Multiple sequence alignment - TraesCS2D01G222200

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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 TraesCS2D01G222200 chr2D 100.000 2897 0 0 1 2897 189376137 189379033 0.000000e+00 5350.0
1 TraesCS2D01G222200 chr2B 91.661 1499 60 19 609 2087 245784088 245785541 0.000000e+00 2015.0
2 TraesCS2D01G222200 chr2B 92.388 670 33 7 3 672 245691074 245691725 0.000000e+00 939.0
3 TraesCS2D01G222200 chr2B 92.857 154 11 0 667 820 245691753 245691906 1.040000e-54 224.0
4 TraesCS2D01G222200 chr2B 89.423 104 5 2 525 622 245773236 245773339 3.030000e-25 126.0
5 TraesCS2D01G222200 chr2B 79.487 117 18 6 11 124 245319763 245319876 8.610000e-11 78.7
6 TraesCS2D01G222200 chr2A 90.510 980 77 12 1928 2897 203308027 203309000 0.000000e+00 1280.0
7 TraesCS2D01G222200 chr2A 90.817 893 61 12 969 1859 203297553 203298426 0.000000e+00 1175.0
8 TraesCS2D01G222200 chr2A 88.319 351 25 6 317 666 203297226 203297561 9.660000e-110 407.0
9 TraesCS2D01G222200 chr2A 91.386 267 17 1 1 267 203288188 203288448 7.630000e-96 361.0
10 TraesCS2D01G222200 chr2A 77.778 117 20 6 11 124 203257481 203257594 1.860000e-07 67.6
11 TraesCS2D01G222200 chr5B 91.492 717 58 3 2182 2897 658178791 658179505 0.000000e+00 983.0
12 TraesCS2D01G222200 chr5B 91.353 717 59 3 2182 2897 425113401 425112687 0.000000e+00 977.0
13 TraesCS2D01G222200 chr4D 91.213 717 61 2 2182 2897 51987449 51988164 0.000000e+00 974.0
14 TraesCS2D01G222200 chr3A 91.226 718 58 5 2182 2897 743535950 743535236 0.000000e+00 972.0
15 TraesCS2D01G222200 chr3A 81.818 803 106 23 1031 1823 70721150 70721922 3.150000e-179 638.0
16 TraesCS2D01G222200 chrUn 90.934 717 62 3 2182 2897 53927894 53928608 0.000000e+00 961.0
17 TraesCS2D01G222200 chr6B 90.934 717 61 4 2182 2897 561640561 561641274 0.000000e+00 961.0
18 TraesCS2D01G222200 chr6B 90.503 716 65 3 2183 2897 114411806 114411093 0.000000e+00 942.0
19 TraesCS2D01G222200 chr5A 90.934 717 62 3 2182 2897 99023333 99022619 0.000000e+00 961.0
20 TraesCS2D01G222200 chr5A 73.978 538 109 26 1118 1641 546239015 546239535 3.810000e-44 189.0
21 TraesCS2D01G222200 chr5A 73.768 568 105 31 1201 1747 546237964 546237420 1.770000e-42 183.0
22 TraesCS2D01G222200 chr5D 90.390 718 66 3 2182 2897 558037149 558036433 0.000000e+00 941.0
23 TraesCS2D01G222200 chr3D 84.232 742 99 10 1029 1764 61696262 61696991 0.000000e+00 706.0


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 TraesCS2D01G222200 chr2D 189376137 189379033 2896 False 5350.0 5350 100.0000 1 2897 1 chr2D.!!$F1 2896
1 TraesCS2D01G222200 chr2B 245784088 245785541 1453 False 2015.0 2015 91.6610 609 2087 1 chr2B.!!$F3 1478
