Multiple sequence alignment - TraesCS5A01G440700

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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 TraesCS5A01G440700 chr5A 100.000 4602 0 0 855 5456 621859795 621855194 0.000000e+00 8499.0
1 TraesCS5A01G440700 chr5A 100.000 441 0 0 1 441 621860649 621860209 0.000000e+00 815.0
2 TraesCS5A01G440700 chr5D 94.482 2211 66 19 3262 5433 497830722 497828529 0.000000e+00 3356.0
3 TraesCS5A01G440700 chr5D 92.614 1232 71 11 923 2145 497831947 497830727 0.000000e+00 1753.0
4 TraesCS5A01G440700 chr5D 87.826 460 19 15 1 441 497832812 497832371 6.310000e-139 505.0
5 TraesCS5A01G440700 chr5D 88.000 100 3 7 2145 2242 296967924 296968016 5.780000e-20 110.0
6 TraesCS5A01G440700 chr5D 97.959 49 1 0 855 903 497832074 497832026 9.740000e-13 86.1
7 TraesCS5A01G440700 chr5B 91.447 1894 76 23 3262 5113 616973978 616972129 0.000000e+00 2521.0
8 TraesCS5A01G440700 chr5B 94.857 1011 44 7 1138 2145 616974988 616973983 0.000000e+00 1572.0
9 TraesCS5A01G440700 chr5B 94.595 296 9 3 5141 5433 616972133 616971842 8.330000e-123 451.0
10 TraesCS5A01G440700 chr5B 91.065 291 14 6 163 441 616975873 616975583 3.080000e-102 383.0
11 TraesCS5A01G440700 chr5B 87.805 246 29 1 4231 4475 616967620 616967375 2.490000e-73 287.0
12 TraesCS5A01G440700 chr5B 90.179 112 1 2 922 1023 616975190 616975079 2.650000e-28 137.0
13 TraesCS5A01G440700 chr5B 94.253 87 4 1 2156 2242 9500437 9500352 1.230000e-26 132.0
14 TraesCS5A01G440700 chr5B 86.364 66 3 1 1078 1143 616975077 616975018 3.530000e-07 67.6
15 TraesCS5A01G440700 chr5B 100.000 30 0 0 5427 5456 616971833 616971804 7.630000e-04 56.5
16 TraesCS5A01G440700 chr5B 88.889 45 5 0 4182 4226 617175583 617175539 7.630000e-04 56.5
17 TraesCS5A01G440700 chr7D 92.830 1060 42 19 2235 3263 616686623 616685567 0.000000e+00 1506.0
18 TraesCS5A01G440700 chr7D 93.000 100 5 2 2145 2242 8727255 8727354 1.580000e-30 145.0
19 TraesCS5A01G440700 chr7D 76.515 264 37 21 2156 2401 10095459 10095203 2.670000e-23 121.0
20 TraesCS5A01G440700 chr1A 96.387 858 26 3 2410 3264 249430241 249431096 0.000000e+00 1408.0
21 TraesCS5A01G440700 chr2B 91.715 1026 63 16 2256 3267 766174902 766175919 0.000000e+00 1404.0
22 TraesCS5A01G440700 chr2B 95.216 857 37 2 2410 3263 744392864 744393719 0.000000e+00 1352.0
23 TraesCS5A01G440700 chr2B 88.462 104 9 2 2139 2240 159096118 159096220 7.420000e-24 122.0
24 TraesCS5A01G440700 chr3B 96.028 856 28 4 2412 3264 586748188 586749040 0.000000e+00 1387.0
