Multiple sequence alignment - TraesCS5D01G216200

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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 TraesCS5D01G216200 chr5D 100.000 4262 0 0 1 4262 325088564 325084303 0.000000e+00 7871
1 TraesCS5D01G216200 chr5D 83.090 479 63 14 1835 2306 556471331 556471798 1.830000e-113 420
2 TraesCS5D01G216200 chr5D 82.737 475 72 7 1835 2306 556473897 556474364 8.530000e-112 414
3 TraesCS5D01G216200 chr5D 82.561 453 66 9 1842 2290 556460742 556461185 1.860000e-103 387
4 TraesCS5D01G216200 chr5D 81.984 383 58 10 2390 2768 556471828 556472203 8.900000e-82 315
5 TraesCS5D01G216200 chr5D 75.293 769 128 41 2389 3144 556474371 556475090 1.150000e-80 311
6 TraesCS5D01G216200 chr5B 92.305 3236 179 34 209 3405 377538038 377534834 0.000000e+00 4532
7 TraesCS5D01G216200 chr5B 81.876 469 73 9 1841 2305 694248218 694247758 6.690000e-103 385
8 TraesCS5D01G216200 chr5B 81.799 478 69 12 1834 2306 694250806 694250342 6.690000e-103 385
9 TraesCS5D01G216200 chr5B 81.761 477 71 12 1834 2306 694252122 694251658 6.690000e-103 385
10 TraesCS5D01G216200 chr5B 81.450 469 71 13 1841 2305 694249522 694249066 1.870000e-98 370
11 TraesCS5D01G216200 chr5B 80.519 385 60 12 2390 2768 694256854 694256479 9.020000e-72 281
12 TraesCS5D01G216200 chr5B 79.284 391 63 14 2389 2771 694255551 694255171 1.520000e-64 257
13 TraesCS5D01G216200 chr5B 78.571 392 65 15 2389 2771 694250335 694249954 1.530000e-59 241
14 TraesCS5D01G216200 chr5B 91.860 172 7 3 41 210 377539402 377539236 2.560000e-57 233
15 TraesCS5D01G216200 chr5A 90.714 2983 162 53 681 3611 423177311 423174392 0.000000e+00 3868
16 TraesCS5D01G216200 chr5A 88.705 664 36 18 3614 4262 423174345 423173706 0.000000e+00 774
17 TraesCS5D01G216200 chr5A 89.577 614 31 12 5 617 423178001 423177420 0.000000e+00 749
18 TraesCS5D01G216200 chr2B 89.447 199 21 0 2415 2613 105907654 105907852 7.070000e-63 252
19 TraesCS5D01G216200 chr2D 89.231 195 21 0 2419 2613 69503385 69503579 1.180000e-60 244
20 TraesCS5D01G216200 chr2D 72.125 513 134 9 1481 1988 69502668 69503176 3.430000e-31 147
21 TraesCS5D01G216200 chr2A 72.453 530 139 7 1483 2008 69322980 69323506 3.410000e-36 163


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 TraesCS5D01G216200 chr5D 325084303 325088564 4261 True 7871.000000 7871 100.000000 1 4262 1 chr5D.!!$R1 4261
1 TraesCS5D01G216200 chr5D 556471331 556475090 3759 False 365.000000 420 80.776000 1835 3144 4 chr5D.!!$F2 1309
2 TraesCS5D01G216200 chr5B 377534834 377539402 4568 True 2382.500000 4532 92.082500 41 3405 2 chr5B.!!$R1 3364
3 TraesCS5D01G216200 chr5B 694247758 694256854 9096 True 329.142857 385 80.751429 1834 2771 7 chr5B.!!$R2 937
4 TraesCS5D01G216200 chr5A 423173706 423178001 4295 True 1797.000000 3868 89.665333 5 4262 3 chr5A.!!$R1 4257

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
503 1717 0.179023 AAAAGCCCCAAACCGACGTA 60.179 50.000 0.0 0.0 0.00 3.57 F
