Multiple sequence alignment - TraesCS5B01G427900

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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 TraesCS5B01G427900 chr5B 100.000 2905 0 0 1 2905 603942239 603939335 0.000000e+00 5365.0
1 TraesCS5B01G427900 chr5A 88.250 2017 189 26 1 1993 611332856 611330864 0.000000e+00 2368.0
2 TraesCS5B01G427900 chr5A 86.578 678 72 12 1 670 611334008 611333342 0.000000e+00 730.0
3 TraesCS5B01G427900 chr5A 93.842 341 18 1 1964 2304 611330858 611330521 7.180000e-141 510.0
4 TraesCS5B01G427900 chr5A 82.581 620 50 19 2296 2877 611325504 611324905 7.230000e-136 494.0
5 TraesCS5B01G427900 chr5D 89.020 1530 118 25 485 1993 489755275 489753775 0.000000e+00 1849.0
6 TraesCS5B01G427900 chr5D 92.063 504 31 8 1962 2463 489753771 489753275 0.000000e+00 701.0
7 TraesCS5B01G427900 chr5D 88.958 480 42 9 2436 2905 489753276 489752798 1.500000e-162 582.0
8 TraesCS5B01G427900 chr5D 95.181 332 15 1 1 331 489770749 489770418 9.220000e-145 523.0
9 TraesCS5B01G427900 chr5D 97.917 96 2 0 399 494 489769847 489769752 1.790000e-37 167.0
10 TraesCS5B01G427900 chr5D 97.333 75 2 0 328 402 489770152 489770078 8.450000e-26 128.0
11 TraesCS5B01G427900 chr1D 77.654 537 101 12 6 529 199015676 199015146 2.810000e-80 309.0
12 TraesCS5B01G427900 chr6D 88.571 175 18 2 1758 1932 382208272 382208100 8.160000e-51 211.0
13 TraesCS5B01G427900 chr6D 87.059 170 20 2 1764 1931 427706008 427705839 1.060000e-44 191.0
14 TraesCS5B01G427900 chr2D 87.719 171 19 2 1764 1932 15520343 15520513 6.350000e-47 198.0
15 TraesCS5B01G427900 chr2D 87.209 172 20 2 1764 1933 575765852 575766023 8.210000e-46 195.0
16 TraesCS5B01G427900 chr1B 86.592 179 24 0 1755 1933 458013748 458013926 6.350000e-47 198.0
17 TraesCS5B01G427900 chr6B 86.857 175 18 4 1759 1930 680996388 680996560 1.060000e-44 191.0
18 TraesCS5B01G427900 chr3A 85.000 180 18 8 1761 1934 108032170 108031994 1.070000e-39 174.0
19 TraesCS5B01G427900 chr4A 72.355 293 71 9 226 514 646083796 646084082 1.860000e-12 84.2


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 TraesCS5B01G427900 chr5B 603939335 603942239 2904 True 5365.000000 5365 100.000000 1 2905 1 chr5B.!!$R1 2904
1 TraesCS5B01G427900 chr5A 611330521 611334008 3487 True 1202.666667 2368 89.556667 1 2304 3 chr5A.!!$R2 2303
2 TraesCS5B01G427900 chr5A 611324905 611325504 599 True 494.000000 494 82.581000 2296 2877 1 chr5A.!!$R1 581
3 TraesCS5B01G427900 chr5D 489752798 489755275 2477 True 1044.000000 1849 90.013667 485 2905 3 chr5D.!!$R1 2420
4 TraesCS5B01G427900 chr5D 489769752 489770749 997 True 272.666667 523 96.810333 1 494 3 chr5D.!!$R2 493
