Multiple sequence alignment - TraesCS7A01G364900

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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 TraesCS7A01G364900 chr7A 100.000 3336 0 0 1 3336 538821188 538824523 0.000000e+00 6161.0
1 TraesCS7A01G364900 chr7A 94.485 689 33 4 1 689 725469887 725469204 0.000000e+00 1057.0
2 TraesCS7A01G364900 chr7A 91.966 697 45 5 1 687 709855656 709856351 0.000000e+00 966.0
3 TraesCS7A01G364900 chr7A 91.457 199 7 2 2336 2534 538836975 538837163 7.100000e-67 265.0
4 TraesCS7A01G364900 chr7A 75.872 344 42 22 1494 1832 538807597 538807290 1.610000e-28 137.0
5 TraesCS7A01G364900 chr7A 74.926 339 41 27 1494 1829 538819742 538819445 7.560000e-22 115.0
6 TraesCS7A01G364900 chr7D 86.322 1623 148 36 751 2333 460794459 460792871 0.000000e+00 1700.0
7 TraesCS7A01G364900 chr7D 86.990 1030 87 23 2338 3336 631463754 631464767 0.000000e+00 1116.0
8 TraesCS7A01G364900 chr7D 76.577 333 47 20 1504 1829 461142332 461142640 1.600000e-33 154.0
9 TraesCS7A01G364900 chr7D 82.353 187 12 6 810 996 461130005 461129840 3.470000e-30 143.0
10 TraesCS7A01G364900 chr7D 75.915 328 44 23 1504 1829 460795966 460796260 5.810000e-28 135.0
11 TraesCS7A01G364900 chr7B 86.249 1549 134 51 682 2175 483329894 483328370 0.000000e+00 1607.0
12 TraesCS7A01G364900 chr7B 79.548 753 132 17 2588 3326 554177556 554178300 4.930000e-143 518.0
13 TraesCS7A01G364900 chr7B 84.182 373 33 12 1272 1624 483343353 483342987 4.120000e-89 339.0
14 TraesCS7A01G364900 chr7B 77.778 468 50 27 1377 1829 483329988 483330416 4.300000e-59 239.0
15 TraesCS7A01G364900 chr7B 75.140 358 47 28 1494 1829 483765844 483766181 2.700000e-26 130.0
16 TraesCS7A01G364900 chr7B 75.535 327 43 26 1504 1829 483759681 483759971 3.490000e-25 126.0
17 TraesCS7A01G364900 chr3B 88.574 1024 70 18 2337 3336 673837909 673838909 0.000000e+00 1199.0
18 TraesCS7A01G364900 chr3B 81.034 812 112 18 2559 3336 747734403 747735206 2.850000e-170 608.0
19 TraesCS7A01G364900 chr3B 85.427 199 18 2 2336 2534 673840075 673840262 2.630000e-46 196.0
20 TraesCS7A01G364900 chr3B 87.619 105 9 3 2217 2319 625886908 625886806 5.850000e-23 119.0
21 TraesCS7A01G364900 chr4A 94.493 690 34 2 1 689 539142611 539143297 0.000000e+00 1061.0
22 TraesCS7A01G364900 chr2A 94.477 688 30 3 1 683 35939744 35940428 0.000000e+00 1053.0
23 TraesCS7A01G364900 chr2A 91.849 687 52 3 1 686 421914025 421914708 0.000000e+00 955.0
24 TraesCS7A01G364900 chr4B 87.965 914 69 21 2437 3324 665983381 665984279 0.000000e+00 1040.0
25 TraesCS7A01G364900 chr5A 92.286 700 44 8 1 698 589307219 589306528 0.000000e+00 985.0
26 TraesCS7A01G364900 chr1A 92.587 688 47 3 1 685 520127996 520128682 0.000000e+00 985.0
27 TraesCS7A01G364900 chrUn 92.052 692 47 3 1 686 150817874 150817185 0.000000e+00 966.0
