Multiple sequence alignment - TraesCS6A01G234400

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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 TraesCS6A01G234400 chr6A 100.000 5022 0 0 1 5022 442392090 442397111 0.000000e+00 9274
1 TraesCS6A01G234400 chr6A 92.771 166 12 0 3462 3627 297641216 297641381 1.810000e-59 241
2 TraesCS6A01G234400 chr6B 94.120 5085 192 44 1 5022 474172215 474177255 0.000000e+00 7635
3 TraesCS6A01G234400 chr6D 89.684 2782 161 49 1 2733 306703102 306705806 0.000000e+00 3432
4 TraesCS6A01G234400 chr6D 93.261 1558 83 14 3481 5022 306707971 306709522 0.000000e+00 2276
5 TraesCS6A01G234400 chr6D 95.859 483 19 1 3007 3488 306707254 306707736 0.000000e+00 780
6 TraesCS6A01G234400 chr6D 90.071 141 13 1 2740 2879 306707104 306707244 1.110000e-41 182
7 TraesCS6A01G234400 chr4B 93.333 165 11 0 3463 3627 28724140 28724304 1.400000e-60 244
8 TraesCS6A01G234400 chr2A 92.899 169 11 1 3460 3628 249754625 249754458 1.400000e-60 244
9 TraesCS6A01G234400 chr3B 93.293 164 11 0 3464 3627 519860082 519860245 5.020000e-60 243
10 TraesCS6A01G234400 chr4D 91.860 172 12 1 3466 3637 465125471 465125302 6.500000e-59 239
11 TraesCS6A01G234400 chr2D 92.308 169 12 1 3460 3628 250630892 250630725 6.500000e-59 239
12 TraesCS6A01G234400 chr1A 89.674 184 16 3 3446 3628 291255803 291255984 1.090000e-56 231


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 TraesCS6A01G234400 chr6A 442392090 442397111 5021 False 9274.0 9274 100.00000 1 5022 1 chr6A.!!$F2 5021
1 TraesCS6A01G234400 chr6B 474172215 474177255 5040 False 7635.0 7635 94.12000 1 5022 1 chr6B.!!$F1 5021
2 TraesCS6A01G234400 chr6D 306703102 306709522 6420 False 1667.5 3432 92.21875 1 5022 4 chr6D.!!$F1 5021

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
193 196 0.252284 TCCAAGACCAGGAGGACCTC 60.252 60.000 13.6 13.6 45.94 3.85 F
1192 1236 0.242825 TCTAAGAGCAACGGTCGTGG 59.757 55.000 0.0 0.0 35.00 4.94 F
1377 1425 1.134699 TGGCACTGCTAATCTTCTCCG 60.135 52.381 0.0 0.0 0.00 4.63 F
2654 2730 1.341285 CCTTTGTCAGATGGATGGGCA 60.341 52.381 0.0 0.0 0.00 5.36 F
2954 4327 0.321671 TTGTGCCTCTGCCACTAGAC 59.678 55.000 0.0 0.0 36.33 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 1763 0.395586 GGAAGCACACCATGGCCATA 60.396 55.0 20.30 0.00 0.00 2.74 R
2813 4180 0.249120 CGTAGCTCCACCATTGGTCA 59.751 55.0 5.04 0.00 44.35 4.02 R
2879 4252 0.898326 AAATTGTTCCCTCACGCCCC 60.898 55.0 0.00 0.00 0.00 5.80 R
3509 5129 1.466856 TTGCTCCGTATGTAGTCCGT 58.533 50.0 0.00 0.00 0.00 4.69 R
