Multiple sequence alignment - TraesCS4D01G212000

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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 TraesCS4D01G212000 chr4D 100.000 3499 0 0 1 3499 364810172 364813670 0.000000e+00 6462.0
1 TraesCS4D01G212000 chr4D 82.558 86 11 4 606 690 483044759 483044841 4.840000e-09 73.1
2 TraesCS4D01G212000 chr4B 93.114 2367 99 15 247 2597 449766236 449768554 0.000000e+00 3410.0
3 TraesCS4D01G212000 chr4B 87.050 973 64 11 2588 3499 449773525 449774496 0.000000e+00 1042.0
4 TraesCS4D01G212000 chr4A 96.016 2058 55 7 676 2716 100636361 100634314 0.000000e+00 3321.0
5 TraesCS4D01G212000 chr4A 94.550 367 19 1 2712 3077 100634226 100633860 1.820000e-157 566.0
6 TraesCS4D01G212000 chr4A 84.349 607 59 18 79 684 100637114 100636543 2.360000e-156 562.0
7 TraesCS4D01G212000 chr4A 92.105 76 6 0 10 85 100637439 100637364 1.330000e-19 108.0
8 TraesCS4D01G212000 chr5A 90.833 120 10 1 435 554 38793932 38794050 3.610000e-35 159.0
9 TraesCS4D01G212000 chr3A 81.921 177 22 8 521 690 706511946 706511773 1.310000e-29 141.0
10 TraesCS4D01G212000 chr6D 77.068 266 37 13 432 690 71024558 71024806 7.880000e-27 132.0
11 TraesCS4D01G212000 chr7A 76.772 254 41 11 441 690 66718155 66718394 3.670000e-25 126.0
12 TraesCS4D01G212000 chr7A 78.704 108 20 3 449 554 71147310 71147204 6.270000e-08 69.4
13 TraesCS4D01G212000 chr2A 86.842 114 12 3 442 554 183520794 183520683 1.320000e-24 124.0
14 TraesCS4D01G212000 chr7D 76.587 252 41 12 439 688 123219103 123218868 4.740000e-24 122.0
15 TraesCS4D01G212000 chr7D 83.193 119 11 6 581 691 439241712 439241829 2.220000e-17 100.0
16 TraesCS4D01G212000 chr7D 82.301 113 15 4 443 554 638348307 638348415 3.720000e-15 93.5
17 TraesCS4D01G212000 chr7D 82.759 87 13 2 606 690 181973395 181973481 3.750000e-10 76.8
18 TraesCS4D01G212000 chr7D 94.595 37 1 1 438 473 498466625 498466589 4.880000e-04 56.5
19 TraesCS4D01G212000 chr6A 88.571 105 7 5 442 545 554470042 554470142 4.740000e-24 122.0
20 TraesCS4D01G212000 chr6A 87.500 72 7 2 476 547 134689191 134689260 8.050000e-12 82.4
21 TraesCS4D01G212000 chr2D 76.654 257 39 14 441 691 78399733 78399492 4.740000e-24 122.0
22 TraesCS4D01G212000 chr2D 78.400 125 22 5 432 554 636944073 636943952 3.750000e-10 76.8
23 TraesCS4D01G212000 chr1B 79.670 182 24 12 522 697 26362939 26363113 6.140000e-23 119.0
