Multiple sequence alignment - TraesCS5B01G548500

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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 TraesCS5B01G548500 chr5B 100.000 2991 0 0 1 2991 700996225 700999215 0.000000e+00 5524.0
1 TraesCS5B01G548500 chr5B 78.443 501 98 10 1358 1853 687223995 687224490 4.810000e-83 318.0
2 TraesCS5B01G548500 chr5D 94.114 1648 55 18 47 1682 549332193 549330576 0.000000e+00 2468.0
3 TraesCS5B01G548500 chr5D 81.743 849 79 33 2175 2991 549330019 549329215 9.040000e-180 640.0
4 TraesCS5B01G548500 chr5D 90.323 434 22 13 1680 2100 549330489 549330063 4.360000e-153 551.0
5 TraesCS5B01G548500 chr5D 79.200 500 96 8 1358 1853 544799360 544799855 1.030000e-89 340.0
6 TraesCS5B01G548500 chr5D 97.778 45 1 0 1 45 549332262 549332218 8.890000e-11 78.7
7 TraesCS5B01G548500 chr4A 92.436 1137 69 10 47 1172 621011375 621010245 0.000000e+00 1607.0
8 TraesCS5B01G548500 chr4A 92.689 807 27 20 1309 2100 621009788 621008999 0.000000e+00 1134.0
9 TraesCS5B01G548500 chr4A 80.222 809 87 35 2215 2991 621008896 621008129 9.430000e-150 540.0
10 TraesCS5B01G548500 chr4A 84.810 316 40 7 1365 1676 26413808 26413497 8.050000e-81 311.0
11 TraesCS5B01G548500 chr4A 95.556 45 2 0 1 45 621011443 621011399 4.140000e-09 73.1
12 TraesCS5B01G548500 chr3D 80.000 635 117 10 1360 1989 157443377 157442748 7.550000e-126 460.0
13 TraesCS5B01G548500 chr3D 93.750 48 2 1 2366 2413 587051418 587051464 1.490000e-08 71.3
14 TraesCS5B01G548500 chr3B 80.193 621 115 8 1360 1976 228690784 228690168 2.720000e-125 459.0
15 TraesCS5B01G548500 chr3A 80.161 620 114 8 1360 1973 170811690 170812306 3.510000e-124 455.0
16 TraesCS5B01G548500 chr4B 84.566 311 44 3 1362 1670 547205034 547205342 3.750000e-79 305.0
17 TraesCS5B01G548500 chr4D 75.382 524 119 9 1359 1877 441105777 441106295 8.280000e-61 244.0
18 TraesCS5B01G548500 chr4D 72.222 360 70 16 2320 2660 87413555 87413903 1.910000e-12 84.2
19 TraesCS5B01G548500 chr6D 76.498 217 39 11 2333 2545 430268631 430268423 1.130000e-19 108.0
20 TraesCS5B01G548500 chr7B 75.519 241 39 18 2290 2526 85306375 85306599 1.900000e-17 100.0
21 TraesCS5B01G548500 chr6A 78.363 171 25 8 2380 2543 482602933 482602768 1.900000e-17 100.0
22 TraesCS5B01G548500 chr7A 75.385 195 35 9 2355 2544 398939454 398939268 6.870000e-12 82.4
23 TraesCS5B01G548500 chr1D 75.401 187 36 9 2355 2538 135393962 135394141 6.870000e-12 82.4
24 TraesCS5B01G548500 chr7D 83.146 89 12 1 2460 2545 56525337 56525425 8.890000e-11 78.7
25 TraesCS5B01G548500 chr1A 75.127 197 34 11 2355 2545 161678169 161677982 8.890000e-11 78.7
26 TraesCS5B01G548500 chr2D 83.951 81 8 5 2333 2413 336734775 336734700 4.140000e-09 73.1


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 TraesCS5B01G548500 chr5B 700996225 700999215 2990 False 5524.000 5524 100.00000 1 2991 1 chr5B.!!$F2 2990
1 TraesCS5B01G548500 chr5D 549329215 549332262 3047 True 934.425 2468 90.98950 1 2991 4 chr5D.!!$R1 2990
2 TraesCS5B01G548500 chr4A 621008129 621011443 3314 True 838.525 1607 90.22575 1 2991 4 chr4A.!!$R2 2990
3 TraesCS5B01G548500 chr3D 157442748 157443377 629 True 460.000 460 80.00000 1360 1989 1 chr3D.!!$R1 629
4 TraesCS5B01G548500 chr3B 228690168 228690784 616 True 459.000 459 80.19300 1360 1976 1 chr3B.!!$R1 616
5 TraesCS5B01G548500 chr3A 170811690 170812306 616 False 455.000 455 80.16100 1360 1973 1 chr3A.!!$F1 613
6 TraesCS5B01G548500 chr4D 441105777 441106295 518 False 244.000 244 75.38200 1359 1877 1 chr4D.!!$F2 518

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
682 711 0.108186 TCTCAGTTAGGGCACATGCG 60.108 55.0 0.0 0.0 43.26 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2609 0.179119 GCTTGCATGGTTCCTGATGC 60.179 55.0 1.34 0.0 44.42 3.91 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
38 39 8.090788 AGTGTACATACAAGTCCCAATCTAAT 57.909 34.615 0.00 0.00 38.04 1.73
116 140 3.010420 CCTCCTGTTAGTTTAGCCAAGC 58.990 50.000 0.00 0.00 0.00 4.01
131 155 4.599041 AGCCAAGCTAAACCACATATCAA 58.401 39.130 0.00 0.00 36.99 2.57
155 181 0.840617 TGGCACTACCCTGACAACAA 59.159 50.000 0.00 0.00 37.83 2.83
157 183 1.812571 GGCACTACCCTGACAACAATG 59.187 52.381 0.00 0.00 0.00 2.82
