Multiple sequence alignment - TraesCS3B01G439700

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 TraesCS3B01G439700 chr3B 100.000 2724 0 0 1 2724 678709801 678712524 0.000000e+00 5031.0
1 TraesCS3B01G439700 chr3B 79.634 928 128 25 1231 2146 679623945 679623067 6.450000e-171 610.0
2 TraesCS3B01G439700 chr3B 86.747 498 48 12 1858 2341 678712973 678712480 3.090000e-149 538.0
3 TraesCS3B01G439700 chr3B 80.533 750 99 18 515 1224 45865769 45866511 1.440000e-147 532.0
4 TraesCS3B01G439700 chr3B 81.804 632 78 12 515 1116 45962061 45962685 1.880000e-136 496.0
5 TraesCS3B01G439700 chr3B 85.838 346 44 3 515 858 45945616 45945958 1.990000e-96 363.0
6 TraesCS3B01G439700 chr3B 85.838 346 44 3 515 858 45973376 45973718 1.990000e-96 363.0
7 TraesCS3B01G439700 chr3B 85.838 346 44 3 515 858 45995579 45995921 1.990000e-96 363.0
8 TraesCS3B01G439700 chr3B 85.549 346 45 3 515 858 45923083 45923425 9.280000e-95 357.0
9 TraesCS3B01G439700 chr3B 86.585 164 17 4 1227 1388 45758840 45759000 2.790000e-40 176.0
10 TraesCS3B01G439700 chr3B 86.585 164 17 4 1227 1388 45783130 45783290 2.790000e-40 176.0
11 TraesCS3B01G439700 chr3B 86.228 167 18 4 1227 1391 45828853 45829016 2.790000e-40 176.0
12 TraesCS3B01G439700 chr3B 86.585 164 17 4 1227 1388 45946612 45946772 2.790000e-40 176.0
13 TraesCS3B01G439700 chr3B 86.585 164 17 4 1227 1388 45962830 45962990 2.790000e-40 176.0
14 TraesCS3B01G439700 chr3B 100.000 72 0 0 1 72 238314383 238314312 1.700000e-27 134.0
15 TraesCS3B01G439700 chr3B 81.818 165 20 7 1061 1224 679624164 679624009 2.200000e-26 130.0
16 TraesCS3B01G439700 chr3B 85.263 95 7 3 69 162 614214093 614214181 1.040000e-14 91.6
17 TraesCS3B01G439700 chr3D 93.384 1572 80 10 1163 2721 515818927 515820487 0.000000e+00 2305.0
18 TraesCS3B01G439700 chr3D 79.926 1345 157 57 1231 2535 516193952 516192681 0.000000e+00 883.0
19 TraesCS3B01G439700 chr3D 92.654 422 27 2 447 867 515818444 515818862 3.000000e-169 604.0
20 TraesCS3B01G439700 chr3D 81.733 750 85 16 515 1224 27529777 27530514 1.820000e-161 579.0
21 TraesCS3B01G439700 chr3D 86.508 504 48 13 1852 2341 515820943 515820446 1.110000e-148 536.0
22 TraesCS3B01G439700 chr3D 95.434 219 8 1 69 285 515812902 515813120 5.580000e-92 348.0
23 TraesCS3B01G439700 chr3D 88.068 176 12 7 69 241 603058592 603058761 1.650000e-47 200.0
24 TraesCS3B01G439700 chr3D 98.649 74 1 0 1 74 14297343 14297270 6.120000e-27 132.0
25 TraesCS3B01G439700 chr3D 98.649 74 1 0 1 74 332623025 332623098 6.120000e-27 132.0
26 TraesCS3B01G439700 chr3A 86.061 1485 122 40 294 1748 650194395 650195824 0.000000e+00 1517.0
27 TraesCS3B01G439700 chr3A 94.348 867 48 1 1855 2721 650195885 650196750 0.000000e+00 1328.0
28 TraesCS3B01G439700 chr3A 80.114 1227 156 50 1231 2428 651501994 651500827 0.000000e+00 833.0
29 TraesCS3B01G439700 chr3A 87.698 504 44 10 1852 2341 650197208 650196709 3.040000e-159 571.0