25 TraesCS5A01G440700 chr4D 89.516 1116 81 29 2157 3261 7098806 7099896 0.000000e+00 1380.0
26 TraesCS5A01G440700 chr4D 95.460 859 32 5 2410 3263 390837431 390836575 0.000000e+00 1363.0
27 TraesCS5A01G440700 chr4D 95.460 859 32 5 2410 3263 448535168 448536024 0.000000e+00 1363.0
28 TraesCS5A01G440700 chr4D 93.939 99 4 2 2146 2242 448534834 448534932 1.220000e-31 148.0
29 TraesCS5A01G440700 chr1B 95.360 862 32 6 2410 3267 134557724 134558581 0.000000e+00 1363.0
30 TraesCS5A01G440700 chr2A 88.336 1166 72 35 2145 3267 110863008 110864152 0.000000e+00 1341.0
31 TraesCS5A01G440700 chrUn 95.000 100 3 2 2145 2242 464683363 464683264 7.320000e-34 156.0
32 TraesCS5A01G440700 chr6D 91.000 100 5 4 2145 2242 55388485 55388388 1.230000e-26 132.0


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 TraesCS5A01G440700 chr5A 621855194 621860649 5455 True 4657.000000 8499 100.000000 1 5456 2 chr5A.!!$R1 5455
1 TraesCS5A01G440700 chr5D 497828529 497832812 4283 True 1425.025000 3356 93.220250 1 5433 4 chr5D.!!$R1 5432
2 TraesCS5A01G440700 chr5B 616971804 616975873 4069 True 741.157143 2521 92.643857 163 5456 7 chr5B.!!$R4 5293
3 TraesCS5A01G440700 chr7D 616685567 616686623 1056 True 1506.000000 1506 92.830000 2235 3263 1 chr7D.!!$R2 1028
4 TraesCS5A01G440700 chr1A 249430241 249431096 855 False 1408.000000 1408 96.387000 2410 3264 1 chr1A.!!$F1 854
5 TraesCS5A01G440700 chr2B 766174902 766175919 1017 False 1404.000000 1404 91.715000 2256 3267 1 chr2B.!!$F3 1011
6 TraesCS5A01G440700 chr2B 744392864 744393719 855 False 1352.000000 1352 95.216000 2410 3263 1 chr2B.!!$F2 853
7 TraesCS5A01G440700 chr3B 586748188 586749040 852 False 1387.000000 1387 96.028000 2412 3264 1 chr3B.!!$F1 852
8 TraesCS5A01G440700 chr4D 7098806 7099896 1090 False 1380.000000 1380 89.516000 2157 3261 1 chr4D.!!$F1 1104
9 TraesCS5A01G440700 chr4D 390836575 390837431 856 True 1363.000000 1363 95.460000 2410 3263 1 chr4D.!!$R1 853
10 TraesCS5A01G440700 chr4D 448534834 448536024 1190 False 755.500000 1363 94.699500 2146 3263 2 chr4D.!!$F2 1117
11 TraesCS5A01G440700 chr1B 134557724 134558581 857 False 1363.000000 1363 95.360000 2410 3267 1 chr1B.!!$F1 857
12 TraesCS5A01G440700 chr2A 110863008 110864152 1144 False 1341.000000 1341 88.336000 2145 3267 1 chr2A.!!$F1 1122

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
83 84 0.103755 CGAGAGAGCTGCATGCCTTA 59.896 55.0 16.68 0.0 44.23 2.69 F
1232 1368 0.670546 CTGATTTGGCGACCACGTCT 60.671 55.0 0.00 0.0 44.93 4.18 F
