Multiple sequence alignment - TraesCS3A01G264000

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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 TraesCS3A01G264000 chr3A 100.000 3694 0 0 1 3694 487856717 487860410 0.000000e+00 6822
1 TraesCS3A01G264000 chr3D 92.865 3714 165 40 1 3694 365908509 365912142 0.000000e+00 5299
2 TraesCS3A01G264000 chr3B 89.337 2035 117 40 505 2522 476948617 476950568 0.000000e+00 2464
3 TraesCS3A01G264000 chr3B 93.651 1197 55 8 2506 3693 476950582 476951766 0.000000e+00 1770
4 TraesCS3A01G264000 chr3B 87.886 421 23 11 1 414 476947897 476948296 1.550000e-128 470


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 TraesCS3A01G264000 chr3A 487856717 487860410 3693 False 6822 6822 100.000000 1 3694 1 chr3A.!!$F1 3693
1 TraesCS3A01G264000 chr3D 365908509 365912142 3633 False 5299 5299 92.865000 1 3694 1 chr3D.!!$F1 3693
2 TraesCS3A01G264000 chr3B 476947897 476951766 3869 False 1568 2464 90.291333 1 3693 3 chr3B.!!$F1 3692

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
477 491 0.105709 CTCTCCTCTTCCTCCTCCCC 60.106 65.0 0.0 0.0 0.0 4.81 F
1595 1897 0.390492 GCCCATTTAATCCTGCCAGC 59.610 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2491 0.107993 TGGCTGCAGCATGAGTACTC 60.108 55.0 37.63 18.61 44.36 2.59 R
3002 3344 0.107456 AGTGCCTGGTGTCTTCTGTG 59.893 55.0 0.00 0.00 0.00 3.66 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
145 152 0.466124 GGCCTATCTATCCATCCCGC 59.534 60.000 0.00 0.00 0.00 6.13
182 190 4.805744 ACAGGTACCCTATCTTGTAGGAG 58.194 47.826 8.74 0.00 36.85 3.69
191 199 1.429930 TCTTGTAGGAGTGCCCAACA 58.570 50.000 0.00 0.00 37.41 3.33
193 201 2.173782 TCTTGTAGGAGTGCCCAACAAA 59.826 45.455 0.00 0.00 39.01 2.83
195 203 3.019799 TGTAGGAGTGCCCAACAAAAA 57.980 42.857 0.00 0.00 37.41 1.94
218 226 2.288961 ACAATAGTCAGTTACCGGCG 57.711 50.000 0.00 0.00 0.00 6.46
284 292 3.614092 GCCATCAGGTGATTCTTCTCAA 58.386 45.455 0.00 0.00 37.19 3.02
285 293 4.012374 GCCATCAGGTGATTCTTCTCAAA 58.988 43.478 0.00 0.00 37.19 2.69
287 295 5.392811 GCCATCAGGTGATTCTTCTCAAAAG 60.393 44.000 0.00 0.00 37.19 2.27
289 297 6.432162 CCATCAGGTGATTCTTCTCAAAAGAA 59.568 38.462 2.96 2.96 40.17 2.52
290 298 6.867662 TCAGGTGATTCTTCTCAAAAGAAC 57.132 37.500 2.55 0.00 38.88 3.01
291 299 5.765182 TCAGGTGATTCTTCTCAAAAGAACC 59.235 40.000 2.55 1.58 38.88 3.62
292 300 5.532406 CAGGTGATTCTTCTCAAAAGAACCA 59.468 40.000 2.55 0.00 38.88 3.67
293 301 6.039717 CAGGTGATTCTTCTCAAAAGAACCAA 59.960 38.462 2.55 0.00 38.88 3.67
294 302 6.607198 AGGTGATTCTTCTCAAAAGAACCAAA 59.393 34.615 2.55 0.00 38.88 3.28
295 303 7.288621 AGGTGATTCTTCTCAAAAGAACCAAAT 59.711 33.333 2.55 0.00 38.88 2.32
296 304 8.576442 GGTGATTCTTCTCAAAAGAACCAAATA 58.424 33.333 2.55 0.00 38.88 1.40
319 327 2.509336 CAACGGAGGCCAGTAGCG 60.509 66.667 5.01 0.00 45.17 4.26
321 329 4.753662 ACGGAGGCCAGTAGCGGA 62.754 66.667 5.01 0.00 45.17 5.54