30 TraesCS3B01G439700 chr3A 95.876 194 7 1 69 261 650193132 650193325 2.040000e-81 313.0
31 TraesCS3B01G439700 chr3A 80.168 358 62 6 1470 1827 37589951 37590299 2.690000e-65 259.0
32 TraesCS3B01G439700 chr3A 80.757 317 54 3 1470 1786 37630750 37631059 9.750000e-60 241.0
33 TraesCS3B01G439700 chr3A 87.059 170 14 3 1061 1224 651502226 651502059 4.630000e-43 185.0
34 TraesCS3B01G439700 chr5B 89.017 173 11 4 69 240 509667934 509668099 9.890000e-50 207.0
35 TraesCS3B01G439700 chr5B 96.296 81 2 1 1 80 78791879 78791799 6.120000e-27 132.0
36 TraesCS3B01G439700 chr5A 92.727 110 7 1 131 240 633690326 633690218 1.010000e-34 158.0
37 TraesCS3B01G439700 chr5A 94.000 50 2 1 69 117 633750147 633750098 1.050000e-09 75.0
38 TraesCS3B01G439700 chr6D 100.000 74 0 0 1 74 95294919 95294992 1.320000e-28 137.0
39 TraesCS3B01G439700 chr6D 100.000 72 0 0 1 72 465243698 465243627 1.700000e-27 134.0
40 TraesCS3B01G439700 chr6D 86.538 104 12 1 69 170 12457321 12457424 2.220000e-21 113.0
41 TraesCS3B01G439700 chr6D 98.182 55 1 0 237 291 12457562 12457616 2.230000e-16 97.1
42 TraesCS3B01G439700 chrUn 98.649 74 1 0 1 74 222975840 222975767 6.120000e-27 132.0
43 TraesCS3B01G439700 chrUn 98.649 74 1 0 1 74 303647974 303647901 6.120000e-27 132.0
44 TraesCS3B01G439700 chr1D 96.250 80 1 2 1 78 321677941 321678020 2.200000e-26 130.0
45 TraesCS3B01G439700 chr7B 85.263 95 7 3 69 162 89422808 89422720 1.040000e-14 91.6
46 TraesCS3B01G439700 chr7D 88.462 52 6 0 2324 2375 412179612 412179663 2.260000e-06 63.9


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 TraesCS3B01G439700 chr3B 678709801 678712524 2723 False 5031.000000 5031 100.0000 1 2724 1 chr3B.!!$F9 2723
1 TraesCS3B01G439700 chr3B 45865769 45866511 742 False 532.000000 532 80.5330 515 1224 1 chr3B.!!$F4 709
2 TraesCS3B01G439700 chr3B 679623067 679624164 1097 True 370.000000 610 80.7260 1061 2146 2 chr3B.!!$R3 1085
3 TraesCS3B01G439700 chr3B 45962061 45962990 929 False 336.000000 496 84.1945 515 1388 2 chr3B.!!$F11 873
4 TraesCS3B01G439700 chr3B 45945616 45946772 1156 False 269.500000 363 86.2115 515 1388 2 chr3B.!!$F10 873
5 TraesCS3B01G439700 chr3D 515818444 515820487 2043 False 1454.500000 2305 93.0190 447 2721 2 chr3D.!!$F5 2274
6 TraesCS3B01G439700 chr3D 516192681 516193952 1271 True 883.000000 883 79.9260 1231 2535 1 chr3D.!!$R3 1304
7 TraesCS3B01G439700 chr3D 27529777 27530514 737 False 579.000000 579 81.7330 515 1224 1 chr3D.!!$F1 709
8 TraesCS3B01G439700 chr3A 650193132 650196750 3618 False 1052.666667 1517 92.0950 69 2721 3 chr3A.!!$F3 2652
9 TraesCS3B01G439700 chr3A 651500827 651502226 1399 True 509.000000 833 83.5865 1061 2428 2 chr3A.!!$R2 1367

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
919 2006 0.111061 TGCTCAGGTTGCCAATCTGT 59.889 50.0 16.88 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 3219 0.392327 GAGTTCTTGGGCTCAGAGGC 60.392 60.0 15.82 15.82 40.51 4.7 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