4630 6267 1.795170 ATTTGCGTGCGCTTCAAGGT 61.795 50.0 17.49 0.66 42.51 3.50 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
83 86 2.503943 CGTAGCACGTTGCCTTTAAG 57.496 50.000 6.39 0.00 46.52 1.85
96 99 4.497300 TGCCTTTAAGTATACACGTCACC 58.503 43.478 5.50 0.00 0.00 4.02
160 163 4.390264 ACTTTAGACTTGTTCCTTCAGCC 58.610 43.478 0.00 0.00 0.00 4.85
193 196 0.252284 TCCAAGACCAGGAGGACCTC 60.252 60.000 13.60 13.60 45.94 3.85
279 282 4.533222 CTAGCTCTTTCTAGAAGCGTAGC 58.467 47.826 16.49 16.49 46.02 3.58
350 368 4.640771 AGGTACTCAATTTTCAGCTCCA 57.359 40.909 0.00 0.00 0.00 3.86
351 369 5.184892 AGGTACTCAATTTTCAGCTCCAT 57.815 39.130 0.00 0.00 0.00 3.41
354 372 2.494870 ACTCAATTTTCAGCTCCATGGC 59.505 45.455 6.96 0.00 0.00 4.40
355 373 2.758979 CTCAATTTTCAGCTCCATGGCT 59.241 45.455 6.96 0.00 44.10 4.75
357 375 3.579586 TCAATTTTCAGCTCCATGGCTTT 59.420 39.130 6.96 0.00 41.00 3.51
360 378 5.743636 ATTTTCAGCTCCATGGCTTTTTA 57.256 34.783 6.96 0.00 41.00 1.52
361 379 5.743636 TTTTCAGCTCCATGGCTTTTTAT 57.256 34.783 6.96 0.00 41.00 1.40
362 380 5.743636 TTTCAGCTCCATGGCTTTTTATT 57.256 34.783 6.96 0.00 41.00 1.40
363 381 5.743636 TTCAGCTCCATGGCTTTTTATTT 57.256 34.783 6.96 0.00 41.00 1.40
364 382 5.329035 TCAGCTCCATGGCTTTTTATTTC 57.671 39.130 6.96 0.00 41.00 2.17
365 383 4.160252 TCAGCTCCATGGCTTTTTATTTCC 59.840 41.667 6.96 0.00 41.00 3.13
366 384 4.081531 CAGCTCCATGGCTTTTTATTTCCA 60.082 41.667 6.96 0.00 41.00 3.53
367 385 4.718276 AGCTCCATGGCTTTTTATTTCCAT 59.282 37.500 6.96 0.00 39.86 3.41
368 386 5.052481 GCTCCATGGCTTTTTATTTCCATC 58.948 41.667 6.96 0.00 37.22 3.51
369 387 5.604565 CTCCATGGCTTTTTATTTCCATCC 58.395 41.667 6.96 0.00 37.22 3.51
370 388 4.408596 TCCATGGCTTTTTATTTCCATCCC 59.591 41.667 6.96 0.00 37.22 3.85
371 389 4.163839 CCATGGCTTTTTATTTCCATCCCA 59.836 41.667 0.00 0.00 37.22 4.37
372 390 5.339035 CCATGGCTTTTTATTTCCATCCCAA 60.339 40.000 0.00 0.00 37.22 4.12
373 391 5.419239 TGGCTTTTTATTTCCATCCCAAG 57.581 39.130 0.00 0.00 0.00 3.61
457 475 0.460284 CCGTGCACCATGAGACCTAC 60.460 60.000 12.15 0.00 0.00 3.18
458 476 0.532573 CGTGCACCATGAGACCTACT 59.467 55.000 12.15 0.00 0.00 2.57
459 477 1.749063 CGTGCACCATGAGACCTACTA 59.251 52.381 12.15 0.00 0.00 1.82
607 646 0.877071 CCATTCGCTCAAGTTGCACT 59.123 50.000 0.00 0.00 0.00 4.40
611 650 0.389025 TCGCTCAAGTTGCACTCTCA 59.611 50.000 0.00 0.00 0.00 3.27
623 665 5.766670 AGTTGCACTCTCATTTCTGATTCAA 59.233 36.000 0.00 0.00 0.00 2.69
669 713 3.439129 GGCTAATTAAAGGTGCACGTTCT 59.561 43.478 23.75 15.97 0.00 3.01