5 TraesCS5B01G427900 chr1D 199015146 199015676 530 True 309.000000 309 77.654000 6 529 1 chr1D.!!$R1 523

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
668 2335 0.398696 ACATGTCGGCTAAACCCACA 59.601 50.0 0.0 0.0 33.26 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 4209 0.177836 CACCATCACACGCTCCCATA 59.822 55.0 0.0 0.0 0.0 2.74 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
70 1223 2.166459 CTCAATGCGTAGACCTTCCTGA 59.834 50.000 0.00 0.00 0.00 3.86
171 1332 5.461032 AAAATCAAGTATTTTCCGCACCA 57.539 34.783 0.00 0.00 42.88 4.17
193 1354 3.052036 CAAGTGGCATTTCAAAGAACGG 58.948 45.455 0.00 0.00 0.00 4.44
367 1799 7.427989 AGTTGGTATCCCGAGATAACTAAAA 57.572 36.000 3.50 0.00 42.35 1.52
442 2108 0.802607 TGCCGCGTCCAAAACAAAAC 60.803 50.000 4.92 0.00 0.00 2.43
523 2190 7.906327 ACACCAATTTCATATTTACAGCCTTT 58.094 30.769 0.00 0.00 0.00 3.11
530 2197 9.822185 ATTTCATATTTACAGCCTTTTCCATTC 57.178 29.630 0.00 0.00 0.00 2.67
534 2201 6.625532 ATTTACAGCCTTTTCCATTCCATT 57.374 33.333 0.00 0.00 0.00 3.16
535 2202 5.659440 TTACAGCCTTTTCCATTCCATTC 57.341 39.130 0.00 0.00 0.00 2.67
576 2243 1.824230 TGTGAACAGTTTTGCTTGCCT 59.176 42.857 0.00 0.00 0.00 4.75
668 2335 0.398696 ACATGTCGGCTAAACCCACA 59.601 50.000 0.00 0.00 33.26 4.17
669 2336 1.202830 ACATGTCGGCTAAACCCACAA 60.203 47.619 0.00 0.00 33.26 3.33
748 2416 9.302345 TGTTTTCGTTAACAAATTAAATGAGCA 57.698 25.926 6.39 0.00 35.22 4.26
751 2419 9.522804 TTTCGTTAACAAATTAAATGAGCAAGT 57.477 25.926 6.39 0.00 32.04 3.16
752 2420 8.722342 TCGTTAACAAATTAAATGAGCAAGTC 57.278 30.769 6.39 0.00 32.04 3.01
782 2450 2.267174 ACAGAACAGAATGCAGTGCT 57.733 45.000 17.60 0.00 42.53 4.40
873 2541 1.516169 CGCTTGGCCGCAAATTACC 60.516 57.895 0.00 0.00 0.00 2.85
972 2643 3.370061 GTGGGTACGTCACAGAATTTAGC 59.630 47.826 11.55 0.00 35.39 3.09
997 2668 4.018779 CCTCCACTAGCTAGCTACTAGGAT 60.019 50.000 24.50 5.14 41.22 3.24
1020 2691 7.878644 GGATTAGTATTTAAAGTGAGCTAGGGG 59.121 40.741 0.00 0.00 0.00 4.79
1032 2703 3.622263 TAGGGGGTCCTGGGCAGT 61.622 66.667 0.00 0.00 44.61 4.40
1033 2704 3.943137 TAGGGGGTCCTGGGCAGTG 62.943 68.421 0.00 0.00 44.61 3.66
1041 2713 1.078567 CCTGGGCAGTGAAGAGCTC 60.079 63.158 5.27 5.27 0.00 4.09
1227 2899 9.900710 GTATATATAGCATGCAGTACATACTCC 57.099 37.037 21.98 0.00 36.64 3.85
1228 2900 8.774546 ATATATAGCATGCAGTACATACTCCT 57.225 34.615 21.98 0.00 36.64 3.69
1229 2901 9.868160 ATATATAGCATGCAGTACATACTCCTA 57.132 33.333 21.98 0.00 36.64 2.94
1230 2902 4.592485 AGCATGCAGTACATACTCCTAC 57.408 45.455 21.98 0.00 36.64 3.18
1272 2948 0.390860 CCCTAGGCGATGAAGGTCTG 59.609 60.000 2.05 0.00 0.00 3.51
