Multiple sequence alignment - TraesCS2B01G392900

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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 TraesCS2B01G392900 chr2B 100.000 2756 0 0 1 2756 557228975 557226220 0.000000e+00 5090.0
1 TraesCS2B01G392900 chr2B 97.959 49 1 0 838 886 557228090 557228042 4.890000e-13 86.1
2 TraesCS2B01G392900 chr2B 97.959 49 1 0 886 934 557228138 557228090 4.890000e-13 86.1
3 TraesCS2B01G392900 chr2D 90.689 1858 62 34 886 2703 476346307 476344521 0.000000e+00 2370.0
4 TraesCS2B01G392900 chr2D 91.319 864 36 11 37 886 476347097 476346259 0.000000e+00 1144.0
5 TraesCS2B01G392900 chr2A 88.328 1842 63 53 899 2679 618267771 618266021 0.000000e+00 2071.0
6 TraesCS2B01G392900 chr2A 81.994 933 62 35 1 886 618268609 618267736 0.000000e+00 695.0
7 TraesCS2B01G392900 chr3A 90.777 206 18 1 1371 1576 59431059 59431263 9.720000e-70 274.0
8 TraesCS2B01G392900 chr6A 87.168 226 27 2 1314 1538 614381577 614381801 3.520000e-64 255.0
9 TraesCS2B01G392900 chr3D 82.667 300 33 10 1278 1576 47344707 47344988 5.890000e-62 248.0
10 TraesCS2B01G392900 chr6D 85.593 236 29 5 1304 1534 469205344 469205579 2.740000e-60 243.0


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 TraesCS2B01G392900 chr2B 557226220 557228975 2755 True 1754.066667 5090 98.639333 1 2756 3 chr2B.!!$R1 2755
1 TraesCS2B01G392900 chr2D 476344521 476347097 2576 True 1757.000000 2370 91.004000 37 2703 2 chr2D.!!$R1 2666
2 TraesCS2B01G392900 chr2A 618266021 618268609 2588 True 1383.000000 2071 85.161000 1 2679 2 chr2A.!!$R1 2678

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
118 119 0.169672 CGGCTGAAAATGACCTGCTG 59.83 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2087 0.182061 TGATGCTGCCCAGATTCTCC 59.818 55.0 0.0 0.0 0.0 3.71 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
68 69 4.318050 GCCTTTTGTTTGAAAATGACTCGC 60.318 41.667 0.00 0.00 0.00 5.03
89 90 6.166279 TCGCAGAAATCTGTTTATCAGTCTT 58.834 36.000 11.77 0.00 45.45 3.01
116 117 1.098050 ATCGGCTGAAAATGACCTGC 58.902 50.000 0.00 0.00 0.00 4.85
118 119 0.169672 CGGCTGAAAATGACCTGCTG 59.830 55.000 0.00 0.00 0.00 4.41
119 120 1.251251 GGCTGAAAATGACCTGCTGT 58.749 50.000 0.00 0.00 0.00 4.40
120 121 1.068055 GGCTGAAAATGACCTGCTGTG 60.068 52.381 0.00 0.00 0.00 3.66
121 122 1.610522 GCTGAAAATGACCTGCTGTGT 59.389 47.619 0.00 0.00 0.00 3.72
122 123 2.813754 GCTGAAAATGACCTGCTGTGTA 59.186 45.455 0.00 0.00 0.00 2.90
123 124 3.441572 GCTGAAAATGACCTGCTGTGTAT 59.558 43.478 0.00 0.00 0.00 2.29
