Multiple sequence alignment - TraesCS3B01G598500

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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 TraesCS3B01G598500 chr3B 100.000 2870 0 0 1 2870 820122501 820125370 0.000000e+00 5301.0
1 TraesCS3B01G598500 chr3B 90.916 2466 202 12 422 2870 819991954 819989494 0.000000e+00 3293.0
2 TraesCS3B01G598500 chr3B 85.143 1575 223 5 394 1967 820178996 820177432 0.000000e+00 1602.0
3 TraesCS3B01G598500 chr3B 84.983 1445 211 6 422 1863 820185874 820184433 0.000000e+00 1461.0
4 TraesCS3B01G598500 chr3B 86.673 983 122 5 936 1915 820114793 820115769 0.000000e+00 1081.0
5 TraesCS3B01G598500 chr3B 87.342 395 49 1 422 816 820114409 820114802 4.360000e-123 451.0
6 TraesCS3B01G598500 chr3B 84.348 230 26 7 2311 2536 819990472 819990249 1.730000e-52 217.0
7 TraesCS3B01G598500 chr3B 77.011 174 36 4 2641 2811 819458459 819458287 2.350000e-16 97.1
8 TraesCS3B01G598500 chr3A 86.551 1554 200 7 419 1969 742928941 742930488 0.000000e+00 1703.0
9 TraesCS3B01G598500 chr3A 86.286 1349 117 34 1 1319 742954664 742955974 0.000000e+00 1404.0
10 TraesCS3B01G598500 chr3A 87.728 383 34 2 2311 2681 743018885 743019266 4.390000e-118 435.0
11 TraesCS3B01G598500 chr3A 83.032 277 34 9 1894 2161 743018873 743019145 3.700000e-59 239.0
12 TraesCS3B01G598500 chr3A 81.707 82 14 1 2545 2625 225221438 225221357 1.850000e-07 67.6
13 TraesCS3B01G598500 chr3A 94.444 36 2 0 2501 2536 145647175 145647140 3.990000e-04 56.5
14 TraesCS3B01G598500 chr3A 96.875 32 1 0 2501 2532 50054251 50054220 1.000000e-03 54.7
15 TraesCS3B01G598500 chr3D 86.624 1555 186 12 419 1969 609363817 609365353 0.000000e+00 1700.0
16 TraesCS3B01G598500 chr1A 81.395 1677 270 24 422 2068 578941138 578939474 0.000000e+00 1330.0
17 TraesCS3B01G598500 chr1D 83.281 957 147 9 422 1377 482243461 482242517 0.000000e+00 869.0
18 TraesCS3B01G598500 chr1D 83.857 477 76 1 1401 1877 482242523 482242048 1.210000e-123 453.0
19 TraesCS3B01G598500 chr1D 82.034 295 45 7 34 322 335359530 335359822 7.940000e-61 244.0
20 TraesCS3B01G598500 chr1D 82.069 145 18 7 2637 2775 8278346 8278204 1.810000e-22 117.0
21 TraesCS3B01G598500 chr2A 80.864 162 26 5 2631 2789 726134614 726134455 3.880000e-24 122.0
22 TraesCS3B01G598500 chr2A 85.882 85 8 3 248 328 766842876 766842960 1.420000e-13 87.9
23 TraesCS3B01G598500 chr2A 90.698 43 2 2 2491 2533 255836883 255836923 3.990000e-04 56.5
24 TraesCS3B01G598500 chr7B 81.757 148 24 3 2642 2787 394807051 394806905 1.400000e-23 121.0
25 TraesCS3B01G598500 chr5B 84.034 119 18 1 2680 2797 499386799 499386681 2.340000e-21 113.0
26 TraesCS3B01G598500 chr5B 74.860 179 41 4 1440 1616 644612179 644612003 8.530000e-11 78.7
