Multiple sequence alignment - TraesCS3D01G083200

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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 TraesCS3D01G083200 chr3D 100.000 2982 0 0 981 3962 42341981 42344962 0.000000e+00 5507.0
1 TraesCS3D01G083200 chr3D 100.000 778 0 0 1 778 42341001 42341778 0.000000e+00 1437.0
2 TraesCS3D01G083200 chr3D 83.696 92 15 0 1122 1213 534165875 534165966 1.960000e-13 87.9
3 TraesCS3D01G083200 chr3A 97.169 1448 33 3 981 2423 53344588 53343144 0.000000e+00 2440.0
4 TraesCS3D01G083200 chr3A 96.657 688 19 2 2798 3483 53342858 53342173 0.000000e+00 1140.0
5 TraesCS3D01G083200 chr3A 89.783 783 63 5 1 778 53345490 53344720 0.000000e+00 987.0
6 TraesCS3D01G083200 chr3A 94.488 254 14 0 2468 2721 53343140 53342887 3.710000e-105 392.0
7 TraesCS3D01G083200 chr3A 88.797 241 16 2 3482 3716 53341929 53341694 6.480000e-73 285.0
8 TraesCS3D01G083200 chr3B 96.221 688 17 3 981 1665 65369326 65368645 0.000000e+00 1118.0
9 TraesCS3D01G083200 chr3B 95.785 688 17 8 2807 3483 65367304 65366618 0.000000e+00 1099.0
10 TraesCS3D01G083200 chr3B 94.473 579 31 1 2144 2721 65367921 65367343 0.000000e+00 891.0
11 TraesCS3D01G083200 chr3B 90.291 309 17 3 3482 3777 65366372 65366064 3.710000e-105 392.0
12 TraesCS3D01G083200 chr3B 92.135 267 21 0 1 267 65370602 65370336 1.040000e-100 377.0
13 TraesCS3D01G083200 chr3B 96.789 218 6 1 562 778 65369958 65369741 2.910000e-96 363.0
14 TraesCS3D01G083200 chr3B 89.051 274 21 6 1686 1954 65368591 65368322 8.210000e-87 331.0
15 TraesCS3D01G083200 chr3B 88.079 151 10 5 3813 3962 65366069 65365926 5.260000e-39 172.0
16 TraesCS3D01G083200 chr7D 100.000 56 0 0 2742 2797 37274209 37274154 1.950000e-18 104.0
17 TraesCS3D01G083200 chr5D 98.276 58 1 0 2740 2797 60143252 60143309 7.000000e-18 102.0
18 TraesCS3D01G083200 chr5D 97.917 48 0 1 2739 2785 102608247 102608294 9.130000e-12 82.4
19 TraesCS3D01G083200 chr6D 98.246 57 0 1 2741 2797 404319409 404319464 9.060000e-17 99.0
20 TraesCS3D01G083200 chr4A 98.182 55 0 1 2743 2797 27556679 27556626 1.170000e-15 95.3
21 TraesCS3D01G083200 chr4A 93.103 58 4 0 2740 2797 662057060 662057117 7.050000e-13 86.1
22 TraesCS3D01G083200 chr4A 89.231 65 4 3 2734 2797 589485927 589485865 1.180000e-10 78.7
23 TraesCS3D01G083200 chr6A 93.220 59 3 1 2740 2797 615390808 615390750 7.050000e-13 86.1
24 TraesCS3D01G083200 chr4D 90.323 62 5 1 2737 2797 43643126 43643187 3.280000e-11 80.5


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 TraesCS3D01G083200 chr3D 42341001 42344962 3961 False 3472.000 5507 100.0000 1 3962 2 chr3D.!!$F2 3961
