Multiple sequence alignment - TraesCS3D01G306500

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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 TraesCS3D01G306500 chr3D 100.000 2536 0 0 1 2536 420358424 420360959 0.000000e+00 4684.0
1 TraesCS3D01G306500 chr3D 91.683 2044 130 27 214 2240 571735992 571733972 0.000000e+00 2796.0
2 TraesCS3D01G306500 chr3D 94.915 295 15 0 2241 2535 414965648 414965354 1.780000e-126 462.0
3 TraesCS3D01G306500 chr3D 94.257 296 17 0 2241 2536 446033338 446033043 1.070000e-123 453.0
4 TraesCS3D01G306500 chr3D 94.237 295 17 0 2241 2535 45815142 45814848 3.850000e-123 451.0
5 TraesCS3D01G306500 chr3D 100.000 28 0 0 1384 1411 229426257 229426230 5.000000e-03 52.8
6 TraesCS3D01G306500 chr2A 90.869 2278 151 38 3 2241 259698027 259700286 0.000000e+00 3001.0
7 TraesCS3D01G306500 chr4A 93.103 1566 79 22 1 1556 24488679 24490225 0.000000e+00 2266.0
8 TraesCS3D01G306500 chr4A 88.864 907 54 21 1370 2240 24490083 24490978 0.000000e+00 1072.0
9 TraesCS3D01G306500 chr2D 94.480 1413 67 8 1 1411 397130520 397131923 0.000000e+00 2167.0
10 TraesCS3D01G306500 chr2D 94.257 296 17 0 2241 2536 132383026 132382731 1.070000e-123 453.0
11 TraesCS3D01G306500 chr7A 93.825 1425 79 7 1 1424 220999415 221000831 0.000000e+00 2135.0
12 TraesCS3D01G306500 chr7A 91.214 774 59 8 1469 2239 221000958 221001725 0.000000e+00 1044.0
13 TraesCS3D01G306500 chr6D 93.111 1437 63 22 1 1433 297171440 297170036 0.000000e+00 2073.0
14 TraesCS3D01G306500 chr6D 94.198 293 17 0 2241 2533 392197912 392198204 4.980000e-122 448.0
15 TraesCS3D01G306500 chr6D 93.898 295 18 0 2241 2535 42141691 42141985 1.790000e-121 446.0
16 TraesCS3D01G306500 chr5D 93.101 1435 67 20 1 1433 384512060 384510656 0.000000e+00 2073.0
17 TraesCS3D01G306500 chr5D 92.837 1438 75 20 1 1433 29767629 29766215 0.000000e+00 2060.0
18 TraesCS3D01G306500 chr5A 93.993 1182 67 4 1 1181 384029551 384030729 0.000000e+00 1786.0
19 TraesCS3D01G306500 chr2B 93.004 1215 79 5 1 1214 123795149 123793940 0.000000e+00 1768.0
20 TraesCS3D01G306500 chr2B 91.451 1041 61 8 1209 2241 123776466 123775446 0.000000e+00 1404.0
21 TraesCS3D01G306500 chr7D 96.163 886 32 2 1 885 501764193 501765077 0.000000e+00 1447.0
22 TraesCS3D01G306500 chr7B 85.969 1347 116 39 957 2240 46780927 46782263 0.000000e+00 1373.0
23 TraesCS3D01G306500 chr7B 86.659 862 79 20 1411 2244 715336908 715336055 0.000000e+00 922.0
24 TraesCS3D01G306500 chr7B 85.887 496 44 18 957 1444 692777043 692777520 2.910000e-139 505.0
25 TraesCS3D01G306500 chr7B 87.500 176 11 6 1448 1617 122470989 122471159 2.570000e-45 193.0
26 TraesCS3D01G306500 chr1D 93.092 941 48 7 494 1433 336729686 336728762 0.000000e+00 1362.0
27 TraesCS3D01G306500 chr1D 94.595 296 16 0 2241 2536 359985349 359985644 2.300000e-125 459.0
28 TraesCS3D01G306500 chr1D 94.558 294 16 0 2241 2534 144540953 144541246 2.970000e-124 455.0
29 TraesCS3D01G306500 chr6B 85.661 1346 120 37 957 2240 630177019 630175685 0.000000e+00 1349.0
30 TraesCS3D01G306500 chr6B 91.927 768 45 10 1487 2240 159275281 159274517 0.000000e+00 1059.0
31 TraesCS3D01G306500 chr6B 88.851 888 53 18 1388 2240 2734326 2735202 0.000000e+00 1050.0
32 TraesCS3D01G306500 chr6B 85.360 847 81 24 794 1600 429916075 429915232 0.000000e+00 837.0
33 TraesCS3D01G306500 chr3B 92.995 828 46 6 1 818 318303831 318304656 0.000000e+00 1197.0
34 TraesCS3D01G306500 chr3B 90.194 775 63 12 1473 2240 228479607 228478839 0.000000e+00 998.0
35 TraesCS3D01G306500 chr3B 88.945 796 73 10 1452 2240 765160870 765160083 0.000000e+00 968.0
36 TraesCS3D01G306500 chr6A 90.418 814 52 10 1446 2240 136675482 136676288 0.000000e+00 1048.0
37 TraesCS3D01G306500 chr5B 90.137 801 63 9 1451 2243 345187927 345187135 0.000000e+00 1027.0
38 TraesCS3D01G306500 chr4D 84.601 1091 100 39 794 1847 196954804 196955863 0.000000e+00 1022.0
39 TraesCS3D01G306500 chr4D 93.919 296 18 0 2241 2536 368035205 368034910 4.980000e-122 448.0
40 TraesCS3D01G306500 chr1B 90.078 766 69 6 1476 2240 13210550 13211309 0.000000e+00 987.0
41 TraesCS3D01G306500 chrUn 87.408 818 74 13 1446 2241 281295393 281294583 0.000000e+00 913.0
42 TraesCS3D01G306500 chrUn 87.408 818 74 13 1446 2241 281302313 281301503 0.000000e+00 913.0


