Multiple sequence alignment - TraesCS6A01G170200

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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 TraesCS6A01G170200 chr6A 100.000 2628 0 0 540 3167 180598946 180601573 0.000000e+00 4854.0
1 TraesCS6A01G170200 chr6A 100.000 374 0 0 1 374 180598407 180598780 0.000000e+00 691.0
2 TraesCS6A01G170200 chr6A 86.957 69 5 4 3080 3145 270711429 270711496 1.220000e-09 75.0
3 TraesCS6A01G170200 chr6B 92.677 1543 65 16 784 2311 237359913 237361422 0.000000e+00 2180.0
4 TraesCS6A01G170200 chr6B 88.564 376 41 2 1 374 237357814 237358189 3.720000e-124 455.0
5 TraesCS6A01G170200 chr6B 93.401 197 13 0 580 776 237358255 237358451 3.090000e-75 292.0
6 TraesCS6A01G170200 chr6D 88.847 1336 63 31 789 2065 137786529 137787837 0.000000e+00 1563.0
7 TraesCS6A01G170200 chr6D 88.830 376 30 5 1 374 137784867 137785232 4.820000e-123 451.0
8 TraesCS6A01G170200 chr6D 96.000 225 9 0 549 773 137785496 137785720 1.790000e-97 366.0
9 TraesCS6A01G170200 chr4A 93.985 665 19 6 2341 3001 571127077 571126430 0.000000e+00 987.0
10 TraesCS6A01G170200 chr4A 95.597 159 7 0 3009 3167 571125865 571125707 4.050000e-64 255.0
11 TraesCS6A01G170200 chr4A 87.143 70 9 0 2343 2412 683639965 683639896 2.620000e-11 80.5
12 TraesCS6A01G170200 chr4D 93.722 446 19 6 2560 3001 494603837 494604277 0.000000e+00 660.0
13 TraesCS6A01G170200 chr4D 93.711 159 9 1 3009 3167 494604455 494604612 1.470000e-58 237.0
14 TraesCS6A01G170200 chr3D 89.336 422 17 14 2418 2830 84668980 84668578 3.650000e-139 505.0
15 TraesCS6A01G170200 chr3D 93.711 159 9 1 3009 3167 84668142 84667985 1.470000e-58 237.0
16 TraesCS6A01G170200 chr3D 88.889 45 5 0 3081 3125 84650475 84650431 4.410000e-04 56.5
17 TraesCS6A01G170200 chr7B 77.733 247 43 9 1198 1441 531222276 531222039 1.180000e-29 141.0
18 TraesCS6A01G170200 chr7B 76.953 256 49 7 1188 1441 530869986 530870233 1.530000e-28 137.0
19 TraesCS6A01G170200 chr7D 77.344 256 44 12 1198 1449 501777787 501777542 4.260000e-29 139.0
20 TraesCS6A01G170200 chr7D 93.103 58 4 0 2341 2398 638400653 638400710 5.630000e-13 86.1
21 TraesCS6A01G170200 chr7D 84.615 78 9 2 2360 2436 167577355 167577280 1.220000e-09 75.0
22 TraesCS6A01G170200 chr7D 97.222 36 1 0 3081 3116 550469907 550469872 9.490000e-06 62.1
23 TraesCS6A01G170200 chr5A 88.571 70 8 0 2343 2412 315789732 315789801 5.630000e-13 86.1
24 TraesCS6A01G170200 chr5A 89.062 64 7 0 2335 2398 649783044 649783107 2.620000e-11 80.5
25 TraesCS6A01G170200 chr1D 92.982 57 4 0 2342 2398 320584958 320585014 2.020000e-12 84.2
26 TraesCS6A01G170200 chr1D 95.652 46 2 0 3083 3128 467443603 467443648 1.220000e-09 75.0
