Multiple sequence alignment - TraesCS2D01G379900

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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 TraesCS2D01G379900 chr2D 100.000 3023 0 0 1 3023 484381564 484378542 0.000000e+00 5583.0
1 TraesCS2D01G379900 chr2D 91.212 751 47 11 1 750 484834702 484833970 0.000000e+00 1003.0
2 TraesCS2D01G379900 chr2D 87.248 149 14 4 1859 2003 126970804 126970657 6.700000e-37 165.0
3 TraesCS2D01G379900 chr2B 86.854 1704 117 45 838 2509 569125113 569126741 0.000000e+00 1807.0
4 TraesCS2D01G379900 chr2B 90.800 750 46 11 1 750 569486414 569485688 0.000000e+00 981.0
5 TraesCS2D01G379900 chr2B 87.918 538 51 13 2491 3023 569127446 569127974 3.310000e-174 621.0
6 TraesCS2D01G379900 chr2B 76.809 677 111 32 1850 2501 473766837 473766182 3.730000e-89 339.0
7 TraesCS2D01G379900 chr2B 86.577 149 12 7 1859 2003 796276540 796276684 1.120000e-34 158.0
8 TraesCS2D01G379900 chr2B 93.814 97 6 0 747 843 569113333 569113429 2.430000e-31 147.0
9 TraesCS2D01G379900 chr2B 95.714 70 3 0 681 750 569113204 569113273 2.460000e-21 113.0
10 TraesCS2D01G379900 chr2B 95.238 63 3 0 747 809 569485628 569485566 1.920000e-17 100.0
11 TraesCS2D01G379900 chr2B 90.411 73 6 1 2573 2644 213108223 213108295 8.920000e-16 95.3
12 TraesCS2D01G379900 chr2A 89.846 1428 91 29 881 2284 628678499 628677102 0.000000e+00 1784.0
13 TraesCS2D01G379900 chr2A 85.940 697 67 16 2353 3023 628677077 628676386 0.000000e+00 715.0
14 TraesCS2D01G379900 chr3A 80.122 654 74 32 1862 2505 22532272 22531665 1.290000e-118 436.0
15 TraesCS2D01G379900 chr3A 79.084 655 74 31 1859 2499 7314024 7313419 2.830000e-105 392.0
16 TraesCS2D01G379900 chr3A 76.949 590 75 33 1860 2437 430319223 430318683 2.290000e-71 279.0
17 TraesCS2D01G379900 chr3A 83.444 151 20 4 1859 2006 681124390 681124242 5.260000e-28 135.0
18 TraesCS2D01G379900 chr5D 79.898 587 68 25 1942 2498 389004422 389003856 4.730000e-103 385.0
19 TraesCS2D01G379900 chr5D 82.667 150 17 9 1859 2003 317725861 317726006 1.140000e-24 124.0
20 TraesCS2D01G379900 chr5B 78.419 658 65 36 1859 2497 513715939 513715340 1.030000e-94 357.0
21 TraesCS2D01G379900 chr7B 76.489 655 72 31 1859 2497 125013829 125014417 6.380000e-72 281.0
22 TraesCS2D01G379900 chr7B 78.149 389 52 20 1859 2236 724932507 724932873 1.830000e-52 217.0
23 TraesCS2D01G379900 chr4A 75.149 672 103 38 1863 2485 703165547 703166203 1.080000e-64 257.0
24 TraesCS2D01G379900 chr4A 84.581 227 21 9 2285 2498 684280166 684279941 2.360000e-51 213.0
25 TraesCS2D01G379900 chr4A 76.734 447 56 22 1858 2270 684279944 684280376 3.950000e-49 206.0
26 TraesCS2D01G379900 chr1D 74.924 662 103 44 1860 2500 910548 909929 8.370000e-61 244.0
