Multiple sequence alignment - TraesCS3A01G278400

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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 TraesCS3A01G278400 chr3A 100.000 5113 0 0 1 5113 508162762 508157650 0.000000e+00 9443
1 TraesCS3A01G278400 chr3B 94.644 4500 184 20 1 4467 502639362 502634887 0.000000e+00 6922
2 TraesCS3A01G278400 chr3B 93.773 273 16 1 4841 5113 502631325 502631054 4.770000e-110 409
3 TraesCS3A01G278400 chr3B 88.923 325 14 4 4463 4784 502634842 502634537 1.040000e-101 381
4 TraesCS3A01G278400 chr3D 95.737 4316 113 20 185 4467 386433806 386429529 0.000000e+00 6885
5 TraesCS3A01G278400 chr3D 95.579 656 23 3 4463 5113 386429484 386428830 0.000000e+00 1046
6 TraesCS3A01G278400 chr3D 90.805 174 14 2 1 173 386434305 386434133 1.110000e-56 231
7 TraesCS3A01G278400 chrUn 100.000 402 0 0 3537 3938 478486737 478487138 0.000000e+00 743
8 TraesCS3A01G278400 chr5D 87.379 412 37 8 88 487 371030922 371031330 4.670000e-125 459
9 TraesCS3A01G278400 chr5D 87.535 361 31 3 88 436 479385955 479385597 6.160000e-109 405
10 TraesCS3A01G278400 chr1D 87.379 412 37 8 88 487 469879381 469879789 4.670000e-125 459
11 TraesCS3A01G278400 chr6D 86.861 411 39 4 89 487 418222265 418222672 3.630000e-121 446
12 TraesCS3A01G278400 chr4B 82.081 519 54 15 1 487 62873374 62873885 1.710000e-109 407
13 TraesCS3A01G278400 chr6A 80.800 375 34 13 1 339 598147517 598147889 5.080000e-65 259


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 TraesCS3A01G278400 chr3A 508157650 508162762 5112 True 9443.000000 9443 100.000000 1 5113 1 chr3A.!!$R1 5112
1 TraesCS3A01G278400 chr3B 502631054 502639362 8308 True 2570.666667 6922 92.446667 1 5113 3 chr3B.!!$R1 5112
2 TraesCS3A01G278400 chr3D 386428830 386434305 5475 True 2720.666667 6885 94.040333 1 5113 3 chr3D.!!$R1 5112
3 TraesCS3A01G278400 chr4B 62873374 62873885 511 False 407.000000 407 82.081000 1 487 1 chr4B.!!$F1 486

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
906 1259 0.043334 TAGGGCAGCCTCCTCTTTCT 59.957 55.000 12.43 0.0 35.92 2.52 F
1315 1672 0.530211 CGGAGCTTGAGATGGCAGAG 60.530 60.000 0.00 0.0 0.00 3.35 F
2105 2477 0.698238 GGCAGTATGGATATGGCCCA 59.302 55.000 0.00 0.0 38.19 5.36 F