866 910 4.109766 CGTCAGTGTCTTACAACAGTTGA 58.890 43.478 20.56 0.89 30.33 3.18
916 960 4.459337 CACAGGTTCCTTGGGATAAACTTC 59.541 45.833 0.00 0.00 0.00 3.01
929 973 7.470192 TGGGATAAACTTCTTTCCTTGATCTT 58.530 34.615 0.00 0.00 0.00 2.40
930 974 7.950124 TGGGATAAACTTCTTTCCTTGATCTTT 59.050 33.333 0.00 0.00 0.00 2.52
931 975 9.462606 GGGATAAACTTCTTTCCTTGATCTTTA 57.537 33.333 0.00 0.00 0.00 1.85
943 987 5.654650 TCCTTGATCTTTAGTCTCCAGTCTC 59.345 44.000 0.00 0.00 0.00 3.36
967 1011 3.073735 CAGCTGACCGGCTCTCCT 61.074 66.667 8.42 0.00 41.00 3.69
968 1012 2.757917 AGCTGACCGGCTCTCCTC 60.758 66.667 0.00 0.00 38.24 3.71
979 1023 2.418197 CGGCTCTCCTCCAAATTCGTTA 60.418 50.000 0.00 0.00 0.00 3.18
980 1024 3.741388 CGGCTCTCCTCCAAATTCGTTAT 60.741 47.826 0.00 0.00 0.00 1.89
981 1025 3.810386 GGCTCTCCTCCAAATTCGTTATC 59.190 47.826 0.00 0.00 0.00 1.75
1005 1049 1.481056 ATAGGGTAGCGTCCATGGGC 61.481 60.000 13.02 9.73 0.00 5.36
1029 1073 1.366854 GGGCGTCGAAATGGAAGGAC 61.367 60.000 0.00 0.00 0.00 3.85
1068 1112 3.591254 GAGGCCAAGAAGCGTCGGT 62.591 63.158 5.01 0.00 37.84 4.69
1133 1177 0.522495 GACTTCTCGCAGTCTCTCGC 60.522 60.000 2.88 0.00 40.23 5.03
1143 1187 1.064946 GTCTCTCGCGGATCACCTG 59.935 63.158 6.13 0.00 0.00 4.00
1192 1236 0.242825 TCTAAGAGCAACGGTCGTGG 59.757 55.000 0.00 0.00 35.00 4.94
1275 1319 1.840635 GTGTAGAGGGGATCCTGCTTT 59.159 52.381 12.58 0.00 45.05 3.51
1377 1425 1.134699 TGGCACTGCTAATCTTCTCCG 60.135 52.381 0.00 0.00 0.00 4.63
1396 1444 1.829222 CGGGCTTTGGAAGAGTACCTA 59.171 52.381 0.00 0.00 0.00 3.08
1438 1486 5.409826 GGTGAAAGAAAGTGAGTGTATCCTG 59.590 44.000 0.00 0.00 0.00 3.86
1571 1629 2.457598 AGAGGACGATGCTGAGGTAAA 58.542 47.619 0.00 0.00 0.00 2.01
1572 1630 3.034635 AGAGGACGATGCTGAGGTAAAT 58.965 45.455 0.00 0.00 0.00 1.40
1573 1631 4.215908 AGAGGACGATGCTGAGGTAAATA 58.784 43.478 0.00 0.00 0.00 1.40
1574 1632 4.649674 AGAGGACGATGCTGAGGTAAATAA 59.350 41.667 0.00 0.00 0.00 1.40
1575 1633 5.128827 AGAGGACGATGCTGAGGTAAATAAA 59.871 40.000 0.00 0.00 0.00 1.40
1576 1634 5.741011 AGGACGATGCTGAGGTAAATAAAA 58.259 37.500 0.00 0.00 0.00 1.52
1577 1635 6.357367 AGGACGATGCTGAGGTAAATAAAAT 58.643 36.000 0.00 0.00 0.00 1.82
1705 1763 1.895707 GCTGTCTGTGCTGCACCTT 60.896 57.895 28.17 0.00 32.73 3.50
1738 1796 1.377994 CTTCCTGCAGGCCAACTCT 59.622 57.895 28.91 0.00 34.44 3.24
1808 1866 6.094603 GTCTGAAGGTTAGTCATTCGGTACTA 59.905 42.308 0.00 0.00 41.96 1.82
1994 2054 1.741327 TACTTCCGCAGATACCGCCC 61.741 60.000 0.00 0.00 0.00 6.13
