Multiple sequence alignment - TraesCS2D01G598900

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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 TraesCS2D01G598900 chr2D 100.000 3412 0 0 1 3412 650650046 650653457 0.000000e+00 6301
1 TraesCS2D01G598900 chr2D 76.275 451 70 24 2263 2685 584531386 584531827 4.460000e-49 206
2 TraesCS2D01G598900 chr2D 79.213 178 34 3 1746 1921 620225195 620225371 1.660000e-23 121
3 TraesCS2D01G598900 chr2B 89.394 1584 97 34 165 1717 787814007 787815550 0.000000e+00 1929
4 TraesCS2D01G598900 chr2B 93.585 1138 45 9 1945 3055 787815785 787816921 0.000000e+00 1672
5 TraesCS2D01G598900 chr2B 97.238 362 10 0 3051 3412 787817364 787817725 6.260000e-172 614
6 TraesCS2D01G598900 chr2B 73.289 745 156 36 1962 2684 704238849 704239572 2.050000e-57 233
7 TraesCS2D01G598900 chr2B 96.104 77 3 0 729 805 787814639 787814715 3.570000e-25 126
8 TraesCS2D01G598900 chr2B 98.387 62 1 0 114 175 787809799 787809860 3.600000e-20 110
9 TraesCS2D01G598900 chr2B 94.000 50 1 2 842 889 787814583 787814632 1.310000e-09 75
10 TraesCS2D01G598900 chr2A 90.909 979 62 13 1945 2905 772085595 772086564 0.000000e+00 1290
11 TraesCS2D01G598900 chr2A 90.807 979 63 13 1945 2905 772046000 772046969 0.000000e+00 1284
12 TraesCS2D01G598900 chr2A 90.705 979 64 13 1945 2905 772207814 772208783 0.000000e+00 1279
13 TraesCS2D01G598900 chr2A 91.042 960 59 13 1964 2905 772168470 772169420 0.000000e+00 1271
14 TraesCS2D01G598900 chr2A 90.072 977 65 15 1945 2905 772125698 772126658 0.000000e+00 1238
15 TraesCS2D01G598900 chr2A 91.588 844 51 10 900 1741 772206961 772207786 0.000000e+00 1147
16 TraesCS2D01G598900 chr2A 91.469 844 52 10 900 1741 772124845 772125670 0.000000e+00 1142
17 TraesCS2D01G598900 chr2A 91.351 844 53 10 900 1741 772084742 772085567 0.000000e+00 1136
18 TraesCS2D01G598900 chr2A 90.877 844 57 11 900 1741 772045147 772045972 0.000000e+00 1114
19 TraesCS2D01G598900 chr2A 89.313 917 50 19 4 889 772080731 772081630 0.000000e+00 1107
20 TraesCS2D01G598900 chr2A 89.301 916 52 14 4 889 772161153 772162052 0.000000e+00 1107
21 TraesCS2D01G598900 chr2A 89.301 916 51 20 4 889 772120835 772121733 0.000000e+00 1105
22 TraesCS2D01G598900 chr2A 89.168 914 52 18 4 889 771997584 771998478 0.000000e+00 1096
23 TraesCS2D01G598900 chr2A 88.550 917 51 17 4 889 772202955 772203848 0.000000e+00 1062
24 TraesCS2D01G598900 chr2A 91.205 523 30 9 900 1421 772165164 772165671 0.000000e+00 697
25 TraesCS2D01G598900 chr2A 88.889 441 39 4 2981 3412 772217656 772218095 5.010000e-148 534
26 TraesCS2D01G598900 chr2A 94.627 335 15 1 915 1249 772011761 772012092 1.820000e-142 516
27 TraesCS2D01G598900 chr2A 93.642 346 20 1 904 1249 772081834 772082177 1.820000e-142 516
28 TraesCS2D01G598900 chr2A 93.642 346 20 1 904 1249 772162256 772162599 1.820000e-142 516
29 TraesCS2D01G598900 chr2A 93.353 346 21 1 904 1249 772121937 772122280 8.450000e-141 510
30 TraesCS2D01G598900 chr2A 93.064 346 22 1 904 1249 772204052 772204395 3.930000e-139 505
31 TraesCS2D01G598900 chr2A 92.570 323 21 3 1420 1741 772168015 772168335 8.630000e-126 460
32 TraesCS2D01G598900 chr2A 90.452 199 17 1 326 524 772043386 772043582 9.390000e-66 261
33 TraesCS2D01G598900 chr2A 89.950 199 18 1 326 524 772163372 772163568 4.370000e-64 255
34 TraesCS2D01G598900 chr2A 89.950 199 17 2 326 524 772123053 772123248 1.570000e-63 254
35 TraesCS2D01G598900 chr2A 73.423 745 153 37 1964 2687 718622843 718623563 1.580000e-58 237
36 TraesCS2D01G598900 chr2A 98.020 101 2 0 605 705 772124459 772124559 3.500000e-40 176
37 TraesCS2D01G598900 chr2A 98.020 101 2 0 605 705 772206574 772206674 3.500000e-40 176
38 TraesCS2D01G598900 chr2A 97.030 101 3 0 605 705 772164778 772164878 1.630000e-38 171
39 TraesCS2D01G598900 chr2A 84.756 164 20 5 1740 1899 90037975 90038137 3.520000e-35 159
40 TraesCS2D01G598900 chr2A 88.043 92 7 1 689 780 772044879 772044966 4.660000e-19 106
41 TraesCS2D01G598900 chr2A 88.043 92 7 1 689 780 772084474 772084561 4.660000e-19 106
42 TraesCS2D01G598900 chr1A 87.097 186 22 2 1737 1920 11531689 11531504 3.450000e-50 209
43 TraesCS2D01G598900 chr3D 86.885 183 18 6 1743 1920 549000036 548999855 2.080000e-47 200
44 TraesCS2D01G598900 chr3A 87.662 154 15 3 1771 1920 686281554 686281401 3.500000e-40 176
45 TraesCS2D01G598900 chr3A 81.373 204 26 9 1736 1931 33991365 33991564 4.560000e-34 156
46 TraesCS2D01G598900 chr5A 84.358 179 25 2 1742 1917 469107847 469108025 4.530000e-39 172
47 TraesCS2D01G598900 chr4D 80.899 178 31 3 1746 1921 112721995 112721819 1.650000e-28 137
48 TraesCS2D01G598900 chrUn 80.791 177 31 3 1745 1920 68281242 68281068 5.940000e-28 135


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 TraesCS2D01G598900 chr2D 650650046 650653457 3411 False 6301.000000 6301 100.000000 1 3412 1 chr2D.!!$F3 3411
