Multiple sequence alignment - TraesCS6A01G378500

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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 TraesCS6A01G378500 chr6A 100.000 4546 0 0 1 4546 599258305 599262850 0.000000e+00 8395.0
1 TraesCS6A01G378500 chr6A 87.816 911 96 10 2465 3366 599622007 599622911 0.000000e+00 1053.0
2 TraesCS6A01G378500 chr6A 83.057 1086 127 29 2300 3365 599716223 599717271 0.000000e+00 933.0
3 TraesCS6A01G378500 chr6A 80.475 758 102 27 3581 4318 599623305 599624036 5.170000e-149 538.0
4 TraesCS6A01G378500 chr6A 95.545 202 8 1 1228 1428 599715434 599715635 5.670000e-84 322.0
5 TraesCS6A01G378500 chr6A 89.222 167 14 3 373 537 599714406 599714570 5.960000e-49 206.0
6 TraesCS6A01G378500 chr6A 87.222 180 21 1 1587 1766 599621185 599621362 2.140000e-48 204.0
7 TraesCS6A01G378500 chr6A 76.484 455 47 33 657 1067 599714758 599715196 4.640000e-45 193.0
8 TraesCS6A01G378500 chr6A 85.256 156 15 3 1591 1746 599197393 599197540 2.190000e-33 154.0
9 TraesCS6A01G378500 chr6A 78.516 256 37 11 2006 2252 599715957 599716203 7.880000e-33 152.0
10 TraesCS6A01G378500 chr6D 91.092 1785 124 7 2789 4545 453188502 453190279 0.000000e+00 2383.0
11 TraesCS6A01G378500 chr6D 87.460 1563 94 42 12 1508 453185381 453186907 0.000000e+00 1707.0
12 TraesCS6A01G378500 chr6D 80.769 1586 191 61 2003 3553 453239849 453241355 0.000000e+00 1134.0
13 TraesCS6A01G378500 chr6D 85.098 973 102 28 1848 2800 453187479 453188428 0.000000e+00 953.0
14 TraesCS6A01G378500 chr6D 79.564 1468 189 57 1946 3365 453346310 453347714 0.000000e+00 946.0
15 TraesCS6A01G378500 chr6D 86.427 361 42 7 3570 3928 453241343 453241698 5.520000e-104 388.0
16 TraesCS6A01G378500 chr6D 95.567 203 9 0 1229 1431 453345847 453346049 4.390000e-85 326.0
17 TraesCS6A01G378500 chr6D 76.840 462 47 34 657 1074 453345158 453345603 5.960000e-49 206.0
18 TraesCS6A01G378500 chr6D 88.068 176 18 2 1598 1773 453346148 453346320 5.960000e-49 206.0
19 TraesCS6A01G378500 chr6D 88.024 167 12 7 373 537 453344817 453344977 1.670000e-44 191.0
20 TraesCS6A01G378500 chr6D 91.765 85 5 1 1613 1697 453239695 453239777 2.870000e-22 117.0
21 TraesCS6A01G378500 chr6B 86.444 1800 95 60 128 1851 688759538 688757812 0.000000e+00 1834.0
22 TraesCS6A01G378500 chr6B 88.429 942 66 13 1843 2770 688757766 688756854 0.000000e+00 1096.0
23 TraesCS6A01G378500 chr6B 85.585 992 113 12 3579 4545 688755957 688754971 0.000000e+00 1013.0
24 TraesCS6A01G378500 chr6B 83.163 1075 129 32 2311 3365 688606700 688605658 0.000000e+00 935.0
25 TraesCS6A01G378500 chr6B 81.175 1089 116 37 2300 3366 688665271 688664250 0.000000e+00 793.0
26 TraesCS6A01G378500 chr6B 85.642 787 72 19 2788 3572 688756746 688755999 0.000000e+00 789.0
