Multiple sequence alignment - TraesCS1D01G210900

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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 TraesCS1D01G210900 chr1D 100.000 2804 0 0 1 2804 296980601 296977798 0.000000e+00 5179
1 TraesCS1D01G210900 chr1D 83.451 284 25 12 850 1131 46477006 46477269 7.760000e-61 244
2 TraesCS1D01G210900 chr1B 91.574 2801 127 45 1 2767 398146084 398143359 0.000000e+00 3764
3 TraesCS1D01G210900 chr1B 93.182 484 32 1 1103 1586 683420957 683420475 0.000000e+00 710
4 TraesCS1D01G210900 chr1A 94.839 1395 54 9 996 2382 369497645 369496261 0.000000e+00 2161
5 TraesCS1D01G210900 chr1A 90.000 520 33 12 13 525 369503349 369502842 0.000000e+00 654
6 TraesCS1D01G210900 chr1A 92.771 332 21 3 2444 2773 369496250 369495920 7.030000e-131 477
7 TraesCS1D01G210900 chr2B 90.050 603 46 9 992 1586 44986554 44987150 0.000000e+00 769
8 TraesCS1D01G210900 chr4B 89.002 591 62 3 996 1586 365085753 365086340 0.000000e+00 728
9 TraesCS1D01G210900 chr4B 86.913 596 73 4 992 1586 358486463 358485872 0.000000e+00 664
10 TraesCS1D01G210900 chr5B 92.126 508 39 1 1079 1586 679584408 679584914 0.000000e+00 715
11 TraesCS1D01G210900 chr2D 91.667 456 34 3 1132 1586 36503273 36503725 1.830000e-176 628
12 TraesCS1D01G210900 chr7D 91.009 456 37 3 1132 1586 277456199 277456651 1.850000e-171 612
13 TraesCS1D01G210900 chr5A 84.043 282 27 7 850 1131 299616892 299616629 3.580000e-64 255
14 TraesCS1D01G210900 chr4D 83.039 283 28 12 850 1131 462822409 462822146 3.610000e-59 239
15 TraesCS1D01G210900 chr3D 83.099 284 26 12 850 1131 12137748 12137485 3.610000e-59 239


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 TraesCS1D01G210900 chr1D 296977798 296980601 2803 True 5179 5179 100.000 1 2804 1 chr1D.!!$R1 2803
1 TraesCS1D01G210900 chr1B 398143359 398146084 2725 True 3764 3764 91.574 1 2767 1 chr1B.!!$R1 2766
2 TraesCS1D01G210900 chr1A 369495920 369497645 1725 True 1319 2161 93.805 996 2773 2 chr1A.!!$R2 1777
3 TraesCS1D01G210900 chr1A 369502842 369503349 507 True 654 654 90.000 13 525 1 chr1A.!!$R1 512
4 TraesCS1D01G210900 chr2B 44986554 44987150 596 False 769 769 90.050 992 1586 1 chr2B.!!$F1 594
5 TraesCS1D01G210900 chr4B 365085753 365086340 587 False 728 728 89.002 996 1586 1 chr4B.!!$F1 590
6 TraesCS1D01G210900 chr4B 358485872 358486463 591 True 664 664 86.913 992 1586 1 chr4B.!!$R1 594
7 TraesCS1D01G210900 chr5B 679584408 679584914 506 False 715 715 92.126 1079 1586 1 chr5B.!!$F1 507

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
520 544 0.103937 AAGCGCCATCTGTAGAGAGC 59.896 55.0 2.29 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2128 0.768622 AGATTCCCACAACCCAACGA 59.231 50.0 0.0 0.0 0.0 3.85 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
