Multiple sequence alignment - TraesCS7A01G406800

Loading Multiple Alignment...

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 TraesCS7A01G406800 chr7A 100.000 2810 0 0 1 2810 592046348 592049157 0.000000e+00 5190
1 TraesCS7A01G406800 chr7D 89.588 2065 120 34 1 2022 517219052 517221064 0.000000e+00 2534
2 TraesCS7A01G406800 chr7D 84.655 782 100 12 2042 2810 631235985 631236759 0.000000e+00 761
3 TraesCS7A01G406800 chr7B 91.198 1386 69 25 651 2000 550031341 550032709 0.000000e+00 1834
4 TraesCS7A01G406800 chr7B 91.649 479 19 5 7 469 550030799 550031272 0.000000e+00 643
5 TraesCS7A01G406800 chr7B 95.238 63 3 0 518 580 550031267 550031329 1.780000e-17 100
6 TraesCS7A01G406800 chr4B 86.129 793 95 10 2027 2810 445649051 445648265 0.000000e+00 841
7 TraesCS7A01G406800 chr1D 85.732 792 96 11 2027 2810 256581729 256580947 0.000000e+00 821
8 TraesCS7A01G406800 chr2B 85.354 792 102 9 2027 2810 446046978 446046193 0.000000e+00 808
9 TraesCS7A01G406800 chr2B 84.741 793 104 13 2027 2810 417775145 417774361 0.000000e+00 778
10 TraesCS7A01G406800 chr3A 85.075 804 95 16 2027 2810 171213812 171213014 0.000000e+00 797
11 TraesCS7A01G406800 chr2D 84.780 795 94 13 2024 2810 60771155 60771930 0.000000e+00 773
12 TraesCS7A01G406800 chr1B 84.596 792 106 11 2027 2810 145724790 145725573 0.000000e+00 773
13 TraesCS7A01G406800 chr5D 84.422 796 109 7 2027 2810 484158916 484158124 0.000000e+00 769
14 TraesCS7A01G406800 chr3B 82.787 244 33 5 20 257 172958665 172958425 2.840000e-50 209


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 TraesCS7A01G406800 chr7A 592046348 592049157 2809 False 5190 5190 100.000 1 2810 1 chr7A.!!$F1 2809
1 TraesCS7A01G406800 chr7D 517219052 517221064 2012 False 2534 2534 89.588 1 2022 1 chr7D.!!$F1 2021
2 TraesCS7A01G406800 chr7D 631235985 631236759 774 False 761 761 84.655 2042 2810 1 chr7D.!!$F2 768
3 TraesCS7A01G406800 chr7B 550030799 550032709 1910 False 859 1834 92.695 7 2000 3 chr7B.!!$F1 1993
4 TraesCS7A01G406800 chr4B 445648265 445649051 786 True 841 841 86.129 2027 2810 1 chr4B.!!$R1 783
5 TraesCS7A01G406800 chr1D 256580947 256581729 782 True 821 821 85.732 2027 2810 1 chr1D.!!$R1 783
6 TraesCS7A01G406800 chr2B 446046193 446046978 785 True 808 808 85.354 2027 2810 1 chr2B.!!$R2 783
7 TraesCS7A01G406800 chr2B 417774361 417775145 784 True 778 778 84.741 2027 2810 1 chr2B.!!$R1 783
