Multiple sequence alignment - TraesCS7A01G451000

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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 TraesCS7A01G451000 chr7A 100.000 3594 0 0 1 3594 644455268 644458861 0.000000e+00 6637
1 TraesCS7A01G451000 chr7A 85.983 2019 191 29 908 2863 644441196 644443185 0.000000e+00 2076
2 TraesCS7A01G451000 chr7B 92.161 2041 128 19 1030 3059 608183212 608185231 0.000000e+00 2854
3 TraesCS7A01G451000 chr7B 88.884 2087 129 39 1019 3073 607927742 607929757 0.000000e+00 2473
4 TraesCS7A01G451000 chr7B 86.868 1858 200 20 1029 2863 607909237 607911073 0.000000e+00 2039
5 TraesCS7A01G451000 chr7B 86.004 493 58 8 2378 2863 607930278 607930766 5.320000e-143 518
6 TraesCS7A01G451000 chr7B 93.458 214 14 0 3294 3507 608185439 608185652 5.790000e-83 318
7 TraesCS7A01G451000 chr7B 90.608 181 6 3 3115 3295 608185231 608185400 2.790000e-56 230
8 TraesCS7A01G451000 chr7B 96.000 75 3 0 957 1031 607927648 607927722 4.870000e-24 122
9 TraesCS7A01G451000 chr7B 96.000 75 3 0 957 1031 608183109 608183183 4.870000e-24 122
10 TraesCS7A01G451000 chr7D 84.912 2227 221 41 908 3072 560222165 560224338 0.000000e+00 2145
11 TraesCS7A01G451000 chr3A 98.714 700 8 1 21 720 150464625 150463927 0.000000e+00 1242
12 TraesCS7A01G451000 chr5D 91.348 705 51 10 21 721 420876083 420876781 0.000000e+00 955
13 TraesCS7A01G451000 chr5D 89.986 699 59 9 21 716 71910331 71909641 0.000000e+00 893
14 TraesCS7A01G451000 chr4D 90.612 703 55 11 21 720 260717656 260718350 0.000000e+00 922
15 TraesCS7A01G451000 chrUn 79.055 1418 235 44 1468 2848 143908680 143910072 0.000000e+00 917
16 TraesCS7A01G451000 chrUn 75.305 1065 217 34 1594 2633 26518243 26517200 5.430000e-128 468
17 TraesCS7A01G451000 chrUn 78.245 547 111 4 1596 2135 153435954 153435409 9.550000e-91 344
18 TraesCS7A01G451000 chrUn 82.090 335 57 2 1076 1407 153390165 153390499 2.110000e-72 283
19 TraesCS7A01G451000 chrUn 80.362 387 56 11 1029 1405 153436482 153436106 3.530000e-70 276
20 TraesCS7A01G451000 chr1D 90.254 708 59 7 19 723 454566067 454565367 0.000000e+00 917
21 TraesCS7A01G451000 chr6B 78.293 1488 253 45 1468 2909 84132336 84133799 0.000000e+00 894
22 TraesCS7A01G451000 chr6B 90.235 553 34 2 2390 2935 171038971 171038432 0.000000e+00 704
23 TraesCS7A01G451000 chr6B 74.689 1529 307 55 1580 3070 82957756 82956270 1.100000e-169 606
24 TraesCS7A01G451000 chr6B 75.373 670 139 18 1485 2135 84357357 84358019 2.100000e-77 300
25 TraesCS7A01G451000 chr6B 82.985 335 53 3 1076 1407 84566061 84566394 2.100000e-77 300
26 TraesCS7A01G451000 chr4B 89.704 709 61 12 18 720 285531576 285532278 0.000000e+00 894
27 TraesCS7A01G451000 chr2D 89.900 703 55 14 21 719 218303424 218302734 0.000000e+00 891
28 TraesCS7A01G451000 chr2D 89.150 553 38 3 2390 2935 278848123 278848660 0.000000e+00 669
29 TraesCS7A01G451000 chr3D 89.787 705 56 10 21 719 168369554 168370248 0.000000e+00 889
30 TraesCS7A01G451000 chr1A 89.616 703 64 8 21 719 531019633 531018936 0.000000e+00 885
31 TraesCS7A01G451000 chr6A 78.764 1408 233 41 1468 2848 47956541 47957909 0.000000e+00 883
32 TraesCS7A01G451000 chr6A 81.953 338 52 7 1076 1407 48056944 48056610 9.830000e-71 278


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 TraesCS7A01G451000 chr7A 644455268 644458861 3593 False 6637.000000 6637 100.00000 1 3594 1 chr7A.!!$F2 3593
1 TraesCS7A01G451000 chr7A 644441196 644443185 1989 False 2076.000000 2076 85.98300 908 2863 1 chr7A.!!$F1 1955
2 TraesCS7A01G451000 chr7B 607909237 607911073 1836 False 2039.000000 2039 86.86800 1029 2863 1 chr7B.!!$F1 1834
3 TraesCS7A01G451000 chr7B 607927648 607930766 3118 False 1037.666667 2473 90.29600 957 3073 3 chr7B.!!$F2 2116
4 TraesCS7A01G451000 chr7B 608183109 608185652 2543 False 881.000000 2854 93.05675 957 3507 4 chr7B.!!$F3 2550
5 TraesCS7A01G451000 chr7D 560222165 560224338 2173 False 2145.000000 2145 84.91200 908 3072 1 chr7D.!!$F1 2164
6 TraesCS7A01G451000 chr3A 150463927 150464625 698 True 1242.000000 1242 98.71400 21 720 1 chr3A.!!$R1 699
7 TraesCS7A01G451000 chr5D 420876083 420876781 698 False 955.000000 955 91.34800 21 721 1 chr5D.!!$F1 700
8 TraesCS7A01G451000 chr5D 71909641 71910331 690 True 893.000000 893 89.98600 21 716 1 chr5D.!!$R1 695
9 TraesCS7A01G451000 chr4D 260717656 260718350 694 False 922.000000 922 90.61200 21 720 1 chr4D.!!$F1 699
10 TraesCS7A01G451000 chrUn 143908680 143910072 1392 False 917.000000 917 79.05500 1468 2848 1 chrUn.!!$F1 1380
11 TraesCS7A01G451000 chrUn 26517200 26518243 1043 True 468.000000 468 75.30500 1594 2633 1 chrUn.!!$R1 1039
12 TraesCS7A01G451000 chrUn 153435409 153436482 1073 True 310.000000 344 79.30350 1029 2135 2 chrUn.!!$R2 1106
13 TraesCS7A01G451000 chr1D 454565367 454566067 700 True 917.000000 917 90.25400 19 723 1 chr1D.!!$R1 704
14 TraesCS7A01G451000 chr6B 84132336 84133799 1463 False 894.000000 894 78.29300 1468 2909 1 chr6B.!!$F1 1441
15 TraesCS7A01G451000 chr6B 171038432 171038971 539 True 704.000000 704 90.23500 2390 2935 1 chr6B.!!$R2 545
16 TraesCS7A01G451000 chr6B 82956270 82957756 1486 True 606.000000 606 74.68900 1580 3070 1 chr6B.!!$R1 1490
17 TraesCS7A01G451000 chr6B 84357357 84358019 662 False 300.000000 300 75.37300 1485 2135 1 chr6B.!!$F2 650
18 TraesCS7A01G451000 chr4B 285531576 285532278 702 False 894.000000 894 89.70400 18 720 1 chr4B.!!$F1 702