27 TraesCS3B01G598500 chr2D 80.420 143 27 1 2671 2812 465949915 465950057 1.090000e-19 108.0
28 TraesCS3B01G598500 chr4D 80.420 143 24 4 2632 2771 487357349 487357208 3.910000e-19 106.0
29 TraesCS3B01G598500 chr1B 77.976 168 33 4 2648 2813 390612701 390612536 5.060000e-18 102.0
30 TraesCS3B01G598500 chr2B 73.913 230 52 8 1397 1622 6179666 6179891 5.090000e-13 86.1
31 TraesCS3B01G598500 chr4B 91.111 45 2 2 2488 2532 83482804 83482846 3.090000e-05 60.2
32 TraesCS3B01G598500 chr4A 94.444 36 2 0 2501 2536 148410494 148410459 3.990000e-04 56.5
33 TraesCS3B01G598500 chr4A 88.889 45 3 2 2488 2532 83363168 83363210 1.000000e-03 54.7


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 TraesCS3B01G598500 chr3B 820122501 820125370 2869 False 5301 5301 100.0000 1 2870 1 chr3B.!!$F1 2869
1 TraesCS3B01G598500 chr3B 819989494 819991954 2460 True 1755 3293 87.6320 422 2870 2 chr3B.!!$R4 2448
2 TraesCS3B01G598500 chr3B 820177432 820178996 1564 True 1602 1602 85.1430 394 1967 1 chr3B.!!$R2 1573
3 TraesCS3B01G598500 chr3B 820184433 820185874 1441 True 1461 1461 84.9830 422 1863 1 chr3B.!!$R3 1441
4 TraesCS3B01G598500 chr3B 820114409 820115769 1360 False 766 1081 87.0075 422 1915 2 chr3B.!!$F2 1493
5 TraesCS3B01G598500 chr3A 742928941 742930488 1547 False 1703 1703 86.5510 419 1969 1 chr3A.!!$F1 1550
6 TraesCS3B01G598500 chr3A 742954664 742955974 1310 False 1404 1404 86.2860 1 1319 1 chr3A.!!$F2 1318
7 TraesCS3B01G598500 chr3D 609363817 609365353 1536 False 1700 1700 86.6240 419 1969 1 chr3D.!!$F1 1550
8 TraesCS3B01G598500 chr1A 578939474 578941138 1664 True 1330 1330 81.3950 422 2068 1 chr1A.!!$R1 1646
9 TraesCS3B01G598500 chr1D 482242048 482243461 1413 True 661 869 83.5690 422 1877 2 chr1D.!!$R2 1455

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
92 93 0.028770 AACGGAACATGCGTGTGTTG 59.971 50.0 13.39 7.68 45.62 3.33 F
385 420 0.179161 CTTCTACCTCGACAGTGCCG 60.179 60.0 0.00 0.00 0.00 5.69 F
1455 1495 0.039180 TAGAGCGGACCAAGTGGAGA 59.961 55.0 3.83 0.00 38.94 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1067 1103 0.314302 ACGACTCTCCAACAACTCGG 59.686 55.0 0.00 0.0 0.00 4.63 R
1685 1725 0.622665 CTTGGCCTCCACCTCATCTT 59.377 55.0 3.32 0.0 30.78 2.40 R
2810 2890 0.035439 AACGCCGAGTGAATCCCAAT 60.035 50.0 0.00 0.0 0.00 3.16 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
54 55 0.811616 GAAGGCGGCCATCTACACTG 60.812 60.000 23.09 0.00 0.00 3.66
75 76 4.579869 TGCTTAGAACATCTGGAAGGAAC 58.420 43.478 0.00 0.00 0.00 3.62
92 93 0.028770 AACGGAACATGCGTGTGTTG 59.971 50.000 13.39 7.68 45.62 3.33
115 116 0.529378 CACCATTTGCTCCAGGAAGC 59.471 55.000 0.00 0.00 42.82 3.86
125 126 1.767681 CTCCAGGAAGCTGCTATCCTT 59.232 52.381 22.47 11.22 43.59 3.36
