Multiple sequence alignment - TraesCS6B01G136000

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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 TraesCS6B01G136000 chr6B 100.000 3254 0 0 1 3254 133347751 133351004 0.000000e+00 6010.0
1 TraesCS6B01G136000 chr6B 91.079 1334 66 29 1952 3253 133447377 133446065 0.000000e+00 1755.0
2 TraesCS6B01G136000 chr6B 93.744 1103 53 9 861 1956 133451828 133450735 0.000000e+00 1640.0
3 TraesCS6B01G136000 chr6A 90.689 1815 115 22 917 2692 76100128 76098329 0.000000e+00 2366.0
4 TraesCS6B01G136000 chr6A 89.100 789 81 4 1 789 29170692 29169909 0.000000e+00 976.0
5 TraesCS6B01G136000 chr6A 88.761 783 86 2 1 783 486383215 486383995 0.000000e+00 957.0
6 TraesCS6B01G136000 chr6A 91.923 520 30 7 2737 3253 76098028 76097518 0.000000e+00 717.0
7 TraesCS6B01G136000 chr6A 86.293 321 43 1 464 784 592804433 592804752 6.680000e-92 348.0
8 TraesCS6B01G136000 chr6D 93.359 1536 72 19 850 2374 59747558 59746042 0.000000e+00 2244.0
9 TraesCS6B01G136000 chr6D 88.537 663 41 13 2527 3158 59746039 59745381 0.000000e+00 771.0
10 TraesCS6B01G136000 chr6D 94.737 38 2 0 2565 2602 135459604 135459641 3.510000e-05 60.2
11 TraesCS6B01G136000 chr4A 91.176 782 67 2 1 782 552270836 552271615 0.000000e+00 1061.0
12 TraesCS6B01G136000 chr5D 89.514 782 81 1 3 784 440926631 440925851 0.000000e+00 989.0
13 TraesCS6B01G136000 chr5D 85.496 131 16 3 2378 2507 150835723 150835595 2.040000e-27 134.0
14 TraesCS6B01G136000 chr3A 87.883 784 91 4 1 783 456805536 456806316 0.000000e+00 918.0
15 TraesCS6B01G136000 chr7B 87.468 782 96 2 1 782 493222790 493223569 0.000000e+00 900.0
16 TraesCS6B01G136000 chr7B 82.550 149 21 4 2369 2514 60244541 60244395 3.410000e-25 126.0
17 TraesCS6B01G136000 chr5B 87.229 783 98 2 1 783 94082941 94083721 0.000000e+00 891.0
18 TraesCS6B01G136000 chr1B 86.589 768 102 1 3 770 477490074 477490840 0.000000e+00 846.0
19 TraesCS6B01G136000 chr7D 90.526 380 33 2 403 782 632761039 632760663 1.740000e-137 499.0
20 TraesCS6B01G136000 chr2A 86.508 126 12 5 2382 2505 58152971 58153093 2.040000e-27 134.0
21 TraesCS6B01G136000 chr7A 83.562 146 19 4 2364 2506 719012429 719012572 7.330000e-27 132.0
22 TraesCS6B01G136000 chr7A 82.877 146 20 4 2364 2506 719286298 719286441 3.410000e-25 126.0
23 TraesCS6B01G136000 chr5A 83.803 142 15 7 2373 2510 350268564 350268427 9.480000e-26 128.0
24 TraesCS6B01G136000 chr5A 94.872 39 2 0 2565 2603 471304197 471304235 9.750000e-06 62.1
