Multiple sequence alignment - TraesCS7A01G548200

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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 TraesCS7A01G548200 chr7A 100.000 2957 0 0 1 2957 722776851 722779807 0.000000e+00 5461.0
1 TraesCS7A01G548200 chr7A 81.152 955 147 13 998 1931 722763920 722764862 0.000000e+00 736.0
2 TraesCS7A01G548200 chr7A 79.958 963 180 9 997 1947 725303101 725304062 0.000000e+00 697.0
3 TraesCS7A01G548200 chr7A 88.725 204 16 3 2722 2920 722777347 722777548 2.940000e-60 243.0
4 TraesCS7A01G548200 chr7A 88.725 204 16 3 497 698 722779572 722779770 2.940000e-60 243.0
5 TraesCS7A01G548200 chr7D 92.093 1973 114 21 24 1963 627218376 627220339 0.000000e+00 2741.0
6 TraesCS7A01G548200 chr7D 81.923 957 150 11 997 1931 627227190 627228145 0.000000e+00 787.0
7 TraesCS7A01G548200 chr7D 80.316 950 172 7 997 1934 627232853 627231907 0.000000e+00 704.0
8 TraesCS7A01G548200 chr7D 82.185 769 117 7 952 1701 627169507 627170274 0.000000e+00 643.0
9 TraesCS7A01G548200 chr7D 91.160 362 25 3 2602 2957 627221000 627221360 4.430000e-133 484.0
10 TraesCS7A01G548200 chr7D 91.220 205 15 3 497 698 627221119 627221323 2.900000e-70 276.0
11 TraesCS7A01G548200 chr7D 90.686 204 13 5 2722 2920 627218878 627219080 1.750000e-67 267.0
12 TraesCS7A01G548200 chr7D 88.764 89 9 1 838 926 627140652 627140739 1.120000e-19 108.0
13 TraesCS7A01G548200 chr7D 93.333 60 3 1 706 764 627219033 627219092 1.460000e-13 87.9
14 TraesCS7A01G548200 chr7D 93.750 48 2 1 706 752 627221276 627221323 1.470000e-08 71.3
15 TraesCS7A01G548200 chr7D 97.368 38 1 0 933 970 627141998 627142035 6.840000e-07 65.8
16 TraesCS7A01G548200 chr7D 91.667 48 3 1 2873 2920 627219088 627219134 6.840000e-07 65.8
17 TraesCS7A01G548200 chr7B 92.837 1452 77 7 654 2083 727862924 727864370 0.000000e+00 2080.0
18 TraesCS7A01G548200 chr7B 90.132 831 65 11 722 1543 727439119 727438297 0.000000e+00 1064.0
19 TraesCS7A01G548200 chr7B 92.764 691 40 10 25 710 727423691 727423006 0.000000e+00 990.0
20 TraesCS7A01G548200 chr7B 87.231 791 57 11 7 764 727862200 727862979 0.000000e+00 861.0
21 TraesCS7A01G548200 chr7B 81.894 961 138 16 998 1934 727608283 727607335 0.000000e+00 778.0
22 TraesCS7A01G548200 chr7B 80.042 957 168 8 997 1931 727426840 727425885 0.000000e+00 688.0
23 TraesCS7A01G548200 chr7B 94.639 429 22 1 1535 1963 727437186 727436759 0.000000e+00 664.0
24 TraesCS7A01G548200 chr7B 90.859 361 26 3 2602 2957 727865388 727865746 7.410000e-131 477.0
25 TraesCS7A01G548200 chr7B 90.432 324 20 8 394 710 727439396 727439077 1.640000e-112 416.0
26 TraesCS7A01G548200 chr7B 88.278 273 22 3 1 265 727439942 727439672 4.760000e-83 318.0
27 TraesCS7A01G548200 chr7B 94.595 185 7 2 709 892 727423062 727422880 1.730000e-72 283.0
28 TraesCS7A01G548200 chr7B 89.706 204 14 3 2722 2920 727423219 727423018 1.360000e-63 254.0
29 TraesCS7A01G548200 chr7B 87.435 191 12 3 2735 2920 727862730 727862913 2.990000e-50 209.0
