Multiple sequence alignment - TraesCS6A01G048300

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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 TraesCS6A01G048300 chr6A 100.000 2836 0 0 557 3392 24428051 24425216 0.000000e+00 5238
1 TraesCS6A01G048300 chr6A 100.000 178 0 0 1 178 24428607 24428430 2.520000e-86 329
2 TraesCS6A01G048300 chrUn 93.445 2151 93 23 704 2840 93842020 93839904 0.000000e+00 3147
3 TraesCS6A01G048300 chrUn 92.391 552 18 6 2841 3392 93839773 93839246 0.000000e+00 765
4 TraesCS6A01G048300 chrUn 83.056 602 80 13 1474 2061 337338654 337338061 8.340000e-146 527
5 TraesCS6A01G048300 chrUn 96.154 156 4 2 2 157 93842281 93842128 1.560000e-63 254
6 TraesCS6A01G048300 chr6B 93.323 1887 97 15 970 2840 42817381 42815508 0.000000e+00 2760
7 TraesCS6A01G048300 chr6B 87.748 555 47 6 2841 3390 42815377 42814839 2.220000e-176 628


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 TraesCS6A01G048300 chr6A 24425216 24428607 3391 True 2783.500000 5238 100.000000 1 3392 2 chr6A.!!$R1 3391
1 TraesCS6A01G048300 chrUn 93839246 93842281 3035 True 1388.666667 3147 93.996667 2 3392 3 chrUn.!!$R2 3390
2 TraesCS6A01G048300 chrUn 337338061 337338654 593 True 527.000000 527 83.056000 1474 2061 1 chrUn.!!$R1 587
3 TraesCS6A01G048300 chr6B 42814839 42817381 2542 True 1694.000000 2760 90.535500 970 3390 2 chr6B.!!$R1 2420

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
890 896 0.034198 TCCATTTTCGACACGCAGGA 59.966 50.0 0.0 0.0 0.00 3.86 F
1605 1614 0.041663 CGTTTTGCGATTGTGGTCGT 60.042 50.0 0.0 0.0 44.77 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1771 0.251354 ATCCAGCACAAGATCTGCGT 59.749 50.0 0.00 0.0 39.79 5.24 R
2890 3057 2.418368 AGGACTGTTGCACTTGTCAA 57.582 45.0 12.29 0.0 0.00 3.18 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
170 171 8.614994 ACACGATGAAAACTTTTCTAACAAAG 57.385 30.769 14.05 0.00 39.35 2.77
171 172 8.455682 ACACGATGAAAACTTTTCTAACAAAGA 58.544 29.630 14.05 0.00 37.24 2.52
172 173 9.284594 CACGATGAAAACTTTTCTAACAAAGAA 57.715 29.630 14.05 0.00 42.62 2.52
173 174 9.503427 ACGATGAAAACTTTTCTAACAAAGAAG 57.497 29.630 14.05 0.00 44.95 2.85
175 176 9.249457 GATGAAAACTTTTCTAACAAAGAAGGG 57.751 33.333 14.05 0.00 44.95 3.95
176 177 8.129496 TGAAAACTTTTCTAACAAAGAAGGGT 57.871 30.769 14.05 0.00 44.95 4.34
177 178 8.590204 TGAAAACTTTTCTAACAAAGAAGGGTT 58.410 29.630 14.05 0.00 44.95 4.11
599 600 5.959618 ATAGGTTGGACACTTTTTAGTGC 57.040 39.130 5.27 0.00 43.13 4.40