27 TraesCS6A01G378500 chr6B 94.231 208 12 0 1227 1434 688607578 688607371 7.340000e-83 318.0
28 TraesCS6A01G378500 chr6B 90.654 214 14 2 1227 1434 688666293 688666080 3.460000e-71 279.0
29 TraesCS6A01G378500 chr6B 76.790 461 44 34 656 1071 688608259 688607817 2.770000e-47 200.0
30 TraesCS6A01G378500 chr6B 84.571 175 19 4 1598 1766 688665995 688665823 2.810000e-37 167.0
31 TraesCS6A01G378500 chr6B 91.339 127 3 6 418 537 688667023 688666898 2.810000e-37 167.0
32 TraesCS6A01G378500 chr2A 80.989 263 29 14 2449 2711 625957781 625958022 6.000000e-44 189.0
33 TraesCS6A01G378500 chr7D 79.352 247 30 7 2472 2718 438368652 438368877 2.190000e-33 154.0
34 TraesCS6A01G378500 chr3B 89.062 64 5 2 1259 1321 62315294 62315232 1.360000e-10 78.7


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 TraesCS6A01G378500 chr6A 599258305 599262850 4545 False 8395.000000 8395 100.000000 1 4546 1 chr6A.!!$F2 4545
1 TraesCS6A01G378500 chr6A 599621185 599624036 2851 False 598.333333 1053 85.171000 1587 4318 3 chr6A.!!$F3 2731
2 TraesCS6A01G378500 chr6A 599714406 599717271 2865 False 361.200000 933 84.564800 373 3365 5 chr6A.!!$F4 2992
3 TraesCS6A01G378500 chr6D 453185381 453190279 4898 False 1681.000000 2383 87.883333 12 4545 3 chr6D.!!$F1 4533
4 TraesCS6A01G378500 chr6D 453239695 453241698 2003 False 546.333333 1134 86.320333 1613 3928 3 chr6D.!!$F2 2315
5 TraesCS6A01G378500 chr6D 453344817 453347714 2897 False 375.000000 946 85.612600 373 3365 5 chr6D.!!$F3 2992
6 TraesCS6A01G378500 chr6B 688754971 688759538 4567 True 1183.000000 1834 86.525000 128 4545 4 chr6B.!!$R3 4417
7 TraesCS6A01G378500 chr6B 688605658 688608259 2601 True 484.333333 935 84.728000 656 3365 3 chr6B.!!$R1 2709
8 TraesCS6A01G378500 chr6B 688664250 688667023 2773 True 351.500000 793 86.934750 418 3366 4 chr6B.!!$R2 2948

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
916 1060 1.196012 CTCCCCTACGCTTCTTCCTT 58.804 55.0 0.00 0.00 0.00 3.36 F
1781 2289 0.681887 TAGTGCTCATTCCGTCGGGA 60.682 55.0 12.29 1.83 41.83 5.14 F
3196 4455 0.179124 CTCGACTTCAGCCAGCTACC 60.179 60.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2805 4061 1.308998 ACAAGCATATTAGCACCGCC 58.691 50.0 0.00 0.0 36.85 6.13 R
3511 4784 0.530744 TGAAGAGTGGCGCTTCGTAT 59.469 50.0 7.64 0.0 41.84 3.06 R
4116 5630 0.036388 AGTATATGGCGGGGCATTCG 60.036 55.0 13.15 0.0 0.00 3.34 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
26 27 1.351350 AGGCCACCACCTTTAACTCTC 59.649 52.381 5.01 0.00 36.28 3.20
35 36 4.381079 CCACCTTTAACTCTCGGAGAAGAG 60.381 50.000 9.32 0.18 37.65 2.85
41 42 6.503589 TTAACTCTCGGAGAAGAGAAGAAG 57.496 41.667 9.32 0.00 45.52 2.85
50 51 5.048643 CGGAGAAGAGAAGAAGAACAGTACA 60.049 44.000 0.00 0.00 0.00 2.90
