Multiple sequence alignment - TraesCS2B01G113700

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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 TraesCS2B01G113700 chr2B 100.000 3076 0 0 833 3908 77164698 77167773 0 5681
1 TraesCS2B01G113700 chr2B 100.000 681 0 0 1 681 77163866 77164546 0 1258
2 TraesCS2B01G113700 chr2B 98.686 685 5 1 1 681 800915991 800915307 0 1212
3 TraesCS2B01G113700 chr2D 93.062 1427 75 13 1797 3207 49872933 49874351 0 2065
4 TraesCS2B01G113700 chr2D 90.481 977 53 19 833 1785 49871874 49872834 0 1253
5 TraesCS2B01G113700 chr2D 87.281 684 34 21 3261 3908 49874368 49875034 0 732
6 TraesCS2B01G113700 chr2A 84.996 1293 140 33 2521 3774 51580042 51581319 0 1264
7 TraesCS2B01G113700 chr2A 90.463 713 44 13 1824 2523 51579305 51580006 0 918
8 TraesCS2B01G113700 chr2A 87.380 729 50 20 834 1546 51578314 51579016 0 798
9 TraesCS2B01G113700 chr3B 98.540 685 6 1 1 681 406867674 406868358 0 1206
10 TraesCS2B01G113700 chr3B 98.540 685 6 1 1 681 700792342 700793026 0 1206
11 TraesCS2B01G113700 chr7A 98.538 684 6 1 1 680 705600648 705601331 0 1205
12 TraesCS2B01G113700 chr7A 98.248 685 8 1 1 681 39835814 39835130 0 1195
13 TraesCS2B01G113700 chr6B 98.538 684 6 1 1 680 45785102 45785785 0 1205
14 TraesCS2B01G113700 chr5A 98.392 684 7 1 1 680 2076416 2075733 0 1199
15 TraesCS2B01G113700 chr5A 98.248 685 8 1 1 681 435252996 435253680 0 1195
16 TraesCS2B01G113700 chr6A 98.392 684 4 2 1 680 2964745 2965425 0 1195


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 TraesCS2B01G113700 chr2B 77163866 77167773 3907 False 3469.500000 5681 100.000000 1 3908 2 chr2B.!!$F1 3907
1 TraesCS2B01G113700 chr2B 800915307 800915991 684 True 1212.000000 1212 98.686000 1 681 1 chr2B.!!$R1 680
2 TraesCS2B01G113700 chr2D 49871874 49875034 3160 False 1350.000000 2065 90.274667 833 3908 3 chr2D.!!$F1 3075
3 TraesCS2B01G113700 chr2A 51578314 51581319 3005 False 993.333333 1264 87.613000 834 3774 3 chr2A.!!$F1 2940
4 TraesCS2B01G113700 chr3B 406867674 406868358 684 False 1206.000000 1206 98.540000 1 681 1 chr3B.!!$F1 680
5 TraesCS2B01G113700 chr3B 700792342 700793026 684 False 1206.000000 1206 98.540000 1 681 1 chr3B.!!$F2 680
6 TraesCS2B01G113700 chr7A 705600648 705601331 683 False 1205.000000 1205 98.538000 1 680 1 chr7A.!!$F1 679
7 TraesCS2B01G113700 chr7A 39835130 39835814 684 True 1195.000000 1195 98.248000 1 681 1 chr7A.!!$R1 680
8 TraesCS2B01G113700 chr6B 45785102 45785785 683 False 1205.000000 1205 98.538000 1 680 1 chr6B.!!$F1 679
