Multiple sequence alignment - TraesCS7A01G229500

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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 TraesCS7A01G229500 chr7A 100.000 4923 0 0 1 4923 199857735 199852813 0.000000e+00 9092
1 TraesCS7A01G229500 chr7A 98.299 882 15 0 1 882 649396039 649396920 0.000000e+00 1546
2 TraesCS7A01G229500 chr7A 97.740 885 19 1 1 885 706453911 706454794 0.000000e+00 1522
3 TraesCS7A01G229500 chr7D 92.199 4051 186 39 913 4923 191160583 191156623 0.000000e+00 5611
4 TraesCS7A01G229500 chr7B 91.444 3436 182 48 936 4321 335926288 335922915 0.000000e+00 4614
5 TraesCS7A01G229500 chr7B 97.732 882 20 0 1 882 8915794 8914913 0.000000e+00 1519
6 TraesCS7A01G229500 chr7B 84.817 573 41 20 4357 4923 335898974 335898442 7.250000e-148 534
7 TraesCS7A01G229500 chr6B 98.188 883 16 0 1 883 40128122 40127240 0.000000e+00 1543
8 TraesCS7A01G229500 chr6B 98.070 881 17 0 1 881 551921568 551920688 0.000000e+00 1533
9 TraesCS7A01G229500 chr6B 97.843 881 19 0 1 881 279072524 279071644 0.000000e+00 1522
10 TraesCS7A01G229500 chr1A 97.957 881 18 0 1 881 119733615 119734495 0.000000e+00 1528
11 TraesCS7A01G229500 chr4A 97.624 884 21 0 1 884 629946897 629947780 0.000000e+00 1517
12 TraesCS7A01G229500 chr3B 97.730 881 20 0 1 881 249998645 249997765 0.000000e+00 1517


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 TraesCS7A01G229500 chr7A 199852813 199857735 4922 True 9092 9092 100.000 1 4923 1 chr7A.!!$R1 4922
1 TraesCS7A01G229500 chr7A 649396039 649396920 881 False 1546 1546 98.299 1 882 1 chr7A.!!$F1 881
2 TraesCS7A01G229500 chr7A 706453911 706454794 883 False 1522 1522 97.740 1 885 1 chr7A.!!$F2 884
3 TraesCS7A01G229500 chr7D 191156623 191160583 3960 True 5611 5611 92.199 913 4923 1 chr7D.!!$R1 4010
4 TraesCS7A01G229500 chr7B 335922915 335926288 3373 True 4614 4614 91.444 936 4321 1 chr7B.!!$R3 3385
5 TraesCS7A01G229500 chr7B 8914913 8915794 881 True 1519 1519 97.732 1 882 1 chr7B.!!$R1 881
6 TraesCS7A01G229500 chr7B 335898442 335898974 532 True 534 534 84.817 4357 4923 1 chr7B.!!$R2 566
7 TraesCS7A01G229500 chr6B 40127240 40128122 882 True 1543 1543 98.188 1 883 1 chr6B.!!$R1 882
8 TraesCS7A01G229500 chr6B 551920688 551921568 880 True 1533 1533 98.070 1 881 1 chr6B.!!$R3 880
9 TraesCS7A01G229500 chr6B 279071644 279072524 880 True 1522 1522 97.843 1 881 1 chr6B.!!$R2 880
10 TraesCS7A01G229500 chr1A 119733615 119734495 880 False 1528 1528 97.957 1 881 1 chr1A.!!$F1 880
11 TraesCS7A01G229500 chr4A 629946897 629947780 883 False 1517 1517 97.624 1 884 1 chr4A.!!$F1 883
12 TraesCS7A01G229500 chr3B 249997765 249998645 880 True 1517 1517 97.730 1 881 1 chr3B.!!$R1 880

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
909 911 0.468226 TCAGTCCGTATTCCATGGCC 59.532 55.0 6.96 0.0 32.72 5.36 F
