Multiple sequence alignment - TraesCS6B01G297700

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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 TraesCS6B01G297700 chr6B 100.000 2962 0 0 794 3755 534247143 534244182 0.000000e+00 5470.0
1 TraesCS6B01G297700 chr6B 100.000 574 0 0 1 574 534247936 534247363 0.000000e+00 1061.0
2 TraesCS6B01G297700 chr6D 96.388 2907 91 3 849 3744 346824520 346827423 0.000000e+00 4774.0
3 TraesCS6B01G297700 chr6A 95.612 2803 99 11 944 3744 496629560 496626780 0.000000e+00 4473.0
4 TraesCS6B01G297700 chr6A 92.958 71 5 0 876 946 496629785 496629715 1.840000e-18 104.0
5 TraesCS6B01G297700 chr6A 91.304 69 6 0 876 944 496629652 496629584 1.110000e-15 95.3
6 TraesCS6B01G297700 chr7D 92.321 573 43 1 3 574 156785524 156786096 0.000000e+00 813.0
7 TraesCS6B01G297700 chr7D 91.972 573 44 2 3 574 469200575 469201146 0.000000e+00 802.0
8 TraesCS6B01G297700 chr5D 92.133 572 45 0 3 574 456097837 456097266 0.000000e+00 808.0
9 TraesCS6B01G297700 chr5D 91.459 562 48 0 4 565 502076311 502076872 0.000000e+00 773.0
10 TraesCS6B01G297700 chr5D 90.609 575 53 1 1 574 38281847 38281273 0.000000e+00 761.0
11 TraesCS6B01G297700 chr1D 91.274 573 49 1 3 574 249345855 249346427 0.000000e+00 780.0
12 TraesCS6B01G297700 chr1D 90.767 574 50 3 3 574 274258728 274259300 0.000000e+00 763.0
13 TraesCS6B01G297700 chr2B 91.115 574 49 2 3 574 545174617 545174044 0.000000e+00 776.0
14 TraesCS6B01G297700 chr4A 90.657 578 48 4 3 574 242879382 242879959 0.000000e+00 763.0


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 TraesCS6B01G297700 chr6B 534244182 534247936 3754 True 3265.500000 5470 100.000000 1 3755 2 chr6B.!!$R1 3754
1 TraesCS6B01G297700 chr6D 346824520 346827423 2903 False 4774.000000 4774 96.388000 849 3744 1 chr6D.!!$F1 2895
2 TraesCS6B01G297700 chr6A 496626780 496629785 3005 True 1557.433333 4473 93.291333 876 3744 3 chr6A.!!$R1 2868
3 TraesCS6B01G297700 chr7D 156785524 156786096 572 False 813.000000 813 92.321000 3 574 1 chr7D.!!$F1 571
4 TraesCS6B01G297700 chr7D 469200575 469201146 571 False 802.000000 802 91.972000 3 574 1 chr7D.!!$F2 571
5 TraesCS6B01G297700 chr5D 456097266 456097837 571 True 808.000000 808 92.133000 3 574 1 chr5D.!!$R2 571
6 TraesCS6B01G297700 chr5D 502076311 502076872 561 False 773.000000 773 91.459000 4 565 1 chr5D.!!$F1 561
7 TraesCS6B01G297700 chr5D 38281273 38281847 574 True 761.000000 761 90.609000 1 574 1 chr5D.!!$R1 573
