Multiple sequence alignment - TraesCS5A01G442400

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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 TraesCS5A01G442400 chr5A 100.000 4321 0 0 1 4321 622784336 622780016 0.000000e+00 7980
1 TraesCS5A01G442400 chr5A 82.235 850 144 5 1 847 698224557 698225402 0.000000e+00 726
2 TraesCS5A01G442400 chr5D 91.125 2648 149 26 865 3502 498557178 498554607 0.000000e+00 3509
3 TraesCS5A01G442400 chr5D 83.540 322 35 11 4001 4319 498500460 498500154 7.070000e-73 285
4 TraesCS5A01G442400 chr5D 95.270 148 7 0 4172 4319 498551145 498550998 7.220000e-58 235
5 TraesCS5A01G442400 chr5B 90.859 2516 162 42 1840 4319 617834003 617831520 0.000000e+00 3310
6 TraesCS5A01G442400 chr5B 90.172 641 23 6 898 1501 617836402 617835765 0.000000e+00 798
7 TraesCS5A01G442400 chr5B 96.759 216 7 0 1493 1708 617834318 617834103 1.140000e-95 361
8 TraesCS5A01G442400 chr2B 86.492 2406 264 33 994 3380 762520848 762518485 0.000000e+00 2586
9 TraesCS5A01G442400 chr2B 85.770 1293 164 11 1937 3219 762533313 762532031 0.000000e+00 1351
10 TraesCS5A01G442400 chr2B 88.975 907 78 8 994 1897 762537164 762536277 0.000000e+00 1101
11 TraesCS5A01G442400 chr2B 86.187 847 115 2 3 847 767661793 767662639 0.000000e+00 915
12 TraesCS5A01G442400 chr2B 76.122 1047 224 20 2086 3123 386314596 386313567 3.830000e-145 525
13 TraesCS5A01G442400 chr2D 85.788 1555 187 21 1844 3394 621559701 621558177 0.000000e+00 1616
14 TraesCS5A01G442400 chr2D 90.944 784 50 7 994 1777 621560566 621559804 0.000000e+00 1035
15 TraesCS5A01G442400 chr2D 76.431 1048 219 21 2086 3123 318338408 318337379 3.800000e-150 542
16 TraesCS5A01G442400 chr3B 88.298 846 96 3 3 847 787824057 787823214 0.000000e+00 1011
17 TraesCS5A01G442400 chr7A 83.746 849 130 7 3 847 170588570 170587726 0.000000e+00 797
18 TraesCS5A01G442400 chr1B 83.529 850 132 7 3 847 119130030 119129184 0.000000e+00 787
19 TraesCS5A01G442400 chr1B 80.964 851 150 9 1 847 558926609 558927451 0.000000e+00 664
20 TraesCS5A01G442400 chr7B 83.452 846 126 13 8 846 81771287 81772125 0.000000e+00 774
21 TraesCS5A01G442400 chr3A 82.243 856 147 5 1 852 514044238 514045092 0.000000e+00 734
22 TraesCS5A01G442400 chr2A 81.904 851 145 7 1 847 764904475 764903630 0.000000e+00 710
23 TraesCS5A01G442400 chr2A 76.657 1041 215 21 2086 3116 413324037 413325059 6.320000e-153 551


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 TraesCS5A01G442400 chr5A 622780016 622784336 4320 True 7980.000000 7980 100.000000 1 4321 1 chr5A.!!$R1 4320
1 TraesCS5A01G442400 chr5A 698224557 698225402 845 False 726.000000 726 82.235000 1 847 1 chr5A.!!$F1 846
2 TraesCS5A01G442400 chr5D 498550998 498557178 6180 True 1872.000000 3509 93.197500 865 4319 2 chr5D.!!$R2 3454
3 TraesCS5A01G442400 chr5B 617831520 617836402 4882 True 1489.666667 3310 92.596667 898 4319 3 chr5B.!!$R1 3421
4 TraesCS5A01G442400 chr2B 762518485 762520848 2363 True 2586.000000 2586 86.492000 994 3380 1 chr2B.!!$R2 2386
