Multiple sequence alignment - TraesCS2B01G204800

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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 TraesCS2B01G204800 chr2B 100.000 6053 0 0 1 6053 184488796 184494848 0.000000e+00 11178.0
1 TraesCS2B01G204800 chr2A 93.536 4069 129 44 2044 6032 137125351 137129365 0.000000e+00 5934.0
2 TraesCS2B01G204800 chr2A 91.706 1278 69 13 765 2018 137124089 137125353 0.000000e+00 1738.0
3 TraesCS2B01G204800 chr2D 93.232 3679 128 37 2434 6034 130984316 130987951 0.000000e+00 5302.0
4 TraesCS2B01G204800 chr2D 90.967 1893 109 29 578 2434 130982382 130984248 0.000000e+00 2492.0
5 TraesCS2B01G204800 chr2D 89.304 991 65 17 36 999 130892199 130893175 0.000000e+00 1205.0
6 TraesCS2B01G204800 chr2D 89.164 849 73 10 1010 1847 645265428 645264588 0.000000e+00 1040.0
7 TraesCS2B01G204800 chr2D 94.143 461 20 7 5575 6034 131041860 131042314 0.000000e+00 695.0
8 TraesCS2B01G204800 chr2D 91.204 216 18 1 1844 2058 645256289 645256074 5.930000e-75 292.0
9 TraesCS2B01G204800 chr2D 82.201 309 31 16 4995 5280 131041425 131041732 1.690000e-60 244.0
10 TraesCS2B01G204800 chr2D 83.412 211 32 3 4682 4892 131123895 131124102 6.190000e-45 193.0
11 TraesCS2B01G204800 chr5A 92.683 41 3 0 576 616 622993519 622993559 6.550000e-05 60.2


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 TraesCS2B01G204800 chr2B 184488796 184494848 6052 False 11178.0 11178 100.0000 1 6053 1 chr2B.!!$F1 6052
1 TraesCS2B01G204800 chr2A 137124089 137129365 5276 False 3836.0 5934 92.6210 765 6032 2 chr2A.!!$F1 5267
2 TraesCS2B01G204800 chr2D 130982382 130987951 5569 False 3897.0 5302 92.0995 578 6034 2 chr2D.!!$F3 5456
3 TraesCS2B01G204800 chr2D 130892199 130893175 976 False 1205.0 1205 89.3040 36 999 1 chr2D.!!$F1 963
4 TraesCS2B01G204800 chr2D 645264588 645265428 840 True 1040.0 1040 89.1640 1010 1847 1 chr2D.!!$R2 837
5 TraesCS2B01G204800 chr2D 131041425 131042314 889 False 469.5 695 88.1720 4995 6034 2 chr2D.!!$F4 1039

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
33 34 0.104120 ACGCCGCAATAGCTACATCA 59.896 50.000 0.00 0.00 39.10 3.07 F
1609 1670 0.099436 CTAAGGACTTGCGGCAATGC 59.901 55.000 16.80 10.79 0.00 3.56 F
1618 1679 1.304254 TGCGGCAATGCGTGTATTAT 58.696 45.000 0.00 0.00 37.81 1.28 F
1760 1826 1.500396 GTTTTAGTTGAGCCGGCGG 59.500 57.895 24.35 24.35 0.00 6.13 F
2452 2598 2.915604 ACTATATCATTCTGGGGCTGGG 59.084 50.000 0.00 0.00 0.00 4.45 F
3384 3566 3.058708 ACTTGATCTGATGTTGCACAACG 60.059 43.478 8.85 0.00 43.94 4.10 F
4062 4272 2.972021 TCGGCATCTTGGGATCATTCTA 59.028 45.455 0.00 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1821 1.014352 CCTCATTTTAACCTCCGCCG 58.986 55.000 0.00 0.0 0.00 6.46 R
3549 3732 3.768757 CTGAGACTCTTCAGGTCCAGATT 59.231 47.826 3.68 0.0 40.69 2.40 R
3615 3798 4.306600 CACACAGGCATTACGCATATAGA 58.693 43.478 0.00 0.0 45.17 1.98 R
