Multiple sequence alignment - TraesCS7D01G320300

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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 TraesCS7D01G320300 chr7D 100.000 2966 0 0 1 2966 410061549 410058584 0.000000e+00 5478
1 TraesCS7D01G320300 chr7D 100.000 1535 0 0 3313 4847 410058237 410056703 0.000000e+00 2835
2 TraesCS7D01G320300 chr7D 96.250 640 24 0 1 640 410066481 410065842 0.000000e+00 1050
3 TraesCS7D01G320300 chr7D 96.250 640 23 1 1 640 607000579 606999941 0.000000e+00 1048
4 TraesCS7D01G320300 chr7D 89.844 128 13 0 4628 4755 190130315 190130442 1.080000e-36 165
5 TraesCS7D01G320300 chr7D 96.250 80 3 0 3564 3643 444363112 444363191 1.090000e-26 132
6 TraesCS7D01G320300 chr7D 95.000 80 4 0 3564 3643 444363196 444363117 5.090000e-25 126
7 TraesCS7D01G320300 chr7D 93.827 81 5 0 3563 3643 410057901 410057981 6.590000e-24 122
8 TraesCS7D01G320300 chr7B 96.392 2328 72 5 638 2954 425473278 425475604 0.000000e+00 3823
9 TraesCS7D01G320300 chr7B 91.327 1326 54 10 3319 4633 425475620 425476895 0.000000e+00 1755
10 TraesCS7D01G320300 chr7B 92.500 80 6 0 3564 3643 461222224 461222303 1.100000e-21 115
11 TraesCS7D01G320300 chr7B 92.500 80 6 0 3564 3643 461222308 461222229 1.100000e-21 115
12 TraesCS7D01G320300 chr7B 91.358 81 4 2 4752 4829 425476896 425476976 1.840000e-19 108
13 TraesCS7D01G320300 chr7A 96.398 2332 47 13 638 2966 472121728 472124025 0.000000e+00 3807
14 TraesCS7D01G320300 chr7A 95.231 671 23 2 3704 4374 472124534 472125195 0.000000e+00 1053
15 TraesCS7D01G320300 chr7A 96.233 292 9 1 3313 3602 472124096 472124387 1.220000e-130 477
16 TraesCS7D01G320300 chr7A 92.157 153 12 0 4372 4524 472159525 472159677 2.940000e-52 217
17 TraesCS7D01G320300 chr7A 96.875 64 2 0 3642 3705 472124388 472124451 1.840000e-19 108
18 TraesCS7D01G320300 chr3D 96.677 632 20 1 1 632 591170314 591170944 0.000000e+00 1050
19 TraesCS7D01G320300 chr3D 95.788 641 25 2 1 640 7570266 7569627 0.000000e+00 1033
20 TraesCS7D01G320300 chr3D 91.667 84 7 0 3564 3647 523844523 523844606 3.070000e-22 117
21 TraesCS7D01G320300 chr6D 96.094 640 23 2 1 640 446734915 446734278 0.000000e+00 1042
22 TraesCS7D01G320300 chr6D 95.925 638 25 1 1 638 446730000 446729364 0.000000e+00 1033
23 TraesCS7D01G320300 chr5D 95.944 641 23 3 1 640 496923187 496923825 0.000000e+00 1037
24 TraesCS7D01G320300 chr5D 95.504 645 26 2 1 645 420453609 420452968 0.000000e+00 1027
25 TraesCS7D01G320300 chr1D 95.938 640 25 1 1 640 470896864 470897502 0.000000e+00 1037
26 TraesCS7D01G320300 chr5B 90.551 127 12 0 4622 4748 27357000 27357126 8.340000e-38 169
27 TraesCS7D01G320300 chr5B 89.922 129 13 0 4628 4756 276944663 276944791 3.000000e-37 167