27 TraesCS6A01G170200 chr4B 87.324 71 6 3 2338 2406 104813112 104813043 9.420000e-11 78.7
28 TraesCS6A01G170200 chr3A 81.818 99 13 4 2341 2436 691372305 691372401 9.420000e-11 78.7
29 TraesCS6A01G170200 chr1B 100.000 38 0 0 3081 3118 11642578 11642541 1.580000e-08 71.3
30 TraesCS6A01G170200 chr5D 95.349 43 2 0 3080 3122 462036312 462036270 5.670000e-08 69.4


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 TraesCS6A01G170200 chr6A 180598407 180601573 3166 False 2772.500000 4854 100.000000 1 3167 2 chr6A.!!$F2 3166
1 TraesCS6A01G170200 chr6B 237357814 237361422 3608 False 975.666667 2180 91.547333 1 2311 3 chr6B.!!$F1 2310
2 TraesCS6A01G170200 chr6D 137784867 137787837 2970 False 793.333333 1563 91.225667 1 2065 3 chr6D.!!$F1 2064
3 TraesCS6A01G170200 chr4A 571125707 571127077 1370 True 621.000000 987 94.791000 2341 3167 2 chr4A.!!$R2 826
4 TraesCS6A01G170200 chr4D 494603837 494604612 775 False 448.500000 660 93.716500 2560 3167 2 chr4D.!!$F1 607
5 TraesCS6A01G170200 chr3D 84667985 84668980 995 True 371.000000 505 91.523500 2418 3167 2 chr3D.!!$R2 749

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
840 2914 0.103937 GATCAACTCCTCCGCCTCTG 59.896 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 4471 0.984995 GGCCTGAACAGACCCTTACT 59.015 55.0 0.0 0.0 0.0 2.24 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
54 55 4.942481 AACTCGTCAGCGCGCACA 62.942 61.111 35.10 16.71 38.14 4.57
65 66 0.907171 GCGCGCACACATGATAAAAC 59.093 50.000 29.10 0.00 0.00 2.43
82 84 3.655615 AAACTGTAACCTTGTCACCCA 57.344 42.857 0.00 0.00 0.00 4.51
95 97 1.561542 GTCACCCAGGGAGATGACAAT 59.438 52.381 14.54 0.00 40.95 2.71
99 101 5.071788 GTCACCCAGGGAGATGACAATAATA 59.928 44.000 14.54 0.00 40.95 0.98
102 104 7.038302 TCACCCAGGGAGATGACAATAATATAC 60.038 40.741 14.54 0.00 0.00 1.47
131 133 1.991813 TCCATCAACTTCATCCCACCA 59.008 47.619 0.00 0.00 0.00 4.17
141 143 3.805066 TCATCCCACCAGACAAATTCA 57.195 42.857 0.00 0.00 0.00 2.57
148 150 2.297033 CACCAGACAAATTCAAGGTGGG 59.703 50.000 0.00 0.00 43.72 4.61
201 203 0.604578 AATGCCATTTGTTGAGCGCT 59.395 45.000 11.27 11.27 0.00 5.92
267 269 6.536941 GGTTCAGAGCACCATTAAAACAAAAA 59.463 34.615 0.00 0.00 34.04 1.94
278 281 0.537653 AAACAAAAACGGTGTGGGGG 59.462 50.000 0.00 0.00 0.00 5.40
297 300 3.711190 GGGGGACTTTATTCCATGCAAAT 59.289 43.478 0.00 0.00 37.40 2.32
298 301 4.164030 GGGGGACTTTATTCCATGCAAATT 59.836 41.667 0.00 0.00 37.40 1.82
319 322 2.819595 CCACCATTGTCTCGCCGG 60.820 66.667 0.00 0.00 0.00 6.13
333 336 1.523711 GCCGGCATCGATCAAAGGA 60.524 57.895 24.80 0.00 39.00 3.36