3677 3860 3.059166 GGAACGAAACGTACTTGGCTTA 58.941 45.455 0.00 0.0 39.99 3.09 R
4062 4272 1.153086 GAGCATCCCACTGCCGAAT 60.153 57.895 0.00 0.0 43.33 3.34 R
4462 4673 1.065564 GCAATCAGTGAAGAGCCCTCT 60.066 52.381 0.00 0.0 42.75 3.69 R
5682 5955 0.178964 TTTGGGTCAGGAAAGGGCAG 60.179 55.000 0.00 0.0 0.00 4.85 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
26 27 1.385409 GTTTTCAAACGCCGCAATAGC 59.615 47.619 0.00 0.00 37.42 2.97
27 28 0.878416 TTTCAAACGCCGCAATAGCT 59.122 45.000 0.00 0.00 39.10 3.32
28 29 1.728068 TTCAAACGCCGCAATAGCTA 58.272 45.000 0.00 0.00 39.10 3.32
29 30 1.003851 TCAAACGCCGCAATAGCTAC 58.996 50.000 0.00 0.00 39.10 3.58
30 31 0.724549 CAAACGCCGCAATAGCTACA 59.275 50.000 0.00 0.00 39.10 2.74
31 32 1.330521 CAAACGCCGCAATAGCTACAT 59.669 47.619 0.00 0.00 39.10 2.29
32 33 1.217882 AACGCCGCAATAGCTACATC 58.782 50.000 0.00 0.00 39.10 3.06
33 34 0.104120 ACGCCGCAATAGCTACATCA 59.896 50.000 0.00 0.00 39.10 3.07
34 35 1.217001 CGCCGCAATAGCTACATCAA 58.783 50.000 0.00 0.00 39.10 2.57
48 49 4.201891 GCTACATCAATCCTGCACTCTTTG 60.202 45.833 0.00 0.00 0.00 2.77
88 89 1.743394 CGGGATTTTTGGAGCACTACC 59.257 52.381 0.00 0.00 0.00 3.18
89 90 2.802719 GGGATTTTTGGAGCACTACCA 58.197 47.619 0.00 0.00 35.47 3.25
91 92 3.193479 GGGATTTTTGGAGCACTACCAAG 59.807 47.826 0.00 0.00 46.05 3.61
102 103 2.073816 CACTACCAAGCCCTTGTAACG 58.926 52.381 7.21 0.00 38.85 3.18
167 168 2.380941 ACGCCCAAGTACCAACTTTTT 58.619 42.857 0.00 0.00 43.60 1.94
192 193 6.437928 TGTGACAATACTTGCATTGTTTCTC 58.562 36.000 4.98 0.00 46.53 2.87
196 197 8.845227 TGACAATACTTGCATTGTTTCTCTTTA 58.155 29.630 4.98 0.00 46.53 1.85
201 202 7.750229 ACTTGCATTGTTTCTCTTTATCTCA 57.250 32.000 0.00 0.00 0.00 3.27
241 242 9.952030 TCTGTACTTTGTATTGATTATGGTTGA 57.048 29.630 0.00 0.00 0.00 3.18
260 261 4.850859 TGAAAACAACAGTACACGTCAG 57.149 40.909 0.00 0.00 0.00 3.51
261 262 4.496360 TGAAAACAACAGTACACGTCAGA 58.504 39.130 0.00 0.00 0.00 3.27
278 279 4.245660 GTCAGATGAGAACCGACATTTGA 58.754 43.478 0.00 0.00 36.03 2.69
279 280 4.092091 GTCAGATGAGAACCGACATTTGAC 59.908 45.833 12.43 12.43 44.67 3.18
281 282 4.092529 CAGATGAGAACCGACATTTGACTG 59.907 45.833 0.00 0.00 32.71 3.51
288 289 1.679944 CCGACATTTGACTGGATGGCT 60.680 52.381 0.00 0.00 0.00 4.75
338 339 2.766828 AGGGATCAAACTCTAGGTTCGG 59.233 50.000 0.00 0.00 37.12 4.30
342 343 0.389948 CAAACTCTAGGTTCGGCGCT 60.390 55.000 7.64 0.00 37.12 5.92
346 347 0.108804 CTCTAGGTTCGGCGCTTTGA 60.109 55.000 7.64 0.00 0.00 2.69
438 441 0.635555 GACAGGGGACTAGTAGGGGT 59.364 60.000 0.00 0.00 40.21 4.95
484 487 2.191981 TCCTATCTTTGACCCTCCCC 57.808 55.000 0.00 0.00 0.00 4.81
493 496 4.107311 TCTTTGACCCTCCCCAAAGTATTT 59.893 41.667 12.65 0.00 45.57 1.40
498 501 3.096852 CCCTCCCCAAAGTATTTTGACC 58.903 50.000 11.94 0.00 45.21 4.02
499 502 3.096852 CCTCCCCAAAGTATTTTGACCC 58.903 50.000 11.94 0.00 45.21 4.46
