Multiple sequence alignment - TraesCS3B01G197700

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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 TraesCS3B01G197700 chr3B 100.000 7281 0 0 1 7281 225165919 225173199 0.000000e+00 13446.0
1 TraesCS3B01G197700 chr3B 87.392 1277 126 29 4058 5317 173321568 173322826 0.000000e+00 1434.0
2 TraesCS3B01G197700 chr3B 83.906 1280 137 39 4074 5317 423797146 423798392 0.000000e+00 1158.0
3 TraesCS3B01G197700 chr3B 90.289 484 38 5 4837 5317 370147731 370148208 6.200000e-175 625.0
4 TraesCS3B01G197700 chr3B 85.844 551 66 10 4636 5182 771531515 771532057 6.340000e-160 575.0
5 TraesCS3B01G197700 chr3A 95.958 3934 114 31 1745 5668 176159504 176155606 0.000000e+00 6342.0
6 TraesCS3B01G197700 chr3A 95.935 984 21 5 5664 6647 176150111 176149147 0.000000e+00 1578.0
7 TraesCS3B01G197700 chr3A 92.614 1029 52 9 1 1023 176165441 176164431 0.000000e+00 1458.0
8 TraesCS3B01G197700 chr3A 98.265 634 10 1 6648 7281 176148839 176148207 0.000000e+00 1109.0
9 TraesCS3B01G197700 chr3A 97.565 575 6 5 1184 1758 176160086 176159520 0.000000e+00 977.0
10 TraesCS3B01G197700 chr3A 82.133 1097 101 39 4226 5317 359342798 359343804 0.000000e+00 852.0
11 TraesCS3B01G197700 chr3A 93.514 185 12 0 1013 1197 176164110 176163926 7.200000e-70 276.0
12 TraesCS3B01G197700 chr3A 86.010 193 25 2 1097 1288 686762582 686762773 9.570000e-49 206.0
13 TraesCS3B01G197700 chr3D 96.596 2703 49 7 1914 4590 153501442 153504127 0.000000e+00 4442.0
14 TraesCS3B01G197700 chr3D 95.883 1846 30 8 4803 6647 153504398 153506198 0.000000e+00 2946.0
15 TraesCS3B01G197700 chr3D 97.498 1079 15 3 843 1919 153494007 153495075 0.000000e+00 1832.0
16 TraesCS3B01G197700 chr3D 95.501 689 29 2 85 771 153493322 153494010 0.000000e+00 1099.0
17 TraesCS3B01G197700 chr3D 97.003 634 4 1 6648 7281 153506407 153507025 0.000000e+00 1051.0
18 TraesCS3B01G197700 chr3D 80.699 772 104 32 4446 5182 426853381 426854142 6.380000e-155 558.0
19 TraesCS3B01G197700 chr3D 77.506 409 75 11 195 589 585933659 585934064 5.680000e-56 230.0
20 TraesCS3B01G197700 chr3D 86.010 193 25 2 1097 1288 549490232 549490423 9.570000e-49 206.0
21 TraesCS3B01G197700 chr3D 98.876 89 1 0 1 89 153479350 153479438 7.560000e-35 159.0
22 TraesCS3B01G197700 chr2B 94.418 1666 49 11 2242 3879 405274771 405273122 0.000000e+00 2521.0
23 TraesCS3B01G197700 chr2B 95.266 1014 32 7 5316 6326 405272932 405271932 0.000000e+00 1592.0
24 TraesCS3B01G197700 chr2B 96.321 598 20 2 6651 7248 405271099 405270504 0.000000e+00 981.0
25 TraesCS3B01G197700 chr2B 94.461 343 16 3 1088 1430 405275156 405274817 6.470000e-145 525.0
26 TraesCS3B01G197700 chr2B 83.239 531 73 12 161 679 303103022 303102496 2.380000e-129 473.0
