Multiple sequence alignment - TraesCS5B01G086400

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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 TraesCS5B01G086400 chr5B 100.000 4704 0 0 1 4704 109890071 109885368 0.000000e+00 8687.0
1 TraesCS5B01G086400 chr5B 83.439 314 38 6 3118 3430 311042350 311042050 3.580000e-71 279.0
2 TraesCS5B01G086400 chr5B 78.750 240 41 6 1022 1261 110113544 110113773 8.150000e-33 152.0
3 TraesCS5B01G086400 chr5D 96.657 4158 86 13 1 4112 101461654 101457504 0.000000e+00 6859.0
4 TraesCS5B01G086400 chr5D 81.934 548 52 17 3113 3624 35871877 35871341 2.020000e-113 420.0
5 TraesCS5B01G086400 chr5D 95.902 244 9 1 4236 4478 101457505 101457262 1.230000e-105 394.0
6 TraesCS5B01G086400 chr5D 97.368 190 4 1 4470 4659 101457221 101457033 5.870000e-84 322.0
7 TraesCS5B01G086400 chr5D 79.167 240 42 4 1022 1261 101698395 101698626 4.870000e-35 159.0
8 TraesCS5B01G086400 chr5D 100.000 38 0 0 4667 4704 101457051 101457014 2.350000e-08 71.3
9 TraesCS5B01G086400 chr5A 96.465 4159 99 9 1 4112 98977618 98981775 0.000000e+00 6822.0
10 TraesCS5B01G086400 chr5A 92.623 244 8 3 4236 4478 98981774 98982008 4.510000e-90 342.0
11 TraesCS5B01G086400 chr5A 97.368 190 4 1 4470 4659 98982048 98982236 5.870000e-84 322.0
12 TraesCS5B01G086400 chr5A 79.751 321 29 12 3340 3624 324967038 324967358 2.870000e-47 200.0
13 TraesCS5B01G086400 chr5A 77.736 265 47 6 1022 1285 98453605 98453352 8.150000e-33 152.0
14 TraesCS5B01G086400 chr2D 97.656 128 3 0 4110 4237 328365419 328365292 2.200000e-53 220.0
15 TraesCS5B01G086400 chr2D 94.245 139 8 0 4107 4245 484901263 484901125 3.690000e-51 213.0
16 TraesCS5B01G086400 chr6B 94.815 135 7 0 4104 4238 703667459 703667593 1.330000e-50 211.0
17 TraesCS5B01G086400 chr6B 94.737 133 6 1 4108 4240 10221064 10220933 6.170000e-49 206.0
18 TraesCS5B01G086400 chr4D 94.245 139 7 1 4105 4242 306860410 306860272 1.330000e-50 211.0
19 TraesCS5B01G086400 chr3A 92.361 144 10 1 4098 4241 154641362 154641504 2.220000e-48 204.0
20 TraesCS5B01G086400 chr4B 89.873 158 12 4 4088 4243 89457747 89457592 2.870000e-47 200.0
21 TraesCS5B01G086400 chr7D 89.441 161 11 6 4080 4237 632020383 632020226 1.030000e-46 198.0
22 TraesCS5B01G086400 chr1D 90.260 154 11 4 4109 4261 141715602 141715452 1.030000e-46 198.0


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 TraesCS5B01G086400 chr5B 109885368 109890071 4703 True 8687.000000 8687 100.000000 1 4704 1 chr5B.!!$R1 4703
1 TraesCS5B01G086400 chr5D 101457014 101461654 4640 True 1911.575000 6859 97.481750 1 4704 4 chr5D.!!$R2 4703
2 TraesCS5B01G086400 chr5D 35871341 35871877 536 True 420.000000 420 81.934000 3113 3624 1 chr5D.!!$R1 511
3 TraesCS5B01G086400 chr5A 98977618 98982236 4618 False 2495.333333 6822 95.485333 1 4659 3 chr5A.!!$F2 4658

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
29 30 0.462789 TCGATAAAGCCCCCGACTTC 59.537 55.0 0.00 0.0 0.00 3.01 F
32 33 0.623617 ATAAAGCCCCCGACTTCCCT 60.624 55.0 0.00 0.0 0.00 4.20 F
985 988 1.119684 CCCTGACCACGGATGTATCA 58.880 55.0 0.00 0.0 0.00 2.15 F
2307 2331 0.806492 TACGTGTGTTTGTCAGCGCA 60.806 50.0 11.47 0.0 31.88 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1650 0.807496 AACTACTCGCCCTGTCGTAC 59.193 55.000 0.00 0.0 0.00 3.67 R
