Multiple sequence alignment - TraesCS6D01G301000

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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 TraesCS6D01G301000 chr6D 100.000 2644 0 0 1 2644 410405626 410408269 0.000000e+00 4883
1 TraesCS6D01G301000 chr6B 89.564 2731 136 62 1 2644 617183806 617186474 0.000000e+00 3326
2 TraesCS6D01G301000 chr6A 88.439 2396 112 74 13 2335 555736524 555738827 0.000000e+00 2737
3 TraesCS6D01G301000 chr6A 90.612 245 14 3 2320 2563 555738973 555739209 1.530000e-82 316


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 TraesCS6D01G301000 chr6D 410405626 410408269 2643 False 4883.0 4883 100.0000 1 2644 1 chr6D.!!$F1 2643
1 TraesCS6D01G301000 chr6B 617183806 617186474 2668 False 3326.0 3326 89.5640 1 2644 1 chr6B.!!$F1 2643
2 TraesCS6D01G301000 chr6A 555736524 555739209 2685 False 1526.5 2737 89.5255 13 2563 2 chr6A.!!$F1 2550

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
698 734 0.099436 GCGCTGATCCATTGTTCACC 59.901 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2317 0.179119 GAAGGAAGCATGCATGTGGC 60.179 55.0 26.79 13.7 45.13 5.01 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
206 217 2.427753 GTCCATGCCCTCCGATCC 59.572 66.667 0.00 0.00 0.00 3.36
208 219 3.550431 CCATGCCCTCCGATCCGT 61.550 66.667 0.00 0.00 0.00 4.69
244 255 2.564504 TCTATCCTCCCAAGATCGCATG 59.435 50.000 0.00 0.00 0.00 4.06
247 258 1.895707 CTCCCAAGATCGCATGGCC 60.896 63.158 0.00 0.00 35.28 5.36
291 302 2.124403 GGGCCTGGAGCTGACATG 60.124 66.667 0.84 0.00 43.05 3.21
292 303 2.124403 GGCCTGGAGCTGACATGG 60.124 66.667 0.00 0.00 43.05 3.66
293 304 2.673200 GGCCTGGAGCTGACATGGA 61.673 63.158 0.00 0.00 43.05 3.41
294 305 1.300963 GCCTGGAGCTGACATGGAA 59.699 57.895 0.00 0.00 38.99 3.53
295 306 0.322816 GCCTGGAGCTGACATGGAAA 60.323 55.000 0.00 0.00 38.99 3.13
296 307 1.887956 GCCTGGAGCTGACATGGAAAA 60.888 52.381 0.00 0.00 38.99 2.29
302 313 4.037923 TGGAGCTGACATGGAAAAAGAAAC 59.962 41.667 0.00 0.00 0.00 2.78
316 333 7.042389 TGGAAAAAGAAACACAAAACAACAGTC 60.042 33.333 0.00 0.00 0.00 3.51
380 397 1.069022 GTTGTACAGTGGCATGCAGTG 60.069 52.381 21.36 19.19 0.00 3.66
457 478 2.296073 ACTCGAGAGTCAAGTTCCCT 57.704 50.000 21.68 0.00 36.92 4.20
465 486 3.456277 AGAGTCAAGTTCCCTGTTTCAGT 59.544 43.478 0.00 0.00 0.00 3.41
466 487 4.080299 AGAGTCAAGTTCCCTGTTTCAGTT 60.080 41.667 0.00 0.00 0.00 3.16
