Multiple sequence alignment - TraesCS3B01G077000

Loading Multiple Alignment...

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 TraesCS3B01G077000 chr3B 100.000 3923 0 0 1 3923 47461803 47457881 0.000000e+00 7245.0
1 TraesCS3B01G077000 chr3B 88.941 2568 221 39 665 3211 50342603 50345128 0.000000e+00 3110.0
2 TraesCS3B01G077000 chr3B 83.591 1877 264 27 1404 3248 188492895 188494759 0.000000e+00 1720.0
3 TraesCS3B01G077000 chr3B 83.546 1878 262 29 1404 3248 188464827 188466690 0.000000e+00 1712.0
4 TraesCS3B01G077000 chr3B 91.870 369 25 4 3330 3696 50345141 50345506 9.720000e-141 510.0
5 TraesCS3B01G077000 chr3B 95.597 159 7 0 3765 3923 50346305 50346463 5.030000e-64 255.0
6 TraesCS3B01G077000 chr3A 89.450 3109 250 45 175 3248 38267789 38264724 0.000000e+00 3853.0
7 TraesCS3B01G077000 chr3A 91.076 2398 179 26 862 3248 38260811 38258438 0.000000e+00 3210.0
8 TraesCS3B01G077000 chr3A 86.576 1326 157 12 1836 3141 10271153 10272477 0.000000e+00 1443.0
9 TraesCS3B01G077000 chr3A 85.908 369 13 14 3329 3696 38258440 38258110 1.340000e-94 357.0
10 TraesCS3B01G077000 chr3A 91.667 120 10 0 3804 3923 38264296 38264177 2.420000e-37 167.0
11 TraesCS3B01G077000 chr3A 91.176 102 9 0 3236 3337 54716970 54716869 5.290000e-29 139.0
12 TraesCS3B01G077000 chr3A 91.429 70 6 0 3854 3923 38257838 38257769 3.230000e-16 97.1
13 TraesCS3B01G077000 chr3A 97.500 40 1 0 3697 3736 38258085 38258046 7.030000e-08 69.4
14 TraesCS3B01G077000 chr3D 92.531 1513 97 9 1736 3244 28500677 28499177 0.000000e+00 2154.0
15 TraesCS3B01G077000 chr3D 89.371 1430 103 27 378 1780 28502085 28500678 0.000000e+00 1753.0
16 TraesCS3B01G077000 chr3D 84.050 1837 257 21 1148 2960 4467568 4469392 0.000000e+00 1736.0
17 TraesCS3B01G077000 chr3D 92.093 215 8 2 180 391 28502328 28502120 1.070000e-75 294.0
18 TraesCS3B01G077000 chr3D 86.145 166 15 5 1 164 28502884 28502725 5.210000e-39 172.0
19 TraesCS3B01G077000 chr3D 87.500 152 4 8 3772 3923 28498645 28498509 1.130000e-35 161.0
20 TraesCS3B01G077000 chr3D 96.703 91 2 1 3246 3336 505561940 505561851 2.440000e-32 150.0
21 TraesCS3B01G077000 chr3D 90.741 108 7 3 3229 3333 37369115 37369008 1.470000e-29 141.0
22 TraesCS3B01G077000 chrUn 83.308 1947 275 34 1151 3059 35686092 35684158 0.000000e+00 1749.0
23 TraesCS3B01G077000 chr7D 98.837 86 1 0 3246 3331 531177883 531177968 1.890000e-33 154.0
24 TraesCS3B01G077000 chr2A 96.703 91 3 0 3244 3334 386732357 386732267 6.790000e-33 152.0
25 TraesCS3B01G077000 chr1D 94.737 95 4 1 3240 3333 356580420 356580326 3.160000e-31 147.0
26 TraesCS3B01G077000 chr1D 90.741 108 7 3 3246 3352 439024787 439024892 1.470000e-29 141.0
27 TraesCS3B01G077000 chr5B 90.000 110 6 5 3224 3331 458619899 458620005 1.900000e-28 137.0
28 TraesCS3B01G077000 chr2D 92.553 94 7 0 3245 3338 547844635 547844728 6.840000e-28 135.0


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 TraesCS3B01G077000 chr3B 47457881 47461803 3922 True 7245.000000 7245 100.000000 1 3923 1 chr3B.!!$R1 3922
