Multiple sequence alignment - TraesCS2D01G242300

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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 TraesCS2D01G242300 chr2D 100.000 5225 0 0 1 5225 269740676 269735452 0.000000e+00 9649
1 TraesCS2D01G242300 chr2D 88.998 609 59 8 4621 5225 244457191 244456587 0.000000e+00 747
2 TraesCS2D01G242300 chr2A 93.598 5248 296 21 1 5225 335391969 335397199 0.000000e+00 7793
3 TraesCS2D01G242300 chr2B 90.108 2325 209 14 1891 4198 317758929 317756609 0.000000e+00 3000
4 TraesCS2D01G242300 chr2B 92.320 1276 92 5 568 1842 317760301 317759031 0.000000e+00 1808
5 TraesCS2D01G242300 chr2B 88.545 323 33 2 4227 4546 317756349 317756028 6.350000e-104 388
6 TraesCS2D01G242300 chr7D 88.744 613 57 11 4621 5225 305106142 305106750 0.000000e+00 739
7 TraesCS2D01G242300 chr5A 88.707 611 60 9 4620 5225 256342998 256342392 0.000000e+00 737
8 TraesCS2D01G242300 chr5A 88.543 611 61 9 4620 5225 256361217 256360611 0.000000e+00 732
9 TraesCS2D01G242300 chr1A 88.651 608 62 7 4621 5225 271549430 271550033 0.000000e+00 734
10 TraesCS2D01G242300 chr1D 88.525 610 60 10 4621 5225 139066070 139066674 0.000000e+00 730
11 TraesCS2D01G242300 chr1D 88.361 610 61 10 4621 5225 159584211 159583607 0.000000e+00 725
12 TraesCS2D01G242300 chr3D 88.342 609 64 7 4621 5225 239302912 239303517 0.000000e+00 725


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 TraesCS2D01G242300 chr2D 269735452 269740676 5224 True 9649 9649 100.000000 1 5225 1 chr2D.!!$R2 5224
1 TraesCS2D01G242300 chr2D 244456587 244457191 604 True 747 747 88.998000 4621 5225 1 chr2D.!!$R1 604
2 TraesCS2D01G242300 chr2A 335391969 335397199 5230 False 7793 7793 93.598000 1 5225 1 chr2A.!!$F1 5224
3 TraesCS2D01G242300 chr2B 317756028 317760301 4273 True 1732 3000 90.324333 568 4546 3 chr2B.!!$R1 3978
4 TraesCS2D01G242300 chr7D 305106142 305106750 608 False 739 739 88.744000 4621 5225 1 chr7D.!!$F1 604
5 TraesCS2D01G242300 chr5A 256342392 256342998 606 True 737 737 88.707000 4620 5225 1 chr5A.!!$R1 605
6 TraesCS2D01G242300 chr5A 256360611 256361217 606 True 732 732 88.543000 4620 5225 1 chr5A.!!$R2 605
7 TraesCS2D01G242300 chr1A 271549430 271550033 603 False 734 734 88.651000 4621 5225 1 chr1A.!!$F1 604
8 TraesCS2D01G242300 chr1D 139066070 139066674 604 False 730 730 88.525000 4621 5225 1 chr1D.!!$F1 604
9 TraesCS2D01G242300 chr1D 159583607 159584211 604 True 725 725 88.361000 4621 5225 1 chr1D.!!$R1 604
