Multiple sequence alignment - TraesCS7B01G139500

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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 TraesCS7B01G139500 chr7B 100.000 4861 0 0 1 4861 175999859 175994999 0.000000e+00 8977.0
1 TraesCS7B01G139500 chr7B 82.494 794 113 17 4079 4860 597188421 597189200 0.000000e+00 673.0
2 TraesCS7B01G139500 chr7B 86.818 220 24 5 2445 2662 175998495 175998711 1.750000e-59 241.0
3 TraesCS7B01G139500 chr7B 93.377 151 10 0 2508 2658 25333332 25333182 1.760000e-54 224.0
4 TraesCS7B01G139500 chr7B 89.441 161 15 2 2501 2660 155897706 155897547 8.250000e-48 202.0
5 TraesCS7B01G139500 chr5B 98.877 1514 17 0 1149 2662 239431279 239429766 0.000000e+00 2702.0
6 TraesCS7B01G139500 chr5B 82.948 821 111 17 4057 4853 450042993 450043808 0.000000e+00 713.0
7 TraesCS7B01G139500 chr5B 87.273 220 23 5 2445 2662 239431063 239431279 3.760000e-61 246.0
8 TraesCS7B01G139500 chr6A 97.891 1517 29 3 1148 2662 459869203 459870718 0.000000e+00 2621.0
9 TraesCS7B01G139500 chr6A 98.009 1507 26 4 1154 2658 6899424 6900928 0.000000e+00 2614.0
10 TraesCS7B01G139500 chr2A 97.756 1515 30 4 1148 2659 484295184 484296697 0.000000e+00 2606.0
11 TraesCS7B01G139500 chr2A 82.030 857 118 21 4026 4853 749525299 749526148 0.000000e+00 697.0
12 TraesCS7B01G139500 chr2A 81.797 857 121 21 4026 4853 532077134 532077984 0.000000e+00 686.0
13 TraesCS7B01G139500 chr2A 87.611 113 14 0 3370 3482 750963460 750963572 1.100000e-26 132.0
14 TraesCS7B01G139500 chr3B 96.836 1517 45 3 1149 2663 732888378 732886863 0.000000e+00 2532.0
15 TraesCS7B01G139500 chr3B 95.714 1400 56 4 1149 2545 684083473 684082075 0.000000e+00 2250.0
16 TraesCS7B01G139500 chr3B 83.740 861 110 20 4026 4860 694178713 694177857 0.000000e+00 787.0
17 TraesCS7B01G139500 chr3B 81.567 868 123 19 4017 4860 576020265 576019411 0.000000e+00 682.0
18 TraesCS7B01G139500 chr3B 86.636 217 23 6 1149 1362 732886864 732887077 8.130000e-58 235.0
19 TraesCS7B01G139500 chr1B 96.436 1515 52 2 1150 2662 420750101 420751615 0.000000e+00 2497.0
20 TraesCS7B01G139500 chr7D 91.919 1522 110 12 1148 2662 579547405 579548920 0.000000e+00 2117.0
21 TraesCS7B01G139500 chr7D 96.333 1227 39 1 2657 3877 220979520 220980746 0.000000e+00 2012.0
22 TraesCS7B01G139500 chr7D 94.927 1163 36 5 1 1141 220978376 220979537 0.000000e+00 1799.0
23 TraesCS7B01G139500 chr7D 88.767 454 41 6 3963 4413 220981104 220981550 9.200000e-152 547.0
24 TraesCS7B01G139500 chr4D 93.654 1308 76 7 1356 2659 391722860 391724164 0.000000e+00 1949.0
