Multiple sequence alignment - TraesCS1A01G095600

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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 TraesCS1A01G095600 chr1A 100.000 3420 0 0 1 3420 91173621 91177040 0.000000e+00 6316
1 TraesCS1A01G095600 chr1B 92.993 2469 107 27 303 2730 156839677 156837234 0.000000e+00 3541
2 TraesCS1A01G095600 chr1B 84.629 566 48 17 2748 3292 156836971 156836424 8.410000e-146 527
3 TraesCS1A01G095600 chr1B 88.172 186 19 3 1 184 156839846 156839662 5.750000e-53 219
4 TraesCS1A01G095600 chr1D 91.534 2445 137 39 284 2709 95934926 95937319 0.000000e+00 3304
5 TraesCS1A01G095600 chr1D 87.798 713 44 22 2730 3420 95937565 95938256 0.000000e+00 795
6 TraesCS1A01G095600 chr1D 92.222 180 13 1 1 180 95934773 95934951 1.580000e-63 254
7 TraesCS1A01G095600 chr6B 85.200 973 98 23 1321 2260 35515149 35516108 0.000000e+00 957
8 TraesCS1A01G095600 chr6B 88.312 231 26 1 990 1219 35514875 35515105 3.360000e-70 276
9 TraesCS1A01G095600 chr6A 88.235 799 75 7 1464 2262 20508943 20509722 0.000000e+00 937
10 TraesCS1A01G095600 chr6A 87.097 248 31 1 980 1226 20508466 20508713 2.600000e-71 279
11 TraesCS1A01G095600 chr6D 82.860 1091 121 37 1464 2530 20590306 20591354 0.000000e+00 918
12 TraesCS1A01G095600 chr6D 87.500 248 30 1 980 1226 20589830 20590077 5.590000e-73 285
13 TraesCS1A01G095600 chr6D 76.543 486 83 21 362 836 20588993 20589458 1.590000e-58 237


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 TraesCS1A01G095600 chr1A 91173621 91177040 3419 False 6316.0 6316 100.000 1 3420 1 chr1A.!!$F1 3419
1 TraesCS1A01G095600 chr1B 156836424 156839846 3422 True 1429.0 3541 88.598 1 3292 3 chr1B.!!$R1 3291
2 TraesCS1A01G095600 chr1D 95934773 95938256 3483 False 1451.0 3304 90.518 1 3420 3 chr1D.!!$F1 3419
3 TraesCS1A01G095600 chr6B 35514875 35516108 1233 False 616.5 957 86.756 990 2260 2 chr6B.!!$F1 1270
4 TraesCS1A01G095600 chr6A 20508466 20509722 1256 False 608.0 937 87.666 980 2262 2 chr6A.!!$F1 1282
5 TraesCS1A01G095600 chr6D 20588993 20591354 2361 False 480.0 918 82.301 362 2530 3 chr6D.!!$F1 2168

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
983 1282 0.110678 AGTCGACCACTCAGGAGTCA 59.889 55.0 13.01 0.0 40.2 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2580 3003 0.539438 TTGCGTTTCAGCCCTTGGAT 60.539 50.0 0.0 0.0 36.02 3.41 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
45 46 1.877680 CGACACCAGTGGCTCATTTGA 60.878 52.381 9.78 0.00 36.16 2.69
64 65 8.092068 TCATTTGAAAGTAGAAGACGATTGGTA 58.908 33.333 0.00 0.00 0.00 3.25