657 1887 0.459411 GCTTCTCTCTTGTCTCGGCC 60.459 60.000 0.0 0.0 0.00 6.13 F
1917 3198 1.272490 GTCGGTGACCTGATGTCTTCA 59.728 52.381 0.0 0.0 44.75 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 7695 0.174389 TGATGAAGCGAGACTCAGCC 59.826 55.000 13.34 3.35 0.00 4.85 R
2499 7698 1.404717 GCCTTGATGAAGCGAGACTCA 60.405 52.381 2.82 0.00 0.00 3.41 R
3625 11580 0.820891 ATGGGCCTATTGCTCGCAAG 60.821 55.000 4.53 0.00 46.64 4.01 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 0.179045 GAACCACATGATCGGGAGGG 60.179 60.000 0.00 2.49 0.00 4.30
39 40 2.183679 GATCGGGAGGGAAGATAGCAT 58.816 52.381 0.00 0.00 0.00 3.79
67 68 0.943835 CGTTCATGTCAGTCGGTGCA 60.944 55.000 0.00 0.00 0.00 4.57
69 70 0.392706 TTCATGTCAGTCGGTGCACT 59.607 50.000 17.98 0.00 0.00 4.40
125 126 2.092914 CGTAGGAGAAAGGGGATTGCTT 60.093 50.000 0.00 0.00 0.00 3.91
179 182 2.932614 CTCTGAATCTTGTGGCGTAAGG 59.067 50.000 1.47 0.00 38.28 2.69
227 1429 3.185797 CGACTTAACACTAGTTGGTTGGC 59.814 47.826 8.47 0.00 38.69 4.52
257 1459 7.013464 CCAACTGGTGGTTACTGTAATTAACAA 59.987 37.037 2.79 0.00 43.20 2.83
261 1463 6.016108 TGGTGGTTACTGTAATTAACAAAGCC 60.016 38.462 3.23 0.00 37.74 4.35
271 1473 1.241315 TAACAAAGCCTCCTTGCCGC 61.241 55.000 0.00 0.00 0.00 6.53
316 1519 6.725364 AGAGATCTCTGAACTCTCTTCTCTT 58.275 40.000 24.56 0.00 42.31 2.85
319 1522 7.605449 AGATCTCTGAACTCTCTTCTCTTTTG 58.395 38.462 0.00 0.00 0.00 2.44
325 1528 5.829924 TGAACTCTCTTCTCTTTTGGCATTT 59.170 36.000 0.00 0.00 0.00 2.32
349 1552 1.144057 GACATCCCAGTAGTGCCCG 59.856 63.158 0.00 0.00 0.00 6.13
351 1554 2.040606 ATCCCAGTAGTGCCCGGT 59.959 61.111 0.00 0.00 0.00 5.28
355 1558 1.072505 CCAGTAGTGCCCGGTGTTT 59.927 57.895 0.00 0.00 0.00 2.83
356 1559 0.536460 CCAGTAGTGCCCGGTGTTTT 60.536 55.000 0.00 0.00 0.00 2.43
419 1622 0.740737 CCATTGCTCCCGTGAAATCC 59.259 55.000 0.00 0.00 0.00 3.01
425 1628 0.460284 CTCCCGTGAAATCCTGTCCG 60.460 60.000 0.00 0.00 0.00 4.79
430 1633 1.606994 CGTGAAATCCTGTCCGGTTCA 60.607 52.381 0.00 0.00 0.00 3.18
431 1634 2.076863 GTGAAATCCTGTCCGGTTCAG 58.923 52.381 17.76 17.76 30.83 3.02
432 1635 1.697432 TGAAATCCTGTCCGGTTCAGT 59.303 47.619 21.03 8.52 0.00 3.41
433 1636 2.076863 GAAATCCTGTCCGGTTCAGTG 58.923 52.381 21.03 15.00 0.00 3.66
434 1637 0.321653 AATCCTGTCCGGTTCAGTGC 60.322 55.000 21.03 0.00 0.00 4.40
435 1638 1.480212 ATCCTGTCCGGTTCAGTGCA 61.480 55.000 21.03 10.17 0.00 4.57
436 1639 1.003355 CCTGTCCGGTTCAGTGCAT 60.003 57.895 21.03 0.00 0.00 3.96
437 1640 1.300971 CCTGTCCGGTTCAGTGCATG 61.301 60.000 21.03 0.00 0.00 4.06
438 1641 0.320683 CTGTCCGGTTCAGTGCATGA 60.321 55.000 16.90 0.00 35.62 3.07
439 1642 0.320683 TGTCCGGTTCAGTGCATGAG 60.321 55.000 0.00 0.00 39.68 2.90
440 1643 0.320771 GTCCGGTTCAGTGCATGAGT 60.321 55.000 0.00 0.00 39.68 3.41
501 1715 1.007849 CAAAAGCCCCAAACCGACG 60.008 57.895 0.00 0.00 0.00 5.12
502 1716 1.454295 AAAAGCCCCAAACCGACGT 60.454 52.632 0.00 0.00 0.00 4.34
503 1717 0.179023 AAAAGCCCCAAACCGACGTA 60.179 50.000 0.00 0.00 0.00 3.57
