Multiple sequence alignment - TraesCS3A01G491200

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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 TraesCS3A01G491200 chr3A 100.000 2589 0 0 1 2589 718387481 718384893 0 4782
1 TraesCS3A01G491200 chr3D 87.167 2626 187 73 25 2589 588373241 588370705 0 2844
2 TraesCS3A01G491200 chr3B 84.479 2094 140 84 579 2589 786793757 786791766 0 1895
3 TraesCS3A01G491200 chr3B 93.574 498 26 5 42 537 786794332 786793839 0 737


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 TraesCS3A01G491200 chr3A 718384893 718387481 2588 True 4782 4782 100.0000 1 2589 1 chr3A.!!$R1 2588
1 TraesCS3A01G491200 chr3D 588370705 588373241 2536 True 2844 2844 87.1670 25 2589 1 chr3D.!!$R1 2564
2 TraesCS3A01G491200 chr3B 786791766 786794332 2566 True 1316 1895 89.0265 42 2589 2 chr3B.!!$R1 2547

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
78 84 0.1791 CTACCGCTCACATGGGAGTG 60.179 60.0 28.19 28.19 43.39 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1878 1.470979 GCGATAATGTGTGTCCGTCCT 60.471 52.381 0.0 0.0 0.0 3.85 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
77 83 0.614979 ACTACCGCTCACATGGGAGT 60.615 55.000 25.52 10.09 44.86 3.85
78 84 0.179100 CTACCGCTCACATGGGAGTG 60.179 60.000 28.19 28.19 43.39 3.51
79 85 0.613572 TACCGCTCACATGGGAGTGA 60.614 55.000 34.78 16.90 45.93 3.41
171 177 3.248171 GACGATGTCTGTCCGCGC 61.248 66.667 0.00 0.00 0.00 6.86
192 198 1.052287 CACAAGTCGCGCCAAAATTC 58.948 50.000 0.00 0.00 0.00 2.17
208 214 5.697633 CCAAAATTCTGTTGGTTCCATCTTG 59.302 40.000 0.00 0.00 40.64 3.02
230 236 4.505217 GATCCACGCGCACGCAAG 62.505 66.667 16.04 6.29 45.53 4.01
277 284 3.204827 CCCAAAGCCTCCGCATCG 61.205 66.667 0.00 0.00 37.52 3.84
371 378 1.586028 CTGTCCACCAAAATGCCGG 59.414 57.895 0.00 0.00 0.00 6.13
434 441 0.526524 CATCTCTCTGCCCGACGTTC 60.527 60.000 0.00 0.00 0.00 3.95
642 709 2.610694 CCACAAGCCGACACTGCAG 61.611 63.158 13.48 13.48 0.00 4.41
686 754 3.092403 CCGTCCGTGTACGATCGA 58.908 61.111 24.34 2.23 45.68 3.59
694 762 0.933509 GTGTACGATCGATCACGGGC 60.934 60.000 24.34 10.12 40.21 6.13
731 799 3.833645 CGATTGAGCGACCCCGGA 61.834 66.667 0.73 0.00 36.06 5.14
732 800 2.202892 GATTGAGCGACCCCGGAC 60.203 66.667 0.73 0.00 36.06 4.79
733 801 4.143333 ATTGAGCGACCCCGGACG 62.143 66.667 0.73 7.20 36.06 4.79
745 813 2.046314 CGGACGGGCCATGAGTTT 60.046 61.111 4.39 0.00 35.94 2.66
