Multiple sequence alignment - TraesCS4A01G338800

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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 TraesCS4A01G338800 chr4A 100.000 3725 0 0 1 3725 620705712 620701988 0.000000e+00 6879.0
1 TraesCS4A01G338800 chr4A 89.189 666 62 10 3060 3721 284742826 284742167 0.000000e+00 822.0
2 TraesCS4A01G338800 chr4A 87.573 684 57 17 3060 3721 284753891 284753214 0.000000e+00 767.0
3 TraesCS4A01G338800 chr4A 87.318 686 59 12 3060 3720 285956504 285957186 0.000000e+00 760.0
4 TraesCS4A01G338800 chr4A 86.831 691 59 19 3060 3725 305948403 305947720 0.000000e+00 743.0
5 TraesCS4A01G338800 chr4A 84.604 669 82 18 3060 3721 363393382 363394036 0.000000e+00 645.0
6 TraesCS4A01G338800 chr4A 98.630 73 1 0 2946 3018 620702661 620702589 3.020000e-26 130.0
7 TraesCS4A01G338800 chr4A 80.992 121 7 6 659 765 620647511 620647393 8.570000e-12 82.4
8 TraesCS4A01G338800 chr4A 95.122 41 0 2 2747 2786 620702691 620702652 3.110000e-06 63.9
9 TraesCS4A01G338800 chr4A 95.122 41 0 2 3022 3060 620702966 620702926 3.110000e-06 63.9
10 TraesCS4A01G338800 chr5D 92.416 2901 182 19 14 2896 549263110 549260230 0.000000e+00 4104.0
11 TraesCS4A01G338800 chr5D 90.022 2315 136 29 620 2896 549230170 549227913 0.000000e+00 2907.0
12 TraesCS4A01G338800 chr5D 82.422 1610 231 39 1109 2707 549548153 549546585 0.000000e+00 1358.0
13 TraesCS4A01G338800 chr5D 81.180 1610 248 35 1109 2707 549430068 549428503 0.000000e+00 1243.0
14 TraesCS4A01G338800 chr5B 90.969 2259 137 20 579 2799 700857025 700854796 0.000000e+00 2979.0
15 TraesCS4A01G338800 chr5B 81.502 1638 247 39 1109 2732 701051702 701050107 0.000000e+00 1295.0
16 TraesCS4A01G338800 chr2A 91.952 671 44 7 3060 3725 353256816 353257481 0.000000e+00 931.0
17 TraesCS4A01G338800 chr2A 90.030 672 59 7 3059 3725 354513453 354512785 0.000000e+00 863.0
18 TraesCS4A01G338800 chr2A 84.509 865 106 19 1109 1969 107182762 107181922 0.000000e+00 830.0
19 TraesCS4A01G338800 chr2A 87.645 688 59 15 3060 3725 350450669 350449986 0.000000e+00 776.0
20 TraesCS4A01G338800 chr2A 84.866 674 78 20 3061 3725 377471525 377472183 0.000000e+00 658.0
21 TraesCS4A01G338800 chr2A 83.958 667 89 17 3060 3721 344372846 344372193 1.140000e-174 623.0
22 TraesCS4A01G338800 chr7D 85.977 870 107 11 1103 1959 162823654 162822787 0.000000e+00 917.0
23 TraesCS4A01G338800 chr7A 85.797 866 114 7 1103 1959 163617765 163616900 0.000000e+00 909.0
24 TraesCS4A01G338800 chr7A 88.293 615 52 10 3060 3655 346616513 346615900 0.000000e+00 719.0
25 TraesCS4A01G338800 chr7A 85.693 685 74 7 3060 3723 346582136 346581455 0.000000e+00 701.0
26 TraesCS4A01G338800 chr7A 83.828 674 69 21 3060 3725 650890951 650890310 4.120000e-169 604.0
27 TraesCS4A01G338800 chr7A 82.641 674 92 19 3062 3725 284327914 284328572 1.160000e-159 573.0
28 TraesCS4A01G338800 chr2D 85.069 864 103 17 1109 1969 110843195 110842355 0.000000e+00 857.0
29 TraesCS4A01G338800 chr2B 84.491 864 108 18 1109 1969 159971028 159970188 0.000000e+00 830.0
30 TraesCS4A01G338800 chr2B 95.714 70 3 0 2952 3021 325929925 325929856 3.040000e-21 113.0
31 TraesCS4A01G338800 chr6A 86.861 685 59 13 3060 3720 341446967 341446290 0.000000e+00 737.0
32 TraesCS4A01G338800 chr3A 84.273 674 78 23 3060 3725 365491418 365492071 1.890000e-177 632.0
33 TraesCS4A01G338800 chr1A 98.507 67 1 0 2952 3018 232876788 232876854 6.540000e-23 119.0
34 TraesCS4A01G338800 chr5A 98.462 65 1 0 2954 3018 259073560 259073624 8.450000e-22 115.0
35 TraesCS4A01G338800 chr4D 98.462 65 1 0 2954 3018 208482568 208482632 8.450000e-22 115.0
36 TraesCS4A01G338800 chr6D 97.015 67 2 0 2954 3020 196394049 196394115 3.040000e-21 113.0
37 TraesCS4A01G338800 chr6D 97.015 67 2 0 2954 3020 196401239 196401305 3.040000e-21 113.0
38 TraesCS4A01G338800 chr1D 97.015 67 2 0 2952 3018 164326749 164326815 3.040000e-21 113.0
39 TraesCS4A01G338800 chr1D 97.015 67 2 0 2952 3018 178030873 178030807 3.040000e-21 113.0


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 TraesCS4A01G338800 chr4A 620701988 620705712 3724 True 1784.2 6879 97.2185 1 3725 4 chr4A.!!$R5 3724
1 TraesCS4A01G338800 chr4A 284742167 284742826 659 True 822.0 822 89.1890 3060 3721 1 chr4A.!!$R1 661
2 TraesCS4A01G338800 chr4A 284753214 284753891 677 True 767.0 767 87.5730 3060 3721 1 chr4A.!!$R2 661
3 TraesCS4A01G338800 chr4A 285956504 285957186 682 False 760.0 760 87.3180 3060 3720 1 chr4A.!!$F1 660
4 TraesCS4A01G338800 chr4A 305947720 305948403 683 True 743.0 743 86.8310 3060 3725 1 chr4A.!!$R3 665
5 TraesCS4A01G338800 chr4A 363393382 363394036 654 False 645.0 645 84.6040 3060 3721 1 chr4A.!!$F2 661
6 TraesCS4A01G338800 chr5D 549260230 549263110 2880 True 4104.0 4104 92.4160 14 2896 1 chr5D.!!$R2 2882
7 TraesCS4A01G338800 chr5D 549227913 549230170 2257 True 2907.0 2907 90.0220 620 2896 1 chr5D.!!$R1 2276