10 TraesCS2D01G242300 chr3D 239302912 239303517 605 False 725 725 88.342000 4621 5225 1 chr3D.!!$F1 604

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
277 278 1.409427 GGGATCGACCAACTAGACCAG 59.591 57.143 0.00 0.0 41.20 4.00 F
1966 2037 0.886043 TTGCATGCTCACTCGCACTT 60.886 50.000 20.33 0.0 43.61 3.16 F
2223 2295 0.182775 ACCTTGGGTCGTGCTTTCTT 59.817 50.000 0.00 0.0 0.00 2.52 F
3007 3091 0.544697 ACCTTTGGGTGCCTATACCG 59.455 55.000 0.00 0.0 45.43 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2225 0.044855 ATCCAAGCACTCCCCCTACT 59.955 55.000 0.00 0.0 0.00 2.57 R
3835 3920 1.153369 ATCCTTGGTCGATGCACCG 60.153 57.895 0.00 0.0 39.62 4.94 R
4052 4138 1.135489 CACCTGCATGCTTGTGTCATC 60.135 52.381 23.58 0.0 0.00 2.92 R
4563 4885 0.657840 GACTGGCATGGTAATCACGC 59.342 55.000 0.00 0.0 33.19 5.34 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
70 71 9.606631 ACTAATCTGGATCTTTCAATCTTGTAC 57.393 33.333 0.00 0.00 0.00 2.90
71 72 7.872113 AATCTGGATCTTTCAATCTTGTACC 57.128 36.000 0.00 0.00 0.00 3.34
72 73 6.373005 TCTGGATCTTTCAATCTTGTACCA 57.627 37.500 0.00 0.00 0.00 3.25
119 120 3.316588 TGCAAGCTATTTTTGACCAACGA 59.683 39.130 0.00 0.00 0.00 3.85
126 127 5.334569 GCTATTTTTGACCAACGACTGCTTA 60.335 40.000 0.00 0.00 0.00 3.09
201 202 7.404671 ACCATGTCAAAGTAAAGTCAAAACT 57.595 32.000 0.00 0.00 37.32 2.66
212 213 8.421673 AGTAAAGTCAAAACTTATAGGCGATC 57.578 34.615 0.00 0.00 45.07 3.69
214 215 5.353394 AGTCAAAACTTATAGGCGATCCA 57.647 39.130 0.00 0.00 28.74 3.41
227 228 4.460263 AGGCGATCCAAATACATGCTTTA 58.540 39.130 0.00 0.00 33.74 1.85
277 278 1.409427 GGGATCGACCAACTAGACCAG 59.591 57.143 0.00 0.00 41.20 4.00
299 300 6.547510 CCAGCTAAACTTATGGCCTCTTTTAT 59.452 38.462 3.32 0.00 0.00 1.40
337 338 9.231297 TGAGGAAATTTGTAGGAGTAAGAATTG 57.769 33.333 0.00 0.00 0.00 2.32
348 349 4.762289 AGTAAGAATTGCTCCTGTAGGG 57.238 45.455 0.00 0.00 35.63 3.53
428 429 6.372937 TCATTTTGGTTTGGGTTTCAAAAGAC 59.627 34.615 0.00 0.00 45.74 3.01
479 480 9.013229 TCAAATATCTTTTCTACATGTTGTGCT 57.987 29.630 2.30 0.00 0.00 4.40
504 505 8.442632 TCATAGAACAAGATAAAAGCCATGAG 57.557 34.615 0.00 0.00 0.00 2.90
511 512 6.377996 ACAAGATAAAAGCCATGAGTTGCATA 59.622 34.615 0.00 0.00 34.82 3.14
622 628 3.863400 GCTCCAAACTGCTGCATTTTCAT 60.863 43.478 14.09 0.00 0.00 2.57
721 728 8.912988 CAAAACAAATGGGTCCTATGTATACAT 58.087 33.333 21.57 21.57 40.22 2.29
797 804 3.954258 ACAAGGGTTATTTCTAGCCATGC 59.046 43.478 0.00 0.00 35.81 4.06
798 805 2.851195 AGGGTTATTTCTAGCCATGCG 58.149 47.619 0.00 0.00 35.62 4.73