8 TraesCS6B01G297700 chr1D 249345855 249346427 572 False 780.000000 780 91.274000 3 574 1 chr1D.!!$F1 571
9 TraesCS6B01G297700 chr1D 274258728 274259300 572 False 763.000000 763 90.767000 3 574 1 chr1D.!!$F2 571
10 TraesCS6B01G297700 chr2B 545174044 545174617 573 True 776.000000 776 91.115000 3 574 1 chr2B.!!$R1 571
11 TraesCS6B01G297700 chr4A 242879382 242879959 577 False 763.000000 763 90.657000 3 574 1 chr4A.!!$F1 571

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
846 854 0.393402 GGGGGCGAACGGTTAAAGAT 60.393 55.0 0.0 0.0 0.0 2.40 F
847 855 0.730840 GGGGCGAACGGTTAAAGATG 59.269 55.0 0.0 0.0 0.0 2.90 F
2213 2378 0.679960 ATGGTTAAGGTGAAGGCGGC 60.680 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2271 0.613260 AATACCGCAAGCTCTCACCA 59.387 50.0 0.00 0.0 0.00 4.17 R
2280 2445 1.197910 GAAGTACGTGTGCGGCTATC 58.802 55.0 0.00 0.0 43.45 2.08 R
3428 3594 0.173708 CCGCTAGTGGACTGGACTTC 59.826 60.0 17.96 0.0 0.00 3.01 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 81 5.730550 AGACTATCTTAAATCGTGTGCCAA 58.269 37.500 0.00 0.00 0.00 4.52
137 142 1.379977 AGGAAGGATGTCGAGCGGA 60.380 57.895 0.00 0.00 0.00 5.54
275 281 0.459489 GAGCGAGCAGGAAGAGACAT 59.541 55.000 0.00 0.00 0.00 3.06
281 287 4.245660 CGAGCAGGAAGAGACATTGTTTA 58.754 43.478 0.00 0.00 0.00 2.01
286 292 5.562890 GCAGGAAGAGACATTGTTTAACACC 60.563 44.000 0.00 0.00 0.00 4.16
301 307 8.145316 TGTTTAACACCGAACCATATTATAGC 57.855 34.615 0.00 0.00 0.00 2.97
302 308 7.042590 TGTTTAACACCGAACCATATTATAGCG 60.043 37.037 0.00 0.00 0.00 4.26
346 352 2.347490 CAGCTACCGGCAACCTGT 59.653 61.111 0.00 0.00 44.79 4.00
368 374 2.357009 GCTGCCTTCCTCAATATGTGTG 59.643 50.000 0.00 0.00 0.00 3.82
395 401 1.203038 TCCAAGACCCACATGTGCATT 60.203 47.619 20.81 8.55 0.00 3.56
398 404 3.257873 CCAAGACCCACATGTGCATTAAA 59.742 43.478 20.81 0.00 0.00 1.52
511 519 9.430623 TGTTTGAATTATGAGTCTGATTCGTTA 57.569 29.630 0.00 0.00 32.54 3.18
812 820 0.992802 GGTTGACTTCGAGACGATGC 59.007 55.000 0.00 0.00 35.23 3.91
813 821 1.402984 GGTTGACTTCGAGACGATGCT 60.403 52.381 0.00 0.00 35.23 3.79
814 822 2.159421 GGTTGACTTCGAGACGATGCTA 60.159 50.000 0.00 0.00 35.23 3.49
815 823 3.489398 GGTTGACTTCGAGACGATGCTAT 60.489 47.826 0.00 0.00 35.23 2.97
816 824 4.106197 GTTGACTTCGAGACGATGCTATT 58.894 43.478 0.00 0.00 35.23 1.73
817 825 4.371855 TGACTTCGAGACGATGCTATTT 57.628 40.909 0.00 0.00 35.23 1.40
818 826 4.744570 TGACTTCGAGACGATGCTATTTT 58.255 39.130 0.00 0.00 35.23 1.82
