Multiple sequence alignment - TraesCS5B01G260100

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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 TraesCS5B01G260100 chr5B 100.000 2795 0 0 1 2795 442779388 442776594 0.000000e+00 5162
1 TraesCS5B01G260100 chr5B 91.343 670 54 4 2106 2773 458739823 458739156 0.000000e+00 913
2 TraesCS5B01G260100 chr5B 89.866 671 64 3 2107 2773 315456685 315457355 0.000000e+00 859
3 TraesCS5B01G260100 chr5B 89.312 683 67 5 2096 2774 700474693 700475373 0.000000e+00 852
4 TraesCS5B01G260100 chr5B 86.395 441 51 8 391 822 554672926 554673366 9.060000e-130 473
5 TraesCS5B01G260100 chr5D 90.657 2130 98 43 1 2069 372326340 372324251 0.000000e+00 2737
6 TraesCS5B01G260100 chr5A 89.447 2151 111 51 1 2076 475526908 475524799 0.000000e+00 2608
7 TraesCS5B01G260100 chr6B 90.774 672 58 3 2106 2774 572386612 572385942 0.000000e+00 894
8 TraesCS5B01G260100 chr6B 90.313 671 61 4 2106 2773 45571408 45570739 0.000000e+00 876
9 TraesCS5B01G260100 chr6B 90.193 673 56 8 2107 2773 107818385 107819053 0.000000e+00 869
10 TraesCS5B01G260100 chr6B 90.000 670 59 7 2108 2773 423421458 423420793 0.000000e+00 859
11 TraesCS5B01G260100 chr1B 90.667 675 55 3 2101 2773 647038293 647038961 0.000000e+00 891
12 TraesCS5B01G260100 chr1B 87.330 442 46 9 391 822 635184711 635185152 5.380000e-137 497
13 TraesCS5B01G260100 chr2B 90.732 669 52 5 2108 2774 326510408 326511068 0.000000e+00 883
14 TraesCS5B01G260100 chr2B 86.005 443 50 12 391 822 591286176 591286617 5.450000e-127 464
15 TraesCS5B01G260100 chr7B 87.162 444 43 10 391 822 725331002 725330561 2.500000e-135 492
16 TraesCS5B01G260100 chr3B 87.104 442 47 9 391 822 118816672 118816231 2.500000e-135 492
17 TraesCS5B01G260100 chrUn 86.652 442 49 9 391 822 3176093 3175652 5.410000e-132 481
18 TraesCS5B01G260100 chr4A 86.456 443 47 9 391 822 651139282 651139722 9.060000e-130 473


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 TraesCS5B01G260100 chr5B 442776594 442779388 2794 True 5162 5162 100.000 1 2795 1 chr5B.!!$R1 2794
1 TraesCS5B01G260100 chr5B 458739156 458739823 667 True 913 913 91.343 2106 2773 1 chr5B.!!$R2 667
2 TraesCS5B01G260100 chr5B 315456685 315457355 670 False 859 859 89.866 2107 2773 1 chr5B.!!$F1 666
3 TraesCS5B01G260100 chr5B 700474693 700475373 680 False 852 852 89.312 2096 2774 1 chr5B.!!$F3 678
4 TraesCS5B01G260100 chr5D 372324251 372326340 2089 True 2737 2737 90.657 1 2069 1 chr5D.!!$R1 2068
