Multiple sequence alignment - TraesCS7B01G138500

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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 TraesCS7B01G138500 chr7B 100.000 5675 0 0 1 5675 174066259 174071933 0.000000e+00 10480.0
1 TraesCS7B01G138500 chr7A 95.807 3053 108 14 1735 4781 237507364 237504326 0.000000e+00 4911.0
2 TraesCS7B01G138500 chr7A 95.205 855 27 8 897 1744 237509183 237508336 0.000000e+00 1339.0
3 TraesCS7B01G138500 chr7A 94.963 814 24 5 4879 5675 237504324 237503511 0.000000e+00 1260.0
4 TraesCS7B01G138500 chr7A 78.138 494 105 3 7 498 273009536 273009044 1.540000e-80 311.0
5 TraesCS7B01G138500 chr7D 95.158 2251 89 11 884 3120 222522422 222520178 0.000000e+00 3535.0
6 TraesCS7B01G138500 chr7D 94.177 1580 63 12 3212 4781 222520152 222518592 0.000000e+00 2381.0
7 TraesCS7B01G138500 chr7D 94.963 814 24 4 4879 5675 222518590 222517777 0.000000e+00 1260.0
8 TraesCS7B01G138500 chr4B 97.595 873 21 0 1 873 602771882 602772754 0.000000e+00 1496.0
9 TraesCS7B01G138500 chr3B 97.592 872 21 0 1 872 739044240 739043369 0.000000e+00 1495.0
10 TraesCS7B01G138500 chr3B 94.682 865 45 1 1 864 160835306 160834442 0.000000e+00 1341.0
11 TraesCS7B01G138500 chr3B 73.050 423 80 26 3054 3455 242890342 242889933 9.990000e-23 119.0
12 TraesCS7B01G138500 chr6A 91.743 872 71 1 1 872 583128578 583129448 0.000000e+00 1210.0
13 TraesCS7B01G138500 chr2A 91.065 873 74 3 1 873 677550929 677550061 0.000000e+00 1177.0
14 TraesCS7B01G138500 chr1B 86.957 874 108 6 1 872 689477788 689478657 0.000000e+00 977.0
15 TraesCS7B01G138500 chr1B 84.330 351 52 3 521 871 689636292 689636639 1.960000e-89 340.0
16 TraesCS7B01G138500 chr1B 83.761 351 54 3 521 871 689773199 689773546 4.240000e-86 329.0
17 TraesCS7B01G138500 chr1D 90.818 697 49 6 1762 2446 59066343 59065650 0.000000e+00 918.0
18 TraesCS7B01G138500 chr5A 89.836 610 47 6 1699 2295 466800213 466800820 0.000000e+00 769.0
19 TraesCS7B01G138500 chr5A 92.029 138 11 0 2309 2446 466801204 466801341 1.610000e-45 195.0
20 TraesCS7B01G138500 chr5B 78.882 161 28 5 3054 3212 61373953 61374109 2.800000e-18 104.0
21 TraesCS7B01G138500 chr6B 77.348 181 34 6 3054 3228 619023555 619023376 3.620000e-17 100.0
22 TraesCS7B01G138500 chr5D 100.000 28 0 0 3054 3081 27545609 27545636 1.000000e-02 52.8


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 TraesCS7B01G138500 chr7B 174066259 174071933 5674 False 10480.000000 10480 100.0000 1 5675 1 chr7B.!!$F1 5674
1 TraesCS7B01G138500 chr7A 237503511 237509183 5672 True 2503.333333 4911 95.3250 897 5675 3 chr7A.!!$R2 4778
2 TraesCS7B01G138500 chr7D 222517777 222522422 4645 True 2392.000000 3535 94.7660 884 5675 3 chr7D.!!$R1 4791
3 TraesCS7B01G138500 chr4B 602771882 602772754 872 False 1496.000000 1496 97.5950 1 873 1 chr4B.!!$F1 872
