Multiple sequence alignment - TraesCS3B01G160500

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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 TraesCS3B01G160500 chr3B 100.000 2994 0 0 1 2994 155655733 155658726 0.000000e+00 5529.0
1 TraesCS3B01G160500 chr3B 98.305 177 3 0 171 347 145317752 145317576 8.060000e-81 311.0
2 TraesCS3B01G160500 chr3D 94.206 2330 68 24 344 2651 104402548 104404832 0.000000e+00 3493.0
3 TraesCS3B01G160500 chr3D 93.642 346 20 2 2649 2994 104404936 104405279 1.590000e-142 516.0
4 TraesCS3B01G160500 chr3D 92.126 127 6 1 49 171 104402430 104402556 3.070000e-40 176.0
5 TraesCS3B01G160500 chr3A 88.889 1728 115 34 680 2379 551693287 551691609 0.000000e+00 2056.0
6 TraesCS3B01G160500 chr3A 84.416 308 33 4 2699 2992 551691133 551690827 3.780000e-74 289.0
7 TraesCS3B01G160500 chr2A 98.295 176 3 0 172 347 9676683 9676858 2.900000e-80 309.0
8 TraesCS3B01G160500 chr2A 97.414 116 3 0 172 287 9674946 9675061 6.550000e-47 198.0
9 TraesCS3B01G160500 chr2A 97.222 72 2 0 172 243 12361343 12361272 4.050000e-24 122.0
10 TraesCS3B01G160500 chr2A 97.183 71 2 0 277 347 12361070 12361000 1.460000e-23 121.0
11 TraesCS3B01G160500 chr5B 97.561 164 4 0 184 347 423795613 423795776 6.320000e-72 281.0
12 TraesCS3B01G160500 chr5B 91.848 184 7 1 172 347 400924763 400924580 1.780000e-62 250.0
13 TraesCS3B01G160500 chr5B 95.745 47 2 0 5 51 418319482 418319436 3.200000e-10 76.8
14 TraesCS3B01G160500 chr5B 95.745 47 2 0 5 51 418322673 418322627 3.200000e-10 76.8
15 TraesCS3B01G160500 chr5B 95.745 47 2 0 5 51 418324800 418324754 3.200000e-10 76.8
16 TraesCS3B01G160500 chr4A 95.480 177 7 1 172 347 620259496 620259672 6.320000e-72 281.0
17 TraesCS3B01G160500 chr4A 94.350 177 9 1 172 347 735162173 735162349 1.370000e-68 270.0
18 TraesCS3B01G160500 chr4A 92.655 177 10 3 172 347 39081769 39081943 4.950000e-63 252.0
19 TraesCS3B01G160500 chr6A 92.350 183 8 1 172 348 539530363 539530545 3.830000e-64 255.0
20 TraesCS3B01G160500 chr1B 96.154 52 1 1 2 53 669746020 669746070 1.910000e-12 84.2
21 TraesCS3B01G160500 chr4B 97.826 46 0 1 2 46 44252487 44252532 8.900000e-11 78.7
22 TraesCS3B01G160500 chrUn 95.745 47 2 0 5 51 357738496 357738542 3.200000e-10 76.8
23 TraesCS3B01G160500 chrUn 95.745 47 2 0 5 51 378019357 378019403 3.200000e-10 76.8
24 TraesCS3B01G160500 chrUn 95.745 47 2 0 5 51 452685190 452685236 3.200000e-10 76.8
