Multiple sequence alignment - TraesCS3D01G474400

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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 TraesCS3D01G474400 chr3D 100.000 5405 0 0 1 5405 575600914 575595510 0.000000e+00 9982.0
1 TraesCS3D01G474400 chr3B 96.902 2582 42 14 2100 4676 766377075 766379623 0.000000e+00 4290.0
2 TraesCS3D01G474400 chr3B 96.961 1020 18 7 1 1017 766364020 766365029 0.000000e+00 1700.0
3 TraesCS3D01G474400 chr3B 87.901 686 48 12 1 679 739861815 739861158 0.000000e+00 774.0
4 TraesCS3D01G474400 chr3B 88.820 644 16 13 1458 2090 766376286 766376884 0.000000e+00 739.0
5 TraesCS3D01G474400 chr3B 96.948 426 6 3 1017 1436 766367958 766368382 0.000000e+00 708.0
6 TraesCS3D01G474400 chr3B 95.074 406 15 5 4673 5077 766379846 766380247 7.640000e-178 634.0
7 TraesCS3D01G474400 chr3B 95.593 295 13 0 5065 5359 766380303 766380597 1.760000e-129 473.0
8 TraesCS3D01G474400 chr3B 82.927 123 17 4 5198 5318 808671861 808671741 2.060000e-19 108.0
9 TraesCS3D01G474400 chr3B 97.674 43 1 0 5363 5405 766022037 766021995 2.090000e-09 75.0
10 TraesCS3D01G474400 chr3A 97.396 2227 30 13 2222 4439 711080122 711077915 0.000000e+00 3766.0
11 TraesCS3D01G474400 chr3A 98.142 646 10 2 1 645 711083266 711082622 0.000000e+00 1125.0
12 TraesCS3D01G474400 chr3A 91.626 824 20 16 644 1458 711082316 711081533 0.000000e+00 1094.0
13 TraesCS3D01G474400 chr3A 87.975 474 50 3 13 484 2262861 2262393 2.200000e-153 553.0
14 TraesCS3D01G474400 chr3A 87.949 473 51 3 13 484 2650907 2650440 2.200000e-153 553.0
15 TraesCS3D01G474400 chr3A 87.949 473 51 3 13 484 3661959 3661492 2.200000e-153 553.0
16 TraesCS3D01G474400 chr3A 88.856 341 20 6 5065 5405 711074138 711073816 2.340000e-108 403.0
17 TraesCS3D01G474400 chr3A 88.215 297 6 9 1492 1771 711080643 711080359 1.450000e-85 327.0
18 TraesCS3D01G474400 chr3A 88.476 269 8 7 1807 2065 711080368 711080113 2.450000e-78 303.0
19 TraesCS3D01G474400 chr3A 95.495 111 4 1 4465 4575 711075993 711075884 5.560000e-40 176.0
20 TraesCS3D01G474400 chr3A 85.088 114 13 4 5207 5318 552610403 552610292 4.420000e-21 113.0
21 TraesCS3D01G474400 chr1A 76.159 1661 333 37 2734 4382 551531802 551533411 0.000000e+00 815.0
22 TraesCS3D01G474400 chr1A 75.256 1657 344 42 2738 4382 554880714 554882316 0.000000e+00 728.0
23 TraesCS3D01G474400 chr1A 75.088 1702 319 63 2732 4380 551788008 551786359 0.000000e+00 697.0