77 78 3.285258 TTGGTACCCCAAGGACCTT 57.715 52.632 10.07 0.00 45.93 3.50
127 128 3.429881 GCTTTGTAATGCTTGACTTTGGC 59.570 43.478 0.00 0.00 0.00 4.52
150 151 0.250234 TGGATCTGGTGGCTTCTTCG 59.750 55.000 0.00 0.00 0.00 3.79
186 187 9.803130 GTACGTAGAAAAAGAAAGAATGTAACC 57.197 33.333 0.00 0.00 0.00 2.85
187 188 7.868775 ACGTAGAAAAAGAAAGAATGTAACCC 58.131 34.615 0.00 0.00 0.00 4.11
188 189 7.499895 ACGTAGAAAAAGAAAGAATGTAACCCA 59.500 33.333 0.00 0.00 0.00 4.51
237 238 9.783081 ATTAAATGCATTCATTCTTTATTCCCC 57.217 29.630 13.38 0.00 41.77 4.81
238 239 5.813513 ATGCATTCATTCTTTATTCCCCC 57.186 39.130 0.00 0.00 0.00 5.40
265 266 8.634335 CCCCCAAAAATAAAAAGAATGAATGT 57.366 30.769 0.00 0.00 0.00 2.71
266 267 9.732130 CCCCCAAAAATAAAAAGAATGAATGTA 57.268 29.630 0.00 0.00 0.00 2.29
461 462 4.019174 GTTGAGATCCCAATGGACATTGT 58.981 43.478 20.08 5.52 45.58 2.71
515 517 9.277783 CTAATGGGGAGAAAATCTTGTATACAG 57.722 37.037 5.56 1.19 0.00 2.74
544 546 4.278669 ACACTAGCCGGTATATTCTCACAG 59.721 45.833 1.90 0.00 0.00 3.66
596 598 1.817357 TGGCAGAAGCAAGATGAGTG 58.183 50.000 0.00 0.00 44.61 3.51
597 599 1.348696 TGGCAGAAGCAAGATGAGTGA 59.651 47.619 0.00 0.00 44.61 3.41
602 604 3.072944 AGAAGCAAGATGAGTGAAGCAC 58.927 45.455 0.00 0.00 34.10 4.40
604 606 3.969287 AGCAAGATGAGTGAAGCACTA 57.031 42.857 0.00 0.00 45.44 2.74
605 607 3.594134 AGCAAGATGAGTGAAGCACTAC 58.406 45.455 0.00 0.00 45.44 2.73
674 681 3.505680 AGTGCTATGAAACCGCATCAAAA 59.494 39.130 0.00 0.00 35.93 2.44
747 771 6.481644 TGCCCAAAGAAATAAAATGTGTGAAC 59.518 34.615 0.00 0.00 0.00 3.18
765 793 1.141449 CGAGAGCAAGCCAGAGAGG 59.859 63.158 0.00 0.00 41.84 3.69
766 794 1.521616 GAGAGCAAGCCAGAGAGGG 59.478 63.158 0.00 0.00 38.09 4.30
767 795 1.970352 GAGAGCAAGCCAGAGAGGGG 61.970 65.000 0.00 0.00 38.09 4.79
983 1282 0.110678 AGTCGACCACTCAGGAGTCA 59.889 55.000 13.01 0.00 40.20 3.41
987 1286 0.892063 GACCACTCAGGAGTCAGGAC 59.108 60.000 11.52 3.48 40.20 3.85
1195 1494 3.181485 CCTCGAGAGGTAATCAACTGACC 60.181 52.174 15.71 0.00 43.61 4.02
1201 1500 6.255887 CGAGAGGTAATCAACTGACCATTTAC 59.744 42.308 0.00 0.00 35.56 2.01
1209 1512 8.788325 AATCAACTGACCATTTACTTACCTAC 57.212 34.615 0.00 0.00 0.00 3.18
1211 1514 7.383687 TCAACTGACCATTTACTTACCTACTG 58.616 38.462 0.00 0.00 0.00 2.74
1241 1545 8.674263 ATCAAGTCATGATTAGGAAGCTAAAG 57.326 34.615 0.00 0.00 46.85 1.85
1254 1558 5.841237 AGGAAGCTAAAGATCAGTGGCTATA 59.159 40.000 6.89 0.00 0.00 1.31
1255 1559 6.500049 AGGAAGCTAAAGATCAGTGGCTATAT 59.500 38.462 6.89 0.00 0.00 0.86