1 TraesCS3B01G077000 chr3B 188492895 188494759 1864 False 1720.000000 1720 83.591000 1404 3248 1 chr3B.!!$F2 1844
2 TraesCS3B01G077000 chr3B 188464827 188466690 1863 False 1712.000000 1712 83.546000 1404 3248 1 chr3B.!!$F1 1844
3 TraesCS3B01G077000 chr3B 50342603 50346463 3860 False 1291.666667 3110 92.136000 665 3923 3 chr3B.!!$F3 3258
4 TraesCS3B01G077000 chr3A 10271153 10272477 1324 False 1443.000000 1443 86.576000 1836 3141 1 chr3A.!!$F1 1305
5 TraesCS3B01G077000 chr3A 38257769 38267789 10020 True 1292.250000 3853 91.171667 175 3923 6 chr3A.!!$R2 3748
6 TraesCS3B01G077000 chr3D 4467568 4469392 1824 False 1736.000000 1736 84.050000 1148 2960 1 chr3D.!!$F1 1812
7 TraesCS3B01G077000 chr3D 28498509 28502884 4375 True 906.800000 2154 89.528000 1 3923 5 chr3D.!!$R3 3922
8 TraesCS3B01G077000 chrUn 35684158 35686092 1934 True 1749.000000 1749 83.308000 1151 3059 1 chrUn.!!$R1 1908

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
324 714 0.035534 ATATGACGTGCCAAGTGCCA 60.036 50.0 0.00 0.0 40.16 4.92 F
495 934 0.039764 AGTGATCTCGACCCCACAGA 59.960 55.0 8.44 0.0 32.35 3.41 F
1116 1586 0.178938 ACATCACCAACCAATGCCCA 60.179 50.0 0.00 0.0 0.00 5.36 F
1260 1730 0.318614 CGTTTGACGGCAAAGGCAAT 60.319 50.0 22.18 0.0 44.12 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 8749 0.037232 GGCGTTCCTTGTAGCTGACT 60.037 55.000 0.00 0.0 0.00 3.41 R
2484 9312 0.680921 ATGTCAACCATTCAGGGGCG 60.681 55.000 0.00 0.0 43.89 6.13 R
2756 9584 2.041216 ACCTCGGACATTTTAGGCCTTT 59.959 45.455 12.58 0.0 31.98 3.11 R
3180 10033 1.064060 CGCCCTAGCAGCATTTGTAAC 59.936 52.381 0.00 0.0 39.83 2.50 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
21 22 4.794278 AACCGTTTTTGTTTCAGGTTCT 57.206 36.364 0.00 0.00 37.40 3.01
23 24 5.900865 ACCGTTTTTGTTTCAGGTTCTTA 57.099 34.783 0.00 0.00 0.00 2.10
24 25 5.886992 ACCGTTTTTGTTTCAGGTTCTTAG 58.113 37.500 0.00 0.00 0.00 2.18
62 65 8.239314 TCTGAATATCAGTTGTTGCTGAATTTC 58.761 33.333 7.21 7.01 46.93 2.17
78 81 2.366640 TTTCATTCCACCGTTCCCAA 57.633 45.000 0.00 0.00 0.00 4.12
132 135 7.816945 AATTTATGTTTGAGTGTAAGCATGC 57.183 32.000 10.51 10.51 34.14 4.06
133 136 6.573664 TTTATGTTTGAGTGTAAGCATGCT 57.426 33.333 16.30 16.30 34.14 3.79
134 137 4.691860 ATGTTTGAGTGTAAGCATGCTC 57.308 40.909 22.93 10.31 31.52 4.26
135 138 2.813754 TGTTTGAGTGTAAGCATGCTCC 59.186 45.455 22.93 15.24 0.00 4.70
139 142 2.502947 TGAGTGTAAGCATGCTCCAGAT 59.497 45.455 22.93 11.95 0.00 2.90
148 151 7.775093 TGTAAGCATGCTCCAGATAAAAATAGT 59.225 33.333 22.93 1.25 0.00 2.12
150 153 5.468072 AGCATGCTCCAGATAAAAATAGTCG 59.532 40.000 16.30 0.00 0.00 4.18
151 154 5.683859 CATGCTCCAGATAAAAATAGTCGC 58.316 41.667 0.00 0.00 0.00 5.19
169 172 4.714851 GTCGCGAAGAGAGACTATTATCC 58.285 47.826 12.06 0.00 44.69 2.59
171 174 3.119779 CGCGAAGAGAGACTATTATCCCC 60.120 52.174 0.00 0.00 0.00 4.81
172 175 3.827302 GCGAAGAGAGACTATTATCCCCA 59.173 47.826 0.00 0.00 0.00 4.96
173 176 4.281182 GCGAAGAGAGACTATTATCCCCAA 59.719 45.833 0.00 0.00 0.00 4.12
174 177 5.774630 CGAAGAGAGACTATTATCCCCAAC 58.225 45.833 0.00 0.00 0.00 3.77