8 TraesCS7A01G406800 chr3A 171213014 171213812 798 True 797 797 85.075 2027 2810 1 chr3A.!!$R1 783
9 TraesCS7A01G406800 chr2D 60771155 60771930 775 False 773 773 84.780 2024 2810 1 chr2D.!!$F1 786
10 TraesCS7A01G406800 chr1B 145724790 145725573 783 False 773 773 84.596 2027 2810 1 chr1B.!!$F1 783
11 TraesCS7A01G406800 chr5D 484158124 484158916 792 True 769 769 84.422 2027 2810 1 chr5D.!!$R1 783

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
954 1017 0.325203 GAAGCTGGTCCTCTCCTCCT 60.325 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2766 2880 0.1791 CCGTCATGTAGTCCCAGCTG 60.179 60.0 6.78 6.78 0.0 4.24 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
147 148 1.995626 CTCCATTCCGGGTCCCACT 60.996 63.158 9.12 0.00 34.36 4.00
193 194 2.507992 GATGCTCTGCGCTGTCGT 60.508 61.111 9.73 6.35 40.11 4.34
312 326 6.131961 ACAGGGGAATTTCATAGATTTCTGG 58.868 40.000 0.00 0.00 0.00 3.86
316 330 6.410853 GGGGAATTTCATAGATTTCTGGGAGA 60.411 42.308 0.00 0.00 0.00 3.71
341 358 8.687824 AATTATATTGTAAGTTGTTGCAGTGC 57.312 30.769 8.58 8.58 29.18 4.40
342 359 5.703978 ATATTGTAAGTTGTTGCAGTGCA 57.296 34.783 15.37 15.37 36.47 4.57
350 367 0.392863 TGTTGCAGTGCACACTCAGT 60.393 50.000 19.58 0.00 40.20 3.41
358 375 1.128692 GTGCACACTCAGTAATTCCGC 59.871 52.381 13.17 0.00 0.00 5.54
359 376 1.270571 TGCACACTCAGTAATTCCGCA 60.271 47.619 0.00 0.00 0.00 5.69
595 619 2.185867 GCACCCGCACGGATCTTA 59.814 61.111 11.42 0.00 38.36 2.10
643 667 2.685106 TGGGGCTTCAATGGTGTTAA 57.315 45.000 0.00 0.00 0.00 2.01
671 703 3.139397 TGGGGTCTTGTTCTGGTTGTAAT 59.861 43.478 0.00 0.00 0.00 1.89
688 720 8.301002 TGGTTGTAATTTTACTGCTGTATTTCC 58.699 33.333 4.12 1.11 34.77 3.13
795 850 1.626825 GTGGTGGGAGTACCTTGCTAA 59.373 52.381 0.00 0.00 41.43 3.09
798 853 2.617276 GGTGGGAGTACCTTGCTAAACC 60.617 54.545 0.00 0.00 41.11 3.27
803 858 2.991866 GAGTACCTTGCTAAACCGTGAC 59.008 50.000 0.00 0.00 0.00 3.67
818 873 2.179547 TGACACTGTGTGCCTTGCG 61.180 57.895 19.62 0.00 36.98 4.85
835 893 3.829886 TGCGGAGTGAATGAATGAAAC 57.170 42.857 0.00 0.00 0.00 2.78
836 894 3.145286 TGCGGAGTGAATGAATGAAACA 58.855 40.909 0.00 0.00 0.00 2.83
837 895 3.758023 TGCGGAGTGAATGAATGAAACAT 59.242 39.130 0.00 0.00 0.00 2.71
838 896 4.142622 TGCGGAGTGAATGAATGAAACATC 60.143 41.667 0.00 0.00 0.00 3.06
