Multiple sequence alignment - TraesCS3D01G244400

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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 TraesCS3D01G244400 chr3D 100.000 2914 0 0 1 2914 339816303 339819216 0.000000e+00 5382.0
1 TraesCS3D01G244400 chr3D 87.755 245 27 3 2609 2852 390951112 390951354 1.710000e-72 283.0
2 TraesCS3D01G244400 chr5D 91.158 2409 162 21 1 2379 538686253 538688640 0.000000e+00 3221.0
3 TraesCS3D01G244400 chr5D 89.644 956 84 8 1 953 420018440 420019383 0.000000e+00 1203.0
4 TraesCS3D01G244400 chr5D 86.936 421 31 12 1983 2381 375283729 375283311 4.430000e-123 451.0
5 TraesCS3D01G244400 chr2B 89.053 2430 212 21 1 2383 54563652 54561230 0.000000e+00 2964.0
6 TraesCS3D01G244400 chr2B 90.244 164 13 3 777 940 358758147 358758307 8.180000e-51 211.0
7 TraesCS3D01G244400 chr2B 91.837 98 7 1 856 953 358758065 358758161 5.070000e-28 135.0
8 TraesCS3D01G244400 chr2B 88.182 110 11 2 774 883 54562785 54562678 2.360000e-26 130.0
9 TraesCS3D01G244400 chr2B 92.500 80 6 0 775 854 358758225 358758304 6.600000e-22 115.0
10 TraesCS3D01G244400 chr4B 86.702 2444 227 57 1 2379 535285396 535287806 0.000000e+00 2623.0
11 TraesCS3D01G244400 chr4B 89.446 957 88 9 1 953 449517851 449518798 0.000000e+00 1195.0
12 TraesCS3D01G244400 chr4B 90.188 744 54 8 1653 2385 413506962 413506227 0.000000e+00 952.0
13 TraesCS3D01G244400 chr4A 88.683 1617 147 19 774 2377 629935544 629937137 0.000000e+00 1940.0
14 TraesCS3D01G244400 chr4A 86.142 1638 173 31 775 2379 117699743 117701359 0.000000e+00 1718.0
15 TraesCS3D01G244400 chr4D 85.692 1887 183 32 546 2379 348041508 348039656 0.000000e+00 1908.0
16 TraesCS3D01G244400 chr4D 89.941 1352 105 20 1043 2382 145379899 145378567 0.000000e+00 1714.0
17 TraesCS3D01G244400 chr1D 92.199 1269 76 7 1 1248 80673792 80675058 0.000000e+00 1773.0
18 TraesCS3D01G244400 chr1D 89.547 1148 90 12 1239 2376 80683840 80684967 0.000000e+00 1428.0
19 TraesCS3D01G244400 chr6A 86.090 1675 151 43 775 2382 571574684 571576343 0.000000e+00 1727.0
20 TraesCS3D01G244400 chr7A 88.450 1368 114 22 1048 2378 297775890 297774530 0.000000e+00 1611.0
21 TraesCS3D01G244400 chr7A 92.505 974 49 15 1 953 62735309 62736279 0.000000e+00 1373.0
22 TraesCS3D01G244400 chr7A 85.440 728 71 13 1684 2380 302661473 302662196 0.000000e+00 725.0
23 TraesCS3D01G244400 chr7A 83.371 439 32 17 1985 2390 211154131 211154561 4.590000e-98 368.0
