Multiple sequence alignment - TraesCS5B01G402800

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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 TraesCS5B01G402800 chr5B 100.000 4173 0 0 1 4173 579519053 579523225 0.000000e+00 7707.0
1 TraesCS5B01G402800 chr5B 88.043 920 93 8 1085 1997 579807425 579808334 0.000000e+00 1074.0
2 TraesCS5B01G402800 chr5B 87.056 958 105 10 1078 2027 580073238 580074184 0.000000e+00 1064.0
3 TraesCS5B01G402800 chr5B 87.039 949 108 6 1085 2027 579590939 579591878 0.000000e+00 1057.0
4 TraesCS5B01G402800 chr5B 91.137 519 28 6 1 519 617253180 617253680 0.000000e+00 688.0
5 TraesCS5B01G402800 chr5B 84.651 645 96 3 2450 3092 579593709 579594352 1.270000e-179 640.0
6 TraesCS5B01G402800 chr5B 94.286 70 1 1 3180 3246 672842168 672842237 2.050000e-18 104.0
7 TraesCS5B01G402800 chr5B 76.471 187 32 8 3864 4041 52303763 52303946 1.600000e-14 91.6
8 TraesCS5B01G402800 chr5B 91.379 58 4 1 3583 3639 142658191 142658248 1.240000e-10 78.7
9 TraesCS5B01G402800 chr5A 89.321 1798 94 39 653 2389 592033598 592035358 0.000000e+00 2167.0
10 TraesCS5B01G402800 chr5A 93.231 783 42 5 2381 3158 592035581 592036357 0.000000e+00 1142.0
11 TraesCS5B01G402800 chr5A 86.765 952 115 6 1080 2027 592122410 592123354 0.000000e+00 1050.0
12 TraesCS5B01G402800 chr5A 86.715 956 108 10 1085 2032 592198228 592199172 0.000000e+00 1044.0
13 TraesCS5B01G402800 chr5A 95.539 538 23 1 2597 3133 55273264 55273801 0.000000e+00 859.0
14 TraesCS5B01G402800 chr5A 84.483 638 99 0 2457 3094 592124465 592125102 7.610000e-177 630.0
15 TraesCS5B01G402800 chr5A 90.364 467 41 3 3244 3707 592036360 592036825 9.920000e-171 610.0
16 TraesCS5B01G402800 chr5A 92.060 403 21 2 1903 2298 55272841 55273239 1.310000e-154 556.0
17 TraesCS5B01G402800 chr5A 88.309 479 35 9 3702 4173 592051362 592051826 4.710000e-154 555.0
18 TraesCS5B01G402800 chr5A 75.936 187 33 8 3864 4041 38969564 38969747 7.430000e-13 86.1
19 TraesCS5B01G402800 chr5D 88.108 1850 100 59 652 2389 472519921 472521762 0.000000e+00 2087.0
20 TraesCS5B01G402800 chr5D 94.359 780 35 3 2383 3158 472522001 472522775 0.000000e+00 1188.0
21 TraesCS5B01G402800 chr5D 86.853 966 105 11 1078 2032 472626829 472627783 0.000000e+00 1061.0
22 TraesCS5B01G402800 chr5D 86.701 970 110 8 1070 2027 472568513 472569475 0.000000e+00 1059.0
23 TraesCS5B01G402800 chr5D 86.481 969 85 22 3238 4173 472522771 472523726 0.000000e+00 1022.0
24 TraesCS5B01G402800 chr5D 85.039 635 95 0 2457 3091 472570560 472571194 0.000000e+00 647.0
25 TraesCS5B01G402800 chr5D 84.518 633 97 1 2457 3088 472627867 472628499 3.540000e-175 625.0
26 TraesCS5B01G402800 chr5D 84.444 135 21 0 519 653 354541566 354541700 2.620000e-27 134.0
27 TraesCS5B01G402800 chr5D 83.333 138 17 5 519 653 354541299 354541433 5.670000e-24 122.0
28 TraesCS5B01G402800 chr6B 94.295 596 23 2 1710 2298 650651148 650651739 0.000000e+00 902.0
29 TraesCS5B01G402800 chr6B 95.167 538 25 1 2597 3133 650651764 650652301 0.000000e+00 848.0
30 TraesCS5B01G402800 chr6B 89.060 521 36 5 1 519 667178358 667178859 9.850000e-176 627.0
31 TraesCS5B01G402800 chr6B 93.243 74 1 2 3177 3246 561044810 561044737 5.710000e-19 106.0
32 TraesCS5B01G402800 chr2A 94.128 596 24 2 1710 2298 469818939 469819530 0.000000e+00 896.0
33 TraesCS5B01G402800 chr2A 93.309 538 22 2 2597 3133 469819555 469820079 0.000000e+00 782.0
34 TraesCS5B01G402800 chr2A 85.821 134 19 0 519 652 121136885 121137018 4.350000e-30 143.0
35 TraesCS5B01G402800 chr3A 91.088 662 42 4 2475 3136 497759564 497758920 0.000000e+00 880.0
36 TraesCS5B01G402800 chr3A 90.557 413 21 4 1710 2122 497760016 497759622 7.940000e-147 531.0
37 TraesCS5B01G402800 chr3A 85.156 128 17 2 526 652 742275648 742275522 3.390000e-26 130.0
38 TraesCS5B01G402800 chr3A 92.857 70 2 1 3180 3246 466780566 466780635 9.550000e-17 99.0
39 TraesCS5B01G402800 chr3A 95.238 42 2 0 2121 2162 497759605 497759564 2.690000e-07 67.6
40 TraesCS5B01G402800 chr2B 93.449 519 29 5 1 519 325837429 325837942 0.000000e+00 765.0
41 TraesCS5B01G402800 chr2B 92.620 271 18 2 1 271 737452022 737451754 5.060000e-104 388.0
