Multiple sequence alignment - TraesCS2D01G435100

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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 TraesCS2D01G435100 chr2D 100.000 5350 0 0 1 5350 545944770 545939421 0.000000e+00 9843
1 TraesCS2D01G435100 chr2A 94.113 3686 116 41 1316 4971 687005144 687001530 0.000000e+00 5511
2 TraesCS2D01G435100 chr2A 95.696 883 31 4 10 886 687027931 687027050 0.000000e+00 1413
3 TraesCS2D01G435100 chr2A 82.292 192 12 9 5178 5350 687001013 687000825 4.320000e-31 147
4 TraesCS2D01G435100 chr2A 94.253 87 5 0 2184 2270 687004408 687004322 3.360000e-27 134
5 TraesCS2D01G435100 chr2A 98.413 63 1 0 2122 2184 687004290 687004228 1.580000e-20 111
6 TraesCS2D01G435100 chr2B 96.582 1375 42 2 2558 3928 652620417 652619044 0.000000e+00 2274
7 TraesCS2D01G435100 chr2B 89.879 662 61 6 3926 4585 652618921 652618264 0.000000e+00 846
8 TraesCS2D01G435100 chr2B 91.372 452 21 3 852 1292 652620890 652620446 2.130000e-168 603
9 TraesCS2D01G435100 chr2B 90.244 287 27 1 4681 4966 652617904 652617618 1.820000e-99 374
10 TraesCS2D01G435100 chr2B 81.038 501 62 16 17 509 652822529 652822054 8.470000e-98 368
11 TraesCS2D01G435100 chr2B 89.431 123 11 2 517 637 652821908 652821786 2.580000e-33 154
12 TraesCS2D01G435100 chr6B 80.549 1347 187 45 3050 4358 618938450 618939759 0.000000e+00 966
13 TraesCS2D01G435100 chr6B 86.091 834 73 22 2186 3005 618937639 618938443 0.000000e+00 857
14 TraesCS2D01G435100 chr6B 82.990 582 70 14 1489 2054 618937061 618937629 2.880000e-137 499
15 TraesCS2D01G435100 chr6B 84.411 263 38 3 965 1224 618936460 618936722 6.880000e-64 255
16 TraesCS2D01G435100 chr6A 85.372 834 78 22 2184 3005 556527928 556528729 0.000000e+00 824
17 TraesCS2D01G435100 chr6A 89.408 642 60 6 3050 3688 556528735 556529371 0.000000e+00 802
18 TraesCS2D01G435100 chr6A 82.931 580 68 21 1489 2054 556527358 556527920 1.340000e-135 494
19 TraesCS2D01G435100 chr6A 86.486 259 31 3 965 1219 556526755 556527013 1.130000e-71 281
20 TraesCS2D01G435100 chr6A 83.913 230 22 4 4143 4358 556529848 556530076 7.020000e-49 206
21 TraesCS2D01G435100 chr6D 83.153 831 79 31 2184 3001 411611737 411612519 0.000000e+00 702
22 TraesCS2D01G435100 chr6D 84.256 578 69 12 1489 2054 411611162 411611729 1.310000e-150 544
23 TraesCS2D01G435100 chr6D 89.970 329 27 5 3050 3375 411612528 411612853 2.300000e-113 420
24 TraesCS2D01G435100 chr6D 87.259 259 31 1 3430 3688 411613204 411613460 1.460000e-75 294
25 TraesCS2D01G435100 chr6D 88.085 235 24 2 991 1221 411610555 411610789 5.280000e-70 276
26 TraesCS2D01G435100 chr6D 79.494 356 33 16 4140 4461 411613921 411614270 3.240000e-52 217
27 TraesCS2D01G435100 chr1A 85.845 219 28 2 3481 3699 561151158 561150943 4.170000e-56 230


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 TraesCS2D01G435100 chr2D 545939421 545944770 5349 True 9843.000000 9843 100.00000 1 5350 1 chr2D.!!$R1 5349
1 TraesCS2D01G435100 chr2A 687000825 687005144 4319 True 1475.750000 5511 92.26775 1316 5350 4 chr2A.!!$R2 4034
2 TraesCS2D01G435100 chr2A 687027050 687027931 881 True 1413.000000 1413 95.69600 10 886 1 chr2A.!!$R1 876
3 TraesCS2D01G435100 chr2B 652617618 652620890 3272 True 1024.250000 2274 92.01925 852 4966 4 chr2B.!!$R1 4114
4 TraesCS2D01G435100 chr2B 652821786 652822529 743 True 261.000000 368 85.23450 17 637 2 chr2B.!!$R2 620
5 TraesCS2D01G435100 chr6B 618936460 618939759 3299 False 644.250000 966 83.51025 965 4358 4 chr6B.!!$F1 3393
6 TraesCS2D01G435100 chr6A 556526755 556530076 3321 False 521.400000 824 85.62200 965 4358 5 chr6A.!!$F1 3393
7 TraesCS2D01G435100 chr6D 411610555 411614270 3715 False 408.833333 702 85.36950 991 4461 6 chr6D.!!$F1 3470

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
973 1139 0.112412 ACCAGTCCATTCCACCAACC 59.888 55.000 0.00 0.00 0.00 3.77 F
974 1140 0.611896 CCAGTCCATTCCACCAACCC 60.612 60.000 0.00 0.00 0.00 4.11 F
975 1141 0.960364 CAGTCCATTCCACCAACCCG 60.960 60.000 0.00 0.00 0.00 5.28 F
978 1144 1.075836 CCATTCCACCAACCCGGAA 59.924 57.895 0.73 0.00 45.12 4.30 F
2171 2563 0.679505 TACCTGTGCTCGAGTTGCTT 59.320 50.000 15.13 0.00 0.00 3.91 F
2172 2564 0.679505 ACCTGTGCTCGAGTTGCTTA 59.320 50.000 15.13 0.00 0.00 3.09 F
2173 2565 1.071605 CCTGTGCTCGAGTTGCTTAC 58.928 55.000 15.13 4.95 0.00 2.34 F
2177 2569 1.136224 GTGCTCGAGTTGCTTACTTGC 60.136 52.381 15.13 0.00 38.05 4.01 F
2178 2570 1.148310 GCTCGAGTTGCTTACTTGCA 58.852 50.000 15.13 0.00 38.05 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2549 1.136224 GCAAGTAAGCAACTCGAGCAC 60.136 52.381 13.61 1.63 37.50 4.40 R