1 TraesCS2D01G598900 chr2B 787814007 787817725 3718 False 883.200000 1929 94.064200 165 3412 5 chr2B.!!$F3 3247
2 TraesCS2D01G598900 chr2B 704238849 704239572 723 False 233.000000 233 73.289000 1962 2684 1 chr2B.!!$F1 722
3 TraesCS2D01G598900 chr2A 771997584 771998478 894 False 1096.000000 1096 89.168000 4 889 1 chr2A.!!$F3 885
4 TraesCS2D01G598900 chr2A 772202955 772208783 5828 False 833.800000 1279 92.385400 4 2905 5 chr2A.!!$F10 2901
5 TraesCS2D01G598900 chr2A 772080731 772086564 5833 False 831.000000 1290 90.651600 4 2905 5 chr2A.!!$F7 2901
6 TraesCS2D01G598900 chr2A 772120835 772126658 5823 False 737.500000 1238 92.027500 4 2905 6 chr2A.!!$F8 2901
7 TraesCS2D01G598900 chr2A 772043386 772046969 3583 False 691.250000 1284 90.044750 326 2905 4 chr2A.!!$F6 2579
8 TraesCS2D01G598900 chr2A 772161153 772169420 8267 False 639.571429 1271 92.105714 4 2905 7 chr2A.!!$F9 2901
9 TraesCS2D01G598900 chr2A 718622843 718623563 720 False 237.000000 237 73.423000 1964 2687 1 chr2A.!!$F2 723

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
27 28 0.041238 TGAGAGGGTTCCGGATCTGT 59.959 55.0 4.15 1.74 0.00 3.41 F
436 470 0.249911 CGGGGCATGCTTCCTAGTAC 60.250 60.0 18.92 0.00 0.00 2.73 F
1217 2634 0.882042 CTGAGCTGACAGGCACGTTT 60.882 55.0 4.26 0.00 34.64 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 5688 0.036010 CGTTGAGGTTCATGGGAGCT 60.036 55.0 0.0 0.0 0.00 4.09 R
2259 9271 0.103937 CTCTCGATGAGTTCCAGGCC 59.896 60.0 0.0 0.0 37.99 5.19 R
3126 10617 1.369091 CGACCAGCTACAACCCATGC 61.369 60.0 0.0 0.0 0.00 4.06 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
19 20 0.747852 GAGGACGATGAGAGGGTTCC 59.252 60.000 0.00 0.00 0.00 3.62
27 28 0.041238 TGAGAGGGTTCCGGATCTGT 59.959 55.000 4.15 1.74 0.00 3.41
31 32 1.555533 GAGGGTTCCGGATCTGTTCTT 59.444 52.381 4.15 0.00 0.00 2.52
45 46 2.291741 CTGTTCTTTGTTGTGGAGGAGC 59.708 50.000 0.00 0.00 0.00 4.70
47 48 2.550180 GTTCTTTGTTGTGGAGGAGCTC 59.450 50.000 4.71 4.71 0.00 4.09
100 101 3.095163 AGCTCCCTCCTGCCATGG 61.095 66.667 7.63 7.63 0.00 3.66
285 290 2.213499 GGTGGTATGAAGGATGAAGCG 58.787 52.381 0.00 0.00 0.00 4.68
436 470 0.249911 CGGGGCATGCTTCCTAGTAC 60.250 60.000 18.92 0.00 0.00 2.73
437 471 1.132500 GGGGCATGCTTCCTAGTACT 58.868 55.000 18.92 0.00 0.00 2.73
438 472 2.326428 GGGGCATGCTTCCTAGTACTA 58.674 52.381 18.92 1.89 0.00 1.82
439 473 2.037381 GGGGCATGCTTCCTAGTACTAC 59.963 54.545 18.92 0.00 0.00 2.73
440 474 2.698797 GGGCATGCTTCCTAGTACTACA 59.301 50.000 18.92 0.00 0.00 2.74
441 475 3.325135 GGGCATGCTTCCTAGTACTACAT 59.675 47.826 18.92 0.00 0.00 2.29
442 476 4.527038 GGGCATGCTTCCTAGTACTACATA 59.473 45.833 18.92 0.00 0.00 2.29
443 477 5.011738 GGGCATGCTTCCTAGTACTACATAA 59.988 44.000 18.92 0.00 0.00 1.90
444 478 6.463897 GGGCATGCTTCCTAGTACTACATAAA 60.464 42.308 18.92 0.00 0.00 1.40
445 479 6.647067 GGCATGCTTCCTAGTACTACATAAAG 59.353 42.308 18.92 2.17 0.00 1.85
446 480 7.434492 GCATGCTTCCTAGTACTACATAAAGA 58.566 38.462 11.37 0.00 0.00 2.52
447 481 7.596995 GCATGCTTCCTAGTACTACATAAAGAG 59.403 40.741 11.37 0.00 0.00 2.85
448 482 8.851145 CATGCTTCCTAGTACTACATAAAGAGA 58.149 37.037 0.00 0.00 0.00 3.10
449 483 8.818622 TGCTTCCTAGTACTACATAAAGAGAA 57.181 34.615 0.00 0.00 0.00 2.87
450 484 8.904834 TGCTTCCTAGTACTACATAAAGAGAAG 58.095 37.037 0.00 6.70 0.00 2.85
451 485 8.354426 GCTTCCTAGTACTACATAAAGAGAAGG 58.646 40.741 0.00 0.00 0.00 3.46
455 489 9.005777 CCTAGTACTACATAAAGAGAAGGCTAG 57.994 40.741 0.00 0.00 0.00 3.42
490 544 6.930731 TGCACACACATATCTACTTTAGTCA 58.069 36.000 0.00 0.00 0.00 3.41
495 549 8.679100 ACACACATATCTACTTTAGTCACTCTC 58.321 37.037 0.00 0.00 0.00 3.20
593 1070 3.627577 CGTCCCTGGTGATTAATGAAAGG 59.372 47.826 0.00 0.00 0.00 3.11
742 1936 5.174395 GCATCTATCAGTTGGCTAGGTATG 58.826 45.833 0.00 0.00 0.00 2.39
743 1937 5.047021 GCATCTATCAGTTGGCTAGGTATGA 60.047 44.000 0.00 0.00 0.00 2.15
950 2366 2.111043 ACAAGCACCACTCCACCG 59.889 61.111 0.00 0.00 0.00 4.94
978 2395 2.353208 GAACAGAACTCTGGTGCTCGAT 60.353 50.000 11.31 0.00 45.35 3.59
1119 2536 1.933021 AGGGATACACCGTCAAGACA 58.067 50.000 0.72 0.00 40.11 3.41
1171 2588 1.598430 GCTCTCTATTCGGACGACTGC 60.598 57.143 0.00 0.00 0.00 4.40
1177 2594 0.892755 ATTCGGACGACTGCCTGTTA 59.107 50.000 0.00 0.00 0.00 2.41
1217 2634 0.882042 CTGAGCTGACAGGCACGTTT 60.882 55.000 4.26 0.00 34.64 3.60
1270 5587 0.914417 TCACCCCCATCTCAAGGACC 60.914 60.000 0.00 0.00 0.00 4.46
1281 5598 2.670934 AAGGACCTGCAAGCGCTG 60.671 61.111 12.58 6.58 39.64 5.18
1371 5688 3.573772 CTGTGCCTTCCTCGTCGCA 62.574 63.158 0.00 0.00 0.00 5.10
1377 5694 3.708220 CTTCCTCGTCGCAGCTCCC 62.708 68.421 0.00 0.00 0.00 4.30
1431 8094 3.118038 AGCCTGACCAAAACACTCTGTAA 60.118 43.478 0.00 0.00 0.00 2.41
