Multiple sequence alignment - TraesCS3D01G404100

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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 TraesCS3D01G404100 chr3D 100.000 6674 0 0 1 6674 518157592 518150919 0.000000e+00 12325.0
1 TraesCS3D01G404100 chr3B 95.128 4372 135 47 2136 6451 682789965 682785616 0.000000e+00 6822.0
2 TraesCS3D01G404100 chr3B 90.786 2214 101 46 4 2132 682792113 682789918 0.000000e+00 2863.0
3 TraesCS3D01G404100 chr3B 84.722 72 5 3 6603 6673 682783097 682783031 4.320000e-07 67.6
4 TraesCS3D01G404100 chr3A 95.018 3693 114 49 2771 6416 653854768 653851099 0.000000e+00 5736.0
5 TraesCS3D01G404100 chr3A 91.164 1460 78 24 708 2132 653856880 653855437 0.000000e+00 1934.0
6 TraesCS3D01G404100 chr3A 93.139 787 32 13 2136 2914 653855484 653854712 0.000000e+00 1134.0
7 TraesCS3D01G404100 chr3A 92.517 441 19 9 14 448 653857759 653857327 2.640000e-173 619.0
8 TraesCS3D01G404100 chr3A 81.567 217 27 11 6410 6614 653850741 653850526 4.140000e-37 167.0
9 TraesCS3D01G404100 chr1D 83.730 1051 158 8 4541 5586 362489985 362488943 0.000000e+00 981.0
10 TraesCS3D01G404100 chr1B 83.349 1051 162 8 4541 5586 485289705 485288663 0.000000e+00 959.0
11 TraesCS3D01G404100 chr1A 83.001 1053 165 9 4541 5586 462002135 462001090 0.000000e+00 941.0
12 TraesCS3D01G404100 chr4D 97.059 34 0 1 5118 5150 105587470 105587437 1.000000e-03 56.5


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 TraesCS3D01G404100 chr3D 518150919 518157592 6673 True 12325.000000 12325 100.000 1 6674 1 chr3D.!!$R1 6673
1 TraesCS3D01G404100 chr3B 682783031 682792113 9082 True 3250.866667 6822 90.212 4 6673 3 chr3B.!!$R1 6669
2 TraesCS3D01G404100 chr3A 653850526 653857759 7233 True 1918.000000 5736 90.681 14 6614 5 chr3A.!!$R1 6600
3 TraesCS3D01G404100 chr1D 362488943 362489985 1042 True 981.000000 981 83.730 4541 5586 1 chr1D.!!$R1 1045
4 TraesCS3D01G404100 chr1B 485288663 485289705 1042 True 959.000000 959 83.349 4541 5586 1 chr1B.!!$R1 1045
5 TraesCS3D01G404100 chr1A 462001090 462002135 1045 True 941.000000 941 83.001 4541 5586 1 chr1A.!!$R1 1045

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
459 473 0.037877 TCCGTCCGTCCTCTTCTTCT 59.962 55.0 0.00 0.0 0.00 2.85 F
1655 1913 0.388520 GCATTTCTGGCGGTGGTTTC 60.389 55.0 0.00 0.0 0.00 2.78 F
1999 2258 0.168128 GAATTCGGCAACCTTGGTCG 59.832 55.0 0.00 0.0 0.00 4.79 F
2162 2425 0.389556 TCGCGTGTTTGCCGGTATTA 60.390 50.0 5.77 0.0 0.00 0.98 F
2163 2426 0.443088 CGCGTGTTTGCCGGTATTAA 59.557 50.0 1.90 0.0 0.00 1.40 F
2369 2633 0.598158 GGTGCGGAGAAACGTGTGTA 60.598 55.0 0.00 0.0 35.98 2.90 F
2643 2910 0.607620 TGTAAGCAAAGCAATGGGGC 59.392 50.0 0.00 0.0 0.00 5.80 F
4031 4390 0.667184 CAGCAAAATTGGCCGTGACC 60.667 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2074 0.317799 GTGCACATGGAACCAATGCA 59.682 50.000 23.11 23.11 44.38 3.96 R
2643 2910 1.160137 CTGGTGCTTTCCTTTCCTCG 58.840 55.000 0.00 0.00 0.00 4.63 R
3764 4123 1.888512 TCACTTTCTGGGAGCAATTGC 59.111 47.619 23.05 23.05 42.49 3.56 R
4049 4408 3.153130 CACAAACATCACATGTACCCCA 58.847 45.455 0.00 0.00 44.07 4.96 R
4475 4835 9.802039 AAGTAATACAGGGACAACAATAAAAGA 57.198 29.630 0.00 0.00 0.00 2.52 R
5117 5478 0.541998 TCGCCTTCACCTCCTCTTCA 60.542 55.000 0.00 0.00 0.00 3.02 R
5165 5526 0.179023 GGAGGACGTAGAGGATCGGT 60.179 60.000 0.00 0.00 42.67 4.69 R
6620 9815 0.107017 CGCATGGAAGATGGAACCCT 60.107 55.000 0.00 0.00 0.00 4.34 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
122 130 4.522975 CCCCTCCCCAAATCGCCC 62.523 72.222 0.00 0.00 0.00 6.13
151 163 4.825679 GTCCCTCCCCTCCCCCTG 62.826 77.778 0.00 0.00 0.00 4.45
157 169 4.888325 CCCCTCCCCCTGCGAGAT 62.888 72.222 0.00 0.00 0.00 2.75
160 172 1.147153 CCTCCCCCTGCGAGATTTC 59.853 63.158 0.00 0.00 0.00 2.17
220 232 1.392589 CCGGCAGGCAAAGATTACAT 58.607 50.000 0.00 0.00 0.00 2.29
387 399 0.695347 CCCCCTCTGAGAGCTTTTGT 59.305 55.000 6.17 0.00 0.00 2.83
454 468 3.745803 GCGTCCGTCCGTCCTCTT 61.746 66.667 0.00 0.00 0.00 2.85