360 363 5.590818 TCCTTAGCTATTCCTACCCCTATG 58.409 45.833 0.00 0.00 0.00 2.23
587 680 2.674852 GACGAGAAGATTGAAGCATGCA 59.325 45.455 21.98 0.00 0.00 3.96
678 771 4.161565 ACGCCTCTCAGGTATCATTTGTAA 59.838 41.667 0.00 0.00 37.80 2.41
683 776 4.565166 TCTCAGGTATCATTTGTAAACGCG 59.435 41.667 3.53 3.53 0.00 6.01
754 847 4.079253 TCTTGCACCAACTTTATTCTCCC 58.921 43.478 0.00 0.00 0.00 4.30
787 2846 7.710044 TGAAACTTTGCAAAATTAAGATCAGCA 59.290 29.630 13.84 1.22 0.00 4.41
820 2894 1.172180 AAACCATGCCACAGTCCACG 61.172 55.000 0.00 0.00 0.00 4.94
824 2898 1.091771 CATGCCACAGTCCACGGATC 61.092 60.000 0.00 0.00 0.00 3.36
840 2914 0.103937 GATCAACTCCTCCGCCTCTG 59.896 60.000 0.00 0.00 0.00 3.35
996 3080 2.445654 CTCCCAGCCTCCCTCTCC 60.446 72.222 0.00 0.00 0.00 3.71
1014 3099 1.413445 TCCCCCGTATAAATCACCACG 59.587 52.381 0.00 0.00 0.00 4.94
1057 3142 0.833287 ACCTCCATTGATCCTCGGTG 59.167 55.000 0.00 0.00 0.00 4.94
1058 3143 0.533755 CCTCCATTGATCCTCGGTGC 60.534 60.000 0.00 0.00 0.00 5.01
1059 3144 0.178767 CTCCATTGATCCTCGGTGCA 59.821 55.000 0.00 0.00 0.00 4.57
1091 3176 2.005995 CACACCACACAGACACACG 58.994 57.895 0.00 0.00 0.00 4.49
1092 3177 0.459411 CACACCACACAGACACACGA 60.459 55.000 0.00 0.00 0.00 4.35
1093 3178 0.179111 ACACCACACAGACACACGAG 60.179 55.000 0.00 0.00 0.00 4.18
1105 3190 4.000557 CACGAGCACACCACACGC 62.001 66.667 0.00 0.00 0.00 5.34
1108 3193 3.349006 GAGCACACCACACGCCAG 61.349 66.667 0.00 0.00 0.00 4.85
1132 3217 1.442526 GACCATGAGGAATGCGGCAG 61.443 60.000 9.25 0.00 38.69 4.85
1392 3477 2.436109 GTGGTGGTGGTGATGGCT 59.564 61.111 0.00 0.00 0.00 4.75
1554 3641 5.449304 CAGATCGACGCCGCAATATATATA 58.551 41.667 0.00 0.00 35.37 0.86
1558 3645 4.973663 TCGACGCCGCAATATATATATGTG 59.026 41.667 6.00 7.89 35.37 3.21
1559 3646 4.738252 CGACGCCGCAATATATATATGTGT 59.262 41.667 6.00 6.39 0.00 3.72
1648 3735 9.627123 TTACATCATTTTCCTCCCTAATTACTG 57.373 33.333 0.00 0.00 0.00 2.74
1649 3736 7.062957 ACATCATTTTCCTCCCTAATTACTGG 58.937 38.462 0.00 0.00 0.00 4.00
1776 3872 5.404466 TTTGGTTGCATAAGATTTCCTGG 57.596 39.130 0.00 0.00 0.00 4.45
1833 3946 3.061429 GCTTTTAGCTAGTTCTGCTGACG 59.939 47.826 0.00 0.00 41.32 4.35
1846 3959 1.675483 TGCTGACGTTTGCTTTGATGT 59.325 42.857 13.40 0.00 0.00 3.06
1863 3976 5.164620 TGATGTGACTTGCTATTTCCTGA 57.835 39.130 0.00 0.00 0.00 3.86
1866 3979 5.164620 TGTGACTTGCTATTTCCTGATCA 57.835 39.130 0.00 0.00 0.00 2.92
1976 4109 7.166473 GCAAGAACCGATTTGCAGATATTTAAG 59.834 37.037 4.48 0.00 46.72 1.85
2061 4194 5.653769 AGTTTTGGATGTACATCTTCCCATG 59.346 40.000 29.87 0.00 38.96 3.66
2096 4229 6.753107 TTTCGGGGAACATCTTCTTAATTC 57.247 37.500 0.00 0.00 0.00 2.17