249 275 0.249405 AGCGGTGGTGCAAAAACATG 60.249 50.000 0.00 0.00 37.31 3.21
285 311 2.614520 TGAAAATTTTGCGTCGGTGAGA 59.385 40.909 8.47 0.00 0.00 3.27
302 328 5.107182 CGGTGAGATATAAGTGATACGTCGT 60.107 44.000 2.21 2.21 0.00 4.34
304 330 6.796072 GGTGAGATATAAGTGATACGTCGTTC 59.204 42.308 1.78 1.91 0.00 3.95
378 405 4.800471 GTGGCATAATTAAAGCTTCAGCAC 59.200 41.667 0.00 7.92 45.16 4.40
379 406 4.462132 TGGCATAATTAAAGCTTCAGCACA 59.538 37.500 0.00 0.00 45.16 4.57
395 422 4.887071 TCAGCACACAATTGTCTAACCTTT 59.113 37.500 8.48 0.00 31.66 3.11
396 423 4.977963 CAGCACACAATTGTCTAACCTTTG 59.022 41.667 8.48 0.00 31.66 2.77
397 424 4.037923 AGCACACAATTGTCTAACCTTTGG 59.962 41.667 8.48 0.00 31.66 3.28
468 495 4.530875 ACAAATCCAGGTTGAGATCCATC 58.469 43.478 0.00 0.00 0.00 3.51
600 629 4.503714 TTGGTCAGACTCTTTGTTTCCT 57.496 40.909 0.00 0.00 0.00 3.36
654 683 1.276138 TGATTCTCTCACATGCACGGT 59.724 47.619 0.00 0.00 0.00 4.83
682 711 0.108186 TCTCAGTTAGGGCACATGCG 60.108 55.000 0.00 0.00 43.26 4.73
731 760 4.580868 GCCTAGTTAAACTTCTTGGAGCT 58.419 43.478 0.00 0.00 0.00 4.09
758 787 1.270305 ACATGGTGAACACGTCAGGAG 60.270 52.381 0.00 0.00 36.74 3.69
760 789 1.694844 TGGTGAACACGTCAGGAGTA 58.305 50.000 0.00 0.00 36.74 2.59
811 840 5.841810 TGTGCCAAAAGTCAAATAAGGAAG 58.158 37.500 0.00 0.00 0.00 3.46
992 1035 1.991264 CGCTGTGTCTGTCATCTTCAG 59.009 52.381 0.00 0.00 0.00 3.02
1141 1184 2.138179 GGCTCCGGCACTATGGGTA 61.138 63.158 0.00 0.00 40.87 3.69
1142 1185 1.692173 GGCTCCGGCACTATGGGTAA 61.692 60.000 0.00 0.00 40.87 2.85
1143 1186 0.249911 GCTCCGGCACTATGGGTAAG 60.250 60.000 0.00 0.00 38.54 2.34
1144 1187 1.120530 CTCCGGCACTATGGGTAAGT 58.879 55.000 0.00 0.00 0.00 2.24
1186 1233 7.265673 TCTTTACTTTCCTGTATCATTCTCCG 58.734 38.462 0.00 0.00 0.00 4.63
1201 1248 2.985001 TCCGGTGGAGAGTGCATAA 58.015 52.632 0.00 0.00 0.00 1.90
1203 1250 0.806102 CCGGTGGAGAGTGCATAACG 60.806 60.000 0.00 0.00 0.00 3.18
1204 1251 0.108804 CGGTGGAGAGTGCATAACGT 60.109 55.000 0.00 0.00 0.00 3.99
1205 1252 1.133598 CGGTGGAGAGTGCATAACGTA 59.866 52.381 0.00 0.00 0.00 3.57
1206 1253 2.537401 GGTGGAGAGTGCATAACGTAC 58.463 52.381 0.00 0.00 0.00 3.67
1207 1254 2.182825 GTGGAGAGTGCATAACGTACG 58.817 52.381 15.01 15.01 35.00 3.67
1226 1273 6.369890 ACGTACGTCTAAATCTCTAGTTGTGA 59.630 38.462 16.72 0.00 0.00 3.58
1229 1276 7.216973 ACGTCTAAATCTCTAGTTGTGAAGT 57.783 36.000 0.00 0.00 0.00 3.01
1239 1286 8.780846 TCTCTAGTTGTGAAGTGTGTTTAAAA 57.219 30.769 0.00 0.00 0.00 1.52
1295 1648 7.066781 TGGTGTGATATACTCTACTCATCCAA 58.933 38.462 0.00 0.00 0.00 3.53
1296 1649 7.563556 TGGTGTGATATACTCTACTCATCCAAA 59.436 37.037 0.00 0.00 0.00 3.28
1297 1650 8.589338 GGTGTGATATACTCTACTCATCCAAAT 58.411 37.037 0.00 0.00 0.00 2.32
1298 1651 9.632807 GTGTGATATACTCTACTCATCCAAATC 57.367 37.037 0.00 0.00 0.00 2.17
1335 1706 8.741603 ATGTTGATCTGATGATGTTTGTATCA 57.258 30.769 0.00 0.00 41.00 2.15
1344 1715 9.983804 CTGATGATGTTTGTATCATATGTATGC 57.016 33.333 1.90 0.16 45.30 3.14
1345 1716 9.729281 TGATGATGTTTGTATCATATGTATGCT 57.271 29.630 1.90 0.00 45.30 3.79
1347 1718 8.552083 TGATGTTTGTATCATATGTATGCTCC 57.448 34.615 1.90 0.00 32.39 4.70
1348 1719 8.156165 TGATGTTTGTATCATATGTATGCTCCA 58.844 33.333 1.90 0.00 32.39 3.86
1349 1720 9.170734 GATGTTTGTATCATATGTATGCTCCAT 57.829 33.333 1.90 0.00 33.76 3.41
1350 1721 8.326680 TGTTTGTATCATATGTATGCTCCATG 57.673 34.615 1.90 0.00 33.76 3.66
1351 1722 7.938490 TGTTTGTATCATATGTATGCTCCATGT 59.062 33.333 1.90 0.00 33.76 3.21
1976 2440 1.198759 GGCCACCTACACTTCCTGGA 61.199 60.000 0.00 0.00 0.00 3.86
1992 2456 4.873010 TCCTGGATCAACTTCTACTAGCT 58.127 43.478 0.00 0.00 0.00 3.32
1993 2457 6.014771 TCCTGGATCAACTTCTACTAGCTA 57.985 41.667 0.00 0.00 0.00 3.32
1994 2458 6.065374 TCCTGGATCAACTTCTACTAGCTAG 58.935 44.000 19.44 19.44 0.00 3.42
1995 2459 5.278758 CCTGGATCAACTTCTACTAGCTAGC 60.279 48.000 20.91 6.62 0.00 3.42
1996 2460 4.276183 TGGATCAACTTCTACTAGCTAGCG 59.724 45.833 20.91 12.04 0.00 4.26
1998 2462 2.950309 TCAACTTCTACTAGCTAGCGGG 59.050 50.000 20.91 10.74 0.00 6.13
1999 2463 2.950309 CAACTTCTACTAGCTAGCGGGA 59.050 50.000 20.91 12.82 0.00 5.14
2000 2464 3.294038 ACTTCTACTAGCTAGCGGGAA 57.706 47.619 20.91 18.50 0.00 3.97
