Multiple sequence alignment - TraesCS7A01G406700

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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 TraesCS7A01G406700 chr7A 100.000 2375 0 0 1 2375 592045195 592047569 0.000000e+00 4386
1 TraesCS7A01G406700 chr7D 89.495 1742 94 27 678 2369 517218566 517220268 0.000000e+00 2121
2 TraesCS7A01G406700 chr7B 92.399 842 31 8 804 1622 550030441 550031272 0.000000e+00 1170
3 TraesCS7A01G406700 chr7B 87.432 740 77 12 1 734 550028590 550029319 0.000000e+00 837
4 TraesCS7A01G406700 chr7B 88.663 591 32 13 1804 2369 550031341 550031921 0.000000e+00 688
5 TraesCS7A01G406700 chr7B 95.238 63 3 0 1671 1733 550031267 550031329 1.500000e-17 100
6 TraesCS7A01G406700 chr3B 82.477 428 54 12 1001 1410 172958849 172958425 2.900000e-94 355


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 TraesCS7A01G406700 chr7A 592045195 592047569 2374 False 4386.00 4386 100.000 1 2375 1 chr7A.!!$F1 2374
1 TraesCS7A01G406700 chr7D 517218566 517220268 1702 False 2121.00 2121 89.495 678 2369 1 chr7D.!!$F1 1691
2 TraesCS7A01G406700 chr7B 550028590 550031921 3331 False 698.75 1170 90.933 1 2369 4 chr7B.!!$F1 2368

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
811 1868 0.178861 TGCCCTCCTCCTCTTCCTTT 60.179 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 2827 0.030908 GTCTCTAAGATCCGTGCGGG 59.969 60.0 10.94 0.0 35.59 6.13 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
33 34 3.139077 CAAGTGGGTAGTCAAGTGTTCC 58.861 50.000 0.00 0.00 0.00 3.62
35 36 3.853207 AGTGGGTAGTCAAGTGTTCCTA 58.147 45.455 0.00 0.00 0.00 2.94
41 42 6.327104 TGGGTAGTCAAGTGTTCCTAAAGTTA 59.673 38.462 0.00 0.00 0.00 2.24
44 45 7.384387 GGTAGTCAAGTGTTCCTAAAGTTACAG 59.616 40.741 0.00 0.00 0.00 2.74
48 49 4.642429 AGTGTTCCTAAAGTTACAGCCAG 58.358 43.478 0.00 0.00 0.00 4.85
49 50 4.347000 AGTGTTCCTAAAGTTACAGCCAGA 59.653 41.667 0.00 0.00 0.00 3.86
58 59 3.424703 AGTTACAGCCAGATGTGCAATT 58.575 40.909 0.00 0.00 34.56 2.32
63 64 3.054875 ACAGCCAGATGTGCAATTCTCTA 60.055 43.478 0.00 0.00 30.46 2.43
73 74 5.674525 TGTGCAATTCTCTATGGTTAGGAG 58.325 41.667 0.00 0.00 0.00 3.69
83 84 7.474445 TCTCTATGGTTAGGAGAGCTAATCAT 58.526 38.462 0.00 0.00 40.16 2.45
146 147 6.149142 ACTGAAAAGATTGAAGAGCTAGCTTG 59.851 38.462 20.42 0.00 28.79 4.01
151 152 5.312079 AGATTGAAGAGCTAGCTTGTTGTT 58.688 37.500 20.42 7.74 0.00 2.83
