Multiple sequence alignment - TraesCS4B01G264600

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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 TraesCS4B01G264600 chr4B 100.000 4197 0 0 1 4197 535240495 535244691 0.000000e+00 7751
1 TraesCS4B01G264600 chr4B 86.806 1766 175 26 1444 3167 535290951 535292700 0.000000e+00 1917
2 TraesCS4B01G264600 chr4B 90.329 1003 68 6 1341 2338 535205735 535206713 0.000000e+00 1288
3 TraesCS4B01G264600 chr4B 90.419 835 63 7 2340 3162 535218883 535219712 0.000000e+00 1083
4 TraesCS4B01G264600 chr4B 82.840 979 110 25 2409 3339 535295605 535296573 0.000000e+00 824
5 TraesCS4B01G264600 chr4B 82.041 980 116 28 2409 3339 535378046 535379014 0.000000e+00 780
6 TraesCS4B01G264600 chr4B 89.447 398 24 16 957 1341 535105883 535106275 1.750000e-133 486
7 TraesCS4B01G264600 chr4B 91.667 84 6 1 3236 3319 535219972 535220054 9.540000e-22 115
8 TraesCS4B01G264600 chr4D 89.820 1886 124 23 1320 3169 435058859 435060712 0.000000e+00 2357
9 TraesCS4B01G264600 chr4D 86.523 1766 175 29 1447 3167 435139960 435141707 0.000000e+00 1884
10 TraesCS4B01G264600 chr4D 85.849 954 95 26 2 941 435057351 435058278 0.000000e+00 977
11 TraesCS4B01G264600 chr4D 87.662 308 24 10 957 1251 435058330 435058636 3.110000e-91 346
12 TraesCS4B01G264600 chr4D 83.972 287 19 11 3069 3330 435144763 435145047 2.510000e-62 250
13 TraesCS4B01G264600 chr4D 79.144 187 12 16 3154 3318 435141730 435141911 2.060000e-18 104
14 TraesCS4B01G264600 chr4A 86.580 1766 175 29 1447 3167 36473392 36475140 0.000000e+00 1892
15 TraesCS4B01G264600 chr4A 87.983 1398 89 28 957 2303 36407796 36409165 0.000000e+00 1578
16 TraesCS4B01G264600 chr4A 88.989 890 82 8 2292 3174 36409541 36410421 0.000000e+00 1086
17 TraesCS4B01G264600 chr4A 84.817 955 98 27 2 941 36406822 36407744 0.000000e+00 917
18 TraesCS4B01G264600 chr4A 89.552 134 8 5 3209 3339 36532057 36532187 9.340000e-37 165
19 TraesCS4B01G264600 chr4A 87.218 133 14 3 3206 3337 36410522 36410652 9.400000e-32 148
20 TraesCS4B01G264600 chr3B 99.418 859 5 0 3339 4197 136797849 136796991 0.000000e+00 1559
21 TraesCS4B01G264600 chr3B 93.148 861 55 2 3341 4197 226964005 226964865 0.000000e+00 1260
22 TraesCS4B01G264600 chr7B 96.391 859 31 0 3339 4197 556335613 556334755 0.000000e+00 1415
23 TraesCS4B01G264600 chr2B 96.140 855 33 0 3343 4197 115850965 115850111 0.000000e+00 1397
24 TraesCS4B01G264600 chr2A 94.767 860 44 1 3338 4197 772827514 772828372 0.000000e+00 1338
25 TraesCS4B01G264600 chr1B 94.516 857 46 1 3341 4197 470423592 470422737 0.000000e+00 1321