24 TraesCS4D01G212000 chr3B 84.444 90 12 2 604 692 117563156 117563244 1.730000e-13 87.9
25 TraesCS4D01G212000 chr7B 82.759 87 14 1 606 691 78323058 78323144 3.750000e-10 76.8


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 TraesCS4D01G212000 chr4D 364810172 364813670 3498 False 6462.00 6462 100.000 1 3499 1 chr4D.!!$F1 3498
1 TraesCS4D01G212000 chr4B 449766236 449768554 2318 False 3410.00 3410 93.114 247 2597 1 chr4B.!!$F1 2350
2 TraesCS4D01G212000 chr4B 449773525 449774496 971 False 1042.00 1042 87.050 2588 3499 1 chr4B.!!$F2 911
3 TraesCS4D01G212000 chr4A 100633860 100637439 3579 True 1139.25 3321 91.755 10 3077 4 chr4A.!!$R1 3067

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
656 928 0.035630 AAGTCAGGGCTGATGTGCTC 60.036 55.0 0.0 0.0 42.18 4.26 F
1407 1878 0.739112 GCGAGGACCAGAAGAAGCTG 60.739 60.0 0.0 0.0 35.66 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2541 0.756294 TCTTGAGCTTGTCGTCCCAA 59.244 50.0 0.0 0.0 0.0 4.12 R
2734 3320 0.324275 ATTTGCCCACCCTTGCGTAT 60.324 50.0 0.0 0.0 0.0 3.06 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 1.673168 GTCCACAGATCCATTGGCTC 58.327 55.000 0.00 0.00 0.00 4.70
27 28 3.135348 CCACAGATCCATTGGCTCTAAGA 59.865 47.826 8.69 0.00 0.00 2.10
29 30 4.755629 CACAGATCCATTGGCTCTAAGATG 59.244 45.833 8.69 0.71 0.00 2.90
38 39 5.957771 TTGGCTCTAAGATGTGATAGGTT 57.042 39.130 0.00 0.00 0.00 3.50
43 44 6.071840 GGCTCTAAGATGTGATAGGTTATCGT 60.072 42.308 0.00 0.00 38.02 3.73
108 365 6.088883 GCCAATGTTACGTTTGATTTGGTAAG 59.911 38.462 14.42 0.00 35.64 2.34
180 437 9.249053 TGTGGTCCATATGTACATAATTTGTTT 57.751 29.630 19.11 0.00 39.87 2.83
209 466 3.067180 TCAATAATGTCGGACCGTCCTAC 59.933 47.826 14.79 14.82 33.30 3.18
244 501 7.280876 TGAGAAGAAATTCATTGATAGGTTCGG 59.719 37.037 0.00 0.00 0.00 4.30
346 603 5.734720 TCAGTTTCAGAAGTTGTGAGTTCT 58.265 37.500 2.65 1.30 44.50 3.01
365 622 6.769512 AGTTCTGTGACACCTGTAATATTGT 58.230 36.000 2.45 0.00 0.00 2.71
396 653 4.009370 AGACCCAAGTTTCTTGAGCTAC 57.991 45.455 10.54 0.00 0.00 3.58
455 712 2.269940 AGCTTGGACCCTGATAAGTGT 58.730 47.619 0.00 0.00 0.00 3.55
460 717 3.181329 TGGACCCTGATAAGTGTCACAT 58.819 45.455 5.62 0.00 0.00 3.21
462 719 3.055094 GGACCCTGATAAGTGTCACATGT 60.055 47.826 5.62 0.00 0.00 3.21
485 743 3.648339 GGCATGAACACATGACAACTT 57.352 42.857 13.30 0.00 46.05 2.66
496 754 4.433304 CACATGACAACTTCGAACGTTTTC 59.567 41.667 0.46 14.43 0.00 2.29
