Multiple sequence alignment - TraesCS4A01G085600

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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 TraesCS4A01G085600 chr4A 100.000 2669 0 0 1 2669 90083958 90086626 0.000000e+00 4929
1 TraesCS4A01G085600 chr4B 86.761 1775 98 48 319 2027 460568911 460567208 0.000000e+00 1849
2 TraesCS4A01G085600 chr4B 89.928 139 10 2 186 321 460569332 460569195 2.730000e-40 176
3 TraesCS4A01G085600 chr4B 94.059 101 6 0 1 101 460600396 460600296 1.280000e-33 154
4 TraesCS4A01G085600 chr4B 91.089 101 1 1 98 190 460600268 460600168 2.160000e-26 130
5 TraesCS4A01G085600 chr4B 85.981 107 12 2 584 690 215918432 215918329 7.810000e-21 111
6 TraesCS4A01G085600 chr4D 94.603 630 18 4 1042 1671 374297256 374296643 0.000000e+00 961
7 TraesCS4A01G085600 chr4D 92.979 527 29 6 1684 2202 374296589 374296063 0.000000e+00 761
8 TraesCS4A01G085600 chr4D 91.837 539 28 1 2144 2666 374296036 374295498 0.000000e+00 737
9 TraesCS4A01G085600 chr4D 87.725 668 33 20 319 966 374297924 374297286 0.000000e+00 734
10 TraesCS4A01G085600 chr4D 95.652 299 11 2 23 321 374298455 374298159 1.860000e-131 479
11 TraesCS4A01G085600 chr7D 86.336 666 62 13 2025 2665 472923064 472922403 0.000000e+00 699
12 TraesCS4A01G085600 chr7D 85.970 670 69 8 2024 2668 5285304 5284635 0.000000e+00 693
13 TraesCS4A01G085600 chr3A 86.099 669 68 9 2024 2668 505233587 505234254 0.000000e+00 697
14 TraesCS4A01G085600 chr5D 85.970 670 67 9 2026 2668 527147460 527146791 0.000000e+00 691
15 TraesCS4A01G085600 chr1D 85.928 668 70 9 2024 2668 346392753 346392087 0.000000e+00 691
16 TraesCS4A01G085600 chr2D 85.481 675 67 12 2022 2668 37012312 37012983 0.000000e+00 675
17 TraesCS4A01G085600 chr2D 82.836 670 67 17 2023 2668 60771152 60771797 8.350000e-155 556
18 TraesCS4A01G085600 chr2D 85.223 494 53 5 2023 2496 596591269 596590776 8.590000e-135 490
19 TraesCS4A01G085600 chr2D 82.103 447 55 13 2015 2438 402312424 402312868 2.530000e-95 359
20 TraesCS4A01G085600 chr1B 84.431 668 80 11 2024 2667 231623544 231624211 1.040000e-178 636
21 TraesCS4A01G085600 chr6B 84.122 655 92 8 2025 2668 583589033 583588380 8.110000e-175 623
22 TraesCS4A01G085600 chr6B 81.449 345 48 14 2023 2355 10583920 10584260 4.380000e-68 268
23 TraesCS4A01G085600 chr6D 84.186 645 88 11 2036 2668 159336520 159337162 4.880000e-172 614
24 TraesCS4A01G085600 chr1A 88.125 480 48 7 2197 2668 291971606 291972084 1.790000e-156 562
25 TraesCS4A01G085600 chr2A 85.047 107 13 2 584 690 590402441 590402544 3.630000e-19 106