24 TraesCS3D01G244400 chr3B 85.675 1445 157 25 955 2381 592330391 592328979 0.000000e+00 1476.0
25 TraesCS3D01G244400 chr3B 86.176 774 68 17 1640 2378 576053728 576052959 0.000000e+00 800.0
26 TraesCS3D01G244400 chr3B 100.000 39 0 0 1 39 604141053 604141015 4.030000e-09 73.1
27 TraesCS3D01G244400 chr1A 90.219 1094 99 7 931 2022 80283718 80282631 0.000000e+00 1421.0
28 TraesCS3D01G244400 chr1A 91.604 929 55 12 44 952 80284658 80283733 0.000000e+00 1262.0
29 TraesCS3D01G244400 chr1A 85.399 363 28 12 2028 2381 80282655 80282309 1.280000e-93 353.0
30 TraesCS3D01G244400 chr5A 92.490 972 51 9 1 953 78448533 78449501 0.000000e+00 1371.0
31 TraesCS3D01G244400 chr5A 85.563 471 48 6 1921 2378 78449838 78450301 2.630000e-130 475.0
32 TraesCS3D01G244400 chr2D 92.379 538 39 2 2378 2914 273950534 273949998 0.000000e+00 765.0
33 TraesCS3D01G244400 chr7B 92.880 309 20 2 2608 2914 397442299 397441991 5.730000e-122 448.0
34 TraesCS3D01G244400 chr1B 86.256 422 31 14 1983 2381 313099006 313099423 1.600000e-117 433.0
35 TraesCS3D01G244400 chr1B 90.625 288 24 3 2629 2914 319975421 319975707 2.120000e-101 379.0
36 TraesCS3D01G244400 chr1B 88.065 310 26 5 2608 2914 319918059 319918360 9.930000e-95 357.0
37 TraesCS3D01G244400 chr1B 86.822 258 22 4 2128 2375 419975156 419975411 7.950000e-71 278.0
38 TraesCS3D01G244400 chr7D 86.909 275 23 4 2112 2377 78508525 78508795 2.200000e-76 296.0


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 TraesCS3D01G244400 chr3D 339816303 339819216 2913 False 5382 5382 100.0000 1 2914 1 chr3D.!!$F1 2913
1 TraesCS3D01G244400 chr5D 538686253 538688640 2387 False 3221 3221 91.1580 1 2379 1 chr5D.!!$F2 2378
2 TraesCS3D01G244400 chr5D 420018440 420019383 943 False 1203 1203 89.6440 1 953 1 chr5D.!!$F1 952
3 TraesCS3D01G244400 chr2B 54561230 54563652 2422 True 1547 2964 88.6175 1 2383 2 chr2B.!!$R1 2382
4 TraesCS3D01G244400 chr4B 535285396 535287806 2410 False 2623 2623 86.7020 1 2379 1 chr4B.!!$F2 2378
5 TraesCS3D01G244400 chr4B 449517851 449518798 947 False 1195 1195 89.4460 1 953 1 chr4B.!!$F1 952
6 TraesCS3D01G244400 chr4B 413506227 413506962 735 True 952 952 90.1880 1653 2385 1 chr4B.!!$R1 732
7 TraesCS3D01G244400 chr4A 629935544 629937137 1593 False 1940 1940 88.6830 774 2377 1 chr4A.!!$F2 1603
8 TraesCS3D01G244400 chr4A 117699743 117701359 1616 False 1718 1718 86.1420 775 2379 1 chr4A.!!$F1 1604
