Multiple sequence alignment - TraesCS2A01G159800

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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 TraesCS2A01G159800 chr2A 100.000 3305 0 0 1 3305 108014494 108011190 0.000000e+00 6104.0
1 TraesCS2A01G159800 chr2A 82.820 1979 223 50 880 2775 109574861 109576805 0.000000e+00 1663.0
2 TraesCS2A01G159800 chr2A 94.737 95 2 1 2989 3083 109576910 109577001 9.560000e-31 145.0
3 TraesCS2A01G159800 chr2A 96.250 80 3 0 2895 2974 109576847 109576926 7.440000e-27 132.0
4 TraesCS2A01G159800 chr2B 89.002 1573 109 24 880 2427 160669561 160668028 0.000000e+00 1888.0
5 TraesCS2A01G159800 chr2B 89.542 765 40 14 895 1637 160411691 160410945 0.000000e+00 933.0
6 TraesCS2A01G159800 chr2B 80.156 1028 142 31 1514 2502 160701326 160700322 0.000000e+00 712.0
7 TraesCS2A01G159800 chr2B 79.749 1037 159 30 1322 2331 160705372 160704360 0.000000e+00 704.0
8 TraesCS2A01G159800 chr2B 87.916 571 59 7 90 653 160708349 160707782 0.000000e+00 664.0
9 TraesCS2A01G159800 chr2B 86.382 492 46 14 1622 2097 160410930 160410444 4.890000e-143 518.0
10 TraesCS2A01G159800 chr2B 85.313 463 30 19 880 1311 160705933 160705478 8.420000e-121 444.0
11 TraesCS2A01G159800 chr2B 80.667 600 74 21 2156 2741 160410443 160409872 8.480000e-116 427.0
12 TraesCS2A01G159800 chr2B 93.171 205 11 1 655 856 160706123 160705919 6.930000e-77 298.0
13 TraesCS2A01G159800 chr2B 95.455 132 6 0 1001 1132 153580367 153580498 9.290000e-51 211.0
14 TraesCS2A01G159800 chr2B 90.789 76 7 0 781 856 160669622 160669547 5.830000e-18 102.0
15 TraesCS2A01G159800 chr2D 93.810 1260 43 15 880 2123 110950450 110949210 0.000000e+00 1862.0
16 TraesCS2A01G159800 chr2D 82.359 2069 232 70 880 2864 111228663 111230682 0.000000e+00 1676.0
17 TraesCS2A01G159800 chr2D 88.366 1169 102 14 1616 2769 110946337 110945188 0.000000e+00 1375.0
18 TraesCS2A01G159800 chr2D 97.706 741 12 3 2345 3083 110949216 110948479 0.000000e+00 1269.0
19 TraesCS2A01G159800 chr2D 88.934 732 64 9 130 856 110961021 110960302 0.000000e+00 887.0
20 TraesCS2A01G159800 chr2D 79.923 1036 156 30 1322 2331 110959773 110958764 0.000000e+00 713.0
21 TraesCS2A01G159800 chr2D 95.495 222 1 5 880 1101 110960316 110960104 2.440000e-91 346.0
22 TraesCS2A01G159800 chr2D 96.212 132 5 0 1001 1132 102269845 102269976 2.000000e-52 217.0
23 TraesCS2A01G159800 chr2D 94.737 95 2 1 2989 3083 111230744 111230835 9.560000e-31 145.0
24 TraesCS2A01G159800 chr1A 98.678 227 2 1 3079 3305 146948744 146948969 5.140000e-108 401.0
25 TraesCS2A01G159800 chr7B 99.099 222 2 0 3084 3305 357981088 357980867 1.850000e-107 399.0
26 TraesCS2A01G159800 chr7B 99.099 222 2 0 3084 3305 660661164 660661385 1.850000e-107 399.0
27 TraesCS2A01G159800 chr7B 99.099 222 2 0 3084 3305 740661478 740661257 1.850000e-107 399.0
28 TraesCS2A01G159800 chr7B 90.698 43 2 2 690 731 692284655 692284614 4.610000e-04 56.5
29 TraesCS2A01G159800 chr7A 99.099 222 2 0 3084 3305 292821128 292821349 1.850000e-107 399.0
30 TraesCS2A01G159800 chr7A 99.099 222 2 0 3084 3305 698731062 698730841 1.850000e-107 399.0
31 TraesCS2A01G159800 chr7A 91.892 37 3 0 689 725 10897695 10897731 6.000000e-03 52.8
32 TraesCS2A01G159800 chr5B 99.099 222 2 0 3084 3305 234297569 234297790 1.850000e-107 399.0
33 TraesCS2A01G159800 chr5B 99.099 222 2 0 3084 3305 588769081 588769302 1.850000e-107 399.0
34 TraesCS2A01G159800 chr5B 97.222 36 1 0 2246 2281 679371785 679371750 9.900000e-06 62.1
35 TraesCS2A01G159800 chr5B 100.000 30 0 0 2856 2885 84883315 84883286 4.610000e-04 56.5
36 TraesCS2A01G159800 chr5A 99.099 222 2 0 3084 3305 451711136 451710915 1.850000e-107 399.0
37 TraesCS2A01G159800 chr5A 94.872 39 1 1 2862 2900 622421439 622421402 3.560000e-05 60.2
38 TraesCS2A01G159800 chr3B 94.737 38 2 0 698 735 783102780 783102743 3.560000e-05 60.2
39 TraesCS2A01G159800 chr3B 100.000 29 0 0 2863 2891 480567732 480567704 2.000000e-03 54.7
40 TraesCS2A01G159800 chr6A 100.000 31 0 0 2855 2885 70614017 70613987 1.280000e-04 58.4
41 TraesCS2A01G159800 chr6A 100.000 30 0 0 2856 2885 291332467 291332438 4.610000e-04 56.5
42 TraesCS2A01G159800 chr4B 100.000 30 0 0 2856 2885 438099453 438099424 4.610000e-04 56.5
43 TraesCS2A01G159800 chr3D 100.000 30 0 0 2856 2885 429612223 429612194 4.610000e-04 56.5
44 TraesCS2A01G159800 chr1B 100.000 30 0 0 2856 2885 18112496 18112467 4.610000e-04 56.5
45 TraesCS2A01G159800 chr1B 100.000 30 0 0 2856 2885 93954391 93954362 4.610000e-04 56.5
46 TraesCS2A01G159800 chr7D 92.308 39 2 1 693 731 607212575 607212612 2.000000e-03 54.7


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 TraesCS2A01G159800 chr2A 108011190 108014494 3304 True 6104.000000 6104 100.000000 1 3305 1 chr2A.!!$R1 3304