25 TraesCS7B01G139500 chr7A 94.845 1164 42 8 1 1148 235468091 235469252 0.000000e+00 1801.0
26 TraesCS7B01G139500 chr7A 93.631 1209 52 11 2663 3861 235469244 235470437 0.000000e+00 1783.0
27 TraesCS7B01G139500 chr7A 81.512 860 118 26 4020 4853 715930409 715931253 0.000000e+00 669.0
28 TraesCS7B01G139500 chr7A 85.802 162 15 2 2498 2659 438477248 438477401 1.080000e-36 165.0
29 TraesCS7B01G139500 chr7A 100.000 47 0 0 2612 2658 163226104 163226150 2.410000e-13 87.9
30 TraesCS7B01G139500 chr6D 84.211 855 105 14 4026 4854 97770842 97771692 0.000000e+00 804.0
31 TraesCS7B01G139500 chr6D 80.906 817 122 21 4022 4812 470969999 470970807 8.940000e-172 614.0
32 TraesCS7B01G139500 chr6B 83.455 822 106 16 4057 4853 51135726 51134910 0.000000e+00 737.0
33 TraesCS7B01G139500 chr6B 90.062 161 13 1 2501 2658 6671140 6670980 6.380000e-49 206.0
34 TraesCS7B01G139500 chr6B 88.690 168 17 2 2494 2661 666222723 666222558 2.290000e-48 204.0
35 TraesCS7B01G139500 chr5A 82.143 840 115 23 4041 4853 654558775 654559606 0.000000e+00 688.0
36 TraesCS7B01G139500 chr5D 82.687 774 104 17 4048 4797 530850207 530850974 0.000000e+00 660.0
37 TraesCS7B01G139500 chr5D 83.234 334 49 7 4057 4386 9103925 9104255 2.840000e-77 300.0
38 TraesCS7B01G139500 chr2B 81.062 866 125 22 4026 4860 349932091 349932948 0.000000e+00 654.0
39 TraesCS7B01G139500 chr2B 89.286 168 17 1 2498 2664 579799382 579799549 4.930000e-50 209.0
40 TraesCS7B01G139500 chr3D 83.871 620 73 15 4026 4620 581084250 581083633 2.540000e-157 566.0


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 TraesCS7B01G139500 chr7B 175994999 175999859 4860 True 8977.000000 8977 100.000000 1 4861 1 chr7B.!!$R3 4860
1 TraesCS7B01G139500 chr7B 597188421 597189200 779 False 673.000000 673 82.494000 4079 4860 1 chr7B.!!$F2 781
2 TraesCS7B01G139500 chr5B 239429766 239431279 1513 True 2702.000000 2702 98.877000 1149 2662 1 chr5B.!!$R1 1513
3 TraesCS7B01G139500 chr5B 450042993 450043808 815 False 713.000000 713 82.948000 4057 4853 1 chr5B.!!$F2 796
4 TraesCS7B01G139500 chr6A 459869203 459870718 1515 False 2621.000000 2621 97.891000 1148 2662 1 chr6A.!!$F2 1514
5 TraesCS7B01G139500 chr6A 6899424 6900928 1504 False 2614.000000 2614 98.009000 1154 2658 1 chr6A.!!$F1 1504
6 TraesCS7B01G139500 chr2A 484295184 484296697 1513 False 2606.000000 2606 97.756000 1148 2659 1 chr2A.!!$F1 1511
7 TraesCS7B01G139500 chr2A 749525299 749526148 849 False 697.000000 697 82.030000 4026 4853 1 chr2A.!!$F3 827
8 TraesCS7B01G139500 chr2A 532077134 532077984 850 False 686.000000 686 81.797000 4026 4853 1 chr2A.!!$F2 827