528 786 6.169094 AGTTTAGTGACATGAGGATGACAAG 58.831 40.000 0.00 0.00 36.27 3.16
561 819 7.977789 TCAAGCATGACAACTTTAGTTATCA 57.022 32.000 6.10 6.10 44.33 2.15
562 820 8.389779 TCAAGCATGACAACTTTAGTTATCAA 57.610 30.769 7.59 0.00 43.57 2.57
563 821 8.506437 TCAAGCATGACAACTTTAGTTATCAAG 58.494 33.333 7.59 4.99 43.57 3.02
565 823 5.734498 GCATGACAACTTTAGTTATCAAGCG 59.266 40.000 13.22 5.20 43.13 4.68
566 824 6.402118 GCATGACAACTTTAGTTATCAAGCGA 60.402 38.462 13.22 0.00 43.13 4.93
567 825 6.462073 TGACAACTTTAGTTATCAAGCGAC 57.538 37.500 1.31 0.00 38.37 5.19
568 826 5.986741 TGACAACTTTAGTTATCAAGCGACA 59.013 36.000 1.31 0.00 38.37 4.35
569 827 6.480651 TGACAACTTTAGTTATCAAGCGACAA 59.519 34.615 1.31 0.00 38.37 3.18
570 828 7.172532 TGACAACTTTAGTTATCAAGCGACAAT 59.827 33.333 1.31 0.00 38.37 2.71
571 829 7.871853 ACAACTTTAGTTATCAAGCGACAATT 58.128 30.769 0.00 0.00 36.32 2.32
572 830 8.349983 ACAACTTTAGTTATCAAGCGACAATTT 58.650 29.630 0.00 0.00 36.32 1.82
573 831 9.180678 CAACTTTAGTTATCAAGCGACAATTTT 57.819 29.630 0.00 0.00 36.32 1.82
598 856 6.523676 TTCGAATGGCAAGTTTCATTTTTC 57.476 33.333 0.00 0.00 34.18 2.29
600 858 5.691305 TCGAATGGCAAGTTTCATTTTTCTG 59.309 36.000 0.00 0.00 34.18 3.02
602 860 6.129009 CGAATGGCAAGTTTCATTTTTCTGAG 60.129 38.462 0.00 0.00 34.18 3.35
603 861 4.947645 TGGCAAGTTTCATTTTTCTGAGG 58.052 39.130 0.00 0.00 0.00 3.86
650 922 9.178758 CTTTAGTTTTATAAAGTCAGGGCTGAT 57.821 33.333 0.00 0.00 42.18 2.90
656 928 0.035630 AAGTCAGGGCTGATGTGCTC 60.036 55.000 0.00 0.00 42.18 4.26
764 1235 5.163943 GCGTTTTAGAGACTTGATGAAGGTC 60.164 44.000 0.00 0.00 32.95 3.85
822 1293 1.746727 CGCGAATCAGACTGAAGCGG 61.747 60.000 29.45 18.50 41.48 5.52
881 1352 3.535962 GCCTCCAGCCCTCTCTCG 61.536 72.222 0.00 0.00 34.35 4.04
1407 1878 0.739112 GCGAGGACCAGAAGAAGCTG 60.739 60.000 0.00 0.00 35.66 4.24
1435 1906 4.398358 TCATCTCCAACGAGGTAAGTACTG 59.602 45.833 0.00 0.00 39.02 2.74
1436 1907 3.759581 TCTCCAACGAGGTAAGTACTGT 58.240 45.455 0.00 0.00 39.02 3.55
1469 1948 5.224888 AGCAAATTAACTAGACGAACGTCA 58.775 37.500 25.13 12.68 46.76 4.35
1507 1986 2.099621 GAGAACGATGTACTGTACGCG 58.900 52.381 22.73 22.73 35.91 6.01
1774 2253 3.010584 CCTGAATTTCCCCTTCTCCTTCA 59.989 47.826 0.00 0.00 0.00 3.02
2130 2613 4.096003 GGCAAGCCCTACTCCGCA 62.096 66.667 0.00 0.00 0.00 5.69
2330 2813 0.176449 CTCGACATCATGCCCACAGA 59.824 55.000 0.00 0.00 0.00 3.41
