Multiple sequence alignment - TraesCS1B01G247100

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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 TraesCS1B01G247100 chr1B 100.000 7208 0 0 1 7208 437597701 437604908 0.000000e+00 13311.0
1 TraesCS1B01G247100 chr1B 89.130 92 10 0 2006 2097 56061804 56061713 1.640000e-21 115.0
2 TraesCS1B01G247100 chr1D 95.964 7235 162 44 45 7208 325482566 325489741 0.000000e+00 11623.0
3 TraesCS1B01G247100 chr1D 91.558 154 13 0 3319 3472 111003374 111003527 5.660000e-51 213.0
4 TraesCS1B01G247100 chr1D 90.244 82 8 0 2006 2087 147896238 147896319 2.750000e-19 108.0
5 TraesCS1B01G247100 chr1A 96.014 3512 78 13 3359 6826 419032378 419028885 0.000000e+00 5653.0
6 TraesCS1B01G247100 chr1A 96.017 3289 84 18 114 3375 419035811 419032543 0.000000e+00 5304.0
7 TraesCS1B01G247100 chr1A 93.247 385 23 3 6825 7208 419028797 419028415 1.360000e-156 564.0
8 TraesCS1B01G247100 chr1A 91.765 85 7 0 2006 2090 201745718 201745634 1.270000e-22 119.0
9 TraesCS1B01G247100 chr1A 91.250 80 3 2 1 76 419035890 419035811 9.890000e-19 106.0
10 TraesCS1B01G247100 chr1A 100.000 30 0 0 3664 3693 419032040 419032011 1.000000e-03 56.5
11 TraesCS1B01G247100 chr3B 87.179 429 50 4 4076 4502 750136816 750137241 3.910000e-132 483.0
12 TraesCS1B01G247100 chr3B 82.895 152 26 0 1103 1254 750136030 750136181 3.510000e-28 137.0
13 TraesCS1B01G247100 chr3D 87.179 429 48 5 4076 4502 562698218 562698641 1.410000e-131 481.0
14 TraesCS1B01G247100 chr3D 88.182 110 13 0 1124 1233 562697554 562697663 1.630000e-26 132.0
15 TraesCS1B01G247100 chr3A 88.206 407 43 4 4076 4480 697738247 697738650 1.410000e-131 481.0
16 TraesCS1B01G247100 chr3A 85.496 131 19 0 1103 1233 697737489 697737619 3.510000e-28 137.0
17 TraesCS1B01G247100 chr4B 92.308 156 12 0 3319 3474 613321974 613321819 9.410000e-54 222.0
18 TraesCS1B01G247100 chr4B 91.463 82 6 1 2009 2090 652001015 652000935 2.130000e-20 111.0
19 TraesCS1B01G247100 chr2A 92.308 156 11 1 3319 3474 141506319 141506473 3.390000e-53 220.0
20 TraesCS1B01G247100 chr2A 91.026 156 13 1 3319 3473 79316156 79316001 7.330000e-50 209.0
21 TraesCS1B01G247100 chr2A 93.103 87 6 0 2006 2092 34328129 34328215 2.110000e-25 128.0
22 TraesCS1B01G247100 chr5B 92.763 152 9 1 3319 3470 208523450 208523301 1.220000e-52 219.0