501 504 2.184533 CCCCAAAGTATTTTGACCCCC 58.815 52.381 11.94 0.00 45.21 5.40
606 624 6.564557 TCATAGGGATAAGATATGCATGCA 57.435 37.500 25.04 25.04 0.00 3.96
718 743 3.670105 CTGGTAATGGGCCAGTGTT 57.330 52.632 18.22 6.40 46.22 3.32
721 746 2.238646 CTGGTAATGGGCCAGTGTTCTA 59.761 50.000 18.22 4.29 46.22 2.10
729 754 1.448540 CCAGTGTTCTAGGCCAGCG 60.449 63.158 5.01 0.00 0.00 5.18
752 777 2.170434 GCTCAGCAGCGCTCCTAAC 61.170 63.158 7.13 0.00 36.40 2.34
753 778 1.520342 CTCAGCAGCGCTCCTAACC 60.520 63.158 7.13 0.00 36.40 2.85
794 819 5.705441 CCCAGAACAATGTAAGTAAGCTTGA 59.295 40.000 9.86 0.00 36.22 3.02
815 840 2.682856 AGCGGAAATGCAATAACACGAT 59.317 40.909 0.00 0.00 37.31 3.73
817 842 4.515191 AGCGGAAATGCAATAACACGATAT 59.485 37.500 0.00 0.00 37.31 1.63
820 845 6.128661 GCGGAAATGCAATAACACGATATCTA 60.129 38.462 0.34 0.00 34.15 1.98
876 912 2.683933 GCTCCTCCGAGTTCCCCA 60.684 66.667 0.00 0.00 38.49 4.96
887 924 2.046023 TTCCCCATCGCTGCAGTG 60.046 61.111 21.43 21.43 0.00 3.66
1204 1251 3.255725 TCGGTATGACGCGAATTTTTCT 58.744 40.909 15.93 0.00 0.00 2.52
1358 1408 4.438200 GCGGTAATGAATTCGTGTTTGGAT 60.438 41.667 0.00 0.00 0.00 3.41
1359 1409 5.636837 CGGTAATGAATTCGTGTTTGGATT 58.363 37.500 0.00 0.00 0.00 3.01
1387 1438 5.453567 AATTTTAGAGGTGTTTCTGTGCC 57.546 39.130 0.00 0.00 0.00 5.01
1502 1555 0.255890 GGAAGCAGGAGCCACCATTA 59.744 55.000 0.47 0.00 43.56 1.90
1609 1670 0.099436 CTAAGGACTTGCGGCAATGC 59.901 55.000 16.80 10.79 0.00 3.56
1618 1679 1.304254 TGCGGCAATGCGTGTATTAT 58.696 45.000 0.00 0.00 37.81 1.28
1745 1811 4.277423 CCATTTTCGGTTCACAGTAGGTTT 59.723 41.667 0.00 0.00 0.00 3.27
1755 1821 4.638304 TCACAGTAGGTTTTAGTTGAGCC 58.362 43.478 0.00 0.00 0.00 4.70
1760 1826 1.500396 GTTTTAGTTGAGCCGGCGG 59.500 57.895 24.35 24.35 0.00 6.13
1801 1867 3.947196 TCATCGGTCTGCTTGCATAAATT 59.053 39.130 0.00 0.00 0.00 1.82
1861 1927 5.772169 CCTCTCTATATCATGTCCACACTGA 59.228 44.000 0.00 0.00 0.00 3.41
1895 1961 3.959495 AGCAGGGGATATGTTGTGATT 57.041 42.857 0.00 0.00 0.00 2.57
1905 1971 7.496591 GGGGATATGTTGTGATTAAGTCGTAAA 59.503 37.037 0.00 0.00 0.00 2.01
1926 1992 4.392921 AACTGAGGGACGATAACATCAG 57.607 45.455 4.98 4.98 39.96 2.90
2190 2256 3.876309 ACTTTCCTGCCAAGAAGGTTA 57.124 42.857 0.00 0.00 40.61 2.85
2452 2598 2.915604 ACTATATCATTCTGGGGCTGGG 59.084 50.000 0.00 0.00 0.00 4.45
2514 2660 6.195600 ACTAACCCAACTGAAATCCTGTAA 57.804 37.500 0.00 0.00 0.00 2.41
2558 2704 5.795972 TCAACCGGATCAGTATTGTACAAA 58.204 37.500 13.23 0.00 0.00 2.83
2592 2766 7.851387 TCGTTTACTTGATATGCATAAACCA 57.149 32.000 11.13 6.61 32.28 3.67
2593 2767 8.270080 TCGTTTACTTGATATGCATAAACCAA 57.730 30.769 11.13 13.40 32.28 3.67
2809 2986 8.436046 AAACAGTGTCAATTGTTGCATAAAAT 57.564 26.923 5.13 0.00 36.46 1.82
3034 3212 3.838244 TCCTACCATTGCCAGTATCAC 57.162 47.619 0.00 0.00 0.00 3.06