27 TraesCS2D01G379900 chr6D 87.500 200 18 2 2306 2498 471924919 471924720 1.090000e-54 224.0
28 TraesCS2D01G379900 chr6D 85.816 141 16 4 2823 2961 10339409 10339271 2.430000e-31 147.0
29 TraesCS2D01G379900 chr7D 86.294 197 19 3 2306 2499 567338143 567338334 1.100000e-49 207.0
30 TraesCS2D01G379900 chr7D 85.167 209 21 5 2294 2498 567338106 567337904 3.950000e-49 206.0
31 TraesCS2D01G379900 chr1A 74.603 504 79 23 1859 2348 2538313 2538781 3.100000e-40 176.0
32 TraesCS2D01G379900 chr1A 83.815 173 27 1 2813 2985 558176715 558176544 2.410000e-36 163.0
33 TraesCS2D01G379900 chr3B 80.321 249 33 9 2247 2487 104590523 104590763 1.110000e-39 174.0
34 TraesCS2D01G379900 chr3B 81.046 153 26 3 2834 2985 723267582 723267732 5.290000e-23 119.0
35 TraesCS2D01G379900 chr1B 73.885 471 64 28 1849 2280 3663664 3663214 1.890000e-27 134.0
36 TraesCS2D01G379900 chr7A 81.410 156 24 4 2831 2983 726736320 726736473 4.090000e-24 122.0
37 TraesCS2D01G379900 chr6B 91.304 69 5 1 2577 2644 507505875 507505807 3.210000e-15 93.5


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 TraesCS2D01G379900 chr2D 484378542 484381564 3022 True 5583.0 5583 100.000 1 3023 1 chr2D.!!$R2 3022
1 TraesCS2D01G379900 chr2D 484833970 484834702 732 True 1003.0 1003 91.212 1 750 1 chr2D.!!$R3 749
2 TraesCS2D01G379900 chr2B 569125113 569127974 2861 False 1214.0 1807 87.386 838 3023 2 chr2B.!!$F4 2185
3 TraesCS2D01G379900 chr2B 569485566 569486414 848 True 540.5 981 93.019 1 809 2 chr2B.!!$R2 808
4 TraesCS2D01G379900 chr2B 473766182 473766837 655 True 339.0 339 76.809 1850 2501 1 chr2B.!!$R1 651
5 TraesCS2D01G379900 chr2A 628676386 628678499 2113 True 1249.5 1784 87.893 881 3023 2 chr2A.!!$R1 2142
6 TraesCS2D01G379900 chr3A 22531665 22532272 607 True 436.0 436 80.122 1862 2505 1 chr3A.!!$R2 643
7 TraesCS2D01G379900 chr3A 7313419 7314024 605 True 392.0 392 79.084 1859 2499 1 chr3A.!!$R1 640
8 TraesCS2D01G379900 chr3A 430318683 430319223 540 True 279.0 279 76.949 1860 2437 1 chr3A.!!$R3 577
9 TraesCS2D01G379900 chr5D 389003856 389004422 566 True 385.0 385 79.898 1942 2498 1 chr5D.!!$R1 556
10 TraesCS2D01G379900 chr5B 513715340 513715939 599 True 357.0 357 78.419 1859 2497 1 chr5B.!!$R1 638
11 TraesCS2D01G379900 chr7B 125013829 125014417 588 False 281.0 281 76.489 1859 2497 1 chr7B.!!$F1 638
12 TraesCS2D01G379900 chr4A 703165547 703166203 656 False 257.0 257 75.149 1863 2485 1 chr4A.!!$F2 622
13 TraesCS2D01G379900 chr1D 909929 910548 619 True 244.0 244 74.924 1860 2500 1 chr1D.!!$R1 640

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