2105 4238 8.462811 GGAACATCTTCTTAATTCTCCCTTTTC 58.537 37.037 0.00 0.00 0.00 2.29
2140 4273 9.989296 TCTTCCCAATTTTCATTAGATAAGGAA 57.011 29.630 0.00 0.00 34.62 3.36
2175 4308 9.706529 AGGATCATCCTTTTCTAAATAAAAGCT 57.293 29.630 0.00 0.00 46.91 3.74
2198 4331 5.687166 TCCCAGTGGAATTAGAAATACGT 57.313 39.130 11.95 0.00 37.86 3.57
2199 4332 6.057321 TCCCAGTGGAATTAGAAATACGTT 57.943 37.500 11.95 0.00 37.86 3.99
2200 4333 5.878116 TCCCAGTGGAATTAGAAATACGTTG 59.122 40.000 11.95 0.00 37.86 4.10
2236 4369 4.141620 ACACAGAGTGTTGATCCAGTTCTT 60.142 41.667 0.00 0.00 45.08 2.52
2238 4371 3.677121 CAGAGTGTTGATCCAGTTCTTCG 59.323 47.826 0.00 0.00 0.00 3.79
2249 4382 6.813649 TGATCCAGTTCTTCGAGAGTTAATTG 59.186 38.462 0.00 0.00 0.00 2.32
2280 4413 4.970003 CCTGTACTTCAAAAGCTTTGTTCG 59.030 41.667 13.54 4.96 0.00 3.95
2304 4437 1.275573 GATGGCGGTTCTACCTATCCC 59.724 57.143 0.00 0.00 35.66 3.85
2305 4438 0.031917 TGGCGGTTCTACCTATCCCA 60.032 55.000 0.00 0.00 35.66 4.37
2306 4439 1.349067 GGCGGTTCTACCTATCCCAT 58.651 55.000 0.00 0.00 35.66 4.00
2309 4442 1.623811 CGGTTCTACCTATCCCATGGG 59.376 57.143 26.30 26.30 35.66 4.00
2310 4443 2.758640 CGGTTCTACCTATCCCATGGGA 60.759 54.545 35.57 35.57 41.88 4.37
2311 4444 3.323775 GGTTCTACCTATCCCATGGGAA 58.676 50.000 36.90 23.32 40.73 3.97
2312 4445 3.328050 GGTTCTACCTATCCCATGGGAAG 59.672 52.174 36.90 29.62 40.73 3.46
2313 4446 4.944324 GGTTCTACCTATCCCATGGGAAGA 60.944 50.000 36.90 29.12 40.73 2.87
2314 4447 6.408034 GGTTCTACCTATCCCATGGGAAGAA 61.408 48.000 36.90 32.44 40.73 2.52
2315 4448 8.158084 GGTTCTACCTATCCCATGGGAAGAAG 62.158 50.000 36.90 29.48 40.73 2.85
2322 4455 3.531059 TCCCATGGGAAGAAGAAAGAGA 58.469 45.455 32.09 3.05 42.05 3.10
2323 4456 4.114597 TCCCATGGGAAGAAGAAAGAGAT 58.885 43.478 32.09 0.00 42.05 2.75
2324 4457 4.080129 TCCCATGGGAAGAAGAAAGAGATG 60.080 45.833 32.09 0.00 42.05 2.90
2325 4458 3.631227 CCATGGGAAGAAGAAAGAGATGC 59.369 47.826 2.85 0.00 0.00 3.91
2326 4459 3.356529 TGGGAAGAAGAAAGAGATGCC 57.643 47.619 0.00 0.00 0.00 4.40
2327 4460 2.644299 TGGGAAGAAGAAAGAGATGCCA 59.356 45.455 0.00 0.00 0.00 4.92
2328 4461 3.074390 TGGGAAGAAGAAAGAGATGCCAA 59.926 43.478 0.00 0.00 0.00 4.52
2329 4462 4.264083 TGGGAAGAAGAAAGAGATGCCAAT 60.264 41.667 0.00 0.00 0.00 3.16
2330 4463 4.337836 GGGAAGAAGAAAGAGATGCCAATC 59.662 45.833 0.00 0.00 0.00 2.67
2331 4464 4.946157 GGAAGAAGAAAGAGATGCCAATCA 59.054 41.667 0.00 0.00 35.03 2.57
2332 4465 5.416952 GGAAGAAGAAAGAGATGCCAATCAA 59.583 40.000 0.00 0.00 35.03 2.57
2333 4466 6.096564 GGAAGAAGAAAGAGATGCCAATCAAT 59.903 38.462 0.00 0.00 35.03 2.57
2334 4467 7.363617 GGAAGAAGAAAGAGATGCCAATCAATT 60.364 37.037 0.00 0.00 35.03 2.32