2127 2499 1.068748 CAGCACAGTCACATCAAAGCC 60.069 52.381 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2465 0.111061 GTGCTGATGGGCCATATCCA 59.889 55.000 21.26 12.63 38.82 3.41 R
2245 2617 1.740025 GTCCTGCAACATGCTCCTTAC 59.260 52.381 3.78 0.00 45.31 2.34 R
3995 4367 0.037326 TCTTAAGAGCGGTGTGGCAG 60.037 55.000 0.00 0.00 34.64 4.85 R
4115 4487 3.056536 ACAGCGTAGACATGTCACATTCT 60.057 43.478 27.02 13.76 0.00 2.40 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
74 76 5.719085 AGTGGAGAACATCATAGTCTCAAGT 59.281 40.000 2.64 0.00 0.00 3.16
80 82 5.991933 ACATCATAGTCTCAAGTCAGTGT 57.008 39.130 0.00 0.00 0.00 3.55
82 84 6.162079 ACATCATAGTCTCAAGTCAGTGTTG 58.838 40.000 0.00 0.00 0.00 3.33
83 85 5.791336 TCATAGTCTCAAGTCAGTGTTGT 57.209 39.130 0.00 0.00 0.00 3.32
86 88 3.798202 AGTCTCAAGTCAGTGTTGTTCC 58.202 45.455 0.00 0.00 0.00 3.62
123 145 7.650504 GCACACTTATATACGACACCTAATTGA 59.349 37.037 0.00 0.00 0.00 2.57
220 557 4.997395 TGAACTTATCAGTGAGCTTCCAAC 59.003 41.667 0.00 0.00 31.60 3.77
266 615 0.250234 CTGATCTCCGCACCCTGAAA 59.750 55.000 0.00 0.00 0.00 2.69
667 1016 1.376424 CATGTGCGAGCTTGGTCCT 60.376 57.895 2.37 0.00 0.00 3.85
688 1037 4.042435 CCTTTGGACTGGGGTAGTAGAAAA 59.958 45.833 0.00 0.00 40.53 2.29
689 1038 4.628963 TTGGACTGGGGTAGTAGAAAAC 57.371 45.455 0.00 0.00 40.53 2.43
690 1039 3.865571 TGGACTGGGGTAGTAGAAAACT 58.134 45.455 0.00 0.00 40.53 2.66
691 1040 5.014534 TGGACTGGGGTAGTAGAAAACTA 57.985 43.478 0.00 0.00 40.53 2.24
692 1041 5.021458 TGGACTGGGGTAGTAGAAAACTAG 58.979 45.833 0.00 0.00 41.42 2.57
693 1042 5.222400 TGGACTGGGGTAGTAGAAAACTAGA 60.222 44.000 0.00 0.00 41.42 2.43
694 1043 5.718607 GGACTGGGGTAGTAGAAAACTAGAA 59.281 44.000 0.00 0.00 41.42 2.10
695 1044 6.212187 GGACTGGGGTAGTAGAAAACTAGAAA 59.788 42.308 0.00 0.00 41.42 2.52
696 1045 7.092979 GGACTGGGGTAGTAGAAAACTAGAAAT 60.093 40.741 0.00 0.00 41.42 2.17
697 1046 8.215954 ACTGGGGTAGTAGAAAACTAGAAATT 57.784 34.615 0.00 0.00 41.42 1.82
698 1047 8.319881 ACTGGGGTAGTAGAAAACTAGAAATTC 58.680 37.037 0.00 0.00 41.42 2.17
699 1048 7.325694 TGGGGTAGTAGAAAACTAGAAATTCG 58.674 38.462 0.00 0.00 41.42 3.34
701 1050 8.202811 GGGGTAGTAGAAAACTAGAAATTCGAT 58.797 37.037 0.00 0.00 41.42 3.59
702 1051 9.032420 GGGTAGTAGAAAACTAGAAATTCGATG 57.968 37.037 0.00 0.00 41.42 3.84