5 TraesCS5B01G260100 chr5A 475524799 475526908 2109 True 2608 2608 89.447 1 2076 1 chr5A.!!$R1 2075
6 TraesCS5B01G260100 chr6B 572385942 572386612 670 True 894 894 90.774 2106 2774 1 chr6B.!!$R3 668
7 TraesCS5B01G260100 chr6B 45570739 45571408 669 True 876 876 90.313 2106 2773 1 chr6B.!!$R1 667
8 TraesCS5B01G260100 chr6B 107818385 107819053 668 False 869 869 90.193 2107 2773 1 chr6B.!!$F1 666
9 TraesCS5B01G260100 chr6B 423420793 423421458 665 True 859 859 90.000 2108 2773 1 chr6B.!!$R2 665
10 TraesCS5B01G260100 chr1B 647038293 647038961 668 False 891 891 90.667 2101 2773 1 chr1B.!!$F2 672
11 TraesCS5B01G260100 chr2B 326510408 326511068 660 False 883 883 90.732 2108 2774 1 chr2B.!!$F1 666

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
250 265 0.037877 TCTTCTTCTCCCGTCCTCGT 59.962 55.0 0.0 0.0 35.01 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2188 0.822532 TAGGGTGCTCCTACGCTAGC 60.823 60.0 4.06 4.06 45.98 3.42 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
147 159 1.972588 ATTTAGCCACCACCTCCTCT 58.027 50.000 0.00 0.00 0.00 3.69
250 265 0.037877 TCTTCTTCTCCCGTCCTCGT 59.962 55.000 0.00 0.00 35.01 4.18
262 277 3.787001 CCTCGTCTTCCCTGCCCC 61.787 72.222 0.00 0.00 0.00 5.80
299 315 0.739112 CCTTGAGTTCTCCTCTGCGC 60.739 60.000 0.00 0.00 41.11 6.09
313 329 2.125832 GCGCTTGCAATGCCATGT 60.126 55.556 11.63 0.00 38.92 3.21
314 330 2.162754 GCGCTTGCAATGCCATGTC 61.163 57.895 11.63 0.00 38.92 3.06
315 331 1.870458 CGCTTGCAATGCCATGTCG 60.870 57.895 1.53 0.00 32.62 4.35
316 332 1.507630 GCTTGCAATGCCATGTCGA 59.492 52.632 1.53 0.00 0.00 4.20
317 333 0.799534 GCTTGCAATGCCATGTCGAC 60.800 55.000 9.11 9.11 0.00 4.20
345 361 8.427012 TGTCGTTTACTCGTTATGTAATTTCAC 58.573 33.333 0.00 0.00 31.13 3.18
363 379 7.627585 ATTTCACAGTTTTGTCATGATTTCG 57.372 32.000 0.00 0.00 34.62 3.46
367 383 6.704050 TCACAGTTTTGTCATGATTTCGTCTA 59.296 34.615 0.00 0.00 34.62 2.59
374 390 4.994217 TGTCATGATTTCGTCTACTGCAAA 59.006 37.500 0.00 0.00 0.00 3.68
376 392 6.149308 TGTCATGATTTCGTCTACTGCAAATT 59.851 34.615 0.00 0.00 0.00 1.82
379 395 5.927030 TGATTTCGTCTACTGCAAATTCAC 58.073 37.500 0.00 0.00 0.00 3.18
384 400 1.804151 TCTACTGCAAATTCACGCCAC 59.196 47.619 0.00 0.00 0.00 5.01
402 421 3.707793 CCACTTCGTTAGTAGGATGCTC 58.292 50.000 0.00 0.00 34.56 4.26
413 432 4.745649 AGTAGGATGCTCGTGTAGTTTTC 58.254 43.478 0.00 0.00 0.00 2.29
425 444 5.977725 TCGTGTAGTTTTCTCAGAGTTCTTG 59.022 40.000 0.00 0.00 0.00 3.02
426 445 5.977725 CGTGTAGTTTTCTCAGAGTTCTTGA 59.022 40.000 0.00 0.00 0.00 3.02