23 TraesCS1B01G247100 chr2D 91.667 156 12 1 3319 3473 79056318 79056163 1.570000e-51 215.0
24 TraesCS1B01G247100 chr6A 90.566 159 14 1 3319 3476 118284205 118284363 7.330000e-50 209.0
25 TraesCS1B01G247100 chr6A 90.909 88 8 0 2006 2093 400247533 400247620 1.270000e-22 119.0
26 TraesCS1B01G247100 chr4A 89.888 89 8 1 2006 2093 594380336 594380248 5.910000e-21 113.0


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 TraesCS1B01G247100 chr1B 437597701 437604908 7207 False 13311.0 13311 100.0000 1 7208 1 chr1B.!!$F1 7207
1 TraesCS1B01G247100 chr1D 325482566 325489741 7175 False 11623.0 11623 95.9640 45 7208 1 chr1D.!!$F3 7163
2 TraesCS1B01G247100 chr1A 419028415 419035890 7475 True 2336.7 5653 95.3056 1 7208 5 chr1A.!!$R2 7207
3 TraesCS1B01G247100 chr3B 750136030 750137241 1211 False 310.0 483 85.0370 1103 4502 2 chr3B.!!$F1 3399
4 TraesCS1B01G247100 chr3D 562697554 562698641 1087 False 306.5 481 87.6805 1124 4502 2 chr3D.!!$F1 3378
5 TraesCS1B01G247100 chr3A 697737489 697738650 1161 False 309.0 481 86.8510 1103 4480 2 chr3A.!!$F1 3377

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
367 375 1.427368 ACCAAGACAAATACCAGGCCA 59.573 47.619 5.01 0.0 0.0 5.36 F
1520 1634 2.290260 TGATCGCAATGGACTTCAAGGT 60.290 45.455 0.00 0.0 0.0 3.50 F
2960 3097 0.610174 GGAGATCACACACAGGAGCA 59.390 55.000 0.00 0.0 0.0 4.26 F
3119 3256 1.617947 GGATCCGACCTGTGAAGGCT 61.618 60.000 0.00 0.0 0.0 4.58 F
4291 4644 0.693622 TTGGCCCTGTCGGTGATAAA 59.306 50.000 0.00 0.0 0.0 1.40 F
6018 6389 0.963962 GTGGTGGTTCTGGTAGACGA 59.036 55.000 0.00 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2072 0.596082 GGCCTAACACGCACAATTGT 59.404 50.000 4.92 4.92 0.00 2.71 R
3211 3348 1.211457 GGATCAGTGCATGGAGTTCCT 59.789 52.381 5.71 0.00 36.82 3.36 R
3949 4302 0.887247 ATGGCGTGCAACAGCATTAA 59.113 45.000 11.38 0.00 40.93 1.40 R
4974 5331 0.188342 ACTGAACAGCCACCCCATTT 59.812 50.000 1.46 0.00 0.00 2.32 R
6204 6575 2.829120 ACCTTCTGCTCCAGAGTTCTAC 59.171 50.000 0.00 0.00 41.75 2.59 R
7040 7503 1.153509 CGAACACCCGGTCCATACC 60.154 63.158 0.00 0.00 42.95 2.73 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
31 32 6.775629 AGAAGTGTTAGATGATACTCCCTCTC 59.224 42.308 0.00 0.00 0.00 3.20
32 33 6.019656 AGTGTTAGATGATACTCCCTCTCA 57.980 41.667 0.00 0.00 0.00 3.27