8 TraesCS4A01G338800 chr5D 549546585 549548153 1568 True 1358.0 1358 82.4220 1109 2707 1 chr5D.!!$R4 1598
9 TraesCS4A01G338800 chr5D 549428503 549430068 1565 True 1243.0 1243 81.1800 1109 2707 1 chr5D.!!$R3 1598
10 TraesCS4A01G338800 chr5B 700854796 700857025 2229 True 2979.0 2979 90.9690 579 2799 1 chr5B.!!$R1 2220
11 TraesCS4A01G338800 chr5B 701050107 701051702 1595 True 1295.0 1295 81.5020 1109 2732 1 chr5B.!!$R2 1623
12 TraesCS4A01G338800 chr2A 353256816 353257481 665 False 931.0 931 91.9520 3060 3725 1 chr2A.!!$F1 665
13 TraesCS4A01G338800 chr2A 354512785 354513453 668 True 863.0 863 90.0300 3059 3725 1 chr2A.!!$R4 666
14 TraesCS4A01G338800 chr2A 107181922 107182762 840 True 830.0 830 84.5090 1109 1969 1 chr2A.!!$R1 860
15 TraesCS4A01G338800 chr2A 350449986 350450669 683 True 776.0 776 87.6450 3060 3725 1 chr2A.!!$R3 665
16 TraesCS4A01G338800 chr2A 377471525 377472183 658 False 658.0 658 84.8660 3061 3725 1 chr2A.!!$F2 664
17 TraesCS4A01G338800 chr2A 344372193 344372846 653 True 623.0 623 83.9580 3060 3721 1 chr2A.!!$R2 661
18 TraesCS4A01G338800 chr7D 162822787 162823654 867 True 917.0 917 85.9770 1103 1959 1 chr7D.!!$R1 856
19 TraesCS4A01G338800 chr7A 163616900 163617765 865 True 909.0 909 85.7970 1103 1959 1 chr7A.!!$R1 856
20 TraesCS4A01G338800 chr7A 346615900 346616513 613 True 719.0 719 88.2930 3060 3655 1 chr7A.!!$R3 595
21 TraesCS4A01G338800 chr7A 346581455 346582136 681 True 701.0 701 85.6930 3060 3723 1 chr7A.!!$R2 663
22 TraesCS4A01G338800 chr7A 650890310 650890951 641 True 604.0 604 83.8280 3060 3725 1 chr7A.!!$R4 665
23 TraesCS4A01G338800 chr7A 284327914 284328572 658 False 573.0 573 82.6410 3062 3725 1 chr7A.!!$F1 663
24 TraesCS4A01G338800 chr2D 110842355 110843195 840 True 857.0 857 85.0690 1109 1969 1 chr2D.!!$R1 860
25 TraesCS4A01G338800 chr2B 159970188 159971028 840 True 830.0 830 84.4910 1109 1969 1 chr2B.!!$R1 860
26 TraesCS4A01G338800 chr6A 341446290 341446967 677 True 737.0 737 86.8610 3060 3720 1 chr6A.!!$R1 660
27 TraesCS4A01G338800 chr3A 365491418 365492071 653 False 632.0 632 84.2730 3060 3725 1 chr3A.!!$F1 665

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
199 200 0.035820 TTGTTGTCCTATGTCCCGCC 60.036 55.0 0.0 0.0 0.00 6.13 F
854 903 0.116342 TTCTACAGCTCTCCCACCCA 59.884 55.0 0.0 0.0 0.00 4.51 F
857 906 0.691078 TACAGCTCTCCCACCCATCC 60.691 60.0 0.0 0.0 0.00 3.51 F
2607 2694 0.183492 TCACTTGGAGCAAGCCAGTT 59.817 50.0 0.0 0.0 44.43 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2193 0.956410 CCACCGCGTTTGATGGGTTA 60.956 55.0 4.92 0.0 0.00 2.85 R
2252 2336 0.248012 TTCTCGGATGCACGCCTTAA 59.752 50.0 5.94 0.0 0.00 1.85 R
2640 2727 0.697658 TGGCCAGGAACACATCATGA 59.302 50.0 0.00 0.0 42.41 3.07 R
3600 3719 1.755200 AAGTGAAGGGGTACATGGGT 58.245 50.0 0.00 0.0 0.00 4.51 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
34 35 1.153289 CGCCTGACTTCCCATCTGG 60.153 63.158 0.00 0.00 38.02 3.86
67 68 3.782443 ATCGACGCCTCCCCCAAC 61.782 66.667 0.00 0.00 0.00 3.77
71 72 4.974438 ACGCCTCCCCCAACTCCA 62.974 66.667 0.00 0.00 0.00 3.86
76 77 4.974438 TCCCCCAACTCCACGGCT 62.974 66.667 0.00 0.00 0.00 5.52
89 90 2.742372 CGGCTGCTAACACCGCTT 60.742 61.111 0.00 0.00 40.55 4.68
103 104 2.258591 GCTTCGACGCTCCTCACA 59.741 61.111 6.65 0.00 0.00 3.58
165 166 3.320830 GGCCATGCTTGCCCCAAA 61.321 61.111 0.00 0.00 43.33 3.28
167 168 1.153309 GCCATGCTTGCCCCAAATC 60.153 57.895 0.00 0.00 0.00 2.17
168 169 1.142314 CCATGCTTGCCCCAAATCG 59.858 57.895 0.00 0.00 0.00 3.34
176 177 3.952675 CCCCAAATCGGCGCGATG 61.953 66.667 12.10 0.00 46.30 3.84
183 184 1.095228 AATCGGCGCGATGGATTTGT 61.095 50.000 12.10 0.00 46.30 2.83
186 187 1.506262 GGCGCGATGGATTTGTTGT 59.494 52.632 12.10 0.00 0.00 3.32
189 190 1.086696 CGCGATGGATTTGTTGTCCT 58.913 50.000 0.00 0.00 36.68 3.85
191 192 2.872245 CGCGATGGATTTGTTGTCCTAT 59.128 45.455 0.00 0.00 36.68 2.57
199 200 0.035820 TTGTTGTCCTATGTCCCGCC 60.036 55.000 0.00 0.00 0.00 6.13
225 226 1.602237 CCGCTGGAATGGTACCACT 59.398 57.895 19.09 5.98 33.57 4.00
226 227 0.744414 CCGCTGGAATGGTACCACTG 60.744 60.000 19.09 10.00 33.57 3.66
241 242 2.124942 CTGGCGAGGAAGAAGGCC 60.125 66.667 0.00 0.00 45.76 5.19
304 305 4.351938 CGTCGTGGCTTCGTCCCA 62.352 66.667 3.16 0.00 0.00 4.37
305 306 2.029964 GTCGTGGCTTCGTCCCAA 59.970 61.111 3.16 0.00 33.39 4.12
307 308 2.204461 TCGTGGCTTCGTCCCAAGA 61.204 57.895 4.12 4.12 38.29 3.02
329 333 4.408821 AAGATGAAGGCGGCCGCA 62.409 61.111 46.88 30.39 44.11 5.69
402 411 4.675303 CCCCACCACCTCCCCTCA 62.675 72.222 0.00 0.00 0.00 3.86
405 414 3.706373 CACCACCTCCCCTCACGG 61.706 72.222 0.00 0.00 0.00 4.94
406 415 4.250170 ACCACCTCCCCTCACGGT 62.250 66.667 0.00 0.00 0.00 4.83
408 417 4.394712 CACCTCCCCTCACGGTGC 62.395 72.222 2.51 0.00 41.39 5.01
430 439 2.671070 CATGGTGGAGGAGCCGTT 59.329 61.111 0.00 0.00 40.66 4.44
459 468 5.293324 CCCGTCGTCATCATCTTCAATTTTA 59.707 40.000 0.00 0.00 0.00 1.52
