Multiple sequence alignment - TraesCS1A01G173500

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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 TraesCS1A01G173500 chr1A 100.000 6880 0 0 1 6880 309463696 309456817 0.000000e+00 12706.0
1 TraesCS1A01G173500 chr1A 81.890 508 51 16 444 923 309460846 309460352 2.330000e-104 390.0
2 TraesCS1A01G173500 chr1A 81.890 508 51 16 2851 3345 309463253 309462774 2.330000e-104 390.0
3 TraesCS1A01G173500 chr1A 86.239 327 33 6 2332 2655 309465252 309464935 1.840000e-90 344.0
4 TraesCS1A01G173500 chr1A 85.053 281 32 9 3710 3987 309459917 309459644 1.890000e-70 278.0
5 TraesCS1A01G173500 chr1A 85.000 280 34 7 3780 4053 309459987 309459710 1.890000e-70 278.0
6 TraesCS1A01G173500 chr1A 79.435 248 27 11 1065 1292 309465948 309465705 3.320000e-33 154.0
7 TraesCS1A01G173500 chr1A 90.909 99 7 2 6304 6402 251345788 251345884 1.560000e-26 132.0
8 TraesCS1A01G173500 chr1A 77.419 186 27 11 2669 2853 309464884 309464713 5.680000e-16 97.1
9 TraesCS1A01G173500 chr1B 97.196 2603 57 9 3710 6303 341748075 341750670 0.000000e+00 4388.0
10 TraesCS1A01G173500 chr1B 93.412 759 29 4 2890 3644 341747125 341747866 0.000000e+00 1105.0
11 TraesCS1A01G173500 chr1B 88.604 781 49 18 1 771 341744802 341745552 0.000000e+00 913.0
12 TraesCS1A01G173500 chr1B 89.880 415 38 3 1065 1479 341745613 341746023 1.310000e-146 531.0
13 TraesCS1A01G173500 chr1B 86.966 468 35 10 6421 6880 341750682 341751131 2.860000e-138 503.0
14 TraesCS1A01G173500 chr1B 88.509 409 32 10 3647 4050 341747951 341748349 1.340000e-131 481.0
15 TraesCS1A01G173500 chr1B 85.872 453 40 13 483 923 341747125 341747565 1.750000e-125 460.0
16 TraesCS1A01G173500 chr1B 89.203 389 10 4 2501 2888 341746697 341747054 2.260000e-124 457.0
17 TraesCS1A01G173500 chr1B 96.324 272 8 1 2326 2597 341746427 341746696 4.900000e-121 446.0
18 TraesCS1A01G173500 chr1B 87.966 349 33 4 2331 2676 341743194 341743536 2.990000e-108 403.0
19 TraesCS1A01G173500 chr1B 94.690 226 8 2 1467 1688 341746208 341746433 1.420000e-91 348.0
20 TraesCS1A01G173500 chr1B 85.546 339 34 7 2851 3177 341745217 341745552 2.380000e-89 340.0
21 TraesCS1A01G173500 chr1B 86.331 278 28 10 3780 4050 341748005 341748279 1.880000e-75 294.0
22 TraesCS1A01G173500 chr1B 84.892 278 33 8 3710 3984 341748144 341748415 8.790000e-69 272.0
23 TraesCS1A01G173500 chr1B 92.308 78 4 2 2914 2989 341747053 341747130 7.300000e-20 110.0
24 TraesCS1A01G173500 chr1B 77.419 186 27 12 2669 2853 341743575 341743746 5.680000e-16 97.1
25 TraesCS1A01G173500 chr1D 94.923 2777 68 22 2326 5095 236319301 236322011 0.000000e+00 4279.0
26 TraesCS1A01G173500 chr1D 97.869 1220 19 2 5090 6303 236322309 236323527 0.000000e+00 2102.0
27 TraesCS1A01G173500 chr1D 92.113 1065 64 11 1 1054 236317572 236318627 0.000000e+00 1483.0
28 TraesCS1A01G173500 chr1D 92.197 628 39 5 1065 1688 236318686 236319307 0.000000e+00 880.0
29 TraesCS1A01G173500 chr1D 87.551 490 32 9 6398 6880 236323528 236323995 2.180000e-149 540.0
30 TraesCS1A01G173500 chr1D 84.350 492 53 11 444 923 236319805 236320284 1.750000e-125 460.0
31 TraesCS1A01G173500 chr1D 82.480 508 56 15 2850 3345 236318010 236318496 1.380000e-111 414.0
32 TraesCS1A01G173500 chr1D 87.324 355 36 4 2333 2684 236315264 236315612 1.390000e-106 398.0
33 TraesCS1A01G173500 chr1D 90.909 66 5 1 2789 2853 236315732 236315797 3.420000e-13 87.9
34 TraesCS1A01G173500 chr5D 92.733 633 38 6 1697 2324 5257141 5256512 0.000000e+00 907.0
35 TraesCS1A01G173500 chr5D 91.549 639 48 5 1691 2327 298070731 298070097 0.000000e+00 876.0
36 TraesCS1A01G173500 chr5D 90.881 636 49 5 1691 2324 271901808 271902436 0.000000e+00 845.0
37 TraesCS1A01G173500 chr6D 91.433 642 44 6 1691 2324 451323250 451322612 0.000000e+00 870.0
38 TraesCS1A01G173500 chr4D 91.195 636 53 3 1691 2324 197007394 197006760 0.000000e+00 861.0
39 TraesCS1A01G173500 chr4D 84.298 242 28 4 6526 6762 120352394 120352158 1.930000e-55 228.0
