Multiple sequence alignment - TraesCS2D01G353100

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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 TraesCS2D01G353100 chr2D 100.000 6055 0 0 1 6055 451454106 451460160 0.000000e+00 11182
1 TraesCS2D01G353100 chr2D 95.192 832 26 8 1 830 50475231 50474412 0.000000e+00 1303
2 TraesCS2D01G353100 chr2B 95.648 4251 141 26 917 5144 531714256 531718485 0.000000e+00 6785
3 TraesCS2D01G353100 chr2B 95.842 914 35 3 5143 6055 531718549 531719460 0.000000e+00 1474
4 TraesCS2D01G353100 chr2A 94.963 2700 88 19 899 3579 597853174 597850504 0.000000e+00 4189
5 TraesCS2D01G353100 chr2A 95.343 1181 47 6 3866 5043 597850028 597848853 0.000000e+00 1869
6 TraesCS2D01G353100 chr2A 92.233 824 59 4 5235 6055 597847137 597846316 0.000000e+00 1162
7 TraesCS2D01G353100 chr2A 96.154 286 11 0 3577 3862 597850423 597850138 9.190000e-128 468
8 TraesCS2D01G353100 chr2A 94.286 70 4 0 875 944 597864036 597863967 2.310000e-19 108
9 TraesCS2D01G353100 chr3D 95.272 846 29 4 1 844 6347305 6348141 0.000000e+00 1330
10 TraesCS2D01G353100 chr4A 92.065 857 30 15 3 855 259777040 259777862 0.000000e+00 1171
11 TraesCS2D01G353100 chr1D 92.887 717 25 8 1 708 62336402 62337101 0.000000e+00 1018
12 TraesCS2D01G353100 chr3A 87.161 849 90 16 1 844 712657241 712658075 0.000000e+00 946
13 TraesCS2D01G353100 chr7D 86.826 835 73 17 29 851 511660410 511659601 0.000000e+00 898
14 TraesCS2D01G353100 chr7D 83.117 847 87 31 29 853 599868511 599869323 0.000000e+00 721
15 TraesCS2D01G353100 chr3B 86.790 810 79 19 29 830 769336683 769337472 0.000000e+00 878
16 TraesCS2D01G353100 chr5A 87.928 613 55 10 261 859 631411754 631411147 0.000000e+00 704
17 TraesCS2D01G353100 chr6B 80.874 847 118 25 29 853 454766919 454767743 1.430000e-175 627
18 TraesCS2D01G353100 chr6B 83.840 625 82 13 240 852 489728905 489729522 1.460000e-160 577
19 TraesCS2D01G353100 chr1A 82.792 616 87 13 242 844 59693618 59694227 3.210000e-147 532
20 TraesCS2D01G353100 chr5D 87.742 155 17 1 3206 3360 139954118 139954270 4.820000e-41 180
21 TraesCS2D01G353100 chr7A 88.991 109 12 0 5335 5443 40256687 40256795 1.060000e-27 135


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 TraesCS2D01G353100 chr2D 451454106 451460160 6054 False 11182.0 11182 100.00000 1 6055 1 chr2D.!!$F1 6054
1 TraesCS2D01G353100 chr2D 50474412 50475231 819 True 1303.0 1303 95.19200 1 830 1 chr2D.!!$R1 829
2 TraesCS2D01G353100 chr2B 531714256 531719460 5204 False 4129.5 6785 95.74500 917 6055 2 chr2B.!!$F1 5138