573 598 0.179234 CCCACATGCCCACATACGTA 59.821 55.000 0.00 0.00 33.67 3.57
594 619 2.422276 GGCCATGCCGACATTATTTC 57.578 50.000 0.00 0.00 39.62 2.17
676 712 7.336161 AGCTACTAGTACTGTATTTCACCTG 57.664 40.000 5.39 0.00 0.00 4.00
678 714 8.051535 AGCTACTAGTACTGTATTTCACCTGTA 58.948 37.037 5.39 0.00 0.00 2.74
697 733 1.089920 AGCGCTGATCCATTGTTCAC 58.910 50.000 10.39 0.00 0.00 3.18
698 734 0.099436 GCGCTGATCCATTGTTCACC 59.901 55.000 0.00 0.00 0.00 4.02
699 735 0.734889 CGCTGATCCATTGTTCACCC 59.265 55.000 0.00 0.00 0.00 4.61
700 736 1.679944 CGCTGATCCATTGTTCACCCT 60.680 52.381 0.00 0.00 0.00 4.34
701 737 2.450476 GCTGATCCATTGTTCACCCTT 58.550 47.619 0.00 0.00 0.00 3.95
702 738 2.424956 GCTGATCCATTGTTCACCCTTC 59.575 50.000 0.00 0.00 0.00 3.46
703 739 3.689347 CTGATCCATTGTTCACCCTTCA 58.311 45.455 0.00 0.00 0.00 3.02
746 782 2.696989 TGCATCTCAATCATCACCGT 57.303 45.000 0.00 0.00 0.00 4.83
747 783 2.989909 TGCATCTCAATCATCACCGTT 58.010 42.857 0.00 0.00 0.00 4.44
748 784 3.346315 TGCATCTCAATCATCACCGTTT 58.654 40.909 0.00 0.00 0.00 3.60
749 785 4.512484 TGCATCTCAATCATCACCGTTTA 58.488 39.130 0.00 0.00 0.00 2.01
750 786 4.571984 TGCATCTCAATCATCACCGTTTAG 59.428 41.667 0.00 0.00 0.00 1.85
751 787 4.553547 GCATCTCAATCATCACCGTTTAGC 60.554 45.833 0.00 0.00 0.00 3.09
752 788 3.186909 TCTCAATCATCACCGTTTAGCG 58.813 45.455 0.00 0.00 40.95 4.26
783 819 0.249405 CGGTGCCAAACAATTGCAGT 60.249 50.000 5.05 0.00 35.10 4.40
802 842 2.162681 GTGCACATCTACCCAAAGCTT 58.837 47.619 13.17 0.00 0.00 3.74
821 862 3.424105 ATCCCAAGCAGCTCCCCC 61.424 66.667 0.00 0.00 0.00 5.40
824 865 3.013932 CCAAGCAGCTCCCCCTCT 61.014 66.667 0.00 0.00 0.00 3.69
838 889 4.325719 TCCCCCTCTTCTCCTCTCTATAA 58.674 47.826 0.00 0.00 0.00 0.98
868 919 0.625849 AATCCACCATCACCTCCACC 59.374 55.000 0.00 0.00 0.00 4.61
870 921 1.925455 CCACCATCACCTCCACCCT 60.925 63.158 0.00 0.00 0.00 4.34
875 926 0.251354 CATCACCTCCACCCTCAGTG 59.749 60.000 0.00 0.00 46.83 3.66
923 994 2.203153 ACACGCCAAGACCACCAC 60.203 61.111 0.00 0.00 0.00 4.16
942 1013 1.684450 ACCACCACCTTTTAAAAGCCG 59.316 47.619 20.45 13.36 34.69 5.52
944 1015 1.067821 CACCACCTTTTAAAAGCCGCA 59.932 47.619 20.45 0.00 34.69 5.69
946 1017 1.604438 CCACCTTTTAAAAGCCGCACC 60.604 52.381 20.45 0.00 34.69 5.01
947 1018 0.312729 ACCTTTTAAAAGCCGCACCG 59.687 50.000 20.45 8.99 34.69 4.94
972 1050 2.049433 CACCCAGTCCACGACGAC 60.049 66.667 0.00 0.00 37.67 4.34
978 1056 4.773117 GTCCACGACGACCGAGCC 62.773 72.222 0.00 0.00 41.76 4.70