19 TraesCS7A01G451000 chr2D 218302734 218303424 690 True 891.000000 891 89.90000 21 719 1 chr2D.!!$R1 698
20 TraesCS7A01G451000 chr2D 278848123 278848660 537 False 669.000000 669 89.15000 2390 2935 1 chr2D.!!$F1 545
21 TraesCS7A01G451000 chr3D 168369554 168370248 694 False 889.000000 889 89.78700 21 719 1 chr3D.!!$F1 698
22 TraesCS7A01G451000 chr1A 531018936 531019633 697 True 885.000000 885 89.61600 21 719 1 chr1A.!!$R1 698
23 TraesCS7A01G451000 chr6A 47956541 47957909 1368 False 883.000000 883 78.76400 1468 2848 1 chr6A.!!$F1 1380

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
892 907 0.249657 GATCTGGCGAACCCTAGCTG 60.250 60.0 0.0 0.0 33.59 4.24 F
917 932 0.546122 TCCATCCCAATTCACTCCCG 59.454 55.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1948 0.248458 GCGCACAAATTACCCGGATG 60.248 55.0 0.73 0.0 0.0 3.51 R
2905 4321 0.872388 AGCCAAACCACGAACGATTC 59.128 50.0 0.14 0.0 0.0 2.52 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
32 33 8.375506 TGGATGTTTTCTTGACTAGTAAGATGT 58.624 33.333 12.57 0.00 34.42 3.06
469 481 4.115199 GAGGCGTTGGGGGCAGAT 62.115 66.667 0.00 0.00 34.40 2.90
685 700 1.683365 GGATGGCAGGCACACCATT 60.683 57.895 14.57 0.00 45.56 3.16
776 791 9.766754 AAGTACTCTCATAGATGATACATGGAT 57.233 33.333 0.00 0.00 36.02 3.41
777 792 9.766754 AGTACTCTCATAGATGATACATGGATT 57.233 33.333 0.00 0.00 36.02 3.01
778 793 9.800433 GTACTCTCATAGATGATACATGGATTG 57.200 37.037 0.00 0.00 36.02 2.67
779 794 8.661752 ACTCTCATAGATGATACATGGATTGA 57.338 34.615 0.00 0.00 36.02 2.57
780 795 9.269494 ACTCTCATAGATGATACATGGATTGAT 57.731 33.333 0.00 0.00 36.02 2.57
840 855 5.523438 GAGATTACCATTTCTCGTCTCCT 57.477 43.478 0.00 0.00 29.96 3.69
841 856 6.636562 GAGATTACCATTTCTCGTCTCCTA 57.363 41.667 0.00 0.00 29.96 2.94
842 857 6.642707 AGATTACCATTTCTCGTCTCCTAG 57.357 41.667 0.00 0.00 0.00 3.02
843 858 6.366340 AGATTACCATTTCTCGTCTCCTAGA 58.634 40.000 0.00 0.00 0.00 2.43
844 859 6.834451 AGATTACCATTTCTCGTCTCCTAGAA 59.166 38.462 0.00 0.00 0.00 2.10
845 860 6.845758 TTACCATTTCTCGTCTCCTAGAAA 57.154 37.500 0.00 0.00 43.72 2.52
847 862 6.301169 ACCATTTCTCGTCTCCTAGAAATT 57.699 37.500 7.41 0.00 45.62 1.82
848 863 6.342111 ACCATTTCTCGTCTCCTAGAAATTC 58.658 40.000 7.41 0.00 45.62 2.17
849 864 6.070767 ACCATTTCTCGTCTCCTAGAAATTCA 60.071 38.462 7.41 0.00 45.62 2.57
850 865 6.989169 CCATTTCTCGTCTCCTAGAAATTCAT 59.011 38.462 7.41 0.00 45.62 2.57
851 866 8.144478 CCATTTCTCGTCTCCTAGAAATTCATA 58.856 37.037 7.41 0.00 45.62 2.15
852 867 9.534565 CATTTCTCGTCTCCTAGAAATTCATAA 57.465 33.333 7.41 0.00 45.62 1.90
858 873 9.459640 TCGTCTCCTAGAAATTCATAAATTACG 57.540 33.333 0.00 0.00 33.93 3.18
859 874 9.245962 CGTCTCCTAGAAATTCATAAATTACGT 57.754 33.333 0.00 0.00 33.93 3.57
877 892 8.964476 AATTACGTGAATTACCATCAAGATCT 57.036 30.769 0.00 0.00 35.91 2.75
878 893 7.770801 TTACGTGAATTACCATCAAGATCTG 57.229 36.000 0.00 0.00 31.83 2.90
879 894 5.118990 ACGTGAATTACCATCAAGATCTGG 58.881 41.667 0.00 0.00 38.55 3.86
880 895 4.024556 CGTGAATTACCATCAAGATCTGGC 60.025 45.833 0.00 0.00 35.88 4.85
881 896 4.024556 GTGAATTACCATCAAGATCTGGCG 60.025 45.833 0.00 0.00 35.88 5.69
882 897 4.141733 TGAATTACCATCAAGATCTGGCGA 60.142 41.667 0.00 0.00 35.88 5.54
883 898 3.904800 TTACCATCAAGATCTGGCGAA 57.095 42.857 0.00 0.00 35.88 4.70
884 899 2.029838 ACCATCAAGATCTGGCGAAC 57.970 50.000 0.00 0.00 35.88 3.95
885 900 1.303309 CCATCAAGATCTGGCGAACC 58.697 55.000 0.00 0.00 0.00 3.62
886 901 1.303309 CATCAAGATCTGGCGAACCC 58.697 55.000 0.00 0.00 33.59 4.11
887 902 1.134280 CATCAAGATCTGGCGAACCCT 60.134 52.381 0.00 0.00 33.59 4.34
888 903 1.860641 TCAAGATCTGGCGAACCCTA 58.139 50.000 0.00 0.00 33.59 3.53
889 904 1.757118 TCAAGATCTGGCGAACCCTAG 59.243 52.381 0.00 0.00 33.59 3.02
890 905 0.466124 AAGATCTGGCGAACCCTAGC 59.534 55.000 0.00 0.00 33.59 3.42
891 906 0.397816 AGATCTGGCGAACCCTAGCT 60.398 55.000 0.00 0.00 33.59 3.32
892 907 0.249657 GATCTGGCGAACCCTAGCTG 60.250 60.000 0.00 0.00 33.59 4.24
893 908 2.317149 ATCTGGCGAACCCTAGCTGC 62.317 60.000 0.00 0.00 33.59 5.25
894 909 4.096003 TGGCGAACCCTAGCTGCC 62.096 66.667 0.00 0.00 45.91 4.85
895 910 4.858680 GGCGAACCCTAGCTGCCC 62.859 72.222 0.00 0.00 39.83 5.36
896 911 3.787001 GCGAACCCTAGCTGCCCT 61.787 66.667 0.00 0.00 0.00 5.19
897 912 2.187946 CGAACCCTAGCTGCCCTG 59.812 66.667 0.00 0.00 0.00 4.45
898 913 2.660064 CGAACCCTAGCTGCCCTGT 61.660 63.158 0.00 0.00 0.00 4.00
899 914 1.222113 GAACCCTAGCTGCCCTGTC 59.778 63.158 0.00 0.00 0.00 3.51
900 915 2.258748 GAACCCTAGCTGCCCTGTCC 62.259 65.000 0.00 0.00 0.00 4.02
901 916 2.688666 CCCTAGCTGCCCTGTCCA 60.689 66.667 0.00 0.00 0.00 4.02
902 917 2.074948 CCCTAGCTGCCCTGTCCAT 61.075 63.158 0.00 0.00 0.00 3.41
903 918 1.449353 CCTAGCTGCCCTGTCCATC 59.551 63.158 0.00 0.00 0.00 3.51
904 919 1.449353 CTAGCTGCCCTGTCCATCC 59.551 63.158 0.00 0.00 0.00 3.51
905 920 2.049627 CTAGCTGCCCTGTCCATCCC 62.050 65.000 0.00 0.00 0.00 3.85
906 921 2.838436 TAGCTGCCCTGTCCATCCCA 62.838 60.000 0.00 0.00 0.00 4.37
917 932 0.546122 TCCATCCCAATTCACTCCCG 59.454 55.000 0.00 0.00 0.00 5.14
927 942 2.365635 CACTCCCGACCTCCCCAT 60.366 66.667 0.00 0.00 0.00 4.00
931 946 3.861797 CCCGACCTCCCCATTCCG 61.862 72.222 0.00 0.00 0.00 4.30
933 948 2.499685 CGACCTCCCCATTCCGTC 59.500 66.667 0.00 0.00 0.00 4.79
