Multiple sequence alignment - TraesCS7D01G241800

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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 TraesCS7D01G241800 chr7D 100.000 6062 0 0 1 6062 205945835 205951896 0.000000e+00 11195.0
1 TraesCS7D01G241800 chr7D 95.858 1376 51 4 1873 3243 575713863 575715237 0.000000e+00 2220.0
2 TraesCS7D01G241800 chr7D 97.823 781 16 1 5282 6062 533622696 533623475 0.000000e+00 1347.0
3 TraesCS7D01G241800 chr7D 97.201 786 19 3 5279 6062 156191640 156190856 0.000000e+00 1327.0
4 TraesCS7D01G241800 chr3A 95.706 1374 51 5 1870 3242 13349343 13347977 0.000000e+00 2204.0
5 TraesCS7D01G241800 chr5D 95.369 1382 49 12 1873 3243 372335135 372333758 0.000000e+00 2183.0
6 TraesCS7D01G241800 chr5D 97.823 781 14 2 5282 6062 489893492 489894269 0.000000e+00 1345.0
7 TraesCS7D01G241800 chr2D 95.342 1374 58 4 1873 3242 66155881 66154510 0.000000e+00 2178.0
8 TraesCS7D01G241800 chr2D 94.971 1372 53 8 1875 3244 28833491 28834848 0.000000e+00 2137.0
9 TraesCS7D01G241800 chr2D 98.331 779 13 0 5284 6062 622370720 622371498 0.000000e+00 1367.0
10 TraesCS7D01G241800 chr2D 97.183 781 22 0 5282 6062 629724374 629725154 0.000000e+00 1321.0
11 TraesCS7D01G241800 chr2D 74.324 888 199 22 3761 4637 548976517 548977386 3.480000e-92 350.0
12 TraesCS7D01G241800 chr3B 95.080 1382 56 6 1873 3245 756264531 756263153 0.000000e+00 2165.0
13 TraesCS7D01G241800 chr3B 94.967 1371 65 4 1873 3242 688150607 688151974 0.000000e+00 2146.0
14 TraesCS7D01G241800 chr6B 94.534 1372 70 4 1876 3242 502797573 502796202 0.000000e+00 2113.0
15 TraesCS7D01G241800 chr6B 97.059 782 20 3 5282 6062 607121837 607121058 0.000000e+00 1314.0
16 TraesCS7D01G241800 chr5A 94.538 1373 67 7 1873 3244 343985935 343984570 0.000000e+00 2113.0
17 TraesCS7D01G241800 chrUn 89.670 1578 147 14 3273 4838 45772041 45773614 0.000000e+00 1997.0
18 TraesCS7D01G241800 chrUn 92.506 1201 79 4 3562 4759 214043897 214045089 0.000000e+00 1709.0
19 TraesCS7D01G241800 chrUn 92.506 1201 79 4 3562 4759 240301188 240299996 0.000000e+00 1709.0
20 TraesCS7D01G241800 chrUn 83.266 986 122 20 883 1839 45771009 45771980 0.000000e+00 867.0
21 TraesCS7D01G241800 chrUn 80.548 766 97 27 1140 1861 214042654 214043411 5.340000e-150 542.0
22 TraesCS7D01G241800 chrUn 80.548 766 97 27 1140 1861 240302431 240301674 5.340000e-150 542.0
23 TraesCS7D01G241800 chrUn 92.377 223 10 5 3245 3460 214043397 214043619 1.640000e-80 311.0