3384 3566 3.058708 ACTTGATCTGATGTTGCACAACG 60.059 43.478 8.85 0.00 43.94 4.10
3549 3732 6.617782 AAAGAGAAGGATGAACTCTGATGA 57.382 37.500 0.00 0.00 40.28 2.92
3615 3798 7.839680 ATGTTCTAATCCAAGTTCTTGGTTT 57.160 32.000 24.87 23.78 42.62 3.27
3694 3877 6.399204 AGTTAATAAGCCAAGTACGTTTCG 57.601 37.500 0.00 0.00 0.00 3.46
3710 3893 8.598075 AGTACGTTTCGTTCCATTTTGTATATC 58.402 33.333 0.00 0.00 41.54 1.63
3712 3895 8.706492 ACGTTTCGTTCCATTTTGTATATCTA 57.294 30.769 0.00 0.00 36.35 1.98
3718 3901 9.309516 TCGTTCCATTTTGTATATCTAGTGTTC 57.690 33.333 0.00 0.00 0.00 3.18
3825 4011 7.095313 GGTTCTGTTAAAGTTGTAAGCTACTCC 60.095 40.741 0.00 0.00 30.70 3.85
3878 4068 5.815233 TTCCAGTTATTTGAAAATGGGCA 57.185 34.783 3.55 0.00 43.22 5.36
3898 4088 4.067192 GCATGGGCTTGTTTTTGAAATCT 58.933 39.130 0.00 0.00 36.96 2.40
3899 4089 4.083696 GCATGGGCTTGTTTTTGAAATCTG 60.084 41.667 0.00 0.00 36.96 2.90
3900 4090 4.070630 TGGGCTTGTTTTTGAAATCTGG 57.929 40.909 0.00 0.00 0.00 3.86
4062 4272 2.972021 TCGGCATCTTGGGATCATTCTA 59.028 45.455 0.00 0.00 0.00 2.10
4235 4445 6.659242 GGGATAGGAACAACTTTTCAATCTGA 59.341 38.462 0.00 0.00 0.00 3.27
4259 4469 8.535335 TGAGTGCTGATTTTCTAGTTTATCTCT 58.465 33.333 0.00 0.00 0.00 3.10
4260 4470 8.940768 AGTGCTGATTTTCTAGTTTATCTCTC 57.059 34.615 0.00 0.00 0.00 3.20
4341 4551 7.125811 ACAGTCCATACAGTATATTTGTCCAGT 59.874 37.037 0.00 0.00 0.00 4.00
4357 4567 5.762279 TGTCCAGTGGTCATATGACTAGTA 58.238 41.667 29.87 13.94 44.20 1.82
4462 4673 2.746279 ATTGTTTGGACTGTGGTGGA 57.254 45.000 0.00 0.00 0.00 4.02
4632 4843 4.003648 CAGGAACGACAGCTCCTATTTTT 58.996 43.478 0.00 0.00 40.80 1.94
4815 5026 4.768145 TCTTTCAAATCACTGCGTAAACG 58.232 39.130 0.00 0.00 43.27 3.60
4885 5096 5.045869 TGGACTCCCACAAAGATAAGGTAAG 60.046 44.000 0.00 0.00 37.58 2.34
4909 5121 7.731054 AGCTTTTCATTTTGTGGTTACCATTA 58.269 30.769 7.58 0.00 35.28 1.90
4924 5136 6.354130 GTTACCATTAGCATACTTCTGGGAA 58.646 40.000 0.00 0.00 32.93 3.97
4925 5137 5.450818 ACCATTAGCATACTTCTGGGAAA 57.549 39.130 0.00 0.00 32.93 3.13
5419 5658 5.726980 TTGTGCTCCTTATTTGCTGAAAT 57.273 34.783 0.00 0.00 35.83 2.17
5526 5775 5.500131 GCTTCGGCAACTTTTTGTTTTACTG 60.500 40.000 0.00 0.00 41.33 2.74
5633 5906 2.429930 GTACCTGCCCTGCACACA 59.570 61.111 0.00 0.00 33.79 3.72
5651 5924 3.127533 GCATCTGCACGGTGTCCC 61.128 66.667 10.24 0.00 41.59 4.46
5682 5955 4.218852 AGCCTAAACAGACAGAGTACAGAC 59.781 45.833 0.00 0.00 0.00 3.51
5704 5978 1.272704 GCCCTTTCCTGACCCAAATCT 60.273 52.381 0.00 0.00 0.00 2.40
5790 6064 2.588877 ACTTTCTGCGCACGCTGT 60.589 55.556 16.77 0.02 42.51 4.40
5839 6116 1.273267 ACCTGCTATCTCTCCCACACA 60.273 52.381 0.00 0.00 0.00 3.72
5840 6117 1.833630 CCTGCTATCTCTCCCACACAA 59.166 52.381 0.00 0.00 0.00 3.33
6035 6315 4.659172 CCACCGCTTCCCAAGGCA 62.659 66.667 0.00 0.00 0.00 4.75
6036 6316 3.365265 CACCGCTTCCCAAGGCAC 61.365 66.667 0.00 0.00 0.00 5.01
