Multiple sequence alignment - TraesCS5B01G233100

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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 TraesCS5B01G233100 chr5B 100.000 2696 0 0 1 2696 411035075 411032380 0.000000e+00 4979.0
1 TraesCS5B01G233100 chr5B 94.776 134 6 1 18 150 411034914 411034781 9.780000e-50 207.0
2 TraesCS5B01G233100 chr5B 94.776 134 6 1 162 295 411035058 411034926 9.780000e-50 207.0
3 TraesCS5B01G233100 chr5B 93.204 103 3 4 207 307 411034769 411034869 6.010000e-32 148.0
4 TraesCS5B01G233100 chr5B 96.552 87 1 2 65 150 62940319 62940404 2.800000e-30 143.0
5 TraesCS5B01G233100 chr5D 96.764 1607 48 3 846 2449 350331169 350329564 0.000000e+00 2676.0
6 TraesCS5B01G233100 chr5D 94.382 623 17 3 162 782 350331801 350331195 0.000000e+00 941.0
7 TraesCS5B01G233100 chr5D 94.510 255 13 1 162 415 350332001 350331747 2.520000e-105 392.0
8 TraesCS5B01G233100 chr5D 97.585 207 4 1 2490 2696 350329572 350329367 1.190000e-93 353.0
9 TraesCS5B01G233100 chr5D 98.013 151 2 1 1 150 350332018 350331868 7.400000e-66 261.0
10 TraesCS5B01G233100 chr5D 96.512 86 2 1 66 150 128577584 128577669 1.010000e-29 141.0
11 TraesCS5B01G233100 chr5D 84.507 142 5 5 10 150 350331809 350331684 1.010000e-24 124.0
12 TraesCS5B01G233100 chr5A 96.879 865 27 0 846 1710 450750012 450749148 0.000000e+00 1448.0
13 TraesCS5B01G233100 chr5A 86.825 926 89 19 1750 2655 450749149 450748237 0.000000e+00 1003.0
14 TraesCS5B01G233100 chr5A 93.579 623 22 3 162 782 450750644 450750038 0.000000e+00 913.0
15 TraesCS5B01G233100 chr5A 95.294 255 11 1 162 415 450750844 450750590 1.160000e-108 403.0
16 TraesCS5B01G233100 chr5A 97.351 151 3 1 1 150 450750861 450750711 3.440000e-64 255.0
17 TraesCS5B01G233100 chr5A 84.507 142 5 5 10 150 450750652 450750527 1.010000e-24 124.0
18 TraesCS5B01G233100 chr7D 93.269 104 5 2 202 303 195626084 195626187 4.650000e-33 152.0
19 TraesCS5B01G233100 chr3A 93.939 99 5 1 207 305 57262242 57262145 6.010000e-32 148.0
20 TraesCS5B01G233100 chr3A 92.771 83 3 2 70 150 79380866 79380947 1.700000e-22 117.0
21 TraesCS5B01G233100 chr1B 93.137 102 4 3 197 298 169531158 169531060 2.160000e-31 147.0
22 TraesCS5B01G233100 chr1B 92.929 99 3 3 67 164 151363744 151363649 1.010000e-29 141.0
23 TraesCS5B01G233100 chr2D 94.505 91 4 1 67 156 589522340 589522250 3.620000e-29 139.0
24 TraesCS5B01G233100 chr3D 90.476 105 6 3 68 168 436676898 436677002 4.680000e-28 135.0
25 TraesCS5B01G233100 chr1D 91.000 100 5 3 66 164 58573626 58573722 6.060000e-27 132.0