28 TraesCS7A01G364900 chr6A 91.618 692 47 6 1 685 544168160 544168847 0.000000e+00 946.0
29 TraesCS7A01G364900 chr6A 81.756 1025 139 31 2336 3329 39866931 39867938 0.000000e+00 813.0
30 TraesCS7A01G364900 chr3D 84.385 967 110 27 2401 3336 569804541 569805497 0.000000e+00 911.0
31 TraesCS7A01G364900 chr2D 81.769 927 115 32 2437 3329 184115887 184116793 0.000000e+00 726.0
32 TraesCS7A01G364900 chr2B 82.222 675 108 12 2663 3329 58804195 58803525 3.730000e-159 571.0
33 TraesCS7A01G364900 chr1B 91.139 237 14 4 2401 2637 236947938 236948167 6.950000e-82 315.0
34 TraesCS7A01G364900 chr1B 94.595 37 2 0 2330 2366 236947890 236947926 1.290000e-04 58.4
35 TraesCS7A01G364900 chr1D 87.255 102 13 0 2233 2334 370918940 370919041 2.100000e-22 117.0


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 TraesCS7A01G364900 chr7A 538821188 538824523 3335 False 6161.0 6161 100.0000 1 3336 1 chr7A.!!$F1 3335
1 TraesCS7A01G364900 chr7A 725469204 725469887 683 True 1057.0 1057 94.4850 1 689 1 chr7A.!!$R3 688
2 TraesCS7A01G364900 chr7A 709855656 709856351 695 False 966.0 966 91.9660 1 687 1 chr7A.!!$F3 686
3 TraesCS7A01G364900 chr7D 460792871 460794459 1588 True 1700.0 1700 86.3220 751 2333 1 chr7D.!!$R1 1582
4 TraesCS7A01G364900 chr7D 631463754 631464767 1013 False 1116.0 1116 86.9900 2338 3336 1 chr7D.!!$F3 998
5 TraesCS7A01G364900 chr7B 483328370 483329894 1524 True 1607.0 1607 86.2490 682 2175 1 chr7B.!!$R1 1493
6 TraesCS7A01G364900 chr7B 554177556 554178300 744 False 518.0 518 79.5480 2588 3326 1 chr7B.!!$F4 738
7 TraesCS7A01G364900 chr3B 673837909 673840262 2353 False 697.5 1199 87.0005 2336 3336 2 chr3B.!!$F2 1000
8 TraesCS7A01G364900 chr3B 747734403 747735206 803 False 608.0 608 81.0340 2559 3336 1 chr3B.!!$F1 777
9 TraesCS7A01G364900 chr4A 539142611 539143297 686 False 1061.0 1061 94.4930 1 689 1 chr4A.!!$F1 688
10 TraesCS7A01G364900 chr2A 35939744 35940428 684 False 1053.0 1053 94.4770 1 683 1 chr2A.!!$F1 682
11 TraesCS7A01G364900 chr2A 421914025 421914708 683 False 955.0 955 91.8490 1 686 1 chr2A.!!$F2 685
12 TraesCS7A01G364900 chr4B 665983381 665984279 898 False 1040.0 1040 87.9650 2437 3324 1 chr4B.!!$F1 887
13 TraesCS7A01G364900 chr5A 589306528 589307219 691 True 985.0 985 92.2860 1 698 1 chr5A.!!$R1 697
14 TraesCS7A01G364900 chr1A 520127996 520128682 686 False 985.0 985 92.5870 1 685 1 chr1A.!!$F1 684
15 TraesCS7A01G364900 chrUn 150817185 150817874 689 True 966.0 966 92.0520 1 686 1 chrUn.!!$R1 685
16 TraesCS7A01G364900 chr6A 544168160 544168847 687 False 946.0 946 91.6180 1 685 1 chr6A.!!$F2 684
17 TraesCS7A01G364900 chr6A 39866931 39867938 1007 False 813.0 813 81.7560 2336 3329 1 chr6A.!!$F1 993
18 TraesCS7A01G364900 chr3D 569804541 569805497 956 False 911.0 911 84.3850 2401 3336 1 chr3D.!!$F1 935