6037 6317 4.660938 ACCGCTTCCCAAGGCACC 62.661 66.667 0.00 0.00 0.00 5.01
6040 6320 2.597510 GCTTCCCAAGGCACCGTT 60.598 61.111 0.00 0.00 0.00 4.44
6041 6321 2.626780 GCTTCCCAAGGCACCGTTC 61.627 63.158 0.00 0.00 0.00 3.95
6042 6322 1.971695 CTTCCCAAGGCACCGTTCC 60.972 63.158 0.00 0.00 0.00 3.62
6043 6323 3.501040 TTCCCAAGGCACCGTTCCC 62.501 63.158 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.385409 GCTATTGCGGCGTTTGAAAAC 59.615 47.619 9.37 0.00 35.59 2.43
7 8 1.268352 AGCTATTGCGGCGTTTGAAAA 59.732 42.857 9.37 0.00 45.42 2.29
8 9 0.878416 AGCTATTGCGGCGTTTGAAA 59.122 45.000 9.37 0.00 45.42 2.69
9 10 1.395608 GTAGCTATTGCGGCGTTTGAA 59.604 47.619 9.37 0.00 45.42 2.69
10 11 1.003851 GTAGCTATTGCGGCGTTTGA 58.996 50.000 9.37 0.00 45.42 2.69
11 12 0.724549 TGTAGCTATTGCGGCGTTTG 59.275 50.000 9.37 0.00 45.42 2.93
12 13 1.597663 GATGTAGCTATTGCGGCGTTT 59.402 47.619 9.37 0.00 45.42 3.60
13 14 1.217882 GATGTAGCTATTGCGGCGTT 58.782 50.000 9.37 0.00 45.42 4.84
14 15 0.104120 TGATGTAGCTATTGCGGCGT 59.896 50.000 9.37 0.00 45.42 5.68
15 16 1.217001 TTGATGTAGCTATTGCGGCG 58.783 50.000 0.51 0.51 45.42 6.46
16 17 2.160417 GGATTGATGTAGCTATTGCGGC 59.840 50.000 0.00 0.00 45.42 6.53
17 18 3.434641 CAGGATTGATGTAGCTATTGCGG 59.565 47.826 0.00 0.00 45.42 5.69
18 19 3.120408 GCAGGATTGATGTAGCTATTGCG 60.120 47.826 0.00 0.00 45.42 4.85
19 20 3.817084 TGCAGGATTGATGTAGCTATTGC 59.183 43.478 0.00 0.00 40.05 3.56
20 21 5.061853 AGTGCAGGATTGATGTAGCTATTG 58.938 41.667 0.00 0.00 0.00 1.90
21 22 5.071519 AGAGTGCAGGATTGATGTAGCTATT 59.928 40.000 0.00 0.00 0.00 1.73
22 23 4.592351 AGAGTGCAGGATTGATGTAGCTAT 59.408 41.667 0.00 0.00 0.00 2.97
23 24 3.963374 AGAGTGCAGGATTGATGTAGCTA 59.037 43.478 0.00 0.00 0.00 3.32
24 25 2.770802 AGAGTGCAGGATTGATGTAGCT 59.229 45.455 0.00 0.00 0.00 3.32
25 26 3.191078 AGAGTGCAGGATTGATGTAGC 57.809 47.619 0.00 0.00 0.00 3.58
26 27 5.481200 CAAAGAGTGCAGGATTGATGTAG 57.519 43.478 0.00 0.00 0.00 2.74
48 49 6.228258 TCCCGGAACAAATATATACAAGAGC 58.772 40.000 0.73 0.00 0.00 4.09
58 59 5.395214 GCTCCAAAAATCCCGGAACAAATAT 60.395 40.000 0.73 0.00 0.00 1.28
88 89 1.084289 GCTACCGTTACAAGGGCTTG 58.916 55.000 0.66 0.00 45.58 4.01
89 90 0.981943 AGCTACCGTTACAAGGGCTT 59.018 50.000 0.66 0.00 37.46 4.35
91 92 1.084289 CAAGCTACCGTTACAAGGGC 58.916 55.000 0.66 0.00 37.46 5.19
127 128 1.581934 TTCTTCACTTCACTGCCGTG 58.418 50.000 1.20 1.20 42.59 4.94
128 129 1.940613 GTTTCTTCACTTCACTGCCGT 59.059 47.619 0.00 0.00 0.00 5.68
175 176 9.453572 TGAGATAAAGAGAAACAATGCAAGTAT 57.546 29.630 0.00 0.00 0.00 2.12
182 183 7.818493 TCGAGTGAGATAAAGAGAAACAATG 57.182 36.000 0.00 0.00 0.00 2.82
192 193 8.754096 CAGATCTTTGAATCGAGTGAGATAAAG 58.246 37.037 0.00 0.00 31.98 1.85
196 197 6.219417 ACAGATCTTTGAATCGAGTGAGAT 57.781 37.500 0.00 0.00 0.00 2.75
241 242 5.113383 TCATCTGACGTGTACTGTTGTTTT 58.887 37.500 0.00 0.00 0.00 2.43