600 601 3.626930 AGGTTGGACACTTTTTAGTGCA 58.373 40.909 5.27 0.00 43.13 4.57
601 602 3.380320 AGGTTGGACACTTTTTAGTGCAC 59.620 43.478 9.40 9.40 43.13 4.57
602 603 3.359654 GTTGGACACTTTTTAGTGCACG 58.640 45.455 12.01 0.00 43.13 5.34
603 604 2.907634 TGGACACTTTTTAGTGCACGA 58.092 42.857 12.01 2.52 43.13 4.35
604 605 3.271729 TGGACACTTTTTAGTGCACGAA 58.728 40.909 12.01 10.15 43.13 3.85
605 606 3.880490 TGGACACTTTTTAGTGCACGAAT 59.120 39.130 13.36 0.00 43.13 3.34
606 607 5.057819 TGGACACTTTTTAGTGCACGAATA 58.942 37.500 13.36 5.99 43.13 1.75
607 608 5.527951 TGGACACTTTTTAGTGCACGAATAA 59.472 36.000 13.36 13.26 43.13 1.40
608 609 5.849604 GGACACTTTTTAGTGCACGAATAAC 59.150 40.000 13.36 3.55 43.13 1.89
609 610 6.366315 ACACTTTTTAGTGCACGAATAACA 57.634 33.333 13.36 0.00 43.13 2.41
610 611 6.787225 ACACTTTTTAGTGCACGAATAACAA 58.213 32.000 13.36 2.00 43.13 2.83
611 612 7.422399 ACACTTTTTAGTGCACGAATAACAAT 58.578 30.769 13.36 0.00 43.13 2.71
612 613 7.918562 ACACTTTTTAGTGCACGAATAACAATT 59.081 29.630 13.36 0.00 43.13 2.32
613 614 8.751335 CACTTTTTAGTGCACGAATAACAATTT 58.249 29.630 13.36 0.00 32.72 1.82
614 615 9.308318 ACTTTTTAGTGCACGAATAACAATTTT 57.692 25.926 13.36 0.00 0.00 1.82
653 654 8.789825 AGCATTTGGAAATTATGCAATTAACA 57.210 26.923 11.63 0.00 45.39 2.41
654 655 9.228949 AGCATTTGGAAATTATGCAATTAACAA 57.771 25.926 11.63 0.00 45.39 2.83
655 656 9.837525 GCATTTGGAAATTATGCAATTAACAAA 57.162 25.926 12.00 12.00 43.13 2.83
759 760 7.597369 GCTTAAATTTTCGAGGTAACATTTGGT 59.403 33.333 0.00 0.00 41.41 3.67
760 761 8.804688 TTAAATTTTCGAGGTAACATTTGGTG 57.195 30.769 0.00 0.00 41.41 4.17
823 827 3.429272 CCTGCAAATTCGCATGTACCATT 60.429 43.478 0.00 0.00 42.06 3.16
889 895 1.086696 ATCCATTTTCGACACGCAGG 58.913 50.000 0.00 0.00 0.00 4.85
890 896 0.034198 TCCATTTTCGACACGCAGGA 59.966 50.000 0.00 0.00 0.00 3.86
891 897 0.443869 CCATTTTCGACACGCAGGAG 59.556 55.000 0.00 0.00 0.00 3.69
892 898 0.179215 CATTTTCGACACGCAGGAGC 60.179 55.000 0.00 0.00 37.42 4.70
893 899 0.602638 ATTTTCGACACGCAGGAGCA 60.603 50.000 0.00 0.00 42.27 4.26
894 900 0.602638 TTTTCGACACGCAGGAGCAT 60.603 50.000 0.00 0.00 42.27 3.79
895 901 1.291184 TTTCGACACGCAGGAGCATG 61.291 55.000 0.00 0.00 40.38 4.06
896 902 3.857854 CGACACGCAGGAGCATGC 61.858 66.667 10.51 10.51 37.49 4.06
897 903 2.435586 GACACGCAGGAGCATGCT 60.436 61.111 22.92 22.92 44.24 3.79
898 904 2.435586 ACACGCAGGAGCATGCTC 60.436 61.111 34.99 34.99 44.24 4.26
924 930 1.335872 GCCAAATTGAATATCCGGCCG 60.336 52.381 21.04 21.04 31.76 6.13