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 TraesCS4A01G085600 chr4A 90083958 90086626 2668 False 4929.0 4929 100.0000 1 2669 1 chr4A.!!$F1 2668
1 TraesCS4A01G085600 chr4B 460567208 460569332 2124 True 1012.5 1849 88.3445 186 2027 2 chr4B.!!$R2 1841
2 TraesCS4A01G085600 chr4D 374295498 374298455 2957 True 734.4 961 92.5592 23 2666 5 chr4D.!!$R1 2643
3 TraesCS4A01G085600 chr7D 472922403 472923064 661 True 699.0 699 86.3360 2025 2665 1 chr7D.!!$R2 640
4 TraesCS4A01G085600 chr7D 5284635 5285304 669 True 693.0 693 85.9700 2024 2668 1 chr7D.!!$R1 644
5 TraesCS4A01G085600 chr3A 505233587 505234254 667 False 697.0 697 86.0990 2024 2668 1 chr3A.!!$F1 644
6 TraesCS4A01G085600 chr5D 527146791 527147460 669 True 691.0 691 85.9700 2026 2668 1 chr5D.!!$R1 642
7 TraesCS4A01G085600 chr1D 346392087 346392753 666 True 691.0 691 85.9280 2024 2668 1 chr1D.!!$R1 644
8 TraesCS4A01G085600 chr2D 37012312 37012983 671 False 675.0 675 85.4810 2022 2668 1 chr2D.!!$F1 646
9 TraesCS4A01G085600 chr2D 60771152 60771797 645 False 556.0 556 82.8360 2023 2668 1 chr2D.!!$F2 645
10 TraesCS4A01G085600 chr1B 231623544 231624211 667 False 636.0 636 84.4310 2024 2667 1 chr1B.!!$F1 643
11 TraesCS4A01G085600 chr6B 583588380 583589033 653 True 623.0 623 84.1220 2025 2668 1 chr6B.!!$R1 643
12 TraesCS4A01G085600 chr6D 159336520 159337162 642 False 614.0 614 84.1860 2036 2668 1 chr6D.!!$F1 632

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
863 1180 0.102481 CGCCATTCGGTACAGCTACT 59.898 55.0 0.0 0.0 33.28 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2932 0.459237 GTGCTACGCTGAGTCATGCT 60.459 55.0 11.22 0.0 0.0 3.79 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
19 20 2.730550 CCATTGTCTGAAACTTGGGC 57.269 50.000 0.00 0.00 31.77 5.36
20 21 1.962807 CCATTGTCTGAAACTTGGGCA 59.037 47.619 0.00 0.00 31.77 5.36
21 22 2.564062 CCATTGTCTGAAACTTGGGCAT 59.436 45.455 0.00 0.00 31.77 4.40
97 98 2.472816 CGTTTGGGATGCAATAATGGC 58.527 47.619 0.00 0.00 0.00 4.40
105 106 1.253593 TGCAATAATGGCGGGCACAA 61.254 50.000 6.33 0.00 0.00 3.33
209 210 3.009143 GTGGGTCTAGTTGGTGGAATCTT 59.991 47.826 0.00 0.00 0.00 2.40
217 218 2.700773 GGTGGAATCTTGTGGCCGC 61.701 63.158 10.11 10.11 0.00 6.53
218 219 2.361104 TGGAATCTTGTGGCCGCC 60.361 61.111 15.15 1.04 0.00 6.13
220 221 2.044946 GAATCTTGTGGCCGCCCT 60.045 61.111 15.15 0.00 0.00 5.19
243 244 6.351456 CCTCCCCGCAAAAAGGAAAATATAAA 60.351 38.462 0.00 0.00 0.00 1.40
265 266 3.996150 ACTGAACTTTGGTTGCATCAG 57.004 42.857 7.89 7.89 35.58 2.90
327 617 8.713971 GGAAATCTATTCCCCATTTTTGGTTAT 58.286 33.333 0.00 0.00 32.48 1.89