104 114 0.815734 CGATACACCAGAACCCGTCT 59.184 55.000 0.00 0.00 36.88 4.18
111 121 1.371183 CAGAACCCGTCTTGCTCCA 59.629 57.895 0.00 0.00 32.70 3.86
180 196 2.741092 GCCGGAAGTCAGTCACCA 59.259 61.111 5.05 0.00 0.00 4.17
206 222 2.547640 TAGCTGAGACGGGCGTACCT 62.548 60.000 0.00 0.00 36.97 3.08
214 230 1.216977 CGGGCGTACCTGAATCACA 59.783 57.895 0.00 0.00 46.41 3.58
226 243 6.156748 ACCTGAATCACATGTAGCGTATTA 57.843 37.500 0.00 0.00 0.00 0.98
385 402 5.829924 ACATGATGATGGTCCTTTTGGATAC 59.170 40.000 0.00 0.00 40.91 2.24
430 447 1.664016 GCGTCAGTGCAACATTTGAGG 60.664 52.381 0.00 0.00 41.43 3.86
446 463 3.593442 TGAGGAAGGAAAAAGGAAGCA 57.407 42.857 0.00 0.00 0.00 3.91
451 468 4.082125 GGAAGGAAAAAGGAAGCATCAGA 58.918 43.478 0.00 0.00 0.00 3.27
452 469 4.524328 GGAAGGAAAAAGGAAGCATCAGAA 59.476 41.667 0.00 0.00 0.00 3.02
454 471 5.911378 AGGAAAAAGGAAGCATCAGAATC 57.089 39.130 0.00 0.00 0.00 2.52
456 473 4.439289 GGAAAAAGGAAGCATCAGAATCCG 60.439 45.833 0.00 0.00 37.05 4.18
457 474 1.673168 AAGGAAGCATCAGAATCCGC 58.327 50.000 0.00 0.00 37.05 5.54
458 475 0.835941 AGGAAGCATCAGAATCCGCT 59.164 50.000 0.00 0.00 37.05 5.52
459 476 1.211457 AGGAAGCATCAGAATCCGCTT 59.789 47.619 0.00 0.00 46.90 4.68
460 477 2.435805 AGGAAGCATCAGAATCCGCTTA 59.564 45.455 0.00 0.00 44.40 3.09
461 478 3.072184 AGGAAGCATCAGAATCCGCTTAT 59.928 43.478 0.00 0.00 44.40 1.73
462 479 3.434984 GGAAGCATCAGAATCCGCTTATC 59.565 47.826 0.00 0.00 44.40 1.75
463 480 3.051081 AGCATCAGAATCCGCTTATCC 57.949 47.619 0.00 0.00 0.00 2.59
464 481 2.369860 AGCATCAGAATCCGCTTATCCA 59.630 45.455 0.00 0.00 0.00 3.41
465 482 2.740981 GCATCAGAATCCGCTTATCCAG 59.259 50.000 0.00 0.00 0.00 3.86
466 483 2.533266 TCAGAATCCGCTTATCCAGC 57.467 50.000 0.00 0.00 46.31 4.85
479 496 0.106819 ATCCAGCATCCCAGCTCAAC 60.107 55.000 0.00 0.00 44.54 3.18
499 523 3.000727 ACCAGCCTAATTTCGTTCGAAG 58.999 45.455 0.00 0.00 0.00 3.79
518 542 0.179100 GCAAGCGCCATCTGTAGAGA 60.179 55.000 2.29 0.00 0.00 3.10
519 543 1.850377 CAAGCGCCATCTGTAGAGAG 58.150 55.000 2.29 0.00 0.00 3.20
520 544 0.103937 AAGCGCCATCTGTAGAGAGC 59.896 55.000 2.29 0.00 0.00 4.09
523 547 1.543802 GCGCCATCTGTAGAGAGCTAT 59.456 52.381 0.00 0.00 0.00 2.97
524 548 2.750166 GCGCCATCTGTAGAGAGCTATA 59.250 50.000 0.00 0.00 0.00 1.31
525 549 3.380004 GCGCCATCTGTAGAGAGCTATAT 59.620 47.826 0.00 0.00 0.00 0.86
528 552 6.428465 GCGCCATCTGTAGAGAGCTATATATA 59.572 42.308 0.00 0.00 0.00 0.86
530 554 8.664798 CGCCATCTGTAGAGAGCTATATATATC 58.335 40.741 0.00 0.00 0.00 1.63
531 555 9.513906 GCCATCTGTAGAGAGCTATATATATCA 57.486 37.037 0.00 0.00 0.00 2.15
557 581 5.023533 TCTCCTTTTGGGAATCATCTACG 57.976 43.478 0.00 0.00 44.58 3.51
558 582 4.469945 TCTCCTTTTGGGAATCATCTACGT 59.530 41.667 0.00 0.00 44.58 3.57
559 583 5.659525 TCTCCTTTTGGGAATCATCTACGTA 59.340 40.000 0.00 0.00 44.58 3.57
