Multiple sequence alignment - TraesCS5A01G127600

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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 TraesCS5A01G127600 chr5A 100.000 6050 0 0 1 6050 283630112 283624063 0.000000e+00 11173
1 TraesCS5A01G127600 chr5D 96.123 6087 177 21 1 6050 215480062 215473998 0.000000e+00 9878
2 TraesCS5A01G127600 chr5B 95.990 6085 180 24 1 6050 231275496 231269441 0.000000e+00 9827
3 TraesCS5A01G127600 chr6A 86.168 1576 140 24 2583 4132 611923259 611924782 0.000000e+00 1631
4 TraesCS5A01G127600 chr6A 85.076 918 78 24 4532 5433 611924848 611925722 0.000000e+00 881
5 TraesCS5A01G127600 chr6A 83.008 1024 115 30 1551 2536 611922260 611923262 0.000000e+00 872
6 TraesCS5A01G127600 chr6A 81.773 203 20 10 5482 5684 611925735 611925920 2.920000e-33 154
7 TraesCS5A01G127600 chr6B 82.892 982 103 22 4532 5497 710326226 710327158 0.000000e+00 822
8 TraesCS5A01G127600 chr6B 85.817 416 51 4 2581 2991 710316289 710316701 9.310000e-118 435
9 TraesCS5A01G127600 chr6B 93.548 93 6 0 1979 2071 710316185 710316277 8.180000e-29 139
10 TraesCS5A01G127600 chr6B 91.011 89 5 1 1085 1170 710315152 710315240 3.830000e-22 117


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 TraesCS5A01G127600 chr5A 283624063 283630112 6049 True 11173.000000 11173 100.000000 1 6050 1 chr5A.!!$R1 6049
1 TraesCS5A01G127600 chr5D 215473998 215480062 6064 True 9878.000000 9878 96.123000 1 6050 1 chr5D.!!$R1 6049
2 TraesCS5A01G127600 chr5B 231269441 231275496 6055 True 9827.000000 9827 95.990000 1 6050 1 chr5B.!!$R1 6049
3 TraesCS5A01G127600 chr6A 611922260 611925920 3660 False 884.500000 1631 84.006250 1551 5684 4 chr6A.!!$F1 4133
4 TraesCS5A01G127600 chr6B 710326226 710327158 932 False 822.000000 822 82.892000 4532 5497 1 chr6B.!!$F1 965
5 TraesCS5A01G127600 chr6B 710315152 710316701 1549 False 230.333333 435 90.125333 1085 2991 3 chr6B.!!$F2 1906

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
92 93 0.942252 CATCATGCGCTGCACTGTAT 59.058 50.000 9.73 0.00 43.04 2.29 F
525 535 1.202463 AGCAGCTACCGCACTTGATAG 60.202 52.381 0.00 0.00 39.10 2.08 F
1720 2119 1.302033 CAGTTTCCTCTGTGGCGCT 60.302 57.895 7.64 0.00 35.26 5.92 F
2544 2984 0.107361 TCAGCCAGCACATCAGATGG 60.107 55.000 15.13 5.10 35.84 3.51 F
3017 3475 0.453390 GTGGCAATGCTGAAGTAGGC 59.547 55.000 4.82 0.00 0.00 3.93 F