168 169 4.036262 TGTTGTTTGAATCTTCCACCTTCG 59.964 41.667 0.00 0.00 0.00 3.79
171 172 4.065789 GTTTGAATCTTCCACCTTCGAGT 58.934 43.478 0.00 0.00 0.00 4.18
172 173 3.319137 TGAATCTTCCACCTTCGAGTG 57.681 47.619 0.00 0.00 37.51 3.51
217 219 7.611770 TGTATCTCAACTAAAGCATGTGTACT 58.388 34.615 0.00 0.00 0.00 2.73
228 230 2.423538 GCATGTGTACTTTCCCACCATC 59.576 50.000 0.00 0.00 0.00 3.51
255 257 1.792115 ATCAGCTCTTCCTCCTCCTG 58.208 55.000 0.00 0.00 0.00 3.86
257 259 0.823460 CAGCTCTTCCTCCTCCTGAC 59.177 60.000 0.00 0.00 0.00 3.51
258 260 0.411452 AGCTCTTCCTCCTCCTGACA 59.589 55.000 0.00 0.00 0.00 3.58
267 269 2.233431 CCTCCTCCTGACACTCTTCTTG 59.767 54.545 0.00 0.00 0.00 3.02
293 295 3.904571 TCATGTCAAAATTCTGCAGCAC 58.095 40.909 9.47 0.00 0.00 4.40
301 303 1.237285 ATTCTGCAGCACCGTGTTCC 61.237 55.000 9.47 0.00 0.00 3.62
305 307 1.891919 GCAGCACCGTGTTCCTCAA 60.892 57.895 0.00 0.00 0.00 3.02
306 308 1.941812 CAGCACCGTGTTCCTCAAC 59.058 57.895 0.00 0.00 0.00 3.18
309 311 1.557443 GCACCGTGTTCCTCAACGAG 61.557 60.000 0.00 0.00 34.95 4.18
333 335 3.261580 CATCGTACCATTCTGCAAGTGA 58.738 45.455 0.00 0.00 33.76 3.41
337 339 1.089920 ACCATTCTGCAAGTGATCGC 58.910 50.000 0.00 0.00 33.76 4.58
347 349 2.897436 CAAGTGATCGCTCAATGGAGA 58.103 47.619 9.70 0.00 44.26 3.71
383 385 3.370103 CCGTTGCTACCTGGGAAGATTTA 60.370 47.826 0.00 0.00 0.00 1.40
384 386 4.258543 CGTTGCTACCTGGGAAGATTTAA 58.741 43.478 0.00 0.00 0.00 1.52
386 388 5.357032 CGTTGCTACCTGGGAAGATTTAAAT 59.643 40.000 0.00 0.00 0.00 1.40
411 413 4.828925 GCCAGCAGCTCCCTCGTC 62.829 72.222 0.00 0.00 38.99 4.20
445 448 2.307098 ACAAGATGGTTCTGAAGGAGGG 59.693 50.000 0.00 0.00 30.72 4.30
466 469 3.365265 GTTGTCAAGGGCGCCAGG 61.365 66.667 30.85 16.96 0.00 4.45
485 488 2.024369 AGGGTTAGCGGGAATCCAAATT 60.024 45.455 0.09 0.00 31.32 1.82
497 500 2.766345 TCCAAATTCAAGCAATGGGC 57.234 45.000 0.00 0.00 45.30 5.36
498 501 1.278699 TCCAAATTCAAGCAATGGGCC 59.721 47.619 0.00 0.00 46.50 5.80
499 502 1.003349 CCAAATTCAAGCAATGGGCCA 59.997 47.619 9.61 9.61 46.50 5.36
501 504 0.251073 AATTCAAGCAATGGGCCAGC 59.749 50.000 13.78 11.47 46.50 4.85
503 506 4.137872 CAAGCAATGGGCCAGCGG 62.138 66.667 13.78 4.81 46.50 5.52
521 525 1.677552 GCCCGACCCAGAAAAGAGA 59.322 57.895 0.00 0.00 0.00 3.10
522 526 0.673956 GCCCGACCCAGAAAAGAGAC 60.674 60.000 0.00 0.00 0.00 3.36
532 536 1.340248 AGAAAAGAGACGCGACTTCCA 59.660 47.619 15.93 0.00 0.00 3.53