2158 2550 1.148310 GCAAGTAAGCAACTCGAGCA 58.852 50.000 13.61 0.00 37.50 4.26 R
2159 2551 1.148310 TGCAAGTAAGCAACTCGAGC 58.852 50.000 13.61 0.00 42.46 5.03 R
2200 2592 2.171341 TGCGTGCTTACAACCATACA 57.829 45.000 0.00 0.00 0.00 2.29 R
3875 4613 1.196581 CGGCAACATGATTTGTGTCGA 59.803 47.619 0.00 0.00 38.99 4.20 R
3924 4662 4.856487 CACATGCCAAGTTAACCAAATACG 59.144 41.667 0.88 0.00 0.00 3.06 R
3956 4819 4.989797 TGAAAATCAACATGTTGGATGTGC 59.010 37.500 32.54 20.07 40.78 4.57 R
3960 4823 7.654520 CACTTTCTGAAAATCAACATGTTGGAT 59.345 33.333 32.54 22.53 40.78 3.41 R
4351 5264 1.673033 CGGATCTGAGTGGGTGTTCAC 60.673 57.143 0.00 0.00 37.89 3.18 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
122 123 7.762615 TCTTTAACTGACACGGATATTTAGTGG 59.237 37.037 9.78 0.00 39.95 4.00
302 306 3.906008 CACGAACTTTTCTAAATGTGCGG 59.094 43.478 19.86 9.69 44.70 5.69
308 312 4.819630 ACTTTTCTAAATGTGCGGAGAACA 59.180 37.500 0.00 0.00 0.00 3.18
896 1062 1.550065 CGGATCTGCTGTAACGTCTG 58.450 55.000 0.00 0.00 0.00 3.51
903 1069 3.659089 CTGTAACGTCTGGGGCCGG 62.659 68.421 0.00 0.00 0.00 6.13
967 1133 0.692476 CCACTGACCAGTCCATTCCA 59.308 55.000 0.00 0.00 40.20 3.53
969 1135 0.693049 ACTGACCAGTCCATTCCACC 59.307 55.000 0.00 0.00 36.92 4.61
971 1137 1.073763 CTGACCAGTCCATTCCACCAA 59.926 52.381 0.00 0.00 0.00 3.67
972 1138 1.202879 TGACCAGTCCATTCCACCAAC 60.203 52.381 0.00 0.00 0.00 3.77
973 1139 0.112412 ACCAGTCCATTCCACCAACC 59.888 55.000 0.00 0.00 0.00 3.77
974 1140 0.611896 CCAGTCCATTCCACCAACCC 60.612 60.000 0.00 0.00 0.00 4.11
975 1141 0.960364 CAGTCCATTCCACCAACCCG 60.960 60.000 0.00 0.00 0.00 5.28
976 1142 1.677633 GTCCATTCCACCAACCCGG 60.678 63.158 0.00 0.00 42.50 5.73
977 1143 1.848431 TCCATTCCACCAACCCGGA 60.848 57.895 0.73 0.00 38.63 5.14
978 1144 1.075836 CCATTCCACCAACCCGGAA 59.924 57.895 0.73 0.00 45.12 4.30
994 1160 1.549203 GGAATTCTGCCTTTCCTGCA 58.451 50.000 5.23 0.00 38.68 4.41
1187 1356 1.766059 TGGACACCAGTGAGTGCCT 60.766 57.895 4.48 2.64 41.67 4.75
1195 1365 1.680651 AGTGAGTGCCTCTCTCCCG 60.681 63.158 7.37 0.00 43.13 5.14
1230 1484 6.476053 GCCTTCACTACCTCTACGATTTTTAG 59.524 42.308 0.00 0.00 0.00 1.85
1268 1522 8.924511 AAATATGGTGTATGGATTTAGTGGAG 57.075 34.615 0.00 0.00 0.00 3.86
1291 1545 2.695666 AGTCATGTAGTATGGCTTCGCT 59.304 45.455 0.00 0.00 28.05 4.93
1298 1552 4.341235 TGTAGTATGGCTTCGCTAGTGATT 59.659 41.667 6.86 0.00 0.00 2.57
1301 1555 2.760634 TGGCTTCGCTAGTGATTTGA 57.239 45.000 6.86 0.00 0.00 2.69
1306 1560 4.260538 GGCTTCGCTAGTGATTTGATGAAG 60.261 45.833 6.86 0.00 35.78 3.02
1308 1562 5.501574 GCTTCGCTAGTGATTTGATGAAGTC 60.502 44.000 6.86 0.00 35.29 3.01
1331 1585 6.042781 GTCTGGTGGTTCATATGGTTAGGATA 59.957 42.308 2.13 0.00 0.00 2.59
1373 1632 5.091431 GCAGTGTGCTGTTTGAGATTTATC 58.909 41.667 0.00 0.00 44.32 1.75
1458 1734 1.145119 GGGGGTGAAGAGTGGTTTTCT 59.855 52.381 0.00 0.00 0.00 2.52
1589 1880 3.675348 TTACCTAGTACTAGCCTGGCA 57.325 47.619 22.39 6.04 31.95 4.92
1755 2050 1.335872 GGCACTGGGAAAACATCAACG 60.336 52.381 0.00 0.00 0.00 4.10
1788 2083 2.792890 CGCGAGGAAGATATATGGCTCG 60.793 54.545 0.00 0.00 36.36 5.03
1914 2209 7.985184 TCTTTTGGGTATACACTAAGTGCTATG 59.015 37.037 6.69 0.00 36.98 2.23
2044 2350 5.827797 GCCCTATCATTGTTCTAATGTGGAA 59.172 40.000 0.00 0.00 0.00 3.53
2045 2351 6.238759 GCCCTATCATTGTTCTAATGTGGAAC 60.239 42.308 0.00 0.00 42.17 3.62
2048 2354 7.227512 CCTATCATTGTTCTAATGTGGAACTCC 59.772 40.741 6.13 0.00 42.27 3.85
2049 2355 5.875224 TCATTGTTCTAATGTGGAACTCCA 58.125 37.500 6.13 0.00 45.30 3.86
2058 2364 3.935993 TGGAACTCCAGTAGCTTGC 57.064 52.632 0.00 0.00 42.01 4.01
2059 2365 1.352083 TGGAACTCCAGTAGCTTGCT 58.648 50.000 0.00 0.00 42.01 3.91
2060 2366 2.536066 TGGAACTCCAGTAGCTTGCTA 58.464 47.619 0.00 0.00 42.01 3.49
2061 2367 2.903784 TGGAACTCCAGTAGCTTGCTAA 59.096 45.455 3.72 0.00 42.01 3.09
2062 2368 3.055819 TGGAACTCCAGTAGCTTGCTAAG 60.056 47.826 3.72 1.23 42.01 2.18
2063 2369 3.195825 GGAACTCCAGTAGCTTGCTAAGA 59.804 47.826 3.72 1.83 35.64 2.10
2064 2370 4.322801 GGAACTCCAGTAGCTTGCTAAGAA 60.323 45.833 3.72 0.00 35.64 2.52
2065 2371 4.891992 ACTCCAGTAGCTTGCTAAGAAA 57.108 40.909 3.72 0.00 0.00 2.52
2096 2416 6.534079 CCCTTAGTTTTAACATGAGGTCGTAG 59.466 42.308 0.00 0.00 0.00 3.51
2097 2417 7.095270 CCTTAGTTTTAACATGAGGTCGTAGT 58.905 38.462 0.00 0.00 0.00 2.73
2101 2421 8.891671 AGTTTTAACATGAGGTCGTAGTTTTA 57.108 30.769 0.00 0.00 0.00 1.52
2102 2422 9.328845 AGTTTTAACATGAGGTCGTAGTTTTAA 57.671 29.630 0.00 0.00 0.00 1.52