9 TraesCS3D01G244400 chr4D 348039656 348041508 1852 True 1908 1908 85.6920 546 2379 1 chr4D.!!$R2 1833
10 TraesCS3D01G244400 chr4D 145378567 145379899 1332 True 1714 1714 89.9410 1043 2382 1 chr4D.!!$R1 1339
11 TraesCS3D01G244400 chr1D 80673792 80675058 1266 False 1773 1773 92.1990 1 1248 1 chr1D.!!$F1 1247
12 TraesCS3D01G244400 chr1D 80683840 80684967 1127 False 1428 1428 89.5470 1239 2376 1 chr1D.!!$F2 1137
13 TraesCS3D01G244400 chr6A 571574684 571576343 1659 False 1727 1727 86.0900 775 2382 1 chr6A.!!$F1 1607
14 TraesCS3D01G244400 chr7A 297774530 297775890 1360 True 1611 1611 88.4500 1048 2378 1 chr7A.!!$R1 1330
15 TraesCS3D01G244400 chr7A 62735309 62736279 970 False 1373 1373 92.5050 1 953 1 chr7A.!!$F1 952
16 TraesCS3D01G244400 chr7A 302661473 302662196 723 False 725 725 85.4400 1684 2380 1 chr7A.!!$F3 696
17 TraesCS3D01G244400 chr3B 592328979 592330391 1412 True 1476 1476 85.6750 955 2381 1 chr3B.!!$R2 1426
18 TraesCS3D01G244400 chr3B 576052959 576053728 769 True 800 800 86.1760 1640 2378 1 chr3B.!!$R1 738
19 TraesCS3D01G244400 chr1A 80282309 80284658 2349 True 1012 1421 89.0740 44 2381 3 chr1A.!!$R1 2337
20 TraesCS3D01G244400 chr5A 78448533 78450301 1768 False 923 1371 89.0265 1 2378 2 chr5A.!!$F1 2377
21 TraesCS3D01G244400 chr2D 273949998 273950534 536 True 765 765 92.3790 2378 2914 1 chr2D.!!$R1 536

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
346 350 0.886490 GATGCCGGTTATGGAGCCAG 60.886 60.0 1.90 0.00 0.00 4.85 F
683 688 1.059913 AAGCAAGTGACACTAGGGCT 58.940 50.0 18.41 18.41 33.54 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1646 0.395036 TTGGCCCCGATTGTACCATG 60.395 55.0 0.0 0.0 0.00 3.66 R
2472 2713 0.108615 CAGGTGAACCGAGTAGCCAG 60.109 60.0 0.0 0.0 42.08 4.85 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
126 127 3.462021 GCAGCGGTAGATTTTGATCTCT 58.538 45.455 0.00 0.00 32.36 3.10
128 129 4.437239 CAGCGGTAGATTTTGATCTCTGT 58.563 43.478 0.00 0.00 32.36 3.41
148 149 2.535012 TTCACGTATGTGTTGGCTGA 57.465 45.000 14.63 0.00 46.49 4.26
250 252 8.916062 AGGTAAGGAGTTAGCTTAGATAGAAAC 58.084 37.037 0.00 0.00 43.08 2.78
273 276 5.590259 ACTGTCCATATGTTATTGCCTCAAC 59.410 40.000 1.24 0.00 0.00 3.18
346 350 0.886490 GATGCCGGTTATGGAGCCAG 60.886 60.000 1.90 0.00 0.00 4.85
349 353 2.589540 CGGTTATGGAGCCAGGCA 59.410 61.111 15.80 0.00 0.00 4.75