2337 2820 0.613572 TCATGCCCACAGAGGTACGA 60.614 55.000 0.00 0.00 34.66 3.43
2338 2821 0.465705 CATGCCCACAGAGGTACGAT 59.534 55.000 0.00 0.00 34.66 3.73
2339 2822 1.134401 CATGCCCACAGAGGTACGATT 60.134 52.381 0.00 0.00 34.66 3.34
2342 2825 2.007608 GCCCACAGAGGTACGATTTTC 58.992 52.381 0.00 0.00 34.66 2.29
2344 2827 3.868754 GCCCACAGAGGTACGATTTTCTT 60.869 47.826 0.00 0.00 34.66 2.52
2354 2837 4.857037 GGTACGATTTTCTTTGCAATCACC 59.143 41.667 0.00 0.00 30.84 4.02
2368 2858 3.374745 CAATCACCAGTGCACTTCAAAC 58.625 45.455 18.94 0.00 0.00 2.93
2520 3014 4.223032 AGAACAAGAACGAGGGATACACAT 59.777 41.667 0.00 0.00 39.74 3.21
2661 3155 1.350684 TGCTGTCTCCTACAAATGGCA 59.649 47.619 0.00 0.00 37.74 4.92
2663 3157 2.421424 GCTGTCTCCTACAAATGGCAAG 59.579 50.000 0.00 0.00 37.74 4.01
2700 3194 5.235186 GTGTCGATCCCAAACATCTGAATAG 59.765 44.000 0.00 0.00 0.00 1.73
2730 3316 6.661805 TGAAAAACCAACCTGAAGTAGAAAGT 59.338 34.615 0.00 0.00 0.00 2.66
2734 3320 4.347000 ACCAACCTGAAGTAGAAAGTAGCA 59.653 41.667 0.00 0.00 0.00 3.49
2748 3334 0.814010 GTAGCATACGCAAGGGTGGG 60.814 60.000 0.00 0.00 46.39 4.61
2800 3386 8.904099 AGTGTTTTGCTATACAAGTCTTAACT 57.096 30.769 0.00 0.00 40.06 2.24
2930 3516 6.257630 AGTTGTAACATTGTGACAATTTTGGC 59.742 34.615 20.15 11.39 38.88 4.52
2964 3550 6.707440 TGGCAACTTCAAGACTTCAATTTA 57.293 33.333 0.00 0.00 37.61 1.40
3071 3658 0.825840 CTCCAAAACCAAGCCCGGAA 60.826 55.000 0.73 0.00 0.00 4.30
3093 3699 0.255033 AATTCCGACCTAAGGGGCAC 59.745 55.000 0.00 0.00 41.90 5.01
3117 3723 4.753516 TGGTAATCACATCGATCCTGTT 57.246 40.909 0.00 0.00 31.11 3.16
3121 3727 6.705825 TGGTAATCACATCGATCCTGTTATTG 59.294 38.462 0.00 0.00 31.11 1.90
3141 3747 4.974645 TGTTACCTATGGGCCTATCTTG 57.025 45.455 4.16 0.00 35.63 3.02
3149 3755 6.564927 ACCTATGGGCCTATCTTGGTATTTTA 59.435 38.462 16.14 0.00 35.63 1.52
3168 3796 5.913137 TTTAGTTGCCCCTCAATTATGTG 57.087 39.130 0.00 0.00 36.99 3.21
3212 3840 8.966868 TCACTTGATTGAACCCTAATTAATTCC 58.033 33.333 3.39 0.00 0.00 3.01
3239 3867 3.839490 CCTATGATCATCTCTCCTGGCTT 59.161 47.826 12.53 0.00 0.00 4.35
3259 3887 3.266510 TCGATAGCCTTGTGAAAGCAT 57.733 42.857 0.00 0.00 0.00 3.79
3265 3893 2.157738 GCCTTGTGAAAGCATGACTCT 58.842 47.619 0.00 0.00 0.00 3.24
3268 3896 3.817084 CCTTGTGAAAGCATGACTCTTCA 59.183 43.478 0.00 4.26 35.73 3.02
3277 3905 3.776969 AGCATGACTCTTCAATCCCTACA 59.223 43.478 0.00 0.00 34.61 2.74