2335 4468 8.585471 AAGAAGAAAGAGATGCCAATCAATTA 57.415 30.769 0.00 0.00 35.03 1.40
2336 4469 8.763984 AGAAGAAAGAGATGCCAATCAATTAT 57.236 30.769 0.00 0.00 35.03 1.28
2337 4470 9.857656 AGAAGAAAGAGATGCCAATCAATTATA 57.142 29.630 0.00 0.00 35.03 0.98
2351 4484 9.408648 CCAATCAATTATAAGTAAGGGTCTGTT 57.591 33.333 0.00 0.00 0.00 3.16
2359 4492 1.066071 GTAAGGGTCTGTTCAGGCCTC 60.066 57.143 20.54 12.08 0.00 4.70
2376 4509 5.011431 CAGGCCTCATCTAGATGTGACATAA 59.989 44.000 28.25 11.01 39.72 1.90
2377 4510 5.011533 AGGCCTCATCTAGATGTGACATAAC 59.988 44.000 28.25 14.45 39.72 1.89
2444 4577 4.837860 TCATCACCTATTTGTGGCCTTTTT 59.162 37.500 3.32 0.00 36.87 1.94
2522 4655 3.459232 TGTAGCATCAGTGGTAGCATC 57.541 47.619 0.00 0.00 38.86 3.91
2648 4801 5.122711 ACGCAGTAGTACACTTTGTGTTTTT 59.877 36.000 8.67 0.00 41.82 1.94
2649 4802 5.675444 CGCAGTAGTACACTTTGTGTTTTTC 59.325 40.000 8.67 0.00 45.08 2.29
2650 4803 6.456449 CGCAGTAGTACACTTTGTGTTTTTCT 60.456 38.462 8.67 5.93 45.08 2.52
2651 4804 6.905609 GCAGTAGTACACTTTGTGTTTTTCTC 59.094 38.462 8.67 0.00 45.08 2.87
2652 4805 7.407337 CAGTAGTACACTTTGTGTTTTTCTCC 58.593 38.462 8.67 0.00 45.08 3.71
2653 4806 7.280205 CAGTAGTACACTTTGTGTTTTTCTCCT 59.720 37.037 8.67 0.00 45.08 3.69
2654 4807 7.827729 AGTAGTACACTTTGTGTTTTTCTCCTT 59.172 33.333 8.67 0.00 45.08 3.36
2655 4808 7.462571 AGTACACTTTGTGTTTTTCTCCTTT 57.537 32.000 8.67 0.00 45.08 3.11
2656 4809 7.892609 AGTACACTTTGTGTTTTTCTCCTTTT 58.107 30.769 8.67 0.00 45.08 2.27
2657 4810 7.812669 AGTACACTTTGTGTTTTTCTCCTTTTG 59.187 33.333 8.67 0.00 45.08 2.44
2658 4811 6.521162 ACACTTTGTGTTTTTCTCCTTTTGT 58.479 32.000 0.00 0.00 45.08 2.83
2659 4812 6.989759 ACACTTTGTGTTTTTCTCCTTTTGTT 59.010 30.769 0.00 0.00 45.08 2.83
2660 4813 7.497579 ACACTTTGTGTTTTTCTCCTTTTGTTT 59.502 29.630 0.00 0.00 45.08 2.83
2661 4814 8.341903 CACTTTGTGTTTTTCTCCTTTTGTTTT 58.658 29.630 0.00 0.00 0.00 2.43
2849 5142 9.645059 TTTCTTTTCAAATACACATTGAACACA 57.355 25.926 1.48 0.00 44.14 3.72
3038 5949 3.759418 TGTATTCAAGCTCTTCGACGAG 58.241 45.455 14.25 14.25 0.00 4.18
3129 6040 4.079253 CTGGGGCAACTACAATTACAAGT 58.921 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 7.040686 GGTGACAAGGTTACAGTTTTATCATGT 60.041 37.037 0.00 0.00 0.00 3.21
65 66 1.271379 CCCTGGGTGACAAGGTTACAG 60.271 57.143 3.97 0.00 0.00 2.74
82 84 8.190326 TCAACGTATATTATTGTCATCTCCCT 57.810 34.615 0.00 0.00 0.00 4.20
95 97 7.709269 GTTGATGGAGCTTCAACGTATATTA 57.291 36.000 12.67 0.00 42.35 0.98
131 133 2.105821 TCGACCCACCTTGAATTTGTCT 59.894 45.455 0.00 0.00 0.00 3.41
170 172 2.025156 GGCATTGCTTCATCGCCG 59.975 61.111 8.82 0.00 32.14 6.46
