Multiple sequence alignment - TraesCS7D01G138900

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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 TraesCS7D01G138900 chr7D 100.000 3310 0 0 1 3310 88987364 88990673 0.000000e+00 6113.0
1 TraesCS7D01G138900 chr7D 91.717 821 64 3 1 819 528485870 528486688 0.000000e+00 1136.0
2 TraesCS7D01G138900 chr7D 83.203 1024 139 16 1059 2071 89079389 89080390 0.000000e+00 907.0
3 TraesCS7D01G138900 chr7D 85.369 786 90 13 1059 1836 89017005 89017773 0.000000e+00 791.0
4 TraesCS7D01G138900 chr7D 80.020 986 157 22 1059 2040 89108171 89109120 0.000000e+00 693.0
5 TraesCS7D01G138900 chr7D 81.579 722 125 8 970 1689 89227904 89228619 1.020000e-164 590.0
6 TraesCS7D01G138900 chr7D 81.612 707 120 9 990 1694 89232317 89233015 7.960000e-161 577.0
7 TraesCS7D01G138900 chr7D 89.009 464 37 3 2248 2711 89109476 89109925 2.230000e-156 562.0
8 TraesCS7D01G138900 chr7D 78.559 583 100 9 2148 2705 89018174 89018756 8.730000e-96 361.0
9 TraesCS7D01G138900 chr7D 80.448 491 62 13 2152 2620 89080612 89081090 8.790000e-91 344.0
10 TraesCS7D01G138900 chr7D 83.854 192 16 7 1914 2105 89017771 89017947 5.680000e-38 169.0
11 TraesCS7D01G138900 chr7D 87.121 132 15 2 2616 2746 89090802 89090932 7.400000e-32 148.0
12 TraesCS7D01G138900 chr7D 79.500 200 36 5 2148 2347 89229265 89229459 1.600000e-28 137.0
13 TraesCS7D01G138900 chr7D 83.562 146 23 1 2148 2292 89233806 89233951 5.760000e-28 135.0
14 TraesCS7D01G138900 chr7D 82.667 150 25 1 1850 1998 88899120 88899269 7.450000e-27 132.0
15 TraesCS7D01G138900 chr7B 90.308 1362 103 16 818 2155 39547227 39548583 0.000000e+00 1757.0
16 TraesCS7D01G138900 chr7B 88.160 777 69 14 2252 3008 39548813 39549586 0.000000e+00 904.0
17 TraesCS7D01G138900 chr7B 83.203 1024 116 23 1309 2327 39917369 39918341 0.000000e+00 887.0
18 TraesCS7D01G138900 chr7B 79.713 1183 178 38 967 2135 39959117 39960251 0.000000e+00 798.0
19 TraesCS7D01G138900 chr7B 81.543 1024 123 32 1063 2071 39980019 39980991 0.000000e+00 784.0
20 TraesCS7D01G138900 chr7B 87.424 660 79 4 1059 1716 39383581 39382924 0.000000e+00 756.0
21 TraesCS7D01G138900 chr7B 80.730 986 150 23 1059 2028 40081081 40082042 0.000000e+00 732.0
22 TraesCS7D01G138900 chr7B 81.589 755 90 31 2372 3102 39918470 39919199 2.210000e-161 579.0
23 TraesCS7D01G138900 chr7B 82.842 577 75 15 2152 2705 39981224 39981799 2.290000e-136 496.0
24 TraesCS7D01G138900 chr7B 77.944 603 89 22 2148 2708 39382427 39381827 1.470000e-88 337.0
25 TraesCS7D01G138900 chr7B 81.412 425 59 13 2290 2698 39960528 39960948 2.460000e-86 329.0
26 TraesCS7D01G138900 chr7B 92.683 205 13 2 2248 2452 39918306 39918508 8.980000e-76 294.0
