Multiple sequence alignment - TraesCS3B01G383600

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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 TraesCS3B01G383600 chr3B 100.000 3796 0 0 1 3796 603488582 603492377 0.000000e+00 7011
1 TraesCS3B01G383600 chr3B 94.154 479 11 7 1 465 452748295 452747820 0.000000e+00 713
2 TraesCS3B01G383600 chr3B 95.406 283 9 3 195 474 603485344 603485063 7.480000e-122 448
3 TraesCS3B01G383600 chr3B 88.106 227 22 4 2942 3165 13497387 13497163 8.090000e-67 265
4 TraesCS3B01G383600 chr3D 93.750 2512 105 22 466 2937 456640761 456643260 0.000000e+00 3722
5 TraesCS3B01G383600 chr3D 86.179 123 17 0 2941 3063 308773743 308773621 2.380000e-27 134
6 TraesCS3B01G383600 chr3D 74.227 291 61 12 1113 1399 1279615 1279895 4.010000e-20 110
7 TraesCS3B01G383600 chr3A 91.838 2340 95 45 530 2791 599528013 599530334 0.000000e+00 3175
8 TraesCS3B01G383600 chr3A 73.929 280 61 11 1122 1398 7791470 7791200 6.710000e-18 102
9 TraesCS3B01G383600 chr5B 98.710 465 6 0 3 467 271134507 271134971 0.000000e+00 826
10 TraesCS3B01G383600 chr5B 77.290 797 130 28 2954 3723 11748289 11747517 4.530000e-114 422
11 TraesCS3B01G383600 chr5B 77.011 783 113 39 2975 3723 11798055 11798804 1.650000e-103 387
12 TraesCS3B01G383600 chr5B 84.928 345 44 7 3326 3665 11685353 11685012 3.630000e-90 342
13 TraesCS3B01G383600 chr5B 95.745 188 8 0 278 465 620758661 620758474 1.710000e-78 303
14 TraesCS3B01G383600 chr5B 97.126 174 5 0 303 476 480740395 480740568 1.030000e-75 294
15 TraesCS3B01G383600 chr5B 97.093 172 5 0 304 475 519188488 519188317 1.330000e-74 291
16 TraesCS3B01G383600 chr5B 79.444 180 32 5 2954 3130 11685720 11685543 5.150000e-24 122
17 TraesCS3B01G383600 chr7D 83.131 907 95 21 2941 3796 575307789 575306890 0.000000e+00 774
18 TraesCS3B01G383600 chr7D 78.381 939 114 36 2940 3796 587113816 587112885 9.340000e-146 527
19 TraesCS3B01G383600 chr7D 83.510 473 35 16 3362 3792 458352807 458352336 5.910000e-108 401
20 TraesCS3B01G383600 chr7D 82.891 339 48 5 2943 3272 458353189 458352852 2.870000e-76 296
21 TraesCS3B01G383600 chr7A 95.041 484 6 1 1 466 689960015 689960498 0.000000e+00 745
22 TraesCS3B01G383600 chr7A 92.079 505 20 12 1 491 37854863 37854365 0.000000e+00 693
23 TraesCS3B01G383600 chr7A 77.592 897 142 24 2941 3789 603520781 603519896 4.410000e-134 488
24 TraesCS3B01G383600 chr7A 77.663 676 109 18 2942 3579 206014511 206013840 1.290000e-99 374
25 TraesCS3B01G383600 chr7A 79.960 494 65 18 3321 3789 38115686 38115202 2.190000e-87 333
26 TraesCS3B01G383600 chr7A 97.076 171 5 0 304 474 487485673 487485503 4.800000e-74 289