504 1718 0.604511 AAAGCCCCAAACCGACGTAG 60.605 55.000 0.00 0.00 0.00 3.51
542 1758 5.511545 CCCTTAAAATCTCCGATCGGATCTT 60.512 44.000 35.58 26.69 44.24 2.40
648 1878 1.938926 GCGCTCTTGTGCTTCTCTCTT 60.939 52.381 0.00 0.00 45.43 2.85
654 1884 2.713895 TGTGCTTCTCTCTTGTCTCG 57.286 50.000 0.00 0.00 0.00 4.04
657 1887 0.459411 GCTTCTCTCTTGTCTCGGCC 60.459 60.000 0.00 0.00 0.00 6.13
663 1893 4.148825 CTTGTCTCGGCCGGGGAG 62.149 72.222 28.04 16.22 0.00 4.30
713 1990 7.970614 GGAACTGACTGAATTGGATTTTGATAC 59.029 37.037 0.00 0.00 0.00 2.24
715 1992 9.739276 AACTGACTGAATTGGATTTTGATACTA 57.261 29.630 0.00 0.00 0.00 1.82
721 1998 9.177608 CTGAATTGGATTTTGATACTAGTTGGA 57.822 33.333 0.00 0.00 0.00 3.53
736 2013 6.161381 ACTAGTTGGATTTTACAGTACGTGG 58.839 40.000 0.00 0.00 0.00 4.94
749 2026 3.084039 AGTACGTGGTCGAGTAATTGGA 58.916 45.455 0.00 0.00 40.62 3.53
754 2031 3.551890 CGTGGTCGAGTAATTGGAATCAG 59.448 47.826 0.00 0.00 39.71 2.90
758 2035 5.104527 TGGTCGAGTAATTGGAATCAGGAAT 60.105 40.000 0.00 0.00 0.00 3.01
768 2045 5.937975 TGGAATCAGGAATTTGGGATTTC 57.062 39.130 0.00 0.00 30.60 2.17
774 2051 4.883585 TCAGGAATTTGGGATTTCGATCTG 59.116 41.667 0.00 0.00 0.00 2.90
942 2222 4.699257 GCAATTGACCTCTGATTCAACTCT 59.301 41.667 10.34 0.00 34.61 3.24
943 2223 5.163774 GCAATTGACCTCTGATTCAACTCTC 60.164 44.000 10.34 0.00 34.61 3.20
944 2224 4.543590 TTGACCTCTGATTCAACTCTCC 57.456 45.455 0.00 0.00 0.00 3.71
945 2225 3.510459 TGACCTCTGATTCAACTCTCCA 58.490 45.455 0.00 0.00 0.00 3.86
946 2226 3.513119 TGACCTCTGATTCAACTCTCCAG 59.487 47.826 0.00 0.00 0.00 3.86
1014 2294 1.645455 CGCCATGAGGAAGAATGCG 59.355 57.895 0.00 0.00 36.89 4.73
1096 2376 3.724374 TCGTGGAACATTTTCTCGTCTT 58.276 40.909 8.58 0.00 44.52 3.01
1270 2550 1.888736 GCGTACCGGAACCTCTTCT 59.111 57.895 9.46 0.00 0.00 2.85
1831 3111 1.878088 GCATCCAGGAGTCGTACGATA 59.122 52.381 22.57 0.00 0.00 2.92
1917 3198 1.272490 GTCGGTGACCTGATGTCTTCA 59.728 52.381 0.00 0.00 44.75 3.02
1959 3240 1.958205 CGCGGATGAGATTGGGAGC 60.958 63.158 0.00 0.00 0.00 4.70
2156 4723 2.999355 GTGGACTCAAAGAGATGCTGAC 59.001 50.000 0.31 0.00 33.32 3.51
2185 4754 4.648762 TCTGAAATTGCAGGGAAACTTTGA 59.351 37.500 13.73 0.00 36.55 2.69
2189 4758 4.861102 ATTGCAGGGAAACTTTGAAGAG 57.139 40.909 0.00 0.00 0.00 2.85
2315 7509 3.375299 GCAGCTCAGGTACTTGGTTATTG 59.625 47.826 5.01 0.00 34.60 1.90
2496 7695 2.791383 TTCTCCACAACGCCATTTTG 57.209 45.000 0.00 0.00 0.00 2.44
2622 10453 8.989980 CAACTCTACTTCGGTAAGATTTTCTTT 58.010 33.333 0.00 0.00 37.89 2.52
2623 10454 9.557061 AACTCTACTTCGGTAAGATTTTCTTTT 57.443 29.630 0.00 0.00 37.89 2.27
2624 10455 9.205719 ACTCTACTTCGGTAAGATTTTCTTTTC 57.794 33.333 0.00 0.00 37.89 2.29
2640 10472 7.938140 TTTCTTTTCTTTTCTTCAGGAGTGA 57.062 32.000 0.00 0.00 0.00 3.41
2641 10473 8.525290 TTTCTTTTCTTTTCTTCAGGAGTGAT 57.475 30.769 0.00 0.00 30.85 3.06
2649 10484 8.432805 TCTTTTCTTCAGGAGTGATCTACTTTT 58.567 33.333 0.00 0.00 40.53 2.27
