Multiple sequence alignment - TraesCS6D01G023900

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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 TraesCS6D01G023900 chr6D 100.000 3188 0 0 1 3188 9060973 9064160 0.000000e+00 5888.0
1 TraesCS6D01G023900 chr6D 77.316 1565 275 60 960 2478 7994319 7992789 0.000000e+00 850.0
2 TraesCS6D01G023900 chr6D 78.203 1280 234 34 965 2228 8659857 8658607 0.000000e+00 776.0
3 TraesCS6D01G023900 chr6D 77.471 1305 253 34 978 2268 8245460 8246737 0.000000e+00 743.0
4 TraesCS6D01G023900 chr6D 77.853 1183 232 21 960 2130 16775787 16774623 0.000000e+00 706.0
5 TraesCS6D01G023900 chr6D 76.829 1230 252 23 978 2197 8147208 8146002 0.000000e+00 662.0
6 TraesCS6D01G023900 chr6D 76.761 1235 242 32 978 2197 8249768 8250972 0.000000e+00 649.0
7 TraesCS6D01G023900 chr6D 78.000 1100 190 32 1093 2175 8858277 8859341 0.000000e+00 643.0
8 TraesCS6D01G023900 chr6D 78.795 830 161 15 1427 2248 14518061 14518883 7.780000e-151 544.0
9 TraesCS6D01G023900 chr6D 96.721 122 4 0 2598 2719 348647458 348647337 1.500000e-48 204.0
10 TraesCS6D01G023900 chr6D 89.535 86 9 0 135 220 444510695 444510780 3.360000e-20 110.0
11 TraesCS6D01G023900 chr6B 92.790 1803 107 12 806 2603 16513354 16511570 0.000000e+00 2588.0
12 TraesCS6D01G023900 chr6B 90.795 1749 116 28 867 2605 16607847 16609560 0.000000e+00 2296.0
13 TraesCS6D01G023900 chr6B 89.146 820 63 17 1 812 16514189 16513388 0.000000e+00 998.0
14 TraesCS6D01G023900 chr6B 76.945 1388 276 25 993 2373 16543995 16542645 0.000000e+00 750.0
15 TraesCS6D01G023900 chr6B 77.831 1254 230 38 969 2200 14323492 14324719 0.000000e+00 732.0
16 TraesCS6D01G023900 chr6B 77.019 1201 240 29 992 2183 15397955 15396782 0.000000e+00 656.0
17 TraesCS6D01G023900 chr6B 93.598 328 19 2 2862 3188 16609586 16609912 3.700000e-134 488.0
18 TraesCS6D01G023900 chr6B 95.946 222 8 1 2862 3082 16511521 16511300 3.020000e-95 359.0
19 TraesCS6D01G023900 chr6B 94.286 210 11 1 2980 3188 16653023 16653232 1.430000e-83 320.0
20 TraesCS6D01G023900 chr6B 94.286 210 11 1 2980 3188 16664919 16665128 1.430000e-83 320.0
21 TraesCS6D01G023900 chr6B 76.568 542 116 9 1709 2245 62650852 62650317 1.450000e-73 287.0
22 TraesCS6D01G023900 chr6B 95.276 127 6 0 2596 2722 256326817 256326691 5.390000e-48 202.0
23 TraesCS6D01G023900 chr6B 96.296 54 2 0 2715 2768 16511573 16511520 4.380000e-14 89.8
24 TraesCS6D01G023900 chr6B 82.222 90 12 3 135 220 669060420 669060509 1.230000e-09 75.0
25 TraesCS6D01G023900 chr6B 100.000 38 0 0 2731 2768 16609550 16609587 1.590000e-08 71.3
26 TraesCS6D01G023900 chr6A 92.147 1248 85 8 1357 2603 9572345 9573580 0.000000e+00 1749.0
27 TraesCS6D01G023900 chr6A 90.820 817 45 10 1 809 9570235 9571029 0.000000e+00 1066.0
28 TraesCS6D01G023900 chr6A 96.196 552 18 3 814 1364 9571416 9571965 0.000000e+00 900.0
29 TraesCS6D01G023900 chr6A 77.037 1559 292 45 960 2478 8202382 8200850 0.000000e+00 835.0
30 TraesCS6D01G023900 chr6A 76.864 1435 288 34 962 2383 15873222 15871819 0.000000e+00 771.0
31 TraesCS6D01G023900 chr6A 77.921 1241 233 30 969 2197 8712223 8713434 0.000000e+00 736.0
32 TraesCS6D01G023900 chr6A 92.025 326 9 2 2862 3186 9573629 9573938 2.920000e-120 442.0
33 TraesCS6D01G023900 chr6A 96.296 54 2 0 2715 2768 9573577 9573630 4.380000e-14 89.8
34 TraesCS6D01G023900 chr2B 79.068 1309 222 29 965 2258 709426197 709424926 0.000000e+00 852.0
35 TraesCS6D01G023900 chr1D 77.182 1157 224 28 1069 2210 416356406 416355275 3.470000e-179 638.0
36 TraesCS6D01G023900 chr1D 91.667 108 6 3 2764 2870 225936849 225936954 2.560000e-31 147.0
37 TraesCS6D01G023900 chrUn 94.286 210 11 1 2980 3188 351893715 351893506 1.430000e-83 320.0
38 TraesCS6D01G023900 chr2D 76.471 425 77 10 139 545 410233373 410232954 3.220000e-50 209.0
39 TraesCS6D01G023900 chr2D 96.000 125 4 1 2602 2726 441576673 441576796 5.390000e-48 202.0
40 TraesCS6D01G023900 chr2D 94.574 129 5 2 2594 2722 579092342 579092468 6.980000e-47 198.0
41 TraesCS6D01G023900 chr2D 93.137 102 7 0 2763 2864 98693497 98693598 1.980000e-32 150.0