980 1058 3.129502 CCACGACGACCGAGCCTA 61.130 66.667 0.00 0.00 41.76 3.93
981 1059 2.099831 CACGACGACCGAGCCTAC 59.900 66.667 0.00 0.00 41.76 3.18
982 1060 2.046507 ACGACGACCGAGCCTACT 60.047 61.111 0.00 0.00 41.76 2.57
983 1061 2.396955 ACGACGACCGAGCCTACTG 61.397 63.158 0.00 0.00 41.76 2.74
984 1062 2.104859 CGACGACCGAGCCTACTGA 61.105 63.158 0.00 0.00 41.76 3.41
985 1063 1.437772 CGACGACCGAGCCTACTGAT 61.438 60.000 0.00 0.00 41.76 2.90
986 1064 0.308376 GACGACCGAGCCTACTGATC 59.692 60.000 0.00 0.00 0.00 2.92
987 1065 1.102222 ACGACCGAGCCTACTGATCC 61.102 60.000 0.00 0.00 0.00 3.36
988 1066 1.101635 CGACCGAGCCTACTGATCCA 61.102 60.000 0.00 0.00 0.00 3.41
989 1067 0.671251 GACCGAGCCTACTGATCCAG 59.329 60.000 0.00 0.00 37.52 3.86
990 1068 1.365633 CCGAGCCTACTGATCCAGC 59.634 63.158 0.00 0.00 34.37 4.85
991 1069 1.007964 CGAGCCTACTGATCCAGCG 60.008 63.158 0.00 0.00 34.37 5.18
992 1070 1.300542 GAGCCTACTGATCCAGCGC 60.301 63.158 0.00 0.00 34.37 5.92
993 1071 2.659897 GCCTACTGATCCAGCGCG 60.660 66.667 0.00 0.00 34.37 6.86
994 1072 2.659897 CCTACTGATCCAGCGCGC 60.660 66.667 26.66 26.66 34.37 6.86
995 1073 3.026879 CTACTGATCCAGCGCGCG 61.027 66.667 28.44 28.44 34.37 6.86
996 1074 3.469754 CTACTGATCCAGCGCGCGA 62.470 63.158 37.18 18.77 34.37 5.87
997 1075 3.469754 TACTGATCCAGCGCGCGAG 62.470 63.158 37.18 24.56 34.37 5.03
1011 1089 4.289379 CGAGCGATGGCATGCGTG 62.289 66.667 12.44 0.09 43.41 5.34
1527 1609 4.469586 TCCATGTAGTATCTTTGCAGTCCA 59.530 41.667 0.00 0.00 0.00 4.02
1537 1619 0.036164 TTGCAGTCCACGTTAGCCAT 59.964 50.000 0.00 0.00 0.00 4.40
1566 1660 9.537192 ACAGCATAGTAGTACGCAATTAATTAA 57.463 29.630 0.00 0.00 0.00 1.40
1743 1842 1.135257 CGGTCTTCTCTCATCGTGCTT 60.135 52.381 0.00 0.00 0.00 3.91
1747 1846 1.916651 CTTCTCTCATCGTGCTTGTCG 59.083 52.381 0.00 0.00 0.00 4.35
1748 1847 1.165270 TCTCTCATCGTGCTTGTCGA 58.835 50.000 0.00 0.00 41.45 4.20
1750 1849 2.115595 CTCTCATCGTGCTTGTCGATC 58.884 52.381 0.00 0.00 44.49 3.69
1751 1850 0.842613 CTCATCGTGCTTGTCGATCG 59.157 55.000 9.36 9.36 44.49 3.69
1752 1851 0.170339 TCATCGTGCTTGTCGATCGT 59.830 50.000 15.94 0.00 44.49 3.73
1753 1852 1.399089 TCATCGTGCTTGTCGATCGTA 59.601 47.619 15.94 2.69 44.49 3.43
1943 2092 1.573108 TCCCCATCACCTCACTTCTC 58.427 55.000 0.00 0.00 0.00 2.87
2186 2335 1.895238 GCCACATGCATGCTTCCTT 59.105 52.632 26.53 2.71 40.77 3.36
2193 2342 0.986527 TGCATGCTTCCTTCTCCTCA 59.013 50.000 20.33 0.00 0.00 3.86