25 TraesCS3B01G160500 chr6B 94.118 51 1 2 1 49 120808817 120808767 3.200000e-10 76.8


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 TraesCS3B01G160500 chr3B 155655733 155658726 2993 False 5529.0 5529 100.000000 1 2994 1 chr3B.!!$F1 2993
1 TraesCS3B01G160500 chr3D 104402430 104405279 2849 False 1395.0 3493 93.324667 49 2994 3 chr3D.!!$F1 2945
2 TraesCS3B01G160500 chr3A 551690827 551693287 2460 True 1172.5 2056 86.652500 680 2992 2 chr3A.!!$R1 2312
3 TraesCS3B01G160500 chr2A 9674946 9676858 1912 False 253.5 309 97.854500 172 347 2 chr2A.!!$F1 175

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
45 46 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 F
47 48 0.032813 TTCCGGACGGAGGGAGTAAT 60.033 55.0 13.64 0.0 46.06 1.89 F
94 95 0.103208 CTCCTCCGTCCATGCACTAC 59.897 60.0 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 3306 1.134371 CCGATCTTGAAGGGGAAGACC 60.134 57.143 0.00 0.00 32.3 3.85 R
1650 3432 4.754667 GTGTCCCCGCCCGAGTTC 62.755 72.222 0.00 0.00 0.0 3.01 R
2215 4010 1.671054 ACCTCGGCCGAACAACATG 60.671 57.895 30.53 15.35 0.0 3.21 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
25 26 6.866480 TCCTTTATCCATTTTGATGACAAGC 58.134 36.000 0.00 0.00 37.32 4.01
26 27 6.436847 TCCTTTATCCATTTTGATGACAAGCA 59.563 34.615 0.00 0.00 37.32 3.91
27 28 7.124599 TCCTTTATCCATTTTGATGACAAGCAT 59.875 33.333 0.00 0.00 40.77 3.79
28 29 7.767198 CCTTTATCCATTTTGATGACAAGCATT 59.233 33.333 0.00 0.00 37.34 3.56
29 30 9.158233 CTTTATCCATTTTGATGACAAGCATTT 57.842 29.630 0.00 0.00 37.34 2.32
30 31 8.706492 TTATCCATTTTGATGACAAGCATTTC 57.294 30.769 0.00 0.00 37.34 2.17
31 32 5.481105 TCCATTTTGATGACAAGCATTTCC 58.519 37.500 0.00 0.00 37.34 3.13
32 33 4.327898 CCATTTTGATGACAAGCATTTCCG 59.672 41.667 0.00 0.00 37.34 4.30
33 34 3.574284 TTTGATGACAAGCATTTCCGG 57.426 42.857 0.00 0.00 37.34 5.14
34 35 2.488204 TGATGACAAGCATTTCCGGA 57.512 45.000 0.00 0.00 37.34 5.14
35 36 2.083774 TGATGACAAGCATTTCCGGAC 58.916 47.619 1.83 0.00 37.34 4.79
36 37 1.062587 GATGACAAGCATTTCCGGACG 59.937 52.381 1.83 0.00 37.34 4.79
37 38 0.953471 TGACAAGCATTTCCGGACGG 60.953 55.000 1.83 3.96 0.00 4.79
38 39 0.672401 GACAAGCATTTCCGGACGGA 60.672 55.000 1.83 9.76 43.52 4.69
39 40 0.673644 ACAAGCATTTCCGGACGGAG 60.674 55.000 13.64 3.92 46.06 4.63
40 41 1.078426 AAGCATTTCCGGACGGAGG 60.078 57.895 13.64 8.82 46.06 4.30
41 42 2.513897 GCATTTCCGGACGGAGGG 60.514 66.667 13.64 8.49 46.06 4.30
42 43 3.026431 GCATTTCCGGACGGAGGGA 62.026 63.158 13.64 4.95 46.06 4.20