26 TraesCS4B01G264600 chr2D 94.179 859 43 1 3339 4197 647562403 647561552 0.000000e+00 1303
27 TraesCS4B01G264600 chr6A 93.140 860 58 1 3339 4197 198093893 198094752 0.000000e+00 1260
28 TraesCS4B01G264600 chr7A 93.015 859 60 0 3339 4197 705676921 705676063 0.000000e+00 1254


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 TraesCS4B01G264600 chr4B 535240495 535244691 4196 False 7751.000000 7751 100.00000 1 4197 1 chr4B.!!$F3 4196
1 TraesCS4B01G264600 chr4B 535290951 535296573 5622 False 1370.500000 1917 84.82300 1444 3339 2 chr4B.!!$F6 1895
2 TraesCS4B01G264600 chr4B 535205735 535206713 978 False 1288.000000 1288 90.32900 1341 2338 1 chr4B.!!$F2 997
3 TraesCS4B01G264600 chr4B 535378046 535379014 968 False 780.000000 780 82.04100 2409 3339 1 chr4B.!!$F4 930
4 TraesCS4B01G264600 chr4B 535218883 535220054 1171 False 599.000000 1083 91.04300 2340 3319 2 chr4B.!!$F5 979
5 TraesCS4B01G264600 chr4D 435057351 435060712 3361 False 1226.666667 2357 87.77700 2 3169 3 chr4D.!!$F1 3167
6 TraesCS4B01G264600 chr4D 435139960 435145047 5087 False 746.000000 1884 83.21300 1447 3330 3 chr4D.!!$F2 1883
7 TraesCS4B01G264600 chr4A 36473392 36475140 1748 False 1892.000000 1892 86.58000 1447 3167 1 chr4A.!!$F1 1720
8 TraesCS4B01G264600 chr4A 36406822 36410652 3830 False 932.250000 1578 87.25175 2 3337 4 chr4A.!!$F3 3335
9 TraesCS4B01G264600 chr3B 136796991 136797849 858 True 1559.000000 1559 99.41800 3339 4197 1 chr3B.!!$R1 858
10 TraesCS4B01G264600 chr3B 226964005 226964865 860 False 1260.000000 1260 93.14800 3341 4197 1 chr3B.!!$F1 856
11 TraesCS4B01G264600 chr7B 556334755 556335613 858 True 1415.000000 1415 96.39100 3339 4197 1 chr7B.!!$R1 858
12 TraesCS4B01G264600 chr2B 115850111 115850965 854 True 1397.000000 1397 96.14000 3343 4197 1 chr2B.!!$R1 854
13 TraesCS4B01G264600 chr2A 772827514 772828372 858 False 1338.000000 1338 94.76700 3338 4197 1 chr2A.!!$F1 859
14 TraesCS4B01G264600 chr1B 470422737 470423592 855 True 1321.000000 1321 94.51600 3341 4197 1 chr1B.!!$R1 856
15 TraesCS4B01G264600 chr2D 647561552 647562403 851 True 1303.000000 1303 94.17900 3339 4197 1 chr2D.!!$R1 858
16 TraesCS4B01G264600 chr6A 198093893 198094752 859 False 1260.000000 1260 93.14000 3339 4197 1 chr6A.!!$F1 858
17 TraesCS4B01G264600 chr7A 705676063 705676921 858 True 1254.000000 1254 93.01500 3339 4197 1 chr7A.!!$R1 858

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
581 591 0.037590 TTGGGAGGGACCGACATTTG 59.962 55.0 0.0 0.0 40.11 2.32 F
1263 1330 0.405585 ACCAGTAGCCCAAGTGCATT 59.594 50.0 0.0 0.0 0.00 3.56 F