1319 1640 9.868277 GATCCATCTTAACTAATATGAGTGAGG 57.132 37.037 0.00 0.00 0.00 3.86
1338 1667 5.525378 GTGAGGTCCATGACTGTTAATGATC 59.475 44.000 0.00 0.00 32.47 2.92
1348 1677 4.521146 ACTGTTAATGATCTTGCAGGAGG 58.479 43.478 4.35 0.00 0.00 4.30
1450 1821 5.044624 TGACCTCCCTTTGAATTCATCATCT 60.045 40.000 9.40 0.00 38.03 2.90
1453 1824 5.889853 CCTCCCTTTGAATTCATCATCTTCA 59.110 40.000 9.40 0.00 38.03 3.02
1454 1825 6.550108 CCTCCCTTTGAATTCATCATCTTCAT 59.450 38.462 9.40 0.00 38.03 2.57
1455 1826 7.255520 CCTCCCTTTGAATTCATCATCTTCATC 60.256 40.741 9.40 0.00 38.03 2.92
1458 1829 8.082852 CCCTTTGAATTCATCATCTTCATCATC 58.917 37.037 9.40 0.00 38.03 2.92
1849 2261 3.343421 GCCAACGTGACGTGGTCC 61.343 66.667 12.85 0.00 39.99 4.46
1993 2405 3.083997 GGGGAGGACATGTCGGCT 61.084 66.667 19.33 11.76 0.00 5.52
2029 2441 4.034258 GACGTGGGTCTCGTCGCA 62.034 66.667 0.00 0.00 45.64 5.10
2362 2777 1.098050 GCGCCATGAACAAGGAAGAT 58.902 50.000 0.00 0.00 0.00 2.40
2498 2913 1.009389 CCACGAGGAGCTGTTTCGTC 61.009 60.000 12.28 0.00 44.83 4.20
2518 2933 5.132897 GTCTGACAGAGACTCTTGAATGT 57.867 43.478 5.10 0.00 46.85 2.71
2580 3003 7.383687 ACTAGAAACTTTATGAACCATCGTCA 58.616 34.615 0.00 0.00 0.00 4.35
2651 3074 3.006967 GGGAGCGGCTATTTCTAAGATGA 59.993 47.826 0.60 0.00 0.00 2.92
2652 3075 3.991121 GGAGCGGCTATTTCTAAGATGAC 59.009 47.826 0.60 0.00 0.00 3.06
2658 3081 5.511373 CGGCTATTTCTAAGATGACATGGGA 60.511 44.000 0.00 0.00 0.00 4.37
2700 3123 6.591062 TGGATGATTCAGCTTTGTTTTTATGC 59.409 34.615 1.44 0.00 0.00 3.14
2717 3140 1.294138 GCTGCCCACATTGTGCAAT 59.706 52.632 11.41 0.00 34.06 3.56
2730 3153 6.748658 CACATTGTGCAATTTGATCGACTTAT 59.251 34.615 3.43 0.00 31.91 1.73
2731 3154 7.274033 CACATTGTGCAATTTGATCGACTTATT 59.726 33.333 3.43 0.00 31.91 1.40
2733 3156 8.736742 CATTGTGCAATTTGATCGACTTATTAC 58.263 33.333 0.00 0.00 0.00 1.89
2734 3157 7.371126 TGTGCAATTTGATCGACTTATTACA 57.629 32.000 0.00 0.00 0.00 2.41
2737 3160 9.289303 GTGCAATTTGATCGACTTATTACAAAT 57.711 29.630 0.00 0.00 38.83 2.32
2766 3435 6.466308 ACTTTTGGCGATTTAGAAATTTGC 57.534 33.333 0.00 0.00 32.59 3.68
2787 3456 8.746922 TTTGCAACTCTGATATGAAAATGTTC 57.253 30.769 0.00 0.00 0.00 3.18
2789 3458 7.532571 TGCAACTCTGATATGAAAATGTTCAG 58.467 34.615 4.31 0.00 46.75 3.02
2791 3460 8.239314 GCAACTCTGATATGAAAATGTTCAGAA 58.761 33.333 4.31 0.00 46.75 3.02
2792 3461 9.552114 CAACTCTGATATGAAAATGTTCAGAAC 57.448 33.333 6.32 6.32 46.75 3.01
2793 3462 9.512588 AACTCTGATATGAAAATGTTCAGAACT 57.487 29.630 14.51 0.00 46.75 3.01
2794 3463 9.512588 ACTCTGATATGAAAATGTTCAGAACTT 57.487 29.630 14.51 5.37 46.75 2.66