42 TraesCS5B01G402800 chr2B 92.063 252 19 1 267 518 737451541 737451291 1.850000e-93 353.0
43 TraesCS5B01G402800 chr2B 81.673 251 40 4 273 519 450445294 450445542 1.970000e-48 204.0
44 TraesCS5B01G402800 chr2B 86.667 135 18 0 519 653 760957235 760957369 2.600000e-32 150.0
45 TraesCS5B01G402800 chr2B 85.915 142 17 3 519 659 110468849 110468710 9.350000e-32 148.0
46 TraesCS5B01G402800 chr2B 86.131 137 18 1 519 654 737451253 737451117 3.360000e-31 147.0
47 TraesCS5B01G402800 chr7A 89.753 527 30 12 1 519 424552384 424552894 0.000000e+00 652.0
48 TraesCS5B01G402800 chr7A 85.938 128 18 0 525 652 27897852 27897725 2.020000e-28 137.0
49 TraesCS5B01G402800 chr3B 89.808 520 33 4 1 519 126368612 126368112 0.000000e+00 649.0
50 TraesCS5B01G402800 chr3B 97.059 68 1 1 3180 3246 811742951 811742884 3.410000e-21 113.0
51 TraesCS5B01G402800 chr3B 93.243 74 5 0 3173 3246 745722703 745722630 4.410000e-20 110.0
52 TraesCS5B01G402800 chr3B 94.286 70 1 1 3180 3246 491524242 491524173 2.050000e-18 104.0
53 TraesCS5B01G402800 chr4A 94.033 419 25 0 1 419 650839620 650840038 1.640000e-178 636.0
54 TraesCS5B01G402800 chr4A 91.200 375 18 8 1 373 217133618 217133257 2.900000e-136 496.0
55 TraesCS5B01G402800 chr1B 88.292 521 38 6 1 519 38917664 38917165 1.660000e-168 603.0
56 TraesCS5B01G402800 chr1B 98.305 59 1 0 3188 3246 7968772 7968830 2.050000e-18 104.0
57 TraesCS5B01G402800 chr2D 87.313 134 17 0 519 652 72445483 72445616 2.010000e-33 154.0
58 TraesCS5B01G402800 chr7B 85.714 133 18 1 525 656 687413202 687413070 5.630000e-29 139.0
59 TraesCS5B01G402800 chr7B 96.825 63 1 1 3180 3241 520117220 520117158 2.050000e-18 104.0
60 TraesCS5B01G402800 chr7B 94.286 70 1 1 3180 3246 678852384 678852453 2.050000e-18 104.0


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 TraesCS5B01G402800 chr5B 579519053 579523225 4172 False 7707.000000 7707 100.000000 1 4173 1 chr5B.!!$F3 4172
1 TraesCS5B01G402800 chr5B 579807425 579808334 909 False 1074.000000 1074 88.043000 1085 1997 1 chr5B.!!$F4 912
2 TraesCS5B01G402800 chr5B 580073238 580074184 946 False 1064.000000 1064 87.056000 1078 2027 1 chr5B.!!$F5 949
3 TraesCS5B01G402800 chr5B 579590939 579594352 3413 False 848.500000 1057 85.845000 1085 3092 2 chr5B.!!$F8 2007
4 TraesCS5B01G402800 chr5B 617253180 617253680 500 False 688.000000 688 91.137000 1 519 1 chr5B.!!$F6 518
5 TraesCS5B01G402800 chr5A 592033598 592036825 3227 False 1306.333333 2167 90.972000 653 3707 3 chr5A.!!$F5 3054
6 TraesCS5B01G402800 chr5A 592198228 592199172 944 False 1044.000000 1044 86.715000 1085 2032 1 chr5A.!!$F3 947
7 TraesCS5B01G402800 chr5A 592122410 592125102 2692 False 840.000000 1050 85.624000 1080 3094 2 chr5A.!!$F6 2014
8 TraesCS5B01G402800 chr5A 55272841 55273801 960 False 707.500000 859 93.799500 1903 3133 2 chr5A.!!$F4 1230
9 TraesCS5B01G402800 chr5D 472519921 472523726 3805 False 1432.333333 2087 89.649333 652 4173 3 chr5D.!!$F2 3521
10 TraesCS5B01G402800 chr5D 472568513 472571194 2681 False 853.000000 1059 85.870000 1070 3091 2 chr5D.!!$F3 2021
11 TraesCS5B01G402800 chr5D 472626829 472628499 1670 False 843.000000 1061 85.685500 1078 3088 2 chr5D.!!$F4 2010
12 TraesCS5B01G402800 chr6B 650651148 650652301 1153 False 875.000000 902 94.731000 1710 3133 2 chr6B.!!$F2 1423
13 TraesCS5B01G402800 chr6B 667178358 667178859 501 False 627.000000 627 89.060000 1 519 1 chr6B.!!$F1 518
14 TraesCS5B01G402800 chr2A 469818939 469820079 1140 False 839.000000 896 93.718500 1710 3133 2 chr2A.!!$F2 1423
15 TraesCS5B01G402800 chr3A 497758920 497760016 1096 True 492.866667 880 92.294333 1710 3136 3 chr3A.!!$R2 1426
16 TraesCS5B01G402800 chr2B 325837429 325837942 513 False 765.000000 765 93.449000 1 519 1 chr2B.!!$F1 518
17 TraesCS5B01G402800 chr2B 737451117 737452022 905 True 296.000000 388 90.271333 1 654 3 chr2B.!!$R2 653
18 TraesCS5B01G402800 chr7A 424552384 424552894 510 False 652.000000 652 89.753000 1 519 1 chr7A.!!$F1 518
19 TraesCS5B01G402800 chr3B 126368112 126368612 500 True 649.000000 649 89.808000 1 519 1 chr3B.!!$R1 518

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
639 919 0.034896 CAAGTTGAGGCACCTACGGT 59.965 55.0 0.0 0.0 35.62 4.83 F