9 TraesCS2B01G113700 chr5A 2075733 2076416 683 True 1199.000000 1199 98.392000 1 680 1 chr5A.!!$R1 679
10 TraesCS2B01G113700 chr5A 435252996 435253680 684 False 1195.000000 1195 98.248000 1 681 1 chr5A.!!$F1 680
11 TraesCS2B01G113700 chr6A 2964745 2965425 680 False 1195.000000 1195 98.392000 1 680 1 chr6A.!!$F1 679

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
867 872 2.203422 ATCGCCCTCCTCTCTCGG 60.203 66.667 0.00 0.00 0.00 4.63 F
1303 1316 0.028110 GTTTCGAATCATGGCGAGCC 59.972 55.000 7.26 7.26 37.85 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2568 2782 0.568888 GCATCAATTGCGTTGCATCG 59.431 50.0 12.78 12.78 42.54 3.84 R
3245 3464 0.179045 CCCTCTTTCCAGTATGCCCG 60.179 60.0 0.00 0.00 31.97 6.13 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
145 150 2.909006 AGAAGAAGGAGGAAGCACATGA 59.091 45.455 0.00 0.00 0.00 3.07
866 871 2.612567 CGATCGCCCTCCTCTCTCG 61.613 68.421 0.26 0.00 0.00 4.04
867 872 2.203422 ATCGCCCTCCTCTCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
874 879 4.877619 TCCTCTCTCGGCCGCGAT 62.878 66.667 23.51 0.00 0.00 4.58
1057 1064 4.271816 CCGAGATGGACGAGGGCG 62.272 72.222 0.00 0.00 42.00 6.13
1058 1065 4.271816 CGAGATGGACGAGGGCGG 62.272 72.222 0.00 0.00 43.17 6.13
1059 1066 3.917760 GAGATGGACGAGGGCGGG 61.918 72.222 0.00 0.00 43.17 6.13
1229 1242 1.001924 CCAGGTCAGTCAGATCGATCG 60.002 57.143 19.33 9.36 30.60 3.69
1230 1243 1.673400 CAGGTCAGTCAGATCGATCGT 59.327 52.381 19.33 5.71 30.60 3.73
1236 1249 1.586303 TCAGATCGATCGTGCACGC 60.586 57.895 33.63 19.75 39.60 5.34
1237 1250 1.873572 CAGATCGATCGTGCACGCA 60.874 57.895 33.63 22.17 39.60 5.24
1244 1257 0.298707 GATCGTGCACGCATACACAG 59.701 55.000 33.63 5.25 39.60 3.66
1267 1280 8.047310 ACAGACGTAATTTAATCAAATCCTCCT 58.953 33.333 0.00 0.00 33.09 3.69
1270 1283 8.664211 ACGTAATTTAATCAAATCCTCCTCTC 57.336 34.615 0.00 0.00 33.09 3.20
1303 1316 0.028110 GTTTCGAATCATGGCGAGCC 59.972 55.000 7.26 7.26 37.85 4.70
1356 1369 1.220749 GTGGGTCTCGCCTTATGCA 59.779 57.895 0.00 0.00 41.33 3.96
1360 1373 1.156645 GGTCTCGCCTTATGCAGCAG 61.157 60.000 0.00 0.00 41.33 4.24
1484 1497 5.072741 TGATTTAATCCCTTGGCTATCTGC 58.927 41.667 2.22 0.00 41.94 4.26
1556 1625 3.982475 TGTGACAGTCTGACAGATGAAC 58.018 45.455 8.73 11.45 0.00 3.18
1575 1644 3.485463 ACGATTGGTTCAGGTCAAAGA 57.515 42.857 0.00 0.00 0.00 2.52
1576 1645 3.815809 ACGATTGGTTCAGGTCAAAGAA 58.184 40.909 0.00 0.00 0.00 2.52
1577 1646 4.204012 ACGATTGGTTCAGGTCAAAGAAA 58.796 39.130 0.00 0.00 0.00 2.52