2 TraesCS2D01G222200 chr2B 245691074 245691906 832 False 581.5 939 92.6225 3 820 2 chr2B.!!$F4 817
3 TraesCS2D01G222200 chr2A 203308027 203309000 973 False 1280.0 1280 90.5100 1928 2897 1 chr2A.!!$F3 969
4 TraesCS2D01G222200 chr2A 203297226 203298426 1200 False 791.0 1175 89.5680 317 1859 2 chr2A.!!$F4 1542
5 TraesCS2D01G222200 chr5B 658178791 658179505 714 False 983.0 983 91.4920 2182 2897 1 chr5B.!!$F1 715
6 TraesCS2D01G222200 chr5B 425112687 425113401 714 True 977.0 977 91.3530 2182 2897 1 chr5B.!!$R1 715
7 TraesCS2D01G222200 chr4D 51987449 51988164 715 False 974.0 974 91.2130 2182 2897 1 chr4D.!!$F1 715
8 TraesCS2D01G222200 chr3A 743535236 743535950 714 True 972.0 972 91.2260 2182 2897 1 chr3A.!!$R1 715
9 TraesCS2D01G222200 chr3A 70721150 70721922 772 False 638.0 638 81.8180 1031 1823 1 chr3A.!!$F1 792
10 TraesCS2D01G222200 chrUn 53927894 53928608 714 False 961.0 961 90.9340 2182 2897 1 chrUn.!!$F1 715
11 TraesCS2D01G222200 chr6B 561640561 561641274 713 False 961.0 961 90.9340 2182 2897 1 chr6B.!!$F1 715
12 TraesCS2D01G222200 chr6B 114411093 114411806 713 True 942.0 942 90.5030 2183 2897 1 chr6B.!!$R1 714
13 TraesCS2D01G222200 chr5A 99022619 99023333 714 True 961.0 961 90.9340 2182 2897 1 chr5A.!!$R1 715
14 TraesCS2D01G222200 chr5D 558036433 558037149 716 True 941.0 941 90.3900 2182 2897 1 chr5D.!!$R1 715
15 TraesCS2D01G222200 chr3D 61696262 61696991 729 False 706.0 706 84.2320 1029 1764 1 chr3D.!!$F1 735

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
829 866 0.252467 AGGGGCTCTTGCAGTAGAGT 60.252 55.0 15.22 0.0 42.93 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 2643 0.104855 GGTGCAGCTGGATATCGACA 59.895 55.0 17.12 0.0 0.0 4.35 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
94 95 4.688419 TGGTCGACCGTCGCGTTC 62.688 66.667 28.70 2.88 40.21 3.95
146 147 2.352805 CTGGGGCTGTGAGGTTCC 59.647 66.667 0.00 0.00 0.00 3.62
149 150 3.256960 GGGCTGTGAGGTTCCCCA 61.257 66.667 0.00 0.00 35.75 4.96
156 157 3.308705 GAGGTTCCCCACGTCCGT 61.309 66.667 0.00 0.00 34.67 4.69
189 190 2.509422 GGGGGATTCCACGCCTAC 59.491 66.667 4.80 0.00 41.64 3.18
605 609 1.677217 GCAGAAAGCGGAAGAGATGGT 60.677 52.381 0.00 0.00 0.00 3.55
606 610 2.418746 GCAGAAAGCGGAAGAGATGGTA 60.419 50.000 0.00 0.00 0.00 3.25
607 611 3.452474 CAGAAAGCGGAAGAGATGGTAG 58.548 50.000 0.00 0.00 0.00 3.18
678 715 0.388520 GCCATGCAACTTCCGGAAAC 60.389 55.000 19.39 8.66 0.00 2.78
691 728 4.703379 TCCGGAAACAAAAAGGGTACTA 57.297 40.909 0.00 0.00 0.00 1.82
820 857 1.221021 GTCGGGTTAGGGGCTCTTG 59.779 63.158 0.00 0.00 0.00 3.02
823 860 1.077429 GGGTTAGGGGCTCTTGCAG 60.077 63.158 0.00 0.00 41.91 4.41
