Multiple sequence alignment - TraesCS5A01G347000

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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 TraesCS5A01G347000 chr5A 100.000 5231 0 0 1 5231 549351781 549357011 0.000000e+00 9660.0
1 TraesCS5A01G347000 chr5A 88.283 495 52 3 2586 3077 549353859 549354350 5.840000e-164 588.0
2 TraesCS5A01G347000 chr5A 88.283 495 52 3 2079 2570 549354366 549354857 5.840000e-164 588.0
3 TraesCS5A01G347000 chr5A 81.533 287 42 3 1 279 549359986 549360269 5.270000e-55 226.0
4 TraesCS5A01G347000 chr5A 81.855 248 36 7 3116 3354 549353822 549354069 3.190000e-47 200.0
5 TraesCS5A01G347000 chr5D 95.736 2181 75 7 969 3134 435512568 435514745 0.000000e+00 3496.0
6 TraesCS5A01G347000 chr5D 92.350 2000 101 20 3027 4990 435514746 435516729 0.000000e+00 2798.0
7 TraesCS5A01G347000 chr5D 89.495 495 46 3 2079 2570 435514197 435514688 5.750000e-174 621.0
8 TraesCS5A01G347000 chr5D 89.228 492 50 1 2586 3077 435513693 435514181 3.460000e-171 612.0
9 TraesCS5A01G347000 chr5D 90.526 380 30 4 4 382 435492972 435493346 1.010000e-136 497.0
10 TraesCS5A01G347000 chr5D 89.450 218 21 2 411 626 435493342 435493559 1.860000e-69 274.0
11 TraesCS5A01G347000 chr5D 83.871 248 40 0 2042 2289 435514835 435515082 2.430000e-58 237.0
12 TraesCS5A01G347000 chr5D 83.908 261 27 8 3103 3354 435514153 435514407 8.760000e-58 235.0
13 TraesCS5A01G347000 chr5D 80.122 327 56 6 1 324 435519377 435519697 8.760000e-58 235.0
14 TraesCS5A01G347000 chr5D 94.079 152 1 3 837 980 435512390 435512541 1.900000e-54 224.0
15 TraesCS5A01G347000 chr5D 84.211 228 27 7 3116 3334 435513656 435513883 4.100000e-51 213.0
16 TraesCS5A01G347000 chr5D 97.222 108 3 0 3027 3134 435514692 435514799 3.220000e-42 183.0
17 TraesCS5A01G347000 chr5D 85.816 141 2 3 5041 5179 435516721 435516845 3.290000e-27 134.0
18 TraesCS5A01G347000 chr5D 90.625 96 5 1 728 819 435512309 435512404 1.980000e-24 124.0
19 TraesCS5A01G347000 chr5B 94.596 2017 94 5 2578 4582 528782437 528784450 0.000000e+00 3107.0
20 TraesCS5A01G347000 chr5B 93.876 1927 73 14 837 2722 528780518 528782440 0.000000e+00 2863.0
21 TraesCS5A01G347000 chr5B 86.999 823 52 26 1 819 528779761 528780532 0.000000e+00 876.0
22 TraesCS5A01G347000 chr5B 89.697 495 45 3 2079 2570 528782445 528782936 1.240000e-175 627.0
23 TraesCS5A01G347000 chr5B 87.602 492 58 1 2586 3077 528781800 528782288 7.600000e-158 568.0
24 TraesCS5A01G347000 chr5B 82.661 248 43 0 2042 2289 528782975 528783222 2.450000e-53 220.0
25 TraesCS5A01G347000 chr5B 85.646 209 21 6 3155 3354 528782447 528782655 1.480000e-50 211.0
26 TraesCS5A01G347000 chr5B 88.304 171 14 1 3103 3273 528782260 528782424 3.190000e-47 200.0
27 TraesCS5A01G347000 chr5B 94.118 119 4 2 5064 5179 528784440 528784558 1.500000e-40 178.0
28 TraesCS5A01G347000 chr1B 88.462 832 87 7 3081 3903 259513572 259514403 0.000000e+00 996.0
29 TraesCS5A01G347000 chr1B 86.148 527 52 6 2296 2801 259513333 259513859 2.750000e-152 549.0
30 TraesCS5A01G347000 chr1B 88.306 248 29 0 2042 2289 259513607 259513854 1.100000e-76 298.0
31 TraesCS5A01G347000 chr1B 92.121 165 10 1 1882 2043 259513219 259513383 4.070000e-56 230.0
32 TraesCS5A01G347000 chr1B 85.354 198 14 7 3986 4171 259514639 259514833 1.920000e-44 191.0
33 TraesCS5A01G347000 chr1B 84.946 186 20 6 4178 4362 259514885 259515063 1.160000e-41 182.0
34 TraesCS5A01G347000 chr1A 87.500 832 92 6 3081 3903 236719778 236720606 0.000000e+00 950.0
35 TraesCS5A01G347000 chr1A 86.948 521 53 6 2296 2801 236719545 236720065 5.880000e-159 571.0
36 TraesCS5A01G347000 chr1A 88.189 254 29 1 2042 2294 236719813 236720066 8.510000e-78 302.0
37 TraesCS5A01G347000 chr1A 81.556 347 34 11 4178 4522 236721064 236721382 5.200000e-65 259.0
38 TraesCS5A01G347000 chr1A 93.939 165 7 1 1882 2043 236719431 236719595 4.050000e-61 246.0
39 TraesCS5A01G347000 chr3B 82.000 250 38 4 76 325 752285698 752285940 6.870000e-49 206.0
40 TraesCS5A01G347000 chr6D 85.000 100 15 0 74 173 448646854 448646755 9.270000e-18 102.0
41 TraesCS5A01G347000 chr6A 84.000 100 16 0 74 173 594721520 594721421 4.310000e-16 97.1
42 TraesCS5A01G347000 chr3D 81.633 98 18 0 87 184 14042044 14041947 1.210000e-11 82.4


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 TraesCS5A01G347000 chr5A 549351781 549357011 5230 False 2759.000000 9660 89.605250 1 5231 4 chr5A.!!$F2 5230