24 TraesCS3D01G474400 chr1A 87.478 559 58 5 128 684 223457227 223456679 7.640000e-178 634.0
25 TraesCS3D01G474400 chr1D 76.159 1661 331 40 2734 4382 459521580 459523187 0.000000e+00 813.0
26 TraesCS3D01G474400 chr1D 75.758 1716 347 43 2689 4382 459626544 459624876 0.000000e+00 800.0
27 TraesCS3D01G474400 chr1D 87.183 710 75 7 1 705 160526854 160526156 0.000000e+00 793.0
28 TraesCS3D01G474400 chr1D 75.558 1657 336 44 2738 4382 463007638 463009237 0.000000e+00 752.0
29 TraesCS3D01G474400 chr1B 75.745 1711 350 41 2689 4382 631716565 631718227 0.000000e+00 800.0
30 TraesCS3D01G474400 chr1B 86.696 684 65 9 7 689 478567478 478566820 0.000000e+00 736.0
31 TraesCS3D01G474400 chr1B 74.691 648 143 17 2792 3427 634608125 634608763 8.920000e-68 268.0
32 TraesCS3D01G474400 chr1B 73.232 396 74 22 3813 4186 634498394 634498009 1.230000e-21 115.0
33 TraesCS3D01G474400 chr1B 79.268 164 27 4 3751 3912 634114485 634114327 2.060000e-19 108.0
34 TraesCS3D01G474400 chr2B 86.404 684 66 10 7 689 116323497 116322840 0.000000e+00 723.0
35 TraesCS3D01G474400 chr2B 89.831 59 6 0 1565 1623 11561360 11561302 5.810000e-10 76.8
36 TraesCS3D01G474400 chr2B 89.831 59 6 0 1565 1623 12875672 12875730 5.810000e-10 76.8
37 TraesCS3D01G474400 chr5B 88.578 429 34 9 699 1124 700059178 700058762 1.740000e-139 507.0
38 TraesCS3D01G474400 chr5B 87.760 433 37 10 696 1125 479043482 479043901 4.860000e-135 492.0
39 TraesCS3D01G474400 chr6B 88.399 431 33 8 699 1125 149042281 149041864 2.250000e-138 503.0
40 TraesCS3D01G474400 chr6B 87.379 103 11 2 5194 5295 279176791 279176690 3.420000e-22 117.0
41 TraesCS3D01G474400 chr2A 86.744 430 42 9 699 1125 722809000 722808583 1.060000e-126 464.0
42 TraesCS3D01G474400 chr2D 86.581 313 27 9 699 1007 288138153 288137852 1.120000e-86 331.0
43 TraesCS3D01G474400 chr2D 82.492 297 37 7 5065 5347 459540318 459540023 4.180000e-61 246.0
44 TraesCS3D01G474400 chr5A 89.474 266 15 2 1206 1458 19101726 19101461 1.880000e-84 324.0
45 TraesCS3D01G474400 chr5A 89.098 266 16 2 1206 1458 19099770 19099505 8.740000e-83 318.0
46 TraesCS3D01G474400 chr5A 89.098 266 16 2 1206 1458 19100422 19100157 8.740000e-83 318.0
47 TraesCS3D01G474400 chr5A 89.098 266 16 2 1206 1458 19102379 19102114 8.740000e-83 318.0
48 TraesCS3D01G474400 chr5A 88.722 266 17 2 1206 1458 19101074 19100809 4.060000e-81 313.0