3284 3912 5.552178 ACTCTTCAATCCCTACAAAGTCAC 58.448 41.667 0.00 0.00 0.00 3.67
3308 3936 1.626654 CTGGACATTGCACCGTCGTC 61.627 60.000 8.24 1.19 32.74 4.20
3311 3939 0.666274 GACATTGCACCGTCGTCTGA 60.666 55.000 0.00 0.00 0.00 3.27
3313 3941 1.078709 CATTGCACCGTCGTCTGATT 58.921 50.000 0.00 0.00 0.00 2.57
3314 3942 1.078709 ATTGCACCGTCGTCTGATTG 58.921 50.000 0.00 0.00 0.00 2.67
3320 3948 1.405821 ACCGTCGTCTGATTGAGGATC 59.594 52.381 0.00 0.00 40.96 3.36
3321 3949 1.678627 CCGTCGTCTGATTGAGGATCT 59.321 52.381 0.00 0.00 40.96 2.75
3323 3951 2.616376 CGTCGTCTGATTGAGGATCTCT 59.384 50.000 0.00 0.00 40.96 3.10
3353 3981 2.985282 CGCTTGCCTTGCCCTCAA 60.985 61.111 0.00 0.00 0.00 3.02
3354 3982 2.345760 CGCTTGCCTTGCCCTCAAT 61.346 57.895 0.00 0.00 0.00 2.57
3388 4016 4.647615 CGACGATAGGGGCAGCGG 62.648 72.222 0.00 0.00 43.77 5.52
3409 4038 2.182842 GGCGATGGTGCTCACATCC 61.183 63.158 2.21 4.20 41.22 3.51
3411 4040 1.884464 CGATGGTGCTCACATCCGG 60.884 63.158 0.00 0.00 41.22 5.14
3422 4051 2.496070 CTCACATCCGGTAGACAAAGGA 59.504 50.000 0.00 0.00 37.17 3.36
3447 4076 1.206072 CAGCAAGCGCAGACTCAAC 59.794 57.895 11.47 0.00 42.27 3.18
3450 4079 3.044305 AAGCGCAGACTCAACGGC 61.044 61.111 11.47 0.00 0.00 5.68
3468 4097 0.811616 GCTTGACGGCCTACCATGAG 60.812 60.000 0.00 0.00 34.57 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.678728 GCCAATGGATCTGTGGACGAA 60.679 52.381 2.05 0.00 34.05 3.85
1 2 0.107703 GCCAATGGATCTGTGGACGA 60.108 55.000 2.05 0.00 34.05 4.20
2 3 0.107508 AGCCAATGGATCTGTGGACG 60.108 55.000 2.05 0.00 34.05 4.79
3 4 1.673168 GAGCCAATGGATCTGTGGAC 58.327 55.000 10.73 5.56 34.95 4.02
22 23 7.455641 AGGACGATAACCTATCACATCTTAG 57.544 40.000 0.00 0.00 35.84 2.18
27 28 5.717178 AGCATAGGACGATAACCTATCACAT 59.283 40.000 0.00 0.00 45.47 3.21
29 30 5.646577 AGCATAGGACGATAACCTATCAC 57.353 43.478 0.00 0.00 45.47 3.06
38 39 7.770366 TGATAGGTTAAAGCATAGGACGATA 57.230 36.000 0.00 0.00 0.00 2.92
43 44 7.373617 TGTCATGATAGGTTAAAGCATAGGA 57.626 36.000 0.00 0.00 0.00 2.94
77 78 3.738282 TCAAACGTAACATTGGCATTTGC 59.262 39.130 0.00 0.00 41.14 3.68
85 86 7.114247 CCACTTACCAAATCAAACGTAACATTG 59.886 37.037 0.00 0.00 0.00 2.82
108 365 5.527582 AGATACACAACACAAAGAGAACCAC 59.472 40.000 0.00 0.00 0.00 4.16
180 437 7.385752 GGACGGTCCGACATTATTGATTTATTA 59.614 37.037 20.51 0.00 0.00 0.98