455 469 2.484203 CGTCCGTCCGTCCTCTTC 59.516 66.667 0.00 0.00 0.00 2.87
456 470 2.039405 CGTCCGTCCGTCCTCTTCT 61.039 63.158 0.00 0.00 0.00 2.85
457 471 1.584380 CGTCCGTCCGTCCTCTTCTT 61.584 60.000 0.00 0.00 0.00 2.52
458 472 0.170784 GTCCGTCCGTCCTCTTCTTC 59.829 60.000 0.00 0.00 0.00 2.87
459 473 0.037877 TCCGTCCGTCCTCTTCTTCT 59.962 55.000 0.00 0.00 0.00 2.85
463 477 1.474879 GTCCGTCCTCTTCTTCTCCTG 59.525 57.143 0.00 0.00 0.00 3.86
467 481 1.899142 GTCCTCTTCTTCTCCTGCTGT 59.101 52.381 0.00 0.00 0.00 4.40
469 483 2.178580 CCTCTTCTTCTCCTGCTGTCT 58.821 52.381 0.00 0.00 0.00 3.41
470 484 2.166254 CCTCTTCTTCTCCTGCTGTCTC 59.834 54.545 0.00 0.00 0.00 3.36
500 514 2.833582 CGCCGCTTCCTCCTCCTA 60.834 66.667 0.00 0.00 0.00 2.94
559 573 1.006922 GTGCTGTTCTTGGCTTGCC 60.007 57.895 4.43 4.43 0.00 4.52
593 607 1.465856 GGATGCGTTTTCTCTTTCGGC 60.466 52.381 0.00 0.00 0.00 5.54
619 633 1.372087 CCGCCTGATCTGTTCTTGGC 61.372 60.000 10.90 10.90 39.58 4.52
621 635 1.093159 GCCTGATCTGTTCTTGGCTG 58.907 55.000 12.61 0.00 39.73 4.85
637 673 4.629523 TGTTCCGTTGGGTCGCCC 62.630 66.667 7.87 7.87 45.71 6.13
670 706 2.383527 GGTCGCTGGTTCTTGCTCG 61.384 63.158 0.00 0.00 0.00 5.03
675 711 1.357991 GCTGGTTCTTGCTCGCTCTC 61.358 60.000 0.00 0.00 0.00 3.20
812 1012 3.397482 GCATTGCTCTCCGATATTCACT 58.603 45.455 0.16 0.00 0.00 3.41
813 1013 3.186001 GCATTGCTCTCCGATATTCACTG 59.814 47.826 0.16 0.00 0.00 3.66
829 1029 9.713740 GATATTCACTGTATTTTTCTGCTCTTG 57.286 33.333 0.00 0.00 0.00 3.02
840 1040 1.073923 TCTGCTCTTGTTTTCTCCCCC 59.926 52.381 0.00 0.00 0.00 5.40
881 1085 2.259266 TGCTTGTCTGTTCATCTGCA 57.741 45.000 0.00 0.00 0.00 4.41
892 1096 4.209538 TGTTCATCTGCATATCCCCTTTG 58.790 43.478 0.00 0.00 0.00 2.77
894 1098 1.538512 CATCTGCATATCCCCTTTGCG 59.461 52.381 0.00 0.00 39.23 4.85
895 1099 0.819259 TCTGCATATCCCCTTTGCGC 60.819 55.000 0.00 0.00 39.23 6.09
933 1152 7.769044 GCATTATTTGACTAGGTGAACTCCTTA 59.231 37.037 0.00 0.00 38.86 2.69
934 1153 9.838339 CATTATTTGACTAGGTGAACTCCTTAT 57.162 33.333 0.00 0.00 38.86 1.73
945 1171 2.674796 ACTCCTTATCGTGTTCTGCC 57.325 50.000 0.00 0.00 0.00 4.85
952 1178 0.670546 ATCGTGTTCTGCCGTTCTGG 60.671 55.000 0.00 0.00 42.50 3.86
1055 1287 0.612229 CAGCTCAGAGGAGGCTTCAA 59.388 55.000 0.00 0.00 41.67 2.69
1056 1288 0.903942 AGCTCAGAGGAGGCTTCAAG 59.096 55.000 0.00 0.00 41.67 3.02
1165 1397 3.450115 CCCACCCCTCGACTCGAC 61.450 72.222 0.00 0.00 0.00 4.20
1169 1401 3.141488 CCCCTCGACTCGACCCAG 61.141 72.222 0.00 0.00 0.00 4.45
1249 1483 2.903079 GATGCCGCTTGCGTGCTAAC 62.903 60.000 21.61 12.96 45.60 2.34
1252 1486 1.447140 CCGCTTGCGTGCTAACCTA 60.447 57.895 13.97 0.00 0.00 3.08
1253 1487 1.017177 CCGCTTGCGTGCTAACCTAA 61.017 55.000 13.97 0.00 0.00 2.69
1267 1501 1.153289 CCTAACCTGCAGATGCGCT 60.153 57.895 17.39 0.00 45.83 5.92
1304 1541 4.203618 GCTAACCAAGCCGTCTCC 57.796 61.111 0.00 0.00 46.25 3.71
1385 1623 2.788191 CTTTCCTCTCCGCTGCCGTT 62.788 60.000 0.00 0.00 0.00 4.44
1446 1688 1.204146 TCCCTGATCTTGTAGGTGGC 58.796 55.000 0.00 0.00 31.99 5.01
1486 1729 3.524095 CCTTTATGGCATCCACCCATA 57.476 47.619 1.65 0.00 42.78 2.74
1519 1777 1.560923 CACTTCCCGTTAGAGATGCG 58.439 55.000 0.00 0.00 0.00 4.73
1548 1806 1.581447 GCCCTCTTTTCCGTTGCTG 59.419 57.895 0.00 0.00 0.00 4.41
1588 1846 4.351054 CTGCCGGTTCTTGCCCCT 62.351 66.667 1.90 0.00 0.00 4.79
1655 1913 0.388520 GCATTTCTGGCGGTGGTTTC 60.389 55.000 0.00 0.00 0.00 2.78
1678 1936 5.105187 TCGATCCCATATTTAGGAGATGCTG 60.105 44.000 0.00 0.00 35.08 4.41
1698 1956 4.331968 CTGATAGTTTTGGTAACCCAGCA 58.668 43.478 0.00 0.00 43.15 4.41
1803 2061 5.474189 CCTTGTCACCGAAACCCTATTAAAA 59.526 40.000 0.00 0.00 0.00 1.52
1823 2082 4.785346 AATCTCCTACTGATGCATTGGT 57.215 40.909 0.00 5.69 0.00 3.67
1876 2135 1.511768 GTCAGCTCCGGTACAGTCC 59.488 63.158 0.00 0.00 0.00 3.85
1999 2258 0.168128 GAATTCGGCAACCTTGGTCG 59.832 55.000 0.00 0.00 0.00 4.79
2051 2310 5.449304 GCATTGACGCTACTACAAAGTTTT 58.551 37.500 0.00 0.00 37.15 2.43