3307 3765 0.464554 GGAGCACTGGGTTCCTATGC 60.465 60.000 5.44 5.31 43.15 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2496 0.038166 ACTATGTGTTGGGGCTGTGG 59.962 55.000 0.00 0.0 0.00 4.17 R
2416 2856 0.958382 TTGTGGGTACGATTGCTGCC 60.958 55.000 0.00 0.0 0.00 4.85 R
2998 3456 0.453390 GCCTACTTCAGCATTGCCAC 59.547 55.000 4.70 0.0 0.00 5.01 R
4322 4807 0.455005 GGTCCTTACGAAGACCTCCG 59.545 60.000 1.93 0.0 35.02 4.63 R
4753 5243 0.623723 ATATCCGGCACCAACCAACT 59.376 50.000 0.00 0.0 0.00 3.16 R
5125 5616 4.796369 ACTGAACTACTGAACTAAGCGTC 58.204 43.478 0.00 0.0 0.00 5.19 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
45 46 3.004734 GCAACATAACACCTGCTGAACTT 59.995 43.478 0.00 0.00 0.00 2.66
56 57 3.817647 CCTGCTGAACTTCAAAGCTAACT 59.182 43.478 0.00 0.00 37.82 2.24
64 65 6.926826 TGAACTTCAAAGCTAACTGAATACGA 59.073 34.615 6.34 0.00 31.40 3.43
65 66 6.952935 ACTTCAAAGCTAACTGAATACGAG 57.047 37.500 6.34 0.00 31.40 4.18
92 93 0.942252 CATCATGCGCTGCACTGTAT 59.058 50.000 9.73 0.00 43.04 2.29
226 227 3.005791 CCTTTTTAGTTCAGTTGGCCCTG 59.994 47.826 0.00 0.41 0.00 4.45
266 269 6.765403 ACTATGCAACAGTGTAGGTTCTTTA 58.235 36.000 0.00 0.00 0.00 1.85
270 273 8.630054 ATGCAACAGTGTAGGTTCTTTATTAA 57.370 30.769 0.00 0.00 0.00 1.40
346 356 7.759489 AGAGATAATCTACCAGATGTCTGTC 57.241 40.000 9.03 0.00 38.23 3.51
411 421 5.050363 CACGTTATGGTATAGGCATGTGTTC 60.050 44.000 0.00 0.00 0.00 3.18
438 448 4.390264 TCTCTACTGTATCGTGCTAGCAT 58.610 43.478 22.51 7.71 0.00 3.79
525 535 1.202463 AGCAGCTACCGCACTTGATAG 60.202 52.381 0.00 0.00 39.10 2.08
538 548 5.453587 CGCACTTGATAGCTGAAAAATAAGC 59.546 40.000 0.00 0.00 39.82 3.09
568 578 4.308526 TGGACCCACATGCAATACTTTA 57.691 40.909 0.00 0.00 0.00 1.85
631 641 5.762179 TGGAGAGTGGTGACAATTAGATT 57.238 39.130 0.00 0.00 46.06 2.40
632 642 6.867519 TGGAGAGTGGTGACAATTAGATTA 57.132 37.500 0.00 0.00 46.06 1.75
636 646 5.104485 AGAGTGGTGACAATTAGATTACCCC 60.104 44.000 0.00 0.00 46.06 4.95
691 701 5.080969 AGCAGCTACACCTTTCGTATTTA 57.919 39.130 0.00 0.00 0.00 1.40
733 743 7.349711 TGACTTGCTATTGTTAAAAAGACGAC 58.650 34.615 0.00 0.00 0.00 4.34
829 842 5.619981 GCCATGTGTTGATTACTTGTCTTCC 60.620 44.000 0.00 0.00 0.00 3.46
920 934 4.212214 GGATTTCTGGCTTTAGCTCATACG 59.788 45.833 0.00 0.00 41.70 3.06
