Multiple sequence alignment - TraesCS1D01G305300

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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 TraesCS1D01G305300 chr1D 100.000 4526 0 0 1 4526 402836738 402832213 0.000000e+00 8359
1 TraesCS1D01G305300 chr1D 89.172 157 13 2 679 832 418099669 418099824 4.620000e-45 193
2 TraesCS1D01G305300 chr1D 88.050 159 13 4 679 832 427036560 427036403 2.780000e-42 183
3 TraesCS1D01G305300 chr1D 86.928 153 20 0 680 832 403232146 403232298 6.020000e-39 172
4 TraesCS1D01G305300 chr1B 95.856 2365 80 8 996 3345 540731344 540728983 0.000000e+00 3808
5 TraesCS1D01G305300 chr1B 93.339 1201 54 6 3339 4526 540728884 540727697 0.000000e+00 1751
6 TraesCS1D01G305300 chr1B 85.554 623 63 14 1 613 520363494 520362889 1.070000e-175 627
7 TraesCS1D01G305300 chr1B 84.053 602 59 21 1 588 10486451 10485873 3.080000e-151 545
8 TraesCS1D01G305300 chr1B 83.919 541 26 20 145 678 681859279 681858793 1.150000e-125 460
9 TraesCS1D01G305300 chr1B 79.276 304 42 18 679 965 442962907 442962608 4.620000e-45 193
10 TraesCS1D01G305300 chr1A 95.107 2391 73 19 996 3345 498066241 498063854 0.000000e+00 3727
11 TraesCS1D01G305300 chr1A 96.047 1189 28 7 3339 4526 498063758 498062588 0.000000e+00 1917
12 TraesCS1D01G305300 chr1A 84.333 300 20 18 679 968 533137703 533137421 7.460000e-68 268
13 TraesCS1D01G305300 chr7D 90.585 701 42 11 3 685 117875826 117876520 0.000000e+00 907
14 TraesCS1D01G305300 chr7D 90.058 684 37 15 22 685 184986562 184985890 0.000000e+00 857
15 TraesCS1D01G305300 chr7D 83.699 319 23 9 679 968 36452857 36453175 1.600000e-69 274
16 TraesCS1D01G305300 chr6D 88.842 708 45 13 1 685 470263487 470264183 0.000000e+00 839
17 TraesCS1D01G305300 chr6D 85.000 320 14 7 679 964 448634402 448634721 1.230000e-75 294
18 TraesCS1D01G305300 chr6D 80.308 325 29 12 679 968 115577586 115577910 3.550000e-51 213
19 TraesCS1D01G305300 chr6D 91.558 154 13 0 679 832 470280070 470280223 3.550000e-51 213
20 TraesCS1D01G305300 chr6D 84.571 175 23 2 793 963 17390537 17390711 2.170000e-38 171
21 TraesCS1D01G305300 chr6D 81.699 153 21 3 687 832 473051171 473051019 2.210000e-23 121
22 TraesCS1D01G305300 chr5D 88.336 703 56 12 3 685 445835208 445835904 0.000000e+00 821
23 TraesCS1D01G305300 chr5D 87.618 638 48 14 1 615 520846347 520846976 0.000000e+00 712
24 TraesCS1D01G305300 chr5D 82.364 550 45 26 148 685 433218682 433218173 8.990000e-117 431
25 TraesCS1D01G305300 chr5D 84.333 300 37 5 679 968 557613533 557613832 7.410000e-73 285
26 TraesCS1D01G305300 chr5D 81.620 321 28 14 679 968 481124835 481124515 2.100000e-58 237