4 TraesCS7B01G138500 chr3B 739043369 739044240 871 True 1495.000000 1495 97.5920 1 872 1 chr3B.!!$R3 871
5 TraesCS7B01G138500 chr3B 160834442 160835306 864 True 1341.000000 1341 94.6820 1 864 1 chr3B.!!$R1 863
6 TraesCS7B01G138500 chr6A 583128578 583129448 870 False 1210.000000 1210 91.7430 1 872 1 chr6A.!!$F1 871
7 TraesCS7B01G138500 chr2A 677550061 677550929 868 True 1177.000000 1177 91.0650 1 873 1 chr2A.!!$R1 872
8 TraesCS7B01G138500 chr1B 689477788 689478657 869 False 977.000000 977 86.9570 1 872 1 chr1B.!!$F1 871
9 TraesCS7B01G138500 chr1D 59065650 59066343 693 True 918.000000 918 90.8180 1762 2446 1 chr1D.!!$R1 684
10 TraesCS7B01G138500 chr5A 466800213 466801341 1128 False 482.000000 769 90.9325 1699 2446 2 chr5A.!!$F1 747

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
979 981 1.190833 TTTACGGGCCTTCACGGGTA 61.191 55.000 0.84 0.0 0.00 3.69 F
1410 1418 2.495409 CCGCACTCTATACCGGCCA 61.495 63.158 0.00 0.0 33.77 5.36 F
2183 3180 0.176910 GTAAGCCTCTGACCCTCTGC 59.823 60.000 0.00 0.0 0.00 4.26 F
2887 4269 0.251922 AGAGGTACTGGGCGTTGGTA 60.252 55.000 0.00 0.0 41.55 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 2839 0.247460 GAACCCCAGAAAATGCAGCC 59.753 55.000 0.00 0.0 0.00 4.85 R
3093 4475 0.608035 TTTGCCCTTCGTGCCCTAAG 60.608 55.000 0.00 0.0 0.00 2.18 R
3201 4584 1.002888 ACAGCAGCTGAAGTGTAGCAT 59.997 47.619 29.70 0.0 43.53 3.79 R
4782 6193 0.099968 CGCCCGATCGAGTCTTTGTA 59.900 55.000 18.66 0.0 0.00 2.41 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
171 172 3.247411 TGTTGAGCCGATATGCATTAACG 59.753 43.478 3.54 8.62 0.00 3.18
262 263 8.389366 CCATAATCTTCCTCCAATCTCCTAAAT 58.611 37.037 0.00 0.00 0.00 1.40
506 507 3.492756 GCGAATTGATCCTCTAAGTCAGC 59.507 47.826 0.00 0.00 0.00 4.26
628 629 3.702623 TACTCCCCCTCCCACCCC 61.703 72.222 0.00 0.00 0.00 4.95
723 724 1.688311 CCCCCGATCTCCTGTTGAGTA 60.688 57.143 0.00 0.00 42.12 2.59
874 876 4.990553 GGCGGCGCTAGGGGAATC 62.991 72.222 32.30 7.60 0.00 2.52
876 878 4.664677 CGGCGCTAGGGGAATCGG 62.665 72.222 7.64 0.00 0.00 4.18
877 879 4.990553 GGCGCTAGGGGAATCGGC 62.991 72.222 7.64 2.46 40.08 5.54
878 880 4.235762 GCGCTAGGGGAATCGGCA 62.236 66.667 9.09 0.00 0.00 5.69
879 881 2.029666 CGCTAGGGGAATCGGCAG 59.970 66.667 0.00 0.00 0.00 4.85
880 882 2.281139 GCTAGGGGAATCGGCAGC 60.281 66.667 0.00 0.00 0.00 5.25
881 883 2.427753 CTAGGGGAATCGGCAGCC 59.572 66.667 0.00 0.00 0.00 4.85
882 884 2.040884 TAGGGGAATCGGCAGCCT 60.041 61.111 10.54 0.00 0.00 4.58
910 912 6.597280 CAGTCAGGATATGTCGAGAGATATCA 59.403 42.308 23.05 8.00 42.54 2.15
925 927 1.913778 TATCAAGCGTATCGGGCCTA 58.086 50.000 0.84 0.00 0.00 3.93
979 981 1.190833 TTTACGGGCCTTCACGGGTA 61.191 55.000 0.84 0.00 0.00 3.69