30 TraesCS7A01G548200 chr7B 82.403 233 35 3 1973 2199 727436663 727436431 6.460000e-47 198.0
31 TraesCS7A01G548200 chr7B 90.411 146 13 1 263 407 727439557 727439412 1.080000e-44 191.0
32 TraesCS7A01G548200 chr7B 82.673 202 22 6 2728 2920 727439286 727439089 1.820000e-37 167.0
33 TraesCS7A01G548200 chr7B 91.667 60 4 1 706 764 727862866 727862925 6.790000e-12 82.4
34 TraesCS7A01G548200 chr7B 91.111 45 3 1 2876 2920 727862924 727862967 3.180000e-05 60.2
35 TraesCS7A01G548200 chr7B 91.111 45 3 1 706 749 727865662 727865706 3.180000e-05 60.2
36 TraesCS7A01G548200 chr2B 75.252 893 186 28 1061 1931 796341338 796342217 2.760000e-105 392.0


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 TraesCS7A01G548200 chr7A 722776851 722779807 2956 False 1982.333333 5461 92.483333 1 2957 3 chr7A.!!$F3 2956
1 TraesCS7A01G548200 chr7A 722763920 722764862 942 False 736.000000 736 81.152000 998 1931 1 chr7A.!!$F1 933
2 TraesCS7A01G548200 chr7A 725303101 725304062 961 False 697.000000 697 79.958000 997 1947 1 chr7A.!!$F2 950
3 TraesCS7A01G548200 chr7D 627227190 627228145 955 False 787.000000 787 81.923000 997 1931 1 chr7D.!!$F2 934
4 TraesCS7A01G548200 chr7D 627231907 627232853 946 True 704.000000 704 80.316000 997 1934 1 chr7D.!!$R1 937
5 TraesCS7A01G548200 chr7D 627169507 627170274 767 False 643.000000 643 82.185000 952 1701 1 chr7D.!!$F1 749
6 TraesCS7A01G548200 chr7D 627218376 627221360 2984 False 570.428571 2741 91.987000 24 2957 7 chr7D.!!$F4 2933
7 TraesCS7A01G548200 chr7B 727607335 727608283 948 True 778.000000 778 81.894000 998 1934 1 chr7B.!!$R1 936
8 TraesCS7A01G548200 chr7B 727422880 727426840 3960 True 553.750000 990 89.276750 25 2920 4 chr7B.!!$R2 2895
9 TraesCS7A01G548200 chr7B 727862200 727865746 3546 False 547.114286 2080 90.321571 7 2957 7 chr7B.!!$F1 2950
10 TraesCS7A01G548200 chr7B 727436431 727439942 3511 True 431.142857 1064 88.424000 1 2920 7 chr7B.!!$R3 2919
11 TraesCS7A01G548200 chr2B 796341338 796342217 879 False 392.000000 392 75.252000 1061 1931 1 chr2B.!!$F1 870

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
710 881 0.179084 CTCCATGGACGCCGTACATT 60.179 55.0 13.31 0.0 34.46 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 3695 0.625316 TTGCATAGACCCATGGTGCT 59.375 50.0 21.06 15.09 35.25 4.4 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
62 70 6.613679 AGGTTCCAAAATTCCCTCTACAAAAA 59.386 34.615 0.00 0.00 0.00 1.94
71 79 9.816787 AAATTCCCTCTACAAAAACTATTACCA 57.183 29.630 0.00 0.00 0.00 3.25
118 126 5.695363 GCCGTGGAACCTAGTCTATAATTTC 59.305 44.000 0.00 0.00 0.00 2.17
119 127 5.919141 CCGTGGAACCTAGTCTATAATTTCG 59.081 44.000 0.00 0.00 0.00 3.46
328 454 8.589338 AGCCTAACAAGATATCAGATTCGTAAT 58.411 33.333 5.32 0.00 0.00 1.89
337 463 8.735315 AGATATCAGATTCGTAATGTAGACTGG 58.265 37.037 5.32 0.00 0.00 4.00
338 464 4.933330 TCAGATTCGTAATGTAGACTGGC 58.067 43.478 0.00 0.00 0.00 4.85
477 634 2.470983 TGCAATGTGTCTCGGATTGA 57.529 45.000 0.00 0.00 30.03 2.57