954 969 1.379710 CCATTTCCCCATCCGTGCA 60.380 57.895 0.00 0.00 0.00 4.57
980 1020 1.514087 CATTGCGGCCAAATCTGCT 59.486 52.632 2.24 0.00 39.06 4.24
1435 1538 2.661718 ACAAGGTCCACGGTGAAAAAT 58.338 42.857 10.28 0.00 0.00 1.82
1437 1540 3.566742 ACAAGGTCCACGGTGAAAAATAC 59.433 43.478 10.28 0.00 0.00 1.89
1458 1561 9.515226 AAATACTTACAAGAACTTATTCTGGCA 57.485 29.630 0.00 0.00 44.82 4.92
1660 1763 2.772287 GTGCCTTGAAGAGCTTACACT 58.228 47.619 0.00 0.00 0.00 3.55
1701 1804 1.377202 TTGCCTCCATGTTCGCTCC 60.377 57.895 0.00 0.00 0.00 4.70
1735 1841 1.067142 GTATCTGCTTCCGTGACACCA 60.067 52.381 0.00 0.00 0.00 4.17
1821 1948 1.583054 GCCGAGATGATTGTGGTACC 58.417 55.000 4.43 4.43 0.00 3.34
1852 1979 0.605319 TTGTGCGCCTAAACTGGAGG 60.605 55.000 4.18 0.00 37.12 4.30
1881 2008 2.325761 CCTTTGTTACCTGTCGTCTCG 58.674 52.381 0.00 0.00 0.00 4.04
1896 2026 2.634600 GTCTCGAAGCTCCTAGTCTCA 58.365 52.381 0.00 0.00 0.00 3.27
2016 2210 3.737172 CCGGCTTGGCAAACTCGG 61.737 66.667 16.95 16.95 0.00 4.63
2037 2231 2.020720 TGCACACCGTGAAGATTTTGT 58.979 42.857 5.28 0.00 35.23 2.83
2118 2312 4.350346 CTGTCTTGAGAAGCTCTATGTCG 58.650 47.826 0.00 0.00 0.00 4.35
2166 2364 8.420189 GCTTTAAAACTTCTGATTTGATTGACG 58.580 33.333 0.00 0.00 0.00 4.35
2180 2378 8.736751 ATTTGATTGACGTATTGTTTGTAACC 57.263 30.769 0.00 0.00 0.00 2.85
2205 2406 2.309528 AACACAGAGACGCTTGACAA 57.690 45.000 0.00 0.00 0.00 3.18
2213 2414 5.934625 ACAGAGACGCTTGACAAATTCTTAT 59.065 36.000 0.00 0.00 0.00 1.73
2336 2551 4.385358 ACAGTGGTGTTTGAAACATTCC 57.615 40.909 14.40 11.87 44.35 3.01
2338 2553 5.197451 ACAGTGGTGTTTGAAACATTCCTA 58.803 37.500 14.40 0.00 44.35 2.94
2630 4029 5.121454 CCTGAAGATTGCACTGTTCTTAGTC 59.879 44.000 13.86 0.00 30.11 2.59
2637 4036 4.621991 TGCACTGTTCTTAGTCTCTTGTC 58.378 43.478 0.00 0.00 0.00 3.18
2646 4045 7.610305 TGTTCTTAGTCTCTTGTCCTTGTTTTT 59.390 33.333 0.00 0.00 0.00 1.94
2647 4046 9.106070 GTTCTTAGTCTCTTGTCCTTGTTTTTA 57.894 33.333 0.00 0.00 0.00 1.52
2884 4293 1.824852 GGTAACCCCATCTGCCAAAAG 59.175 52.381 0.00 0.00 0.00 2.27
2905 4321 2.361438 GTCCTACGGTCTTATCCTGTGG 59.639 54.545 0.00 0.00 0.00 4.17
3011 4429 5.774690 ACATGGAAAAAGCAGGAGATGTTTA 59.225 36.000 0.00 0.00 31.28 2.01
3072 4491 3.302365 TTGCTTGATGCTTACAAAGGC 57.698 42.857 0.00 0.00 43.37 4.35
3073 4492 2.517959 TGCTTGATGCTTACAAAGGCT 58.482 42.857 0.00 0.00 43.37 4.58
3074 4493 2.892852 TGCTTGATGCTTACAAAGGCTT 59.107 40.909 0.00 0.00 43.37 4.35
3075 4494 3.057315 TGCTTGATGCTTACAAAGGCTTC 60.057 43.478 0.00 0.00 43.37 3.86
3076 4495 3.057315 GCTTGATGCTTACAAAGGCTTCA 60.057 43.478 0.00 0.00 39.61 3.02
3077 4496 4.381292 GCTTGATGCTTACAAAGGCTTCAT 60.381 41.667 0.00 0.00 40.49 2.57
3078 4497 5.717119 CTTGATGCTTACAAAGGCTTCATT 58.283 37.500 0.00 0.00 40.49 2.57
3079 4498 5.726980 TGATGCTTACAAAGGCTTCATTT 57.273 34.783 0.00 0.00 37.58 2.32
3080 4499 6.832520 TGATGCTTACAAAGGCTTCATTTA 57.167 33.333 0.00 0.00 37.58 1.40
3081 4500 6.855836 TGATGCTTACAAAGGCTTCATTTAG 58.144 36.000 0.00 0.00 37.58 1.85
3082 4501 5.059404 TGCTTACAAAGGCTTCATTTAGC 57.941 39.130 0.00 7.24 40.48 3.09
3083 4502 4.522405 TGCTTACAAAGGCTTCATTTAGCA 59.478 37.500 15.43 15.43 43.02 3.49
3084 4503 4.859245 GCTTACAAAGGCTTCATTTAGCAC 59.141 41.667 0.00 0.00 43.02 4.40
3085 4504 3.942130 ACAAAGGCTTCATTTAGCACC 57.058 42.857 0.00 0.00 43.02 5.01
3086 4505 3.500343 ACAAAGGCTTCATTTAGCACCT 58.500 40.909 0.00 0.00 43.02 4.00
3087 4506 3.256631 ACAAAGGCTTCATTTAGCACCTG 59.743 43.478 0.00 0.00 43.02 4.00
3088 4507 2.887151 AGGCTTCATTTAGCACCTGT 57.113 45.000 0.00 0.00 43.02 4.00
3089 4508 4.301072 AAGGCTTCATTTAGCACCTGTA 57.699 40.909 0.00 0.00 43.02 2.74
3090 4509 3.878778 AGGCTTCATTTAGCACCTGTAG 58.121 45.455 0.00 0.00 43.02 2.74
3091 4510 2.945668 GGCTTCATTTAGCACCTGTAGG 59.054 50.000 0.00 0.00 43.02 3.18
3092 4511 2.356069 GCTTCATTTAGCACCTGTAGGC 59.644 50.000 0.00 0.00 40.89 3.93
3093 4512 3.878778 CTTCATTTAGCACCTGTAGGCT 58.121 45.455 0.00 0.00 43.94 4.58
3094 4513 3.266510 TCATTTAGCACCTGTAGGCTG 57.733 47.619 0.00 0.00 41.25 4.85
3095 4514 2.092968 TCATTTAGCACCTGTAGGCTGG 60.093 50.000 0.00 0.00 41.25 4.85
3096 4515 0.618458 TTTAGCACCTGTAGGCTGGG 59.382 55.000 0.00 0.00 41.25 4.45
3097 4516 1.910580 TTAGCACCTGTAGGCTGGGC 61.911 60.000 0.00 0.00 41.25 5.36
3107 4526 3.825623 GGCTGGGCCCCTATGCTT 61.826 66.667 22.27 0.00 44.06 3.91
3108 4527 2.460853 GGCTGGGCCCCTATGCTTA 61.461 63.158 22.27 0.00 44.06 3.09
3109 4528 1.770324 GCTGGGCCCCTATGCTTAT 59.230 57.895 22.27 0.00 0.00 1.73
3110 4529 0.991920 GCTGGGCCCCTATGCTTATA 59.008 55.000 22.27 0.00 0.00 0.98
3111 4530 1.354368 GCTGGGCCCCTATGCTTATAA 59.646 52.381 22.27 0.00 0.00 0.98
3112 4531 2.225017 GCTGGGCCCCTATGCTTATAAA 60.225 50.000 22.27 0.00 0.00 1.40
3113 4532 3.690460 CTGGGCCCCTATGCTTATAAAG 58.310 50.000 22.27 0.00 0.00 1.85
3114 4533 2.378547 TGGGCCCCTATGCTTATAAAGG 59.621 50.000 22.27 0.00 0.00 3.11
3184 4603 4.326278 GCACAAGATGTTTGATTGCTGATG 59.674 41.667 0.00 0.00 0.00 3.07
3188 4607 5.055642 AGATGTTTGATTGCTGATGTGTG 57.944 39.130 0.00 0.00 0.00 3.82
3189 4608 4.521639 AGATGTTTGATTGCTGATGTGTGT 59.478 37.500 0.00 0.00 0.00 3.72
3190 4609 3.967401 TGTTTGATTGCTGATGTGTGTG 58.033 40.909 0.00 0.00 0.00 3.82
3191 4610 3.380954 TGTTTGATTGCTGATGTGTGTGT 59.619 39.130 0.00 0.00 0.00 3.72
3192 4611 3.629438 TTGATTGCTGATGTGTGTGTG 57.371 42.857 0.00 0.00 0.00 3.82