1 TraesCS2A01G159800 chr2A 109574861 109577001 2140 False 646.666667 1663 91.269000 880 3083 3 chr2A.!!$F1 2203
2 TraesCS2A01G159800 chr2B 160668028 160669622 1594 True 995.000000 1888 89.895500 781 2427 2 chr2B.!!$R2 1646
3 TraesCS2A01G159800 chr2B 160409872 160411691 1819 True 626.000000 933 85.530333 895 2741 3 chr2B.!!$R1 1846
4 TraesCS2A01G159800 chr2B 160700322 160708349 8027 True 564.400000 712 85.261000 90 2502 5 chr2B.!!$R3 2412
5 TraesCS2A01G159800 chr2D 110945188 110950450 5262 True 1502.000000 1862 93.294000 880 3083 3 chr2D.!!$R1 2203
6 TraesCS2A01G159800 chr2D 111228663 111230835 2172 False 910.500000 1676 88.548000 880 3083 2 chr2D.!!$F2 2203
7 TraesCS2A01G159800 chr2D 110958764 110961021 2257 True 648.666667 887 88.117333 130 2331 3 chr2D.!!$R2 2201

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
864 2532 0.030705 CTCTTCCCCCTGATCCCTCA 60.031 60.0 0.0 0.0 0.0 3.86 F
865 2533 0.421495 TCTTCCCCCTGATCCCTCAA 59.579 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 3591 0.679640 TCTTGAATTGCCGCGGGATT 60.680 50.000 29.38 18.72 0.0 3.01 R
2809 8266 1.813753 TCAGGCTAATGTTCGGCGC 60.814 57.895 0.00 0.00 0.0 6.53 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 5.509605 AAACAAAACGAAGAAACAAGTGC 57.490 34.783 0.00 0.00 0.00 4.40
25 26 4.167554 ACAAAACGAAGAAACAAGTGCA 57.832 36.364 0.00 0.00 0.00 4.57
26 27 4.551388 ACAAAACGAAGAAACAAGTGCAA 58.449 34.783 0.00 0.00 0.00 4.08
27 28 4.985409 ACAAAACGAAGAAACAAGTGCAAA 59.015 33.333 0.00 0.00 0.00 3.68
28 29 5.463724 ACAAAACGAAGAAACAAGTGCAAAA 59.536 32.000 0.00 0.00 0.00 2.44
29 30 6.018669 ACAAAACGAAGAAACAAGTGCAAAAA 60.019 30.769 0.00 0.00 0.00 1.94
30 31 5.761818 AACGAAGAAACAAGTGCAAAAAG 57.238 34.783 0.00 0.00 0.00 2.27
31 32 5.054390 ACGAAGAAACAAGTGCAAAAAGA 57.946 34.783 0.00 0.00 0.00 2.52
32 33 5.465935 ACGAAGAAACAAGTGCAAAAAGAA 58.534 33.333 0.00 0.00 0.00 2.52
33 34 6.099341 ACGAAGAAACAAGTGCAAAAAGAAT 58.901 32.000 0.00 0.00 0.00 2.40
34 35 6.034898 ACGAAGAAACAAGTGCAAAAAGAATG 59.965 34.615 0.00 0.00 0.00 2.67
35 36 6.253298 CGAAGAAACAAGTGCAAAAAGAATGA 59.747 34.615 0.00 0.00 0.00 2.57
36 37 7.201427 CGAAGAAACAAGTGCAAAAAGAATGAA 60.201 33.333 0.00 0.00 0.00 2.57
37 38 7.903995 AGAAACAAGTGCAAAAAGAATGAAA 57.096 28.000 0.00 0.00 0.00 2.69
38 39 8.321650 AGAAACAAGTGCAAAAAGAATGAAAA 57.678 26.923 0.00 0.00 0.00 2.29
39 40 8.949177 AGAAACAAGTGCAAAAAGAATGAAAAT 58.051 25.926 0.00 0.00 0.00 1.82
40 41 9.558648 GAAACAAGTGCAAAAAGAATGAAAATT 57.441 25.926 0.00 0.00 0.00 1.82
43 44 9.382275 ACAAGTGCAAAAAGAATGAAAATTAGT 57.618 25.926 0.00 0.00 0.00 2.24
44 45 9.640974 CAAGTGCAAAAAGAATGAAAATTAGTG 57.359 29.630 0.00 0.00 0.00 2.74
45 46 9.598517 AAGTGCAAAAAGAATGAAAATTAGTGA 57.401 25.926 0.00 0.00 0.00 3.41
46 47 9.598517 AGTGCAAAAAGAATGAAAATTAGTGAA 57.401 25.926 0.00 0.00 0.00 3.18
52 53 9.810545 AAAAGAATGAAAATTAGTGAAAACCGA 57.189 25.926 0.00 0.00 0.00 4.69
53 54 9.463443 AAAGAATGAAAATTAGTGAAAACCGAG 57.537 29.630 0.00 0.00 0.00 4.63
54 55 7.593825 AGAATGAAAATTAGTGAAAACCGAGG 58.406 34.615 0.00 0.00 0.00 4.63
55 56 7.447238 AGAATGAAAATTAGTGAAAACCGAGGA 59.553 33.333 0.00 0.00 0.00 3.71
56 57 6.945938 TGAAAATTAGTGAAAACCGAGGAA 57.054 33.333 0.00 0.00 0.00 3.36
57 58 7.336161 TGAAAATTAGTGAAAACCGAGGAAA 57.664 32.000 0.00 0.00 0.00 3.13
58 59 7.773149 TGAAAATTAGTGAAAACCGAGGAAAA 58.227 30.769 0.00 0.00 0.00 2.29
59 60 7.703197 TGAAAATTAGTGAAAACCGAGGAAAAC 59.297 33.333 0.00 0.00 0.00 2.43
60 61 6.702716 AATTAGTGAAAACCGAGGAAAACA 57.297 33.333 0.00 0.00 0.00 2.83
61 62 6.702716 ATTAGTGAAAACCGAGGAAAACAA 57.297 33.333 0.00 0.00 0.00 2.83
62 63 6.512342 TTAGTGAAAACCGAGGAAAACAAA 57.488 33.333 0.00 0.00 0.00 2.83
63 64 5.394224 AGTGAAAACCGAGGAAAACAAAA 57.606 34.783 0.00 0.00 0.00 2.44
64 65 5.785243 AGTGAAAACCGAGGAAAACAAAAA 58.215 33.333 0.00 0.00 0.00 1.94
87 88 8.980143 AAAAGAATGAAAACAAAGAAACTCGA 57.020 26.923 0.00 0.00 0.00 4.04
88 89 8.620533 AAAGAATGAAAACAAAGAAACTCGAG 57.379 30.769 11.84 11.84 0.00 4.04
162 163 8.731275 AGAAAGAACAAAAATAAACAAAGGGG 57.269 30.769 0.00 0.00 0.00 4.79
163 164 7.773224 AGAAAGAACAAAAATAAACAAAGGGGG 59.227 33.333 0.00 0.00 0.00 5.40
169 170 8.830915 ACAAAAATAAACAAAGGGGGAAAAAT 57.169 26.923 0.00 0.00 0.00 1.82
181 183 9.519191 CAAAGGGGGAAAAATAAGAAAAATCAT 57.481 29.630 0.00 0.00 0.00 2.45
224 226 7.200455 ACAAAGAGAATCGGTAAAAACAAAGG 58.800 34.615 0.00 0.00 42.67 3.11
228 230 8.178313 AGAGAATCGGTAAAAACAAAGGAAAT 57.822 30.769 0.00 0.00 42.67 2.17
229 231 9.292195 AGAGAATCGGTAAAAACAAAGGAAATA 57.708 29.630 0.00 0.00 42.67 1.40
230 232 9.556030 GAGAATCGGTAAAAACAAAGGAAATAG 57.444 33.333 0.00 0.00 0.00 1.73