560 584 5.667466 TCCTTTTGGGAATCATCTACGTAC 58.333 41.667 0.00 0.00 41.91 3.67
570 594 7.222999 GGGAATCATCTACGTACTCTTCTTTTG 59.777 40.741 0.00 0.00 0.00 2.44
575 599 7.328737 TCATCTACGTACTCTTCTTTTGCTTTC 59.671 37.037 0.00 0.00 0.00 2.62
576 600 5.924825 TCTACGTACTCTTCTTTTGCTTTCC 59.075 40.000 0.00 0.00 0.00 3.13
577 601 3.493503 ACGTACTCTTCTTTTGCTTTCCG 59.506 43.478 0.00 0.00 0.00 4.30
581 605 5.363979 ACTCTTCTTTTGCTTTCCGAATC 57.636 39.130 0.00 0.00 0.00 2.52
596 620 5.321959 TCCGAATCATCTATCATCTGCTC 57.678 43.478 0.00 0.00 0.00 4.26
600 624 5.336610 CGAATCATCTATCATCTGCTCCAGT 60.337 44.000 0.00 0.00 32.61 4.00
629 653 4.254492 GGAGTGCCTACTTGGTTCTAAAG 58.746 47.826 0.00 0.00 37.25 1.85
630 654 4.262938 GGAGTGCCTACTTGGTTCTAAAGT 60.263 45.833 0.00 0.00 40.82 2.66
631 655 4.895961 AGTGCCTACTTGGTTCTAAAGTC 58.104 43.478 0.00 0.00 38.73 3.01
632 656 4.593634 AGTGCCTACTTGGTTCTAAAGTCT 59.406 41.667 0.00 0.00 38.73 3.24
633 657 5.778750 AGTGCCTACTTGGTTCTAAAGTCTA 59.221 40.000 0.00 0.00 38.73 2.59
634 658 6.269307 AGTGCCTACTTGGTTCTAAAGTCTAA 59.731 38.462 0.00 0.00 38.73 2.10
635 659 6.932960 GTGCCTACTTGGTTCTAAAGTCTAAA 59.067 38.462 0.00 0.00 38.73 1.85
654 679 4.830826 AAACCTCGAATCACCTTGTTTC 57.169 40.909 0.00 0.00 0.00 2.78
660 685 4.373527 TCGAATCACCTTGTTTCGAGAAA 58.626 39.130 14.85 0.00 46.88 2.52
711 736 1.284982 CTCCGTGCAAGTCCGTGAAG 61.285 60.000 0.00 0.00 0.00 3.02
765 790 2.125350 CTGTTCCTCGCAGGCTCC 60.125 66.667 0.00 0.00 34.61 4.70
785 810 2.352814 CCGAGGCCAGTAAGATAATCCG 60.353 54.545 5.01 0.00 0.00 4.18
786 811 2.557056 CGAGGCCAGTAAGATAATCCGA 59.443 50.000 5.01 0.00 0.00 4.55
789 814 3.067833 GGCCAGTAAGATAATCCGAAGC 58.932 50.000 0.00 0.00 0.00 3.86
790 815 2.731976 GCCAGTAAGATAATCCGAAGCG 59.268 50.000 0.00 0.00 0.00 4.68
866 891 2.125512 CACCGCTCGCCTTAAGCT 60.126 61.111 0.00 0.00 40.39 3.74
910 935 1.271102 GAAACCGCTCACTCACTCTCT 59.729 52.381 0.00 0.00 0.00 3.10
914 939 1.138671 GCTCACTCACTCTCTCGCC 59.861 63.158 0.00 0.00 0.00 5.54
952 977 4.130281 GTACCGCACGCTCGCAAC 62.130 66.667 0.00 0.00 0.00 4.17
956 981 3.838795 CGCACGCTCGCAACCTAC 61.839 66.667 0.00 0.00 0.00 3.18
957 982 3.488090 GCACGCTCGCAACCTACC 61.488 66.667 0.00 0.00 0.00 3.18
958 983 3.179265 CACGCTCGCAACCTACCG 61.179 66.667 0.00 0.00 0.00 4.02
960 985 2.879462 CGCTCGCAACCTACCGAC 60.879 66.667 0.00 0.00 0.00 4.79
961 986 2.508663 GCTCGCAACCTACCGACC 60.509 66.667 0.00 0.00 0.00 4.79
962 987 2.202570 CTCGCAACCTACCGACCG 60.203 66.667 0.00 0.00 0.00 4.79
963 988 3.695022 CTCGCAACCTACCGACCGG 62.695 68.421 6.94 6.94 42.03 5.28
966 991 4.807039 CAACCTACCGACCGGCCG 62.807 72.222 21.04 21.04 39.32 6.13
1288 1314 3.961414 GGAAGCCCAACCCGTCCA 61.961 66.667 0.00 0.00 32.13 4.02
1677 1709 4.659172 TTCTGGGGCGCCAACCTG 62.659 66.667 30.85 23.64 0.00 4.00