376 385 2.854967 ACTGGATGTTTGGGATCTCCAT 59.145 45.455 4.04 0.00 46.52 3.41
425 434 1.911471 CTCCTCCCAAGCCCTTCTC 59.089 63.158 0.00 0.00 0.00 2.87
435 444 0.178861 AGCCCTTCTCCCCTTCTTGA 60.179 55.000 0.00 0.00 0.00 3.02
436 445 0.922626 GCCCTTCTCCCCTTCTTGAT 59.077 55.000 0.00 0.00 0.00 2.57
471 484 3.181443 CCTCTCCTACTCTCCTCTTCCTC 60.181 56.522 0.00 0.00 0.00 3.71
477 491 0.105709 CTCTCCTCTTCCTCCTCCCC 60.106 65.000 0.00 0.00 0.00 4.81
710 1000 1.816074 TCATGGCCCTTTTCGTGTAC 58.184 50.000 0.00 0.00 0.00 2.90
751 1041 0.610509 TGGGCGCATGGCTCTTTTAA 60.611 50.000 10.83 0.00 44.88 1.52
804 1097 1.468914 GGTGGAATGGAAAGACGCTTC 59.531 52.381 0.00 0.00 0.00 3.86
836 1133 1.363744 CTTTCCTGCCATCTCGTGTC 58.636 55.000 0.00 0.00 0.00 3.67
848 1145 0.943835 CTCGTGTCATGTTCGTGGCA 60.944 55.000 0.00 0.00 0.00 4.92
855 1152 2.989909 TCATGTTCGTGGCATGATTCT 58.010 42.857 10.74 0.00 45.18 2.40
940 1238 4.659111 TCGATATAGCGTCCCTGAAAAA 57.341 40.909 10.57 0.00 0.00 1.94
941 1239 5.209818 TCGATATAGCGTCCCTGAAAAAT 57.790 39.130 10.57 0.00 0.00 1.82
942 1240 5.227908 TCGATATAGCGTCCCTGAAAAATC 58.772 41.667 10.57 0.00 0.00 2.17
946 1247 2.094675 AGCGTCCCTGAAAAATCATGG 58.905 47.619 0.00 0.00 0.00 3.66
1071 1372 1.971505 TTCAGGGCGCCATCTTCGAT 61.972 55.000 30.85 0.00 0.00 3.59
1251 1552 1.153469 GCTTTCTGCTCCTCTCCCG 60.153 63.158 0.00 0.00 38.95 5.14
1259 1560 1.745264 CTCCTCTCCCGGCTTGATC 59.255 63.158 0.00 0.00 0.00 2.92
1272 1573 3.119955 CGGCTTGATCATTCCATATGCTG 60.120 47.826 12.52 0.00 0.00 4.41
1274 1575 4.082895 GGCTTGATCATTCCATATGCTGTC 60.083 45.833 0.00 0.00 0.00 3.51
1280 1581 8.694581 TGATCATTCCATATGCTGTCAAATTA 57.305 30.769 0.00 0.00 0.00 1.40
1282 1583 9.784680 GATCATTCCATATGCTGTCAAATTATC 57.215 33.333 0.00 0.00 0.00 1.75
1286 1587 7.514784 TCCATATGCTGTCAAATTATCCTTG 57.485 36.000 0.00 0.00 0.00 3.61
1287 1588 6.491062 TCCATATGCTGTCAAATTATCCTTGG 59.509 38.462 0.00 0.00 0.00 3.61
1297 1598 7.925483 TGTCAAATTATCCTTGGTTGTTCAAAG 59.075 33.333 0.00 0.00 0.00 2.77
1303 1604 4.199310 TCCTTGGTTGTTCAAAGTCTGAG 58.801 43.478 0.00 0.00 34.81 3.35
1327 1628 5.009610 GCACCAGAAATAACCTCAAGTTGAA 59.990 40.000 7.06 0.00 39.67 2.69
1346 1647 7.092137 GTTGAAAACCCGCTTATTATTACCT 57.908 36.000 0.00 0.00 42.21 3.08
1347 1648 6.930667 TGAAAACCCGCTTATTATTACCTC 57.069 37.500 0.00 0.00 0.00 3.85
1348 1649 5.524646 TGAAAACCCGCTTATTATTACCTCG 59.475 40.000 0.00 0.00 0.00 4.63
1349 1650 4.677673 AACCCGCTTATTATTACCTCGT 57.322 40.909 0.00 0.00 0.00 4.18
1350 1651 4.248691 ACCCGCTTATTATTACCTCGTC 57.751 45.455 0.00 0.00 0.00 4.20
1371 1673 4.984295 TCCATCTTCAACAATGGAACAGA 58.016 39.130 1.67 0.00 46.51 3.41
1373 1675 6.036826 TCCATCTTCAACAATGGAACAGAGG 61.037 44.000 1.67 0.00 46.51 3.69
1432 1734 5.279256 CCACCGGGAACACAAATTTCTATTT 60.279 40.000 6.32 0.00 35.59 1.40
1433 1735 5.861787 CACCGGGAACACAAATTTCTATTTC 59.138 40.000 6.32 0.00 31.63 2.17