533 537 1.721926 GAAAAGAGACGCGACTTCCAG 59.278 52.381 15.93 0.00 0.00 3.86
559 563 0.396435 TGCAGGTCGTCAATTGGTCT 59.604 50.000 5.42 0.00 0.00 3.85
560 564 1.202758 TGCAGGTCGTCAATTGGTCTT 60.203 47.619 5.42 0.00 0.00 3.01
580 584 6.653183 GTCTTTGACCTAGTAACGTTTTTCC 58.347 40.000 5.91 0.00 0.00 3.13
581 585 6.258507 GTCTTTGACCTAGTAACGTTTTTCCA 59.741 38.462 5.91 0.00 0.00 3.53
582 586 5.989551 TTGACCTAGTAACGTTTTTCCAC 57.010 39.130 5.91 0.00 0.00 4.02
589 594 9.321562 ACCTAGTAACGTTTTTCCACATATATG 57.678 33.333 5.91 11.29 0.00 1.78
595 600 7.324354 ACGTTTTTCCACATATATGGTTACC 57.676 36.000 16.96 0.00 40.95 2.85
596 601 7.114095 ACGTTTTTCCACATATATGGTTACCT 58.886 34.615 16.96 0.00 40.95 3.08
597 602 8.266473 ACGTTTTTCCACATATATGGTTACCTA 58.734 33.333 16.96 0.00 40.95 3.08
598 603 8.770828 CGTTTTTCCACATATATGGTTACCTAG 58.229 37.037 16.96 0.00 40.95 3.02
599 604 8.565416 GTTTTTCCACATATATGGTTACCTAGC 58.435 37.037 16.96 0.00 40.95 3.42
600 605 6.368779 TTCCACATATATGGTTACCTAGCC 57.631 41.667 16.96 0.00 40.95 3.93
601 606 4.464951 TCCACATATATGGTTACCTAGCCG 59.535 45.833 16.96 0.00 40.95 5.52
602 607 4.222145 CCACATATATGGTTACCTAGCCGT 59.778 45.833 16.96 0.00 34.77 5.68
603 608 5.419788 CCACATATATGGTTACCTAGCCGTA 59.580 44.000 16.96 0.00 34.77 4.02
604 609 6.405508 CCACATATATGGTTACCTAGCCGTAG 60.406 46.154 16.96 0.00 32.64 3.51
609 614 1.534805 GGTTACCTAGCCGTAGCGTTC 60.535 57.143 0.00 0.00 46.67 3.95
657 662 2.494059 TGAAACTTGGCGAGGAAGAAG 58.506 47.619 6.71 0.00 0.00 2.85
692 697 5.635700 GCCGGCTTGTAATTTTGAATTGTAA 59.364 36.000 22.15 0.00 0.00 2.41
693 698 6.400621 GCCGGCTTGTAATTTTGAATTGTAAC 60.401 38.462 22.15 0.00 0.00 2.50
703 708 4.610605 TTGAATTGTAACGAGGTGAGGA 57.389 40.909 0.00 0.00 0.00 3.71
709 714 2.701951 TGTAACGAGGTGAGGAAGGTTT 59.298 45.455 0.00 0.00 0.00 3.27
756 761 1.339631 ACTTCGGCCATGGAATTCGAA 60.340 47.619 18.40 20.84 38.04 3.71
772 777 3.549299 TCGAACTTCGTGGTCTAGTTC 57.451 47.619 10.88 0.00 42.61 3.01
811 1868 0.178861 TGCCCTCCTCCTCTTCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
838 1897 3.126001 TCCGACAGTGAGCTTGAAAAT 57.874 42.857 0.00 0.00 0.00 1.82
879 1938 2.036733 TGCCAGACCAGTAACAGTGTAC 59.963 50.000 0.00 0.00 0.00 2.90
917 1981 1.602377 GTGCACGGCTTAAGTTTCACT 59.398 47.619 0.00 0.00 0.00 3.41
1014 2078 2.036098 CTCATGGCACCCCAGCAA 59.964 61.111 0.00 0.00 46.24 3.91