196 199 7.422399 GTTCCTTGCTTTAAGTTAATCACACA 58.578 34.615 0.00 0.00 34.45 3.72
332 351 4.620982 AGCAAAATTAACAAGCCAGACAC 58.379 39.130 0.00 0.00 0.00 3.67
333 352 3.425193 GCAAAATTAACAAGCCAGACACG 59.575 43.478 0.00 0.00 0.00 4.49
334 353 4.606961 CAAAATTAACAAGCCAGACACGT 58.393 39.130 0.00 0.00 0.00 4.49
335 354 3.896648 AATTAACAAGCCAGACACGTG 57.103 42.857 15.48 15.48 0.00 4.49
365 384 4.092091 CACACAAAAAGCGAGAGGAGATAC 59.908 45.833 0.00 0.00 0.00 2.24
366 385 3.304559 CACAAAAAGCGAGAGGAGATACG 59.695 47.826 0.00 0.00 0.00 3.06
369 388 5.163540 ACAAAAAGCGAGAGGAGATACGTAT 60.164 40.000 8.05 8.05 0.00 3.06
370 389 4.752661 AAAGCGAGAGGAGATACGTATC 57.247 45.455 25.00 25.00 0.00 2.24
371 390 3.688694 AGCGAGAGGAGATACGTATCT 57.311 47.619 32.86 32.86 45.26 1.98
395 432 8.330247 TCTAGAGAGAGATGATGATGATGATGA 58.670 37.037 0.00 0.00 0.00 2.92
397 434 7.781056 AGAGAGAGATGATGATGATGATGATG 58.219 38.462 0.00 0.00 0.00 3.07
398 435 7.617723 AGAGAGAGATGATGATGATGATGATGA 59.382 37.037 0.00 0.00 0.00 2.92
399 436 8.317776 AGAGAGATGATGATGATGATGATGAT 57.682 34.615 0.00 0.00 0.00 2.45
400 437 8.203485 AGAGAGATGATGATGATGATGATGATG 58.797 37.037 0.00 0.00 0.00 3.07
401 438 8.083828 AGAGATGATGATGATGATGATGATGA 57.916 34.615 0.00 0.00 0.00 2.92
402 439 7.984617 AGAGATGATGATGATGATGATGATGAC 59.015 37.037 0.00 0.00 0.00 3.06
403 440 6.758886 AGATGATGATGATGATGATGATGACG 59.241 38.462 0.00 0.00 0.00 4.35
404 441 6.032956 TGATGATGATGATGATGATGACGA 57.967 37.500 0.00 0.00 0.00 4.20
405 442 5.867716 TGATGATGATGATGATGATGACGAC 59.132 40.000 0.00 0.00 0.00 4.34
408 445 3.632189 TGATGATGATGATGACGACGAC 58.368 45.455 0.00 0.00 0.00 4.34
547 619 4.033776 TGGGGCTTCCTTGCGAGG 62.034 66.667 14.59 14.59 45.02 4.63
566 638 2.813165 TTGGGTCACCTCCTCCCCT 61.813 63.158 0.00 0.00 40.41 4.79
681 803 3.827898 CACCTCCTCCGTCTCCGC 61.828 72.222 0.00 0.00 0.00 5.54
690 812 2.159085 CCTCCGTCTCCGCTTAATTTCT 60.159 50.000 0.00 0.00 0.00 2.52
814 952 1.961277 CACACGCAGGGAGGTTGAC 60.961 63.158 0.00 0.00 0.00 3.18
832 974 3.462678 GGAGACCTCCGGACTGGC 61.463 72.222 9.62 1.61 40.36 4.85
916 1060 1.196012 CTCCCCTACGCTTCTTCCTT 58.804 55.000 0.00 0.00 0.00 3.36
1118 1344 5.994250 TCCACTATCTTGCTAGCTCAATTT 58.006 37.500 17.23 0.00 0.00 1.82
1120 1346 5.008415 CCACTATCTTGCTAGCTCAATTTGG 59.992 44.000 17.23 10.32 0.00 3.28
1121 1347 5.587844 CACTATCTTGCTAGCTCAATTTGGT 59.412 40.000 17.23 2.96 0.00 3.67
1122 1348 4.978083 ATCTTGCTAGCTCAATTTGGTG 57.022 40.909 17.23 0.00 0.00 4.17
1149 1388 3.389329 ACTGGAAGCGACATCCATAGATT 59.611 43.478 4.95 0.00 45.57 2.40
1153 1392 5.304357 TGGAAGCGACATCCATAGATTTCTA 59.696 40.000 0.68 0.00 41.98 2.10
1155 1394 6.367422 GGAAGCGACATCCATAGATTTCTAAG 59.633 42.308 0.00 0.00 36.92 2.18
