TGCCTTCCCTGGACAGATTA 58.035 50.000 0.00 0.00 0.00 1.75
3620 4734 5.343307 AATTTGTTGGCTAATCCCACATC 57.657 39.130 0.00 0.00 39.87 3.06
3785 4911 3.160679 AGGCCTACATTGAATATGCCC 57.839 47.619 1.29 0.00 34.76 5.36
3802 4928 1.144057 CCACATAGCCGTCCTGGTC 59.856 63.158 0.00 0.00 41.21 4.02
4489 5620 8.663025 GTTAGTAGGAATGTAGTAAAAGGCAAC 58.337 37.037 0.00 0.00 0.00 4.17
4490 5621 6.178324 AGTAGGAATGTAGTAAAAGGCAACC 58.822 40.000 0.00 0.00 37.17 3.77
4491 5622 4.341487 AGGAATGTAGTAAAAGGCAACCC 58.659 43.478 0.00 0.00 37.17 4.11
4492 5623 4.083565 GGAATGTAGTAAAAGGCAACCCA 58.916 43.478 0.00 0.00 37.17 4.51
4493 5624 4.709886 GGAATGTAGTAAAAGGCAACCCAT 59.290 41.667 0.00 0.00 37.17 4.00
4494 5625 5.889289 GGAATGTAGTAAAAGGCAACCCATA 59.111 40.000 0.00 0.00 37.17 2.74
4495 5626 6.378848 GGAATGTAGTAAAAGGCAACCCATAA 59.621 38.462 0.00 0.00 37.17 1.90
4496 5627 7.093684 GGAATGTAGTAAAAGGCAACCCATAAA 60.094 37.037 0.00 0.00 37.17 1.40
4497 5628 7.971368 ATGTAGTAAAAGGCAACCCATAAAT 57.029 32.000 0.00 0.00 37.17 1.40
4498 5629 7.784470 TGTAGTAAAAGGCAACCCATAAATT 57.216 32.000 0.00 0.00 37.17 1.82
4499 5630 8.196378 TGTAGTAAAAGGCAACCCATAAATTT 57.804 30.769 0.00 0.00 37.17 1.82
4500 5631 8.308207 TGTAGTAAAAGGCAACCCATAAATTTC 58.692 33.333 0.00 0.00 37.17 2.17
4501 5632 7.309770 AGTAAAAGGCAACCCATAAATTTCA 57.690 32.000 0.00 0.00 37.17 2.69
4502 5633 7.386059 AGTAAAAGGCAACCCATAAATTTCAG 58.614 34.615 0.00 0.00 37.17 3.02
4503 5634 5.823861 AAAGGCAACCCATAAATTTCAGT 57.176 34.783 0.00 0.00 37.17 3.41
4504 5635 5.823861 AAGGCAACCCATAAATTTCAGTT 57.176 34.783 0.00 0.00 37.17 3.16
4505 5636 5.823861 AGGCAACCCATAAATTTCAGTTT 57.176 34.783 0.00 0.00 37.17 2.66
4506 5637 6.186420 AGGCAACCCATAAATTTCAGTTTT 57.814 33.333 0.00 0.00 37.17 2.43
4507 5638 6.230472 AGGCAACCCATAAATTTCAGTTTTC 58.770 36.000 0.00 0.00 37.17 2.29
4508 5639 5.994668 GGCAACCCATAAATTTCAGTTTTCA 59.005 36.000 0.00 0.00 0.00 2.69
4509 5640 6.073276 GGCAACCCATAAATTTCAGTTTTCAC 60.073 38.462 0.00 0.00 0.00 3.18
4510 5641 6.073276 GCAACCCATAAATTTCAGTTTTCACC 60.073 38.462 0.00 0.00 0.00 4.02
4511 5642 6.994421 ACCCATAAATTTCAGTTTTCACCT 57.006 33.333 0.00 0.00 0.00 4.00
4512 5643 6.758254 ACCCATAAATTTCAGTTTTCACCTG 58.242 36.000 0.00 0.00 0.00 4.00
4513 5644 6.165577 CCCATAAATTTCAGTTTTCACCTGG 58.834 40.000 0.00 0.00 0.00 4.45
4514 5645 6.165577 CCATAAATTTCAGTTTTCACCTGGG 58.834 40.000 0.00 0.00 0.00 4.45
4515 5646 6.014669 CCATAAATTTCAGTTTTCACCTGGGA 60.015 38.462 0.00 0.00 0.00 4.37
4516 5647 5.948742 AAATTTCAGTTTTCACCTGGGAA 57.051 34.783 0.00 0.00 0.00 3.97
4517 5648 5.535753 AATTTCAGTTTTCACCTGGGAAG 57.464 39.130 0.00 0.00 0.00 3.46
4518 5649 3.662759 TTCAGTTTTCACCTGGGAAGT 57.337 42.857 0.00 0.00 0.00 3.01
4519 5650 3.662759 TCAGTTTTCACCTGGGAAGTT 57.337 42.857 0.00 0.00 0.00 2.66
4520 5651 3.287222 TCAGTTTTCACCTGGGAAGTTG 58.713 45.455 0.00 0.27 0.00 3.16
4521 5652 2.031870 AGTTTTCACCTGGGAAGTTGC 58.968 47.619 0.00 0.00 0.00 4.17
4522 5653 2.031870 GTTTTCACCTGGGAAGTTGCT 58.968 47.619 0.00 0.00 0.00 3.91