427 446 6.642950 CGTGTAGTTTTCTCAGAGTTCTTGAT 59.357 38.462 0.00 0.00 0.00 2.57
430 449 6.432403 AGTTTTCTCAGAGTTCTTGATCCT 57.568 37.500 0.00 0.00 0.00 3.24
435 454 2.026822 TCAGAGTTCTTGATCCTTGGGC 60.027 50.000 0.00 0.00 0.00 5.36
459 493 2.548057 TGAGATTTCTGCGTTTGTGTCC 59.452 45.455 0.00 0.00 0.00 4.02
517 551 2.744202 GAGATTGTGTGATCGCTTGGTT 59.256 45.455 7.94 0.00 0.00 3.67
529 563 1.598701 GCTTGGTTTAGGCAGGCAGG 61.599 60.000 0.00 0.00 0.00 4.85
542 576 2.851195 CAGGCAGGAAAGTGTTACAGT 58.149 47.619 0.00 0.00 0.00 3.55
722 767 3.053842 AGTGATCCTGATGCCTGAAATGT 60.054 43.478 0.00 0.00 0.00 2.71
723 768 4.164796 AGTGATCCTGATGCCTGAAATGTA 59.835 41.667 0.00 0.00 0.00 2.29
725 770 5.533903 GTGATCCTGATGCCTGAAATGTATT 59.466 40.000 0.00 0.00 0.00 1.89
729 774 6.866480 TCCTGATGCCTGAAATGTATTTTTC 58.134 36.000 0.00 0.00 36.38 2.29
730 775 6.664816 TCCTGATGCCTGAAATGTATTTTTCT 59.335 34.615 0.00 0.00 36.71 2.52
731 776 7.178983 TCCTGATGCCTGAAATGTATTTTTCTT 59.821 33.333 0.00 0.00 36.71 2.52
734 779 7.814107 TGATGCCTGAAATGTATTTTTCTTGTC 59.186 33.333 0.00 0.00 36.71 3.18
735 780 7.048629 TGCCTGAAATGTATTTTTCTTGTCA 57.951 32.000 0.00 0.00 36.71 3.58
736 781 6.922957 TGCCTGAAATGTATTTTTCTTGTCAC 59.077 34.615 0.00 0.00 36.71 3.67
738 783 7.359595 CCTGAAATGTATTTTTCTTGTCACGA 58.640 34.615 0.00 0.00 36.71 4.35
800 890 4.627035 TCTGAATGCTGAAACATACACTCG 59.373 41.667 0.00 0.00 0.00 4.18
844 934 7.332678 GCCGTTTTTCTTCTTCTTGGTAGTATA 59.667 37.037 0.00 0.00 0.00 1.47
845 935 9.211485 CCGTTTTTCTTCTTCTTGGTAGTATAA 57.789 33.333 0.00 0.00 0.00 0.98
866 956 4.825546 ATAGTATCAAGCAGCAACATGC 57.174 40.909 0.00 0.00 46.88 4.06
902 992 4.037446 TCAAACCACCACAAAGTATTCAGC 59.963 41.667 0.00 0.00 0.00 4.26
913 1003 6.017605 CACAAAGTATTCAGCTTCTGAGTTGT 60.018 38.462 0.00 2.98 41.75 3.32
938 1029 4.508124 AGTTGTAACGCTCTCTGAAACTTG 59.492 41.667 0.00 0.00 0.00 3.16
998 1089 2.629656 GCAAGCAAGCGGTGGTGAT 61.630 57.895 0.00 0.00 38.21 3.06
1004 1095 1.077501 AAGCGGTGGTGATCATGGG 60.078 57.895 0.00 0.00 0.00 4.00
1027 1118 2.122167 AAAGCGGCCGTTTTCACCA 61.122 52.632 31.08 0.00 0.00 4.17
1204 1295 1.752198 CCGTTCCACACCTTCCTCA 59.248 57.895 0.00 0.00 0.00 3.86
1205 1296 0.602905 CCGTTCCACACCTTCCTCAC 60.603 60.000 0.00 0.00 0.00 3.51
1224 1315 1.272769 ACCTACCTGCAGAAGACGAAC 59.727 52.381 17.39 0.00 0.00 3.95
1231 1322 0.992802 GCAGAAGACGAACGTGATCC 59.007 55.000 4.19 0.00 0.00 3.36
1335 1426 1.821088 AGTCCACCTTCTCCAACCTT 58.179 50.000 0.00 0.00 0.00 3.50
