Multiple sequence alignment - TraesCS4B01G201700

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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 TraesCS4B01G201700 chr4B 100.000 3521 0 0 1 3521 432259275 432255755 0.000000e+00 6503.0
1 TraesCS4B01G201700 chr4B 83.117 77 13 0 1680 1756 455011815 455011739 1.750000e-08 71.3
2 TraesCS4B01G201700 chr4D 91.685 2730 150 27 831 3520 349411736 349409044 0.000000e+00 3712.0
3 TraesCS4B01G201700 chr4D 95.055 546 20 5 1 540 349421070 349420526 0.000000e+00 852.0
4 TraesCS4B01G201700 chr4D 91.946 149 9 3 536 684 349411966 349411821 4.610000e-49 206.0
5 TraesCS4B01G201700 chr4D 85.047 107 7 3 697 803 349411834 349411737 2.240000e-17 100.0
6 TraesCS4B01G201700 chr4D 76.879 173 40 0 1584 1756 369861931 369861759 8.040000e-17 99.0
7 TraesCS4B01G201700 chr4D 75.723 173 42 0 1581 1753 369874646 369874818 1.740000e-13 87.9
8 TraesCS4B01G201700 chr4A 94.374 1653 84 9 1872 3521 115575136 115576782 0.000000e+00 2529.0
9 TraesCS4B01G201700 chr4A 89.442 1847 78 36 3 1821 115573092 115574849 0.000000e+00 2222.0
10 TraesCS4B01G201700 chr4A 75.706 177 35 6 1581 1753 94824109 94824281 8.100000e-12 82.4
11 TraesCS4B01G201700 chr3D 73.175 630 149 16 2908 3521 281893063 281892438 3.560000e-50 209.0
12 TraesCS4B01G201700 chr3D 94.444 36 1 1 801 835 610998891 610998856 2.000000e-03 54.7
13 TraesCS4B01G201700 chr1A 100.000 28 0 0 804 831 585074971 585074998 6.000000e-03 52.8


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 TraesCS4B01G201700 chr4B 432255755 432259275 3520 True 6503.000000 6503 100.000000 1 3521 1 chr4B.!!$R1 3520
1 TraesCS4B01G201700 chr4D 349409044 349411966 2922 True 1339.333333 3712 89.559333 536 3520 3 chr4D.!!$R3 2984
2 TraesCS4B01G201700 chr4D 349420526 349421070 544 True 852.000000 852 95.055000 1 540 1 chr4D.!!$R1 539
3 TraesCS4B01G201700 chr4A 115573092 115576782 3690 False 2375.500000 2529 91.908000 3 3521 2 chr4A.!!$F2 3518
4 TraesCS4B01G201700 chr3D 281892438 281893063 625 True 209.000000 209 73.175000 2908 3521 1 chr3D.!!$R1 613

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
813 823 0.106708 GATCCCGTGGAGCAATGCTA 59.893 55.0 8.12 0.00 39.88 3.49 F
814 824 0.179045 ATCCCGTGGAGCAATGCTAC 60.179 55.0 11.21 11.21 39.88 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2239 1.503800 ACCCGGTATTTACCCTCAGG 58.496 55.000 0.0 0.0 43.51 3.86 R
2797 3110 1.628846 AGCGTGGGGAAGTAAGACATT 59.371 47.619 0.0 0.0 0.00 2.71 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
63 64 1.936547 CTAGAAAAGCTGGGTCATCGC 59.063 52.381 0.00 0.00 0.00 4.58