703 1052 8.541312 GGTAGTAGAAAACTAGAAATTCGATGC 58.459 37.037 0.00 0.00 41.42 3.91
709 1062 5.567138 AACTAGAAATTCGATGCAAAGGG 57.433 39.130 0.00 0.00 0.00 3.95
746 1099 1.435346 AAAAGCCCAGCCCAGTAGGT 61.435 55.000 0.00 0.00 38.26 3.08
848 1201 3.860930 ATTCCCACCACCACACCGC 62.861 63.158 0.00 0.00 0.00 5.68
902 1255 2.443016 CGTAGGGCAGCCTCCTCT 60.443 66.667 12.43 1.83 35.92 3.69
903 1256 2.060980 CGTAGGGCAGCCTCCTCTT 61.061 63.158 12.43 0.00 35.92 2.85
904 1257 1.617947 CGTAGGGCAGCCTCCTCTTT 61.618 60.000 12.43 0.00 35.92 2.52
905 1258 0.179234 GTAGGGCAGCCTCCTCTTTC 59.821 60.000 12.43 0.00 35.92 2.62
906 1259 0.043334 TAGGGCAGCCTCCTCTTTCT 59.957 55.000 12.43 0.00 35.92 2.52
907 1260 0.844221 AGGGCAGCCTCCTCTTTCTT 60.844 55.000 12.43 0.00 0.00 2.52
941 1294 3.839432 GGGGCTCTTCGTCTCCGG 61.839 72.222 0.00 0.00 33.95 5.14
1229 1583 4.142838 TGTGCTCATTTGCGATAGAAACAG 60.143 41.667 0.00 0.00 29.09 3.16
1244 1598 4.973168 AGAAACAGAGCCACATGAGTTAA 58.027 39.130 0.00 0.00 0.00 2.01
1246 1600 5.239525 AGAAACAGAGCCACATGAGTTAAAC 59.760 40.000 0.00 0.00 0.00 2.01
1315 1672 0.530211 CGGAGCTTGAGATGGCAGAG 60.530 60.000 0.00 0.00 0.00 3.35
1341 1698 3.620427 AAACACATACGCCCACTCATA 57.380 42.857 0.00 0.00 0.00 2.15
1351 1708 2.299013 CGCCCACTCATAGCACCTTATA 59.701 50.000 0.00 0.00 0.00 0.98
1375 1732 2.532531 CAGTGTGCTGAAAATAGCCG 57.467 50.000 0.00 0.00 45.28 5.52
1390 1747 4.506255 CCGGCCACCTCAATCCCC 62.506 72.222 2.24 0.00 0.00 4.81
1411 1768 8.096621 TCCCCTATAATTTCAGTGTTCACATA 57.903 34.615 5.74 0.00 0.00 2.29
1417 1774 6.403866 AATTTCAGTGTTCACATAGCCAAA 57.596 33.333 5.74 0.00 0.00 3.28
1433 1790 2.543653 GCCAAACAGATTGCTTTGACGT 60.544 45.455 0.00 0.00 37.73 4.34
1435 1792 3.300009 CAAACAGATTGCTTTGACGTCC 58.700 45.455 14.12 0.00 31.00 4.79
1440 1797 1.611491 GATTGCTTTGACGTCCCCAAA 59.389 47.619 14.12 6.91 33.12 3.28
1449 1806 2.342650 CGTCCCCAAATGGCCACTG 61.343 63.158 8.16 8.91 0.00 3.66
1467 1824 3.612423 CACTGTGATTTCTTCGACGCATA 59.388 43.478 0.32 0.00 0.00 3.14
1481 1838 2.682856 GACGCATATTTCTTGCCTGGAA 59.317 45.455 0.00 0.00 36.75 3.53
1495 1852 4.580868 TGCCTGGAAATTAACGTGACATA 58.419 39.130 0.00 0.00 0.00 2.29
1543 1900 1.303317 AAAGAGGATGCCCGCGTTT 60.303 52.632 4.92 0.00 37.33 3.60