2055 2316 7.949903 TTGACGCTACTACAAAGTTTTCATA 57.050 32.000 0.00 0.00 37.15 2.15
2103 2366 1.268335 GGCTTTTCTTCGCGTGTTTGA 60.268 47.619 5.77 0.00 0.00 2.69
2118 2381 6.061429 CGTGTTTGACGGTATTAAAATTGC 57.939 37.500 0.00 0.00 44.85 3.56
2119 2382 5.219695 CGTGTTTGACGGTATTAAAATTGCG 60.220 40.000 0.00 0.00 44.85 4.85
2120 2383 5.852229 GTGTTTGACGGTATTAAAATTGCGA 59.148 36.000 0.00 0.00 0.00 5.10
2121 2384 6.360148 GTGTTTGACGGTATTAAAATTGCGAA 59.640 34.615 0.00 0.00 0.00 4.70
2122 2385 6.916387 TGTTTGACGGTATTAAAATTGCGAAA 59.084 30.769 0.00 0.00 0.00 3.46
2123 2386 7.595502 TGTTTGACGGTATTAAAATTGCGAAAT 59.404 29.630 0.00 0.00 0.00 2.17
2124 2387 7.499438 TTGACGGTATTAAAATTGCGAAATG 57.501 32.000 0.00 0.00 0.00 2.32
2125 2388 6.030849 TGACGGTATTAAAATTGCGAAATGG 58.969 36.000 0.00 0.00 0.00 3.16
2126 2389 6.127980 TGACGGTATTAAAATTGCGAAATGGA 60.128 34.615 0.00 0.00 0.00 3.41
2127 2390 6.262601 ACGGTATTAAAATTGCGAAATGGAG 58.737 36.000 0.00 0.00 0.00 3.86
2128 2391 6.094325 ACGGTATTAAAATTGCGAAATGGAGA 59.906 34.615 0.00 0.00 0.00 3.71
2129 2392 6.632834 CGGTATTAAAATTGCGAAATGGAGAG 59.367 38.462 0.00 0.00 0.00 3.20
2130 2393 7.480810 GGTATTAAAATTGCGAAATGGAGAGT 58.519 34.615 0.00 0.00 0.00 3.24
2131 2394 7.432252 GGTATTAAAATTGCGAAATGGAGAGTG 59.568 37.037 0.00 0.00 0.00 3.51
2132 2395 6.567687 TTAAAATTGCGAAATGGAGAGTGA 57.432 33.333 0.00 0.00 0.00 3.41
2133 2396 4.425577 AAATTGCGAAATGGAGAGTGAC 57.574 40.909 0.00 0.00 0.00 3.67
2134 2397 2.542020 TTGCGAAATGGAGAGTGACA 57.458 45.000 0.00 0.00 0.00 3.58
2135 2398 2.084610 TGCGAAATGGAGAGTGACAG 57.915 50.000 0.00 0.00 0.00 3.51
2136 2399 0.723981 GCGAAATGGAGAGTGACAGC 59.276 55.000 0.00 0.00 0.00 4.40
2137 2400 1.674221 GCGAAATGGAGAGTGACAGCT 60.674 52.381 0.00 0.00 0.00 4.24
2138 2401 2.693069 CGAAATGGAGAGTGACAGCTT 58.307 47.619 0.00 0.00 0.00 3.74
2139 2402 3.070018 CGAAATGGAGAGTGACAGCTTT 58.930 45.455 0.00 0.00 0.00 3.51
2140 2403 3.499918 CGAAATGGAGAGTGACAGCTTTT 59.500 43.478 0.00 0.00 0.00 2.27
2141 2404 4.377841 CGAAATGGAGAGTGACAGCTTTTC 60.378 45.833 0.00 0.00 0.00 2.29
2142 2405 4.363991 AATGGAGAGTGACAGCTTTTCT 57.636 40.909 0.00 0.00 0.00 2.52
2143 2406 3.845781 TGGAGAGTGACAGCTTTTCTT 57.154 42.857 0.00 0.00 0.00 2.52
2144 2407 3.733337 TGGAGAGTGACAGCTTTTCTTC 58.267 45.455 0.00 0.00 0.00 2.87
2145 2408 2.734079 GGAGAGTGACAGCTTTTCTTCG 59.266 50.000 0.00 0.00 0.00 3.79
2146 2409 2.139118 AGAGTGACAGCTTTTCTTCGC 58.861 47.619 0.00 0.00 0.00 4.70
2147 2410 0.861837 AGTGACAGCTTTTCTTCGCG 59.138 50.000 0.00 0.00 0.00 5.87
2148 2411 0.582005 GTGACAGCTTTTCTTCGCGT 59.418 50.000 5.77 0.00 0.00 6.01
2149 2412 0.581529 TGACAGCTTTTCTTCGCGTG 59.418 50.000 5.77 0.00 0.00 5.34
2150 2413 0.582005 GACAGCTTTTCTTCGCGTGT 59.418 50.000 5.77 0.00 0.00 4.49
2151 2414 1.003866 GACAGCTTTTCTTCGCGTGTT 60.004 47.619 5.77 0.00 0.00 3.32
2152 2415 1.400494 ACAGCTTTTCTTCGCGTGTTT 59.600 42.857 5.77 0.00 0.00 2.83
2153 2416 1.775208 CAGCTTTTCTTCGCGTGTTTG 59.225 47.619 5.77 0.00 0.00 2.93
2154 2417 0.498511 GCTTTTCTTCGCGTGTTTGC 59.501 50.000 5.77 0.00 0.00 3.68
2155 2418 1.120437 CTTTTCTTCGCGTGTTTGCC 58.880 50.000 5.77 0.00 0.00 4.52
2156 2419 0.590230 TTTTCTTCGCGTGTTTGCCG 60.590 50.000 5.77 0.00 0.00 5.69
2157 2420 2.381665 TTTCTTCGCGTGTTTGCCGG 62.382 55.000 5.77 0.00 0.00 6.13
2158 2421 3.645975 CTTCGCGTGTTTGCCGGT 61.646 61.111 5.77 0.00 0.00 5.28
2159 2422 2.279985 TTCGCGTGTTTGCCGGTA 60.280 55.556 5.77 0.00 0.00 4.02
2160 2423 1.632046 CTTCGCGTGTTTGCCGGTAT 61.632 55.000 5.77 0.00 0.00 2.73
2161 2424 1.229315 TTCGCGTGTTTGCCGGTATT 61.229 50.000 5.77 0.00 0.00 1.89
2162 2425 0.389556 TCGCGTGTTTGCCGGTATTA 60.390 50.000 5.77 0.00 0.00 0.98
2163 2426 0.443088 CGCGTGTTTGCCGGTATTAA 59.557 50.000 1.90 0.00 0.00 1.40
2164 2427 1.136029 CGCGTGTTTGCCGGTATTAAA 60.136 47.619 1.90 0.00 0.00 1.52
2165 2428 2.664971 CGCGTGTTTGCCGGTATTAAAA 60.665 45.455 1.90 0.00 0.00 1.52
2166 2429 3.503891 GCGTGTTTGCCGGTATTAAAAT 58.496 40.909 1.90 0.00 0.00 1.82
