Multiple sequence alignment - TraesCS5B01G467200

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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 TraesCS5B01G467200 chr5B 100.000 2847 0 0 1 2847 641134958 641132112 0.000000e+00 5258
1 TraesCS5B01G467200 chr5B 89.591 538 39 8 2317 2847 641393860 641393333 0.000000e+00 667
2 TraesCS5B01G467200 chr5B 92.814 167 9 2 2680 2846 35516322 35516159 3.670000e-59 239
3 TraesCS5B01G467200 chr5D 91.202 2330 126 41 2 2315 510129537 510127271 0.000000e+00 3094
4 TraesCS5B01G467200 chr5D 94.247 817 42 3 653 1465 510163936 510163121 0.000000e+00 1243
5 TraesCS5B01G467200 chr5D 92.019 639 48 3 1625 2261 510163121 510162484 0.000000e+00 894
6 TraesCS5B01G467200 chr5D 85.174 634 50 22 2 632 510164587 510163995 6.740000e-171 610
7 TraesCS5B01G467200 chr5A 87.870 709 55 15 426 1122 638604754 638604065 0.000000e+00 804
8 TraesCS5B01G467200 chr5A 90.426 564 34 6 1626 2186 638603583 638603037 0.000000e+00 725
9 TraesCS5B01G467200 chr5A 89.354 526 31 11 2 523 638605262 638604758 3.090000e-179 638
10 TraesCS5B01G467200 chr5A 93.294 343 18 3 1121 1461 638603927 638603588 4.230000e-138 501
11 TraesCS5B01G467200 chr5A 88.485 165 17 2 1460 1623 605231142 605231305 6.220000e-47 198
12 TraesCS5B01G467200 chr7B 94.220 173 10 0 2675 2847 706773355 706773527 6.050000e-67 265
13 TraesCS5B01G467200 chr7A 94.220 173 10 0 2675 2847 20478987 20479159 6.050000e-67 265
14 TraesCS5B01G467200 chr1D 92.655 177 13 0 2670 2846 31156704 31156880 3.640000e-64 255
15 TraesCS5B01G467200 chr1D 88.535 157 17 1 1467 1623 434740622 434740467 3.740000e-44 189
16 TraesCS5B01G467200 chr4D 94.012 167 10 0 2681 2847 400237869 400237703 1.310000e-63 254
17 TraesCS5B01G467200 chr4D 88.623 167 17 2 1458 1623 117421355 117421190 4.810000e-48 202
18 TraesCS5B01G467200 chr4D 87.647 170 16 4 1455 1623 326382445 326382610 2.890000e-45 193
19 TraesCS5B01G467200 chr4A 92.655 177 9 1 2675 2847 713739017 713738841 4.710000e-63 252
20 TraesCS5B01G467200 chr3A 82.069 290 48 4 1786 2074 65893104 65893390 7.880000e-61 244
21 TraesCS5B01G467200 chr3A 87.500 168 19 2 1457 1623 600920851 600921017 2.890000e-45 193
22 TraesCS5B01G467200 chr2D 91.379 174 12 3 2674 2847 559301917 559301747 4.740000e-58 235
23 TraesCS5B01G467200 chr4B 89.560 182 19 0 2499 2680 4712939 4712758 6.130000e-57 231
24 TraesCS5B01G467200 chr4B 88.679 159 17 1 1464 1622 650273375 650273218 2.890000e-45 193
25 TraesCS5B01G467200 chr3B 90.230 174 15 1 2674 2847 727262697 727262526 2.850000e-55 226
26 TraesCS5B01G467200 chr3B 76.639 244 38 13 1210 1436 88986168 88986409 1.790000e-22 117