1449 8112 8.552296 ACTCTGTAATAGGGTCAGATTTGATTT 58.448 33.333 0.00 0.00 33.91 2.17
1513 8182 0.901124 AAGAAGTGATCGAGCTGGCT 59.099 50.000 0.90 0.00 0.00 4.75
1526 8195 4.680237 TGGCTGTCAGCGGAACCG 62.680 66.667 18.44 9.00 43.62 4.44
1600 8269 2.348104 ATCGTCAGTGGCGGCTGTA 61.348 57.895 18.43 0.00 37.70 2.74
1741 8627 7.654568 AGTAGTTCCGTTCCCTTTAAATTTTG 58.345 34.615 0.00 0.00 0.00 2.44
1742 8628 5.849510 AGTTCCGTTCCCTTTAAATTTTGG 58.150 37.500 0.00 0.00 0.00 3.28
1743 8629 4.875561 TCCGTTCCCTTTAAATTTTGGG 57.124 40.909 14.04 14.04 40.95 4.12
1745 8631 5.088026 TCCGTTCCCTTTAAATTTTGGGAT 58.912 37.500 20.00 0.00 46.80 3.85
1746 8632 5.544562 TCCGTTCCCTTTAAATTTTGGGATT 59.455 36.000 20.00 0.00 46.80 3.01
1747 8633 5.641636 CCGTTCCCTTTAAATTTTGGGATTG 59.358 40.000 20.00 16.15 46.80 2.67
1748 8634 5.121611 CGTTCCCTTTAAATTTTGGGATTGC 59.878 40.000 20.00 14.42 46.80 3.56
1749 8635 6.237901 GTTCCCTTTAAATTTTGGGATTGCT 58.762 36.000 20.00 0.00 46.80 3.91
1750 8636 7.390823 GTTCCCTTTAAATTTTGGGATTGCTA 58.609 34.615 20.00 8.20 46.80 3.49
1751 8637 7.560796 TCCCTTTAAATTTTGGGATTGCTAA 57.439 32.000 17.17 0.84 43.20 3.09
1752 8638 7.978925 TCCCTTTAAATTTTGGGATTGCTAAA 58.021 30.769 17.17 0.49 43.20 1.85
1753 8639 8.610369 TCCCTTTAAATTTTGGGATTGCTAAAT 58.390 29.630 17.17 0.00 43.20 1.40
1754 8640 8.892723 CCCTTTAAATTTTGGGATTGCTAAATC 58.107 33.333 14.72 0.00 42.11 2.17
1755 8641 9.671279 CCTTTAAATTTTGGGATTGCTAAATCT 57.329 29.630 0.00 0.00 41.74 2.40
1762 8648 4.922206 TGGGATTGCTAAATCTCAGTTGT 58.078 39.130 0.00 0.00 46.30 3.32
1763 8649 4.943705 TGGGATTGCTAAATCTCAGTTGTC 59.056 41.667 0.00 0.00 46.30 3.18
1764 8650 5.189180 GGGATTGCTAAATCTCAGTTGTCT 58.811 41.667 0.00 0.00 42.13 3.41
1765 8651 5.065731 GGGATTGCTAAATCTCAGTTGTCTG 59.934 44.000 0.00 0.00 42.13 3.51
1766 8652 5.877012 GGATTGCTAAATCTCAGTTGTCTGA 59.123 40.000 0.00 0.00 46.29 3.27
1779 8665 7.548196 TCAGTTGTCTGAAAATTAACGAAGT 57.452 32.000 0.00 0.00 45.92 3.01
1780 8666 7.627340 TCAGTTGTCTGAAAATTAACGAAGTC 58.373 34.615 0.00 0.00 44.16 3.01
1781 8667 7.494625 TCAGTTGTCTGAAAATTAACGAAGTCT 59.505 33.333 0.00 0.00 44.16 3.24
1782 8668 7.794349 CAGTTGTCTGAAAATTAACGAAGTCTC 59.206 37.037 0.00 0.00 42.08 3.36
1783 8669 7.494625 AGTTGTCTGAAAATTAACGAAGTCTCA 59.505 33.333 0.00 0.00 45.00 3.27
1784 8670 7.408132 TGTCTGAAAATTAACGAAGTCTCAG 57.592 36.000 0.00 0.00 45.00 3.35
1785 8671 6.984474 TGTCTGAAAATTAACGAAGTCTCAGT 59.016 34.615 0.00 0.00 45.00 3.41
1786 8672 7.169308 TGTCTGAAAATTAACGAAGTCTCAGTC 59.831 37.037 0.00 0.00 45.00 3.51
1787 8673 6.362551 TCTGAAAATTAACGAAGTCTCAGTCG 59.637 38.462 0.00 0.00 45.00 4.18
1788 8674 6.210796 TGAAAATTAACGAAGTCTCAGTCGA 58.789 36.000 0.00 0.00 45.00 4.20
1789 8675 6.866770 TGAAAATTAACGAAGTCTCAGTCGAT 59.133 34.615 0.00 0.00 45.00 3.59
1790 8676 6.633668 AAATTAACGAAGTCTCAGTCGATG 57.366 37.500 0.00 0.00 45.00 3.84
1791 8677 1.983972 AACGAAGTCTCAGTCGATGC 58.016 50.000 0.00 0.00 45.00 3.91
1792 8678 1.169577 ACGAAGTCTCAGTCGATGCT 58.830 50.000 0.00 0.00 29.74 3.79
1793 8679 2.357075 ACGAAGTCTCAGTCGATGCTA 58.643 47.619 0.00 0.00 29.74 3.49
1794 8680 2.946329 ACGAAGTCTCAGTCGATGCTAT 59.054 45.455 0.00 0.00 29.74 2.97
1795 8681 4.127907 ACGAAGTCTCAGTCGATGCTATA 58.872 43.478 0.00 0.00 29.74 1.31
1796 8682 4.757657 ACGAAGTCTCAGTCGATGCTATAT 59.242 41.667 0.00 0.00 29.74 0.86
1797 8683 5.239744 ACGAAGTCTCAGTCGATGCTATATT 59.760 40.000 0.00 0.00 29.74 1.28
1798 8684 5.792962 CGAAGTCTCAGTCGATGCTATATTC 59.207 44.000 0.00 0.00 39.64 1.75
1799 8685 5.289917 AGTCTCAGTCGATGCTATATTCG 57.710 43.478 0.00 0.00 36.72 3.34
1800 8686 4.757657 AGTCTCAGTCGATGCTATATTCGT 59.242 41.667 0.00 0.00 36.74 3.85
1801 8687 5.239744 AGTCTCAGTCGATGCTATATTCGTT 59.760 40.000 0.00 0.00 36.74 3.85
1802 8688 6.427242 AGTCTCAGTCGATGCTATATTCGTTA 59.573 38.462 0.00 0.00 36.74 3.18
1803 8689 6.739100 GTCTCAGTCGATGCTATATTCGTTAG 59.261 42.308 0.00 0.00 36.74 2.34
1804 8690 6.649557 TCTCAGTCGATGCTATATTCGTTAGA 59.350 38.462 0.00 0.00 36.74 2.10
1805 8691 7.334671 TCTCAGTCGATGCTATATTCGTTAGAT 59.665 37.037 0.00 0.00 36.74 1.98
1806 8692 7.465173 TCAGTCGATGCTATATTCGTTAGATC 58.535 38.462 0.00 0.00 36.74 2.75
1807 8693 7.334671 TCAGTCGATGCTATATTCGTTAGATCT 59.665 37.037 0.00 0.00 36.74 2.75
1808 8694 7.965655 CAGTCGATGCTATATTCGTTAGATCTT 59.034 37.037 0.00 0.00 36.74 2.40
1809 8695 9.163899 AGTCGATGCTATATTCGTTAGATCTTA 57.836 33.333 0.00 0.00 36.74 2.10
1810 8696 9.212687 GTCGATGCTATATTCGTTAGATCTTAC 57.787 37.037 0.00 0.00 36.74 2.34
1811 8697 8.114905 TCGATGCTATATTCGTTAGATCTTACG 58.885 37.037 24.39 24.39 39.03 3.18
1812 8698 7.903946 CGATGCTATATTCGTTAGATCTTACGT 59.096 37.037 27.64 15.83 38.79 3.57
1813 8699 8.897457 ATGCTATATTCGTTAGATCTTACGTG 57.103 34.615 27.64 15.43 38.79 4.49
1814 8700 7.868775 TGCTATATTCGTTAGATCTTACGTGT 58.131 34.615 27.64 20.56 38.79 4.49