26 TraesCS5B01G233100 chr1D 84.071 113 14 4 68 178 468550705 468550815 3.670000e-19 106.0
27 TraesCS5B01G233100 chr6A 86.667 105 12 2 66 169 499008433 499008536 6.100000e-22 115.0
28 TraesCS5B01G233100 chr4D 89.655 87 7 2 66 150 303079253 303079339 2.840000e-20 110.0
29 TraesCS5B01G233100 chr6B 81.553 103 15 3 69 170 12535599 12535698 6.190000e-12 82.4


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 TraesCS5B01G233100 chr5B 411032380 411035075 2695 True 1797.666667 4979 96.517333 1 2696 3 chr5B.!!$R1 2695
1 TraesCS5B01G233100 chr5D 350329367 350332018 2651 True 791.166667 2676 94.293500 1 2696 6 chr5D.!!$R1 2695
2 TraesCS5B01G233100 chr5A 450748237 450750861 2624 True 691.000000 1448 92.405833 1 2655 6 chr5A.!!$R1 2654

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
504 563 0.956633 CACAGCATCTTGTGTTGCCT 59.043 50.0 0.0 0.0 42.2 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2584 0.106419 TTCCTTGAAAACCGGTGCCT 60.106 50.0 8.52 0.0 0.0 4.75 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
149 150 8.380742 ACACTCTTATATTTCTTTCAGAGGGA 57.619 34.615 3.29 0.00 35.67 4.20
150 151 8.261522 ACACTCTTATATTTCTTTCAGAGGGAC 58.738 37.037 3.29 0.00 35.67 4.46
152 153 8.482128 ACTCTTATATTTCTTTCAGAGGGACTG 58.518 37.037 0.00 0.00 46.97 3.51
153 154 7.275920 TCTTATATTTCTTTCAGAGGGACTGC 58.724 38.462 0.00 0.00 45.38 4.40
154 155 5.707066 ATATTTCTTTCAGAGGGACTGCT 57.293 39.130 0.00 0.00 45.38 4.24
155 156 6.814954 ATATTTCTTTCAGAGGGACTGCTA 57.185 37.500 0.00 0.00 45.38 3.49
156 157 4.543590 TTTCTTTCAGAGGGACTGCTAG 57.456 45.455 0.00 0.00 45.38 3.42
157 158 3.458044 TCTTTCAGAGGGACTGCTAGA 57.542 47.619 0.00 0.00 45.38 2.43
159 160 3.511934 TCTTTCAGAGGGACTGCTAGAAC 59.488 47.826 0.00 0.00 45.38 3.01
193 250 9.311916 CTCCACTTCTTATAAGAGTTTGAGATG 57.688 37.037 14.63 9.66 36.22 2.90
224 281 6.491383 TCAAACTGTATAGTACTCCCTCTGT 58.509 40.000 0.00 0.00 35.69 3.41
225 282 7.636579 TCAAACTGTATAGTACTCCCTCTGTA 58.363 38.462 0.00 0.00 35.69 2.74
226 283 8.111545 TCAAACTGTATAGTACTCCCTCTGTAA 58.888 37.037 0.00 0.00 35.69 2.41
227 284 8.746530 CAAACTGTATAGTACTCCCTCTGTAAA 58.253 37.037 0.00 0.00 35.69 2.01
228 285 8.522542 AACTGTATAGTACTCCCTCTGTAAAG 57.477 38.462 0.00 0.00 35.69 1.85
229 286 7.870027 ACTGTATAGTACTCCCTCTGTAAAGA 58.130 38.462 0.00 0.00 34.74 2.52
230 287 8.334734 ACTGTATAGTACTCCCTCTGTAAAGAA 58.665 37.037 0.00 0.00 34.74 2.52
231 288 9.186837 CTGTATAGTACTCCCTCTGTAAAGAAA 57.813 37.037 0.00 0.00 0.00 2.52
