Multiple sequence alignment - TraesCS3A01G297700

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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 TraesCS3A01G297700 chr3A 100.000 4717 0 0 1 4717 532452100 532447384 0.000000e+00 8711
1 TraesCS3A01G297700 chr3B 92.175 4128 223 45 639 4693 545066195 545070295 0.000000e+00 5742
2 TraesCS3A01G297700 chr3B 84.420 276 33 8 1 268 545064339 545064612 3.620000e-66 263
3 TraesCS3A01G297700 chr3B 93.103 87 3 2 315 401 545064929 545065012 1.780000e-24 124
4 TraesCS3A01G297700 chr3D 91.562 4136 211 68 639 4701 418727143 418731213 0.000000e+00 5578
5 TraesCS3A01G297700 chr3D 85.614 285 22 5 2 268 418725297 418725580 9.990000e-72 281
6 TraesCS3A01G297700 chr3D 93.333 180 12 0 421 600 8534532 8534711 2.800000e-67 267
7 TraesCS3A01G297700 chr5A 97.778 180 4 0 421 600 534072732 534072911 1.270000e-80 311
8 TraesCS3A01G297700 chr5B 97.238 181 5 0 420 600 642597193 642597373 1.650000e-79 307
9 TraesCS3A01G297700 chr5B 91.803 183 15 0 418 600 522371604 522371786 6.060000e-64 255
10 TraesCS3A01G297700 chr5B 89.447 199 21 0 402 600 522370440 522370638 7.840000e-63 252
11 TraesCS3A01G297700 chr4B 97.222 180 5 0 421 600 619367084 619366905 5.930000e-79 305
12 TraesCS3A01G297700 chr1B 97.222 180 5 0 421 600 407901335 407901514 5.930000e-79 305
13 TraesCS3A01G297700 chr1B 91.083 157 14 0 919 1075 572295414 572295258 3.700000e-51 213
14 TraesCS3A01G297700 chr2D 94.444 180 10 0 421 600 317053303 317053482 1.290000e-70 278
15 TraesCS3A01G297700 chr2D 93.889 180 11 0 421 600 317056486 317056665 6.010000e-69 272
16 TraesCS3A01G297700 chr1A 92.357 157 12 0 919 1075 518974118 518973962 1.710000e-54 224
17 TraesCS3A01G297700 chr1D 91.083 157 14 0 919 1075 423043280 423043124 3.700000e-51 213


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 TraesCS3A01G297700 chr3A 532447384 532452100 4716 True 8711.0 8711 100.000000 1 4717 1 chr3A.!!$R1 4716
1 TraesCS3A01G297700 chr3B 545064339 545070295 5956 False 2043.0 5742 89.899333 1 4693 3 chr3B.!!$F1 4692
2 TraesCS3A01G297700 chr3D 418725297 418731213 5916 False 2929.5 5578 88.588000 2 4701 2 chr3D.!!$F2 4699
3 TraesCS3A01G297700 chr5B 522370440 522371786 1346 False 253.5 255 90.625000 402 600 2 chr5B.!!$F2 198
4 TraesCS3A01G297700 chr2D 317053303 317056665 3362 False 275.0 278 94.166500 421 600 2 chr2D.!!$F1 179

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
370 679 0.100682 CTCGTCCGTCGGATCACAAT 59.899 55.000 18.75 0.0 40.32 2.71 F
472 5250 1.620323 GCACTTTGAGGATTTGCCCTT 59.380 47.619 0.00 0.0 36.49 3.95 F
1942 6754 1.065551 GCGCAGGGTAATTTGATCCAC 59.934 52.381 0.30 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 5973 0.179067 AAACCCGACACTCGAAAGCA 60.179 50.0 0.0 0.0 43.74 3.91 R