43 44 1.144057 CATTTCCGGACGGAGGGAG 59.856 63.158 13.64 2.33 46.06 4.30
44 45 1.305887 ATTTCCGGACGGAGGGAGT 60.306 57.895 13.64 0.00 46.06 3.85
45 46 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
46 47 0.251742 TTTCCGGACGGAGGGAGTAA 60.252 55.000 13.64 1.47 46.06 2.24
47 48 0.032813 TTCCGGACGGAGGGAGTAAT 60.033 55.000 13.64 0.00 46.06 1.89
48 49 0.846015 TCCGGACGGAGGGAGTAATA 59.154 55.000 9.76 0.00 39.76 0.98
49 50 1.215173 TCCGGACGGAGGGAGTAATAA 59.785 52.381 9.76 0.00 39.76 1.40
50 51 2.158415 TCCGGACGGAGGGAGTAATAAT 60.158 50.000 9.76 0.00 39.76 1.28
51 52 3.074390 TCCGGACGGAGGGAGTAATAATA 59.926 47.826 9.76 0.00 39.76 0.98
52 53 3.192212 CCGGACGGAGGGAGTAATAATAC 59.808 52.174 4.40 0.00 37.50 1.89
53 54 3.192212 CGGACGGAGGGAGTAATAATACC 59.808 52.174 0.00 0.00 32.08 2.73
92 93 3.023949 GCTCCTCCGTCCATGCACT 62.024 63.158 0.00 0.00 0.00 4.40
94 95 0.103208 CTCCTCCGTCCATGCACTAC 59.897 60.000 0.00 0.00 0.00 2.73
140 145 1.579429 GTGGAACGAACCCATGCAC 59.421 57.895 0.00 0.00 35.91 4.57
159 164 1.003718 GCACGGGACCAAAGCTAGT 60.004 57.895 0.00 0.00 0.00 2.57
195 200 7.277981 GCCAATAATCCTACATCTACGTAATGG 59.722 40.741 16.69 4.71 0.00 3.16
258 2000 3.410541 CCCCCTGATTTCGTGGGA 58.589 61.111 9.27 0.00 43.47 4.37
347 2089 4.868171 TGCCTTTTACGTAGATGTAGCAAG 59.132 41.667 0.00 0.00 0.00 4.01
348 2090 4.868734 GCCTTTTACGTAGATGTAGCAAGT 59.131 41.667 0.00 0.00 0.00 3.16
349 2091 5.350640 GCCTTTTACGTAGATGTAGCAAGTT 59.649 40.000 0.00 0.00 0.00 2.66
350 2092 6.672357 GCCTTTTACGTAGATGTAGCAAGTTG 60.672 42.308 0.00 0.00 0.00 3.16
351 2093 5.773239 TTTACGTAGATGTAGCAAGTTGC 57.227 39.130 20.44 20.44 45.46 4.17
367 2109 1.855213 TTGCAAAGCAGCGCCTACTG 61.855 55.000 2.29 0.00 40.61 2.74
376 2118 2.949678 CGCCTACTGCTACGTGCG 60.950 66.667 0.00 0.00 46.63 5.34
377 2119 2.181021 GCCTACTGCTACGTGCGT 59.819 61.111 0.00 2.05 46.63 5.24
378 2120 1.430632 GCCTACTGCTACGTGCGTA 59.569 57.895 0.00 4.35 46.63 4.42
420 2162 2.258013 CGGAAGGCGCCTGAAAACA 61.258 57.895 33.60 0.00 0.00 2.83
452 2194 5.239744 TCAGTAACATAATCTCTCCTCGCTC 59.760 44.000 0.00 0.00 0.00 5.03
469 2211 1.399343 GCTCGGCTTTTCCACGTAAAC 60.399 52.381 0.00 0.00 34.01 2.01
470 2212 1.868498 CTCGGCTTTTCCACGTAAACA 59.132 47.619 0.00 0.00 34.01 2.83
508 2250 1.310904 GGTCCGTAAAAAGCACACCA 58.689 50.000 0.00 0.00 0.00 4.17
537 2279 8.296000 TCCCACATAATTGCGACATATAAAATG 58.704 33.333 0.00 0.00 0.00 2.32
