Multiple sequence alignment - TraesCS3A01G387400

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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 TraesCS3A01G387400 chr3A 100.000 3089 0 0 1 3089 636542101 636539013 0.000000e+00 5705.0
1 TraesCS3A01G387400 chr3A 87.115 1560 177 20 821 2370 655628941 655630486 0.000000e+00 1746.0
2 TraesCS3A01G387400 chr3A 87.573 1368 150 13 821 2182 655896976 655895623 0.000000e+00 1567.0
3 TraesCS3A01G387400 chr3A 85.417 192 25 3 2490 2680 655895533 655895344 2.430000e-46 196.0
4 TraesCS3A01G387400 chr3A 84.444 180 27 1 2485 2663 655630582 655630761 3.170000e-40 176.0
5 TraesCS3A01G387400 chr3B 91.787 2070 137 16 316 2370 658486653 658488704 0.000000e+00 2850.0
6 TraesCS3A01G387400 chr3B 88.041 878 91 8 821 1695 684762789 684763655 0.000000e+00 1027.0
7 TraesCS3A01G387400 chr3B 80.688 1134 196 18 879 2004 684770132 684771250 0.000000e+00 859.0
8 TraesCS3A01G387400 chr3B 88.199 483 52 5 1703 2182 684763723 684764203 3.460000e-159 571.0
9 TraesCS3A01G387400 chr3B 93.146 321 21 1 1 320 658486289 658486609 1.300000e-128 470.0
10 TraesCS3A01G387400 chr3B 86.691 278 30 7 2390 2662 658488694 658488969 5.010000e-78 302.0
11 TraesCS3A01G387400 chr3B 84.896 192 25 4 2490 2680 684764295 684764483 1.130000e-44 191.0
12 TraesCS3A01G387400 chr3B 89.855 69 7 0 232 300 684747679 684747747 4.240000e-14 89.8
13 TraesCS3A01G387400 chr3B 88.406 69 8 0 1809 1877 658491076 658491144 1.970000e-12 84.2
14 TraesCS3A01G387400 chr3D 93.353 1384 81 6 316 1695 497864927 497866303 0.000000e+00 2036.0
15 TraesCS3A01G387400 chr3D 87.604 1557 168 18 821 2370 520322409 520320871 0.000000e+00 1783.0
16 TraesCS3A01G387400 chr3D 89.377 706 55 11 1682 2370 497866322 497867024 0.000000e+00 870.0
17 TraesCS3A01G387400 chr3D 80.671 1133 194 16 907 2029 520315728 520314611 0.000000e+00 856.0
18 TraesCS3A01G387400 chr3D 76.195 1151 232 34 908 2038 520318960 520317832 1.240000e-158 569.0
19 TraesCS3A01G387400 chr3D 79.028 720 134 9 877 1592 569900466 569901172 7.750000e-131 477.0
20 TraesCS3A01G387400 chr3D 84.350 492 50 15 2621 3088 520320677 520320189 1.010000e-124 457.0
21 TraesCS3A01G387400 chr3D 93.182 308 21 0 13 320 497864576 497864883 1.310000e-123 453.0
22 TraesCS3A01G387400 chr5A 76.467 1602 297 53 621 2182 401317666 401316105 0.000000e+00 797.0


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 TraesCS3A01G387400 chr3A 636539013 636542101 3088 True 5705.000000 5705 100.000000 1 3089 1 chr3A.!!$R1 3088
1 TraesCS3A01G387400 chr3A 655628941 655630761 1820 False 961.000000 1746 85.779500 821 2663 2 chr3A.!!$F1 1842
