Multiple sequence alignment - TraesCS2A01G581100

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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 TraesCS2A01G581100 chr2A 100.000 2543 0 0 1 2543 773296191 773298733 0.000000e+00 4697.0
1 TraesCS2A01G581100 chr2A 81.527 812 142 7 839 1646 540770652 540769845 0.000000e+00 662.0
2 TraesCS2A01G581100 chr2A 88.235 153 8 6 429 572 773380543 773380392 9.350000e-40 174.0
3 TraesCS2A01G581100 chr2A 89.474 57 6 0 2374 2430 495110723 495110667 3.510000e-09 73.1
4 TraesCS2A01G581100 chr7D 93.635 1524 85 3 1020 2543 184213854 184212343 0.000000e+00 2266.0
5 TraesCS2A01G581100 chr7D 78.448 116 20 5 1631 1744 104335563 104335675 1.260000e-08 71.3
6 TraesCS2A01G581100 chr2B 81.713 1471 266 2 996 2463 638009206 638010676 0.000000e+00 1223.0
7 TraesCS2A01G581100 chr2B 79.393 461 40 25 401 806 571963713 571963253 8.960000e-70 274.0
8 TraesCS2A01G581100 chr2B 79.348 460 40 27 401 806 571877278 571876820 3.220000e-69 272.0
9 TraesCS2A01G581100 chr2B 79.130 460 42 24 401 806 571851404 571850945 4.170000e-68 268.0
10 TraesCS2A01G581100 chr2B 79.004 462 41 26 401 806 789406335 789405874 5.390000e-67 265.0
11 TraesCS2A01G581100 chr2B 78.959 461 42 24 401 806 789424716 789424256 1.940000e-66 263.0
12 TraesCS2A01G581100 chr2B 78.742 461 42 27 401 806 571833370 571832911 9.030000e-65 257.0
13 TraesCS2A01G581100 chr2B 86.875 160 17 3 651 806 789326349 789326190 2.600000e-40 176.0
14 TraesCS2A01G581100 chr2B 82.609 115 13 5 213 325 571833524 571833415 7.490000e-16 95.3
15 TraesCS2A01G581100 chr2D 90.753 876 45 12 1 844 646086153 646085282 0.000000e+00 1136.0
16 TraesCS2A01G581100 chr2D 79.700 734 77 35 152 842 646053967 646054671 4.960000e-127 464.0
17 TraesCS2A01G581100 chr2D 79.402 301 56 5 2246 2543 376834004 376834301 9.220000e-50 207.0
18 TraesCS2A01G581100 chr4A 81.879 298 54 0 2246 2543 603123812 603123515 4.200000e-63 252.0
19 TraesCS2A01G581100 chr6A 80.693 202 37 2 2248 2448 77104545 77104745 3.390000e-34 156.0
20 TraesCS2A01G581100 chr6A 92.857 42 1 2 2473 2512 386905740 386905781 2.730000e-05 60.2
21 TraesCS2A01G581100 chr1D 84.564 149 20 3 2302 2450 9911008 9910863 7.330000e-31 145.0
22 TraesCS2A01G581100 chr1D 75.845 207 42 8 2341 2543 421069810 421070012 5.790000e-17 99.0


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 TraesCS2A01G581100 chr2A 773296191 773298733 2542 False 4697 4697 100.000 1 2543 1 chr2A.!!$F1 2542