1410 1418 2.495409 CCGCACTCTATACCGGCCA 61.495 63.158 0.00 0.00 33.77 5.36
1422 1433 4.640771 ATACCGGCCATGTTATCATCTT 57.359 40.909 0.00 0.00 31.15 2.40
1428 1439 2.808543 GCCATGTTATCATCTTCGGTCC 59.191 50.000 0.00 0.00 31.15 4.46
1441 1452 9.799106 ATCATCTTCGGTCCTATTAATGAAAAT 57.201 29.630 0.00 0.00 0.00 1.82
1492 1506 4.210331 ACACATAAGAAGGGGATTGCATC 58.790 43.478 0.00 0.00 0.00 3.91
1509 1523 4.725359 TGCATCGTTCTCAAATGTGAATG 58.275 39.130 9.91 9.91 36.45 2.67
1520 1534 5.049167 TCAAATGTGAATGGCTTGTTCAAC 58.951 37.500 2.93 0.00 37.34 3.18
1653 1668 5.649557 CCATTGATTGATTCGCTTTGGTAA 58.350 37.500 0.00 0.00 0.00 2.85
1694 1709 8.997621 TCTATCATTTCACTACCAGTTTACAC 57.002 34.615 0.00 0.00 0.00 2.90
1842 2839 8.970859 AAGAAGGTATGTAATGAAGAATCCAG 57.029 34.615 0.00 0.00 0.00 3.86
1847 2844 3.282021 TGTAATGAAGAATCCAGGCTGC 58.718 45.455 9.56 0.00 0.00 5.25
2183 3180 0.176910 GTAAGCCTCTGACCCTCTGC 59.823 60.000 0.00 0.00 0.00 4.26
2505 3885 0.839946 ATGGGAATGAAGAGGGTCCG 59.160 55.000 0.00 0.00 0.00 4.79
2603 3985 0.663153 GTTTGTGAGTGCAGGTCCAC 59.337 55.000 0.00 0.00 35.98 4.02
2887 4269 0.251922 AGAGGTACTGGGCGTTGGTA 60.252 55.000 0.00 0.00 41.55 3.25
2945 4327 5.086104 TGCTCCTCTCACAAAGGTATTAC 57.914 43.478 0.00 0.00 35.29 1.89
2946 4328 4.113354 GCTCCTCTCACAAAGGTATTACG 58.887 47.826 0.00 0.00 35.29 3.18
3093 4475 4.215613 CCTAAAATAGGGCATAACCGCTTC 59.784 45.833 0.00 0.00 42.42 3.86
3120 4503 1.358759 CGAAGGGCAAAAACGCTGT 59.641 52.632 0.00 0.00 32.43 4.40
3121 4504 0.660300 CGAAGGGCAAAAACGCTGTC 60.660 55.000 0.00 0.00 32.43 3.51
3198 4581 1.756430 TACAGCACCAAGTGTTGCAA 58.244 45.000 10.92 0.00 46.08 4.08
3199 4582 0.894141 ACAGCACCAAGTGTTGCAAA 59.106 45.000 0.00 0.00 46.08 3.68
3200 4583 1.481772 ACAGCACCAAGTGTTGCAAAT 59.518 42.857 0.00 0.00 46.08 2.32
3201 4584 2.692557 ACAGCACCAAGTGTTGCAAATA 59.307 40.909 0.00 0.00 46.08 1.40
3205 4588 3.861886 GCACCAAGTGTTGCAAATATGCT 60.862 43.478 0.00 0.00 43.42 3.79
3347 4748 6.045072 AGACAACCGTGATGTATTTTAGGA 57.955 37.500 0.00 0.00 0.00 2.94
3348 4749 6.469410 AGACAACCGTGATGTATTTTAGGAA 58.531 36.000 0.00 0.00 0.00 3.36
3349 4750 6.370718 AGACAACCGTGATGTATTTTAGGAAC 59.629 38.462 0.00 0.00 0.00 3.62
3350 4751 5.413523 ACAACCGTGATGTATTTTAGGAACC 59.586 40.000 0.00 0.00 0.00 3.62
3351 4752 5.168647 ACCGTGATGTATTTTAGGAACCA 57.831 39.130 0.00 0.00 0.00 3.67
3352 4753 5.562635 ACCGTGATGTATTTTAGGAACCAA 58.437 37.500 0.00 0.00 0.00 3.67
3353 4754 6.184789 ACCGTGATGTATTTTAGGAACCAAT 58.815 36.000 0.00 0.00 0.00 3.16
3354 4755 6.661805 ACCGTGATGTATTTTAGGAACCAATT 59.338 34.615 0.00 0.00 0.00 2.32
3355 4756 7.177744 ACCGTGATGTATTTTAGGAACCAATTT 59.822 33.333 0.00 0.00 0.00 1.82
3356 4757 8.032451 CCGTGATGTATTTTAGGAACCAATTTT 58.968 33.333 0.00 0.00 0.00 1.82