336 626 6.937465 TCCCCATTTTTGGTTATAAAGTTTGC 59.063 34.615 0.00 0.00 0.00 3.68
343 633 8.426881 TTTTGGTTATAAAGTTTGCCTTGTTC 57.573 30.769 0.00 0.00 32.32 3.18
395 685 7.815840 TTGAAGTTAAATGTCACATTCCTCA 57.184 32.000 2.74 0.30 0.00 3.86
397 687 8.231692 TGAAGTTAAATGTCACATTCCTCAAA 57.768 30.769 2.74 0.00 0.00 2.69
398 688 8.690884 TGAAGTTAAATGTCACATTCCTCAAAA 58.309 29.630 2.74 0.00 0.00 2.44
399 689 9.185192 GAAGTTAAATGTCACATTCCTCAAAAG 57.815 33.333 2.74 0.00 0.00 2.27
423 713 2.226962 AAAGTCAGATGCCCTGCAAT 57.773 45.000 0.00 0.00 43.62 3.56
430 720 4.098349 GTCAGATGCCCTGCAATAATGAAA 59.902 41.667 0.00 0.00 43.62 2.69
439 729 7.022979 GCCCTGCAATAATGAAAAATTTGAAC 58.977 34.615 0.00 0.00 0.00 3.18
505 795 1.353022 AGGGCGTTTCAATAGGGTTCA 59.647 47.619 0.00 0.00 0.00 3.18
518 808 3.733443 AGGGTTCATTGTGTTTTGAGC 57.267 42.857 0.00 0.00 0.00 4.26
549 839 2.294233 AGTCATTGGTGTGTGCATTGAC 59.706 45.455 0.00 0.00 33.84 3.18
656 973 9.283420 CTGTATTTCAGTGCTAGATATACATCG 57.717 37.037 12.95 0.00 38.40 3.84
674 991 5.467705 ACATCGGTTAGAGTGACAAGTAAC 58.532 41.667 0.00 0.00 0.00 2.50
681 998 6.313905 GGTTAGAGTGACAAGTAACATGGATG 59.686 42.308 0.00 0.00 0.00 3.51
682 999 4.836825 AGAGTGACAAGTAACATGGATGG 58.163 43.478 0.00 0.00 0.00 3.51
719 1036 3.189606 TCCCAAGAGAAGGAATTGGCTA 58.810 45.455 0.00 0.00 41.79 3.93
858 1175 1.813753 CCCACGCCATTCGGTACAG 60.814 63.158 0.00 0.00 43.86 2.74
859 1176 2.461110 CCACGCCATTCGGTACAGC 61.461 63.158 0.00 0.00 43.86 4.40
860 1177 1.447838 CACGCCATTCGGTACAGCT 60.448 57.895 0.00 0.00 43.86 4.24
861 1178 0.179121 CACGCCATTCGGTACAGCTA 60.179 55.000 0.00 0.00 43.86 3.32
862 1179 0.179119 ACGCCATTCGGTACAGCTAC 60.179 55.000 0.00 0.00 43.86 3.58
863 1180 0.102481 CGCCATTCGGTACAGCTACT 59.898 55.000 0.00 0.00 33.28 2.57
909 1226 2.543687 CTACAGTAGTGCGCTGCCGT 62.544 60.000 10.80 9.91 37.47 5.68
910 1227 2.537792 TACAGTAGTGCGCTGCCGTC 62.538 60.000 10.80 0.00 37.47 4.79
911 1228 3.374402 AGTAGTGCGCTGCCGTCT 61.374 61.111 10.80 0.15 36.67 4.18
912 1229 2.044555 AGTAGTGCGCTGCCGTCTA 61.045 57.895 10.80 0.00 36.67 2.59
913 1230 1.065928 GTAGTGCGCTGCCGTCTAT 59.934 57.895 10.80 0.00 36.67 1.98
914 1231 0.935366 GTAGTGCGCTGCCGTCTATC 60.935 60.000 10.80 0.00 36.67 2.08
915 1232 1.381165 TAGTGCGCTGCCGTCTATCA 61.381 55.000 10.80 0.00 36.67 2.15
916 1233 2.104928 TGCGCTGCCGTCTATCAG 59.895 61.111 9.73 0.00 36.67 2.90
1010 1327 1.111277 GTCCACAGCAAAACCCAACT 58.889 50.000 0.00 0.00 0.00 3.16
1013 1330 1.067516 CCACAGCAAAACCCAACTGAG 59.932 52.381 0.00 0.00 34.25 3.35
1017 1334 2.030805 CAGCAAAACCCAACTGAGCTAC 60.031 50.000 0.00 0.00 31.67 3.58