1288 2964 3.057174 AGGTCTGAATCTTGTGTCGTCTC 60.057 47.826 0.00 0.00 0.00 3.36
1345 3025 5.907207 TCTCAGGTATGCTAATCAAGTCAC 58.093 41.667 0.00 0.00 0.00 3.67
1346 3026 5.422012 TCTCAGGTATGCTAATCAAGTCACA 59.578 40.000 0.00 0.00 0.00 3.58
1359 3039 7.664082 AATCAAGTCACAGTGATAAACTCTG 57.336 36.000 6.51 2.21 43.24 3.35
1378 3058 6.129179 ACTCTGATTTTCTTTTCTTGTGGGA 58.871 36.000 0.00 0.00 0.00 4.37
1384 3064 2.863809 TCTTTTCTTGTGGGAAGAGGC 58.136 47.619 0.00 0.00 31.14 4.70
1433 3117 7.704899 GCGAGCTTAATTTATAATGGGTTTTGT 59.295 33.333 0.00 0.00 0.00 2.83
1476 3160 4.953940 TTTGAGCTGGCAAAACCTAATT 57.046 36.364 0.00 0.00 40.22 1.40
1478 3162 6.412362 TTTGAGCTGGCAAAACCTAATTAA 57.588 33.333 0.00 0.00 40.22 1.40
1481 3165 6.630071 TGAGCTGGCAAAACCTAATTAATTC 58.370 36.000 3.39 0.00 40.22 2.17
1486 3170 7.063426 GCTGGCAAAACCTAATTAATTCTCAAC 59.937 37.037 3.39 0.00 40.22 3.18
1497 3181 5.512942 TTAATTCTCAACCTGTGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
1498 3182 3.641434 ATTCTCAACCTGTGGATGGAG 57.359 47.619 0.00 0.00 0.00 3.86
1499 3183 2.325661 TCTCAACCTGTGGATGGAGA 57.674 50.000 0.00 0.00 0.00 3.71
1507 3191 6.603201 TCAACCTGTGGATGGAGAAAATAATC 59.397 38.462 0.00 0.00 0.00 1.75
1511 3195 7.675619 ACCTGTGGATGGAGAAAATAATCTTTT 59.324 33.333 0.00 0.00 0.00 2.27
1528 3212 1.195347 TTTGTTGTTGCACGCGATTG 58.805 45.000 15.93 1.64 0.00 2.67
1634 3318 1.960040 ATCAACTGCTCGGCCGATGA 61.960 55.000 31.19 28.00 30.82 2.92
1713 3397 7.586349 TCCAGATTGAAGCTCCCTATATTTTT 58.414 34.615 0.00 0.00 0.00 1.94
1736 3420 9.436957 TTTTCTGCATTTCTTCCTTAGTAGTAG 57.563 33.333 0.00 0.00 0.00 2.57
1737 3421 7.719871 TCTGCATTTCTTCCTTAGTAGTAGT 57.280 36.000 0.00 0.00 0.00 2.73
1739 3423 8.684520 TCTGCATTTCTTCCTTAGTAGTAGTAC 58.315 37.037 0.00 0.00 0.00 2.73
1741 3425 6.417339 GCATTTCTTCCTTAGTAGTAGTACGC 59.583 42.308 2.04 0.00 33.97 4.42
1747 3431 3.242543 CCTTAGTAGTAGTACGCCACGTG 60.243 52.174 9.08 9.08 41.39 4.49
1753 3437 2.159421 AGTAGTACGCCACGTGAATCAG 60.159 50.000 19.30 0.00 41.39 2.90
1756 3440 0.599060 TACGCCACGTGAATCAGTCA 59.401 50.000 19.30 0.00 41.39 3.41
1780 3464 5.057149 CCTACGCATAGCTTTTGGTCTTAT 58.943 41.667 0.00 0.00 0.00 1.73
1790 3474 4.919754 GCTTTTGGTCTTATGACTTTGCTG 59.080 41.667 8.51 0.00 42.54 4.41
1791 3475 5.452078 TTTTGGTCTTATGACTTTGCTGG 57.548 39.130 8.51 0.00 42.54 4.85
1795 3480 3.366374 GGTCTTATGACTTTGCTGGTTGC 60.366 47.826 8.51 0.00 42.54 4.17
1819 3504 4.085884 GGTGTGTTTTCGCGTATATGTTG 58.914 43.478 5.77 0.00 0.00 3.33
1826 3511 1.207570 TCGCGTATATGTTGGGTTGGT 59.792 47.619 5.77 0.00 0.00 3.67
1829 3514 2.750712 GCGTATATGTTGGGTTGGTTGT 59.249 45.455 0.00 0.00 0.00 3.32