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 TraesCS3D01G306500 chr3D 420358424 420360959 2535 False 4684.0 4684 100.0000 1 2536 1 chr3D.!!$F1 2535
1 TraesCS3D01G306500 chr3D 571733972 571735992 2020 True 2796.0 2796 91.6830 214 2240 1 chr3D.!!$R5 2026
2 TraesCS3D01G306500 chr2A 259698027 259700286 2259 False 3001.0 3001 90.8690 3 2241 1 chr2A.!!$F1 2238
3 TraesCS3D01G306500 chr4A 24488679 24490978 2299 False 1669.0 2266 90.9835 1 2240 2 chr4A.!!$F1 2239
4 TraesCS3D01G306500 chr2D 397130520 397131923 1403 False 2167.0 2167 94.4800 1 1411 1 chr2D.!!$F1 1410
5 TraesCS3D01G306500 chr7A 220999415 221001725 2310 False 1589.5 2135 92.5195 1 2239 2 chr7A.!!$F1 2238
6 TraesCS3D01G306500 chr6D 297170036 297171440 1404 True 2073.0 2073 93.1110 1 1433 1 chr6D.!!$R1 1432
7 TraesCS3D01G306500 chr5D 384510656 384512060 1404 True 2073.0 2073 93.1010 1 1433 1 chr5D.!!$R2 1432
8 TraesCS3D01G306500 chr5D 29766215 29767629 1414 True 2060.0 2060 92.8370 1 1433 1 chr5D.!!$R1 1432
9 TraesCS3D01G306500 chr5A 384029551 384030729 1178 False 1786.0 1786 93.9930 1 1181 1 chr5A.!!$F1 1180
10 TraesCS3D01G306500 chr2B 123793940 123795149 1209 True 1768.0 1768 93.0040 1 1214 1 chr2B.!!$R2 1213
11 TraesCS3D01G306500 chr2B 123775446 123776466 1020 True 1404.0 1404 91.4510 1209 2241 1 chr2B.!!$R1 1032
12 TraesCS3D01G306500 chr7D 501764193 501765077 884 False 1447.0 1447 96.1630 1 885 1 chr7D.!!$F1 884
13 TraesCS3D01G306500 chr7B 46780927 46782263 1336 False 1373.0 1373 85.9690 957 2240 1 chr7B.!!$F1 1283
14 TraesCS3D01G306500 chr7B 715336055 715336908 853 True 922.0 922 86.6590 1411 2244 1 chr7B.!!$R1 833
15 TraesCS3D01G306500 chr1D 336728762 336729686 924 True 1362.0 1362 93.0920 494 1433 1 chr1D.!!$R1 939
16 TraesCS3D01G306500 chr6B 630175685 630177019 1334 True 1349.0 1349 85.6610 957 2240 1 chr6B.!!$R3 1283
17 TraesCS3D01G306500 chr6B 159274517 159275281 764 True 1059.0 1059 91.9270 1487 2240 1 chr6B.!!$R1 753
18 TraesCS3D01G306500 chr6B 2734326 2735202 876 False 1050.0 1050 88.8510 1388 2240 1 chr6B.!!$F1 852
19 TraesCS3D01G306500 chr6B 429915232 429916075 843 True 837.0 837 85.3600 794 1600 1 chr6B.!!$R2 806
20 TraesCS3D01G306500 chr3B 318303831 318304656 825 False 1197.0 1197 92.9950 1 818 1 chr3B.!!$F1 817
21 TraesCS3D01G306500 chr3B 228478839 228479607 768 True 998.0 998 90.1940 1473 2240 1 chr3B.!!$R1 767
22 TraesCS3D01G306500 chr3B 765160083 765160870 787 True 968.0 968 88.9450 1452 2240 1 chr3B.!!$R2 788
23 TraesCS3D01G306500 chr6A 136675482 136676288 806 False 1048.0 1048 90.4180 1446 2240 1 chr6A.!!$F1 794
24 TraesCS3D01G306500 chr5B 345187135 345187927 792 True 1027.0 1027 90.1370 1451 2243 1 chr5B.!!$R1 792
25 TraesCS3D01G306500 chr4D 196954804 196955863 1059 False 1022.0 1022 84.6010 794 1847 1 chr4D.!!$F1 1053
26 TraesCS3D01G306500 chr1B 13210550 13211309 759 False 987.0 987 90.0780 1476 2240 1 chr1B.!!$F1 764
27 TraesCS3D01G306500 chrUn 281294583 281295393 810 True 913.0 913 87.4080 1446 2241 1 chrUn.!!$R1 795
28 TraesCS3D01G306500 chrUn 281301503 281302313 810 True 913.0 913 87.4080 1446 2241 1 chrUn.!!$R2 795

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
532 562 4.060205 GCCAGCTTTGATGTTGTTTGATT 58.94 39.13 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2672 0.031043 CTCATCTCGAGAGCCAGCAG 59.969 60.0 21.52 6.05 45.45 4.24 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
310 312 8.579006 ACATTTCTGATTCTTGCTGAATAACAA 58.421 29.630 5.70 0.00 44.70 2.83
532 562 4.060205 GCCAGCTTTGATGTTGTTTGATT 58.940 39.130 0.00 0.00 0.00 2.57
731 795 6.599638 GCCATCTTATATAGAACCACCATTCC 59.400 42.308 0.00 0.00 36.22 3.01
1053 1120 1.597742 GTGAAGAGCCAAAGTCTGCA 58.402 50.000 0.00 0.00 0.00 4.41
1070 1140 5.532406 AGTCTGCAGCTAAAATTGTTGAAGA 59.468 36.000 9.47 0.00 29.62 2.87
1071 1141 6.039717 AGTCTGCAGCTAAAATTGTTGAAGAA 59.960 34.615 9.47 0.00 33.21 2.52
1072 1142 6.361748 GTCTGCAGCTAAAATTGTTGAAGAAG 59.638 38.462 9.47 0.00 33.21 2.85
1080 1150 7.383300 GCTAAAATTGTTGAAGAAGTGCTCAAT 59.617 33.333 0.00 0.00 0.00 2.57
1098 1168 4.637276 TCAATACCGAAGTCAAGCAAAGA 58.363 39.130 0.00 0.00 0.00 2.52
1268 1338 2.567169 TCAAGATGAAGGCGGAAGAAGA 59.433 45.455 0.00 0.00 0.00 2.87
1399 1525 2.412870 TGTCGTAGTTTGATGGCTGTG 58.587 47.619 0.00 0.00 0.00 3.66
1449 1642 0.394216 TTGCACTTGTGAGCCTGTGT 60.394 50.000 4.79 0.00 33.44 3.72