1434 1736 5.773176 ACCGGGAACACAAATTTCTATTTCT 59.227 36.000 6.32 0.00 31.63 2.52
1435 1737 6.092748 CCGGGAACACAAATTTCTATTTCTG 58.907 40.000 0.00 0.00 31.63 3.02
1437 1739 6.801862 CGGGAACACAAATTTCTATTTCTGTC 59.198 38.462 0.00 0.00 33.48 3.51
1484 1786 5.477607 TTTCTTCTCTGTTATCGGAACCA 57.522 39.130 0.00 0.00 0.00 3.67
1502 1804 2.752903 ACCAAATCGGATTTTTCGAGGG 59.247 45.455 13.09 12.20 40.09 4.30
1505 1807 4.097892 CCAAATCGGATTTTTCGAGGGATT 59.902 41.667 13.09 0.00 40.09 3.01
1506 1808 5.273944 CAAATCGGATTTTTCGAGGGATTC 58.726 41.667 13.09 0.00 40.09 2.52
1551 1853 7.250445 CATGATTTTCATGTAGATTCGACCA 57.750 36.000 8.92 0.00 46.80 4.02
1560 1862 5.687166 TGTAGATTCGACCACCCTTTTAT 57.313 39.130 0.00 0.00 0.00 1.40
1585 1887 4.518278 TTCCTAGCAGATGCCCATTTAA 57.482 40.909 0.14 0.00 43.38 1.52
1594 1896 1.779221 TGCCCATTTAATCCTGCCAG 58.221 50.000 0.00 0.00 0.00 4.85
1595 1897 0.390492 GCCCATTTAATCCTGCCAGC 59.610 55.000 0.00 0.00 0.00 4.85
1596 1898 1.043022 CCCATTTAATCCTGCCAGCC 58.957 55.000 0.00 0.00 0.00 4.85
1597 1899 1.688942 CCCATTTAATCCTGCCAGCCA 60.689 52.381 0.00 0.00 0.00 4.75
1598 1900 2.109774 CCATTTAATCCTGCCAGCCAA 58.890 47.619 0.00 0.00 0.00 4.52
1599 1901 2.159057 CCATTTAATCCTGCCAGCCAAC 60.159 50.000 0.00 0.00 0.00 3.77
1600 1902 2.300956 TTTAATCCTGCCAGCCAACA 57.699 45.000 0.00 0.00 0.00 3.33
1610 1912 1.269723 GCCAGCCAACAGAGGTTTTAC 59.730 52.381 0.00 0.00 34.21 2.01
1770 2072 2.871453 TCAGTTTGCCCTTTACTTCCC 58.129 47.619 0.00 0.00 0.00 3.97
1771 2073 2.445525 TCAGTTTGCCCTTTACTTCCCT 59.554 45.455 0.00 0.00 0.00 4.20
1947 2249 6.569127 TGGTGCTTAAGATCCTTGGTAATA 57.431 37.500 6.67 0.00 0.00 0.98
1953 2256 9.693739 TGCTTAAGATCCTTGGTAATATTTTCA 57.306 29.630 6.67 0.00 0.00 2.69
1972 2275 2.707791 TCATCCAAGAAGGGCCTATCTG 59.292 50.000 6.41 3.89 38.24 2.90
2013 2316 1.988956 ACTGCAGGAGAGCTGGAGG 60.989 63.158 19.93 0.00 43.21 4.30
2056 2359 3.358118 TGGAGAAAACGTTTCCCAAACT 58.642 40.909 15.01 7.17 39.23 2.66
2058 2361 3.113322 GAGAAAACGTTTCCCAAACTGC 58.887 45.455 15.01 0.00 39.23 4.40
2061 2364 0.744281 AACGTTTCCCAAACTGCTGG 59.256 50.000 0.00 0.00 39.23 4.85
2071 2374 1.530013 AAACTGCTGGTCATGCTGCC 61.530 55.000 0.00 0.00 33.58 4.85
2174 2481 6.486657 TGCTATAGAATGTAAACCTTCCATGC 59.513 38.462 3.21 0.00 0.00 4.06
2175 2482 6.486657 GCTATAGAATGTAAACCTTCCATGCA 59.513 38.462 3.21 0.00 0.00 3.96
2176 2483 7.175641 GCTATAGAATGTAAACCTTCCATGCAT 59.824 37.037 3.21 0.00 0.00 3.96
2177 2484 5.841957 AGAATGTAAACCTTCCATGCATC 57.158 39.130 0.00 0.00 0.00 3.91
2178 2485 5.513233 AGAATGTAAACCTTCCATGCATCT 58.487 37.500 0.00 0.00 0.00 2.90
2179 2486 5.359009 AGAATGTAAACCTTCCATGCATCTG 59.641 40.000 0.00 0.00 0.00 2.90
2180 2487 3.355378 TGTAAACCTTCCATGCATCTGG 58.645 45.455 0.00 0.00 37.66 3.86
2181 2488 1.188863 AAACCTTCCATGCATCTGGC 58.811 50.000 0.00 0.00 45.13 4.85
2219 2526 2.032054 CAGCCAACTAACGCATATGTGG 59.968 50.000 19.94 10.95 0.00 4.17