19 TraesCS7A01G364900 chr2D 184115887 184116793 906 False 726.0 726 81.7690 2437 3329 1 chr2D.!!$F1 892
20 TraesCS7A01G364900 chr2B 58803525 58804195 670 True 571.0 571 82.2220 2663 3329 1 chr2B.!!$R1 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
733 756 0.246635 CGGAGACTGGTTGACGGATT 59.753 55.0 0.00 0.00 0.00 3.01 F
1739 1830 0.108520 GTGCATGGCCTTGTTCATGG 60.109 55.0 19.05 1.09 40.59 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1978 0.108585 AACCGTGATGAACAGCAGGT 59.891 50.0 10.82 9.23 34.87 4.00 R
3276 3443 1.041447 CCCTGGTTACCGAGGACGAT 61.041 60.0 17.46 0.00 42.66 3.73 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
428 446 4.715523 CGTCCATGGGTGCGGGTT 62.716 66.667 13.02 0.00 0.00 4.11
473 492 0.793617 TGGAGGGGGAGAAGAAGAGT 59.206 55.000 0.00 0.00 0.00 3.24
646 665 2.981400 AAAACGGACGATTTTGCGAT 57.019 40.000 0.00 0.00 33.96 4.58
652 671 2.309764 GACGATTTTGCGATGCGGCT 62.310 55.000 0.00 0.00 34.83 5.52
662 681 1.154205 CGATGCGGCTCCTGTTTAGG 61.154 60.000 0.00 0.00 46.06 2.69
666 685 2.124695 GGCTCCTGTTTAGGGCGG 60.125 66.667 0.00 0.00 44.70 6.13
705 728 2.258591 GCGTCGTCTTGCCTGAGA 59.741 61.111 0.00 0.00 0.00 3.27
730 753 1.080705 GACGGAGACTGGTTGACGG 60.081 63.158 0.00 0.00 0.00 4.79
733 756 0.246635 CGGAGACTGGTTGACGGATT 59.753 55.000 0.00 0.00 0.00 3.01
734 757 1.726853 GGAGACTGGTTGACGGATTG 58.273 55.000 0.00 0.00 0.00 2.67
735 758 1.002087 GGAGACTGGTTGACGGATTGT 59.998 52.381 0.00 0.00 0.00 2.71
736 759 2.550208 GGAGACTGGTTGACGGATTGTT 60.550 50.000 0.00 0.00 0.00 2.83
737 760 2.480419 GAGACTGGTTGACGGATTGTTG 59.520 50.000 0.00 0.00 0.00 3.33
749 772 6.664515 TGACGGATTGTTGCTTAAACTAAAG 58.335 36.000 0.00 0.00 39.70 1.85
750 773 6.009115 ACGGATTGTTGCTTAAACTAAAGG 57.991 37.500 0.00 0.00 39.70 3.11
768 791 2.399611 GAAGAAATCCACGCGGCG 59.600 61.111 22.36 22.36 0.00 6.46
838 868 3.680490 GTCTTTCCTTCCTTCCTTCCTG 58.320 50.000 0.00 0.00 0.00 3.86
851 881 1.065199 CCTTCCTGGCTGTGCTTATCA 60.065 52.381 0.00 0.00 0.00 2.15
889 919 4.988598 ACGAAGGCCGGTGTGCTG 62.989 66.667 1.90 0.00 43.93 4.41
891 921 4.329545 GAAGGCCGGTGTGCTGGA 62.330 66.667 1.90 0.00 43.97 3.86
903 943 4.096231 CGGTGTGCTGGATCAAATCAAATA 59.904 41.667 0.00 0.00 0.00 1.40
917 957 1.060713 CAAATAGCGGATCCGTAGCG 58.939 55.000 33.33 14.75 42.09 4.26
952 998 2.202987 GCAGAGGAGATGCCACGG 60.203 66.667 0.00 0.00 40.02 4.94
970 1016 1.429148 GGATGGACGAATCGGTGCAC 61.429 60.000 8.80 8.80 41.15 4.57
990 1036 2.099831 CACGACGGAGGAGTACGC 59.900 66.667 0.00 0.00 0.00 4.42
1038 1084 4.319190 GGCATAATTACACGCGCTGATTAA 60.319 41.667 5.73 0.43 0.00 1.40
1057 1103 2.126914 ATGATTAGCAGAGACGACGC 57.873 50.000 0.00 0.00 0.00 5.19
1092 1138 2.065899 TTCTGCTCTAGGCTCCTCTC 57.934 55.000 0.00 0.00 42.39 3.20
1093 1139 1.221635 TCTGCTCTAGGCTCCTCTCT 58.778 55.000 0.00 0.00 42.39 3.10