1410 1501 2.042831 GCTGGCGCAGTTCAGGAAT 61.043 57.895 10.83 0.00 33.43 3.01
1749 1840 2.202479 GGTGCCGCGAATTGCTTC 60.202 61.111 8.23 0.00 43.27 3.86
1802 1893 1.620819 GCTCCTGTGGTGAGAGAGAAA 59.379 52.381 0.00 0.00 31.26 2.52
1803 1894 2.353605 GCTCCTGTGGTGAGAGAGAAAG 60.354 54.545 0.00 0.00 31.26 2.62
1804 1895 2.233431 CTCCTGTGGTGAGAGAGAAAGG 59.767 54.545 0.00 0.00 31.26 3.11
1806 1897 2.634940 CCTGTGGTGAGAGAGAAAGGAA 59.365 50.000 0.00 0.00 0.00 3.36
1808 1899 3.576118 CTGTGGTGAGAGAGAAAGGAAGA 59.424 47.826 0.00 0.00 0.00 2.87
1809 1900 3.322254 TGTGGTGAGAGAGAAAGGAAGAC 59.678 47.826 0.00 0.00 0.00 3.01
1810 1901 2.900546 TGGTGAGAGAGAAAGGAAGACC 59.099 50.000 0.00 0.00 0.00 3.85
1864 1955 6.647481 TGAATTTGATTTTGAGCTGGTTGATG 59.353 34.615 0.00 0.00 0.00 3.07
1869 1960 1.067295 TTGAGCTGGTTGATGGGAGT 58.933 50.000 0.00 0.00 0.00 3.85
1891 1982 7.364762 GGAGTCATTCTTTTGGACATAGTAGGA 60.365 40.741 0.00 0.00 34.04 2.94
1913 2004 5.453339 GGAATGATGTTAGGATTGAGTCGGA 60.453 44.000 0.00 0.00 0.00 4.55
2019 2118 4.662468 ATCATGATGACTACTGCTTCGT 57.338 40.909 7.59 0.00 0.00 3.85
2031 2130 1.847999 CTGCTTCGTTTGCTTGTGTTG 59.152 47.619 0.00 0.00 0.00 3.33
2036 2135 1.330521 TCGTTTGCTTGTGTTGCTCTC 59.669 47.619 0.00 0.00 0.00 3.20
2037 2136 1.331756 CGTTTGCTTGTGTTGCTCTCT 59.668 47.619 0.00 0.00 0.00 3.10
2065 2164 3.273434 TCTATGCAGATTGCCAAGTGAC 58.727 45.455 0.00 0.00 44.23 3.67
2069 2168 2.749076 TGCAGATTGCCAAGTGACATAC 59.251 45.455 0.00 0.00 44.23 2.39
2073 2172 5.622914 GCAGATTGCCAAGTGACATACAAAT 60.623 40.000 0.00 0.00 37.42 2.32
2076 2175 3.407698 TGCCAAGTGACATACAAATCGT 58.592 40.909 0.00 0.00 0.00 3.73
2077 2176 4.570930 TGCCAAGTGACATACAAATCGTA 58.429 39.130 0.00 0.00 0.00 3.43
2078 2177 5.182487 TGCCAAGTGACATACAAATCGTAT 58.818 37.500 0.00 0.00 41.74 3.06
2079 2178 6.342111 TGCCAAGTGACATACAAATCGTATA 58.658 36.000 0.00 0.00 38.85 1.47
2080 2179 6.478673 TGCCAAGTGACATACAAATCGTATAG 59.521 38.462 0.00 0.00 38.85 1.31
2081 2180 6.700081 GCCAAGTGACATACAAATCGTATAGA 59.300 38.462 0.00 0.00 38.85 1.98
2082 2181 7.385205 GCCAAGTGACATACAAATCGTATAGAT 59.615 37.037 0.00 0.00 38.85 1.98
2177 2277 1.944024 TGCAGTTCACGGAAAAACGAT 59.056 42.857 0.00 0.00 37.61 3.73
2296 2401 3.758931 TCTGCTCTTGCGCCGCTA 61.759 61.111 11.67 0.48 43.34 4.26
2456 2571 9.233649 ACTTGTCCCGAATACAAATACAAATAA 57.766 29.630 0.00 0.00 36.46 1.40
2488 2604 6.491394 TGGAAAAATGAGTTTGTTACTGTCG 58.509 36.000 0.00 0.00 37.17 4.35