24 TraesCS7D01G241800 chrUn 92.377 223 10 5 3245 3460 240301688 240301466 1.640000e-80 311.0
25 TraesCS7D01G241800 chrUn 80.251 319 27 12 270 585 45770588 45770873 2.210000e-49 207.0
26 TraesCS7D01G241800 chrUn 94.545 55 3 0 169 223 214037314 214037368 1.080000e-12 86.1
27 TraesCS7D01G241800 chr3D 89.128 1582 145 19 3273 4838 592867525 592869095 0.000000e+00 1943.0
28 TraesCS7D01G241800 chr3D 89.128 1582 145 19 3273 4838 592873266 592874836 0.000000e+00 1943.0
29 TraesCS7D01G241800 chr3D 98.207 781 14 0 5282 6062 15906379 15905599 0.000000e+00 1365.0
30 TraesCS7D01G241800 chr3D 83.994 1287 143 28 617 1858 592871971 592873239 0.000000e+00 1177.0
31 TraesCS7D01G241800 chr3D 83.916 1287 143 29 617 1858 592866231 592867498 0.000000e+00 1171.0
32 TraesCS7D01G241800 chr7A 91.937 1389 86 10 95 1465 218260876 218262256 0.000000e+00 1921.0
33 TraesCS7D01G241800 chr7A 94.074 810 35 6 4476 5284 218263687 218264484 0.000000e+00 1218.0
34 TraesCS7D01G241800 chr7A 95.969 521 21 0 3673 4193 218263172 218263692 0.000000e+00 846.0
35 TraesCS7D01G241800 chr7A 88.488 443 41 7 3244 3678 218262596 218263036 1.500000e-145 527.0
36 TraesCS7D01G241800 chr7A 92.500 360 24 1 1503 1862 218262256 218262612 4.190000e-141 512.0
37 TraesCS7D01G241800 chr7A 74.237 885 213 14 3755 4631 693207076 693206199 2.080000e-94 357.0
38 TraesCS7D01G241800 chr7B 92.239 1237 69 10 637 1862 196280819 196279599 0.000000e+00 1727.0
39 TraesCS7D01G241800 chr7B 93.049 892 39 11 3244 4125 196279615 196278737 0.000000e+00 1282.0
40 TraesCS7D01G241800 chr7B 94.529 658 25 7 4627 5282 196278375 196277727 0.000000e+00 1005.0
41 TraesCS7D01G241800 chr7B 90.388 541 39 11 1 541 196281400 196280873 0.000000e+00 699.0
42 TraesCS7D01G241800 chr7B 95.957 371 15 0 4166 4536 196278740 196278370 2.420000e-168 603.0
43 TraesCS7D01G241800 chr1A 96.807 783 22 2 5282 6062 482801841 482801060 0.000000e+00 1304.0
44 TraesCS7D01G241800 chr1A 96.807 783 22 2 5282 6062 482808521 482807740 0.000000e+00 1304.0
45 TraesCS7D01G241800 chr2A 76.703 910 190 17 3739 4637 764771385 764770487 2.540000e-133 486.0


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 TraesCS7D01G241800 chr7D 205945835 205951896 6061 False 11195.000000 11195 100.000000 1 6062 1 chr7D.!!$F1 6061
1 TraesCS7D01G241800 chr7D 575713863 575715237 1374 False 2220.000000 2220 95.858000 1873 3243 1 chr7D.!!$F3 1370