1578 1647 4.275936 ACGATTGGTTCAGGTCAAAGAAAG 59.724 41.667 0.00 0.00 0.00 2.62
1579 1648 4.515191 CGATTGGTTCAGGTCAAAGAAAGA 59.485 41.667 0.00 0.00 0.00 2.52
1580 1649 5.182001 CGATTGGTTCAGGTCAAAGAAAGAT 59.818 40.000 0.00 0.00 0.00 2.40
1582 1651 4.792068 TGGTTCAGGTCAAAGAAAGATGT 58.208 39.130 0.00 0.00 0.00 3.06
1583 1652 5.935945 TGGTTCAGGTCAAAGAAAGATGTA 58.064 37.500 0.00 0.00 0.00 2.29
1584 1653 5.997746 TGGTTCAGGTCAAAGAAAGATGTAG 59.002 40.000 0.00 0.00 0.00 2.74
1608 1684 7.550712 AGAGAATATTGAACATTTTCCTTGGC 58.449 34.615 0.00 0.00 0.00 4.52
1650 1726 1.295746 GACTTCACCTTCCCCGACC 59.704 63.158 0.00 0.00 0.00 4.79
1702 1778 1.142870 CTCCCACCTGTCAACTTTGGA 59.857 52.381 0.00 0.00 0.00 3.53
1703 1779 1.780309 TCCCACCTGTCAACTTTGGAT 59.220 47.619 0.00 0.00 0.00 3.41
1705 1781 3.009033 TCCCACCTGTCAACTTTGGATAG 59.991 47.826 0.00 0.00 0.00 2.08
1707 1783 4.398319 CCACCTGTCAACTTTGGATAGTT 58.602 43.478 0.00 0.00 38.87 2.24
1708 1784 4.827284 CCACCTGTCAACTTTGGATAGTTT 59.173 41.667 0.00 0.00 36.24 2.66
1710 1786 6.149474 CCACCTGTCAACTTTGGATAGTTTAG 59.851 42.308 0.00 0.00 36.24 1.85
1711 1787 6.710744 CACCTGTCAACTTTGGATAGTTTAGT 59.289 38.462 0.00 0.00 36.24 2.24
1712 1788 7.228706 CACCTGTCAACTTTGGATAGTTTAGTT 59.771 37.037 0.00 0.00 36.24 2.24
1759 1836 1.670811 ACTGGCAGTTTGTGTCTTTCG 59.329 47.619 15.88 0.00 0.00 3.46
1785 1863 9.357652 GTTGATGTGTTTATTACCGAACTACTA 57.642 33.333 0.00 0.00 0.00 1.82
1786 1864 8.915871 TGATGTGTTTATTACCGAACTACTAC 57.084 34.615 0.00 0.00 0.00 2.73
1788 1866 6.321717 TGTGTTTATTACCGAACTACTACCG 58.678 40.000 0.00 0.00 0.00 4.02
1790 1868 5.650266 TGTTTATTACCGAACTACTACCGGA 59.350 40.000 9.46 0.00 45.58 5.14
1791 1869 6.151985 TGTTTATTACCGAACTACTACCGGAA 59.848 38.462 9.46 0.00 45.58 4.30
1792 1870 4.907879 ATTACCGAACTACTACCGGAAG 57.092 45.455 9.46 2.00 45.58 3.46
1793 1871 2.206576 ACCGAACTACTACCGGAAGT 57.793 50.000 9.46 2.73 45.58 3.01
1794 1872 2.087646 ACCGAACTACTACCGGAAGTC 58.912 52.381 9.46 0.00 45.58 3.01
1795 1873 1.403323 CCGAACTACTACCGGAAGTCC 59.597 57.143 9.46 0.00 45.58 3.85
1893 2066 9.846248 GTGTATAGCATCTGTTCTGAAAATTTT 57.154 29.630 2.28 2.28 0.00 1.82
1898 2071 5.754890 GCATCTGTTCTGAAAATTTTGTGGT 59.245 36.000 8.47 0.00 0.00 4.16
1903 2076 9.349713 TCTGTTCTGAAAATTTTGTGGTATACT 57.650 29.630 8.47 0.00 0.00 2.12
1951 2124 3.496870 GGCCTACCTATCTTGTCAATGGG 60.497 52.174 0.00 0.00 0.00 4.00
1964 2138 3.117474 TGTCAATGGGTTTTACCACCTCA 60.117 43.478 0.00 0.00 44.72 3.86