49 TraesCS3D01G474400 chr5A 88.346 266 18 2 1206 1458 19103031 19102766 1.890000e-79 307.0
50 TraesCS3D01G474400 chr5A 87.868 272 14 10 1205 1458 19103687 19103417 8.800000e-78 302.0
51 TraesCS3D01G474400 chr7A 89.179 268 16 6 1204 1458 19710599 19710866 6.750000e-84 322.0
52 TraesCS3D01G474400 chr7A 83.607 122 18 2 5198 5318 11383126 11383006 4.420000e-21 113.0
53 TraesCS3D01G474400 chr7D 85.350 314 29 11 699 1007 379612617 379612918 5.260000e-80 309.0
54 TraesCS3D01G474400 chr7D 86.325 117 12 4 5198 5312 388645963 388646077 2.040000e-24 124.0
55 TraesCS3D01G474400 chr7D 82.270 141 17 7 5198 5333 500118233 500118370 1.230000e-21 115.0
56 TraesCS3D01G474400 chr5D 85.563 284 26 6 5065 5334 125975217 125974935 3.190000e-72 283.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G474400 chr3D 575595510 575600914 5404 True 9982.000000 9982 100.000000 1 5405 1 chr3D.!!$R1 5404
1 TraesCS3D01G474400 chr3B 766376286 766380597 4311 False 1534.000000 4290 94.097250 1458 5359 4 chr3B.!!$F2 3901
2 TraesCS3D01G474400 chr3B 766364020 766368382 4362 False 1204.000000 1700 96.954500 1 1436 2 chr3B.!!$F1 1435
3 TraesCS3D01G474400 chr3B 739861158 739861815 657 True 774.000000 774 87.901000 1 679 1 chr3B.!!$R1 678
4 TraesCS3D01G474400 chr3A 711073816 711083266 9450 True 1027.714286 3766 92.600857 1 5405 7 chr3A.!!$R5 5404
5 TraesCS3D01G474400 chr1A 551531802 551533411 1609 False 815.000000 815 76.159000 2734 4382 1 chr1A.!!$F1 1648
6 TraesCS3D01G474400 chr1A 554880714 554882316 1602 False 728.000000 728 75.256000 2738 4382 1 chr1A.!!$F2 1644
7 TraesCS3D01G474400 chr1A 551786359 551788008 1649 True 697.000000 697 75.088000 2732 4380 1 chr1A.!!$R2 1648
8 TraesCS3D01G474400 chr1A 223456679 223457227 548 True 634.000000 634 87.478000 128 684 1 chr1A.!!$R1 556
9 TraesCS3D01G474400 chr1D 459521580 459523187 1607 False 813.000000 813 76.159000 2734 4382 1 chr1D.!!$F1 1648
10 TraesCS3D01G474400 chr1D 459624876 459626544 1668 True 800.000000 800 75.758000 2689 4382 1 chr1D.!!$R2 1693
11 TraesCS3D01G474400 chr1D 160526156 160526854 698 True 793.000000 793 87.183000 1 705 1 chr1D.!!$R1 704
12 TraesCS3D01G474400 chr1D 463007638 463009237 1599 False 752.000000 752 75.558000 2738 4382 1 chr1D.!!$F2 1644
13 TraesCS3D01G474400 chr1B 631716565 631718227 1662 False 800.000000 800 75.745000 2689 4382 1 chr1B.!!$F1 1693
14 TraesCS3D01G474400 chr1B 478566820 478567478 658 True 736.000000 736 86.696000 7 689 1 chr1B.!!$R1 682
