Multiple sequence alignment - TraesCS3D01G068800

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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 TraesCS3D01G068800 chr3D 100.000 5051 0 0 1 5051 30277327 30282377 0.000000e+00 9328.0
1 TraesCS3D01G068800 chr3D 79.907 1508 261 30 2777 4266 30060226 30061709 0.000000e+00 1068.0
2 TraesCS3D01G068800 chr3D 99.176 364 3 0 4463 4826 30287408 30287771 0.000000e+00 656.0
3 TraesCS3D01G068800 chr3D 82.642 530 62 22 4538 5051 562416006 562415491 4.640000e-120 442.0
4 TraesCS3D01G068800 chr3A 94.538 4504 183 26 1 4462 42015896 42020378 0.000000e+00 6896.0
5 TraesCS3D01G068800 chr3A 83.111 3369 520 28 795 4137 40936175 40939520 0.000000e+00 3024.0
6 TraesCS3D01G068800 chr3A 82.592 3194 507 36 880 4040 41149837 41153014 0.000000e+00 2772.0
7 TraesCS3D01G068800 chr3A 82.661 3097 508 17 956 4035 41537183 41540267 0.000000e+00 2717.0
8 TraesCS3D01G068800 chr3A 82.361 754 128 3 3285 4034 40919879 40920631 0.000000e+00 651.0
9 TraesCS3D01G068800 chr3A 88.276 145 16 1 4905 5049 561674891 561674748 6.720000e-39 172.0
10 TraesCS3D01G068800 chr3B 95.836 3482 132 3 792 4273 52742843 52739375 0.000000e+00 5614.0
11 TraesCS3D01G068800 chr3B 96.659 2484 73 2 789 3272 51856899 51859372 0.000000e+00 4119.0
12 TraesCS3D01G068800 chr3B 83.328 3365 479 51 880 4207 51726922 51730241 0.000000e+00 3031.0
13 TraesCS3D01G068800 chr3B 83.105 3214 486 43 910 4092 52777840 52774653 0.000000e+00 2874.0
14 TraesCS3D01G068800 chr3B 82.452 3140 523 19 910 4036 52426244 52429368 0.000000e+00 2721.0
15 TraesCS3D01G068800 chr3B 95.978 547 22 0 3305 3851 51859370 51859916 0.000000e+00 889.0
16 TraesCS3D01G068800 chr3B 84.183 765 75 20 60 786 52743688 52742932 0.000000e+00 701.0
17 TraesCS3D01G068800 chr3B 81.677 775 137 3 3286 4056 52456923 52457696 1.530000e-179 640.0
18 TraesCS3D01G068800 chr3B 90.037 271 23 2 4007 4273 51859915 51860185 1.040000e-91 348.0
19 TraesCS3D01G068800 chr3B 79.737 380 21 23 254 603 51856365 51856718 1.830000e-54 224.0
20 TraesCS3D01G068800 chr3B 84.375 96 5 3 4263 4354 52739363 52739274 9.010000e-13 86.1
21 TraesCS3D01G068800 chr3B 100.000 32 0 0 1 32 52743725 52743694 5.460000e-05 60.2
22 TraesCS3D01G068800 chr5A 83.961 611 69 16 4460 5051 87986649 87987249 4.420000e-155 558.0