3 TraesCS2D01G353100 chr2A 597846316 597853174 6858 True 1922.0 4189 94.67325 899 6055 4 chr2A.!!$R2 5156
4 TraesCS2D01G353100 chr3D 6347305 6348141 836 False 1330.0 1330 95.27200 1 844 1 chr3D.!!$F1 843
5 TraesCS2D01G353100 chr4A 259777040 259777862 822 False 1171.0 1171 92.06500 3 855 1 chr4A.!!$F1 852
6 TraesCS2D01G353100 chr1D 62336402 62337101 699 False 1018.0 1018 92.88700 1 708 1 chr1D.!!$F1 707
7 TraesCS2D01G353100 chr3A 712657241 712658075 834 False 946.0 946 87.16100 1 844 1 chr3A.!!$F1 843
8 TraesCS2D01G353100 chr7D 511659601 511660410 809 True 898.0 898 86.82600 29 851 1 chr7D.!!$R1 822
9 TraesCS2D01G353100 chr7D 599868511 599869323 812 False 721.0 721 83.11700 29 853 1 chr7D.!!$F1 824
10 TraesCS2D01G353100 chr3B 769336683 769337472 789 False 878.0 878 86.79000 29 830 1 chr3B.!!$F1 801
11 TraesCS2D01G353100 chr5A 631411147 631411754 607 True 704.0 704 87.92800 261 859 1 chr5A.!!$R1 598
12 TraesCS2D01G353100 chr6B 454766919 454767743 824 False 627.0 627 80.87400 29 853 1 chr6B.!!$F1 824
13 TraesCS2D01G353100 chr6B 489728905 489729522 617 False 577.0 577 83.84000 240 852 1 chr6B.!!$F2 612
14 TraesCS2D01G353100 chr1A 59693618 59694227 609 False 532.0 532 82.79200 242 844 1 chr1A.!!$F1 602

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
897 1011 0.109913 GTCGTTTGAAAGGGAGGGGT 59.890 55.000 0.00 0.0 0.00 4.95 F
1068 1198 0.036875 CCGCTTCCTCTTTCTGGGTT 59.963 55.000 0.00 0.0 0.00 4.11 F
1613 1744 0.316204 ATTTGTGCTCCTTGTGCTGC 59.684 50.000 0.00 0.0 0.00 5.25 F
1784 1916 0.971386 CAAGCCTGGTTCAAGCCATT 59.029 50.000 0.00 0.0 37.96 3.16 F
2104 2236 1.202336 ACGGCGTAACAGTAGGTATGC 60.202 52.381 12.58 0.0 0.00 3.14 F
3603 3820 2.154462 GTTTGCTATCCTGCAGTGTGT 58.846 47.619 13.81 0.0 44.27 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2307 0.455815 GACCAACAATGCGGGATTCC 59.544 55.000 0.00 0.00 0.00 3.01 R
2228 2360 1.335964 CGTGAGGAAGCTTCTTCGACA 60.336 52.381 27.44 12.93 36.21 4.35 R
3188 3322 2.049228 CTTGCTGAAGCTTTTTCTGCG 58.951 47.619 0.00 0.00 43.44 5.18 R
3635 3852 3.258372 TCTTGAACAGAAGATGGCTACGT 59.742 43.478 0.00 0.00 0.00 3.57 R
3990 4313 3.649502 TGGATCTGCACCATATCAGATGT 59.350 43.478 9.18 0.00 46.60 3.06 R
5408 7341 0.311790 CACAATGTGCTTTCACGCCT 59.688 50.000 0.00 0.00 46.01 5.52 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
116 118 5.354845 GCTTTTTGCTACCACAGTTGGCT 62.355 47.826 0.00 0.00 42.08 4.75
210 219 3.057526 GGTCTTTGATTTTTGCTACCGCT 60.058 43.478 0.00 0.00 36.97 5.52
360 383 8.546083 ACACCCCATTTATGATATTTTTGCTA 57.454 30.769 0.00 0.00 0.00 3.49
438 487 1.377725 CGTGGAGGGAGCTGCAAAT 60.378 57.895 7.79 0.00 0.00 2.32
