Multiple sequence alignment - TraesCS7D01G029900

Loading Multiple Alignment...

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 TraesCS7D01G029900 chr7D 100.000 3102 0 0 1 3102 15631889 15628788 0.000000e+00 5729
1 TraesCS7D01G029900 chr4D 89.196 3073 243 47 48 3102 150015773 150018774 0.000000e+00 3753
2 TraesCS7D01G029900 chr4D 95.255 1391 44 11 49 1437 507735293 507736663 0.000000e+00 2183
3 TraesCS7D01G029900 chr4D 93.460 1208 77 2 631 1837 43327037 43328243 0.000000e+00 1792
4 TraesCS7D01G029900 chr4D 86.003 1286 131 23 1848 3101 278205207 278203939 0.000000e+00 1332
5 TraesCS7D01G029900 chr4D 95.278 593 17 6 48 640 43326034 43326615 0.000000e+00 929
6 TraesCS7D01G029900 chr5A 91.387 2148 140 20 48 2192 605327476 605325371 0.000000e+00 2900
7 TraesCS7D01G029900 chr1A 85.487 2260 245 36 876 3102 336239098 336236889 0.000000e+00 2279
8 TraesCS7D01G029900 chr1A 84.215 1286 147 28 1848 3102 320271440 320270180 0.000000e+00 1199
9 TraesCS7D01G029900 chr7A 85.172 2266 256 34 868 3101 148015682 148013465 0.000000e+00 2250
10 TraesCS7D01G029900 chr7A 89.616 963 93 2 876 1837 6709670 6710626 0.000000e+00 1218
11 TraesCS7D01G029900 chr7A 84.479 902 101 17 2232 3102 6745805 6746698 0.000000e+00 854
12 TraesCS7D01G029900 chr7A 90.909 341 28 3 1848 2186 6710609 6710948 3.650000e-124 455
13 TraesCS7D01G029900 chr7A 90.909 264 17 5 48 311 82158057 82157801 6.370000e-92 348
14 TraesCS7D01G029900 chr6B 93.987 1264 67 2 48 1311 37031486 37032740 0.000000e+00 1905
15 TraesCS7D01G029900 chr7B 94.597 1166 38 4 203 1363 611608465 611609610 0.000000e+00 1781
16 TraesCS7D01G029900 chr7B 90.827 1330 109 9 513 1837 651186945 651188266 0.000000e+00 1768
17 TraesCS7D01G029900 chr7B 90.605 777 39 8 48 823 680542460 680543203 0.000000e+00 1000
18 TraesCS7D01G029900 chr3B 87.552 1454 136 23 919 2367 802584283 802585696 0.000000e+00 1640
19 TraesCS7D01G029900 chr3B 90.722 776 39 7 48 823 736319330 736318588 0.000000e+00 1003
20 TraesCS7D01G029900 chr6A 86.929 1446 146 22 926 2367 58005132 58003726 0.000000e+00 1583
21 TraesCS7D01G029900 chr6A 85.058 1285 147 21 1848 3102 10050153 10048884 0.000000e+00 1267
22 TraesCS7D01G029900 chr6A 84.657 1284 148 21 1848 3102 90086566 90087829 0.000000e+00 1234
23 TraesCS7D01G029900 chr5B 90.217 920 87 2 919 1837 607045234 607046151 0.000000e+00 1197
24 TraesCS7D01G029900 chr5B 87.430 891 82 24 2231 3102 607046562 607047441 0.000000e+00 998
25 TraesCS7D01G029900 chr5B 87.318 891 83 25 2231 3102 607103400 607104279 0.000000e+00 992
26 TraesCS7D01G029900 chr5B 91.244 434 29 4 1848 2280 607046134 607046559 1.600000e-162 582