15 TraesCS3D01G474400 chr1B 634608125 634608763 638 False 268.000000 268 74.691000 2792 3427 1 chr1B.!!$F2 635
16 TraesCS3D01G474400 chr2B 116322840 116323497 657 True 723.000000 723 86.404000 7 689 1 chr2B.!!$R2 682
17 TraesCS3D01G474400 chr5A 19099505 19103687 4182 True 314.285714 324 88.814857 1205 1458 7 chr5A.!!$R1 253

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
101 107 3.003689 CCCTGCAAACTACAGTTCTTGTG 59.996 47.826 0.00 0.00 41.10 3.33 F
1130 4395 0.179012 TGGTGGGTCGGTTTTCTTCC 60.179 55.000 0.00 0.00 0.00 3.46 F
1889 6797 0.322546 CCTCAAGCCTAACCCACACC 60.323 60.000 0.00 0.00 0.00 4.16 F
2155 7250 0.596859 GGATGCTCGGGTTAGCGTAC 60.597 60.000 0.00 0.00 45.85 3.67 F
2156 7251 0.933509 GATGCTCGGGTTAGCGTACG 60.934 60.000 11.84 11.84 45.85 3.67 F
2157 7252 1.660560 ATGCTCGGGTTAGCGTACGT 61.661 55.000 17.90 6.37 45.85 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 6388 0.401356 TTACCTCCGTTCCCCCAAAC 59.599 55.000 0.00 0.00 0.00 2.93 R
2024 6938 0.869880 GTTTCCGCAGCCAACAACAC 60.870 55.000 0.00 0.00 0.00 3.32 R
3165 8280 2.229792 TGAAAAGTGCAAGAGCCGATT 58.770 42.857 0.00 0.00 41.13 3.34 R
4382 9550 2.110420 GGCTGCCGGTATGGTACC 59.890 66.667 4.43 4.43 45.52 3.34 R
4383 9551 2.279918 CGGCTGCCGGTATGGTAC 60.280 66.667 32.37 0.00 44.15 3.34 R
4562 11634 9.899661 ACTGCAGAAATGTAAATATGTACCTTA 57.100 29.630 23.35 0.00 0.00 2.69 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
101 107 3.003689 CCCTGCAAACTACAGTTCTTGTG 59.996 47.826 0.00 0.00 41.10 3.33
433 453 6.994496 GTCACCTGATAGGATTTCATGATTGA 59.006 38.462 0.00 0.00 37.67 2.57
609 631 8.043113 TCAGATGCATTACTTAAGAACACTGAT 58.957 33.333 10.09 0.00 0.00 2.90
883 1219 3.679639 GCCAGGGAAAAATATTGCTGGTG 60.680 47.826 0.00 0.00 33.64 4.17
925 1261 3.756963 GTCCTCGCCAAAATTTACTCCTT 59.243 43.478 0.00 0.00 0.00 3.36
1130 4395 0.179012 TGGTGGGTCGGTTTTCTTCC 60.179 55.000 0.00 0.00 0.00 3.46
1282 4575 4.734398 AGAAGATGATGGAGAGACACAC 57.266 45.455 0.00 0.00 0.00 3.82
1459 4756 2.381725 GTTCAACTAGAGGAACGGGG 57.618 55.000 12.92 0.00 34.69 5.73
1489 6292 6.174720 TCAATCCCCATTATGAGTGTCTAC 57.825 41.667 0.00 0.00 0.00 2.59
1500 6388 9.623350 CATTATGAGTGTCTACATACATCTCTG 57.377 37.037 7.78 3.39 32.97 3.35
1528 6416 4.439968 GGGAACGGAGGTAATAGAAACTG 58.560 47.826 0.00 0.00 0.00 3.16
1642 6530 4.517703 CGACTCGCCGTCCGACTC 62.518 72.222 0.00 0.00 41.89 3.36