85 86 1.933853 GCACCTCATGGTCGTGAATAC 59.066 52.381 10.65 0.00 46.60 1.89
248 249 4.593206 TCCTGAGAGAACCTTGTGTTGTAT 59.407 41.667 0.00 0.00 37.29 2.29
357 359 7.455058 TCCTCTGCCTTTGTTGTACTATAAAA 58.545 34.615 0.00 0.00 0.00 1.52
361 363 8.154856 TCTGCCTTTGTTGTACTATAAAAGACT 58.845 33.333 13.29 0.00 31.01 3.24
396 402 9.574458 GTATGTATGTATGTATAGACAAGCTGG 57.426 37.037 0.00 0.00 39.59 4.85
433 439 2.080286 ATGTACACCTTCTGACGTGC 57.920 50.000 0.00 0.00 33.09 5.34
457 467 5.914033 TGGTGGTGTTCTATACTTCTATGC 58.086 41.667 0.00 0.00 0.00 3.14
476 486 3.286353 TGCATTTTCCTGTGAGTGAACA 58.714 40.909 0.00 0.00 0.00 3.18
484 494 8.463930 TTTTCCTGTGAGTGAACATAAGAAAT 57.536 30.769 0.00 0.00 30.32 2.17
505 515 4.771590 TGCCTAAGAGCATTTTGAACAG 57.228 40.909 0.00 0.00 38.00 3.16
529 539 8.960591 CAGATGATGTAAAACTGGTTTCCTAAT 58.039 33.333 0.00 0.00 31.45 1.73
595 605 8.947940 GCATTAAAGCAAAACTTGATACGATAG 58.052 33.333 0.00 0.00 39.09 2.08
616 626 9.694520 CGATAGTTAAAACTCATGTCAAGAATG 57.305 33.333 0.00 0.00 40.37 2.67
622 632 9.958180 TTAAAACTCATGTCAAGAATGGAGATA 57.042 29.630 0.00 0.00 0.00 1.98
688 698 4.703645 GGAAATACTCCAGGAACAAAGC 57.296 45.455 0.00 0.00 44.67 3.51
689 699 3.127030 GGAAATACTCCAGGAACAAAGCG 59.873 47.826 0.00 0.00 44.67 4.68
690 700 3.695830 AATACTCCAGGAACAAAGCGA 57.304 42.857 0.00 0.00 0.00 4.93
691 701 3.695830 ATACTCCAGGAACAAAGCGAA 57.304 42.857 0.00 0.00 0.00 4.70
692 702 2.568623 ACTCCAGGAACAAAGCGAAT 57.431 45.000 0.00 0.00 0.00 3.34
693 703 2.154462 ACTCCAGGAACAAAGCGAATG 58.846 47.619 0.00 0.00 0.00 2.67
694 704 1.470098 CTCCAGGAACAAAGCGAATGG 59.530 52.381 0.00 0.00 0.00 3.16
695 705 1.073125 TCCAGGAACAAAGCGAATGGA 59.927 47.619 0.00 0.00 33.11 3.41
696 706 1.885887 CCAGGAACAAAGCGAATGGAA 59.114 47.619 0.00 0.00 0.00 3.53
697 707 2.295909 CCAGGAACAAAGCGAATGGAAA 59.704 45.455 0.00 0.00 0.00 3.13
698 708 3.056607 CCAGGAACAAAGCGAATGGAAAT 60.057 43.478 0.00 0.00 0.00 2.17
699 709 4.157656 CCAGGAACAAAGCGAATGGAAATA 59.842 41.667 0.00 0.00 0.00 1.40
700 710 5.095490 CAGGAACAAAGCGAATGGAAATAC 58.905 41.667 0.00 0.00 0.00 1.89
701 711 5.010282 AGGAACAAAGCGAATGGAAATACT 58.990 37.500 0.00 0.00 0.00 2.12
702 712 5.123979 AGGAACAAAGCGAATGGAAATACTC 59.876 40.000 0.00 0.00 0.00 2.59
703 713 4.965119 ACAAAGCGAATGGAAATACTCC 57.035 40.909 0.00 0.00 45.64 3.85
751 761 6.490040 GCCAACTAATCAGCCTCCAATAATTA 59.510 38.462 0.00 0.00 0.00 1.40
752 762 7.177392 GCCAACTAATCAGCCTCCAATAATTAT 59.823 37.037 0.00 0.00 0.00 1.28
753 763 8.734386 CCAACTAATCAGCCTCCAATAATTATC 58.266 37.037 0.00 0.00 0.00 1.75
754 764 9.288576 CAACTAATCAGCCTCCAATAATTATCA 57.711 33.333 0.00 0.00 0.00 2.15