256 257 4.092091 GTCAAATGTCGGTTCTCATCTGAC 59.908 45.833 0.00 0.00 35.75 3.51
260 261 3.372206 CCAGTCAAATGTCGGTTCTCATC 59.628 47.826 0.00 0.00 0.00 2.92
261 262 3.007940 TCCAGTCAAATGTCGGTTCTCAT 59.992 43.478 0.00 0.00 0.00 2.90
278 279 0.339859 TGTCCTCCTAGCCATCCAGT 59.660 55.000 0.00 0.00 0.00 4.00
279 280 1.500474 TTGTCCTCCTAGCCATCCAG 58.500 55.000 0.00 0.00 0.00 3.86
281 282 1.072965 CCATTGTCCTCCTAGCCATCC 59.927 57.143 0.00 0.00 0.00 3.51
316 317 3.197983 CCGAACCTAGAGTTTGATCCCTT 59.802 47.826 11.06 0.00 41.81 3.95
338 339 4.404507 TCTTTACAAGATGTCAAAGCGC 57.595 40.909 0.00 0.00 31.20 5.92
380 383 4.052608 TCTTGCTATTGACGAAAACGTCA 58.947 39.130 18.89 18.89 45.63 4.35
393 396 0.246635 ACTGCGGACGTCTTGCTATT 59.753 50.000 25.75 12.66 0.00 1.73
429 432 0.397254 GCAGAGCCAGACCCCTACTA 60.397 60.000 0.00 0.00 0.00 1.82
438 441 2.346766 TTTTGAACAGCAGAGCCAGA 57.653 45.000 0.00 0.00 0.00 3.86
499 502 3.339093 GGTGTTGGGAGGAGGGGG 61.339 72.222 0.00 0.00 0.00 5.40
501 504 1.725169 TTTGGGTGTTGGGAGGAGGG 61.725 60.000 0.00 0.00 0.00 4.30
503 506 2.080654 TTTTTGGGTGTTGGGAGGAG 57.919 50.000 0.00 0.00 0.00 3.69
606 624 7.236529 ACATATACTCTTCCCAATGAATGCAT 58.763 34.615 0.00 0.00 35.92 3.96
642 660 6.514063 ACCTGTACTGTTTTTCTAGAGACAC 58.486 40.000 0.00 0.00 0.00 3.67
680 705 2.910319 AGCTGGGACCTGTAATGTGTTA 59.090 45.455 0.00 0.00 0.00 2.41
681 706 1.705186 AGCTGGGACCTGTAATGTGTT 59.295 47.619 0.00 0.00 0.00 3.32
682 707 1.003580 CAGCTGGGACCTGTAATGTGT 59.996 52.381 5.57 0.00 0.00 3.72
683 708 1.679944 CCAGCTGGGACCTGTAATGTG 60.680 57.143 26.14 0.00 40.01 3.21
684 709 0.620556 CCAGCTGGGACCTGTAATGT 59.379 55.000 26.14 0.00 40.01 2.71
740 765 0.818296 AGTGTAGGTTAGGAGCGCTG 59.182 55.000 18.48 0.00 0.00 5.18
741 766 0.818296 CAGTGTAGGTTAGGAGCGCT 59.182 55.000 11.27 11.27 0.00 5.92
742 767 0.179108 CCAGTGTAGGTTAGGAGCGC 60.179 60.000 0.00 0.00 0.00 5.92
743 768 0.460311 CCCAGTGTAGGTTAGGAGCG 59.540 60.000 0.00 0.00 0.00 5.03
744 769 0.178301 GCCCAGTGTAGGTTAGGAGC 59.822 60.000 0.00 0.00 0.00 4.70
748 773 1.568504 TCTGGCCCAGTGTAGGTTAG 58.431 55.000 11.27 0.00 32.61 2.34
749 774 1.906574 CTTCTGGCCCAGTGTAGGTTA 59.093 52.381 11.27 0.00 32.61 2.85
750 775 0.693049 CTTCTGGCCCAGTGTAGGTT 59.307 55.000 11.27 0.00 32.61 3.50
752 777 1.078143 GCTTCTGGCCCAGTGTAGG 60.078 63.158 11.27 0.00 32.61 3.18
753 778 4.625800 GCTTCTGGCCCAGTGTAG 57.374 61.111 11.27 8.13 32.61 2.74
794 819 2.080693 TCGTGTTATTGCATTTCCGCT 58.919 42.857 0.00 0.00 0.00 5.52
859 888 2.034048 GATGGGGAACTCGGAGGAGC 62.034 65.000 10.23 0.00 44.48 4.70
1039 1086 4.087892 AGGCGGCAGCTTCGTGAT 62.088 61.111 13.08 0.00 44.37 3.06
1204 1251 3.989817 GAGCGACCGGTTTAGTAGAAAAA 59.010 43.478 9.42 0.00 0.00 1.94
1366 1417 4.469657 TGGCACAGAAACACCTCTAAAAT 58.530 39.130 0.00 0.00 0.00 1.82
1387 1438 3.641437 ATTTTCACAACCACGTCCATG 57.359 42.857 0.00 0.00 0.00 3.66