452 456 2.743636 TCAACCTTAGGCACTCTTCG 57.256 50.000 0.00 0.00 41.75 3.79
457 461 1.476891 CCTTAGGCACTCTTCGCTACA 59.523 52.381 0.00 0.00 41.75 2.74
492 496 2.646798 AGGGCTTTTGGATCTCTCAAGT 59.353 45.455 0.00 0.00 0.00 3.16
517 521 7.116233 GTGGCGTTTCAAAATTTTAGATGATGT 59.884 33.333 2.44 0.00 0.00 3.06
518 522 7.116090 TGGCGTTTCAAAATTTTAGATGATGTG 59.884 33.333 2.44 0.00 0.00 3.21
548 552 6.583912 TTCTTTACTTTCTCGACACAAGTG 57.416 37.500 8.68 0.00 32.88 3.16
567 571 6.072508 ACAAGTGGACATTGTTATAGCTTGTG 60.073 38.462 17.15 2.84 41.29 3.33
611 615 7.646314 CACTATCACAAGGGATTGATGAATTC 58.354 38.462 0.00 0.00 34.28 2.17
683 688 1.059913 AAGCAAGTGACACTAGGGCT 58.940 50.000 18.41 18.41 33.54 5.19
739 744 4.537135 TGTGGGAAGATAGACAACTCAC 57.463 45.455 0.00 0.00 0.00 3.51
788 904 8.296000 CACACTCCATGTATTTGAACAATGTAA 58.704 33.333 0.00 0.00 40.64 2.41
808 924 8.692110 ATGTAATTGTGATGTTTATGCAACTG 57.308 30.769 0.00 0.00 36.21 3.16
850 967 6.422333 TGGCTGGACAGATTGTATCATTTAA 58.578 36.000 3.00 0.00 0.00 1.52
879 996 8.028354 TCATTTGAACCATGTAATTGTGATGTC 58.972 33.333 0.00 0.00 0.00 3.06
917 1034 6.602410 TGAATTTATTTGATGGCTGGACAA 57.398 33.333 0.00 0.00 0.00 3.18
1065 1213 5.161135 AGATCTGGGATCATTGTATGGACT 58.839 41.667 9.71 0.00 0.00 3.85
1107 1257 2.419990 GCTTGGTTTTTGGCTGGTCTTT 60.420 45.455 0.00 0.00 0.00 2.52
1112 1262 1.933247 TTTTGGCTGGTCTTTTTGCG 58.067 45.000 0.00 0.00 0.00 4.85
1113 1263 1.107114 TTTGGCTGGTCTTTTTGCGA 58.893 45.000 0.00 0.00 0.00 5.10
1140 1290 1.192793 GAGAACTTCGAGCGGATTCG 58.807 55.000 0.00 0.00 41.79 3.34
1162 1312 4.147321 GGGGATGTGCATCATAGACAATT 58.853 43.478 13.37 0.00 39.54 2.32
1169 1319 3.444388 TGCATCATAGACAATTTGCTGCA 59.556 39.130 0.00 0.00 39.40 4.41
1257 1407 1.186200 GAAGATTTGGGGAAGGGTGC 58.814 55.000 0.00 0.00 0.00 5.01
1370 1527 1.144708 TGCTTCTCACCCCACAAATCA 59.855 47.619 0.00 0.00 0.00 2.57
1379 1537 3.765511 CACCCCACAAATCAGATGTCATT 59.234 43.478 0.00 0.00 0.00 2.57
1390 1548 9.146984 CAAATCAGATGTCATTTTATGTTTGCT 57.853 29.630 0.00 0.00 0.00 3.91
1415 1573 8.999220 TTTATGCTAATCATTTTGCACAATGA 57.001 26.923 25.92 25.92 44.33 2.57
1416 1574 8.999220 TTATGCTAATCATTTTGCACAATGAA 57.001 26.923 27.07 14.05 44.48 2.57
1488 1646 1.405872 TCATGCCATGGCTTCCATTC 58.594 50.000 35.53 6.53 42.23 2.67
1562 1720 9.748708 CTTCTTTCTATTGATCTCGAAGAAGAT 57.251 33.333 16.68 0.00 34.09 2.40