2001 2465 3.834938 ACTTCTACTAGCTAGCGGGAAT 58.165 45.455 20.91 2.54 0.00 3.01
2002 2466 3.570550 ACTTCTACTAGCTAGCGGGAATG 59.429 47.826 20.91 15.42 0.00 2.67
2004 2468 0.596577 TACTAGCTAGCGGGAATGCG 59.403 55.000 20.91 0.00 40.67 4.73
2005 2469 1.373497 CTAGCTAGCGGGAATGCGG 60.373 63.158 8.05 0.00 40.67 5.69
2006 2470 2.771763 CTAGCTAGCGGGAATGCGGG 62.772 65.000 8.05 0.00 40.67 6.13
2017 2491 1.284982 GAATGCGGGATCATCGACGG 61.285 60.000 11.13 0.00 0.00 4.79
2025 2499 1.485838 GATCATCGACGGCACTGCTG 61.486 60.000 8.40 8.40 41.29 4.41
2039 2513 4.153835 GGCACTGCTGCTTAATCTATCATC 59.846 45.833 0.00 0.00 43.66 2.92
2040 2514 4.996122 GCACTGCTGCTTAATCTATCATCT 59.004 41.667 0.00 0.00 40.63 2.90
2041 2515 5.469421 GCACTGCTGCTTAATCTATCATCTT 59.531 40.000 0.00 0.00 40.63 2.40
2094 2571 3.093278 GCCCTCTGTTGCGATTCG 58.907 61.111 0.62 0.62 0.00 3.34
2124 2601 4.853924 ACTTGTGTTTTAGATGGGCTTG 57.146 40.909 0.00 0.00 0.00 4.01
2125 2602 3.005791 ACTTGTGTTTTAGATGGGCTTGC 59.994 43.478 0.00 0.00 0.00 4.01
2126 2603 1.539388 TGTGTTTTAGATGGGCTTGCG 59.461 47.619 0.00 0.00 0.00 4.85
2127 2604 1.539827 GTGTTTTAGATGGGCTTGCGT 59.460 47.619 0.00 0.00 0.00 5.24
2128 2605 2.745281 GTGTTTTAGATGGGCTTGCGTA 59.255 45.455 0.00 0.00 0.00 4.42
2130 2607 4.013728 TGTTTTAGATGGGCTTGCGTATT 58.986 39.130 0.00 0.00 0.00 1.89
2131 2608 5.065474 GTGTTTTAGATGGGCTTGCGTATTA 59.935 40.000 0.00 0.00 0.00 0.98
2132 2609 5.295787 TGTTTTAGATGGGCTTGCGTATTAG 59.704 40.000 0.00 0.00 0.00 1.73
2134 2611 1.140852 AGATGGGCTTGCGTATTAGCA 59.859 47.619 0.00 0.00 46.54 3.49
2147 2624 3.187227 CGTATTAGCATCAGGAACCATGC 59.813 47.826 7.72 7.72 43.25 4.06
2149 2626 2.804986 TAGCATCAGGAACCATGCAA 57.195 45.000 15.19 0.00 44.77 4.08
2150 2627 1.471119 AGCATCAGGAACCATGCAAG 58.529 50.000 15.19 0.00 44.77 4.01
2151 2628 0.179119 GCATCAGGAACCATGCAAGC 60.179 55.000 10.07 0.00 42.68 4.01
2152 2629 1.179152 CATCAGGAACCATGCAAGCA 58.821 50.000 0.00 0.00 0.00 3.91
2153 2630 1.135199 CATCAGGAACCATGCAAGCAC 60.135 52.381 0.00 0.00 0.00 4.40
2155 2632 2.126346 GGAACCATGCAAGCACGC 60.126 61.111 0.00 0.00 0.00 5.34
2157 2634 1.007502 GAACCATGCAAGCACGCAA 60.008 52.632 4.03 0.00 46.87 4.85
2158 2635 1.277495 GAACCATGCAAGCACGCAAC 61.277 55.000 4.03 0.00 46.87 4.17
2159 2636 2.431260 CCATGCAAGCACGCAACC 60.431 61.111 4.03 0.00 46.87 3.77
2160 2637 2.335729 CATGCAAGCACGCAACCA 59.664 55.556 4.03 0.00 46.87 3.67
2161 2638 1.300003 CATGCAAGCACGCAACCAA 60.300 52.632 4.03 0.00 46.87 3.67
2162 2639 1.007038 ATGCAAGCACGCAACCAAG 60.007 52.632 4.03 0.00 46.87 3.61
2163 2640 1.454572 ATGCAAGCACGCAACCAAGA 61.455 50.000 4.03 0.00 46.87 3.02
2164 2641 1.065600 GCAAGCACGCAACCAAGAA 59.934 52.632 0.00 0.00 0.00 2.52
2165 2642 0.318955 GCAAGCACGCAACCAAGAAT 60.319 50.000 0.00 0.00 0.00 2.40
2166 2643 1.869342 GCAAGCACGCAACCAAGAATT 60.869 47.619 0.00 0.00 0.00 2.17
2195 2672 2.476619 CACACTCTTTCTTGCACCTACG 59.523 50.000 0.00 0.00 0.00 3.51
2240 2730 1.330306 GCACACAATGCGCAACTAAG 58.670 50.000 17.11 6.42 46.55 2.18
2243 2733 3.825308 CACACAATGCGCAACTAAGAAT 58.175 40.909 17.11 0.00 0.00 2.40
2244 2734 4.229096 CACACAATGCGCAACTAAGAATT 58.771 39.130 17.11 0.00 0.00 2.17
2255 2745 7.753132 TGCGCAACTAAGAATTATTGTAAAAGG 59.247 33.333 8.16 0.00 0.00 3.11
2285 2775 2.205074 CGAAATGAAGACGGCATAGCT 58.795 47.619 0.00 0.00 0.00 3.32
2286 2776 3.181479 ACGAAATGAAGACGGCATAGCTA 60.181 43.478 0.00 0.00 0.00 3.32
2287 2777 3.426859 CGAAATGAAGACGGCATAGCTAG 59.573 47.826 0.00 0.00 0.00 3.42
2288 2778 4.372656 GAAATGAAGACGGCATAGCTAGT 58.627 43.478 0.00 0.00 0.00 2.57
2300 2790 0.189080 TAGCTAGTGGGGGCGGATTA 59.811 55.000 0.00 0.00 0.00 1.75
2350 2842 7.173047 GCAATCCATTTTTCTTTTGGCTTTCTA 59.827 33.333 0.00 0.00 0.00 2.10
2420 2912 9.729023 TTAAGTTTCGTTTGCATATATTCATGG 57.271 29.630 0.00 0.00 0.00 3.66
2430 2922 7.500720 TGCATATATTCATGGTTCTTGTGAG 57.499 36.000 0.00 0.00 0.00 3.51
2433 2925 7.308229 GCATATATTCATGGTTCTTGTGAGGAC 60.308 40.741 0.00 0.00 0.00 3.85
2435 2927 1.691976 TCATGGTTCTTGTGAGGACGT 59.308 47.619 0.00 0.00 31.60 4.34
2436 2928 2.104111 TCATGGTTCTTGTGAGGACGTT 59.896 45.455 0.00 0.00 31.60 3.99