755 765 9.866655 AACTAATCAGCCTCCAATAATTATCAA 57.133 29.630 0.00 0.00 0.00 2.57
803 813 0.170561 GATACGATCCGATCCCGTGG 59.829 60.000 2.69 0.00 37.69 4.94
804 814 0.251033 ATACGATCCGATCCCGTGGA 60.251 55.000 2.69 0.00 37.69 4.02
805 815 0.887836 TACGATCCGATCCCGTGGAG 60.888 60.000 2.69 0.00 37.76 3.86
806 816 2.340443 GATCCGATCCCGTGGAGC 59.660 66.667 0.00 0.00 37.76 4.70
807 817 2.443952 ATCCGATCCCGTGGAGCA 60.444 61.111 8.57 0.00 38.11 4.26
808 818 2.028125 GATCCGATCCCGTGGAGCAA 62.028 60.000 8.57 0.00 38.11 3.91
809 819 1.410850 ATCCGATCCCGTGGAGCAAT 61.411 55.000 8.57 0.00 38.11 3.56
810 820 1.889105 CCGATCCCGTGGAGCAATG 60.889 63.158 8.57 0.00 38.11 2.82
811 821 2.537560 CGATCCCGTGGAGCAATGC 61.538 63.158 0.00 0.00 38.11 3.56
812 822 1.153086 GATCCCGTGGAGCAATGCT 60.153 57.895 7.79 7.79 43.88 3.79
813 823 0.106708 GATCCCGTGGAGCAATGCTA 59.893 55.000 8.12 0.00 39.88 3.49
814 824 0.179045 ATCCCGTGGAGCAATGCTAC 60.179 55.000 11.21 11.21 39.88 3.58
821 831 2.549926 TGGAGCAATGCTACACATACG 58.450 47.619 17.45 0.00 42.40 3.06
822 832 2.093711 TGGAGCAATGCTACACATACGT 60.094 45.455 17.45 0.00 42.40 3.57
823 833 3.131400 TGGAGCAATGCTACACATACGTA 59.869 43.478 17.45 0.00 42.40 3.57
824 834 3.736252 GGAGCAATGCTACACATACGTAG 59.264 47.826 13.46 0.00 39.71 3.51
825 835 4.499188 GGAGCAATGCTACACATACGTAGA 60.499 45.833 13.46 0.00 39.71 2.59
826 836 4.360563 AGCAATGCTACACATACGTAGAC 58.639 43.478 5.69 0.00 41.21 2.59
827 837 4.098044 AGCAATGCTACACATACGTAGACT 59.902 41.667 5.69 0.00 41.21 3.24
828 838 4.804139 GCAATGCTACACATACGTAGACTT 59.196 41.667 0.08 0.00 41.21 3.01
829 839 5.975344 GCAATGCTACACATACGTAGACTTA 59.025 40.000 0.08 0.00 41.21 2.24
979 989 2.686915 GCATCAAGAACCCAAGATCCAG 59.313 50.000 0.00 0.00 0.00 3.86
987 1001 1.059006 CCCAAGATCCAGGCTAGGCT 61.059 60.000 14.10 14.10 0.00 4.58
1097 1123 2.159421 GCGTCTTCCTCAACTACATCGA 60.159 50.000 0.00 0.00 0.00 3.59
1098 1124 3.427243 CGTCTTCCTCAACTACATCGAC 58.573 50.000 0.00 0.00 0.00 4.20
1156 1188 3.195002 CCGCGGTCGACTACGGTA 61.195 66.667 29.52 0.00 40.77 4.02
1342 1376 2.119611 TCTTCGACCCAGCCCTGA 59.880 61.111 0.00 0.00 0.00 3.86
1414 1448 5.368989 AGAAGTTCGACCTCATTGAGTTTT 58.631 37.500 12.54 0.00 0.00 2.43
1493 1539 1.418637 TGAACCGGCTGTAGAACCTTT 59.581 47.619 0.00 0.00 0.00 3.11
1494 1540 1.804748 GAACCGGCTGTAGAACCTTTG 59.195 52.381 0.00 0.00 0.00 2.77
1495 1541 0.605589 ACCGGCTGTAGAACCTTTGC 60.606 55.000 0.00 0.00 0.00 3.68
1496 1542 1.305930 CCGGCTGTAGAACCTTTGCC 61.306 60.000 0.00 0.00 37.24 4.52
1497 1543 0.605319 CGGCTGTAGAACCTTTGCCA 60.605 55.000 0.00 0.00 40.27 4.92
1498 1544 1.616159 GGCTGTAGAACCTTTGCCAA 58.384 50.000 0.00 0.00 40.04 4.52