28 TraesCS7D01G320300 chr5B 89.313 131 14 0 4624 4754 689670615 689670745 1.080000e-36 165
29 TraesCS7D01G320300 chr2B 89.474 133 14 0 4624 4756 20671902 20672034 8.340000e-38 169
30 TraesCS7D01G320300 chr2B 88.722 133 15 0 4622 4754 77863000 77863132 3.880000e-36 163
31 TraesCS7D01G320300 chr6B 89.922 129 13 0 4627 4755 629166437 629166565 3.000000e-37 167
32 TraesCS7D01G320300 chr6B 89.231 130 14 0 4627 4756 717007454 717007325 3.880000e-36 163
33 TraesCS7D01G320300 chr2D 88.406 138 12 4 4633 4768 565942827 565942962 3.880000e-36 163
34 TraesCS7D01G320300 chr4B 93.590 78 3 2 3567 3643 604049695 604049619 1.100000e-21 115
35 TraesCS7D01G320300 chr3A 90.476 84 8 0 3564 3647 658755079 658755162 1.430000e-20 111
36 TraesCS7D01G320300 chr4A 89.011 91 7 3 3564 3652 85905013 85904924 5.130000e-20 110


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 TraesCS7D01G320300 chr7D 410056703 410061549 4846 True 4156.500000 5478 100.000000 1 4847 2 chr7D.!!$R4 4846
1 TraesCS7D01G320300 chr7D 410065842 410066481 639 True 1050.000000 1050 96.250000 1 640 1 chr7D.!!$R1 639
2 TraesCS7D01G320300 chr7D 606999941 607000579 638 True 1048.000000 1048 96.250000 1 640 1 chr7D.!!$R3 639
3 TraesCS7D01G320300 chr7B 425473278 425476976 3698 False 1895.333333 3823 93.025667 638 4829 3 chr7B.!!$F2 4191
4 TraesCS7D01G320300 chr7A 472121728 472125195 3467 False 1361.250000 3807 96.184250 638 4374 4 chr7A.!!$F2 3736
5 TraesCS7D01G320300 chr3D 591170314 591170944 630 False 1050.000000 1050 96.677000 1 632 1 chr3D.!!$F2 631
6 TraesCS7D01G320300 chr3D 7569627 7570266 639 True 1033.000000 1033 95.788000 1 640 1 chr3D.!!$R1 639
7 TraesCS7D01G320300 chr6D 446734278 446734915 637 True 1042.000000 1042 96.094000 1 640 1 chr6D.!!$R2 639
8 TraesCS7D01G320300 chr6D 446729364 446730000 636 True 1033.000000 1033 95.925000 1 638 1 chr6D.!!$R1 637
9 TraesCS7D01G320300 chr5D 496923187 496923825 638 False 1037.000000 1037 95.944000 1 640 1 chr5D.!!$F1 639
10 TraesCS7D01G320300 chr5D 420452968 420453609 641 True 1027.000000 1027 95.504000 1 645 1 chr5D.!!$R1 644
11 TraesCS7D01G320300 chr1D 470896864 470897502 638 False 1037.000000 1037 95.938000 1 640 1 chr1D.!!$F1 639

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
569 571 0.538287 GAAGTGGGCTTCTGCACCTT 60.538 55.000 0.58 0.00 45.68 3.50 F
1254 1265 0.687757 TATGCCGCTTCCTCCACTCT 60.688 55.000 0.00 0.00 0.00 3.24 F
1952 1963 1.134367 CAGCAAGCATCTGTCATTGGG 59.866 52.381 0.00 0.00 0.00 4.12 F
2935 2952 0.394192 CACCCTGTGCTCTGAACAGA 59.606 55.000 10.35 4.45 46.55 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1854 0.975556 TACCCAGCCATCGCAGAGAA 60.976 55.000 0.00 0.0 43.63 2.87 R