27 TraesCS3B01G197700 chr2B 90.678 236 15 3 1930 2158 405275523 405275288 2.550000e-79 307.0
28 TraesCS3B01G197700 chr2B 92.237 219 13 2 825 1041 405281901 405281685 2.550000e-79 307.0
29 TraesCS3B01G197700 chr2B 97.368 152 4 0 1085 1236 405275672 405275521 7.250000e-65 259.0
30 TraesCS3B01G197700 chr2B 88.119 202 17 6 4060 4258 2530776 2530579 4.390000e-57 233.0
31 TraesCS3B01G197700 chr2B 94.326 141 6 2 3880 4018 405273084 405272944 1.590000e-51 215.0
32 TraesCS3B01G197700 chr2B 92.029 138 3 3 6330 6467 405271658 405271529 3.470000e-43 187.0
33 TraesCS3B01G197700 chr2B 94.643 56 3 0 1037 1092 405279189 405279134 3.620000e-13 87.9
34 TraesCS3B01G197700 chr2A 92.066 1399 63 17 818 2169 448509418 448508021 0.000000e+00 1925.0
35 TraesCS3B01G197700 chr2A 94.357 638 33 3 2200 2836 448508037 448507402 0.000000e+00 976.0
36 TraesCS3B01G197700 chr2A 93.323 644 21 8 2867 3495 448507411 448506775 0.000000e+00 931.0
37 TraesCS3B01G197700 chr2A 93.874 604 32 5 6651 7254 448499377 448498779 0.000000e+00 905.0
38 TraesCS3B01G197700 chr2A 93.236 547 30 6 5318 5864 448501256 448500717 0.000000e+00 798.0
39 TraesCS3B01G197700 chr2A 81.351 681 99 21 148 814 609504998 609505664 5.000000e-146 529.0
40 TraesCS3B01G197700 chr2A 91.071 336 19 6 6135 6467 448500335 448500008 1.860000e-120 444.0
41 TraesCS3B01G197700 chr2A 86.245 269 27 6 5859 6122 448500658 448500395 4.300000e-72 283.0
42 TraesCS3B01G197700 chr2A 89.256 121 10 3 3551 3669 448501575 448501456 1.640000e-31 148.0
43 TraesCS3B01G197700 chr2A 90.179 112 11 0 3768 3879 448501416 448501305 5.890000e-31 147.0
44 TraesCS3B01G197700 chr2A 100.000 34 0 0 3883 3916 100646340 100646307 6.100000e-06 63.9
45 TraesCS3B01G197700 chr2D 94.453 1262 48 8 926 2169 338671181 338669924 0.000000e+00 1923.0
46 TraesCS3B01G197700 chr2D 91.408 838 32 12 2867 3669 338669315 338668483 0.000000e+00 1112.0
47 TraesCS3B01G197700 chr2D 95.110 634 28 3 2200 2832 338669940 338669309 0.000000e+00 996.0
48 TraesCS3B01G197700 chr2D 94.205 604 31 4 6651 7254 338666284 338665685 0.000000e+00 918.0
49 TraesCS3B01G197700 chr2D 93.419 547 30 6 5318 5864 338668156 338667616 0.000000e+00 806.0
50 TraesCS3B01G197700 chr2D 90.606 330 28 3 148 474 641620449 641620120 1.120000e-117 435.0
51 TraesCS3B01G197700 chr2D 88.657 335 14 5 6135 6467 338667235 338666923 3.190000e-103 387.0
52 TraesCS3B01G197700 chr2D 83.883 273 25 8 5859 6122 338667557 338667295 7.300000e-60 243.0
53 TraesCS3B01G197700 chr2D 95.614 114 3 1 818 929 338673166 338673053 1.610000e-41 182.0
54 TraesCS3B01G197700 chr2D 82.667 75 10 3 548 620 621047496 621047423 6.100000e-06 63.9
55 TraesCS3B01G197700 chr7D 84.976 1258 119 32 4077 5317 385034362 385033158 0.000000e+00 1212.0
56 TraesCS3B01G197700 chr7D 84.158 303 30 11 4472 4774 31480804 31481088 2.000000e-70 278.0