176 179 5.063017 AGAGAGACTATTATCCCCAACGA 57.937 43.478 0.00 0.00 0.00 3.85
178 181 5.302313 AGAGAGACTATTATCCCCAACGAAC 59.698 44.000 0.00 0.00 0.00 3.95
243 630 1.487976 TGATGAGCTCCATTCCTCCAC 59.512 52.381 12.15 0.00 35.17 4.02
298 688 9.254133 CATGACAACTTGTAATCGAGATAGATT 57.746 33.333 0.00 0.00 42.77 2.40
312 702 7.084486 TCGAGATAGATTGGTTGAATATGACG 58.916 38.462 0.00 0.00 0.00 4.35
315 705 4.882671 AGATTGGTTGAATATGACGTGC 57.117 40.909 0.00 0.00 0.00 5.34
316 706 3.627577 AGATTGGTTGAATATGACGTGCC 59.372 43.478 0.00 0.00 0.00 5.01
317 707 2.481289 TGGTTGAATATGACGTGCCA 57.519 45.000 0.00 0.00 0.00 4.92
324 714 0.035534 ATATGACGTGCCAAGTGCCA 60.036 50.000 0.00 0.00 40.16 4.92
356 747 2.923020 CACAAAAATAATGCACGAGGCC 59.077 45.455 0.00 0.00 43.89 5.19
399 838 1.586154 CCGCCATTGTTGACCTCCAC 61.586 60.000 0.00 0.00 0.00 4.02
453 892 2.817396 GACCAAGCTCAGCTCGCC 60.817 66.667 0.00 0.00 38.25 5.54
495 934 0.039764 AGTGATCTCGACCCCACAGA 59.960 55.000 8.44 0.00 32.35 3.41
496 935 1.115467 GTGATCTCGACCCCACAGAT 58.885 55.000 0.00 0.00 0.00 2.90
497 936 1.482593 GTGATCTCGACCCCACAGATT 59.517 52.381 0.00 0.00 0.00 2.40
501 940 4.767409 TGATCTCGACCCCACAGATTATAG 59.233 45.833 0.00 0.00 0.00 1.31
578 1017 1.194772 CTGACGCAGCATGAGCATATG 59.805 52.381 10.58 0.00 40.66 1.78
617 1056 5.070847 AGGAATGAACACCTGAAGCAAAAAT 59.929 36.000 0.00 0.00 34.99 1.82
756 1216 4.072131 TGGTAAGGATGTTCAACAAGAGC 58.928 43.478 0.00 0.00 0.00 4.09
781 1246 7.094592 GCTTGAAAGGAGCTAAGAAGTAAACAT 60.095 37.037 0.00 0.00 37.18 2.71
785 1250 9.654663 GAAAGGAGCTAAGAAGTAAACATCTAA 57.345 33.333 0.00 0.00 0.00 2.10
807 1277 1.949525 ACAAGCAGCAATCAAGTCGTT 59.050 42.857 0.00 0.00 0.00 3.85
865 1335 1.134788 GTGAGTTAGGCCATACGCTGT 60.135 52.381 5.01 0.00 37.74 4.40
904 1374 8.692110 TTGAACATTTTCAACATGCAGATATC 57.308 30.769 2.88 0.00 45.08 1.63
940 1410 4.837860 ACTGATCTAGACCTCCATTCCATC 59.162 45.833 0.00 0.00 0.00 3.51
983 1453 4.561254 AGAGGGGTCATATTACCAGACT 57.439 45.455 8.33 3.15 41.67 3.24
1048 1518 2.641746 CCACCTCCCCTCCTCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
1062 1532 2.186384 CTCTTGCTCCGCCTCCTG 59.814 66.667 0.00 0.00 0.00 3.86
1093 1563 1.002659 TCGTCACCACCCAAACCATAG 59.997 52.381 0.00 0.00 0.00 2.23
1109 1579 3.073798 ACCATAGTCAACATCACCAACCA 59.926 43.478 0.00 0.00 0.00 3.67
1116 1586 0.178938 ACATCACCAACCAATGCCCA 60.179 50.000 0.00 0.00 0.00 5.36
1122 1592 1.077005 ACCAACCAATGCCCATACACT 59.923 47.619 0.00 0.00 0.00 3.55
1260 1730 0.318614 CGTTTGACGGCAAAGGCAAT 60.319 50.000 22.18 0.00 44.12 3.56
1314 1784 0.815213 TCGCCTGCAAGACATATGGC 60.815 55.000 7.80 3.43 34.07 4.40
1318 1788 1.315690 CTGCAAGACATATGGCCAGG 58.684 55.000 13.05 5.88 34.07 4.45
1336 1806 2.103042 GCACCCATCACGTCTGCTC 61.103 63.158 0.00 0.00 0.00 4.26
1407 1877 1.373435 CCAGGGCTTCAACGTACCA 59.627 57.895 0.00 0.00 0.00 3.25
1553 2023 1.383080 CGCATGCGATGTGTTCAAAAC 59.617 47.619 35.82 0.00 42.83 2.43
1579 2055 4.020218 AGTCCAATTTGTACTGCTGCTCTA 60.020 41.667 0.00 0.00 0.00 2.43