1899 1922 3.318275 GCAGTGCTAGTAGTACATGGCTA 59.682 47.826 19.00 0.0 32.98 3.93 R
2572 2596 0.106015 AACTGCAGTGGGGCTTTTCT 60.106 50.000 22.49 0.0 34.04 2.52 R
4111 4175 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.0 46.06 3.85 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
24 25 3.670625 TCATTAATCGATAAAGCCCCCG 58.329 45.455 0.00 0.00 0.00 5.73
29 30 0.462789 TCGATAAAGCCCCCGACTTC 59.537 55.000 0.00 0.00 0.00 3.01
32 33 0.623617 ATAAAGCCCCCGACTTCCCT 60.624 55.000 0.00 0.00 0.00 4.20
33 34 1.559065 TAAAGCCCCCGACTTCCCTG 61.559 60.000 0.00 0.00 0.00 4.45
36 37 3.646715 CCCCCGACTTCCCTGCAA 61.647 66.667 0.00 0.00 0.00 4.08
68 69 1.349627 GTGCATGCCGATTCGTCTG 59.650 57.895 16.68 0.87 0.00 3.51
96 97 5.199982 TCATTTACCTGCCATTTTAGGGA 57.800 39.130 0.00 0.00 38.42 4.20
227 229 5.200368 TGATGTTTTTCTTTTCCTCTGGC 57.800 39.130 0.00 0.00 0.00 4.85
232 234 5.891551 TGTTTTTCTTTTCCTCTGGCTAACT 59.108 36.000 0.00 0.00 0.00 2.24
235 237 2.087646 CTTTTCCTCTGGCTAACTGGC 58.912 52.381 0.00 0.00 42.18 4.85
985 988 1.119684 CCCTGACCACGGATGTATCA 58.880 55.000 0.00 0.00 0.00 2.15
1223 1226 3.068024 TGTGTCATGGAGGAAAAAGCAAC 59.932 43.478 0.00 0.00 0.00 4.17
1636 1650 8.633561 TGTACACATTCTAGGATGTCATCTAAG 58.366 37.037 14.13 3.93 38.15 2.18
2014 2037 3.788333 TTGATTGCTAATCCTTGCTGC 57.212 42.857 0.00 0.00 37.09 5.25
2027 2050 3.005684 TCCTTGCTGCGTTGAATGAATTT 59.994 39.130 0.00 0.00 0.00 1.82
2307 2331 0.806492 TACGTGTGTTTGTCAGCGCA 60.806 50.000 11.47 0.00 31.88 6.09
2663 2687 7.708752 CAGAGTTAACCCAGAGAGCTTAATAAG 59.291 40.741 0.88 0.00 0.00 1.73
2671 2695 8.718656 ACCCAGAGAGCTTAATAAGTGAATAAT 58.281 33.333 1.68 0.00 0.00 1.28
2916 2942 8.540388 GGGATTCATGGATATTAGTGCTACTTA 58.460 37.037 0.00 0.00 0.00 2.24
3172 3198 7.996644 ACCTCAAAGTTCTTTTACAGACCATAA 59.003 33.333 0.00 0.00 0.00 1.90
3178 3204 4.585879 TCTTTTACAGACCATAACCTGCC 58.414 43.478 0.00 0.00 33.90 4.85
3390 3416 3.258123 CCCGTGATTTGGAATCAAAAGGT 59.742 43.478 5.03 0.00 44.83 3.50
3647 3710 4.112634 AGGAGTATCTCTTAGGAGCTGG 57.887 50.000 0.00 0.00 39.31 4.85
3772 3835 3.947834 CACATTTACCCCTCCATGAGTTC 59.052 47.826 0.00 0.00 0.00 3.01
3796 3859 5.049405 CGTAGACTTTTGTGCTTCCAGAAAT 60.049 40.000 0.00 0.00 34.64 2.17
3819 3882 5.649602 TTTTGCCGAAAATCACAATGTTC 57.350 34.783 0.00 0.00 0.00 3.18
3913 3977 8.503458 AGATGAAGATAAGAACATGTCTTTGG 57.497 34.615 13.40 0.00 44.64 3.28
4021 4085 3.818210 TCGTGCAGTACCATGAATGTTTT 59.182 39.130 0.00 0.00 0.00 2.43
4123 4187 6.854091 AATTAGATTATACTCCCTCCGTCC 57.146 41.667 0.00 0.00 0.00 4.79
4124 4188 2.792878 AGATTATACTCCCTCCGTCCG 58.207 52.381 0.00 0.00 0.00 4.79
4125 4189 1.817447 GATTATACTCCCTCCGTCCGG 59.183 57.143 0.00 0.00 0.00 5.14
4126 4190 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
4127 4191 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