33 34 5.830991 AGTGTTAGATGATACTCCCTCTCAC 59.169 44.000 0.00 0.00 0.00 3.51
34 35 5.830991 GTGTTAGATGATACTCCCTCTCACT 59.169 44.000 0.00 0.00 0.00 3.41
66 71 8.867097 AGTTTACAGATGGAGTAGTTACTTTCA 58.133 33.333 0.00 0.00 36.50 2.69
168 174 6.293462 GGGACACTTAGCTAAGTTCTTTTGTG 60.293 42.308 31.90 21.84 43.57 3.33
178 184 6.811665 GCTAAGTTCTTTTGTGGTTTTTCTGT 59.188 34.615 0.00 0.00 0.00 3.41
367 375 1.427368 ACCAAGACAAATACCAGGCCA 59.573 47.619 5.01 0.00 0.00 5.36
638 646 6.605471 TGACAAAGACCAGTCATACATAGT 57.395 37.500 0.00 0.00 39.65 2.12
639 647 7.004555 TGACAAAGACCAGTCATACATAGTT 57.995 36.000 0.00 0.00 39.65 2.24
640 648 8.129496 TGACAAAGACCAGTCATACATAGTTA 57.871 34.615 0.00 0.00 39.65 2.24
641 649 8.033038 TGACAAAGACCAGTCATACATAGTTAC 58.967 37.037 0.00 0.00 39.65 2.50
642 650 7.903145 ACAAAGACCAGTCATACATAGTTACA 58.097 34.615 0.00 0.00 0.00 2.41
643 651 8.540388 ACAAAGACCAGTCATACATAGTTACAT 58.460 33.333 0.00 0.00 0.00 2.29
650 658 9.411801 CCAGTCATACATAGTTACATACACATC 57.588 37.037 0.00 0.00 0.00 3.06
727 736 6.262601 ACACACAGTTTTTCCGTTATTGAAG 58.737 36.000 0.00 0.00 0.00 3.02
728 737 6.094325 ACACACAGTTTTTCCGTTATTGAAGA 59.906 34.615 0.00 0.00 0.00 2.87
748 757 7.504403 TGAAGAAAATAGGCAACCAATTCAAA 58.496 30.769 0.00 0.00 37.17 2.69
1457 1571 4.274214 TGCTGAGTTCTTGATCACAACTTG 59.726 41.667 16.79 14.07 32.27 3.16
1520 1634 2.290260 TGATCGCAATGGACTTCAAGGT 60.290 45.455 0.00 0.00 0.00 3.50
1833 1948 3.751175 TCTGGATTGCTTCTTTGTTACCG 59.249 43.478 0.00 0.00 0.00 4.02
1862 1984 8.581578 TCTCGCCTTTTAACCATTAATTTTTCT 58.418 29.630 0.00 0.00 0.00 2.52
1863 1985 9.849166 CTCGCCTTTTAACCATTAATTTTTCTA 57.151 29.630 0.00 0.00 0.00 2.10
1949 2071 4.097551 TGTCATGACAAATCCAAGTCCA 57.902 40.909 26.02 0.00 38.56 4.02
1950 2072 4.468713 TGTCATGACAAATCCAAGTCCAA 58.531 39.130 26.02 0.00 38.56 3.53
1959 2081 3.665745 ATCCAAGTCCAACAATTGTGC 57.334 42.857 12.82 3.40 0.00 4.57
2131 2253 4.201812 TGCGTACTTGCATTATTCTTCTGC 60.202 41.667 0.00 0.00 40.62 4.26
2149 2271 0.669318 GCGGTTGTTGATCTGGTCGA 60.669 55.000 0.00 0.00 0.00 4.20
2227 2349 5.007430 CAGTGAGTGAATTGATCTGCATACC 59.993 44.000 0.00 0.00 0.00 2.73
2526 2648 6.373495 TCAATTCATTCTGTCTCTGGTTGATG 59.627 38.462 0.00 0.00 0.00 3.07
2528 2650 3.584406 TCATTCTGTCTCTGGTTGATGGT 59.416 43.478 0.00 0.00 0.00 3.55
