Multiple sequence alignment - TraesCS2A01G209500

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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 TraesCS2A01G209500 chr2A 100.000 5112 0 0 1 5112 193703999 193709110 0.000000e+00 9441.0
1 TraesCS2A01G209500 chr2B 90.101 5142 296 94 9 5060 236044186 236049204 0.000000e+00 6479.0
2 TraesCS2A01G209500 chr2D 93.117 2339 122 20 2386 4703 179133287 179135607 0.000000e+00 3391.0
3 TraesCS2A01G209500 chr2D 90.399 1229 51 26 369 1580 179131328 179132506 0.000000e+00 1554.0
4 TraesCS2A01G209500 chr2D 93.369 377 14 6 4731 5101 179135602 179135973 9.680000e-152 547.0
5 TraesCS2A01G209500 chr2D 88.406 414 14 5 2000 2390 179132818 179133220 7.750000e-128 468.0
6 TraesCS2A01G209500 chr2D 89.572 374 26 2 9 381 179130951 179131312 3.610000e-126 462.0
7 TraesCS2A01G209500 chr2D 92.763 304 16 1 1650 1953 179132517 179132814 7.860000e-118 435.0
8 TraesCS2A01G209500 chr5D 81.500 200 18 7 4372 4568 422035236 422035419 4.120000e-31 147.0
9 TraesCS2A01G209500 chr3B 93.023 43 1 2 1551 1592 4423667 4423626 1.540000e-05 62.1


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 TraesCS2A01G209500 chr2A 193703999 193709110 5111 False 9441.000000 9441 100.000 1 5112 1 chr2A.!!$F1 5111
1 TraesCS2A01G209500 chr2B 236044186 236049204 5018 False 6479.000000 6479 90.101 9 5060 1 chr2B.!!$F1 5051
2 TraesCS2A01G209500 chr2D 179130951 179135973 5022 False 1142.833333 3391 91.271 9 5101 6 chr2D.!!$F1 5092

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
963 1020 0.336737 GACAGGAAGAGGGAGGGAGA 59.663 60.000 0.00 0.00 0.00 3.71 F
1310 1367 0.391793 GAGCTAACTCTTGGCCGCTT 60.392 55.000 0.00 0.00 40.03 4.68 F
1311 1368 0.674895 AGCTAACTCTTGGCCGCTTG 60.675 55.000 0.00 0.00 37.96 4.01 F
2988 3189 1.100510 CATCTGTGGCAAGATGTGGG 58.899 55.000 21.43 6.16 45.68 4.61 F
3022 3223 2.615912 GTGCTTTATCCTCCATGTCTGC 59.384 50.000 0.00 0.00 0.00 4.26 F
3135 3337 4.218417 GCAACATACTCTTGTTCCCATTGT 59.782 41.667 0.00 0.00 37.73 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2264 1.879380 TGACAAGCAAGAAATGGACGG 59.121 47.619 0.00 0.00 0.00 4.79 R
3155 3357 2.558359 ACAGCTCAAGTAAACCAATGGC 59.442 45.455 0.00 0.00 0.00 4.40 R
3227 3430 6.183360 AGCCATTGCCTGAAATAGTTTCATAC 60.183 38.462 5.67 2.75 40.65 2.39 R
4027 4231 0.182299 TGTCCATGCCACACAACTCA 59.818 50.000 0.00 0.00 0.00 3.41 R
4061 4265 0.463295 AGCGGCTGATGTTCATCAGG 60.463 55.000 30.95 21.40 46.08 3.86 R
4162 4366 0.725117 CCCCTTTCGATAACACGCAC 59.275 55.000 0.00 0.00 0.00 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
87 88 0.988832 TAGGAACGGCTTTGGGTCAT 59.011 50.000 0.00 0.00 0.00 3.06
157 159 7.391833 CCTTAGATCAACAAAAGAAAGCCTACT 59.608 37.037 0.00 0.00 0.00 2.57
168 170 5.622346 AGAAAGCCTACTATCCTTCCTTG 57.378 43.478 0.00 0.00 0.00 3.61
232 235 7.649306 AGAGAGAAATGAAAATTGTTTCCAACG 59.351 33.333 0.00 0.00 42.20 4.10
238 241 5.046529 TGAAAATTGTTTCCAACGATGTGG 58.953 37.500 0.00 0.00 42.20 4.17
