Multiple sequence alignment - TraesCS3D01G251000

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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 TraesCS3D01G251000 chr3D 100.000 3389 0 0 1 3389 351286270 351289658 0.000000e+00 6259.0
1 TraesCS3D01G251000 chr3D 88.182 110 6 5 2543 2646 5867020 5866912 1.280000e-24 124.0
2 TraesCS3D01G251000 chr3D 97.368 38 1 0 416 453 351286621 351286658 7.850000e-07 65.8
3 TraesCS3D01G251000 chr3B 94.032 2128 89 23 732 2827 449846111 449848232 0.000000e+00 3192.0
4 TraesCS3D01G251000 chr3B 94.746 571 27 3 2820 3388 521479512 521480081 0.000000e+00 885.0
5 TraesCS3D01G251000 chr3A 97.100 1655 39 2 863 2508 469668842 469670496 0.000000e+00 2782.0
6 TraesCS3D01G251000 chr3A 84.474 599 78 14 1 589 700822352 700822945 8.150000e-161 577.0
7 TraesCS3D01G251000 chr3A 93.082 159 8 2 724 879 469668665 469668823 2.630000e-56 230.0
8 TraesCS3D01G251000 chr5B 96.106 565 21 1 2825 3388 82447850 82448414 0.000000e+00 920.0
9 TraesCS3D01G251000 chr5B 88.095 84 10 0 2521 2604 676925326 676925243 2.150000e-17 100.0
10 TraesCS3D01G251000 chr6D 95.936 566 21 2 2825 3388 295109033 295108468 0.000000e+00 917.0
11 TraesCS3D01G251000 chr6D 96.970 33 1 0 1368 1400 316564968 316565000 4.720000e-04 56.5
12 TraesCS3D01G251000 chrUn 95.575 565 24 1 2825 3388 47578351 47578915 0.000000e+00 904.0
13 TraesCS3D01G251000 chrUn 95.221 565 26 1 2825 3388 109549157 109549721 0.000000e+00 893.0
14 TraesCS3D01G251000 chr2D 95.398 565 25 1 2825 3388 499157396 499157960 0.000000e+00 898.0
15 TraesCS3D01G251000 chr4B 95.079 569 27 1 2821 3388 630003312 630002744 0.000000e+00 894.0
16 TraesCS3D01G251000 chr4B 86.173 716 73 13 1 708 13388208 13387511 0.000000e+00 750.0
17 TraesCS3D01G251000 chr4B 85.675 719 75 18 1 708 660538523 660539224 0.000000e+00 732.0
18 TraesCS3D01G251000 chr2A 94.728 569 28 2 2822 3388 723177712 723178280 0.000000e+00 883.0
19 TraesCS3D01G251000 chr2A 85.335 716 71 13 1 708 680348954 680349643 0.000000e+00 710.0
20 TraesCS3D01G251000 chr4A 94.867 565 28 1 2825 3388 683537338 683537902 0.000000e+00 881.0
21 TraesCS3D01G251000 chr4A 87.021 678 63 14 3 673 581957392 581958051 0.000000e+00 741.0
22 TraesCS3D01G251000 chr4A 84.895 715 84 12 1 708 642841168 642840471 0.000000e+00 701.0
23 TraesCS3D01G251000 chr4A 83.036 112 14 4 2515 2625 122051185 122051078 2.780000e-16 97.1
24 TraesCS3D01G251000 chr4A 97.368 38 1 0 416 453 581957742 581957779 7.850000e-07 65.8
25 TraesCS3D01G251000 chr1B 85.056 716 74 18 2 708 262524636 262523945 0.000000e+00 699.0
26 TraesCS3D01G251000 chr1B 86.144 599 68 11 1 589 633308500 633309093 1.720000e-177 632.0