746 814 1.674322 CGGACGGGCCATGAGTTTT 60.674 57.895 4.39 0.00 35.94 2.43
747 815 0.391927 CGGACGGGCCATGAGTTTTA 60.392 55.000 4.39 0.00 35.94 1.52
823 891 4.760047 CGTCTGCCCAACCCGAGG 62.760 72.222 0.00 0.00 0.00 4.63
830 898 4.785453 CCAACCCGAGGCCAGCTC 62.785 72.222 5.01 0.00 0.00 4.09
831 899 4.785453 CAACCCGAGGCCAGCTCC 62.785 72.222 5.01 0.00 0.00 4.70
893 961 0.602638 TGTTCATCGGCACTCCACAC 60.603 55.000 0.00 0.00 0.00 3.82
894 962 0.320771 GTTCATCGGCACTCCACACT 60.321 55.000 0.00 0.00 0.00 3.55
895 963 0.320683 TTCATCGGCACTCCACACTG 60.321 55.000 0.00 0.00 0.00 3.66
896 964 2.046892 ATCGGCACTCCACACTGC 60.047 61.111 0.00 0.00 0.00 4.40
900 968 2.203195 GCACTCCACACTGCCACA 60.203 61.111 0.00 0.00 0.00 4.17
901 969 2.256591 GCACTCCACACTGCCACAG 61.257 63.158 0.00 0.00 37.52 3.66
902 970 2.111878 ACTCCACACTGCCACAGC 59.888 61.111 0.00 0.00 34.37 4.40
903 971 2.670934 CTCCACACTGCCACAGCC 60.671 66.667 0.00 0.00 38.69 4.85
904 972 4.269523 TCCACACTGCCACAGCCC 62.270 66.667 0.00 0.00 38.69 5.19
905 973 4.584518 CCACACTGCCACAGCCCA 62.585 66.667 0.00 0.00 38.69 5.36
906 974 3.289834 CACACTGCCACAGCCCAC 61.290 66.667 0.00 0.00 38.69 4.61
907 975 3.807839 ACACTGCCACAGCCCACA 61.808 61.111 0.00 0.00 38.69 4.17
908 976 2.981909 CACTGCCACAGCCCACAG 60.982 66.667 0.00 0.00 38.69 3.66
909 977 4.962836 ACTGCCACAGCCCACAGC 62.963 66.667 0.00 0.00 44.25 4.40
933 1010 4.865698 AGATCAACAATCTAGCAGCTTGCA 60.866 41.667 0.00 0.00 43.17 4.08
934 1011 6.654746 AGATCAACAATCTAGCAGCTTGCAG 61.655 44.000 0.00 0.00 43.17 4.41
943 1020 1.502163 GCAGCTTGCAGTCGAGTTGT 61.502 55.000 0.00 0.00 44.26 3.32
971 1052 4.476410 CGTAGAGCTCGCCGCACA 62.476 66.667 8.37 0.00 42.61 4.57
973 1054 1.946650 GTAGAGCTCGCCGCACATC 60.947 63.158 8.37 0.00 42.61 3.06
974 1055 2.121538 TAGAGCTCGCCGCACATCT 61.122 57.895 8.37 0.00 42.61 2.90
975 1056 0.818040 TAGAGCTCGCCGCACATCTA 60.818 55.000 8.37 0.00 42.61 1.98
976 1057 1.659954 GAGCTCGCCGCACATCTAG 60.660 63.158 0.00 0.00 42.61 2.43
980 1061 0.386605 CTCGCCGCACATCTAGCTAG 60.387 60.000 15.01 15.01 0.00 3.42
981 1062 0.818040 TCGCCGCACATCTAGCTAGA 60.818 55.000 25.23 25.23 36.65 2.43
988 1069 3.065655 GCACATCTAGCTAGATTGCCAG 58.934 50.000 33.32 25.24 40.91 4.85
995 1090 3.634397 AGCTAGATTGCCAGCTAACAA 57.366 42.857 0.00 3.30 46.14 2.83
996 1091 3.955471 AGCTAGATTGCCAGCTAACAAA 58.045 40.909 4.83 0.00 46.14 2.83