2175 2186 1.756538 GAGAGGAGCAGGAAGAAGAGG 59.243 57.143 0.00 0.0 0.00 3.69 R
3810 3922 1.135199 TGTTCATCGAGTTAGGCCGTC 60.135 52.381 0.00 0.0 0.00 4.79 R
4382 4494 0.176680 CTGGAGCTGCCTACACGATT 59.823 55.000 1.53 0.0 37.63 3.34 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
406 408 6.069963 CCTTCAATCTTCCTCTTCTTCCCTTA 60.070 42.308 0.00 0.00 0.00 2.69
425 427 5.164954 CCTTACTCTCTTGGTTTTCTCTCG 58.835 45.833 0.00 0.00 0.00 4.04
465 467 6.147164 GGATGAACTGATTTTCGTCACACTTA 59.853 38.462 7.24 0.00 41.52 2.24
505 507 1.147817 GGGTAAAGCATCCCCATCCAT 59.852 52.381 0.00 0.00 38.37 3.41
507 509 3.308401 GGTAAAGCATCCCCATCCATTT 58.692 45.455 0.00 0.00 0.00 2.32
551 553 5.102783 ACCCTAGGTCATAACTCTAATGGGA 60.103 44.000 8.29 0.00 34.27 4.37
569 571 0.538287 GAAGTGGGCTTCTGCACCTT 60.538 55.000 0.58 0.00 45.68 3.50
618 621 1.222936 CATCTCCTCACAGCCCACC 59.777 63.158 0.00 0.00 0.00 4.61
623 626 1.915266 CCTCACAGCCCACCTGAGA 60.915 63.158 0.00 0.00 44.64 3.27
632 635 2.050144 GCCCACCTGAGAAGGATATCA 58.950 52.381 4.83 0.00 0.00 2.15
635 638 3.181461 CCCACCTGAGAAGGATATCACAC 60.181 52.174 4.83 0.00 0.00 3.82
658 661 7.761038 ACCAAAGTGATACCCTTTCTTTTAG 57.239 36.000 0.00 0.00 29.89 1.85
713 720 7.010160 TGTTTCCCAAAGAAATAGGAAGACAT 58.990 34.615 0.00 0.00 45.99 3.06
736 743 1.134521 TGGCCGATAAGCACGAAATCT 60.135 47.619 0.00 0.00 0.00 2.40
752 759 3.644966 AATCTCCCGGAAAGTTGCATA 57.355 42.857 0.73 0.00 0.00 3.14
753 760 3.864789 ATCTCCCGGAAAGTTGCATAT 57.135 42.857 0.73 0.00 0.00 1.78
939 950 3.225940 AGGTGGAGAAAAGAAAAGGCAG 58.774 45.455 0.00 0.00 0.00 4.85
1254 1265 0.687757 TATGCCGCTTCCTCCACTCT 60.688 55.000 0.00 0.00 0.00 3.24
1717 1728 2.667318 CGTGAGGCGATGTTGCGTT 61.667 57.895 0.00 0.00 44.77 4.84
1952 1963 1.134367 CAGCAAGCATCTGTCATTGGG 59.866 52.381 0.00 0.00 0.00 4.12
2175 2186 3.373565 CGCAAACCAGGGAAGGCC 61.374 66.667 0.00 0.00 0.00 5.19
2406 2417 0.546598 AGGGCATTGCTACTGGGTAC 59.453 55.000 8.82 0.00 0.00 3.34
2451 2462 1.071071 CCCGGGTCACTGTTTGTTCTA 59.929 52.381 14.18 0.00 0.00 2.10
2697 2708 7.981789 GTCATAGTTGATTACAGATTCCAGACA 59.018 37.037 0.00 0.00 33.56 3.41
2725 2741 7.745594 CCAATTGCTGGTTAATTTGAAAAATCG 59.254 33.333 0.00 0.00 40.78 3.34
2756 2772 2.289274 TGTTGCGACATGTACCAAACTG 59.711 45.455 1.50 0.00 0.00 3.16
2757 2773 2.535012 TGCGACATGTACCAAACTGA 57.465 45.000 0.00 0.00 0.00 3.41
2766 2782 5.763204 ACATGTACCAAACTGAAACTGGTAG 59.237 40.000 0.00 0.00 44.39 3.18
2769 2785 3.626930 ACCAAACTGAAACTGGTAGCAA 58.373 40.909 0.00 0.00 41.72 3.91
2935 2952 0.394192 CACCCTGTGCTCTGAACAGA 59.606 55.000 10.35 4.45 46.55 3.41
2957 2974 2.541556 GACTTCGTCATGACTAAGGGC 58.458 52.381 31.87 23.19 38.12 5.19