927 933 2.616376 CAAATTGAATATCCGGCCGTCA 59.384 45.455 26.12 17.98 0.00 4.35
943 949 4.498345 GGCCGTCATGTTGAAAAACTTGTA 60.498 41.667 0.00 0.00 31.91 2.41
944 950 4.439776 GCCGTCATGTTGAAAAACTTGTAC 59.560 41.667 0.00 0.00 31.91 2.90
945 951 5.732247 GCCGTCATGTTGAAAAACTTGTACT 60.732 40.000 0.00 0.00 31.91 2.73
946 952 5.681105 CCGTCATGTTGAAAAACTTGTACTG 59.319 40.000 0.00 0.00 31.91 2.74
947 953 6.255215 CGTCATGTTGAAAAACTTGTACTGT 58.745 36.000 0.00 0.00 31.91 3.55
948 954 7.403421 CGTCATGTTGAAAAACTTGTACTGTA 58.597 34.615 0.00 0.00 31.91 2.74
986 992 3.388552 AGCCCCTCCAAAATTCCTTAG 57.611 47.619 0.00 0.00 0.00 2.18
1374 1383 4.785453 GCCCTCAACGCCCTCCTG 62.785 72.222 0.00 0.00 0.00 3.86
1419 1428 2.515991 CTCGCCGAGCTCCTCTCT 60.516 66.667 8.47 0.00 39.70 3.10
1422 1431 2.705821 CGCCGAGCTCCTCTCTGTT 61.706 63.158 8.47 0.00 39.70 3.16
1473 1482 2.939103 GTGCACCTACAACATCCTCATC 59.061 50.000 5.22 0.00 0.00 2.92
1476 1485 1.139058 ACCTACAACATCCTCATCCGC 59.861 52.381 0.00 0.00 0.00 5.54
1477 1486 1.491670 CTACAACATCCTCATCCGCG 58.508 55.000 0.00 0.00 0.00 6.46
1478 1487 0.529773 TACAACATCCTCATCCGCGC 60.530 55.000 0.00 0.00 0.00 6.86
1479 1488 2.586079 AACATCCTCATCCGCGCG 60.586 61.111 25.67 25.67 0.00 6.86
1480 1489 4.592192 ACATCCTCATCCGCGCGG 62.592 66.667 42.13 42.13 0.00 6.46
1605 1614 0.041663 CGTTTTGCGATTGTGGTCGT 60.042 50.000 0.00 0.00 44.77 4.34
1626 1643 2.504244 GAGGAGGCGTTCGACGTG 60.504 66.667 0.00 0.00 44.73 4.49
1642 1659 2.046023 TGAAGGACGCCATGGCTG 60.046 61.111 33.07 26.84 39.32 4.85
1683 1700 1.315690 ATGCTCATGTGTATGCCAGC 58.684 50.000 0.00 0.00 35.69 4.85
1728 1745 1.303317 GGATGTGGACAAGGCGGTT 60.303 57.895 0.00 0.00 0.00 4.44
1752 1769 0.620556 TCAAAGAGGAGATGGTGGCC 59.379 55.000 0.00 0.00 0.00 5.36
1753 1770 0.745845 CAAAGAGGAGATGGTGGCCG 60.746 60.000 0.00 0.00 0.00 6.13
1754 1771 0.909610 AAAGAGGAGATGGTGGCCGA 60.910 55.000 0.00 0.00 0.00 5.54
1766 1783 2.125512 GGCCGACGCAGATCTTGT 60.126 61.111 0.00 0.00 36.38 3.16
1860 1880 1.661463 TGCTGGAAGAGATGAAGGGT 58.339 50.000 0.00 0.00 34.07 4.34
1932 1952 1.303309 GTGAGGATGAGGGCGATTTG 58.697 55.000 0.00 0.00 0.00 2.32
1941 1961 2.025156 GGCGATTTGGATGCTGCG 59.975 61.111 0.00 0.00 0.00 5.18
1988 2008 2.360350 CGGGTGCAAGGCAGATGT 60.360 61.111 0.00 0.00 40.08 3.06
2121 2141 3.242543 CGTACAGAATGCTCTTTGATGGC 60.243 47.826 0.00 0.00 42.53 4.40
2130 2150 2.749076 GCTCTTTGATGGCATGTGTGTA 59.251 45.455 3.81 0.00 0.00 2.90
2139 2159 1.002257 CATGTGTGTAGCTGGGGCA 60.002 57.895 0.00 0.00 41.70 5.36