1157 1209 3.041940 GGTCAACCACGCACGAGG 61.042 66.667 4.92 4.92 35.64 4.63
1158 1210 3.712881 GTCAACCACGCACGAGGC 61.713 66.667 6.42 0.00 39.90 4.70
1159 1211 4.980805 TCAACCACGCACGAGGCC 62.981 66.667 6.42 0.00 40.31 5.19
1183 1235 2.456000 CGTCCAACGGAACCATGAG 58.544 57.895 0.00 0.00 38.08 2.90
1218 1270 2.253452 GCAAGCGCAACACCTGAG 59.747 61.111 11.47 0.00 38.36 3.35
1340 1407 0.734253 CGTGTCTGTGCAGCTCCTAC 60.734 60.000 0.00 0.00 0.00 3.18
1344 1411 2.038952 TGTCTGTGCAGCTCCTACAAAT 59.961 45.455 0.00 0.00 0.00 2.32
1345 1412 3.260632 TGTCTGTGCAGCTCCTACAAATA 59.739 43.478 0.00 0.00 0.00 1.40
1379 1446 4.322349 GCGATGCACTCTTCCTAATCCTAT 60.322 45.833 0.00 0.00 0.00 2.57
1418 1485 1.992538 AGCAGCAAAGCCTCTTTTCT 58.007 45.000 0.00 0.00 34.23 2.52
1419 1486 1.885233 AGCAGCAAAGCCTCTTTTCTC 59.115 47.619 0.00 0.00 34.23 2.87
1432 1499 4.588528 CCTCTTTTCTCCATCCTCCTCTAG 59.411 50.000 0.00 0.00 0.00 2.43
1459 1527 2.234661 TGATCGCTTCAGGAAGACACAT 59.765 45.455 13.01 0.00 40.79 3.21
1467 1535 5.645497 GCTTCAGGAAGACACATCAGTAATT 59.355 40.000 13.01 0.00 40.79 1.40
1696 1787 2.296471 TCTTGTTCGTCCCTTCTGAGTC 59.704 50.000 0.00 0.00 0.00 3.36
1703 1794 1.548269 GTCCCTTCTGAGTCCTGTCTG 59.452 57.143 0.00 0.00 0.00 3.51
1705 1796 0.108898 CCTTCTGAGTCCTGTCTGCG 60.109 60.000 0.00 0.00 0.00 5.18
1706 1797 0.735632 CTTCTGAGTCCTGTCTGCGC 60.736 60.000 0.00 0.00 0.00 6.09
1707 1798 1.463553 TTCTGAGTCCTGTCTGCGCA 61.464 55.000 10.98 10.98 0.00 6.09
1708 1799 1.217511 CTGAGTCCTGTCTGCGCAT 59.782 57.895 12.24 0.00 0.00 4.73
1739 1830 0.108520 GTGCATGGCCTTGTTCATGG 60.109 55.000 19.05 1.09 40.59 3.66
1740 1831 0.542467 TGCATGGCCTTGTTCATGGT 60.542 50.000 19.05 0.00 40.59 3.55
1771 1869 5.876612 ATCATGTTTGTCTGCTTCTTCTC 57.123 39.130 0.00 0.00 0.00 2.87
1839 1937 5.638783 CCTGCTTCTGATCAAGTCAATTTC 58.361 41.667 0.00 0.00 36.14 2.17
1844 1942 6.127814 GCTTCTGATCAAGTCAATTTCATCCA 60.128 38.462 0.00 0.00 36.14 3.41
1845 1943 7.416438 GCTTCTGATCAAGTCAATTTCATCCAT 60.416 37.037 0.00 0.00 36.14 3.41
1853 1951 2.609002 TCAATTTCATCCATCGTGCTCG 59.391 45.455 0.81 0.81 38.55 5.03
1858 1956 1.067060 TCATCCATCGTGCTCGGTTAG 59.933 52.381 8.49 0.00 37.69 2.34
1860 1958 1.883084 CCATCGTGCTCGGTTAGGC 60.883 63.158 8.49 0.00 37.69 3.93
1868 1966 1.226888 CTCGGTTAGGCTACGTGGC 60.227 63.158 16.51 16.51 42.15 5.01
1876 1974 4.083746 GCTACGTGGCCTAACGAC 57.916 61.111 21.25 7.32 46.49 4.34
1880 1978 1.525718 TACGTGGCCTAACGACTGCA 61.526 55.000 21.25 0.00 46.49 4.41
1915 2013 0.541863 GGTTGATGTGGAGTCCGGAT 59.458 55.000 7.81 0.00 0.00 4.18
1921 2019 0.824109 TGTGGAGTCCGGATGTCATC 59.176 55.000 7.81 4.06 0.00 2.92
1927 2027 4.142790 GGAGTCCGGATGTCATCTAGTAA 58.857 47.826 7.81 0.00 0.00 2.24
1992 2092 2.288395 GCAGTGCTATTTGTTGGTTGCT 60.288 45.455 8.18 0.00 0.00 3.91