2416 3057 0.171007 GCCGTGGTGGTTTCATCATG 59.829 55.0 0.0 0.0 39.95 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2303 0.034283 ACCAGTCCTCCTCGTAGTCC 60.034 60.000 0.00 0.0 0.0 3.85 R
2488 3174 0.390866 CAGCGACAACCTGCAGAGAT 60.391 55.000 17.39 0.0 0.0 2.75 R
3428 11201 2.469826 TGTAATGCCGCGAGAGTAATG 58.530 47.619 8.23 0.0 0.0 1.90 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 1.071699 GAACATAAGATGGCCCGGCTA 59.928 52.381 9.86 2.83 33.60 3.93
51 52 7.916450 AGTTTATCTCGTTTAGCTAGCTACAAG 59.084 37.037 24.09 19.13 0.00 3.16
55 56 4.360563 TCGTTTAGCTAGCTACAAGATGC 58.639 43.478 24.09 4.82 0.00 3.91
56 57 3.180584 CGTTTAGCTAGCTACAAGATGCG 59.819 47.826 24.09 12.79 0.00 4.73
355 362 9.801873 AATGTTTACATTCATAAAGAAATCCCG 57.198 29.630 2.33 0.00 42.45 5.14
376 383 8.874744 TCCCGAAGTTTATTTTTACCTTTTTG 57.125 30.769 0.00 0.00 0.00 2.44
412 419 9.826574 AAAGGTTATTTTTAAGGGAAAGACAAC 57.173 29.630 0.00 0.00 0.00 3.32
421 428 8.990163 TTTAAGGGAAAGACAACTTGATAACT 57.010 30.769 0.00 0.00 36.39 2.24
430 437 9.708092 AAAGACAACTTGATAACTAGTAGAACC 57.292 33.333 3.59 0.00 36.39 3.62
453 463 0.883833 AAAATCTGGCTTCCACGCTG 59.116 50.000 0.00 0.00 0.00 5.18
468 478 1.376609 CGCTGGTAATCTGGGTTGGC 61.377 60.000 0.00 0.00 0.00 4.52
490 500 2.224066 CCAGTCGGTGAGTCACTCTTTT 60.224 50.000 22.18 3.04 34.40 2.27
493 503 1.070134 TCGGTGAGTCACTCTTTTGGG 59.930 52.381 22.18 3.25 34.40 4.12
494 504 1.070134 CGGTGAGTCACTCTTTTGGGA 59.930 52.381 22.18 0.00 34.40 4.37
496 506 2.368875 GGTGAGTCACTCTTTTGGGAGA 59.631 50.000 22.18 0.00 37.13 3.71
497 507 3.181454 GGTGAGTCACTCTTTTGGGAGAA 60.181 47.826 22.18 0.00 37.13 2.87
516 526 6.321717 GGAGAAATCAACATTTAATCGCACA 58.678 36.000 0.00 0.00 31.94 4.57
535 545 2.501723 ACAGAGCGACCAATATGACCTT 59.498 45.455 0.00 0.00 0.00 3.50
538 548 3.389329 AGAGCGACCAATATGACCTTGAT 59.611 43.478 0.00 0.00 0.00 2.57
540 550 5.247110 AGAGCGACCAATATGACCTTGATAT 59.753 40.000 0.00 0.00 0.00 1.63
571 581 2.921221 AGACTCATTCTTTGGGAGGGA 58.079 47.619 0.00 0.00 32.98 4.20
574 584 0.618458 TCATTCTTTGGGAGGGACCG 59.382 55.000 0.00 0.00 40.11 4.79
575 585 0.618458 CATTCTTTGGGAGGGACCGA 59.382 55.000 0.00 0.00 40.11 4.69
580 590 0.774908 TTTGGGAGGGACCGACATTT 59.225 50.000 0.00 0.00 40.11 2.32
581 591 0.037590 TTGGGAGGGACCGACATTTG 59.962 55.000 0.00 0.00 40.11 2.32
582 592 1.077716 GGGAGGGACCGACATTTGG 60.078 63.158 0.00 0.00 40.11 3.28
583 593 1.683441 GGAGGGACCGACATTTGGT 59.317 57.895 0.00 0.00 44.10 3.67
597 607 4.943822 TGGTCGCACAGAACAACA 57.056 50.000 0.00 0.00 44.92 3.33
618 628 9.784531 ACAACAAATAGGACATCCATAGAATAG 57.215 33.333 0.00 0.00 38.89 1.73