27 TraesCS7D01G029900 chr5B 89.931 437 32 6 1848 2280 607102969 607103397 1.260000e-153 553
28 TraesCS7D01G029900 chr1D 83.994 1287 139 27 1848 3102 22168936 22170187 0.000000e+00 1173
29 TraesCS7D01G029900 chr6D 87.303 890 86 22 2231 3102 341372431 341373311 0.000000e+00 992
30 TraesCS7D01G029900 chr1B 92.523 428 27 2 48 475 626455251 626454829 2.650000e-170 608
31 TraesCS7D01G029900 chr1B 87.931 232 24 3 564 793 606311791 606312020 1.420000e-68 270
32 TraesCS7D01G029900 chr5D 89.224 232 21 3 564 793 531289146 531289375 1.410000e-73 287


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 TraesCS7D01G029900 chr7D 15628788 15631889 3101 True 5729.000000 5729 100.000000 1 3102 1 chr7D.!!$R1 3101
1 TraesCS7D01G029900 chr4D 150015773 150018774 3001 False 3753.000000 3753 89.196000 48 3102 1 chr4D.!!$F1 3054
2 TraesCS7D01G029900 chr4D 507735293 507736663 1370 False 2183.000000 2183 95.255000 49 1437 1 chr4D.!!$F2 1388
3 TraesCS7D01G029900 chr4D 43326034 43328243 2209 False 1360.500000 1792 94.369000 48 1837 2 chr4D.!!$F3 1789
4 TraesCS7D01G029900 chr4D 278203939 278205207 1268 True 1332.000000 1332 86.003000 1848 3101 1 chr4D.!!$R1 1253
5 TraesCS7D01G029900 chr5A 605325371 605327476 2105 True 2900.000000 2900 91.387000 48 2192 1 chr5A.!!$R1 2144
6 TraesCS7D01G029900 chr1A 336236889 336239098 2209 True 2279.000000 2279 85.487000 876 3102 1 chr1A.!!$R2 2226
7 TraesCS7D01G029900 chr1A 320270180 320271440 1260 True 1199.000000 1199 84.215000 1848 3102 1 chr1A.!!$R1 1254
8 TraesCS7D01G029900 chr7A 148013465 148015682 2217 True 2250.000000 2250 85.172000 868 3101 1 chr7A.!!$R2 2233
9 TraesCS7D01G029900 chr7A 6745805 6746698 893 False 854.000000 854 84.479000 2232 3102 1 chr7A.!!$F1 870
10 TraesCS7D01G029900 chr7A 6709670 6710948 1278 False 836.500000 1218 90.262500 876 2186 2 chr7A.!!$F2 1310
11 TraesCS7D01G029900 chr6B 37031486 37032740 1254 False 1905.000000 1905 93.987000 48 1311 1 chr6B.!!$F1 1263
12 TraesCS7D01G029900 chr7B 611608465 611609610 1145 False 1781.000000 1781 94.597000 203 1363 1 chr7B.!!$F1 1160
13 TraesCS7D01G029900 chr7B 651186945 651188266 1321 False 1768.000000 1768 90.827000 513 1837 1 chr7B.!!$F2 1324
14 TraesCS7D01G029900 chr7B 680542460 680543203 743 False 1000.000000 1000 90.605000 48 823 1 chr7B.!!$F3 775
15 TraesCS7D01G029900 chr3B 802584283 802585696 1413 False 1640.000000 1640 87.552000 919 2367 1 chr3B.!!$F1 1448
16 TraesCS7D01G029900 chr3B 736318588 736319330 742 True 1003.000000 1003 90.722000 48 823 1 chr3B.!!$R1 775
17 TraesCS7D01G029900 chr6A 58003726 58005132 1406 True 1583.000000 1583 86.929000 926 2367 1 chr6A.!!$R2 1441
18 TraesCS7D01G029900 chr6A 10048884 10050153 1269 True 1267.000000 1267 85.058000 1848 3102 1 chr6A.!!$R1 1254