2234 7074 0.779997 AGGTTGGTTTCAGCCAGGAT 59.220 50.0 0.0 0.0 45.35 3.24 R
3750 8611 0.613777 AGTGGAAGAACCCGATGGAC 59.386 55.0 0.0 0.0 38.00 4.02 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
29 30 0.404040 TCCAGATTGCCCGGAACTTT 59.596 50.000 0.73 0.00 0.00 2.66
103 108 0.991920 GGAACTCCCCAACTGGATCA 59.008 55.000 0.00 0.00 37.39 2.92
148 153 0.391130 GTCCACATTACAGCGCCTCA 60.391 55.000 2.29 0.00 0.00 3.86
272 295 3.066814 CCAGCAGCAGGCCCTTTC 61.067 66.667 0.00 0.00 46.50 2.62
276 558 0.543646 AGCAGCAGGCCCTTTCAATT 60.544 50.000 0.00 0.00 46.50 2.32
282 564 2.613725 GCAGGCCCTTTCAATTTTGAGG 60.614 50.000 0.00 0.00 38.61 3.86
289 571 3.575687 CCTTTCAATTTTGAGGCTCCAGT 59.424 43.478 12.86 0.00 38.61 4.00
292 574 2.813754 TCAATTTTGAGGCTCCAGTTCG 59.186 45.455 12.86 0.00 32.50 3.95
304 586 2.169789 CAGTTCGAGGGCGCTGATG 61.170 63.158 8.56 0.00 37.46 3.07
326 635 2.409948 AGATTAGCTGAGCCACCAAC 57.590 50.000 0.00 0.00 0.00 3.77
327 636 1.009829 GATTAGCTGAGCCACCAACG 58.990 55.000 0.00 0.00 0.00 4.10
355 664 1.021390 CGGCAATTTGAGCTCCTCGT 61.021 55.000 12.15 0.00 32.35 4.18
369 678 1.504900 CTCGTCCGTCGGATCACAA 59.495 57.895 18.75 0.78 40.32 3.33
370 679 0.100682 CTCGTCCGTCGGATCACAAT 59.899 55.000 18.75 0.00 40.32 2.71
472 5250 1.620323 GCACTTTGAGGATTTGCCCTT 59.380 47.619 0.00 0.00 36.49 3.95
477 5255 5.243730 CACTTTGAGGATTTGCCCTTCTTTA 59.756 40.000 0.00 0.00 36.49 1.85
486 5264 7.068716 AGGATTTGCCCTTCTTTATATTGACAC 59.931 37.037 0.00 0.00 37.37 3.67
509 5287 5.021033 TGATGATTTGCCACAACTTTGTT 57.979 34.783 0.00 0.00 39.91 2.83
600 5378 3.070015 ACTCTTGCCAAAACCAATCCAAG 59.930 43.478 0.00 0.00 0.00 3.61
601 5379 3.303938 TCTTGCCAAAACCAATCCAAGA 58.696 40.909 0.00 0.00 37.08 3.02
602 5380 3.708631 TCTTGCCAAAACCAATCCAAGAA 59.291 39.130 0.00 0.00 36.66 2.52
603 5381 3.749665 TGCCAAAACCAATCCAAGAAG 57.250 42.857 0.00 0.00 0.00 2.85
604 5382 3.303938 TGCCAAAACCAATCCAAGAAGA 58.696 40.909 0.00 0.00 0.00 2.87
609 5387 5.105351 CCAAAACCAATCCAAGAAGATACCC 60.105 44.000 0.00 0.00 0.00 3.69
625 5403 1.954035 ACCCCTTCTACCCTTCACTC 58.046 55.000 0.00 0.00 0.00 3.51
628 5406 2.292587 CCCCTTCTACCCTTCACTCTCT 60.293 54.545 0.00 0.00 0.00 3.10
631 5409 3.699038 CCTTCTACCCTTCACTCTCTCTG 59.301 52.174 0.00 0.00 0.00 3.35
632 5410 4.340617 CTTCTACCCTTCACTCTCTCTGT 58.659 47.826 0.00 0.00 0.00 3.41
633 5411 5.502079 CTTCTACCCTTCACTCTCTCTGTA 58.498 45.833 0.00 0.00 0.00 2.74
634 5412 5.105567 TCTACCCTTCACTCTCTCTGTAG 57.894 47.826 0.00 0.00 0.00 2.74
635 5413 4.783763 TCTACCCTTCACTCTCTCTGTAGA 59.216 45.833 0.00 0.00 33.13 2.59
636 5414 3.692690 ACCCTTCACTCTCTCTGTAGAC 58.307 50.000 0.00 0.00 0.00 2.59