619 629 9.784531 CAACAAATAGGACATCCATAGAATAGT 57.215 33.333 0.00 0.00 38.89 2.12
621 631 8.378565 ACAAATAGGACATCCATAGAATAGTGG 58.621 37.037 0.00 0.00 38.89 4.00
649 659 8.090250 AGACTCACTTATTGTATAGAGTAGCG 57.910 38.462 0.00 0.00 36.56 4.26
686 696 5.759506 TGTCGGTACACAATGAACATTTT 57.240 34.783 0.00 0.00 0.00 1.82
713 723 8.641499 AAATGCACGTTGAAGATTCTTTTAAA 57.359 26.923 0.00 0.00 0.00 1.52
862 872 9.675464 ATTTCTTGATGTTTTAAATGCCATGAT 57.325 25.926 0.00 0.00 0.00 2.45
1079 1134 9.701098 ATGTTCAATGTGCATATGGAAAATATC 57.299 29.630 14.23 3.52 0.00 1.63
1233 1300 3.888930 GGAACCTTCTGAAAACCACATGA 59.111 43.478 0.00 0.00 0.00 3.07
1260 1327 1.269723 GAAAACCAGTAGCCCAAGTGC 59.730 52.381 0.00 0.00 0.00 4.40
1263 1330 0.405585 ACCAGTAGCCCAAGTGCATT 59.594 50.000 0.00 0.00 0.00 3.56
1335 1556 0.955905 GGGTTTACTGCCGAGCAAAA 59.044 50.000 0.35 0.00 38.41 2.44
1336 1557 1.068541 GGGTTTACTGCCGAGCAAAAG 60.069 52.381 0.35 0.00 38.41 2.27
1338 1559 2.034179 GGTTTACTGCCGAGCAAAAGTT 59.966 45.455 0.35 0.00 38.41 2.66
1339 1560 3.251487 GGTTTACTGCCGAGCAAAAGTTA 59.749 43.478 0.35 0.00 38.41 2.24
1364 1589 4.466015 ACTTATATGTTGGGTTGGGCTTTG 59.534 41.667 0.00 0.00 0.00 2.77
1392 1620 8.574196 AAAAATAACTCCACGAATTGTCAAAG 57.426 30.769 0.00 0.00 0.00 2.77
1713 1950 3.667282 CGTGGACACCCGTCTCGT 61.667 66.667 0.00 0.00 42.21 4.18
1723 1960 4.538283 CGTCTCGTCGATGCGCCT 62.538 66.667 4.18 0.00 0.00 5.52
1756 1993 4.309950 GCCTTCGTGGACCACCGT 62.310 66.667 19.11 0.00 39.42 4.83
2063 2301 3.021456 TCGACACCGACGACGAAA 58.979 55.556 9.28 0.00 40.30 3.46
2064 2302 1.369209 TCGACACCGACGACGAAAC 60.369 57.895 9.28 0.00 40.30 2.78
2065 2303 2.690817 CGACACCGACGACGAAACG 61.691 63.158 9.28 4.39 42.66 3.60
2100 2353 2.126031 GTTGTCCTCGGACTCGGC 60.126 66.667 16.41 1.86 44.80 5.54
2101 2354 3.744719 TTGTCCTCGGACTCGGCG 61.745 66.667 16.41 0.00 44.80 6.46
2103 2356 4.176851 GTCCTCGGACTCGGCGTC 62.177 72.222 6.85 0.00 41.57 5.19
2110 2363 3.210528 GACTCGGCGTCGGAGGAT 61.211 66.667 10.62 0.00 36.95 3.24
2167 2420 2.504244 GTCGAGGCGAAGGACACG 60.504 66.667 0.00 0.00 37.72 4.49
2264 2517 4.367023 CGTTCGTCCGGGAAGGCA 62.367 66.667 10.12 0.00 40.77 4.75
2266 2519 2.602267 TTCGTCCGGGAAGGCAGA 60.602 61.111 10.12 0.00 40.77 4.26
2269 2522 3.394836 GTCCGGGAAGGCAGAGCT 61.395 66.667 0.00 0.00 40.77 4.09
2270 2523 3.077556 TCCGGGAAGGCAGAGCTC 61.078 66.667 5.27 5.27 40.77 4.09
2272 2525 3.393970 CGGGAAGGCAGAGCTCCA 61.394 66.667 10.93 0.00 0.00 3.86
2278 2531 3.005539 GGCAGAGCTCCAGGGACA 61.006 66.667 10.93 0.00 0.00 4.02
2338 2978 4.821805 CACGGAATGGCATTTTATCTACCT 59.178 41.667 14.93 0.00 0.00 3.08