19 TraesCS7D01G029900 chr6A 90086566 90087829 1263 False 1234.000000 1234 84.657000 1848 3102 1 chr6A.!!$F1 1254
20 TraesCS7D01G029900 chr5B 607045234 607047441 2207 False 925.666667 1197 89.630333 919 3102 3 chr5B.!!$F1 2183
21 TraesCS7D01G029900 chr5B 607102969 607104279 1310 False 772.500000 992 88.624500 1848 3102 2 chr5B.!!$F2 1254
22 TraesCS7D01G029900 chr1D 22168936 22170187 1251 False 1173.000000 1173 83.994000 1848 3102 1 chr1D.!!$F1 1254
23 TraesCS7D01G029900 chr6D 341372431 341373311 880 False 992.000000 992 87.303000 2231 3102 1 chr6D.!!$F1 871

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
648 1093 0.452122 CGCCGCTACGAAGGTTTTTG 60.452 55.0 0.0 0.0 34.06 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2940 1.068921 GTGCAACGCCCACCAAAAT 59.931 52.632 0.0 0.0 0.0 1.82 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 8.751335 GCGAATCTGAAAACAAAACTTATTTCA 58.249 29.630 0.00 0.00 38.92 2.69
32 33 8.406172 TGAAAACAAAACTTATTTCAGACTGC 57.594 30.769 0.00 0.00 36.99 4.40
33 34 7.491048 TGAAAACAAAACTTATTTCAGACTGCC 59.509 33.333 0.00 0.00 36.99 4.85
34 35 5.453567 ACAAAACTTATTTCAGACTGCCC 57.546 39.130 0.00 0.00 0.00 5.36
35 36 5.140454 ACAAAACTTATTTCAGACTGCCCT 58.860 37.500 0.00 0.00 0.00 5.19
36 37 5.010012 ACAAAACTTATTTCAGACTGCCCTG 59.990 40.000 0.00 0.00 35.55 4.45
37 38 4.373156 AACTTATTTCAGACTGCCCTGT 57.627 40.909 0.00 0.00 35.71 4.00
38 39 4.373156 ACTTATTTCAGACTGCCCTGTT 57.627 40.909 0.00 0.00 35.71 3.16
39 40 4.729868 ACTTATTTCAGACTGCCCTGTTT 58.270 39.130 0.00 0.00 35.71 2.83
40 41 4.520492 ACTTATTTCAGACTGCCCTGTTTG 59.480 41.667 0.00 0.00 35.71 2.93
41 42 2.727123 TTTCAGACTGCCCTGTTTGA 57.273 45.000 0.00 0.00 35.71 2.69
42 43 2.957402 TTCAGACTGCCCTGTTTGAT 57.043 45.000 0.00 0.00 32.38 2.57
43 44 4.365514 TTTCAGACTGCCCTGTTTGATA 57.634 40.909 0.00 0.00 32.38 2.15
44 45 3.616956 TCAGACTGCCCTGTTTGATAG 57.383 47.619 0.00 0.00 35.71 2.08
45 46 2.012673 CAGACTGCCCTGTTTGATAGC 58.987 52.381 0.00 0.00 0.00 2.97
46 47 1.630369 AGACTGCCCTGTTTGATAGCA 59.370 47.619 0.00 0.00 0.00 3.49
206 209 8.768501 AAGAACCTCAGACCTCTTTTTAAAAT 57.231 30.769 0.55 0.00 0.00 1.82
252 255 1.206371 CACGTCGTTATCCTTCCCCTT 59.794 52.381 0.00 0.00 0.00 3.95
373 377 1.814248 GCAACGGAGAGACCAAAGGTT 60.814 52.381 0.00 0.00 35.25 3.50
374 378 2.549349 GCAACGGAGAGACCAAAGGTTA 60.549 50.000 0.00 0.00 35.25 2.85
375 379 3.326747 CAACGGAGAGACCAAAGGTTAG 58.673 50.000 0.00 0.00 35.25 2.34
376 380 2.606378 ACGGAGAGACCAAAGGTTAGT 58.394 47.619 0.00 0.00 35.25 2.24
377 381 3.771216 ACGGAGAGACCAAAGGTTAGTA 58.229 45.455 0.00 0.00 35.25 1.82