2080 2140 4.566987 ACGTCTACTGAATTCTTTGGTCC 58.433 43.478 7.05 0.00 0.00 4.46
2196 2257 8.670804 TTTGATGATTTTTGTTTTGCAAAGTG 57.329 26.923 12.41 0.00 46.40 3.16
2209 2270 5.843673 TTGCAAAGTGTAAGGACAAATCA 57.156 34.783 0.00 0.00 37.31 2.57
2277 2353 3.814842 TCTGTCACATTGGTTGCAAGTAG 59.185 43.478 0.00 0.00 0.00 2.57
2336 2412 5.305585 TCTTGGGATGTTTGAGTGACTTAC 58.694 41.667 0.00 0.00 0.00 2.34
2417 2493 1.871039 GCCACTTTAGCAGTCAAACGA 59.129 47.619 0.00 0.00 30.92 3.85
2470 2546 3.251972 CAGCAGGTGTTTCTTCTTTCTCC 59.748 47.826 0.00 0.00 0.00 3.71
2475 2551 3.815962 GGTGTTTCTTCTTTCTCCCAGAC 59.184 47.826 0.00 0.00 0.00 3.51
2483 2559 7.808279 TCTTCTTTCTCCCAGACCTATTTTA 57.192 36.000 0.00 0.00 0.00 1.52
2499 2575 8.895141 ACCTATTTTAAAGGGCTTATGAAGTT 57.105 30.769 0.00 0.00 38.54 2.66
2524 2600 3.879892 GAGCATATGGGTCTGTTCTTTCC 59.120 47.826 4.56 0.00 40.87 3.13
2544 2620 8.689061 TCTTTCCCATCATACTTCATCATTTTG 58.311 33.333 0.00 0.00 0.00 2.44
2569 2645 4.852134 TTGCATTCAACAGCTATTGTGT 57.148 36.364 4.34 0.00 40.74 3.72
2574 2650 5.973565 GCATTCAACAGCTATTGTGTAATCC 59.026 40.000 4.34 0.00 40.74 3.01
2585 2661 8.730680 AGCTATTGTGTAATCCTTTTGTACTTG 58.269 33.333 0.00 0.00 0.00 3.16
2627 2703 7.392494 TCTACAGATTAAGGATAGCATACCG 57.608 40.000 0.00 0.00 0.00 4.02
2642 2718 1.344065 TACCGGAGCTTCCTTTGTCA 58.656 50.000 9.46 0.00 33.30 3.58
2654 2730 1.341285 CCTTTGTCAGATGGATGGGCA 60.341 52.381 0.00 0.00 0.00 5.36
2870 4243 2.290287 TGTACCGCCCAGCTCATGT 61.290 57.895 0.00 0.00 0.00 3.21
2879 4252 0.803117 CCAGCTCATGTGCAGAACTG 59.197 55.000 20.92 10.14 34.99 3.16
2893 4266 3.192103 AACTGGGGCGTGAGGGAAC 62.192 63.158 0.00 0.00 0.00 3.62
2896 4269 2.355115 GGGGCGTGAGGGAACAAT 59.645 61.111 0.00 0.00 0.00 2.71
2918 4291 1.746991 GTGCTCACCTTAGCCTGGC 60.747 63.158 11.65 11.65 42.05 4.85
2954 4327 0.321671 TTGTGCCTCTGCCACTAGAC 59.678 55.000 0.00 0.00 36.33 2.59
2979 4352 7.286775 ACGCAACCTTACATATCCCATTTAAAT 59.713 33.333 0.00 0.00 0.00 1.40
3476 4854 4.836175 TGCATTGTATAATACTCCCTCCGA 59.164 41.667 0.00 0.00 0.00 4.55
3638 5259 5.671493 ACGGAGGGAGTAGTTGAATATTTG 58.329 41.667 0.00 0.00 0.00 2.32
4212 5834 6.715718 TCGACCAGTTAAAATGAATTACCCAA 59.284 34.615 0.00 0.00 0.00 4.12
4370 5999 3.126000 GCTGCTCACTAAAATCACAGGAC 59.874 47.826 0.00 0.00 0.00 3.85
4491 6125 5.741388 TTGCAGAGAACTTCAAGAGAAAC 57.259 39.130 0.00 0.00 32.35 2.78
4492 6126 4.769688 TGCAGAGAACTTCAAGAGAAACA 58.230 39.130 0.00 0.00 32.35 2.83
4493 6127 5.371526 TGCAGAGAACTTCAAGAGAAACAT 58.628 37.500 0.00 0.00 32.35 2.71