2044 2407 4.220602 GGTGGATTGCTAGTGACCAAAATT 59.779 41.667 0.00 0.00 32.32 1.82
2098 2464 9.102757 TCTAGTCATAAACGTCTACGACTATTT 57.897 33.333 5.39 2.10 43.02 1.40
2128 2494 7.868775 AGAAAGGTCGTTAATTTCAGTTTACC 58.131 34.615 0.00 0.00 35.79 2.85
2244 2610 5.428253 TGACATATTTCTTGTAGTGGAGGC 58.572 41.667 0.00 0.00 0.00 4.70
2245 2611 4.781934 ACATATTTCTTGTAGTGGAGGCC 58.218 43.478 0.00 0.00 0.00 5.19
2246 2612 4.475016 ACATATTTCTTGTAGTGGAGGCCT 59.525 41.667 3.86 3.86 0.00 5.19
2247 2613 3.636153 ATTTCTTGTAGTGGAGGCCTC 57.364 47.619 25.59 25.59 0.00 4.70
2257 2623 2.281345 GAGGCCTCCGCATCATGG 60.281 66.667 23.19 0.00 45.17 3.66
2258 2624 3.839353 GAGGCCTCCGCATCATGGG 62.839 68.421 23.19 0.00 45.17 4.00
2259 2625 4.195334 GGCCTCCGCATCATGGGT 62.195 66.667 0.00 0.00 36.38 4.51
2260 2626 2.903855 GCCTCCGCATCATGGGTG 60.904 66.667 0.36 0.00 34.03 4.61
2261 2627 2.903855 CCTCCGCATCATGGGTGC 60.904 66.667 12.28 12.28 39.18 5.01
2262 2628 2.903855 CTCCGCATCATGGGTGCC 60.904 66.667 15.33 2.46 39.39 5.01
2263 2629 4.504596 TCCGCATCATGGGTGCCC 62.505 66.667 15.33 0.00 39.39 5.36
2264 2630 4.511246 CCGCATCATGGGTGCCCT 62.511 66.667 15.33 0.00 39.39 5.19
2265 2631 2.903855 CGCATCATGGGTGCCCTC 60.904 66.667 15.33 0.00 39.39 4.30
2266 2632 2.903855 GCATCATGGGTGCCCTCG 60.904 66.667 8.91 0.00 36.61 4.63
2267 2633 2.591753 CATCATGGGTGCCCTCGT 59.408 61.111 8.91 0.00 36.94 4.18
2268 2634 1.524621 CATCATGGGTGCCCTCGTC 60.525 63.158 8.91 0.00 36.94 4.20
2269 2635 3.094062 ATCATGGGTGCCCTCGTCG 62.094 63.158 8.91 0.00 36.94 5.12
2270 2636 4.082523 CATGGGTGCCCTCGTCGT 62.083 66.667 8.91 0.00 36.94 4.34
2271 2637 2.363276 ATGGGTGCCCTCGTCGTA 60.363 61.111 8.91 0.00 36.94 3.43
2272 2638 2.423898 ATGGGTGCCCTCGTCGTAG 61.424 63.158 8.91 0.00 36.94 3.51
2273 2639 3.066814 GGGTGCCCTCGTCGTAGT 61.067 66.667 0.00 0.00 0.00 2.73
2274 2640 2.181021 GGTGCCCTCGTCGTAGTG 59.819 66.667 0.00 0.00 0.00 2.74
2275 2641 2.181021 GTGCCCTCGTCGTAGTGG 59.819 66.667 0.00 0.00 0.00 4.00
2276 2642 2.282674 TGCCCTCGTCGTAGTGGT 60.283 61.111 0.00 0.00 0.00 4.16
2277 2643 2.181021 GCCCTCGTCGTAGTGGTG 59.819 66.667 0.00 0.00 0.00 4.17
2278 2644 2.338015 GCCCTCGTCGTAGTGGTGA 61.338 63.158 0.00 0.00 0.00 4.02
2279 2645 1.801332 CCCTCGTCGTAGTGGTGAG 59.199 63.158 0.00 0.00 0.00 3.51
2280 2646 0.959372 CCCTCGTCGTAGTGGTGAGT 60.959 60.000 0.00 0.00 0.00 3.41
2281 2647 0.879765 CCTCGTCGTAGTGGTGAGTT 59.120 55.000 0.00 0.00 0.00 3.01
2282 2648 1.401148 CCTCGTCGTAGTGGTGAGTTG 60.401 57.143 0.00 0.00 0.00 3.16
2283 2649 0.039798 TCGTCGTAGTGGTGAGTTGC 60.040 55.000 0.00 0.00 0.00 4.17
2284 2650 1.007336 CGTCGTAGTGGTGAGTTGCC 61.007 60.000 0.00 0.00 0.00 4.52
2285 2651 0.317479 GTCGTAGTGGTGAGTTGCCT 59.683 55.000 0.00 0.00 0.00 4.75
2286 2652 0.317160 TCGTAGTGGTGAGTTGCCTG 59.683 55.000 0.00 0.00 0.00 4.85
2287 2653 0.317160 CGTAGTGGTGAGTTGCCTGA 59.683 55.000 0.00 0.00 0.00 3.86
2288 2654 1.670087 CGTAGTGGTGAGTTGCCTGAG 60.670 57.143 0.00 0.00 0.00 3.35
2289 2655 0.321671 TAGTGGTGAGTTGCCTGAGC 59.678 55.000 0.00 0.00 40.48 4.26
2290 2656 1.968540 GTGGTGAGTTGCCTGAGCC 60.969 63.158 0.00 0.00 38.69 4.70
2291 2657 2.743928 GGTGAGTTGCCTGAGCCG 60.744 66.667 0.00 0.00 38.69 5.52
2292 2658 3.426568 GTGAGTTGCCTGAGCCGC 61.427 66.667 0.00 0.00 38.69 6.53
2293 2659 3.630013 TGAGTTGCCTGAGCCGCT 61.630 61.111 0.00 0.00 38.69 5.52
2294 2660 2.817396 GAGTTGCCTGAGCCGCTC 60.817 66.667 13.81 13.81 38.69 5.03
2295 2661 3.308014 GAGTTGCCTGAGCCGCTCT 62.308 63.158 20.87 0.00 38.69 4.09
2296 2662 3.123620 GTTGCCTGAGCCGCTCTG 61.124 66.667 20.87 19.30 38.69 3.35
2314 2680 4.982701 GGCACCAACCTGCTGGCT 62.983 66.667 9.95 0.00 40.45 4.75
2315 2681 3.368571 GCACCAACCTGCTGGCTC 61.369 66.667 9.95 0.00 40.45 4.70
2316 2682 2.433446 CACCAACCTGCTGGCTCT 59.567 61.111 9.95 0.00 40.45 4.09
2317 2683 1.673665 CACCAACCTGCTGGCTCTC 60.674 63.158 9.95 0.00 40.45 3.20
2318 2684 2.435586 CCAACCTGCTGGCTCTCG 60.436 66.667 9.95 0.00 36.63 4.04
2319 2685 2.659016 CAACCTGCTGGCTCTCGA 59.341 61.111 9.95 0.00 36.63 4.04
2320 2686 1.447489 CAACCTGCTGGCTCTCGAG 60.447 63.158 9.95 5.93 36.63 4.04
2321 2687 1.607756 AACCTGCTGGCTCTCGAGA 60.608 57.895 15.70 15.70 36.63 4.04
2322 2688 0.975040 AACCTGCTGGCTCTCGAGAT 60.975 55.000 17.03 0.00 36.63 2.75
2323 2689 1.067749 CCTGCTGGCTCTCGAGATG 59.932 63.158 17.03 11.23 0.00 2.90