2714 2836 6.422701 TGGTAGTATGCTAAATTGATGTACGC 59.577 38.462 0.00 0.00 0.00 4.42
2728 2850 5.694816 TGATGTACGCAACCATTAACTTTG 58.305 37.500 0.00 0.00 0.00 2.77
2758 2880 7.225145 GCATTATTTCTTCTTTTGGCATGCATA 59.775 33.333 21.36 4.71 34.68 3.14
2759 2881 8.545420 CATTATTTCTTCTTTTGGCATGCATAC 58.455 33.333 21.36 2.31 0.00 2.39
2761 2883 5.726980 TTCTTCTTTTGGCATGCATACTT 57.273 34.783 21.36 0.00 0.00 2.24
2763 2885 3.872511 TCTTTTGGCATGCATACTTGG 57.127 42.857 21.36 3.15 0.00 3.61
2764 2886 2.496871 TCTTTTGGCATGCATACTTGGG 59.503 45.455 21.36 1.63 0.00 4.12
2766 2888 1.766494 TTGGCATGCATACTTGGGAG 58.234 50.000 21.36 0.00 0.00 4.30
2767 2889 0.625316 TGGCATGCATACTTGGGAGT 59.375 50.000 21.36 0.00 39.97 3.85
2889 3024 5.944007 ACATAAACTGGCAAGTAAAGGTAGG 59.056 40.000 0.00 0.00 34.77 3.18
2947 3084 4.142293 GGAAACAATGCCTTCAAGGAGATC 60.142 45.833 7.98 0.00 37.67 2.75
2960 3097 0.610174 GGAGATCACACACAGGAGCA 59.390 55.000 0.00 0.00 0.00 4.26
3119 3256 1.617947 GGATCCGACCTGTGAAGGCT 61.618 60.000 0.00 0.00 0.00 4.58
3159 3296 5.696724 CCTGAGAAATAGAAGTGTTGACGTT 59.303 40.000 0.00 0.00 0.00 3.99
3211 3348 4.720902 CCGCTCATGGCCACCACA 62.721 66.667 8.16 0.00 35.80 4.17
3229 3366 1.632409 ACAGGAACTCCATGCACTGAT 59.368 47.619 3.95 0.00 34.60 2.90
3279 3416 8.821147 TTAGAAGACATTTACATTGTGTACGT 57.179 30.769 0.00 0.00 31.69 3.57
3663 3989 5.590530 AGTCATTGTTTTTGTAACAGGCA 57.409 34.783 0.00 0.00 0.00 4.75
3722 4054 7.592938 CATGTGGCAAGTGTTAAGAAAATAGA 58.407 34.615 0.00 0.00 0.00 1.98
3723 4055 7.759489 TGTGGCAAGTGTTAAGAAAATAGAT 57.241 32.000 0.00 0.00 0.00 1.98
3724 4056 7.816640 TGTGGCAAGTGTTAAGAAAATAGATC 58.183 34.615 0.00 0.00 0.00 2.75
3783 4118 8.816640 ATGTAAACATGATTTCTCAAACAACC 57.183 30.769 0.00 0.00 34.83 3.77
3849 4184 3.926616 TCTGCTTCTTGTTGCCTACTAC 58.073 45.455 0.00 0.00 0.00 2.73
3939 4292 8.487028 ACATATCTCAGTTACCCTCTTTTTAGG 58.513 37.037 0.00 0.00 36.30 2.69
3949 4302 8.863086 GTTACCCTCTTTTTAGGTGGTAAATTT 58.137 33.333 0.00 0.00 34.56 1.82
4291 4644 0.693622 TTGGCCCTGTCGGTGATAAA 59.306 50.000 0.00 0.00 0.00 1.40
4306 4659 5.278758 CGGTGATAAAACCCATGTTTCAACT 60.279 40.000 0.00 0.00 43.80 3.16
4726 5079 2.299582 TGTTGCCACCAAATCAGGAATG 59.700 45.455 0.00 0.00 31.68 2.67
4751 5104 7.840210 TGTTTTAGGGACCCTTTCTTTCTTTTA 59.160 33.333 20.96 0.00 34.61 1.52