40 TraesCS1A01G173500 chr4D 91.919 99 6 2 6304 6402 9492947 9493043 3.350000e-28 137.0
41 TraesCS1A01G173500 chr4D 90.909 99 9 0 6304 6402 13198283 13198381 4.330000e-27 134.0
42 TraesCS1A01G173500 chr3D 90.439 638 54 7 1691 2324 374957165 374957799 0.000000e+00 833.0
43 TraesCS1A01G173500 chr3D 82.031 256 36 7 6526 6775 298594879 298595130 6.990000e-50 209.0
44 TraesCS1A01G173500 chr3D 90.816 98 9 0 6304 6401 448433609 448433706 1.560000e-26 132.0
45 TraesCS1A01G173500 chr2D 90.409 636 58 3 1694 2327 423469210 423468576 0.000000e+00 833.0
46 TraesCS1A01G173500 chr2D 90.252 636 60 2 1691 2324 236114151 236114786 0.000000e+00 830.0
47 TraesCS1A01G173500 chr2D 87.166 187 22 1 6552 6738 158246165 158245981 1.940000e-50 211.0
48 TraesCS1A01G173500 chr2D 89.720 107 10 1 6294 6400 566267674 566267569 1.200000e-27 135.0
49 TraesCS1A01G173500 chr3A 90.252 636 56 5 1691 2324 387179789 387180420 0.000000e+00 826.0
50 TraesCS1A01G173500 chr3A 85.909 220 25 2 6553 6766 69662762 69662543 5.370000e-56 230.0
51 TraesCS1A01G173500 chr3A 83.333 240 31 2 6526 6760 91026505 91026740 5.410000e-51 213.0
52 TraesCS1A01G173500 chr2A 85.223 291 40 3 3700 3987 555339343 555339633 5.220000e-76 296.0
53 TraesCS1A01G173500 chr2A 82.133 347 49 11 3780 4116 555339353 555339696 1.130000e-72 285.0
54 TraesCS1A01G173500 chr2A 91.089 101 9 0 6304 6404 660286776 660286876 3.350000e-28 137.0
55 TraesCS1A01G173500 chr2A 91.753 97 8 0 6304 6400 68155919 68155823 1.200000e-27 135.0
56 TraesCS1A01G173500 chr3B 85.909 220 25 2 6553 6766 97756112 97755893 5.370000e-56 230.0
57 TraesCS1A01G173500 chr3B 83.268 257 30 7 6526 6775 394097771 394098021 2.500000e-54 224.0
58 TraesCS1A01G173500 chr3B 90.816 98 9 0 6304 6401 588476645 588476742 1.560000e-26 132.0
59 TraesCS1A01G173500 chr7A 83.544 237 29 4 6526 6757 561386261 561386492 5.410000e-51 213.0
60 TraesCS1A01G173500 chr7D 89.423 104 10 1 6300 6402 420091659 420091762 5.600000e-26 130.0


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 TraesCS1A01G173500 chr1A 309456817 309463696 6879 True 12706.000000 12706 100.000000 1 6880 1 chr1A.!!$R1 6879
1 TraesCS1A01G173500 chr1A 309459644 309465948 6304 True 275.871429 390 82.418000 444 4053 7 chr1A.!!$R2 3609
2 TraesCS1A01G173500 chr1B 341743194 341751131 7937 False 696.756250 4388 89.069875 1 6880 16 chr1B.!!$F1 6879
3 TraesCS1A01G173500 chr1D 236315264 236323995 8731 False 1182.655556 4279 89.968444 1 6880 9 chr1D.!!$F1 6879
4 TraesCS1A01G173500 chr5D 5256512 5257141 629 True 907.000000 907 92.733000 1697 2324 1 chr5D.!!$R1 627
5 TraesCS1A01G173500 chr5D 298070097 298070731 634 True 876.000000 876 91.549000 1691 2327 1 chr5D.!!$R2 636
6 TraesCS1A01G173500 chr5D 271901808 271902436 628 False 845.000000 845 90.881000 1691 2324 1 chr5D.!!$F1 633
7 TraesCS1A01G173500 chr6D 451322612 451323250 638 True 870.000000 870 91.433000 1691 2324 1 chr6D.!!$R1 633
8 TraesCS1A01G173500 chr4D 197006760 197007394 634 True 861.000000 861 91.195000 1691 2324 1 chr4D.!!$R2 633
9 TraesCS1A01G173500 chr3D 374957165 374957799 634 False 833.000000 833 90.439000 1691 2324 1 chr3D.!!$F2 633
10 TraesCS1A01G173500 chr2D 423468576 423469210 634 True 833.000000 833 90.409000 1694 2327 1 chr2D.!!$R2 633
11 TraesCS1A01G173500 chr2D 236114151 236114786 635 False 830.000000 830 90.252000 1691 2324 1 chr2D.!!$F1 633
12 TraesCS1A01G173500 chr3A 387179789 387180420 631 False 826.000000 826 90.252000 1691 2324 1 chr3A.!!$F2 633

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
36 1645 0.036388 GCCTCGTGGTCATTCTTCCA 60.036 55.000 5.26 0.0 35.27 3.53 F
426 2035 0.536460 AAGCGGACGAAATGGGTTGT 60.536 50.000 0.00 0.0 0.00 3.32 F
2709 6103 1.074405 TGCTGAAATCTCTTGTGGGCT 59.926 47.619 0.00 0.0 0.00 5.19 F
2710 6104 2.305635 TGCTGAAATCTCTTGTGGGCTA 59.694 45.455 0.00 0.0 0.00 3.93 F
5002 8670 0.537143 TCGTGTGCCCAATGAGCTTT 60.537 50.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2795 6219 5.121380 ACATGCAGATTAGGAAGAATGGT 57.879 39.130 0.00 0.00 0.00 3.55 R