1 TraesCS3D01G083200 chr3A 53341694 53345490 3796 True 1048.800 2440 93.3788 1 3716 5 chr3A.!!$R1 3715
2 TraesCS3D01G083200 chr3B 65365926 65370602 4676 True 592.875 1118 92.8530 1 3962 8 chr3B.!!$R1 3961

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
68 69 0.035820 CCTAAGTTAAGCGGGGCACA 60.036 55.0 0.00 0.00 0.00 4.57 F
70 71 0.671163 TAAGTTAAGCGGGGCACACG 60.671 55.0 0.00 0.00 0.00 4.49 F
1594 1952 0.035439 CATCCAAAGGTACCGTGGCT 60.035 55.0 25.36 17.16 32.10 4.75 F
2684 3346 0.395173 AAGGGAACAGGTGCGTTGTT 60.395 50.0 0.59 0.59 41.21 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1855 1.078567 GAGCAGCTTGACCTCCTGG 60.079 63.158 0.00 0.0 39.83 4.45 R
1961 2362 2.910319 AGGTCCATACTTTGCCACTACA 59.090 45.455 0.00 0.0 0.00 2.74 R
2686 3348 0.740737 AGCACAACAAGACTGCCAAC 59.259 50.000 0.00 0.0 0.00 3.77 R
3530 4454 0.871722 AACGCGCAAACTGCTATCAA 59.128 45.000 5.73 0.0 42.25 2.57 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
68 69 0.035820 CCTAAGTTAAGCGGGGCACA 60.036 55.000 0.00 0.00 0.00 4.57
70 71 0.671163 TAAGTTAAGCGGGGCACACG 60.671 55.000 0.00 0.00 0.00 4.49
82 83 2.959372 CACACGACGACTGCCCTA 59.041 61.111 0.00 0.00 0.00 3.53
185 186 7.876896 AGAGAACACGAGAAAGATAGAAAAC 57.123 36.000 0.00 0.00 0.00 2.43
225 226 4.961551 GCACGTACACATTTATACACATGC 59.038 41.667 0.00 0.00 0.00 4.06
272 273 3.885521 GACCGGTAGCGAGGGACG 61.886 72.222 17.33 0.00 45.66 4.79
296 297 1.600485 ACAACAAAACACGTCGGATCC 59.400 47.619 0.00 0.00 0.00 3.36
319 320 2.820197 TCAGAGCAACACATCTCTACGT 59.180 45.455 0.00 0.00 37.56 3.57
364 418 4.581824 TGTCTTGGTTGAGTTACTCTACGT 59.418 41.667 17.63 0.00 37.17 3.57
372 426 0.893447 GTTACTCTACGTGTGGGGCT 59.107 55.000 0.00 0.00 0.00 5.19
381 474 1.594833 GTGTGGGGCTACGATGACA 59.405 57.895 0.00 0.00 0.00 3.58
383 476 1.521681 GTGGGGCTACGATGACAGC 60.522 63.158 0.00 0.00 37.05 4.40
457 582 6.319048 ACCAAACATATCAGGTGAAGAGAT 57.681 37.500 0.00 0.00 32.04 2.75
461 586 5.543507 ACATATCAGGTGAAGAGATGTCC 57.456 43.478 0.00 0.00 42.41 4.02
489 614 6.398234 TGAGTTGTTCTGGATCTATCTAGC 57.602 41.667 0.00 0.00 35.61 3.42
554 684 5.450818 ACTCATAAACATGGAAAGCCCTA 57.549 39.130 0.00 0.00 35.38 3.53
660 802 4.856801 ATAGCCCGCCAACGCCAG 62.857 66.667 0.00 0.00 38.22 4.85
1027 1385 2.043852 TCCTCTGCGACTCCTCCC 60.044 66.667 0.00 0.00 0.00 4.30
1594 1952 0.035439 CATCCAAAGGTACCGTGGCT 60.035 55.000 25.36 17.16 32.10 4.75
1810 2209 7.298122 TGCGTTTCTTGATTCTTTCTTATGTC 58.702 34.615 0.00 0.00 0.00 3.06
1962 2363 2.520982 CCCTGGCATGGGCTGATG 60.521 66.667 8.75 0.00 40.84 3.07
2017 2418 7.514784 TGATTGATATCCAGCCTGTTAATTG 57.485 36.000 0.00 0.00 0.00 2.32
2032 2433 7.574967 GCCTGTTAATTGTGCTGTAGTACATTT 60.575 37.037 2.82 12.47 40.21 2.32