4783 5138 7.675161 TGATGAATTACTATCACTTGAGGGA 57.325 36.000 0.00 0.00 0.00 4.20
4788 5143 8.041323 TGAATTACTATCACTTGAGGGACTTTC 58.959 37.037 0.00 0.00 41.55 2.62
4805 5160 7.121315 AGGGACTTTCATTTTCTATTTCCTTCG 59.879 37.037 0.00 0.00 27.25 3.79
4908 5265 1.497991 TTTCTTGAACGCTGTCTCCG 58.502 50.000 0.00 0.00 0.00 4.63
4920 5277 3.056304 GCTGTCTCCGAAAGCTATCATC 58.944 50.000 0.00 0.00 39.61 2.92
4981 5338 7.712204 AAGGTTATGTTACTTACAAATGGGG 57.288 36.000 0.00 0.00 40.89 4.96
5070 5427 3.432378 ACCACTGAGATTAGTTCCTCGT 58.568 45.455 0.00 0.00 32.30 4.18
5121 5478 4.466567 TCACACATCGCTGTTGTAAAAG 57.533 40.909 0.00 0.00 31.62 2.27
5260 5617 8.632679 TGGATCCTTGAATGTTATTGCTTAATC 58.367 33.333 14.23 0.00 0.00 1.75
5302 5659 3.596214 ACACCATACTAAACAGCCTTCG 58.404 45.455 0.00 0.00 0.00 3.79
5584 5955 4.438336 CCAACTATTGCAGCTCACTCATTG 60.438 45.833 0.00 0.00 0.00 2.82
5951 6322 4.081198 TCCAGATCTGAGGAGAAAAGAAGC 60.081 45.833 24.62 0.00 0.00 3.86
6018 6389 0.963962 GTGGTGGTTCTGGTAGACGA 59.036 55.000 0.00 0.00 0.00 4.20
6204 6575 4.210120 GGCAGCTTCGATAGTACAAATGAG 59.790 45.833 0.00 0.00 37.40 2.90
6399 6770 5.013079 TCTCTTCCACACAAATATCACCACT 59.987 40.000 0.00 0.00 0.00 4.00
6540 6913 2.630580 AGAACTGTTCTGAGGAGGACAC 59.369 50.000 21.47 0.00 38.91 3.67
6898 7360 3.193479 CAGATAAGCCCAGGGTTGTTTTC 59.807 47.826 7.55 3.83 37.08 2.29
6935 7397 9.982291 TTGCTCAAACTAATTATATTTGTCGAC 57.018 29.630 9.11 9.11 35.33 4.20
6938 7400 8.133754 TCAAACTAATTATATTTGTCGACGGG 57.866 34.615 11.62 0.00 35.33 5.28
7040 7503 5.527582 GGGGCATGTTACAAGTAGTAATCAG 59.472 44.000 0.00 0.00 44.06 2.90
7093 7556 2.830923 CTCCACCTGTGTCATCTTCTCT 59.169 50.000 0.00 0.00 0.00 3.10
7104 7567 1.066358 CATCTTCTCTGTCCTGCAGCA 60.066 52.381 8.66 0.31 44.66 4.41
7111 7574 2.591715 GTCCTGCAGCACCGTTGT 60.592 61.111 8.66 0.00 0.00 3.32
7172 7635 3.723348 GTCGTTGCGGCTTGGGAC 61.723 66.667 0.00 0.05 0.00 4.46
7173 7636 4.243008 TCGTTGCGGCTTGGGACA 62.243 61.111 0.00 0.00 0.00 4.02
7174 7637 4.025401 CGTTGCGGCTTGGGACAC 62.025 66.667 0.00 0.00 39.29 3.67
7175 7638 4.025401 GTTGCGGCTTGGGACACG 62.025 66.667 0.00 0.00 39.29 4.49
7198 7662 2.264480 CGACGCCCAGAATCCACA 59.736 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
367 375 7.301868 ACCATAAAATCAACAATGTTCCTGT 57.698 32.000 0.00 0.00 0.00 4.00