2221 2528 2.422127 GCCAACTAACGCATATGTGGTT 59.578 45.455 19.94 17.36 0.00 3.67
2223 2530 3.242284 CCAACTAACGCATATGTGGTTCG 60.242 47.826 19.94 14.08 0.00 3.95
2271 2578 3.712881 GGTGCTCCGTGACGCAAC 61.713 66.667 0.00 0.00 37.97 4.17
2328 2635 2.899900 TGGCACTGATCACTGTAAGAGT 59.100 45.455 0.00 0.00 37.43 3.24
2399 2706 6.072649 TGTGATTCATGGGCAATTCTGATAT 58.927 36.000 0.00 0.00 0.00 1.63
2405 2712 5.479027 TCATGGGCAATTCTGATATGGATTG 59.521 40.000 0.00 0.00 0.00 2.67
2462 2769 3.637229 CGGAGTTGTCATACCCATCTACT 59.363 47.826 0.00 0.00 0.00 2.57
2542 2879 1.480954 ACCCATGTCCAGTCACGTATC 59.519 52.381 0.00 0.00 0.00 2.24
2548 2885 5.872617 CCATGTCCAGTCACGTATCTAAAAA 59.127 40.000 0.00 0.00 0.00 1.94
2573 2910 6.180472 ACCTCGGTTTCAATCAGAATGTAAT 58.820 36.000 0.00 0.00 35.83 1.89
2632 2969 4.323562 GCCAGTTACAGAACCTGTAGGAAT 60.324 45.833 4.64 0.00 45.83 3.01
2640 2977 4.020218 CAGAACCTGTAGGAATTGAGGACA 60.020 45.833 4.64 0.00 38.94 4.02
2643 2980 3.261897 ACCTGTAGGAATTGAGGACACAG 59.738 47.826 4.64 0.00 38.94 3.66
2734 3071 5.570205 TGGTGGTTAGGTTCTGTCAAATA 57.430 39.130 0.00 0.00 0.00 1.40
2735 3072 6.134535 TGGTGGTTAGGTTCTGTCAAATAT 57.865 37.500 0.00 0.00 0.00 1.28
2736 3073 6.548321 TGGTGGTTAGGTTCTGTCAAATATT 58.452 36.000 0.00 0.00 0.00 1.28
2789 3126 1.615883 ACGCTGGCTGTCATAGGATAG 59.384 52.381 0.00 0.00 35.54 2.08
2798 3135 5.480073 GGCTGTCATAGGATAGAGAAGATGT 59.520 44.000 5.24 0.00 34.44 3.06
3002 3344 1.872952 GTGAAAATTTTGTGCCCAGCC 59.127 47.619 8.47 0.00 0.00 4.85
3072 3414 6.721318 AGCAGGGAAACTCTGTATGAAAATA 58.279 36.000 0.00 0.00 34.89 1.40
3120 3474 5.552870 AATACAGTACATCATGTCCCTCC 57.447 43.478 0.00 0.00 0.00 4.30
3121 3475 3.121929 ACAGTACATCATGTCCCTCCT 57.878 47.619 0.00 0.00 0.00 3.69
3134 3488 2.040939 TCCCTCCTGTTCGTTTACACA 58.959 47.619 0.00 0.00 0.00 3.72
3179 3533 5.010213 GTGTTCTCTTACTCTCTGTCCTTGT 59.990 44.000 0.00 0.00 0.00 3.16
3249 3610 8.778358 GGATAAAATTGAGCTACAACATAGAGG 58.222 37.037 0.00 0.00 41.52 3.69
3259 3620 5.472137 GCTACAACATAGAGGGAAAAACACA 59.528 40.000 0.00 0.00 0.00 3.72
3402 3763 0.760567 TCACCTGCACCTCTGTCTGT 60.761 55.000 0.00 0.00 0.00 3.41
3496 3857 6.656902 ACATGATGTTATGACCTGAAGACAT 58.343 36.000 0.00 0.00 0.00 3.06
3557 3918 2.213499 AGTTTCAGAGAGTTTGCACGG 58.787 47.619 0.00 0.00 0.00 4.94
3627 3988 6.566079 AGATTCCCAATACATCACTCTGAA 57.434 37.500 0.00 0.00 0.00 3.02
3628 3989 6.590068 AGATTCCCAATACATCACTCTGAAG 58.410 40.000 0.00 0.00 0.00 3.02
3629 3990 4.142609 TCCCAATACATCACTCTGAAGC 57.857 45.455 0.00 0.00 0.00 3.86
3630 3991 3.519107 TCCCAATACATCACTCTGAAGCA 59.481 43.478 0.00 0.00 0.00 3.91
3631 3992 4.019411 TCCCAATACATCACTCTGAAGCAA 60.019 41.667 0.00 0.00 0.00 3.91
3632 3993 4.701651 CCCAATACATCACTCTGAAGCAAA 59.298 41.667 0.00 0.00 0.00 3.68
3633 3994 5.163683 CCCAATACATCACTCTGAAGCAAAG 60.164 44.000 0.00 0.00 0.00 2.77
3634 3995 5.645067 CCAATACATCACTCTGAAGCAAAGA 59.355 40.000 0.00 0.00 0.00 2.52