1831 3516 3.426963 CGTATATGTTGGGTTGGTTGTGC 60.427 47.826 0.00 0.00 0.00 4.57
1833 3518 1.040339 ATGTTGGGTTGGTTGTGCGT 61.040 50.000 0.00 0.00 0.00 5.24
1840 3525 1.199097 GGTTGGTTGTGCGTATCCTTG 59.801 52.381 0.00 0.00 0.00 3.61
1848 3533 2.935849 TGTGCGTATCCTTGTTATGCAG 59.064 45.455 0.00 0.00 41.05 4.41
1851 3536 3.132111 TGCGTATCCTTGTTATGCAGAGA 59.868 43.478 0.00 0.00 36.82 3.10
1856 3541 1.656652 CTTGTTATGCAGAGACCGGG 58.343 55.000 6.32 0.00 0.00 5.73
1872 3557 1.165907 CGGGTGTGTGCTCATTGTGT 61.166 55.000 0.00 0.00 0.00 3.72
1887 3572 7.066163 TGCTCATTGTGTTATGTATCTTCTTGG 59.934 37.037 0.00 0.00 0.00 3.61
1892 3577 6.941857 TGTGTTATGTATCTTCTTGGTGCTA 58.058 36.000 0.00 0.00 0.00 3.49
1901 3586 6.899393 ATCTTCTTGGTGCTACATTTTGAA 57.101 33.333 0.00 0.00 0.00 2.69
1959 3649 3.429272 CCGCACATAGTTTACCTCGGTAA 60.429 47.826 4.47 4.47 38.63 2.85
1967 3657 2.991866 GTTTACCTCGGTAAGTGCTCAC 59.008 50.000 8.42 0.62 40.98 3.51
1983 3710 4.009675 TGCTCACATGAGGTAATTTCCAC 58.990 43.478 10.81 0.00 42.29 4.02
1993 3720 5.880332 TGAGGTAATTTCCACAGATTGCTAC 59.120 40.000 3.73 0.00 0.00 3.58
1997 3724 6.260271 GGTAATTTCCACAGATTGCTACCTAC 59.740 42.308 0.00 0.00 0.00 3.18
2009 3736 2.029623 GCTACCTACCTCGACATTCCA 58.970 52.381 0.00 0.00 0.00 3.53
2015 3742 3.684788 CCTACCTCGACATTCCAAGTTTG 59.315 47.826 0.00 0.00 0.00 2.93
2066 3793 4.196971 CCTGCTTGATGATGATGTTCTCA 58.803 43.478 0.00 0.00 38.53 3.27
2127 3854 5.993748 TTTTAAATCAATCAGGGTGGTCC 57.006 39.130 0.00 0.00 0.00 4.46
2223 3950 8.954350 AGAGTTTCATTAATCAATCTCAGTTGG 58.046 33.333 11.34 0.00 0.00 3.77
2260 3987 7.901029 TGGCCACAATGATCAACTTTTATTTA 58.099 30.769 0.00 0.00 0.00 1.40
2261 3988 8.538701 TGGCCACAATGATCAACTTTTATTTAT 58.461 29.630 0.00 0.00 0.00 1.40
2262 3989 9.382275 GGCCACAATGATCAACTTTTATTTATT 57.618 29.630 0.00 0.00 0.00 1.40
2286 4013 0.661483 GAACAAAGACGCAAGCTGCC 60.661 55.000 0.00 0.00 41.12 4.85
2324 4051 9.732130 AAATTAATAAAGCCCACAAATTAAGCA 57.268 25.926 0.00 0.00 0.00 3.91
2375 4103 9.583765 AAACAAATAAAACAAGGTAAAACGCTA 57.416 25.926 0.00 0.00 0.00 4.26
2415 4143 2.430465 CATAACAGAGCACACAGGCTT 58.570 47.619 0.00 0.00 45.99 4.35
2454 4209 1.898154 CTACCTAGGCAGCAACCGT 59.102 57.895 9.30 0.00 33.69 4.83
2456 4211 1.687123 CTACCTAGGCAGCAACCGTAT 59.313 52.381 9.30 0.00 33.69 3.06
2471 4226 0.875908 CGTATGGGAGCGTGTGATGG 60.876 60.000 0.00 0.00 0.00 3.51
2542 4325 0.322546 GACGCTTCCCCAATGGAGTT 60.323 55.000 0.00 0.00 46.24 3.01
2603 4386 6.211584 GCCATCTGGAGATTCAATAGTAGGTA 59.788 42.308 0.00 0.00 37.39 3.08
2704 4487 7.766278 TGAGATGAAAGAATAGTTAGCAACTCC 59.234 37.037 5.04 0.00 41.77 3.85
2710 4501 0.248289 TAGTTAGCAACTCCGTGCCC 59.752 55.000 5.04 0.00 46.14 5.36