2324 2690 1.390383 CCTGCTGGCTCTCGAGATGA 61.390 60.000 17.03 1.74 0.00 2.92
2325 2691 0.031043 CTGCTGGCTCTCGAGATGAG 59.969 60.000 17.03 12.66 46.72 2.90
2326 2692 1.363443 GCTGGCTCTCGAGATGAGG 59.637 63.158 17.03 5.23 45.32 3.86
2327 2693 1.391157 GCTGGCTCTCGAGATGAGGT 61.391 60.000 17.03 0.00 45.32 3.85
2328 2694 1.974265 CTGGCTCTCGAGATGAGGTA 58.026 55.000 17.03 0.00 45.32 3.08
2329 2695 2.302260 CTGGCTCTCGAGATGAGGTAA 58.698 52.381 17.03 0.00 45.32 2.85
2330 2696 2.293122 CTGGCTCTCGAGATGAGGTAAG 59.707 54.545 17.03 2.43 45.32 2.34
2331 2697 1.000717 GGCTCTCGAGATGAGGTAAGC 60.001 57.143 17.03 12.77 45.32 3.09
2332 2698 1.678627 GCTCTCGAGATGAGGTAAGCA 59.321 52.381 17.03 0.00 45.32 3.91
2333 2699 2.542824 GCTCTCGAGATGAGGTAAGCAC 60.543 54.545 17.03 0.00 45.32 4.40
2334 2700 2.685388 CTCTCGAGATGAGGTAAGCACA 59.315 50.000 17.03 0.00 45.32 4.57
2335 2701 3.291584 TCTCGAGATGAGGTAAGCACAT 58.708 45.455 12.08 0.00 45.32 3.21
2336 2702 3.067320 TCTCGAGATGAGGTAAGCACATG 59.933 47.826 12.08 0.00 45.32 3.21
2337 2703 1.863454 CGAGATGAGGTAAGCACATGC 59.137 52.381 0.00 0.00 42.49 4.06
2338 2704 2.739609 CGAGATGAGGTAAGCACATGCA 60.740 50.000 6.64 0.00 45.16 3.96
2339 2705 2.611292 GAGATGAGGTAAGCACATGCAC 59.389 50.000 6.64 0.00 45.16 4.57
2340 2706 1.328680 GATGAGGTAAGCACATGCACG 59.671 52.381 6.64 0.00 45.16 5.34
2341 2707 1.298157 TGAGGTAAGCACATGCACGC 61.298 55.000 6.64 0.00 45.16 5.34
2342 2708 1.003355 AGGTAAGCACATGCACGCT 60.003 52.632 6.64 1.40 45.16 5.07
2343 2709 1.135315 GGTAAGCACATGCACGCTG 59.865 57.895 6.64 0.00 45.16 5.18
2344 2710 1.298157 GGTAAGCACATGCACGCTGA 61.298 55.000 6.64 0.00 45.16 4.26
2345 2711 0.095935 GTAAGCACATGCACGCTGAG 59.904 55.000 6.64 0.00 45.16 3.35
2346 2712 0.037419 TAAGCACATGCACGCTGAGA 60.037 50.000 6.64 0.00 45.16 3.27
2347 2713 0.886043 AAGCACATGCACGCTGAGAA 60.886 50.000 6.64 0.00 45.16 2.87
2348 2714 0.886043 AGCACATGCACGCTGAGAAA 60.886 50.000 6.64 0.00 45.16 2.52
2349 2715 0.040157 GCACATGCACGCTGAGAAAA 60.040 50.000 0.00 0.00 41.59 2.29
2350 2716 1.678360 CACATGCACGCTGAGAAAAC 58.322 50.000 0.00 0.00 0.00 2.43
2351 2717 1.002576 CACATGCACGCTGAGAAAACA 60.003 47.619 0.00 0.00 0.00 2.83
2352 2718 1.002468 ACATGCACGCTGAGAAAACAC 60.002 47.619 0.00 0.00 0.00 3.32
2353 2719 0.593128 ATGCACGCTGAGAAAACACC 59.407 50.000 0.00 0.00 0.00 4.16
2354 2720 0.463654 TGCACGCTGAGAAAACACCT 60.464 50.000 0.00 0.00 0.00 4.00
2355 2721 0.235926 GCACGCTGAGAAAACACCTC 59.764 55.000 0.00 0.00 0.00 3.85
2356 2722 0.508641 CACGCTGAGAAAACACCTCG 59.491 55.000 0.00 0.00 33.51 4.63
2357 2723 0.104304 ACGCTGAGAAAACACCTCGT 59.896 50.000 0.00 0.00 33.51 4.18
2358 2724 1.338973 ACGCTGAGAAAACACCTCGTA 59.661 47.619 0.00 0.00 33.51 3.43
2359 2725 1.719780 CGCTGAGAAAACACCTCGTAC 59.280 52.381 0.00 0.00 33.51 3.67
2360 2726 2.607282 CGCTGAGAAAACACCTCGTACT 60.607 50.000 0.00 0.00 33.51 2.73
2361 2727 2.987821 GCTGAGAAAACACCTCGTACTC 59.012 50.000 0.00 0.00 33.51 2.59
2362 2728 3.305471 GCTGAGAAAACACCTCGTACTCT 60.305 47.826 0.00 0.00 33.51 3.24
2363 2729 4.796618 GCTGAGAAAACACCTCGTACTCTT 60.797 45.833 0.00 0.00 33.51 2.85
2364 2730 4.868067 TGAGAAAACACCTCGTACTCTTC 58.132 43.478 0.00 0.00 33.51 2.87
2365 2731 3.898529 AGAAAACACCTCGTACTCTTCG 58.101 45.455 0.00 0.00 0.00 3.79
2366 2732 3.317430 AGAAAACACCTCGTACTCTTCGT 59.683 43.478 0.00 0.00 0.00 3.85
2367 2733 2.985406 AACACCTCGTACTCTTCGTC 57.015 50.000 0.00 0.00 0.00 4.20
2368 2734 0.795085 ACACCTCGTACTCTTCGTCG 59.205 55.000 0.00 0.00 0.00 5.12
2369 2735 1.073964 CACCTCGTACTCTTCGTCGA 58.926 55.000 0.00 0.00 0.00 4.20
2370 2736 1.462283 CACCTCGTACTCTTCGTCGAA 59.538 52.381 7.57 7.57 32.12 3.71
2371 2737 1.731160 ACCTCGTACTCTTCGTCGAAG 59.269 52.381 25.76 25.76 40.65 3.79
2372 2738 1.062294 CCTCGTACTCTTCGTCGAAGG 59.938 57.143 29.52 22.66 39.82 3.46
2373 2739 0.445436 TCGTACTCTTCGTCGAAGGC 59.555 55.000 29.52 17.84 39.82 4.35
2374 2740 0.167470 CGTACTCTTCGTCGAAGGCA 59.833 55.000 29.52 14.22 39.82 4.75
2375 2741 1.615502 GTACTCTTCGTCGAAGGCAC 58.384 55.000 29.52 21.11 39.82 5.01
2376 2742 0.524862 TACTCTTCGTCGAAGGCACC 59.475 55.000 29.52 0.00 39.82 5.01
2377 2743 1.801913 CTCTTCGTCGAAGGCACCG 60.802 63.158 29.52 12.82 39.82 4.94
2378 2744 2.196382 CTCTTCGTCGAAGGCACCGA 62.196 60.000 29.52 12.47 39.82 4.69