2 TraesCS7D01G241800 chr7D 533622696 533623475 779 False 1347.000000 1347 97.823000 5282 6062 1 chr7D.!!$F2 780
3 TraesCS7D01G241800 chr7D 156190856 156191640 784 True 1327.000000 1327 97.201000 5279 6062 1 chr7D.!!$R1 783
4 TraesCS7D01G241800 chr3A 13347977 13349343 1366 True 2204.000000 2204 95.706000 1870 3242 1 chr3A.!!$R1 1372
5 TraesCS7D01G241800 chr5D 372333758 372335135 1377 True 2183.000000 2183 95.369000 1873 3243 1 chr5D.!!$R1 1370
6 TraesCS7D01G241800 chr5D 489893492 489894269 777 False 1345.000000 1345 97.823000 5282 6062 1 chr5D.!!$F1 780
7 TraesCS7D01G241800 chr2D 66154510 66155881 1371 True 2178.000000 2178 95.342000 1873 3242 1 chr2D.!!$R1 1369
8 TraesCS7D01G241800 chr2D 28833491 28834848 1357 False 2137.000000 2137 94.971000 1875 3244 1 chr2D.!!$F1 1369
9 TraesCS7D01G241800 chr2D 622370720 622371498 778 False 1367.000000 1367 98.331000 5284 6062 1 chr2D.!!$F3 778
10 TraesCS7D01G241800 chr2D 629724374 629725154 780 False 1321.000000 1321 97.183000 5282 6062 1 chr2D.!!$F4 780
11 TraesCS7D01G241800 chr2D 548976517 548977386 869 False 350.000000 350 74.324000 3761 4637 1 chr2D.!!$F2 876
12 TraesCS7D01G241800 chr3B 756263153 756264531 1378 True 2165.000000 2165 95.080000 1873 3245 1 chr3B.!!$R1 1372
13 TraesCS7D01G241800 chr3B 688150607 688151974 1367 False 2146.000000 2146 94.967000 1873 3242 1 chr3B.!!$F1 1369
14 TraesCS7D01G241800 chr6B 502796202 502797573 1371 True 2113.000000 2113 94.534000 1876 3242 1 chr6B.!!$R1 1366
15 TraesCS7D01G241800 chr6B 607121058 607121837 779 True 1314.000000 1314 97.059000 5282 6062 1 chr6B.!!$R2 780
16 TraesCS7D01G241800 chr5A 343984570 343985935 1365 True 2113.000000 2113 94.538000 1873 3244 1 chr5A.!!$R1 1371
17 TraesCS7D01G241800 chrUn 45770588 45773614 3026 False 1023.666667 1997 84.395667 270 4838 3 chrUn.!!$F2 4568
18 TraesCS7D01G241800 chrUn 214042654 214045089 2435 False 854.000000 1709 88.477000 1140 4759 3 chrUn.!!$F3 3619
19 TraesCS7D01G241800 chrUn 240299996 240302431 2435 True 854.000000 1709 88.477000 1140 4759 3 chrUn.!!$R1 3619
20 TraesCS7D01G241800 chr3D 592866231 592874836 8605 False 1558.500000 1943 86.541500 617 4838 4 chr3D.!!$F1 4221
21 TraesCS7D01G241800 chr3D 15905599 15906379 780 True 1365.000000 1365 98.207000 5282 6062 1 chr3D.!!$R1 780
22 TraesCS7D01G241800 chr7A 218260876 218264484 3608 False 1004.800000 1921 92.593600 95 5284 5 chr7A.!!$F1 5189
23 TraesCS7D01G241800 chr7A 693206199 693207076 877 True 357.000000 357 74.237000 3755 4631 1 chr7A.!!$R1 876