42 TraesCS6D01G023900 chr2D 79.602 201 38 3 157 356 410401886 410401688 1.190000e-29 141.0
43 TraesCS6D01G023900 chr3D 98.305 118 2 0 2601 2718 337959626 337959509 1.160000e-49 207.0
44 TraesCS6D01G023900 chr3D 97.479 119 3 0 2602 2720 607000538 607000656 1.500000e-48 204.0
45 TraesCS6D01G023900 chr3D 90.323 62 3 3 500 559 6952362 6952302 9.480000e-11 78.7
46 TraesCS6D01G023900 chr5B 93.478 138 6 3 2596 2731 472739672 472739536 5.390000e-48 202.0
47 TraesCS6D01G023900 chr5A 95.968 124 4 1 2596 2719 505594264 505594142 1.940000e-47 200.0
48 TraesCS6D01G023900 chr4D 94.574 129 6 1 2594 2721 15768035 15768163 6.980000e-47 198.0
49 TraesCS6D01G023900 chr5D 75.721 416 70 17 153 543 450702186 450701777 2.530000e-41 180.0
50 TraesCS6D01G023900 chr5D 81.928 83 14 1 730 812 383227222 383227303 5.710000e-08 69.4
51 TraesCS6D01G023900 chr2A 74.438 489 91 18 140 601 578378536 578378055 2.530000e-41 180.0
52 TraesCS6D01G023900 chr2A 94.059 101 6 0 2766 2866 68155921 68155821 1.530000e-33 154.0
53 TraesCS6D01G023900 chr7B 91.743 109 7 2 2760 2867 134634114 134634221 1.980000e-32 150.0
54 TraesCS6D01G023900 chr7B 93.878 98 6 0 2767 2864 478835037 478835134 7.120000e-32 148.0
55 TraesCS6D01G023900 chr7A 93.137 102 7 0 2763 2864 61815918 61816019 1.980000e-32 150.0
56 TraesCS6D01G023900 chr7A 89.908 109 11 0 2765 2873 735412102 735412210 1.190000e-29 141.0
57 TraesCS6D01G023900 chr7D 90.179 112 11 0 2765 2876 632327990 632327879 2.560000e-31 147.0
58 TraesCS6D01G023900 chr4A 88.189 127 10 5 2752 2875 724808110 724808234 2.560000e-31 147.0


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 TraesCS6D01G023900 chr6D 9060973 9064160 3187 False 5888.000000 5888 100.000000 1 3188 1 chr6D.!!$F2 3187
1 TraesCS6D01G023900 chr6D 7992789 7994319 1530 True 850.000000 850 77.316000 960 2478 1 chr6D.!!$R1 1518
2 TraesCS6D01G023900 chr6D 8658607 8659857 1250 True 776.000000 776 78.203000 965 2228 1 chr6D.!!$R3 1263
3 TraesCS6D01G023900 chr6D 16774623 16775787 1164 True 706.000000 706 77.853000 960 2130 1 chr6D.!!$R4 1170
4 TraesCS6D01G023900 chr6D 8245460 8250972 5512 False 696.000000 743 77.116000 978 2268 2 chr6D.!!$F5 1290
5 TraesCS6D01G023900 chr6D 8146002 8147208 1206 True 662.000000 662 76.829000 978 2197 1 chr6D.!!$R2 1219
6 TraesCS6D01G023900 chr6D 8858277 8859341 1064 False 643.000000 643 78.000000 1093 2175 1 chr6D.!!$F1 1082
7 TraesCS6D01G023900 chr6D 14518061 14518883 822 False 544.000000 544 78.795000 1427 2248 1 chr6D.!!$F3 821
8 TraesCS6D01G023900 chr6B 16511300 16514189 2889 True 1008.700000 2588 93.544500 1 3082 4 chr6B.!!$R5 3081
9 TraesCS6D01G023900 chr6B 16607847 16609912 2065 False 951.766667 2296 94.797667 867 3188 3 chr6B.!!$F5 2321
10 TraesCS6D01G023900 chr6B 16542645 16543995 1350 True 750.000000 750 76.945000 993 2373 1 chr6B.!!$R2 1380
11 TraesCS6D01G023900 chr6B 14323492 14324719 1227 False 732.000000 732 77.831000 969 2200 1 chr6B.!!$F1 1231
12 TraesCS6D01G023900 chr6B 15396782 15397955 1173 True 656.000000 656 77.019000 992 2183 1 chr6B.!!$R1 1191
13 TraesCS6D01G023900 chr6B 62650317 62650852 535 True 287.000000 287 76.568000 1709 2245 1 chr6B.!!$R3 536
14 TraesCS6D01G023900 chr6A 9570235 9573938 3703 False 849.360000 1749 93.496800 1 3186 5 chr6A.!!$F2 3185
15 TraesCS6D01G023900 chr6A 8200850 8202382 1532 True 835.000000 835 77.037000 960 2478 1 chr6A.!!$R1 1518
16 TraesCS6D01G023900 chr6A 15871819 15873222 1403 True 771.000000 771 76.864000 962 2383 1 chr6A.!!$R2 1421
17 TraesCS6D01G023900 chr6A 8712223 8713434 1211 False 736.000000 736 77.921000 969 2197 1 chr6A.!!$F1 1228
18 TraesCS6D01G023900 chr2B 709424926 709426197 1271 True 852.000000 852 79.068000 965 2258 1 chr2B.!!$R1 1293
19 TraesCS6D01G023900 chr1D 416355275 416356406 1131 True 638.000000 638 77.182000 1069 2210 1 chr1D.!!$R1 1141

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
863 1256 0.189822 AGCCCTCCCCTCTATGAGAC 59.81 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 7801 0.032813 TTCCGGACGGAGGGAATACT 60.033 55.0 13.64 0.0 46.06 2.12 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