9 TraesCS7B01G139500 chr3B 732886863 732888378 1515 True 2532.000000 2532 96.836000 1149 2663 1 chr3B.!!$R4 1514
10 TraesCS7B01G139500 chr3B 684082075 684083473 1398 True 2250.000000 2250 95.714000 1149 2545 1 chr3B.!!$R2 1396
11 TraesCS7B01G139500 chr3B 694177857 694178713 856 True 787.000000 787 83.740000 4026 4860 1 chr3B.!!$R3 834
12 TraesCS7B01G139500 chr3B 576019411 576020265 854 True 682.000000 682 81.567000 4017 4860 1 chr3B.!!$R1 843
13 TraesCS7B01G139500 chr1B 420750101 420751615 1514 False 2497.000000 2497 96.436000 1150 2662 1 chr1B.!!$F1 1512
14 TraesCS7B01G139500 chr7D 579547405 579548920 1515 False 2117.000000 2117 91.919000 1148 2662 1 chr7D.!!$F1 1514
15 TraesCS7B01G139500 chr7D 220978376 220981550 3174 False 1452.666667 2012 93.342333 1 4413 3 chr7D.!!$F2 4412
16 TraesCS7B01G139500 chr4D 391722860 391724164 1304 False 1949.000000 1949 93.654000 1356 2659 1 chr4D.!!$F1 1303
17 TraesCS7B01G139500 chr7A 235468091 235470437 2346 False 1792.000000 1801 94.238000 1 3861 2 chr7A.!!$F4 3860
18 TraesCS7B01G139500 chr7A 715930409 715931253 844 False 669.000000 669 81.512000 4020 4853 1 chr7A.!!$F3 833
19 TraesCS7B01G139500 chr6D 97770842 97771692 850 False 804.000000 804 84.211000 4026 4854 1 chr6D.!!$F1 828
20 TraesCS7B01G139500 chr6D 470969999 470970807 808 False 614.000000 614 80.906000 4022 4812 1 chr6D.!!$F2 790
21 TraesCS7B01G139500 chr6B 51134910 51135726 816 True 737.000000 737 83.455000 4057 4853 1 chr6B.!!$R2 796
22 TraesCS7B01G139500 chr5A 654558775 654559606 831 False 688.000000 688 82.143000 4041 4853 1 chr5A.!!$F1 812
23 TraesCS7B01G139500 chr5D 530850207 530850974 767 False 660.000000 660 82.687000 4048 4797 1 chr5D.!!$F2 749
24 TraesCS7B01G139500 chr2B 349932091 349932948 857 False 654.000000 654 81.062000 4026 4860 1 chr2B.!!$F1 834
25 TraesCS7B01G139500 chr3D 581083633 581084250 617 True 566.000000 566 83.871000 4026 4620 1 chr3D.!!$R1 594

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
549 550 0.254178 AAGATGTACCCTGCCTGCAG 59.746 55.000 12.17 12.17 43.26 4.41 F
1089 1113 2.165998 GCACAGCCATTCTCTTCCTTT 58.834 47.619 0.00 0.00 0.00 3.11 F
1699 1723 0.108019 GAACCAAACCACTCGGAGGT 59.892 55.000 10.23 0.00 42.34 3.85 F
2725 2815 1.884464 CCACATCGGCCAGATCACG 60.884 63.158 2.24 0.00 37.52 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1626 2.573869 CGAGTGCACCGGATGTCT 59.426 61.111 14.63 6.07 0.0 3.41 R
2861 2961 0.827089 CAAGGCAATGGTGGTGGTGA 60.827 55.000 0.00 0.00 0.0 4.02 R