380 384 4.142425 CGGAGAGACCAAAGGTTAGTAGAC 60.142 50.000 0.00 0.00 35.25 2.59
397 411 0.833949 GACTGTCCTTCATCCTCCCC 59.166 60.000 0.00 0.00 0.00 4.81
457 471 4.530857 CCTCCGCCCGTGATGGAC 62.531 72.222 0.00 0.00 42.00 4.02
648 1093 0.452122 CGCCGCTACGAAGGTTTTTG 60.452 55.000 0.00 0.00 34.06 2.44
837 1284 1.771255 AGAGGTCATCCCCTTACATGC 59.229 52.381 0.00 0.00 34.03 4.06
934 1382 7.171337 ACGCTTTATTTGATGCATTTTGTTTCT 59.829 29.630 0.00 0.00 0.00 2.52
964 1412 5.401674 GCAGAAAAGAAAAACAGAGCATCAG 59.598 40.000 0.00 0.00 37.82 2.90
973 1421 1.273267 ACAGAGCATCAGGGACCACTA 60.273 52.381 0.00 0.00 37.82 2.74
1100 1548 3.120199 CGCTTGAACAATCAGTTTCCGAT 60.120 43.478 0.00 0.00 41.51 4.18
1111 1559 8.184192 ACAATCAGTTTCCGATAGCTAATTTTG 58.816 33.333 0.00 0.00 0.00 2.44
1211 1659 5.355910 GTGGCTTCGGTTTTGATCCTATTAA 59.644 40.000 0.00 0.00 0.00 1.40
1212 1660 5.355910 TGGCTTCGGTTTTGATCCTATTAAC 59.644 40.000 0.00 0.00 0.00 2.01
1220 1668 7.759433 CGGTTTTGATCCTATTAACAAAATGCT 59.241 33.333 0.00 0.00 41.74 3.79
1344 1797 5.179742 TGGTACGTTGGTTTCACATGTAATC 59.820 40.000 0.00 0.00 0.00 1.75
1400 1853 7.931015 TTACAATCTATTCCTCTGTACCCAT 57.069 36.000 0.00 0.00 0.00 4.00
1407 1860 8.331931 TCTATTCCTCTGTACCCATGTAAATT 57.668 34.615 0.00 0.00 0.00 1.82
1417 1870 1.880027 CCATGTAAATTAGCGGAGGGC 59.120 52.381 0.00 0.00 44.05 5.19
1437 1890 3.421844 GCAAGGGTTGTAAGAGGACAAT 58.578 45.455 0.00 0.00 41.21 2.71
1438 1891 4.566907 GGCAAGGGTTGTAAGAGGACAATA 60.567 45.833 0.00 0.00 41.21 1.90
1455 1908 6.098124 AGGACAATAGATCAGGTTGAAGAGAG 59.902 42.308 10.49 0.00 0.00 3.20
1475 1928 3.362706 AGGTTCAGTTCGGCTACAGATA 58.637 45.455 0.00 0.00 0.00 1.98
1556 2010 0.251916 CCAACATTACCGGCTCCAGA 59.748 55.000 0.00 0.00 0.00 3.86
1608 2062 4.193826 AGGCATATATGGTGACGATGTC 57.806 45.455 14.51 0.00 0.00 3.06
1675 2129 2.504367 ACCAATTTCCCACAGAAGACG 58.496 47.619 0.00 0.00 35.40 4.18
1717 2171 3.053619 ACCACCTATGAAAAAGGCTAGGG 60.054 47.826 2.53 0.00 37.67 3.53
1767 2221 3.281727 AAGAGAGGCAAAGACACAACA 57.718 42.857 0.00 0.00 0.00 3.33
1837 2291 6.149633 GTGGATGTAAAGACGAAGCAAATTT 58.850 36.000 0.00 0.00 0.00 1.82
1838 2292 6.640907 GTGGATGTAAAGACGAAGCAAATTTT 59.359 34.615 0.00 0.00 0.00 1.82
1839 2293 7.169140 GTGGATGTAAAGACGAAGCAAATTTTT 59.831 33.333 0.00 0.00 0.00 1.94
1963 2423 5.771469 TGCATTGTCAAACTTAAGACCATG 58.229 37.500 10.09 5.96 39.53 3.66
1995 2455 4.060900 TCAGCAAGTGAACATCTGAAGAC 58.939 43.478 0.00 0.00 31.62 3.01
2022 2482 4.564769 CGAGTATCTGAAAGGACAAAGAGC 59.435 45.833 0.00 0.00 0.00 4.09
2059 2519 2.103537 TGACAGTGGAGCATGATGTG 57.896 50.000 0.00 0.00 0.00 3.21
2194 2654 8.929827 TCGATTCATATTACTTTCGGTTTACA 57.070 30.769 0.00 0.00 0.00 2.41