57 TraesCS3B01G197700 chr7A 82.143 1260 171 38 4070 5301 29428468 29427235 0.000000e+00 1031.0
58 TraesCS3B01G197700 chr7A 97.143 35 1 0 3880 3914 13797397 13797431 7.890000e-05 60.2
59 TraesCS3B01G197700 chr4D 86.876 922 109 9 4399 5318 23480468 23479557 0.000000e+00 1022.0
60 TraesCS3B01G197700 chr4D 90.323 62 3 3 3918 3977 360600892 360600952 2.180000e-10 78.7
61 TraesCS3B01G197700 chr1A 89.027 483 45 6 4838 5317 104386317 104385840 6.290000e-165 592.0
62 TraesCS3B01G197700 chr6D 87.444 446 46 6 149 585 450244574 450245018 8.430000e-139 505.0
63 TraesCS3B01G197700 chr1B 82.836 536 83 9 148 678 430332501 430333032 8.550000e-129 472.0
64 TraesCS3B01G197700 chr1B 89.785 186 16 3 4058 4243 570478138 570478320 1.220000e-57 235.0
65 TraesCS3B01G197700 chr1B 92.308 52 4 0 3926 3977 6761209 6761158 2.820000e-09 75.0
66 TraesCS3B01G197700 chr6B 86.925 413 43 9 149 551 682912089 682912500 3.100000e-123 453.0
67 TraesCS3B01G197700 chr6B 86.165 412 47 8 149 551 682945667 682946077 3.120000e-118 436.0
68 TraesCS3B01G197700 chr6B 79.348 92 18 1 548 638 662173992 662173901 6.100000e-06 63.9
69 TraesCS3B01G197700 chr6B 94.737 38 2 0 548 585 407177363 407177400 7.890000e-05 60.2
70 TraesCS3B01G197700 chr4B 88.942 208 17 6 4054 4259 38021923 38022126 1.210000e-62 252.0
71 TraesCS3B01G197700 chr4B 90.164 61 4 2 3918 3977 445646906 445646965 2.180000e-10 78.7
72 TraesCS3B01G197700 chr6A 91.573 178 12 3 4066 4243 94207797 94207971 7.300000e-60 243.0
73 TraesCS3B01G197700 chr6A 97.059 34 0 1 7249 7281 169514767 169514800 1.000000e-03 56.5
74 TraesCS3B01G197700 chr1D 87.562 201 20 5 4060 4259 328903353 328903157 2.040000e-55 228.0
75 TraesCS3B01G197700 chr1D 90.625 64 3 3 3916 3977 476217809 476217747 1.680000e-11 82.4
76 TraesCS3B01G197700 chr1D 88.710 62 4 3 3918 3977 467358641 467358701 1.010000e-08 73.1
77 TraesCS3B01G197700 chr4A 93.220 59 1 3 3921 3977 104266069 104266012 4.680000e-12 84.2
78 TraesCS3B01G197700 chr5D 100.000 38 0 0 3883 3920 250419450 250419413 3.640000e-08 71.3
79 TraesCS3B01G197700 chrUn 100.000 29 0 0 7253 7281 88784914 88784886 4.000000e-03 54.7
80 TraesCS3B01G197700 chr7B 92.105 38 3 0 3879 3916 537654887 537654850 4.000000e-03 54.7


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 TraesCS3B01G197700 chr3B 225165919 225173199 7280 False 13446.000000 13446 100.000000 1 7281 1 chr3B.!!$F2 7280
1 TraesCS3B01G197700 chr3B 173321568 173322826 1258 False 1434.000000 1434 87.392000 4058 5317 1 chr3B.!!$F1 1259
2 TraesCS3B01G197700 chr3B 423797146 423798392 1246 False 1158.000000 1158 83.906000 4074 5317 1 chr3B.!!$F4 1243
3 TraesCS3B01G197700 chr3B 771531515 771532057 542 False 575.000000 575 85.844000 4636 5182 1 chr3B.!!$F5 546
