Multiple sequence alignment - TraesCS2B01G493200

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 TraesCS2B01G493200 chr2B 100.000 3029 0 0 1 3029 690964880 690961852 0.000000e+00 5594
1 TraesCS2B01G493200 chr2B 94.824 850 44 0 2180 3029 25740055 25740904 0.000000e+00 1327
2 TraesCS2B01G493200 chr2B 93.783 756 27 14 1 738 690973883 690973130 0.000000e+00 1118
3 TraesCS2B01G493200 chr2D 89.972 1785 98 44 408 2158 574825592 574823855 0.000000e+00 2230
4 TraesCS2B01G493200 chr5B 94.529 859 44 3 2174 3029 115905404 115906262 0.000000e+00 1323
5 TraesCS2B01G493200 chr4D 94.712 851 42 2 2182 3029 498607558 498606708 0.000000e+00 1319
6 TraesCS2B01G493200 chr4D 94.386 855 46 2 2177 3029 15242420 15241566 0.000000e+00 1312
7 TraesCS2B01G493200 chr5D 94.805 847 41 2 2183 3029 36488060 36487217 0.000000e+00 1317
8 TraesCS2B01G493200 chr2A 94.700 849 44 1 2181 3029 592830554 592831401 0.000000e+00 1317
9 TraesCS2B01G493200 chr2A 91.055 872 66 5 981 1849 713165875 713165013 0.000000e+00 1168
10 TraesCS2B01G493200 chr2A 93.193 617 36 2 1428 2044 713151007 713150397 0.000000e+00 902
11 TraesCS2B01G493200 chr2A 77.473 1132 197 41 935 2039 713143511 713142411 2.560000e-175 625
12 TraesCS2B01G493200 chr2A 90.728 302 16 5 600 892 713176690 713176392 2.830000e-105 392
13 TraesCS2B01G493200 chr2A 87.390 341 20 13 1845 2183 713155969 713155650 1.330000e-98 370
14 TraesCS2B01G493200 chr2A 86.220 254 14 10 341 591 713177219 713176984 3.880000e-64 255
15 TraesCS2B01G493200 chr6D 94.588 850 45 1 2181 3029 61138862 61139711 0.000000e+00 1314
16 TraesCS2B01G493200 chr1D 94.588 850 44 2 2180 3029 53166082 53166929 0.000000e+00 1314
17 TraesCS2B01G493200 chr4A 94.464 849 46 1 2181 3029 583935827 583934980 0.000000e+00 1306


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 TraesCS2B01G493200 chr2B 690961852 690964880 3028 True 5594.0 5594 100.000 1 3029 1 chr2B.!!$R1 3028
1 TraesCS2B01G493200 chr2B 25740055 25740904 849 False 1327.0 1327 94.824 2180 3029 1 chr2B.!!$F1 849
2 TraesCS2B01G493200 chr2B 690973130 690973883 753 True 1118.0 1118 93.783 1 738 1 chr2B.!!$R2 737
3 TraesCS2B01G493200 chr2D 574823855 574825592 1737 True 2230.0 2230 89.972 408 2158 1 chr2D.!!$R1 1750
4 TraesCS2B01G493200 chr5B 115905404 115906262 858 False 1323.0 1323 94.529 2174 3029 1 chr5B.!!$F1 855
5 TraesCS2B01G493200 chr4D 498606708 498607558 850 True 1319.0 1319 94.712 2182 3029 1 chr4D.!!$R2 847
6 TraesCS2B01G493200 chr4D 15241566 15242420 854 True 1312.0 1312 94.386 2177 3029 1 chr4D.!!$R1 852
7 TraesCS2B01G493200 chr5D 36487217 36488060 843 True 1317.0 1317 94.805 2183 3029 1 chr5D.!!$R1 846