2033 2417 0.317160 CTCTGTGTGCGGTAAGTCCA 59.683 55.0 0.0 0.0 35.57 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2500 5361 1.153086 GAGCGACATGGCCCATTCT 60.153 57.895 0.0 0.0 0.00 2.40 R
3852 6741 0.038526 CGGGATGTATAGCCGGTCAC 60.039 60.000 1.9 0.0 31.45 3.67 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
111 114 3.057174 AGTTCAGCCTCTTCGAAGTACAG 60.057 47.826 23.85 14.23 0.00 2.74
259 268 6.812160 AGAAATTTGTAGAGTGATACGTGGAC 59.188 38.462 0.00 0.00 0.00 4.02
304 545 7.906160 GCTTTGTAGCTAATAGTTGAATTCGA 58.094 34.615 0.00 0.00 44.27 3.71
305 546 8.388103 GCTTTGTAGCTAATAGTTGAATTCGAA 58.612 33.333 0.00 0.00 44.27 3.71
306 547 9.907576 CTTTGTAGCTAATAGTTGAATTCGAAG 57.092 33.333 3.35 0.00 0.00 3.79
307 548 7.464830 TGTAGCTAATAGTTGAATTCGAAGC 57.535 36.000 3.35 7.87 0.00 3.86
308 549 7.039270 TGTAGCTAATAGTTGAATTCGAAGCA 58.961 34.615 15.50 1.35 0.00 3.91
309 550 7.710907 TGTAGCTAATAGTTGAATTCGAAGCAT 59.289 33.333 15.50 6.40 0.00 3.79
310 551 9.193133 GTAGCTAATAGTTGAATTCGAAGCATA 57.807 33.333 15.50 5.70 0.00 3.14
311 552 8.077836 AGCTAATAGTTGAATTCGAAGCATAC 57.922 34.615 15.50 6.13 0.00 2.39
312 553 7.928706 AGCTAATAGTTGAATTCGAAGCATACT 59.071 33.333 15.50 12.00 0.00 2.12
313 554 8.552034 GCTAATAGTTGAATTCGAAGCATACTT 58.448 33.333 3.35 0.00 39.43 2.24
528 808 1.533469 ATAGGCGGGCGTCCTGATAC 61.533 60.000 3.66 0.00 35.21 2.24
534 814 0.387929 GGGCGTCCTGATACGAATGA 59.612 55.000 0.00 0.00 45.68 2.57
536 816 2.128035 GGCGTCCTGATACGAATGAAG 58.872 52.381 0.00 0.00 45.68 3.02
538 818 2.128035 CGTCCTGATACGAATGAAGGC 58.872 52.381 0.00 0.00 45.68 4.35
540 820 2.866762 GTCCTGATACGAATGAAGGCAC 59.133 50.000 0.00 0.00 0.00 5.01
548 828 2.418628 ACGAATGAAGGCACCGTATTTG 59.581 45.455 0.00 0.00 35.71 2.32
549 829 2.675844 CGAATGAAGGCACCGTATTTGA 59.324 45.455 0.00 0.00 0.00 2.69
578 858 1.940613 ACAAGTTCGAGCACCAGTTTC 59.059 47.619 1.01 0.00 0.00 2.78
588 868 4.853196 CGAGCACCAGTTTCATGTATTTTG 59.147 41.667 0.00 0.00 0.00 2.44
597 877 8.487176 CCAGTTTCATGTATTTTGCAACTTTAC 58.513 33.333 0.00 2.15 29.89 2.01
598 878 8.207252 CAGTTTCATGTATTTTGCAACTTTACG 58.793 33.333 0.00 0.00 29.89 3.18
616 896 0.567968 CGCACTAAACTGATCGCTCG 59.432 55.000 0.00 0.00 0.00 5.03
617 897 0.924090 GCACTAAACTGATCGCTCGG 59.076 55.000 0.00 0.00 0.00 4.63
630 910 2.035442 GCTCGGGACAAGTTGAGGC 61.035 63.158 10.54 0.00 0.00 4.70
635 915 0.690762 GGGACAAGTTGAGGCACCTA 59.309 55.000 10.54 0.00 0.00 3.08
637 917 1.429463 GACAAGTTGAGGCACCTACG 58.571 55.000 10.54 0.00 0.00 3.51
639 919 0.034896 CAAGTTGAGGCACCTACGGT 59.965 55.000 0.00 0.00 35.62 4.83
663 943 8.456471 GGTGTATTTAACTCTAATTTCACCACC 58.544 37.037 0.00 0.00 37.93 4.61
684 964 6.163476 CACCTGTATACTCTGCAAGTAAACA 58.837 40.000 4.17 1.43 43.61 2.83
685 965 6.090898 CACCTGTATACTCTGCAAGTAAACAC 59.909 42.308 4.17 10.13 43.61 3.32
768 1049 4.766375 TCAGAGTTTCTTGTTTCGGAAGT 58.234 39.130 0.00 0.00 0.00 3.01
776 1061 5.286267 TCTTGTTTCGGAAGTAAAGGTCT 57.714 39.130 8.39 0.00 0.00 3.85
779 1064 4.628074 TGTTTCGGAAGTAAAGGTCTCAG 58.372 43.478 0.00 0.00 0.00 3.35
797 1082 1.479323 CAGGATGCAGAACCCCAATTG 59.521 52.381 0.00 0.00 0.00 2.32
814 1099 0.463620 TTGGAGTTGGCCTTTTGCAC 59.536 50.000 3.32 0.00 43.89 4.57
817 1102 1.322442 GAGTTGGCCTTTTGCACTCT 58.678 50.000 3.32 0.00 43.89 3.24
866 1152 1.153997 GGAGAACGAGACGAGGCAC 60.154 63.158 0.00 0.00 0.00 5.01
917 1235 1.521681 GGCGCTAAACTCCATCGCT 60.522 57.895 7.64 0.00 44.51 4.93
921 1239 2.862530 GCGCTAAACTCCATCGCTATGA 60.863 50.000 0.00 0.00 42.19 2.15
965 1284 1.154150 CTTAAGCTGCACCGCAAGC 60.154 57.895 1.02 0.00 38.41 4.01
1021 1350 2.202236 ATATAGGCCCGCCATGCAGG 62.202 60.000 8.74 0.00 38.92 4.85
1042 1373 4.968719 AGGGTACATACATCCAATCAGTCA 59.031 41.667 0.00 0.00 0.00 3.41
1045 1376 3.813443 ACATACATCCAATCAGTCAGCC 58.187 45.455 0.00 0.00 0.00 4.85
1076 1436 1.961180 GATCCCCACAGACCACGGAG 61.961 65.000 0.00 0.00 0.00 4.63
1628 1997 2.659610 GTGGAGCTCAAGCGGAGT 59.340 61.111 17.19 0.00 45.88 3.85
1769 2138 1.000283 GACGAGATCATCCCGCTCATT 60.000 52.381 0.00 0.00 0.00 2.57
1892 2261 3.390017 CATCGGCTCATCGACGCG 61.390 66.667 3.53 3.53 46.15 6.01