2201 2350 3.556999 CTTCCTTCTCCTCATCCGTCTA 58.443 50.000 0.00 0.00 0.00 2.59
2291 2440 4.300743 GATCGAGCGAGCGAGCGA 62.301 66.667 11.47 11.47 44.26 4.93
2292 2441 4.306471 ATCGAGCGAGCGAGCGAG 62.306 66.667 13.62 0.41 44.26 5.03
2294 2443 4.936248 CGAGCGAGCGAGCGAGAG 62.936 72.222 1.41 0.00 43.00 3.20
2335 2653 0.326264 GGGAACATGTCCTCTGCACT 59.674 55.000 0.00 0.00 46.92 4.40
2382 2700 4.152045 CGGCTAGATCGGTGTTAGTAGTAG 59.848 50.000 0.00 0.00 0.00 2.57
2463 2788 4.578105 GCAGGAGAAAATCAATAGTGGGAG 59.422 45.833 0.00 0.00 0.00 4.30
2464 2789 5.749462 CAGGAGAAAATCAATAGTGGGAGT 58.251 41.667 0.00 0.00 0.00 3.85
2538 2864 2.660064 CCGTAGGCTGCCAGAAGGT 61.660 63.158 22.65 0.61 46.14 3.50
2579 2905 8.708378 TGTATAAGATGATAATGGGATAGGCAG 58.292 37.037 0.00 0.00 0.00 4.85
2602 2928 2.456000 CACAAGGTCCGTGGAATCG 58.544 57.895 9.75 0.00 0.00 3.34
2607 2933 0.178068 AGGTCCGTGGAATCGATTGG 59.822 55.000 16.96 10.62 0.00 3.16
2619 2945 1.210931 CGATTGGTGGCAGCACTTG 59.789 57.895 20.46 14.30 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 217 2.225068 AGATCGCAAGTCCCAATACG 57.775 50.000 0.00 0.00 39.48 3.06
208 219 4.160329 AGGATAGATCGCAAGTCCCAATA 58.840 43.478 0.00 0.00 39.48 1.90
291 302 7.184800 ACTGTTGTTTTGTGTTTCTTTTTCC 57.815 32.000 0.00 0.00 0.00 3.13
292 303 7.287950 GGACTGTTGTTTTGTGTTTCTTTTTC 58.712 34.615 0.00 0.00 0.00 2.29
293 304 6.074034 CGGACTGTTGTTTTGTGTTTCTTTTT 60.074 34.615 0.00 0.00 0.00 1.94
294 305 5.404066 CGGACTGTTGTTTTGTGTTTCTTTT 59.596 36.000 0.00 0.00 0.00 2.27
295 306 4.920927 CGGACTGTTGTTTTGTGTTTCTTT 59.079 37.500 0.00 0.00 0.00 2.52
296 307 4.022676 ACGGACTGTTGTTTTGTGTTTCTT 60.023 37.500 0.00 0.00 0.00 2.52
302 313 2.162608 TGGAACGGACTGTTGTTTTGTG 59.837 45.455 3.87 0.00 42.09 3.33
333 350 2.262423 ACCTTTTCACTGAGAGCACC 57.738 50.000 0.00 0.00 0.00 5.01
380 397 0.108138 AAGACCGCCACAGCATACTC 60.108 55.000 0.00 0.00 39.83 2.59
410 428 2.993937 TCTGAAACTTGAAACCGTGGT 58.006 42.857 0.00 0.00 0.00 4.16
414 432 2.665519 CGGCATCTGAAACTTGAAACCG 60.666 50.000 0.00 0.00 0.00 4.44
416 434 3.003275 TCACGGCATCTGAAACTTGAAAC 59.997 43.478 0.00 0.00 0.00 2.78
457 478 9.500785 TCATCTGTCATTACATTAACTGAAACA 57.499 29.630 0.00 0.00 34.37 2.83
465 486 6.539826 CAGCCACTCATCTGTCATTACATTAA 59.460 38.462 0.00 0.00 34.37 1.40
466 487 6.051074 CAGCCACTCATCTGTCATTACATTA 58.949 40.000 0.00 0.00 34.37 1.90