2379 2745 1.801913 CTTCGTCGAAGGCACCGAG 60.802 63.158 24.37 0.00 36.16 4.63
2380 2746 3.277211 TTCGTCGAAGGCACCGAGG 62.277 63.158 2.90 12.69 41.52 4.63
2381 2747 4.796231 CGTCGAAGGCACCGAGGG 62.796 72.222 11.54 0.99 38.00 4.30
2382 2748 3.692406 GTCGAAGGCACCGAGGGT 61.692 66.667 1.56 0.00 36.66 4.34
2394 2760 3.388841 GAGGGTGGCCTCGAGAAA 58.611 61.111 15.71 0.00 0.00 2.52
2395 2761 1.677552 GAGGGTGGCCTCGAGAAAA 59.322 57.895 15.71 0.00 0.00 2.29
2396 2762 0.673956 GAGGGTGGCCTCGAGAAAAC 60.674 60.000 15.71 8.34 0.00 2.43
2397 2763 2.033194 GGGTGGCCTCGAGAAAACG 61.033 63.158 15.71 0.00 0.00 3.60
2398 2764 2.677979 GGTGGCCTCGAGAAAACGC 61.678 63.158 15.71 8.12 0.00 4.84
2399 2765 2.358247 TGGCCTCGAGAAAACGCC 60.358 61.111 15.71 17.87 40.16 5.68
2400 2766 2.358247 GGCCTCGAGAAAACGCCA 60.358 61.111 20.64 0.00 39.50 5.69
2401 2767 2.677979 GGCCTCGAGAAAACGCCAC 61.678 63.158 20.64 0.00 39.50 5.01
2402 2768 3.011760 GCCTCGAGAAAACGCCACG 62.012 63.158 15.71 0.00 0.00 4.94
2403 2769 1.372499 CCTCGAGAAAACGCCACGA 60.372 57.895 15.71 0.00 0.00 4.35
2404 2770 0.942410 CCTCGAGAAAACGCCACGAA 60.942 55.000 15.71 0.00 32.85 3.85
2405 2771 0.161024 CTCGAGAAAACGCCACGAAC 59.839 55.000 6.58 0.00 32.85 3.95
2406 2772 0.249155 TCGAGAAAACGCCACGAACT 60.249 50.000 0.00 0.00 0.00 3.01
2407 2773 0.111266 CGAGAAAACGCCACGAACTG 60.111 55.000 0.00 0.00 0.00 3.16
2408 2774 0.935196 GAGAAAACGCCACGAACTGT 59.065 50.000 0.00 0.00 0.00 3.55
2409 2775 0.935196 AGAAAACGCCACGAACTGTC 59.065 50.000 0.00 0.00 0.00 3.51
2421 2787 2.560896 CGAACTGTCGTTTAAAGCAGC 58.439 47.619 11.86 0.00 42.53 5.25
2422 2788 2.661979 CGAACTGTCGTTTAAAGCAGCC 60.662 50.000 11.86 6.08 42.53 4.85
2423 2789 1.961793 ACTGTCGTTTAAAGCAGCCA 58.038 45.000 11.86 0.00 32.65 4.75
2424 2790 2.294074 ACTGTCGTTTAAAGCAGCCAA 58.706 42.857 11.86 0.00 32.65 4.52
2425 2791 2.032924 ACTGTCGTTTAAAGCAGCCAAC 59.967 45.455 11.86 0.00 32.65 3.77
2426 2792 1.335496 TGTCGTTTAAAGCAGCCAACC 59.665 47.619 0.00 0.00 0.00 3.77
2427 2793 0.589223 TCGTTTAAAGCAGCCAACCG 59.411 50.000 0.00 0.00 0.00 4.44
2428 2794 1.001745 CGTTTAAAGCAGCCAACCGC 61.002 55.000 0.00 0.00 37.98 5.68
2429 2795 1.001745 GTTTAAAGCAGCCAACCGCG 61.002 55.000 0.00 0.00 44.76 6.46
2430 2796 1.448922 TTTAAAGCAGCCAACCGCGT 61.449 50.000 4.92 0.00 44.76 6.01
2431 2797 1.448922 TTAAAGCAGCCAACCGCGTT 61.449 50.000 4.92 0.00 44.76 4.84
2432 2798 2.123988 TAAAGCAGCCAACCGCGTTG 62.124 55.000 4.92 9.81 44.76 4.10
2495 2861 2.043227 GGTACTCCTCCAAGATCTGGG 58.957 57.143 10.27 10.27 46.44 4.45
2496 2862 2.043227 GTACTCCTCCAAGATCTGGGG 58.957 57.143 16.63 11.55 46.75 4.96
2500 2866 1.826024 CTCCAAGATCTGGGGGTCG 59.174 63.158 16.63 0.00 42.85 4.79
2501 2867 1.689233 TCCAAGATCTGGGGGTCGG 60.689 63.158 16.63 0.00 46.44 4.79
2502 2868 2.190578 CAAGATCTGGGGGTCGGC 59.809 66.667 0.00 0.00 0.00 5.54
2503 2869 2.285368 AAGATCTGGGGGTCGGCA 60.285 61.111 0.00 0.00 0.00 5.69
2504 2870 2.670148 AAGATCTGGGGGTCGGCAC 61.670 63.158 0.00 0.00 0.00 5.01
2518 2884 2.410469 GCACGAATGGCAGCCATC 59.590 61.111 27.82 18.45 44.40 3.51
2519 2885 2.711311 CACGAATGGCAGCCATCG 59.289 61.111 29.53 29.53 44.40 3.84
2520 2886 3.204827 ACGAATGGCAGCCATCGC 61.205 61.111 30.39 23.33 44.40 4.58
2521 2887 3.204119 CGAATGGCAGCCATCGCA 61.204 61.111 27.82 0.00 44.40 5.10
2522 2888 2.763273 CGAATGGCAGCCATCGCAA 61.763 57.895 27.82 0.00 44.40 4.85
2523 2889 1.226773 GAATGGCAGCCATCGCAAC 60.227 57.895 27.82 12.49 44.40 4.17
2524 2890 2.618312 GAATGGCAGCCATCGCAACC 62.618 60.000 27.82 8.91 44.40 3.77
2525 2891 3.650298 ATGGCAGCCATCGCAACCT 62.650 57.895 22.36 0.00 40.74 3.50
2526 2892 3.512516 GGCAGCCATCGCAACCTC 61.513 66.667 6.55 0.00 37.52 3.85
2527 2893 2.747460 GCAGCCATCGCAACCTCA 60.747 61.111 0.00 0.00 37.52 3.86
2528 2894 2.117156 GCAGCCATCGCAACCTCAT 61.117 57.895 0.00 0.00 37.52 2.90
2529 2895 2.020131 CAGCCATCGCAACCTCATC 58.980 57.895 0.00 0.00 37.52 2.92
2530 2896 1.153086 AGCCATCGCAACCTCATCC 60.153 57.895 0.00 0.00 37.52 3.51
2531 2897 2.537560 GCCATCGCAACCTCATCCG 61.538 63.158 0.00 0.00 34.03 4.18
2532 2898 2.537560 CCATCGCAACCTCATCCGC 61.538 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 149 2.138320 CATCTTGTTCGACACACAGCT 58.862 47.619 0.00 0.00 33.98 4.24
148 150 2.135139 TCATCTTGTTCGACACACAGC 58.865 47.619 0.00 0.00 33.98 4.40