3362 4763 7.676468 TGTATTTTAGGAACCAATTTTAGGGCT 59.324 33.333 0.00 0.00 0.00 5.19
3366 4767 8.673456 TTTAGGAACCAATTTTAGGGCTATTT 57.327 30.769 0.00 0.00 0.00 1.40
3398 4803 9.450807 GATGAACATTTTTCGGTTATAATCCAG 57.549 33.333 0.00 0.00 0.00 3.86
3473 4878 4.061596 GCACCTATTGGAGATGCTCTTAC 58.938 47.826 0.00 0.00 37.04 2.34
3480 4885 3.445008 TGGAGATGCTCTTACCACTCTT 58.555 45.455 0.00 0.00 0.00 2.85
3520 4925 0.554792 CATCCCTGGCTCCTTTCCAT 59.445 55.000 0.00 0.00 32.37 3.41
3699 5104 1.134310 TCTGGCATAGATGGTGCACAG 60.134 52.381 20.43 3.11 44.25 3.66
3732 5137 2.307768 GAGTATCGAGTGATGGGACCA 58.692 52.381 0.00 0.00 35.99 4.02
3927 5333 3.955524 TTTACCCCTTCAACACCTGAA 57.044 42.857 0.00 0.00 41.93 3.02
3931 5337 3.653164 ACCCCTTCAACACCTGAATTTT 58.347 40.909 0.00 0.00 43.20 1.82
3932 5338 3.387699 ACCCCTTCAACACCTGAATTTTG 59.612 43.478 0.00 0.00 43.20 2.44
3935 5341 5.049828 CCCTTCAACACCTGAATTTTGTTC 58.950 41.667 0.00 0.00 43.20 3.18
4004 5410 8.663911 TGAAAATTTTCAACTGAAATCACCAAC 58.336 29.630 27.22 0.00 43.62 3.77
4033 5439 3.243816 TGACCCTGCTGCAGCTCA 61.244 61.111 36.61 28.29 42.66 4.26
4131 5537 1.227383 GCAGAATCCCCAACCGGAT 59.773 57.895 9.46 0.00 44.94 4.18
4143 5549 1.000717 CAACCGGATTTTGAGCCGTTT 60.001 47.619 9.46 0.00 45.85 3.60
4146 5552 2.081462 CCGGATTTTGAGCCGTTTACT 58.919 47.619 0.00 0.00 45.85 2.24
4261 5667 0.541863 GATGGTGGTCCCGAACATCT 59.458 55.000 0.84 0.00 36.06 2.90
4403 5809 3.703001 AATGTCTTCCTACCTGGTGTG 57.297 47.619 10.23 2.03 37.07 3.82
4406 5812 2.567169 TGTCTTCCTACCTGGTGTGATG 59.433 50.000 10.23 8.08 37.07 3.07
4416 5822 5.772393 ACCTGGTGTGATGGTTTATCTTA 57.228 39.130 0.00 0.00 36.71 2.10
4649 6055 2.857592 ATCAGCGAACAATTGATGCC 57.142 45.000 13.59 0.00 30.76 4.40
4651 6057 1.199789 TCAGCGAACAATTGATGCCAC 59.800 47.619 13.59 0.00 0.00 5.01
4652 6058 0.527565 AGCGAACAATTGATGCCACC 59.472 50.000 13.59 0.00 0.00 4.61
4654 6060 1.135024 GCGAACAATTGATGCCACCAT 60.135 47.619 13.59 0.00 0.00 3.55
4781 6192 4.983671 TCACTGTACATCGTAGCATCTT 57.016 40.909 0.00 0.00 0.00 2.40
4782 6193 5.324784 TCACTGTACATCGTAGCATCTTT 57.675 39.130 0.00 0.00 0.00 2.52
4783 6194 6.445357 TCACTGTACATCGTAGCATCTTTA 57.555 37.500 0.00 0.00 0.00 1.85
4784 6195 6.263344 TCACTGTACATCGTAGCATCTTTAC 58.737 40.000 0.00 0.00 0.00 2.01
4785 6196 6.033966 CACTGTACATCGTAGCATCTTTACA 58.966 40.000 0.00 0.00 0.00 2.41
4786 6197 6.530181 CACTGTACATCGTAGCATCTTTACAA 59.470 38.462 0.00 0.00 0.00 2.41
4787 6198 7.062956 CACTGTACATCGTAGCATCTTTACAAA 59.937 37.037 0.00 0.00 0.00 2.83
4788 6199 7.275779 ACTGTACATCGTAGCATCTTTACAAAG 59.724 37.037 0.00 0.00 37.36 2.77
4790 6201 6.648725 ACATCGTAGCATCTTTACAAAGAC 57.351 37.500 6.56 0.00 46.80 3.01
4791 6202 6.398918 ACATCGTAGCATCTTTACAAAGACT 58.601 36.000 6.56 3.84 46.80 3.24