2438 2930 2.557317 TGGTTCTTGTGAGGACGTTTC 58.443 47.619 0.00 0.00 31.60 2.78
2440 2932 2.801111 GGTTCTTGTGAGGACGTTTCTC 59.199 50.000 11.44 11.44 31.60 2.87
2441 2933 3.454375 GTTCTTGTGAGGACGTTTCTCA 58.546 45.455 15.54 15.54 38.75 3.27
2444 2936 3.869246 TCTTGTGAGGACGTTTCTCAAAC 59.131 43.478 19.45 11.60 42.13 2.93
2454 2946 3.039670 GTTTCTCAAACGCGATCCATC 57.960 47.619 15.93 0.00 0.00 3.51
2461 2953 4.438148 TCAAACGCGATCCATCTTGAATA 58.562 39.130 15.93 0.00 0.00 1.75
2462 2954 4.270084 TCAAACGCGATCCATCTTGAATAC 59.730 41.667 15.93 0.00 0.00 1.89
2463 2955 3.452755 ACGCGATCCATCTTGAATACA 57.547 42.857 15.93 0.00 0.00 2.29
2464 2956 3.995199 ACGCGATCCATCTTGAATACAT 58.005 40.909 15.93 0.00 0.00 2.29
2465 2957 4.380531 ACGCGATCCATCTTGAATACATT 58.619 39.130 15.93 0.00 0.00 2.71
2466 2958 4.816385 ACGCGATCCATCTTGAATACATTT 59.184 37.500 15.93 0.00 0.00 2.32
2467 2959 5.296780 ACGCGATCCATCTTGAATACATTTT 59.703 36.000 15.93 0.00 0.00 1.82
2468 2960 5.622448 CGCGATCCATCTTGAATACATTTTG 59.378 40.000 0.00 0.00 0.00 2.44
2469 2961 6.511605 CGCGATCCATCTTGAATACATTTTGA 60.512 38.462 0.00 0.00 0.00 2.69
2470 2962 6.634436 GCGATCCATCTTGAATACATTTTGAC 59.366 38.462 0.00 0.00 0.00 3.18
2471 2963 6.847792 CGATCCATCTTGAATACATTTTGACG 59.152 38.462 0.00 0.00 0.00 4.35
2472 2964 7.254421 CGATCCATCTTGAATACATTTTGACGA 60.254 37.037 0.00 0.00 0.00 4.20
2473 2965 7.307493 TCCATCTTGAATACATTTTGACGAG 57.693 36.000 0.00 0.00 0.00 4.18
2474 2966 6.878923 TCCATCTTGAATACATTTTGACGAGT 59.121 34.615 0.00 0.00 0.00 4.18
2475 2967 7.390440 TCCATCTTGAATACATTTTGACGAGTT 59.610 33.333 0.00 0.00 0.00 3.01
2476 2968 8.023128 CCATCTTGAATACATTTTGACGAGTTT 58.977 33.333 0.00 0.00 0.00 2.66
2477 2969 9.055248 CATCTTGAATACATTTTGACGAGTTTC 57.945 33.333 0.00 0.00 0.00 2.78
2478 2970 8.378172 TCTTGAATACATTTTGACGAGTTTCT 57.622 30.769 0.00 0.00 0.00 2.52
2479 2971 9.483916 TCTTGAATACATTTTGACGAGTTTCTA 57.516 29.630 0.00 0.00 0.00 2.10
2480 2972 9.746711 CTTGAATACATTTTGACGAGTTTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
2481 2973 9.483916 TTGAATACATTTTGACGAGTTTCTAGA 57.516 29.630 0.00 0.00 0.00 2.43
2482 2974 9.483916 TGAATACATTTTGACGAGTTTCTAGAA 57.516 29.630 0.00 0.00 0.00 2.10
2483 2975 9.742552 GAATACATTTTGACGAGTTTCTAGAAC 57.257 33.333 4.18 0.89 0.00 3.01
2484 2976 9.490379 AATACATTTTGACGAGTTTCTAGAACT 57.510 29.630 4.18 6.00 0.00 3.01
2485 2977 7.787725 ACATTTTGACGAGTTTCTAGAACTT 57.212 32.000 4.18 0.00 0.00 2.66
2486 2978 7.852516 ACATTTTGACGAGTTTCTAGAACTTC 58.147 34.615 4.18 5.10 0.00 3.01
2487 2979 6.839820 TTTTGACGAGTTTCTAGAACTTCC 57.160 37.500 4.18 0.00 0.00 3.46
2518 3010 4.756642 TCAACTGCTGAAACTTGGTATGAG 59.243 41.667 0.00 0.00 0.00 2.90
2519 3011 3.077359 ACTGCTGAAACTTGGTATGAGC 58.923 45.455 0.00 0.00 0.00 4.26
2520 3012 2.076100 TGCTGAAACTTGGTATGAGCG 58.924 47.619 0.00 0.00 0.00 5.03
2523 3015 3.424962 GCTGAAACTTGGTATGAGCGAAC 60.425 47.826 0.00 0.00 0.00 3.95
2524 3016 3.734463 TGAAACTTGGTATGAGCGAACA 58.266 40.909 0.00 0.00 0.00 3.18
2525 3017 4.130857 TGAAACTTGGTATGAGCGAACAA 58.869 39.130 0.00 0.00 0.00 2.83
2528 3020 5.705609 AACTTGGTATGAGCGAACAAAAT 57.294 34.783 0.00 0.00 0.00 1.82
2529 3021 5.296813 ACTTGGTATGAGCGAACAAAATC 57.703 39.130 0.00 0.00 0.00 2.17
2530 3022 4.142902 ACTTGGTATGAGCGAACAAAATCG 60.143 41.667 0.00 0.00 45.41 3.34
2532 3024 4.496360 TGGTATGAGCGAACAAAATCGTA 58.504 39.130 0.00 0.00 44.49 3.43
2533 3025 4.930405 TGGTATGAGCGAACAAAATCGTAA 59.070 37.500 0.00 0.00 44.49 3.18
2534 3026 5.062934 TGGTATGAGCGAACAAAATCGTAAG 59.937 40.000 0.00 0.00 44.49 2.34
2535 3027 5.063060 GGTATGAGCGAACAAAATCGTAAGT 59.937 40.000 0.00 0.00 44.49 2.24
2536 3028 5.607119 ATGAGCGAACAAAATCGTAAGTT 57.393 34.783 0.00 0.00 44.49 2.66
2537 3029 5.412526 TGAGCGAACAAAATCGTAAGTTT 57.587 34.783 0.00 0.00 44.49 2.66
2538 3030 5.437263 TGAGCGAACAAAATCGTAAGTTTC 58.563 37.500 0.00 0.00 44.49 2.78
2539 3031 5.006844 TGAGCGAACAAAATCGTAAGTTTCA 59.993 36.000 0.00 0.00 44.49 2.69
2540 3032 5.997385 AGCGAACAAAATCGTAAGTTTCAT 58.003 33.333 0.00 0.00 44.49 2.57
2543 3035 8.071368 AGCGAACAAAATCGTAAGTTTCATAAA 58.929 29.630 0.00 0.00 44.49 1.40
2544 3036 8.145312 GCGAACAAAATCGTAAGTTTCATAAAC 58.855 33.333 0.00 0.00 44.49 2.01