3509 3535 4.677779 AAACCTTAGTTGTTGCACTGCAAG 60.678 41.667 16.91 5.38 41.68 4.01
3549 3577 7.917720 TTTTTAAAGACTAACCATTTGCGAC 57.082 32.000 0.00 0.00 0.00 5.19
3602 3630 3.955771 TGTAAGACGTTTTGGCAGTTC 57.044 42.857 0.83 0.00 0.00 3.01
3603 3631 3.271729 TGTAAGACGTTTTGGCAGTTCA 58.728 40.909 0.83 0.00 0.00 3.18
3604 3632 3.690139 TGTAAGACGTTTTGGCAGTTCAA 59.310 39.130 0.83 0.00 0.00 2.69
3605 3633 3.859411 AAGACGTTTTGGCAGTTCAAA 57.141 38.095 0.00 0.00 35.15 2.69
3606 3634 4.385358 AAGACGTTTTGGCAGTTCAAAT 57.615 36.364 0.00 0.00 36.63 2.32
3607 3635 4.385358 AGACGTTTTGGCAGTTCAAATT 57.615 36.364 0.00 0.00 36.63 1.82
3608 3636 4.111916 AGACGTTTTGGCAGTTCAAATTG 58.888 39.130 0.00 0.00 36.63 2.32
3609 3637 4.109050 GACGTTTTGGCAGTTCAAATTGA 58.891 39.130 0.00 0.00 36.63 2.57
3697 3725 5.632244 TCTTCAATTGATGACATGGTGTG 57.368 39.130 17.55 0.00 37.92 3.82
3699 3727 5.947566 TCTTCAATTGATGACATGGTGTGAT 59.052 36.000 17.55 0.00 37.92 3.06
3810 3922 4.082274 TCATTGTTGCGCTACTCATTTG 57.918 40.909 22.01 12.07 0.00 2.32
3822 3934 2.973945 ACTCATTTGACGGCCTAACTC 58.026 47.619 0.00 0.00 0.00 3.01
4090 4202 7.334421 GGAAATGGCATCGATATACATAACTGT 59.666 37.037 0.00 0.00 39.49 3.55
4115 4227 8.903820 GTTATGTCCTTATCTTGGTTATTTGCT 58.096 33.333 0.00 0.00 0.00 3.91
4132 4244 5.971895 TTTGCTTGCTTCTGCTTTAAAAG 57.028 34.783 0.00 0.00 40.48 2.27
4182 4294 2.036098 CATTCAGCACCAGGCCCA 59.964 61.111 0.00 0.00 46.50 5.36
4331 4443 6.732154 AGCTCATTTGTGTCATACATTATGC 58.268 36.000 0.00 0.00 39.48 3.14
4386 4498 9.611284 TTGAAGAACTATTGATTGTTCAAATCG 57.389 29.630 16.58 0.00 42.80 3.34
4451 4563 0.322975 AGTAACCTCAGCTGTGCCTG 59.677 55.000 14.67 1.24 0.00 4.85
4464 4576 2.816087 CTGTGCCTGTAAGAGCATTTGT 59.184 45.455 0.00 0.00 41.07 2.83
4511 4623 2.599408 TCTAGGAACTTCGGTGGTCT 57.401 50.000 0.00 0.00 41.75 3.85
4524 4636 2.661675 CGGTGGTCTTCGCATAATATCG 59.338 50.000 0.00 0.00 0.00 2.92
4538 4650 6.115446 GCATAATATCGATCCCAAGATTCCA 58.885 40.000 0.00 0.00 30.90 3.53
4539 4651 6.037610 GCATAATATCGATCCCAAGATTCCAC 59.962 42.308 0.00 0.00 30.90 4.02
4540 4652 5.567037 AATATCGATCCCAAGATTCCACA 57.433 39.130 0.00 0.00 30.90 4.17
4541 4653 5.768980 ATATCGATCCCAAGATTCCACAT 57.231 39.130 0.00 0.00 30.90 3.21
4542 4654 3.931907 TCGATCCCAAGATTCCACATT 57.068 42.857 0.00 0.00 30.90 2.71
4543 4655 3.808728 TCGATCCCAAGATTCCACATTC 58.191 45.455 0.00 0.00 30.90 2.67
4544 4656 3.199727 TCGATCCCAAGATTCCACATTCA 59.800 43.478 0.00 0.00 30.90 2.57
4545 4657 3.313526 CGATCCCAAGATTCCACATTCAC 59.686 47.826 0.00 0.00 30.90 3.18
4546 4658 3.805066 TCCCAAGATTCCACATTCACA 57.195 42.857 0.00 0.00 0.00 3.58
4547 4659 3.420893 TCCCAAGATTCCACATTCACAC 58.579 45.455 0.00 0.00 0.00 3.82