4792 6203 6.531948 ACATCGTAGCATCTTTACAAAGACTC 59.468 38.462 6.56 2.55 46.80 3.36
4793 6204 5.093457 TCGTAGCATCTTTACAAAGACTCG 58.907 41.667 6.56 7.63 46.80 4.18
4794 6205 5.093457 CGTAGCATCTTTACAAAGACTCGA 58.907 41.667 6.56 0.00 46.80 4.04
4795 6206 5.744345 CGTAGCATCTTTACAAAGACTCGAT 59.256 40.000 6.56 1.19 46.80 3.59
4796 6207 6.075310 CGTAGCATCTTTACAAAGACTCGATC 60.075 42.308 6.56 0.00 46.80 3.69
4797 6208 4.800993 AGCATCTTTACAAAGACTCGATCG 59.199 41.667 9.36 9.36 46.80 3.69
4798 6209 4.026475 GCATCTTTACAAAGACTCGATCGG 60.026 45.833 16.41 8.65 46.80 4.18
4799 6210 4.106029 TCTTTACAAAGACTCGATCGGG 57.894 45.455 14.88 14.88 39.95 5.14
4800 6211 2.288961 TTACAAAGACTCGATCGGGC 57.711 50.000 16.63 8.21 0.00 6.13
4801 6212 0.099968 TACAAAGACTCGATCGGGCG 59.900 55.000 16.63 6.67 0.00 6.13
4802 6213 1.878522 CAAAGACTCGATCGGGCGG 60.879 63.158 16.63 5.87 0.00 6.13
4803 6214 2.348888 AAAGACTCGATCGGGCGGT 61.349 57.895 16.63 9.14 0.00 5.68
4804 6215 2.280823 AAAGACTCGATCGGGCGGTC 62.281 60.000 16.63 16.90 34.15 4.79
4805 6216 4.267503 GACTCGATCGGGCGGTCC 62.268 72.222 16.63 0.00 0.00 4.46
4807 6218 4.271816 CTCGATCGGGCGGTCCAG 62.272 72.222 16.41 0.00 34.36 3.86
4808 6219 4.807631 TCGATCGGGCGGTCCAGA 62.808 66.667 16.41 0.00 40.79 3.86
4809 6220 4.271816 CGATCGGGCGGTCCAGAG 62.272 72.222 7.38 0.00 39.89 3.35
4810 6221 2.833582 GATCGGGCGGTCCAGAGA 60.834 66.667 0.00 0.00 39.89 3.10
4811 6222 2.835431 ATCGGGCGGTCCAGAGAG 60.835 66.667 0.00 0.00 39.89 3.20
4836 6247 5.606348 GGGCATGTTCCCATTATTGTTAA 57.394 39.130 3.64 0.00 45.82 2.01
4837 6248 6.173427 GGGCATGTTCCCATTATTGTTAAT 57.827 37.500 3.64 0.00 45.82 1.40
4838 6249 6.591001 GGGCATGTTCCCATTATTGTTAATT 58.409 36.000 3.64 0.00 45.82 1.40
4839 6250 6.482973 GGGCATGTTCCCATTATTGTTAATTG 59.517 38.462 3.64 0.00 45.82 2.32
4840 6251 6.482973 GGCATGTTCCCATTATTGTTAATTGG 59.517 38.462 0.00 0.00 33.72 3.16
4841 6252 7.047271 GCATGTTCCCATTATTGTTAATTGGT 58.953 34.615 0.00 0.00 33.99 3.67
4842 6253 7.011295 GCATGTTCCCATTATTGTTAATTGGTG 59.989 37.037 0.00 0.00 33.99 4.17
4843 6254 7.782897 TGTTCCCATTATTGTTAATTGGTGA 57.217 32.000 0.00 0.00 33.99 4.02
4844 6255 7.607250 TGTTCCCATTATTGTTAATTGGTGAC 58.393 34.615 0.00 0.00 33.99 3.67
4845 6256 7.233553 TGTTCCCATTATTGTTAATTGGTGACA 59.766 33.333 0.00 0.00 33.99 3.58
4846 6257 7.969690 TCCCATTATTGTTAATTGGTGACAT 57.030 32.000 0.00 0.00 42.32 3.06
4847 6258 7.780064 TCCCATTATTGTTAATTGGTGACATG 58.220 34.615 0.00 0.00 42.32 3.21
4848 6259 6.479660 CCCATTATTGTTAATTGGTGACATGC 59.520 38.462 0.00 0.00 42.32 4.06
4849 6260 7.267128 CCATTATTGTTAATTGGTGACATGCT 58.733 34.615 0.00 0.00 42.32 3.79
4850 6261 7.436080 CCATTATTGTTAATTGGTGACATGCTC 59.564 37.037 0.00 0.00 42.32 4.26
4851 6262 5.981088 ATTGTTAATTGGTGACATGCTCA 57.019 34.783 0.00 0.00 42.32 4.26