24 TraesCS7D01G241800 chr7B 196277727 196281400 3673 True 1063.200000 1727 93.232400 1 5282 5 chr7B.!!$R1 5281
25 TraesCS7D01G241800 chr1A 482801060 482801841 781 True 1304.000000 1304 96.807000 5282 6062 1 chr1A.!!$R1 780
26 TraesCS7D01G241800 chr1A 482807740 482808521 781 True 1304.000000 1304 96.807000 5282 6062 1 chr1A.!!$R2 780
27 TraesCS7D01G241800 chr2A 764770487 764771385 898 True 486.000000 486 76.703000 3739 4637 1 chr2A.!!$R1 898

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
234 235 2.036992 ACTCAGTCAGCTTTGGAGTCTG 59.963 50.000 2.20 0.0 33.84 3.51 F
1361 1494 0.670546 CCTGCAGGTACCACTTGTCG 60.671 60.000 25.53 0.0 0.00 4.35 F
1806 7712 0.676782 GTTGGCATGGCTACGAAGGT 60.677 55.000 21.08 0.0 0.00 3.50 F
2613 8552 1.092921 AGCGTCGTTTTGTGGAGCAA 61.093 50.000 0.00 0.0 34.87 3.91 F
2860 8799 1.987855 CAGGGAGGAGGTGCCGTTA 60.988 63.158 0.00 0.0 43.04 3.18 F
4127 10450 1.137872 CACTCCACTATCAGTGCCCTC 59.862 57.143 0.64 0.0 44.63 4.30 F
4549 10872 0.250513 GCAAGTCATCGAGGAAGGGT 59.749 55.000 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 7770 1.371595 GCGGGCGTTACCTCAAATTA 58.628 50.000 0.00 0.00 39.10 1.40 R
2584 8522 0.608640 AAACGACGCTCCCAAGAGAT 59.391 50.000 0.00 0.00 43.39 2.75 R
3626 9808 0.750850 GCCTATTCCTACCGCAGTGA 59.249 55.000 0.00 0.00 0.00 3.41 R
3855 10178 0.609406 GGCCTCCACCTCCAAGTTTC 60.609 60.000 0.00 0.00 0.00 2.78 R
4356 10679 1.007038 GAGTCGCCGTGTGTGGTAA 60.007 57.895 0.00 0.00 0.00 2.85 R
5043 11374 0.320421 TCTAACTTGAGGCACGTGGC 60.320 55.000 32.77 32.77 43.74 5.01 R
5708 12042 0.673644 GATTGTCTGGGGTCGTGGTG 60.674 60.000 0.00 0.00 0.00 4.17 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
26 27 6.496565 TCCATTAAATGCTTCCTCTTTTTGGA 59.503 34.615 0.00 0.00 0.00 3.53
29 30 9.874205 CATTAAATGCTTCCTCTTTTTGGATTA 57.126 29.630 0.00 0.00 33.09 1.75
71 72 3.512724 AGGCATTAGTCTTTGCAAGCAAT 59.487 39.130 8.46 0.00 40.66 3.56
81 82 5.961263 GTCTTTGCAAGCAATTTCAAAACTG 59.039 36.000 8.46 0.00 35.70 3.16
234 235 2.036992 ACTCAGTCAGCTTTGGAGTCTG 59.963 50.000 2.20 0.00 33.84 3.51
531 550 2.533916 TGCCAGGCATTTGGACAATTA 58.466 42.857 11.22 0.00 40.87 1.40
541 560 4.846779 TTTGGACAATTAGACTTGGCAC 57.153 40.909 0.00 0.00 35.75 5.01
542 561 3.788227 TGGACAATTAGACTTGGCACT 57.212 42.857 0.00 0.00 35.75 4.40
544 563 3.820467 TGGACAATTAGACTTGGCACTTG 59.180 43.478 0.00 0.00 35.75 3.16