46 47 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
47 48 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
48 49 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
49 50 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
50 51 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
51 52 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
52 53 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
58 59 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
59 60 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
60 61 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
61 62 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
62 63 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
63 64 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
64 65 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
65 66 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
66 67 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
67 68 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
91 92 4.598036 ACATGAATTTCTCCTGGGTGAT 57.402 40.909 0.00 0.00 0.00 3.06
117 119 1.069668 ACAGACCGTGTCCAGGTTTAC 59.930 52.381 1.06 0.00 43.01 2.01
125 127 2.798847 GTGTCCAGGTTTACGAGAACAC 59.201 50.000 0.00 0.00 0.00 3.32
189 191 9.390795 CACAACATGTCAAAGAAAATAAGAGAG 57.609 33.333 0.00 0.00 0.00 3.20
271 1258 6.455360 TCTCTGAATTTTGCTTGTTCTTGT 57.545 33.333 0.00 0.00 0.00 3.16
291 1278 3.697542 TGTGTGATGTACGCCTGTAGTAT 59.302 43.478 0.00 0.00 39.06 2.12
292 1279 4.883006 TGTGTGATGTACGCCTGTAGTATA 59.117 41.667 0.00 0.00 39.06 1.47
296 1335 8.077991 GTGTGATGTACGCCTGTAGTATATTTA 58.922 37.037 0.00 0.00 33.65 1.40
318 1357 7.576750 TTATTTCTTGTACGTGTAGCTTCAG 57.423 36.000 0.00 0.00 0.00 3.02
332 1371 2.435805 AGCTTCAGAGTTGTGAGTGGAA 59.564 45.455 0.00 0.00 0.00 3.53
342 1381 4.818546 AGTTGTGAGTGGAAATGTCAGAAG 59.181 41.667 0.00 0.00 0.00 2.85
354 1393 9.739276 TGGAAATGTCAGAAGTAAACATCTAAT 57.261 29.630 0.00 0.00 32.63 1.73
400 1444 5.548406 ACAGGTGTTCCTTACATTCTACAC 58.452 41.667 0.00 0.00 43.07 2.90
403 1447 5.187186 AGGTGTTCCTTACATTCTACACGAT 59.813 40.000 0.00 0.00 42.12 3.73
415 1459 3.610495 TCTACACGATGTAATACGCACG 58.390 45.455 0.00 0.00 31.67 5.34
424 1468 6.128472 ACGATGTAATACGCACGATGTAGATA 60.128 38.462 0.00 0.00 0.00 1.98
434 1478 4.158579 GCACGATGTAGATAGGATGATCCA 59.841 45.833 14.90 0.00 39.61 3.41
440 1484 6.724893 TGTAGATAGGATGATCCAAAACGA 57.275 37.500 14.90 0.00 39.61 3.85
443 1487 8.304596 TGTAGATAGGATGATCCAAAACGATAC 58.695 37.037 14.90 7.54 39.61 2.24
444 1488 7.303182 AGATAGGATGATCCAAAACGATACA 57.697 36.000 14.90 0.00 39.61 2.29
445 1489 7.155328 AGATAGGATGATCCAAAACGATACAC 58.845 38.462 14.90 0.00 39.61 2.90
469 1513 0.806102 GCTGGATGCACACGATACGT 60.806 55.000 0.00 0.00 40.60 3.57
500 1544 2.512515 GGCCAGCGTCCAGTCATC 60.513 66.667 0.00 0.00 0.00 2.92