2167 2430 3.921630 GCGTGTTTGCCGGTATTAAAATT 59.078 39.130 1.90 0.00 0.00 1.82
2168 2431 4.386350 GCGTGTTTGCCGGTATTAAAATTT 59.614 37.500 1.90 0.00 0.00 1.82
2169 2432 5.666670 GCGTGTTTGCCGGTATTAAAATTTG 60.667 40.000 1.90 0.00 0.00 2.32
2193 2456 2.508891 CGGAGCGTGCTGTCGATTC 61.509 63.158 0.00 0.00 0.00 2.52
2366 2630 2.632136 TTCGGTGCGGAGAAACGTGT 62.632 55.000 0.00 0.00 35.98 4.49
2368 2632 1.885850 GGTGCGGAGAAACGTGTGT 60.886 57.895 0.00 0.00 35.98 3.72
2369 2633 0.598158 GGTGCGGAGAAACGTGTGTA 60.598 55.000 0.00 0.00 35.98 2.90
2579 2846 1.000171 GCAGCCTCCAAGAAAAACCAG 60.000 52.381 0.00 0.00 0.00 4.00
2589 2856 4.499696 CCAAGAAAAACCAGACACCATCAC 60.500 45.833 0.00 0.00 0.00 3.06
2643 2910 0.607620 TGTAAGCAAAGCAATGGGGC 59.392 50.000 0.00 0.00 0.00 5.80
2690 2957 4.082245 TGGCTTGCTTGTAGGCTTATTTTC 60.082 41.667 0.00 0.00 38.84 2.29
2722 2989 4.133820 TGGTACAAGTGGTTGTTCTGATG 58.866 43.478 0.00 0.00 45.00 3.07
2863 3134 6.751888 CAGAGTTTTGGTTTTGGACTAACAAG 59.248 38.462 0.00 0.00 0.00 3.16
2866 3137 7.768240 AGTTTTGGTTTTGGACTAACAAGTAG 58.232 34.615 0.00 0.00 35.75 2.57
2867 3138 7.395206 AGTTTTGGTTTTGGACTAACAAGTAGT 59.605 33.333 0.00 0.00 46.23 2.73
2987 3345 1.809567 GCCAAAGTTCCCAGTGCCTG 61.810 60.000 0.00 0.00 0.00 4.85
3007 3365 4.158579 CCTGTTGAGTGTCTAGCATCTACA 59.841 45.833 0.00 0.00 0.00 2.74
3048 3406 7.940178 AAAGTAAAACGGAAACAAATCATCC 57.060 32.000 0.00 0.00 0.00 3.51
3071 3429 6.071952 TCCTCCTGCATAACAAAATGAAAGTC 60.072 38.462 0.00 0.00 0.00 3.01
3099 3457 2.430332 AGAACTCTACTGCTCTCATGGC 59.570 50.000 0.00 0.00 0.00 4.40
3764 4123 1.202651 ACTGAGTTTGGGTCTTGGACG 60.203 52.381 0.00 0.00 32.65 4.79
3989 4348 0.678048 GGTGGTCCAGAGATGTTGCC 60.678 60.000 0.00 0.00 0.00 4.52
4031 4390 0.667184 CAGCAAAATTGGCCGTGACC 60.667 55.000 0.00 0.00 0.00 4.02
4436 4796 5.930135 ACATATAGGAACATCACCACCTTC 58.070 41.667 0.00 0.00 34.42 3.46
4826 5187 1.244019 AATTCCGGTTGTGGCAGCTC 61.244 55.000 0.00 0.00 0.00 4.09
5117 5478 1.302907 AGCATTTCTGGGAGGGTGAT 58.697 50.000 0.00 0.00 0.00 3.06
5156 5517 1.122019 AGAAGACCCAGCTGTTCGGT 61.122 55.000 13.81 13.02 0.00 4.69
5165 5526 2.203280 CTGTTCGGTGCCAACCCA 60.203 61.111 0.00 0.00 44.42 4.51
5267 5628 1.764571 TACTGCGGGAGTTTGCCAGT 61.765 55.000 7.67 0.00 35.96 4.00
5593 5960 0.896226 GTGTAGATATCCTCCCCCGC 59.104 60.000 0.00 0.00 0.00 6.13
5667 6036 6.426633 TCCATTCCATACAATACACAATAGCG 59.573 38.462 0.00 0.00 0.00 4.26
5712 6081 1.522580 GCTGCTCCTAGGCCTTTCG 60.523 63.158 12.58 0.00 0.00 3.46
5863 6262 1.905637 AGGTAAACTTTTCCGGGCAG 58.094 50.000 0.00 0.00 0.00 4.85
5935 6334 6.943146 TGTAATGTAATGTGTGTATGGTGGTT 59.057 34.615 0.00 0.00 0.00 3.67
6070 6494 4.514577 CTGCTCGGCGATTCGGGT 62.515 66.667 11.27 0.00 32.39 5.28
6071 6495 4.508128 TGCTCGGCGATTCGGGTC 62.508 66.667 11.27 0.00 32.39 4.46
6079 6503 4.557605 GATTCGGGTCGCGGCGTA 62.558 66.667 22.90 6.35 0.00 4.42
6091 6518 2.717044 CGGCGTATGGGGAGTGTCA 61.717 63.158 0.00 0.00 0.00 3.58
6107 6534 6.071728 GGGAGTGTCATCTGAAATTGTTCATT 60.072 38.462 0.00 0.00 42.85 2.57
6170 6603 1.932511 GTTGGTTTGGTTGCATGTGTG 59.067 47.619 0.00 0.00 0.00 3.82
6171 6604 1.189752 TGGTTTGGTTGCATGTGTGT 58.810 45.000 0.00 0.00 0.00 3.72
6172 6605 1.134877 TGGTTTGGTTGCATGTGTGTG 60.135 47.619 0.00 0.00 0.00 3.82
6173 6606 1.134848 GGTTTGGTTGCATGTGTGTGT 60.135 47.619 0.00 0.00 0.00 3.72
6174 6607 1.925847 GTTTGGTTGCATGTGTGTGTG 59.074 47.619 0.00 0.00 0.00 3.82
6175 6608 0.179116 TTGGTTGCATGTGTGTGTGC 60.179 50.000 0.00 0.00 41.61 4.57
6254 6688 4.720902 TGGGTGCGGGCAGATGTG 62.721 66.667 0.00 0.00 0.00 3.21
6265 6699 0.179936 GCAGATGTGGAAGAGGAGGG 59.820 60.000 0.00 0.00 0.00 4.30
6317 6751 4.704833 CCTCCCGTGCCAGTGGTG 62.705 72.222 11.74 0.94 0.00 4.17
6322 6756 3.740397 CGTGCCAGTGGTGCCATG 61.740 66.667 11.74 1.96 0.00 3.66
6324 6758 3.578286 TGCCAGTGGTGCCATGGA 61.578 61.111 18.40 0.00 36.09 3.41
6325 6759 2.753043 GCCAGTGGTGCCATGGAG 60.753 66.667 18.40 0.00 36.09 3.86