232 289 9.710818 TGTATAGTACTCCCTCTGTAAAGAAAT 57.289 33.333 0.00 0.00 0.00 2.17
240 297 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
504 563 0.956633 CACAGCATCTTGTGTTGCCT 59.043 50.000 0.00 0.00 42.20 4.75
514 573 6.694411 GCATCTTGTGTTGCCTTTTCATATAG 59.306 38.462 0.00 0.00 33.94 1.31
566 625 3.139077 CGTGTAGGGAAAATATCAGGGC 58.861 50.000 0.00 0.00 0.00 5.19
571 630 6.019748 TGTAGGGAAAATATCAGGGCAAAAA 58.980 36.000 0.00 0.00 0.00 1.94
669 728 8.280084 TCAGACTGTATAGTTCCTTATACACCT 58.720 37.037 1.59 1.69 40.05 4.00
675 734 8.505246 TGTATAGTTCCTTATACACCTGTAGGA 58.495 37.037 4.64 0.00 40.05 2.94
732 791 9.643693 GTGACATCAACCATTTAATTTCTTCAT 57.356 29.630 0.00 0.00 0.00 2.57
779 838 9.886132 CATATATCAACCATCAATCAGATCTCA 57.114 33.333 0.00 0.00 33.72 3.27
782 841 6.303903 TCAACCATCAATCAGATCTCAAGA 57.696 37.500 0.00 0.00 33.72 3.02
783 842 6.346896 TCAACCATCAATCAGATCTCAAGAG 58.653 40.000 0.00 0.00 33.72 2.85
784 843 5.954153 ACCATCAATCAGATCTCAAGAGT 57.046 39.130 0.00 0.00 33.72 3.24
785 844 5.672503 ACCATCAATCAGATCTCAAGAGTG 58.327 41.667 0.00 0.00 33.72 3.51
786 845 5.057819 CCATCAATCAGATCTCAAGAGTGG 58.942 45.833 8.56 3.56 33.72 4.00
787 846 5.163332 CCATCAATCAGATCTCAAGAGTGGA 60.163 44.000 8.56 0.00 33.72 4.02
788 847 5.595257 TCAATCAGATCTCAAGAGTGGAG 57.405 43.478 8.56 0.00 0.00 3.86
789 848 4.121317 CAATCAGATCTCAAGAGTGGAGC 58.879 47.826 0.00 0.00 32.38 4.70
790 849 2.812658 TCAGATCTCAAGAGTGGAGCA 58.187 47.619 0.00 0.00 32.38 4.26
791 850 3.168292 TCAGATCTCAAGAGTGGAGCAA 58.832 45.455 0.00 0.00 32.38 3.91
792 851 3.580022 TCAGATCTCAAGAGTGGAGCAAA 59.420 43.478 0.00 0.00 32.38 3.68
794 853 4.758674 CAGATCTCAAGAGTGGAGCAAAAA 59.241 41.667 0.00 0.00 32.38 1.94
819 878 9.859152 AAAGATCCCTCTAAAAATATCCTTCTG 57.141 33.333 0.00 0.00 0.00 3.02
820 879 7.983363 AGATCCCTCTAAAAATATCCTTCTGG 58.017 38.462 0.00 0.00 0.00 3.86
834 893 5.683876 TCCTTCTGGATACTTTTGGAGAG 57.316 43.478 0.00 0.00 37.46 3.20
835 894 5.094387 TCCTTCTGGATACTTTTGGAGAGT 58.906 41.667 0.00 0.00 37.46 3.24
836 895 5.187967 TCCTTCTGGATACTTTTGGAGAGTC 59.812 44.000 0.00 0.00 37.46 3.36
837 896 5.188751 CCTTCTGGATACTTTTGGAGAGTCT 59.811 44.000 0.00 0.00 34.57 3.24
838 897 6.381420 CCTTCTGGATACTTTTGGAGAGTCTA 59.619 42.308 0.00 0.00 34.57 2.59
839 898 7.411486 TTCTGGATACTTTTGGAGAGTCTAG 57.589 40.000 0.00 0.00 37.61 2.43
840 899 5.894393 TCTGGATACTTTTGGAGAGTCTAGG 59.106 44.000 0.00 0.00 37.61 3.02
841 900 5.838955 TGGATACTTTTGGAGAGTCTAGGA 58.161 41.667 0.00 0.00 37.61 2.94
