Multiple sequence alignment - TraesCS2D01G291400

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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 TraesCS2D01G291400 chr2D 100.000 3163 0 0 1 3163 373654664 373651502 0.000000e+00 5842
1 TraesCS2D01G291400 chr2D 94.332 2082 86 16 407 2470 373750012 373752079 0.000000e+00 3162
2 TraesCS2D01G291400 chr2D 88.703 239 24 2 2488 2724 609889998 609889761 3.990000e-74 289
3 TraesCS2D01G291400 chr2D 86.975 238 30 1 2488 2724 373651048 373651285 1.870000e-67 267
4 TraesCS2D01G291400 chr2D 94.286 70 4 0 2987 3056 641372897 641372966 1.200000e-19 108
5 TraesCS2D01G291400 chr2A 91.426 2799 159 38 409 3159 505080486 505077721 0.000000e+00 3764
6 TraesCS2D01G291400 chr2A 92.422 1821 100 19 586 2376 505208565 505210377 0.000000e+00 2564
7 TraesCS2D01G291400 chr2A 85.652 230 23 4 10 238 729555216 729554996 1.900000e-57 233
8 TraesCS2D01G291400 chr2A 83.969 131 16 3 274 403 509069230 509069356 1.540000e-23 121
9 TraesCS2D01G291400 chr2B 93.232 2497 106 20 1 2451 443149383 443146904 0.000000e+00 3616
10 TraesCS2D01G291400 chr2B 94.171 1990 78 20 407 2376 443223072 443225043 0.000000e+00 2998
11 TraesCS2D01G291400 chr2B 78.838 241 46 5 2487 2724 109204130 109203892 1.170000e-34 158
12 TraesCS2D01G291400 chr3D 75.090 554 123 12 1408 1952 566081016 566081563 8.760000e-61 244
13 TraesCS2D01G291400 chr3D 85.463 227 23 4 10 235 590751783 590752000 8.830000e-56 228
14 TraesCS2D01G291400 chr3D 78.926 242 48 3 2485 2724 442981737 442981977 9.080000e-36 161
15 TraesCS2D01G291400 chr3D 83.929 168 24 3 2559 2724 527681315 527681481 1.170000e-34 158
16 TraesCS2D01G291400 chr3D 83.234 167 25 3 2560 2724 517743564 517743399 1.970000e-32 150
17 TraesCS2D01G291400 chr3B 75.045 557 118 18 1408 1952 755806067 755806614 4.080000e-59 239
18 TraesCS2D01G291400 chr3B 85.903 227 22 4 10 235 727161164 727161381 1.900000e-57 233
19 TraesCS2D01G291400 chr7A 86.087 230 20 5 10 235 252954085 252954306 1.470000e-58 237
20 TraesCS2D01G291400 chr3A 75.000 560 115 19 1407 1952 701218937 701218389 5.270000e-58 235
21 TraesCS2D01G291400 chr6B 84.322 236 36 1 2490 2724 566638865 566639100 2.450000e-56 230
22 TraesCS2D01G291400 chr7B 85.088 228 21 8 12 238 603248319 603248104 1.480000e-53 220
23 TraesCS2D01G291400 chr6A 85.022 227 23 5 10 235 22626345 22626561 1.480000e-53 220
24 TraesCS2D01G291400 chr6A 84.416 231 26 4 6 235 539231882 539232103 5.310000e-53 219
25 TraesCS2D01G291400 chr5A 84.581 227 25 4 10 235 91625573 91625790 1.910000e-52 217
26 TraesCS2D01G291400 chr7D 81.863 204 32 5 2524 2724 559111882 559111681 1.950000e-37 167