2 TraesCS3A01G387400 chr3A 655895344 655896976 1632 True 881.500000 1567 86.495000 821 2680 2 chr3A.!!$R2 1859
3 TraesCS3A01G387400 chr3B 658486289 658491144 4855 False 926.550000 2850 90.007500 1 2662 4 chr3B.!!$F3 2661
4 TraesCS3A01G387400 chr3B 684770132 684771250 1118 False 859.000000 859 80.688000 879 2004 1 chr3B.!!$F2 1125
5 TraesCS3A01G387400 chr3B 684762789 684764483 1694 False 596.333333 1027 87.045333 821 2680 3 chr3B.!!$F4 1859
6 TraesCS3A01G387400 chr3D 497864576 497867024 2448 False 1119.666667 2036 91.970667 13 2370 3 chr3D.!!$F2 2357
7 TraesCS3A01G387400 chr3D 520314611 520322409 7798 True 916.250000 1783 82.205000 821 3088 4 chr3D.!!$R1 2267
8 TraesCS3A01G387400 chr3D 569900466 569901172 706 False 477.000000 477 79.028000 877 1592 1 chr3D.!!$F1 715
9 TraesCS3A01G387400 chr5A 401316105 401317666 1561 True 797.000000 797 76.467000 621 2182 1 chr5A.!!$R1 1561

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
618 668 0.76706 AAGGTCTTCGGAGGTTGGGT 60.767 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 2616 0.034574 AAGTCACACACCAGTTGCCA 60.035 50.0 0.0 0.0 0.0 4.92 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
44 45 7.289310 TGTATGGTCCATGACAATATGTGAAT 58.711 34.615 15.10 0.00 32.01 2.57
53 54 8.509690 CCATGACAATATGTGAATACTCCAATC 58.490 37.037 0.00 0.00 0.00 2.67
141 142 6.430616 CCGGTAAAGAAACAATGTAGGGTAAA 59.569 38.462 0.00 0.00 0.00 2.01
142 143 7.300320 CGGTAAAGAAACAATGTAGGGTAAAC 58.700 38.462 0.00 0.00 0.00 2.01
221 222 9.918630 ATGTCAAATAATAATAATTCTGCTGGC 57.081 29.630 0.00 0.00 0.00 4.85
256 257 0.767375 ATCTGGCAGTGACAGGTTGT 59.233 50.000 25.86 7.17 39.54 3.32
360 410 2.029649 ACTGTGCAATCAAAGTCATGGC 60.030 45.455 0.00 0.00 35.96 4.40
494 544 2.158696 AGCCCCTGAGATTGATAAGCAC 60.159 50.000 0.00 0.00 0.00 4.40
505 555 3.965379 TGATAAGCACGTTGACCCTAA 57.035 42.857 0.00 0.00 0.00 2.69
543 593 6.428385 AGCAGTCTGAACAGCATATAAAAC 57.572 37.500 3.32 0.00 40.16 2.43
558 608 8.579863 AGCATATAAAACATAGAATTGAAGGGC 58.420 33.333 0.00 0.00 0.00 5.19
618 668 0.767060 AAGGTCTTCGGAGGTTGGGT 60.767 55.000 0.00 0.00 0.00 4.51
659 709 1.701704 CTTCCAAAAAGATGGCGCAC 58.298 50.000 10.83 0.00 40.46 5.34
667 717 3.698029 AAAGATGGCGCACATTATGAC 57.302 42.857 10.83 0.00 40.72 3.06
693 743 4.892198 AGGACAAGGGGAAACTAGCTATA 58.108 43.478 0.00 0.00 0.00 1.31
764 827 2.557056 TGTTGACTCTACGGTCTCTTGG 59.443 50.000 0.00 0.00 37.16 3.61
935 1003 4.392047 TGCTGAGCAGAAGAAGATGAAAA 58.608 39.130 1.40 0.00 33.32 2.29
936 1004 4.823442 TGCTGAGCAGAAGAAGATGAAAAA 59.177 37.500 1.40 0.00 33.32 1.94