1577 1735 5.163509 CGAAGAAGATGAGAATGGTGAGGTA 60.164 44.000 0.00 0.00 0.00 3.08
1628 1786 2.209315 CCCCAAAGCACCACCCAAG 61.209 63.158 0.00 0.00 0.00 3.61
1746 1907 3.259123 CGGAGATGATGATGACATACCCA 59.741 47.826 0.00 0.00 36.82 4.51
1758 1919 3.075283 TGACATACCCAATGACCTTTGGT 59.925 43.478 11.98 3.63 43.92 3.67
1839 2004 1.809133 TGTGGACAACCCCAAGACTA 58.191 50.000 0.00 0.00 38.06 2.59
1868 2033 4.298332 CCTTCATGAAACTTTCCCAAACG 58.702 43.478 9.88 0.00 0.00 3.60
1937 2102 7.054124 AGATTCGATATGGTTGTATGGTTGTT 58.946 34.615 0.00 0.00 0.00 2.83
1938 2103 8.208224 AGATTCGATATGGTTGTATGGTTGTTA 58.792 33.333 0.00 0.00 0.00 2.41
1969 2135 5.693104 GTGAACTTGACACGTATGGTTCTAA 59.307 40.000 14.95 0.89 35.52 2.10
1997 2164 4.335400 TTGGTTGCTTTTGGAGATTTCC 57.665 40.909 0.00 0.00 44.31 3.13
2036 2205 3.563808 GTGTGGCTGTCAAGTATGTGAAA 59.436 43.478 0.00 0.00 0.00 2.69
2046 2215 6.072563 TGTCAAGTATGTGAAATGGACATGTG 60.073 38.462 1.15 0.00 35.62 3.21
2058 2230 2.305635 TGGACATGTGTGGCTCTATTGT 59.694 45.455 1.15 0.00 32.35 2.71
2078 2251 5.606348 TGTACTTTGGTTGCTTTTGGAAT 57.394 34.783 0.00 0.00 31.02 3.01
2081 2283 6.536941 TGTACTTTGGTTGCTTTTGGAATTTC 59.463 34.615 0.00 0.00 31.02 2.17
2082 2284 5.495640 ACTTTGGTTGCTTTTGGAATTTCA 58.504 33.333 0.00 0.00 31.02 2.69
2083 2285 6.121590 ACTTTGGTTGCTTTTGGAATTTCAT 58.878 32.000 0.00 0.00 31.02 2.57
2258 2498 0.820871 TGCTTCCAACCAAACACCAC 59.179 50.000 0.00 0.00 0.00 4.16
2286 2527 2.707257 ACCAACCCGTTCCTCTCTTTTA 59.293 45.455 0.00 0.00 0.00 1.52
2327 2568 0.902531 GAACGGACCCATTCCTCTGA 59.097 55.000 0.00 0.00 43.25 3.27
2404 2645 3.476552 CAACAGAGTAGAAGGGCAAACA 58.523 45.455 0.00 0.00 0.00 2.83
2405 2646 4.074970 CAACAGAGTAGAAGGGCAAACAT 58.925 43.478 0.00 0.00 0.00 2.71
2408 2649 1.398390 GAGTAGAAGGGCAAACATGCG 59.602 52.381 0.00 0.00 35.24 4.73
2472 2713 2.113986 ACACAGGTTGCTGGCTCC 59.886 61.111 0.00 0.00 0.00 4.70
2473 2714 2.433446 CACAGGTTGCTGGCTCCT 59.567 61.111 0.00 4.69 0.00 3.69
2476 2717 4.357279 AGGTTGCTGGCTCCTGGC 62.357 66.667 8.45 0.00 40.90 4.85
2491 2732 0.108615 CTGGCTACTCGGTTCACCTG 60.109 60.000 0.00 0.00 0.00 4.00
2494 2735 1.972198 CTACTCGGTTCACCTGGCA 59.028 57.895 0.00 0.00 0.00 4.92
2495 2736 0.108615 CTACTCGGTTCACCTGGCAG 60.109 60.000 7.75 7.75 0.00 4.85
2562 2803 3.338249 CAGCGCTTATTATAGCCACCAT 58.662 45.455 7.50 0.00 37.90 3.55
2563 2804 3.125829 CAGCGCTTATTATAGCCACCATG 59.874 47.826 7.50 0.00 37.90 3.66