27 TraesCS3B01G383600 chr1A 94.617 483 8 2 1 465 286245388 286244906 0.000000e+00 732
28 TraesCS3B01G383600 chr1A 93.608 485 13 1 1 467 287786024 287785540 0.000000e+00 708
29 TraesCS3B01G383600 chr1A 78.652 356 61 10 1106 1455 490023434 490023088 4.940000e-54 222
30 TraesCS3B01G383600 chr5A 94.203 483 10 2 1 465 535685754 535686236 0.000000e+00 721
31 TraesCS3B01G383600 chr5A 93.069 505 14 12 1 490 618275971 618275473 0.000000e+00 719
32 TraesCS3B01G383600 chr5A 89.881 504 11 8 1 465 510261021 510260519 2.510000e-171 612
33 TraesCS3B01G383600 chr1B 93.621 486 13 2 1 468 365464734 365465219 0.000000e+00 710
34 TraesCS3B01G383600 chr1B 92.961 483 16 2 1 465 111684044 111684526 0.000000e+00 688
35 TraesCS3B01G383600 chr1B 76.923 572 93 14 2951 3495 10760921 10760362 4.800000e-74 289
36 TraesCS3B01G383600 chr1B 79.661 354 61 7 1106 1455 526432666 526432320 1.050000e-60 244
37 TraesCS3B01G383600 chr6A 94.043 470 19 9 1 467 71531608 71531145 0.000000e+00 704
38 TraesCS3B01G383600 chr7B 93.528 479 13 8 1 465 718888394 718888868 0.000000e+00 697
39 TraesCS3B01G383600 chr4A 93.333 480 15 8 1 466 135353089 135353565 0.000000e+00 693
40 TraesCS3B01G383600 chr2A 81.527 904 105 30 2941 3796 618999959 618999070 0.000000e+00 688
41 TraesCS3B01G383600 chr2A 81.719 826 103 23 3009 3796 521070 521885 0.000000e+00 645
42 TraesCS3B01G383600 chr2A 96.460 113 4 0 2551 2663 429784014 429783902 1.800000e-43 187
43 TraesCS3B01G383600 chr2A 79.638 221 35 7 2924 3138 207970805 207971021 2.360000e-32 150
44 TraesCS3B01G383600 chr2A 93.750 80 4 1 3714 3793 711858118 711858040 6.660000e-23 119
45 TraesCS3B01G383600 chr4B 80.595 907 105 31 2941 3796 494024530 494025416 5.350000e-178 634
46 TraesCS3B01G383600 chr4B 86.520 408 42 11 3321 3723 659701580 659701979 1.620000e-118 436
47 TraesCS3B01G383600 chr4B 96.040 202 7 1 280 481 601828696 601828896 1.020000e-85 327
48 TraesCS3B01G383600 chr4B 97.838 185 3 1 283 467 447642153 447642336 6.120000e-83 318
49 TraesCS3B01G383600 chr2B 80.440 910 111 27 2938 3796 692868276 692869169 1.920000e-177 632
50 TraesCS3B01G383600 chr2B 88.950 362 30 9 3366 3723 798843790 798844145 4.500000e-119 438
51 TraesCS3B01G383600 chr4D 86.649 367 22 12 3452 3792 9594929 9595294 7.690000e-102 381
52 TraesCS3B01G383600 chr1D 76.222 450 92 10 1106 1549 395881911 395881471 1.370000e-54 224
53 TraesCS3B01G383600 chr6B 82.353 255 39 5 2941 3190 641951663 641951410 2.300000e-52 217
54 TraesCS3B01G383600 chrUn 73.852 283 58 13 1122 1399 281636408 281636137 8.680000e-17 99
55 TraesCS3B01G383600 chrUn 73.852 283 58 13 1122 1399 281643282 281643011 8.680000e-17 99