247 249 5.047188 CCGTTTTTGTTTTAATGGTGCTCT 58.953 37.500 0.00 0.00 0.00 4.09
248 250 4.806775 ACCGTTTTTGTTTTAATGGTGCTC 59.193 37.500 0.00 0.00 41.04 4.26
278 281 5.723492 GCAATTTGCATGGAATAAAGTCC 57.277 39.130 16.35 0.00 44.26 3.85
297 300 0.955428 GCGAGACAATGGTGGAGCAA 60.955 55.000 0.00 0.00 0.00 3.91
298 301 1.375908 GCGAGACAATGGTGGAGCA 60.376 57.895 0.00 0.00 0.00 4.26
319 322 4.907879 AGGATTTTCCTTTGATCGATGC 57.092 40.909 0.54 0.00 46.91 3.91
333 336 5.917682 AGGGGTAGGAATAGCTAAGGATTTT 59.082 40.000 0.00 0.00 0.00 1.82
542 545 3.470567 GACCAGAGCGAACGCACG 61.471 66.667 20.66 10.65 44.88 5.34
543 546 2.049063 AGACCAGAGCGAACGCAC 60.049 61.111 20.66 14.57 44.88 5.34
544 547 2.258591 GAGACCAGAGCGAACGCA 59.741 61.111 20.66 0.00 44.88 5.24
545 548 2.876645 CGAGACCAGAGCGAACGC 60.877 66.667 11.31 11.31 42.33 4.84
546 549 2.876645 GCGAGACCAGAGCGAACG 60.877 66.667 0.00 0.00 0.00 3.95
547 550 1.347817 CTTGCGAGACCAGAGCGAAC 61.348 60.000 0.00 0.00 0.00 3.95
678 771 2.695359 AGATTGGTGATGTTACGCGTT 58.305 42.857 20.78 0.00 0.00 4.84
807 2881 1.763546 TTGATCCGTGGACTGTGGCA 61.764 55.000 0.00 0.00 0.00 4.92
824 2898 2.125350 GCAGAGGCGGAGGAGTTG 60.125 66.667 0.00 0.00 0.00 3.16
840 2914 4.862574 AGAAACTCAAAACGAAAAGTTGGC 59.137 37.500 0.00 0.00 43.37 4.52
996 3080 1.223187 GCGTGGTGATTTATACGGGG 58.777 55.000 0.00 0.00 37.06 5.73
1014 3099 1.883021 CGATGTTGGGGTTGAAGGC 59.117 57.895 0.00 0.00 0.00 4.35
1057 3142 2.662857 TGCTCGTGTGTCTGCTGC 60.663 61.111 0.00 0.00 0.00 5.25
1058 3143 1.592400 TGTGCTCGTGTGTCTGCTG 60.592 57.895 0.00 0.00 0.00 4.41
1059 3144 1.592669 GTGTGCTCGTGTGTCTGCT 60.593 57.895 0.00 0.00 0.00 4.24
1091 3176 3.349006 CTGGCGTGTGGTGTGCTC 61.349 66.667 0.00 0.00 0.00 4.26
1105 3190 0.325933 TTCCTCATGGTCTGTGCTGG 59.674 55.000 0.00 0.00 34.23 4.85
1108 3193 0.737219 GCATTCCTCATGGTCTGTGC 59.263 55.000 0.00 0.00 32.81 4.57
1132 3217 1.327292 CCGTTCATTTGCGCGTCAAC 61.327 55.000 8.43 0.02 33.73 3.18
1353 3438 2.607750 GGCACCTCCCTGTCCAGA 60.608 66.667 0.00 0.00 0.00 3.86
1443 3528 3.315142 CTGCACCTTAGCCGCCTCA 62.315 63.158 0.00 0.00 0.00 3.86
1452 3537 3.383681 TACGGGCGCTGCACCTTA 61.384 61.111 7.64 0.00 0.00 2.69
1532 3619 2.941453 ATATATTGCGGCGTCGATCT 57.059 45.000 16.53 0.00 39.00 2.75
1617 3704 9.628500 ATTAGGGAGGAAAATGATGTAAACTAC 57.372 33.333 0.00 0.00 0.00 2.73
1645 3732 2.949644 GTTGCACCAAAACTACTCCAGT 59.050 45.455 0.00 0.00 40.05 4.00
1646 3733 2.032030 CGTTGCACCAAAACTACTCCAG 60.032 50.000 0.00 0.00 0.00 3.86
1647 3734 1.944024 CGTTGCACCAAAACTACTCCA 59.056 47.619 0.00 0.00 0.00 3.86
1648 3735 2.215196 TCGTTGCACCAAAACTACTCC 58.785 47.619 0.00 0.00 0.00 3.85