1910 2282 2.413765 GAGCGACGGAGGATGGAC 59.586 66.667 0.00 0.00 0.00 4.02
1911 2283 3.471244 GAGCGACGGAGGATGGACG 62.471 68.421 0.00 0.00 0.00 4.79
1912 2284 3.515286 GCGACGGAGGATGGACGA 61.515 66.667 0.00 0.00 0.00 4.20
1913 2285 2.716244 CGACGGAGGATGGACGAG 59.284 66.667 0.00 0.00 0.00 4.18
1914 2286 2.835705 CGACGGAGGATGGACGAGG 61.836 68.421 0.00 0.00 0.00 4.63
1915 2287 2.442272 ACGGAGGATGGACGAGGG 60.442 66.667 0.00 0.00 0.00 4.30
1916 2288 3.917760 CGGAGGATGGACGAGGGC 61.918 72.222 0.00 0.00 0.00 5.19
1917 2289 3.917760 GGAGGATGGACGAGGGCG 61.918 72.222 0.00 0.00 44.79 6.13
1918 2290 3.917760 GAGGATGGACGAGGGCGG 61.918 72.222 0.00 0.00 43.17 6.13
1940 2324 4.430765 GGCGACGAGGGCGAGAAA 62.431 66.667 0.00 0.00 41.64 2.52
1952 2336 2.424956 GGGCGAGAAAAAGAGCATGATT 59.575 45.455 0.00 0.00 0.00 2.57
2033 2417 0.317160 CTCTGTGTGCGGTAAGTCCA 59.683 55.000 0.00 0.00 35.57 4.02
2061 2622 4.457810 CACTTGTATGCTTCTCACAAACG 58.542 43.478 0.00 0.00 32.16 3.60
2079 2640 1.335689 ACGCGAGTACTTCAACTGTCC 60.336 52.381 15.93 0.00 46.88 4.02
2087 2966 5.425630 AGTACTTCAACTGTCCGTTTCTTT 58.574 37.500 0.00 0.00 32.27 2.52
2164 3283 4.970611 CGACCAGAGTCATTATGTTAGTCG 59.029 45.833 0.00 0.00 43.73 4.18
2324 3720 4.516365 TTTTCCCACTCTCGAGTACTTC 57.484 45.455 13.13 0.00 40.20 3.01
2325 3721 2.125773 TCCCACTCTCGAGTACTTCC 57.874 55.000 13.13 0.00 40.20 3.46
2327 3723 2.025226 TCCCACTCTCGAGTACTTCCAT 60.025 50.000 13.13 0.00 40.20 3.41
2328 3724 3.201487 TCCCACTCTCGAGTACTTCCATA 59.799 47.826 13.13 0.00 40.20 2.74
2339 3735 7.229308 TCGAGTACTTCCATATTAAGGCTCTA 58.771 38.462 0.00 6.11 32.62 2.43
2500 5361 1.822990 GAGACCACCTCAACCACGATA 59.177 52.381 0.00 0.00 41.58 2.92
2509 5370 1.134220 TCAACCACGATAGAATGGGCC 60.134 52.381 0.00 0.00 40.59 5.80
2950 5811 1.078848 GCAGTGCTTCGACTGGGAT 60.079 57.895 8.18 0.00 43.17 3.85
3095 5957 2.359900 GATCGAACTTGTTGGCATCCT 58.640 47.619 0.00 0.00 0.00 3.24
3139 6001 2.731691 ATCGTCCCGTATGCATGGCC 62.732 60.000 10.16 0.00 0.00 5.36
3158 6020 2.542595 GCCCGATACCGTTTTGATGTAG 59.457 50.000 0.00 0.00 0.00 2.74
3159 6021 3.788937 CCCGATACCGTTTTGATGTAGT 58.211 45.455 0.00 0.00 0.00 2.73
3160 6022 4.737352 GCCCGATACCGTTTTGATGTAGTA 60.737 45.833 0.00 0.00 0.00 1.82
3161 6023 4.741676 CCCGATACCGTTTTGATGTAGTAC 59.258 45.833 0.00 0.00 0.00 2.73
3162 6024 5.450965 CCCGATACCGTTTTGATGTAGTACT 60.451 44.000 0.00 0.00 0.00 2.73
3163 6025 5.457799 CCGATACCGTTTTGATGTAGTACTG 59.542 44.000 5.39 0.00 0.00 2.74
3164 6026 6.032094 CGATACCGTTTTGATGTAGTACTGT 58.968 40.000 5.39 0.00 0.00 3.55
3165 6027 7.188834 CGATACCGTTTTGATGTAGTACTGTA 58.811 38.462 5.39 0.00 0.00 2.74
3166 6028 7.375280 CGATACCGTTTTGATGTAGTACTGTAG 59.625 40.741 5.39 0.00 0.00 2.74
3167 6029 6.336842 ACCGTTTTGATGTAGTACTGTAGT 57.663 37.500 5.39 0.22 0.00 2.73
3168 6030 7.452880 ACCGTTTTGATGTAGTACTGTAGTA 57.547 36.000 5.39 0.00 0.00 1.82
3203 6065 4.904253 TTTTTAACTACTTGGCGCACTT 57.096 36.364 10.83 0.00 0.00 3.16
3204 6066 4.904253 TTTTAACTACTTGGCGCACTTT 57.096 36.364 10.83 0.00 0.00 2.66
3205 6067 6.374565 TTTTTAACTACTTGGCGCACTTTA 57.625 33.333 10.83 0.00 0.00 1.85
3206 6068 6.563222 TTTTAACTACTTGGCGCACTTTAT 57.437 33.333 10.83 0.00 0.00 1.40
3207 6069 6.563222 TTTAACTACTTGGCGCACTTTATT 57.437 33.333 10.83 0.00 0.00 1.40
3208 6070 7.670009 TTTAACTACTTGGCGCACTTTATTA 57.330 32.000 10.83 0.00 0.00 0.98
3209 6071 7.670009 TTAACTACTTGGCGCACTTTATTAA 57.330 32.000 10.83 2.83 0.00 1.40
3210 6072 6.563222 AACTACTTGGCGCACTTTATTAAA 57.437 33.333 10.83 0.00 0.00 1.52
3211 6073 5.934921 ACTACTTGGCGCACTTTATTAAAC 58.065 37.500 10.83 0.00 0.00 2.01
3212 6074 5.704053 ACTACTTGGCGCACTTTATTAAACT 59.296 36.000 10.83 0.00 0.00 2.66
3213 6075 5.043189 ACTTGGCGCACTTTATTAAACTC 57.957 39.130 10.83 0.00 0.00 3.01
3214 6076 4.517453 ACTTGGCGCACTTTATTAAACTCA 59.483 37.500 10.83 0.00 0.00 3.41
3215 6077 5.183140 ACTTGGCGCACTTTATTAAACTCAT 59.817 36.000 10.83 0.00 0.00 2.90
3216 6078 6.373216 ACTTGGCGCACTTTATTAAACTCATA 59.627 34.615 10.83 0.00 0.00 2.15
3217 6079 6.935741 TGGCGCACTTTATTAAACTCATAT 57.064 33.333 10.83 0.00 0.00 1.78
3218 6080 6.954944 TGGCGCACTTTATTAAACTCATATC 58.045 36.000 10.83 0.00 0.00 1.63