1776 2133 3.487376 CGGTGTCAATGCACATTATGGAC 60.487 47.826 9.30 1.14 40.89 4.02
1854 2226 1.070758 AGCCATATACCGGTGCAAGAG 59.929 52.381 19.93 2.42 0.00 2.85
1969 2341 1.553704 TCATCAGCAGCAGAGTGTCAT 59.446 47.619 0.00 0.00 0.00 3.06
2040 2412 4.808895 GTGACGTTACTGGATATGATTGCA 59.191 41.667 2.75 0.00 0.00 4.08
2093 2465 5.258051 GAGAGCTATACTAGTGGGCAGTAT 58.742 45.833 5.39 1.49 41.13 2.12
2105 2477 0.698238 GGCAGTATGGATATGGCCCA 59.302 55.000 0.00 0.00 38.19 5.36
2127 2499 1.068748 CAGCACAGTCACATCAAAGCC 60.069 52.381 0.00 0.00 0.00 4.35
2156 2528 3.498774 AGTGACCAGCAAGTCTTTCAT 57.501 42.857 7.54 0.00 37.66 2.57
2211 2583 1.615392 ACTTCAACAAGCCTGGCAATC 59.385 47.619 22.65 0.00 32.09 2.67
2245 2617 1.237285 CCAACTCCAAGCAGTTCCCG 61.237 60.000 0.00 0.00 34.17 5.14
2346 2718 3.766545 AGTGCATACAATCACCCAAGTT 58.233 40.909 0.00 0.00 33.90 2.66
2465 2837 8.629821 ACTATAATGGTAGGCAGAATGGATAT 57.370 34.615 0.00 0.00 35.86 1.63
2539 2911 8.565416 GCAGAATGATTATCAAAGTCATGATCA 58.435 33.333 0.00 0.00 38.70 2.92
2576 2948 7.035162 TGTGAATTCTGCCTCACAGTATCCA 62.035 44.000 7.05 0.00 45.31 3.41
2604 2976 3.919834 AGCCATTTCCATAAGGAGCATT 58.080 40.909 0.00 0.00 46.74 3.56
2629 3001 1.098050 GTATTCCAGCAAGGCCACAG 58.902 55.000 5.01 0.00 37.29 3.66
2710 3082 3.986996 TGACAGGCAGAGAAATCATCA 57.013 42.857 0.00 0.00 0.00 3.07
3377 3749 1.134946 GCCTGTGGAATTTTGGGATCG 59.865 52.381 0.00 0.00 0.00 3.69
3438 3810 8.533569 GAAGGATTTTGGTATAATTCCTTCCA 57.466 34.615 19.56 0.00 46.59 3.53
3941 4313 6.567959 AGCTGTTAGTTACGGTCTTATAACC 58.432 40.000 0.00 0.00 35.43 2.85
3971 4343 2.203401 CGTTCGCCAATTCGGGTTATA 58.797 47.619 0.00 0.00 34.06 0.98
3977 4349 4.333372 TCGCCAATTCGGGTTATAAAGAAC 59.667 41.667 0.00 0.00 34.06 3.01
4008 4380 2.433318 GAGACTGCCACACCGCTC 60.433 66.667 0.00 0.00 0.00 5.03
4010 4382 2.031163 GACTGCCACACCGCTCTT 59.969 61.111 0.00 0.00 0.00 2.85
4055 4427 1.576356 GTCAGATCATTGCGAGGGAC 58.424 55.000 0.00 0.00 0.00 4.46
4141 4513 5.570234 TGTGACATGTCTACGCTGTTATA 57.430 39.130 25.55 0.00 0.00 0.98
4148 4520 9.769093 GACATGTCTACGCTGTTATAAAATTTT 57.231 29.630 18.83 8.75 0.00 1.82
4422 4795 6.952773 TGTTGGTAACTTTTTGTGCTAGAT 57.047 33.333 0.00 0.00 37.61 1.98
4435 4808 5.324784 TGTGCTAGATGACTTGTACGAAT 57.675 39.130 0.00 0.00 37.31 3.34