5 TraesCS5A01G442400 chr2B 762532031 762537164 5133 True 1226.000000 1351 87.372500 994 3219 2 chr2B.!!$R3 2225
6 TraesCS5A01G442400 chr2B 767661793 767662639 846 False 915.000000 915 86.187000 3 847 1 chr2B.!!$F1 844
7 TraesCS5A01G442400 chr2B 386313567 386314596 1029 True 525.000000 525 76.122000 2086 3123 1 chr2B.!!$R1 1037
8 TraesCS5A01G442400 chr2D 621558177 621560566 2389 True 1325.500000 1616 88.366000 994 3394 2 chr2D.!!$R2 2400
9 TraesCS5A01G442400 chr2D 318337379 318338408 1029 True 542.000000 542 76.431000 2086 3123 1 chr2D.!!$R1 1037
10 TraesCS5A01G442400 chr3B 787823214 787824057 843 True 1011.000000 1011 88.298000 3 847 1 chr3B.!!$R1 844
11 TraesCS5A01G442400 chr7A 170587726 170588570 844 True 797.000000 797 83.746000 3 847 1 chr7A.!!$R1 844
12 TraesCS5A01G442400 chr1B 119129184 119130030 846 True 787.000000 787 83.529000 3 847 1 chr1B.!!$R1 844
13 TraesCS5A01G442400 chr1B 558926609 558927451 842 False 664.000000 664 80.964000 1 847 1 chr1B.!!$F1 846
14 TraesCS5A01G442400 chr7B 81771287 81772125 838 False 774.000000 774 83.452000 8 846 1 chr7B.!!$F1 838
15 TraesCS5A01G442400 chr3A 514044238 514045092 854 False 734.000000 734 82.243000 1 852 1 chr3A.!!$F1 851
16 TraesCS5A01G442400 chr2A 764903630 764904475 845 True 710.000000 710 81.904000 1 847 1 chr2A.!!$R1 846
17 TraesCS5A01G442400 chr2A 413324037 413325059 1022 False 551.000000 551 76.657000 2086 3116 1 chr2A.!!$F1 1030

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
333 334 0.394192 CAGCAACCAGTGAGACCTCA 59.606 55.000 0.00 0.0 37.24 3.86 F
1150 1171 1.773635 CAATGGTCCAACCTCCCCA 59.226 57.895 0.00 0.0 39.58 4.96 F
2738 7230 0.109086 ACACCTCGAGCAATGAGACG 60.109 55.000 6.99 0.0 35.43 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 6738 0.462225 TGCCGGTTTGTCGTTGAGAA 60.462 50.0 1.9 0.0 0.0 2.87 R
2981 7473 0.035458 GCTGAGGGAATATGGGGACG 59.965 60.0 0.0 0.0 0.0 4.79 R
4035 11805 0.102300 GTGGACAGGTTGGTGCAAAC 59.898 55.0 0.0 0.0 40.9 2.93 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
33 34 4.166539 AGGCATGCTCTCCTAGAATGTAT 58.833 43.478 18.92 0.00 42.69 2.29
145 146 3.181451 TGGAGATGCATGACCAACTATCC 60.181 47.826 16.12 3.17 0.00 2.59
257 258 5.104374 CCCAAGGAACGAATCAATTCATTG 58.896 41.667 12.07 12.07 43.04 2.82
302 303 2.541907 ATTGCAGGTGTGGGGAGCT 61.542 57.895 0.00 0.00 0.00 4.09
333 334 0.394192 CAGCAACCAGTGAGACCTCA 59.606 55.000 0.00 0.00 37.24 3.86
352 353 2.044806 ATCACTGGATAGCGCCACCC 62.045 60.000 2.29 2.70 33.52 4.61
481 485 1.886655 GCTCTTGTTGTCGGGGGAATT 60.887 52.381 0.00 0.00 0.00 2.17
487 491 2.375845 TGTTGTCGGGGGAATTAAGGAA 59.624 45.455 0.00 0.00 0.00 3.36
550 554 4.633126 GCACTTGCTGAAGATCTCAACATA 59.367 41.667 0.00 0.00 38.21 2.29
649 653 9.585099 GGAGCTATTCTACATGAAATCATAGAG 57.415 37.037 0.00 0.00 38.29 2.43
663 667 2.423892 TCATAGAGCACAGTTCCTCGTC 59.576 50.000 0.00 0.00 33.39 4.20
675 679 4.872691 CAGTTCCTCGTCTATTTCTTGCAT 59.127 41.667 0.00 0.00 0.00 3.96