242 251 2.283298 AGCTAGGCATGACAAATGACG 58.717 47.619 0.00 0.00 30.86 4.35
253 278 2.484264 GACAAATGACGTTTCAGAGGGG 59.516 50.000 0.00 0.00 34.35 4.79
258 283 0.896226 GACGTTTCAGAGGGGCTACT 59.104 55.000 0.00 0.00 0.00 2.57
288 313 1.210545 GGAATGCAATGCGAATGCGG 61.211 55.000 0.00 0.00 46.76 5.69
289 314 1.814211 GAATGCAATGCGAATGCGGC 61.814 55.000 0.00 0.00 46.76 6.53
290 315 2.560051 AATGCAATGCGAATGCGGCA 62.560 50.000 4.58 4.58 46.76 5.69
302 333 1.255882 ATGCGGCATGACCAAGAAAA 58.744 45.000 15.87 0.00 39.03 2.29
316 347 6.017440 TGACCAAGAAAATTGTAAACCTCGAG 60.017 38.462 5.13 5.13 0.00 4.04
372 406 5.604231 TGAGCAAGGTGAGGTGAGATAATAT 59.396 40.000 0.00 0.00 0.00 1.28
373 407 6.107901 AGCAAGGTGAGGTGAGATAATATC 57.892 41.667 0.00 0.00 0.00 1.63
534 582 1.520494 CACTGCACTGCACTTCAGAT 58.480 50.000 0.00 0.00 45.72 2.90
545 593 2.816087 GCACTTCAGATTTCTTGAGCCA 59.184 45.455 0.00 0.00 0.00 4.75
557 605 1.108727 TTGAGCCAAGTGCCCAAGTG 61.109 55.000 0.00 0.00 42.71 3.16
558 606 2.914097 AGCCAAGTGCCCAAGTGC 60.914 61.111 0.00 0.00 42.71 4.40
666 716 4.210331 AGCTGAAACCTCATGTTCAAACT 58.790 39.130 0.00 0.00 35.67 2.66
673 723 3.003689 ACCTCATGTTCAAACTCGCAAAG 59.996 43.478 0.00 0.00 0.00 2.77
674 724 3.558505 CTCATGTTCAAACTCGCAAAGG 58.441 45.455 0.00 0.00 0.00 3.11
704 754 2.507484 CACCTCATGTTCAAGCTGGAA 58.493 47.619 0.00 0.00 0.00 3.53
725 779 8.909708 TGGAATCATAATTTTCGTCACAATTC 57.090 30.769 0.00 0.00 0.00 2.17
730 784 6.806249 TCATAATTTTCGTCACAATTCCTTGC 59.194 34.615 0.00 0.00 35.69 4.01
760 814 9.942850 TTATTTTTCATCAGAGAGACATGTGTA 57.057 29.630 1.15 0.00 0.00 2.90
761 815 8.853077 ATTTTTCATCAGAGAGACATGTGTAA 57.147 30.769 1.15 0.00 0.00 2.41
762 816 7.658179 TTTTCATCAGAGAGACATGTGTAAC 57.342 36.000 1.15 0.00 37.35 2.50
763 817 5.330455 TCATCAGAGAGACATGTGTAACC 57.670 43.478 1.15 0.00 34.36 2.85
764 818 4.772100 TCATCAGAGAGACATGTGTAACCA 59.228 41.667 1.15 0.00 34.36 3.67
790 844 4.616802 CCAACAACTTCATACGTGCATTTC 59.383 41.667 0.00 0.00 0.00 2.17
830 890 1.827344 TCCTCATGCAGAGTCGAACAT 59.173 47.619 10.86 0.00 43.12 2.71
871 936 4.556942 TTTTTCTGACATGCACACTCAG 57.443 40.909 9.79 9.79 33.94 3.35
872 937 3.473923 TTTCTGACATGCACACTCAGA 57.526 42.857 13.34 13.34 38.92 3.27
873 938 3.473923 TTCTGACATGCACACTCAGAA 57.526 42.857 20.74 20.74 44.87 3.02
874 939 3.473923 TCTGACATGCACACTCAGAAA 57.526 42.857 14.49 0.00 37.97 2.52
875 940 4.011966 TCTGACATGCACACTCAGAAAT 57.988 40.909 14.49 0.00 37.97 2.17
876 941 3.749609 TCTGACATGCACACTCAGAAATG 59.250 43.478 14.49 0.00 37.97 2.32
