Multiple sequence alignment - TraesCS7D01G482200

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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 TraesCS7D01G482200 chr7D 100.000 3911 0 0 1 3911 592631322 592635232 0.000000e+00 7223.0
1 TraesCS7D01G482200 chr7D 93.075 852 55 3 5 856 599905970 599906817 0.000000e+00 1243.0
2 TraesCS7D01G482200 chr7D 92.666 859 62 1 1 858 39581933 39581075 0.000000e+00 1236.0
3 TraesCS7D01G482200 chr7D 92.494 866 54 8 1 858 108617266 108616404 0.000000e+00 1229.0
4 TraesCS7D01G482200 chr7D 92.640 856 57 5 1 856 634181507 634180658 0.000000e+00 1227.0
5 TraesCS7D01G482200 chr7D 86.857 700 87 5 980 1675 592677373 592678071 0.000000e+00 778.0
6 TraesCS7D01G482200 chr7D 87.045 687 62 10 982 1668 592816338 592816997 0.000000e+00 750.0
7 TraesCS7D01G482200 chr7D 80.590 1051 117 51 1929 2949 592818441 592819434 0.000000e+00 730.0
8 TraesCS7D01G482200 chr7D 83.810 735 82 12 973 1685 592860224 592859505 0.000000e+00 664.0
9 TraesCS7D01G482200 chr4D 93.946 859 49 3 1 858 449911002 449911858 0.000000e+00 1295.0
10 TraesCS7D01G482200 chr4D 82.266 203 34 2 3106 3306 362794218 362794016 1.440000e-39 174.0
11 TraesCS7D01G482200 chr1A 93.692 856 50 4 1 855 94476330 94475478 0.000000e+00 1279.0
12 TraesCS7D01G482200 chr1A 80.135 297 35 14 2515 2794 544193872 544193583 2.380000e-47 200.0
13 TraesCS7D01G482200 chr3D 93.590 858 48 6 1 858 8293526 8292676 0.000000e+00 1273.0
14 TraesCS7D01G482200 chr3A 93.248 859 51 5 1 858 37296040 37296892 0.000000e+00 1258.0
15 TraesCS7D01G482200 chr3A 92.974 854 54 5 5 858 634685901 634686748 0.000000e+00 1240.0
16 TraesCS7D01G482200 chr7A 89.210 899 69 9 861 1738 684292400 684293291 0.000000e+00 1098.0
17 TraesCS7D01G482200 chr7A 81.620 1099 112 36 2228 3293 684296584 684297625 0.000000e+00 828.0
18 TraesCS7D01G482200 chr7A 80.218 1193 144 49 1819 2949 685213593 685214755 0.000000e+00 811.0
19 TraesCS7D01G482200 chr7A 86.938 689 84 4 986 1668 685230681 685229993 0.000000e+00 769.0
20 TraesCS7D01G482200 chr7A 85.442 735 81 11 980 1707 685212662 685213377 0.000000e+00 741.0
21 TraesCS7D01G482200 chr7A 85.734 708 78 8 991 1688 685090140 685090834 0.000000e+00 726.0
22 TraesCS7D01G482200 chr7A 81.743 482 70 11 2468 2941 685095395 685095866 1.700000e-103 387.0
23 TraesCS7D01G482200 chr7A 91.617 167 14 0 3398 3564 684297976 684298142 8.450000e-57 231.0
24 TraesCS7D01G482200 chr7A 81.955 266 40 5 3045 3308 304150294 304150553 6.580000e-53 219.0
25 TraesCS7D01G482200 chr7A 97.778 45 1 0 1765 1809 684293381 684293425 1.170000e-10 78.7
26 TraesCS7D01G482200 chr7B 86.505 741 87 5 980 1707 668907226 668907966 0.000000e+00 802.0
27 TraesCS7D01G482200 chr7B 86.648 704 87 5 980 1678 669141454 669140753 0.000000e+00 773.0
28 TraesCS7D01G482200 chr7B 85.515 718 69 18 980 1690 668930642 668929953 0.000000e+00 717.0
29 TraesCS7D01G482200 chr7B 91.618 513 38 4 3311 3823 669640391 669639884 0.000000e+00 704.0
30 TraesCS7D01G482200 chr7B 85.185 189 22 3 1819 2002 669140591 669140404 5.160000e-44 189.0
31 TraesCS7D01G482200 chr7B 78.333 180 30 6 3363 3536 669139239 669139063 1.490000e-19 108.0
32 TraesCS7D01G482200 chr2A 79.612 412 60 16 2515 2912 737478792 737478391 1.380000e-69 274.0
33 TraesCS7D01G482200 chr5D 84.211 266 33 6 3045 3308 546697972 546697714 2.330000e-62 250.0
34 TraesCS7D01G482200 chr4A 83.643 269 39 2 3045 3313 62950255 62950518 8.390000e-62 248.0
35 TraesCS7D01G482200 chr2B 82.482 274 38 7 3045 3317 632643847 632643583 8.450000e-57 231.0
36 TraesCS7D01G482200 chr1D 85.859 198 23 3 3110 3307 299925057 299925249 5.120000e-49 206.0
37 TraesCS7D01G482200 chr1D 79.924 264 48 2 3045 3308 126334068 126334326 5.160000e-44 189.0
38 TraesCS7D01G482200 chr1B 81.590 239 33 8 3044 3279 550372543 550372773 1.860000e-43 187.0
39 TraesCS7D01G482200 chr6B 86.111 108 10 4 2230 2337 200510914 200510812 1.150000e-20 111.0
40 TraesCS7D01G482200 chr6D 84.259 108 12 5 2230 2337 111568915 111568813 2.490000e-17 100.0
41 TraesCS7D01G482200 chr6A 84.259 108 12 4 2230 2337 136542660 136542762 2.490000e-17 100.0


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 TraesCS7D01G482200 chr7D 592631322 592635232 3910 False 7223.000000 7223 100.000000 1 3911 1 chr7D.!!$F1 3910
1 TraesCS7D01G482200 chr7D 599905970 599906817 847 False 1243.000000 1243 93.075000 5 856 1 chr7D.!!$F3 851
2 TraesCS7D01G482200 chr7D 39581075 39581933 858 True 1236.000000 1236 92.666000 1 858 1 chr7D.!!$R1 857
3 TraesCS7D01G482200 chr7D 108616404 108617266 862 True 1229.000000 1229 92.494000 1 858 1 chr7D.!!$R2 857
4 TraesCS7D01G482200 chr7D 634180658 634181507 849 True 1227.000000 1227 92.640000 1 856 1 chr7D.!!$R4 855
5 TraesCS7D01G482200 chr7D 592677373 592678071 698 False 778.000000 778 86.857000 980 1675 1 chr7D.!!$F2 695
6 TraesCS7D01G482200 chr7D 592816338 592819434 3096 False 740.000000 750 83.817500 982 2949 2 chr7D.!!$F4 1967
7 TraesCS7D01G482200 chr7D 592859505 592860224 719 True 664.000000 664 83.810000 973 1685 1 chr7D.!!$R3 712