27 TraesCS2D01G291400 chr6D 83.929 168 24 3 2559 2724 456819563 456819729 1.170000e-34 158


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 TraesCS2D01G291400 chr2D 373651502 373654664 3162 True 5842 5842 100.000 1 3163 1 chr2D.!!$R1 3162
1 TraesCS2D01G291400 chr2D 373750012 373752079 2067 False 3162 3162 94.332 407 2470 1 chr2D.!!$F2 2063
2 TraesCS2D01G291400 chr2A 505077721 505080486 2765 True 3764 3764 91.426 409 3159 1 chr2A.!!$R1 2750
3 TraesCS2D01G291400 chr2A 505208565 505210377 1812 False 2564 2564 92.422 586 2376 1 chr2A.!!$F1 1790
4 TraesCS2D01G291400 chr2B 443146904 443149383 2479 True 3616 3616 93.232 1 2451 1 chr2B.!!$R2 2450
5 TraesCS2D01G291400 chr2B 443223072 443225043 1971 False 2998 2998 94.171 407 2376 1 chr2B.!!$F1 1969
6 TraesCS2D01G291400 chr3D 566081016 566081563 547 False 244 244 75.090 1408 1952 1 chr3D.!!$F3 544
7 TraesCS2D01G291400 chr3B 755806067 755806614 547 False 239 239 75.045 1408 1952 1 chr3B.!!$F2 544
8 TraesCS2D01G291400 chr3A 701218389 701218937 548 True 235 235 75.000 1407 1952 1 chr3A.!!$R1 545

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
71 72 0.108041 CGCACACCTTACCCGGTTAT 60.108 55.0 0.00 0.0 34.29 1.89 F
177 179 0.388649 CGTCTTCTCCCACTGAACGG 60.389 60.0 0.00 0.0 0.00 4.44 F
1009 1097 0.807667 GCAGTGATCGATGGCGTCTT 60.808 55.0 0.54 0.0 38.98 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1591 1.795170 GCGTTGATGTGCAGGTTGGT 61.795 55.000 0.00 0.0 0.00 3.67 R
1658 1767 2.994995 TCGACGGGCACACCATCT 60.995 61.111 0.00 0.0 40.22 2.90 R
2626 2768 0.183492 GGCCTGGCCTGTCATAATCA 59.817 55.000 30.42 0.0 46.69 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
22 23 1.555477 TGCATACGCTCATACACACG 58.445 50.000 0.00 0.00 39.64 4.49
23 24 0.229753 GCATACGCTCATACACACGC 59.770 55.000 0.00 0.00 34.30 5.34
35 36 1.282248 ACACACGCGCATACACTCAC 61.282 55.000 5.73 0.00 0.00 3.51
45 46 3.123804 GCATACACTCACCCTATGAACG 58.876 50.000 0.00 0.00 36.69 3.95
53 54 0.669318 ACCCTATGAACGCACACACG 60.669 55.000 0.00 0.00 39.50 4.49
64 65 1.938861 CACACACGCACACCTTACC 59.061 57.895 0.00 0.00 0.00 2.85
71 72 0.108041 CGCACACCTTACCCGGTTAT 60.108 55.000 0.00 0.00 34.29 1.89
83 84 1.909302 CCCGGTTATCCCTATGAGCAT 59.091 52.381 0.00 0.00 0.00 3.79
87 88 3.766591 CGGTTATCCCTATGAGCATCTCT 59.233 47.826 0.00 0.00 34.92 3.10
149 151 1.746615 TCGTAGGCGCCTCGTAGTT 60.747 57.895 36.73 10.36 38.14 2.24
172 174 3.516578 GGAACGTCTTCTCCCACTG 57.483 57.895 0.00 0.00 0.00 3.66
177 179 0.388649 CGTCTTCTCCCACTGAACGG 60.389 60.000 0.00 0.00 0.00 4.44
208 210 7.920682 CACCGGAAATCCTAAAATAAATTCAGG 59.079 37.037 9.46 0.00 36.92 3.86