2103 2423 9.373750 GTTTTAACATGAGGTCGTAGTTTTAAC 57.626 33.333 0.00 0.00 0.00 2.01
2105 2425 8.836268 TTAACATGAGGTCGTAGTTTTAACAT 57.164 30.769 0.00 0.00 0.00 2.71
2106 2426 9.926158 TTAACATGAGGTCGTAGTTTTAACATA 57.074 29.630 0.00 0.00 0.00 2.29
2108 2428 8.475331 ACATGAGGTCGTAGTTTTAACATAAG 57.525 34.615 0.00 0.00 0.00 1.73
2109 2429 8.308931 ACATGAGGTCGTAGTTTTAACATAAGA 58.691 33.333 0.00 0.00 0.00 2.10
2110 2430 9.146984 CATGAGGTCGTAGTTTTAACATAAGAA 57.853 33.333 0.00 0.00 0.00 2.52
2112 2432 9.199982 TGAGGTCGTAGTTTTAACATAAGAAAG 57.800 33.333 0.00 0.00 0.00 2.62
2163 2555 8.559536 ACAATATGAATTAAATACCTGTGCTCG 58.440 33.333 0.00 0.00 0.00 5.03
2164 2556 8.773645 CAATATGAATTAAATACCTGTGCTCGA 58.226 33.333 0.00 0.00 0.00 4.04
2165 2557 6.851222 ATGAATTAAATACCTGTGCTCGAG 57.149 37.500 8.45 8.45 0.00 4.04
2166 2558 5.730550 TGAATTAAATACCTGTGCTCGAGT 58.269 37.500 15.13 0.00 0.00 4.18
2167 2559 6.170506 TGAATTAAATACCTGTGCTCGAGTT 58.829 36.000 15.13 0.00 0.00 3.01
2168 2560 6.092122 TGAATTAAATACCTGTGCTCGAGTTG 59.908 38.462 15.13 1.95 0.00 3.16
2169 2561 1.726853 AATACCTGTGCTCGAGTTGC 58.273 50.000 15.13 0.48 0.00 4.17
2170 2562 0.898320 ATACCTGTGCTCGAGTTGCT 59.102 50.000 15.13 0.00 0.00 3.91
2171 2563 0.679505 TACCTGTGCTCGAGTTGCTT 59.320 50.000 15.13 0.00 0.00 3.91
2172 2564 0.679505 ACCTGTGCTCGAGTTGCTTA 59.320 50.000 15.13 0.00 0.00 3.09
2173 2565 1.071605 CCTGTGCTCGAGTTGCTTAC 58.928 55.000 15.13 4.95 0.00 2.34
2174 2566 1.337260 CCTGTGCTCGAGTTGCTTACT 60.337 52.381 15.13 0.00 40.71 2.24
2175 2567 2.408050 CTGTGCTCGAGTTGCTTACTT 58.592 47.619 15.13 0.00 37.17 2.24
2176 2568 2.135139 TGTGCTCGAGTTGCTTACTTG 58.865 47.619 15.13 1.58 37.17 3.16
2177 2569 1.136224 GTGCTCGAGTTGCTTACTTGC 60.136 52.381 15.13 0.00 38.05 4.01
2178 2570 1.148310 GCTCGAGTTGCTTACTTGCA 58.852 50.000 15.13 0.00 38.05 4.08
2179 2571 1.734465 GCTCGAGTTGCTTACTTGCAT 59.266 47.619 15.13 0.00 42.96 3.96
2180 2572 2.475187 GCTCGAGTTGCTTACTTGCATG 60.475 50.000 15.13 0.00 42.96 4.06
2181 2573 1.464608 TCGAGTTGCTTACTTGCATGC 59.535 47.619 11.82 11.82 42.96 4.06
2182 2574 1.787989 CGAGTTGCTTACTTGCATGCG 60.788 52.381 14.09 1.59 42.96 4.73
2183 2575 1.197721 GAGTTGCTTACTTGCATGCGT 59.802 47.619 14.09 8.38 42.96 5.24
2184 2576 2.415168 GAGTTGCTTACTTGCATGCGTA 59.585 45.455 14.09 7.29 42.96 4.42
2185 2577 2.416547 AGTTGCTTACTTGCATGCGTAG 59.583 45.455 14.09 15.05 42.96 3.51
2186 2578 2.093306 TGCTTACTTGCATGCGTAGT 57.907 45.000 23.44 23.44 38.12 2.73
2187 2579 2.422597 TGCTTACTTGCATGCGTAGTT 58.577 42.857 24.62 12.67 38.12 2.24
2188 2580 2.811431 TGCTTACTTGCATGCGTAGTTT 59.189 40.909 24.62 8.68 38.12 2.66
2189 2581 3.252215 TGCTTACTTGCATGCGTAGTTTT 59.748 39.130 24.62 8.09 38.12 2.43
2190 2582 4.452795 TGCTTACTTGCATGCGTAGTTTTA 59.547 37.500 24.62 9.35 38.12 1.52
2191 2583 5.049336 TGCTTACTTGCATGCGTAGTTTTAA 60.049 36.000 24.62 14.88 38.12 1.52
2192 2584 5.283012 GCTTACTTGCATGCGTAGTTTTAAC 59.717 40.000 24.62 10.90 0.00 2.01
2193 2585 4.822036 ACTTGCATGCGTAGTTTTAACA 57.178 36.364 16.88 0.00 0.00 2.41
2194 2586 5.371115 ACTTGCATGCGTAGTTTTAACAT 57.629 34.783 16.88 0.00 0.00 2.71
2195 2587 5.153513 ACTTGCATGCGTAGTTTTAACATG 58.846 37.500 16.88 0.00 40.80 3.21
2196 2588 5.049060 ACTTGCATGCGTAGTTTTAACATGA 60.049 36.000 16.88 0.00 40.39 3.07
2197 2589 4.968626 TGCATGCGTAGTTTTAACATGAG 58.031 39.130 14.09 0.00 40.39 2.90
2198 2590 4.142708 TGCATGCGTAGTTTTAACATGAGG 60.143 41.667 14.09 0.00 40.39 3.86
2199 2591 4.142687 GCATGCGTAGTTTTAACATGAGGT 60.143 41.667 0.00 0.00 40.39 3.85
2200 2592 5.619086 GCATGCGTAGTTTTAACATGAGGTT 60.619 40.000 0.00 0.00 40.39 3.50
2201 2593 5.351233 TGCGTAGTTTTAACATGAGGTTG 57.649 39.130 0.00 0.00 40.73 3.77
2202 2594 4.817464 TGCGTAGTTTTAACATGAGGTTGT 59.183 37.500 0.00 0.00 40.73 3.32
2203 2595 5.990386 TGCGTAGTTTTAACATGAGGTTGTA 59.010 36.000 0.00 0.00 40.73 2.41
2204 2596 6.651643 TGCGTAGTTTTAACATGAGGTTGTAT 59.348 34.615 0.00 0.00 40.73 2.29
2205 2597 6.959311 GCGTAGTTTTAACATGAGGTTGTATG 59.041 38.462 0.00 0.00 40.73 2.39
2206 2598 7.461107 CGTAGTTTTAACATGAGGTTGTATGG 58.539 38.462 0.00 0.00 40.73 2.74
2207 2599 7.118680 CGTAGTTTTAACATGAGGTTGTATGGT 59.881 37.037 0.00 0.00 40.73 3.55
2208 2600 7.833285 AGTTTTAACATGAGGTTGTATGGTT 57.167 32.000 0.00 0.00 40.73 3.67
2209 2601 7.657336 AGTTTTAACATGAGGTTGTATGGTTG 58.343 34.615 0.00 0.00 40.73 3.77
2210 2602 7.286775 AGTTTTAACATGAGGTTGTATGGTTGT 59.713 33.333 0.00 0.00 40.73 3.32
2211 2603 8.569641 GTTTTAACATGAGGTTGTATGGTTGTA 58.430 33.333 0.00 0.00 40.73 2.41