1169 1284 2.034066 CGAAGGCCAGGGCAAGAA 59.966 61.111 16.94 0.00 44.11 2.52
1257 1372 1.440060 CAACGATGGCCGCTAGGTA 59.560 57.895 0.00 0.00 43.32 3.08
1283 1398 2.126888 CACGTTGGCCGCACATTC 60.127 61.111 0.00 0.00 41.42 2.67
1286 1401 2.699768 CGTTGGCCGCACATTCCAT 61.700 57.895 0.00 0.00 0.00 3.41
1324 1439 1.035385 TAGCTGTTCGATCTGCCCGA 61.035 55.000 18.33 5.31 33.76 5.14
1433 1556 3.741249 TGTGATCCCTAGCTACTACTCG 58.259 50.000 0.00 0.00 0.00 4.18
1478 1606 4.767255 GAGCTCCCGCCCACTGTG 62.767 72.222 0.87 0.00 36.60 3.66
1487 1615 2.359602 CCCACTGTGCCTCTGCTG 60.360 66.667 1.29 0.00 38.71 4.41
1488 1616 2.745698 CCACTGTGCCTCTGCTGA 59.254 61.111 1.29 0.00 38.71 4.26
1500 1633 4.038522 TGCCTCTGCTGACTAATCTGTATC 59.961 45.833 0.00 0.00 38.71 2.24
1513 1646 9.419297 GACTAATCTGTATCAAGTGTACAAACA 57.581 33.333 0.00 0.00 32.15 2.83
1519 1652 7.330946 TCTGTATCAAGTGTACAAACATGCTAC 59.669 37.037 0.00 1.93 38.08 3.58
1577 1723 1.118838 GTGCCTAGCCTCTGATCACT 58.881 55.000 0.00 0.00 0.00 3.41
1578 1724 1.068434 GTGCCTAGCCTCTGATCACTC 59.932 57.143 0.00 0.00 0.00 3.51
1589 1735 5.465056 GCCTCTGATCACTCACTAAATAAGC 59.535 44.000 0.00 0.00 0.00 3.09
1590 1736 6.685116 GCCTCTGATCACTCACTAAATAAGCT 60.685 42.308 0.00 0.00 0.00 3.74
1593 1739 6.381133 TCTGATCACTCACTAAATAAGCTCCA 59.619 38.462 0.00 0.00 0.00 3.86
1650 1796 2.346099 TGCACGCTTTATTTTCTGCC 57.654 45.000 0.00 0.00 0.00 4.85
1651 1797 1.611006 TGCACGCTTTATTTTCTGCCA 59.389 42.857 0.00 0.00 0.00 4.92
1670 1817 3.251487 GCCAATGCTTTGACAAAAATGCT 59.749 39.130 13.58 0.00 34.60 3.79
1710 1860 2.166870 GGATCTGGAACATGCATGCAAA 59.833 45.455 26.68 1.26 38.20 3.68
1726 1876 1.067821 GCAAAATGAACGTGGGTGGAA 59.932 47.619 0.00 0.00 0.00 3.53
1728 1878 3.786635 CAAAATGAACGTGGGTGGAAAA 58.213 40.909 0.00 0.00 0.00 2.29
1762 1912 0.171679 TATCGCTTTCGCCGAGACAA 59.828 50.000 0.00 0.00 38.20 3.18
1763 1913 0.460284 ATCGCTTTCGCCGAGACAAT 60.460 50.000 0.00 0.00 38.20 2.71
1802 1952 1.079681 CAATGCGTGCTGCCCAATT 60.080 52.632 0.00 0.00 45.60 2.32
1889 2045 4.649088 ACGGATAAATCTGTCGTGATCA 57.351 40.909 0.00 0.00 42.52 2.92
1908 2064 2.231478 TCAAAGGACTACAAGAGAGGCG 59.769 50.000 0.00 0.00 0.00 5.52
1914 2070 4.896482 AGGACTACAAGAGAGGCGATTTAT 59.104 41.667 0.00 0.00 0.00 1.40
1930 2086 4.142491 CGATTTATCTGGGGAGATCTCGAG 60.142 50.000 16.46 5.93 32.00 4.04