839 897 4.095483 GCGGAGTGAATGAATGAAACATCT 59.905 41.667 0.00 0.00 0.00 2.90
840 898 5.566623 CGGAGTGAATGAATGAAACATCTG 58.433 41.667 0.00 0.00 0.00 2.90
887 945 3.584250 CTGCTTGAACGTGCGGCTG 62.584 63.158 11.67 7.99 0.00 4.85
906 964 0.385723 GCCATCGGTCGATCTCGTAC 60.386 60.000 2.59 0.00 40.80 3.67
954 1017 0.325203 GAAGCTGGTCCTCTCCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
985 1051 1.889530 CTTCCCCACCTCACCGACTC 61.890 65.000 0.00 0.00 0.00 3.36
989 1055 2.657237 CACCTCACCGACTCCCAC 59.343 66.667 0.00 0.00 0.00 4.61
1176 1242 3.648339 TGAAGTAGCGTCGTAAAACCT 57.352 42.857 0.00 0.00 0.00 3.50
1183 1249 1.620413 CGTCGTAAAACCTCGTGCCC 61.620 60.000 0.00 0.00 0.00 5.36
1216 1282 1.063567 TCCCTCTCCCTGACTAGCTTC 60.064 57.143 0.00 0.00 0.00 3.86
1219 1285 1.064946 CTCCCTGACTAGCTTCGCG 59.935 63.158 0.00 0.00 0.00 5.87
1352 1419 9.635404 TTTTCTGTTCCCTTCAGTTTATTCTTA 57.365 29.630 0.00 0.00 34.86 2.10
1364 1431 2.857592 TATTCTTACACGGCCGTCTC 57.142 50.000 31.80 0.00 0.00 3.36
1368 1435 1.068474 CTTACACGGCCGTCTCAAAG 58.932 55.000 31.80 23.30 0.00 2.77
1372 1439 0.319211 CACGGCCGTCTCAAAGTGTA 60.319 55.000 31.80 0.00 0.00 2.90
1373 1440 0.038526 ACGGCCGTCTCAAAGTGTAG 60.039 55.000 28.70 0.00 0.00 2.74
1374 1441 1.352156 CGGCCGTCTCAAAGTGTAGC 61.352 60.000 19.50 0.00 0.00 3.58
1375 1442 0.320421 GGCCGTCTCAAAGTGTAGCA 60.320 55.000 0.00 0.00 0.00 3.49
1376 1443 1.508632 GCCGTCTCAAAGTGTAGCAA 58.491 50.000 0.00 0.00 0.00 3.91
1377 1444 2.076863 GCCGTCTCAAAGTGTAGCAAT 58.923 47.619 0.00 0.00 0.00 3.56
1378 1445 2.484264 GCCGTCTCAAAGTGTAGCAATT 59.516 45.455 0.00 0.00 0.00 2.32
1381 1448 5.147162 CCGTCTCAAAGTGTAGCAATTTTC 58.853 41.667 0.00 0.00 29.07 2.29
1382 1449 5.277779 CCGTCTCAAAGTGTAGCAATTTTCA 60.278 40.000 0.00 0.00 29.07 2.69
1383 1450 5.621228 CGTCTCAAAGTGTAGCAATTTTCAC 59.379 40.000 0.00 0.00 29.07 3.18
1385 1452 5.592282 TCTCAAAGTGTAGCAATTTTCACCA 59.408 36.000 0.00 0.00 29.07 4.17
1386 1453 5.830912 TCAAAGTGTAGCAATTTTCACCAG 58.169 37.500 0.00 0.00 29.07 4.00
1387 1454 5.359576 TCAAAGTGTAGCAATTTTCACCAGT 59.640 36.000 0.00 0.00 29.07 4.00
1390 1457 4.024048 AGTGTAGCAATTTTCACCAGTTCG 60.024 41.667 0.00 0.00 0.00 3.95
1391 1458 3.880490 TGTAGCAATTTTCACCAGTTCGT 59.120 39.130 0.00 0.00 0.00 3.85
1392 1459 5.049954 GTGTAGCAATTTTCACCAGTTCGTA 60.050 40.000 0.00 0.00 0.00 3.43
1393 1460 5.703592 TGTAGCAATTTTCACCAGTTCGTAT 59.296 36.000 0.00 0.00 0.00 3.06