99 101 1.416480 GGGGAGGATAAGGGGAACGG 61.416 65.000 0.00 0.00 0.00 4.44
252 254 5.932303 TGGACTCTCTTTCAAGATAAAACCG 59.068 40.000 0.00 0.00 33.93 4.44
334 338 5.007234 CCGAGATTGTTGTGTGTTTCTTACA 59.993 40.000 0.00 0.00 0.00 2.41
409 413 8.452868 AGAGAACTCCTATACATGACTTCCTAT 58.547 37.037 0.00 0.00 0.00 2.57
440 444 4.641094 AGTATACGACAAGTCTTCAGGAGG 59.359 45.833 0.00 0.00 0.00 4.30
559 563 0.759436 AGACCACAACCGAGACACCT 60.759 55.000 0.00 0.00 0.00 4.00
573 577 2.309162 AGACACCTCTAGTAGCCACTGA 59.691 50.000 0.00 0.00 36.14 3.41
583 587 2.037772 AGTAGCCACTGAACCAGTCTTG 59.962 50.000 0.00 0.00 43.43 3.02
585 589 2.047061 AGCCACTGAACCAGTCTTGTA 58.953 47.619 0.00 0.00 43.43 2.41
614 618 2.814336 ACACTCCTCAATTTTTCCGAGC 59.186 45.455 0.00 0.00 0.00 5.03
615 619 2.813754 CACTCCTCAATTTTTCCGAGCA 59.186 45.455 0.00 0.00 0.00 4.26
616 620 3.253188 CACTCCTCAATTTTTCCGAGCAA 59.747 43.478 0.00 0.00 0.00 3.91
635 639 4.614946 GCAATTCTTCTGCTTGAGTTGTT 58.385 39.130 0.00 0.00 36.84 2.83
671 675 4.768448 TGGTTCAACGAGTCCTCACTTATA 59.232 41.667 0.00 0.00 30.63 0.98
812 823 8.267894 AGGTAAGAGAGAGCATGCTAAAATTTA 58.732 33.333 22.74 13.78 0.00 1.40
813 824 8.338986 GGTAAGAGAGAGCATGCTAAAATTTAC 58.661 37.037 22.74 22.74 0.00 2.01
863 1256 0.189822 AGCCCTCCCCTCTATGAGAC 59.810 60.000 0.00 0.00 0.00 3.36
1127 1597 1.566231 CTTTTCCCCAGACCCTAGCAT 59.434 52.381 0.00 0.00 0.00 3.79
1748 6918 4.024218 GGATGCTGTCTCATTCATAAGTGC 60.024 45.833 0.00 0.00 0.00 4.40
2279 7456 6.869388 GTGTTTATTTTTCCGCCTAAATGGAA 59.131 34.615 0.00 0.00 42.35 3.53
2295 7472 5.930837 AATGGAAGTTGGTTTTCTGTTCA 57.069 34.783 0.00 0.00 0.00 3.18
2308 7487 2.551270 TCTGTTCAAGTATCCCTGCCT 58.449 47.619 0.00 0.00 0.00 4.75
2369 7555 9.638176 AGTGAAGCTGATAATTTTATTCCTGAT 57.362 29.630 0.00 0.00 0.00 2.90
2551 7753 7.609918 TGATTTCCGTTCATTCCAGATTTTCTA 59.390 33.333 0.00 0.00 0.00 2.10
2598 7800 8.919145 TCTTTTGTTTTCCACCATATGTAAGTT 58.081 29.630 1.24 0.00 0.00 2.66
2601 7803 8.927675 TTGTTTTCCACCATATGTAAGTTAGT 57.072 30.769 1.24 0.00 0.00 2.24
2606 7808 9.841295 TTTCCACCATATGTAAGTTAGTATTCC 57.159 33.333 1.24 0.00 0.00 3.01
2607 7809 7.970102 TCCACCATATGTAAGTTAGTATTCCC 58.030 38.462 1.24 0.00 0.00 3.97
2608 7810 7.792736 TCCACCATATGTAAGTTAGTATTCCCT 59.207 37.037 1.24 0.00 0.00 4.20
2609 7811 8.095169 CCACCATATGTAAGTTAGTATTCCCTC 58.905 40.741 1.24 0.00 0.00 4.30
2610 7812 8.095169 CACCATATGTAAGTTAGTATTCCCTCC 58.905 40.741 1.24 0.00 0.00 4.30
2611 7813 7.039223 ACCATATGTAAGTTAGTATTCCCTCCG 60.039 40.741 1.24 0.00 0.00 4.63
2612 7814 7.039223 CCATATGTAAGTTAGTATTCCCTCCGT 60.039 40.741 1.24 0.00 0.00 4.69
2613 7815 5.841957 TGTAAGTTAGTATTCCCTCCGTC 57.158 43.478 0.00 0.00 0.00 4.79
2614 7816 4.646492 TGTAAGTTAGTATTCCCTCCGTCC 59.354 45.833 0.00 0.00 0.00 4.79
2615 7817 2.305009 AGTTAGTATTCCCTCCGTCCG 58.695 52.381 0.00 0.00 0.00 4.79
2616 7818 1.339291 GTTAGTATTCCCTCCGTCCGG 59.661 57.143 0.00 0.00 0.00 5.14
2617 7819 0.846015 TAGTATTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2618 7820 0.032813 AGTATTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2619 7821 0.826062 GTATTCCCTCCGTCCGGAAA 59.174 55.000 5.23 1.92 44.66 3.13
2620 7822 1.415289 GTATTCCCTCCGTCCGGAAAT 59.585 52.381 5.23 9.21 44.66 2.17
2621 7823 1.797320 ATTCCCTCCGTCCGGAAATA 58.203 50.000 5.23 0.00 44.66 1.40
2622 7824 0.826062 TTCCCTCCGTCCGGAAATAC 59.174 55.000 5.23 0.00 44.66 1.89
2623 7825 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2624 7826 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2625 7827 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2626 7828 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2627 7829 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2628 7830 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2629 7831 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
2630 7832 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
2631 7833 3.103738 CGTCCGGAAATACTTGTCGTAG 58.896 50.000 5.23 0.00 0.00 3.51
2632 7834 3.181507 CGTCCGGAAATACTTGTCGTAGA 60.182 47.826 5.23 0.00 0.00 2.59