2892 2998 0.868406 GTGACGGCAACAAGGAAGAG 59.132 55.000 0.00 0.00 0.0 2.85 R
4414 4811 0.108329 ACGACTGGGTCCTTATTGCG 60.108 55.000 0.00 0.00 0.0 4.85 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
49 50 2.492088 TCTCACCATACACCAGTTCTCG 59.508 50.000 0.00 0.00 0.00 4.04
59 60 1.625818 ACCAGTTCTCGCATTTCCTCT 59.374 47.619 0.00 0.00 0.00 3.69
130 131 1.743996 GCCCTGATGTTTGAGAGACC 58.256 55.000 0.00 0.00 0.00 3.85
276 277 6.710744 TGGTAATCAGAGAAGTTTTTCCTGAC 59.289 38.462 0.00 0.00 40.33 3.51
302 303 7.307396 CGACCAAGCTACTATAACATTCATTGG 60.307 40.741 0.00 0.00 39.43 3.16
426 427 3.549299 AGAAGAAGCAGCAAAACGATG 57.451 42.857 0.00 0.00 0.00 3.84
529 530 0.987081 AGACCCTGCATCTCTGGCAT 60.987 55.000 0.00 0.00 41.06 4.40
541 542 3.928754 TCTCTGGCATAAGATGTACCCT 58.071 45.455 0.00 0.00 0.00 4.34
549 550 0.254178 AAGATGTACCCTGCCTGCAG 59.746 55.000 12.17 12.17 43.26 4.41
573 586 4.754667 GGGACTCCGGTTGGTCGC 62.755 72.222 19.01 19.01 38.01 5.19
817 831 4.633565 GTGAGAATTGTTAGCTTGGAGGAG 59.366 45.833 0.00 0.00 0.00 3.69
832 846 2.170607 GGAGGAGCAGGTGCATAACTTA 59.829 50.000 4.48 0.00 45.16 2.24
834 848 3.873952 GAGGAGCAGGTGCATAACTTAAG 59.126 47.826 4.48 0.00 45.16 1.85
837 851 4.442706 GAGCAGGTGCATAACTTAAGCTA 58.557 43.478 1.29 0.00 45.16 3.32
845 859 7.287927 AGGTGCATAACTTAAGCTAGTCAGATA 59.712 37.037 1.29 0.00 0.00 1.98
996 1010 3.112709 GTTGCCGAGACAGCGACC 61.113 66.667 0.00 0.00 38.48 4.79
1089 1113 2.165998 GCACAGCCATTCTCTTCCTTT 58.834 47.619 0.00 0.00 0.00 3.11
1141 1165 2.773993 TAAAATCGCGAGGGAAAGGT 57.226 45.000 16.66 0.00 0.00 3.50
1473 1497 2.983402 ATCTTCGTCTCGTCGAAACA 57.017 45.000 0.00 4.95 46.55 2.83
1511 1535 4.730949 AAATCGTCTTAATCCGAGGTCA 57.269 40.909 3.49 0.00 36.41 4.02
1699 1723 0.108019 GAACCAAACCACTCGGAGGT 59.892 55.000 10.23 0.00 42.34 3.85
2691 2781 2.039624 ATCCCGCCTCTGACACCT 59.960 61.111 0.00 0.00 0.00 4.00
2700 2790 3.402681 CTGACACCTCGGCCCCAT 61.403 66.667 0.00 0.00 0.00 4.00
2725 2815 1.884464 CCACATCGGCCAGATCACG 60.884 63.158 2.24 0.00 37.52 4.35
2861 2961 4.451150 ATGCCGTCGTCGCACCAT 62.451 61.111 0.00 0.00 35.54 3.55
2892 2998 1.201429 TTGCCTTGTCCTCCTCCTCC 61.201 60.000 0.00 0.00 0.00 4.30
3295 3401 1.226323 CGATCTCCTTCGCGTTCGT 60.226 57.895 5.77 0.00 36.96 3.85
3633 3739 2.355363 CGAGGAACGACGCCAACA 60.355 61.111 0.00 0.00 45.77 3.33
3635 3741 1.300697 GAGGAACGACGCCAACACT 60.301 57.895 0.00 0.00 0.00 3.55
3830 3936 1.435256 AGGGACTGTGTAGCAAAGGT 58.565 50.000 0.00 0.00 37.18 3.50
3869 3975 0.608640 ACCAGGAGTAGTCGGCTTTG 59.391 55.000 0.00 0.00 0.00 2.77
3887 3993 4.712425 GCGTGGCCTGCTTTGCTG 62.712 66.667 3.32 0.00 0.00 4.41