490 647 4.282449 TCTCGGATTGAGGTGTTCACTTTA 59.718 41.667 2.98 0.00 45.32 1.85
547 707 6.546395 CACGGAGACAATAAGAGAAATTTGG 58.454 40.000 0.00 0.00 0.00 3.28
681 852 9.731819 TGTTTCTTTGCTATAGATAGTAACGAG 57.268 33.333 3.21 0.00 35.72 4.18
682 853 9.182933 GTTTCTTTGCTATAGATAGTAACGAGG 57.817 37.037 3.21 0.00 35.72 4.63
683 854 8.461249 TTCTTTGCTATAGATAGTAACGAGGT 57.539 34.615 3.21 0.00 35.72 3.85
684 855 9.565090 TTCTTTGCTATAGATAGTAACGAGGTA 57.435 33.333 3.21 0.00 35.72 3.08
685 856 9.565090 TCTTTGCTATAGATAGTAACGAGGTAA 57.435 33.333 3.21 0.00 35.25 2.85
686 857 9.609950 CTTTGCTATAGATAGTAACGAGGTAAC 57.390 37.037 3.21 0.00 35.25 2.50
687 858 8.915057 TTGCTATAGATAGTAACGAGGTAACT 57.085 34.615 3.21 0.00 38.74 2.24
688 859 8.320396 TGCTATAGATAGTAACGAGGTAACTG 57.680 38.462 3.21 0.00 38.94 3.16
689 860 7.935755 TGCTATAGATAGTAACGAGGTAACTGT 59.064 37.037 3.21 0.00 38.94 3.55
690 861 9.429359 GCTATAGATAGTAACGAGGTAACTGTA 57.571 37.037 3.21 0.00 38.94 2.74
701 872 3.160777 GGTAACTGTACTCCATGGACG 57.839 52.381 11.44 9.93 0.00 4.79
702 873 2.537401 GTAACTGTACTCCATGGACGC 58.463 52.381 11.44 4.41 0.00 5.19
703 874 0.249398 AACTGTACTCCATGGACGCC 59.751 55.000 11.44 1.38 0.00 5.68
704 875 1.226974 CTGTACTCCATGGACGCCG 60.227 63.158 11.44 3.42 0.00 6.46
705 876 1.945354 CTGTACTCCATGGACGCCGT 61.945 60.000 11.44 10.06 0.00 5.68
706 877 0.680601 TGTACTCCATGGACGCCGTA 60.681 55.000 11.44 8.95 0.00 4.02
707 878 0.248784 GTACTCCATGGACGCCGTAC 60.249 60.000 20.22 20.22 0.00 3.67
708 879 0.680601 TACTCCATGGACGCCGTACA 60.681 55.000 11.44 3.81 0.00 2.90
709 880 1.327690 ACTCCATGGACGCCGTACAT 61.328 55.000 9.66 9.66 37.63 2.29
710 881 0.179084 CTCCATGGACGCCGTACATT 60.179 55.000 13.31 0.00 34.46 2.71
711 882 0.250793 TCCATGGACGCCGTACATTT 59.749 50.000 13.31 0.00 34.46 2.32
712 883 1.091537 CCATGGACGCCGTACATTTT 58.908 50.000 13.31 0.00 34.46 1.82
713 884 1.470890 CCATGGACGCCGTACATTTTT 59.529 47.619 13.31 0.00 34.46 1.94
714 885 2.477189 CCATGGACGCCGTACATTTTTC 60.477 50.000 13.31 0.00 34.46 2.29
715 886 2.172851 TGGACGCCGTACATTTTTCT 57.827 45.000 0.00 0.00 0.00 2.52
716 887 2.496111 TGGACGCCGTACATTTTTCTT 58.504 42.857 0.00 0.00 0.00 2.52
717 888 2.224549 TGGACGCCGTACATTTTTCTTG 59.775 45.455 0.00 0.00 0.00 3.02
718 889 2.413634 GGACGCCGTACATTTTTCTTGG 60.414 50.000 0.00 0.00 0.00 3.61
719 890 1.068816 ACGCCGTACATTTTTCTTGGC 60.069 47.619 0.00 0.00 37.66 4.52
720 891 1.731098 CGCCGTACATTTTTCTTGGCC 60.731 52.381 0.00 0.00 37.75 5.36
817 1096 5.565592 TTCTGTCATCCATGCATACAAAC 57.434 39.130 0.00 0.00 0.00 2.93
829 1108 6.363088 CCATGCATACAAACTTACAAACACAG 59.637 38.462 0.00 0.00 0.00 3.66
830 1109 6.685527 TGCATACAAACTTACAAACACAGA 57.314 33.333 0.00 0.00 0.00 3.41
899 1178 1.979855 TTGCTGCCTAGTTCTTGCAA 58.020 45.000 0.00 0.00 37.96 4.08
932 1211 7.886212 CGCGACACATATATATAAAAACGTGAG 59.114 37.037 0.00 8.75 0.00 3.51
1497 1818 1.521681 GGAGCGCGCTAAGTCCAAT 60.522 57.895 36.69 8.91 0.00 3.16
1999 3542 5.128827 ACCAGCGAGACTTATTTTAGGATGA 59.871 40.000 0.00 0.00 0.00 2.92