3219 6081 6.540551 TGGCGCACTTTATTAAACTCATATCA 59.459 34.615 10.83 0.00 0.00 2.15
3220 6082 7.066404 TGGCGCACTTTATTAAACTCATATCAA 59.934 33.333 10.83 0.00 0.00 2.57
3221 6083 7.913297 GGCGCACTTTATTAAACTCATATCAAA 59.087 33.333 10.83 0.00 0.00 2.69
3222 6084 8.947940 GCGCACTTTATTAAACTCATATCAAAG 58.052 33.333 0.30 0.00 0.00 2.77
3223 6085 9.988350 CGCACTTTATTAAACTCATATCAAAGT 57.012 29.630 0.00 0.00 35.86 2.66
3236 6098 9.671279 ACTCATATCAAAGTTACATCATTCACA 57.329 29.630 0.00 0.00 0.00 3.58
3254 6116 5.041951 TCACAATGTCCGAATAAACTTGC 57.958 39.130 0.00 0.00 0.00 4.01
3386 6250 2.679837 ACATTTGATCCGCACATGTCTC 59.320 45.455 0.00 0.00 42.63 3.36
3407 6271 1.244019 ACAGAAACGCCAGCCCAATC 61.244 55.000 0.00 0.00 0.00 2.67
3416 6280 3.390521 AGCCCAATCCGCAGACGA 61.391 61.111 0.00 0.00 43.93 4.20
3417 6281 2.203070 GCCCAATCCGCAGACGAT 60.203 61.111 0.00 0.00 43.93 3.73
3420 6284 1.948104 CCCAATCCGCAGACGATAAA 58.052 50.000 0.00 0.00 43.93 1.40
3430 6294 4.214119 CCGCAGACGATAAATCCAAATCAT 59.786 41.667 0.00 0.00 43.93 2.45
3508 6376 5.882557 GTGTTTACAAGGACATGAGATGGAT 59.117 40.000 0.00 0.00 33.60 3.41
3521 6389 1.207811 AGATGGATGCGTCACACATCA 59.792 47.619 19.50 4.99 44.68 3.07
3526 6394 3.119884 TGGATGCGTCACACATCATTTTC 60.120 43.478 8.07 0.00 44.68 2.29
3532 6400 3.664276 CGTCACACATCATTTTCGTGTCC 60.664 47.826 0.00 0.00 41.79 4.02
3612 6481 2.668632 GGAATCGTCCAGGCCACA 59.331 61.111 5.01 0.00 44.26 4.17
3655 6524 4.360405 GAAAGGGGGCGGCCTCAA 62.360 66.667 31.84 0.00 0.00 3.02
3664 6533 1.250840 GGCGGCCTCAACCATTTCTT 61.251 55.000 12.87 0.00 0.00 2.52
3714 6603 3.998672 TGTTCCCTCGTCCGCCAC 61.999 66.667 0.00 0.00 0.00 5.01
3718 6607 4.530857 CCCTCGTCCGCCACCATC 62.531 72.222 0.00 0.00 0.00 3.51
3763 6652 1.289109 GCAAGCATGGCAAGCACAAG 61.289 55.000 17.75 4.58 32.79 3.16
3768 6657 0.249531 CATGGCAAGCACAAGCACAA 60.250 50.000 0.00 0.00 45.49 3.33
3769 6658 0.032952 ATGGCAAGCACAAGCACAAG 59.967 50.000 0.00 0.00 45.49 3.16
3770 6659 1.952635 GGCAAGCACAAGCACAAGC 60.953 57.895 0.00 0.00 45.49 4.01
3771 6660 1.227031 GCAAGCACAAGCACAAGCA 60.227 52.632 0.00 0.00 45.49 3.91
3772 6661 1.485032 GCAAGCACAAGCACAAGCAC 61.485 55.000 0.00 0.00 45.49 4.40
3778 6667 1.135024 CACAAGCACAAGCACAAGGTT 60.135 47.619 0.00 0.00 45.49 3.50
3818 6707 1.447317 AACTTCACCTTGGCAGCACG 61.447 55.000 0.00 0.00 0.00 5.34
3839 6728 1.771565 TAGTGGTAGGGGACATCACG 58.228 55.000 0.00 0.00 33.85 4.35
3843 6732 3.151710 TAGGGGACATCACGGCCG 61.152 66.667 26.86 26.86 0.00 6.13
3899 6793 1.514553 GTACCACTGGGAGTACCGC 59.485 63.158 0.00 0.00 44.64 5.68
3923 6817 2.743928 CTGCCGTGGCCAGACTTC 60.744 66.667 5.11 0.00 41.09 3.01
3937 6832 2.474359 CAGACTTCAACTCTTGCACGAG 59.526 50.000 17.99 17.99 37.07 4.18
3947 6842 2.994387 CTTGCACGAGTGGCACCTCA 62.994 60.000 15.27 2.45 41.75 3.86
3953 6848 2.450502 AGTGGCACCTCAACCCCT 60.451 61.111 15.27 0.00 0.00 4.79
3969 6864 0.326927 CCCTACCACATTCCGGTGTT 59.673 55.000 0.00 0.00 37.33 3.32
3974 6869 1.900981 CACATTCCGGTGTTGGCCA 60.901 57.895 0.00 0.00 34.09 5.36
4051 6946 0.179100 CCGGAGCAATGTCGTGATCT 60.179 55.000 0.00 0.00 34.32 2.75
4059 6954 3.691498 CAATGTCGTGATCTAGCGTACA 58.309 45.455 0.00 4.09 0.00 2.90
4086 6982 2.304180 ACTCCTTGAACTGGGATGTCTG 59.696 50.000 0.00 0.00 0.00 3.51
4091 6987 2.054021 TGAACTGGGATGTCTGGTTCA 58.946 47.619 0.00 0.00 42.23 3.18
4100 6996 0.032130 TGTCTGGTTCACGACTGAGC 59.968 55.000 0.00 0.00 0.00 4.26
4130 7026 2.715624 GCCATCCAAATCGACGCC 59.284 61.111 0.00 0.00 0.00 5.68
4147 7043 4.864334 CTGCCCTCCACCGCCATC 62.864 72.222 0.00 0.00 0.00 3.51
4164 7060 2.913054 ATCGTCGGCTGTGAGGCATG 62.913 60.000 0.00 0.00 41.44 4.06
4169 7065 1.300963 GGCTGTGAGGCATGAGGAA 59.699 57.895 0.00 0.00 40.97 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 181 8.647143 AGTTTCATAATGCATAAATTTTCCCG 57.353 30.769 0.00 0.00 0.00 5.14
303 544 0.462759 AGCTGGCCGAAGTATGCTTC 60.463 55.000 13.07 13.07 45.68 3.86
304 545 0.745845 CAGCTGGCCGAAGTATGCTT 60.746 55.000 5.57 0.00 37.71 3.91
305 546 1.153289 CAGCTGGCCGAAGTATGCT 60.153 57.895 5.57 0.00 0.00 3.79
306 547 2.182842 CCAGCTGGCCGAAGTATGC 61.183 63.158 22.33 0.00 0.00 3.14