4523 5654 3.117663 AGTTTTCACCTGGGAAGTTGCTA 60.118 43.478 0.00 0.00 0.00 3.49
4524 5655 3.586470 TTTCACCTGGGAAGTTGCTAA 57.414 42.857 0.00 0.00 0.00 3.09
4525 5656 2.859165 TCACCTGGGAAGTTGCTAAG 57.141 50.000 0.00 0.00 0.00 2.18
4526 5657 1.168714 CACCTGGGAAGTTGCTAAGC 58.831 55.000 0.00 0.00 0.00 3.09
4527 5658 1.068121 ACCTGGGAAGTTGCTAAGCT 58.932 50.000 0.00 0.00 0.00 3.74
4528 5659 1.271597 ACCTGGGAAGTTGCTAAGCTG 60.272 52.381 0.00 0.00 0.00 4.24
4529 5660 1.457346 CTGGGAAGTTGCTAAGCTGG 58.543 55.000 0.00 0.00 0.00 4.85
4530 5661 1.003580 CTGGGAAGTTGCTAAGCTGGA 59.996 52.381 0.00 0.00 0.00 3.86
4531 5662 1.003580 TGGGAAGTTGCTAAGCTGGAG 59.996 52.381 0.00 0.00 0.00 3.86
4532 5663 1.279271 GGGAAGTTGCTAAGCTGGAGA 59.721 52.381 0.03 0.00 0.00 3.71
4533 5664 2.626840 GGAAGTTGCTAAGCTGGAGAG 58.373 52.381 0.03 0.00 0.00 3.20
4534 5665 2.234908 GGAAGTTGCTAAGCTGGAGAGA 59.765 50.000 0.03 0.00 0.00 3.10
4535 5666 3.307059 GGAAGTTGCTAAGCTGGAGAGAA 60.307 47.826 0.03 0.00 0.00 2.87
4536 5667 4.512484 GAAGTTGCTAAGCTGGAGAGAAT 58.488 43.478 0.03 0.00 0.00 2.40
4537 5668 4.566426 AGTTGCTAAGCTGGAGAGAATT 57.434 40.909 0.03 0.00 0.00 2.17
4538 5669 4.260170 AGTTGCTAAGCTGGAGAGAATTG 58.740 43.478 0.03 0.00 0.00 2.32
4539 5670 4.019860 AGTTGCTAAGCTGGAGAGAATTGA 60.020 41.667 0.03 0.00 0.00 2.57
4540 5671 4.558226 TGCTAAGCTGGAGAGAATTGAA 57.442 40.909 0.03 0.00 0.00 2.69
4541 5672 5.108187 TGCTAAGCTGGAGAGAATTGAAT 57.892 39.130 0.03 0.00 0.00 2.57
4542 5673 5.503927 TGCTAAGCTGGAGAGAATTGAATT 58.496 37.500 0.03 0.00 0.00 2.17
4543 5674 5.948162 TGCTAAGCTGGAGAGAATTGAATTT 59.052 36.000 0.03 0.00 0.00 1.82
4544 5675 6.127814 TGCTAAGCTGGAGAGAATTGAATTTG 60.128 38.462 0.03 0.00 0.00 2.32
4545 5676 6.127786 GCTAAGCTGGAGAGAATTGAATTTGT 60.128 38.462 0.03 0.00 0.00 2.83
4546 5677 6.661304 AAGCTGGAGAGAATTGAATTTGTT 57.339 33.333 0.00 0.00 0.00 2.83
4547 5678 7.765695 AAGCTGGAGAGAATTGAATTTGTTA 57.234 32.000 0.00 0.00 0.00 2.41
4548 5679 7.388460 AGCTGGAGAGAATTGAATTTGTTAG 57.612 36.000 0.00 0.00 0.00 2.34
4549 5680 6.944862 AGCTGGAGAGAATTGAATTTGTTAGT 59.055 34.615 0.00 0.00 0.00 2.24
4550 5681 8.103305 AGCTGGAGAGAATTGAATTTGTTAGTA 58.897 33.333 0.00 0.00 0.00 1.82
4551 5682 8.394121 GCTGGAGAGAATTGAATTTGTTAGTAG 58.606 37.037 0.00 0.00 0.00 2.57
4552 5683 8.792830 TGGAGAGAATTGAATTTGTTAGTAGG 57.207 34.615 0.00 0.00 0.00 3.18
4553 5684 8.602424 TGGAGAGAATTGAATTTGTTAGTAGGA 58.398 33.333 0.00 0.00 0.00 2.94
4554 5685 9.449719 GGAGAGAATTGAATTTGTTAGTAGGAA 57.550 33.333 0.00 0.00 0.00 3.36
4559 5690 9.490663 GAATTGAATTTGTTAGTAGGAATGTCG 57.509 33.333 0.00 0.00 0.00 4.35
4560 5691 7.972832 TTGAATTTGTTAGTAGGAATGTCGT 57.027 32.000 0.00 0.00 0.00 4.34
4561 5692 9.661563 ATTGAATTTGTTAGTAGGAATGTCGTA 57.338 29.630 0.00 0.00 0.00 3.43
4562 5693 8.697846 TGAATTTGTTAGTAGGAATGTCGTAG 57.302 34.615 0.00 0.00 0.00 3.51
4563 5694 8.525316 TGAATTTGTTAGTAGGAATGTCGTAGA 58.475 33.333 0.00 0.00 0.00 2.59
4564 5695 9.362539 GAATTTGTTAGTAGGAATGTCGTAGAA 57.637 33.333 0.00 0.00 39.69 2.10
4565 5696 8.928270 ATTTGTTAGTAGGAATGTCGTAGAAG 57.072 34.615 0.00 0.00 39.69 2.85