637 5415 3.074687 ACCCTTCACTCTCTCTGTAGACA 59.925 47.826 0.00 0.00 0.00 3.41
647 5435 2.685388 TCTCTGTAGACATTGCGAGAGG 59.315 50.000 0.00 0.00 0.00 3.69
783 5579 2.028484 GATTCGCCGGCCACGATA 59.972 61.111 23.46 9.80 44.60 2.92
798 5594 2.278206 ATACACAGCTCGCTCGCG 60.278 61.111 0.00 0.00 41.35 5.87
799 5595 2.648320 GATACACAGCTCGCTCGCGA 62.648 60.000 9.26 9.26 46.87 5.87
1177 5973 2.859992 GGCACGAGGAATTTCTGCT 58.140 52.632 0.00 0.00 0.00 4.24
1204 6015 2.097250 CGAGTGTCGGGTTTAACGAAAC 60.097 50.000 0.18 0.18 46.23 2.78
1393 6205 2.594303 CTGAACACGGCCTTGGCA 60.594 61.111 14.57 10.17 0.00 4.92
1428 6240 2.623416 GGTAAGTTTCTGCTGGTTGCTT 59.377 45.455 0.00 0.00 43.37 3.91
1532 6344 5.943706 TTGGATTTGAACCAATGCAAATG 57.056 34.783 0.00 0.00 42.81 2.32
1626 6438 4.387256 GTGCTGACAAGTGTTGATAGAGAC 59.613 45.833 0.00 0.00 0.00 3.36
1697 6509 8.584157 AGCTTTGAAGGTCTATCTCATATACTG 58.416 37.037 0.00 0.00 29.15 2.74
1698 6510 8.364142 GCTTTGAAGGTCTATCTCATATACTGT 58.636 37.037 0.00 0.00 0.00 3.55
1715 6527 9.161629 CATATACTGTATTGGTGTGTCTTTCAA 57.838 33.333 5.52 0.00 0.00 2.69
1716 6528 9.905713 ATATACTGTATTGGTGTGTCTTTCAAT 57.094 29.630 5.52 0.00 34.65 2.57
1718 6530 9.733556 ATACTGTATTGGTGTGTCTTTCAATAA 57.266 29.630 0.00 0.00 34.95 1.40
1719 6531 8.099364 ACTGTATTGGTGTGTCTTTCAATAAG 57.901 34.615 0.00 0.00 34.95 1.73
1761 6573 4.187694 CCATGCTAAAGACTTCTGGACTC 58.812 47.826 0.00 0.00 0.00 3.36
1767 6579 5.129650 GCTAAAGACTTCTGGACTCCCTATT 59.870 44.000 0.00 0.00 0.00 1.73
1872 6684 6.925718 CCGATTCTAATCTAGATGTCTTTGCA 59.074 38.462 5.86 0.00 34.22 4.08
1876 6688 6.036470 TCTAATCTAGATGTCTTTGCACACG 58.964 40.000 5.86 0.00 0.00 4.49
1942 6754 1.065551 GCGCAGGGTAATTTGATCCAC 59.934 52.381 0.30 0.00 0.00 4.02
1953 6765 8.749354 GGGTAATTTGATCCACTGATTTTAGTT 58.251 33.333 0.00 0.00 0.00 2.24
1966 6778 7.061441 CACTGATTTTAGTTGCATGACATTGTC 59.939 37.037 9.93 9.93 0.00 3.18
2071 6886 4.764823 TCAACAATTCCGGAACAGCTAAAT 59.235 37.500 21.56 0.00 0.00 1.40
2103 6918 2.412089 CGCTACTTCCGGTTTCTTTCTG 59.588 50.000 0.00 0.00 0.00 3.02
2104 6919 3.400255 GCTACTTCCGGTTTCTTTCTGT 58.600 45.455 0.00 0.00 0.00 3.41
2110 6925 5.884232 ACTTCCGGTTTCTTTCTGTTTTACT 59.116 36.000 0.00 0.00 0.00 2.24
2127 6942 9.103861 CTGTTTTACTTTCTGATATTCTCCTCC 57.896 37.037 0.00 0.00 0.00 4.30
2164 6979 5.524281 GGCTAGAGGTTTGAAACACTATAGC 59.476 44.000 26.70 26.70 42.34 2.97
2166 6981 6.763610 GCTAGAGGTTTGAAACACTATAGCAT 59.236 38.462 28.10 6.76 42.46 3.79
2167 6982 7.042389 GCTAGAGGTTTGAAACACTATAGCATC 60.042 40.741 28.10 13.15 42.46 3.91
2168 6983 6.116126 AGAGGTTTGAAACACTATAGCATCC 58.884 40.000 10.53 0.00 0.00 3.51