2565 2806 3.120199 GCGCTTATTATAGCCACCATGTG 60.120 47.826 0.00 0.00 37.90 3.21
2567 2808 5.234752 CGCTTATTATAGCCACCATGTGTA 58.765 41.667 0.00 0.00 37.90 2.90
2600 2841 1.142748 GTCTCCAGTGGATCCAGCG 59.857 63.158 16.81 9.15 0.00 5.18
2617 2858 2.493278 CAGCGGAAATCCAAGGAAATGT 59.507 45.455 0.00 0.00 35.14 2.71
2624 2865 6.159293 GGAAATCCAAGGAAATGTTGAAGAC 58.841 40.000 0.00 0.00 35.64 3.01
2626 2867 5.712152 ATCCAAGGAAATGTTGAAGACAC 57.288 39.130 0.00 0.00 42.04 3.67
2698 2939 8.752005 TCAATTCCCTACATAATGAAAAGGAG 57.248 34.615 0.00 0.00 0.00 3.69
2703 2944 8.101309 TCCCTACATAATGAAAAGGAGATCAA 57.899 34.615 0.00 0.00 0.00 2.57
2750 2991 8.359875 AGTGTAGATCCTACAGATAATCCATG 57.640 38.462 7.03 0.00 34.42 3.66
2763 3004 7.940688 ACAGATAATCCATGCATGAACAAGATA 59.059 33.333 28.31 10.69 0.00 1.98
2771 3012 8.377799 TCCATGCATGAACAAGATAGTACATAT 58.622 33.333 28.31 0.00 0.00 1.78
2811 3052 6.450845 TTGAAATTACAAGCGCAAAATCAG 57.549 33.333 11.47 0.00 0.00 2.90
2831 3072 8.532977 AATCAGCGCTAAAATGTAAACAAAAT 57.467 26.923 10.99 0.00 0.00 1.82
2832 3073 9.632807 AATCAGCGCTAAAATGTAAACAAAATA 57.367 25.926 10.99 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 2.289274 CAGCCAACACATACGTGAAACA 59.711 45.455 0.00 0.00 46.80 2.83
128 129 2.839975 TCAGCCAACACATACGTGAAA 58.160 42.857 0.00 0.00 46.80 2.69
148 149 0.251341 GTGTGCTGACCCTTCCCAAT 60.251 55.000 0.00 0.00 0.00 3.16
173 174 1.076332 ACGCATCAGCTAAAACGGTC 58.924 50.000 0.00 0.00 39.10 4.79
231 232 7.773149 TGGACAGTTTCTATCTAAGCTAACTC 58.227 38.462 0.00 0.00 31.43 3.01
236 237 8.256356 ACATATGGACAGTTTCTATCTAAGCT 57.744 34.615 7.80 0.00 0.00 3.74
250 252 5.589855 TGTTGAGGCAATAACATATGGACAG 59.410 40.000 7.80 0.00 32.30 3.51
290 294 8.716646 ACTTTCCTAAAAAGGTGAAACAAATG 57.283 30.769 2.91 0.00 39.98 2.32
346 350 1.673337 GGTGGTAAGAACCCGTGCC 60.673 63.158 0.00 0.00 46.16 5.01
349 353 2.807837 CGAAAAGGTGGTAAGAACCCGT 60.808 50.000 0.00 0.00 46.16 5.28
452 456 1.671845 CTCTCTACCGTCACCTGTAGC 59.328 57.143 0.00 0.00 35.50 3.58
457 461 1.380112 GCCCTCTCTACCGTCACCT 60.380 63.158 0.00 0.00 0.00 4.00
492 496 7.116090 CACATCATCTAAAATTTTGAAACGCCA 59.884 33.333 13.76 0.00 0.00 5.69
517 521 6.764085 TGTCGAGAAAGTAAAGAATGGTTTCA 59.236 34.615 0.00 0.00 34.08 2.69
518 522 7.070183 GTGTCGAGAAAGTAAAGAATGGTTTC 58.930 38.462 0.00 0.00 0.00 2.78
548 552 4.700213 ACACCACAAGCTATAACAATGTCC 59.300 41.667 0.00 0.00 0.00 4.02