2223 2884 3.067461 ACAAGGAGAGATGTATCGCTGTC 59.933 47.826 2.80 0.00 37.07 3.51
2319 2980 1.066573 CAGTACACAGAGGAGGGCTTG 60.067 57.143 0.00 0.00 0.00 4.01
2388 3049 2.158769 TGATATTGCCATCGAGTGCCTT 60.159 45.455 6.50 0.00 0.00 4.35
2424 3085 6.990349 TCAAGAGAGAAGTTTTCGTGGTAAAT 59.010 34.615 0.00 0.00 34.02 1.40
2449 3110 8.437360 TTCAATAAACTCGCTGATATGATGTT 57.563 30.769 0.00 0.00 0.00 2.71
2480 3142 7.679783 TCCTCTCATTTCTGTTATTTCTGTCA 58.320 34.615 0.00 0.00 0.00 3.58
2495 3157 2.637382 TCTGTCAATAGAACTGGCCACA 59.363 45.455 0.00 0.00 0.00 4.17
2530 3192 7.971722 CAGCATTTTACATGTTGATCTGATTGA 59.028 33.333 2.30 0.00 32.96 2.57
2616 3278 1.122019 ACTGCGTGTTCTTCCTCCCT 61.122 55.000 0.00 0.00 0.00 4.20
2684 3346 0.395173 AAGGGAACAGGTGCGTTGTT 60.395 50.000 0.59 0.59 41.21 2.83
2686 3348 1.358759 GGAACAGGTGCGTTGTTGG 59.641 57.895 5.20 0.00 38.78 3.77
2721 3383 2.615447 TGTGCTTTCTTCTGCAAGTCAG 59.385 45.455 0.00 0.00 44.21 3.51
2722 3384 1.605710 TGCTTTCTTCTGCAAGTCAGC 59.394 47.619 0.00 0.00 42.56 4.26
2723 3385 1.068679 GCTTTCTTCTGCAAGTCAGCC 60.069 52.381 0.00 0.00 42.56 4.85
2725 3387 2.645838 TTCTTCTGCAAGTCAGCCTT 57.354 45.000 0.00 0.00 42.56 4.35
2726 3388 3.769739 TTCTTCTGCAAGTCAGCCTTA 57.230 42.857 0.00 0.00 42.56 2.69
2728 3390 1.736681 CTTCTGCAAGTCAGCCTTAGC 59.263 52.381 0.00 0.00 42.56 3.09
2729 3391 0.979665 TCTGCAAGTCAGCCTTAGCT 59.020 50.000 0.00 0.00 43.50 3.32
2765 3427 4.916358 GAGGGAAGGCCATCATGG 57.084 61.111 10.67 0.00 44.29 3.66
2781 3443 7.551035 CCATCATGGCTAGCTTTATTAGATC 57.449 40.000 15.72 0.00 0.00 2.75
2782 3444 7.108194 CCATCATGGCTAGCTTTATTAGATCA 58.892 38.462 15.72 0.00 0.00 2.92
2783 3445 7.609146 CCATCATGGCTAGCTTTATTAGATCAA 59.391 37.037 15.72 0.00 0.00 2.57
2784 3446 9.006839 CATCATGGCTAGCTTTATTAGATCAAA 57.993 33.333 15.72 0.00 0.00 2.69
2785 3447 8.978874 TCATGGCTAGCTTTATTAGATCAAAA 57.021 30.769 15.72 0.00 0.00 2.44
2786 3448 9.407380 TCATGGCTAGCTTTATTAGATCAAAAA 57.593 29.630 15.72 0.00 0.00 1.94
2835 3497 6.659242 TCTCTTCAGTTTTGTTTCCTGTTTCT 59.341 34.615 0.00 0.00 0.00 2.52
2849 3511 8.308207 GTTTCCTGTTTCTCTGTCTAAGTAGAT 58.692 37.037 0.00 0.00 34.39 1.98
3163 3830 4.206200 GGCGTTTTCTGTTGTTGTATGTTG 59.794 41.667 0.00 0.00 0.00 3.33
3244 3911 1.208642 GCTTCTTGTTGTTGTGCGCC 61.209 55.000 4.18 0.00 0.00 6.53
3245 3912 0.594796 CTTCTTGTTGTTGTGCGCCC 60.595 55.000 4.18 0.00 0.00 6.13
3342 4015 3.667448 GCATATGCTCGGACAGTCA 57.333 52.632 20.64 0.00 38.21 3.41
3453 4129 4.454728 AGCTTTGTTCACAAACATGTGT 57.545 36.364 0.00 0.00 44.59 3.72
3530 4454 2.025981 TGCAACCACAAGAGCATATCCT 60.026 45.455 0.00 0.00 31.05 3.24