2734 4525 6.284459 CAGGAGGGATTCTAAACTGTATCAC 58.716 44.000 0.00 0.00 0.00 3.06
2743 4534 2.105006 AACTGTATCACTGGCAGCTG 57.895 50.000 15.89 10.11 33.87 4.24
2774 4565 1.601903 CCACGTGAAGCAAACTAAGCA 59.398 47.619 19.30 0.00 0.00 3.91
2812 4605 4.703897 GTGATTCACATCCTCCGGAATAA 58.296 43.478 5.23 0.00 34.34 1.40
2817 4610 3.262151 TCACATCCTCCGGAATAACACAA 59.738 43.478 5.23 0.00 34.34 3.33
2843 4642 1.209747 GTGATTTCCGTTCTAGGGGCT 59.790 52.381 0.00 0.00 0.00 5.19
2855 4654 0.549169 TAGGGGCTGTTAGGCTTGGT 60.549 55.000 0.00 0.00 41.09 3.67
2886 4685 4.124851 AGATGTAGGTAAGCGGTTTCTG 57.875 45.455 4.64 0.00 0.00 3.02
2894 4693 4.583073 AGGTAAGCGGTTTCTGAACATTTT 59.417 37.500 4.64 0.00 37.51 1.82
2896 4695 3.643159 AGCGGTTTCTGAACATTTTCC 57.357 42.857 0.00 0.00 37.51 3.13
2897 4696 2.031157 AGCGGTTTCTGAACATTTTCCG 60.031 45.455 0.00 0.00 37.51 4.30
2899 4698 3.549221 GCGGTTTCTGAACATTTTCCGAA 60.549 43.478 0.00 0.00 39.17 4.30
2901 4700 4.546570 GGTTTCTGAACATTTTCCGAAGG 58.453 43.478 0.00 0.00 43.55 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 1194 3.046390 GTCTACGCATTGAGGATCTTCG 58.954 50.000 0.00 0.00 34.92 3.79
70 1223 1.224592 CTTGTGCCGGCCTAAGGAT 59.775 57.895 26.77 0.00 0.00 3.24
171 1332 3.490761 CCGTTCTTTGAAATGCCACTTGT 60.491 43.478 0.00 0.00 0.00 3.16
193 1354 7.277174 ACAAGTTTGCCTATATTTATGCTCC 57.723 36.000 0.00 0.00 0.00 4.70
367 1799 2.191400 TGTGAGATTGCTAAGCTCCCT 58.809 47.619 10.31 0.00 43.08 4.20
442 2108 2.969443 ATTTTCACAAGAGCGAACGG 57.031 45.000 0.00 0.00 0.00 4.44
523 2190 5.528600 TTTAGTGGAGGAATGGAATGGAA 57.471 39.130 0.00 0.00 0.00 3.53
530 2197 9.853177 ATAATACTTCTTTTAGTGGAGGAATGG 57.147 33.333 0.00 0.00 0.00 3.16
534 2201 9.042450 TCACATAATACTTCTTTTAGTGGAGGA 57.958 33.333 0.00 0.00 0.00 3.71
535 2202 9.667107 TTCACATAATACTTCTTTTAGTGGAGG 57.333 33.333 0.00 0.00 0.00 4.30
562 2229 1.406539 ACACTGAGGCAAGCAAAACTG 59.593 47.619 0.00 0.00 0.00 3.16
576 2243 8.154203 TGACTGATTTTGGTAAGATAACACTGA 58.846 33.333 0.00 0.00 0.00 3.41
721 2389 9.777843 GCTCATTTAATTTGTTAACGAAAACAG 57.222 29.630 12.26 4.36 40.29 3.16
745 2413 7.615403 TGTTCTGTTCTATTCTATGACTTGCT 58.385 34.615 0.00 0.00 0.00 3.91
750 2418 8.547069 GCATTCTGTTCTGTTCTATTCTATGAC 58.453 37.037 0.00 0.00 0.00 3.06
751 2419 8.260114 TGCATTCTGTTCTGTTCTATTCTATGA 58.740 33.333 0.00 0.00 0.00 2.15
752 2420 8.429493 TGCATTCTGTTCTGTTCTATTCTATG 57.571 34.615 0.00 0.00 0.00 2.23
754 2422 7.547019 CACTGCATTCTGTTCTGTTCTATTCTA 59.453 37.037 0.00 0.00 0.00 2.10
755 2423 6.370994 CACTGCATTCTGTTCTGTTCTATTCT 59.629 38.462 0.00 0.00 0.00 2.40