468 477 6.435430 TCATCTTCAATTTTACATCACCCG 57.565 37.500 0.00 0.00 0.00 5.28
498 507 6.728200 GCACTAGCTATTTTTACATCATGCA 58.272 36.000 0.00 0.00 37.91 3.96
499 508 7.365741 GCACTAGCTATTTTTACATCATGCAT 58.634 34.615 0.00 0.00 37.91 3.96
500 509 7.325338 GCACTAGCTATTTTTACATCATGCATG 59.675 37.037 21.07 21.07 36.77 4.06
514 523 1.317613 TGCATGTGTTGGAGTTGGAC 58.682 50.000 0.00 0.00 0.00 4.02
515 524 1.317613 GCATGTGTTGGAGTTGGACA 58.682 50.000 0.00 0.00 0.00 4.02
587 597 5.943706 TGGAGATGCTCTATAAGTACGTC 57.056 43.478 0.00 0.00 0.00 4.34
725 774 0.251634 GCTGTCCCTTCTCTTGGAGG 59.748 60.000 0.00 0.00 0.00 4.30
785 834 3.896648 ACGGTGTAAACTTGCAATCAG 57.103 42.857 0.00 0.00 0.00 2.90
851 900 2.167487 CCTTCTTCTACAGCTCTCCCAC 59.833 54.545 0.00 0.00 0.00 4.61
854 903 0.116342 TTCTACAGCTCTCCCACCCA 59.884 55.000 0.00 0.00 0.00 4.51
856 905 0.755686 CTACAGCTCTCCCACCCATC 59.244 60.000 0.00 0.00 0.00 3.51
857 906 0.691078 TACAGCTCTCCCACCCATCC 60.691 60.000 0.00 0.00 0.00 3.51
858 907 2.367512 AGCTCTCCCACCCATCCC 60.368 66.667 0.00 0.00 0.00 3.85
859 908 2.692368 GCTCTCCCACCCATCCCA 60.692 66.667 0.00 0.00 0.00 4.37
860 909 3.049080 GCTCTCCCACCCATCCCAC 62.049 68.421 0.00 0.00 0.00 4.61
864 913 3.743017 CCCACCCATCCCACCCTG 61.743 72.222 0.00 0.00 0.00 4.45
948 997 4.100035 TGTTCTGATCTCTGCGTCCAATAT 59.900 41.667 0.00 0.00 0.00 1.28
955 1004 3.764434 TCTCTGCGTCCAATATATCCCTC 59.236 47.826 0.00 0.00 0.00 4.30
961 1010 1.548719 TCCAATATATCCCTCCGTGCG 59.451 52.381 0.00 0.00 0.00 5.34
1048 1098 1.019673 AATGCTGGTGCTATTGCTCG 58.980 50.000 0.00 0.00 40.48 5.03
1335 1385 4.814294 CGCCCGCTAACCTTCGCT 62.814 66.667 0.00 0.00 0.00 4.93
1372 1422 0.734942 CGGATACAAGAACGCCGTGT 60.735 55.000 0.00 2.99 40.51 4.49
1407 1457 1.153289 CCAGTGGAGGAAGATGCGG 60.153 63.158 1.68 0.00 0.00 5.69
1587 1646 1.450312 GAGGCACTACTGCGGCAAT 60.450 57.895 3.44 0.00 45.31 3.56
1713 1775 3.597728 CTCGGGCTCCTCTACGCC 61.598 72.222 0.00 0.00 45.55 5.68
1798 1860 4.660938 AGGAGGCCAACGCAACCC 62.661 66.667 5.01 0.00 36.38 4.11
1859 1921 1.906824 AGTGGAAGTCCGGCGAGAA 60.907 57.895 9.30 0.00 39.43 2.87
2047 2118 2.301346 AGGTGCAAAGAAAGTGGACTG 58.699 47.619 0.00 0.00 37.47 3.51
2109 2193 1.904287 TAACCTTTGCAGCCGTTGAT 58.096 45.000 5.03 0.00 0.00 2.57
2151 2235 2.044650 GCCCTTGCAGAGATGGCA 60.045 61.111 8.56 0.00 41.76 4.92
2251 2335 2.561209 TATCCCCCAACTCAGCTACA 57.439 50.000 0.00 0.00 0.00 2.74
2252 2336 1.898863 ATCCCCCAACTCAGCTACAT 58.101 50.000 0.00 0.00 0.00 2.29
2253 2337 1.668826 TCCCCCAACTCAGCTACATT 58.331 50.000 0.00 0.00 0.00 2.71
2272 2356 0.248012 TAAGGCGTGCATCCGAGAAA 59.752 50.000 0.24 0.00 0.00 2.52
2316 2400 0.725784 CTTTCAACGTGCCGCATGTC 60.726 55.000 18.42 0.00 31.86 3.06
2342 2426 2.962786 CGACACCAACGTTGCCGA 60.963 61.111 22.93 0.00 37.88 5.54
2433 2517 1.748329 ATGAGCCGCTCCGCTTCATA 61.748 55.000 17.81 0.00 39.87 2.15
2607 2694 0.183492 TCACTTGGAGCAAGCCAGTT 59.817 50.000 0.00 0.00 44.43 3.16
2640 2727 4.635765 GCTATAGATCTCAGCGAGTCAGAT 59.364 45.833 12.14 0.00 0.00 2.90
2646 2733 3.220940 TCTCAGCGAGTCAGATCATGAT 58.779 45.455 8.25 8.25 40.92 2.45
2680 2767 4.321008 CCAAGCCATTGATGATGTATGCTC 60.321 45.833 0.00 0.00 38.83 4.26
2801 2888 2.306805 TGATGTGAGCCAAGATCACCTT 59.693 45.455 10.20 0.00 46.70 3.50
2819 2906 4.020218 CACCTTGATCTCCACCTGAAGTAA 60.020 45.833 0.00 0.00 0.00 2.24
2831 2918 4.036734 CACCTGAAGTAAGTTTGTGTGCAT 59.963 41.667 0.00 0.00 0.00 3.96
2845 2932 1.271934 TGTGCATACATGTTGTTGGCC 59.728 47.619 2.30 0.00 30.40 5.36
2900 2987 9.489084 AATCATTTTCATTGATAGCCATTGATG 57.511 29.630 0.00 0.00 35.73 3.07
2901 2988 6.926826 TCATTTTCATTGATAGCCATTGATGC 59.073 34.615 0.00 0.00 35.73 3.91
2902 2989 4.492791 TTCATTGATAGCCATTGATGCG 57.507 40.909 0.00 0.00 35.73 4.73
2903 2990 2.815503 TCATTGATAGCCATTGATGCGG 59.184 45.455 0.00 0.00 32.14 5.69
2904 2991 2.636647 TTGATAGCCATTGATGCGGA 57.363 45.000 0.00 0.00 0.00 5.54
2905 2992 2.174363 TGATAGCCATTGATGCGGAG 57.826 50.000 0.00 0.00 0.00 4.63
2926 3013 5.858381 GAGCATCCCACTTGATACATAAGA 58.142 41.667 0.00 0.00 0.00 2.10
2927 3014 6.445451 AGCATCCCACTTGATACATAAGAT 57.555 37.500 0.00 0.00 0.00 2.40
2928 3015 6.236409 AGCATCCCACTTGATACATAAGATG 58.764 40.000 0.00 0.00 0.00 2.90
2929 3016 6.043590 AGCATCCCACTTGATACATAAGATGA 59.956 38.462 0.00 0.00 0.00 2.92
2930 3017 6.370994 GCATCCCACTTGATACATAAGATGAG 59.629 42.308 0.00 0.00 0.00 2.90
2931 3018 7.674120 CATCCCACTTGATACATAAGATGAGA 58.326 38.462 0.00 0.00 0.00 3.27
2932 3019 7.055667 TCCCACTTGATACATAAGATGAGAC 57.944 40.000 0.00 0.00 0.00 3.36
2933 3020 6.042093 TCCCACTTGATACATAAGATGAGACC 59.958 42.308 0.00 0.00 0.00 3.85
2934 3021 6.042552 CCCACTTGATACATAAGATGAGACCT 59.957 42.308 0.00 0.00 0.00 3.85
2935 3022 7.151308 CCACTTGATACATAAGATGAGACCTC 58.849 42.308 0.00 0.00 0.00 3.85
2936 3023 6.860539 CACTTGATACATAAGATGAGACCTCG 59.139 42.308 0.00 0.00 0.00 4.63