591 592 0.037975 GTTTTGCCTCCATGGTGCAG 60.038 55.0 23.93 10.97 36.21 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 2526 0.036306 GAGGGTTTGACCACGACCAT 59.964 55.0 0.0 0.0 41.02 3.55 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
68 69 3.467119 ATGCACGACGCGAACGAC 61.467 61.111 28.40 21.19 46.97 4.34
131 132 2.811317 CCAGCGTGCTTCTCGTCC 60.811 66.667 0.00 0.00 0.00 4.79
236 237 2.046988 CACAGATCCTGCACGCCA 60.047 61.111 0.00 0.00 34.37 5.69
325 326 1.535462 CCCGAAGTTGTTGATGACCAC 59.465 52.381 0.00 0.00 0.00 4.16
368 369 1.975407 GTGGTCCTCGAGGTCGGAA 60.975 63.158 30.17 8.66 40.29 4.30
437 438 1.216710 GACGAGACCCAGAGCAAGG 59.783 63.158 0.00 0.00 0.00 3.61
512 513 2.341176 GCAGTCACCGTACCCGTT 59.659 61.111 0.00 0.00 0.00 4.44
522 523 1.579429 GTACCCGTTTGGCTGCTTG 59.421 57.895 0.00 0.00 37.83 4.01
524 525 0.466555 TACCCGTTTGGCTGCTTGTT 60.467 50.000 0.00 0.00 37.83 2.83
559 560 3.774702 GTTGTTCGTCGCTCCGGC 61.775 66.667 0.00 0.00 0.00 6.13
579 580 0.936297 CGTGCTGCAGAAGTTTTGCC 60.936 55.000 20.43 2.24 40.81 4.52
589 590 0.681175 AAGTTTTGCCTCCATGGTGC 59.319 50.000 12.58 16.10 38.35 5.01
590 591 0.469705 AGTTTTGCCTCCATGGTGCA 60.470 50.000 22.29 22.29 38.35 4.57
591 592 0.037975 GTTTTGCCTCCATGGTGCAG 60.038 55.000 23.93 10.97 36.21 4.41
592 593 0.469705 TTTTGCCTCCATGGTGCAGT 60.470 50.000 23.93 0.00 36.21 4.40
593 594 1.180456 TTTGCCTCCATGGTGCAGTG 61.180 55.000 23.93 7.41 36.21 3.66
594 595 2.753043 GCCTCCATGGTGCAGTGG 60.753 66.667 19.70 11.39 38.35 4.00
595 596 2.044650 CCTCCATGGTGCAGTGGG 60.045 66.667 12.58 0.57 36.15 4.61
658 659 9.892130 ATTAAAGATAAAGATGTCTCGTTTCCT 57.108 29.630 0.00 0.00 0.00 3.36
666 667 0.109226 GTCTCGTTTCCTGTCCTCGG 60.109 60.000 0.00 0.00 0.00 4.63
683 684 7.120716 TGTCCTCGGGTACATTATGCTATATA 58.879 38.462 0.00 0.00 0.00 0.86
684 685 7.783119 TGTCCTCGGGTACATTATGCTATATAT 59.217 37.037 0.00 0.00 0.00 0.86
685 686 9.293404 GTCCTCGGGTACATTATGCTATATATA 57.707 37.037 0.00 0.00 0.00 0.86
777 841 7.946768 CGTAAGATGATTAAGTTGTGCATATCG 59.053 37.037 0.00 0.00 43.02 2.92
791 855 2.413453 GCATATCGATTTCGGAGAAGGC 59.587 50.000 1.71 0.00 45.90 4.35
803 867 3.574396 TCGGAGAAGGCTATCAATCGATT 59.426 43.478 4.39 4.39 32.73 3.34
814 878 3.266510 TCAATCGATTGAGTTCCCCTG 57.733 47.619 31.83 8.27 41.51 4.45
815 879 2.571653 TCAATCGATTGAGTTCCCCTGT 59.428 45.455 31.83 0.00 41.51 4.00
816 880 2.679837 CAATCGATTGAGTTCCCCTGTG 59.320 50.000 30.12 1.31 40.14 3.66
817 881 0.613260 TCGATTGAGTTCCCCTGTGG 59.387 55.000 0.00 0.00 0.00 4.17
828 892 3.642078 CCTGTGGGGGAATCGCTA 58.358 61.111 0.00 0.00 0.00 4.26
829 893 1.146263 CCTGTGGGGGAATCGCTAC 59.854 63.158 0.00 0.00 37.72 3.58
830 894 1.146263 CTGTGGGGGAATCGCTACC 59.854 63.158 0.00 0.00 36.68 3.18
831 895 2.108362 GTGGGGGAATCGCTACCG 59.892 66.667 0.00 0.00 32.53 4.02