330 332 4.938226 CCCTTACGCTCTTCTTTCTGAATT 59.062 41.667 0.00 0.00 33.71 2.17
532 562 5.562696 GCTCCGAATCAAACAACATCAAAGA 60.563 40.000 0.00 0.00 0.00 2.52
1053 1120 6.039717 TGAGCACTTCTTCAACAATTTTAGCT 59.960 34.615 0.00 0.00 0.00 3.32
1070 1140 3.678056 TGACTTCGGTATTGAGCACTT 57.322 42.857 0.00 0.00 0.00 3.16
1071 1141 3.589988 CTTGACTTCGGTATTGAGCACT 58.410 45.455 0.00 0.00 0.00 4.40
1072 1142 2.094417 GCTTGACTTCGGTATTGAGCAC 59.906 50.000 0.00 0.00 0.00 4.40
1080 1150 3.799366 TGTTCTTTGCTTGACTTCGGTA 58.201 40.909 0.00 0.00 0.00 4.02
1268 1338 1.904852 CTTGTCGCGTGCAGCTTCAT 61.905 55.000 5.77 0.00 45.59 2.57
1399 1525 0.947244 CTGCACAGGTTCACAGGTTC 59.053 55.000 0.00 0.00 0.00 3.62
1442 1605 1.202405 CCAGGTTCAAACAACACAGGC 60.202 52.381 0.00 0.00 0.00 4.85
1449 1642 1.064017 ACAGCTCCCAGGTTCAAACAA 60.064 47.619 0.00 0.00 0.00 2.83
1533 1848 2.886523 CCAGGTTCAAACAGCAAGATCA 59.113 45.455 0.00 0.00 0.00 2.92
1677 2027 7.174253 ACAAACTTTGTTCTTACAGTCAACTCA 59.826 33.333 1.00 0.00 42.22 3.41
1694 2044 4.448732 GGATGCAGCCTTTTACAAACTTTG 59.551 41.667 15.35 0.00 0.00 2.77
2098 2464 6.990349 ACTGAAATTAACGACCTTTCTTCTGA 59.010 34.615 0.00 0.00 31.66 3.27
2128 2494 2.644992 GGTCAAAAGCTGGCCGTG 59.355 61.111 0.00 0.00 40.90 4.94
2244 2610 2.903855 GCACCCATGATGCGGAGG 60.904 66.667 6.21 0.00 32.45 4.30
2245 2611 2.903855 GGCACCCATGATGCGGAG 60.904 66.667 13.67 1.06 44.37 4.63
2258 2624 2.181021 CCACTACGACGAGGGCAC 59.819 66.667 0.00 0.00 0.00 5.01
2259 2625 2.282674 ACCACTACGACGAGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
2260 2626 2.181021 CACCACTACGACGAGGGC 59.819 66.667 0.00 0.00 0.00 5.19
2261 2627 0.959372 ACTCACCACTACGACGAGGG 60.959 60.000 0.00 0.00 0.00 4.30
2262 2628 0.879765 AACTCACCACTACGACGAGG 59.120 55.000 0.00 0.08 0.00 4.63
2263 2629 1.965083 CAACTCACCACTACGACGAG 58.035 55.000 0.00 0.00 0.00 4.18
2264 2630 0.039798 GCAACTCACCACTACGACGA 60.040 55.000 0.00 0.00 0.00 4.20
2265 2631 1.007336 GGCAACTCACCACTACGACG 61.007 60.000 0.00 0.00 0.00 5.12
2266 2632 2.823628 GGCAACTCACCACTACGAC 58.176 57.895 0.00 0.00 0.00 4.34
2279 2645 3.123620 CAGAGCGGCTCAGGCAAC 61.124 66.667 29.88 3.57 40.87 4.17
2280 2646 4.399395 CCAGAGCGGCTCAGGCAA 62.399 66.667 29.88 0.00 40.87 4.52
2291 2657 2.674380 CAGGTTGGTGCCCAGAGC 60.674 66.667 0.00 0.00 44.14 4.09
2292 2658 2.674380 GCAGGTTGGTGCCCAGAG 60.674 66.667 0.00 0.00 37.49 3.35
2293 2659 3.177884 AGCAGGTTGGTGCCCAGA 61.178 61.111 0.00 0.00 45.20 3.86
2294 2660 2.987547 CAGCAGGTTGGTGCCCAG 60.988 66.667 0.00 0.00 45.20 4.45
2295 2661 4.601794 CCAGCAGGTTGGTGCCCA 62.602 66.667 2.88 0.00 45.20 5.36
2297 2663 4.982701 AGCCAGCAGGTTGGTGCC 62.983 66.667 4.07 0.00 45.20 5.01
2298 2664 3.368571 GAGCCAGCAGGTTGGTGC 61.369 66.667 4.07 0.00 43.92 5.01
2299 2665 1.673665 GAGAGCCAGCAGGTTGGTG 60.674 63.158 4.07 1.47 44.79 4.17
2300 2666 2.753029 GAGAGCCAGCAGGTTGGT 59.247 61.111 4.07 0.00 40.49 3.67
2301 2667 2.435586 CGAGAGCCAGCAGGTTGG 60.436 66.667 0.00 0.00 41.35 3.77
2302 2668 1.447489 CTCGAGAGCCAGCAGGTTG 60.447 63.158 6.58 0.00 37.19 3.77
2303 2669 0.975040 ATCTCGAGAGCCAGCAGGTT 60.975 55.000 21.52 0.00 37.19 3.50
2304 2670 1.381056 ATCTCGAGAGCCAGCAGGT 60.381 57.895 21.52 0.00 37.19 4.00
2305 2671 1.067749 CATCTCGAGAGCCAGCAGG 59.932 63.158 21.52 0.00 38.23 4.85
2306 2672 0.031043 CTCATCTCGAGAGCCAGCAG 59.969 60.000 21.52 6.05 45.45 4.24
2307 2673 1.390383 CCTCATCTCGAGAGCCAGCA 61.390 60.000 21.52 0.00 45.45 4.41
2308 2674 1.363443 CCTCATCTCGAGAGCCAGC 59.637 63.158 21.52 0.00 45.45 4.85
2309 2675 1.974265 TACCTCATCTCGAGAGCCAG 58.026 55.000 21.52 14.84 45.45 4.85
2310 2676 2.302260 CTTACCTCATCTCGAGAGCCA 58.698 52.381 21.52 5.95 45.45 4.75
2311 2677 1.000717 GCTTACCTCATCTCGAGAGCC 60.001 57.143 21.52 0.00 45.45 4.70
2312 2678 1.678627 TGCTTACCTCATCTCGAGAGC 59.321 52.381 21.52 15.63 45.45 4.09
2313 2679 2.685388 TGTGCTTACCTCATCTCGAGAG 59.315 50.000 21.52 12.70 45.45 3.20
2314 2680 2.723273 TGTGCTTACCTCATCTCGAGA 58.277 47.619 19.19 19.19 45.45 4.04
2315 2681 3.379240 CATGTGCTTACCTCATCTCGAG 58.621 50.000 5.93 5.93 41.89 4.04
2316 2682 2.481969 GCATGTGCTTACCTCATCTCGA 60.482 50.000 0.00 0.00 38.21 4.04
2317 2683 1.863454 GCATGTGCTTACCTCATCTCG 59.137 52.381 0.00 0.00 38.21 4.04
2318 2684 2.611292 GTGCATGTGCTTACCTCATCTC 59.389 50.000 6.55 0.00 42.66 2.75