2014 2114 5.420725 TCAGCACCATTTCTGTGTAGTAT 57.579 39.130 0.00 0.00 36.11 2.12
2015 2115 5.178061 TCAGCACCATTTCTGTGTAGTATG 58.822 41.667 0.00 0.00 36.11 2.39
2028 2133 5.418676 TGTGTAGTATGTCATGGTGATGTG 58.581 41.667 0.00 0.00 0.00 3.21
2031 2136 1.949525 GTATGTCATGGTGATGTGGCC 59.050 52.381 0.00 0.00 0.00 5.36
2056 2161 7.442364 CCCGATCTCTTGTACATTGATTATGTT 59.558 37.037 0.00 0.00 45.19 2.71
2057 2162 9.476202 CCGATCTCTTGTACATTGATTATGTTA 57.524 33.333 0.00 0.00 45.19 2.41
2118 2231 6.535508 AGTCGCTTCACCTCTTCAATTTATAC 59.464 38.462 0.00 0.00 0.00 1.47
2143 2257 2.621763 GCTGATGGAGCCATAACCG 58.378 57.895 1.21 0.00 42.54 4.44
2164 2278 3.064987 CTCGCTTCGGTGGGACGAT 62.065 63.158 0.00 0.00 43.11 3.73
2228 2342 5.525012 TCAAAGATGTTGTCTCAAGTCACTG 59.475 40.000 0.00 0.00 35.67 3.66
2230 2344 2.988010 TGTTGTCTCAAGTCACTGCT 57.012 45.000 0.00 0.00 0.00 4.24
2231 2345 3.266510 TGTTGTCTCAAGTCACTGCTT 57.733 42.857 0.00 0.00 0.00 3.91
2251 2365 4.615223 GCTTAACCGTTTGATTCACCCTTC 60.615 45.833 0.00 0.00 0.00 3.46
2254 2368 1.200020 CCGTTTGATTCACCCTTCTGC 59.800 52.381 0.00 0.00 0.00 4.26
2256 2370 2.293122 CGTTTGATTCACCCTTCTGCAA 59.707 45.455 0.00 0.00 0.00 4.08
2274 2388 7.589958 TCTGCAAGGGTTTGATAAAAACTAA 57.410 32.000 0.00 0.00 36.36 2.24
2309 2424 8.760980 TTTCAATAGGGGAAGGTTACATATTG 57.239 34.615 0.00 0.00 32.85 1.90
2319 2434 3.463329 AGGTTACATATTGGTGATGGCCT 59.537 43.478 3.32 0.00 0.00 5.19
2321 2436 4.760204 GGTTACATATTGGTGATGGCCTAC 59.240 45.833 3.32 0.00 0.00 3.18
2379 2494 9.695526 TTGTACATTATGTAACGTTGTACTCTT 57.304 29.630 19.54 2.97 41.86 2.85
2426 2543 5.076182 CCTAGATTGTAGGATCTGAGCTCA 58.924 45.833 17.19 17.19 37.01 4.26
2427 2544 5.716228 CCTAGATTGTAGGATCTGAGCTCAT 59.284 44.000 18.63 2.44 37.01 2.90
2456 2575 1.153549 CCTGCGTGCCTAACTCTCC 60.154 63.158 0.00 0.00 0.00 3.71
2460 2579 1.888018 CGTGCCTAACTCTCCGGAA 59.112 57.895 5.23 0.00 0.00 4.30
2461 2580 0.458025 CGTGCCTAACTCTCCGGAAC 60.458 60.000 5.23 0.00 0.00 3.62
2462 2581 0.606604 GTGCCTAACTCTCCGGAACA 59.393 55.000 5.23 0.00 0.00 3.18
2485 2604 6.897966 ACATTCTCTCCCTCTCTATGTAAACA 59.102 38.462 0.00 0.00 0.00 2.83
2489 2610 5.827756 TCTCCCTCTCTATGTAAACACTGA 58.172 41.667 0.00 0.00 0.00 3.41
2495 2616 7.707035 CCCTCTCTATGTAAACACTGATTGTAC 59.293 40.741 0.00 0.00 37.51 2.90
2585 2708 0.107831 CGGACGATCTCTCCTCCTCT 59.892 60.000 0.00 0.00 0.00 3.69
2586 2709 1.876416 CGGACGATCTCTCCTCCTCTC 60.876 61.905 0.00 0.00 0.00 3.20
2587 2710 1.544759 GGACGATCTCTCCTCCTCTCC 60.545 61.905 0.00 0.00 0.00 3.71
2711 2870 2.354401 CCTCTTCAGCGGCTCCTCA 61.354 63.158 0.00 0.00 0.00 3.86
2755 2916 2.599281 TCTCTTCACCACCGCCGA 60.599 61.111 0.00 0.00 0.00 5.54
2835 2997 4.338118 ACATCACGAACCACATCAAGTTTT 59.662 37.500 0.00 0.00 0.00 2.43
2977 3141 3.069980 GAGCTCGACGCCCACATCT 62.070 63.158 0.00 0.00 40.39 2.90
