Multiple sequence alignment - TraesCS2D01G482900

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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 TraesCS2D01G482900 chr2D 100.000 2663 0 0 1 2663 584866314 584868976 0.000000e+00 4918.0
1 TraesCS2D01G482900 chr2D 89.922 903 51 13 802 1684 584858764 584857882 0.000000e+00 1127.0
2 TraesCS2D01G482900 chr2D 94.156 154 4 1 2187 2335 584873380 584873533 2.060000e-56 230.0
3 TraesCS2D01G482900 chr2A 91.474 1208 48 24 707 1907 718975612 718976771 0.000000e+00 1609.0
4 TraesCS2D01G482900 chr2A 93.194 720 42 4 969 1682 718965695 718964977 0.000000e+00 1051.0
5 TraesCS2D01G482900 chr2A 88.847 529 56 3 182 708 718974829 718975356 0.000000e+00 647.0
6 TraesCS2D01G482900 chr2A 81.679 131 9 5 812 927 718965821 718965691 7.850000e-16 95.3
7 TraesCS2D01G482900 chr2B 95.767 756 30 2 961 1716 705357392 705358145 0.000000e+00 1218.0
8 TraesCS2D01G482900 chr2B 93.014 730 43 6 961 1684 705348894 705348167 0.000000e+00 1059.0
9 TraesCS2D01G482900 chr2B 84.624 917 77 23 1 879 705356463 705357353 0.000000e+00 854.0
10 TraesCS2D01G482900 chr2B 95.407 479 18 3 2187 2663 12992548 12992072 0.000000e+00 760.0
11 TraesCS2D01G482900 chr2B 88.728 346 22 8 1846 2187 705347910 705347578 8.880000e-110 407.0
12 TraesCS2D01G482900 chr2B 82.086 441 14 22 1748 2185 705359093 705359471 1.540000e-82 316.0
13 TraesCS2D01G482900 chr2B 90.260 154 12 2 2187 2339 12978081 12977930 5.810000e-47 198.0
14 TraesCS2D01G482900 chr2B 88.000 100 8 2 710 806 705349122 705349024 6.020000e-22 115.0
15 TraesCS2D01G482900 chr2B 94.203 69 3 1 113 181 705356531 705356598 1.300000e-18 104.0
16 TraesCS2D01G482900 chr3D 89.150 682 69 5 985 1664 41746656 41745978 0.000000e+00 845.0
17 TraesCS2D01G482900 chr3D 83.077 325 37 12 182 494 488881726 488882044 2.020000e-71 279.0
18 TraesCS2D01G482900 chr3A 88.939 669 70 4 998 1664 53257335 53256669 0.000000e+00 822.0
19 TraesCS2D01G482900 chr3A 84.000 325 37 10 182 494 632367740 632367419 5.570000e-77 298.0
20 TraesCS2D01G482900 chr3B 87.714 700 76 7 968 1664 65269476 65268784 0.000000e+00 808.0
21 TraesCS2D01G482900 chr3B 82.323 396 57 12 2273 2661 10382154 10381765 5.490000e-87 331.0
22 TraesCS2D01G482900 chr3B 84.146 328 37 11 182 497 651609621 651609297 1.200000e-78 303.0
23 TraesCS2D01G482900 chr6B 92.562 484 27 3 2187 2663 64227078 64226597 0.000000e+00 686.0
24 TraesCS2D01G482900 chr6B 91.667 144 9 2 2187 2329 64205028 64204887 2.090000e-46 196.0
25 TraesCS2D01G482900 chrUn 88.732 568 46 10 1131 1683 49875915 49875351 0.000000e+00 678.0