4128 4192 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4129 4193 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4130 4194 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4131 4195 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4132 4196 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4133 4197 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4134 4198 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4135 4199 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4136 4200 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4137 4201 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4138 4202 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4139 4203 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4140 4204 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4141 4205 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4142 4206 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4143 4207 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4144 4208 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4145 4209 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
4146 4210 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
4147 4211 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
4148 4212 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
4149 4213 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
4155 4219 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
4156 4220 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
4157 4221 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
4158 4222 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
4159 4223 8.064389 TGTCATCAAAATGGATAAAAGGGGATA 58.936 33.333 0.00 0.00 33.42 2.59
4160 4224 9.093458 GTCATCAAAATGGATAAAAGGGGATAT 57.907 33.333 0.00 0.00 33.42 1.63
4223 4287 9.179552 TGTTCATTTTGATGACAAGTATTTTCG 57.820 29.630 0.00 0.00 37.32 3.46
4224 4288 8.638565 GTTCATTTTGATGACAAGTATTTTCGG 58.361 33.333 0.00 0.00 37.32 4.30
4225 4289 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
4226 4290 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
4227 4291 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
4228 4292 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
4229 4293 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
4230 4294 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
4231 4295 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4232 4296 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4233 4297 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
4234 4298 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
4235 4299 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
4322 4386 3.215587 AAGGCAGGCTGGTGGAAGG 62.216 63.158 17.64 0.00 0.00 3.46
4361 4425 9.959749 TTTACTGTTCTTTGAATCGCTTTAATT 57.040 25.926 0.00 0.00 0.00 1.40
4363 4427 8.507470 ACTGTTCTTTGAATCGCTTTAATTTC 57.493 30.769 0.00 0.00 0.00 2.17
4557 4671 5.091261 AGTAGCAAACCTATGGTGAAGAG 57.909 43.478 0.00 0.00 35.34 2.85
4633 4747 3.018856 TGGCAGAACATTGTCATGATCC 58.981 45.455 0.00 0.00 33.59 3.36
4640 4754 3.411446 ACATTGTCATGATCCGTGTGTT 58.589 40.909 0.00 0.00 34.11 3.32
4641 4755 4.574892 ACATTGTCATGATCCGTGTGTTA 58.425 39.130 0.00 0.00 34.11 2.41
4642 4756 5.185454 ACATTGTCATGATCCGTGTGTTAT 58.815 37.500 0.00 0.00 34.11 1.89
4643 4757 5.065090 ACATTGTCATGATCCGTGTGTTATG 59.935 40.000 0.00 0.00 34.11 1.90
4644 4758 4.200838 TGTCATGATCCGTGTGTTATGT 57.799 40.909 0.00 0.00 0.00 2.29
4645 4759 3.932089 TGTCATGATCCGTGTGTTATGTG 59.068 43.478 0.00 0.00 0.00 3.21
4646 4760 4.180817 GTCATGATCCGTGTGTTATGTGA 58.819 43.478 0.00 0.00 0.00 3.58