1026 2090 1.078567 CCAGCAACAGCTCCTCCTC 60.079 63.158 0.00 0.00 36.19 3.71
1300 2370 1.995626 CTCCATTCCGGGTCCCACT 60.996 63.158 9.12 0.00 34.36 4.00
1346 2416 2.507992 GATGCTCTGCGCTGTCGT 60.508 61.111 9.73 6.35 40.11 4.34
1465 2548 6.131961 ACAGGGGAATTTCATAGATTTCTGG 58.868 40.000 0.00 0.00 0.00 3.86
1469 2552 6.410853 GGGGAATTTCATAGATTTCTGGGAGA 60.411 42.308 0.00 0.00 0.00 3.71
1494 2580 8.687824 AATTATATTGTAAGTTGTTGCAGTGC 57.312 30.769 8.58 8.58 29.18 4.40
1495 2581 5.703978 ATATTGTAAGTTGTTGCAGTGCA 57.296 34.783 15.37 15.37 36.47 4.57
1503 2589 0.392863 TGTTGCAGTGCACACTCAGT 60.393 50.000 19.58 0.00 40.20 3.41
1511 2597 1.128692 GTGCACACTCAGTAATTCCGC 59.871 52.381 13.17 0.00 0.00 5.54
1512 2598 1.270571 TGCACACTCAGTAATTCCGCA 60.271 47.619 0.00 0.00 0.00 5.69
1748 2841 2.185867 GCACCCGCACGGATCTTA 59.814 61.111 11.42 0.00 38.36 2.10
1796 2889 2.685106 TGGGGCTTCAATGGTGTTAA 57.315 45.000 0.00 0.00 0.00 2.01
1824 2925 3.139397 TGGGGTCTTGTTCTGGTTGTAAT 59.861 43.478 0.00 0.00 0.00 1.89
1841 2942 8.301002 TGGTTGTAATTTTACTGCTGTATTTCC 58.699 33.333 4.12 1.11 34.77 3.13
1948 3072 1.626825 GTGGTGGGAGTACCTTGCTAA 59.373 52.381 0.00 0.00 41.43 3.09
1951 3075 2.617276 GGTGGGAGTACCTTGCTAAACC 60.617 54.545 0.00 0.00 41.11 3.27
1956 3080 2.991866 GAGTACCTTGCTAAACCGTGAC 59.008 50.000 0.00 0.00 0.00 3.67
1971 3095 2.179547 TGACACTGTGTGCCTTGCG 61.180 57.895 19.62 0.00 36.98 4.85
1988 3115 3.829886 TGCGGAGTGAATGAATGAAAC 57.170 42.857 0.00 0.00 0.00 2.78
1989 3116 3.145286 TGCGGAGTGAATGAATGAAACA 58.855 40.909 0.00 0.00 0.00 2.83
1990 3117 3.758023 TGCGGAGTGAATGAATGAAACAT 59.242 39.130 0.00 0.00 0.00 2.71
1991 3118 4.142622 TGCGGAGTGAATGAATGAAACATC 60.143 41.667 0.00 0.00 0.00 3.06
1992 3119 4.095483 GCGGAGTGAATGAATGAAACATCT 59.905 41.667 0.00 0.00 0.00 2.90
1993 3120 5.566623 CGGAGTGAATGAATGAAACATCTG 58.433 41.667 0.00 0.00 0.00 2.90
2040 3167 3.584250 CTGCTTGAACGTGCGGCTG 62.584 63.158 11.67 7.99 0.00 4.85
2059 3186 0.385723 GCCATCGGTCGATCTCGTAC 60.386 60.000 2.59 0.00 40.80 3.67
2107 3239 0.325203 GAAGCTGGTCCTCTCCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
2138 3273 1.889530 CTTCCCCACCTCACCGACTC 61.890 65.000 0.00 0.00 0.00 3.36
2142 3277 2.657237 CACCTCACCGACTCCCAC 59.343 66.667 0.00 0.00 0.00 4.61
2329 3464 3.648339 TGAAGTAGCGTCGTAAAACCT 57.352 42.857 0.00 0.00 0.00 3.50
2336 3471 1.620413 CGTCGTAAAACCTCGTGCCC 61.620 60.000 0.00 0.00 0.00 5.36