25 TraesCS6B01G136000 chr4B 83.333 138 19 3 2372 2507 453048505 453048640 1.230000e-24 124.0
26 TraesCS6B01G136000 chrUn 94.737 38 2 0 2565 2602 216513763 216513800 3.510000e-05 60.2
27 TraesCS6B01G136000 chrUn 94.737 38 2 0 2565 2602 286269620 286269583 3.510000e-05 60.2
28 TraesCS6B01G136000 chrUn 94.737 38 2 0 2565 2602 379971536 379971573 3.510000e-05 60.2
29 TraesCS6B01G136000 chrUn 94.737 38 2 0 2565 2602 410662031 410661994 3.510000e-05 60.2
30 TraesCS6B01G136000 chrUn 94.737 38 2 0 2565 2602 418329323 418329360 3.510000e-05 60.2
31 TraesCS6B01G136000 chrUn 94.737 38 2 0 2565 2602 420150264 420150227 3.510000e-05 60.2


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 TraesCS6B01G136000 chr6B 133347751 133351004 3253 False 6010.0 6010 100.0000 1 3254 1 chr6B.!!$F1 3253
1 TraesCS6B01G136000 chr6B 133446065 133451828 5763 True 1697.5 1755 92.4115 861 3253 2 chr6B.!!$R1 2392
2 TraesCS6B01G136000 chr6A 76097518 76100128 2610 True 1541.5 2366 91.3060 917 3253 2 chr6A.!!$R2 2336
3 TraesCS6B01G136000 chr6A 29169909 29170692 783 True 976.0 976 89.1000 1 789 1 chr6A.!!$R1 788
4 TraesCS6B01G136000 chr6A 486383215 486383995 780 False 957.0 957 88.7610 1 783 1 chr6A.!!$F1 782
5 TraesCS6B01G136000 chr6D 59745381 59747558 2177 True 1507.5 2244 90.9480 850 3158 2 chr6D.!!$R1 2308
6 TraesCS6B01G136000 chr4A 552270836 552271615 779 False 1061.0 1061 91.1760 1 782 1 chr4A.!!$F1 781
7 TraesCS6B01G136000 chr5D 440925851 440926631 780 True 989.0 989 89.5140 3 784 1 chr5D.!!$R2 781
8 TraesCS6B01G136000 chr3A 456805536 456806316 780 False 918.0 918 87.8830 1 783 1 chr3A.!!$F1 782
9 TraesCS6B01G136000 chr7B 493222790 493223569 779 False 900.0 900 87.4680 1 782 1 chr7B.!!$F1 781
10 TraesCS6B01G136000 chr5B 94082941 94083721 780 False 891.0 891 87.2290 1 783 1 chr5B.!!$F1 782
11 TraesCS6B01G136000 chr1B 477490074 477490840 766 False 846.0 846 86.5890 3 770 1 chr1B.!!$F1 767


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
542 545 0.438445 CACTTTTTCGCGCTCGATGA 59.562 50.0 5.56 0.0 45.04 2.92 F
1021 1051 0.109272 GCAGACCGATGTCGACAGAA 60.109 55.0 24.41 0.0 46.51 3.02 F
1113 1146 0.970427 TCCACTACAGCATCCTCGCA 60.970 55.0 0.00 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1546 0.895530 CGAGGTGGTAGCTTTCCTGA 59.104 55.000 0.00 0.00 0.0 3.86 R
1843 1880 1.439228 CTGACACCATCGCGATCCT 59.561 57.895 20.85 3.62 0.0 3.24 R