3536 4460 5.862845 ACCACAAGAGCATATCCTTGATAG 58.137 41.667 13.10 6.29 41.56 2.08
3589 4513 8.039603 TCATTTTTATAGCAGTGTCACGATTT 57.960 30.769 0.00 0.00 0.00 2.17
3718 4653 3.277416 AGTAGGTGGATTATCCCTCCC 57.723 52.381 8.98 6.22 39.96 4.30
3727 4662 1.946984 TTATCCCTCCCAACACGAGT 58.053 50.000 0.00 0.00 0.00 4.18
3728 4663 1.946984 TATCCCTCCCAACACGAGTT 58.053 50.000 0.00 0.00 38.88 3.01
3729 4664 1.946984 ATCCCTCCCAACACGAGTTA 58.053 50.000 0.00 0.00 35.85 2.24
3730 4665 1.263356 TCCCTCCCAACACGAGTTAG 58.737 55.000 0.00 0.00 35.85 2.34
3736 4673 3.093814 TCCCAACACGAGTTAGCTCATA 58.906 45.455 7.41 0.00 41.71 2.15
3760 4697 3.445096 GCAACTGCATTTGACTCCCTATT 59.555 43.478 19.89 0.00 41.59 1.73
3767 4704 6.186957 TGCATTTGACTCCCTATTACAATGT 58.813 36.000 0.00 0.00 0.00 2.71
3771 4708 8.739039 CATTTGACTCCCTATTACAATGTTGAA 58.261 33.333 0.00 0.00 0.00 2.69
3772 4709 8.877864 TTTGACTCCCTATTACAATGTTGAAT 57.122 30.769 0.00 0.00 0.00 2.57
3773 4710 7.864108 TGACTCCCTATTACAATGTTGAATG 57.136 36.000 0.00 0.00 0.00 2.67
3774 4711 7.629157 TGACTCCCTATTACAATGTTGAATGA 58.371 34.615 0.00 0.00 0.00 2.57
3775 4712 8.274322 TGACTCCCTATTACAATGTTGAATGAT 58.726 33.333 0.00 0.00 0.00 2.45
3776 4713 8.455903 ACTCCCTATTACAATGTTGAATGATG 57.544 34.615 0.00 0.00 0.00 3.07
3777 4714 8.274322 ACTCCCTATTACAATGTTGAATGATGA 58.726 33.333 0.00 0.00 0.00 2.92
3778 4715 8.450578 TCCCTATTACAATGTTGAATGATGAC 57.549 34.615 0.00 0.00 0.00 3.06
3779 4716 7.502226 TCCCTATTACAATGTTGAATGATGACC 59.498 37.037 0.00 0.00 0.00 4.02
3780 4717 7.503566 CCCTATTACAATGTTGAATGATGACCT 59.496 37.037 0.00 0.00 0.00 3.85
3781 4718 8.906867 CCTATTACAATGTTGAATGATGACCTT 58.093 33.333 0.00 0.00 0.00 3.50
3784 4721 6.029346 ACAATGTTGAATGATGACCTTTCC 57.971 37.500 0.00 0.00 0.00 3.13
3785 4722 5.539574 ACAATGTTGAATGATGACCTTTCCA 59.460 36.000 0.00 0.00 0.00 3.53
3786 4723 6.041865 ACAATGTTGAATGATGACCTTTCCAA 59.958 34.615 0.00 0.00 0.00 3.53
3787 4724 6.669125 ATGTTGAATGATGACCTTTCCAAA 57.331 33.333 0.00 0.00 0.00 3.28
3788 4725 6.088016 TGTTGAATGATGACCTTTCCAAAG 57.912 37.500 0.00 0.00 35.79 2.77
3789 4726 5.598005 TGTTGAATGATGACCTTTCCAAAGT 59.402 36.000 0.00 0.00 34.20 2.66
3790 4727 5.964958 TGAATGATGACCTTTCCAAAGTC 57.035 39.130 0.00 0.00 34.20 3.01
3791 4728 5.634118 TGAATGATGACCTTTCCAAAGTCT 58.366 37.500 0.00 0.00 34.20 3.24
3792 4729 6.778821 TGAATGATGACCTTTCCAAAGTCTA 58.221 36.000 0.00 0.00 34.20 2.59
3793 4730 6.881065 TGAATGATGACCTTTCCAAAGTCTAG 59.119 38.462 0.00 0.00 34.20 2.43
3794 4731 5.165961 TGATGACCTTTCCAAAGTCTAGG 57.834 43.478 0.00 0.00 34.20 3.02
3795 4732 4.844085 TGATGACCTTTCCAAAGTCTAGGA 59.156 41.667 0.00 0.00 34.20 2.94