540 593 3.562635 CGAAAGCTGGAACCGTCC 58.437 61.111 0.00 0.00 45.21 4.79
647 750 4.980805 GTGGTGCGGCGAGGACAA 62.981 66.667 12.98 0.00 43.57 3.18
797 911 3.444388 ACAAAAAGACAAACTAACGCCCA 59.556 39.130 0.00 0.00 0.00 5.36
879 993 7.845066 AAAAAGACAAACTAGAACTTCGAGT 57.155 32.000 0.00 0.00 33.72 4.18
880 994 7.466193 AAAAGACAAACTAGAACTTCGAGTC 57.534 36.000 5.15 0.00 31.03 3.36
881 995 4.785417 AGACAAACTAGAACTTCGAGTCG 58.215 43.478 6.09 6.09 31.03 4.18
882 996 4.275443 AGACAAACTAGAACTTCGAGTCGT 59.725 41.667 13.12 6.05 31.03 4.34
883 997 4.929781 ACAAACTAGAACTTCGAGTCGTT 58.070 39.130 13.12 0.00 31.03 3.85
884 998 5.346522 ACAAACTAGAACTTCGAGTCGTTT 58.653 37.500 13.12 4.52 31.03 3.60
885 999 5.231568 ACAAACTAGAACTTCGAGTCGTTTG 59.768 40.000 13.12 13.83 43.14 2.93
886 1000 4.825546 ACTAGAACTTCGAGTCGTTTGA 57.174 40.909 13.12 0.00 25.23 2.69
887 1001 5.179045 ACTAGAACTTCGAGTCGTTTGAA 57.821 39.130 13.12 0.00 25.23 2.69
888 1002 5.585390 ACTAGAACTTCGAGTCGTTTGAAA 58.415 37.500 13.12 0.00 25.23 2.69
889 1003 5.686397 ACTAGAACTTCGAGTCGTTTGAAAG 59.314 40.000 13.12 10.61 25.23 2.62
890 1004 3.802685 AGAACTTCGAGTCGTTTGAAAGG 59.197 43.478 13.12 0.00 0.00 3.11
891 1005 2.480845 ACTTCGAGTCGTTTGAAAGGG 58.519 47.619 13.12 0.00 0.00 3.95
892 1006 2.101917 ACTTCGAGTCGTTTGAAAGGGA 59.898 45.455 13.12 0.00 0.00 4.20
893 1007 2.433868 TCGAGTCGTTTGAAAGGGAG 57.566 50.000 13.12 0.00 0.00 4.30
894 1008 1.000506 TCGAGTCGTTTGAAAGGGAGG 59.999 52.381 13.12 0.00 0.00 4.30
895 1009 1.809684 GAGTCGTTTGAAAGGGAGGG 58.190 55.000 0.00 0.00 0.00 4.30
896 1010 0.400594 AGTCGTTTGAAAGGGAGGGG 59.599 55.000 0.00 0.00 0.00 4.79
897 1011 0.109913 GTCGTTTGAAAGGGAGGGGT 59.890 55.000 0.00 0.00 0.00 4.95
898 1012 1.348696 GTCGTTTGAAAGGGAGGGGTA 59.651 52.381 0.00 0.00 0.00 3.69
899 1013 1.348696 TCGTTTGAAAGGGAGGGGTAC 59.651 52.381 0.00 0.00 0.00 3.34
900 1014 1.350019 CGTTTGAAAGGGAGGGGTACT 59.650 52.381 0.00 0.00 0.00 2.73
901 1015 2.224695 CGTTTGAAAGGGAGGGGTACTT 60.225 50.000 0.00 0.00 0.00 2.24
902 1016 3.154710 GTTTGAAAGGGAGGGGTACTTG 58.845 50.000 0.00 0.00 0.00 3.16
903 1017 2.127651 TGAAAGGGAGGGGTACTTGT 57.872 50.000 0.00 0.00 0.00 3.16
904 1018 2.424793 TGAAAGGGAGGGGTACTTGTT 58.575 47.619 0.00 0.00 0.00 2.83
905 1019 3.600433 TGAAAGGGAGGGGTACTTGTTA 58.400 45.455 0.00 0.00 0.00 2.41
1036 1150 2.294078 CCGCCTTTCACCCTCCTCT 61.294 63.158 0.00 0.00 0.00 3.69
1061 1191 2.266055 CGCCTCCGCTTCCTCTTT 59.734 61.111 0.00 0.00 0.00 2.52
1064 1194 0.742635 GCCTCCGCTTCCTCTTTCTG 60.743 60.000 0.00 0.00 0.00 3.02