1 TraesCS5A01G347000 chr5D 435512309 435519697 7388 False 759.333333 3496 88.888583 1 5179 12 chr5D.!!$F2 5178
2 TraesCS5A01G347000 chr5D 435492972 435493559 587 False 385.500000 497 89.988000 4 626 2 chr5D.!!$F1 622
3 TraesCS5A01G347000 chr5B 528779761 528784558 4797 False 983.333333 3107 89.277667 1 5179 9 chr5B.!!$F1 5178
4 TraesCS5A01G347000 chr1B 259513219 259515063 1844 False 407.666667 996 87.556167 1882 4362 6 chr1B.!!$F1 2480
5 TraesCS5A01G347000 chr1A 236719431 236721382 1951 False 465.600000 950 87.626400 1882 4522 5 chr1A.!!$F1 2640

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
663 669 0.336737 GGGGAGGAAGACTGAGAGGA 59.663 60.0 0.00 0.00 0.0 3.71 F
1341 1394 0.457443 TCTCCTGCAGCGTATGTGAG 59.543 55.0 8.66 7.87 0.0 3.51 F
2644 2748 0.107643 TTCAACACGACATGGGCTGA 59.892 50.0 0.00 0.00 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2341 0.182537 TGTGTGGGTGGAAGTGGAAG 59.817 55.0 0.00 0.0 0.00 3.46 R
3015 3260 0.179936 GTTGATGCTCTGAGAGGGGG 59.820 60.0 12.01 0.0 0.00 5.40 R
4546 5133 0.540830 ACTCTGAGCGAACCCTGAGT 60.541 55.0 4.19 0.0 36.96 3.41 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
20 21 1.386533 GGTCACGGTATCGGAGAAGA 58.613 55.000 0.00 0.00 43.58 2.87
29 30 3.188873 GGTATCGGAGAAGACTATGGACG 59.811 52.174 0.00 0.00 43.58 4.79
250 251 2.338015 CGGCTTCCTTGCTGCACAT 61.338 57.895 0.00 0.00 32.21 3.21
328 329 2.485426 CCGACACAGAATGAGCAAACAT 59.515 45.455 0.00 0.00 39.69 2.71
340 341 1.001181 AGCAAACATGCGGCAAAGATT 59.999 42.857 6.82 0.90 40.27 2.40
343 344 0.968405 AACATGCGGCAAAGATTGGT 59.032 45.000 6.82 0.00 0.00 3.67
356 357 5.473039 CAAAGATTGGTAAAGAAGCCAAGG 58.527 41.667 0.00 0.00 46.41 3.61
384 385 1.183676 AAGTTACCTCTGGTCGCCGT 61.184 55.000 0.00 0.00 37.09 5.68
385 386 1.153881 GTTACCTCTGGTCGCCGTC 60.154 63.158 0.00 0.00 37.09 4.79
386 387 1.303888 TTACCTCTGGTCGCCGTCT 60.304 57.895 0.00 0.00 37.09 4.18
387 388 1.310933 TTACCTCTGGTCGCCGTCTC 61.311 60.000 0.00 0.00 37.09 3.36
388 389 3.827898 CCTCTGGTCGCCGTCTCC 61.828 72.222 0.00 0.00 0.00 3.71
389 390 4.180946 CTCTGGTCGCCGTCTCCG 62.181 72.222 0.00 0.00 0.00 4.63
484 485 3.177920 GCGACGTGAGCAGAGCAG 61.178 66.667 0.00 0.00 34.19 4.24
538 544 0.477597 TGTTGGTGGGGGAGAGGAAT 60.478 55.000 0.00 0.00 0.00 3.01
559 565 4.884257 GCGGGTCAGCGGCGAATA 62.884 66.667 12.98 0.00 0.00 1.75
568 574 4.036971 GGTCAGCGGCGAATAGATATAGAT 59.963 45.833 12.98 0.00 0.00 1.98
586 592 4.086178 CGTCACCGCGTCGAGTCT 62.086 66.667 4.92 0.00 0.00 3.24
618 624 1.367665 GCGATCGCCGTGCATTAAC 60.368 57.895 29.48 0.00 41.15 2.01
640 646 2.720758 CTCGAGCAACACGAAGCGG 61.721 63.158 0.00 0.00 39.23 5.52
641 647 3.036084 CGAGCAACACGAAGCGGT 61.036 61.111 0.00 0.00 35.48 5.68
643 649 2.954753 GAGCAACACGAAGCGGTGG 61.955 63.158 9.76 0.00 42.23 4.61
645 651 3.353836 CAACACGAAGCGGTGGGG 61.354 66.667 9.76 0.00 42.23 4.96
646 652 4.636435 AACACGAAGCGGTGGGGG 62.636 66.667 9.76 0.00 42.23 5.40
661 667 2.909140 GGGGGAGGAAGACTGAGAG 58.091 63.158 0.00 0.00 0.00 3.20
662 668 0.689412 GGGGGAGGAAGACTGAGAGG 60.689 65.000 0.00 0.00 0.00 3.69
663 669 0.336737 GGGGAGGAAGACTGAGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
664 670 1.273324 GGGGAGGAAGACTGAGAGGAA 60.273 57.143 0.00 0.00 0.00 3.36
665 671 1.828595 GGGAGGAAGACTGAGAGGAAC 59.171 57.143 0.00 0.00 0.00 3.62
666 672 2.530701 GGAGGAAGACTGAGAGGAACA 58.469 52.381 0.00 0.00 0.00 3.18
667 673 2.232696 GGAGGAAGACTGAGAGGAACAC 59.767 54.545 0.00 0.00 0.00 3.32
668 674 1.889829 AGGAAGACTGAGAGGAACACG 59.110 52.381 0.00 0.00 0.00 4.49
669 675 1.067495 GGAAGACTGAGAGGAACACGG 60.067 57.143 0.00 0.00 0.00 4.94
670 676 0.969894 AAGACTGAGAGGAACACGGG 59.030 55.000 0.00 0.00 0.00 5.28
671 677 0.900647 AGACTGAGAGGAACACGGGG 60.901 60.000 0.00 0.00 0.00 5.73
672 678 1.889530 GACTGAGAGGAACACGGGGG 61.890 65.000 0.00 0.00 0.00 5.40
716 722 4.388499 GCTCCGTGCGAGGGGAAA 62.388 66.667 0.78 0.00 39.22 3.13
717 723 2.434359 CTCCGTGCGAGGGGAAAC 60.434 66.667 0.00 0.00 34.67 2.78
718 724 4.367023 TCCGTGCGAGGGGAAACG 62.367 66.667 0.00 0.00 35.85 3.60
764 770 2.472934 GCCCGTTTAAGCGTGTCG 59.527 61.111 10.88 0.00 0.00 4.35
770 776 1.136721 CGTTTAAGCGTGTCGAACCTG 60.137 52.381 3.26 0.00 0.00 4.00