2369 3504 1.063567 TCCCTCTCCCTGACTAGCTTC 60.064 57.143 0.00 0.00 0.00 3.86
2370 3505 1.028905 CCTCTCCCTGACTAGCTTCG 58.971 60.000 0.00 0.00 0.00 3.79
2371 3506 0.383949 CTCTCCCTGACTAGCTTCGC 59.616 60.000 0.00 0.00 0.00 4.70
2372 3507 1.064946 CTCCCTGACTAGCTTCGCG 59.935 63.158 0.00 0.00 0.00 5.87
2373 3508 1.658686 CTCCCTGACTAGCTTCGCGT 61.659 60.000 5.77 0.00 0.00 6.01
2374 3509 1.226717 CCCTGACTAGCTTCGCGTC 60.227 63.158 5.77 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.758784 GCTGTAACTTTAGGAACACTTGACT 59.241 40.000 0.00 0.00 0.00 3.41
22 23 5.049612 GGCTGTAACTTTAGGAACACTTGAC 60.050 44.000 0.00 0.00 0.00 3.18
33 34 4.002982 TGCACATCTGGCTGTAACTTTAG 58.997 43.478 0.00 0.00 0.00 1.85
35 36 2.862541 TGCACATCTGGCTGTAACTTT 58.137 42.857 0.00 0.00 0.00 2.66
41 42 2.089980 GAGAATTGCACATCTGGCTGT 58.910 47.619 5.21 0.00 0.00 4.40
44 45 3.252701 CCATAGAGAATTGCACATCTGGC 59.747 47.826 5.21 0.00 0.00 4.85
48 49 6.291377 TCCTAACCATAGAGAATTGCACATC 58.709 40.000 0.00 0.00 0.00 3.06
49 50 6.100279 TCTCCTAACCATAGAGAATTGCACAT 59.900 38.462 0.00 0.00 0.00 3.21
58 59 6.853490 TGATTAGCTCTCCTAACCATAGAGA 58.147 40.000 0.00 0.00 39.29 3.10
87 88 5.656859 GGCCCCACAGTATTTAAAAGAGAAT 59.343 40.000 0.00 0.00 0.00 2.40
99 100 2.190398 TGACATAGGCCCCACAGTAT 57.810 50.000 0.00 0.00 0.00 2.12
146 147 4.274950 TCGAAGGTGGAAGATTCAAACAAC 59.725 41.667 0.00 0.00 0.00 3.32
151 152 3.664107 CACTCGAAGGTGGAAGATTCAA 58.336 45.455 0.00 0.00 33.95 2.69
168 169 5.200483 TGGATAATTGGGTGAATTCCACTC 58.800 41.667 2.27 2.18 46.52 3.51
171 172 5.527385 ACATGGATAATTGGGTGAATTCCA 58.473 37.500 2.27 0.00 35.74 3.53
172 173 7.671398 AGATACATGGATAATTGGGTGAATTCC 59.329 37.037 2.27 0.00 35.74 3.01
179 180 7.154191 AGTTGAGATACATGGATAATTGGGT 57.846 36.000 0.00 0.00 0.00 4.51
228 230 3.431486 GGAGGAAGAGCTGATTGTACCTG 60.431 52.174 0.00 0.00 0.00 4.00
255 257 4.636249 ACATGAACCTCAAGAAGAGTGTC 58.364 43.478 0.00 0.00 43.12 3.67
257 259 4.635223 TGACATGAACCTCAAGAAGAGTG 58.365 43.478 0.00 0.00 43.12 3.51
258 260 4.963318 TGACATGAACCTCAAGAAGAGT 57.037 40.909 0.00 0.00 43.12 3.24
267 269 5.125100 TGCAGAATTTTGACATGAACCTC 57.875 39.130 0.00 0.00 0.00 3.85
306 308 3.112484 GCAGAATGGTACGATGTCCTCG 61.112 54.545 0.00 0.00 45.38 4.63
309 311 2.309528 TGCAGAATGGTACGATGTCC 57.690 50.000 0.00 0.00 35.86 4.02
323 325 2.004733 CATTGAGCGATCACTTGCAGA 58.995 47.619 1.08 0.00 33.84 4.26