1068 1198 0.036875 CCGCTTCCTCTTTCTGGGTT 59.963 55.000 0.00 0.00 0.00 4.11
1305 1436 0.318699 CTGCACGAGGACGACTTGAA 60.319 55.000 6.21 0.00 42.66 2.69
1560 1691 0.329596 CCCTTCTCTTCAACCCCCAG 59.670 60.000 0.00 0.00 0.00 4.45
1613 1744 0.316204 ATTTGTGCTCCTTGTGCTGC 59.684 50.000 0.00 0.00 0.00 5.25
1709 1841 2.540361 GCATTGGCATGTCTTGATCGTC 60.540 50.000 0.00 0.00 40.72 4.20
1784 1916 0.971386 CAAGCCTGGTTCAAGCCATT 59.029 50.000 0.00 0.00 37.96 3.16
2074 2206 5.762825 ATTTTCATCGATGAACTGGATGG 57.237 39.130 34.51 3.08 45.63 3.51
2104 2236 1.202336 ACGGCGTAACAGTAGGTATGC 60.202 52.381 12.58 0.00 0.00 3.14
2228 2360 9.484806 AACTCTGATGGATGGAAATAAGAAATT 57.515 29.630 0.00 0.00 0.00 1.82
2586 2719 8.613482 TCTACTATCTTTGTGATGACTTCTACG 58.387 37.037 0.00 0.00 36.65 3.51
2700 2833 2.426522 TCACTTGCCACTGCTTGATAC 58.573 47.619 0.00 0.00 38.71 2.24
2817 2950 8.775527 GTCTAATAGGCCTTATTTTTGTAGCTC 58.224 37.037 12.58 0.00 33.96 4.09
3078 3211 6.434302 TCCAACTGTTTCATGGGATGATATT 58.566 36.000 0.00 0.00 39.39 1.28
3188 3322 2.224281 TGATGACGATTGTCCCTATGCC 60.224 50.000 10.69 0.00 44.86 4.40
3376 3510 9.184523 TCTTTTCTTTGAGGTTTGTCATAGAAA 57.815 29.630 12.56 12.56 45.18 2.52
3495 3629 3.299503 ACATGAAGTTTTTCTGGGCACT 58.700 40.909 0.00 0.00 34.31 4.40
3560 3694 8.562892 CATCAAGCTGGTTTATTAATAGGAGTG 58.437 37.037 0.00 0.00 0.00 3.51
3603 3820 2.154462 GTTTGCTATCCTGCAGTGTGT 58.846 47.619 13.81 0.00 44.27 3.72
3847 4064 2.367567 GCCCCTAAACGGTATGAGATCA 59.632 50.000 0.00 0.00 0.00 2.92
3990 4313 8.846943 TTGCAACTATCTGATCAAGAAACTTA 57.153 30.769 0.00 0.00 38.79 2.24
4011 4334 4.283363 ACATCTGATATGGTGCAGATCC 57.717 45.455 0.00 0.00 45.99 3.36
4164 4488 2.159393 TGAACTTCAGTTGTGCACTTGC 60.159 45.455 19.41 8.02 38.56 4.01
4173 4497 2.404265 TGTGCACTTGCGAATCTTTG 57.596 45.000 19.41 0.00 45.83 2.77
4240 4564 6.621316 TTGCAACGAAATAACTTAGGTTGA 57.379 33.333 0.00 0.00 37.53 3.18
4863 5187 4.094294 TGACAAAAACAGAAGTTGACGAGG 59.906 41.667 0.00 0.00 38.17 4.63
4958 5285 5.034152 AGTTCGTGTTACACAAGCATTTTG 58.966 37.500 16.09 0.00 33.40 2.44
5021 5348 5.869753 AATGATATATTTGTGCGGCTCTC 57.130 39.130 0.00 0.00 0.00 3.20
5026 5353 6.318648 TGATATATTTGTGCGGCTCTCTTTTT 59.681 34.615 0.00 0.00 0.00 1.94
5062 5425 1.663135 GAGAATTCAAGCGACTCTGGC 59.337 52.381 8.44 0.00 0.00 4.85
5105 5468 6.833342 TTTTCTCTACAACCGTCTAAACAC 57.167 37.500 0.00 0.00 0.00 3.32
5230 7162 3.777465 GTGCATTGAATCATCAGCACT 57.223 42.857 20.30 0.00 46.36 4.40
5384 7317 0.175760 TCTTGCAGTAGGTCGATGCC 59.824 55.000 5.55 0.00 39.22 4.40
5408 7341 1.132527 TCCTTCCCTTCAGAGGTTGGA 60.133 52.381 0.00 0.00 41.85 3.53