2175 2195 3.955471 TCAGGTTTTGGATGAGATGACC 58.045 45.455 0.00 0.00 0.00 4.02
2207 2227 2.575461 GCCAAGCAAGGATGGTGC 59.425 61.111 0.00 0.00 42.55 5.01
2268 2288 4.796290 GCAGTGTTGCTAGAGTCAGTGTTA 60.796 45.833 0.00 0.00 46.95 2.41
2289 2309 1.079127 CCGTCTGGCGAAGGTGAAT 60.079 57.895 1.87 0.00 44.77 2.57
2293 2313 0.391661 TCTGGCGAAGGTGAATGCTC 60.392 55.000 0.00 0.00 0.00 4.26
2295 2315 0.901827 TGGCGAAGGTGAATGCTCTA 59.098 50.000 0.00 0.00 0.00 2.43
2303 2323 4.734398 AGGTGAATGCTCTAGAGTCAAG 57.266 45.455 20.75 0.00 0.00 3.02
2340 2360 0.950555 TCACCAGTGCGCTGAATGAC 60.951 55.000 28.54 0.00 45.28 3.06
2357 2377 1.208052 TGACCCTGCAGAGCTTATGAC 59.792 52.381 17.39 0.00 0.00 3.06
2396 2416 7.281100 GGATAGTTTAAGATTCACTTGACTGGG 59.719 40.741 0.00 0.00 39.38 4.45
2417 2437 5.130477 TGGGTCTCTGGATACTTGATTAACC 59.870 44.000 0.00 0.00 37.61 2.85
2525 2545 4.226761 GTTTTCCTACGCAATTCAGGTTG 58.773 43.478 0.00 0.00 0.00 3.77
2829 2866 6.174049 GTGCTCTTCTAAATACCCTTTGACT 58.826 40.000 0.00 0.00 0.00 3.41
2870 3037 6.886459 AGAATTAGCAAATGCCAGAAAGAGTA 59.114 34.615 0.94 0.00 43.38 2.59
2890 3057 8.164057 AGAGTAAAGATATTGGGGAAAAGACT 57.836 34.615 0.00 0.00 0.00 3.24
2929 3097 9.512588 CAGTCCTATGGCTATCTTATCAATTTT 57.487 33.333 0.00 0.00 0.00 1.82
2932 3100 9.219603 TCCTATGGCTATCTTATCAATTTTTCG 57.780 33.333 0.00 0.00 0.00 3.46
2933 3101 7.965107 CCTATGGCTATCTTATCAATTTTTCGC 59.035 37.037 0.00 0.00 0.00 4.70
2934 3102 6.072112 TGGCTATCTTATCAATTTTTCGCC 57.928 37.500 0.00 0.00 0.00 5.54
2935 3103 5.827797 TGGCTATCTTATCAATTTTTCGCCT 59.172 36.000 0.00 0.00 33.99 5.52
2936 3104 6.321181 TGGCTATCTTATCAATTTTTCGCCTT 59.679 34.615 0.00 0.00 33.99 4.35
2937 3105 7.147915 TGGCTATCTTATCAATTTTTCGCCTTT 60.148 33.333 0.00 0.00 33.99 3.11
2938 3106 7.379797 GGCTATCTTATCAATTTTTCGCCTTTC 59.620 37.037 0.00 0.00 0.00 2.62
2939 3107 7.915397 GCTATCTTATCAATTTTTCGCCTTTCA 59.085 33.333 0.00 0.00 0.00 2.69
2940 3108 9.787532 CTATCTTATCAATTTTTCGCCTTTCAA 57.212 29.630 0.00 0.00 0.00 2.69
2942 3110 8.879342 TCTTATCAATTTTTCGCCTTTCAAAA 57.121 26.923 0.00 0.00 0.00 2.44
2943 3111 8.760569 TCTTATCAATTTTTCGCCTTTCAAAAC 58.239 29.630 0.00 0.00 0.00 2.43
2944 3112 8.655651 TTATCAATTTTTCGCCTTTCAAAACT 57.344 26.923 0.00 0.00 0.00 2.66
2945 3113 6.343226 TCAATTTTTCGCCTTTCAAAACTG 57.657 33.333 0.00 0.00 0.00 3.16
2946 3114 6.102663 TCAATTTTTCGCCTTTCAAAACTGA 58.897 32.000 0.00 0.00 0.00 3.41
2947 3115 6.591834 TCAATTTTTCGCCTTTCAAAACTGAA 59.408 30.769 0.00 0.00 0.00 3.02