4906 6317 6.110411 ACTACCTTGTTGCACTAGTGTAAT 57.890 37.500 26.05 14.16 37.50 1.89
5009 6420 2.055310 TAGTACGTCCATCGCCGCTG 62.055 60.000 0.00 0.00 44.19 5.18
5235 6651 2.741985 CATGTGCTCGGCGGTGAA 60.742 61.111 7.21 0.00 0.00 3.18
5236 6652 2.031919 ATGTGCTCGGCGGTGAAA 59.968 55.556 7.21 0.00 0.00 2.69
5638 7066 2.981302 CGGGACATCTCCTGCACA 59.019 61.111 0.00 0.00 36.06 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 3.444388 AGGAGTACGATGGTTTCTCTGAC 59.556 47.826 10.62 0.00 0.00 3.51
262 263 5.189928 TCTTTTTCTTGTTCAGTGCCACTA 58.810 37.500 0.00 0.00 0.00 2.74
264 265 4.370364 TCTTTTTCTTGTTCAGTGCCAC 57.630 40.909 0.00 0.00 0.00 5.01
506 507 1.300233 GACTATCCCGGAGCTTGCG 60.300 63.158 0.73 0.00 0.00 4.85
723 724 0.530650 CTACGTGCATGGCGGATTCT 60.531 55.000 11.36 0.00 0.00 2.40
833 835 4.409247 GCTAGGGTTCCAAAATCTCCTCTA 59.591 45.833 0.00 0.00 0.00 2.43
881 883 1.683385 TCGACATATCCTGACTGGCAG 59.317 52.381 14.16 14.16 44.49 4.85
882 884 1.683385 CTCGACATATCCTGACTGGCA 59.317 52.381 0.00 0.00 35.26 4.92
910 912 2.505167 GGGTAGGCCCGATACGCTT 61.505 63.158 0.00 0.00 46.51 4.68
1410 1418 9.658799 CATTAATAGGACCGAAGATGATAACAT 57.341 33.333 0.00 0.00 39.67 2.71
1422 1433 8.564574 GTGCAATATTTTCATTAATAGGACCGA 58.435 33.333 0.00 0.00 0.00 4.69
1481 1495 1.750193 TTGAGAACGATGCAATCCCC 58.250 50.000 0.00 0.00 41.39 4.81
1492 1506 3.837213 AGCCATTCACATTTGAGAACG 57.163 42.857 0.00 0.00 31.71 3.95
1509 1523 0.237498 GCCTACACGTTGAACAAGCC 59.763 55.000 0.00 0.00 0.00 4.35
1520 1534 3.189910 TCGCCACTATAATAGCCTACACG 59.810 47.826 0.00 0.00 0.00 4.49
1694 1709 3.056678 TGAAAACAATGCCTACATGCAGG 60.057 43.478 7.71 7.71 45.93 4.85
1839 2836 1.610554 CCCCAGAAAATGCAGCCTGG 61.611 60.000 15.47 15.47 44.29 4.45
1842 2839 0.247460 GAACCCCAGAAAATGCAGCC 59.753 55.000 0.00 0.00 0.00 4.85
1847 2844 6.648879 TCACTAAAAGAACCCCAGAAAATG 57.351 37.500 0.00 0.00 0.00 2.32
2099 3096 7.547019 TCATGCAAGAAACTAATCAGAGTACAG 59.453 37.037 0.00 0.00 0.00 2.74
2151 3148 1.524008 GGCTTACACAACTGCCCACC 61.524 60.000 0.00 0.00 39.49 4.61
2183 3180 7.750458 CCTGTATGCACAAGTTAATTTACTGTG 59.250 37.037 16.20 16.20 33.22 3.66
2603 3985 3.562141 CACTAGTATCTCTGTCCAGTCGG 59.438 52.174 0.00 0.00 0.00 4.79
2887 4269 2.225908 ACTCTCTGTAGGGGTCCCAATT 60.226 50.000 10.98 0.00 38.92 2.32
3041 4423 8.609483 ACCTATTGGAGATGCAAATATGACTAT 58.391 33.333 0.00 0.00 37.04 2.12
3049 4431 2.961062 GGCACCTATTGGAGATGCAAAT 59.039 45.455 0.00 0.00 35.36 2.32
3093 4475 0.608035 TTTGCCCTTCGTGCCCTAAG 60.608 55.000 0.00 0.00 0.00 2.18
3120 4503 2.422803 GCATATAAGGCACCTGTTGGGA 60.423 50.000 0.00 0.00 38.76 4.37
3121 4504 1.956477 GCATATAAGGCACCTGTTGGG 59.044 52.381 0.00 0.00 41.89 4.12
3198 4581 3.875727 CAGCAGCTGAAGTGTAGCATATT 59.124 43.478 20.43 0.00 43.53 1.28