1003 1071 2.758434 TGCAGCCCAGCAAGATGA 59.242 55.556 0.00 0.00 42.46 2.92
1060 1128 1.866601 CGCTTGCATTGGTATCGATCA 59.133 47.619 0.00 0.00 0.00 2.92
1193 1261 1.664649 TCACGCTCCGTCAAAGCAG 60.665 57.895 0.00 0.00 38.32 4.24
1205 1277 0.455633 CAAAGCAGCGATCCTGTTGC 60.456 55.000 11.37 7.08 45.21 4.17
1325 1397 3.668447 AGGTGTGAGTTTGATGCTACTG 58.332 45.455 0.00 0.00 0.00 2.74
1376 1454 6.801539 TGACTCTGTAAGCAAAACCTTATG 57.198 37.500 0.00 0.00 30.68 1.90
1404 1482 5.221925 ACAGGCTCCAGAAGATCTAACAAAA 60.222 40.000 0.00 0.00 0.00 2.44
1695 1777 8.432110 TTTTCTAGCATGTATCTTTTGCGATA 57.568 30.769 0.00 0.00 41.22 2.92
1701 1815 6.201806 AGCATGTATCTTTTGCGATAGAACTC 59.798 38.462 0.00 0.00 41.22 3.01
1707 1883 0.800683 TTGCGATAGAACTCGTGCGG 60.801 55.000 0.00 0.00 40.73 5.69
1711 1887 1.146358 GATAGAACTCGTGCGGGCAC 61.146 60.000 13.61 13.61 43.01 5.01
1760 1936 8.110271 TGGTTATATAAACAGGGTGTGATTGAA 58.890 33.333 9.20 0.00 0.00 2.69
1798 1976 8.860088 GTTCCTTTTATGGGCTATTGTATGAAT 58.140 33.333 0.00 0.00 0.00 2.57
1803 1981 8.635765 TTTATGGGCTATTGTATGAATCTTCC 57.364 34.615 0.00 0.00 0.00 3.46
1918 2096 4.284550 GCACCCCAGGCAGGTTCA 62.285 66.667 0.00 0.00 34.56 3.18
1929 2108 2.039084 AGGCAGGTTCACGAGATTTCTT 59.961 45.455 0.00 0.00 0.00 2.52
1991 2170 5.430886 AGATGTCATGGATGAATTCGTGAA 58.569 37.500 4.51 0.00 38.75 3.18
1996 2175 3.694043 TGGATGAATTCGTGAAGACCA 57.306 42.857 4.51 2.91 0.00 4.02
2038 2217 0.326264 GGGAAGCTTGCAAGAGGAGA 59.674 55.000 30.39 0.00 0.00 3.71
2109 2288 7.691791 GCATGATTATCAGGTCCCTAAAGGTAA 60.692 40.741 8.65 0.00 36.75 2.85
2155 2336 2.888834 TGCTTTCTTTGAGGCCAAAC 57.111 45.000 5.01 0.00 37.36 2.93
2172 2353 0.951558 AACGTGTGCCCACTTGATTC 59.048 50.000 0.00 0.00 39.55 2.52
2173 2354 0.889186 ACGTGTGCCCACTTGATTCC 60.889 55.000 0.00 0.00 39.55 3.01
2177 2358 1.338674 TGTGCCCACTTGATTCCGTAG 60.339 52.381 0.00 0.00 0.00 3.51
2185 2366 6.113411 CCCACTTGATTCCGTAGACTAAAAT 58.887 40.000 0.00 0.00 0.00 1.82
2190 2371 8.701895 ACTTGATTCCGTAGACTAAAATCCATA 58.298 33.333 9.39 0.00 0.00 2.74
2244 2425 9.825972 GATGTATACCATATGCACATGTTTAAC 57.174 33.333 3.92 0.00 32.56 2.01
2284 2475 4.646040 GGAACATGGTCATGGATGAATTCA 59.354 41.667 13.90 11.26 42.91 2.57
2316 2507 1.601759 GAAGCACTGGAGCCTGCAA 60.602 57.895 3.94 0.00 35.73 4.08
2338 2537 3.951332 GCTCGCAAGCTGTGTGTA 58.049 55.556 0.00 0.00 45.55 2.90
2339 2538 1.493311 GCTCGCAAGCTGTGTGTAC 59.507 57.895 0.00 0.00 45.55 2.90
2340 2539 1.901650 GCTCGCAAGCTGTGTGTACC 61.902 60.000 0.00 0.00 45.55 3.34
2370 2569 3.535561 AGAGTGATGCTGGTTTTATCGG 58.464 45.455 0.00 0.00 0.00 4.18