1643 6531 4.176851 GACTCGCCGTCCGACTCC 62.177 72.222 0.00 0.00 41.89 3.85
1725 6630 3.313526 CAGCGATCCATCTTTTAACTGGG 59.686 47.826 0.00 0.00 0.00 4.45
1726 6631 2.033424 GCGATCCATCTTTTAACTGGGC 59.967 50.000 0.00 0.00 0.00 5.36
1727 6632 3.545703 CGATCCATCTTTTAACTGGGCT 58.454 45.455 0.00 0.00 0.00 5.19
1728 6633 3.313526 CGATCCATCTTTTAACTGGGCTG 59.686 47.826 0.00 0.00 0.00 4.85
1729 6634 3.806949 TCCATCTTTTAACTGGGCTGT 57.193 42.857 0.00 0.00 0.00 4.40
1730 6635 4.112634 TCCATCTTTTAACTGGGCTGTT 57.887 40.909 2.54 2.54 0.00 3.16
1884 6792 1.210722 CTCCTTCCTCAAGCCTAACCC 59.789 57.143 0.00 0.00 0.00 4.11
1885 6793 0.991920 CCTTCCTCAAGCCTAACCCA 59.008 55.000 0.00 0.00 0.00 4.51
1886 6794 1.340114 CCTTCCTCAAGCCTAACCCAC 60.340 57.143 0.00 0.00 0.00 4.61
1887 6795 1.351017 CTTCCTCAAGCCTAACCCACA 59.649 52.381 0.00 0.00 0.00 4.17
1888 6796 0.690762 TCCTCAAGCCTAACCCACAC 59.309 55.000 0.00 0.00 0.00 3.82
1889 6797 0.322546 CCTCAAGCCTAACCCACACC 60.323 60.000 0.00 0.00 0.00 4.16
1890 6798 0.322546 CTCAAGCCTAACCCACACCC 60.323 60.000 0.00 0.00 0.00 4.61
1891 6799 1.674322 CAAGCCTAACCCACACCCG 60.674 63.158 0.00 0.00 0.00 5.28
1892 6800 3.562732 AAGCCTAACCCACACCCGC 62.563 63.158 0.00 0.00 0.00 6.13
1894 6802 4.770874 CCTAACCCACACCCGCCG 62.771 72.222 0.00 0.00 0.00 6.46
1911 6819 2.184167 CGCGGTCTCTCTCTCCTCC 61.184 68.421 0.00 0.00 0.00 4.30
1986 6894 2.049985 GATCCGTGGCGATCCTCG 60.050 66.667 0.00 0.00 45.91 4.63
2024 6938 3.417224 CATCGGCATCGGCATCGG 61.417 66.667 0.00 0.00 43.71 4.18
2080 6994 3.059051 GCAAGTACGTATACTCTCCTCGG 60.059 52.174 0.00 0.00 41.00 4.63
2090 7004 7.076983 CGTATACTCTCCTCGGTTATTTCTTC 58.923 42.308 0.56 0.00 0.00 2.87
2091 7005 7.041235 CGTATACTCTCCTCGGTTATTTCTTCT 60.041 40.741 0.56 0.00 0.00 2.85
2092 7006 7.663043 ATACTCTCCTCGGTTATTTCTTCTT 57.337 36.000 0.00 0.00 0.00 2.52
2093 7007 8.763984 ATACTCTCCTCGGTTATTTCTTCTTA 57.236 34.615 0.00 0.00 0.00 2.10
2094 7008 6.865411 ACTCTCCTCGGTTATTTCTTCTTAC 58.135 40.000 0.00 0.00 0.00 2.34
2095 7009 6.664384 ACTCTCCTCGGTTATTTCTTCTTACT 59.336 38.462 0.00 0.00 0.00 2.24
2096 7010 6.864342 TCTCCTCGGTTATTTCTTCTTACTG 58.136 40.000 0.00 0.00 0.00 2.74
2097 7011 6.436532 TCTCCTCGGTTATTTCTTCTTACTGT 59.563 38.462 0.00 0.00 0.00 3.55
2098 7012 7.613022 TCTCCTCGGTTATTTCTTCTTACTGTA 59.387 37.037 0.00 0.00 0.00 2.74
2154 7249 1.038681 TGGATGCTCGGGTTAGCGTA 61.039 55.000 0.00 0.00 45.85 4.42