3193 4612 2.574450 TGATTGCTGATGTGTGTGTGT 58.426 42.857 0.00 0.00 0.00 3.72
3194 4613 2.291190 TGATTGCTGATGTGTGTGTGTG 59.709 45.455 0.00 0.00 0.00 3.82
3195 4614 1.748950 TTGCTGATGTGTGTGTGTGT 58.251 45.000 0.00 0.00 0.00 3.72
3196 4615 1.015868 TGCTGATGTGTGTGTGTGTG 58.984 50.000 0.00 0.00 0.00 3.82
3197 4616 1.016627 GCTGATGTGTGTGTGTGTGT 58.983 50.000 0.00 0.00 0.00 3.72
3267 4686 0.765510 CAACCTGTAGGATAGGCCCC 59.234 60.000 0.00 0.00 38.96 5.80
3295 4714 8.596781 ATGCTTTTCTAGTTAGGAGAGTTCTA 57.403 34.615 0.00 0.00 0.00 2.10
3296 4715 8.057536 TGCTTTTCTAGTTAGGAGAGTTCTAG 57.942 38.462 0.00 0.00 0.00 2.43
3373 4832 1.554160 CTCTCTCCAGCTGGAACATGT 59.446 52.381 34.30 0.00 44.91 3.21
3382 4841 3.560481 CAGCTGGAACATGTGATGATCTC 59.440 47.826 5.57 0.00 38.20 2.75
3391 4850 5.215903 ACATGTGATGATCTCGTCGTATTC 58.784 41.667 0.00 0.00 34.69 1.75
3393 4852 5.243426 TGTGATGATCTCGTCGTATTCAA 57.757 39.130 0.00 0.00 34.69 2.69
3400 4859 7.416154 TGATCTCGTCGTATTCAAAAGTTTT 57.584 32.000 0.00 0.00 0.00 2.43
3448 4907 5.176774 GCCACCTTGTACAAATTTACAAAGC 59.823 40.000 10.03 5.52 40.59 3.51
3478 4937 2.430332 CCTTTCCTGTTGCAAGAACCAA 59.570 45.455 0.00 0.00 0.00 3.67
3494 4953 4.984161 AGAACCAACATTGAATTTTGCTCG 59.016 37.500 0.00 0.00 0.00 5.03
3497 4956 4.037923 ACCAACATTGAATTTTGCTCGAGT 59.962 37.500 15.13 0.00 0.00 4.18
3507 4966 2.433868 TTGCTCGAGTACCTGAACAC 57.566 50.000 15.13 0.00 0.00 3.32
3508 4967 1.617322 TGCTCGAGTACCTGAACACT 58.383 50.000 15.13 0.00 0.00 3.55
3509 4968 1.540267 TGCTCGAGTACCTGAACACTC 59.460 52.381 15.13 0.00 38.24 3.51
3510 4969 1.540267 GCTCGAGTACCTGAACACTCA 59.460 52.381 15.13 0.00 41.04 3.41
3511 4970 2.164624 GCTCGAGTACCTGAACACTCAT 59.835 50.000 15.13 0.00 41.04 2.90
3512 4971 3.732471 GCTCGAGTACCTGAACACTCATC 60.732 52.174 15.13 0.00 41.04 2.92
3513 4972 3.418047 TCGAGTACCTGAACACTCATCA 58.582 45.455 2.98 0.00 41.04 3.07
3514 4973 3.824443 TCGAGTACCTGAACACTCATCAA 59.176 43.478 2.98 0.00 41.04 2.57
3515 4974 3.921021 CGAGTACCTGAACACTCATCAAC 59.079 47.826 2.98 0.00 41.04 3.18
3516 4975 4.321304 CGAGTACCTGAACACTCATCAACT 60.321 45.833 2.98 0.00 41.04 3.16
3517 4976 5.542779 GAGTACCTGAACACTCATCAACTT 58.457 41.667 0.00 0.00 40.74 2.66
3518 4977 5.300752 AGTACCTGAACACTCATCAACTTG 58.699 41.667 0.00 0.00 0.00 3.16
3519 4978 4.156455 ACCTGAACACTCATCAACTTGT 57.844 40.909 0.00 0.00 0.00 3.16
3520 4979 4.526970 ACCTGAACACTCATCAACTTGTT 58.473 39.130 0.00 0.00 34.88 2.83
3521 4980 4.949856 ACCTGAACACTCATCAACTTGTTT 59.050 37.500 0.00 0.00 32.34 2.83
3522 4981 5.418840 ACCTGAACACTCATCAACTTGTTTT 59.581 36.000 0.00 0.00 32.34 2.43
3523 4982 6.071391 ACCTGAACACTCATCAACTTGTTTTT 60.071 34.615 0.00 0.00 32.34 1.94
3524 4983 6.473455 CCTGAACACTCATCAACTTGTTTTTC 59.527 38.462 0.00 0.00 32.34 2.29
3525 4984 7.156876 TGAACACTCATCAACTTGTTTTTCT 57.843 32.000 0.00 0.00 32.34 2.52
3526 4985 7.028962 TGAACACTCATCAACTTGTTTTTCTG 58.971 34.615 0.00 0.00 32.34 3.02
3527 4986 5.343249 ACACTCATCAACTTGTTTTTCTGC 58.657 37.500 0.00 0.00 0.00 4.26
3528 4987 5.105797 ACACTCATCAACTTGTTTTTCTGCA 60.106 36.000 0.00 0.00 0.00 4.41
3529 4988 5.981315 CACTCATCAACTTGTTTTTCTGCAT 59.019 36.000 0.00 0.00 0.00 3.96
3530 4989 6.477688 CACTCATCAACTTGTTTTTCTGCATT 59.522 34.615 0.00 0.00 0.00 3.56
3531 4990 6.477688 ACTCATCAACTTGTTTTTCTGCATTG 59.522 34.615 0.00 0.00 0.00 2.82
3532 4991 6.571605 TCATCAACTTGTTTTTCTGCATTGA 58.428 32.000 0.00 0.00 0.00 2.57
3533 4992 7.211573 TCATCAACTTGTTTTTCTGCATTGAT 58.788 30.769 0.00 0.00 36.28 2.57
3534 4993 6.831727 TCAACTTGTTTTTCTGCATTGATG 57.168 33.333 0.00 0.00 0.00 3.07
3535 4994 6.339730 TCAACTTGTTTTTCTGCATTGATGT 58.660 32.000 0.00 0.00 0.00 3.06
3536 4995 6.817641 TCAACTTGTTTTTCTGCATTGATGTT 59.182 30.769 0.00 0.00 0.00 2.71
3537 4996 7.333921 TCAACTTGTTTTTCTGCATTGATGTTT 59.666 29.630 0.00 0.00 0.00 2.83
3538 4997 7.007313 ACTTGTTTTTCTGCATTGATGTTTG 57.993 32.000 0.00 0.00 0.00 2.93
3539 4998 5.406767 TGTTTTTCTGCATTGATGTTTGC 57.593 34.783 0.00 0.00 39.33 3.68
3540 4999 4.272991 TGTTTTTCTGCATTGATGTTTGCC 59.727 37.500 0.00 0.00 38.08 4.52
3541 5000 3.747854 TTTCTGCATTGATGTTTGCCA 57.252 38.095 0.00 0.00 38.08 4.92
3542 5001 3.747854 TTCTGCATTGATGTTTGCCAA 57.252 38.095 0.00 0.00 38.08 4.52
3543 5002 3.747854 TCTGCATTGATGTTTGCCAAA 57.252 38.095 0.00 0.00 38.08 3.28
3544 5003 4.069300 TCTGCATTGATGTTTGCCAAAA 57.931 36.364 0.00 0.00 38.08 2.44
3545 5004 4.059511 TCTGCATTGATGTTTGCCAAAAG 58.940 39.130 0.00 0.00 38.08 2.27
3546 5005 4.059511 CTGCATTGATGTTTGCCAAAAGA 58.940 39.130 0.00 0.00 38.08 2.52
3547 5006 4.449131 TGCATTGATGTTTGCCAAAAGAA 58.551 34.783 0.00 0.00 38.08 2.52
3548 5007 4.880120 TGCATTGATGTTTGCCAAAAGAAA 59.120 33.333 0.00 0.00 38.08 2.52
3549 5008 5.356190 TGCATTGATGTTTGCCAAAAGAAAA 59.644 32.000 0.00 0.00 38.08 2.29
3550 5009 5.910723 GCATTGATGTTTGCCAAAAGAAAAG 59.089 36.000 0.00 0.00 32.66 2.27
3551 5010 6.238429 GCATTGATGTTTGCCAAAAGAAAAGA 60.238 34.615 0.00 0.00 32.66 2.52
3552 5011 7.679164 GCATTGATGTTTGCCAAAAGAAAAGAA 60.679 33.333 0.00 0.00 32.66 2.52
3553 5012 7.678947 TTGATGTTTGCCAAAAGAAAAGAAA 57.321 28.000 0.00 0.00 0.00 2.52
3554 5013 7.678947 TGATGTTTGCCAAAAGAAAAGAAAA 57.321 28.000 0.00 0.00 0.00 2.29
3555 5014 7.750769 TGATGTTTGCCAAAAGAAAAGAAAAG 58.249 30.769 0.00 0.00 0.00 2.27
3556 5015 6.493449 TGTTTGCCAAAAGAAAAGAAAAGG 57.507 33.333 0.00 0.00 0.00 3.11