819 825 0.679960 GCCCAGCGGTCCAACTTATT 60.680 55.000 0.00 0.00 0.00 1.40
820 826 1.379527 CCCAGCGGTCCAACTTATTC 58.620 55.000 0.00 0.00 0.00 1.75
821 827 1.065418 CCCAGCGGTCCAACTTATTCT 60.065 52.381 0.00 0.00 0.00 2.40
822 828 2.618045 CCCAGCGGTCCAACTTATTCTT 60.618 50.000 0.00 0.00 0.00 2.52
823 829 2.678336 CCAGCGGTCCAACTTATTCTTC 59.322 50.000 0.00 0.00 0.00 2.87
824 830 3.600388 CAGCGGTCCAACTTATTCTTCT 58.400 45.455 0.00 0.00 0.00 2.85
825 831 3.619038 CAGCGGTCCAACTTATTCTTCTC 59.381 47.826 0.00 0.00 0.00 2.87
826 832 3.260884 AGCGGTCCAACTTATTCTTCTCA 59.739 43.478 0.00 0.00 0.00 3.27
827 833 4.000988 GCGGTCCAACTTATTCTTCTCAA 58.999 43.478 0.00 0.00 0.00 3.02
828 834 4.454504 GCGGTCCAACTTATTCTTCTCAAA 59.545 41.667 0.00 0.00 0.00 2.69
829 835 5.048991 GCGGTCCAACTTATTCTTCTCAAAA 60.049 40.000 0.00 0.00 0.00 2.44
830 836 6.514376 GCGGTCCAACTTATTCTTCTCAAAAA 60.514 38.462 0.00 0.00 0.00 1.94
1341 1394 0.457443 TCTCCTGCAGCGTATGTGAG 59.543 55.000 8.66 7.87 0.00 3.51
1347 1400 3.193263 CTGCAGCGTATGTGAGAGAATT 58.807 45.455 0.00 0.00 0.00 2.17
1355 1408 4.500545 CGTATGTGAGAGAATTGAGGAGGG 60.501 50.000 0.00 0.00 0.00 4.30
1362 1445 3.350031 AATTGAGGAGGGCCAGGCG 62.350 63.158 6.18 0.00 36.29 5.52
1420 1503 2.203408 GCCTGCTAAGGGGGCATC 60.203 66.667 0.00 0.00 44.67 3.91
1452 1535 4.360964 GGGCTGCGCATGTGCAAA 62.361 61.111 31.75 12.91 45.74 3.68
1536 1619 4.326766 CGGCACACGCAAACAGGG 62.327 66.667 0.00 0.00 41.24 4.45
1761 1847 3.165875 TCGGAAAGATCACTTCCTCTGT 58.834 45.455 19.09 0.00 35.05 3.41
1782 1868 1.163420 AAGATGACGCGTGTTTGGCA 61.163 50.000 20.70 7.68 0.00 4.92
1833 1919 3.076621 GGAGATCAACAGACACAATGCA 58.923 45.455 0.00 0.00 0.00 3.96
1872 1958 1.079750 GTCTCGTGCCCAGAGGAAC 60.080 63.158 1.25 0.00 38.54 3.62
1974 2060 1.209019 GCTCACCATGACAGACCTGAT 59.791 52.381 3.76 0.00 0.00 2.90
1975 2061 2.902523 CTCACCATGACAGACCTGATG 58.097 52.381 3.76 0.00 0.00 3.07
2056 2142 2.690881 ATAGCGCAGGGGGTTCCA 60.691 61.111 11.47 0.00 38.24 3.53
2077 2163 2.353889 ACGATGCTTGCTGATGAATCAC 59.646 45.455 0.00 0.00 32.50 3.06
2089 2175 2.859165 TGAATCACTGTTCCCTCCAC 57.141 50.000 0.00 0.00 0.00 4.02
2178 2264 2.555325 TCTTGCATCAAGGCTTCAACAG 59.445 45.455 0.00 0.00 41.33 3.16
2255 2341 5.736951 AATCCTGAGATAGTACCTCATGC 57.263 43.478 0.00 0.00 39.62 4.06
2396 2500 2.087009 GTTCGGCCAGTTCTCGTCG 61.087 63.158 2.24 0.00 0.00 5.12
2397 2501 2.558286 TTCGGCCAGTTCTCGTCGT 61.558 57.895 2.24 0.00 0.00 4.34
2398 2502 2.467946 TTCGGCCAGTTCTCGTCGTC 62.468 60.000 2.24 0.00 0.00 4.20
2517 2621 1.153745 CTCGTTTGCTCCCCTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
2633 2737 2.097466 ACAAAGGTTCTGCTTCAACACG 59.903 45.455 0.00 0.00 0.00 4.49
2637 2741 1.873591 GGTTCTGCTTCAACACGACAT 59.126 47.619 0.00 0.00 0.00 3.06
2644 2748 0.107643 TTCAACACGACATGGGCTGA 59.892 50.000 0.00 0.00 0.00 4.26
2647 2751 0.951558 AACACGACATGGGCTGAAAC 59.048 50.000 0.00 0.00 0.00 2.78
2798 3043 1.550524 GACATGTCCTACACCTGAGCA 59.449 52.381 15.31 0.00 0.00 4.26
2954 3199 4.083271 CGAACAATTGTCTTTTCCTCCTCC 60.083 45.833 12.39 0.00 0.00 4.30
3034 3279 0.179936 CCCCCTCTCAGAGCATCAAC 59.820 60.000 0.00 0.00 37.82 3.18
3392 3763 0.246910 GGGTCTTCTCACCTTCGGAC 59.753 60.000 0.00 0.00 36.57 4.79
3424 3795 2.034685 TCGACAAGAGATAATGGGCTCG 59.965 50.000 0.00 0.00 36.29 5.03
3441 3812 3.958860 GTGCCACCTGCCTCCAGT 61.959 66.667 0.00 0.00 40.16 4.00
3549 3920 4.272018 CAGGCATCATCAAGTACAGCTTAC 59.728 45.833 0.00 0.00 35.27 2.34
3559 3930 5.121142 TCAAGTACAGCTTACGGCAATAAAC 59.879 40.000 0.00 0.00 44.79 2.01
3568 3939 7.498256 GCTTACGGCAATAAACACCAAGTGT 62.498 44.000 0.00 0.00 44.08 3.55
3585 3956 0.535780 TGTCACCTCAAAGCAGCCAG 60.536 55.000 0.00 0.00 0.00 4.85
3595 3966 3.756727 GCAGCCAGCCTTTGCCTC 61.757 66.667 0.00 0.00 38.69 4.70
3638 4009 1.611491 GAACAACGCCCTCATGGAAAA 59.389 47.619 0.00 0.00 35.39 2.29
3878 4249 3.389002 AGCCTGAAAGAAAATGGCAGTTT 59.611 39.130 13.30 13.30 45.42 2.66
3992 4516 2.697229 CACTATCTGCTGGAGGTGATCA 59.303 50.000 0.00 0.00 35.31 2.92
4171 4752 2.356432 CCTGATGATGTGAGCCCTGAAA 60.356 50.000 0.00 0.00 0.00 2.69
4188 4769 5.273944 CCTGAAAGAAACGTTTGGAAGAAG 58.726 41.667 20.10 8.51 34.07 2.85
4280 4862 2.253452 CGTTCAGCAGCTGGTTGC 59.747 61.111 22.62 8.29 44.41 4.17
4350 4933 2.606725 CGTCGTCTATGTAGAAGGTCGT 59.393 50.000 3.71 0.00 33.47 4.34