27 TraesCS7D01G138900 chr7B 87.795 254 15 4 3044 3296 39549582 39549820 1.940000e-72 283.0
28 TraesCS7D01G138900 chr7B 82.692 312 40 13 2153 2452 39548629 39548938 7.040000e-67 265.0
29 TraesCS7D01G138900 chr7B 83.333 204 19 7 1914 2117 39382830 39382642 1.220000e-39 174.0
30 TraesCS7D01G138900 chr7B 85.567 97 13 1 2149 2244 40090185 40090281 2.100000e-17 100.0
31 TraesCS7D01G138900 chr7B 83.000 100 11 6 2776 2874 39981834 39981928 5.890000e-13 86.1
32 TraesCS7D01G138900 chr6D 91.932 818 65 1 2 819 48470546 48471362 0.000000e+00 1144.0
33 TraesCS7D01G138900 chr4D 91.941 819 62 2 1 819 449446039 449446853 0.000000e+00 1144.0
34 TraesCS7D01G138900 chr4D 91.697 819 63 5 1 819 21137747 21138560 0.000000e+00 1131.0
35 TraesCS7D01G138900 chr4D 91.575 819 68 1 1 819 409313694 409314511 0.000000e+00 1129.0
36 TraesCS7D01G138900 chr1D 91.697 819 67 1 1 819 421527149 421526332 0.000000e+00 1134.0
37 TraesCS7D01G138900 chr1D 80.180 111 14 4 2963 3073 60322257 60322359 3.540000e-10 76.8
38 TraesCS7D01G138900 chrUn 91.697 819 64 2 1 819 5440183 5440997 0.000000e+00 1133.0
39 TraesCS7D01G138900 chr3D 91.697 819 65 2 1 819 24875594 24876409 0.000000e+00 1133.0
40 TraesCS7D01G138900 chr2B 91.575 819 67 2 1 819 227254869 227254053 0.000000e+00 1129.0
41 TraesCS7D01G138900 chr2B 87.234 47 6 0 3098 3144 548968251 548968205 2.000000e-03 54.7
42 TraesCS7D01G138900 chr7A 85.294 782 100 9 1059 1838 90364326 90365094 0.000000e+00 793.0
43 TraesCS7D01G138900 chr7A 81.818 968 127 21 950 1887 90424072 90425020 0.000000e+00 767.0
44 TraesCS7D01G138900 chr7A 84.786 631 71 13 2248 2874 90445153 90445762 7.850000e-171 610.0
45 TraesCS7D01G138900 chr7A 83.005 559 72 13 2152 2709 90425312 90425848 4.970000e-133 484.0
46 TraesCS7D01G138900 chr7A 90.580 138 12 1 2148 2284 90365493 90365630 7.300000e-42 182.0
47 TraesCS7D01G138900 chr7A 80.392 204 25 7 1914 2117 90365090 90365278 1.240000e-29 141.0
48 TraesCS7D01G138900 chr7A 87.379 103 13 0 2372 2474 90377237 90377339 5.800000e-23 119.0
49 TraesCS7D01G138900 chr5B 84.884 86 11 2 2979 3063 640547262 640547346 5.890000e-13 86.1
50 TraesCS7D01G138900 chr2A 95.745 47 2 0 2974 3020 102289017 102289063 3.540000e-10 76.8
51 TraesCS7D01G138900 chr1A 84.615 78 9 3 2963 3040 58950766 58950840 1.270000e-09 75.0


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 TraesCS7D01G138900 chr7D 88987364 88990673 3309 False 6113.000000 6113 100.000000 1 3310 1 chr7D.!!$F2 3309
1 TraesCS7D01G138900 chr7D 528485870 528486688 818 False 1136.000000 1136 91.717000 1 819 1 chr7D.!!$F4 818
2 TraesCS7D01G138900 chr7D 89108171 89109925 1754 False 627.500000 693 84.514500 1059 2711 2 chr7D.!!$F7 1652