2341 2981 5.049405 CGGAATGGCATTTTATCTACCTGAC 60.049 44.000 14.93 0.00 0.00 3.51
2401 3041 1.153628 GCTCTACGTCCATTGCCGT 60.154 57.895 0.00 5.21 40.87 5.68
2416 3057 0.171007 GCCGTGGTGGTTTCATCATG 59.829 55.000 0.00 0.00 39.95 3.07
2453 3113 6.150474 CCAATCATCATAGCAGCATCACATAA 59.850 38.462 0.00 0.00 0.00 1.90
2482 3168 8.689972 AGCTACTGATAATTTGCTTGCTAAATT 58.310 29.630 14.76 14.76 40.00 1.82
2513 3208 1.595109 CAGGTTGTCGCTGCTGACA 60.595 57.895 18.47 18.47 46.63 3.58
2674 3380 1.869754 CGAAGAATCACCGATGGCGAT 60.870 52.381 0.00 0.00 40.82 4.58
2751 7149 1.205893 TGCGCCAAAACCTTCAAAACT 59.794 42.857 4.18 0.00 0.00 2.66
2767 7165 5.360591 TCAAAACTCAGAGAAGTCTTGGAC 58.639 41.667 3.79 0.00 29.91 4.02
2797 7195 1.486310 TCCCAGGAGACCGAAATCATG 59.514 52.381 0.00 0.00 0.00 3.07
2828 7228 4.812476 TGCCGCGAATGGGACTCG 62.812 66.667 8.23 0.00 39.33 4.18
2831 7231 2.417516 CGCGAATGGGACTCGGAT 59.582 61.111 0.00 0.00 36.80 4.18
2853 7253 1.792301 GATGATGATGATGGCGCCG 59.208 57.895 23.90 0.00 0.00 6.46
2860 7260 0.952497 GATGATGGCGCCGATGTCAT 60.952 55.000 26.26 26.26 32.59 3.06
2917 7344 4.352298 GGATTTCTTGGGGTATCATCCTCT 59.648 45.833 0.00 0.00 0.00 3.69
3017 7444 1.806542 CTTGGTGATCTTTGTCCGGTG 59.193 52.381 0.00 0.00 0.00 4.94
3021 7449 0.327924 TGATCTTTGTCCGGTGCCAT 59.672 50.000 0.00 0.00 0.00 4.40
3233 10889 9.717892 GTAAATTTAGACTAGCCTTTACAATGC 57.282 33.333 0.00 0.00 32.21 3.56
3275 11047 9.410556 GAACTCAATGCTTTTTACATGTACATT 57.589 29.630 5.37 8.74 0.00 2.71
3311 11083 9.511144 AAATTACTTTGCACAGTAAGTTTACAC 57.489 29.630 24.96 0.00 42.18 2.90
3326 11098 4.632688 AGTTTACACTGCTACACACGTTTT 59.367 37.500 0.00 0.00 0.00 2.43
3330 11102 3.247648 ACACTGCTACACACGTTTTCATC 59.752 43.478 0.00 0.00 0.00 2.92
3331 11103 3.494626 CACTGCTACACACGTTTTCATCT 59.505 43.478 0.00 0.00 0.00 2.90
3332 11104 3.494626 ACTGCTACACACGTTTTCATCTG 59.505 43.478 0.00 0.00 0.00 2.90
3428 11201 2.258726 AAGCGGCGGACAAAGGAAC 61.259 57.895 9.78 0.00 0.00 3.62
3721 11494 1.611673 CCAAGCCACGGAAGAATGTCT 60.612 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.202927 CCGGGCCATCTTATGTTCCAT 60.203 52.381 4.39 0.00 0.00 3.41
18 19 2.884894 AACGAGATAAACTAGCCGGG 57.115 50.000 2.18 0.00 0.00 5.73
19 20 3.734735 GCTAAACGAGATAAACTAGCCGG 59.265 47.826 0.00 0.00 0.00 6.13
25 26 7.330900 TGTAGCTAGCTAAACGAGATAAACT 57.669 36.000 25.74 0.00 0.00 2.66
51 52 1.886542 ACCTTTTCCTGAAACCGCATC 59.113 47.619 0.00 0.00 0.00 3.91
347 354 9.701098 AAAGGTAAAAATAAACTTCGGGATTTC 57.299 29.630 0.00 0.00 0.00 2.17
407 414 7.533426 TCGGTTCTACTAGTTATCAAGTTGTC 58.467 38.462 0.00 0.00 0.00 3.18
