Multiple sequence alignment - TraesCS1B01G347400

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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 TraesCS1B01G347400 chr1B 100.000 3085 0 0 1 3085 576520456 576523540 0.000000e+00 5698.0
1 TraesCS1B01G347400 chr1A 90.470 2214 118 36 38 2186 521737737 521739922 0.000000e+00 2833.0
2 TraesCS1B01G347400 chr1A 97.143 35 1 0 2171 2205 521741213 521741247 3.320000e-05 60.2
3 TraesCS1B01G347400 chr5A 99.199 874 7 0 2212 3085 701082413 701081540 0.000000e+00 1576.0
4 TraesCS1B01G347400 chr5A 98.866 882 9 1 2204 3085 312472860 312471980 0.000000e+00 1572.0
5 TraesCS1B01G347400 chr5A 98.750 880 9 2 2207 3085 174283312 174284190 0.000000e+00 1563.0
6 TraesCS1B01G347400 chr5A 98.749 879 11 0 2207 3085 321903049 321902171 0.000000e+00 1563.0
7 TraesCS1B01G347400 chr6A 98.865 881 10 0 2205 3085 464536274 464537154 0.000000e+00 1572.0
8 TraesCS1B01G347400 chr6B 98.756 884 9 2 2202 3085 479170760 479171641 0.000000e+00 1570.0
9 TraesCS1B01G347400 chr5B 99.084 873 8 0 2213 3085 287808846 287807974 0.000000e+00 1568.0
10 TraesCS1B01G347400 chr5B 89.444 180 18 1 1252 1430 488559780 488559959 3.100000e-55 226.0
11 TraesCS1B01G347400 chr5B 97.297 37 1 0 1 37 678422842 678422878 2.570000e-06 63.9
12 TraesCS1B01G347400 chr7A 98.639 882 12 0 2204 3085 692289190 692290071 0.000000e+00 1563.0
13 TraesCS1B01G347400 chr4B 98.749 879 11 0 2207 3085 10445985 10445107 0.000000e+00 1563.0
14 TraesCS1B01G347400 chr1D 93.447 1053 48 7 743 1789 426651747 426652784 0.000000e+00 1543.0
15 TraesCS1B01G347400 chr1D 91.906 593 26 7 94 664 426650967 426651559 0.000000e+00 809.0
16 TraesCS1B01G347400 chr1D 86.835 357 33 7 1856 2207 426659859 426660206 1.340000e-103 387.0
17 TraesCS1B01G347400 chr3B 89.252 214 17 5 1222 1435 532667438 532667231 2.360000e-66 263.0
18 TraesCS1B01G347400 chr3A 89.252 214 17 5 1222 1435 544969600 544969807 2.360000e-66 263.0
19 TraesCS1B01G347400 chr3D 88.785 214 18 5 1222 1435 406772760 406772553 1.100000e-64 257.0
20 TraesCS1B01G347400 chr3D 84.459 148 21 2 1250 1396 376169961 376169815 8.920000e-31 145.0
21 TraesCS1B01G347400 chr3D 86.441 59 7 1 38 95 15260580 15260522 2.570000e-06 63.9
22 TraesCS1B01G347400 chr3D 100.000 33 0 0 5 37 1911238 1911270 9.240000e-06 62.1
23 TraesCS1B01G347400 chr3D 100.000 33 0 0 5 37 585232580 585232612 9.240000e-06 62.1