4647 4761 4.811024 GTCATGATCCGTGTGTTATGTGAT 59.189 41.667 0.00 0.00 0.00 3.06
4648 4762 5.049828 TCATGATCCGTGTGTTATGTGATC 58.950 41.667 0.00 0.00 0.00 2.92
4649 4763 3.443976 TGATCCGTGTGTTATGTGATCG 58.556 45.455 0.00 0.00 33.10 3.69
4650 4764 3.119280 TGATCCGTGTGTTATGTGATCGT 60.119 43.478 0.00 0.00 33.10 3.73
4651 4765 3.306917 TCCGTGTGTTATGTGATCGTT 57.693 42.857 0.00 0.00 0.00 3.85
4652 4766 3.655486 TCCGTGTGTTATGTGATCGTTT 58.345 40.909 0.00 0.00 0.00 3.60
4653 4767 4.807443 TCCGTGTGTTATGTGATCGTTTA 58.193 39.130 0.00 0.00 0.00 2.01
4654 4768 4.860352 TCCGTGTGTTATGTGATCGTTTAG 59.140 41.667 0.00 0.00 0.00 1.85
4655 4769 4.624024 CCGTGTGTTATGTGATCGTTTAGT 59.376 41.667 0.00 0.00 0.00 2.24
4656 4770 5.801444 CCGTGTGTTATGTGATCGTTTAGTA 59.199 40.000 0.00 0.00 0.00 1.82
4657 4771 6.237384 CCGTGTGTTATGTGATCGTTTAGTAC 60.237 42.308 0.00 0.00 0.00 2.73
4658 4772 6.525628 CGTGTGTTATGTGATCGTTTAGTACT 59.474 38.462 0.00 0.00 0.00 2.73
4659 4773 7.253223 CGTGTGTTATGTGATCGTTTAGTACTC 60.253 40.741 0.00 0.00 0.00 2.59
4660 4774 6.744082 TGTGTTATGTGATCGTTTAGTACTCG 59.256 38.462 0.00 0.00 0.00 4.18
4661 4775 6.744537 GTGTTATGTGATCGTTTAGTACTCGT 59.255 38.462 0.00 0.00 0.00 4.18
4662 4776 6.744082 TGTTATGTGATCGTTTAGTACTCGTG 59.256 38.462 0.00 0.00 0.00 4.35
4663 4777 4.754372 TGTGATCGTTTAGTACTCGTGT 57.246 40.909 0.00 0.00 0.00 4.49
4664 4778 4.469552 TGTGATCGTTTAGTACTCGTGTG 58.530 43.478 0.00 0.00 0.00 3.82
4665 4779 3.300066 GTGATCGTTTAGTACTCGTGTGC 59.700 47.826 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.673333 AGACGAATCGGCATGCACAA 60.673 50.000 21.36 4.00 37.34 3.33
49 50 1.079197 AGACGAATCGGCATGCACA 60.079 52.632 21.36 4.98 37.34 4.57
56 57 1.202302 TGATCAGTCAGACGAATCGGC 60.202 52.381 7.80 3.13 33.59 5.54
57 58 2.851805 TGATCAGTCAGACGAATCGG 57.148 50.000 7.80 0.00 0.00 4.18
68 69 5.841957 AAATGGCAGGTAAATGATCAGTC 57.158 39.130 0.09 0.00 0.00 3.51
96 97 2.901839 ACAGAGAAAATGCAATTGGGCT 59.098 40.909 7.72 0.00 36.10 5.19
144 145 0.177836 CATCCACGGTGAGGCATACA 59.822 55.000 10.28 0.00 0.00 2.29
214 216 2.290323 GCCAGTTAGCCAGAGGAAAAGA 60.290 50.000 0.00 0.00 0.00 2.52
227 229 5.239306 TGAAAACTCAGTCATTGCCAGTTAG 59.761 40.000 0.00 0.00 0.00 2.34
232 234 3.819368 TCTGAAAACTCAGTCATTGCCA 58.181 40.909 2.28 0.00 38.75 4.92
317 319 8.645814 AATCGGAACCTAGGAAAATAAAACTT 57.354 30.769 17.98 0.00 0.00 2.66
446 448 8.721019 AAAATTATATGTGTGGGCATGAAAAG 57.279 30.769 0.00 0.00 0.00 2.27
686 689 9.976511 CTCATTTGTCTGCATATTCCAAATATT 57.023 29.630 0.00 0.00 34.82 1.28
809 812 5.389859 TCATGAGGTGCCAAAATAACAAG 57.610 39.130 0.00 0.00 0.00 3.16
925 928 9.965902 ACAATCTTTACTGTCCTCAGAATTTAT 57.034 29.630 2.17 0.00 43.76 1.40
985 988 6.780522 ACCAATTATTGTGGAAACCAGTAACT 59.219 34.615 4.15 0.00 39.62 2.24
1229 1232 6.770785 AGAGTTTTTACCATTCTGTTGTAGCA 59.229 34.615 0.00 0.00 0.00 3.49
1300 1303 2.695359 TCAAAGTTATCACCCAGACGC 58.305 47.619 0.00 0.00 0.00 5.19
1306 1309 3.125316 CGAGCACTTCAAAGTTATCACCC 59.875 47.826 0.00 0.00 37.08 4.61
1448 1451 3.423539 AAGTTGCATAGCAGAGACCAA 57.576 42.857 0.00 0.00 40.61 3.67
1573 1587 4.090761 ACTGTGACTCACCATGTGAAAT 57.909 40.909 6.72 0.00 42.26 2.17
1636 1650 0.807496 AACTACTCGCCCTGTCGTAC 59.193 55.000 0.00 0.00 0.00 3.67
1899 1922 3.318275 GCAGTGCTAGTAGTACATGGCTA 59.682 47.826 19.00 0.00 32.98 3.93