4 TraesCS3B01G197700 chr3A 176155606 176165441 9835 True 2263.250000 6342 94.912750 1 5668 4 chr3A.!!$R2 5667
5 TraesCS3B01G197700 chr3A 176148207 176150111 1904 True 1343.500000 1578 97.100000 5664 7281 2 chr3A.!!$R1 1617
6 TraesCS3B01G197700 chr3A 359342798 359343804 1006 False 852.000000 852 82.133000 4226 5317 1 chr3A.!!$F1 1091
7 TraesCS3B01G197700 chr3D 153501442 153507025 5583 False 2813.000000 4442 96.494000 1914 7281 3 chr3D.!!$F6 5367
8 TraesCS3B01G197700 chr3D 153493322 153495075 1753 False 1465.500000 1832 96.499500 85 1919 2 chr3D.!!$F5 1834
9 TraesCS3B01G197700 chr3D 426853381 426854142 761 False 558.000000 558 80.699000 4446 5182 1 chr3D.!!$F2 736
10 TraesCS3B01G197700 chr2B 405270504 405281901 11397 True 698.190000 2521 94.174700 825 7248 10 chr2B.!!$R3 6423
11 TraesCS3B01G197700 chr2B 303102496 303103022 526 True 473.000000 473 83.239000 161 679 1 chr2B.!!$R2 518
12 TraesCS3B01G197700 chr2A 448506775 448509418 2643 True 1277.333333 1925 93.248667 818 3495 3 chr2A.!!$R3 2677
13 TraesCS3B01G197700 chr2A 609504998 609505664 666 False 529.000000 529 81.351000 148 814 1 chr2A.!!$F1 666
14 TraesCS3B01G197700 chr2A 448498779 448501575 2796 True 454.166667 905 90.643500 3551 7254 6 chr2A.!!$R2 3703
15 TraesCS3B01G197700 chr2D 338665685 338673166 7481 True 820.875000 1923 92.093625 818 7254 8 chr2D.!!$R3 6436
16 TraesCS3B01G197700 chr7D 385033158 385034362 1204 True 1212.000000 1212 84.976000 4077 5317 1 chr7D.!!$R1 1240
17 TraesCS3B01G197700 chr7A 29427235 29428468 1233 True 1031.000000 1031 82.143000 4070 5301 1 chr7A.!!$R1 1231
18 TraesCS3B01G197700 chr4D 23479557 23480468 911 True 1022.000000 1022 86.876000 4399 5318 1 chr4D.!!$R1 919
19 TraesCS3B01G197700 chr1B 430332501 430333032 531 False 472.000000 472 82.836000 148 678 1 chr1B.!!$F1 530

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
499 513 0.037605 GTCGTCTCCGTTCCAACCAT 60.038 55.000 0.00 0.0 35.01 3.55 F
1173 9393 1.220206 CGAGAGCAATGGCAGGAGT 59.780 57.895 0.00 0.0 44.61 3.85 F
1389 13471 1.528309 CCGGTGCCCTGTTCTTTGT 60.528 57.895 0.00 0.0 0.00 2.83 F
3019 15589 1.444895 GCTGCCATTCACGCCAAAG 60.445 57.895 0.00 0.0 0.00 2.77 F
3951 16766 1.350019 CATCCTATGATGCAGAGGCCA 59.650 52.381 5.01 0.0 42.04 5.36 F
4512 17407 3.845259 GCGGACGGCTGGTGGATA 61.845 66.667 0.00 0.0 39.11 2.59 F
5688 18722 0.026803 GAGTTGTCGATTCATGGCGC 59.973 55.000 0.00 0.0 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 14946 1.268743 GGCAAACAGTCAAGACACTGC 60.269 52.381 2.72 5.39 46.81 4.40 R
3019 15589 0.235665 CGCATCAACCATCATACCGC 59.764 55.000 0.00 0.00 0.00 5.68 R
3311 15889 2.613026 TCGGTGTCTTCTTTTGCAGA 57.387 45.000 0.00 0.00 0.00 4.26 R
4774 17712 0.398696 ACCACAACGGCTAATGGACA 59.601 50.000 0.00 0.00 39.03 4.02 R