2545 3037 9.160576 CGAACAAAATCGTAAGTTTCATAAACA 57.839 29.630 5.42 0.00 39.58 2.83
2550 3042 9.673454 AAAATCGTAAGTTTCATAAACAAGACC 57.327 29.630 5.42 0.00 43.79 3.85
2551 3043 6.790285 TCGTAAGTTTCATAAACAAGACCC 57.210 37.500 5.42 0.00 43.79 4.46
2560 3058 0.036306 AAACAAGACCCGTGCCCTAG 59.964 55.000 0.00 0.00 0.00 3.02
2572 3070 3.006728 CCCTAGTGCGGGGTCCAA 61.007 66.667 0.00 0.00 40.75 3.53
2576 3074 2.830704 CTAGTGCGGGGTCCAACGAC 62.831 65.000 9.16 5.03 38.38 4.34
2620 3118 2.668632 CCCGGCAAGGCTAGACAA 59.331 61.111 0.00 0.00 39.21 3.18
2641 3139 2.031012 CGTGCTCCTTCACCTGCA 59.969 61.111 0.00 0.00 33.57 4.41
2676 3174 3.795623 TCCGAGCATACTTCCAACTAC 57.204 47.619 0.00 0.00 0.00 2.73
2691 3195 4.530553 TCCAACTACAGCCATTTCACTAGA 59.469 41.667 0.00 0.00 0.00 2.43
2723 3235 3.825014 ACCGAGCTAAACTAGTCACTTGA 59.175 43.478 0.00 0.00 0.00 3.02
2732 3244 7.095017 GCTAAACTAGTCACTTGAGAAAGCAAT 60.095 37.037 0.00 0.00 0.00 3.56
2735 3247 6.291377 ACTAGTCACTTGAGAAAGCAATTCA 58.709 36.000 0.00 0.00 40.72 2.57
2737 3249 6.455360 AGTCACTTGAGAAAGCAATTCAAA 57.545 33.333 5.24 0.00 40.72 2.69
2768 3280 4.332543 AGCCCCACCTCCCTCGAA 62.333 66.667 0.00 0.00 0.00 3.71
2772 3284 0.983378 CCCCACCTCCCTCGAAGAAT 60.983 60.000 0.00 0.00 34.09 2.40
2773 3285 1.691482 CCCCACCTCCCTCGAAGAATA 60.691 57.143 0.00 0.00 34.09 1.75
2778 3290 2.228059 CCTCCCTCGAAGAATACGCTA 58.772 52.381 0.00 0.00 34.09 4.26
2794 3308 0.657840 GCTACCATTGGACATGACGC 59.342 55.000 10.37 0.00 0.00 5.19
2836 3350 1.307084 AAGGTGGTAGGGGGAGCTC 60.307 63.158 4.71 4.71 0.00 4.09
2902 3416 1.168714 CTTGCTTTTCGAGGAAGGGG 58.831 55.000 11.20 0.00 46.63 4.79
2906 3420 1.544759 GCTTTTCGAGGAAGGGGTGAA 60.545 52.381 11.20 0.00 0.00 3.18
2917 3431 0.771755 AGGGGTGAAGTGGTTTCCTC 59.228 55.000 0.00 0.00 34.77 3.71
2918 3432 0.476771 GGGGTGAAGTGGTTTCCTCA 59.523 55.000 0.00 0.00 34.77 3.86
2922 3436 3.263425 GGGTGAAGTGGTTTCCTCATCTA 59.737 47.826 0.00 0.00 34.77 1.98
2928 3442 4.899502 AGTGGTTTCCTCATCTACACAAG 58.100 43.478 0.00 0.00 0.00 3.16
2940 3455 2.093869 TCTACACAAGATACAACGGGGC 60.094 50.000 0.00 0.00 0.00 5.80
2960 3475 3.740832 GGCTTTTTGCACACAATAAGGTC 59.259 43.478 9.83 0.00 42.04 3.85
2977 3492 2.220586 TCCCAACGAGCCACCATCA 61.221 57.895 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.878116 AGGTATGCTACGCACTAAATTTCAA 59.122 36.000 0.00 0.00 43.04 2.69
45 46 2.031420 CGCTAGGTATGCTACGCACTAA 60.031 50.000 0.00 0.00 43.04 2.24
116 140 6.531240 GTGCCATGTTTTGATATGTGGTTTAG 59.469 38.462 0.00 0.00 0.00 1.85
121 145 4.724074 AGTGCCATGTTTTGATATGTGG 57.276 40.909 0.00 0.00 0.00 4.17
155 181 3.154710 CATGAGCCTATGTGCATTCCAT 58.845 45.455 0.00 0.00 0.00 3.41
157 183 2.579873 ACATGAGCCTATGTGCATTCC 58.420 47.619 0.00 0.00 39.68 3.01
179 205 1.302033 ACACAAGGCAAGAGCTCCG 60.302 57.895 10.93 2.85 41.70 4.63
266 292 3.915437 ATCTCACCGACGCAAAATTTT 57.085 38.095 0.00 0.00 0.00 1.82
273 299 2.946990 TCACTTATATCTCACCGACGCA 59.053 45.455 0.00 0.00 0.00 5.24
285 311 7.803659 CACATCTGAACGACGTATCACTTATAT 59.196 37.037 0.00 0.00 0.00 0.86
302 328 8.659925 AATTAACATGTTTTTGCACATCTGAA 57.340 26.923 17.78 0.03 35.03 3.02
304 330 9.160576 CAAAATTAACATGTTTTTGCACATCTG 57.839 29.630 17.78 2.27 35.03 2.90
378 405 3.564511 CGCCAAAGGTTAGACAATTGTG 58.435 45.455 17.58 0.00 0.00 3.33
379 406 2.556622 CCGCCAAAGGTTAGACAATTGT 59.443 45.455 11.78 11.78 0.00 2.71
468 495 2.224161 CCAGCTCTAAATCTCCTTCCGG 60.224 54.545 0.00 0.00 0.00 5.14
483 510 6.803642 ATTTAATGAAAATCAGCTCCAGCTC 58.196 36.000 0.00 0.00 39.26 4.09
600 629 6.729690 AAAATTCAACCAGAACAAGATGGA 57.270 33.333 0.00 0.00 39.49 3.41
654 683 2.187958 CCCTAACTGAGATCCACACCA 58.812 52.381 0.00 0.00 0.00 4.17
731 760 3.275143 ACGTGTTCACCATGTTCTTGAA 58.725 40.909 0.00 0.00 40.46 2.69
811 840 1.984288 AACTTAGCCGCCCTCCATCC 61.984 60.000 0.00 0.00 0.00 3.51
863 901 3.345508 TGATGAGCATGCATATCCTCC 57.654 47.619 21.98 2.46 0.00 4.30
992 1035 1.125633 ATGCTTCCCCATTGGATTGC 58.874 50.000 3.62 3.84 44.66 3.56
1141 1184 0.765510 AGCGGAAGGGAAACTGACTT 59.234 50.000 0.00 0.00 0.00 3.01
1142 1185 0.765510 AAGCGGAAGGGAAACTGACT 59.234 50.000 0.00 0.00 0.00 3.41