545 564 3.191371 GGACAATTAGACTTGGCACTTGG 59.809 47.826 0.00 0.00 35.75 3.61
546 565 2.558359 ACAATTAGACTTGGCACTTGGC 59.442 45.455 0.00 0.00 43.74 4.52
565 584 4.151121 TGGCAGATTTGAAGTTTCCATCA 58.849 39.130 0.00 0.00 0.00 3.07
728 761 8.738645 AGAAATAGAAAGGTAAGCAGGTATTG 57.261 34.615 0.00 0.00 0.00 1.90
832 875 6.456988 GCAGTTTCACACTACAATGGCTATAC 60.457 42.308 0.00 0.00 32.76 1.47
834 877 6.594159 AGTTTCACACTACAATGGCTATACAC 59.406 38.462 0.00 0.00 31.97 2.90
968 1074 3.525537 CCACCATGTTAGTGCTAGTCTG 58.474 50.000 0.00 0.00 33.75 3.51
969 1075 3.195610 CCACCATGTTAGTGCTAGTCTGA 59.804 47.826 0.00 0.00 33.75 3.27
995 1101 3.511595 CGCATCGCCCAACTGCAT 61.512 61.111 0.00 0.00 35.64 3.96
1248 1360 0.976073 GGTCAGTCCCCCTCGATGAA 60.976 60.000 0.00 0.00 0.00 2.57
1361 1494 0.670546 CCTGCAGGTACCACTTGTCG 60.671 60.000 25.53 0.00 0.00 4.35
1725 7631 2.106338 TGACTTTGGATGCCTCAGTGAA 59.894 45.455 0.00 0.00 0.00 3.18
1755 7661 3.073946 AGTGCCTTGTGTACCATAAACCT 59.926 43.478 0.00 0.00 0.00 3.50
1806 7712 0.676782 GTTGGCATGGCTACGAAGGT 60.677 55.000 21.08 0.00 0.00 3.50
1856 7769 4.664064 AGGTATGCTACTAGACTCCCTGTA 59.336 45.833 0.00 0.00 0.00 2.74
1857 7770 5.313772 AGGTATGCTACTAGACTCCCTGTAT 59.686 44.000 0.00 0.00 0.00 2.29
1858 7771 6.504634 AGGTATGCTACTAGACTCCCTGTATA 59.495 42.308 0.00 0.00 0.00 1.47
1859 7772 7.018349 AGGTATGCTACTAGACTCCCTGTATAA 59.982 40.741 0.00 0.00 0.00 0.98
1860 7773 7.835181 GGTATGCTACTAGACTCCCTGTATAAT 59.165 40.741 0.00 0.00 0.00 1.28
1861 7774 9.245481 GTATGCTACTAGACTCCCTGTATAATT 57.755 37.037 0.00 0.00 0.00 1.40
1862 7775 8.728596 ATGCTACTAGACTCCCTGTATAATTT 57.271 34.615 0.00 0.00 0.00 1.82
1863 7776 7.952671 TGCTACTAGACTCCCTGTATAATTTG 58.047 38.462 0.00 0.00 0.00 2.32
1864 7777 7.783119 TGCTACTAGACTCCCTGTATAATTTGA 59.217 37.037 0.00 0.00 0.00 2.69
1865 7778 8.301002 GCTACTAGACTCCCTGTATAATTTGAG 58.699 40.741 0.00 0.00 0.00 3.02
1866 7779 7.604657 ACTAGACTCCCTGTATAATTTGAGG 57.395 40.000 0.00 0.00 0.00 3.86
1867 7780 7.133483 ACTAGACTCCCTGTATAATTTGAGGT 58.867 38.462 0.00 0.00 0.00 3.85
1868 7781 8.287350 ACTAGACTCCCTGTATAATTTGAGGTA 58.713 37.037 0.00 0.00 0.00 3.08
1869 7782 7.989947 AGACTCCCTGTATAATTTGAGGTAA 57.010 36.000 0.00 0.00 0.00 2.85
1870 7783 7.793036 AGACTCCCTGTATAATTTGAGGTAAC 58.207 38.462 0.00 0.00 0.00 2.50
1871 7784 6.579865 ACTCCCTGTATAATTTGAGGTAACG 58.420 40.000 0.00 0.00 46.39 3.18
2337 8275 1.280457 GGTGGTGGTCATCTCTTCCT 58.720 55.000 0.00 0.00 0.00 3.36