26 TraesCS2D01G482900 chrUn 86.982 169 17 4 1865 2032 49875272 49875108 4.530000e-43 185.0
27 TraesCS2D01G482900 chr7A 89.353 479 41 4 2187 2663 130625972 130625502 6.350000e-166 593.0
28 TraesCS2D01G482900 chr7B 93.827 324 20 0 2340 2663 697490452 697490775 3.080000e-134 488.0
29 TraesCS2D01G482900 chr7B 91.200 125 8 1 2185 2309 697490100 697490221 1.640000e-37 167.0
30 TraesCS2D01G482900 chr1A 82.093 430 63 9 2230 2649 249883571 249883996 3.260000e-94 355.0
31 TraesCS2D01G482900 chr1A 82.012 328 59 0 2336 2663 499768515 499768842 2.020000e-71 279.0
32 TraesCS2D01G482900 chr1B 85.981 321 44 1 2336 2655 3180500 3180820 2.540000e-90 342.0
33 TraesCS2D01G482900 chr4B 86.120 317 35 9 183 494 85364523 85364211 1.530000e-87 333.0
34 TraesCS2D01G482900 chr5D 80.692 347 66 1 2318 2663 543371520 543371174 4.370000e-68 268.0
35 TraesCS2D01G482900 chr5D 86.905 168 18 3 1865 2032 483375216 483375053 4.530000e-43 185.0
36 TraesCS2D01G482900 chr4A 80.488 328 61 3 2330 2655 494542974 494543300 5.690000e-62 248.0
37 TraesCS2D01G482900 chr4D 87.500 168 17 3 1865 2032 487463014 487462851 9.730000e-45 191.0


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 TraesCS2D01G482900 chr2D 584866314 584868976 2662 False 4918.00 4918 100.0000 1 2663 1 chr2D.!!$F1 2662
1 TraesCS2D01G482900 chr2D 584857882 584858764 882 True 1127.00 1127 89.9220 802 1684 1 chr2D.!!$R1 882
2 TraesCS2D01G482900 chr2A 718974829 718976771 1942 False 1128.00 1609 90.1605 182 1907 2 chr2A.!!$F1 1725
3 TraesCS2D01G482900 chr2A 718964977 718965821 844 True 573.15 1051 87.4365 812 1682 2 chr2A.!!$R1 870
4 TraesCS2D01G482900 chr2B 705356463 705359471 3008 False 623.00 1218 89.1700 1 2185 4 chr2B.!!$F1 2184
5 TraesCS2D01G482900 chr2B 705347578 705349122 1544 True 527.00 1059 89.9140 710 2187 3 chr2B.!!$R3 1477
6 TraesCS2D01G482900 chr3D 41745978 41746656 678 True 845.00 845 89.1500 985 1664 1 chr3D.!!$R1 679
7 TraesCS2D01G482900 chr3A 53256669 53257335 666 True 822.00 822 88.9390 998 1664 1 chr3A.!!$R1 666
8 TraesCS2D01G482900 chr3B 65268784 65269476 692 True 808.00 808 87.7140 968 1664 1 chr3B.!!$R2 696
9 TraesCS2D01G482900 chrUn 49875108 49875915 807 True 431.50 678 87.8570 1131 2032 2 chrUn.!!$R1 901
10 TraesCS2D01G482900 chr7B 697490100 697490775 675 False 327.50 488 92.5135 2185 2663 2 chr7B.!!$F1 478

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
458 474 0.527565 CCGACATTTCAAAGGCTGGG 59.472 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 3690 0.098905 CACGATCATCTCCACGTCGT 59.901 55.0 0.0 0.0 45.27 4.34 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