1502 1555 1.275291 CTAACCCAGTCATCGTGTGGT 59.725 52.381 0.00 0.00 0.00 4.16
1609 1670 8.826710 ACTTCATCCAATTGTACATAATACACG 58.173 33.333 4.43 0.00 0.00 4.49
1618 1679 3.760738 TGCCACTTCATCCAATTGTACA 58.239 40.909 4.43 0.00 0.00 2.90
1710 1776 1.132262 CGAAAATGGACACAATCGGGG 59.868 52.381 0.00 0.00 31.69 5.73
1711 1777 1.132262 CCGAAAATGGACACAATCGGG 59.868 52.381 11.44 0.00 42.62 5.14
1712 1778 2.542766 CCGAAAATGGACACAATCGG 57.457 50.000 0.00 0.00 41.57 4.18
1713 1779 3.058570 TGAACCGAAAATGGACACAATCG 60.059 43.478 0.00 0.00 33.68 3.34
1718 1784 2.616842 ACTGTGAACCGAAAATGGACAC 59.383 45.455 0.00 0.00 38.87 3.67
1745 1811 2.577059 CTCCGCCGGCTCAACTAA 59.423 61.111 26.68 0.38 0.00 2.24
1755 1821 1.014352 CCTCATTTTAACCTCCGCCG 58.986 55.000 0.00 0.00 0.00 6.46
1760 1826 6.148480 CCGATGATGATCCTCATTTTAACCTC 59.852 42.308 13.84 0.59 37.20 3.85
1847 1913 2.046292 TGGAAGTCAGTGTGGACATGA 58.954 47.619 0.00 0.00 40.29 3.07
1861 1927 1.625818 CCCTGCTTCTACAGTGGAAGT 59.374 52.381 23.48 0.00 41.36 3.01
1895 1961 3.820467 TCGTCCCTCAGTTTTACGACTTA 59.180 43.478 0.00 0.00 37.63 2.24
1905 1971 3.430929 GCTGATGTTATCGTCCCTCAGTT 60.431 47.826 0.00 0.00 34.13 3.16
2097 2163 7.703058 ACCTTCATAAATCGTTTCCTTGATT 57.297 32.000 0.00 0.00 36.41 2.57
2217 2283 5.235305 AGCCATAAACGTTCTATTGCTTG 57.765 39.130 16.24 3.23 26.42 4.01
2310 2376 5.780958 AGGGTTAGCTCCTTTTAGTTGAT 57.219 39.130 0.00 0.00 0.00 2.57
2311 2377 5.578157 AAGGGTTAGCTCCTTTTAGTTGA 57.422 39.130 0.00 0.00 41.47 3.18
2452 2598 6.198216 TGTTGAATCTTTTAACTCGCAAAAGC 59.802 34.615 3.29 0.00 40.97 3.51
2485 2631 6.002082 GGATTTCAGTTGGGTTAGTTAGTGT 58.998 40.000 0.00 0.00 0.00 3.55
2514 2660 7.039714 GGTTGAGACACCAAAGAGGATATTTTT 60.040 37.037 0.00 0.00 41.22 1.94
3034 3212 5.008019 AGTTTGCTTCAAGATACATATGGCG 59.992 40.000 7.80 0.00 0.00 5.69
3159 3337 5.480422 ACAAGTCTTGGAAAAGGAAAACTGT 59.520 36.000 16.85 0.00 34.12 3.55
3406 3588 8.567285 AAAATACGTTCAGAAGAAATCAGGAT 57.433 30.769 0.00 0.00 35.08 3.24
3407 3589 7.979444 AAAATACGTTCAGAAGAAATCAGGA 57.021 32.000 0.00 0.00 35.08 3.86
3408 3590 7.750903 GGAAAAATACGTTCAGAAGAAATCAGG 59.249 37.037 0.00 0.00 35.08 3.86
3409 3591 7.478667 CGGAAAAATACGTTCAGAAGAAATCAG 59.521 37.037 0.00 0.00 35.08 2.90
3410 3592 7.041644 ACGGAAAAATACGTTCAGAAGAAATCA 60.042 33.333 0.00 0.00 40.99 2.57
3411 3593 7.295930 ACGGAAAAATACGTTCAGAAGAAATC 58.704 34.615 0.00 0.00 40.99 2.17
3412 3594 7.198306 ACGGAAAAATACGTTCAGAAGAAAT 57.802 32.000 0.00 0.00 40.99 2.17
3549 3732 3.768757 CTGAGACTCTTCAGGTCCAGATT 59.231 47.826 3.68 0.00 40.69 2.40
3605 3788 6.851330 GCATTACGCATATAGAAACCAAGAAC 59.149 38.462 0.00 0.00 41.79 3.01
3615 3798 4.306600 CACACAGGCATTACGCATATAGA 58.693 43.478 0.00 0.00 45.17 1.98
3670 3853 7.090173 ACGAAACGTACTTGGCTTATTAACTA 58.910 34.615 0.00 0.00 38.73 2.24