133 134 4.444022 GGAAGCTGCTATCCTTCATCTCAA 60.444 45.833 17.89 0.00 39.30 3.02
146 155 5.391736 CCTTCATCTCAACAAGCAAGACATC 60.392 44.000 0.00 0.00 0.00 3.06
155 164 3.326006 ACAAGCAAGACATCTCTCTTCCA 59.674 43.478 0.00 0.00 0.00 3.53
158 167 4.032310 AGCAAGACATCTCTCTTCCATCT 58.968 43.478 0.00 0.00 0.00 2.90
171 180 3.818210 TCTTCCATCTATCTCTGCTCGTC 59.182 47.826 0.00 0.00 0.00 4.20
172 181 3.214696 TCCATCTATCTCTGCTCGTCA 57.785 47.619 0.00 0.00 0.00 4.35
192 201 2.419324 CAGCTTTCTGATGCAGAGAACC 59.581 50.000 9.86 5.59 41.75 3.62
197 206 0.742281 CTGATGCAGAGAACCCACCG 60.742 60.000 0.00 0.00 32.44 4.94
202 211 1.003718 CAGAGAACCCACCGGAACC 60.004 63.158 9.46 0.00 0.00 3.62
203 212 1.152096 AGAGAACCCACCGGAACCT 60.152 57.895 9.46 0.00 0.00 3.50
204 213 1.003718 GAGAACCCACCGGAACCTG 60.004 63.158 9.46 0.00 0.00 4.00
205 214 1.460689 AGAACCCACCGGAACCTGA 60.461 57.895 9.46 0.00 0.00 3.86
206 215 1.003718 GAACCCACCGGAACCTGAG 60.004 63.158 9.46 0.00 0.00 3.35
207 216 3.192103 AACCCACCGGAACCTGAGC 62.192 63.158 9.46 0.00 0.00 4.26
209 218 3.636231 CCACCGGAACCTGAGCCA 61.636 66.667 9.46 0.00 0.00 4.75
229 258 6.248433 AGCCAGACTGATCCTTTTATTTTCA 58.752 36.000 3.32 0.00 0.00 2.69
233 262 7.417116 CCAGACTGATCCTTTTATTTTCATGGG 60.417 40.741 3.32 0.00 0.00 4.00
262 291 1.276989 CCGTAACCCCACACTGTGTAT 59.723 52.381 13.89 0.88 0.00 2.29
264 293 2.028839 CGTAACCCCACACTGTGTATCA 60.029 50.000 13.89 0.00 0.00 2.15
275 304 7.309133 CCCACACTGTGTATCATAACATTTGTT 60.309 37.037 13.89 1.08 41.73 2.83
351 386 6.426646 AGAATTTCCACGCTCCTCTATATT 57.573 37.500 0.00 0.00 0.00 1.28
357 392 7.956328 TTCCACGCTCCTCTATATTGTATAT 57.044 36.000 0.00 0.00 0.00 0.86
377 412 4.571369 ATCCGGATATCTTCTACCTCGA 57.429 45.455 17.43 0.00 0.00 4.04
385 420 0.179161 CTTCTACCTCGACAGTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
411 446 1.963515 AGTGCCACCTCCAAAACATTC 59.036 47.619 0.00 0.00 0.00 2.67
416 451 3.769300 GCCACCTCCAAAACATTCCTAAT 59.231 43.478 0.00 0.00 0.00 1.73
454 489 2.428622 GGTGTTGTACCCTGGCGT 59.571 61.111 0.00 0.00 44.15 5.68
456 491 1.670083 GTGTTGTACCCTGGCGTCC 60.670 63.158 0.00 0.00 0.00 4.79
563 598 3.555168 CGTCCTTTAAGTTGCCAGTCTCT 60.555 47.826 0.00 0.00 0.00 3.10
615 651 1.482182 CACATCCGTCCATCTCCTTCA 59.518 52.381 0.00 0.00 0.00 3.02
624 660 3.198635 GTCCATCTCCTTCAATGTCCTCA 59.801 47.826 0.00 0.00 0.00 3.86
625 661 4.042884 TCCATCTCCTTCAATGTCCTCAT 58.957 43.478 0.00 0.00 35.59 2.90
643 679 0.477204 ATGTCCATCCATGCTCCAGG 59.523 55.000 0.00 0.00 0.00 4.45
691 727 5.590530 TTCTTACTCATTCTCCAGCTCTC 57.409 43.478 0.00 0.00 0.00 3.20
693 729 1.846007 ACTCATTCTCCAGCTCTCGT 58.154 50.000 0.00 0.00 0.00 4.18