1818 1850 0.454620 CCTAGATGATACGCCGTCGC 60.455 60.000 0.00 0.00 39.84 5.19
1826 1858 3.902162 TACGCCGTCGCAGTGTTCC 62.902 63.158 0.00 0.00 39.84 3.62
1858 1891 2.608825 TACGCCGCGTTGCATGTTT 61.609 52.632 25.47 0.00 41.54 2.83
1859 1892 2.119147 TACGCCGCGTTGCATGTTTT 62.119 50.000 25.47 0.00 41.54 2.43
1860 1893 1.441182 CGCCGCGTTGCATGTTTTA 60.441 52.632 4.92 0.00 0.00 1.52
1929 1966 7.552687 TGGCCATGTAAAATTTCTCAGTAGTAG 59.447 37.037 0.00 0.00 0.00 2.57
1930 1967 7.553044 GGCCATGTAAAATTTCTCAGTAGTAGT 59.447 37.037 0.00 0.00 0.00 2.73
1956 1993 0.036164 AGCGAATGCAACTGGTACCA 59.964 50.000 15.39 15.39 46.23 3.25
2091 2128 4.712337 AGTAGAGTTCAGTTCCGAATCCAT 59.288 41.667 0.00 0.00 0.00 3.41
2102 2139 1.448985 CGAATCCATCGTTGGGTTGT 58.551 50.000 15.72 0.00 46.73 3.32
2199 2244 2.267188 TTACAACGTCGGAATCGGAG 57.733 50.000 0.00 0.00 36.95 4.63
2202 2247 1.132199 CAACGTCGGAATCGGAGTCG 61.132 60.000 0.00 0.00 36.95 4.18
2231 2276 2.127758 CGTCCGAACTTGTTGCGC 60.128 61.111 0.00 0.00 0.00 6.09
2232 2277 2.594962 CGTCCGAACTTGTTGCGCT 61.595 57.895 9.73 0.00 0.00 5.92
2233 2278 1.082756 GTCCGAACTTGTTGCGCTG 60.083 57.895 9.73 0.00 0.00 5.18
2234 2279 1.522806 TCCGAACTTGTTGCGCTGT 60.523 52.632 9.73 0.00 0.00 4.40
2235 2280 1.092921 TCCGAACTTGTTGCGCTGTT 61.093 50.000 9.73 6.00 0.00 3.16
2236 2281 0.929824 CCGAACTTGTTGCGCTGTTG 60.930 55.000 9.73 0.00 0.00 3.33
2237 2282 1.531522 CGAACTTGTTGCGCTGTTGC 61.532 55.000 9.73 0.00 0.00 4.17
2238 2283 0.248621 GAACTTGTTGCGCTGTTGCT 60.249 50.000 9.73 0.00 36.97 3.91
2239 2284 0.526096 AACTTGTTGCGCTGTTGCTG 60.526 50.000 9.73 0.00 36.97 4.41
2240 2285 2.278726 TTGTTGCGCTGTTGCTGC 60.279 55.556 9.73 0.00 38.50 5.25
2241 2286 2.672908 CTTGTTGCGCTGTTGCTGCT 62.673 55.000 9.73 0.00 38.69 4.24
2242 2287 2.728383 GTTGCGCTGTTGCTGCTG 60.728 61.111 9.73 0.00 38.69 4.41
2243 2288 4.634133 TTGCGCTGTTGCTGCTGC 62.634 61.111 9.73 8.89 38.69 5.25
2362 2427 1.079819 CTTGGTCGCCGTCATCACT 60.080 57.895 0.00 0.00 0.00 3.41
2389 2454 0.319555 TCTTCCACTTTCCGCTCACG 60.320 55.000 0.00 0.00 39.67 4.35
2431 2496 1.424493 CCTCGTCGAATCTTGGCAGC 61.424 60.000 0.00 0.00 0.00 5.25
2432 2497 1.424493 CTCGTCGAATCTTGGCAGCC 61.424 60.000 3.66 3.66 0.00 4.85
2433 2498 1.741401 CGTCGAATCTTGGCAGCCA 60.741 57.895 11.22 11.22 0.00 4.75
2434 2499 1.091771 CGTCGAATCTTGGCAGCCAT 61.092 55.000 17.09 0.00 31.53 4.40
2435 2500 0.379669 GTCGAATCTTGGCAGCCATG 59.620 55.000 17.09 18.44 31.53 3.66
2436 2501 0.749091 TCGAATCTTGGCAGCCATGG 60.749 55.000 23.74 16.03 31.53 3.66
2640 2706 2.745492 GTGCTGCAGCTGGACCTC 60.745 66.667 36.61 15.40 42.66 3.85
2659 2725 2.892425 GCTCCATGGCTTCCGTCG 60.892 66.667 6.96 0.00 0.00 5.12
2722 2789 6.758886 CCTCAACATCCTCATGTAAGAACTAC 59.241 42.308 0.00 0.00 42.89 2.73