1205 1477 2.239907 GTTTAGCAGGAGGAGGGTTCAT 59.760 50.000 0.00 0.00 0.00 2.57
1317 1602 2.116983 CTGGTGTGCCACTACCTGCT 62.117 60.000 14.64 0.00 40.46 4.24
1474 1765 2.836981 CCTCTCCTCTGTTCCATTCACT 59.163 50.000 0.00 0.00 0.00 3.41
1480 1771 4.827284 TCCTCTGTTCCATTCACTTTTTCC 59.173 41.667 0.00 0.00 0.00 3.13
1481 1772 4.829492 CCTCTGTTCCATTCACTTTTTCCT 59.171 41.667 0.00 0.00 0.00 3.36
1482 1773 6.003950 CCTCTGTTCCATTCACTTTTTCCTA 58.996 40.000 0.00 0.00 0.00 2.94
1483 1774 6.072452 CCTCTGTTCCATTCACTTTTTCCTAC 60.072 42.308 0.00 0.00 0.00 3.18
1488 1779 7.660208 TGTTCCATTCACTTTTTCCTACTACTC 59.340 37.037 0.00 0.00 0.00 2.59
1508 1799 7.985752 ACTACTCCATTAATTACCACAGTTAGC 59.014 37.037 0.00 0.00 0.00 3.09
1517 1808 2.399580 ACCACAGTTAGCTATCCCCTC 58.600 52.381 0.00 0.00 0.00 4.30
1518 1809 2.292918 ACCACAGTTAGCTATCCCCTCA 60.293 50.000 0.00 0.00 0.00 3.86
1622 2120 4.713824 TCGATCTTGATCCAGTACGTTT 57.286 40.909 0.00 0.00 0.00 3.60
1737 2245 3.119101 GCTCTAATTCGGACTTGTCCTCA 60.119 47.826 16.60 4.56 0.00 3.86
1778 2286 4.804139 ACTAAATTAGTGCTCATTCCGTCG 59.196 41.667 4.66 0.00 37.69 5.12
1781 2289 0.681887 TAGTGCTCATTCCGTCGGGA 60.682 55.000 12.29 1.83 41.83 5.14
1797 2305 4.616373 CGTCGGGATTTATTAGGCTCTCTC 60.616 50.000 0.00 0.00 0.00 3.20
1814 2322 6.237969 GGCTCTCTCGTATTTTGAGTCAAATC 60.238 42.308 18.69 11.27 33.19 2.17
1973 2539 8.948145 ACTAGTACTACTACTCATCAACTTGTG 58.052 37.037 0.00 0.00 34.79 3.33
1980 2546 6.102663 ACTACTCATCAACTTGTGATACTGC 58.897 40.000 0.00 0.00 45.69 4.40
1982 2548 5.174395 ACTCATCAACTTGTGATACTGCTC 58.826 41.667 0.00 0.00 45.69 4.26
2123 2944 1.068895 TCAAGTGGGCAGCATTGTTTG 59.931 47.619 0.00 0.00 0.00 2.93
2183 3015 8.597662 ATGTGGCATTTTATATCAGCATTTTC 57.402 30.769 0.00 0.00 0.00 2.29
2225 3125 7.375053 TGGAGTATTTGCCTATTTCAACAAAC 58.625 34.615 0.00 0.00 35.06 2.93
2511 3582 1.470285 GCTTCCGTGACCGCAAGTATA 60.470 52.381 0.00 0.00 0.00 1.47
2780 3949 7.269477 GCTCTTGCAATATAAACCTGATCTT 57.731 36.000 0.00 0.00 39.41 2.40
2781 3950 8.383318 GCTCTTGCAATATAAACCTGATCTTA 57.617 34.615 0.00 0.00 39.41 2.10
2782 3951 8.840321 GCTCTTGCAATATAAACCTGATCTTAA 58.160 33.333 0.00 0.00 39.41 1.85
2821 4077 2.417379 CGATAGGCGGTGCTAATATGCT 60.417 50.000 0.00 0.00 36.03 3.79
2851 4107 5.682422 GCATTTGAATTTTGTTTGTTCAGGC 59.318 36.000 0.00 0.00 33.82 4.85
3175 4434 1.921230 GCTGCTGAGCTACGAAACTAC 59.079 52.381 5.83 0.00 42.52 2.73
3193 4452 2.654079 CCCTCGACTTCAGCCAGCT 61.654 63.158 0.00 0.00 0.00 4.24
3196 4455 0.179124 CTCGACTTCAGCCAGCTACC 60.179 60.000 0.00 0.00 0.00 3.18
3351 4620 2.153034 TGATGTAGATCCGTGGGTGA 57.847 50.000 0.00 0.00 0.00 4.02
3424 4693 4.013728 CAACAAATCATAAGACCGGGGAA 58.986 43.478 6.32 0.00 0.00 3.97