4354 4937 4.696877 TCGTCTATGTAGAAGGTCGTTTCA 59.303 41.667 3.71 0.00 33.47 2.69
4370 4956 6.202188 GGTCGTTTCATTTGAGTCTAGTTTCA 59.798 38.462 0.00 0.00 0.00 2.69
4433 5020 6.539103 GTGAGGATGGAACTTGAAATAGTACC 59.461 42.308 0.00 0.00 0.00 3.34
4516 5103 6.747280 CGAATTCTACCAATGATTTTGTGTCC 59.253 38.462 3.52 0.00 0.00 4.02
4519 5106 6.573664 TCTACCAATGATTTTGTGTCCTTG 57.426 37.500 0.00 0.00 0.00 3.61
4522 5109 3.991773 CCAATGATTTTGTGTCCTTGCAG 59.008 43.478 0.00 0.00 0.00 4.41
4550 5137 9.998106 AAAAACTCTCTATAGCAAGTTTACTCA 57.002 29.630 22.21 0.00 40.16 3.41
4563 5150 1.919240 TTACTCAGGGTTCGCTCAGA 58.081 50.000 0.00 0.00 0.00 3.27
4614 5203 8.903570 ATGCGAAAATTTGAAATACATAACGA 57.096 26.923 0.00 0.00 0.00 3.85
4708 5304 5.089970 TCCATGTATGTGGAGAAGTTCAG 57.910 43.478 5.50 0.00 43.20 3.02
4712 5308 6.037940 CCATGTATGTGGAGAAGTTCAGAATG 59.962 42.308 5.50 0.00 42.02 2.67
4719 5315 8.463930 TGTGGAGAAGTTCAGAATGTAAAAAT 57.536 30.769 5.50 0.00 37.40 1.82
4720 5316 8.352201 TGTGGAGAAGTTCAGAATGTAAAAATG 58.648 33.333 5.50 0.00 37.40 2.32
4723 5319 7.746475 GGAGAAGTTCAGAATGTAAAAATGACG 59.254 37.037 5.50 0.00 37.40 4.35
4760 5369 9.366216 GAAAAAGTAAGAAAAAGAAAAGGAGCA 57.634 29.630 0.00 0.00 0.00 4.26
4795 5404 3.622166 GGAACCCCTGAGAATAAACGA 57.378 47.619 0.00 0.00 0.00 3.85
4796 5405 3.532542 GGAACCCCTGAGAATAAACGAG 58.467 50.000 0.00 0.00 0.00 4.18
4797 5406 3.197116 GGAACCCCTGAGAATAAACGAGA 59.803 47.826 0.00 0.00 0.00 4.04
4798 5407 4.323257 GGAACCCCTGAGAATAAACGAGAA 60.323 45.833 0.00 0.00 0.00 2.87
4799 5408 4.903045 ACCCCTGAGAATAAACGAGAAA 57.097 40.909 0.00 0.00 0.00 2.52
4800 5409 4.833390 ACCCCTGAGAATAAACGAGAAAG 58.167 43.478 0.00 0.00 0.00 2.62
4801 5410 4.530946 ACCCCTGAGAATAAACGAGAAAGA 59.469 41.667 0.00 0.00 0.00 2.52
4802 5411 5.112686 CCCCTGAGAATAAACGAGAAAGAG 58.887 45.833 0.00 0.00 0.00 2.85
4803 5412 5.105310 CCCCTGAGAATAAACGAGAAAGAGA 60.105 44.000 0.00 0.00 0.00 3.10
4804 5413 6.039616 CCCTGAGAATAAACGAGAAAGAGAG 58.960 44.000 0.00 0.00 0.00 3.20
4805 5414 5.518487 CCTGAGAATAAACGAGAAAGAGAGC 59.482 44.000 0.00 0.00 0.00 4.09
4806 5415 6.025749 TGAGAATAAACGAGAAAGAGAGCA 57.974 37.500 0.00 0.00 0.00 4.26
4807 5416 5.864474 TGAGAATAAACGAGAAAGAGAGCAC 59.136 40.000 0.00 0.00 0.00 4.40
4808 5417 5.784177 AGAATAAACGAGAAAGAGAGCACA 58.216 37.500 0.00 0.00 0.00 4.57
4822 5431 0.820871 AGCACAAAAGAAAACCGCCA 59.179 45.000 0.00 0.00 0.00 5.69
4836 5445 2.316108 ACCGCCAGAACCAAAGAAAAT 58.684 42.857 0.00 0.00 0.00 1.82
4852 5461 2.453983 AAATTTGTCACATTGCCCCG 57.546 45.000 0.00 0.00 0.00 5.73
4859 5468 1.400494 GTCACATTGCCCCGTATGTTC 59.600 52.381 0.00 0.00 32.88 3.18
4902 5511 3.801698 AGCATCACATAGCGAATTCTGT 58.198 40.909 3.52 0.00 35.48 3.41
4913 5522 1.325640 CGAATTCTGTGACGAGGCATG 59.674 52.381 3.52 0.00 0.00 4.06
4914 5523 2.350522 GAATTCTGTGACGAGGCATGT 58.649 47.619 0.00 0.00 0.00 3.21
4938 5547 8.357402 TGTATTTTGGCTAGAGTTTTCCTTTTC 58.643 33.333 0.00 0.00 0.00 2.29
4976 5585 7.333672 GGGAAAATGTCTAGTAGTTGTGGTAAG 59.666 40.741 0.00 0.00 0.00 2.34
4981 5590 4.097589 GTCTAGTAGTTGTGGTAAGCCGAT 59.902 45.833 0.00 0.00 37.67 4.18
4982 5591 5.297776 GTCTAGTAGTTGTGGTAAGCCGATA 59.702 44.000 0.00 0.00 37.67 2.92
4983 5592 4.382345 AGTAGTTGTGGTAAGCCGATAC 57.618 45.455 0.00 0.00 37.67 2.24
4984 5593 3.765511 AGTAGTTGTGGTAAGCCGATACA 59.234 43.478 0.00 0.00 37.67 2.29
4985 5594 2.968675 AGTTGTGGTAAGCCGATACAC 58.031 47.619 0.00 0.00 37.67 2.90
4986 5595 2.300723 AGTTGTGGTAAGCCGATACACA 59.699 45.455 0.00 0.00 37.67 3.72
4987 5596 3.055385 AGTTGTGGTAAGCCGATACACAT 60.055 43.478 0.00 0.00 37.67 3.21
4988 5597 2.899976 TGTGGTAAGCCGATACACATG 58.100 47.619 0.00 0.00 37.67 3.21
4989 5598 2.235155 TGTGGTAAGCCGATACACATGT 59.765 45.455 0.00 0.00 37.67 3.21
4990 5599 2.864343 GTGGTAAGCCGATACACATGTC 59.136 50.000 0.00 0.00 37.67 3.06
4991 5600 2.498078 TGGTAAGCCGATACACATGTCA 59.502 45.455 0.00 0.00 37.67 3.58
4992 5601 3.133901 TGGTAAGCCGATACACATGTCAT 59.866 43.478 0.00 0.00 37.67 3.06
4993 5602 3.494626 GGTAAGCCGATACACATGTCATG 59.505 47.826 11.41 11.41 0.00 3.07
4994 5603 3.541996 AAGCCGATACACATGTCATGA 57.458 42.857 19.77 0.00 0.00 3.07
4995 5604 2.826428 AGCCGATACACATGTCATGAC 58.174 47.619 19.27 19.27 0.00 3.06
4996 5605 1.522676 GCCGATACACATGTCATGACG 59.477 52.381 19.77 10.04 0.00 4.35