2503 2619 0.326595 TGTCGAGCCCTTTGCCAATA 59.673 50.000 0.00 0.00 42.71 1.90
2588 2704 5.238432 TGTTTGAAGAAAAGCTCTAATGCGA 59.762 36.000 0.00 0.00 38.13 5.10
2601 2718 5.126384 GCTCTAATGCGATTAGGGTCTCTAT 59.874 44.000 13.74 0.00 43.68 1.98
2611 2728 6.015010 CGATTAGGGTCTCTATCTGGTTTGAT 60.015 42.308 0.00 0.00 0.00 2.57
2703 2820 8.388768 TGTGAAGGATAACACAACATGTCATGT 61.389 37.037 12.87 12.87 42.31 3.21
2719 2836 4.137543 GTCATGTTGTTCTTCAAGGTCCT 58.862 43.478 0.00 0.00 36.66 3.85
2723 2840 5.623956 TGTTGTTCTTCAAGGTCCTCTTA 57.376 39.130 0.00 0.00 36.66 2.10
2767 2884 7.099266 CATGAACAATGGCAAACCTAGATTA 57.901 36.000 0.00 0.00 36.63 1.75
2774 2891 7.818930 ACAATGGCAAACCTAGATTACAAAATG 59.181 33.333 0.00 0.00 36.63 2.32
2775 2892 6.909550 TGGCAAACCTAGATTACAAAATGT 57.090 33.333 0.00 0.00 36.63 2.71
2776 2893 6.919721 TGGCAAACCTAGATTACAAAATGTC 58.080 36.000 0.00 0.00 36.63 3.06
2777 2894 6.719370 TGGCAAACCTAGATTACAAAATGTCT 59.281 34.615 0.00 0.00 36.63 3.41
2778 2895 7.029563 GGCAAACCTAGATTACAAAATGTCTG 58.970 38.462 0.00 0.00 0.00 3.51
2779 2896 6.528072 GCAAACCTAGATTACAAAATGTCTGC 59.472 38.462 0.00 0.00 0.00 4.26
2780 2897 7.575720 GCAAACCTAGATTACAAAATGTCTGCT 60.576 37.037 0.00 0.00 0.00 4.24
2781 2898 6.992063 ACCTAGATTACAAAATGTCTGCTG 57.008 37.500 0.00 0.00 0.00 4.41
2782 2899 5.355350 ACCTAGATTACAAAATGTCTGCTGC 59.645 40.000 0.00 0.00 0.00 5.25
2783 2900 5.587844 CCTAGATTACAAAATGTCTGCTGCT 59.412 40.000 0.00 0.00 0.00 4.24
2784 2901 5.306532 AGATTACAAAATGTCTGCTGCTG 57.693 39.130 0.00 0.00 0.00 4.41
2785 2902 5.005740 AGATTACAAAATGTCTGCTGCTGA 58.994 37.500 5.03 5.03 0.00 4.26
2786 2903 5.474532 AGATTACAAAATGTCTGCTGCTGAA 59.525 36.000 10.92 2.85 0.00 3.02
2787 2904 5.512753 TTACAAAATGTCTGCTGCTGAAA 57.487 34.783 10.92 6.32 0.00 2.69
2788 2905 3.973657 ACAAAATGTCTGCTGCTGAAAG 58.026 40.909 10.92 0.00 0.00 2.62
2789 2906 3.382546 ACAAAATGTCTGCTGCTGAAAGT 59.617 39.130 10.92 2.13 35.30 2.66
2790 2907 4.142093 ACAAAATGTCTGCTGCTGAAAGTT 60.142 37.500 10.92 8.58 35.30 2.66
2791 2908 4.660789 AAATGTCTGCTGCTGAAAGTTT 57.339 36.364 10.92 9.29 35.30 2.66
2792 2909 3.637998 ATGTCTGCTGCTGAAAGTTTG 57.362 42.857 10.92 0.00 35.30 2.93
2793 2910 2.642427 TGTCTGCTGCTGAAAGTTTGA 58.358 42.857 10.92 0.00 35.30 2.69
2794 2911 3.016031 TGTCTGCTGCTGAAAGTTTGAA 58.984 40.909 10.92 0.00 35.30 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 159 1.706575 CAGGGAGGAGGAGGAGGAA 59.293 63.158 0.00 0.00 0.00 3.36
262 277 2.747855 GGGGAGCAAACCTGAGCG 60.748 66.667 0.00 0.00 35.48 5.03