2223 2684 4.926860 TCAAAAGATATCACTGTGCACG 57.073 40.909 13.13 9.67 0.00 5.34
2260 2721 8.673711 CCATGAATAAAAAGAGGAACACGAATA 58.326 33.333 0.00 0.00 0.00 1.75
2292 2805 7.605449 AGCATACATTTGTTTCAGCACTAAAT 58.395 30.769 0.00 0.00 0.00 1.40
2312 2826 4.961438 ATTTGGTTTTGATGGTGCTCTT 57.039 36.364 0.00 0.00 0.00 2.85
2316 2830 5.389859 TGGTTTTGATGGTGCTCTTATTG 57.610 39.130 0.00 0.00 0.00 1.90
2320 2834 4.970662 TTGATGGTGCTCTTATTGCTTC 57.029 40.909 0.00 0.00 0.00 3.86
2327 2841 5.125417 TGGTGCTCTTATTGCTTCCATAAAC 59.875 40.000 0.00 0.00 33.34 2.01
2336 2852 5.554822 TTGCTTCCATAAACGTACAATCC 57.445 39.130 0.00 0.00 0.00 3.01
2339 2855 5.353123 TGCTTCCATAAACGTACAATCCTTC 59.647 40.000 0.00 0.00 0.00 3.46
2361 2878 5.457140 TCAATTTTGTTACTTCCGTCATGC 58.543 37.500 0.00 0.00 0.00 4.06
2367 2884 6.811253 TTGTTACTTCCGTCATGCTATTTT 57.189 33.333 0.00 0.00 0.00 1.82
2377 2894 2.023673 CATGCTATTTTTGCTCCCGGA 58.976 47.619 0.73 0.00 0.00 5.14
2380 2897 3.892284 TGCTATTTTTGCTCCCGGATTA 58.108 40.909 0.73 0.00 0.00 1.75
2382 2899 4.892934 TGCTATTTTTGCTCCCGGATTATT 59.107 37.500 0.73 0.00 0.00 1.40
2447 2968 0.317436 GGCGTTGCACGTTTGATCAA 60.317 50.000 3.38 3.38 44.73 2.57
2480 3001 7.550906 AGAAGAAAATAGCATTGTAGAGGACAC 59.449 37.037 0.00 0.00 37.96 3.67
2481 3002 6.711277 AGAAAATAGCATTGTAGAGGACACA 58.289 36.000 0.00 0.00 37.96 3.72
2482 3003 7.168219 AGAAAATAGCATTGTAGAGGACACAA 58.832 34.615 0.00 0.00 37.96 3.33
2483 3004 7.665559 AGAAAATAGCATTGTAGAGGACACAAA 59.334 33.333 0.00 0.00 39.22 2.83
2496 3017 5.182001 AGAGGACACAAACACTCATATTTGC 59.818 40.000 0.00 0.00 39.03 3.68
2502 3024 3.855689 AACACTCATATTTGCTGCACC 57.144 42.857 0.00 0.00 0.00 5.01
2527 3049 7.095313 CCAGTTGATAGCTGCATCTTACATTAG 60.095 40.741 1.02 0.00 32.93 1.73
2626 3168 8.635765 TTTATTCTAGCTTCAACAATTCCACT 57.364 30.769 0.00 0.00 0.00 4.00
2650 3192 5.363939 AGTCATGTGCTATTTCTTCTAGCC 58.636 41.667 0.00 0.00 40.72 3.93
2667 3209 1.068753 CCCGCTCCTGCAGATACTG 59.931 63.158 17.39 0.00 39.64 2.74
2678 3220 4.036262 CCTGCAGATACTGACAGTAGTCTC 59.964 50.000 17.39 12.74 45.20 3.36
2819 3362 3.525609 TGGTCAATATTGGAGCCAACCTA 59.474 43.478 15.36 3.52 38.88 3.08
2866 3411 8.667987 TCGTGATTGCAAATAAAGTTATGAAC 57.332 30.769 1.71 0.00 0.00 3.18
2910 3457 6.078456 TCAGGTTGAGATTCAATTGGGTAT 57.922 37.500 5.42 0.00 38.79 2.73
2916 3463 7.253422 GTTGAGATTCAATTGGGTATTGTGAG 58.747 38.462 5.42 0.00 43.41 3.51
3060 3607 3.347216 AGCTTGCTCGTTCAAATGGTAT 58.653 40.909 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.491048 GGCAGTCTGAAATAAGTTTTGTTTTCA 59.509 33.333 3.32 0.00 36.80 2.69
8 9 7.042725 GGGCAGTCTGAAATAAGTTTTGTTTTC 60.043 37.037 3.32 0.00 0.00 2.29