871 877 2.040813 AGGGTGAATGTGTGATGAAGCT 59.959 45.455 0.00 0.00 0.00 3.74
878 884 3.988379 TGTGTGATGAAGCTTGAAACC 57.012 42.857 2.10 0.00 0.00 3.27
903 909 4.704965 AGGTTAAGGTGTCAACTGAACTC 58.295 43.478 16.35 7.95 0.00 3.01
936 942 6.343155 GCGCGATCGTGAAATATTTGTTTAAG 60.343 38.462 31.43 0.00 38.14 1.85
1150 1171 1.773635 CAATGGTCCAACCTCCCCA 59.226 57.895 0.00 0.00 39.58 4.96
1209 1230 4.816984 ACCTCCGGCGACCTCGAT 62.817 66.667 9.30 0.00 43.02 3.59
1480 1523 2.437895 ACGAGGCGGACGAGATGA 60.438 61.111 8.47 0.00 34.70 2.92
1565 3069 2.766229 GGAGGAGTGGGAGGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
1732 3236 2.289694 ACATGGTGAACTGTGCCTACTC 60.290 50.000 0.00 0.00 0.00 2.59
1757 3264 8.575589 TCATACTAATTTTGTGCTGACATTGTT 58.424 29.630 0.00 0.00 30.13 2.83
1764 3271 9.630098 AATTTTGTGCTGACATTGTTATCTAAG 57.370 29.630 0.00 0.00 30.13 2.18
1777 3284 9.708222 CATTGTTATCTAAGAGTTTGATTTCCG 57.292 33.333 0.00 0.00 0.00 4.30
1786 3293 6.743575 AGAGTTTGATTTCCGGATAAACAG 57.256 37.500 23.88 0.00 34.58 3.16
1787 3294 5.648092 AGAGTTTGATTTCCGGATAAACAGG 59.352 40.000 23.88 0.00 34.58 4.00
1798 3345 3.620488 GGATAAACAGGGCTCATTGTCA 58.380 45.455 0.00 0.00 0.00 3.58
1806 3353 2.309755 AGGGCTCATTGTCAGAAATCCA 59.690 45.455 0.00 0.00 0.00 3.41
1811 3358 5.415701 GGCTCATTGTCAGAAATCCAAGTTA 59.584 40.000 0.00 0.00 0.00 2.24
1818 3365 6.855836 TGTCAGAAATCCAAGTTAATGATGC 58.144 36.000 0.00 0.00 0.00 3.91
1826 3373 5.101628 TCCAAGTTAATGATGCGCAAAATC 58.898 37.500 17.11 8.66 0.00 2.17
1838 3385 5.686159 TGCGCAAAATCATTTTCCATTTT 57.314 30.435 8.16 0.00 33.37 1.82
1849 3396 8.786710 ATCATTTTCCATTTTAGATGGGATCA 57.213 30.769 1.81 0.00 39.60 2.92
1863 3410 4.371624 TGGGATCATCTCAAAGTTGTGT 57.628 40.909 0.00 0.00 0.00 3.72
1867 3414 6.430925 TGGGATCATCTCAAAGTTGTGTAAAG 59.569 38.462 0.00 0.00 0.00 1.85
1874 3421 9.651718 CATCTCAAAGTTGTGTAAAGTTTAGTC 57.348 33.333 0.00 0.00 0.00 2.59
1921 6402 9.098355 TGATATACAGTCTAGTTTTTGTGATGC 57.902 33.333 0.00 0.00 0.00 3.91
1922 6403 9.098355 GATATACAGTCTAGTTTTTGTGATGCA 57.902 33.333 0.00 0.00 0.00 3.96
1923 6404 7.744087 ATACAGTCTAGTTTTTGTGATGCAA 57.256 32.000 0.00 0.00 34.87 4.08
1924 6405 5.821204 ACAGTCTAGTTTTTGTGATGCAAC 58.179 37.500 0.00 0.00 36.72 4.17
1925 6406 5.215160 CAGTCTAGTTTTTGTGATGCAACC 58.785 41.667 0.00 0.00 36.72 3.77
1926 6407 4.887071 AGTCTAGTTTTTGTGATGCAACCA 59.113 37.500 0.00 0.00 36.72 3.67
1927 6408 5.536161 AGTCTAGTTTTTGTGATGCAACCAT 59.464 36.000 0.00 0.00 36.72 3.55
1929 6410 3.731089 AGTTTTTGTGATGCAACCATGG 58.269 40.909 11.19 11.19 36.72 3.66
1934 6415 4.987408 TTGTGATGCAACCATGGAATAG 57.013 40.909 21.47 5.93 31.07 1.73
1939 6420 6.656270 TGTGATGCAACCATGGAATAGATATC 59.344 38.462 21.47 12.31 0.00 1.63
1969 6456 3.068024 GCTCATGGTTTCAAGTTCCAACA 59.932 43.478 0.00 0.00 34.80 3.33
1970 6457 4.441356 GCTCATGGTTTCAAGTTCCAACAA 60.441 41.667 0.00 0.00 34.80 2.83
1973 6460 4.181309 TGGTTTCAAGTTCCAACAACAC 57.819 40.909 0.00 0.00 0.00 3.32