284 300 1.357991 GCAAGCGCAGAGGAGAACTC 61.358 60.000 11.47 0.00 46.98 3.01
286 302 1.669115 TGCAAGCGCAGAGGAGAAC 60.669 57.895 11.47 0.00 45.36 3.01
299 315 0.522626 TGTCGACATGGCATTGCAAG 59.477 50.000 15.76 1.91 0.00 4.01
314 330 7.044510 ATTACATAACGAGTAAACGACATGTCG 60.045 37.037 39.08 39.08 43.79 4.35
315 331 7.496704 TTACATAACGAGTAAACGACATGTC 57.503 36.000 16.21 16.21 39.56 3.06
316 332 8.470040 AATTACATAACGAGTAAACGACATGT 57.530 30.769 0.00 0.00 40.69 3.21
317 333 9.405083 GAAATTACATAACGAGTAAACGACATG 57.595 33.333 0.00 0.00 35.33 3.21
345 361 7.011773 CAGTAGACGAAATCATGACAAAACTG 58.988 38.462 0.00 0.90 0.00 3.16
350 366 4.565022 TGCAGTAGACGAAATCATGACAA 58.435 39.130 0.00 0.00 0.00 3.18
363 379 1.804151 TGGCGTGAATTTGCAGTAGAC 59.196 47.619 0.00 0.00 0.00 2.59
367 383 1.001378 GAAGTGGCGTGAATTTGCAGT 60.001 47.619 0.00 0.00 0.00 4.40
374 390 2.450609 ACTAACGAAGTGGCGTGAAT 57.549 45.000 0.00 0.00 45.00 2.57
376 392 1.200716 CCTACTAACGAAGTGGCGTGA 59.799 52.381 5.60 0.00 45.00 4.35
379 395 2.460918 CATCCTACTAACGAAGTGGCG 58.539 52.381 5.60 0.00 45.00 5.69
384 400 3.181499 ACACGAGCATCCTACTAACGAAG 60.181 47.826 0.00 0.00 0.00 3.79
402 421 5.977725 TCAAGAACTCTGAGAAAACTACACG 59.022 40.000 12.44 0.00 0.00 4.49
413 432 3.871485 CCCAAGGATCAAGAACTCTGAG 58.129 50.000 2.45 2.45 0.00 3.35
425 444 2.557920 AATCTCATCGCCCAAGGATC 57.442 50.000 0.00 0.00 0.00 3.36
426 445 2.441001 AGAAATCTCATCGCCCAAGGAT 59.559 45.455 0.00 0.00 0.00 3.24
427 446 1.839994 AGAAATCTCATCGCCCAAGGA 59.160 47.619 0.00 0.00 0.00 3.36
430 449 1.382522 GCAGAAATCTCATCGCCCAA 58.617 50.000 0.00 0.00 0.00 4.12
435 454 3.120546 ACACAAACGCAGAAATCTCATCG 60.121 43.478 0.00 0.00 0.00 3.84
459 493 3.857052 AGAAAGCAATGCCATCATGTTG 58.143 40.909 0.00 0.00 32.23 3.33
517 551 0.771127 ACACTTTCCTGCCTGCCTAA 59.229 50.000 0.00 0.00 0.00 2.69
529 563 6.094464 ACCAACTACCAAACTGTAACACTTTC 59.906 38.462 0.00 0.00 0.00 2.62
542 576 0.537828 GGCCCGAACCAACTACCAAA 60.538 55.000 0.00 0.00 0.00 3.28
677 721 5.051409 AGATCCAGTGTAGGACCTACTAC 57.949 47.826 27.95 22.87 41.30 2.73
722 767 7.330946 CCACTCACTATCGTGACAAGAAAAATA 59.669 37.037 0.00 0.00 44.85 1.40
723 768 6.147821 CCACTCACTATCGTGACAAGAAAAAT 59.852 38.462 0.00 0.00 44.85 1.82
725 770 4.988540 CCACTCACTATCGTGACAAGAAAA 59.011 41.667 0.00 0.00 44.85 2.29
729 774 3.850122 TCCACTCACTATCGTGACAAG 57.150 47.619 0.00 0.00 44.85 3.16
730 775 3.181500 CGATCCACTCACTATCGTGACAA 60.181 47.826 0.00 0.00 44.85 3.18