1074 1089 1.440938 TTTGCCCTGTTTGTCGGACG 61.441 55.000 3.34 0.00 0.00 4.79
1241 1626 1.620822 AAGGGAGTGATTTGTGCACC 58.379 50.000 15.69 0.00 36.95 5.01
1261 1646 5.706916 CACCGTACAGTGAGTTTAGTGTAT 58.293 41.667 2.91 0.00 40.34 2.29
1272 1657 8.867097 AGTGAGTTTAGTGTATTTGGAAGTAGA 58.133 33.333 0.00 0.00 0.00 2.59
1451 1839 1.656652 CTTGTGCCTATGGGAACTCG 58.343 55.000 7.89 0.00 41.79 4.18
1558 1947 8.087982 TCATGTCTCAAAGTGATTTGTTCTAC 57.912 34.615 0.00 0.00 33.82 2.59
1720 2119 1.302033 CAGTTTCCTCTGTGGCGCT 60.302 57.895 7.64 0.00 35.26 5.92
1872 2292 3.132925 GCAGTTGCACCACAAATTCAAT 58.867 40.909 0.00 0.00 40.82 2.57
2076 2496 2.768492 CCTCAATTCCTGCAGCCGC 61.768 63.158 8.66 0.00 39.24 6.53
2093 2513 1.304052 GCCACAGCCCCAACACATA 60.304 57.895 0.00 0.00 0.00 2.29
2238 2674 4.052199 ACCTATAGCCCATACCCAAGTTT 58.948 43.478 0.00 0.00 0.00 2.66
2321 2758 2.618816 GCAACCTCATCCTCCACATCAA 60.619 50.000 0.00 0.00 0.00 2.57
2380 2820 1.310933 CCACCTCAGCAGCAACATCC 61.311 60.000 0.00 0.00 0.00 3.51
2416 2856 1.968017 ACCAGCATCCACAAGTGCG 60.968 57.895 0.00 0.00 45.69 5.34
2494 2934 3.055819 TCTCAGAACCCTTCAGTACATGC 60.056 47.826 0.00 0.00 0.00 4.06
2544 2984 0.107361 TCAGCCAGCACATCAGATGG 60.107 55.000 15.13 5.10 35.84 3.51
2660 3100 1.464734 TTCCGTTGCAAGGTCAACAA 58.535 45.000 17.23 1.28 44.80 2.83
2811 3259 3.192422 CACACCTGTTCCTTCACAAACAA 59.808 43.478 0.00 0.00 35.13 2.83
2855 3303 3.884693 TGCACTCATCACAACAACAGATT 59.115 39.130 0.00 0.00 0.00 2.40
3017 3475 0.453390 GTGGCAATGCTGAAGTAGGC 59.547 55.000 4.82 0.00 0.00 3.93
3036 3494 3.146066 GGCGATAATACAAATGGAGGCA 58.854 45.455 0.00 0.00 0.00 4.75
3196 3654 1.912043 AGGAAAGGATGAGTCTGGTGG 59.088 52.381 0.00 0.00 0.00 4.61
3307 3765 0.464554 GGAGCACTGGGTTCCTATGC 60.465 60.000 5.44 5.31 43.15 3.14
3357 3815 3.653164 TCTGGACCTGATACCATGCTTA 58.347 45.455 0.00 0.00 35.54 3.09
3403 3864 0.676466 CCATGTACGCAAGCCCAGAA 60.676 55.000 0.00 0.00 45.62 3.02
3437 3898 3.054655 GGCCACCTAGTCATAGTTTTCCA 60.055 47.826 0.00 0.00 0.00 3.53
3505 3966 0.482446 TCTGAAATGGCACCAAGGGT 59.518 50.000 0.00 0.00 35.62 4.34
3566 4038 2.158784 TGATGATGGCATGATTCGACCA 60.159 45.455 3.81 0.00 34.11 4.02
3693 4165 3.923461 TGCAAACACTTTTGAGTTTTCCG 59.077 39.130 1.29 0.00 44.38 4.30
3772 4250 4.761739 TGTTCAGGAATGAGAAATGGTGTC 59.238 41.667 0.00 0.00 0.00 3.67