819 827 5.886992 TGACTTCGAGACGATGCTATTTTA 58.113 37.500 0.00 0.00 35.23 1.52
820 828 6.327154 TGACTTCGAGACGATGCTATTTTAA 58.673 36.000 0.00 0.00 35.23 1.52
821 829 6.978659 TGACTTCGAGACGATGCTATTTTAAT 59.021 34.615 0.00 0.00 35.23 1.40
822 830 7.491372 TGACTTCGAGACGATGCTATTTTAATT 59.509 33.333 0.00 0.00 35.23 1.40
823 831 8.197988 ACTTCGAGACGATGCTATTTTAATTT 57.802 30.769 0.00 0.00 35.23 1.82
824 832 8.328864 ACTTCGAGACGATGCTATTTTAATTTC 58.671 33.333 0.00 0.00 35.23 2.17
825 833 6.863230 TCGAGACGATGCTATTTTAATTTCG 58.137 36.000 0.00 0.00 0.00 3.46
826 834 6.474427 TCGAGACGATGCTATTTTAATTTCGT 59.526 34.615 0.00 0.00 40.62 3.85
827 835 6.566427 CGAGACGATGCTATTTTAATTTCGTG 59.434 38.462 1.15 0.00 38.34 4.35
828 836 6.715464 AGACGATGCTATTTTAATTTCGTGG 58.285 36.000 1.15 0.00 38.34 4.94
829 837 5.816919 ACGATGCTATTTTAATTTCGTGGG 58.183 37.500 0.00 0.00 37.02 4.61
830 838 5.212194 CGATGCTATTTTAATTTCGTGGGG 58.788 41.667 0.00 0.00 0.00 4.96
831 839 4.993029 TGCTATTTTAATTTCGTGGGGG 57.007 40.909 0.00 0.00 0.00 5.40
832 840 3.131400 TGCTATTTTAATTTCGTGGGGGC 59.869 43.478 0.00 0.00 0.00 5.80
833 841 2.951457 ATTTTAATTTCGTGGGGGCG 57.049 45.000 0.00 0.00 0.00 6.13
834 842 1.906990 TTTTAATTTCGTGGGGGCGA 58.093 45.000 0.00 0.00 39.28 5.54
841 849 4.376176 CGTGGGGGCGAACGGTTA 62.376 66.667 0.00 0.00 36.17 2.85
842 850 2.032376 GTGGGGGCGAACGGTTAA 59.968 61.111 0.00 0.00 0.00 2.01
843 851 1.600356 GTGGGGGCGAACGGTTAAA 60.600 57.895 0.00 0.00 0.00 1.52
844 852 1.302671 TGGGGGCGAACGGTTAAAG 60.303 57.895 0.00 0.00 0.00 1.85
845 853 1.003476 GGGGGCGAACGGTTAAAGA 60.003 57.895 0.00 0.00 0.00 2.52
846 854 0.393402 GGGGGCGAACGGTTAAAGAT 60.393 55.000 0.00 0.00 0.00 2.40
847 855 0.730840 GGGGCGAACGGTTAAAGATG 59.269 55.000 0.00 0.00 0.00 2.90
850 858 1.062148 GGCGAACGGTTAAAGATGCTC 59.938 52.381 0.00 0.00 0.00 4.26
861 869 7.604927 ACGGTTAAAGATGCTCTAAACATTACA 59.395 33.333 0.00 0.00 29.21 2.41
873 881 4.513198 AAACATTACAATGGACCGGTTG 57.487 40.909 9.42 5.29 40.70 3.77
900 908 6.260714 GTGCAATTTGAAAGGGAAAAACTGAT 59.739 34.615 0.00 0.00 0.00 2.90
1048 1213 3.127533 GCACCGTCATGCCACTCC 61.128 66.667 0.00 0.00 39.86 3.85
1533 1698 4.292178 CTCATCTCCGCCCGCCTC 62.292 72.222 0.00 0.00 0.00 4.70
1658 1823 4.019860 CCCCCTTGTCGATGATCTTATGAT 60.020 45.833 0.00 0.00 35.26 2.45
1983 2148 1.637553 AGAGTTGGGTTGGCAGATGAT 59.362 47.619 0.00 0.00 0.00 2.45
1989 2154 1.673168 GGTTGGCAGATGATGAGGTC 58.327 55.000 0.00 0.00 0.00 3.85