1972 2146 4.506802 GGGTTTTACCACCTCAGTCTCATT 60.507 45.833 0.00 0.00 41.02 2.57
1990 2164 6.150140 GTCTCATTTTTGCCATAAGAGACTGT 59.850 38.462 11.26 0.00 44.20 3.55
1995 2169 9.888878 CATTTTTGCCATAAGAGACTGTATATG 57.111 33.333 0.00 0.00 0.00 1.78
1996 2170 9.632638 ATTTTTGCCATAAGAGACTGTATATGT 57.367 29.630 0.00 0.00 0.00 2.29
1999 2173 8.706322 TTGCCATAAGAGACTGTATATGTAGA 57.294 34.615 0.00 0.00 0.00 2.59
2020 2194 9.647918 TGTAGATCTTCTTACTCATATGGTTCT 57.352 33.333 0.00 1.41 0.00 3.01
2259 2434 1.693606 TCTCATCAACCAGCAGTGACA 59.306 47.619 0.00 0.00 0.00 3.58
2260 2435 2.104622 TCTCATCAACCAGCAGTGACAA 59.895 45.455 0.00 0.00 0.00 3.18
2269 2445 0.609131 AGCAGTGACAATTTCCCCCG 60.609 55.000 0.00 0.00 0.00 5.73
2283 2459 1.213430 TCCCCCGAAACTGAAACTTGT 59.787 47.619 0.00 0.00 0.00 3.16
2299 2475 8.351495 TGAAACTTGTTGAAATAACATGCTTC 57.649 30.769 11.59 11.59 34.12 3.86
2434 2610 3.032459 GACGGGGAAAGAAGATACCTCT 58.968 50.000 0.00 0.00 0.00 3.69
2568 2782 3.411446 TGGTATCCATTTGATCATCGGC 58.589 45.455 0.00 0.00 34.76 5.54
2673 2888 1.049289 GCTACGGGTTCCAGATCCCT 61.049 60.000 11.22 2.78 41.40 4.20
2927 3142 2.900528 GCTTACCGTAGCGCATGAT 58.099 52.632 11.47 0.00 0.00 2.45
2954 3169 4.261888 GCCGAACAGAAGCGAGAA 57.738 55.556 0.00 0.00 0.00 2.87
2976 3191 3.331889 AGATTTTCACCCCTCATGTCTGT 59.668 43.478 0.00 0.00 0.00 3.41
2997 3212 2.726691 CGGTCGGATCGTGCACAAC 61.727 63.158 18.64 7.00 0.00 3.32
3135 3351 1.810151 GCTCATACGCCTGGTTTTGAA 59.190 47.619 0.00 0.00 0.00 2.69
3160 3376 3.004002 TGCTCAACTGCTCATGAACAAAG 59.996 43.478 0.00 0.00 0.00 2.77
3164 3380 4.639755 TCAACTGCTCATGAACAAAGTTGA 59.360 37.500 24.19 24.19 46.71 3.18
3180 3399 8.947055 ACAAAGTTGATGCTGTTTAAATTCTT 57.053 26.923 0.00 0.00 0.00 2.52
3245 3464 1.575447 AAGGGGGTGATCTGCTTCCC 61.575 60.000 0.00 0.00 39.22 3.97
3250 3469 3.008517 TGATCTGCTTCCCGGGCA 61.009 61.111 18.49 10.03 38.10 5.36
3253 3472 0.603975 GATCTGCTTCCCGGGCATAC 60.604 60.000 18.49 5.56 39.07 2.39
3396 3624 3.276642 AACCGCGTGGGGGCTATTT 62.277 57.895 21.14 0.00 41.60 1.40
3504 3732 3.190849 CACAGAGATGCACGGGCG 61.191 66.667 4.58 0.00 45.35 6.13
3565 3794 3.259374 CCTGGTAGAGCATGATCCGTATT 59.741 47.826 7.49 0.00 0.00 1.89
3586 3815 8.491152 CGTATTTTTGCAAATTTCCATGTGTTA 58.509 29.630 13.65 0.00 34.29 2.41
3587 3816 9.592720 GTATTTTTGCAAATTTCCATGTGTTAC 57.407 29.630 13.65 0.00 34.29 2.50
3589 3818 3.906998 TGCAAATTTCCATGTGTTACCG 58.093 40.909 0.00 0.00 0.00 4.02
3590 3819 3.319405 TGCAAATTTCCATGTGTTACCGT 59.681 39.130 0.00 0.00 0.00 4.83