611 615 4.393062 GTCCATGTCACTTCTGGTGTAATG 59.607 45.833 0.00 0.00 45.50 1.90
683 688 1.004628 TGTAGCCTACGGTCTACCACA 59.995 52.381 0.00 0.00 34.12 4.17
739 744 4.623167 GCCACACTCATAGATTAGCATACG 59.377 45.833 0.00 0.00 0.00 3.06
808 924 6.539464 TCCAGCCATCAAATAAATTCAAATGC 59.461 34.615 0.00 0.00 0.00 3.56
854 971 8.030692 AGACATCACAATTACATGGTTCAAATG 58.969 33.333 0.00 0.00 0.00 2.32
1045 1193 7.392766 AATTAGTCCATACAATGATCCCAGA 57.607 36.000 0.00 0.00 0.00 3.86
1065 1213 6.357579 AGCATGGTTTTTGTCATGGAATTA 57.642 33.333 0.00 0.00 40.59 1.40
1107 1257 3.140325 AGTTCTCTTCCCATTCGCAAA 57.860 42.857 0.00 0.00 0.00 3.68
1112 1262 2.933260 GCTCGAAGTTCTCTTCCCATTC 59.067 50.000 0.56 0.00 45.02 2.67
1113 1263 2.675317 CGCTCGAAGTTCTCTTCCCATT 60.675 50.000 0.56 0.00 45.02 3.16
1130 1280 1.595382 CACATCCCCGAATCCGCTC 60.595 63.158 0.00 0.00 0.00 5.03
1133 1283 1.227943 ATGCACATCCCCGAATCCG 60.228 57.895 0.00 0.00 0.00 4.18
1140 1290 2.936919 TGTCTATGATGCACATCCCC 57.063 50.000 8.11 0.00 40.07 4.81
1162 1312 1.533756 GCTCGTTCAAAACTGCAGCAA 60.534 47.619 15.27 0.00 0.00 3.91
1169 1319 4.044426 GCTTGAATTGCTCGTTCAAAACT 58.956 39.130 11.08 0.00 42.91 2.66
1257 1407 8.302438 AGCTCCACTTAAATTCTTCAAATTGAG 58.698 33.333 0.00 0.00 0.00 3.02
1370 1527 9.090692 GCATAAAGCAAACATAAAATGACATCT 57.909 29.630 0.00 0.00 44.79 2.90
1390 1548 8.999220 TCATTGTGCAAAATGATTAGCATAAA 57.001 26.923 25.40 2.55 40.72 1.40
1415 1573 3.788227 TCAGCTTTGTGGGTCTACATT 57.212 42.857 0.00 0.00 0.00 2.71
1416 1574 3.614092 CATCAGCTTTGTGGGTCTACAT 58.386 45.455 0.00 0.00 0.00 2.29
1488 1646 0.395036 TTGGCCCCGATTGTACCATG 60.395 55.000 0.00 0.00 0.00 3.66
1493 1651 2.685534 CCCCTTGGCCCCGATTGTA 61.686 63.158 0.00 0.00 0.00 2.41
1530 1688 9.689976 TTCGAGATCAATAGAAAGAAGATCATC 57.310 33.333 0.00 0.00 38.00 2.92
1562 1720 3.070446 ACGTGTTTACCTCACCATTCTCA 59.930 43.478 0.00 0.00 32.86 3.27
1577 1735 3.157932 CCAACATTTGGTGACGTGTTT 57.842 42.857 0.00 0.00 45.93 2.83
1628 1786 2.514803 TGCTTTACCTTGGCCTTCTTC 58.485 47.619 3.32 0.00 0.00 2.87
1746 1907 5.487488 TGGAGACTACATACCAAAGGTCATT 59.513 40.000 0.00 0.00 37.09 2.57
1758 1919 7.559335 AATCTGGCAATATGGAGACTACATA 57.441 36.000 9.89 9.89 35.48 2.29
1839 2004 4.279420 GGAAAGTTTCATGAAGGCTCTTGT 59.721 41.667 17.16 4.52 0.00 3.16
1868 2033 3.279434 ACTCACCCAAACAGACTTGTTC 58.721 45.455 0.00 0.00 46.54 3.18