825 862 0.909623 GGTTAGGGGCTCTTGCAGTA 59.090 55.000 0.00 0.00 41.91 2.74
826 863 1.134371 GGTTAGGGGCTCTTGCAGTAG 60.134 57.143 0.00 0.00 41.91 2.57
827 864 1.831736 GTTAGGGGCTCTTGCAGTAGA 59.168 52.381 0.00 0.00 41.91 2.59
828 865 1.781786 TAGGGGCTCTTGCAGTAGAG 58.218 55.000 10.54 10.54 43.66 2.43
829 866 0.252467 AGGGGCTCTTGCAGTAGAGT 60.252 55.000 15.22 0.00 42.93 3.24
831 868 1.410882 GGGGCTCTTGCAGTAGAGTAG 59.589 57.143 15.22 0.00 42.93 2.57
833 870 2.159170 GGGCTCTTGCAGTAGAGTAGTG 60.159 54.545 15.22 0.00 42.93 2.74
852 905 3.503748 AGTGCAGTAGAAATTGGCAACTC 59.496 43.478 0.00 2.19 36.08 3.01
855 908 1.732259 AGTAGAAATTGGCAACTCGCG 59.268 47.619 0.00 0.00 43.84 5.87
901 954 2.982130 ACGGGCAGTCAGTCCATC 59.018 61.111 0.00 0.00 44.49 3.51
902 955 1.610673 ACGGGCAGTCAGTCCATCT 60.611 57.895 0.00 0.00 44.49 2.90
903 956 1.194781 ACGGGCAGTCAGTCCATCTT 61.195 55.000 0.00 0.00 44.49 2.40
904 957 0.460987 CGGGCAGTCAGTCCATCTTC 60.461 60.000 0.00 0.00 44.49 2.87
905 958 0.908198 GGGCAGTCAGTCCATCTTCT 59.092 55.000 0.00 0.00 43.39 2.85
906 959 1.134551 GGGCAGTCAGTCCATCTTCTC 60.135 57.143 0.00 0.00 43.39 2.87
907 960 1.470632 GGCAGTCAGTCCATCTTCTCG 60.471 57.143 0.00 0.00 0.00 4.04
908 961 1.470632 GCAGTCAGTCCATCTTCTCGG 60.471 57.143 0.00 0.00 0.00 4.63
909 962 1.821753 CAGTCAGTCCATCTTCTCGGT 59.178 52.381 0.00 0.00 0.00 4.69
910 963 2.096248 AGTCAGTCCATCTTCTCGGTC 58.904 52.381 0.00 0.00 0.00 4.79
911 964 2.096248 GTCAGTCCATCTTCTCGGTCT 58.904 52.381 0.00 0.00 0.00 3.85
912 965 2.098443 GTCAGTCCATCTTCTCGGTCTC 59.902 54.545 0.00 0.00 0.00 3.36
913 966 1.407258 CAGTCCATCTTCTCGGTCTCC 59.593 57.143 0.00 0.00 0.00 3.71
914 967 1.006043 AGTCCATCTTCTCGGTCTCCA 59.994 52.381 0.00 0.00 0.00 3.86
929 982 1.065345 TCTCCACTCGGTCTCCAGTAG 60.065 57.143 0.00 0.00 0.00 2.57
930 983 0.697079 TCCACTCGGTCTCCAGTAGT 59.303 55.000 0.00 0.00 0.00 2.73
931 984 1.911357 TCCACTCGGTCTCCAGTAGTA 59.089 52.381 0.00 0.00 0.00 1.82
932 985 2.306805 TCCACTCGGTCTCCAGTAGTAA 59.693 50.000 0.00 0.00 0.00 2.24
933 986 3.087031 CCACTCGGTCTCCAGTAGTAAA 58.913 50.000 0.00 0.00 0.00 2.01
934 987 3.508793 CCACTCGGTCTCCAGTAGTAAAA 59.491 47.826 0.00 0.00 0.00 1.52
935 988 4.380655 CCACTCGGTCTCCAGTAGTAAAAG 60.381 50.000 0.00 0.00 0.00 2.27
936 989 4.217983 CACTCGGTCTCCAGTAGTAAAAGT 59.782 45.833 0.00 0.00 0.00 2.66
937 990 4.217983 ACTCGGTCTCCAGTAGTAAAAGTG 59.782 45.833 0.00 0.00 0.00 3.16
993 1046 1.877637 TGCCATACACACAGACACAC 58.122 50.000 0.00 0.00 0.00 3.82
1013 1066 0.108585 AACACAATGAGCCACCTCGT 59.891 50.000 0.00 0.00 41.13 4.18
1112 1165 1.358759 CCAACTTCACGGCCAACAC 59.641 57.895 2.24 0.00 0.00 3.32