1000 1005 0.451383 CTCGCTGTCTCAGTCTCCAG 59.549 60.0 0.00 0.0 33.43 3.86 F
2277 2304 0.609131 AGACAAATTGGCGGTCCCAG 60.609 55.0 0.00 0.0 46.39 4.45 F
3348 3422 0.460722 GTGGTGCCATGCATGCATTA 59.539 50.0 30.32 16.6 41.91 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2371 0.394352 GGACCTGAATTCCGCACCAT 60.394 55.000 2.27 0.00 0.00 3.55 R
2971 3021 1.021920 TCTCTGTCGAGTCTCGCAGG 61.022 60.000 29.53 23.49 41.14 4.85 R
3625 3699 1.379576 GAAGAAGCAGGCTGCCCAT 60.380 57.895 34.33 21.64 46.52 4.00 R
4683 4788 0.034896 GGTTGAACTTCCTCTCGGCA 59.965 55.000 0.00 0.00 0.00 5.69 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
280 281 2.031768 GCTCCATCCCCTGCGATC 59.968 66.667 0.00 0.00 0.00 3.69
728 729 2.957680 TGGAAAGTGCTGATTTGCAAGA 59.042 40.909 0.00 0.00 45.12 3.02
871 873 1.630369 ACTGCCAACTGCTCCATTAGA 59.370 47.619 0.00 0.00 42.00 2.10
885 887 8.484214 TGCTCCATTAGAAGTAGAGATTACAT 57.516 34.615 0.00 0.00 0.00 2.29
886 888 8.580720 TGCTCCATTAGAAGTAGAGATTACATC 58.419 37.037 0.00 0.00 0.00 3.06
887 889 8.032451 GCTCCATTAGAAGTAGAGATTACATCC 58.968 40.741 0.00 0.00 0.00 3.51
888 890 9.083422 CTCCATTAGAAGTAGAGATTACATCCA 57.917 37.037 0.00 0.00 0.00 3.41
889 891 9.083422 TCCATTAGAAGTAGAGATTACATCCAG 57.917 37.037 0.00 0.00 0.00 3.86
890 892 8.865090 CCATTAGAAGTAGAGATTACATCCAGT 58.135 37.037 0.00 0.00 0.00 4.00
891 893 9.906660 CATTAGAAGTAGAGATTACATCCAGTC 57.093 37.037 0.00 0.00 0.00 3.51
892 894 9.647918 ATTAGAAGTAGAGATTACATCCAGTCA 57.352 33.333 0.00 0.00 0.00 3.41
893 895 7.581213 AGAAGTAGAGATTACATCCAGTCAG 57.419 40.000 0.00 0.00 0.00 3.51
894 896 7.122715 AGAAGTAGAGATTACATCCAGTCAGT 58.877 38.462 0.00 0.00 0.00 3.41
895 897 6.952773 AGTAGAGATTACATCCAGTCAGTC 57.047 41.667 0.00 0.00 0.00 3.51
896 898 5.830991 AGTAGAGATTACATCCAGTCAGTCC 59.169 44.000 0.00 0.00 0.00 3.85
897 899 3.634448 AGAGATTACATCCAGTCAGTCCG 59.366 47.826 0.00 0.00 0.00 4.79
898 900 3.366396 AGATTACATCCAGTCAGTCCGT 58.634 45.455 0.00 0.00 0.00 4.69
899 901 4.533815 AGATTACATCCAGTCAGTCCGTA 58.466 43.478 0.00 0.00 0.00 4.02
900 902 5.141182 AGATTACATCCAGTCAGTCCGTAT 58.859 41.667 0.00 0.00 0.00 3.06
901 903 5.598830 AGATTACATCCAGTCAGTCCGTATT 59.401 40.000 0.00 0.00 0.00 1.89
902 904 3.802948 ACATCCAGTCAGTCCGTATTC 57.197 47.619 0.00 0.00 0.00 1.75
903 905 2.431057 ACATCCAGTCAGTCCGTATTCC 59.569 50.000 0.00 0.00 0.00 3.01
904 906 2.225382 TCCAGTCAGTCCGTATTCCA 57.775 50.000 0.00 0.00 0.00 3.53
905 907 2.747177 TCCAGTCAGTCCGTATTCCAT 58.253 47.619 0.00 0.00 0.00 3.41
906 908 2.430694 TCCAGTCAGTCCGTATTCCATG 59.569 50.000 0.00 0.00 0.00 3.66
907 909 2.483714 CCAGTCAGTCCGTATTCCATGG 60.484 54.545 4.97 4.97 34.18 3.66
908 910 1.139058 AGTCAGTCCGTATTCCATGGC 59.861 52.381 6.96 0.00 32.72 4.40
909 911 0.468226 TCAGTCCGTATTCCATGGCC 59.532 55.000 6.96 0.00 32.72 5.36
910 912 0.469917 CAGTCCGTATTCCATGGCCT 59.530 55.000 6.96 0.00 32.72 5.19