2633 7835 4.672542 CGTCCGGAAATACTTGTCGTAGAA 60.673 45.833 5.23 0.00 39.69 2.10
2634 7836 5.163513 GTCCGGAAATACTTGTCGTAGAAA 58.836 41.667 5.23 0.00 39.69 2.52
2635 7837 5.809051 GTCCGGAAATACTTGTCGTAGAAAT 59.191 40.000 5.23 0.00 39.69 2.17
2636 7838 5.808540 TCCGGAAATACTTGTCGTAGAAATG 59.191 40.000 0.00 0.00 39.69 2.32
2637 7839 5.006358 CCGGAAATACTTGTCGTAGAAATGG 59.994 44.000 0.00 0.00 39.69 3.16
2638 7840 5.808540 CGGAAATACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
2639 7841 6.479001 CGGAAATACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
2640 7842 7.650504 CGGAAATACTTGTCGTAGAAATGGATA 59.349 37.037 0.00 0.00 39.69 2.59
2641 7843 8.762426 GGAAATACTTGTCGTAGAAATGGATAC 58.238 37.037 0.00 0.00 39.69 2.24
2688 7890 8.423906 AAATACATCTAGATACGTCCATTCCT 57.576 34.615 4.54 0.00 0.00 3.36
2689 7891 5.968528 ACATCTAGATACGTCCATTCCTC 57.031 43.478 4.54 0.00 0.00 3.71
2690 7892 4.456222 ACATCTAGATACGTCCATTCCTCG 59.544 45.833 4.54 0.00 0.00 4.63
2691 7893 3.409570 TCTAGATACGTCCATTCCTCGG 58.590 50.000 0.00 0.00 0.00 4.63
2692 7894 2.359981 AGATACGTCCATTCCTCGGA 57.640 50.000 0.00 0.00 0.00 4.55
2701 7903 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
2702 7904 4.766375 TCCATTCCTCGGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
2703 7905 3.877508 CCATTCCTCGGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
2709 7911 1.648504 GGACAAGTATTTCCGGACGG 58.351 55.000 1.83 3.96 0.00 4.79
2710 7912 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
2711 7913 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2712 7914 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2713 7915 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2772 7974 9.174166 TCTAAATTGTGCTTAGAAAATACTCCC 57.826 33.333 0.00 0.00 33.47 4.30
2773 7975 9.178758 CTAAATTGTGCTTAGAAAATACTCCCT 57.821 33.333 0.00 0.00 0.00 4.20
2774 7976 7.631717 AATTGTGCTTAGAAAATACTCCCTC 57.368 36.000 0.00 0.00 0.00 4.30
2775 7977 5.099042 TGTGCTTAGAAAATACTCCCTCC 57.901 43.478 0.00 0.00 0.00 4.30
2776 7978 4.120589 GTGCTTAGAAAATACTCCCTCCG 58.879 47.826 0.00 0.00 0.00 4.63
2777 7979 3.773119 TGCTTAGAAAATACTCCCTCCGT 59.227 43.478 0.00 0.00 0.00 4.69
2778 7980 4.142004 TGCTTAGAAAATACTCCCTCCGTC 60.142 45.833 0.00 0.00 0.00 4.79
2779 7981 4.740034 GCTTAGAAAATACTCCCTCCGTCC 60.740 50.000 0.00 0.00 0.00 4.79
2780 7982 2.117051 AGAAAATACTCCCTCCGTCCC 58.883 52.381 0.00 0.00 0.00 4.46
2781 7983 1.835531 GAAAATACTCCCTCCGTCCCA 59.164 52.381 0.00 0.00 0.00 4.37
2782 7984 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
2783 7985 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2784 7986 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2785 7987 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2786 7988 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2787 7989 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2788 7990 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2789 7991 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2790 7992 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2791 7993 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2792 7994 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2793 7995 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2794 7996 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2795 7997 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2796 7998 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2797 7999 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2798 8000 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2799 8001 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2800 8002 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2801 8003 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2802 8004 5.691754 CCCAAAATAAGTGTCTCAACTTTGC 59.308 40.000 0.00 0.00 40.77 3.68
2803 8005 5.691754 CCAAAATAAGTGTCTCAACTTTGCC 59.308 40.000 0.00 0.00 40.77 4.52
2804 8006 5.453567 AAATAAGTGTCTCAACTTTGCCC 57.546 39.130 0.00 0.00 40.77 5.36
2805 8007 2.736670 AAGTGTCTCAACTTTGCCCT 57.263 45.000 0.00 0.00 37.05 5.19