2653 10488 5.489792 TCAGGAGTGATCTACTTTTTGCT 57.510 39.130 0.00 0.00 40.53 3.91
2654 10489 5.240891 TCAGGAGTGATCTACTTTTTGCTG 58.759 41.667 0.00 0.00 40.53 4.41
2656 10491 3.753272 GGAGTGATCTACTTTTTGCTGCA 59.247 43.478 0.00 0.00 40.53 4.41
2657 10492 4.142730 GGAGTGATCTACTTTTTGCTGCAG 60.143 45.833 10.11 10.11 40.53 4.41
2658 10493 3.190118 AGTGATCTACTTTTTGCTGCAGC 59.810 43.478 31.89 31.89 35.67 5.25
2661 10496 7.965296 AGTGATCTACTTTTTGCTGCAGCATT 61.965 38.462 39.83 23.30 43.74 3.56
2674 10510 4.436332 CTGCAGCATTATCAGTGTCACTA 58.564 43.478 4.85 0.00 0.00 2.74
2698 10534 7.878477 ACATCTTGTTCGATTTTCTAACGTA 57.122 32.000 0.00 0.00 0.00 3.57
2780 10646 1.404035 GGCAACTTCGACAACCAGTTT 59.596 47.619 0.00 0.00 0.00 2.66
2787 10653 1.065345 TCGACAACCAGTTTTGGGTCA 60.065 47.619 0.00 0.00 42.06 4.02
2889 10755 3.739810 GTGAGTAAGAAACCACGAACTCC 59.260 47.826 0.00 0.00 33.94 3.85
2890 10756 3.640029 TGAGTAAGAAACCACGAACTCCT 59.360 43.478 0.00 0.00 33.94 3.69
2896 10762 4.822026 AGAAACCACGAACTCCTAGATTG 58.178 43.478 0.00 0.00 0.00 2.67
3051 10919 2.107953 GGCGACAGGATGCTCTCC 59.892 66.667 0.00 0.00 42.53 3.71
3268 11139 1.134159 GGAGCAAGCAGTGATGGAGAT 60.134 52.381 0.00 0.00 0.00 2.75
3271 11142 1.941294 GCAAGCAGTGATGGAGATGAG 59.059 52.381 0.00 0.00 0.00 2.90
3272 11143 2.419713 GCAAGCAGTGATGGAGATGAGA 60.420 50.000 0.00 0.00 0.00 3.27
3303 11177 1.211709 CGTGGAAATGCGGGGTTTC 59.788 57.895 0.00 0.00 35.38 2.78
3304 11178 1.519751 CGTGGAAATGCGGGGTTTCA 61.520 55.000 0.00 0.00 37.32 2.69
3305 11179 0.894835 GTGGAAATGCGGGGTTTCAT 59.105 50.000 0.00 0.00 37.32 2.57
3317 11191 4.803613 GCGGGGTTTCATTGTGATTTTATC 59.196 41.667 0.00 0.00 0.00 1.75
3357 11239 2.808543 CAGTTCTTAGCTTGGGTGTGTC 59.191 50.000 0.00 0.00 0.00 3.67
3360 11242 3.334583 TCTTAGCTTGGGTGTGTCATC 57.665 47.619 0.00 0.00 0.00 2.92
3364 11246 1.556911 AGCTTGGGTGTGTCATCCTAG 59.443 52.381 6.23 6.23 39.75 3.02
3365 11247 1.279271 GCTTGGGTGTGTCATCCTAGT 59.721 52.381 10.89 0.00 39.16 2.57
3367 11249 3.430929 GCTTGGGTGTGTCATCCTAGTAG 60.431 52.174 10.89 0.00 39.16 2.57
3409 11305 3.243569 CCGTATGAGTTTGGTTTTTGCCA 60.244 43.478 0.00 0.00 36.62 4.92
3411 11307 4.261405 CGTATGAGTTTGGTTTTTGCCAGA 60.261 41.667 0.00 0.00 40.01 3.86
3415 11311 4.874966 TGAGTTTGGTTTTTGCCAGAAATG 59.125 37.500 0.00 0.00 40.01 2.32
3416 11312 5.096443 AGTTTGGTTTTTGCCAGAAATGA 57.904 34.783 0.00 0.00 40.01 2.57
3418 11314 6.825610 AGTTTGGTTTTTGCCAGAAATGATA 58.174 32.000 0.00 0.00 40.01 2.15
3419 11315 6.930722 AGTTTGGTTTTTGCCAGAAATGATAG 59.069 34.615 0.00 0.00 40.01 2.08
3425 11334 7.869429 GGTTTTTGCCAGAAATGATAGGATATG 59.131 37.037 0.00 0.00 0.00 1.78
3427 11336 9.639563 TTTTTGCCAGAAATGATAGGATATGTA 57.360 29.630 0.00 0.00 0.00 2.29
3428 11337 9.812347 TTTTGCCAGAAATGATAGGATATGTAT 57.188 29.630 0.00 0.00 0.00 2.29
3432 11341 9.553064 GCCAGAAATGATAGGATATGTATAAGG 57.447 37.037 0.00 0.00 0.00 2.69
3525 11434 9.478768 TGTAATGAAAACTACGACTGTTGAATA 57.521 29.630 1.15 0.00 0.00 1.75