2937 3024 6.773200 ACTTGATACATAAGATGAGACCTCGA 59.227 38.462 0.00 0.00 0.00 4.04
2938 3025 6.561737 TGATACATAAGATGAGACCTCGAC 57.438 41.667 0.00 0.00 0.00 4.20
2939 3026 6.299922 TGATACATAAGATGAGACCTCGACT 58.700 40.000 0.00 0.00 0.00 4.18
2940 3027 7.450903 TGATACATAAGATGAGACCTCGACTA 58.549 38.462 0.00 0.00 0.00 2.59
2941 3028 7.388224 TGATACATAAGATGAGACCTCGACTAC 59.612 40.741 0.00 0.00 0.00 2.73
2942 3029 5.686753 ACATAAGATGAGACCTCGACTACT 58.313 41.667 0.00 0.00 0.00 2.57
2943 3030 5.761234 ACATAAGATGAGACCTCGACTACTC 59.239 44.000 0.00 0.00 0.00 2.59
2944 3031 4.497291 AAGATGAGACCTCGACTACTCT 57.503 45.455 0.00 0.00 0.00 3.24
2945 3032 4.067972 AGATGAGACCTCGACTACTCTC 57.932 50.000 0.00 4.17 0.00 3.20
2946 3033 2.695127 TGAGACCTCGACTACTCTCC 57.305 55.000 0.00 0.00 0.00 3.71
2947 3034 1.907255 TGAGACCTCGACTACTCTCCA 59.093 52.381 0.00 0.00 0.00 3.86
2948 3035 2.506231 TGAGACCTCGACTACTCTCCAT 59.494 50.000 0.00 0.00 0.00 3.41
2949 3036 2.875933 GAGACCTCGACTACTCTCCATG 59.124 54.545 0.00 0.00 0.00 3.66
2950 3037 2.506231 AGACCTCGACTACTCTCCATGA 59.494 50.000 0.00 0.00 0.00 3.07
2951 3038 3.054287 AGACCTCGACTACTCTCCATGAA 60.054 47.826 0.00 0.00 0.00 2.57
2952 3039 3.886505 GACCTCGACTACTCTCCATGAAT 59.113 47.826 0.00 0.00 0.00 2.57
2953 3040 3.634448 ACCTCGACTACTCTCCATGAATG 59.366 47.826 0.00 0.00 0.00 2.67
2954 3041 3.634448 CCTCGACTACTCTCCATGAATGT 59.366 47.826 0.00 0.00 0.00 2.71
2955 3042 4.098654 CCTCGACTACTCTCCATGAATGTT 59.901 45.833 0.00 0.00 0.00 2.71
2956 3043 5.250235 TCGACTACTCTCCATGAATGTTC 57.750 43.478 0.00 0.00 0.00 3.18
2957 3044 4.705023 TCGACTACTCTCCATGAATGTTCA 59.295 41.667 0.00 0.00 42.14 3.18
2959 3046 5.689514 CGACTACTCTCCATGAATGTTCATC 59.310 44.000 5.30 0.00 45.62 2.92
2960 3047 5.923204 ACTACTCTCCATGAATGTTCATCC 58.077 41.667 5.30 0.00 45.62 3.51
2961 3048 5.664908 ACTACTCTCCATGAATGTTCATCCT 59.335 40.000 5.30 0.00 45.62 3.24
2962 3049 5.447778 ACTCTCCATGAATGTTCATCCTT 57.552 39.130 5.30 0.00 45.62 3.36
2963 3050 6.566079 ACTCTCCATGAATGTTCATCCTTA 57.434 37.500 5.30 0.00 45.62 2.69
2964 3051 7.146715 ACTCTCCATGAATGTTCATCCTTAT 57.853 36.000 5.30 0.00 45.62 1.73
2965 3052 6.996879 ACTCTCCATGAATGTTCATCCTTATG 59.003 38.462 5.30 0.00 45.62 1.90
2966 3053 6.903516 TCTCCATGAATGTTCATCCTTATGT 58.096 36.000 5.30 0.00 45.62 2.29
2967 3054 8.033178 TCTCCATGAATGTTCATCCTTATGTA 57.967 34.615 5.30 0.00 45.62 2.29
2968 3055 7.933577 TCTCCATGAATGTTCATCCTTATGTAC 59.066 37.037 5.30 0.00 45.62 2.90
2969 3056 7.572814 TCCATGAATGTTCATCCTTATGTACA 58.427 34.615 0.00 0.00 45.62 2.90
2970 3057 7.498900 TCCATGAATGTTCATCCTTATGTACAC 59.501 37.037 0.00 0.00 45.62 2.90
2971 3058 7.500227 CCATGAATGTTCATCCTTATGTACACT 59.500 37.037 0.00 0.00 45.62 3.55
2972 3059 8.554528 CATGAATGTTCATCCTTATGTACACTC 58.445 37.037 0.00 1.04 45.62 3.51
2973 3060 7.047891 TGAATGTTCATCCTTATGTACACTCC 58.952 38.462 0.00 0.00 43.48 3.85
2974 3061 5.006153 TGTTCATCCTTATGTACACTCCG 57.994 43.478 0.00 0.00 38.16 4.63
2975 3062 4.707934 TGTTCATCCTTATGTACACTCCGA 59.292 41.667 0.00 0.00 38.16 4.55
2976 3063 4.913335 TCATCCTTATGTACACTCCGAC 57.087 45.455 0.00 0.00 34.50 4.79
2977 3064 4.533815 TCATCCTTATGTACACTCCGACT 58.466 43.478 0.00 0.00 34.50 4.18
2978 3065 5.687780 TCATCCTTATGTACACTCCGACTA 58.312 41.667 0.00 0.00 34.50 2.59
2979 3066 5.530171 TCATCCTTATGTACACTCCGACTAC 59.470 44.000 0.00 0.00 34.50 2.73
2980 3067 5.108187 TCCTTATGTACACTCCGACTACT 57.892 43.478 0.00 0.00 0.00 2.57
2981 3068 5.121811 TCCTTATGTACACTCCGACTACTC 58.878 45.833 0.00 0.00 0.00 2.59
2982 3069 5.104610 TCCTTATGTACACTCCGACTACTCT 60.105 44.000 0.00 0.00 0.00 3.24
2983 3070 5.236911 CCTTATGTACACTCCGACTACTCTC 59.763 48.000 0.00 0.00 0.00 3.20
2984 3071 2.983229 TGTACACTCCGACTACTCTCC 58.017 52.381 0.00 0.00 0.00 3.71
2985 3072 2.303890 TGTACACTCCGACTACTCTCCA 59.696 50.000 0.00 0.00 0.00 3.86
2986 3073 2.581216 ACACTCCGACTACTCTCCAA 57.419 50.000 0.00 0.00 0.00 3.53
2987 3074 2.438411 ACACTCCGACTACTCTCCAAG 58.562 52.381 0.00 0.00 0.00 3.61
2988 3075 1.133407 CACTCCGACTACTCTCCAAGC 59.867 57.143 0.00 0.00 0.00 4.01
2989 3076 0.741915 CTCCGACTACTCTCCAAGCC 59.258 60.000 0.00 0.00 0.00 4.35
2990 3077 0.683504 TCCGACTACTCTCCAAGCCC 60.684 60.000 0.00 0.00 0.00 5.19
2991 3078 1.677637 CCGACTACTCTCCAAGCCCC 61.678 65.000 0.00 0.00 0.00 5.80
2992 3079 0.970937 CGACTACTCTCCAAGCCCCA 60.971 60.000 0.00 0.00 0.00 4.96
2993 3080 1.276622 GACTACTCTCCAAGCCCCAA 58.723 55.000 0.00 0.00 0.00 4.12
2994 3081 1.208293 GACTACTCTCCAAGCCCCAAG 59.792 57.143 0.00 0.00 0.00 3.61
2995 3082 0.543749 CTACTCTCCAAGCCCCAAGG 59.456 60.000 0.00 0.00 0.00 3.61
2996 3083 0.118346 TACTCTCCAAGCCCCAAGGA 59.882 55.000 0.00 0.00 33.47 3.36
2997 3084 0.551131 ACTCTCCAAGCCCCAAGGAT 60.551 55.000 0.00 0.00 33.47 3.24
2998 3085 1.274416 ACTCTCCAAGCCCCAAGGATA 60.274 52.381 0.00 0.00 33.47 2.59
2999 3086 1.141858 CTCTCCAAGCCCCAAGGATAC 59.858 57.143 0.00 0.00 33.47 2.24