1170 1223 0.250234 TGCCCAAGAACATCTCCTCG 59.750 55.000 0.00 0.00 0.00 4.63
1175 1228 0.818296 AAGAACATCTCCTCGTCCCG 59.182 55.000 0.00 0.00 0.00 5.14
1177 1230 2.630592 GAACATCTCCTCGTCCCGGC 62.631 65.000 0.00 0.00 0.00 6.13
1384 1437 4.760047 CCAACGCCACCTCCCTCG 62.760 72.222 0.00 0.00 0.00 4.63
1395 1448 1.840650 CTCCCTCGCCTCCATGGAT 60.841 63.158 16.63 0.00 38.35 3.41
1645 1699 3.664025 CTCGCCGGACTCATTGCCA 62.664 63.158 5.05 0.00 0.00 4.92
1646 1700 2.745884 CGCCGGACTCATTGCCAA 60.746 61.111 5.05 0.00 0.00 4.52
1651 1705 1.545582 CCGGACTCATTGCCAAAATGT 59.454 47.619 0.00 0.00 0.00 2.71
1653 1707 2.489329 CGGACTCATTGCCAAAATGTCT 59.511 45.455 6.90 0.00 0.00 3.41
1863 1926 7.442062 GGTGAGTCTTCCTACTACAGTATACTC 59.558 44.444 1.26 0.00 0.00 2.59
1864 1927 7.986320 GTGAGTCTTCCTACTACAGTATACTCA 59.014 40.741 1.26 0.00 0.00 3.41
1901 1964 2.936498 CGTCGTGGCATCCTTAAAGAAT 59.064 45.455 0.00 0.00 0.00 2.40
1908 1971 3.242870 GGCATCCTTAAAGAATGCGTGAG 60.243 47.826 3.73 0.00 38.99 3.51
1909 1972 3.375299 GCATCCTTAAAGAATGCGTGAGT 59.625 43.478 0.00 0.00 0.00 3.41
1986 2049 2.648059 AGCAATCATTCAGTGGCTACC 58.352 47.619 0.00 0.00 0.00 3.18
2060 2127 3.063997 GCTATCCATCGTTGACAACTTGG 59.936 47.826 22.12 22.12 35.10 3.61
2087 2154 6.938507 TGCATGCATCTAGAAAAAGGAAAAT 58.061 32.000 18.46 0.00 0.00 1.82
2104 2171 4.025979 GGAAAATTCTACGTACGCCATCTG 60.026 45.833 16.72 0.00 0.00 2.90
2123 2190 6.638063 CCATCTGTAATTTTGTTCACACACAG 59.362 38.462 0.00 0.00 30.32 3.66
2143 2210 3.070018 AGCATTAGACTTGCACAGTGTC 58.930 45.455 1.61 3.81 42.62 3.67
2149 2216 3.201290 AGACTTGCACAGTGTCAAGAAG 58.799 45.455 29.24 15.68 41.50 2.85
2156 2223 4.639755 TGCACAGTGTCAAGAAGATTTCAA 59.360 37.500 1.61 0.00 0.00 2.69
2190 2265 1.414181 AGGATGTACCCGCATCTGAAG 59.586 52.381 6.11 0.00 43.41 3.02
2198 2273 2.158769 ACCCGCATCTGAAGAATGCATA 60.159 45.455 0.00 0.00 41.05 3.14
2269 2344 4.777896 AGTAAGTCTGAAGCCACCATCTTA 59.222 41.667 0.00 0.00 0.00 2.10
2289 2364 3.446310 AACGACACATGTCACTACACA 57.554 42.857 12.32 0.00 44.99 3.72
2332 2407 2.296471 CCGAATGTCCGAGCCTAATACT 59.704 50.000 0.00 0.00 0.00 2.12
2347 2422 5.696724 GCCTAATACTAAACAGACATCGCAT 59.303 40.000 0.00 0.00 0.00 4.73
2354 2429 4.836125 AAACAGACATCGCATCAAAACT 57.164 36.364 0.00 0.00 0.00 2.66
2392 2467 0.773644 GTCCCATCCCAGCCACATAT 59.226 55.000 0.00 0.00 0.00 1.78
2437 2512 2.970639 GCACTCACCGAGGCTACA 59.029 61.111 0.00 0.00 33.35 2.74
2475 2550 4.346418 CCTAACCATCTTCAGAGCAGGTAT 59.654 45.833 0.00 0.00 31.98 2.73
2477 2552 3.378512 ACCATCTTCAGAGCAGGTATCA 58.621 45.455 0.00 0.00 30.94 2.15
2567 2643 1.452651 CCATCCAGCCGCATCTGTT 60.453 57.895 0.00 0.00 32.32 3.16