2757 2995 0.251608 TGGTGGTGATCTCGGTGAGA 60.252 55.0 0.00 0.0 43.20 3.27 F
3583 3826 0.250234 CTTGGCTGCAGGTGCTACTA 59.750 55.0 17.12 0.0 42.66 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 1569 0.322456 TGCCCTTCTTAAGCGCACAT 60.322 50.000 11.47 0.00 37.39 3.21 R
3000 3239 1.582937 GATGCGACGTCGACGACAT 60.583 57.895 41.52 35.02 43.02 3.06 R
4380 4662 0.036952 CTTCAGGAGAAGCGGCTTCA 60.037 55.000 36.12 18.28 44.25 3.02 R
4911 5195 0.336737 AGACTGTAGCCTAGCCTGGT 59.663 55.000 0.00 0.00 0.00 4.00 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
24 25 3.126858 GCATTGGTCTTACGAAGATGCAA 59.873 43.478 0.00 0.00 38.83 4.08
32 33 2.554806 ACGAAGATGCAACGACGATA 57.445 45.000 18.24 0.00 0.00 2.92
56 57 4.452890 AAATCACGTTCGTGTTCTCAAG 57.547 40.909 21.61 0.00 37.40 3.02
79 80 3.628193 CGCGAGAGAGCTGCATGC 61.628 66.667 11.82 11.82 43.29 4.06
80 81 3.270839 GCGAGAGAGCTGCATGCC 61.271 66.667 16.68 0.00 44.23 4.40
83 84 0.103755 CGAGAGAGCTGCATGCCTTA 59.896 55.000 16.68 0.00 44.23 2.69
85 86 2.806019 CGAGAGAGCTGCATGCCTTATT 60.806 50.000 16.68 0.00 44.23 1.40
88 89 3.380637 AGAGAGCTGCATGCCTTATTTTG 59.619 43.478 16.68 0.00 44.23 2.44
89 90 3.359033 AGAGCTGCATGCCTTATTTTGA 58.641 40.909 16.68 0.00 44.23 2.69
91 92 2.159142 AGCTGCATGCCTTATTTTGAGC 60.159 45.455 16.68 13.73 44.23 4.26
92 93 2.456989 CTGCATGCCTTATTTTGAGCG 58.543 47.619 16.68 0.00 0.00 5.03
93 94 2.090760 TGCATGCCTTATTTTGAGCGA 58.909 42.857 16.68 0.00 0.00 4.93
94 95 2.097954 TGCATGCCTTATTTTGAGCGAG 59.902 45.455 16.68 0.00 0.00 5.03
95 96 2.355756 GCATGCCTTATTTTGAGCGAGA 59.644 45.455 6.36 0.00 0.00 4.04
96 97 3.547613 GCATGCCTTATTTTGAGCGAGAG 60.548 47.826 6.36 0.00 0.00 3.20
150 151 3.366052 AACAGGTGTGGACAGTTTCTT 57.634 42.857 0.00 0.00 0.00 2.52
152 153 3.279434 ACAGGTGTGGACAGTTTCTTTC 58.721 45.455 0.00 0.00 0.00 2.62
153 154 3.054361 ACAGGTGTGGACAGTTTCTTTCT 60.054 43.478 0.00 0.00 0.00 2.52
156 157 4.640647 AGGTGTGGACAGTTTCTTTCTTTC 59.359 41.667 0.00 0.00 0.00 2.62
159 160 6.350194 GGTGTGGACAGTTTCTTTCTTTCTTT 60.350 38.462 0.00 0.00 0.00 2.52
160 161 6.747739 GTGTGGACAGTTTCTTTCTTTCTTTC 59.252 38.462 0.00 0.00 0.00 2.62
241 244 4.670606 GCTAATGCAAACGAGGCG 57.329 55.556 0.00 0.00 39.41 5.52
254 257 2.757917 AGGCGCCCACTCTCTCTC 60.758 66.667 26.15 0.00 0.00 3.20
255 258 2.757917 GGCGCCCACTCTCTCTCT 60.758 66.667 18.11 0.00 0.00 3.10
256 259 2.493973 GCGCCCACTCTCTCTCTG 59.506 66.667 0.00 0.00 0.00 3.35
257 260 2.493973 CGCCCACTCTCTCTCTGC 59.506 66.667 0.00 0.00 0.00 4.26