2811 6235 4.759183 TGTGCATTAGAACAAGTACATGCA 59.241 37.500 8.63 8.63 43.56 3.96 R
4100 7767 0.466543 TACAGGCGTGTGTGAGGTTT 59.533 50.000 21.78 0.00 37.52 3.27 R
5315 9285 0.890996 GGCATATTCCCGCCCTTGAG 60.891 60.000 0.00 0.00 42.82 3.02 R
6478 10471 1.073199 ACCTTCACTCCCCGCAAAG 59.927 57.895 0.00 0.00 0.00 2.77 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
17 18 3.790437 ACCCCGATGAGCTGCTGG 61.790 66.667 7.01 2.97 0.00 4.85
36 1645 0.036388 GCCTCGTGGTCATTCTTCCA 60.036 55.000 5.26 0.00 35.27 3.53
37 1646 1.610624 GCCTCGTGGTCATTCTTCCAA 60.611 52.381 5.26 0.00 35.38 3.53
72 1681 1.677552 CGACTAGGGCTGGGTTGTT 59.322 57.895 0.00 0.00 0.00 2.83
73 1682 0.673644 CGACTAGGGCTGGGTTGTTG 60.674 60.000 0.00 0.00 0.00 3.33
85 1694 3.585428 TTGTTGGGCGGATGGGGT 61.585 61.111 0.00 0.00 0.00 4.95
111 1720 2.482839 GGCAAGAGGAAGAAGAGGATCG 60.483 54.545 0.00 0.00 42.67 3.69
134 1743 4.716784 GGGGAGGAAAGCATTAAAAAGGAT 59.283 41.667 0.00 0.00 0.00 3.24
156 1765 1.822371 GGTGTGGACTGGTTTTGTTGT 59.178 47.619 0.00 0.00 0.00 3.32
216 1825 4.198224 CGGTGGGTGGTGGTTGGT 62.198 66.667 0.00 0.00 0.00 3.67
318 1927 1.608109 CCAAATTTGGGGCAAAAGTGC 59.392 47.619 26.87 0.00 44.13 4.40
347 1956 3.876300 GCACCGAGCGAACAGAAT 58.124 55.556 0.00 0.00 0.00 2.40
348 1957 2.162716 GCACCGAGCGAACAGAATT 58.837 52.632 0.00 0.00 0.00 2.17
350 1959 1.730064 GCACCGAGCGAACAGAATTTA 59.270 47.619 0.00 0.00 0.00 1.40
351 1960 2.222819 GCACCGAGCGAACAGAATTTAG 60.223 50.000 0.00 0.00 0.00 1.85
352 1961 2.348666 CACCGAGCGAACAGAATTTAGG 59.651 50.000 0.00 0.00 0.00 2.69
359 1968 3.364565 GCGAACAGAATTTAGGTTTGCGA 60.365 43.478 11.73 0.00 40.78 5.10
393 2002 1.670791 GTGGTTTTTGGTCTCGTGGA 58.329 50.000 0.00 0.00 0.00 4.02
426 2035 0.536460 AAGCGGACGAAATGGGTTGT 60.536 50.000 0.00 0.00 0.00 3.32
439 2048 1.340211 TGGGTTGTCGTGTTGGAGTTT 60.340 47.619 0.00 0.00 0.00 2.66
2442 5738 6.749036 TCTTCAAATACCCCTTATCCTCTC 57.251 41.667 0.00 0.00 0.00 3.20
2443 5739 5.607171 TCTTCAAATACCCCTTATCCTCTCC 59.393 44.000 0.00 0.00 0.00 3.71
2708 6102 1.200948 GTGCTGAAATCTCTTGTGGGC 59.799 52.381 0.00 0.00 0.00 5.36
2709 6103 1.074405 TGCTGAAATCTCTTGTGGGCT 59.926 47.619 0.00 0.00 0.00 5.19
2710 6104 2.305635 TGCTGAAATCTCTTGTGGGCTA 59.694 45.455 0.00 0.00 0.00 3.93
2711 6105 2.680339 GCTGAAATCTCTTGTGGGCTAC 59.320 50.000 0.00 0.00 0.00 3.58
2712 6106 3.620966 GCTGAAATCTCTTGTGGGCTACT 60.621 47.826 1.79 0.00 0.00 2.57
2713 6107 4.187694 CTGAAATCTCTTGTGGGCTACTC 58.812 47.826 1.79 0.00 0.00 2.59
2714 6108 3.840666 TGAAATCTCTTGTGGGCTACTCT 59.159 43.478 1.79 0.00 0.00 3.24
2791 6215 7.938490 TGCATATACCATTCTTCTTAATCTGCA 59.062 33.333 0.00 0.00 0.00 4.41
2792 6216 8.954350 GCATATACCATTCTTCTTAATCTGCAT 58.046 33.333 0.00 0.00 0.00 3.96
2796 6220 7.559590 ACCATTCTTCTTAATCTGCATGTAC 57.440 36.000 0.00 0.00 0.00 2.90
2797 6221 6.543831 ACCATTCTTCTTAATCTGCATGTACC 59.456 38.462 0.00 0.00 0.00 3.34
2798 6222 6.543465 CCATTCTTCTTAATCTGCATGTACCA 59.457 38.462 0.00 0.00 0.00 3.25
2799 6223 7.230108 CCATTCTTCTTAATCTGCATGTACCAT 59.770 37.037 0.00 0.00 0.00 3.55
2800 6224 8.627403 CATTCTTCTTAATCTGCATGTACCATT 58.373 33.333 0.00 0.00 0.00 3.16
2801 6225 7.792374 TCTTCTTAATCTGCATGTACCATTC 57.208 36.000 0.00 0.00 0.00 2.67
2802 6226 7.568349 TCTTCTTAATCTGCATGTACCATTCT 58.432 34.615 0.00 0.00 0.00 2.40
2803 6227 8.049117 TCTTCTTAATCTGCATGTACCATTCTT 58.951 33.333 0.00 0.00 0.00 2.52
2804 6228 7.792374 TCTTAATCTGCATGTACCATTCTTC 57.208 36.000 0.00 0.00 0.00 2.87
2805 6229 6.767902 TCTTAATCTGCATGTACCATTCTTCC 59.232 38.462 0.00 0.00 0.00 3.46
2806 6230 4.785346 ATCTGCATGTACCATTCTTCCT 57.215 40.909 0.00 0.00 0.00 3.36
2807 6231 5.894298 ATCTGCATGTACCATTCTTCCTA 57.106 39.130 0.00 0.00 0.00 2.94
2808 6232 5.692115 TCTGCATGTACCATTCTTCCTAA 57.308 39.130 0.00 0.00 0.00 2.69
2809 6233 6.252599 TCTGCATGTACCATTCTTCCTAAT 57.747 37.500 0.00 0.00 0.00 1.73
2810 6234 6.291377 TCTGCATGTACCATTCTTCCTAATC 58.709 40.000 0.00 0.00 0.00 1.75