756 2424 6.541086 CACTGCATTCTGTTCTGTTCTATTC 58.459 40.000 0.00 0.00 0.00 1.75
758 2426 4.394300 GCACTGCATTCTGTTCTGTTCTAT 59.606 41.667 0.00 0.00 0.00 1.98
764 2432 3.637998 AAAGCACTGCATTCTGTTCTG 57.362 42.857 3.30 0.00 0.00 3.02
782 2450 1.883275 CCCACTACAATCGCCACAAAA 59.117 47.619 0.00 0.00 0.00 2.44
873 2541 1.189524 TGGTCCCCCTATAATCGCGG 61.190 60.000 6.13 0.00 0.00 6.46
972 2643 1.146152 AGTAGCTAGCTAGTGGAGGGG 59.854 57.143 27.62 0.00 31.56 4.79
997 2668 6.675303 ACCCCCTAGCTCACTTTAAATACTAA 59.325 38.462 0.00 0.00 0.00 2.24
1020 2691 1.298014 CTCTTCACTGCCCAGGACC 59.702 63.158 0.00 0.00 0.00 4.46
1058 2730 4.826556 CTGGAATACCTAGCTTATGGAGC 58.173 47.826 0.00 0.00 43.53 4.70
1072 2744 1.398390 CGGTGCAAGAAGCTGGAATAC 59.602 52.381 0.00 0.00 45.94 1.89
1074 2746 0.962356 CCGGTGCAAGAAGCTGGAAT 60.962 55.000 0.00 0.00 45.94 3.01
1075 2747 1.600636 CCGGTGCAAGAAGCTGGAA 60.601 57.895 0.00 0.00 45.94 3.53
1076 2748 2.032528 CCGGTGCAAGAAGCTGGA 59.967 61.111 0.00 0.00 45.94 3.86
1077 2749 3.741476 GCCGGTGCAAGAAGCTGG 61.741 66.667 1.90 0.00 45.94 4.85
1078 2750 3.741476 GGCCGGTGCAAGAAGCTG 61.741 66.667 1.90 0.00 45.94 4.24
1175 2847 4.539083 TGCGTCCTTGTGCACGGT 62.539 61.111 13.13 0.00 35.90 4.83
1179 2851 2.661537 CGACTGCGTCCTTGTGCA 60.662 61.111 3.65 0.00 39.13 4.57
1225 2897 7.017254 AGGAGGAATTCTAGTTTTGTTGTAGGA 59.983 37.037 5.23 0.00 0.00 2.94
1226 2898 7.168905 AGGAGGAATTCTAGTTTTGTTGTAGG 58.831 38.462 5.23 0.00 0.00 3.18
1227 2899 7.334671 GGAGGAGGAATTCTAGTTTTGTTGTAG 59.665 40.741 5.23 0.00 0.00 2.74
1228 2900 7.166167 GGAGGAGGAATTCTAGTTTTGTTGTA 58.834 38.462 5.23 0.00 0.00 2.41
1229 2901 6.004574 GGAGGAGGAATTCTAGTTTTGTTGT 58.995 40.000 5.23 0.00 0.00 3.32
1230 2902 5.416013 GGGAGGAGGAATTCTAGTTTTGTTG 59.584 44.000 5.23 0.00 0.00 3.33
1272 2948 2.920490 GCAGAGAGACGACACAAGATTC 59.080 50.000 0.00 0.00 0.00 2.52
1288 2964 1.742140 CTCACCAGCAGCTGCAGAG 60.742 63.158 38.24 30.64 45.16 3.35
1335 3015 7.445121 TCAGAGTTTATCACTGTGACTTGATT 58.555 34.615 13.50 0.00 46.33 2.57
1359 3039 6.450545 CCTCTTCCCACAAGAAAAGAAAATC 58.549 40.000 0.00 0.00 0.00 2.17
1370 3050 0.689623 AGAGTGCCTCTTCCCACAAG 59.310 55.000 0.00 0.00 37.60 3.16
1378 3058 5.487131 AGGAGAGAAAATTAGAGTGCCTCTT 59.513 40.000 9.58 0.00 41.50 2.85
1384 3064 4.328440 CGTGCAGGAGAGAAAATTAGAGTG 59.672 45.833 0.00 0.00 0.00 3.51
1433 3117 4.976224 TCAACCTTCGATCGATCACTAA 57.024 40.909 24.40 13.87 0.00 2.24
1476 3160 4.782691 TCTCCATCCACAGGTTGAGAATTA 59.217 41.667 0.00 0.00 0.00 1.40
1478 3162 3.184628 TCTCCATCCACAGGTTGAGAAT 58.815 45.455 0.00 0.00 0.00 2.40
1481 3165 3.423539 TTTCTCCATCCACAGGTTGAG 57.576 47.619 0.00 0.00 0.00 3.02