56 TraesCS3B01G383600 chrUn 73.852 283 58 13 1122 1399 312316266 312315995 8.680000e-17 99


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 TraesCS3B01G383600 chr3B 603488582 603492377 3795 False 7011.0 7011 100.0000 1 3796 1 chr3B.!!$F1 3795
1 TraesCS3B01G383600 chr3D 456640761 456643260 2499 False 3722.0 3722 93.7500 466 2937 1 chr3D.!!$F2 2471
2 TraesCS3B01G383600 chr3A 599528013 599530334 2321 False 3175.0 3175 91.8380 530 2791 1 chr3A.!!$F1 2261
3 TraesCS3B01G383600 chr5B 11747517 11748289 772 True 422.0 422 77.2900 2954 3723 1 chr5B.!!$R1 769
4 TraesCS3B01G383600 chr5B 11798055 11798804 749 False 387.0 387 77.0110 2975 3723 1 chr5B.!!$F1 748
5 TraesCS3B01G383600 chr5B 11685012 11685720 708 True 232.0 342 82.1860 2954 3665 2 chr5B.!!$R4 711
6 TraesCS3B01G383600 chr7D 575306890 575307789 899 True 774.0 774 83.1310 2941 3796 1 chr7D.!!$R1 855
7 TraesCS3B01G383600 chr7D 587112885 587113816 931 True 527.0 527 78.3810 2940 3796 1 chr7D.!!$R2 856
8 TraesCS3B01G383600 chr7D 458352336 458353189 853 True 348.5 401 83.2005 2943 3792 2 chr7D.!!$R3 849
9 TraesCS3B01G383600 chr7A 603519896 603520781 885 True 488.0 488 77.5920 2941 3789 1 chr7A.!!$R5 848
10 TraesCS3B01G383600 chr7A 206013840 206014511 671 True 374.0 374 77.6630 2942 3579 1 chr7A.!!$R3 637
11 TraesCS3B01G383600 chr5A 510260519 510261021 502 True 612.0 612 89.8810 1 465 1 chr5A.!!$R1 464
12 TraesCS3B01G383600 chr1B 10760362 10760921 559 True 289.0 289 76.9230 2951 3495 1 chr1B.!!$R1 544
13 TraesCS3B01G383600 chr2A 618999070 618999959 889 True 688.0 688 81.5270 2941 3796 1 chr2A.!!$R2 855
14 TraesCS3B01G383600 chr2A 521070 521885 815 False 645.0 645 81.7190 3009 3796 1 chr2A.!!$F1 787
15 TraesCS3B01G383600 chr4B 494024530 494025416 886 False 634.0 634 80.5950 2941 3796 1 chr4B.!!$F2 855
16 TraesCS3B01G383600 chr2B 692868276 692869169 893 False 632.0 632 80.4400 2938 3796 1 chr2B.!!$F1 858

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
431 471 0.257616 GGGGGAAATCGGTCCATCAA 59.742 55.0 3.61 0.0 39.7 2.57 F
1822 1943 0.094730 GTGTGCTTATTCCGTGACGC 59.905 55.0 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2052 0.245539 TAACGCCACTGTCACTAGCC 59.754 55.0 0.00 0.0 0.00 3.93 R
3165 3310 0.039798 AAGACTCTTTACGTCGCGCA 60.040 50.0 8.75 0.0 36.53 6.09 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
103 104 2.279810 TTGACTCACCATCGGGCGA 61.280 57.895 0.00 0.00 37.90 5.54
261 301 3.407967 GACCGGCTCCCCCAATCA 61.408 66.667 0.00 0.00 0.00 2.57
331 371 5.605488 AGGAGACTAGTCAAAACCACCTAAA 59.395 40.000 24.44 0.00 40.61 1.85