832 896 3.158648 TGGGGGAATCGCTACCGG 61.159 66.667 0.00 0.00 34.56 5.28
833 897 2.841044 GGGGGAATCGCTACCGGA 60.841 66.667 9.46 0.00 34.56 5.14
834 898 2.437396 GGGGGAATCGCTACCGGAA 61.437 63.158 9.46 0.00 34.56 4.30
835 899 1.752833 GGGGAATCGCTACCGGAAT 59.247 57.895 9.46 0.00 34.56 3.01
836 900 0.602905 GGGGAATCGCTACCGGAATG 60.603 60.000 9.46 0.00 34.56 2.67
837 901 0.602905 GGGAATCGCTACCGGAATGG 60.603 60.000 9.46 0.00 46.41 3.16
861 925 2.095668 CGCACTAGAGATCGATGGTACC 60.096 54.545 0.54 4.43 0.00 3.34
863 927 3.057876 GCACTAGAGATCGATGGTACCAG 60.058 52.174 21.41 7.83 0.00 4.00
984 1048 4.567558 CGTACACGCACCTCCATAATTTTA 59.432 41.667 0.00 0.00 0.00 1.52
985 1049 5.235616 CGTACACGCACCTCCATAATTTTAT 59.764 40.000 0.00 0.00 0.00 1.40
986 1050 6.238266 CGTACACGCACCTCCATAATTTTATT 60.238 38.462 0.00 0.00 0.00 1.40
987 1051 6.524101 ACACGCACCTCCATAATTTTATTT 57.476 33.333 0.00 0.00 0.00 1.40
988 1052 6.930731 ACACGCACCTCCATAATTTTATTTT 58.069 32.000 0.00 0.00 0.00 1.82
989 1053 7.382898 ACACGCACCTCCATAATTTTATTTTT 58.617 30.769 0.00 0.00 0.00 1.94
1040 1104 2.810852 GCTGGCTCCTGCAATATAAGTC 59.189 50.000 12.12 0.00 41.91 3.01
1081 1146 3.355378 TCGGCCTCAACAATCAATCAAT 58.645 40.909 0.00 0.00 0.00 2.57
1096 1161 9.464714 CAATCAATCAATCATGGAGAAAGAATC 57.535 33.333 0.00 0.00 0.00 2.52
1107 1172 3.375299 GGAGAAAGAATCGACCCATGTTG 59.625 47.826 0.00 0.00 0.00 3.33
1190 1256 1.150567 CCTTCTCCTTCGCAGCATCG 61.151 60.000 0.00 0.00 0.00 3.84
1229 1298 4.081406 TCATCAATCTGGTTCCAGGTTTG 58.919 43.478 13.90 17.36 35.45 2.93
1247 1316 7.383843 CCAGGTTTGTGTATTTTTCGCTTTATT 59.616 33.333 0.00 0.00 0.00 1.40
1315 1384 0.599204 TCAACGCGTTCAGGAGTTCC 60.599 55.000 23.92 0.00 0.00 3.62
1720 1792 2.158300 CAAGGTTGCATCGCGTGTA 58.842 52.632 5.77 0.07 0.00 2.90
1775 1847 1.834263 ACTTCATGACTAGGGCAGACC 59.166 52.381 0.00 0.00 40.67 3.85
1788 1860 1.239347 GCAGACCAGGAGTTTTGACC 58.761 55.000 0.00 0.00 0.00 4.02
1820 1897 2.787249 CAGCACGAATTCCCAGCG 59.213 61.111 0.00 0.00 0.00 5.18
1839 1922 4.253352 GCGTATGCGTCTGTTATTTTCA 57.747 40.909 4.81 0.00 40.81 2.69
1840 1923 4.833126 GCGTATGCGTCTGTTATTTTCAT 58.167 39.130 4.81 0.00 40.81 2.57
1841 1924 5.969741 GCGTATGCGTCTGTTATTTTCATA 58.030 37.500 4.81 0.00 40.81 2.15
2003 2133 1.270550 GCATGTTGACCAGGGTTTGAG 59.729 52.381 0.00 0.00 0.00 3.02
2013 2143 2.242043 CAGGGTTTGAGCAGGTTTGAT 58.758 47.619 0.00 0.00 0.00 2.57
2110 2255 1.871676 TGCGTTTGGTGCGTGTAAATA 59.128 42.857 0.00 0.00 34.24 1.40
2133 2279 5.253330 AGTTGTGGTCAAATAACATCCGAT 58.747 37.500 0.00 0.00 35.20 4.18
2142 2288 6.870965 GTCAAATAACATCCGATGAGCTCTAT 59.129 38.462 16.19 6.82 0.00 1.98