2798 3467 9.695526 TGATATGAAAATGTTCAGAACTTTTGG 57.304 29.630 21.75 0.00 46.75 3.28
2799 3468 6.849588 ATGAAAATGTTCAGAACTTTTGGC 57.150 33.333 21.75 17.76 46.75 4.52
2800 3469 4.803088 TGAAAATGTTCAGAACTTTTGGCG 59.197 37.500 21.75 0.00 38.88 5.69
2801 3470 4.647424 AAATGTTCAGAACTTTTGGCGA 57.353 36.364 20.83 0.00 37.36 5.54
2802 3471 4.853924 AATGTTCAGAACTTTTGGCGAT 57.146 36.364 14.51 0.00 0.00 4.58
2803 3472 4.853924 ATGTTCAGAACTTTTGGCGATT 57.146 36.364 14.51 0.00 0.00 3.34
2810 3479 5.049680 TCAGAACTTTTGGCGATTTAGACAC 60.050 40.000 0.00 0.00 0.00 3.67
2879 3557 2.504367 GTTGGCACCTACATGTTCAGT 58.496 47.619 2.30 0.00 0.00 3.41
2894 3572 4.883083 TGTTCAGTACATGTTGGTCTCTC 58.117 43.478 2.30 0.00 0.00 3.20
2895 3573 4.588951 TGTTCAGTACATGTTGGTCTCTCT 59.411 41.667 2.30 0.00 0.00 3.10
2897 3575 5.392767 TCAGTACATGTTGGTCTCTCTTC 57.607 43.478 2.30 0.00 0.00 2.87
2898 3576 4.832823 TCAGTACATGTTGGTCTCTCTTCA 59.167 41.667 2.30 0.00 0.00 3.02
2979 3658 4.340381 TCCTCAAAGTATTACTCCCGCTAC 59.660 45.833 0.00 0.00 0.00 3.58
2992 3671 1.269102 CCCGCTACCTGATTACTCACG 60.269 57.143 0.00 0.00 0.00 4.35
3026 3711 5.234972 CACTTTCAACAAAATGGAGCCTTTC 59.765 40.000 0.00 0.00 0.00 2.62
3030 3715 6.024552 TCAACAAAATGGAGCCTTTCATAC 57.975 37.500 0.00 0.00 0.00 2.39
3088 3774 6.477053 TTTTTGACTCATTTGATTCCACCA 57.523 33.333 0.00 0.00 0.00 4.17
3112 3798 9.280174 CCACTGAAAAGTTATGGTCTAGTTAAA 57.720 33.333 0.00 0.00 0.00 1.52
3154 3840 5.068460 CCTGGCCGGATTTGTATGATTTTTA 59.932 40.000 15.09 0.00 33.16 1.52
3155 3841 6.239289 CCTGGCCGGATTTGTATGATTTTTAT 60.239 38.462 15.09 0.00 33.16 1.40
3232 3931 0.106918 TTTTCCGACACAAGCACCCT 60.107 50.000 0.00 0.00 0.00 4.34
3239 3938 2.286772 CGACACAAGCACCCTAAAACAC 60.287 50.000 0.00 0.00 0.00 3.32
3264 3963 7.551262 ACGTGCCATCTCAACATTTTACTTATA 59.449 33.333 0.00 0.00 0.00 0.98
3338 4037 2.354403 GCCCACAACCATCGTAGTACTT 60.354 50.000 0.00 0.00 0.00 2.24
3405 4109 5.342259 CGATCGACGCATTACAAGATATGAA 59.658 40.000 10.26 0.00 34.51 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.326826 TCTACTTTCAAATGAGCCACTGG 58.673 43.478 0.00 0.00 0.00 4.00
31 32 5.702670 TCTTCTACTTTCAAATGAGCCACTG 59.297 40.000 0.00 0.00 0.00 3.66
64 65 1.384191 GCATCAAGGTCCTTGGGGT 59.616 57.895 27.79 13.84 41.33 4.95
127 128 2.114616 AGAAGCCACCAGATCCACTAG 58.885 52.381 0.00 0.00 0.00 2.57
211 212 9.783081 GGGGAATAAAGAATGAATGCATTTAAT 57.217 29.630 14.33 8.00 44.47 1.40
212 213 8.210265 GGGGGAATAAAGAATGAATGCATTTAA 58.790 33.333 14.33 5.79 44.47 1.52