1434 1502 6.476243 TTGTCAAATTTCCGCTTACTACTC 57.524 37.500 0.00 0.00 0.00 2.59
1439 1507 4.820894 ATTTCCGCTTACTACTCACCTT 57.179 40.909 0.00 0.00 0.00 3.50
1466 1534 1.435515 GTAGTGAGCAGGAGGAGCG 59.564 63.158 0.00 0.00 37.01 5.03
1701 1769 2.169832 AGCGTTGCTTTGCTTCTCTA 57.830 45.000 0.00 0.00 38.57 2.43
1794 1862 3.499918 CCGCATTTATCATCTTCCAGTCC 59.500 47.826 0.00 0.00 0.00 3.85
1816 1884 2.034685 GGATCGTCGGACTGATCAATCA 59.965 50.000 27.61 0.00 42.19 2.57
1820 1888 2.455032 GTCGGACTGATCAATCACTCG 58.545 52.381 6.49 0.85 32.50 4.18
1833 1901 6.493449 TCAATCACTCGATGTTAATTTGCA 57.507 33.333 0.00 0.00 30.13 4.08
1834 1902 7.087409 TCAATCACTCGATGTTAATTTGCAT 57.913 32.000 0.00 0.00 30.13 3.96
1837 1905 6.252967 TCACTCGATGTTAATTTGCATTGT 57.747 33.333 0.00 2.21 0.00 2.71
1895 1966 1.017387 GCTTCCCAAAGGCGTCTATG 58.983 55.000 0.00 0.00 32.79 2.23
1896 1967 1.406887 GCTTCCCAAAGGCGTCTATGA 60.407 52.381 0.00 0.00 32.79 2.15
1897 1968 2.280628 CTTCCCAAAGGCGTCTATGAC 58.719 52.381 0.00 0.00 0.00 3.06
1898 1969 0.539986 TCCCAAAGGCGTCTATGACC 59.460 55.000 0.00 0.00 0.00 4.02
1949 2026 9.778993 CATGGCATATTTTGTATTAGCATCTAC 57.221 33.333 0.00 0.00 0.00 2.59
2118 2197 5.649557 TCACAAAGGTTTGACAAGAACATG 58.350 37.500 9.42 0.00 40.55 3.21
2134 2213 2.501261 ACATGCATCAATCCATCCGAG 58.499 47.619 0.00 0.00 0.00 4.63
2148 2227 2.665000 CGAGGCCACCACTCACAT 59.335 61.111 5.01 0.00 34.66 3.21
2156 2235 4.413520 AGGCCACCACTCACATCTATAAAT 59.586 41.667 5.01 0.00 0.00 1.40
2198 2278 4.291792 TCACTCCCCATATCTAAAACCGA 58.708 43.478 0.00 0.00 0.00 4.69
2215 2295 0.866061 CGATGTCGTCGGTGATCCAC 60.866 60.000 6.56 0.00 46.47 4.02
2249 2329 1.227438 CGGAACCAACAGTCGGTGT 60.227 57.895 0.00 0.00 43.24 4.16
2288 2381 2.878406 ACATGCACACGTTTTAGAAGCT 59.122 40.909 0.00 0.00 0.00 3.74
2291 2384 1.663161 GCACACGTTTTAGAAGCTGCC 60.663 52.381 0.00 0.00 0.00 4.85
2292 2385 0.865769 ACACGTTTTAGAAGCTGCCG 59.134 50.000 0.00 0.00 0.00 5.69
2293 2386 0.865769 CACGTTTTAGAAGCTGCCGT 59.134 50.000 0.00 0.00 0.00 5.68
2311 2404 2.159057 CCGTCATCATCATCAGACCACA 60.159 50.000 0.00 0.00 0.00 4.17
2312 2405 3.524541 CGTCATCATCATCAGACCACAA 58.475 45.455 0.00 0.00 0.00 3.33
2315 2408 4.940046 GTCATCATCATCAGACCACAAACT 59.060 41.667 0.00 0.00 0.00 2.66
2343 2437 3.640498 TCAGAAGAGAGATCCGCATCATT 59.360 43.478 0.00 0.00 0.00 2.57