198 455 4.824289 TCAAGTTTATTGTAGGACGGTCC 58.176 43.478 19.61 19.61 36.58 4.46
201 458 6.395629 TCTTCTCAAGTTTATTGTAGGACGG 58.604 40.000 0.00 0.00 0.00 4.79
233 490 1.134699 CAGCTTCTGCCGAACCTATCA 60.135 52.381 0.00 0.00 40.80 2.15
326 583 5.351465 TCACAGAACTCACAACTTCTGAAAC 59.649 40.000 13.06 0.00 44.22 2.78
346 603 4.839121 GGGACAATATTACAGGTGTCACA 58.161 43.478 5.12 0.00 42.71 3.58
365 622 3.611025 AACTTGGGTCTTTGATTGGGA 57.389 42.857 0.00 0.00 0.00 4.37
414 671 9.965824 CAAGCTAAATTAGTTCCTCAAAAGAAA 57.034 29.630 1.68 0.00 0.00 2.52
421 678 5.497474 GGTCCAAGCTAAATTAGTTCCTCA 58.503 41.667 1.68 0.00 0.00 3.86
424 681 4.640647 CAGGGTCCAAGCTAAATTAGTTCC 59.359 45.833 1.68 0.00 0.00 3.62
469 726 3.000825 CGTTCGAAGTTGTCATGTGTTCA 59.999 43.478 0.00 0.00 0.00 3.18
485 743 1.256895 CTTGCGACAGAAAACGTTCGA 59.743 47.619 9.11 0.00 38.90 3.71
496 754 3.740832 TCATGTCACTAAACTTGCGACAG 59.259 43.478 0.00 0.00 39.74 3.51
515 773 9.388506 CTTGATAACTAAACTTGTCATCCTCAT 57.611 33.333 0.00 0.00 0.00 2.90
516 774 7.334421 GCTTGATAACTAAACTTGTCATCCTCA 59.666 37.037 0.00 0.00 0.00 3.86
572 830 6.917217 AAATGAAACTTGCCATTCGAAAAA 57.083 29.167 0.00 0.00 32.36 1.94
573 831 6.917217 AAAATGAAACTTGCCATTCGAAAA 57.083 29.167 0.00 0.00 32.36 2.29
577 835 5.691305 TCAGAAAAATGAAACTTGCCATTCG 59.309 36.000 0.00 0.00 32.36 3.34
623 881 8.380099 TCAGCCCTGACTTTATAAAACTAAAGA 58.620 33.333 9.82 0.00 40.41 2.52
624 882 8.561738 TCAGCCCTGACTTTATAAAACTAAAG 57.438 34.615 0.00 2.82 42.08 1.85
625 883 8.956426 CATCAGCCCTGACTTTATAAAACTAAA 58.044 33.333 0.00 0.00 43.11 1.85
626 884 8.107095 ACATCAGCCCTGACTTTATAAAACTAA 58.893 33.333 0.00 0.00 43.11 2.24
627 885 7.552687 CACATCAGCCCTGACTTTATAAAACTA 59.447 37.037 0.00 0.00 43.11 2.24
628 886 6.375455 CACATCAGCCCTGACTTTATAAAACT 59.625 38.462 0.00 0.00 43.11 2.66
629 887 6.555315 CACATCAGCCCTGACTTTATAAAAC 58.445 40.000 0.00 0.00 43.11 2.43
630 888 5.125417 GCACATCAGCCCTGACTTTATAAAA 59.875 40.000 0.00 0.00 43.11 1.52
631 889 4.640201 GCACATCAGCCCTGACTTTATAAA 59.360 41.667 0.00 0.00 43.11 1.40
632 890 4.080356 AGCACATCAGCCCTGACTTTATAA 60.080 41.667 0.00 0.00 43.11 0.98
633 891 3.455910 AGCACATCAGCCCTGACTTTATA 59.544 43.478 0.00 0.00 43.11 0.98
634 892 2.240667 AGCACATCAGCCCTGACTTTAT 59.759 45.455 0.00 0.00 43.11 1.40
635 893 1.630369 AGCACATCAGCCCTGACTTTA 59.370 47.619 0.00 0.00 43.11 1.85
636 894 0.403271 AGCACATCAGCCCTGACTTT 59.597 50.000 0.00 0.00 43.11 2.66