1649 3736 3.810373 CATCGTTGCACCAAAACTACTC 58.190 45.455 0.00 0.00 0.00 2.59
1788 3884 7.107542 AGCCAAATCATGCTCACATTTAATTT 58.892 30.769 0.00 0.00 32.87 1.82
1789 3885 6.646267 AGCCAAATCATGCTCACATTTAATT 58.354 32.000 0.00 0.00 32.87 1.40
1790 3886 6.229936 AGCCAAATCATGCTCACATTTAAT 57.770 33.333 0.00 0.00 32.87 1.40
1833 3946 3.709987 AGCAAGTCACATCAAAGCAAAC 58.290 40.909 0.00 0.00 0.00 2.93
1846 3959 6.053650 CAGATGATCAGGAAATAGCAAGTCA 58.946 40.000 0.09 0.00 0.00 3.41
1863 3976 9.781425 ACTGGATATATCTTTAGGTCAGATGAT 57.219 33.333 12.42 0.00 32.94 2.45
1866 3979 9.253832 CTCACTGGATATATCTTTAGGTCAGAT 57.746 37.037 12.42 0.00 35.13 2.90
2096 4229 4.876679 GGAAGATACCTTTCGAAAAGGGAG 59.123 45.833 19.81 5.15 41.71 4.30
2105 4238 6.509418 TGAAAATTGGGAAGATACCTTTCG 57.491 37.500 0.00 0.00 31.62 3.46
2154 4287 8.531146 TGGGAAGCTTTTATTTAGAAAAGGATG 58.469 33.333 0.00 0.00 43.63 3.51
2155 4288 8.664669 TGGGAAGCTTTTATTTAGAAAAGGAT 57.335 30.769 0.00 0.00 43.63 3.24
2177 4310 5.646360 ACAACGTATTTCTAATTCCACTGGG 59.354 40.000 0.00 0.00 0.00 4.45
2192 4325 5.873164 GTGTCTCAAATAGGGACAACGTATT 59.127 40.000 0.00 0.00 40.86 1.89
2193 4326 5.046878 TGTGTCTCAAATAGGGACAACGTAT 60.047 40.000 0.00 0.00 40.86 3.06
2194 4327 4.281435 TGTGTCTCAAATAGGGACAACGTA 59.719 41.667 0.00 0.00 40.86 3.57
2195 4328 3.070446 TGTGTCTCAAATAGGGACAACGT 59.930 43.478 0.00 0.00 40.86 3.99
2196 4329 3.659786 TGTGTCTCAAATAGGGACAACG 58.340 45.455 0.00 0.00 40.86 4.10
2197 4330 4.894784 TCTGTGTCTCAAATAGGGACAAC 58.105 43.478 0.00 0.00 40.86 3.32
2198 4331 4.593206 ACTCTGTGTCTCAAATAGGGACAA 59.407 41.667 0.00 0.00 40.86 3.18
2199 4332 4.021104 CACTCTGTGTCTCAAATAGGGACA 60.021 45.833 0.00 0.00 37.60 4.02
2200 4333 4.021016 ACACTCTGTGTCTCAAATAGGGAC 60.021 45.833 0.00 0.00 43.92 4.46
2226 4359 6.936279 TCAATTAACTCTCGAAGAACTGGAT 58.064 36.000 2.28 0.00 34.09 3.41
2236 4369 7.837863 ACAGGAATAGTTCAATTAACTCTCGA 58.162 34.615 0.00 0.00 45.64 4.04
2249 4382 7.674471 AGCTTTTGAAGTACAGGAATAGTTC 57.326 36.000 0.00 0.00 35.76 3.01
2267 4400 2.035832 CCATCCACCGAACAAAGCTTTT 59.964 45.455 9.53 0.00 0.00 2.27
2280 4413 1.153229 GGTAGAACCGCCATCCACC 60.153 63.158 0.00 0.00 0.00 4.61
2304 4437 3.631227 GGCATCTCTTTCTTCTTCCCATG 59.369 47.826 0.00 0.00 0.00 3.66
2305 4438 3.267812 TGGCATCTCTTTCTTCTTCCCAT 59.732 43.478 0.00 0.00 0.00 4.00
2306 4439 2.644299 TGGCATCTCTTTCTTCTTCCCA 59.356 45.455 0.00 0.00 0.00 4.37
2309 4442 6.506500 TTGATTGGCATCTCTTTCTTCTTC 57.493 37.500 0.00 0.00 0.00 2.87
2310 4443 7.477945 AATTGATTGGCATCTCTTTCTTCTT 57.522 32.000 0.00 0.00 0.00 2.52