27 TraesCS3D01G251000 chr4D 87.046 633 57 16 1 625 2825698 2825083 0.000000e+00 691.0
28 TraesCS3D01G251000 chr1D 91.287 505 32 8 2 498 465075725 465076225 0.000000e+00 678.0
29 TraesCS3D01G251000 chr1D 97.368 38 1 0 416 453 465076075 465076112 7.850000e-07 65.8
30 TraesCS3D01G251000 chr6B 77.723 404 60 13 100 497 21095515 21095136 1.580000e-53 220.0
31 TraesCS3D01G251000 chr6B 77.723 404 60 13 100 497 21098042 21097663 1.580000e-53 220.0
32 TraesCS3D01G251000 chr6B 77.723 404 60 13 100 497 21101871 21101492 1.580000e-53 220.0
33 TraesCS3D01G251000 chr6B 84.733 131 14 4 2520 2646 2069644 2069516 3.550000e-25 126.0
34 TraesCS3D01G251000 chr6B 88.764 89 10 0 2520 2608 5789112 5789024 3.580000e-20 110.0
35 TraesCS3D01G251000 chr6B 100.000 30 0 0 1371 1400 507795235 507795206 4.720000e-04 56.5
36 TraesCS3D01G251000 chr2B 84.615 117 12 4 2517 2633 740319867 740319757 9.940000e-21 111.0
37 TraesCS3D01G251000 chr7B 81.679 131 19 5 2520 2647 564189764 564189636 1.660000e-18 104.0
38 TraesCS3D01G251000 chr5A 84.416 77 12 0 2523 2599 440939529 440939605 3.630000e-10 76.8
39 TraesCS3D01G251000 chr6A 96.970 33 1 0 1368 1400 454547095 454547127 4.720000e-04 56.5


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 TraesCS3D01G251000 chr3D 351286270 351289658 3388 False 3162.4 6259 98.6840 1 3389 2 chr3D.!!$F1 3388
1 TraesCS3D01G251000 chr3B 449846111 449848232 2121 False 3192.0 3192 94.0320 732 2827 1 chr3B.!!$F1 2095
2 TraesCS3D01G251000 chr3B 521479512 521480081 569 False 885.0 885 94.7460 2820 3388 1 chr3B.!!$F2 568
3 TraesCS3D01G251000 chr3A 469668665 469670496 1831 False 1506.0 2782 95.0910 724 2508 2 chr3A.!!$F2 1784
4 TraesCS3D01G251000 chr3A 700822352 700822945 593 False 577.0 577 84.4740 1 589 1 chr3A.!!$F1 588
5 TraesCS3D01G251000 chr5B 82447850 82448414 564 False 920.0 920 96.1060 2825 3388 1 chr5B.!!$F1 563
6 TraesCS3D01G251000 chr6D 295108468 295109033 565 True 917.0 917 95.9360 2825 3388 1 chr6D.!!$R1 563
7 TraesCS3D01G251000 chrUn 47578351 47578915 564 False 904.0 904 95.5750 2825 3388 1 chrUn.!!$F1 563
8 TraesCS3D01G251000 chrUn 109549157 109549721 564 False 893.0 893 95.2210 2825 3388 1 chrUn.!!$F2 563
9 TraesCS3D01G251000 chr2D 499157396 499157960 564 False 898.0 898 95.3980 2825 3388 1 chr2D.!!$F1 563
10 TraesCS3D01G251000 chr4B 630002744 630003312 568 True 894.0 894 95.0790 2821 3388 1 chr4B.!!$R2 567
11 TraesCS3D01G251000 chr4B 13387511 13388208 697 True 750.0 750 86.1730 1 708 1 chr4B.!!$R1 707
12 TraesCS3D01G251000 chr4B 660538523 660539224 701 False 732.0 732 85.6750 1 708 1 chr4B.!!$F1 707