4566 5697 6.446781 TGTTAGTAGGAATGTCGTAGAAGG 57.553 41.667 0.00 0.00 39.69 3.46
4567 5698 5.163581 TGTTAGTAGGAATGTCGTAGAAGGC 60.164 44.000 0.00 0.00 39.69 4.35
4568 5699 3.362706 AGTAGGAATGTCGTAGAAGGCA 58.637 45.455 0.00 0.00 39.69 4.75
4569 5700 3.767673 AGTAGGAATGTCGTAGAAGGCAA 59.232 43.478 0.00 0.00 39.69 4.52
4585 5716 5.185828 AGAAGGCAACCCATAAATTTCAGTC 59.814 40.000 0.00 0.00 37.17 3.51
4713 5844 5.636903 AGGACTTGCATGAACCATATACT 57.363 39.130 6.60 0.00 0.00 2.12
4830 5963 3.356290 CTTGTTGGTATCCCCTTTCTGG 58.644 50.000 0.00 0.00 0.00 3.86
4843 5976 4.884164 CCCCTTTCTGGATCTTGTAATGAC 59.116 45.833 0.00 0.00 38.35 3.06
4849 5982 9.994432 CTTTCTGGATCTTGTAATGACAATAAC 57.006 33.333 0.00 0.00 44.53 1.89
4890 6023 2.038164 GCAGCCATATCTCCATGAGTCA 59.962 50.000 0.00 0.00 0.00 3.41
4891 6024 3.495629 GCAGCCATATCTCCATGAGTCAA 60.496 47.826 0.00 0.00 0.00 3.18
4956 6089 4.084013 CGGTTTCTTAACGCAAAGTCAGAT 60.084 41.667 0.00 0.00 35.00 2.90
5006 6139 0.242017 AAAGACAAGCAGAATGGCGC 59.758 50.000 0.00 0.00 39.27 6.53
5215 6348 2.486203 CCGCTCTGCTCTATAGTAGTGG 59.514 54.545 0.00 3.91 36.84 4.00
5292 6426 7.667043 TGGTTTCTACATTCTGTACAATGAC 57.333 36.000 13.29 2.28 37.24 3.06
5481 6619 7.765695 AAATCTGGGTATACATAATGGCTTG 57.234 36.000 5.01 0.00 0.00 4.01
5499 6640 1.291272 GGCCTGCAGCTTTCTTTGG 59.709 57.895 8.66 0.00 43.05 3.28
5591 6732 1.071239 CCTCGCGATAAGATGTTTGCG 60.071 52.381 10.36 9.33 46.27 4.85
5597 6738 3.060873 GCGATAAGATGTTTGCGTCTCTC 60.061 47.826 0.00 0.00 39.89 3.20
5706 6851 2.284190 GTCAGTCAGGCCTGAATTAGC 58.716 52.381 36.66 23.22 42.81 3.09
5740 7013 6.911250 TTGAATCTTACTTTCTTTTCCCCC 57.089 37.500 0.00 0.00 0.00 5.40
5755 7028 4.265206 CCCCCTCATGGACATTGC 57.735 61.111 0.00 0.00 35.39 3.56
5874 7147 3.906014 TTCTCGAGAACACTGACTGAG 57.094 47.619 23.74 0.00 0.00 3.35
5886 7159 5.201243 ACACTGACTGAGGCATATACTACA 58.799 41.667 0.00 0.00 0.00 2.74
6000 7274 0.531974 TCCAACGTCACTGTCTTGGC 60.532 55.000 0.00 0.00 34.29 4.52
6011 7285 1.521457 GTCTTGGCGATGCGGATGA 60.521 57.895 0.00 0.00 0.00 2.92
6015 7289 3.032609 GGCGATGCGGATGAGACG 61.033 66.667 0.00 0.00 0.00 4.18
6023 7297 2.980568 TGCGGATGAGACGGTAAAAAT 58.019 42.857 0.00 0.00 0.00 1.82
6025 7299 4.699637 TGCGGATGAGACGGTAAAAATAT 58.300 39.130 0.00 0.00 0.00 1.28
6026 7300 5.120399 TGCGGATGAGACGGTAAAAATATT 58.880 37.500 0.00 0.00 0.00 1.28
6027 7301 5.587043 TGCGGATGAGACGGTAAAAATATTT 59.413 36.000 0.00 0.00 0.00 1.40
6072 7347 9.632638 ATGACCATGCTGTAAATTAAGAAGTAT 57.367 29.630 0.00 0.00 0.00 2.12
6073 7348 8.892723 TGACCATGCTGTAAATTAAGAAGTATG 58.107 33.333 0.00 0.00 32.68 2.39
6074 7349 8.807948 ACCATGCTGTAAATTAAGAAGTATGT 57.192 30.769 0.00 0.00 31.45 2.29
6075 7350 9.899661 ACCATGCTGTAAATTAAGAAGTATGTA 57.100 29.630 0.00 0.00 31.45 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.783708 AGTGGTCATCAAGGTTTTTGTTTA 57.216 33.333 0.00 0.00 0.00 2.01
1 2 5.675684 AGTGGTCATCAAGGTTTTTGTTT 57.324 34.783 0.00 0.00 0.00 2.83
2 3 5.675684 AAGTGGTCATCAAGGTTTTTGTT 57.324 34.783 0.00 0.00 0.00 2.83