213 214 7.734942 GGGGGAATAAAGAATGAATGCATTTA 58.265 34.615 14.33 10.23 44.47 1.40
214 215 6.594744 GGGGGAATAAAGAATGAATGCATTT 58.405 36.000 14.33 0.00 44.47 2.32
215 216 6.178607 GGGGGAATAAAGAATGAATGCATT 57.821 37.500 12.83 12.83 47.00 3.56
216 217 5.813513 GGGGGAATAAAGAATGAATGCAT 57.186 39.130 0.00 0.00 35.92 3.96
240 241 8.634335 ACATTCATTCTTTTTATTTTTGGGGG 57.366 30.769 0.00 0.00 0.00 5.40
461 462 3.136443 GTCCTCCAACACCATCCATCATA 59.864 47.826 0.00 0.00 0.00 2.15
510 512 1.476891 CGGCTAGTGTGTGTCCTGTAT 59.523 52.381 0.00 0.00 0.00 2.29
515 517 0.822164 ATACCGGCTAGTGTGTGTCC 59.178 55.000 0.00 0.00 0.00 4.02
544 546 4.686091 TGATCACTCGTTGTTGATGAGAAC 59.314 41.667 0.00 0.00 42.92 3.01
596 598 3.738590 GCCAACTAGCTAGGTAGTGCTTC 60.739 52.174 30.00 17.54 40.35 3.86
597 599 2.168728 GCCAACTAGCTAGGTAGTGCTT 59.831 50.000 30.00 15.47 40.35 3.91
661 668 2.432510 TGGGAAAGTTTTGATGCGGTTT 59.567 40.909 0.00 0.00 0.00 3.27
700 724 3.552875 ACGAGTAGGAGCAATACTAGCA 58.447 45.455 0.00 0.00 33.64 3.49
710 734 0.321298 TTTGGGCAACGAGTAGGAGC 60.321 55.000 0.00 0.00 37.60 4.70
747 771 1.141449 CCTCTCTGGCTTGCTCTCG 59.859 63.158 0.00 0.00 0.00 4.04
868 1162 5.185454 TCGATGGAGAATGCAAGTATGTTT 58.815 37.500 0.00 0.00 42.43 2.83
970 1269 1.274728 CTTGTCCTGACTCCTGAGTGG 59.725 57.143 4.19 0.99 42.66 4.00
977 1276 2.104170 CTACCTCCTTGTCCTGACTCC 58.896 57.143 0.00 0.00 0.00 3.85
978 1277 1.478916 GCTACCTCCTTGTCCTGACTC 59.521 57.143 0.00 0.00 0.00 3.36
983 1282 1.207791 CATGGCTACCTCCTTGTCCT 58.792 55.000 0.00 0.00 0.00 3.85
987 1286 1.524621 CGCCATGGCTACCTCCTTG 60.525 63.158 33.07 11.50 39.32 3.61
1192 1491 6.403878 TCAAGCAGTAGGTAAGTAAATGGTC 58.596 40.000 0.00 0.00 0.00 4.02
1195 1494 8.492673 TTGATCAAGCAGTAGGTAAGTAAATG 57.507 34.615 3.38 0.00 0.00 2.32
1201 1500 5.724328 TGACTTGATCAAGCAGTAGGTAAG 58.276 41.667 30.95 8.09 41.99 2.34
1209 1512 6.053650 TCCTAATCATGACTTGATCAAGCAG 58.946 40.000 30.95 21.07 44.51 4.24
1211 1514 6.513066 GCTTCCTAATCATGACTTGATCAAGC 60.513 42.308 30.95 23.59 44.51 4.01
1231 1535 3.274095 AGCCACTGATCTTTAGCTTCC 57.726 47.619 0.00 0.00 0.00 3.46
1234 1538 7.093156 TGCATATATAGCCACTGATCTTTAGCT 60.093 37.037 0.00 0.00 0.00 3.32
1240 1544 8.586744 CATCTATGCATATATAGCCACTGATCT 58.413 37.037 6.92 0.00 32.01 2.75
1241 1545 8.760103 CATCTATGCATATATAGCCACTGATC 57.240 38.462 6.92 0.00 32.01 2.92
1262 1566 7.716799 TTTTAATAGGTGTTGGATTGCATCT 57.283 32.000 0.00 0.00 0.00 2.90
1319 1640 5.355071 TGCAAGATCATTAACAGTCATGGAC 59.645 40.000 0.00 0.00 0.00 4.02
1338 1667 3.793144 GCGCGTTCCTCCTGCAAG 61.793 66.667 8.43 0.00 0.00 4.01