2106 2277 1.665916 GCTCGTGCTGCTGTGAAGA 60.666 57.895 1.41 0.00 36.03 2.87
2158 2329 1.084370 GCCGTGTGAAGAAGATCCGG 61.084 60.000 0.00 0.00 37.08 5.14
2166 2337 5.063564 GTGTGAAGAAGATCCGGTTAATCAC 59.936 44.000 0.00 9.10 36.19 3.06
2188 2359 2.354259 GCCATCACACTCTTCTTCCTG 58.646 52.381 0.00 0.00 0.00 3.86
2232 2403 9.632638 ATGTGTATGAATAGGAAGCTAACAATT 57.367 29.630 0.00 0.00 0.00 2.32
2262 2433 8.076178 AGTACTGTGAAATAGTGTGAAAATTGC 58.924 33.333 0.00 0.00 39.27 3.56
2274 2445 3.430895 GTGAAAATTGCTGAATGGCTGTG 59.569 43.478 0.00 0.00 0.00 3.66
2278 2449 2.798976 TTGCTGAATGGCTGTGTTTC 57.201 45.000 0.00 0.00 0.00 2.78
2310 2481 6.525578 TTAGTTCGTACATCTGTGGATTCT 57.474 37.500 0.00 0.00 0.00 2.40
2311 2482 5.407407 AGTTCGTACATCTGTGGATTCTT 57.593 39.130 0.00 0.00 0.00 2.52
2312 2483 5.411781 AGTTCGTACATCTGTGGATTCTTC 58.588 41.667 0.00 0.00 0.00 2.87
2313 2484 4.028852 TCGTACATCTGTGGATTCTTCG 57.971 45.455 0.00 0.00 0.00 3.79
2314 2485 2.535984 CGTACATCTGTGGATTCTTCGC 59.464 50.000 0.00 0.00 0.00 4.70
2315 2486 2.029838 ACATCTGTGGATTCTTCGCC 57.970 50.000 0.00 0.00 0.00 5.54
2316 2487 0.933097 CATCTGTGGATTCTTCGCCG 59.067 55.000 0.00 0.00 0.00 6.46
2317 2488 0.537188 ATCTGTGGATTCTTCGCCGT 59.463 50.000 0.00 0.00 0.00 5.68
2318 2489 0.108804 TCTGTGGATTCTTCGCCGTC 60.109 55.000 0.00 0.00 0.00 4.79
2319 2490 0.389817 CTGTGGATTCTTCGCCGTCA 60.390 55.000 0.00 0.00 0.00 4.35
2320 2491 0.389817 TGTGGATTCTTCGCCGTCAG 60.390 55.000 0.00 0.00 0.00 3.51
2321 2492 0.108804 GTGGATTCTTCGCCGTCAGA 60.109 55.000 0.00 0.00 0.00 3.27
2322 2493 0.824109 TGGATTCTTCGCCGTCAGAT 59.176 50.000 0.00 0.00 0.00 2.90
2323 2494 1.202417 TGGATTCTTCGCCGTCAGATC 60.202 52.381 0.00 0.00 0.00 2.75
2324 2495 1.492720 GATTCTTCGCCGTCAGATCC 58.507 55.000 0.00 0.00 0.00 3.36
2325 2496 0.105039 ATTCTTCGCCGTCAGATCCC 59.895 55.000 0.00 0.00 0.00 3.85
2342 2513 2.182030 CTCGCCGTCAGAACCCTC 59.818 66.667 0.00 0.00 0.00 4.30
2359 2530 2.771435 TCGCCTTGATCGTACGAGA 58.229 52.632 23.89 10.40 0.00 4.04
2534 2709 1.598130 GTTCTGGCTGTGAACCGCT 60.598 57.895 7.14 0.00 38.19 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 83 1.005037 ATGCTGAAACGACGCCTCA 60.005 52.632 0.00 0.00 0.00 3.86
78 84 1.710339 GATGCTGAAACGACGCCTC 59.290 57.895 0.00 0.00 0.00 4.70
79 85 2.094659 CGATGCTGAAACGACGCCT 61.095 57.895 0.00 0.00 0.00 5.52
80 86 1.897398 AACGATGCTGAAACGACGCC 61.897 55.000 0.00 0.00 0.00 5.68