440 448 3.054361 TGGCCAAGAGAAACCTAAGATCC 60.054 47.826 0.61 0.00 0.00 3.36
538 546 7.380423 AATTCCTAGCCTCTTAGAGCAAATA 57.620 36.000 3.26 0.00 0.00 1.40
635 643 6.614694 ACAACCCTGATGTGTATGTAACTA 57.385 37.500 0.00 0.00 0.00 2.24
636 644 5.499004 ACAACCCTGATGTGTATGTAACT 57.501 39.130 0.00 0.00 0.00 2.24
637 645 7.335924 ACATAACAACCCTGATGTGTATGTAAC 59.664 37.037 10.15 0.00 35.59 2.50
638 646 7.398829 ACATAACAACCCTGATGTGTATGTAA 58.601 34.615 10.15 0.00 35.59 2.41
639 647 6.953101 ACATAACAACCCTGATGTGTATGTA 58.047 36.000 10.15 0.00 35.59 2.29
640 648 5.815581 ACATAACAACCCTGATGTGTATGT 58.184 37.500 0.00 0.00 34.25 2.29
641 649 6.757897 AACATAACAACCCTGATGTGTATG 57.242 37.500 0.00 0.00 32.92 2.39
642 650 9.120538 GATTAACATAACAACCCTGATGTGTAT 57.879 33.333 0.00 0.00 32.92 2.29
643 651 8.325787 AGATTAACATAACAACCCTGATGTGTA 58.674 33.333 0.00 0.00 32.92 2.90
727 736 8.321650 TCAATTTGAATTGGTTGCCTATTTTC 57.678 30.769 14.53 0.00 44.51 2.29
728 737 8.688747 TTCAATTTGAATTGGTTGCCTATTTT 57.311 26.923 14.53 0.00 44.51 1.82
748 757 6.460676 GCATCCAATTTCGAATCCTCTTCAAT 60.461 38.462 0.00 0.00 0.00 2.57
981 993 6.351117 GCAACATAGGTAAGGTGAACTACTCT 60.351 42.308 0.00 0.00 0.00 3.24
1457 1571 6.146837 CAGCCTGCACAGTAGACAATATAATC 59.853 42.308 0.00 0.00 0.00 1.75
1833 1948 8.926715 AAATTAATGGTTAAAAGGCGAGAATC 57.073 30.769 0.00 0.00 0.00 2.52
1863 1985 9.173021 TCATTGAAATAGAAACCGTGACATTAT 57.827 29.630 0.00 0.00 0.00 1.28
1945 2067 2.202295 AACACGCACAATTGTTGGAC 57.798 45.000 8.77 0.00 34.61 4.02
1946 2068 2.292016 CCTAACACGCACAATTGTTGGA 59.708 45.455 8.77 0.00 36.57 3.53
1947 2069 2.660490 CCTAACACGCACAATTGTTGG 58.340 47.619 8.77 6.22 36.61 3.77
1948 2070 2.050691 GCCTAACACGCACAATTGTTG 58.949 47.619 8.77 7.79 36.61 3.33
1949 2071 1.000717 GGCCTAACACGCACAATTGTT 60.001 47.619 8.77 0.00 39.31 2.83
1950 2072 0.596082 GGCCTAACACGCACAATTGT 59.404 50.000 4.92 4.92 0.00 2.71
1959 2081 4.037089 ACTTTAAAACCTTGGCCTAACACG 59.963 41.667 3.32 0.00 0.00 4.49
2079 2201 2.236395 GCTTAAGCAAGTACTCCCTCCA 59.764 50.000 22.59 0.00 41.59 3.86
2131 2253 1.068474 GTCGACCAGATCAACAACCG 58.932 55.000 3.51 0.00 0.00 4.44
2149 2271 8.862325 TCAAAACTGTTGAATATATGACCAGT 57.138 30.769 0.00 0.00 0.00 4.00
2227 2349 7.362662 TGAGATACAGCAAAACTTAGCTTTTG 58.637 34.615 0.00 0.00 41.96 2.44