5439 7372 1.739466 CACATTGTGAGATCCCCAACG 59.261 52.381 11.45 0.00 35.23 4.10
5524 7457 1.086696 GCAAGCTCGATAAACCAGCA 58.913 50.000 0.00 0.00 35.46 4.41
5591 7524 7.230849 AGAATGTATGCAATCTGGTGAAAAA 57.769 32.000 0.02 0.00 33.88 1.94
5601 7534 6.347079 GCAATCTGGTGAAAAATTGACACATG 60.347 38.462 0.00 0.00 36.42 3.21
5623 7556 3.737559 TGCTATCATGTCCCCTTGTTT 57.262 42.857 0.00 0.00 0.00 2.83
5640 7573 3.338249 TGTTTAGGAGAAGAGTGCATGC 58.662 45.455 11.82 11.82 0.00 4.06
5643 7576 2.399916 AGGAGAAGAGTGCATGCTTC 57.600 50.000 20.33 18.48 40.54 3.86
5645 7578 2.239150 AGGAGAAGAGTGCATGCTTCAT 59.761 45.455 24.41 9.60 42.21 2.57
5694 7627 1.000866 GCAAGGAAAGGGCCTGGAT 59.999 57.895 6.92 0.00 38.58 3.41
5697 7630 2.690936 GCAAGGAAAGGGCCTGGATAAT 60.691 50.000 6.92 0.00 38.58 1.28
5703 7636 2.514726 AGGGCCTGGATAATGTACCT 57.485 50.000 4.50 0.00 0.00 3.08
5803 7736 0.603707 CGGGCACAGCTTCTTCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
5911 7844 4.799564 TTTCCCAAACTCCAATGTATGC 57.200 40.909 0.00 0.00 0.00 3.14
5985 7918 4.260538 CGATGCAGAGCTTGGAATAACTTC 60.261 45.833 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 2.032979 GCAAATTTTTGGACTGGTTGCG 60.033 45.455 5.28 0.00 38.57 4.85
210 219 3.117663 AGGTGGGAGCAAAAACTAAGACA 60.118 43.478 0.00 0.00 0.00 3.41
402 449 2.228822 CACGCCATTTACAGCCTTCTTT 59.771 45.455 0.00 0.00 0.00 2.52
540 593 3.369546 ACGGTTGAAGCTTTTTCCATG 57.630 42.857 0.00 0.00 0.00 3.66
763 877 3.807622 TGTCTTTTTGTCCATCGTCAGAC 59.192 43.478 0.00 0.00 0.00 3.51
797 911 4.077184 TTCGGCCGGTCGCATCTT 62.077 61.111 26.77 0.00 40.31 2.40
860 974 4.535116 ACGACTCGAAGTTCTAGTTTGTC 58.465 43.478 11.05 4.71 0.00 3.18
861 975 4.564940 ACGACTCGAAGTTCTAGTTTGT 57.435 40.909 11.05 10.04 0.00 2.83
862 976 5.457799 TCAAACGACTCGAAGTTCTAGTTTG 59.542 40.000 20.08 20.08 44.71 2.93
863 977 5.585390 TCAAACGACTCGAAGTTCTAGTTT 58.415 37.500 11.05 7.93 0.00 2.66
864 978 5.179045 TCAAACGACTCGAAGTTCTAGTT 57.821 39.130 11.05 2.85 0.00 2.24
865 979 4.825546 TCAAACGACTCGAAGTTCTAGT 57.174 40.909 9.65 9.65 0.00 2.57
866 980 5.117287 CCTTTCAAACGACTCGAAGTTCTAG 59.883 44.000 5.20 2.96 0.00 2.43
867 981 4.980434 CCTTTCAAACGACTCGAAGTTCTA 59.020 41.667 5.20 0.00 0.00 2.10
868 982 3.802685 CCTTTCAAACGACTCGAAGTTCT 59.197 43.478 5.20 0.00 0.00 3.01
869 983 3.059800 CCCTTTCAAACGACTCGAAGTTC 60.060 47.826 5.20 0.00 0.00 3.01
870 984 2.870411 CCCTTTCAAACGACTCGAAGTT 59.130 45.455 5.20 0.00 0.00 2.66
871 985 2.101917 TCCCTTTCAAACGACTCGAAGT 59.898 45.455 5.20 0.00 0.00 3.01
872 986 2.731976 CTCCCTTTCAAACGACTCGAAG 59.268 50.000 5.20 0.00 0.00 3.79