2212 2604 8.693120 TTTAACATGAGGTTGTATGGTTGTAA 57.307 30.769 0.00 0.00 40.73 2.41
2213 2605 6.817765 AACATGAGGTTGTATGGTTGTAAG 57.182 37.500 0.00 0.00 38.60 2.34
2214 2606 4.700213 ACATGAGGTTGTATGGTTGTAAGC 59.300 41.667 0.00 0.00 0.00 3.09
2215 2607 4.359434 TGAGGTTGTATGGTTGTAAGCA 57.641 40.909 0.00 0.00 41.10 3.91
2216 2608 4.069304 TGAGGTTGTATGGTTGTAAGCAC 58.931 43.478 0.00 0.00 39.48 4.40
2217 2609 3.071479 AGGTTGTATGGTTGTAAGCACG 58.929 45.455 0.00 0.00 39.48 5.34
2218 2610 2.413634 GGTTGTATGGTTGTAAGCACGC 60.414 50.000 0.00 0.00 39.48 5.34
2219 2611 2.171341 TGTATGGTTGTAAGCACGCA 57.829 45.000 0.00 0.00 39.48 5.24
2220 2612 2.495084 TGTATGGTTGTAAGCACGCAA 58.505 42.857 0.00 0.00 39.48 4.85
2221 2613 3.078097 TGTATGGTTGTAAGCACGCAAT 58.922 40.909 0.00 0.00 39.48 3.56
2222 2614 3.504134 TGTATGGTTGTAAGCACGCAATT 59.496 39.130 0.00 0.00 39.48 2.32
2223 2615 4.695928 TGTATGGTTGTAAGCACGCAATTA 59.304 37.500 0.00 0.00 39.48 1.40
2224 2616 3.546002 TGGTTGTAAGCACGCAATTAC 57.454 42.857 0.00 0.00 33.42 1.89
2225 2617 2.879026 TGGTTGTAAGCACGCAATTACA 59.121 40.909 3.58 3.58 39.48 2.41
2226 2618 3.315470 TGGTTGTAAGCACGCAATTACAA 59.685 39.130 12.84 12.84 45.08 2.41
2229 2621 5.621197 TTGTAAGCACGCAATTACAATCT 57.379 34.783 12.84 0.00 43.41 2.40
2230 2622 4.968626 TGTAAGCACGCAATTACAATCTG 58.031 39.130 4.90 0.00 38.57 2.90
2231 2623 4.693095 TGTAAGCACGCAATTACAATCTGA 59.307 37.500 4.90 0.00 38.57 3.27
2232 2624 4.764679 AAGCACGCAATTACAATCTGAA 57.235 36.364 0.00 0.00 0.00 3.02
2233 2625 4.970662 AGCACGCAATTACAATCTGAAT 57.029 36.364 0.00 0.00 0.00 2.57
2234 2626 5.314923 AGCACGCAATTACAATCTGAATT 57.685 34.783 0.00 0.00 0.00 2.17
2235 2627 6.435430 AGCACGCAATTACAATCTGAATTA 57.565 33.333 0.00 0.00 0.00 1.40
2236 2628 6.851609 AGCACGCAATTACAATCTGAATTAA 58.148 32.000 0.00 0.00 0.00 1.40
2237 2629 7.312154 AGCACGCAATTACAATCTGAATTAAA 58.688 30.769 0.00 0.00 0.00 1.52
2238 2630 7.975616 AGCACGCAATTACAATCTGAATTAAAT 59.024 29.630 0.00 0.00 0.00 1.40
2239 2631 9.232082 GCACGCAATTACAATCTGAATTAAATA 57.768 29.630 0.00 0.00 0.00 1.40
3270 3682 9.793259 AATGTACTCCTAATTACCATTACCATG 57.207 33.333 0.00 0.00 0.00 3.66
3271 3683 7.221450 TGTACTCCTAATTACCATTACCATGC 58.779 38.462 0.00 0.00 0.00 4.06
3875 4613 5.520376 AGTCAACTAAGCAAAGCAACAAT 57.480 34.783 0.00 0.00 0.00 2.71
3924 4662 3.193267 TGCCACACTCCAAAGCATAATTC 59.807 43.478 0.00 0.00 0.00 2.17
3956 4819 2.224606 ACTTGGCATGTGTGTTCTCTG 58.775 47.619 5.09 0.00 0.00 3.35
3960 4823 0.946528 GCATGTGTGTTCTCTGCACA 59.053 50.000 0.00 0.00 45.48 4.57
4401 5333 6.547141 TGATGGGGCAGTTTATTTATCTTCTG 59.453 38.462 0.00 0.00 0.00 3.02
4405 5337 6.183360 GGGGCAGTTTATTTATCTTCTGTGTC 60.183 42.308 0.00 0.00 0.00 3.67
4461 5394 1.273606 TGCTAGAACTGTCTGTCTGCC 59.726 52.381 0.00 0.00 35.12 4.85
4464 5397 1.709578 AGAACTGTCTGTCTGCCTGA 58.290 50.000 0.00 0.00 30.83 3.86
4465 5398 1.342819 AGAACTGTCTGTCTGCCTGAC 59.657 52.381 0.00 0.00 45.54 3.51
4532 5465 6.582636 TCAGGTTTAGGTGATGTACATGATC 58.417 40.000 14.43 5.03 0.00 2.92
4538 5471 2.409715 GGTGATGTACATGATCGATGCG 59.590 50.000 14.43 0.00 35.15 4.73
4585 5518 4.751060 TCACGACTCAAGTAAACACTGTT 58.249 39.130 0.00 0.00 0.00 3.16
4586 5519 5.893687 TCACGACTCAAGTAAACACTGTTA 58.106 37.500 0.00 0.00 0.00 2.41
4587 5520 6.509656 TCACGACTCAAGTAAACACTGTTAT 58.490 36.000 0.00 0.00 0.00 1.89
4588 5521 6.419710 TCACGACTCAAGTAAACACTGTTATG 59.580 38.462 0.00 0.00 0.00 1.90
4589 5522 6.419710 CACGACTCAAGTAAACACTGTTATGA 59.580 38.462 0.00 0.00 0.00 2.15
4590 5523 6.641314 ACGACTCAAGTAAACACTGTTATGAG 59.359 38.462 17.14 17.14 39.09 2.90
4591 5524 6.641314 CGACTCAAGTAAACACTGTTATGAGT 59.359 38.462 20.96 20.96 46.34 3.41
4629 5562 8.856490 AAAAACATTTTGAGCAACTACTAGTG 57.144 30.769 5.39 0.00 0.00 2.74
4630 5563 7.568199 AAACATTTTGAGCAACTACTAGTGT 57.432 32.000 5.39 0.00 0.00 3.55
4631 5564 7.568199 AACATTTTGAGCAACTACTAGTGTT 57.432 32.000 5.39 5.31 0.00 3.32
4632 5565 6.959361 ACATTTTGAGCAACTACTAGTGTTG 58.041 36.000 22.98 22.98 45.23 3.33
4639 5572 3.799035 CAACTACTAGTGTTGCAAAGCG 58.201 45.455 18.68 0.00 38.36 4.68
4640 5573 3.380479 ACTACTAGTGTTGCAAAGCGA 57.620 42.857 5.39 0.00 0.00 4.93
4641 5574 3.318017 ACTACTAGTGTTGCAAAGCGAG 58.682 45.455 5.39 5.42 0.00 5.03
4642 5575 2.526304 ACTAGTGTTGCAAAGCGAGA 57.474 45.000 0.00 0.00 0.00 4.04
4643 5576 2.833794 ACTAGTGTTGCAAAGCGAGAA 58.166 42.857 0.00 0.00 0.00 2.87
4647 5696 2.111756 GTGTTGCAAAGCGAGAAACAG 58.888 47.619 0.00 0.00 31.80 3.16
4691 5896 4.631813 GTGACACCAACAATCTATCCTGTC 59.368 45.833 0.00 0.00 0.00 3.51