930 937 2.041485 TGCATGGTTGAATGGAGAGGAA 59.959 45.455 0.00 0.00 0.00 3.36
1096 1103 5.276584 CGCAATATCGAGCTAGCATAATTCC 60.277 44.000 18.83 0.00 0.00 3.01
1142 1149 5.276440 AGGAAACATGTTATTGCCCCATTA 58.724 37.500 12.39 0.00 0.00 1.90
1168 1175 6.044404 AGGAGGAAGTGAGAGAATTGGTTAAA 59.956 38.462 0.00 0.00 0.00 1.52
1176 1192 6.923508 GTGAGAGAATTGGTTAAAAAGGTTGG 59.076 38.462 0.00 0.00 0.00 3.77
1379 1395 9.607285 GTGCATTATATTTCCGTAATTTGTAGG 57.393 33.333 0.00 0.00 0.00 3.18
1415 1431 6.575162 ACTTGGGCACAAATAAGTAGAAAG 57.425 37.500 1.48 0.00 35.89 2.62
1771 1787 3.823281 TGGGTAAGTTCACGTCTTTCA 57.177 42.857 0.00 0.00 0.00 2.69
1966 2037 0.886043 TTGCATGCTCACTCGCACTT 60.886 50.000 20.33 0.00 43.61 3.16
1999 2070 1.786937 AATGCCACCCTTTGTTGTCA 58.213 45.000 0.00 0.00 0.00 3.58
2001 2072 1.327303 TGCCACCCTTTGTTGTCATC 58.673 50.000 0.00 0.00 0.00 2.92
2004 2075 1.888512 CCACCCTTTGTTGTCATCTGG 59.111 52.381 0.00 0.00 0.00 3.86
2032 2103 6.428083 TTGATTACACTAGGAAAGGTCACA 57.572 37.500 0.00 0.00 0.00 3.58
2035 2106 8.319057 TGATTACACTAGGAAAGGTCACATAT 57.681 34.615 0.00 0.00 0.00 1.78
2074 2145 5.085219 ACCTACTATACACTTATGAGGGCC 58.915 45.833 0.00 0.00 0.00 5.80
2087 2158 1.912731 TGAGGGCCTGTGTATGCTAAA 59.087 47.619 12.95 0.00 0.00 1.85
2105 2176 4.399303 GCTAAATGTGTACCCTTGATGCTT 59.601 41.667 0.00 0.00 0.00 3.91
2109 2180 3.146066 TGTGTACCCTTGATGCTTTGAC 58.854 45.455 0.00 0.00 0.00 3.18
2147 2219 6.542852 ACGCAACATGTAGTCATTTATCAAC 58.457 36.000 0.00 0.00 31.15 3.18
2149 2221 6.542852 GCAACATGTAGTCATTTATCAACGT 58.457 36.000 0.00 0.00 31.15 3.99
2153 2225 8.766000 ACATGTAGTCATTTATCAACGTTACA 57.234 30.769 0.00 0.00 31.15 2.41
2157 2229 9.563898 TGTAGTCATTTATCAACGTTACAGTAG 57.436 33.333 0.00 0.00 0.00 2.57
2197 2269 5.524281 ACCAAAGACGAGAAAGAGAAACTTC 59.476 40.000 0.00 0.00 37.93 3.01
2223 2295 0.182775 ACCTTGGGTCGTGCTTTCTT 59.817 50.000 0.00 0.00 0.00 2.52
2225 2297 2.158726 ACCTTGGGTCGTGCTTTCTTAA 60.159 45.455 0.00 0.00 0.00 1.85
2277 2349 4.713553 TCTTGAAGACCAGCATAACAACA 58.286 39.130 0.00 0.00 0.00 3.33
2382 2459 1.152963 ACCCAGGCGGTGCATAATC 60.153 57.895 0.00 0.00 46.09 1.75
2397 2474 7.518370 CGGTGCATAATCTTGGTATTAGTGTTC 60.518 40.741 0.00 0.00 0.00 3.18
2442 2519 6.894339 TTCCTTTCAACCCTAAATGACTTC 57.106 37.500 0.00 0.00 0.00 3.01
2452 2529 4.881850 CCCTAAATGACTTCCGTTAGCATT 59.118 41.667 0.00 0.00 0.00 3.56
2514 2591 5.631929 CACACATCATTTGTTTCACATGAGG 59.368 40.000 0.00 8.34 38.01 3.86