307 548 4.131376 CCAGCTGGCCGAAGTATG 57.869 61.111 22.33 0.00 0.00 2.39
408 651 4.122046 AGAAAAGCCATCAAAAACACTGC 58.878 39.130 0.00 0.00 0.00 4.40
488 731 0.528470 AGTGTCTAAGAGGCGCTGAC 59.472 55.000 7.64 7.24 39.51 3.51
489 732 2.962882 AGTGTCTAAGAGGCGCTGA 58.037 52.632 7.64 0.00 39.51 4.26
528 808 2.675844 TCAAATACGGTGCCTTCATTCG 59.324 45.455 0.00 0.00 0.00 3.34
548 828 0.599204 TCGAACTTGTCAGGCCGTTC 60.599 55.000 8.43 8.43 34.07 3.95
549 829 0.600255 CTCGAACTTGTCAGGCCGTT 60.600 55.000 0.00 0.00 0.00 4.44
578 858 5.629020 AGTGCGTAAAGTTGCAAAATACATG 59.371 36.000 0.00 0.00 43.75 3.21
588 868 4.461992 TCAGTTTAGTGCGTAAAGTTGC 57.538 40.909 0.00 0.00 32.74 4.17
597 877 0.567968 CGAGCGATCAGTTTAGTGCG 59.432 55.000 0.00 0.00 0.00 5.34
598 878 0.924090 CCGAGCGATCAGTTTAGTGC 59.076 55.000 0.00 0.00 0.00 4.40
616 896 0.690762 TAGGTGCCTCAACTTGTCCC 59.309 55.000 0.00 0.00 31.86 4.46
617 897 1.809684 GTAGGTGCCTCAACTTGTCC 58.190 55.000 0.00 0.00 31.86 4.02
635 915 7.879160 TGGTGAAATTAGAGTTAAATACACCGT 59.121 33.333 0.00 0.00 41.51 4.83
637 917 8.456471 GGTGGTGAAATTAGAGTTAAATACACC 58.544 37.037 0.00 0.00 40.42 4.16
639 919 9.226606 CAGGTGGTGAAATTAGAGTTAAATACA 57.773 33.333 0.00 0.00 0.00 2.29
642 922 9.975218 ATACAGGTGGTGAAATTAGAGTTAAAT 57.025 29.630 0.00 0.00 0.00 1.40
644 924 9.880157 GTATACAGGTGGTGAAATTAGAGTTAA 57.120 33.333 0.00 0.00 0.00 2.01
645 925 9.263446 AGTATACAGGTGGTGAAATTAGAGTTA 57.737 33.333 5.50 0.00 0.00 2.24
646 926 8.147244 AGTATACAGGTGGTGAAATTAGAGTT 57.853 34.615 5.50 0.00 0.00 3.01
647 927 7.620094 AGAGTATACAGGTGGTGAAATTAGAGT 59.380 37.037 5.50 0.00 0.00 3.24
648 928 7.923344 CAGAGTATACAGGTGGTGAAATTAGAG 59.077 40.741 5.50 0.00 0.00 2.43
649 929 7.632898 GCAGAGTATACAGGTGGTGAAATTAGA 60.633 40.741 5.50 0.00 0.00 2.10
650 930 6.480320 GCAGAGTATACAGGTGGTGAAATTAG 59.520 42.308 5.50 0.00 0.00 1.73
663 943 6.183360 GCTGTGTTTACTTGCAGAGTATACAG 60.183 42.308 20.94 22.04 46.46 2.74
684 964 1.134280 ACTGACTTTGTGAGCAGCTGT 60.134 47.619 16.64 1.59 34.73 4.40
685 965 1.263484 CACTGACTTTGTGAGCAGCTG 59.737 52.381 10.11 10.11 37.60 4.24
741 1022 4.083802 CCGAAACAAGAAACTCTGATGGAC 60.084 45.833 0.00 0.00 0.00 4.02
768 1049 3.055094 GGTTCTGCATCCTGAGACCTTTA 60.055 47.826 0.00 0.00 0.00 1.85
776 1061 1.002069 ATTGGGGTTCTGCATCCTGA 58.998 50.000 0.00 0.00 0.00 3.86
779 1064 0.826062 CCAATTGGGGTTCTGCATCC 59.174 55.000 17.36 0.00 0.00 3.51
797 1082 0.315251 GAGTGCAAAAGGCCAACTCC 59.685 55.000 5.01 0.00 43.89 3.85
814 1099 0.908198 CCAGACCCCTTCCTTCAGAG 59.092 60.000 0.00 0.00 0.00 3.35
817 1102 1.584724 GATCCAGACCCCTTCCTTCA 58.415 55.000 0.00 0.00 0.00 3.02
850 1136 2.561885 CGTGCCTCGTCTCGTTCT 59.438 61.111 0.00 0.00 34.52 3.01
855 1141 0.459585 TATTTGGCGTGCCTCGTCTC 60.460 55.000 12.84 0.00 45.15 3.36
860 1146 2.423538 ACAGAATTATTTGGCGTGCCTC 59.576 45.455 12.84 0.00 36.94 4.70
861 1147 2.423538 GACAGAATTATTTGGCGTGCCT 59.576 45.455 12.84 0.00 36.94 4.75
866 1152 5.490139 ACTGATGACAGAATTATTTGGCG 57.510 39.130 0.00 0.00 46.03 5.69
894 1204 1.103398 ATGGAGTTTAGCGCCCATGC 61.103 55.000 12.09 0.00 37.94 4.06
917 1235 0.809636 CGCCATGCCTGACGTTCATA 60.810 55.000 0.00 0.00 0.00 2.15
921 1239 0.392461 AATACGCCATGCCTGACGTT 60.392 50.000 8.76 0.00 39.78 3.99
965 1284 3.078836 CCCCATGGCTTGGCTTGG 61.079 66.667 13.72 18.05 44.97 3.61
1021 1350 4.752101 GCTGACTGATTGGATGTATGTACC 59.248 45.833 0.00 0.00 0.00 3.34
1022 1351 4.752101 GGCTGACTGATTGGATGTATGTAC 59.248 45.833 0.00 0.00 0.00 2.90
1042 1373 0.908198 GGATCTGTCTTGAGGTGGCT 59.092 55.000 0.00 0.00 0.00 4.75
1045 1376 1.065854 GTGGGGATCTGTCTTGAGGTG 60.066 57.143 0.00 0.00 0.00 4.00
1076 1436 1.602311 CCTTATCCATGGCTGACTGC 58.398 55.000 6.96 0.00 41.94 4.40
1199 1565 3.006728 AAGAACGGGATGGCCGGA 61.007 61.111 5.05 0.00 37.87 5.14
1391 1757 1.817099 CATCTGCGAGGGGAACTGC 60.817 63.158 0.00 0.00 0.00 4.40
1892 2261 2.833582 TCCATCCTCCGTCGCTCC 60.834 66.667 0.00 0.00 0.00 4.70
1898 2267 2.442272 CCCTCGTCCATCCTCCGT 60.442 66.667 0.00 0.00 0.00 4.69
2033 2417 5.181748 GTGAGAAGCATACAAGTGGAAGAT 58.818 41.667 0.00 0.00 0.00 2.40
2061 2622 1.335689 ACGGACAGTTGAAGTACTCGC 60.336 52.381 0.00 0.00 0.00 5.03