258 261 2.888414 GGGTTCAATGGGAGAACGAAAA 59.112 45.455 0.00 0.00 44.78 2.29
272 275 1.268625 ACGAAAAAGAACGGCCATTCC 59.731 47.619 8.18 0.00 0.00 3.01
298 301 1.677052 GGTTTGGCCGAACAACTAACA 59.323 47.619 32.31 0.00 0.00 2.41
300 303 3.243602 GGTTTGGCCGAACAACTAACAAT 60.244 43.478 32.31 0.00 0.00 2.71
342 347 2.829914 GAGCATGATGCCCGCCAA 60.830 61.111 14.72 0.00 46.52 4.52
351 356 4.733542 GCCCGCCAAGTTGCCCTA 62.734 66.667 0.00 0.00 0.00 3.53
354 359 1.584495 CCGCCAAGTTGCCCTAAAC 59.416 57.895 0.00 0.00 0.00 2.01
358 363 2.482142 CGCCAAGTTGCCCTAAACAAAA 60.482 45.455 0.00 0.00 32.21 2.44
590 633 4.028490 CCAACCACCGCCAGGCTA 62.028 66.667 10.54 0.00 42.76 3.93
591 634 2.746277 CAACCACCGCCAGGCTAC 60.746 66.667 10.54 0.00 42.76 3.58
592 635 2.928396 AACCACCGCCAGGCTACT 60.928 61.111 10.54 0.00 42.76 2.57
593 636 2.955881 AACCACCGCCAGGCTACTC 61.956 63.158 10.54 0.00 42.76 2.59
594 637 4.162690 CCACCGCCAGGCTACTCC 62.163 72.222 10.54 0.00 42.76 3.85
596 639 2.760385 ACCGCCAGGCTACTCCTC 60.760 66.667 10.54 0.00 45.52 3.71
597 640 3.541713 CCGCCAGGCTACTCCTCC 61.542 72.222 10.54 0.00 45.52 4.30
598 641 3.541713 CGCCAGGCTACTCCTCCC 61.542 72.222 10.54 0.00 45.52 4.30
599 642 2.041405 GCCAGGCTACTCCTCCCT 60.041 66.667 3.29 0.00 45.52 4.20
643 686 3.788937 ACGTTATTATTAGCAGCCACGT 58.211 40.909 0.00 0.00 34.92 4.49
669 712 6.990447 GCTAATTGCCCGATTTAACCATCGA 61.990 44.000 10.43 0.00 44.85 3.59
780 823 2.203280 CACCTCACCGTGGGCAAA 60.203 61.111 0.00 0.00 0.00 3.68
813 856 1.668151 GAGTGCGAACAGGTGGGTC 60.668 63.158 0.00 0.00 0.00 4.46
827 871 3.905331 GGGTCTTCTCCCAAATCCC 57.095 57.895 0.00 0.00 46.30 3.85
844 888 0.820891 CCCATCGGAGATGCCCTTTG 60.821 60.000 4.60 0.00 45.12 2.77
892 944 9.213819 GCTTATTAATAAGACGTTAAAAACCCG 57.786 33.333 30.76 7.30 41.72 5.28
898 950 2.945206 GTTAAAAACCCGCCGCGA 59.055 55.556 15.93 0.00 0.00 5.87
899 951 1.440850 GTTAAAAACCCGCCGCGAC 60.441 57.895 15.93 0.00 0.00 5.19
914 966 2.488820 GACACGGGACCGAGTAGC 59.511 66.667 18.80 1.00 42.66 3.58
917 969 2.035312 ACGGGACCGAGTAGCAGT 59.965 61.111 18.80 0.00 42.83 4.40
923 976 0.860618 GACCGAGTAGCAGTAACGCG 60.861 60.000 3.53 3.53 39.44 6.01
924 977 1.136147 CCGAGTAGCAGTAACGCGT 59.864 57.895 5.58 5.58 38.29 6.01
963 1020 0.336737 GACAGGAAGAGGGAGGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
967 1024 0.759060 GGAAGAGGGAGGGAGAGAGC 60.759 65.000 0.00 0.00 0.00 4.09
975 1032 3.591835 GGGAGAGAGCGAGCGAGG 61.592 72.222 0.00 0.00 0.00 4.63
979 1036 3.591835 GAGAGCGAGCGAGGGAGG 61.592 72.222 0.00 0.00 0.00 4.30
980 1037 4.116585 AGAGCGAGCGAGGGAGGA 62.117 66.667 0.00 0.00 0.00 3.71
981 1038 3.591835 GAGCGAGCGAGGGAGGAG 61.592 72.222 0.00 0.00 0.00 3.69
982 1039 4.116585 AGCGAGCGAGGGAGGAGA 62.117 66.667 0.00 0.00 0.00 3.71
983 1040 3.591835 GCGAGCGAGGGAGGAGAG 61.592 72.222 0.00 0.00 0.00 3.20
984 1041 3.591835 CGAGCGAGGGAGGAGAGC 61.592 72.222 0.00 0.00 0.00 4.09