1815 8701 8.992073 TGCTATATTCGTTAGATCTTACGTGTA 58.008 33.333 27.64 21.68 38.79 2.90
1816 8702 9.475505 GCTATATTCGTTAGATCTTACGTGTAG 57.524 37.037 27.64 21.58 38.79 2.74
1820 8706 6.536731 TCGTTAGATCTTACGTGTAGATCC 57.463 41.667 27.64 16.41 39.24 3.36
1821 8707 5.176406 TCGTTAGATCTTACGTGTAGATCCG 59.824 44.000 27.64 23.09 39.24 4.18
1822 8708 5.050499 CGTTAGATCTTACGTGTAGATCCGT 60.050 44.000 26.13 17.27 39.24 4.69
1823 8709 4.815040 AGATCTTACGTGTAGATCCGTG 57.185 45.455 26.13 0.00 39.24 4.94
1824 8710 4.197750 AGATCTTACGTGTAGATCCGTGT 58.802 43.478 26.13 13.57 39.24 4.49
1825 8711 5.363101 AGATCTTACGTGTAGATCCGTGTA 58.637 41.667 26.13 0.00 39.24 2.90
1826 8712 5.819379 AGATCTTACGTGTAGATCCGTGTAA 59.181 40.000 26.13 0.00 39.24 2.41
1827 8713 5.878332 TCTTACGTGTAGATCCGTGTAAA 57.122 39.130 0.00 0.00 37.91 2.01
1828 8714 6.252967 TCTTACGTGTAGATCCGTGTAAAA 57.747 37.500 0.00 0.00 37.91 1.52
1829 8715 6.855836 TCTTACGTGTAGATCCGTGTAAAAT 58.144 36.000 0.00 0.00 37.91 1.82
1830 8716 7.315142 TCTTACGTGTAGATCCGTGTAAAATT 58.685 34.615 0.00 0.00 37.91 1.82
1831 8717 7.814107 TCTTACGTGTAGATCCGTGTAAAATTT 59.186 33.333 0.00 0.00 37.91 1.82
1832 8718 6.790285 ACGTGTAGATCCGTGTAAAATTTT 57.210 33.333 8.75 8.75 35.69 1.82
1833 8719 6.824557 ACGTGTAGATCCGTGTAAAATTTTC 58.175 36.000 6.72 0.37 35.69 2.29
1834 8720 6.647895 ACGTGTAGATCCGTGTAAAATTTTCT 59.352 34.615 6.72 0.00 35.69 2.52
1835 8721 7.172019 ACGTGTAGATCCGTGTAAAATTTTCTT 59.828 33.333 6.72 0.00 35.69 2.52
1836 8722 8.013378 CGTGTAGATCCGTGTAAAATTTTCTTT 58.987 33.333 6.72 0.00 0.00 2.52
1837 8723 9.673454 GTGTAGATCCGTGTAAAATTTTCTTTT 57.327 29.630 6.72 0.00 0.00 2.27
1880 8766 9.942850 TCTATATGTTTTGTCATTTGACTGAGA 57.057 29.630 11.67 0.00 44.99 3.27
1881 8767 9.979270 CTATATGTTTTGTCATTTGACTGAGAC 57.021 33.333 11.67 6.76 44.99 3.36
1882 8768 6.949352 ATGTTTTGTCATTTGACTGAGACT 57.051 33.333 11.67 0.00 44.99 3.24
1883 8769 6.757897 TGTTTTGTCATTTGACTGAGACTT 57.242 33.333 11.67 0.00 44.99 3.01
1884 8770 6.785191 TGTTTTGTCATTTGACTGAGACTTC 58.215 36.000 11.67 0.00 44.99 3.01
1885 8771 5.657470 TTTGTCATTTGACTGAGACTTCG 57.343 39.130 11.67 0.00 44.99 3.79
1886 8772 4.322080 TGTCATTTGACTGAGACTTCGT 57.678 40.909 11.67 0.00 44.99 3.85
1887 8773 4.693283 TGTCATTTGACTGAGACTTCGTT 58.307 39.130 11.67 0.00 44.99 3.85
1888 8774 5.838529 TGTCATTTGACTGAGACTTCGTTA 58.161 37.500 11.67 0.00 44.99 3.18
1889 8775 6.277605 TGTCATTTGACTGAGACTTCGTTAA 58.722 36.000 11.67 0.00 44.99 2.01
1890 8776 6.420903 TGTCATTTGACTGAGACTTCGTTAAG 59.579 38.462 11.67 0.00 44.99 1.85
1891 8777 6.421202 GTCATTTGACTGAGACTTCGTTAAGT 59.579 38.462 3.45 0.00 43.76 2.24
1904 8790 7.976135 ACTTCGTTAAGTCTCAGTCTACTAA 57.024 36.000 0.00 0.00 42.42 2.24
1905 8791 8.031848 ACTTCGTTAAGTCTCAGTCTACTAAG 57.968 38.462 0.00 0.00 42.42 2.18
1906 8792 7.877097 ACTTCGTTAAGTCTCAGTCTACTAAGA 59.123 37.037 0.00 0.00 42.42 2.10
1907 8793 8.789825 TTCGTTAAGTCTCAGTCTACTAAGAT 57.210 34.615 0.00 0.00 33.30 2.40
1908 8794 8.422973 TCGTTAAGTCTCAGTCTACTAAGATC 57.577 38.462 0.00 0.00 33.30 2.75
1909 8795 8.259411 TCGTTAAGTCTCAGTCTACTAAGATCT 58.741 37.037 0.00 0.00 33.30 2.75
1910 8796 9.531942 CGTTAAGTCTCAGTCTACTAAGATCTA 57.468 37.037 0.00 0.00 33.30 1.98
1914 8800 8.313944 AGTCTCAGTCTACTAAGATCTAGTCA 57.686 38.462 0.00 0.00 33.30 3.41
1915 8801 8.202137 AGTCTCAGTCTACTAAGATCTAGTCAC 58.798 40.741 0.00 1.90 33.30 3.67
1916 8802 7.982919 GTCTCAGTCTACTAAGATCTAGTCACA 59.017 40.741 0.00 0.00 33.30 3.58
1917 8803 7.982919 TCTCAGTCTACTAAGATCTAGTCACAC 59.017 40.741 0.00 0.00 33.30 3.82
1918 8804 7.049133 TCAGTCTACTAAGATCTAGTCACACC 58.951 42.308 0.00 0.00 33.30 4.16
1919 8805 6.261381 CAGTCTACTAAGATCTAGTCACACCC 59.739 46.154 0.00 0.00 33.30 4.61
1920 8806 6.069556 AGTCTACTAAGATCTAGTCACACCCA 60.070 42.308 0.00 0.00 33.30 4.51
1921 8807 6.602406 GTCTACTAAGATCTAGTCACACCCAA 59.398 42.308 0.00 0.00 33.30 4.12
1922 8808 5.662674 ACTAAGATCTAGTCACACCCAAC 57.337 43.478 0.00 0.00 0.00 3.77
1923 8809 5.334421 ACTAAGATCTAGTCACACCCAACT 58.666 41.667 0.00 0.00 0.00 3.16
1924 8810 5.780793 ACTAAGATCTAGTCACACCCAACTT 59.219 40.000 0.00 0.00 0.00 2.66
1925 8811 4.810191 AGATCTAGTCACACCCAACTTC 57.190 45.455 0.00 0.00 0.00 3.01
1926 8812 4.421131 AGATCTAGTCACACCCAACTTCT 58.579 43.478 0.00 0.00 0.00 2.85
1927 8813 5.580998 AGATCTAGTCACACCCAACTTCTA 58.419 41.667 0.00 0.00 0.00 2.10
1928 8814 6.017192 AGATCTAGTCACACCCAACTTCTAA 58.983 40.000 0.00 0.00 0.00 2.10
1929 8815 6.670027 AGATCTAGTCACACCCAACTTCTAAT 59.330 38.462 0.00 0.00 0.00 1.73
1930 8816 6.681729 TCTAGTCACACCCAACTTCTAATT 57.318 37.500 0.00 0.00 0.00 1.40
1939 8825 4.014406 CCCAACTTCTAATTTTAGGGCGT 58.986 43.478 0.00 0.00 0.00 5.68
1944 8830 6.046290 ACTTCTAATTTTAGGGCGTGTAGT 57.954 37.500 0.00 0.00 0.00 2.73