333 335 0.179062 GTGCCTCTCCATTGAGCGAT 60.179 55.000 0.00 0.00 38.58 4.58
337 339 1.938577 CATTCGTGCCTCTCCATTGAG 59.061 52.381 0.00 0.00 40.17 3.02
362 364 2.403252 AATCTTCCCAGGTAGCAACG 57.597 50.000 0.00 0.00 0.00 4.10
395 397 3.368190 CTGACGAGGGAGCTGCTGG 62.368 68.421 7.01 0.00 0.00 4.85
397 399 2.283532 ACTGACGAGGGAGCTGCT 60.284 61.111 0.00 0.00 0.00 4.24
398 400 2.125753 CACTGACGAGGGAGCTGC 60.126 66.667 0.00 0.00 0.00 5.25
410 412 1.059584 TCTTGTCCCCAAGCCACTGA 61.060 55.000 0.00 0.00 46.33 3.41
411 413 0.038744 ATCTTGTCCCCAAGCCACTG 59.961 55.000 0.00 0.00 46.33 3.66
429 432 2.715295 CCCCCTCCTTCAGAACCAT 58.285 57.895 0.00 0.00 0.00 3.55
430 433 4.250699 CCCCCTCCTTCAGAACCA 57.749 61.111 0.00 0.00 0.00 3.67
449 452 3.365265 CCTGGCGCCCTTGACAAC 61.365 66.667 26.77 0.00 0.00 3.32
453 456 2.931105 TAACCCTGGCGCCCTTGA 60.931 61.111 26.77 3.41 0.00 3.02
463 466 0.254747 TTGGATTCCCGCTAACCCTG 59.745 55.000 0.00 0.00 34.29 4.45
466 469 3.020984 TGAATTTGGATTCCCGCTAACC 58.979 45.455 0.00 0.00 40.79 2.85
473 476 4.193865 CCATTGCTTGAATTTGGATTCCC 58.806 43.478 0.00 0.00 40.79 3.97
485 488 3.063704 CGCTGGCCCATTGCTTGA 61.064 61.111 0.00 0.00 40.92 3.02
501 504 2.746277 CTTTTCTGGGTCGGGCCG 60.746 66.667 22.51 22.51 38.44 6.13
503 506 0.673956 GTCTCTTTTCTGGGTCGGGC 60.674 60.000 0.00 0.00 0.00 6.13
505 508 1.014564 GCGTCTCTTTTCTGGGTCGG 61.015 60.000 0.00 0.00 0.00 4.79
559 563 5.879223 TGTGGAAAAACGTTACTAGGTCAAA 59.121 36.000 0.00 0.00 0.00 2.69
560 564 5.426504 TGTGGAAAAACGTTACTAGGTCAA 58.573 37.500 0.00 0.00 0.00 3.18
567 571 8.570068 AACCATATATGTGGAAAAACGTTACT 57.430 30.769 23.95 0.00 42.02 2.24
573 577 8.565416 GCTAGGTAACCATATATGTGGAAAAAC 58.435 37.037 23.95 14.47 42.02 2.43
578 582 4.464951 CGGCTAGGTAACCATATATGTGGA 59.535 45.833 23.95 0.55 42.02 4.02
580 584 5.401531 ACGGCTAGGTAACCATATATGTG 57.598 43.478 11.73 5.92 37.17 3.21
581 585 5.126707 GCTACGGCTAGGTAACCATATATGT 59.873 44.000 11.73 0.00 35.22 2.29
582 586 5.589192 GCTACGGCTAGGTAACCATATATG 58.411 45.833 5.68 5.68 35.22 1.78
589 594 0.457443 AACGCTACGGCTAGGTAACC 59.543 55.000 0.00 0.00 36.09 2.85
595 600 1.121240 CATTCGAACGCTACGGCTAG 58.879 55.000 0.00 0.00 36.09 3.42
596 601 0.734309 TCATTCGAACGCTACGGCTA 59.266 50.000 0.00 0.00 36.09 3.93
597 602 0.801067 GTCATTCGAACGCTACGGCT 60.801 55.000 0.00 0.00 36.09 5.52