409 416 8.752766 TTTCGGTTCTACTAGTTATCAAGTTG 57.247 34.615 0.00 0.00 0.00 3.16
410 417 9.768662 TTTTTCGGTTCTACTAGTTATCAAGTT 57.231 29.630 0.00 0.00 0.00 2.66
438 445 1.476845 TTACCAGCGTGGAAGCCAGA 61.477 55.000 10.46 0.00 40.96 3.86
439 446 0.392998 ATTACCAGCGTGGAAGCCAG 60.393 55.000 10.46 0.00 40.96 4.85
440 447 0.392461 GATTACCAGCGTGGAAGCCA 60.392 55.000 10.46 0.00 40.96 4.75
441 448 0.107654 AGATTACCAGCGTGGAAGCC 60.108 55.000 10.46 0.00 40.96 4.35
442 449 1.009829 CAGATTACCAGCGTGGAAGC 58.990 55.000 10.46 0.00 40.96 3.86
444 451 0.251916 CCCAGATTACCAGCGTGGAA 59.748 55.000 10.46 0.00 40.96 3.53
445 452 0.907704 ACCCAGATTACCAGCGTGGA 60.908 55.000 10.46 0.00 40.96 4.02
447 454 1.086696 CAACCCAGATTACCAGCGTG 58.913 55.000 0.00 0.00 0.00 5.34
448 455 0.035439 CCAACCCAGATTACCAGCGT 60.035 55.000 0.00 0.00 0.00 5.07
468 478 0.896019 AGAGTGACTCACCGACTGGG 60.896 60.000 15.86 0.00 40.75 4.45
490 500 5.417266 TGCGATTAAATGTTGATTTCTCCCA 59.583 36.000 0.00 0.00 33.63 4.37
493 503 7.243487 TCTGTGCGATTAAATGTTGATTTCTC 58.757 34.615 0.00 0.00 33.63 2.87
494 504 7.144722 TCTGTGCGATTAAATGTTGATTTCT 57.855 32.000 0.00 0.00 33.63 2.52
496 506 5.801947 GCTCTGTGCGATTAAATGTTGATTT 59.198 36.000 0.00 0.00 35.83 2.17
497 507 5.335127 GCTCTGTGCGATTAAATGTTGATT 58.665 37.500 0.00 0.00 0.00 2.57
516 526 2.766263 TCAAGGTCATATTGGTCGCTCT 59.234 45.455 0.00 0.00 0.00 4.09
574 584 1.601903 TGTTCTGTGCGACCAAATGTC 59.398 47.619 0.00 0.00 40.81 3.06
575 585 1.674359 TGTTCTGTGCGACCAAATGT 58.326 45.000 0.00 0.00 0.00 2.71
580 590 1.454201 TTTGTTGTTCTGTGCGACCA 58.546 45.000 0.00 0.00 0.00 4.02
581 591 2.774439 ATTTGTTGTTCTGTGCGACC 57.226 45.000 0.00 0.00 0.00 4.79
582 592 3.496884 TCCTATTTGTTGTTCTGTGCGAC 59.503 43.478 0.00 0.00 0.00 5.19
583 593 3.496884 GTCCTATTTGTTGTTCTGTGCGA 59.503 43.478 0.00 0.00 0.00 5.10
584 594 3.249799 TGTCCTATTTGTTGTTCTGTGCG 59.750 43.478 0.00 0.00 0.00 5.34
585 595 4.829064 TGTCCTATTTGTTGTTCTGTGC 57.171 40.909 0.00 0.00 0.00 4.57
592 602 9.784531 CTATTCTATGGATGTCCTATTTGTTGT 57.215 33.333 0.09 0.00 36.82 3.32
597 607 8.742125 TCCACTATTCTATGGATGTCCTATTT 57.258 34.615 0.09 0.00 40.17 1.40
618 628 9.522804 CTCTATACAATAAGTGAGTCTTTCCAC 57.477 37.037 0.00 0.00 37.56 4.02
619 629 9.256228 ACTCTATACAATAAGTGAGTCTTTCCA 57.744 33.333 0.00 0.00 37.56 3.53
649 659 4.096732 ACCGACAATAAATGAGCTTTGC 57.903 40.909 0.00 0.00 0.00 3.68
655 665 7.302350 TCATTGTGTACCGACAATAAATGAG 57.698 36.000 10.32 0.37 43.29 2.90
686 696 9.737427 TTAAAAGAATCTTCAACGTGCATTTTA 57.263 25.926 0.00 0.00 0.00 1.52
713 723 9.182933 GCACATTAAAAATGTTCATTTTGCATT 57.817 25.926 19.62 9.89 34.34 3.56