13 TraesCS3D01G251000 chr2A 723177712 723178280 568 False 883.0 883 94.7280 2822 3388 1 chr2A.!!$F2 566
14 TraesCS3D01G251000 chr2A 680348954 680349643 689 False 710.0 710 85.3350 1 708 1 chr2A.!!$F1 707
15 TraesCS3D01G251000 chr4A 683537338 683537902 564 False 881.0 881 94.8670 2825 3388 1 chr4A.!!$F1 563
16 TraesCS3D01G251000 chr4A 642840471 642841168 697 True 701.0 701 84.8950 1 708 1 chr4A.!!$R2 707
17 TraesCS3D01G251000 chr4A 581957392 581958051 659 False 403.4 741 92.1945 3 673 2 chr4A.!!$F2 670
18 TraesCS3D01G251000 chr1B 262523945 262524636 691 True 699.0 699 85.0560 2 708 1 chr1B.!!$R1 706
19 TraesCS3D01G251000 chr1B 633308500 633309093 593 False 632.0 632 86.1440 1 589 1 chr1B.!!$F1 588
20 TraesCS3D01G251000 chr4D 2825083 2825698 615 True 691.0 691 87.0460 1 625 1 chr4D.!!$R1 624
21 TraesCS3D01G251000 chr1D 465075725 465076225 500 False 371.9 678 94.3275 2 498 2 chr1D.!!$F1 496
22 TraesCS3D01G251000 chr6B 21095136 21101871 6735 True 220.0 220 77.7230 100 497 3 chr6B.!!$R4 397

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
222 226 0.454957 CCATGCGAAAAGAACAGCGG 60.455 55.000 0.0 0.0 0.0 5.52 F
775 4652 1.001378 CAAGCAAGGAAAGTTGACGGG 60.001 52.381 0.0 0.0 0.0 5.28 F
823 4703 1.577328 CTGGCACATTGACACGGGAC 61.577 60.000 0.0 0.0 38.2 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 5890 0.966920 TCACGTGGGGAGACTTCTTC 59.033 55.000 17.00 0.0 0.0 2.87 R
2076 5998 1.003839 CCGGTTCACCTGCAGCTTA 60.004 57.895 8.66 0.0 0.0 3.09 R
2681 6653 1.064463 TGGGTACGATTAGGTCCGACT 60.064 52.381 0.00 0.0 0.0 4.18 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
26 27 4.522022 AGAAAAGATGTTGAGAGGGCTTTG 59.478 41.667 0.00 0.00 0.00 2.77
59 60 3.763097 TCTCAATTTGCTATTGTGCGG 57.237 42.857 10.54 3.28 35.36 5.69
63 64 1.846007 ATTTGCTATTGTGCGGGGAA 58.154 45.000 0.00 0.00 35.36 3.97
64 65 1.846007 TTTGCTATTGTGCGGGGAAT 58.154 45.000 0.00 0.00 35.36 3.01
154 156 2.002586 CATTGAGAACGAGCGTGGAAT 58.997 47.619 0.00 0.00 0.00 3.01
155 157 2.163818 TTGAGAACGAGCGTGGAATT 57.836 45.000 0.00 0.00 0.00 2.17
157 159 2.489971 TGAGAACGAGCGTGGAATTTT 58.510 42.857 0.00 0.00 0.00 1.82
158 160 2.875933 TGAGAACGAGCGTGGAATTTTT 59.124 40.909 0.00 0.00 0.00 1.94
222 226 0.454957 CCATGCGAAAAGAACAGCGG 60.455 55.000 0.00 0.00 0.00 5.52
227 231 1.398390 GCGAAAAGAACAGCGGATCAT 59.602 47.619 0.00 0.00 0.00 2.45
236 240 2.268298 ACAGCGGATCATACGTTTCAC 58.732 47.619 0.00 0.00 0.00 3.18
237 241 2.267426 CAGCGGATCATACGTTTCACA 58.733 47.619 0.00 0.00 0.00 3.58
313 320 6.950041 AGATTTGATGGAAGAGTTGGAAATGA 59.050 34.615 0.00 0.00 0.00 2.57
328 335 2.119801 AATGACATGGCGAAAGAGCT 57.880 45.000 0.00 0.00 37.29 4.09