2806 8008 3.857157 AAGTGTCTCAACTTTGCCCTA 57.143 42.857 0.00 0.00 37.05 3.53
2807 8009 3.857157 AGTGTCTCAACTTTGCCCTAA 57.143 42.857 0.00 0.00 0.00 2.69
2808 8010 4.373156 AGTGTCTCAACTTTGCCCTAAT 57.627 40.909 0.00 0.00 0.00 1.73
2809 8011 4.729868 AGTGTCTCAACTTTGCCCTAATT 58.270 39.130 0.00 0.00 0.00 1.40
2810 8012 5.140454 AGTGTCTCAACTTTGCCCTAATTT 58.860 37.500 0.00 0.00 0.00 1.82
2811 8013 5.598417 AGTGTCTCAACTTTGCCCTAATTTT 59.402 36.000 0.00 0.00 0.00 1.82
2812 8014 6.775629 AGTGTCTCAACTTTGCCCTAATTTTA 59.224 34.615 0.00 0.00 0.00 1.52
2813 8015 7.040409 AGTGTCTCAACTTTGCCCTAATTTTAG 60.040 37.037 0.00 0.00 0.00 1.85
2814 8016 6.775629 TGTCTCAACTTTGCCCTAATTTTAGT 59.224 34.615 0.00 0.00 0.00 2.24
2815 8017 7.940137 TGTCTCAACTTTGCCCTAATTTTAGTA 59.060 33.333 0.00 0.00 0.00 1.82
2816 8018 8.235226 GTCTCAACTTTGCCCTAATTTTAGTAC 58.765 37.037 0.00 0.00 0.00 2.73
2817 8019 7.940137 TCTCAACTTTGCCCTAATTTTAGTACA 59.060 33.333 0.00 0.00 0.00 2.90
2818 8020 8.466617 TCAACTTTGCCCTAATTTTAGTACAA 57.533 30.769 0.00 0.00 0.00 2.41
2819 8021 8.915036 TCAACTTTGCCCTAATTTTAGTACAAA 58.085 29.630 0.00 11.40 34.89 2.83
2820 8022 9.191995 CAACTTTGCCCTAATTTTAGTACAAAG 57.808 33.333 23.76 23.76 45.43 2.77
2821 8023 8.473358 ACTTTGCCCTAATTTTAGTACAAAGT 57.527 30.769 24.52 24.52 46.41 2.66
2823 8025 9.191995 CTTTGCCCTAATTTTAGTACAAAGTTG 57.808 33.333 20.68 0.00 41.23 3.16
2824 8026 7.826918 TGCCCTAATTTTAGTACAAAGTTGT 57.173 32.000 1.75 1.75 44.86 3.32
2825 8027 8.921353 TGCCCTAATTTTAGTACAAAGTTGTA 57.079 30.769 0.00 0.00 42.35 2.41
2840 8042 8.429493 ACAAAGTTGTACTAAAGGTAAGACAC 57.571 34.615 0.00 0.00 40.16 3.67
2841 8043 8.262933 ACAAAGTTGTACTAAAGGTAAGACACT 58.737 33.333 0.00 0.00 40.16 3.55
2842 8044 9.106070 CAAAGTTGTACTAAAGGTAAGACACTT 57.894 33.333 0.00 0.00 31.56 3.16
2850 8052 8.631480 ACTAAAGGTAAGACACTTATTTTGGG 57.369 34.615 0.44 0.00 0.00 4.12
2851 8053 8.442374 ACTAAAGGTAAGACACTTATTTTGGGA 58.558 33.333 0.44 0.00 0.00 4.37
2852 8054 7.520451 AAAGGTAAGACACTTATTTTGGGAC 57.480 36.000 0.00 0.00 0.00 4.46
2853 8055 6.195600 AGGTAAGACACTTATTTTGGGACA 57.804 37.500 0.00 0.00 0.00 4.02
2854 8056 6.238648 AGGTAAGACACTTATTTTGGGACAG 58.761 40.000 0.00 0.00 42.39 3.51
2855 8057 6.043938 AGGTAAGACACTTATTTTGGGACAGA 59.956 38.462 0.00 0.00 42.39 3.41
2856 8058 6.371825 GGTAAGACACTTATTTTGGGACAGAG 59.628 42.308 0.00 0.00 42.39 3.35
2857 8059 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
2858 8060 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
2859 8061 3.655777 ACACTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
2860 8062 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
2878 8080 4.225267 AGGGAGTATGTTTCTGTTGGGTAG 59.775 45.833 0.00 0.00 0.00 3.18
2889 8091 1.211949 TGTTGGGTAGCTTCTATGCCC 59.788 52.381 0.00 0.00 42.56 5.36
3161 8364 7.114095 AGAGAACAGTTTGGTTGGTAACTAAA 58.886 34.615 0.02 0.02 39.16 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.536662 CTTATCCTCCCCCTCCCGG 60.537 68.421 0.00 0.00 0.00 5.73
74 75 1.536662 CCTTATCCTCCCCCTCCCG 60.537 68.421 0.00 0.00 0.00 5.14
78 79 0.028955 GTTCCCCTTATCCTCCCCCT 60.029 60.000 0.00 0.00 0.00 4.79
99 101 0.392461 TCGGGTGATTTGTAGCCAGC 60.392 55.000 0.00 0.00 35.46 4.85
252 254 6.699063 GCAATAAAATGCAAGCAAGATGTAC 58.301 36.000 0.00 0.00 45.70 2.90
334 338 1.518367 TAAATCGAGGGATGGGGCTT 58.482 50.000 0.00 0.00 31.83 4.35
409 413 7.121611 TGAAGACTTGTCGTATACTCCACAATA 59.878 37.037 10.58 0.00 0.00 1.90
440 444 3.921677 CCCATGGCATATGAAATGAAGC 58.078 45.455 6.09 0.00 0.00 3.86
477 481 1.359848 CTATGTCGGTTCACCAGTGC 58.640 55.000 0.00 0.00 35.14 4.40
559 563 3.090037 GACTGGTTCAGTGGCTACTAGA 58.910 50.000 0.95 0.12 45.44 2.43
583 587 4.810191 ATTGAGGAGTGTCCAGACTTAC 57.190 45.455 0.00 0.00 39.61 2.34
585 589 4.713792 AAATTGAGGAGTGTCCAGACTT 57.286 40.909 0.00 0.00 39.61 3.01
595 599 3.140325 TGCTCGGAAAAATTGAGGAGT 57.860 42.857 0.00 0.00 0.00 3.85
614 618 4.980434 CCAACAACTCAAGCAGAAGAATTG 59.020 41.667 0.00 0.00 0.00 2.32
615 619 4.646492 ACCAACAACTCAAGCAGAAGAATT 59.354 37.500 0.00 0.00 0.00 2.17
616 620 4.210331 ACCAACAACTCAAGCAGAAGAAT 58.790 39.130 0.00 0.00 0.00 2.40