3425 4694 3.886123 ACAAATCATAAGACCGGGGAAG 58.114 45.455 6.32 0.00 0.00 3.46
3438 4707 1.482593 CGGGGAAGTAGACAAGCTGAT 59.517 52.381 0.00 0.00 0.00 2.90
3441 4710 3.135530 GGGGAAGTAGACAAGCTGATCAT 59.864 47.826 0.00 0.00 0.00 2.45
3443 4712 4.574013 GGGAAGTAGACAAGCTGATCATTG 59.426 45.833 7.38 7.38 0.00 2.82
3469 4742 1.466856 ACACCGGCTACGATAAGACA 58.533 50.000 0.00 0.00 44.60 3.41
3482 4755 0.831966 TAAGACACACACCCAACGGT 59.168 50.000 0.00 0.00 46.31 4.83
3508 4781 7.630082 ACAGGTATGGACATTTGTTACATAGT 58.370 34.615 8.42 0.00 32.67 2.12
3509 4782 8.764558 ACAGGTATGGACATTTGTTACATAGTA 58.235 33.333 8.42 0.00 32.67 1.82
3510 4783 9.778741 CAGGTATGGACATTTGTTACATAGTAT 57.221 33.333 8.42 0.00 32.67 2.12
3526 4799 3.555917 AGTATATACGAAGCGCCACTC 57.444 47.619 2.29 0.00 0.00 3.51
3535 4811 0.460284 AAGCGCCACTCTTCATACCG 60.460 55.000 2.29 0.00 0.00 4.02
3654 5162 8.882415 TCTTGAAAGCTTAATTACTATACCCG 57.118 34.615 0.00 0.00 0.00 5.28
3662 5170 4.612264 AATTACTATACCCGCGTTCCAT 57.388 40.909 4.92 0.00 0.00 3.41
3686 5194 9.165035 CATAATAATTGATGTTTTGGGCTTGTT 57.835 29.630 0.00 0.00 0.00 2.83
3898 5407 7.722795 AAAACTTGAATTATTTTGGAACGGG 57.277 32.000 0.00 0.00 0.00 5.28
3900 5409 5.081032 ACTTGAATTATTTTGGAACGGGGA 58.919 37.500 0.00 0.00 0.00 4.81
4132 5646 2.672996 GCGAATGCCCCGCCATAT 60.673 61.111 0.00 0.00 46.22 1.78
4327 5864 3.274095 TGTTGTCCTGTTGTGATGTGA 57.726 42.857 0.00 0.00 0.00 3.58
4362 5899 5.336372 CCAAAACCTTGTTCAGAGTTTGTCA 60.336 40.000 0.00 0.00 32.97 3.58
4370 5907 7.389803 TTGTTCAGAGTTTGTCAATGAAGAA 57.610 32.000 5.54 5.54 32.68 2.52
4391 5928 2.282674 ACTGTGCGGTCGGTCCTA 60.283 61.111 0.00 0.00 0.00 2.94
4406 5943 2.467880 GTCCTACAGTCTCCCCATTGA 58.532 52.381 0.00 0.00 0.00 2.57
4427 5964 3.221771 ACTTCCACAGCTGCAATAACAA 58.778 40.909 15.27 0.00 0.00 2.83
4429 5966 3.921119 TCCACAGCTGCAATAACAAAG 57.079 42.857 15.27 0.00 0.00 2.77
4450 5987 2.033424 GCCCTTTACAAATGAGATCCGC 59.967 50.000 0.00 0.00 0.00 5.54
4452 5989 3.278574 CCTTTACAAATGAGATCCGCCA 58.721 45.455 0.00 0.00 0.00 5.69
4468 6005 2.159626 CCGCCAGGTGTTTAAACATACG 60.160 50.000 23.11 19.47 41.59 3.06
4471 6008 3.119637 GCCAGGTGTTTAAACATACGCAT 60.120 43.478 23.11 6.19 41.59 4.73
4491 6028 5.873712 CGCATCTCCATAAGAGCTTCATTAT 59.126 40.000 0.00 0.00 42.90 1.28
4521 6058 0.464036 TCACGACCAAGCAAGTGTCT 59.536 50.000 0.00 0.00 36.16 3.41
4537 6074 1.214175 TGTCTCAAAGCCAACCCAAGA 59.786 47.619 0.00 0.00 0.00 3.02
4545 6082 0.540597 GCCAACCCAAGAAAGCCTCT 60.541 55.000 0.00 0.00 35.13 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.546714 AAGGTGGTGGCCTACGTGC 62.547 63.158 3.32 0.00 38.03 5.34
1 2 0.322322 TAAAGGTGGTGGCCTACGTG 59.678 55.000 3.32 0.00 38.03 4.49
2 3 1.058284 TTAAAGGTGGTGGCCTACGT 58.942 50.000 3.32 0.00 38.03 3.57