27 TraesCS1D01G305300 chr7A 88.193 703 51 12 3 685 369578778 369578088 0.000000e+00 809
28 TraesCS1D01G305300 chr2D 86.809 705 61 10 1 685 567054037 567054729 0.000000e+00 758
29 TraesCS1D01G305300 chr2D 86.742 709 53 15 1 685 444369134 444368443 0.000000e+00 750
30 TraesCS1D01G305300 chr2D 84.848 297 33 7 679 964 567056393 567056688 5.730000e-74 289
31 TraesCS1D01G305300 chr2D 82.392 301 37 8 679 964 179289418 179289119 9.720000e-62 248
32 TraesCS1D01G305300 chr7B 86.944 697 62 14 4 685 113914679 113913997 0.000000e+00 756
33 TraesCS1D01G305300 chr7B 85.714 273 29 7 679 945 650636629 650636361 3.450000e-71 279
34 TraesCS1D01G305300 chr7B 81.994 311 29 9 681 964 113912947 113912637 5.850000e-59 239
35 TraesCS1D01G305300 chr2B 86.063 696 51 14 3 685 407214638 407213976 0.000000e+00 706
36 TraesCS1D01G305300 chr2B 82.935 586 44 23 119 685 143941525 143942073 1.140000e-130 477
37 TraesCS1D01G305300 chr2B 81.964 560 35 27 145 685 71729575 71730087 9.060000e-112 414
38 TraesCS1D01G305300 chr2B 84.451 328 28 13 375 685 751793421 751793100 7.360000e-78 302
39 TraesCS1D01G305300 chr5A 82.720 706 68 29 3 685 332573376 332574050 3.040000e-161 579
40 TraesCS1D01G305300 chr5A 85.343 539 44 14 162 685 631351221 631350703 4.010000e-145 525
41 TraesCS1D01G305300 chr5A 94.565 184 9 1 430 612 40387392 40387575 2.670000e-72 283
42 TraesCS1D01G305300 chr3B 82.295 706 80 17 3 685 33501777 33502460 1.830000e-158 569
43 TraesCS1D01G305300 chr3B 79.632 707 76 24 3 689 24397347 24396689 3.210000e-121 446
44 TraesCS1D01G305300 chr4B 79.469 565 86 21 71 615 650774879 650774325 1.540000e-99 374
45 TraesCS1D01G305300 chr4B 85.382 301 33 4 679 968 566209948 566210248 7.360000e-78 302
46 TraesCS1D01G305300 chr4D 88.636 308 21 7 679 973 30280314 30280008 3.330000e-96 363
47 TraesCS1D01G305300 chr4D 83.333 312 26 5 679 964 461767023 461767334 9.650000e-67 265
48 TraesCS1D01G305300 chr4D 81.505 319 30 7 679 968 351687430 351687748 7.570000e-58 235
49 TraesCS1D01G305300 chr4D 86.335 161 14 3 679 832 63583556 63583715 7.790000e-38 169
50 TraesCS1D01G305300 chr3D 88.552 297 23 6 679 968 384267324 384267616 2.590000e-92 350
51 TraesCS1D01G305300 chr3D 82.637 311 25 11 679 964 474509134 474508828 9.720000e-62 248
52 TraesCS1D01G305300 chr3A 85.050 301 30 9 679 968 41243567 41243271 4.430000e-75 292
53 TraesCS1D01G305300 chr6A 82.911 316 27 12 679 968 614976353 614976667 4.490000e-65 259
54 TraesCS1D01G305300 chr6A 81.270 315 30 10 679 964 495468269 495468583 1.270000e-55 228


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 TraesCS1D01G305300 chr1D 402832213 402836738 4525 True 8359.0 8359 100.0000 1 4526 1 chr1D.!!$R1 4525