3 TraesCS7D01G138900 chr7D 89079389 89081090 1701 False 625.500000 907 81.825500 1059 2620 2 chr7D.!!$F6 1561
4 TraesCS7D01G138900 chr7D 89017005 89018756 1751 False 440.333333 791 82.594000 1059 2705 3 chr7D.!!$F5 1646
5 TraesCS7D01G138900 chr7D 89227904 89233951 6047 False 359.750000 590 81.563250 970 2347 4 chr7D.!!$F8 1377
6 TraesCS7D01G138900 chr7B 39547227 39549820 2593 False 802.250000 1757 87.238750 818 3296 4 chr7B.!!$F3 2478
7 TraesCS7D01G138900 chr7B 40081081 40082042 961 False 732.000000 732 80.730000 1059 2028 1 chr7B.!!$F1 969
8 TraesCS7D01G138900 chr7B 39917369 39919199 1830 False 586.666667 887 85.825000 1309 3102 3 chr7B.!!$F4 1793
9 TraesCS7D01G138900 chr7B 39959117 39960948 1831 False 563.500000 798 80.562500 967 2698 2 chr7B.!!$F5 1731
10 TraesCS7D01G138900 chr7B 39980019 39981928 1909 False 455.366667 784 82.461667 1063 2874 3 chr7B.!!$F6 1811
11 TraesCS7D01G138900 chr7B 39381827 39383581 1754 True 422.333333 756 82.900333 1059 2708 3 chr7B.!!$R1 1649
12 TraesCS7D01G138900 chr6D 48470546 48471362 816 False 1144.000000 1144 91.932000 2 819 1 chr6D.!!$F1 817
13 TraesCS7D01G138900 chr4D 449446039 449446853 814 False 1144.000000 1144 91.941000 1 819 1 chr4D.!!$F3 818
14 TraesCS7D01G138900 chr4D 21137747 21138560 813 False 1131.000000 1131 91.697000 1 819 1 chr4D.!!$F1 818
15 TraesCS7D01G138900 chr4D 409313694 409314511 817 False 1129.000000 1129 91.575000 1 819 1 chr4D.!!$F2 818
16 TraesCS7D01G138900 chr1D 421526332 421527149 817 True 1134.000000 1134 91.697000 1 819 1 chr1D.!!$R1 818
17 TraesCS7D01G138900 chrUn 5440183 5440997 814 False 1133.000000 1133 91.697000 1 819 1 chrUn.!!$F1 818
18 TraesCS7D01G138900 chr3D 24875594 24876409 815 False 1133.000000 1133 91.697000 1 819 1 chr3D.!!$F1 818
19 TraesCS7D01G138900 chr2B 227254053 227254869 816 True 1129.000000 1129 91.575000 1 819 1 chr2B.!!$R1 818
20 TraesCS7D01G138900 chr7A 90424072 90425848 1776 False 625.500000 767 82.411500 950 2709 2 chr7A.!!$F4 1759
21 TraesCS7D01G138900 chr7A 90445153 90445762 609 False 610.000000 610 84.786000 2248 2874 1 chr7A.!!$F2 626
22 TraesCS7D01G138900 chr7A 90364326 90365630 1304 False 372.000000 793 85.422000 1059 2284 3 chr7A.!!$F3 1225

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
928 936 0.032130 TTCGTCACCACTCTGCAGTC 59.968 55.0 14.67 0.0 0.00 3.51 F
1224 1256 0.179073 GGTCCATCTGCGTGTATGCT 60.179 55.0 0.00 0.0 35.36 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2340 0.104855 GTATCCGTCATGCCTGCTGA 59.895 55.0 0.0 0.0 0.0 4.26 R
3022 3890 0.101399 TTGTTTTGTTCGCCACGCAT 59.899 45.0 0.0 0.0 0.0 4.73 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
44 45 2.078452 CCACTCCCCACCTGTCAAT 58.922 57.895 0.00 0.00 0.00 2.57