8 TraesCS2B01G493200 chr2A 592830554 592831401 847 False 1317.0 1317 94.700 2181 3029 1 chr2A.!!$F1 848
9 TraesCS2B01G493200 chr2A 713165013 713165875 862 True 1168.0 1168 91.055 981 1849 1 chr2A.!!$R4 868
10 TraesCS2B01G493200 chr2A 713150397 713151007 610 True 902.0 902 93.193 1428 2044 1 chr2A.!!$R2 616
11 TraesCS2B01G493200 chr2A 713142411 713143511 1100 True 625.0 625 77.473 935 2039 1 chr2A.!!$R1 1104
12 TraesCS2B01G493200 chr2A 713176392 713177219 827 True 323.5 392 88.474 341 892 2 chr2A.!!$R5 551
13 TraesCS2B01G493200 chr6D 61138862 61139711 849 False 1314.0 1314 94.588 2181 3029 1 chr6D.!!$F1 848
14 TraesCS2B01G493200 chr1D 53166082 53166929 847 False 1314.0 1314 94.588 2180 3029 1 chr1D.!!$F1 849
15 TraesCS2B01G493200 chr4A 583934980 583935827 847 True 1306.0 1306 94.464 2181 3029 1 chr4A.!!$R1 848

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
698 1015 0.036164 TTGAATGGACCAGGTCACCG 59.964 55.0 21.75 0.0 33.68 4.94 F
898 1234 0.382636 GTTGCAAGCGTGTCGTGTAC 60.383 55.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1974 0.592148 GAGGTAGAGGTATGCGTCGG 59.408 60.0 0.0 0.0 34.93 4.79 R
2686 3055 0.968393 GAGGCAGGGAGACGAAGACT 60.968 60.0 0.0 0.0 33.76 3.24 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
112 114 4.165372 ACAACTAGGAAAGGTGAGACCAAA 59.835 41.667 0.00 0.00 46.79 3.28
151 154 7.299134 TCCTCCCCAGTTTTCTTTTTGTAATA 58.701 34.615 0.00 0.00 0.00 0.98
154 157 9.996554 CTCCCCAGTTTTCTTTTTGTAATATTT 57.003 29.630 0.00 0.00 0.00 1.40
194 200 2.804647 TCTTACCGCATATGTCACGTG 58.195 47.619 9.94 9.94 0.00 4.49
265 271 9.413048 TGGTAAACAAGAAAAACAAGTAACAAG 57.587 29.630 0.00 0.00 0.00 3.16
384 393 6.441093 TTGTGAAGCCTGATTGTAATGATC 57.559 37.500 0.00 0.00 0.00 2.92
385 394 4.571984 TGTGAAGCCTGATTGTAATGATCG 59.428 41.667 0.00 0.00 0.00 3.69
386 395 4.811024 GTGAAGCCTGATTGTAATGATCGA 59.189 41.667 0.00 0.00 0.00 3.59
387 396 5.468072 GTGAAGCCTGATTGTAATGATCGAT 59.532 40.000 0.00 0.00 0.00 3.59
388 397 5.698089 TGAAGCCTGATTGTAATGATCGATC 59.302 40.000 18.72 18.72 0.00 3.69
439 451 0.249531 GCCGGCTTAGCTACTTCCTC 60.250 60.000 22.15 0.00 0.00 3.71
487 503 2.560542 ACTTGAATTGCCGGCATGTTTA 59.439 40.909 33.25 21.29 0.00 2.01
625 934 4.650972 TGGTGCTTACTTACCAAATCCT 57.349 40.909 0.00 0.00 43.60 3.24
698 1015 0.036164 TTGAATGGACCAGGTCACCG 59.964 55.000 21.75 0.00 33.68 4.94
699 1016 1.745489 GAATGGACCAGGTCACCGC 60.745 63.158 21.75 4.28 33.68 5.68
700 1017 3.605749 AATGGACCAGGTCACCGCG 62.606 63.158 21.75 0.00 33.68 6.46
895 1231 0.925267 CAAGTTGCAAGCGTGTCGTG 60.925 55.000 0.00 0.00 0.00 4.35