3557 5016 6.234177 TGTTTGCCAAAAGAAAAGAAAAGGA 58.766 32.000 0.00 0.00 0.00 3.36
3558 5017 6.712547 TGTTTGCCAAAAGAAAAGAAAAGGAA 59.287 30.769 0.00 0.00 0.00 3.36
3559 5018 7.229506 TGTTTGCCAAAAGAAAAGAAAAGGAAA 59.770 29.630 0.00 0.00 0.00 3.13
3560 5019 6.983474 TGCCAAAAGAAAAGAAAAGGAAAG 57.017 33.333 0.00 0.00 0.00 2.62
3561 5020 6.706295 TGCCAAAAGAAAAGAAAAGGAAAGA 58.294 32.000 0.00 0.00 0.00 2.52
3562 5021 7.164803 TGCCAAAAGAAAAGAAAAGGAAAGAA 58.835 30.769 0.00 0.00 0.00 2.52
3563 5022 7.334171 TGCCAAAAGAAAAGAAAAGGAAAGAAG 59.666 33.333 0.00 0.00 0.00 2.85
3564 5023 7.549134 GCCAAAAGAAAAGAAAAGGAAAGAAGA 59.451 33.333 0.00 0.00 0.00 2.87
3565 5024 9.435688 CCAAAAGAAAAGAAAAGGAAAGAAGAA 57.564 29.630 0.00 0.00 0.00 2.52
3570 5029 9.862371 AGAAAAGAAAAGGAAAGAAGAAAGAAC 57.138 29.630 0.00 0.00 0.00 3.01
3571 5030 9.862371 GAAAAGAAAAGGAAAGAAGAAAGAACT 57.138 29.630 0.00 0.00 0.00 3.01
3573 5032 9.645059 AAAGAAAAGGAAAGAAGAAAGAACTTG 57.355 29.630 0.00 0.00 0.00 3.16
3574 5033 8.354711 AGAAAAGGAAAGAAGAAAGAACTTGT 57.645 30.769 0.00 0.00 0.00 3.16
3575 5034 8.807118 AGAAAAGGAAAGAAGAAAGAACTTGTT 58.193 29.630 0.00 0.00 35.43 2.83
3576 5035 9.424319 GAAAAGGAAAGAAGAAAGAACTTGTTT 57.576 29.630 0.00 0.00 42.88 2.83
3577 5036 9.778741 AAAAGGAAAGAAGAAAGAACTTGTTTT 57.221 25.926 0.00 0.00 41.23 2.43
3578 5037 9.778741 AAAGGAAAGAAGAAAGAACTTGTTTTT 57.221 25.926 0.00 0.00 41.23 1.94
3579 5038 8.988064 AGGAAAGAAGAAAGAACTTGTTTTTC 57.012 30.769 0.00 10.33 41.23 2.29
3580 5039 8.807118 AGGAAAGAAGAAAGAACTTGTTTTTCT 58.193 29.630 0.00 12.96 41.23 2.52
3581 5040 8.864024 GGAAAGAAGAAAGAACTTGTTTTTCTG 58.136 33.333 16.40 0.00 41.23 3.02
3582 5041 7.818493 AAGAAGAAAGAACTTGTTTTTCTGC 57.182 32.000 16.40 15.36 40.12 4.26
3583 5042 6.924111 AGAAGAAAGAACTTGTTTTTCTGCA 58.076 32.000 19.23 0.00 40.12 4.41
3584 5043 7.550712 AGAAGAAAGAACTTGTTTTTCTGCAT 58.449 30.769 19.23 9.86 40.12 3.96
3585 5044 8.037166 AGAAGAAAGAACTTGTTTTTCTGCATT 58.963 29.630 19.23 9.66 40.12 3.56
3586 5045 7.529880 AGAAAGAACTTGTTTTTCTGCATTG 57.470 32.000 15.64 0.00 39.12 2.82
3587 5046 5.723492 AAGAACTTGTTTTTCTGCATTGC 57.277 34.783 0.46 0.46 33.46 3.56
3588 5047 5.014808 AGAACTTGTTTTTCTGCATTGCT 57.985 34.783 10.49 0.00 31.88 3.91
3589 5048 4.807304 AGAACTTGTTTTTCTGCATTGCTG 59.193 37.500 10.49 9.74 31.88 4.41
3590 5049 4.389890 ACTTGTTTTTCTGCATTGCTGA 57.610 36.364 13.50 13.50 34.87 4.26
3591 5050 4.114794 ACTTGTTTTTCTGCATTGCTGAC 58.885 39.130 16.67 7.71 36.32 3.51
3592 5051 3.797451 TGTTTTTCTGCATTGCTGACA 57.203 38.095 16.67 8.79 36.32 3.58
3593 5052 3.708890 TGTTTTTCTGCATTGCTGACAG 58.291 40.909 16.67 0.00 36.32 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.881775 ACTAGTCAAGAAAACATCCAAGTTT 57.118 32.000 0.00 0.00 43.13 2.66
2 3 8.974060 TTACTAGTCAAGAAAACATCCAAGTT 57.026 30.769 0.00 0.00 0.00 2.66
3 4 8.429641 TCTTACTAGTCAAGAAAACATCCAAGT 58.570 33.333 0.00 0.00 0.00 3.16
4 5 8.833231 TCTTACTAGTCAAGAAAACATCCAAG 57.167 34.615 0.00 0.00 0.00 3.61
5 6 9.219603 CATCTTACTAGTCAAGAAAACATCCAA 57.780 33.333 0.00 0.00 35.73 3.53
6 7 8.375506 ACATCTTACTAGTCAAGAAAACATCCA 58.624 33.333 0.00 0.00 35.73 3.41
7 8 8.779354 ACATCTTACTAGTCAAGAAAACATCC 57.221 34.615 0.00 0.00 35.73 3.51
8 9 8.874816 GGACATCTTACTAGTCAAGAAAACATC 58.125 37.037 0.00 3.38 35.73 3.06
9 10 7.545965 CGGACATCTTACTAGTCAAGAAAACAT 59.454 37.037 0.00 0.00 35.73 2.71
10 11 6.866770 CGGACATCTTACTAGTCAAGAAAACA 59.133 38.462 0.00 0.00 35.73 2.83
11 12 6.867293 ACGGACATCTTACTAGTCAAGAAAAC 59.133 38.462 0.00 3.81 35.73 2.43
12 13 6.866770 CACGGACATCTTACTAGTCAAGAAAA 59.133 38.462 0.00 0.00 35.73 2.29
13 14 6.387465 CACGGACATCTTACTAGTCAAGAAA 58.613 40.000 0.00 0.00 35.73 2.52
14 15 5.621555 GCACGGACATCTTACTAGTCAAGAA 60.622 44.000 0.00 0.00 35.73 2.52
15 16 4.142447 GCACGGACATCTTACTAGTCAAGA 60.142 45.833 0.00 7.86 36.50 3.02
16 17 4.106197 GCACGGACATCTTACTAGTCAAG 58.894 47.826 0.00 2.31 34.04 3.02
17 18 3.508402 TGCACGGACATCTTACTAGTCAA 59.492 43.478 0.00 0.00 34.04 3.18
512 526 4.958581 TCACTTCATCTAGCCATCTCAGAA 59.041 41.667 0.00 0.00 0.00 3.02
685 700 7.455058 TCTTATAAAAAGCTGAGTTGGTGGTA 58.545 34.615 0.00 0.00 0.00 3.25
750 765 9.766754 ATCCATGTATCATCTATGAGAGTACTT 57.233 33.333 0.00 0.00 40.64 2.24
751 766 9.766754 AATCCATGTATCATCTATGAGAGTACT 57.233 33.333 0.00 0.00 40.64 2.73
752 767 9.800433 CAATCCATGTATCATCTATGAGAGTAC 57.200 37.037 0.00 0.00 40.64 2.73
753 768 9.759473 TCAATCCATGTATCATCTATGAGAGTA 57.241 33.333 0.00 0.00 40.64 2.59
754 769 8.661752 TCAATCCATGTATCATCTATGAGAGT 57.338 34.615 0.00 0.00 40.64 3.24
818 833 5.523438 AGGAGACGAGAAATGGTAATCTC 57.477 43.478 0.00 0.00 38.94 2.75
819 834 6.366340 TCTAGGAGACGAGAAATGGTAATCT 58.634 40.000 0.00 0.00 39.28 2.40
820 835 6.636562 TCTAGGAGACGAGAAATGGTAATC 57.363 41.667 0.00 0.00 39.28 1.75
832 847 9.459640 CGTAATTTATGAATTTCTAGGAGACGA 57.540 33.333 0.26 0.00 36.82 4.20
833 848 9.245962 ACGTAATTTATGAATTTCTAGGAGACG 57.754 33.333 0.26 5.20 36.82 4.18
851 866 9.396022 AGATCTTGATGGTAATTCACGTAATTT 57.604 29.630 7.84 0.00 38.71 1.82
852 867 8.830580 CAGATCTTGATGGTAATTCACGTAATT 58.169 33.333 0.00 0.00 40.87 1.40
853 868 7.442364 CCAGATCTTGATGGTAATTCACGTAAT 59.558 37.037 0.00 0.00 0.00 1.89
854 869 6.761242 CCAGATCTTGATGGTAATTCACGTAA 59.239 38.462 0.00 0.00 0.00 3.18
855 870 6.280643 CCAGATCTTGATGGTAATTCACGTA 58.719 40.000 0.00 0.00 0.00 3.57