3635 3996 6.149973 CCAATACATCACTCTGAAGCAAAGAA 59.850 38.462 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 67 1.443872 CGTCCACCGCTGTACAGAC 60.444 63.158 27.08 15.90 0.00 3.51
65 69 1.154016 CTCGTCCACCGCTGTACAG 60.154 63.158 18.93 18.93 36.19 2.74
67 71 1.019673 TATCTCGTCCACCGCTGTAC 58.980 55.000 0.00 0.00 36.19 2.90
145 152 1.080230 CTGTCTGCTCCCGTCAGTG 60.080 63.158 0.00 0.00 33.48 3.66
195 203 4.083696 CGCCGGTAACTGACTATTGTTTTT 60.084 41.667 1.90 0.00 0.00 1.94
196 204 3.434299 CGCCGGTAACTGACTATTGTTTT 59.566 43.478 1.90 0.00 0.00 2.43
197 205 2.997986 CGCCGGTAACTGACTATTGTTT 59.002 45.455 1.90 0.00 0.00 2.83
198 206 2.613691 CGCCGGTAACTGACTATTGTT 58.386 47.619 1.90 0.00 0.00 2.83
199 207 1.134907 CCGCCGGTAACTGACTATTGT 60.135 52.381 1.90 0.00 0.00 2.71
200 208 1.567504 CCGCCGGTAACTGACTATTG 58.432 55.000 1.90 0.00 0.00 1.90
201 209 0.462789 CCCGCCGGTAACTGACTATT 59.537 55.000 1.90 0.00 0.00 1.73
202 210 0.396139 TCCCGCCGGTAACTGACTAT 60.396 55.000 1.90 0.00 0.00 2.12
203 211 1.001020 TCCCGCCGGTAACTGACTA 60.001 57.895 1.90 0.00 0.00 2.59
204 212 2.283388 TCCCGCCGGTAACTGACT 60.283 61.111 1.90 0.00 0.00 3.41
205 213 2.125793 GTCCCGCCGGTAACTGAC 60.126 66.667 1.90 0.00 0.00 3.51
262 270 2.208431 GAGAAGAATCACCTGATGGCG 58.792 52.381 0.00 0.00 34.49 5.69
279 287 6.565234 TGCGTTTTATTTGGTTCTTTTGAGA 58.435 32.000 0.00 0.00 0.00 3.27
280 288 6.820470 TGCGTTTTATTTGGTTCTTTTGAG 57.180 33.333 0.00 0.00 0.00 3.02
281 289 6.237595 CGTTGCGTTTTATTTGGTTCTTTTGA 60.238 34.615 0.00 0.00 0.00 2.69
282 290 5.893726 CGTTGCGTTTTATTTGGTTCTTTTG 59.106 36.000 0.00 0.00 0.00 2.44
284 292 4.504826 CCGTTGCGTTTTATTTGGTTCTTT 59.495 37.500 0.00 0.00 0.00 2.52
285 293 4.045783 CCGTTGCGTTTTATTTGGTTCTT 58.954 39.130 0.00 0.00 0.00 2.52
287 295 3.630101 TCCGTTGCGTTTTATTTGGTTC 58.370 40.909 0.00 0.00 0.00 3.62
289 297 2.030628 CCTCCGTTGCGTTTTATTTGGT 60.031 45.455 0.00 0.00 0.00 3.67
290 298 2.591133 CCTCCGTTGCGTTTTATTTGG 58.409 47.619 0.00 0.00 0.00 3.28
291 299 1.982913 GCCTCCGTTGCGTTTTATTTG 59.017 47.619 0.00 0.00 0.00 2.32
292 300 1.068125 GGCCTCCGTTGCGTTTTATTT 60.068 47.619 0.00 0.00 0.00 1.40
293 301 0.524414 GGCCTCCGTTGCGTTTTATT 59.476 50.000 0.00 0.00 0.00 1.40
294 302 0.606944 TGGCCTCCGTTGCGTTTTAT 60.607 50.000 3.32 0.00 0.00 1.40
295 303 1.227883 TGGCCTCCGTTGCGTTTTA 60.228 52.632 3.32 0.00 0.00 1.52
296 304 2.517402 TGGCCTCCGTTGCGTTTT 60.517 55.556 3.32 0.00 0.00 2.43
319 327 1.996070 GATGGGTTAGGTGGCCCTCC 61.996 65.000 0.00 2.52 45.06 4.30
321 329 2.375345 CGATGGGTTAGGTGGCCCT 61.375 63.158 0.00 0.00 45.06 5.19
402 411 4.120755 GGCTTGGGAGGAGCAGGG 62.121 72.222 0.00 0.00 41.89 4.45
403 412 4.120755 GGGCTTGGGAGGAGCAGG 62.121 72.222 0.00 0.00 41.89 4.85
404 413 2.549169 GAAGGGCTTGGGAGGAGCAG 62.549 65.000 0.00 0.00 41.89 4.24
425 434 1.273327 GCCAACAACATCAAGAAGGGG 59.727 52.381 0.00 0.00 0.00 4.79