2169 6984 5.815581 AGGTTTGAAACACTATAGCATCCA 58.184 37.500 10.53 0.00 0.00 3.41
2259 7099 2.691011 TGGCTGAAACCAACCTAACAAC 59.309 45.455 0.00 0.00 36.55 3.32
2280 7120 6.567769 AACGTTAAACAAATGTTGCTTCTG 57.432 33.333 0.00 0.00 44.01 3.02
2313 7153 3.811497 TGCTCTGACACTTGAATCAGTTG 59.189 43.478 1.48 0.00 42.52 3.16
2464 7315 7.332213 CAAATGTGGATGTGTACCATATCAA 57.668 36.000 0.00 0.00 38.06 2.57
2473 7324 7.015292 GGATGTGTACCATATCAAGAGACCTTA 59.985 40.741 3.85 0.00 34.41 2.69
2531 7382 6.857777 ATTTGATCAGTGAGTTGCTATAGC 57.142 37.500 18.18 18.18 42.50 2.97
2613 7464 5.777449 TCCCTAGTATCTGGATGTCTTCAA 58.223 41.667 0.00 0.00 0.00 2.69
2760 7617 9.401058 CCTTGTATCTTCTTTTCTCATGGTATT 57.599 33.333 0.00 0.00 0.00 1.89
2801 7658 8.260818 TCTCTTATGACCTCTCATTTTTACAGG 58.739 37.037 0.00 0.00 38.21 4.00
2909 7766 2.610727 GGAAACTGACGAGGAGGTGAAG 60.611 54.545 0.00 0.00 0.00 3.02
3070 7928 6.403866 TGATGTTACAGCCAACAGAAAAAT 57.596 33.333 0.00 0.00 41.48 1.82
3135 7993 5.512942 TTTGGAAGGAGTATGGTGAATCA 57.487 39.130 0.00 0.00 0.00 2.57
3282 8140 5.748402 TCTTGATTGCCCATGCTATATAGG 58.252 41.667 11.72 0.00 38.71 2.57
3574 8432 2.356135 CAAGCATACAAACGTAGCCCT 58.644 47.619 0.00 0.00 0.00 5.19
3575 8433 2.311124 AGCATACAAACGTAGCCCTC 57.689 50.000 0.00 0.00 0.00 4.30
3607 8468 4.060205 GCCATTTGCATGAACTCACTTTT 58.940 39.130 0.00 0.00 40.77 2.27
3609 8470 5.333568 GCCATTTGCATGAACTCACTTTTTC 60.334 40.000 0.00 0.00 40.77 2.29
3613 8474 4.923893 TGCATGAACTCACTTTTTCTGTG 58.076 39.130 0.00 0.00 36.82 3.66
3691 8552 8.887717 CGAGAATTTGGTCAGAAATAAGAAGAT 58.112 33.333 0.00 0.00 0.00 2.40
3706 8567 3.818180 AGAAGATTAAGCCTGCATCTGG 58.182 45.455 0.00 0.00 0.00 3.86
3736 8597 8.134202 TCTTAAGTCTCAACCAAGATATGTCA 57.866 34.615 1.63 0.00 0.00 3.58
3750 8611 6.992063 AGATATGTCAACCTACAAAAGCAG 57.008 37.500 0.00 0.00 32.02 4.24
3759 8620 2.009774 CTACAAAAGCAGTCCATCGGG 58.990 52.381 0.00 0.00 0.00 5.14
3769 8630 0.613777 GTCCATCGGGTTCTTCCACT 59.386 55.000 0.00 0.00 38.11 4.00
3770 8631 1.003233 GTCCATCGGGTTCTTCCACTT 59.997 52.381 0.00 0.00 38.11 3.16
3817 8683 1.454847 GGGGGCGGCACAATCATTA 60.455 57.895 15.31 0.00 0.00 1.90
3828 8694 6.968904 GCGGCACAATCATTATATTATTCTGG 59.031 38.462 0.00 0.00 0.00 3.86
3878 8745 7.529158 TGAATATGCACACACACTTTTGATAG 58.471 34.615 0.00 0.00 0.00 2.08
3897 8764 5.838521 TGATAGTTATCACTGTAGATGCCCA 59.161 40.000 0.00 0.00 37.76 5.36
3911 8779 0.036199 TGCCCAGATGCCATTTTTGC 60.036 50.000 0.00 0.00 0.00 3.68
3961 8829 6.874288 ATAGCAAAAGCTATTCATGAGTCC 57.126 37.500 4.26 0.00 29.66 3.85
3962 8830 4.592942 AGCAAAAGCTATTCATGAGTCCA 58.407 39.130 0.00 0.00 0.00 4.02
3964 8832 4.156556 GCAAAAGCTATTCATGAGTCCACA 59.843 41.667 0.00 0.00 0.00 4.17