2014 2037 4.216257 AGTGTCCCTCAAATTCATTCAACG 59.784 41.667 0.00 0.00 0.00 4.10
2307 2331 8.582437 CATAAAGATTCATCAGGGCATTACATT 58.418 33.333 0.00 0.00 0.00 2.71
2572 2596 0.106015 AACTGCAGTGGGGCTTTTCT 60.106 50.000 22.49 0.00 34.04 2.52
3172 3198 3.011708 ACCAAATGATAAGGAAGGCAGGT 59.988 43.478 0.00 0.00 0.00 4.00
3178 3204 6.359804 TCATCTCCACCAAATGATAAGGAAG 58.640 40.000 0.00 0.00 0.00 3.46
3390 3416 2.574018 CGAGTGGCTGTCCTGTCCA 61.574 63.158 0.00 0.00 0.00 4.02
3772 3835 3.390135 TCTGGAAGCACAAAAGTCTACG 58.610 45.455 0.00 0.00 0.00 3.51
3796 3859 5.814705 AGAACATTGTGATTTTCGGCAAAAA 59.185 32.000 0.00 0.00 40.98 1.94
3913 3977 5.077134 ACAGGAGGTACCAAATTACGTAC 57.923 43.478 15.94 6.48 42.04 3.67
4111 4175 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4112 4176 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4113 4177 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4114 4178 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4115 4179 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4116 4180 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4117 4181 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4118 4182 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4119 4183 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4120 4184 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4121 4185 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
4122 4186 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
4123 4187 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
4129 4193 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
4130 4194 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
4131 4195 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
4132 4196 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
4133 4197 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
4134 4198 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
4197 4261 9.179552 CGAAAATACTTGTCATCAAAATGAACA 57.820 29.630 0.00 0.00 43.42 3.18
4198 4262 8.638565 CCGAAAATACTTGTCATCAAAATGAAC 58.361 33.333 0.00 0.00 43.42 3.18
4199 4263 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
4200 4264 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
4201 4265 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
4202 4266 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
4203 4267 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
4204 4268 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
4205 4269 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
4206 4270 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
4207 4271 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
4208 4272 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
4209 4273 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
4210 4274 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4211 4275 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4212 4276 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4213 4277 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
4214 4278 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
4215 4279 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
4216 4280 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