2371 2570 2.614057 GAGTGATGCTGGTTTTATCGGG 59.386 50.000 0.00 0.00 0.00 5.14
2372 2571 1.676006 GTGATGCTGGTTTTATCGGGG 59.324 52.381 0.00 0.00 0.00 5.73
2388 2587 2.347630 GGGGGTTTTCGACAAAGGG 58.652 57.895 0.00 0.00 0.00 3.95
2389 2588 0.468585 GGGGGTTTTCGACAAAGGGT 60.469 55.000 0.00 0.00 0.00 4.34
2390 2589 0.671796 GGGGTTTTCGACAAAGGGTG 59.328 55.000 0.00 0.00 0.00 4.61
2391 2590 0.671796 GGGTTTTCGACAAAGGGTGG 59.328 55.000 0.00 0.00 0.00 4.61
2392 2591 1.682740 GGTTTTCGACAAAGGGTGGA 58.317 50.000 0.00 0.00 31.87 4.02
2393 2592 2.235891 GGTTTTCGACAAAGGGTGGAT 58.764 47.619 0.00 0.00 34.00 3.41
2394 2593 2.626266 GGTTTTCGACAAAGGGTGGATT 59.374 45.455 0.00 0.00 34.00 3.01
2395 2594 3.069016 GGTTTTCGACAAAGGGTGGATTT 59.931 43.478 0.00 0.00 34.00 2.17
2396 2595 4.442332 GGTTTTCGACAAAGGGTGGATTTT 60.442 41.667 0.00 0.00 34.00 1.82
2397 2596 5.221283 GGTTTTCGACAAAGGGTGGATTTTA 60.221 40.000 0.00 0.00 34.00 1.52
2398 2597 6.452242 GTTTTCGACAAAGGGTGGATTTTAT 58.548 36.000 0.00 0.00 34.00 1.40
2399 2598 5.890424 TTCGACAAAGGGTGGATTTTATC 57.110 39.130 0.00 0.00 34.00 1.75
2419 2618 2.026641 CCTTACCAAGGCATGACATGG 58.973 52.381 21.34 21.34 42.78 3.66
2445 2644 4.344102 ACTGGTGTGTGACTTCTTAGCTTA 59.656 41.667 0.00 0.00 0.00 3.09
2451 2651 8.630917 GGTGTGTGACTTCTTAGCTTATATCTA 58.369 37.037 0.00 0.00 0.00 1.98
2465 2665 6.827251 AGCTTATATCTATCACAATGGCATGG 59.173 38.462 0.00 0.00 0.00 3.66
2561 2788 6.539103 GTGTTTGTATCTTCCCCTTATCTGAC 59.461 42.308 0.00 0.00 0.00 3.51
2577 2805 9.653287 CCTTATCTGACAATGTAGTTGAGTTTA 57.347 33.333 0.00 0.00 40.37 2.01
2596 2824 7.498900 TGAGTTTAATATTGATGTTCCGCTGAT 59.501 33.333 0.00 0.00 0.00 2.90
2681 2993 2.770802 ACAGAACATGCCATCTCTAGCT 59.229 45.455 0.00 0.00 0.00 3.32
2711 3023 0.322098 CCCATCAGTGGCGGTTTACA 60.322 55.000 0.00 0.00 44.62 2.41
2712 3024 1.086696 CCATCAGTGGCGGTTTACAG 58.913 55.000 0.00 0.00 39.01 2.74
2713 3025 1.086696 CATCAGTGGCGGTTTACAGG 58.913 55.000 0.00 0.00 0.00 4.00
2716 3028 0.953960 CAGTGGCGGTTTACAGGACC 60.954 60.000 0.00 0.00 0.00 4.46
2723 3035 0.252197 GGTTTACAGGACCGCCAGAT 59.748 55.000 0.00 0.00 36.29 2.90
2757 3074 2.497675 GTCAGTCCATCAGAGGCAGTTA 59.502 50.000 0.00 0.00 0.00 2.24
2758 3075 2.497675 TCAGTCCATCAGAGGCAGTTAC 59.502 50.000 0.00 0.00 0.00 2.50
2760 3077 1.555075 GTCCATCAGAGGCAGTTACCA 59.445 52.381 0.00 0.00 0.00 3.25
2762 3079 2.027192 TCCATCAGAGGCAGTTACCAAC 60.027 50.000 0.00 0.00 0.00 3.77
2763 3080 2.359900 CATCAGAGGCAGTTACCAACC 58.640 52.381 0.00 0.00 0.00 3.77
2768 3085 3.263941 GCAGTTACCAACCGCCTG 58.736 61.111 0.00 0.00 0.00 4.85