3965 8833 5.163581 GCAAAAGCTATTCATGAGTCCACAT 60.164 40.000 0.00 0.00 0.00 3.21
3966 8834 6.263344 CAAAAGCTATTCATGAGTCCACATG 58.737 40.000 0.00 0.00 46.01 3.21
3998 8871 4.084849 CCTCTGTCGTTTGATTATGCGATC 60.085 45.833 0.00 0.00 35.78 3.69
4014 8887 4.129380 TGCGATCCTTTATCCATCACTTG 58.871 43.478 0.00 0.00 0.00 3.16
4027 8900 0.684535 TCACTTGGGAGAACGCATCA 59.315 50.000 0.00 0.00 38.67 3.07
4205 9113 8.621532 ATTCACAGTTCAATTTGAAGTAGCTA 57.378 30.769 16.99 6.39 37.91 3.32
4207 9115 6.426937 TCACAGTTCAATTTGAAGTAGCTACC 59.573 38.462 20.31 6.72 37.91 3.18
4300 9211 9.678941 TTGTGACACAGTCGATATATTATCTTC 57.321 33.333 8.55 0.00 34.95 2.87
4328 9239 5.617252 TGTTCCTAGAATTTTCCGTGACTT 58.383 37.500 0.00 0.00 0.00 3.01
4358 9269 7.772166 TGTGAAGTTCTCAGAATCATATACGT 58.228 34.615 4.17 0.00 33.60 3.57
4374 9285 1.408969 ACGTGGGTGCTGGAATTTTT 58.591 45.000 0.00 0.00 0.00 1.94
4431 9342 2.675889 GCCGGAAATACTCCAAACTCGA 60.676 50.000 5.05 0.00 45.74 4.04
4432 9343 3.187700 CCGGAAATACTCCAAACTCGAG 58.812 50.000 11.84 11.84 45.74 4.04
4548 9459 5.565834 GCGGTTTCTTTAATGGAAATGGACA 60.566 40.000 7.18 0.00 35.55 4.02
4578 9489 7.333423 AGCTTGTTGTTTTAAAGAAAAGGTTCC 59.667 33.333 7.67 0.00 35.21 3.62
4600 9511 6.565974 TCCTAATAATCCTCTGGTAGAGCAT 58.434 40.000 0.31 0.00 40.98 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.221924 TCTTCACTGTCCGATCCAATTGTA 59.778 41.667 4.43 0.00 0.00 2.41
122 127 0.744414 CTGTAATGTGGACGGGGCAG 60.744 60.000 0.00 0.00 0.00 4.85
268 291 4.861102 ACTGGAGCCTCAAAATTGAAAG 57.139 40.909 0.00 0.00 36.64 2.62
269 292 4.261572 CGAACTGGAGCCTCAAAATTGAAA 60.262 41.667 0.00 0.00 36.64 2.69
270 293 3.253188 CGAACTGGAGCCTCAAAATTGAA 59.747 43.478 0.00 0.00 36.64 2.69
271 294 2.813754 CGAACTGGAGCCTCAAAATTGA 59.186 45.455 0.00 0.00 35.57 2.57
272 295 2.813754 TCGAACTGGAGCCTCAAAATTG 59.186 45.455 0.00 0.00 0.00 2.32
276 558 0.321671 CCTCGAACTGGAGCCTCAAA 59.678 55.000 0.00 0.00 32.57 2.69
304 586 0.817229 GGTGGCTCAGCTAATCTGGC 60.817 60.000 0.00 0.00 43.06 4.85
306 588 2.012673 GTTGGTGGCTCAGCTAATCTG 58.987 52.381 0.00 0.00 44.21 2.90
308 590 1.009829 CGTTGGTGGCTCAGCTAATC 58.990 55.000 0.00 0.00 32.61 1.75
309 591 0.613260 TCGTTGGTGGCTCAGCTAAT 59.387 50.000 0.00 0.00 32.61 1.73
310 592 0.037326 CTCGTTGGTGGCTCAGCTAA 60.037 55.000 0.00 0.00 32.61 3.09
311 593 1.591703 CTCGTTGGTGGCTCAGCTA 59.408 57.895 0.00 0.00 32.61 3.32
326 635 0.095935 CAAATTGCCGTGAGAGCTCG 59.904 55.000 8.37 0.00 0.00 5.03
327 636 1.396301 CTCAAATTGCCGTGAGAGCTC 59.604 52.381 5.27 5.27 43.32 4.09
355 664 2.223947 CCATACATTGTGATCCGACGGA 60.224 50.000 20.85 20.85 35.55 4.69
369 678 5.707242 AACGATCAGATACGTCCATACAT 57.293 39.130 0.00 0.00 41.87 2.29