1348 1677 3.799755 GACATGGGTGGCGCGTTC 61.800 66.667 8.43 0.58 0.00 3.95
1419 1755 0.890683 CAAAGGGAGGTCAATGGTGC 59.109 55.000 0.00 0.00 0.00 5.01
1470 1851 5.949787 CGTACGTGCAATACATGTTACTTTC 59.050 40.000 2.30 0.00 46.67 2.62
1849 2261 4.686695 TGGAGGACGATCCAGAGG 57.313 61.111 4.95 0.00 44.56 3.69
1927 2339 4.609018 AGCGACTGCACCGTGCTT 62.609 61.111 23.52 11.14 45.31 3.91
1972 2384 4.530857 GACATGTCCTCCCCGCCG 62.531 72.222 15.31 0.00 0.00 6.46
2362 2777 1.008194 CGGTTTCACCTCGTCGTCA 60.008 57.895 0.00 0.00 35.66 4.35
2379 2794 0.753848 GGTTCTCCTCTCCTCCTCCG 60.754 65.000 0.00 0.00 0.00 4.63
2391 2806 2.087646 GTGAATCCAGCTTGGTTCTCC 58.912 52.381 11.72 0.00 39.03 3.71
2498 2913 6.035866 GCATTACATTCAAGAGTCTCTGTCAG 59.964 42.308 2.28 0.00 0.00 3.51
2518 2933 9.002600 CATTTCCTAGTGCTGTATTATGCATTA 57.997 33.333 3.54 0.00 41.45 1.90
2580 3003 0.539438 TTGCGTTTCAGCCCTTGGAT 60.539 50.000 0.00 0.00 36.02 3.41
2610 3033 5.298989 TCCCGTTACATACCAGCAATTAT 57.701 39.130 0.00 0.00 0.00 1.28
2611 3034 4.699637 CTCCCGTTACATACCAGCAATTA 58.300 43.478 0.00 0.00 0.00 1.40
2612 3035 3.541632 CTCCCGTTACATACCAGCAATT 58.458 45.455 0.00 0.00 0.00 2.32
2674 3097 7.201496 GCATAAAAACAAAGCTGAATCATCCAG 60.201 37.037 0.00 0.00 34.88 3.86
2740 3409 8.655970 GCAAATTTCTAAATCGCCAAAAGTTAT 58.344 29.630 0.00 0.00 0.00 1.89
2763 3432 7.884257 TGAACATTTTCATATCAGAGTTGCAA 58.116 30.769 0.00 0.00 36.79 4.08
2764 3433 7.391275 TCTGAACATTTTCATATCAGAGTTGCA 59.609 33.333 0.00 0.00 41.01 4.08
2766 3435 9.552114 GTTCTGAACATTTTCATATCAGAGTTG 57.448 33.333 15.34 0.00 45.04 3.16
2779 3448 5.004922 TCGCCAAAAGTTCTGAACATTTT 57.995 34.783 21.50 18.95 30.68 1.82
2787 3456 5.147162 GTGTCTAAATCGCCAAAAGTTCTG 58.853 41.667 0.00 0.00 0.00 3.02
2789 3458 5.103290 TGTGTCTAAATCGCCAAAAGTTC 57.897 39.130 0.00 0.00 0.00 3.01
2791 3460 4.578928 AGTTGTGTCTAAATCGCCAAAAGT 59.421 37.500 0.00 0.00 0.00 2.66
2792 3461 5.108385 AGTTGTGTCTAAATCGCCAAAAG 57.892 39.130 0.00 0.00 0.00 2.27
2793 3462 5.508200 AAGTTGTGTCTAAATCGCCAAAA 57.492 34.783 0.00 0.00 0.00 2.44
2794 3463 5.333492 CGTAAGTTGTGTCTAAATCGCCAAA 60.333 40.000 0.00 0.00 0.00 3.28
2795 3464 4.150980 CGTAAGTTGTGTCTAAATCGCCAA 59.849 41.667 0.00 0.00 0.00 4.52
2796 3465 3.676172 CGTAAGTTGTGTCTAAATCGCCA 59.324 43.478 0.00 0.00 0.00 5.69
2797 3466 3.061697 CCGTAAGTTGTGTCTAAATCGCC 59.938 47.826 0.00 0.00 0.00 5.54
2798 3467 3.676646 ACCGTAAGTTGTGTCTAAATCGC 59.323 43.478 0.00 0.00 0.00 4.58
2799 3468 6.803320 TCTTACCGTAAGTTGTGTCTAAATCG 59.197 38.462 16.23 0.00 37.10 3.34