896 1232 1.366111 AAGTTGCAAGCGTGTCGTGT 61.366 50.000 0.00 0.00 0.00 4.49
897 1233 0.528901 AGTTGCAAGCGTGTCGTGTA 60.529 50.000 0.00 0.00 0.00 2.90
898 1234 0.382636 GTTGCAAGCGTGTCGTGTAC 60.383 55.000 0.00 0.00 0.00 2.90
899 1235 0.806492 TTGCAAGCGTGTCGTGTACA 60.806 50.000 0.00 0.00 35.06 2.90
902 1238 1.924524 GCAAGCGTGTCGTGTACATAT 59.075 47.619 0.00 0.00 41.10 1.78
907 1243 6.452480 GCAAGCGTGTCGTGTACATATATATG 60.452 42.308 19.21 19.21 41.10 1.78
908 1244 6.490566 AGCGTGTCGTGTACATATATATGA 57.509 37.500 26.05 9.59 41.10 2.15
909 1245 7.085052 AGCGTGTCGTGTACATATATATGAT 57.915 36.000 26.05 14.08 41.10 2.45
910 1246 8.205131 AGCGTGTCGTGTACATATATATGATA 57.795 34.615 26.05 13.23 41.10 2.15
911 1247 8.837389 AGCGTGTCGTGTACATATATATGATAT 58.163 33.333 26.05 9.20 41.10 1.63
931 1267 1.721664 ATGCATGCATGGCACGAGAC 61.722 55.000 31.74 9.08 45.23 3.36
947 1283 2.223294 CGAGACGACTCTCCATAACCAC 60.223 54.545 12.88 0.00 40.10 4.16
948 1284 3.018149 GAGACGACTCTCCATAACCACT 58.982 50.000 7.68 0.00 37.56 4.00
951 1287 2.681848 ACGACTCTCCATAACCACTACG 59.318 50.000 0.00 0.00 0.00 3.51
1005 1345 5.470098 ACTCACAAATTAAGACAAGATGCGT 59.530 36.000 0.00 0.00 0.00 5.24
1020 1360 2.161486 GCGTGCCTCATCACTCGTC 61.161 63.158 0.00 0.00 34.92 4.20
1023 1363 0.798771 GTGCCTCATCACTCGTCGAC 60.799 60.000 5.18 5.18 34.29 4.20
1038 1378 4.314440 GACCACTGCGCCACCTCA 62.314 66.667 4.18 0.00 0.00 3.86
1056 1396 1.900016 ACTGGTCGTCGTGGTGCTA 60.900 57.895 0.00 0.00 0.00 3.49
1060 1400 1.577922 GTCGTCGTGGTGCTACTCA 59.422 57.895 0.00 0.00 0.00 3.41
1210 1571 1.837051 TGGACCAGCGTCTCCTGTT 60.837 57.895 0.00 0.00 39.15 3.16
1211 1572 1.079750 GGACCAGCGTCTCCTGTTC 60.080 63.158 0.00 0.00 39.15 3.18
1215 1576 2.600769 AGCGTCTCCTGTTCCGGT 60.601 61.111 0.00 0.00 0.00 5.28
1216 1577 2.432628 GCGTCTCCTGTTCCGGTG 60.433 66.667 0.00 0.00 0.00 4.94
1217 1578 2.927580 GCGTCTCCTGTTCCGGTGA 61.928 63.158 0.00 0.00 0.00 4.02
1261 1625 4.308458 TCGGCGTGTCCTTGGTGG 62.308 66.667 6.85 0.00 37.10 4.61
1610 1974 1.970352 CTGCTCCTCAGGAAGGCCTC 61.970 65.000 5.23 0.00 44.80 4.70
1722 2089 0.536460 ACAACGGTTTCAAGGGCGAT 60.536 50.000 0.00 0.00 0.00 4.58
2025 2392 1.529244 ACTTCCACCCTGCAAGCAC 60.529 57.895 0.00 0.00 0.00 4.40
2031 2398 1.001641 ACCCTGCAAGCACTGATCC 60.002 57.895 0.00 0.00 0.00 3.36
2039 2406 0.453793 AAGCACTGATCCTCGTCTCG 59.546 55.000 0.00 0.00 0.00 4.04
2044 2411 1.208535 ACTGATCCTCGTCTCGACTCT 59.791 52.381 0.00 0.00 0.00 3.24
2045 2412 1.864711 CTGATCCTCGTCTCGACTCTC 59.135 57.143 0.00 0.00 0.00 3.20
2046 2413 1.483004 TGATCCTCGTCTCGACTCTCT 59.517 52.381 0.00 0.00 0.00 3.10