2723 2790 7.364232 CCTCAACATCCTCATGTAAGAACTACT 60.364 40.741 0.00 0.00 42.89 2.57
2724 2791 8.589701 TCAACATCCTCATGTAAGAACTACTA 57.410 34.615 0.00 0.00 42.89 1.82
2726 2793 9.307121 CAACATCCTCATGTAAGAACTACTAAG 57.693 37.037 0.00 0.00 42.89 2.18
2727 2794 8.824756 ACATCCTCATGTAAGAACTACTAAGA 57.175 34.615 0.00 0.00 41.81 2.10
2738 2805 9.141400 GTAAGAACTACTAAGAACATCCACAAG 57.859 37.037 0.00 0.00 0.00 3.16
2740 2807 7.607250 AGAACTACTAAGAACATCCACAAGAG 58.393 38.462 0.00 0.00 0.00 2.85
2767 2835 3.550437 AGCGACCTCTCTATTTGCATT 57.450 42.857 0.00 0.00 0.00 3.56
2773 2841 6.037172 GCGACCTCTCTATTTGCATTAAGAAA 59.963 38.462 0.00 0.00 0.00 2.52
2774 2842 7.254932 GCGACCTCTCTATTTGCATTAAGAAAT 60.255 37.037 0.00 0.00 0.00 2.17
2775 2843 8.066595 CGACCTCTCTATTTGCATTAAGAAATG 58.933 37.037 0.00 0.00 44.53 2.32
2776 2844 8.230472 ACCTCTCTATTTGCATTAAGAAATGG 57.770 34.615 0.00 0.00 42.39 3.16
2777 2845 8.055181 ACCTCTCTATTTGCATTAAGAAATGGA 58.945 33.333 0.00 0.00 42.39 3.41
2778 2846 8.348507 CCTCTCTATTTGCATTAAGAAATGGAC 58.651 37.037 0.00 0.00 42.38 4.02
2779 2847 8.806429 TCTCTATTTGCATTAAGAAATGGACA 57.194 30.769 0.00 0.00 42.38 4.02
2780 2848 8.896744 TCTCTATTTGCATTAAGAAATGGACAG 58.103 33.333 0.00 0.00 42.38 3.51
2781 2849 8.806429 TCTATTTGCATTAAGAAATGGACAGA 57.194 30.769 0.00 0.00 42.38 3.41
2782 2850 9.241919 TCTATTTGCATTAAGAAATGGACAGAA 57.758 29.630 0.00 0.00 42.38 3.02
2783 2851 9.859427 CTATTTGCATTAAGAAATGGACAGAAA 57.141 29.630 0.00 0.00 42.38 2.52
2785 2853 8.761575 TTTGCATTAAGAAATGGACAGAAATC 57.238 30.769 0.00 0.00 42.38 2.17
2786 2854 7.707624 TGCATTAAGAAATGGACAGAAATCT 57.292 32.000 0.72 0.00 42.39 2.40
2787 2855 8.125978 TGCATTAAGAAATGGACAGAAATCTT 57.874 30.769 0.72 0.00 42.39 2.40
2788 2856 8.030692 TGCATTAAGAAATGGACAGAAATCTTG 58.969 33.333 0.00 0.00 42.39 3.02
2789 2857 7.009907 GCATTAAGAAATGGACAGAAATCTTGC 59.990 37.037 0.00 0.00 42.39 4.01
2790 2858 5.397142 AAGAAATGGACAGAAATCTTGCC 57.603 39.130 0.00 0.00 0.00 4.52
2791 2859 3.766051 AGAAATGGACAGAAATCTTGCCC 59.234 43.478 0.00 0.00 0.00 5.36
2792 2860 1.755179 ATGGACAGAAATCTTGCCCG 58.245 50.000 0.00 0.00 0.00 6.13
2793 2861 0.400213 TGGACAGAAATCTTGCCCGT 59.600 50.000 0.00 0.00 0.00 5.28
2794 2862 0.804989 GGACAGAAATCTTGCCCGTG 59.195 55.000 0.00 0.00 0.00 4.94
2795 2863 0.804989 GACAGAAATCTTGCCCGTGG 59.195 55.000 0.00 0.00 0.00 4.94
2796 2864 0.110486 ACAGAAATCTTGCCCGTGGT 59.890 50.000 0.00 0.00 0.00 4.16
2797 2865 1.247567 CAGAAATCTTGCCCGTGGTT 58.752 50.000 0.00 0.00 0.00 3.67
2798 2866 1.068333 CAGAAATCTTGCCCGTGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
2799 2867 0.388520 GAAATCTTGCCCGTGGTTGC 60.389 55.000 0.00 0.00 0.00 4.17
2800 2868 1.112315 AAATCTTGCCCGTGGTTGCA 61.112 50.000 0.00 0.00 35.27 4.08
2801 2869 1.805428 AATCTTGCCCGTGGTTGCAC 61.805 55.000 0.00 0.00 37.18 4.57