2079 2640 6.616947 TGCCAATGTCCTTAATAAAGAAACG 58.383 36.000 0.00 0.00 34.37 3.60
2087 2966 5.188555 TGCCAAATTGCCAATGTCCTTAATA 59.811 36.000 0.00 0.00 0.00 0.98
2194 3394 8.948145 GTGACCACTATCTGATTAGATATACGT 58.052 37.037 7.60 0.00 43.19 3.57
2195 3395 9.168451 AGTGACCACTATCTGATTAGATATACG 57.832 37.037 7.60 0.20 43.19 3.06
2302 3668 4.081586 GGAAGTACTCGAGAGTGGGAAAAT 60.082 45.833 21.68 0.00 42.52 1.82
2339 3735 3.119495 GCACAAATCCTACGAAGGCAAAT 60.119 43.478 0.00 0.00 43.31 2.32
2451 5301 4.579869 GGCCACAAAGAGATTCTGTAAGA 58.420 43.478 0.00 0.00 44.68 2.10
2452 5302 3.372206 CGGCCACAAAGAGATTCTGTAAG 59.628 47.826 2.24 0.00 0.00 2.34
2455 5316 1.611673 CCGGCCACAAAGAGATTCTGT 60.612 52.381 2.24 0.00 0.00 3.41
2462 5323 2.325082 CCGTTCCGGCCACAAAGAG 61.325 63.158 2.24 0.00 41.17 2.85
2500 5361 1.153086 GAGCGACATGGCCCATTCT 60.153 57.895 0.00 0.00 0.00 2.40
2728 5589 2.124983 ATCAGCATCGTGCCGCTT 60.125 55.556 6.39 0.00 46.52 4.68
3050 5911 0.107945 AGCTTCTGAAGGACATCGCC 60.108 55.000 18.38 0.01 0.00 5.54
3095 5957 8.756486 TGCTACTGGAAACTACTGTACATATA 57.244 34.615 0.00 0.00 0.00 0.86
3139 6001 5.457799 CAGTACTACATCAAAACGGTATCGG 59.542 44.000 0.00 0.00 41.39 4.18
3182 6044 4.904253 AAGTGCGCCAAGTAGTTAAAAA 57.096 36.364 4.18 0.00 0.00 1.94
3183 6045 4.904253 AAAGTGCGCCAAGTAGTTAAAA 57.096 36.364 4.18 0.00 0.00 1.52
3184 6046 6.563222 AATAAAGTGCGCCAAGTAGTTAAA 57.437 33.333 4.18 0.00 0.00 1.52
3185 6047 7.670009 TTAATAAAGTGCGCCAAGTAGTTAA 57.330 32.000 4.18 0.00 0.00 2.01
3186 6048 7.388500 AGTTTAATAAAGTGCGCCAAGTAGTTA 59.612 33.333 4.18 0.00 0.00 2.24
3187 6049 6.206048 AGTTTAATAAAGTGCGCCAAGTAGTT 59.794 34.615 4.18 0.00 0.00 2.24
3188 6050 5.704053 AGTTTAATAAAGTGCGCCAAGTAGT 59.296 36.000 4.18 0.00 0.00 2.73
3189 6051 6.128391 TGAGTTTAATAAAGTGCGCCAAGTAG 60.128 38.462 4.18 0.00 0.00 2.57
3190 6052 5.701750 TGAGTTTAATAAAGTGCGCCAAGTA 59.298 36.000 4.18 0.00 0.00 2.24
3191 6053 4.517453 TGAGTTTAATAAAGTGCGCCAAGT 59.483 37.500 4.18 0.00 0.00 3.16
3192 6054 5.041951 TGAGTTTAATAAAGTGCGCCAAG 57.958 39.130 4.18 0.00 0.00 3.61
3193 6055 5.637006 ATGAGTTTAATAAAGTGCGCCAA 57.363 34.783 4.18 0.00 0.00 4.52
3194 6056 6.540551 TGATATGAGTTTAATAAAGTGCGCCA 59.459 34.615 4.18 0.00 0.00 5.69
3195 6057 6.954944 TGATATGAGTTTAATAAAGTGCGCC 58.045 36.000 4.18 0.00 0.00 6.53
3196 6058 8.835467 TTTGATATGAGTTTAATAAAGTGCGC 57.165 30.769 0.00 0.00 0.00 6.09
3197 6059 9.988350 ACTTTGATATGAGTTTAATAAAGTGCG 57.012 29.630 0.00 0.00 36.22 5.34
3210 6072 9.671279 TGTGAATGATGTAACTTTGATATGAGT 57.329 29.630 0.00 0.00 0.00 3.41
3216 6078 8.246180 GGACATTGTGAATGATGTAACTTTGAT 58.754 33.333 3.35 0.00 41.46 2.57
3217 6079 7.572910 CGGACATTGTGAATGATGTAACTTTGA 60.573 37.037 3.35 0.00 41.46 2.69
3218 6080 6.524239 CGGACATTGTGAATGATGTAACTTTG 59.476 38.462 3.35 0.00 41.46 2.77
3219 6081 6.429692 TCGGACATTGTGAATGATGTAACTTT 59.570 34.615 3.35 0.00 41.46 2.66
3220 6082 5.937540 TCGGACATTGTGAATGATGTAACTT 59.062 36.000 3.35 0.00 41.46 2.66
3221 6083 5.487433 TCGGACATTGTGAATGATGTAACT 58.513 37.500 3.35 0.00 41.46 2.24
3222 6084 5.794687 TCGGACATTGTGAATGATGTAAC 57.205 39.130 3.35 0.00 41.46 2.50
3223 6085 8.499403 TTATTCGGACATTGTGAATGATGTAA 57.501 30.769 10.91 0.00 41.46 2.41
3224 6086 8.394877 GTTTATTCGGACATTGTGAATGATGTA 58.605 33.333 10.91 0.00 41.46 2.29
3225 6087 7.121168 AGTTTATTCGGACATTGTGAATGATGT 59.879 33.333 10.91 0.00 41.46 3.06
3226 6088 7.475015 AGTTTATTCGGACATTGTGAATGATG 58.525 34.615 10.91 0.00 41.46 3.07
3227 6089 7.630242 AGTTTATTCGGACATTGTGAATGAT 57.370 32.000 10.91 0.00 41.46 2.45
3228 6090 7.304735 CAAGTTTATTCGGACATTGTGAATGA 58.695 34.615 10.91 2.72 41.46 2.57
3229 6091 6.033831 GCAAGTTTATTCGGACATTGTGAATG 59.966 38.462 10.91 0.00 44.48 2.67
3230 6092 6.071952 AGCAAGTTTATTCGGACATTGTGAAT 60.072 34.615 0.00 0.87 36.40 2.57
3231 6093 5.240623 AGCAAGTTTATTCGGACATTGTGAA 59.759 36.000 0.00 0.00 0.00 3.18
3232 6094 4.759693 AGCAAGTTTATTCGGACATTGTGA 59.240 37.500 0.00 0.00 0.00 3.58
3233 6095 4.853196 CAGCAAGTTTATTCGGACATTGTG 59.147 41.667 0.00 0.00 0.00 3.33
3234 6096 4.615912 GCAGCAAGTTTATTCGGACATTGT 60.616 41.667 0.00 0.00 0.00 2.71