1 TraesCS1D01G305300 chr1B 540727697 540731344 3647 True 2779.5 3808 94.5975 996 4526 2 chr1B.!!$R5 3530
2 TraesCS1D01G305300 chr1B 520362889 520363494 605 True 627.0 627 85.5540 1 613 1 chr1B.!!$R3 612
3 TraesCS1D01G305300 chr1B 10485873 10486451 578 True 545.0 545 84.0530 1 588 1 chr1B.!!$R1 587
4 TraesCS1D01G305300 chr1A 498062588 498066241 3653 True 2822.0 3727 95.5770 996 4526 2 chr1A.!!$R2 3530
5 TraesCS1D01G305300 chr7D 117875826 117876520 694 False 907.0 907 90.5850 3 685 1 chr7D.!!$F2 682
6 TraesCS1D01G305300 chr7D 184985890 184986562 672 True 857.0 857 90.0580 22 685 1 chr7D.!!$R1 663
7 TraesCS1D01G305300 chr6D 470263487 470264183 696 False 839.0 839 88.8420 1 685 1 chr6D.!!$F4 684
8 TraesCS1D01G305300 chr5D 445835208 445835904 696 False 821.0 821 88.3360 3 685 1 chr5D.!!$F1 682
9 TraesCS1D01G305300 chr5D 520846347 520846976 629 False 712.0 712 87.6180 1 615 1 chr5D.!!$F2 614
10 TraesCS1D01G305300 chr5D 433218173 433218682 509 True 431.0 431 82.3640 148 685 1 chr5D.!!$R1 537
11 TraesCS1D01G305300 chr7A 369578088 369578778 690 True 809.0 809 88.1930 3 685 1 chr7A.!!$R1 682
12 TraesCS1D01G305300 chr2D 444368443 444369134 691 True 750.0 750 86.7420 1 685 1 chr2D.!!$R2 684
13 TraesCS1D01G305300 chr2D 567054037 567056688 2651 False 523.5 758 85.8285 1 964 2 chr2D.!!$F1 963
14 TraesCS1D01G305300 chr7B 113912637 113914679 2042 True 497.5 756 84.4690 4 964 2 chr7B.!!$R2 960
15 TraesCS1D01G305300 chr2B 407213976 407214638 662 True 706.0 706 86.0630 3 685 1 chr2B.!!$R1 682
16 TraesCS1D01G305300 chr2B 143941525 143942073 548 False 477.0 477 82.9350 119 685 1 chr2B.!!$F2 566
17 TraesCS1D01G305300 chr2B 71729575 71730087 512 False 414.0 414 81.9640 145 685 1 chr2B.!!$F1 540
18 TraesCS1D01G305300 chr5A 332573376 332574050 674 False 579.0 579 82.7200 3 685 1 chr5A.!!$F2 682
19 TraesCS1D01G305300 chr5A 631350703 631351221 518 True 525.0 525 85.3430 162 685 1 chr5A.!!$R1 523
20 TraesCS1D01G305300 chr3B 33501777 33502460 683 False 569.0 569 82.2950 3 685 1 chr3B.!!$F1 682
21 TraesCS1D01G305300 chr3B 24396689 24397347 658 True 446.0 446 79.6320 3 689 1 chr3B.!!$R1 686
22 TraesCS1D01G305300 chr4B 650774325 650774879 554 True 374.0 374 79.4690 71 615 1 chr4B.!!$R1 544

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
899 2745 0.033504 CGCCCAACTCTATATGCCGT 59.966 55.0 0.00 0.00 0.00 5.68 F
979 2831 0.036732 ATTTCGGCTCAGCTGTTGGA 59.963 50.0 14.67 4.58 36.18 3.53 F
1367 3230 0.038166 CTTGGCCTACCTCCAGCAAA 59.962 55.0 3.32 0.00 34.66 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 4708 0.960286 GAGGAGTACCATACCGGCTC 59.040 60.000 0.00 0.0 39.03 4.70 R