2047 2414 2.132762 GATCCTCGTCTCGACTCTCTC 58.867 57.143 0.00 0.00 0.00 3.20
2048 2415 1.187974 TCCTCGTCTCGACTCTCTCT 58.812 55.000 0.00 0.00 0.00 3.10
2049 2416 1.135527 TCCTCGTCTCGACTCTCTCTC 59.864 57.143 0.00 0.00 0.00 3.20
2050 2417 1.197055 CTCGTCTCGACTCTCTCTCG 58.803 60.000 0.00 0.00 0.00 4.04
2051 2418 0.810016 TCGTCTCGACTCTCTCTCGA 59.190 55.000 0.00 0.00 37.82 4.04
2052 2419 0.918619 CGTCTCGACTCTCTCTCGAC 59.081 60.000 0.00 0.00 35.26 4.20
2053 2420 1.283736 GTCTCGACTCTCTCTCGACC 58.716 60.000 0.00 0.00 35.26 4.79
2064 2431 4.436998 CTCGACCACCAGCCCGTC 62.437 72.222 0.00 0.00 0.00 4.79
2158 2526 3.492829 GCATCCCTGTGGCTTACTACTAC 60.493 52.174 0.00 0.00 0.00 2.73
2159 2527 3.752359 TCCCTGTGGCTTACTACTACT 57.248 47.619 0.00 0.00 0.00 2.57
2160 2528 3.629087 TCCCTGTGGCTTACTACTACTC 58.371 50.000 0.00 0.00 0.00 2.59
2161 2529 2.694109 CCCTGTGGCTTACTACTACTCC 59.306 54.545 0.00 0.00 0.00 3.85
2162 2530 3.627747 CCCTGTGGCTTACTACTACTCCT 60.628 52.174 0.00 0.00 0.00 3.69
2163 2531 4.386088 CCCTGTGGCTTACTACTACTCCTA 60.386 50.000 0.00 0.00 0.00 2.94
2164 2532 4.579753 CCTGTGGCTTACTACTACTCCTAC 59.420 50.000 0.00 0.00 0.00 3.18
2165 2533 5.438833 CTGTGGCTTACTACTACTCCTACT 58.561 45.833 0.00 0.00 0.00 2.57
2166 2534 5.191426 TGTGGCTTACTACTACTCCTACTG 58.809 45.833 0.00 0.00 0.00 2.74
2167 2535 5.192176 GTGGCTTACTACTACTCCTACTGT 58.808 45.833 0.00 0.00 0.00 3.55
2168 2536 5.651576 GTGGCTTACTACTACTCCTACTGTT 59.348 44.000 0.00 0.00 0.00 3.16
2169 2537 6.152492 GTGGCTTACTACTACTCCTACTGTTT 59.848 42.308 0.00 0.00 0.00 2.83
2170 2538 7.337942 GTGGCTTACTACTACTCCTACTGTTTA 59.662 40.741 0.00 0.00 0.00 2.01
2171 2539 7.337942 TGGCTTACTACTACTCCTACTGTTTAC 59.662 40.741 0.00 0.00 0.00 2.01
2172 2540 7.555914 GGCTTACTACTACTCCTACTGTTTACT 59.444 40.741 0.00 0.00 0.00 2.24
2173 2541 8.397148 GCTTACTACTACTCCTACTGTTTACTG 58.603 40.741 0.00 0.00 0.00 2.74
2174 2542 6.756299 ACTACTACTCCTACTGTTTACTGC 57.244 41.667 0.00 0.00 0.00 4.40
2175 2543 6.243900 ACTACTACTCCTACTGTTTACTGCA 58.756 40.000 0.00 0.00 0.00 4.41
2176 2544 6.890814 ACTACTACTCCTACTGTTTACTGCAT 59.109 38.462 0.00 0.00 0.00 3.96
2177 2545 5.967088 ACTACTCCTACTGTTTACTGCATG 58.033 41.667 0.00 0.00 0.00 4.06
2178 2546 4.891992 ACTCCTACTGTTTACTGCATGT 57.108 40.909 0.00 0.00 0.00 3.21
2245 2614 6.942576 ACAAAGTAGTTGATCCTTACAAGCAT 59.057 34.615 0.00 0.00 39.87 3.79
2261 2630 4.229096 CAAGCATACTGAAACGCAAACAT 58.771 39.130 0.00 0.00 0.00 2.71
2270 2639 4.283678 TGAAACGCAAACATAAAGAACCG 58.716 39.130 0.00 0.00 0.00 4.44
2279 2648 2.803956 ACATAAAGAACCGTGAACACCG 59.196 45.455 0.00 0.00 0.00 4.94