4548 4660 3.156293 CCCAAGATTCCACATTCACACA 58.844 45.455 0.00 0.00 0.00 3.72
4549 4661 3.573538 CCCAAGATTCCACATTCACACAA 59.426 43.478 0.00 0.00 0.00 3.33
4550 4662 4.549458 CCAAGATTCCACATTCACACAAC 58.451 43.478 0.00 0.00 0.00 3.32
4551 4663 4.037803 CCAAGATTCCACATTCACACAACA 59.962 41.667 0.00 0.00 0.00 3.33
4552 4664 5.279106 CCAAGATTCCACATTCACACAACAT 60.279 40.000 0.00 0.00 0.00 2.71
4553 4665 6.218019 CAAGATTCCACATTCACACAACATT 58.782 36.000 0.00 0.00 0.00 2.71
4554 4666 6.017400 AGATTCCACATTCACACAACATTC 57.983 37.500 0.00 0.00 0.00 2.67
4555 4667 4.582701 TTCCACATTCACACAACATTCC 57.417 40.909 0.00 0.00 0.00 3.01
4573 4685 3.462483 TCCACATTCACACAACGTACT 57.538 42.857 0.00 0.00 0.00 2.73
4596 4708 4.991687 TCATGAAAACGTGCACACTATGTA 59.008 37.500 18.64 0.00 0.00 2.29
4637 4749 9.326413 ACAACAGATTATAAAATACTCCCTTCG 57.674 33.333 0.00 0.00 0.00 3.79
4638 4750 9.326413 CAACAGATTATAAAATACTCCCTTCGT 57.674 33.333 0.00 0.00 0.00 3.85
4639 4751 9.901172 AACAGATTATAAAATACTCCCTTCGTT 57.099 29.630 0.00 0.00 0.00 3.85
4640 4752 9.901172 ACAGATTATAAAATACTCCCTTCGTTT 57.099 29.630 0.00 0.00 0.00 3.60
4653 4765 8.415192 ACTCCCTTCGTTTTAAAATTTTTGTC 57.585 30.769 9.06 0.00 0.00 3.18
4654 4766 8.255206 ACTCCCTTCGTTTTAAAATTTTTGTCT 58.745 29.630 9.06 0.00 0.00 3.41
4655 4767 9.093970 CTCCCTTCGTTTTAAAATTTTTGTCTT 57.906 29.630 9.06 0.00 0.00 3.01
4705 4817 9.990360 TCAAGTCATGTTTTAGTATTAGACACA 57.010 29.630 0.00 0.00 0.00 3.72
4741 4853 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
4742 4854 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
4743 4855 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
4744 4856 9.546428 CAAATTTAAGACAAGAATTTTGGGACT 57.454 29.630 0.00 0.00 32.35 3.85
4745 4857 9.546428 AAATTTAAGACAAGAATTTTGGGACTG 57.454 29.630 0.00 0.00 31.00 3.51
4746 4858 7.889873 TTTAAGACAAGAATTTTGGGACTGA 57.110 32.000 5.68 0.00 0.00 3.41
4747 4859 7.889873 TTAAGACAAGAATTTTGGGACTGAA 57.110 32.000 5.68 0.00 0.00 3.02
4748 4860 6.790232 AAGACAAGAATTTTGGGACTGAAA 57.210 33.333 5.68 0.00 0.00 2.69
4749 4861 6.396829 AGACAAGAATTTTGGGACTGAAAG 57.603 37.500 5.68 0.00 42.29 2.62
4750 4862 6.129179 AGACAAGAATTTTGGGACTGAAAGA 58.871 36.000 5.68 0.00 37.43 2.52
4758 4870 5.576563 TTTGGGACTGAAAGAGTATTCCA 57.423 39.130 0.00 0.00 37.43 3.53
4762 4874 5.119694 GGGACTGAAAGAGTATTCCACATC 58.880 45.833 0.00 0.00 37.43 3.06
4770 4882 9.513906 TGAAAGAGTATTCCACATCAACAATAA 57.486 29.630 0.00 0.00 0.00 1.40
4833 4948 8.570068 ACAACCAAAATCCAACTTATATACGT 57.430 30.769 0.00 0.00 0.00 3.57
4834 4949 9.669887 ACAACCAAAATCCAACTTATATACGTA 57.330 29.630 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