842 901 6.261435 TGGATACTTTTGGAGAGTCTAGGAA 58.739 40.000 0.00 0.00 37.61 3.36
843 902 6.729100 TGGATACTTTTGGAGAGTCTAGGAAA 59.271 38.462 0.00 0.00 37.61 3.13
844 903 7.403231 TGGATACTTTTGGAGAGTCTAGGAAAT 59.597 37.037 0.00 0.00 37.61 2.17
940 999 7.438757 TCAATGGACAATGTGAATTTTCTTGTG 59.561 33.333 0.00 0.00 30.63 3.33
976 1035 3.535561 ACTTGATACGCTAAGCATGCTT 58.464 40.909 33.70 33.70 39.83 3.91
983 1042 3.535561 ACGCTAAGCATGCTTATCTTGT 58.464 40.909 34.14 25.88 37.81 3.16
994 1053 4.253685 TGCTTATCTTGTACTTGCAGTCC 58.746 43.478 0.00 0.00 0.00 3.85
1003 1062 3.578282 TGTACTTGCAGTCCTCAAGATGA 59.422 43.478 9.40 0.00 42.52 2.92
1005 1064 1.998315 CTTGCAGTCCTCAAGATGACG 59.002 52.381 0.00 0.00 42.52 4.35
1037 1096 3.812053 AGGAGCATGAAATATTCGTCTGC 59.188 43.478 0.00 0.00 34.44 4.26
1062 1121 4.430007 AGCTCAGATCAACGCGTTATTTA 58.570 39.130 26.11 10.94 0.00 1.40
1272 1331 3.138304 CCACTCAAATTGTCTCGACCAA 58.862 45.455 0.00 0.00 0.00 3.67
1305 1364 4.416738 AGAAGCCCAGGAAGCGGC 62.417 66.667 0.00 0.00 46.09 6.53
1575 1634 0.674269 TGCAAGACATGATCTGCGCA 60.674 50.000 10.98 10.98 41.88 6.09
1598 1657 0.610174 AGCTCGTCAATGCTCCAAGA 59.390 50.000 0.00 0.00 33.90 3.02
1729 1788 4.201753 CGGACTTTGTTGCTCTGTGATATG 60.202 45.833 0.00 0.00 0.00 1.78
1772 1832 3.308866 AGAAAATGACGTGCTATTACCGC 59.691 43.478 0.00 0.00 0.00 5.68
1777 1837 0.742505 ACGTGCTATTACCGCTAGCA 59.257 50.000 16.45 0.76 46.97 3.49
1793 1853 4.021894 CGCTAGCATAACCTCCTACAGAAT 60.022 45.833 16.45 0.00 0.00 2.40
1813 1873 5.777732 AGAATTTGAGACCTGACAGAGTAGT 59.222 40.000 3.32 0.00 0.00 2.73
1814 1874 4.855715 TTTGAGACCTGACAGAGTAGTG 57.144 45.455 3.32 0.00 0.00 2.74
1845 1905 4.837860 GGATCTGTTCTCAGGGAGTATGAT 59.162 45.833 0.00 0.00 41.59 2.45
1869 1930 9.507329 GATTGGCCTATATTCAGAAGAAACATA 57.493 33.333 3.32 0.00 37.29 2.29
1924 1985 6.548321 AGTGGTGGAATGGTTTGAATAGTTA 58.452 36.000 0.00 0.00 0.00 2.24
2154 2220 4.997395 CAGGTATCCAATATCTTGAACGGG 59.003 45.833 0.00 0.00 34.04 5.28
2184 2251 7.513371 AAGTTACAAAAACCCGATATGAACA 57.487 32.000 0.00 0.00 0.00 3.18
2209 2276 6.720309 TGACATCCACTATTTTGAAGATGGA 58.280 36.000 0.00 0.00 40.39 3.41
2341 2409 4.442403 GCGGTGCGTCTCATATATCATATG 59.558 45.833 0.00 0.00 0.00 1.78
2371 2439 2.243602 TTCACGGGTACAACTTGGAC 57.756 50.000 0.00 0.00 0.00 4.02
2394 2462 2.368548 GAGGTTTTCATTTGGCTTGGGT 59.631 45.455 0.00 0.00 0.00 4.51
2433 2501 7.674471 AGTGAATAGTTTCTTTCCTAAGCAC 57.326 36.000 0.00 0.00 32.78 4.40
2434 2502 7.224297 AGTGAATAGTTTCTTTCCTAAGCACA 58.776 34.615 0.00 0.00 32.78 4.57