3310 5211 6.749923 TCACTATCCTCAGATGTATGATCG 57.250 41.667 0.00 0.0 33.67 3.69 R
3613 5620 0.111446 TTTCAACCATCCTTCGGCCA 59.889 50.000 2.24 0.0 0.00 5.36 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
65 66 1.859398 GTTTGCAGTGCGTCGATCA 59.141 52.632 11.20 0.00 0.00 2.92
82 83 2.983030 ATCTGTTTTGGCGCGGCA 60.983 55.556 33.04 33.04 0.00 5.69
321 378 4.202243 CCACAACATCATCCAACCAAGTTT 60.202 41.667 0.00 0.00 0.00 2.66
407 482 2.601029 CGTCCTCGTCTTCATCTCATCG 60.601 54.545 0.00 0.00 0.00 3.84
432 507 1.709578 CGATTCATCCTCCTCCTCCA 58.290 55.000 0.00 0.00 0.00 3.86
584 697 3.415087 GGTGCTCCCATGCCTCCT 61.415 66.667 0.00 0.00 0.00 3.69
654 767 1.898154 GCTCCGAAGCCACCTAAGA 59.102 57.895 0.00 0.00 43.10 2.10
867 2711 1.926510 CAAATACACAGCTCGCGATGA 59.073 47.619 16.17 0.19 0.00 2.92
899 2745 0.033504 CGCCCAACTCTATATGCCGT 59.966 55.000 0.00 0.00 0.00 5.68
913 2761 3.864686 CCGTGCGCGCTTATTGCT 61.865 61.111 33.29 0.00 40.11 3.91
923 2771 0.999406 GCTTATTGCTCGTTCGCTGA 59.001 50.000 0.00 0.00 38.95 4.26
964 2816 3.978855 ACGCGCTAAAAAGGACAAATTTC 59.021 39.130 5.73 0.00 0.00 2.17
965 2817 3.057609 CGCGCTAAAAAGGACAAATTTCG 59.942 43.478 5.56 0.00 0.00 3.46
966 2818 3.363724 GCGCTAAAAAGGACAAATTTCGG 59.636 43.478 0.00 0.00 0.00 4.30
967 2819 3.363724 CGCTAAAAAGGACAAATTTCGGC 59.636 43.478 0.00 0.00 0.00 5.54
968 2820 4.556233 GCTAAAAAGGACAAATTTCGGCT 58.444 39.130 0.00 0.00 0.00 5.52
969 2821 4.621460 GCTAAAAAGGACAAATTTCGGCTC 59.379 41.667 0.00 0.00 0.00 4.70
970 2822 4.664150 AAAAAGGACAAATTTCGGCTCA 57.336 36.364 0.00 0.00 0.00 4.26
971 2823 3.923017 AAAGGACAAATTTCGGCTCAG 57.077 42.857 0.00 0.00 0.00 3.35
972 2824 1.168714 AGGACAAATTTCGGCTCAGC 58.831 50.000 0.00 0.00 0.00 4.26
973 2825 1.168714 GGACAAATTTCGGCTCAGCT 58.831 50.000 0.00 0.00 0.00 4.24
974 2826 1.135575 GGACAAATTTCGGCTCAGCTG 60.136 52.381 7.63 7.63 36.06 4.24
975 2827 1.537202 GACAAATTTCGGCTCAGCTGT 59.463 47.619 14.67 0.00 36.18 4.40
976 2828 1.956477 ACAAATTTCGGCTCAGCTGTT 59.044 42.857 14.67 0.00 36.18 3.16
977 2829 2.287788 ACAAATTTCGGCTCAGCTGTTG 60.288 45.455 14.67 9.78 36.18 3.33
978 2830 0.883833 AATTTCGGCTCAGCTGTTGG 59.116 50.000 14.67 6.67 36.18 3.77
979 2831 0.036732 ATTTCGGCTCAGCTGTTGGA 59.963 50.000 14.67 4.58 36.18 3.53
980 2832 0.603707 TTTCGGCTCAGCTGTTGGAG 60.604 55.000 14.67 4.56 36.18 3.86
981 2833 1.471829 TTCGGCTCAGCTGTTGGAGA 61.472 55.000 14.67 5.65 36.18 3.71
982 2834 1.220206 CGGCTCAGCTGTTGGAGAT 59.780 57.895 14.67 0.00 32.87 2.75
983 2835 1.088340 CGGCTCAGCTGTTGGAGATG 61.088 60.000 14.67 0.00 39.65 2.90