406 408 3.892588 AGACGAGAGAAAACCAAGAGAGT 59.107 43.478 0.00 0.00 0.00 3.24
425 427 4.466015 AGTTCATCCTCCAAGAGAGAAGAC 59.534 45.833 0.00 0.00 46.50 3.01
465 467 2.353958 CATCCAGCAGCCACCACT 59.646 61.111 0.00 0.00 0.00 4.00
505 507 5.988561 GGTCATTTTGGACTTTGCACATAAA 59.011 36.000 0.00 0.00 37.91 1.40
507 509 4.021544 GGGTCATTTTGGACTTTGCACATA 60.022 41.667 0.00 0.00 37.91 2.29
551 553 0.106015 AAAGGTGCAGAAGCCCACTT 60.106 50.000 0.00 0.00 41.13 3.16
618 621 5.583854 CACTTTGGTGTGATATCCTTCTCAG 59.416 44.000 0.00 0.00 40.12 3.35
632 635 4.724279 AGAAAGGGTATCACTTTGGTGT 57.276 40.909 1.59 0.00 43.41 4.16
635 638 7.996098 TCTAAAAGAAAGGGTATCACTTTGG 57.004 36.000 1.59 0.00 38.21 3.28
663 666 9.203421 CAAGGTGACGCTGTATATGATATTTTA 57.797 33.333 0.00 0.00 0.00 1.52
713 720 0.320858 TTCGTGCTTATCGGCCAACA 60.321 50.000 2.24 0.00 0.00 3.33
736 743 3.054728 TCTCAATATGCAACTTTCCGGGA 60.055 43.478 0.00 0.00 0.00 5.14
939 950 0.944386 TGTGGCGTCTGCTTCTTTTC 59.056 50.000 0.00 0.00 42.25 2.29
1254 1265 3.636231 CCTTGGAGCGGGGACACA 61.636 66.667 0.00 0.00 0.00 3.72
1717 1728 1.236616 CCGCTGGACTCAATGTGCAA 61.237 55.000 0.00 0.00 46.14 4.08
1809 1820 3.386237 ACCCTCTCACCAGCGCTC 61.386 66.667 7.13 0.00 0.00 5.03
1843 1854 0.975556 TACCCAGCCATCGCAGAGAA 60.976 55.000 0.00 0.00 43.63 2.87
1952 1963 3.131661 CTAGCGCGCAAGAACTCGC 62.132 63.158 35.10 0.00 46.98 5.03
2175 2186 1.756538 GAGAGGAGCAGGAAGAAGAGG 59.243 57.143 0.00 0.00 0.00 3.69
2725 2741 3.236816 CATGTCGCAACAGATTTTGTCC 58.763 45.455 0.00 0.00 39.73 4.02
2756 2772 4.006319 AGAGCTCATTTGCTACCAGTTTC 58.994 43.478 17.77 0.00 44.17 2.78
2757 2773 4.026356 AGAGCTCATTTGCTACCAGTTT 57.974 40.909 17.77 0.00 44.17 2.66
2766 2782 5.557891 ACAACTGATAAGAGCTCATTTGC 57.442 39.130 17.77 1.57 37.00 3.68
2769 2785 7.044798 GGTCTAACAACTGATAAGAGCTCATT 58.955 38.462 17.77 9.84 0.00 2.57
3602 3630 4.111916 AGACGTTTTGGCAGTTCAATTTG 58.888 39.130 0.00 0.00 0.00 2.32
3603 3631 4.385358 AGACGTTTTGGCAGTTCAATTT 57.615 36.364 0.00 0.00 0.00 1.82
3604 3632 4.385358 AAGACGTTTTGGCAGTTCAATT 57.615 36.364 0.00 0.00 0.00 2.32
3605 3633 4.336993 TGTAAGACGTTTTGGCAGTTCAAT 59.663 37.500 0.83 0.00 0.00 2.57
3606 3634 3.690139 TGTAAGACGTTTTGGCAGTTCAA 59.310 39.130 0.83 0.00 0.00 2.69
3607 3635 3.271729 TGTAAGACGTTTTGGCAGTTCA 58.728 40.909 0.83 0.00 0.00 3.18
3608 3636 3.955771 TGTAAGACGTTTTGGCAGTTC 57.044 42.857 0.83 0.00 0.00 3.01
3609 3637 4.911514 AATGTAAGACGTTTTGGCAGTT 57.088 36.364 0.83 0.00 0.00 3.16
3620 3648 5.699458 ACCCTTTGTTCACTAATGTAAGACG 59.301 40.000 0.00 0.00 0.00 4.18
3699 3727 9.886132 GAAGAACCAATGGTTACTTTCTATCTA 57.114 33.333 18.76 0.00 46.95 1.98
3810 3922 1.135199 TGTTCATCGAGTTAGGCCGTC 60.135 52.381 0.00 0.00 0.00 4.79