1018 1335 1.069227 GCAAAACCCAACTGAGCTACG 60.069 52.381 0.00 0.00 0.00 3.51
1019 1336 2.218603 CAAAACCCAACTGAGCTACGT 58.781 47.619 0.00 0.00 0.00 3.57
1020 1337 3.395639 CAAAACCCAACTGAGCTACGTA 58.604 45.455 0.00 0.00 0.00 3.57
1023 1340 5.410355 AAACCCAACTGAGCTACGTATAA 57.590 39.130 0.00 0.00 0.00 0.98
1024 1341 4.382345 ACCCAACTGAGCTACGTATAAC 57.618 45.455 0.00 0.00 0.00 1.89
1025 1342 4.021916 ACCCAACTGAGCTACGTATAACT 58.978 43.478 0.00 0.00 0.00 2.24
1039 1356 5.430007 ACGTATAACTAGTCACTCTGCTCT 58.570 41.667 0.00 0.00 0.00 4.09
1047 1364 1.472480 GTCACTCTGCTCTCTCACTCC 59.528 57.143 0.00 0.00 0.00 3.85
1051 1368 0.962855 TCTGCTCTCTCACTCCACCG 60.963 60.000 0.00 0.00 0.00 4.94
1092 1416 0.907230 AGAGAAGCACCAGGGGAGTC 60.907 60.000 0.00 0.00 0.00 3.36
1093 1417 1.904990 GAGAAGCACCAGGGGAGTCC 61.905 65.000 0.00 0.00 0.00 3.85
1094 1418 3.316573 GAAGCACCAGGGGAGTCCG 62.317 68.421 2.26 0.00 41.52 4.79
1325 1649 2.496070 CACAGTCGATTACTCCTTCCCA 59.504 50.000 0.00 0.00 35.76 4.37
1326 1650 2.496470 ACAGTCGATTACTCCTTCCCAC 59.504 50.000 0.00 0.00 35.76 4.61
1327 1651 2.108970 AGTCGATTACTCCTTCCCACC 58.891 52.381 0.00 0.00 30.33 4.61
1343 1667 1.209128 CACCGTTGCTCCGTATCATC 58.791 55.000 0.00 0.00 0.00 2.92
1378 1702 4.177026 GTGATGCGTGTCTTTGATCTACT 58.823 43.478 0.00 0.00 0.00 2.57
1402 1726 1.045407 AGTGTTCAGCTACAACCCGA 58.955 50.000 5.48 0.00 0.00 5.14
1403 1727 1.623811 AGTGTTCAGCTACAACCCGAT 59.376 47.619 5.48 0.00 0.00 4.18
1588 1912 0.383491 CGTCACTGCAAACTGAAGCG 60.383 55.000 0.00 0.00 0.00 4.68
1589 1913 0.937304 GTCACTGCAAACTGAAGCGA 59.063 50.000 0.00 0.00 0.00 4.93
1590 1914 1.070309 GTCACTGCAAACTGAAGCGAG 60.070 52.381 0.00 0.00 0.00 5.03
1591 1915 0.940126 CACTGCAAACTGAAGCGAGT 59.060 50.000 0.00 0.00 0.00 4.18
1592 1916 1.070309 CACTGCAAACTGAAGCGAGTC 60.070 52.381 0.00 0.00 0.00 3.36
1614 1938 1.871772 CTGCAGCTTCCGGTTTCAG 59.128 57.895 0.00 0.00 0.00 3.02
1672 1997 6.363088 CGCATGTGAAAACATCAATAAAGTGT 59.637 34.615 0.00 0.00 40.50 3.55
1695 2062 1.079750 GAACTCAGTGACTCCCCGC 60.080 63.158 0.00 0.00 0.00 6.13
1768 2144 1.142748 GATGCAGAGACGGAGGTGG 59.857 63.158 0.00 0.00 0.00 4.61
1936 2312 3.331150 TGTTTCCAACAGTACGCATAGG 58.669 45.455 0.00 0.00 36.25 2.57
1950 2326 1.427809 CATAGGGAGCCATGGTCTGA 58.572 55.000 14.67 0.00 0.00 3.27
2006 2382 2.435805 AGCTTTGAACCACTCTCACTCA 59.564 45.455 0.00 0.00 0.00 3.41
2009 2385 4.635223 CTTTGAACCACTCTCACTCATGA 58.365 43.478 0.00 0.00 0.00 3.07
2055 2434 1.587066 AAGAAGGTTATACCCCGGCA 58.413 50.000 0.00 0.00 39.75 5.69