8 TraesCS7D01G482200 chr4D 449911002 449911858 856 False 1295.000000 1295 93.946000 1 858 1 chr4D.!!$F1 857
9 TraesCS7D01G482200 chr1A 94475478 94476330 852 True 1279.000000 1279 93.692000 1 855 1 chr1A.!!$R1 854
10 TraesCS7D01G482200 chr3D 8292676 8293526 850 True 1273.000000 1273 93.590000 1 858 1 chr3D.!!$R1 857
11 TraesCS7D01G482200 chr3A 37296040 37296892 852 False 1258.000000 1258 93.248000 1 858 1 chr3A.!!$F1 857
12 TraesCS7D01G482200 chr3A 634685901 634686748 847 False 1240.000000 1240 92.974000 5 858 1 chr3A.!!$F2 853
13 TraesCS7D01G482200 chr7A 685212662 685214755 2093 False 776.000000 811 82.830000 980 2949 2 chr7A.!!$F5 1969
14 TraesCS7D01G482200 chr7A 685229993 685230681 688 True 769.000000 769 86.938000 986 1668 1 chr7A.!!$R1 682
15 TraesCS7D01G482200 chr7A 685090140 685090834 694 False 726.000000 726 85.734000 991 1688 1 chr7A.!!$F2 697
16 TraesCS7D01G482200 chr7A 684292400 684298142 5742 False 558.925000 1098 90.056250 861 3564 4 chr7A.!!$F4 2703
17 TraesCS7D01G482200 chr7B 668907226 668907966 740 False 802.000000 802 86.505000 980 1707 1 chr7B.!!$F1 727
18 TraesCS7D01G482200 chr7B 668929953 668930642 689 True 717.000000 717 85.515000 980 1690 1 chr7B.!!$R1 710
19 TraesCS7D01G482200 chr7B 669639884 669640391 507 True 704.000000 704 91.618000 3311 3823 1 chr7B.!!$R2 512
20 TraesCS7D01G482200 chr7B 669139063 669141454 2391 True 356.666667 773 83.388667 980 3536 3 chr7B.!!$R3 2556

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
926 940 0.179045 GACCACAGCACAACCTCACT 60.179 55.0 0.0 0.0 0.00 3.41 F
1145 1198 0.108615 CACGAGGGGGCGATGATATC 60.109 60.0 0.0 0.0 34.83 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 6625 0.107831 AGCACGTGGAACCTAAAGCA 59.892 50.0 18.88 0.0 0.0 3.91 R
3009 7445 0.035739 TGTCGCTGTTTAACCCCCTC 59.964 55.0 0.00 0.0 0.0 4.30 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
104 105 7.768582 TGTTATCAATTCAAGCTCGATTCCTAA 59.231 33.333 0.00 0.00 0.00 2.69
108 109 7.050377 TCAATTCAAGCTCGATTCCTAATTCT 58.950 34.615 0.00 0.00 0.00 2.40
121 122 8.673711 CGATTCCTAATTCTAAACATGTTTGGA 58.326 33.333 27.60 27.60 38.10 3.53
280 281 5.976458 TCAAACACCTTTTTCTTGATTGCT 58.024 33.333 0.00 0.00 0.00 3.91
312 313 3.305720 AGTTCTATGGCGGATAGTCCAA 58.694 45.455 0.00 0.00 35.91 3.53
506 507 4.513198 TTTTGCAGGTTATTTTCCGAGG 57.487 40.909 0.00 0.00 0.00 4.63
511 513 1.276989 AGGTTATTTTCCGAGGCACGA 59.723 47.619 5.74 0.00 45.77 4.35
538 540 0.316772 CCGTATGTGGTCGCTACTCG 60.317 60.000 0.00 0.00 40.15 4.18
601 603 2.109181 GGGAGATGGTAGCACGGC 59.891 66.667 0.00 0.00 0.00 5.68
638 640 4.365514 TTGGATGGCGGTCATGTAATAT 57.634 40.909 0.00 0.00 35.97 1.28
641 643 3.935203 GGATGGCGGTCATGTAATATGAG 59.065 47.826 0.00 0.00 35.97 2.90
665 667 8.325477 AGAGGCAATTAGTTTACCTATCTCTT 57.675 34.615 0.00 0.00 0.00 2.85
695 702 0.593773 CGGTTGTGGCGTCCTTTTTG 60.594 55.000 0.00 0.00 0.00 2.44
720 727 1.413118 AGTTTGTCCTTTGGCCCTTG 58.587 50.000 0.00 0.00 0.00 3.61
773 785 6.257193 TCGTTTTGAGACTTTAAGACCTTGTC 59.743 38.462 0.00 0.00 0.00 3.18
830 844 3.627395 ATCGTTTTGATGTAGAGGCCA 57.373 42.857 5.01 0.00 35.45 5.36
877 891 7.914427 AAAAACTCTCTCCCTTTTTAACCAT 57.086 32.000 0.00 0.00 0.00 3.55
878 892 6.901081 AAACTCTCTCCCTTTTTAACCATG 57.099 37.500 0.00 0.00 0.00 3.66
903 917 4.660938 GCGCCCTCCACCACCTTT 62.661 66.667 0.00 0.00 0.00 3.11
907 921 0.322546 GCCCTCCACCACCTTTACAG 60.323 60.000 0.00 0.00 0.00 2.74
909 923 1.003233 CCCTCCACCACCTTTACAGAC 59.997 57.143 0.00 0.00 0.00 3.51
911 925 1.697432 CTCCACCACCTTTACAGACCA 59.303 52.381 0.00 0.00 0.00 4.02
913 927 1.142060 CCACCACCTTTACAGACCACA 59.858 52.381 0.00 0.00 0.00 4.17
926 940 0.179045 GACCACAGCACAACCTCACT 60.179 55.000 0.00 0.00 0.00 3.41
936 950 3.162666 CACAACCTCACTAGTCCCTACA 58.837 50.000 0.00 0.00 0.00 2.74
937 951 3.769844 CACAACCTCACTAGTCCCTACAT 59.230 47.826 0.00 0.00 0.00 2.29
945 959 6.015856 CCTCACTAGTCCCTACATTCACATAG 60.016 46.154 0.00 0.00 0.00 2.23
946 960 5.833667 TCACTAGTCCCTACATTCACATAGG 59.166 44.000 0.00 0.00 38.18 2.57
969 983 3.764466 CGAGCACGAGCCTCCCTT 61.764 66.667 0.00 0.00 43.56 3.95
998 1030 1.004440 GACCACTCACTCAGGCCAC 60.004 63.158 5.01 0.00 0.00 5.01
1007 1039 1.078918 CTCAGGCCACGATGAGCAA 60.079 57.895 5.01 0.00 36.80 3.91
1023 1055 2.746277 AACGGCAGGATGAACGCC 60.746 61.111 0.00 0.00 40.78 5.68
1145 1198 0.108615 CACGAGGGGGCGATGATATC 60.109 60.000 0.00 0.00 34.83 1.63
1193 1246 2.385091 CCGCCTTCAACCGGTTACG 61.385 63.158 21.79 17.46 39.67 3.18
1324 1389 2.601702 ATGGCCATGGACGGTCACA 61.602 57.895 20.04 6.15 45.24 3.58
1692 1795 2.656069 CCCCCACACCCACTCTACG 61.656 68.421 0.00 0.00 0.00 3.51
1693 1796 1.911766 CCCCACACCCACTCTACGT 60.912 63.158 0.00 0.00 0.00 3.57
1738 1841 3.608796 ACGTTACAGTAGGTCTCTCTCC 58.391 50.000 0.00 0.00 0.00 3.71
1739 1842 2.608546 CGTTACAGTAGGTCTCTCTCCG 59.391 54.545 0.00 0.00 0.00 4.63
1742 1845 1.292061 CAGTAGGTCTCTCTCCGTCG 58.708 60.000 0.00 0.00 0.00 5.12
1743 1846 1.134759 CAGTAGGTCTCTCTCCGTCGA 60.135 57.143 0.00 0.00 0.00 4.20
1744 1847 1.554160 AGTAGGTCTCTCTCCGTCGAA 59.446 52.381 0.00 0.00 0.00 3.71