2155 7250 0.596859 GGATGCTCGGGTTAGCGTAC 60.597 60.000 0.00 0.00 45.85 3.67
2156 7251 0.933509 GATGCTCGGGTTAGCGTACG 60.934 60.000 11.84 11.84 45.85 3.67
2157 7252 1.660560 ATGCTCGGGTTAGCGTACGT 61.661 55.000 17.90 6.37 45.85 3.57
2391 7486 4.335315 TCGGCTCAAATAAACCATCATCAC 59.665 41.667 0.00 0.00 0.00 3.06
2393 7488 4.037690 GCTCAAATAAACCATCATCACGC 58.962 43.478 0.00 0.00 0.00 5.34
2501 7603 7.959651 GCTGTCAACAAAGTATTCAGATACAAG 59.040 37.037 0.00 0.00 40.51 3.16
2707 7809 8.868522 TTAGATTTATTATTGCAGCCAGCTAT 57.131 30.769 0.00 1.06 45.94 2.97
2708 7810 9.958180 TTAGATTTATTATTGCAGCCAGCTATA 57.042 29.630 0.00 0.13 45.94 1.31
2709 7811 8.503458 AGATTTATTATTGCAGCCAGCTATAG 57.497 34.615 0.00 0.00 45.94 1.31
2710 7812 8.324306 AGATTTATTATTGCAGCCAGCTATAGA 58.676 33.333 3.21 0.00 45.94 1.98
2711 7813 9.118300 GATTTATTATTGCAGCCAGCTATAGAT 57.882 33.333 3.21 0.00 45.94 1.98
2713 7815 8.948631 TTATTATTGCAGCCAGCTATAGATAC 57.051 34.615 3.21 0.00 45.94 2.24
3165 8280 7.222611 GCTGCAAGTTCAATTCAGTTTCTTAAA 59.777 33.333 0.00 0.00 35.30 1.52
4382 9550 2.279517 GCCCTGTAGTCGATGCCG 60.280 66.667 0.00 0.00 37.07 5.69
4383 9551 2.417516 CCCTGTAGTCGATGCCGG 59.582 66.667 0.00 0.00 36.24 6.13
4384 9552 2.423898 CCCTGTAGTCGATGCCGGT 61.424 63.158 1.90 0.00 36.24 5.28
4385 9553 1.105167 CCCTGTAGTCGATGCCGGTA 61.105 60.000 1.90 0.00 36.24 4.02
4386 9554 0.030369 CCTGTAGTCGATGCCGGTAC 59.970 60.000 1.90 0.00 36.24 3.34
4387 9555 0.030369 CTGTAGTCGATGCCGGTACC 59.970 60.000 1.90 0.16 36.24 3.34
4533 11605 4.629634 TCAACTATAGCACACATGAAACCG 59.370 41.667 0.00 0.00 0.00 4.44
4656 11728 4.808895 TGCTAAACGATGGTATTGCTAGTG 59.191 41.667 0.00 0.00 0.00 2.74
4695 13518 4.339247 TCCTTTTTCAGTTGCCTTCTTCAG 59.661 41.667 0.00 0.00 0.00 3.02
4731 13555 5.737860 TGTGCATACAAGTCTTGATGATCT 58.262 37.500 19.53 0.00 32.88 2.75
4745 13569 3.792053 GATCTACCGCACGGCCCAG 62.792 68.421 9.43 4.36 39.32 4.45
4753 13577 2.342279 CACGGCCCAGAACGAGAA 59.658 61.111 0.00 0.00 0.00 2.87
4794 13618 1.647545 CCATGCGCTTCATCACCGTT 61.648 55.000 9.73 0.00 31.79 4.44
4797 13621 2.965147 GCGCTTCATCACCGTTGCA 61.965 57.895 0.00 0.00 0.00 4.08
4873 13697 5.411781 ACGAGAGAACATTTATCAGACACC 58.588 41.667 0.00 0.00 0.00 4.16
4948 13772 4.985413 TCGATTGCTTTATGCTTCAAAGG 58.015 39.130 7.17 0.00 43.37 3.11
5176 14065 1.813786 GTAGTTCAGGCACTCTCTCGT 59.186 52.381 0.00 0.00 34.60 4.18