985 1042 3.591835 GAGCGAGGGAGGAGAGCG 61.592 72.222 0.00 0.00 0.00 5.03
1005 1062 3.474570 GAGGCTCCGTCCATGGCT 61.475 66.667 6.96 0.00 39.33 4.75
1310 1367 0.391793 GAGCTAACTCTTGGCCGCTT 60.392 55.000 0.00 0.00 40.03 4.68
1311 1368 0.674895 AGCTAACTCTTGGCCGCTTG 60.675 55.000 0.00 0.00 37.96 4.01
1378 1435 4.278513 TGGTTGCCACGGGGAAGG 62.279 66.667 8.67 0.00 32.69 3.46
1397 1458 6.040729 GGGAAGGTTGGAGATTCTACTAGTAC 59.959 46.154 0.00 0.00 0.00 2.73
1441 1502 2.652941 TGATTTTCTGCGGATTTGGC 57.347 45.000 0.00 0.00 0.00 4.52
1460 1521 1.368641 CCATAAACTGCGCTGCTGTA 58.631 50.000 14.80 4.54 39.66 2.74
1493 1557 9.445878 CCAACTCGATATGGAATACTAGTACTA 57.554 37.037 4.31 1.89 39.12 1.82
1617 1684 2.230508 CTGCTTGAAATGCCATCAGTGT 59.769 45.455 0.00 0.00 35.91 3.55
1724 1798 3.621558 AGGTCTTTGCCTAATTAGTGCC 58.378 45.455 17.82 6.01 37.04 5.01
1757 1831 3.995705 GGAGCATACTTCATCTCTGATGC 59.004 47.826 2.93 0.00 35.05 3.91
1773 1847 2.159000 TGATGCAGACTCGCAGATGATT 60.159 45.455 0.00 0.00 46.99 2.57
1774 1848 2.391616 TGCAGACTCGCAGATGATTT 57.608 45.000 0.00 0.00 36.86 2.17
1777 1851 4.053983 TGCAGACTCGCAGATGATTTATC 58.946 43.478 0.00 0.00 36.86 1.75
1781 1855 6.367149 GCAGACTCGCAGATGATTTATCATAA 59.633 38.462 5.25 0.00 46.84 1.90
1814 1888 6.289064 TCAAGGTTTAGTTTCTCTCTTGGAC 58.711 40.000 0.00 0.00 33.23 4.02
1840 1914 2.599659 GTTGGTTAACTCGAGTACCGG 58.400 52.381 25.33 0.00 39.14 5.28
1867 1941 9.466497 AAAGTATTTCCTAGCTTGAATCATGAA 57.534 29.630 0.00 0.00 27.08 2.57
1868 1942 9.638176 AAGTATTTCCTAGCTTGAATCATGAAT 57.362 29.630 0.00 0.00 0.00 2.57
1869 1943 9.064706 AGTATTTCCTAGCTTGAATCATGAATG 57.935 33.333 0.00 0.00 0.00 2.67
1870 1944 9.060347 GTATTTCCTAGCTTGAATCATGAATGA 57.940 33.333 0.00 0.00 41.70 2.57
1871 1945 7.943079 TTTCCTAGCTTGAATCATGAATGAA 57.057 32.000 0.00 0.00 40.69 2.57
1872 1946 7.943079 TTCCTAGCTTGAATCATGAATGAAA 57.057 32.000 0.00 0.00 40.69 2.69
1958 2038 4.156455 TCTGAACTTCTGCCTTTGTTCT 57.844 40.909 0.00 0.00 39.38 3.01
1962 2042 6.428159 TCTGAACTTCTGCCTTTGTTCTATTC 59.572 38.462 0.00 0.00 39.38 1.75
1963 2043 5.179368 TGAACTTCTGCCTTTGTTCTATTCG 59.821 40.000 0.00 0.00 39.38 3.34
1971 2052 4.691216 GCCTTTGTTCTATTCGACTGTCTT 59.309 41.667 6.21 0.00 0.00 3.01
2059 2140 2.096069 GGGTTCTTCGCTTTAACGTTCC 60.096 50.000 2.82 0.00 0.00 3.62
2137 2218 2.611225 GAGCCAATCTCGGATCTTGT 57.389 50.000 0.00 0.00 38.48 3.16
2183 2264 3.609853 TGAGCAACTTATGACCATGTCC 58.390 45.455 0.00 0.00 0.00 4.02
2219 2300 4.260334 GCTTGTCATTTTTCTGTGCCAAAC 60.260 41.667 0.00 0.00 0.00 2.93
2222 2303 3.242712 GTCATTTTTCTGTGCCAAACGTG 59.757 43.478 0.00 0.00 0.00 4.49
2390 2565 9.594936 AGTAGACTATTCTTGATATAGTTGCCT 57.405 33.333 0.00 0.00 38.57 4.75
2497 2676 8.000780 AGAGGTGGAATATTTTGTTAGAATGC 57.999 34.615 0.00 0.00 0.00 3.56
2536 2715 7.315142 TGTTGAAATGAATGCTTACTTCCATC 58.685 34.615 0.00 0.00 0.00 3.51
2588 2767 7.176865 AGCTGTCTTCTGACTAGTTATACAACA 59.823 37.037 0.00 0.00 43.29 3.33