623 2365 2.446435 TGGTAGAAAATGCAAGGAGCC 58.554 47.619 0.00 0.00 44.83 4.70
654 2396 2.420022 GCCGTGCAAGATCACAACTTAT 59.580 45.455 0.00 0.00 36.80 1.73
655 2397 3.485877 GCCGTGCAAGATCACAACTTATC 60.486 47.826 0.00 0.00 36.80 1.75
673 2415 7.098074 ACTTATCACGGAGTAGTTTCTTAGG 57.902 40.000 0.00 0.00 41.61 2.69
754 2504 1.403780 GGATGGTCACCACGTACTCAC 60.404 57.143 0.00 0.00 35.80 3.51
941 2697 4.824515 ACGCCTCCCTCCTCCTCG 62.825 72.222 0.00 0.00 0.00 4.63
1051 2807 3.879892 GAGCAAAAGTTGTTCCACTCTCT 59.120 43.478 0.00 0.00 35.19 3.10
1052 2808 3.879892 AGCAAAAGTTGTTCCACTCTCTC 59.120 43.478 0.00 0.00 0.00 3.20
1055 2811 4.713792 AAAGTTGTTCCACTCTCTCCAT 57.286 40.909 0.00 0.00 0.00 3.41
1056 2812 4.713792 AAGTTGTTCCACTCTCTCCATT 57.286 40.909 0.00 0.00 0.00 3.16
1057 2813 4.013267 AGTTGTTCCACTCTCTCCATTG 57.987 45.455 0.00 0.00 0.00 2.82
1135 2897 1.064946 GGCTCGACGGTGATCTCTG 59.935 63.158 2.01 2.01 0.00 3.35
1136 2898 1.587613 GCTCGACGGTGATCTCTGC 60.588 63.158 3.48 0.00 0.00 4.26
2299 4094 6.476706 GCTTGTGAAAAATGCATAATCCTACC 59.523 38.462 0.00 0.00 0.00 3.18
2320 4116 8.674607 CCTACCTAGTAAATTGGTTGATTTGTC 58.325 37.037 0.00 0.00 38.13 3.18
2439 4264 7.851387 TTCATTCCGTACATAATAAGCAACA 57.149 32.000 0.00 0.00 0.00 3.33
2468 4296 6.315891 AGCTTATATACCTACCGAGATCGTTC 59.684 42.308 1.09 0.00 37.74 3.95
2577 4412 1.303561 AGCTGACCCGTACGTACCA 60.304 57.895 19.67 10.67 0.00 3.25
2578 4413 0.682209 AGCTGACCCGTACGTACCAT 60.682 55.000 19.67 5.47 0.00 3.55
2579 4414 1.024271 GCTGACCCGTACGTACCATA 58.976 55.000 19.67 1.95 0.00 2.74
2580 4415 1.268743 GCTGACCCGTACGTACCATAC 60.269 57.143 19.67 9.78 0.00 2.39
2581 4416 2.292267 CTGACCCGTACGTACCATACT 58.708 52.381 19.67 0.00 0.00 2.12
2603 4442 7.659652 ACTGTCTAGTCTTTTAACTTCATGC 57.340 36.000 0.00 0.00 28.79 4.06
2687 4774 3.320826 GGGTGAATGTTACCTTTGTTGCT 59.679 43.478 0.00 0.00 38.30 3.91
2741 4828 1.808411 TGATTTCAGCCCGTTCACTC 58.192 50.000 0.00 0.00 0.00 3.51
2799 4888 1.327303 TTGGGGTGCACTAGCTTTTG 58.673 50.000 17.98 0.00 42.74 2.44
2812 4901 6.360329 CACTAGCTTTTGTGTACGTTTTAGG 58.640 40.000 0.00 0.00 0.00 2.69
2813 4902 6.201425 CACTAGCTTTTGTGTACGTTTTAGGA 59.799 38.462 0.00 0.00 0.00 2.94
2814 4903 5.668558 AGCTTTTGTGTACGTTTTAGGAG 57.331 39.130 0.00 0.00 0.00 3.69
2817 4906 6.423001 AGCTTTTGTGTACGTTTTAGGAGTAG 59.577 38.462 0.00 0.00 0.00 2.57
2818 4907 6.201615 GCTTTTGTGTACGTTTTAGGAGTAGT 59.798 38.462 0.00 0.00 0.00 2.73