2656 2733 2.603560 GCGCGGGCAGATTACTATTATC 59.396 50.000 20.76 0.00 39.62 1.75
2682 2759 5.465935 TCTATTTTCGAAACACAATTGGGC 58.534 37.500 10.79 0.00 0.00 5.36
2704 2781 3.675698 CAGGAAAGTCAACTAGCTCGAAC 59.324 47.826 0.00 0.00 0.00 3.95
2719 2796 5.469479 AGCTCGAACCCAATAAAATGTTTG 58.531 37.500 0.00 0.00 0.00 2.93
2746 2823 8.188139 TGATGAGTAGAACCAAAACAAGAAAAC 58.812 33.333 0.00 0.00 0.00 2.43
2802 2879 7.038017 TCCCTTACCCATTTTGAAATGCAAATA 60.038 33.333 10.26 0.00 45.30 1.40
2867 2949 7.338196 TGATGGACGACATTATTGTGGTAAATT 59.662 33.333 5.54 0.00 43.78 1.82
2870 2952 7.810282 TGGACGACATTATTGTGGTAAATTTTG 59.190 33.333 5.54 0.00 43.78 2.44
2872 2954 9.187455 GACGACATTATTGTGGTAAATTTTGTT 57.813 29.630 5.54 0.00 43.78 2.83
2873 2955 9.535878 ACGACATTATTGTGGTAAATTTTGTTT 57.464 25.926 0.00 0.00 42.21 2.83
2903 2985 6.712547 AGAGGAATAATTACTGCAAGGCATAC 59.287 38.462 0.00 0.00 38.13 2.39
2943 3025 2.954318 CAATCCGCATCTTCCTTCCAAT 59.046 45.455 0.00 0.00 0.00 3.16
2975 3057 7.321153 GTGCTTAAGACAGTAATCCTAGTTCA 58.679 38.462 6.67 0.00 0.00 3.18
3007 3091 0.544697 ACCTTTGGGTGCCTATACCG 59.455 55.000 0.00 0.00 45.43 4.02
3081 3165 5.692204 AGCATTGAATTCTACCGTAATCGAG 59.308 40.000 7.05 0.00 39.71 4.04
3125 3209 3.958147 TGGGCACGTGAGAAGAGATATAA 59.042 43.478 22.23 0.00 0.00 0.98
3173 3257 1.291132 GCATCCGCTACCTTTGAGTC 58.709 55.000 0.00 0.00 34.30 3.36
3291 3375 2.204059 AGGGGAGGTTCTGCTGCT 60.204 61.111 0.00 0.00 0.00 4.24
3403 3487 8.301002 GTGCAACTTTAATTTAAGTGACCCATA 58.699 33.333 10.40 0.00 38.33 2.74
3405 3489 7.973944 GCAACTTTAATTTAAGTGACCCATAGG 59.026 37.037 10.40 0.00 38.33 2.57
3586 3671 1.074090 TGTTGGTGACTCCCCTCCA 60.074 57.895 0.00 0.00 34.77 3.86
3661 3746 3.452264 CCTCTATGGATGTCACAACAGGA 59.548 47.826 0.00 0.00 39.20 3.86
3750 3835 0.673022 GACAAGGCAGCTGAGGACAG 60.673 60.000 20.43 3.79 45.91 3.51
3904 3989 1.522569 GCTAACTCTGGTGGCCGAT 59.477 57.895 0.00 0.00 0.00 4.18
3969 4054 2.095059 CCCTTGTTTGGAGATGAAAGCG 60.095 50.000 0.00 0.00 0.00 4.68
4024 4109 1.993956 TTGGTTGGATCAAGTGGTGG 58.006 50.000 0.00 0.00 0.00 4.61
4194 4280 3.189606 ACCCATTGTCCTGTTCCAGATA 58.810 45.455 0.00 0.00 32.44 1.98
4195 4281 3.788142 ACCCATTGTCCTGTTCCAGATAT 59.212 43.478 0.00 0.00 32.44 1.63
4290 4609 8.564574 TGTGAAAGGACACAAAAGTCAATATAC 58.435 33.333 0.00 0.00 45.81 1.47
4296 4615 6.653320 GGACACAAAAGTCAATATACAGACCA 59.347 38.462 0.00 0.00 40.29 4.02
4443 4762 8.173775 CACTTTACAAGAGCTACATCATTCAAG 58.826 37.037 0.00 0.00 0.00 3.02
4475 4794 7.695055 TGTAGAATAAAAGAAGGGGATCACAA 58.305 34.615 0.00 0.00 0.00 3.33