49 50 1.273327 CTCCCCACCTGTCAATTTTGC 59.727 52.381 0.00 0.00 0.00 3.68
174 175 5.082425 AGAGAAAGAGATTTGCCCAAATGT 58.918 37.500 10.69 7.00 40.77 2.71
194 195 6.859112 ATGTAAGAGAGTGCTAGAAAGGAA 57.141 37.500 0.00 0.00 0.00 3.36
254 255 0.675083 TCGTTCGAAACCCTGCACTA 59.325 50.000 0.00 0.00 0.00 2.74
268 269 4.404640 CCTGCACTATCATGGGATGAAAT 58.595 43.478 0.00 0.00 43.50 2.17
304 305 3.069289 TGATGACTGCTTGTGTGATCAC 58.931 45.455 19.27 19.27 44.08 3.06
344 345 2.033550 GGACGAGCGTGATGAGAGTATT 59.966 50.000 0.00 0.00 0.00 1.89
476 477 6.103997 CACCCATTTGGATCTTCAAAATGAG 58.896 40.000 15.69 7.77 39.64 2.90
657 660 3.064271 TGGACGTGCAAACTAGTTTTGAC 59.936 43.478 18.25 15.29 46.76 3.18
701 704 3.083997 GACGGACAGGATGGGGCT 61.084 66.667 0.00 0.00 43.62 5.19
704 707 0.694444 ACGGACAGGATGGGGCTAAT 60.694 55.000 0.00 0.00 43.62 1.73
716 719 3.887868 GCTAATGGTTGCGGCCGG 61.888 66.667 29.38 8.95 0.00 6.13
717 720 2.124901 CTAATGGTTGCGGCCGGA 60.125 61.111 29.38 24.35 0.00 5.14
746 749 1.119684 CACGGTCACCATATCCCAGA 58.880 55.000 0.00 0.00 0.00 3.86
763 766 1.449601 GAACACGCCCGGACATGAT 60.450 57.895 0.73 0.00 0.00 2.45
771 774 1.748403 CCGGACATGATCCCATCGT 59.252 57.895 0.00 0.00 46.04 3.73
806 809 2.142319 CAAAATTTGGCCAAACCGGAG 58.858 47.619 32.62 17.32 43.94 4.63
860 863 4.034742 GGTTTGTCTCACGCTTTCTTTGTA 59.965 41.667 0.00 0.00 0.00 2.41
869 872 1.909700 CTTTCTTTGTAGCCCAGCCA 58.090 50.000 0.00 0.00 0.00 4.75
871 874 0.609131 TTCTTTGTAGCCCAGCCAGC 60.609 55.000 0.00 0.00 0.00 4.85
872 875 2.035626 TTTGTAGCCCAGCCAGCC 59.964 61.111 0.00 0.00 0.00 4.85
873 876 2.769652 CTTTGTAGCCCAGCCAGCCA 62.770 60.000 0.00 0.00 0.00 4.75
875 878 2.751837 GTAGCCCAGCCAGCCAAC 60.752 66.667 0.00 0.00 0.00 3.77
876 879 3.256178 TAGCCCAGCCAGCCAACA 61.256 61.111 0.00 0.00 0.00 3.33
877 880 2.839609 TAGCCCAGCCAGCCAACAA 61.840 57.895 0.00 0.00 0.00 2.83
878 881 2.364722 TAGCCCAGCCAGCCAACAAA 62.365 55.000 0.00 0.00 0.00 2.83
879 882 3.053828 CCCAGCCAGCCAACAAAG 58.946 61.111 0.00 0.00 0.00 2.77
881 884 2.341176 CAGCCAGCCAACAAAGCC 59.659 61.111 0.00 0.00 0.00 4.35
882 885 3.297620 AGCCAGCCAACAAAGCCG 61.298 61.111 0.00 0.00 0.00 5.52
884 887 2.597217 CCAGCCAACAAAGCCGGA 60.597 61.111 5.05 0.00 28.48 5.14
885 888 1.978617 CCAGCCAACAAAGCCGGAT 60.979 57.895 5.05 0.00 28.48 4.18
886 889 0.679640 CCAGCCAACAAAGCCGGATA 60.680 55.000 5.05 0.00 28.48 2.59
888 891 0.394352 AGCCAACAAAGCCGGATAGG 60.394 55.000 5.05 0.00 44.97 2.57
899 907 1.963172 CCGGATAGGTACAAAAGGGC 58.037 55.000 0.00 0.00 34.51 5.19
915 923 2.355837 GCTCACTGCGGTTCGTCA 60.356 61.111 0.00 0.00 0.00 4.35
916 924 2.658707 GCTCACTGCGGTTCGTCAC 61.659 63.158 0.00 0.00 0.00 3.67