1 TraesCS2A01G581100 chr2A 540769845 540770652 807 True 662 662 81.527 839 1646 1 chr2A.!!$R2 807
2 TraesCS2A01G581100 chr7D 184212343 184213854 1511 True 2266 2266 93.635 1020 2543 1 chr7D.!!$R1 1523
3 TraesCS2A01G581100 chr2B 638009206 638010676 1470 False 1223 1223 81.713 996 2463 1 chr2B.!!$F1 1467
4 TraesCS2A01G581100 chr2D 646085282 646086153 871 True 1136 1136 90.753 1 844 1 chr2D.!!$R1 843
5 TraesCS2A01G581100 chr2D 646053967 646054671 704 False 464 464 79.700 152 842 1 chr2D.!!$F2 690

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
46 47 0.032813 CACAGCCCCCAATTGGAGAT 60.033 55.0 26.6 12.59 37.39 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2093 0.179004 TCTTGGGTGCGGTTTGTGAT 60.179 50.0 0.0 0.0 0.0 3.06 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
33 34 2.945668 GGACAATGAATCCTACACAGCC 59.054 50.000 0.00 0.00 33.03 4.85
46 47 0.032813 CACAGCCCCCAATTGGAGAT 60.033 55.000 26.60 12.59 37.39 2.75
139 146 3.181508 ACGTACGTTGGGTTCTTTGTTTG 60.182 43.478 16.72 0.00 0.00 2.93
281 289 4.915085 ACTTTCGCAATTACCGAACATTTG 59.085 37.500 11.30 4.79 43.48 2.32
290 298 7.464710 GCAATTACCGAACATTTGTGAAAAACA 60.465 33.333 0.00 0.00 36.85 2.83
293 301 6.159419 ACCGAACATTTGTGAAAAACAAAC 57.841 33.333 5.83 0.00 44.97 2.93
295 303 5.350091 CCGAACATTTGTGAAAAACAAACCT 59.650 36.000 5.83 0.00 44.97 3.50
443 471 2.370281 TGGAAATCAGACAGACTCGC 57.630 50.000 0.00 0.00 0.00 5.03
542 581 3.423996 TTGTGTTTTACTTTGACCGCC 57.576 42.857 0.00 0.00 0.00 6.13
632 688 2.165437 GCAATTCGCCCCAATAAACTGA 59.835 45.455 0.00 0.00 32.94 3.41
635 691 3.644966 TTCGCCCCAATAAACTGAGAT 57.355 42.857 0.00 0.00 0.00 2.75
640 696 4.196971 GCCCCAATAAACTGAGATTACGT 58.803 43.478 0.00 0.00 0.00 3.57
662 718 7.364970 ACGTTTTTCCAACAGAATATTGTACC 58.635 34.615 0.00 0.00 33.44 3.34
757 816 5.759506 TTGAGTTTCAATTTGTAGGCGAA 57.240 34.783 0.00 0.00 30.26 4.70
758 817 5.356882 TGAGTTTCAATTTGTAGGCGAAG 57.643 39.130 0.00 0.00 0.00 3.79
759 818 4.215399 TGAGTTTCAATTTGTAGGCGAAGG 59.785 41.667 0.00 0.00 0.00 3.46
760 819 8.654937 TTGAGTTTCAATTTGTAGGCGAAGGC 62.655 42.308 0.00 0.00 42.36 4.35
783 846 1.672881 CAGATCCGACTTGATTTGCCC 59.327 52.381 0.00 0.00 0.00 5.36
785 848 0.331278 ATCCGACTTGATTTGCCCCA 59.669 50.000 0.00 0.00 0.00 4.96
844 911 1.130373 CACACAATCAATTCCCCGTCG 59.870 52.381 0.00 0.00 0.00 5.12