731 776 2.354821 CGATCCACTCACTATCGTGACA 59.645 50.000 0.00 0.00 44.85 3.58
734 779 2.287069 GGTCGATCCACTCACTATCGTG 60.287 54.545 0.00 0.00 42.32 4.35
735 780 1.948145 GGTCGATCCACTCACTATCGT 59.052 52.381 0.00 0.00 42.32 3.73
736 781 1.947456 TGGTCGATCCACTCACTATCG 59.053 52.381 0.00 0.00 41.93 2.92
754 820 8.875803 CAGATCAATAATTTCAACATTTGGTGG 58.124 33.333 0.00 0.00 32.52 4.61
794 860 4.138290 AGATCTATCATCCGTTCGAGTGT 58.862 43.478 0.00 0.00 0.00 3.55
800 890 2.989840 CGGCAAGATCTATCATCCGTTC 59.010 50.000 0.00 0.00 33.61 3.95
844 934 5.179045 GCATGTTGCTGCTTGATACTATT 57.821 39.130 0.00 0.00 40.96 1.73
845 935 4.825546 GCATGTTGCTGCTTGATACTAT 57.174 40.909 0.00 0.00 40.96 2.12
902 992 5.462398 AGCGTTACAACTTACAACTCAGAAG 59.538 40.000 0.00 0.00 0.00 2.85
913 1003 5.839621 AGTTTCAGAGAGCGTTACAACTTA 58.160 37.500 0.00 0.00 0.00 2.24
938 1029 2.202987 CCCCTGAGATCACGCAGC 60.203 66.667 0.00 0.00 41.40 5.25
998 1089 1.976474 GCCGCTTTGAACCCCATGA 60.976 57.895 0.00 0.00 0.00 3.07
1004 1095 0.937699 GAAAACGGCCGCTTTGAACC 60.938 55.000 29.73 12.44 0.00 3.62
1204 1295 1.272769 GTTCGTCTTCTGCAGGTAGGT 59.727 52.381 15.13 0.00 0.00 3.08
1205 1296 1.732732 CGTTCGTCTTCTGCAGGTAGG 60.733 57.143 15.13 5.62 0.00 3.18
1224 1315 3.748863 CTGGAAGGTCTGGATCACG 57.251 57.895 0.00 0.00 0.00 4.35
1299 1390 3.354499 CTTCTTGAGCGCGGCGAAC 62.354 63.158 28.54 18.40 0.00 3.95
1305 1396 2.383527 GGTGGACTTCTTGAGCGCG 61.384 63.158 0.00 0.00 0.00 6.86
1335 1426 2.992689 TTGAGCTGGTCGCCGGTA 60.993 61.111 1.90 0.00 40.39 4.02
1410 1501 2.973899 GGGTTGAGCGAGCTGAGA 59.026 61.111 0.84 0.00 0.00 3.27
1809 1900 3.753272 ACAAATGACAAGAACCATCGAGG 59.247 43.478 0.00 0.00 45.67 4.63
1810 1901 6.480524 TTACAAATGACAAGAACCATCGAG 57.519 37.500 0.00 0.00 0.00 4.04
1811 1902 5.106712 GCTTACAAATGACAAGAACCATCGA 60.107 40.000 0.00 0.00 0.00 3.59
1812 1903 5.088739 GCTTACAAATGACAAGAACCATCG 58.911 41.667 4.48 0.00 0.00 3.84
1813 1904 5.858581 GTGCTTACAAATGACAAGAACCATC 59.141 40.000 4.48 0.00 0.00 3.51
1814 1905 5.536161 AGTGCTTACAAATGACAAGAACCAT 59.464 36.000 6.88 0.00 29.36 3.55
1815 1906 4.887071 AGTGCTTACAAATGACAAGAACCA 59.113 37.500 6.88 0.00 29.36 3.67
1817 1908 6.494842 TCAAGTGCTTACAAATGACAAGAAC 58.505 36.000 4.48 4.13 0.00 3.01
1819 1910 6.691754 TTCAAGTGCTTACAAATGACAAGA 57.308 33.333 4.48 0.00 0.00 3.02
1821 1912 7.978414 TCAAATTCAAGTGCTTACAAATGACAA 59.022 29.630 0.00 0.00 0.00 3.18
1864 1955 5.501156 ACTATGTCCAAAAGAATGACTCCC 58.499 41.667 0.00 0.00 0.00 4.30