1143 1186 1.157585 GAAGCGGAAGGGAAACTGAC 58.842 55.000 0.00 0.00 0.00 3.51
1144 1187 1.056660 AGAAGCGGAAGGGAAACTGA 58.943 50.000 0.00 0.00 0.00 3.41
1186 1233 2.537401 GTACGTTATGCACTCTCCACC 58.463 52.381 0.00 0.00 0.00 4.61
1201 1248 6.369890 TCACAACTAGAGATTTAGACGTACGT 59.630 38.462 23.04 23.04 0.00 3.57
1203 1250 8.235905 ACTTCACAACTAGAGATTTAGACGTAC 58.764 37.037 0.00 0.00 0.00 3.67
1204 1251 8.235226 CACTTCACAACTAGAGATTTAGACGTA 58.765 37.037 0.00 0.00 0.00 3.57
1205 1252 7.085116 CACTTCACAACTAGAGATTTAGACGT 58.915 38.462 0.00 0.00 0.00 4.34
1206 1253 7.061210 CACACTTCACAACTAGAGATTTAGACG 59.939 40.741 0.00 0.00 0.00 4.18
1207 1254 7.868415 ACACACTTCACAACTAGAGATTTAGAC 59.132 37.037 0.00 0.00 0.00 2.59
1226 1273 8.026396 TCTACTCTACCCTTTTAAACACACTT 57.974 34.615 0.00 0.00 0.00 3.16
1229 1276 9.856162 AAAATCTACTCTACCCTTTTAAACACA 57.144 29.630 0.00 0.00 0.00 3.72
1263 1613 7.928103 AGTAGAGTATATCACACCAAACGTAG 58.072 38.462 0.00 0.00 0.00 3.51
1295 1648 6.598457 CAGATCAACATCACTTCTCCTTGATT 59.402 38.462 0.00 0.00 30.35 2.57
1296 1649 6.070366 TCAGATCAACATCACTTCTCCTTGAT 60.070 38.462 0.00 0.00 32.35 2.57
1297 1650 5.246883 TCAGATCAACATCACTTCTCCTTGA 59.753 40.000 0.00 0.00 0.00 3.02
1298 1651 5.485620 TCAGATCAACATCACTTCTCCTTG 58.514 41.667 0.00 0.00 0.00 3.61
1335 1706 7.567458 TGCATACATACATGGAGCATACATAT 58.433 34.615 0.00 0.00 31.44 1.78
1342 1713 2.705127 TCCTGCATACATACATGGAGCA 59.295 45.455 0.00 0.00 41.56 4.26
1343 1714 3.332919 CTCCTGCATACATACATGGAGC 58.667 50.000 0.00 0.00 41.56 4.70
1344 1715 3.867600 GCCTCCTGCATACATACATGGAG 60.868 52.174 6.00 6.00 42.29 3.86
1345 1716 2.038952 GCCTCCTGCATACATACATGGA 59.961 50.000 0.00 0.00 40.77 3.41
1346 1717 2.430465 GCCTCCTGCATACATACATGG 58.570 52.381 0.00 0.00 40.77 3.66
1347 1718 2.071540 CGCCTCCTGCATACATACATG 58.928 52.381 0.00 0.00 41.33 3.21
1348 1719 1.609061 GCGCCTCCTGCATACATACAT 60.609 52.381 0.00 0.00 41.33 2.29
1349 1720 0.249868 GCGCCTCCTGCATACATACA 60.250 55.000 0.00 0.00 41.33 2.29
1350 1721 1.284982 CGCGCCTCCTGCATACATAC 61.285 60.000 0.00 0.00 41.33 2.39
1351 1722 1.006220 CGCGCCTCCTGCATACATA 60.006 57.895 0.00 0.00 41.33 2.29
1976 2440 3.570550 CCCGCTAGCTAGTAGAAGTTGAT 59.429 47.826 21.62 0.00 0.00 2.57
1992 2456 1.480212 ATGATCCCGCATTCCCGCTA 61.480 55.000 0.00 0.00 0.00 4.26
1993 2457 2.738213 GATGATCCCGCATTCCCGCT 62.738 60.000 0.00 0.00 0.00 5.52
1994 2458 2.281761 ATGATCCCGCATTCCCGC 60.282 61.111 0.00 0.00 0.00 6.13
1995 2459 2.029288 CGATGATCCCGCATTCCCG 61.029 63.158 0.00 0.00 0.00 5.14
1996 2460 0.951040 GTCGATGATCCCGCATTCCC 60.951 60.000 0.00 0.00 0.00 3.97
1998 2462 1.284982 CCGTCGATGATCCCGCATTC 61.285 60.000 6.11 0.00 0.00 2.67
1999 2463 1.300931 CCGTCGATGATCCCGCATT 60.301 57.895 6.11 0.00 0.00 3.56
2000 2464 2.340078 CCGTCGATGATCCCGCAT 59.660 61.111 6.11 0.00 0.00 4.73
2001 2465 4.585526 GCCGTCGATGATCCCGCA 62.586 66.667 6.11 0.00 0.00 5.69
2002 2466 4.585526 TGCCGTCGATGATCCCGC 62.586 66.667 6.11 0.72 0.00 6.13
2004 2468 1.592669 CAGTGCCGTCGATGATCCC 60.593 63.158 6.11 0.00 0.00 3.85
2005 2469 2.240500 GCAGTGCCGTCGATGATCC 61.241 63.158 6.11 0.00 0.00 3.36
2006 2470 1.227089 AGCAGTGCCGTCGATGATC 60.227 57.895 12.58 0.00 0.00 2.92
2053 2527 7.040271 GGCGCCCCTTATGAATTTTAATACTTA 60.040 37.037 18.11 0.00 0.00 2.24
2098 2575 9.337396 CAAGCCCATCTAAAACACAAGTATATA 57.663 33.333 0.00 0.00 0.00 0.86
2099 2576 7.201821 GCAAGCCCATCTAAAACACAAGTATAT 60.202 37.037 0.00 0.00 0.00 0.86
2113 2590 2.367241 TGCTAATACGCAAGCCCATCTA 59.633 45.455 0.00 0.00 45.62 1.98
2114 2591 1.140852 TGCTAATACGCAAGCCCATCT 59.859 47.619 0.00 0.00 45.62 2.90
2115 2592 1.593196 TGCTAATACGCAAGCCCATC 58.407 50.000 0.00 0.00 45.62 3.51
2117 2594 1.134250 TGATGCTAATACGCAAGCCCA 60.134 47.619 0.00 0.00 44.06 5.36
2118 2595 1.532868 CTGATGCTAATACGCAAGCCC 59.467 52.381 0.00 0.00 44.06 5.19
2119 2596 1.532868 CCTGATGCTAATACGCAAGCC 59.467 52.381 0.00 0.00 44.06 4.35
2122 2599 3.202906 GGTTCCTGATGCTAATACGCAA 58.797 45.455 0.00 0.00 44.06 4.85
2123 2600 2.169561 TGGTTCCTGATGCTAATACGCA 59.830 45.455 0.00 0.00 45.10 5.24
2124 2601 2.833794 TGGTTCCTGATGCTAATACGC 58.166 47.619 0.00 0.00 0.00 4.42