1948 8834 8.428186 TTCTAATTTTAGGGCGTGTAGTAATG 57.572 34.615 0.00 0.00 0.00 1.90
1950 8836 6.673154 AATTTTAGGGCGTGTAGTAATGTC 57.327 37.500 0.00 0.00 0.00 3.06
1951 8837 4.804868 TTTAGGGCGTGTAGTAATGTCA 57.195 40.909 0.00 0.00 0.00 3.58
1952 8838 2.961526 AGGGCGTGTAGTAATGTCAG 57.038 50.000 0.00 0.00 0.00 3.51
1953 8839 2.176889 AGGGCGTGTAGTAATGTCAGT 58.823 47.619 0.00 0.00 0.00 3.41
1954 8840 2.094182 AGGGCGTGTAGTAATGTCAGTG 60.094 50.000 0.00 0.00 0.00 3.66
1957 8855 3.314553 GCGTGTAGTAATGTCAGTGTGT 58.685 45.455 0.00 0.00 0.00 3.72
2071 9057 1.969589 CTTGTTACGGTGTGCCCCC 60.970 63.158 0.00 0.00 0.00 5.40
2123 9109 4.704833 CCACACCAGCGTCCCCAG 62.705 72.222 0.00 0.00 0.00 4.45
2176 9162 2.485426 ACCAAGTCAAGATGCAACGATG 59.515 45.455 0.00 0.00 0.00 3.84
2246 9258 5.689514 GTGAATGATTATCTCAGGTGACGAG 59.310 44.000 0.00 0.00 37.28 4.18
2311 9323 1.758440 ATCCCGATGGTCCATGTCCG 61.758 60.000 9.76 6.78 0.00 4.79
2383 9401 3.269178 GAAGATATATCTGCAGCTGCCC 58.731 50.000 34.64 10.46 41.18 5.36
2384 9402 2.549082 AGATATATCTGCAGCTGCCCT 58.451 47.619 34.64 21.03 41.18 5.19
2386 9404 0.689055 TATATCTGCAGCTGCCCTGG 59.311 55.000 34.64 21.14 42.03 4.45
2423 9441 0.978146 GGAGCTAGCCACCTTCCTGA 60.978 60.000 12.13 0.00 0.00 3.86
2510 9539 1.162698 AGTTCCGACGTTCTCGATCA 58.837 50.000 0.00 0.00 46.14 2.92
2519 9559 4.290969 GACGTTCTCGATCATGAATAGCA 58.709 43.478 0.00 0.00 40.62 3.49
2740 9780 1.144691 TGGTTGGATGTCTGGAACCA 58.855 50.000 0.00 0.00 44.40 3.67
2929 9973 2.028420 TGATCAAGAGATGGCCGTTG 57.972 50.000 0.00 0.00 33.72 4.10
2944 9988 0.041312 CGTTGTTCCTGTTTCTGCCG 60.041 55.000 0.00 0.00 0.00 5.69
3004 10048 9.567776 TGACTATTTTCCTTCTTTTGTGTATCA 57.432 29.630 0.00 0.00 0.00 2.15
3048 10092 9.897744 AGCGATTGATAAATTTGTAATGTATGG 57.102 29.630 0.00 0.00 0.00 2.74
3049 10093 9.891828 GCGATTGATAAATTTGTAATGTATGGA 57.108 29.630 0.00 0.00 0.00 3.41
3059 10550 9.474313 AATTTGTAATGTATGGATACTTGGTGT 57.526 29.630 0.00 0.00 34.41 4.16
3062 10553 7.204604 TGTAATGTATGGATACTTGGTGTACG 58.795 38.462 0.00 0.00 33.45 3.67
3126 10617 6.454715 CGGATGATGCGTGTTCTTGATATATG 60.455 42.308 0.00 0.00 0.00 1.78
3144 10635 0.322456 TGCATGGGTTGTAGCTGGTC 60.322 55.000 0.00 0.00 0.00 4.02
3145 10636 1.369091 GCATGGGTTGTAGCTGGTCG 61.369 60.000 0.00 0.00 0.00 4.79
3232 10723 6.804534 TTCAGTTCAAACTAAACATTTGCG 57.195 33.333 0.00 0.00 37.08 4.85
3270 10761 2.049433 ACCAACTTCGTCGGAGCG 60.049 61.111 0.00 0.00 0.00 5.03
3274 10765 3.493830 AACTTCGTCGGAGCGTGCA 62.494 57.895 0.00 0.00 0.00 4.57
3377 10868 1.337260 CCGTGTCCAAAGAGAGACCTG 60.337 57.143 0.00 0.00 31.76 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.747852 GGAACCCTCTCATCGTCCTC 59.252 60.000 0.00 0.00 0.00 3.71
1 2 1.038130 CGGAACCCTCTCATCGTCCT 61.038 60.000 0.00 0.00 0.00 3.85
2 3 1.437986 CGGAACCCTCTCATCGTCC 59.562 63.158 0.00 0.00 0.00 4.79
19 20 3.138304 TCCACAACAAAGAACAGATCCG 58.862 45.455 0.00 0.00 0.00 4.18
27 28 2.806745 CGAGCTCCTCCACAACAAAGAA 60.807 50.000 8.47 0.00 0.00 2.52
31 32 1.301716 GCGAGCTCCTCCACAACAA 60.302 57.895 8.47 0.00 0.00 2.83
45 46 3.610669 CCTCCATCCTCCGGCGAG 61.611 72.222 9.30 3.68 35.72 5.03
47 48 3.917760 GACCTCCATCCTCCGGCG 61.918 72.222 0.00 0.00 0.00 6.46
53 54 2.060980 GCCACTCGACCTCCATCCT 61.061 63.158 0.00 0.00 0.00 3.24
57 58 4.988716 ACCGCCACTCGACCTCCA 62.989 66.667 0.00 0.00 41.67 3.86
96 97 1.187974 TTTCTGCAATGCCTCCCATG 58.812 50.000 1.53 0.00 33.49 3.66
98 99 1.187974 CATTTCTGCAATGCCTCCCA 58.812 50.000 1.53 0.00 36.05 4.37
100 101 3.193267 TGTTACATTTCTGCAATGCCTCC 59.807 43.478 1.53 0.00 45.74 4.30
106 107 7.665690 TGGTACAAATGTTACATTTCTGCAAT 58.334 30.769 19.05 5.29 31.92 3.56
141 142 9.591792 TGAAGATGCATAGTGCTAATGTATATC 57.408 33.333 0.00 0.00 45.31 1.63
311 317 3.327464 TGATGATGGCCCGATGATAAAGA 59.673 43.478 0.00 0.00 0.00 2.52
355 362 4.668289 CACAAAGTAAGTTTTCGTTGGCT 58.332 39.130 9.62 0.00 0.00 4.75
426 460 8.354426 GCCTTCTCTTTATGTAGTACTAGGAAG 58.646 40.741 1.87 7.37 0.00 3.46
436 470 8.447833 CGATAGTCTAGCCTTCTCTTTATGTAG 58.552 40.741 0.00 0.00 0.00 2.74
437 471 7.390996 CCGATAGTCTAGCCTTCTCTTTATGTA 59.609 40.741 0.00 0.00 0.00 2.29
438 472 6.207810 CCGATAGTCTAGCCTTCTCTTTATGT 59.792 42.308 0.00 0.00 0.00 2.29
439 473 6.616947 CCGATAGTCTAGCCTTCTCTTTATG 58.383 44.000 0.00 0.00 0.00 1.90
440 474 5.184287 GCCGATAGTCTAGCCTTCTCTTTAT 59.816 44.000 0.00 0.00 0.00 1.40
441 475 4.519730 GCCGATAGTCTAGCCTTCTCTTTA 59.480 45.833 0.00 0.00 0.00 1.85
442 476 3.319689 GCCGATAGTCTAGCCTTCTCTTT 59.680 47.826 0.00 0.00 0.00 2.52
443 477 2.888414 GCCGATAGTCTAGCCTTCTCTT 59.112 50.000 0.00 0.00 0.00 2.85
444 478 2.158593 TGCCGATAGTCTAGCCTTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
445 479 2.231529 TGCCGATAGTCTAGCCTTCTC 58.768 52.381 0.00 0.00 0.00 2.87
446 480 2.366640 TGCCGATAGTCTAGCCTTCT 57.633 50.000 0.00 0.00 0.00 2.85