4485 4804 6.980577 AGAAGGGGATCACAATACCAAATAA 58.019 36.000 0.00 0.00 37.67 1.40
4512 4834 7.533900 CAGGAGTAAATGTAAATGTGTGTTTCG 59.466 37.037 0.00 0.00 0.00 3.46
4513 4835 6.799925 GGAGTAAATGTAAATGTGTGTTTCGG 59.200 38.462 0.00 0.00 0.00 4.30
4558 4880 7.719483 TGACCCAAATATTTACGTAGACTAGG 58.281 38.462 0.00 0.60 0.00 3.02
4563 4885 9.627395 CCAAATATTTACGTAGACTAGGATCTG 57.373 37.037 9.12 0.00 0.00 2.90
4568 4890 2.210961 CGTAGACTAGGATCTGCGTGA 58.789 52.381 11.18 0.00 46.06 4.35
4585 4907 1.064758 GTGATTACCATGCCAGTCCCA 60.065 52.381 0.00 0.00 0.00 4.37
4599 4921 4.999950 GCCAGTCCCAGTATCAATTGATAG 59.000 45.833 25.14 15.68 37.67 2.08
4601 4923 5.455183 CCAGTCCCAGTATCAATTGATAGCA 60.455 44.000 25.14 6.83 37.67 3.49
4606 4928 7.826252 GTCCCAGTATCAATTGATAGCACATAT 59.174 37.037 25.14 3.25 37.67 1.78
4650 4972 0.543410 TAGAGGCAAAGGTGTCCCGA 60.543 55.000 0.00 0.00 35.12 5.14
4651 4973 1.072505 GAGGCAAAGGTGTCCCGAA 59.927 57.895 0.00 0.00 35.12 4.30
4664 4987 3.067742 GTGTCCCGAATTTCGAGGAGATA 59.932 47.826 19.91 10.58 43.74 1.98
4668 4991 3.068307 CCCGAATTTCGAGGAGATAGTGT 59.932 47.826 19.91 0.00 43.74 3.55
4717 5040 3.326836 TGATCCGACTACAAACATGCA 57.673 42.857 0.00 0.00 0.00 3.96
4788 5111 1.673477 TGCCAGAGCACGATCAACT 59.327 52.632 0.00 0.00 46.52 3.16
4819 5142 7.323656 CACGATGGTCTATTTTCTTCAAACAAC 59.676 37.037 0.00 0.00 0.00 3.32
4820 5143 7.012894 ACGATGGTCTATTTTCTTCAAACAACA 59.987 33.333 0.00 0.00 0.00 3.33
4831 5154 6.817765 TCTTCAAACAACAGAAGAACAAGT 57.182 33.333 2.65 0.00 45.13 3.16
4844 5167 9.110502 ACAGAAGAACAAGTAAGAAAACTAAGG 57.889 33.333 0.00 0.00 0.00 2.69
4872 5196 7.823799 TGCATCTGGATATTGCGAATATAAGAA 59.176 33.333 12.49 0.00 39.23 2.52
4896 5222 8.650143 AAGAAAGCTTTATTAATCAAGGTGGA 57.350 30.769 17.11 0.00 31.15 4.02
4905 5231 3.864789 AATCAAGGTGGAGTTCTGTGT 57.135 42.857 0.00 0.00 0.00 3.72
5055 5385 0.476771 TTTGTGACCCCTTGGAGGAC 59.523 55.000 0.00 0.00 37.67 3.85
5090 5421 1.338769 CCCTAACTCTGTTTCCCCACG 60.339 57.143 0.00 0.00 0.00 4.94
5186 5517 4.515567 GGCAACACCTATAATAACCTCTGC 59.484 45.833 0.00 0.00 34.51 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 9.806203 TCTTTTGTTGCATTATGATCTAAATGG 57.194 29.630 17.04 5.06 34.37 3.16
86 87 5.851047 AAATAGCTTGCATCTTTTGTTGC 57.149 34.783 0.00 0.00 43.42 4.17
103 104 4.749245 AGCAGTCGTTGGTCAAAAATAG 57.251 40.909 0.00 0.00 29.81 1.73
105 106 5.705609 ATAAGCAGTCGTTGGTCAAAAAT 57.294 34.783 0.00 0.00 36.24 1.82