877 942 3.479489 TGACATGCACACTCAGAAATGT 58.521 40.909 0.00 0.00 0.00 2.71
878 943 8.162578 TTCTGACATGCACACTCAGAAATGTG 62.163 42.308 21.70 9.33 44.37 3.21
879 944 3.216800 ACATGCACACTCAGAAATGTGT 58.783 40.909 13.57 2.91 46.48 3.72
880 945 4.388485 ACATGCACACTCAGAAATGTGTA 58.612 39.130 13.57 10.63 46.48 2.90
882 947 5.556355 ATGCACACTCAGAAATGTGTATG 57.444 39.130 13.99 0.00 46.31 2.39
883 948 4.640364 TGCACACTCAGAAATGTGTATGA 58.360 39.130 13.57 0.00 46.48 2.15
884 949 4.452114 TGCACACTCAGAAATGTGTATGAC 59.548 41.667 13.57 1.29 46.48 3.06
885 950 4.692625 GCACACTCAGAAATGTGTATGACT 59.307 41.667 13.57 0.00 46.48 3.41
886 951 5.163913 GCACACTCAGAAATGTGTATGACTC 60.164 44.000 13.57 0.00 46.48 3.36
887 952 5.928264 CACACTCAGAAATGTGTATGACTCA 59.072 40.000 6.38 0.00 44.43 3.41
888 953 6.592994 CACACTCAGAAATGTGTATGACTCAT 59.407 38.462 6.38 0.00 44.43 2.90
889 954 7.761249 CACACTCAGAAATGTGTATGACTCATA 59.239 37.037 6.38 0.00 44.43 2.15
890 955 8.481314 ACACTCAGAAATGTGTATGACTCATAT 58.519 33.333 2.00 0.00 44.40 1.78
891 956 8.762426 CACTCAGAAATGTGTATGACTCATATG 58.238 37.037 2.00 0.00 31.84 1.78
892 957 7.440556 ACTCAGAAATGTGTATGACTCATATGC 59.559 37.037 2.00 0.24 31.84 3.14
893 958 6.421801 TCAGAAATGTGTATGACTCATATGCG 59.578 38.462 2.00 0.00 31.84 4.73
894 959 4.997905 AATGTGTATGACTCATATGCGC 57.002 40.909 0.00 0.00 31.84 6.09
895 960 3.451141 TGTGTATGACTCATATGCGCA 57.549 42.857 14.96 14.96 0.00 6.09
896 961 3.993920 TGTGTATGACTCATATGCGCAT 58.006 40.909 28.23 28.23 0.00 4.73
897 962 4.379652 TGTGTATGACTCATATGCGCATT 58.620 39.130 30.42 10.21 0.00 3.56
898 963 4.815846 TGTGTATGACTCATATGCGCATTT 59.184 37.500 30.42 18.82 0.00 2.32
899 964 5.296531 TGTGTATGACTCATATGCGCATTTT 59.703 36.000 30.42 14.09 0.00 1.82
900 965 6.183360 TGTGTATGACTCATATGCGCATTTTT 60.183 34.615 30.42 11.32 0.00 1.94
938 1003 7.283127 ACACTCAGAAATGTGTATGACTTTGTT 59.717 33.333 0.00 0.00 44.40 2.83
945 1010 9.117145 GAAATGTGTATGACTTTGTTGTACATG 57.883 33.333 0.00 0.00 0.00 3.21
956 1021 2.939756 TGTTGTACATGCTTGTGACGTT 59.060 40.909 15.08 0.00 36.53 3.99
958 1023 3.870723 TGTACATGCTTGTGACGTTTC 57.129 42.857 15.08 0.00 36.53 2.78
959 1024 3.198872 TGTACATGCTTGTGACGTTTCA 58.801 40.909 15.08 0.00 36.53 2.69
960 1025 3.247411 TGTACATGCTTGTGACGTTTCAG 59.753 43.478 15.08 0.00 36.53 3.02
961 1026 2.560504 ACATGCTTGTGACGTTTCAGA 58.439 42.857 4.14 0.00 33.85 3.27
962 1027 2.545526 ACATGCTTGTGACGTTTCAGAG 59.454 45.455 4.14 0.00 33.85 3.35