1499 1545 1.541588 GGCTGTAGAACCTTTGCCAAG 59.458 52.381 0.00 0.00 40.04 3.61
1500 1546 2.504367 GCTGTAGAACCTTTGCCAAGA 58.496 47.619 0.00 0.00 30.57 3.02
1501 1547 2.226674 GCTGTAGAACCTTTGCCAAGAC 59.773 50.000 0.00 0.00 30.57 3.01
1502 1548 3.476552 CTGTAGAACCTTTGCCAAGACA 58.523 45.455 0.00 0.00 30.57 3.41
1503 1549 3.476552 TGTAGAACCTTTGCCAAGACAG 58.523 45.455 0.00 0.00 30.57 3.51
1504 1550 2.736670 AGAACCTTTGCCAAGACAGT 57.263 45.000 0.00 0.00 30.57 3.55
1512 1558 0.684535 TGCCAAGACAGTCCATCGAA 59.315 50.000 0.00 0.00 0.00 3.71
1578 1624 1.471676 CCTGTGTTCTCATCGGCTACC 60.472 57.143 0.00 0.00 0.00 3.18
1633 1681 1.078848 GGCTGTCAAGACGATGGCT 60.079 57.895 0.00 0.00 0.00 4.75
1707 1755 1.740296 GTGTGTATTGGCGAGGCGT 60.740 57.895 0.00 0.00 0.00 5.68
1774 1822 7.619050 CATCCTAGATCCAAGTGCATAACTAT 58.381 38.462 0.00 0.00 38.56 2.12
1918 2230 5.116528 GCGAGTAAATTTGTGTTTTGTAGGC 59.883 40.000 0.00 0.00 0.00 3.93
1927 2239 9.908152 AATTTGTGTTTTGTAGGCTATCTTTAC 57.092 29.630 0.00 0.00 0.00 2.01
1929 2241 6.775708 TGTGTTTTGTAGGCTATCTTTACCT 58.224 36.000 0.00 0.00 37.61 3.08
1932 2244 7.064728 GTGTTTTGTAGGCTATCTTTACCTGAG 59.935 40.741 0.00 0.00 34.92 3.35
1960 2272 5.796424 ATACCGGGTACTTAATACACCAG 57.204 43.478 9.50 0.00 33.05 4.00
1987 2299 2.798976 TGAGGAAAGCAAACATGCAC 57.201 45.000 3.41 0.00 37.25 4.57
1989 2301 1.266718 GAGGAAAGCAAACATGCACGA 59.733 47.619 3.41 0.00 37.25 4.35
1992 2304 0.743688 AAAGCAAACATGCACGACCA 59.256 45.000 3.41 0.00 37.25 4.02
2016 2328 4.788925 TCTTGGGAAGTCAGAAAAAGGA 57.211 40.909 0.00 0.00 0.00 3.36
2022 2334 5.073144 TGGGAAGTCAGAAAAAGGAGTGTAT 59.927 40.000 0.00 0.00 0.00 2.29
2057 2369 5.492895 TCACAAGTACAACAACCTTCTTCA 58.507 37.500 0.00 0.00 0.00 3.02
2058 2370 5.584649 TCACAAGTACAACAACCTTCTTCAG 59.415 40.000 0.00 0.00 0.00 3.02
2527 2839 9.607333 TTTCAGAGACTCCTCCATAATATGTAT 57.393 33.333 0.00 0.00 40.30 2.29
2566 2878 4.462508 TGAACTGCAAATGGTTCAACAA 57.537 36.364 14.76 0.00 45.54 2.83
2664 2977 7.819415 CACAATCTTCTGAGGTAGTTTGTCATA 59.181 37.037 8.15 0.00 33.56 2.15
2785 3098 7.549839 AGTACCGCAAAGTGTAGAAACATATA 58.450 34.615 0.00 0.00 38.08 0.86
2856 3170 3.366679 GCATGCAAAAGTAGTCATGTGCT 60.367 43.478 14.21 0.00 38.72 4.40
2880 3194 4.945292 TGAAATCGTGTCAAATTTTGCG 57.055 36.364 4.19 3.20 0.00 4.85
2947 3262 7.010738 GTGAAAAGGCATTCATCAATGGTAATG 59.989 37.037 8.65 0.00 41.09 1.90
3038 3356 1.824852 CCACAAAGTCCTTTATGGGCC 59.175 52.381 8.86 0.00 41.97 5.80
3055 3373 0.969409 GCCCAAGCAAGCTCCTTGAT 60.969 55.000 21.99 0.00 43.42 2.57
3110 3429 2.573915 AGAAGGGCTTCAAACTAGGAGG 59.426 50.000 0.00 0.00 41.84 4.30