3000 3087 0.918983 CTCCAAGCCCCAAGGATACA 59.081 55.000 0.00 0.00 41.41 2.29
3001 3088 1.496429 CTCCAAGCCCCAAGGATACAT 59.504 52.381 0.00 0.00 41.41 2.29
3002 3089 2.711009 CTCCAAGCCCCAAGGATACATA 59.289 50.000 0.00 0.00 41.41 2.29
3003 3090 3.127250 TCCAAGCCCCAAGGATACATAA 58.873 45.455 0.00 0.00 41.41 1.90
3004 3091 3.138283 TCCAAGCCCCAAGGATACATAAG 59.862 47.826 0.00 0.00 41.41 1.73
3005 3092 3.138283 CCAAGCCCCAAGGATACATAAGA 59.862 47.826 0.00 0.00 41.41 2.10
3006 3093 4.202609 CCAAGCCCCAAGGATACATAAGAT 60.203 45.833 0.00 0.00 41.41 2.40
3007 3094 4.647564 AGCCCCAAGGATACATAAGATG 57.352 45.455 0.00 0.00 41.41 2.90
3008 3095 4.242811 AGCCCCAAGGATACATAAGATGA 58.757 43.478 0.00 0.00 41.41 2.92
3009 3096 4.288105 AGCCCCAAGGATACATAAGATGAG 59.712 45.833 0.00 0.00 41.41 2.90
3010 3097 4.287067 GCCCCAAGGATACATAAGATGAGA 59.713 45.833 0.00 0.00 41.41 3.27
3011 3098 5.799213 CCCCAAGGATACATAAGATGAGAC 58.201 45.833 0.00 0.00 41.41 3.36
3012 3099 5.280215 CCCCAAGGATACATAAGATGAGACC 60.280 48.000 0.00 0.00 41.41 3.85
3013 3100 5.545723 CCCAAGGATACATAAGATGAGACCT 59.454 44.000 0.00 0.00 41.41 3.85
3014 3101 6.295575 CCCAAGGATACATAAGATGAGACCTC 60.296 46.154 0.00 0.00 41.41 3.85
3015 3102 6.385843 CAAGGATACATAAGATGAGACCTCG 58.614 44.000 0.00 0.00 41.41 4.63
3016 3103 5.882040 AGGATACATAAGATGAGACCTCGA 58.118 41.667 0.00 0.00 41.41 4.04
3017 3104 5.708230 AGGATACATAAGATGAGACCTCGAC 59.292 44.000 0.00 0.00 41.41 4.20
3018 3105 5.106078 GGATACATAAGATGAGACCTCGACC 60.106 48.000 0.00 0.00 0.00 4.79
3019 3106 3.632333 ACATAAGATGAGACCTCGACCA 58.368 45.455 0.00 0.00 0.00 4.02
3020 3107 3.381908 ACATAAGATGAGACCTCGACCAC 59.618 47.826 0.00 0.00 0.00 4.16
3021 3108 2.223803 AAGATGAGACCTCGACCACT 57.776 50.000 0.00 0.00 0.00 4.00
3022 3109 2.223803 AGATGAGACCTCGACCACTT 57.776 50.000 0.00 0.00 0.00 3.16
3023 3110 1.821753 AGATGAGACCTCGACCACTTG 59.178 52.381 0.00 0.00 0.00 3.16
3024 3111 1.819288 GATGAGACCTCGACCACTTGA 59.181 52.381 0.00 0.00 0.00 3.02
3025 3112 1.699730 TGAGACCTCGACCACTTGAA 58.300 50.000 0.00 0.00 0.00 2.69
3026 3113 2.036387 TGAGACCTCGACCACTTGAAA 58.964 47.619 0.00 0.00 0.00 2.69
3027 3114 2.432874 TGAGACCTCGACCACTTGAAAA 59.567 45.455 0.00 0.00 0.00 2.29
3028 3115 3.071023 TGAGACCTCGACCACTTGAAAAT 59.929 43.478 0.00 0.00 0.00 1.82
3029 3116 4.282449 TGAGACCTCGACCACTTGAAAATA 59.718 41.667 0.00 0.00 0.00 1.40
3030 3117 5.221561 TGAGACCTCGACCACTTGAAAATAA 60.222 40.000 0.00 0.00 0.00 1.40
3031 3118 5.805728 AGACCTCGACCACTTGAAAATAAT 58.194 37.500 0.00 0.00 0.00 1.28
3032 3119 6.942976 AGACCTCGACCACTTGAAAATAATA 58.057 36.000 0.00 0.00 0.00 0.98
3033 3120 7.565680 AGACCTCGACCACTTGAAAATAATAT 58.434 34.615 0.00 0.00 0.00 1.28
3034 3121 8.701895 AGACCTCGACCACTTGAAAATAATATA 58.298 33.333 0.00 0.00 0.00 0.86
3035 3122 8.888579 ACCTCGACCACTTGAAAATAATATAG 57.111 34.615 0.00 0.00 0.00 1.31
3036 3123 7.441458 ACCTCGACCACTTGAAAATAATATAGC 59.559 37.037 0.00 0.00 0.00 2.97
3037 3124 7.657761 CCTCGACCACTTGAAAATAATATAGCT 59.342 37.037 0.00 0.00 0.00 3.32
3038 3125 8.589335 TCGACCACTTGAAAATAATATAGCTC 57.411 34.615 0.00 0.00 0.00 4.09
3039 3126 8.201464 TCGACCACTTGAAAATAATATAGCTCA 58.799 33.333 0.00 0.00 0.00 4.26
3040 3127 8.826710 CGACCACTTGAAAATAATATAGCTCAA 58.173 33.333 0.00 0.00 0.00 3.02
3053 3140 9.797642 ATAATATAGCTCAATTGATTGTCACCA 57.202 29.630 8.96 0.00 38.84 4.17
3054 3141 8.701908 AATATAGCTCAATTGATTGTCACCAT 57.298 30.769 8.96 0.00 38.84 3.55
3055 3142 4.713824 AGCTCAATTGATTGTCACCATG 57.286 40.909 8.96 0.00 38.84 3.66
3056 3143 4.338012 AGCTCAATTGATTGTCACCATGA 58.662 39.130 8.96 0.00 38.84 3.07
3057 3144 4.398358 AGCTCAATTGATTGTCACCATGAG 59.602 41.667 8.96 9.62 38.84 2.90
3245 3333 4.101114 TCAGGTACATAGAGGAAAGCCAA 58.899 43.478 0.00 0.00 36.29 4.52
3488 3606 4.373116 GCGCCACCTCAACCGAGA 62.373 66.667 0.00 0.00 42.34 4.04
3515 3633 0.594602 CCGGACGTCTGACAAGTACA 59.405 55.000 26.01 0.00 0.00 2.90
3562 3680 2.012902 GATGTCCGGTACCTGTCGGG 62.013 65.000 10.90 3.17 45.69 5.14
3600 3719 3.301554 CCATGTGTTGGGCCGCAA 61.302 61.111 0.00 0.00 42.33 4.85
3711 3843 6.385033 GCTCATATTTTGTGTGAGAGCTTTT 58.615 36.000 5.84 0.00 45.87 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.612453 GGCGTGGGGTGGGAATTTTA 60.612 55.000 0.00 0.00 0.00 1.52
1 2 1.911269 GGCGTGGGGTGGGAATTTT 60.911 57.895 0.00 0.00 0.00 1.82
2 3 2.283604 GGCGTGGGGTGGGAATTT 60.284 61.111 0.00 0.00 0.00 1.82
3 4 3.264845 AGGCGTGGGGTGGGAATT 61.265 61.111 0.00 0.00 0.00 2.17
4 5 4.047125 CAGGCGTGGGGTGGGAAT 62.047 66.667 0.00 0.00 0.00 3.01
8 9 3.901797 GAAGTCAGGCGTGGGGTGG 62.902 68.421 6.56 0.00 0.00 4.61
9 10 2.358737 GAAGTCAGGCGTGGGGTG 60.359 66.667 6.56 0.00 0.00 4.61
10 11 3.637273 GGAAGTCAGGCGTGGGGT 61.637 66.667 6.56 0.00 0.00 4.95
11 12 4.410400 GGGAAGTCAGGCGTGGGG 62.410 72.222 6.56 0.00 0.00 4.96
12 13 2.876368 GATGGGAAGTCAGGCGTGGG 62.876 65.000 6.56 0.00 0.00 4.61