1913 2078 6.861065 ACAACCATACAACCATATCGAATC 57.139 37.500 0.00 0.00 0.00 2.52
1937 2102 7.329962 CCATACGTGTCAAGTTCACATACTTTA 59.670 37.037 0.00 0.00 36.24 1.85
1938 2103 6.147164 CCATACGTGTCAAGTTCACATACTTT 59.853 38.462 0.00 0.00 36.24 2.66
1969 2135 2.170187 TCCAAAAGCAACCAAAGTGCAT 59.830 40.909 0.00 0.00 0.00 3.96
1997 2164 2.975193 CACACACATCAAGTTCGCATTG 59.025 45.455 0.00 0.00 0.00 2.82
2002 2169 1.069703 CAGCCACACACATCAAGTTCG 60.070 52.381 0.00 0.00 0.00 3.95
2036 2205 3.054139 ACAATAGAGCCACACATGTCCAT 60.054 43.478 0.00 0.00 0.00 3.41
2046 2215 4.379499 GCAACCAAAGTACAATAGAGCCAC 60.379 45.833 0.00 0.00 0.00 5.01
2058 2230 6.644347 TGAAATTCCAAAAGCAACCAAAGTA 58.356 32.000 0.00 0.00 0.00 2.24
2082 2284 9.830975 TGCACATAGTTAACATAGTTGTCATAT 57.169 29.630 8.61 0.00 34.06 1.78
2083 2285 9.093970 GTGCACATAGTTAACATAGTTGTCATA 57.906 33.333 13.17 0.00 34.06 2.15
2234 2474 1.748493 TGTTTGGTTGGAAGCACAGAC 59.252 47.619 0.00 0.00 35.94 3.51
2286 2527 3.244911 CCATTCCTGTGTTTGGTAGGAGT 60.245 47.826 0.00 0.00 41.33 3.85
2408 2649 0.179084 TGGATGCCGCAAGTAGTAGC 60.179 55.000 0.00 0.00 0.00 3.58
2411 2652 1.450312 GCTGGATGCCGCAAGTAGT 60.450 57.895 0.00 0.00 35.15 2.73
2472 2713 0.108615 CAGGTGAACCGAGTAGCCAG 60.109 60.000 0.00 0.00 42.08 4.85
2473 2714 1.541310 CCAGGTGAACCGAGTAGCCA 61.541 60.000 0.00 0.00 42.08 4.75
2476 2717 0.108615 CTGCCAGGTGAACCGAGTAG 60.109 60.000 0.00 0.00 42.08 2.57
2520 2761 2.811317 CGACTGCACGGAGAAGCC 60.811 66.667 0.00 0.00 0.00 4.35
2544 2785 4.065088 ACACATGGTGGCTATAATAAGCG 58.935 43.478 0.00 0.00 43.74 4.68
2582 2823 1.142748 CGCTGGATCCACTGGAGAC 59.857 63.158 11.44 0.00 34.05 3.36
2600 2841 6.159293 GTCTTCAACATTTCCTTGGATTTCC 58.841 40.000 0.00 0.00 0.00 3.13
2685 2926 7.909485 AAGCCATTGATCTCCTTTTCATTAT 57.091 32.000 0.00 0.00 0.00 1.28
2686 2927 9.071276 GATAAGCCATTGATCTCCTTTTCATTA 57.929 33.333 0.00 0.00 0.00 1.90
2750 2991 7.875041 ACCTCATATGTACTATCTTGTTCATGC 59.125 37.037 1.90 0.00 31.93 4.06
2783 3024 7.757097 TTTTGCGCTTGTAATTTCAAGTTAA 57.243 28.000 21.42 13.32 44.41 2.01
2795 3036 3.674225 CGCTGATTTTGCGCTTGTA 57.326 47.368 9.73 0.00 46.72 2.41
2796 3037 4.539152 CGCTGATTTTGCGCTTGT 57.461 50.000 9.73 0.00 46.72 3.16
2841 3083 9.586435 GTATTTAAGCAAGCTAACATTTGGATT 57.414 29.630 0.00 0.00 0.00 3.01
2854 3096 9.887406 TTACTTAGTTTGTGTATTTAAGCAAGC 57.113 29.630 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.