2083 2462 2.953648 TCAATCGATGCATGAAGCCATT 59.046 40.909 2.46 0.00 44.83 3.16
2091 2470 7.140705 TCGATGCATGAAGCCATTTTTATTAG 58.859 34.615 2.46 0.00 44.83 1.73
2181 2564 6.950842 ACTTGATAATGTGGAGTGATCTCAA 58.049 36.000 0.00 0.00 42.05 3.02
2233 2717 0.396435 TCGGAATCAACAGCTGGTGT 59.604 50.000 30.13 13.43 43.24 4.16
2279 2763 1.463444 GCACACGTTTTAGAAGCCGAT 59.537 47.619 0.00 0.00 0.00 4.18
2308 2792 1.470632 CGGAGCACTGACTCATCTTCC 60.471 57.143 0.00 0.00 38.50 3.46
2355 2843 3.338126 GACATCCGTCGACGCCACT 62.338 63.158 31.73 13.80 38.18 4.00
2444 2932 1.599518 CGTAGCACCTGCCAACCAA 60.600 57.895 0.00 0.00 43.38 3.67
2649 3149 0.107456 CCCCGAAGCAGCATGAGTAT 59.893 55.000 0.00 0.00 39.69 2.12
2668 3168 1.842720 TGTCGACAACAGTTACACGG 58.157 50.000 17.62 0.00 32.81 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.962807 TGCCCAAGTTTCAGACAATGG 59.037 47.619 0.00 0.00 37.29 3.16
1 2 3.006110 ACATGCCCAAGTTTCAGACAATG 59.994 43.478 0.00 0.00 0.00 2.82
2 3 3.233507 ACATGCCCAAGTTTCAGACAAT 58.766 40.909 0.00 0.00 0.00 2.71
5 6 2.029918 GGAACATGCCCAAGTTTCAGAC 60.030 50.000 0.00 0.00 0.00 3.51
7 8 1.962807 TGGAACATGCCCAAGTTTCAG 59.037 47.619 5.06 0.00 30.13 3.02
8 9 1.962807 CTGGAACATGCCCAAGTTTCA 59.037 47.619 8.54 0.00 38.20 2.69
9 10 1.963515 ACTGGAACATGCCCAAGTTTC 59.036 47.619 8.54 0.00 38.20 2.78
10 11 1.963515 GACTGGAACATGCCCAAGTTT 59.036 47.619 8.54 0.00 38.20 2.66
11 12 1.133513 TGACTGGAACATGCCCAAGTT 60.134 47.619 8.54 0.00 38.20 2.66
12 13 0.478072 TGACTGGAACATGCCCAAGT 59.522 50.000 8.54 8.51 38.20 3.16
13 14 1.171308 CTGACTGGAACATGCCCAAG 58.829 55.000 8.54 5.99 38.20 3.61
14 15 0.251297 CCTGACTGGAACATGCCCAA 60.251 55.000 8.54 0.00 38.20 4.12
15 16 1.379916 CCTGACTGGAACATGCCCA 59.620 57.895 7.16 7.16 38.20 5.36
16 17 2.048603 GCCTGACTGGAACATGCCC 61.049 63.158 1.91 0.00 38.20 5.36
17 18 1.303561 TGCCTGACTGGAACATGCC 60.304 57.895 1.91 0.00 38.20 4.40
18 19 0.607489 ACTGCCTGACTGGAACATGC 60.607 55.000 1.91 0.00 38.20 4.06
19 20 1.271001 TGACTGCCTGACTGGAACATG 60.271 52.381 1.91 0.00 38.20 3.21
20 21 1.059098 TGACTGCCTGACTGGAACAT 58.941 50.000 1.91 0.00 38.20 2.71
21 22 0.106708 GTGACTGCCTGACTGGAACA 59.893 55.000 1.91 0.00 38.35 3.18
52 53 0.036010 ATGAACCAAGAGCCCGTGAG 60.036 55.000 0.00 0.00 0.00 3.51
105 106 4.141688 GCTTTAGGTGTACTTATCCAGGCT 60.142 45.833 0.00 0.00 0.00 4.58
139 140 0.830023 TGTAAACCAAAGCCCCCTGC 60.830 55.000 0.00 0.00 41.71 4.85
217 218 0.830023 TTTCCTTTTTGCGGGGAGGG 60.830 55.000 0.00 0.00 0.00 4.30
218 219 1.044611 TTTTCCTTTTTGCGGGGAGG 58.955 50.000 0.00 0.00 0.00 4.30
220 221 6.607004 TTTATATTTTCCTTTTTGCGGGGA 57.393 33.333 0.00 0.00 0.00 4.81