67 68 8.738645 AACACAAGAGAATTTAGACAAGTCTT 57.261 30.769 8.17 0.00 40.93 3.01
166 167 9.231297 ACAAGTACACAAACATCATAATAGCTT 57.769 29.630 0.00 0.00 0.00 3.74
206 221 2.100197 ACATACTCGCAAGCTCCACTA 58.900 47.619 0.00 0.00 37.18 2.74
214 229 2.096218 CGCAAGCTCCACTAAGTTCAAC 60.096 50.000 0.00 0.00 0.00 3.18
219 234 4.557205 AGCTCCACTAAGTTCAACTTACG 58.443 43.478 5.86 5.72 39.51 3.18
220 235 3.123116 GCTCCACTAAGTTCAACTTACGC 59.877 47.826 5.86 1.48 39.51 4.42
231 246 6.831769 AGTTCAACTTACGCACATAAATGAG 58.168 36.000 0.00 0.00 0.00 2.90
237 252 5.699001 ACTTACGCACATAAATGAGAACACA 59.301 36.000 0.00 0.00 0.00 3.72
381 397 3.745799 ACACCGATGTAACAATCCAACA 58.254 40.909 0.00 0.00 37.26 3.33
392 408 7.699566 TGTAACAATCCAACACTTTCACTTAC 58.300 34.615 0.00 0.00 0.00 2.34
401 417 1.140252 ACTTTCACTTACGGGCAGTGT 59.860 47.619 0.00 0.00 42.12 3.55
403 419 0.753867 TTCACTTACGGGCAGTGTCA 59.246 50.000 0.00 0.00 42.12 3.58
425 441 4.808414 TCACAAGACAATCAGAGGTAGG 57.192 45.455 0.00 0.00 0.00 3.18
440 456 1.832366 GGTAGGGAACTGAGGAAGACC 59.168 57.143 0.00 0.00 43.88 3.85
458 474 0.527565 CCGACATTTCAAAGGCTGGG 59.472 55.000 0.00 0.00 0.00 4.45
479 495 5.414454 TGGGTGATGGCGAAAATTATATAGC 59.586 40.000 0.00 0.00 0.00 2.97
521 537 5.063204 TGACATTTCAAAGACAATCCTCGT 58.937 37.500 0.00 0.00 0.00 4.18
522 538 5.179368 TGACATTTCAAAGACAATCCTCGTC 59.821 40.000 0.00 0.00 0.00 4.20
579 595 4.007644 CCGTCTCAGGTGGCAGCA 62.008 66.667 20.04 0.00 0.00 4.41
609 625 0.549413 GGGAAGGGGAAGGTGGTAGT 60.549 60.000 0.00 0.00 0.00 2.73
610 626 0.618981 GGAAGGGGAAGGTGGTAGTG 59.381 60.000 0.00 0.00 0.00 2.74
643 676 3.692406 GTCCCCGAGTCGCCTTGT 61.692 66.667 7.12 0.00 0.00 3.16
719 1009 1.658596 GCACAATTATGCTCGACGACA 59.341 47.619 0.26 0.00 42.62 4.35
770 1063 2.173669 CACTCGTTGCTATGCCCGG 61.174 63.158 0.00 0.00 0.00 5.73
773 1066 2.824041 CGTTGCTATGCCCGGCTT 60.824 61.111 11.61 7.04 0.00 4.35
774 1067 2.406616 CGTTGCTATGCCCGGCTTT 61.407 57.895 11.61 0.55 0.00 3.51
860 1195 1.565305 GCATCGACTGGTAGCTGAAG 58.435 55.000 5.76 0.00 0.00 3.02
861 1196 1.135139 GCATCGACTGGTAGCTGAAGA 59.865 52.381 5.76 4.91 0.00 2.87
864 1199 2.723273 TCGACTGGTAGCTGAAGATCA 58.277 47.619 5.76 0.00 0.00 2.92
921 1269 3.462021 GGCAGTGTCATCCAAGATCTAC 58.538 50.000 0.00 0.00 0.00 2.59
922 1270 3.133721 GGCAGTGTCATCCAAGATCTACT 59.866 47.826 0.00 0.00 0.00 2.57
923 1271 4.342378 GGCAGTGTCATCCAAGATCTACTA 59.658 45.833 0.00 0.00 0.00 1.82
924 1272 5.508825 GGCAGTGTCATCCAAGATCTACTAG 60.509 48.000 0.00 0.00 0.00 2.57