2724 2903 2.242043 CATTGGCAAGTCAACCCTCTT 58.758 47.619 5.96 0.00 0.00 2.85
2749 2928 5.927030 CAAGTATAACGTGCAGTGTCATTT 58.073 37.500 0.00 0.00 0.00 2.32
2861 3046 2.892852 CCAGATTGAAGCCCACAAGAAA 59.107 45.455 0.00 0.00 0.00 2.52
2870 3055 5.241506 TGAAGCCCACAAGAAATTGACTTAG 59.758 40.000 0.00 0.00 0.00 2.18
2937 3122 3.719173 TTTTGGTAAGGTTTCGCAAGG 57.281 42.857 0.00 0.00 38.47 3.61
2938 3123 2.351706 TTGGTAAGGTTTCGCAAGGT 57.648 45.000 0.00 0.00 38.47 3.50
2939 3124 3.488778 TTGGTAAGGTTTCGCAAGGTA 57.511 42.857 0.00 0.00 38.47 3.08
2988 3189 1.100510 CATCTGTGGCAAGATGTGGG 58.899 55.000 21.43 6.16 45.68 4.61
3022 3223 2.615912 GTGCTTTATCCTCCATGTCTGC 59.384 50.000 0.00 0.00 0.00 4.26
3028 3229 5.848286 TTATCCTCCATGTCTGCCAATAT 57.152 39.130 0.00 0.00 0.00 1.28
3135 3337 4.218417 GCAACATACTCTTGTTCCCATTGT 59.782 41.667 0.00 0.00 37.73 2.71
3227 3430 9.515020 GAACTCTTATTCACTCTTCTGATACAG 57.485 37.037 0.00 0.00 0.00 2.74
3395 3598 4.891992 TCCGAAGAAGAATCAGGAAACT 57.108 40.909 0.00 0.00 46.44 2.66
3596 3799 6.913873 TTGAGTTAATATTGGTAGTTCGGC 57.086 37.500 0.00 0.00 0.00 5.54
3807 4011 5.368230 TGCCAGGTTATATACATTCAGACCA 59.632 40.000 1.42 0.00 0.00 4.02
3958 4162 4.626771 CGGGGTGATACCATTTGTTTAGGA 60.627 45.833 0.00 0.00 41.02 2.94
4027 4231 5.963865 ACCATTTGTGCTTATAAAATCCCCT 59.036 36.000 0.00 0.00 0.00 4.79
4056 4260 4.581824 GTGTGGCATGGACAGAATATCAAT 59.418 41.667 0.00 0.00 0.00 2.57
4060 4264 4.021719 GGCATGGACAGAATATCAATTGGG 60.022 45.833 5.42 0.00 0.00 4.12
4061 4265 4.560108 GCATGGACAGAATATCAATTGGGC 60.560 45.833 5.42 0.00 0.00 5.36
4092 4296 4.148825 GCCGCTCGTCCCATCAGT 62.149 66.667 0.00 0.00 0.00 3.41
4162 4366 3.601443 AAAGAACAGGTGGATCTCTCG 57.399 47.619 0.00 0.00 0.00 4.04
4181 4385 0.725117 GTGCGTGTTATCGAAAGGGG 59.275 55.000 0.00 0.00 0.00 4.79
4216 4421 0.397675 TCAGTGGATCCCTCTGCGAT 60.398 55.000 21.86 0.00 42.71 4.58
4455 4661 0.313043 GCGAGATTGGGCATGAATGG 59.687 55.000 0.00 0.00 0.00 3.16
4483 4692 6.698329 TCAAATGTTCTGCTTCTTTGATGTTG 59.302 34.615 0.00 0.00 32.52 3.33
4484 4693 5.779529 ATGTTCTGCTTCTTTGATGTTGT 57.220 34.783 0.00 0.00 0.00 3.32
4485 4694 5.581126 TGTTCTGCTTCTTTGATGTTGTT 57.419 34.783 0.00 0.00 0.00 2.83
4497 4706 8.696410 TCTTTGATGTTGTTTCTTGTAAAACC 57.304 30.769 0.00 0.00 38.16 3.27
4498 4707 7.762159 TCTTTGATGTTGTTTCTTGTAAAACCC 59.238 33.333 0.00 0.00 38.16 4.11
4509 4718 2.599677 TGTAAAACCCGCCTTCCATTT 58.400 42.857 0.00 0.00 0.00 2.32
4510 4719 2.966516 TGTAAAACCCGCCTTCCATTTT 59.033 40.909 0.00 0.00 0.00 1.82
4514 4723 2.009681 ACCCGCCTTCCATTTTTCTT 57.990 45.000 0.00 0.00 0.00 2.52
4534 4743 9.691362 TTTTCTTTGCTAACATCATTTACCTTC 57.309 29.630 0.00 0.00 0.00 3.46
4626 4850 9.506018 CATAACAAAAGAGGGGATCAAAATTTT 57.494 29.630 0.00 0.00 0.00 1.82
4635 4859 8.659527 AGAGGGGATCAAAATTTTTGTGTTTAT 58.340 29.630 18.69 7.11 0.00 1.40
4636 4860 9.283768 GAGGGGATCAAAATTTTTGTGTTTATT 57.716 29.630 18.69 4.24 0.00 1.40