6373 6809 1.772063 ATTATTTCGCCGTGCTCCGC 61.772 55.000 0.00 0.00 34.38 5.54
6393 6834 2.357034 GGTTCGTTCCAGCTGCGA 60.357 61.111 8.66 9.66 0.00 5.10
6395 6836 1.372997 GTTCGTTCCAGCTGCGAGA 60.373 57.895 8.66 1.59 36.00 4.04
6463 8008 3.851955 CGCCCTACGTCCACCTAT 58.148 61.111 0.00 0.00 36.87 2.57
6464 8009 1.362717 CGCCCTACGTCCACCTATG 59.637 63.158 0.00 0.00 36.87 2.23
6470 8041 2.167693 CCTACGTCCACCTATGAAAGCA 59.832 50.000 0.00 0.00 0.00 3.91
6473 8044 2.002586 CGTCCACCTATGAAAGCACTG 58.997 52.381 0.00 0.00 0.00 3.66
6480 8051 3.838317 ACCTATGAAAGCACTGGTACTGA 59.162 43.478 0.00 0.00 33.11 3.41
6489 8060 2.838736 CACTGGTACTGATGGTATGGC 58.161 52.381 0.00 0.00 32.56 4.40
6496 8067 0.184451 CTGATGGTATGGCTTGCCCT 59.816 55.000 9.35 1.69 0.00 5.19
6499 8070 1.421646 GATGGTATGGCTTGCCCTAGT 59.578 52.381 9.35 0.00 0.00 2.57
6501 8072 1.064758 TGGTATGGCTTGCCCTAGTTG 60.065 52.381 9.35 0.00 0.00 3.16
6503 8074 1.211949 GTATGGCTTGCCCTAGTTGGA 59.788 52.381 9.35 0.00 38.35 3.53
6505 8076 1.750780 GGCTTGCCCTAGTTGGAGC 60.751 63.158 0.00 0.00 38.35 4.70
6506 8077 1.301293 GCTTGCCCTAGTTGGAGCT 59.699 57.895 0.00 0.00 38.35 4.09
6508 8079 0.326264 CTTGCCCTAGTTGGAGCTGT 59.674 55.000 0.00 0.00 38.35 4.40
6510 8081 0.835971 TGCCCTAGTTGGAGCTGTGA 60.836 55.000 0.00 0.00 38.35 3.58
6513 8084 1.139853 CCCTAGTTGGAGCTGTGATCC 59.860 57.143 0.00 0.00 38.35 3.36
6514 8085 1.139853 CCTAGTTGGAGCTGTGATCCC 59.860 57.143 0.00 0.00 38.35 3.85
6516 8087 1.293062 AGTTGGAGCTGTGATCCCAT 58.707 50.000 0.00 0.00 35.86 4.00
6517 8088 1.064906 AGTTGGAGCTGTGATCCCATG 60.065 52.381 0.00 0.00 35.86 3.66
6521 8092 2.190313 GCTGTGATCCCATGGCGA 59.810 61.111 6.09 5.75 0.00 5.54
6570 8149 7.523293 TTTAAATTGCTTCCAGATCTGAACA 57.477 32.000 24.62 12.70 0.00 3.18
6586 8165 2.288457 TGAACACACTGTAGCTGAGCTC 60.288 50.000 11.68 6.82 40.44 4.09
6589 8168 2.288702 ACACACTGTAGCTGAGCTCAAG 60.289 50.000 18.85 14.02 40.44 3.02
6638 9833 2.149973 AAGGGTTCCATCTTCCATGC 57.850 50.000 0.00 0.00 0.00 4.06
6641 9836 1.017387 GGTTCCATCTTCCATGCGAC 58.983 55.000 0.00 0.00 0.00 5.19
6673 9868 1.885850 GCTGTGACAACGAACGGGT 60.886 57.895 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.303928 GGGCTCGAGGATACCCGG 61.304 72.222 15.58 0.00 37.58 5.73
1 2 1.472662 ATTGGGCTCGAGGATACCCG 61.473 60.000 15.58 0.00 46.02 5.28
2 3 0.321996 GATTGGGCTCGAGGATACCC 59.678 60.000 15.58 16.17 43.14 3.69
122 130 2.204151 AGGGACCAGGAGGGGTTG 60.204 66.667 0.00 0.00 42.53 3.77
153 165 3.514417 GGCAAGGGGCGAAATCTC 58.486 61.111 0.00 0.00 46.16 2.75
331 343 9.832445 GAGAGAGTTTTATAGAGAGAGAGAGAA 57.168 37.037 0.00 0.00 0.00 2.87
387 399 3.740495 CTCCGGCTGCCCCTCTCTA 62.740 68.421 14.12 0.00 0.00 2.43
408 422 4.988486 GTGGCTGTGCGCTTGTGC 62.988 66.667 9.73 7.84 39.13 4.57
450 464 2.166254 GGAGACAGCAGGAGAAGAAGAG 59.834 54.545 0.00 0.00 0.00 2.85
451 465 2.175202 GGAGACAGCAGGAGAAGAAGA 58.825 52.381 0.00 0.00 0.00 2.87
452 466 1.135141 CGGAGACAGCAGGAGAAGAAG 60.135 57.143 0.00 0.00 0.00 2.85
454 468 1.599606 GCGGAGACAGCAGGAGAAGA 61.600 60.000 0.00 0.00 34.19 2.87
455 469 1.153667 GCGGAGACAGCAGGAGAAG 60.154 63.158 0.00 0.00 34.19 2.85
456 470 2.650116 GGCGGAGACAGCAGGAGAA 61.650 63.158 0.00 0.00 31.66 2.87
457 471 3.071206 GGCGGAGACAGCAGGAGA 61.071 66.667 0.00 0.00 31.66 3.71
540 554 1.370900 GCAAGCCAAGAACAGCACG 60.371 57.895 0.00 0.00 0.00 5.34
542 556 2.202395 GGGCAAGCCAAGAACAGCA 61.202 57.895 13.87 0.00 37.98 4.41
601 615 2.093216 GCCAAGAACAGATCAGGCG 58.907 57.895 0.00 0.00 40.29 5.52
619 633 3.047877 GGCGACCCAACGGAACAG 61.048 66.667 0.00 0.00 0.00 3.16
637 673 3.739077 GACCAAATCGGGCAAATGG 57.261 52.632 0.00 0.00 45.64 3.16
712 910 6.362820 GCTCAAAGCATCTGAGAAAGAAAAAG 59.637 38.462 12.40 0.00 42.51 2.27
812 1012 7.425606 GGAGAAAACAAGAGCAGAAAAATACA 58.574 34.615 0.00 0.00 0.00 2.29
813 1013 6.863645 GGGAGAAAACAAGAGCAGAAAAATAC 59.136 38.462 0.00 0.00 0.00 1.89
840 1040 3.499737 GGGATGAACAGTGGCGCG 61.500 66.667 0.00 0.00 0.00 6.86