27 TraesCS5B01G467200 chr3D 88.024 167 18 2 1457 1622 87926165 87926000 2.240000e-46 196
28 TraesCS5B01G467200 chr3D 79.094 287 42 13 1164 1436 56570325 56570607 6.270000e-42 182
29 TraesCS5B01G467200 chr3D 89.344 122 12 1 1771 1891 56570760 56570881 4.910000e-33 152
30 TraesCS5B01G467200 chr2A 88.415 164 17 2 1461 1623 758586738 758586576 2.240000e-46 196


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 TraesCS5B01G467200 chr5B 641132112 641134958 2846 True 5258.000000 5258 100.000 1 2847 1 chr5B.!!$R2 2846
1 TraesCS5B01G467200 chr5B 641393333 641393860 527 True 667.000000 667 89.591 2317 2847 1 chr5B.!!$R3 530
2 TraesCS5B01G467200 chr5D 510127271 510129537 2266 True 3094.000000 3094 91.202 2 2315 1 chr5D.!!$R1 2313
3 TraesCS5B01G467200 chr5D 510162484 510164587 2103 True 915.666667 1243 90.480 2 2261 3 chr5D.!!$R2 2259
4 TraesCS5B01G467200 chr5A 638603037 638605262 2225 True 667.000000 804 90.236 2 2186 4 chr5A.!!$R1 2184

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
280 281 1.058695 GCCGTACGATCAGTTTCAACG 59.941 52.381 18.76 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2188 0.32005 TGGTCACACGCTTAGCATGA 59.68 50.0 7.44 2.89 0.0 3.07 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
65 66 4.072131 GACACAGGGAAGAAGCAAACATA 58.928 43.478 0.00 0.00 0.00 2.29
66 67 4.666512 ACACAGGGAAGAAGCAAACATAT 58.333 39.130 0.00 0.00 0.00 1.78
67 68 5.815581 ACACAGGGAAGAAGCAAACATATA 58.184 37.500 0.00 0.00 0.00 0.86
68 69 6.426587 ACACAGGGAAGAAGCAAACATATAT 58.573 36.000 0.00 0.00 0.00 0.86
121 122 4.631377 TGATAAACTCTCAAGATGCAACCG 59.369 41.667 0.00 0.00 0.00 4.44
155 156 7.073342 ACGCATTATTCTGGAAGTTTCTTAC 57.927 36.000 0.00 0.00 33.76 2.34
156 157 6.879458 ACGCATTATTCTGGAAGTTTCTTACT 59.121 34.615 0.00 0.00 39.32 2.24
157 158 8.038944 ACGCATTATTCTGGAAGTTTCTTACTA 58.961 33.333 0.00 0.00 35.54 1.82
158 159 9.046296 CGCATTATTCTGGAAGTTTCTTACTAT 57.954 33.333 0.00 0.00 35.54 2.12
233 234 1.237285 GCAGGGCGCAATATACCCAG 61.237 60.000 10.83 0.00 46.88 4.45
248 249 1.628340 ACCCAGATCAATCCGTGTCAA 59.372 47.619 0.00 0.00 0.00 3.18
280 281 1.058695 GCCGTACGATCAGTTTCAACG 59.941 52.381 18.76 0.00 0.00 4.10
308 309 2.283298 CAGTGCGCCAATCAATCTAGT 58.717 47.619 4.18 0.00 0.00 2.57
309 310 2.286294 CAGTGCGCCAATCAATCTAGTC 59.714 50.000 4.18 0.00 0.00 2.59
310 311 2.169352 AGTGCGCCAATCAATCTAGTCT 59.831 45.455 4.18 0.00 0.00 3.24
311 312 3.384789 AGTGCGCCAATCAATCTAGTCTA 59.615 43.478 4.18 0.00 0.00 2.59
312 313 3.738282 GTGCGCCAATCAATCTAGTCTAG 59.262 47.826 4.18 0.00 0.00 2.43
324 325 7.489160 TCAATCTAGTCTAGCGCAAATTAAGA 58.511 34.615 11.47 6.03 0.00 2.10