236 240 7.921745 CGGTAAAAACAAAGGAAATAGAAACCA 59.078 33.333 0.00 0.00 0.00 3.67
248 252 7.710907 AGGAAATAGAAACCAAAGAAAAAGTGC 59.289 33.333 0.00 0.00 0.00 4.40
269 273 4.862018 TGCTGAAGAAACAAAAGAAAACCG 59.138 37.500 0.00 0.00 0.00 4.44
315 319 4.019321 TGGAATAGCAGAAAAGCCAGTACT 60.019 41.667 0.00 0.00 34.23 2.73
326 330 3.449227 CAGTACTCCCGCCGAGCA 61.449 66.667 0.00 0.00 43.01 4.26
418 426 7.878477 TTGTCTTACCACACTCTTTATTACG 57.122 36.000 0.00 0.00 0.00 3.18
438 446 4.253685 ACGGAACATAGACAAGGTTGATG 58.746 43.478 0.00 0.00 0.00 3.07
502 510 3.131046 GCGTCCCAATGAAAATCCAAGAT 59.869 43.478 0.00 0.00 0.00 2.40
517 525 2.484417 CCAAGATCATGCTTAGCGAGGT 60.484 50.000 0.00 0.00 0.00 3.85
613 621 1.881973 TCTCCTTGACAATGCTTGCAC 59.118 47.619 0.00 0.00 0.00 4.57
625 633 3.496309 CTTGCACACTGGCCTCCCA 62.496 63.158 3.32 0.00 39.32 4.37
669 2334 4.937015 ACCATACTTTTGCAATTTGATGCC 59.063 37.500 0.00 0.00 45.83 4.40
674 2339 5.064558 ACTTTTGCAATTTGATGCCATGAA 58.935 33.333 0.00 0.00 45.83 2.57
823 2491 1.583709 GCTTGCTACAATTCCGCGC 60.584 57.895 0.00 0.00 0.00 6.86
824 2492 1.296867 CTTGCTACAATTCCGCGCG 60.297 57.895 25.67 25.67 0.00 6.86
831 2499 3.122278 GCTACAATTCCGCGCGATAAATA 59.878 43.478 34.63 14.74 0.00 1.40
841 2509 3.457596 GCGCGATAAATATCACAACGAC 58.542 45.455 12.10 0.00 32.98 4.34
842 2510 3.660904 GCGCGATAAATATCACAACGACC 60.661 47.826 12.10 0.00 32.98 4.79
843 2511 3.734231 CGCGATAAATATCACAACGACCT 59.266 43.478 0.00 0.00 32.98 3.85
844 2512 4.208460 CGCGATAAATATCACAACGACCTT 59.792 41.667 0.00 0.00 32.98 3.50
845 2513 5.609696 CGCGATAAATATCACAACGACCTTC 60.610 44.000 0.00 0.00 32.98 3.46
846 2514 5.462398 GCGATAAATATCACAACGACCTTCT 59.538 40.000 0.00 0.00 32.98 2.85
847 2515 6.345882 GCGATAAATATCACAACGACCTTCTC 60.346 42.308 0.00 0.00 32.98 2.87
848 2516 6.918569 CGATAAATATCACAACGACCTTCTCT 59.081 38.462 0.00 0.00 32.98 3.10
849 2517 7.435488 CGATAAATATCACAACGACCTTCTCTT 59.565 37.037 0.00 0.00 32.98 2.85
850 2518 6.969828 AAATATCACAACGACCTTCTCTTC 57.030 37.500 0.00 0.00 0.00 2.87
851 2519 2.814280 TCACAACGACCTTCTCTTCC 57.186 50.000 0.00 0.00 0.00 3.46
852 2520 1.343465 TCACAACGACCTTCTCTTCCC 59.657 52.381 0.00 0.00 0.00 3.97
853 2521 0.685660 ACAACGACCTTCTCTTCCCC 59.314 55.000 0.00 0.00 0.00 4.81
854 2522 0.036294 CAACGACCTTCTCTTCCCCC 60.036 60.000 0.00 0.00 0.00 5.40
855 2523 0.178900 AACGACCTTCTCTTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
856 2524 0.905337 ACGACCTTCTCTTCCCCCTG 60.905 60.000 0.00 0.00 0.00 4.45
857 2525 0.614979 CGACCTTCTCTTCCCCCTGA 60.615 60.000 0.00 0.00 0.00 3.86
858 2526 1.886422 GACCTTCTCTTCCCCCTGAT 58.114 55.000 0.00 0.00 0.00 2.90
859 2527 1.765904 GACCTTCTCTTCCCCCTGATC 59.234 57.143 0.00 0.00 0.00 2.92
860 2528 1.135960 CCTTCTCTTCCCCCTGATCC 58.864 60.000 0.00 0.00 0.00 3.36
861 2529 1.135960 CTTCTCTTCCCCCTGATCCC 58.864 60.000 0.00 0.00 0.00 3.85
862 2530 0.725133 TTCTCTTCCCCCTGATCCCT 59.275 55.000 0.00 0.00 0.00 4.20
863 2531 0.266152 TCTCTTCCCCCTGATCCCTC 59.734 60.000 0.00 0.00 0.00 4.30
864 2532 0.030705 CTCTTCCCCCTGATCCCTCA 60.031 60.000 0.00 0.00 0.00 3.86
865 2533 0.421495 TCTTCCCCCTGATCCCTCAA 59.579 55.000 0.00 0.00 0.00 3.02
866 2534 1.203557 TCTTCCCCCTGATCCCTCAAA 60.204 52.381 0.00 0.00 0.00 2.69
867 2535 1.640670 CTTCCCCCTGATCCCTCAAAA 59.359 52.381 0.00 0.00 0.00 2.44
868 2536 1.766951 TCCCCCTGATCCCTCAAAAA 58.233 50.000 0.00 0.00 0.00 1.94
1206 2943 0.453282 CGTCTGATTTGCTTGGTGCG 60.453 55.000 0.00 0.00 46.63 5.34
1212 2949 1.252904 ATTTGCTTGGTGCGGCAGAT 61.253 50.000 1.18 0.00 46.63 2.90
1422 3262 9.077885 AGGTCTAAATCTTGCTTAATTTCAACA 57.922 29.630 0.00 0.00 0.00 3.33
1522 3387 2.310052 AGGCCAAAGAGCTCAATAACCT 59.690 45.455 17.77 13.67 0.00 3.50
1567 3432 1.684983 CATCAAGCCCATGACCCATTC 59.315 52.381 0.00 0.00 30.82 2.67
1670 3572 3.487544 GGCTTACTCGATGTTGATTTGGC 60.488 47.826 0.00 0.00 0.00 4.52
1687 3591 0.106708 GGCCGGATATCTTGCAGACA 59.893 55.000 5.05 0.00 0.00 3.41
1721 3625 4.744795 TTCAAGAAGAGCTATCTCCCAC 57.255 45.455 2.20 0.00 40.22 4.61
1949 3853 6.864342 TGGAACTCGAGGTATCTCTTAAAAG 58.136 40.000 18.41 0.00 37.86 2.27
2140 7453 5.643348 TGATGTTGATCGAGTTACTGCATTT 59.357 36.000 0.00 0.00 0.00 2.32
2314 7629 1.414919 ACCACTGTTGACGCCTTTAGA 59.585 47.619 0.00 0.00 0.00 2.10
2450 7863 3.819564 TTACTATGATGCTTCGTGCCT 57.180 42.857 4.63 0.00 42.00 4.75
2551 7966 5.574970 AGTCTTGAAGAGGAAATTCTGGT 57.425 39.130 0.00 0.00 0.00 4.00
2601 8023 0.457509 TGTTTTGCTGTTGTGCACGG 60.458 50.000 13.13 3.54 43.20 4.94
2616 8038 4.925054 TGTGCACGGTAGTTAAACTATGAC 59.075 41.667 13.13 0.00 32.65 3.06
2618 8040 3.549070 GCACGGTAGTTAAACTATGACGG 59.451 47.826 0.00 0.00 32.65 4.79