637 895 0.035630 GAGCACATCAGCCCTGACTT 60.036 55.000 0.00 0.00 43.11 3.01
703 1165 7.750229 ACATGATGATTTATTGATTACGCCT 57.250 32.000 0.00 0.00 0.00 5.52
822 1293 0.460284 ATTGTGAGGATGTCGTCGCC 60.460 55.000 12.14 1.11 39.65 5.54
881 1352 2.639286 CTGCGGTTTGTGTGGCTC 59.361 61.111 0.00 0.00 0.00 4.70
1032 1503 2.283894 TGGCGGGAGAGCAGAAGA 60.284 61.111 0.00 0.00 39.27 2.87
1086 1557 4.168291 CTGCTTCCGGGCCTCCTC 62.168 72.222 0.84 0.00 0.00 3.71
1189 1660 1.743321 CTGCTCCTCTTCCTAGCCGG 61.743 65.000 0.00 0.00 35.33 6.13
1407 1878 0.179134 CCTCGTTGGAGATGACGTCC 60.179 60.000 14.12 0.00 43.27 4.79
1435 1906 9.518906 GTCTAGTTAATTTGCTTACTCCTAGAC 57.481 37.037 0.00 0.00 36.49 2.59
1436 1907 8.404000 CGTCTAGTTAATTTGCTTACTCCTAGA 58.596 37.037 0.00 0.00 0.00 2.43
1469 1948 6.704493 TCGTTCTCAGTTAGTAATTGCTGTTT 59.296 34.615 6.28 0.00 0.00 2.83
1593 2072 1.440938 CCGAGTAGCTCTCCTCCACG 61.441 65.000 0.00 0.00 39.84 4.94
2058 2541 0.756294 TCTTGAGCTTGTCGTCCCAA 59.244 50.000 0.00 0.00 0.00 4.12
2330 2813 5.335661 GGTGATTGCAAAGAAAATCGTACCT 60.336 40.000 1.71 0.00 35.89 3.08
2337 2820 4.060205 GCACTGGTGATTGCAAAGAAAAT 58.940 39.130 1.71 0.00 38.68 1.82
2338 2821 3.118847 TGCACTGGTGATTGCAAAGAAAA 60.119 39.130 1.71 0.00 45.65 2.29
2339 2822 2.429971 TGCACTGGTGATTGCAAAGAAA 59.570 40.909 1.71 0.00 45.65 2.52
2354 2837 2.005537 GCGCGTTTGAAGTGCACTG 61.006 57.895 22.49 7.76 43.84 3.66
2368 2858 1.705337 ATCTCCAATTCAACCGCGCG 61.705 55.000 25.67 25.67 0.00 6.86
2557 3051 8.197439 GCATTACAAGAAAAGGGCTACATTATT 58.803 33.333 0.00 0.00 0.00 1.40
2661 3155 6.289064 GGATCGACACCATTATAACCTTCTT 58.711 40.000 5.72 0.00 0.00 2.52
2663 3157 4.995487 GGGATCGACACCATTATAACCTTC 59.005 45.833 11.69 0.00 0.00 3.46
2700 3194 4.099419 ACTTCAGGTTGGTTTTTCATGGTC 59.901 41.667 0.00 0.00 0.00 4.02
2730 3316 1.524961 CCCACCCTTGCGTATGCTA 59.475 57.895 8.69 0.00 43.34 3.49
2734 3320 0.324275 ATTTGCCCACCCTTGCGTAT 60.324 50.000 0.00 0.00 0.00 3.06
2748 3334 5.066505 ACTTCTGATCCGATTTGGTATTTGC 59.933 40.000 0.00 0.00 39.52 3.68
2875 3461 7.512130 AGGCAGTGAAATGTGATAGAATGATA 58.488 34.615 0.00 0.00 0.00 2.15
2964 3550 7.489239 AGTAGAGAGCTCCTAAAAATTGTCT 57.511 36.000 10.93 5.08 0.00 3.41
3071 3658 1.508256 CCCCTTAGGTCGGAATTCCT 58.492 55.000 22.05 6.07 37.80 3.36
3077 3664 0.912487 ATTGTGCCCCTTAGGTCGGA 60.912 55.000 0.00 0.00 38.26 4.55