23 TraesCS3D01G068800 chr5A 88.219 365 38 4 4463 4826 88020750 88021110 1.000000e-116 431.0
24 TraesCS3D01G068800 chr5A 80.455 440 68 16 4462 4894 314680234 314679806 2.270000e-83 320.0
25 TraesCS3D01G068800 chr6D 81.690 568 83 19 4491 5050 71534581 71534027 2.140000e-123 453.0
26 TraesCS3D01G068800 chr6D 93.333 45 3 0 4991 5035 22988917 22988873 3.260000e-07 67.6
27 TraesCS3D01G068800 chr2A 78.161 609 95 26 4463 5051 694731864 694732454 2.240000e-93 353.0
28 TraesCS3D01G068800 chr2A 78.723 376 56 19 4463 4827 694737486 694737848 3.930000e-56 230.0
29 TraesCS3D01G068800 chr2A 82.192 73 10 3 4966 5035 103794771 103794843 5.460000e-05 60.2
30 TraesCS3D01G068800 chr2D 78.533 368 68 9 4463 4826 634070421 634070781 1.090000e-56 231.0
31 TraesCS3D01G068800 chr6B 77.748 373 59 19 4463 4826 536858432 536858789 1.840000e-49 207.0
32 TraesCS3D01G068800 chr1B 80.000 270 38 13 4534 4798 157461101 157460843 8.640000e-43 185.0
33 TraesCS3D01G068800 chr6A 73.127 387 75 25 4534 4907 172051655 172051285 1.490000e-20 111.0


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 TraesCS3D01G068800 chr3D 30277327 30282377 5050 False 9328.000 9328 100.00000 1 5051 1 chr3D.!!$F2 5050
1 TraesCS3D01G068800 chr3D 30060226 30061709 1483 False 1068.000 1068 79.90700 2777 4266 1 chr3D.!!$F1 1489
2 TraesCS3D01G068800 chr3D 562415491 562416006 515 True 442.000 442 82.64200 4538 5051 1 chr3D.!!$R1 513
3 TraesCS3D01G068800 chr3A 42015896 42020378 4482 False 6896.000 6896 94.53800 1 4462 1 chr3A.!!$F5 4461
4 TraesCS3D01G068800 chr3A 40936175 40939520 3345 False 3024.000 3024 83.11100 795 4137 1 chr3A.!!$F2 3342
5 TraesCS3D01G068800 chr3A 41149837 41153014 3177 False 2772.000 2772 82.59200 880 4040 1 chr3A.!!$F3 3160
6 TraesCS3D01G068800 chr3A 41537183 41540267 3084 False 2717.000 2717 82.66100 956 4035 1 chr3A.!!$F4 3079
7 TraesCS3D01G068800 chr3A 40919879 40920631 752 False 651.000 651 82.36100 3285 4034 1 chr3A.!!$F1 749
8 TraesCS3D01G068800 chr3B 51726922 51730241 3319 False 3031.000 3031 83.32800 880 4207 1 chr3B.!!$F1 3327
9 TraesCS3D01G068800 chr3B 52774653 52777840 3187 True 2874.000 2874 83.10500 910 4092 1 chr3B.!!$R1 3182
10 TraesCS3D01G068800 chr3B 52426244 52429368 3124 False 2721.000 2721 82.45200 910 4036 1 chr3B.!!$F2 3126
11 TraesCS3D01G068800 chr3B 52739274 52743725 4451 True 1615.325 5614 91.09850 1 4354 4 chr3B.!!$R2 4353