3 4 1.002773 AGTTAAAGGTGGTGGCCTACG 59.997 52.381 3.32 0.00 38.03 3.51
4 5 2.305052 AGAGTTAAAGGTGGTGGCCTAC 59.695 50.000 3.32 0.00 38.03 3.18
5 6 2.570302 GAGAGTTAAAGGTGGTGGCCTA 59.430 50.000 3.32 0.00 38.03 3.93
6 7 1.351350 GAGAGTTAAAGGTGGTGGCCT 59.649 52.381 3.32 0.00 41.41 5.19
7 8 1.822506 GAGAGTTAAAGGTGGTGGCC 58.177 55.000 0.00 0.00 0.00 5.36
8 9 1.439679 CGAGAGTTAAAGGTGGTGGC 58.560 55.000 0.00 0.00 0.00 5.01
9 10 1.621814 TCCGAGAGTTAAAGGTGGTGG 59.378 52.381 0.00 0.00 0.00 4.61
10 11 2.561419 TCTCCGAGAGTTAAAGGTGGTG 59.439 50.000 0.00 0.00 0.00 4.17
15 16 5.416326 TCTTCTCTTCTCCGAGAGTTAAAGG 59.584 44.000 0.00 0.00 42.96 3.11
26 27 4.513198 ACTGTTCTTCTTCTCTTCTCCG 57.487 45.455 0.00 0.00 0.00 4.63
50 51 8.713971 TCTATCATGTGTCCCAATTTACAGTAT 58.286 33.333 0.00 0.00 0.00 2.12
196 199 5.015603 ACATAGCTGGGGATTAATTATGGCT 59.984 40.000 0.00 0.00 0.00 4.75
208 212 1.352083 GAGGCATACATAGCTGGGGA 58.648 55.000 0.00 0.00 0.00 4.81
266 285 2.167693 CGTACAGAGGATTAACAGGGCA 59.832 50.000 0.00 0.00 0.00 5.36
335 354 1.584920 CGCTTTTTGTGTGCGTACGC 61.585 55.000 32.49 32.49 44.00 4.42
352 371 4.746729 TCTAGATACGTATCTCCTCTCGC 58.253 47.826 35.15 8.93 41.85 5.03
365 384 8.553696 CATCATCATCATCTCTCTCTAGATACG 58.446 40.741 0.00 0.00 34.40 3.06
366 385 9.617523 TCATCATCATCATCTCTCTCTAGATAC 57.382 37.037 0.00 0.00 34.40 2.24
369 388 8.330247 TCATCATCATCATCATCTCTCTCTAGA 58.670 37.037 0.00 0.00 0.00 2.43
370 389 8.514330 TCATCATCATCATCATCTCTCTCTAG 57.486 38.462 0.00 0.00 0.00 2.43
371 390 8.908903 CATCATCATCATCATCATCTCTCTCTA 58.091 37.037 0.00 0.00 0.00 2.43
395 432 3.360533 GTTACATCGTCGTCGTCATCAT 58.639 45.455 1.33 0.00 38.33 2.45
397 434 1.766301 CGTTACATCGTCGTCGTCATC 59.234 52.381 1.33 0.00 38.33 2.92
398 435 1.394572 TCGTTACATCGTCGTCGTCAT 59.605 47.619 1.33 0.00 38.33 3.06
399 436 0.789601 TCGTTACATCGTCGTCGTCA 59.210 50.000 1.33 0.00 38.33 4.35
400 437 1.766301 CATCGTTACATCGTCGTCGTC 59.234 52.381 1.33 0.00 38.33 4.20
401 438 1.394572 TCATCGTTACATCGTCGTCGT 59.605 47.619 1.33 0.00 38.33 4.34
402 439 2.081336 TCATCGTTACATCGTCGTCG 57.919 50.000 0.00 0.00 38.55 5.12
403 440 3.165890 TGTTCATCGTTACATCGTCGTC 58.834 45.455 0.00 0.00 0.00 4.20
404 441 3.168963 CTGTTCATCGTTACATCGTCGT 58.831 45.455 0.00 0.00 0.00 4.34
405 442 2.035674 GCTGTTCATCGTTACATCGTCG 60.036 50.000 0.00 0.00 0.00 5.12
408 445 1.331161 GCGCTGTTCATCGTTACATCG 60.331 52.381 0.00 0.00 37.07 3.84
547 619 2.603652 GGGGAGGAGGTGACCCAAC 61.604 68.421 0.00 0.00 44.87 3.77
566 638 2.003830 TGGGAGGAAGAGAGAAGAGGA 58.996 52.381 0.00 0.00 0.00 3.71
640 739 4.120331 GGACATGCTTGTGCGCCC 62.120 66.667 10.37 0.00 43.34 6.13
648 747 1.566298 GGTGGGGAGAGGACATGCTT 61.566 60.000 0.00 0.00 0.00 3.91