5185 14074 3.805307 CTCTCTCGTGGTCGCGCT 61.805 66.667 5.56 0.00 36.96 5.92
5186 14075 4.103103 TCTCTCGTGGTCGCGCTG 62.103 66.667 5.56 0.00 36.96 5.18
5296 14186 2.203280 CGACCAAGGTTGTGCCCA 60.203 61.111 0.00 0.00 38.26 5.36
5374 14264 1.081175 GCCCTCAAGAAAACTGCGC 60.081 57.895 0.00 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
433 453 7.599998 GCAGAACCTATTTCATGACAAAACAAT 59.400 33.333 0.00 0.00 36.57 2.71
584 605 7.601073 TCAGTGTTCTTAAGTAATGCATCTG 57.399 36.000 0.00 0.00 0.00 2.90
668 1000 1.513158 CTCGACGCTCCATCCAACT 59.487 57.895 0.00 0.00 0.00 3.16
925 1261 6.582677 ATGTTTAACCAAATCGGATGACAA 57.417 33.333 0.00 0.00 38.63 3.18
1130 4395 3.739401 ACAGGGGGTCAATAAAGAAGG 57.261 47.619 0.00 0.00 0.00 3.46
1397 4694 5.481105 TGCTTTCAGAATTTGCTTTATGGG 58.519 37.500 5.34 0.00 0.00 4.00
1458 4755 6.782494 ACTCATAATGGGGATTGAATTTACCC 59.218 38.462 6.59 6.59 41.84 3.69
1459 4756 7.287696 ACACTCATAATGGGGATTGAATTTACC 59.712 37.037 0.00 0.00 0.00 2.85
1489 6292 3.931907 TCCCCCAAACAGAGATGTATG 57.068 47.619 0.00 0.00 0.00 2.39
1500 6388 0.401356 TTACCTCCGTTCCCCCAAAC 59.599 55.000 0.00 0.00 0.00 2.93
1725 6630 1.589716 CTAGGCCCAACAGCAACAGC 61.590 60.000 0.00 0.00 0.00 4.40
1726 6631 0.962356 CCTAGGCCCAACAGCAACAG 60.962 60.000 0.00 0.00 0.00 3.16
1727 6632 1.074775 CCTAGGCCCAACAGCAACA 59.925 57.895 0.00 0.00 0.00 3.33
1728 6633 1.678970 CCCTAGGCCCAACAGCAAC 60.679 63.158 2.05 0.00 0.00 4.17
1729 6634 2.763215 CCCTAGGCCCAACAGCAA 59.237 61.111 2.05 0.00 0.00 3.91
1730 6635 3.338250 CCCCTAGGCCCAACAGCA 61.338 66.667 2.05 0.00 0.00 4.41
1786 6691 4.208666 CGCCGCTCTATCTTTTACCTTTAC 59.791 45.833 0.00 0.00 0.00 2.01
1848 6756 2.034376 AGGTCGCGGTGAGAGAGT 59.966 61.111 6.13 0.00 0.00 3.24
1890 6798 4.244802 GAGAGAGAGACCGCGGCG 62.245 72.222 28.58 16.78 0.00 6.46
1891 6799 3.894947 GGAGAGAGAGACCGCGGC 61.895 72.222 28.58 18.62 0.00 6.53
1892 6800 2.124487 AGGAGAGAGAGACCGCGG 60.124 66.667 26.86 26.86 0.00 6.46
1893 6801 2.184167 GGAGGAGAGAGAGACCGCG 61.184 68.421 0.00 0.00 0.00 6.46
1894 6802 1.077357 TGGAGGAGAGAGAGACCGC 60.077 63.158 0.00 0.00 0.00 5.68
1895 6803 1.101049 GCTGGAGGAGAGAGAGACCG 61.101 65.000 0.00 0.00 0.00 4.79
1896 6804 0.755327 GGCTGGAGGAGAGAGAGACC 60.755 65.000 0.00 0.00 0.00 3.85
1911 6819 1.890979 GCGACATGGATGGAGGCTG 60.891 63.158 0.00 0.00 0.00 4.85
1999 6907 3.630148 GATGCCGATGCCGTGTCG 61.630 66.667 0.00 0.00 38.75 4.35