3114 3280 1.740380 CGCTTCATGATCCTCAACCGT 60.740 52.381 0.00 0.00 0.00 4.83
3118 3284 2.972625 TCATGATCCTCAACCGTCAAC 58.027 47.619 0.00 0.00 0.00 3.18
3151 3318 5.012458 TCAAACAGGATGATCTCTCTGTGTT 59.988 40.000 13.29 11.08 39.69 3.32
3162 3329 1.810755 TCTCTGTGTTCGAGTACGCAT 59.189 47.619 4.09 0.00 37.84 4.73
3259 3426 0.674581 CTTCATGGCCTCGACAAGCA 60.675 55.000 3.32 0.00 0.00 3.91
3276 3443 3.381983 AGCTCGACACCATCCGCA 61.382 61.111 0.00 0.00 0.00 5.69
3330 3497 2.664851 TGCTCTCCCGCGTTGTTG 60.665 61.111 4.92 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
335 336 2.598787 CCACAAACCCTAGCCCGGA 61.599 63.158 0.73 0.00 0.00 5.14
621 640 1.149987 AAATCGTCCGTTTTAGCGCA 58.850 45.000 11.47 0.00 0.00 6.09
646 665 2.668632 CCCTAAACAGGAGCCGCA 59.331 61.111 0.00 0.00 0.00 5.69
652 671 1.774894 AACAGCCGCCCTAAACAGGA 61.775 55.000 0.00 0.00 0.00 3.86
662 681 3.512516 GCATCTCCAACAGCCGCC 61.513 66.667 0.00 0.00 0.00 6.13
715 738 1.002087 ACAATCCGTCAACCAGTCTCC 59.998 52.381 0.00 0.00 0.00 3.71
730 753 7.882179 TCTTCCCTTTAGTTTAAGCAACAATC 58.118 34.615 0.00 0.00 37.93 2.67
733 756 7.648039 TTTCTTCCCTTTAGTTTAAGCAACA 57.352 32.000 0.00 0.00 37.93 3.33
734 757 7.813148 GGATTTCTTCCCTTTAGTTTAAGCAAC 59.187 37.037 0.00 0.00 38.75 4.17
735 758 7.507616 TGGATTTCTTCCCTTTAGTTTAAGCAA 59.492 33.333 0.00 0.00 44.77 3.91
736 759 7.007723 TGGATTTCTTCCCTTTAGTTTAAGCA 58.992 34.615 0.00 0.00 44.77 3.91
737 760 7.313646 GTGGATTTCTTCCCTTTAGTTTAAGC 58.686 38.462 0.00 0.00 44.77 3.09
749 772 2.761195 GCCGCGTGGATTTCTTCCC 61.761 63.158 21.76 0.00 44.77 3.97
750 773 2.791927 GCCGCGTGGATTTCTTCC 59.208 61.111 21.76 0.00 45.69 3.46
820 850 1.075536 GCCAGGAAGGAAGGAAGGAAA 59.924 52.381 0.00 0.00 41.22 3.13
876 906 4.101448 GATCCAGCACACCGGCCT 62.101 66.667 0.00 0.00 0.00 5.19
883 913 4.201940 CGCTATTTGATTTGATCCAGCACA 60.202 41.667 0.00 0.00 0.00 4.57
889 919 4.142816 CGGATCCGCTATTTGATTTGATCC 60.143 45.833 23.37 0.00 42.05 3.36
891 921 4.389374 ACGGATCCGCTATTTGATTTGAT 58.611 39.130 33.62 6.17 44.19 2.57
917 957 1.028868 GCTCTGGATGCAGTTGACCC 61.029 60.000 14.43 0.00 0.00 4.46
952 998 1.752501 CGTGCACCGATTCGTCCATC 61.753 60.000 12.15 0.00 39.56 3.51
970 1016 3.129502 TACTCCTCCGTCGTGGCG 61.130 66.667 0.00 0.00 37.80 5.69
990 1036 1.732259 GCTCAACCGTGTTGGACTATG 59.268 52.381 14.23 3.42 42.00 2.23
1038 1084 1.269309 GGCGTCGTCTCTGCTAATCAT 60.269 52.381 0.00 0.00 0.00 2.45
1057 1103 0.673644 AGAAATCCAAGACGCCACGG 60.674 55.000 0.00 0.00 0.00 4.94
1092 1138 2.723746 GTGCACCACACCAAGCAG 59.276 61.111 5.22 0.00 44.02 4.24
1358 1425 5.247110 TGGATAGGATTAGGAAGAGTGCATC 59.753 44.000 0.00 0.00 0.00 3.91
1379 1446 4.413189 TGCTATGAAGATGAAGGGAATGGA 59.587 41.667 0.00 0.00 0.00 3.41
1432 1499 2.386661 TCCTGAAGCGATCAAGAACC 57.613 50.000 0.00 0.00 37.67 3.62