4997 5606 2.127251 CCGATACACATGTCATGACGG 58.873 52.381 19.77 16.94 0.00 4.79
4998 5607 2.481276 CCGATACACATGTCATGACGGT 60.481 50.000 19.77 17.57 34.39 4.83
4999 5608 2.535574 CGATACACATGTCATGACGGTG 59.464 50.000 32.24 32.24 41.75 4.94
5000 5609 2.378445 TACACATGTCATGACGGTGG 57.622 50.000 34.56 23.89 40.93 4.61
5001 5610 0.684535 ACACATGTCATGACGGTGGA 59.315 50.000 34.56 17.01 40.93 4.02
5002 5611 1.071542 ACACATGTCATGACGGTGGAA 59.928 47.619 34.56 16.41 40.93 3.53
5003 5612 1.464608 CACATGTCATGACGGTGGAAC 59.535 52.381 29.07 6.33 36.33 3.62
5004 5613 0.721154 CATGTCATGACGGTGGAACG 59.279 55.000 20.54 0.00 38.12 3.95
5020 5629 2.430921 CGTCCAGCGTGGTGTCTC 60.431 66.667 4.33 0.00 39.03 3.36
5021 5630 2.734591 GTCCAGCGTGGTGTCTCA 59.265 61.111 4.33 0.00 39.03 3.27
5022 5631 1.293498 GTCCAGCGTGGTGTCTCAT 59.707 57.895 4.33 0.00 39.03 2.90
5023 5632 1.016130 GTCCAGCGTGGTGTCTCATG 61.016 60.000 4.33 0.00 39.03 3.07
5024 5633 1.004560 CCAGCGTGGTGTCTCATGT 60.005 57.895 0.00 0.00 31.35 3.21
5025 5634 1.016130 CCAGCGTGGTGTCTCATGTC 61.016 60.000 0.00 0.00 31.35 3.06
5026 5635 0.319813 CAGCGTGGTGTCTCATGTCA 60.320 55.000 0.00 0.00 0.00 3.58
5027 5636 0.610174 AGCGTGGTGTCTCATGTCAT 59.390 50.000 0.00 0.00 0.00 3.06
5028 5637 0.723414 GCGTGGTGTCTCATGTCATG 59.277 55.000 6.47 6.47 0.00 3.07
5029 5638 1.941209 GCGTGGTGTCTCATGTCATGT 60.941 52.381 12.54 0.00 0.00 3.21
5030 5639 1.728425 CGTGGTGTCTCATGTCATGTG 59.272 52.381 12.54 10.33 0.00 3.21
5031 5640 1.466167 GTGGTGTCTCATGTCATGTGC 59.534 52.381 12.54 7.35 0.00 4.57
5032 5641 1.072015 TGGTGTCTCATGTCATGTGCA 59.928 47.619 12.54 9.54 0.00 4.57
5033 5642 2.153645 GGTGTCTCATGTCATGTGCAA 58.846 47.619 12.54 0.00 0.00 4.08
5034 5643 2.161012 GGTGTCTCATGTCATGTGCAAG 59.839 50.000 12.54 3.10 0.00 4.01
5035 5644 2.161012 GTGTCTCATGTCATGTGCAAGG 59.839 50.000 12.54 0.00 0.00 3.61
5036 5645 2.224597 TGTCTCATGTCATGTGCAAGGT 60.225 45.455 12.54 0.00 0.00 3.50
5037 5646 2.161012 GTCTCATGTCATGTGCAAGGTG 59.839 50.000 12.54 0.00 0.00 4.00
5038 5647 2.156917 CTCATGTCATGTGCAAGGTGT 58.843 47.619 12.54 0.00 0.00 4.16
5039 5648 2.555325 CTCATGTCATGTGCAAGGTGTT 59.445 45.455 12.54 0.00 0.00 3.32
5121 5730 4.466828 CCACATTCAGATGAAACGTGTTC 58.533 43.478 19.09 0.00 38.64 3.18
5125 5734 6.358030 CACATTCAGATGAAACGTGTTCTTTC 59.642 38.462 15.26 0.00 37.05 2.62
5180 5790 6.902771 AAGAGCTCTTCTAAGTACTGTTCA 57.097 37.500 23.49 0.00 34.14 3.18
5181 5791 6.902771 AGAGCTCTTCTAAGTACTGTTCAA 57.097 37.500 11.45 0.00 33.23 2.69
5182 5792 7.475137 AGAGCTCTTCTAAGTACTGTTCAAT 57.525 36.000 11.45 0.00 33.23 2.57
5184 5794 8.463607 AGAGCTCTTCTAAGTACTGTTCAATAC 58.536 37.037 11.45 0.00 33.23 1.89
5185 5795 8.356000 AGCTCTTCTAAGTACTGTTCAATACT 57.644 34.615 0.00 0.00 32.93 2.12
5186 5796 8.463607 AGCTCTTCTAAGTACTGTTCAATACTC 58.536 37.037 0.00 0.00 31.15 2.59
5188 5798 8.064336 TCTTCTAAGTACTGTTCAATACTCCC 57.936 38.462 0.00 0.00 31.15 4.30
5189 5799 7.894364 TCTTCTAAGTACTGTTCAATACTCCCT 59.106 37.037 0.00 0.00 31.15 4.20
5194 5804 4.618920 ACTGTTCAATACTCCCTTCGTT 57.381 40.909 0.00 0.00 0.00 3.85
5196 5806 3.933332 CTGTTCAATACTCCCTTCGTTCC 59.067 47.826 0.00 0.00 0.00 3.62
5198 5808 4.773674 TGTTCAATACTCCCTTCGTTCCTA 59.226 41.667 0.00 0.00 0.00 2.94
5199 5809 5.246656 TGTTCAATACTCCCTTCGTTCCTAA 59.753 40.000 0.00 0.00 0.00 2.69
5202 5812 7.664552 TCAATACTCCCTTCGTTCCTAAATA 57.335 36.000 0.00 0.00 0.00 1.40
5204 5814 6.667558 ATACTCCCTTCGTTCCTAAATAGG 57.332 41.667 0.00 0.00 45.02 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.158900 CCTGAGCCATTTCGTCCATAGT 60.159 50.000 0.00 0.00 0.00 2.12
29 30 2.486796 GCAGGACCTGAGCCATTTC 58.513 57.895 26.25 0.40 32.44 2.17
68 69 1.007271 CATTCGCCTCGACGCCTAT 60.007 57.895 0.63 0.00 34.89 2.57
238 239 1.088340 CGAGAGGATGTGCAGCAAGG 61.088 60.000 0.00 0.00 0.00 3.61
308 309 3.485633 CATGTTTGCTCATTCTGTGTCG 58.514 45.455 0.00 0.00 0.00 4.35
328 329 2.509569 TCTTTACCAATCTTTGCCGCA 58.490 42.857 0.00 0.00 0.00 5.69
340 341 2.500229 CGAACCTTGGCTTCTTTACCA 58.500 47.619 0.00 0.00 0.00 3.25
343 344 1.877443 GTGCGAACCTTGGCTTCTTTA 59.123 47.619 0.00 0.00 32.75 1.85
407 408 3.432051 GAGCACTCCATCGGACGGG 62.432 68.421 0.00 0.00 0.00 5.28
484 485 1.414550 GAGATGGCTTAGGGGAGTGAC 59.585 57.143 0.00 0.00 0.00 3.67