4637 4861 9.639563 AGGGGATCAAAATTTTTGTGTTTATTT 57.360 25.926 18.69 1.08 0.00 1.40
4657 4881 9.814507 TTTATTTAGCTTACACAAATACACACG 57.185 29.630 0.00 0.00 0.00 4.49
4704 4928 1.940613 GATTCCATTCGCCAGTACACC 59.059 52.381 0.00 0.00 0.00 4.16
4724 4950 2.149578 CTGCTGGAGGTTTCAGAACAG 58.850 52.381 0.00 0.00 37.51 3.16
4735 4961 4.096382 GGTTTCAGAACAGAAAAGAGCACA 59.904 41.667 0.00 0.00 39.05 4.57
4736 4962 5.221126 GGTTTCAGAACAGAAAAGAGCACAT 60.221 40.000 0.00 0.00 39.05 3.21
4737 4963 5.428496 TTCAGAACAGAAAAGAGCACATG 57.572 39.130 0.00 0.00 0.00 3.21
4879 5107 0.327924 ACATGCGGGATGACCTTTCA 59.672 50.000 16.77 0.00 35.80 2.69
4897 5125 8.992835 ACCTTTCAATTTCTTAATCAATCTGC 57.007 30.769 0.00 0.00 0.00 4.26
4975 5203 7.136822 TGCCAAACCACTAGAATGTCTATAT 57.863 36.000 0.00 0.00 0.00 0.86
5016 5247 3.573967 ACGGATTTGGCATCTTTTCTTGT 59.426 39.130 0.00 0.00 0.00 3.16
5075 5308 6.640518 TCAACTATCCTAGCTTACTTTGTGG 58.359 40.000 0.00 0.00 0.00 4.17
5092 5325 0.770499 TGGTGATCACAGCCCAAAGA 59.230 50.000 26.47 0.00 42.95 2.52
5101 5334 2.298163 CACAGCCCAAAGAAGCAGAAAT 59.702 45.455 0.00 0.00 0.00 2.17
5102 5335 2.298163 ACAGCCCAAAGAAGCAGAAATG 59.702 45.455 0.00 0.00 0.00 2.32
5103 5336 2.559668 CAGCCCAAAGAAGCAGAAATGA 59.440 45.455 0.00 0.00 0.00 2.57
5104 5337 3.194968 CAGCCCAAAGAAGCAGAAATGAT 59.805 43.478 0.00 0.00 0.00 2.45
5105 5338 3.194968 AGCCCAAAGAAGCAGAAATGATG 59.805 43.478 0.00 0.00 0.00 3.07
5106 5339 3.056322 GCCCAAAGAAGCAGAAATGATGT 60.056 43.478 0.00 0.00 0.00 3.06
5107 5340 4.158394 GCCCAAAGAAGCAGAAATGATGTA 59.842 41.667 0.00 0.00 0.00 2.29
5108 5341 5.678107 GCCCAAAGAAGCAGAAATGATGTAG 60.678 44.000 0.00 0.00 0.00 2.74
5109 5342 5.163581 CCCAAAGAAGCAGAAATGATGTAGG 60.164 44.000 0.00 0.00 0.00 3.18
5110 5343 5.163581 CCAAAGAAGCAGAAATGATGTAGGG 60.164 44.000 0.00 0.00 0.00 3.53
5111 5344 4.851639 AGAAGCAGAAATGATGTAGGGT 57.148 40.909 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.408634 GGCCTTCTGCTAGTTTTGTACA 58.591 45.455 0.00 0.00 40.92 2.90
151 153 1.768870 TGCCAAGGAAGGATAGTAGGC 59.231 52.381 0.00 0.00 41.15 3.93
157 159 7.404104 ACATCTATATCATGCCAAGGAAGGATA 59.596 37.037 4.05 4.05 0.00 2.59
194 196 8.994429 TTTCATTTCTCTCTTAGTCTCATGTC 57.006 34.615 0.00 0.00 0.00 3.06
232 235 2.755103 GTTCTCCCATTGAACCCACATC 59.245 50.000 0.00 0.00 38.19 3.06
238 241 4.277423 TCTTTTTCGTTCTCCCATTGAACC 59.723 41.667 0.00 0.00 40.26 3.62
272 275 1.299544 GTTCGGCCAAACCCAAACG 60.300 57.895 2.24 0.00 33.26 3.60
342 347 4.828072 TTTGGTTTTGTTTAGGGCAACT 57.172 36.364 0.00 0.00 0.00 3.16
351 356 3.563390 CGGGCAATCATTTGGTTTTGTTT 59.437 39.130 0.00 0.00 33.22 2.83
354 359 1.464219 GCGGGCAATCATTTGGTTTTG 59.536 47.619 0.00 0.00 33.22 2.44
358 363 1.190833 TTGGCGGGCAATCATTTGGT 61.191 50.000 13.46 0.00 33.22 3.67
414 449 2.799207 CGTGCACCTCAAATTTTGCAGT 60.799 45.455 14.04 1.73 45.31 4.40
590 633 3.369388 GGGGGAGGAGGGAGGAGT 61.369 72.222 0.00 0.00 0.00 3.85