911 913 0.759346 AGTCCGTATTCCATGGCCTC 59.241 55.000 6.96 0.00 32.72 4.70
1000 1005 0.451383 CTCGCTGTCTCAGTCTCCAG 59.549 60.000 0.00 0.00 33.43 3.86
1009 1014 3.249559 GTCTCAGTCTCCAGCAACAAAAG 59.750 47.826 0.00 0.00 0.00 2.27
1071 1076 1.945354 TACGCACAGACTAGGCAGCC 61.945 60.000 1.84 1.84 0.00 4.85
1100 1105 1.066143 CCTCCACTACACCATCACCAC 60.066 57.143 0.00 0.00 0.00 4.16
1104 1109 0.984230 ACTACACCATCACCACCCTG 59.016 55.000 0.00 0.00 0.00 4.45
1126 1131 2.747855 CCGCAACCTGCCTCCTTC 60.748 66.667 0.00 0.00 41.12 3.46
1127 1132 2.348998 CGCAACCTGCCTCCTTCT 59.651 61.111 0.00 0.00 41.12 2.85
1128 1133 2.037136 CGCAACCTGCCTCCTTCTG 61.037 63.158 0.00 0.00 41.12 3.02
1139 1144 3.818787 CCTTCTGCACGCCATGGC 61.819 66.667 27.67 27.67 37.85 4.40
1293 1298 3.240134 TTCCGTCTGCCAGCTCACC 62.240 63.158 0.00 0.00 0.00 4.02
1296 1301 3.325753 GTCTGCCAGCTCACCCCT 61.326 66.667 0.00 0.00 0.00 4.79
1458 1466 1.739562 CAGCAGGTGGTCGAAGCTC 60.740 63.158 0.00 0.00 32.35 4.09
1754 1762 2.360475 GCTGAACCTGGTGAGGCC 60.360 66.667 0.00 0.00 44.33 5.19
1768 1776 1.168714 GAGGCCACACATTCAGAACC 58.831 55.000 5.01 0.00 0.00 3.62
1813 1821 6.487689 AGAAAAAGAACTGCAGTACTATGC 57.512 37.500 22.01 7.50 46.68 3.14
1979 1987 7.415653 CCCTTTTTATCTGTTTAGATGTCAGGC 60.416 40.741 0.00 0.00 43.41 4.85
1997 2005 2.432510 AGGCACACAGAGTAGGATAAGC 59.567 50.000 0.00 0.00 0.00 3.09
2046 2054 6.996509 TGAGCATCATGAATACTAGCATACA 58.003 36.000 0.00 0.00 42.56 2.29
2112 2129 6.472887 TCATTACCAAACACCAAAACCAAAA 58.527 32.000 0.00 0.00 0.00 2.44
2113 2130 6.371825 TCATTACCAAACACCAAAACCAAAAC 59.628 34.615 0.00 0.00 0.00 2.43
2114 2131 3.413327 ACCAAACACCAAAACCAAAACC 58.587 40.909 0.00 0.00 0.00 3.27
2115 2132 3.181443 ACCAAACACCAAAACCAAAACCA 60.181 39.130 0.00 0.00 0.00 3.67
2116 2133 3.821033 CCAAACACCAAAACCAAAACCAA 59.179 39.130 0.00 0.00 0.00 3.67
2117 2134 4.278419 CCAAACACCAAAACCAAAACCAAA 59.722 37.500 0.00 0.00 0.00 3.28
2118 2135 5.221244 CCAAACACCAAAACCAAAACCAAAA 60.221 36.000 0.00 0.00 0.00 2.44
2119 2136 5.440234 AACACCAAAACCAAAACCAAAAC 57.560 34.783 0.00 0.00 0.00 2.43
2120 2137 3.821600 ACACCAAAACCAAAACCAAAACC 59.178 39.130 0.00 0.00 0.00 3.27
2121 2138 3.821033 CACCAAAACCAAAACCAAAACCA 59.179 39.130 0.00 0.00 0.00 3.67
2122 2139 4.278419 CACCAAAACCAAAACCAAAACCAA 59.722 37.500 0.00 0.00 0.00 3.67
2123 2140 4.893524 ACCAAAACCAAAACCAAAACCAAA 59.106 33.333 0.00 0.00 0.00 3.28
2164 2181 5.807909 TGAGCTTGCATATATAGGCATCAA 58.192 37.500 21.60 7.41 42.93 2.57
2165 2182 5.878669 TGAGCTTGCATATATAGGCATCAAG 59.121 40.000 21.60 16.75 42.93 3.02
2182 2200 2.664568 TCAAGTACACAAATACGCGAGC 59.335 45.455 15.93 0.00 0.00 5.03
2277 2304 0.609131 AGACAAATTGGCGGTCCCAG 60.609 55.000 0.00 0.00 46.39 4.45
2280 2307 0.609131 CAAATTGGCGGTCCCAGTCT 60.609 55.000 0.00 0.00 46.39 3.24
2344 2371 4.069304 CCAACAAGGAGTCACGGAAAATA 58.931 43.478 0.00 0.00 41.22 1.40