856 871 5.118990 CCAGATCTTGATGGTAATTCACGT 58.881 41.667 0.00 0.00 0.00 4.49
857 872 4.024556 GCCAGATCTTGATGGTAATTCACG 60.025 45.833 0.00 0.00 38.91 4.35
858 873 4.024556 CGCCAGATCTTGATGGTAATTCAC 60.025 45.833 0.00 0.00 38.91 3.18
859 874 4.129380 CGCCAGATCTTGATGGTAATTCA 58.871 43.478 0.00 0.00 38.91 2.57
860 875 4.380531 TCGCCAGATCTTGATGGTAATTC 58.619 43.478 0.00 0.00 38.91 2.17
861 876 4.422073 TCGCCAGATCTTGATGGTAATT 57.578 40.909 0.00 0.00 38.91 1.40
862 877 4.130118 GTTCGCCAGATCTTGATGGTAAT 58.870 43.478 0.00 0.00 38.91 1.89
863 878 3.531538 GTTCGCCAGATCTTGATGGTAA 58.468 45.455 0.00 0.00 38.91 2.85
864 879 2.158957 GGTTCGCCAGATCTTGATGGTA 60.159 50.000 0.00 0.00 38.91 3.25
865 880 1.407437 GGTTCGCCAGATCTTGATGGT 60.407 52.381 0.00 0.00 38.91 3.55
866 881 1.303309 GGTTCGCCAGATCTTGATGG 58.697 55.000 0.00 0.00 39.73 3.51
867 882 1.134280 AGGGTTCGCCAGATCTTGATG 60.134 52.381 0.00 0.00 39.65 3.07
868 883 1.207791 AGGGTTCGCCAGATCTTGAT 58.792 50.000 0.00 0.00 39.65 2.57
869 884 1.757118 CTAGGGTTCGCCAGATCTTGA 59.243 52.381 0.00 0.00 39.65 3.02
870 885 1.808133 GCTAGGGTTCGCCAGATCTTG 60.808 57.143 0.00 0.00 39.65 3.02
871 886 0.466124 GCTAGGGTTCGCCAGATCTT 59.534 55.000 0.00 0.00 39.65 2.40
872 887 0.397816 AGCTAGGGTTCGCCAGATCT 60.398 55.000 0.00 0.00 39.65 2.75
873 888 0.249657 CAGCTAGGGTTCGCCAGATC 60.250 60.000 0.00 0.00 39.65 2.75
874 889 1.826024 CAGCTAGGGTTCGCCAGAT 59.174 57.895 0.00 0.00 39.65 2.90
875 890 3.019003 GCAGCTAGGGTTCGCCAGA 62.019 63.158 0.00 0.00 39.65 3.86
876 891 2.512515 GCAGCTAGGGTTCGCCAG 60.513 66.667 0.00 0.00 39.65 4.85
877 892 4.096003 GGCAGCTAGGGTTCGCCA 62.096 66.667 4.21 0.00 42.50 5.69
878 893 4.858680 GGGCAGCTAGGGTTCGCC 62.859 72.222 0.40 0.40 42.21 5.54
879 894 3.787001 AGGGCAGCTAGGGTTCGC 61.787 66.667 0.00 0.00 0.00 4.70
880 895 2.187946 CAGGGCAGCTAGGGTTCG 59.812 66.667 0.00 0.00 0.00 3.95
881 896 1.222113 GACAGGGCAGCTAGGGTTC 59.778 63.158 0.00 0.00 0.00 3.62
882 897 2.301738 GGACAGGGCAGCTAGGGTT 61.302 63.158 0.00 0.00 0.00 4.11
883 898 2.689034 GGACAGGGCAGCTAGGGT 60.689 66.667 0.00 0.00 0.00 4.34
884 899 2.049627 GATGGACAGGGCAGCTAGGG 62.050 65.000 0.00 0.00 0.00 3.53
885 900 1.449353 GATGGACAGGGCAGCTAGG 59.551 63.158 0.00 0.00 0.00 3.02
886 901 1.449353 GGATGGACAGGGCAGCTAG 59.551 63.158 0.00 0.00 0.00 3.42
887 902 2.072487 GGGATGGACAGGGCAGCTA 61.072 63.158 0.00 0.00 0.00 3.32
888 903 3.415087 GGGATGGACAGGGCAGCT 61.415 66.667 0.00 0.00 0.00 4.24
889 904 2.578586 ATTGGGATGGACAGGGCAGC 62.579 60.000 0.00 0.00 0.00 5.25
890 905 0.032813 AATTGGGATGGACAGGGCAG 60.033 55.000 0.00 0.00 0.00 4.85
891 906 0.033208 GAATTGGGATGGACAGGGCA 60.033 55.000 0.00 0.00 0.00 5.36
892 907 0.033208 TGAATTGGGATGGACAGGGC 60.033 55.000 0.00 0.00 0.00 5.19
893 908 1.285962 AGTGAATTGGGATGGACAGGG 59.714 52.381 0.00 0.00 0.00 4.45
894 909 2.648059 GAGTGAATTGGGATGGACAGG 58.352 52.381 0.00 0.00 0.00 4.00
895 910 2.648059 GGAGTGAATTGGGATGGACAG 58.352 52.381 0.00 0.00 0.00 3.51
896 911 1.284785 GGGAGTGAATTGGGATGGACA 59.715 52.381 0.00 0.00 0.00 4.02
897 912 1.747206 CGGGAGTGAATTGGGATGGAC 60.747 57.143 0.00 0.00 0.00 4.02
898 913 0.546122 CGGGAGTGAATTGGGATGGA 59.454 55.000 0.00 0.00 0.00 3.41
899 914 0.546122 TCGGGAGTGAATTGGGATGG 59.454 55.000 0.00 0.00 0.00 3.51
900 915 1.668419 GTCGGGAGTGAATTGGGATG 58.332 55.000 0.00 0.00 0.00 3.51
901 916 0.546598 GGTCGGGAGTGAATTGGGAT 59.453 55.000 0.00 0.00 0.00 3.85
902 917 0.546747 AGGTCGGGAGTGAATTGGGA 60.547 55.000 0.00 0.00 0.00 4.37
903 918 0.107654 GAGGTCGGGAGTGAATTGGG 60.108 60.000 0.00 0.00 0.00 4.12
904 919 0.107654 GGAGGTCGGGAGTGAATTGG 60.108 60.000 0.00 0.00 0.00 3.16
905 920 0.107654 GGGAGGTCGGGAGTGAATTG 60.108 60.000 0.00 0.00 0.00 2.32
906 921 1.272554 GGGGAGGTCGGGAGTGAATT 61.273 60.000 0.00 0.00 0.00 2.17
917 932 2.743179 GGGACGGAATGGGGAGGTC 61.743 68.421 0.00 0.00 0.00 3.85
927 942 2.618449 GGGGAAATGGGGGACGGAA 61.618 63.158 0.00 0.00 0.00 4.30
931 946 1.233080 GGATGGGGAAATGGGGGAC 59.767 63.158 0.00 0.00 0.00 4.46
933 948 2.198426 CGGATGGGGAAATGGGGG 59.802 66.667 0.00 0.00 0.00 5.40
954 969 3.064324 GGCCGCAATGCTCCACTT 61.064 61.111 2.94 0.00 0.00 3.16
1435 1538 8.372459 TCTTGCCAGAATAAGTTCTTGTAAGTA 58.628 33.333 14.77 5.07 43.72 2.24
1437 1540 7.672983 TCTTGCCAGAATAAGTTCTTGTAAG 57.327 36.000 11.28 11.28 44.18 2.34
1458 1561 1.315257 ATGGCGGCAGCGAAATTCTT 61.315 50.000 19.29 0.00 46.35 2.52
1487 1590 0.324830 GAGGAGGGTAGGTGCAGAGT 60.325 60.000 0.00 0.00 0.00 3.24
1660 1763 1.890041 CACCACGAACTTCGGCCAA 60.890 57.895 15.42 0.00 45.59 4.52
1735 1841 5.622460 CGATGACAAGCTCTACTTTACCAGT 60.622 44.000 0.00 0.00 36.04 4.00
1821 1948 0.248458 GCGCACAAATTACCCGGATG 60.248 55.000 0.73 0.00 0.00 3.51
1852 1979 2.758423 CAGGTAACAAAGGGCCCAATAC 59.242 50.000 27.56 17.70 41.41 1.89
1881 2008 2.452505 ACCTGTGAGACTAGGAGCTTC 58.547 52.381 0.00 0.00 37.52 3.86
1896 2026 6.294473 GTTTGAGGATGATGATGATACCTGT 58.706 40.000 0.00 0.00 0.00 4.00
2016 2210 2.223479 ACAAAATCTTCACGGTGTGCAC 60.223 45.455 10.75 10.75 32.98 4.57
2037 2231 4.871822 TCATATCCAGAACACCTGAGAGA 58.128 43.478 0.00 0.00 45.78 3.10
2118 2312 3.360249 AGCAAAATGAGCACTCACAAC 57.640 42.857 1.71 0.00 43.11 3.32
2166 2364 6.911511 TGTGTTAAAGCGGTTACAAACAATAC 59.088 34.615 18.46 10.86 0.00 1.89
2180 2378 1.419374 AGCGTCTCTGTGTTAAAGCG 58.581 50.000 0.00 0.00 0.00 4.68