925 1273 5.527951 CAGTGTCATCCAAGATCTACTAGC 58.472 45.833 0.00 0.00 0.00 3.42
926 1274 5.301551 CAGTGTCATCCAAGATCTACTAGCT 59.698 44.000 0.00 0.00 0.00 3.32
927 1275 6.488344 CAGTGTCATCCAAGATCTACTAGCTA 59.512 42.308 0.00 0.00 0.00 3.32
931 1279 6.208599 GTCATCCAAGATCTACTAGCTAGCTT 59.791 42.308 24.88 8.55 0.00 3.74
953 1301 2.957491 CTCAAGAGCCAGTCGAAGAT 57.043 50.000 0.00 0.00 40.67 2.40
954 1302 3.244033 CTCAAGAGCCAGTCGAAGATT 57.756 47.619 0.00 0.00 40.67 2.40
955 1303 2.928757 CTCAAGAGCCAGTCGAAGATTG 59.071 50.000 0.00 0.00 44.22 2.67
983 1331 2.909006 AGAAACCAGCTCAAGATCCAGA 59.091 45.455 0.00 0.00 0.00 3.86
988 1336 1.554160 CAGCTCAAGATCCAGACAGGT 59.446 52.381 0.00 0.00 39.02 4.00
989 1337 1.830477 AGCTCAAGATCCAGACAGGTC 59.170 52.381 0.00 0.00 39.02 3.85
1490 1850 2.046217 GGAGAACAAGACGGGGGC 60.046 66.667 0.00 0.00 0.00 5.80
1877 3269 9.658799 ATTTCAATCCTATATTCGACGATGAAT 57.341 29.630 0.00 10.71 41.32 2.57
1884 3276 6.473778 CCTATATTCGACGATGAATGATGGAC 59.526 42.308 14.28 0.00 38.92 4.02
1885 3277 2.119671 TCGACGATGAATGATGGACG 57.880 50.000 0.00 0.00 31.21 4.79
1889 3281 2.726760 GACGATGAATGATGGACGTAGC 59.273 50.000 0.00 0.00 34.26 3.58
1890 3282 2.100749 ACGATGAATGATGGACGTAGCA 59.899 45.455 0.00 0.00 32.42 3.49
1931 3347 5.525378 GCAAATCTAGATGGAGTGTTACCTG 59.475 44.000 5.86 0.00 0.00 4.00
2049 3465 5.485708 AGAATCTAGGCCTGTTAGTCAAGTT 59.514 40.000 17.99 0.00 0.00 2.66
2050 3466 6.668283 AGAATCTAGGCCTGTTAGTCAAGTTA 59.332 38.462 17.99 0.00 0.00 2.24
2051 3467 7.345914 AGAATCTAGGCCTGTTAGTCAAGTTAT 59.654 37.037 17.99 0.00 0.00 1.89
2052 3468 6.869206 TCTAGGCCTGTTAGTCAAGTTATT 57.131 37.500 17.99 0.00 0.00 1.40
2053 3469 7.966339 TCTAGGCCTGTTAGTCAAGTTATTA 57.034 36.000 17.99 0.00 0.00 0.98
2054 3470 7.779073 TCTAGGCCTGTTAGTCAAGTTATTAC 58.221 38.462 17.99 0.00 0.00 1.89
2209 3630 8.908786 ATTGAAGATTAACAGAGAGTTTCACA 57.091 30.769 0.00 0.00 41.64 3.58
2210 3631 7.715265 TGAAGATTAACAGAGAGTTTCACAC 57.285 36.000 0.00 0.00 41.64 3.82
2211 3632 6.706270 TGAAGATTAACAGAGAGTTTCACACC 59.294 38.462 0.00 0.00 41.64 4.16
2233 3654 3.616956 TGCTTTGAGAGTACATGGAGG 57.383 47.619 0.00 0.00 0.00 4.30
2237 3658 1.015609 TGAGAGTACATGGAGGGGGA 58.984 55.000 0.00 0.00 0.00 4.81
2249 3670 4.626942 TGGAGGGGGATACATATAGAGG 57.373 50.000 0.00 0.00 39.74 3.69
2309 3730 1.729470 CCTCGATCGTGGGAGGTGAG 61.729 65.000 25.06 7.87 43.91 3.51
2310 3731 1.729470 CTCGATCGTGGGAGGTGAGG 61.729 65.000 15.94 0.00 0.00 3.86
2311 3732 2.786495 CGATCGTGGGAGGTGAGGG 61.786 68.421 7.03 0.00 0.00 4.30