4630 6267 2.954318 GTGGTTACTAGCCGAGGATACA 59.046 50.000 0.00 0.00 41.41 2.29
4654 6291 1.198867 TGAAGCGCACGCAAATAACAT 59.801 42.857 18.24 0.00 44.88 2.71
4715 6352 6.131972 CCATACAATGGGTCCTCAATCTAT 57.868 41.667 0.00 0.00 46.86 1.98
4718 6355 7.772292 CCATACAATGGGTCCTCAATCTATATG 59.228 40.741 0.00 0.00 46.86 1.78
4849 6487 3.604130 GCACCGAACATGCATACAC 57.396 52.632 0.00 0.00 42.88 2.90
4984 6622 8.041323 CCTCAACAACTATAACACCATAACTCT 58.959 37.037 0.00 0.00 0.00 3.24
5014 6652 5.728471 AGACACCAATAGAGAATCACACTG 58.272 41.667 0.00 0.00 37.82 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 86 8.644318 AAAATCTAGAATGGTGACGTGTATAC 57.356 34.615 0.00 0.00 0.00 1.47
96 99 8.175716 GGGAAACGAGTTGTAAAATCTAGAATG 58.824 37.037 0.00 0.00 39.08 2.67
160 163 1.630369 TCTTGGAGTTGGAGGTGATGG 59.370 52.381 0.00 0.00 0.00 3.51
193 196 0.317479 AACTGGAGGAGAACGAACGG 59.683 55.000 0.00 0.00 0.00 4.44
279 282 4.266502 GTCTTGCAGCAAAGATACGTAGAG 59.733 45.833 9.65 0.00 38.41 2.43
280 283 4.174009 GTCTTGCAGCAAAGATACGTAGA 58.826 43.478 9.65 0.00 38.41 2.59
281 284 3.926527 TGTCTTGCAGCAAAGATACGTAG 59.073 43.478 9.65 0.00 38.41 3.51
350 368 5.488561 ACTTGGGATGGAAATAAAAAGCCAT 59.511 36.000 0.00 0.00 43.46 4.40
351 369 4.843516 ACTTGGGATGGAAATAAAAAGCCA 59.156 37.500 0.00 0.00 34.45 4.75
354 372 7.670364 ACTGAACTTGGGATGGAAATAAAAAG 58.330 34.615 0.00 0.00 0.00 2.27
355 373 7.610580 ACTGAACTTGGGATGGAAATAAAAA 57.389 32.000 0.00 0.00 0.00 1.94
357 375 8.581578 GTTTACTGAACTTGGGATGGAAATAAA 58.418 33.333 0.00 0.00 35.31 1.40
360 378 5.480422 GGTTTACTGAACTTGGGATGGAAAT 59.520 40.000 0.00 0.00 38.35 2.17
361 379 4.830600 GGTTTACTGAACTTGGGATGGAAA 59.169 41.667 0.00 0.00 38.35 3.13
362 380 4.403734 GGTTTACTGAACTTGGGATGGAA 58.596 43.478 0.00 0.00 38.35 3.53
363 381 3.245122 GGGTTTACTGAACTTGGGATGGA 60.245 47.826 0.00 0.00 38.35 3.41
364 382 3.089284 GGGTTTACTGAACTTGGGATGG 58.911 50.000 0.00 0.00 38.35 3.51
365 383 4.034285 AGGGTTTACTGAACTTGGGATG 57.966 45.455 0.00 0.00 38.35 3.51
366 384 4.508584 GGAAGGGTTTACTGAACTTGGGAT 60.509 45.833 0.00 0.00 38.35 3.85
367 385 3.181437 GGAAGGGTTTACTGAACTTGGGA 60.181 47.826 0.00 0.00 38.35 4.37
368 386 3.154710 GGAAGGGTTTACTGAACTTGGG 58.845 50.000 0.00 0.00 38.35 4.12
369 387 3.827722 TGGAAGGGTTTACTGAACTTGG 58.172 45.455 0.00 0.00 38.35 3.61
370 388 5.772521 CAATGGAAGGGTTTACTGAACTTG 58.227 41.667 0.00 0.00 38.35 3.16
371 389 4.280929 GCAATGGAAGGGTTTACTGAACTT 59.719 41.667 0.00 0.00 38.35 2.66