2311 4444 8.763984 ATAATTGATTGGCATCTCTTTCTTCT 57.236 30.769 0.00 0.00 0.00 2.85
2314 4447 9.638176 ACTTATAATTGATTGGCATCTCTTTCT 57.362 29.630 0.00 0.00 0.00 2.52
2318 4451 9.512588 CCTTACTTATAATTGATTGGCATCTCT 57.487 33.333 0.00 0.00 0.00 3.10
2319 4452 8.734386 CCCTTACTTATAATTGATTGGCATCTC 58.266 37.037 0.00 0.00 0.00 2.75
2320 4453 8.227507 ACCCTTACTTATAATTGATTGGCATCT 58.772 33.333 0.00 0.00 0.00 2.90
2321 4454 8.409358 ACCCTTACTTATAATTGATTGGCATC 57.591 34.615 0.00 0.00 0.00 3.91
2322 4455 8.227507 AGACCCTTACTTATAATTGATTGGCAT 58.772 33.333 0.00 0.00 0.00 4.40
2323 4456 7.502226 CAGACCCTTACTTATAATTGATTGGCA 59.498 37.037 0.00 0.00 0.00 4.92
2324 4457 7.502561 ACAGACCCTTACTTATAATTGATTGGC 59.497 37.037 0.00 0.00 0.00 4.52
2325 4458 8.980481 ACAGACCCTTACTTATAATTGATTGG 57.020 34.615 0.00 0.00 0.00 3.16
2328 4461 9.838339 CTGAACAGACCCTTACTTATAATTGAT 57.162 33.333 0.00 0.00 0.00 2.57
2329 4462 8.265055 CCTGAACAGACCCTTACTTATAATTGA 58.735 37.037 3.19 0.00 0.00 2.57
2330 4463 7.012421 GCCTGAACAGACCCTTACTTATAATTG 59.988 40.741 3.19 0.00 0.00 2.32
2331 4464 7.054751 GCCTGAACAGACCCTTACTTATAATT 58.945 38.462 3.19 0.00 0.00 1.40
2332 4465 6.409349 GGCCTGAACAGACCCTTACTTATAAT 60.409 42.308 0.00 0.00 0.00 1.28
2333 4466 5.104652 GGCCTGAACAGACCCTTACTTATAA 60.105 44.000 0.00 0.00 0.00 0.98
2334 4467 4.407945 GGCCTGAACAGACCCTTACTTATA 59.592 45.833 0.00 0.00 0.00 0.98
2335 4468 3.200165 GGCCTGAACAGACCCTTACTTAT 59.800 47.826 0.00 0.00 0.00 1.73
2336 4469 2.570302 GGCCTGAACAGACCCTTACTTA 59.430 50.000 0.00 0.00 0.00 2.24
2337 4470 1.351350 GGCCTGAACAGACCCTTACTT 59.649 52.381 0.00 0.00 0.00 2.24
2338 4471 0.984995 GGCCTGAACAGACCCTTACT 59.015 55.000 0.00 0.00 0.00 2.24
2339 4472 0.984995 AGGCCTGAACAGACCCTTAC 59.015 55.000 3.11 0.00 30.45 2.34
2351 4484 2.961741 GTCACATCTAGATGAGGCCTGA 59.038 50.000 34.16 24.09 41.20 3.86
2352 4485 2.697229 TGTCACATCTAGATGAGGCCTG 59.303 50.000 34.16 22.45 41.20 4.85
2502 4635 2.103094 GGATGCTACCACTGATGCTACA 59.897 50.000 0.00 0.00 0.00 2.74
2522 4655 3.431486 GGTCTCTCCTTAAGTCATGCTGG 60.431 52.174 0.97 0.00 0.00 4.85
2533 4666 2.656002 CACGATCTGGGTCTCTCCTTA 58.344 52.381 0.00 0.00 36.25 2.69
2588 4723 2.486982 GGAGGTAGCGATCGTATTAGCA 59.513 50.000 17.81 0.00 0.00 3.49
3007 5331 9.559958 CGAAGAGCTTGAATACATAAACATTTT 57.440 29.630 0.00 0.00 0.00 1.82
3038 5949 1.142474 GGCTGTCTTGTGCATTTTGC 58.858 50.000 0.00 0.00 45.29 3.68
3044 5955 0.534877 ATCAACGGCTGTCTTGTGCA 60.535 50.000 0.00 0.00 0.00 4.57
3054 5965 1.317613 TTGCTTGTGAATCAACGGCT 58.682 45.000 0.00 0.00 31.35 5.52
3129 6040 2.416836 CCTTAATCGACTCGCAACTGGA 60.417 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.