311 325 4.786609 GCAGTCCAGTCAAAGAAAAAGTCG 60.787 45.833 0.00 0.00 0.00 4.18
897 918 3.979497 GGTGGGGGTGGGGTTCTG 61.979 72.222 0.00 0.00 0.00 3.02
898 919 4.678743 GTGGGGGTGGGGTTCTGC 62.679 72.222 0.00 0.00 0.00 4.26
1030 1130 2.372837 ACCAGAGGCCAATGCAAATTTT 59.627 40.909 5.01 0.00 40.13 1.82
1035 1135 2.107901 AGGCCAATGCAAATTTTTGGGA 59.892 40.909 17.73 0.00 40.22 4.37
1038 1138 4.487019 GCCAATGCAAATTTTTGGGATTG 58.513 39.130 17.73 14.70 40.22 2.67
1070 1170 6.169800 TGTACTCGATGAATTTTCCACATGA 58.830 36.000 0.00 0.00 0.00 3.07
1080 1180 0.950836 TTCCACATGACACGCCTTTG 59.049 50.000 0.00 0.00 0.00 2.77
1232 1368 0.670546 CTGATTTGGCGACCACGTCT 60.671 55.000 0.00 0.00 44.93 4.18
1275 1411 1.446792 CTGCGGCTCAGACGTGATT 60.447 57.895 0.00 0.00 45.72 2.57
1350 1486 6.072673 AGGTACATGTTCCGATTTTTCTTCAC 60.073 38.462 15.04 0.00 0.00 3.18
1399 1535 3.019799 TGGGCTACAAGTGTTTTTGGA 57.980 42.857 0.00 0.00 32.32 3.53
1433 1569 1.203758 CATTTTCAGGCTGCAGCATCA 59.796 47.619 37.63 18.75 44.36 3.07
1434 1570 1.552578 TTTTCAGGCTGCAGCATCAT 58.447 45.000 37.63 18.86 44.36 2.45
1448 1584 2.713011 GCATCATGTGCGCTTAAGAAG 58.287 47.619 9.73 0.00 45.23 2.85
1495 1631 2.662700 GATGCTCACGGAGGTTATACG 58.337 52.381 3.56 0.00 0.00 3.06
1687 1824 4.362279 TGCTGTTGTTGATCTGCTTTTTC 58.638 39.130 0.00 0.00 0.00 2.29
1695 1833 6.732154 TGTTGATCTGCTTTTTCTTTCTGAG 58.268 36.000 0.00 0.00 0.00 3.35
1813 1951 0.898320 GAGCTGGTGAGTCCTTGCTA 59.102 55.000 0.00 0.00 42.80 3.49
1868 2006 6.403866 TTTCTTGTATTTGTGTCATTGGCT 57.596 33.333 0.00 0.00 0.00 4.75
1877 2015 2.308570 TGTGTCATTGGCTCCCTACATT 59.691 45.455 0.00 0.00 0.00 2.71
1933 2071 9.553064 CACTAGAGATTAGACCTATGCATTTTT 57.447 33.333 3.54 0.00 0.00 1.94
1938 2076 6.830324 AGATTAGACCTATGCATTTTTCAGCA 59.170 34.615 3.54 0.00 45.92 4.41
1942 2080 4.813027 ACCTATGCATTTTTCAGCAAGTG 58.187 39.130 3.54 0.00 44.88 3.16
1954 2092 1.009222 GCAAGTGCTATGGCGATGC 60.009 57.895 9.16 9.16 42.25 3.91
2045 2183 2.691409 CTCCTGGTGAGGCGATTTTA 57.309 50.000 0.00 0.00 39.57 1.52
2059 2197 4.142249 GGCGATTTTAACTAGGCCACATTT 60.142 41.667 5.01 0.00 40.24 2.32
2223 2366 2.204624 TCCCCCTCCCCTCTCTCA 60.205 66.667 0.00 0.00 0.00 3.27
2757 2995 0.251608 TGGTGGTGATCTCGGTGAGA 60.252 55.000 0.00 0.00 43.20 3.27
3000 3239 4.980805 GACACGTCCGGGCAGCAA 62.981 66.667 6.96 0.00 0.00 3.91
3001 3240 4.329545 ACACGTCCGGGCAGCAAT 62.330 61.111 6.96 0.00 0.00 3.56
3462 3705 5.014544 ACTGACCTGTTACCTACACTACCTA 59.985 44.000 0.00 0.00 32.10 3.08
3487 3730 7.727181 AGTTAGAATGGTATCGCAGTAGAAAT 58.273 34.615 0.00 0.00 0.00 2.17