9 10 6.761242 GGGCAGTCTGAAATAAGTTTTGTTTT 59.239 34.615 3.32 0.00 0.00 2.43
10 11 6.098266 AGGGCAGTCTGAAATAAGTTTTGTTT 59.902 34.615 3.32 0.00 0.00 2.83
11 12 5.598417 AGGGCAGTCTGAAATAAGTTTTGTT 59.402 36.000 3.32 0.00 0.00 2.83
12 13 5.010012 CAGGGCAGTCTGAAATAAGTTTTGT 59.990 40.000 3.32 0.00 36.93 2.83
13 14 5.010012 ACAGGGCAGTCTGAAATAAGTTTTG 59.990 40.000 3.32 0.00 38.11 2.44
14 15 5.140454 ACAGGGCAGTCTGAAATAAGTTTT 58.860 37.500 3.32 0.00 38.11 2.43
15 16 4.729868 ACAGGGCAGTCTGAAATAAGTTT 58.270 39.130 3.32 0.00 38.11 2.66
16 17 4.373156 ACAGGGCAGTCTGAAATAAGTT 57.627 40.909 3.32 0.00 38.11 2.66
17 18 4.373156 AACAGGGCAGTCTGAAATAAGT 57.627 40.909 3.32 0.00 38.11 2.24
18 19 4.761739 TCAAACAGGGCAGTCTGAAATAAG 59.238 41.667 3.32 0.00 38.11 1.73
19 20 4.724399 TCAAACAGGGCAGTCTGAAATAA 58.276 39.130 3.32 0.00 38.11 1.40
20 21 4.365514 TCAAACAGGGCAGTCTGAAATA 57.634 40.909 3.32 0.00 38.11 1.40
21 22 3.228188 TCAAACAGGGCAGTCTGAAAT 57.772 42.857 3.32 0.00 38.11 2.17
22 23 2.727123 TCAAACAGGGCAGTCTGAAA 57.273 45.000 3.32 0.00 38.11 2.69
23 24 2.957402 ATCAAACAGGGCAGTCTGAA 57.043 45.000 3.32 0.00 38.11 3.02
24 25 2.355108 GCTATCAAACAGGGCAGTCTGA 60.355 50.000 3.32 0.00 38.11 3.27
25 26 2.012673 GCTATCAAACAGGGCAGTCTG 58.987 52.381 0.00 0.00 40.40 3.51
26 27 1.630369 TGCTATCAAACAGGGCAGTCT 59.370 47.619 0.00 0.00 0.00 3.24
27 28 2.113860 TGCTATCAAACAGGGCAGTC 57.886 50.000 0.00 0.00 0.00 3.51
28 29 2.584835 TTGCTATCAAACAGGGCAGT 57.415 45.000 0.00 0.00 34.37 4.40
29 30 2.821969 ACTTTGCTATCAAACAGGGCAG 59.178 45.455 0.00 0.00 37.28 4.85
30 31 2.875296 ACTTTGCTATCAAACAGGGCA 58.125 42.857 0.00 0.00 37.28 5.36
31 32 5.582689 AATACTTTGCTATCAAACAGGGC 57.417 39.130 0.00 0.00 37.28 5.19
32 33 7.601856 TCAAAATACTTTGCTATCAAACAGGG 58.398 34.615 0.00 0.00 41.53 4.45
42 43 8.832521 CGGTGGTATTATCAAAATACTTTGCTA 58.167 33.333 7.58 0.00 41.53 3.49
43 44 7.338449 ACGGTGGTATTATCAAAATACTTTGCT 59.662 33.333 7.58 0.00 41.53 3.91
44 45 7.477494 ACGGTGGTATTATCAAAATACTTTGC 58.523 34.615 7.58 0.00 41.53 3.68
45 46 9.849166 AAACGGTGGTATTATCAAAATACTTTG 57.151 29.630 7.58 0.00 42.88 2.77
112 115 7.589958 ATTAAAACCACAGTTGTTATGGACA 57.410 32.000 0.00 0.00 35.97 4.02
206 209 2.233922 CCTTCTTTTCGGCTCCTCTGTA 59.766 50.000 0.00 0.00 0.00 2.74
252 255 3.202906 CGAGTTGTTGAACAAAGAGGGA 58.797 45.455 12.89 0.00 40.15 4.20
326 330 2.034999 GTTTCCCCATGGCCGACA 59.965 61.111 6.09 0.00 0.00 4.35
373 377 4.386536 GGGAGGATGAAGGACAGTCTACTA 60.387 50.000 0.00 0.00 0.00 1.82
374 378 3.628769 GGGAGGATGAAGGACAGTCTACT 60.629 52.174 0.00 0.00 0.00 2.57
375 379 2.696187 GGGAGGATGAAGGACAGTCTAC 59.304 54.545 0.00 0.00 0.00 2.59