873 987 2.547218 CCTCCCTTTCAAACGACTCGAA 60.547 50.000 5.20 0.00 0.00 3.71
874 988 1.000506 CCTCCCTTTCAAACGACTCGA 59.999 52.381 5.20 0.00 0.00 4.04
875 989 1.429463 CCTCCCTTTCAAACGACTCG 58.571 55.000 0.00 0.00 0.00 4.18
876 990 1.610886 CCCCTCCCTTTCAAACGACTC 60.611 57.143 0.00 0.00 0.00 3.36
877 991 0.400594 CCCCTCCCTTTCAAACGACT 59.599 55.000 0.00 0.00 0.00 4.18
878 992 0.109913 ACCCCTCCCTTTCAAACGAC 59.890 55.000 0.00 0.00 0.00 4.34
879 993 1.348696 GTACCCCTCCCTTTCAAACGA 59.651 52.381 0.00 0.00 0.00 3.85
880 994 1.350019 AGTACCCCTCCCTTTCAAACG 59.650 52.381 0.00 0.00 0.00 3.60
881 995 3.154710 CAAGTACCCCTCCCTTTCAAAC 58.845 50.000 0.00 0.00 0.00 2.93
882 996 2.787035 ACAAGTACCCCTCCCTTTCAAA 59.213 45.455 0.00 0.00 0.00 2.69
883 997 2.424793 ACAAGTACCCCTCCCTTTCAA 58.575 47.619 0.00 0.00 0.00 2.69
884 998 2.127651 ACAAGTACCCCTCCCTTTCA 57.872 50.000 0.00 0.00 0.00 2.69
885 999 4.645863 TTAACAAGTACCCCTCCCTTTC 57.354 45.455 0.00 0.00 0.00 2.62
886 1000 4.355889 ACATTAACAAGTACCCCTCCCTTT 59.644 41.667 0.00 0.00 0.00 3.11
887 1001 3.920841 ACATTAACAAGTACCCCTCCCTT 59.079 43.478 0.00 0.00 0.00 3.95
888 1002 3.265995 CACATTAACAAGTACCCCTCCCT 59.734 47.826 0.00 0.00 0.00 4.20
889 1003 3.617284 CACATTAACAAGTACCCCTCCC 58.383 50.000 0.00 0.00 0.00 4.30
890 1004 3.014623 GCACATTAACAAGTACCCCTCC 58.985 50.000 0.00 0.00 0.00 4.30
891 1005 3.014623 GGCACATTAACAAGTACCCCTC 58.985 50.000 0.00 0.00 0.00 4.30
892 1006 2.617021 CGGCACATTAACAAGTACCCCT 60.617 50.000 0.00 0.00 0.00 4.79
893 1007 1.741145 CGGCACATTAACAAGTACCCC 59.259 52.381 0.00 0.00 0.00 4.95
894 1008 1.131693 GCGGCACATTAACAAGTACCC 59.868 52.381 0.00 0.00 0.00 3.69
895 1009 1.807742 TGCGGCACATTAACAAGTACC 59.192 47.619 0.00 0.00 0.00 3.34
896 1010 2.482721 AGTGCGGCACATTAACAAGTAC 59.517 45.455 32.29 3.11 36.74 2.73
897 1011 2.482336 CAGTGCGGCACATTAACAAGTA 59.518 45.455 32.29 0.00 36.74 2.24
898 1012 1.266718 CAGTGCGGCACATTAACAAGT 59.733 47.619 32.29 7.86 36.74 3.16
899 1013 1.535028 TCAGTGCGGCACATTAACAAG 59.465 47.619 32.29 12.61 36.74 3.16
900 1014 1.598882 TCAGTGCGGCACATTAACAA 58.401 45.000 32.29 8.60 36.74 2.83
901 1015 1.535028 CTTCAGTGCGGCACATTAACA 59.465 47.619 32.29 10.80 36.74 2.41
902 1016 1.135689 CCTTCAGTGCGGCACATTAAC 60.136 52.381 32.29 6.90 36.74 2.01
903 1017 1.164411 CCTTCAGTGCGGCACATTAA 58.836 50.000 32.29 21.13 36.74 1.40
904 1018 1.305219 GCCTTCAGTGCGGCACATTA 61.305 55.000 32.29 15.72 45.59 1.90
905 1019 2.629656 GCCTTCAGTGCGGCACATT 61.630 57.895 32.29 12.40 45.59 2.71
1023 1137 1.612442 CGGGGAGAGGAGGGTGAAA 60.612 63.158 0.00 0.00 0.00 2.69