616 622 0.387929 TCGTGTTGCTCGAGGAAGTT 59.612 50.000 20.52 0.00 33.38 2.66
618 624 1.063806 CTTCGTGTTGCTCGAGGAAG 58.936 55.000 20.52 14.89 38.52 3.46
643 649 0.689412 CCTCTCAGTCTTCCTCCCCC 60.689 65.000 0.00 0.00 0.00 5.40
645 651 1.828595 GTTCCTCTCAGTCTTCCTCCC 59.171 57.143 0.00 0.00 0.00 4.30
646 652 2.232696 GTGTTCCTCTCAGTCTTCCTCC 59.767 54.545 0.00 0.00 0.00 4.30
648 654 1.889829 CGTGTTCCTCTCAGTCTTCCT 59.110 52.381 0.00 0.00 0.00 3.36
649 655 1.067495 CCGTGTTCCTCTCAGTCTTCC 60.067 57.143 0.00 0.00 0.00 3.46
650 656 1.067495 CCCGTGTTCCTCTCAGTCTTC 60.067 57.143 0.00 0.00 0.00 2.87
651 657 0.969894 CCCGTGTTCCTCTCAGTCTT 59.030 55.000 0.00 0.00 0.00 3.01
652 658 0.900647 CCCCGTGTTCCTCTCAGTCT 60.901 60.000 0.00 0.00 0.00 3.24
653 659 1.592223 CCCCGTGTTCCTCTCAGTC 59.408 63.158 0.00 0.00 0.00 3.51
654 660 1.913762 CCCCCGTGTTCCTCTCAGT 60.914 63.158 0.00 0.00 0.00 3.41
655 661 2.982130 CCCCCGTGTTCCTCTCAG 59.018 66.667 0.00 0.00 0.00 3.35
669 675 3.412408 GTCTCTCCCCTTGCCCCC 61.412 72.222 0.00 0.00 0.00 5.40
670 676 3.412408 GGTCTCTCCCCTTGCCCC 61.412 72.222 0.00 0.00 0.00 5.80
679 685 1.334243 CGTCGAATAGTGGGTCTCTCC 59.666 57.143 0.00 0.00 0.00 3.71
685 691 1.814527 GGAGCGTCGAATAGTGGGT 59.185 57.895 0.00 0.00 0.00 4.51
688 694 1.472276 GCACGGAGCGTCGAATAGTG 61.472 60.000 8.61 1.70 38.32 2.74
711 717 4.683334 GTGCTGCGTGCGTTTCCC 62.683 66.667 0.00 0.00 46.63 3.97
712 718 3.862063 CTGTGCTGCGTGCGTTTCC 62.862 63.158 0.00 0.00 46.63 3.13
713 719 2.425773 CTGTGCTGCGTGCGTTTC 60.426 61.111 0.00 0.00 46.63 2.78
714 720 3.952675 CCTGTGCTGCGTGCGTTT 61.953 61.111 0.00 0.00 46.63 3.60
770 776 1.516423 GTAAGGCGGTGGAGAGACC 59.484 63.158 0.00 0.00 39.54 3.85
1341 1394 0.182299 CCTGGCCCTCCTCAATTCTC 59.818 60.000 0.00 0.00 0.00 2.87
1380 1463 0.108585 TGGTCTTGAAGGTGCTGTCC 59.891 55.000 0.00 0.00 0.00 4.02
1420 1503 2.401766 GCCCATGCTTGTCGGACAG 61.402 63.158 11.14 7.02 33.53 3.51
1452 1535 0.772124 TCCTCCCCTCCAAGCAAAGT 60.772 55.000 0.00 0.00 0.00 2.66
1536 1619 1.078143 GCCATCCACCTCAGTGTCC 60.078 63.158 0.00 0.00 42.88 4.02
1761 1847 0.865111 CCAAACACGCGTCATCTTCA 59.135 50.000 9.86 0.00 0.00 3.02
1782 1868 5.163612 GCTCTGGAAGACAACAAACTTCTTT 60.164 40.000 0.00 0.00 38.67 2.52
1872 1958 0.384309 TAGGTATCTGAAGTGCGGCG 59.616 55.000 0.51 0.51 0.00 6.46
1952 2038 0.322975 AGGTCTGTCATGGTGAGCAC 59.677 55.000 12.51 0.00 0.00 4.40
1974 2060 3.053693 CCACAGGTAATGAGAAATCCCCA 60.054 47.826 0.00 0.00 0.00 4.96
1975 2061 3.202151 TCCACAGGTAATGAGAAATCCCC 59.798 47.826 0.00 0.00 0.00 4.81
2056 2142 2.353889 GTGATTCATCAGCAAGCATCGT 59.646 45.455 0.00 0.00 37.51 3.73
2077 2163 1.002868 CAGGCAGTGGAGGGAACAG 60.003 63.158 0.00 0.00 0.00 3.16
2089 2175 2.154462 CTTGTTACTTGACCCAGGCAG 58.846 52.381 0.00 0.00 0.00 4.85
2178 2264 1.218316 CACGGTGCCCTTCCTAGAC 59.782 63.158 0.00 0.00 0.00 2.59
2255 2341 0.182537 TGTGTGGGTGGAAGTGGAAG 59.817 55.000 0.00 0.00 0.00 3.46
2396 2500 2.552031 GACCATTCCCTAAGCTTCGAC 58.448 52.381 0.00 0.00 0.00 4.20
2397 2501 1.136305 CGACCATTCCCTAAGCTTCGA 59.864 52.381 0.00 0.00 0.00 3.71
2398 2502 1.571919 CGACCATTCCCTAAGCTTCG 58.428 55.000 0.00 0.00 0.00 3.79
2517 2621 4.752101 AGCGTATTACTTGATTGATGCTCC 59.248 41.667 0.00 0.00 0.00 4.70
2523 2627 4.119862 GAGCCAGCGTATTACTTGATTGA 58.880 43.478 0.00 0.00 0.00 2.57
2633 2737 2.867647 GCAAAAGGTTTCAGCCCATGTC 60.868 50.000 0.00 0.00 0.00 3.06
2637 2741 2.373335 TAGCAAAAGGTTTCAGCCCA 57.627 45.000 0.00 0.00 0.00 5.36
2644 2748 5.914898 AGTGTGTTCTTAGCAAAAGGTTT 57.085 34.783 0.00 0.00 0.00 3.27
2647 2751 4.044426 GCAAGTGTGTTCTTAGCAAAAGG 58.956 43.478 0.00 0.00 0.00 3.11
2798 3043 3.790437 CAGTGCCATCCCGCTCCT 61.790 66.667 0.00 0.00 0.00 3.69
3015 3260 0.179936 GTTGATGCTCTGAGAGGGGG 59.820 60.000 12.01 0.00 0.00 5.40
3034 3279 1.080093 CAGCCAGTGCATGCTTTGG 60.080 57.895 26.81 26.81 41.13 3.28
3292 3663 4.472833 AGGCACTATCTCAGGATTTTCAGT 59.527 41.667 0.00 0.00 36.02 3.41
3392 3763 4.703645 TCTCTTGTCGATTGAGGTACAG 57.296 45.455 10.78 0.00 0.00 2.74
3441 3812 2.041485 TCTGGAATTCCATGCTGAACCA 59.959 45.455 27.20 1.24 46.46 3.67
3559 3930 1.334869 GCTTTGAGGTGACACTTGGTG 59.665 52.381 5.39 0.00 39.75 4.17
3568 3939 1.601759 GCTGGCTGCTTTGAGGTGA 60.602 57.895 9.31 0.00 38.95 4.02
3585 3956 2.672996 TCCGCAAGAGGCAAAGGC 60.673 61.111 0.00 0.00 45.17 4.35