2006 2171 1.080093 TCGATGTGGCGGTGAAGAC 60.080 57.895 0.00 0.00 0.00 3.01
2075 2240 1.228094 TGCGTGCAATGGGACTGAA 60.228 52.632 0.00 0.00 32.44 3.02
2082 2247 2.292267 GCAATGGGACTGAATCATCGT 58.708 47.619 0.00 0.00 0.00 3.73
2106 2271 2.307098 CCTGGAGAAGATTTCTGGTGGT 59.693 50.000 0.00 0.00 40.87 4.16
2142 2307 5.558273 GCGGTATTTATCACCAGATTTCGTG 60.558 44.000 0.00 0.00 35.67 4.35
2152 2317 3.517901 ACCAGATTTCGTGTTGGAGGATA 59.482 43.478 0.00 0.00 34.76 2.59
2210 2375 3.421844 ACAGAATGGTTAAGGTGAAGGC 58.578 45.455 0.00 0.00 43.62 4.35
2213 2378 0.679960 ATGGTTAAGGTGAAGGCGGC 60.680 55.000 0.00 0.00 0.00 6.53
2280 2445 3.129287 GCATTGGGTATGGTGAGAACAAG 59.871 47.826 0.00 0.00 34.66 3.16
2282 2447 4.927267 TTGGGTATGGTGAGAACAAGAT 57.073 40.909 0.00 0.00 0.00 2.40
2284 2449 5.614324 TGGGTATGGTGAGAACAAGATAG 57.386 43.478 0.00 0.00 0.00 2.08
2293 2458 0.370273 GAACAAGATAGCCGCACACG 59.630 55.000 0.00 0.00 39.67 4.49
2445 2610 6.349611 GCAAGGAGATGCTCAATGAAAAGTTA 60.350 38.462 0.00 0.00 43.06 2.24
2578 2743 3.440522 GTGGCTCCAAAGTTATGGTCTTC 59.559 47.826 0.00 0.00 41.46 2.87
2636 2801 6.652900 GCTAACTCAGAGAAGAGGTTCATTTT 59.347 38.462 3.79 0.00 39.97 1.82
2847 3012 1.628846 TGCTTTCCCTCAGAAGGTACC 59.371 52.381 2.73 2.73 41.59 3.34
3207 3372 2.554032 GTGGATGATATTTTCCGGGCTG 59.446 50.000 0.00 0.00 34.58 4.85
3239 3404 3.452264 CCATGGTATCTTCTCTGGTGACA 59.548 47.826 2.57 0.00 39.59 3.58
3399 3565 1.198713 GGTGCTCCCTCTGATCTGAA 58.801 55.000 3.72 0.00 0.00 3.02
3437 3603 4.667573 TCTGTGTGAGATAGAAGTCCAGT 58.332 43.478 0.00 0.00 0.00 4.00
3442 3608 4.020543 GTGAGATAGAAGTCCAGTCCACT 58.979 47.826 0.00 0.00 0.00 4.00
3445 3611 4.211920 AGATAGAAGTCCAGTCCACTAGC 58.788 47.826 0.00 0.00 0.00 3.42
3483 3649 4.048470 GCTCGGGCCCCTCCTTTT 62.048 66.667 18.66 0.00 34.39 2.27
3529 3695 2.573462 CCACCATTCTTCTCCTCCTTCA 59.427 50.000 0.00 0.00 0.00 3.02
3548 3714 1.294426 ATCCTCTCCCCGTGGTAGGA 61.294 60.000 11.75 11.75 43.98 2.94
3550 3716 1.000019 CTCTCCCCGTGGTAGGACA 60.000 63.158 0.00 0.00 0.00 4.02
3588 3754 2.043450 CTCCGCTCCTCCCTGTCT 60.043 66.667 0.00 0.00 0.00 3.41
3594 3760 0.902516 GCTCCTCCCTGTCTGTCAGT 60.903 60.000 0.00 0.00 42.19 3.41
3744 3910 7.389053 AGAAAGCCATTGTAGAAGAGTTAAGTG 59.611 37.037 0.00 0.00 0.00 3.16
3745 3911 5.491982 AGCCATTGTAGAAGAGTTAAGTGG 58.508 41.667 0.00 0.00 0.00 4.00
3746 3912 5.013183 AGCCATTGTAGAAGAGTTAAGTGGT 59.987 40.000 0.00 0.00 0.00 4.16