746 782 1.439679 GAGCCGTCGACCAGAAAAAT 58.560 50.000 10.58 0.00 0.00 1.82
760 796 5.127682 ACCAGAAAAATCTTGCACTCTGTTT 59.872 36.000 0.00 0.00 30.55 2.83
828 864 1.007336 GCGTCCCTGTCTACACGTTG 61.007 60.000 0.00 0.00 34.69 4.10
832 868 2.033372 TCCCTGTCTACACGTTGTTCA 58.967 47.619 0.00 0.00 0.00 3.18
866 902 2.584608 CCTGTCAGCCCTAACCCG 59.415 66.667 0.00 0.00 0.00 5.28
964 1000 1.363807 CCGATGCCAGCGTCTCATA 59.636 57.895 0.28 0.00 0.00 2.15
973 1009 3.801638 GCCAGCGTCTCATATCATCAAGT 60.802 47.826 0.00 0.00 0.00 3.16
989 1025 6.188407 TCATCAAGTAACTACTAGAGCACCT 58.812 40.000 0.00 0.00 34.99 4.00
990 1026 7.344134 TCATCAAGTAACTACTAGAGCACCTA 58.656 38.462 0.00 0.00 34.99 3.08
1066 1102 2.401766 GGCATCCTGCTGAACACGG 61.402 63.158 0.00 0.00 44.28 4.94
1067 1103 3.044059 GCATCCTGCTGAACACGGC 62.044 63.158 0.00 0.00 40.96 5.68
1089 1125 0.249911 AGTTGTTGGAGAGTCGTGCC 60.250 55.000 0.00 0.00 0.00 5.01
1163 1199 1.252215 TACTGCGTTGGTCCATCGGA 61.252 55.000 20.99 17.97 0.00 4.55
1190 1229 1.318158 GGCACCAAGGATGAAGGCAG 61.318 60.000 0.00 0.00 0.00 4.85
1195 1234 1.615116 CCAAGGATGAAGGCAGAGCAA 60.615 52.381 0.00 0.00 0.00 3.91
1254 1293 0.823356 ACCGCAGCATTGTGTTCCTT 60.823 50.000 0.00 0.00 32.87 3.36
1259 1298 2.796593 GCAGCATTGTGTTCCTTTGTTC 59.203 45.455 0.00 0.00 0.00 3.18
1262 1301 2.223711 GCATTGTGTTCCTTTGTTCCGT 60.224 45.455 0.00 0.00 0.00 4.69
1352 1391 2.845752 TTCCTATGGTCCGTGCGCAC 62.846 60.000 30.42 30.42 0.00 5.34
1381 1421 3.119096 GCGACAGCCCGGAGAAAC 61.119 66.667 0.73 0.00 37.42 2.78
1450 1490 2.501261 GGTTTTTAGAGCGGACCAAGT 58.499 47.619 0.00 0.00 0.00 3.16
1452 1492 2.178912 TTTTAGAGCGGACCAAGTGG 57.821 50.000 0.00 0.00 42.17 4.00
1455 1495 0.039180 TAGAGCGGACCAAGTGGAGA 59.961 55.000 3.83 0.00 38.94 3.71
1498 1538 4.994744 CACAGATGGACGTGCTCA 57.005 55.556 8.99 0.00 0.00 4.26
1638 1678 5.130705 AGGTGTCTATGACAGAGGACATA 57.869 43.478 0.20 0.00 43.57 2.29
1641 1681 4.890581 GTGTCTATGACAGAGGACATAGGT 59.109 45.833 0.00 0.00 43.57 3.08
1670 1710 1.622811 GGAGCTGGAGGGATACATGAG 59.377 57.143 0.00 0.00 39.74 2.90
1685 1725 7.420214 GGGATACATGAGAGGTTTTATCAAGGA 60.420 40.741 0.00 0.00 39.74 3.36
1728 1768 0.393808 GGCTGGTAATTGAGGGCGAA 60.394 55.000 0.00 0.00 0.00 4.70
1808 1848 2.120718 AGAAGGTGGCCCGTCTCT 59.879 61.111 0.00 0.00 45.15 3.10
1871 1911 1.841302 AAGCAGCTCGGGGAATGACA 61.841 55.000 0.00 0.00 0.00 3.58
1999 2051 5.294552 AGCACCTTCTTTATAAATCGTCTGC 59.705 40.000 0.00 4.22 0.00 4.26
2007 2059 3.895232 ATAAATCGTCTGCCTGAGTGT 57.105 42.857 0.00 0.00 0.00 3.55
2011 2063 2.340078 GTCTGCCTGAGTGTCGCA 59.660 61.111 0.00 0.00 0.00 5.10
2022 2074 0.669318 AGTGTCGCATACCGTGGTTG 60.669 55.000 0.00 0.00 38.35 3.77