3199 4582 3.118482 ACAGCAGCTGAAGTGTAGCATAT 60.118 43.478 29.70 0.00 43.53 1.78
3200 4583 2.234661 ACAGCAGCTGAAGTGTAGCATA 59.765 45.455 29.70 0.00 43.53 3.14
3201 4584 1.002888 ACAGCAGCTGAAGTGTAGCAT 59.997 47.619 29.70 0.00 43.53 3.79
3205 4588 1.229428 GCAACAGCAGCTGAAGTGTA 58.771 50.000 29.70 0.00 35.18 2.90
3312 4699 1.680338 GGTTGTCTTCTTGCAGGTGT 58.320 50.000 0.00 0.00 0.00 4.16
3317 4704 1.872952 CATCACGGTTGTCTTCTTGCA 59.127 47.619 0.00 0.00 0.00 4.08
3398 4803 8.831550 TGGAGTAAAATTTACAATGCCAAAAAC 58.168 29.630 17.00 0.00 0.00 2.43
3406 4811 7.867403 AGTGTGCTTGGAGTAAAATTTACAATG 59.133 33.333 17.00 6.68 0.00 2.82
3407 4812 7.951591 AGTGTGCTTGGAGTAAAATTTACAAT 58.048 30.769 17.00 0.00 0.00 2.71
3473 4878 3.244561 ACTGTGGTGGTTGATAAGAGTGG 60.245 47.826 0.00 0.00 0.00 4.00
3548 4953 8.631480 ATCGTTACTACATATGAGTATGACCA 57.369 34.615 10.38 0.00 40.12 4.02
3578 4983 6.757237 TGTGACAAATCTTGCCATTAAACAT 58.243 32.000 0.00 0.00 0.00 2.71
3699 5104 2.950309 TCGATACTCAGTAACAGCCTCC 59.050 50.000 0.00 0.00 0.00 4.30
3854 5259 9.162764 GGCGTATCCATAATACAAGATGTTAAT 57.837 33.333 0.00 0.00 40.34 1.40
3981 5387 7.337938 AGGTTGGTGATTTCAGTTGAAAATTT 58.662 30.769 10.96 0.00 45.81 1.82
4004 5410 2.171448 AGCAGGGTCAGCATAGTTTAGG 59.829 50.000 0.00 0.00 0.00 2.69
4033 5439 1.301244 CTTCCGCACAGTGCACTCT 60.301 57.895 25.19 1.33 45.36 3.24
4056 5462 4.850193 CCAACAATGGGAGTGCCT 57.150 55.556 1.06 0.00 43.51 4.75
4131 5537 1.143277 TCCCCAGTAAACGGCTCAAAA 59.857 47.619 0.00 0.00 0.00 2.44
4143 5549 2.238646 CAGCTTGTATGGTTCCCCAGTA 59.761 50.000 0.00 0.00 46.15 2.74
4261 5667 3.493699 CCGGTGTTACTCAGGAACTTTGA 60.494 47.826 0.25 0.00 34.60 2.69
4432 5838 5.738619 TGCAACTTAAGAGGAGTGACATA 57.261 39.130 10.09 0.00 0.00 2.29
4578 5984 4.285863 ACCTGACAATCCCAAAGAAAACA 58.714 39.130 0.00 0.00 0.00 2.83
4689 6096 7.389053 GGAAGAGTCTTTGTAAGATGATTGTGT 59.611 37.037 6.88 0.00 40.18 3.72
4762 6173 6.203808 TGTAAAGATGCTACGATGTACAGT 57.796 37.500 0.33 0.00 0.00 3.55
4781 6192 1.468565 CGCCCGATCGAGTCTTTGTAA 60.469 52.381 18.66 0.00 0.00 2.41
4782 6193 0.099968 CGCCCGATCGAGTCTTTGTA 59.900 55.000 18.66 0.00 0.00 2.41
4783 6194 1.153823 CGCCCGATCGAGTCTTTGT 60.154 57.895 18.66 0.00 0.00 2.83
4784 6195 1.878522 CCGCCCGATCGAGTCTTTG 60.879 63.158 18.66 0.00 0.00 2.77
4785 6196 2.280823 GACCGCCCGATCGAGTCTTT 62.281 60.000 18.66 0.00 31.61 2.52
4786 6197 2.754658 ACCGCCCGATCGAGTCTT 60.755 61.111 18.66 0.00 0.00 3.01
4787 6198 3.210528 GACCGCCCGATCGAGTCT 61.211 66.667 18.66 0.00 31.61 3.24
4788 6199 4.267503 GGACCGCCCGATCGAGTC 62.268 72.222 18.66 16.29 0.00 3.36
4790 6201 4.271816 CTGGACCGCCCGATCGAG 62.272 72.222 18.66 3.84 37.93 4.04
4791 6202 4.807631 TCTGGACCGCCCGATCGA 62.808 66.667 18.66 0.00 37.93 3.59
4792 6203 4.271816 CTCTGGACCGCCCGATCG 62.272 72.222 8.51 8.51 37.93 3.69