447 481 2.928731 GCATGCCGATAGTCTAGCCTTC 60.929 54.545 6.36 0.00 0.00 3.46
448 482 1.001406 GCATGCCGATAGTCTAGCCTT 59.999 52.381 6.36 0.00 0.00 4.35
449 483 0.605589 GCATGCCGATAGTCTAGCCT 59.394 55.000 6.36 0.00 0.00 4.58
450 484 0.318441 TGCATGCCGATAGTCTAGCC 59.682 55.000 16.68 0.00 0.00 3.93
451 485 1.269778 TGTGCATGCCGATAGTCTAGC 60.270 52.381 16.68 0.00 0.00 3.42
455 489 0.652592 GTGTGTGCATGCCGATAGTC 59.347 55.000 16.68 0.00 0.00 2.59
490 544 3.458189 CTGTTGTCGGTTTTCAGAGAGT 58.542 45.455 0.00 0.00 0.00 3.24
495 549 4.036262 TGAAATCCTGTTGTCGGTTTTCAG 59.964 41.667 9.88 0.00 41.62 3.02
543 1009 7.712639 TGTGATGAAAGGAGCACTTATAGAATC 59.287 37.037 0.00 0.00 38.85 2.52
545 1011 6.946340 TGTGATGAAAGGAGCACTTATAGAA 58.054 36.000 0.00 0.00 38.85 2.10
593 1070 5.163923 GGCAGGTTAGTTTATCACGTTGTAC 60.164 44.000 0.00 0.00 0.00 2.90
726 1918 5.604231 AGATTGATCATACCTAGCCAACTGA 59.396 40.000 0.00 0.00 0.00 3.41
756 1950 9.476202 GTTAGATGCTTTCCAACTTGTATTTTT 57.524 29.630 0.00 0.00 0.00 1.94
950 2366 0.390472 CAGAGTTCTGTTCCTCGGCC 60.390 60.000 0.00 0.00 39.09 6.13
953 2369 1.937108 GCACCAGAGTTCTGTTCCTCG 60.937 57.143 8.23 0.00 42.27 4.63
978 2395 3.003173 CCGGCTGGAGGTGGAGAA 61.003 66.667 5.28 0.00 37.49 2.87
1171 2588 6.930667 TCATCACATTCACATCATAACAGG 57.069 37.500 0.00 0.00 0.00 4.00
1177 2594 6.412214 TCAGAGTTCATCACATTCACATCAT 58.588 36.000 0.00 0.00 0.00 2.45
1281 5598 1.563577 GGAAGACCTCCAAGGGACCC 61.564 65.000 0.59 0.59 44.67 4.46
1355 5672 2.811317 CTGCGACGAGGAAGGCAC 60.811 66.667 0.00 0.00 0.00 5.01
1371 5688 0.036010 CGTTGAGGTTCATGGGAGCT 60.036 55.000 0.00 0.00 0.00 4.09
1377 5694 2.084610 TCTCTGCGTTGAGGTTCATG 57.915 50.000 6.90 0.00 34.98 3.07
1418 5735 6.681729 TCTGACCCTATTACAGAGTGTTTT 57.318 37.500 0.00 0.00 36.04 2.43
1431 8094 8.434589 TTTTCCAAAATCAAATCTGACCCTAT 57.565 30.769 0.00 0.00 33.30 2.57
1473 8142 9.941325 CTTCTTTCTGCCATGAGATATATAACT 57.059 33.333 0.00 0.00 0.00 2.24
1476 8145 9.093458 TCACTTCTTTCTGCCATGAGATATATA 57.907 33.333 0.00 0.00 0.00 0.86
1477 8146 7.971201 TCACTTCTTTCTGCCATGAGATATAT 58.029 34.615 0.00 0.00 0.00 0.86
1513 8182 0.940519 CGTTAACGGTTCCGCTGACA 60.941 55.000 20.24 0.00 35.37 3.58
1526 8195 2.027214 CGCACGACCTCATTACGTTAAC 59.973 50.000 0.00 0.00 38.18 2.01
1639 8308 1.739049 GCTCCAGGACTCCTCATCG 59.261 63.158 0.00 0.00 0.00 3.84
1720 8606 4.992319 CCCAAAATTTAAAGGGAACGGAAC 59.008 41.667 14.94 0.00 44.30 3.62
1734 8620 7.910584 ACTGAGATTTAGCAATCCCAAAATTT 58.089 30.769 0.00 0.00 39.95 1.82
1741 8627 5.065731 CAGACAACTGAGATTTAGCAATCCC 59.934 44.000 0.00 0.00 46.03 3.85
1742 8628 5.877012 TCAGACAACTGAGATTTAGCAATCC 59.123 40.000 0.00 0.00 46.55 3.01
1743 8629 6.974932 TCAGACAACTGAGATTTAGCAATC 57.025 37.500 0.00 0.00 46.55 2.67
1756 8642 7.630924 AGACTTCGTTAATTTTCAGACAACTG 58.369 34.615 0.00 0.00 44.66 3.16
1757 8643 7.494625 TGAGACTTCGTTAATTTTCAGACAACT 59.505 33.333 0.00 0.00 0.00 3.16
1758 8644 7.627340 TGAGACTTCGTTAATTTTCAGACAAC 58.373 34.615 0.00 0.00 0.00 3.32
1759 8645 7.494625 ACTGAGACTTCGTTAATTTTCAGACAA 59.505 33.333 5.29 0.00 35.84 3.18
1760 8646 6.984474 ACTGAGACTTCGTTAATTTTCAGACA 59.016 34.615 5.29 0.00 35.84 3.41
1761 8647 7.409465 ACTGAGACTTCGTTAATTTTCAGAC 57.591 36.000 5.29 0.00 35.84 3.51
1762 8648 6.362551 CGACTGAGACTTCGTTAATTTTCAGA 59.637 38.462 5.29 0.00 35.84 3.27
1763 8649 6.362551 TCGACTGAGACTTCGTTAATTTTCAG 59.637 38.462 0.00 0.00 36.60 3.02
1764 8650 6.210796 TCGACTGAGACTTCGTTAATTTTCA 58.789 36.000 0.00 0.00 36.60 2.69
1765 8651 6.686130 TCGACTGAGACTTCGTTAATTTTC 57.314 37.500 0.00 0.00 36.60 2.29
1766 8652 6.401153 GCATCGACTGAGACTTCGTTAATTTT 60.401 38.462 0.00 0.00 36.60 1.82
1767 8653 5.062308 GCATCGACTGAGACTTCGTTAATTT 59.938 40.000 0.00 0.00 36.60 1.82
1768 8654 4.563184 GCATCGACTGAGACTTCGTTAATT 59.437 41.667 0.00 0.00 36.60 1.40
1769 8655 4.106197 GCATCGACTGAGACTTCGTTAAT 58.894 43.478 0.00 0.00 36.60 1.40
1770 8656 3.190744 AGCATCGACTGAGACTTCGTTAA 59.809 43.478 0.00 0.00 36.60 2.01
1771 8657 2.747989 AGCATCGACTGAGACTTCGTTA 59.252 45.455 0.00 0.00 36.60 3.18
1772 8658 1.542030 AGCATCGACTGAGACTTCGTT 59.458 47.619 0.00 0.00 36.60 3.85
1773 8659 1.169577 AGCATCGACTGAGACTTCGT 58.830 50.000 0.00 0.00 36.60 3.85
1774 8660 3.617540 ATAGCATCGACTGAGACTTCG 57.382 47.619 0.00 0.00 36.55 3.79
1775 8661 5.792962 CGAATATAGCATCGACTGAGACTTC 59.207 44.000 0.00 0.00 41.43 3.01
1776 8662 5.239744 ACGAATATAGCATCGACTGAGACTT 59.760 40.000 11.05 0.00 41.43 3.01
1777 8663 4.757657 ACGAATATAGCATCGACTGAGACT 59.242 41.667 11.05 0.00 41.43 3.24
1778 8664 5.037015 ACGAATATAGCATCGACTGAGAC 57.963 43.478 11.05 0.00 41.43 3.36
1779 8665 5.690997 AACGAATATAGCATCGACTGAGA 57.309 39.130 11.05 0.00 41.43 3.27
1780 8666 6.832804 TCTAACGAATATAGCATCGACTGAG 58.167 40.000 11.05 4.45 41.43 3.35