3563 11472 8.830201 AAATCATTCAAACGATTTTCATTCCA 57.170 26.923 0.00 0.00 38.39 3.53
3566 11475 7.377398 TCATTCAAACGATTTTCATTCCACAT 58.623 30.769 0.00 0.00 0.00 3.21
3593 11502 5.493133 TTCACTGTCAATTTTGTAGCGTT 57.507 34.783 0.00 0.00 0.00 4.84
3625 11580 2.673368 CGGTCTTGCTAAATGTGACCTC 59.327 50.000 0.00 0.00 43.45 3.85
3638 11593 1.929836 GTGACCTCTTGCGAGCAATAG 59.070 52.381 11.15 12.77 35.90 1.73
3658 11613 1.526686 CCCATAAGCCTGCATCGCA 60.527 57.895 8.47 0.00 36.92 5.10
3692 11647 1.243902 TGGGCCGAATCTTGTTTGTC 58.756 50.000 0.00 0.00 0.00 3.18
3701 11668 6.128391 GCCGAATCTTGTTTGTCATAGTGTTA 60.128 38.462 0.00 0.00 0.00 2.41
3833 11800 6.754209 CACCTCTATGTAACAGATTCAGTGTC 59.246 42.308 0.00 0.00 0.00 3.67
3843 11810 3.430218 CAGATTCAGTGTCCGTGAGAAAC 59.570 47.826 0.00 0.00 32.16 2.78
3853 11821 6.073222 AGTGTCCGTGAGAAACAAATATTCAC 60.073 38.462 0.00 0.00 34.82 3.18
3872 11840 9.743057 ATATTCACGTGTTTCAAAAATGAAGAA 57.257 25.926 16.51 0.00 0.00 2.52
4043 12011 8.579682 TTCATGTGTATGAAGATAGATGTTCG 57.420 34.615 0.00 0.00 45.77 3.95
4045 12013 7.649306 TCATGTGTATGAAGATAGATGTTCGTG 59.351 37.037 4.76 0.00 40.26 4.35
4049 12017 8.656849 GTGTATGAAGATAGATGTTCGTGTTTT 58.343 33.333 4.76 0.00 33.20 2.43
4195 12164 9.762933 AAATGCAAACTGAAGTAAACAACATAT 57.237 25.926 0.00 0.00 0.00 1.78
4230 12199 1.832998 GTTGGCCCATGTTCCATTGAT 59.167 47.619 0.00 0.00 31.54 2.57
4233 12202 0.031178 GCCCATGTTCCATTGATCGC 59.969 55.000 0.00 0.00 0.00 4.58
4252 12221 1.605710 GCAGTCACACACATGAAAGCT 59.394 47.619 0.00 0.00 31.41 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.183679 GCTATCTTCCCTCCCGATCAT 58.816 52.381 0.00 0.00 0.00 2.45
20 21 2.334006 ATGCTATCTTCCCTCCCGAT 57.666 50.000 0.00 0.00 0.00 4.18
29 30 5.466728 TGAACGCTGGATTTATGCTATCTTC 59.533 40.000 0.00 0.00 0.00 2.87
39 40 3.932710 GACTGACATGAACGCTGGATTTA 59.067 43.478 0.00 0.00 0.00 1.40
67 68 0.673985 TGCGTTGAGTACTGAGCAGT 59.326 50.000 0.00 8.35 45.02 4.40
69 70 2.068519 CATTGCGTTGAGTACTGAGCA 58.931 47.619 0.00 3.48 0.00 4.26
125 126 2.580815 CCAGCCATGTCAGAGCGA 59.419 61.111 0.00 0.00 0.00 4.93
179 182 2.434359 GTAGGTCGGTGGCACTGC 60.434 66.667 21.67 15.66 0.00 4.40
257 1459 4.329545 TTCGCGGCAAGGAGGCTT 62.330 61.111 6.13 0.00 41.46 4.35
271 1473 0.304705 GCCATGCTATGTTCCGTTCG 59.695 55.000 0.00 0.00 0.00 3.95
312 1515 1.804151 TCGACGGAAATGCCAAAAGAG 59.196 47.619 0.00 0.00 35.94 2.85
314 1517 1.265635 TGTCGACGGAAATGCCAAAAG 59.734 47.619 11.62 0.00 35.94 2.27
316 1519 1.466950 GATGTCGACGGAAATGCCAAA 59.533 47.619 11.62 0.00 35.94 3.28
319 1522 1.436983 GGGATGTCGACGGAAATGCC 61.437 60.000 11.62 9.63 40.68 4.40
325 1528 0.034767 ACTACTGGGATGTCGACGGA 60.035 55.000 11.62 0.00 0.00 4.69
419 1622 0.320683 TCATGCACTGAACCGGACAG 60.321 55.000 23.69 23.69 40.68 3.51
425 1628 1.734465 GCACTACTCATGCACTGAACC 59.266 52.381 0.00 0.00 42.88 3.62
430 1633 0.891373 ACTCGCACTACTCATGCACT 59.109 50.000 0.00 0.00 43.57 4.40
431 1634 0.994995 CACTCGCACTACTCATGCAC 59.005 55.000 0.00 0.00 43.57 4.57