4793 6204 2.833582 TCTCTGGACCGCCCGATC 60.834 66.667 0.00 0.00 37.93 3.69
4794 6205 2.835431 CTCTCTGGACCGCCCGAT 60.835 66.667 0.00 0.00 37.93 4.18
4819 6230 7.233553 TGTCACCAATTAACAATAATGGGAACA 59.766 33.333 8.63 8.92 43.02 3.18
4820 6231 7.607250 TGTCACCAATTAACAATAATGGGAAC 58.393 34.615 8.63 7.00 43.02 3.62
4821 6232 7.782897 TGTCACCAATTAACAATAATGGGAA 57.217 32.000 8.63 0.00 43.02 3.97
4822 6233 7.632462 GCATGTCACCAATTAACAATAATGGGA 60.632 37.037 8.63 0.00 43.02 4.37
4823 6234 6.479660 GCATGTCACCAATTAACAATAATGGG 59.520 38.462 0.00 1.26 45.03 4.00
4824 6235 7.267128 AGCATGTCACCAATTAACAATAATGG 58.733 34.615 0.00 0.00 32.06 3.16
4825 6236 7.975058 TGAGCATGTCACCAATTAACAATAATG 59.025 33.333 0.00 0.00 32.06 1.90
4826 6237 8.065473 TGAGCATGTCACCAATTAACAATAAT 57.935 30.769 0.00 0.00 33.06 1.28
4827 6238 7.459795 TGAGCATGTCACCAATTAACAATAA 57.540 32.000 0.00 0.00 0.00 1.40
4829 6240 5.981088 TGAGCATGTCACCAATTAACAAT 57.019 34.783 0.00 0.00 0.00 2.71
4842 6253 3.854666 AGTGACATACTGTGAGCATGTC 58.145 45.455 12.36 12.36 45.66 3.06
4843 6254 3.969287 AGTGACATACTGTGAGCATGT 57.031 42.857 0.00 0.00 38.49 3.21
4865 6276 6.174760 AGGTAGTAGTACATGGATCGAGATC 58.825 44.000 9.89 4.58 37.11 2.75
4866 6277 6.129414 AGGTAGTAGTACATGGATCGAGAT 57.871 41.667 9.89 0.00 0.00 2.75
4867 6278 5.563876 AGGTAGTAGTACATGGATCGAGA 57.436 43.478 9.89 0.00 0.00 4.04
4868 6279 5.531659 ACAAGGTAGTAGTACATGGATCGAG 59.468 44.000 9.89 0.00 0.00 4.04
4869 6280 5.443283 ACAAGGTAGTAGTACATGGATCGA 58.557 41.667 9.89 0.00 0.00 3.59
4870 6281 5.769484 ACAAGGTAGTAGTACATGGATCG 57.231 43.478 9.89 0.00 0.00 3.69
4871 6282 5.753921 GCAACAAGGTAGTAGTACATGGATC 59.246 44.000 9.89 0.00 0.00 3.36
4872 6283 5.188948 TGCAACAAGGTAGTAGTACATGGAT 59.811 40.000 9.89 0.00 0.00 3.41
4873 6284 4.528987 TGCAACAAGGTAGTAGTACATGGA 59.471 41.667 9.89 0.00 0.00 3.41
4874 6285 4.630069 GTGCAACAAGGTAGTAGTACATGG 59.370 45.833 9.89 2.68 36.32 3.66
4875 6286 5.479306 AGTGCAACAAGGTAGTAGTACATG 58.521 41.667 9.89 9.88 41.43 3.21
4876 6287 5.740290 AGTGCAACAAGGTAGTAGTACAT 57.260 39.130 9.89 0.00 41.43 2.29
4877 6288 5.771666 ACTAGTGCAACAAGGTAGTAGTACA 59.228 40.000 9.89 0.00 41.43 2.90
4906 6317 3.196254 TGATCTTCATCAGTGCAGCACTA 59.804 43.478 27.80 16.02 43.43 2.74
5235 6651 1.341383 GCATGTTCTGGGACCTCCATT 60.341 52.381 0.00 0.00 46.01 3.16
5236 6652 0.257039 GCATGTTCTGGGACCTCCAT 59.743 55.000 0.00 0.00 46.01 3.41
5321 6737 1.227497 GCGCCTTCCTGGAGATGAG 60.227 63.158 0.00 0.00 37.90 2.90
5440 6856 0.317479 ACTACAAGCTCGGCGAGTTT 59.683 50.000 34.41 31.90 33.57 2.66
5624 7040 1.079543 ACGCTGTGCAGGAGATGTC 60.080 57.895 1.11 0.00 0.00 3.06
5625 7041 1.079543 GACGCTGTGCAGGAGATGT 60.080 57.895 1.11 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.