372 390 3.826729 GCAATGGAAGGGTTTACTGAACT 59.173 43.478 0.00 0.00 38.35 3.01
373 391 3.826729 AGCAATGGAAGGGTTTACTGAAC 59.173 43.478 0.00 0.00 37.53 3.18
457 475 3.839293 AGTACTCGAAAAGCAGTGCTAG 58.161 45.455 20.09 14.14 38.25 3.42
458 476 3.936372 AGTACTCGAAAAGCAGTGCTA 57.064 42.857 20.09 0.38 38.25 3.49
459 477 2.821991 AGTACTCGAAAAGCAGTGCT 57.178 45.000 13.14 13.14 42.56 4.40
494 524 4.336713 GGGTTAGCTGAGCTGGAAATTAAG 59.663 45.833 18.79 0.00 40.10 1.85
623 665 4.941263 TCGCTTGTTCCTGCACTAATAATT 59.059 37.500 0.00 0.00 0.00 1.40
669 713 2.905075 CCGCACTGATAATCTGAACCA 58.095 47.619 0.00 0.00 0.00 3.67
866 910 4.039488 TGAAACCAAAGCTCAGCAATCAAT 59.961 37.500 0.00 0.00 0.00 2.57
916 960 6.706295 ACTGGAGACTAAAGATCAAGGAAAG 58.294 40.000 0.00 0.00 0.00 2.62
929 973 2.897969 GGTTGTGGAGACTGGAGACTAA 59.102 50.000 0.00 0.00 0.00 2.24
930 974 2.158370 TGGTTGTGGAGACTGGAGACTA 60.158 50.000 0.00 0.00 0.00 2.59
931 975 1.343069 GGTTGTGGAGACTGGAGACT 58.657 55.000 0.00 0.00 0.00 3.24
932 976 1.001406 CTGGTTGTGGAGACTGGAGAC 59.999 57.143 0.00 0.00 0.00 3.36
933 977 1.342074 CTGGTTGTGGAGACTGGAGA 58.658 55.000 0.00 0.00 0.00 3.71
934 978 0.321122 GCTGGTTGTGGAGACTGGAG 60.321 60.000 0.00 0.00 0.00 3.86
935 979 0.764369 AGCTGGTTGTGGAGACTGGA 60.764 55.000 0.00 0.00 0.00 3.86
943 987 2.669569 CCGGTCAGCTGGTTGTGG 60.670 66.667 15.13 5.47 36.39 4.17
967 1011 4.988540 CCTATCTGCGATAACGAATTTGGA 59.011 41.667 0.00 0.00 42.66 3.53
968 1012 4.152402 CCCTATCTGCGATAACGAATTTGG 59.848 45.833 0.00 0.00 42.66 3.28
1005 1049 2.398554 CCATTTCGACGCCCCACAG 61.399 63.158 0.00 0.00 0.00 3.66
1068 1112 2.654802 GAGGAAGACGACCACCTCA 58.345 57.895 17.57 0.00 45.53 3.86
1133 1177 0.460987 GCTCTTGTCCAGGTGATCCG 60.461 60.000 0.00 0.00 39.05 4.18
1143 1187 1.374758 CTCCACCGTGCTCTTGTCC 60.375 63.158 0.00 0.00 0.00 4.02
1192 1236 1.578583 GATTCCTGCATTGCCATTGC 58.421 50.000 6.12 4.66 40.55 3.56
1224 1268 2.815647 GTCCTTCGCCTCGGCTTG 60.816 66.667 6.35 0.00 39.32 4.01
1275 1319 1.413118 TATGTAGCAGGCTAGCAGCA 58.587 50.000 26.63 13.95 44.75 4.41
1377 1425 2.093075 GGTAGGTACTCTTCCAAAGCCC 60.093 54.545 0.00 0.00 41.75 5.19
1669 1727 1.133976 AGCACCTCATACCAAGCATCC 60.134 52.381 0.00 0.00 0.00 3.51
1705 1763 0.395586 GGAAGCACACCATGGCCATA 60.396 55.000 20.30 0.00 0.00 2.74
1738 1796 1.561643 ATGACCTCGGAAGAAGCAGA 58.438 50.000 0.00 0.00 41.32 4.26
1783 1841 4.189639 ACCGAATGACTAACCTTCAGAC 57.810 45.455 0.00 0.00 0.00 3.51
2220 2281 9.780413 GTTCAGTTTTGGATGAGATTAAGAATC 57.220 33.333 0.00 0.00 38.20 2.52