3747 3913 6.212791 AGCCATTGTAGAAGAGTTAAGTGGTA 59.787 38.462 0.00 0.00 0.00 3.25
3748 3914 6.877322 GCCATTGTAGAAGAGTTAAGTGGTAA 59.123 38.462 0.00 0.00 0.00 2.85
3749 3915 7.553044 GCCATTGTAGAAGAGTTAAGTGGTAAT 59.447 37.037 0.00 0.00 0.00 1.89
3750 3916 9.449719 CCATTGTAGAAGAGTTAAGTGGTAATT 57.550 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.380339 CGGATAGATGTCATCTGCTAGGTG 60.380 50.000 23.17 5.08 40.51 4.00
77 81 3.558109 GCAAAGTAGGAGTTCTTGCCTCT 60.558 47.826 0.00 0.00 35.73 3.69
275 281 8.614346 GCTATAATATGGTTCGGTGTTAAACAA 58.386 33.333 0.00 0.00 0.00 2.83
281 287 5.204409 TCGCTATAATATGGTTCGGTGTT 57.796 39.130 0.00 0.00 0.00 3.32
286 292 4.421948 GACCCTCGCTATAATATGGTTCG 58.578 47.826 0.00 0.00 0.00 3.95
346 352 2.025981 ACACATATTGAGGAAGGCAGCA 60.026 45.455 0.00 0.00 0.00 4.41
368 374 1.573108 TGTGGGTCTTGGATCTCCTC 58.427 55.000 0.00 0.00 36.82 3.71
395 401 4.081406 ACCAGATCATGCTGCAGTTTTTA 58.919 39.130 16.64 0.00 34.56 1.52
398 404 1.816835 CACCAGATCATGCTGCAGTTT 59.183 47.619 16.64 0.00 34.56 2.66
522 530 5.295292 AGTTCATCGCAGAAATCAATACAGG 59.705 40.000 0.00 0.00 43.58 4.00
523 531 6.355397 AGTTCATCGCAGAAATCAATACAG 57.645 37.500 0.00 0.00 43.58 2.74
793 801 0.992802 GCATCGTCTCGAAGTCAACC 59.007 55.000 0.00 0.00 39.99 3.77
794 802 1.983972 AGCATCGTCTCGAAGTCAAC 58.016 50.000 0.00 0.00 39.99 3.18
795 803 4.371855 AATAGCATCGTCTCGAAGTCAA 57.628 40.909 0.00 0.00 39.99 3.18
796 804 4.371855 AAATAGCATCGTCTCGAAGTCA 57.628 40.909 0.00 0.00 39.99 3.41
797 805 6.807708 TTAAAATAGCATCGTCTCGAAGTC 57.192 37.500 0.00 0.00 39.99 3.01
798 806 7.772332 AATTAAAATAGCATCGTCTCGAAGT 57.228 32.000 0.00 0.00 39.99 3.01
799 807 7.524201 CGAAATTAAAATAGCATCGTCTCGAAG 59.476 37.037 0.00 0.00 39.99 3.79
800 808 7.009815 ACGAAATTAAAATAGCATCGTCTCGAA 59.990 33.333 0.00 0.00 39.99 3.71
801 809 6.474427 ACGAAATTAAAATAGCATCGTCTCGA 59.526 34.615 0.00 0.00 37.48 4.04
802 810 6.566427 CACGAAATTAAAATAGCATCGTCTCG 59.434 38.462 0.00 0.00 39.72 4.04
803 811 6.846283 CCACGAAATTAAAATAGCATCGTCTC 59.154 38.462 0.00 0.00 39.72 3.36
804 812 6.238374 CCCACGAAATTAAAATAGCATCGTCT 60.238 38.462 0.00 0.00 39.72 4.18
805 813 5.907391 CCCACGAAATTAAAATAGCATCGTC 59.093 40.000 0.00 0.00 39.72 4.20
806 814 5.220970 CCCCACGAAATTAAAATAGCATCGT 60.221 40.000 0.00 0.00 42.10 3.73
807 815 5.212194 CCCCACGAAATTAAAATAGCATCG 58.788 41.667 0.00 0.00 35.16 3.84
808 816 5.528870 CCCCCACGAAATTAAAATAGCATC 58.471 41.667 0.00 0.00 0.00 3.91