225 227 6.949352 ATTCAGGATAAATGTAAGCACCAG 57.051 37.500 0.00 0.00 0.00 4.00
264 290 5.235305 ACCATCGCATCACAATTTAGTTC 57.765 39.130 0.00 0.00 0.00 3.01
270 296 4.675146 CGCATCACAATTTAGTTCCCAAGG 60.675 45.833 0.00 0.00 0.00 3.61
279 305 8.049721 ACAATTTAGTTCCCAAGGAATCTAGAG 58.950 37.037 0.00 0.00 44.04 2.43
321 347 5.220912 GGCGTACTTTTTGTGTTAGGTCTTT 60.221 40.000 0.00 0.00 0.00 2.52
327 353 7.200455 ACTTTTTGTGTTAGGTCTTTGCATAC 58.800 34.615 0.00 0.00 0.00 2.39
328 354 6.952773 TTTTGTGTTAGGTCTTTGCATACT 57.047 33.333 0.00 0.00 0.00 2.12
353 379 2.014857 CAGATGTCTGCACATTCTGGG 58.985 52.381 0.00 0.00 43.79 4.45
379 405 5.625311 CGTTAAAAATGTTGCACTCTCCTTC 59.375 40.000 0.00 0.00 0.00 3.46
381 407 5.444663 AAAAATGTTGCACTCTCCTTCTC 57.555 39.130 0.00 0.00 0.00 2.87
468 495 2.246719 ACTTGACACCTTGTGCTCTC 57.753 50.000 0.00 0.00 36.98 3.20
473 500 4.415881 TGACACCTTGTGCTCTCTTAAA 57.584 40.909 0.00 0.00 36.98 1.52
661 717 4.466015 GGATAAATTTTTGTCCTGGCTGGA 59.534 41.667 9.30 9.30 42.93 3.86
712 768 1.532868 GCAGATGACACTTGACACCAC 59.467 52.381 0.00 0.00 0.00 4.16
753 823 2.161609 GGATTTGAATCAACCGTTCGCT 59.838 45.455 0.00 0.00 37.15 4.93
978 1066 3.802948 ACTAGCAGTAAAGATCACCCG 57.197 47.619 0.00 0.00 0.00 5.28
1008 1096 1.227089 GCAGTGATCGATGGCGTCT 60.227 57.895 0.54 0.00 38.98 4.18
1009 1097 0.807667 GCAGTGATCGATGGCGTCTT 60.808 55.000 0.54 0.00 38.98 3.01
1345 1448 2.600867 GCAGCTGAAGTTACTGATCGAC 59.399 50.000 20.43 0.00 33.10 4.20
1488 1591 1.881903 CTTCTGCCTGCTCTCCGACA 61.882 60.000 0.00 0.00 0.00 4.35
1628 1737 1.686110 GAGGACGGTCACCTGGGAT 60.686 63.158 10.76 0.00 37.93 3.85
1658 1767 0.968901 ACCGCCTCGTCATCACCTTA 60.969 55.000 0.00 0.00 0.00 2.69
1661 1770 1.338337 CGCCTCGTCATCACCTTAGAT 59.662 52.381 0.00 0.00 0.00 1.98
2257 2386 5.286438 TGCTATGCTACGTTATTGGTAGTG 58.714 41.667 0.00 0.00 39.60 2.74
2286 2415 5.052172 CGCATTTGCTTTCCGAATAAATCAG 60.052 40.000 0.51 0.00 39.32 2.90
2295 2427 2.289002 CCGAATAAATCAGCTGCTGGTC 59.711 50.000 27.79 14.52 31.51 4.02
2362 2503 0.960364 GGAAATCCAGGCGTTGCTCA 60.960 55.000 0.00 0.00 35.64 4.26
2474 2616 2.806244 ACAGTATTTCGTTGAGCCACAC 59.194 45.455 0.00 0.00 0.00 3.82
2503 2645 7.611213 AAGTTCGGGAGTGAATAACATAAAG 57.389 36.000 0.00 0.00 0.00 1.85
2507 2649 7.062749 TCGGGAGTGAATAACATAAAGCTAT 57.937 36.000 0.00 0.00 0.00 2.97
2517 2659 9.107367 GAATAACATAAAGCTATCACAATTCGC 57.893 33.333 0.00 0.00 0.00 4.70
2527 2669 3.799137 TCACAATTCGCGTTAAGGTTC 57.201 42.857 5.77 0.00 0.00 3.62
2530 2672 2.224784 ACAATTCGCGTTAAGGTTCCAC 59.775 45.455 5.77 0.00 0.00 4.02
2552 2694 8.311836 TCCACAAAACTACCACAAATTTGTTTA 58.688 29.630 21.10 13.71 40.98 2.01