2317 2686 6.773638 ACAACCATAACACAAGAAGATCTCT 58.226 36.000 0.00 0.00 35.13 3.10
2364 2733 1.349026 CTTGAGAGAAGACCCCTGCAA 59.651 52.381 0.00 0.00 0.00 4.08
2376 2745 2.912956 ACCCCTGCAACAGAAAGATCTA 59.087 45.455 0.00 0.00 33.50 1.98
2397 2766 1.157870 AACCAGTCGCAAACAGGTCG 61.158 55.000 4.11 0.00 46.32 4.79
2632 3001 1.992519 ATCTCCCACCAGCATCAGCC 61.993 60.000 0.00 0.00 43.56 4.85
2686 3055 8.477419 AATCATACCAACAAGGAAGAAGAAAA 57.523 30.769 0.00 0.00 41.22 2.29
2731 3102 1.486310 CCCATCTGAGGATCCAAACGA 59.514 52.381 15.82 5.03 0.00 3.85
2738 3109 1.002087 GAGGATCCAAACGACCAGTGT 59.998 52.381 15.82 0.00 0.00 3.55
2748 3119 1.218316 GACCAGTGTCGATGGACCC 59.782 63.158 10.49 0.00 42.73 4.46
2760 3131 2.037208 GGACCCCCAACCACCATG 59.963 66.667 0.00 0.00 0.00 3.66
2864 3235 2.170817 GAGCCCGGAGAAACTTATTCCT 59.829 50.000 0.73 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 7.713942 GTCTCACCTTTCCTAGTTGTTTCTTTA 59.286 37.037 0.00 0.00 0.00 1.85
90 92 4.351874 TTGGTCTCACCTTTCCTAGTTG 57.648 45.455 0.00 0.00 39.58 3.16
160 163 6.576662 TGCGGTAAGAAATCCAAACATTTA 57.423 33.333 0.00 0.00 0.00 1.40
163 169 6.321181 ACATATGCGGTAAGAAATCCAAACAT 59.679 34.615 1.58 0.00 0.00 2.71
181 187 4.939509 AAAGTAACCACGTGACATATGC 57.060 40.909 19.30 1.72 0.00 3.14
194 200 9.500864 TCAAACGTAATTGTACAAAAAGTAACC 57.499 29.630 13.23 0.00 33.72 2.85
265 271 3.994789 GGTAAGCCGAACATTTTACGTC 58.005 45.455 0.00 0.00 0.00 4.34
439 451 1.626654 GGTCATGCCTCGTGAACGTG 61.627 60.000 2.37 0.15 40.80 4.49
487 503 2.492025 TGCTCCTCCAATCCAAGGTAT 58.508 47.619 0.00 0.00 34.12 2.73
625 934 6.314648 ACGACTGTCTGACTCACGTTATATTA 59.685 38.462 9.51 0.00 0.00 0.98
633 942 0.586802 TGACGACTGTCTGACTCACG 59.413 55.000 9.51 12.90 45.70 4.35
703 1020 1.906994 TTTACGCACGTGCTGATGGC 61.907 55.000 35.27 10.38 39.32 4.40
705 1022 2.525750 AATTTACGCACGTGCTGATG 57.474 45.000 35.27 23.08 39.32 3.07
706 1023 2.414029 CCAAATTTACGCACGTGCTGAT 60.414 45.455 35.27 23.31 39.32 2.90
707 1024 1.069568 CCAAATTTACGCACGTGCTGA 60.070 47.619 35.27 21.52 39.32 4.26
708 1025 1.326576 CCAAATTTACGCACGTGCTG 58.673 50.000 35.27 29.06 39.32 4.41
709 1026 0.386731 GCCAAATTTACGCACGTGCT 60.387 50.000 35.27 24.47 39.32 4.40
797 1123 3.386932 ACTACGTACCCTAACCATGGA 57.613 47.619 21.47 0.00 0.00 3.41
899 1235 9.914834 TGCCATGCATGCATATATCATATATAT 57.085 29.630 31.73 3.67 34.91 0.86
902 1238 6.148150 CGTGCCATGCATGCATATATCATATA 59.852 38.462 31.73 8.96 41.91 0.86
907 1243 2.679336 TCGTGCCATGCATGCATATATC 59.321 45.455 31.73 20.12 44.29 1.63
908 1244 2.681344 CTCGTGCCATGCATGCATATAT 59.319 45.455 31.73 9.52 44.29 0.86