5148 18159 0.398696 TGCGAAAGTAGGCCTCCAAA 59.601 50.000 9.68 0.00 0.00 3.28 R
5897 19061 1.135915 AGACGTGGCAAAACATTTGCA 59.864 42.857 24.22 11.36 46.58 4.08 R
7245 21316 5.186198 CACTTATCAGGGTCCTACTTTTGG 58.814 45.833 0.00 0.00 0.00 3.28 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
69 70 5.649557 TGCCAACATGTATATTGTCAAAGC 58.350 37.500 0.00 0.00 0.00 3.51
230 234 5.920193 ATCAACAACATAATGTTCCCCAG 57.080 39.130 0.00 0.00 41.44 4.45
411 420 1.622811 GGATTGGGCAACAAATCCACA 59.377 47.619 8.63 0.00 43.46 4.17
445 454 7.403312 TTCAAATCTGAAGTTCTTTGGACAA 57.597 32.000 13.23 2.31 36.62 3.18
447 456 8.010733 TCAAATCTGAAGTTCTTTGGACAAAT 57.989 30.769 13.23 0.00 31.20 2.32
478 487 2.283532 AGTGGAGAGAGCCGCTGT 60.284 61.111 0.00 0.00 46.53 4.40
499 513 0.037605 GTCGTCTCCGTTCCAACCAT 60.038 55.000 0.00 0.00 35.01 3.55
724 741 2.125552 CATCGCCTTGCTGTCGGA 60.126 61.111 0.00 0.00 0.00 4.55
737 754 2.333926 CTGTCGGACGCTACATGAAAA 58.666 47.619 0.00 0.00 0.00 2.29
790 808 7.904461 CAGTTCATTTTGCGAAATCTTTTTGTT 59.096 29.630 9.06 0.00 33.25 2.83
805 823 9.991388 AATCTTTTTGTTCACATGTCAATTTTG 57.009 25.926 0.00 0.00 0.00 2.44
949 2861 7.380870 CACTAAACTGCACTGCTCTGTATATAG 59.619 40.741 1.98 0.00 0.00 1.31
950 2862 5.860941 AACTGCACTGCTCTGTATATAGT 57.139 39.130 1.98 0.00 0.00 2.12
1173 9393 1.220206 CGAGAGCAATGGCAGGAGT 59.780 57.895 0.00 0.00 44.61 3.85
1389 13471 1.528309 CCGGTGCCCTGTTCTTTGT 60.528 57.895 0.00 0.00 0.00 2.83
1407 13489 3.208747 TGTTCAGGTCCCTTCAACTTC 57.791 47.619 6.52 0.00 0.00 3.01
2379 14946 3.808466 TGTGGACAGATAGCAAGCTAG 57.192 47.619 7.91 0.00 31.45 3.42
2486 15053 6.311690 GCCAAGAAAATATAGATAGAGTCCGC 59.688 42.308 0.00 0.00 0.00 5.54
2563 15130 4.949856 TCCAAATTCTGTAAGGCCTCAATC 59.050 41.667 5.23 0.00 0.00 2.67
2841 15408 9.061435 TGCACGGTATGAAAATTATATCAATGA 57.939 29.630 0.00 0.00 0.00 2.57
3019 15589 1.444895 GCTGCCATTCACGCCAAAG 60.445 57.895 0.00 0.00 0.00 2.77
3311 15889 6.740411 TGTTAACACCGAGTAACTTGTTTT 57.260 33.333 3.59 0.00 34.15 2.43
3639 16259 8.429237 TTTATTGTGGGTAAATTGGTTCAGAT 57.571 30.769 0.00 0.00 0.00 2.90
3747 16367 6.946009 CCTTTCTTGGTACCTGGAATAGAAAA 59.054 38.462 14.36 1.21 31.92 2.29
3789 16436 3.824443 ACCTTTAACCCACATGCTTACAC 59.176 43.478 0.00 0.00 0.00 2.90
3951 16766 1.350019 CATCCTATGATGCAGAGGCCA 59.650 52.381 5.01 0.00 42.04 5.36
4325 17218 4.451150 GGACAGATGCGTGGCCGA 62.451 66.667 0.00 0.00 35.28 5.54
4486 17380 4.497984 TTGGCTGGTGCGTGTGGT 62.498 61.111 0.00 0.00 40.82 4.16
4512 17407 3.845259 GCGGACGGCTGGTGGATA 61.845 66.667 0.00 0.00 39.11 2.59
4901 17863 4.175337 GGCTGGTCGCTATGGCCA 62.175 66.667 8.56 8.56 42.08 5.36
5095 18106 5.016173 CCAGGTGAAAACCATGATCCTTTA 58.984 41.667 0.00 0.00 0.00 1.85
5148 18159 1.374758 CTTCTTGAAGGCGCCGTCT 60.375 57.895 36.30 19.98 0.00 4.18