2230 2442 6.430925 TCTTATCCATCTCTTTGTGTTTGTGG 59.569 38.462 0.00 0.00 0.00 4.17
2336 2551 4.454678 TCAAGCTGTTTATCATGGCCTAG 58.545 43.478 3.32 0.00 0.00 3.02
2338 2553 3.285484 CTCAAGCTGTTTATCATGGCCT 58.715 45.455 3.32 0.00 0.00 5.19
2419 2634 3.780804 ACACTGTTGTAGGCACCATAA 57.219 42.857 0.00 0.00 32.60 1.90
2646 4045 9.481340 CGATCTTCAGGAATCAATATTGTCTTA 57.519 33.333 14.97 0.00 0.00 2.10
2647 4046 7.041508 GCGATCTTCAGGAATCAATATTGTCTT 60.042 37.037 14.97 9.93 0.00 3.01
2905 4321 0.872388 AGCCAAACCACGAACGATTC 59.128 50.000 0.14 0.00 0.00 2.52
2973 4391 7.595130 GCTTTTTCCATGTACTAACTGAAAAGG 59.405 37.037 15.64 13.33 33.77 3.11
3032 4451 7.046292 AGCAAATGATATATGCACACACATT 57.954 32.000 0.00 0.00 42.45 2.71
3033 4452 6.644248 AGCAAATGATATATGCACACACAT 57.356 33.333 0.00 0.00 42.45 3.21
3072 4491 3.624861 CAGCCTACAGGTGCTAAATGAAG 59.375 47.826 0.00 0.00 37.12 3.02
3073 4492 3.609853 CAGCCTACAGGTGCTAAATGAA 58.390 45.455 0.00 0.00 37.12 2.57
3074 4493 2.092968 CCAGCCTACAGGTGCTAAATGA 60.093 50.000 0.00 0.00 42.90 2.57
3075 4494 2.292267 CCAGCCTACAGGTGCTAAATG 58.708 52.381 0.00 0.00 42.90 2.32
3076 4495 1.212935 CCCAGCCTACAGGTGCTAAAT 59.787 52.381 0.00 0.00 42.90 1.40
3077 4496 0.618458 CCCAGCCTACAGGTGCTAAA 59.382 55.000 0.00 0.00 42.90 1.85
3078 4497 1.910580 GCCCAGCCTACAGGTGCTAA 61.911 60.000 0.00 0.00 42.90 3.09
3079 4498 2.367202 GCCCAGCCTACAGGTGCTA 61.367 63.158 0.00 0.00 42.90 3.49
3080 4499 3.721706 GCCCAGCCTACAGGTGCT 61.722 66.667 0.00 0.00 42.90 4.40
3081 4500 4.803908 GGCCCAGCCTACAGGTGC 62.804 72.222 0.00 0.00 46.69 5.01
3091 4510 0.991920 TATAAGCATAGGGGCCCAGC 59.008 55.000 27.72 24.61 0.00 4.85
3092 4511 3.562176 CCTTTATAAGCATAGGGGCCCAG 60.562 52.174 27.72 15.46 0.00 4.45
3093 4512 2.378547 CCTTTATAAGCATAGGGGCCCA 59.621 50.000 27.72 11.59 0.00 5.36
3094 4513 2.884304 GCCTTTATAAGCATAGGGGCCC 60.884 54.545 17.12 17.12 33.57 5.80
3095 4514 2.041755 AGCCTTTATAAGCATAGGGGCC 59.958 50.000 0.00 0.00 37.06 5.80
3096 4515 3.441500 AGCCTTTATAAGCATAGGGGC 57.558 47.619 3.64 0.00 36.84 5.80
3097 4516 5.509670 GCAAAAGCCTTTATAAGCATAGGGG 60.510 44.000 3.64 0.00 0.00 4.79
3098 4517 5.068987 TGCAAAAGCCTTTATAAGCATAGGG 59.931 40.000 3.64 0.00 0.00 3.53
3099 4518 6.147864 TGCAAAAGCCTTTATAAGCATAGG 57.852 37.500 0.00 0.00 0.00 2.57
3100 4519 7.428020 TCATGCAAAAGCCTTTATAAGCATAG 58.572 34.615 14.66 11.12 39.22 2.23
3101 4520 7.345422 TCATGCAAAAGCCTTTATAAGCATA 57.655 32.000 14.66 5.91 39.22 3.14
3102 4521 6.224665 TCATGCAAAAGCCTTTATAAGCAT 57.775 33.333 11.24 11.24 41.64 3.79
3103 4522 5.657826 TCATGCAAAAGCCTTTATAAGCA 57.342 34.783 8.34 8.34 35.03 3.91
3104 4523 6.332630 TCTTCATGCAAAAGCCTTTATAAGC 58.667 36.000 7.21 0.00 0.00 3.09
3105 4524 8.937634 ATTCTTCATGCAAAAGCCTTTATAAG 57.062 30.769 7.21 0.00 0.00 1.73
3106 4525 9.723601 AAATTCTTCATGCAAAAGCCTTTATAA 57.276 25.926 7.21 0.00 0.00 0.98
3107 4526 9.153721 CAAATTCTTCATGCAAAAGCCTTTATA 57.846 29.630 7.21 0.00 0.00 0.98
3108 4527 7.662669 ACAAATTCTTCATGCAAAAGCCTTTAT 59.337 29.630 7.21 0.00 0.00 1.40
3109 4528 6.991531 ACAAATTCTTCATGCAAAAGCCTTTA 59.008 30.769 7.21 0.00 0.00 1.85
3110 4529 5.824097 ACAAATTCTTCATGCAAAAGCCTTT 59.176 32.000 7.21 6.65 0.00 3.11
3111 4530 5.370679 ACAAATTCTTCATGCAAAAGCCTT 58.629 33.333 7.21 1.92 0.00 4.35
3112 4531 4.964593 ACAAATTCTTCATGCAAAAGCCT 58.035 34.783 7.21 0.00 0.00 4.58
3113 4532 4.992951 AGACAAATTCTTCATGCAAAAGCC 59.007 37.500 7.21 0.00 0.00 4.35
3114 4533 6.535274 AAGACAAATTCTTCATGCAAAAGC 57.465 33.333 7.21 0.00 40.98 3.51
3149 4568 9.317936 TCAAACATCTTGTGCTTCTGTATATAG 57.682 33.333 0.00 0.00 0.00 1.31
3156 4575 4.384846 GCAATCAAACATCTTGTGCTTCTG 59.615 41.667 0.00 0.00 0.00 3.02
3166 4585 4.521639 ACACACATCAGCAATCAAACATCT 59.478 37.500 0.00 0.00 0.00 2.90
3184 4603 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3188 4607 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3189 4608 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3190 4609 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3191 4610 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3192 4611 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3193 4612 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3194 4613 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3195 4614 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3196 4615 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3197 4616 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3238 4657 1.913419 CCTACAGGTTGCCCTTCCTAA 59.087 52.381 0.00 0.00 39.89 2.69
3267 4686 9.308318 GAACTCTCCTAACTAGAAAAGCATAAG 57.692 37.037 0.00 0.00 0.00 1.73
3295 4714 2.373707 GGGGCTGCTGAGGATCACT 61.374 63.158 0.00 0.00 42.56 3.41
3296 4715 2.191641 GGGGCTGCTGAGGATCAC 59.808 66.667 0.00 0.00 42.56 3.06
3329 4788 4.520179 TGATGACTATTGCAGCATTCAGT 58.480 39.130 0.00 0.00 0.00 3.41
3373 4832 6.330278 ACTTTTGAATACGACGAGATCATCA 58.670 36.000 0.00 0.00 0.00 3.07
3382 4841 9.853921 AGTAAACTAAAACTTTTGAATACGACG 57.146 29.630 0.00 0.00 0.00 5.12
3400 4859 8.296713 GGCAATTGAATTCACTTCAGTAAACTA 58.703 33.333 10.34 0.00 44.48 2.24
3419 4878 6.703607 TGTAAATTTGTACAAGGTGGCAATTG 59.296 34.615 8.56 11.09 31.03 2.32
3420 4879 6.821388 TGTAAATTTGTACAAGGTGGCAATT 58.179 32.000 8.56 1.20 31.03 2.32
3448 4907 4.954875 TGCAACAGGAAAGGGTAAAATTG 58.045 39.130 0.00 0.00 0.00 2.32