984 2836 1.375098 GGCTCAGCTGTTGGAGATGC 61.375 60.000 14.67 6.42 38.04 3.91
985 2837 0.392729 GCTCAGCTGTTGGAGATGCT 60.393 55.000 14.67 0.00 38.04 3.79
986 2838 1.134580 GCTCAGCTGTTGGAGATGCTA 60.135 52.381 14.67 0.00 38.04 3.49
987 2839 2.485124 GCTCAGCTGTTGGAGATGCTAT 60.485 50.000 14.67 0.00 38.04 2.97
988 2840 3.244009 GCTCAGCTGTTGGAGATGCTATA 60.244 47.826 14.67 0.00 38.04 1.31
989 2841 4.741837 GCTCAGCTGTTGGAGATGCTATAA 60.742 45.833 14.67 0.00 38.04 0.98
990 2842 4.953667 TCAGCTGTTGGAGATGCTATAAG 58.046 43.478 14.67 0.00 38.04 1.73
991 2843 4.063689 CAGCTGTTGGAGATGCTATAAGG 58.936 47.826 5.25 0.00 29.56 2.69
992 2844 2.810852 GCTGTTGGAGATGCTATAAGGC 59.189 50.000 0.00 0.00 0.00 4.35
993 2845 3.745480 GCTGTTGGAGATGCTATAAGGCA 60.745 47.826 0.00 0.00 46.63 4.75
994 2846 4.063689 CTGTTGGAGATGCTATAAGGCAG 58.936 47.826 0.00 0.00 45.75 4.85
1027 2879 2.980548 ACCTAGTTTACAGGTGGTCCA 58.019 47.619 0.00 0.00 44.89 4.02
1040 2892 0.898789 TGGTCCACTCTTCTCCGGAC 60.899 60.000 0.00 0.00 45.95 4.79
1046 2898 1.472878 CACTCTTCTCCGGACGATGAA 59.527 52.381 0.00 1.17 0.00 2.57
1049 2901 2.924290 CTCTTCTCCGGACGATGAAAAC 59.076 50.000 0.00 0.00 0.00 2.43
1052 2904 1.475280 TCTCCGGACGATGAAAACGAT 59.525 47.619 0.00 0.00 34.88 3.73
1054 2906 0.650512 CCGGACGATGAAAACGATGG 59.349 55.000 0.00 0.00 34.88 3.51
1083 2941 1.078347 GGCCAAACCCTCAATCCCA 59.922 57.895 0.00 0.00 0.00 4.37
1089 2947 3.434309 CAAACCCTCAATCCCAATCACT 58.566 45.455 0.00 0.00 0.00 3.41
1091 2949 3.091633 ACCCTCAATCCCAATCACTTG 57.908 47.619 0.00 0.00 0.00 3.16
1107 2966 7.124750 CCAATCACTTGAATAAAAAGATCCCCT 59.875 37.037 0.00 0.00 34.04 4.79
1176 3035 2.905996 GCTGGTGTGGTGGGATCCA 61.906 63.158 15.23 0.00 34.85 3.41
1214 3074 0.677731 TTGGAGATTTGCGCCTGGAG 60.678 55.000 4.18 0.00 37.36 3.86
1348 3208 2.784347 CAACTCCCTTCCTGTTCTTCC 58.216 52.381 0.00 0.00 0.00 3.46
1367 3230 0.038166 CTTGGCCTACCTCCAGCAAA 59.962 55.000 3.32 0.00 34.66 3.68
1413 3282 2.045280 CCGCCTCTACTCCATCCAG 58.955 63.158 0.00 0.00 0.00 3.86
1464 3333 1.801178 CCAAAGGTCAGCGACTTCTTC 59.199 52.381 8.26 0.00 32.47 2.87
1471 3340 2.480802 GTCAGCGACTTCTTCCTTTTCC 59.519 50.000 0.00 0.00 0.00 3.13
1499 3373 4.672801 GCTTAGTTTCGAGCAAAAGATGGG 60.673 45.833 4.45 0.00 38.73 4.00
1522 3396 0.406361 TTTGGGGGTTGCTAATCCGT 59.594 50.000 0.00 0.00 0.00 4.69
1564 3441 1.811266 CACGGAGCCTGTTCCATCG 60.811 63.158 0.89 0.00 37.05 3.84
1700 3580 1.880675 TCGCCGCTAAATTTGTTTCCA 59.119 42.857 0.00 0.00 0.00 3.53
1767 3649 3.564225 TCCCTTGTTTTCGCTCTTCTTTC 59.436 43.478 0.00 0.00 0.00 2.62
1833 3719 0.262876 ATTCTTGGGCTGGGAATCCC 59.737 55.000 12.39 12.39 45.71 3.85