4439 4812 7.148137 TGTGCTAGATGACTTGTACGAATCTTA 60.148 37.037 0.00 0.00 37.31 2.10
4467 4840 4.808767 ACCCCTTCTTTTGTACTCCTTT 57.191 40.909 0.00 0.00 0.00 3.11
4469 4842 5.628130 ACCCCTTCTTTTGTACTCCTTTAC 58.372 41.667 0.00 0.00 0.00 2.01
4471 4844 5.705905 CCCCTTCTTTTGTACTCCTTTACTG 59.294 44.000 0.00 0.00 0.00 2.74
4472 4845 5.705905 CCCTTCTTTTGTACTCCTTTACTGG 59.294 44.000 0.00 0.00 0.00 4.00
4473 4846 6.296803 CCTTCTTTTGTACTCCTTTACTGGT 58.703 40.000 0.00 0.00 0.00 4.00
4474 4847 6.204882 CCTTCTTTTGTACTCCTTTACTGGTG 59.795 42.308 0.00 0.00 0.00 4.17
4477 4899 2.616524 TGTACTCCTTTACTGGTGGCT 58.383 47.619 0.00 0.00 0.00 4.75
4553 4977 4.384940 GAAAGAGCCTCACTGAAGAAGTT 58.615 43.478 0.00 0.00 36.83 2.66
4613 5041 2.675348 GTGCACTTCTGTAGCTGGAATC 59.325 50.000 10.32 0.00 0.00 2.52
4621 5049 1.009829 GTAGCTGGAATCGTGCCAAG 58.990 55.000 0.00 0.00 34.44 3.61
4622 5050 0.744414 TAGCTGGAATCGTGCCAAGC 60.744 55.000 0.00 0.00 34.44 4.01
4762 5191 1.669265 CACTGGAGCATCGTACGAGTA 59.331 52.381 23.89 0.05 34.37 2.59
4803 6396 1.800286 GCATCCGGCTTTGAATTCTGC 60.800 52.381 7.05 8.33 40.25 4.26
4899 8483 1.134280 CAGGATCTCGCATTCCCAAGT 60.134 52.381 0.00 0.00 32.05 3.16
5097 8681 1.334869 CTTCACAAGCGGATTATGGGC 59.665 52.381 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.331845 TGCTTATACCGAACTTTGATCGTTA 58.668 36.000 0.00 0.00 38.60 3.18
26 27 5.172934 TGCTTATACCGAACTTTGATCGTT 58.827 37.500 0.00 0.00 38.60 3.85
37 38 4.020928 TGTTCTCCACTTGCTTATACCGAA 60.021 41.667 0.00 0.00 0.00 4.30
82 84 4.600692 AGTGTGCCCTTTAATTTGGAAC 57.399 40.909 0.00 0.00 0.00 3.62
83 85 6.926630 ATAAGTGTGCCCTTTAATTTGGAA 57.073 33.333 0.00 0.00 0.00 3.53
86 88 8.832521 TCGTATATAAGTGTGCCCTTTAATTTG 58.167 33.333 0.00 0.00 0.00 2.32
189 526 5.521735 GCTCACTGATAAGTTCACCTATGTG 59.478 44.000 0.00 0.00 44.18 3.21
201 538 4.328440 CGAAGTTGGAAGCTCACTGATAAG 59.672 45.833 0.00 0.00 0.00 1.73
266 615 1.488705 TTTGGGTGCGAGAGATGGGT 61.489 55.000 0.00 0.00 0.00 4.51
514 863 4.694233 CAGCCACAGTCGCCTGCT 62.694 66.667 0.00 0.00 42.81 4.24
544 893 3.414700 GCCGCGCCTATGGATTCG 61.415 66.667 0.00 0.00 0.00 3.34
667 1016 4.661709 AGTTTTCTACTACCCCAGTCCAAA 59.338 41.667 0.00 0.00 38.80 3.28
688 1037 4.843728 TCCCTTTGCATCGAATTTCTAGT 58.156 39.130 0.00 0.00 0.00 2.57