3478 4937 5.003804 AGGTACTCGAGCAAAATTCAATGT 58.996 37.500 13.61 0.00 0.00 2.71
3494 4953 5.140747 AGTTGATGAGTGTTCAGGTACTC 57.859 43.478 0.00 0.00 42.77 2.59
3497 4956 5.290493 ACAAGTTGATGAGTGTTCAGGTA 57.710 39.130 10.54 0.00 36.61 3.08
3507 4966 6.698329 TCAATGCAGAAAAACAAGTTGATGAG 59.302 34.615 10.54 0.00 0.00 2.90
3508 4967 6.571605 TCAATGCAGAAAAACAAGTTGATGA 58.428 32.000 10.54 0.00 0.00 2.92
3509 4968 6.831727 TCAATGCAGAAAAACAAGTTGATG 57.168 33.333 10.54 0.00 0.00 3.07
3510 4969 6.987992 ACATCAATGCAGAAAAACAAGTTGAT 59.012 30.769 10.54 0.00 35.97 2.57
3511 4970 6.339730 ACATCAATGCAGAAAAACAAGTTGA 58.660 32.000 10.54 0.00 0.00 3.18
3512 4971 6.592798 ACATCAATGCAGAAAAACAAGTTG 57.407 33.333 0.00 0.00 0.00 3.16
3513 4972 7.465989 CAAACATCAATGCAGAAAAACAAGTT 58.534 30.769 0.00 0.00 0.00 2.66
3514 4973 6.457257 GCAAACATCAATGCAGAAAAACAAGT 60.457 34.615 0.00 0.00 42.12 3.16
3515 4974 5.905181 GCAAACATCAATGCAGAAAAACAAG 59.095 36.000 0.00 0.00 42.12 3.16
3516 4975 5.220815 GGCAAACATCAATGCAGAAAAACAA 60.221 36.000 0.00 0.00 44.32 2.83
3517 4976 4.272991 GGCAAACATCAATGCAGAAAAACA 59.727 37.500 0.00 0.00 44.32 2.83
3518 4977 4.272991 TGGCAAACATCAATGCAGAAAAAC 59.727 37.500 0.00 0.00 44.32 2.43
3519 4978 4.449131 TGGCAAACATCAATGCAGAAAAA 58.551 34.783 0.00 0.00 44.32 1.94
3520 4979 4.069300 TGGCAAACATCAATGCAGAAAA 57.931 36.364 0.00 0.00 44.32 2.29
3521 4980 3.747854 TGGCAAACATCAATGCAGAAA 57.252 38.095 0.00 0.00 44.32 2.52
3522 4981 3.747854 TTGGCAAACATCAATGCAGAA 57.252 38.095 0.00 0.00 44.32 3.02
3523 4982 3.747854 TTTGGCAAACATCAATGCAGA 57.252 38.095 8.93 0.00 44.32 4.26
3524 4983 4.059511 TCTTTTGGCAAACATCAATGCAG 58.940 39.130 13.10 4.21 44.32 4.41
3525 4984 4.069300 TCTTTTGGCAAACATCAATGCA 57.931 36.364 13.10 0.00 44.32 3.96
3526 4985 5.421212 TTTCTTTTGGCAAACATCAATGC 57.579 34.783 13.10 0.00 41.82 3.56
3527 4986 7.249186 TCTTTTCTTTTGGCAAACATCAATG 57.751 32.000 13.10 6.14 0.00 2.82
3528 4987 7.862512 TTCTTTTCTTTTGGCAAACATCAAT 57.137 28.000 13.10 0.00 0.00 2.57
3529 4988 7.678947 TTTCTTTTCTTTTGGCAAACATCAA 57.321 28.000 13.10 3.19 0.00 2.57
3530 4989 7.148272 CCTTTTCTTTTCTTTTGGCAAACATCA 60.148 33.333 13.10 0.00 0.00 3.07
3531 4990 7.065683 TCCTTTTCTTTTCTTTTGGCAAACATC 59.934 33.333 13.10 0.00 0.00 3.06
3532 4991 6.883756 TCCTTTTCTTTTCTTTTGGCAAACAT 59.116 30.769 13.10 0.00 0.00 2.71
3533 4992 6.234177 TCCTTTTCTTTTCTTTTGGCAAACA 58.766 32.000 13.10 0.00 0.00 2.83
3534 4993 6.735678 TCCTTTTCTTTTCTTTTGGCAAAC 57.264 33.333 13.10 0.00 0.00 2.93
3535 4994 7.663493 TCTTTCCTTTTCTTTTCTTTTGGCAAA 59.337 29.630 8.93 8.93 0.00 3.68
3536 4995 7.164803 TCTTTCCTTTTCTTTTCTTTTGGCAA 58.835 30.769 0.00 0.00 0.00 4.52
3537 4996 6.706295 TCTTTCCTTTTCTTTTCTTTTGGCA 58.294 32.000 0.00 0.00 0.00 4.92
3538 4997 7.549134 TCTTCTTTCCTTTTCTTTTCTTTTGGC 59.451 33.333 0.00 0.00 0.00 4.52
3539 4998 9.435688 TTCTTCTTTCCTTTTCTTTTCTTTTGG 57.564 29.630 0.00 0.00 0.00 3.28
3544 5003 9.862371 GTTCTTTCTTCTTTCCTTTTCTTTTCT 57.138 29.630 0.00 0.00 0.00 2.52
3545 5004 9.862371 AGTTCTTTCTTCTTTCCTTTTCTTTTC 57.138 29.630 0.00 0.00 0.00 2.29
3547 5006 9.645059 CAAGTTCTTTCTTCTTTCCTTTTCTTT 57.355 29.630 0.00 0.00 0.00 2.52
3548 5007 8.807118 ACAAGTTCTTTCTTCTTTCCTTTTCTT 58.193 29.630 0.00 0.00 0.00 2.52
3549 5008 8.354711 ACAAGTTCTTTCTTCTTTCCTTTTCT 57.645 30.769 0.00 0.00 0.00 2.52
3550 5009 8.988064 AACAAGTTCTTTCTTCTTTCCTTTTC 57.012 30.769 0.00 0.00 0.00 2.29
3551 5010 9.778741 AAAACAAGTTCTTTCTTCTTTCCTTTT 57.221 25.926 0.00 0.00 0.00 2.27
3552 5011 9.778741 AAAAACAAGTTCTTTCTTCTTTCCTTT 57.221 25.926 0.00 0.00 0.00 3.11
3553 5012 9.424319 GAAAAACAAGTTCTTTCTTCTTTCCTT 57.576 29.630 10.53 0.00 0.00 3.36
3554 5013 8.807118 AGAAAAACAAGTTCTTTCTTCTTTCCT 58.193 29.630 12.83 0.00 36.27 3.36
3555 5014 8.864024 CAGAAAAACAAGTTCTTTCTTCTTTCC 58.136 33.333 14.58 0.00 37.31 3.13
3556 5015 8.376203 GCAGAAAAACAAGTTCTTTCTTCTTTC 58.624 33.333 14.58 7.10 37.31 2.62
3557 5016 7.872483 TGCAGAAAAACAAGTTCTTTCTTCTTT 59.128 29.630 14.58 0.07 37.31 2.52
3558 5017 7.378181 TGCAGAAAAACAAGTTCTTTCTTCTT 58.622 30.769 14.58 0.00 37.31 2.52
3559 5018 6.924111 TGCAGAAAAACAAGTTCTTTCTTCT 58.076 32.000 14.58 5.22 37.31 2.85
3560 5019 7.761651 ATGCAGAAAAACAAGTTCTTTCTTC 57.238 32.000 14.58 12.33 37.31 2.87
3561 5020 7.413328 GCAATGCAGAAAAACAAGTTCTTTCTT 60.413 33.333 0.00 5.04 37.31 2.52
3562 5021 6.036408 GCAATGCAGAAAAACAAGTTCTTTCT 59.964 34.615 0.00 12.83 39.42 2.52
3563 5022 6.036408 AGCAATGCAGAAAAACAAGTTCTTTC 59.964 34.615 8.35 10.11 32.96 2.62
3564 5023 5.876460 AGCAATGCAGAAAAACAAGTTCTTT 59.124 32.000 8.35 0.00 32.96 2.52
3565 5024 5.292589 CAGCAATGCAGAAAAACAAGTTCTT 59.707 36.000 8.35 0.00 32.96 2.52
3566 5025 4.807304 CAGCAATGCAGAAAAACAAGTTCT 59.193 37.500 8.35 0.00 35.69 3.01
3567 5026 4.805192 TCAGCAATGCAGAAAAACAAGTTC 59.195 37.500 8.35 0.00 0.00 3.01
3568 5027 4.567959 GTCAGCAATGCAGAAAAACAAGTT 59.432 37.500 8.35 0.00 0.00 2.66
3569 5028 4.114794 GTCAGCAATGCAGAAAAACAAGT 58.885 39.130 8.35 0.00 0.00 3.16
3570 5029 4.114073 TGTCAGCAATGCAGAAAAACAAG 58.886 39.130 8.35 0.00 0.00 3.16
3571 5030 4.114073 CTGTCAGCAATGCAGAAAAACAA 58.886 39.130 8.35 0.00 32.39 2.83
3572 5031 3.708890 CTGTCAGCAATGCAGAAAAACA 58.291 40.909 8.35 0.00 32.39 2.83


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

AutoCloner maintained by Alex Coulton.