3583 3826 0.250234 CTTGGCTGCAGGTGCTACTA 59.750 55.000 17.12 0.00 42.66 1.82
3658 3901 5.801012 GAAGGATTCGTTTATCTTGTGAGC 58.199 41.667 0.00 0.00 34.17 4.26
3980 4239 6.978659 CACTCGATTTGGTAACTAGCTCATAA 59.021 38.462 0.00 0.00 37.61 1.90
4037 4296 4.609783 GCACGCTCAAATGTAAACTTACGT 60.610 41.667 0.00 0.00 36.45 3.57
4101 4360 7.604657 ACTATAACCCTCTTCTCATTGGTAG 57.395 40.000 0.00 0.00 0.00 3.18
4317 4599 8.840867 GTTTCGATAGCTTTTCTGTTTGTAATG 58.159 33.333 0.00 0.00 0.00 1.90
4363 4645 1.093972 TGTGATTATTGGCAGTGCGG 58.906 50.000 9.45 0.00 0.00 5.69
4375 4657 0.512952 CAGTGCGGTTGTTAGACAGC 59.487 55.000 0.00 0.00 40.47 4.40
4380 4662 0.034896 CGGTTGTTAGACAGCTGGGT 59.965 55.000 19.93 7.01 32.86 4.51
4707 4990 6.363577 TCGAGGAAAAATATTGTGAGATGC 57.636 37.500 0.00 0.00 0.00 3.91
4720 5003 4.256110 TGTGAGATGCAGTGTTCTTATGG 58.744 43.478 0.00 0.00 0.00 2.74
4751 5034 9.887862 ATATGGAATGTTAGAATTTGGAAGGAT 57.112 29.630 0.00 0.00 0.00 3.24
4772 5055 1.649321 TGTCCTGAGAGGAGCAACAT 58.351 50.000 0.00 0.00 46.90 2.71
4800 5083 3.056607 GTCCATGGTGCATTTATATGGCC 60.057 47.826 12.58 0.00 38.49 5.36
4833 5116 4.448720 TGCCATCTGAATCCATCATTCT 57.551 40.909 0.00 0.00 41.58 2.40
4897 5181 1.625818 TCTTCTTGCCCTCTTCAGGAC 59.374 52.381 0.00 0.00 43.65 3.85
4932 5216 0.749649 CAGGCTAGGCTACAGTCTGG 59.250 60.000 19.78 0.00 41.16 3.86
4944 5228 1.203313 ACAGTCTGGTCCCCACTGTAT 60.203 52.381 17.56 0.00 38.51 2.29
4975 5259 6.228273 TGATAACTTCTTGTTTCAAGCTCG 57.772 37.500 4.82 0.00 39.89 5.03
5001 5285 9.983804 GTATTTATTTCGTACTCTTCCTTTTGG 57.016 33.333 0.00 0.00 42.21 3.28
5045 5332 2.923020 CAGTCAAACATTTTATGCGCCC 59.077 45.455 4.18 0.00 0.00 6.13
5110 5399 6.124340 TCTGGTATGTTTACTGTATCCGAGA 58.876 40.000 0.00 0.00 0.00 4.04
5123 5412 0.036732 TCCGAGATGCATATTGGGGC 59.963 55.000 24.38 0.00 0.00 5.80
5144 5433 2.541346 CTGTATACTTGTCATGCAGCCG 59.459 50.000 4.17 0.00 30.93 5.52
5291 5581 8.621532 TGTCAGCATTTCATATAAGATTACCC 57.378 34.615 0.00 0.00 0.00 3.69
5317 5607 0.819582 GTGGCACAATTGGAGGATGG 59.180 55.000 13.86 0.00 44.16 3.51
5318 5608 0.703488 TGGCACAATTGGAGGATGGA 59.297 50.000 10.83 0.00 31.92 3.41
5319 5609 1.288633 TGGCACAATTGGAGGATGGAT 59.711 47.619 10.83 0.00 31.92 3.41
5320 5610 1.684983 GGCACAATTGGAGGATGGATG 59.315 52.381 10.83 0.00 0.00 3.51
5337 5627 2.102252 GGATGAGAGTAGCAAGGACAGG 59.898 54.545 0.00 0.00 0.00 4.00
5377 5669 2.488347 CCTTTCCCTTTCCTGAACCGAA 60.488 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.944049 TTTACTATCGTCGTTGCATCTTC 57.056 39.130 0.00 0.00 0.00 2.87