909 1245 2.078392 CTCGTGCCATGCATGCATATA 58.922 47.619 31.73 18.01 44.29 0.86
910 1246 0.879090 CTCGTGCCATGCATGCATAT 59.121 50.000 31.73 10.77 44.29 1.78
911 1247 0.179051 TCTCGTGCCATGCATGCATA 60.179 50.000 31.73 15.14 44.29 3.14
912 1248 1.452470 TCTCGTGCCATGCATGCAT 60.452 52.632 27.46 27.46 44.29 3.96
913 1249 2.046120 TCTCGTGCCATGCATGCA 60.046 55.556 25.04 25.04 44.29 3.96
914 1250 2.406401 GTCTCGTGCCATGCATGC 59.594 61.111 21.69 11.82 44.29 4.06
915 1251 1.810853 TCGTCTCGTGCCATGCATG 60.811 57.895 20.19 20.19 45.79 4.06
931 1267 2.033049 CCGTAGTGGTTATGGAGAGTCG 59.967 54.545 0.00 0.00 40.37 4.18
947 1283 3.883489 TGGTGAGTGAGATGATACCGTAG 59.117 47.826 0.00 0.00 0.00 3.51
948 1284 3.893521 TGGTGAGTGAGATGATACCGTA 58.106 45.455 0.00 0.00 0.00 4.02
951 1287 5.282055 TGAATGGTGAGTGAGATGATACC 57.718 43.478 0.00 0.00 0.00 2.73
1005 1345 1.506718 GTCGACGAGTGATGAGGCA 59.493 57.895 0.00 0.00 0.00 4.75
1023 1363 4.320456 AGTGAGGTGGCGCAGTGG 62.320 66.667 10.83 0.00 0.00 4.00
1036 1376 2.725641 CACCACGACGACCAGTGA 59.274 61.111 0.00 0.00 40.56 3.41
1037 1377 2.137425 TAGCACCACGACGACCAGTG 62.137 60.000 0.00 4.48 38.05 3.66
1038 1378 1.900016 TAGCACCACGACGACCAGT 60.900 57.895 0.00 0.00 0.00 4.00
1149 1510 3.430929 GCGTCCATGAGTTGAAGTAGGAT 60.431 47.826 0.00 0.00 0.00 3.24
1188 1549 2.276116 GGAGACGCTGGTCCACTCA 61.276 63.158 8.93 0.00 44.54 3.41
1329 1693 2.331451 GGCACGTTGTTCAGCACC 59.669 61.111 0.00 0.00 0.00 5.01
1399 1763 2.362397 TGGAGATGATGTCGAGTAAGCC 59.638 50.000 0.00 0.00 0.00 4.35
1404 1768 0.741326 CCGTGGAGATGATGTCGAGT 59.259 55.000 0.00 0.00 0.00 4.18
1488 1852 2.617274 GCCCGTGAGCTTGTTGGAC 61.617 63.158 0.00 0.00 0.00 4.02
1530 1894 3.039011 GAGGAAGTAGAGGTTGGGCATA 58.961 50.000 0.00 0.00 0.00 3.14
1610 1974 0.592148 GAGGTAGAGGTATGCGTCGG 59.408 60.000 0.00 0.00 34.93 4.79
1615 1979 1.964933 GTGGGAGAGGTAGAGGTATGC 59.035 57.143 0.00 0.00 0.00 3.14
1678 2045 0.898320 AGGTCGATGGTCCAGAAGTG 59.102 55.000 0.00 0.00 0.00 3.16
1680 2047 0.898320 ACAGGTCGATGGTCCAGAAG 59.102 55.000 0.00 0.00 0.00 2.85
1722 2089 3.691342 CCGAACAGGGACGAGGCA 61.691 66.667 0.00 0.00 35.97 4.75
2025 2392 1.864711 GAGAGTCGAGACGAGGATCAG 59.135 57.143 0.00 0.00 36.23 2.90
2031 2398 1.197055 CGAGAGAGAGTCGAGACGAG 58.803 60.000 0.00 0.00 39.92 4.18
2039 2406 1.091537 CTGGTGGTCGAGAGAGAGTC 58.908 60.000 0.00 0.00 43.49 3.36
2044 2411 2.680352 GGGCTGGTGGTCGAGAGA 60.680 66.667 0.00 0.00 38.16 3.10
2045 2412 4.135153 CGGGCTGGTGGTCGAGAG 62.135 72.222 0.00 0.00 0.00 3.20
2046 2413 4.988716 ACGGGCTGGTGGTCGAGA 62.989 66.667 0.00 0.00 0.00 4.04