2035 2087 2.556622 CCGTGGTTGCCTCTACAAAATT 59.443 45.455 0.00 0.00 0.00 1.82
2105 2157 7.908453 AGCTAAAGTGTGAGAAGTACCTAATT 58.092 34.615 0.00 0.00 0.00 1.40
2147 2199 7.652909 CAGTTACCAATTGAATTCACATGTGTT 59.347 33.333 24.63 13.25 0.00 3.32
2172 2224 4.782691 TGTTCTTGGGAGTGGATAATCTCA 59.217 41.667 0.00 0.00 32.93 3.27
2174 2226 4.883759 TCTTGGGAGTGGATAATCTCAGA 58.116 43.478 0.00 0.00 32.27 3.27
2218 2270 7.063456 CGCAGTAGTATGTACATTTATGTTGC 58.937 38.462 14.77 15.07 41.97 4.17
2232 2284 2.327325 TGTTGCCTTCTACTCCCTCT 57.673 50.000 0.00 0.00 0.00 3.69
2233 2285 1.902508 TGTTGCCTTCTACTCCCTCTG 59.097 52.381 0.00 0.00 0.00 3.35
2237 2289 2.567615 TGCCTTCTACTCCCTCTGTTTC 59.432 50.000 0.00 0.00 0.00 2.78
2315 2367 1.541588 GAAATGGAGGGACTGTGTTGC 59.458 52.381 0.00 0.00 41.55 4.17
2400 2467 6.350906 TCTACCACCTTGTTAATAAATCGGG 58.649 40.000 0.00 0.00 0.00 5.14
2404 2471 6.071784 ACCACCTTGTTAATAAATCGGGTTTC 60.072 38.462 0.00 0.00 0.00 2.78
2626 2705 2.905415 ATGATGCCCTTTTGAGGACA 57.095 45.000 0.00 0.00 0.00 4.02
2645 2724 0.107459 AGCGGGAGGAATCTTGCTTC 60.107 55.000 0.00 0.00 0.00 3.86
2662 2741 4.058817 TGCTTCGTTTTGGTGTTTTTGTT 58.941 34.783 0.00 0.00 0.00 2.83
2663 2742 5.227908 TGCTTCGTTTTGGTGTTTTTGTTA 58.772 33.333 0.00 0.00 0.00 2.41
2664 2743 5.346281 TGCTTCGTTTTGGTGTTTTTGTTAG 59.654 36.000 0.00 0.00 0.00 2.34
2678 2757 7.436970 GTGTTTTTGTTAGTTCATTTAGGGGTG 59.563 37.037 0.00 0.00 0.00 4.61
2689 2768 2.242882 TTAGGGGTGGTGTCCTACTC 57.757 55.000 0.00 0.00 35.56 2.59
2749 2828 1.464734 GGTTTTCCTGCCTAGCCTTC 58.535 55.000 0.00 0.00 36.94 3.46
2750 2829 1.271926 GGTTTTCCTGCCTAGCCTTCA 60.272 52.381 0.00 0.00 36.94 3.02
2756 2836 0.548031 CTGCCTAGCCTTCATTCCCA 59.452 55.000 0.00 0.00 0.00 4.37
2782 2862 1.869767 CGTCTAGCATCATTGAAGGGC 59.130 52.381 0.00 0.00 0.00 5.19
2789 2869 2.288030 GCATCATTGAAGGGCATGTAGC 60.288 50.000 0.00 0.00 44.65 3.58
2810 2890 3.118408 GCCATGTGTTACCAGTGGATCTA 60.118 47.826 18.40 0.00 31.99 1.98
2821 2901 4.141390 ACCAGTGGATCTATTGGGATTCAC 60.141 45.833 22.04 7.57 46.91 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.534203 GGCCGTTCCTTGAAGACACA 60.534 55.000 0.00 0.00 0.00 3.72
54 55 3.619038 CGTTCCTTCCAGATGTTCTAAGC 59.381 47.826 0.00 0.00 0.00 3.09
75 76 1.082169 CCAACACACGCATGTTCCG 60.082 57.895 2.06 0.00 40.89 4.30
107 108 1.487976 TGAAGGATAGCAGCTTCCTGG 59.512 52.381 20.54 0.00 41.58 4.45
108 109 2.996249 TGAAGGATAGCAGCTTCCTG 57.004 50.000 20.54 0.00 41.58 3.86
109 110 3.316501 AGATGAAGGATAGCAGCTTCCT 58.683 45.455 16.35 16.35 44.35 3.36
110 111 3.070734 TGAGATGAAGGATAGCAGCTTCC 59.929 47.826 0.00 7.88 29.81 3.46
111 112 4.333913 TGAGATGAAGGATAGCAGCTTC 57.666 45.455 0.00 0.00 29.81 3.86