3079 3666 0.748005 CCATTGTGCCCCTTAGGTCG 60.748 60.000 0.00 0.00 38.26 4.79
3080 3667 0.331616 ACCATTGTGCCCCTTAGGTC 59.668 55.000 0.00 0.00 38.26 3.85
3093 3699 5.059161 ACAGGATCGATGTGATTACCATTG 58.941 41.667 0.54 0.00 37.47 2.82
3117 3723 6.012858 CCAAGATAGGCCCATAGGTAACAATA 60.013 42.308 0.00 0.00 41.41 1.90
3121 3727 3.651423 ACCAAGATAGGCCCATAGGTAAC 59.349 47.826 0.00 0.00 34.57 2.50
3141 3747 5.932619 AATTGAGGGGCAACTAAAATACC 57.067 39.130 0.00 0.00 39.78 2.73
3149 3755 3.091545 CACACATAATTGAGGGGCAACT 58.908 45.455 0.00 0.00 39.78 3.16
3168 3796 6.763135 TCAAGTGATGATTATGTTAGGAGCAC 59.237 38.462 0.00 0.00 31.50 4.40
3210 3838 6.666980 CAGGAGAGATGATCATAGGTTATGGA 59.333 42.308 8.54 0.00 36.81 3.41
3212 3840 6.629963 GCCAGGAGAGATGATCATAGGTTATG 60.630 46.154 8.54 4.51 37.52 1.90
3226 3854 1.892474 GCTATCGAAGCCAGGAGAGAT 59.108 52.381 7.98 0.00 46.25 2.75
3239 3867 2.760634 TGCTTTCACAAGGCTATCGA 57.239 45.000 0.00 0.00 0.00 3.59
3254 3882 4.225942 TGTAGGGATTGAAGAGTCATGCTT 59.774 41.667 0.00 0.00 32.48 3.91
3255 3883 3.776969 TGTAGGGATTGAAGAGTCATGCT 59.223 43.478 0.00 0.00 32.48 3.79
3259 3887 5.306937 TGACTTTGTAGGGATTGAAGAGTCA 59.693 40.000 0.00 0.00 38.76 3.41
3265 3893 6.605594 AGTTTTGTGACTTTGTAGGGATTGAA 59.394 34.615 0.00 0.00 0.00 2.69
3268 3896 5.301805 CCAGTTTTGTGACTTTGTAGGGATT 59.698 40.000 0.00 0.00 0.00 3.01
3277 3905 4.081752 TGCAATGTCCAGTTTTGTGACTTT 60.082 37.500 0.00 0.00 0.00 2.66
3284 3912 1.066908 ACGGTGCAATGTCCAGTTTTG 59.933 47.619 0.00 0.00 0.00 2.44
3308 3936 5.595257 TCTTGTCAGAGATCCTCAATCAG 57.405 43.478 0.00 0.00 36.79 2.90
3321 3949 3.880591 GCGCATGCTCTTGTCAGA 58.119 55.556 17.13 0.00 38.39 3.27
3336 3964 2.345760 ATTGAGGGCAAGGCAAGCG 61.346 57.895 0.00 0.00 37.45 4.68
3353 3981 2.491022 GCTACCGAGGACGAGCCAT 61.491 63.158 0.00 0.00 42.66 4.40
3354 3982 3.138798 GCTACCGAGGACGAGCCA 61.139 66.667 0.00 0.00 42.66 4.75
3393 4021 1.884464 CCGGATGTGAGCACCATCG 60.884 63.158 0.00 0.00 0.00 3.84
3409 4038 3.199677 TGTTGTTGTCCTTTGTCTACCG 58.800 45.455 0.00 0.00 0.00 4.02
3411 4040 3.625764 TGCTGTTGTTGTCCTTTGTCTAC 59.374 43.478 0.00 0.00 0.00 2.59
3422 4051 1.064621 CTGCGCTTGCTGTTGTTGT 59.935 52.632 9.73 0.00 40.12 3.32
3450 4079 0.537188 ACTCATGGTAGGCCGTCAAG 59.463 55.000 0.00 0.00 37.67 3.02


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

AutoCloner maintained by Alex Coulton.