2802 2870 2.974692 ATCTTGCCCGTGGTTGCACA 62.975 55.000 0.00 0.00 37.18 4.57
2803 2871 2.520500 TTGCCCGTGGTTGCACAT 60.521 55.556 0.00 0.00 37.18 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 23 3.259374 CAGTTTCTTCTGCTGAGGACCTA 59.741 47.826 4.86 0.00 32.39 3.08
80 90 0.179081 GGTTCTGGTGTATCGCCCTC 60.179 60.000 0.00 0.00 32.22 4.30
111 121 1.068121 AGCAAAGCCTTCCAGTACCT 58.932 50.000 0.00 0.00 0.00 3.08
180 196 1.178276 CCCGTCTCAGCTACAAGACT 58.822 55.000 16.56 0.00 39.80 3.24
206 222 8.432110 ACAAATAATACGCTACATGTGATTCA 57.568 30.769 9.11 0.00 0.00 2.57
214 230 7.528481 TCGACAAACAAATAATACGCTACAT 57.472 32.000 0.00 0.00 0.00 2.29
226 243 2.297701 AGGTGTGCTCGACAAACAAAT 58.702 42.857 9.53 0.00 38.37 2.32
385 402 4.091509 CGTTCTCCGTACCATTTTCTTCTG 59.908 45.833 0.00 0.00 0.00 3.02
430 447 5.712152 TTCTGATGCTTCCTTTTTCCTTC 57.288 39.130 0.00 0.00 0.00 3.46
446 463 3.051081 GCTGGATAAGCGGATTCTGAT 57.949 47.619 0.00 0.00 43.45 2.90
457 474 1.419012 TGAGCTGGGATGCTGGATAAG 59.581 52.381 0.00 0.00 44.17 1.73
458 475 1.510492 TGAGCTGGGATGCTGGATAA 58.490 50.000 0.00 0.00 44.17 1.75
459 476 1.141657 GTTGAGCTGGGATGCTGGATA 59.858 52.381 0.00 0.00 44.17 2.59
460 477 0.106819 GTTGAGCTGGGATGCTGGAT 60.107 55.000 0.00 0.00 44.17 3.41
461 478 1.300963 GTTGAGCTGGGATGCTGGA 59.699 57.895 0.00 0.00 44.17 3.86
462 479 1.751927 GGTTGAGCTGGGATGCTGG 60.752 63.158 0.00 0.00 44.17 4.85
463 480 1.001764 TGGTTGAGCTGGGATGCTG 60.002 57.895 0.00 0.00 44.17 4.41
464 481 2.833604 GCTGGTTGAGCTGGGATGCT 62.834 60.000 0.00 0.00 45.21 3.79
465 482 2.413142 GCTGGTTGAGCTGGGATGC 61.413 63.158 0.00 0.00 45.21 3.91
466 483 3.915575 GCTGGTTGAGCTGGGATG 58.084 61.111 0.00 0.00 45.21 3.51
479 496 2.223044 GCTTCGAACGAAATTAGGCTGG 60.223 50.000 10.68 0.00 33.34 4.85
499 523 0.179100 TCTCTACAGATGGCGCTTGC 60.179 55.000 7.64 0.00 38.11 4.01
519 543 9.995003 CCAAAAGGAGAGGATGATATATATAGC 57.005 37.037 0.87 0.87 0.00 2.97
537 561 4.837093 ACGTAGATGATTCCCAAAAGGA 57.163 40.909 0.00 0.00 45.68 3.36
538 562 5.671493 AGTACGTAGATGATTCCCAAAAGG 58.329 41.667 0.00 0.00 0.00 3.11
539 563 6.574350 AGAGTACGTAGATGATTCCCAAAAG 58.426 40.000 0.00 0.00 0.00 2.27
557 581 5.668558 TTCGGAAAGCAAAAGAAGAGTAC 57.331 39.130 0.00 0.00 0.00 2.73
558 582 5.995282 TGATTCGGAAAGCAAAAGAAGAGTA 59.005 36.000 0.00 0.00 0.00 2.59
559 583 4.821805 TGATTCGGAAAGCAAAAGAAGAGT 59.178 37.500 0.00 0.00 0.00 3.24
560 584 5.362556 TGATTCGGAAAGCAAAAGAAGAG 57.637 39.130 0.00 0.00 0.00 2.85
570 594 5.163874 GCAGATGATAGATGATTCGGAAAGC 60.164 44.000 0.00 0.00 0.00 3.51
575 599 4.081807 TGGAGCAGATGATAGATGATTCGG 60.082 45.833 0.00 0.00 0.00 4.30
576 600 5.069501 TGGAGCAGATGATAGATGATTCG 57.930 43.478 0.00 0.00 0.00 3.34
577 601 6.040209 ACTGGAGCAGATGATAGATGATTC 57.960 41.667 0.00 0.00 35.18 2.52