2619 8041 4.737054 CACGGTAGTTAAACTATGACGGT 58.263 43.478 0.00 0.00 32.65 4.83
2809 8266 4.874970 AGTTGCTATTTTGCCTTTGTGAG 58.125 39.130 0.00 0.00 0.00 3.51
2866 8374 9.726232 GTTTCGGTTCCCATAAAAATTATACTC 57.274 33.333 0.00 0.00 0.00 2.59
2867 8375 8.454570 TTCGGTTCCCATAAAAATTATACTCC 57.545 34.615 0.00 0.00 0.00 3.85
2868 8376 6.999871 TCGGTTCCCATAAAAATTATACTCCC 59.000 38.462 0.00 0.00 0.00 4.30
2871 8379 7.450634 GGTTCCCATAAAAATTATACTCCCTCC 59.549 40.741 0.00 0.00 0.00 4.30
2872 8380 6.775708 TCCCATAAAAATTATACTCCCTCCG 58.224 40.000 0.00 0.00 0.00 4.63
2873 8381 6.330778 TCCCATAAAAATTATACTCCCTCCGT 59.669 38.462 0.00 0.00 0.00 4.69
2874 8382 6.653740 CCCATAAAAATTATACTCCCTCCGTC 59.346 42.308 0.00 0.00 0.00 4.79
2875 8383 6.653740 CCATAAAAATTATACTCCCTCCGTCC 59.346 42.308 0.00 0.00 0.00 4.79
2876 8384 4.701651 AAAATTATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
2877 8385 3.339713 AATTATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
2879 8387 4.687262 ATTATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
2880 8388 4.474303 TTATACTCCCTCCGTCCCATAA 57.526 45.455 0.00 0.00 0.00 1.90
2882 8390 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2883 8391 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2884 8392 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2885 8393 4.351127 ACTCCCTCCGTCCCATAATATAC 58.649 47.826 0.00 0.00 0.00 1.47
2886 8394 3.359033 TCCCTCCGTCCCATAATATACG 58.641 50.000 0.00 0.00 35.20 3.06
2893 8401 3.380637 CGTCCCATAATATACGGAGGGAG 59.619 52.174 0.00 0.00 45.39 4.30
2894 8402 4.351127 GTCCCATAATATACGGAGGGAGT 58.649 47.826 0.00 0.00 45.39 3.85
2897 8405 5.254737 TCCCATAATATACGGAGGGAGTAGT 59.745 44.000 0.00 0.00 40.26 2.73
2898 8406 6.448061 TCCCATAATATACGGAGGGAGTAGTA 59.552 42.308 0.00 0.00 40.26 1.82
2963 10550 8.621532 TGTAGAACTGAATCAAATTAGTTGCT 57.378 30.769 0.00 0.00 37.13 3.91
2964 10551 9.066892 TGTAGAACTGAATCAAATTAGTTGCTT 57.933 29.630 0.00 0.00 37.13 3.91
2965 10552 9.548208 GTAGAACTGAATCAAATTAGTTGCTTC 57.452 33.333 2.62 2.62 40.99 3.86
2967 10554 8.078596 AGAACTGAATCAAATTAGTTGCTTCAC 58.921 33.333 7.44 0.37 43.82 3.18
2969 10556 6.491403 ACTGAATCAAATTAGTTGCTTCACCT 59.509 34.615 7.44 0.00 43.82 4.00
2971 10558 8.402798 TGAATCAAATTAGTTGCTTCACCTTA 57.597 30.769 7.44 0.00 43.82 2.69
2973 10560 6.254281 TCAAATTAGTTGCTTCACCTTAGC 57.746 37.500 0.00 0.00 37.13 3.09
2974 10561 6.003950 TCAAATTAGTTGCTTCACCTTAGCT 58.996 36.000 0.00 0.00 39.38 3.32
2975 10562 6.149474 TCAAATTAGTTGCTTCACCTTAGCTC 59.851 38.462 0.00 0.00 39.38 4.09
2976 10563 2.481289 AGTTGCTTCACCTTAGCTCC 57.519 50.000 0.00 0.00 39.38 4.70
2978 10565 0.036388 TTGCTTCACCTTAGCTCCCG 60.036 55.000 0.00 0.00 39.38 5.14
2979 10566 1.815840 GCTTCACCTTAGCTCCCGC 60.816 63.158 0.00 0.00 35.74 6.13
2980 10567 1.596934 CTTCACCTTAGCTCCCGCA 59.403 57.895 0.00 0.00 39.10 5.69
2981 10568 0.036388 CTTCACCTTAGCTCCCGCAA 60.036 55.000 0.00 0.00 39.10 4.85
2982 10569 0.398696 TTCACCTTAGCTCCCGCAAA 59.601 50.000 0.00 0.00 39.10 3.68
2983 10570 0.398696 TCACCTTAGCTCCCGCAAAA 59.601 50.000 0.00 0.00 39.10 2.44
2984 10571 1.202830 TCACCTTAGCTCCCGCAAAAA 60.203 47.619 0.00 0.00 39.10 1.94
3068 11421 6.438186 TGCAGGATGGAAATATATGACTGA 57.562 37.500 0.00 0.00 35.86 3.41
3084 11437 3.681417 TGACTGAAGCGAAGATCAATGTG 59.319 43.478 0.00 0.00 0.00 3.21
3086 11439 3.681897 ACTGAAGCGAAGATCAATGTGTC 59.318 43.478 0.00 0.00 0.00 3.67
3087 11440 3.663025 TGAAGCGAAGATCAATGTGTCA 58.337 40.909 0.00 0.00 0.00 3.58
3088 11441 4.256110 TGAAGCGAAGATCAATGTGTCAT 58.744 39.130 0.00 0.00 0.00 3.06
3089 11442 4.093850 TGAAGCGAAGATCAATGTGTCATG 59.906 41.667 0.00 0.00 0.00 3.07
3090 11443 3.603532 AGCGAAGATCAATGTGTCATGT 58.396 40.909 0.00 0.00 0.00 3.21
3091 11444 3.373130 AGCGAAGATCAATGTGTCATGTG 59.627 43.478 0.00 0.00 0.00 3.21
3092 11445 3.486375 GCGAAGATCAATGTGTCATGTGG 60.486 47.826 0.00 0.00 0.00 4.17
3093 11446 3.064408 CGAAGATCAATGTGTCATGTGGG 59.936 47.826 0.00 0.00 0.00 4.61
3094 11447 3.008835 AGATCAATGTGTCATGTGGGG 57.991 47.619 0.00 0.00 0.00 4.96
3096 11449 0.112025 TCAATGTGTCATGTGGGGCA 59.888 50.000 0.00 0.00 0.00 5.36
3097 11450 0.244450 CAATGTGTCATGTGGGGCAC 59.756 55.000 0.00 0.00 34.56 5.01
3098 11451 1.243342 AATGTGTCATGTGGGGCACG 61.243 55.000 0.00 0.00 37.14 5.34
3099 11452 2.281484 GTGTCATGTGGGGCACGT 60.281 61.111 0.00 0.00 37.14 4.49
3100 11453 2.031919 TGTCATGTGGGGCACGTC 59.968 61.111 0.00 0.00 37.14 4.34
3104 11457 1.449601 CATGTGGGGCACGTCCTAC 60.450 63.158 3.16 3.16 37.14 3.18
3105 11458 2.524640 TGTGGGGCACGTCCTACA 60.525 61.111 8.20 8.20 44.34 2.74
3106 11459 2.264794 GTGGGGCACGTCCTACAG 59.735 66.667 5.09 0.00 38.07 2.74