2346 2373 5.391950 CCAACAAGGAGTCACGGAAAATATG 60.392 44.000 0.00 0.00 41.22 1.78
2351 2378 2.006888 AGTCACGGAAAATATGGTGCG 58.993 47.619 0.00 0.00 34.44 5.34
2369 2396 2.124278 GAATTCAGGTCCCGGGCC 60.124 66.667 18.49 20.85 0.00 5.80
2426 2453 4.331968 AGGAACAGTGCGAAAATCCATAA 58.668 39.130 0.00 0.00 0.00 1.90
2427 2454 4.949856 AGGAACAGTGCGAAAATCCATAAT 59.050 37.500 0.00 0.00 0.00 1.28
2428 2455 5.036737 GGAACAGTGCGAAAATCCATAATG 58.963 41.667 0.00 0.00 0.00 1.90
2429 2456 4.637483 ACAGTGCGAAAATCCATAATGG 57.363 40.909 0.00 0.00 39.43 3.16
2488 2515 3.800506 GCATGCCTGAACTTTCATATTGC 59.199 43.478 6.36 0.00 36.46 3.56
2517 2544 5.712152 AAAACTTAACTGAATGGGAGCAG 57.288 39.130 0.00 0.00 38.10 4.24
2530 2557 2.108168 GGGAGCAGGAGTACATGTACA 58.892 52.381 32.02 0.00 38.48 2.90
2562 2591 6.127591 TGCCATTGCAGTAATAAAACCGTTAT 60.128 34.615 0.00 0.00 44.23 1.89
2563 2592 6.754675 GCCATTGCAGTAATAAAACCGTTATT 59.245 34.615 0.00 0.00 37.47 1.40
2564 2593 7.916450 GCCATTGCAGTAATAAAACCGTTATTA 59.084 33.333 0.00 0.00 37.47 0.98
2577 2610 7.867445 AAACCGTTATTAAAAGCTGATTGTG 57.133 32.000 0.00 0.00 0.00 3.33
2601 2634 6.943718 TGGTAAATAAACCTGGTGAACCTAAG 59.056 38.462 0.00 0.00 40.44 2.18
2618 2651 6.029346 ACCTAAGCCATTCAACTGAATTTG 57.971 37.500 2.11 0.00 42.41 2.32
2837 2887 2.855770 AAGCAAGGCATCCCACCCA 61.856 57.895 0.00 0.00 0.00 4.51
2876 2926 4.452733 GGACCCGACCGCTTCCAG 62.453 72.222 0.00 0.00 0.00 3.86
2877 2927 3.692406 GACCCGACCGCTTCCAGT 61.692 66.667 0.00 0.00 0.00 4.00
2878 2928 3.236003 GACCCGACCGCTTCCAGTT 62.236 63.158 0.00 0.00 0.00 3.16
2879 2929 2.434359 CCCGACCGCTTCCAGTTC 60.434 66.667 0.00 0.00 0.00 3.01
2880 2930 2.434359 CCGACCGCTTCCAGTTCC 60.434 66.667 0.00 0.00 0.00 3.62
2881 2931 2.342279 CGACCGCTTCCAGTTCCA 59.658 61.111 0.00 0.00 0.00 3.53
2920 2970 7.229106 TGGTTGCTTTACTAGTAATTTTTCGGT 59.771 33.333 15.92 0.00 30.90 4.69
2928 2978 7.125536 ACTAGTAATTTTTCGGTACAGCAAC 57.874 36.000 0.00 0.00 0.00 4.17
2971 3021 1.087501 GTCAAGGGAAATGTCTCCGC 58.912 55.000 0.00 0.00 36.21 5.54
3216 3289 1.801242 TTGACCTCCACAGTTCCTGA 58.199 50.000 0.00 0.00 35.18 3.86
3217 3290 1.342074 TGACCTCCACAGTTCCTGAG 58.658 55.000 0.00 0.00 35.18 3.35
3264 3337 3.673338 TCAAAATTACTGTCGCTCACTCG 59.327 43.478 0.00 0.00 0.00 4.18
3348 3422 0.460722 GTGGTGCCATGCATGCATTA 59.539 50.000 30.32 16.60 41.91 1.90
3734 3808 3.935828 GCGGTCTCTTTGCTATTTCTTCT 59.064 43.478 0.00 0.00 0.00 2.85
3735 3809 4.201763 GCGGTCTCTTTGCTATTTCTTCTG 60.202 45.833 0.00 0.00 0.00 3.02
3931 4006 1.656652 CTACGTCTTGCATTCCAGGG 58.343 55.000 0.00 0.00 0.00 4.45
3967 4042 2.836154 TGGTCCACCCAGAACTGC 59.164 61.111 0.00 0.00 38.72 4.40
4000 4075 2.125912 CGAGCAGTCGTCCTTGGG 60.126 66.667 0.00 0.00 41.57 4.12
4028 4117 0.733566 GGTTGACACATGGCGCATTG 60.734 55.000 10.83 8.68 0.00 2.82