2796 3117 5.419542 GACAATATGTGAGCACTCCAGTTA 58.580 41.667 1.99 0.00 0.00 2.24
2797 3118 5.423015 ACAATATGTGAGCACTCCAGTTAG 58.577 41.667 1.99 0.00 0.00 2.34
2799 3120 6.154534 ACAATATGTGAGCACTCCAGTTAGTA 59.845 38.462 1.99 0.00 0.00 1.82
2800 3121 6.985653 ATATGTGAGCACTCCAGTTAGTAT 57.014 37.500 1.99 0.00 0.00 2.12
2801 3122 4.720649 TGTGAGCACTCCAGTTAGTATC 57.279 45.455 1.99 0.00 0.00 2.24
2803 3124 4.158579 TGTGAGCACTCCAGTTAGTATCTG 59.841 45.833 1.99 1.76 0.00 2.90
2804 3125 4.399618 GTGAGCACTCCAGTTAGTATCTGA 59.600 45.833 9.42 0.00 35.20 3.27
2806 3127 5.658634 TGAGCACTCCAGTTAGTATCTGATT 59.341 40.000 9.42 0.00 35.20 2.57
2807 3128 5.911752 AGCACTCCAGTTAGTATCTGATTG 58.088 41.667 9.42 5.10 35.20 2.67
2809 3130 6.607600 AGCACTCCAGTTAGTATCTGATTGTA 59.392 38.462 9.42 0.00 35.20 2.41
2810 3131 7.288852 AGCACTCCAGTTAGTATCTGATTGTAT 59.711 37.037 9.42 0.00 35.20 2.29
2811 3132 8.577296 GCACTCCAGTTAGTATCTGATTGTATA 58.423 37.037 9.42 0.00 35.20 1.47
2838 3162 6.260714 TCAATATGGTGCTTGTGTAATGCTAG 59.739 38.462 0.00 0.00 0.00 3.42
2845 3169 6.250819 GTGCTTGTGTAATGCTAGTATTGTG 58.749 40.000 15.50 1.93 0.00 3.33
2898 3230 7.519008 GCCGGAAATTCAGTTAGTATCTGATTG 60.519 40.741 5.05 0.00 40.83 2.67
2952 3284 4.843728 ACCATGTCAAATAACGATCCTGT 58.156 39.130 0.00 0.00 0.00 4.00
3003 3335 7.133891 AGTGACAGATTGTTTTTCTTATCCG 57.866 36.000 0.00 0.00 0.00 4.18
3008 3340 9.278734 GACAGATTGTTTTTCTTATCCGAATTC 57.721 33.333 0.00 0.00 0.00 2.17
3019 3351 5.361857 TCTTATCCGAATTCGACCCTTTAGT 59.638 40.000 28.76 6.32 43.02 2.24
3028 3360 4.715527 TCGACCCTTTAGTCTTTCTAGC 57.284 45.455 0.00 0.00 34.46 3.42
3045 3380 3.860681 CTGGCCCAAACAGCAGTT 58.139 55.556 0.00 0.00 40.40 3.16
3049 3384 1.036707 GGCCCAAACAGCAGTTACAA 58.963 50.000 0.00 0.00 36.84 2.41
3088 3423 4.829968 CACATTGACCATTTTATTGCCCA 58.170 39.130 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 8.735692 TTAGCATTAACATGATCACAATGAGA 57.264 30.769 18.31 7.68 29.65 3.27
80 81 8.454570 ACATGATTAGCATTAACATGATCACA 57.545 30.769 0.00 0.00 40.13 3.58
124 125 8.106247 TGATTGAGTTTACCCTACATTGTTTC 57.894 34.615 0.00 0.00 0.00 2.78
227 228 6.423776 TGTCACTGCCAGATATGATATTGA 57.576 37.500 0.00 0.00 0.00 2.57
228 229 5.642491 CCTGTCACTGCCAGATATGATATTG 59.358 44.000 0.00 0.00 31.38 1.90
256 257 9.973661 TGAAGGGTCAAATTCAGATAAGAATAA 57.026 29.630 0.00 0.00 37.24 1.40
334 384 3.066621 TGACTTTGATTGCACAGTGGAAC 59.933 43.478 10.03 5.19 35.29 3.62
360 410 5.381174 TCAGCAGATTTGTCATTTTGAGG 57.619 39.130 0.00 0.00 0.00 3.86
440 490 5.184892 AGGTTGCATGAAAGATTAGGTCT 57.815 39.130 0.00 0.00 39.43 3.85