3117 3436 3.807209 GCTTCAAACTAGGAGGCACTGAA 60.807 47.826 0.00 0.00 41.55 3.02
3215 3535 7.758076 TGACAATACTAACTCTCATTACAACGG 59.242 37.037 0.00 0.00 0.00 4.44
3225 3545 6.038271 ACTCTCATTACAACGGATAATTTGCC 59.962 38.462 0.00 0.00 0.00 4.52
3245 3566 5.830912 TGCCAAATTAATAGCCGAAGAATG 58.169 37.500 0.00 0.00 0.00 2.67
3316 3640 4.911610 GTCAACAACGGAATGACATCTTTG 59.088 41.667 7.68 0.00 42.31 2.77
3345 3670 2.416836 GGAAAAATACCTCAAAGCCGCC 60.417 50.000 0.00 0.00 0.00 6.13
3458 3784 6.189677 TCAACAAAAAGGTATATTGCTCCG 57.810 37.500 0.00 0.00 0.00 4.63
3472 3801 0.603065 GCTCCGTTGGCTTTCCATTT 59.397 50.000 0.00 0.00 43.05 2.32
3503 3832 3.117550 TGCATCTAGGCCCAACATTATGT 60.118 43.478 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 5.122512 ACGATATTCACGAGTCCTAATGG 57.877 43.478 0.00 0.00 34.70 3.16
129 130 8.600625 CATGGCAATAAAATGAATCAAGACTTG 58.399 33.333 9.03 9.03 0.00 3.16
283 284 5.396484 CCATGTGAGCTTCTAACAAATGTG 58.604 41.667 0.00 0.00 27.50 3.21
396 402 3.708451 ACATTTTATTCCCCTGACCACC 58.292 45.455 0.00 0.00 0.00 4.61
433 439 5.986135 GCATAGAAGTATAGAACACCACCAG 59.014 44.000 0.00 0.00 0.00 4.00
457 467 7.439157 TCTTATGTTCACTCACAGGAAAATG 57.561 36.000 0.00 0.00 0.00 2.32
484 494 4.397420 TCTGTTCAAAATGCTCTTAGGCA 58.603 39.130 0.00 0.00 46.63 4.75
497 507 7.581213 ACCAGTTTTACATCATCTGTTCAAA 57.419 32.000 0.00 0.00 39.39 2.69
500 510 7.040409 AGGAAACCAGTTTTACATCATCTGTTC 60.040 37.037 0.00 0.00 34.55 3.18
577 587 9.821662 AGTTTTAACTATCGTATCAAGTTTTGC 57.178 29.630 0.00 0.00 37.52 3.68
595 605 8.099364 TCTCCATTCTTGACATGAGTTTTAAC 57.901 34.615 0.00 0.00 0.00 2.01
633 643 1.595093 ATCGCGCCCAAAAAGGAAGG 61.595 55.000 0.00 0.00 41.22 3.46
693 703 4.700692 GGTTCTTGTTCCTGGAGTATTTCC 59.299 45.833 0.00 0.00 46.98 3.13
694 704 4.392138 CGGTTCTTGTTCCTGGAGTATTTC 59.608 45.833 0.00 0.00 0.00 2.17
695 705 4.041198 TCGGTTCTTGTTCCTGGAGTATTT 59.959 41.667 0.00 0.00 0.00 1.40
696 706 3.581332 TCGGTTCTTGTTCCTGGAGTATT 59.419 43.478 0.00 0.00 0.00 1.89
697 707 3.170717 TCGGTTCTTGTTCCTGGAGTAT 58.829 45.455 0.00 0.00 0.00 2.12
698 708 2.600790 TCGGTTCTTGTTCCTGGAGTA 58.399 47.619 0.00 0.00 0.00 2.59
699 709 1.420430 TCGGTTCTTGTTCCTGGAGT 58.580 50.000 0.00 0.00 0.00 3.85
700 710 2.622436 GATCGGTTCTTGTTCCTGGAG 58.378 52.381 0.00 0.00 0.00 3.86
701 711 1.067142 CGATCGGTTCTTGTTCCTGGA 60.067 52.381 7.38 0.00 0.00 3.86
702 712 1.359848 CGATCGGTTCTTGTTCCTGG 58.640 55.000 7.38 0.00 0.00 4.45
703 713 1.359848 CCGATCGGTTCTTGTTCCTG 58.640 55.000 26.35 0.00 0.00 3.86
704 714 3.834732 CCGATCGGTTCTTGTTCCT 57.165 52.632 26.35 0.00 0.00 3.36