1869 1960 8.548025 TCATTCCTACTATGTCCAAAAGAATGA 58.452 33.333 7.34 7.34 42.68 2.57
1891 1982 5.129485 ACTCCGACTCAATCCTAACATCATT 59.871 40.000 0.00 0.00 0.00 2.57
2000 2099 4.726021 GCAAACGAAGCAGTAGTCATCATG 60.726 45.833 0.00 0.00 0.00 3.07
2019 2118 4.454728 AAAAGAGAGCAACACAAGCAAA 57.545 36.364 0.00 0.00 0.00 3.68
2031 2130 7.360269 GCAATCTGCATAGAGATAAAAGAGAGC 60.360 40.741 0.00 0.00 44.26 4.09
2073 2172 7.966753 CCTACGCTAGCAATTAAATCTATACGA 59.033 37.037 16.45 0.00 0.00 3.43
2076 2175 7.974501 GCTCCTACGCTAGCAATTAAATCTATA 59.025 37.037 16.45 0.00 38.63 1.31
2077 2176 6.814146 GCTCCTACGCTAGCAATTAAATCTAT 59.186 38.462 16.45 0.00 38.63 1.98
2078 2177 6.157211 GCTCCTACGCTAGCAATTAAATCTA 58.843 40.000 16.45 0.00 38.63 1.98
2079 2178 4.991687 GCTCCTACGCTAGCAATTAAATCT 59.008 41.667 16.45 0.00 38.63 2.40
2080 2179 4.750098 TGCTCCTACGCTAGCAATTAAATC 59.250 41.667 16.45 0.00 45.36 2.17
2081 2180 4.703897 TGCTCCTACGCTAGCAATTAAAT 58.296 39.130 16.45 0.00 45.36 1.40
2082 2181 4.131649 TGCTCCTACGCTAGCAATTAAA 57.868 40.909 16.45 0.00 45.36 1.52
2083 2182 3.812156 TGCTCCTACGCTAGCAATTAA 57.188 42.857 16.45 0.00 45.36 1.40
2088 2187 2.423898 GGGTGCTCCTACGCTAGCA 61.424 63.158 16.45 0.00 46.11 3.49
2089 2188 0.822532 TAGGGTGCTCCTACGCTAGC 60.823 60.000 4.06 4.06 45.98 3.42
2090 2189 3.416253 TAGGGTGCTCCTACGCTAG 57.584 57.895 4.53 0.00 45.98 3.42
2192 2292 4.749310 CTGCTTCTGCGCCGTCCT 62.749 66.667 4.18 0.00 43.34 3.85
2261 2365 4.697756 CCTCGCAAAGCCGACCCA 62.698 66.667 0.00 0.00 33.12 4.51
2460 2575 8.695456 ACAGTAACAAACTCATTTTTCCATTCT 58.305 29.630 0.00 0.00 35.76 2.40
2488 2604 0.457443 GCACTATTGGCAAAGGGCTC 59.543 55.000 21.51 2.39 44.01 4.70
2503 2619 2.435069 CAGGAGGATCTCATTGAGCACT 59.565 50.000 8.89 6.56 33.73 4.40
2588 2704 7.039644 CGTATCAAACCAGATAGAGACCCTAAT 60.040 40.741 0.00 0.00 31.50 1.73
2601 2718 1.483415 GGGTAGCCGTATCAAACCAGA 59.517 52.381 0.00 0.00 31.58 3.86
2622 2739 5.177696 ACTTGAAGTTCTTCTACGACAATGC 59.822 40.000 12.74 0.00 0.00 3.56
2653 2770 8.805175 ACAATATGATTCTCGAAGATGAGAGAT 58.195 33.333 0.00 0.00 45.23 2.75
2703 2820 5.280521 GGGATAAGAGGACCTTGAAGAACAA 60.281 44.000 0.00 0.00 36.34 2.83
2719 2836 3.008594 TCCTGCTCGTTTTTGGGATAAGA 59.991 43.478 0.00 0.00 0.00 2.10
2723 2840 1.534729 GTCCTGCTCGTTTTTGGGAT 58.465 50.000 0.00 0.00 0.00 3.85
2767 2884 3.382546 ACTTTCAGCAGCAGACATTTTGT 59.617 39.130 0.00 0.00 0.00 2.83
2774 2891 3.698029 TTCAAACTTTCAGCAGCAGAC 57.302 42.857 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.