4726 5931 7.662258 TGTATTTCGTAAGTCATTCCAAAAGGA 59.338 33.333 0.00 0.00 39.48 3.36
4752 5957 6.292865 GCAAAAAGGCAACAGAAAGGAATAAC 60.293 38.462 0.00 0.00 41.41 1.89
4845 6051 2.606795 GCTGTGTTTTCGGCATTAGCAA 60.607 45.455 0.00 0.00 44.61 3.91
5006 6212 6.931281 CCCTAAATATATATCACATCCTGCCG 59.069 42.308 0.00 0.00 0.00 5.69
5007 6213 7.419057 CCCTAAATATATATCACATCCTGCCGT 60.419 40.741 0.00 0.00 0.00 5.68
5008 6214 7.987458 CCTAAATATATATCACATCCTGCCGTT 59.013 37.037 0.00 0.00 0.00 4.44
5009 6215 9.383519 CTAAATATATATCACATCCTGCCGTTT 57.616 33.333 0.00 0.00 0.00 3.60
5010 6216 8.635765 AAATATATATCACATCCTGCCGTTTT 57.364 30.769 0.00 0.00 0.00 2.43
5011 6217 8.635765 AATATATATCACATCCTGCCGTTTTT 57.364 30.769 0.00 0.00 0.00 1.94
5012 6218 4.900635 ATATCACATCCTGCCGTTTTTC 57.099 40.909 0.00 0.00 0.00 2.29
5013 6219 1.243902 TCACATCCTGCCGTTTTTCC 58.756 50.000 0.00 0.00 0.00 3.13
5014 6220 0.958091 CACATCCTGCCGTTTTTCCA 59.042 50.000 0.00 0.00 0.00 3.53
5015 6221 1.339610 CACATCCTGCCGTTTTTCCAA 59.660 47.619 0.00 0.00 0.00 3.53
5016 6222 2.029110 CACATCCTGCCGTTTTTCCAAT 60.029 45.455 0.00 0.00 0.00 3.16
5017 6223 2.632512 ACATCCTGCCGTTTTTCCAATT 59.367 40.909 0.00 0.00 0.00 2.32
5018 6224 3.070878 ACATCCTGCCGTTTTTCCAATTT 59.929 39.130 0.00 0.00 0.00 1.82
5019 6225 3.828875 TCCTGCCGTTTTTCCAATTTT 57.171 38.095 0.00 0.00 0.00 1.82
5020 6226 4.143986 TCCTGCCGTTTTTCCAATTTTT 57.856 36.364 0.00 0.00 0.00 1.94
5085 6592 4.342862 CGGAGGGACATCTGTGAATATT 57.657 45.455 0.00 0.00 0.00 1.28
5163 6712 7.432350 TCATGGTGAACAATTTTTAATTGGC 57.568 32.000 14.55 8.10 33.56 4.52
5164 6713 6.429385 TCATGGTGAACAATTTTTAATTGGCC 59.571 34.615 14.55 0.00 33.56 5.36
5166 6715 5.994668 TGGTGAACAATTTTTAATTGGCCTC 59.005 36.000 3.32 9.34 33.56 4.70
5167 6716 5.411361 GGTGAACAATTTTTAATTGGCCTCC 59.589 40.000 3.32 11.53 33.56 4.30
5168 6717 5.411361 GTGAACAATTTTTAATTGGCCTCCC 59.589 40.000 3.32 0.02 33.56 4.30
5169 6718 4.200838 ACAATTTTTAATTGGCCTCCCG 57.799 40.909 3.32 0.00 33.56 5.14
5171 6720 1.633774 TTTTTAATTGGCCTCCCGCA 58.366 45.000 3.32 0.00 40.31 5.69
5172 6721 1.633774 TTTTAATTGGCCTCCCGCAA 58.366 45.000 3.32 0.00 40.31 4.85
5173 6722 1.633774 TTTAATTGGCCTCCCGCAAA 58.366 45.000 3.32 0.00 40.31 3.68
5174 6723 1.633774 TTAATTGGCCTCCCGCAAAA 58.366 45.000 3.32 0.00 40.31 2.44
5175 6724 1.633774 TAATTGGCCTCCCGCAAAAA 58.366 45.000 3.32 0.00 40.31 1.94
5239 6788 8.897752 AGAACATTTATTTCTAGGAACATGAGC 58.102 33.333 0.00 0.00 31.28 4.26
5240 6789 8.579850 AACATTTATTTCTAGGAACATGAGCA 57.420 30.769 0.00 0.00 0.00 4.26
5246 6812 6.959639 TTTCTAGGAACATGAGCAGTTTTT 57.040 33.333 0.00 0.00 0.00 1.94
5254 6820 8.082242 AGGAACATGAGCAGTTTTTATTTACAC 58.918 33.333 0.00 0.00 0.00 2.90
5258 6824 9.840427 ACATGAGCAGTTTTTATTTACACATAC 57.160 29.630 0.00 0.00 0.00 2.39
5276 6842 6.015180 ACACATACAAAACTCTCCATTGCAAT 60.015 34.615 5.99 5.99 0.00 3.56
5278 6844 8.028354 CACATACAAAACTCTCCATTGCAATAA 58.972 33.333 12.53 2.49 0.00 1.40
5283 6849 9.995003 ACAAAACTCTCCATTGCAATAATTTTA 57.005 25.926 12.53 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.442047 TCACATTGTTTTAGGAAAATGTTTTGT 57.558 25.926 0.00 0.00 28.54 2.83
11 12 9.442047 TGTTCACATTGTTTTAGGAAAATGTTT 57.558 25.926 0.00 0.00 28.54 2.83
13 14 9.612066 AATGTTCACATTGTTTTAGGAAAATGT 57.388 25.926 4.32 0.00 44.22 2.71
106 107 2.504175 ACCAGCCACTAAATATCCGTGT 59.496 45.455 0.00 0.00 0.00 4.49
250 254 9.906660 TGTAGAAAAATGGCTGTAACTTTTATG 57.093 29.630 0.00 0.00 0.00 1.90
263 267 2.225491 TCGTGCAGTGTAGAAAAATGGC 59.775 45.455 0.00 0.00 0.00 4.40
373 378 5.518847 CGTTTTGTCTTCTTTTTCCCTTTCC 59.481 40.000 0.00 0.00 0.00 3.13
474 486 1.820481 GACGGTAGCTCTCCTCGCT 60.820 63.158 0.00 0.00 41.35 4.93
728 880 6.269769 AGCAAATGAGAACAAAAATCCCCTTA 59.730 34.615 0.00 0.00 0.00 2.69
837 992 2.327325 AGTATAGACCGGCCCATCAT 57.673 50.000 0.00 0.00 0.00 2.45
846 1001 5.179742 CCTAACTGACAGCTAGTATAGACCG 59.820 48.000 11.10 0.00 42.77 4.79
948 1114 0.692476 TGGAATGGACTGGTCAGTGG 59.308 55.000 8.49 0.00 42.66 4.00
967 1133 1.304134 GGCAGAATTCCGGGTTGGT 60.304 57.895 0.00 0.00 39.52 3.67
969 1135 1.202348 GAAAGGCAGAATTCCGGGTTG 59.798 52.381 0.00 0.00 0.00 3.77
971 1137 0.323451 GGAAAGGCAGAATTCCGGGT 60.323 55.000 0.00 0.00 36.09 5.28
972 1138 2.493547 GGAAAGGCAGAATTCCGGG 58.506 57.895 0.00 0.00 36.09 5.73
975 1141 1.549203 TGCAGGAAAGGCAGAATTCC 58.451 50.000 0.65 0.00 44.45 3.01
1187 1356 3.373226 CGGAACCAACGGGAGAGA 58.627 61.111 0.00 0.00 38.05 3.10