2584 8522 1.957186 GGCACTGCGGTGTCGTTTA 60.957 57.895 26.00 0.00 44.65 2.01
2613 8552 1.092921 AGCGTCGTTTTGTGGAGCAA 61.093 50.000 0.00 0.00 34.87 3.91
2860 8799 1.987855 CAGGGAGGAGGTGCCGTTA 60.988 63.158 0.00 0.00 43.04 3.18
3104 9043 5.129485 CCTTCATCAACTGGATAGGTGTAGT 59.871 44.000 0.00 0.00 42.42 2.73
3113 9052 5.047235 ACTGGATAGGTGTAGTGACAGTTTC 60.047 44.000 0.00 0.00 35.82 2.78
3610 9792 3.136443 AGACCCAAGCCGATTGATTATGA 59.864 43.478 0.00 0.00 41.83 2.15
3626 9808 8.827832 TTGATTATGAATTCTCCAGGATTTGT 57.172 30.769 7.05 0.00 0.00 2.83
3654 9836 2.420129 GGTAGGAATAGGCAGTGGTGTG 60.420 54.545 0.00 0.00 0.00 3.82
3678 10001 4.994217 GGCACTCTTCTAATTATCCTCAGC 59.006 45.833 0.00 0.00 0.00 4.26
3705 10028 7.137490 TCTGATTGTAAGACAAAAGCTCATG 57.863 36.000 0.00 0.00 41.96 3.07
3810 10133 4.071423 TCGCTGAAAGGATGATGTTCAAA 58.929 39.130 0.00 0.00 31.21 2.69
3855 10178 2.295253 ATAAGTTTGACGAGGCTCGG 57.705 50.000 36.81 20.85 45.59 4.63
3947 10270 9.956720 CATCAAGAAGTCAAAAGTTGTAATTCT 57.043 29.630 0.00 0.00 33.00 2.40
4125 10448 3.768633 CACTCCACTATCAGTGCCC 57.231 57.895 0.64 0.00 44.63 5.36
4127 10450 1.137872 CACTCCACTATCAGTGCCCTC 59.862 57.143 0.64 0.00 44.63 4.30
4253 10576 4.395231 TGTACTACTTGACGATCACCTCAG 59.605 45.833 0.00 0.00 0.00 3.35
4356 10679 8.506083 ACTTTTGGATATTTGGATCCTGAGTAT 58.494 33.333 14.23 8.19 45.07 2.12
4420 10743 0.764271 TGGTGTCATGCTTGTGGAGA 59.236 50.000 0.00 0.00 0.00 3.71
4492 10815 6.592994 CAGTCTAACTGCTGAATTCATCTTGA 59.407 38.462 8.96 0.00 39.62 3.02
4549 10872 0.250513 GCAAGTCATCGAGGAAGGGT 59.749 55.000 0.00 0.00 0.00 4.34
4617 10940 3.117851 GCTTAAAGGGTGAAGATAGGCCT 60.118 47.826 11.78 11.78 0.00 5.19
4785 11109 3.181469 TGCCTCGGTAACCTGATTGATAC 60.181 47.826 0.00 0.00 0.00 2.24
4796 11120 9.197306 GTAACCTGATTGATACCCCTTTTATTT 57.803 33.333 0.00 0.00 0.00 1.40
4828 11158 2.129555 GAAGCTGGTGCCCTTCCTGA 62.130 60.000 0.00 0.00 40.80 3.86
4866 11197 9.630098 TTGCTATCAAAAATAAAAGAGCTCTTG 57.370 29.630 29.09 14.93 36.12 3.02
4941 11272 5.932303 GCTTACAGACAGGTTTCAGTAATCA 59.068 40.000 0.00 0.00 29.96 2.57
5065 11396 2.353704 CCACGTGCCTCAAGTTAGATGA 60.354 50.000 10.91 0.00 0.00 2.92
5510 11844 3.722295 ACCACGAAACGCCGCATG 61.722 61.111 0.00 0.00 0.00 4.06
5708 12042 0.481128 TTTCTCCCAACCTCCAACCC 59.519 55.000 0.00 0.00 0.00 4.11
5724 12058 3.238497 CCACCACGACCCCAGACA 61.238 66.667 0.00 0.00 0.00 3.41