2047 2414 4.436998 GACGGGCTGGTGGTCGAG 62.437 72.222 0.00 0.00 0.00 4.04
2064 2431 1.959042 ATTCAGATTACTGCAGCCGG 58.041 50.000 15.27 0.00 43.17 6.13
2067 2434 6.092396 CCATCAGATATTCAGATTACTGCAGC 59.908 42.308 15.27 0.00 43.17 5.25
2069 2436 7.307131 TCCATCAGATATTCAGATTACTGCA 57.693 36.000 0.00 0.00 43.17 4.41
2071 2438 8.537858 TCCATCCATCAGATATTCAGATTACTG 58.462 37.037 0.00 0.00 38.34 2.74
2072 2439 8.676397 TCCATCCATCAGATATTCAGATTACT 57.324 34.615 0.00 0.00 32.37 2.24
2117 2485 9.259832 AGGGATGCTTTTATTCATTTTCTTAGT 57.740 29.630 0.00 0.00 0.00 2.24
2118 2486 9.525409 CAGGGATGCTTTTATTCATTTTCTTAG 57.475 33.333 0.00 0.00 0.00 2.18
2126 2494 3.385755 GCCACAGGGATGCTTTTATTCAT 59.614 43.478 0.00 0.00 35.59 2.57
2127 2495 2.760092 GCCACAGGGATGCTTTTATTCA 59.240 45.455 0.00 0.00 35.59 2.57
2128 2496 3.026694 AGCCACAGGGATGCTTTTATTC 58.973 45.455 0.00 0.00 35.59 1.75
2130 2498 2.834638 AGCCACAGGGATGCTTTTAT 57.165 45.000 0.00 0.00 35.59 1.40
2131 2499 2.603075 AAGCCACAGGGATGCTTTTA 57.397 45.000 0.00 0.00 42.37 1.52
2132 2500 2.171003 GTAAGCCACAGGGATGCTTTT 58.829 47.619 0.94 0.00 42.37 2.27
2133 2501 1.355720 AGTAAGCCACAGGGATGCTTT 59.644 47.619 0.94 0.00 42.37 3.51
2134 2502 0.995024 AGTAAGCCACAGGGATGCTT 59.005 50.000 0.00 0.00 46.37 3.91
2158 2526 7.849804 AAATACATGCAGTAAACAGTAGGAG 57.150 36.000 0.00 0.00 36.05 3.69
2159 2527 8.630054 AAAAATACATGCAGTAAACAGTAGGA 57.370 30.769 0.00 0.00 36.05 2.94
2245 2614 6.432107 GGTTCTTTATGTTTGCGTTTCAGTA 58.568 36.000 0.00 0.00 0.00 2.74
2261 2630 2.361757 TCTCGGTGTTCACGGTTCTTTA 59.638 45.455 9.59 0.00 0.00 1.85
2270 2639 1.254954 AGGGTACTCTCGGTGTTCAC 58.745 55.000 0.00 0.00 0.00 3.18
2279 2648 6.154021 TGTTATGGTTGTCTTAGGGTACTCTC 59.846 42.308 0.00 0.00 0.00 3.20
2317 2686 1.065199 GGATGATGACACAGGGCTTCA 60.065 52.381 0.00 0.00 0.00 3.02
2364 2733 4.810790 CGACTGGTTGTAGATCTTTCTGT 58.189 43.478 0.00 0.00 33.17 3.41
2376 2745 2.404083 CCTGTTTGCGACTGGTTGT 58.596 52.632 7.52 0.00 41.19 3.32
2436 2805 1.946768 CGCTGGTGTCAAGAAAGGAAA 59.053 47.619 0.00 0.00 0.00 3.13
2437 2806 1.593196 CGCTGGTGTCAAGAAAGGAA 58.407 50.000 0.00 0.00 0.00 3.36
2632 3001 2.354604 GCTGTTCTTCTCCTTCCTCTGG 60.355 54.545 0.00 0.00 0.00 3.86
2686 3055 0.968393 GAGGCAGGGAGACGAAGACT 60.968 60.000 0.00 0.00 33.76 3.24
2731 3102 2.291043 GGGGTCCATCGACACTGGT 61.291 63.158 3.55 0.00 42.53 4.00
2738 3109 2.204013 TGGTTGGGGGTCCATCGA 60.204 61.111 0.00 0.00 43.63 3.59
2800 3171 1.142097 GCCTTCGTCTAGGAGCCAC 59.858 63.158 5.39 0.00 37.50 5.01


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

AutoCloner maintained by Alex Coulton.