12 TraesCS3D01G068800 chr3B 51856365 51860185 3820 False 1395.000 4119 90.60275 254 4273 4 chr3B.!!$F4 4019
13 TraesCS3D01G068800 chr3B 52456923 52457696 773 False 640.000 640 81.67700 3286 4056 1 chr3B.!!$F3 770
14 TraesCS3D01G068800 chr5A 87986649 87987249 600 False 558.000 558 83.96100 4460 5051 1 chr5A.!!$F1 591
15 TraesCS3D01G068800 chr6D 71534027 71534581 554 True 453.000 453 81.69000 4491 5050 1 chr6D.!!$R2 559
16 TraesCS3D01G068800 chr2A 694731864 694732454 590 False 353.000 353 78.16100 4463 5051 1 chr2A.!!$F2 588

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
158 159 0.107703 TAACGCAGGCTGGATTCAGG 60.108 55.000 17.64 0.0 41.19 3.86 F
437 458 0.109597 CCTGGCTTGCGTTCAACATC 60.110 55.000 0.00 0.0 0.00 3.06 F
446 467 0.708370 CGTTCAACATCGTGAGGTCG 59.292 55.000 0.00 0.0 0.00 4.79 F
447 468 1.664874 CGTTCAACATCGTGAGGTCGA 60.665 52.381 0.00 0.0 43.86 4.20 F
2073 2226 1.896220 TGAGAAACACAGGCATGGAC 58.104 50.000 2.31 0.0 0.00 4.02 F
3618 3784 2.187946 GGAGAGGATGGTGGTGCG 59.812 66.667 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1498 1.667830 CAACATCGTGGCGTGACCT 60.668 57.895 0.00 0.00 40.22 3.85 R
2241 2394 0.098200 TCAGACGATGCGGTAACTCG 59.902 55.000 0.00 0.00 38.34 4.18 R
2569 2722 4.415881 TCTTACTGACAACAGAAAGGCA 57.584 40.909 0.00 0.00 46.03 4.75 R
2670 2826 5.821470 TCTCTTGAAGAATGCATCCTCAATC 59.179 40.000 14.78 7.50 37.74 2.67 R
3799 3965 1.291588 CAAGGAGCTCGAGCACTGT 59.708 57.895 36.87 18.48 45.16 3.55 R
4523 4731 1.404986 CGGCCGTCCATCTAACTGAAA 60.405 52.381 19.50 0.00 0.00 2.69 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
48 49 8.777865 TGAAGATATTATTTGCCCTATTCTCG 57.222 34.615 0.00 0.00 0.00 4.04
51 52 3.569194 TTATTTGCCCTATTCTCGCCA 57.431 42.857 0.00 0.00 0.00 5.69
75 76 2.296190 TGATCGCGGTATGCATCTACTT 59.704 45.455 6.13 0.00 46.97 2.24
81 82 3.643763 CGGTATGCATCTACTTCACTCC 58.356 50.000 0.19 0.00 0.00 3.85
107 108 2.400896 ATTTTGTCTTGGCGCGCGTT 62.401 50.000 32.35 0.00 0.00 4.84
108 109 2.975167 TTTTGTCTTGGCGCGCGTTC 62.975 55.000 32.35 23.28 0.00 3.95
125 126 2.155924 CGTTCTCGTTCCTTTGCTCTTC 59.844 50.000 0.00 0.00 0.00 2.87
143 144 4.421058 TCTTCGTCCATTGATCACTAACG 58.579 43.478 11.59 11.59 0.00 3.18
146 147 2.282555 CGTCCATTGATCACTAACGCAG 59.717 50.000 0.00 0.00 0.00 5.18
158 159 0.107703 TAACGCAGGCTGGATTCAGG 60.108 55.000 17.64 0.00 41.19 3.86