591 634 3.368501 TGGGGGAGGAGGGAGGAG 61.369 72.222 0.00 0.00 0.00 3.69
592 635 3.368501 CTGGGGGAGGAGGGAGGA 61.369 72.222 0.00 0.00 0.00 3.71
593 636 3.368501 TCTGGGGGAGGAGGGAGG 61.369 72.222 0.00 0.00 0.00 4.30
594 637 2.041405 GTCTGGGGGAGGAGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
595 638 3.695825 GGTCTGGGGGAGGAGGGA 61.696 72.222 0.00 0.00 0.00 4.20
596 639 4.024984 TGGTCTGGGGGAGGAGGG 62.025 72.222 0.00 0.00 0.00 4.30
597 640 2.689034 GTGGTCTGGGGGAGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
598 641 3.077556 CGTGGTCTGGGGGAGGAG 61.078 72.222 0.00 0.00 0.00 3.69
669 712 1.300697 GACGAGGCGCCCGAATTAT 60.301 57.895 33.94 17.56 0.00 1.28
813 856 1.490490 TCCGATGGGATTTGGGAGAAG 59.510 52.381 0.00 0.00 37.43 2.85
827 871 2.028130 GCAAAGGGCATCTCCGATG 58.972 57.895 0.00 0.00 43.97 3.84
844 888 3.878667 CCGATTGGGAGAGGGGGC 61.879 72.222 0.00 0.00 38.47 5.80
898 950 2.282674 TGCTACTCGGTCCCGTGT 60.283 61.111 16.47 16.47 45.84 4.49
899 951 1.028330 TACTGCTACTCGGTCCCGTG 61.028 60.000 5.52 5.92 40.74 4.94
908 960 1.836555 CGTAACGCGTTACTGCTACTC 59.163 52.381 42.15 24.41 42.31 2.59
914 966 3.486408 TTGTTTCGTAACGCGTTACTG 57.514 42.857 42.15 35.88 42.31 2.74
917 969 4.891516 AGTTTTTGTTTCGTAACGCGTTA 58.108 34.783 26.87 26.87 42.13 3.18
923 976 6.316319 TGTCCTGAAGTTTTTGTTTCGTAAC 58.684 36.000 0.00 0.00 34.75 2.50
924 977 6.403855 CCTGTCCTGAAGTTTTTGTTTCGTAA 60.404 38.462 0.00 0.00 0.00 3.18
963 1020 4.116585 TCCTCCCTCGCTCGCTCT 62.117 66.667 0.00 0.00 0.00 4.09
967 1024 3.591835 GCTCTCCTCCCTCGCTCG 61.592 72.222 0.00 0.00 0.00 5.03
985 1042 4.899239 CATGGACGGAGCCTCGCC 62.899 72.222 0.00 0.64 0.00 5.54
986 1043 4.899239 CCATGGACGGAGCCTCGC 62.899 72.222 5.56 0.00 0.00 5.03
1310 1367 7.015098 ACCAATACAGGTTTGATGAATGAAACA 59.985 33.333 7.51 0.00 39.34 2.83
1311 1368 7.378181 ACCAATACAGGTTTGATGAATGAAAC 58.622 34.615 0.00 0.00 39.34 2.78
1341 1398 0.953960 CCGAAAACAGGTCCTTCCGG 60.954 60.000 0.00 0.00 41.99 5.14
1378 1435 8.454570 AAGCTAGTACTAGTAGAATCTCCAAC 57.545 38.462 26.76 8.94 35.65 3.77
1397 1458 8.719648 CAATATGGAAAGATTGAGCTAAGCTAG 58.280 37.037 0.00 0.00 39.88 3.42
1441 1502 1.368641 TACAGCAGCGCAGTTTATGG 58.631 50.000 11.47 0.00 29.63 2.74
1460 1521 8.103305 AGTATTCCATATCGAGTTGGCATAAAT 58.897 33.333 10.77 8.28 32.80 1.40
1493 1557 4.542662 GCAGTATTCATGCGAGACAAAT 57.457 40.909 0.00 0.00 33.31 2.32
1588 1655 4.025360 TGGCATTTCAAGCAGTATCCATT 58.975 39.130 0.00 0.00 0.00 3.16
1640 1707 9.989869 GCTAGGAAGAACTAACAAATAAATGAC 57.010 33.333 0.00 0.00 0.00 3.06
1647 1714 8.870075 ATTGAAGCTAGGAAGAACTAACAAAT 57.130 30.769 0.00 0.00 0.00 2.32
1648 1715 7.117812 CGATTGAAGCTAGGAAGAACTAACAAA 59.882 37.037 0.00 0.00 0.00 2.83
1655 1722 3.619038 CCACGATTGAAGCTAGGAAGAAC 59.381 47.826 0.00 0.00 0.00 3.01
1668 1735 3.074412 GCCTTTCTTCTTCCACGATTGA 58.926 45.455 0.00 0.00 0.00 2.57
1724 1798 1.209019 AGTATGCTCCAAGGACAGCTG 59.791 52.381 13.48 13.48 0.00 4.24