3888 3994 4.712425 CGTGGCCTGCTTTGCTGC 62.712 66.667 3.32 0.00 0.00 5.25
3889 3995 4.712425 GTGGCCTGCTTTGCTGCG 62.712 66.667 3.32 0.00 35.36 5.18
3892 3998 3.434319 GCCTGCTTTGCTGCGCTA 61.434 61.111 9.73 0.00 35.36 4.26
3909 4031 6.268825 TGCGCTATTGTTGGGTTTATAAAA 57.731 33.333 9.73 0.00 0.00 1.52
3911 4033 6.809196 TGCGCTATTGTTGGGTTTATAAAAAG 59.191 34.615 9.73 0.00 0.00 2.27
3920 4044 9.974980 TGTTGGGTTTATAAAAAGAAACTCATC 57.025 29.630 0.00 2.11 43.64 2.92
3921 4045 9.124807 GTTGGGTTTATAAAAAGAAACTCATCG 57.875 33.333 0.00 0.00 43.64 3.84
3923 4047 8.293867 TGGGTTTATAAAAAGAAACTCATCGTG 58.706 33.333 0.00 0.00 40.30 4.35
3939 4227 8.895932 ACTCATCGTGTTTTAAAATTAGATGC 57.104 30.769 23.16 6.57 35.53 3.91
3945 4233 9.828852 TCGTGTTTTAAAATTAGATGCGTTATT 57.171 25.926 3.52 0.00 0.00 1.40
4052 4431 3.328382 AAGCACGTCTAAGCATACCAA 57.672 42.857 0.00 0.00 0.00 3.67
4132 4514 3.935872 CGCACACACCACACCACG 61.936 66.667 0.00 0.00 0.00 4.94
4185 4567 4.092675 GCAAAGCAAGCTACAACACAAAAA 59.907 37.500 0.00 0.00 0.00 1.94
4218 4600 3.688330 GACACACACACCGCGTCG 61.688 66.667 4.92 0.00 0.00 5.12
4249 4632 1.003233 GGACATTTCCGAAGACCACCT 59.997 52.381 0.00 0.00 29.98 4.00
4266 4649 3.195825 CCACCTCTTTCCGTAGAACATCT 59.804 47.826 0.00 0.00 0.00 2.90
4268 4651 3.447944 ACCTCTTTCCGTAGAACATCTCC 59.552 47.826 0.00 0.00 0.00 3.71
4287 4670 2.048597 GTCGACGCACCATCCACA 60.049 61.111 0.00 0.00 0.00 4.17
4302 4685 0.037326 CCACACTGAGCGCCTAAGAA 60.037 55.000 2.29 0.00 0.00 2.52
4385 4782 1.879737 TAGCGCCGCAAAGTACCAGA 61.880 55.000 13.36 0.00 0.00 3.86
4430 4827 1.141053 GGATCGCAATAAGGACCCAGT 59.859 52.381 0.00 0.00 0.00 4.00
4471 4871 2.031807 CCAACAGAGATACGACGTCGAT 59.968 50.000 41.52 28.74 43.02 3.59
4487 4887 1.075979 CGATGACGCCGTCAATGTGA 61.076 55.000 25.07 0.00 45.96 3.58
4511 4913 4.673580 CGATCCAACTGAATCAAGGCTTTG 60.674 45.833 1.35 1.35 35.57 2.77
4525 4927 1.377994 CTTTGGCCCAGAGACAGCT 59.622 57.895 0.00 0.00 0.00 4.24
4539 4941 3.177228 AGACAGCTACCAACTCCAAGAT 58.823 45.455 0.00 0.00 0.00 2.40
4550 4953 0.329261 CTCCAAGATGTGAGGGGCAA 59.671 55.000 0.00 0.00 0.00 4.52
4553 4956 0.038744 CAAGATGTGAGGGGCAAGGT 59.961 55.000 0.00 0.00 0.00 3.50
4555 4958 0.842030 AGATGTGAGGGGCAAGGTGA 60.842 55.000 0.00 0.00 0.00 4.02
4666 5070 1.878070 CATTGCACATCACCACGCT 59.122 52.632 0.00 0.00 0.00 5.07
4676 5080 3.189287 ACATCACCACGCTTCTTGAAATC 59.811 43.478 0.00 0.00 0.00 2.17
4677 5081 3.126001 TCACCACGCTTCTTGAAATCT 57.874 42.857 0.00 0.00 0.00 2.40
4732 5136 0.723981 CCGCAACTCTAAGCAGAAGC 59.276 55.000 0.00 0.00 42.56 3.86