24 TraesCS1B01G347400 chr7B 87.560 209 20 5 1222 1430 712841420 712841622 1.430000e-58 237.0
25 TraesCS1B01G347400 chr7B 89.444 180 18 1 1252 1430 712841874 712842053 3.100000e-55 226.0
26 TraesCS1B01G347400 chr4D 86.441 59 7 1 38 95 327712362 327712304 2.570000e-06 63.9
27 TraesCS1B01G347400 chr7D 100.000 33 0 0 5 37 2487634 2487602 9.240000e-06 62.1
28 TraesCS1B01G347400 chr2D 100.000 33 0 0 5 37 54665623 54665591 9.240000e-06 62.1
29 TraesCS1B01G347400 chr2D 96.970 33 1 0 38 70 420892931 420892963 4.300000e-04 56.5


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 TraesCS1B01G347400 chr1B 576520456 576523540 3084 False 5698.0 5698 100.0000 1 3085 1 chr1B.!!$F1 3084
1 TraesCS1B01G347400 chr1A 521737737 521741247 3510 False 1446.6 2833 93.8065 38 2205 2 chr1A.!!$F1 2167
2 TraesCS1B01G347400 chr5A 701081540 701082413 873 True 1576.0 1576 99.1990 2212 3085 1 chr5A.!!$R3 873
3 TraesCS1B01G347400 chr5A 312471980 312472860 880 True 1572.0 1572 98.8660 2204 3085 1 chr5A.!!$R1 881
4 TraesCS1B01G347400 chr5A 174283312 174284190 878 False 1563.0 1563 98.7500 2207 3085 1 chr5A.!!$F1 878
5 TraesCS1B01G347400 chr5A 321902171 321903049 878 True 1563.0 1563 98.7490 2207 3085 1 chr5A.!!$R2 878
6 TraesCS1B01G347400 chr6A 464536274 464537154 880 False 1572.0 1572 98.8650 2205 3085 1 chr6A.!!$F1 880
7 TraesCS1B01G347400 chr6B 479170760 479171641 881 False 1570.0 1570 98.7560 2202 3085 1 chr6B.!!$F1 883
8 TraesCS1B01G347400 chr5B 287807974 287808846 872 True 1568.0 1568 99.0840 2213 3085 1 chr5B.!!$R1 872
9 TraesCS1B01G347400 chr7A 692289190 692290071 881 False 1563.0 1563 98.6390 2204 3085 1 chr7A.!!$F1 881
10 TraesCS1B01G347400 chr4B 10445107 10445985 878 True 1563.0 1563 98.7490 2207 3085 1 chr4B.!!$R1 878
11 TraesCS1B01G347400 chr1D 426650967 426652784 1817 False 1176.0 1543 92.6765 94 1789 2 chr1D.!!$F2 1695
12 TraesCS1B01G347400 chr7B 712841420 712842053 633 False 231.5 237 88.5020 1222 1430 2 chr7B.!!$F1 208

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
699 724 0.251916 TCGATTTCACCCAGCGGAAT 59.748 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2259 0.322277 ACACTCCGCTTCCGTCTCTA 60.322 55.0 0.0 0.0 0.0 2.43 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 6.751514 AACAAGATCATTACGTAATTGCCA 57.248 33.333 18.06 3.60 0.00 4.92
25 26 6.942532 ACAAGATCATTACGTAATTGCCAT 57.057 33.333 18.06 8.05 0.00 4.40