3796 4733 5.488919 TGATGACCTTTCCAAAGTCTAGGAT 59.511 40.000 0.00 0.00 34.20 3.24
3797 4734 6.672218 TGATGACCTTTCCAAAGTCTAGGATA 59.328 38.462 0.00 0.00 34.20 2.59
3798 4735 6.945636 TGACCTTTCCAAAGTCTAGGATAA 57.054 37.500 0.00 0.00 34.20 1.75
3799 4736 7.324388 TGACCTTTCCAAAGTCTAGGATAAA 57.676 36.000 0.00 0.00 34.20 1.40
3800 4737 7.751646 TGACCTTTCCAAAGTCTAGGATAAAA 58.248 34.615 0.00 0.00 34.20 1.52
3801 4738 8.390921 TGACCTTTCCAAAGTCTAGGATAAAAT 58.609 33.333 0.00 0.00 34.20 1.82
3802 4739 8.581253 ACCTTTCCAAAGTCTAGGATAAAATG 57.419 34.615 0.00 0.00 34.20 2.32
3803 4740 7.122799 ACCTTTCCAAAGTCTAGGATAAAATGC 59.877 37.037 0.00 0.00 34.20 3.56
3804 4741 7.340487 CCTTTCCAAAGTCTAGGATAAAATGCT 59.660 37.037 0.00 0.00 34.20 3.79
3805 4742 7.630242 TTCCAAAGTCTAGGATAAAATGCTG 57.370 36.000 0.00 0.00 33.10 4.41
3806 4743 6.957631 TCCAAAGTCTAGGATAAAATGCTGA 58.042 36.000 0.00 0.00 31.56 4.26
3807 4744 7.577303 TCCAAAGTCTAGGATAAAATGCTGAT 58.423 34.615 0.00 0.00 31.56 2.90
3808 4745 7.500227 TCCAAAGTCTAGGATAAAATGCTGATG 59.500 37.037 0.00 0.00 31.56 3.07
3809 4746 7.500227 CCAAAGTCTAGGATAAAATGCTGATGA 59.500 37.037 0.00 0.00 31.56 2.92
3810 4747 8.896744 CAAAGTCTAGGATAAAATGCTGATGAA 58.103 33.333 0.00 0.00 31.56 2.57
3811 4748 8.674263 AAGTCTAGGATAAAATGCTGATGAAG 57.326 34.615 0.00 0.00 31.56 3.02
3819 4756 4.585955 AAATGCTGATGAAGATGATGCC 57.414 40.909 0.00 0.00 0.00 4.40
3848 4785 0.975556 TTCATAGCCTCCGCCACTGA 60.976 55.000 0.00 0.00 34.57 3.41
3852 4789 2.597578 TAGCCTCCGCCACTGATATA 57.402 50.000 0.00 0.00 34.57 0.86
3853 4790 0.969894 AGCCTCCGCCACTGATATAC 59.030 55.000 0.00 0.00 34.57 1.47
3854 4791 0.679505 GCCTCCGCCACTGATATACA 59.320 55.000 0.00 0.00 0.00 2.29
3880 4817 4.982241 TCAGATTGAACAAAGAGGGAGT 57.018 40.909 0.00 0.00 0.00 3.85
3882 4819 3.755378 CAGATTGAACAAAGAGGGAGTGG 59.245 47.826 0.00 0.00 0.00 4.00
3883 4820 1.981256 TTGAACAAAGAGGGAGTGGC 58.019 50.000 0.00 0.00 0.00 5.01
3884 4821 0.843309 TGAACAAAGAGGGAGTGGCA 59.157 50.000 0.00 0.00 0.00 4.92
3886 4823 0.538287 AACAAAGAGGGAGTGGCAGC 60.538 55.000 0.00 0.00 0.00 5.25
3888 4825 2.911926 AAAGAGGGAGTGGCAGCCC 61.912 63.158 15.80 15.80 45.04 5.19
3907 4844 3.096633 AACCGGCAACCGTCACTCA 62.097 57.895 0.00 0.00 46.80 3.41
3908 4845 2.738521 CCGGCAACCGTCACTCAG 60.739 66.667 5.17 0.00 46.80 3.35
3927 4864 1.394917 AGCGATGAAATCACGAGCAAC 59.605 47.619 0.00 0.00 45.97 4.17
3932 4869 3.811722 TGAAATCACGAGCAACATCAC 57.188 42.857 0.00 0.00 0.00 3.06
3938 4875 0.249280 ACGAGCAACATCACGTGTGA 60.249 50.000 16.51 4.99 41.14 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.002379 AGTCTAGGGCAGTCGTCGT 60.002 57.895 0.00 0.00 0.00 4.34