4739 5143 0.603065 TCTAAGCAGAAGCAGTCGCA 59.397 50.000 0.00 0.00 45.49 5.10
4771 5176 4.539083 ACGACCGGCTGCACAACA 62.539 61.111 0.00 0.00 0.00 3.33
4825 5231 0.944386 CTGGACAGAAACCACAACCG 59.056 55.000 0.00 0.00 33.57 4.44
4843 5249 4.020617 CCCGCACCTCTGGCAAGA 62.021 66.667 0.00 0.00 0.00 3.02
4860 5266 0.987294 AGATCCAAGACCACCCACAG 59.013 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.198853 AGAGGTTGGAGTAGAGGAAATGC 59.801 47.826 0.00 0.00 0.00 3.56
59 60 2.759355 CATGGGGTAGAGGTTGGAGTA 58.241 52.381 0.00 0.00 0.00 2.59
276 277 7.307396 CCAATGAATGTTATAGTAGCTTGGTCG 60.307 40.741 0.00 0.00 0.00 4.79
302 303 3.976306 GCATTTTGTTTTTGCTCCATTGC 59.024 39.130 0.00 0.00 33.61 3.56
426 427 3.559238 GATCGAGCTGGAGATCTTCTC 57.441 52.381 4.31 4.24 42.66 2.87
529 530 1.486310 CTGCAGGCAGGGTACATCTTA 59.514 52.381 13.39 0.00 40.17 2.10
549 550 1.228154 AACCGGAGTCCCTTGTTGC 60.228 57.895 9.46 0.00 0.00 4.17
817 831 4.192317 ACTAGCTTAAGTTATGCACCTGC 58.808 43.478 19.55 0.00 42.50 4.85
832 846 6.015519 GTGATCCATGACTATCTGACTAGCTT 60.016 42.308 0.00 0.00 0.00 3.74
834 848 5.476599 AGTGATCCATGACTATCTGACTAGC 59.523 44.000 0.00 0.00 0.00 3.42
837 851 4.039004 GCAGTGATCCATGACTATCTGACT 59.961 45.833 0.00 0.00 0.00 3.41
845 859 0.463204 CCTCGCAGTGATCCATGACT 59.537 55.000 0.00 0.00 0.00 3.41
980 994 4.373116 GGGTCGCTGTCTCGGCAA 62.373 66.667 1.60 0.00 35.49 4.52
1089 1113 3.071206 GGTGAGGCGAGGCTGAGA 61.071 66.667 3.24 0.00 0.00 3.27
1511 1535 6.364701 TGTTTTGGCTCTATAGGTTGCATAT 58.635 36.000 0.00 0.00 0.00 1.78
1602 1626 2.573869 CGAGTGCACCGGATGTCT 59.426 61.111 14.63 6.07 0.00 3.41
2700 2790 4.408821 GGCCGATGTGGACCTGCA 62.409 66.667 0.00 0.00 41.58 4.41
2725 2815 2.315386 GGTTTGACTCGTGGCGGTC 61.315 63.158 0.00 0.00 0.00 4.79
2861 2961 0.827089 CAAGGCAATGGTGGTGGTGA 60.827 55.000 0.00 0.00 0.00 4.02
2892 2998 0.868406 GTGACGGCAACAAGGAAGAG 59.132 55.000 0.00 0.00 0.00 2.85
2965 3071 4.787280 CCTCCTCCTGCGGGGACT 62.787 72.222 12.87 0.00 39.58 3.85
3335 3441 1.677552 GGACCTCGGAAAGAAGCCA 59.322 57.895 0.00 0.00 0.00 4.75
3815 3921 0.537371 GGCCACCTTTGCTACACAGT 60.537 55.000 0.00 0.00 0.00 3.55
3821 3927 1.295423 GAGACGGCCACCTTTGCTA 59.705 57.895 2.24 0.00 0.00 3.49
3872 3978 4.712425 CGCAGCAAAGCAGGCCAC 62.712 66.667 5.01 0.00 0.00 5.01
3885 3991 5.493133 TTATAAACCCAACAATAGCGCAG 57.507 39.130 11.47 0.00 0.00 5.18
3886 3992 5.899120 TTTATAAACCCAACAATAGCGCA 57.101 34.783 11.47 0.00 0.00 6.09
3887 3993 7.030768 TCTTTTTATAAACCCAACAATAGCGC 58.969 34.615 0.00 0.00 0.00 5.92