176 177 1.906824 GTGGTCCGGTGGAGACAGA 60.907 63.158 0.00 0.00 44.46 3.41
184 185 2.135933 CGGTGGAGACAGAAAACAGTC 58.864 52.381 0.00 0.00 44.46 3.51
222 224 2.419739 GCACGTCCCTCTCTCCTCC 61.420 68.421 0.00 0.00 0.00 4.30
293 306 2.093288 TCATCTCAATGGTCTGCACCTC 60.093 50.000 0.00 0.00 44.17 3.85
334 354 2.480419 CGGCACTCCTTTTGTTCACTAG 59.520 50.000 0.00 0.00 0.00 2.57
381 402 3.831333 TGGCAGCATGGTTTTATTCTTCA 59.169 39.130 0.00 0.00 35.86 3.02
424 445 7.682787 TCTCTTCTCTATTTTTATCCTGGCT 57.317 36.000 0.00 0.00 0.00 4.75
429 450 4.523083 TCTATTTTTATCCTGGCTTGCGT 58.477 39.130 0.00 0.00 0.00 5.24
435 456 0.537143 ATCCTGGCTTGCGTTCAACA 60.537 50.000 0.00 0.00 0.00 3.33
437 458 0.109597 CCTGGCTTGCGTTCAACATC 60.110 55.000 0.00 0.00 0.00 3.06
446 467 0.708370 CGTTCAACATCGTGAGGTCG 59.292 55.000 0.00 0.00 0.00 4.79
447 468 1.664874 CGTTCAACATCGTGAGGTCGA 60.665 52.381 0.00 0.00 43.86 4.20
449 470 2.347697 TCAACATCGTGAGGTCGAAG 57.652 50.000 0.00 0.00 42.99 3.79
483 528 8.066595 GTCTTCAAGGTCATCAATATTGATTCG 58.933 37.037 25.16 16.40 45.13 3.34
523 569 2.294512 CCTTGTTGGAAGACAGCTTTCC 59.705 50.000 8.49 8.49 38.35 3.13
541 587 7.391833 CAGCTTTCCAAGGTAAAGACTAATCTT 59.608 37.037 12.27 0.00 41.28 2.40
645 691 2.031120 TGGCCCTTCAACTGACAAAAG 58.969 47.619 0.00 0.00 0.00 2.27
707 754 8.479280 GCACATGTAAATTTGTAAAACACAGAG 58.521 33.333 0.00 0.00 38.72 3.35
709 756 9.950680 ACATGTAAATTTGTAAAACACAGAGAG 57.049 29.630 0.00 0.00 38.72 3.20
730 777 9.851686 AGAGAGTGAAAATATATAATGCCAACA 57.148 29.630 0.00 0.00 0.00 3.33
752 799 7.448748 ACACAGGATTTTTAGACCACAATAC 57.551 36.000 0.00 0.00 0.00 1.89
768 815 2.139323 ATACGTGGCACTACTCAGGA 57.861 50.000 16.72 0.00 0.00 3.86
786 833 7.285566 ACTCAGGATGCTGAATTTGTATGTAT 58.714 34.615 18.24 0.00 34.76 2.29
787 834 7.228108 ACTCAGGATGCTGAATTTGTATGTATG 59.772 37.037 18.24 4.26 34.76 2.39
790 837 7.646526 CAGGATGCTGAATTTGTATGTATGTTG 59.353 37.037 8.85 0.00 0.00 3.33
853 983 6.578023 AGCAAGTCACTAGTGATATCTTTCC 58.422 40.000 27.54 17.21 42.18 3.13
874 1005 3.071023 CCCACCTTGTAAGACTTGTCTCA 59.929 47.826 3.58 0.00 0.00 3.27
875 1006 4.310769 CCACCTTGTAAGACTTGTCTCAG 58.689 47.826 3.58 0.00 0.00 3.35
876 1007 4.039245 CCACCTTGTAAGACTTGTCTCAGA 59.961 45.833 3.58 0.00 0.00 3.27
877 1008 4.985409 CACCTTGTAAGACTTGTCTCAGAC 59.015 45.833 0.00 0.00 0.00 3.51