1195 1365 0.035739 TAGTGAAGGCCGGAACCAAC 59.964 55.000 5.05 0.00 0.00 3.77
1262 1516 4.585162 GCCATACTACATGACTACTCCACT 59.415 45.833 0.00 0.00 0.00 4.00
1291 1545 5.013079 ACCACCAGACTTCATCAAATCACTA 59.987 40.000 0.00 0.00 0.00 2.74
1298 1552 3.855255 TGAACCACCAGACTTCATCAA 57.145 42.857 0.00 0.00 0.00 2.57
1301 1555 4.228210 ACCATATGAACCACCAGACTTCAT 59.772 41.667 3.65 0.00 38.08 2.57
1306 1560 4.163458 TCCTAACCATATGAACCACCAGAC 59.837 45.833 3.65 0.00 0.00 3.51
1308 1562 4.771114 TCCTAACCATATGAACCACCAG 57.229 45.455 3.65 0.00 0.00 4.00
1331 1585 8.147058 CACACTGCTATATTAGAGAAGTCCAAT 58.853 37.037 0.00 0.00 0.00 3.16
1373 1632 6.981559 GTCTAACCTAACCTCTAAAGCATCAG 59.018 42.308 0.00 0.00 0.00 2.90
1458 1734 6.373186 ACAGATACATACGAAATCACTCGA 57.627 37.500 0.00 0.00 41.44 4.04
1494 1770 3.513515 AGCTTGATTTTGGGGCGAAAATA 59.486 39.130 5.99 0.00 36.00 1.40
1562 1853 8.810041 GCCAGGCTAGTACTAGGTAATAATAAA 58.190 37.037 27.24 0.00 33.87 1.40
1755 2050 1.227639 TCCTCGCGACAGCTAGTATC 58.772 55.000 3.71 0.00 42.32 2.24
1788 2083 4.096833 TCAAGAATCATGTTGCCATACTGC 59.903 41.667 0.00 0.00 30.21 4.40
2044 2350 4.891992 TTTCTTAGCAAGCTACTGGAGT 57.108 40.909 0.40 0.00 0.00 3.85
2045 2351 4.633565 CCTTTTCTTAGCAAGCTACTGGAG 59.366 45.833 0.40 0.00 0.00 3.86
2048 2354 5.295540 GGATCCTTTTCTTAGCAAGCTACTG 59.704 44.000 3.84 0.00 0.00 2.74
2049 2355 5.432645 GGATCCTTTTCTTAGCAAGCTACT 58.567 41.667 3.84 0.00 0.00 2.57
2050 2356 4.576873 GGGATCCTTTTCTTAGCAAGCTAC 59.423 45.833 12.58 0.00 0.00 3.58
2051 2357 4.475016 AGGGATCCTTTTCTTAGCAAGCTA 59.525 41.667 12.58 0.00 0.00 3.32
2052 2358 3.268072 AGGGATCCTTTTCTTAGCAAGCT 59.732 43.478 12.58 0.00 0.00 3.74
2053 2359 3.625853 AGGGATCCTTTTCTTAGCAAGC 58.374 45.455 12.58 0.00 0.00 4.01
2054 2360 6.418946 ACTAAGGGATCCTTTTCTTAGCAAG 58.581 40.000 24.39 13.45 41.69 4.01
2055 2361 6.388619 ACTAAGGGATCCTTTTCTTAGCAA 57.611 37.500 24.39 4.06 41.69 3.91
2056 2362 6.388619 AACTAAGGGATCCTTTTCTTAGCA 57.611 37.500 24.39 4.66 41.69 3.49
2057 2363 7.704578 AAAACTAAGGGATCCTTTTCTTAGC 57.295 36.000 24.39 3.74 41.69 3.09
2060 2366 9.601810 ATGTTAAAACTAAGGGATCCTTTTCTT 57.398 29.630 15.13 10.09 41.69 2.52
2061 2367 9.025041 CATGTTAAAACTAAGGGATCCTTTTCT 57.975 33.333 15.13 0.00 41.69 2.52
2062 2368 9.020731 TCATGTTAAAACTAAGGGATCCTTTTC 57.979 33.333 15.13 0.00 41.69 2.29
2063 2369 8.950007 TCATGTTAAAACTAAGGGATCCTTTT 57.050 30.769 15.13 13.23 41.69 2.27
2064 2370 7.615757 CCTCATGTTAAAACTAAGGGATCCTTT 59.384 37.037 14.31 14.31 41.69 3.11
2065 2371 7.119387 CCTCATGTTAAAACTAAGGGATCCTT 58.881 38.462 12.58 0.00 46.63 3.36
2155 2547 2.071688 AGTAAGCAACTCGAGCACAG 57.928 50.000 13.61 0.71 30.33 3.66
2156 2548 2.135139 CAAGTAAGCAACTCGAGCACA 58.865 47.619 13.61 0.00 37.50 4.57
2157 2549 1.136224 GCAAGTAAGCAACTCGAGCAC 60.136 52.381 13.61 1.63 37.50 4.40
2158 2550 1.148310 GCAAGTAAGCAACTCGAGCA 58.852 50.000 13.61 0.00 37.50 4.26
2159 2551 1.148310 TGCAAGTAAGCAACTCGAGC 58.852 50.000 13.61 0.00 42.46 5.03
2168 2560 3.471495 AAACTACGCATGCAAGTAAGC 57.529 42.857 19.57 0.00 0.00 3.09
2169 2561 6.367421 TGTTAAAACTACGCATGCAAGTAAG 58.633 36.000 19.57 9.12 0.00 2.34
2170 2562 6.301687 TGTTAAAACTACGCATGCAAGTAA 57.698 33.333 19.57 8.82 0.00 2.24
2171 2563 5.926214 TGTTAAAACTACGCATGCAAGTA 57.074 34.783 19.57 11.60 0.00 2.24
2172 2564 4.822036 TGTTAAAACTACGCATGCAAGT 57.178 36.364 19.57 17.06 0.00 3.16
2173 2565 5.389778 TCATGTTAAAACTACGCATGCAAG 58.610 37.500 19.57 16.38 37.44 4.01
2174 2566 5.363979 TCATGTTAAAACTACGCATGCAA 57.636 34.783 19.57 3.82 37.44 4.08
2175 2567 4.142708 CCTCATGTTAAAACTACGCATGCA 60.143 41.667 19.57 0.00 37.44 3.96
2176 2568 4.142687 ACCTCATGTTAAAACTACGCATGC 60.143 41.667 7.91 7.91 37.44 4.06
2177 2569 5.545658 ACCTCATGTTAAAACTACGCATG 57.454 39.130 0.00 0.00 38.49 4.06
2178 2570 5.472137 ACAACCTCATGTTAAAACTACGCAT 59.528 36.000 0.00 0.00 34.69 4.73
2179 2571 4.817464 ACAACCTCATGTTAAAACTACGCA 59.183 37.500 0.00 0.00 34.69 5.24
2180 2572 5.352643 ACAACCTCATGTTAAAACTACGC 57.647 39.130 0.00 0.00 34.69 4.42
2181 2573 7.118680 ACCATACAACCTCATGTTAAAACTACG 59.881 37.037 0.00 0.00 34.69 3.51
2182 2574 8.331730 ACCATACAACCTCATGTTAAAACTAC 57.668 34.615 0.00 0.00 34.69 2.73
2183 2575 8.788806 CAACCATACAACCTCATGTTAAAACTA 58.211 33.333 0.00 0.00 34.69 2.24
2184 2576 7.286775 ACAACCATACAACCTCATGTTAAAACT 59.713 33.333 0.00 0.00 34.69 2.66
2185 2577 7.430441 ACAACCATACAACCTCATGTTAAAAC 58.570 34.615 0.00 0.00 34.69 2.43
2186 2578 7.589958 ACAACCATACAACCTCATGTTAAAA 57.410 32.000 0.00 0.00 34.69 1.52