881 1085 1.215423 AGGAAAGCGCAAAGGGGATAT 59.785 47.619 11.47 0.00 0.00 1.63
894 1098 3.427161 AATAATGCTTCGCAGGAAAGC 57.573 42.857 1.01 1.01 43.65 3.51
895 1099 4.795278 GTCAAATAATGCTTCGCAGGAAAG 59.205 41.667 0.00 0.00 43.65 2.62
905 1109 6.599638 GGAGTTCACCTAGTCAAATAATGCTT 59.400 38.462 0.00 0.00 0.00 3.91
917 1121 4.342359 ACACGATAAGGAGTTCACCTAGT 58.658 43.478 0.00 0.00 39.62 2.57
920 1124 3.833070 AGAACACGATAAGGAGTTCACCT 59.167 43.478 0.00 0.00 42.69 4.00
922 1126 3.368236 GCAGAACACGATAAGGAGTTCAC 59.632 47.826 0.00 0.00 39.71 3.18
933 1152 0.670546 CCAGAACGGCAGAACACGAT 60.671 55.000 0.00 0.00 0.00 3.73
934 1153 1.300620 CCAGAACGGCAGAACACGA 60.301 57.895 0.00 0.00 0.00 4.35
945 1171 3.124297 GCTTCTCATCTGAAACCAGAACG 59.876 47.826 0.00 0.00 43.22 3.95
952 1178 1.202009 GCGCTGCTTCTCATCTGAAAC 60.202 52.381 0.00 0.00 0.00 2.78
1039 1271 0.612229 TGCTTGAAGCCTCCTCTGAG 59.388 55.000 15.43 0.00 41.51 3.35
1040 1272 0.322975 GTGCTTGAAGCCTCCTCTGA 59.677 55.000 15.43 0.00 41.51 3.27
1055 1287 0.104855 TCGCTTTCAGTCTGTGTGCT 59.895 50.000 0.00 0.00 0.00 4.40
1056 1288 0.510359 CTCGCTTTCAGTCTGTGTGC 59.490 55.000 0.00 2.20 0.00 4.57
1165 1397 4.576330 AGTGGGTATTTTTCTCTCTGGG 57.424 45.455 0.00 0.00 0.00 4.45
1169 1401 7.511959 ACAGAAAAGTGGGTATTTTTCTCTC 57.488 36.000 8.73 0.00 44.58 3.20
1249 1483 1.153289 AGCGCATCTGCAGGTTAGG 60.153 57.895 15.13 0.00 42.21 2.69
1252 1486 2.667418 AGAGCGCATCTGCAGGTT 59.333 55.556 15.13 0.00 42.21 3.50
1385 1623 3.445687 CCATGGACGGACGGACGA 61.446 66.667 5.56 0.00 37.61 4.20
1417 1659 5.428184 ACAAGATCAGGGAAGTTAAGGAG 57.572 43.478 0.00 0.00 0.00 3.69
1446 1688 4.326766 CTGCAACCACCAACGGCG 62.327 66.667 4.80 4.80 0.00 6.46
1548 1806 2.268920 TGGCAGTTCGGGCATCTC 59.731 61.111 0.00 0.00 38.55 2.75
1655 1913 5.105187 TCAGCATCTCCTAAATATGGGATCG 60.105 44.000 0.00 0.00 35.39 3.69
1708 1966 1.373536 TGGCCCCACCATAGTAACAA 58.626 50.000 0.00 0.00 46.36 2.83
1803 2061 4.445448 GGAACCAATGCATCAGTAGGAGAT 60.445 45.833 0.00 0.00 0.00 2.75
1815 2074 0.317799 GTGCACATGGAACCAATGCA 59.682 50.000 23.11 23.11 44.38 3.96
1847 2106 0.458716 GGAGCTGACCTACTCAACGC 60.459 60.000 0.00 0.00 34.48 4.84
2051 2310 4.234550 AGCAATCCCAGGTGTAGATATGA 58.765 43.478 0.00 0.00 0.00 2.15
2055 2316 2.481441 TGAGCAATCCCAGGTGTAGAT 58.519 47.619 0.00 0.00 0.00 1.98
2103 2366 6.094325 TCTCCATTTCGCAATTTTAATACCGT 59.906 34.615 0.00 0.00 0.00 4.83
2118 2381 2.376808 AGCTGTCACTCTCCATTTCG 57.623 50.000 0.00 0.00 0.00 3.46
2119 2382 4.759183 AGAAAAGCTGTCACTCTCCATTTC 59.241 41.667 0.00 0.00 0.00 2.17
2120 2383 4.723309 AGAAAAGCTGTCACTCTCCATTT 58.277 39.130 0.00 0.00 0.00 2.32
2121 2384 4.363991 AGAAAAGCTGTCACTCTCCATT 57.636 40.909 0.00 0.00 0.00 3.16
2122 2385 4.322567 GAAGAAAAGCTGTCACTCTCCAT 58.677 43.478 0.00 0.00 0.00 3.41
2123 2386 3.733337 GAAGAAAAGCTGTCACTCTCCA 58.267 45.455 0.00 0.00 0.00 3.86
2124 2387 2.734079 CGAAGAAAAGCTGTCACTCTCC 59.266 50.000 0.00 0.00 0.00 3.71
2125 2388 2.156697 GCGAAGAAAAGCTGTCACTCTC 59.843 50.000 0.00 0.00 0.00 3.20
2126 2389 2.139118 GCGAAGAAAAGCTGTCACTCT 58.861 47.619 0.00 0.00 0.00 3.24
2127 2390 1.136502 CGCGAAGAAAAGCTGTCACTC 60.137 52.381 0.00 0.00 0.00 3.51
2128 2391 0.861837 CGCGAAGAAAAGCTGTCACT 59.138 50.000 0.00 0.00 0.00 3.41
2129 2392 0.582005 ACGCGAAGAAAAGCTGTCAC 59.418 50.000 15.93 0.00 0.00 3.67
2130 2393 0.581529 CACGCGAAGAAAAGCTGTCA 59.418 50.000 15.93 0.00 0.00 3.58
2131 2394 0.582005 ACACGCGAAGAAAAGCTGTC 59.418 50.000 15.93 0.00 0.00 3.51
2132 2395 1.014352 AACACGCGAAGAAAAGCTGT 58.986 45.000 15.93 0.00 0.00 4.40
2133 2396 1.775208 CAAACACGCGAAGAAAAGCTG 59.225 47.619 15.93 0.00 0.00 4.24
2134 2397 1.859998 GCAAACACGCGAAGAAAAGCT 60.860 47.619 15.93 0.00 0.00 3.74
2135 2398 0.498511 GCAAACACGCGAAGAAAAGC 59.501 50.000 15.93 3.87 0.00 3.51
2136 2399 1.120437 GGCAAACACGCGAAGAAAAG 58.880 50.000 15.93 0.00 0.00 2.27
2137 2400 0.590230 CGGCAAACACGCGAAGAAAA 60.590 50.000 15.93 0.00 0.00 2.29