70 71 0.743701 TCGAGTCTAGGGCAGTCGTC 60.744 60.000 6.95 0.00 32.49 4.20
82 83 2.037772 ACAAGCAGGAAACATCGAGTCT 59.962 45.455 0.00 0.00 0.00 3.24
185 186 1.331756 GTGCCGGCTTCACATATCTTG 59.668 52.381 29.70 0.00 34.73 3.02
207 208 4.130857 CCCCGCATGTGTATAAATGTGTA 58.869 43.478 5.38 0.00 33.40 2.90
214 215 0.464735 GTGGCCCCGCATGTGTATAA 60.465 55.000 0.00 0.00 0.00 0.98
272 273 1.710418 CGACGTGTTTTGTTGTCGTC 58.290 50.000 0.00 0.00 46.56 4.20
296 297 3.733380 CGTAGAGATGTGTTGCTCTGAGG 60.733 52.174 6.83 0.00 41.34 3.86
364 418 1.897423 CTGTCATCGTAGCCCCACA 59.103 57.895 0.00 0.00 0.00 4.17
372 426 1.067416 GCCATCCGCTGTCATCGTA 59.933 57.895 0.00 0.00 0.00 3.43
381 474 0.676466 TTTTGATGTCGCCATCCGCT 60.676 50.000 3.66 0.00 45.78 5.52
383 476 0.801872 TGTTTTGATGTCGCCATCCG 59.198 50.000 3.66 0.00 45.78 4.18
404 497 4.732568 TTGCGAGGGCTGCAATAA 57.267 50.000 0.50 0.00 46.62 1.40
457 582 2.549992 CCAGAACAACTCAATCGGGACA 60.550 50.000 0.00 0.00 31.06 4.02
461 586 3.866651 AGATCCAGAACAACTCAATCGG 58.133 45.455 0.00 0.00 0.00 4.18
489 614 6.986424 GAACAAAAATGTTAGGTTCCTTCG 57.014 37.500 0.00 0.00 33.52 3.79
670 812 2.979120 TTACCGTTGGTTGCCGCC 60.979 61.111 0.00 0.00 37.09 6.13
1284 1642 3.654143 TCGGACTCGACCTCCCCA 61.654 66.667 0.00 0.00 40.88 4.96
1497 1855 1.078567 GAGCAGCTTGACCTCCTGG 60.079 63.158 0.00 0.00 39.83 4.45
1810 2209 3.529634 TTGGTGTTCTTACGCGAATTG 57.470 42.857 15.93 0.00 35.59 2.32
1960 2361 3.523564 AGGTCCATACTTTGCCACTACAT 59.476 43.478 0.00 0.00 0.00 2.29
1961 2362 2.910319 AGGTCCATACTTTGCCACTACA 59.090 45.455 0.00 0.00 0.00 2.74
1962 2363 3.629142 AGGTCCATACTTTGCCACTAC 57.371 47.619 0.00 0.00 0.00 2.73
2114 2731 7.531857 TGAAAGAAGCATAATGGTACCAAAA 57.468 32.000 20.76 10.50 0.00 2.44
2223 2884 1.603172 GCCCAACTATCTCCATCGTCG 60.603 57.143 0.00 0.00 0.00 5.12
2319 2980 1.576356 GGTTCTCATCGATGGTCAGC 58.424 55.000 24.61 13.84 0.00 4.26
2388 3049 0.318441 CTCTCTTGAACTCGGTGGCA 59.682 55.000 0.00 0.00 0.00 4.92
2424 3085 8.437360 AACATCATATCAGCGAGTTTATTGAA 57.563 30.769 0.00 0.00 0.00 2.69
2453 3114 8.924511 ACAGAAATAACAGAAATGAGAGGAAA 57.075 30.769 0.00 0.00 0.00 3.13
2456 3117 7.912056 TGACAGAAATAACAGAAATGAGAGG 57.088 36.000 0.00 0.00 0.00 3.69
2466 3128 7.414540 GGCCAGTTCTATTGACAGAAATAACAG 60.415 40.741 0.00 0.00 36.34 3.16
2470 3132 5.880332 GTGGCCAGTTCTATTGACAGAAATA 59.120 40.000 5.11 0.00 36.34 1.40
2495 3157 6.271488 ACATGTAAAATGCTGCATACAACT 57.729 33.333 16.58 3.69 32.53 3.16
2530 3192 5.348451 GTCAATGCCGCACAAATAAAAGATT 59.652 36.000 0.00 0.00 0.00 2.40
2684 3346 1.102154 CACAACAAGACTGCCAACCA 58.898 50.000 0.00 0.00 0.00 3.67