2948 3116 6.588348 ATTTTTCGCCTTTCAAAACTGAAG 57.412 33.333 0.00 0.00 0.00 3.02
3093 3281 6.610830 TCTCCTGTTTATCTTTGAAAACCCT 58.389 36.000 0.00 0.00 35.23 4.34
3152 3340 5.772825 TTCCTGAACACAATTTCCTGAAG 57.227 39.130 0.00 0.00 0.00 3.02
3182 3370 7.493645 AGAAAACCTCAAAGCTTCTGATTTTTG 59.506 33.333 20.58 8.84 28.28 2.44
3251 3439 2.039480 AGCACTCTTCTCCTTGATTGCA 59.961 45.455 0.00 0.00 40.02 4.08
3310 3498 4.158394 TCGCCGGTTAATGTCTAGTTTAGT 59.842 41.667 1.90 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.231317 AGTGAGTGTTAAAAATGGTCATCACAT 59.769 33.333 0.00 0.00 36.63 3.21
573 574 9.169592 GCACTAAAAAGTGTCCAACCTATATTA 57.830 33.333 7.32 0.00 41.53 0.98
574 575 7.668052 TGCACTAAAAAGTGTCCAACCTATATT 59.332 33.333 7.32 0.00 41.53 1.28
575 576 7.120726 GTGCACTAAAAAGTGTCCAACCTATAT 59.879 37.037 10.32 0.00 41.53 0.86
576 577 6.428771 GTGCACTAAAAAGTGTCCAACCTATA 59.571 38.462 10.32 0.00 41.53 1.31
577 578 5.240844 GTGCACTAAAAAGTGTCCAACCTAT 59.759 40.000 10.32 0.00 41.53 2.57
578 579 4.577283 GTGCACTAAAAAGTGTCCAACCTA 59.423 41.667 10.32 0.00 41.53 3.08
579 580 3.380320 GTGCACTAAAAAGTGTCCAACCT 59.620 43.478 10.32 0.00 41.53 3.50
580 581 3.702330 GTGCACTAAAAAGTGTCCAACC 58.298 45.455 10.32 0.00 41.53 3.77
581 582 3.064271 TCGTGCACTAAAAAGTGTCCAAC 59.936 43.478 16.19 1.58 41.53 3.77
582 583 3.271729 TCGTGCACTAAAAAGTGTCCAA 58.728 40.909 16.19 0.00 41.53 3.53
583 584 2.907634 TCGTGCACTAAAAAGTGTCCA 58.092 42.857 16.19 0.00 41.53 4.02
584 585 3.955771 TTCGTGCACTAAAAAGTGTCC 57.044 42.857 16.19 0.00 41.53 4.02
585 586 6.423862 TGTTATTCGTGCACTAAAAAGTGTC 58.576 36.000 16.19 1.31 41.53 3.67
586 587 6.366315 TGTTATTCGTGCACTAAAAAGTGT 57.634 33.333 16.19 0.00 41.53 3.55
587 588 7.851822 ATTGTTATTCGTGCACTAAAAAGTG 57.148 32.000 16.19 1.14 42.32 3.16
588 589 8.865590 AAATTGTTATTCGTGCACTAAAAAGT 57.134 26.923 16.19 4.94 0.00 2.66
627 628 9.228949 TGTTAATTGCATAATTTCCAAATGCTT 57.771 25.926 10.60 2.17 44.96 3.91
628 629 8.789825 TGTTAATTGCATAATTTCCAAATGCT 57.210 26.923 10.60 0.00 44.96 3.79
629 630 9.837525 TTTGTTAATTGCATAATTTCCAAATGC 57.162 25.926 3.62 3.62 44.94 3.56
700 701 9.920946 ACCACACTAATATGGACATCTAAATTT 57.079 29.630 0.00 0.00 39.46 1.82
712 713 6.942532 AGCACATTTACCACACTAATATGG 57.057 37.500 0.00 0.00 42.13 2.74
823 827 2.291209 ATGCTCATTGTCACACCCAA 57.709 45.000 0.00 0.00 0.00 4.12
872 878 0.443869 CTCCTGCGTGTCGAAAATGG 59.556 55.000 0.00 0.00 0.00 3.16
896 902 5.641209 CGGATATTCAATTTGGCTCTAGGAG 59.359 44.000 0.00 0.00 0.00 3.69