2456 2579 8.354011 CACAGGTGCTTATTTGTATAGTAGAC 57.646 38.462 0.00 0.00 0.00 2.59
2457 2580 7.979537 CACAGGTGCTTATTTGTATAGTAGACA 59.020 37.037 0.00 0.00 0.00 3.41
2458 2581 7.980099 ACAGGTGCTTATTTGTATAGTAGACAC 59.020 37.037 0.00 0.00 0.00 3.67
2459 2582 8.198109 CAGGTGCTTATTTGTATAGTAGACACT 58.802 37.037 0.00 0.00 38.91 3.55
2460 2583 8.759782 AGGTGCTTATTTGTATAGTAGACACTT 58.240 33.333 0.00 0.00 36.14 3.16
2464 2587 9.194271 GCTTATTTGTATAGTAGACACTTAGGC 57.806 37.037 0.00 1.66 36.14 3.93
2467 2590 6.461110 TTGTATAGTAGACACTTAGGCACC 57.539 41.667 0.00 0.00 36.14 5.01
2468 2591 4.577693 TGTATAGTAGACACTTAGGCACCG 59.422 45.833 0.00 0.00 36.14 4.94
2469 2592 1.183549 AGTAGACACTTAGGCACCGG 58.816 55.000 0.00 0.00 0.00 5.28
2470 2593 0.893447 GTAGACACTTAGGCACCGGT 59.107 55.000 0.00 0.00 0.00 5.28
2471 2594 1.274447 GTAGACACTTAGGCACCGGTT 59.726 52.381 2.97 0.00 0.00 4.44
2472 2595 0.763035 AGACACTTAGGCACCGGTTT 59.237 50.000 2.97 0.00 0.00 3.27
2473 2596 1.142262 AGACACTTAGGCACCGGTTTT 59.858 47.619 2.97 0.00 0.00 2.43
2474 2597 1.534163 GACACTTAGGCACCGGTTTTC 59.466 52.381 2.97 0.00 0.00 2.29
2475 2598 1.134037 ACACTTAGGCACCGGTTTTCA 60.134 47.619 2.97 0.00 0.00 2.69
2476 2599 1.950909 CACTTAGGCACCGGTTTTCAA 59.049 47.619 2.97 0.00 0.00 2.69
2477 2600 2.031157 CACTTAGGCACCGGTTTTCAAG 60.031 50.000 2.97 9.29 0.00 3.02
2478 2601 1.539827 CTTAGGCACCGGTTTTCAAGG 59.460 52.381 2.97 0.00 0.00 3.61
2479 2602 0.766131 TAGGCACCGGTTTTCAAGGA 59.234 50.000 2.97 0.00 0.00 3.36
2480 2603 0.106419 AGGCACCGGTTTTCAAGGAA 60.106 50.000 2.97 0.00 0.00 3.36
2481 2604 0.747852 GGCACCGGTTTTCAAGGAAA 59.252 50.000 2.97 0.00 0.00 3.13
2482 2605 1.137282 GGCACCGGTTTTCAAGGAAAA 59.863 47.619 2.97 0.28 38.90 2.29
2483 2606 2.418884 GGCACCGGTTTTCAAGGAAAAA 60.419 45.455 2.97 0.00 42.09 1.94
2484 2607 2.605818 GCACCGGTTTTCAAGGAAAAAC 59.394 45.455 2.97 8.96 43.35 2.43
2546 2672 5.122239 GCGTATATGATGCTTATTGCTTGGA 59.878 40.000 0.00 0.00 43.37 3.53
2572 2698 4.759516 TTGAAAAGAGCATAACGGGTTC 57.240 40.909 0.00 0.00 0.00 3.62
2676 2805 0.753262 TCTCCTCTTATCCGCCTTGC 59.247 55.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 5.543507 ATTATGTTCTAGCAGTCCCTCTG 57.456 43.478 0.00 0.00 46.12 3.35
143 144 6.385467 AGAAATTATGTTCTAGCAGTCCCTCT 59.615 38.462 0.00 0.00 36.06 3.69
144 145 6.587273 AGAAATTATGTTCTAGCAGTCCCTC 58.413 40.000 0.00 0.00 36.06 4.30
145 146 6.408662 GGAGAAATTATGTTCTAGCAGTCCCT 60.409 42.308 0.00 0.00 37.98 4.20