580 1636 7.715265 AGACAGACAACTTGTTATTACTGTG 57.285 36.000 14.67 0.00 37.45 3.66
724 1784 7.011763 GCTCATCTATATGCAGAAAGAAACACA 59.988 37.037 0.00 0.00 32.76 3.72
778 1838 1.135527 CTGGCGGTGATGCATGAATTT 59.864 47.619 2.46 0.00 36.28 1.82
792 1852 4.439289 GCATGAATTTGTAGAGGCAAGGAC 60.439 45.833 0.00 0.00 0.00 3.85
882 1969 0.325110 CCCTCCTCTCCTCTTGCTGA 60.325 60.000 0.00 0.00 0.00 4.26
919 2006 0.111061 TGCTCAGGTTGCCAATCTGT 59.889 50.000 16.88 0.00 0.00 3.41
920 2007 1.251251 GCTCAGGTTGCCAATCTGTT 58.749 50.000 16.88 0.00 0.00 3.16
1006 2218 3.431486 GGAGTTGTAGAGGAAGATGGCTG 60.431 52.174 0.00 0.00 0.00 4.85
1073 2286 1.446792 CTGACGATTCAGCACGGCT 60.447 57.895 0.00 0.00 42.99 5.52
1139 2361 4.829968 CAGCAGGTATGATCCTCTATTGG 58.170 47.826 0.00 0.00 35.37 3.16
1218 2449 4.985413 ACGCAATTCTGTGTTAATGGATG 58.015 39.130 0.00 0.00 43.89 3.51
1233 2594 5.526506 AATGGATGCTAGGCAAATCTTTC 57.473 39.130 0.00 0.00 43.62 2.62
1247 2609 5.050091 GCAAATCTTTCTGTCTCGAAGAACA 60.050 40.000 0.00 0.00 33.46 3.18
1251 2613 5.416083 TCTTTCTGTCTCGAAGAACAACAA 58.584 37.500 0.00 0.00 33.46 2.83
1350 2713 8.044908 TCCAATCCCTGAACTAGTTAACATTAC 58.955 37.037 8.42 0.00 0.00 1.89
1351 2714 8.047310 CCAATCCCTGAACTAGTTAACATTACT 58.953 37.037 8.42 0.00 0.00 2.24
1371 2734 9.927668 CATTACTAGGGAAAACAATTCACAAAT 57.072 29.630 0.00 0.00 0.00 2.32
1373 2736 7.839680 ACTAGGGAAAACAATTCACAAATCT 57.160 32.000 0.00 0.00 0.00 2.40
1460 2864 5.456779 AGAACCTGATCTGATCTGATCTGA 58.543 41.667 32.55 23.67 41.72 3.27
1461 2865 6.079336 AGAACCTGATCTGATCTGATCTGAT 58.921 40.000 32.55 28.98 46.44 2.90
1476 2882 8.564509 TCTGATCTGATCTGTATGACTATCTG 57.435 38.462 17.82 0.00 0.00 2.90
1487 2893 7.717436 TCTGTATGACTATCTGACACTCCTAAG 59.283 40.741 0.00 0.00 0.00 2.18
1528 2934 5.105917 TGGTTTCTTCAAAATTAGGGATCGC 60.106 40.000 0.54 0.54 0.00 4.58
1550 2962 1.071471 GGATGGGAGCATGGTACCG 59.929 63.158 21.14 0.00 0.00 4.02
1556 2968 1.408266 GGGAGCATGGTACCGTGATTT 60.408 52.381 33.81 19.41 35.09 2.17
1558 2970 3.496160 GGGAGCATGGTACCGTGATTTAT 60.496 47.826 33.81 15.23 35.09 1.40
1560 2972 4.377021 GAGCATGGTACCGTGATTTATGA 58.623 43.478 33.81 0.63 35.09 2.15
1579 2991 4.916983 TGAAAACAGACATTGGAAGTGG 57.083 40.909 0.00 0.00 0.00 4.00
1593 3005 0.400594 AAGTGGAAGTACTGCCCCAC 59.599 55.000 24.01 24.01 46.97 4.61
1639 3051 2.719426 GCCTCAAGCATCATATTGCC 57.281 50.000 0.00 0.00 43.83 4.52
1661 3073 1.153147 GGCAGTAGCAGGGTAAGGC 60.153 63.158 0.00 0.00 44.61 4.35
1663 3075 1.144057 CAGTAGCAGGGTAAGGCCG 59.856 63.158 0.00 0.00 38.44 6.13
1746 3158 3.875838 CGGAAACCGCAAAAATGGA 57.124 47.368 0.00 0.00 41.17 3.41
1747 3159 1.414378 CGGAAACCGCAAAAATGGAC 58.586 50.000 0.00 0.00 41.17 4.02
1748 3160 1.414378 GGAAACCGCAAAAATGGACG 58.586 50.000 0.00 0.00 0.00 4.79
1749 3161 1.001158 GGAAACCGCAAAAATGGACGA 60.001 47.619 0.00 0.00 0.00 4.20