3822 3934 2.420022 CCTAAGCAAAGGGTGTTCATCG 59.580 50.000 0.00 0.00 32.55 3.84
4027 4139 2.041620 AGTGGCATTTCCTTGAGGCTAA 59.958 45.455 0.00 0.00 35.26 3.09
4030 4142 1.260544 AAGTGGCATTTCCTTGAGGC 58.739 50.000 0.00 0.00 35.26 4.70
4090 4202 9.474313 AAGCAAATAACCAAGATAAGGACATAA 57.526 29.630 0.00 0.00 0.00 1.90
4115 4227 5.105554 TGGACAACTTTTAAAGCAGAAGCAA 60.106 36.000 4.42 0.00 45.49 3.91
4132 4244 6.366061 GCTCATTCCTTTTAAATGTGGACAAC 59.634 38.462 5.07 0.00 35.92 3.32
4182 4294 2.167075 GCCATTTTAGCACTTGGAGCAT 59.833 45.455 0.00 0.00 0.00 3.79
4279 4391 2.935201 GTGAGATCAGTCATGGCAGTTC 59.065 50.000 0.00 0.00 0.00 3.01
4331 4443 3.264897 GCACTAGGCACATCCGCG 61.265 66.667 0.00 0.00 43.97 6.46
4382 4494 0.176680 CTGGAGCTGCCTACACGATT 59.823 55.000 1.53 0.00 37.63 3.34
4384 4496 1.304134 TCTGGAGCTGCCTACACGA 60.304 57.895 1.53 0.00 37.63 4.35
4511 4623 5.400066 TCTTGGGATCGATATTATGCGAA 57.600 39.130 0.00 0.00 40.20 4.70
4524 4636 4.096984 GTGTGAATGTGGAATCTTGGGATC 59.903 45.833 0.00 0.00 0.00 3.36
4538 4650 5.068855 TGAATGTGGAATGTTGTGTGAATGT 59.931 36.000 0.00 0.00 0.00 2.71
4539 4651 5.403166 GTGAATGTGGAATGTTGTGTGAATG 59.597 40.000 0.00 0.00 0.00 2.67
4540 4652 5.068855 TGTGAATGTGGAATGTTGTGTGAAT 59.931 36.000 0.00 0.00 0.00 2.57
4541 4653 4.400567 TGTGAATGTGGAATGTTGTGTGAA 59.599 37.500 0.00 0.00 0.00 3.18
4542 4654 3.950395 TGTGAATGTGGAATGTTGTGTGA 59.050 39.130 0.00 0.00 0.00 3.58
4543 4655 4.043750 GTGTGAATGTGGAATGTTGTGTG 58.956 43.478 0.00 0.00 0.00 3.82
4544 4656 3.698539 TGTGTGAATGTGGAATGTTGTGT 59.301 39.130 0.00 0.00 0.00 3.72
4545 4657 4.304537 TGTGTGAATGTGGAATGTTGTG 57.695 40.909 0.00 0.00 0.00 3.33
4546 4658 4.681744 GTTGTGTGAATGTGGAATGTTGT 58.318 39.130 0.00 0.00 0.00 3.32
4547 4659 3.730215 CGTTGTGTGAATGTGGAATGTTG 59.270 43.478 0.00 0.00 0.00 3.33
4548 4660 3.380004 ACGTTGTGTGAATGTGGAATGTT 59.620 39.130 0.00 0.00 0.00 2.71
4549 4661 2.948979 ACGTTGTGTGAATGTGGAATGT 59.051 40.909 0.00 0.00 0.00 2.71
4550 4662 3.624326 ACGTTGTGTGAATGTGGAATG 57.376 42.857 0.00 0.00 0.00 2.67
4551 4663 4.385825 AGTACGTTGTGTGAATGTGGAAT 58.614 39.130 0.00 0.00 0.00 3.01
4552 4664 3.799366 AGTACGTTGTGTGAATGTGGAA 58.201 40.909 0.00 0.00 0.00 3.53
4553 4665 3.181474 TGAGTACGTTGTGTGAATGTGGA 60.181 43.478 0.00 0.00 0.00 4.02
4554 4666 3.127589 TGAGTACGTTGTGTGAATGTGG 58.872 45.455 0.00 0.00 0.00 4.17
4555 4667 4.447389 TCATGAGTACGTTGTGTGAATGTG 59.553 41.667 0.00 0.00 0.00 3.21
4573 4685 3.812609 ACATAGTGTGCACGTTTTCATGA 59.187 39.130 13.13 0.00 36.20 3.07
4596 4708 3.070446 TCTGTTGTGATACCGACCTTGTT 59.930 43.478 0.00 0.00 0.00 2.83
4679 4791 9.990360 TGTGTCTAATACTAAAACATGACTTGA 57.010 29.630 0.00 0.00 0.00 3.02