689 1038 4.274459 CCTCCCTTTGCATCGAATTTCTAG 59.726 45.833 0.00 0.00 0.00 2.43
690 1039 4.080582 TCCTCCCTTTGCATCGAATTTCTA 60.081 41.667 0.00 0.00 0.00 2.10
691 1040 3.019564 CCTCCCTTTGCATCGAATTTCT 58.980 45.455 0.00 0.00 0.00 2.52
692 1041 3.016736 TCCTCCCTTTGCATCGAATTTC 58.983 45.455 0.00 0.00 0.00 2.17
693 1042 3.085952 TCCTCCCTTTGCATCGAATTT 57.914 42.857 0.00 0.00 0.00 1.82
694 1043 2.806945 TCCTCCCTTTGCATCGAATT 57.193 45.000 0.00 0.00 0.00 2.17
695 1044 2.648059 CTTCCTCCCTTTGCATCGAAT 58.352 47.619 0.00 0.00 0.00 3.34
696 1045 1.340017 CCTTCCTCCCTTTGCATCGAA 60.340 52.381 0.00 0.00 0.00 3.71
697 1046 0.253044 CCTTCCTCCCTTTGCATCGA 59.747 55.000 0.00 0.00 0.00 3.59
698 1047 1.379642 GCCTTCCTCCCTTTGCATCG 61.380 60.000 0.00 0.00 0.00 3.84
699 1048 1.039785 GGCCTTCCTCCCTTTGCATC 61.040 60.000 0.00 0.00 0.00 3.91
701 1050 2.162906 AGGCCTTCCTCCCTTTGCA 61.163 57.895 0.00 0.00 38.72 4.08
702 1051 1.680314 CAGGCCTTCCTCCCTTTGC 60.680 63.158 0.00 0.00 41.93 3.68
703 1052 0.405585 TTCAGGCCTTCCTCCCTTTG 59.594 55.000 0.00 0.00 41.93 2.77
709 1062 2.568623 TTCACTTTCAGGCCTTCCTC 57.431 50.000 0.00 0.00 41.93 3.71
746 1099 1.612442 GGTCCACTGGGCCTCACTA 60.612 63.158 11.92 0.00 0.00 2.74
791 1144 0.602060 GACGGGTGGGTATAGCTAGC 59.398 60.000 6.62 6.62 0.00 3.42
792 1145 1.254954 GGACGGGTGGGTATAGCTAG 58.745 60.000 0.00 0.00 0.00 3.42
793 1146 0.538057 CGGACGGGTGGGTATAGCTA 60.538 60.000 0.00 0.00 0.00 3.32
794 1147 1.831286 CGGACGGGTGGGTATAGCT 60.831 63.158 1.32 0.00 0.00 3.32
880 1233 4.715130 AGGCTGCCCTACGGTGGA 62.715 66.667 16.57 0.00 40.58 4.02
1229 1583 6.595716 ACTTCTATGTTTAACTCATGTGGCTC 59.404 38.462 0.00 0.00 0.00 4.70
1279 1636 3.202906 CTCCGGCCGAAATTGATTTCTA 58.797 45.455 30.73 0.00 42.96 2.10
1315 1672 4.690122 AGTGGGCGTATGTGTTTAGTATC 58.310 43.478 0.00 0.00 0.00 2.24
1341 1698 5.567138 GCACACTGAAATTATAAGGTGCT 57.433 39.130 13.83 0.00 44.97 4.40
1375 1732 1.742308 TATAGGGGATTGAGGTGGCC 58.258 55.000 0.00 0.00 0.00 5.36
1390 1747 8.437360 TGGCTATGTGAACACTGAAATTATAG 57.563 34.615 6.51 4.73 0.00 1.31
1411 1768 2.287788 CGTCAAAGCAATCTGTTTGGCT 60.288 45.455 1.08 0.00 36.35 4.75
1417 1774 1.523758 GGGACGTCAAAGCAATCTGT 58.476 50.000 18.91 0.00 0.00 3.41