331 332 8.894768 AGTCTAGCGCAAATTAAGAATCTAAT 57.105 30.769 11.47 0.00 0.00 1.73
336 337 8.894768 AGCGCAAATTAAGAATCTAATCTACT 57.105 30.769 11.47 0.00 0.00 2.57
337 338 8.983724 AGCGCAAATTAAGAATCTAATCTACTC 58.016 33.333 11.47 0.00 0.00 2.59
338 339 8.224437 GCGCAAATTAAGAATCTAATCTACTCC 58.776 37.037 0.30 0.00 0.00 3.85
339 340 9.482627 CGCAAATTAAGAATCTAATCTACTCCT 57.517 33.333 0.00 0.00 0.00 3.69
424 432 1.268184 TGTACGTACATCCGATCACGC 60.268 52.381 24.10 0.00 37.92 5.34
546 651 7.783042 AGTGTTCTACAGTAATTCCTATGGTC 58.217 38.462 0.00 0.00 28.20 4.02
551 656 7.285566 TCTACAGTAATTCCTATGGTCGTACT 58.714 38.462 0.00 0.00 0.00 2.73
642 794 8.181487 TCACTCGTCAACATAAATAGTTTAGC 57.819 34.615 0.00 0.00 0.00 3.09
647 799 9.589111 TCGTCAACATAAATAGTTTAGCACATA 57.411 29.630 0.00 0.00 0.00 2.29
717 869 8.052748 TCATAAAATGTATGAACTAGCTGGGTT 58.947 33.333 0.85 4.27 31.66 4.11
782 934 3.312736 TTCTTTTGGGAAGGAACTGCT 57.687 42.857 0.00 0.00 40.86 4.24
786 938 4.042809 TCTTTTGGGAAGGAACTGCTATCA 59.957 41.667 0.00 0.00 40.86 2.15
802 954 7.646314 ACTGCTATCATATTTTTCAGACATGC 58.354 34.615 0.00 0.00 0.00 4.06
876 1032 4.191544 TCAAATACATGGCTTTCGAGAGG 58.808 43.478 4.98 0.00 0.00 3.69
901 1057 4.323336 CGGTCAAATCACAATTTTTAGCCG 59.677 41.667 0.00 0.00 32.69 5.52
954 1110 8.768397 TGTCTTAGATCTAGCCTTGGAATTAAA 58.232 33.333 2.02 0.00 0.00 1.52
1024 1181 0.679505 TCGAACTAAGTGCACAGCCT 59.320 50.000 21.04 2.71 0.00 4.58
1079 1236 3.871594 CACCTTCGGGCTTTCTATGTAAG 59.128 47.826 0.00 0.00 39.10 2.34
1268 1564 4.491676 GAACTGTTGCTCTTCGGTATGTA 58.508 43.478 0.00 0.00 0.00 2.29
1270 1566 5.086104 ACTGTTGCTCTTCGGTATGTATT 57.914 39.130 0.00 0.00 0.00 1.89
1272 1568 4.827692 TGTTGCTCTTCGGTATGTATTGT 58.172 39.130 0.00 0.00 0.00 2.71
1311 1607 4.790937 TGCTTGGATTATTATGAGGTGCA 58.209 39.130 0.00 0.00 0.00 4.57
1333 1629 5.563475 GCATGTGTTTCATACTCTTGTGCTT 60.563 40.000 0.00 0.00 34.67 3.91
1335 1631 5.122519 TGTGTTTCATACTCTTGTGCTTCA 58.877 37.500 0.00 0.00 0.00 3.02
1397 1693 5.188359 ACTTATAAGGAAGCTACCGTTCCAA 59.812 40.000 16.73 0.00 45.30 3.53
1400 1696 1.003233 AGGAAGCTACCGTTCCAAAGG 59.997 52.381 4.25 0.00 45.30 3.11
1531 1832 8.876790 TGAACTACATACGGATGTATATAGACG 58.123 37.037 20.64 9.79 45.42 4.18
1846 2149 1.153168 GGAGGCAGCCGAAGCATAA 60.153 57.895 5.55 0.00 43.56 1.90
2196 2500 1.317613 TTGATTGGGTGTCACAGTGC 58.682 50.000 5.12 0.00 0.00 4.40
2200 2504 2.032681 GGGTGTCACAGTGCCTCC 59.967 66.667 5.12 0.00 0.00 4.30
2202 2506 2.357517 GTGTCACAGTGCCTCCCG 60.358 66.667 0.00 0.00 0.00 5.14
2203 2507 2.842462 TGTCACAGTGCCTCCCGT 60.842 61.111 0.00 0.00 0.00 5.28