374 414 2.427095 GGGAGAATTGATCCGGTTTTGG 59.573 50.000 0.00 0.00 37.75 3.28
385 425 2.039348 TCCGGTTTTGGAGAGTTTAGGG 59.961 50.000 0.00 0.00 33.05 3.53
397 437 3.137360 AGAGTTTAGGGGCTGATTGATCC 59.863 47.826 0.00 0.00 0.00 3.36
430 470 1.919771 GGGGGAAATCGGTCCATCA 59.080 57.895 3.61 0.00 39.70 3.07
431 471 0.257616 GGGGGAAATCGGTCCATCAA 59.742 55.000 3.61 0.00 39.70 2.57
436 476 3.343617 GGAAATCGGTCCATCAAACAGA 58.656 45.455 0.00 0.00 37.65 3.41
441 481 4.764679 TCGGTCCATCAAACAGAATTTG 57.235 40.909 0.00 0.00 0.00 2.32
444 484 4.379813 CGGTCCATCAAACAGAATTTGAGG 60.380 45.833 7.99 7.48 41.13 3.86
614 657 8.779303 AGATACGTCTACTCATTTCTACATCTG 58.221 37.037 0.00 0.00 31.36 2.90
641 684 0.958091 TGATTTGGTTGGCAGTTCGG 59.042 50.000 0.00 0.00 0.00 4.30
667 710 3.202467 GAGGTCGACAGCTCCTCC 58.798 66.667 18.91 0.00 40.74 4.30
671 714 1.040339 GGTCGACAGCTCCTCCTGAT 61.040 60.000 18.91 0.00 36.67 2.90
672 715 0.820871 GTCGACAGCTCCTCCTGATT 59.179 55.000 11.55 0.00 36.67 2.57
673 716 2.025155 GTCGACAGCTCCTCCTGATTA 58.975 52.381 11.55 0.00 36.67 1.75
674 717 2.427453 GTCGACAGCTCCTCCTGATTAA 59.573 50.000 11.55 0.00 36.67 1.40
675 718 2.690497 TCGACAGCTCCTCCTGATTAAG 59.310 50.000 0.00 0.00 36.67 1.85
676 719 2.428890 CGACAGCTCCTCCTGATTAAGT 59.571 50.000 0.00 0.00 36.67 2.24
677 720 3.632604 CGACAGCTCCTCCTGATTAAGTA 59.367 47.826 0.00 0.00 36.67 2.24
678 721 4.279671 CGACAGCTCCTCCTGATTAAGTAT 59.720 45.833 0.00 0.00 36.67 2.12
825 883 0.535328 CTCGATCGTCCCTGGCTCTA 60.535 60.000 15.94 0.00 0.00 2.43
902 973 5.786401 AAAGAATCGTGACAGATAGCAAC 57.214 39.130 0.00 0.00 0.00 4.17
1013 1087 1.571955 CCAAAAATGGGGCCTAAGCT 58.428 50.000 0.84 0.00 39.73 3.74
1021 1113 4.893601 GGCCTAAGCTCGCGTCCC 62.894 72.222 5.77 0.00 39.73 4.46
1345 1437 1.432251 CTGACGGTCGCGGACTTAT 59.568 57.895 6.13 0.00 32.47 1.73
1626 1718 3.382227 TCGGCAACCTTCGATCTTACATA 59.618 43.478 0.00 0.00 0.00 2.29
1633 1725 7.262772 CAACCTTCGATCTTACATACAGGTAA 58.737 38.462 0.00 0.00 32.91 2.85
1634 1726 7.414222 ACCTTCGATCTTACATACAGGTAAA 57.586 36.000 0.00 0.00 33.18 2.01
1779 1879 3.688694 ATAACCACAGTAGGCGTTGAA 57.311 42.857 0.00 0.00 0.00 2.69
1780 1880 2.561478 AACCACAGTAGGCGTTGAAT 57.439 45.000 0.00 0.00 0.00 2.57
1796 1917 5.283060 GTTGAATAACGAACAGCTGTCAT 57.717 39.130 21.95 5.00 0.00 3.06
1799 1920 4.388773 TGAATAACGAACAGCTGTCATGTC 59.611 41.667 21.95 13.03 0.00 3.06
1817 1938 0.981183 TCTGGGTGTGCTTATTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
1822 1943 0.094730 GTGTGCTTATTCCGTGACGC 59.905 55.000 0.00 0.00 0.00 5.19
1881 2002 2.027073 GAGGACACGCGCAATCACA 61.027 57.895 5.73 0.00 0.00 3.58