3107 11460 3.000819 TGGGGCACGTCCTACAGG 61.001 66.667 0.00 0.00 34.39 4.00
3108 11461 4.468689 GGGGCACGTCCTACAGGC 62.469 72.222 0.00 0.00 34.44 4.85
3110 11463 4.065281 GGCACGTCCTACAGGCGT 62.065 66.667 10.60 10.60 44.39 5.68
3113 11466 3.379445 ACGTCCTACAGGCGTGGG 61.379 66.667 11.67 3.33 44.99 4.61
3161 11514 2.659897 GCATCAGGCGAGGCGTAG 60.660 66.667 0.86 0.00 39.45 3.51
3162 11515 2.028190 CATCAGGCGAGGCGTAGG 59.972 66.667 0.00 0.00 0.00 3.18
3173 11526 4.537433 GCGTAGGCTGGGCAGGAG 62.537 72.222 0.00 0.00 35.83 3.69
3174 11527 3.077556 CGTAGGCTGGGCAGGAGT 61.078 66.667 0.00 0.00 0.00 3.85
3175 11528 2.904131 GTAGGCTGGGCAGGAGTC 59.096 66.667 0.00 0.00 0.00 3.36
3176 11529 2.365635 TAGGCTGGGCAGGAGTCC 60.366 66.667 0.00 0.00 41.04 3.85
3189 11670 1.646447 AGGAGTCCTGGTCCTGATACA 59.354 52.381 12.07 0.00 43.24 2.29
3192 11673 4.078571 AGGAGTCCTGGTCCTGATACATTA 60.079 45.833 12.07 0.00 43.24 1.90
3193 11674 4.282195 GGAGTCCTGGTCCTGATACATTAG 59.718 50.000 0.41 0.00 0.00 1.73
3194 11675 4.884961 AGTCCTGGTCCTGATACATTAGT 58.115 43.478 0.00 0.00 0.00 2.24
3195 11676 5.281314 AGTCCTGGTCCTGATACATTAGTT 58.719 41.667 0.00 0.00 0.00 2.24
3198 11679 4.656112 CCTGGTCCTGATACATTAGTTCCT 59.344 45.833 0.00 0.00 0.00 3.36
3202 11683 7.130099 TGGTCCTGATACATTAGTTCCTAGAA 58.870 38.462 0.00 0.00 0.00 2.10
3204 11685 9.310449 GGTCCTGATACATTAGTTCCTAGAATA 57.690 37.037 0.00 0.00 0.00 1.75
3246 11727 8.997621 TGTATAGGTTTCTAGTTTGTTAGCAG 57.002 34.615 0.00 0.00 0.00 4.24
3248 11729 4.072839 AGGTTTCTAGTTTGTTAGCAGCC 58.927 43.478 0.00 0.00 0.00 4.85
3249 11730 3.190744 GGTTTCTAGTTTGTTAGCAGCCC 59.809 47.826 0.00 0.00 0.00 5.19
3250 11731 3.780804 TTCTAGTTTGTTAGCAGCCCA 57.219 42.857 0.00 0.00 0.00 5.36
3251 11732 4.301072 TTCTAGTTTGTTAGCAGCCCAT 57.699 40.909 0.00 0.00 0.00 4.00
3252 11733 3.609853 TCTAGTTTGTTAGCAGCCCATG 58.390 45.455 0.00 0.00 0.00 3.66
3253 11734 1.549203 AGTTTGTTAGCAGCCCATGG 58.451 50.000 4.14 4.14 0.00 3.66
3268 11749 3.820557 CCCATGGGGCCTTTATATATCG 58.179 50.000 24.53 0.00 35.35 2.92
3269 11750 3.202151 CCCATGGGGCCTTTATATATCGT 59.798 47.826 24.53 0.00 35.35 3.73
3272 11753 6.271391 CCCATGGGGCCTTTATATATCGTATA 59.729 42.308 24.53 0.00 35.35 1.47
3273 11754 7.202149 CCCATGGGGCCTTTATATATCGTATAA 60.202 40.741 24.53 0.00 35.35 0.98
3274 11755 8.383175 CCATGGGGCCTTTATATATCGTATAAT 58.617 37.037 2.85 0.00 0.00 1.28
3275 11756 9.436957 CATGGGGCCTTTATATATCGTATAATC 57.563 37.037 0.84 0.00 0.00 1.75
3278 11759 7.603024 GGGGCCTTTATATATCGTATAATCAGC 59.397 40.741 0.84 0.00 0.00 4.26
3279 11760 8.148351 GGGCCTTTATATATCGTATAATCAGCA 58.852 37.037 0.84 0.00 0.00 4.41
3280 11761 8.979574 GGCCTTTATATATCGTATAATCAGCAC 58.020 37.037 0.00 0.00 0.00 4.40
3281 11762 8.979574 GCCTTTATATATCGTATAATCAGCACC 58.020 37.037 0.00 0.00 0.00 5.01
3282 11763 9.477484 CCTTTATATATCGTATAATCAGCACCC 57.523 37.037 0.00 0.00 0.00 4.61
3286 11767 8.948631 ATATATCGTATAATCAGCACCCTTTG 57.051 34.615 0.00 0.00 0.00 2.77
3287 11768 4.746535 TCGTATAATCAGCACCCTTTGA 57.253 40.909 0.00 0.00 0.00 2.69
3301 11782 3.959535 CCTTTGAGGGCAAGCAATAAA 57.040 42.857 0.00 0.00 35.04 1.40
3302 11783 3.853475 CCTTTGAGGGCAAGCAATAAAG 58.147 45.455 0.00 0.00 35.04 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.018669 TGCACTTGTTTCTTCGTTTTGTTTTT 60.019 30.769 0.00 0.00 0.00 1.94
1 2 5.463724 TGCACTTGTTTCTTCGTTTTGTTTT 59.536 32.000 0.00 0.00 0.00 2.43
2 3 4.985409 TGCACTTGTTTCTTCGTTTTGTTT 59.015 33.333 0.00 0.00 0.00 2.83
3 4 4.551388 TGCACTTGTTTCTTCGTTTTGTT 58.449 34.783 0.00 0.00 0.00 2.83
4 5 4.167554 TGCACTTGTTTCTTCGTTTTGT 57.832 36.364 0.00 0.00 0.00 2.83
5 6 5.508124 TTTGCACTTGTTTCTTCGTTTTG 57.492 34.783 0.00 0.00 0.00 2.44
6 7 6.422400 TCTTTTTGCACTTGTTTCTTCGTTTT 59.578 30.769 0.00 0.00 0.00 2.43
7 8 5.923684 TCTTTTTGCACTTGTTTCTTCGTTT 59.076 32.000 0.00 0.00 0.00 3.60
8 9 5.465935 TCTTTTTGCACTTGTTTCTTCGTT 58.534 33.333 0.00 0.00 0.00 3.85
9 10 5.054390 TCTTTTTGCACTTGTTTCTTCGT 57.946 34.783 0.00 0.00 0.00 3.85
10 11 6.253298 TCATTCTTTTTGCACTTGTTTCTTCG 59.747 34.615 0.00 0.00 0.00 3.79
11 12 7.524294 TCATTCTTTTTGCACTTGTTTCTTC 57.476 32.000 0.00 0.00 0.00 2.87
12 13 7.903995 TTCATTCTTTTTGCACTTGTTTCTT 57.096 28.000 0.00 0.00 0.00 2.52
13 14 7.903995 TTTCATTCTTTTTGCACTTGTTTCT 57.096 28.000 0.00 0.00 0.00 2.52
14 15 9.558648 AATTTTCATTCTTTTTGCACTTGTTTC 57.441 25.926 0.00 0.00 0.00 2.78
17 18 9.382275 ACTAATTTTCATTCTTTTTGCACTTGT 57.618 25.926 0.00 0.00 0.00 3.16
18 19 9.640974 CACTAATTTTCATTCTTTTTGCACTTG 57.359 29.630 0.00 0.00 0.00 3.16
19 20 9.598517 TCACTAATTTTCATTCTTTTTGCACTT 57.401 25.926 0.00 0.00 0.00 3.16
20 21 9.598517 TTCACTAATTTTCATTCTTTTTGCACT 57.401 25.926 0.00 0.00 0.00 4.40