2823 4912 7.491682 TGTGTACGTTTTAGGAGTAGTTTTCT 58.508 34.615 0.00 0.00 0.00 2.52
2862 4951 4.410228 TGATTAGGCTTTCTCTATGGTGCT 59.590 41.667 0.00 0.00 0.00 4.40
2899 4997 4.487714 TCCCGGGATCATAAATCTATGC 57.512 45.455 22.63 0.00 35.75 3.14
2901 4999 3.198068 CCGGGATCATAAATCTATGCCG 58.802 50.000 7.42 7.42 37.92 5.69
2911 5009 8.262601 TCATAAATCTATGCCGGATATATGGT 57.737 34.615 5.05 0.00 35.75 3.55
2934 5032 5.567154 GTCATGTCATCGTCTTATCGATCTG 59.433 44.000 0.00 0.00 46.64 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.976925 GCTTGTCATCAAAATGGATAAAGGAG 59.023 38.462 0.00 0.00 33.42 3.69
1 2 6.436847 TGCTTGTCATCAAAATGGATAAAGGA 59.563 34.615 0.00 0.00 33.42 3.36
2 3 6.632909 TGCTTGTCATCAAAATGGATAAAGG 58.367 36.000 0.00 0.00 33.42 3.11
3 4 8.712285 AATGCTTGTCATCAAAATGGATAAAG 57.288 30.769 0.00 0.00 33.40 1.85
4 5 9.153721 GAAATGCTTGTCATCAAAATGGATAAA 57.846 29.630 0.00 0.00 33.40 1.40
6 7 7.267128 GGAAATGCTTGTCATCAAAATGGATA 58.733 34.615 0.00 0.00 33.40 2.59
7 8 6.110707 GGAAATGCTTGTCATCAAAATGGAT 58.889 36.000 0.00 0.00 33.40 3.41
8 9 5.481105 GGAAATGCTTGTCATCAAAATGGA 58.519 37.500 0.00 0.00 33.40 3.41
9 10 4.327898 CGGAAATGCTTGTCATCAAAATGG 59.672 41.667 0.00 0.00 33.40 3.16
10 11 4.327898 CCGGAAATGCTTGTCATCAAAATG 59.672 41.667 0.00 0.00 33.40 2.32
11 12 4.220382 TCCGGAAATGCTTGTCATCAAAAT 59.780 37.500 0.00 0.00 33.40 1.82
12 13 3.571828 TCCGGAAATGCTTGTCATCAAAA 59.428 39.130 0.00 0.00 33.40 2.44
13 14 3.057596 GTCCGGAAATGCTTGTCATCAAA 60.058 43.478 5.23 0.00 33.40 2.69
14 15 2.487762 GTCCGGAAATGCTTGTCATCAA 59.512 45.455 5.23 0.00 33.40 2.57
15 16 2.083774 GTCCGGAAATGCTTGTCATCA 58.916 47.619 5.23 0.00 33.40 3.07
16 17 1.062587 CGTCCGGAAATGCTTGTCATC 59.937 52.381 5.23 0.00 33.40 2.92
17 18 1.086696 CGTCCGGAAATGCTTGTCAT 58.913 50.000 5.23 0.00 36.87 3.06
18 19 0.953471 CCGTCCGGAAATGCTTGTCA 60.953 55.000 5.23 0.00 37.50 3.58
19 20 0.672401 TCCGTCCGGAAATGCTTGTC 60.672 55.000 5.23 0.00 42.05 3.18
20 21 0.673644 CTCCGTCCGGAAATGCTTGT 60.674 55.000 5.23 0.00 44.66 3.16
21 22 1.369091 CCTCCGTCCGGAAATGCTTG 61.369 60.000 5.23 0.00 44.66 4.01
22 23 1.078426 CCTCCGTCCGGAAATGCTT 60.078 57.895 5.23 0.00 44.66 3.91
23 24 2.584608 CCTCCGTCCGGAAATGCT 59.415 61.111 5.23 0.00 44.66 3.79
24 25 2.513897 CCCTCCGTCCGGAAATGC 60.514 66.667 5.23 0.00 44.66 3.56
25 26 1.144057 CTCCCTCCGTCCGGAAATG 59.856 63.158 5.23 0.00 44.66 2.32
26 27 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