5405 18438 8.376942 GTTTTTCTTTTGCGAATAACTCACAAA 58.623 29.630 0.00 0.00 34.29 2.83
5688 18722 0.026803 GAGTTGTCGATTCATGGCGC 59.973 55.000 0.00 0.00 0.00 6.53
5838 18872 1.866601 TGCGCCAATTGATAGATGACG 59.133 47.619 7.12 0.00 0.00 4.35
5912 19076 3.472283 ACAGATGCAAATGTTTTGCCA 57.528 38.095 19.09 9.91 44.32 4.92
6172 19389 6.712547 ACAAGAGTTTATTATATGGCTGAGGC 59.287 38.462 0.00 0.00 37.82 4.70
6229 19448 2.037772 CACTGTTCCTGAGTACAAGCCT 59.962 50.000 0.00 0.00 0.00 4.58
6376 19865 9.653287 TGTAGATTTTGATAAAGACTGTACCTG 57.347 33.333 0.00 0.00 0.00 4.00
6377 19866 9.654663 GTAGATTTTGATAAAGACTGTACCTGT 57.345 33.333 0.00 0.00 0.00 4.00
6379 19868 9.654663 AGATTTTGATAAAGACTGTACCTGTAC 57.345 33.333 0.45 0.45 36.63 2.90
6380 19869 8.788325 ATTTTGATAAAGACTGTACCTGTACC 57.212 34.615 5.07 0.00 35.26 3.34
6404 19893 5.004448 TGTACCTGTTTTCAGTGTGAAACA 58.996 37.500 19.17 19.17 45.03 2.83
6451 19940 5.622770 AAATTTCCGCGTACATTCTCTTT 57.377 34.783 4.92 0.00 0.00 2.52
6473 20001 2.989840 CTGAGCGTTAGAAACACCAGAG 59.010 50.000 0.00 0.00 0.00 3.35
6698 20768 3.443099 TGTCTCGTGCAGAATGGATAG 57.557 47.619 0.00 0.00 39.99 2.08
7143 21213 4.395959 ACAAGTGTAAACGTTGGAGAGA 57.604 40.909 0.00 0.00 0.00 3.10
7164 21234 8.100135 AGAGAGGTATGAGATCATTTTCCTTT 57.900 34.615 0.00 3.17 37.76 3.11
7245 21316 9.185192 GTATGATTAAAGCAGATGCCAAAATAC 57.815 33.333 0.14 3.97 43.38 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 6.271488 TGCTTCCATAAGGATTTGAAACAG 57.729 37.500 0.00 0.00 45.26 3.16
230 234 8.943909 AGCCTATGTAGATTACTTGTAAACAC 57.056 34.615 0.00 0.00 0.00 3.32
350 357 5.973124 TCCTCCAATCCCTTTCTTTCTATCT 59.027 40.000 0.00 0.00 0.00 1.98
445 454 1.849039 CCACTCCCCCTCTCAATCATT 59.151 52.381 0.00 0.00 0.00 2.57
447 456 0.417437 TCCACTCCCCCTCTCAATCA 59.583 55.000 0.00 0.00 0.00 2.57
499 513 1.075836 CCCCACCCATTCGTTCCAA 59.924 57.895 0.00 0.00 0.00 3.53
724 741 3.402628 ACTGACCTTTTCATGTAGCGT 57.597 42.857 0.00 0.00 32.17 5.07
759 776 5.403466 AGATTTCGCAAAATGAACTGCTTTC 59.597 36.000 0.00 0.00 35.21 2.62
790 808 6.587990 ACAAAAACGACAAAATTGACATGTGA 59.412 30.769 1.15 0.00 0.00 3.58
805 823 7.860872 AGTCCTTCAAAATATGACAAAAACGAC 59.139 33.333 0.00 0.00 37.92 4.34
949 2861 5.119743 GGGATTCGGCAAGACGTTAATATAC 59.880 44.000 0.00 0.00 34.94 1.47
950 2862 5.011329 AGGGATTCGGCAAGACGTTAATATA 59.989 40.000 0.00 0.00 34.94 0.86
964 2876 4.268687 CGATAGCAGGGATTCGGC 57.731 61.111 0.00 0.00 36.81 5.54
1173 9393 2.826128 CAGCACCAGGTAGTAGAACAGA 59.174 50.000 0.00 0.00 0.00 3.41
1389 13471 2.037251 CTCGAAGTTGAAGGGACCTGAA 59.963 50.000 0.00 0.00 0.00 3.02
1567 13655 7.667043 AAAATACTGCTCGTTCTATGACAAA 57.333 32.000 0.00 0.00 0.00 2.83
2178 14674 2.293399 GCTCCCGCAAAAAGAAGAAGAA 59.707 45.455 0.00 0.00 35.78 2.52