1905 2026 2.284798 AATCGCGCCTGTCTCATCGT 62.285 55.000 0.00 0.00 0.00 3.73
1973 2100 2.819552 GCACGCACGAACCACTTGT 61.820 57.895 0.00 0.00 0.00 3.16
1980 2107 2.609737 GCACGAACCACTTGTAGCTAGT 60.610 50.000 0.00 0.00 0.00 2.57
2011 2138 1.962822 CTCCAGCAAGCAAGCGTCA 60.963 57.895 0.00 0.00 40.15 4.35
2017 2144 2.096335 CAGCAAGCAAGCGTCATAATCA 59.904 45.455 0.00 0.00 40.15 2.57
2123 2250 2.096169 CGTACGTGGTTTAAAGCATGCA 60.096 45.455 30.17 20.18 44.88 3.96
2145 2272 4.968812 TCGTCATGCATCAAATGTGAAT 57.031 36.364 0.00 0.00 37.30 2.57
2197 2326 2.016961 CATGCAGGCCATGTACGAC 58.983 57.895 5.01 0.00 45.05 4.34
2269 2398 3.200593 CTGCAGCTGACGATGGCC 61.201 66.667 20.43 0.00 0.00 5.36
2277 2406 4.819761 GACGATGGCCGAGCTGCA 62.820 66.667 1.02 0.00 41.76 4.41
2347 2476 0.951040 AGTGCTACAACGCCAAGCTC 60.951 55.000 0.00 0.00 37.16 4.09
2468 2597 1.076485 TACGGTGAGTAGGGGCCTC 60.076 63.158 0.84 0.00 0.00 4.70
2470 2599 3.155167 GGTGAGTAGGGGCCTCCG 61.155 72.222 0.00 0.00 41.52 4.63
2471 2600 3.851128 GTGAGTAGGGGCCTCCGC 61.851 72.222 0.00 0.00 41.52 5.54
2561 2692 1.266175 CGAGACGGTGTCTACTGTTGT 59.734 52.381 3.67 0.00 46.22 3.32
2696 2827 4.764336 CGCGACGCCGTCCAAGTA 62.764 66.667 15.34 0.00 38.24 2.24
2783 2914 1.024579 ACCAACATCATCCGGTTCGC 61.025 55.000 0.00 0.00 0.00 4.70
2796 2927 1.198867 CGGTTCGCCAATTGATGTGAA 59.801 47.619 7.12 6.80 37.00 3.18
2801 2932 2.427812 TCGCCAATTGATGTGAATGCAT 59.572 40.909 7.12 0.00 0.00 3.96
2804 2935 4.619760 CGCCAATTGATGTGAATGCATATC 59.380 41.667 7.12 3.46 41.45 1.63
2830 2962 1.813786 AGACGGTCTAAGAGAGTGTGC 59.186 52.381 9.33 0.00 0.00 4.57
2835 2967 2.030185 GGTCTAAGAGAGTGTGCGTCAA 60.030 50.000 0.00 0.00 0.00 3.18
2878 3010 3.020984 TGTTGAAGTTCAGGGTGGAAAC 58.979 45.455 5.56 0.00 0.00 2.78
2883 3015 3.223674 AGTTCAGGGTGGAAACGAAAT 57.776 42.857 0.00 0.00 0.00 2.17
2892 3024 4.387559 GGGTGGAAACGAAATTGTATTTGC 59.612 41.667 0.00 0.00 0.00 3.68
2898 3030 6.021468 GGAAACGAAATTGTATTTGCGAGATG 60.021 38.462 0.00 0.00 0.00 2.90
2901 3033 5.106712 ACGAAATTGTATTTGCGAGATGTGT 60.107 36.000 0.00 0.00 0.00 3.72
2902 3034 5.449113 CGAAATTGTATTTGCGAGATGTGTC 59.551 40.000 0.00 0.00 0.00 3.67
2916 3048 2.913777 TGTGTCTACGATTCGGTCAG 57.086 50.000 11.29 4.80 0.00 3.51
2918 3050 1.135489 GTGTCTACGATTCGGTCAGCA 60.135 52.381 11.29 4.81 0.00 4.41
2979 3113 7.728847 AACCTTGAATTTATTGTCAAAAGCC 57.271 32.000 0.00 0.00 33.52 4.35
3056 3190 2.159379 CGGCCTATTTTCAACCTTGAGC 60.159 50.000 0.00 0.00 38.61 4.26
3057 3191 2.825532 GGCCTATTTTCAACCTTGAGCA 59.174 45.455 0.00 0.00 38.61 4.26
3067 3201 3.130340 TCAACCTTGAGCAAGTTTCCAAC 59.870 43.478 9.18 0.00 36.72 3.77