123 129 1.353103 CGGCGTACCACCGTACTAG 59.647 63.158 12.66 0.00 45.70 2.57
171 177 2.141122 ATTTTGGCGCGACTTGTGGG 62.141 55.000 15.80 0.00 0.00 4.61
192 198 2.094390 CCATGCAAGATGGAACCAACAG 60.094 50.000 0.00 0.00 41.64 3.16
252 258 4.204028 AGGCTTTGGGCACGTGGT 62.204 61.111 18.88 0.00 44.01 4.16
371 378 0.667184 CATGGGCGTGCCAAGAAAAC 60.667 55.000 13.76 0.00 37.98 2.43
434 441 2.278596 CGTACGTGGCCATCGAGG 60.279 66.667 27.07 15.34 41.84 4.63
492 499 1.493950 GCGTCTGCATGGATTCTCCG 61.494 60.000 0.00 0.00 39.45 4.63
493 500 2.315246 GCGTCTGCATGGATTCTCC 58.685 57.895 0.00 0.00 42.15 3.71
505 512 1.269166 GTAACTCCATCGTGCGTCTG 58.731 55.000 0.00 0.00 0.00 3.51
627 694 2.031012 TCCTGCAGTGTCGGCTTG 59.969 61.111 13.81 0.00 0.00 4.01
642 709 1.214373 TGTTACCGAACGCAACGTCC 61.214 55.000 0.00 0.00 39.99 4.79
727 795 3.622060 AAACTCATGGCCCGTCCGG 62.622 63.158 0.00 0.00 37.80 5.14
729 797 2.052782 ATAAAACTCATGGCCCGTCC 57.947 50.000 0.00 0.00 0.00 4.79
730 798 4.450082 AAAATAAAACTCATGGCCCGTC 57.550 40.909 0.00 0.00 0.00 4.79
731 799 5.068591 GGATAAAATAAAACTCATGGCCCGT 59.931 40.000 0.00 0.00 0.00 5.28
732 800 5.068460 TGGATAAAATAAAACTCATGGCCCG 59.932 40.000 0.00 0.00 0.00 6.13
733 801 6.478512 TGGATAAAATAAAACTCATGGCCC 57.521 37.500 0.00 0.00 0.00 5.80
745 813 8.316946 TGCATGTGGTTTTCATGGATAAAATAA 58.683 29.630 7.78 0.00 41.77 1.40
746 814 7.763528 GTGCATGTGGTTTTCATGGATAAAATA 59.236 33.333 7.78 0.00 43.21 1.40
747 815 6.594937 GTGCATGTGGTTTTCATGGATAAAAT 59.405 34.615 7.78 0.00 43.21 1.82
782 850 1.385409 GCGCTCGGCAACAAATAAAAC 59.615 47.619 0.00 0.00 42.87 2.43
783 851 1.667467 GGCGCTCGGCAACAAATAAAA 60.667 47.619 7.64 0.00 46.16 1.52
786 854 1.376683 AGGCGCTCGGCAACAAATA 60.377 52.632 17.74 0.00 46.16 1.40
806 874 4.760047 CCTCGGGTTGGGCAGACG 62.760 72.222 0.00 0.00 0.00 4.18
814 882 4.785453 GGAGCTGGCCTCGGGTTG 62.785 72.222 3.32 0.00 41.71 3.77
828 896 1.970352 GAGGAGAAGCCAGCCAGGAG 61.970 65.000 0.00 0.00 41.22 3.69
829 897 1.992277 GAGGAGAAGCCAGCCAGGA 60.992 63.158 0.00 0.00 41.22 3.86
830 898 2.588989 GAGGAGAAGCCAGCCAGG 59.411 66.667 0.00 0.00 40.02 4.45
831 899 2.588989 GGAGGAGAAGCCAGCCAG 59.411 66.667 0.00 0.00 40.02 4.85
832 900 3.011517 GGGAGGAGAAGCCAGCCA 61.012 66.667 0.00 0.00 40.02 4.75
833 901 2.264120 GAAGGGAGGAGAAGCCAGCC 62.264 65.000 0.00 0.00 40.02 4.85