4048 4137 0.390124 TACGGATAATCGTGGTGCCC 59.610 55.000 0.00 0.00 43.70 5.36
4099 4189 9.750125 AAATAAAAACTCAAAAGTCAGTCCATC 57.250 29.630 0.00 0.00 33.48 3.51
4175 4265 6.744112 TCATAATTTGGACACTTGGTTCAAC 58.256 36.000 0.00 0.00 44.74 3.18
4190 4280 8.730680 ACTTGGTTCAACAGTTGTGATAATATC 58.269 33.333 13.14 0.00 0.00 1.63
4219 4309 6.597832 TTGTCTTTCTTTTTGGAAACCTCA 57.402 33.333 0.00 0.00 32.63 3.86
4220 4310 6.597832 TGTCTTTCTTTTTGGAAACCTCAA 57.402 33.333 0.00 0.00 32.63 3.02
4259 4349 1.269936 GCTTCAGGTGTTTGCAGCAAT 60.270 47.619 9.12 0.00 44.89 3.56
4297 4387 3.030291 AGCTCTCATTCCTCCTGTACTG 58.970 50.000 0.00 0.00 0.00 2.74
4310 4400 3.948473 TCCTGTACTGAGATTCTCGAAGG 59.052 47.826 9.07 10.26 32.35 3.46
4388 4479 3.735237 TCCCTGCTTCGAGCTATTTAG 57.265 47.619 8.07 0.00 42.97 1.85
4396 4488 7.148407 CCTGCTTCGAGCTATTTAGAAAAGAAA 60.148 37.037 8.07 0.00 42.97 2.52
4403 4495 8.989767 CGAGCTATTTAGAAAAGAAAAACATCG 58.010 33.333 0.00 0.00 0.00 3.84
4611 4716 8.885494 TTGAAAAACCTCAAAATTCACATAGG 57.115 30.769 0.00 0.00 32.39 2.57
4612 4717 8.243961 TGAAAAACCTCAAAATTCACATAGGA 57.756 30.769 0.00 0.00 0.00 2.94
4613 4718 8.700051 TGAAAAACCTCAAAATTCACATAGGAA 58.300 29.630 0.00 0.00 0.00 3.36
4614 4719 9.541143 GAAAAACCTCAAAATTCACATAGGAAA 57.459 29.630 0.00 0.00 0.00 3.13
4624 4729 9.829507 AAAATTCACATAGGAAAACACATGAAA 57.170 25.926 0.00 0.00 0.00 2.69
4629 4734 7.448161 TCACATAGGAAAACACATGAAAGTCAT 59.552 33.333 0.00 0.00 37.65 3.06
4637 4742 8.450578 AAAACACATGAAAGTCATAGAAGACA 57.549 30.769 0.00 0.00 40.98 3.41
4638 4743 8.450578 AAACACATGAAAGTCATAGAAGACAA 57.549 30.769 0.00 0.00 40.98 3.18
4695 4800 3.556004 AGAAAGTTCTTGCCGAGAGGAAG 60.556 47.826 0.00 0.00 45.36 3.46
4696 4801 6.019960 AGAAAGTTCTTGCCGAGAGGAAGT 62.020 45.833 0.00 0.00 45.36 3.01
4697 4802 7.432010 AGAAAGTTCTTGCCGAGAGGAAGTT 62.432 44.000 0.00 0.00 45.36 2.66
4710 4815 7.900782 CGAGAGGAAGTTCAACCTATAAAAA 57.099 36.000 5.01 0.00 36.57 1.94
4711 4816 7.740246 CGAGAGGAAGTTCAACCTATAAAAAC 58.260 38.462 5.01 0.00 36.57 2.43
4712 4817 7.386848 CGAGAGGAAGTTCAACCTATAAAAACA 59.613 37.037 5.01 0.00 36.57 2.83
4713 4818 8.990163 AGAGGAAGTTCAACCTATAAAAACAA 57.010 30.769 5.01 0.00 36.57 2.83
4714 4819 9.416284 AGAGGAAGTTCAACCTATAAAAACAAA 57.584 29.630 5.01 0.00 36.57 2.83
4764 4869 5.576447 AAAAACAACTTCACGGAGTTCAT 57.424 34.783 0.00 0.00 41.61 2.57
4863 4971 3.974642 GGGACTAGTTCACATTAGGGGAT 59.025 47.826 2.92 0.00 0.00 3.85
4871 4979 3.469859 TCACATTAGGGGATCCAGGAAA 58.530 45.455 15.23 2.25 34.83 3.13
4884 4992 4.740154 TCCAGGAAATTCCAGAAAAGGA 57.260 40.909 15.21 8.24 39.61 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.613977 CCACTACTGCCCTCAACTTCTG 60.614 54.545 0.00 0.00 0.00 3.02
728 729 5.715279 GGTTTATTTACCCCTCAGCTCTTTT 59.285 40.000 0.00 0.00 31.71 2.27
854 856 2.716217 ACTTCTAATGGAGCAGTTGGC 58.284 47.619 0.00 0.00 45.30 4.52