2686 3348 0.740737 AGCACAACAAGACTGCCAAC 59.259 50.000 0.00 0.00 0.00 3.77
2743 3405 2.692709 TGATGGCCTTCCCTCAAAAA 57.307 45.000 15.62 0.00 34.64 1.94
2748 3410 4.916358 CCATGATGGCCTTCCCTC 57.084 61.111 15.62 0.14 0.00 4.30
2757 3419 7.108194 TGATCTAATAAAGCTAGCCATGATGG 58.892 38.462 12.13 7.21 41.55 3.51
2758 3420 8.557592 TTGATCTAATAAAGCTAGCCATGATG 57.442 34.615 12.13 0.00 0.00 3.07
2759 3421 9.578576 TTTTGATCTAATAAAGCTAGCCATGAT 57.421 29.630 12.13 5.94 0.00 2.45
2760 3422 8.978874 TTTTGATCTAATAAAGCTAGCCATGA 57.021 30.769 12.13 0.99 0.00 3.07
2803 3465 7.442666 AGGAAACAAAACTGAAGAGATAGACAC 59.557 37.037 0.00 0.00 0.00 3.67
2835 3497 8.840200 AAGATTTGGGTATCTACTTAGACAGA 57.160 34.615 0.00 0.00 33.81 3.41
2849 3511 2.170166 CTGCAGGCAAAGATTTGGGTA 58.830 47.619 5.57 0.00 38.57 3.69
3163 3830 3.105283 AGTCAGAACCTACCATACCACC 58.895 50.000 0.00 0.00 0.00 4.61
3342 4015 6.780457 AATTCAATGAATCGGTTCCATTCT 57.220 33.333 9.11 0.00 30.29 2.40
3453 4129 9.607988 CATCCATTATTACAAGTACCAGTTGTA 57.392 33.333 2.88 2.88 41.57 2.41
3530 4454 0.871722 AACGCGCAAACTGCTATCAA 59.128 45.000 5.73 0.00 42.25 2.57
3536 4460 3.024043 CCACAACGCGCAAACTGC 61.024 61.111 5.73 0.00 40.69 4.40
3545 4469 0.951558 ATGGTCAAACTCCACAACGC 59.048 50.000 0.00 0.00 37.81 4.84
3552 4476 7.771183 TGCTATAAAAATGATGGTCAAACTCC 58.229 34.615 0.00 0.00 0.00 3.85
3589 4513 4.170468 AGAAAGAAAGAGGGAAAGCACA 57.830 40.909 0.00 0.00 0.00 4.57
3689 4624 5.104485 GGATAATCCACCTACTTTGTCCTGT 60.104 44.000 0.00 0.00 36.28 4.00
3718 4653 4.506838 GCTTATGAGCTAACTCGTGTTG 57.493 45.455 12.89 4.63 46.69 3.33
3736 4673 1.615392 GGGAGTCAAATGCAGTTGCTT 59.385 47.619 21.53 11.83 42.66 3.91
3760 4697 6.718912 TGGAAAGGTCATCATTCAACATTGTA 59.281 34.615 0.00 0.00 0.00 2.41
3777 4714 7.122799 GCATTTTATCCTAGACTTTGGAAAGGT 59.877 37.037 4.23 0.00 39.64 3.50
3778 4715 7.340487 AGCATTTTATCCTAGACTTTGGAAAGG 59.660 37.037 4.23 0.00 40.31 3.11
3779 4716 8.186821 CAGCATTTTATCCTAGACTTTGGAAAG 58.813 37.037 0.00 0.00 41.73 2.62
3780 4717 7.888021 TCAGCATTTTATCCTAGACTTTGGAAA 59.112 33.333 0.00 0.00 35.81 3.13
3781 4718 7.402054 TCAGCATTTTATCCTAGACTTTGGAA 58.598 34.615 0.00 0.00 35.81 3.53
3782 4719 6.957631 TCAGCATTTTATCCTAGACTTTGGA 58.042 36.000 0.00 0.24 36.72 3.53
3783 4720 7.500227 TCATCAGCATTTTATCCTAGACTTTGG 59.500 37.037 0.00 0.00 0.00 3.28
3784 4721 8.442632 TCATCAGCATTTTATCCTAGACTTTG 57.557 34.615 0.00 0.00 0.00 2.77
3785 4722 9.118300 CTTCATCAGCATTTTATCCTAGACTTT 57.882 33.333 0.00 0.00 0.00 2.66
3786 4723 8.489489 TCTTCATCAGCATTTTATCCTAGACTT 58.511 33.333 0.00 0.00 0.00 3.01
3787 4724 8.027524 TCTTCATCAGCATTTTATCCTAGACT 57.972 34.615 0.00 0.00 0.00 3.24