2008 6495 7.506599 TCCAACATCATCAGCATTTGGTATAAT 59.493 33.333 0.00 0.00 35.87 1.28
2251 6738 0.757188 ATCCTCCGCGATCTCCAAGT 60.757 55.000 8.23 0.00 0.00 3.16
2252 6739 0.970937 TCCTCCGCGATCTCCAAGTT 60.971 55.000 8.23 0.00 0.00 2.66
2279 6766 2.606108 GACAAACCGGCAATCATTTCC 58.394 47.619 0.00 0.00 0.00 3.13
2516 7008 0.623194 TCAGAATGCCCGGGAATTCA 59.377 50.000 42.95 28.03 41.48 2.57
2732 7224 1.202417 CCGATGTACACCTCGAGCAAT 60.202 52.381 18.12 0.00 36.35 3.56
2736 7228 2.167662 TGTACACCTCGAGCAATGAGA 58.832 47.619 6.99 0.00 35.43 3.27
2738 7230 0.109086 ACACCTCGAGCAATGAGACG 60.109 55.000 6.99 0.00 35.43 4.18
2749 7241 0.966920 AATGAGACGAAGGACACGGT 59.033 50.000 0.00 0.00 34.93 4.83
2795 7287 0.846427 TGGAGCCCCTCTTTGTGGAT 60.846 55.000 0.00 0.00 0.00 3.41
2861 7353 1.005215 AGGTTCTGCCCCATGAAGAAG 59.995 52.381 0.00 0.00 38.26 2.85
2981 7473 2.930562 AGGCCTGACCACCCTGAC 60.931 66.667 3.11 0.00 43.14 3.51
3110 7602 2.594131 CATGATGGGCAAGTCCATGAT 58.406 47.619 11.53 5.26 46.67 2.45
3204 7696 3.386402 GGAGAAGATGAGGTACTTGGGAG 59.614 52.174 0.00 0.00 41.55 4.30
3279 7771 4.315803 TGTTAGAAAGAAGAAGAAGGCGG 58.684 43.478 0.00 0.00 0.00 6.13
3280 7772 4.039973 TGTTAGAAAGAAGAAGAAGGCGGA 59.960 41.667 0.00 0.00 0.00 5.54
3281 7773 3.326836 AGAAAGAAGAAGAAGGCGGAG 57.673 47.619 0.00 0.00 0.00 4.63
3302 7794 1.591703 TGCAGGATGGAGTCGTGTC 59.408 57.895 0.00 0.00 43.07 3.67
3320 7812 3.445805 GTGTCCAAGAAGAGGAGTCCTAG 59.554 52.174 12.99 0.00 35.42 3.02
3330 7822 5.523883 AGAGGAGTCCTAGTTACTTCACT 57.476 43.478 12.99 0.00 31.76 3.41
3333 7825 5.258051 AGGAGTCCTAGTTACTTCACTCTG 58.742 45.833 10.94 0.00 32.49 3.35
3337 7829 5.047660 AGTCCTAGTTACTTCACTCTGCTTG 60.048 44.000 0.00 0.00 0.00 4.01
3369 7865 6.127196 TGTGTTGGTAATTGCTCTTCCTTTTT 60.127 34.615 0.00 0.00 0.00 1.94
3421 7917 3.566742 TGTCTAGACACGACAGCAACTAA 59.433 43.478 21.74 0.00 36.54 2.24
3423 7919 5.162075 GTCTAGACACGACAGCAACTAAAT 58.838 41.667 18.20 0.00 0.00 1.40
3424 7920 6.072342 TGTCTAGACACGACAGCAACTAAATA 60.072 38.462 21.74 0.00 36.54 1.40
3425 7921 6.250951 GTCTAGACACGACAGCAACTAAATAC 59.749 42.308 18.20 0.00 0.00 1.89
3426 7922 4.878439 AGACACGACAGCAACTAAATACA 58.122 39.130 0.00 0.00 0.00 2.29
3427 7923 4.923871 AGACACGACAGCAACTAAATACAG 59.076 41.667 0.00 0.00 0.00 2.74
3433 7929 6.365247 ACGACAGCAACTAAATACAGTACTTG 59.635 38.462 0.00 0.00 0.00 3.16
3448 7944 5.305644 ACAGTACTTGGTCTTCAGATTCACT 59.694 40.000 0.00 0.00 0.00 3.41
3450 7946 4.013267 ACTTGGTCTTCAGATTCACTGG 57.987 45.455 0.00 0.00 45.76 4.00
3535 11273 1.480789 TCCCAGCGCTTACTGATGTA 58.519 50.000 7.50 0.00 40.25 2.29
3536 11274 1.136305 TCCCAGCGCTTACTGATGTAC 59.864 52.381 7.50 0.00 40.25 2.90
3537 11275 1.134818 CCCAGCGCTTACTGATGTACA 60.135 52.381 7.50 0.00 40.25 2.90
3570 11314 6.778834 TGGTTGATGTATTGCTGATGAATT 57.221 33.333 0.00 0.00 0.00 2.17
3571 11315 6.798482 TGGTTGATGTATTGCTGATGAATTC 58.202 36.000 0.00 0.00 0.00 2.17
3621 11365 2.317530 TGTGGTGTGTTGATTGTCGA 57.682 45.000 0.00 0.00 0.00 4.20