1895 3781 1.376037 CCTCGGCTTCAGTTGGGTC 60.376 63.158 0.00 0.00 0.00 4.46
1950 3836 4.184629 CCACTCCTGTTCCTAAAGAATCG 58.815 47.826 0.00 0.00 36.69 3.34
2018 3904 4.402056 TCTTCTCCTTGTTCTTGTTCGT 57.598 40.909 0.00 0.00 0.00 3.85
2031 3917 3.194329 TCTTGTTCGTCATGCTGATCTCT 59.806 43.478 0.00 0.00 0.00 3.10
2076 3962 2.805671 TGCAGTGTGGAATTTAGTCACG 59.194 45.455 0.00 0.00 34.43 4.35
2248 4137 3.243068 GCACGGTTCACAGATTTGACTTT 60.243 43.478 0.00 0.00 0.00 2.66
2747 4648 8.086522 GCAAATAATGATGATGGTTTGCTAGAT 58.913 33.333 15.42 0.00 44.63 1.98
2807 4708 1.402968 CATTTGGCTGAGAATGACCCG 59.597 52.381 0.00 0.00 35.74 5.28
3310 5211 6.650807 TGATCTTCTCCAGTGTTGTGAATAAC 59.349 38.462 0.00 0.00 0.00 1.89
3548 5555 1.440618 TGGCCTTCTTACCTTCCACA 58.559 50.000 3.32 0.00 0.00 4.17
3595 5602 4.101448 CCGGTAGCTTGCCTGCCT 62.101 66.667 0.00 0.00 43.52 4.75
3602 5609 4.864334 CTTGCCTGCCTAGCCCCG 62.864 72.222 0.00 0.00 0.00 5.73
3648 5655 7.849804 TGGTTGAAAAGATTATGAGTAGAGC 57.150 36.000 0.00 0.00 0.00 4.09
3716 5723 6.722129 AGGTATTGTTGCCCAAAAGTATACAA 59.278 34.615 5.50 0.00 36.44 2.41
3827 5836 2.907910 AACAGTGCATCGCTTTGATC 57.092 45.000 0.00 0.00 34.13 2.92
4077 6087 4.162509 GTCCTATTCCTCTGCTTACCTGTT 59.837 45.833 0.00 0.00 0.00 3.16
4081 6091 5.700402 ATTCCTCTGCTTACCTGTTACAT 57.300 39.130 0.00 0.00 0.00 2.29
4105 6115 1.442769 TTGCTCCAAGTTGATCGCTC 58.557 50.000 3.87 0.00 0.00 5.03
4117 6127 0.462759 GATCGCTCCCCCTTGTCTTG 60.463 60.000 0.00 0.00 0.00 3.02
4170 6180 3.376636 TGCCATGGGATTGAAATGATGT 58.623 40.909 15.13 0.00 0.00 3.06
4444 6464 0.601046 TTCTTGAGTGCCAGACTGCG 60.601 55.000 0.00 0.00 33.83 5.18
4511 6531 3.744660 ACTCCACCAGTGAATGTTCTTC 58.255 45.455 0.00 0.00 32.26 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.731709 CCAAAACAGATGATCGACGCA 59.268 47.619 0.00 0.00 0.00 5.24
65 66 2.981560 CTGCCGCGCCAAAACAGAT 61.982 57.895 0.00 0.00 0.00 2.90
321 378 4.693566 GTGTCATGAACTTGGTTCGGATTA 59.306 41.667 0.00 0.00 44.55 1.75
407 482 1.616374 GAGGAGGATGAATCGGAGGAC 59.384 57.143 0.00 0.00 0.00 3.85
432 507 3.445987 AGGAGGAGGAAGAATCGTCTTT 58.554 45.455 0.00 0.00 44.42 2.52
584 697 3.618594 GCATGAGTTTTGCGTCTCTCATA 59.381 43.478 0.00 0.00 43.07 2.15
724 2547 0.252742 CCTCACCCCTTCCTACACCT 60.253 60.000 0.00 0.00 0.00 4.00
913 2761 1.327690 ATAGGGGCTTCAGCGAACGA 61.328 55.000 0.00 0.00 43.26 3.85
917 2765 0.888619 CGATATAGGGGCTTCAGCGA 59.111 55.000 0.00 0.00 43.26 4.93
923 2771 2.612972 CGTGCAATCGATATAGGGGCTT 60.613 50.000 0.00 0.00 0.00 4.35
964 2816 1.088340 CATCTCCAACAGCTGAGCCG 61.088 60.000 23.35 5.09 0.00 5.52
965 2817 1.375098 GCATCTCCAACAGCTGAGCC 61.375 60.000 23.35 0.00 0.00 4.70