2245 2420 1.127701 CACAAATTTTCACGCACCCG 58.872 50.000 0.00 0.00 41.14 5.28
2334 2518 9.685276 TGAATGTACTATTCATCAATCAAACCT 57.315 29.630 13.39 0.00 33.55 3.50
2341 2525 5.452078 TTCATCAATCAAACCTGGTCAAC 57.548 39.130 0.00 0.00 0.00 3.18
2342 2526 4.468713 TCATCAATCAAACCTGGTCAACA 58.531 39.130 0.00 0.00 0.00 3.33
2343 2527 5.078949 TCATCAATCAAACCTGGTCAACAT 58.921 37.500 0.00 0.00 0.00 2.71
2344 2528 4.852134 TCAATCAAACCTGGTCAACATG 57.148 40.909 0.00 0.00 0.00 3.21
2345 2529 3.573538 TCAATCAAACCTGGTCAACATGG 59.426 43.478 0.00 0.00 0.00 3.66
2346 2530 2.746279 TCAAACCTGGTCAACATGGT 57.254 45.000 0.00 0.00 33.73 3.55
2375 2579 2.457366 ACCCTCTCAACGTGCTTAAG 57.543 50.000 0.00 0.00 0.00 1.85
2397 2601 6.544928 AGATCTTGTTTTGGACCAAACTTT 57.455 33.333 19.42 1.89 32.79 2.66
2470 2678 5.880887 CCAAGTCTATACTTTTGGGGAACTC 59.119 44.000 0.00 0.00 43.60 3.01
2537 3469 7.919385 ATGGGGTGCTTTATTCAGATAAAAT 57.081 32.000 0.00 0.00 37.30 1.82
2545 3477 9.060347 TGCTTTATTCAGATAAAATAGCTCCAG 57.940 33.333 0.00 0.00 37.30 3.86
2555 3487 8.824783 AGATAAAATAGCTCCAGAATCTGCTAT 58.175 33.333 4.40 6.27 46.67 2.97
2714 3666 4.996434 GCAGGCTGACGTGGCACT 62.996 66.667 20.86 2.45 34.73 4.40
2739 3691 6.170506 ACTTAACATCTCAGATTTAACGGCA 58.829 36.000 0.00 0.00 0.00 5.69
2788 3740 0.698238 TCCACCTGTCATTGGAAGGG 59.302 55.000 9.48 0.00 39.04 3.95
2824 3778 0.108520 TGGTTTTAGCCCGACTAGCG 60.109 55.000 0.00 0.00 40.47 4.26
2884 3838 2.223456 CCGCCGATCAATGTTATTTGCA 60.223 45.455 0.00 0.00 0.00 4.08
2913 3867 9.498176 AAAGATTACCGTAGACATAGTGTTTTT 57.502 29.630 0.00 0.00 0.00 1.94
2985 3942 6.424509 ACATGATGGTTTTGTGCAATTTACTG 59.575 34.615 0.00 0.00 0.00 2.74
3005 3962 1.821759 CACACCGAACAAGTGGCCA 60.822 57.895 0.00 0.00 39.63 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.774702 GAAGCACCGGTCGTTCGC 61.775 66.667 2.59 4.54 0.00 4.70
120 121 2.125552 CATGGCGGACGAGAAGCA 60.126 61.111 0.00 0.00 0.00 3.91
154 155 2.762875 GAGGGGTGGGTCTACCGG 60.763 72.222 0.00 0.00 44.64 5.28
191 192 0.868406 CCAAGTGCTCCACGAAGTTC 59.132 55.000 0.00 0.00 41.61 3.01
251 252 3.066900 CAGTGGTCTTATACGGAGGAGTG 59.933 52.174 0.00 0.00 0.00 3.51
307 308 1.194547 CCGTGGTCATCAACAACTTCG 59.805 52.381 0.00 0.00 28.55 3.79
325 326 1.683790 GCGGACGTTCAATCTCACCG 61.684 60.000 0.00 0.00 41.44 4.94
368 369 3.153024 CGTGGTCATGGACGGATTT 57.847 52.632 0.00 0.00 32.65 2.17
449 450 2.794981 CGTTCTGTGTATAGTCGGCCTG 60.795 54.545 0.00 0.00 0.00 4.85
512 513 3.294493 GCCGGAACAAGCAGCCAA 61.294 61.111 5.05 0.00 0.00 4.52
522 523 4.508128 TCGATGGAGCGCCGGAAC 62.508 66.667 5.05 0.00 36.79 3.62
524 525 4.207281 CTTCGATGGAGCGCCGGA 62.207 66.667 5.05 0.00 36.79 5.14
559 560 0.936297 GCAAAACTTCTGCAGCACGG 60.936 55.000 9.47 1.19 39.69 4.94