3665 11409 5.715429 CTCATGTGTCTTGAGCTGAATAC 57.285 43.478 0.00 0.00 34.68 1.89
3681 11425 4.585879 TGAATACAAGCCAGTAGGTTTCC 58.414 43.478 0.00 0.00 36.02 3.13
3682 11426 3.646736 ATACAAGCCAGTAGGTTTCCC 57.353 47.619 0.00 0.00 36.02 3.97
3833 11580 4.952262 TGGAGATTTTCTTCGCATTCAG 57.048 40.909 0.00 0.00 0.00 3.02
3840 11587 7.824672 AGATTTTCTTCGCATTCAGAGAAATT 58.175 30.769 0.00 0.00 35.57 1.82
3852 11599 8.814235 GCATTCAGAGAAATTTATGACAATTGG 58.186 33.333 10.83 0.00 0.00 3.16
3953 11708 0.034059 CAGGAGTCGACAAAGTGGCT 59.966 55.000 19.50 0.00 0.00 4.75
3955 11710 2.093973 CAGGAGTCGACAAAGTGGCTAT 60.094 50.000 19.50 0.00 0.00 2.97
3967 11722 6.289064 ACAAAGTGGCTATAACTGCTATACC 58.711 40.000 0.00 0.00 0.00 2.73
3968 11723 6.126883 ACAAAGTGGCTATAACTGCTATACCA 60.127 38.462 0.00 0.00 0.00 3.25
3981 11736 2.868839 GCTATACCACACACAACACGGT 60.869 50.000 0.00 0.00 0.00 4.83
3999 11754 5.300792 ACACGGTGAACAATTTAACCAGATT 59.699 36.000 16.29 0.00 32.69 2.40
4000 11755 5.629020 CACGGTGAACAATTTAACCAGATTG 59.371 40.000 0.74 0.00 38.79 2.67
4017 11787 5.647658 CCAGATTGTAGTATTCTGTGGCAAA 59.352 40.000 0.00 0.00 35.83 3.68
4035 11805 3.738899 GCAAATGTATGCATCAGTTGGGG 60.739 47.826 25.85 12.26 45.70 4.96
4066 11837 0.304705 CTGTCCACTTGTGTTGTCGC 59.695 55.000 0.00 0.00 0.00 5.19
4068 11839 1.092921 GTCCACTTGTGTTGTCGCCA 61.093 55.000 0.00 0.00 0.00 5.69
4071 11842 0.732571 CACTTGTGTTGTCGCCAGTT 59.267 50.000 0.00 0.00 29.53 3.16
4086 11857 1.265905 CCAGTTGCTTGTTTCCGGTAC 59.734 52.381 0.00 1.45 0.00 3.34
4094 11865 1.447314 GTTTCCGGTACCTCTGCCG 60.447 63.158 10.90 0.00 46.80 5.69
4163 11934 0.893727 TGCTCTGGTACTCAGACGCA 60.894 55.000 20.72 20.72 46.71 5.24
4196 11967 2.674462 GCCGTTCTCCTCAAAGTACTCC 60.674 54.545 0.00 0.00 0.00 3.85
4319 12090 1.671742 GCTCAAGAACCCGACCTGA 59.328 57.895 0.00 0.00 0.00 3.86
4320 12091 0.390472 GCTCAAGAACCCGACCTGAG 60.390 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.752747 CGCCCATATGCATCTTGACATAA 59.247 43.478 0.19 0.00 32.77 1.90
145 146 1.533625 TCCGGACAAAATGCTCTTGG 58.466 50.000 0.00 0.00 0.00 3.61
302 303 1.036707 GGTTGCTGTTTTACCTGGCA 58.963 50.000 0.00 0.00 0.00 4.92
333 334 1.447643 GGTGGCGCTATCCAGTGAT 59.552 57.895 7.64 0.00 36.67 3.06
352 353 3.242091 CGTTGATCTTAGCACATCGGTTG 60.242 47.826 0.00 0.00 0.00 3.77
470 474 1.282738 TGGTTCCTTAATTCCCCCGAC 59.717 52.381 0.00 0.00 0.00 4.79
473 477 1.006639 TGCTGGTTCCTTAATTCCCCC 59.993 52.381 0.00 0.00 0.00 5.40
481 485 0.669318 CGAGCGTTGCTGGTTCCTTA 60.669 55.000 0.00 0.00 39.88 2.69
487 491 3.044305 GCTTCGAGCGTTGCTGGT 61.044 61.111 0.00 0.00 39.88 4.00
550 554 2.325082 GGCAACGTGAATCCTGCGT 61.325 57.895 1.88 0.00 40.81 5.24
649 653 3.851098 AGAAATAGACGAGGAACTGTGC 58.149 45.455 0.00 0.00 41.55 4.57
675 679 4.584325 AGCTCCTAAACTCATGCACAAAAA 59.416 37.500 0.00 0.00 0.00 1.94
767 771 2.839228 AGAGAGATTACCAGGGTTGCT 58.161 47.619 0.00 0.00 0.00 3.91
847 853 3.627395 TCATCACACATTCACCCTACC 57.373 47.619 0.00 0.00 0.00 3.18