1745 1848 2.027377 AGTAGGTCTCTCTCCGTCGAAA 60.027 50.000 0.00 0.00 0.00 3.46
1746 1849 1.166989 AGGTCTCTCTCCGTCGAAAC 58.833 55.000 0.00 0.00 0.00 2.78
1809 1983 4.876107 TCAGTCTTCACTCAGTTTTTGGTC 59.124 41.667 0.00 0.00 0.00 4.02
1811 1985 3.002348 GTCTTCACTCAGTTTTTGGTCCG 59.998 47.826 0.00 0.00 0.00 4.79
1813 1987 2.993937 TCACTCAGTTTTTGGTCCGTT 58.006 42.857 0.00 0.00 0.00 4.44
1868 2095 5.751243 ACACAAAACTCAACTCCATGTAC 57.249 39.130 0.00 0.00 0.00 2.90
1878 2105 4.759693 TCAACTCCATGTACCACAAACATC 59.240 41.667 0.00 0.00 35.39 3.06
1950 3324 6.965500 CAGGATCACGAAATGAAAAAGAGATG 59.035 38.462 0.00 0.00 41.93 2.90
1996 3370 4.775236 AGTTTTCAGACTTCAGACTGCTT 58.225 39.130 0.00 0.00 37.65 3.91
2043 6182 1.680314 GCAGCCTTTTGCCCTAGCT 60.680 57.895 0.00 0.00 42.71 3.32
2045 6184 1.955208 GCAGCCTTTTGCCCTAGCTAA 60.955 52.381 0.00 0.00 42.71 3.09
2046 6185 2.659428 CAGCCTTTTGCCCTAGCTAAT 58.341 47.619 0.00 0.00 42.71 1.73
2047 6186 2.620585 CAGCCTTTTGCCCTAGCTAATC 59.379 50.000 0.00 0.00 42.71 1.75
2048 6187 2.511637 AGCCTTTTGCCCTAGCTAATCT 59.488 45.455 0.00 0.00 42.71 2.40
2049 6188 2.881513 GCCTTTTGCCCTAGCTAATCTC 59.118 50.000 0.00 0.00 40.80 2.75
2050 6189 3.434310 GCCTTTTGCCCTAGCTAATCTCT 60.434 47.826 0.00 0.00 40.80 3.10
2051 6190 4.133078 CCTTTTGCCCTAGCTAATCTCTG 58.867 47.826 0.00 0.00 40.80 3.35
2052 6191 2.918712 TTGCCCTAGCTAATCTCTGC 57.081 50.000 0.00 0.00 40.80 4.26
2053 6192 2.094100 TGCCCTAGCTAATCTCTGCT 57.906 50.000 0.00 0.00 42.67 4.24
2054 6193 1.967066 TGCCCTAGCTAATCTCTGCTC 59.033 52.381 0.00 0.00 40.35 4.26
2057 6196 3.816118 GCCCTAGCTAATCTCTGCTCCTA 60.816 52.174 0.00 0.00 40.35 2.94
2187 6449 2.973420 GAAGGATTCTGGTACGCGG 58.027 57.895 12.47 0.00 43.23 6.46
2188 6450 0.175073 GAAGGATTCTGGTACGCGGT 59.825 55.000 12.47 0.00 43.23 5.68
2202 6465 0.739813 CGCGGTTTAGCTTAGCCTGT 60.740 55.000 0.00 0.00 34.40 4.00
2217 6618 3.467803 AGCCTGTGTTGTTCTTGTACTC 58.532 45.455 0.00 0.00 0.00 2.59
2224 6625 6.119536 TGTGTTGTTCTTGTACTCTGGATTT 58.880 36.000 0.00 0.00 0.00 2.17
2310 6711 2.047274 CACAACCATCGCCGGAGT 60.047 61.111 5.05 0.00 0.00 3.85
2380 6781 0.395862 TTCCAAGAAACCCAACGCCA 60.396 50.000 0.00 0.00 0.00 5.69
2404 6805 1.075970 ATCTCCAGCTCCTACGCCA 60.076 57.895 0.00 0.00 0.00 5.69
2407 6808 3.390521 CCAGCTCCTACGCCACCA 61.391 66.667 0.00 0.00 0.00 4.17
2425 6826 3.078837 ACCAACAATAACAGTAAGCCGG 58.921 45.455 0.00 0.00 0.00 6.13
2449 6850 5.465056 GCACCTTTGCTTTAACTAATTGCAA 59.535 36.000 0.00 0.00 46.17 4.08
2450 6851 6.346838 GCACCTTTGCTTTAACTAATTGCAAG 60.347 38.462 4.94 0.00 46.17 4.01
2451 6852 6.701400 CACCTTTGCTTTAACTAATTGCAAGT 59.299 34.615 4.94 4.58 43.13 3.16
2453 6854 7.768582 ACCTTTGCTTTAACTAATTGCAAGTTT 59.231 29.630 4.05 0.00 43.13 2.66
2454 6855 8.063630 CCTTTGCTTTAACTAATTGCAAGTTTG 58.936 33.333 4.05 1.18 43.13 2.93
2475 6876 3.181475 TGCAGCCTATCTAGTAGTGCAAC 60.181 47.826 8.07 0.00 38.63 4.17
2505 6909 7.721842 TCATCATTTATCGGGGCTAATTTGTAA 59.278 33.333 0.00 0.00 0.00 2.41
2509 6913 9.010029 CATTTATCGGGGCTAATTTGTAAGTAT 57.990 33.333 0.00 0.00 0.00 2.12
2510 6914 7.972832 TTATCGGGGCTAATTTGTAAGTATG 57.027 36.000 0.00 0.00 0.00 2.39
2511 6915 4.131596 TCGGGGCTAATTTGTAAGTATGC 58.868 43.478 0.00 0.00 0.00 3.14
2512 6916 3.880490 CGGGGCTAATTTGTAAGTATGCA 59.120 43.478 0.00 0.00 0.00 3.96
2513 6917 4.518970 CGGGGCTAATTTGTAAGTATGCAT 59.481 41.667 3.79 3.79 0.00 3.96
2547 6952 2.127232 GCTTTGAGCGCGACCAAC 60.127 61.111 12.10 0.00 0.00 3.77
2562 6967 1.336887 ACCAACAAGTCGACCATCTCG 60.337 52.381 13.01 0.00 44.44 4.04
2607 7012 0.609131 TTAAGCAAGTCCAGGCCAGC 60.609 55.000 5.01 0.00 0.00 4.85
2661 7069 2.125350 GTGCCGCCAGAGAAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
2706 7114 1.604308 CATGCAGCTCCACCACCAA 60.604 57.895 0.00 0.00 0.00 3.67
2708 7116 3.357079 GCAGCTCCACCACCAACG 61.357 66.667 0.00 0.00 0.00 4.10
2727 7135 0.964358 GGGAGCAGCAGCACTTCATT 60.964 55.000 3.17 0.00 45.49 2.57
2744 7152 1.134280 CATTACCTCCCTCCTGCACAG 60.134 57.143 0.00 0.00 0.00 3.66
2745 7153 0.116342 TTACCTCCCTCCTGCACAGA 59.884 55.000 0.00 0.00 0.00 3.41
2749 7157 0.671781 CTCCCTCCTGCACAGAAACG 60.672 60.000 0.00 0.00 0.00 3.60
2754 7162 1.261619 CTCCTGCACAGAAACGTCAAC 59.738 52.381 0.00 0.00 0.00 3.18
2781 7189 3.693085 GCAACATCATGTCATGTTCCTCT 59.307 43.478 12.54 0.00 43.75 3.69
2845 7260 3.980583 GTCTCCGACCAGAACAACA 57.019 52.632 0.00 0.00 0.00 3.33
2868 7289 1.047596 ACACCAATGGCAGCAACCAA 61.048 50.000 0.00 0.00 44.65 3.67
2885 7306 0.032952 CAAGCCAACAACAGCATGCT 59.967 50.000 16.30 16.30 42.53 3.79
2967 7403 7.865706 ATGATCAGAAAACCACATTAGGTAC 57.134 36.000 0.09 0.00 42.25 3.34
2983 7419 3.816994 AGGTACTTGGTGGAAGTGTTTC 58.183 45.455 0.00 0.00 45.05 2.78
2989 7425 4.021807 ACTTGGTGGAAGTGTTTCGTTTTT 60.022 37.500 0.00 0.00 43.71 1.94
2990 7426 4.099380 TGGTGGAAGTGTTTCGTTTTTC 57.901 40.909 0.00 0.00 33.98 2.29
2993 7429 2.427812 TGGAAGTGTTTCGTTTTTCCCC 59.572 45.455 0.00 0.00 37.17 4.81
2994 7430 2.691526 GGAAGTGTTTCGTTTTTCCCCT 59.308 45.455 0.00 0.00 33.98 4.79
2995 7431 3.490249 GGAAGTGTTTCGTTTTTCCCCTG 60.490 47.826 0.00 0.00 33.98 4.45