1781 8667 6.796705 TCTAACGAATATAGCATCGACTGA 57.203 37.500 11.05 4.62 41.43 3.41
1782 8668 7.468441 AGATCTAACGAATATAGCATCGACTG 58.532 38.462 11.05 0.00 41.43 3.51
1783 8669 7.618502 AGATCTAACGAATATAGCATCGACT 57.381 36.000 11.05 0.00 41.43 4.18
1784 8670 9.212687 GTAAGATCTAACGAATATAGCATCGAC 57.787 37.037 11.05 0.00 41.43 4.20
1785 8671 8.114905 CGTAAGATCTAACGAATATAGCATCGA 58.885 37.037 11.05 0.00 41.55 3.59
1786 8672 7.903946 ACGTAAGATCTAACGAATATAGCATCG 59.096 37.037 0.00 4.40 41.55 3.84
1787 8673 9.001049 CACGTAAGATCTAACGAATATAGCATC 57.999 37.037 0.00 0.00 41.55 3.91
1788 8674 8.512956 ACACGTAAGATCTAACGAATATAGCAT 58.487 33.333 0.00 0.00 41.55 3.79
1789 8675 7.868775 ACACGTAAGATCTAACGAATATAGCA 58.131 34.615 0.00 0.00 41.55 3.49
1790 8676 9.475505 CTACACGTAAGATCTAACGAATATAGC 57.524 37.037 0.00 0.00 41.55 2.97
1794 8680 8.715998 GGATCTACACGTAAGATCTAACGAATA 58.284 37.037 26.69 0.00 41.55 1.75
1795 8681 7.570875 CGGATCTACACGTAAGATCTAACGAAT 60.571 40.741 26.69 3.11 41.55 3.34
1796 8682 6.292542 CGGATCTACACGTAAGATCTAACGAA 60.293 42.308 26.69 0.00 41.55 3.85
1797 8683 5.176406 CGGATCTACACGTAAGATCTAACGA 59.824 44.000 26.69 1.44 41.55 3.85
1798 8684 5.050499 ACGGATCTACACGTAAGATCTAACG 60.050 44.000 26.69 24.06 42.15 3.18
1799 8685 6.134730 CACGGATCTACACGTAAGATCTAAC 58.865 44.000 26.69 16.18 42.04 2.34
1800 8686 5.819379 ACACGGATCTACACGTAAGATCTAA 59.181 40.000 26.69 0.70 42.04 2.10
1801 8687 5.363101 ACACGGATCTACACGTAAGATCTA 58.637 41.667 26.69 0.99 42.04 1.98
1802 8688 4.197750 ACACGGATCTACACGTAAGATCT 58.802 43.478 26.69 14.03 42.04 2.75
1803 8689 4.548991 ACACGGATCTACACGTAAGATC 57.451 45.455 22.82 22.82 42.04 2.75
1804 8690 6.441093 TTTACACGGATCTACACGTAAGAT 57.559 37.500 11.32 11.32 42.04 2.40
1805 8691 5.878332 TTTACACGGATCTACACGTAAGA 57.122 39.130 2.57 2.57 42.04 2.10
1806 8692 7.515957 AATTTTACACGGATCTACACGTAAG 57.484 36.000 0.00 0.00 42.04 2.34
1807 8693 7.887996 AAATTTTACACGGATCTACACGTAA 57.112 32.000 0.00 0.00 42.04 3.18
1808 8694 7.814107 AGAAAATTTTACACGGATCTACACGTA 59.186 33.333 2.75 0.00 42.04 3.57
1809 8695 6.647895 AGAAAATTTTACACGGATCTACACGT 59.352 34.615 2.75 0.00 45.25 4.49
1810 8696 7.057149 AGAAAATTTTACACGGATCTACACG 57.943 36.000 2.75 0.00 0.00 4.49
1811 8697 9.673454 AAAAGAAAATTTTACACGGATCTACAC 57.327 29.630 2.75 0.00 0.00 2.90
1860 8746 8.746927 ACGAAGTCTCAGTCAAATGACAAAACA 61.747 37.037 15.38 0.00 42.62 2.83
1861 8747 6.456988 ACGAAGTCTCAGTCAAATGACAAAAC 60.457 38.462 15.38 7.93 42.62 2.43
1862 8748 5.584649 ACGAAGTCTCAGTCAAATGACAAAA 59.415 36.000 15.38 0.33 42.62 2.44
1863 8749 5.116180 ACGAAGTCTCAGTCAAATGACAAA 58.884 37.500 15.38 2.61 42.62 2.83
1864 8750 4.693283 ACGAAGTCTCAGTCAAATGACAA 58.307 39.130 15.38 2.94 42.62 3.18
1865 8751 4.322080 ACGAAGTCTCAGTCAAATGACA 57.678 40.909 15.38 0.00 42.62 3.58
1866 8752 6.421202 ACTTAACGAAGTCTCAGTCAAATGAC 59.579 38.462 5.40 5.40 45.00 3.06
1867 8753 6.513180 ACTTAACGAAGTCTCAGTCAAATGA 58.487 36.000 0.00 0.00 45.00 2.57
1868 8754 6.771188 ACTTAACGAAGTCTCAGTCAAATG 57.229 37.500 0.00 0.00 45.00 2.32
1881 8767 8.254178 TCTTAGTAGACTGAGACTTAACGAAG 57.746 38.462 0.27 0.00 34.24 3.79
1882 8768 8.789825 ATCTTAGTAGACTGAGACTTAACGAA 57.210 34.615 6.33 0.00 40.68 3.85
1883 8769 8.259411 AGATCTTAGTAGACTGAGACTTAACGA 58.741 37.037 6.33 0.00 40.68 3.85
1884 8770 8.428186 AGATCTTAGTAGACTGAGACTTAACG 57.572 38.462 6.33 0.00 40.68 3.18
1888 8774 8.764558 TGACTAGATCTTAGTAGACTGAGACTT 58.235 37.037 0.00 1.71 40.68 3.01
1889 8775 8.202137 GTGACTAGATCTTAGTAGACTGAGACT 58.798 40.741 0.00 8.38 40.68 3.24
1890 8776 7.982919 TGTGACTAGATCTTAGTAGACTGAGAC 59.017 40.741 0.00 2.30 40.68 3.36
1891 8777 7.982919 GTGTGACTAGATCTTAGTAGACTGAGA 59.017 40.741 0.00 6.62 41.83 3.27
1892 8778 7.225931 GGTGTGACTAGATCTTAGTAGACTGAG 59.774 44.444 0.00 0.00 31.99 3.35
1893 8779 7.049133 GGTGTGACTAGATCTTAGTAGACTGA 58.951 42.308 0.00 0.00 31.99 3.41
1894 8780 6.261381 GGGTGTGACTAGATCTTAGTAGACTG 59.739 46.154 0.00 0.00 31.99 3.51
1895 8781 6.069556 TGGGTGTGACTAGATCTTAGTAGACT 60.070 42.308 0.00 0.00 31.99 3.24
1896 8782 6.120905 TGGGTGTGACTAGATCTTAGTAGAC 58.879 44.000 0.00 4.32 31.99 2.59
1897 8783 6.323210 TGGGTGTGACTAGATCTTAGTAGA 57.677 41.667 0.00 0.00 34.21 2.59
1898 8784 6.603997 AGTTGGGTGTGACTAGATCTTAGTAG 59.396 42.308 0.00 0.00 0.00 2.57
1899 8785 6.491383 AGTTGGGTGTGACTAGATCTTAGTA 58.509 40.000 0.00 0.00 0.00 1.82
1900 8786 5.334421 AGTTGGGTGTGACTAGATCTTAGT 58.666 41.667 0.00 2.42 0.00 2.24
1901 8787 5.923733 AGTTGGGTGTGACTAGATCTTAG 57.076 43.478 0.00 0.00 0.00 2.18
1902 8788 6.017192 AGAAGTTGGGTGTGACTAGATCTTA 58.983 40.000 0.00 0.00 0.00 2.10
1903 8789 4.841246 AGAAGTTGGGTGTGACTAGATCTT 59.159 41.667 0.00 0.00 0.00 2.40
1904 8790 4.421131 AGAAGTTGGGTGTGACTAGATCT 58.579 43.478 0.00 0.00 0.00 2.75