3 4 6.605594 TCTTAAGTGGTCATCAAGGTTTTTGT 59.394 34.615 1.63 0.00 0.00 2.83
4 5 7.038154 TCTTAAGTGGTCATCAAGGTTTTTG 57.962 36.000 1.63 0.00 0.00 2.44
5 6 7.654022 TTCTTAAGTGGTCATCAAGGTTTTT 57.346 32.000 1.63 0.00 0.00 1.94
6 7 7.417456 GGTTTCTTAAGTGGTCATCAAGGTTTT 60.417 37.037 1.63 0.00 0.00 2.43
7 8 6.040504 GGTTTCTTAAGTGGTCATCAAGGTTT 59.959 38.462 1.63 0.00 0.00 3.27
8 9 5.535030 GGTTTCTTAAGTGGTCATCAAGGTT 59.465 40.000 1.63 0.00 0.00 3.50
9 10 5.070685 GGTTTCTTAAGTGGTCATCAAGGT 58.929 41.667 1.63 0.00 0.00 3.50
10 11 4.459337 GGGTTTCTTAAGTGGTCATCAAGG 59.541 45.833 1.63 0.00 0.00 3.61
11 12 5.070001 TGGGTTTCTTAAGTGGTCATCAAG 58.930 41.667 1.63 0.00 0.00 3.02
12 13 5.055265 TGGGTTTCTTAAGTGGTCATCAA 57.945 39.130 1.63 0.00 0.00 2.57
13 14 4.715534 TGGGTTTCTTAAGTGGTCATCA 57.284 40.909 1.63 0.00 0.00 3.07
14 15 5.048013 CCTTTGGGTTTCTTAAGTGGTCATC 60.048 44.000 1.63 0.00 0.00 2.92
15 16 4.832823 CCTTTGGGTTTCTTAAGTGGTCAT 59.167 41.667 1.63 0.00 0.00 3.06
68 71 1.200020 CAGCCATTGAACCGAACCTTC 59.800 52.381 0.00 0.00 0.00 3.46
90 93 0.755327 AAGCTTCCGGGTGCTTGTTT 60.755 50.000 26.02 9.14 46.25 2.83
112 125 1.743394 GATGGACGGATGGAAACCAAC 59.257 52.381 0.00 0.00 36.95 3.77
114 127 0.254747 GGATGGACGGATGGAAACCA 59.745 55.000 0.00 0.00 38.19 3.67
115 128 0.254747 TGGATGGACGGATGGAAACC 59.745 55.000 0.00 0.00 0.00 3.27
118 131 0.830648 GAGTGGATGGACGGATGGAA 59.169 55.000 0.00 0.00 0.00 3.53
119 132 1.391933 CGAGTGGATGGACGGATGGA 61.392 60.000 0.00 0.00 0.00 3.41
120 133 1.068083 CGAGTGGATGGACGGATGG 59.932 63.158 0.00 0.00 0.00 3.51
126 139 0.318784 GTATCGGCGAGTGGATGGAC 60.319 60.000 17.22 0.00 0.00 4.02
170 186 3.764972 GAGGATAAGAGGGTATTCTCGGG 59.235 52.174 0.00 0.00 38.71 5.14
171 187 4.668636 AGAGGATAAGAGGGTATTCTCGG 58.331 47.826 0.00 0.00 40.00 4.63
280 322 1.448069 GAGGGGGCGAGAGAATTCC 59.552 63.158 0.65 0.00 0.00 3.01
281 323 1.068250 CGAGGGGGCGAGAGAATTC 59.932 63.158 0.00 0.00 0.00 2.17
282 324 3.095347 GCGAGGGGGCGAGAGAATT 62.095 63.158 0.00 0.00 0.00 2.17
283 325 3.541713 GCGAGGGGGCGAGAGAAT 61.542 66.667 0.00 0.00 0.00 2.40
525 572 4.986708 GCGGGGGCAAGGGTTCAA 62.987 66.667 0.00 0.00 0.00 2.69
541 599 1.377725 CAGACACATGGACAGGGGC 60.378 63.158 0.00 0.00 0.00 5.80
548 606 1.552799 ATCCACCGCAGACACATGGA 61.553 55.000 0.00 0.00 43.42 3.41
595 653 2.124983 CCCCACGCCATGACTGAG 60.125 66.667 0.00 0.00 0.00 3.35
637 696 3.181499 CCACTACTGCGAAGGTACTACTG 60.181 52.174 0.00 0.00 38.49 2.74
777 870 8.630037 AGCTTATTTCTGTTTATTTATTCCCCG 58.370 33.333 0.00 0.00 0.00 5.73
867 961 0.755327 AGACCAAACCGCAAAGGCTT 60.755 50.000 0.00 0.00 46.52 4.35
868 962 1.152756 AGACCAAACCGCAAAGGCT 60.153 52.632 0.00 0.00 46.52 4.58
872 966 0.882927 CTCCGAGACCAAACCGCAAA 60.883 55.000 0.00 0.00 0.00 3.68
877 971 4.623002 GATATCTTCTCCGAGACCAAACC 58.377 47.826 0.00 0.00 0.00 3.27
940 1034 1.419374 CTCGGAGAAAAGACACGGTG 58.581 55.000 6.58 6.58 34.09 4.94
979 1073 2.223745 GGTTTGTTACTTTCCGAGGCA 58.776 47.619 0.00 0.00 0.00 4.75
1068 1162 2.098233 GTACCGCCATGTCCGTGTG 61.098 63.158 0.00 0.00 0.00 3.82