845 912 1.002659 ACACAATCAATTCCCCGTCGA 59.997 47.619 0.00 0.00 0.00 4.20
846 913 1.665679 CACAATCAATTCCCCGTCGAG 59.334 52.381 0.00 0.00 0.00 4.04
852 919 1.104630 AATTCCCCGTCGAGAGTCTC 58.895 55.000 10.33 10.33 0.00 3.36
868 935 1.154376 CTCTCTATCGTAGCGGCGC 60.154 63.158 26.86 26.86 0.00 6.53
870 937 1.154376 CTCTATCGTAGCGGCGCTC 60.154 63.158 39.97 26.65 40.44 5.03
883 950 3.733960 CGCTCCCGCCGATCGATA 61.734 66.667 18.66 0.00 41.67 2.92
887 954 0.811915 CTCCCGCCGATCGATAATCT 59.188 55.000 18.66 0.00 41.67 2.40
888 955 0.809385 TCCCGCCGATCGATAATCTC 59.191 55.000 18.66 0.00 41.67 2.75
898 965 2.074579 TCGATAATCTCTCCCCTCCCT 58.925 52.381 0.00 0.00 0.00 4.20
899 966 2.041891 TCGATAATCTCTCCCCTCCCTC 59.958 54.545 0.00 0.00 0.00 4.30
902 969 2.319410 AATCTCTCCCCTCCCTCCCG 62.319 65.000 0.00 0.00 0.00 5.14
903 970 3.756783 CTCTCCCCTCCCTCCCGT 61.757 72.222 0.00 0.00 0.00 5.28
909 976 2.364961 CCTCCCTCCCGTTCTCCT 59.635 66.667 0.00 0.00 0.00 3.69
912 979 2.362632 CCCTCCCGTTCTCCTCGT 60.363 66.667 0.00 0.00 0.00 4.18
917 984 1.977544 CCCGTTCTCCTCGTCTGGT 60.978 63.158 0.00 0.00 0.00 4.00
918 985 1.533469 CCCGTTCTCCTCGTCTGGTT 61.533 60.000 0.00 0.00 0.00 3.67
919 986 0.317479 CCGTTCTCCTCGTCTGGTTT 59.683 55.000 0.00 0.00 0.00 3.27
921 988 1.792949 CGTTCTCCTCGTCTGGTTTTG 59.207 52.381 0.00 0.00 0.00 2.44
922 989 1.531578 GTTCTCCTCGTCTGGTTTTGC 59.468 52.381 0.00 0.00 0.00 3.68
923 990 1.048601 TCTCCTCGTCTGGTTTTGCT 58.951 50.000 0.00 0.00 0.00 3.91
924 991 1.151668 CTCCTCGTCTGGTTTTGCTG 58.848 55.000 0.00 0.00 0.00 4.41
929 996 0.588252 CGTCTGGTTTTGCTGTCCAG 59.412 55.000 4.30 4.30 46.94 3.86
950 1017 3.151022 GACTGAGAGGGGGCGAGG 61.151 72.222 0.00 0.00 0.00 4.63
964 1031 3.379445 GAGGGTCTCGTTCGCCCA 61.379 66.667 8.56 0.00 44.69 5.36
965 1032 3.358076 GAGGGTCTCGTTCGCCCAG 62.358 68.421 8.56 0.00 44.69 4.45
966 1033 3.379445 GGGTCTCGTTCGCCCAGA 61.379 66.667 0.00 0.00 41.93 3.86
967 1034 2.654877 GGTCTCGTTCGCCCAGAA 59.345 61.111 0.00 0.00 36.31 3.02
968 1035 1.446272 GGTCTCGTTCGCCCAGAAG 60.446 63.158 0.00 0.00 39.95 2.85
975 1043 0.241213 GTTCGCCCAGAAGGAAAAGC 59.759 55.000 0.00 0.00 39.95 3.51
976 1044 1.234615 TTCGCCCAGAAGGAAAAGCG 61.235 55.000 0.00 0.00 41.37 4.68
984 1052 2.226674 CAGAAGGAAAAGCGAGGGTTTC 59.773 50.000 0.00 0.00 31.82 2.78
985 1053 2.106684 AGAAGGAAAAGCGAGGGTTTCT 59.893 45.455 0.00 0.00 34.74 2.52