594 619 4.685169 ACAATGTCGGCATTTCAGTAAG 57.315 40.909 13.64 2.30 42.91 2.34
648 678 9.433153 GGTGAAATACAGTACTAGTAGCTTTTT 57.567 33.333 1.87 0.73 0.00 1.94
660 693 3.550678 GCGCTACAGGTGAAATACAGTAC 59.449 47.826 0.00 0.00 0.00 2.73
676 712 2.030946 GTGAACAATGGATCAGCGCTAC 59.969 50.000 10.99 4.56 0.00 3.58
678 714 1.089920 GTGAACAATGGATCAGCGCT 58.910 50.000 2.64 2.64 0.00 5.92
697 733 0.109723 TTTTCTCCACCGGTGAAGGG 59.890 55.000 36.07 20.08 36.70 3.95
698 734 1.235724 GTTTTCTCCACCGGTGAAGG 58.764 55.000 36.07 22.74 36.70 3.46
699 735 1.873591 CTGTTTTCTCCACCGGTGAAG 59.126 52.381 36.07 26.78 36.70 3.02
700 736 1.961793 CTGTTTTCTCCACCGGTGAA 58.038 50.000 36.07 16.59 34.05 3.18
701 737 0.534203 GCTGTTTTCTCCACCGGTGA 60.534 55.000 36.07 19.89 0.00 4.02
702 738 0.535102 AGCTGTTTTCTCCACCGGTG 60.535 55.000 28.26 28.26 0.00 4.94
703 739 0.250338 GAGCTGTTTTCTCCACCGGT 60.250 55.000 0.00 0.00 0.00 5.28
746 782 2.029110 ACCGCCTGTAGTAAACGCTAAA 60.029 45.455 0.00 0.00 0.00 1.85
747 783 1.545582 ACCGCCTGTAGTAAACGCTAA 59.454 47.619 0.00 0.00 0.00 3.09
748 784 1.135315 CACCGCCTGTAGTAAACGCTA 60.135 52.381 0.00 0.00 0.00 4.26
749 785 0.389426 CACCGCCTGTAGTAAACGCT 60.389 55.000 0.00 0.00 0.00 5.07
750 786 1.963190 GCACCGCCTGTAGTAAACGC 61.963 60.000 0.00 0.00 0.00 4.84
751 787 1.356527 GGCACCGCCTGTAGTAAACG 61.357 60.000 0.00 0.00 46.69 3.60
752 788 2.463592 GGCACCGCCTGTAGTAAAC 58.536 57.895 0.00 0.00 46.69 2.01
783 819 2.224744 TGAAGCTTTGGGTAGATGTGCA 60.225 45.455 0.00 0.00 0.00 4.57
802 842 2.683465 GGGGAGCTGCTTGGGATGA 61.683 63.158 2.53 0.00 0.00 2.92
821 862 7.256154 GGATGGGTTTTATAGAGAGGAGAAGAG 60.256 44.444 0.00 0.00 0.00 2.85
824 865 6.209774 TGGATGGGTTTTATAGAGAGGAGAA 58.790 40.000 0.00 0.00 0.00 2.87
838 889 2.711895 TGGTGGATTTGGATGGGTTT 57.288 45.000 0.00 0.00 0.00 3.27
868 919 0.966920 ACTGTTACGGGTCACTGAGG 59.033 55.000 0.00 0.00 0.00 3.86
870 921 0.032952 GCACTGTTACGGGTCACTGA 59.967 55.000 0.00 0.00 0.00 3.41
875 926 2.046604 GGGGCACTGTTACGGGTC 60.047 66.667 0.00 0.00 0.00 4.46
923 994 1.604438 GCGGCTTTTAAAAGGTGGTGG 60.604 52.381 25.40 3.78 36.53 4.61
946 1017 4.767255 GACTGGGTGCCTGCTCCG 62.767 72.222 4.32 0.00 0.00 4.63
947 1018 4.416738 GGACTGGGTGCCTGCTCC 62.417 72.222 1.62 1.62 0.00 4.70
949 1020 3.958860 GTGGACTGGGTGCCTGCT 61.959 66.667 0.00 0.00 0.00 4.24
951 1022 3.625897 TCGTGGACTGGGTGCCTG 61.626 66.667 0.00 0.00 0.00 4.85
952 1023 3.626924 GTCGTGGACTGGGTGCCT 61.627 66.667 0.00 0.00 0.00 4.75