751 761 7.039784 CCATCCGGGTAACATGATAAAATTGAT 60.040 37.037 0.00 0.00 39.74 2.57
752 762 6.264292 CCATCCGGGTAACATGATAAAATTGA 59.736 38.462 0.00 0.00 39.74 2.57
753 763 6.446318 CCATCCGGGTAACATGATAAAATTG 58.554 40.000 0.00 0.00 39.74 2.32
754 764 5.010617 GCCATCCGGGTAACATGATAAAATT 59.989 40.000 0.00 0.00 39.65 1.82
755 765 4.522789 GCCATCCGGGTAACATGATAAAAT 59.477 41.667 0.00 0.00 39.65 1.82
756 766 3.886505 GCCATCCGGGTAACATGATAAAA 59.113 43.478 0.00 0.00 39.65 1.52
757 767 3.482436 GCCATCCGGGTAACATGATAAA 58.518 45.455 0.00 0.00 39.65 1.40
758 768 2.224670 GGCCATCCGGGTAACATGATAA 60.225 50.000 0.00 0.00 39.65 1.75
759 769 1.349688 GGCCATCCGGGTAACATGATA 59.650 52.381 0.00 0.00 39.65 2.15
803 813 4.441415 GTCTACGTATGTGTAGCATTGCTC 59.559 45.833 15.81 7.72 41.29 4.26
804 814 4.098044 AGTCTACGTATGTGTAGCATTGCT 59.902 41.667 16.63 16.63 41.29 3.91
805 815 4.360563 AGTCTACGTATGTGTAGCATTGC 58.639 43.478 0.00 0.00 41.29 3.56
806 816 6.970613 TGTAAGTCTACGTATGTGTAGCATTG 59.029 38.462 0.00 0.00 41.29 2.82
807 817 7.092137 TGTAAGTCTACGTATGTGTAGCATT 57.908 36.000 0.00 2.82 41.29 3.56
808 818 6.688637 TGTAAGTCTACGTATGTGTAGCAT 57.311 37.500 0.00 0.00 41.29 3.79
809 819 6.688637 ATGTAAGTCTACGTATGTGTAGCA 57.311 37.500 0.00 0.00 41.29 3.49
810 820 6.417044 CCAATGTAAGTCTACGTATGTGTAGC 59.583 42.308 0.00 0.00 41.29 3.58
811 821 6.916387 CCCAATGTAAGTCTACGTATGTGTAG 59.084 42.308 0.00 0.00 42.57 2.74
812 822 6.377996 ACCCAATGTAAGTCTACGTATGTGTA 59.622 38.462 0.00 0.00 0.00 2.90
813 823 5.186409 ACCCAATGTAAGTCTACGTATGTGT 59.814 40.000 0.00 0.00 0.00 3.72
814 824 5.657474 ACCCAATGTAAGTCTACGTATGTG 58.343 41.667 0.00 0.00 0.00 3.21
815 825 5.655532 AGACCCAATGTAAGTCTACGTATGT 59.344 40.000 0.00 0.00 39.06 2.29
816 826 6.145338 AGACCCAATGTAAGTCTACGTATG 57.855 41.667 0.00 0.00 39.06 2.39
817 827 6.786967 AAGACCCAATGTAAGTCTACGTAT 57.213 37.500 0.00 0.00 39.92 3.06
818 828 6.392354 CAAAGACCCAATGTAAGTCTACGTA 58.608 40.000 0.00 0.00 39.92 3.57
819 829 5.235516 CAAAGACCCAATGTAAGTCTACGT 58.764 41.667 0.00 0.00 39.92 3.57
820 830 4.630069 CCAAAGACCCAATGTAAGTCTACG 59.370 45.833 0.00 0.00 39.92 3.51
821 831 4.941873 CCCAAAGACCCAATGTAAGTCTAC 59.058 45.833 0.00 0.00 39.92 2.59
822 832 4.566907 GCCCAAAGACCCAATGTAAGTCTA 60.567 45.833 0.00 0.00 39.92 2.59
823 833 3.814316 GCCCAAAGACCCAATGTAAGTCT 60.814 47.826 0.00 0.00 42.58 3.24
824 834 2.492088 GCCCAAAGACCCAATGTAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
825 835 2.158385 TGCCCAAAGACCCAATGTAAGT 60.158 45.455 0.00 0.00 0.00 2.24
826 836 2.524306 TGCCCAAAGACCCAATGTAAG 58.476 47.619 0.00 0.00 0.00 2.34
827 837 2.685106 TGCCCAAAGACCCAATGTAA 57.315 45.000 0.00 0.00 0.00 2.41