1083 1177 0.599204 CCATGTCCCCGTATGCGTAC 60.599 60.000 5.98 5.98 36.15 3.67
1109 1203 3.451141 TGGCAGCTTTTTCGAAAATGT 57.549 38.095 27.36 16.66 0.00 2.71
1117 1211 0.108662 CCCCGAATGGCAGCTTTTTC 60.109 55.000 0.00 0.00 0.00 2.29
1118 1212 0.541764 TCCCCGAATGGCAGCTTTTT 60.542 50.000 0.00 0.00 0.00 1.94
1125 1219 0.034756 CGACATATCCCCGAATGGCA 59.965 55.000 0.00 0.00 29.94 4.92
1193 1293 5.593909 TGATCTCATCTCTGTTTCTCTCCTC 59.406 44.000 0.00 0.00 0.00 3.71
1442 1556 2.877097 TGCTTGATGTTAGGGAGCAA 57.123 45.000 0.00 0.00 40.09 3.91
1535 1701 2.545810 CCTCTCCTCAACCTCTTCCTT 58.454 52.381 0.00 0.00 0.00 3.36
1574 1777 2.972505 CGGCAACCACGCTCAACT 60.973 61.111 0.00 0.00 0.00 3.16
1575 1778 3.236618 GACGGCAACCACGCTCAAC 62.237 63.158 0.00 0.00 34.00 3.18
1576 1779 2.970324 GACGGCAACCACGCTCAA 60.970 61.111 0.00 0.00 34.00 3.02
1594 1797 1.459455 CCGCATGGACTCGATCTCCT 61.459 60.000 9.96 0.00 37.49 3.69
1599 1802 4.592192 CCGCCGCATGGACTCGAT 62.592 66.667 0.00 0.00 37.49 3.59
1721 2454 1.097547 CAATAACAGCCTCGGCCCTG 61.098 60.000 3.92 0.21 43.17 4.45
1817 2557 2.433444 TATCCCCCAGTATCCCTTGG 57.567 55.000 0.00 0.00 0.00 3.61
1835 2575 1.070134 GGACACGCTGGGATAAGCATA 59.930 52.381 0.00 0.00 43.73 3.14
1837 2577 1.220749 GGACACGCTGGGATAAGCA 59.779 57.895 0.00 0.00 43.73 3.91
1871 2611 2.279918 CGTCCTAATTCGGCGGGG 60.280 66.667 7.21 2.26 0.00 5.73
1933 2673 6.293027 GGTTCAAAATTGACATGGCAAAGAAG 60.293 38.462 19.96 9.33 36.83 2.85
1959 2699 6.070078 CCCTACCTAGTAGCTACTACTGCTAT 60.070 46.154 26.36 12.30 45.52 2.97
2029 2769 3.094572 CCAATTCCATGAGCCAAGAGTT 58.905 45.455 0.00 0.00 0.00 3.01
2063 2803 6.900186 ACAAATACAATATCCCAATTCCCACA 59.100 34.615 0.00 0.00 0.00 4.17
2134 2874 4.333913 AGCTATTAGACATGACAGCTGG 57.666 45.455 19.93 1.96 37.93 4.85
2174 2914 6.332976 ACAGATAAGGAATGAAATCCCAGT 57.667 37.500 0.00 0.00 40.59 4.00
2268 3010 4.127171 CGACTGGGAATTTATGGTGTAGG 58.873 47.826 0.00 0.00 0.00 3.18
2472 3217 2.017049 GGGTGTGACATAATCTGTGGC 58.983 52.381 0.00 0.00 38.54 5.01
2682 3436 2.981859 ACGACCAACCCATAGTGATC 57.018 50.000 0.00 0.00 0.00 2.92
2704 3458 3.776969 AGTCAGGCAGAAGAATCCATACA 59.223 43.478 0.00 0.00 0.00 2.29
2815 3578 3.101019 GGCAAATCCCAAACGTTCG 57.899 52.632 0.00 0.00 0.00 3.95
2876 3639 2.887152 GTCAACTGAACTTGCCATCCTT 59.113 45.455 0.00 0.00 0.00 3.36
2939 3702 1.580845 GCAAGTGTAGCTGGTGGCAG 61.581 60.000 0.00 0.00 44.79 4.85
2948 3711 1.399791 GCAAGAGATGGCAAGTGTAGC 59.600 52.381 0.00 0.00 0.00 3.58
3007 3770 2.081462 CCTAAACGTTCGGGATTTGCT 58.919 47.619 0.00 0.00 0.00 3.91
3112 4028 6.948309 AGGAAATGATGCAGTTTAACCTAACT 59.052 34.615 0.00 0.00 38.87 2.24
3197 4114 9.716507 ATAATCAACATTGCACGTCTAATTAAC 57.283 29.630 0.00 0.00 0.00 2.01
3229 4146 3.339141 TGTTATATGCGAACTGTGGCAA 58.661 40.909 10.27 2.46 42.19 4.52
3277 4387 4.940046 AGTTTTATGTGATCAGTGAGCTGG 59.060 41.667 10.19 0.00 42.78 4.85
3286 4396 7.701539 ACAGGCAAATAGTTTTATGTGATCA 57.298 32.000 0.00 0.00 27.40 2.92
3363 4473 8.434589 AGCTAGAAGCAGAGAGGAATATATTT 57.565 34.615 0.00 0.00 45.56 1.40