370 679 5.278604 CAAACGATCAGATACGTCCATACA 58.721 41.667 0.00 0.00 41.87 2.29
472 5250 8.623903 GGCAAATCATCAGTGTCAATATAAAGA 58.376 33.333 0.00 0.00 0.00 2.52
477 5255 5.653330 TGTGGCAAATCATCAGTGTCAATAT 59.347 36.000 0.00 0.00 0.00 1.28
486 5264 4.624015 ACAAAGTTGTGGCAAATCATCAG 58.376 39.130 0.00 0.00 40.49 2.90
509 5287 6.326323 AGAAAGGGCAAATCCTCAAGTTTTTA 59.674 34.615 0.00 0.00 35.80 1.52
600 5378 4.101274 GTGAAGGGTAGAAGGGGTATCTTC 59.899 50.000 0.00 0.00 42.43 2.87
601 5379 4.038633 GTGAAGGGTAGAAGGGGTATCTT 58.961 47.826 0.00 0.00 0.00 2.40
602 5380 3.275228 AGTGAAGGGTAGAAGGGGTATCT 59.725 47.826 0.00 0.00 0.00 1.98
603 5381 3.642377 GAGTGAAGGGTAGAAGGGGTATC 59.358 52.174 0.00 0.00 0.00 2.24
604 5382 3.275228 AGAGTGAAGGGTAGAAGGGGTAT 59.725 47.826 0.00 0.00 0.00 2.73
609 5387 3.699038 CAGAGAGAGTGAAGGGTAGAAGG 59.301 52.174 0.00 0.00 0.00 3.46
625 5403 3.243035 CCTCTCGCAATGTCTACAGAGAG 60.243 52.174 15.21 15.21 46.57 3.20
628 5406 2.447443 ACCTCTCGCAATGTCTACAGA 58.553 47.619 0.00 0.00 0.00 3.41
631 5409 2.271800 CCAACCTCTCGCAATGTCTAC 58.728 52.381 0.00 0.00 0.00 2.59
632 5410 1.405526 GCCAACCTCTCGCAATGTCTA 60.406 52.381 0.00 0.00 0.00 2.59
633 5411 0.674895 GCCAACCTCTCGCAATGTCT 60.675 55.000 0.00 0.00 0.00 3.41
634 5412 1.648467 GGCCAACCTCTCGCAATGTC 61.648 60.000 0.00 0.00 0.00 3.06
635 5413 1.675641 GGCCAACCTCTCGCAATGT 60.676 57.895 0.00 0.00 0.00 2.71
636 5414 2.753966 CGGCCAACCTCTCGCAATG 61.754 63.158 2.24 0.00 0.00 2.82
637 5415 2.436646 CGGCCAACCTCTCGCAAT 60.437 61.111 2.24 0.00 0.00 3.56
1177 5973 0.179067 AAACCCGACACTCGAAAGCA 60.179 50.000 0.00 0.00 43.74 3.91
1204 6015 3.698820 GCCCCCAAAAGCAGCAGG 61.699 66.667 0.00 0.00 0.00 4.85
1267 6079 3.112126 GATGGTCGCCGTGGCAATG 62.112 63.158 12.06 0.00 42.06 2.82
1393 6205 1.216930 ACTTACCCCCAACTTGCAACT 59.783 47.619 0.00 0.00 0.00 3.16
1532 6344 3.419264 TCATGCATCGTAAATTGGCAC 57.581 42.857 0.00 0.00 37.30 5.01
1536 6348 7.408910 TCTGTGTAATCATGCATCGTAAATTG 58.591 34.615 0.00 0.00 0.00 2.32
1641 6453 0.968405 GAGCAAAATGGCCACTTCCA 59.032 50.000 8.16 0.00 40.97 3.53
1683 6495 9.847706 GACACACCAATACAGTATATGAGATAG 57.152 37.037 0.00 0.00 0.00 2.08
1686 6498 7.898014 AGACACACCAATACAGTATATGAGA 57.102 36.000 0.00 0.00 0.00 3.27
1751 6563 3.640967 CTCCTGAATAGGGAGTCCAGAAG 59.359 52.174 12.30 0.00 44.70 2.85
1761 6573 2.507471 AGGTTTGAGCTCCTGAATAGGG 59.493 50.000 12.15 0.00 44.70 3.53
1872 6684 2.872245 CCTCACAGTTTCAATGTCGTGT 59.128 45.455 0.00 0.00 0.00 4.49
1876 6688 4.450419 CAGACTCCTCACAGTTTCAATGTC 59.550 45.833 0.00 0.00 0.00 3.06
1923 6735 2.355756 CAGTGGATCAAATTACCCTGCG 59.644 50.000 0.00 0.00 0.00 5.18
1942 6754 7.272731 CAGACAATGTCATGCAACTAAAATCAG 59.727 37.037 16.38 0.00 34.60 2.90