3595 3966 2.464459 GCCGAACATCCTCCGCAAG 61.464 63.158 0.00 0.00 0.00 4.01
3878 4249 7.889873 TTCTCTTTCAAGGTAATGGTTTCAA 57.110 32.000 0.00 0.00 0.00 2.69
3992 4516 1.412343 ACGCCTTTGAAATGGCAACTT 59.588 42.857 17.25 0.00 46.42 2.66
4171 4752 2.949644 CACCCTTCTTCCAAACGTTTCT 59.050 45.455 11.37 0.00 0.00 2.52
4350 4933 8.836413 ACGAAATGAAACTAGACTCAAATGAAA 58.164 29.630 0.00 0.00 0.00 2.69
4354 4937 8.926710 CAGTACGAAATGAAACTAGACTCAAAT 58.073 33.333 0.00 0.00 0.00 2.32
4370 4956 6.084326 ACCAGCAAAAATTCAGTACGAAAT 57.916 33.333 0.00 0.00 37.12 2.17
4407 4994 5.501156 ACTATTTCAAGTTCCATCCTCACC 58.499 41.667 0.00 0.00 0.00 4.02
4433 5020 1.492873 CCACGAACATGACACTGCG 59.507 57.895 0.00 0.00 0.00 5.18
4546 5133 0.540830 ACTCTGAGCGAACCCTGAGT 60.541 55.000 4.19 0.00 36.96 3.41
4547 5134 0.605589 AACTCTGAGCGAACCCTGAG 59.394 55.000 4.19 0.00 35.39 3.35
4548 5135 1.048601 AAACTCTGAGCGAACCCTGA 58.951 50.000 4.19 0.00 0.00 3.86
4549 5136 1.884235 AAAACTCTGAGCGAACCCTG 58.116 50.000 4.19 0.00 0.00 4.45
4550 5137 2.222027 CAAAAACTCTGAGCGAACCCT 58.778 47.619 4.19 0.00 0.00 4.34
4590 5179 8.729529 TTCGTTATGTATTTCAAATTTTCGCA 57.270 26.923 0.00 0.00 0.00 5.10
4686 5277 4.777366 TCTGAACTTCTCCACATACATGGA 59.223 41.667 0.00 0.00 46.92 3.41
4687 5278 5.089970 TCTGAACTTCTCCACATACATGG 57.910 43.478 0.00 0.00 41.57 3.66
4688 5279 6.596888 ACATTCTGAACTTCTCCACATACATG 59.403 38.462 0.00 0.00 0.00 3.21
4689 5280 6.715280 ACATTCTGAACTTCTCCACATACAT 58.285 36.000 0.00 0.00 0.00 2.29
4690 5281 6.114187 ACATTCTGAACTTCTCCACATACA 57.886 37.500 0.00 0.00 0.00 2.29
4691 5282 8.547967 TTTACATTCTGAACTTCTCCACATAC 57.452 34.615 0.00 0.00 0.00 2.39
4692 5283 9.567776 TTTTTACATTCTGAACTTCTCCACATA 57.432 29.630 0.00 0.00 0.00 2.29
4693 5284 8.463930 TTTTTACATTCTGAACTTCTCCACAT 57.536 30.769 0.00 0.00 0.00 3.21
4697 5293 7.746475 CGTCATTTTTACATTCTGAACTTCTCC 59.254 37.037 0.00 0.00 0.00 3.71
4734 5330 9.366216 TGCTCCTTTTCTTTTTCTTACTTTTTC 57.634 29.630 0.00 0.00 0.00 2.29
4737 5333 9.719355 TTTTGCTCCTTTTCTTTTTCTTACTTT 57.281 25.926 0.00 0.00 0.00 2.66
4780 5389 5.967088 TCTCTTTCTCGTTTATTCTCAGGG 58.033 41.667 0.00 0.00 0.00 4.45
4781 5390 5.518487 GCTCTCTTTCTCGTTTATTCTCAGG 59.482 44.000 0.00 0.00 0.00 3.86
4793 5402 5.409643 TTTCTTTTGTGCTCTCTTTCTCG 57.590 39.130 0.00 0.00 0.00 4.04
4794 5403 5.974158 GGTTTTCTTTTGTGCTCTCTTTCTC 59.026 40.000 0.00 0.00 0.00 2.87
4795 5404 5.449177 CGGTTTTCTTTTGTGCTCTCTTTCT 60.449 40.000 0.00 0.00 0.00 2.52
4796 5405 4.735338 CGGTTTTCTTTTGTGCTCTCTTTC 59.265 41.667 0.00 0.00 0.00 2.62
4797 5406 4.672409 CGGTTTTCTTTTGTGCTCTCTTT 58.328 39.130 0.00 0.00 0.00 2.52
4798 5407 3.489229 GCGGTTTTCTTTTGTGCTCTCTT 60.489 43.478 0.00 0.00 0.00 2.85
4799 5408 2.033424 GCGGTTTTCTTTTGTGCTCTCT 59.967 45.455 0.00 0.00 0.00 3.10
4800 5409 2.385315 GCGGTTTTCTTTTGTGCTCTC 58.615 47.619 0.00 0.00 0.00 3.20
4801 5410 1.067060 GGCGGTTTTCTTTTGTGCTCT 59.933 47.619 0.00 0.00 0.00 4.09
4802 5411 1.202359 TGGCGGTTTTCTTTTGTGCTC 60.202 47.619 0.00 0.00 0.00 4.26
4803 5412 0.820871 TGGCGGTTTTCTTTTGTGCT 59.179 45.000 0.00 0.00 0.00 4.40
4804 5413 1.202359 TCTGGCGGTTTTCTTTTGTGC 60.202 47.619 0.00 0.00 0.00 4.57
4805 5414 2.857748 GTTCTGGCGGTTTTCTTTTGTG 59.142 45.455 0.00 0.00 0.00 3.33
4806 5415 2.159156 GGTTCTGGCGGTTTTCTTTTGT 60.159 45.455 0.00 0.00 0.00 2.83
4807 5416 2.159170 TGGTTCTGGCGGTTTTCTTTTG 60.159 45.455 0.00 0.00 0.00 2.44
4808 5417 2.104170 TGGTTCTGGCGGTTTTCTTTT 58.896 42.857 0.00 0.00 0.00 2.27
4822 5431 7.201635 GCAATGTGACAAATTTTCTTTGGTTCT 60.202 33.333 0.00 0.00 33.92 3.01
4836 5445 1.815613 CATACGGGGCAATGTGACAAA 59.184 47.619 0.00 0.00 0.00 2.83
4852 5461 2.158957 TCAGATTGCGGGGAGAACATAC 60.159 50.000 0.00 0.00 0.00 2.39
4859 5468 2.892425 GCGTCAGATTGCGGGGAG 60.892 66.667 0.00 0.00 0.00 4.30
4888 5497 2.791560 CCTCGTCACAGAATTCGCTATG 59.208 50.000 0.00 0.00 0.00 2.23
4902 5511 1.742831 GCCAAAATACATGCCTCGTCA 59.257 47.619 0.00 0.00 0.00 4.35
4913 5522 8.577296 AGAAAAGGAAAACTCTAGCCAAAATAC 58.423 33.333 0.00 0.00 0.00 1.89
4914 5523 8.706322 AGAAAAGGAAAACTCTAGCCAAAATA 57.294 30.769 0.00 0.00 0.00 1.40
4923 5532 7.700656 CGCAAGAAAAAGAAAAGGAAAACTCTA 59.299 33.333 0.00 0.00 43.02 2.43
4927 5536 5.220586 CCCGCAAGAAAAAGAAAAGGAAAAC 60.221 40.000 0.00 0.00 43.02 2.43