26 27 9.810545 TCGGTTTTCACTAATTTTCATTCTTTT 57.189 25.926 0.00 0.00 0.00 2.27
27 28 9.463443 CTCGGTTTTCACTAATTTTCATTCTTT 57.537 29.630 0.00 0.00 0.00 2.52
28 29 8.082242 CCTCGGTTTTCACTAATTTTCATTCTT 58.918 33.333 0.00 0.00 0.00 2.52
29 30 7.447238 TCCTCGGTTTTCACTAATTTTCATTCT 59.553 33.333 0.00 0.00 0.00 2.40
30 31 7.590279 TCCTCGGTTTTCACTAATTTTCATTC 58.410 34.615 0.00 0.00 0.00 2.67
31 32 7.519032 TCCTCGGTTTTCACTAATTTTCATT 57.481 32.000 0.00 0.00 0.00 2.57
32 33 7.519032 TTCCTCGGTTTTCACTAATTTTCAT 57.481 32.000 0.00 0.00 0.00 2.57
33 34 6.945938 TTCCTCGGTTTTCACTAATTTTCA 57.054 33.333 0.00 0.00 0.00 2.69
34 35 7.703197 TGTTTTCCTCGGTTTTCACTAATTTTC 59.297 33.333 0.00 0.00 0.00 2.29
35 36 7.548967 TGTTTTCCTCGGTTTTCACTAATTTT 58.451 30.769 0.00 0.00 0.00 1.82
36 37 7.102847 TGTTTTCCTCGGTTTTCACTAATTT 57.897 32.000 0.00 0.00 0.00 1.82
37 38 6.702716 TGTTTTCCTCGGTTTTCACTAATT 57.297 33.333 0.00 0.00 0.00 1.40
38 39 6.702716 TTGTTTTCCTCGGTTTTCACTAAT 57.297 33.333 0.00 0.00 0.00 1.73
39 40 6.512342 TTTGTTTTCCTCGGTTTTCACTAA 57.488 33.333 0.00 0.00 0.00 2.24
40 41 6.512342 TTTTGTTTTCCTCGGTTTTCACTA 57.488 33.333 0.00 0.00 0.00 2.74
41 42 5.394224 TTTTGTTTTCCTCGGTTTTCACT 57.606 34.783 0.00 0.00 0.00 3.41
61 62 9.418045 TCGAGTTTCTTTGTTTTCATTCTTTTT 57.582 25.926 0.00 0.00 0.00 1.94
62 63 8.980143 TCGAGTTTCTTTGTTTTCATTCTTTT 57.020 26.923 0.00 0.00 0.00 2.27
63 64 8.458843 TCTCGAGTTTCTTTGTTTTCATTCTTT 58.541 29.630 13.13 0.00 0.00 2.52
64 65 7.985476 TCTCGAGTTTCTTTGTTTTCATTCTT 58.015 30.769 13.13 0.00 0.00 2.52
65 66 7.553881 TCTCGAGTTTCTTTGTTTTCATTCT 57.446 32.000 13.13 0.00 0.00 2.40
66 67 8.614994 TTTCTCGAGTTTCTTTGTTTTCATTC 57.385 30.769 13.13 0.00 0.00 2.67
67 68 8.860128 GTTTTCTCGAGTTTCTTTGTTTTCATT 58.140 29.630 13.13 0.00 0.00 2.57
68 69 8.026607 TGTTTTCTCGAGTTTCTTTGTTTTCAT 58.973 29.630 13.13 0.00 0.00 2.57
69 70 7.364200 TGTTTTCTCGAGTTTCTTTGTTTTCA 58.636 30.769 13.13 0.00 0.00 2.69
70 71 7.790861 TGTTTTCTCGAGTTTCTTTGTTTTC 57.209 32.000 13.13 0.00 0.00 2.29
71 72 8.484799 GTTTGTTTTCTCGAGTTTCTTTGTTTT 58.515 29.630 13.13 0.00 0.00 2.43
72 73 7.650104 TGTTTGTTTTCTCGAGTTTCTTTGTTT 59.350 29.630 13.13 0.00 0.00 2.83
73 74 7.142680 TGTTTGTTTTCTCGAGTTTCTTTGTT 58.857 30.769 13.13 0.00 0.00 2.83
74 75 6.674066 TGTTTGTTTTCTCGAGTTTCTTTGT 58.326 32.000 13.13 0.00 0.00 2.83
75 76 7.561237 TTGTTTGTTTTCTCGAGTTTCTTTG 57.439 32.000 13.13 0.00 0.00 2.77
76 77 8.079809 TCTTTGTTTGTTTTCTCGAGTTTCTTT 58.920 29.630 13.13 0.00 0.00 2.52
77 78 7.590279 TCTTTGTTTGTTTTCTCGAGTTTCTT 58.410 30.769 13.13 0.00 0.00 2.52
78 79 7.141100 TCTTTGTTTGTTTTCTCGAGTTTCT 57.859 32.000 13.13 0.00 0.00 2.52
79 80 7.790861 TTCTTTGTTTGTTTTCTCGAGTTTC 57.209 32.000 13.13 2.83 0.00 2.78
80 81 8.582433 TTTTCTTTGTTTGTTTTCTCGAGTTT 57.418 26.923 13.13 0.00 0.00 2.66
81 82 8.582433 TTTTTCTTTGTTTGTTTTCTCGAGTT 57.418 26.923 13.13 0.00 0.00 3.01
82 83 8.757164 ATTTTTCTTTGTTTGTTTTCTCGAGT 57.243 26.923 13.13 0.00 0.00 4.18
123 124 6.293004 TGTTCTTTCTTGGTTTTCATTGGT 57.707 33.333 0.00 0.00 0.00 3.67
136 137 9.173021 CCCCTTTGTTTATTTTTGTTCTTTCTT 57.827 29.630 0.00 0.00 0.00 2.52
206 208 9.902196 TTCTATTTCCTTTGTTTTTACCGATTC 57.098 29.630 0.00 0.00 0.00 2.52
209 211 8.136800 GGTTTCTATTTCCTTTGTTTTTACCGA 58.863 33.333 0.00 0.00 0.00 4.69
224 226 8.542953 CAGCACTTTTTCTTTGGTTTCTATTTC 58.457 33.333 0.00 0.00 0.00 2.17
228 230 6.767524 TCAGCACTTTTTCTTTGGTTTCTA 57.232 33.333 0.00 0.00 0.00 2.10
229 231 5.659440 TCAGCACTTTTTCTTTGGTTTCT 57.341 34.783 0.00 0.00 0.00 2.52
230 232 6.099341 TCTTCAGCACTTTTTCTTTGGTTTC 58.901 36.000 0.00 0.00 0.00 2.78
236 240 7.961325 TTTGTTTCTTCAGCACTTTTTCTTT 57.039 28.000 0.00 0.00 0.00 2.52
248 252 7.575332 TTTCGGTTTTCTTTTGTTTCTTCAG 57.425 32.000 0.00 0.00 0.00 3.02
292 296 3.439857 ACTGGCTTTTCTGCTATTCCA 57.560 42.857 0.00 0.00 0.00 3.53
297 301 2.236395 GGGAGTACTGGCTTTTCTGCTA 59.764 50.000 0.00 0.00 0.00 3.49
304 308 2.669240 GGCGGGAGTACTGGCTTT 59.331 61.111 0.00 0.00 46.91 3.51
418 426 3.947834 CCCATCAACCTTGTCTATGTTCC 59.052 47.826 0.00 0.00 0.00 3.62
438 446 5.510430 ACTCTGGACCTAAATTGAATTCCC 58.490 41.667 2.27 0.00 0.00 3.97
502 510 1.001974 ACACAACCTCGCTAAGCATGA 59.998 47.619 0.00 0.00 0.00 3.07
517 525 5.754782 AGATACCAATATTGAGGCACACAA 58.245 37.500 17.23 0.00 43.97 3.33
570 578 2.472695 TAGCGGCATCAAGACACTTT 57.527 45.000 1.45 0.00 0.00 2.66
573 581 4.310769 AGATTATAGCGGCATCAAGACAC 58.689 43.478 1.45 0.00 0.00 3.67
613 621 0.181350 GAAGGTATGGGAGGCCAGTG 59.819 60.000 5.01 0.00 0.00 3.66
625 633 6.194235 TGGTAAATGCCATCAAAGAAGGTAT 58.806 36.000 0.00 0.00 32.81 2.73
650 658 5.791666 TCATGGCATCAAATTGCAAAAGTA 58.208 33.333 1.71 0.00 44.59 2.24