955 1033 2.049433 GTCGTCGTGGACTGGGTG 60.049 66.667 0.00 0.00 34.09 4.61
957 1035 4.415332 CGGTCGTCGTGGACTGGG 62.415 72.222 8.84 0.00 39.20 4.45
972 1050 1.365633 GCTGGATCAGTAGGCTCGG 59.634 63.158 0.00 0.00 33.43 4.63
978 1056 3.026879 CGCGCGCTGGATCAGTAG 61.027 66.667 30.48 5.07 33.43 2.57
979 1057 3.469754 CTCGCGCGCTGGATCAGTA 62.470 63.158 30.48 1.98 33.43 2.74
980 1058 4.862092 CTCGCGCGCTGGATCAGT 62.862 66.667 30.48 0.00 33.43 3.41
994 1072 4.289379 CACGCATGCCATCGCTCG 62.289 66.667 13.15 0.00 35.36 5.03
995 1073 2.463620 TTCACGCATGCCATCGCTC 61.464 57.895 13.15 0.00 35.36 5.03
996 1074 2.436469 TTCACGCATGCCATCGCT 60.436 55.556 13.15 0.00 35.36 4.93
997 1075 2.277501 GTTCACGCATGCCATCGC 60.278 61.111 13.15 0.00 0.00 4.58
998 1076 0.590481 CATGTTCACGCATGCCATCG 60.590 55.000 13.15 0.00 39.59 3.84
999 1077 3.245443 CATGTTCACGCATGCCATC 57.755 52.632 13.15 0.00 39.59 3.51
1011 1089 1.073177 CGTCCGGGTTGTACATGTTC 58.927 55.000 2.30 0.00 0.00 3.18
1062 1140 3.371097 GAAGGAGATGCGCGGACCA 62.371 63.158 8.83 0.00 0.00 4.02
1065 1143 2.786495 GGAGAAGGAGATGCGCGGA 61.786 63.158 8.83 5.00 0.00 5.54
1527 1609 2.691409 ATGCTGTACATGGCTAACGT 57.309 45.000 8.39 0.00 37.70 3.99
1537 1619 4.968812 TTGCGTACTACTATGCTGTACA 57.031 40.909 0.00 0.00 37.11 2.90
1566 1660 9.412460 TCATCCAACAGCTCTTAATCAATTAAT 57.588 29.630 0.00 0.00 32.36 1.40
1567 1661 8.806429 TCATCCAACAGCTCTTAATCAATTAA 57.194 30.769 0.00 0.00 0.00 1.40
1568 1662 8.806429 TTCATCCAACAGCTCTTAATCAATTA 57.194 30.769 0.00 0.00 0.00 1.40
1569 1663 7.395489 ACTTCATCCAACAGCTCTTAATCAATT 59.605 33.333 0.00 0.00 0.00 2.32
1570 1664 6.888632 ACTTCATCCAACAGCTCTTAATCAAT 59.111 34.615 0.00 0.00 0.00 2.57
1571 1665 6.149973 CACTTCATCCAACAGCTCTTAATCAA 59.850 38.462 0.00 0.00 0.00 2.57
1572 1666 5.645067 CACTTCATCCAACAGCTCTTAATCA 59.355 40.000 0.00 0.00 0.00 2.57
1573 1667 5.877012 TCACTTCATCCAACAGCTCTTAATC 59.123 40.000 0.00 0.00 0.00 1.75
1682 1781 1.605753 GCGAGGAAGAAGGTGGTTTT 58.394 50.000 0.00 0.00 0.00 2.43
1688 1787 1.517832 CGATGGCGAGGAAGAAGGT 59.482 57.895 0.00 0.00 40.82 3.50
1712 1811 1.002087 GAGAAGACCGGTGAACATGGT 59.998 52.381 14.63 0.00 39.12 3.55
1743 1842 1.000385 ACCCAAAACGTACGATCGACA 60.000 47.619 24.34 6.06 34.70 4.35
1747 1846 0.445043 GCCACCCAAAACGTACGATC 59.555 55.000 24.41 0.00 0.00 3.69
1748 1847 0.956902 GGCCACCCAAAACGTACGAT 60.957 55.000 24.41 7.40 0.00 3.73