1750 3162 2.048498 GAAACCGCAAAAATGGACGAC 58.952 47.619 0.00 0.00 0.00 4.34
1751 3163 1.025812 AACCGCAAAAATGGACGACA 58.974 45.000 0.00 0.00 0.00 4.35
1752 3164 0.309612 ACCGCAAAAATGGACGACAC 59.690 50.000 0.00 0.00 0.00 3.67
1753 3165 0.309302 CCGCAAAAATGGACGACACA 59.691 50.000 0.00 0.00 0.00 3.72
1754 3166 1.268794 CCGCAAAAATGGACGACACAA 60.269 47.619 0.00 0.00 0.00 3.33
1755 3167 2.455032 CGCAAAAATGGACGACACAAA 58.545 42.857 0.00 0.00 0.00 2.83
1756 3168 2.854777 CGCAAAAATGGACGACACAAAA 59.145 40.909 0.00 0.00 0.00 2.44
1757 3169 3.304559 CGCAAAAATGGACGACACAAAAA 59.695 39.130 0.00 0.00 0.00 1.94
1758 3170 4.547966 CGCAAAAATGGACGACACAAAAAG 60.548 41.667 0.00 0.00 0.00 2.27
1759 3171 4.781883 GCAAAAATGGACGACACAAAAAGC 60.782 41.667 0.00 0.00 0.00 3.51
1760 3172 4.385358 AAAATGGACGACACAAAAAGCT 57.615 36.364 0.00 0.00 0.00 3.74
1761 3173 5.508200 AAAATGGACGACACAAAAAGCTA 57.492 34.783 0.00 0.00 0.00 3.32
1762 3174 5.705609 AAATGGACGACACAAAAAGCTAT 57.294 34.783 0.00 0.00 0.00 2.97
1827 3254 3.700038 AGAACTCTATACCCTTGACCACG 59.300 47.826 0.00 0.00 0.00 4.94
1835 3262 1.635663 CCCTTGACCACGCATTCGAC 61.636 60.000 0.00 0.00 39.41 4.20
1841 3268 0.670546 ACCACGCATTCGACAGAAGG 60.671 55.000 0.00 0.00 40.09 3.46
1887 3317 1.200020 GAAAACAGTGCATTCCCCTCG 59.800 52.381 0.00 0.00 0.00 4.63
2024 3460 6.600882 TGGTGGAGGTCTAGTAGTAAAAAG 57.399 41.667 0.00 0.00 0.00 2.27
2111 3552 7.337938 TGAGGATGCTTCATACAGTATTTTCA 58.662 34.615 1.64 0.00 0.00 2.69
2222 3681 0.594602 TTGCTACACTACACGTCGCT 59.405 50.000 0.00 0.00 0.00 4.93
2311 3770 5.600069 TCTCAATCTACTGGTGCATATCTGT 59.400 40.000 0.00 0.00 0.00 3.41
2418 3883 5.554822 TTTATGTATCGCCTTTTGTGGTC 57.445 39.130 0.00 0.00 0.00 4.02
2491 3956 4.284490 AGAAGACTGACAAGCCATAGTTGA 59.716 41.667 0.00 0.00 0.00 3.18
2535 4000 5.591099 TCAAGATGAAACTTTTGGCTGTTC 58.409 37.500 0.00 0.00 0.00 3.18
2536 4001 5.360714 TCAAGATGAAACTTTTGGCTGTTCT 59.639 36.000 0.00 0.00 0.00 3.01
2570 4035 7.029563 GGCATGATTTGTTTTACTCAAGGTAG 58.970 38.462 0.00 0.00 0.00 3.18
2654 4120 9.360093 CAAAACAATTAGTTACCTGAAACAACA 57.640 29.630 0.00 0.00 40.26 3.33
2721 4187 6.148315 ACATTCACATTATCAGATATGCACCG 59.852 38.462 0.00 0.00 0.00 4.94
2722 4188 4.568956 TCACATTATCAGATATGCACCGG 58.431 43.478 0.00 0.00 0.00 5.28
2723 4189 4.040339 TCACATTATCAGATATGCACCGGT 59.960 41.667 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
24 25 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
25 26 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
26 27 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
32 33 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
33 34 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
34 35 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
35 36 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
36 37 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
37 38 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