598 603 1.629504 GTCATTCGAACGCTACGGC 59.370 57.895 0.00 0.00 0.00 5.68
599 604 0.795735 ACGTCATTCGAACGCTACGG 60.796 55.000 20.36 8.64 43.76 4.02
600 605 1.801618 TACGTCATTCGAACGCTACG 58.198 50.000 16.87 16.87 43.76 3.51
601 606 4.551056 TTTTACGTCATTCGAACGCTAC 57.449 40.909 0.00 0.00 43.76 3.58
625 630 2.547218 CCAAGTTTCAATTGCTGCAGCT 60.547 45.455 36.61 17.63 42.66 4.24
626 631 1.796459 CCAAGTTTCAATTGCTGCAGC 59.204 47.619 31.89 31.89 42.50 5.25
628 633 1.868469 GCCAAGTTTCAATTGCTGCA 58.132 45.000 0.00 0.00 0.00 4.41
629 634 0.785979 CGCCAAGTTTCAATTGCTGC 59.214 50.000 0.00 0.00 0.00 5.25
630 635 2.322161 CTCGCCAAGTTTCAATTGCTG 58.678 47.619 0.00 0.00 0.00 4.41
635 640 3.140325 TCTTCCTCGCCAAGTTTCAAT 57.860 42.857 0.00 0.00 0.00 2.57
670 675 6.579292 TCGTTACAATTCAAAATTACAAGCCG 59.421 34.615 0.00 0.00 0.00 5.52
671 676 7.061789 CCTCGTTACAATTCAAAATTACAAGCC 59.938 37.037 0.00 0.00 0.00 4.35
692 697 0.396811 CCAAACCTTCCTCACCTCGT 59.603 55.000 0.00 0.00 0.00 4.18
693 698 0.396811 ACCAAACCTTCCTCACCTCG 59.603 55.000 0.00 0.00 0.00 4.63
703 708 2.965147 CACAGGAATTCCACCAAACCTT 59.035 45.455 26.22 0.00 38.89 3.50
709 714 2.307496 ATTGCACAGGAATTCCACCA 57.693 45.000 26.22 13.58 38.89 4.17
772 777 2.642139 AAATCCTCATTTGCAGCACG 57.358 45.000 0.00 0.00 30.49 5.34
811 1868 1.347707 AGCTCACTGTCGGATGGAAAA 59.652 47.619 0.00 0.00 0.00 2.29
838 1897 3.315191 GCACCAGACAAAGCTTTCAAGTA 59.685 43.478 9.23 0.00 0.00 2.24
895 1959 1.601903 TGAAACTTAAGCCGTGCACTG 59.398 47.619 16.19 9.93 0.00 3.66
896 1960 1.602377 GTGAAACTTAAGCCGTGCACT 59.398 47.619 16.19 0.00 0.00 4.40
897 1961 2.032414 GTGAAACTTAAGCCGTGCAC 57.968 50.000 6.82 6.82 0.00 4.57
1014 2078 1.685421 GAGCAGGAGGAGGAGCTGT 60.685 63.158 0.00 0.00 37.48 4.40
1026 2090 3.478274 GCCAGGAGGAGGAGCAGG 61.478 72.222 0.00 0.00 36.89 4.85
1110 2174 4.139038 GCGGAGGAGAGTAGTAGAAGAAT 58.861 47.826 0.00 0.00 0.00 2.40
1300 2370 4.056125 CTGCACTCCGGTCTGCGA 62.056 66.667 17.54 8.84 0.00 5.10
1346 2416 1.437573 CATAGGAGAAGTGCGGCGA 59.562 57.895 12.98 0.00 0.00 5.54
1379 2449 4.994471 TGAGTGGCACAGCAGCGG 62.994 66.667 21.41 0.00 41.80 5.52
1465 2548 9.722056 CTGCAACAACTTACAATATAATTCTCC 57.278 33.333 0.00 0.00 0.00 3.71
1469 2552 8.303156 TGCACTGCAACAACTTACAATATAATT 58.697 29.630 0.00 0.00 34.76 1.40
1485 2571 1.581934 TACTGAGTGTGCACTGCAAC 58.418 50.000 19.41 7.71 42.66 4.17
1494 2580 2.002586 CCTGCGGAATTACTGAGTGTG 58.997 52.381 0.00 0.00 0.00 3.82