1750 1849 2.619165 GGGCCACCCAAAACGTACG 61.619 63.158 15.01 15.01 44.65 3.67
1751 1850 2.619165 CGGGCCACCCAAAACGTAC 61.619 63.158 4.39 0.00 45.83 3.67
1752 1851 2.127027 ATCGGGCCACCCAAAACGTA 62.127 55.000 4.39 0.00 45.83 3.57
1753 1852 2.987355 AATCGGGCCACCCAAAACGT 62.987 55.000 4.39 0.00 45.83 3.99
1866 1976 6.096987 AGAGCGGATCACTTATGAAAGTAGAA 59.903 38.462 0.00 0.00 44.28 2.10
1870 1983 6.891490 TCGAGAGCGGATCACTTATGAAAGT 61.891 44.000 0.00 0.00 41.47 2.66
1943 2092 4.926140 AACAAAGCTTGGAAGAAGAAGG 57.074 40.909 8.15 0.00 34.12 3.46
2168 2317 0.179119 GAAGGAAGCATGCATGTGGC 60.179 55.000 26.79 13.70 45.13 5.01
2186 2335 0.924090 TGGGTAGACGGATGAGGAGA 59.076 55.000 0.00 0.00 0.00 3.71
2193 2342 1.826921 ATCGCGTGGGTAGACGGAT 60.827 57.895 5.77 0.00 39.81 4.18
2285 2434 1.487452 CCGTCTCTCTCTCTCGCTCG 61.487 65.000 0.00 0.00 0.00 5.03
2289 2438 2.404215 GATCTCCGTCTCTCTCTCTCG 58.596 57.143 0.00 0.00 0.00 4.04
2290 2439 2.035449 TCGATCTCCGTCTCTCTCTCTC 59.965 54.545 0.00 0.00 39.75 3.20
2291 2440 2.036387 TCGATCTCCGTCTCTCTCTCT 58.964 52.381 0.00 0.00 39.75 3.10
2292 2441 2.519377 TCGATCTCCGTCTCTCTCTC 57.481 55.000 0.00 0.00 39.75 3.20
2293 2442 2.609491 CGATCGATCTCCGTCTCTCTCT 60.609 54.545 22.43 0.00 39.75 3.10
2294 2443 1.724623 CGATCGATCTCCGTCTCTCTC 59.275 57.143 22.43 0.00 39.75 3.20
2335 2653 0.249447 GGACGACGATGATGCATCCA 60.249 55.000 23.67 12.20 37.57 3.41
2348 2666 4.208686 CTAGCCGGCCAGGACGAC 62.209 72.222 26.15 3.65 45.00 4.34
2382 2700 6.932960 ACGGGCCAATACAATAAGATTAGTAC 59.067 38.462 4.39 0.00 0.00 2.73
2463 2788 0.249489 CTAGCATAGCCGTCCCACAC 60.249 60.000 0.00 0.00 0.00 3.82
2464 2789 2.124293 CTAGCATAGCCGTCCCACA 58.876 57.895 0.00 0.00 0.00 4.17
2534 2860 2.370849 ACAAATCCACTACGACCACCTT 59.629 45.455 0.00 0.00 0.00 3.50
2535 2861 1.975680 ACAAATCCACTACGACCACCT 59.024 47.619 0.00 0.00 0.00 4.00
2538 2864 6.778834 TCTTATACAAATCCACTACGACCA 57.221 37.500 0.00 0.00 0.00 4.02
2567 2893 1.697394 TGGTGCCTGCCTATCCCAT 60.697 57.895 0.00 0.00 0.00 4.00
2568 2894 2.286045 TGGTGCCTGCCTATCCCA 60.286 61.111 0.00 0.00 0.00 4.37
2569 2895 2.193248 GTGGTGCCTGCCTATCCC 59.807 66.667 0.00 0.00 0.00 3.85
2602 2928 0.895100 TCCAAGTGCTGCCACCAATC 60.895 55.000 0.00 0.00 43.09 2.67
2607 2933 3.357079 CCGTCCAAGTGCTGCCAC 61.357 66.667 0.00 0.00 42.39 5.01


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

AutoCloner maintained by Alex Coulton.