543 593 4.037208 GTGATGGTGCCCTTCAATTCTATG 59.963 45.833 10.16 0.00 38.98 2.23
558 608 1.842562 AGGAAGGAGATGGTGATGGTG 59.157 52.381 0.00 0.00 0.00 4.17
641 691 1.035923 TGTGCGCCATCTTTTTGGAA 58.964 45.000 4.18 0.00 39.25 3.53
659 709 4.080356 TCCCCTTGTCCTTGAGTCATAATG 60.080 45.833 0.00 0.00 0.00 1.90
667 717 2.959465 AGTTTCCCCTTGTCCTTGAG 57.041 50.000 0.00 0.00 0.00 3.02
748 800 3.157750 AGTTCCAAGAGACCGTAGAGT 57.842 47.619 0.00 0.00 0.00 3.24
764 827 3.339141 AGAATCTTCGGAAGCCAAGTTC 58.661 45.455 12.90 10.76 0.00 3.01
935 1003 1.202879 TGACCGCTTCAATCAGGGTTT 60.203 47.619 0.00 0.00 0.00 3.27
936 1004 0.400213 TGACCGCTTCAATCAGGGTT 59.600 50.000 0.00 0.00 0.00 4.11
937 1005 0.620556 ATGACCGCTTCAATCAGGGT 59.379 50.000 0.00 0.00 37.92 4.34
1003 1071 0.107508 CAGCCCAAGTCCACGATCAT 60.108 55.000 0.00 0.00 0.00 2.45
1060 1128 2.264794 GTGGATCGCCTCAACGGT 59.735 61.111 0.00 0.00 34.25 4.83
1081 1149 3.319122 GGTTGCTGGAACTGAAGACAATT 59.681 43.478 11.83 0.00 34.66 2.32
1193 1261 2.434185 TCACGGCAACAGGATCGC 60.434 61.111 0.00 0.00 0.00 4.58
1376 1454 4.479786 AGATCTTCTGGAGCCTGTAAAC 57.520 45.455 0.00 0.00 0.00 2.01
1404 1482 5.314718 TGTCATATGCTGGGATGAGATTT 57.685 39.130 0.00 0.00 32.81 2.17
1455 1533 1.318158 GCCTCAAGCACCATGGGAAG 61.318 60.000 18.09 6.72 42.97 3.46
1456 1534 1.304381 GCCTCAAGCACCATGGGAA 60.304 57.895 18.09 0.00 42.97 3.97
1707 1883 6.471146 AGATCATGAGGTCAAATATAGTGCC 58.529 40.000 0.09 0.00 0.00 5.01
1764 1940 6.247229 AGCCCATAAAAGGAACAAACTTTT 57.753 33.333 8.06 8.06 46.51 2.27
1768 1944 6.697395 ACAATAGCCCATAAAAGGAACAAAC 58.303 36.000 0.00 0.00 0.00 2.93
1769 1945 6.926630 ACAATAGCCCATAAAAGGAACAAA 57.073 33.333 0.00 0.00 0.00 2.83
1772 1948 7.817418 TCATACAATAGCCCATAAAAGGAAC 57.183 36.000 0.00 0.00 0.00 3.62
1821 1999 2.174424 GGAGCCCTCTTCTTGGATGATT 59.826 50.000 0.00 0.00 0.00 2.57
1918 2096 6.706270 TCAAACAAAGCTCTAAGAAATCTCGT 59.294 34.615 0.00 0.00 0.00 4.18
1929 2108 1.071699 ACCGGCTCAAACAAAGCTCTA 59.928 47.619 0.00 0.00 39.75 2.43
2038 2217 2.983296 AGCATAAGGACATCTAGCCCT 58.017 47.619 0.00 0.00 0.00 5.19
2172 2353 4.680110 CACGCTATGGATTTTAGTCTACGG 59.320 45.833 0.00 0.00 0.00 4.02
2173 2354 4.148348 GCACGCTATGGATTTTAGTCTACG 59.852 45.833 0.00 0.00 0.00 3.51
2177 2358 5.064707 TCAAAGCACGCTATGGATTTTAGTC 59.935 40.000 0.00 0.00 0.00 2.59
2185 2366 1.003118 ACCTTCAAAGCACGCTATGGA 59.997 47.619 0.00 0.00 0.00 3.41
2190 2371 2.778299 TGAATACCTTCAAAGCACGCT 58.222 42.857 0.00 0.00 38.43 5.07
2226 2407 4.891627 TCCGTTAAACATGTGCATATGG 57.108 40.909 24.94 7.74 32.32 2.74
2284 2475 2.092323 GTGCTTCTTTTCGGCCCTTAT 58.908 47.619 0.00 0.00 0.00 1.73