924 932 3.952811 GGTTCGTCACCACTCTGC 58.047 61.111 2.10 0.00 46.42 4.26
926 934 0.946221 GGTTCGTCACCACTCTGCAG 60.946 60.000 7.63 7.63 46.42 4.41
928 936 0.032130 TTCGTCACCACTCTGCAGTC 59.968 55.000 14.67 0.00 0.00 3.51
929 937 0.823769 TCGTCACCACTCTGCAGTCT 60.824 55.000 14.67 0.00 0.00 3.24
930 938 0.665670 CGTCACCACTCTGCAGTCTG 60.666 60.000 14.67 9.81 0.00 3.51
931 939 0.948141 GTCACCACTCTGCAGTCTGC 60.948 60.000 18.32 18.32 45.29 4.26
946 954 3.239464 TGCAGTGCAGGTCCAAGA 58.761 55.556 15.37 0.00 33.32 3.02
970 978 2.756283 AGGGAAGGAGGAGACGCG 60.756 66.667 3.53 3.53 0.00 6.01
1118 1150 3.054503 CCAGGACGAGGTCGACGT 61.055 66.667 11.12 11.12 46.58 4.34
1126 1158 3.973267 GAGGTCGACGTGCTCTGCC 62.973 68.421 16.63 0.00 0.00 4.85
1132 1164 2.358003 ACGTGCTCTGCCAGAAGC 60.358 61.111 0.00 2.62 44.14 3.86
1224 1256 0.179073 GGTCCATCTGCGTGTATGCT 60.179 55.000 0.00 0.00 35.36 3.79
1345 1377 2.511600 GCGTCATGGAGGGGTTCG 60.512 66.667 0.00 0.00 0.00 3.95
1499 1535 4.856801 CTTCACGGGGATGCCGGG 62.857 72.222 15.29 3.45 35.17 5.73
1676 1769 4.664677 GAGTGCTCACGGTGGCGT 62.665 66.667 8.50 2.62 36.20 5.68
1716 1809 4.514577 CTCCCTGCTACGTGCCCG 62.515 72.222 0.00 0.00 42.00 6.13
1865 2026 5.824904 ATTTCTGAACATCGAAATCCCTG 57.175 39.130 0.00 0.00 35.55 4.45
1925 2101 1.141657 GTGCTTCTAGGCATGGATCCA 59.858 52.381 18.88 18.88 44.34 3.41
1937 2113 4.263199 GGCATGGATCCATCTGTCTATGAA 60.263 45.833 24.93 0.00 35.94 2.57
1963 2139 2.125350 GGTTCTGCTGGCGGAGAG 60.125 66.667 0.00 0.00 38.90 3.20
2042 2275 1.521450 GGGAGAACGACGGACACTCA 61.521 60.000 0.00 0.00 0.00 3.41
2054 2287 1.006102 ACACTCACCGCCTCTTTCG 60.006 57.895 0.00 0.00 0.00 3.46
2095 2340 3.560251 ACCGCCACAGCACTTCCT 61.560 61.111 0.00 0.00 39.83 3.36
2105 2374 1.378250 GCACTTCCTCAGCAGGCAT 60.378 57.895 0.00 0.00 40.12 4.40
2112 2381 1.145598 CTCAGCAGGCATGACGGAT 59.854 57.895 1.57 0.00 0.00 4.18
2338 2989 1.883544 CGAGCTCTCCGCGTCTCTA 60.884 63.158 12.85 0.00 45.59 2.43
2535 3315 1.510383 CGGAGACTGAGCTGGTGAG 59.490 63.158 0.00 0.00 0.00 3.51
2620 3406 1.992277 GCTCCTGGCCTCTGAGGAA 60.992 63.158 27.53 13.05 37.67 3.36
2712 3498 3.031660 GTGCTGCCTGAGTACGTAC 57.968 57.895 18.10 18.10 0.00 3.67
2755 3558 6.183360 GGAATTTAAAACCTTCTATGCGCTCT 60.183 38.462 9.73 0.00 0.00 4.09
2836 3658 4.290985 CCTCTATCCTGGAGATCCACTCTA 59.709 50.000 1.52 0.00 44.37 2.43
2842 3664 7.937700 ATCCTGGAGATCCACTCTATTTTTA 57.062 36.000 1.52 0.00 44.37 1.52
2861 3683 0.250901 AGTTGCCGCAGTTTCCTGAT 60.251 50.000 0.00 0.00 41.50 2.90
2865 3687 0.727398 GCCGCAGTTTCCTGATGTAC 59.273 55.000 0.00 0.00 41.50 2.90
2869 3691 3.555956 CCGCAGTTTCCTGATGTACATAC 59.444 47.826 8.71 2.05 41.50 2.39
2870 3692 4.180817 CGCAGTTTCCTGATGTACATACA 58.819 43.478 8.71 7.93 41.50 2.29