3591 3820 3.917985 GCAAATTTCCATGTGTTACCGTC 59.082 43.478 0.00 0.00 0.00 4.79
3594 3823 5.622770 AATTTCCATGTGTTACCGTCTTC 57.377 39.130 0.00 0.00 0.00 2.87
3647 3912 6.752351 TCTTGATCTTCTATGTTGTTCGCTAC 59.248 38.462 0.00 0.00 0.00 3.58
3648 3913 5.961272 TGATCTTCTATGTTGTTCGCTACA 58.039 37.500 0.00 0.00 37.27 2.74
3659 3924 6.074642 TGTTGTTCGCTACATACATTTTTCG 58.925 36.000 0.00 0.00 36.44 3.46
3663 3928 6.092944 TGTTCGCTACATACATTTTTCGGAAT 59.907 34.615 0.00 0.00 0.00 3.01
3669 3934 8.774586 GCTACATACATTTTTCGGAATGTCTAT 58.225 33.333 13.39 3.98 44.65 1.98
3677 3942 3.819564 TCGGAATGTCTATTGTGGAGG 57.180 47.619 0.00 0.00 0.00 4.30
3698 3963 9.502091 TGGAGGTGTAAATATAATTGTGCTATC 57.498 33.333 0.00 0.00 0.00 2.08
3762 4029 7.767250 AGAGGAATTTTGGAAGACTTTTAGG 57.233 36.000 0.00 0.00 0.00 2.69
3770 4037 2.737252 GGAAGACTTTTAGGCGTGTGAG 59.263 50.000 0.00 0.00 0.00 3.51
3772 4039 3.746045 AGACTTTTAGGCGTGTGAGAA 57.254 42.857 0.00 0.00 0.00 2.87
3773 4040 3.654414 AGACTTTTAGGCGTGTGAGAAG 58.346 45.455 0.00 0.00 0.00 2.85
3774 4041 3.069729 AGACTTTTAGGCGTGTGAGAAGT 59.930 43.478 0.00 0.00 0.00 3.01
3775 4042 4.280174 AGACTTTTAGGCGTGTGAGAAGTA 59.720 41.667 0.00 0.00 0.00 2.24
3776 4043 5.047235 AGACTTTTAGGCGTGTGAGAAGTAT 60.047 40.000 0.00 0.00 0.00 2.12
3777 4044 6.152323 AGACTTTTAGGCGTGTGAGAAGTATA 59.848 38.462 0.00 0.00 0.00 1.47
3778 4045 6.098017 ACTTTTAGGCGTGTGAGAAGTATAC 58.902 40.000 0.00 0.00 0.00 1.47
3779 4046 2.846039 AGGCGTGTGAGAAGTATACG 57.154 50.000 0.00 0.00 36.03 3.06
3780 4047 2.089980 AGGCGTGTGAGAAGTATACGT 58.910 47.619 0.00 0.00 35.49 3.57
3781 4048 2.159421 AGGCGTGTGAGAAGTATACGTG 60.159 50.000 0.00 0.00 35.49 4.49
3782 4049 1.582502 GCGTGTGAGAAGTATACGTGC 59.417 52.381 0.00 0.00 35.49 5.34
3783 4050 1.838345 CGTGTGAGAAGTATACGTGCG 59.162 52.381 0.00 0.00 0.00 5.34
3784 4051 2.475022 CGTGTGAGAAGTATACGTGCGA 60.475 50.000 0.00 0.00 0.00 5.10
3785 4052 2.844804 GTGTGAGAAGTATACGTGCGAC 59.155 50.000 0.00 0.00 0.00 5.19
3786 4053 2.159476 TGTGAGAAGTATACGTGCGACC 60.159 50.000 0.00 0.00 0.00 4.79
3787 4054 1.402968 TGAGAAGTATACGTGCGACCC 59.597 52.381 0.00 0.00 0.00 4.46
3828 4095 5.107220 CGTAGAAGCCGTGTATTTGTTCTTT 60.107 40.000 0.00 0.00 0.00 2.52
3832 4099 6.261381 AGAAGCCGTGTATTTGTTCTTTACAA 59.739 34.615 0.00 0.00 44.81 2.41
3888 4155 2.037136 GCCACAATCGAGCAGCTGT 61.037 57.895 16.64 1.59 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 150 1.400737 GGGTCGTGGTACTGCTATCT 58.599 55.000 0.00 0.00 0.00 1.98