64 65 0.602638 TGTTAGCAGCCGTGGAGTTG 60.603 55.000 0.00 0.00 0.00 3.16
65 66 0.602905 GTGTTAGCAGCCGTGGAGTT 60.603 55.000 0.00 0.00 0.00 3.01
67 68 1.741770 GGTGTTAGCAGCCGTGGAG 60.742 63.158 0.00 0.00 37.15 3.86
71 72 3.530910 AAGCGGTGTTAGCAGCCGT 62.531 57.895 17.07 6.31 46.41 5.68
76 77 1.731613 CGTCGAAGCGGTGTTAGCA 60.732 57.895 0.00 0.00 37.01 3.49
78 79 1.403972 GAGCGTCGAAGCGGTGTTAG 61.404 60.000 17.57 0.00 42.89 2.34
89 90 1.215382 CCATTGTGAGGAGCGTCGA 59.785 57.895 0.00 0.00 0.00 4.20
162 163 0.029300 AAATCCATCGCGCCGATTTG 59.971 50.000 19.97 9.17 44.59 2.32
167 168 1.583451 CAACAAATCCATCGCGCCG 60.583 57.895 0.00 0.00 0.00 6.46
168 169 0.523335 GACAACAAATCCATCGCGCC 60.523 55.000 0.00 0.00 0.00 6.53
173 174 4.580580 GGGACATAGGACAACAAATCCATC 59.419 45.833 0.00 0.00 38.86 3.51
175 176 3.621214 CGGGACATAGGACAACAAATCCA 60.621 47.826 0.00 0.00 38.86 3.41
176 177 2.943033 CGGGACATAGGACAACAAATCC 59.057 50.000 0.00 0.00 36.38 3.01
183 184 2.897207 CGGCGGGACATAGGACAA 59.103 61.111 0.00 0.00 0.00 3.18
208 209 0.744414 CCAGTGGTACCATTCCAGCG 60.744 60.000 19.72 1.04 35.49 5.18
209 210 1.032114 GCCAGTGGTACCATTCCAGC 61.032 60.000 19.72 12.39 35.49 4.85
210 211 0.744414 CGCCAGTGGTACCATTCCAG 60.744 60.000 19.72 6.08 35.49 3.86
211 212 1.195442 TCGCCAGTGGTACCATTCCA 61.195 55.000 19.72 0.00 0.00 3.53
212 213 0.462047 CTCGCCAGTGGTACCATTCC 60.462 60.000 19.72 5.25 0.00 3.01
225 226 4.082523 CGGCCTTCTTCCTCGCCA 62.083 66.667 0.00 0.00 41.71 5.69
252 253 4.856801 CTTGGGGATCCGGTGGCG 62.857 72.222 5.45 0.00 35.24 5.69
261 262 3.090532 GGAGGCGTCCTTGGGGAT 61.091 66.667 18.26 0.00 44.33 3.85
304 305 2.679349 GCCGCCTTCATCTTCTTCTCTT 60.679 50.000 0.00 0.00 0.00 2.85
305 306 1.134551 GCCGCCTTCATCTTCTTCTCT 60.135 52.381 0.00 0.00 0.00 3.10
307 308 0.107459 GGCCGCCTTCATCTTCTTCT 60.107 55.000 0.71 0.00 0.00 2.85
418 427 4.373116 GCGTCAACGGCTCCTCCA 62.373 66.667 4.54 0.00 40.23 3.86
445 454 5.943416 ACGGGTGATGTAAAATTGAAGATGA 59.057 36.000 0.00 0.00 0.00 2.92
459 468 1.302511 GTGCTCCAACGGGTGATGT 60.303 57.895 0.00 0.00 34.93 3.06
496 505 1.317613 TGTCCAACTCCAACACATGC 58.682 50.000 0.00 0.00 0.00 4.06
497 506 4.589216 AAATGTCCAACTCCAACACATG 57.411 40.909 0.00 0.00 0.00 3.21
498 507 5.612725 AAAAATGTCCAACTCCAACACAT 57.387 34.783 0.00 0.00 0.00 3.21
725 774 4.438744 GGGAATACATTAAGTGCAGTGTGC 60.439 45.833 0.00 0.00 45.29 4.57
785 834 4.664150 ATGCTAGCTAGGTTTCTCACTC 57.336 45.455 22.10 2.10 0.00 3.51
857 906 4.609018 CGCGCTATCCCAGGGTGG 62.609 72.222 5.01 0.00 42.43 4.61
859 908 1.332144 TAAACGCGCTATCCCAGGGT 61.332 55.000 5.73 0.00 39.38 4.34
860 909 0.878961 GTAAACGCGCTATCCCAGGG 60.879 60.000 5.73 0.00 40.15 4.45
864 913 0.782384 CATCGTAAACGCGCTATCCC 59.218 55.000 5.73 0.00 39.60 3.85
927 976 4.944619 ATATTGGACGCAGAGATCAGAA 57.055 40.909 0.00 0.00 0.00 3.02
948 997 1.452953 CTAGCACGCACGGAGGGATA 61.453 60.000 0.00 0.00 0.00 2.59
1048 1098 1.338655 GAGGACGAGGTAGATGAAGGC 59.661 57.143 0.00 0.00 0.00 4.35
1147 1197 1.906995 TGAGCATCATCTCCGGCAA 59.093 52.632 0.00 0.00 42.56 4.52
1356 1406 1.796459 GACAACACGGCGTTCTTGTAT 59.204 47.619 24.95 10.23 34.86 2.29
1372 1422 2.592287 GTCCCCAAACGGCGACAA 60.592 61.111 16.62 0.00 33.98 3.18
1653 1715 2.365105 TCTACCTCCAAGGGCCCG 60.365 66.667 18.44 2.08 40.58 6.13
1668 1730 1.376424 CAAGGCGTCCATGTGCTCT 60.376 57.895 0.00 0.00 0.00 4.09
1798 1860 3.414700 GTCGTGCAGCCGGTTCAG 61.415 66.667 1.90 0.00 0.00 3.02
1859 1921 3.055240 CAGGAAGTCATCAAGCTCCTTCT 60.055 47.826 0.00 0.00 33.66 2.85
1971 2033 9.743581 ATGCATATGTGACTTCATAATATTGGA 57.256 29.630 0.00 0.00 34.58 3.53
2047 2118 3.730662 CGTATGCAACACATTAGTTGGCC 60.731 47.826 0.00 0.00 46.81 5.36
2109 2193 0.956410 CCACCGCGTTTGATGGGTTA 60.956 55.000 4.92 0.00 0.00 2.85
2139 2223 2.679934 CGCGTTTGCCATCTCTGCA 61.680 57.895 0.00 0.00 38.08 4.41
2151 2235 4.388499 ATCACCTCCGGCGCGTTT 62.388 61.111 8.43 0.00 0.00 3.60
2206 2290 4.478371 CTGCATCAGCCGCTCCCA 62.478 66.667 0.00 0.00 41.13 4.37
2251 2335 0.464036 TCTCGGATGCACGCCTTAAT 59.536 50.000 5.94 0.00 0.00 1.40
2252 2336 0.248012 TTCTCGGATGCACGCCTTAA 59.752 50.000 5.94 0.00 0.00 1.85
2253 2337 0.248012 TTTCTCGGATGCACGCCTTA 59.752 50.000 5.94 0.00 0.00 2.69
2272 2356 3.650950 AGGGTGCAGCCGGAATGT 61.651 61.111 28.24 7.85 38.44 2.71
2342 2426 3.372675 GCTTCCCTTGGGTATGTGGTAAT 60.373 47.826 5.51 0.00 0.00 1.89
2433 2517 3.141398 CATATTAATGTGGCGCTCTGGT 58.859 45.455 7.64 0.00 0.00 4.00
2607 2694 2.497675 GAGATCTATAGCCGCCAATCCA 59.502 50.000 0.00 0.00 0.00 3.41
2640 2727 0.697658 TGGCCAGGAACACATCATGA 59.302 50.000 0.00 0.00 42.41 3.07
2801 2888 5.071788 ACAAACTTACTTCAGGTGGAGATCA 59.928 40.000 0.00 0.00 0.00 2.92
2819 2906 4.916983 ACAACATGTATGCACACAAACT 57.083 36.364 0.00 0.00 37.54 2.66
2831 2918 1.202710 AGTCACGGCCAACAACATGTA 60.203 47.619 2.24 0.00 0.00 2.29
2845 2932 1.508632 CCAACTGGGTTGTAGTCACG 58.491 55.000 9.14 0.00 41.41 4.35