26 27 8.445275 AACAAGATCATTACGTAATTGCCATA 57.555 30.769 18.06 1.17 0.00 2.74
27 28 8.621532 ACAAGATCATTACGTAATTGCCATAT 57.378 30.769 18.06 5.61 0.00 1.78
28 29 9.719355 ACAAGATCATTACGTAATTGCCATATA 57.281 29.630 18.06 0.00 0.00 0.86
29 30 9.973246 CAAGATCATTACGTAATTGCCATATAC 57.027 33.333 18.06 3.55 0.00 1.47
30 31 8.407457 AGATCATTACGTAATTGCCATATACG 57.593 34.615 18.06 7.89 45.76 3.06
31 32 6.397831 TCATTACGTAATTGCCATATACGC 57.602 37.500 18.06 0.00 44.55 4.42
32 33 5.349270 TCATTACGTAATTGCCATATACGCC 59.651 40.000 18.06 0.00 44.55 5.68
33 34 3.114668 ACGTAATTGCCATATACGCCA 57.885 42.857 9.02 0.00 44.55 5.69
34 35 3.468770 ACGTAATTGCCATATACGCCAA 58.531 40.909 9.02 0.00 44.55 4.52
35 36 3.878103 ACGTAATTGCCATATACGCCAAA 59.122 39.130 9.02 0.00 44.55 3.28
36 37 4.517453 ACGTAATTGCCATATACGCCAAAT 59.483 37.500 9.02 0.00 44.55 2.32
47 48 7.077605 CCATATACGCCAAATCATGTTTACTG 58.922 38.462 0.00 0.00 0.00 2.74
152 154 6.951256 AACACTTTTCAACAGAAAGAAAGC 57.049 33.333 3.83 0.00 37.50 3.51
155 157 6.928492 ACACTTTTCAACAGAAAGAAAGCAAA 59.072 30.769 3.83 0.00 37.50 3.68
242 261 5.742838 CCTAAAGGAAAGCTTTTGCATTGGT 60.743 40.000 14.05 0.00 42.85 3.67
332 351 2.723124 TTCGCAAGCATTTCCCTTTC 57.277 45.000 0.00 0.00 37.18 2.62
333 352 1.614996 TCGCAAGCATTTCCCTTTCA 58.385 45.000 0.00 0.00 37.18 2.69
388 407 1.067060 GGAAAAGACACAAAAGGCGCT 59.933 47.619 7.64 0.00 0.00 5.92
419 438 0.515564 GCCAAAGCGAGTAAAGCGAA 59.484 50.000 0.00 0.00 40.04 4.70
453 473 6.145338 TCGGATAGTCTTTATCGCTTTTCT 57.855 37.500 0.00 0.00 0.00 2.52
527 548 4.671766 GCCATCTTTCGTCGCTTTTACATT 60.672 41.667 0.00 0.00 0.00 2.71
619 643 2.281831 TGCGTCGAAAATGGGCCA 60.282 55.556 9.61 9.61 0.00 5.36
657 682 7.533289 AAACAAGCTTAATTAGGCCTGTTTA 57.467 32.000 31.77 10.33 45.20 2.01
664 689 6.150474 GCTTAATTAGGCCTGTTTAGAACACA 59.850 38.462 17.99 0.00 36.25 3.72
665 690 5.959618 AATTAGGCCTGTTTAGAACACAC 57.040 39.130 17.99 0.00 36.25 3.82
669 694 1.541670 GCCTGTTTAGAACACACGGGA 60.542 52.381 0.00 0.00 39.06 5.14
677 702 6.752815 TGTTTAGAACACACGGGAAATTTTTC 59.247 34.615 0.00 0.00 36.25 2.29
678 703 4.993029 AGAACACACGGGAAATTTTTCA 57.007 36.364 0.00 0.00 38.92 2.69
689 714 5.342259 CGGGAAATTTTTCAGTCGATTTCAC 59.658 40.000 5.48 5.28 39.22 3.18
692 717 5.782893 AATTTTTCAGTCGATTTCACCCA 57.217 34.783 0.00 0.00 0.00 4.51
693 718 4.829064 TTTTTCAGTCGATTTCACCCAG 57.171 40.909 0.00 0.00 0.00 4.45