3888 3994 8.973835 TTCTTTTTATAAACCCAACAATAGCG 57.026 30.769 0.00 0.00 0.00 4.26
4032 4408 3.328382 TTGGTATGCTTAGACGTGCTT 57.672 42.857 0.00 0.00 0.00 3.91
4035 4414 5.607119 AAGTTTTGGTATGCTTAGACGTG 57.393 39.130 0.00 0.00 0.00 4.49
4090 4469 0.725784 CGTTGTTCGCAATGAGTGGC 60.726 55.000 0.00 0.00 44.64 5.01
4132 4514 2.069273 CGTCTGTGGACTTGATCAACC 58.931 52.381 3.38 6.09 40.10 3.77
4185 4567 4.256920 GTGTGTCAGCTGAGGATATGTTT 58.743 43.478 18.89 0.00 0.00 2.83
4235 4618 1.346722 GGAAAGAGGTGGTCTTCGGAA 59.653 52.381 0.00 0.00 45.44 4.30
4249 4632 4.087182 ACAGGAGATGTTCTACGGAAAGA 58.913 43.478 0.00 0.00 39.96 2.52
4266 4649 2.571757 GATGGTGCGTCGACAGGA 59.428 61.111 17.16 6.94 0.00 3.86
4268 4651 2.094659 GTGGATGGTGCGTCGACAG 61.095 63.158 17.16 9.59 30.38 3.51
4287 4670 1.896465 ACTTCTTCTTAGGCGCTCAGT 59.104 47.619 7.64 0.00 0.00 3.41
4302 4685 1.302832 CCTTCCGCTTGCCACTTCT 60.303 57.895 0.00 0.00 0.00 2.85
4334 4717 1.819229 CCGGTGTCTCCCTCAGATG 59.181 63.158 0.00 0.00 32.08 2.90
4385 4782 0.535335 TGTTCGCCGCTATCCTCTTT 59.465 50.000 0.00 0.00 0.00 2.52
4413 4810 0.174845 CGACTGGGTCCTTATTGCGA 59.825 55.000 0.00 0.00 0.00 5.10
4414 4811 0.108329 ACGACTGGGTCCTTATTGCG 60.108 55.000 0.00 0.00 0.00 4.85
4471 4871 3.945436 GTCACATTGACGGCGTCA 58.055 55.556 36.29 36.29 41.09 4.35
4479 4879 3.676291 TCAGTTGGATCGTCACATTGA 57.324 42.857 0.00 0.00 0.00 2.57
4487 4887 2.026822 AGCCTTGATTCAGTTGGATCGT 60.027 45.455 6.61 0.00 0.00 3.73
4511 4913 1.553690 TTGGTAGCTGTCTCTGGGCC 61.554 60.000 0.00 0.00 0.00 5.80
4516 4918 2.310779 TGGAGTTGGTAGCTGTCTCT 57.689 50.000 0.00 0.00 0.00 3.10
4525 4927 2.571653 CCCTCACATCTTGGAGTTGGTA 59.428 50.000 0.00 0.00 0.00 3.25
4539 4941 1.150536 GTTCACCTTGCCCCTCACA 59.849 57.895 0.00 0.00 0.00 3.58
4550 4953 4.681978 GCCGAGGCGTGTTCACCT 62.682 66.667 0.00 0.00 39.65 4.00
4620 5023 4.032960 TGAAAATCTTGCTTGGCTCCTA 57.967 40.909 0.00 0.00 0.00 2.94
4623 5026 3.733077 CGGATGAAAATCTTGCTTGGCTC 60.733 47.826 0.00 0.00 0.00 4.70
4666 5070 2.293122 CGGTGTTGCCAGATTTCAAGAA 59.707 45.455 0.00 0.00 36.97 2.52
4676 5080 1.468520 CTAATTGGACGGTGTTGCCAG 59.531 52.381 0.00 0.00 36.97 4.85
4677 5081 1.529226 CTAATTGGACGGTGTTGCCA 58.471 50.000 0.00 0.00 36.97 4.92
4711 5115 2.674177 GCTTCTGCTTAGAGTTGCGGTA 60.674 50.000 0.00 0.00 36.94 4.02
4739 5143 0.942884 GTCGTCGGTCTTCGGCTTTT 60.943 55.000 0.00 0.00 42.07 2.27
4785 5190 2.112297 GGGAGTTTGGTGCGGTCA 59.888 61.111 0.00 0.00 0.00 4.02
4786 5191 1.966451 CTGGGAGTTTGGTGCGGTC 60.966 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.