1580 2056 4.878397 GTCCAATTTGTACTGCTGCTCTAT 59.122 41.667 0.00 0.00 0.00 1.98
1586 2062 2.166459 TGTACTGCTGCTCTATGACACC 59.834 50.000 0.00 0.00 0.00 4.16
1660 2136 5.220739 GCAATAAGTTACTCCAGTGATGCTG 60.221 44.000 0.00 0.00 44.63 4.41
1661 2137 5.683876 ATAAGTTACTCCAGTGATGCTGT 57.316 39.130 0.00 0.00 43.55 4.40
1713 2189 5.104485 GGATACCAACTACCAGGTCATCTTT 60.104 44.000 0.00 0.00 39.31 2.52
1893 2438 1.129326 GAAGAACACGACGACACCAG 58.871 55.000 0.00 0.00 0.00 4.00
1917 8745 0.616111 TGGAGGAAGAGGAGGCAGAC 60.616 60.000 0.00 0.00 0.00 3.51
1920 8748 1.480545 GAGGAAGAGGAGGCAGACTTC 59.519 57.143 0.00 0.00 38.26 3.01
1921 8749 1.203237 AGGAAGAGGAGGCAGACTTCA 60.203 52.381 0.00 0.00 39.99 3.02
1938 8766 2.724977 TCAGTCAGCTACAAGGAACG 57.275 50.000 0.00 0.00 0.00 3.95
2310 9138 5.125367 TCACTGACATAGCTAAGGGTCTA 57.875 43.478 18.52 8.91 0.00 2.59
2452 9280 4.492646 TGATAGGGATATGAGCCAAGTGA 58.507 43.478 0.00 0.00 0.00 3.41
2638 9466 4.047627 ACCCTATTGGAAGAAAAGGTGG 57.952 45.455 0.00 0.00 38.00 4.61
2643 9471 5.649831 CCTATTGGAAGAAAAGGTGGAGAAG 59.350 44.000 0.00 0.00 34.57 2.85
2857 9685 5.006165 GTCGCAACAAATGAACCAAATTTCA 59.994 36.000 0.00 0.00 39.79 2.69
2953 9782 4.559862 ATCCCGAGAAGACAGACAATTT 57.440 40.909 0.00 0.00 0.00 1.82
3096 9946 6.321181 TGAACCTTCTTGTTTTACAGCAGAAT 59.679 34.615 0.00 0.00 28.19 2.40
3135 9988 5.352569 ACAGTTTGTTCAGTTTCTCTCTGTG 59.647 40.000 0.00 0.00 34.86 3.66
3142 9995 3.001414 CAGTTTCTCTCTGTGATGCAGG 58.999 50.000 0.00 0.00 45.08 4.85
3151 10004 2.104622 TCTGTGATGCAGGTCTGTTTCA 59.895 45.455 0.00 1.29 45.08 2.69
3160 10013 4.518970 TGCAGGTCTGTTTCAAGTTATTCC 59.481 41.667 0.00 0.00 0.00 3.01
3177 10030 6.998673 AGTTATTCCAGTTGAAACTAACAGCT 59.001 34.615 7.96 0.00 37.08 4.24
3178 10031 8.154856 AGTTATTCCAGTTGAAACTAACAGCTA 58.845 33.333 7.96 0.00 37.08 3.32
3179 10032 8.947115 GTTATTCCAGTTGAAACTAACAGCTAT 58.053 33.333 0.00 0.00 37.08 2.97
3180 10033 6.801539 TTCCAGTTGAAACTAACAGCTATG 57.198 37.500 0.00 0.00 37.08 2.23
3194 10047 4.627611 CAGCTATGTTACAAATGCTGCT 57.372 40.909 18.54 7.58 40.75 4.24
3195 10048 5.739752 CAGCTATGTTACAAATGCTGCTA 57.260 39.130 18.54 0.00 40.75 3.49
3196 10049 5.745514 CAGCTATGTTACAAATGCTGCTAG 58.254 41.667 18.54 3.68 40.75 3.42
3197 10050 4.818546 AGCTATGTTACAAATGCTGCTAGG 59.181 41.667 0.00 0.00 0.00 3.02
3198 10051 4.023707 GCTATGTTACAAATGCTGCTAGGG 60.024 45.833 0.00 0.00 0.00 3.53
3199 10052 2.091541 TGTTACAAATGCTGCTAGGGC 58.908 47.619 0.00 0.00 39.26 5.19
3200 10053 1.064060 GTTACAAATGCTGCTAGGGCG 59.936 52.381 0.00 0.00 42.25 6.13
3230 10091 5.769835 TCCAATAAAGGCAGAGAAATGGAT 58.230 37.500 0.00 0.00 29.93 3.41
3252 10113 9.225682 TGGATAGACTGAATTAAAATACTCCCT 57.774 33.333 0.00 0.00 0.00 4.20
3253 10114 9.713713 GGATAGACTGAATTAAAATACTCCCTC 57.286 37.037 0.00 0.00 0.00 4.30
3256 10117 8.152023 AGACTGAATTAAAATACTCCCTCTGT 57.848 34.615 0.00 0.00 0.00 3.41
3257 10118 9.268282 AGACTGAATTAAAATACTCCCTCTGTA 57.732 33.333 0.00 0.00 0.00 2.74
3258 10119 9.886132 GACTGAATTAAAATACTCCCTCTGTAA 57.114 33.333 0.00 0.00 0.00 2.41