653 661 4.820173 TGTTCATGGCATCAAATTGCAAAA 59.180 33.333 1.71 0.00 44.59 2.44
674 2339 2.824936 CTCCTCTCTCTGTCACATGTGT 59.175 50.000 24.63 0.00 0.00 3.72
813 2481 4.081761 GTGATATTTATCGCGCGGAATTG 58.918 43.478 31.69 0.00 35.48 2.32
823 2491 6.918569 AGAGAAGGTCGTTGTGATATTTATCG 59.081 38.462 0.00 0.00 35.48 2.92
824 2492 8.649973 AAGAGAAGGTCGTTGTGATATTTATC 57.350 34.615 0.00 0.00 0.00 1.75
831 2499 2.028020 GGGAAGAGAAGGTCGTTGTGAT 60.028 50.000 0.00 0.00 0.00 3.06
841 2509 1.135960 GGATCAGGGGGAAGAGAAGG 58.864 60.000 0.00 0.00 0.00 3.46
842 2510 1.135960 GGGATCAGGGGGAAGAGAAG 58.864 60.000 0.00 0.00 0.00 2.85
843 2511 0.725133 AGGGATCAGGGGGAAGAGAA 59.275 55.000 0.00 0.00 0.00 2.87
844 2512 0.266152 GAGGGATCAGGGGGAAGAGA 59.734 60.000 0.00 0.00 0.00 3.10
845 2513 0.030705 TGAGGGATCAGGGGGAAGAG 60.031 60.000 0.00 0.00 0.00 2.85
846 2514 0.421495 TTGAGGGATCAGGGGGAAGA 59.579 55.000 0.00 0.00 0.00 2.87
847 2515 1.298953 TTTGAGGGATCAGGGGGAAG 58.701 55.000 0.00 0.00 0.00 3.46
848 2516 1.766951 TTTTGAGGGATCAGGGGGAA 58.233 50.000 0.00 0.00 0.00 3.97
849 2517 1.766951 TTTTTGAGGGATCAGGGGGA 58.233 50.000 0.00 0.00 0.00 4.81
873 2541 4.816048 AAGGAGGAAGAGAAGGGTTTTT 57.184 40.909 0.00 0.00 0.00 1.94
874 2542 4.816048 AAAGGAGGAAGAGAAGGGTTTT 57.184 40.909 0.00 0.00 0.00 2.43
875 2543 4.079154 ACAAAAGGAGGAAGAGAAGGGTTT 60.079 41.667 0.00 0.00 0.00 3.27
876 2544 3.463704 ACAAAAGGAGGAAGAGAAGGGTT 59.536 43.478 0.00 0.00 0.00 4.11
877 2545 3.056832 ACAAAAGGAGGAAGAGAAGGGT 58.943 45.455 0.00 0.00 0.00 4.34
878 2546 3.797559 ACAAAAGGAGGAAGAGAAGGG 57.202 47.619 0.00 0.00 0.00 3.95
921 2591 4.204028 CGGGGCGATTTGGGGGAT 62.204 66.667 0.00 0.00 0.00 3.85
923 2593 4.751820 AACGGGGCGATTTGGGGG 62.752 66.667 0.00 0.00 0.00 5.40
924 2594 2.678580 AAACGGGGCGATTTGGGG 60.679 61.111 0.00 0.00 0.00 4.96
1206 2943 0.179051 CTTCAGCTCCTGGATCTGCC 60.179 60.000 20.10 0.00 31.51 4.85
1397 3233 9.346725 CTGTTGAAATTAAGCAAGATTTAGACC 57.653 33.333 0.00 0.00 0.00 3.85
1422 3262 5.170198 TCCCCTTCTATTAACATATGCCCT 58.830 41.667 1.58 0.00 0.00 5.19
1522 3387 2.587247 GGGTGAGCAGAGGACAGCA 61.587 63.158 0.00 0.00 34.36 4.41
1567 3432 1.299541 CAAGCTACCCGTGGCATAAG 58.700 55.000 5.95 0.00 39.73 1.73
1687 3591 0.679640 TCTTGAATTGCCGCGGGATT 60.680 50.000 29.38 18.72 0.00 3.01
1721 3625 5.007430 CCAGAAAGATCATCTCATCAAACCG 59.993 44.000 0.00 0.00 0.00 4.44
2140 7453 6.869315 TGTTCATTTGTATTCCAGTTTCGA 57.131 33.333 0.00 0.00 0.00 3.71
2190 7504 9.106070 GTAAATTAATATACATGGATCGTCCCC 57.894 37.037 0.00 0.00 35.03 4.81
2314 7629 3.818210 TGTTGTGGTCGCAATAGTTGAAT 59.182 39.130 0.14 0.00 0.00 2.57
2363 7774 5.046910 ACACTTGAATTATTGCGAACCAG 57.953 39.130 0.00 0.00 0.00 4.00
2405 7818 6.500684 AAGAAATGGTTACATAGCACACAG 57.499 37.500 0.00 0.00 37.02 3.66
2407 7820 9.124807 GTAAAAAGAAATGGTTACATAGCACAC 57.875 33.333 0.00 0.00 37.02 3.82
2450 7863 8.884124 AATGGAGAAAGAATCATTAAGGTTGA 57.116 30.769 0.00 0.00 0.00 3.18
2616 8038 5.768317 ACCTTCAACATGATGTTTAAACCG 58.232 37.500 15.59 0.00 38.77 4.44
2799 8256 3.353836 TTCGGCGCTCACAAAGGC 61.354 61.111 7.64 0.00 0.00 4.35
2809 8266 1.813753 TCAGGCTAATGTTCGGCGC 60.814 57.895 0.00 0.00 0.00 6.53
2864 8372 3.380637 CGTATATTATGGGACGGAGGGAG 59.619 52.174 0.00 0.00 0.00 4.30
2866 8374 3.795623 CGTATATTATGGGACGGAGGG 57.204 52.381 0.00 0.00 0.00 4.30
2871 8379 3.359033 TCCCTCCGTATATTATGGGACG 58.641 50.000 0.00 0.00 38.67 4.79
2872 8380 4.351127 ACTCCCTCCGTATATTATGGGAC 58.649 47.826 0.00 0.00 38.67 4.46
2873 8381 4.687262 ACTCCCTCCGTATATTATGGGA 57.313 45.455 0.00 0.00 40.99 4.37
2874 8382 5.516984 ACTACTCCCTCCGTATATTATGGG 58.483 45.833 0.00 0.00 35.49 4.00
2875 8383 7.447853 GGATACTACTCCCTCCGTATATTATGG 59.552 44.444 0.00 0.00 36.13 2.74
2876 8384 7.997223 TGGATACTACTCCCTCCGTATATTATG 59.003 40.741 0.00 0.00 34.12 1.90
2877 8385 8.110743 TGGATACTACTCCCTCCGTATATTAT 57.889 38.462 0.00 0.00 34.12 1.28
2879 8387 6.398655 TGGATACTACTCCCTCCGTATATT 57.601 41.667 0.00 0.00 34.12 1.28
2880 8388 6.390461 AGATGGATACTACTCCCTCCGTATAT 59.610 42.308 0.00 0.00 32.14 0.86
2882 8390 4.540906 AGATGGATACTACTCCCTCCGTAT 59.459 45.833 0.00 0.00 32.14 3.06
2883 8391 3.915073 AGATGGATACTACTCCCTCCGTA 59.085 47.826 0.00 0.00 32.14 4.02
2884 8392 2.717515 AGATGGATACTACTCCCTCCGT 59.282 50.000 0.00 0.00 32.14 4.69
2885 8393 3.443145 AGATGGATACTACTCCCTCCG 57.557 52.381 0.00 0.00 32.14 4.63
2886 8394 6.502074 AAAAAGATGGATACTACTCCCTCC 57.498 41.667 0.00 0.00 32.14 4.30
2936 10523 9.282247 GCAACTAATTTGATTCAGTTCTACATG 57.718 33.333 0.00 0.00 37.39 3.21
2958 10545 1.454201 GGGAGCTAAGGTGAAGCAAC 58.546 55.000 0.00 0.00 42.62 4.17
2961 10548 4.522971 CGGGAGCTAAGGTGAAGC 57.477 61.111 0.00 0.00 40.40 3.86