2811 6235 6.100279 TCTGCATGTACCATTCTTCCTAATCT 59.900 38.462 0.00 0.00 0.00 2.40
2812 6236 6.057533 TGCATGTACCATTCTTCCTAATCTG 58.942 40.000 0.00 0.00 0.00 2.90
2813 6237 5.049129 GCATGTACCATTCTTCCTAATCTGC 60.049 44.000 0.00 0.00 0.00 4.26
4100 7767 9.582431 CTAAAAATTAATGTACTCGGAGTCTCA 57.418 33.333 15.05 14.97 0.00 3.27
4108 7775 1.614413 ACTCGGAGTCTCAAACCTCAC 59.386 52.381 4.45 0.00 0.00 3.51
4278 7946 4.096231 CCATATTTGTTTGCATGTCGAGGA 59.904 41.667 0.00 0.00 0.00 3.71
4309 7977 8.812329 CATACTTCTTCTCACTAGTTATTGCAC 58.188 37.037 0.00 0.00 0.00 4.57
4313 7981 6.993079 TCTTCTCACTAGTTATTGCACTGAA 58.007 36.000 0.00 0.00 0.00 3.02
4390 8058 9.659830 AACTAACTTGTTTCATTTTATCACGAC 57.340 29.630 0.00 0.00 0.00 4.34
4417 8085 8.212995 TGTACTCATTCATATGTGTTCATGGAT 58.787 33.333 1.90 0.00 38.85 3.41
5002 8670 0.537143 TCGTGTGCCCAATGAGCTTT 60.537 50.000 0.00 0.00 0.00 3.51
5121 9091 8.839310 ATCTGTGTAGCCATTGAATCTATAAC 57.161 34.615 0.00 0.00 0.00 1.89
5952 9922 3.186909 CGAGCCAGTCATTCGTAAATCA 58.813 45.455 0.00 0.00 0.00 2.57
5980 9950 1.134491 GCATCGGTAAGCTGTAACCCT 60.134 52.381 7.40 0.00 31.68 4.34
6128 10098 6.712095 ACTCAGAAACATATGCTTTGAAGTGA 59.288 34.615 1.58 3.32 0.00 3.41
6171 10147 3.814842 TCATCGTGTTTCTTTCATGCACT 59.185 39.130 0.00 0.00 0.00 4.40
6231 10207 5.163131 GGAAATAACCCAGGTTGGCTATCTA 60.163 44.000 12.41 0.00 38.92 1.98
6246 10222 4.342665 GGCTATCTACAAGCTGGTACTTCT 59.657 45.833 0.00 0.00 39.97 2.85
6265 10241 5.181433 ACTTCTTTCGGTGCCTTTATTCTTC 59.819 40.000 0.00 0.00 0.00 2.87
6303 10279 5.240891 TCCAATTTGTTTGTTGTTTGAGCA 58.759 33.333 0.00 0.00 33.15 4.26
6304 10280 5.121454 TCCAATTTGTTTGTTGTTTGAGCAC 59.879 36.000 0.00 0.00 33.15 4.40
6305 10281 5.122082 CCAATTTGTTTGTTGTTTGAGCACT 59.878 36.000 0.00 0.00 33.15 4.40
6306 10282 6.242829 CAATTTGTTTGTTGTTTGAGCACTC 58.757 36.000 0.00 0.00 0.00 3.51
6307 10283 4.782019 TTGTTTGTTGTTTGAGCACTCT 57.218 36.364 0.00 0.00 0.00 3.24
6308 10284 4.355543 TGTTTGTTGTTTGAGCACTCTC 57.644 40.909 0.00 0.00 39.78 3.20
6309 10285 4.009675 TGTTTGTTGTTTGAGCACTCTCT 58.990 39.130 0.00 0.00 40.03 3.10
6310 10286 4.094887 TGTTTGTTGTTTGAGCACTCTCTC 59.905 41.667 0.00 0.00 40.03 3.20
6311 10287 2.838736 TGTTGTTTGAGCACTCTCTCC 58.161 47.619 0.00 0.00 40.03 3.71
6312 10288 1.795286 GTTGTTTGAGCACTCTCTCCG 59.205 52.381 0.00 0.00 40.03 4.63
6313 10289 1.040646 TGTTTGAGCACTCTCTCCGT 58.959 50.000 0.00 0.00 40.03 4.69
6314 10290 1.412710 TGTTTGAGCACTCTCTCCGTT 59.587 47.619 0.00 0.00 40.03 4.44
6315 10291 2.062519 GTTTGAGCACTCTCTCCGTTC 58.937 52.381 0.00 0.00 40.03 3.95
6316 10292 0.603569 TTGAGCACTCTCTCCGTTCC 59.396 55.000 0.00 0.00 40.03 3.62
6317 10293 0.539669 TGAGCACTCTCTCCGTTCCA 60.540 55.000 0.00 0.00 40.03 3.53
6318 10294 0.603569 GAGCACTCTCTCCGTTCCAA 59.396 55.000 0.00 0.00 36.42 3.53
6319 10295 1.000955 GAGCACTCTCTCCGTTCCAAA 59.999 52.381 0.00 0.00 36.42 3.28
6320 10296 1.416401 AGCACTCTCTCCGTTCCAAAA 59.584 47.619 0.00 0.00 0.00 2.44
6321 10297 2.039084 AGCACTCTCTCCGTTCCAAAAT 59.961 45.455 0.00 0.00 0.00 1.82
6322 10298 3.260884 AGCACTCTCTCCGTTCCAAAATA 59.739 43.478 0.00 0.00 0.00 1.40
6323 10299 4.000988 GCACTCTCTCCGTTCCAAAATAA 58.999 43.478 0.00 0.00 0.00 1.40
6324 10300 4.093556 GCACTCTCTCCGTTCCAAAATAAG 59.906 45.833 0.00 0.00 0.00 1.73
6325 10301 5.238583 CACTCTCTCCGTTCCAAAATAAGT 58.761 41.667 0.00 0.00 0.00 2.24
6326 10302 5.120830 CACTCTCTCCGTTCCAAAATAAGTG 59.879 44.000 0.00 0.00 0.00 3.16
6327 10303 5.221661 ACTCTCTCCGTTCCAAAATAAGTGT 60.222 40.000 0.00 0.00 0.00 3.55
6328 10304 5.235516 TCTCTCCGTTCCAAAATAAGTGTC 58.764 41.667 0.00 0.00 0.00 3.67
6329 10305 5.011738 TCTCTCCGTTCCAAAATAAGTGTCT 59.988 40.000 0.00 0.00 0.00 3.41
6330 10306 5.235516 TCTCCGTTCCAAAATAAGTGTCTC 58.764 41.667 0.00 0.00 0.00 3.36
6331 10307 4.963373 TCCGTTCCAAAATAAGTGTCTCA 58.037 39.130 0.00 0.00 0.00 3.27
6332 10308 5.369833 TCCGTTCCAAAATAAGTGTCTCAA 58.630 37.500 0.00 0.00 0.00 3.02
6333 10309 6.001460 TCCGTTCCAAAATAAGTGTCTCAAT 58.999 36.000 0.00 0.00 0.00 2.57