829 971 3.751049 CTACCCCCTAGCTCGGCCA 62.751 68.421 2.24 0.00 0.00 5.36
832 974 0.824182 CTGTCTACCCCCTAGCTCGG 60.824 65.000 0.00 0.00 0.00 4.63
841 983 1.209747 CTACAAAGGCCTGTCTACCCC 59.790 57.143 5.69 0.00 0.00 4.95
916 1060 7.224297 GGAAGGAATAATTGTATGTAGCCAGA 58.776 38.462 0.00 0.00 0.00 3.86
1118 1344 1.005037 CGCTTCCAGTACAGCACCA 60.005 57.895 0.00 0.00 35.60 4.17
1120 1346 0.319555 TGTCGCTTCCAGTACAGCAC 60.320 55.000 0.00 0.00 35.60 4.40
1121 1347 0.608130 ATGTCGCTTCCAGTACAGCA 59.392 50.000 0.00 0.00 35.60 4.41
1122 1348 1.281899 GATGTCGCTTCCAGTACAGC 58.718 55.000 0.00 0.00 0.00 4.40
1153 1392 9.720874 TCTACAATCTATGGATAGATATGGCTT 57.279 33.333 9.16 0.00 46.49 4.35
1155 1394 9.360901 TCTCTACAATCTATGGATAGATATGGC 57.639 37.037 9.16 0.00 46.49 4.40
1187 1448 2.518407 TCTATGAACCCTCCTCCTGCTA 59.482 50.000 0.00 0.00 0.00 3.49
1317 1602 2.203480 GGTTGGCCACCTTGCTGA 60.203 61.111 3.88 0.00 43.29 4.26
1436 1727 5.431402 AGGAGAGGAGCCTTTTGATCTAAAT 59.569 40.000 2.77 0.00 29.44 1.40
1437 1728 4.785376 AGGAGAGGAGCCTTTTGATCTAAA 59.215 41.667 2.38 2.38 29.44 1.85
1438 1729 4.366267 AGGAGAGGAGCCTTTTGATCTAA 58.634 43.478 0.00 0.00 29.44 2.10
1439 1730 3.964031 GAGGAGAGGAGCCTTTTGATCTA 59.036 47.826 0.00 0.00 35.44 1.98
1482 1773 7.985752 GCTAACTGTGGTAATTAATGGAGTAGT 59.014 37.037 0.00 0.00 0.00 2.73
1483 1774 8.204836 AGCTAACTGTGGTAATTAATGGAGTAG 58.795 37.037 0.00 0.00 0.00 2.57
1488 1779 7.390718 GGGATAGCTAACTGTGGTAATTAATGG 59.609 40.741 0.00 0.00 0.00 3.16
1622 2120 3.714144 AGCTTGCTAGAGAGGGACTAAA 58.286 45.455 0.00 0.00 41.55 1.85
1771 2279 2.701951 AGCCTAATAAATCCCGACGGAA 59.298 45.455 17.49 0.00 43.10 4.30
1778 2286 4.875561 ACGAGAGAGCCTAATAAATCCC 57.124 45.455 0.00 0.00 0.00 3.85
1781 2289 9.482627 CTCAAAATACGAGAGAGCCTAATAAAT 57.517 33.333 0.00 0.00 31.84 1.40
2018 2637 2.613595 TGTGCTAGAAACAACACAGCAG 59.386 45.455 0.00 0.00 42.50 4.24
2183 3015 2.204306 AAGGAAGGAGGGGGTGGG 60.204 66.667 0.00 0.00 0.00 4.61
2800 4056 1.927174 GCATATTAGCACCGCCTATCG 59.073 52.381 0.00 0.00 38.08 2.92
2805 4061 1.308998 ACAAGCATATTAGCACCGCC 58.691 50.000 0.00 0.00 36.85 6.13
2821 4077 8.807667 AACAAACAAAATTCAAATGCAAACAA 57.192 23.077 0.00 0.00 0.00 2.83
2851 4107 4.624364 TGCACAGCACCCAGTCCG 62.624 66.667 0.00 0.00 31.71 4.79
3104 4363 4.933563 TGCAAGACGCCTGCTGCA 62.934 61.111 0.88 0.88 41.33 4.41
3121 4380 0.593128 GAAAGCGTCCACATTGCTGT 59.407 50.000 0.00 0.00 39.30 4.40
3175 4434 1.323271 TAGCTGGCTGAAGTCGAGGG 61.323 60.000 5.25 0.00 0.00 4.30
3292 4551 2.404215 AGCTGTTGTAGTTGTAGTGCG 58.596 47.619 0.00 0.00 0.00 5.34
3343 4612 3.879682 CGGCATGCATCACCCACG 61.880 66.667 21.36 7.19 0.00 4.94
3414 4683 1.558233 CTTGTCTACTTCCCCGGTCT 58.442 55.000 0.00 0.00 0.00 3.85