2472 2582 2.280628 GCATGACTTAGTGTAGCACCC 58.719 52.381 0.00 0.00 34.49 4.61
2495 2605 4.100479 CCAGGCATGGCTTGACAA 57.900 55.556 20.85 0.00 40.52 3.18
2496 2606 2.353858 CCAGGCATGGCTTGACAAA 58.646 52.632 20.85 0.00 40.52 2.83
2520 2630 0.601046 CTGAAGCTCCGTGCAAGACA 60.601 55.000 0.00 0.00 45.94 3.41
2544 2655 2.063378 GCTCCACCTCCTCCTCTGG 61.063 68.421 0.00 0.00 0.00 3.86
2548 2659 1.204113 CCACCTCCTCCTCTGGCTTT 61.204 60.000 0.00 0.00 0.00 3.51
2563 2674 3.020026 CTTTCAGCGCTGCTCCACG 62.020 63.158 32.44 12.75 36.40 4.94
2595 2706 3.479269 GAGAGAAACGGCACCGCG 61.479 66.667 9.43 0.00 44.19 6.46
2600 2711 4.303993 AAACGGCACCGCGGTACT 62.304 61.111 33.70 7.60 41.05 2.73
2658 2769 1.005748 CCTGAAGCAGCACGAGTGA 60.006 57.895 7.50 0.00 0.00 3.41
2662 2773 0.319040 GAAGCAGCACGAGTGAGTCA 60.319 55.000 7.50 0.00 0.00 3.41
2683 2794 3.088194 ACAACAGTTACACGACGATGT 57.912 42.857 0.00 5.07 36.56 3.06
2688 2799 3.252701 ACAGTTACACGACGATGTCTTCT 59.747 43.478 0.00 0.20 33.85 2.85
2690 2801 5.049198 ACAGTTACACGACGATGTCTTCTTA 60.049 40.000 0.00 0.00 33.85 2.10
2719 2832 4.398598 GCAAAACGCCGCCATCGT 62.399 61.111 0.00 0.00 42.54 3.73
2766 2880 3.600388 CAACTATGTCTCCCCAACTCAC 58.400 50.000 0.00 0.00 0.00 3.51
2778 2892 1.338200 CCAACTCACAGCTGGGACTAC 60.338 57.143 16.58 0.00 27.93 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 4.056125 CTGCACTCCGGTCTGCGA 62.056 66.667 17.54 8.84 0.00 5.10
193 194 1.437573 CATAGGAGAAGTGCGGCGA 59.562 57.895 12.98 0.00 0.00 5.54
226 227 4.994471 TGAGTGGCACAGCAGCGG 62.994 66.667 21.41 0.00 41.80 5.52
312 326 9.722056 CTGCAACAACTTACAATATAATTCTCC 57.278 33.333 0.00 0.00 0.00 3.71
316 330 8.303156 TGCACTGCAACAACTTACAATATAATT 58.697 29.630 0.00 0.00 34.76 1.40
332 349 1.581934 TACTGAGTGTGCACTGCAAC 58.418 50.000 19.41 7.71 42.66 4.17
341 358 2.002586 CCTGCGGAATTACTGAGTGTG 58.997 52.381 0.00 0.00 0.00 3.82
342 359 1.066143 CCCTGCGGAATTACTGAGTGT 60.066 52.381 0.00 0.00 0.00 3.55
350 367 2.702592 AATCGAACCCTGCGGAATTA 57.297 45.000 0.00 0.00 0.00 1.40
358 375 2.222027 GGCCAGATTAATCGAACCCTG 58.778 52.381 9.78 1.93 0.00 4.45
359 376 1.843851 TGGCCAGATTAATCGAACCCT 59.156 47.619 0.00 0.00 0.00 4.34
581 605 0.030908 GTCTCTAAGATCCGTGCGGG 59.969 60.000 10.94 0.00 35.59 6.13
586 610 4.764050 TCTCTCTGTCTCTAAGATCCGT 57.236 45.455 0.00 0.00 0.00 4.69