3103 3238 2.034558 GTGGCATGTTAAATCCCGGATG 59.965 50.000 0.73 0.00 0.00 3.51
3165 3310 8.387354 CACGAAGCAAGTTTTATTTTCCTTTTT 58.613 29.630 0.00 0.00 0.00 1.94
3207 3365 6.391227 TTCTCTTCCTTAAAAAGCCAAGTG 57.609 37.500 0.00 0.00 0.00 3.16
3244 3411 2.303311 GCTGAGTAGAACTTGGGACCTT 59.697 50.000 0.00 0.00 0.00 3.50
3245 3412 3.514309 GCTGAGTAGAACTTGGGACCTTA 59.486 47.826 0.00 0.00 0.00 2.69
3250 3417 5.342866 AGTAGAACTTGGGACCTTACAGAT 58.657 41.667 0.00 0.00 0.00 2.90
3255 3422 5.319043 ACTTGGGACCTTACAGATTTGAA 57.681 39.130 0.00 0.00 0.00 2.69
3262 3429 5.292101 GGACCTTACAGATTTGAACTCATCG 59.708 44.000 0.00 0.00 0.00 3.84
3263 3430 5.794894 ACCTTACAGATTTGAACTCATCGT 58.205 37.500 0.00 0.00 0.00 3.73
3278 3445 1.405463 CATCGTGCTAGCCACTAGTGA 59.595 52.381 24.68 3.38 42.42 3.41
3282 3449 2.478709 CGTGCTAGCCACTAGTGAAGAG 60.479 54.545 24.68 16.83 42.42 2.85
3296 3463 5.590530 AGTGAAGAGAACTATGAGCGATT 57.409 39.130 0.00 0.00 0.00 3.34
3302 3474 8.129840 TGAAGAGAACTATGAGCGATTTAGTAC 58.870 37.037 0.00 0.00 0.00 2.73
3324 3513 3.813166 CGAGCCCCGTTGTATTTATTGAT 59.187 43.478 0.00 0.00 0.00 2.57
3411 3600 8.901748 CCGAACATTTTATAAAGTGTGAACAAG 58.098 33.333 22.48 12.31 38.60 3.16
3515 3723 8.411318 TGAAAGCTGAAGAAAATTTGAAAGTC 57.589 30.769 0.00 0.00 0.00 3.01
3516 3724 8.253113 TGAAAGCTGAAGAAAATTTGAAAGTCT 58.747 29.630 0.00 0.00 0.00 3.24
3695 3921 7.872163 TTCAAATATGTGCTTGTGACATTTC 57.128 32.000 0.00 0.00 35.62 2.17
3701 3927 5.776519 TGTGCTTGTGACATTTCAAAAAC 57.223 34.783 0.00 0.00 31.90 2.43
3735 3983 7.224297 ACAATGTAGAAAAGTGTGTCATACCT 58.776 34.615 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 202 2.034687 CCAACCTCCCTGTGCCTG 59.965 66.667 0.00 0.00 0.00 4.85
261 301 4.344679 TGGCAGATTTCAGGTGTTTTCATT 59.655 37.500 0.00 0.00 0.00 2.57
374 414 3.914426 TCAATCAGCCCCTAAACTCTC 57.086 47.619 0.00 0.00 0.00 3.20
385 425 3.312697 GTCTAAAACCGGATCAATCAGCC 59.687 47.826 9.46 0.00 0.00 4.85
430 470 4.202212 CGTTTTCCCCCTCAAATTCTGTTT 60.202 41.667 0.00 0.00 0.00 2.83
431 471 3.320826 CGTTTTCCCCCTCAAATTCTGTT 59.679 43.478 0.00 0.00 0.00 3.16
436 476 4.930696 AGTATCGTTTTCCCCCTCAAATT 58.069 39.130 0.00 0.00 0.00 1.82
441 481 3.276857 GGAAAGTATCGTTTTCCCCCTC 58.723 50.000 5.63 0.00 45.02 4.30
614 657 4.700213 ACTGCCAACCAAATCACTGTATAC 59.300 41.667 0.00 0.00 0.00 1.47
641 684 1.433534 CTGTCGACCTCCTTCTTTGC 58.566 55.000 14.12 0.00 0.00 3.68
677 720 8.405531 GGCACATCATAACACATGTACTTAAAT 58.594 33.333 0.00 0.00 31.78 1.40
678 721 7.391833 TGGCACATCATAACACATGTACTTAAA 59.608 33.333 0.00 0.00 31.78 1.52