3272 10133 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
3274 10135 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
3325 10186 9.760077 AACACTCTTATATTAGTTTACGGATGG 57.240 33.333 0.00 0.00 0.00 3.51
3326 10187 9.139734 ACACTCTTATATTAGTTTACGGATGGA 57.860 33.333 0.00 0.00 0.00 3.41
3327 10188 9.627395 CACTCTTATATTAGTTTACGGATGGAG 57.373 37.037 0.00 0.00 0.00 3.86
3386 10249 9.822185 AACAATTAGAAATCAGAAGTGCTTTTT 57.178 25.926 0.00 0.00 0.00 1.94
3492 10355 5.693769 TGATACTAGCTTTTAGGCTTGGT 57.306 39.130 0.00 0.00 42.97 3.67
3570 10434 1.338674 CGGGCATACTGGTGTTCTCAA 60.339 52.381 0.00 0.00 0.00 3.02
3655 10519 3.628032 TCCAGTGTGTTTTTATTGCACGA 59.372 39.130 0.00 0.00 36.04 4.35
3662 10526 6.853872 GTGTGTTTTTATTGCACGAATACTGA 59.146 34.615 0.00 0.00 36.04 3.41
3692 10636 7.676338 GCATACACAGAAAGCGTATTTGTACAT 60.676 37.037 0.00 0.00 0.00 2.29
3724 10692 0.327924 ATGAAAGATCCACCGTGCCA 59.672 50.000 0.00 0.00 0.00 4.92
3768 11387 2.086094 CTGTGACCATGTAATGCTGCA 58.914 47.619 4.13 4.13 44.97 4.41
3770 11389 2.228582 TGTGACCATGTAATGCTGCAAC 59.771 45.455 6.36 1.29 44.97 4.17
3783 11457 7.706607 TGTAATGCTGCAACTTGATAGTACTAG 59.293 37.037 6.36 0.00 33.17 2.57
3790 11464 7.759465 TGCAACTTGATAGTACTAGTAGTCAC 58.241 38.462 13.60 9.64 33.17 3.67
3850 11553 4.282957 CCTCTGGATTATTGCTCTGAGCTA 59.717 45.833 28.04 22.11 42.97 3.32
3859 11562 1.753649 TGCTCTGAGCTAAGTAGGCTG 59.246 52.381 28.04 0.00 42.97 4.85
3866 11569 1.760029 AGCTAAGTAGGCTGAAGCTCC 59.240 52.381 0.00 0.00 39.34 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.806149 AAACTAAGAACCTGAAACAAAAACG 57.194 32.000 0.00 0.00 0.00 3.60
19 20 9.892130 GATATTCAGAGGAAAGGAAAACTAAGA 57.108 33.333 0.00 0.00 36.43 2.10
20 21 9.672673 TGATATTCAGAGGAAAGGAAAACTAAG 57.327 33.333 0.00 0.00 36.43 2.18
62 65 1.745087 CTCATTGGGAACGGTGGAATG 59.255 52.381 0.00 0.00 0.00 2.67
109 112 7.161773 AGCATGCTTACACTCAAACATAAAT 57.838 32.000 16.30 0.00 0.00 1.40
110 113 6.349280 GGAGCATGCTTACACTCAAACATAAA 60.349 38.462 23.61 0.00 0.00 1.40
117 120 2.302733 TCTGGAGCATGCTTACACTCAA 59.697 45.455 23.61 0.00 0.00 3.02
120 123 4.760530 TTATCTGGAGCATGCTTACACT 57.239 40.909 23.61 13.56 0.00 3.55
124 127 7.171508 CGACTATTTTTATCTGGAGCATGCTTA 59.828 37.037 23.61 13.31 0.00 3.09
125 128 6.017605 CGACTATTTTTATCTGGAGCATGCTT 60.018 38.462 23.61 7.98 0.00 3.91
128 131 5.613360 CGCGACTATTTTTATCTGGAGCATG 60.613 44.000 0.00 0.00 0.00 4.06
129 132 4.449068 CGCGACTATTTTTATCTGGAGCAT 59.551 41.667 0.00 0.00 0.00 3.79
130 133 3.802139 CGCGACTATTTTTATCTGGAGCA 59.198 43.478 0.00 0.00 0.00 4.26
131 134 4.049186 TCGCGACTATTTTTATCTGGAGC 58.951 43.478 3.71 0.00 0.00 4.70
132 135 5.977725 TCTTCGCGACTATTTTTATCTGGAG 59.022 40.000 9.15 0.00 0.00 3.86
133 136 5.898174 TCTTCGCGACTATTTTTATCTGGA 58.102 37.500 9.15 0.00 0.00 3.86
134 137 5.977725 TCTCTTCGCGACTATTTTTATCTGG 59.022 40.000 9.15 0.00 0.00 3.86
135 138 6.913132 TCTCTCTTCGCGACTATTTTTATCTG 59.087 38.462 9.15 0.00 0.00 2.90
139 142 6.192234 AGTCTCTCTTCGCGACTATTTTTA 57.808 37.500 9.15 0.00 36.33 1.52