695 720 0.389817 TCAGTCGATTTCACCCAGCG 60.390 55.000 0.00 0.00 0.00 5.18
696 721 1.079127 AGTCGATTTCACCCAGCGG 60.079 57.895 0.00 0.00 0.00 5.52
697 722 1.079405 GTCGATTTCACCCAGCGGA 60.079 57.895 0.00 0.00 0.00 5.54
698 723 0.672401 GTCGATTTCACCCAGCGGAA 60.672 55.000 0.00 0.00 0.00 4.30
699 724 0.251916 TCGATTTCACCCAGCGGAAT 59.748 50.000 0.00 0.00 0.00 3.01
700 725 1.094785 CGATTTCACCCAGCGGAATT 58.905 50.000 0.00 0.00 0.00 2.17
730 857 2.734606 CGAAGTTCACGTAGCCAAATGA 59.265 45.455 3.32 0.00 0.00 2.57
731 858 3.185594 CGAAGTTCACGTAGCCAAATGAA 59.814 43.478 3.32 0.00 0.00 2.57
773 907 2.672996 GCAATGGAGTGTGGCCGT 60.673 61.111 0.00 0.00 0.00 5.68
818 952 2.024868 CACGAACCGAACGGCATCA 61.025 57.895 13.32 0.00 39.32 3.07
848 982 0.620030 TATCCCACATGCACTGCACT 59.380 50.000 5.67 0.00 43.04 4.40
878 1012 3.748989 GCTGTTCCTTTTCCTTCACCTCT 60.749 47.826 0.00 0.00 0.00 3.69
948 1087 4.519350 CACAGAGCACGTATCCTATTCCTA 59.481 45.833 0.00 0.00 0.00 2.94
949 1088 5.009710 CACAGAGCACGTATCCTATTCCTAA 59.990 44.000 0.00 0.00 0.00 2.69
1003 1142 0.032130 TGAGACACACTTCTCCGTGC 59.968 55.000 0.00 0.00 41.34 5.34
1015 1154 1.953231 CTCCGTGCCATCAGAGAGCA 61.953 60.000 0.00 0.00 0.00 4.26
1110 1249 2.031919 AAGGTCATCACGCGGCAA 59.968 55.556 12.47 0.00 0.00 4.52
1187 1329 3.272334 GGCGCCCATGTCGTCATC 61.272 66.667 18.11 0.00 31.15 2.92
1194 1336 0.866061 CCATGTCGTCATCGTCGTCC 60.866 60.000 0.00 0.00 38.33 4.79
1200 1342 1.296722 GTCATCGTCGTCCTCGTCG 60.297 63.158 0.00 1.62 46.06 5.12
1550 1692 1.690893 CGATCATGGATGGTCTCAGGT 59.309 52.381 0.00 0.00 35.78 4.00
1623 1765 1.478510 CTCGTTCATCAGTACCCAGCT 59.521 52.381 0.00 0.00 0.00 4.24
1677 1819 1.202463 CCTTCGTCTCTGCGGATCAAT 60.202 52.381 0.00 0.00 0.00 2.57
1781 1924 3.249080 GTCGATTGAAACTTCGGGTTTGA 59.751 43.478 11.02 2.02 46.77 2.69
1816 1978 4.160736 TCAATCGATGCTATAGTGGTCG 57.839 45.455 0.00 13.70 0.00 4.79
1818 1980 1.244816 TCGATGCTATAGTGGTCGGG 58.755 55.000 17.35 0.00 33.46 5.14
1941 2105 1.610886 GCGCTTCCTTGAAACTAGGGT 60.611 52.381 0.00 0.00 33.41 4.34
1966 2131 1.578583 AAAAAGTGGACACGGACGAG 58.421 50.000 0.00 0.00 36.20 4.18
1974 2139 0.813184 GACACGGACGAGATTGGGTA 59.187 55.000 0.00 0.00 0.00 3.69
1975 2140 1.407979 GACACGGACGAGATTGGGTAT 59.592 52.381 0.00 0.00 0.00 2.73
1982 2147 3.214328 GACGAGATTGGGTATTGCCATT 58.786 45.455 0.00 0.00 39.65 3.16