848 854 3.375299 GCTTCATCACACATTCACCCTAC 59.625 47.826 0.00 0.00 0.00 3.18
849 855 3.264193 AGCTTCATCACACATTCACCCTA 59.736 43.478 0.00 0.00 0.00 3.53
850 856 2.040813 AGCTTCATCACACATTCACCCT 59.959 45.455 0.00 0.00 0.00 4.34
851 857 2.440409 AGCTTCATCACACATTCACCC 58.560 47.619 0.00 0.00 0.00 4.61
852 858 3.503363 TCAAGCTTCATCACACATTCACC 59.497 43.478 0.00 0.00 0.00 4.02
854 860 5.507817 GGTTTCAAGCTTCATCACACATTCA 60.508 40.000 0.00 0.00 0.00 2.57
855 861 4.919754 GGTTTCAAGCTTCATCACACATTC 59.080 41.667 0.00 0.00 0.00 2.67
856 862 4.557296 CGGTTTCAAGCTTCATCACACATT 60.557 41.667 0.00 0.00 0.00 2.71
857 863 3.058016 CGGTTTCAAGCTTCATCACACAT 60.058 43.478 0.00 0.00 0.00 3.21
858 864 2.290367 CGGTTTCAAGCTTCATCACACA 59.710 45.455 0.00 0.00 0.00 3.72
859 865 2.350772 CCGGTTTCAAGCTTCATCACAC 60.351 50.000 0.00 0.00 0.00 3.82
860 866 1.879380 CCGGTTTCAAGCTTCATCACA 59.121 47.619 0.00 0.00 0.00 3.58
861 867 2.151202 TCCGGTTTCAAGCTTCATCAC 58.849 47.619 0.00 0.00 0.00 3.06
862 868 2.426522 CTCCGGTTTCAAGCTTCATCA 58.573 47.619 0.00 0.00 0.00 3.07
863 869 1.740025 CCTCCGGTTTCAAGCTTCATC 59.260 52.381 0.00 0.00 0.00 2.92
871 877 2.173143 ACACCTTAACCTCCGGTTTCAA 59.827 45.455 0.00 0.00 44.33 2.69
878 884 2.036733 TCAGTTGACACCTTAACCTCCG 59.963 50.000 0.00 0.00 0.00 4.63
887 893 4.780815 TCATTTGAGTTCAGTTGACACCT 58.219 39.130 0.00 0.00 0.00 4.00
903 909 0.369931 TCACGATCGCGCTTCATTTG 59.630 50.000 16.60 2.39 42.48 2.32
936 942 2.588314 CGGGCAGCTCAGATCAGC 60.588 66.667 0.00 0.00 39.99 4.26
949 955 1.009829 CTTAATGACTGTGCTCGGGC 58.990 55.000 0.00 0.00 39.26 6.13
952 958 4.627467 AGCTTAACTTAATGACTGTGCTCG 59.373 41.667 0.00 0.00 0.00 5.03
1059 1080 4.699522 GTCGTGGTGGAGGTGGCC 62.700 72.222 0.00 0.00 0.00 5.36
1060 1081 4.699522 GGTCGTGGTGGAGGTGGC 62.700 72.222 0.00 0.00 0.00 5.01
1209 1230 0.686769 GGAGGAGGAAGCCGAGGTAA 60.687 60.000 0.00 0.00 0.00 2.85
1480 1523 2.591715 GCACACGAACAGCACCCT 60.592 61.111 0.00 0.00 0.00 4.34
1690 3194 3.376546 GTCACTACCTTGTAGGAGTACCG 59.623 52.174 6.25 0.00 37.67 4.02
1732 3236 8.746922 AACAATGTCAGCACAAAATTAGTATG 57.253 30.769 0.00 0.00 35.64 2.39
1764 3271 5.163652 CCCTGTTTATCCGGAAATCAAACTC 60.164 44.000 23.38 8.97 31.85 3.01
1777 3284 3.620488 TGACAATGAGCCCTGTTTATCC 58.380 45.455 0.00 0.00 0.00 2.59
1786 3293 2.726821 TGGATTTCTGACAATGAGCCC 58.273 47.619 0.00 0.00 0.00 5.19
1787 3294 3.760684 ACTTGGATTTCTGACAATGAGCC 59.239 43.478 0.00 0.00 0.00 4.70
1798 3345 4.398988 TGCGCATCATTAACTTGGATTTCT 59.601 37.500 5.66 0.00 0.00 2.52
1806 3353 7.599630 AAATGATTTTGCGCATCATTAACTT 57.400 28.000 28.53 15.98 46.29 2.66
1818 3365 8.117988 CCATCTAAAATGGAAAATGATTTTGCG 58.882 33.333 15.65 2.74 42.97 4.85
1849 3396 9.614792 AGACTAAACTTTACACAACTTTGAGAT 57.385 29.630 0.00 0.00 0.00 2.75
1867 3414 9.747293 ACTGAAGTTAGTGTTCTAAGACTAAAC 57.253 33.333 12.45 8.32 43.55 2.01
1913 6394 4.598022 TCTATTCCATGGTTGCATCACAA 58.402 39.130 12.58 0.00 35.33 3.33
1916 6397 7.024345 AGATATCTATTCCATGGTTGCATCA 57.976 36.000 12.58 0.00 0.00 3.07