6334 10310 6.488683 TCCGTTCCAAAATAAGTGTCTCAATT 59.511 34.615 0.00 0.00 0.00 2.32
6335 10311 7.013846 TCCGTTCCAAAATAAGTGTCTCAATTT 59.986 33.333 0.00 0.00 0.00 1.82
6336 10312 7.651704 CCGTTCCAAAATAAGTGTCTCAATTTT 59.348 33.333 0.00 0.00 33.07 1.82
6337 10313 8.479280 CGTTCCAAAATAAGTGTCTCAATTTTG 58.521 33.333 10.80 10.80 43.77 2.44
6338 10314 9.313118 GTTCCAAAATAAGTGTCTCAATTTTGT 57.687 29.630 14.67 0.00 43.14 2.83
6340 10316 9.959749 TCCAAAATAAGTGTCTCAATTTTGTAC 57.040 29.630 14.67 0.00 43.14 2.90
6341 10317 9.965824 CCAAAATAAGTGTCTCAATTTTGTACT 57.034 29.630 14.67 0.00 43.14 2.73
6376 10352 8.429493 ACAAAGTTGTACTAAGGTTAAGACAC 57.571 34.615 0.00 0.00 40.16 3.67
6377 10353 8.262933 ACAAAGTTGTACTAAGGTTAAGACACT 58.737 33.333 0.00 0.00 40.16 3.55
6378 10354 9.106070 CAAAGTTGTACTAAGGTTAAGACACTT 57.894 33.333 0.00 0.00 0.00 3.16
6396 10372 9.508642 AAGACACTTATTTTAGGAAAGAGGAAG 57.491 33.333 0.00 0.00 0.00 3.46
6408 10384 7.444703 AGGAAAGAGGAAGTATATTTCTGCT 57.555 36.000 7.79 3.45 31.96 4.24
6409 10385 7.278875 AGGAAAGAGGAAGTATATTTCTGCTG 58.721 38.462 7.79 0.00 31.96 4.41
6410 10386 7.051000 GGAAAGAGGAAGTATATTTCTGCTGT 58.949 38.462 7.79 1.69 31.96 4.40
6411 10387 7.225734 GGAAAGAGGAAGTATATTTCTGCTGTC 59.774 40.741 7.79 9.08 31.96 3.51
6412 10388 6.798427 AGAGGAAGTATATTTCTGCTGTCA 57.202 37.500 7.79 0.00 0.00 3.58
6413 10389 7.372260 AGAGGAAGTATATTTCTGCTGTCAT 57.628 36.000 7.79 0.00 0.00 3.06
6414 10390 7.215789 AGAGGAAGTATATTTCTGCTGTCATG 58.784 38.462 7.79 0.00 0.00 3.07
6415 10391 6.893583 AGGAAGTATATTTCTGCTGTCATGT 58.106 36.000 7.79 0.00 0.00 3.21
6416 10392 8.023021 AGGAAGTATATTTCTGCTGTCATGTA 57.977 34.615 7.79 0.00 0.00 2.29
6417 10393 8.147058 AGGAAGTATATTTCTGCTGTCATGTAG 58.853 37.037 7.79 0.00 0.00 2.74
6418 10394 7.095439 GGAAGTATATTTCTGCTGTCATGTAGC 60.095 40.741 14.89 14.89 41.49 3.58
6458 10446 0.798771 GCTTGTCTGAGGCTACGTCG 60.799 60.000 0.00 0.00 0.00 5.12
6469 10462 0.731855 GCTACGTCGGTGAAGGTGTC 60.732 60.000 0.00 0.00 0.00 3.67
6470 10463 0.594602 CTACGTCGGTGAAGGTGTCA 59.405 55.000 0.00 0.00 0.00 3.58
6471 10464 1.001048 CTACGTCGGTGAAGGTGTCAA 60.001 52.381 0.00 0.00 38.23 3.18
6472 10465 0.529119 ACGTCGGTGAAGGTGTCAAC 60.529 55.000 0.00 0.00 40.94 3.18
6473 10466 0.528901 CGTCGGTGAAGGTGTCAACA 60.529 55.000 0.00 0.00 45.06 3.33
6478 10471 3.314080 TCGGTGAAGGTGTCAACATTTTC 59.686 43.478 0.00 0.00 45.06 2.29
6485 10478 2.794350 GGTGTCAACATTTTCTTTGCGG 59.206 45.455 0.00 0.00 0.00 5.69
6512 10505 6.588204 AGTGAAGGTGTTAACATTAGTGTGA 58.412 36.000 12.26 0.00 38.92 3.58
6513 10506 7.224297 AGTGAAGGTGTTAACATTAGTGTGAT 58.776 34.615 12.26 0.00 38.92 3.06
6541 10534 7.618442 ACTTAACTATTTCATAATGTCGTGCG 58.382 34.615 0.00 0.00 0.00 5.34
6542 10535 7.277098 ACTTAACTATTTCATAATGTCGTGCGT 59.723 33.333 0.00 0.00 0.00 5.24
6543 10536 8.631676 TTAACTATTTCATAATGTCGTGCGTA 57.368 30.769 0.00 0.00 0.00 4.42
6544 10537 7.709269 AACTATTTCATAATGTCGTGCGTAT 57.291 32.000 0.00 0.00 0.00 3.06
6545 10538 8.806177 AACTATTTCATAATGTCGTGCGTATA 57.194 30.769 0.00 0.00 0.00 1.47
6546 10539 8.449085 ACTATTTCATAATGTCGTGCGTATAG 57.551 34.615 0.00 0.00 0.00 1.31
6547 10540 8.080417 ACTATTTCATAATGTCGTGCGTATAGT 58.920 33.333 0.00 0.00 0.00 2.12
6548 10541 7.709269 ATTTCATAATGTCGTGCGTATAGTT 57.291 32.000 0.00 0.00 0.00 2.24
6549 10542 7.528481 TTTCATAATGTCGTGCGTATAGTTT 57.472 32.000 0.00 0.00 0.00 2.66
6550 10543 7.528481 TTCATAATGTCGTGCGTATAGTTTT 57.472 32.000 0.00 0.00 0.00 2.43
6551 10544 7.528481 TCATAATGTCGTGCGTATAGTTTTT 57.472 32.000 0.00 0.00 0.00 1.94
6768 10766 5.450592 TGCACTGCATTATGAACAGAAAA 57.549 34.783 0.00 0.00 35.38 2.29
6796 10796 2.148916 TACACTTGAACGCAGTGGAG 57.851 50.000 6.15 0.00 45.00 3.86
6797 10797 0.464036 ACACTTGAACGCAGTGGAGA 59.536 50.000 6.15 0.00 45.00 3.71
6834 10834 8.467598 TCCTGTGATACTATCTTACACTGAAAC 58.532 37.037 0.00 0.00 34.19 2.78
6869 10869 5.717119 ATGGAGGGTGCTATTTAAGAACT 57.283 39.130 0.00 0.00 33.67 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.790437 CCAGCAGCTCATCGGGGT 61.790 66.667 0.00 0.00 0.00 4.95