435 444 0.610232 GAGAGGCAGGCCAACAACAT 60.610 55.000 13.63 0.00 38.92 2.71
436 445 1.228245 GAGAGGCAGGCCAACAACA 60.228 57.895 13.63 0.00 38.92 3.33
489 503 0.918258 TGATATGCAAGCCACCAGGA 59.082 50.000 0.00 0.00 36.89 3.86
655 945 1.682344 GAGGGGGTGCAAATGGGAC 60.682 63.158 0.00 0.00 37.06 4.46
695 985 0.675837 GGAGGTACACGAAAAGGGCC 60.676 60.000 0.00 0.00 0.00 5.80
751 1041 6.749923 CTTTGCTTACAGAAAGGAGCTAAT 57.250 37.500 0.00 0.00 36.82 1.73
804 1097 2.865276 GCAGGAAAGGCAGCTCTTTTTG 60.865 50.000 9.45 11.21 37.13 2.44
836 1133 3.770263 AAGAATCATGCCACGAACATG 57.230 42.857 9.69 9.69 45.08 3.21
848 1145 3.119743 CGCACCACATGACAAAGAATCAT 60.120 43.478 0.00 0.00 37.27 2.45
855 1152 1.674359 AAGTCGCACCACATGACAAA 58.326 45.000 0.00 0.00 35.09 2.83
911 1209 2.987821 GGACGCTATATCGAAAAGGAGC 59.012 50.000 2.48 0.00 0.00 4.70
946 1247 4.818546 ACAGCTGTGGATAACATAAGCATC 59.181 41.667 20.97 0.00 41.51 3.91
1029 1330 1.613317 TTGCCTCCGTGATCATCCGT 61.613 55.000 0.00 0.00 0.00 4.69
1234 1535 1.519719 CCGGGAGAGGAGCAGAAAG 59.480 63.158 0.00 0.00 0.00 2.62
1251 1552 3.825014 ACAGCATATGGAATGATCAAGCC 59.175 43.478 0.00 4.78 0.00 4.35
1259 1560 8.118976 AGGATAATTTGACAGCATATGGAATG 57.881 34.615 4.56 0.00 0.00 2.67
1272 1573 7.926018 ACTTTGAACAACCAAGGATAATTTGAC 59.074 33.333 0.00 0.00 0.00 3.18
1274 1575 8.143835 AGACTTTGAACAACCAAGGATAATTTG 58.856 33.333 0.00 0.00 0.00 2.32
1280 1581 4.792068 TCAGACTTTGAACAACCAAGGAT 58.208 39.130 0.00 0.00 31.34 3.24
1282 1583 3.243201 GCTCAGACTTTGAACAACCAAGG 60.243 47.826 0.00 0.00 34.81 3.61
1286 1587 2.033424 GGTGCTCAGACTTTGAACAACC 59.967 50.000 0.00 0.00 34.24 3.77
1287 1588 2.682856 TGGTGCTCAGACTTTGAACAAC 59.317 45.455 0.00 0.00 39.53 3.32
1303 1604 4.518970 TCAACTTGAGGTTATTTCTGGTGC 59.481 41.667 0.00 0.00 36.23 5.01
1327 1628 5.027293 ACGAGGTAATAATAAGCGGGTTT 57.973 39.130 0.00 0.00 0.00 3.27
1333 1634 7.152645 TGAAGATGGACGAGGTAATAATAAGC 58.847 38.462 0.00 0.00 0.00 3.09
1343 1644 3.338249 CATTGTTGAAGATGGACGAGGT 58.662 45.455 0.00 0.00 0.00 3.85
1344 1645 2.679837 CCATTGTTGAAGATGGACGAGG 59.320 50.000 2.23 0.00 44.49 4.63
1345 1646 3.599343 TCCATTGTTGAAGATGGACGAG 58.401 45.455 6.20 0.00 45.14 4.18
1346 1647 3.694043 TCCATTGTTGAAGATGGACGA 57.306 42.857 6.20 0.00 45.14 4.20
1350 1651 4.157289 CCTCTGTTCCATTGTTGAAGATGG 59.843 45.833 2.03 2.03 43.36 3.51
1432 1734 5.360999 CACTGATAGTGGTATGGAAGACAGA 59.639 44.000 0.00 0.00 42.35 3.41
1433 1735 5.360999 TCACTGATAGTGGTATGGAAGACAG 59.639 44.000 8.91 0.00 45.94 3.51
1434 1736 5.269189 TCACTGATAGTGGTATGGAAGACA 58.731 41.667 8.91 0.00 45.94 3.41
1435 1737 5.854010 TCACTGATAGTGGTATGGAAGAC 57.146 43.478 8.91 0.00 45.94 3.01
1437 1739 9.784531 AATAATTCACTGATAGTGGTATGGAAG 57.215 33.333 8.91 0.00 45.94 3.46
1445 1747 9.829507 AGAGAAGAAATAATTCACTGATAGTGG 57.170 33.333 8.91 0.00 45.94 4.00
1484 1786 5.193679 AGAATCCCTCGAAAAATCCGATTT 58.806 37.500 0.17 0.17 35.35 2.17