148 151 3.752222 GGGATAATAGTCTCTCTTCGCGA 59.248 47.826 3.71 3.71 0.00 5.87
150 153 3.827302 TGGGGATAATAGTCTCTCTTCGC 59.173 47.826 0.00 0.00 0.00 4.70
151 154 5.563085 CGTTGGGGATAATAGTCTCTCTTCG 60.563 48.000 0.00 0.00 0.00 3.79
171 174 1.577328 ATTCAGCAGCCCGTTCGTTG 61.577 55.000 0.00 0.00 0.00 4.10
172 175 1.302511 ATTCAGCAGCCCGTTCGTT 60.303 52.632 0.00 0.00 0.00 3.85
173 176 2.034879 CATTCAGCAGCCCGTTCGT 61.035 57.895 0.00 0.00 0.00 3.85
174 177 2.753966 CCATTCAGCAGCCCGTTCG 61.754 63.158 0.00 0.00 0.00 3.95
176 179 1.973281 CACCATTCAGCAGCCCGTT 60.973 57.895 0.00 0.00 0.00 4.44
178 181 1.442526 GATCACCATTCAGCAGCCCG 61.443 60.000 0.00 0.00 0.00 6.13
243 630 5.464389 CCAAGCTTTTTGGAAGTGAAAGATG 59.536 40.000 0.00 0.00 42.06 2.90
298 688 2.481289 TGGCACGTCATATTCAACCA 57.519 45.000 0.00 0.00 0.00 3.67
315 705 0.318120 GTTGGGATGTTGGCACTTGG 59.682 55.000 0.00 0.00 0.00 3.61
316 706 0.318120 GGTTGGGATGTTGGCACTTG 59.682 55.000 0.00 0.00 0.00 3.16
317 707 0.105760 TGGTTGGGATGTTGGCACTT 60.106 50.000 0.00 0.00 0.00 3.16
324 714 5.704978 GCATTATTTTTGTGGTTGGGATGTT 59.295 36.000 0.00 0.00 0.00 2.71
356 747 1.604593 CTTGGGTGGTGGGCAGAAG 60.605 63.158 0.00 0.00 0.00 2.85
399 838 1.075425 CGTCGAAGCAGCTTGAGGAG 61.075 60.000 13.91 0.00 0.00 3.69
453 892 2.965716 GAACAGGATCATGGGGGCCG 62.966 65.000 12.66 0.00 0.00 6.13
495 934 1.867233 CAGCAACGCGAAGGCTATAAT 59.133 47.619 15.93 0.00 35.82 1.28
496 935 1.286501 CAGCAACGCGAAGGCTATAA 58.713 50.000 15.93 0.00 35.82 0.98
497 936 1.151777 GCAGCAACGCGAAGGCTATA 61.152 55.000 15.93 0.00 35.82 1.31
561 1000 1.947013 GCATATGCTCATGCTGCGT 59.053 52.632 20.64 9.54 46.35 5.24
578 1017 4.965814 TCATTCCTGGTCTAATCTGATGC 58.034 43.478 0.00 0.00 0.00 3.91
679 1130 0.383737 TTTTTGCTTACGACAGCGCG 60.384 50.000 0.00 0.00 43.37 6.86
706 1157 4.340666 ACCATACATGCAAACTGTTGACAA 59.659 37.500 0.00 0.00 36.83 3.18
756 1216 7.730364 TGTTTACTTCTTAGCTCCTTTCAAG 57.270 36.000 0.00 0.00 0.00 3.02
781 1246 4.136796 ACTTGATTGCTGCTTGTGTTAGA 58.863 39.130 0.00 0.00 0.00 2.10
785 1250 1.265095 CGACTTGATTGCTGCTTGTGT 59.735 47.619 0.00 0.00 0.00 3.72
807 1277 1.846007 ACAAACAGTTTGACAGGCCA 58.154 45.000 29.10 0.00 43.26 5.36
865 1335 1.408340 TGTTCAACGGTCTACGGTCAA 59.592 47.619 0.00 0.00 39.00 3.18
904 1374 9.290988 AGGTCTAGATCAGTGTATACTTGTATG 57.709 37.037 5.64 0.00 34.07 2.39
940 1410 5.309020 TCTTGGATGAGATGATAAAGGAGGG 59.691 44.000 0.00 0.00 0.00 4.30
983 1453 2.356022 CCCATAACTGCCATCTGTGTCA 60.356 50.000 0.00 0.00 0.00 3.58
1062 1532 2.109126 GGTGACGAATGGCAGGAGC 61.109 63.158 0.00 0.00 41.10 4.70
1093 1563 2.610232 GGCATTGGTTGGTGATGTTGAC 60.610 50.000 0.00 0.00 0.00 3.18
1109 1579 2.586425 GCCATACAGTGTATGGGCATT 58.414 47.619 42.65 13.22 43.52 3.56
1116 1586 1.450211 GGCCGGCCATACAGTGTAT 59.550 57.895 40.73 10.10 35.81 2.29
1260 1730 3.080641 CCTGTCTGGCATGACCCA 58.919 61.111 0.00 0.00 37.83 4.51
1314 1784 2.436646 GACGTGATGGGTGCCTGG 60.437 66.667 0.00 0.00 0.00 4.45
1318 1788 2.046892 AGCAGACGTGATGGGTGC 60.047 61.111 0.00 0.00 0.00 5.01