2871 3693 4.629634 CGCAGTTTCCTGATGTACATACAA 59.370 41.667 8.71 0.00 41.50 2.41
2875 3697 7.362056 GCAGTTTCCTGATGTACATACAACATT 60.362 37.037 8.71 0.00 41.50 2.71
2878 3700 5.495640 TCCTGATGTACATACAACATTGCA 58.504 37.500 8.71 0.00 38.13 4.08
3045 3913 2.029849 GCGTGGCGAACAAAACAAAATT 59.970 40.909 0.00 0.00 0.00 1.82
3047 3915 3.304559 CGTGGCGAACAAAACAAAATTGA 59.695 39.130 0.00 0.00 0.00 2.57
3135 4099 7.795431 TTATGATGAAACTTTGCGAACATTC 57.205 32.000 0.00 1.36 0.00 2.67
3177 4141 2.579787 CGGCCTAACGTGAGCTCG 60.580 66.667 9.64 0.45 0.00 5.03
3179 4143 2.707849 GGCCTAACGTGAGCTCGGA 61.708 63.158 9.64 0.00 34.94 4.55
3252 5227 3.515630 CTCATAAGAGCTCAGCGAACAA 58.484 45.455 17.77 0.00 34.61 2.83
3254 5229 5.262588 TCATAAGAGCTCAGCGAACAATA 57.737 39.130 17.77 0.00 0.00 1.90
3264 5239 5.107875 GCTCAGCGAACAATAAAACCAAAAG 60.108 40.000 0.00 0.00 0.00 2.27
3307 5283 9.883142 AAAAATTCTGATTTTACTCACCAAACA 57.117 25.926 0.00 0.00 42.97 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.284408 GTGGCCGTTGATCGCAAAA 59.716 52.632 0.00 0.00 35.42 2.44
49 50 1.138036 TACTCGTGGCCGTTGATCG 59.862 57.895 0.00 0.00 39.52 3.69
63 64 7.449086 AGCTAGATAGTATCCCTTGTTGTACTC 59.551 40.741 6.53 0.00 0.00 2.59
174 175 5.186021 CCACTTCCTTTCTAGCACTCTCTTA 59.814 44.000 0.00 0.00 0.00 2.10
194 195 2.101249 CACACCAAAAGCATGTTCCACT 59.899 45.455 0.00 0.00 0.00 4.00
254 255 6.183361 CCCAAAGCTTTATTTCATCCCATGAT 60.183 38.462 12.25 0.00 39.39 2.45
268 269 3.330701 AGTCATCACCTCCCAAAGCTTTA 59.669 43.478 12.25 0.00 0.00 1.85
304 305 1.716050 CCTCGACGATCATATTGTGCG 59.284 52.381 0.00 0.00 0.00 5.34
344 345 7.148086 CCTTGATAATCAAATCCTTGGTCGAAA 60.148 37.037 0.00 0.00 35.73 3.46
455 456 6.592607 CCAACTCATTTTGAAGATCCAAATGG 59.407 38.462 13.62 0.00 36.12 3.16
476 477 1.355210 CCACACGTGCTCAACCAAC 59.645 57.895 17.22 0.00 0.00 3.77
537 538 8.193953 ACCAAATCAAAATTGTCTAGAATGGT 57.806 30.769 0.00 0.00 0.00 3.55
538 539 8.928733 CAACCAAATCAAAATTGTCTAGAATGG 58.071 33.333 0.00 0.00 0.00 3.16
580 583 9.549078 TTTTACAACCCAATAAAAATTGTCTCC 57.451 29.630 0.00 0.00 35.26 3.71
685 688 0.694444 ATTAGCCCCATCCTGTCCGT 60.694 55.000 0.00 0.00 0.00 4.69
701 704 2.437002 GTCCGGCCGCAACCATTA 60.437 61.111 22.85 0.00 0.00 1.90
732 735 1.134521 GCGTGTTCTGGGATATGGTGA 60.135 52.381 0.00 0.00 0.00 4.02
738 741 2.727392 CCGGGCGTGTTCTGGGATA 61.727 63.158 0.00 0.00 0.00 2.59
746 749 1.449601 GATCATGTCCGGGCGTGTT 60.450 57.895 26.79 19.49 0.00 3.32
763 766 2.047061 CCTTTGGATAGGACGATGGGA 58.953 52.381 0.00 0.00 37.50 4.37
771 774 6.603940 CAAATTTTGTCCCTTTGGATAGGA 57.396 37.500 0.78 0.00 44.28 2.94
792 795 2.114411 GACCTCCGGTTTGGCCAA 59.886 61.111 16.05 16.05 35.25 4.52