1505 1807 7.448469 TCATGATTCTATCGACACAAGGATAGA 59.552 37.037 6.65 6.65 45.66 1.98
1506 1808 7.597386 TCATGATTCTATCGACACAAGGATAG 58.403 38.462 0.00 2.43 42.14 2.08
1531 1833 4.881850 GGGTGGTCGAATCTACATGAAAAT 59.118 41.667 0.00 0.00 0.00 1.82
1568 1870 4.401022 CAGGATTAAATGGGCATCTGCTA 58.599 43.478 1.70 0.00 41.70 3.49
1585 1887 1.302285 CTCTGTTGGCTGGCAGGAT 59.698 57.895 17.64 0.00 33.81 3.24
1594 1896 4.338400 AGTTCAAGTAAAACCTCTGTTGGC 59.662 41.667 0.00 0.00 34.13 4.52
1595 1897 6.766467 ACTAGTTCAAGTAAAACCTCTGTTGG 59.234 38.462 0.00 0.00 34.13 3.77
1596 1898 7.787725 ACTAGTTCAAGTAAAACCTCTGTTG 57.212 36.000 0.00 0.00 34.13 3.33
1597 1899 8.674607 CAAACTAGTTCAAGTAAAACCTCTGTT 58.325 33.333 8.95 0.00 35.82 3.16
1598 1900 7.827729 ACAAACTAGTTCAAGTAAAACCTCTGT 59.172 33.333 8.95 1.38 0.00 3.41
1599 1901 8.209917 ACAAACTAGTTCAAGTAAAACCTCTG 57.790 34.615 8.95 0.73 0.00 3.35
1600 1902 8.674607 CAACAAACTAGTTCAAGTAAAACCTCT 58.325 33.333 8.95 0.00 0.00 3.69
1610 1912 3.316308 AGGCAGCAACAAACTAGTTCAAG 59.684 43.478 8.95 4.94 0.00 3.02
1770 2072 5.181009 TGAAGACTGATGATGGCTTTACAG 58.819 41.667 0.00 0.00 0.00 2.74
1771 2073 5.164620 TGAAGACTGATGATGGCTTTACA 57.835 39.130 0.00 0.00 0.00 2.41
1823 2125 3.375299 GTGCCATAGGTAGCAAAGACAAG 59.625 47.826 0.00 0.00 41.48 3.16
1830 2132 0.617935 TGCTGTGCCATAGGTAGCAA 59.382 50.000 0.00 0.00 40.99 3.91
1947 2249 3.479866 AGGCCCTTCTTGGATGAAAAT 57.520 42.857 0.00 0.00 38.35 1.82
1953 2256 2.708325 GTCAGATAGGCCCTTCTTGGAT 59.292 50.000 0.00 0.00 38.35 3.41
1956 2259 3.495806 GGATGTCAGATAGGCCCTTCTTG 60.496 52.174 0.00 0.00 0.00 3.02
1957 2260 2.708325 GGATGTCAGATAGGCCCTTCTT 59.292 50.000 0.00 0.00 0.00 2.52
1972 2275 1.967779 GAAGAGAGGGCCTAGGATGTC 59.032 57.143 14.75 5.54 0.00 3.06
2013 2316 2.413453 GCGTTGAGATTCTCTGGTGTTC 59.587 50.000 14.54 0.00 0.00 3.18
2022 2325 3.685139 TTTCTCCAGCGTTGAGATTCT 57.315 42.857 0.00 0.00 38.58 2.40
2071 2374 0.877071 AGTCAAAGCTTGATGTGCCG 59.123 50.000 0.00 0.00 42.47 5.69
2174 2481 2.467838 CATGAGTACTCGTGCCAGATG 58.532 52.381 27.60 15.32 39.43 2.90
2175 2482 2.879002 CATGAGTACTCGTGCCAGAT 57.121 50.000 27.60 7.83 39.43 2.90
2181 2488 1.275505 CTGCAGCATGAGTACTCGTG 58.724 55.000 32.17 32.17 46.52 4.35
2182 2489 0.459237 GCTGCAGCATGAGTACTCGT 60.459 55.000 33.36 15.05 39.69 4.18
2183 2490 1.150567 GGCTGCAGCATGAGTACTCG 61.151 60.000 37.63 5.93 44.36 4.18
2184 2491 0.107993 TGGCTGCAGCATGAGTACTC 60.108 55.000 37.63 18.61 44.36 2.59
2185 2492 0.325933 TTGGCTGCAGCATGAGTACT 59.674 50.000 37.63 0.00 44.36 2.73
2186 2493 0.449388 GTTGGCTGCAGCATGAGTAC 59.551 55.000 37.63 20.06 44.36 2.73
2187 2494 0.325933 AGTTGGCTGCAGCATGAGTA 59.674 50.000 37.63 14.85 44.36 2.59
2188 2495 0.325933 TAGTTGGCTGCAGCATGAGT 59.674 50.000 37.63 25.64 44.36 3.41
2219 2526 2.290641 ACTGAAGGTGCATGTTTCGAAC 59.709 45.455 0.00 0.00 0.00 3.95