4938 5547 3.727726 ACATTTTCCCCGCAAGAAAAAG 58.272 40.909 8.93 7.67 44.09 2.27
4976 5585 1.522676 CGTCATGACATGTGTATCGGC 59.477 52.381 24.93 0.00 0.00 5.54
4981 5590 1.896465 TCCACCGTCATGACATGTGTA 59.104 47.619 29.26 19.45 34.08 2.90
4982 5591 0.684535 TCCACCGTCATGACATGTGT 59.315 50.000 29.26 17.87 34.08 3.72
4983 5592 1.464608 GTTCCACCGTCATGACATGTG 59.535 52.381 26.90 26.90 35.05 3.21
4984 5593 1.808411 GTTCCACCGTCATGACATGT 58.192 50.000 24.93 17.73 0.00 3.21
4985 5594 0.721154 CGTTCCACCGTCATGACATG 59.279 55.000 24.93 20.38 0.00 3.21
4986 5595 0.320374 ACGTTCCACCGTCATGACAT 59.680 50.000 24.93 10.09 35.95 3.06
4987 5596 1.743391 ACGTTCCACCGTCATGACA 59.257 52.632 24.93 2.54 35.95 3.58
4988 5597 4.667420 ACGTTCCACCGTCATGAC 57.333 55.556 16.21 16.21 35.95 3.06
4994 5603 4.657824 CGCTGGACGTTCCACCGT 62.658 66.667 11.32 0.00 42.67 4.83
5004 5613 1.016130 CATGAGACACCACGCTGGAC 61.016 60.000 10.46 3.04 40.96 4.02
5005 5614 1.293179 CATGAGACACCACGCTGGA 59.707 57.895 10.46 0.00 40.96 3.86
5006 5615 1.004560 ACATGAGACACCACGCTGG 60.005 57.895 0.00 2.92 45.02 4.85
5007 5616 0.319813 TGACATGAGACACCACGCTG 60.320 55.000 0.00 0.00 0.00 5.18
5008 5617 0.610174 ATGACATGAGACACCACGCT 59.390 50.000 0.00 0.00 0.00 5.07
5009 5618 0.723414 CATGACATGAGACACCACGC 59.277 55.000 10.03 0.00 0.00 5.34
5010 5619 1.728425 CACATGACATGAGACACCACG 59.272 52.381 22.19 0.00 0.00 4.94
5011 5620 1.466167 GCACATGACATGAGACACCAC 59.534 52.381 22.19 0.00 0.00 4.16
5012 5621 1.072015 TGCACATGACATGAGACACCA 59.928 47.619 22.19 4.81 0.00 4.17
5013 5622 1.812235 TGCACATGACATGAGACACC 58.188 50.000 22.19 2.26 0.00 4.16
5014 5623 2.161012 CCTTGCACATGACATGAGACAC 59.839 50.000 22.19 6.69 0.00 3.67
5015 5624 2.224597 ACCTTGCACATGACATGAGACA 60.225 45.455 22.19 12.91 0.00 3.41
5016 5625 2.161012 CACCTTGCACATGACATGAGAC 59.839 50.000 22.19 10.61 0.00 3.36
5017 5626 2.224597 ACACCTTGCACATGACATGAGA 60.225 45.455 22.19 2.35 0.00 3.27
5018 5627 2.156917 ACACCTTGCACATGACATGAG 58.843 47.619 22.19 15.06 0.00 2.90
5019 5628 2.275134 ACACCTTGCACATGACATGA 57.725 45.000 22.19 0.00 0.00 3.07
5020 5629 3.374220 AAACACCTTGCACATGACATG 57.626 42.857 14.02 14.02 0.00 3.21
5021 5630 3.888323 TGTAAACACCTTGCACATGACAT 59.112 39.130 0.00 0.00 0.00 3.06
5022 5631 3.282885 TGTAAACACCTTGCACATGACA 58.717 40.909 0.00 0.00 0.00 3.58
5023 5632 3.980646 TGTAAACACCTTGCACATGAC 57.019 42.857 0.00 0.00 0.00 3.06
5024 5633 5.709631 ACATATGTAAACACCTTGCACATGA 59.290 36.000 6.56 0.00 36.85 3.07
5025 5634 5.953183 ACATATGTAAACACCTTGCACATG 58.047 37.500 6.56 0.00 39.60 3.21
5026 5635 6.588719 AACATATGTAAACACCTTGCACAT 57.411 33.333 9.21 0.00 31.94 3.21
5027 5636 6.183360 ACAAACATATGTAAACACCTTGCACA 60.183 34.615 9.21 0.00 31.94 4.57
5028 5637 6.143758 CACAAACATATGTAAACACCTTGCAC 59.856 38.462 9.21 0.00 31.94 4.57
5029 5638 6.039829 TCACAAACATATGTAAACACCTTGCA 59.960 34.615 9.21 0.00 33.84 4.08
5030 5639 6.442952 TCACAAACATATGTAAACACCTTGC 58.557 36.000 9.21 0.00 30.84 4.01
5031 5640 8.864069 TTTCACAAACATATGTAAACACCTTG 57.136 30.769 9.21 10.33 30.84 3.61
5032 5641 9.308318 GTTTTCACAAACATATGTAAACACCTT 57.692 29.630 18.34 3.60 41.85 3.50
5033 5642 8.470805 TGTTTTCACAAACATATGTAAACACCT 58.529 29.630 20.58 0.00 46.06 4.00
5034 5643 8.635877 TGTTTTCACAAACATATGTAAACACC 57.364 30.769 20.58 6.49 46.06 4.16
5121 5730 6.817765 TGGCTAGTGGAACAAATAAGAAAG 57.182 37.500 0.00 0.00 44.16 2.62
5125 5734 6.924111 ACAAATGGCTAGTGGAACAAATAAG 58.076 36.000 0.00 0.00 44.16 1.73
5172 5782 5.337009 GGAACGAAGGGAGTATTGAACAGTA 60.337 44.000 0.00 0.00 0.00 2.74
5173 5783 4.562963 GGAACGAAGGGAGTATTGAACAGT 60.563 45.833 0.00 0.00 0.00 3.55
5174 5784 3.933332 GGAACGAAGGGAGTATTGAACAG 59.067 47.826 0.00 0.00 0.00 3.16
5175 5785 3.581332 AGGAACGAAGGGAGTATTGAACA 59.419 43.478 0.00 0.00 0.00 3.18
5176 5786 4.203654 AGGAACGAAGGGAGTATTGAAC 57.796 45.455 0.00 0.00 0.00 3.18
5178 5788 6.555463 ATTTAGGAACGAAGGGAGTATTGA 57.445 37.500 0.00 0.00 0.00 2.57
5179 5789 6.929606 CCTATTTAGGAACGAAGGGAGTATTG 59.070 42.308 0.00 0.00 46.63 1.90
5180 5790 7.063934 CCTATTTAGGAACGAAGGGAGTATT 57.936 40.000 0.00 0.00 46.63 1.89
5181 5791 6.667558 CCTATTTAGGAACGAAGGGAGTAT 57.332 41.667 0.00 0.00 46.63 2.12


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

AutoCloner maintained by Alex Coulton.