428 436 6.464222 TCTCGTGGATTTGAAGAACTATGTT 58.536 36.000 0.00 0.00 0.00 2.71
429 437 6.368791 TCTCGTGGATTTGAAGAACTATGTTG 59.631 38.462 0.00 0.00 0.00 3.33
434 442 9.559958 GTGGATTTGAAGAACTATGTTGTATTG 57.440 33.333 0.00 0.00 0.00 1.90
437 445 8.970691 ATTTGAAGAACTATGTTGTATTGTGC 57.029 30.769 0.00 0.00 0.00 4.57
438 446 7.503521 TTGAAGAACTATGTTGTATTGTGCA 57.496 32.000 0.00 0.00 0.00 4.57
440 448 7.935520 TGAAGAACTATGTTGTATTGTGCAAA 58.064 30.769 0.00 0.00 0.00 3.68
442 450 8.574196 AAGAACTATGTTGTATTGTGCAAAAC 57.426 30.769 0.00 0.00 0.00 2.43
444 452 9.062524 AGAACTATGTTGTATTGTGCAAAACTA 57.937 29.630 0.00 0.00 0.00 2.24
447 455 8.792633 ACTATGTTGTATTGTGCAAAACTATGT 58.207 29.630 0.00 0.00 0.00 2.29
564 623 5.387279 GCCGATTTTACATCTTCGTTTTGA 58.613 37.500 0.00 0.00 0.00 2.69
566 625 6.361214 GCCGATTTTACATCTTCGTTTTGAAA 59.639 34.615 0.00 0.00 35.79 2.69
618 4465 8.366359 ACAGCTCCATTTTAAACCATCTATTT 57.634 30.769 0.00 0.00 0.00 1.40
643 4517 6.545666 TGAGTTGAGCCTTTTTCAAAGATGTA 59.454 34.615 0.00 0.00 36.41 2.29
694 4571 6.618287 TTTTATATCATCGGTTTGGAGCAG 57.382 37.500 0.00 0.00 0.00 4.24
708 4585 5.422666 TTGGAGCAGCAAAATATACATCG 57.577 39.130 0.00 0.00 0.00 3.84
709 4586 3.814842 TGGAGCAGCAAAATATACATCGG 59.185 43.478 0.00 0.00 0.00 4.18
710 4587 4.065088 GGAGCAGCAAAATATACATCGGA 58.935 43.478 0.00 0.00 0.00 4.55
711 4588 4.153117 GGAGCAGCAAAATATACATCGGAG 59.847 45.833 0.00 0.00 0.00 4.63
712 4589 4.960938 AGCAGCAAAATATACATCGGAGA 58.039 39.130 0.00 0.00 45.75 3.71
713 4590 5.555017 AGCAGCAAAATATACATCGGAGAT 58.445 37.500 0.00 0.00 45.12 2.75
714 4591 5.410746 AGCAGCAAAATATACATCGGAGATG 59.589 40.000 8.33 8.33 45.12 2.90
715 4592 5.625251 CAGCAAAATATACATCGGAGATGC 58.375 41.667 9.67 0.00 45.12 3.91
716 4593 5.410746 CAGCAAAATATACATCGGAGATGCT 59.589 40.000 9.67 0.00 45.12 3.79
717 4594 5.641209 AGCAAAATATACATCGGAGATGCTC 59.359 40.000 9.67 0.00 45.12 4.26
718 4595 5.641209 GCAAAATATACATCGGAGATGCTCT 59.359 40.000 9.67 0.00 45.12 4.09
719 4596 6.813649 GCAAAATATACATCGGAGATGCTCTA 59.186 38.462 9.67 0.90 45.12 2.43
720 4597 7.331934 GCAAAATATACATCGGAGATGCTCTAA 59.668 37.037 9.67 0.00 45.12 2.10
721 4598 8.651588 CAAAATATACATCGGAGATGCTCTAAC 58.348 37.037 9.67 0.00 45.12 2.34
722 4599 7.710676 AATATACATCGGAGATGCTCTAACT 57.289 36.000 9.67 0.00 45.12 2.24
770 4647 4.252878 ACCAAAACAAGCAAGGAAAGTTG 58.747 39.130 0.00 0.00 0.00 3.16
772 4649 4.329801 CCAAAACAAGCAAGGAAAGTTGAC 59.670 41.667 0.00 0.00 0.00 3.18
775 4652 1.001378 CAAGCAAGGAAAGTTGACGGG 60.001 52.381 0.00 0.00 0.00 5.28
811 4691 1.891919 GAAACGGCAGTCTGGCACA 60.892 57.895 24.57 0.00 43.94 4.57