1917 6398 7.934855 AAGATATCTATTCCATGGTTGCATC 57.065 36.000 12.58 6.92 0.00 3.91
1918 6399 7.946219 TGAAAGATATCTATTCCATGGTTGCAT 59.054 33.333 12.58 2.86 0.00 3.96
1919 6400 7.289310 TGAAAGATATCTATTCCATGGTTGCA 58.711 34.615 12.58 0.00 0.00 4.08
1920 6401 7.750229 TGAAAGATATCTATTCCATGGTTGC 57.250 36.000 12.58 0.00 0.00 4.17
1922 6403 9.678260 GCTATGAAAGATATCTATTCCATGGTT 57.322 33.333 12.58 3.29 0.00 3.67
1923 6404 9.055689 AGCTATGAAAGATATCTATTCCATGGT 57.944 33.333 12.58 0.00 0.00 3.55
1924 6405 9.545105 GAGCTATGAAAGATATCTATTCCATGG 57.455 37.037 4.97 4.97 0.00 3.66
1934 6415 8.613060 TGAAACCATGAGCTATGAAAGATATC 57.387 34.615 0.00 0.00 39.21 1.63
1939 6420 6.506500 ACTTGAAACCATGAGCTATGAAAG 57.493 37.500 0.00 0.00 39.21 2.62
1953 6438 4.181309 TGTGTTGTTGGAACTTGAAACC 57.819 40.909 0.00 0.00 0.00 3.27
1969 6456 3.827876 TGATGTTGGATGCTCATTGTGTT 59.172 39.130 0.00 0.00 0.00 3.32
1970 6457 3.423749 TGATGTTGGATGCTCATTGTGT 58.576 40.909 0.00 0.00 0.00 3.72
1973 6460 4.793028 GCTGATGATGTTGGATGCTCATTG 60.793 45.833 0.00 0.00 0.00 2.82
2008 6495 4.633175 TGTGGCGTAGAATGAGTGTTTAA 58.367 39.130 0.00 0.00 0.00 1.52
2012 6499 3.262420 GAATGTGGCGTAGAATGAGTGT 58.738 45.455 0.00 0.00 0.00 3.55
2014 6501 3.262420 GTGAATGTGGCGTAGAATGAGT 58.738 45.455 0.00 0.00 0.00 3.41
2015 6502 2.609459 GGTGAATGTGGCGTAGAATGAG 59.391 50.000 0.00 0.00 0.00 2.90
2024 6511 4.155826 TCAAAAGATTAGGTGAATGTGGCG 59.844 41.667 0.00 0.00 0.00 5.69
2251 6738 0.462225 TGCCGGTTTGTCGTTGAGAA 60.462 50.000 1.90 0.00 0.00 2.87
2252 6739 0.462225 TTGCCGGTTTGTCGTTGAGA 60.462 50.000 1.90 0.00 0.00 3.27
2279 6766 2.528743 GCTGATGTCGCCGATGTGG 61.529 63.158 0.00 0.00 42.50 4.17
2516 7008 2.446036 GTGCCGGTAGGGAGGGAT 60.446 66.667 1.90 0.00 39.06 3.85
2732 7224 0.313043 GAACCGTGTCCTTCGTCTCA 59.687 55.000 0.00 0.00 0.00 3.27
2736 7228 0.249322 CTGTGAACCGTGTCCTTCGT 60.249 55.000 0.00 0.00 0.00 3.85
2738 7230 0.602905 CCCTGTGAACCGTGTCCTTC 60.603 60.000 0.00 0.00 0.00 3.46
2749 7241 1.487976 GGATCATCTGCTCCCTGTGAA 59.512 52.381 0.00 0.00 0.00 3.18
2861 7353 1.993370 GACGTGTTGAGGCACTGATAC 59.007 52.381 0.00 0.00 41.55 2.24
2981 7473 0.035458 GCTGAGGGAATATGGGGACG 59.965 60.000 0.00 0.00 0.00 4.79
3110 7602 2.542205 CGGCGACAGTATTTCGACCATA 60.542 50.000 0.00 0.00 41.79 2.74
3279 7771 0.102120 CGACTCCATCCTGCAGACTC 59.898 60.000 17.39 0.00 0.00 3.36
3280 7772 0.613292 ACGACTCCATCCTGCAGACT 60.613 55.000 17.39 0.00 0.00 3.24
3281 7773 0.459237 CACGACTCCATCCTGCAGAC 60.459 60.000 17.39 0.00 0.00 3.51
3298 7790 2.252714 AGGACTCCTCTTCTTGGACAC 58.747 52.381 0.00 0.00 0.00 3.67
3302 7794 5.265989 AGTAACTAGGACTCCTCTTCTTGG 58.734 45.833 0.00 0.00 34.61 3.61
3308 7800 5.252164 AGAGTGAAGTAACTAGGACTCCTCT 59.748 44.000 0.00 12.90 34.61 3.69
3320 7812 2.410053 CGAGCAAGCAGAGTGAAGTAAC 59.590 50.000 0.00 0.00 0.00 2.50
3330 7822 1.063912 CAACACAAACGAGCAAGCAGA 59.936 47.619 0.00 0.00 0.00 4.26
3333 7825 0.100503 ACCAACACAAACGAGCAAGC 59.899 50.000 0.00 0.00 0.00 4.01