834 902 1.223211 GAAGGGAGGAGAAGCCAGC 59.777 63.158 0.00 0.00 40.02 4.85
835 903 2.166907 TAGAAGGGAGGAGAAGCCAG 57.833 55.000 0.00 0.00 40.02 4.85
836 904 2.877154 ATAGAAGGGAGGAGAAGCCA 57.123 50.000 0.00 0.00 40.02 4.75
837 905 4.041075 CCTTTATAGAAGGGAGGAGAAGCC 59.959 50.000 0.00 0.00 33.56 4.35
838 906 4.504165 GCCTTTATAGAAGGGAGGAGAAGC 60.504 50.000 1.84 0.00 37.88 3.86
839 907 4.041075 GGCCTTTATAGAAGGGAGGAGAAG 59.959 50.000 1.84 0.00 37.88 2.85
840 908 3.974642 GGCCTTTATAGAAGGGAGGAGAA 59.025 47.826 1.84 0.00 37.88 2.87
841 909 3.051341 TGGCCTTTATAGAAGGGAGGAGA 60.051 47.826 3.32 0.00 37.88 3.71
842 910 3.318313 TGGCCTTTATAGAAGGGAGGAG 58.682 50.000 3.32 0.00 37.88 3.69
873 941 0.320683 TGTGGAGTGCCGATGAACAG 60.321 55.000 0.00 0.00 36.79 3.16
893 961 4.960866 TGCTGTGGGCTGTGGCAG 62.961 66.667 0.00 0.00 42.39 4.85
894 962 4.960866 CTGCTGTGGGCTGTGGCA 62.961 66.667 0.00 0.00 42.39 4.92
895 963 3.933048 ATCTGCTGTGGGCTGTGGC 62.933 63.158 0.00 0.00 42.39 5.01
896 964 1.748122 GATCTGCTGTGGGCTGTGG 60.748 63.158 0.00 0.00 42.39 4.17
899 967 0.607217 TGTTGATCTGCTGTGGGCTG 60.607 55.000 0.00 0.00 42.39 4.85
900 968 0.111061 TTGTTGATCTGCTGTGGGCT 59.889 50.000 0.00 0.00 42.39 5.19
901 969 1.133790 GATTGTTGATCTGCTGTGGGC 59.866 52.381 0.00 0.00 42.22 5.36
902 970 2.719739 AGATTGTTGATCTGCTGTGGG 58.280 47.619 0.00 0.00 43.52 4.61
903 971 3.311871 GCTAGATTGTTGATCTGCTGTGG 59.688 47.826 0.00 0.00 44.80 4.17
904 972 3.937079 TGCTAGATTGTTGATCTGCTGTG 59.063 43.478 0.00 0.00 44.80 3.66
905 973 4.190001 CTGCTAGATTGTTGATCTGCTGT 58.810 43.478 0.00 0.00 44.80 4.40
906 974 3.002451 GCTGCTAGATTGTTGATCTGCTG 59.998 47.826 0.00 6.10 44.80 4.41
907 975 3.118334 AGCTGCTAGATTGTTGATCTGCT 60.118 43.478 0.00 0.00 44.80 4.24
908 976 3.204526 AGCTGCTAGATTGTTGATCTGC 58.795 45.455 0.00 2.33 44.80 4.26
909 977 4.496010 GCAAGCTGCTAGATTGTTGATCTG 60.496 45.833 0.90 0.00 43.06 2.90
933 1010 2.429236 CGCGCTCACAACTCGACT 60.429 61.111 5.56 0.00 0.00 4.18
934 1011 4.122515 GCGCGCTCACAACTCGAC 62.123 66.667 26.67 0.00 0.00 4.20
940 1017 4.649310 TACGTGGCGCGCTCACAA 62.649 61.111 35.04 25.63 46.11 3.33
943 1020 4.476410 CTCTACGTGGCGCGCTCA 62.476 66.667 32.29 23.70 46.11 4.26
963 1044 0.242286 ATCTAGCTAGATGTGCGGCG 59.758 55.000 31.03 0.51 41.28 6.46
965 1046 2.064762 GCAATCTAGCTAGATGTGCGG 58.935 52.381 31.86 22.77 41.96 5.69