24 25 4.024438 CGAACGTGATTTACTATCGTCGT 58.976 43.478 0.00 0.00 34.62 4.34
46 47 1.591158 TCGCGTTTCACTTGAGAACAC 59.409 47.619 5.77 0.00 0.00 3.32
56 57 1.950098 GCAGCTCTCTCGCGTTTCAC 61.950 60.000 5.77 0.00 34.40 3.18
100 101 6.636850 GCTCTCGCTCAAAATTTGTCTAAAAA 59.363 34.615 5.56 0.00 0.00 1.94
101 102 6.017109 AGCTCTCGCTCAAAATTTGTCTAAAA 60.017 34.615 5.56 0.00 45.15 1.52
102 103 5.470098 AGCTCTCGCTCAAAATTTGTCTAAA 59.530 36.000 5.56 0.00 45.15 1.85
103 104 4.997395 AGCTCTCGCTCAAAATTTGTCTAA 59.003 37.500 5.56 0.00 45.15 2.10
104 105 4.389992 CAGCTCTCGCTCAAAATTTGTCTA 59.610 41.667 5.56 0.00 45.15 2.59
105 106 3.188048 CAGCTCTCGCTCAAAATTTGTCT 59.812 43.478 5.56 0.00 45.15 3.41
106 107 3.486584 CAGCTCTCGCTCAAAATTTGTC 58.513 45.455 5.56 0.00 45.15 3.18
118 119 1.080995 CACCTGTTAGCAGCTCTCGC 61.081 60.000 0.00 0.00 41.26 5.03
131 132 3.054361 AGAAAGAAACTGTCCACACCTGT 60.054 43.478 0.00 0.00 0.00 4.00
150 151 4.736464 GCCGCCTCAAAAAGAAAGAAAGAA 60.736 41.667 0.00 0.00 0.00 2.52
152 153 3.052745 GCCGCCTCAAAAAGAAAGAAAG 58.947 45.455 0.00 0.00 0.00 2.62
153 154 2.542824 CGCCGCCTCAAAAAGAAAGAAA 60.543 45.455 0.00 0.00 0.00 2.52
156 157 0.591170 TCGCCGCCTCAAAAAGAAAG 59.409 50.000 0.00 0.00 0.00 2.62
159 160 1.964373 GGTCGCCGCCTCAAAAAGA 60.964 57.895 0.00 0.00 0.00 2.52
160 161 1.515521 AAGGTCGCCGCCTCAAAAAG 61.516 55.000 0.67 0.00 38.03 2.27
241 244 0.612744 AAAGCAGAGAGAGAGTGGGC 59.387 55.000 0.00 0.00 0.00 5.36
256 259 0.092519 GTCGTAACGAAGCCGAAAGC 59.907 55.000 0.00 0.00 37.72 3.51
292 306 3.554324 CGTCGACTTTTTCTTTGACTGGA 59.446 43.478 14.70 0.00 0.00 3.86
311 325 2.740055 CTGCAGTGAGGTGGCGTC 60.740 66.667 5.25 0.00 0.00 5.19
903 924 4.764336 TTCGCTACACCGACGCCG 62.764 66.667 0.00 0.00 36.90 6.46
904 925 2.257286 TAGTTCGCTACACCGACGCC 62.257 60.000 0.00 0.00 36.90 5.68
1030 1130 3.936453 GAGTACATGTAACGCAATCCCAA 59.064 43.478 7.25 0.00 0.00 4.12
1035 1135 4.678622 TCATCGAGTACATGTAACGCAAT 58.321 39.130 21.18 12.35 0.00 3.56
1038 1138 5.637104 AATTCATCGAGTACATGTAACGC 57.363 39.130 21.18 11.69 0.00 4.84
1080 1180 2.000447 CTGCTAGTACTGTTTTCCGCC 59.000 52.381 5.39 0.00 0.00 6.13
1141 1276 2.433436 AGCCGAACACCCTAAAATGAC 58.567 47.619 0.00 0.00 0.00 3.06
1232 1368 0.397114 TAGGATCCTCAGCGCCTTCA 60.397 55.000 20.22 0.00 32.04 3.02
1350 1486 6.973474 ACAAGTACTACTAAAGCTGATAAGCG 59.027 38.462 0.00 0.00 40.27 4.68
1399 1535 5.484715 CCTGAAAATGAAATGGCTGTGAAT 58.515 37.500 0.00 0.00 0.00 2.57