2652 2729 2.046892 CTCCTGGCAACCTCCACG 60.047 66.667 0.00 0.00 31.74 4.94
2694 2771 0.325671 ACGGAGTCCATCACCCAGAT 60.326 55.000 10.49 0.00 29.74 2.90
2695 2772 1.063190 ACGGAGTCCATCACCCAGATA 60.063 52.381 10.49 0.00 29.74 1.98
2710 2787 2.352225 CCAGATAATCTCTCCGCCGAAG 60.352 54.545 0.00 0.00 29.16 3.79
2729 2806 1.827399 GAGCGGAACCTCCCAAGACA 61.827 60.000 0.00 0.00 31.13 3.41
2730 2807 1.072505 GCGGAACCTCCCAAGACAA 59.927 57.895 0.00 0.00 31.13 3.18
2760 2837 1.722636 GAGGGTACGACGCGAAGGAT 61.723 60.000 15.93 0.00 36.04 3.24
2784 2861 2.908015 GCCGCCCAATCCAGACTA 59.092 61.111 0.00 0.00 0.00 2.59
2862 2939 3.834732 CTCCACGGAGGGTAACAAG 57.165 57.895 5.08 0.00 38.51 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.117661 GGAGCTTCGACGCGACCT 62.118 66.667 15.93 0.00 34.89 3.85
149 150 2.633509 GCACCTACTCCACGGACGT 61.634 63.158 0.00 0.00 0.00 4.34
189 190 2.097038 CAGCGCTTCCTGGACTTCG 61.097 63.158 7.50 1.28 0.00 3.79
230 231 2.125326 TCGCCATCTACCAGGACGG 61.125 63.158 0.00 0.00 42.50 4.79
553 557 4.514577 CTCGGCGGCATCCTCGTT 62.515 66.667 10.53 0.00 0.00 3.85
575 579 0.795085 CGCTTTCTGCCAGAGACAAG 59.205 55.000 0.00 0.00 38.78 3.16
603 607 2.271800 CCAACTCGTGCTTGATCTACC 58.728 52.381 0.00 0.00 0.00 3.18
605 609 1.550524 AGCCAACTCGTGCTTGATCTA 59.449 47.619 0.00 0.00 32.94 1.98
606 610 0.322975 AGCCAACTCGTGCTTGATCT 59.677 50.000 0.00 0.00 32.94 2.75
607 611 0.445436 CAGCCAACTCGTGCTTGATC 59.555 55.000 0.00 0.00 35.12 2.92
672 676 4.319984 GCAGTAGTACCCTTTTTGTTTCCG 60.320 45.833 0.00 0.00 0.00 4.30
678 715 4.023193 CCACTTGCAGTAGTACCCTTTTTG 60.023 45.833 0.00 0.00 0.00 2.44
691 728 2.035066 GTCAAAATCAGCCACTTGCAGT 59.965 45.455 0.00 0.00 44.83 4.40
757 794 2.048597 TCGTGCGCTTGGGTAGTG 60.049 61.111 9.73 0.00 37.43 2.74
820 857 4.966965 TTCTACTGCACTACTCTACTGC 57.033 45.455 0.00 0.00 0.00 4.40
823 860 5.520649 GCCAATTTCTACTGCACTACTCTAC 59.479 44.000 0.00 0.00 0.00 2.59
825 862 4.020218 TGCCAATTTCTACTGCACTACTCT 60.020 41.667 0.00 0.00 0.00 3.24
826 863 4.253685 TGCCAATTTCTACTGCACTACTC 58.746 43.478 0.00 0.00 0.00 2.59
827 864 4.286297 TGCCAATTTCTACTGCACTACT 57.714 40.909 0.00 0.00 0.00 2.57
828 865 4.455877 AGTTGCCAATTTCTACTGCACTAC 59.544 41.667 0.00 0.00 0.00 2.73
829 866 4.651778 AGTTGCCAATTTCTACTGCACTA 58.348 39.130 0.00 0.00 0.00 2.74
831 868 3.667960 CGAGTTGCCAATTTCTACTGCAC 60.668 47.826 0.00 0.00 0.00 4.57
833 870 2.729156 GCGAGTTGCCAATTTCTACTGC 60.729 50.000 0.00 0.00 37.76 4.40
834 871 2.474526 CGCGAGTTGCCAATTTCTACTG 60.475 50.000 0.00 0.00 42.08 2.74
836 873 1.463444 ACGCGAGTTGCCAATTTCTAC 59.537 47.619 15.93 0.00 46.40 2.59