2236 2540 3.181524 CGAGCCTATTTTTCGCGAAAAGA 60.182 43.478 36.58 28.83 40.35 2.52
2237 2541 4.668177 CGAGCCTATTTTTCGCGAAAAGAA 60.668 41.667 36.58 27.63 40.35 2.52
2267 2571 3.045492 CGTTGTACGTGGGGCACC 61.045 66.667 0.00 0.00 42.62 5.01
2269 2573 2.157305 CGTTGTACGTGGGGCACCTA 62.157 60.000 6.53 0.00 42.84 3.08
2324 2628 2.945668 GCCTGGGTATGCTTCTTAACAG 59.054 50.000 0.00 0.00 0.00 3.16
2328 2632 4.585879 TGGGTATGCTTCTTAACAGTTCC 58.414 43.478 0.00 0.00 0.00 3.62
2343 2648 3.821841 CAGTTCCGCCACTGTTTTTATC 58.178 45.455 4.46 0.00 39.59 1.75
2370 2675 7.699709 TGGGGTATTTCTACATGAAGGAATA 57.300 36.000 0.00 0.00 35.89 1.75
2395 2700 6.575162 ACATGACTACTTTGATCCCAAAAC 57.425 37.500 0.00 0.00 41.28 2.43
2442 2747 3.746045 TCTTCTTTTGTGAGTACGCCT 57.254 42.857 0.00 0.00 0.00 5.52
2493 2798 5.476752 GCTATAGCAAACCAGAGTCAAAG 57.523 43.478 20.01 0.00 41.59 2.77
2494 2799 4.201861 GCTATAGCAAACCAGAGTCAAAGC 60.202 45.833 20.01 0.00 41.59 3.51
2496 2801 2.590821 AGCAAACCAGAGTCAAAGCAT 58.409 42.857 0.00 0.00 0.00 3.79
2498 2803 4.338879 AGCAAACCAGAGTCAAAGCATAT 58.661 39.130 0.00 0.00 0.00 1.78
2500 2805 6.125029 AGCAAACCAGAGTCAAAGCATATAT 58.875 36.000 0.00 0.00 0.00 0.86
2501 2806 6.261826 AGCAAACCAGAGTCAAAGCATATATC 59.738 38.462 0.00 0.00 0.00 1.63
2502 2807 6.038603 GCAAACCAGAGTCAAAGCATATATCA 59.961 38.462 0.00 0.00 0.00 2.15
2503 2808 7.255381 GCAAACCAGAGTCAAAGCATATATCAT 60.255 37.037 0.00 0.00 0.00 2.45
2504 2809 8.627403 CAAACCAGAGTCAAAGCATATATCATT 58.373 33.333 0.00 0.00 0.00 2.57
2505 2810 8.757982 AACCAGAGTCAAAGCATATATCATTT 57.242 30.769 0.00 0.00 0.00 2.32
2506 2811 8.757982 ACCAGAGTCAAAGCATATATCATTTT 57.242 30.769 0.00 0.00 0.00 1.82
2507 2812 9.193806 ACCAGAGTCAAAGCATATATCATTTTT 57.806 29.630 0.00 0.00 0.00 1.94
2527 2832 2.728690 TTTTCATTTGCTGCAGCGAT 57.271 40.000 32.11 24.79 45.83 4.58
2556 2861 4.281941 TCCCATTATGATCTCGAAGGACTG 59.718 45.833 0.00 0.00 0.00 3.51
2572 2877 1.464997 GACTGCTCGTTGGATTTGACC 59.535 52.381 0.00 0.00 0.00 4.02
2612 2917 2.599281 TCGTCGGTGAGGGCTCAA 60.599 61.111 0.00 0.00 41.85 3.02
2624 2929 1.578206 GGGCTCAAACAAGGACTCGC 61.578 60.000 0.00 0.00 0.00 5.03
2647 2952 4.803426 GTGAGGCACCGGAGCGAG 62.803 72.222 17.93 0.00 34.64 5.03
2678 2989 4.982916 AGAAACTACTGCAGTCAACTTACG 59.017 41.667 25.56 5.33 36.04 3.18
2679 2990 3.299340 ACTACTGCAGTCAACTTACGG 57.701 47.619 25.56 5.98 28.33 4.02
2692 3003 3.891056 ACTTACGGAAAAAGGCTTTCG 57.109 42.857 13.76 14.73 0.00 3.46
2729 3040 0.251354 AGCAATGATCGACAGCACCT 59.749 50.000 0.00 0.00 0.00 4.00
2732 3043 1.662629 CAATGATCGACAGCACCTGAC 59.337 52.381 0.00 0.00 35.18 3.51