27 28 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
28 29 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
29 30 0.846015 TATTACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
30 31 1.696063 TTATTACTCCCTCCGTCCGG 58.304 55.000 0.00 0.00 0.00 5.14
31 32 3.192212 GGTATTATTACTCCCTCCGTCCG 59.808 52.174 0.00 0.00 0.00 4.79
32 33 3.192212 CGGTATTATTACTCCCTCCGTCC 59.808 52.174 0.00 0.00 33.39 4.79
33 34 3.192212 CCGGTATTATTACTCCCTCCGTC 59.808 52.174 0.00 0.00 35.78 4.79
34 35 3.160269 CCGGTATTATTACTCCCTCCGT 58.840 50.000 0.00 0.00 35.78 4.69
35 36 3.424703 TCCGGTATTATTACTCCCTCCG 58.575 50.000 0.00 0.00 37.04 4.63
36 37 4.020751 GGTTCCGGTATTATTACTCCCTCC 60.021 50.000 0.00 0.00 0.00 4.30
37 38 4.020751 GGGTTCCGGTATTATTACTCCCTC 60.021 50.000 0.00 0.00 0.00 4.30
38 39 3.906218 GGGTTCCGGTATTATTACTCCCT 59.094 47.826 0.00 0.00 0.00 4.20
39 40 3.906218 AGGGTTCCGGTATTATTACTCCC 59.094 47.826 0.00 0.00 0.00 4.30
40 41 4.590222 TCAGGGTTCCGGTATTATTACTCC 59.410 45.833 0.00 0.00 0.00 3.85
41 42 5.796424 TCAGGGTTCCGGTATTATTACTC 57.204 43.478 0.00 0.00 0.00 2.59
42 43 6.564557 TTTCAGGGTTCCGGTATTATTACT 57.435 37.500 0.00 0.00 0.00 2.24
43 44 6.206048 CCATTTCAGGGTTCCGGTATTATTAC 59.794 42.308 0.00 0.00 0.00 1.89
44 45 6.300703 CCATTTCAGGGTTCCGGTATTATTA 58.699 40.000 0.00 0.00 0.00 0.98
45 46 5.137551 CCATTTCAGGGTTCCGGTATTATT 58.862 41.667 0.00 0.00 0.00 1.40
46 47 4.725490 CCATTTCAGGGTTCCGGTATTAT 58.275 43.478 0.00 0.00 0.00 1.28
47 48 3.686120 GCCATTTCAGGGTTCCGGTATTA 60.686 47.826 0.00 0.00 0.00 0.98
48 49 2.948600 GCCATTTCAGGGTTCCGGTATT 60.949 50.000 0.00 0.00 0.00 1.89
49 50 1.409661 GCCATTTCAGGGTTCCGGTAT 60.410 52.381 0.00 0.00 0.00 2.73
50 51 0.034863 GCCATTTCAGGGTTCCGGTA 60.035 55.000 0.00 0.00 0.00 4.02
51 52 1.304134 GCCATTTCAGGGTTCCGGT 60.304 57.895 0.00 0.00 0.00 5.28
52 53 1.304052 TGCCATTTCAGGGTTCCGG 60.304 57.895 0.00 0.00 0.00 5.14
53 54 2.183409 CTGCCATTTCAGGGTTCCG 58.817 57.895 0.00 0.00 0.00 4.30
112 113 1.707239 TTCGTTCCACGTTGGCACAC 61.707 55.000 7.35 0.00 43.14 3.82
140 145 2.047655 TAGCTTTGGTCCCGTGCG 60.048 61.111 0.00 0.00 0.00 5.34
159 164 3.088532 AGGATTATTGGCAAGTTGCGAA 58.911 40.909 24.69 24.69 46.21 4.70
195 200 7.821652 AGAAGGTTACGTAAGGTTAAGTAGAC 58.178 38.462 8.60 0.00 46.39 2.59
347 2089 1.442688 GTAGGCGCTGCTTTGCAAC 60.443 57.895 7.64 0.00 38.41 4.17
348 2090 1.600636 AGTAGGCGCTGCTTTGCAA 60.601 52.632 7.64 0.00 38.41 4.08