809 817 4.202212 GCCCCCACGAAATTAAAATAGCAT 60.202 41.667 0.00 0.00 0.00 3.79
810 818 3.131400 GCCCCCACGAAATTAAAATAGCA 59.869 43.478 0.00 0.00 0.00 3.49
811 819 3.713288 GCCCCCACGAAATTAAAATAGC 58.287 45.455 0.00 0.00 0.00 2.97
812 820 3.628487 TCGCCCCCACGAAATTAAAATAG 59.372 43.478 0.00 0.00 39.54 1.73
813 821 3.618351 TCGCCCCCACGAAATTAAAATA 58.382 40.909 0.00 0.00 39.54 1.40
814 822 2.448453 TCGCCCCCACGAAATTAAAAT 58.552 42.857 0.00 0.00 39.54 1.82
815 823 1.906990 TCGCCCCCACGAAATTAAAA 58.093 45.000 0.00 0.00 39.54 1.52
816 824 3.646787 TCGCCCCCACGAAATTAAA 57.353 47.368 0.00 0.00 39.54 1.52
824 832 3.880162 TTAACCGTTCGCCCCCACG 62.880 63.158 0.00 0.00 36.12 4.94
825 833 1.579964 CTTTAACCGTTCGCCCCCAC 61.580 60.000 0.00 0.00 0.00 4.61
826 834 1.302671 CTTTAACCGTTCGCCCCCA 60.303 57.895 0.00 0.00 0.00 4.96
827 835 0.393402 ATCTTTAACCGTTCGCCCCC 60.393 55.000 0.00 0.00 0.00 5.40
828 836 0.730840 CATCTTTAACCGTTCGCCCC 59.269 55.000 0.00 0.00 0.00 5.80
829 837 0.098200 GCATCTTTAACCGTTCGCCC 59.902 55.000 0.00 0.00 0.00 6.13
830 838 1.062148 GAGCATCTTTAACCGTTCGCC 59.938 52.381 0.00 0.00 0.00 5.54
831 839 2.437308 GAGCATCTTTAACCGTTCGC 57.563 50.000 0.00 0.00 0.00 4.70
840 848 9.679661 TCCATTGTAATGTTTAGAGCATCTTTA 57.320 29.630 4.12 0.00 39.69 1.85
841 849 8.462016 GTCCATTGTAATGTTTAGAGCATCTTT 58.538 33.333 4.12 0.00 39.69 2.52
842 850 7.067494 GGTCCATTGTAATGTTTAGAGCATCTT 59.933 37.037 4.12 0.00 39.69 2.40
843 851 6.543831 GGTCCATTGTAATGTTTAGAGCATCT 59.456 38.462 4.12 0.00 41.19 2.90
844 852 6.511767 CGGTCCATTGTAATGTTTAGAGCATC 60.512 42.308 4.12 0.00 34.60 3.91
845 853 5.296780 CGGTCCATTGTAATGTTTAGAGCAT 59.703 40.000 4.12 0.00 34.60 3.79
846 854 4.634004 CGGTCCATTGTAATGTTTAGAGCA 59.366 41.667 4.12 0.00 34.60 4.26
847 855 4.035208 CCGGTCCATTGTAATGTTTAGAGC 59.965 45.833 0.00 3.28 34.60 4.09
850 858 5.392595 CCAACCGGTCCATTGTAATGTTTAG 60.393 44.000 8.04 0.00 34.60 1.85
861 869 2.282887 GCACCCAACCGGTCCATT 60.283 61.111 8.04 0.00 43.58 3.16
863 871 2.648613 AATTGCACCCAACCGGTCCA 62.649 55.000 8.04 0.00 43.58 4.02
873 881 3.483808 TTTCCCTTTCAAATTGCACCC 57.516 42.857 0.00 0.00 0.00 4.61
967 1132 1.536418 CAGGGCCAGGGGATATCGA 60.536 63.158 6.18 0.00 0.00 3.59
1033 1198 1.898154 GTAGGAGTGGCATGACGGT 59.102 57.895 0.00 0.00 0.00 4.83
1377 1542 1.032794 TGAGATCGGAATCGGTGGAG 58.967 55.000 0.00 0.00 36.97 3.86
1533 1698 2.202623 CTTTCCTCGAGGGCGACG 60.203 66.667 30.80 11.41 42.51 5.12