2068 3617 0.389296 CGGTCAGGCGATACACACAA 60.389 55.000 0.00 0.00 0.00 3.33
2093 3693 1.082366 GGGTTACTTGTTGTGCGCG 60.082 57.895 0.00 0.00 0.00 6.86
2095 3695 0.305313 GGTTACTTGTTGTGCGCGAA 59.695 50.000 12.10 0.00 0.00 4.70
2121 3996 4.586001 ACCATGGGTCTATGCAAATGATTC 59.414 41.667 18.09 0.00 0.00 2.52
2140 4018 4.570874 GCCCGGCCTCATCTTCCC 62.571 72.222 0.00 0.00 0.00 3.97
2158 4036 1.954382 CCCTGCATGATGTCATCAAGG 59.046 52.381 19.17 19.23 43.50 3.61
2162 4040 1.961394 GCATGATGTCATCAAGGCCAT 59.039 47.619 22.78 5.36 43.50 4.40
2170 4048 5.389859 TGTCATCAAGGCCATTGTTTTAG 57.610 39.130 5.01 0.00 40.05 1.85
2223 5184 2.989824 CAGACGACGACCAGGGGT 60.990 66.667 0.00 0.00 39.44 4.95
2225 5186 1.035932 CAGACGACGACCAGGGGTAT 61.036 60.000 0.00 0.00 35.25 2.73
2226 5187 1.035932 AGACGACGACCAGGGGTATG 61.036 60.000 0.00 0.00 35.25 2.39
2233 5194 0.107654 GACCAGGGGTATGCTGTGTC 60.108 60.000 0.00 0.00 35.25 3.67
2239 5200 1.479323 GGGGTATGCTGTGTCTACGAA 59.521 52.381 0.00 0.00 0.00 3.85
2247 5208 2.431539 GTGTCTACGAACACGCCAG 58.568 57.895 0.00 0.00 40.09 4.85
2288 5250 1.138266 GCGACCTTGGCCTTATACTCA 59.862 52.381 3.32 0.00 0.00 3.41
2308 5315 3.816523 TCACCCAACTTCGTTTTCATACC 59.183 43.478 0.00 0.00 0.00 2.73
2346 5647 1.203225 AGCCCTTCTTTTGAGCCCATT 60.203 47.619 0.00 0.00 0.00 3.16
2360 5661 1.299648 CCATTGGTCCTCTTGCGGA 59.700 57.895 0.00 0.00 0.00 5.54
2362 5663 0.804989 CATTGGTCCTCTTGCGGAAC 59.195 55.000 0.00 0.00 41.30 3.62
2411 5712 4.886247 TTAAAACTTCCAACACGTCTGG 57.114 40.909 6.84 6.84 35.05 3.86
2412 5713 1.021968 AAACTTCCAACACGTCTGGC 58.978 50.000 8.14 0.00 33.63 4.85
2413 5714 0.818040 AACTTCCAACACGTCTGGCC 60.818 55.000 8.14 0.00 33.63 5.36
2414 5715 1.966451 CTTCCAACACGTCTGGCCC 60.966 63.158 0.00 0.00 33.63 5.80
2415 5716 2.674563 CTTCCAACACGTCTGGCCCA 62.675 60.000 0.00 0.00 33.63 5.36
2416 5717 2.203280 CCAACACGTCTGGCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
2417 5718 1.603455 CCAACACGTCTGGCCCAAT 60.603 57.895 0.00 0.00 0.00 3.16
2418 5719 1.178534 CCAACACGTCTGGCCCAATT 61.179 55.000 0.00 0.00 0.00 2.32
2419 5720 0.673437 CAACACGTCTGGCCCAATTT 59.327 50.000 0.00 0.00 0.00 1.82
2420 5721 0.673437 AACACGTCTGGCCCAATTTG 59.327 50.000 0.00 0.00 0.00 2.32
2421 5722 1.080569 CACGTCTGGCCCAATTTGC 60.081 57.895 0.00 0.00 0.00 3.68
2422 5723 1.228552 ACGTCTGGCCCAATTTGCT 60.229 52.632 0.00 0.00 0.00 3.91
2423 5724 1.244019 ACGTCTGGCCCAATTTGCTC 61.244 55.000 0.00 0.00 0.00 4.26
2424 5725 1.243342 CGTCTGGCCCAATTTGCTCA 61.243 55.000 0.00 0.00 0.00 4.26
2425 5726 0.968405 GTCTGGCCCAATTTGCTCAA 59.032 50.000 0.00 0.00 0.00 3.02
2426 5727 1.344114 GTCTGGCCCAATTTGCTCAAA 59.656 47.619 0.00 0.00 34.46 2.69
2427 5728 2.045524 TCTGGCCCAATTTGCTCAAAA 58.954 42.857 0.00 0.00 33.56 2.44
2428 5729 2.437281 TCTGGCCCAATTTGCTCAAAAA 59.563 40.909 0.00 0.00 33.56 1.94
2469 5770 0.467290 ACACGGCATGGACCAAGTTT 60.467 50.000 0.00 0.00 0.00 2.66