1997 2164 4.849111 TGCCATTTGTTTTCGTGTTTTC 57.151 36.364 0.00 0.00 0.00 2.29
2000 2167 5.163913 TGCCATTTGTTTTCGTGTTTTCTTG 60.164 36.000 0.00 0.00 0.00 3.02
2002 2169 6.035112 GCCATTTGTTTTCGTGTTTTCTTGTA 59.965 34.615 0.00 0.00 0.00 2.41
2003 2170 7.412020 GCCATTTGTTTTCGTGTTTTCTTGTAA 60.412 33.333 0.00 0.00 0.00 2.41
2004 2171 8.436200 CCATTTGTTTTCGTGTTTTCTTGTAAA 58.564 29.630 0.00 0.00 0.00 2.01
2007 2174 9.634300 TTTGTTTTCGTGTTTTCTTGTAAAAAC 57.366 25.926 5.51 5.51 45.25 2.43
2020 2190 5.757320 TCTTGTAAAAACGGAACCGATACAA 59.243 36.000 20.14 21.50 42.83 2.41
2046 2216 3.632604 TGCCGGAAACAAATACAGAAACA 59.367 39.130 5.05 0.00 0.00 2.83
2048 2218 5.044558 GCCGGAAACAAATACAGAAACAAA 58.955 37.500 5.05 0.00 0.00 2.83
2089 2259 6.942532 ATAAAGCGAATACAACATGGACAT 57.057 33.333 0.00 0.00 0.00 3.06
2092 2262 5.276461 AGCGAATACAACATGGACATAGA 57.724 39.130 0.00 0.00 0.00 1.98
2095 2265 5.175856 GCGAATACAACATGGACATAGAGAC 59.824 44.000 0.00 0.00 0.00 3.36
2103 2273 0.030908 GGACATAGAGACGGAAGCGG 59.969 60.000 0.00 0.00 0.00 5.52
2113 2283 2.027625 CGGAAGCGGAGTGTTCACC 61.028 63.158 0.00 0.00 0.00 4.02
2128 2298 4.153655 GTGTTCACCGAAACTAAAGATCCC 59.846 45.833 0.00 0.00 0.00 3.85
2142 2312 7.339482 ACTAAAGATCCCTTGAAACATAGACC 58.661 38.462 0.00 0.00 31.91 3.85
2143 2313 4.779993 AGATCCCTTGAAACATAGACCC 57.220 45.455 0.00 0.00 0.00 4.46
2144 2314 4.111577 AGATCCCTTGAAACATAGACCCA 58.888 43.478 0.00 0.00 0.00 4.51
2145 2315 4.540099 AGATCCCTTGAAACATAGACCCAA 59.460 41.667 0.00 0.00 0.00 4.12
2146 2316 4.733077 TCCCTTGAAACATAGACCCAAA 57.267 40.909 0.00 0.00 0.00 3.28
2147 2317 5.068215 TCCCTTGAAACATAGACCCAAAA 57.932 39.130 0.00 0.00 0.00 2.44
2388 3865 3.063180 CGCTAGAGTCCAATCTTTTGCTG 59.937 47.826 0.00 0.00 0.00 4.41
2938 4614 2.803285 TCTGGGGAGAGCTGGATATT 57.197 50.000 0.00 0.00 0.00 1.28
2969 4645 0.824109 CCCATAGCTGGACGAACTGA 59.176 55.000 0.00 0.00 46.37 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.781138 TGGCAATTACGTAATGATCTTGTTC 58.219 36.000 21.00 12.20 0.00 3.18
3 4 9.973246 GTATATGGCAATTACGTAATGATCTTG 57.027 33.333 21.00 16.02 0.00 3.02
4 5 8.869897 CGTATATGGCAATTACGTAATGATCTT 58.130 33.333 21.00 12.82 0.00 2.40
5 6 7.010183 GCGTATATGGCAATTACGTAATGATCT 59.990 37.037 21.00 3.00 36.63 2.75
6 7 7.117454 GCGTATATGGCAATTACGTAATGATC 58.883 38.462 21.00 13.14 36.63 2.92
7 8 6.036735 GGCGTATATGGCAATTACGTAATGAT 59.963 38.462 21.00 12.77 36.63 2.45