146 147 5.760743 GGAGAAATTATGTTCTAGCAGTCCC 59.239 44.000 0.00 0.00 37.98 4.46
149 150 6.951971 AGTGGAGAAATTATGTTCTAGCAGT 58.048 36.000 0.00 0.00 37.98 4.40
150 151 7.768120 AGAAGTGGAGAAATTATGTTCTAGCAG 59.232 37.037 0.00 0.00 37.98 4.24
151 152 7.624549 AGAAGTGGAGAAATTATGTTCTAGCA 58.375 34.615 0.00 0.00 37.98 3.49
152 153 8.499403 AAGAAGTGGAGAAATTATGTTCTAGC 57.501 34.615 0.00 0.00 37.98 3.42
193 250 7.494952 GGGAGTACTATACAGTTTGATTCAACC 59.505 40.741 0.00 0.00 36.14 3.77
231 288 9.509956 AGAGTAGTGATCTAAACGCTCTTATAT 57.490 33.333 0.00 0.00 33.87 0.86
232 289 8.905660 AGAGTAGTGATCTAAACGCTCTTATA 57.094 34.615 0.00 0.00 33.87 0.98
233 290 7.811117 AGAGTAGTGATCTAAACGCTCTTAT 57.189 36.000 0.00 0.00 33.87 1.73
234 291 7.986320 ACTAGAGTAGTGATCTAAACGCTCTTA 59.014 37.037 13.02 4.45 37.69 2.10
235 292 6.824704 ACTAGAGTAGTGATCTAAACGCTCTT 59.175 38.462 13.02 0.80 37.69 2.85
236 293 6.350906 ACTAGAGTAGTGATCTAAACGCTCT 58.649 40.000 0.00 12.65 37.69 4.09
237 294 6.607735 ACTAGAGTAGTGATCTAAACGCTC 57.392 41.667 0.00 0.00 37.69 5.03
442 501 6.451393 TGTCACAAACTTTTGCTGTTTTACT 58.549 32.000 1.49 0.00 41.79 2.24
528 587 7.037438 CCCTACACGTGTACAAGTAAATGTAT 58.963 38.462 24.10 0.00 38.03 2.29
571 630 2.971330 TGGATGTCACCCATTTTTGCTT 59.029 40.909 0.00 0.00 32.56 3.91
595 654 5.064452 ACAAGATGCTGCGAAGAGATTAAAG 59.936 40.000 0.00 0.00 0.00 1.85
602 661 1.436600 ACACAAGATGCTGCGAAGAG 58.563 50.000 0.00 0.00 0.00 2.85
687 746 5.892119 TGTCACCCCATTTTACTGTTTTACA 59.108 36.000 0.00 0.00 0.00 2.41
702 761 2.692709 AAATGGTTGATGTCACCCCA 57.307 45.000 3.79 3.79 33.34 4.96
732 791 2.512692 AAGGGCAACACATGATGCTA 57.487 45.000 13.03 0.00 42.51 3.49
794 853 8.443979 CCAGAAGGATATTTTTAGAGGGATCTT 58.556 37.037 0.00 0.00 36.89 2.40
796 855 7.978925 TCCAGAAGGATATTTTTAGAGGGATC 58.021 38.462 0.00 0.00 39.61 3.36
797 856 7.954539 TCCAGAAGGATATTTTTAGAGGGAT 57.045 36.000 0.00 0.00 39.61 3.85
813 872 5.188751 AGACTCTCCAAAAGTATCCAGAAGG 59.811 44.000 0.00 0.00 0.00 3.46
814 873 6.293004 AGACTCTCCAAAAGTATCCAGAAG 57.707 41.667 0.00 0.00 0.00 2.85
815 874 6.381420 CCTAGACTCTCCAAAAGTATCCAGAA 59.619 42.308 0.00 0.00 0.00 3.02
816 875 5.894393 CCTAGACTCTCCAAAAGTATCCAGA 59.106 44.000 0.00 0.00 0.00 3.86
817 876 5.894393 TCCTAGACTCTCCAAAAGTATCCAG 59.106 44.000 0.00 0.00 0.00 3.86
818 877 5.838955 TCCTAGACTCTCCAAAAGTATCCA 58.161 41.667 0.00 0.00 0.00 3.41
819 878 6.793505 TTCCTAGACTCTCCAAAAGTATCC 57.206 41.667 0.00 0.00 0.00 2.59
820 879 7.225734 GCATTTCCTAGACTCTCCAAAAGTATC 59.774 40.741 0.00 0.00 0.00 2.24