2984 10571 3.960755 AGGCTAAGGTGAAGCAACTTTTT 59.039 39.130 2.76 0.00 38.32 1.94
3021 10608 4.243007 GCACTGAGCAAACCAATTAGTT 57.757 40.909 0.00 0.00 44.79 2.24
3068 11421 4.005650 ACATGACACATTGATCTTCGCTT 58.994 39.130 0.00 0.00 0.00 4.68
3084 11437 1.895020 TAGGACGTGCCCCACATGAC 61.895 60.000 2.38 0.00 38.75 3.06
3086 11439 1.449601 GTAGGACGTGCCCCACATG 60.450 63.158 2.38 0.00 41.41 3.21
3087 11440 1.899437 CTGTAGGACGTGCCCCACAT 61.899 60.000 2.38 0.00 37.37 3.21
3088 11441 2.524640 TGTAGGACGTGCCCCACA 60.525 61.111 2.38 2.87 37.37 4.17
3089 11442 2.264794 CTGTAGGACGTGCCCCAC 59.735 66.667 2.38 0.00 37.37 4.61
3090 11443 3.000819 CCTGTAGGACGTGCCCCA 61.001 66.667 2.38 0.00 37.37 4.96
3091 11444 4.468689 GCCTGTAGGACGTGCCCC 62.469 72.222 2.38 0.00 37.37 5.80
3092 11445 4.814294 CGCCTGTAGGACGTGCCC 62.814 72.222 2.38 0.00 37.37 5.36
3093 11446 4.065281 ACGCCTGTAGGACGTGCC 62.065 66.667 15.88 0.00 42.88 5.01
3096 11449 3.379445 CCCACGCCTGTAGGACGT 61.379 66.667 12.42 12.42 44.39 4.34
3097 11450 4.814294 GCCCACGCCTGTAGGACG 62.814 72.222 1.17 7.56 39.44 4.79
3144 11497 2.659897 CTACGCCTCGCCTGATGC 60.660 66.667 0.00 0.00 32.98 3.91
3145 11498 2.028190 CCTACGCCTCGCCTGATG 59.972 66.667 0.00 0.00 0.00 3.07
3146 11499 3.917760 GCCTACGCCTCGCCTGAT 61.918 66.667 0.00 0.00 0.00 2.90
3148 11501 4.880537 CAGCCTACGCCTCGCCTG 62.881 72.222 0.00 0.00 34.57 4.85
3153 11506 4.537433 CTGCCCAGCCTACGCCTC 62.537 72.222 0.00 0.00 34.57 4.70
3156 11509 4.537433 CTCCTGCCCAGCCTACGC 62.537 72.222 0.00 0.00 0.00 4.42
3157 11510 3.077556 ACTCCTGCCCAGCCTACG 61.078 66.667 0.00 0.00 0.00 3.51
3158 11511 2.736826 GGACTCCTGCCCAGCCTAC 61.737 68.421 0.00 0.00 0.00 3.18
3159 11512 2.365635 GGACTCCTGCCCAGCCTA 60.366 66.667 0.00 0.00 0.00 3.93
3160 11513 4.345286 AGGACTCCTGCCCAGCCT 62.345 66.667 0.00 0.00 29.57 4.58
3161 11514 4.106925 CAGGACTCCTGCCCAGCC 62.107 72.222 12.34 0.00 45.13 4.85
3169 11522 1.646447 TGTATCAGGACCAGGACTCCT 59.354 52.381 0.00 0.00 38.84 3.69
3170 11523 2.160721 TGTATCAGGACCAGGACTCC 57.839 55.000 0.00 0.00 0.00 3.85
3171 11524 4.896482 ACTAATGTATCAGGACCAGGACTC 59.104 45.833 0.00 0.00 0.00 3.36
3172 11525 4.884961 ACTAATGTATCAGGACCAGGACT 58.115 43.478 0.00 0.00 0.00 3.85
3173 11526 5.453480 GGAACTAATGTATCAGGACCAGGAC 60.453 48.000 0.00 0.00 0.00 3.85
3174 11527 4.654262 GGAACTAATGTATCAGGACCAGGA 59.346 45.833 0.00 0.00 0.00 3.86
3175 11528 4.656112 AGGAACTAATGTATCAGGACCAGG 59.344 45.833 0.00 0.00 36.02 4.45
3176 11529 5.878406 AGGAACTAATGTATCAGGACCAG 57.122 43.478 0.00 0.00 36.02 4.00
3178 11531 7.598759 TTCTAGGAACTAATGTATCAGGACC 57.401 40.000 0.00 0.00 42.17 4.46
3220 11701 9.601217 CTGCTAACAAACTAGAAACCTATACAT 57.399 33.333 0.00 0.00 0.00 2.29
3221 11702 7.548075 GCTGCTAACAAACTAGAAACCTATACA 59.452 37.037 0.00 0.00 0.00 2.29
3222 11703 7.011202 GGCTGCTAACAAACTAGAAACCTATAC 59.989 40.741 0.00 0.00 0.00 1.47
3224 11705 5.880887 GGCTGCTAACAAACTAGAAACCTAT 59.119 40.000 0.00 0.00 0.00 2.57
3225 11706 5.243207 GGCTGCTAACAAACTAGAAACCTA 58.757 41.667 0.00 0.00 0.00 3.08
3227 11708 3.190744 GGGCTGCTAACAAACTAGAAACC 59.809 47.826 0.00 0.00 0.00 3.27
3228 11709 3.818773 TGGGCTGCTAACAAACTAGAAAC 59.181 43.478 0.00 0.00 0.00 2.78
3231 11712 3.609853 CATGGGCTGCTAACAAACTAGA 58.390 45.455 0.00 0.00 0.00 2.43
3233 11714 2.620367 CCCATGGGCTGCTAACAAACTA 60.620 50.000 20.41 0.00 0.00 2.24
3235 11716 0.532115 CCCATGGGCTGCTAACAAAC 59.468 55.000 20.41 0.00 0.00 2.93
3236 11717 0.614415 CCCCATGGGCTGCTAACAAA 60.614 55.000 26.87 0.00 35.35 2.83
3238 11719 2.682846 CCCCATGGGCTGCTAACA 59.317 61.111 26.87 0.00 35.35 2.41
3248 11729 4.503714 ACGATATATAAAGGCCCCATGG 57.496 45.455 4.14 4.14 0.00 3.66
3249 11730 9.436957 GATTATACGATATATAAAGGCCCCATG 57.563 37.037 0.00 0.00 0.00 3.66
3250 11731 9.166222 TGATTATACGATATATAAAGGCCCCAT 57.834 33.333 0.00 0.00 0.00 4.00
3251 11732 8.555896 TGATTATACGATATATAAAGGCCCCA 57.444 34.615 0.00 0.00 0.00 4.96
3252 11733 7.603024 GCTGATTATACGATATATAAAGGCCCC 59.397 40.741 0.00 0.00 0.00 5.80
3253 11734 8.148351 TGCTGATTATACGATATATAAAGGCCC 58.852 37.037 0.00 0.00 0.00 5.80
3255 11736 8.979574 GGTGCTGATTATACGATATATAAAGGC 58.020 37.037 0.00 0.00 0.00 4.35
3256 11737 9.477484 GGGTGCTGATTATACGATATATAAAGG 57.523 37.037 0.00 0.00 0.00 3.11
3266 11747 4.442893 CCTCAAAGGGTGCTGATTATACGA 60.443 45.833 0.00 0.00 0.00 3.43
3267 11748 3.809832 CCTCAAAGGGTGCTGATTATACG 59.190 47.826 0.00 0.00 0.00 3.06
3281 11762 3.259123 ACTTTATTGCTTGCCCTCAAAGG 59.741 43.478 0.00 0.00 34.30 3.11
3282 11763 4.525912 ACTTTATTGCTTGCCCTCAAAG 57.474 40.909 0.00 0.00 0.00 2.77
3283 11764 4.953940 AACTTTATTGCTTGCCCTCAAA 57.046 36.364 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.