1307 1403 5.047519 GCTCGGCAGTAAACCCTCTATTATA 60.048 44.000 0.00 0.00 0.00 0.98
1309 1405 3.069158 GCTCGGCAGTAAACCCTCTATTA 59.931 47.826 0.00 0.00 0.00 0.98
1310 1406 2.158943 GCTCGGCAGTAAACCCTCTATT 60.159 50.000 0.00 0.00 0.00 1.73
1335 1556 7.002276 GCCCAACCCAACATATAAGTATAACT 58.998 38.462 0.00 0.00 0.00 2.24
1336 1557 7.002276 AGCCCAACCCAACATATAAGTATAAC 58.998 38.462 0.00 0.00 0.00 1.89
1338 1559 6.773583 AGCCCAACCCAACATATAAGTATA 57.226 37.500 0.00 0.00 0.00 1.47
1339 1560 5.663158 AGCCCAACCCAACATATAAGTAT 57.337 39.130 0.00 0.00 0.00 2.12
1629 1866 1.407299 CCTCGGCCATGTTGATGAAGA 60.407 52.381 2.24 0.00 0.00 2.87
1699 1936 2.404995 ATCGACGAGACGGGTGTCC 61.405 63.158 3.01 0.00 46.74 4.02
1713 1950 2.758327 ACCTGGTAGGCGCATCGA 60.758 61.111 10.83 0.00 39.63 3.59
1738 1975 4.003788 CGGTGGTCCACGAAGGCT 62.004 66.667 15.93 0.00 37.29 4.58
1756 1993 2.656069 GCACAGGAGGAGCCCGTTA 61.656 63.158 0.00 0.00 37.37 3.18
2033 2271 4.593864 GTCGATCTGAGGCGGCCC 62.594 72.222 17.02 8.02 0.00 5.80
2034 2272 3.838271 TGTCGATCTGAGGCGGCC 61.838 66.667 12.11 12.11 0.00 6.13
2055 2293 0.164647 CTCGTAGTCCGTTTCGTCGT 59.835 55.000 0.00 0.00 37.94 4.34
2056 2294 0.519999 CCTCGTAGTCCGTTTCGTCG 60.520 60.000 0.00 0.00 37.94 5.12
2057 2295 0.798776 TCCTCGTAGTCCGTTTCGTC 59.201 55.000 0.00 0.00 37.94 4.20
2058 2296 0.801251 CTCCTCGTAGTCCGTTTCGT 59.199 55.000 0.00 0.00 37.94 3.85
2059 2297 0.098376 CCTCCTCGTAGTCCGTTTCG 59.902 60.000 0.00 0.00 37.94 3.46
2060 2298 1.132073 GTCCTCCTCGTAGTCCGTTTC 59.868 57.143 0.00 0.00 37.94 2.78
2061 2299 1.172175 GTCCTCCTCGTAGTCCGTTT 58.828 55.000 0.00 0.00 37.94 3.60
2062 2300 0.327591 AGTCCTCCTCGTAGTCCGTT 59.672 55.000 0.00 0.00 37.94 4.44
2063 2301 0.392729 CAGTCCTCCTCGTAGTCCGT 60.393 60.000 0.00 0.00 37.94 4.69
2064 2302 1.096386 CCAGTCCTCCTCGTAGTCCG 61.096 65.000 0.00 0.00 38.13 4.79
2065 2303 0.034283 ACCAGTCCTCCTCGTAGTCC 60.034 60.000 0.00 0.00 0.00 3.85
2066 2304 1.473278 CAACCAGTCCTCCTCGTAGTC 59.527 57.143 0.00 0.00 0.00 2.59
2067 2305 1.203025 ACAACCAGTCCTCCTCGTAGT 60.203 52.381 0.00 0.00 0.00 2.73
2068 2306 1.473278 GACAACCAGTCCTCCTCGTAG 59.527 57.143 0.00 0.00 41.56 3.51
2069 2307 1.542492 GACAACCAGTCCTCCTCGTA 58.458 55.000 0.00 0.00 41.56 3.43
2104 2357 1.521681 CTTCCGCGGTTCATCCTCC 60.522 63.158 27.15 0.00 0.00 4.30
2105 2358 2.174319 GCTTCCGCGGTTCATCCTC 61.174 63.158 27.15 3.20 0.00 3.71
2167 2420 0.752658 GCCATTCCATAAGCCCCAAC 59.247 55.000 0.00 0.00 0.00 3.77
2264 2517 1.611851 CCACTGTCCCTGGAGCTCT 60.612 63.158 14.64 0.00 0.00 4.09