837 874 1.803334 ACGCGAGTTGCCAATTTCTA 58.197 45.000 15.93 0.00 46.40 2.10
838 875 2.629002 ACGCGAGTTGCCAATTTCT 58.371 47.368 15.93 0.00 46.40 2.52
852 905 0.168788 ATCATCAACTTGGCAACGCG 59.831 50.000 3.53 3.53 42.51 6.01
855 908 5.121142 CCAATCAAATCATCAACTTGGCAAC 59.879 40.000 0.00 0.00 0.00 4.17
860 913 5.097529 CGACCCAATCAAATCATCAACTTG 58.902 41.667 0.00 0.00 0.00 3.16
901 954 0.961358 ACCGAGTGGAGACCGAGAAG 60.961 60.000 0.00 0.00 39.21 2.85
902 955 0.959372 GACCGAGTGGAGACCGAGAA 60.959 60.000 0.00 0.00 39.21 2.87
903 956 1.376942 GACCGAGTGGAGACCGAGA 60.377 63.158 0.00 0.00 39.21 4.04
904 957 1.370587 GAGACCGAGTGGAGACCGAG 61.371 65.000 0.00 0.00 39.21 4.63
905 958 1.376942 GAGACCGAGTGGAGACCGA 60.377 63.158 0.00 0.00 39.21 4.69
906 959 2.408241 GGAGACCGAGTGGAGACCG 61.408 68.421 0.00 0.00 39.21 4.79
907 960 1.304217 TGGAGACCGAGTGGAGACC 60.304 63.158 0.00 0.00 39.21 3.85
908 961 0.609681 ACTGGAGACCGAGTGGAGAC 60.610 60.000 0.00 0.00 39.21 3.36
909 962 0.989602 TACTGGAGACCGAGTGGAGA 59.010 55.000 0.00 0.00 39.21 3.71
910 963 1.340211 ACTACTGGAGACCGAGTGGAG 60.340 57.143 0.00 0.00 39.21 3.86
911 964 0.697079 ACTACTGGAGACCGAGTGGA 59.303 55.000 0.00 0.00 39.21 4.02
912 965 2.414994 TACTACTGGAGACCGAGTGG 57.585 55.000 0.00 0.00 42.84 4.00
913 966 4.217983 ACTTTTACTACTGGAGACCGAGTG 59.782 45.833 0.00 0.00 0.00 3.51
914 967 4.217983 CACTTTTACTACTGGAGACCGAGT 59.782 45.833 0.00 0.00 0.00 4.18
929 982 8.713737 ATCGGACTATTAAGGAACACTTTTAC 57.286 34.615 0.00 0.00 40.64 2.01
930 983 9.374838 GAATCGGACTATTAAGGAACACTTTTA 57.625 33.333 0.00 0.00 40.64 1.52
931 984 7.064253 CGAATCGGACTATTAAGGAACACTTTT 59.936 37.037 0.00 0.00 40.64 2.27
932 985 6.534079 CGAATCGGACTATTAAGGAACACTTT 59.466 38.462 0.00 0.00 40.64 2.66
933 986 6.040878 CGAATCGGACTATTAAGGAACACTT 58.959 40.000 0.00 0.00 43.28 3.16
934 987 5.359009 TCGAATCGGACTATTAAGGAACACT 59.641 40.000 1.76 0.00 0.00 3.55
935 988 5.585390 TCGAATCGGACTATTAAGGAACAC 58.415 41.667 1.76 0.00 0.00 3.32
936 989 5.840243 TCGAATCGGACTATTAAGGAACA 57.160 39.130 1.76 0.00 0.00 3.18
937 990 6.362820 GTGATCGAATCGGACTATTAAGGAAC 59.637 42.308 1.76 0.00 0.00 3.62
993 1046 0.518636 CGAGGTGGCTCATTGTGTTG 59.481 55.000 0.00 0.00 0.00 3.33
1013 1066 4.077184 GGGATGCCACGACCACGA 62.077 66.667 0.00 0.00 42.66 4.35
1112 1165 2.359478 GGTTGGCCTGGTACGTGG 60.359 66.667 3.32 0.00 0.00 4.94
1384 1437 0.600255 CCGACGTTATCCATGGAGGC 60.600 60.000 21.33 7.59 37.29 4.70
1417 1470 1.005347 CGTGACGTTCTGGTTGTTGAC 60.005 52.381 0.00 0.00 0.00 3.18
1555 1608 4.366684 CACCCTGGGGAACTGGCC 62.367 72.222 18.88 0.00 38.96 5.36
1645 1699 2.433436 GGTGAACCGCCTAGACATTTT 58.567 47.619 0.00 0.00 0.00 1.82