2997 7433 3.093814 AGTGTTTCGTTTTTCCCCTGTT 58.906 40.909 0.00 0.00 0.00 3.16
2998 7434 4.271661 AGTGTTTCGTTTTTCCCCTGTTA 58.728 39.130 0.00 0.00 0.00 2.41
3000 7436 5.185442 AGTGTTTCGTTTTTCCCCTGTTAAA 59.815 36.000 0.00 0.00 0.00 1.52
3003 7439 6.590677 TGTTTCGTTTTTCCCCTGTTAAAAAG 59.409 34.615 0.00 0.00 35.77 2.27
3006 7442 5.045215 CGTTTTTCCCCTGTTAAAAAGGAC 58.955 41.667 6.97 0.00 40.35 3.85
3007 7443 5.362263 GTTTTTCCCCTGTTAAAAAGGACC 58.638 41.667 6.97 0.00 35.77 4.46
3008 7444 2.572209 TCCCCTGTTAAAAAGGACCG 57.428 50.000 6.97 0.00 36.91 4.79
3009 7445 1.074244 TCCCCTGTTAAAAAGGACCGG 59.926 52.381 0.00 0.00 36.91 5.28
3010 7446 1.074244 CCCCTGTTAAAAAGGACCGGA 59.926 52.381 9.46 0.00 36.91 5.14
3011 7447 2.433436 CCCTGTTAAAAAGGACCGGAG 58.567 52.381 9.46 0.00 36.91 4.63
3025 7479 1.743995 CGGAGGGGGTTAAACAGCG 60.744 63.158 0.00 0.00 0.00 5.18
3042 7496 1.726791 AGCGACAAAGCAATGTACTCG 59.273 47.619 0.00 0.00 40.15 4.18
3043 7497 1.724623 GCGACAAAGCAATGTACTCGA 59.275 47.619 0.00 0.00 37.05 4.04
3046 7500 3.000322 CGACAAAGCAATGTACTCGATCC 60.000 47.826 0.00 0.00 32.57 3.36
3048 7502 3.055094 ACAAAGCAATGTACTCGATCCCT 60.055 43.478 0.00 0.00 0.00 4.20
3050 7504 1.689273 AGCAATGTACTCGATCCCTCC 59.311 52.381 0.00 0.00 0.00 4.30
3051 7505 1.603172 GCAATGTACTCGATCCCTCCG 60.603 57.143 0.00 0.00 0.00 4.63
3055 7509 0.754587 GTACTCGATCCCTCCGGGTT 60.755 60.000 0.00 0.00 44.74 4.11
3056 7510 0.032813 TACTCGATCCCTCCGGGTTT 60.033 55.000 0.00 0.00 44.74 3.27
3086 7540 8.273780 AGTCTGTATTTAAGATTTGCCTGAAG 57.726 34.615 0.00 0.00 0.00 3.02
3089 7543 7.882791 TCTGTATTTAAGATTTGCCTGAAGTCA 59.117 33.333 0.00 0.00 0.00 3.41
3091 7545 9.023962 TGTATTTAAGATTTGCCTGAAGTCAAT 57.976 29.630 0.00 0.00 0.00 2.57
3092 7546 9.860898 GTATTTAAGATTTGCCTGAAGTCAATT 57.139 29.630 0.00 0.00 0.00 2.32
3114 7568 6.981762 TTGTCGTAAAGTTTAGTTTGACCA 57.018 33.333 0.00 0.00 0.00 4.02
3204 7663 7.384932 ACGACGCATCTAATGATATTGATTTCA 59.615 33.333 0.00 0.00 0.00 2.69
3298 7757 9.778741 TCTTATATGCATACTAAAAAGGACCTG 57.221 33.333 8.99 0.00 0.00 4.00
3299 7758 9.778741 CTTATATGCATACTAAAAAGGACCTGA 57.221 33.333 8.99 0.00 0.00 3.86
3300 7759 9.778741 TTATATGCATACTAAAAAGGACCTGAG 57.221 33.333 8.99 0.00 0.00 3.35
3301 7760 4.843728 TGCATACTAAAAAGGACCTGAGG 58.156 43.478 0.00 0.00 0.00 3.86
3302 7761 4.200092 GCATACTAAAAAGGACCTGAGGG 58.800 47.826 2.38 0.00 38.88 4.30
3303 7762 4.080526 GCATACTAAAAAGGACCTGAGGGA 60.081 45.833 2.38 0.00 36.25 4.20
3304 7763 5.675538 CATACTAAAAAGGACCTGAGGGAG 58.324 45.833 2.38 0.00 36.25 4.30
3305 7764 3.599348 ACTAAAAAGGACCTGAGGGAGT 58.401 45.455 2.38 0.00 36.25 3.85
3306 7765 4.759953 ACTAAAAAGGACCTGAGGGAGTA 58.240 43.478 2.38 0.00 36.25 2.59
3307 7766 4.531339 ACTAAAAAGGACCTGAGGGAGTAC 59.469 45.833 2.38 0.00 36.25 2.73
3308 7767 3.277416 AAAAGGACCTGAGGGAGTACT 57.723 47.619 2.38 0.00 36.25 2.73
3309 7768 4.415224 AAAAGGACCTGAGGGAGTACTA 57.585 45.455 2.38 0.00 36.25 1.82
3321 7780 5.473846 TGAGGGAGTACTAGCTAATTCATCG 59.526 44.000 0.00 0.00 0.00 3.84
3517 8226 2.752903 ACAAACCAGTCCACACAACTTC 59.247 45.455 0.00 0.00 0.00 3.01
3568 8277 8.894768 ATCTCAAGAGATTTAAAATACCCTCG 57.105 34.615 6.75 0.00 45.31 4.63
3569 8278 8.074613 TCTCAAGAGATTTAAAATACCCTCGA 57.925 34.615 0.00 0.00 31.41 4.04
3607 8316 0.675083 CAGCAGCAACCCACAATTGA 59.325 50.000 13.59 0.00 0.00 2.57
3619 8328 4.405358 ACCCACAATTGACAAGACAACAAT 59.595 37.500 13.59 0.00 36.07 2.71
3621 8330 6.151691 CCCACAATTGACAAGACAACAATAG 58.848 40.000 13.59 0.00 34.48 1.73
3625 8334 9.299963 CACAATTGACAAGACAACAATAGAAAA 57.700 29.630 13.59 0.00 34.48 2.29
3663 8372 3.766591 CTGTCCCATCCGCTAATCTATCT 59.233 47.826 0.00 0.00 0.00 1.98
3667 8376 6.440647 TGTCCCATCCGCTAATCTATCTATTT 59.559 38.462 0.00 0.00 0.00 1.40
3691 8400 4.677584 TCTCAAATTGTTGAACCAAACGG 58.322 39.130 0.00 0.00 43.18 4.44
3692 8401 4.399618 TCTCAAATTGTTGAACCAAACGGA 59.600 37.500 0.00 0.00 43.18 4.69
3694 8403 4.865365 TCAAATTGTTGAACCAAACGGAAC 59.135 37.500 0.00 0.00 40.87 3.62
3753 8462 7.537715 TGCAACATACGAATCAAATTTCATCT 58.462 30.769 0.00 0.00 0.00 2.90
3757 8466 9.559958 AACATACGAATCAAATTTCATCTCAAC 57.440 29.630 0.00 0.00 0.00 3.18
3759 8468 9.218359 CATACGAATCAAATTTCATCTCAACTG 57.782 33.333 0.00 0.00 0.00 3.16
3769 8478 8.597662 AATTTCATCTCAACTGGACATTTTTG 57.402 30.769 0.00 0.00 0.00 2.44
3770 8479 6.713762 TTCATCTCAACTGGACATTTTTGT 57.286 33.333 0.00 0.00 0.00 2.83
3771 8480 6.075762 TCATCTCAACTGGACATTTTTGTG 57.924 37.500 0.00 0.00 0.00 3.33
3810 8519 9.877178 AGTGTTGGTTATAATGTTTTGTTTTCA 57.123 25.926 0.00 0.00 0.00 2.69
3823 8532 7.821652 TGTTTTGTTTTCACTAACATGTGAGA 58.178 30.769 17.67 1.54 46.02 3.27
3824 8533 8.465999 TGTTTTGTTTTCACTAACATGTGAGAT 58.534 29.630 17.67 0.00 46.02 2.75
3825 8534 8.745837 GTTTTGTTTTCACTAACATGTGAGATG 58.254 33.333 17.67 11.09 46.02 2.90
3826 8535 6.558771 TGTTTTCACTAACATGTGAGATGG 57.441 37.500 17.67 6.14 46.02 3.51
3827 8536 6.061441 TGTTTTCACTAACATGTGAGATGGT 58.939 36.000 17.67 0.00 46.02 3.55
3828 8537 6.204688 TGTTTTCACTAACATGTGAGATGGTC 59.795 38.462 17.67 3.71 46.02 4.02