3808 4286 2.044908 AGGAAATTCCAGGGCTTTCCAT 59.955 45.455 24.57 13.53 46.75 3.41
3824 4302 5.418840 GCTTTCCATGAAGAAGGGTTCAATA 59.581 40.000 0.00 0.00 39.84 1.90
3852 4330 1.539827 GGAACATTTCAGGTCGTTGGG 59.460 52.381 0.00 0.00 0.00 4.12
3991 4470 6.825944 TTTGATGGTTTCGATTCATTACCA 57.174 33.333 0.00 0.00 42.57 3.25
4051 4530 5.072329 TCCTATAGGCTTCCCTGAAGATTTG 59.928 44.000 14.50 0.00 41.71 2.32
4155 4634 2.193993 GCCTAGAAACCCAGGTAAGGA 58.806 52.381 10.18 0.00 34.18 3.36
4163 4642 7.766736 AGAAACCCAGGTAAGGATTATAAGT 57.233 36.000 0.00 0.00 30.46 2.24
4193 4672 6.266103 TCAAGGCTTGATTTGAAACTTCATCT 59.734 34.615 25.38 0.00 34.09 2.90
4241 4726 7.423844 TGAATGAAGAGGAGCTTACTTGATA 57.576 36.000 5.89 0.00 36.83 2.15
4265 4750 7.250445 ACTTTTCACAATTTTTCAATGGCTC 57.750 32.000 0.00 0.00 0.00 4.70
4266 4751 7.049754 ACTTTTCACAATTTTTCAATGGCTCT 58.950 30.769 0.00 0.00 0.00 4.09
4267 4752 6.847956 TTTCACAATTTTTCAATGGCTCTG 57.152 33.333 0.00 0.00 0.00 3.35
4268 4753 5.534207 TCACAATTTTTCAATGGCTCTGT 57.466 34.783 0.00 0.00 0.00 3.41
4269 4754 6.647334 TCACAATTTTTCAATGGCTCTGTA 57.353 33.333 0.00 0.00 0.00 2.74
4270 4755 7.048629 TCACAATTTTTCAATGGCTCTGTAA 57.951 32.000 0.00 0.00 0.00 2.41
4271 4756 7.669427 TCACAATTTTTCAATGGCTCTGTAAT 58.331 30.769 0.00 0.00 0.00 1.89
4272 4757 7.599621 TCACAATTTTTCAATGGCTCTGTAATG 59.400 33.333 0.00 0.00 0.00 1.90
4322 4807 2.592308 GGGATGACAGCTGGTCCC 59.408 66.667 27.71 27.71 46.38 4.46
4393 4878 6.883217 AGTAGACAGCATGATTTTGACAATCT 59.117 34.615 0.00 0.00 39.69 2.40
4421 4906 2.654863 CCTCATACACATTTCCACCCC 58.345 52.381 0.00 0.00 0.00 4.95
4521 5006 1.959226 CACCGGTTCCAAGGACACG 60.959 63.158 2.97 5.03 0.00 4.49
4609 5094 2.093181 TCAGTTCGGTGGGTTATGGATG 60.093 50.000 0.00 0.00 0.00 3.51
4617 5102 4.159506 CGGTGGGTTATGGATGTTGAATTT 59.840 41.667 0.00 0.00 0.00 1.82
4753 5243 4.202326 GGTGGTTTCTTCAGTAGTGGAGAA 60.202 45.833 16.15 16.15 45.28 2.87
4876 5366 6.384224 TGTTCTGAAAATGAAGCATGATGTC 58.616 36.000 0.00 0.00 0.00 3.06
5131 5622 2.357517 CCCTCAAGTGCGACGCTT 60.358 61.111 22.08 4.79 34.27 4.68
5164 5656 0.482887 AGTTAGTTGCTTTGCCCCCT 59.517 50.000 0.00 0.00 0.00 4.79
5392 5896 5.660417 TGACTCTGAGGATGCTTCTATTTCT 59.340 40.000 9.85 0.00 0.00 2.52
5593 6098 4.348863 AGCCATAGATGTGAAGTCATCC 57.651 45.455 3.52 0.00 43.46 3.51