563 564 0.038801 GGAGGCAAAACTTCTGCAGC 60.039 55.000 9.47 0.00 41.78 5.25
564 565 1.321474 TGGAGGCAAAACTTCTGCAG 58.679 50.000 7.63 7.63 41.78 4.41
567 568 2.029649 CACCATGGAGGCAAAACTTCTG 60.030 50.000 21.47 0.00 43.14 3.02
570 571 0.681175 GCACCATGGAGGCAAAACTT 59.319 50.000 21.47 0.00 43.14 2.66
579 580 1.377725 GACCCACTGCACCATGGAG 60.378 63.158 21.47 12.70 41.93 3.86
589 590 2.193447 CGTGAATACATCGACCCACTG 58.807 52.381 0.00 0.00 0.00 3.66
590 591 1.470979 GCGTGAATACATCGACCCACT 60.471 52.381 0.00 0.00 0.00 4.00
591 592 0.928229 GCGTGAATACATCGACCCAC 59.072 55.000 0.00 0.00 0.00 4.61
592 593 0.526739 CGCGTGAATACATCGACCCA 60.527 55.000 0.00 0.00 0.00 4.51
593 594 1.818221 GCGCGTGAATACATCGACCC 61.818 60.000 8.43 0.00 0.00 4.46
594 595 1.558383 GCGCGTGAATACATCGACC 59.442 57.895 8.43 0.00 0.00 4.79
595 596 1.195985 CGCGCGTGAATACATCGAC 59.804 57.895 24.19 0.00 0.00 4.20
641 642 3.325135 AGGACAGGAAACGAGACATCTTT 59.675 43.478 0.00 0.00 0.00 2.52
642 643 2.900546 AGGACAGGAAACGAGACATCTT 59.099 45.455 0.00 0.00 0.00 2.40
643 644 2.494073 GAGGACAGGAAACGAGACATCT 59.506 50.000 0.00 0.00 0.00 2.90
644 645 2.732597 CGAGGACAGGAAACGAGACATC 60.733 54.545 0.00 0.00 0.00 3.06
645 646 1.202582 CGAGGACAGGAAACGAGACAT 59.797 52.381 0.00 0.00 0.00 3.06
646 647 0.596577 CGAGGACAGGAAACGAGACA 59.403 55.000 0.00 0.00 0.00 3.41
647 648 0.109226 CCGAGGACAGGAAACGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
648 649 1.248785 CCCGAGGACAGGAAACGAGA 61.249 60.000 0.00 0.00 0.00 4.04
658 659 2.394632 AGCATAATGTACCCGAGGACA 58.605 47.619 0.00 0.00 0.00 4.02
683 684 3.711704 CTGTCTGGGACTGTGGGTTATAT 59.288 47.826 0.00 0.00 33.15 0.86
684 685 3.104512 CTGTCTGGGACTGTGGGTTATA 58.895 50.000 0.00 0.00 33.15 0.98
685 686 1.909302 CTGTCTGGGACTGTGGGTTAT 59.091 52.381 0.00 0.00 33.15 1.89
686 687 1.348064 CTGTCTGGGACTGTGGGTTA 58.652 55.000 0.00 0.00 33.15 2.85
687 688 2.056906 GCTGTCTGGGACTGTGGGTT 62.057 60.000 6.47 0.00 34.68 4.11
689 690 2.348998 GCTGTCTGGGACTGTGGG 59.651 66.667 6.47 0.00 34.68 4.61
690 691 2.348998 GGCTGTCTGGGACTGTGG 59.651 66.667 6.47 0.00 34.68 4.17
691 692 2.348998 GGGCTGTCTGGGACTGTG 59.651 66.667 6.47 0.00 34.68 3.66
692 693 3.314331 CGGGCTGTCTGGGACTGT 61.314 66.667 6.47 0.00 34.68 3.55
693 694 4.087892 CCGGGCTGTCTGGGACTG 62.088 72.222 0.00 0.38 38.27 3.51
694 695 3.625632 ATCCGGGCTGTCTGGGACT 62.626 63.158 7.39 0.00 42.31 3.85
695 696 3.083997 ATCCGGGCTGTCTGGGAC 61.084 66.667 7.39 0.00 42.31 4.46
696 697 2.764128 GATCCGGGCTGTCTGGGA 60.764 66.667 7.39 0.94 42.31 4.37
726 727 5.705441 GTCAAATCCTACATGAACTCCACAA 59.295 40.000 0.00 0.00 0.00 3.33
777 841 4.387256 CGATTGATAGCCTTCTCCGAAATC 59.613 45.833 0.00 0.00 0.00 2.17