3829 8538 5.745312 TTCACTAACATGTGAGATGGTCT 57.255 39.130 17.67 0.00 46.02 3.85
3830 8539 5.745312 TCACTAACATGTGAGATGGTCTT 57.255 39.130 17.67 0.00 41.43 3.01
3831 8540 5.724328 TCACTAACATGTGAGATGGTCTTC 58.276 41.667 17.67 0.00 41.43 2.87
3832 8541 5.245977 TCACTAACATGTGAGATGGTCTTCA 59.754 40.000 17.67 0.00 41.43 3.02
3833 8542 5.579904 CACTAACATGTGAGATGGTCTTCAG 59.420 44.000 17.67 0.00 40.12 3.02
3834 8543 4.897509 AACATGTGAGATGGTCTTCAGA 57.102 40.909 0.00 0.00 0.00 3.27
3835 8544 4.897509 ACATGTGAGATGGTCTTCAGAA 57.102 40.909 0.00 0.00 0.00 3.02
3836 8545 4.829968 ACATGTGAGATGGTCTTCAGAAG 58.170 43.478 3.45 3.45 0.00 2.85
3837 8546 4.529769 ACATGTGAGATGGTCTTCAGAAGA 59.470 41.667 8.95 8.95 34.51 2.87
3838 8547 4.797800 TGTGAGATGGTCTTCAGAAGAG 57.202 45.455 13.53 0.00 38.41 2.85
3839 8548 4.411013 TGTGAGATGGTCTTCAGAAGAGA 58.589 43.478 13.53 3.79 38.41 3.10
3840 8549 5.022122 TGTGAGATGGTCTTCAGAAGAGAT 58.978 41.667 13.53 8.53 38.41 2.75
3841 8550 6.190587 TGTGAGATGGTCTTCAGAAGAGATA 58.809 40.000 13.53 3.50 38.41 1.98
3842 8551 6.665248 TGTGAGATGGTCTTCAGAAGAGATAA 59.335 38.462 13.53 0.23 38.41 1.75
3843 8552 7.344093 TGTGAGATGGTCTTCAGAAGAGATAAT 59.656 37.037 13.53 5.02 38.41 1.28
3844 8553 7.867403 GTGAGATGGTCTTCAGAAGAGATAATC 59.133 40.741 13.53 12.83 38.41 1.75
3845 8554 7.784073 TGAGATGGTCTTCAGAAGAGATAATCT 59.216 37.037 13.53 16.62 41.27 2.40
3846 8555 8.181904 AGATGGTCTTCAGAAGAGATAATCTC 57.818 38.462 13.53 4.39 43.70 2.75
3847 8556 7.784073 AGATGGTCTTCAGAAGAGATAATCTCA 59.216 37.037 13.53 2.42 45.73 3.27
3848 8557 7.345422 TGGTCTTCAGAAGAGATAATCTCAG 57.655 40.000 13.53 0.00 45.73 3.35
3849 8558 7.122048 TGGTCTTCAGAAGAGATAATCTCAGA 58.878 38.462 13.53 0.00 45.73 3.27
3850 8559 7.285172 TGGTCTTCAGAAGAGATAATCTCAGAG 59.715 40.741 13.53 0.00 45.73 3.35
3851 8560 7.285401 GGTCTTCAGAAGAGATAATCTCAGAGT 59.715 40.741 13.53 0.00 45.73 3.24
3852 8561 9.337396 GTCTTCAGAAGAGATAATCTCAGAGTA 57.663 37.037 13.53 0.00 45.73 2.59
3864 8573 9.921637 GATAATCTCAGAGTATTCTTACTTGGG 57.078 37.037 0.00 0.00 38.81 4.12
3865 8574 5.599999 TCTCAGAGTATTCTTACTTGGGC 57.400 43.478 0.00 0.00 38.81 5.36
3866 8575 5.023452 TCTCAGAGTATTCTTACTTGGGCA 58.977 41.667 0.00 0.00 38.81 5.36
3867 8576 5.663106 TCTCAGAGTATTCTTACTTGGGCAT 59.337 40.000 0.00 0.00 38.81 4.40
3868 8577 5.674525 TCAGAGTATTCTTACTTGGGCATG 58.325 41.667 0.00 0.00 38.81 4.06
3869 8578 5.189736 TCAGAGTATTCTTACTTGGGCATGT 59.810 40.000 0.00 0.00 38.81 3.21
3870 8579 5.882557 CAGAGTATTCTTACTTGGGCATGTT 59.117 40.000 0.00 0.00 38.81 2.71
3871 8580 5.882557 AGAGTATTCTTACTTGGGCATGTTG 59.117 40.000 0.00 0.00 38.81 3.33
3872 8581 5.815581 AGTATTCTTACTTGGGCATGTTGA 58.184 37.500 0.00 0.00 34.99 3.18
3873 8582 6.245408 AGTATTCTTACTTGGGCATGTTGAA 58.755 36.000 0.00 0.00 34.99 2.69
3874 8583 5.649782 ATTCTTACTTGGGCATGTTGAAG 57.350 39.130 0.00 0.00 0.00 3.02
3875 8584 4.098914 TCTTACTTGGGCATGTTGAAGT 57.901 40.909 9.40 9.40 33.32 3.01
3876 8585 4.072131 TCTTACTTGGGCATGTTGAAGTC 58.928 43.478 8.17 0.00 31.25 3.01
3877 8586 2.363306 ACTTGGGCATGTTGAAGTCA 57.637 45.000 0.00 0.00 0.00 3.41
3878 8587 2.665165 ACTTGGGCATGTTGAAGTCAA 58.335 42.857 0.00 0.00 0.00 3.18
3891 8600 5.883503 TTGAAGTCAACCTTTACGTTGTT 57.116 34.783 0.00 0.00 43.02 2.83
3892 8601 5.224562 TGAAGTCAACCTTTACGTTGTTG 57.775 39.130 0.00 3.44 43.02 3.33
3893 8602 4.936411 TGAAGTCAACCTTTACGTTGTTGA 59.064 37.500 14.59 14.59 44.32 3.18
3894 8603 5.587043 TGAAGTCAACCTTTACGTTGTTGAT 59.413 36.000 18.86 9.38 46.92 2.57
3895 8604 6.094325 TGAAGTCAACCTTTACGTTGTTGATT 59.906 34.615 18.86 14.52 46.92 2.57
3896 8605 6.445357 AGTCAACCTTTACGTTGTTGATTT 57.555 33.333 18.86 11.66 46.92 2.17
3897 8606 6.492254 AGTCAACCTTTACGTTGTTGATTTC 58.508 36.000 18.86 10.81 46.92 2.17
3898 8607 6.317893 AGTCAACCTTTACGTTGTTGATTTCT 59.682 34.615 18.86 12.22 46.92 2.52
3899 8608 6.631636 GTCAACCTTTACGTTGTTGATTTCTC 59.368 38.462 18.86 8.01 46.92 2.87
3900 8609 6.316640 TCAACCTTTACGTTGTTGATTTCTCA 59.683 34.615 14.59 0.00 42.36 3.27
3901 8610 6.300354 ACCTTTACGTTGTTGATTTCTCAG 57.700 37.500 0.00 0.00 31.68 3.35
3902 8611 6.053005 ACCTTTACGTTGTTGATTTCTCAGA 58.947 36.000 0.00 0.00 31.68 3.27
3903 8612 6.540914 ACCTTTACGTTGTTGATTTCTCAGAA 59.459 34.615 0.00 0.00 31.68 3.02
3904 8613 7.066525 ACCTTTACGTTGTTGATTTCTCAGAAA 59.933 33.333 1.30 1.30 31.68 2.52
3905 8614 7.913297 CCTTTACGTTGTTGATTTCTCAGAAAA 59.087 33.333 3.35 0.00 31.68 2.29
3906 8615 9.450807 CTTTACGTTGTTGATTTCTCAGAAAAT 57.549 29.630 3.35 0.00 31.68 1.82
3909 8618 7.078228 ACGTTGTTGATTTCTCAGAAAATAGC 58.922 34.615 3.35 0.00 31.68 2.97
3910 8619 7.077605 CGTTGTTGATTTCTCAGAAAATAGCA 58.922 34.615 3.35 1.98 31.68 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 9.480053 CTTTGACATTCCAAACATGTTTAGAAT 57.520 29.630 28.34 28.34 39.99 2.40
108 109 7.206687 GGACTTTGACATTCCAAACATGTTTA 58.793 34.615 22.87 9.04 34.89 2.01
312 313 8.514330 TCGGTGGAGTAATATTAAAAGCAATT 57.486 30.769 0.00 0.00 0.00 2.32
506 507 0.570734 CATACGGATCAACGTCGTGC 59.429 55.000 9.23 0.00 45.08 5.34