828 838 2.733956 GATGCCCAAAGACCCAATGTA 58.266 47.619 0.00 0.00 0.00 2.29
829 839 1.560505 GATGCCCAAAGACCCAATGT 58.439 50.000 0.00 0.00 0.00 2.71
894 904 1.208706 TGGGCGGGATATCAACTCAA 58.791 50.000 4.83 0.00 0.00 3.02
952 962 0.401356 TGGGTTCTTGATGCAGAGCA 59.599 50.000 0.00 0.00 44.86 4.26
987 1001 2.982643 ATCCATGGCTTCCACGGCA 61.983 57.895 6.96 0.00 36.72 5.69
992 1006 0.109153 CGGATCATCCATGGCTTCCA 59.891 55.000 6.96 0.00 35.91 3.53
1098 1124 4.388499 AACCGTGGCCGCCAGTAG 62.388 66.667 13.92 7.04 32.34 2.57
1156 1188 1.982938 CGGGGAGGAAGTCGAGGTT 60.983 63.158 0.00 0.00 0.00 3.50
1342 1376 2.167398 AACACCTCGTAGCCATGCGT 62.167 55.000 0.00 0.00 35.83 5.24
1414 1448 3.489355 ACATGTCATCCAGCAAAGACAA 58.511 40.909 0.00 0.00 43.38 3.18
1493 1539 0.684535 TTCGATGGACTGTCTTGGCA 59.315 50.000 7.85 0.00 0.00 4.92
1494 1540 1.066858 TCTTCGATGGACTGTCTTGGC 60.067 52.381 7.85 0.00 0.00 4.52
1495 1541 2.232452 AGTCTTCGATGGACTGTCTTGG 59.768 50.000 17.11 0.00 41.76 3.61
1496 1542 3.584406 AGTCTTCGATGGACTGTCTTG 57.416 47.619 17.11 0.00 41.76 3.02
1497 1543 3.862642 GCAAGTCTTCGATGGACTGTCTT 60.863 47.826 18.11 4.46 42.39 3.01
1498 1544 2.353208 GCAAGTCTTCGATGGACTGTCT 60.353 50.000 18.11 4.74 42.39 3.41
1499 1545 1.996191 GCAAGTCTTCGATGGACTGTC 59.004 52.381 18.11 0.00 42.39 3.51
1500 1546 1.344438 TGCAAGTCTTCGATGGACTGT 59.656 47.619 18.11 8.96 42.39 3.55
1501 1547 2.084610 TGCAAGTCTTCGATGGACTG 57.915 50.000 18.11 13.94 42.39 3.51
1502 1548 2.736719 CGATGCAAGTCTTCGATGGACT 60.737 50.000 13.54 13.54 44.73 3.85
1503 1549 1.590238 CGATGCAAGTCTTCGATGGAC 59.410 52.381 0.33 10.00 42.78 4.02
1504 1550 1.204704 ACGATGCAAGTCTTCGATGGA 59.795 47.619 13.21 0.00 42.78 3.41
1512 1558 1.148310 CCGTCAAACGATGCAAGTCT 58.852 50.000 0.24 0.00 46.05 3.24
1578 1624 2.681778 ACCTCTCCTGCCACTCCG 60.682 66.667 0.00 0.00 0.00 4.63
1707 1755 1.795872 CACGACAATGGACGTAAAGCA 59.204 47.619 0.00 0.00 43.18 3.91
1752 1800 9.778741 TTTTATAGTTATGCACTTGGATCTAGG 57.221 33.333 0.00 0.00 36.88 3.02
1760 1808 8.398665 GGAAGGAGTTTTATAGTTATGCACTTG 58.601 37.037 0.00 0.00 36.88 3.16
1886 2197 8.920509 AAACACAAATTTACTCGCTAAAAGTT 57.079 26.923 0.00 0.00 0.00 2.66
1888 2199 8.803799 ACAAAACACAAATTTACTCGCTAAAAG 58.196 29.630 0.00 0.00 0.00 2.27
1898 2210 9.908152 AAGATAGCCTACAAAACACAAATTTAC 57.092 29.630 0.00 0.00 0.00 2.01
1927 2239 1.503800 ACCCGGTATTTACCCTCAGG 58.496 55.000 0.00 0.00 43.51 3.86
1929 2241 3.403228 AGTACCCGGTATTTACCCTCA 57.597 47.619 0.00 0.00 43.51 3.86
1932 2244 6.929049 GTGTATTAAGTACCCGGTATTTACCC 59.071 42.308 11.14 4.61 36.42 3.69
1948 2260 9.667107 TTCCTCAAAATCTACTGGTGTATTAAG 57.333 33.333 0.00 0.00 0.00 1.85