2611 6032 1.923148 CCACTCCCCTGAAATAACCCT 59.077 52.381 0.00 0.00 0.0 4.34 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
86 87 1.266989 GCGACCCAAGGTTTCAAGAAG 59.733 52.381 0.00 0.00 35.25 2.85
91 92 2.294512 CCCAAGGTTTCAAGAAGCTGAC 59.705 50.000 0.00 0.00 0.00 3.51
168 169 6.506500 AACACATGATAAGGAAAGCTCAAG 57.493 37.500 0.00 0.00 0.00 3.02
171 172 4.205587 CATGATAAGGAAAGCTCAAGCCT 58.794 43.478 0.00 0.00 43.38 4.58
182 185 2.373502 AGCTCAAGCCTAGTCCAGTTTT 59.626 45.455 0.00 0.00 43.38 2.43
183 186 3.149981 GCTCAAGCCTAGTCCAGTTTTT 58.850 45.455 0.00 0.00 34.31 1.94
198 201 4.697352 CCAGTTTTTGAGATCGATCAAGGT 59.303 41.667 26.47 6.38 40.16 3.50
245 248 0.890996 GGAGCACACCAAAGTCCTGG 60.891 60.000 0.00 0.00 42.68 4.45
253 256 1.224592 CAAAGTCCTGGCCGGCTAT 59.775 57.895 28.56 0.94 0.00 2.97
275 278 3.003763 GGAGACCGCCTGAGGGTT 61.004 66.667 0.00 0.00 38.07 4.11
279 282 1.209747 GAGACCGCCTGAGGGTTATTT 59.790 52.381 0.00 0.00 38.07 1.40
344 347 2.692368 GGGGTGCAGGAGGGATCA 60.692 66.667 0.00 0.00 0.00 2.92
475 478 2.262915 CGAGGCTTCCTGCGAGTT 59.737 61.111 0.00 0.00 44.05 3.01
499 502 1.067295 TGGAGGTTGACTGCAAGGAT 58.933 50.000 0.00 0.00 45.18 3.24
504 507 2.906389 AGGTTGACTGCAAGGATGTAGA 59.094 45.455 0.90 0.00 41.33 2.59
542 545 0.438445 CACTTTTTCGCGCTCGATGA 59.562 50.000 5.56 0.00 45.04 2.92
557 560 2.222678 TCGATGATAGCGTCCGTTCTAC 59.777 50.000 0.00 0.00 0.00 2.59
570 573 5.124645 GTCCGTTCTACTGGAGATAGAAGA 58.875 45.833 0.00 0.00 38.91 2.87
577 580 6.901300 TCTACTGGAGATAGAAGAACTAGCA 58.099 40.000 0.00 0.00 39.63 3.49
630 633 9.686683 AACATGTATCTAGAAAAGCCAATACTT 57.313 29.630 0.00 0.00 0.00 2.24
639 642 0.995024 AGCCAATACTTCAGCCCACT 59.005 50.000 0.00 0.00 0.00 4.00
674 677 1.878948 GCTTGCACGTTAGGGGTTACA 60.879 52.381 0.00 0.00 0.00 2.41
705 708 2.999928 TGGACTCCCCTCCTAGTTTTT 58.000 47.619 0.00 0.00 35.38 1.94
726 729 6.624352 TTTTCATGACTAGCATTATGGCTC 57.376 37.500 0.00 0.00 44.54 4.70
761 764 9.336171 GGAGCTAGAGATGATTGAATAAAGTTT 57.664 33.333 0.00 0.00 0.00 2.66
774 777 6.399743 TGAATAAAGTTTTTATTTCCCCGCC 58.600 36.000 7.89 0.00 0.00 6.13
800 803 4.953940 AAAAAGTCTAGCCATGCCAAAA 57.046 36.364 0.00 0.00 0.00 2.44
801 804 3.942130 AAAGTCTAGCCATGCCAAAAC 57.058 42.857 0.00 0.00 0.00 2.43
802 805 2.584835 AGTCTAGCCATGCCAAAACA 57.415 45.000 0.00 0.00 0.00 2.83
803 806 2.162681 AGTCTAGCCATGCCAAAACAC 58.837 47.619 0.00 0.00 0.00 3.32