791 855 4.993584 CAGGGGAACTCAATCGATTGATAG 59.006 45.833 34.40 26.79 44.92 2.08
811 875 1.146263 GTAGCGATTCCCCCACAGG 59.854 63.158 0.00 0.00 0.00 4.00
812 876 1.146263 GGTAGCGATTCCCCCACAG 59.854 63.158 0.00 0.00 0.00 3.66
813 877 2.727392 CGGTAGCGATTCCCCCACA 61.727 63.158 9.07 0.00 0.00 4.17
814 878 2.108362 CGGTAGCGATTCCCCCAC 59.892 66.667 9.07 0.00 0.00 4.61
815 879 3.158648 CCGGTAGCGATTCCCCCA 61.159 66.667 17.33 0.00 0.00 4.96
816 880 1.765597 ATTCCGGTAGCGATTCCCCC 61.766 60.000 17.33 0.00 0.00 5.40
817 881 0.602905 CATTCCGGTAGCGATTCCCC 60.603 60.000 17.33 0.00 0.00 4.81
818 882 0.602905 CCATTCCGGTAGCGATTCCC 60.603 60.000 17.33 0.00 0.00 3.97
819 883 2.914379 CCATTCCGGTAGCGATTCC 58.086 57.895 17.33 0.00 0.00 3.01
829 893 2.125310 TAGTGCGCACCATTCCGG 60.125 61.111 35.51 0.00 42.50 5.14
830 894 1.148157 CTCTAGTGCGCACCATTCCG 61.148 60.000 35.51 17.53 0.00 4.30
831 895 0.175760 TCTCTAGTGCGCACCATTCC 59.824 55.000 35.51 11.40 0.00 3.01
832 896 2.131183 GATCTCTAGTGCGCACCATTC 58.869 52.381 35.51 19.64 0.00 2.67
833 897 1.536922 CGATCTCTAGTGCGCACCATT 60.537 52.381 35.51 20.80 0.00 3.16
834 898 0.031314 CGATCTCTAGTGCGCACCAT 59.969 55.000 35.51 21.57 0.00 3.55
835 899 1.029947 TCGATCTCTAGTGCGCACCA 61.030 55.000 35.51 23.16 0.00 4.17
836 900 0.312416 ATCGATCTCTAGTGCGCACC 59.688 55.000 35.51 17.89 0.00 5.01
837 901 1.403493 CATCGATCTCTAGTGCGCAC 58.597 55.000 32.79 32.79 0.00 5.34
838 902 0.312102 CCATCGATCTCTAGTGCGCA 59.688 55.000 5.66 5.66 0.00 6.09
839 903 0.312416 ACCATCGATCTCTAGTGCGC 59.688 55.000 0.00 0.00 0.00 6.09
840 904 2.095668 GGTACCATCGATCTCTAGTGCG 60.096 54.545 7.15 0.00 0.00 5.34
841 905 2.885266 TGGTACCATCGATCTCTAGTGC 59.115 50.000 11.60 0.00 0.00 4.40
842 906 4.138290 ACTGGTACCATCGATCTCTAGTG 58.862 47.826 16.75 0.90 0.00 2.74
843 907 4.440826 ACTGGTACCATCGATCTCTAGT 57.559 45.455 16.75 2.40 0.00 2.57
844 908 5.776173 AAACTGGTACCATCGATCTCTAG 57.224 43.478 16.75 1.69 0.00 2.43
845 909 6.540438 AAAAACTGGTACCATCGATCTCTA 57.460 37.500 16.75 0.00 0.00 2.43
1001 1065 2.923655 CAGCGACCGCCTTGTATATATG 59.076 50.000 11.03 0.00 43.17 1.78
1040 1104 1.153289 CTGTCCCCCAAGCAGATCG 60.153 63.158 0.00 0.00 32.39 3.69
1081 1146 2.837591 TGGGTCGATTCTTTCTCCATGA 59.162 45.455 0.00 0.00 0.00 3.07
1107 1172 0.038310 CAGAAAACCCCTCCCCAGTC 59.962 60.000 0.00 0.00 0.00 3.51
1117 1182 2.594131 ACCAGCTAAACCAGAAAACCC 58.406 47.619 0.00 0.00 0.00 4.11
1247 1316 6.272318 CACCTGTTTGATTTGAAAGCTTGTA 58.728 36.000 0.00 0.00 0.00 2.41
1410 1479 3.277211 TTCGTCCGCCTGTTCTCCG 62.277 63.158 0.00 0.00 0.00 4.63
1424 1493 2.203294 GTTGCCCACCCACTTCGT 60.203 61.111 0.00 0.00 0.00 3.85