2267 2389 8.482852 AACTAGGTAACCACTAAAACTCTACA 57.517 34.615 0.00 0.00 37.17 2.74
2526 2648 2.438021 TGCAGGTTATCCCAGACATACC 59.562 50.000 0.00 0.00 34.66 2.73
2528 2650 4.853468 TTTGCAGGTTATCCCAGACATA 57.147 40.909 0.00 0.00 34.66 2.29
2582 2704 9.753674 TCCTTTCTGATTTACAACTGGAAATAT 57.246 29.630 0.00 0.00 0.00 1.28
2714 2836 8.761575 AATAATGCACTCAAAGTTAATGGTTG 57.238 30.769 0.00 0.00 0.00 3.77
2728 2850 6.158598 TGCCAAAAGAAGAAATAATGCACTC 58.841 36.000 0.00 0.00 0.00 3.51
2852 2987 6.491745 TGCCAGTTTATGTAATCTGTTTTGGA 59.508 34.615 9.00 0.00 33.35 3.53
2947 3084 1.677576 ACAACATTGCTCCTGTGTGTG 59.322 47.619 0.00 0.00 0.00 3.82
2960 3097 3.071892 TGGTTCCGACTTCCTACAACATT 59.928 43.478 0.00 0.00 0.00 2.71
3119 3256 1.418264 TCAGGTGAAAACCCGTGATCA 59.582 47.619 0.00 0.00 0.00 2.92
3159 3296 2.778299 AGCCACTACGATTTTCAAGCA 58.222 42.857 0.00 0.00 0.00 3.91
3211 3348 1.211457 GGATCAGTGCATGGAGTTCCT 59.789 52.381 5.71 0.00 36.82 3.36
3279 3416 7.674471 TGTCGTATAAACCACATTGAATCAA 57.326 32.000 0.00 0.00 0.00 2.57
3459 3777 3.926058 TGCAAAGTATTACTCCCTCCC 57.074 47.619 0.00 0.00 0.00 4.30
3625 3951 7.218228 ACAATGACTTCTTCATGTAATTGCA 57.782 32.000 0.00 0.00 44.86 4.08
3663 3989 2.862541 TCTTAACACTTGCCACATGCT 58.137 42.857 0.00 0.00 42.00 3.79
3699 4031 7.446931 TGATCTATTTTCTTAACACTTGCCACA 59.553 33.333 0.00 0.00 0.00 4.17
3700 4032 7.816640 TGATCTATTTTCTTAACACTTGCCAC 58.183 34.615 0.00 0.00 0.00 5.01
3701 4033 7.994425 TGATCTATTTTCTTAACACTTGCCA 57.006 32.000 0.00 0.00 0.00 4.92
3702 4034 9.508567 GATTGATCTATTTTCTTAACACTTGCC 57.491 33.333 0.00 0.00 0.00 4.52
3722 4054 6.944290 TCAATTCAGAAGTTCCAGTGATTGAT 59.056 34.615 0.00 0.00 0.00 2.57
3723 4055 6.298361 TCAATTCAGAAGTTCCAGTGATTGA 58.702 36.000 0.00 10.03 0.00 2.57
3724 4056 6.564709 TCAATTCAGAAGTTCCAGTGATTG 57.435 37.500 0.00 8.26 0.00 2.67
3763 4098 5.363580 AGGTGGTTGTTTGAGAAATCATGTT 59.636 36.000 0.00 0.00 0.00 2.71
3783 4118 7.094420 CGGAGCATCTGGATATAGATATAGGTG 60.094 44.444 0.00 0.00 38.01 4.00
3939 4292 6.589454 GTGCAACAGCATTAAAATTTACCAC 58.411 36.000 0.00 0.00 40.93 4.16
3949 4302 0.887247 ATGGCGTGCAACAGCATTAA 59.113 45.000 11.38 0.00 40.93 1.40
4291 4644 2.650322 ACACGAGTTGAAACATGGGTT 58.350 42.857 0.00 0.00 39.43 4.11