821 880 7.051000 GCATTTCCTAGACTCTCCAAAAGTAT 58.949 38.462 0.00 0.00 0.00 2.12
822 881 6.013725 TGCATTTCCTAGACTCTCCAAAAGTA 60.014 38.462 0.00 0.00 0.00 2.24
823 882 5.221925 TGCATTTCCTAGACTCTCCAAAAGT 60.222 40.000 0.00 0.00 0.00 2.66
824 883 5.248640 TGCATTTCCTAGACTCTCCAAAAG 58.751 41.667 0.00 0.00 0.00 2.27
825 884 5.241403 TGCATTTCCTAGACTCTCCAAAA 57.759 39.130 0.00 0.00 0.00 2.44
826 885 4.908601 TGCATTTCCTAGACTCTCCAAA 57.091 40.909 0.00 0.00 0.00 3.28
827 886 4.908601 TTGCATTTCCTAGACTCTCCAA 57.091 40.909 0.00 0.00 0.00 3.53
828 887 4.908601 TTTGCATTTCCTAGACTCTCCA 57.091 40.909 0.00 0.00 0.00 3.86
912 971 8.995220 CAAGAAAATTCACATTGTCCATTGAAT 58.005 29.630 0.00 0.00 39.78 2.57
914 973 7.438757 CACAAGAAAATTCACATTGTCCATTGA 59.561 33.333 0.00 0.00 32.01 2.57
940 999 7.541437 AGCGTATCAAGTCTTACAAAGTCTAAC 59.459 37.037 0.00 0.00 0.00 2.34
953 1012 3.126831 GCATGCTTAGCGTATCAAGTCT 58.873 45.455 11.37 0.00 0.00 3.24
956 1015 5.852005 GATAAGCATGCTTAGCGTATCAAG 58.148 41.667 35.85 0.00 46.05 3.02
994 1053 6.902341 TCCTTGAATTTTTCGTCATCTTGAG 58.098 36.000 0.00 0.00 0.00 3.02
1003 1062 5.452078 TTCATGCTCCTTGAATTTTTCGT 57.548 34.783 0.00 0.00 0.00 3.85
1037 1096 0.457509 ACGCGTTGATCTGAGCTCAG 60.458 55.000 33.73 33.73 45.08 3.35
1272 1331 4.202305 GGGCTTCTGCATGACTCTATAAGT 60.202 45.833 0.00 0.00 40.40 2.24
1305 1364 1.815613 ACTATCGAGCCTGGATCATCG 59.184 52.381 13.04 8.50 36.54 3.84
1598 1657 1.747355 GCAACATGGCAGACAATAGCT 59.253 47.619 0.00 0.00 0.00 3.32
1729 1788 2.160219 TCATGTTTCTGCGAGCAATCAC 59.840 45.455 0.00 0.00 0.00 3.06
1772 1832 7.500992 TCAAATTCTGTAGGAGGTTATGCTAG 58.499 38.462 0.00 0.00 31.67 3.42
1777 1837 6.674419 AGGTCTCAAATTCTGTAGGAGGTTAT 59.326 38.462 0.00 0.00 0.00 1.89
1778 1838 6.023603 AGGTCTCAAATTCTGTAGGAGGTTA 58.976 40.000 0.00 0.00 0.00 2.85
1793 1853 3.574396 CCACTACTCTGTCAGGTCTCAAA 59.426 47.826 0.00 0.00 0.00 2.69
1813 1873 1.003580 GAGAACAGATCCAGGCAACCA 59.996 52.381 0.00 0.00 37.17 3.67
1814 1874 1.003580 TGAGAACAGATCCAGGCAACC 59.996 52.381 0.00 0.00 37.17 3.77
1845 1905 9.342308 CTTATGTTTCTTCTGAATATAGGCCAA 57.658 33.333 5.01 0.00 31.56 4.52
1869 1930 5.569428 GCACCTTTAAATCCATGAAAGCCTT 60.569 40.000 0.00 0.00 0.00 4.35
1924 1985 5.139727 TGGACAGACATGAACTTCCAAAAT 58.860 37.500 0.00 0.00 30.08 1.82
2154 2220 9.498307 CATATCGGGTTTTTGTAACTTTCATAC 57.502 33.333 0.00 0.00 0.00 2.39
2184 2251 7.348815 TCCATCTTCAAAATAGTGGATGTCAT 58.651 34.615 0.00 0.00 31.24 3.06