2221 2528 2.254546 ACTGAAGGTGCATGTTTCGA 57.745 45.000 0.00 0.00 0.00 3.71
2223 2530 3.988379 TCAACTGAAGGTGCATGTTTC 57.012 42.857 0.00 0.00 0.00 2.78
2328 2635 9.152327 AGATCTAATCAGGTTACATGATTCAGA 57.848 33.333 25.15 22.86 44.27 3.27
2399 2706 2.349590 CTGTCTCATCAACGCAATCCA 58.650 47.619 0.00 0.00 0.00 3.41
2405 2712 1.018226 AGCAGCTGTCTCATCAACGC 61.018 55.000 16.64 0.00 0.00 4.84
2548 2885 4.398319 ACATTCTGATTGAAACCGAGGTT 58.602 39.130 0.93 0.93 38.29 3.50
2549 2886 4.021102 ACATTCTGATTGAAACCGAGGT 57.979 40.909 6.56 0.00 38.29 3.85
2606 2943 1.140252 ACAGGTTCTGTAACTGGCGTT 59.860 47.619 4.34 0.87 43.46 4.84
2632 2969 0.972134 CAGGCTCTCTGTGTCCTCAA 59.028 55.000 0.00 0.00 38.64 3.02
2735 3072 9.547753 GCTAACTTCATCCAATGAGACTAATAA 57.452 33.333 0.00 0.00 40.94 1.40
2736 3073 7.867909 CGCTAACTTCATCCAATGAGACTAATA 59.132 37.037 0.00 0.00 40.94 0.98
2789 3126 8.025445 ACACTTGCAATGATTTTACATCTTCTC 58.975 33.333 0.00 0.00 0.00 2.87
2798 3135 9.979578 AACATCTTTACACTTGCAATGATTTTA 57.020 25.926 0.00 0.00 0.00 1.52
3002 3344 0.107456 AGTGCCTGGTGTCTTCTGTG 59.893 55.000 0.00 0.00 0.00 3.66
3072 3414 2.645802 TGTAACCGTGAACTTTTGCCT 58.354 42.857 0.00 0.00 0.00 4.75
3110 3464 2.185004 AAACGAACAGGAGGGACATG 57.815 50.000 0.00 0.00 36.29 3.21
3111 3465 2.635915 TGTAAACGAACAGGAGGGACAT 59.364 45.455 0.00 0.00 0.00 3.06
3112 3466 2.040939 TGTAAACGAACAGGAGGGACA 58.959 47.619 0.00 0.00 0.00 4.02
3113 3467 2.224113 TGTGTAAACGAACAGGAGGGAC 60.224 50.000 0.00 0.00 0.00 4.46
3114 3468 2.040939 TGTGTAAACGAACAGGAGGGA 58.959 47.619 0.00 0.00 0.00 4.20
3115 3469 2.536761 TGTGTAAACGAACAGGAGGG 57.463 50.000 0.00 0.00 0.00 4.30
3116 3470 3.001939 GTGTTGTGTAAACGAACAGGAGG 59.998 47.826 0.00 0.00 30.41 4.30
3117 3471 3.619483 TGTGTTGTGTAAACGAACAGGAG 59.381 43.478 0.00 0.00 30.41 3.69
3118 3472 3.597255 TGTGTTGTGTAAACGAACAGGA 58.403 40.909 0.00 0.00 30.41 3.86
3119 3473 4.343811 TTGTGTTGTGTAAACGAACAGG 57.656 40.909 0.00 0.00 30.41 4.00
3120 3474 6.677027 TTTTTGTGTTGTGTAAACGAACAG 57.323 33.333 0.00 0.00 30.41 3.16
3121 3475 7.502339 CAATTTTTGTGTTGTGTAAACGAACA 58.498 30.769 0.00 0.00 0.00 3.18
3134 3488 8.491331 AACACTTATGAAGCAATTTTTGTGTT 57.509 26.923 0.00 0.00 39.20 3.32
3179 3533 3.140325 CTGGCAGTCCTTTCCAGTTTA 57.860 47.619 6.28 0.00 41.76 2.01
3249 3610 3.381045 GCCAGCTTAAGTGTGTTTTTCC 58.619 45.455 4.02 0.00 0.00 3.13
3259 3620 1.523758 CGTGAAAGGCCAGCTTAAGT 58.476 50.000 5.01 0.00 0.00 2.24
3294 3655 1.451936 GGGTCTCAAGTGTGCACCT 59.548 57.895 15.69 8.25 31.25 4.00
3402 3763 3.681593 CGGAAATTTGGTAAGGAGGACA 58.318 45.455 0.00 0.00 0.00 4.02
3496 3857 9.162764 GTCCTGTAGAATTGAAACTTATGCTTA 57.837 33.333 0.00 0.00 0.00 3.09
3518 3879 6.497259 TGAAACTCTTATCTTACACCAGTCCT 59.503 38.462 0.00 0.00 0.00 3.85
3557 3918 3.067833 GCCTTGTGGTCAGTACTTTCTC 58.932 50.000 0.00 0.00 35.27 2.87


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

AutoCloner maintained by Alex Coulton.