1757 1831 7.880059 TTATGATAAATCATCTGCGAGTCTG 57.120 36.000 8.69 0.00 43.72 3.51
1814 1888 5.866092 GGTACTCGAGTTAACCAACCTAAAG 59.134 44.000 25.95 0.00 35.05 1.85
1840 1914 9.113838 TCATGATTCAAGCTAGGAAATACTTTC 57.886 33.333 5.00 0.00 38.94 2.62
1958 2038 8.504005 GGAATCTTTTTCAAAGACAGTCGAATA 58.496 33.333 1.02 0.00 0.00 1.75
1962 2042 6.060028 TGGAATCTTTTTCAAAGACAGTCG 57.940 37.500 1.02 0.00 0.00 4.18
1963 2043 8.877808 AAATGGAATCTTTTTCAAAGACAGTC 57.122 30.769 1.02 0.00 0.00 3.51
1971 2052 6.930722 GCAGAGGAAAATGGAATCTTTTTCAA 59.069 34.615 17.12 0.00 0.00 2.69
2137 2218 6.906901 AGGGTATTATCTGTACCTGAAGGAAA 59.093 38.462 2.62 0.00 41.11 3.13
2183 2264 1.879380 TGACAAGCAAGAAATGGACGG 59.121 47.619 0.00 0.00 0.00 4.79
2222 2303 3.926616 ACCTACACAGCAATGTGACTAC 58.073 45.455 14.85 0.00 42.02 2.73
2262 2366 4.041321 GGTTTCCTACTTCCTACCAACAGT 59.959 45.833 0.00 0.00 0.00 3.55
2449 2628 6.895756 TCTCTAGCATTAGGAGGAAGTTGTTA 59.104 38.462 0.00 0.00 0.00 2.41
2452 2631 5.221422 CCTCTCTAGCATTAGGAGGAAGTTG 60.221 48.000 0.00 0.00 41.79 3.16
2497 2676 8.592105 TTCATTTCAACAAATTTAGCAAGAGG 57.408 30.769 0.00 0.00 28.97 3.69
2588 2767 9.788889 TCAAACATCATATGCATTATCTTCTCT 57.211 29.630 3.54 0.00 0.00 3.10
2605 2784 3.635836 TCACATTGGCAAGTCAAACATCA 59.364 39.130 5.96 0.00 0.00 3.07
2743 2922 8.041323 TCTCTAGTTTATGTTGGAGGAAATGAC 58.959 37.037 0.00 0.00 0.00 3.06
2749 2928 7.921041 ATGATCTCTAGTTTATGTTGGAGGA 57.079 36.000 0.00 0.00 0.00 3.71
2844 3029 4.590222 AGTCAATTTCTTGTGGGCTTCAAT 59.410 37.500 0.00 0.00 33.87 2.57
2846 3031 3.565307 AGTCAATTTCTTGTGGGCTTCA 58.435 40.909 0.00 0.00 33.87 3.02
2988 3189 7.100458 AGGATAAAGCACATTTGGTTGATAC 57.900 36.000 0.00 0.00 42.74 2.24
3022 3223 8.706492 AACACAAATTTATCAGCACATATTGG 57.294 30.769 0.00 0.00 0.00 3.16
3028 3229 8.196771 AGAGAAAAACACAAATTTATCAGCACA 58.803 29.630 0.00 0.00 31.05 4.57
3107 3308 3.253188 GGAACAAGAGTATGTTGCAGCAA 59.747 43.478 7.52 2.83 44.23 3.91
3155 3357 2.558359 ACAGCTCAAGTAAACCAATGGC 59.442 45.455 0.00 0.00 0.00 4.40
3227 3430 6.183360 AGCCATTGCCTGAAATAGTTTCATAC 60.183 38.462 5.67 2.75 40.65 2.39
3328 3531 2.104963 AGAGAACAGAACCAAGTCCCAC 59.895 50.000 0.00 0.00 0.00 4.61
3395 3598 7.713507 CAGAAATACTTACCCGGATATTGAACA 59.286 37.037 0.73 0.00 0.00 3.18
3449 3652 5.517054 GTGCACTAGTAAGCTGTAATCTGTC 59.483 44.000 10.32 0.00 0.00 3.51
3537 3740 7.432252 CAGTTATTGTTCATTCGATTAAAGCCC 59.568 37.037 0.00 0.00 0.00 5.19
3596 3799 4.016444 ACATACAAACTGGCAAGGGTATG 58.984 43.478 19.90 19.90 39.90 2.39
3843 4047 7.078249 ACAACTGTGAGGCCAATATATATCA 57.922 36.000 5.01 0.00 0.00 2.15
3845 4049 7.078249 TGACAACTGTGAGGCCAATATATAT 57.922 36.000 5.01 0.00 0.00 0.86
3846 4050 6.493189 TGACAACTGTGAGGCCAATATATA 57.507 37.500 5.01 0.00 0.00 0.86
3958 4162 3.070015 CCTTGTTTCCTTCACCATTGCTT 59.930 43.478 0.00 0.00 0.00 3.91
4027 4231 0.182299 TGTCCATGCCACACAACTCA 59.818 50.000 0.00 0.00 0.00 3.41