590 614 7.555087 CCAAACAATCTCTCTGTCTCTAAGAT 58.445 38.462 0.00 0.00 0.00 2.40
595 619 3.616076 CGCCAAACAATCTCTCTGTCTCT 60.616 47.826 0.00 0.00 0.00 3.10
626 650 3.006859 AGCTTTTAACACCATTGAAGCCC 59.993 43.478 0.00 0.00 40.10 5.19
643 667 2.310538 CAGAACAAGACCCCAAGCTTT 58.689 47.619 0.00 0.00 0.00 3.51
671 703 4.624024 CGAGACGGAAATACAGCAGTAAAA 59.376 41.667 0.00 0.00 33.13 1.52
688 720 1.388093 CAGCAAGAACACATCGAGACG 59.612 52.381 0.00 0.00 0.00 4.18
749 781 6.302535 TCGGGGAAGACTTAACATGAATTA 57.697 37.500 0.00 0.00 0.00 1.40
763 795 2.221299 CCACCACCTTCGGGGAAGA 61.221 63.158 6.93 0.00 41.71 2.87
768 800 1.611261 TACTCCCACCACCTTCGGG 60.611 63.158 0.00 0.00 41.76 5.14
782 814 2.991866 GTCACGGTTTAGCAAGGTACTC 59.008 50.000 0.00 0.00 38.49 2.59
784 816 2.477754 GTGTCACGGTTTAGCAAGGTAC 59.522 50.000 0.00 0.00 0.00 3.34
787 819 1.531149 CAGTGTCACGGTTTAGCAAGG 59.469 52.381 0.00 0.00 0.00 3.61
795 850 1.817941 GGCACACAGTGTCACGGTT 60.818 57.895 2.14 0.00 38.14 4.44
798 853 1.643292 CAAGGCACACAGTGTCACG 59.357 57.895 2.14 0.00 41.04 4.35
818 873 6.748333 TCAGATGTTTCATTCATTCACTCC 57.252 37.500 0.00 0.00 0.00 3.85
887 945 0.385723 GTACGAGATCGACCGATGGC 60.386 60.000 9.83 0.95 43.02 4.40
906 964 4.683832 CTTCCTTGTAGACACCTTATCGG 58.316 47.826 0.00 0.00 39.35 4.18
942 1005 0.185175 GAGGAGGAGGAGGAGAGGAC 59.815 65.000 0.00 0.00 0.00 3.85
954 1017 2.647949 GGGGAAGGGAGGAGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
985 1051 4.936575 CATGGATGGATGGGTGGG 57.063 61.111 0.00 0.00 0.00 4.61
1129 1195 2.088423 TGCACGCGGATAAAAGGATTT 58.912 42.857 12.47 0.00 42.41 2.17
1176 1242 1.949847 GCTAGCTCAAGAGGGCACGA 61.950 60.000 7.70 0.00 0.00 4.35
1183 1249 1.956477 GAGAGGGAGCTAGCTCAAGAG 59.044 57.143 38.32 0.00 44.40 2.85
1219 1285 2.527951 ATTGCCTGCACGGAGAGGAC 62.528 60.000 6.40 0.00 33.16 3.85
1352 1419 1.594293 CACTTTGAGACGGCCGTGT 60.594 57.895 39.65 34.74 0.00 4.49
1364 1431 5.591099 ACTGGTGAAAATTGCTACACTTTG 58.409 37.500 0.00 0.00 34.28 2.77
1368 1435 4.219033 CGAACTGGTGAAAATTGCTACAC 58.781 43.478 0.00 0.00 0.00 2.90
1372 1439 5.460646 CAATACGAACTGGTGAAAATTGCT 58.539 37.500 0.00 0.00 0.00 3.91
1373 1440 4.089923 GCAATACGAACTGGTGAAAATTGC 59.910 41.667 0.00 0.00 40.56 3.56
1374 1441 4.621034 GGCAATACGAACTGGTGAAAATTG 59.379 41.667 0.00 0.00 0.00 2.32
1375 1442 4.321675 GGGCAATACGAACTGGTGAAAATT 60.322 41.667 0.00 0.00 0.00 1.82