976 1057 4.415735 GTTTTGTTAGCTGGCAATCTAGC 58.584 43.478 0.00 0.00 40.18 3.42
980 1061 3.658757 TGGTTTTGTTAGCTGGCAATC 57.341 42.857 0.00 0.00 0.00 2.67
981 1062 3.577848 TCATGGTTTTGTTAGCTGGCAAT 59.422 39.130 0.00 0.00 0.00 3.56
988 1069 2.834689 CGACGTCATGGTTTTGTTAGC 58.165 47.619 17.16 0.00 0.00 3.09
990 1071 1.192757 CGCGACGTCATGGTTTTGTTA 59.807 47.619 17.16 0.00 0.00 2.41
995 1090 3.419759 GGCGCGACGTCATGGTTT 61.420 61.111 17.16 0.00 0.00 3.27
996 1091 4.673298 TGGCGCGACGTCATGGTT 62.673 61.111 17.16 0.00 36.25 3.67
1035 1135 2.878429 TCGAAGTCGAGAGGCAGC 59.122 61.111 0.00 0.00 44.22 5.25
1324 1439 2.033194 GCTAGGCCGTCGTGCTTTT 61.033 57.895 0.00 0.00 0.00 2.27
1478 1606 2.977772 ACAGATTAGTCAGCAGAGGC 57.022 50.000 0.00 0.00 41.61 4.70
1487 1615 9.419297 TGTTTGTACACTTGATACAGATTAGTC 57.581 33.333 0.00 0.00 34.15 2.59
1488 1616 9.944376 ATGTTTGTACACTTGATACAGATTAGT 57.056 29.630 0.00 0.00 37.03 2.24
1500 1633 7.421530 AAGTAGTAGCATGTTTGTACACTTG 57.578 36.000 0.00 0.00 37.03 3.16
1577 1723 6.859112 AGAACTCTGGAGCTTATTTAGTGA 57.141 37.500 0.00 0.00 0.00 3.41
1578 1724 6.536941 GGAAGAACTCTGGAGCTTATTTAGTG 59.463 42.308 0.00 0.00 0.00 2.74
1589 1735 4.081198 ACAGCTTATGGAAGAACTCTGGAG 60.081 45.833 0.00 0.00 34.25 3.86
1590 1736 3.840666 ACAGCTTATGGAAGAACTCTGGA 59.159 43.478 0.00 0.00 34.25 3.86
1593 1739 5.690464 ATCACAGCTTATGGAAGAACTCT 57.310 39.130 0.00 0.00 34.25 3.24
1650 1796 8.283992 TCATTTAGCATTTTTGTCAAAGCATTG 58.716 29.630 9.82 0.00 37.92 2.82
1651 1797 8.380743 TCATTTAGCATTTTTGTCAAAGCATT 57.619 26.923 9.82 0.00 0.00 3.56
1710 1860 1.960689 CCTTTTCCACCCACGTTCATT 59.039 47.619 0.00 0.00 0.00 2.57
1726 1876 3.259064 CGATAATGTGTGTCCGTCCTTT 58.741 45.455 0.00 0.00 0.00 3.11
1728 1878 1.470979 GCGATAATGTGTGTCCGTCCT 60.471 52.381 0.00 0.00 0.00 3.85
1762 1912 2.528743 GCAGTAGACGCATGCGCAT 61.529 57.895 38.15 28.23 44.19 4.73
1763 1913 3.188100 GCAGTAGACGCATGCGCA 61.188 61.111 38.15 21.69 44.19 6.09
1775 1925 3.577229 CACGCATTGCAGGCAGTA 58.423 55.556 9.69 0.00 0.00 2.74
1889 2045 2.526432 TCGCCTCTCTTGTAGTCCTTT 58.474 47.619 0.00 0.00 0.00 3.11
1908 2064 5.013547 TCTCGAGATCTCCCCAGATAAATC 58.986 45.833 17.13 0.00 39.71 2.17
1914 2070 2.828661 TTTCTCGAGATCTCCCCAGA 57.171 50.000 17.44 12.41 0.00 3.86
1930 2086 5.663920 CGTAATCGTTTTTACGTCCGATTTC 59.336 40.000 18.17 14.24 44.87 2.17
1953 2109 2.165845 AGTACCTTCGATTTCCACTCCG 59.834 50.000 0.00 0.00 0.00 4.63