825 883 0.109086 CGCGAACCACTCATCTCAGT 60.109 55.000 0.00 0.00 0.00 3.41
883 950 2.535984 CCGTTGCTATCTGTCACGATTC 59.464 50.000 0.00 0.00 0.00 2.52
885 952 1.802880 GCCGTTGCTATCTGTCACGAT 60.803 52.381 0.00 0.00 33.53 3.73
1329 1421 1.298938 GGATAAGTCCGCGACCGTC 60.299 63.158 8.23 2.77 34.13 4.79
1342 1434 1.895020 AAGCAGACGCCCGTGGATAA 61.895 55.000 0.00 0.00 39.83 1.75
1345 1437 4.373116 GAAGCAGACGCCCGTGGA 62.373 66.667 0.00 0.00 39.83 4.02
1483 1575 0.680061 ACCGACTTCTTCACCACCTC 59.320 55.000 0.00 0.00 0.00 3.85
1626 1718 7.454225 AGCAAGAAAAGAGATACTTTACCTGT 58.546 34.615 0.00 0.00 46.55 4.00
1669 1762 2.006056 GCAGTCAAGCTCGATCTTGCT 61.006 52.381 21.32 18.04 42.29 3.91
1779 1879 3.928992 CAGACATGACAGCTGTTCGTTAT 59.071 43.478 22.65 8.10 0.00 1.89
1780 1880 3.317150 CAGACATGACAGCTGTTCGTTA 58.683 45.455 22.65 6.01 0.00 3.18
1796 1917 1.338674 CGGAATAAGCACACCCAGACA 60.339 52.381 0.00 0.00 0.00 3.41
1799 1920 1.086696 CACGGAATAAGCACACCCAG 58.913 55.000 0.00 0.00 0.00 4.45
1817 1938 1.731700 GGCCACTATCTACGCGTCA 59.268 57.895 18.63 3.51 0.00 4.35
1822 1943 1.792949 GATTTGCGGCCACTATCTACG 59.207 52.381 2.24 0.00 0.00 3.51
1881 2002 0.382515 GAGACAGGCGCGATTCTAGT 59.617 55.000 12.10 4.97 0.00 2.57
1905 2026 2.939640 GCCTCACCGCCTTTCTTTCATA 60.940 50.000 0.00 0.00 0.00 2.15
1931 2052 0.245539 TAACGCCACTGTCACTAGCC 59.754 55.000 0.00 0.00 0.00 3.93
1973 2100 2.905880 GAGCGCCCGGACTAGCTA 60.906 66.667 0.73 0.00 40.39 3.32
2011 2138 7.455953 TCTGCATTCTACTGTAGGGATGATTAT 59.544 37.037 23.80 4.65 30.69 1.28
2017 2144 4.262808 GCATCTGCATTCTACTGTAGGGAT 60.263 45.833 14.47 6.85 41.59 3.85
2123 2250 4.968812 TTCACATTTGATGCATGACGAT 57.031 36.364 2.46 0.00 0.00 3.73
2330 2459 1.671054 GGAGCTTGGCGTTGTAGCA 60.671 57.895 0.00 0.00 39.27 3.49
2470 2599 4.796495 GTGGGTGGTCGGATGGGC 62.796 72.222 0.00 0.00 0.00 5.36
2471 2600 3.326578 TGTGGGTGGTCGGATGGG 61.327 66.667 0.00 0.00 0.00 4.00
2474 2603 1.198094 TCATGTGTGGGTGGTCGGAT 61.198 55.000 0.00 0.00 0.00 4.18
2503 2633 1.269831 GGATCCCTGCACGTCTATCAC 60.270 57.143 0.00 0.00 0.00 3.06
2506 2636 0.398522 TGGGATCCCTGCACGTCTAT 60.399 55.000 31.05 0.00 36.94 1.98
2510 2640 2.591753 CATGGGATCCCTGCACGT 59.408 61.111 31.05 7.82 36.94 4.49
2549 2680 7.307751 GCAAGCAGTTAATAACAACAGTAGACA 60.308 37.037 5.89 0.00 0.00 3.41
2684 2815 0.719465 GAACATGTACTTGGACGGCG 59.281 55.000 4.80 4.80 0.00 6.46
2692 2823 2.233922 CGGAGTCCCAGAACATGTACTT 59.766 50.000 2.80 0.00 0.00 2.24
2696 2827 2.759985 ACGGAGTCCCAGAACATGT 58.240 52.632 2.80 0.00 29.74 3.21
2783 2914 6.156519 CCAGATATGCATTCACATCAATTGG 58.843 40.000 3.54 2.24 28.67 3.16