2125 2602 3.187227 GCATGGTTCCTGATGCTAATACG 59.813 47.826 0.00 0.00 41.52 3.06
2126 2603 4.136796 TGCATGGTTCCTGATGCTAATAC 58.863 43.478 12.91 0.00 44.46 1.89
2127 2604 4.436113 TGCATGGTTCCTGATGCTAATA 57.564 40.909 12.91 0.00 44.46 0.98
2128 2605 3.301794 TGCATGGTTCCTGATGCTAAT 57.698 42.857 12.91 0.00 44.46 1.73
2130 2607 2.646930 CTTGCATGGTTCCTGATGCTA 58.353 47.619 12.91 6.82 44.46 3.49
2131 2608 1.471119 CTTGCATGGTTCCTGATGCT 58.529 50.000 12.91 0.00 44.46 3.79
2132 2609 0.179119 GCTTGCATGGTTCCTGATGC 60.179 55.000 1.34 0.00 44.42 3.91
2134 2611 1.180029 GTGCTTGCATGGTTCCTGAT 58.820 50.000 0.00 0.00 0.00 2.90
2135 2612 1.236616 CGTGCTTGCATGGTTCCTGA 61.237 55.000 6.91 0.00 0.00 3.86
2136 2613 1.210931 CGTGCTTGCATGGTTCCTG 59.789 57.895 6.91 0.00 0.00 3.86
2137 2614 2.629656 GCGTGCTTGCATGGTTCCT 61.630 57.895 15.43 0.00 34.15 3.36
2138 2615 2.126346 GCGTGCTTGCATGGTTCC 60.126 61.111 15.43 0.00 34.15 3.62
2139 2616 1.007502 TTGCGTGCTTGCATGGTTC 60.008 52.632 15.43 1.35 45.78 3.62
2140 2617 1.300080 GTTGCGTGCTTGCATGGTT 60.300 52.632 15.43 0.00 45.78 3.67
2141 2618 2.336088 GTTGCGTGCTTGCATGGT 59.664 55.556 15.43 0.00 45.78 3.55
2142 2619 2.431260 GGTTGCGTGCTTGCATGG 60.431 61.111 15.43 4.89 45.78 3.66
2147 2624 1.788308 CAATTCTTGGTTGCGTGCTTG 59.212 47.619 0.00 0.00 0.00 4.01
2149 2626 0.314935 CCAATTCTTGGTTGCGTGCT 59.685 50.000 0.00 0.00 45.93 4.40
2150 2627 2.813100 CCAATTCTTGGTTGCGTGC 58.187 52.632 0.00 0.00 45.93 5.34
2169 2646 3.625764 GGTGCAAGAAAGAGTGTGTTACA 59.374 43.478 0.00 0.00 0.00 2.41
2170 2647 3.877508 AGGTGCAAGAAAGAGTGTGTTAC 59.122 43.478 0.00 0.00 0.00 2.50
2171 2648 4.150897 AGGTGCAAGAAAGAGTGTGTTA 57.849 40.909 0.00 0.00 0.00 2.41
2172 2649 3.004752 AGGTGCAAGAAAGAGTGTGTT 57.995 42.857 0.00 0.00 0.00 3.32
2173 2650 2.717639 AGGTGCAAGAAAGAGTGTGT 57.282 45.000 0.00 0.00 0.00 3.72
2209 2693 0.459489 TTGTGTGCTTGCCTGGTTTC 59.541 50.000 0.00 0.00 0.00 2.78
2255 2745 5.283012 GCCGTCTTCATTTCGTACAATTTTC 59.717 40.000 0.00 0.00 0.00 2.29
2285 2775 1.383386 TGCTAATCCGCCCCCACTA 60.383 57.895 0.00 0.00 0.00 2.74
2286 2776 2.690881 TGCTAATCCGCCCCCACT 60.691 61.111 0.00 0.00 0.00 4.00
2287 2777 2.203209 CTGCTAATCCGCCCCCAC 60.203 66.667 0.00 0.00 0.00 4.61
2288 2778 4.189580 GCTGCTAATCCGCCCCCA 62.190 66.667 0.00 0.00 0.00 4.96
2320 2810 4.456914 CAAAAGAAAAATGGATTGCGTGC 58.543 39.130 0.00 0.00 0.00 5.34
2403 2895 8.190122 TCACAAGAACCATGAATATATGCAAAC 58.810 33.333 0.00 0.00 0.00 2.93
2413 2905 3.244561 ACGTCCTCACAAGAACCATGAAT 60.245 43.478 0.00 0.00 0.00 2.57
2415 2907 1.691976 ACGTCCTCACAAGAACCATGA 59.308 47.619 0.00 0.00 0.00 3.07
2416 2908 2.169832 ACGTCCTCACAAGAACCATG 57.830 50.000 0.00 0.00 0.00 3.66
2417 2909 2.930826 AACGTCCTCACAAGAACCAT 57.069 45.000 0.00 0.00 0.00 3.55
2420 2912 3.454375 TGAGAAACGTCCTCACAAGAAC 58.546 45.455 14.32 0.00 35.89 3.01
2435 2927 2.972625 AGATGGATCGCGTTTGAGAAA 58.027 42.857 5.77 0.00 0.00 2.52
2436 2928 2.672874 CAAGATGGATCGCGTTTGAGAA 59.327 45.455 5.77 0.00 0.00 2.87
2438 2930 2.270923 TCAAGATGGATCGCGTTTGAG 58.729 47.619 5.77 0.00 0.00 3.02
2440 2932 3.680642 ATTCAAGATGGATCGCGTTTG 57.319 42.857 5.77 1.47 0.00 2.93
2441 2933 4.188462 TGTATTCAAGATGGATCGCGTTT 58.812 39.130 5.77 0.00 0.00 3.60
2444 2936 4.997905 AATGTATTCAAGATGGATCGCG 57.002 40.909 0.00 0.00 0.00 5.87
2446 2938 6.847792 CGTCAAAATGTATTCAAGATGGATCG 59.152 38.462 0.00 0.00 0.00 3.69
2454 2946 9.746711 CTAGAAACTCGTCAAAATGTATTCAAG 57.253 33.333 0.00 0.00 0.00 3.02
2461 2953 7.041984 GGAAGTTCTAGAAACTCGTCAAAATGT 60.042 37.037 6.78 0.00 0.00 2.71
2462 2954 7.171678 AGGAAGTTCTAGAAACTCGTCAAAATG 59.828 37.037 6.78 0.00 0.00 2.32
2463 2955 7.217906 AGGAAGTTCTAGAAACTCGTCAAAAT 58.782 34.615 6.78 0.00 0.00 1.82
2464 2956 6.579865 AGGAAGTTCTAGAAACTCGTCAAAA 58.420 36.000 6.78 0.00 0.00 2.44
2465 2957 6.158023 AGGAAGTTCTAGAAACTCGTCAAA 57.842 37.500 6.78 0.00 0.00 2.69
2466 2958 5.786264 AGGAAGTTCTAGAAACTCGTCAA 57.214 39.130 6.78 0.00 0.00 3.18
2467 2959 5.786264 AAGGAAGTTCTAGAAACTCGTCA 57.214 39.130 6.78 0.00 0.00 4.35
2468 2960 7.369607 ACTTAAGGAAGTTCTAGAAACTCGTC 58.630 38.462 6.78 3.06 43.70 4.20
2469 2961 7.287512 ACTTAAGGAAGTTCTAGAAACTCGT 57.712 36.000 6.78 5.68 43.70 4.18