2229 2304 6.419484 TGAGTAGTTCAGTTTTGGATGAGA 57.581 37.500 0.00 0.00 0.00 3.27
2336 2412 3.881688 CTCCCTGTAGCATTTGAAGATGG 59.118 47.826 0.00 0.00 0.00 3.51
2417 2493 1.337823 ACCATCTCGCAAGCTAAACGT 60.338 47.619 0.00 0.00 37.18 3.99
2470 2546 7.060421 TCATAAGCCCTTTAAAATAGGTCTGG 58.940 38.462 0.00 0.00 0.00 3.86
2483 2559 5.509498 TGCTCATAACTTCATAAGCCCTTT 58.491 37.500 0.00 0.00 0.00 3.11
2499 2575 5.894298 AAGAACAGACCCATATGCTCATA 57.106 39.130 0.00 0.00 0.00 2.15
2544 2620 6.018832 ACACAATAGCTGTTGAATGCAAAAAC 60.019 34.615 27.54 0.00 35.47 2.43
2627 2703 2.026822 TCCATCTGACAAAGGAAGCTCC 60.027 50.000 0.00 0.00 36.58 4.70
2813 4180 0.249120 CGTAGCTCCACCATTGGTCA 59.751 55.000 5.04 0.00 44.35 4.02
2870 4243 3.535629 CTCACGCCCCAGTTCTGCA 62.536 63.158 0.00 0.00 0.00 4.41
2879 4252 0.898326 AAATTGTTCCCTCACGCCCC 60.898 55.000 0.00 0.00 0.00 5.80
2893 4266 3.256631 AGGCTAAGGTGAGCACAAAATTG 59.743 43.478 2.75 0.00 44.76 2.32
2896 4269 2.229792 CAGGCTAAGGTGAGCACAAAA 58.770 47.619 2.75 0.00 44.76 2.44
2918 4291 2.493278 CACAAAGAAATAGCTGGGTGGG 59.507 50.000 0.00 0.00 0.00 4.61
2954 4327 6.627395 TTAAATGGGATATGTAAGGTTGCG 57.373 37.500 0.00 0.00 0.00 4.85
2979 4352 4.141733 TGTGTGATCTGGTGAAGACTTCAA 60.142 41.667 19.32 4.64 42.15 2.69
3040 4414 7.252708 GTCTCTAGTTAGCAAGGTAAAGAGAC 58.747 42.308 23.75 23.75 46.52 3.36
3297 4671 4.844655 ACAGTAGTAGATTTGGGACAGGTT 59.155 41.667 0.00 0.00 42.39 3.50
3509 5129 1.466856 TTGCTCCGTATGTAGTCCGT 58.533 50.000 0.00 0.00 0.00 4.69
3511 5131 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
3556 5176 8.322828 ACGGACTACATACAGATGTCTATAGAT 58.677 37.037 5.57 0.00 43.01 1.98
3617 5238 7.339482 AGTTCAAATATTCAACTACTCCCTCC 58.661 38.462 9.87 0.00 0.00 4.30
3638 5259 6.961218 GCTTCAAGCAAAACTCTGCAAGTTC 61.961 44.000 3.89 3.91 43.52 3.01
3753 5374 4.005650 TGGAGCTTGCTTAATGTCTCTTG 58.994 43.478 0.00 0.00 0.00 3.02
4212 5834 3.251484 TCTTCAGATCCTTGGACCTTGT 58.749 45.455 0.00 0.00 0.00 3.16
4370 5999 3.599343 TCACAGAATGGACTGAAATCCG 58.401 45.455 0.00 0.00 43.62 4.18
4553 6187 8.931385 AGCACCATGTTTCAAAATATGTATTC 57.069 30.769 10.18 0.12 36.23 1.75
4555 6189 7.981225 GGAAGCACCATGTTTCAAAATATGTAT 59.019 33.333 10.18 0.00 39.01 2.29
4630 6267 1.795170 ATTTGCGTGCGCTTCAAGGT 61.795 50.000 17.49 0.66 42.51 3.50
4718 6355 9.793259 TTCTTCTTAATGGATGGGTTATACATC 57.207 33.333 0.00 0.00 39.51 3.06


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

AutoCloner maintained by Alex Coulton.