4306 4659 3.199071 AGCCATAAGTTCCCATAACACGA 59.801 43.478 0.00 0.00 0.00 4.35
4705 5058 9.259347 TAAAACATTCCTGATTTGGTGGCAACA 62.259 37.037 0.00 0.00 34.93 3.33
4726 5079 6.726490 AAAGAAAGAAAGGGTCCCTAAAAC 57.274 37.500 12.06 3.21 31.13 2.43
4783 5138 7.174946 TCTGCGAAGGAAATAGAAAATGAAAGT 59.825 33.333 0.00 0.00 0.00 2.66
4788 5143 7.019774 TGATCTGCGAAGGAAATAGAAAATG 57.980 36.000 0.00 0.00 0.00 2.32
4805 5160 9.282569 AGAGTTCAAAAGGATAATATGATCTGC 57.717 33.333 0.00 0.00 0.00 4.26
4845 5202 6.150641 ACGAAGTAACAGTGAATAGCAGTCTA 59.849 38.462 0.00 0.00 41.94 2.59
4846 5203 5.047943 ACGAAGTAACAGTGAATAGCAGTCT 60.048 40.000 0.00 0.00 41.94 3.24
4974 5331 0.188342 ACTGAACAGCCACCCCATTT 59.812 50.000 1.46 0.00 0.00 2.32
4981 5338 1.537202 CCTAAGCAACTGAACAGCCAC 59.463 52.381 1.46 0.00 0.00 5.01
5070 5427 8.736244 TGAGAATGACGTGGATCGATAAATATA 58.264 33.333 0.00 0.00 42.86 0.86
5260 5617 9.104965 TGGTGTTATTAGAGGATTAATTGTTCG 57.895 33.333 0.00 0.00 0.00 3.95
5302 5659 5.095490 CCATAATTCGAAAAGAGTGGTTGC 58.905 41.667 0.00 0.00 0.00 4.17
5375 5732 7.356641 ACTTAGCATACATTCGCATTCATAG 57.643 36.000 0.00 0.00 0.00 2.23
5584 5955 9.502091 TCAACTATAAGGCATCCAACATTATAC 57.498 33.333 0.00 0.00 0.00 1.47
5605 5976 3.554544 CGAGCCTGCATATCAGATCAACT 60.555 47.826 0.00 0.00 45.72 3.16
5951 6322 5.605564 TTCATACTTCGATGTTGTTGTGG 57.394 39.130 9.44 0.00 0.00 4.17
6018 6389 2.995746 TCCCTATCATCCAAGCCTGAT 58.004 47.619 0.00 0.00 36.19 2.90
6204 6575 2.829120 ACCTTCTGCTCCAGAGTTCTAC 59.171 50.000 0.00 0.00 41.75 2.59
6359 6730 4.570369 GGAAGAGAGAAACTATGAAGCAGC 59.430 45.833 0.00 0.00 0.00 5.25
6399 6770 1.634757 GCGTGTCGATGGTGATTGCA 61.635 55.000 0.00 0.00 0.00 4.08
6481 6854 0.684535 TTCCAGCCAGATGTCGTTCA 59.315 50.000 0.00 0.00 0.00 3.18
6540 6913 3.474600 AGAGGCTCATTTGATTGGATCG 58.525 45.455 18.26 0.00 0.00 3.69
6688 7061 6.573485 TGTCACAATACAGACGTATGGAACAT 60.573 38.462 15.60 0.00 39.60 2.71
6898 7360 2.689983 AGTTTGAGCAAAGTTGGACCAG 59.310 45.455 0.00 0.00 30.25 4.00
7040 7503 1.153509 CGAACACCCGGTCCATACC 60.154 63.158 0.00 0.00 42.95 2.73
7093 7556 2.591429 CAACGGTGCTGCAGGACA 60.591 61.111 34.97 14.93 38.19 4.02
7104 7567 2.430367 GGAGAAGGGCACAACGGT 59.570 61.111 0.00 0.00 0.00 4.83
7111 7574 1.680989 TCATCGACGGAGAAGGGCA 60.681 57.895 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.