3337 7829 2.724174 GCAATTACCAACACAAACGAGC 59.276 45.455 0.00 0.00 0.00 5.03
3369 7865 7.712204 TTGGTGTCTAGATATGTTACAGTGA 57.288 36.000 0.00 0.00 0.00 3.41
3421 7917 7.819900 GTGAATCTGAAGACCAAGTACTGTATT 59.180 37.037 0.00 0.00 0.00 1.89
3423 7919 6.493802 AGTGAATCTGAAGACCAAGTACTGTA 59.506 38.462 0.00 0.00 0.00 2.74
3424 7920 5.305644 AGTGAATCTGAAGACCAAGTACTGT 59.694 40.000 0.00 0.00 0.00 3.55
3425 7921 5.636965 CAGTGAATCTGAAGACCAAGTACTG 59.363 44.000 0.00 0.00 46.27 2.74
3426 7922 5.279708 CCAGTGAATCTGAAGACCAAGTACT 60.280 44.000 0.00 0.00 46.27 2.73
3427 7923 4.932200 CCAGTGAATCTGAAGACCAAGTAC 59.068 45.833 0.00 0.00 46.27 2.73
3433 7929 2.479566 TGCCAGTGAATCTGAAGACC 57.520 50.000 0.00 0.00 46.27 3.85
3535 11273 6.710597 ATACATCAACCATCGTAGTACTGT 57.289 37.500 5.39 0.00 0.00 3.55
3536 11274 6.074302 GCAATACATCAACCATCGTAGTACTG 60.074 42.308 5.39 0.00 0.00 2.74
3537 11275 5.983720 GCAATACATCAACCATCGTAGTACT 59.016 40.000 0.00 0.00 0.00 2.73
3582 11326 7.866898 CACCACAATGAACAAGATGAACAAATA 59.133 33.333 0.00 0.00 0.00 1.40
3621 11365 4.469227 AGCACTGGACTAGAAGAATCACAT 59.531 41.667 0.00 0.00 0.00 3.21
3681 11425 2.737252 GTGCTTCGACAAGAAAGGTAGG 59.263 50.000 0.00 0.00 38.57 3.18
3682 11426 2.408704 CGTGCTTCGACAAGAAAGGTAG 59.591 50.000 0.00 0.00 42.86 3.18
3740 11484 6.653526 AATGTTCAAATGATTCTCACACCA 57.346 33.333 0.00 0.00 0.00 4.17
3770 11516 7.390440 GGCAGCAGTAATATATTGACATGGTAA 59.610 37.037 8.28 0.00 0.00 2.85
3771 11517 6.878923 GGCAGCAGTAATATATTGACATGGTA 59.121 38.462 8.28 0.00 0.00 3.25
3772 11518 5.707298 GGCAGCAGTAATATATTGACATGGT 59.293 40.000 8.28 4.52 0.00 3.55
3811 11558 5.003160 TCTGAATGCGAAGAAAATCTCCAA 58.997 37.500 0.00 0.00 0.00 3.53
3913 11666 2.423538 GCTCTTGGTGTGAGTTTGTTGT 59.576 45.455 0.00 0.00 34.30 3.32
3953 11708 6.814644 GTGTTGTGTGTGGTATAGCAGTTATA 59.185 38.462 4.51 0.00 0.00 0.98
3955 11710 4.992319 GTGTTGTGTGTGGTATAGCAGTTA 59.008 41.667 4.51 0.00 0.00 2.24
3967 11722 0.799393 TGTTCACCGTGTTGTGTGTG 59.201 50.000 0.00 0.00 37.51 3.82
3968 11723 1.524848 TTGTTCACCGTGTTGTGTGT 58.475 45.000 0.00 0.00 37.51 3.72
3999 11754 6.038161 GCATACATTTGCCACAGAATACTACA 59.962 38.462 0.00 0.00 36.60 2.74
4000 11755 6.038161 TGCATACATTTGCCACAGAATACTAC 59.962 38.462 0.00 0.00 42.06 2.73
4017 11787 3.386932 AACCCCAACTGATGCATACAT 57.613 42.857 0.00 0.00 39.98 2.29
4028 11798 4.796408 TTGGTGCAAACCCCAACT 57.204 50.000 2.51 0.00 35.84 3.16
4035 11805 0.102300 GTGGACAGGTTGGTGCAAAC 59.898 55.000 0.00 0.00 40.90 2.93
4066 11837 1.265905 GTACCGGAAACAAGCAACTGG 59.734 52.381 9.46 0.00 35.21 4.00
4068 11839 1.142262 AGGTACCGGAAACAAGCAACT 59.858 47.619 9.46 0.00 0.00 3.16
4071 11842 1.053424 AGAGGTACCGGAAACAAGCA 58.947 50.000 9.46 0.00 0.00 3.91
4163 11934 0.608582 AGAACGGCGAGTACCTGAGT 60.609 55.000 16.62 0.00 0.00 3.41
4196 11967 2.095567 CAGATTCCTGAAACGCTTGGTG 60.096 50.000 0.00 0.00 43.02 4.17


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

AutoCloner maintained by Alex Coulton.