5604 6112 5.674525 TGTGAAGTCATCCCTACATGAATC 58.325 41.667 0.00 0.00 34.50 2.52
5630 6138 7.134815 CCTCGTATTTTGAAAGGATATTGCAG 58.865 38.462 0.00 0.00 0.00 4.41
5661 6169 5.815233 TGGCCTTGTATTTTGAAATGGAA 57.185 34.783 3.32 0.00 0.00 3.53
5699 6207 7.098845 TCCATGTATATCCACTAGGTAGACA 57.901 40.000 0.00 0.00 35.89 3.41
5722 6230 4.124238 TGAGTTTTGTCGTTCTTACTGGG 58.876 43.478 0.00 0.00 0.00 4.45
5736 6244 2.930826 ACTGGGGCCTAAATATCACG 57.069 50.000 0.84 0.00 0.00 4.35
5842 6357 4.705023 GGCACTCCTGGTATGTAAAATTGT 59.295 41.667 0.00 0.00 0.00 2.71
5865 6380 7.721402 TGTCACCAGTTTGCTTATGTTAAATT 58.279 30.769 0.00 0.00 0.00 1.82
5934 6449 2.170166 CACTGCTCCAAATAAAGGCCA 58.830 47.619 5.01 0.00 0.00 5.36
5943 6458 6.179906 TCCAAATAAAGGCCATTGTGAAAA 57.820 33.333 5.01 0.00 0.00 2.29
5951 6466 2.096318 GGCCATTGTGAAAACGCATTTG 60.096 45.455 0.00 0.00 0.00 2.32
5964 6479 1.895238 CATTTGAAGGCCAGGCTGG 59.105 57.895 29.44 29.44 41.55 4.85
6025 6540 6.920569 AGGGCGTTGTTTAGTAGAAATATG 57.079 37.500 0.00 0.00 0.00 1.78
6030 6545 8.112449 GGCGTTGTTTAGTAGAAATATGTGTAC 58.888 37.037 0.00 0.00 0.00 2.90
6035 6550 7.182387 TGTTTAGTAGAAATATGTGTACCCCCA 59.818 37.037 0.00 0.00 0.00 4.96
6039 6554 3.134081 AGAAATATGTGTACCCCCAGTCG 59.866 47.826 0.00 0.00 0.00 4.18
6046 6561 1.608336 TACCCCCAGTCGACCACAG 60.608 63.158 13.01 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.526142 TGTTGCCAAATAACCAAGTTACATA 57.474 32.000 0.00 0.00 30.49 2.29
45 46 4.081642 AGGCTCGTATTCAGTTAGCTTTGA 60.082 41.667 0.00 0.00 33.67 2.69
56 57 4.335400 TGATGCATTAGGCTCGTATTCA 57.665 40.909 0.00 0.00 45.15 2.57
64 65 0.536687 AGCGCATGATGCATTAGGCT 60.537 50.000 23.08 14.02 45.36 4.58
65 66 0.386858 CAGCGCATGATGCATTAGGC 60.387 55.000 17.17 17.17 45.36 3.93
92 93 3.324846 ACAGCCATAAGAAGAGTGACACA 59.675 43.478 8.59 0.00 0.00 3.72
137 138 9.906660 GAGTATAGAGGATGTCTAATTCTGTTG 57.093 37.037 0.00 0.00 41.31 3.33
166 167 1.895798 CAGTAGGTCAGACTCCAAGCA 59.104 52.381 0.00 0.00 0.00 3.91
270 273 7.612677 ACTCGATCTTAAACCACAGTAAGAAT 58.387 34.615 0.00 0.00 39.23 2.40
279 282 3.614616 CAGCTGACTCGATCTTAAACCAC 59.385 47.826 8.42 0.00 0.00 4.16
411 421 7.492994 TGCTAGCACGATACAGTAGAGATATAG 59.507 40.741 14.93 0.00 0.00 1.31
438 448 4.228824 AGAGTACCCGCAAATCCCTAATA 58.771 43.478 0.00 0.00 0.00 0.98
484 494 2.869233 TGTTCAGAACAAGGCAAAGC 57.131 45.000 13.90 0.00 38.72 3.51