2266 2519 3.325753 GCCACTGTCCCTGGAGCT 61.326 66.667 0.00 0.00 0.00 4.09
2269 2522 4.631740 TCGGCCACTGTCCCTGGA 62.632 66.667 2.24 0.00 0.00 3.86
2270 2523 4.394712 GTCGGCCACTGTCCCTGG 62.395 72.222 2.24 0.00 0.00 4.45
2272 2525 2.607750 ATGTCGGCCACTGTCCCT 60.608 61.111 2.24 0.00 0.00 4.20
2278 2531 2.347490 GACCACATGTCGGCCACT 59.653 61.111 2.24 0.00 33.49 4.00
2325 2965 3.809832 CCCGCAGTCAGGTAGATAAAATG 59.190 47.826 0.00 0.00 0.00 2.32
2401 3041 3.329225 TGTACCTCATGATGAAACCACCA 59.671 43.478 4.88 0.00 0.00 4.17
2416 3057 6.148480 GCTATGATGATTGGTTCATGTACCTC 59.852 42.308 20.70 12.23 45.29 3.85
2453 3113 6.352516 AGCAAGCAAATTATCAGTAGCTAGT 58.647 36.000 0.00 0.00 0.00 2.57
2482 3168 4.559502 GCGACAACCTGCAGAGATATGATA 60.560 45.833 17.39 0.00 0.00 2.15
2488 3174 0.390866 CAGCGACAACCTGCAGAGAT 60.391 55.000 17.39 0.00 0.00 2.75
2513 3208 5.476945 GGTTTTGATCACCACATACTTTCCT 59.523 40.000 0.00 0.00 34.04 3.36
2674 3380 3.716195 CCATCTCCCACACCGGCA 61.716 66.667 0.00 0.00 0.00 5.69
2736 7134 6.856895 ACTTCTCTGAGTTTTGAAGGTTTTG 58.143 36.000 4.32 0.00 39.90 2.44
2751 7149 2.251818 CAGGGTCCAAGACTTCTCTGA 58.748 52.381 0.00 0.00 32.47 3.27
2828 7228 3.308053 CGCCATCATCATCATCGTTATCC 59.692 47.826 0.00 0.00 0.00 2.59
2831 7231 2.068519 GCGCCATCATCATCATCGTTA 58.931 47.619 0.00 0.00 0.00 3.18
2837 7237 0.952010 CATCGGCGCCATCATCATCA 60.952 55.000 28.98 0.00 0.00 3.07
2853 7253 4.367450 CCTTCTTCTTCTCCGATGACATC 58.633 47.826 5.28 5.28 0.00 3.06
2860 7260 1.605058 CCCGCCTTCTTCTTCTCCGA 61.605 60.000 0.00 0.00 0.00 4.55
2863 7263 1.549170 TGTACCCGCCTTCTTCTTCTC 59.451 52.381 0.00 0.00 0.00 2.87
2917 7344 3.221771 CCCAACAACACAATCTCCTTGA 58.778 45.455 0.00 0.00 38.29 3.02
3017 7444 2.097825 GGATAATGCTCATCCCATGGC 58.902 52.381 6.09 0.00 36.69 4.40
3084 7512 4.597004 ACACCATTCTCATCAGAAAGCAT 58.403 39.130 0.00 0.00 42.14 3.79
3204 10838 8.488651 TGTAAAGGCTAGTCTAAATTTACAGC 57.511 34.615 13.01 1.57 37.88 4.40
3233 10889 2.749621 GAGTTCCACCTGGCAATTACAG 59.250 50.000 0.00 3.05 35.74 2.74
3275 11047 4.507388 GTGCAAAGTAATTTCAGCAAGCAA 59.493 37.500 2.70 0.00 33.35 3.91
3311 11083 3.120546 CCAGATGAAAACGTGTGTAGCAG 60.121 47.826 0.00 0.00 0.00 4.24
3417 11190 3.371285 GCGAGAGTAATGTTCCTTTGTCC 59.629 47.826 0.00 0.00 0.00 4.02
3428 11201 2.469826 TGTAATGCCGCGAGAGTAATG 58.530 47.619 8.23 0.00 0.00 1.90
3721 11494 2.808523 TCACATTGCGCATTTGGAAA 57.191 40.000 12.75 0.00 0.00 3.13
3972 11749 9.670442 AGTTCACTAAGGATGGGATTTATACTA 57.330 33.333 0.00 0.00 0.00 1.82
3975 11752 8.437575 GGAAGTTCACTAAGGATGGGATTTATA 58.562 37.037 5.01 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.