581 605 5.718724 TGTACTGGAGCAGATGATAGATG 57.281 43.478 0.00 0.00 35.18 2.90
596 620 0.687354 AGGCACTCCACTTGTACTGG 59.313 55.000 0.00 0.00 33.74 4.00
600 624 2.301870 CCAAGTAGGCACTCCACTTGTA 59.698 50.000 17.15 0.00 42.88 2.41
629 653 4.566987 ACAAGGTGATTCGAGGTTTAGAC 58.433 43.478 0.00 0.00 0.00 2.59
630 654 4.884668 ACAAGGTGATTCGAGGTTTAGA 57.115 40.909 0.00 0.00 0.00 2.10
631 655 5.928153 GAAACAAGGTGATTCGAGGTTTAG 58.072 41.667 0.00 0.00 0.00 1.85
632 656 5.934935 GAAACAAGGTGATTCGAGGTTTA 57.065 39.130 0.00 0.00 0.00 2.01
633 657 4.830826 GAAACAAGGTGATTCGAGGTTT 57.169 40.909 0.00 0.00 0.00 3.27
765 790 2.557056 TCGGATTATCTTACTGGCCTCG 59.443 50.000 3.32 0.00 0.00 4.63
889 914 0.318762 AGAGTGAGTGAGCGGTTTCC 59.681 55.000 0.00 0.00 0.00 3.13
892 917 0.885196 GAGAGAGTGAGTGAGCGGTT 59.115 55.000 0.00 0.00 0.00 4.44
896 921 1.138671 GGCGAGAGAGTGAGTGAGC 59.861 63.158 0.00 0.00 0.00 4.26
897 922 0.884514 TTGGCGAGAGAGTGAGTGAG 59.115 55.000 0.00 0.00 0.00 3.51
943 968 2.879462 GTCGGTAGGTTGCGAGCG 60.879 66.667 0.00 0.00 37.89 5.03
949 974 4.807039 CGGCCGGTCGGTAGGTTG 62.807 72.222 23.57 0.00 37.65 3.77
983 1008 3.064987 ATCGGCGGTGAACGGAGAG 62.065 63.158 7.21 0.00 44.51 3.20
984 1009 3.066190 ATCGGCGGTGAACGGAGA 61.066 61.111 7.21 0.00 44.51 3.71
985 1010 2.885644 CATCGGCGGTGAACGGAG 60.886 66.667 16.62 0.00 44.51 4.63
989 1014 3.186047 CGGACATCGGCGGTGAAC 61.186 66.667 29.09 18.97 34.75 3.18
1677 1709 2.436824 GGCAGGAGGAAGGCGAAC 60.437 66.667 0.00 0.00 0.00 3.95
1826 1858 2.802667 GCGTACGCAGCCATCACAG 61.803 63.158 33.90 0.00 41.49 3.66
1858 1891 8.685838 AAAGCAACAAACTACTGGAGTAATAA 57.314 30.769 0.00 0.00 37.44 1.40
1859 1892 8.685838 AAAAGCAACAAACTACTGGAGTAATA 57.314 30.769 0.00 0.00 37.44 0.98
1860 1893 7.502561 AGAAAAGCAACAAACTACTGGAGTAAT 59.497 33.333 0.00 0.00 37.44 1.89
1929 1966 1.466167 AGTTGCATTCGCTGACATCAC 59.534 47.619 0.00 0.00 39.64 3.06
1930 1967 1.465777 CAGTTGCATTCGCTGACATCA 59.534 47.619 0.00 0.00 39.64 3.07
2091 2128 0.768622 AGATTCCCACAACCCAACGA 59.231 50.000 0.00 0.00 0.00 3.85
2102 2139 7.675161 TTATGACTATTGACAGAGATTCCCA 57.325 36.000 0.00 0.00 0.00 4.37
2199 2244 1.499049 GGACGGGCTAATGATTCGAC 58.501 55.000 0.00 0.00 0.00 4.20
2202 2247 1.865340 GTTCGGACGGGCTAATGATTC 59.135 52.381 0.00 0.00 0.00 2.52
2243 2288 2.513204 CATCAGTCGGCCAGCAGG 60.513 66.667 2.24 0.00 38.23 4.85
2362 2427 2.038033 CGGAAAGTGGAAGAAGGTACCA 59.962 50.000 15.94 0.00 0.00 3.25
2389 2454 1.748122 CATGCTGACAGCTCACCCC 60.748 63.158 26.94 0.00 42.97 4.95
2399 2464 1.079543 ACGAGGACAGCATGCTGAC 60.080 57.895 45.50 39.08 46.30 3.51
2431 2496 2.401766 GCTCACGAGGTTGCCATGG 61.402 63.158 7.63 7.63 0.00 3.66
2432 2497 1.376424 AGCTCACGAGGTTGCCATG 60.376 57.895 0.00 0.00 35.28 3.66
2433 2498 1.376424 CAGCTCACGAGGTTGCCAT 60.376 57.895 0.00 0.00 36.98 4.40