3491 4601 1.481871 AGGCATGGGAATTTGCTCAG 58.518 50.000 0.00 0.00 0.00 3.35
3525 4635 5.713861 ACAAGAAAGCAATAGAAGAGGCAAT 59.286 36.000 0.00 0.00 0.00 3.56
3620 4734 0.535780 TTGACCCTGCTGAGCACAAG 60.536 55.000 1.40 0.00 33.79 3.16
3785 4911 1.144057 GGACCAGGACGGCTATGTG 59.856 63.158 0.00 0.00 39.03 3.21
3802 4928 6.566753 GCAAAGTTACTTCTCACTTGCTAAGG 60.567 42.308 9.20 0.00 33.38 2.69
3869 4995 4.756642 CACCAGTTTGATGAGCTGAACTAA 59.243 41.667 0.00 0.00 38.75 2.24
4384 5514 7.056635 TCCACCTTCTTCCATATCAGAAATTC 58.943 38.462 0.00 0.00 0.00 2.17
4489 5620 6.165577 CCAGGTGAAAACTGAAATTTATGGG 58.834 40.000 0.00 0.00 38.20 4.00
4490 5621 6.014669 TCCCAGGTGAAAACTGAAATTTATGG 60.015 38.462 0.00 0.00 38.20 2.74
4491 5622 6.991938 TCCCAGGTGAAAACTGAAATTTATG 58.008 36.000 0.00 0.00 38.20 1.90
4492 5623 7.290014 ACTTCCCAGGTGAAAACTGAAATTTAT 59.710 33.333 0.00 0.00 38.20 1.40
4493 5624 6.609616 ACTTCCCAGGTGAAAACTGAAATTTA 59.390 34.615 0.00 0.00 38.20 1.40
4494 5625 5.425217 ACTTCCCAGGTGAAAACTGAAATTT 59.575 36.000 0.00 0.00 38.20 1.82
4495 5626 4.962362 ACTTCCCAGGTGAAAACTGAAATT 59.038 37.500 0.00 0.00 38.20 1.82
4496 5627 4.546674 ACTTCCCAGGTGAAAACTGAAAT 58.453 39.130 0.00 0.00 38.20 2.17
4497 5628 3.976015 ACTTCCCAGGTGAAAACTGAAA 58.024 40.909 0.00 0.00 38.20 2.69
4498 5629 3.662759 ACTTCCCAGGTGAAAACTGAA 57.337 42.857 0.00 0.00 38.20 3.02
4499 5630 3.287222 CAACTTCCCAGGTGAAAACTGA 58.713 45.455 0.00 0.00 40.69 3.41
4500 5631 2.223805 GCAACTTCCCAGGTGAAAACTG 60.224 50.000 0.00 0.00 40.69 3.16
4501 5632 2.031870 GCAACTTCCCAGGTGAAAACT 58.968 47.619 0.00 0.00 40.69 2.66
4502 5633 2.031870 AGCAACTTCCCAGGTGAAAAC 58.968 47.619 0.00 0.00 40.69 2.43
4503 5634 2.452600 AGCAACTTCCCAGGTGAAAA 57.547 45.000 0.00 0.00 40.69 2.29
4504 5635 3.486383 CTTAGCAACTTCCCAGGTGAAA 58.514 45.455 0.00 0.00 40.69 2.69
4505 5636 2.814097 GCTTAGCAACTTCCCAGGTGAA 60.814 50.000 0.00 0.00 40.69 3.18
4506 5637 1.271379 GCTTAGCAACTTCCCAGGTGA 60.271 52.381 0.00 0.00 40.69 4.02
4507 5638 1.168714 GCTTAGCAACTTCCCAGGTG 58.831 55.000 0.00 0.00 41.25 4.00
4508 5639 1.068121 AGCTTAGCAACTTCCCAGGT 58.932 50.000 7.07 0.00 0.00 4.00
4509 5640 1.457346 CAGCTTAGCAACTTCCCAGG 58.543 55.000 7.07 0.00 0.00 4.45
4510 5641 1.003580 TCCAGCTTAGCAACTTCCCAG 59.996 52.381 7.07 0.00 0.00 4.45
4511 5642 1.003580 CTCCAGCTTAGCAACTTCCCA 59.996 52.381 7.07 0.00 0.00 4.37
4512 5643 1.279271 TCTCCAGCTTAGCAACTTCCC 59.721 52.381 7.07 0.00 0.00 3.97
4513 5644 2.234908 TCTCTCCAGCTTAGCAACTTCC 59.765 50.000 7.07 0.00 0.00 3.46
4514 5645 3.601443 TCTCTCCAGCTTAGCAACTTC 57.399 47.619 7.07 0.00 0.00 3.01
4515 5646 4.566426 ATTCTCTCCAGCTTAGCAACTT 57.434 40.909 7.07 0.00 0.00 2.66
4516 5647 4.019860 TCAATTCTCTCCAGCTTAGCAACT 60.020 41.667 7.07 0.00 0.00 3.16
4517 5648 4.256920 TCAATTCTCTCCAGCTTAGCAAC 58.743 43.478 7.07 0.00 0.00 4.17
4518 5649 4.558226 TCAATTCTCTCCAGCTTAGCAA 57.442 40.909 7.07 0.00 0.00 3.91
4519 5650 4.558226 TTCAATTCTCTCCAGCTTAGCA 57.442 40.909 7.07 0.00 0.00 3.49
4520 5651 6.127786 ACAAATTCAATTCTCTCCAGCTTAGC 60.128 38.462 0.00 0.00 0.00 3.09