963 1028 0.937304 TGCTTGTGACGTTTCAGAGC 59.063 50.000 0.00 5.54 40.31 4.09
1129 1201 1.375013 GCCACCCGAACGAAAGCTA 60.375 57.895 0.00 0.00 0.00 3.32
1878 1960 2.724520 AGGTGTTCCTGCTTGCTTG 58.275 52.632 0.00 0.00 43.33 4.01
1879 1961 1.006922 GGTGTTCCTGCTTGCTTGC 60.007 57.895 0.00 0.00 0.00 4.01
1880 1962 1.006922 GTGTTCCTGCTTGCTTGCC 60.007 57.895 0.00 0.00 0.00 4.52
1916 1998 1.901159 TGGCTTGCCCTACGTACTTTA 59.099 47.619 9.35 0.00 0.00 1.85
1917 1999 2.502538 TGGCTTGCCCTACGTACTTTAT 59.497 45.455 9.35 0.00 0.00 1.40
1918 2000 3.129109 GGCTTGCCCTACGTACTTTATC 58.871 50.000 0.00 0.00 0.00 1.75
1919 2001 3.431207 GGCTTGCCCTACGTACTTTATCA 60.431 47.826 0.00 0.00 0.00 2.15
1920 2002 4.377897 GCTTGCCCTACGTACTTTATCAT 58.622 43.478 0.00 0.00 0.00 2.45
1921 2003 4.814771 GCTTGCCCTACGTACTTTATCATT 59.185 41.667 0.00 0.00 0.00 2.57
1922 2004 5.296035 GCTTGCCCTACGTACTTTATCATTT 59.704 40.000 0.00 0.00 0.00 2.32
1923 2005 6.183360 GCTTGCCCTACGTACTTTATCATTTT 60.183 38.462 0.00 0.00 0.00 1.82
1997 2087 5.789643 TTTTGGTCTGGGAAGAAAGAATG 57.210 39.130 0.00 0.00 0.00 2.67
2007 2101 4.886489 GGGAAGAAAGAATGGAGAATCTGG 59.114 45.833 0.00 0.00 33.73 3.86
2107 2208 5.606505 TGTGATTGTGCTTGTCACTAGTTA 58.393 37.500 0.00 0.00 45.81 2.24
2136 2237 0.738063 TGTATTACGCCACTGCCACG 60.738 55.000 0.00 0.00 0.00 4.94
2137 2238 1.153529 TATTACGCCACTGCCACGG 60.154 57.895 0.00 0.00 0.00 4.94
2167 2268 1.662608 CCTGCTGTCTGTGACGAGT 59.337 57.895 0.00 0.00 34.95 4.18
2222 2323 2.043411 CCACTCGATTGTTGTTTTGCG 58.957 47.619 1.83 0.00 0.00 4.85
2285 2417 2.507484 CAAAGGCTCTGGTGTGATTGA 58.493 47.619 0.00 0.00 0.00 2.57
2339 2471 1.304381 ATGACCCATTTGGCGCACT 60.304 52.632 10.83 0.00 37.83 4.40
2356 2488 2.030457 GCACTGCCATCACATTACGTAC 59.970 50.000 0.00 0.00 0.00 3.67
2357 2489 2.281498 CACTGCCATCACATTACGTACG 59.719 50.000 15.01 15.01 0.00 3.67
2399 2536 2.355756 TGCTGCGGAAGAATGATTTAGC 59.644 45.455 0.00 0.00 0.00 3.09
2443 2581 1.729284 TCGTGGGTTCGCTTTTATCC 58.271 50.000 0.00 0.00 0.00 2.59
2525 2678 1.372087 GATGAAAGGCTCCGGCTGTG 61.372 60.000 0.00 0.00 38.81 3.66
2575 2728 3.777910 CCATTTGGCTGGCTGGGC 61.778 66.667 2.00 0.00 0.00 5.36
2576 2729 2.998480 CATTTGGCTGGCTGGGCA 60.998 61.111 2.00 3.59 39.99 5.36
2577 2730 2.682494 ATTTGGCTGGCTGGGCAG 60.682 61.111 17.96 17.96 42.50 4.85
2592 2745 1.748500 GCAGGAAAGAGAGCTGCCC 60.749 63.158 0.00 0.00 35.26 5.36
2593 2746 1.989620 CAGGAAAGAGAGCTGCCCT 59.010 57.895 0.00 0.00 0.00 5.19
2594 2747 0.392729 CAGGAAAGAGAGCTGCCCTG 60.393 60.000 0.00 0.00 37.84 4.45