987 1055 0.241213 GGAAAAGCGAGGGTTTCTGC 59.759 55.000 0.00 0.00 34.74 4.26
988 1056 0.951558 GAAAAGCGAGGGTTTCTGCA 59.048 50.000 0.00 0.00 31.82 4.41
989 1057 1.336755 GAAAAGCGAGGGTTTCTGCAA 59.663 47.619 0.00 0.00 31.82 4.08
992 1060 1.302511 GCGAGGGTTTCTGCAAGGA 60.303 57.895 0.00 0.00 0.00 3.36
994 1062 1.406887 GCGAGGGTTTCTGCAAGGATA 60.407 52.381 0.00 0.00 0.00 2.59
1018 1086 1.004745 GGATGGGTTCTCAGGCTGAAA 59.995 52.381 19.29 12.52 0.00 2.69
1026 1094 0.676151 CTCAGGCTGAAACAGGAGGC 60.676 60.000 19.29 0.00 35.02 4.70
1038 1106 0.319555 CAGGAGGCTCGAAACAACGA 60.320 55.000 8.69 0.00 40.00 3.85
1053 1121 1.934220 AACGAGCTGAGCCGATCGAA 61.934 55.000 18.66 0.00 38.50 3.71
1089 1157 4.082190 CGTCTGGAACTACAAGAGGATGAA 60.082 45.833 0.00 0.00 0.00 2.57
1120 1188 4.527038 AGTTCGTATGGGAAGAAGAGTTCA 59.473 41.667 0.00 0.00 0.00 3.18
1199 1267 0.112995 TTCAGCCCATCTGCCTTGTT 59.887 50.000 0.00 0.00 42.56 2.83
1271 1339 5.350504 AAGATCGAGGACAATCTGTTCAT 57.649 39.130 0.00 0.00 32.62 2.57
1309 1377 0.036010 AGGAGATTGGAACACTGCCG 60.036 55.000 0.00 0.00 39.29 5.69
1353 1421 3.711704 TCCGAGATCAAGGGCTTCTTATT 59.288 43.478 6.64 0.00 33.68 1.40
1437 1505 5.813157 GGCTAGAATTCTGAAACTACCAGAC 59.187 44.000 18.47 2.18 40.05 3.51
1524 1592 2.032681 ACTCTGCCGGCTGGTTTC 59.967 61.111 30.13 0.00 37.67 2.78
1525 1593 2.032528 CTCTGCCGGCTGGTTTCA 59.967 61.111 30.13 11.98 37.67 2.69
1527 1595 3.726517 CTGCCGGCTGGTTTCACG 61.727 66.667 29.70 0.57 37.67 4.35
1540 1608 2.103432 GGTTTCACGGGGGAATTTGTTT 59.897 45.455 0.00 0.00 0.00 2.83
1551 1619 6.243148 GGGGGAATTTGTTTGAGTTAGAGTA 58.757 40.000 0.00 0.00 0.00 2.59
1606 1674 4.222124 GTGGGTATCACAAGGAATGAGT 57.778 45.455 0.00 0.00 45.39 3.41
1626 1694 7.770366 TGAGTTCACTGATTACTACCAAGTA 57.230 36.000 0.00 0.00 37.15 2.24
1646 1714 9.099454 CCAAGTACAATATGAGAAACTTCCTAC 57.901 37.037 0.00 0.00 0.00 3.18
1698 1766 1.906574 TGGTATGAGGAGTGTGGAACC 59.093 52.381 0.00 0.00 34.36 3.62
1767 1835 2.683933 GGAGGAAGAGGCCGTGGA 60.684 66.667 0.00 0.00 0.00 4.02
1863 1934 0.390472 GTGGAAGAGGACAAGAGCCG 60.390 60.000 0.00 0.00 0.00 5.52
1906 1977 4.020307 TGATGAACAGCTGGAGACATAACA 60.020 41.667 19.93 9.53 41.51 2.41
1911 1982 3.257393 CAGCTGGAGACATAACACACTC 58.743 50.000 5.57 0.00 41.51 3.51
1955 2026 5.704354 AGACATGGAGACTGATAGAGATGT 58.296 41.667 0.00 0.00 0.00 3.06
1956 2027 5.535783 AGACATGGAGACTGATAGAGATGTG 59.464 44.000 0.00 0.00 0.00 3.21