4521 5652 7.388460 ACAAATTCAATTCTCTCCAGCTTAG 57.612 36.000 0.00 0.00 0.00 2.18
4522 5653 7.765695 AACAAATTCAATTCTCTCCAGCTTA 57.234 32.000 0.00 0.00 0.00 3.09
4523 5654 6.661304 AACAAATTCAATTCTCTCCAGCTT 57.339 33.333 0.00 0.00 0.00 3.74
4524 5655 6.944862 ACTAACAAATTCAATTCTCTCCAGCT 59.055 34.615 0.00 0.00 0.00 4.24
4525 5656 7.150783 ACTAACAAATTCAATTCTCTCCAGC 57.849 36.000 0.00 0.00 0.00 4.85
4526 5657 8.887717 CCTACTAACAAATTCAATTCTCTCCAG 58.112 37.037 0.00 0.00 0.00 3.86
4527 5658 8.602424 TCCTACTAACAAATTCAATTCTCTCCA 58.398 33.333 0.00 0.00 0.00 3.86
4528 5659 9.449719 TTCCTACTAACAAATTCAATTCTCTCC 57.550 33.333 0.00 0.00 0.00 3.71
4533 5664 9.490663 CGACATTCCTACTAACAAATTCAATTC 57.509 33.333 0.00 0.00 0.00 2.17
4534 5665 9.010029 ACGACATTCCTACTAACAAATTCAATT 57.990 29.630 0.00 0.00 0.00 2.32
4535 5666 8.561738 ACGACATTCCTACTAACAAATTCAAT 57.438 30.769 0.00 0.00 0.00 2.57
4536 5667 7.972832 ACGACATTCCTACTAACAAATTCAA 57.027 32.000 0.00 0.00 0.00 2.69
4537 5668 8.525316 TCTACGACATTCCTACTAACAAATTCA 58.475 33.333 0.00 0.00 0.00 2.57
4538 5669 8.922058 TCTACGACATTCCTACTAACAAATTC 57.078 34.615 0.00 0.00 0.00 2.17
4539 5670 9.367444 CTTCTACGACATTCCTACTAACAAATT 57.633 33.333 0.00 0.00 0.00 1.82
4540 5671 7.980099 CCTTCTACGACATTCCTACTAACAAAT 59.020 37.037 0.00 0.00 0.00 2.32
4541 5672 7.318141 CCTTCTACGACATTCCTACTAACAAA 58.682 38.462 0.00 0.00 0.00 2.83
4542 5673 6.626623 GCCTTCTACGACATTCCTACTAACAA 60.627 42.308 0.00 0.00 0.00 2.83
4543 5674 5.163581 GCCTTCTACGACATTCCTACTAACA 60.164 44.000 0.00 0.00 0.00 2.41
4544 5675 5.163581 TGCCTTCTACGACATTCCTACTAAC 60.164 44.000 0.00 0.00 0.00 2.34
4545 5676 4.951715 TGCCTTCTACGACATTCCTACTAA 59.048 41.667 0.00 0.00 0.00 2.24
4546 5677 4.529897 TGCCTTCTACGACATTCCTACTA 58.470 43.478 0.00 0.00 0.00 1.82
4547 5678 3.362706 TGCCTTCTACGACATTCCTACT 58.637 45.455 0.00 0.00 0.00 2.57
4548 5679 3.795623 TGCCTTCTACGACATTCCTAC 57.204 47.619 0.00 0.00 0.00 3.18
4549 5680 3.118884 GGTTGCCTTCTACGACATTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
4550 5681 2.354805 GGTTGCCTTCTACGACATTCCT 60.355 50.000 0.00 0.00 0.00 3.36
4551 5682 2.007608 GGTTGCCTTCTACGACATTCC 58.992 52.381 0.00 0.00 0.00 3.01
4552 5683 2.007608 GGGTTGCCTTCTACGACATTC 58.992 52.381 0.00 0.00 0.00 2.67
4553 5684 1.349688 TGGGTTGCCTTCTACGACATT 59.650 47.619 0.00 0.00 0.00 2.71
4554 5685 0.981183 TGGGTTGCCTTCTACGACAT 59.019 50.000 0.00 0.00 0.00 3.06
4555 5686 0.981183 ATGGGTTGCCTTCTACGACA 59.019 50.000 0.00 0.00 0.00 4.35
4556 5687 2.973694 TATGGGTTGCCTTCTACGAC 57.026 50.000 0.00 0.00 0.00 4.34
4557 5688 3.985019 TTTATGGGTTGCCTTCTACGA 57.015 42.857 0.00 0.00 0.00 3.43
4558 5689 5.124776 TGAAATTTATGGGTTGCCTTCTACG 59.875 40.000 0.00 0.00 0.00 3.51
4559 5690 6.152831 ACTGAAATTTATGGGTTGCCTTCTAC 59.847 38.462 0.00 0.00 0.00 2.59
4560 5691 6.252995 ACTGAAATTTATGGGTTGCCTTCTA 58.747 36.000 0.00 0.00 0.00 2.10
4561 5692 5.086621 ACTGAAATTTATGGGTTGCCTTCT 58.913 37.500 0.00 0.00 0.00 2.85
4562 5693 5.405935 ACTGAAATTTATGGGTTGCCTTC 57.594 39.130 0.00 0.00 0.00 3.46