187 192 7.758076 CGTCCACATTGAGTTTGTAGTAATCTA 59.242 37.037 0.00 0.00 0.00 1.98
349 354 2.573462 TCTGAAAGTGCTAATGCCTCCT 59.427 45.455 0.00 0.00 38.71 3.69
1229 1242 1.282248 ACGTCTGTGTATGCGTGCAC 61.282 55.000 19.04 19.04 40.83 4.57
1230 1243 0.241481 TACGTCTGTGTATGCGTGCA 59.759 50.000 0.00 0.00 38.10 4.57
1244 1257 8.664211 AGAGGAGGATTTGATTAAATTACGTC 57.336 34.615 0.00 4.12 36.66 4.34
1303 1316 0.332632 TGGGGATTTGGAGGCAAGAG 59.667 55.000 0.00 0.00 0.00 2.85
1416 1429 2.103042 CGTGGCTGGCTGCTCTAAC 61.103 63.158 16.14 8.67 42.39 2.34
1484 1497 5.812127 TCATTCAGATAACAATGACGACAGG 59.188 40.000 0.00 0.00 34.71 4.00
1556 1625 4.515191 TCTTTCTTTGACCTGAACCAATCG 59.485 41.667 0.00 0.00 0.00 3.34
1582 1651 8.686334 GCCAAGGAAAATGTTCAATATTCTCTA 58.314 33.333 0.00 0.00 35.25 2.43
1583 1652 7.550712 GCCAAGGAAAATGTTCAATATTCTCT 58.449 34.615 0.00 0.00 35.25 3.10
1584 1653 6.473455 CGCCAAGGAAAATGTTCAATATTCTC 59.527 38.462 0.00 0.00 35.25 2.87
1608 1684 8.113062 GTCAATCTGTTCAGTATTTCAATCTCG 58.887 37.037 0.00 0.00 0.00 4.04
1717 1793 9.893305 CCAGTGGTTTTCTTTTACAGTATAAAG 57.107 33.333 0.00 8.08 33.65 1.85
1759 1836 8.248117 AGTAGTTCGGTAATAAACACATCAAC 57.752 34.615 0.00 0.00 0.00 3.18
1785 1863 7.125356 ACTCTGTTAATATTAAGGACTTCCGGT 59.875 37.037 8.18 1.92 42.08 5.28
1786 1864 7.498443 ACTCTGTTAATATTAAGGACTTCCGG 58.502 38.462 8.18 0.00 42.08 5.14
1791 1869 9.798994 CGTGTAACTCTGTTAATATTAAGGACT 57.201 33.333 8.18 2.26 31.75 3.85
1792 1870 9.028185 CCGTGTAACTCTGTTAATATTAAGGAC 57.972 37.037 8.18 0.00 31.75 3.85
1793 1871 8.970020 TCCGTGTAACTCTGTTAATATTAAGGA 58.030 33.333 8.18 8.82 31.75 3.36
1794 1872 9.245962 CTCCGTGTAACTCTGTTAATATTAAGG 57.754 37.037 8.18 5.23 31.75 2.69
1795 1873 9.798994 ACTCCGTGTAACTCTGTTAATATTAAG 57.201 33.333 8.18 0.00 31.75 1.85
1869 2034 9.846248 ACAAAATTTTCAGAACAGATGCTATAC 57.154 29.630 0.00 0.00 0.00 1.47
1906 2079 9.227777 GGCCTTCAGACTTTTAGTTAAGAAATA 57.772 33.333 0.00 0.00 0.00 1.40
1907 2080 7.945109 AGGCCTTCAGACTTTTAGTTAAGAAAT 59.055 33.333 0.00 0.00 0.00 2.17
1911 2084 6.594547 GGTAGGCCTTCAGACTTTTAGTTAAG 59.405 42.308 12.58 0.00 0.00 1.85
1912 2085 6.271624 AGGTAGGCCTTCAGACTTTTAGTTAA 59.728 38.462 12.58 0.00 44.18 2.01
1915 2088 4.168883 AGGTAGGCCTTCAGACTTTTAGT 58.831 43.478 12.58 0.00 44.18 2.24
1917 2090 6.203072 AGATAGGTAGGCCTTCAGACTTTTA 58.797 40.000 12.58 0.00 44.18 1.52
1929 2102 3.496870 CCCATTGACAAGATAGGTAGGCC 60.497 52.174 0.00 0.00 0.00 5.19
1949 2122 2.370849 TGAGACTGAGGTGGTAAAACCC 59.629 50.000 0.00 0.00 41.54 4.11