2595 2748 1.748500 GGAAAGAGAGCTGCCCTGC 60.749 63.158 0.00 0.00 0.00 4.85
2596 2749 1.748500 GAAAGAGAGCTGCCCTGCC 60.749 63.158 0.00 0.00 0.00 4.85
2597 2750 3.279504 AAAGAGAGCTGCCCTGCCC 62.280 63.158 0.00 0.00 0.00 5.36
2598 2751 4.737476 AGAGAGCTGCCCTGCCCT 62.737 66.667 0.00 0.00 0.00 5.19
2599 2752 2.765807 GAGAGCTGCCCTGCCCTA 60.766 66.667 0.00 0.00 0.00 3.53
2600 2753 3.086600 AGAGCTGCCCTGCCCTAC 61.087 66.667 0.00 0.00 0.00 3.18
2601 2754 4.182433 GAGCTGCCCTGCCCTACC 62.182 72.222 0.00 0.00 0.00 3.18
2691 2844 3.717707 TCGCAGATATTAAGTGCTCCAC 58.282 45.455 0.00 0.00 34.92 4.02
2703 2856 5.705609 AAGTGCTCCACGTAAATTTCAAT 57.294 34.783 0.00 0.00 39.64 2.57
2704 2857 6.811253 AAGTGCTCCACGTAAATTTCAATA 57.189 33.333 0.00 0.00 39.64 1.90
2705 2858 7.391148 AAGTGCTCCACGTAAATTTCAATAT 57.609 32.000 0.00 0.00 39.64 1.28
2706 2859 8.500753 AAGTGCTCCACGTAAATTTCAATATA 57.499 30.769 0.00 0.00 39.64 0.86
2707 2860 8.677148 AGTGCTCCACGTAAATTTCAATATAT 57.323 30.769 0.00 0.00 39.64 0.86
2708 2861 9.772973 AGTGCTCCACGTAAATTTCAATATATA 57.227 29.630 0.00 0.00 39.64 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.359478 GGCCAGGTTACGGGTGTG 60.359 66.667 0.00 0.00 34.09 3.82
31 32 1.712000 AAAGGCCAGGTTACGGGTGT 61.712 55.000 5.01 0.00 34.09 4.16
89 90 4.035558 GTCATTTTCAGCCGATATTCAGCA 59.964 41.667 0.00 0.00 0.00 4.41
116 117 2.101582 GGAGACCCAGCTACATACACAG 59.898 54.545 0.00 0.00 0.00 3.66
118 119 2.108168 TGGAGACCCAGCTACATACAC 58.892 52.381 0.00 0.00 37.58 2.90
119 120 2.543037 TGGAGACCCAGCTACATACA 57.457 50.000 0.00 0.00 37.58 2.29
190 199 3.187637 CGTCCGTATGCAAAGAAAGGAAA 59.812 43.478 0.00 0.00 0.00 3.13
242 251 1.183549 TCGAGTAGCCCCTCTGAAAC 58.816 55.000 0.00 0.00 0.00 2.78
253 278 2.024176 TTCCATTGGCTTCGAGTAGC 57.976 50.000 0.20 0.20 40.48 3.58
258 283 1.543607 TTGCATTCCATTGGCTTCGA 58.456 45.000 0.00 0.00 0.00 3.71
288 313 6.223120 AGGTTTACAATTTTCTTGGTCATGC 58.777 36.000 0.00 0.00 0.00 4.06
289 314 6.582295 CGAGGTTTACAATTTTCTTGGTCATG 59.418 38.462 0.00 0.00 0.00 3.07
290 315 6.488683 TCGAGGTTTACAATTTTCTTGGTCAT 59.511 34.615 0.00 0.00 0.00 3.06
291 316 5.823570 TCGAGGTTTACAATTTTCTTGGTCA 59.176 36.000 0.00 0.00 0.00 4.02
292 317 6.204108 TCTCGAGGTTTACAATTTTCTTGGTC 59.796 38.462 13.56 0.00 0.00 4.02
293 318 6.059484 TCTCGAGGTTTACAATTTTCTTGGT 58.941 36.000 13.56 0.00 0.00 3.67
294 319 6.204882 ACTCTCGAGGTTTACAATTTTCTTGG 59.795 38.462 13.56 0.00 0.00 3.61
302 333 6.347859 AGAAGAACTCTCGAGGTTTACAAT 57.652 37.500 13.56 2.48 0.00 2.71