2337 2536 2.614481 GCATCACTCTCGGGTTTTGGTA 60.614 50.000 0.00 0.00 0.00 3.25
2338 2537 1.882352 GCATCACTCTCGGGTTTTGGT 60.882 52.381 0.00 0.00 0.00 3.67
2339 2538 0.804989 GCATCACTCTCGGGTTTTGG 59.195 55.000 0.00 0.00 0.00 3.28
2340 2539 1.466167 CAGCATCACTCTCGGGTTTTG 59.534 52.381 0.00 0.00 0.00 2.44
2370 2569 0.468585 ACCCTTTGTCGAAAACCCCC 60.469 55.000 0.00 0.00 0.00 5.40
2371 2570 0.671796 CACCCTTTGTCGAAAACCCC 59.328 55.000 0.00 0.00 0.00 4.95
2372 2571 0.671796 CCACCCTTTGTCGAAAACCC 59.328 55.000 0.00 0.00 0.00 4.11
2374 2573 4.316205 AAATCCACCCTTTGTCGAAAAC 57.684 40.909 0.00 0.00 0.00 2.43
2375 2574 6.658188 ATAAAATCCACCCTTTGTCGAAAA 57.342 33.333 0.00 0.00 0.00 2.29
2376 2575 6.262193 GATAAAATCCACCCTTTGTCGAAA 57.738 37.500 0.00 0.00 0.00 3.46
2377 2576 5.890424 GATAAAATCCACCCTTTGTCGAA 57.110 39.130 0.00 0.00 0.00 3.71
2400 2599 1.406539 GCCATGTCATGCCTTGGTAAG 59.593 52.381 10.04 0.00 33.37 2.34
2401 2600 1.272369 TGCCATGTCATGCCTTGGTAA 60.272 47.619 10.04 0.00 33.37 2.85
2417 2616 0.034574 AAGTCACACACCAGTTGCCA 60.035 50.000 0.00 0.00 0.00 4.92
2419 2618 1.668419 AGAAGTCACACACCAGTTGC 58.332 50.000 0.00 0.00 0.00 4.17
2421 2620 3.134804 AGCTAAGAAGTCACACACCAGTT 59.865 43.478 0.00 0.00 0.00 3.16
2445 2644 4.925836 TGCCATGCCATTGTGATAGATAT 58.074 39.130 0.00 0.00 0.00 1.63
2451 2651 1.491668 ACATGCCATGCCATTGTGAT 58.508 45.000 4.17 0.00 0.00 3.06
2456 2656 1.761449 TACGAACATGCCATGCCATT 58.239 45.000 4.17 0.00 0.00 3.16
2465 2665 6.370593 TGTCTCTTCAATTTTACGAACATGC 58.629 36.000 0.00 0.00 0.00 4.06
2532 2759 4.993705 AGGGGAAGATACAAACACTTGA 57.006 40.909 0.00 0.00 36.33 3.02
2546 2773 6.240549 ACTACATTGTCAGATAAGGGGAAG 57.759 41.667 0.00 0.00 0.00 3.46
2577 2805 7.550551 CCTATACATCAGCGGAACATCAATATT 59.449 37.037 0.00 0.00 0.00 1.28
2590 2818 4.899502 AGGGAATTTCCTATACATCAGCG 58.100 43.478 14.95 0.00 36.57 5.18
2596 2824 7.265599 TGAACAGAAGGGAATTTCCTATACA 57.734 36.000 5.46 0.00 36.57 2.29
2638 2866 7.567994 TCTGTACTAGTGAGGAGTCCTATTCTA 59.432 40.741 12.99 13.25 31.76 2.10
2640 2868 6.593807 TCTGTACTAGTGAGGAGTCCTATTC 58.406 44.000 12.99 5.66 31.76 1.75
2711 3023 2.362503 TGACGATCTGGCGGTCCT 60.363 61.111 0.00 0.00 35.12 3.85
2712 3024 2.105128 CTGACGATCTGGCGGTCC 59.895 66.667 0.00 0.00 35.12 4.46
2713 3025 1.517257 CACTGACGATCTGGCGGTC 60.517 63.158 2.38 0.00 35.12 4.79
2716 3028 1.335415 CCTATCACTGACGATCTGGCG 60.335 57.143 0.00 0.00 37.29 5.69
2723 3035 2.290705 TGGACTGACCTATCACTGACGA 60.291 50.000 0.00 0.00 39.86 4.20
2757 3074 1.228154 GTCCTTTCAGGCGGTTGGT 60.228 57.895 0.00 0.00 34.61 3.67