1433 1790 1.228831 CACAGTGGCCATTTGGGGA 60.229 57.895 9.72 0.00 37.04 4.81
1435 1792 1.269012 AATCACAGTGGCCATTTGGG 58.731 50.000 9.72 12.80 40.85 4.12
1440 1797 2.086869 CGAAGAAATCACAGTGGCCAT 58.913 47.619 9.72 0.00 0.00 4.40
1449 1806 6.037423 AGAAATATGCGTCGAAGAAATCAC 57.963 37.500 1.37 0.00 39.69 3.06
1467 1824 5.242838 TCACGTTAATTTCCAGGCAAGAAAT 59.757 36.000 8.45 8.45 43.95 2.17
1481 1838 9.935682 CAGAATAGCAAATATGTCACGTTAATT 57.064 29.630 0.00 0.00 0.00 1.40
1495 1852 6.716628 TGGAAGACTGAAACAGAATAGCAAAT 59.283 34.615 5.76 0.00 35.18 2.32
1543 1900 1.582610 GCCTCGATGCGGAACCAAAA 61.583 55.000 0.00 0.00 0.00 2.44
1554 1911 4.827087 ACTGCCAGCGCCTCGATG 62.827 66.667 2.29 0.00 43.13 3.84
1650 2007 5.009911 TGAAATGATCAGGTGAGTGTTTTGG 59.990 40.000 0.09 0.00 33.04 3.28
1694 2051 1.561542 GAAGAATGAGCTGAAGGGGGA 59.438 52.381 0.00 0.00 0.00 4.81
1707 2064 7.563888 TTCTATCAATGCCTTCTGAAGAATG 57.436 36.000 18.68 11.01 33.01 2.67
1776 2133 3.252215 TGGTAAGGTTGTTCAGAATTGCG 59.748 43.478 0.00 0.00 0.00 4.85
1854 2226 1.066430 TCCAGGTGGCTCGTTATTCAC 60.066 52.381 0.00 0.00 34.44 3.18
1963 2335 4.455877 GGCCATTAATAGCAGGTATGACAC 59.544 45.833 8.15 0.00 0.00 3.67
1969 2341 5.376625 CAGAAAGGCCATTAATAGCAGGTA 58.623 41.667 5.01 0.00 0.00 3.08
2040 2412 2.398588 TCGGGAATTGTATCCAGAGCT 58.601 47.619 0.00 0.00 38.53 4.09
2093 2465 0.111061 GTGCTGATGGGCCATATCCA 59.889 55.000 21.26 12.63 38.82 3.41
2105 2477 2.486982 GCTTTGATGTGACTGTGCTGAT 59.513 45.455 0.00 0.00 0.00 2.90
2245 2617 1.740025 GTCCTGCAACATGCTCCTTAC 59.260 52.381 3.78 0.00 45.31 2.34
2265 2637 4.233013 CACCATTGTGGCCTTGTTGAGG 62.233 54.545 3.32 0.00 42.67 3.86
2320 2692 4.260985 TGGGTGATTGTATGCACTACTTG 58.739 43.478 0.00 0.00 35.43 3.16
2325 2697 3.439857 ACTTGGGTGATTGTATGCACT 57.560 42.857 0.00 0.00 35.43 4.40
2539 2911 4.098960 CAGAATTCACAGGCCTATTTGCAT 59.901 41.667 3.98 0.00 0.00 3.96
2576 2948 6.717084 GCTCCTTATGGAAATGGCTAGTATTT 59.283 38.462 6.76 6.76 42.66 1.40
2604 2976 2.446435 GCCTTGCTGGAATACTGGAAA 58.554 47.619 0.49 0.00 38.35 3.13
2629 3001 5.841957 AGCATTGTATCCAAAATCACCTC 57.158 39.130 0.00 0.00 33.44 3.85
2695 3067 3.276857 TGCTCTTGATGATTTCTCTGCC 58.723 45.455 0.00 0.00 0.00 4.85
3377 3749 1.875963 CAACATGCCCTCGTCAACC 59.124 57.895 0.00 0.00 0.00 3.77