897 903 5.513094 CCGGATATTCAATTTGGCTCTAGGA 60.513 44.000 0.00 0.00 0.00 2.94
898 904 4.697352 CCGGATATTCAATTTGGCTCTAGG 59.303 45.833 0.00 0.00 0.00 3.02
899 905 4.154918 GCCGGATATTCAATTTGGCTCTAG 59.845 45.833 5.05 0.00 38.00 2.43
900 906 4.072131 GCCGGATATTCAATTTGGCTCTA 58.928 43.478 5.05 0.00 38.00 2.43
901 907 2.887152 GCCGGATATTCAATTTGGCTCT 59.113 45.455 5.05 0.00 38.00 4.09
924 930 9.730420 AATACAGTACAAGTTTTTCAACATGAC 57.270 29.630 0.00 0.00 35.54 3.06
943 949 1.985159 TGGCCTGGTCAGAAATACAGT 59.015 47.619 3.32 0.00 0.00 3.55
944 950 2.787473 TGGCCTGGTCAGAAATACAG 57.213 50.000 3.32 0.00 0.00 2.74
945 951 3.737559 ATTGGCCTGGTCAGAAATACA 57.262 42.857 3.32 0.00 0.00 2.29
946 952 3.565902 GCTATTGGCCTGGTCAGAAATAC 59.434 47.826 3.32 0.00 34.27 1.89
947 953 3.820557 GCTATTGGCCTGGTCAGAAATA 58.179 45.455 3.32 0.00 34.27 1.40
948 954 2.659428 GCTATTGGCCTGGTCAGAAAT 58.341 47.619 3.32 0.00 34.27 2.17
973 979 3.119495 CCCGAACTGCTAAGGAATTTTGG 60.119 47.826 0.00 0.00 0.00 3.28
986 992 1.522580 GGCATCTCTCCCGAACTGC 60.523 63.158 0.00 0.00 0.00 4.40
1023 1032 1.001048 TGGTACGACGAGAACTTGGTG 60.001 52.381 0.00 0.00 0.00 4.17
1188 1197 4.424711 TCCATGGCCGGGAAGTGC 62.425 66.667 13.26 0.00 0.00 4.40
1191 1200 2.190578 GACTCCATGGCCGGGAAG 59.809 66.667 16.04 12.37 33.11 3.46
1605 1614 2.046604 TCGAACGCCTCCTCGAGA 60.047 61.111 15.71 0.00 39.07 4.04
1642 1659 1.339055 TGGCCTCACATTGTACTGCTC 60.339 52.381 3.32 0.00 0.00 4.26
1683 1700 1.280133 TGACAGAGCCCCTTCATCAAG 59.720 52.381 0.00 0.00 0.00 3.02
1728 1745 2.768527 CACCATCTCCTCTTTGAGCCTA 59.231 50.000 0.00 0.00 32.22 3.93
1752 1769 1.690283 CCAGCACAAGATCTGCGTCG 61.690 60.000 0.00 0.00 39.79 5.12
1753 1770 0.390340 TCCAGCACAAGATCTGCGTC 60.390 55.000 0.00 0.00 39.79 5.19
1754 1771 0.251354 ATCCAGCACAAGATCTGCGT 59.749 50.000 0.00 0.00 39.79 5.24
1766 1783 0.478072 ATAAATGGCGGGATCCAGCA 59.522 50.000 33.41 21.51 39.89 4.41
1860 1880 4.155709 CTCTATCAGCCTGAATGTCCCTA 58.844 47.826 0.00 0.00 0.00 3.53
1896 1916 2.606725 CTCACAGAAACCTGCGATCATC 59.393 50.000 0.00 0.00 35.09 2.92
1941 1961 1.132640 GTCATCAAGCACCGCGAAC 59.867 57.895 8.23 0.00 0.00 3.95
1988 2008 5.406175 GCAACCAACGTGTTATAACTCACTA 59.594 40.000 16.33 0.00 33.07 2.74
2039 2059 3.499338 TCAACCAACTCATTTGCATCCT 58.501 40.909 0.00 0.00 33.34 3.24
2121 2141 0.394762 ATGCCCCAGCTACACACATG 60.395 55.000 0.00 0.00 40.80 3.21
2130 2150 1.481871 CTTCATGAAATGCCCCAGCT 58.518 50.000 9.88 0.00 46.21 4.24
2139 2159 6.395629 CAAAACCTGATCTGCTTCATGAAAT 58.604 36.000 9.88 0.00 0.00 2.17