2187 2579 8.693120 TTACAACCATACAACCTCATGTTAAA 57.307 30.769 0.00 0.00 34.69 1.52
2188 2580 7.094549 GCTTACAACCATACAACCTCATGTTAA 60.095 37.037 0.00 0.00 34.69 2.01
2189 2581 6.373216 GCTTACAACCATACAACCTCATGTTA 59.627 38.462 0.00 0.00 34.69 2.41
2190 2582 5.183140 GCTTACAACCATACAACCTCATGTT 59.817 40.000 0.00 0.00 37.80 2.71
2191 2583 4.700213 GCTTACAACCATACAACCTCATGT 59.300 41.667 0.00 0.00 37.32 3.21
2192 2584 4.699735 TGCTTACAACCATACAACCTCATG 59.300 41.667 0.00 0.00 0.00 3.07
2193 2585 4.700213 GTGCTTACAACCATACAACCTCAT 59.300 41.667 0.00 0.00 0.00 2.90
2194 2586 4.069304 GTGCTTACAACCATACAACCTCA 58.931 43.478 0.00 0.00 0.00 3.86
2195 2587 3.124636 CGTGCTTACAACCATACAACCTC 59.875 47.826 0.00 0.00 0.00 3.85
2196 2588 3.071479 CGTGCTTACAACCATACAACCT 58.929 45.455 0.00 0.00 0.00 3.50
2197 2589 2.413634 GCGTGCTTACAACCATACAACC 60.414 50.000 0.00 0.00 0.00 3.77
2198 2590 2.224549 TGCGTGCTTACAACCATACAAC 59.775 45.455 0.00 0.00 0.00 3.32
2199 2591 2.495084 TGCGTGCTTACAACCATACAA 58.505 42.857 0.00 0.00 0.00 2.41
2200 2592 2.171341 TGCGTGCTTACAACCATACA 57.829 45.000 0.00 0.00 0.00 2.29
2201 2593 3.757745 ATTGCGTGCTTACAACCATAC 57.242 42.857 0.00 0.00 0.00 2.39
2202 2594 4.695928 TGTAATTGCGTGCTTACAACCATA 59.304 37.500 4.72 0.00 35.50 2.74
2203 2595 3.504134 TGTAATTGCGTGCTTACAACCAT 59.496 39.130 4.72 0.00 35.50 3.55
2204 2596 2.879026 TGTAATTGCGTGCTTACAACCA 59.121 40.909 4.72 0.00 35.50 3.67
2205 2597 3.546002 TGTAATTGCGTGCTTACAACC 57.454 42.857 4.72 0.00 35.50 3.77
2206 2598 5.283717 CAGATTGTAATTGCGTGCTTACAAC 59.716 40.000 16.68 12.38 45.48 3.32
2207 2599 5.180304 TCAGATTGTAATTGCGTGCTTACAA 59.820 36.000 16.68 16.68 46.23 2.41
2208 2600 4.693095 TCAGATTGTAATTGCGTGCTTACA 59.307 37.500 3.42 3.42 36.36 2.41
2209 2601 5.216566 TCAGATTGTAATTGCGTGCTTAC 57.783 39.130 0.00 0.00 0.00 2.34
2210 2602 5.871465 TTCAGATTGTAATTGCGTGCTTA 57.129 34.783 0.00 0.00 0.00 3.09
2211 2603 4.764679 TTCAGATTGTAATTGCGTGCTT 57.235 36.364 0.00 0.00 0.00 3.91
2212 2604 4.970662 ATTCAGATTGTAATTGCGTGCT 57.029 36.364 0.00 0.00 0.00 4.40
2213 2605 7.504922 TTTAATTCAGATTGTAATTGCGTGC 57.495 32.000 0.00 0.00 0.00 5.34
2215 2607 9.730420 GGTATTTAATTCAGATTGTAATTGCGT 57.270 29.630 0.00 0.00 0.00 5.24
2216 2608 9.950680 AGGTATTTAATTCAGATTGTAATTGCG 57.049 29.630 0.00 0.00 0.00 4.85
2221 2613 9.461312 AGCACAGGTATTTAATTCAGATTGTAA 57.539 29.630 0.00 0.00 0.00 2.41
2223 2615 7.944729 AGCACAGGTATTTAATTCAGATTGT 57.055 32.000 0.00 0.00 0.00 2.71
2224 2616 9.330063 TCTAGCACAGGTATTTAATTCAGATTG 57.670 33.333 0.00 0.00 0.00 2.67
2225 2617 9.553064 CTCTAGCACAGGTATTTAATTCAGATT 57.447 33.333 0.00 0.00 0.00 2.40
2226 2618 8.709308 ACTCTAGCACAGGTATTTAATTCAGAT 58.291 33.333 0.00 0.00 0.00 2.90
2227 2619 8.079211 ACTCTAGCACAGGTATTTAATTCAGA 57.921 34.615 0.00 0.00 0.00 3.27
2228 2620 8.607459 CAACTCTAGCACAGGTATTTAATTCAG 58.393 37.037 0.00 0.00 0.00 3.02
2229 2621 7.065803 GCAACTCTAGCACAGGTATTTAATTCA 59.934 37.037 0.00 0.00 0.00 2.57
2230 2622 7.281100 AGCAACTCTAGCACAGGTATTTAATTC 59.719 37.037 0.00 0.00 0.00 2.17
2231 2623 7.112779 AGCAACTCTAGCACAGGTATTTAATT 58.887 34.615 0.00 0.00 0.00 1.40
2232 2624 6.653989 AGCAACTCTAGCACAGGTATTTAAT 58.346 36.000 0.00 0.00 0.00 1.40
2233 2625 6.049955 AGCAACTCTAGCACAGGTATTTAA 57.950 37.500 0.00 0.00 0.00 1.52
2234 2626 5.677319 AGCAACTCTAGCACAGGTATTTA 57.323 39.130 0.00 0.00 0.00 1.40
2235 2627 4.559862 AGCAACTCTAGCACAGGTATTT 57.440 40.909 0.00 0.00 0.00 1.40
2236 2628 4.559862 AAGCAACTCTAGCACAGGTATT 57.440 40.909 0.00 0.00 0.00 1.89
2237 2629 4.712337 AGTAAGCAACTCTAGCACAGGTAT 59.288 41.667 0.00 0.00 30.33 2.73
2238 2630 4.087182 AGTAAGCAACTCTAGCACAGGTA 58.913 43.478 0.00 0.00 30.33 3.08
2239 2631 2.900546 AGTAAGCAACTCTAGCACAGGT 59.099 45.455 0.00 0.00 30.33 4.00
2240 2632 3.601443 AGTAAGCAACTCTAGCACAGG 57.399 47.619 0.00 0.00 30.33 4.00
3020 3431 7.880160 ACAATACAGCAGCTTTGGAATATTA 57.120 32.000 9.61 0.00 0.00 0.98
3027 3438 4.398988 TGGATAACAATACAGCAGCTTTGG 59.601 41.667 9.61 0.00 0.00 3.28
3270 3682 7.972277 ACACATTTAGATCATGAATTGTGAAGC 59.028 33.333 22.95 0.00 38.38 3.86
3271 3683 9.285770 CACACATTTAGATCATGAATTGTGAAG 57.714 33.333 22.95 15.95 38.38 3.02
3875 4613 1.196581 CGGCAACATGATTTGTGTCGA 59.803 47.619 0.00 0.00 38.99 4.20
3924 4662 4.856487 CACATGCCAAGTTAACCAAATACG 59.144 41.667 0.88 0.00 0.00 3.06
3956 4819 4.989797 TGAAAATCAACATGTTGGATGTGC 59.010 37.500 32.54 20.07 40.78 4.57
3960 4823 7.654520 CACTTTCTGAAAATCAACATGTTGGAT 59.345 33.333 32.54 22.53 40.78 3.41
4351 5264 1.673033 CGGATCTGAGTGGGTGTTCAC 60.673 57.143 0.00 0.00 37.89 3.18