1989 6801 7.330946 GGAATTAAGTTATTGGTGCTTCAAACC 59.669 37.037 0.00 0.00 38.26 3.27
2035 6850 5.502382 CGGAATTGTTGATGAGTGGTAATCG 60.502 44.000 0.00 0.00 0.00 3.34
2071 6886 4.178540 CCGGAAGTAGCGATTCTTTGTAA 58.821 43.478 0.00 0.00 0.00 2.41
2103 6918 9.449719 TTGGAGGAGAATATCAGAAAGTAAAAC 57.550 33.333 0.00 0.00 0.00 2.43
2104 6919 9.672673 CTTGGAGGAGAATATCAGAAAGTAAAA 57.327 33.333 0.00 0.00 0.00 1.52
2110 6925 5.965033 AGCTTGGAGGAGAATATCAGAAA 57.035 39.130 0.00 0.00 0.00 2.52
2127 6942 5.220710 ACCTCTAGCCATTGTATAGCTTG 57.779 43.478 0.00 0.00 38.06 4.01
2220 7060 9.752228 TTTCAGCCAGGATTATGCATATTATTA 57.248 29.630 7.36 0.00 0.00 0.98
2234 7074 0.779997 AGGTTGGTTTCAGCCAGGAT 59.220 50.000 0.00 0.00 45.35 3.24
2259 7099 6.252441 TGAACAGAAGCAACATTTGTTTAACG 59.748 34.615 0.00 0.00 35.83 3.18
2280 7120 2.481952 GTGTCAGAGCACCAGAATGAAC 59.518 50.000 0.00 0.00 39.69 3.18
2473 7324 4.894784 TCTGCTTTTGATCGAACCTAAGT 58.105 39.130 0.00 0.00 0.00 2.24
2479 7330 6.521133 CAGTAACATTCTGCTTTTGATCGAAC 59.479 38.462 0.00 0.00 0.00 3.95
2658 7509 9.542462 GTCTAGCATTTATATCAACAGGTGTAA 57.458 33.333 0.00 0.00 0.00 2.41
2659 7510 7.865889 CGTCTAGCATTTATATCAACAGGTGTA 59.134 37.037 0.00 0.00 0.00 2.90
2660 7511 6.701841 CGTCTAGCATTTATATCAACAGGTGT 59.298 38.462 0.00 0.00 0.00 4.16
2661 7512 6.923508 TCGTCTAGCATTTATATCAACAGGTG 59.076 38.462 0.00 0.00 0.00 4.00
2662 7513 7.050970 TCGTCTAGCATTTATATCAACAGGT 57.949 36.000 0.00 0.00 0.00 4.00
2760 7617 2.260639 AGAGATCCTTCCAGAGCCAA 57.739 50.000 0.00 0.00 0.00 4.52
2801 7658 3.451141 ACAGCTAAGCTCTGCTCATAC 57.549 47.619 10.03 0.00 38.25 2.39
2849 7706 6.846505 TGATAGAAGACTTGGTTATCATCCCT 59.153 38.462 0.00 0.00 0.00 4.20
3070 7928 7.478322 GTCACATACTCTCTAACCGTCAAATA 58.522 38.462 0.00 0.00 0.00 1.40
3135 7993 6.928492 CACTAGCAACATAACAAAAACCCAAT 59.072 34.615 0.00 0.00 0.00 3.16
3282 8140 8.451748 GGACCAGAAACTGTATTTCTTGATTAC 58.548 37.037 7.30 0.00 36.69 1.89
3342 8200 4.253685 CGGGCTATTATGGAACTACATGG 58.746 47.826 0.00 0.00 32.39 3.66
3430 8288 8.041323 TCAGACTCCTGAACTATTAACCATTTC 58.959 37.037 0.00 0.00 45.74 2.17
3574 8432 1.961378 CAAATGGCTGCACTGCTGA 59.039 52.632 11.81 0.00 0.00 4.26
3575 8433 1.736645 GCAAATGGCTGCACTGCTG 60.737 57.895 0.50 2.86 42.17 4.41
3585 8446 3.308438 AAGTGAGTTCATGCAAATGGC 57.692 42.857 0.00 0.00 45.13 4.40
3586 8447 5.987347 AGAAAAAGTGAGTTCATGCAAATGG 59.013 36.000 0.00 0.00 0.00 3.16
3587 8448 6.477688 ACAGAAAAAGTGAGTTCATGCAAATG 59.522 34.615 0.00 0.00 0.00 2.32
3607 8468 2.143122 GACAAGAATCGCACCACAGAA 58.857 47.619 0.00 0.00 0.00 3.02
3609 8470 1.462283 CTGACAAGAATCGCACCACAG 59.538 52.381 0.00 0.00 0.00 3.66