5750 12084 1.450312 GCGCTCCACCATACTTGCT 60.450 57.895 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 9.255304 GCAGGTTTTATTGATACAGTTTTGAAA 57.745 29.630 0.00 0.00 0.00 2.69
81 82 7.352739 CGACTAATGGCAGGTTTTATTGATAC 58.647 38.462 0.00 0.00 0.00 2.24
284 300 8.865001 CAAGGAATCGCTAGAATTACTATAAGC 58.135 37.037 0.00 0.00 0.00 3.09
379 398 2.032054 TCTCTGCACAGAAAAAGCAACG 59.968 45.455 1.42 0.00 37.89 4.10
531 550 0.403271 ATCTGCCAAGTGCCAAGTCT 59.597 50.000 0.00 0.00 40.16 3.24
541 560 4.589216 TGGAAACTTCAAATCTGCCAAG 57.411 40.909 0.00 0.00 0.00 3.61
542 561 4.588106 TGATGGAAACTTCAAATCTGCCAA 59.412 37.500 0.00 0.00 41.09 4.52
544 563 4.789012 TGATGGAAACTTCAAATCTGCC 57.211 40.909 6.15 0.00 41.09 4.85
708 741 7.676683 AGATCAATACCTGCTTACCTTTCTA 57.323 36.000 0.00 0.00 0.00 2.10
728 761 5.633927 ACGGCGGTAACAAATAAAAAGATC 58.366 37.500 13.24 0.00 0.00 2.75
943 1049 0.112218 AGCACTAACATGGTGGCCAA 59.888 50.000 7.24 0.00 36.95 4.52
968 1074 2.325857 GCGATGCGATGTTGGCTC 59.674 61.111 0.00 0.00 0.00 4.70
969 1075 3.204827 GGCGATGCGATGTTGGCT 61.205 61.111 0.00 0.00 0.00 4.75
995 1101 2.406596 TATGTTGCTGCATCTGCTGA 57.593 45.000 1.84 0.00 41.71 4.26
1006 1112 4.080015 TGGGTAAGGTATGCTTATGTTGCT 60.080 41.667 0.00 0.00 0.00 3.91
1248 1360 5.246429 GTCTGCTAACACCCTATATAGGCTT 59.754 44.000 21.75 14.21 42.26 4.35
1578 1743 1.446907 CAAGGCTGGTGTCAGATGAC 58.553 55.000 6.01 6.01 43.49 3.06
1694 7600 3.676646 GCATCCAAAGTCACTTGAATTGC 59.323 43.478 0.00 0.00 32.24 3.56
1695 7601 4.021719 AGGCATCCAAAGTCACTTGAATTG 60.022 41.667 0.00 0.00 32.24 2.32
1696 7602 4.154942 AGGCATCCAAAGTCACTTGAATT 58.845 39.130 0.00 0.00 33.37 2.17
1725 7631 2.128771 ACACAAGGCACTCACTGTTT 57.871 45.000 0.00 0.00 38.49 2.83
1755 7661 1.996798 AACCTCCTCTTGAGTCGTCA 58.003 50.000 0.00 0.00 39.65 4.35
1856 7769 1.944709 GCGGGCGTTACCTCAAATTAT 59.055 47.619 0.00 0.00 39.10 1.28
1857 7770 1.371595 GCGGGCGTTACCTCAAATTA 58.628 50.000 0.00 0.00 39.10 1.40
1858 7771 1.641123 CGCGGGCGTTACCTCAAATT 61.641 55.000 4.64 0.00 39.10 1.82
1859 7772 2.104253 CGCGGGCGTTACCTCAAAT 61.104 57.895 4.64 0.00 39.10 2.32
1860 7773 2.739287 CGCGGGCGTTACCTCAAA 60.739 61.111 4.64 0.00 39.10 2.69
2292 8230 1.204704 CTGCACCGGTCAGAACAGATA 59.795 52.381 22.23 0.00 33.54 1.98
2337 8275 2.203788 AGGCCGACCACCTCTGAA 60.204 61.111 0.00 0.00 39.06 3.02
2584 8522 0.608640 AAACGACGCTCCCAAGAGAT 59.391 50.000 0.00 0.00 43.39 2.75
2613 8552 2.164865 CTGCCTCTGACTTCCAGCGT 62.165 60.000 0.00 0.00 42.62 5.07