2024 6938 0.869880 GTTTCCGCAGCCAACAACAC 60.870 55.000 0.00 0.00 0.00 3.32
2027 6941 2.054140 GACGTTTCCGCAGCCAACAA 62.054 55.000 0.00 0.00 37.70 2.83
2093 7007 8.934697 ACTGTTTGGGATATACATACATACAGT 58.065 33.333 10.84 10.84 44.00 3.55
2094 7008 9.778741 AACTGTTTGGGATATACATACATACAG 57.221 33.333 9.93 9.93 42.67 2.74
2098 7012 9.693739 TTGAAACTGTTTGGGATATACATACAT 57.306 29.630 11.03 0.00 31.23 2.29
2154 7249 9.118300 ACATAAAAGAGTATAGTAGTAGCACGT 57.882 33.333 0.00 0.00 0.00 4.49
2155 7250 9.383462 CACATAAAAGAGTATAGTAGTAGCACG 57.617 37.037 0.00 0.00 0.00 5.34
2391 7486 4.202161 ACTTGAGGAATATCAGTACCAGCG 60.202 45.833 0.00 0.00 0.00 5.18
2393 7488 5.525378 GCAACTTGAGGAATATCAGTACCAG 59.475 44.000 0.00 0.00 0.00 4.00
2501 7603 7.857885 GTGCCAGCAGTTATGATAAAGAATTAC 59.142 37.037 0.00 0.00 0.00 1.89
2712 7814 9.476928 AAGGTTCATCAGTTATACTGTAGTAGT 57.523 33.333 6.71 0.00 46.03 2.73
2713 7815 9.737427 CAAGGTTCATCAGTTATACTGTAGTAG 57.263 37.037 6.71 0.00 46.03 2.57
3165 8280 2.229792 TGAAAAGTGCAAGAGCCGATT 58.770 42.857 0.00 0.00 41.13 3.34
4382 9550 2.110420 GGCTGCCGGTATGGTACC 59.890 66.667 4.43 4.43 45.52 3.34
4383 9551 2.279918 CGGCTGCCGGTATGGTAC 60.280 66.667 32.37 0.00 44.15 3.34
4562 11634 9.899661 ACTGCAGAAATGTAAATATGTACCTTA 57.100 29.630 23.35 0.00 0.00 2.69
4582 11654 6.398918 ACCATACAACTAAACTAGACTGCAG 58.601 40.000 13.48 13.48 0.00 4.41
4623 11695 1.438651 TCGTTTAGCACATCAGCACC 58.561 50.000 0.00 0.00 36.85 5.01
4711 13535 5.403766 CGGTAGATCATCAAGACTTGTATGC 59.596 44.000 14.75 6.25 0.00 3.14
4731 13555 4.382320 GTTCTGGGCCGTGCGGTA 62.382 66.667 12.46 0.00 37.65 4.02
4745 13569 0.711118 GAGCGTGCTTCTTCTCGTTC 59.289 55.000 0.00 0.00 0.00 3.95
4749 13573 2.448705 GGCGAGCGTGCTTCTTCTC 61.449 63.158 0.00 0.00 34.52 2.87
4753 13577 2.816958 CATGGCGAGCGTGCTTCT 60.817 61.111 0.00 0.00 34.52 2.85
4873 13697 0.877649 CGTGCTCAATCGATCCCCAG 60.878 60.000 0.00 0.00 0.00 4.45
5038 13862 1.766461 CCGAGGAAGGGGCTACCAT 60.766 63.158 0.97 0.00 43.89 3.55
5039 13863 2.252012 ATCCGAGGAAGGGGCTACCA 62.252 60.000 0.00 0.00 43.89 3.25
5273 14163 2.424302 CAACCTTGGTCGGACCGT 59.576 61.111 21.52 11.13 42.58 4.83
5296 14186 3.900892 CGGAGCGCCACGATACCT 61.901 66.667 15.25 0.00 0.00 3.08
5374 14264 3.248266 GTTGCTATTGCCTTGCTTCTTG 58.752 45.455 0.00 0.00 38.71 3.02


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

AutoCloner maintained by Alex Coulton.