793 796 3.961414 GGACCTCCGGTTTGGCCA 61.961 66.667 0.00 0.00 35.25 5.36
821 824 3.442273 ACAAACCGAAAGTGCTCTTTTGA 59.558 39.130 23.93 0.00 43.87 2.69
822 825 3.769536 ACAAACCGAAAGTGCTCTTTTG 58.230 40.909 17.89 17.89 42.99 2.44
860 863 3.754586 TTTGTTGGCTGGCTGGGCT 62.755 57.895 2.00 0.00 0.00 5.19
869 872 0.394352 CCTATCCGGCTTTGTTGGCT 60.394 55.000 0.00 0.00 0.00 4.75
871 874 2.285977 GTACCTATCCGGCTTTGTTGG 58.714 52.381 0.00 0.00 35.61 3.77
872 875 2.980568 TGTACCTATCCGGCTTTGTTG 58.019 47.619 0.00 0.00 35.61 3.33
873 876 3.706600 TTGTACCTATCCGGCTTTGTT 57.293 42.857 0.00 0.00 35.61 2.83
875 878 3.377172 CCTTTTGTACCTATCCGGCTTTG 59.623 47.826 0.00 0.00 35.61 2.77
876 879 3.617284 CCTTTTGTACCTATCCGGCTTT 58.383 45.455 0.00 0.00 35.61 3.51
877 880 2.092592 CCCTTTTGTACCTATCCGGCTT 60.093 50.000 0.00 0.00 35.61 4.35
878 881 1.489230 CCCTTTTGTACCTATCCGGCT 59.511 52.381 0.00 0.00 35.61 5.52
879 882 1.963172 CCCTTTTGTACCTATCCGGC 58.037 55.000 0.00 0.00 35.61 6.13
881 884 2.169769 TGAGCCCTTTTGTACCTATCCG 59.830 50.000 0.00 0.00 0.00 4.18
882 885 3.200165 AGTGAGCCCTTTTGTACCTATCC 59.800 47.826 0.00 0.00 0.00 2.59
884 887 3.622455 GCAGTGAGCCCTTTTGTACCTAT 60.622 47.826 0.00 0.00 37.23 2.57
885 888 2.290071 GCAGTGAGCCCTTTTGTACCTA 60.290 50.000 0.00 0.00 37.23 3.08
886 889 1.545651 GCAGTGAGCCCTTTTGTACCT 60.546 52.381 0.00 0.00 37.23 3.08
888 891 0.517316 CGCAGTGAGCCCTTTTGTAC 59.483 55.000 0.00 0.00 41.38 2.90
899 907 2.022129 GGTGACGAACCGCAGTGAG 61.022 63.158 0.00 0.00 39.81 3.51
929 937 1.227943 GTCTTGGACCTGCACTGCA 60.228 57.895 3.11 3.11 36.92 4.41
930 938 1.227943 TGTCTTGGACCTGCACTGC 60.228 57.895 0.00 0.00 0.00 4.40
931 939 0.604780 CCTGTCTTGGACCTGCACTG 60.605 60.000 0.00 0.00 0.00 3.66
932 940 1.757306 CCTGTCTTGGACCTGCACT 59.243 57.895 0.00 0.00 0.00 4.40
933 941 1.302832 CCCTGTCTTGGACCTGCAC 60.303 63.158 0.00 0.00 0.00 4.57
934 942 3.160585 CCCTGTCTTGGACCTGCA 58.839 61.111 0.00 0.00 0.00 4.41
935 943 2.360475 GCCCTGTCTTGGACCTGC 60.360 66.667 0.00 0.00 0.00 4.85
936 944 1.002868 CTGCCCTGTCTTGGACCTG 60.003 63.158 0.00 0.00 0.00 4.00
938 946 2.352805 CCTGCCCTGTCTTGGACC 59.647 66.667 0.00 0.00 0.00 4.46
939 947 1.779061 TTCCCTGCCCTGTCTTGGAC 61.779 60.000 0.00 0.00 0.00 4.02
940 948 1.463214 TTCCCTGCCCTGTCTTGGA 60.463 57.895 0.00 0.00 0.00 3.53
941 949 1.001641 CTTCCCTGCCCTGTCTTGG 60.002 63.158 0.00 0.00 0.00 3.61
944 952 1.614824 CTCCTTCCCTGCCCTGTCT 60.615 63.158 0.00 0.00 0.00 3.41
946 954 2.612115 CCTCCTTCCCTGCCCTGT 60.612 66.667 0.00 0.00 0.00 4.00
1126 1158 2.813908 GGGTACGCCGTGCTTCTG 60.814 66.667 5.11 0.00 34.97 3.02
1132 1164 1.520787 GATCCTTGGGTACGCCGTG 60.521 63.158 7.55 0.00 34.97 4.94