509 519 1.202417 TCAGCTATCAAGTGCGGTAGC 60.202 52.381 0.00 0.00 45.41 3.58
525 535 5.407387 CCATATGCCATGCTTATTTTTCAGC 59.593 40.000 0.00 0.00 36.49 4.26
538 548 1.890489 CATGTGGGTCCATATGCCATG 59.110 52.381 12.58 8.07 38.37 3.66
568 578 1.560505 CCATAAAAGGCAAGCCACCT 58.439 50.000 14.40 0.00 40.02 4.00
598 608 2.508716 ACCACTCTCCATGATCAATGCT 59.491 45.455 0.00 0.00 34.67 3.79
631 641 6.500751 GGATCAGGACAAAGAATATAGGGGTA 59.499 42.308 0.00 0.00 0.00 3.69
632 642 5.310857 GGATCAGGACAAAGAATATAGGGGT 59.689 44.000 0.00 0.00 0.00 4.95
636 646 9.650539 CATACTGGATCAGGACAAAGAATATAG 57.349 37.037 0.00 0.00 35.51 1.31
691 701 8.854614 AGCAAGTCAAATATTAGAAGTCAACT 57.145 30.769 0.00 0.00 0.00 3.16
730 740 2.489329 ACAATGCTGAAGAAATGGGTCG 59.511 45.455 0.00 0.00 0.00 4.79
733 743 2.028839 TGCACAATGCTGAAGAAATGGG 60.029 45.455 2.02 0.00 45.31 4.00
829 842 9.801714 GAAGCAAATACAAAATTTCATTCACAG 57.198 29.630 0.00 0.00 0.00 3.66
907 921 5.868257 TGCATTCAAACGTATGAGCTAAAG 58.132 37.500 0.19 0.00 0.00 1.85
954 969 1.065126 AGTAAGGGTTCTGATGCCTGC 60.065 52.381 0.00 0.00 0.00 4.85
1074 1089 2.143925 GCTTCGTTGGGGTATATGAGC 58.856 52.381 0.00 0.00 0.00 4.26
1241 1626 6.864685 TCCAAATACACTAAACTCACTGTACG 59.135 38.462 0.00 0.00 0.00 3.67
1261 1646 5.382664 ACAAAGAGGGTTCTACTTCCAAA 57.617 39.130 0.00 0.00 31.96 3.28
1272 1657 5.256806 AGCAGGTTATAACAAAGAGGGTT 57.743 39.130 17.16 0.00 0.00 4.11
1451 1839 2.159352 ACAACGGTTACAAACAACAGGC 60.159 45.455 0.00 0.00 0.00 4.85
1597 1992 1.134848 TGCCCTGCAAAGACACAAAAC 60.135 47.619 0.00 0.00 34.76 2.43
1834 2254 2.304180 ACTGCTTGACCTTGAGTAGCAT 59.696 45.455 0.00 0.00 40.66 3.79
1872 2292 3.288484 CTGGTACTGCTCGGCTGA 58.712 61.111 9.15 0.00 0.00 4.26
2076 2496 0.038166 ACTATGTGTTGGGGCTGTGG 59.962 55.000 0.00 0.00 0.00 4.17
2093 2513 1.151450 CTGGGACTGGTTTGGCACT 59.849 57.895 0.00 0.00 0.00 4.40
2238 2674 3.523547 GCATTGCAAATGGCTGATTACA 58.476 40.909 1.71 0.00 45.15 2.41
2334 2771 2.713927 ATTTGCGGTTGTTGCTGGGC 62.714 55.000 0.00 0.00 0.00 5.36
2380 2820 1.941294 GGTGCTGCATCTGAGATTGAG 59.059 52.381 5.27 0.00 0.00 3.02
2416 2856 0.958382 TTGTGGGTACGATTGCTGCC 60.958 55.000 0.00 0.00 0.00 4.85
2494 2934 2.602257 TGATTGATGACCTGCTACCG 57.398 50.000 0.00 0.00 0.00 4.02
2811 3259 5.126061 GCATTCCTTGTTGGTATGATTGACT 59.874 40.000 5.66 0.00 43.66 3.41