2312 3733 3.083997 ATCGTGGGAGGTGAGGGC 61.084 66.667 0.00 0.00 0.00 5.19
2313 3734 3.924013 ATCGTGGGAGGTGAGGGCA 62.924 63.158 0.00 0.00 0.00 5.36
2314 3735 4.087892 CGTGGGAGGTGAGGGCAG 62.088 72.222 0.00 0.00 0.00 4.85
2315 3736 2.607750 GTGGGAGGTGAGGGCAGA 60.608 66.667 0.00 0.00 0.00 4.26
2316 3737 2.607750 TGGGAGGTGAGGGCAGAC 60.608 66.667 0.00 0.00 0.00 3.51
2317 3738 3.403558 GGGAGGTGAGGGCAGACC 61.404 72.222 0.00 0.00 40.67 3.85
2318 3739 3.775654 GGAGGTGAGGGCAGACCG 61.776 72.222 0.00 0.00 46.96 4.79
2319 3740 2.680352 GAGGTGAGGGCAGACCGA 60.680 66.667 0.00 0.00 46.96 4.69
2320 3741 2.203788 AGGTGAGGGCAGACCGAA 60.204 61.111 0.00 0.00 46.96 4.30
2321 3742 1.613630 AGGTGAGGGCAGACCGAAT 60.614 57.895 0.00 0.00 46.96 3.34
2322 3743 1.153349 GGTGAGGGCAGACCGAATC 60.153 63.158 0.00 0.00 46.96 2.52
2323 3744 1.153349 GTGAGGGCAGACCGAATCC 60.153 63.158 0.00 0.00 46.96 3.01
2324 3745 1.612146 TGAGGGCAGACCGAATCCA 60.612 57.895 0.00 0.00 46.96 3.41
2325 3746 1.153349 GAGGGCAGACCGAATCCAC 60.153 63.158 0.00 0.00 46.96 4.02
2326 3747 1.899437 GAGGGCAGACCGAATCCACA 61.899 60.000 0.00 0.00 46.96 4.17
2327 3748 1.745489 GGGCAGACCGAATCCACAC 60.745 63.158 0.00 0.00 36.48 3.82
2328 3749 1.296715 GGCAGACCGAATCCACACT 59.703 57.895 0.00 0.00 0.00 3.55
2329 3750 0.741221 GGCAGACCGAATCCACACTC 60.741 60.000 0.00 0.00 0.00 3.51
2330 3751 0.247736 GCAGACCGAATCCACACTCT 59.752 55.000 0.00 0.00 0.00 3.24
2331 3752 1.476891 GCAGACCGAATCCACACTCTA 59.523 52.381 0.00 0.00 0.00 2.43
2332 3753 2.094182 GCAGACCGAATCCACACTCTAA 60.094 50.000 0.00 0.00 0.00 2.10
2333 3754 3.512680 CAGACCGAATCCACACTCTAAC 58.487 50.000 0.00 0.00 0.00 2.34
2334 3755 3.056821 CAGACCGAATCCACACTCTAACA 60.057 47.826 0.00 0.00 0.00 2.41
2335 3756 3.056749 AGACCGAATCCACACTCTAACAC 60.057 47.826 0.00 0.00 0.00 3.32
2336 3757 2.028385 ACCGAATCCACACTCTAACACC 60.028 50.000 0.00 0.00 0.00 4.16
2337 3758 2.618053 CGAATCCACACTCTAACACCC 58.382 52.381 0.00 0.00 0.00 4.61
2338 3759 2.677037 CGAATCCACACTCTAACACCCC 60.677 54.545 0.00 0.00 0.00 4.95
2398 4019 0.591741 GCGTATGTCGAGGAAGGTCG 60.592 60.000 0.00 0.00 42.86 4.79
2400 4021 0.739561 GTATGTCGAGGAAGGTCGCT 59.260 55.000 0.00 0.00 39.90 4.93
2462 4083 0.638746 GTCGGTACATGAAGAACGCG 59.361 55.000 3.53 3.53 0.00 6.01
2470 4091 0.608640 ATGAAGAACGCGAACCTCCT 59.391 50.000 15.93 0.00 0.00 3.69
2471 4092 0.038526 TGAAGAACGCGAACCTCCTC 60.039 55.000 15.93 3.61 0.00 3.71
2494 4115 7.122948 CCTCTAAAGCTACCTTCTCTCTTACAA 59.877 40.741 0.00 0.00 0.00 2.41
2499 4120 7.246171 AGCTACCTTCTCTCTTACAAAATGA 57.754 36.000 0.00 0.00 0.00 2.57