432 1635 0.603065 ACACTCGCACTACTCATGCA 59.397 50.000 0.00 0.00 43.57 3.96
433 1636 0.994995 CACACTCGCACTACTCATGC 59.005 55.000 0.00 0.00 39.81 4.06
434 1637 0.994995 GCACACTCGCACTACTCATG 59.005 55.000 0.00 0.00 0.00 3.07
435 1638 0.456824 CGCACACTCGCACTACTCAT 60.457 55.000 0.00 0.00 0.00 2.90
436 1639 1.081442 CGCACACTCGCACTACTCA 60.081 57.895 0.00 0.00 0.00 3.41
437 1640 3.755404 CGCACACTCGCACTACTC 58.245 61.111 0.00 0.00 0.00 2.59
469 1683 1.606668 GCTTTTGACACCACGGATGAA 59.393 47.619 0.00 0.00 0.00 2.57
627 1857 1.681945 GAGAGAAGCACAAGAGCGCG 61.682 60.000 0.00 0.00 40.15 6.86
648 1878 4.689549 TTCTCCCCGGCCGAGACA 62.690 66.667 30.73 7.98 36.11 3.41
654 1884 2.253403 AAACGATCTTCTCCCCGGCC 62.253 60.000 0.00 0.00 0.00 6.13
657 1887 2.271800 CAAGAAACGATCTTCTCCCCG 58.728 52.381 5.46 0.00 45.42 5.73
663 1893 4.333926 AGCCTAATGCAAGAAACGATCTTC 59.666 41.667 0.00 0.00 46.80 2.87
713 1990 6.161381 ACCACGTACTGTAAAATCCAACTAG 58.839 40.000 0.00 0.00 0.00 2.57
715 1992 4.964593 ACCACGTACTGTAAAATCCAACT 58.035 39.130 0.00 0.00 0.00 3.16
721 1998 4.510038 ACTCGACCACGTACTGTAAAAT 57.490 40.909 0.00 0.00 40.69 1.82
728 2005 3.084039 TCCAATTACTCGACCACGTACT 58.916 45.455 0.00 0.00 40.69 2.73
736 2013 6.927294 AATTCCTGATTCCAATTACTCGAC 57.073 37.500 0.00 0.00 0.00 4.20
749 2026 6.040166 CAGATCGAAATCCCAAATTCCTGATT 59.960 38.462 0.00 0.00 31.78 2.57
754 2031 3.243535 GCCAGATCGAAATCCCAAATTCC 60.244 47.826 0.00 0.00 31.78 3.01
758 2035 1.284785 AGGCCAGATCGAAATCCCAAA 59.715 47.619 5.01 0.00 31.78 3.28
768 2045 3.947834 ACCAAATTAAAGAGGCCAGATCG 59.052 43.478 5.01 0.00 0.00 3.69
942 2222 1.902508 GTGATCTTGGTGGAGACTGGA 59.097 52.381 0.00 0.00 0.00 3.86
943 2223 1.905215 AGTGATCTTGGTGGAGACTGG 59.095 52.381 0.00 0.00 0.00 4.00
944 2224 2.830923 AGAGTGATCTTGGTGGAGACTG 59.169 50.000 0.00 0.00 0.00 3.51
945 2225 3.182887 AGAGTGATCTTGGTGGAGACT 57.817 47.619 0.00 0.00 0.00 3.24
946 2226 3.971245 AAGAGTGATCTTGGTGGAGAC 57.029 47.619 0.00 0.00 0.00 3.36
971 2251 0.813610 CGATCAATTAGGCACCCGCA 60.814 55.000 0.00 0.00 41.24 5.69
972 2252 1.507141 CCGATCAATTAGGCACCCGC 61.507 60.000 0.00 0.00 37.44 6.13
1014 2294 4.041723 CCAAAATCAACAGGACAAACGAC 58.958 43.478 0.00 0.00 0.00 4.34
1077 2357 3.493503 ACGAAGACGAGAAAATGTTCCAC 59.506 43.478 0.00 0.00 42.66 4.02
1270 2550 4.212913 GATCTCGCCGCAGCTGGA 62.213 66.667 17.12 2.92 36.60 3.86
1434 2714 2.297597 CAGGAAGAACTCGAGGAACACT 59.702 50.000 18.41 4.73 0.00 3.55
1539 2819 3.358076 CTCCTCCGCCGACTTGGAC 62.358 68.421 0.00 0.00 42.00 4.02
1831 3111 3.411517 CATCCCGTCCCCCAGCTT 61.412 66.667 0.00 0.00 0.00 3.74
1917 3198 1.542492 CCTGCAGAACCAGCATCTTT 58.458 50.000 17.39 0.00 41.82 2.52
2122 4681 2.146342 GAGTCCACAGTCCACACATTG 58.854 52.381 0.00 0.00 0.00 2.82
2156 4723 7.381323 AGTTTCCCTGCAATTTCAGATAAAAG 58.619 34.615 6.67 0.00 36.19 2.27
2185 4754 2.036346 GCCCAAACAGTGCAAATCTCTT 59.964 45.455 0.00 0.00 0.00 2.85