966 2818 0.392729 AGCATCTCCAACAGCTGAGC 60.393 55.000 23.35 10.36 35.72 4.26
967 2819 2.975732 TAGCATCTCCAACAGCTGAG 57.024 50.000 23.35 12.34 37.94 3.35
968 2820 4.202295 CCTTATAGCATCTCCAACAGCTGA 60.202 45.833 23.35 0.00 37.94 4.26
969 2821 4.063689 CCTTATAGCATCTCCAACAGCTG 58.936 47.826 13.48 13.48 37.94 4.24
970 2822 3.495806 GCCTTATAGCATCTCCAACAGCT 60.496 47.826 0.00 0.00 40.92 4.24
971 2823 2.810852 GCCTTATAGCATCTCCAACAGC 59.189 50.000 0.00 0.00 0.00 4.40
972 2824 4.063689 CTGCCTTATAGCATCTCCAACAG 58.936 47.826 0.00 0.00 43.09 3.16
973 2825 3.711190 TCTGCCTTATAGCATCTCCAACA 59.289 43.478 0.00 0.00 43.09 3.33
974 2826 4.342862 TCTGCCTTATAGCATCTCCAAC 57.657 45.455 0.00 0.00 43.09 3.77
975 2827 4.444876 GGTTCTGCCTTATAGCATCTCCAA 60.445 45.833 0.00 0.00 43.09 3.53
976 2828 3.071602 GGTTCTGCCTTATAGCATCTCCA 59.928 47.826 0.00 0.00 43.09 3.86
977 2829 3.558109 GGGTTCTGCCTTATAGCATCTCC 60.558 52.174 0.00 0.00 43.09 3.71
978 2830 3.071602 TGGGTTCTGCCTTATAGCATCTC 59.928 47.826 0.00 0.00 43.09 2.75
979 2831 3.048600 TGGGTTCTGCCTTATAGCATCT 58.951 45.455 0.00 0.00 43.09 2.90
980 2832 3.492102 TGGGTTCTGCCTTATAGCATC 57.508 47.619 0.00 0.00 43.09 3.91
981 2833 3.395607 TGATGGGTTCTGCCTTATAGCAT 59.604 43.478 0.00 0.00 43.09 3.79
982 2834 2.777114 TGATGGGTTCTGCCTTATAGCA 59.223 45.455 0.00 0.00 41.46 3.49
983 2835 3.406764 CTGATGGGTTCTGCCTTATAGC 58.593 50.000 0.00 0.00 37.43 2.97
984 2836 3.808618 GCCTGATGGGTTCTGCCTTATAG 60.809 52.174 0.00 0.00 37.43 1.31
985 2837 2.106511 GCCTGATGGGTTCTGCCTTATA 59.893 50.000 0.00 0.00 37.43 0.98
986 2838 1.133668 GCCTGATGGGTTCTGCCTTAT 60.134 52.381 0.00 0.00 37.43 1.73
987 2839 0.255890 GCCTGATGGGTTCTGCCTTA 59.744 55.000 0.00 0.00 37.43 2.69
988 2840 1.000396 GCCTGATGGGTTCTGCCTT 60.000 57.895 0.00 0.00 37.43 4.35
989 2841 2.233566 TGCCTGATGGGTTCTGCCT 61.234 57.895 0.00 0.00 37.43 4.75
990 2842 2.048603 GTGCCTGATGGGTTCTGCC 61.049 63.158 0.00 0.00 37.43 4.85
991 2843 2.048603 GGTGCCTGATGGGTTCTGC 61.049 63.158 0.00 0.00 37.43 4.26
992 2844 0.911769 TAGGTGCCTGATGGGTTCTG 59.088 55.000 0.12 0.00 37.43 3.02
993 2845 1.207791 CTAGGTGCCTGATGGGTTCT 58.792 55.000 0.12 0.00 37.43 3.01
994 2846 0.912486 ACTAGGTGCCTGATGGGTTC 59.088 55.000 0.12 0.00 37.43 3.62
1024 2876 0.034380 ATCGTCCGGAGAAGAGTGGA 60.034 55.000 3.06 0.00 33.85 4.02
1027 2879 1.835494 TTCATCGTCCGGAGAAGAGT 58.165 50.000 3.06 0.00 33.85 3.24
1040 2892 2.480419 GGATAGGCCATCGTTTTCATCG 59.520 50.000 5.01 0.00 34.12 3.84
1083 2941 9.768215 TTAGGGGATCTTTTTATTCAAGTGATT 57.232 29.630 0.00 0.00 0.00 2.57
1107 2966 5.865552 GCATGCAAAGCTTCTGATCTTTTTA 59.134 36.000 14.21 0.00 30.79 1.52