1959 2115 3.869832 GCTACCAAGTACCTTCGATTTCC 59.130 47.826 0.00 0.00 0.00 3.13
2001 2165 3.240069 ACAATGTAACGAGCACTACGAC 58.760 45.455 0.00 0.00 34.70 4.34
2106 2277 1.460305 AGATGGGCGAGGGTATGCT 60.460 57.895 0.00 0.00 0.00 3.79
2142 2313 5.063564 GTGATTAACCGGATCTTCTTCACAC 59.936 44.000 9.46 1.46 33.08 3.82
2158 2329 2.351726 GAGTGTGATGGCCGTGATTAAC 59.648 50.000 0.00 0.00 0.00 2.01
2166 2337 1.363744 GAAGAAGAGTGTGATGGCCG 58.636 55.000 0.00 0.00 0.00 6.13
2188 2359 6.259550 ACACATTCTACTCCTGAAATTTGC 57.740 37.500 0.00 0.00 0.00 3.68
2205 2376 9.632638 ATTGTTAGCTTCCTATTCATACACATT 57.367 29.630 0.00 0.00 0.00 2.71
2237 2408 8.076178 AGCAATTTTCACACTATTTCACAGTAC 58.924 33.333 0.00 0.00 0.00 2.73
2242 2413 7.928908 TTCAGCAATTTTCACACTATTTCAC 57.071 32.000 0.00 0.00 0.00 3.18
2262 2433 3.250762 TCGAAAGAAACACAGCCATTCAG 59.749 43.478 0.00 0.00 37.03 3.02
2278 2449 7.893236 CACAGATGTACGAACTAAAATCGAAAG 59.107 37.037 2.65 0.00 42.76 2.62
2310 2481 2.771639 CGAGGGATCTGACGGCGAA 61.772 63.158 16.62 0.00 0.00 4.70
2311 2482 3.209812 CGAGGGATCTGACGGCGA 61.210 66.667 16.62 0.00 0.00 5.54
2312 2483 4.933064 GCGAGGGATCTGACGGCG 62.933 72.222 4.80 4.80 0.00 6.46
2313 2484 4.593864 GGCGAGGGATCTGACGGC 62.594 72.222 13.64 13.64 42.98 5.68
2314 2485 4.271816 CGGCGAGGGATCTGACGG 62.272 72.222 0.00 0.00 0.00 4.79
2315 2486 3.471244 GACGGCGAGGGATCTGACG 62.471 68.421 16.62 0.00 0.00 4.35
2316 2487 2.343163 CTGACGGCGAGGGATCTGAC 62.343 65.000 16.62 0.00 0.00 3.51
2317 2488 2.044352 TGACGGCGAGGGATCTGA 60.044 61.111 16.62 0.00 0.00 3.27
2318 2489 1.667154 TTCTGACGGCGAGGGATCTG 61.667 60.000 16.62 4.31 0.00 2.90
2319 2490 1.379977 TTCTGACGGCGAGGGATCT 60.380 57.895 16.62 0.00 0.00 2.75
2320 2491 1.227002 GTTCTGACGGCGAGGGATC 60.227 63.158 16.62 0.00 0.00 3.36
2321 2492 2.722201 GGTTCTGACGGCGAGGGAT 61.722 63.158 16.62 0.00 0.00 3.85
2322 2493 3.379445 GGTTCTGACGGCGAGGGA 61.379 66.667 16.62 5.04 0.00 4.20
2323 2494 4.452733 GGGTTCTGACGGCGAGGG 62.453 72.222 16.62 2.33 0.00 4.30
2324 2495 3.358076 GAGGGTTCTGACGGCGAGG 62.358 68.421 16.62 2.73 0.00 4.63
2325 2496 2.182030 GAGGGTTCTGACGGCGAG 59.818 66.667 16.62 0.25 0.00 5.03
2342 2513 2.121116 ATTCTCGTACGATCAAGGCG 57.879 50.000 19.87 5.21 0.00 5.52
2534 2709 0.947660 CTTGCAGCGCTCTCAGTTCA 60.948 55.000 7.13 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.