1951 2124 6.635030 AAAATGAGACTGAGGTGGTAAAAC 57.365 37.500 0.00 0.00 0.00 2.43
1964 2138 6.749923 GTCTCTTATGGCAAAAATGAGACT 57.250 37.500 22.62 0.00 42.99 3.24
1972 2146 9.764363 CTACATATACAGTCTCTTATGGCAAAA 57.236 33.333 0.00 0.00 0.00 2.44
2022 2196 9.445878 CTGCCATACAAGATATATCAAAGTGAT 57.554 33.333 15.08 0.00 40.72 3.06
2023 2197 8.650490 TCTGCCATACAAGATATATCAAAGTGA 58.350 33.333 15.08 1.07 0.00 3.41
2024 2198 8.837788 TCTGCCATACAAGATATATCAAAGTG 57.162 34.615 15.08 9.21 0.00 3.16
2025 2199 7.605691 GCTCTGCCATACAAGATATATCAAAGT 59.394 37.037 15.08 11.53 0.00 2.66
2259 2434 3.572642 AGTTTCAGTTTCGGGGGAAATT 58.427 40.909 0.00 0.00 32.52 1.82
2260 2435 3.238788 AGTTTCAGTTTCGGGGGAAAT 57.761 42.857 0.00 0.00 32.52 2.17
2299 2475 7.984391 TGTATGTTTGGCACTATCAGTATTTG 58.016 34.615 0.00 0.00 0.00 2.32
2434 2610 1.475403 GTCTCACAGGGAAGATCGGA 58.525 55.000 0.00 0.00 0.00 4.55
2568 2782 0.568888 GCATCAATTGCGTTGCATCG 59.431 50.000 12.78 12.78 42.54 3.84
2673 2888 1.118965 TGGCGAACTCCTTGTCCTCA 61.119 55.000 0.00 0.00 0.00 3.86
2856 3071 1.067354 GTGACGTACTTGGACCGGAAT 60.067 52.381 9.46 0.00 0.00 3.01
2954 3169 3.331889 ACAGACATGAGGGGTGAAAATCT 59.668 43.478 0.00 0.00 0.00 2.40
2997 3212 7.872163 TGAAAATTACAGCTTGTTTATGCAG 57.128 32.000 0.00 0.00 0.00 4.41
3056 3272 3.631145 TTCTTGACAAATGACTGCAGC 57.369 42.857 15.27 7.45 0.00 5.25
3135 3351 0.689055 TCATGAGCAGTTGAGCACCT 59.311 50.000 0.00 0.00 36.85 4.00
3225 3444 0.332972 GGAAGCAGATCACCCCCTTT 59.667 55.000 0.00 0.00 0.00 3.11
3226 3445 1.575447 GGGAAGCAGATCACCCCCTT 61.575 60.000 0.00 0.00 36.65 3.95
3227 3446 2.003548 GGGAAGCAGATCACCCCCT 61.004 63.158 0.00 0.00 36.65 4.79
3228 3447 2.597903 GGGAAGCAGATCACCCCC 59.402 66.667 0.00 0.00 36.65 5.40
3229 3448 2.190578 CGGGAAGCAGATCACCCC 59.809 66.667 0.00 0.00 39.20 4.95
3230 3449 2.190578 CCGGGAAGCAGATCACCC 59.809 66.667 0.00 0.00 39.02 4.61
3233 3452 1.053835 TATGCCCGGGAAGCAGATCA 61.054 55.000 29.31 10.65 44.90 2.92
3238 3457 2.589540 CAGTATGCCCGGGAAGCA 59.410 61.111 29.31 16.65 45.94 3.91
3239 3458 2.203209 CCAGTATGCCCGGGAAGC 60.203 66.667 29.31 11.81 31.97 3.86
3245 3464 0.179045 CCCTCTTTCCAGTATGCCCG 60.179 60.000 0.00 0.00 31.97 6.13
3250 3469 2.293586 TGGGCTACCCTCTTTCCAGTAT 60.294 50.000 3.93 0.00 45.70 2.12
3253 3472 0.543749 CTGGGCTACCCTCTTTCCAG 59.456 60.000 3.93 0.00 45.70 3.86
3391 3619 4.130118 CAGGGGAGAAATGACGGAAATAG 58.870 47.826 0.00 0.00 0.00 1.73
3392 3620 3.521937 ACAGGGGAGAAATGACGGAAATA 59.478 43.478 0.00 0.00 0.00 1.40