878 1009 4.896482 ACCTTGTAAGACTTGTCTCAGACT 59.104 41.667 6.33 0.00 33.15 3.24
946 1084 2.679642 TTTTGCTGCCATCCCCCG 60.680 61.111 0.00 0.00 0.00 5.73
989 1131 2.583520 GGCCTCCTGAGCTGAGTG 59.416 66.667 0.00 0.00 0.00 3.51
1295 1448 4.079970 GACCATCCATCATCATCAAGCAT 58.920 43.478 0.00 0.00 0.00 3.79
1345 1498 6.321181 AGTTTCCTCTTGCTTTTGTAACATCA 59.679 34.615 0.00 0.00 0.00 3.07
1443 1596 9.284968 ACATTTTTAACATTCAGCACTAGTACT 57.715 29.630 0.00 0.00 0.00 2.73
1938 2091 6.046593 GGTAACCACACGAGATGATCAAATA 58.953 40.000 0.00 0.00 0.00 1.40
2073 2226 1.896220 TGAGAAACACAGGCATGGAC 58.104 50.000 2.31 0.00 0.00 4.02
2184 2337 7.039993 TGGAGAAAGTTTTTAGGCAAATACTCC 60.040 37.037 0.00 0.00 35.62 3.85
2241 2394 4.439016 GGCGCTCTATACCTAAGCTATGAC 60.439 50.000 7.64 0.00 33.83 3.06
2569 2722 6.460123 GGGTGAGAATATGTCAAAATTGCGAT 60.460 38.462 0.00 0.00 0.00 4.58
2670 2826 5.404466 TTGCTTTTTATGGTCCATGGAAG 57.596 39.130 18.20 14.78 0.00 3.46
3600 3766 5.363580 AGTGGAAAATGTTGTTGATGAAGGT 59.636 36.000 0.00 0.00 0.00 3.50
3618 3784 2.187946 GGAGAGGATGGTGGTGCG 59.812 66.667 0.00 0.00 0.00 5.34
4069 4245 3.688694 AGATGGCAATGCAAACACAAT 57.311 38.095 7.79 0.00 0.00 2.71
4479 4687 2.037772 GGTGTGTCAGGACTGAAGATGT 59.962 50.000 3.18 0.00 41.85 3.06
4481 4689 2.072298 GTGTCAGGACTGAAGATGTGC 58.928 52.381 3.18 0.00 41.85 4.57
4505 4713 8.478066 TGCTGATATGATTCAGTTAACTGTAGT 58.522 33.333 29.83 18.86 44.10 2.73
4511 4719 6.759272 TGATTCAGTTAACTGTAGTTGCTCT 58.241 36.000 29.83 8.44 44.12 4.09
4520 4728 3.319405 ACTGTAGTTGCTCTAGCGCATAT 59.681 43.478 11.47 2.95 45.83 1.78
4523 4731 1.338337 AGTTGCTCTAGCGCATATCGT 59.662 47.619 11.47 0.00 45.83 3.73
4542 4753 2.007608 GTTTCAGTTAGATGGACGGCC 58.992 52.381 0.00 0.00 0.00 6.13
4582 4794 2.352115 GCTCGTCGCTAGCCGTAC 60.352 66.667 9.66 4.30 38.35 3.67
4604 4816 3.434299 CGATGCCCTTTGTAACGTTACTT 59.566 43.478 32.10 11.83 34.77 2.24
4618 4833 4.531332 ACGTTACTTCGTCAGTTACTGTC 58.469 43.478 12.41 5.90 40.04 3.51
4620 4835 4.609113 CGTTACTTCGTCAGTTACTGTCGA 60.609 45.833 25.22 25.22 46.15 4.20
4776 4994 0.823769 GGCGGAATTCCCCAATCTCC 60.824 60.000 19.01 5.18 0.00 3.71
4777 4995 0.183731 GCGGAATTCCCCAATCTCCT 59.816 55.000 19.01 0.00 0.00 3.69
4810 5029 3.014623 CCTAGATCGCGTCCCATATACA 58.985 50.000 5.77 0.00 0.00 2.29
4845 5065 5.711506 TGACAAATTGGTATCATGAGCAGTT 59.288 36.000 0.09 0.00 0.00 3.16