2899 2986 1.913951 ATCAAGTGGGATGCTCCGCA 61.914 55.000 7.41 0.00 44.86 5.69
2900 2987 0.106708 TATCAAGTGGGATGCTCCGC 59.893 55.000 0.00 0.00 37.43 5.54
2901 2988 1.138859 TGTATCAAGTGGGATGCTCCG 59.861 52.381 0.00 0.00 37.43 4.63
2902 2989 3.498774 ATGTATCAAGTGGGATGCTCC 57.501 47.619 0.00 0.00 35.23 4.70
2903 2990 5.858381 TCTTATGTATCAAGTGGGATGCTC 58.142 41.667 0.00 0.00 31.99 4.26
2904 2991 5.894298 TCTTATGTATCAAGTGGGATGCT 57.106 39.130 0.00 0.00 31.99 3.79
2905 2992 6.233434 TCATCTTATGTATCAAGTGGGATGC 58.767 40.000 0.00 0.00 0.00 3.91
2906 2993 7.601886 GTCTCATCTTATGTATCAAGTGGGATG 59.398 40.741 0.00 0.00 0.00 3.51
2907 2994 7.256475 GGTCTCATCTTATGTATCAAGTGGGAT 60.256 40.741 0.00 0.00 0.00 3.85
2908 2995 6.042093 GGTCTCATCTTATGTATCAAGTGGGA 59.958 42.308 0.00 0.00 0.00 4.37
2909 2996 6.042552 AGGTCTCATCTTATGTATCAAGTGGG 59.957 42.308 0.00 0.00 0.00 4.61
2910 2997 7.060383 AGGTCTCATCTTATGTATCAAGTGG 57.940 40.000 0.00 0.00 0.00 4.00
2911 2998 6.860539 CGAGGTCTCATCTTATGTATCAAGTG 59.139 42.308 0.00 0.00 0.00 3.16
2912 2999 6.773200 TCGAGGTCTCATCTTATGTATCAAGT 59.227 38.462 0.00 0.00 0.00 3.16
2913 3000 7.040755 AGTCGAGGTCTCATCTTATGTATCAAG 60.041 40.741 0.00 0.00 0.00 3.02
2914 3001 6.773200 AGTCGAGGTCTCATCTTATGTATCAA 59.227 38.462 0.00 0.00 0.00 2.57
2915 3002 6.299922 AGTCGAGGTCTCATCTTATGTATCA 58.700 40.000 0.00 0.00 0.00 2.15
2916 3003 6.811253 AGTCGAGGTCTCATCTTATGTATC 57.189 41.667 0.00 0.00 0.00 2.24
2917 3004 7.455058 AGTAGTCGAGGTCTCATCTTATGTAT 58.545 38.462 0.00 0.00 0.00 2.29
2918 3005 6.828788 AGTAGTCGAGGTCTCATCTTATGTA 58.171 40.000 0.00 0.00 0.00 2.29
2919 3006 5.686753 AGTAGTCGAGGTCTCATCTTATGT 58.313 41.667 0.00 0.00 0.00 2.29
2920 3007 5.995282 AGAGTAGTCGAGGTCTCATCTTATG 59.005 44.000 11.44 0.00 0.00 1.90
2921 3008 6.182507 AGAGTAGTCGAGGTCTCATCTTAT 57.817 41.667 11.44 0.00 0.00 1.73
2922 3009 5.453621 GGAGAGTAGTCGAGGTCTCATCTTA 60.454 48.000 12.72 0.00 37.73 2.10
2923 3010 4.448210 GAGAGTAGTCGAGGTCTCATCTT 58.552 47.826 11.44 0.00 36.29 2.40
2924 3011 3.181458 GGAGAGTAGTCGAGGTCTCATCT 60.181 52.174 12.72 3.11 37.73 2.90
2925 3012 3.135994 GGAGAGTAGTCGAGGTCTCATC 58.864 54.545 12.72 7.83 37.73 2.92
2926 3013 2.506231 TGGAGAGTAGTCGAGGTCTCAT 59.494 50.000 12.72 1.35 37.73 2.90
2927 3014 1.907255 TGGAGAGTAGTCGAGGTCTCA 59.093 52.381 12.72 1.09 37.73 3.27
2928 3015 2.695127 TGGAGAGTAGTCGAGGTCTC 57.305 55.000 0.00 0.00 35.64 3.36
2929 3016 2.506231 TCATGGAGAGTAGTCGAGGTCT 59.494 50.000 0.00 0.00 0.00 3.85
2930 3017 2.920524 TCATGGAGAGTAGTCGAGGTC 58.079 52.381 0.00 0.00 0.00 3.85
2931 3018 3.367646 TTCATGGAGAGTAGTCGAGGT 57.632 47.619 0.00 0.00 0.00 3.85
2932 3019 3.634448 ACATTCATGGAGAGTAGTCGAGG 59.366 47.826 0.00 0.00 0.00 4.63
2933 3020 4.909696 ACATTCATGGAGAGTAGTCGAG 57.090 45.455 0.00 0.00 0.00 4.04
2934 3021 4.705023 TGAACATTCATGGAGAGTAGTCGA 59.295 41.667 0.00 0.00 31.01 4.20
2935 3022 4.998788 TGAACATTCATGGAGAGTAGTCG 58.001 43.478 0.00 0.00 31.01 4.18
2948 3035 7.047891 GGAGTGTACATAAGGATGAACATTCA 58.952 38.462 0.00 0.00 42.14 2.57
2949 3036 6.201044 CGGAGTGTACATAAGGATGAACATTC 59.799 42.308 0.00 0.00 36.48 2.67
2950 3037 6.049149 CGGAGTGTACATAAGGATGAACATT 58.951 40.000 0.00 0.00 36.48 2.71
2951 3038 5.362717 TCGGAGTGTACATAAGGATGAACAT 59.637 40.000 0.00 0.00 36.48 2.71
2952 3039 4.707934 TCGGAGTGTACATAAGGATGAACA 59.292 41.667 0.00 0.00 36.48 3.18
2953 3040 5.041940 GTCGGAGTGTACATAAGGATGAAC 58.958 45.833 0.00 0.00 36.48 3.18
2954 3041 4.954202 AGTCGGAGTGTACATAAGGATGAA 59.046 41.667 0.00 0.00 36.48 2.57
2955 3042 4.533815 AGTCGGAGTGTACATAAGGATGA 58.466 43.478 0.00 0.00 36.48 2.92
2956 3043 4.920640 AGTCGGAGTGTACATAAGGATG 57.079 45.455 0.00 0.00 39.16 3.51
2957 3044 5.692928 AGTAGTCGGAGTGTACATAAGGAT 58.307 41.667 0.00 0.00 0.00 3.24
2958 3045 5.104610 AGAGTAGTCGGAGTGTACATAAGGA 60.105 44.000 0.00 0.00 0.00 3.36
2959 3046 5.124645 AGAGTAGTCGGAGTGTACATAAGG 58.875 45.833 0.00 0.00 0.00 2.69
2960 3047 5.236911 GGAGAGTAGTCGGAGTGTACATAAG 59.763 48.000 0.00 0.00 0.00 1.73
2961 3048 5.121811 GGAGAGTAGTCGGAGTGTACATAA 58.878 45.833 0.00 0.00 0.00 1.90
2962 3049 4.162888 TGGAGAGTAGTCGGAGTGTACATA 59.837 45.833 0.00 0.00 0.00 2.29
2963 3050 3.054582 TGGAGAGTAGTCGGAGTGTACAT 60.055 47.826 0.00 0.00 0.00 2.29
2964 3051 2.303890 TGGAGAGTAGTCGGAGTGTACA 59.696 50.000 0.00 0.00 0.00 2.90
2965 3052 2.983229 TGGAGAGTAGTCGGAGTGTAC 58.017 52.381 0.00 0.00 0.00 2.90
2966 3053 3.607741 CTTGGAGAGTAGTCGGAGTGTA 58.392 50.000 0.00 0.00 0.00 2.90
2967 3054 2.438411 CTTGGAGAGTAGTCGGAGTGT 58.562 52.381 0.00 0.00 0.00 3.55
2968 3055 1.133407 GCTTGGAGAGTAGTCGGAGTG 59.867 57.143 0.00 0.00 0.00 3.51
2969 3056 1.465794 GCTTGGAGAGTAGTCGGAGT 58.534 55.000 0.00 0.00 0.00 3.85
2970 3057 0.741915 GGCTTGGAGAGTAGTCGGAG 59.258 60.000 0.00 0.00 0.00 4.63
2971 3058 0.683504 GGGCTTGGAGAGTAGTCGGA 60.684 60.000 0.00 0.00 0.00 4.55