1376 1443 3.192633 GGGCAATACGAACTGGTGAAAAT 59.807 43.478 0.00 0.00 0.00 1.82
1377 1444 2.554893 GGGCAATACGAACTGGTGAAAA 59.445 45.455 0.00 0.00 0.00 2.29
1378 1445 2.156098 GGGCAATACGAACTGGTGAAA 58.844 47.619 0.00 0.00 0.00 2.69
1381 1448 1.086696 CTGGGCAATACGAACTGGTG 58.913 55.000 0.00 0.00 0.00 4.17
1382 1449 0.981183 TCTGGGCAATACGAACTGGT 59.019 50.000 0.00 0.00 0.00 4.00
1383 1450 1.656652 CTCTGGGCAATACGAACTGG 58.343 55.000 0.00 0.00 0.00 4.00
1385 1452 0.905357 AGCTCTGGGCAATACGAACT 59.095 50.000 0.74 0.00 44.79 3.01
1386 1453 1.009829 CAGCTCTGGGCAATACGAAC 58.990 55.000 0.74 0.00 44.79 3.95
1387 1454 0.107703 CCAGCTCTGGGCAATACGAA 60.108 55.000 0.74 0.00 46.81 3.85
1434 1502 3.746492 GCTCACTACCAAGTACAAAGGTG 59.254 47.826 12.50 5.97 36.87 4.00
1439 1507 3.236047 TCCTGCTCACTACCAAGTACAA 58.764 45.455 0.00 0.00 33.48 2.41
1466 1534 2.035530 CTCAGGGATTTGAGCCTCAC 57.964 55.000 0.00 0.00 38.28 3.51
1477 1545 3.023949 GCACCTCACGCTCAGGGAT 62.024 63.158 0.00 0.00 35.01 3.85
1660 1728 2.029288 CACGCACTCACGCTTCCAT 61.029 57.895 0.00 0.00 36.19 3.41
1701 1769 0.537188 CCATCAGCCCTACGTTCTGT 59.463 55.000 0.00 0.00 0.00 3.41
1794 1862 0.380733 TTGATCAGTCCGACGATCCG 59.619 55.000 20.72 0.00 37.77 4.18
1806 1874 7.375280 GCAAATTAACATCGAGTGATTGATCAG 59.625 37.037 0.00 0.00 37.51 2.90
1816 1884 6.363088 CACAACAATGCAAATTAACATCGAGT 59.637 34.615 0.00 0.00 0.00 4.18
1820 1888 7.872163 TCTCACAACAATGCAAATTAACATC 57.128 32.000 0.00 0.00 0.00 3.06
1859 1930 3.553096 GGAAGCAAGAGAGACAACTCGAA 60.553 47.826 0.00 0.00 46.64 3.71
1871 1942 0.890996 ACGCCTTTGGGAAGCAAGAG 60.891 55.000 0.00 0.00 33.58 2.85
2022 2099 8.461249 AGGTTTACCTCCTTTTCTAAAAGAAC 57.539 34.615 15.16 10.30 44.77 3.01
2118 2197 1.239968 GGCCTCGGATGGATTGATGC 61.240 60.000 0.00 0.00 0.00 3.91
2134 2213 3.838244 TTATAGATGTGAGTGGTGGCC 57.162 47.619 0.00 0.00 0.00 5.36
2148 2227 9.764363 AGCACTTCACATTATCGAATTTATAGA 57.236 29.630 0.00 0.00 0.00 1.98
2156 2235 4.864806 GTGAGAGCACTTCACATTATCGAA 59.135 41.667 9.52 0.00 41.84 3.71
2198 2278 1.515954 GGTGGATCACCGACGACAT 59.484 57.895 0.00 0.00 44.95 3.06
2207 2287 1.461897 CGTTTTACGTGGGTGGATCAC 59.538 52.381 0.00 0.00 36.74 3.06
2220 2300 4.448732 ACTGTTGGTTCCGATACGTTTTAC 59.551 41.667 0.00 0.00 0.00 2.01
2223 2303 3.062042 GACTGTTGGTTCCGATACGTTT 58.938 45.455 0.00 0.00 0.00 3.60