2494 5796 2.965147 AGTTTGTTTTGTAGCCTGCCAT 59.035 40.909 0.00 0.00 0.00 4.40
2517 5819 8.720562 CCATATATCGCTGTTGAAATTCATGTA 58.279 33.333 0.00 0.00 0.00 2.29
2553 5855 3.408634 CTTCAACCGTGGTATGAGGTTT 58.591 45.455 0.00 0.00 45.04 3.27
2554 5856 2.773487 TCAACCGTGGTATGAGGTTTG 58.227 47.619 0.00 0.00 45.04 2.93
2557 5904 1.975680 ACCGTGGTATGAGGTTTGTCT 59.024 47.619 0.00 0.00 33.96 3.41
2596 5943 4.715534 TGGTATGAGGTCCACTGAAAAA 57.284 40.909 0.00 0.00 0.00 1.94
2666 6013 3.243301 GCTATGTGCAATGGGATGTTCTG 60.243 47.826 0.00 0.00 42.31 3.02
2674 6098 1.133181 TGGGATGTTCTGCTCACCCA 61.133 55.000 0.00 0.00 43.96 4.51
2688 6112 0.179140 CACCCATTCAAATTCGGCGG 60.179 55.000 7.21 0.00 0.00 6.13
2701 6125 3.712907 GGCGGGCTTACCACCTCA 61.713 66.667 0.00 0.00 40.22 3.86
2713 6137 5.334879 GCTTACCACCTCAAATGTTACACAG 60.335 44.000 0.00 0.00 0.00 3.66
2909 7011 6.656693 TGGCTATAGATAGTAACGAGGTAACC 59.343 42.308 3.21 0.00 32.96 2.85
2910 7012 6.656693 GGCTATAGATAGTAACGAGGTAACCA 59.343 42.308 3.21 0.00 32.96 3.67
2940 7042 6.256321 CCATGTTTTAATAATGCTCAGTTGCC 59.744 38.462 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 30 7.531857 TTTGGAACCTGCTTCATGTTTTATA 57.468 32.000 0.00 0.00 0.00 0.98
62 70 8.943594 TTTGTTGGGAAATAACTGGTAATAGT 57.056 30.769 0.00 0.00 0.00 2.12
68 76 6.074648 TGATCTTTGTTGGGAAATAACTGGT 58.925 36.000 0.00 0.00 0.00 4.00
71 79 6.295292 GGCTTGATCTTTGTTGGGAAATAACT 60.295 38.462 0.00 0.00 0.00 2.24
118 126 7.233689 TGTCGAATCTGATTTGTAATTTGTCG 58.766 34.615 15.46 6.21 0.00 4.35
166 174 8.986477 ATGTAATACAGTTTCTGGCAAAATTC 57.014 30.769 0.00 0.00 35.51 2.17
362 490 7.979537 GGTTGGTCTCTTTTTAACAAACTTCAT 59.020 33.333 0.00 0.00 29.44 2.57
364 492 6.755141 GGGTTGGTCTCTTTTTAACAAACTTC 59.245 38.462 0.00 0.00 29.44 3.01
374 502 3.806157 GCTAGTCGGGTTGGTCTCTTTTT 60.806 47.826 0.00 0.00 0.00 1.94
379 507 0.456628 GAGCTAGTCGGGTTGGTCTC 59.543 60.000 0.00 0.00 0.00 3.36
477 634 2.127651 TCCCCCTAAAGTGAACACCT 57.872 50.000 1.11 0.00 0.00 4.00
547 707 9.229784 CACATAATTGTATGTCTGAATTTGAGC 57.770 33.333 0.00 0.00 46.01 4.26
663 834 7.935755 ACAGTTACCTCGTTACTATCTATAGCA 59.064 37.037 0.00 0.00 33.68 3.49
667 838 9.487790 GAGTACAGTTACCTCGTTACTATCTAT 57.512 37.037 0.00 0.00 0.00 1.98
668 839 7.928706 GGAGTACAGTTACCTCGTTACTATCTA 59.071 40.741 0.00 0.00 0.00 1.98
669 840 6.765512 GGAGTACAGTTACCTCGTTACTATCT 59.234 42.308 0.00 0.00 0.00 1.98
670 841 6.540189 TGGAGTACAGTTACCTCGTTACTATC 59.460 42.308 0.00 0.00 0.00 2.08
671 842 6.418101 TGGAGTACAGTTACCTCGTTACTAT 58.582 40.000 0.00 0.00 0.00 2.12
672 843 5.804639 TGGAGTACAGTTACCTCGTTACTA 58.195 41.667 0.00 0.00 0.00 1.82
673 844 4.655963 TGGAGTACAGTTACCTCGTTACT 58.344 43.478 0.00 0.00 0.00 2.24
674 845 5.338365 CATGGAGTACAGTTACCTCGTTAC 58.662 45.833 0.00 0.00 0.00 2.50
675 846 4.400251 CCATGGAGTACAGTTACCTCGTTA 59.600 45.833 5.56 0.00 0.00 3.18
676 847 3.194968 CCATGGAGTACAGTTACCTCGTT 59.805 47.826 5.56 0.00 0.00 3.85
677 848 2.758979 CCATGGAGTACAGTTACCTCGT 59.241 50.000 5.56 0.00 0.00 4.18