1430 1462 2.152016 GACAGTACCACCCTTTCTTGC 58.848 52.381 0.00 0.00 0.00 4.01
1676 1769 2.832129 AGGTTCCTAAGATCAACAGCGA 59.168 45.455 0.00 0.00 0.00 4.93
1800 1899 6.489361 AGGAAGTAGTACGAGTTGAAGAAGAA 59.511 38.462 0.30 0.00 0.00 2.52
1801 1900 6.002704 AGGAAGTAGTACGAGTTGAAGAAGA 58.997 40.000 0.30 0.00 0.00 2.87
1865 2026 2.939103 CTCGATGAAACAGGGGAATCAC 59.061 50.000 0.00 0.00 0.00 3.06
1925 2101 8.492782 AGAACCTTCATCATTTCATAGACAGAT 58.507 33.333 0.00 0.00 0.00 2.90
1937 2113 2.097825 GCCAGCAGAACCTTCATCATT 58.902 47.619 0.00 0.00 0.00 2.57
2095 2340 0.104855 GTATCCGTCATGCCTGCTGA 59.895 55.000 0.00 0.00 0.00 4.26
2105 2374 1.807226 CAGCTCCGTGTATCCGTCA 59.193 57.895 0.00 0.00 0.00 4.35
2112 2381 2.262603 CTGCAGCAGCTCCGTGTA 59.737 61.111 10.14 0.00 42.74 2.90
2159 2710 3.655211 CTGGCCACCAGCTTCCCT 61.655 66.667 0.00 0.00 45.13 4.20
2360 3059 3.049674 CTCCGCCGCTTGCTTTGA 61.050 61.111 0.00 0.00 38.05 2.69
2535 3315 2.935740 GCAAGCTTGGCCTTCACCC 61.936 63.158 27.10 3.94 0.00 4.61
2712 3498 2.235016 TCCAAAAACCCATCGACAAGG 58.765 47.619 0.00 0.00 0.00 3.61
2750 3538 1.144565 CTCCAGCGATGAACAGAGCG 61.145 60.000 0.06 0.00 34.34 5.03
2755 3558 4.670896 TTATGATCTCCAGCGATGAACA 57.329 40.909 0.06 0.00 0.00 3.18
2836 3658 3.320826 AGGAAACTGCGGCAACTAAAAAT 59.679 39.130 3.44 0.00 41.13 1.82
2861 3683 8.829612 CAGATAATCTGCAATGTTGTATGTACA 58.170 33.333 0.00 0.00 37.72 2.90
2865 3687 7.041303 AGCTCAGATAATCTGCAATGTTGTATG 60.041 37.037 0.00 0.00 43.95 2.39
2869 3691 5.296035 TGAGCTCAGATAATCTGCAATGTTG 59.704 40.000 13.74 0.00 43.95 3.33
2870 3692 5.434408 TGAGCTCAGATAATCTGCAATGTT 58.566 37.500 13.74 0.00 43.95 2.71
2871 3693 5.032327 TGAGCTCAGATAATCTGCAATGT 57.968 39.130 13.74 0.00 43.95 2.71
2875 3697 3.464907 GCTTGAGCTCAGATAATCTGCA 58.535 45.455 17.43 0.00 43.95 4.41
2904 3726 8.871686 ATCATTTGTTTGGTTTTACTGTTCTC 57.128 30.769 0.00 0.00 0.00 2.87
2961 3790 8.434661 GCAATCAAAATATTTGACGATGTTTGT 58.565 29.630 7.61 0.00 0.00 2.83
3022 3890 0.101399 TTGTTTTGTTCGCCACGCAT 59.899 45.000 0.00 0.00 0.00 4.73
3101 4065 9.962759 GCAAAGTTTCATCATAAAATGACATTC 57.037 29.630 0.05 0.00 43.01 2.67
3102 4066 8.649841 CGCAAAGTTTCATCATAAAATGACATT 58.350 29.630 0.00 0.00 43.01 2.71
3103 4067 8.028354 TCGCAAAGTTTCATCATAAAATGACAT 58.972 29.630 0.00 0.00 43.01 3.06
3108 4072 8.761575 ATGTTCGCAAAGTTTCATCATAAAAT 57.238 26.923 0.00 0.00 0.00 1.82
3135 4099 7.467623 GGTATGCAGACTTTTAGAATGTTCTG 58.532 38.462 11.87 0.00 38.19 3.02
3177 4141 1.120530 TAGAATGCCCTTCTCGGTCC 58.879 55.000 2.18 0.00 43.32 4.46
3179 4143 3.713826 TTTTAGAATGCCCTTCTCGGT 57.286 42.857 2.18 0.00 43.32 4.69


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

AutoCloner maintained by Alex Coulton.