3613 8474 1.079503 GACCTGACAAGAATCGCACC 58.920 55.000 0.00 0.00 0.00 5.01
3706 8567 3.963428 TGGTTGAGACTTAAGAGGAGC 57.037 47.619 10.09 1.07 0.00 4.70
3736 8597 3.074412 CGATGGACTGCTTTTGTAGGTT 58.926 45.455 0.00 0.00 36.42 3.50
3750 8611 0.613777 AGTGGAAGAACCCGATGGAC 59.386 55.000 0.00 0.00 38.00 4.02
3759 8620 6.566753 GCTCTGAACATACAAAGTGGAAGAAC 60.567 42.308 0.00 0.00 0.00 3.01
3769 8630 2.813754 GGTGCTGCTCTGAACATACAAA 59.186 45.455 0.00 0.00 0.00 2.83
3770 8631 2.224499 TGGTGCTGCTCTGAACATACAA 60.224 45.455 0.00 0.00 0.00 2.41
3817 8683 7.062957 CAGGGGACAAACTTCCAGAATAATAT 58.937 38.462 0.00 0.00 37.40 1.28
3828 8694 2.587522 AGAAAGCAGGGGACAAACTTC 58.412 47.619 0.00 0.00 0.00 3.01
3878 8745 4.672587 TCTGGGCATCTACAGTGATAAC 57.327 45.455 0.00 0.00 36.17 1.89
3897 8764 3.756933 ACAACAGCAAAAATGGCATCT 57.243 38.095 0.00 0.00 0.00 2.90
3942 8810 5.885230 TGTGGACTCATGAATAGCTTTTG 57.115 39.130 0.00 0.00 0.00 2.44
3960 8828 0.617413 AGAGGGACAGCTTCATGTGG 59.383 55.000 0.00 0.00 32.25 4.17
3961 8829 1.002888 ACAGAGGGACAGCTTCATGTG 59.997 52.381 0.00 0.00 32.25 3.21
3962 8830 1.277557 GACAGAGGGACAGCTTCATGT 59.722 52.381 0.00 0.00 35.68 3.21
3964 8832 0.534412 CGACAGAGGGACAGCTTCAT 59.466 55.000 0.00 0.00 0.00 2.57
3965 8833 0.827925 ACGACAGAGGGACAGCTTCA 60.828 55.000 0.00 0.00 0.00 3.02
3966 8834 0.318762 AACGACAGAGGGACAGCTTC 59.681 55.000 0.00 0.00 0.00 3.86
3967 8835 0.759346 AAACGACAGAGGGACAGCTT 59.241 50.000 0.00 0.00 0.00 3.74
4014 8887 0.674895 AGTGCTTGATGCGTTCTCCC 60.675 55.000 0.00 0.00 46.63 4.30
4027 8900 6.115448 AGTACCTAAGACATGAAAGTGCTT 57.885 37.500 0.00 0.00 0.00 3.91
4156 9041 7.972832 TTCGGACAATTTAACACTCTATTGT 57.027 32.000 0.00 0.00 42.22 2.71
4157 9042 9.490663 GAATTCGGACAATTTAACACTCTATTG 57.509 33.333 0.00 0.00 34.87 1.90
4158 9043 9.226606 TGAATTCGGACAATTTAACACTCTATT 57.773 29.630 0.04 0.00 0.00 1.73
4159 9044 8.665685 GTGAATTCGGACAATTTAACACTCTAT 58.334 33.333 0.04 0.00 0.00 1.98
4175 9083 6.039270 ACTTCAAATTGAACTGTGAATTCGGA 59.961 34.615 4.03 0.00 32.21 4.55
4205 9113 8.757982 AAATGACAAATCTAGCTATGAATGGT 57.242 30.769 0.00 0.00 0.00 3.55
4300 9211 6.426937 TCACGGAAAATTCTAGGAACAAAGAG 59.573 38.462 0.00 0.00 0.00 2.85
4358 9269 2.102252 GTGACAAAAATTCCAGCACCCA 59.898 45.455 0.00 0.00 0.00 4.51
4374 9285 8.638873 TCTGAGAACTTTACAATAAGAGTGACA 58.361 33.333 0.00 0.00 0.00 3.58
4431 9342 2.447443 TCAACCTATCACGTGCTCTCT 58.553 47.619 11.67 0.00 0.00 3.10
4432 9343 2.941453 TCAACCTATCACGTGCTCTC 57.059 50.000 11.67 0.00 0.00 3.20
4548 9459 7.549134 CCTTTTCTTTAAAACAACAAGCTCCTT 59.451 33.333 0.00 0.00 31.37 3.36


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

AutoCloner maintained by Alex Coulton.