4563 5694 4.222810 GGACTGAAATTTATGGGTTGCCTT 59.777 41.667 0.00 0.00 0.00 4.35
4564 5695 3.769300 GGACTGAAATTTATGGGTTGCCT 59.231 43.478 0.00 0.00 0.00 4.75
4565 5696 3.513515 TGGACTGAAATTTATGGGTTGCC 59.486 43.478 0.00 0.00 0.00 4.52
4566 5697 4.494484 GTGGACTGAAATTTATGGGTTGC 58.506 43.478 0.00 0.00 0.00 4.17
4567 5698 4.772100 AGGTGGACTGAAATTTATGGGTTG 59.228 41.667 0.00 0.00 0.00 3.77
4568 5699 5.010708 AGGTGGACTGAAATTTATGGGTT 57.989 39.130 0.00 0.00 0.00 4.11
4569 5700 4.675063 AGGTGGACTGAAATTTATGGGT 57.325 40.909 0.00 0.00 0.00 4.51
4585 5716 1.826385 CTTAGCAACTTCCCAGGTGG 58.174 55.000 0.00 0.00 38.31 4.61
4713 5844 3.803021 GCAAATTGGCACTGGAAACATCA 60.803 43.478 0.00 0.00 41.51 3.07
4843 5976 6.127925 ACAATGTAGGCACATGTCAGTTATTG 60.128 38.462 0.00 6.10 44.83 1.90
4849 5982 2.159476 GCACAATGTAGGCACATGTCAG 60.159 50.000 0.00 0.00 44.83 3.51
4956 6089 5.356190 GGAATCAGAATGCTCTTCATTGTCA 59.644 40.000 0.00 0.00 44.95 3.58
5073 6206 5.469421 CCTTCTAGCATCTCATTCATGGTTC 59.531 44.000 0.00 0.00 33.96 3.62
5240 6373 1.094785 AACACGGACCAATATGCTGC 58.905 50.000 0.00 0.00 0.00 5.25
5241 6374 2.731968 GCAAACACGGACCAATATGCTG 60.732 50.000 0.00 0.00 0.00 4.41
5242 6375 1.472480 GCAAACACGGACCAATATGCT 59.528 47.619 0.00 0.00 0.00 3.79
5243 6376 1.472480 AGCAAACACGGACCAATATGC 59.528 47.619 0.00 0.00 0.00 3.14
5244 6377 2.159393 CCAGCAAACACGGACCAATATG 60.159 50.000 0.00 0.00 0.00 1.78
5245 6378 2.091541 CCAGCAAACACGGACCAATAT 58.908 47.619 0.00 0.00 0.00 1.28
5246 6379 1.202830 ACCAGCAAACACGGACCAATA 60.203 47.619 0.00 0.00 0.00 1.90
5304 6438 3.369451 CCGGAACACAAAAACCACAAAAG 59.631 43.478 0.00 0.00 0.00 2.27
5305 6439 3.326747 CCGGAACACAAAAACCACAAAA 58.673 40.909 0.00 0.00 0.00 2.44
5306 6440 2.353803 CCCGGAACACAAAAACCACAAA 60.354 45.455 0.73 0.00 0.00 2.83
5307 6441 1.204941 CCCGGAACACAAAAACCACAA 59.795 47.619 0.73 0.00 0.00 3.33
5308 6442 0.818296 CCCGGAACACAAAAACCACA 59.182 50.000 0.73 0.00 0.00 4.17
5481 6619 1.291272 CCAAAGAAAGCTGCAGGCC 59.709 57.895 17.12 0.00 43.05 5.19
5591 6732 7.885922 TGGACAAGATATATACCAGAGAGAGAC 59.114 40.741 0.00 0.00 0.00 3.36
5597 6738 8.811017 ACTCAATGGACAAGATATATACCAGAG 58.189 37.037 0.00 0.00 0.00 3.35
5706 6851 8.190784 AGAAAGTAAGATTCAAAAGTGTGGTTG 58.809 33.333 0.00 0.00 0.00 3.77
5740 7013 2.380941 TGATTGCAATGTCCATGAGGG 58.619 47.619 18.59 0.00 34.83 4.30
5742 7015 5.298527 ACAGTATGATTGCAATGTCCATGAG 59.701 40.000 18.59 10.40 39.69 2.90
5743 7016 5.195185 ACAGTATGATTGCAATGTCCATGA 58.805 37.500 18.59 1.52 39.69 3.07
5745 7018 5.195185 TGACAGTATGATTGCAATGTCCAT 58.805 37.500 18.59 16.00 39.69 3.41
5755 7028 7.311364 TGTTCATGTGATGACAGTATGATTG 57.689 36.000 0.00 0.00 41.26 2.67
5799 7072 5.163343 TGTTAACTTCCATCTTATCGAGGGG 60.163 44.000 7.22 0.00 43.73 4.79
5874 7147 4.345837 TGTACCCCAACTGTAGTATATGCC 59.654 45.833 0.00 0.00 0.00 4.40
5886 7159 3.814316 GCAAGAAAGGATGTACCCCAACT 60.814 47.826 4.49 0.00 40.05 3.16
6000 7274 0.030235 TTACCGTCTCATCCGCATCG 59.970 55.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.