1336 1806 5.580691 TGTTATACTGGTTGAGCGAGAATTG 59.419 40.000 0.00 0.00 0.00 2.32
1407 1877 1.551883 GGCATTGGCAAGAACTCCATT 59.448 47.619 5.96 0.00 43.71 3.16
1470 1940 2.625823 CGTGATGTTGGCCCCACAC 61.626 63.158 7.01 9.93 0.00 3.82
1539 2009 3.559655 TGGACTGAGTTTTGAACACATCG 59.440 43.478 0.00 0.00 31.68 3.84
1542 2012 5.913137 AATTGGACTGAGTTTTGAACACA 57.087 34.783 0.00 0.00 0.00 3.72
1579 2055 2.108075 TGTTGGATTCACAGGGTGTCAT 59.892 45.455 0.00 0.00 34.79 3.06
1580 2056 1.492599 TGTTGGATTCACAGGGTGTCA 59.507 47.619 0.00 0.00 34.79 3.58
1586 2062 4.094887 CCGAGTATTTGTTGGATTCACAGG 59.905 45.833 0.00 0.00 0.00 4.00
1660 2136 4.035208 ACAACTGAATGAAGTTTCCGTGAC 59.965 41.667 0.00 0.00 38.34 3.67
1661 2137 4.196193 ACAACTGAATGAAGTTTCCGTGA 58.804 39.130 0.00 0.00 38.34 4.35
1713 2189 2.752354 CGTTAGATTGATTGGTGGGCAA 59.248 45.455 0.00 0.00 0.00 4.52
1893 2438 1.715785 CCTCCTCTTCCTCCATCTCC 58.284 60.000 0.00 0.00 0.00 3.71
1917 8745 2.989840 CGTTCCTTGTAGCTGACTGAAG 59.010 50.000 0.00 0.00 0.00 3.02
1920 8748 1.071605 GCGTTCCTTGTAGCTGACTG 58.928 55.000 0.00 0.00 0.00 3.51
1921 8749 0.037232 GGCGTTCCTTGTAGCTGACT 60.037 55.000 0.00 0.00 0.00 3.41
1938 8766 3.907894 TGAAACGTAAACCTCATTGGC 57.092 42.857 0.00 0.00 40.22 4.52
2310 9138 5.282055 TGCAATCCTCGTGAAGATAAGAT 57.718 39.130 0.00 0.00 0.00 2.40
2452 9280 4.018960 AGGTGTGCCTCTCATTCTTGTAAT 60.019 41.667 0.00 0.00 42.67 1.89
2484 9312 0.680921 ATGTCAACCATTCAGGGGCG 60.681 55.000 0.00 0.00 43.89 6.13
2638 9466 7.678947 TCAAATCTTCCAACTGATTCTTCTC 57.321 36.000 0.00 0.00 32.43 2.87
2643 9471 7.596494 TGTCAATCAAATCTTCCAACTGATTC 58.404 34.615 0.00 0.00 35.15 2.52
2756 9584 2.041216 ACCTCGGACATTTTAGGCCTTT 59.959 45.455 12.58 0.00 31.98 3.11
2857 9685 5.564550 AGAGTTCACATTTCCAGCAATACT 58.435 37.500 0.00 0.00 0.00 2.12
2953 9782 8.750515 TCATTTCATTTAGCACCTGATAATCA 57.249 30.769 0.00 0.00 0.00 2.57
3071 9921 5.189928 TCTGCTGTAAAACAAGAAGGTTCA 58.810 37.500 0.00 0.00 0.00 3.18
3135 9988 5.886960 ATAACTTGAAACAGACCTGCATC 57.113 39.130 0.00 0.00 0.00 3.91
3142 9995 7.259290 TCAACTGGAATAACTTGAAACAGAC 57.741 36.000 0.00 0.00 0.00 3.51
3151 10004 7.502561 AGCTGTTAGTTTCAACTGGAATAACTT 59.497 33.333 2.26 0.00 40.07 2.66
3160 10013 8.083462 TGTAACATAGCTGTTAGTTTCAACTG 57.917 34.615 0.00 0.00 45.95 3.16
3169 10022 5.967674 GCAGCATTTGTAACATAGCTGTTAG 59.032 40.000 16.40 0.00 45.95 2.34
3177 10030 3.882888 GCCCTAGCAGCATTTGTAACATA 59.117 43.478 0.00 0.00 39.53 2.29
3178 10031 2.689983 GCCCTAGCAGCATTTGTAACAT 59.310 45.455 0.00 0.00 39.53 2.71
3179 10032 2.091541 GCCCTAGCAGCATTTGTAACA 58.908 47.619 0.00 0.00 39.53 2.41
3180 10033 1.064060 CGCCCTAGCAGCATTTGTAAC 59.936 52.381 0.00 0.00 39.83 2.50
3183 10036 2.409870 GCGCCCTAGCAGCATTTGT 61.410 57.895 0.00 0.00 39.83 2.83
3184 10037 2.410469 GCGCCCTAGCAGCATTTG 59.590 61.111 0.00 0.00 39.83 2.32
3198 10051 1.230324 CCTTTATTGGAGCTAGGCGC 58.770 55.000 0.00 0.00 39.57 6.53
3199 10052 1.230324 GCCTTTATTGGAGCTAGGCG 58.770 55.000 5.70 0.00 41.65 5.52
3230 10091 9.268282 ACAGAGGGAGTATTTTAATTCAGTCTA 57.732 33.333 0.00 0.00 0.00 2.59