2502 4123 9.601217 GCTACCTTCTCTCTTACAAAATGAATA 57.399 33.333 0.00 0.00 0.00 1.75
2560 4181 5.047590 ACAGGATTAGACGACATGTACACAA 60.048 40.000 0.00 0.00 0.00 3.33
2583 4204 7.488150 ACAACTGATACATTATCACAGTACACG 59.512 37.037 0.00 0.00 40.09 4.49
2601 4222 1.217585 CGATGGTAGCCTGATGCACG 61.218 60.000 0.00 0.00 44.83 5.34
2630 4251 2.383527 GCTCGGTGAGAAGTTGCCG 61.384 63.158 0.00 0.00 44.95 5.69
2640 4261 0.884704 GAAGTTGCCGAAGCCAGACA 60.885 55.000 0.00 0.00 38.69 3.41
2653 4274 1.233019 CCAGACAGTTTCAGCCACAG 58.767 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 7.477422 GCTATTATGACGTTTGTGTACTTGTTG 59.523 37.037 0.00 0.00 0.00 3.33
206 221 7.172532 TCTCATTTATGTGCGTAAGTTGAACTT 59.827 33.333 15.57 15.57 41.97 2.66
214 229 6.164408 TGTGTTCTCATTTATGTGCGTAAG 57.836 37.500 0.00 0.00 43.44 2.34
231 246 7.801716 TGTCCCTGCTTATTATTATGTGTTC 57.198 36.000 0.00 0.00 0.00 3.18
237 252 8.664079 AGTGAAGATGTCCCTGCTTATTATTAT 58.336 33.333 0.00 0.00 0.00 1.28
363 378 5.049060 TGAAAGTGTTGGATTGTTACATCGG 60.049 40.000 0.00 0.00 0.00 4.18
374 389 3.408634 CCCGTAAGTGAAAGTGTTGGAT 58.591 45.455 0.00 0.00 0.00 3.41
375 390 2.841215 CCCGTAAGTGAAAGTGTTGGA 58.159 47.619 0.00 0.00 0.00 3.53
376 391 1.265905 GCCCGTAAGTGAAAGTGTTGG 59.734 52.381 0.00 0.00 0.00 3.77
377 392 1.944024 TGCCCGTAAGTGAAAGTGTTG 59.056 47.619 0.00 0.00 0.00 3.33
381 397 1.140252 ACACTGCCCGTAAGTGAAAGT 59.860 47.619 14.19 0.00 46.55 2.66
392 408 0.320683 TCTTGTGATGACACTGCCCG 60.321 55.000 0.00 0.00 46.07 6.13
401 417 4.897509 ACCTCTGATTGTCTTGTGATGA 57.102 40.909 0.00 0.00 0.00 2.92
403 419 4.163078 CCCTACCTCTGATTGTCTTGTGAT 59.837 45.833 0.00 0.00 0.00 3.06
425 441 0.966920 TGTCGGTCTTCCTCAGTTCC 59.033 55.000 0.00 0.00 0.00 3.62
440 456 1.068333 CACCCAGCCTTTGAAATGTCG 60.068 52.381 0.00 0.00 0.00 4.35
458 474 5.560148 CGGCTATATAATTTTCGCCATCAC 58.440 41.667 8.63 0.00 37.39 3.06
479 495 0.033504 AGTGCGGGAGTATATTGCGG 59.966 55.000 0.00 0.00 0.00 5.69
579 595 2.461637 CCTTCCCCCTCCTCCCTT 59.538 66.667 0.00 0.00 0.00 3.95
627 643 3.691342 CACAAGGCGACTCGGGGA 61.691 66.667 0.00 0.00 42.68 4.81
654 687 1.768077 CCTCCCTCCCCATGTCCTC 60.768 68.421 0.00 0.00 0.00 3.71
658 691 1.930656 CAACCCTCCCTCCCCATGT 60.931 63.158 0.00 0.00 0.00 3.21
719 1009 0.321671 CAGTCAACGGGTCTGGTCAT 59.678 55.000 0.00 0.00 0.00 3.06
774 1067 0.102120 CCTGACAGCAACGGCAAAAA 59.898 50.000 0.00 0.00 44.61 1.94
824 1119 3.015383 CGGATTGGGGGATTGGGT 58.985 61.111 0.00 0.00 0.00 4.51
925 1273 2.430332 ACTGGCTCTTGAGCTAAGCTAG 59.570 50.000 20.12 16.55 46.48 3.42