1055 1185 1.580845 CGCTGCAACCCAGAAAGAGG 61.581 60.000 0.00 0.00 44.64 3.69
1061 1191 2.031012 CTGTCGCTGCAACCCAGA 59.969 61.111 0.00 0.00 44.64 3.86
1126 1257 4.924187 CGCGGGGAGGGAGAGGAT 62.924 72.222 0.00 0.00 34.27 3.24
1284 1415 3.575351 AAGTCGTCCTCGTGCAGGC 62.575 63.158 0.35 0.00 43.08 4.85
1285 1416 1.734477 CAAGTCGTCCTCGTGCAGG 60.734 63.158 0.00 0.00 45.15 4.85
1287 1418 0.318699 CTTCAAGTCGTCCTCGTGCA 60.319 55.000 0.00 0.00 38.33 4.57
1288 1419 0.318784 ACTTCAAGTCGTCCTCGTGC 60.319 55.000 0.00 0.00 38.33 5.34
1289 1420 1.666311 GGACTTCAAGTCGTCCTCGTG 60.666 57.143 11.52 0.00 45.96 4.35
1292 1423 0.246910 GGGGACTTCAAGTCGTCCTC 59.753 60.000 16.92 0.59 45.96 3.71
1294 1425 1.295746 GGGGGACTTCAAGTCGTCC 59.704 63.158 11.52 14.28 45.96 4.79
1296 1427 1.752833 GTGGGGGACTTCAAGTCGT 59.247 57.895 11.52 0.00 45.96 4.34
1382 1513 2.432300 CGCCGTCCTCCCCATTAGT 61.432 63.158 0.00 0.00 0.00 2.24
1438 1569 1.917336 GAAGGGCCATACGGTTCCCA 61.917 60.000 6.18 0.00 37.11 4.37
1539 1670 1.691823 GGGGTTGAAGAGAAGGGGG 59.308 63.158 0.00 0.00 0.00 5.40
1560 1691 1.062587 CCCGTCAGACGATGAAATTGC 59.937 52.381 24.88 0.00 46.05 3.56
1643 1774 2.820037 GGGCCGTAGAGCAGCAAC 60.820 66.667 0.00 0.00 0.00 4.17
1709 1841 3.253188 CCACACTGGTCAACATTTGTAGG 59.747 47.826 0.00 0.00 31.35 3.18
1735 1867 8.329203 ACAAGAAGAACAAGAATCAATCCTAC 57.671 34.615 0.00 0.00 0.00 3.18
1784 1916 0.955428 GGGCACTGCATTCTCGAACA 60.955 55.000 2.82 0.00 0.00 3.18
2042 2174 1.606668 TCGATGAAAATAATGGCCGGC 59.393 47.619 21.18 21.18 0.00 6.13
2074 2206 3.047796 CTGTTACGCCGTGGACATATAC 58.952 50.000 0.00 0.00 0.00 1.47
2104 2236 9.590451 AAGCACCAAAAATGATAACATGATAAG 57.410 29.630 0.00 0.00 36.79 1.73
2175 2307 0.455815 GACCAACAATGCGGGATTCC 59.544 55.000 0.00 0.00 0.00 3.01
2228 2360 1.335964 CGTGAGGAAGCTTCTTCGACA 60.336 52.381 27.44 12.93 36.21 4.35
2383 2515 7.813852 ACGAGACAAGATATTGTTTCAGTAC 57.186 36.000 19.90 1.96 36.27 2.73
2564 2697 7.463383 GCAACGTAGAAGTCATCACAAAGATAG 60.463 40.741 0.00 0.00 34.43 2.08
2565 2698 6.310467 GCAACGTAGAAGTCATCACAAAGATA 59.690 38.462 0.00 0.00 34.43 1.98
2566 2699 5.120830 GCAACGTAGAAGTCATCACAAAGAT 59.879 40.000 0.00 0.00 37.48 2.40
2570 2703 3.723260 TGCAACGTAGAAGTCATCACAA 58.277 40.909 0.00 0.00 0.00 3.33
2700 2833 6.009115 ACATTTTAGGCTCGGTACAAAAAG 57.991 37.500 0.00 0.00 0.00 2.27
2817 2950 8.410912 TCATCAAGATGCAGATTTTTGGAATAG 58.589 33.333 5.19 0.00 38.65 1.73
3078 3211 6.003950 CACCTTTAGATCTTTCAAACCTCCA 58.996 40.000 0.00 0.00 0.00 3.86
3188 3322 2.049228 CTTGCTGAAGCTTTTTCTGCG 58.951 47.619 0.00 0.00 43.44 5.18