8 9 5.349270 GGCGTATATGGCAATTACGTAATGA 59.651 40.000 21.00 6.78 36.63 2.57
9 10 5.120986 TGGCGTATATGGCAATTACGTAATG 59.879 40.000 21.00 15.25 41.96 1.90
10 11 5.239351 TGGCGTATATGGCAATTACGTAAT 58.761 37.500 24.19 15.07 41.96 1.89
11 12 4.629092 TGGCGTATATGGCAATTACGTAA 58.371 39.130 24.19 11.02 41.96 3.18
12 13 4.254402 TGGCGTATATGGCAATTACGTA 57.746 40.909 24.19 15.60 41.96 3.57
13 14 3.114668 TGGCGTATATGGCAATTACGT 57.885 42.857 24.19 0.00 41.96 3.57
20 21 3.485394 ACATGATTTGGCGTATATGGCA 58.515 40.909 16.69 16.69 43.36 4.92
21 22 4.503741 AACATGATTTGGCGTATATGGC 57.496 40.909 11.47 11.47 0.00 4.40
22 23 7.077605 CAGTAAACATGATTTGGCGTATATGG 58.922 38.462 0.00 0.00 0.00 2.74
23 24 7.639039 ACAGTAAACATGATTTGGCGTATATG 58.361 34.615 0.00 0.00 0.00 1.78
24 25 7.801716 ACAGTAAACATGATTTGGCGTATAT 57.198 32.000 0.00 0.00 0.00 0.86
25 26 7.618502 AACAGTAAACATGATTTGGCGTATA 57.381 32.000 0.00 0.00 0.00 1.47
26 27 6.509418 AACAGTAAACATGATTTGGCGTAT 57.491 33.333 0.00 0.00 0.00 3.06
27 28 5.950758 AACAGTAAACATGATTTGGCGTA 57.049 34.783 0.00 0.00 0.00 4.42
28 29 4.846779 AACAGTAAACATGATTTGGCGT 57.153 36.364 0.00 0.00 0.00 5.68
29 30 6.378582 AGTAAACAGTAAACATGATTTGGCG 58.621 36.000 0.00 0.00 0.00 5.69
30 31 7.367285 TGAGTAAACAGTAAACATGATTTGGC 58.633 34.615 0.00 0.00 0.00 4.52
31 32 9.345517 CATGAGTAAACAGTAAACATGATTTGG 57.654 33.333 0.00 0.00 36.70 3.28
32 33 9.345517 CCATGAGTAAACAGTAAACATGATTTG 57.654 33.333 0.00 0.00 36.70 2.32
33 34 9.295825 TCCATGAGTAAACAGTAAACATGATTT 57.704 29.630 0.00 0.00 36.70 2.17
34 35 8.862325 TCCATGAGTAAACAGTAAACATGATT 57.138 30.769 0.00 0.00 36.70 2.57
35 36 9.466497 AATCCATGAGTAAACAGTAAACATGAT 57.534 29.630 0.00 0.00 36.70 2.45
36 37 8.862325 AATCCATGAGTAAACAGTAAACATGA 57.138 30.769 0.00 0.00 36.70 3.07
101 103 5.353956 TGTGCAGTAATGATGTGGTATTCAC 59.646 40.000 0.00 0.00 46.23 3.18
109 111 5.626543 GTGTTTTCTGTGCAGTAATGATGTG 59.373 40.000 0.00 0.00 0.00 3.21
158 160 9.620259 TTCTTTCTTTCTTTCTTTAGAGCTTCT 57.380 29.630 0.00 0.00 0.00 2.85
190 208 3.254892 GTGCCACTTTGTAGCTAGACTC 58.745 50.000 0.00 0.00 0.00 3.36
225 244 3.258123 TCCCTACCAATGCAAAAGCTTTC 59.742 43.478 13.10 1.15 0.00 2.62
306 325 2.159517 GGAAATGCTTGCGAATCGTCTT 60.160 45.455 4.07 0.00 0.00 3.01
388 407 1.603455 CTTTGGCTGCGGAAAGGGA 60.603 57.895 12.53 0.00 0.00 4.20
419 438 2.567615 AGACTATCCGAAACAAGGTGCT 59.432 45.455 0.00 0.00 0.00 4.40