1658 1823 0.986019 ACCCAATCCTCCATACGCCA 60.986 55.000 0.00 0.00 0.00 5.69
1887 2052 3.274288 CCCAGGATTGCTCAGTAAGAAC 58.726 50.000 0.00 0.00 0.00 3.01
1983 2148 2.994995 ACCGCCACATCGACCTCA 60.995 61.111 0.00 0.00 0.00 3.86
1989 2154 2.444624 CGTCTTCACCGCCACATCG 61.445 63.158 0.00 0.00 0.00 3.84
2006 2171 2.395360 CCAACCACATACGGGTGCG 61.395 63.158 0.00 0.00 42.91 5.34
2075 2240 5.365021 AATCTTCTCCAGGAAACGATGAT 57.635 39.130 0.00 0.00 33.07 2.45
2082 2247 4.507335 CCACCAGAAATCTTCTCCAGGAAA 60.507 45.833 0.00 0.00 38.11 3.13
2106 2271 0.613260 AATACCGCAAGCTCTCACCA 59.387 50.000 0.00 0.00 0.00 4.17
2142 2307 9.256228 TCCATATCATAACTAGTATCCTCCAAC 57.744 37.037 0.00 0.00 0.00 3.77
2152 2317 6.864421 TCTCCACCTCCATATCATAACTAGT 58.136 40.000 0.00 0.00 0.00 2.57
2210 2375 2.023741 GCTGTGCATTCATCGCCG 59.976 61.111 0.00 0.00 0.00 6.46
2280 2445 1.197910 GAAGTACGTGTGCGGCTATC 58.802 55.000 0.00 0.00 43.45 2.08
2282 2447 1.213537 GGAAGTACGTGTGCGGCTA 59.786 57.895 0.00 0.00 43.45 3.93
2284 2449 2.048503 AGGAAGTACGTGTGCGGC 60.049 61.111 0.00 0.00 43.45 6.53
2418 2583 1.562942 TCATTGAGCATCTCCTTGCCT 59.437 47.619 0.00 0.00 43.83 4.75
2445 2610 4.163078 CCCAGATCCAGAGTCATGTAGTTT 59.837 45.833 0.00 0.00 0.00 2.66
2578 2743 3.381590 GCAGGGGCTAATGGTCTTTTAAG 59.618 47.826 0.00 0.00 36.96 1.85
2636 2801 5.614308 CAGGATGCATATTGTAGAGGTTGA 58.386 41.667 0.00 0.00 0.00 3.18
2733 2898 9.170734 GCTAATTATTCATTATCTGGATGCTGA 57.829 33.333 0.00 0.00 0.00 4.26
2771 2936 2.289002 CGGCTCTGATAATCTTGCCAAC 59.711 50.000 0.00 0.00 40.27 3.77
2778 2943 2.390225 ACCTCCGGCTCTGATAATCT 57.610 50.000 0.00 0.00 0.00 2.40
3115 3280 5.951747 TGATATGAGGATGATGGTACGATCA 59.048 40.000 20.92 20.92 36.78 2.92
3184 3349 2.814336 GCCCGGAAAATATCATCCACTC 59.186 50.000 0.73 0.00 35.34 3.51
3207 3372 4.040217 AGAAGATACCATGGCTGAGTGATC 59.960 45.833 13.04 3.78 0.00 2.92
3415 3581 4.667573 ACTGGACTTCTATCTCACACAGA 58.332 43.478 0.00 0.00 34.78 3.41
3428 3594 0.173708 CCGCTAGTGGACTGGACTTC 59.826 60.000 17.96 0.00 0.00 3.01
3483 3649 1.514678 AAGCAATGGAAACGAGCGCA 61.515 50.000 11.47 0.00 0.00 6.09
3529 3695 1.233369 CCTACCACGGGGAGAGGAT 59.767 63.158 20.86 0.00 40.93 3.24
3588 3754 0.598562 GCTCAAGACGGAGACTGACA 59.401 55.000 0.00 0.00 37.05 3.58
3594 3760 2.650116 GCCCTGCTCAAGACGGAGA 61.650 63.158 0.00 0.00 37.05 3.71


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

AutoCloner maintained by Alex Coulton.