38 39 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
39 40 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
40 41 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
41 42 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
42 43 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
43 44 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
44 45 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
45 46 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
46 47 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
47 48 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
48 49 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
49 50 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
50 51 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
51 52 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
52 53 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
53 54 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
54 55 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
55 56 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
56 57 0.396695 TCATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
57 58 1.481871 TTCATGTACTCCCTCCGTCC 58.518 55.000 0.00 0.00 0.00 4.79
58 59 3.821421 AATTCATGTACTCCCTCCGTC 57.179 47.619 0.00 0.00 0.00 4.79
59 60 3.775316 AGAAATTCATGTACTCCCTCCGT 59.225 43.478 0.00 0.00 0.00 4.69
60 61 4.372656 GAGAAATTCATGTACTCCCTCCG 58.627 47.826 0.00 0.00 0.00 4.63
61 62 4.410555 AGGAGAAATTCATGTACTCCCTCC 59.589 45.833 0.00 14.10 45.53 4.30
62 63 5.363939 CAGGAGAAATTCATGTACTCCCTC 58.636 45.833 0.00 8.17 45.53 4.30
63 64 4.164988 CCAGGAGAAATTCATGTACTCCCT 59.835 45.833 0.00 0.00 45.53 4.20
64 65 4.455606 CCAGGAGAAATTCATGTACTCCC 58.544 47.826 0.00 0.00 45.53 4.30
65 66 4.080299 ACCCAGGAGAAATTCATGTACTCC 60.080 45.833 0.00 0.00 44.97 3.85
66 67 4.878397 CACCCAGGAGAAATTCATGTACTC 59.122 45.833 0.00 0.00 35.86 2.59
67 68 4.536090 TCACCCAGGAGAAATTCATGTACT 59.464 41.667 0.00 0.00 35.86 2.73
100 102 0.314935 TCGTAAACCTGGACACGGTC 59.685 55.000 0.00 0.00 35.21 4.79
104 106 2.798847 GTGTTCTCGTAAACCTGGACAC 59.201 50.000 0.00 0.00 0.00 3.67
117 119 5.294306 AGCACCATAATACATTGTGTTCTCG 59.706 40.000 1.74 0.00 0.00 4.04
125 127 4.464008 ACCAGGAGCACCATAATACATTG 58.536 43.478 2.07 0.00 38.94 2.82
189 191 3.182967 CAGCGAGGTGTCAAACTATCTC 58.817 50.000 0.00 0.00 0.00 2.75
235 237 2.724977 TCAGAGATGTGGTTGTCGTC 57.275 50.000 0.00 0.00 0.00 4.20
271 1258 6.644248 AATATACTACAGGCGTACATCACA 57.356 37.500 0.00 0.00 0.00 3.58
291 1278 9.642327 TGAAGCTACACGTACAAGAAATAAATA 57.358 29.630 0.00 0.00 0.00 1.40
292 1279 8.542497 TGAAGCTACACGTACAAGAAATAAAT 57.458 30.769 0.00 0.00 0.00 1.40
296 1335 5.779922 TCTGAAGCTACACGTACAAGAAAT 58.220 37.500 0.00 0.00 0.00 2.17
299 1338 3.819337 ACTCTGAAGCTACACGTACAAGA 59.181 43.478 0.00 0.00 0.00 3.02