871 873 6.322712 GGACTGACTGGATGTAATCTCTACTT 59.677 42.308 0.00 0.00 44.71 2.24
885 887 2.225382 TGGAATACGGACTGACTGGA 57.775 50.000 0.00 0.00 0.00 3.86
886 888 2.483714 CCATGGAATACGGACTGACTGG 60.484 54.545 5.56 0.00 0.00 4.00
887 889 2.826428 CCATGGAATACGGACTGACTG 58.174 52.381 5.56 0.00 0.00 3.51
888 890 1.139058 GCCATGGAATACGGACTGACT 59.861 52.381 18.40 0.00 0.00 3.41
889 891 1.583054 GCCATGGAATACGGACTGAC 58.417 55.000 18.40 0.00 0.00 3.51
890 892 0.468226 GGCCATGGAATACGGACTGA 59.532 55.000 18.40 0.00 0.00 3.41
891 893 0.469917 AGGCCATGGAATACGGACTG 59.530 55.000 18.40 0.00 36.55 3.51
892 894 0.759346 GAGGCCATGGAATACGGACT 59.241 55.000 18.40 0.00 42.46 3.85
893 895 0.468226 TGAGGCCATGGAATACGGAC 59.532 55.000 18.40 0.00 0.00 4.79
894 896 0.758734 CTGAGGCCATGGAATACGGA 59.241 55.000 18.40 0.00 0.00 4.69
895 897 0.469917 ACTGAGGCCATGGAATACGG 59.530 55.000 18.40 10.59 0.00 4.02
896 898 2.158900 AGAACTGAGGCCATGGAATACG 60.159 50.000 18.40 2.36 0.00 3.06
897 899 3.118261 TGAGAACTGAGGCCATGGAATAC 60.118 47.826 18.40 1.61 0.00 1.89
898 900 3.114606 TGAGAACTGAGGCCATGGAATA 58.885 45.455 18.40 0.00 0.00 1.75
899 901 1.918262 TGAGAACTGAGGCCATGGAAT 59.082 47.619 18.40 1.43 0.00 3.01
900 902 1.361204 TGAGAACTGAGGCCATGGAA 58.639 50.000 18.40 0.00 0.00 3.53
901 903 1.361204 TTGAGAACTGAGGCCATGGA 58.639 50.000 18.40 0.00 0.00 3.41
902 904 2.205022 TTTGAGAACTGAGGCCATGG 57.795 50.000 7.63 7.63 0.00 3.66
903 905 3.618351 AGATTTGAGAACTGAGGCCATG 58.382 45.455 5.01 0.00 0.00 3.66
904 906 4.015084 CAAGATTTGAGAACTGAGGCCAT 58.985 43.478 5.01 0.00 0.00 4.40
905 907 3.415212 CAAGATTTGAGAACTGAGGCCA 58.585 45.455 5.01 0.00 0.00 5.36
906 908 2.751806 CCAAGATTTGAGAACTGAGGCC 59.248 50.000 0.00 0.00 0.00 5.19
907 909 3.679389 TCCAAGATTTGAGAACTGAGGC 58.321 45.455 0.00 0.00 0.00 4.70
908 910 4.260170 CCTCCAAGATTTGAGAACTGAGG 58.740 47.826 0.00 0.00 0.00 3.86
909 911 3.688673 GCCTCCAAGATTTGAGAACTGAG 59.311 47.826 0.00 0.00 0.00 3.35
910 912 3.560025 GGCCTCCAAGATTTGAGAACTGA 60.560 47.826 0.00 0.00 0.00 3.41
911 913 2.751806 GGCCTCCAAGATTTGAGAACTG 59.248 50.000 0.00 0.00 0.00 3.16
1000 1005 2.287608 GGTAGTGTGCTCCTTTTGTTGC 60.288 50.000 0.00 0.00 0.00 4.17
1009 1014 2.269241 GGCAGGGTAGTGTGCTCC 59.731 66.667 0.00 0.00 39.76 4.70
1071 1076 1.878522 GTAGTGGAGGCGACGCATG 60.879 63.158 23.09 0.00 0.00 4.06
1104 1109 4.400961 AGGCAGGTTGCGGAGAGC 62.401 66.667 0.00 0.00 46.21 4.09
1113 1118 1.073897 GTGCAGAAGGAGGCAGGTT 59.926 57.895 0.00 0.00 41.35 3.50
1587 1595 2.431771 TCGCACGTCGTCCCATTG 60.432 61.111 0.00 0.00 39.67 2.82
1754 1762 2.558359 GGAAAGGGGTTCTGAATGTGTG 59.442 50.000 0.00 0.00 36.40 3.82
1768 1776 2.200170 CTGCGGCGAAAAGGAAAGGG 62.200 60.000 12.98 0.00 0.00 3.95
1882 1890 6.088616 GCATTCATCAAAGCTCACAGTTTAAC 59.911 38.462 0.00 0.00 0.00 2.01