823 4703 1.577328 CTGGCACATTGACACGGGAC 61.577 60.000 0.00 0.00 38.20 4.46
1161 5083 2.507992 CTTCTCTGCGGCGACCTG 60.508 66.667 12.98 0.00 0.00 4.00
1968 5890 4.775746 GAGCTCTCCGTGAACTCG 57.224 61.111 6.43 0.00 29.58 4.18
2076 5998 2.955881 CGGGGAGAAGGGCGAGTTT 61.956 63.158 0.00 0.00 0.00 2.66
2178 6100 1.007238 TGGTGGGTGGAAAGGAACAAA 59.993 47.619 0.00 0.00 0.00 2.83
2345 6267 3.576078 TCAAGGCAAGAAGAAGACCAA 57.424 42.857 0.00 0.00 0.00 3.67
2352 6274 2.808543 CAAGAAGAAGACCAAGGGAACG 59.191 50.000 0.00 0.00 0.00 3.95
2414 6336 6.793492 TGTGAATACGTGAATGATTGAACA 57.207 33.333 0.00 0.00 0.00 3.18
2510 6435 2.475818 TGTGTGGTGTGTCGTGTAATC 58.524 47.619 0.00 0.00 0.00 1.75
2518 6443 6.091577 GTGGTGTGTCGTGTAATCAATATCAA 59.908 38.462 0.00 0.00 0.00 2.57
2524 6449 8.523464 GTGTCGTGTAATCAATATCAATTTTGC 58.477 33.333 0.00 0.00 0.00 3.68
2539 6464 7.194607 TCAATTTTGCTAAGTCTCAGTTGAG 57.805 36.000 2.69 2.69 43.36 3.02
2541 6466 7.931407 TCAATTTTGCTAAGTCTCAGTTGAGTA 59.069 33.333 8.85 0.00 42.60 2.59
2554 6479 8.704234 GTCTCAGTTGAGTAAGACTTTGTTATG 58.296 37.037 8.85 0.00 42.60 1.90
2559 6484 7.873505 AGTTGAGTAAGACTTTGTTATGTCTCC 59.126 37.037 0.00 0.00 42.02 3.71
2566 6491 5.421056 AGACTTTGTTATGTCTCCGTGGATA 59.579 40.000 0.00 0.00 39.04 2.59
2586 6511 8.940952 GTGGATACTATATTCCTTTGATCTTGC 58.059 37.037 0.00 0.00 32.95 4.01
2659 6631 3.917329 TCACTTGTAAGTCTCAGTCGG 57.083 47.619 0.00 0.00 37.08 4.79
2660 6632 3.483421 TCACTTGTAAGTCTCAGTCGGA 58.517 45.455 0.00 0.00 37.08 4.55
2661 6633 3.252701 TCACTTGTAAGTCTCAGTCGGAC 59.747 47.826 0.00 0.00 37.08 4.79
2662 6634 3.253677 CACTTGTAAGTCTCAGTCGGACT 59.746 47.826 4.45 4.45 44.73 3.85
2669 6641 2.683867 AGTCTCAGTCGGACTTTATCGG 59.316 50.000 8.18 0.00 40.65 4.18
2670 6642 2.681848 GTCTCAGTCGGACTTTATCGGA 59.318 50.000 8.18 0.69 34.46 4.55
2671 6643 3.128242 GTCTCAGTCGGACTTTATCGGAA 59.872 47.826 8.18 0.00 38.31 4.30
2672 6644 3.760151 TCTCAGTCGGACTTTATCGGAAA 59.240 43.478 8.18 0.00 38.31 3.13
2673 6645 4.219070 TCTCAGTCGGACTTTATCGGAAAA 59.781 41.667 8.18 0.00 38.31 2.29
2674 6646 4.885413 TCAGTCGGACTTTATCGGAAAAA 58.115 39.130 8.18 0.00 38.31 1.94
2692 6664 4.950205 AAAAAGTCTCAGTCGGACCTAA 57.050 40.909 4.14 0.00 34.56 2.69
2695 6667 2.290464 AGTCTCAGTCGGACCTAATCG 58.710 52.381 4.14 0.00 34.56 3.34
2705 6677 3.451902 TCGGACCTAATCGTACCCAATTT 59.548 43.478 0.00 0.00 0.00 1.82
2706 6678 4.648762 TCGGACCTAATCGTACCCAATTTA 59.351 41.667 0.00 0.00 0.00 1.40
2709 6681 7.015098 TCGGACCTAATCGTACCCAATTTAATA 59.985 37.037 0.00 0.00 0.00 0.98
2710 6682 7.820872 CGGACCTAATCGTACCCAATTTAATAT 59.179 37.037 0.00 0.00 0.00 1.28
2711 6683 9.159364 GGACCTAATCGTACCCAATTTAATATC 57.841 37.037 0.00 0.00 0.00 1.63