2800 3469 8.524870 TTCTTACCGTAAGTTGTGTCTAAATC 57.475 34.615 16.23 0.00 37.10 2.17
2801 3470 9.498176 AATTCTTACCGTAAGTTGTGTCTAAAT 57.502 29.630 16.23 4.76 37.10 1.40
2802 3471 8.891671 AATTCTTACCGTAAGTTGTGTCTAAA 57.108 30.769 16.23 2.84 37.10 1.85
2803 3472 9.979578 TTAATTCTTACCGTAAGTTGTGTCTAA 57.020 29.630 16.23 3.45 37.10 2.10
2840 3518 1.004745 ACCGGCCAAGACAGATCAAAT 59.995 47.619 0.00 0.00 0.00 2.32
2879 3557 5.245977 TCATGTGAAGAGAGACCAACATGTA 59.754 40.000 0.00 0.00 36.22 2.29
2894 3572 8.854979 TTTAAACTTGTGACAATCATGTGAAG 57.145 30.769 0.00 0.00 40.74 3.02
2895 3573 9.299963 CTTTTAAACTTGTGACAATCATGTGAA 57.700 29.630 0.00 0.00 40.74 3.18
2897 3575 8.854979 TCTTTTAAACTTGTGACAATCATGTG 57.145 30.769 0.00 0.00 40.74 3.21
2898 3576 8.137437 CCTCTTTTAAACTTGTGACAATCATGT 58.863 33.333 0.00 0.00 44.25 3.21
2979 3658 8.681806 AGTGATATATGATCGTGAGTAATCAGG 58.318 37.037 6.54 6.54 35.49 3.86
3008 3693 5.170748 GGTATGAAAGGCTCCATTTTGTTG 58.829 41.667 7.51 0.00 0.00 3.33
3026 3711 3.328931 AGATAAGCATGAGTGGGGGTATG 59.671 47.826 0.00 0.00 0.00 2.39
3030 3715 4.566488 GGATAAGATAAGCATGAGTGGGGG 60.566 50.000 0.00 0.00 0.00 5.40
3081 3767 4.798882 ACCATAACTTTTCAGTGGTGGAA 58.201 39.130 11.32 0.00 41.38 3.53
3082 3768 4.104102 AGACCATAACTTTTCAGTGGTGGA 59.896 41.667 11.32 0.00 42.87 4.02
3088 3774 9.281371 GGTTTAACTAGACCATAACTTTTCAGT 57.719 33.333 0.00 0.00 35.95 3.41
3112 3798 1.228862 GCCACCACAAATCCTGGGT 60.229 57.895 0.00 0.00 32.45 4.51
3154 3840 3.496870 GGGTGCCCTCGAAAGATATGAAT 60.497 47.826 0.00 0.00 40.84 2.57
3155 3841 2.158813 GGGTGCCCTCGAAAGATATGAA 60.159 50.000 0.00 0.00 40.84 2.57
3175 3874 4.226168 AGGATGACAAAGTTAAGAGAGGGG 59.774 45.833 0.00 0.00 0.00 4.79
3221 3920 1.673920 ACGTGTTTTAGGGTGCTTGTG 59.326 47.619 0.00 0.00 0.00 3.33
3230 3929 2.422597 TGAGATGGCACGTGTTTTAGG 58.577 47.619 18.38 0.00 0.00 2.69
3232 3931 3.206964 TGTTGAGATGGCACGTGTTTTA 58.793 40.909 18.38 1.48 0.00 1.52
3239 3938 4.685169 AGTAAAATGTTGAGATGGCACG 57.315 40.909 0.00 0.00 0.00 5.34
3277 3976 2.011947 GTGCACTCATGATGCTTGCTA 58.988 47.619 22.27 7.11 43.77 3.49
3338 4037 4.067896 ACTCTCGTCGTCTTACCTTGTTA 58.932 43.478 0.00 0.00 0.00 2.41
3370 4069 2.538037 TGCGTCGATCGACATTTATTGG 59.462 45.455 38.62 24.39 44.77 3.16
3371 4070 3.834435 TGCGTCGATCGACATTTATTG 57.166 42.857 38.62 25.01 44.77 1.90
3372 4071 5.460748 TGTAATGCGTCGATCGACATTTATT 59.539 36.000 38.62 30.96 44.77 1.40


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

AutoCloner maintained by Alex Coulton.