243 244 5.048504 CACTGATGCAACCAAAGTTCAGTAT 60.049 40.000 13.39 0.00 36.00 2.12
265 266 2.412089 CGATTCGACCTTGGAACTTCAC 59.588 50.000 0.00 0.00 0.00 3.18
322 612 9.569167 GATAAGAACAAGGCAAACTTTATAACC 57.431 33.333 0.00 0.00 37.29 2.85
327 617 6.311735 AGGGATAAGAACAAGGCAAACTTTA 58.688 36.000 0.00 0.00 37.29 1.85
336 626 6.497259 TGTAGGCTATAGGGATAAGAACAAGG 59.503 42.308 0.00 0.00 0.00 3.61
343 633 6.493802 TCAAGTGTGTAGGCTATAGGGATAAG 59.506 42.308 0.00 0.00 0.00 1.73
409 699 4.659111 TTTCATTATTGCAGGGCATCTG 57.341 40.909 2.37 2.37 46.03 2.90
475 765 5.975693 ATTGAAACGCCCTAAATGAAGAA 57.024 34.783 0.00 0.00 0.00 2.52
505 795 5.324409 TCCTATTCCTGCTCAAAACACAAT 58.676 37.500 0.00 0.00 0.00 2.71
518 808 4.194640 CACACCAATGACTCCTATTCCTG 58.805 47.826 0.00 0.00 0.00 3.86
650 967 6.207221 TGTTACTTGTCACTCTAACCGATGTA 59.793 38.462 0.00 0.00 0.00 2.29
651 968 5.010314 TGTTACTTGTCACTCTAACCGATGT 59.990 40.000 0.00 0.00 0.00 3.06
656 973 5.790593 TCCATGTTACTTGTCACTCTAACC 58.209 41.667 0.00 0.00 0.00 2.85
674 991 0.037877 GATGCTCCCTCCCATCCATG 59.962 60.000 0.00 0.00 33.43 3.66
681 998 1.283321 GGGATAATGATGCTCCCTCCC 59.717 57.143 5.54 0.00 44.49 4.30
682 999 2.797177 GGGATAATGATGCTCCCTCC 57.203 55.000 5.54 0.00 44.49 4.30
858 1175 7.110043 ACCAAAATGGAGTAGTAGTAGTAGC 57.890 40.000 2.85 0.00 40.96 3.58
887 1204 1.135199 GGCAGCGCACTACTGTAGTTA 60.135 52.381 17.46 0.00 36.76 2.24
888 1205 0.389948 GGCAGCGCACTACTGTAGTT 60.390 55.000 17.46 0.96 36.76 2.24
889 1206 1.215647 GGCAGCGCACTACTGTAGT 59.784 57.895 14.53 14.53 40.28 2.73
898 1215 2.202743 TGATAGACGGCAGCGCAC 60.203 61.111 11.47 0.00 0.00 5.34
901 1218 0.945099 TAGACTGATAGACGGCAGCG 59.055 55.000 0.00 0.00 35.57 5.18
916 1233 5.059833 GGATCCAATCACAAGTCCATAGAC 58.940 45.833 6.95 0.00 43.89 2.59
993 1310 1.067516 CTCAGTTGGGTTTTGCTGTGG 59.932 52.381 0.00 0.00 0.00 4.17
1010 1327 6.479331 CAGAGTGACTAGTTATACGTAGCTCA 59.521 42.308 0.08 0.00 0.00 4.26
1013 1330 5.236911 AGCAGAGTGACTAGTTATACGTAGC 59.763 44.000 0.08 4.56 0.00 3.58
1017 1334 5.756347 AGAGAGCAGAGTGACTAGTTATACG 59.244 44.000 0.00 0.00 0.00 3.06
1018 1335 6.764085 TGAGAGAGCAGAGTGACTAGTTATAC 59.236 42.308 0.00 0.00 0.00 1.47
1019 1336 6.764085 GTGAGAGAGCAGAGTGACTAGTTATA 59.236 42.308 0.00 0.00 0.00 0.98
1020 1337 5.588648 GTGAGAGAGCAGAGTGACTAGTTAT 59.411 44.000 0.00 0.00 0.00 1.89
1023 1340 3.009033 AGTGAGAGAGCAGAGTGACTAGT 59.991 47.826 0.00 0.00 0.00 2.57
1024 1341 3.609853 AGTGAGAGAGCAGAGTGACTAG 58.390 50.000 0.00 0.00 0.00 2.57
1025 1342 3.605634 GAGTGAGAGAGCAGAGTGACTA 58.394 50.000 0.00 0.00 0.00 2.59