2249 2329 1.070615 TGGTGTGCGCTTTCTGCTA 59.929 52.632 9.73 0.00 40.11 3.49
2288 2381 1.202568 GGTCTGATGATGATGACGGCA 60.203 52.381 0.00 0.00 0.00 5.69
2291 2384 3.169355 TGTGGTCTGATGATGATGACG 57.831 47.619 0.00 0.00 0.00 4.35
2292 2385 4.940046 AGTTTGTGGTCTGATGATGATGAC 59.060 41.667 0.00 0.00 0.00 3.06
2293 2386 5.169992 AGTTTGTGGTCTGATGATGATGA 57.830 39.130 0.00 0.00 0.00 2.92
2311 2404 6.405731 CGGATCTCTCTTCTGAAGATGAGTTT 60.406 42.308 27.18 21.22 43.10 2.66
2312 2405 5.067674 CGGATCTCTCTTCTGAAGATGAGTT 59.932 44.000 27.18 23.27 43.10 3.01
2315 2408 3.317711 GCGGATCTCTCTTCTGAAGATGA 59.682 47.826 19.61 19.09 36.82 2.92
2343 2437 1.338105 CGGATGTCTGGACTTGCAAGA 60.338 52.381 32.50 9.84 0.00 3.02
2395 2499 4.794439 TCGCGTCTGCACGGATGG 62.794 66.667 5.77 0.00 46.80 3.51
2403 2511 0.944311 TCCAGAGTTTTCGCGTCTGC 60.944 55.000 15.92 2.40 37.06 4.26
2460 2570 2.703798 GCCGACGGGTGCTACACTA 61.704 63.158 17.22 0.00 34.40 2.74
2487 2597 2.555757 AGCTTCAGTGGATTTGTCAAGC 59.444 45.455 1.73 1.73 35.95 4.01
2495 2605 0.674895 GCACGGAGCTTCAGTGGATT 60.675 55.000 15.66 0.00 41.75 3.01
2496 2606 1.078848 GCACGGAGCTTCAGTGGAT 60.079 57.895 15.66 0.00 41.75 3.41
2520 2630 2.930562 AGGAGGTGGAGCGGCTTT 60.931 61.111 2.97 0.00 0.00 3.51
2548 2659 3.989787 TTCGTGGAGCAGCGCTGA 61.990 61.111 40.21 17.52 39.88 4.26
2563 2674 1.478510 TCTCTCTTGGGAGCATCGTTC 59.521 52.381 0.00 0.00 39.31 3.95
2595 2706 0.318784 GATCGGACGATGGCAGTACC 60.319 60.000 12.40 0.00 34.60 3.34
2600 2711 0.534873 TTTCAGATCGGACGATGGCA 59.465 50.000 12.40 0.00 34.60 4.92
2642 2753 0.319040 GACTCACTCGTGCTGCTTCA 60.319 55.000 0.00 0.00 0.00 3.02
2658 2769 2.855963 CGTCGTGTAACTGTTGTTGACT 59.144 45.455 2.69 0.00 37.59 3.41
2662 2773 3.450578 ACATCGTCGTGTAACTGTTGTT 58.549 40.909 2.69 0.00 39.98 2.83
2683 2794 4.339872 TGCACCGTTACCTTTAAGAAGA 57.660 40.909 0.00 0.00 34.71 2.87
2688 2799 3.791455 GCGTTTTGCACCGTTACCTTTAA 60.791 43.478 0.00 0.00 45.45 1.52
2690 2801 1.534385 GCGTTTTGCACCGTTACCTTT 60.534 47.619 0.00 0.00 45.45 3.11
2723 2836 1.228533 GGTGAAAACCGAGCCGTTTA 58.771 50.000 0.00 0.00 34.89 2.01
2724 2837 2.027325 GGTGAAAACCGAGCCGTTT 58.973 52.632 0.00 0.00 37.56 3.60
2766 2880 0.179100 CCGTCATGTAGTCCCAGCTG 60.179 60.000 6.78 6.78 0.00 4.24


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

AutoCloner maintained by Alex Coulton.