188 189 7.279313 TGGATCGCCTATAAGTTTTGACTTTAC 59.721 37.037 0.00 0.00 34.31 2.01
197 198 7.308589 GCATGTATTTGGATCGCCTATAAGTTT 60.309 37.037 0.00 0.00 34.31 2.66
201 202 5.804639 AGCATGTATTTGGATCGCCTATAA 58.195 37.500 0.00 0.00 34.31 0.98
244 245 5.977635 TGGTCGATCCCATGATAATGTATC 58.022 41.667 0.00 0.00 33.89 2.24
277 278 7.996385 TGAATAAAAGAGGCCATAAGTTTAGC 58.004 34.615 5.01 0.42 0.00 3.09
337 338 5.248477 TGGATGAATAATACCCTACAGGAGC 59.752 44.000 0.00 0.00 39.89 4.70
404 405 6.550843 GTCTTTTGAAACCCAAACCAAAATG 58.449 36.000 0.00 0.00 43.82 2.32
405 406 5.352846 CGTCTTTTGAAACCCAAACCAAAAT 59.647 36.000 0.00 0.00 43.82 1.82
461 462 7.601073 TCTATGAGCACAACATGTAGAAAAG 57.399 36.000 0.00 0.00 0.00 2.27
479 480 8.049117 ACTCATGGCTTTTATCTTGTTCTATGA 58.951 33.333 0.00 0.00 0.00 2.15
557 558 8.973182 GGGAATAGGAAAACACATAAACCATAA 58.027 33.333 0.00 0.00 0.00 1.90
559 560 6.096282 CGGGAATAGGAAAACACATAAACCAT 59.904 38.462 0.00 0.00 0.00 3.55
622 628 1.529226 CAGTGCAAAACGATGGGGTA 58.471 50.000 0.00 0.00 0.00 3.69
730 737 6.871492 TCGTACAATATGATGTTGTTGTGTCT 59.129 34.615 12.70 0.00 40.13 3.41
738 745 8.703336 CCTTGAGTATCGTACAATATGATGTTG 58.297 37.037 0.08 0.08 38.61 3.33
930 937 2.629017 AGGGCCAAGAACCATTTGAT 57.371 45.000 6.18 0.00 0.00 2.57
1096 1103 1.540267 TCTCTTTGTCTCTTCGTCCCG 59.460 52.381 0.00 0.00 0.00 5.14
1102 1109 7.321745 TGTTTCCTTTTCTCTTTGTCTCTTC 57.678 36.000 0.00 0.00 0.00 2.87
1142 1149 3.913163 ACCAATTCTCTCACTTCCTCCTT 59.087 43.478 0.00 0.00 0.00 3.36
1176 1192 4.734370 GCAACAAAAATGAACATTGGTTGC 59.266 37.500 27.48 27.48 45.44 4.17
1345 1361 7.270757 ACGGAAATATAATGCACTGCAAATA 57.729 32.000 8.03 9.48 43.62 1.40
1379 1395 3.498777 GTGCCCAAGTAGTCTTCTTGAAC 59.501 47.826 18.05 11.02 43.17 3.18
1415 1431 5.763698 GCTCATGTCCTTTATAAACTACCCC 59.236 44.000 0.00 0.00 0.00 4.95
1690 1706 1.407437 GGTCCATCCCATCCGATATGC 60.407 57.143 0.00 0.00 0.00 3.14
1809 1825 9.949174 GCAAAACAAATATTGTGAAAATCCTTT 57.051 25.926 0.00 0.00 44.59 3.11
1922 1992 3.921119 AAGTCGCATGCTTTCATTTCA 57.079 38.095 17.13 0.00 0.00 2.69
1966 2037 1.969208 TGGCATTTTGAGAATGTGGCA 59.031 42.857 0.00 0.00 42.08 4.92
1999 2070 7.862274 TCCTAGTGTAATCAATGATCCAGAT 57.138 36.000 0.00 0.00 0.00 2.90
2001 2072 7.443575 CCTTTCCTAGTGTAATCAATGATCCAG 59.556 40.741 0.00 0.00 0.00 3.86
2004 2075 7.987458 TGACCTTTCCTAGTGTAATCAATGATC 59.013 37.037 0.00 0.00 0.00 2.92
2067 2138 1.578897 TTAGCATACACAGGCCCTCA 58.421 50.000 0.00 0.00 29.59 3.86
2074 2145 5.428253 AGGGTACACATTTAGCATACACAG 58.572 41.667 0.00 0.00 0.00 3.66