635 639 3.563808 CGTTGAACCAGATCTCAAAACCA 59.436 43.478 0.00 0.00 33.52 3.67
671 675 5.491070 TCGATCCAGTGATCAAGAAATTGT 58.509 37.500 0.00 0.00 46.50 2.71
775 786 5.397334 GCTCTCTCTTACCTCCCATTTTCAT 60.397 44.000 0.00 0.00 0.00 2.57
950 1344 2.204213 AGGGAAGGGCTGGAGCTT 60.204 61.111 0.00 0.00 41.70 3.74
1108 1572 1.564348 GATGCTAGGGTCTGGGGAAAA 59.436 52.381 0.00 0.00 0.00 2.29
1127 1597 1.001764 TACTCCTCCACGGCGAAGA 60.002 57.895 16.62 8.82 0.00 2.87
1299 6075 4.504916 CAGAGGAGCTGCGGGTCG 62.505 72.222 18.07 0.84 40.51 4.79
1748 6918 0.391130 TTTGGTGGCGATCTTCTCCG 60.391 55.000 0.00 0.00 0.00 4.63
2141 7313 5.574443 GTGAATTTGAAATTAGCTGGCACTC 59.426 40.000 2.71 0.00 0.00 3.51
2260 7434 5.478407 CAACTTCCATTTAGGCGGAAAAAT 58.522 37.500 0.00 0.00 40.71 1.82
2279 7456 5.535030 GGGATACTTGAACAGAAAACCAACT 59.465 40.000 0.00 0.00 0.00 3.16
2308 7487 1.423541 ACCAAACCAGTATGTGCCAGA 59.576 47.619 0.00 0.00 0.00 3.86
2349 7535 7.667219 TCAGGGATCAGGAATAAAATTATCAGC 59.333 37.037 0.00 0.00 0.00 4.26
2369 7555 5.241403 ACTAAATGACAACACATCAGGGA 57.759 39.130 0.00 0.00 0.00 4.20
2551 7753 9.617523 AAAAGACACTGAAATGAAAATGGAAAT 57.382 25.926 0.00 0.00 0.00 2.17
2598 7800 0.846015 TCCGGACGGAGGGAATACTA 59.154 55.000 9.76 0.00 39.76 1.82
2599 7801 0.032813 TTCCGGACGGAGGGAATACT 60.033 55.000 13.64 0.00 46.06 2.12
2600 7802 0.826062 TTTCCGGACGGAGGGAATAC 59.174 55.000 13.64 0.00 46.06 1.89
2601 7803 1.797320 ATTTCCGGACGGAGGGAATA 58.203 50.000 13.64 0.00 46.06 1.75
2602 7804 1.415289 GTATTTCCGGACGGAGGGAAT 59.585 52.381 13.64 12.81 46.06 3.01
2603 7805 0.826062 GTATTTCCGGACGGAGGGAA 59.174 55.000 13.64 6.20 46.06 3.97
2604 7806 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2605 7807 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2606 7808 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2607 7809 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2608 7810 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2609 7811 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2610 7812 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
2611 7813 4.361451 TCTACGACAAGTATTTCCGGAC 57.639 45.455 1.83 0.00 34.34 4.79
2612 7814 5.389859 TTTCTACGACAAGTATTTCCGGA 57.610 39.130 0.00 0.00 34.34 5.14
2613 7815 5.006358 CCATTTCTACGACAAGTATTTCCGG 59.994 44.000 0.00 0.00 34.34 5.14
2614 7816 5.808540 TCCATTTCTACGACAAGTATTTCCG 59.191 40.000 0.00 0.00 34.34 4.30
2615 7817 7.787725 ATCCATTTCTACGACAAGTATTTCC 57.212 36.000 0.00 0.00 34.34 3.13
2616 7818 9.309516 TGTATCCATTTCTACGACAAGTATTTC 57.690 33.333 0.00 0.00 34.34 2.17
2617 7819 9.661563 TTGTATCCATTTCTACGACAAGTATTT 57.338 29.630 0.00 0.00 34.34 1.40
2618 7820 9.661563 TTTGTATCCATTTCTACGACAAGTATT 57.338 29.630 0.00 0.00 34.34 1.89
2619 7821 9.832445 ATTTGTATCCATTTCTACGACAAGTAT 57.168 29.630 0.00 0.00 34.34 2.12
2620 7822 9.093970 CATTTGTATCCATTTCTACGACAAGTA 57.906 33.333 0.00 0.00 0.00 2.24
2621 7823 7.065803 CCATTTGTATCCATTTCTACGACAAGT 59.934 37.037 0.00 0.00 0.00 3.16
2622 7824 7.279981 TCCATTTGTATCCATTTCTACGACAAG 59.720 37.037 0.00 0.00 0.00 3.16
2623 7825 7.106890 TCCATTTGTATCCATTTCTACGACAA 58.893 34.615 0.00 0.00 0.00 3.18
2624 7826 6.645306 TCCATTTGTATCCATTTCTACGACA 58.355 36.000 0.00 0.00 0.00 4.35
2625 7827 7.226720 ACATCCATTTGTATCCATTTCTACGAC 59.773 37.037 0.00 0.00 0.00 4.34
2626 7828 7.279615 ACATCCATTTGTATCCATTTCTACGA 58.720 34.615 0.00 0.00 0.00 3.43
2627 7829 7.496529 ACATCCATTTGTATCCATTTCTACG 57.503 36.000 0.00 0.00 0.00 3.51
2662 7864 8.871125 AGGAATGGACGTATCTAGATGTATTTT 58.129 33.333 15.79 0.90 0.00 1.82
2663 7865 8.423906 AGGAATGGACGTATCTAGATGTATTT 57.576 34.615 15.79 1.04 0.00 1.40
2664 7866 7.148222 CGAGGAATGGACGTATCTAGATGTATT 60.148 40.741 15.79 3.66 0.00 1.89
2665 7867 6.316640 CGAGGAATGGACGTATCTAGATGTAT 59.683 42.308 15.79 0.00 0.00 2.29
2666 7868 5.642491 CGAGGAATGGACGTATCTAGATGTA 59.358 44.000 15.79 0.00 0.00 2.29
2667 7869 4.456222 CGAGGAATGGACGTATCTAGATGT 59.544 45.833 15.79 5.44 0.00 3.06
2668 7870 4.142578 CCGAGGAATGGACGTATCTAGATG 60.143 50.000 15.79 1.92 0.00 2.90