1905 8791 4.810191 AGAAGTTGGGTGTGACTAGATC 57.190 45.455 0.00 0.00 0.00 2.75
1906 8792 6.875972 ATTAGAAGTTGGGTGTGACTAGAT 57.124 37.500 0.00 0.00 0.00 1.98
1907 8793 6.681729 AATTAGAAGTTGGGTGTGACTAGA 57.318 37.500 0.00 0.00 0.00 2.43
1908 8794 7.745620 AAAATTAGAAGTTGGGTGTGACTAG 57.254 36.000 0.00 0.00 0.00 2.57
1909 8795 7.881232 CCTAAAATTAGAAGTTGGGTGTGACTA 59.119 37.037 1.75 0.00 32.47 2.59
1910 8796 6.715264 CCTAAAATTAGAAGTTGGGTGTGACT 59.285 38.462 1.75 0.00 32.47 3.41
1911 8797 6.072119 CCCTAAAATTAGAAGTTGGGTGTGAC 60.072 42.308 1.75 0.00 32.47 3.67
1912 8798 6.007703 CCCTAAAATTAGAAGTTGGGTGTGA 58.992 40.000 1.75 0.00 32.47 3.58
1913 8799 5.336451 GCCCTAAAATTAGAAGTTGGGTGTG 60.336 44.000 1.75 0.00 36.00 3.82
1914 8800 4.770531 GCCCTAAAATTAGAAGTTGGGTGT 59.229 41.667 1.75 0.00 36.00 4.16
1915 8801 4.142469 CGCCCTAAAATTAGAAGTTGGGTG 60.142 45.833 1.75 0.00 37.60 4.61
1916 8802 4.014406 CGCCCTAAAATTAGAAGTTGGGT 58.986 43.478 1.75 0.00 36.00 4.51
1917 8803 4.014406 ACGCCCTAAAATTAGAAGTTGGG 58.986 43.478 1.75 0.00 36.63 4.12
1918 8804 4.457949 ACACGCCCTAAAATTAGAAGTTGG 59.542 41.667 1.75 0.00 32.47 3.77
1919 8805 5.622770 ACACGCCCTAAAATTAGAAGTTG 57.377 39.130 1.75 0.00 32.47 3.16
1920 8806 6.470278 ACTACACGCCCTAAAATTAGAAGTT 58.530 36.000 1.75 0.00 32.47 2.66
1921 8807 6.046290 ACTACACGCCCTAAAATTAGAAGT 57.954 37.500 1.75 0.00 32.47 3.01
1922 8808 8.548721 CATTACTACACGCCCTAAAATTAGAAG 58.451 37.037 1.75 0.00 32.47 2.85
1923 8809 8.042515 ACATTACTACACGCCCTAAAATTAGAA 58.957 33.333 1.75 0.00 32.47 2.10
1924 8810 7.558604 ACATTACTACACGCCCTAAAATTAGA 58.441 34.615 1.75 0.00 32.47 2.10
1925 8811 7.493320 TGACATTACTACACGCCCTAAAATTAG 59.507 37.037 0.00 0.00 0.00 1.73
1926 8812 7.329499 TGACATTACTACACGCCCTAAAATTA 58.671 34.615 0.00 0.00 0.00 1.40
1927 8813 6.174760 TGACATTACTACACGCCCTAAAATT 58.825 36.000 0.00 0.00 0.00 1.82
1928 8814 5.736813 TGACATTACTACACGCCCTAAAAT 58.263 37.500 0.00 0.00 0.00 1.82
1929 8815 5.149973 TGACATTACTACACGCCCTAAAA 57.850 39.130 0.00 0.00 0.00 1.52
1930 8816 4.221262 ACTGACATTACTACACGCCCTAAA 59.779 41.667 0.00 0.00 0.00 1.85
1939 8825 4.979815 CGTCAACACACTGACATTACTACA 59.020 41.667 4.75 0.00 45.03 2.74
1944 8830 2.542178 GCACGTCAACACACTGACATTA 59.458 45.455 4.75 0.00 45.03 1.90
1948 8834 1.006832 AAGCACGTCAACACACTGAC 58.993 50.000 0.00 0.00 41.98 3.51
1950 8836 0.589729 GCAAGCACGTCAACACACTG 60.590 55.000 0.00 0.00 0.00 3.66
1951 8837 1.721487 GCAAGCACGTCAACACACT 59.279 52.632 0.00 0.00 0.00 3.55
1952 8838 1.651132 CGCAAGCACGTCAACACAC 60.651 57.895 0.00 0.00 0.00 3.82
1953 8839 2.103647 ACGCAAGCACGTCAACACA 61.104 52.632 0.00 0.00 44.43 3.72
1954 8840 1.651132 CACGCAAGCACGTCAACAC 60.651 57.895 0.00 0.00 46.34 3.32
1957 8855 3.947841 GGCACGCAAGCACGTCAA 61.948 61.111 0.00 0.00 46.34 3.18
2034 9020 2.580815 CTGATGCCGCTGTCCTGA 59.419 61.111 0.00 0.00 0.00 3.86
2071 9057 2.398554 CCTCGCCAACCGTGAATGG 61.399 63.158 0.00 0.00 39.80 3.16
2073 9059 2.746277 GCCTCGCCAACCGTGAAT 60.746 61.111 0.00 0.00 38.35 2.57
2122 9108 4.137543 CCAGTTAGCAAAGAAAGGACACT 58.862 43.478 0.00 0.00 0.00 3.55
2123 9109 3.883489 ACCAGTTAGCAAAGAAAGGACAC 59.117 43.478 0.00 0.00 0.00 3.67
2246 9258 3.541713 AGGCCGCGGATCTTCTCC 61.542 66.667 33.48 19.06 41.07 3.71
2259 9271 0.103937 CTCTCGATGAGTTCCAGGCC 59.896 60.000 0.00 0.00 37.99 5.19
2423 9441 4.388499 CTGCGGGTACTTGGCGGT 62.388 66.667 0.00 0.00 0.00 5.68
2510 9539 9.577110 CTGAAAACAAACATACATGCTATTCAT 57.423 29.630 0.00 0.00 35.31 2.57
2519 9559 5.300792 ACCGAACCTGAAAACAAACATACAT 59.699 36.000 0.00 0.00 0.00 2.29
2718 9758 2.489073 GGTTCCAGACATCCAACCAACT 60.489 50.000 0.00 0.00 38.57 3.16
2929 9973 2.556287 CGCGGCAGAAACAGGAAC 59.444 61.111 0.00 0.00 0.00 3.62
2944 9988 1.399791 CCTTTGATCTTCTCCTTGCGC 59.600 52.381 0.00 0.00 0.00 6.09
3004 10048 9.875691 TCAATCGCTAGCTATATAAATGTGAAT 57.124 29.630 13.93 0.00 0.00 2.57
3046 10090 4.932799 CACATTTCGTACACCAAGTATCCA 59.067 41.667 0.00 0.00 34.67 3.41
3048 10092 6.367969 ACTTCACATTTCGTACACCAAGTATC 59.632 38.462 0.00 0.00 34.67 2.24
3049 10093 6.228258 ACTTCACATTTCGTACACCAAGTAT 58.772 36.000 0.00 0.00 34.67 2.12
3126 10617 1.369091 CGACCAGCTACAACCCATGC 61.369 60.000 0.00 0.00 0.00 4.06
3144 10635 1.401905 GACCATGCCTTTAGCCTTTCG 59.598 52.381 0.00 0.00 42.71 3.46
3145 10636 1.751351 GGACCATGCCTTTAGCCTTTC 59.249 52.381 0.00 0.00 42.71 2.62
3270 10761 1.566018 GCTTGGGTGTAGTCGTGCAC 61.566 60.000 6.82 6.82 38.50 4.57
3274 10765 0.249741 GTGTGCTTGGGTGTAGTCGT 60.250 55.000 0.00 0.00 0.00 4.34
3307 10798 6.128035 TGACCTATCAATCAAACATGGTTTCG 60.128 38.462 0.00 0.00 0.00 3.46
3377 10868 0.515564 ATTGCTAAACCGTGTGCGAC 59.484 50.000 0.00 0.00 41.33 5.19


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

AutoCloner maintained by Alex Coulton.