2757 3068 1.727467 GCACACCCTCACAACACAC 59.273 57.895 0.00 0.00 0.00 3.82
2758 3069 1.029408 GCACACCCTCACAACACACA 61.029 55.000 0.00 0.00 0.00 3.72
2774 3085 2.112198 ACACACACACGCACCCAAG 61.112 57.895 0.00 0.00 0.00 3.61
2776 3087 3.286751 CACACACGCACCCAAGGG 61.287 66.667 2.91 2.91 42.03 3.95
2779 3090 3.953775 ACACGCACCCAAGGGAGG 61.954 66.667 13.15 4.68 38.96 4.30
2790 3101 2.289694 CCCAAGGGAGGATACATAAGCG 60.290 54.545 0.00 0.00 41.41 4.68
2791 3102 2.417719 CAAGGGAGGATACATAAGCGC 58.582 52.381 0.00 0.00 41.41 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.294659 GCCTGAGGTCTGAACAAGCG 61.295 60.000 0.00 0.00 0.00 4.68
48 49 4.829492 GCCATATATGTTTGCTTCTTCCCT 59.171 41.667 11.73 0.00 0.00 4.20
121 122 6.954944 TCCAGAATAATGCGTAATTAAGCAC 58.045 36.000 25.13 13.79 46.83 4.40
157 158 9.232882 TGGTTTTCCTAAATCCTAGTGGTATAT 57.767 33.333 0.00 0.00 41.38 0.86
158 159 8.488668 GTGGTTTTCCTAAATCCTAGTGGTATA 58.511 37.037 0.00 0.00 41.38 1.47
159 160 7.344134 GTGGTTTTCCTAAATCCTAGTGGTAT 58.656 38.462 0.00 0.00 41.38 2.73
161 162 5.567430 GTGGTTTTCCTAAATCCTAGTGGT 58.433 41.667 0.00 0.00 41.38 4.16
162 163 4.634443 CGTGGTTTTCCTAAATCCTAGTGG 59.366 45.833 0.00 0.00 41.38 4.00
233 234 3.186909 TCGATGTTGACACGGATTGATC 58.813 45.455 0.00 0.00 0.00 2.92
248 249 1.653115 GTACGGCTCGGATCGATGT 59.347 57.895 0.54 0.00 34.61 3.06
310 311 9.982651 AGTAGATTAGATTCTTAATTTGCGCTA 57.017 29.630 9.73 0.00 0.00 4.26
311 312 8.894768 AGTAGATTAGATTCTTAATTTGCGCT 57.105 30.769 9.73 0.00 0.00 5.92
312 313 8.224437 GGAGTAGATTAGATTCTTAATTTGCGC 58.776 37.037 0.00 0.00 0.00 6.09
324 325 9.810870 AACCGACTTATAGGAGTAGATTAGATT 57.189 33.333 0.00 0.00 0.00 2.40
331 332 5.028549 ACGAACCGACTTATAGGAGTAGA 57.971 43.478 0.00 0.00 0.00 2.59
334 335 3.557595 CGTACGAACCGACTTATAGGAGT 59.442 47.826 10.44 0.00 0.00 3.85
335 336 3.557595 ACGTACGAACCGACTTATAGGAG 59.442 47.826 24.41 0.00 0.00 3.69
336 337 3.309682 CACGTACGAACCGACTTATAGGA 59.690 47.826 24.41 0.00 0.00 2.94
337 338 3.611517 CACGTACGAACCGACTTATAGG 58.388 50.000 24.41 0.00 0.00 2.57
338 339 3.031812 GCACGTACGAACCGACTTATAG 58.968 50.000 24.41 0.00 0.00 1.31
339 340 2.223249 GGCACGTACGAACCGACTTATA 60.223 50.000 24.41 0.00 0.00 0.98
340 341 1.468054 GGCACGTACGAACCGACTTAT 60.468 52.381 24.41 0.00 0.00 1.73
341 342 0.109781 GGCACGTACGAACCGACTTA 60.110 55.000 24.41 0.00 0.00 2.24
377 382 1.420514 GAGAGGGGGCAGGGTATTTAC 59.579 57.143 0.00 0.00 0.00 2.01
424 432 2.028130 ACTAGTTGATCGAGGGCTGAG 58.972 52.381 0.00 0.00 0.00 3.35
504 609 5.178809 AGAACACTTGAAACGGCTTACATAC 59.821 40.000 0.00 0.00 0.00 2.39