926 1274 2.428890 GACTGGCTCTTGAGCTAAGCTA 59.571 50.000 20.12 3.63 39.88 3.32
927 1275 1.206849 GACTGGCTCTTGAGCTAAGCT 59.793 52.381 20.12 10.07 43.88 3.74
931 1279 1.474478 CTTCGACTGGCTCTTGAGCTA 59.526 52.381 20.12 14.43 34.73 3.32
946 1294 3.074412 GTTTCTTGAGCCCAATCTTCGA 58.926 45.455 0.00 0.00 0.00 3.71
948 1296 3.157087 TGGTTTCTTGAGCCCAATCTTC 58.843 45.455 0.00 0.00 0.00 2.87
949 1297 3.160269 CTGGTTTCTTGAGCCCAATCTT 58.840 45.455 0.00 0.00 0.00 2.40
950 1298 2.800250 CTGGTTTCTTGAGCCCAATCT 58.200 47.619 0.00 0.00 0.00 2.40
951 1299 1.203287 GCTGGTTTCTTGAGCCCAATC 59.797 52.381 0.00 0.00 0.00 2.67
952 1300 1.203100 AGCTGGTTTCTTGAGCCCAAT 60.203 47.619 0.00 0.00 32.86 3.16
953 1301 0.185901 AGCTGGTTTCTTGAGCCCAA 59.814 50.000 0.00 0.00 32.86 4.12
954 1302 0.250901 GAGCTGGTTTCTTGAGCCCA 60.251 55.000 0.00 0.00 32.86 5.36
955 1303 0.250901 TGAGCTGGTTTCTTGAGCCC 60.251 55.000 0.00 0.00 32.86 5.19
956 1304 1.538950 CTTGAGCTGGTTTCTTGAGCC 59.461 52.381 0.00 0.00 32.86 4.70
957 1305 2.498167 TCTTGAGCTGGTTTCTTGAGC 58.502 47.619 0.00 0.00 0.00 4.26
958 1306 3.688673 GGATCTTGAGCTGGTTTCTTGAG 59.311 47.826 0.00 0.00 0.00 3.02
959 1307 3.072915 TGGATCTTGAGCTGGTTTCTTGA 59.927 43.478 0.00 0.00 0.00 3.02
983 1331 1.922369 ATGGCTGGCTGAGACCTGT 60.922 57.895 2.00 0.00 0.00 4.00
988 1336 2.045634 GCACATGGCTGGCTGAGA 60.046 61.111 2.00 0.00 40.25 3.27
1239 1593 3.017232 CGTGAGCGAGAGGTTGTAC 57.983 57.895 0.00 0.00 45.11 2.90
1387 1747 2.633657 GTGCACCTGTGTCTTGCG 59.366 61.111 5.22 0.00 39.22 4.85
1490 1850 2.347490 CCACCTCCACCTGGAACG 59.653 66.667 0.00 0.00 44.91 3.95
1877 3269 2.224042 GGATGATGTGCTACGTCCATCA 60.224 50.000 17.09 17.09 46.33 3.07
1884 3276 0.933097 GCTGTGGATGATGTGCTACG 59.067 55.000 0.00 0.00 0.00 3.51
1885 3277 2.028420 TGCTGTGGATGATGTGCTAC 57.972 50.000 0.00 0.00 0.00 3.58
1889 3281 1.542472 TGCTTTGCTGTGGATGATGTG 59.458 47.619 0.00 0.00 0.00 3.21
1890 3282 1.913778 TGCTTTGCTGTGGATGATGT 58.086 45.000 0.00 0.00 0.00 3.06
1931 3347 8.225777 CACGAGTTTTCTGGTTTAAATAGGTAC 58.774 37.037 0.00 0.00 36.76 3.34
2201 3622 3.620488 TCTCAAAGCAAGGTGTGAAACT 58.380 40.909 0.00 0.00 38.04 2.66
2206 3627 3.466836 TGTACTCTCAAAGCAAGGTGTG 58.533 45.455 0.00 0.00 0.00 3.82
2207 3628 3.838244 TGTACTCTCAAAGCAAGGTGT 57.162 42.857 0.00 0.00 0.00 4.16
2208 3629 3.438087 CCATGTACTCTCAAAGCAAGGTG 59.562 47.826 0.00 0.00 0.00 4.00
2209 3630 3.327757 TCCATGTACTCTCAAAGCAAGGT 59.672 43.478 0.00 0.00 0.00 3.50
2210 3631 3.937706 CTCCATGTACTCTCAAAGCAAGG 59.062 47.826 0.00 0.00 0.00 3.61