2022 2093 1.956477 GGAAAAAGGACAGCAGCAGAA 59.044 47.619 0.00 0.00 0.00 3.02
2039 2110 0.671251 GAATCACAAACCGCACCCAA 59.329 50.000 0.00 0.00 0.00 4.12
2042 2113 1.098712 TCACAAACCGCACCCAAGAC 61.099 55.000 0.00 0.00 0.00 3.01
2069 2140 0.034896 ACAGAATTGGCGGTCGTTCT 59.965 50.000 0.00 0.00 0.00 3.01
2109 2180 1.681793 TCGGCTGTAGCTAATCTGGTC 59.318 52.381 0.00 0.00 41.70 4.02
2115 2186 3.211865 TGTAGCTAATCTGGTCGATCGT 58.788 45.455 15.94 0.00 0.00 3.73
2178 2249 3.794911 AGGAAATCCCCAGAAAAATGCT 58.205 40.909 0.00 0.00 36.42 3.79
2215 2286 4.263905 ACAAGGGAAAAGATGGTGATGCTA 60.264 41.667 0.00 0.00 0.00 3.49
2217 2288 5.912149 AGGGAAAAGATGGTGATGCTATA 57.088 39.130 0.00 0.00 0.00 1.31
2233 2304 5.215252 TGCTATAGATAGTTCAAGTGGGC 57.785 43.478 3.21 0.00 32.96 5.36
2240 2311 6.067217 AGATAGTTCAAGTGGGCTACAAAT 57.933 37.500 3.15 0.00 0.00 2.32
2241 2312 6.116126 AGATAGTTCAAGTGGGCTACAAATC 58.884 40.000 3.15 0.00 0.00 2.17
2295 2366 0.534203 ACCGGACGCAATGAAACTGT 60.534 50.000 9.46 0.00 0.00 3.55
2319 2390 4.097361 GGAACTGCCGGGGACTCC 62.097 72.222 2.18 0.00 0.00 3.85
2506 2577 8.929487 TGGAGGTTTAGTTTTGTTTTGGAATAT 58.071 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.172934 GTGTAGGATTCATTGTCCGTGTAA 58.827 41.667 0.00 0.00 40.76 2.41
33 34 4.417426 ACTTACGTATCTCCAATTGGGG 57.583 45.455 24.29 21.86 37.22 4.96
106 113 6.449635 ACCCAACGTACGTATGAGTTATTA 57.550 37.500 23.12 0.00 0.00 0.98
161 169 9.393512 TCAAAAATTGTTCACAGATCCAAAAAT 57.606 25.926 0.00 0.00 0.00 1.82
256 264 2.239201 GTTCGGTAATTGCGAAAGTGC 58.761 47.619 0.00 0.00 0.00 4.40
259 267 4.915085 ACAAATGTTCGGTAATTGCGAAAG 59.085 37.500 0.00 0.00 0.00 2.62
443 471 7.427606 ACGAGAAAAAGAATATGTACGTAGTCG 59.572 37.037 14.93 5.89 43.93 4.18
582 638 2.063979 CACACGGGAGCCCCTGATA 61.064 63.158 0.00 0.00 42.67 2.15
583 639 3.402681 CACACGGGAGCCCCTGAT 61.403 66.667 0.00 0.00 42.67 2.90
626 682 7.066525 TCTGTTGGAAAAACGTAATCTCAGTTT 59.933 33.333 0.00 0.00 39.45 2.66
632 688 9.840427 CAATATTCTGTTGGAAAAACGTAATCT 57.160 29.630 0.00 0.00 37.49 2.40
635 691 9.881529 GTACAATATTCTGTTGGAAAAACGTAA 57.118 29.630 0.00 0.00 37.49 3.18
670 726 6.018751 TCGACTACGTACGTATTTTGCTATCT 60.019 38.462 26.98 0.00 40.69 1.98
671 727 6.129393 TCGACTACGTACGTATTTTGCTATC 58.871 40.000 26.98 13.32 40.69 2.08
672 728 6.018751 TCTCGACTACGTACGTATTTTGCTAT 60.019 38.462 26.98 6.88 40.69 2.97