4875 5095 1.550524 CGGAGATGAGTTTCAGTGGGA 59.449 52.381 0.00 0.00 0.00 4.37
4947 5178 0.808060 GAGCTTAGAGAGGCGTTGGC 60.808 60.000 0.00 0.00 38.90 4.52
4959 5190 3.656045 GTTGGCGTCGGGGTTGTG 61.656 66.667 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.212935 ACTGGCGAGAATAGGGCAAAT 59.787 47.619 1.44 0.00 38.32 2.32
36 37 0.107703 CAACTGGCGAGAATAGGGCA 60.108 55.000 1.44 0.00 37.18 5.36
48 49 1.934463 CATACCGCGATCAACTGGC 59.066 57.895 8.23 0.00 0.00 4.85
51 52 1.069204 AGATGCATACCGCGATCAACT 59.931 47.619 8.23 0.00 46.97 3.16
75 76 4.351874 AGACAAAATTTCCTCGGAGTGA 57.648 40.909 4.02 0.00 0.00 3.41
81 82 2.584791 CGCCAAGACAAAATTTCCTCG 58.415 47.619 0.00 0.00 0.00 4.63
107 108 1.340248 ACGAAGAGCAAAGGAACGAGA 59.660 47.619 0.00 0.00 0.00 4.04
108 109 1.721926 GACGAAGAGCAAAGGAACGAG 59.278 52.381 0.00 0.00 0.00 4.18
125 126 2.267426 TGCGTTAGTGATCAATGGACG 58.733 47.619 21.63 21.63 0.00 4.79
143 144 1.751927 CCACCTGAATCCAGCCTGC 60.752 63.158 0.00 0.00 39.07 4.85
146 147 1.077429 GGACCACCTGAATCCAGCC 60.077 63.158 0.00 0.00 39.07 4.85
158 159 1.469335 TTCTGTCTCCACCGGACCAC 61.469 60.000 9.46 0.00 33.22 4.16
176 177 2.292267 CACAGAGCCACAGACTGTTTT 58.708 47.619 5.04 0.00 41.93 2.43
210 212 2.433994 GCTGCAGGAGGAGAGAGGG 61.434 68.421 17.12 0.00 34.74 4.30
258 271 9.872684 ACCATTGAGATGAAATATTTACCTGAT 57.127 29.630 0.00 0.00 35.16 2.90
266 279 6.040166 GGTGCAGACCATTGAGATGAAATATT 59.960 38.462 0.00 0.00 42.59 1.28
272 285 1.911357 AGGTGCAGACCATTGAGATGA 59.089 47.619 0.00 0.00 45.98 2.92
307 327 0.535102 CAAAAGGAGTGCCGGACAGT 60.535 55.000 5.05 5.65 39.96 3.55
308 328 0.535102 ACAAAAGGAGTGCCGGACAG 60.535 55.000 5.05 0.00 39.96 3.51
309 329 0.106918 AACAAAAGGAGTGCCGGACA 60.107 50.000 5.05 0.00 39.96 4.02
310 330 0.591659 GAACAAAAGGAGTGCCGGAC 59.408 55.000 5.05 0.00 39.96 4.79
311 331 0.181587 TGAACAAAAGGAGTGCCGGA 59.818 50.000 5.05 0.00 39.96 5.14
312 332 0.310854 GTGAACAAAAGGAGTGCCGG 59.689 55.000 0.00 0.00 39.96 6.13
313 333 1.308998 AGTGAACAAAAGGAGTGCCG 58.691 50.000 0.00 0.00 39.96 5.69
334 354 8.768955 CATCACCTGCAGTAGATATCTAAAAAC 58.231 37.037 14.09 4.71 0.00 2.43
381 402 8.487848 AGAAGAGAAGATCATCAATCAAGTCAT 58.512 33.333 0.10 0.00 36.79 3.06
424 445 0.865111 CCTCACGATGTTGAACGCAA 59.135 50.000 0.00 0.00 0.00 4.85
429 450 2.295070 TCTTCGACCTCACGATGTTGAA 59.705 45.455 0.00 5.40 41.82 2.69