505 610 5.302360 AGAACACTTGAAACGGCTTACATA 58.698 37.500 0.00 0.00 0.00 2.29
506 611 4.134563 AGAACACTTGAAACGGCTTACAT 58.865 39.130 0.00 0.00 0.00 2.29
507 612 3.537580 AGAACACTTGAAACGGCTTACA 58.462 40.909 0.00 0.00 0.00 2.41
546 651 7.478322 TCAAGAAATACTAAGGCTACAGTACG 58.522 38.462 10.19 0.00 30.36 3.67
551 656 6.889198 AGCATCAAGAAATACTAAGGCTACA 58.111 36.000 0.00 0.00 0.00 2.74
642 794 7.724305 AAACAAGGTTGTGTAGTAGTATGTG 57.276 36.000 0.00 0.00 41.31 3.21
647 799 6.317893 CAGGAAAAACAAGGTTGTGTAGTAGT 59.682 38.462 0.00 0.00 41.31 2.73
649 801 5.591067 CCAGGAAAAACAAGGTTGTGTAGTA 59.409 40.000 0.00 0.00 41.31 1.82
650 802 4.401202 CCAGGAAAAACAAGGTTGTGTAGT 59.599 41.667 0.00 0.00 41.31 2.73
651 803 4.736464 GCCAGGAAAAACAAGGTTGTGTAG 60.736 45.833 0.00 0.00 41.31 2.74
656 808 3.552890 GCTAGCCAGGAAAAACAAGGTTG 60.553 47.826 2.29 0.00 0.00 3.77
702 854 7.136822 TCACATAATAACCCAGCTAGTTCAT 57.863 36.000 4.66 0.00 0.00 2.57
717 869 9.601810 AGTATAGGTCCAAGTGATCACATAATA 57.398 33.333 27.02 10.71 0.00 0.98
786 938 8.905850 TGTGATACATGCATGTCTGAAAAATAT 58.094 29.630 34.54 19.20 41.97 1.28
853 1009 4.818546 CCTCTCGAAAGCCATGTATTTGAT 59.181 41.667 0.00 0.00 0.00 2.57
861 1017 0.807667 CCGTCCTCTCGAAAGCCATG 60.808 60.000 0.00 0.00 0.00 3.66
876 1032 5.344933 GGCTAAAAATTGTGATTTGACCGTC 59.655 40.000 0.00 0.00 35.69 4.79
901 1057 5.065988 TGAAACAAAAGCAACTACTCACTCC 59.934 40.000 0.00 0.00 0.00 3.85
1024 1181 1.756408 TTTCCGCCGGTGGACTTACA 61.756 55.000 36.16 18.94 37.89 2.41
1079 1236 2.007608 GTCGGAGCCAAAGGTGTAATC 58.992 52.381 0.00 0.00 0.00 1.75
1214 1510 1.293498 GCGAGGCTTCTTCACTCCA 59.707 57.895 0.00 0.00 0.00 3.86
1311 1607 5.764686 TGAAGCACAAGAGTATGAAACACAT 59.235 36.000 0.00 0.00 42.39 3.21
1333 1629 9.108284 TCTGATATTTGCGAATTTCACTATTGA 57.892 29.630 13.91 8.23 32.28 2.57
1335 1631 9.941664 CTTCTGATATTTGCGAATTTCACTATT 57.058 29.630 13.91 0.00 32.28 1.73
1397 1693 1.615384 GCAATCTCCCTGACAAGCCTT 60.615 52.381 0.00 0.00 0.00 4.35
1400 1696 1.034292 GGGCAATCTCCCTGACAAGC 61.034 60.000 0.00 0.00 43.13 4.01
1613 1914 5.816955 ATCTGAAATAAGCCTACTCCCTC 57.183 43.478 0.00 0.00 0.00 4.30
1615 1916 5.243283 TCGTATCTGAAATAAGCCTACTCCC 59.757 44.000 0.00 0.00 0.00 4.30
1745 2048 9.632638 AGAAGCCAAAGAAAATAGATATAAGCA 57.367 29.630 0.00 0.00 0.00 3.91
1846 2149 3.222603 GTCTTCAAACAGTCCCACCAAT 58.777 45.455 0.00 0.00 0.00 3.16
1885 2188 0.320050 TGGTCACACGCTTAGCATGA 59.680 50.000 7.44 2.89 0.00 3.07
2118 2421 6.686130 ACAGTAAAGAATTTAGACGTGACG 57.314 37.500 2.24 2.24 41.97 4.35
2182 2486 2.818169 GGAGGCACTGTGACACCCA 61.818 63.158 18.20 0.00 41.55 4.51
2196 2500 1.592223 GTTCCAGTGAGACGGGAGG 59.408 63.158 0.00 0.00 43.14 4.30