112 113 4.080695 TGTTGAGATGAAGGATAGCAGCTT 60.081 41.667 0.00 0.00 29.81 3.74
113 114 3.453717 TGTTGAGATGAAGGATAGCAGCT 59.546 43.478 0.00 0.00 32.77 4.24
114 115 3.801698 TGTTGAGATGAAGGATAGCAGC 58.198 45.455 0.00 0.00 0.00 5.25
115 116 4.272991 GCTTGTTGAGATGAAGGATAGCAG 59.727 45.833 0.00 0.00 0.00 4.24
125 126 4.903054 AGATGTCTTGCTTGTTGAGATGA 58.097 39.130 0.00 0.00 0.00 2.92
133 134 3.326006 TGGAAGAGAGATGTCTTGCTTGT 59.674 43.478 11.52 0.00 43.38 3.16
146 155 4.154737 CGAGCAGAGATAGATGGAAGAGAG 59.845 50.000 0.00 0.00 0.00 3.20
171 180 2.419324 GGTTCTCTGCATCAGAAAGCTG 59.581 50.000 9.29 0.00 40.18 4.24
172 181 2.617532 GGGTTCTCTGCATCAGAAAGCT 60.618 50.000 9.29 0.00 40.18 3.74
184 193 1.003718 GGTTCCGGTGGGTTCTCTG 60.004 63.158 0.00 0.00 33.83 3.35
192 201 3.612247 CTGGCTCAGGTTCCGGTGG 62.612 68.421 0.00 0.00 0.00 4.61
197 206 0.908198 ATCAGTCTGGCTCAGGTTCC 59.092 55.000 0.00 0.00 31.51 3.62
202 211 3.347077 AAAAGGATCAGTCTGGCTCAG 57.653 47.619 0.00 0.00 0.00 3.35
203 212 5.441718 AATAAAAGGATCAGTCTGGCTCA 57.558 39.130 0.00 0.00 0.00 4.26
204 213 6.375455 TGAAAATAAAAGGATCAGTCTGGCTC 59.625 38.462 0.00 0.00 0.00 4.70
205 214 6.248433 TGAAAATAAAAGGATCAGTCTGGCT 58.752 36.000 0.00 0.00 0.00 4.75
206 215 6.515272 TGAAAATAAAAGGATCAGTCTGGC 57.485 37.500 0.00 0.00 0.00 4.85
207 216 7.417116 CCCATGAAAATAAAAGGATCAGTCTGG 60.417 40.741 0.00 0.00 0.00 3.86
209 218 6.608808 CCCCATGAAAATAAAAGGATCAGTCT 59.391 38.462 0.00 0.00 0.00 3.24
244 273 3.688694 TGATACACAGTGTGGGGTTAC 57.311 47.619 26.40 11.86 37.94 2.50
245 274 5.248705 TGTTATGATACACAGTGTGGGGTTA 59.751 40.000 26.40 10.65 37.94 2.85
287 319 8.353423 CAGTTGGGCTGCCTTAATATAATAAT 57.647 34.615 19.68 0.00 38.52 1.28
351 386 6.990939 CGAGGTAGAAGATATCCGGATATACA 59.009 42.308 32.15 11.99 34.36 2.29
357 392 3.072038 TGTCGAGGTAGAAGATATCCGGA 59.928 47.826 6.61 6.61 0.00 5.14
377 412 4.935495 CACTGGCACCGGCACTGT 62.935 66.667 0.00 0.00 43.71 3.55
411 446 5.350914 CAGTCTGCTTCTTCTTGACATTAGG 59.649 44.000 0.00 0.00 0.00 2.69
416 451 3.461061 CACAGTCTGCTTCTTCTTGACA 58.539 45.455 0.00 0.00 0.00 3.58
456 491 2.202171 GCAAACATGACCGACGCG 60.202 61.111 3.53 3.53 0.00 6.01
471 506 2.993008 GAGCTCTGTCATGGGGCA 59.007 61.111 6.43 0.00 0.00 5.36
534 569 2.488153 GCAACTTAAAGGACGGCTTGAT 59.512 45.455 0.00 0.00 0.00 2.57
543 578 3.244561 CCAGAGACTGGCAACTTAAAGGA 60.245 47.826 4.84 0.00 45.13 3.36
596 632 1.866015 TGAAGGAGATGGACGGATGT 58.134 50.000 0.00 0.00 0.00 3.06
597 633 2.988010 TTGAAGGAGATGGACGGATG 57.012 50.000 0.00 0.00 0.00 3.51
624 660 0.477204 CCTGGAGCATGGATGGACAT 59.523 55.000 0.00 0.00 0.00 3.06
625 661 1.917495 CCTGGAGCATGGATGGACA 59.083 57.895 0.00 0.00 0.00 4.02
691 727 5.849604 TCGAACTGCTCATTATAATCGTACG 59.150 40.000 9.53 9.53 0.00 3.67