673 729 5.290885 TCTCGACTACGTACGTATTTTGCTA 59.709 40.000 26.98 5.83 40.69 3.49
757 816 0.965866 TCAAGTCGGATCTGTCGCCT 60.966 55.000 0.42 0.00 0.00 5.52
758 817 0.103208 ATCAAGTCGGATCTGTCGCC 59.897 55.000 0.42 0.00 0.00 5.54
759 818 1.927895 AATCAAGTCGGATCTGTCGC 58.072 50.000 0.42 0.00 0.00 5.19
760 819 2.029728 GCAAATCAAGTCGGATCTGTCG 59.970 50.000 0.42 0.00 0.00 4.35
763 822 1.672881 GGGCAAATCAAGTCGGATCTG 59.327 52.381 0.00 0.00 0.00 2.90
764 823 1.408822 GGGGCAAATCAAGTCGGATCT 60.409 52.381 0.00 0.00 0.00 2.75
797 860 1.139058 CGCACAGCCCCCTATATATCC 59.861 57.143 0.00 0.00 0.00 2.59
844 911 2.991190 CCGCTACGATAGAGAGACTCTC 59.009 54.545 22.72 22.72 43.70 3.20
845 912 2.868839 GCCGCTACGATAGAGAGACTCT 60.869 54.545 4.14 4.14 43.83 3.24
846 913 1.461897 GCCGCTACGATAGAGAGACTC 59.538 57.143 0.00 0.00 41.38 3.36
852 919 1.154376 GAGCGCCGCTACGATAGAG 60.154 63.158 13.54 0.00 39.88 2.43
868 935 0.811915 AGATTATCGATCGGCGGGAG 59.188 55.000 16.41 0.00 39.85 4.30
870 937 0.811915 AGAGATTATCGATCGGCGGG 59.188 55.000 16.41 0.00 39.85 6.13
878 945 2.041891 GAGGGAGGGGAGAGATTATCGA 59.958 54.545 0.00 0.00 0.00 3.59
879 946 2.452505 GAGGGAGGGGAGAGATTATCG 58.547 57.143 0.00 0.00 0.00 2.92
881 948 1.439143 GGGAGGGAGGGGAGAGATTAT 59.561 57.143 0.00 0.00 0.00 1.28
883 950 1.635051 GGGAGGGAGGGGAGAGATT 59.365 63.158 0.00 0.00 0.00 2.40
887 954 3.281787 AACGGGAGGGAGGGGAGA 61.282 66.667 0.00 0.00 0.00 3.71
888 955 2.764547 GAACGGGAGGGAGGGGAG 60.765 72.222 0.00 0.00 0.00 4.30
898 965 1.677966 CCAGACGAGGAGAACGGGA 60.678 63.158 0.00 0.00 34.93 5.14
899 966 1.533469 AACCAGACGAGGAGAACGGG 61.533 60.000 0.00 0.00 34.93 5.28
902 969 1.531578 GCAAAACCAGACGAGGAGAAC 59.468 52.381 0.00 0.00 0.00 3.01
903 970 1.416401 AGCAAAACCAGACGAGGAGAA 59.584 47.619 0.00 0.00 0.00 2.87
909 976 0.179234 TGGACAGCAAAACCAGACGA 59.821 50.000 0.00 0.00 0.00 4.20
934 1001 4.787280 CCCTCGCCCCCTCTCAGT 62.787 72.222 0.00 0.00 0.00 3.41
935 1002 4.787280 ACCCTCGCCCCCTCTCAG 62.787 72.222 0.00 0.00 0.00 3.35
936 1003 4.779733 GACCCTCGCCCCCTCTCA 62.780 72.222 0.00 0.00 0.00 3.27
938 1005 4.467107 GAGACCCTCGCCCCCTCT 62.467 72.222 0.00 0.00 0.00 3.69
950 1017 1.446272 CTTCTGGGCGAACGAGACC 60.446 63.158 0.00 0.00 33.34 3.85
960 1027 1.308783 CCTCGCTTTTCCTTCTGGGC 61.309 60.000 0.00 0.00 34.39 5.36
962 1029 0.036875 ACCCTCGCTTTTCCTTCTGG 59.963 55.000 0.00 0.00 0.00 3.86