678 849 3.021695 TCCATGGAGTACAGTTACCTCG 58.978 50.000 11.44 0.00 0.00 4.63
679 850 3.181489 CGTCCATGGAGTACAGTTACCTC 60.181 52.174 16.81 0.00 0.00 3.85
680 851 2.758979 CGTCCATGGAGTACAGTTACCT 59.241 50.000 16.81 0.00 0.00 3.08
681 852 2.737679 GCGTCCATGGAGTACAGTTACC 60.738 54.545 16.81 0.00 0.00 2.85
682 853 2.537401 GCGTCCATGGAGTACAGTTAC 58.463 52.381 16.81 0.00 0.00 2.50
683 854 1.479323 GGCGTCCATGGAGTACAGTTA 59.521 52.381 16.81 0.00 0.00 2.24
684 855 0.249398 GGCGTCCATGGAGTACAGTT 59.751 55.000 16.81 0.00 0.00 3.16
685 856 1.898154 GGCGTCCATGGAGTACAGT 59.102 57.895 16.81 0.00 0.00 3.55
686 857 1.226974 CGGCGTCCATGGAGTACAG 60.227 63.158 16.81 4.47 0.00 2.74
687 858 0.680601 TACGGCGTCCATGGAGTACA 60.681 55.000 19.21 0.00 0.00 2.90
688 859 0.248784 GTACGGCGTCCATGGAGTAC 60.249 60.000 19.21 19.01 0.00 2.73
689 860 0.680601 TGTACGGCGTCCATGGAGTA 60.681 55.000 19.21 11.12 0.00 2.59
690 861 1.327690 ATGTACGGCGTCCATGGAGT 61.328 55.000 19.21 12.24 0.00 3.85
691 862 0.179084 AATGTACGGCGTCCATGGAG 60.179 55.000 18.89 10.69 0.00 3.86
692 863 0.250793 AAATGTACGGCGTCCATGGA 59.749 50.000 18.89 11.44 0.00 3.41
693 864 1.091537 AAAATGTACGGCGTCCATGG 58.908 50.000 18.89 4.97 0.00 3.66
694 865 2.418628 AGAAAAATGTACGGCGTCCATG 59.581 45.455 18.89 0.00 0.00 3.66
695 866 2.706890 AGAAAAATGTACGGCGTCCAT 58.293 42.857 19.21 15.47 0.00 3.41
696 867 2.172851 AGAAAAATGTACGGCGTCCA 57.827 45.000 19.21 13.23 0.00 4.02
697 868 2.413634 CCAAGAAAAATGTACGGCGTCC 60.414 50.000 19.21 5.43 0.00 4.79
698 869 2.846693 CCAAGAAAAATGTACGGCGTC 58.153 47.619 19.21 9.31 0.00 5.19
699 870 1.068816 GCCAAGAAAAATGTACGGCGT 60.069 47.619 19.64 19.64 0.00 5.68
700 871 1.613270 GCCAAGAAAAATGTACGGCG 58.387 50.000 4.80 4.80 0.00 6.46
701 872 1.271102 TGGCCAAGAAAAATGTACGGC 59.729 47.619 0.61 0.00 37.33 5.68
702 873 3.866883 ATGGCCAAGAAAAATGTACGG 57.133 42.857 10.96 0.00 0.00 4.02
703 874 5.811399 TCTATGGCCAAGAAAAATGTACG 57.189 39.130 10.96 0.00 0.00 3.67
704 875 8.451908 ACTATCTATGGCCAAGAAAAATGTAC 57.548 34.615 10.96 0.00 0.00 2.90
706 877 8.903820 GTTACTATCTATGGCCAAGAAAAATGT 58.096 33.333 10.96 11.53 0.00 2.71
707 878 8.070171 CGTTACTATCTATGGCCAAGAAAAATG 58.930 37.037 10.96 8.90 0.00 2.32
708 879 7.990886 TCGTTACTATCTATGGCCAAGAAAAAT 59.009 33.333 10.96 1.98 0.00 1.82
709 880 7.332557 TCGTTACTATCTATGGCCAAGAAAAA 58.667 34.615 10.96 5.29 0.00 1.94
710 881 6.880484 TCGTTACTATCTATGGCCAAGAAAA 58.120 36.000 10.96 6.38 0.00 2.29
711 882 6.462487 CCTCGTTACTATCTATGGCCAAGAAA 60.462 42.308 10.96 2.83 0.00 2.52
712 883 5.010719 CCTCGTTACTATCTATGGCCAAGAA 59.989 44.000 10.96 0.00 0.00 2.52
713 884 4.523173 CCTCGTTACTATCTATGGCCAAGA 59.477 45.833 10.96 14.76 0.00 3.02
714 885 4.281182 ACCTCGTTACTATCTATGGCCAAG 59.719 45.833 10.96 9.18 0.00 3.61
715 886 4.220724 ACCTCGTTACTATCTATGGCCAA 58.779 43.478 10.96 0.00 0.00 4.52
716 887 3.840991 ACCTCGTTACTATCTATGGCCA 58.159 45.455 8.56 8.56 0.00 5.36