3424 4693 4.679106 CGGTCAATGATCAGCTTGTCTACT 60.679 45.833 0.09 0.00 0.00 2.57
3425 4694 3.553511 CGGTCAATGATCAGCTTGTCTAC 59.446 47.826 0.09 0.00 0.00 2.59
3482 4755 8.764558 ACTATGTAACAAATGTCCATACCTGTA 58.235 33.333 3.21 0.00 0.00 2.74
3508 4781 3.566742 TGAAGAGTGGCGCTTCGTATATA 59.433 43.478 7.64 0.00 41.84 0.86
3509 4782 2.361119 TGAAGAGTGGCGCTTCGTATAT 59.639 45.455 7.64 0.00 41.84 0.86
3510 4783 1.746787 TGAAGAGTGGCGCTTCGTATA 59.253 47.619 7.64 0.00 41.84 1.47
3511 4784 0.530744 TGAAGAGTGGCGCTTCGTAT 59.469 50.000 7.64 0.00 41.84 3.06
3607 5115 6.188400 GAGGAAATAAGTTCTTCTTGGCAG 57.812 41.667 0.00 0.00 38.87 4.85
3654 5162 7.042791 CCCAAAACATCAATTATTATGGAACGC 60.043 37.037 0.00 0.00 0.00 4.84
3662 5170 8.370940 TGAACAAGCCCAAAACATCAATTATTA 58.629 29.630 0.00 0.00 0.00 0.98
3746 5254 8.742125 AAGAATCCCATGAGACTAATATGGTA 57.258 34.615 0.00 0.00 39.74 3.25
3781 5289 8.524870 AACGAAATACACGTAGTACTGAAAAT 57.475 30.769 5.39 0.00 41.61 1.82
3787 5295 8.289618 TCTACAAAACGAAATACACGTAGTACT 58.710 33.333 0.00 0.00 41.61 2.73
3803 5311 3.617540 TGTGCCAACATCTACAAAACG 57.382 42.857 0.00 0.00 0.00 3.60
3958 5468 3.118956 ACGCCTCTCTCGAATCTTGAATT 60.119 43.478 0.00 0.00 0.00 2.17
3959 5469 2.428890 ACGCCTCTCTCGAATCTTGAAT 59.571 45.455 0.00 0.00 0.00 2.57
4116 5630 0.036388 AGTATATGGCGGGGCATTCG 60.036 55.000 13.15 0.00 0.00 3.34
4132 5646 5.829062 TGTAAACTTTAAGGGCCTCAGTA 57.171 39.130 6.46 0.00 0.00 2.74
4202 5716 2.766263 TGGTCTCTTCCGAGCATGTATT 59.234 45.455 0.00 0.00 36.58 1.89
4210 5724 4.508662 AGCTAATTTTGGTCTCTTCCGAG 58.491 43.478 0.00 0.00 38.67 4.63
4320 5857 1.629861 TGGGAGCTTCATGTCACATCA 59.370 47.619 0.00 0.00 0.00 3.07
4327 5864 2.629617 CAAGGTTTTGGGAGCTTCATGT 59.370 45.455 0.00 0.00 35.33 3.21
4362 5899 2.146342 CCGCACAGTGACTTCTTCATT 58.854 47.619 4.15 0.00 36.32 2.57
4370 5907 3.208884 GACCGACCGCACAGTGACT 62.209 63.158 4.15 0.00 0.00 3.41
4391 5928 1.630878 GGAAGTCAATGGGGAGACTGT 59.369 52.381 0.00 0.00 0.00 3.55
4406 5943 2.862541 TGTTATTGCAGCTGTGGAAGT 58.137 42.857 16.64 0.00 37.44 3.01
4427 5964 3.947834 CGGATCTCATTTGTAAAGGGCTT 59.052 43.478 0.00 0.00 0.00 4.35
4429 5966 2.033424 GCGGATCTCATTTGTAAAGGGC 59.967 50.000 0.00 0.00 0.00 5.19
4450 5987 4.394920 AGATGCGTATGTTTAAACACCTGG 59.605 41.667 22.78 13.19 42.51 4.45
4452 5989 4.634443 GGAGATGCGTATGTTTAAACACCT 59.366 41.667 22.78 11.08 42.51 4.00
4468 6005 7.009999 CGTATAATGAAGCTCTTATGGAGATGC 59.990 40.741 0.00 0.00 44.45 3.91
4471 6008 7.761038 TCGTATAATGAAGCTCTTATGGAGA 57.239 36.000 0.00 0.00 44.45 3.71
4491 6028 1.465794 TGGTCGTGATGGACATCGTA 58.534 50.000 7.70 0.00 40.63 3.43
4521 6058 1.412343 GCTTTCTTGGGTTGGCTTTGA 59.588 47.619 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.