963 1030 1.897560 AACCCTCGCTTTTCCTTCTG 58.102 50.000 0.00 0.00 0.00 3.02
964 1031 2.106684 AGAAACCCTCGCTTTTCCTTCT 59.893 45.455 0.00 0.00 32.98 2.85
965 1032 2.226674 CAGAAACCCTCGCTTTTCCTTC 59.773 50.000 0.00 0.00 32.98 3.46
966 1033 2.230660 CAGAAACCCTCGCTTTTCCTT 58.769 47.619 0.00 0.00 32.98 3.36
967 1034 1.897560 CAGAAACCCTCGCTTTTCCT 58.102 50.000 0.00 0.00 32.98 3.36
968 1035 0.241213 GCAGAAACCCTCGCTTTTCC 59.759 55.000 0.00 0.00 32.98 3.13
975 1043 2.691409 TATCCTTGCAGAAACCCTCG 57.309 50.000 0.00 0.00 0.00 4.63
976 1044 4.133078 CTGATATCCTTGCAGAAACCCTC 58.867 47.826 0.00 0.00 0.00 4.30
984 1052 2.374504 ACCCATCCTGATATCCTTGCAG 59.625 50.000 0.00 0.00 0.00 4.41
985 1053 2.421725 ACCCATCCTGATATCCTTGCA 58.578 47.619 0.00 0.00 0.00 4.08
987 1055 4.349048 TGAGAACCCATCCTGATATCCTTG 59.651 45.833 0.00 0.00 0.00 3.61
988 1056 4.570926 TGAGAACCCATCCTGATATCCTT 58.429 43.478 0.00 0.00 0.00 3.36
989 1057 4.166539 CTGAGAACCCATCCTGATATCCT 58.833 47.826 0.00 0.00 0.00 3.24
992 1060 2.641815 GCCTGAGAACCCATCCTGATAT 59.358 50.000 0.00 0.00 0.00 1.63
994 1062 0.842635 GCCTGAGAACCCATCCTGAT 59.157 55.000 0.00 0.00 0.00 2.90
1018 1086 0.600255 CGTTGTTTCGAGCCTCCTGT 60.600 55.000 0.00 0.00 0.00 4.00
1038 1106 1.435515 GTCTTCGATCGGCTCAGCT 59.564 57.895 16.41 0.00 0.00 4.24
1053 1121 2.283532 AGACGCTCCAGCAGGTCT 60.284 61.111 3.93 3.93 42.21 3.85
1089 1157 1.006758 TCCCATACGAACTGGTCCTCT 59.993 52.381 0.00 0.00 31.44 3.69
1120 1188 2.430921 CGCGACCTGCTCTTCGTT 60.431 61.111 0.00 0.00 43.27 3.85
1139 1207 2.032634 GCGATCGCCAACCACTTCA 61.033 57.895 29.48 0.00 34.56 3.02
1199 1267 0.249955 TGCCGATCTCATGTCAGCAA 59.750 50.000 0.00 0.00 0.00 3.91
1239 1307 1.944676 CTCGATCTTACGCCACCGC 60.945 63.158 0.00 0.00 38.22 5.68
1248 1316 5.914898 TGAACAGATTGTCCTCGATCTTA 57.085 39.130 0.00 0.00 41.41 2.10
1271 1339 2.432444 CTAAGCAACCGAATTGGACCA 58.568 47.619 0.00 0.00 42.00 4.02
1309 1377 0.846693 AGCCAGGGACCCATATTCAC 59.153 55.000 14.60 0.00 0.00 3.18
1353 1421 9.354673 GGGTTCTTAAATCCATCATATTCTTCA 57.645 33.333 0.00 0.00 35.54 3.02
1437 1505 1.869767 GCCGCTGGAATCAGATAGTTG 59.130 52.381 0.00 0.00 43.49 3.16
1524 1592 1.960689 ACTCAAACAAATTCCCCCGTG 59.039 47.619 0.00 0.00 0.00 4.94
1525 1593 2.375014 ACTCAAACAAATTCCCCCGT 57.625 45.000 0.00 0.00 0.00 5.28
1527 1595 5.077564 ACTCTAACTCAAACAAATTCCCCC 58.922 41.667 0.00 0.00 0.00 5.40