1646 1700 2.109425 GGTGAACCGCCTAGACATTT 57.891 50.000 0.00 0.00 0.00 2.32
1667 1721 3.492311 GATCTCCCTCCGACGCTGC 62.492 68.421 0.00 0.00 0.00 5.25
1669 1723 1.527380 GAGATCTCCCTCCGACGCT 60.527 63.158 12.00 0.00 0.00 5.07
1796 1859 2.983592 GAACCGTGGGCCCAACTG 60.984 66.667 30.64 20.39 0.00 3.16
1863 1926 2.153817 CGACGCGACCAGATGAAATATG 59.846 50.000 15.93 0.00 34.73 1.78
1864 1927 2.223735 ACGACGCGACCAGATGAAATAT 60.224 45.455 15.93 0.00 0.00 1.28
1901 1964 2.959599 GTGTCACGCACTCACGCA 60.960 61.111 0.00 0.00 44.41 5.24
1909 1972 1.254026 AGGTAAGCTAGTGTCACGCA 58.746 50.000 5.76 0.00 0.00 5.24
1986 2049 7.807977 AGCATGTTAATCTTTGTGTATAGGG 57.192 36.000 0.00 0.00 0.00 3.53
2087 2154 4.906065 ATTACAGATGGCGTACGTAGAA 57.094 40.909 17.90 0.36 0.00 2.10
2104 2171 6.826893 AATGCTGTGTGTGAACAAAATTAC 57.173 33.333 0.00 0.00 0.00 1.89
2123 2190 2.807967 TGACACTGTGCAAGTCTAATGC 59.192 45.455 7.90 0.00 44.08 3.56
2165 2232 1.968493 GATGCGGGTACATCCTCCTTA 59.032 52.381 0.00 0.00 40.52 2.69
2166 2233 0.759346 GATGCGGGTACATCCTCCTT 59.241 55.000 0.00 0.00 40.52 3.36
2180 2247 4.277258 GTTGTATGCATTCTTCAGATGCG 58.723 43.478 3.54 0.00 43.69 4.73
2219 2294 7.476540 TGTAATGCTTTGTAAGGTCTCTAGA 57.523 36.000 0.00 0.00 0.00 2.43
2220 2295 7.981789 TGATGTAATGCTTTGTAAGGTCTCTAG 59.018 37.037 0.00 0.00 0.00 2.43
2221 2296 7.847096 TGATGTAATGCTTTGTAAGGTCTCTA 58.153 34.615 0.00 0.00 0.00 2.43
2289 2364 3.749954 GCACCCCTGCATCAAAGAGATAT 60.750 47.826 0.00 0.00 43.62 1.63
2332 2407 5.940192 AGTTTTGATGCGATGTCTGTTTA 57.060 34.783 0.00 0.00 0.00 2.01
2347 2422 5.941058 TCCGGCATTAGATGTTAAGTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
2374 2449 1.067295 GATATGTGGCTGGGATGGGA 58.933 55.000 0.00 0.00 0.00 4.37
2392 2467 0.400213 GGTGTGTGACCCATTCCTGA 59.600 55.000 0.00 0.00 39.10 3.86
2437 2512 1.344953 TTAGGTGGATGATGGCGGCT 61.345 55.000 11.43 0.00 0.00 5.52
2567 2643 0.104855 GGTGCAGCTGGATATCGACA 59.895 55.000 17.12 0.00 0.00 4.35
2616 2693 1.226030 GGTGCGCCGTTGTTTCTACT 61.226 55.000 4.18 0.00 0.00 2.57
2694 2771 0.669077 GCTCTTCGGCGGAGAGATTA 59.331 55.000 41.53 11.35 33.03 1.75
2695 2772 1.439644 GCTCTTCGGCGGAGAGATT 59.560 57.895 41.53 0.00 33.03 2.40
2710 2787 1.079057 GTCTTGGGAGGTTCCGCTC 60.079 63.158 0.00 0.00 37.43 5.03
2714 2791 1.235281 GCGTTGTCTTGGGAGGTTCC 61.235 60.000 0.00 0.00 35.23 3.62
2803 2880 2.284699 CACCTCCGAACCCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
2862 2939 2.267681 ATTGGCGACGTCTCTCGACC 62.268 60.000 14.70 7.34 41.36 4.79
2879 2956 3.981308 CTTGTTCGGTCCGGCATT 58.019 55.556 12.29 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.