5 6 2.588314 CGAGGCCAGCAGCTCATC 60.588 66.667 5.01 0.00 43.05 2.92
6 7 3.397439 ACGAGGCCAGCAGCTCAT 61.397 61.111 5.01 0.00 43.05 2.90
7 8 4.383861 CACGAGGCCAGCAGCTCA 62.384 66.667 5.01 0.00 43.05 4.26
12 13 2.803155 GAATGACCACGAGGCCAGCA 62.803 60.000 5.01 0.00 39.06 4.41
13 14 2.045926 AATGACCACGAGGCCAGC 60.046 61.111 5.01 0.00 39.06 4.85
17 18 0.036388 TGGAAGAATGACCACGAGGC 60.036 55.000 0.00 0.00 39.06 4.70
18 19 2.472695 TTGGAAGAATGACCACGAGG 57.527 50.000 0.00 0.00 42.21 4.63
25 1634 5.064441 CCATGAGGTTTTGGAAGAATGAC 57.936 43.478 0.00 0.00 34.81 3.06
64 1673 2.282816 CATCCGCCCAACAACCCA 60.283 61.111 0.00 0.00 0.00 4.51
87 1696 0.254462 CTCTTCTTCCTCTTGCCCCC 59.746 60.000 0.00 0.00 0.00 5.40
88 1697 0.254462 CCTCTTCTTCCTCTTGCCCC 59.746 60.000 0.00 0.00 0.00 5.80
91 1700 2.482839 CCGATCCTCTTCTTCCTCTTGC 60.483 54.545 0.00 0.00 0.00 4.01
93 1702 2.393646 CCCGATCCTCTTCTTCCTCTT 58.606 52.381 0.00 0.00 0.00 2.85
94 1703 1.412361 CCCCGATCCTCTTCTTCCTCT 60.412 57.143 0.00 0.00 0.00 3.69
95 1704 1.044611 CCCCGATCCTCTTCTTCCTC 58.955 60.000 0.00 0.00 0.00 3.71
96 1705 0.637195 TCCCCGATCCTCTTCTTCCT 59.363 55.000 0.00 0.00 0.00 3.36
97 1706 1.044611 CTCCCCGATCCTCTTCTTCC 58.955 60.000 0.00 0.00 0.00 3.46
111 1720 4.093743 TCCTTTTTAATGCTTTCCTCCCC 58.906 43.478 0.00 0.00 0.00 4.81
134 1743 0.333312 ACAAAACCAGTCCACACCCA 59.667 50.000 0.00 0.00 0.00 4.51
172 1781 0.793861 TAAATTCCACGCGTGCACTC 59.206 50.000 33.17 5.91 0.00 3.51
175 1784 2.353269 CCTATTAAATTCCACGCGTGCA 59.647 45.455 33.17 18.18 0.00 4.57
234 1843 4.778415 CGGTCGGTGTCTGCCTCG 62.778 72.222 0.00 0.00 0.00 4.63
331 1940 2.348666 CCTAAATTCTGTTCGCTCGGTG 59.651 50.000 0.00 0.00 0.00 4.94
332 1941 2.028385 ACCTAAATTCTGTTCGCTCGGT 60.028 45.455 0.00 0.00 0.00 4.69
333 1942 2.618053 ACCTAAATTCTGTTCGCTCGG 58.382 47.619 0.00 0.00 0.00 4.63
334 1943 4.394795 CAAACCTAAATTCTGTTCGCTCG 58.605 43.478 0.00 0.00 0.00 5.03
335 1944 4.159120 GCAAACCTAAATTCTGTTCGCTC 58.841 43.478 0.00 0.00 0.00 5.03
336 1945 3.364964 CGCAAACCTAAATTCTGTTCGCT 60.365 43.478 0.00 0.00 0.00 4.93
339 1948 4.148891 CGTCGCAAACCTAAATTCTGTTC 58.851 43.478 0.00 0.00 0.00 3.18
340 1949 3.058501 CCGTCGCAAACCTAAATTCTGTT 60.059 43.478 0.00 0.00 0.00 3.16
341 1950 2.482721 CCGTCGCAAACCTAAATTCTGT 59.517 45.455 0.00 0.00 0.00 3.41
343 1952 1.467342 GCCGTCGCAAACCTAAATTCT 59.533 47.619 0.00 0.00 34.03 2.40
344 1953 1.467342 AGCCGTCGCAAACCTAAATTC 59.533 47.619 0.00 0.00 37.52 2.17
345 1954 1.530323 AGCCGTCGCAAACCTAAATT 58.470 45.000 0.00 0.00 37.52 1.82
346 1955 1.199097 CAAGCCGTCGCAAACCTAAAT 59.801 47.619 0.00 0.00 37.52 1.40
347 1956 0.589223 CAAGCCGTCGCAAACCTAAA 59.411 50.000 0.00 0.00 37.52 1.85
348 1957 0.533308 ACAAGCCGTCGCAAACCTAA 60.533 50.000 0.00 0.00 37.52 2.69
350 1959 1.822186 AACAAGCCGTCGCAAACCT 60.822 52.632 0.00 0.00 37.52 3.50
351 1960 1.657181 CAACAAGCCGTCGCAAACC 60.657 57.895 0.00 0.00 37.52 3.27
352 1961 1.657181 CCAACAAGCCGTCGCAAAC 60.657 57.895 0.00 0.00 37.52 2.93
393 2002 1.184970 CCGCTTTGGTCCATTTGGGT 61.185 55.000 0.00 0.00 38.11 4.51
426 2035 2.623878 TAAGGCAAACTCCAACACGA 57.376 45.000 0.00 0.00 0.00 4.35
439 2048 3.517296 TCATCAAGGGTGTTTAAGGCA 57.483 42.857 0.00 0.00 0.00 4.75
2793 6217 6.058183 ACATGCAGATTAGGAAGAATGGTAC 58.942 40.000 0.00 0.00 0.00 3.34
2794 6218 6.252599 ACATGCAGATTAGGAAGAATGGTA 57.747 37.500 0.00 0.00 0.00 3.25
2795 6219 5.121380 ACATGCAGATTAGGAAGAATGGT 57.879 39.130 0.00 0.00 0.00 3.55
2796 6220 6.294473 AGTACATGCAGATTAGGAAGAATGG 58.706 40.000 0.00 0.00 0.00 3.16
2797 6221 7.281774 ACAAGTACATGCAGATTAGGAAGAATG 59.718 37.037 0.00 0.00 0.00 2.67
2798 6222 7.341805 ACAAGTACATGCAGATTAGGAAGAAT 58.658 34.615 0.00 0.00 0.00 2.40
2799 6223 6.711277 ACAAGTACATGCAGATTAGGAAGAA 58.289 36.000 0.00 0.00 0.00 2.52
2800 6224 6.299805 ACAAGTACATGCAGATTAGGAAGA 57.700 37.500 0.00 0.00 0.00 2.87
2801 6225 6.820656 AGAACAAGTACATGCAGATTAGGAAG 59.179 38.462 0.00 0.00 0.00 3.46