2189 4758 1.787012 CTGCCCAAACAGTGCAAATC 58.213 50.000 0.00 0.00 34.06 2.17
2442 7641 3.127533 GCCGCGAAGATGTTGGCT 61.128 61.111 8.23 0.00 42.44 4.75
2478 7677 0.958091 CCAAAATGGCGTTGTGGAGA 59.042 50.000 22.03 0.00 46.65 3.71
2496 7695 0.174389 TGATGAAGCGAGACTCAGCC 59.826 55.000 13.34 3.35 0.00 4.85
2499 7698 1.404717 GCCTTGATGAAGCGAGACTCA 60.405 52.381 2.82 0.00 0.00 3.41
2622 10453 7.546250 AGTAGATCACTCCTGAAGAAAAGAA 57.454 36.000 0.00 0.00 28.33 2.52
2623 10454 7.546250 AAGTAGATCACTCCTGAAGAAAAGA 57.454 36.000 0.00 0.00 36.04 2.52
2624 10455 8.614469 AAAAGTAGATCACTCCTGAAGAAAAG 57.386 34.615 0.00 0.00 36.04 2.27
2635 10467 4.671250 GCTGCAGCAAAAAGTAGATCACTC 60.671 45.833 33.36 0.00 41.59 3.51
2636 10468 3.190118 GCTGCAGCAAAAAGTAGATCACT 59.810 43.478 33.36 0.00 41.59 3.41
2637 10469 3.496155 GCTGCAGCAAAAAGTAGATCAC 58.504 45.455 33.36 0.00 41.59 3.06
2653 10488 3.339253 AGTGACACTGATAATGCTGCA 57.661 42.857 7.47 4.13 0.00 4.41
2654 10489 4.183865 TGTAGTGACACTGATAATGCTGC 58.816 43.478 18.58 0.00 0.00 5.25
2656 10491 6.477053 AGATGTAGTGACACTGATAATGCT 57.523 37.500 18.58 3.75 38.76 3.79
2657 10492 6.536582 ACAAGATGTAGTGACACTGATAATGC 59.463 38.462 18.58 1.57 38.76 3.56
2658 10493 8.484641 AACAAGATGTAGTGACACTGATAATG 57.515 34.615 18.58 11.75 38.76 1.90
2661 10496 6.150474 TCGAACAAGATGTAGTGACACTGATA 59.850 38.462 18.58 4.67 38.76 2.15
2665 10501 4.848562 TCGAACAAGATGTAGTGACACT 57.151 40.909 13.68 13.68 38.76 3.55
2666 10502 6.467723 AAATCGAACAAGATGTAGTGACAC 57.532 37.500 0.00 0.00 38.76 3.67
2674 10510 6.780706 ACGTTAGAAAATCGAACAAGATGT 57.219 33.333 0.00 0.00 32.57 3.06
2698 10534 0.031994 GCACAAACCTGCCGAAACAT 59.968 50.000 0.00 0.00 0.00 2.71
2780 10646 0.850100 ACACCTTGGACATGACCCAA 59.150 50.000 18.38 18.38 41.04 4.12
2889 10755 6.108687 TGTAAGTGCACAATCTCCAATCTAG 58.891 40.000 21.04 0.00 0.00 2.43
2890 10756 6.048732 TGTAAGTGCACAATCTCCAATCTA 57.951 37.500 21.04 0.00 0.00 1.98
2896 10762 6.072112 TCTTTTTGTAAGTGCACAATCTCC 57.928 37.500 21.04 0.86 38.18 3.71
2904 10770 5.843673 TCAACCATCTTTTTGTAAGTGCA 57.156 34.783 0.00 0.00 0.00 4.57
2940 10808 6.549364 AGTCCCTGAAATACAATGTTTGAACA 59.451 34.615 0.00 0.00 44.06 3.18
2941 10809 6.981722 AGTCCCTGAAATACAATGTTTGAAC 58.018 36.000 0.00 0.00 0.00 3.18
2943 10811 6.370442 CGTAGTCCCTGAAATACAATGTTTGA 59.630 38.462 0.00 0.00 0.00 2.69
2944 10812 6.370442 TCGTAGTCCCTGAAATACAATGTTTG 59.630 38.462 0.00 0.00 0.00 2.93
2952 10820 5.805994 CAGAACTTCGTAGTCCCTGAAATAC 59.194 44.000 14.92 0.00 37.25 1.89
3155 11026 3.636313 TACCTCCGGCGAGTTTGCG 62.636 63.158 9.30 0.00 33.93 4.85
3268 11139 2.483876 CACGAGGAGCAAAAACTCTCA 58.516 47.619 0.00 0.00 36.87 3.27
3271 11142 1.878953 TCCACGAGGAGCAAAAACTC 58.121 50.000 0.00 0.00 39.61 3.01
3272 11143 2.341846 TTCCACGAGGAGCAAAAACT 57.658 45.000 0.78 0.00 46.74 2.66
3303 11177 7.495934 ACCCTCTTCGTAGATAAAATCACAATG 59.504 37.037 0.00 0.00 35.04 2.82
3304 11178 7.565680 ACCCTCTTCGTAGATAAAATCACAAT 58.434 34.615 0.00 0.00 35.04 2.71