349 2091 2.032528 AGTAGGCGCTGCTTTGCA 59.967 55.556 7.64 0.00 36.92 4.08
350 2092 2.482374 CAGTAGGCGCTGCTTTGC 59.518 61.111 7.64 0.00 0.00 3.68
376 2118 4.884247 AGCTTCCAGACAAACAGTACTAC 58.116 43.478 0.00 0.00 0.00 2.73
377 2119 5.510861 GGAAGCTTCCAGACAAACAGTACTA 60.511 44.000 35.71 0.00 46.76 1.82
378 2120 4.381411 GAAGCTTCCAGACAAACAGTACT 58.619 43.478 15.97 0.00 0.00 2.73
379 2121 3.498777 GGAAGCTTCCAGACAAACAGTAC 59.501 47.826 35.71 7.18 46.76 2.73
452 2194 2.759538 TTGTTTACGTGGAAAAGCCG 57.240 45.000 0.00 0.00 40.66 5.52
469 2211 2.159254 CCGTATGGAAAGGTGCCAATTG 60.159 50.000 0.00 0.00 39.21 2.32
470 2212 2.099405 CCGTATGGAAAGGTGCCAATT 58.901 47.619 0.00 0.00 39.21 2.32
508 2250 6.899393 ATATGTCGCAATTATGTGGGAAAT 57.101 33.333 1.23 1.23 41.55 2.17
537 2279 6.625081 GCATGGAAAGTTACTGGTTATTCCAC 60.625 42.308 15.18 3.57 46.36 4.02
548 2290 3.440173 CCGTTCATGCATGGAAAGTTACT 59.560 43.478 25.97 0.00 0.00 2.24
561 2303 2.997621 TTTGCGTGCACCGTTCATGC 62.998 55.000 12.15 8.26 44.41 4.06
580 2322 1.770294 TTTTTCAACAGAAGGGGCGT 58.230 45.000 0.00 0.00 0.00 5.68
629 2371 3.120385 TGATCTTGCACGGCAGCG 61.120 61.111 0.00 0.00 40.61 5.18
654 2396 3.057033 GTGCCTAAGAAACTACTCCGTGA 60.057 47.826 0.00 0.00 0.00 4.35
655 2397 3.251571 GTGCCTAAGAAACTACTCCGTG 58.748 50.000 0.00 0.00 0.00 4.94
736 2486 0.606604 GGTGAGTACGTGGTGACCAT 59.393 55.000 7.94 0.00 35.28 3.55
754 2504 0.030773 ACCGATGACGATGATGACGG 59.969 55.000 0.00 0.00 42.66 4.79
845 2601 0.029700 GTAACGTTGGTTGTGTGGCC 59.970 55.000 11.99 0.00 36.90 5.36
846 2602 0.316360 CGTAACGTTGGTTGTGTGGC 60.316 55.000 11.99 0.00 36.90 5.01
847 2603 0.316360 GCGTAACGTTGGTTGTGTGG 60.316 55.000 11.99 0.00 36.90 4.17
848 2604 0.653636 AGCGTAACGTTGGTTGTGTG 59.346 50.000 11.99 0.00 36.90 3.82
849 2605 0.932399 GAGCGTAACGTTGGTTGTGT 59.068 50.000 11.99 0.00 36.90 3.72
850 2606 0.233848 GGAGCGTAACGTTGGTTGTG 59.766 55.000 11.99 0.00 36.90 3.33
851 2607 0.105408 AGGAGCGTAACGTTGGTTGT 59.895 50.000 11.99 0.00 36.90 3.32
955 2711 3.083686 GCCGTATTTAAAGGCCCGA 57.916 52.632 0.00 0.00 44.80 5.14
976 2732 4.129148 AATGGGAAGCGGAGGCCC 62.129 66.667 0.00 0.00 41.24 5.80
1056 2812 1.300080 GGCTTCGCTTTGCTTTGCA 60.300 52.632 0.00 0.00 36.47 4.08
1057 2813 1.300080 TGGCTTCGCTTTGCTTTGC 60.300 52.632 0.00 0.00 0.00 3.68
1380 3150 4.144703 GCGAGGAGGTCCCGGAAC 62.145 72.222 0.73 0.00 40.87 3.62
1470 3240 1.153429 GGGGTCGTGCTGGTACATC 60.153 63.158 0.00 0.00 38.20 3.06