2802 6226 6.711277 AGAACAAGTACATGCAGATTAGGAA 58.289 36.000 0.00 0.00 0.00 3.36
2803 6227 6.299805 AGAACAAGTACATGCAGATTAGGA 57.700 37.500 0.00 0.00 0.00 2.94
2804 6228 8.554528 CATTAGAACAAGTACATGCAGATTAGG 58.445 37.037 0.00 0.00 0.00 2.69
2805 6229 8.066595 GCATTAGAACAAGTACATGCAGATTAG 58.933 37.037 0.00 0.00 37.54 1.73
2806 6230 7.552330 TGCATTAGAACAAGTACATGCAGATTA 59.448 33.333 8.63 0.00 41.52 1.75
2807 6231 6.375174 TGCATTAGAACAAGTACATGCAGATT 59.625 34.615 8.63 0.00 41.52 2.40
2808 6232 5.882000 TGCATTAGAACAAGTACATGCAGAT 59.118 36.000 8.63 0.00 41.52 2.90
2809 6233 5.122239 GTGCATTAGAACAAGTACATGCAGA 59.878 40.000 12.03 0.00 45.69 4.26
2810 6234 5.106594 TGTGCATTAGAACAAGTACATGCAG 60.107 40.000 12.03 0.00 45.69 4.41
2811 6235 4.759183 TGTGCATTAGAACAAGTACATGCA 59.241 37.500 8.63 8.63 43.56 3.96
2812 6236 5.295431 TGTGCATTAGAACAAGTACATGC 57.705 39.130 0.00 0.97 38.00 4.06
2813 6237 9.838975 TTTATTGTGCATTAGAACAAGTACATG 57.161 29.630 0.00 0.00 46.22 3.21
3261 6771 9.290988 TGTGTGCTCCTTCTAATACAAAATAAA 57.709 29.630 0.00 0.00 0.00 1.40
3262 6772 8.856153 TGTGTGCTCCTTCTAATACAAAATAA 57.144 30.769 0.00 0.00 0.00 1.40
3263 6773 8.856153 TTGTGTGCTCCTTCTAATACAAAATA 57.144 30.769 0.00 0.00 0.00 1.40
3264 6774 7.759489 TTGTGTGCTCCTTCTAATACAAAAT 57.241 32.000 0.00 0.00 0.00 1.82
3265 6775 7.284489 AGTTTGTGTGCTCCTTCTAATACAAAA 59.716 33.333 0.00 0.00 38.16 2.44
3266 6776 6.770785 AGTTTGTGTGCTCCTTCTAATACAAA 59.229 34.615 0.00 0.00 35.27 2.83
3267 6777 6.296026 AGTTTGTGTGCTCCTTCTAATACAA 58.704 36.000 0.00 0.00 0.00 2.41
4100 7767 0.466543 TACAGGCGTGTGTGAGGTTT 59.533 50.000 21.78 0.00 37.52 3.27
4108 7775 1.804326 GCGTACCTACAGGCGTGTG 60.804 63.158 21.78 8.71 37.52 3.82
4226 7894 4.943705 ACTAGGTACAACATGAGCCAATTG 59.056 41.667 0.00 0.00 0.00 2.32
4237 7905 6.801718 ATATGGTAAGCACTAGGTACAACA 57.198 37.500 0.00 0.00 0.00 3.33
4278 7946 7.726033 AACTAGTGAGAAGAAGTATGGTGAT 57.274 36.000 0.00 0.00 0.00 3.06
4390 8058 7.712205 TCCATGAACACATATGAATGAGTACAG 59.288 37.037 10.38 0.00 36.10 2.74
4417 8085 4.235079 AGCTTGTGCCCAAATATGAGTA 57.765 40.909 0.00 0.00 40.80 2.59
4928 8596 8.251750 TGTAATGCAGATTTAATATAGCGGAC 57.748 34.615 0.00 0.00 0.00 4.79
5315 9285 0.890996 GGCATATTCCCGCCCTTGAG 60.891 60.000 0.00 0.00 42.82 3.02
5723 9693 1.870458 CATTCGCTGGCATGCAACG 60.870 57.895 21.36 18.86 0.00 4.10
5726 9696 1.731093 CATCATTCGCTGGCATGCA 59.269 52.632 21.36 4.79 0.00 3.96
5738 9708 5.579753 AGATACCTTCATCCAGCATCATT 57.420 39.130 0.00 0.00 0.00 2.57
5952 9922 2.874701 CAGCTTACCGATGCTTTGCTAT 59.125 45.455 0.00 0.00 37.44 2.97
6128 10098 4.283978 TGAATCCAAGTCCAATGCAAACAT 59.716 37.500 0.00 0.00 38.49 2.71
6171 10147 1.214424 GGCCTGGAAATAGCCTAACCA 59.786 52.381 0.00 0.00 43.62 3.67
6231 10207 2.104281 ACCGAAAGAAGTACCAGCTTGT 59.896 45.455 0.00 0.00 0.00 3.16
6246 10222 3.757270 TGGAAGAATAAAGGCACCGAAA 58.243 40.909 0.00 0.00 0.00 3.46
6303 10279 5.221661 ACACTTATTTTGGAACGGAGAGAGT 60.222 40.000 0.00 0.00 0.00 3.24
6304 10280 5.238583 ACACTTATTTTGGAACGGAGAGAG 58.761 41.667 0.00 0.00 0.00 3.20
6305 10281 5.011738 AGACACTTATTTTGGAACGGAGAGA 59.988 40.000 0.00 0.00 0.00 3.10
6306 10282 5.238583 AGACACTTATTTTGGAACGGAGAG 58.761 41.667 0.00 0.00 0.00 3.20
6307 10283 5.221561 TGAGACACTTATTTTGGAACGGAGA 60.222 40.000 0.00 0.00 0.00 3.71
6308 10284 4.994852 TGAGACACTTATTTTGGAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
6309 10285 4.963373 TGAGACACTTATTTTGGAACGGA 58.037 39.130 0.00 0.00 0.00 4.69
6310 10286 5.682943 TTGAGACACTTATTTTGGAACGG 57.317 39.130 0.00 0.00 0.00 4.44
6311 10287 8.479280 CAAAATTGAGACACTTATTTTGGAACG 58.521 33.333 16.22 0.00 41.13 3.95
6312 10288 9.313118 ACAAAATTGAGACACTTATTTTGGAAC 57.687 29.630 21.75 0.00 45.43 3.62
6314 10290 9.959749 GTACAAAATTGAGACACTTATTTTGGA 57.040 29.630 21.75 16.72 45.43 3.53
6315 10291 9.965824 AGTACAAAATTGAGACACTTATTTTGG 57.034 29.630 21.75 9.08 45.43 3.28
6350 10326 9.533253 GTGTCTTAACCTTAGTACAACTTTGTA 57.467 33.333 0.00 0.00 42.35 2.41