2855 3303 1.004745 GGCTGGAAAGGTTGAGGATGA 59.995 52.381 0.00 0.00 0.00 2.92
2998 3456 0.453390 GCCTACTTCAGCATTGCCAC 59.547 55.000 4.70 0.00 0.00 5.01
3017 3475 5.056480 TCACTGCCTCCATTTGTATTATCG 58.944 41.667 0.00 0.00 0.00 2.92
3064 3522 6.098695 CCCATTCACATTTTTATCACCCAGAT 59.901 38.462 0.00 0.00 40.86 2.90
3196 3654 4.154918 CAGACTGTGAATTACTTTCCTGGC 59.845 45.833 0.00 0.00 33.04 4.85
3335 3793 2.481441 AGCATGGTATCAGGTCCAGAA 58.519 47.619 0.00 0.00 37.14 3.02
3403 3864 3.525199 ACTAGGTGGCCTCATTTGATTCT 59.475 43.478 3.32 0.00 34.61 2.40
3437 3898 1.628846 ACTGTAGGCCGGACATTTTCT 59.371 47.619 11.69 0.00 0.00 2.52
3507 3968 1.439644 GCGGAAGGTTTGGTGCAAA 59.560 52.632 0.00 0.00 0.00 3.68
3541 4010 3.324556 TCGAATCATGCCATCATCAGGTA 59.675 43.478 0.00 0.00 0.00 3.08
3693 4165 6.694877 AGAAAACTCAAGTGTCCCTAAAAC 57.305 37.500 0.00 0.00 0.00 2.43
3772 4250 1.945354 TTCCTAGTTGCTCTCCGCCG 61.945 60.000 0.00 0.00 38.05 6.46
3784 4262 3.309193 GGAAAGCCCTGGAATTTCCTAGT 60.309 47.826 24.13 0.00 45.57 2.57
3808 4286 4.994852 CGTGAAGTATTGAACCCTTCTTCA 59.005 41.667 0.00 0.00 38.84 3.02
3824 4302 2.158667 ACCTGAAATGTTCCCGTGAAGT 60.159 45.455 0.00 0.00 0.00 3.01
3991 4470 0.850883 TTGGGAATGGAGGCCTTCCT 60.851 55.000 18.69 1.71 46.92 3.36
4051 4530 1.923356 TTGAATGGGGCTTCCTTGAC 58.077 50.000 0.00 0.00 36.20 3.18
4163 4642 6.819284 AGTTTCAAATCAAGCCTTGAATCAA 58.181 32.000 11.81 0.00 43.95 2.57
4193 4672 2.957402 ACCCATGAAGACTTGCTGAA 57.043 45.000 0.00 0.00 0.00 3.02
4241 4726 7.011669 CAGAGCCATTGAAAAATTGTGAAAAGT 59.988 33.333 0.00 0.00 0.00 2.66
4265 4750 6.222389 TGAAAACCATTTGAAGCCATTACAG 58.778 36.000 0.00 0.00 0.00 2.74
4266 4751 6.166984 TGAAAACCATTTGAAGCCATTACA 57.833 33.333 0.00 0.00 0.00 2.41
4267 4752 5.639082 CCTGAAAACCATTTGAAGCCATTAC 59.361 40.000 0.00 0.00 0.00 1.89
4268 4753 5.306678 ACCTGAAAACCATTTGAAGCCATTA 59.693 36.000 0.00 0.00 0.00 1.90
4269 4754 4.102996 ACCTGAAAACCATTTGAAGCCATT 59.897 37.500 0.00 0.00 0.00 3.16
4270 4755 3.647590 ACCTGAAAACCATTTGAAGCCAT 59.352 39.130 0.00 0.00 0.00 4.40
4271 4756 3.037549 ACCTGAAAACCATTTGAAGCCA 58.962 40.909 0.00 0.00 0.00 4.75
4272 4757 3.751479 ACCTGAAAACCATTTGAAGCC 57.249 42.857 0.00 0.00 0.00 4.35
4322 4807 0.455005 GGTCCTTACGAAGACCTCCG 59.545 60.000 1.93 0.00 35.02 4.63