1979 1987 6.108687 TGAAATGCTTATCCTACTCTGTGTG 58.891 40.000 0.00 0.00 0.00 3.82
2038 2046 9.791801 ACATGGAATATGTTTGTATGTATGCTA 57.208 29.630 0.00 0.00 0.00 3.49
2039 2047 8.696043 ACATGGAATATGTTTGTATGTATGCT 57.304 30.769 0.00 0.00 0.00 3.79
2046 2054 5.178623 CCGCGTACATGGAATATGTTTGTAT 59.821 40.000 4.92 0.00 33.76 2.29
2120 2137 3.904136 ACTCAATCTCGCCAAGTTTTG 57.096 42.857 0.00 0.00 0.00 2.44
2121 2138 3.882888 TCAACTCAATCTCGCCAAGTTTT 59.117 39.130 0.00 0.00 0.00 2.43
2122 2139 3.476552 TCAACTCAATCTCGCCAAGTTT 58.523 40.909 0.00 0.00 0.00 2.66
2123 2140 3.070018 CTCAACTCAATCTCGCCAAGTT 58.930 45.455 0.00 0.00 0.00 2.66
2164 2181 1.067425 TGGCTCGCGTATTTGTGTACT 60.067 47.619 5.77 0.00 0.00 2.73
2165 2182 1.352114 TGGCTCGCGTATTTGTGTAC 58.648 50.000 5.77 0.00 0.00 2.90
2182 2200 3.624861 CCTCGTGATCCTTCTTCATTTGG 59.375 47.826 0.00 0.00 0.00 3.28
2235 2262 2.903079 GATTAGTGCACTTGCCGCGC 62.903 60.000 27.06 0.00 41.18 6.86
2251 2278 2.014128 CCGCCAATTTGTCTACCGATT 58.986 47.619 0.00 0.00 0.00 3.34
2299 2326 3.056201 ACCGATAAATACTGGGACCCT 57.944 47.619 13.00 0.00 0.00 4.34
2344 2371 0.394352 GGACCTGAATTCCGCACCAT 60.394 55.000 2.27 0.00 0.00 3.55
2346 2373 1.749258 GGGACCTGAATTCCGCACC 60.749 63.158 2.27 2.93 33.43 5.01
2351 2378 2.124278 GCCCGGGACCTGAATTCC 60.124 66.667 29.31 0.00 0.00 3.01
2426 2453 3.128938 GTGACTGCGACTTACTACTCCAT 59.871 47.826 0.00 0.00 0.00 3.41
2427 2454 2.486982 GTGACTGCGACTTACTACTCCA 59.513 50.000 0.00 0.00 0.00 3.86
2428 2455 2.475852 CGTGACTGCGACTTACTACTCC 60.476 54.545 0.00 0.00 0.00 3.85
2429 2456 2.475852 CCGTGACTGCGACTTACTACTC 60.476 54.545 0.00 0.00 0.00 2.59
2430 2457 1.467734 CCGTGACTGCGACTTACTACT 59.532 52.381 0.00 0.00 0.00 2.57
2488 2515 4.157105 CCATTCAGTTAAGTTTTACCCGGG 59.843 45.833 22.25 22.25 0.00 5.73
2517 2544 3.927142 GCAGAGTGTTGTACATGTACTCC 59.073 47.826 30.69 22.16 38.76 3.85
2562 2591 9.699703 GGTTTATTTACCACAATCAGCTTTTAA 57.300 29.630 0.00 0.00 38.12 1.52
2563 2592 9.084533 AGGTTTATTTACCACAATCAGCTTTTA 57.915 29.630 0.00 0.00 40.82 1.52
2564 2593 7.872483 CAGGTTTATTTACCACAATCAGCTTTT 59.128 33.333 0.00 0.00 40.82 2.27
2577 2610 6.127814 GCTTAGGTTCACCAGGTTTATTTACC 60.128 42.308 0.00 0.00 38.89 2.85
2601 2634 2.027837 AGGGCAAATTCAGTTGAATGGC 60.028 45.455 16.97 16.97 43.41 4.40
2618 2651 2.442236 TCATTCAATCCTTCCAGGGC 57.558 50.000 0.00 0.00 35.59 5.19
2876 2926 2.365293 ACCAATGCTTTGTCCTTGGAAC 59.635 45.455 11.03 0.00 40.48 3.62
2877 2927 2.676748 ACCAATGCTTTGTCCTTGGAA 58.323 42.857 11.03 0.00 40.48 3.53
2878 2928 2.364970 CAACCAATGCTTTGTCCTTGGA 59.635 45.455 11.03 0.00 40.48 3.53
2879 2929 2.758009 CAACCAATGCTTTGTCCTTGG 58.242 47.619 11.03 0.00 43.06 3.61
2920 2970 4.324719 CCCTAAATTACTGGGGTTGCTGTA 60.325 45.833 3.20 0.00 37.37 2.74
2971 3021 1.021920 TCTCTGTCGAGTCTCGCAGG 61.022 60.000 29.53 23.49 41.14 4.85
3091 3148 2.331132 GCTCTCACACAAGCTGGCC 61.331 63.158 0.00 0.00 35.60 5.36