316 347 7.551035 AACATTGATCTGCATAGAAGAACTC 57.449 36.000 0.00 0.00 36.32 3.01
372 406 4.001652 CTCTACGGACGGCTCTATTATGA 58.998 47.826 0.00 0.00 0.00 2.15
373 407 3.127203 CCTCTACGGACGGCTCTATTATG 59.873 52.174 0.00 0.00 33.16 1.90
534 582 2.732289 GGGCACTTGGCTCAAGAAA 58.268 52.632 18.22 0.00 44.81 2.52
557 605 2.159517 CCTGAAAACCTGAATGTAGCGC 60.160 50.000 0.00 0.00 0.00 5.92
558 606 2.420022 CCCTGAAAACCTGAATGTAGCG 59.580 50.000 0.00 0.00 0.00 4.26
666 716 2.557372 GGCCGGTTTTCCTTTGCGA 61.557 57.895 1.90 0.00 37.95 5.10
673 723 1.304134 ATGAGGTGGCCGGTTTTCC 60.304 57.895 1.90 0.82 0.00 3.13
674 724 0.893727 ACATGAGGTGGCCGGTTTTC 60.894 55.000 1.90 0.00 0.00 2.29
704 754 7.489113 GCAAGGAATTGTGACGAAAATTATGAT 59.511 33.333 0.00 0.00 0.00 2.45
725 779 8.991243 TCTCTGATGAAAAATAATTTGCAAGG 57.009 30.769 0.00 0.00 37.62 3.61
760 814 4.399934 ACGTATGAAGTTGTTGGTTTGGTT 59.600 37.500 0.00 0.00 0.00 3.67
761 815 3.949113 ACGTATGAAGTTGTTGGTTTGGT 59.051 39.130 0.00 0.00 0.00 3.67
762 816 4.286910 CACGTATGAAGTTGTTGGTTTGG 58.713 43.478 0.00 0.00 0.00 3.28
763 817 3.728718 GCACGTATGAAGTTGTTGGTTTG 59.271 43.478 0.00 0.00 0.00 2.93
764 818 3.378742 TGCACGTATGAAGTTGTTGGTTT 59.621 39.130 0.00 0.00 0.00 3.27
790 844 4.755123 AGGAAAATACACTGACTTTGTCGG 59.245 41.667 5.12 5.12 43.83 4.79
871 936 5.050159 TGCGCATATGAGTCATACACATTTC 60.050 40.000 15.07 2.66 31.94 2.17
872 937 4.815846 TGCGCATATGAGTCATACACATTT 59.184 37.500 15.07 0.00 31.94 2.32
873 938 4.379652 TGCGCATATGAGTCATACACATT 58.620 39.130 15.07 0.00 31.94 2.71
874 939 3.993920 TGCGCATATGAGTCATACACAT 58.006 40.909 15.07 0.00 33.99 3.21
875 940 3.451141 TGCGCATATGAGTCATACACA 57.549 42.857 15.07 8.25 0.00 3.72
876 941 4.997905 AATGCGCATATGAGTCATACAC 57.002 40.909 25.61 9.18 0.00 2.90
877 942 6.375945 AAAAATGCGCATATGAGTCATACA 57.624 33.333 25.61 9.01 0.00 2.29
898 963 4.198530 TCTGAGTGTGCATGTCAGAAAAA 58.801 39.130 18.24 2.08 42.91 1.94
899 964 3.807553 TCTGAGTGTGCATGTCAGAAAA 58.192 40.909 18.24 2.36 42.91 2.29
900 965 3.473923 TCTGAGTGTGCATGTCAGAAA 57.526 42.857 18.24 2.92 42.91 2.52
902 967 3.473923 TTTCTGAGTGTGCATGTCAGA 57.526 42.857 17.17 17.17 43.91 3.27
903 968 3.501062 ACATTTCTGAGTGTGCATGTCAG 59.499 43.478 13.89 13.89 39.31 3.51
904 969 3.251487 CACATTTCTGAGTGTGCATGTCA 59.749 43.478 10.83 0.00 39.23 3.58
905 970 3.818387 CACATTTCTGAGTGTGCATGTC 58.182 45.455 10.83 0.00 39.23 3.06
906 971 3.909776 CACATTTCTGAGTGTGCATGT 57.090 42.857 10.83 0.00 39.23 3.21
913 978 7.194607 ACAAAGTCATACACATTTCTGAGTG 57.805 36.000 0.00 0.00 41.40 3.51