318 1357 4.380531 TCTGACATTTCCACTCACAACTC 58.619 43.478 0.00 0.00 0.00 3.01
354 1393 6.995686 TGTCAATAGGAACAAGCAGTAAGAAA 59.004 34.615 0.00 0.00 0.00 2.52
363 1402 3.412386 ACACCTGTCAATAGGAACAAGC 58.588 45.455 0.00 0.00 40.42 4.01
400 1444 4.460505 TCTACATCGTGCGTATTACATCG 58.539 43.478 0.00 0.00 0.00 3.84
403 1447 5.702209 TCCTATCTACATCGTGCGTATTACA 59.298 40.000 0.00 0.00 0.00 2.41
415 1459 7.378966 TCGTTTTGGATCATCCTATCTACATC 58.621 38.462 4.96 0.00 37.46 3.06
424 1468 4.119862 CGTGTATCGTTTTGGATCATCCT 58.880 43.478 4.96 0.00 34.41 3.24
434 1478 2.006888 CCAGCATCCGTGTATCGTTTT 58.993 47.619 0.00 0.00 37.94 2.43
440 1484 3.312404 GCATCCAGCATCCGTGTAT 57.688 52.632 0.00 0.00 44.79 2.29
546 1602 7.120923 ACAAGTTGTCTGTCTAAGGTAGAAA 57.879 36.000 1.64 0.00 36.40 2.52
547 1603 6.726490 ACAAGTTGTCTGTCTAAGGTAGAA 57.274 37.500 1.64 0.00 36.40 2.10
548 1604 6.726490 AACAAGTTGTCTGTCTAAGGTAGA 57.274 37.500 9.40 0.00 0.00 2.59
559 1615 6.136071 GTGCACAGTAATAACAAGTTGTCTG 58.864 40.000 13.17 13.63 0.00 3.51
580 1636 3.272334 GCCGGATCCATGACGTGC 61.272 66.667 13.41 0.00 0.00 5.34
663 1720 1.547372 ACACACGCGTTAGGAATAGGT 59.453 47.619 10.22 0.00 0.00 3.08
778 1838 2.038557 GGTTTCTGTCCTTGCCTCTACA 59.961 50.000 0.00 0.00 0.00 2.74
792 1852 0.598065 CCAAAAGGCTCGGGTTTCTG 59.402 55.000 0.00 0.00 0.00 3.02
882 1969 2.079925 GCAGAAAGCTTCCACGAGAAT 58.920 47.619 0.00 0.00 41.15 2.40
920 2007 6.407525 CCCAAACCAACCATTAGAGACAAAAA 60.408 38.462 0.00 0.00 0.00 1.94
929 2016 1.899142 CCCACCCAAACCAACCATTAG 59.101 52.381 0.00 0.00 0.00 1.73
1059 2272 0.179137 TGTAGAGCCGTGCTGAATCG 60.179 55.000 2.98 0.00 39.88 3.34
1073 2286 3.081409 GCCGGGGCCTCTTGTAGA 61.081 66.667 2.18 0.00 34.56 2.59
1139 2361 2.287373 CAGAATCCTGCAAGCGAGAATC 59.713 50.000 0.00 0.00 33.07 2.52
1218 2449 3.308323 CGAGACAGAAAGATTTGCCTAGC 59.692 47.826 0.00 0.00 0.00 3.42
1233 2594 5.914085 AGATTTGTTGTTCTTCGAGACAG 57.086 39.130 0.00 0.00 0.00 3.51
1371 2734 5.566016 GCACGTGCGATTTTTGTTTATTAGA 59.434 36.000 26.77 0.00 0.00 2.10
1373 2736 5.732849 GCACGTGCGATTTTTGTTTATTA 57.267 34.783 26.77 0.00 0.00 0.98
1460 2864 6.609876 AGGAGTGTCAGATAGTCATACAGAT 58.390 40.000 4.53 0.00 0.00 2.90
1461 2865 6.007485 AGGAGTGTCAGATAGTCATACAGA 57.993 41.667 4.53 0.00 0.00 3.41
1463 2867 7.347252 ACTTAGGAGTGTCAGATAGTCATACA 58.653 38.462 4.53 0.00 33.99 2.29
1464 2868 7.811117 ACTTAGGAGTGTCAGATAGTCATAC 57.189 40.000 4.53 0.00 33.99 2.39
1465 2869 8.824756 AAACTTAGGAGTGTCAGATAGTCATA 57.175 34.615 4.53 0.00 35.91 2.15
1466 2870 7.726033 AAACTTAGGAGTGTCAGATAGTCAT 57.274 36.000 4.53 0.00 35.91 3.06
1467 2871 7.540474 AAAACTTAGGAGTGTCAGATAGTCA 57.460 36.000 4.53 0.00 35.91 3.41
1468 2872 8.521176 TGTAAAACTTAGGAGTGTCAGATAGTC 58.479 37.037 0.00 0.00 35.91 2.59
1476 2882 5.405873 GCACTCTGTAAAACTTAGGAGTGTC 59.594 44.000 17.96 9.71 46.83 3.67
1487 2893 4.568152 AACCATGTGCACTCTGTAAAAC 57.432 40.909 19.41 0.00 0.00 2.43