3216 3289 1.408702 ACTGCAAAATTCACCGTTGCT 59.591 42.857 11.85 0.00 46.19 3.91
3217 3290 1.851658 ACTGCAAAATTCACCGTTGC 58.148 45.000 5.09 5.09 46.21 4.17
3264 3337 4.392921 TCTAGCTTACTCCAACTCATGC 57.607 45.455 0.00 0.00 0.00 4.06
3625 3699 1.379576 GAAGAAGCAGGCTGCCCAT 60.380 57.895 34.33 21.64 46.52 4.00
3931 4006 5.235305 ACCATATCAGTGAAATGCGTTTC 57.765 39.130 22.03 22.03 43.22 2.78
3967 4042 4.807834 ACTGCTCGTATGTGATCATTTCTG 59.192 41.667 0.00 0.00 35.70 3.02
4000 4075 1.806542 CATGTGTCAACCAGCCAGTAC 59.193 52.381 0.00 0.00 0.00 2.73
4028 4117 1.494824 GGCACCACGATTATCCGTAC 58.505 55.000 0.00 0.00 41.29 3.67
4048 4137 3.536956 TTATGTAGGGAGCTGTTTCGG 57.463 47.619 0.00 0.00 0.00 4.30
4089 4178 7.946207 TGAAACTAGATCATAGATGGACTGAC 58.054 38.462 0.00 0.00 0.00 3.51
4153 4243 6.323739 ACTGTTGAACCAAGTGTCCAAATTAT 59.676 34.615 0.00 0.00 0.00 1.28
4259 4349 3.513119 AGAGCTTAGCATGAAGTGTCTCA 59.487 43.478 7.07 0.00 0.00 3.27
4588 4680 9.541143 TTTCCTATGTGAATTTTGAGGTTTTTC 57.459 29.630 0.00 0.00 0.00 2.29
4606 4711 9.166173 TCTATGACTTTCATGTGTTTTCCTATG 57.834 33.333 0.00 0.00 37.70 2.23
4607 4712 9.739276 TTCTATGACTTTCATGTGTTTTCCTAT 57.261 29.630 0.00 0.00 37.70 2.57
4608 4713 9.219603 CTTCTATGACTTTCATGTGTTTTCCTA 57.780 33.333 0.00 0.00 37.70 2.94
4609 4714 7.939039 TCTTCTATGACTTTCATGTGTTTTCCT 59.061 33.333 0.00 0.00 37.70 3.36
4610 4715 8.017946 GTCTTCTATGACTTTCATGTGTTTTCC 58.982 37.037 0.00 0.00 37.70 3.13
4611 4716 8.559536 TGTCTTCTATGACTTTCATGTGTTTTC 58.440 33.333 0.00 0.00 37.70 2.29
4612 4717 8.450578 TGTCTTCTATGACTTTCATGTGTTTT 57.549 30.769 0.00 0.00 37.70 2.43
4613 4718 8.450578 TTGTCTTCTATGACTTTCATGTGTTT 57.549 30.769 0.00 0.00 37.70 2.83
4614 4719 8.450578 TTTGTCTTCTATGACTTTCATGTGTT 57.549 30.769 0.00 0.00 37.70 3.32
4648 4753 6.743575 ATTTTTCATCTTTGTACTCTCGGG 57.256 37.500 0.00 0.00 0.00 5.14
4664 4769 7.012894 TCTCGGCAAGAACTTTCTTATTTTTCA 59.987 33.333 3.91 0.00 45.23 2.69
4678 4783 2.070028 GAACTTCCTCTCGGCAAGAAC 58.930 52.381 0.00 0.00 32.23 3.01
4683 4788 0.034896 GGTTGAACTTCCTCTCGGCA 59.965 55.000 0.00 0.00 0.00 5.69
4685 4790 5.593679 TTATAGGTTGAACTTCCTCTCGG 57.406 43.478 0.00 0.00 35.51 4.63
4747 4852 2.766313 TCCATGAACTCCGTGAAGTTG 58.234 47.619 0.00 0.00 39.55 3.16
4841 4949 3.381335 TCCCCTAATGTGAACTAGTCCC 58.619 50.000 0.00 0.00 0.00 4.46
4842 4950 4.040584 GGATCCCCTAATGTGAACTAGTCC 59.959 50.000 0.00 0.00 0.00 3.85
4854 4962 4.061657 TGGAATTTCCTGGATCCCCTAAT 58.938 43.478 16.25 1.10 37.46 1.73
4856 4964 3.056080 CTGGAATTTCCTGGATCCCCTA 58.944 50.000 16.25 0.00 37.46 3.53
4857 4965 1.855599 CTGGAATTTCCTGGATCCCCT 59.144 52.381 16.25 0.00 37.46 4.79
4863 4971 4.740154 TCCTTTTCTGGAATTTCCTGGA 57.260 40.909 18.88 10.29 37.46 3.86


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

AutoCloner maintained by Alex Coulton.