453 473 2.981350 GCTTTTTCGTGGCGGGGA 60.981 61.111 0.00 0.00 0.00 4.81
527 548 2.083774 CTAATCACTTTTGCGGCAGGA 58.916 47.619 1.67 0.00 0.00 3.86
619 643 3.005791 AGCTTGTTTTAGCGCCAAGAAAT 59.994 39.130 22.33 8.32 45.82 2.17
657 682 4.401202 ACTGAAAAATTTCCCGTGTGTTCT 59.599 37.500 3.60 0.00 36.36 3.01
664 689 5.009210 TGAAATCGACTGAAAAATTTCCCGT 59.991 36.000 3.60 1.42 37.33 5.28
665 690 5.342259 GTGAAATCGACTGAAAAATTTCCCG 59.658 40.000 3.60 5.17 37.33 5.14
669 694 6.155475 TGGGTGAAATCGACTGAAAAATTT 57.845 33.333 0.00 0.00 0.00 1.82
677 702 1.361668 CCGCTGGGTGAAATCGACTG 61.362 60.000 0.00 0.00 0.00 3.51
678 703 1.079127 CCGCTGGGTGAAATCGACT 60.079 57.895 0.00 0.00 0.00 4.18
689 714 2.068519 GCAAAAAGAAATTCCGCTGGG 58.931 47.619 0.00 0.00 0.00 4.45
692 717 3.243401 ACTTCGCAAAAAGAAATTCCGCT 60.243 39.130 0.00 0.00 0.00 5.52
693 718 3.049912 ACTTCGCAAAAAGAAATTCCGC 58.950 40.909 0.00 0.00 0.00 5.54
695 720 5.331532 CGTGAACTTCGCAAAAAGAAATTCC 60.332 40.000 3.32 0.00 34.21 3.01
696 721 5.229260 ACGTGAACTTCGCAAAAAGAAATTC 59.771 36.000 3.32 0.00 35.27 2.17
697 722 5.099575 ACGTGAACTTCGCAAAAAGAAATT 58.900 33.333 3.32 0.00 0.00 1.82
698 723 4.668289 ACGTGAACTTCGCAAAAAGAAAT 58.332 34.783 3.32 0.00 0.00 2.17
699 724 4.086199 ACGTGAACTTCGCAAAAAGAAA 57.914 36.364 3.32 0.00 0.00 2.52
700 725 3.750639 ACGTGAACTTCGCAAAAAGAA 57.249 38.095 3.32 0.00 0.00 2.52
857 991 4.068599 GAGAGGTGAAGGAAAAGGAACAG 58.931 47.826 0.00 0.00 0.00 3.16
878 1012 5.656549 TTTCCTCTTTCCTTTAACAGGGA 57.343 39.130 4.51 0.00 44.12 4.20
965 1104 4.515567 TCTCATCGGCCGTATATATAGCTG 59.484 45.833 27.15 8.11 0.00 4.24
1003 1142 1.153208 GCCCTGTGCTCTCTGATGG 60.153 63.158 0.00 0.00 36.87 3.51
1015 1154 2.510906 GGTCAGTGTGTGCCCTGT 59.489 61.111 0.00 0.00 0.00 4.00
1017 1156 2.842462 TCGGTCAGTGTGTGCCCT 60.842 61.111 0.00 0.00 0.00 5.19
1575 1717 1.134995 CACTGCTCCATCTCTGCGTTA 60.135 52.381 0.00 0.00 0.00 3.18
1576 1718 0.390866 CACTGCTCCATCTCTGCGTT 60.391 55.000 0.00 0.00 0.00 4.84
1580 1722 0.462225 CCAGCACTGCTCCATCTCTG 60.462 60.000 0.00 0.00 36.40 3.35
1623 1765 1.752198 CCCGTTGACCTGACCTTGA 59.248 57.895 0.00 0.00 0.00 3.02
1816 1978 1.278238 CGAATCTCTGCGTACAACCC 58.722 55.000 0.00 0.00 0.00 4.11
1818 1980 3.243336 AGAACGAATCTCTGCGTACAAC 58.757 45.455 0.00 0.00 40.23 3.32
1956 2121 1.481871 ATACCCAATCTCGTCCGTGT 58.518 50.000 0.00 0.00 0.00 4.49