2557 2699 8.568732 AAACTACCACAAATTTGTTTATGACG 57.431 30.769 21.10 8.18 39.91 4.35
2574 2716 8.851416 GTTTATGACGGATAACTATCAGAATCG 58.149 37.037 4.20 0.00 34.40 3.34
2580 2722 2.510768 AACTATCAGAATCGGCGTCC 57.489 50.000 6.85 0.00 0.00 4.79
2625 2767 2.095110 CCGAGTGCTTTGCAATTGATCA 60.095 45.455 10.34 0.00 39.99 2.92
2626 2768 3.428452 CCGAGTGCTTTGCAATTGATCAT 60.428 43.478 10.34 0.00 39.99 2.45
2628 2770 4.673320 CGAGTGCTTTGCAATTGATCATGA 60.673 41.667 10.34 0.00 39.99 3.07
2636 2778 7.436970 GCTTTGCAATTGATCATGATTATGACA 59.563 33.333 10.14 0.00 45.54 3.58
2637 2779 8.865590 TTTGCAATTGATCATGATTATGACAG 57.134 30.769 10.14 0.00 45.54 3.51
2638 2780 6.977213 TGCAATTGATCATGATTATGACAGG 58.023 36.000 10.14 0.00 45.54 4.00
2639 2781 5.862323 GCAATTGATCATGATTATGACAGGC 59.138 40.000 10.14 4.71 45.54 4.85
2640 2782 6.387465 CAATTGATCATGATTATGACAGGCC 58.613 40.000 10.14 0.00 45.54 5.19
2641 2783 4.710313 TGATCATGATTATGACAGGCCA 57.290 40.909 10.14 0.00 45.54 5.36
2642 2784 4.648651 TGATCATGATTATGACAGGCCAG 58.351 43.478 10.14 0.00 45.54 4.85
2643 2785 3.497103 TCATGATTATGACAGGCCAGG 57.503 47.619 5.01 0.00 38.37 4.45
2644 2786 1.884579 CATGATTATGACAGGCCAGGC 59.115 52.381 5.01 1.26 36.36 4.85
2645 2787 3.398062 CATGATTATGACAGGCCAGGCC 61.398 54.545 24.90 24.90 42.13 5.19
2655 2797 2.489751 GCCAGGCCGCACATAAAC 59.510 61.111 0.00 0.00 0.00 2.01
2679 2821 4.081322 ACCATCTGTTTGACCGTTTACT 57.919 40.909 0.00 0.00 0.00 2.24
2684 2826 6.459024 CCATCTGTTTGACCGTTTACTTTGAA 60.459 38.462 0.00 0.00 0.00 2.69
2686 2828 4.649977 TGTTTGACCGTTTACTTTGAACG 58.350 39.130 2.68 2.68 46.82 3.95
2703 2845 2.025418 CGTTACCTGACGTGTGGGC 61.025 63.158 0.00 0.00 38.19 5.36
2880 3022 4.049640 GACAAATGGCGCCGGCAA 62.050 61.111 28.98 12.05 42.43 4.52
2901 3043 3.231889 CTGCAGTGTCCAGGTCGCT 62.232 63.158 5.25 0.00 0.00 4.93
2917 3059 2.816958 CTACAGCAGCGTGGCAGG 60.817 66.667 2.14 2.14 35.83 4.85
2962 3104 4.554363 CTCGCCGGCTGTAGGTCG 62.554 72.222 26.68 6.06 43.42 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.370494 CGCGTGTGTATGAGCGTA 57.630 55.556 0.00 0.00 46.48 4.42
18 19 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
19 20 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
22 23 1.068588 TCATAGGGTGAGTGTATGCGC 59.931 52.381 0.00 0.00 31.80 6.09
23 24 3.123804 GTTCATAGGGTGAGTGTATGCG 58.876 50.000 0.00 0.00 38.29 4.73
35 36 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
45 46 1.278637 GTAAGGTGTGCGTGTGTGC 59.721 57.895 0.00 0.00 0.00 4.57
53 54 1.660167 GATAACCGGGTAAGGTGTGC 58.340 55.000 1.67 0.00 45.21 4.57