601 603 4.036734 CCATCCAAACCGGTTGAAGATATG 59.963 45.833 23.08 17.08 39.87 1.78
665 667 1.142748 CACAACCGGCTGGCAAAAA 59.857 52.632 12.89 0.00 39.70 1.94
695 702 1.269723 GCCAAAGGACAAACTAGCCAC 59.730 52.381 0.00 0.00 0.00 5.01
858 872 4.156739 GTGCATGGTTAAAAAGGGAGAGAG 59.843 45.833 0.00 0.00 0.00 3.20
859 873 4.079253 GTGCATGGTTAAAAAGGGAGAGA 58.921 43.478 0.00 0.00 0.00 3.10
863 877 3.161866 GAGGTGCATGGTTAAAAAGGGA 58.838 45.455 0.00 0.00 0.00 4.20
897 911 1.873591 GTGCTGTGGTCTGTAAAGGTG 59.126 52.381 0.00 0.00 0.00 4.00
903 917 1.070134 GAGGTTGTGCTGTGGTCTGTA 59.930 52.381 0.00 0.00 0.00 2.74
907 921 0.179045 AGTGAGGTTGTGCTGTGGTC 60.179 55.000 0.00 0.00 0.00 4.02
909 923 1.070758 ACTAGTGAGGTTGTGCTGTGG 59.929 52.381 0.00 0.00 0.00 4.17
911 925 1.344763 GGACTAGTGAGGTTGTGCTGT 59.655 52.381 0.00 0.00 0.00 4.40
913 927 0.977395 GGGACTAGTGAGGTTGTGCT 59.023 55.000 0.00 0.00 0.00 4.40
936 950 1.001406 GCTCGCTAGCCCTATGTGAAT 59.999 52.381 9.66 0.00 43.40 2.57
937 951 0.389391 GCTCGCTAGCCCTATGTGAA 59.611 55.000 9.66 0.00 43.40 3.18
959 973 0.466555 TAGCTCGAGAAGGGAGGCTC 60.467 60.000 18.75 5.78 32.10 4.70
973 987 1.131504 CTGAGTGAGTGGTCGTAGCTC 59.868 57.143 0.00 0.00 0.00 4.09
998 1030 1.522355 ATCCTGCCGTTGCTCATCG 60.522 57.895 0.00 0.00 38.71 3.84
1174 1227 1.301953 GTAACCGGTTGAAGGCGGT 60.302 57.895 30.08 1.96 36.15 5.68
1243 1296 3.857521 TAAGGACCAGCCCACCGGT 62.858 63.158 0.00 0.00 38.56 5.28
1315 1380 0.308684 TACACGTCACTGTGACCGTC 59.691 55.000 29.42 10.18 44.20 4.79
1324 1389 2.599578 AGCCGGGTACACGTCACT 60.600 61.111 17.68 7.96 0.00 3.41
1374 1448 2.196229 CCGATCCTCCCCTCGTCT 59.804 66.667 0.00 0.00 33.11 4.18
1379 1453 1.306997 TTCAAGCCGATCCTCCCCT 60.307 57.895 0.00 0.00 0.00 4.79
1520 1594 2.205462 AGTCCTCCACCTGGCACT 59.795 61.111 0.00 0.00 34.44 4.40
1693 1796 2.024273 ACGTTCCTAGAGAGGGATGGAA 60.024 50.000 0.00 0.00 41.38 3.53
1728 1831 0.179194 CGTTTCGACGGAGAGAGACC 60.179 60.000 0.00 0.00 0.00 3.85
1729 1832 0.795085 TCGTTTCGACGGAGAGAGAC 59.205 55.000 0.00 0.00 0.00 3.36
1738 1841 2.311450 TCAGTTCTCTCGTTTCGACG 57.689 50.000 0.00 0.00 0.00 5.12
1739 1842 3.566523 ACATCAGTTCTCTCGTTTCGAC 58.433 45.455 0.00 0.00 0.00 4.20
1756 1876 1.135859 CAGTTTGCGCTGGAGAACATC 60.136 52.381 9.73 0.00 33.11 3.06
1811 1985 2.742372 ATGACTGGTCGCCGCAAC 60.742 61.111 0.00 0.00 0.00 4.17
1813 1987 3.932580 GACATGACTGGTCGCCGCA 62.933 63.158 0.00 0.00 0.00 5.69
1817 2040 4.678509 TTTATTTGACATGACTGGTCGC 57.321 40.909 0.00 0.00 38.10 5.19
1855 2078 4.157849 TGTTTGTGGTACATGGAGTTGA 57.842 40.909 0.00 0.00 44.52 3.18
1857 2080 4.724399 TGATGTTTGTGGTACATGGAGTT 58.276 39.130 0.00 0.00 44.52 3.01
1868 2095 3.731652 TGGAAAAGCTGATGTTTGTGG 57.268 42.857 0.00 0.00 0.00 4.17
1878 2105 2.061028 GAAAACGCCATGGAAAAGCTG 58.939 47.619 18.40 0.00 0.00 4.24
1965 3339 5.197451 TGAAGTCTGAAAACTAGCCCAAAA 58.803 37.500 0.00 0.00 0.00 2.44
1976 3350 3.804325 CGAAGCAGTCTGAAGTCTGAAAA 59.196 43.478 3.32 0.00 33.96 2.29
1977 3351 3.181475 ACGAAGCAGTCTGAAGTCTGAAA 60.181 43.478 3.32 0.00 33.96 2.69
2040 6179 5.948742 AAAAGTAGGAGCAGAGATTAGCT 57.051 39.130 0.00 0.00 45.25 3.32
2141 6315 9.846248 AGTTGTAGTACGTACCTATAACAAAAG 57.154 33.333 26.55 0.00 30.53 2.27
2146 6405 9.495754 CTTCAAGTTGTAGTACGTACCTATAAC 57.504 37.037 21.80 22.14 0.00 1.89
2151 6410 5.072741 TCCTTCAAGTTGTAGTACGTACCT 58.927 41.667 21.80 8.73 0.00 3.08
2160 6422 5.577164 CGTACCAGAATCCTTCAAGTTGTAG 59.423 44.000 2.11 2.41 0.00 2.74
2177 6439 2.190981 CTAAGCTAAACCGCGTACCAG 58.809 52.381 4.92 0.00 34.40 4.00
2182 6444 0.739813 CAGGCTAAGCTAAACCGCGT 60.740 55.000 4.92 0.00 34.40 6.01
2184 6446 0.727398 CACAGGCTAAGCTAAACCGC 59.273 55.000 0.00 0.00 0.00 5.68
2186 6448 3.146847 ACAACACAGGCTAAGCTAAACC 58.853 45.455 0.00 0.00 0.00 3.27
2187 6449 4.515567 AGAACAACACAGGCTAAGCTAAAC 59.484 41.667 0.00 0.00 0.00 2.01
2188 6450 4.714632 AGAACAACACAGGCTAAGCTAAA 58.285 39.130 0.00 0.00 0.00 1.85
2202 6465 5.008613 GCAAATCCAGAGTACAAGAACAACA 59.991 40.000 0.00 0.00 0.00 3.33
2217 6618 3.119849 CGTGGAACCTAAAGCAAATCCAG 60.120 47.826 0.00 0.00 37.62 3.86
2224 6625 0.107831 AGCACGTGGAACCTAAAGCA 59.892 50.000 18.88 0.00 0.00 3.91
2253 6654 2.650116 GCTCCTCTTGGCCTCGTCA 61.650 63.158 3.32 0.00 0.00 4.35
2348 6749 3.126703 TTGGAAGGTGGCGCCAAGA 62.127 57.895 34.66 5.51 40.61 3.02
2355 6756 0.469144 TGGGTTTCTTGGAAGGTGGC 60.469 55.000 0.00 0.00 0.00 5.01
2380 6781 2.936160 TAGGAGCTGGAGATGCCGCT 62.936 60.000 0.00 0.00 45.04 5.52
2404 6805 3.078837 CCGGCTTACTGTTATTGTTGGT 58.921 45.455 0.00 0.00 0.00 3.67
2407 6808 2.486592 GTGCCGGCTTACTGTTATTGTT 59.513 45.455 29.70 0.00 0.00 2.83
2449 6850 4.442192 GCACTACTAGATAGGCTGCAAACT 60.442 45.833 0.50 0.00 34.50 2.66
2450 6851 3.804873 GCACTACTAGATAGGCTGCAAAC 59.195 47.826 0.50 0.00 34.50 2.93
2451 6852 3.450817 TGCACTACTAGATAGGCTGCAAA 59.549 43.478 0.50 0.00 39.00 3.68
2453 6854 2.666317 TGCACTACTAGATAGGCTGCA 58.334 47.619 0.50 5.35 39.40 4.41
2454 6855 3.068873 AGTTGCACTACTAGATAGGCTGC 59.931 47.826 0.00 2.95 34.79 5.25
2456 6857 3.639094 CCAGTTGCACTACTAGATAGGCT 59.361 47.826 0.00 0.00 34.89 4.58