914 979 7.283127 ACAACAAAGTCATACACATTTCTGAGT 59.717 33.333 0.00 0.00 0.00 3.41
918 983 8.445275 TGTACAACAAAGTCATACACATTTCT 57.555 30.769 0.00 0.00 0.00 2.52
938 1003 3.198872 TGAAACGTCACAAGCATGTACA 58.801 40.909 0.00 0.00 37.82 2.90
945 1010 0.235926 GGCTCTGAAACGTCACAAGC 59.764 55.000 0.00 4.83 37.00 4.01
963 1028 8.463930 TTGTATATTCTTTTTATGCCCTCTGG 57.536 34.615 0.00 0.00 0.00 3.86
995 1066 1.503542 GGCTGGAGTTTCATGTGCG 59.496 57.895 0.00 0.00 0.00 5.34
1129 1201 2.678934 CATGGCTGCTGGTGGCTT 60.679 61.111 0.00 0.00 42.39 4.35
1208 1284 2.910360 CCATCGTCTGGGGCATGA 59.090 61.111 0.00 0.00 41.82 3.07
1213 1289 2.484062 GCATTGCCATCGTCTGGGG 61.484 63.158 0.00 0.00 46.06 4.96
1593 1675 4.704833 TGCAGCGCCTCCCAGAAC 62.705 66.667 2.29 0.00 0.00 3.01
1787 1869 2.006587 GATCACGTAGAGAGCGCGC 61.007 63.158 26.66 26.66 0.00 6.86
1791 1873 1.403493 CATGCGATCACGTAGAGAGC 58.597 55.000 0.00 0.00 41.98 4.09
1792 1874 1.403493 GCATGCGATCACGTAGAGAG 58.597 55.000 0.00 0.00 41.98 3.20
1793 1875 0.317020 CGCATGCGATCACGTAGAGA 60.317 55.000 35.82 0.00 42.83 3.10
1794 1876 1.870268 GCGCATGCGATCACGTAGAG 61.870 60.000 41.98 10.38 42.83 2.43
1823 1905 0.394899 GAATTAGGCAGCAGGGCACT 60.395 55.000 0.00 0.00 46.44 4.40
1878 1960 3.667282 CACCACACAGCAGCAGGC 61.667 66.667 0.00 0.00 45.30 4.85
1879 1961 2.203252 ACACCACACAGCAGCAGG 60.203 61.111 0.00 0.00 0.00 4.85
1880 1962 2.549198 CCACACCACACAGCAGCAG 61.549 63.158 0.00 0.00 0.00 4.24
1916 1998 7.015974 AGGAGAAAGGAAGCAAAAGAAAATGAT 59.984 33.333 0.00 0.00 0.00 2.45
1917 1999 6.324770 AGGAGAAAGGAAGCAAAAGAAAATGA 59.675 34.615 0.00 0.00 0.00 2.57
1918 2000 6.519382 AGGAGAAAGGAAGCAAAAGAAAATG 58.481 36.000 0.00 0.00 0.00 2.32
1919 2001 6.737720 AGGAGAAAGGAAGCAAAAGAAAAT 57.262 33.333 0.00 0.00 0.00 1.82
1920 2002 6.544928 AAGGAGAAAGGAAGCAAAAGAAAA 57.455 33.333 0.00 0.00 0.00 2.29
1921 2003 6.340522 CAAAGGAGAAAGGAAGCAAAAGAAA 58.659 36.000 0.00 0.00 0.00 2.52
1922 2004 5.682212 GCAAAGGAGAAAGGAAGCAAAAGAA 60.682 40.000 0.00 0.00 0.00 2.52
1923 2005 4.202151 GCAAAGGAGAAAGGAAGCAAAAGA 60.202 41.667 0.00 0.00 0.00 2.52
1997 2087 0.182061 TGATGCTGCCCAGATTCTCC 59.818 55.000 0.00 0.00 0.00 3.71
2007 2101 1.948145 CTTGGAATCTCTGATGCTGCC 59.052 52.381 0.00 0.00 0.00 4.85
2107 2208 6.461110 AGTGGCGTAATACACTGTAGTAAT 57.539 37.500 0.00 0.00 45.54 1.89
2137 2238 2.119655 CAGCAGGGAATGGCAGAGC 61.120 63.158 0.00 0.00 0.00 4.09
2138 2239 0.747283 GACAGCAGGGAATGGCAGAG 60.747 60.000 0.00 0.00 0.00 3.35