2200 2504 1.444553 GCTCGTTCCAGTGAGACGG 60.445 63.158 15.15 9.14 37.39 4.79
2202 2506 1.174783 TAGGCTCGTTCCAGTGAGAC 58.825 55.000 0.00 0.00 40.72 3.36
2203 2507 2.145397 ATAGGCTCGTTCCAGTGAGA 57.855 50.000 0.00 0.00 34.04 3.27
2315 2619 2.489971 CAGTGGCGGAACTGTTAAGAA 58.510 47.619 0.00 0.00 42.21 2.52
2324 2628 2.817844 AGGATAAAAACAGTGGCGGAAC 59.182 45.455 0.00 0.00 0.00 3.62
2328 2632 2.094752 CCCAAGGATAAAAACAGTGGCG 60.095 50.000 0.00 0.00 0.00 5.69
2343 2648 5.104109 TCCTTCATGTAGAAATACCCCAAGG 60.104 44.000 0.12 0.00 35.40 3.61
2370 2675 8.109634 AGTTTTGGGATCAAAGTAGTCATGTAT 58.890 33.333 0.00 0.00 42.93 2.29
2507 2812 2.505628 TCGCTGCAGCAAATGAAAAA 57.494 40.000 36.03 8.35 42.21 1.94
2508 2813 2.030096 TCATCGCTGCAGCAAATGAAAA 60.030 40.909 34.38 21.35 38.84 2.29
2509 2814 1.540707 TCATCGCTGCAGCAAATGAAA 59.459 42.857 34.38 21.88 38.84 2.69
2510 2815 1.166989 TCATCGCTGCAGCAAATGAA 58.833 45.000 34.38 23.84 38.84 2.57
2527 2832 5.869649 TCGAGATCATAATGGGAAGTTCA 57.130 39.130 5.01 0.00 0.00 3.18
2556 2861 1.136057 GTTCGGTCAAATCCAACGAGC 60.136 52.381 0.00 0.00 34.85 5.03
2572 2877 2.144680 GTCGTCTCGCTTCGGTTCG 61.145 63.158 0.00 0.00 0.00 3.95
2612 2917 2.657237 CTCCGGCGAGTCCTTGTT 59.343 61.111 9.30 0.00 0.00 2.83
2649 2954 1.903183 ACTGCAGTAGTTTCTCTCCCC 59.097 52.381 20.16 0.00 35.67 4.81
2651 2956 3.944055 TGACTGCAGTAGTTTCTCTCC 57.056 47.619 21.73 3.44 40.53 3.71
2653 2958 4.946478 AGTTGACTGCAGTAGTTTCTCT 57.054 40.909 21.73 8.62 40.53 3.10
2655 2960 4.982916 CGTAAGTTGACTGCAGTAGTTTCT 59.017 41.667 21.73 11.07 40.53 2.52
2657 2962 4.056050 CCGTAAGTTGACTGCAGTAGTTT 58.944 43.478 21.73 14.01 40.53 2.66
2658 2963 3.319972 TCCGTAAGTTGACTGCAGTAGTT 59.680 43.478 21.73 16.44 40.53 2.24
2712 3023 1.662629 GTCAGGTGCTGTCGATCATTG 59.337 52.381 0.00 0.00 32.61 2.82
2724 3035 3.279116 TGCGCTTGTGTCAGGTGC 61.279 61.111 9.73 9.76 45.06 5.01
2729 3040 2.899838 GGGTGTGCGCTTGTGTCA 60.900 61.111 9.73 0.00 0.00 3.58
2732 3043 2.591429 TGAGGGTGTGCGCTTGTG 60.591 61.111 9.73 0.00 38.06 3.33
2757 3068 2.715005 CTTGGGTGCGTGTGTGTG 59.285 61.111 0.00 0.00 0.00 3.82
2758 3069 2.515991 CCTTGGGTGCGTGTGTGT 60.516 61.111 0.00 0.00 0.00 3.72
2774 3085 1.618837 TCAGCGCTTATGTATCCTCCC 59.381 52.381 7.50 0.00 0.00 4.30
2776 3087 2.333014 GCTCAGCGCTTATGTATCCTC 58.667 52.381 7.50 0.00 35.14 3.71
2791 3102 2.545596 TTGGTGTTGCTGCGCTCAG 61.546 57.895 9.73 0.00 43.16 3.35
2797 3108 1.067916 CTTGGGTTGGTGTTGCTGC 59.932 57.895 0.00 0.00 0.00 5.25
2803 3114 0.548989 TGTAGTGCTTGGGTTGGTGT 59.451 50.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.