2712 6684 9.715121 GACCTAATCGTACCCAATTTAATATCA 57.285 33.333 0.00 0.00 0.00 2.15
2734 6706 5.049060 TCAATGGTTGATAAGTTTGTGTCCG 60.049 40.000 0.00 0.00 34.08 4.79
2753 6725 6.316390 GTGTCCGAAAGAATATTTCTGATGGT 59.684 38.462 0.00 0.00 40.59 3.55
2757 6729 8.044309 TCCGAAAGAATATTTCTGATGGTTGTA 58.956 33.333 0.00 0.00 40.59 2.41
2808 6786 6.265196 TGTCTGGAATTAACTGTTGCTGAAAT 59.735 34.615 2.69 0.00 29.63 2.17
2823 6801 5.918608 TGCTGAAATGGAGAGAGTAATACC 58.081 41.667 0.00 0.00 0.00 2.73
3061 7040 3.253432 ACGCTTCCTTCTTCAAATCAACC 59.747 43.478 0.00 0.00 0.00 3.77
3388 7844 7.335627 TCTCCACATTACTAATGGGTTGTAAG 58.664 38.462 12.48 5.30 40.76 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.806366 CAAATTGAGATTGCAAAATCCCC 57.194 39.130 1.71 0.00 0.00 4.81
59 60 7.502060 TTGATCCCAGAATCTAGATATTCCC 57.498 40.000 5.46 0.00 36.68 3.97
170 172 5.105997 GGAATGCCCATCAAGTGATATAAGC 60.106 44.000 0.00 0.00 32.63 3.09
174 176 4.141088 ACAGGAATGCCCATCAAGTGATAT 60.141 41.667 0.00 0.00 37.41 1.63
222 226 5.607119 ACACCTTTGTGAAACGTATGATC 57.393 39.130 0.00 0.00 45.76 2.92
227 231 4.622313 CGCTATACACCTTTGTGAAACGTA 59.378 41.667 0.00 0.00 45.76 3.57
236 240 6.858993 GTCTCTAATCTCGCTATACACCTTTG 59.141 42.308 0.00 0.00 0.00 2.77
237 241 6.546403 TGTCTCTAATCTCGCTATACACCTTT 59.454 38.462 0.00 0.00 0.00 3.11
313 320 0.679002 ATGCAGCTCTTTCGCCATGT 60.679 50.000 0.00 0.00 0.00 3.21
504 524 0.816825 CTGTTCAGCCACTGTGCAGT 60.817 55.000 1.29 0.00 43.61 4.40
508 528 1.947013 CTGCTGTTCAGCCACTGTG 59.053 57.895 19.91 0.00 35.78 3.66
564 623 4.961438 AAAGCAACTCCAATGGATGTTT 57.039 36.364 0.87 0.36 0.00 2.83
566 625 4.961438 AAAAAGCAACTCCAATGGATGT 57.039 36.364 0.87 0.14 0.00 3.06
589 4436 8.366359 AGATGGTTTAAAATGGAGCTGTAAAT 57.634 30.769 0.00 0.00 0.00 1.40
596 4443 8.470002 ACTCAAATAGATGGTTTAAAATGGAGC 58.530 33.333 0.00 0.00 0.00 4.70
618 4465 5.360714 ACATCTTTGAAAAAGGCTCAACTCA 59.639 36.000 0.00 0.00 32.61 3.41
676 4553 1.209261 TGCTGCTCCAAACCGATGATA 59.791 47.619 0.00 0.00 0.00 2.15
681 4558 1.327303 ATTTTGCTGCTCCAAACCGA 58.673 45.000 0.00 0.00 34.68 4.69
694 4571 5.862811 GAGCATCTCCGATGTATATTTTGC 58.137 41.667 5.81 0.00 0.00 3.68
711 4588 3.618594 TCATGCGTTCAAGTTAGAGCATC 59.381 43.478 0.00 0.00 42.52 3.91
712 4589 3.599343 TCATGCGTTCAAGTTAGAGCAT 58.401 40.909 0.00 0.00 44.85 3.79
713 4590 3.038788 TCATGCGTTCAAGTTAGAGCA 57.961 42.857 0.00 0.00 39.02 4.26
714 4591 3.001736 GGATCATGCGTTCAAGTTAGAGC 59.998 47.826 0.00 0.00 0.00 4.09
715 4592 4.183865 TGGATCATGCGTTCAAGTTAGAG 58.816 43.478 0.00 0.00 0.00 2.43
716 4593 4.200838 TGGATCATGCGTTCAAGTTAGA 57.799 40.909 0.00 0.00 0.00 2.10