1459 1527 5.366477 TGGTAGCTCATGATGGAATTACTGA 59.634 40.000 0.00 0.00 0.00 3.41
1467 1535 1.415289 CTGCTGGTAGCTCATGATGGA 59.585 52.381 0.00 0.00 42.97 3.41
1703 1794 3.957535 CGGGAAGGATGCATGCGC 61.958 66.667 14.09 0.00 39.24 6.09
1705 1796 3.113745 CACGGGAAGGATGCATGC 58.886 61.111 11.82 11.82 0.00 4.06
1706 1797 1.750018 TGCACGGGAAGGATGCATG 60.750 57.895 2.46 0.00 44.17 4.06
1707 1798 2.676608 TGCACGGGAAGGATGCAT 59.323 55.556 0.00 0.00 44.17 3.96
1739 1830 5.514204 GCAGACAAACATGATTAAGCATCAC 59.486 40.000 2.53 0.00 45.12 3.06
1740 1831 5.416639 AGCAGACAAACATGATTAAGCATCA 59.583 36.000 2.53 0.00 46.41 3.07
1790 1888 3.896356 GAGGCAGCAGCAGCACAGA 62.896 63.158 12.41 0.00 45.49 3.41
1839 1937 1.491670 CTAACCGAGCACGATGGATG 58.508 55.000 4.70 0.00 42.66 3.51
1844 1942 0.384669 GTAGCCTAACCGAGCACGAT 59.615 55.000 4.70 0.00 42.66 3.73
1845 1943 1.805254 GTAGCCTAACCGAGCACGA 59.195 57.895 4.70 0.00 42.66 4.35
1860 1958 0.801067 GCAGTCGTTAGGCCACGTAG 60.801 60.000 14.56 7.64 41.16 3.51
1868 1966 1.016130 CAGCAGGTGCAGTCGTTAGG 61.016 60.000 4.48 0.00 45.16 2.69
1871 1969 1.153168 AACAGCAGGTGCAGTCGTT 60.153 52.632 4.48 0.00 45.16 3.85
1876 1974 0.520404 GTGATGAACAGCAGGTGCAG 59.480 55.000 4.48 0.00 38.84 4.41
1880 1978 0.108585 AACCGTGATGAACAGCAGGT 59.891 50.000 10.82 9.23 34.87 4.00
1915 2013 9.349713 AGGAAAACAAACAATTACTAGATGACA 57.650 29.630 0.00 0.00 0.00 3.58
1927 2027 6.403092 CCAAGCGAAAAAGGAAAACAAACAAT 60.403 34.615 0.00 0.00 0.00 2.71
1972 2072 3.004629 TGAGCAACCAACAAATAGCACTG 59.995 43.478 0.00 0.00 0.00 3.66
1976 2076 2.030007 TGCTGAGCAACCAACAAATAGC 60.030 45.455 3.81 0.00 34.76 2.97
1992 2092 3.769739 ACTACACAGAAATGGTGCTGA 57.230 42.857 0.00 0.00 39.87 4.26
2014 2114 1.001020 GGGCCACATCACCATGACA 60.001 57.895 4.39 0.00 33.72 3.58
2015 2115 2.114670 CGGGCCACATCACCATGAC 61.115 63.158 4.39 0.00 33.72 3.06
2028 2133 2.158957 TCAATGTACAAGAGATCGGGCC 60.159 50.000 0.00 0.00 0.00 5.80
2067 2172 7.279981 TGTTGCACAGTGATATTACTAACCATC 59.720 37.037 4.15 0.00 0.00 3.51
2094 2207 5.803020 ATAAATTGAAGAGGTGAAGCGAC 57.197 39.130 0.00 0.00 0.00 5.19
2143 2257 3.760035 TCCCACCGAAGCGAGCTC 61.760 66.667 2.73 2.73 0.00 4.09
2156 2270 0.617535 ATCCACACTCCATCGTCCCA 60.618 55.000 0.00 0.00 0.00 4.37
2164 2278 5.012664 ACACAATAACTGTATCCACACTCCA 59.987 40.000 0.00 0.00 36.10 3.86
2191 2305 8.121305 ACAACATCTTTGAGTGCCAATATTTA 57.879 30.769 0.00 0.00 34.23 1.40
2199 2313 3.141398 TGAGACAACATCTTTGAGTGCC 58.859 45.455 0.00 0.00 38.00 5.01
2200 2314 4.274459 ACTTGAGACAACATCTTTGAGTGC 59.726 41.667 0.00 0.00 38.00 4.40
2207 2321 3.812053 GCAGTGACTTGAGACAACATCTT 59.188 43.478 0.00 0.00 38.00 2.40
2228 2342 2.817844 AGGGTGAATCAAACGGTTAAGC 59.182 45.455 0.00 0.00 0.00 3.09
2230 2344 4.517453 CAGAAGGGTGAATCAAACGGTTAA 59.483 41.667 0.00 0.00 0.00 2.01