2379 14946 1.268743 GGCAAACAGTCAAGACACTGC 60.269 52.381 2.72 5.39 46.81 4.40
2486 15053 3.454447 TCTGGTACATGGACATTACCCAG 59.546 47.826 10.99 7.04 38.20 4.45
2563 15130 2.174363 TCCTGCAGATGACAACACAG 57.826 50.000 17.39 0.00 0.00 3.66
3019 15589 0.235665 CGCATCAACCATCATACCGC 59.764 55.000 0.00 0.00 0.00 5.68
3311 15889 2.613026 TCGGTGTCTTCTTTTGCAGA 57.387 45.000 0.00 0.00 0.00 4.26
3543 16134 5.347635 TCACGTTCTTTACATTGAATCGAGG 59.652 40.000 0.00 0.00 0.00 4.63
3789 16436 4.754372 AAGCACAACACATGTACATCAG 57.246 40.909 5.07 3.93 41.46 2.90
4310 17203 4.457496 CCTCGGCCACGCATCTGT 62.457 66.667 2.24 0.00 40.69 3.41
4312 17205 4.457496 CACCTCGGCCACGCATCT 62.457 66.667 2.24 0.00 40.69 2.90
4442 17336 3.745803 GAGAGGGCGTCGACCGTT 61.746 66.667 12.53 3.37 34.63 4.44
4452 17346 1.760029 CCAAAGAGTAGAGGAGAGGGC 59.240 57.143 0.00 0.00 0.00 5.19
4774 17712 0.398696 ACCACAACGGCTAATGGACA 59.601 50.000 0.00 0.00 39.03 4.02
5148 18159 0.398696 TGCGAAAGTAGGCCTCCAAA 59.601 50.000 9.68 0.00 0.00 3.28
5300 18331 4.278919 TCCACAATACCGAAAAAGGGTTTC 59.721 41.667 0.00 0.00 38.99 2.78
5405 18438 8.276252 ACTAACAAAGTGACAAAGTTACACAT 57.724 30.769 0.00 0.00 36.93 3.21
5517 18550 2.955660 TCGGAAAAATGCAAAGGTGAGT 59.044 40.909 0.00 0.00 0.00 3.41
5815 18849 3.076621 TCATCTATCAATTGGCGCATCC 58.923 45.455 10.83 0.00 0.00 3.51
5838 18872 7.763356 TGCTAGTTATGTTAGACAGAGTTCTC 58.237 38.462 0.00 0.00 0.00 2.87
5894 19058 2.224018 ACGTGGCAAAACATTTGCATCT 60.224 40.909 24.22 5.70 46.58 2.90
5897 19061 1.135915 AGACGTGGCAAAACATTTGCA 59.864 42.857 24.22 11.36 46.58 4.08
5912 19076 7.028361 GCAACTCTACTTAACTAATGAGACGT 58.972 38.462 0.00 0.00 0.00 4.34
6172 19389 3.996150 AACATGGTGCTTGTCAGAAAG 57.004 42.857 0.00 0.00 0.00 2.62
6229 19448 4.570772 GTGTAGAATGCCAGCGATTCTTTA 59.429 41.667 16.80 8.41 40.09 1.85
6375 19864 4.162698 ACACTGAAAACAGGTACAGGTACA 59.837 41.667 11.35 0.00 37.78 2.90
6376 19865 4.510340 CACACTGAAAACAGGTACAGGTAC 59.490 45.833 0.93 0.93 35.08 3.34
6377 19866 4.406326 TCACACTGAAAACAGGTACAGGTA 59.594 41.667 0.00 0.00 35.08 3.08
6378 19867 3.199071 TCACACTGAAAACAGGTACAGGT 59.801 43.478 0.00 0.00 35.08 4.00
6379 19868 3.804036 TCACACTGAAAACAGGTACAGG 58.196 45.455 0.00 0.00 35.08 4.00
6380 19869 5.123186 TGTTTCACACTGAAAACAGGTACAG 59.877 40.000 0.00 0.00 46.53 2.74
6404 19893 5.324409 TCAGAGCCTTGGATTGTTTATTGT 58.676 37.500 0.00 0.00 0.00 2.71
6451 19940 2.626266 TCTGGTGTTTCTAACGCTCAGA 59.374 45.455 14.54 14.54 41.96 3.27
6473 20001 7.965107 CAGTTTTATGTCTATTTCACCTGCTTC 59.035 37.037 0.00 0.00 0.00 3.86
6698 20768 8.128582 TCAGTGTGTTTCTGATGTCATTTTAAC 58.871 33.333 0.00 0.00 37.07 2.01
7245 21316 5.186198 CACTTATCAGGGTCCTACTTTTGG 58.814 45.833 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.