717 4594 4.024556 GGATGGATCATGCGTTCAAGTTAG 60.025 45.833 0.00 0.00 0.00 2.34
718 4595 3.876914 GGATGGATCATGCGTTCAAGTTA 59.123 43.478 0.00 0.00 0.00 2.24
719 4596 2.684881 GGATGGATCATGCGTTCAAGTT 59.315 45.455 0.00 0.00 0.00 2.66
720 4597 2.292267 GGATGGATCATGCGTTCAAGT 58.708 47.619 0.00 0.00 0.00 3.16
721 4598 2.291365 TGGATGGATCATGCGTTCAAG 58.709 47.619 0.00 0.00 34.93 3.02
722 4599 2.416680 TGGATGGATCATGCGTTCAA 57.583 45.000 0.00 0.00 34.93 2.69
811 4691 2.358247 GCACCGTCCCGTGTCAAT 60.358 61.111 0.00 0.00 36.08 2.57
823 4703 2.566010 CCGGGAACATTTGCACCG 59.434 61.111 0.00 2.86 43.89 4.94
996 4918 3.490031 TTGGCTGGCGTCCATGTGT 62.490 57.895 0.00 0.00 32.92 3.72
1008 4930 3.710722 AGGAGGACGCCTTGGCTG 61.711 66.667 10.12 6.07 33.46 4.85
1161 5083 1.080025 GTCGTAGGTGACCTGGCAC 60.080 63.158 15.83 3.38 34.61 5.01
1968 5890 0.966920 TCACGTGGGGAGACTTCTTC 59.033 55.000 17.00 0.00 0.00 2.87
2061 5983 1.066071 AGCTTAAACTCGCCCTTCTCC 60.066 52.381 0.00 0.00 0.00 3.71
2076 5998 1.003839 CCGGTTCACCTGCAGCTTA 60.004 57.895 8.66 0.00 0.00 3.09
2288 6210 2.092914 GGCTCCTTACTGCTAATGGTGT 60.093 50.000 0.00 0.00 0.00 4.16
2352 6274 1.831580 AGCATGCAGGGAGAAACTTC 58.168 50.000 21.98 0.00 0.00 3.01
2436 6358 8.100791 TCAAAAGCCATTATTCACAGTAGTACT 58.899 33.333 0.00 0.00 0.00 2.73
2437 6359 8.263940 TCAAAAGCCATTATTCACAGTAGTAC 57.736 34.615 0.00 0.00 0.00 2.73
2518 6443 8.150945 TCTTACTCAACTGAGACTTAGCAAAAT 58.849 33.333 13.61 0.00 44.74 1.82
2532 6457 8.594881 AGACATAACAAAGTCTTACTCAACTG 57.405 34.615 0.00 0.00 42.12 3.16
2536 6461 6.015688 ACGGAGACATAACAAAGTCTTACTCA 60.016 38.462 0.00 0.00 44.61 3.41
2539 6464 5.347907 CCACGGAGACATAACAAAGTCTTAC 59.652 44.000 0.00 0.00 44.61 2.34
2541 6466 4.039973 TCCACGGAGACATAACAAAGTCTT 59.960 41.667 0.00 0.00 44.61 3.01
2548 6473 8.645814 AATATAGTATCCACGGAGACATAACA 57.354 34.615 13.06 0.00 38.66 2.41
2554 6479 6.837471 AAGGAATATAGTATCCACGGAGAC 57.163 41.667 2.52 2.52 38.23 3.36
2559 6484 9.144747 CAAGATCAAAGGAATATAGTATCCACG 57.855 37.037 0.00 0.00 38.23 4.94
2566 6491 8.985315 TTCATGCAAGATCAAAGGAATATAGT 57.015 30.769 0.00 0.00 0.00 2.12
2651 6623 3.777465 TTCCGATAAAGTCCGACTGAG 57.223 47.619 0.65 0.00 0.00 3.35
2671 6643 4.950205 TTAGGTCCGACTGAGACTTTTT 57.050 40.909 0.00 0.00 34.56 1.94
2672 6644 4.380655 CGATTAGGTCCGACTGAGACTTTT 60.381 45.833 0.00 0.00 34.56 2.27
2673 6645 3.128938 CGATTAGGTCCGACTGAGACTTT 59.871 47.826 0.00 0.00 34.56 2.66
2674 6646 2.683867 CGATTAGGTCCGACTGAGACTT 59.316 50.000 0.00 0.00 34.56 3.01
2675 6647 2.290464 CGATTAGGTCCGACTGAGACT 58.710 52.381 0.00 0.00 34.56 3.24