2231 2345 4.069304 CAGAAGGGTGAATCAAACGGTTA 58.931 43.478 0.00 0.00 0.00 2.85
2251 2365 6.868339 CCTTAGTTTTTATCAAACCCTTGCAG 59.132 38.462 0.00 0.00 32.14 4.41
2254 2368 7.170828 GCAACCTTAGTTTTTATCAAACCCTTG 59.829 37.037 0.00 0.00 32.45 3.61
2256 2370 6.553476 AGCAACCTTAGTTTTTATCAAACCCT 59.447 34.615 0.00 0.00 32.45 4.34
2287 2401 6.490040 CACCAATATGTAACCTTCCCCTATTG 59.510 42.308 0.00 0.00 0.00 1.90
2288 2402 6.391649 TCACCAATATGTAACCTTCCCCTATT 59.608 38.462 0.00 0.00 0.00 1.73
2290 2404 5.290335 TCACCAATATGTAACCTTCCCCTA 58.710 41.667 0.00 0.00 0.00 3.53
2291 2405 4.116113 TCACCAATATGTAACCTTCCCCT 58.884 43.478 0.00 0.00 0.00 4.79
2292 2406 4.513406 TCACCAATATGTAACCTTCCCC 57.487 45.455 0.00 0.00 0.00 4.81
2293 2407 4.827284 CCATCACCAATATGTAACCTTCCC 59.173 45.833 0.00 0.00 0.00 3.97
2295 2409 4.278419 GGCCATCACCAATATGTAACCTTC 59.722 45.833 0.00 0.00 0.00 3.46
2302 2417 2.782925 TGGTAGGCCATCACCAATATGT 59.217 45.455 18.58 0.00 41.83 2.29
2309 2424 1.141053 CCTAGTTGGTAGGCCATCACC 59.859 57.143 5.01 10.08 45.56 4.02
2321 2436 2.036733 TCAACACCGAGAACCTAGTTGG 59.963 50.000 0.00 0.00 37.52 3.77
2328 2443 1.949465 ACAACTCAACACCGAGAACC 58.051 50.000 0.00 0.00 36.47 3.62
2333 2448 7.656542 TGTACAAAATATACAACTCAACACCGA 59.343 33.333 0.00 0.00 29.59 4.69
2334 2449 7.798801 TGTACAAAATATACAACTCAACACCG 58.201 34.615 0.00 0.00 29.59 4.94
2456 2575 2.383855 AGAGAGGGAGAGAATGTTCCG 58.616 52.381 0.00 0.00 34.17 4.30
2460 2579 6.897966 TGTTTACATAGAGAGGGAGAGAATGT 59.102 38.462 0.00 0.00 0.00 2.71
2461 2580 7.069331 AGTGTTTACATAGAGAGGGAGAGAATG 59.931 40.741 0.00 0.00 0.00 2.67
2462 2581 7.069331 CAGTGTTTACATAGAGAGGGAGAGAAT 59.931 40.741 0.00 0.00 0.00 2.40
2485 2604 5.290493 TGAGTGTTTCTGGTACAATCAGT 57.710 39.130 2.45 0.00 43.24 3.41
2489 2610 7.639113 TTTTCTTGAGTGTTTCTGGTACAAT 57.361 32.000 0.00 0.00 38.70 2.71
2495 2616 8.352201 TGTTATGATTTTCTTGAGTGTTTCTGG 58.648 33.333 0.00 0.00 0.00 3.86
2755 2916 4.070552 GTGGCGCGGGAGAAGAGT 62.071 66.667 8.83 0.00 0.00 3.24
2835 2997 3.006728 ATCCGCGGGGTTGAGGAA 61.007 61.111 27.83 1.69 41.33 3.36
3031 3195 3.633116 GGCGTAGGTGGTGGTGGT 61.633 66.667 0.00 0.00 0.00 4.16
3114 3280 2.285083 CTGTTTGAGGTTCGGTGTTGA 58.715 47.619 0.00 0.00 0.00 3.18
3118 3284 1.806542 CATCCTGTTTGAGGTTCGGTG 59.193 52.381 0.00 0.00 43.37 4.94
3136 3303 4.034626 CGTACTCGAACACAGAGAGATCAT 59.965 45.833 0.00 0.00 38.97 2.45
3151 3318 2.101575 GACGGCATGCGTACTCGA 59.898 61.111 18.14 0.00 39.71 4.04
3162 3329 1.908299 TGAGGAGCTTCAGACGGCA 60.908 57.895 0.00 0.00 0.00 5.69
3259 3426 2.635229 GATGCGGATGGTGTCGAGCT 62.635 60.000 0.00 0.00 33.87 4.09
3276 3443 1.041447 CCCTGGTTACCGAGGACGAT 61.041 60.000 17.46 0.00 42.66 3.73


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

AutoCloner maintained by Alex Coulton.