3246 10107 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
3248 10109 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
3299 10160 9.760077 CCATCCGTAAACTAATATAAGAGTGTT 57.240 33.333 0.00 0.00 0.00 3.32
3300 10161 9.139734 TCCATCCGTAAACTAATATAAGAGTGT 57.860 33.333 0.00 0.00 0.00 3.55
3301 10162 9.627395 CTCCATCCGTAAACTAATATAAGAGTG 57.373 37.037 0.00 0.00 0.00 3.51
3302 10163 9.364653 ACTCCATCCGTAAACTAATATAAGAGT 57.635 33.333 0.00 0.00 0.00 3.24
3311 10172 9.590451 CTAAAATGTACTCCATCCGTAAACTAA 57.410 33.333 0.00 0.00 31.75 2.24
3312 10173 8.199449 CCTAAAATGTACTCCATCCGTAAACTA 58.801 37.037 0.00 0.00 31.75 2.24
3313 10174 7.046033 CCTAAAATGTACTCCATCCGTAAACT 58.954 38.462 0.00 0.00 31.75 2.66
3314 10175 7.043565 TCCTAAAATGTACTCCATCCGTAAAC 58.956 38.462 0.00 0.00 31.75 2.01
3315 10176 7.093201 ACTCCTAAAATGTACTCCATCCGTAAA 60.093 37.037 0.00 0.00 31.75 2.01
3316 10177 6.381994 ACTCCTAAAATGTACTCCATCCGTAA 59.618 38.462 0.00 0.00 31.75 3.18
3317 10178 5.895534 ACTCCTAAAATGTACTCCATCCGTA 59.104 40.000 0.00 0.00 31.75 4.02
3318 10179 4.715297 ACTCCTAAAATGTACTCCATCCGT 59.285 41.667 0.00 0.00 31.75 4.69
3319 10180 5.277857 ACTCCTAAAATGTACTCCATCCG 57.722 43.478 0.00 0.00 31.75 4.18
3320 10181 6.239629 CCCTACTCCTAAAATGTACTCCATCC 60.240 46.154 0.00 0.00 31.75 3.51
3321 10182 6.553852 TCCCTACTCCTAAAATGTACTCCATC 59.446 42.308 0.00 0.00 31.75 3.51
3322 10183 6.449956 TCCCTACTCCTAAAATGTACTCCAT 58.550 40.000 0.00 0.00 34.36 3.41
3323 10184 5.845734 TCCCTACTCCTAAAATGTACTCCA 58.154 41.667 0.00 0.00 0.00 3.86
3324 10185 6.803366 TTCCCTACTCCTAAAATGTACTCC 57.197 41.667 0.00 0.00 0.00 3.85
3325 10186 9.761504 GTTATTCCCTACTCCTAAAATGTACTC 57.238 37.037 0.00 0.00 0.00 2.59
3326 10187 9.503369 AGTTATTCCCTACTCCTAAAATGTACT 57.497 33.333 0.00 0.00 0.00 2.73
3372 10234 5.063880 GGGAGAACTAAAAAGCACTTCTGA 58.936 41.667 0.00 0.00 0.00 3.27
3373 10235 4.821805 TGGGAGAACTAAAAAGCACTTCTG 59.178 41.667 0.00 0.00 0.00 3.02
3374 10236 5.048846 TGGGAGAACTAAAAAGCACTTCT 57.951 39.130 0.00 0.00 0.00 2.85
3375 10237 5.767816 TTGGGAGAACTAAAAAGCACTTC 57.232 39.130 0.00 0.00 0.00 3.01
3386 10249 4.993705 ACACTGGAAATTGGGAGAACTA 57.006 40.909 0.00 0.00 0.00 2.24
3505 10368 4.959839 AGCCAACAAAAGAAGTAGGGAAAA 59.040 37.500 0.00 0.00 0.00 2.29
3506 10369 4.340950 CAGCCAACAAAAGAAGTAGGGAAA 59.659 41.667 0.00 0.00 0.00 3.13
3606 10470 0.817634 TCTCCAACACACGCCCAAAG 60.818 55.000 0.00 0.00 0.00 2.77
3692 10636 4.458397 GATCTTTCATTCCATGAGCCTCA 58.542 43.478 0.00 0.00 40.94 3.86
3768 11387 8.783833 TTCGTGACTACTAGTACTATCAAGTT 57.216 34.615 2.33 0.00 37.15 2.66
3770 11389 8.645730 TCTTCGTGACTACTAGTACTATCAAG 57.354 38.462 2.33 6.90 0.00 3.02
3783 11457 2.155924 GCAGCAACTTCTTCGTGACTAC 59.844 50.000 0.00 0.00 0.00 2.73
3790 11464 1.126846 CGGTAAGCAGCAACTTCTTCG 59.873 52.381 0.00 0.00 0.00 3.79
3850 11553 0.820871 CGAGGAGCTTCAGCCTACTT 59.179 55.000 0.00 0.00 43.38 2.24


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

AutoCloner maintained by Alex Coulton.