2669 7871 4.011023 CCGAGGAATGGACGTATCTAGAT 58.989 47.826 10.73 10.73 0.00 1.98
2670 7872 3.072038 TCCGAGGAATGGACGTATCTAGA 59.928 47.826 0.00 0.00 0.00 2.43
2671 7873 3.188873 GTCCGAGGAATGGACGTATCTAG 59.811 52.174 0.00 0.00 45.82 2.43
2672 7874 3.144506 GTCCGAGGAATGGACGTATCTA 58.855 50.000 0.00 0.00 45.82 1.98
2673 7875 1.955080 GTCCGAGGAATGGACGTATCT 59.045 52.381 0.00 0.00 45.82 1.98
2674 7876 2.418983 GTCCGAGGAATGGACGTATC 57.581 55.000 0.00 0.00 45.82 2.24
2680 7882 4.383770 GGAAATACTTGTCCGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
2681 7883 3.877508 GGAAATACTTGTCCGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
2690 7892 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
2691 7893 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2692 7894 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2693 7895 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2694 7896 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2695 7897 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2696 7898 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2697 7899 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2698 7900 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2699 7901 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2700 7902 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2701 7903 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2702 7904 0.107017 TTAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
2703 7905 1.307097 CTTAGTACTCCCTCCGTCCG 58.693 60.000 0.00 0.00 0.00 4.79
2704 7906 2.433662 ACTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2705 7907 5.735638 GCAATAACTTAGTACTCCCTCCGTC 60.736 48.000 0.00 0.00 0.00 4.79
2706 7908 4.099113 GCAATAACTTAGTACTCCCTCCGT 59.901 45.833 0.00 0.00 0.00 4.69
2707 7909 4.098960 TGCAATAACTTAGTACTCCCTCCG 59.901 45.833 0.00 0.00 0.00 4.63
2708 7910 5.128991 ACTGCAATAACTTAGTACTCCCTCC 59.871 44.000 0.00 0.00 0.00 4.30
2709 7911 6.223351 ACTGCAATAACTTAGTACTCCCTC 57.777 41.667 0.00 0.00 0.00 4.30
2710 7912 6.212791 TGAACTGCAATAACTTAGTACTCCCT 59.787 38.462 0.00 0.00 0.00 4.20
2711 7913 6.403878 TGAACTGCAATAACTTAGTACTCCC 58.596 40.000 0.00 0.00 0.00 4.30
2712 7914 7.097834 ACTGAACTGCAATAACTTAGTACTCC 58.902 38.462 0.00 0.00 0.00 3.85
2713 7915 9.804758 ATACTGAACTGCAATAACTTAGTACTC 57.195 33.333 0.00 0.00 0.00 2.59
2766 7968 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2767 7969 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2768 7970 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2769 7971 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2770 7972 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2771 7973 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2772 7974 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2773 7975 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2774 7976 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2775 7977 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
2776 7978 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2777 7979 6.460953 GCAAAGTTGAGACACTTATTTTGGGA 60.461 38.462 0.00 0.00 35.87 4.37
2778 7980 5.691754 GCAAAGTTGAGACACTTATTTTGGG 59.308 40.000 0.00 0.00 35.87 4.12
2779 7981 5.691754 GGCAAAGTTGAGACACTTATTTTGG 59.308 40.000 0.00 0.00 35.87 3.28
2780 7982 5.691754 GGGCAAAGTTGAGACACTTATTTTG 59.308 40.000 0.00 0.00 35.87 2.44
2781 7983 5.598417 AGGGCAAAGTTGAGACACTTATTTT 59.402 36.000 0.00 0.00 35.87 1.82
2782 7984 5.140454 AGGGCAAAGTTGAGACACTTATTT 58.860 37.500 0.00 0.00 35.87 1.40
2783 7985 4.729868 AGGGCAAAGTTGAGACACTTATT 58.270 39.130 0.00 0.00 35.87 1.40
2784 7986 4.373156 AGGGCAAAGTTGAGACACTTAT 57.627 40.909 0.00 0.00 35.87 1.73
2785 7987 3.857157 AGGGCAAAGTTGAGACACTTA 57.143 42.857 0.00 0.00 35.87 2.24
2786 7988 2.736670 AGGGCAAAGTTGAGACACTT 57.263 45.000 0.00 0.00 38.74 3.16
2787 7989 3.857157 TTAGGGCAAAGTTGAGACACT 57.143 42.857 0.00 0.00 0.00 3.55
2788 7990 5.453567 AAATTAGGGCAAAGTTGAGACAC 57.546 39.130 0.00 0.00 0.00 3.67
2789 7991 6.775629 ACTAAAATTAGGGCAAAGTTGAGACA 59.224 34.615 5.27 0.00 35.08 3.41