4521 5006 7.999679 TCAAAATTTGGATCATCTGGATGTAC 58.000 34.615 5.83 6.04 39.72 2.90
4647 5132 9.159364 GCATATAGAAACTCATAATGCATCAGA 57.841 33.333 0.00 0.00 33.25 3.27
4706 5193 4.203226 TGGACAATACAACAGCAGTTCAA 58.797 39.130 0.00 0.00 35.28 2.69
4753 5243 0.623723 ATATCCGGCACCAACCAACT 59.376 50.000 0.00 0.00 0.00 3.16
5125 5616 4.796369 ACTGAACTACTGAACTAAGCGTC 58.204 43.478 0.00 0.00 0.00 5.19
5131 5622 7.286215 AGCAACTAACTGAACTACTGAACTA 57.714 36.000 0.00 0.00 0.00 2.24
5392 5896 3.889134 CTGGAAGGCTGCACGCTCA 62.889 63.158 0.50 0.00 39.13 4.26
5570 6074 5.046014 GGGATGACTTCACATCTATGGCTAT 60.046 44.000 0.00 0.00 44.02 2.97
5593 6098 6.288294 TCAAAATACGAGGGATTCATGTAGG 58.712 40.000 0.00 0.00 0.00 3.18
5604 6112 6.039270 TGCAATATCCTTTCAAAATACGAGGG 59.961 38.462 0.00 0.00 0.00 4.30
5630 6138 4.584327 AAATACAAGGCCAACAGTGTTC 57.416 40.909 5.01 0.00 0.00 3.18
5661 6169 1.623811 ACATGGAAGTCAAGTACGCCT 59.376 47.619 0.00 0.00 0.00 5.52
5699 6207 4.755123 CCCAGTAAGAACGACAAAACTCAT 59.245 41.667 0.00 0.00 0.00 2.90
5722 6230 7.492352 AACAATTCTACGTGATATTTAGGCC 57.508 36.000 0.00 0.00 0.00 5.19
5824 6334 5.882040 TGGTGACAATTTTACATACCAGGA 58.118 37.500 0.00 0.00 37.44 3.86
5825 6335 6.194796 CTGGTGACAATTTTACATACCAGG 57.805 41.667 11.60 0.00 46.09 4.45
5827 6337 7.429633 CAAACTGGTGACAATTTTACATACCA 58.570 34.615 0.00 0.00 36.10 3.25
5828 6338 6.364976 GCAAACTGGTGACAATTTTACATACC 59.635 38.462 0.00 0.00 36.10 2.73
5829 6339 7.145323 AGCAAACTGGTGACAATTTTACATAC 58.855 34.615 0.00 0.00 36.10 2.39
5842 6357 8.177119 AGAATTTAACATAAGCAAACTGGTGA 57.823 30.769 0.00 0.00 0.00 4.02
5875 6390 6.378280 GGTTCATTTCAATAGAAGGTGATGGT 59.622 38.462 0.00 0.00 34.71 3.55
5934 6449 3.494251 GCCTTCAAATGCGTTTTCACAAT 59.506 39.130 0.00 0.00 0.00 2.71
5943 6458 2.639327 GCCTGGCCTTCAAATGCGT 61.639 57.895 7.66 0.00 0.00 5.24
5951 6466 0.328258 TTTCTACCAGCCTGGCCTTC 59.672 55.000 16.57 0.00 42.67 3.46
5998 6513 4.178545 TCTACTAAACAACGCCCTACAC 57.821 45.455 0.00 0.00 0.00 2.90
6006 6521 8.598075 GGGTACACATATTTCTACTAAACAACG 58.402 37.037 0.00 0.00 0.00 4.10
6025 6540 1.909781 TGGTCGACTGGGGGTACAC 60.910 63.158 16.46 0.00 0.00 2.90
6030 6545 1.553690 AATCTGTGGTCGACTGGGGG 61.554 60.000 16.46 2.90 0.00 5.40


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

AutoCloner maintained by Alex Coulton.