1717 1789 0.389817 GTGACGGCTGATGCAGTACA 60.390 55.000 0.00 0.00 46.89 2.90
1775 1847 1.734465 GCAGATCGGTCAAAACTCCTG 59.266 52.381 0.00 0.00 0.00 3.86
1933 2021 5.761165 TCCGGTTTTGAGACTTAAAAAGG 57.239 39.130 15.98 15.98 32.75 3.11
1935 2023 8.454570 ACTTATCCGGTTTTGAGACTTAAAAA 57.545 30.769 6.71 0.63 0.00 1.94
1936 2024 8.454570 AACTTATCCGGTTTTGAGACTTAAAA 57.545 30.769 0.00 1.23 0.00 1.52
1967 2055 6.922957 GTCAACATGCTCAAAATCTGGTTTTA 59.077 34.615 0.00 0.00 37.93 1.52
2003 2133 8.986477 ATTTACTGTTTATCAATCAAACCTGC 57.014 30.769 0.00 0.00 35.46 4.85
2110 2255 4.647611 TCGGATGTTATTTGACCACAACT 58.352 39.130 0.00 0.00 35.63 3.16
2245 2420 0.961019 TTGTGGCAACCAAGATGCTC 59.039 50.000 0.00 0.00 43.34 4.26
2313 2497 7.552687 TGACCAGGTTTGATTGATGAATAGTAC 59.447 37.037 0.00 0.00 0.00 2.73
2318 2502 5.539574 TGTTGACCAGGTTTGATTGATGAAT 59.460 36.000 0.00 0.00 0.00 2.57
2334 2518 0.250124 GACCACGACCATGTTGACCA 60.250 55.000 0.00 0.00 0.00 4.02
2341 2525 0.250727 AGGGTTTGACCACGACCATG 60.251 55.000 0.00 0.00 41.02 3.66
2342 2526 0.036306 GAGGGTTTGACCACGACCAT 59.964 55.000 0.00 0.00 41.02 3.55
2343 2527 1.052124 AGAGGGTTTGACCACGACCA 61.052 55.000 0.00 0.00 41.02 4.02
2344 2528 0.320508 GAGAGGGTTTGACCACGACC 60.321 60.000 0.00 0.00 41.02 4.79
2345 2529 0.391597 TGAGAGGGTTTGACCACGAC 59.608 55.000 0.00 0.00 41.02 4.34
2346 2530 1.124780 TTGAGAGGGTTTGACCACGA 58.875 50.000 0.00 0.00 41.02 4.35
2375 2579 7.489160 ACTAAAGTTTGGTCCAAAACAAGATC 58.511 34.615 18.74 4.81 41.56 2.75
2397 2601 5.623956 TGGTCCTTCAAGTCTCAAAACTA 57.376 39.130 0.00 0.00 0.00 2.24
2493 2702 6.900743 CCCCATATTCCCCTAAAGAAAAAGAA 59.099 38.462 0.00 0.00 0.00 2.52
2537 3469 3.831333 CCTCATAGCAGATTCTGGAGCTA 59.169 47.826 15.28 10.58 42.99 3.32
2545 3477 5.118990 TGTAACAAGCCTCATAGCAGATTC 58.881 41.667 0.00 0.00 34.23 2.52
2555 3487 6.354130 AGTAGTTTTCTTGTAACAAGCCTCA 58.646 36.000 0.00 0.00 0.00 3.86
2706 3658 3.845178 TGAGATGTTAAGTAGTGCCACG 58.155 45.455 0.00 0.00 0.00 4.94
2714 3666 7.324935 TGCCGTTAAATCTGAGATGTTAAGTA 58.675 34.615 0.00 0.00 0.00 2.24
2739 3691 1.338655 GGCCACACATTACCAAACGTT 59.661 47.619 0.00 0.00 0.00 3.99
2804 3756 1.673626 CGCTAGTCGGGCTAAAACCAA 60.674 52.381 0.00 0.00 33.78 3.67
2816 3770 4.301027 GATGGGGCCCGCTAGTCG 62.301 72.222 19.83 0.00 38.08 4.18
2821 3775 0.252696 TATGATAGATGGGGCCCGCT 60.253 55.000 19.83 19.90 0.00 5.52
2824 3778 4.451900 CGTATTTATGATAGATGGGGCCC 58.548 47.826 18.17 18.17 0.00 5.80
2962 3919 5.409214 GCAGTAAATTGCACAAAACCATCAT 59.591 36.000 0.00 0.00 43.53 2.45
2985 3942 3.030652 CCACTTGTTCGGTGTGGC 58.969 61.111 0.00 0.00 43.61 5.01


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

AutoCloner maintained by Alex Coulton.