1039 1356 2.131067 TGTGTGCGGTGGAGTGAGA 61.131 57.895 0.00 0.00 0.00 3.27
1047 1364 1.217585 CTCTGTGAGTGTGTGCGGTG 61.218 60.000 0.00 0.00 0.00 4.94
1051 1368 0.601311 GTCCCTCTGTGAGTGTGTGC 60.601 60.000 0.00 0.00 0.00 4.57
1092 1416 1.825191 CCATTGCCATCACTCCCGG 60.825 63.158 0.00 0.00 0.00 5.73
1093 1417 2.484062 GCCATTGCCATCACTCCCG 61.484 63.158 0.00 0.00 0.00 5.14
1094 1418 1.076485 AGCCATTGCCATCACTCCC 60.076 57.895 0.00 0.00 38.69 4.30
1095 1419 0.394762 TGAGCCATTGCCATCACTCC 60.395 55.000 0.00 0.00 38.69 3.85
1096 1420 1.022735 CTGAGCCATTGCCATCACTC 58.977 55.000 0.00 0.00 38.69 3.51
1097 1421 0.395311 CCTGAGCCATTGCCATCACT 60.395 55.000 0.00 0.00 38.69 3.41
1325 1649 0.821517 TGATGATACGGAGCAACGGT 59.178 50.000 0.00 2.74 38.39 4.83
1326 1650 1.209128 GTGATGATACGGAGCAACGG 58.791 55.000 0.00 0.00 38.39 4.44
1327 1651 1.202417 AGGTGATGATACGGAGCAACG 60.202 52.381 0.00 0.00 40.31 4.10
1343 1667 1.284657 GCATCACATGAGACGAGGTG 58.715 55.000 0.00 0.00 0.00 4.00
1378 1702 0.531753 TTGTAGCTGAACACTGCGCA 60.532 50.000 10.98 10.98 34.51 6.09
1643 1968 0.976963 GATGTTTTCACATGCGCACG 59.023 50.000 14.90 7.29 44.22 5.34
1672 1997 1.416401 GGGAGTCACTGAGTTCCACAA 59.584 52.381 6.34 0.00 31.10 3.33
1695 2062 5.464057 TGTTAACAACTCAGGATACAACACG 59.536 40.000 5.64 0.00 41.41 4.49
1761 2134 3.532542 CGAAAAGAAGGATACCACCTCC 58.467 50.000 0.00 0.00 39.62 4.30
1787 2163 5.126396 ACTGGCTGCTGTATTTTTCTTTC 57.874 39.130 0.00 0.00 0.00 2.62
1817 2193 3.071023 ACCCTCCATATCCACACATAACG 59.929 47.826 0.00 0.00 0.00 3.18
1936 2312 1.622811 CCTAGATCAGACCATGGCTCC 59.377 57.143 13.04 0.91 0.00 4.70
1950 2326 4.762251 GGCTAATTGGAATTTCGCCTAGAT 59.238 41.667 13.65 0.00 39.07 1.98
2046 2423 0.767998 TTGATGCATATGCCGGGGTA 59.232 50.000 24.54 5.39 41.18 3.69
2091 2470 7.739498 TCCTGTTAGACTTTTGTGGAATAAC 57.261 36.000 0.00 0.00 0.00 1.89
2129 2511 1.534476 TGAGTGGTGGCTTCGGGTA 60.534 57.895 0.00 0.00 0.00 3.69
2181 2564 6.215431 TGTGGATCGATTTTAGATATGGGGAT 59.785 38.462 0.00 0.00 0.00 3.85
2233 2717 1.202533 GGATGCGCTTTAGGTCTGCTA 60.203 52.381 9.73 0.00 0.00 3.49
2279 2763 3.225940 AGTCAGTGCTCCGATGATGATA 58.774 45.455 0.00 0.00 0.00 2.15
2308 2792 3.383620 CAAGGATTGGATCTCTCTCCG 57.616 52.381 0.00 0.00 43.94 4.63
2444 2932 0.459237 GTGCTACGCTGAGTCATGCT 60.459 55.000 11.22 0.00 0.00 3.79
2590 3086 1.953138 CAGATCGGACGATGGCAGC 60.953 63.158 12.40 0.00 34.60 5.25
2649 3149 1.842720 CCGTGTAACTGTTGTCGACA 58.157 50.000 15.76 15.76 36.65 4.35


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

AutoCloner maintained by Alex Coulton.