3788 4725 8.719648 CATCTTCATCAGCATTTTATCCTAGAC 58.280 37.037 0.00 0.00 0.00 2.59
3789 4726 8.654094 TCATCTTCATCAGCATTTTATCCTAGA 58.346 33.333 0.00 0.00 0.00 2.43
3790 4727 8.843885 TCATCTTCATCAGCATTTTATCCTAG 57.156 34.615 0.00 0.00 0.00 3.02
3791 4728 9.227777 CATCATCTTCATCAGCATTTTATCCTA 57.772 33.333 0.00 0.00 0.00 2.94
3792 4729 7.309255 GCATCATCTTCATCAGCATTTTATCCT 60.309 37.037 0.00 0.00 0.00 3.24
3793 4730 6.807230 GCATCATCTTCATCAGCATTTTATCC 59.193 38.462 0.00 0.00 0.00 2.59
3794 4731 6.807230 GGCATCATCTTCATCAGCATTTTATC 59.193 38.462 0.00 0.00 0.00 1.75
3795 4732 6.569801 CGGCATCATCTTCATCAGCATTTTAT 60.570 38.462 0.00 0.00 0.00 1.40
3796 4733 5.278120 CGGCATCATCTTCATCAGCATTTTA 60.278 40.000 0.00 0.00 0.00 1.52
3797 4734 4.499188 CGGCATCATCTTCATCAGCATTTT 60.499 41.667 0.00 0.00 0.00 1.82
3798 4735 3.004419 CGGCATCATCTTCATCAGCATTT 59.996 43.478 0.00 0.00 0.00 2.32
3799 4736 2.552743 CGGCATCATCTTCATCAGCATT 59.447 45.455 0.00 0.00 0.00 3.56
3800 4737 2.152016 CGGCATCATCTTCATCAGCAT 58.848 47.619 0.00 0.00 0.00 3.79
3801 4738 1.139455 TCGGCATCATCTTCATCAGCA 59.861 47.619 0.00 0.00 0.00 4.41
3802 4739 1.799403 CTCGGCATCATCTTCATCAGC 59.201 52.381 0.00 0.00 0.00 4.26
3803 4740 3.058450 GACTCGGCATCATCTTCATCAG 58.942 50.000 0.00 0.00 0.00 2.90
3804 4741 2.224137 GGACTCGGCATCATCTTCATCA 60.224 50.000 0.00 0.00 0.00 3.07
3805 4742 2.224137 TGGACTCGGCATCATCTTCATC 60.224 50.000 0.00 0.00 0.00 2.92
3806 4743 1.764723 TGGACTCGGCATCATCTTCAT 59.235 47.619 0.00 0.00 0.00 2.57
3807 4744 1.194218 TGGACTCGGCATCATCTTCA 58.806 50.000 0.00 0.00 0.00 3.02
3808 4745 2.208431 CTTGGACTCGGCATCATCTTC 58.792 52.381 0.00 0.00 0.00 2.87
3809 4746 1.556911 ACTTGGACTCGGCATCATCTT 59.443 47.619 0.00 0.00 0.00 2.40
3810 4747 1.198713 ACTTGGACTCGGCATCATCT 58.801 50.000 0.00 0.00 0.00 2.90
3811 4748 1.936547 GAACTTGGACTCGGCATCATC 59.063 52.381 0.00 0.00 0.00 2.92
3819 4756 2.482142 GGAGGCTATGAACTTGGACTCG 60.482 54.545 0.00 0.00 34.89 4.18
3852 4789 6.239120 CCCTCTTTGTTCAATCTGATTGTTGT 60.239 38.462 25.08 0.00 41.02 3.32
3853 4790 6.016024 TCCCTCTTTGTTCAATCTGATTGTTG 60.016 38.462 25.08 6.70 41.02 3.33
3854 4791 6.070656 TCCCTCTTTGTTCAATCTGATTGTT 58.929 36.000 25.08 0.00 41.02 2.83
3893 4830 3.414700 CGCTGAGTGACGGTTGCC 61.415 66.667 0.00 0.00 0.00 4.52
3894 4831 1.738099 ATCGCTGAGTGACGGTTGC 60.738 57.895 0.00 0.00 0.00 4.17
3907 4844 1.394917 GTTGCTCGTGATTTCATCGCT 59.605 47.619 0.00 0.00 37.64 4.93
3908 4845 1.128507 TGTTGCTCGTGATTTCATCGC 59.871 47.619 0.00 0.00 36.47 4.58


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

AutoCloner maintained by Alex Coulton.