693 729 6.362551 GCTTCGAACTGCTCATTATAATCGTA 59.637 38.462 0.00 0.00 0.00 3.43
739 775 6.097412 AGGAAAACAGAGTGCAAGATTTTTCT 59.903 34.615 15.65 8.72 33.79 2.52
746 782 2.102420 TCGAGGAAAACAGAGTGCAAGA 59.898 45.455 0.00 0.00 0.00 3.02
760 796 2.743664 CAATGCAGAACATGTCGAGGAA 59.256 45.455 0.00 0.00 39.60 3.36
828 864 2.435059 GAGGCGCTCCCTGTGAAC 60.435 66.667 7.64 0.00 46.60 3.18
832 868 4.479993 GCATGAGGCGCTCCCTGT 62.480 66.667 7.64 0.00 46.60 4.00
866 902 0.603975 GGCAATCAGTATCGGGAGCC 60.604 60.000 0.00 0.00 0.00 4.70
964 1000 6.836527 AGGTGCTCTAGTAGTTACTTGATGAT 59.163 38.462 4.37 0.00 37.42 2.45
973 1009 7.803131 TCATCTTCTAGGTGCTCTAGTAGTTA 58.197 38.462 15.23 4.48 44.45 2.24
989 1025 3.432749 GGCCTTGCACATCTCATCTTCTA 60.433 47.826 0.00 0.00 0.00 2.10
990 1026 2.641305 GCCTTGCACATCTCATCTTCT 58.359 47.619 0.00 0.00 0.00 2.85
1066 1102 1.009389 CGACTCTCCAACAACTCGGC 61.009 60.000 0.00 0.00 0.00 5.54
1067 1103 0.314302 ACGACTCTCCAACAACTCGG 59.686 55.000 0.00 0.00 0.00 4.63
1089 1125 4.087892 CCCCTGGGAGACTGCACG 62.088 72.222 16.20 0.00 37.50 5.34
1163 1199 4.974721 CCTTGGTGCCCTTGCCGT 62.975 66.667 0.00 0.00 36.33 5.68
1187 1226 1.512926 TTCGTTCCTCTTTGCTCTGC 58.487 50.000 0.00 0.00 0.00 4.26
1190 1229 1.131315 GGCATTCGTTCCTCTTTGCTC 59.869 52.381 0.00 0.00 0.00 4.26
1195 1234 3.442996 CGAGGCATTCGTTCCTCTT 57.557 52.632 6.70 0.00 45.12 2.85
1254 1293 1.896660 GCCCTTGCTCACGGAACAA 60.897 57.895 0.00 0.00 33.53 2.83
1312 1351 2.373707 GCTGCCCTGACCTCTCCAT 61.374 63.158 0.00 0.00 0.00 3.41
1352 1391 2.031012 TGTCGCTTCCAGCAGGTG 59.969 61.111 0.00 0.00 42.58 4.00
1407 1447 2.172483 GAGGAAGGAGCACGCCAAGA 62.172 60.000 0.00 0.00 0.00 3.02
1434 1474 1.275291 CTCCACTTGGTCCGCTCTAAA 59.725 52.381 0.00 0.00 36.34 1.85
1450 1490 2.680352 GACGACCAGGCCTCTCCA 60.680 66.667 0.00 0.00 37.29 3.86
1452 1492 1.216710 CTTGACGACCAGGCCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
1455 1495 2.932234 CGACTTGACGACCAGGCCT 61.932 63.158 0.00 0.00 35.09 5.19
1536 1576 1.079543 CTCCAGCACCGAGTTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
1567 1607 2.672996 GCACAACATCGGCACCCT 60.673 61.111 0.00 0.00 0.00 4.34
1648 1688 1.983691 CATGTATCCCTCCAGCTCCAT 59.016 52.381 0.00 0.00 0.00 3.41
1670 1710 6.317391 CACCTCATCTTCCTTGATAAAACCTC 59.683 42.308 0.00 0.00 0.00 3.85
1685 1725 0.622665 CTTGGCCTCCACCTCATCTT 59.377 55.000 3.32 0.00 30.78 2.40
1728 1768 1.994507 CCTGAGCTGCCTCCCTTCT 60.995 63.158 0.00 0.00 37.29 2.85
1829 1869 3.118775 TCCAAGACTATCCACATCCAACG 60.119 47.826 0.00 0.00 0.00 4.10
1915 1965 1.173913 ATGTAAACAAGGGCGGCTTC 58.826 50.000 9.56 0.00 0.00 3.86
1999 2051 0.802222 CACGGTATGCGACACTCAGG 60.802 60.000 0.00 0.00 0.00 3.86