1957 2122 2.201732 CAATACCCAATCTCGTCCGTG 58.798 52.381 0.00 0.00 0.00 4.94
1966 2131 5.063312 CGAAAACAAATGGCAATACCCAATC 59.937 40.000 0.00 0.00 38.61 2.67
1974 2139 5.584251 AGAAAACACGAAAACAAATGGCAAT 59.416 32.000 0.00 0.00 0.00 3.56
1975 2140 4.932200 AGAAAACACGAAAACAAATGGCAA 59.068 33.333 0.00 0.00 0.00 4.52
1982 2147 7.997104 CGTTTTTACAAGAAAACACGAAAACAA 59.003 29.630 12.10 0.00 45.35 2.83
1997 2164 5.594724 TGTATCGGTTCCGTTTTTACAAG 57.405 39.130 11.04 0.00 0.00 3.16
2000 2167 7.617731 GCATTTTTGTATCGGTTCCGTTTTTAC 60.618 37.037 11.04 9.33 0.00 2.01
2002 2169 5.176039 GCATTTTTGTATCGGTTCCGTTTTT 59.824 36.000 11.04 0.00 0.00 1.94
2003 2170 4.682401 GCATTTTTGTATCGGTTCCGTTTT 59.318 37.500 11.04 1.09 0.00 2.43
2004 2171 4.231439 GCATTTTTGTATCGGTTCCGTTT 58.769 39.130 11.04 3.38 0.00 3.60
2007 2174 2.789779 CGGCATTTTTGTATCGGTTCCG 60.790 50.000 4.74 4.74 0.00 4.30
2008 2175 2.478879 CCGGCATTTTTGTATCGGTTCC 60.479 50.000 0.00 0.00 33.63 3.62
2009 2176 2.420722 TCCGGCATTTTTGTATCGGTTC 59.579 45.455 0.00 0.00 38.70 3.62
2010 2177 2.438411 TCCGGCATTTTTGTATCGGTT 58.562 42.857 0.00 0.00 38.70 4.44
2011 2178 2.116827 TCCGGCATTTTTGTATCGGT 57.883 45.000 0.00 0.00 38.70 4.69
2012 2179 3.175929 GTTTCCGGCATTTTTGTATCGG 58.824 45.455 0.00 0.00 38.92 4.18
2013 2180 3.827625 TGTTTCCGGCATTTTTGTATCG 58.172 40.909 0.00 0.00 0.00 2.92
2020 2190 5.461032 TCTGTATTTGTTTCCGGCATTTT 57.539 34.783 0.00 0.00 0.00 1.82
2068 2238 6.112734 TCTATGTCCATGTTGTATTCGCTTT 58.887 36.000 0.00 0.00 0.00 3.51
2069 2239 5.670485 TCTATGTCCATGTTGTATTCGCTT 58.330 37.500 0.00 0.00 0.00 4.68
2073 2243 5.692204 CCGTCTCTATGTCCATGTTGTATTC 59.308 44.000 0.00 0.00 0.00 1.75
2089 2259 0.322277 ACACTCCGCTTCCGTCTCTA 60.322 55.000 0.00 0.00 0.00 2.43
2092 2262 1.289380 GAACACTCCGCTTCCGTCT 59.711 57.895 0.00 0.00 0.00 4.18
2095 2265 2.027625 GGTGAACACTCCGCTTCCG 61.028 63.158 4.96 0.00 0.00 4.30
2103 2273 5.120363 GGATCTTTAGTTTCGGTGAACACTC 59.880 44.000 4.96 0.00 31.94 3.51
2113 2283 6.554334 TGTTTCAAGGGATCTTTAGTTTCG 57.446 37.500 0.00 0.00 0.00 3.46
2153 2323 6.538945 ACAAGTTATGTTGGTTTCCTTGTT 57.461 33.333 0.00 0.00 40.06 2.83
2388 3865 3.559242 GTCATGCACAAGATAAGAGAGGC 59.441 47.826 0.00 0.00 0.00 4.70
2938 4614 3.581770 CCAGCTATGGGATCTCATCTCAA 59.418 47.826 12.48 0.00 44.21 3.02
2969 4645 1.968017 CACGGCAGAGCACATTGGT 60.968 57.895 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.