1486 3170 7.651027 AAAGATTATTTTCTCCATCCACAGG 57.349 36.000 0.00 0.00 0.00 4.00
1497 3181 7.516627 GCGTGCAACAACAAAAGATTATTTTCT 60.517 33.333 0.00 0.00 35.74 2.52
1498 3182 6.569693 GCGTGCAACAACAAAAGATTATTTTC 59.430 34.615 0.00 0.00 35.74 2.29
1499 3183 6.418141 GCGTGCAACAACAAAAGATTATTTT 58.582 32.000 0.00 0.00 35.74 1.82
1507 3191 1.476074 ATCGCGTGCAACAACAAAAG 58.524 45.000 5.77 0.00 35.74 2.27
1511 3195 1.656875 GCAATCGCGTGCAACAACA 60.657 52.632 15.93 0.00 44.29 3.33
1528 3212 0.381089 GATCTCAACATGCTGCAGGC 59.619 55.000 17.12 8.54 42.22 4.85
1650 3334 7.694388 TTGATTCGTGAATTACTTAGGATCG 57.306 36.000 0.00 0.00 0.00 3.69
1713 3397 7.719871 ACTACTACTAAGGAAGAAATGCAGA 57.280 36.000 0.00 0.00 0.00 4.26
1729 3413 2.099141 TCACGTGGCGTACTACTACT 57.901 50.000 17.00 0.00 38.32 2.57
1733 3417 2.182825 CTGATTCACGTGGCGTACTAC 58.817 52.381 17.00 0.19 38.32 2.73
1736 3420 0.989890 GACTGATTCACGTGGCGTAC 59.010 55.000 17.00 4.15 38.32 3.67
1737 3421 0.599060 TGACTGATTCACGTGGCGTA 59.401 50.000 17.00 0.00 38.32 4.42
1739 3423 1.781555 GTGACTGATTCACGTGGCG 59.218 57.895 17.00 2.50 45.33 5.69
1747 3431 3.053455 GCTATGCGTAGGTGACTGATTC 58.947 50.000 14.75 0.00 43.88 2.52
1753 3437 2.351726 CCAAAAGCTATGCGTAGGTGAC 59.648 50.000 17.98 0.00 38.59 3.67
1756 3440 2.236395 AGACCAAAAGCTATGCGTAGGT 59.764 45.455 11.89 11.89 40.24 3.08
1761 3445 4.572389 AGTCATAAGACCAAAAGCTATGCG 59.428 41.667 0.00 0.00 46.15 4.73
1790 3474 1.298788 CGAAAACACACCGGCAACC 60.299 57.895 0.00 0.00 0.00 3.77
1791 3475 1.942223 GCGAAAACACACCGGCAAC 60.942 57.895 0.00 0.00 0.00 4.17
1795 3480 1.348276 TATACGCGAAAACACACCGG 58.652 50.000 15.93 0.00 0.00 5.28
1819 3504 0.322187 AGGATACGCACAACCAACCC 60.322 55.000 0.00 0.00 46.39 4.11
1826 3511 3.339141 TGCATAACAAGGATACGCACAA 58.661 40.909 0.00 0.00 46.39 3.33
1829 3514 3.132111 TCTCTGCATAACAAGGATACGCA 59.868 43.478 0.00 0.00 46.39 5.24
1831 3516 4.051922 GGTCTCTGCATAACAAGGATACG 58.948 47.826 0.00 0.00 46.39 3.06
1833 3518 3.069586 CCGGTCTCTGCATAACAAGGATA 59.930 47.826 0.00 0.00 0.00 2.59
1840 3525 0.249398 ACACCCGGTCTCTGCATAAC 59.751 55.000 0.00 0.00 0.00 1.89
1848 3533 2.048127 GAGCACACACCCGGTCTC 60.048 66.667 0.00 0.00 0.00 3.36
1851 3536 1.600636 CAATGAGCACACACCCGGT 60.601 57.895 0.00 0.00 0.00 5.28
1856 3541 4.488126 ACATAACACAATGAGCACACAC 57.512 40.909 0.00 0.00 0.00 3.82
1872 3557 9.461312 AAAATGTAGCACCAAGAAGATACATAA 57.539 29.630 4.09 0.00 33.84 1.90
1928 3613 7.438564 AGGTAAACTATGTGCGGAAAATTTTT 58.561 30.769 4.63 0.00 0.00 1.94
1929 3614 6.988522 AGGTAAACTATGTGCGGAAAATTTT 58.011 32.000 2.28 2.28 0.00 1.82
1930 3615 6.584185 AGGTAAACTATGTGCGGAAAATTT 57.416 33.333 0.00 0.00 0.00 1.82