64 65 2.834549 AGATGCTCATAGGGATAACCGG 59.165 50.000 0.00 0.00 46.96 5.28
71 72 3.397282 TCTCTCAGAGATGCTCATAGGGA 59.603 47.826 0.00 0.00 33.35 4.20
83 84 0.393673 CCGGCTCAGTCTCTCAGAGA 60.394 60.000 0.00 0.00 36.22 3.10
87 88 1.683707 ATGCCGGCTCAGTCTCTCA 60.684 57.895 29.70 2.45 0.00 3.27
208 210 9.516314 GTTTAAATCCTGGTGCTTACATTTATC 57.484 33.333 0.00 0.00 0.00 1.75
215 217 6.315642 GGTAGAGTTTAAATCCTGGTGCTTAC 59.684 42.308 0.00 0.00 0.00 2.34
217 219 5.254115 GGTAGAGTTTAAATCCTGGTGCTT 58.746 41.667 0.00 0.00 0.00 3.91
225 227 4.743644 CGATGGTCGGTAGAGTTTAAATCC 59.256 45.833 0.00 0.00 36.00 3.01
264 290 5.615289 CATACAACCTCTAGATTCCTTGGG 58.385 45.833 0.00 0.00 0.00 4.12
270 296 7.170658 GTGAAGATGCATACAACCTCTAGATTC 59.829 40.741 0.00 0.00 0.00 2.52
279 305 1.064060 GCCGTGAAGATGCATACAACC 59.936 52.381 0.00 0.00 0.00 3.77
321 347 3.429960 GCAGACATCTGAGACAGTATGCA 60.430 47.826 23.10 0.00 46.59 3.96
327 353 2.738013 TGTGCAGACATCTGAGACAG 57.262 50.000 13.15 0.00 46.59 3.51
328 354 3.260128 AGAATGTGCAGACATCTGAGACA 59.740 43.478 13.15 13.36 46.59 3.41
353 379 3.638484 AGAGTGCAACATTTTTAACGGC 58.362 40.909 0.00 0.00 41.43 5.68
379 405 1.095600 TCATCGAAGACCACGAGGAG 58.904 55.000 5.68 0.00 43.51 3.69
381 407 0.526211 TGTCATCGAAGACCACGAGG 59.474 55.000 17.41 0.00 42.51 4.63
575 602 9.467258 CCACCAAAAATTGCACAATATATAGAG 57.533 33.333 0.00 0.00 0.00 2.43
581 631 4.009002 GGCCACCAAAAATTGCACAATAT 58.991 39.130 0.00 0.00 0.00 1.28
582 632 3.181451 TGGCCACCAAAAATTGCACAATA 60.181 39.130 0.00 0.00 0.00 1.90
661 717 2.496070 TGGCTAAGCAGAATCTACGTGT 59.504 45.455 0.00 0.00 0.00 4.49
712 768 2.956964 GGCGCTTGGTCTCGATCG 60.957 66.667 9.36 9.36 0.00 3.69
978 1066 1.335496 GATCACTGCTAGTCGGTCTCC 59.665 57.143 0.00 0.00 30.14 3.71
1191 1279 2.124570 ACCGGGATCATGCACTGC 60.125 61.111 6.32 0.00 0.00 4.40
1192 1280 2.475466 GCACCGGGATCATGCACTG 61.475 63.158 6.32 0.00 39.23 3.66
1313 1405 2.816087 ACTTCAGCTGCGAAATGAATGT 59.184 40.909 9.47 0.00 32.82 2.71
1328 1420 3.172050 CACGGTCGATCAGTAACTTCAG 58.828 50.000 0.00 0.00 0.00 3.02
1488 1591 1.795170 GCGTTGATGTGCAGGTTGGT 61.795 55.000 0.00 0.00 0.00 3.67
1658 1767 2.994995 TCGACGGGCACACCATCT 60.995 61.111 0.00 0.00 40.22 2.90
1721 1830 4.717629 CGGAAGACGGACAGCGCA 62.718 66.667 11.47 0.00 39.42 6.09
2286 2415 1.630244 GACACGACATGACCAGCAGC 61.630 60.000 0.00 0.00 0.00 5.25
2295 2427 2.348872 GCTGACACAAAGACACGACATG 60.349 50.000 0.00 0.00 0.00 3.21
2362 2503 2.364972 AAAAAGTAGCCTGGCACACT 57.635 45.000 22.65 19.57 0.00 3.55
2426 2568 8.339344 TCTGACACATGTAACATGAAAATCAT 57.661 30.769 0.00 0.00 37.65 2.45
2448 2590 5.005779 GTGGCTCAACGAAATACTGTATCTG 59.994 44.000 0.00 0.00 0.00 2.90