3376 3510 5.258456 ACAATGTACACGGTAATCGATCT 57.742 39.130 0.00 0.00 42.43 2.75
3560 3694 7.198306 ACATACTACAACTAAACCAGCAAAC 57.802 36.000 0.00 0.00 0.00 2.93
3635 3852 3.258372 TCTTGAACAGAAGATGGCTACGT 59.742 43.478 0.00 0.00 0.00 3.57
3786 4003 6.932356 TCAAAGAATATGATGCTTGGAGAC 57.068 37.500 0.00 0.00 0.00 3.36
3835 4052 7.770801 TTTAAGACACATTGATCTCATACCG 57.229 36.000 0.00 0.00 0.00 4.02
3990 4313 3.649502 TGGATCTGCACCATATCAGATGT 59.350 43.478 9.18 0.00 46.60 3.06
4011 4334 7.643764 ACACGAAATACAACAAGTTTCTTCATG 59.356 33.333 0.00 0.00 31.42 3.07
4181 4505 0.877071 GACGGTCAGTACTCGGTTGA 59.123 55.000 2.62 0.00 0.00 3.18
4240 4564 3.198409 TCTGCAAGATCACACAAGTGT 57.802 42.857 0.00 0.00 42.07 3.55
4914 5241 7.269937 CGAACTTGAACAAAAGCTCAATAGATG 59.730 37.037 0.00 0.00 31.40 2.90
4958 5285 2.725221 ATCCAAGGCTTGACTGATCC 57.275 50.000 28.18 0.00 0.00 3.36
5030 5357 9.935682 GTCGCTTGAATTCTCATATTTCATTAA 57.064 29.630 7.05 0.00 29.90 1.40
5032 5359 8.218338 AGTCGCTTGAATTCTCATATTTCATT 57.782 30.769 7.05 0.00 29.90 2.57
5035 5398 7.343691 CAGAGTCGCTTGAATTCTCATATTTC 58.656 38.462 7.05 0.00 0.00 2.17
5105 5468 1.148310 CAATATAGCCAAGGCCGTCG 58.852 55.000 7.62 0.00 43.17 5.12
5194 7126 5.048083 TCAATGCACATAAAGTTCCTGTTCC 60.048 40.000 0.00 0.00 0.00 3.62
5384 7317 0.540923 CCTCTGAAGGGAAGGAGCTG 59.459 60.000 0.00 0.00 39.21 4.24
5408 7341 0.311790 CACAATGTGCTTTCACGCCT 59.688 50.000 0.00 0.00 46.01 5.52
5439 7372 2.970974 GCTTCTGTGAAGGCGGCAC 61.971 63.158 13.08 5.41 36.81 5.01
5524 7457 7.083062 TGATATCACCCTGCAAAGATAGATT 57.917 36.000 0.00 0.00 0.00 2.40
5601 7534 3.498774 ACAAGGGGACATGATAGCATC 57.501 47.619 0.00 0.00 30.68 3.91
5623 7556 2.833943 TGAAGCATGCACTCTTCTCCTA 59.166 45.455 21.98 7.16 39.41 2.94
5640 7573 6.149973 TGCCTTGAAAACTCATCACTATGAAG 59.850 38.462 0.00 0.00 41.57 3.02
5643 7576 5.885230 TGCCTTGAAAACTCATCACTATG 57.115 39.130 0.00 0.00 0.00 2.23
5645 7578 5.559770 TCATGCCTTGAAAACTCATCACTA 58.440 37.500 0.00 0.00 0.00 2.74
5694 7627 1.276705 TGGACGCTGCAAGGTACATTA 59.723 47.619 0.00 0.00 0.00 1.90
5697 7630 1.301401 GTGGACGCTGCAAGGTACA 60.301 57.895 0.00 0.00 0.00 2.90
5703 7636 2.203195 AGCTTGTGGACGCTGCAA 60.203 55.556 0.00 0.00 34.69 4.08
5722 7655 3.198872 CAGAAGAAAGGGAATAGCGTCC 58.801 50.000 0.00 0.00 36.90 4.79
5803 7736 1.915078 GCCCTGGTGCCATAGTCTGT 61.915 60.000 0.00 0.00 0.00 3.41
5911 7844 1.884579 ACTGAATCAGCACAGGCAAAG 59.115 47.619 10.62 0.00 44.61 2.77
5985 7918 0.796312 ACCGATAAAAGCAGCACACG 59.204 50.000 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.