2211 3632 3.937706 CCTCCATGTACTCTCAAAGCAAG 59.062 47.826 0.00 0.00 0.00 4.01
2233 3654 4.342665 GCTAGCACCTCTATATGTATCCCC 59.657 50.000 10.63 0.00 0.00 4.81
2237 3658 4.640789 GCGCTAGCACCTCTATATGTAT 57.359 45.455 16.45 0.00 44.35 2.29
2269 3690 0.098905 CACGATCATCTCCACGTCGT 59.901 55.000 0.00 0.00 45.27 4.34
2270 3691 0.592500 CCACGATCATCTCCACGTCG 60.593 60.000 0.00 0.00 36.86 5.12
2309 3730 1.745489 GTGTGGATTCGGTCTGCCC 60.745 63.158 0.00 0.00 0.00 5.36
2310 3731 0.741221 GAGTGTGGATTCGGTCTGCC 60.741 60.000 0.00 0.00 0.00 4.85
2311 3732 0.247736 AGAGTGTGGATTCGGTCTGC 59.752 55.000 0.00 0.00 0.00 4.26
2312 3733 3.056821 TGTTAGAGTGTGGATTCGGTCTG 60.057 47.826 0.00 0.00 0.00 3.51
2313 3734 3.056749 GTGTTAGAGTGTGGATTCGGTCT 60.057 47.826 0.00 0.00 0.00 3.85
2314 3735 3.251571 GTGTTAGAGTGTGGATTCGGTC 58.748 50.000 0.00 0.00 0.00 4.79
2315 3736 2.028385 GGTGTTAGAGTGTGGATTCGGT 60.028 50.000 0.00 0.00 0.00 4.69
2316 3737 2.618053 GGTGTTAGAGTGTGGATTCGG 58.382 52.381 0.00 0.00 0.00 4.30
2317 3738 2.618053 GGGTGTTAGAGTGTGGATTCG 58.382 52.381 0.00 0.00 0.00 3.34
2318 3739 2.355818 GGGGGTGTTAGAGTGTGGATTC 60.356 54.545 0.00 0.00 0.00 2.52
2319 3740 1.633945 GGGGGTGTTAGAGTGTGGATT 59.366 52.381 0.00 0.00 0.00 3.01
2320 3741 1.286248 GGGGGTGTTAGAGTGTGGAT 58.714 55.000 0.00 0.00 0.00 3.41
2321 3742 2.768046 GGGGGTGTTAGAGTGTGGA 58.232 57.895 0.00 0.00 0.00 4.02
2364 3985 0.520404 TACGCTCCAGTCTCAACGTC 59.480 55.000 0.00 0.00 35.15 4.34
2374 3995 0.738975 TTCCTCGACATACGCTCCAG 59.261 55.000 0.00 0.00 42.26 3.86
2442 4063 1.705256 GCGTTCTTCATGTACCGACA 58.295 50.000 0.00 0.00 40.72 4.35
2448 4069 2.602878 GAGGTTCGCGTTCTTCATGTA 58.397 47.619 5.77 0.00 0.00 2.29
2454 4075 1.542492 TAGAGGAGGTTCGCGTTCTT 58.458 50.000 5.77 0.00 0.00 2.52
2462 4083 4.712829 AGAAGGTAGCTTTAGAGGAGGTTC 59.287 45.833 8.87 0.00 0.00 3.62
2470 4091 8.418597 TTTGTAAGAGAGAAGGTAGCTTTAGA 57.581 34.615 8.87 0.00 0.00 2.10
2471 4092 9.660180 ATTTTGTAAGAGAGAAGGTAGCTTTAG 57.340 33.333 8.87 0.00 0.00 1.85
2528 4149 3.678548 GTCGTCTAATCCTGTTCAACACC 59.321 47.826 0.00 0.00 0.00 4.16
2560 4181 7.329588 TCGTGTACTGTGATAATGTATCAGT 57.670 36.000 0.00 0.00 45.16 3.41
2583 4204 0.882042 CCGTGCATCAGGCTACCATC 60.882 60.000 0.00 0.00 45.15 3.51
2601 4222 1.519455 CACCGAGCTTCATCGTCCC 60.519 63.158 0.00 0.00 41.12 4.46
2630 4251 0.877743 GGCTGAAACTGTCTGGCTTC 59.122 55.000 0.00 0.00 44.47 3.86
2640 4261 0.956633 CACATGCTGTGGCTGAAACT 59.043 50.000 8.03 0.00 44.27 2.66


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

AutoCloner maintained by Alex Coulton.