717 888 5.476254 AGTTACCTCGTTACTATCTATGGCC 59.524 44.000 0.00 0.00 0.00 5.36
718 889 6.016443 ACAGTTACCTCGTTACTATCTATGGC 60.016 42.308 0.00 0.00 0.00 4.40
719 890 7.507733 ACAGTTACCTCGTTACTATCTATGG 57.492 40.000 0.00 0.00 0.00 2.74
817 1096 2.405357 CGAGAGCGTCTGTGTTTGTAAG 59.595 50.000 0.00 0.00 0.00 2.34
829 1108 0.591236 GTGAGCTGATCGAGAGCGTC 60.591 60.000 12.26 10.78 41.61 5.19
830 1109 1.431440 GTGAGCTGATCGAGAGCGT 59.569 57.895 12.26 3.16 41.61 5.07
899 1178 0.379316 TATATGTGTCGCGCTCGTGT 59.621 50.000 5.56 0.46 36.96 4.49
932 1211 1.452108 CCAGAAGCGGTGGGGAATC 60.452 63.158 0.00 0.00 0.00 2.52
934 1213 4.344865 GCCAGAAGCGGTGGGGAA 62.345 66.667 3.90 0.00 35.39 3.97
1147 1444 2.506438 GTCACCGCAGTACTCCGC 60.506 66.667 0.00 0.00 0.00 5.54
1204 1519 4.572571 AACGCCGCCACCAAAGGA 62.573 61.111 0.00 0.00 0.00 3.36
1497 1818 1.599518 CACGCTTGGGGTGCAGTAA 60.600 57.895 0.00 0.00 39.43 2.24
1779 3220 1.144057 GGTGATCACGCCGAATCCT 59.856 57.895 19.33 0.00 36.93 3.24
2030 3577 8.458843 CCTGACCGTTGAAATATCTTGTTTTAT 58.541 33.333 0.00 0.00 0.00 1.40
2068 3617 4.438148 GCACAACAAGTAACCCACAATTT 58.562 39.130 0.00 0.00 0.00 1.82
2093 3693 1.312815 GCATAGACCCATGGTGCTTC 58.687 55.000 15.19 4.74 35.25 3.86
2095 3695 0.625316 TTGCATAGACCCATGGTGCT 59.375 50.000 21.06 15.09 35.25 4.40
2098 3698 3.668141 TCATTTGCATAGACCCATGGT 57.332 42.857 11.73 0.00 39.44 3.55
2099 3699 4.320714 CGAATCATTTGCATAGACCCATGG 60.321 45.833 4.14 4.14 0.00 3.66
2101 3701 3.822735 CCGAATCATTTGCATAGACCCAT 59.177 43.478 0.00 0.00 0.00 4.00
2102 3702 3.213506 CCGAATCATTTGCATAGACCCA 58.786 45.455 0.00 0.00 0.00 4.51
2103 3703 2.030805 GCCGAATCATTTGCATAGACCC 60.031 50.000 0.00 0.00 0.00 4.46
2104 3704 2.030805 GGCCGAATCATTTGCATAGACC 60.031 50.000 0.00 0.00 0.00 3.85
2108 3711 0.950836 CGGGCCGAATCATTTGCATA 59.049 50.000 24.41 0.00 0.00 3.14
2133 4011 3.137728 TGATGACATCATGCAGGGAAGAT 59.862 43.478 14.24 0.00 36.57 2.40
2140 4018 1.337071 GGCCTTGATGACATCATGCAG 59.663 52.381 27.89 19.37 39.39 4.41
2158 4036 2.414161 GCGTCACTCCTAAAACAATGGC 60.414 50.000 0.00 0.00 0.00 4.40
2162 4040 1.504359 CGGCGTCACTCCTAAAACAA 58.496 50.000 0.00 0.00 0.00 2.83
2217 5178 1.202417 CGTAGACACAGCATACCCCTG 60.202 57.143 0.00 0.00 36.41 4.45
2223 5184 2.858839 CGTGTTCGTAGACACAGCATA 58.141 47.619 15.68 0.00 38.04 3.14
2225 5186 0.937699 GCGTGTTCGTAGACACAGCA 60.938 55.000 19.24 0.00 38.04 4.41
2226 5187 1.615107 GGCGTGTTCGTAGACACAGC 61.615 60.000 15.68 16.77 38.04 4.40
2233 5194 2.813908 GCCCTGGCGTGTTCGTAG 60.814 66.667 0.00 0.00 39.49 3.51
2308 5315 0.798776 CTAACAAGCTCGCCAAGTGG 59.201 55.000 0.00 0.00 38.53 4.00
2346 5647 2.204461 TCGTTCCGCAAGAGGACCA 61.204 57.895 0.00 0.00 40.56 4.02
2360 5661 3.764237 ATGAGTAACCAACCAGTCGTT 57.236 42.857 0.00 0.00 33.90 3.85
2362 5663 3.926616 AGAATGAGTAACCAACCAGTCG 58.073 45.455 0.00 0.00 32.28 4.18
2392 5693 1.404035 GCCAGACGTGTTGGAAGTTTT 59.596 47.619 17.55 0.00 37.96 2.43
2393 5694 1.021968 GCCAGACGTGTTGGAAGTTT 58.978 50.000 17.55 0.00 37.96 2.66