2087 2158 3.758554 GTCAAAGCATCAAGGGTACACAT 59.241 43.478 0.00 0.00 0.00 3.21
2105 2176 2.855187 GCGTTATTGTGTTTGGCGTCAA 60.855 45.455 0.00 0.00 0.00 3.18
2109 2180 1.450161 GTTGCGTTATTGTGTTTGGCG 59.550 47.619 0.00 0.00 0.00 5.69
2147 2219 0.175073 GCACTCCCCCTACTGTAACG 59.825 60.000 0.00 0.00 0.00 3.18
2149 2221 1.906574 CAAGCACTCCCCCTACTGTAA 59.093 52.381 0.00 0.00 0.00 2.41
2153 2225 0.044855 ATCCAAGCACTCCCCCTACT 59.955 55.000 0.00 0.00 0.00 2.57
2157 2229 1.279025 TGGTATCCAAGCACTCCCCC 61.279 60.000 0.00 0.00 0.00 5.40
2223 2295 6.554419 GCAATTGACATTGTCACATAGCTTA 58.446 36.000 18.84 2.64 42.60 3.09
2225 2297 4.437794 CGCAATTGACATTGTCACATAGCT 60.438 41.667 18.84 0.00 42.60 3.32
2372 2449 7.282224 TGAACACTAATACCAAGATTATGCACC 59.718 37.037 0.00 0.00 0.00 5.01
2382 2459 7.134815 GCAGCATATTGAACACTAATACCAAG 58.865 38.462 0.00 0.00 0.00 3.61
2397 2474 1.674441 CCTCTGTGGTGCAGCATATTG 59.326 52.381 23.18 13.81 44.66 1.90
2514 2591 9.851043 GTGTAGAAAAGTTAAGATTCATATCGC 57.149 33.333 0.00 0.00 35.85 4.58
2656 2733 7.411804 GCCCAATTGTGTTTCGAAAATAGAATG 60.412 37.037 13.10 8.32 0.00 2.67
2682 2759 3.577649 TCGAGCTAGTTGACTTTCCTG 57.422 47.619 0.00 0.00 0.00 3.86
2704 2781 8.739039 TCTACTCATCACAAACATTTTATTGGG 58.261 33.333 0.00 0.00 0.00 4.12
2719 2796 6.861065 TCTTGTTTTGGTTCTACTCATCAC 57.139 37.500 0.00 0.00 0.00 3.06
2802 2879 2.439507 TGGTTTCACTTGCCTCTCTTCT 59.560 45.455 0.00 0.00 0.00 2.85
2870 2952 8.718102 TGCAGTAATTATTCCTCTAGACAAAC 57.282 34.615 0.00 0.00 0.00 2.93
2872 2954 7.987458 CCTTGCAGTAATTATTCCTCTAGACAA 59.013 37.037 0.00 0.00 0.00 3.18
2873 2955 7.500992 CCTTGCAGTAATTATTCCTCTAGACA 58.499 38.462 0.00 0.00 0.00 3.41
2886 2968 4.641989 CCTCTTGTATGCCTTGCAGTAATT 59.358 41.667 0.00 0.00 43.65 1.40
2893 2975 2.113860 TGTCCTCTTGTATGCCTTGC 57.886 50.000 0.00 0.00 0.00 4.01
2903 2985 6.512903 CGGATTGAATTCATGATGTCCTCTTG 60.513 42.308 9.40 0.00 0.00 3.02
2943 3025 8.472413 AGGATTACTGTCTTAAGCACGTTATTA 58.528 33.333 0.00 0.00 0.00 0.98
2975 3057 2.158755 CCCAAAGGTGAGCTCGGAATAT 60.159 50.000 9.64 0.00 0.00 1.28
3081 3165 7.308229 GCCCATAGTGTATGAGACAAATTCATC 60.308 40.741 0.00 0.00 40.66 2.92
3291 3375 2.274542 TGAGAAGCCCATGGGTTAGAA 58.725 47.619 31.58 11.07 43.92 2.10
3661 3746 6.154363 CCTTCTTCTCCAAGATCTCAGTACTT 59.846 42.308 0.00 0.00 38.50 2.24
3817 3902 1.898154 GCCACTTCCTTCGGAGCTA 59.102 57.895 0.00 0.00 31.21 3.32
3835 3920 1.153369 ATCCTTGGTCGATGCACCG 60.153 57.895 0.00 0.00 39.62 4.94