1931 3616 5.163794 CGAGGTAAACTATGTGCGGAAAATT 60.164 40.000 0.00 0.00 0.00 1.82
1932 3617 4.331717 CGAGGTAAACTATGTGCGGAAAAT 59.668 41.667 0.00 0.00 0.00 1.82
1946 3634 2.991866 GTGAGCACTTACCGAGGTAAAC 59.008 50.000 14.78 6.40 39.69 2.01
1959 3649 4.263462 TGGAAATTACCTCATGTGAGCACT 60.263 41.667 4.48 0.00 40.75 4.40
1967 3657 5.359009 AGCAATCTGTGGAAATTACCTCATG 59.641 40.000 0.00 0.00 33.84 3.07
1983 3710 2.688446 TGTCGAGGTAGGTAGCAATCTG 59.312 50.000 0.00 0.00 0.00 2.90
1993 3720 3.611766 AACTTGGAATGTCGAGGTAGG 57.388 47.619 0.00 0.00 0.00 3.18
1997 3724 1.200020 GGCAAACTTGGAATGTCGAGG 59.800 52.381 0.00 0.00 0.00 4.63
2009 3736 4.379339 ACAACATAAACACGGCAAACTT 57.621 36.364 0.00 0.00 0.00 2.66
2015 3742 5.915758 TGTTCATTTACAACATAAACACGGC 59.084 36.000 0.00 0.00 0.00 5.68
2097 3824 6.959366 ACCCTGATTGATTTAAAAATCCTGGA 59.041 34.615 16.65 0.00 43.19 3.86
2203 3930 5.525012 CGCTCCAACTGAGATTGATTAATGA 59.475 40.000 0.00 0.00 44.42 2.57
2260 3987 5.687285 CAGCTTGCGTCTTTGTTCTAAAAAT 59.313 36.000 0.00 0.00 0.00 1.82
2261 3988 5.034152 CAGCTTGCGTCTTTGTTCTAAAAA 58.966 37.500 0.00 0.00 0.00 1.94
2262 3989 4.597079 CAGCTTGCGTCTTTGTTCTAAAA 58.403 39.130 0.00 0.00 0.00 1.52
2321 4048 3.074412 CCGAACCTATGTCACTTTTGCT 58.926 45.455 0.00 0.00 0.00 3.91
2324 4051 5.861727 AGTTACCGAACCTATGTCACTTTT 58.138 37.500 0.00 0.00 36.08 2.27
2375 4103 3.043999 GCCTTCGGCCATGTACCCT 62.044 63.158 2.24 0.00 44.06 4.34
2415 4143 3.389329 AGCAGTCTCCTTTTGTTCTCTCA 59.611 43.478 0.00 0.00 0.00 3.27
2454 4209 0.177836 CACCATCACACGCTCCCATA 59.822 55.000 0.00 0.00 0.00 2.74
2456 4211 2.347114 CACCATCACACGCTCCCA 59.653 61.111 0.00 0.00 0.00 4.37
2471 4226 3.262420 ACAAGCTTCGACATATCCACAC 58.738 45.455 0.00 0.00 0.00 3.82
2542 4325 3.434167 GCCTCCTATTCCTTCAGCATTGA 60.434 47.826 0.00 0.00 0.00 2.57
2582 4365 8.783660 AACATACCTACTATTGAATCTCCAGA 57.216 34.615 0.00 0.00 0.00 3.86
2669 4452 4.462508 TTCTTTCATCTCAGAGCGATGT 57.537 40.909 0.00 0.00 39.36 3.06
2710 4501 6.098982 AGTGATACAGTTTAGAATCCCTCCTG 59.901 42.308 0.00 0.00 0.00 3.86
2727 4518 0.975887 TGACAGCTGCCAGTGATACA 59.024 50.000 15.27 0.00 0.00 2.29
2728 4519 1.363744 GTGACAGCTGCCAGTGATAC 58.636 55.000 15.27 0.00 0.00 2.24
2734 4525 1.670406 GTGAGGTGACAGCTGCCAG 60.670 63.158 15.27 0.00 0.00 4.85
2817 4610 4.261801 CCTAGAACGGAAATCACATGGTT 58.738 43.478 0.00 0.00 0.00 3.67
2843 4642 2.158534 ACCAATGTCACCAAGCCTAACA 60.159 45.455 0.00 0.00 0.00 2.41
2855 4654 5.451381 CGCTTACCTACATCTACCAATGTCA 60.451 44.000 0.00 0.00 40.32 3.58


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

AutoCloner maintained by Alex Coulton.