3438 3810 4.077108 ACAATGCTCGCATAATGATCCAT 58.923 39.130 4.63 0.00 35.31 3.41
3941 4313 3.414700 GGCGAACGGACAGCACTG 61.415 66.667 0.00 0.00 0.00 3.66
3971 4343 1.543429 CCACAGGAGCGAAGGTTCTTT 60.543 52.381 0.00 0.00 44.25 2.52
3995 4367 0.037326 TCTTAAGAGCGGTGTGGCAG 60.037 55.000 0.00 0.00 34.64 4.85
4004 4376 7.865385 ACAAGCTTAGAGATTATCTTAAGAGCG 59.135 37.037 11.53 12.07 39.64 5.03
4008 4380 8.555361 GCCAACAAGCTTAGAGATTATCTTAAG 58.445 37.037 0.00 14.22 39.64 1.85
4010 4382 6.992715 GGCCAACAAGCTTAGAGATTATCTTA 59.007 38.462 0.00 0.00 39.64 2.10
4103 4475 8.044060 ACATGTCACATTCTGTTTACCAATAG 57.956 34.615 0.00 0.00 0.00 1.73
4115 4487 3.056536 ACAGCGTAGACATGTCACATTCT 60.057 43.478 27.02 13.76 0.00 2.40
4116 4488 3.254060 ACAGCGTAGACATGTCACATTC 58.746 45.455 27.02 11.85 0.00 2.67
4121 4493 8.487313 AATTTTATAACAGCGTAGACATGTCA 57.513 30.769 27.02 10.87 0.00 3.58
4148 4520 9.213777 ACAACTGATTTTGGATCTCTACCTATA 57.786 33.333 0.00 0.00 0.00 1.31
4282 4654 6.546034 GCTTCAAGCTAATAAATTCCAGGGTA 59.454 38.462 0.71 0.00 38.45 3.69
4283 4655 5.360999 GCTTCAAGCTAATAAATTCCAGGGT 59.639 40.000 0.71 0.00 38.45 4.34
4422 4795 5.717078 ACCAGTAAGATTCGTACAAGTCA 57.283 39.130 11.51 0.00 0.00 3.41
4467 4840 6.262273 GCTAAAGCATATAAAAGCCACCAGTA 59.738 38.462 0.00 0.00 41.59 2.74
4469 4842 5.523369 GCTAAAGCATATAAAAGCCACCAG 58.477 41.667 0.00 0.00 41.59 4.00
4471 4844 4.036380 ACGCTAAAGCATATAAAAGCCACC 59.964 41.667 2.44 0.00 42.21 4.61
4472 4845 5.169836 ACGCTAAAGCATATAAAAGCCAC 57.830 39.130 2.44 0.00 42.21 5.01
4473 4846 5.220970 GGAACGCTAAAGCATATAAAAGCCA 60.221 40.000 2.44 0.00 42.21 4.75
4474 4847 5.212934 GGAACGCTAAAGCATATAAAAGCC 58.787 41.667 2.44 0.00 42.21 4.35
4477 4899 9.944663 CTTATTGGAACGCTAAAGCATATAAAA 57.055 29.630 2.44 0.00 42.21 1.52
4553 4977 2.036217 CCATCAAAGCTCCAAGTTGCAA 59.964 45.455 0.00 0.00 0.00 4.08
4613 5041 1.442520 CATTTCACCGCTTGGCACG 60.443 57.895 0.00 0.00 35.53 5.34
4621 5049 1.068541 GTTGGACTTCCATTTCACCGC 60.069 52.381 0.00 0.00 46.97 5.68
4622 5050 2.031157 GTGTTGGACTTCCATTTCACCG 60.031 50.000 0.00 0.00 46.97 4.94
4762 5191 0.110486 AACCATGCCACTTCGACCTT 59.890 50.000 0.00 0.00 0.00 3.50
4899 8483 2.787473 ATGATTTCTCCAACTCCGCA 57.213 45.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.