3671 3854 5.928264 ACGAAACGTACTTGGCTTATTAACT 59.072 36.000 0.00 0.00 38.73 2.24
3672 3855 6.156932 ACGAAACGTACTTGGCTTATTAAC 57.843 37.500 0.00 0.00 38.73 2.01
3673 3856 6.128580 GGAACGAAACGTACTTGGCTTATTAA 60.129 38.462 0.00 0.00 39.99 1.40
3677 3860 3.059166 GGAACGAAACGTACTTGGCTTA 58.941 45.455 0.00 0.00 39.99 3.09
3718 3901 9.754382 AGCAGCATATACAAAATGGAATAAAAG 57.246 29.630 0.00 0.00 0.00 2.27
3835 4021 5.187186 GGAATAAAGAGGTCCAGTCACTACA 59.813 44.000 0.00 0.00 0.00 2.74
3878 4068 4.102996 ACCAGATTTCAAAAACAAGCCCAT 59.897 37.500 0.00 0.00 0.00 4.00
4062 4272 1.153086 GAGCATCCCACTGCCGAAT 60.153 57.895 0.00 0.00 43.33 3.34
4235 4445 8.535335 TGAGAGATAAACTAGAAAATCAGCACT 58.465 33.333 0.00 0.00 0.00 4.40
4259 4469 4.699735 TCAGTTTGCAAGAGACAAAACTGA 59.300 37.500 20.18 20.18 39.71 3.41
4260 4470 4.985413 TCAGTTTGCAAGAGACAAAACTG 58.015 39.130 16.99 16.99 38.64 3.16
4288 4498 2.292569 TGGGTCGATAATAGAGTGCGTC 59.707 50.000 0.00 0.00 0.00 5.19
4341 4551 5.696030 AGAGCTGTACTAGTCATATGACCA 58.304 41.667 28.26 16.92 45.85 4.02
4357 4567 7.493971 CAGTTATAAACAGAGCAATAGAGCTGT 59.506 37.037 0.00 0.00 46.75 4.40
4462 4673 1.065564 GCAATCAGTGAAGAGCCCTCT 60.066 52.381 0.00 0.00 42.75 3.69
4632 4843 3.386078 AGCTTGAGTGTGAAGAGAACTGA 59.614 43.478 0.00 0.00 0.00 3.41
4815 5026 5.576774 GCAGGAGCAAAACCATTAATTGTAC 59.423 40.000 0.00 0.00 41.58 2.90
4885 5096 6.859420 AATGGTAACCACAAAATGAAAAGC 57.141 33.333 0.00 0.00 35.80 3.51
4924 5136 6.263842 TGAGTTCTGTTGAGCATCTCATTTTT 59.736 34.615 0.00 0.00 40.39 1.94
4925 5137 5.766670 TGAGTTCTGTTGAGCATCTCATTTT 59.233 36.000 0.00 0.00 40.39 1.82
5100 5334 9.965824 ATTGTTTAAAACGATTCAAACTGAGAT 57.034 25.926 5.85 0.00 31.35 2.75
5141 5376 6.405731 GGCTGGTTATGCAAGATGAAATACAA 60.406 38.462 0.00 0.00 0.00 2.41
5143 5378 5.300286 AGGCTGGTTATGCAAGATGAAATAC 59.700 40.000 0.00 0.00 0.00 1.89
5205 5440 3.144506 AGTCTGGATTGAACAGCTGTTG 58.855 45.455 35.67 19.18 38.56 3.33
5419 5658 7.492524 TGTTATAATGTGTTGGCTTTTCACAA 58.507 30.769 0.00 0.00 43.59 3.33
5474 5717 8.986477 AAACAATCTGGAATTTAACATGCTAC 57.014 30.769 0.00 0.00 0.00 3.58
5512 5755 5.754890 AGGAATGCTGCAGTAAAACAAAAAG 59.245 36.000 16.64 0.00 0.00 2.27
5633 5906 2.046892 GGACACCGTGCAGATGCT 60.047 61.111 6.35 0.00 42.66 3.79
5651 5924 1.537202 GTCTGTTTAGGCTGCAGTTGG 59.463 52.381 16.64 0.00 0.00 3.77
5682 5955 0.178964 TTTGGGTCAGGAAAGGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
5704 5978 5.728637 TTCAGAGTCTACATCTGCTCAAA 57.271 39.130 0.00 0.00 43.20 2.69
5790 6064 7.070696 TGCTTGCTATTTATAGGGTACAGAAGA 59.929 37.037 0.00 0.00 0.00 2.87
5839 6116 2.094752 GCAGTGTGGTTTGAGTGTTGTT 60.095 45.455 0.00 0.00 0.00 2.83
5840 6117 1.472480 GCAGTGTGGTTTGAGTGTTGT 59.528 47.619 0.00 0.00 0.00 3.32
5963 6243 2.031508 GGTCTCTTCTAGGATTCTCGCG 60.032 54.545 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.