2007 2059 2.435234 GGCAACCACGGTATGCGA 60.435 61.111 13.53 0.00 40.94 5.10
2011 2063 1.563924 TGTAGAGGCAACCACGGTAT 58.436 50.000 0.00 0.00 37.17 2.73
2035 2087 6.429692 TCGCCAGAAAGAGAAAACATCATAAA 59.570 34.615 0.00 0.00 0.00 1.40
2050 2102 1.787155 CCGTCGATTATCGCCAGAAAG 59.213 52.381 10.02 0.00 40.21 2.62
2068 2120 6.455647 TCACACTTTAGCTATGGATAATCCG 58.544 40.000 0.00 0.00 40.17 4.18
2105 2157 8.774890 TTGGTAACTGAGCACGTTATTTATAA 57.225 30.769 0.00 0.00 34.56 0.98
2147 2199 6.615316 TGAGATTATCCACTCCCAAGAACATA 59.385 38.462 0.00 0.00 32.84 2.29
2172 2224 0.669932 CACTCGCTGAGCTGCTTTCT 60.670 55.000 2.53 0.00 32.04 2.52
2174 2226 0.948141 GTCACTCGCTGAGCTGCTTT 60.948 55.000 2.53 0.00 32.04 3.51
2218 2270 3.173965 TGGAAACAGAGGGAGTAGAAGG 58.826 50.000 0.00 0.00 35.01 3.46
2232 2284 6.197364 ACTACGACAACAATTTTGGAAACA 57.803 33.333 0.00 0.00 39.83 2.83
2233 2285 7.514573 AAACTACGACAACAATTTTGGAAAC 57.485 32.000 0.00 0.00 0.00 2.78
2237 2289 6.915843 AGCTAAAACTACGACAACAATTTTGG 59.084 34.615 0.00 0.00 0.00 3.28
2300 2352 0.977395 ACTAGCAACACAGTCCCTCC 59.023 55.000 0.00 0.00 0.00 4.30
2315 2367 0.693049 ACAAGGGTGGCTTGGACTAG 59.307 55.000 0.00 0.00 36.23 2.57
2338 2390 6.392354 AGTGATTGACCATGCAACTAAAATG 58.608 36.000 0.00 0.00 0.00 2.32
2400 2467 1.798813 CGGTACTTGGCACTCAGAAAC 59.201 52.381 0.00 0.00 0.00 2.78
2404 2471 0.670546 CCACGGTACTTGGCACTCAG 60.671 60.000 1.68 0.00 41.99 3.35
2494 2561 9.367160 TCATAGATTCAGTATTCCTCATACACA 57.633 33.333 0.00 0.00 40.49 3.72
2516 2583 9.070179 CCATGTGAATTGAGGACATTATTCATA 57.930 33.333 0.00 0.00 36.39 2.15
2626 2705 0.107459 GAAGCAAGATTCCTCCCGCT 60.107 55.000 0.00 0.00 32.34 5.52
2645 2724 6.692232 TGAACTAACAAAAACACCAAAACG 57.308 33.333 0.00 0.00 0.00 3.60
2662 2741 3.264964 GGACACCACCCCTAAATGAACTA 59.735 47.826 0.00 0.00 0.00 2.24
2663 2742 2.041216 GGACACCACCCCTAAATGAACT 59.959 50.000 0.00 0.00 0.00 3.01
2664 2743 2.041216 AGGACACCACCCCTAAATGAAC 59.959 50.000 0.00 0.00 0.00 3.18
2689 2768 2.650116 CCACCACCTCGTCCTCCTG 61.650 68.421 0.00 0.00 0.00 3.86
2749 2828 1.802960 GCTAGACGCATCATGGGAATG 59.197 52.381 9.03 0.00 38.92 2.67
2750 2829 1.417517 TGCTAGACGCATCATGGGAAT 59.582 47.619 9.03 0.00 45.47 3.01
2789 2869 3.634397 AGATCCACTGGTAACACATGG 57.366 47.619 0.00 0.40 46.17 3.66
2791 2871 5.397899 CCCAATAGATCCACTGGTAACACAT 60.398 44.000 0.00 0.00 46.17 3.21
2810 2890 0.035439 AACGCCGAGTGAATCCCAAT 60.035 50.000 0.00 0.00 0.00 3.16
2821 2901 1.153823 ATCGAAGACCAACGCCGAG 60.154 57.895 0.00 0.00 42.51 4.63
2823 2903 2.452813 CCATCGAAGACCAACGCCG 61.453 63.158 0.00 0.00 42.51 6.46


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

AutoCloner maintained by Alex Coulton.