3305 11179 6.942976 ACCCTCTTCGTAGATAAAATCACAA 58.057 36.000 0.00 0.00 35.04 3.33
3317 11191 1.359459 GCCGCAAACCCTCTTCGTAG 61.359 60.000 0.00 0.00 0.00 3.51
3357 11239 5.227238 ACAAACGACGTACTACTAGGATG 57.773 43.478 0.00 0.00 0.00 3.51
3360 11242 6.470235 CCAAATACAAACGACGTACTACTAGG 59.530 42.308 0.00 0.00 0.00 3.02
3364 11246 4.201618 GGCCAAATACAAACGACGTACTAC 60.202 45.833 0.00 0.00 0.00 2.73
3365 11247 3.925913 GGCCAAATACAAACGACGTACTA 59.074 43.478 0.00 0.00 0.00 1.82
3367 11249 2.159667 GGGCCAAATACAAACGACGTAC 60.160 50.000 4.39 0.00 0.00 3.67
3443 11352 8.933653 TCAACATCCTTATACATATCCTCACAA 58.066 33.333 0.00 0.00 0.00 3.33
3497 11406 7.623770 TCAACAGTCGTAGTTTTCATTACAAC 58.376 34.615 0.00 0.00 0.00 3.32
3525 11434 9.878599 CGTTTGAATGATTTACAGTAAAGAGTT 57.121 29.630 11.41 5.80 0.00 3.01
3600 11509 3.123621 GTCACATTTAGCAAGACCGACTG 59.876 47.826 0.00 0.00 0.00 3.51
3601 11510 3.326747 GTCACATTTAGCAAGACCGACT 58.673 45.455 0.00 0.00 0.00 4.18
3602 11511 2.415512 GGTCACATTTAGCAAGACCGAC 59.584 50.000 0.00 0.00 39.33 4.79
3603 11512 2.695359 GGTCACATTTAGCAAGACCGA 58.305 47.619 0.00 0.00 39.33 4.69
3606 11515 4.378874 GCAAGAGGTCACATTTAGCAAGAC 60.379 45.833 0.00 0.00 0.00 3.01
3607 11516 3.753272 GCAAGAGGTCACATTTAGCAAGA 59.247 43.478 0.00 0.00 0.00 3.02
3608 11517 3.425359 CGCAAGAGGTCACATTTAGCAAG 60.425 47.826 0.00 0.00 43.02 4.01
3610 11519 2.076100 CGCAAGAGGTCACATTTAGCA 58.924 47.619 0.00 0.00 43.02 3.49
3611 11520 2.346803 TCGCAAGAGGTCACATTTAGC 58.653 47.619 0.00 0.00 45.01 3.09
3625 11580 0.820891 ATGGGCCTATTGCTCGCAAG 60.821 55.000 4.53 0.00 46.64 4.01
3658 11613 3.149196 CGGCCCATGTATAAAGCTTCAT 58.851 45.455 0.00 0.00 0.00 2.57
3803 11770 7.851228 TGAATCTGTTACATAGAGGTGAACAT 58.149 34.615 0.00 0.00 30.16 2.71
3853 11821 9.412390 CATTTTCTTCTTCATTTTTGAAACACG 57.588 29.630 0.00 0.00 0.00 4.49
3943 11911 6.804677 TGTGATATGTGTGTTTTTCTTTGCT 58.195 32.000 0.00 0.00 0.00 3.91
3944 11912 7.462109 TTGTGATATGTGTGTTTTTCTTTGC 57.538 32.000 0.00 0.00 0.00 3.68
3955 11923 9.791820 ACATGAACATTTATTGTGATATGTGTG 57.208 29.630 0.00 0.00 38.99 3.82
4021 11989 7.492524 ACACGAACATCTATCTTCATACACAT 58.507 34.615 0.00 0.00 0.00 3.21
4032 12000 9.445786 TTTCTTTTCAAAACACGAACATCTATC 57.554 29.630 0.00 0.00 0.00 2.08
4033 12001 9.965824 ATTTCTTTTCAAAACACGAACATCTAT 57.034 25.926 0.00 0.00 0.00 1.98
4039 12007 9.829637 GTGAATATTTCTTTTCAAAACACGAAC 57.170 29.630 0.00 0.00 33.90 3.95
4139 12108 6.405278 AAAACTTTGTTTCCACCTATCCTG 57.595 37.500 0.00 0.00 0.00 3.86
4169 12138 9.762933 ATATGTTGTTTACTTCAGTTTGCATTT 57.237 25.926 0.00 0.00 0.00 2.32
4195 12164 5.642165 TGGGCCAACCTAGTAACATTTTTA 58.358 37.500 2.13 0.00 41.11 1.52
4196 12165 4.484912 TGGGCCAACCTAGTAACATTTTT 58.515 39.130 2.13 0.00 41.11 1.94
4230 12199 1.866601 CTTTCATGTGTGTGACTGCGA 59.133 47.619 0.00 0.00 0.00 5.10
4233 12202 2.031420 CCAGCTTTCATGTGTGTGACTG 60.031 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.