3396 3624 1.358152 AACAGGGGAGAAATGACGGA 58.642 50.000 0.00 0.00 0.00 4.69
3504 3732 2.396157 CGCTCCGTTAGGGCCAAAC 61.396 63.158 6.18 7.68 38.33 2.93
3565 3794 5.235186 CGGTAACACATGGAAATTTGCAAAA 59.765 36.000 17.19 0.00 30.51 2.44
3586 3815 4.581077 ACGAAAAGAGTTAGAAGACGGT 57.419 40.909 0.00 0.00 0.00 4.83
3587 3816 6.091437 ACATACGAAAAGAGTTAGAAGACGG 58.909 40.000 0.00 0.00 0.00 4.79
3647 3912 9.225201 CACAATAGACATTCCGAAAAATGTATG 57.775 33.333 12.58 10.58 46.99 2.39
3648 3913 8.405531 CCACAATAGACATTCCGAAAAATGTAT 58.594 33.333 9.71 9.51 46.99 2.29
3659 3924 4.222124 ACACCTCCACAATAGACATTCC 57.778 45.455 0.00 0.00 0.00 3.01
3669 3934 7.613801 AGCACAATTATATTTACACCTCCACAA 59.386 33.333 0.00 0.00 0.00 3.33
3670 3935 7.116075 AGCACAATTATATTTACACCTCCACA 58.884 34.615 0.00 0.00 0.00 4.17
3698 3963 4.392138 GGTGTCCTTTTCTTAACGAGGATG 59.608 45.833 0.00 0.00 40.21 3.51
3762 4029 1.582502 GCACGTATACTTCTCACACGC 59.417 52.381 0.56 0.00 36.11 5.34
3770 4037 2.282701 TTGGGTCGCACGTATACTTC 57.717 50.000 0.56 0.00 0.00 3.01
3772 4039 2.747396 TTTTGGGTCGCACGTATACT 57.253 45.000 0.56 0.00 0.00 2.12
3773 4040 2.995258 TCTTTTTGGGTCGCACGTATAC 59.005 45.455 0.00 0.00 0.00 1.47
3774 4041 3.316071 TCTTTTTGGGTCGCACGTATA 57.684 42.857 0.00 0.00 0.00 1.47
3775 4042 2.172851 TCTTTTTGGGTCGCACGTAT 57.827 45.000 0.00 0.00 0.00 3.06
3776 4043 2.172851 ATCTTTTTGGGTCGCACGTA 57.827 45.000 0.00 0.00 0.00 3.57
3777 4044 1.265905 GAATCTTTTTGGGTCGCACGT 59.734 47.619 0.00 0.00 0.00 4.49
3778 4045 1.401018 GGAATCTTTTTGGGTCGCACG 60.401 52.381 0.00 0.00 0.00 5.34
3779 4046 1.611491 TGGAATCTTTTTGGGTCGCAC 59.389 47.619 0.00 0.00 0.00 5.34
3780 4047 1.988293 TGGAATCTTTTTGGGTCGCA 58.012 45.000 0.00 0.00 0.00 5.10
3781 4048 3.486875 CGTATGGAATCTTTTTGGGTCGC 60.487 47.826 0.00 0.00 0.00 5.19
3782 4049 3.486875 GCGTATGGAATCTTTTTGGGTCG 60.487 47.826 0.00 0.00 0.00 4.79
3783 4050 3.486875 CGCGTATGGAATCTTTTTGGGTC 60.487 47.826 0.00 0.00 0.00 4.46
3784 4051 2.422127 CGCGTATGGAATCTTTTTGGGT 59.578 45.455 0.00 0.00 0.00 4.51
3785 4052 2.422127 ACGCGTATGGAATCTTTTTGGG 59.578 45.455 11.67 0.00 0.00 4.12
3786 4053 3.757745 ACGCGTATGGAATCTTTTTGG 57.242 42.857 11.67 0.00 0.00 3.28
3787 4054 5.712217 TCTACGCGTATGGAATCTTTTTG 57.288 39.130 20.91 3.13 0.00 2.44
3828 4095 9.146984 GGCGTCATAGCATAGTATTATTTTGTA 57.853 33.333 0.00 0.00 39.27 2.41
3832 4099 9.751542 GATAGGCGTCATAGCATAGTATTATTT 57.248 33.333 0.00 0.00 36.81 1.40


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

AutoCloner maintained by Alex Coulton.