1495 2581 1.066143 CCCTGCGGAATTACTGAGTGT 60.066 52.381 0.00 0.00 0.00 3.55
1503 2589 2.702592 AATCGAACCCTGCGGAATTA 57.297 45.000 0.00 0.00 0.00 1.40
1511 2597 2.222027 GGCCAGATTAATCGAACCCTG 58.778 52.381 9.78 1.93 0.00 4.45
1512 2598 1.843851 TGGCCAGATTAATCGAACCCT 59.156 47.619 0.00 0.00 0.00 4.34
1734 2827 0.030908 GTCTCTAAGATCCGTGCGGG 59.969 60.000 10.94 0.00 35.59 6.13
1739 2832 4.764050 TCTCTCTGTCTCTAAGATCCGT 57.236 45.455 0.00 0.00 0.00 4.69
1743 2836 7.555087 CCAAACAATCTCTCTGTCTCTAAGAT 58.445 38.462 0.00 0.00 0.00 2.40
1748 2841 3.616076 CGCCAAACAATCTCTCTGTCTCT 60.616 47.826 0.00 0.00 0.00 3.10
1779 2872 3.006859 AGCTTTTAACACCATTGAAGCCC 59.993 43.478 0.00 0.00 40.10 5.19
1796 2889 2.310538 CAGAACAAGACCCCAAGCTTT 58.689 47.619 0.00 0.00 0.00 3.51
1824 2925 4.624024 CGAGACGGAAATACAGCAGTAAAA 59.376 41.667 0.00 0.00 33.13 1.52
1841 2942 1.388093 CAGCAAGAACACATCGAGACG 59.612 52.381 0.00 0.00 0.00 4.18
1902 3003 6.302535 TCGGGGAAGACTTAACATGAATTA 57.697 37.500 0.00 0.00 0.00 1.40
1916 3017 2.221299 CCACCACCTTCGGGGAAGA 61.221 63.158 6.93 0.00 41.71 2.87
1921 3022 1.611261 TACTCCCACCACCTTCGGG 60.611 63.158 0.00 0.00 41.76 5.14
1935 3036 2.991866 GTCACGGTTTAGCAAGGTACTC 59.008 50.000 0.00 0.00 38.49 2.59
1937 3038 2.477754 GTGTCACGGTTTAGCAAGGTAC 59.522 50.000 0.00 0.00 0.00 3.34
1940 3041 1.531149 CAGTGTCACGGTTTAGCAAGG 59.469 52.381 0.00 0.00 0.00 3.61
1948 3072 1.817941 GGCACACAGTGTCACGGTT 60.818 57.895 2.14 0.00 38.14 4.44
1951 3075 1.643292 CAAGGCACACAGTGTCACG 59.357 57.895 2.14 0.00 41.04 4.35
1971 3095 6.748333 TCAGATGTTTCATTCATTCACTCC 57.252 37.500 0.00 0.00 0.00 3.85
2040 3167 0.385723 GTACGAGATCGACCGATGGC 60.386 60.000 9.83 0.95 43.02 4.40
2059 3186 4.683832 CTTCCTTGTAGACACCTTATCGG 58.316 47.826 0.00 0.00 39.35 4.18
2095 3227 0.185175 GAGGAGGAGGAGGAGAGGAC 59.815 65.000 0.00 0.00 0.00 3.85
2107 3239 2.647949 GGGGAAGGGAGGAGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
2138 3273 4.936575 CATGGATGGATGGGTGGG 57.063 61.111 0.00 0.00 0.00 4.61
2282 3417 2.088423 TGCACGCGGATAAAAGGATTT 58.912 42.857 12.47 0.00 42.41 2.17
2329 3464 1.949847 GCTAGCTCAAGAGGGCACGA 61.950 60.000 7.70 0.00 0.00 4.35
2336 3471 1.956477 GAGAGGGAGCTAGCTCAAGAG 59.044 57.143 38.32 0.00 44.40 2.85


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

AutoCloner maintained by Alex Coulton.