1348 3208 0.038166 TTTGCTGGAGGTAGGCCAAG 59.962 55.000 5.01 0.00 34.44 3.61
1367 3230 2.040278 CCTGCTCCCAGTCCTCCT 59.960 66.667 0.00 0.00 37.38 3.69
1402 3271 1.216930 TGGATCGGACTGGATGGAGTA 59.783 52.381 0.00 0.00 0.00 2.59
1413 3282 0.679505 TGGATCGGATTGGATCGGAC 59.320 55.000 0.00 0.00 43.00 4.79
1464 3333 4.695455 TCGAAACTAAGCATCAGGAAAAGG 59.305 41.667 0.00 0.00 0.00 3.11
1522 3396 3.969250 GATTTGGAGCACGCCGGGA 62.969 63.158 2.18 0.00 0.00 5.14
1564 3441 2.365095 ATTCGATTCGACGGGAGGGC 62.365 60.000 8.55 0.00 34.89 5.19
1618 3498 2.280524 CCGAACGAACAGGCACCA 60.281 61.111 0.00 0.00 0.00 4.17
1700 3580 4.704833 ACAACATCGGGCTGCGCT 62.705 61.111 9.73 0.00 0.00 5.92
1780 3666 2.485479 CCATTCTACGGGGAACAGGATG 60.485 54.545 0.00 0.00 46.00 3.51
1833 3719 2.279784 GGCGGAGATCAAGAGCCG 60.280 66.667 0.00 0.00 46.14 5.52
1863 3749 2.413765 GAGGCGACACCGAGATCC 59.586 66.667 0.00 0.00 46.52 3.36
1950 3836 6.914259 ACACAAAGCTAGCTCTAATTTTTCC 58.086 36.000 19.65 0.00 0.00 3.13
1966 3852 3.503748 AGGTCTTGCATCTAACACAAAGC 59.496 43.478 0.00 0.00 0.00 3.51
2031 3917 3.216800 GGCAATCAGGCATATCTCACAA 58.783 45.455 0.00 0.00 43.51 3.33
2269 4158 2.890474 CGCCAATCCTTCGGTCGG 60.890 66.667 0.00 0.00 0.00 4.79
2747 4648 1.001120 TGCCCCGAGGACATACTCA 59.999 57.895 0.00 0.00 37.34 3.41
2807 4708 0.960286 GAGGAGTACCATACCGGCTC 59.040 60.000 0.00 0.00 39.03 4.70
3310 5211 6.749923 TCACTATCCTCAGATGTATGATCG 57.250 41.667 0.00 0.00 33.67 3.69
3548 5555 3.379057 GCTTCGTAGAAGCTTCTAGAGGT 59.621 47.826 31.81 12.12 45.90 3.85
3595 5602 0.892755 CATTCGCCTATACGGGGCTA 59.107 55.000 3.25 0.00 46.73 3.93
3613 5620 0.111446 TTTCAACCATCCTTCGGCCA 59.889 50.000 2.24 0.00 0.00 5.36
3628 5635 7.187824 ACAGGCTCTACTCATAATCTTTTCA 57.812 36.000 0.00 0.00 0.00 2.69
3648 5655 4.446371 CATTAGCTTGACTTCCCTACAGG 58.554 47.826 0.00 0.00 0.00 4.00
3716 5723 4.265073 AGCTTGAGTTGTCTTCAAACAGT 58.735 39.130 0.00 0.00 35.20 3.55
3816 5825 4.162040 AGAGGAATTGGATCAAAGCGAT 57.838 40.909 0.00 0.00 36.91 4.58
3827 5836 3.054802 AGCTACCTGTCAAGAGGAATTGG 60.055 47.826 0.00 0.00 36.51 3.16
4041 6051 9.454859 CAGAGGAATAGGACATTTCTTTAAACT 57.545 33.333 0.00 0.00 0.00 2.66
4077 6087 5.843673 TCAACTTGGAGCAAACAAATGTA 57.156 34.783 0.00 0.00 0.00 2.29
4081 6091 3.795150 GCGATCAACTTGGAGCAAACAAA 60.795 43.478 0.00 0.00 0.00 2.83
4105 6115 2.356667 GGGCTCAAGACAAGGGGG 59.643 66.667 0.00 0.00 0.00 5.40
4117 6127 1.708341 ATGGGCAATAATGTGGGCTC 58.292 50.000 0.00 0.00 0.00 4.70
4444 6464 0.032540 CAGCAGGTTTTTGGCACCTC 59.967 55.000 0.00 0.00 43.30 3.85


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

AutoCloner maintained by Alex Coulton.