3235 6097 3.853671 GCAGCAAGTTTATTCGGACATTG 59.146 43.478 0.00 0.00 0.00 2.82
3236 6098 3.426159 CGCAGCAAGTTTATTCGGACATT 60.426 43.478 0.00 0.00 0.00 2.71
3237 6099 2.095853 CGCAGCAAGTTTATTCGGACAT 59.904 45.455 0.00 0.00 0.00 3.06
3238 6100 1.463056 CGCAGCAAGTTTATTCGGACA 59.537 47.619 0.00 0.00 0.00 4.02
3239 6101 1.730064 TCGCAGCAAGTTTATTCGGAC 59.270 47.619 0.00 0.00 0.00 4.79
3240 6102 1.730064 GTCGCAGCAAGTTTATTCGGA 59.270 47.619 0.00 0.00 0.00 4.55
3254 6116 4.508124 GGTTATTATGGTCTGAAGTCGCAG 59.492 45.833 0.00 0.00 37.24 5.18
3386 6250 3.423154 GGGCTGGCGTTTCTGTCG 61.423 66.667 0.00 0.00 0.00 4.35
3407 6271 3.559655 TGATTTGGATTTATCGTCTGCGG 59.440 43.478 0.00 0.00 38.89 5.69
3416 6280 5.008613 CCGAACGGACATGATTTGGATTTAT 59.991 40.000 7.53 0.00 37.50 1.40
3417 6281 4.334203 CCGAACGGACATGATTTGGATTTA 59.666 41.667 7.53 0.00 37.50 1.40
3420 6284 2.288666 CCGAACGGACATGATTTGGAT 58.711 47.619 7.53 0.00 37.50 3.41
3450 6314 2.158971 AGTTTGGGCTGAAAATGCGTTT 60.159 40.909 0.00 0.00 0.00 3.60
3508 6376 1.870402 ACGAAAATGATGTGTGACGCA 59.130 42.857 0.00 0.00 0.00 5.24
3521 6389 3.870606 CGAGGCGGACACGAAAAT 58.129 55.556 0.00 0.00 44.60 1.82
3532 6400 2.660552 AACACGTGTTCCGAGGCG 60.661 61.111 27.70 0.00 40.70 5.52
3540 6408 3.251332 TGGTTGACCAACACGTGTT 57.749 47.368 27.70 27.70 44.35 3.32
3612 6481 4.244862 CACGCTTGCCATTTAAAAAGGAT 58.755 39.130 12.75 0.00 0.00 3.24
3655 6524 5.163152 ACTGGAGTGAGAAAGAAGAAATGGT 60.163 40.000 0.00 0.00 0.00 3.55
3664 6533 4.590647 AGATGTTGACTGGAGTGAGAAAGA 59.409 41.667 0.00 0.00 0.00 2.52
3714 6603 1.339055 TGAAGAAGTCCCTTGCGATGG 60.339 52.381 0.00 0.00 0.00 3.51
3718 6607 0.603707 TGCTGAAGAAGTCCCTTGCG 60.604 55.000 0.00 0.00 0.00 4.85
3721 6610 2.175715 ACCTTTGCTGAAGAAGTCCCTT 59.824 45.455 2.50 0.00 37.57 3.95
3763 6652 1.592400 GCCAACCTTGTGCTTGTGC 60.592 57.895 0.00 0.00 40.20 4.57
3768 6657 0.957395 CGATGAGCCAACCTTGTGCT 60.957 55.000 1.93 1.93 37.39 4.40
3769 6658 1.503542 CGATGAGCCAACCTTGTGC 59.496 57.895 0.00 0.00 0.00 4.57
3770 6659 1.503542 GCGATGAGCCAACCTTGTG 59.496 57.895 0.00 0.00 40.81 3.33
3771 6660 2.034879 CGCGATGAGCCAACCTTGT 61.035 57.895 0.00 0.00 44.76 3.16
3772 6661 1.699656 CTCGCGATGAGCCAACCTTG 61.700 60.000 10.36 0.00 44.76 3.61
3814 6703 0.388294 GTCCCCTACCACTATCGTGC 59.612 60.000 0.00 0.00 39.86 5.34
3818 6707 2.296471 CGTGATGTCCCCTACCACTATC 59.704 54.545 0.00 0.00 0.00 2.08
3823 6712 2.363975 GCCGTGATGTCCCCTACCA 61.364 63.158 0.00 0.00 0.00 3.25
3826 6715 3.151710 CGGCCGTGATGTCCCCTA 61.152 66.667 19.50 0.00 0.00 3.53
3851 6740 0.320697 GGGATGTATAGCCGGTCACC 59.679 60.000 1.90 0.00 31.45 4.02
3852 6741 0.038526 CGGGATGTATAGCCGGTCAC 60.039 60.000 1.90 0.00 31.45 3.67
3853 6742 1.183030 CCGGGATGTATAGCCGGTCA 61.183 60.000 1.90 0.00 38.96 4.02
3862 6751 2.203015 GCGTGCACCGGGATGTAT 60.203 61.111 12.15 0.00 36.94 2.29
3909 6803 0.951040 GAGTTGAAGTCTGGCCACGG 60.951 60.000 0.00 0.00 0.00 4.94
3917 6811 2.748605 CTCGTGCAAGAGTTGAAGTCT 58.251 47.619 20.05 0.00 33.75 3.24
3937 6832 1.002502 GTAGGGGTTGAGGTGCCAC 60.003 63.158 0.00 0.00 0.00 5.01
3947 6842 0.843343 ACCGGAATGTGGTAGGGGTT 60.843 55.000 9.46 0.00 38.15 4.11
3953 6848 0.606944 GCCAACACCGGAATGTGGTA 60.607 55.000 9.46 0.00 40.62 3.25
3990 6885 3.558411 GATCTCAGCCGTGCGCAC 61.558 66.667 30.42 30.42 41.38 5.34
3991 6886 4.819761 GGATCTCAGCCGTGCGCA 62.820 66.667 5.66 5.66 41.38 6.09
4041 6936 2.819422 GTGTACGCTAGATCACGACA 57.181 50.000 9.40 6.82 0.00 4.35
4059 6954 1.071471 CAGTTCAAGGAGTGGGCGT 59.929 57.895 0.00 0.00 0.00 5.68
4086 6982 1.071605 GTCATGCTCAGTCGTGAACC 58.928 55.000 0.00 0.00 34.16 3.62
4091 6987 4.559835 CACGTCATGCTCAGTCGT 57.440 55.556 0.00 0.00 35.12 4.34
4110 7006 2.715624 GTCGATTTGGATGGCGGC 59.284 61.111 0.00 0.00 0.00 6.53
4116 7012 1.819632 GGCAGGCGTCGATTTGGAT 60.820 57.895 0.00 0.00 0.00 3.41
4121 7017 4.162690 GGAGGGCAGGCGTCGATT 62.163 66.667 10.30 0.00 0.00 3.34
4130 7026 4.864334 GATGGCGGTGGAGGGCAG 62.864 72.222 0.00 0.00 43.57 4.85
4146 7042 3.381983 ATGCCTCACAGCCGACGA 61.382 61.111 0.00 0.00 0.00 4.20
4147 7043 3.190849 CATGCCTCACAGCCGACG 61.191 66.667 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.