2483 2975 6.377327 TTCAGCAGTTGAAACTTAAGGAAG 57.623 37.500 7.53 0.00 42.69 3.46
2518 3010 7.769719 TTATGAAACTTACGATTTTGTTCGC 57.230 32.000 0.00 0.00 42.82 4.70
2519 3011 9.160576 TGTTTATGAAACTTACGATTTTGTTCG 57.839 29.630 3.92 0.00 42.02 3.95
2524 3016 9.673454 GGTCTTGTTTATGAAACTTACGATTTT 57.327 29.630 3.92 0.00 41.90 1.82
2525 3017 8.294577 GGGTCTTGTTTATGAAACTTACGATTT 58.705 33.333 3.92 0.00 41.90 2.17
2528 3020 5.406175 CGGGTCTTGTTTATGAAACTTACGA 59.594 40.000 3.92 0.00 41.90 3.43
2529 3021 5.178067 ACGGGTCTTGTTTATGAAACTTACG 59.822 40.000 3.92 0.00 41.90 3.18
2530 3022 6.368213 CACGGGTCTTGTTTATGAAACTTAC 58.632 40.000 3.92 0.36 41.90 2.34
2532 3024 4.261447 GCACGGGTCTTGTTTATGAAACTT 60.261 41.667 3.92 0.00 41.90 2.66
2533 3025 3.252458 GCACGGGTCTTGTTTATGAAACT 59.748 43.478 3.92 0.00 41.90 2.66
2534 3026 3.561503 GCACGGGTCTTGTTTATGAAAC 58.438 45.455 0.00 0.00 41.73 2.78
2535 3027 2.554893 GGCACGGGTCTTGTTTATGAAA 59.445 45.455 0.00 0.00 0.00 2.69
2536 3028 2.156098 GGCACGGGTCTTGTTTATGAA 58.844 47.619 0.00 0.00 0.00 2.57
2537 3029 1.612199 GGGCACGGGTCTTGTTTATGA 60.612 52.381 0.00 0.00 0.00 2.15
2538 3030 0.808755 GGGCACGGGTCTTGTTTATG 59.191 55.000 0.00 0.00 0.00 1.90
2539 3031 0.696501 AGGGCACGGGTCTTGTTTAT 59.303 50.000 0.00 0.00 0.00 1.40
2540 3032 1.276989 CTAGGGCACGGGTCTTGTTTA 59.723 52.381 0.00 0.00 0.00 2.01
2543 3035 1.535687 ACTAGGGCACGGGTCTTGT 60.536 57.895 0.00 0.00 0.00 3.16
2544 3036 1.079127 CACTAGGGCACGGGTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
2545 3037 2.955881 GCACTAGGGCACGGGTCTT 61.956 63.158 13.43 0.00 0.00 3.01
2546 3038 3.391382 GCACTAGGGCACGGGTCT 61.391 66.667 13.43 0.00 0.00 3.85
2547 3039 4.814294 CGCACTAGGGCACGGGTC 62.814 72.222 18.96 0.00 0.00 4.46
2560 3058 3.819877 AAGTCGTTGGACCCCGCAC 62.820 63.158 0.00 0.00 44.54 5.34
2566 3064 0.872388 ATTCGCAAAGTCGTTGGACC 59.128 50.000 0.60 0.00 44.54 4.46
2567 3065 1.529438 TGATTCGCAAAGTCGTTGGAC 59.471 47.619 0.60 0.00 43.76 4.02
2572 3070 1.060713 CTCGTGATTCGCAAAGTCGT 58.939 50.000 0.00 0.00 39.67 4.34
2576 3074 0.516877 TTGCCTCGTGATTCGCAAAG 59.483 50.000 0.00 0.00 38.23 2.77
2603 3101 1.450312 CTTGTCTAGCCTTGCCGGG 60.450 63.158 2.18 0.00 0.00 5.73
2622 3120 3.957260 CAGGTGAAGGAGCACGTG 58.043 61.111 12.28 12.28 44.76 4.49
2623 3121 2.031163 GCAGGTGAAGGAGCACGT 59.969 61.111 0.00 0.00 39.66 4.49
2641 3139 2.044946 GGAAACTCGCAGGGGCAT 60.045 61.111 0.00 0.00 41.24 4.40
2676 3174 8.341173 GTTTGAGATAATCTAGTGAAATGGCTG 58.659 37.037 0.00 0.00 0.00 4.85
2723 3235 3.389002 AGGGTTGCTTTGAATTGCTTTCT 59.611 39.130 0.00 0.00 35.23 2.52
2732 3244 0.536233 TGCGCTAGGGTTGCTTTGAA 60.536 50.000 9.73 0.00 0.00 2.69
2735 3247 2.335712 GCTGCGCTAGGGTTGCTTT 61.336 57.895 9.73 0.00 0.00 3.51
2737 3249 4.785453 GGCTGCGCTAGGGTTGCT 62.785 66.667 9.73 0.00 0.00 3.91
2768 3280 4.100963 TCATGTCCAATGGTAGCGTATTCT 59.899 41.667 0.00 0.00 0.00 2.40
2772 3284 2.480587 CGTCATGTCCAATGGTAGCGTA 60.481 50.000 0.00 0.00 0.00 4.42
2773 3285 1.739035 CGTCATGTCCAATGGTAGCGT 60.739 52.381 0.00 0.00 0.00 5.07
2778 3290 1.745115 CCGCGTCATGTCCAATGGT 60.745 57.895 4.92 0.00 0.00 3.55
2829 3343 1.079750 GTGTTCACCTCGAGCTCCC 60.080 63.158 6.99 0.00 0.00 4.30
2836 3350 2.654912 GGCGTTCGTGTTCACCTCG 61.655 63.158 0.00 2.09 0.00 4.63
2864 3378 3.598562 CGCACGCTCGTCGATGTC 61.599 66.667 4.21 0.00 41.67 3.06
2872 3386 2.430080 AAAAGCAAGTCGCACGCTCG 62.430 55.000 0.00 0.00 46.13 5.03
2902 3416 4.691216 GTGTAGATGAGGAAACCACTTCAC 59.309 45.833 0.00 0.00 35.55 3.18
2906 3420 4.593206 TCTTGTGTAGATGAGGAAACCACT 59.407 41.667 0.00 0.00 0.00 4.00
2917 3431 4.119862 CCCCGTTGTATCTTGTGTAGATG 58.880 47.826 0.00 0.00 43.52 2.90
2918 3432 3.431766 GCCCCGTTGTATCTTGTGTAGAT 60.432 47.826 0.00 0.00 45.59 1.98
2922 3436 0.690762 AGCCCCGTTGTATCTTGTGT 59.309 50.000 0.00 0.00 0.00 3.72
2928 3442 1.271102 TGCAAAAAGCCCCGTTGTATC 59.729 47.619 0.00 0.00 44.83 2.24
2940 3455 4.202202 TGGGACCTTATTGTGTGCAAAAAG 60.202 41.667 0.00 0.00 38.21 2.27
2954 3469 1.675219 GTGGCTCGTTGGGACCTTA 59.325 57.895 0.00 0.00 0.00 2.69
2960 3475 1.077501 ATGATGGTGGCTCGTTGGG 60.078 57.895 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.