1960 2272 6.089954 GCATGTTTGCTTTCCTCAAAATCTAC 59.910 38.462 0.00 0.00 45.77 2.59
1992 2304 7.032598 TCCTTTTTCTGACTTCCCAAGATAT 57.967 36.000 0.00 0.00 0.00 1.63
2007 2319 5.298276 TGTCGCAAAATACACTCCTTTTTCT 59.702 36.000 0.00 0.00 0.00 2.52
2016 2328 5.431420 TGTGAATTGTCGCAAAATACACT 57.569 34.783 0.00 0.00 41.30 3.55
2072 2384 4.422073 TCTATTGGACCGCTTGATTCAT 57.578 40.909 0.00 0.00 0.00 2.57
2098 2410 7.106890 TCAAGCTCGATAGTATGCTCTAGTAT 58.893 38.462 0.00 0.00 37.28 2.12
2104 2416 5.053140 TCATCAAGCTCGATAGTATGCTC 57.947 43.478 0.00 0.00 37.28 4.26
2280 2592 3.278574 CTGTTCTTCACAACCACCTTGA 58.721 45.455 0.00 0.00 33.87 3.02
2527 2839 5.182950 CAGTTCACATATGGTAACCTTTGCA 59.817 40.000 7.80 0.00 0.00 4.08
2566 2878 8.409358 ACTTTAGGATACACTTTTTCTTGCAT 57.591 30.769 0.00 0.00 41.41 3.96
2637 2950 6.174720 ACAAACTACCTCAGAAGATTGTGA 57.825 37.500 2.98 0.00 0.00 3.58
2638 2951 5.991606 TGACAAACTACCTCAGAAGATTGTG 59.008 40.000 7.18 0.00 30.58 3.33
2639 2952 6.174720 TGACAAACTACCTCAGAAGATTGT 57.825 37.500 3.32 3.32 32.89 2.71
2685 2998 5.138125 ACTGGTTGGTTCAAATGCATAAG 57.862 39.130 0.00 0.00 0.00 1.73
2749 3062 5.061808 CACTTTGCGGTACTTACATGTAGAC 59.938 44.000 5.56 5.97 0.00 2.59
2785 3098 7.827729 GGGAAGTAAGACATTTGTAACCAGTAT 59.172 37.037 0.00 0.00 0.00 2.12
2797 3110 1.628846 AGCGTGGGGAAGTAAGACATT 59.371 47.619 0.00 0.00 0.00 2.71
2856 3170 6.181255 CGCAAAATTTGACACGATTTCAAAA 58.819 32.000 10.26 0.00 44.14 2.44
2860 3174 3.421698 GGCGCAAAATTTGACACGATTTC 60.422 43.478 10.83 0.00 0.00 2.17
2947 3262 6.260050 TGTTTGACACATAGTTCTTCCTTGAC 59.740 38.462 0.00 0.00 0.00 3.18
3038 3356 2.125773 AGATCAAGGAGCTTGCTTGG 57.874 50.000 14.18 1.41 44.54 3.61
3055 3373 7.482169 ACTTCTTGAGTGTATCATACCAAGA 57.518 36.000 9.67 9.67 37.89 3.02
3110 3429 2.999355 GTGAAGAGAGTGGATTCAGTGC 59.001 50.000 0.00 0.00 33.83 4.40
3117 3436 5.511386 AAGATTTGGTGAAGAGAGTGGAT 57.489 39.130 0.00 0.00 0.00 3.41
3215 3535 8.810652 TTCGGCTATTAATTTGGCAAATTATC 57.189 30.769 33.86 24.49 41.51 1.75
3225 3545 8.909708 TTTGACATTCTTCGGCTATTAATTTG 57.090 30.769 0.00 0.00 0.00 2.32
3245 3566 2.034124 CCCCCATCATGGACATTTGAC 58.966 52.381 4.75 0.00 40.96 3.18
3316 3640 6.128145 GCTTTGAGGTATTTTTCCTGAGAGAC 60.128 42.308 0.00 0.00 35.20 3.36
3345 3670 8.500773 CCAATTTTCCATGAAACATTTCTTCAG 58.499 33.333 5.97 0.00 36.30 3.02
3431 3757 8.250332 GGAGCAATATACCTTTTTGTTGAATGA 58.750 33.333 0.00 0.00 0.00 2.57
3472 3801 2.104792 GGGCCTAGATGCACACAGATAA 59.895 50.000 0.84 0.00 33.82 1.75


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

AutoCloner maintained by Alex Coulton.