2139 2240 1.203441 AGACAGCAGGGAATGGCAGA 61.203 55.000 0.00 0.00 0.00 4.26
2140 2241 1.030488 CAGACAGCAGGGAATGGCAG 61.030 60.000 0.00 0.00 0.00 4.85
2141 2242 1.001764 CAGACAGCAGGGAATGGCA 60.002 57.895 0.00 0.00 0.00 4.92
2142 2243 1.001641 ACAGACAGCAGGGAATGGC 60.002 57.895 0.00 0.00 0.00 4.40
2143 2244 0.325933 TCACAGACAGCAGGGAATGG 59.674 55.000 0.00 0.00 0.00 3.16
2144 2245 1.446907 GTCACAGACAGCAGGGAATG 58.553 55.000 0.00 0.00 32.09 2.67
2145 2246 0.036952 CGTCACAGACAGCAGGGAAT 60.037 55.000 0.00 0.00 32.09 3.01
2146 2247 1.112916 TCGTCACAGACAGCAGGGAA 61.113 55.000 0.00 0.00 32.09 3.97
2167 2268 6.209361 GCACTGTGTTAGATAGATCAATCGA 58.791 40.000 9.86 0.00 0.00 3.59
2222 2323 4.407296 ACAGATAGAGGGACTTCCATTGAC 59.593 45.833 0.00 0.00 41.55 3.18
2285 2417 0.885879 TCGACAGTTACCGCAGATGT 59.114 50.000 0.00 0.00 0.00 3.06
2339 2471 2.658373 ACGTACGTAATGTGATGGCA 57.342 45.000 21.41 0.00 0.00 4.92
2568 2721 1.077858 CTCTCTTTCCTGCCCAGCC 60.078 63.158 0.00 0.00 0.00 4.85
2569 2722 1.748500 GCTCTCTTTCCTGCCCAGC 60.749 63.158 0.00 0.00 0.00 4.85
2570 2723 0.392729 CAGCTCTCTTTCCTGCCCAG 60.393 60.000 0.00 0.00 0.00 4.45
2571 2724 1.681666 CAGCTCTCTTTCCTGCCCA 59.318 57.895 0.00 0.00 0.00 5.36
2572 2725 1.748500 GCAGCTCTCTTTCCTGCCC 60.749 63.158 0.62 0.00 44.60 5.36
2573 2726 3.902318 GCAGCTCTCTTTCCTGCC 58.098 61.111 0.62 0.00 44.60 4.85
2575 2728 0.392729 CAGGGCAGCTCTCTTTCCTG 60.393 60.000 0.00 0.00 35.21 3.86
2576 2729 1.989620 CAGGGCAGCTCTCTTTCCT 59.010 57.895 0.00 0.00 0.00 3.36
2577 2730 1.748500 GCAGGGCAGCTCTCTTTCC 60.749 63.158 0.00 0.00 0.00 3.13
2592 2745 1.049289 GGTGAGGTAGGGTAGGGCAG 61.049 65.000 0.00 0.00 0.00 4.85
2593 2746 1.002533 GGTGAGGTAGGGTAGGGCA 59.997 63.158 0.00 0.00 0.00 5.36
2594 2747 1.049289 CAGGTGAGGTAGGGTAGGGC 61.049 65.000 0.00 0.00 0.00 5.19
2595 2748 0.635009 TCAGGTGAGGTAGGGTAGGG 59.365 60.000 0.00 0.00 0.00 3.53
2596 2749 1.777941 GTCAGGTGAGGTAGGGTAGG 58.222 60.000 0.00 0.00 0.00 3.18
2597 2750 1.390565 CGTCAGGTGAGGTAGGGTAG 58.609 60.000 0.00 0.00 0.00 3.18
2598 2751 0.033796 CCGTCAGGTGAGGTAGGGTA 60.034 60.000 0.00 0.00 0.00 3.69
2599 2752 1.305046 CCGTCAGGTGAGGTAGGGT 60.305 63.158 0.00 0.00 0.00 4.34
2600 2753 0.613853 TTCCGTCAGGTGAGGTAGGG 60.614 60.000 0.00 0.00 39.05 3.53
2601 2754 1.137086 CATTCCGTCAGGTGAGGTAGG 59.863 57.143 0.00 0.00 39.05 3.18
2642 2795 1.227913 CGTAAACCGTTGGGGGTGT 60.228 57.895 0.00 0.00 41.08 4.16


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

AutoCloner maintained by Alex Coulton.