2972 3059 1.677637 GGGGCTTGGAGAGTAGTCGG 61.678 65.000 0.00 0.00 0.00 4.79
2973 3060 0.970937 TGGGGCTTGGAGAGTAGTCG 60.971 60.000 0.00 0.00 0.00 4.18
2974 3061 1.208293 CTTGGGGCTTGGAGAGTAGTC 59.792 57.143 0.00 0.00 0.00 2.59
2975 3062 1.280457 CTTGGGGCTTGGAGAGTAGT 58.720 55.000 0.00 0.00 0.00 2.73
2976 3063 0.543749 CCTTGGGGCTTGGAGAGTAG 59.456 60.000 0.00 0.00 0.00 2.57
2977 3064 0.118346 TCCTTGGGGCTTGGAGAGTA 59.882 55.000 0.00 0.00 0.00 2.59
2978 3065 0.551131 ATCCTTGGGGCTTGGAGAGT 60.551 55.000 0.00 0.00 32.95 3.24
2979 3066 1.141858 GTATCCTTGGGGCTTGGAGAG 59.858 57.143 0.00 0.00 32.95 3.20
2980 3067 1.213296 GTATCCTTGGGGCTTGGAGA 58.787 55.000 0.00 0.00 32.95 3.71
2981 3068 0.918983 TGTATCCTTGGGGCTTGGAG 59.081 55.000 0.00 0.00 32.95 3.86
2982 3069 1.607225 ATGTATCCTTGGGGCTTGGA 58.393 50.000 0.00 0.00 0.00 3.53
2983 3070 3.138283 TCTTATGTATCCTTGGGGCTTGG 59.862 47.826 0.00 0.00 0.00 3.61
2984 3071 4.437682 TCTTATGTATCCTTGGGGCTTG 57.562 45.455 0.00 0.00 0.00 4.01
2985 3072 4.665009 TCATCTTATGTATCCTTGGGGCTT 59.335 41.667 0.00 0.00 0.00 4.35
2986 3073 4.242811 TCATCTTATGTATCCTTGGGGCT 58.757 43.478 0.00 0.00 0.00 5.19
2987 3074 4.287067 TCTCATCTTATGTATCCTTGGGGC 59.713 45.833 0.00 0.00 0.00 5.80
2988 3075 5.280215 GGTCTCATCTTATGTATCCTTGGGG 60.280 48.000 0.00 0.00 0.00 4.96
2989 3076 5.545723 AGGTCTCATCTTATGTATCCTTGGG 59.454 44.000 0.00 0.00 0.00 4.12
2990 3077 6.571344 CGAGGTCTCATCTTATGTATCCTTGG 60.571 46.154 0.00 0.00 0.00 3.61
2991 3078 6.207614 TCGAGGTCTCATCTTATGTATCCTTG 59.792 42.308 0.00 0.00 32.59 3.61
2992 3079 6.207810 GTCGAGGTCTCATCTTATGTATCCTT 59.792 42.308 0.00 0.00 0.00 3.36
2993 3080 5.708230 GTCGAGGTCTCATCTTATGTATCCT 59.292 44.000 0.00 0.00 0.00 3.24
2994 3081 5.106078 GGTCGAGGTCTCATCTTATGTATCC 60.106 48.000 0.00 0.00 0.00 2.59
2995 3082 5.473846 TGGTCGAGGTCTCATCTTATGTATC 59.526 44.000 0.00 0.00 0.00 2.24
2996 3083 5.241949 GTGGTCGAGGTCTCATCTTATGTAT 59.758 44.000 0.00 0.00 0.00 2.29
2997 3084 4.579340 GTGGTCGAGGTCTCATCTTATGTA 59.421 45.833 0.00 0.00 0.00 2.29
2998 3085 3.381908 GTGGTCGAGGTCTCATCTTATGT 59.618 47.826 0.00 0.00 0.00 2.29
2999 3086 3.634448 AGTGGTCGAGGTCTCATCTTATG 59.366 47.826 0.00 0.00 0.00 1.90
3000 3087 3.904717 AGTGGTCGAGGTCTCATCTTAT 58.095 45.455 0.00 0.00 0.00 1.73
3001 3088 3.367646 AGTGGTCGAGGTCTCATCTTA 57.632 47.619 0.00 0.00 0.00 2.10
3002 3089 2.223803 AGTGGTCGAGGTCTCATCTT 57.776 50.000 0.00 0.00 0.00 2.40
3003 3090 1.821753 CAAGTGGTCGAGGTCTCATCT 59.178 52.381 0.00 0.00 0.00 2.90
3004 3091 1.819288 TCAAGTGGTCGAGGTCTCATC 59.181 52.381 0.00 0.00 0.00 2.92
3005 3092 1.924731 TCAAGTGGTCGAGGTCTCAT 58.075 50.000 0.00 0.00 0.00 2.90
3006 3093 1.699730 TTCAAGTGGTCGAGGTCTCA 58.300 50.000 0.00 0.00 0.00 3.27
3007 3094 2.814280 TTTCAAGTGGTCGAGGTCTC 57.186 50.000 0.00 0.00 0.00 3.36
3008 3095 3.771577 ATTTTCAAGTGGTCGAGGTCT 57.228 42.857 0.00 0.00 0.00 3.85
3009 3096 7.787725 ATATTATTTTCAAGTGGTCGAGGTC 57.212 36.000 0.00 0.00 0.00 3.85
3010 3097 7.441458 GCTATATTATTTTCAAGTGGTCGAGGT 59.559 37.037 0.00 0.00 0.00 3.85
3011 3098 7.657761 AGCTATATTATTTTCAAGTGGTCGAGG 59.342 37.037 0.00 0.00 0.00 4.63
3012 3099 8.594881 AGCTATATTATTTTCAAGTGGTCGAG 57.405 34.615 0.00 0.00 0.00 4.04
3013 3100 8.201464 TGAGCTATATTATTTTCAAGTGGTCGA 58.799 33.333 0.00 0.00 0.00 4.20
3014 3101 8.365399 TGAGCTATATTATTTTCAAGTGGTCG 57.635 34.615 0.00 0.00 0.00 4.79
3027 3114 9.797642 TGGTGACAATCAATTGAGCTATATTAT 57.202 29.630 14.54 0.00 40.14 1.28
3045 3132 8.491374 CATAAGGATGAACACTCATGGTGACAA 61.491 40.741 17.76 5.96 42.60 3.18
3046 3133 7.075968 CATAAGGATGAACACTCATGGTGACA 61.076 42.308 17.76 15.99 42.60 3.58
3047 3134 5.295292 CATAAGGATGAACACTCATGGTGAC 59.705 44.000 17.76 12.31 42.60 3.67
3048 3135 5.045651 ACATAAGGATGAACACTCATGGTGA 60.046 40.000 17.76 0.51 42.60 4.02
3049 3136 5.188434 ACATAAGGATGAACACTCATGGTG 58.812 41.667 11.40 11.40 42.60 4.17
3050 3137 5.441718 ACATAAGGATGAACACTCATGGT 57.558 39.130 0.00 0.00 42.60 3.55
3051 3138 6.258727 GTGTACATAAGGATGAACACTCATGG 59.741 42.308 0.00 0.00 42.60 3.66
3052 3139 7.044181 AGTGTACATAAGGATGAACACTCATG 58.956 38.462 0.00 0.00 42.60 3.07
3053 3140 7.187824 AGTGTACATAAGGATGAACACTCAT 57.812 36.000 0.00 0.00 45.34 2.90
3054 3141 6.605471 AGTGTACATAAGGATGAACACTCA 57.395 37.500 0.00 0.00 36.48 3.41
3055 3142 6.043411 GGAGTGTACATAAGGATGAACACTC 58.957 44.000 19.88 19.88 46.88 3.51
3056 3143 5.394224 CGGAGTGTACATAAGGATGAACACT 60.394 44.000 0.00 5.67 39.51 3.55
3057 3144 4.804139 CGGAGTGTACATAAGGATGAACAC 59.196 45.833 0.00 0.00 36.48 3.32
3068 3155 4.162888 TGGAGAGTAGTCGGAGTGTACATA 59.837 45.833 0.00 0.00 0.00 2.29
3245 3333 1.380302 GTTGGATGTGGTGGCTCCT 59.620 57.895 7.19 0.00 37.07 3.69
3346 3446 2.430367 GGTGGGTCTTCAGGCGTT 59.570 61.111 0.00 0.00 0.00 4.84
3600 3719 1.755200 AAGTGAAGGGGTACATGGGT 58.245 50.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.