2209 2276 5.447279 GCGTTCAGTTTTTCACGGATCATAT 60.447 40.000 0.00 0.00 33.17 1.78
2341 2409 0.887933 ACCCGTGAATTGTCATTGGC 59.112 50.000 0.00 0.00 35.80 4.52
2371 2439 2.610232 CCAAGCCAAATGAAAACCTCCG 60.610 50.000 0.00 0.00 0.00 4.63
2394 2462 6.119536 ACTATTCACTTTCACAGTTGTGGAA 58.880 36.000 11.98 8.90 45.65 3.53
2410 2478 7.361286 CCTGTGCTTAGGAAAGAAACTATTCAC 60.361 40.741 0.00 0.00 40.42 3.18
2433 2501 8.198109 AGTGTCTACTATACAAATAAGCACCTG 58.802 37.037 0.00 0.00 34.74 4.00
2434 2502 8.307582 AGTGTCTACTATACAAATAAGCACCT 57.692 34.615 0.00 0.00 34.74 4.00
2446 2569 4.023365 CCGGTGCCTAAGTGTCTACTATAC 60.023 50.000 0.00 0.00 35.69 1.47
2447 2570 4.139786 CCGGTGCCTAAGTGTCTACTATA 58.860 47.826 0.00 0.00 35.69 1.31
2448 2571 2.957006 CCGGTGCCTAAGTGTCTACTAT 59.043 50.000 0.00 0.00 35.69 2.12
2449 2572 2.291153 ACCGGTGCCTAAGTGTCTACTA 60.291 50.000 6.12 0.00 35.69 1.82
2450 2573 1.183549 CCGGTGCCTAAGTGTCTACT 58.816 55.000 0.00 0.00 39.32 2.57
2451 2574 0.893447 ACCGGTGCCTAAGTGTCTAC 59.107 55.000 6.12 0.00 0.00 2.59
2452 2575 1.636148 AACCGGTGCCTAAGTGTCTA 58.364 50.000 8.52 0.00 0.00 2.59
2453 2576 0.763035 AAACCGGTGCCTAAGTGTCT 59.237 50.000 8.52 0.00 0.00 3.41
2454 2577 1.534163 GAAAACCGGTGCCTAAGTGTC 59.466 52.381 8.52 0.00 0.00 3.67
2455 2578 1.134037 TGAAAACCGGTGCCTAAGTGT 60.134 47.619 8.52 0.00 0.00 3.55
2456 2579 1.600023 TGAAAACCGGTGCCTAAGTG 58.400 50.000 8.52 0.00 0.00 3.16
2457 2580 2.227194 CTTGAAAACCGGTGCCTAAGT 58.773 47.619 8.52 0.00 0.00 2.24
2458 2581 1.539827 CCTTGAAAACCGGTGCCTAAG 59.460 52.381 8.52 11.22 0.00 2.18
2459 2582 1.143277 TCCTTGAAAACCGGTGCCTAA 59.857 47.619 8.52 0.68 0.00 2.69
2460 2583 0.766131 TCCTTGAAAACCGGTGCCTA 59.234 50.000 8.52 0.00 0.00 3.93
2461 2584 0.106419 TTCCTTGAAAACCGGTGCCT 60.106 50.000 8.52 0.00 0.00 4.75
2462 2585 0.747852 TTTCCTTGAAAACCGGTGCC 59.252 50.000 8.52 0.14 0.00 5.01
2463 2586 2.588027 TTTTCCTTGAAAACCGGTGC 57.412 45.000 8.52 0.77 36.73 5.01
2492 2615 9.959721 AAAGTGCTTAGAGAGGTGATTATAAAA 57.040 29.630 0.00 0.00 0.00 1.52
2493 2616 9.383519 CAAAGTGCTTAGAGAGGTGATTATAAA 57.616 33.333 0.00 0.00 0.00 1.40
2494 2617 7.495934 GCAAAGTGCTTAGAGAGGTGATTATAA 59.504 37.037 0.00 0.00 40.96 0.98
2495 2618 6.986817 GCAAAGTGCTTAGAGAGGTGATTATA 59.013 38.462 0.00 0.00 40.96 0.98
2546 2672 5.476945 ACCCGTTATGCTCTTTTCAAATCTT 59.523 36.000 0.00 0.00 0.00 2.40
2572 2698 3.181461 CCTGGGGCAACAAGAGTATAGAG 60.181 52.174 0.00 0.00 39.74 2.43


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

AutoCloner maintained by Alex Coulton.