4217 4281 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
4218 4282 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
4219 4283 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
4220 4284 2.965671 ATATACTCCCTCCGTCCGAA 57.034 50.000 0.00 0.00 0.00 4.30
4221 4285 2.909006 ACTATATACTCCCTCCGTCCGA 59.091 50.000 0.00 0.00 0.00 4.55
4222 4286 3.347077 ACTATATACTCCCTCCGTCCG 57.653 52.381 0.00 0.00 0.00 4.79
4223 4287 4.522114 GGTACTATATACTCCCTCCGTCC 58.478 52.174 0.00 0.00 0.00 4.79
4224 4288 4.018960 TGGGTACTATATACTCCCTCCGTC 60.019 50.000 11.22 0.00 38.95 4.79
4225 4289 3.918912 TGGGTACTATATACTCCCTCCGT 59.081 47.826 11.22 0.00 38.95 4.69
4226 4290 4.581309 TGGGTACTATATACTCCCTCCG 57.419 50.000 11.22 0.00 38.95 4.63
4227 4291 8.906238 TTTAATGGGTACTATATACTCCCTCC 57.094 38.462 11.22 0.00 38.95 4.30
4322 4386 5.491982 AGAACAGTAAATCACCTCCATGTC 58.508 41.667 0.00 0.00 0.00 3.06
4361 4425 5.966935 AGGTCCAGAATTTCTAGGATCTGAA 59.033 40.000 20.61 0.00 41.38 3.02
4363 4427 5.885449 AGGTCCAGAATTTCTAGGATCTG 57.115 43.478 20.61 0.00 35.38 2.90
4633 4747 5.756950 ACTAAACGATCACATAACACACG 57.243 39.130 0.00 0.00 0.00 4.49
4640 4754 6.253013 CACACGAGTACTAAACGATCACATA 58.747 40.000 9.21 0.00 0.00 2.29
4641 4755 5.093457 CACACGAGTACTAAACGATCACAT 58.907 41.667 9.21 0.00 0.00 3.21
4642 4756 4.469552 CACACGAGTACTAAACGATCACA 58.530 43.478 9.21 0.00 0.00 3.58
4643 4757 3.300066 GCACACGAGTACTAAACGATCAC 59.700 47.826 9.21 0.00 0.00 3.06
4644 4758 3.189910 AGCACACGAGTACTAAACGATCA 59.810 43.478 9.21 0.00 0.00 2.92
4645 4759 3.756069 AGCACACGAGTACTAAACGATC 58.244 45.455 9.21 0.00 0.00 3.69
4646 4760 3.844577 AGCACACGAGTACTAAACGAT 57.155 42.857 9.21 0.00 0.00 3.73
4647 4761 4.154737 ACATAGCACACGAGTACTAAACGA 59.845 41.667 9.21 0.00 27.86 3.85
4648 4762 4.262277 CACATAGCACACGAGTACTAAACG 59.738 45.833 0.00 0.00 27.86 3.60
4649 4763 5.396484 TCACATAGCACACGAGTACTAAAC 58.604 41.667 0.00 0.00 27.86 2.01
4650 4764 5.632244 TCACATAGCACACGAGTACTAAA 57.368 39.130 0.00 0.00 27.86 1.85
4651 4765 5.503520 CGATCACATAGCACACGAGTACTAA 60.504 44.000 0.00 0.00 27.86 2.24
4652 4766 4.025145 CGATCACATAGCACACGAGTACTA 60.025 45.833 0.00 0.00 0.00 1.82
4653 4767 3.242772 CGATCACATAGCACACGAGTACT 60.243 47.826 0.00 0.00 0.00 2.73
4654 4768 3.036633 CGATCACATAGCACACGAGTAC 58.963 50.000 0.00 0.00 0.00 2.73
4655 4769 2.681344 ACGATCACATAGCACACGAGTA 59.319 45.455 0.00 0.00 0.00 2.59
4656 4770 1.472878 ACGATCACATAGCACACGAGT 59.527 47.619 0.00 0.00 0.00 4.18
4657 4771 2.194800 ACGATCACATAGCACACGAG 57.805 50.000 0.00 0.00 0.00 4.18
4658 4772 2.647529 AACGATCACATAGCACACGA 57.352 45.000 0.00 0.00 0.00 4.35
4659 4773 3.857665 ACTAAACGATCACATAGCACACG 59.142 43.478 0.00 0.00 0.00 4.49
4660 4774 6.020599 CAGTACTAAACGATCACATAGCACAC 60.021 42.308 0.00 0.00 0.00 3.82
4661 4775 6.033966 CAGTACTAAACGATCACATAGCACA 58.966 40.000 0.00 0.00 0.00 4.57
4662 4776 5.051641 GCAGTACTAAACGATCACATAGCAC 60.052 44.000 0.00 0.00 0.00 4.40
4663 4777 5.041287 GCAGTACTAAACGATCACATAGCA 58.959 41.667 0.00 0.00 0.00 3.49
4664 4778 4.444720 GGCAGTACTAAACGATCACATAGC 59.555 45.833 0.00 0.00 0.00 2.97
4665 4779 5.833082 AGGCAGTACTAAACGATCACATAG 58.167 41.667 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.