3904 3989 7.737972 TTACAATTCGTGATCCTTTTCTTCA 57.262 32.000 0.00 0.00 0.00 3.02
3949 4034 2.554032 ACGCTTTCATCTCCAAACAAGG 59.446 45.455 0.00 0.00 0.00 3.61
3952 4037 3.126858 GCATACGCTTTCATCTCCAAACA 59.873 43.478 0.00 0.00 34.30 2.83
3953 4038 3.685058 GCATACGCTTTCATCTCCAAAC 58.315 45.455 0.00 0.00 34.30 2.93
4052 4138 1.135489 CACCTGCATGCTTGTGTCATC 60.135 52.381 23.58 0.00 0.00 2.92
4296 4615 4.825377 GTTGTGCGCCAACCTTTT 57.175 50.000 23.18 0.00 46.39 2.27
4443 4762 8.047310 TCCCCTTCTTTTATTCTACAAGATGTC 58.953 37.037 0.00 0.00 0.00 3.06
4485 4804 7.817418 AACACACATTTACATTTACTCCTGT 57.183 32.000 0.00 0.00 0.00 4.00
4512 4834 6.206829 GGTCATTACATAGCCCATAAACTTCC 59.793 42.308 0.00 0.00 0.00 3.46
4513 4835 6.206829 GGGTCATTACATAGCCCATAAACTTC 59.793 42.308 0.00 0.00 39.13 3.01
4558 4880 1.532868 GGCATGGTAATCACGCAGATC 59.467 52.381 0.00 0.00 36.10 2.75
4563 4885 0.657840 GACTGGCATGGTAATCACGC 59.342 55.000 0.00 0.00 33.19 5.34
4568 4890 1.298953 ACTGGGACTGGCATGGTAAT 58.701 50.000 0.00 0.00 0.00 1.89
4581 4903 5.628797 TGTGCTATCAATTGATACTGGGA 57.371 39.130 21.67 12.36 36.05 4.37
4650 4972 7.825331 TGATAGACACTATCTCCTCGAAATT 57.175 36.000 16.30 0.00 39.04 1.82
4651 4973 8.415950 AATGATAGACACTATCTCCTCGAAAT 57.584 34.615 16.30 1.28 39.04 2.17
4664 4987 5.880901 ACTCCACCAAAAATGATAGACACT 58.119 37.500 0.00 0.00 0.00 3.55
4668 4991 7.496346 AGTCTACTCCACCAAAAATGATAGA 57.504 36.000 0.00 0.00 0.00 1.98
4717 5040 2.472695 TGCTAAGGCACGACATTCTT 57.527 45.000 0.00 0.00 44.28 2.52
4811 5134 7.915293 TCTTACTTGTTCTTCTGTTGTTTGA 57.085 32.000 0.00 0.00 0.00 2.69
4819 5142 8.070769 GCCTTAGTTTTCTTACTTGTTCTTCTG 58.929 37.037 0.00 0.00 0.00 3.02
4820 5143 7.993758 AGCCTTAGTTTTCTTACTTGTTCTTCT 59.006 33.333 0.00 0.00 0.00 2.85
4831 5154 4.943705 CCAGATGCAGCCTTAGTTTTCTTA 59.056 41.667 0.00 0.00 0.00 2.10
4844 5167 1.516161 TCGCAATATCCAGATGCAGC 58.484 50.000 0.00 0.00 40.04 5.25
4872 5196 7.890655 ACTCCACCTTGATTAATAAAGCTTTCT 59.109 33.333 16.57 2.47 0.00 2.52
4896 5222 3.244353 CCAGACCAAGATGACACAGAACT 60.244 47.826 0.00 0.00 0.00 3.01
4905 5231 1.967779 TCAACGACCAGACCAAGATGA 59.032 47.619 0.00 0.00 0.00 2.92
5019 5346 2.043115 ACAAAATTCCCCCTCTCTTCCC 59.957 50.000 0.00 0.00 0.00 3.97
5090 5421 4.938226 AGGCTGTTTTTAGAGTCTGTATGC 59.062 41.667 1.86 0.00 0.00 3.14
5160 5491 4.957296 AGGTTATTATAGGTGTTGCCTCG 58.043 43.478 0.00 0.00 46.96 4.63
5186 5517 7.762615 ACAAGATGCCACTTCATAAATTTCATG 59.237 33.333 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.