2434 2499 2.031012 CAGCTCACGAGGTTGCCA 59.969 61.111 0.00 0.00 36.98 4.92
2435 2500 2.029844 GTCAGCTCACGAGGTTGCC 61.030 63.158 0.00 0.00 36.98 4.52
2436 2501 1.300931 TGTCAGCTCACGAGGTTGC 60.301 57.895 0.00 0.00 36.98 4.17
2437 2502 0.946221 GGTGTCAGCTCACGAGGTTG 60.946 60.000 0.00 0.00 39.00 3.77
2438 2503 1.367840 GGTGTCAGCTCACGAGGTT 59.632 57.895 0.00 0.00 39.00 3.50
2439 2504 2.920645 CGGTGTCAGCTCACGAGGT 61.921 63.158 0.00 0.00 39.00 3.85
2469 2534 2.182791 CTCGACGCACCTGCAGAT 59.817 61.111 17.39 0.00 42.21 2.90
2640 2706 1.817099 GACGGAAGCCATGGAGCTG 60.817 63.158 18.40 10.94 44.11 4.24
2659 2725 4.951963 CTCCGCGGCGAATCTCCC 62.952 72.222 25.92 0.00 0.00 4.30
2722 2789 5.426504 AGATGCTCTTGTGGATGTTCTTAG 58.573 41.667 0.00 0.00 0.00 2.18
2723 2790 5.426689 AGATGCTCTTGTGGATGTTCTTA 57.573 39.130 0.00 0.00 0.00 2.10
2724 2791 4.298103 AGATGCTCTTGTGGATGTTCTT 57.702 40.909 0.00 0.00 0.00 2.52
2726 2793 4.034975 GCTTAGATGCTCTTGTGGATGTTC 59.965 45.833 0.00 0.00 0.00 3.18
2727 2794 3.944015 GCTTAGATGCTCTTGTGGATGTT 59.056 43.478 0.00 0.00 0.00 2.71
2738 2805 1.953686 AGAGAGGTCGCTTAGATGCTC 59.046 52.381 0.00 0.00 0.00 4.26
2740 2807 4.513198 AATAGAGAGGTCGCTTAGATGC 57.487 45.455 0.00 0.00 0.00 3.91
2745 2812 4.672587 ATGCAAATAGAGAGGTCGCTTA 57.327 40.909 0.00 0.00 0.00 3.09
2746 2813 3.550437 ATGCAAATAGAGAGGTCGCTT 57.450 42.857 0.00 0.00 0.00 4.68
2748 2815 5.050490 TCTTAATGCAAATAGAGAGGTCGC 58.950 41.667 0.00 0.00 0.00 5.19
2750 2817 8.348507 CCATTTCTTAATGCAAATAGAGAGGTC 58.651 37.037 0.00 0.00 39.87 3.85
2767 2835 5.418840 GGGCAAGATTTCTGTCCATTTCTTA 59.581 40.000 0.00 0.00 0.00 2.10
2773 2841 1.004745 ACGGGCAAGATTTCTGTCCAT 59.995 47.619 0.00 0.00 0.00 3.41
2774 2842 0.400213 ACGGGCAAGATTTCTGTCCA 59.600 50.000 0.00 0.00 0.00 4.02
2775 2843 0.804989 CACGGGCAAGATTTCTGTCC 59.195 55.000 0.00 0.00 0.00 4.02
2776 2844 0.804989 CCACGGGCAAGATTTCTGTC 59.195 55.000 0.00 0.00 0.00 3.51
2777 2845 0.110486 ACCACGGGCAAGATTTCTGT 59.890 50.000 0.00 0.00 0.00 3.41
2778 2846 1.068333 CAACCACGGGCAAGATTTCTG 60.068 52.381 0.00 0.00 0.00 3.02
2779 2847 1.247567 CAACCACGGGCAAGATTTCT 58.752 50.000 0.00 0.00 0.00 2.52
2780 2848 0.388520 GCAACCACGGGCAAGATTTC 60.389 55.000 0.00 0.00 0.00 2.17
2781 2849 1.112315 TGCAACCACGGGCAAGATTT 61.112 50.000 0.00 0.00 37.03 2.17
2782 2850 1.530419 TGCAACCACGGGCAAGATT 60.530 52.632 0.00 0.00 37.03 2.40
2783 2851 2.115052 TGCAACCACGGGCAAGAT 59.885 55.556 0.00 0.00 37.03 2.40
2784 2852 2.904866 GTGCAACCACGGGCAAGA 60.905 61.111 0.00 0.00 42.45 3.02
2785 2853 2.563798 ATGTGCAACCACGGGCAAG 61.564 57.895 0.00 0.00 45.04 4.01
2786 2854 2.520500 ATGTGCAACCACGGGCAA 60.521 55.556 0.00 0.00 45.04 4.52


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

AutoCloner maintained by Alex Coulton.