2319 2685 2.636830 GTGCATGTGCTTACCTCATCT 58.363 47.619 6.55 0.00 42.66 2.90
2320 2686 1.328680 CGTGCATGTGCTTACCTCATC 59.671 52.381 6.55 0.00 42.66 2.92
2321 2687 1.372582 CGTGCATGTGCTTACCTCAT 58.627 50.000 6.55 0.00 42.66 2.90
2322 2688 1.298157 GCGTGCATGTGCTTACCTCA 61.298 55.000 7.93 0.00 42.66 3.86
2323 2689 1.021390 AGCGTGCATGTGCTTACCTC 61.021 55.000 7.93 0.00 38.57 3.85
2324 2690 1.003355 AGCGTGCATGTGCTTACCT 60.003 52.632 7.93 0.00 38.57 3.08
2325 2691 1.135315 CAGCGTGCATGTGCTTACC 59.865 57.895 7.93 0.00 40.03 2.85
2326 2692 0.095935 CTCAGCGTGCATGTGCTTAC 59.904 55.000 7.93 0.00 40.03 2.34
2327 2693 0.037419 TCTCAGCGTGCATGTGCTTA 60.037 50.000 7.93 0.29 40.03 3.09
2328 2694 0.886043 TTCTCAGCGTGCATGTGCTT 60.886 50.000 7.93 0.00 40.03 3.91
2329 2695 0.886043 TTTCTCAGCGTGCATGTGCT 60.886 50.000 7.93 6.51 43.58 4.40
2330 2696 0.040157 TTTTCTCAGCGTGCATGTGC 60.040 50.000 7.93 4.03 42.50 4.57
2331 2697 1.002576 TGTTTTCTCAGCGTGCATGTG 60.003 47.619 7.93 5.08 0.00 3.21
2332 2698 1.002468 GTGTTTTCTCAGCGTGCATGT 60.002 47.619 7.93 0.00 0.00 3.21
2333 2699 1.664016 GGTGTTTTCTCAGCGTGCATG 60.664 52.381 0.09 0.09 0.00 4.06
2334 2700 0.593128 GGTGTTTTCTCAGCGTGCAT 59.407 50.000 0.00 0.00 0.00 3.96
2335 2701 0.463654 AGGTGTTTTCTCAGCGTGCA 60.464 50.000 0.00 0.00 40.23 4.57
2336 2702 0.235926 GAGGTGTTTTCTCAGCGTGC 59.764 55.000 0.00 0.00 40.23 5.34
2337 2703 0.508641 CGAGGTGTTTTCTCAGCGTG 59.491 55.000 0.00 0.00 40.23 5.34
2338 2704 0.104304 ACGAGGTGTTTTCTCAGCGT 59.896 50.000 0.00 0.00 40.23 5.07
2339 2705 1.719780 GTACGAGGTGTTTTCTCAGCG 59.280 52.381 0.00 0.00 40.23 5.18
2340 2706 2.987821 GAGTACGAGGTGTTTTCTCAGC 59.012 50.000 0.00 0.00 36.27 4.26
2341 2707 4.506886 AGAGTACGAGGTGTTTTCTCAG 57.493 45.455 0.00 0.00 0.00 3.35
2342 2708 4.556104 CGAAGAGTACGAGGTGTTTTCTCA 60.556 45.833 0.00 0.00 0.00 3.27
2343 2709 3.913163 CGAAGAGTACGAGGTGTTTTCTC 59.087 47.826 0.00 0.00 0.00 2.87
2344 2710 3.317430 ACGAAGAGTACGAGGTGTTTTCT 59.683 43.478 0.00 0.00 34.70 2.52
2345 2711 3.636381 ACGAAGAGTACGAGGTGTTTTC 58.364 45.455 0.00 0.00 34.70 2.29
2346 2712 3.636381 GACGAAGAGTACGAGGTGTTTT 58.364 45.455 0.00 0.00 34.70 2.43
2347 2713 2.350197 CGACGAAGAGTACGAGGTGTTT 60.350 50.000 0.00 0.00 34.70 2.83
2348 2714 1.196354 CGACGAAGAGTACGAGGTGTT 59.804 52.381 0.00 0.00 34.70 3.32
2349 2715 0.795085 CGACGAAGAGTACGAGGTGT 59.205 55.000 0.00 0.00 34.70 4.16
2350 2716 1.073964 TCGACGAAGAGTACGAGGTG 58.926 55.000 0.00 0.00 32.01 4.00
2351 2717 1.731160 CTTCGACGAAGAGTACGAGGT 59.269 52.381 29.40 0.00 41.71 3.85
2352 2718 1.062294 CCTTCGACGAAGAGTACGAGG 59.938 57.143 33.52 15.26 41.71 4.63
2353 2719 1.529418 GCCTTCGACGAAGAGTACGAG 60.529 57.143 33.52 18.32 41.71 4.18
2354 2720 0.445436 GCCTTCGACGAAGAGTACGA 59.555 55.000 33.52 0.14 41.71 3.43
2355 2721 0.167470 TGCCTTCGACGAAGAGTACG 59.833 55.000 33.52 19.59 41.71 3.67
2356 2722 1.615502 GTGCCTTCGACGAAGAGTAC 58.384 55.000 33.52 26.55 41.71 2.73
2357 2723 0.524862 GGTGCCTTCGACGAAGAGTA 59.475 55.000 33.52 21.33 41.71 2.59
2358 2724 1.289380 GGTGCCTTCGACGAAGAGT 59.711 57.895 33.52 0.00 41.71 3.24
2359 2725 1.801913 CGGTGCCTTCGACGAAGAG 60.802 63.158 33.52 24.38 41.71 2.85
2360 2726 2.196382 CTCGGTGCCTTCGACGAAGA 62.196 60.000 33.52 15.88 41.71 2.87
2361 2727 1.801913 CTCGGTGCCTTCGACGAAG 60.802 63.158 27.01 27.01 39.17 3.79
2362 2728 2.257371 CTCGGTGCCTTCGACGAA 59.743 61.111 10.34 10.34 34.70 3.85
2363 2729 3.744719 CCTCGGTGCCTTCGACGA 61.745 66.667 0.00 0.00 32.86 4.20
2364 2730 4.796231 CCCTCGGTGCCTTCGACG 62.796 72.222 0.00 0.00 32.86 5.12
2365 2731 3.692406 ACCCTCGGTGCCTTCGAC 61.692 66.667 0.00 0.00 32.98 4.20
2378 2744 1.375326 GTTTTCTCGAGGCCACCCT 59.625 57.895 13.56 0.00 46.74 4.34
2379 2745 2.033194 CGTTTTCTCGAGGCCACCC 61.033 63.158 13.56 0.00 0.00 4.61
2380 2746 2.677979 GCGTTTTCTCGAGGCCACC 61.678 63.158 13.56 0.00 0.00 4.61
2381 2747 2.677979 GGCGTTTTCTCGAGGCCAC 61.678 63.158 20.64 10.66 45.05 5.01
2382 2748 2.358247 GGCGTTTTCTCGAGGCCA 60.358 61.111 20.64 0.79 45.05 5.36
2383 2749 2.358247 TGGCGTTTTCTCGAGGCC 60.358 61.111 19.26 19.26 45.71 5.19
2384 2750 2.861006 GTGGCGTTTTCTCGAGGC 59.139 61.111 13.56 7.35 0.00 4.70
2385 2751 0.942410 TTCGTGGCGTTTTCTCGAGG 60.942 55.000 13.56 0.00 32.39 4.63
2386 2752 0.161024 GTTCGTGGCGTTTTCTCGAG 59.839 55.000 5.93 5.93 32.39 4.04