4483 5416 5.779922 AGCAATCAGTTACAGTCGAGTTAA 58.220 37.500 0.00 0.00 0.00 2.01
4484 5417 5.386958 AGCAATCAGTTACAGTCGAGTTA 57.613 39.130 0.00 0.00 0.00 2.24
4520 5453 1.391485 GCCGCATCGATCATGTACATC 59.609 52.381 5.07 0.00 34.56 3.06
4578 5511 7.394016 TCCAATGTCATAACTCATAACAGTGT 58.606 34.615 0.00 0.00 34.97 3.55
4621 5554 3.575630 TCTCGCTTTGCAACACTAGTAG 58.424 45.455 0.00 0.00 0.00 2.57
4622 5555 3.653539 TCTCGCTTTGCAACACTAGTA 57.346 42.857 0.00 0.00 0.00 1.82
4623 5556 2.526304 TCTCGCTTTGCAACACTAGT 57.474 45.000 0.00 0.00 0.00 2.57
4624 5557 3.002246 TGTTTCTCGCTTTGCAACACTAG 59.998 43.478 0.00 0.00 0.00 2.57
4625 5558 2.939756 TGTTTCTCGCTTTGCAACACTA 59.060 40.909 0.00 0.00 0.00 2.74
4626 5559 1.742831 TGTTTCTCGCTTTGCAACACT 59.257 42.857 0.00 0.00 0.00 3.55
4627 5560 2.111756 CTGTTTCTCGCTTTGCAACAC 58.888 47.619 0.00 0.00 0.00 3.32
4629 5562 2.223249 TGACTGTTTCTCGCTTTGCAAC 60.223 45.455 0.00 0.00 0.00 4.17
4630 5563 2.013400 TGACTGTTTCTCGCTTTGCAA 58.987 42.857 0.00 0.00 0.00 4.08
4631 5564 1.662517 TGACTGTTTCTCGCTTTGCA 58.337 45.000 0.00 0.00 0.00 4.08
4632 5565 2.977405 ATGACTGTTTCTCGCTTTGC 57.023 45.000 0.00 0.00 0.00 3.68
4634 5567 4.380531 TCTGAATGACTGTTTCTCGCTTT 58.619 39.130 0.00 0.00 0.00 3.51
4635 5568 3.995199 TCTGAATGACTGTTTCTCGCTT 58.005 40.909 0.00 0.00 0.00 4.68
4636 5569 3.667497 TCTGAATGACTGTTTCTCGCT 57.333 42.857 0.00 0.00 0.00 4.93
4637 5570 3.422343 CGTTCTGAATGACTGTTTCTCGC 60.422 47.826 3.49 0.00 0.00 5.03
4638 5571 3.121944 CCGTTCTGAATGACTGTTTCTCG 59.878 47.826 11.11 0.00 0.00 4.04
4639 5572 4.307432 TCCGTTCTGAATGACTGTTTCTC 58.693 43.478 11.11 0.00 0.00 2.87
4640 5573 4.336889 TCCGTTCTGAATGACTGTTTCT 57.663 40.909 11.11 0.00 0.00 2.52
4641 5574 5.205565 GTTTCCGTTCTGAATGACTGTTTC 58.794 41.667 11.11 0.00 0.00 2.78
4642 5575 4.638421 TGTTTCCGTTCTGAATGACTGTTT 59.362 37.500 11.11 0.00 0.00 2.83
4643 5576 4.196193 TGTTTCCGTTCTGAATGACTGTT 58.804 39.130 11.11 0.00 0.00 3.16
4647 5696 3.564225 ACCTTGTTTCCGTTCTGAATGAC 59.436 43.478 11.11 2.56 0.00 3.06
4691 5896 7.812309 TGACTTACGAAATACAGATGTCTTG 57.188 36.000 0.00 0.00 0.00 3.02
4726 5931 2.765699 TCCTTTCTGTTGCCTTTTTGCT 59.234 40.909 0.00 0.00 0.00 3.91
4752 5957 2.352960 GCCATTTCTCGGAAGCTAACAG 59.647 50.000 0.00 0.00 0.00 3.16
4867 6073 3.857052 CGTATTGCTCAGGTAACCTTGA 58.143 45.455 0.00 0.00 37.17 3.02
4981 6187 6.931281 CGGCAGGATGTGATATATATTTAGGG 59.069 42.308 0.00 0.00 39.31 3.53
4982 6188 7.500992 ACGGCAGGATGTGATATATATTTAGG 58.499 38.462 0.00 0.00 39.31 2.69
4983 6189 8.948631 AACGGCAGGATGTGATATATATTTAG 57.051 34.615 0.00 0.00 39.31 1.85
4984 6190 9.733556 AAAACGGCAGGATGTGATATATATTTA 57.266 29.630 0.00 0.00 39.31 1.40
4985 6191 8.635765 AAAACGGCAGGATGTGATATATATTT 57.364 30.769 0.00 0.00 39.31 1.40
4986 6192 8.635765 AAAAACGGCAGGATGTGATATATATT 57.364 30.769 0.00 0.00 39.31 1.28
4987 6193 7.336931 GGAAAAACGGCAGGATGTGATATATAT 59.663 37.037 0.00 0.00 39.31 0.86
4988 6194 6.653320 GGAAAAACGGCAGGATGTGATATATA 59.347 38.462 0.00 0.00 39.31 0.86
4989 6195 5.473504 GGAAAAACGGCAGGATGTGATATAT 59.526 40.000 0.00 0.00 39.31 0.86
4990 6196 4.819630 GGAAAAACGGCAGGATGTGATATA 59.180 41.667 0.00 0.00 39.31 0.86
4991 6197 3.632145 GGAAAAACGGCAGGATGTGATAT 59.368 43.478 0.00 0.00 39.31 1.63
4992 6198 3.013921 GGAAAAACGGCAGGATGTGATA 58.986 45.455 0.00 0.00 39.31 2.15
4993 6199 1.818674 GGAAAAACGGCAGGATGTGAT 59.181 47.619 0.00 0.00 39.31 3.06
4994 6200 1.243902 GGAAAAACGGCAGGATGTGA 58.756 50.000 0.00 0.00 39.31 3.58
4995 6201 0.958091 TGGAAAAACGGCAGGATGTG 59.042 50.000 0.00 0.00 39.31 3.21
4996 6202 1.698506 TTGGAAAAACGGCAGGATGT 58.301 45.000 0.00 0.00 39.31 3.06
4997 6203 3.317603 AATTGGAAAAACGGCAGGATG 57.682 42.857 0.00 0.00 40.87 3.51
4998 6204 4.350368 AAAATTGGAAAAACGGCAGGAT 57.650 36.364 0.00 0.00 0.00 3.24
4999 6205 3.828875 AAAATTGGAAAAACGGCAGGA 57.171 38.095 0.00 0.00 0.00 3.86
5047 6547 8.053963 TGTCCCTCCGGAAATACAAAATATAAA 58.946 33.333 5.23 0.00 40.92 1.40
5048 6548 7.575505 TGTCCCTCCGGAAATACAAAATATAA 58.424 34.615 5.23 0.00 40.92 0.98
5049 6549 7.139287 TGTCCCTCCGGAAATACAAAATATA 57.861 36.000 5.23 0.00 40.92 0.86
5064 6564 4.342862 AATATTCACAGATGTCCCTCCG 57.657 45.455 0.00 0.00 0.00 4.63
5090 6597 9.165035 TCTTTTGAAAAGTTCATGAATTGCTTT 57.835 25.926 16.41 13.18 39.84 3.51
5150 6699 2.569404 TGCGGGAGGCCAATTAAAAATT 59.431 40.909 5.01 0.00 42.61 1.82
5254 6820 9.590451 AATTATTGCAATGGAGAGTTTTGTATG 57.410 29.630 22.27 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.