2796 2927 2.036475 GACCGTCTCACCAGATATGCAT 59.964 50.000 3.79 3.79 0.00 3.96
2801 2932 4.163649 TCTCTTAGACCGTCTCACCAGATA 59.836 45.833 3.74 0.00 0.00 1.98
2804 2935 2.680841 CTCTCTTAGACCGTCTCACCAG 59.319 54.545 3.74 0.00 0.00 4.00
2830 2962 4.324402 GTCAAGCCATTATTTGCTTTGACG 59.676 41.667 0.00 0.00 45.09 4.35
2878 3010 5.323900 ACACATCTCGCAAATACAATTTCG 58.676 37.500 0.00 0.00 0.00 3.46
2883 3015 4.561213 CGTAGACACATCTCGCAAATACAA 59.439 41.667 0.00 0.00 36.29 2.41
2892 3024 2.031807 ACCGAATCGTAGACACATCTCG 59.968 50.000 0.82 0.00 42.51 4.04
2898 3030 1.135489 TGCTGACCGAATCGTAGACAC 60.135 52.381 0.82 0.00 42.51 3.67
2901 3033 1.542472 TGTTGCTGACCGAATCGTAGA 59.458 47.619 0.82 0.00 45.75 2.59
2902 3034 1.654105 GTGTTGCTGACCGAATCGTAG 59.346 52.381 0.82 0.00 0.00 3.51
2969 3103 3.432890 GGGGTTTGATTTGGCTTTTGACA 60.433 43.478 0.00 0.00 34.22 3.58
2971 3105 2.774234 TGGGGTTTGATTTGGCTTTTGA 59.226 40.909 0.00 0.00 0.00 2.69
2979 3113 7.040755 GGGATTTAAAGTTTGGGGTTTGATTTG 60.041 37.037 0.00 0.00 0.00 2.32
3067 3201 1.447838 CCACGTCGACAATCCCTGG 60.448 63.158 17.16 5.76 0.00 4.45
3103 3238 2.354203 CCAGTTGAGTCCAGAGCTAACC 60.354 54.545 0.00 0.00 0.00 2.85
3154 3291 1.268845 ACGTCGCGCAAAAAGGAAAAT 60.269 42.857 8.75 0.00 0.00 1.82
3165 3310 0.039798 AAGACTCTTTACGTCGCGCA 60.040 50.000 8.75 0.00 36.53 6.09
3216 3374 3.118956 CCAAGTTCTACTCAGCCCTAGTG 60.119 52.174 0.00 0.00 0.00 2.74
3220 3378 1.203313 TCCCAAGTTCTACTCAGCCCT 60.203 52.381 0.00 0.00 0.00 5.19
3230 3397 5.073144 TCAAATCTGTAAGGTCCCAAGTTCT 59.927 40.000 0.00 0.00 0.00 3.01
3244 3411 4.820897 AGCACGATGAGTTCAAATCTGTA 58.179 39.130 0.00 0.00 0.00 2.74
3245 3412 3.668447 AGCACGATGAGTTCAAATCTGT 58.332 40.909 0.00 0.00 0.00 3.41
3250 3417 2.289382 TGGCTAGCACGATGAGTTCAAA 60.289 45.455 18.24 0.00 0.00 2.69
3255 3422 1.678627 CTAGTGGCTAGCACGATGAGT 59.321 52.381 18.24 0.00 0.00 3.41
3262 3429 2.755655 TCTCTTCACTAGTGGCTAGCAC 59.244 50.000 22.48 12.66 37.57 4.40
3263 3430 3.087370 TCTCTTCACTAGTGGCTAGCA 57.913 47.619 22.48 0.00 37.57 3.49
3278 3445 7.012138 TCGTACTAAATCGCTCATAGTTCTCTT 59.988 37.037 0.00 0.00 32.44 2.85
3282 3449 5.340138 GCTCGTACTAAATCGCTCATAGTTC 59.660 44.000 0.00 0.00 32.44 3.01
3302 3474 3.199677 TCAATAAATACAACGGGGCTCG 58.800 45.455 4.58 4.58 45.88 5.03
3383 3572 8.788806 TGTTCACACTTTATAAAATGTTCGGAT 58.211 29.630 9.49 0.00 0.00 4.18
3495 3702 7.489113 TGTTCAGACTTTCAAATTTTCTTCAGC 59.511 33.333 0.00 0.00 0.00 4.26
3701 3927 9.811655 CACACTTTTCTACATTGTATACACTTG 57.188 33.333 4.68 9.06 0.00 3.16


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

AutoCloner maintained by Alex Coulton.