2175 2195 2.403259 CTTGGCGCAAAACCCTTAAAG 58.597 47.619 10.83 0.00 0.00 1.85
2207 2227 2.472695 TCCCTGAATGAACTTGGTCG 57.527 50.000 0.00 0.00 0.00 4.79
2280 2300 4.727507 TGACTCTAGAGCATTCACCTTC 57.272 45.455 19.97 6.94 0.00 3.46
2289 2309 2.093816 CCATGCACTTGACTCTAGAGCA 60.094 50.000 19.97 15.08 42.04 4.26
2293 2313 2.762887 TCTCCCATGCACTTGACTCTAG 59.237 50.000 0.00 0.00 0.00 2.43
2295 2315 1.649321 TCTCCCATGCACTTGACTCT 58.351 50.000 0.00 0.00 0.00 3.24
2303 2323 0.807496 GACAGCTTTCTCCCATGCAC 59.193 55.000 0.00 0.00 0.00 4.57
2340 2360 1.483827 TCTGTCATAAGCTCTGCAGGG 59.516 52.381 15.13 12.70 0.00 4.45
2357 2377 9.829507 ATCTTAAACTATCCAGATGTTTCTCTG 57.170 33.333 9.79 0.00 41.93 3.35
2375 2395 5.998363 AGACCCAGTCAAGTGAATCTTAAAC 59.002 40.000 0.00 0.00 34.60 2.01
2396 2416 6.127026 ACCAGGTTAATCAAGTATCCAGAGAC 60.127 42.308 0.00 0.00 0.00 3.36
2417 2437 8.542132 CAATCATACTTTCAAAACAACAACCAG 58.458 33.333 0.00 0.00 0.00 4.00
2829 2866 6.547880 TGCTAATTCTTGTAACCTGTGGAAAA 59.452 34.615 0.00 0.00 0.00 2.29
2870 3037 7.010160 TGTCAAGTCTTTTCCCCAATATCTTT 58.990 34.615 0.00 0.00 0.00 2.52
2890 3057 2.418368 AGGACTGTTGCACTTGTCAA 57.582 45.000 12.29 0.00 0.00 3.18
2929 3097 6.038825 TGAATACTTCAGTTTTGAAAGGCGAA 59.961 34.615 0.00 0.00 42.48 4.70
2930 3098 5.529430 TGAATACTTCAGTTTTGAAAGGCGA 59.471 36.000 0.00 0.00 42.48 5.54
2931 3099 5.757886 TGAATACTTCAGTTTTGAAAGGCG 58.242 37.500 0.00 0.00 42.48 5.52
2944 3112 6.998074 ACATCTGTTTCCAACTGAATACTTCA 59.002 34.615 0.98 0.00 41.66 3.02
2945 3113 7.440523 ACATCTGTTTCCAACTGAATACTTC 57.559 36.000 0.98 0.00 41.66 3.01
2946 3114 8.157476 ACTACATCTGTTTCCAACTGAATACTT 58.843 33.333 0.98 0.00 41.66 2.24
2947 3115 7.604164 CACTACATCTGTTTCCAACTGAATACT 59.396 37.037 0.98 0.00 41.66 2.12
2948 3116 7.602644 TCACTACATCTGTTTCCAACTGAATAC 59.397 37.037 0.98 0.00 41.66 1.89
2964 3152 8.350722 CGTGGTAAACATATACTCACTACATCT 58.649 37.037 0.00 0.00 30.93 2.90
3044 3232 2.759973 CAGTCCAGGCTCCGGCTA 60.760 66.667 0.00 0.00 36.44 3.93
3074 3262 5.659079 ACACCAGGGTTTTCAAAGATAAACA 59.341 36.000 0.00 0.00 36.27 2.83
3093 3281 3.507162 ACAACCTTCATGATGACACCA 57.493 42.857 10.07 0.00 0.00 4.17
3152 3340 3.885901 AGAAGCTTTGAGGTTTTCTGTCC 59.114 43.478 0.00 0.00 35.86 4.02
3243 3431 7.568349 ACTTCTTCCTAGATGTATGCAATCAA 58.432 34.615 0.00 0.00 37.11 2.57
3251 3439 7.430760 AGCAGAAACTTCTTCCTAGATGTAT 57.569 36.000 0.00 0.00 37.69 2.29


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

AutoCloner maintained by Alex Coulton.