376 380 2.359355 GGGGAGGATGAAGGACAGTCTA 60.359 54.545 0.00 0.00 0.00 2.59
377 381 1.623834 GGGGAGGATGAAGGACAGTCT 60.624 57.143 0.00 0.00 0.00 3.24
380 384 0.621571 TGGGGGAGGATGAAGGACAG 60.622 60.000 0.00 0.00 0.00 3.51
397 411 0.466922 GATGTGGGAGGAGCCAATGG 60.467 60.000 0.00 0.00 38.95 3.16
457 471 0.972883 GATCTAGTGCCCTGGCCTAG 59.027 60.000 19.47 19.47 40.28 3.02
546 560 8.705594 CATACCAGACTTTATAAAGGAGAAGGA 58.294 37.037 25.25 10.07 40.31 3.36
648 1093 3.451141 CCTCTGAGCAATCTGAGGTAC 57.549 52.381 18.12 0.00 45.24 3.34
837 1284 3.077229 TCCATGCTTTTGTTCAACACG 57.923 42.857 0.00 0.00 0.00 4.49
934 1382 6.256321 GCTCTGTTTTTCTTTTCTGCAATTGA 59.744 34.615 10.34 0.00 0.00 2.57
964 1412 4.031611 AGGTCTAATTGAGTAGTGGTCCC 58.968 47.826 0.00 0.00 0.00 4.46
973 1421 8.091449 CACAGAAACTAGAAGGTCTAATTGAGT 58.909 37.037 0.00 0.00 0.00 3.41
1400 1853 2.639065 CTTGCCCTCCGCTAATTTACA 58.361 47.619 0.00 0.00 38.78 2.41
1407 1860 2.609610 AACCCTTGCCCTCCGCTA 60.610 61.111 0.00 0.00 38.78 4.26
1417 1870 6.049955 TCTATTGTCCTCTTACAACCCTTG 57.950 41.667 0.00 0.00 41.89 3.61
1437 1890 5.333581 TGAACCTCTCTTCAACCTGATCTA 58.666 41.667 0.00 0.00 0.00 1.98
1438 1891 4.163427 TGAACCTCTCTTCAACCTGATCT 58.837 43.478 0.00 0.00 0.00 2.75
1455 1908 2.674796 ATCTGTAGCCGAACTGAACC 57.325 50.000 0.00 0.00 32.08 3.62
1475 1928 1.860696 AGGTTTCCCCTTGTGGCAT 59.139 52.632 0.00 0.00 42.73 4.40
1556 2010 7.884877 TCCACTCATAATGTTGATCTTCAAAGT 59.115 33.333 0.00 0.00 38.22 2.66
1608 2062 6.491394 TGTGTTTTCAACAGGAAATACTTCG 58.509 36.000 0.00 0.00 44.59 3.79
1639 2093 9.067986 GGGAAATTGGTTACTATTATTCTCCAG 57.932 37.037 0.00 0.00 0.00 3.86
1675 2129 1.134220 TGGGTCAGGAAGTGTGTTCAC 60.134 52.381 0.00 0.00 44.15 3.18
1717 2171 4.400567 ACCTTCATCATTGCCTTTAGAAGC 59.599 41.667 0.00 0.00 31.99 3.86
1767 2221 6.240894 TCTAACTGCAACCAGATCTTCAATT 58.759 36.000 0.00 0.00 41.77 2.32
1838 2292 8.696410 ATTTGCTTCGTCTTTACTTTCAAAAA 57.304 26.923 0.00 0.00 0.00 1.94
1839 2293 8.591312 CAATTTGCTTCGTCTTTACTTTCAAAA 58.409 29.630 0.00 0.00 0.00 2.44
1840 2294 7.971168 TCAATTTGCTTCGTCTTTACTTTCAAA 59.029 29.630 0.00 0.00 0.00 2.69
1841 2295 7.476667 TCAATTTGCTTCGTCTTTACTTTCAA 58.523 30.769 0.00 0.00 0.00 2.69
1842 2296 7.011950 TCTCAATTTGCTTCGTCTTTACTTTCA 59.988 33.333 0.00 0.00 0.00 2.69
1843 2297 7.352739 TCTCAATTTGCTTCGTCTTTACTTTC 58.647 34.615 0.00 0.00 0.00 2.62
1844 2298 7.259290 TCTCAATTTGCTTCGTCTTTACTTT 57.741 32.000 0.00 0.00 0.00 2.66
1845 2299 6.566753 GCTCTCAATTTGCTTCGTCTTTACTT 60.567 38.462 0.00 0.00 0.00 2.24
1846 2300 5.106908 GCTCTCAATTTGCTTCGTCTTTACT 60.107 40.000 0.00 0.00 0.00 2.24
1920 2377 3.310501 GCAATTGGCAATGCAATAAGGAC 59.689 43.478 14.47 0.00 43.97 3.85