2138 2401 1.010574 CGGCAAACACGCGAAGAAA 60.011 52.632 15.93 0.00 0.00 2.52
2139 2402 2.629210 CGGCAAACACGCGAAGAA 59.371 55.556 15.93 0.00 0.00 2.52
2140 2403 2.696409 TACCGGCAAACACGCGAAGA 62.696 55.000 15.93 0.00 0.00 2.87
2141 2404 1.632046 ATACCGGCAAACACGCGAAG 61.632 55.000 15.93 7.57 0.00 3.79
2142 2405 1.229315 AATACCGGCAAACACGCGAA 61.229 50.000 15.93 0.00 0.00 4.70
2143 2406 0.389556 TAATACCGGCAAACACGCGA 60.390 50.000 15.93 0.00 0.00 5.87
2144 2407 0.443088 TTAATACCGGCAAACACGCG 59.557 50.000 3.53 3.53 0.00 6.01
2145 2408 2.615489 TTTAATACCGGCAAACACGC 57.385 45.000 0.00 0.00 0.00 5.34
2146 2409 5.666670 GCAAATTTTAATACCGGCAAACACG 60.667 40.000 0.00 0.00 0.00 4.49
2147 2410 5.407084 AGCAAATTTTAATACCGGCAAACAC 59.593 36.000 0.00 0.00 0.00 3.32
2148 2411 5.542779 AGCAAATTTTAATACCGGCAAACA 58.457 33.333 0.00 0.00 0.00 2.83
2149 2412 7.583860 TTAGCAAATTTTAATACCGGCAAAC 57.416 32.000 0.00 0.00 0.00 2.93
2150 2413 7.221067 CGATTAGCAAATTTTAATACCGGCAAA 59.779 33.333 0.00 0.00 0.00 3.68
2151 2414 6.693545 CGATTAGCAAATTTTAATACCGGCAA 59.306 34.615 0.00 0.00 0.00 4.52
2152 2415 6.202937 CGATTAGCAAATTTTAATACCGGCA 58.797 36.000 0.00 0.00 0.00 5.69
2153 2416 5.627780 CCGATTAGCAAATTTTAATACCGGC 59.372 40.000 0.00 0.00 0.00 6.13
2154 2417 6.961576 TCCGATTAGCAAATTTTAATACCGG 58.038 36.000 0.00 0.00 0.00 5.28
2155 2418 6.577427 GCTCCGATTAGCAAATTTTAATACCG 59.423 38.462 0.00 0.00 42.30 4.02
2156 2419 6.577427 CGCTCCGATTAGCAAATTTTAATACC 59.423 38.462 5.45 0.00 42.91 2.73
2157 2420 7.111593 CACGCTCCGATTAGCAAATTTTAATAC 59.888 37.037 5.45 0.00 42.91 1.89
2158 2421 7.129622 CACGCTCCGATTAGCAAATTTTAATA 58.870 34.615 5.45 0.00 42.91 0.98
2159 2422 5.971202 CACGCTCCGATTAGCAAATTTTAAT 59.029 36.000 5.45 0.00 42.91 1.40
2160 2423 5.328691 CACGCTCCGATTAGCAAATTTTAA 58.671 37.500 5.45 0.00 42.91 1.52
2161 2424 4.729458 GCACGCTCCGATTAGCAAATTTTA 60.729 41.667 5.45 0.00 42.91 1.52
2162 2425 3.758300 CACGCTCCGATTAGCAAATTTT 58.242 40.909 5.45 0.00 42.91 1.82
2163 2426 2.477863 GCACGCTCCGATTAGCAAATTT 60.478 45.455 5.45 0.00 42.91 1.82
2164 2427 1.064060 GCACGCTCCGATTAGCAAATT 59.936 47.619 5.45 0.00 42.91 1.82
2165 2428 0.657840 GCACGCTCCGATTAGCAAAT 59.342 50.000 5.45 0.00 42.91 2.32
2166 2429 0.391130 AGCACGCTCCGATTAGCAAA 60.391 50.000 5.45 0.00 42.91 3.68
2167 2430 1.083806 CAGCACGCTCCGATTAGCAA 61.084 55.000 5.45 0.00 42.91 3.91
2168 2431 1.519234 CAGCACGCTCCGATTAGCA 60.519 57.895 5.45 0.00 42.91 3.49
2169 2432 1.483424 GACAGCACGCTCCGATTAGC 61.483 60.000 0.00 0.00 39.21 3.09
2193 2456 1.453155 CCCCATGTTTCTTGGTCTCG 58.547 55.000 0.00 0.00 31.99 4.04
2366 2630 3.396611 AGGCTAAGGGGAACAAAAGTACA 59.603 43.478 0.00 0.00 0.00 2.90
2368 2632 4.734843 AAGGCTAAGGGGAACAAAAGTA 57.265 40.909 0.00 0.00 0.00 2.24
2369 2633 3.612795 AAGGCTAAGGGGAACAAAAGT 57.387 42.857 0.00 0.00 0.00 2.66
2579 2846 2.681097 GCTTTCCTAGGGTGATGGTGTC 60.681 54.545 9.46 0.00 0.00 3.67
2589 2856 3.879892 GCTTTCATAGTGCTTTCCTAGGG 59.120 47.826 9.46 0.00 0.00 3.53
2643 2910 1.160137 CTGGTGCTTTCCTTTCCTCG 58.840 55.000 0.00 0.00 0.00 4.63
2987 3345 6.090088 CACTTTGTAGATGCTAGACACTCAAC 59.910 42.308 0.00 0.00 0.00 3.18
3048 3406 6.680810 TGACTTTCATTTTGTTATGCAGGAG 58.319 36.000 0.00 0.00 0.00 3.69
3764 4123 1.888512 TCACTTTCTGGGAGCAATTGC 59.111 47.619 23.05 23.05 42.49 3.56
4049 4408 3.153130 CACAAACATCACATGTACCCCA 58.847 45.455 0.00 0.00 44.07 4.96
4475 4835 9.802039 AAGTAATACAGGGACAACAATAAAAGA 57.198 29.630 0.00 0.00 0.00 2.52
5117 5478 0.541998 TCGCCTTCACCTCCTCTTCA 60.542 55.000 0.00 0.00 0.00 3.02
5156 5517 2.933287 AGGATCGGTGGGTTGGCA 60.933 61.111 0.00 0.00 0.00 4.92
5165 5526 0.179023 GGAGGACGTAGAGGATCGGT 60.179 60.000 0.00 0.00 42.67 4.69
5593 5960 7.864686 TCATCATCTGGTATGCTAAAATTTCG 58.135 34.615 0.00 0.00 0.00 3.46
5667 6036 3.408634 TGGCTACCTTTACAAAGCTGTC 58.591 45.455 0.00 0.00 36.96 3.51
5712 6081 6.267496 ACAAAATGTATAGCTGTTGGGAAC 57.733 37.500 0.00 0.00 0.00 3.62