3104 9043 3.390135 CCGTCTAAGCAAGAAACTGTCA 58.610 45.455 0.00 0.00 35.47 3.58
3113 9052 1.298859 AAAGCCGCCGTCTAAGCAAG 61.299 55.000 0.00 0.00 0.00 4.01
3245 9187 9.893975 AGTAATGGTACTAATTATACAGGGAGT 57.106 33.333 0.00 0.00 38.87 3.85
3484 9533 7.591006 ATCAAAGTATTTTGCAATCTTGCTG 57.409 32.000 15.32 3.19 45.93 4.41
3610 9792 3.760684 GCAGTGACAAATCCTGGAGAATT 59.239 43.478 1.52 0.00 0.00 2.17
3626 9808 0.750850 GCCTATTCCTACCGCAGTGA 59.249 55.000 0.00 0.00 0.00 3.41
3654 9836 5.546526 CTGAGGATAATTAGAAGAGTGCCC 58.453 45.833 0.00 0.00 0.00 5.36
3678 10001 5.990408 AGCTTTTGTCTTACAATCAGAACG 58.010 37.500 0.00 0.00 38.00 3.95
3705 10028 2.693074 TGACTTCCTTGCTTTCCAAACC 59.307 45.455 0.00 0.00 31.94 3.27
3784 10107 5.467735 TGAACATCATCCTTTCAGCGATATG 59.532 40.000 0.00 0.00 0.00 1.78
3810 10133 4.833478 TGCCTTCTCAAGCTCTTCTAAT 57.167 40.909 0.00 0.00 0.00 1.73
3855 10178 0.609406 GGCCTCCACCTCCAAGTTTC 60.609 60.000 0.00 0.00 0.00 2.78
4125 10448 4.619336 GCTATTCTTAGCCGATCTTTCGAG 59.381 45.833 0.00 0.00 43.36 4.04
4127 10450 4.894798 GCTATTCTTAGCCGATCTTTCG 57.105 45.455 0.00 0.00 44.29 3.46
4253 10576 6.032717 GCTCCAAAATCTGATACTTTTGCTC 58.967 40.000 8.67 0.00 39.75 4.26
4356 10679 1.007038 GAGTCGCCGTGTGTGGTAA 60.007 57.895 0.00 0.00 0.00 2.85
4420 10743 6.891908 ACACATGGCTTCTTCCTTGTTAATAT 59.108 34.615 0.00 0.00 41.01 1.28
4492 10815 5.753921 CGAAGAGTTTGTCTTGGTTTACTCT 59.246 40.000 0.00 0.00 46.21 3.24
4549 10872 3.316308 GCAACTTCTTTGGCTTCTTCAGA 59.684 43.478 0.00 0.00 35.51 3.27
4617 10940 4.350368 TGTCTCAACTTGCCTCATTGTA 57.650 40.909 0.00 0.00 0.00 2.41
4796 11120 5.229423 GCACCAGCTTCATTAATTGAAACA 58.771 37.500 0.00 0.00 43.64 2.83
5043 11374 0.320421 TCTAACTTGAGGCACGTGGC 60.320 55.000 32.77 32.77 43.74 5.01
5065 11396 5.687780 TGTGAAAGATATGCCTGATGATGT 58.312 37.500 0.00 0.00 0.00 3.06
5075 11406 7.432350 CTAGGAAGGATTGTGAAAGATATGC 57.568 40.000 0.00 0.00 0.00 3.14
5174 11505 6.128200 TGCTGCAGTCTTTTTACACATATCAG 60.128 38.462 16.64 0.00 0.00 2.90
5510 11844 1.032014 TCTTGAAGGTGTTGCTTGGC 58.968 50.000 0.00 0.00 0.00 4.52
5708 12042 0.673644 GATTGTCTGGGGTCGTGGTG 60.674 60.000 0.00 0.00 0.00 4.17
5724 12058 2.203070 GGTGGAGCGCGATGGATT 60.203 61.111 12.10 0.00 0.00 3.01
5750 12084 1.077858 TGGCGCATATTGGCAGACA 60.078 52.632 10.83 0.00 36.93 3.41


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

AutoCloner maintained by Alex Coulton.