2491 2633 9.107367 GCGAATTGTGATAGCTTTATGTTATTC 57.893 33.333 0.00 0.00 0.00 1.75
2496 2638 4.570772 ACGCGAATTGTGATAGCTTTATGT 59.429 37.500 15.93 0.00 0.00 2.29
2503 2645 3.308866 ACCTTAACGCGAATTGTGATAGC 59.691 43.478 15.93 0.00 0.00 2.97
2507 2649 2.481185 GGAACCTTAACGCGAATTGTGA 59.519 45.455 15.93 0.00 0.00 3.58
2515 2657 2.032426 AGTTTTGTGGAACCTTAACGCG 59.968 45.455 3.53 3.53 34.36 6.01
2517 2659 4.575645 TGGTAGTTTTGTGGAACCTTAACG 59.424 41.667 0.00 0.00 34.36 3.18
2527 2669 6.976636 AACAAATTTGTGGTAGTTTTGTGG 57.023 33.333 23.93 0.00 41.31 4.17
2552 2694 5.622460 GCCGATTCTGATAGTTATCCGTCAT 60.622 44.000 0.00 0.00 31.71 3.06
2557 2699 4.167268 GACGCCGATTCTGATAGTTATCC 58.833 47.826 0.00 0.00 31.71 2.59
2574 2716 1.503818 TTTTTGAGACAGCGGACGCC 61.504 55.000 13.63 0.00 43.17 5.68
2625 2767 1.202976 GGCCTGGCCTGTCATAATCAT 60.203 52.381 30.42 0.00 46.69 2.45
2626 2768 0.183492 GGCCTGGCCTGTCATAATCA 59.817 55.000 30.42 0.00 46.69 2.57
2637 2779 2.753849 TTTATGTGCGGCCTGGCC 60.754 61.111 28.17 28.17 46.75 5.36
2638 2780 1.872197 TTGTTTATGTGCGGCCTGGC 61.872 55.000 11.05 11.05 0.00 4.85
2639 2781 0.600557 TTTGTTTATGTGCGGCCTGG 59.399 50.000 0.00 0.00 0.00 4.45
2640 2782 1.668628 GGTTTGTTTATGTGCGGCCTG 60.669 52.381 0.00 0.00 0.00 4.85
2641 2783 0.601057 GGTTTGTTTATGTGCGGCCT 59.399 50.000 0.00 0.00 0.00 5.19
2642 2784 0.315568 TGGTTTGTTTATGTGCGGCC 59.684 50.000 0.00 0.00 0.00 6.13
2643 2785 2.094752 AGATGGTTTGTTTATGTGCGGC 60.095 45.455 0.00 0.00 0.00 6.53
2644 2786 3.057596 ACAGATGGTTTGTTTATGTGCGG 60.058 43.478 0.00 0.00 0.00 5.69
2645 2787 4.159377 ACAGATGGTTTGTTTATGTGCG 57.841 40.909 0.00 0.00 0.00 5.34
2686 2828 1.670083 GGCCCACACGTCAGGTAAC 60.670 63.158 0.00 0.00 0.00 2.50
2798 2940 9.657728 TTTCAAAAACTTTTAGGGACCCTATTA 57.342 29.630 21.41 9.73 35.87 0.98
2799 2941 8.555896 TTTCAAAAACTTTTAGGGACCCTATT 57.444 30.769 21.41 9.59 35.87 1.73
2832 2974 2.134933 GCTTCTCCTAGGGACCCGG 61.135 68.421 9.46 0.76 0.00 5.73
2880 3022 1.810606 CGACCTGGACACTGCAGAGT 61.811 60.000 23.35 20.07 38.14 3.24
2889 3031 1.877576 CTGCTGTAGCGACCTGGACA 61.878 60.000 0.00 0.00 45.83 4.02
2952 3094 4.208686 CCTCCCGCGACCTACAGC 62.209 72.222 8.23 0.00 0.00 4.40
2955 3097 4.208686 CTGCCTCCCGCGACCTAC 62.209 72.222 8.23 0.00 42.08 3.18
2980 3122 3.749064 TCGAGCTGCTCCACCGAC 61.749 66.667 22.97 0.00 0.00 4.79
2981 3123 3.749064 GTCGAGCTGCTCCACCGA 61.749 66.667 22.97 14.82 0.00 4.69
3061 3203 3.983420 CCCCCTTCTTGGCAGCCA 61.983 66.667 11.22 11.22 0.00 4.75


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

AutoCloner maintained by Alex Coulton.