2676 6648 2.015587 ACGATTAGGTCCGACTGAGAC 58.984 52.381 0.00 0.00 0.00 3.36
2677 6649 2.414994 ACGATTAGGTCCGACTGAGA 57.585 50.000 0.00 0.00 0.00 3.27
2678 6650 2.290093 GGTACGATTAGGTCCGACTGAG 59.710 54.545 0.00 0.00 0.00 3.35
2679 6651 2.292267 GGTACGATTAGGTCCGACTGA 58.708 52.381 0.00 0.00 0.00 3.41
2680 6652 1.336125 GGGTACGATTAGGTCCGACTG 59.664 57.143 0.00 0.00 0.00 3.51
2681 6653 1.064463 TGGGTACGATTAGGTCCGACT 60.064 52.381 0.00 0.00 0.00 4.18
2682 6654 1.392589 TGGGTACGATTAGGTCCGAC 58.607 55.000 0.00 0.00 0.00 4.79
2683 6655 2.142356 TTGGGTACGATTAGGTCCGA 57.858 50.000 0.00 0.00 0.00 4.55
2684 6656 3.464111 AATTGGGTACGATTAGGTCCG 57.536 47.619 0.00 0.00 0.00 4.79
2685 6657 9.159364 GATATTAAATTGGGTACGATTAGGTCC 57.841 37.037 0.00 0.00 30.40 4.46
2692 6664 8.934023 ACCATTGATATTAAATTGGGTACGAT 57.066 30.769 5.22 0.00 0.00 3.73
2710 6682 5.049060 CGGACACAAACTTATCAACCATTGA 60.049 40.000 0.00 0.00 45.01 2.57
2711 6683 5.049060 TCGGACACAAACTTATCAACCATTG 60.049 40.000 0.00 0.00 0.00 2.82
2712 6684 5.067273 TCGGACACAAACTTATCAACCATT 58.933 37.500 0.00 0.00 0.00 3.16
2732 6704 7.088589 ACAACCATCAGAAATATTCTTTCGG 57.911 36.000 0.00 0.00 38.11 4.30
2771 6749 9.047947 AGTTAATTCCAGACAAAGGAGTAGTAT 57.952 33.333 0.00 0.00 36.33 2.12
2772 6750 8.311836 CAGTTAATTCCAGACAAAGGAGTAGTA 58.688 37.037 0.00 0.00 36.33 1.82
2773 6751 7.162082 CAGTTAATTCCAGACAAAGGAGTAGT 58.838 38.462 0.00 0.00 36.33 2.73
2776 6754 5.941788 ACAGTTAATTCCAGACAAAGGAGT 58.058 37.500 0.00 0.00 36.33 3.85
2778 6756 5.009610 GCAACAGTTAATTCCAGACAAAGGA 59.990 40.000 0.00 0.00 0.00 3.36
2779 6757 5.010012 AGCAACAGTTAATTCCAGACAAAGG 59.990 40.000 0.00 0.00 0.00 3.11
2780 6758 5.916883 CAGCAACAGTTAATTCCAGACAAAG 59.083 40.000 0.00 0.00 0.00 2.77
2781 6759 5.592282 TCAGCAACAGTTAATTCCAGACAAA 59.408 36.000 0.00 0.00 0.00 2.83
2782 6760 5.129634 TCAGCAACAGTTAATTCCAGACAA 58.870 37.500 0.00 0.00 0.00 3.18
2783 6761 4.713553 TCAGCAACAGTTAATTCCAGACA 58.286 39.130 0.00 0.00 0.00 3.41
2784 6762 5.689383 TTCAGCAACAGTTAATTCCAGAC 57.311 39.130 0.00 0.00 0.00 3.51
2785 6763 6.294675 CCATTTCAGCAACAGTTAATTCCAGA 60.295 38.462 0.00 0.00 0.00 3.86
2786 6764 5.865552 CCATTTCAGCAACAGTTAATTCCAG 59.134 40.000 0.00 0.00 0.00 3.86
2787 6765 5.538053 TCCATTTCAGCAACAGTTAATTCCA 59.462 36.000 0.00 0.00 0.00 3.53
2788 6766 6.024552 TCCATTTCAGCAACAGTTAATTCC 57.975 37.500 0.00 0.00 0.00 3.01
2873 6851 4.631813 AGAGCTGTAACGAATGATTGTTCC 59.368 41.667 0.00 0.00 34.86 3.62
2875 6853 5.617751 GCAAGAGCTGTAACGAATGATTGTT 60.618 40.000 0.00 0.00 36.06 2.83
3020 6999 2.989840 CGTTGAGTGTCTCCAAGATGAC 59.010 50.000 0.00 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.