2394 5695 0.818040 GGCCAGACGTGTTGGAAGTT 60.818 55.000 17.55 0.00 37.96 2.66
2400 5701 0.673437 AAATTGGGCCAGACGTGTTG 59.327 50.000 6.23 0.00 0.00 3.33
2401 5702 0.673437 CAAATTGGGCCAGACGTGTT 59.327 50.000 6.23 0.00 0.00 3.32
2408 5709 2.547299 TTTTGAGCAAATTGGGCCAG 57.453 45.000 6.23 0.00 0.00 4.85
2427 5728 1.345415 CAGCACTCCATTGGGCTTTTT 59.655 47.619 2.09 0.00 33.60 1.94
2428 5729 0.971386 CAGCACTCCATTGGGCTTTT 59.029 50.000 2.09 0.00 33.60 2.27
2443 5744 1.228094 TCCATGCCGTGTTTCAGCA 60.228 52.632 0.00 0.00 41.50 4.41
2469 5770 3.779759 CAGGCTACAAAACAAACTGCAA 58.220 40.909 0.00 0.00 0.00 4.08
2494 5796 8.229811 GCATACATGAATTTCAACAGCGATATA 58.770 33.333 0.00 0.00 0.00 0.86
2517 5819 2.558359 GTTGAAGGTAACCAAGCAGCAT 59.442 45.455 0.00 0.00 37.17 3.79
2575 5922 4.715534 TTTTTCAGTGGACCTCATACCA 57.284 40.909 0.00 0.00 0.00 3.25
2598 5945 4.344104 CCCATCCTCATACCACAGTTTTT 58.656 43.478 0.00 0.00 0.00 1.94
2599 5946 3.877735 GCCCATCCTCATACCACAGTTTT 60.878 47.826 0.00 0.00 0.00 2.43
2600 5947 2.357154 GCCCATCCTCATACCACAGTTT 60.357 50.000 0.00 0.00 0.00 2.66
2603 5950 0.839277 TGCCCATCCTCATACCACAG 59.161 55.000 0.00 0.00 0.00 3.66
2604 5951 0.839277 CTGCCCATCCTCATACCACA 59.161 55.000 0.00 0.00 0.00 4.17
2605 5952 1.131638 TCTGCCCATCCTCATACCAC 58.868 55.000 0.00 0.00 0.00 4.16
2606 5953 1.701292 CATCTGCCCATCCTCATACCA 59.299 52.381 0.00 0.00 0.00 3.25
2607 5954 1.004044 CCATCTGCCCATCCTCATACC 59.996 57.143 0.00 0.00 0.00 2.73
2608 5955 1.980765 TCCATCTGCCCATCCTCATAC 59.019 52.381 0.00 0.00 0.00 2.39
2609 5956 2.421197 TCCATCTGCCCATCCTCATA 57.579 50.000 0.00 0.00 0.00 2.15
2610 5957 1.526315 TTCCATCTGCCCATCCTCAT 58.474 50.000 0.00 0.00 0.00 2.90
2611 5958 1.064463 GTTTCCATCTGCCCATCCTCA 60.064 52.381 0.00 0.00 0.00 3.86
2612 5959 1.685148 GTTTCCATCTGCCCATCCTC 58.315 55.000 0.00 0.00 0.00 3.71
2616 5963 0.916086 TACGGTTTCCATCTGCCCAT 59.084 50.000 0.00 0.00 0.00 4.00
2618 5965 1.339727 ACTTACGGTTTCCATCTGCCC 60.340 52.381 0.00 0.00 0.00 5.36
2666 6013 1.469767 GCCGAATTTGAATGGGTGAGC 60.470 52.381 0.00 0.00 0.00 4.26
2674 6098 1.404035 GTAAGCCCGCCGAATTTGAAT 59.596 47.619 0.00 0.00 0.00 2.57
2688 6112 4.076394 TGTAACATTTGAGGTGGTAAGCC 58.924 43.478 0.00 0.00 0.00 4.35
2742 6838 6.358178 TCTCTAATTGTCTCCGTGATCTAGT 58.642 40.000 0.00 0.00 0.00 2.57
2743 6839 6.869315 TCTCTAATTGTCTCCGTGATCTAG 57.131 41.667 0.00 0.00 0.00 2.43
2744 6840 7.640597 TTTCTCTAATTGTCTCCGTGATCTA 57.359 36.000 0.00 0.00 0.00 1.98
2745 6841 6.531503 TTTCTCTAATTGTCTCCGTGATCT 57.468 37.500 0.00 0.00 0.00 2.75
2746 6842 7.306283 CGAATTTCTCTAATTGTCTCCGTGATC 60.306 40.741 0.00 0.00 36.59 2.92
2747 6843 6.477033 CGAATTTCTCTAATTGTCTCCGTGAT 59.523 38.462 0.00 0.00 36.59 3.06
2748 6844 5.805486 CGAATTTCTCTAATTGTCTCCGTGA 59.195 40.000 0.00 0.00 36.59 4.35
2931 7033 0.605319 TTAGTTGGGCGGCAACTGAG 60.605 55.000 25.76 0.00 42.21 3.35


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

AutoCloner maintained by Alex Coulton.