2758 3075 0.821711 TTGTCCTTTCAGGCGGTTGG 60.822 55.000 0.00 0.00 34.61 3.77
2760 3077 2.871096 TATTGTCCTTTCAGGCGGTT 57.129 45.000 0.00 0.00 34.61 4.44
2762 3079 2.355756 CACATATTGTCCTTTCAGGCGG 59.644 50.000 0.00 0.00 34.61 6.13
2763 3080 3.270027 TCACATATTGTCCTTTCAGGCG 58.730 45.455 0.00 0.00 34.61 5.52
2766 3083 4.940046 AGTGCTCACATATTGTCCTTTCAG 59.060 41.667 2.63 0.00 0.00 3.02
2767 3084 4.910195 AGTGCTCACATATTGTCCTTTCA 58.090 39.130 2.63 0.00 0.00 2.69
2768 3085 4.333926 GGAGTGCTCACATATTGTCCTTTC 59.666 45.833 2.63 0.00 0.00 2.62
2799 3120 9.970553 AGCACCATATTGAATATACAATCAGAT 57.029 29.630 0.00 0.00 40.36 2.90
2800 3121 9.797642 AAGCACCATATTGAATATACAATCAGA 57.202 29.630 0.00 0.00 40.36 3.27
2801 3122 9.836076 CAAGCACCATATTGAATATACAATCAG 57.164 33.333 0.00 0.00 40.36 2.90
2803 3124 9.616634 CACAAGCACCATATTGAATATACAATC 57.383 33.333 0.00 0.00 40.36 2.67
2804 3125 9.135189 ACACAAGCACCATATTGAATATACAAT 57.865 29.630 0.00 0.00 42.17 2.71
2806 3127 9.620259 TTACACAAGCACCATATTGAATATACA 57.380 29.630 0.00 0.00 0.00 2.29
2809 3130 8.084073 GCATTACACAAGCACCATATTGAATAT 58.916 33.333 0.00 0.00 0.00 1.28
2810 3131 7.285172 AGCATTACACAAGCACCATATTGAATA 59.715 33.333 0.00 0.00 0.00 1.75
2811 3132 6.097270 AGCATTACACAAGCACCATATTGAAT 59.903 34.615 0.00 0.00 0.00 2.57
2813 3134 4.949238 AGCATTACACAAGCACCATATTGA 59.051 37.500 0.00 0.00 0.00 2.57
2814 3135 5.252969 AGCATTACACAAGCACCATATTG 57.747 39.130 0.00 0.00 0.00 1.90
2816 3137 5.684704 ACTAGCATTACACAAGCACCATAT 58.315 37.500 0.00 0.00 0.00 1.78
2817 3138 5.097742 ACTAGCATTACACAAGCACCATA 57.902 39.130 0.00 0.00 0.00 2.74
2872 3204 5.357257 TCAGATACTAACTGAATTTCCGGC 58.643 41.667 0.00 0.00 40.70 6.13
2952 3284 8.822805 ACTACAGAGGATATTTGTTTAGACCAA 58.177 33.333 0.00 0.00 0.00 3.67
2987 3319 7.248437 GGTCGAATTCGGATAAGAAAAACAAT 58.752 34.615 26.47 0.00 40.29 2.71
2989 3321 5.122711 GGGTCGAATTCGGATAAGAAAAACA 59.877 40.000 26.47 0.41 40.29 2.83
2992 3324 5.093849 AGGGTCGAATTCGGATAAGAAAA 57.906 39.130 26.47 1.93 40.29 2.29
2993 3325 4.748277 AGGGTCGAATTCGGATAAGAAA 57.252 40.909 26.47 2.69 40.29 2.52
3003 3335 6.256104 GCTAGAAAGACTAAAGGGTCGAATTC 59.744 42.308 0.00 0.00 40.76 2.17
3008 3340 4.425520 CAGCTAGAAAGACTAAAGGGTCG 58.574 47.826 0.00 0.00 40.76 4.79
3019 3351 1.423541 TGTTTGGGCCAGCTAGAAAGA 59.576 47.619 6.23 0.00 0.00 2.52
3028 3360 0.598065 GTAACTGCTGTTTGGGCCAG 59.402 55.000 14.54 0.00 37.59 4.85
3045 3380 7.977789 TGTGCTTCTCAATCTGTTATTTGTA 57.022 32.000 0.00 0.00 0.00 2.41
3049 3384 7.362401 GGTCAATGTGCTTCTCAATCTGTTATT 60.362 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.