2790 7992 7.215719 ACTAAAATTAGGGCAAAGTTGAGAC 57.784 36.000 5.27 0.00 35.08 3.36
2791 7993 7.940137 TGTACTAAAATTAGGGCAAAGTTGAGA 59.060 33.333 5.27 0.00 35.08 3.27
2792 7994 8.106247 TGTACTAAAATTAGGGCAAAGTTGAG 57.894 34.615 5.27 0.00 35.08 3.02
2793 7995 8.466617 TTGTACTAAAATTAGGGCAAAGTTGA 57.533 30.769 5.27 0.00 35.08 3.18
2794 7996 9.191995 CTTTGTACTAAAATTAGGGCAAAGTTG 57.808 33.333 24.41 13.14 42.83 3.16
2797 7999 9.191995 CAACTTTGTACTAAAATTAGGGCAAAG 57.808 33.333 27.26 27.26 46.76 2.77
2798 8000 8.697292 ACAACTTTGTACTAAAATTAGGGCAAA 58.303 29.630 16.23 16.23 40.16 3.68
2799 8001 8.240267 ACAACTTTGTACTAAAATTAGGGCAA 57.760 30.769 5.27 6.42 40.16 4.52
2800 8002 7.826918 ACAACTTTGTACTAAAATTAGGGCA 57.173 32.000 5.27 1.17 40.16 5.36
2814 8016 9.533253 GTGTCTTACCTTTAGTACAACTTTGTA 57.467 33.333 0.00 0.00 42.35 2.41
2815 8017 8.262933 AGTGTCTTACCTTTAGTACAACTTTGT 58.737 33.333 0.00 0.00 44.86 2.83
2816 8018 8.658499 AGTGTCTTACCTTTAGTACAACTTTG 57.342 34.615 0.00 0.00 0.00 2.77
2824 8026 9.729281 CCCAAAATAAGTGTCTTACCTTTAGTA 57.271 33.333 0.00 0.00 0.00 1.82
2825 8027 8.442374 TCCCAAAATAAGTGTCTTACCTTTAGT 58.558 33.333 0.00 0.00 0.00 2.24
2826 8028 8.727910 GTCCCAAAATAAGTGTCTTACCTTTAG 58.272 37.037 0.00 0.00 0.00 1.85
2827 8029 8.219178 TGTCCCAAAATAAGTGTCTTACCTTTA 58.781 33.333 0.00 0.00 0.00 1.85
2828 8030 7.064229 TGTCCCAAAATAAGTGTCTTACCTTT 58.936 34.615 0.00 0.00 0.00 3.11
2829 8031 6.607019 TGTCCCAAAATAAGTGTCTTACCTT 58.393 36.000 0.00 0.00 0.00 3.50
2830 8032 6.043938 TCTGTCCCAAAATAAGTGTCTTACCT 59.956 38.462 0.00 0.00 0.00 3.08
2831 8033 6.235664 TCTGTCCCAAAATAAGTGTCTTACC 58.764 40.000 0.00 0.00 0.00 2.85
2832 8034 6.371825 CCTCTGTCCCAAAATAAGTGTCTTAC 59.628 42.308 0.00 0.00 0.00 2.34
2833 8035 6.472887 CCTCTGTCCCAAAATAAGTGTCTTA 58.527 40.000 0.00 0.00 0.00 2.10
2834 8036 5.316987 CCTCTGTCCCAAAATAAGTGTCTT 58.683 41.667 0.00 0.00 0.00 3.01
2835 8037 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
2836 8038 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
2837 8039 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
2838 8040 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
2839 8041 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
2840 8042 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
2841 8043 5.491078 ACATACTCCCTCTGTCCCAAAATAA 59.509 40.000 0.00 0.00 0.00 1.40
2842 8044 5.036916 ACATACTCCCTCTGTCCCAAAATA 58.963 41.667 0.00 0.00 0.00 1.40
2843 8045 3.852578 ACATACTCCCTCTGTCCCAAAAT 59.147 43.478 0.00 0.00 0.00 1.82
2844 8046 3.256704 ACATACTCCCTCTGTCCCAAAA 58.743 45.455 0.00 0.00 0.00 2.44
2845 8047 2.915869 ACATACTCCCTCTGTCCCAAA 58.084 47.619 0.00 0.00 0.00 3.28
2846 8048 2.642171 ACATACTCCCTCTGTCCCAA 57.358 50.000 0.00 0.00 0.00 4.12
2847 8049 2.642171 AACATACTCCCTCTGTCCCA 57.358 50.000 0.00 0.00 0.00 4.37
2848 8050 3.108376 AGAAACATACTCCCTCTGTCCC 58.892 50.000 0.00 0.00 0.00 4.46
2849 8051 3.515901 ACAGAAACATACTCCCTCTGTCC 59.484 47.826 0.00 0.00 42.27 4.02
2850 8052 4.810191 ACAGAAACATACTCCCTCTGTC 57.190 45.455 0.00 0.00 42.27 3.51
2851 8053 4.263068 CCAACAGAAACATACTCCCTCTGT 60.263 45.833 0.00 0.00 46.61 3.41
2852 8054 4.256920 CCAACAGAAACATACTCCCTCTG 58.743 47.826 0.00 0.00 39.53 3.35
2853 8055 3.264450 CCCAACAGAAACATACTCCCTCT 59.736 47.826 0.00 0.00 0.00 3.69
2854 8056 3.009143 ACCCAACAGAAACATACTCCCTC 59.991 47.826 0.00 0.00 0.00 4.30
2855 8057 2.986728 ACCCAACAGAAACATACTCCCT 59.013 45.455 0.00 0.00 0.00 4.20
2856 8058 3.434940 ACCCAACAGAAACATACTCCC 57.565 47.619 0.00 0.00 0.00 4.30
2857 8059 3.939592 GCTACCCAACAGAAACATACTCC 59.060 47.826 0.00 0.00 0.00 3.85
2858 8060 4.833390 AGCTACCCAACAGAAACATACTC 58.167 43.478 0.00 0.00 0.00 2.59
2859 8061 4.910458 AGCTACCCAACAGAAACATACT 57.090 40.909 0.00 0.00 0.00 2.12
2860 8062 5.246307 AGAAGCTACCCAACAGAAACATAC 58.754 41.667 0.00 0.00 0.00 2.39
2878 8080 5.588958 AAGAAATCAAAGGGCATAGAAGC 57.411 39.130 0.00 0.00 0.00 3.86
2889 8091 7.617329 AGAAGGATAAGGGGAAAGAAATCAAAG 59.383 37.037 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.