435 456 1.402456 CGGTTTCTTCGACCTCACGAT 60.402 52.381 0.00 0.00 41.82 3.73
437 458 0.318445 ACGGTTTCTTCGACCTCACG 60.318 55.000 0.00 0.00 34.95 4.35
446 467 3.203716 ACCTTGAAGACACGGTTTCTTC 58.796 45.455 23.56 23.56 44.48 2.87
447 468 3.203716 GACCTTGAAGACACGGTTTCTT 58.796 45.455 9.17 9.17 46.32 2.52
449 470 2.557317 TGACCTTGAAGACACGGTTTC 58.443 47.619 0.00 0.00 46.32 2.78
516 562 7.021998 AGATTAGTCTTTACCTTGGAAAGCT 57.978 36.000 0.00 0.00 44.44 3.74
586 632 7.391833 TGCATAACAGTGTACATATTGAACCAA 59.608 33.333 0.00 0.00 0.00 3.67
617 663 1.355381 AGTTGAAGGGCCATCACATGA 59.645 47.619 11.65 0.00 0.00 3.07
707 754 9.669353 CTGTGTTGGCATTATATATTTTCACTC 57.331 33.333 0.00 0.00 0.00 3.51
709 756 8.629158 TCCTGTGTTGGCATTATATATTTTCAC 58.371 33.333 0.00 0.00 0.00 3.18
730 777 6.148811 CACGTATTGTGGTCTAAAAATCCTGT 59.851 38.462 0.00 0.00 45.21 4.00
752 799 0.807667 GCATCCTGAGTAGTGCCACG 60.808 60.000 0.00 0.00 0.00 4.94
768 815 6.865411 TGCAACATACATACAAATTCAGCAT 58.135 32.000 0.00 0.00 0.00 3.79
786 833 3.349927 AGCATAATGAAGCTCTGCAACA 58.650 40.909 0.00 0.00 36.00 3.33
787 834 5.490139 TTAGCATAATGAAGCTCTGCAAC 57.510 39.130 0.00 0.00 42.05 4.17
790 837 9.688592 AATAAATTTAGCATAATGAAGCTCTGC 57.311 29.630 3.94 0.00 42.05 4.26
822 952 9.119329 GATATCACTAGTGACTTGCTATTTACG 57.881 37.037 27.41 0.00 43.11 3.18
853 983 4.039245 TCTGAGACAAGTCTTACAAGGTGG 59.961 45.833 3.96 0.00 40.61 4.61
874 1005 5.128919 ACATGCTTTCAAAACTGAGAGTCT 58.871 37.500 0.00 0.00 0.00 3.24
875 1006 5.429957 ACATGCTTTCAAAACTGAGAGTC 57.570 39.130 0.00 0.00 0.00 3.36
876 1007 5.841957 AACATGCTTTCAAAACTGAGAGT 57.158 34.783 0.00 0.00 0.00 3.24
877 1008 6.638468 GGTAAACATGCTTTCAAAACTGAGAG 59.362 38.462 0.00 0.00 0.00 3.20
878 1009 6.321181 AGGTAAACATGCTTTCAAAACTGAGA 59.679 34.615 0.00 0.00 0.00 3.27
921 1057 2.995939 GGATGGCAGCAAAACTAAAAGC 59.004 45.455 4.64 0.00 0.00 3.51
926 1063 0.324275 GGGGGATGGCAGCAAAACTA 60.324 55.000 4.64 0.00 0.00 2.24
989 1131 3.275540 ATGGTTGCCATTGATCTGAGGC 61.276 50.000 13.65 13.65 42.23 4.70
1295 1448 6.101150 TGAAAGGCCTTTATAGGAAGCTGATA 59.899 38.462 30.47 0.00 45.05 2.15
1345 1498 1.667830 CAACATCGTGGCGTGACCT 60.668 57.895 0.00 0.00 40.22 3.85
1443 1596 3.713826 GGACCATTTCCAGTAGGTTGA 57.286 47.619 0.00 0.00 45.10 3.18
1675 1828 4.320861 CGAAACACAAATCCATGCCTGTAA 60.321 41.667 0.00 0.00 0.00 2.41