1963 2423 1.206610 TCACTTGCTGAGAGATCTGGC 59.793 52.381 0.00 0.00 0.00 4.85
1995 2455 4.553756 TGTCCTTTCAGATACTCGATCG 57.446 45.455 9.36 9.36 39.80 3.69
2022 2482 3.996363 TGTCATGAAGATTTCACGGTCAG 59.004 43.478 0.00 0.00 43.48 3.51
2059 2519 4.019771 ACTTTCTTGAGGATCTCCAGAACC 60.020 45.833 9.90 0.00 40.39 3.62
2194 2654 9.846248 GCACAGTGATATCTTTTGAACTAAAAT 57.154 29.630 4.15 0.00 37.61 1.82
2199 2659 5.106948 CGTGCACAGTGATATCTTTTGAACT 60.107 40.000 18.64 0.00 0.00 3.01
2264 2725 7.161773 AGTGCTGAAACAAATGTATGCTAAT 57.838 32.000 0.00 0.00 0.00 1.73
2266 2727 7.680442 TTAGTGCTGAAACAAATGTATGCTA 57.320 32.000 0.00 0.00 0.00 3.49
2292 2805 6.222389 CAATAAGAGCACCATCAAAACCAAA 58.778 36.000 0.00 0.00 0.00 3.28
2312 2826 7.051623 AGGATTGTACGTTTATGGAAGCAATA 58.948 34.615 0.00 0.00 0.00 1.90
2316 2830 5.353123 TGAAGGATTGTACGTTTATGGAAGC 59.647 40.000 0.00 0.00 0.00 3.86
2320 2834 8.859156 CAAAATTGAAGGATTGTACGTTTATGG 58.141 33.333 0.00 0.00 0.00 2.74
2327 2841 9.113876 GAAGTAACAAAATTGAAGGATTGTACG 57.886 33.333 0.00 0.00 35.09 3.67
2361 2878 5.301805 ACCAATAATCCGGGAGCAAAAATAG 59.698 40.000 0.00 0.00 0.00 1.73
2367 2884 1.409521 CCACCAATAATCCGGGAGCAA 60.410 52.381 0.00 0.00 0.00 3.91
2377 2894 6.717289 ACACACATGTACTACCACCAATAAT 58.283 36.000 0.00 0.00 37.26 1.28
2380 2897 4.634012 ACACACATGTACTACCACCAAT 57.366 40.909 0.00 0.00 37.26 3.16
2382 2899 3.134985 ACAACACACATGTACTACCACCA 59.865 43.478 0.00 0.00 38.45 4.17
2419 2940 1.068921 GTGCAACGCCCACCAAAAT 59.931 52.632 0.00 0.00 0.00 1.82
2464 2985 3.815401 GTGTTTGTGTCCTCTACAATGCT 59.185 43.478 0.00 0.00 40.63 3.79
2480 3001 3.922240 GGTGCAGCAAATATGAGTGTTTG 59.078 43.478 11.86 0.00 38.86 2.93
2481 3002 3.573538 TGGTGCAGCAAATATGAGTGTTT 59.426 39.130 17.80 0.00 0.00 2.83
2482 3003 3.156293 TGGTGCAGCAAATATGAGTGTT 58.844 40.909 17.80 0.00 0.00 3.32
2483 3004 2.751259 CTGGTGCAGCAAATATGAGTGT 59.249 45.455 20.60 0.00 0.00 3.55
2502 3024 6.615264 AATGTAAGATGCAGCTATCAACTG 57.385 37.500 4.15 0.00 38.22 3.16
2626 3168 6.463049 GGGCTAGAAGAAATAGCACATGACTA 60.463 42.308 0.00 0.71 46.77 2.59
2667 3209 3.357203 TCCATGTGGAGAGACTACTGTC 58.643 50.000 0.00 0.00 39.78 3.51
2766 3308 7.888514 ATAGTTGATATTCCAAGTGGGGATA 57.111 36.000 0.00 0.00 41.56 2.59
2797 3340 2.311542 AGGTTGGCTCCAATATTGACCA 59.688 45.455 17.23 16.69 38.28 4.02
2819 3362 2.490902 GGGGGAGAACAATGGTTTGACT 60.491 50.000 0.00 0.00 37.36 3.41
2880 3425 7.012138 CCAATTGAATCTCAACCTGATAGTCAG 59.988 40.741 7.12 0.00 39.45 3.51
2910 3457 3.814842 CAGTATTGAAGTGTGCCTCACAA 59.185 43.478 10.84 0.00 46.28 3.33
2916 3463 2.489938 TCCCAGTATTGAAGTGTGCC 57.510 50.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.