4715 4827 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
4716 4828 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
4717 4829 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
4718 4830 9.546428 AGTCCCAAAATTCTTGTCTTAAATTTG 57.454 29.630 0.00 0.00 33.95 2.32
4719 4831 9.546428 CAGTCCCAAAATTCTTGTCTTAAATTT 57.454 29.630 0.00 0.00 34.86 1.82
4720 4832 8.923270 TCAGTCCCAAAATTCTTGTCTTAAATT 58.077 29.630 0.00 0.00 0.00 1.82
4721 4833 8.477419 TCAGTCCCAAAATTCTTGTCTTAAAT 57.523 30.769 0.00 0.00 0.00 1.40
4722 4834 7.889873 TCAGTCCCAAAATTCTTGTCTTAAA 57.110 32.000 0.00 0.00 0.00 1.52
4723 4835 7.889873 TTCAGTCCCAAAATTCTTGTCTTAA 57.110 32.000 0.00 0.00 0.00 1.85
4724 4836 7.777910 TCTTTCAGTCCCAAAATTCTTGTCTTA 59.222 33.333 0.00 0.00 0.00 2.10
4725 4837 6.607198 TCTTTCAGTCCCAAAATTCTTGTCTT 59.393 34.615 0.00 0.00 0.00 3.01
4726 4838 6.129179 TCTTTCAGTCCCAAAATTCTTGTCT 58.871 36.000 0.00 0.00 0.00 3.41
4727 4839 6.039829 ACTCTTTCAGTCCCAAAATTCTTGTC 59.960 38.462 0.00 0.00 0.00 3.18
4728 4840 5.893824 ACTCTTTCAGTCCCAAAATTCTTGT 59.106 36.000 0.00 0.00 0.00 3.16
4729 4841 6.396829 ACTCTTTCAGTCCCAAAATTCTTG 57.603 37.500 0.00 0.00 0.00 3.02
4730 4842 8.712228 AATACTCTTTCAGTCCCAAAATTCTT 57.288 30.769 0.00 0.00 36.43 2.52
4731 4843 7.394641 GGAATACTCTTTCAGTCCCAAAATTCT 59.605 37.037 0.00 0.00 36.43 2.40
4732 4844 7.176690 TGGAATACTCTTTCAGTCCCAAAATTC 59.823 37.037 0.00 0.00 36.43 2.17
4733 4845 7.010160 TGGAATACTCTTTCAGTCCCAAAATT 58.990 34.615 0.00 0.00 36.43 1.82
4734 4846 6.434340 GTGGAATACTCTTTCAGTCCCAAAAT 59.566 38.462 0.00 0.00 36.43 1.82
4735 4847 5.768164 GTGGAATACTCTTTCAGTCCCAAAA 59.232 40.000 0.00 0.00 36.43 2.44
4736 4848 5.163141 TGTGGAATACTCTTTCAGTCCCAAA 60.163 40.000 0.00 0.00 36.43 3.28
4737 4849 4.349636 TGTGGAATACTCTTTCAGTCCCAA 59.650 41.667 0.00 0.00 36.43 4.12
4738 4850 3.907474 TGTGGAATACTCTTTCAGTCCCA 59.093 43.478 0.00 0.00 36.43 4.37
4739 4851 4.553330 TGTGGAATACTCTTTCAGTCCC 57.447 45.455 0.00 0.00 36.43 4.46
4740 4852 5.734720 TGATGTGGAATACTCTTTCAGTCC 58.265 41.667 0.00 0.00 36.43 3.85
4741 4853 6.650807 TGTTGATGTGGAATACTCTTTCAGTC 59.349 38.462 0.00 0.00 36.43 3.51
4742 4854 6.533730 TGTTGATGTGGAATACTCTTTCAGT 58.466 36.000 0.00 0.00 39.41 3.41
4743 4855 7.439157 TTGTTGATGTGGAATACTCTTTCAG 57.561 36.000 0.00 0.00 0.00 3.02
4744 4856 9.513906 TTATTGTTGATGTGGAATACTCTTTCA 57.486 29.630 0.00 0.00 0.00 2.69
4781 4896 5.070580 AGACCCTGGTTGTATAAGATACTGC 59.929 44.000 0.00 0.00 0.00 4.40
4798 4913 4.586841 TGGATTTTGGTTGTAAAGACCCTG 59.413 41.667 0.00 0.00 36.30 4.45


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

AutoCloner maintained by Alex Coulton.