1540 1608 5.946377 TGACATTCAGCTCTACTCTAACTCA 59.054 40.000 0.00 0.00 0.00 3.41
1551 1619 3.667497 TTCTTCGTGACATTCAGCTCT 57.333 42.857 0.00 0.00 0.00 4.09
1596 1664 7.038302 TGGTAGTAATCAGTGAACTCATTCCTT 60.038 37.037 0.00 0.00 33.49 3.36
1626 1694 8.043710 CAGAAGGTAGGAAGTTTCTCATATTGT 58.956 37.037 0.00 0.00 0.00 2.71
1646 1714 1.273327 GGCCACAATTTCCACAGAAGG 59.727 52.381 0.00 0.00 32.35 3.46
1698 1766 0.382873 TCGATACGTCATGTTCCCCG 59.617 55.000 0.00 0.00 0.00 5.73
1842 1913 0.390472 GCTCTTGTCCTCTTCCACGG 60.390 60.000 0.00 0.00 0.00 4.94
1863 1934 0.690762 TACCTCCTCCAGCACCAAAC 59.309 55.000 0.00 0.00 0.00 2.93
1906 1977 2.443255 ACCCATCCTTGTTGAAGAGTGT 59.557 45.455 0.00 0.00 0.00 3.55
1911 1982 1.962807 TGCAACCCATCCTTGTTGAAG 59.037 47.619 6.56 0.00 43.50 3.02
1955 2026 4.408276 ACTAGAGTTCTGGTGAAGTAGCA 58.592 43.478 0.00 0.00 36.28 3.49
1956 2027 4.459685 TGACTAGAGTTCTGGTGAAGTAGC 59.540 45.833 2.68 0.00 37.82 3.58
2022 2093 0.179004 TCTTGGGTGCGGTTTGTGAT 60.179 50.000 0.00 0.00 0.00 3.06
2086 2157 2.036475 CCAGATTAGCTACAGCCGATGT 59.964 50.000 0.00 0.00 46.45 3.06
2109 2180 1.654954 CCGCCCCCTCTATACGATCG 61.655 65.000 14.88 14.88 0.00 3.69
2115 2186 2.282958 CGCTCCGCCCCCTCTATA 60.283 66.667 0.00 0.00 0.00 1.31
2145 2216 4.010349 GGGGATTTCCTTCACTAGTTGTG 58.990 47.826 0.00 0.00 41.01 3.33
2146 2217 3.655777 TGGGGATTTCCTTCACTAGTTGT 59.344 43.478 0.00 0.00 35.95 3.32
2160 2231 5.046376 CCTGTTAGCATTTTTCTGGGGATTT 60.046 40.000 0.00 0.00 0.00 2.17
2162 2233 4.026052 CCTGTTAGCATTTTTCTGGGGAT 58.974 43.478 0.00 0.00 0.00 3.85
2166 2237 6.073602 GCTTTTTCCTGTTAGCATTTTTCTGG 60.074 38.462 0.00 0.00 33.88 3.86
2178 2249 3.904717 TCCCTTGTGCTTTTTCCTGTTA 58.095 40.909 0.00 0.00 0.00 2.41
2215 2286 6.808321 TTGTAGCCCACTTGAACTATCTAT 57.192 37.500 0.00 0.00 0.00 1.98
2217 2288 5.499004 TTTGTAGCCCACTTGAACTATCT 57.501 39.130 0.00 0.00 0.00 1.98
2233 2304 5.092105 CGCCGATATCTCTGAGATTTGTAG 58.908 45.833 23.98 11.44 36.20 2.74
2240 2311 1.072489 AGGACGCCGATATCTCTGAGA 59.928 52.381 10.23 10.23 0.00 3.27
2241 2312 1.466950 GAGGACGCCGATATCTCTGAG 59.533 57.143 0.34 0.00 0.00 3.35
2295 2366 1.077787 CCCGGCAGTTCCATGCTAA 60.078 57.895 0.00 0.00 45.75 3.09
2507 2578 8.724310 AGTGCTAACCTATGGACCTTAATATTT 58.276 33.333 0.00 0.00 0.00 1.40
2519 2590 4.696479 AGGATCAAGTGCTAACCTATGG 57.304 45.455 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.