1938 2091 5.439721 TGTTGTATGCCTATTCTCATTGCT 58.560 37.500 0.00 0.00 0.00 3.91
2073 2226 4.104776 GGCGACCACATTTATCAACAATG 58.895 43.478 0.00 0.00 37.60 2.82
2184 2337 1.190833 AGAGCATCCTATGGGAGCCG 61.191 60.000 3.45 0.00 45.86 5.52
2241 2394 0.098200 TCAGACGATGCGGTAACTCG 59.902 55.000 0.00 0.00 38.34 4.18
2569 2722 4.415881 TCTTACTGACAACAGAAAGGCA 57.584 40.909 0.00 0.00 46.03 4.75
2670 2826 5.821470 TCTCTTGAAGAATGCATCCTCAATC 59.179 40.000 14.78 7.50 37.74 2.67
2982 3140 6.287589 AGAAATCCTCGTAATTCAGTGAGT 57.712 37.500 0.00 0.00 0.00 3.41
3200 3360 7.118245 CGGCATTGCTAACATCTTCTGAATATA 59.882 37.037 8.82 0.00 0.00 0.86
3466 3629 1.489560 GGTTCACCCACCCTGTAGCT 61.490 60.000 0.00 0.00 0.00 3.32
3497 3660 5.010617 TCAAGTTTAGGGAAAGCAATGAACC 59.989 40.000 0.00 0.00 0.00 3.62
3600 3766 2.659063 CGCACCACCATCCTCTCCA 61.659 63.158 0.00 0.00 0.00 3.86
3618 3784 3.507786 GGCATCACCGTTACAAATTTCC 58.492 45.455 0.00 0.00 0.00 3.13
3799 3965 1.291588 CAAGGAGCTCGAGCACTGT 59.708 57.895 36.87 18.48 45.16 3.55
4069 4245 6.048509 CCAGTATACATGCAGTGTTCATACA 58.951 40.000 5.50 0.00 42.29 2.29
4164 4346 7.281040 TCCAATATGATGAGGCAGAAAATTC 57.719 36.000 0.00 0.00 0.00 2.17
4484 4692 9.319143 GAGCAACTACAGTTAACTGAATCATAT 57.681 33.333 36.14 17.88 46.59 1.78
4511 4719 5.177725 TCTAACTGAAACGATATGCGCTA 57.822 39.130 9.73 0.00 46.04 4.26
4520 4728 2.673043 GCCGTCCATCTAACTGAAACGA 60.673 50.000 0.00 0.00 33.77 3.85
4523 4731 1.404986 CGGCCGTCCATCTAACTGAAA 60.405 52.381 19.50 0.00 0.00 2.69
4582 4794 2.997986 AGTAACGTTACAAAGGGCATCG 59.002 45.455 33.43 0.00 36.12 3.84
4618 4833 2.613506 GGCAACGGGGTGAAACTCG 61.614 63.158 0.00 0.00 39.25 4.18
4776 4994 3.556004 GCGATCTAGGGATTTGGAGGAAG 60.556 52.174 0.00 0.00 31.46 3.46
4777 4995 2.368875 GCGATCTAGGGATTTGGAGGAA 59.631 50.000 0.00 0.00 31.46 3.36
4810 5029 4.729868 ACCAATTTGTCAGGAACTAGCTT 58.270 39.130 0.00 0.00 36.02 3.74
4903 5133 1.971357 GCCGATCAGAAGGATAAGGGA 59.029 52.381 0.00 0.00 36.00 4.20
4947 5178 1.959226 CAGAACCACAACCCCGACG 60.959 63.158 0.00 0.00 0.00 5.12
4961 5192 3.283684 CAAACACCGCCGCCAGAA 61.284 61.111 0.00 0.00 0.00 3.02
4999 5232 2.094906 CGACTGATCTGTACCCGAACAA 60.095 50.000 5.09 0.00 0.00 2.83
5000 5233 1.471287 CGACTGATCTGTACCCGAACA 59.529 52.381 5.09 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.