1536 3306 1.134371 CCGATCTTGAAGGGGAAGACC 60.134 57.143 0.00 0.00 32.30 3.85
1650 3432 4.754667 GTGTCCCCGCCCGAGTTC 62.755 72.222 0.00 0.00 0.00 3.01
2215 4010 1.671054 ACCTCGGCCGAACAACATG 60.671 57.895 30.53 15.35 0.00 3.21
2439 4264 7.441760 CGATCTCGGTAGGTATATAAGCTGTAT 59.558 40.741 0.00 0.00 34.90 2.29
2448 4273 5.802465 TCTGAACGATCTCGGTAGGTATAT 58.198 41.667 4.44 0.00 40.66 0.86
2468 4296 3.969352 GTCAGACTTATGTACGCGATCTG 59.031 47.826 15.93 11.79 34.68 2.90
2473 4301 4.088638 GCATATGTCAGACTTATGTACGCG 59.911 45.833 26.08 3.53 38.06 6.01
2534 4369 5.382616 CATGATTCCATCTCCAAAGATCCA 58.617 41.667 0.00 0.00 40.38 3.41
2540 4375 2.691526 GCTGCATGATTCCATCTCCAAA 59.308 45.455 0.00 0.00 0.00 3.28
2563 4398 2.017049 ACAGTATGGTACGTACGGGTC 58.983 52.381 21.06 8.98 43.62 4.46
2577 4412 9.372369 GCATGAAGTTAAAAGACTAGACAGTAT 57.628 33.333 0.00 0.00 34.21 2.12
2578 4413 7.817962 GGCATGAAGTTAAAAGACTAGACAGTA 59.182 37.037 0.00 0.00 34.21 2.74
2579 4414 6.651225 GGCATGAAGTTAAAAGACTAGACAGT 59.349 38.462 0.00 0.00 37.87 3.55
2580 4415 6.092807 GGGCATGAAGTTAAAAGACTAGACAG 59.907 42.308 0.00 0.00 0.00 3.51
2581 4416 5.938125 GGGCATGAAGTTAAAAGACTAGACA 59.062 40.000 0.00 0.00 0.00 3.41
2687 4774 7.095816 CGACAAGTTATGATTGATTATACGGCA 60.096 37.037 0.00 0.00 0.00 5.69
2741 4828 6.032094 GGTGTTGTAATCATGAGCAAGATTG 58.968 40.000 10.27 0.00 36.07 2.67
2782 4871 0.598065 CACAAAAGCTAGTGCACCCC 59.402 55.000 14.63 1.68 42.74 4.95
2799 4888 7.568315 GCAGAAAACTACTCCTAAAACGTACAC 60.568 40.741 0.00 0.00 0.00 2.90
2812 4901 5.527582 TCACTTTCAAGGCAGAAAACTACTC 59.472 40.000 6.60 0.00 37.09 2.59
2813 4902 5.437060 TCACTTTCAAGGCAGAAAACTACT 58.563 37.500 6.60 0.00 37.09 2.57
2814 4903 5.751243 TCACTTTCAAGGCAGAAAACTAC 57.249 39.130 6.60 0.00 37.09 2.73
2817 4906 4.800471 CACTTCACTTTCAAGGCAGAAAAC 59.200 41.667 6.60 0.00 37.09 2.43
2818 4907 4.704540 TCACTTCACTTTCAAGGCAGAAAA 59.295 37.500 6.60 0.00 37.09 2.29
2823 4912 4.761739 CCTAATCACTTCACTTTCAAGGCA 59.238 41.667 0.00 0.00 0.00 4.75
2862 4951 5.213519 TCCCGGGATATTCTAAAAGTCTCA 58.786 41.667 22.63 0.00 0.00 3.27
2899 4997 4.142160 ACGATGACATGACCATATATCCGG 60.142 45.833 0.00 0.00 0.00 5.14
2901 4999 6.214191 AGACGATGACATGACCATATATCC 57.786 41.667 0.00 0.00 0.00 2.59
2934 5032 5.481473 ACATATATGGGACCATGGAATTTGC 59.519 40.000 21.47 0.00 37.82 3.68


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

AutoCloner maintained by Alex Coulton.