1528 2934 2.301346 GTACCATGCTCCCATCCTTTG 58.699 52.381 0.00 0.00 0.00 2.77
1550 2962 9.132521 CTTCCAATGTCTGTTTTCATAAATCAC 57.867 33.333 0.00 0.00 0.00 3.06
1556 2968 6.303054 TCCACTTCCAATGTCTGTTTTCATA 58.697 36.000 0.00 0.00 0.00 2.15
1558 2970 4.531854 TCCACTTCCAATGTCTGTTTTCA 58.468 39.130 0.00 0.00 0.00 2.69
1560 2972 4.956075 ACTTCCACTTCCAATGTCTGTTTT 59.044 37.500 0.00 0.00 0.00 2.43
1579 2991 0.953960 CAACCGTGGGGCAGTACTTC 60.954 60.000 0.00 0.00 36.48 3.01
1639 3051 1.895020 TTACCCTGCTACTGCCACCG 61.895 60.000 0.00 0.00 38.71 4.94
1661 3073 1.971505 TTGGGAGCAGATAGGCACGG 61.972 60.000 0.00 0.00 35.83 4.94
1663 3075 1.210478 TCTTTGGGAGCAGATAGGCAC 59.790 52.381 0.00 0.00 35.83 5.01
1668 3080 3.389329 GGAGACATCTTTGGGAGCAGATA 59.611 47.826 0.00 0.00 0.00 1.98
1705 3117 2.554032 CTCCTACTGCCCAACAAACAAG 59.446 50.000 0.00 0.00 0.00 3.16
1738 3150 4.754322 AGCTTTTTGTGTCGTCCATTTTT 58.246 34.783 0.00 0.00 0.00 1.94
1742 3154 5.351465 CAGTATAGCTTTTTGTGTCGTCCAT 59.649 40.000 0.00 0.00 0.00 3.41
1746 3158 5.526111 ACAACAGTATAGCTTTTTGTGTCGT 59.474 36.000 0.00 0.00 32.47 4.34
1747 3159 5.845953 CACAACAGTATAGCTTTTTGTGTCG 59.154 40.000 9.84 0.00 40.44 4.35
1748 3160 5.625311 GCACAACAGTATAGCTTTTTGTGTC 59.375 40.000 15.99 8.53 43.69 3.67
1749 3161 5.067153 TGCACAACAGTATAGCTTTTTGTGT 59.933 36.000 15.99 3.04 43.69 3.72
1750 3162 5.518812 TGCACAACAGTATAGCTTTTTGTG 58.481 37.500 12.43 12.43 44.14 3.33
1751 3163 5.762045 CTGCACAACAGTATAGCTTTTTGT 58.238 37.500 0.00 0.00 41.86 2.83
1791 3218 0.839853 AGTTCTTGGGCTCAGAGGCT 60.840 55.000 22.57 0.00 41.09 4.58
1792 3219 0.392327 GAGTTCTTGGGCTCAGAGGC 60.392 60.000 15.82 15.82 40.51 4.70
1827 3254 1.808411 TGGAACCTTCTGTCGAATGC 58.192 50.000 0.00 0.00 0.00 3.56
1841 3268 7.349645 TCAGAATCTGTCTCCGTCATGGAAC 62.350 48.000 10.36 0.00 38.38 3.62
1887 3317 2.538333 GCGTGTCATGAATGATGCTGAC 60.538 50.000 0.00 0.00 39.30 3.51
2024 3460 6.717997 TCCCAGAGGTTAAGGTAACAATTTTC 59.282 38.462 0.96 0.00 40.39 2.29
2077 3518 6.763135 TGTATGAAGCATCCTCAAGTTACATC 59.237 38.462 0.00 0.00 0.00 3.06
2111 3552 1.489649 CTGACAGCATCCTCCCAAGAT 59.510 52.381 0.00 0.00 0.00 2.40
2222 3681 6.039616 GTGGAACAACTTTTAGCATTCAACA 58.960 36.000 0.00 0.00 44.16 3.33
2311 3770 6.931840 TGTAGTGCTGTGTACATTCACATTAA 59.068 34.615 19.91 6.72 45.38 1.40
2329 3788 8.812329 CACTTAACAGATCTATTCTTGTAGTGC 58.188 37.037 0.00 0.00 29.93 4.40
2335 3794 8.768955 GGTATGCACTTAACAGATCTATTCTTG 58.231 37.037 0.00 0.00 29.93 3.02
2491 3956 2.191128 ATTTTCACTCGCTCTGCCTT 57.809 45.000 0.00 0.00 0.00 4.35
2535 4000 4.713824 ACAAATCATGCCATGAACAGAG 57.286 40.909 12.08 3.31 43.50 3.35
2536 4001 5.471556 AAACAAATCATGCCATGAACAGA 57.528 34.783 12.08 0.00 43.50 3.41
2654 4120 5.803470 GCCAAAACACTTCCAGTAGGACTAT 60.803 44.000 0.00 0.00 45.73 2.12


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

AutoCloner maintained by Alex Coulton.