1433 1569 0.322456 TGCCCTTCTTAAGCGCACAT 60.322 50.000 11.47 0.00 37.39 3.21
1434 1570 1.072332 TGCCCTTCTTAAGCGCACA 59.928 52.632 11.47 0.00 37.39 4.57
1448 1584 0.741221 CAGAACCGAGCTTAGTGCCC 60.741 60.000 0.00 0.00 44.23 5.36
1495 1631 5.127031 AGAACTATTGGACAAGAGAGCTCTC 59.873 44.000 32.45 32.45 39.39 3.20
1687 1824 7.170998 AGCAAGCAAATCAATTTTCTCAGAAAG 59.829 33.333 0.00 0.00 0.00 2.62
1695 1833 6.475207 CAGCATAGCAAGCAAATCAATTTTC 58.525 36.000 0.00 0.00 0.00 2.29
1699 1837 3.118920 TGCAGCATAGCAAGCAAATCAAT 60.119 39.130 6.66 0.00 42.46 2.57
1813 1951 6.595326 ACACGAACATTACATGACAAGATGAT 59.405 34.615 0.00 0.00 0.00 2.45
1868 2006 6.043243 GGACCTAAAGATGATCAATGTAGGGA 59.957 42.308 22.56 0.00 32.56 4.20
1938 2076 2.213499 GTAAGCATCGCCATAGCACTT 58.787 47.619 0.00 0.00 39.83 3.16
1954 2092 9.967346 TTCAGGTTCTAGATAATTCGATGTAAG 57.033 33.333 0.00 0.00 0.00 2.34
2045 2183 6.127619 GCTGAATTTCTAAATGTGGCCTAGTT 60.128 38.462 3.32 0.96 0.00 2.24
2059 2197 3.609853 ACCAGATTGCGCTGAATTTCTA 58.390 40.909 9.73 0.00 38.14 2.10
2352 2545 2.696125 AAGATCCCCCGCCACCAT 60.696 61.111 0.00 0.00 0.00 3.55
2483 2711 3.407967 ATCCACCCGCCCATCGTT 61.408 61.111 0.00 0.00 36.19 3.85
2484 2712 4.175337 CATCCACCCGCCCATCGT 62.175 66.667 0.00 0.00 36.19 3.73
3000 3239 1.582937 GATGCGACGTCGACGACAT 60.583 57.895 41.52 35.02 43.02 3.06
3001 3240 2.202260 GATGCGACGTCGACGACA 60.202 61.111 41.52 32.54 43.02 4.35
3162 3402 4.329801 CACAACAAGCCCAAAGAAAAGAAC 59.670 41.667 0.00 0.00 0.00 3.01
3302 3545 1.202855 AGTGCAGCCTGATCAACTTGT 60.203 47.619 0.00 0.00 0.00 3.16
3305 3548 1.209019 CCTAGTGCAGCCTGATCAACT 59.791 52.381 0.00 0.00 0.00 3.16
3383 3626 9.599866 TTCATGACCATACAGTTTAACATAGAG 57.400 33.333 0.00 0.00 0.00 2.43
3384 3627 9.952030 TTTCATGACCATACAGTTTAACATAGA 57.048 29.630 0.00 0.00 0.00 1.98
3390 3633 9.913310 TGGATATTTCATGACCATACAGTTTAA 57.087 29.630 0.00 0.00 0.00 1.52
3462 3705 6.710597 TTCTACTGCGATACCATTCTAACT 57.289 37.500 0.00 0.00 0.00 2.24
3523 3766 9.726232 GTTAAACGAATAAACTCAAGAAAACCT 57.274 29.630 0.00 0.00 0.00 3.50
3524 3767 8.675888 CGTTAAACGAATAAACTCAAGAAAACC 58.324 33.333 0.00 0.00 46.05 3.27
3548 3791 6.127758 TGCAGCCAAGTGAAAATATAAATCGT 60.128 34.615 0.00 0.00 0.00 3.73
3583 3826 1.273886 GTTGGTGTGGTTGGTGTTGTT 59.726 47.619 0.00 0.00 0.00 2.83
3658 3901 4.495422 AGCAAATAGTAGGTGTCTTGACG 58.505 43.478 0.00 0.00 0.00 4.35
3789 4037 8.131100 CCAAGATGACAAATTATATGGTGTGTC 58.869 37.037 5.84 5.84 36.71 3.67