2387 2753 0.249155 AGTTCGTGGCGTTTTCTCGA 60.249 50.000 0.00 0.00 0.00 4.04
2388 2754 0.111266 CAGTTCGTGGCGTTTTCTCG 60.111 55.000 0.00 0.00 0.00 4.04
2389 2755 0.935196 ACAGTTCGTGGCGTTTTCTC 59.065 50.000 0.00 0.00 0.00 2.87
2390 2756 0.935196 GACAGTTCGTGGCGTTTTCT 59.065 50.000 0.00 0.00 0.00 2.52
2391 2757 3.432759 GACAGTTCGTGGCGTTTTC 57.567 52.632 0.00 0.00 0.00 2.29
2402 2768 2.289547 TGGCTGCTTTAAACGACAGTTC 59.710 45.455 0.00 4.54 40.18 3.01
2403 2769 2.294074 TGGCTGCTTTAAACGACAGTT 58.706 42.857 0.00 0.00 43.50 3.16
2404 2770 1.961793 TGGCTGCTTTAAACGACAGT 58.038 45.000 0.00 0.00 32.65 3.55
2405 2771 2.604614 GGTTGGCTGCTTTAAACGACAG 60.605 50.000 0.00 4.49 0.00 3.51
2406 2772 1.335496 GGTTGGCTGCTTTAAACGACA 59.665 47.619 0.00 0.00 0.00 4.35
2407 2773 1.662026 CGGTTGGCTGCTTTAAACGAC 60.662 52.381 13.86 0.98 36.69 4.34
2408 2774 0.589223 CGGTTGGCTGCTTTAAACGA 59.411 50.000 13.86 0.00 36.69 3.85
2409 2775 1.001745 GCGGTTGGCTGCTTTAAACG 61.002 55.000 14.45 14.45 43.44 3.60
2410 2776 1.001745 CGCGGTTGGCTGCTTTAAAC 61.002 55.000 0.00 0.00 44.55 2.01
2411 2777 1.284408 CGCGGTTGGCTGCTTTAAA 59.716 52.632 0.00 0.00 44.55 1.52
2412 2778 1.448922 AACGCGGTTGGCTGCTTTAA 61.449 50.000 12.47 0.00 44.55 1.52
2413 2779 1.894756 AACGCGGTTGGCTGCTTTA 60.895 52.632 12.47 0.00 44.55 1.85
2414 2780 3.216292 AACGCGGTTGGCTGCTTT 61.216 55.556 12.47 0.00 44.55 3.51
2415 2781 3.964875 CAACGCGGTTGGCTGCTT 61.965 61.111 12.47 0.00 44.55 3.91
2439 2805 4.829518 TCGATGCCTCGCACGACG 62.830 66.667 6.51 0.00 43.04 5.12
2440 2806 3.248171 GTCGATGCCTCGCACGAC 61.248 66.667 18.55 18.55 46.17 4.34
2441 2807 4.829518 CGTCGATGCCTCGCACGA 62.830 66.667 21.78 7.05 44.03 4.35
2442 2808 4.829518 TCGTCGATGCCTCGCACG 62.830 66.667 20.93 20.93 43.04 5.34
2443 2809 2.278857 ATCGTCGATGCCTCGCAC 60.279 61.111 7.00 5.41 43.04 5.34
2444 2810 2.278792 CATCGTCGATGCCTCGCA 60.279 61.111 21.42 0.00 44.65 5.10
2445 2811 3.032609 CCATCGTCGATGCCTCGC 61.033 66.667 26.43 1.53 44.65 5.03
2446 2812 3.032609 GCCATCGTCGATGCCTCG 61.033 66.667 26.43 15.37 46.41 4.63
2447 2813 2.663188 GGCCATCGTCGATGCCTC 60.663 66.667 26.43 17.33 38.59 4.70
2448 2814 3.157217 GAGGCCATCGTCGATGCCT 62.157 63.158 32.79 32.79 43.61 4.75
2449 2815 2.663188 GAGGCCATCGTCGATGCC 60.663 66.667 26.43 26.96 38.59 4.40
2465 2831 2.821366 GGAGTACCTCGCCGTCGA 60.821 66.667 0.00 0.00 43.28 4.20
2466 2832 2.823147 AGGAGTACCTCGCCGTCG 60.823 66.667 0.00 0.00 44.13 5.12
2485 2851 2.190578 GCCGACCCCCAGATCTTG 59.809 66.667 0.00 0.00 0.00 3.02
2486 2852 2.285368 TGCCGACCCCCAGATCTT 60.285 61.111 0.00 0.00 0.00 2.40
2487 2853 3.083997 GTGCCGACCCCCAGATCT 61.084 66.667 0.00 0.00 0.00 2.75
2488 2854 4.530857 CGTGCCGACCCCCAGATC 62.531 72.222 0.00 0.00 0.00 2.75
2491 2857 4.096003 ATTCGTGCCGACCCCCAG 62.096 66.667 0.00 0.00 34.89 4.45
2492 2858 4.402528 CATTCGTGCCGACCCCCA 62.403 66.667 0.00 0.00 34.89 4.96
2496 2862 3.499737 CTGCCATTCGTGCCGACC 61.500 66.667 0.00 0.00 34.89 4.79
2497 2863 4.166011 GCTGCCATTCGTGCCGAC 62.166 66.667 0.00 0.00 34.89 4.79
2500 2866 3.129913 GATGGCTGCCATTCGTGCC 62.130 63.158 32.94 16.71 45.26 5.01
2501 2867 2.410469 GATGGCTGCCATTCGTGC 59.590 61.111 32.94 17.42 45.26 5.34
2502 2868 2.711311 CGATGGCTGCCATTCGTG 59.289 61.111 32.94 19.59 45.26 4.35
2503 2869 3.204827 GCGATGGCTGCCATTCGT 61.205 61.111 33.03 19.45 45.26 3.85
2504 2870 2.763273 TTGCGATGGCTGCCATTCG 61.763 57.895 32.94 31.83 45.26 3.34
2505 2871 1.226773 GTTGCGATGGCTGCCATTC 60.227 57.895 32.94 26.00 45.26 2.67
2506 2872 2.713967 GGTTGCGATGGCTGCCATT 61.714 57.895 32.94 18.08 45.26 3.16
2508 2874 4.349503 AGGTTGCGATGGCTGCCA 62.350 61.111 25.65 25.65 40.82 4.92
2509 2875 3.512516 GAGGTTGCGATGGCTGCC 61.513 66.667 12.87 12.87 40.82 4.85
2510 2876 2.056481 GATGAGGTTGCGATGGCTGC 62.056 60.000 0.15 0.00 40.82 5.25
2511 2877 1.442526 GGATGAGGTTGCGATGGCTG 61.443 60.000 0.15 0.00 40.82 4.85
2512 2878 1.153086 GGATGAGGTTGCGATGGCT 60.153 57.895 0.15 0.00 40.82 4.75
2513 2879 2.537560 CGGATGAGGTTGCGATGGC 61.538 63.158 0.00 0.00 40.52 4.40
2514 2880 2.537560 GCGGATGAGGTTGCGATGG 61.538 63.158 0.00 0.00 31.44 3.51
2515 2881 3.017323 GCGGATGAGGTTGCGATG 58.983 61.111 0.00 0.00 31.44 3.84


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

AutoCloner maintained by Alex Coulton.