6351 10327 8.262933 AGTGTCTTAACCTTAGTACAACTTTGT 58.737 33.333 0.00 0.00 44.86 2.83
6352 10328 8.658499 AGTGTCTTAACCTTAGTACAACTTTG 57.342 34.615 0.00 0.00 0.00 2.77
6370 10346 9.508642 CTTCCTCTTTCCTAAAATAAGTGTCTT 57.491 33.333 0.00 0.00 0.00 3.01
6371 10347 8.661345 ACTTCCTCTTTCCTAAAATAAGTGTCT 58.339 33.333 0.00 0.00 0.00 3.41
6372 10348 8.850007 ACTTCCTCTTTCCTAAAATAAGTGTC 57.150 34.615 0.00 0.00 0.00 3.67
6381 10357 9.614792 GCAGAAATATACTTCCTCTTTCCTAAA 57.385 33.333 0.00 0.00 0.00 1.85
6382 10358 8.993424 AGCAGAAATATACTTCCTCTTTCCTAA 58.007 33.333 0.00 0.00 0.00 2.69
6383 10359 8.424918 CAGCAGAAATATACTTCCTCTTTCCTA 58.575 37.037 0.00 0.00 0.00 2.94
6384 10360 7.092668 ACAGCAGAAATATACTTCCTCTTTCCT 60.093 37.037 0.00 0.00 0.00 3.36
6385 10361 7.051000 ACAGCAGAAATATACTTCCTCTTTCC 58.949 38.462 0.00 0.00 0.00 3.13
6386 10362 7.766278 TGACAGCAGAAATATACTTCCTCTTTC 59.234 37.037 0.00 0.00 0.00 2.62
6387 10363 7.624549 TGACAGCAGAAATATACTTCCTCTTT 58.375 34.615 0.00 0.00 0.00 2.52
6388 10364 7.187824 TGACAGCAGAAATATACTTCCTCTT 57.812 36.000 0.00 0.00 0.00 2.85
6389 10365 6.798427 TGACAGCAGAAATATACTTCCTCT 57.202 37.500 0.00 0.00 0.00 3.69
6390 10366 6.989169 ACATGACAGCAGAAATATACTTCCTC 59.011 38.462 0.00 0.00 0.00 3.71
6391 10367 6.893583 ACATGACAGCAGAAATATACTTCCT 58.106 36.000 0.00 0.00 0.00 3.36
6392 10368 7.095439 GCTACATGACAGCAGAAATATACTTCC 60.095 40.741 15.98 0.00 38.93 3.46
6393 10369 7.439356 TGCTACATGACAGCAGAAATATACTTC 59.561 37.037 18.57 0.00 43.90 3.01
6394 10370 7.275183 TGCTACATGACAGCAGAAATATACTT 58.725 34.615 18.57 0.00 43.90 2.24
6395 10371 6.820335 TGCTACATGACAGCAGAAATATACT 58.180 36.000 18.57 0.00 43.90 2.12
6408 10384 3.131046 AGATCACGACATGCTACATGACA 59.869 43.478 14.17 0.00 0.00 3.58
6409 10385 3.711086 AGATCACGACATGCTACATGAC 58.289 45.455 14.17 7.21 0.00 3.06
6410 10386 4.363138 GAAGATCACGACATGCTACATGA 58.637 43.478 14.17 0.00 0.00 3.07
6411 10387 3.492383 GGAAGATCACGACATGCTACATG 59.508 47.826 6.03 6.03 0.00 3.21
6412 10388 3.386078 AGGAAGATCACGACATGCTACAT 59.614 43.478 0.00 0.00 0.00 2.29
6413 10389 2.760650 AGGAAGATCACGACATGCTACA 59.239 45.455 0.00 0.00 0.00 2.74
6414 10390 3.444703 AGGAAGATCACGACATGCTAC 57.555 47.619 0.00 0.00 0.00 3.58
6415 10391 3.318275 GGTAGGAAGATCACGACATGCTA 59.682 47.826 0.00 0.00 0.00 3.49
6416 10392 2.101582 GGTAGGAAGATCACGACATGCT 59.898 50.000 0.00 0.00 0.00 3.79
6417 10393 2.101582 AGGTAGGAAGATCACGACATGC 59.898 50.000 0.00 0.00 0.00 4.06
6418 10394 3.711086 CAGGTAGGAAGATCACGACATG 58.289 50.000 0.00 0.00 0.00 3.21
6419 10395 2.101582 GCAGGTAGGAAGATCACGACAT 59.898 50.000 0.00 0.00 0.00 3.06
6458 10446 4.918810 AGAAAATGTTGACACCTTCACC 57.081 40.909 8.75 0.00 32.26 4.02
6469 10462 2.035832 ACTCCCCGCAAAGAAAATGTTG 59.964 45.455 0.00 0.00 0.00 3.33
6470 10463 2.035832 CACTCCCCGCAAAGAAAATGTT 59.964 45.455 0.00 0.00 0.00 2.71
6471 10464 1.613437 CACTCCCCGCAAAGAAAATGT 59.387 47.619 0.00 0.00 0.00 2.71
6472 10465 1.885887 TCACTCCCCGCAAAGAAAATG 59.114 47.619 0.00 0.00 0.00 2.32
6473 10466 2.286365 TCACTCCCCGCAAAGAAAAT 57.714 45.000 0.00 0.00 0.00 1.82
6478 10471 1.073199 ACCTTCACTCCCCGCAAAG 59.927 57.895 0.00 0.00 0.00 2.77
6485 10478 5.411669 CACTAATGTTAACACCTTCACTCCC 59.588 44.000 11.22 0.00 0.00 4.30
6520 10513 7.709269 ATACGCACGACATTATGAAATAGTT 57.291 32.000 0.00 0.00 0.00 2.24
6523 10516 8.806177 AACTATACGCACGACATTATGAAATA 57.194 30.769 0.00 0.00 0.00 1.40
6766 10764 7.817962 ACTGCGTTCAAGTGTAAGATAGTATTT 59.182 33.333 0.00 0.00 0.00 1.40
6767 10765 7.275779 CACTGCGTTCAAGTGTAAGATAGTATT 59.724 37.037 0.00 0.00 0.00 1.89
6768 10766 6.752351 CACTGCGTTCAAGTGTAAGATAGTAT 59.248 38.462 0.00 0.00 0.00 2.12
6784 10784 1.795768 TCAACATCTCCACTGCGTTC 58.204 50.000 0.00 0.00 0.00 3.95
6796 10796 1.795768 TCACAGGAGCGTTCAACATC 58.204 50.000 0.53 0.00 0.00 3.06
6797 10797 2.479566 ATCACAGGAGCGTTCAACAT 57.520 45.000 0.53 0.00 0.00 2.71
6844 10844 6.603599 AGTTCTTAAATAGCACCCTCCATTTC 59.396 38.462 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.