2457 6858 3.385111 ACCAGTTGCACTACTAGATAGGC 59.615 47.826 0.00 2.14 34.89 3.93
2458 6859 4.645136 TGACCAGTTGCACTACTAGATAGG 59.355 45.833 0.00 0.00 34.89 2.57
2459 6860 5.836821 TGACCAGTTGCACTACTAGATAG 57.163 43.478 0.00 0.00 36.89 2.08
2460 6861 5.891551 TGATGACCAGTTGCACTACTAGATA 59.108 40.000 0.00 0.00 0.00 1.98
2461 6862 4.711846 TGATGACCAGTTGCACTACTAGAT 59.288 41.667 0.00 0.00 0.00 1.98
2462 6863 4.086457 TGATGACCAGTTGCACTACTAGA 58.914 43.478 0.00 0.00 0.00 2.43
2463 6864 4.456280 TGATGACCAGTTGCACTACTAG 57.544 45.455 0.00 0.00 0.00 2.57
2464 6865 5.420725 AATGATGACCAGTTGCACTACTA 57.579 39.130 0.00 0.00 0.00 1.82
2465 6866 3.988976 ATGATGACCAGTTGCACTACT 57.011 42.857 0.00 0.00 0.00 2.57
2466 6867 6.510157 CGATAAATGATGACCAGTTGCACTAC 60.510 42.308 0.00 0.00 34.59 2.73
2475 6876 2.154462 GCCCCGATAAATGATGACCAG 58.846 52.381 0.00 0.00 0.00 4.00
2505 6909 2.546789 TCGACGATCGTACATGCATACT 59.453 45.455 22.79 0.00 41.35 2.12
2509 6913 1.332375 TGATCGACGATCGTACATGCA 59.668 47.619 27.66 12.89 41.51 3.96
2510 6914 1.972640 CTGATCGACGATCGTACATGC 59.027 52.381 27.66 7.31 41.51 4.06
2511 6915 1.972640 GCTGATCGACGATCGTACATG 59.027 52.381 27.66 11.56 41.51 3.21
2512 6916 1.874231 AGCTGATCGACGATCGTACAT 59.126 47.619 27.66 15.68 41.51 2.29
2513 6917 1.296727 AGCTGATCGACGATCGTACA 58.703 50.000 27.66 16.78 41.51 2.90
2562 6967 3.764049 GTCGCGCTCGTGTTGGAC 61.764 66.667 5.56 0.00 36.96 4.02
2590 6995 2.282745 GCTGGCCTGGACTTGCTT 60.283 61.111 12.06 0.00 0.00 3.91
2595 7000 3.775654 GCTACGCTGGCCTGGACT 61.776 66.667 12.06 0.00 0.00 3.85
2685 7093 3.969119 TGGTGGAGCTGCATGGCA 61.969 61.111 12.38 0.00 36.92 4.92
2706 7114 3.890936 GAAGTGCTGCTGCTCCCGT 62.891 63.158 17.00 3.22 40.48 5.28
2708 7116 0.964358 AATGAAGTGCTGCTGCTCCC 60.964 55.000 17.00 8.55 40.48 4.30
2727 7135 0.116342 TTCTGTGCAGGAGGGAGGTA 59.884 55.000 0.00 0.00 0.00 3.08
2744 7152 2.857618 TGTTGCTGTTGTTGACGTTTC 58.142 42.857 0.00 0.00 0.00 2.78
2745 7153 2.999507 TGTTGCTGTTGTTGACGTTT 57.000 40.000 0.00 0.00 0.00 3.60
2749 7157 3.968649 ACATGATGTTGCTGTTGTTGAC 58.031 40.909 0.00 0.00 0.00 3.18
2754 7162 4.168922 ACATGACATGATGTTGCTGTTG 57.831 40.909 22.19 0.00 32.38 3.33
2845 7260 0.829333 TTGCTGCCATTGGTGTTGTT 59.171 45.000 4.26 0.00 0.00 2.83
2868 7289 1.619654 TAAGCATGCTGTTGTTGGCT 58.380 45.000 23.48 4.27 0.00 4.75
2885 7306 8.154203 TCTACATGAAGTCAACCTCAAACATAA 58.846 33.333 0.00 0.00 0.00 1.90
2953 7389 3.653836 TCCACCAAGTACCTAATGTGGTT 59.346 43.478 13.85 0.00 40.63 3.67
2964 7400 3.200483 ACGAAACACTTCCACCAAGTAC 58.800 45.455 0.00 0.00 44.14 2.73
2967 7403 3.775661 AAACGAAACACTTCCACCAAG 57.224 42.857 0.00 0.00 38.21 3.61
2983 7419 5.045215 GTCCTTTTTAACAGGGGAAAAACG 58.955 41.667 0.00 0.00 32.56 3.60
2989 7425 1.074244 CCGGTCCTTTTTAACAGGGGA 59.926 52.381 0.00 0.00 31.50 4.81
2990 7426 1.074244 TCCGGTCCTTTTTAACAGGGG 59.926 52.381 0.00 0.00 31.50 4.79
2993 7429 2.433436 CCCTCCGGTCCTTTTTAACAG 58.567 52.381 0.00 0.00 0.00 3.16
2994 7430 1.074244 CCCCTCCGGTCCTTTTTAACA 59.926 52.381 0.00 0.00 0.00 2.41
2995 7431 1.615116 CCCCCTCCGGTCCTTTTTAAC 60.615 57.143 0.00 0.00 0.00 2.01
2997 7433 0.476219 ACCCCCTCCGGTCCTTTTTA 60.476 55.000 0.00 0.00 0.00 1.52
2998 7434 1.365894 AACCCCCTCCGGTCCTTTTT 61.366 55.000 0.00 0.00 33.98 1.94
3000 7436 0.476219 TTAACCCCCTCCGGTCCTTT 60.476 55.000 0.00 0.00 33.98 3.11
3003 7439 1.300963 GTTTAACCCCCTCCGGTCC 59.699 63.158 0.00 0.00 33.98 4.46
3006 7442 1.378119 GCTGTTTAACCCCCTCCGG 60.378 63.158 0.00 0.00 0.00 5.14
3007 7443 1.743995 CGCTGTTTAACCCCCTCCG 60.744 63.158 0.00 0.00 0.00 4.63
3008 7444 0.675837 GTCGCTGTTTAACCCCCTCC 60.676 60.000 0.00 0.00 0.00 4.30
3009 7445 0.035739 TGTCGCTGTTTAACCCCCTC 59.964 55.000 0.00 0.00 0.00 4.30
3010 7446 0.475044 TTGTCGCTGTTTAACCCCCT 59.525 50.000 0.00 0.00 0.00 4.79
3011 7447 1.268625 CTTTGTCGCTGTTTAACCCCC 59.731 52.381 0.00 0.00 0.00 5.40
3025 7479 3.309954 GGGATCGAGTACATTGCTTTGTC 59.690 47.826 0.00 0.00 0.00 3.18
3067 7521 9.859427 CAATTGACTTCAGGCAAATCTTAAATA 57.141 29.630 0.00 0.00 0.00 1.40
3070 7524 7.288810 ACAATTGACTTCAGGCAAATCTTAA 57.711 32.000 13.59 0.00 0.00 1.85
3074 7528 4.161333 CGACAATTGACTTCAGGCAAATC 58.839 43.478 13.59 0.00 0.00 2.17
3080 7534 5.924475 ACTTTACGACAATTGACTTCAGG 57.076 39.130 13.59 0.00 0.00 3.86
3086 7540 8.940924 GTCAAACTAAACTTTACGACAATTGAC 58.059 33.333 13.59 4.95 36.25 3.18
3089 7543 7.911727 GTGGTCAAACTAAACTTTACGACAATT 59.088 33.333 0.00 0.00 0.00 2.32
3091 7545 6.370994 TGTGGTCAAACTAAACTTTACGACAA 59.629 34.615 0.00 0.00 0.00 3.18
3092 7546 5.873712 TGTGGTCAAACTAAACTTTACGACA 59.126 36.000 0.00 0.00 0.00 4.35
3134 7588 8.769891 TGTGTAACTTCAGTATTGTACATGTTG 58.230 33.333 2.30 0.00 38.04 3.33
3135 7589 8.896320 TGTGTAACTTCAGTATTGTACATGTT 57.104 30.769 2.30 0.00 38.04 2.71
3136 7590 8.896320 TTGTGTAACTTCAGTATTGTACATGT 57.104 30.769 2.69 2.69 38.04 3.21
3179 7638 7.732664 TGAAATCAATATCATTAGATGCGTCG 58.267 34.615 0.00 0.00 35.67 5.12
3285 7744 4.778427 AGTACTCCCTCAGGTCCTTTTTAG 59.222 45.833 0.00 0.00 0.00 1.85