3980 4239 1.349026 ACAGCACTCACCTGCATAACT 59.651 47.619 0.00 0.00 39.86 2.24
4037 4296 3.580022 TCTCCTGAAGAAGATGCTCAACA 59.420 43.478 0.00 0.00 0.00 3.33
4101 4360 7.256756 AGAGCAGATTTCTATACACAAATGC 57.743 36.000 0.00 0.00 0.00 3.56
4363 4645 2.543777 TCACCCAGCTGTCTAACAAC 57.456 50.000 13.81 0.00 0.00 3.32
4375 4657 1.743252 GAGAAGCGGCTTCACCCAG 60.743 63.158 36.12 0.00 42.37 4.45
4380 4662 0.036952 CTTCAGGAGAAGCGGCTTCA 60.037 55.000 36.12 18.28 44.25 3.02
4707 4990 6.364701 TCCATATTTCCCCATAAGAACACTG 58.635 40.000 0.00 0.00 0.00 3.66
4720 5003 8.923270 TCCAAATTCTAACATTCCATATTTCCC 58.077 33.333 0.00 0.00 0.00 3.97
4751 5034 1.768275 TGTTGCTCCTCTCAGGACAAA 59.232 47.619 8.33 0.00 40.06 2.83
4772 5055 7.394077 CCATATAAATGCACCATGGACTTATCA 59.606 37.037 21.47 6.77 38.77 2.15
4800 5083 2.094597 TCAGATGGCAAAATTCAAGCGG 60.095 45.455 0.00 0.00 0.00 5.52
4833 5116 5.878332 TTTCAGCGCATAGAAAATGAGAA 57.122 34.783 11.47 0.00 31.35 2.87
4910 5194 0.747852 GACTGTAGCCTAGCCTGGTC 59.252 60.000 0.00 0.00 0.00 4.02
4911 5195 0.336737 AGACTGTAGCCTAGCCTGGT 59.663 55.000 0.00 0.00 0.00 4.00
4912 5196 0.749649 CAGACTGTAGCCTAGCCTGG 59.250 60.000 0.00 0.00 0.00 4.45
4944 5228 4.085357 ACAAGAAGTTATCAGCACACCA 57.915 40.909 0.00 0.00 0.00 4.17
4952 5236 5.758296 ACGAGCTTGAAACAAGAAGTTATCA 59.242 36.000 8.31 0.00 40.26 2.15
4975 5259 9.983804 CCAAAAGGAAGAGTACGAAATAAATAC 57.016 33.333 0.00 0.00 0.00 1.89
5001 5285 6.016718 TGCGCGTTTACTAAAACACATATTC 58.983 36.000 8.43 0.00 44.37 1.75
5021 5308 2.026742 CGCATAAAATGTTTGACTGCGC 59.973 45.455 0.00 0.00 43.39 6.09
5060 5349 9.632638 AATTATATTGTACCAAAGCATCTGTCT 57.367 29.630 0.00 0.00 0.00 3.41
5092 5381 5.276461 TGCATCTCGGATACAGTAAACAT 57.724 39.130 0.00 0.00 0.00 2.71
5110 5399 4.934797 AGTATACAGCCCCAATATGCAT 57.065 40.909 3.79 3.79 0.00 3.96
5123 5412 2.541346 CGGCTGCATGACAAGTATACAG 59.459 50.000 5.50 0.00 0.00 2.74
5143 5432 9.974750 GAAAGAATCTCACCTTTTATTTCTACG 57.025 33.333 0.00 0.00 33.23 3.51
5291 5581 1.411977 TCCAATTGTGCCACAAACCAG 59.588 47.619 15.17 4.30 41.96 4.00
5317 5607 3.027412 TCCTGTCCTTGCTACTCTCATC 58.973 50.000 0.00 0.00 0.00 2.92
5318 5608 3.107402 TCCTGTCCTTGCTACTCTCAT 57.893 47.619 0.00 0.00 0.00 2.90
5319 5609 2.563179 GTTCCTGTCCTTGCTACTCTCA 59.437 50.000 0.00 0.00 0.00 3.27
5320 5610 2.093921 GGTTCCTGTCCTTGCTACTCTC 60.094 54.545 0.00 0.00 0.00 3.20
5337 5627 5.774498 AAGGTCTGAAAAGTCAATGGTTC 57.226 39.130 0.00 0.00 31.88 3.62


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

AutoCloner maintained by Alex Coulton.