4056 4260 1.956636 GCTGATGTTCATCAGGCCCAA 60.957 52.381 30.95 5.96 46.08 4.12
4061 4265 0.463295 AGCGGCTGATGTTCATCAGG 60.463 55.000 30.95 21.40 46.08 3.86
4092 4296 1.002430 CTTACTCCTGCTCTGGTTGCA 59.998 52.381 0.00 0.00 38.81 4.08
4162 4366 0.725117 CCCCTTTCGATAACACGCAC 59.275 55.000 0.00 0.00 0.00 5.34
4216 4421 3.657398 ATCACAGGGCTGATGATTTCA 57.343 42.857 0.00 0.00 31.90 2.69
4233 4438 3.554934 ACAACAAACAGGCAGAGAATCA 58.445 40.909 0.00 0.00 37.82 2.57
4444 4650 4.411256 ACATTTGATTCCATTCATGCCC 57.589 40.909 0.00 0.00 0.00 5.36
4455 4661 7.597743 ACATCAAAGAAGCAGAACATTTGATTC 59.402 33.333 8.34 0.00 44.17 2.52
4483 4692 3.551454 GGAAGGCGGGTTTTACAAGAAAC 60.551 47.826 0.00 0.00 38.49 2.78
4484 4693 2.624364 GGAAGGCGGGTTTTACAAGAAA 59.376 45.455 0.00 0.00 0.00 2.52
4485 4694 2.232399 GGAAGGCGGGTTTTACAAGAA 58.768 47.619 0.00 0.00 0.00 2.52
4497 4706 2.068519 GCAAAGAAAAATGGAAGGCGG 58.931 47.619 0.00 0.00 0.00 6.13
4498 4707 3.030668 AGCAAAGAAAAATGGAAGGCG 57.969 42.857 0.00 0.00 0.00 5.52
4509 4718 9.077885 AGAAGGTAAATGATGTTAGCAAAGAAA 57.922 29.630 0.00 0.00 34.58 2.52
4510 4719 8.635765 AGAAGGTAAATGATGTTAGCAAAGAA 57.364 30.769 0.00 0.00 34.58 2.52
4541 4750 9.896645 ACACATGTAATTATCAATTCTCAGAGT 57.103 29.630 0.00 0.00 32.38 3.24
4592 4802 5.045213 TCCCCTCTTTTGTTATGTGCTATGA 60.045 40.000 0.00 0.00 0.00 2.15
4635 4859 5.334260 GCCGTGTGTATTTGTGTAAGCTAAA 60.334 40.000 0.00 0.00 0.00 1.85
4636 4860 4.152759 GCCGTGTGTATTTGTGTAAGCTAA 59.847 41.667 0.00 0.00 0.00 3.09
4637 4861 3.680937 GCCGTGTGTATTTGTGTAAGCTA 59.319 43.478 0.00 0.00 0.00 3.32
4638 4862 2.482721 GCCGTGTGTATTTGTGTAAGCT 59.517 45.455 0.00 0.00 0.00 3.74
4654 4878 3.423154 GCTTCTTCCACGGCCGTG 61.423 66.667 44.04 44.04 45.02 4.94
4656 4880 1.982073 GATTGCTTCTTCCACGGCCG 61.982 60.000 26.86 26.86 0.00 6.13
4657 4881 1.657751 GGATTGCTTCTTCCACGGCC 61.658 60.000 0.00 0.00 31.99 6.13
4666 4890 0.970937 TCGTCTCCCGGATTGCTTCT 60.971 55.000 0.73 0.00 37.11 2.85
4704 4928 2.149578 CTGTTCTGAAACCTCCAGCAG 58.850 52.381 0.00 0.00 34.28 4.24
4724 4950 6.017109 TCCTAACAAAGTCATGTGCTCTTTTC 60.017 38.462 0.00 0.00 32.81 2.29
4735 4961 7.611467 TGCATCACTTTATCCTAACAAAGTCAT 59.389 33.333 0.00 0.00 41.78 3.06
4736 4962 6.939730 TGCATCACTTTATCCTAACAAAGTCA 59.060 34.615 0.00 0.00 41.78 3.41
4737 4963 7.377766 TGCATCACTTTATCCTAACAAAGTC 57.622 36.000 0.00 0.00 41.78 3.01
4879 5107 8.571336 CCCTTATCGCAGATTGATTAAGAAATT 58.429 33.333 0.00 0.00 45.12 1.82
4897 5125 1.616374 GAGCTTCCTCCTCCCTTATCG 59.384 57.143 0.00 0.00 31.68 2.92
4975 5203 1.902918 GGGGCACATGCAAGACACA 60.903 57.895 6.15 0.00 44.36 3.72
5059 5292 4.631813 GTGATCACCACAAAGTAAGCTAGG 59.368 45.833 15.31 0.00 45.03 3.02
5072 5305 0.883833 CTTTGGGCTGTGATCACCAC 59.116 55.000 22.85 14.22 45.88 4.16
5075 5308 1.200948 GCTTCTTTGGGCTGTGATCAC 59.799 52.381 19.27 19.27 0.00 3.06
5083 5316 2.880443 TCATTTCTGCTTCTTTGGGCT 58.120 42.857 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.