3286 7745 4.759953 AGTACTCCCTCAGGTCCTTTTTA 58.240 43.478 0.00 0.00 0.00 1.52
3291 7750 1.215924 GCTAGTACTCCCTCAGGTCCT 59.784 57.143 0.00 0.00 0.00 3.85
3292 7751 1.215924 AGCTAGTACTCCCTCAGGTCC 59.784 57.143 0.00 0.00 0.00 4.46
3293 7752 2.740506 AGCTAGTACTCCCTCAGGTC 57.259 55.000 0.00 0.00 0.00 3.85
3294 7753 4.817874 ATTAGCTAGTACTCCCTCAGGT 57.182 45.455 0.00 0.00 0.00 4.00
3295 7754 5.141182 TGAATTAGCTAGTACTCCCTCAGG 58.859 45.833 0.00 0.00 0.00 3.86
3296 7755 6.348950 CGATGAATTAGCTAGTACTCCCTCAG 60.349 46.154 0.00 0.00 0.00 3.35
3297 7756 5.473846 CGATGAATTAGCTAGTACTCCCTCA 59.526 44.000 0.00 0.00 0.00 3.86
3298 7757 5.706369 TCGATGAATTAGCTAGTACTCCCTC 59.294 44.000 0.00 0.00 0.00 4.30
3299 7758 5.474189 GTCGATGAATTAGCTAGTACTCCCT 59.526 44.000 0.00 0.00 0.00 4.20
3300 7759 5.241064 TGTCGATGAATTAGCTAGTACTCCC 59.759 44.000 0.00 0.00 0.00 4.30
3301 7760 6.315091 TGTCGATGAATTAGCTAGTACTCC 57.685 41.667 0.00 0.00 0.00 3.85
3302 7761 7.364200 ACATGTCGATGAATTAGCTAGTACTC 58.636 38.462 0.00 0.00 33.36 2.59
3303 7762 7.278461 ACATGTCGATGAATTAGCTAGTACT 57.722 36.000 0.00 0.00 33.36 2.73
3304 7763 7.932120 AACATGTCGATGAATTAGCTAGTAC 57.068 36.000 0.00 0.00 33.36 2.73
3305 7764 8.847196 AGTAACATGTCGATGAATTAGCTAGTA 58.153 33.333 0.00 0.00 33.36 1.82
3306 7765 7.717568 AGTAACATGTCGATGAATTAGCTAGT 58.282 34.615 0.00 0.00 33.36 2.57
3307 7766 8.581057 AAGTAACATGTCGATGAATTAGCTAG 57.419 34.615 0.00 0.00 33.36 3.42
3309 7768 8.942338 TTAAGTAACATGTCGATGAATTAGCT 57.058 30.769 0.00 0.00 33.36 3.32
3337 7796 5.891198 TGCTAAGGGGTTGATATTATGCAT 58.109 37.500 3.79 3.79 0.00 3.96
3350 7809 0.698238 TGAGTTGCATGCTAAGGGGT 59.302 50.000 20.33 0.00 0.00 4.95
3437 8145 4.214545 TCTTCCACGTAAAACGATTGCATT 59.785 37.500 6.44 0.00 46.05 3.56
3517 8226 5.760253 GTGTACCCATTGATTCTCATAGTGG 59.240 44.000 0.00 0.00 0.00 4.00
3568 8277 3.056328 GCGGGTTGGCAAGGTCTC 61.056 66.667 0.00 0.00 0.00 3.36
3588 8297 0.675083 TCAATTGTGGGTTGCTGCTG 59.325 50.000 5.13 0.00 0.00 4.41
3663 8372 9.528018 GTTTGGTTCAACAATTTGAGAGAAATA 57.472 29.630 2.79 0.00 42.79 1.40
3667 8376 5.449862 CCGTTTGGTTCAACAATTTGAGAGA 60.450 40.000 2.79 0.00 42.79 3.10
3733 8442 9.218359 CAGTTGAGATGAAATTTGATTCGTATG 57.782 33.333 0.00 0.00 31.80 2.39
3796 8505 8.994429 TCACATGTTAGTGAAAACAAAACATT 57.006 26.923 0.00 0.00 44.92 2.71
3810 8519 5.481824 TCTGAAGACCATCTCACATGTTAGT 59.518 40.000 6.92 0.00 0.00 2.24
3823 8532 7.784073 TCTGAGATTATCTCTTCTGAAGACCAT 59.216 37.037 21.08 12.65 43.73 3.55
3824 8533 7.122048 TCTGAGATTATCTCTTCTGAAGACCA 58.878 38.462 21.08 6.41 43.73 4.02
3825 8534 7.285401 ACTCTGAGATTATCTCTTCTGAAGACC 59.715 40.741 21.08 2.51 43.73 3.85
3826 8535 8.225603 ACTCTGAGATTATCTCTTCTGAAGAC 57.774 38.462 21.08 5.77 43.73 3.01
3838 8547 9.921637 CCCAAGTAAGAATACTCTGAGATTATC 57.078 37.037 12.44 4.31 41.57 1.75
3839 8548 8.371699 GCCCAAGTAAGAATACTCTGAGATTAT 58.628 37.037 12.44 1.88 41.57 1.28
3840 8549 7.344612 TGCCCAAGTAAGAATACTCTGAGATTA 59.655 37.037 12.44 0.00 41.57 1.75
3841 8550 6.156949 TGCCCAAGTAAGAATACTCTGAGATT 59.843 38.462 12.44 6.84 41.57 2.40
3842 8551 5.663106 TGCCCAAGTAAGAATACTCTGAGAT 59.337 40.000 12.44 0.00 41.57 2.75
3843 8552 5.023452 TGCCCAAGTAAGAATACTCTGAGA 58.977 41.667 12.44 0.00 41.57 3.27
3844 8553 5.344743 TGCCCAAGTAAGAATACTCTGAG 57.655 43.478 2.45 2.45 41.57 3.35
3845 8554 5.189736 ACATGCCCAAGTAAGAATACTCTGA 59.810 40.000 0.00 0.00 41.57 3.27
3846 8555 5.431765 ACATGCCCAAGTAAGAATACTCTG 58.568 41.667 0.00 0.00 41.57 3.35
3847 8556 5.700402 ACATGCCCAAGTAAGAATACTCT 57.300 39.130 0.00 0.00 41.57 3.24
3848 8557 5.880332 TCAACATGCCCAAGTAAGAATACTC 59.120 40.000 0.00 0.00 41.57 2.59
3849 8558 5.815581 TCAACATGCCCAAGTAAGAATACT 58.184 37.500 0.00 0.00 44.33 2.12
3850 8559 6.151144 ACTTCAACATGCCCAAGTAAGAATAC 59.849 38.462 0.00 0.00 0.00 1.89
3851 8560 6.245408 ACTTCAACATGCCCAAGTAAGAATA 58.755 36.000 0.00 0.00 0.00 1.75
3852 8561 5.079643 ACTTCAACATGCCCAAGTAAGAAT 58.920 37.500 0.00 0.00 0.00 2.40
3853 8562 4.469657 ACTTCAACATGCCCAAGTAAGAA 58.530 39.130 0.00 0.00 0.00 2.52
3854 8563 4.072131 GACTTCAACATGCCCAAGTAAGA 58.928 43.478 0.00 0.00 0.00 2.10
3855 8564 3.820467 TGACTTCAACATGCCCAAGTAAG 59.180 43.478 0.00 0.00 0.00 2.34
3856 8565 3.826524 TGACTTCAACATGCCCAAGTAA 58.173 40.909 0.00 0.00 0.00 2.24
3857 8566 3.500448 TGACTTCAACATGCCCAAGTA 57.500 42.857 0.00 0.00 0.00 2.24
3858 8567 2.363306 TGACTTCAACATGCCCAAGT 57.637 45.000 3.97 3.97 0.00 3.16
3877 8586 6.540914 TCTGAGAAATCAACAACGTAAAGGTT 59.459 34.615 0.00 0.00 0.00 3.50
3878 8587 6.053005 TCTGAGAAATCAACAACGTAAAGGT 58.947 36.000 0.00 0.00 0.00 3.50
3879 8588 6.539649 TCTGAGAAATCAACAACGTAAAGG 57.460 37.500 0.00 0.00 0.00 3.11
3880 8589 8.835467 TTTTCTGAGAAATCAACAACGTAAAG 57.165 30.769 8.64 0.00 0.00 1.85
3883 8592 8.227791 GCTATTTTCTGAGAAATCAACAACGTA 58.772 33.333 8.64 0.00 31.96 3.57
3884 8593 7.078228 GCTATTTTCTGAGAAATCAACAACGT 58.922 34.615 8.64 0.00 31.96 3.99
3885 8594 7.077605 TGCTATTTTCTGAGAAATCAACAACG 58.922 34.615 8.64 0.00 31.96 4.10


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

AutoCloner maintained by Alex Coulton.