5863 6262 0.543749 AGCCAGCCATAGACAAGTCC 59.456 55.000 0.00 0.00 0.00 3.85
5935 6334 0.817634 CCGGAGCCAACAGTTCAACA 60.818 55.000 0.00 0.00 0.00 3.33
6073 6497 2.028125 ATGACACTCCCCATACGCCG 62.028 60.000 0.00 0.00 0.00 6.46
6076 6500 2.031870 TCAGATGACACTCCCCATACG 58.968 52.381 0.00 0.00 0.00 3.06
6077 6501 4.487714 TTTCAGATGACACTCCCCATAC 57.512 45.455 0.00 0.00 0.00 2.39
6078 6502 5.044919 ACAATTTCAGATGACACTCCCCATA 60.045 40.000 0.00 0.00 0.00 2.74
6079 6503 4.264083 ACAATTTCAGATGACACTCCCCAT 60.264 41.667 0.00 0.00 0.00 4.00
6083 6507 5.947228 TGAACAATTTCAGATGACACTCC 57.053 39.130 0.00 0.00 36.79 3.85
6084 6508 7.864379 ACAAATGAACAATTTCAGATGACACTC 59.136 33.333 8.40 0.00 45.07 3.51
6085 6509 7.650504 CACAAATGAACAATTTCAGATGACACT 59.349 33.333 8.40 0.00 45.07 3.55
6087 6514 7.490840 ACACAAATGAACAATTTCAGATGACA 58.509 30.769 8.40 0.00 45.07 3.58
6091 6518 8.819974 GTCAAACACAAATGAACAATTTCAGAT 58.180 29.630 0.00 0.00 45.07 2.90
6107 6534 3.582714 TGCACAACATGTCAAACACAA 57.417 38.095 0.00 0.00 38.97 3.33
6170 6603 1.154338 GAGCTCAATGCACGCACAC 60.154 57.895 9.40 0.00 45.94 3.82
6171 6604 1.571215 CTGAGCTCAATGCACGCACA 61.571 55.000 18.85 0.00 45.94 4.57
6172 6605 1.134075 CTGAGCTCAATGCACGCAC 59.866 57.895 18.85 0.00 45.94 5.34
6173 6606 2.683859 GCTGAGCTCAATGCACGCA 61.684 57.895 18.85 0.00 45.94 5.24
6174 6607 2.099831 GCTGAGCTCAATGCACGC 59.900 61.111 18.85 12.64 45.94 5.34
6175 6608 2.398429 CGCTGAGCTCAATGCACG 59.602 61.111 23.16 15.51 45.94 5.34
6213 6646 0.108992 CAGCAGCACGCCATTTCAAT 60.109 50.000 0.00 0.00 44.04 2.57
6254 6688 0.393537 CATGTGTGCCCTCCTCTTCC 60.394 60.000 0.00 0.00 0.00 3.46
6265 6699 4.501714 CATGCGCCCCATGTGTGC 62.502 66.667 4.18 10.21 45.05 4.57
6312 6746 2.044946 GTCCCTCCATGGCACCAC 60.045 66.667 6.96 0.00 0.00 4.16
6318 6752 4.530857 GGCGACGTCCCTCCATGG 62.531 72.222 10.58 4.97 0.00 3.66
6319 6753 4.530857 GGGCGACGTCCCTCCATG 62.531 72.222 7.42 2.12 43.13 3.66
6393 6834 1.677217 GCGGCCTCAACAAAGATCTCT 60.677 52.381 0.00 0.00 0.00 3.10
6395 6836 0.326264 AGCGGCCTCAACAAAGATCT 59.674 50.000 0.00 0.00 0.00 2.75
6463 8008 2.371841 ACCATCAGTACCAGTGCTTTCA 59.628 45.455 0.00 0.00 0.00 2.69
6464 8009 3.059352 ACCATCAGTACCAGTGCTTTC 57.941 47.619 0.00 0.00 0.00 2.62
6470 8041 2.764269 AGCCATACCATCAGTACCAGT 58.236 47.619 0.00 0.00 32.46 4.00
6473 8044 2.222027 GCAAGCCATACCATCAGTACC 58.778 52.381 0.00 0.00 32.46 3.34
6480 8051 1.522900 ACTAGGGCAAGCCATACCAT 58.477 50.000 13.87 0.00 37.98 3.55
6489 8060 0.326264 ACAGCTCCAACTAGGGCAAG 59.674 55.000 0.00 0.00 36.41 4.01
6496 8067 1.951209 TGGGATCACAGCTCCAACTA 58.049 50.000 0.00 0.00 34.24 2.24
6499 8070 0.256752 CCATGGGATCACAGCTCCAA 59.743 55.000 2.98 0.00 34.24 3.53
6501 8072 1.527844 GCCATGGGATCACAGCTCC 60.528 63.158 15.13 0.00 0.00 4.70
6503 8074 1.703014 ATCGCCATGGGATCACAGCT 61.703 55.000 15.13 0.00 29.10 4.24
6505 8076 0.887836 CCATCGCCATGGGATCACAG 60.888 60.000 15.13 3.09 45.63 3.66
6506 8077 1.148949 CCATCGCCATGGGATCACA 59.851 57.895 15.13 0.00 45.63 3.58
6521 8092 1.329256 CCTACTAGCAGTACGGCCAT 58.671 55.000 14.67 3.09 0.00 4.40
6526 8104 8.524870 TTTAAAAGAAACCTACTAGCAGTACG 57.475 34.615 0.00 0.00 0.00 3.67
6531 8109 8.404107 AGCAATTTAAAAGAAACCTACTAGCA 57.596 30.769 0.00 0.00 0.00 3.49
6532 8110 9.343103 GAAGCAATTTAAAAGAAACCTACTAGC 57.657 33.333 0.00 0.00 0.00 3.42
6570 8149 1.274728 CCTTGAGCTCAGCTACAGTGT 59.725 52.381 17.43 0.00 39.88 3.55
6614 9809 5.129320 GCATGGAAGATGGAACCCTTTTTAT 59.871 40.000 0.00 0.00 0.00 1.40
6620 9815 0.107017 CGCATGGAAGATGGAACCCT 60.107 55.000 0.00 0.00 0.00 4.34
6623 9818 2.029838 AGTCGCATGGAAGATGGAAC 57.970 50.000 0.00 0.00 0.00 3.62
6625 9820 1.069204 GCTAGTCGCATGGAAGATGGA 59.931 52.381 0.00 0.00 38.92 3.41
6626 9821 1.202568 TGCTAGTCGCATGGAAGATGG 60.203 52.381 0.00 0.00 45.47 3.51
6627 9822 2.229675 TGCTAGTCGCATGGAAGATG 57.770 50.000 0.00 0.00 45.47 2.90


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

AutoCloner maintained by Alex Coulton.