804 807 1.885887 GTCTAGCCATGCCAAAACACA 59.114 47.619 0.00 0.00 0.00 3.72
805 808 2.295909 GTCTAGCCATGCCAAAACACAA 59.704 45.455 0.00 0.00 0.00 3.33
806 809 2.295909 TCTAGCCATGCCAAAACACAAC 59.704 45.455 0.00 0.00 0.00 3.32
807 810 0.829333 AGCCATGCCAAAACACAACA 59.171 45.000 0.00 0.00 0.00 3.33
808 811 0.936600 GCCATGCCAAAACACAACAC 59.063 50.000 0.00 0.00 0.00 3.32
809 812 1.207390 CCATGCCAAAACACAACACG 58.793 50.000 0.00 0.00 0.00 4.49
810 813 0.576328 CATGCCAAAACACAACACGC 59.424 50.000 0.00 0.00 0.00 5.34
811 814 0.529555 ATGCCAAAACACAACACGCC 60.530 50.000 0.00 0.00 0.00 5.68
812 815 2.227568 GCCAAAACACAACACGCCG 61.228 57.895 0.00 0.00 0.00 6.46
813 816 2.227568 CCAAAACACAACACGCCGC 61.228 57.895 0.00 0.00 0.00 6.53
814 817 1.515088 CAAAACACAACACGCCGCA 60.515 52.632 0.00 0.00 0.00 5.69
815 818 1.515304 AAAACACAACACGCCGCAC 60.515 52.632 0.00 0.00 0.00 5.34
816 819 2.875684 AAAACACAACACGCCGCACC 62.876 55.000 0.00 0.00 0.00 5.01
820 823 3.893763 CAACACGCCGCACCCAAA 61.894 61.111 0.00 0.00 0.00 3.28
821 824 3.894947 AACACGCCGCACCCAAAC 61.895 61.111 0.00 0.00 0.00 2.93
822 825 4.868116 ACACGCCGCACCCAAACT 62.868 61.111 0.00 0.00 0.00 2.66
823 826 4.326766 CACGCCGCACCCAAACTG 62.327 66.667 0.00 0.00 0.00 3.16
824 827 4.555709 ACGCCGCACCCAAACTGA 62.556 61.111 0.00 0.00 0.00 3.41
825 828 3.283684 CGCCGCACCCAAACTGAA 61.284 61.111 0.00 0.00 0.00 3.02
826 829 2.335011 GCCGCACCCAAACTGAAC 59.665 61.111 0.00 0.00 0.00 3.18
827 830 3.039134 CCGCACCCAAACTGAACC 58.961 61.111 0.00 0.00 0.00 3.62
828 831 2.637025 CGCACCCAAACTGAACCG 59.363 61.111 0.00 0.00 0.00 4.44
829 832 1.890041 CGCACCCAAACTGAACCGA 60.890 57.895 0.00 0.00 0.00 4.69
830 833 1.440938 CGCACCCAAACTGAACCGAA 61.441 55.000 0.00 0.00 0.00 4.30
831 834 0.958822 GCACCCAAACTGAACCGAAT 59.041 50.000 0.00 0.00 0.00 3.34
832 835 2.156098 GCACCCAAACTGAACCGAATA 58.844 47.619 0.00 0.00 0.00 1.75
833 836 2.095415 GCACCCAAACTGAACCGAATAC 60.095 50.000 0.00 0.00 0.00 1.89
834 837 3.408634 CACCCAAACTGAACCGAATACT 58.591 45.455 0.00 0.00 0.00 2.12
835 838 3.188460 CACCCAAACTGAACCGAATACTG 59.812 47.826 0.00 0.00 0.00 2.74
836 839 2.747446 CCCAAACTGAACCGAATACTGG 59.253 50.000 0.00 0.00 0.00 4.00
837 840 3.408634 CCAAACTGAACCGAATACTGGT 58.591 45.455 0.00 0.00 42.98 4.00
842 845 3.148340 AACCGAATACTGGTTCCGC 57.852 52.632 0.00 0.00 46.61 5.54
843 846 0.738412 AACCGAATACTGGTTCCGCG 60.738 55.000 0.00 0.00 46.61 6.46
844 847 2.522638 CCGAATACTGGTTCCGCGC 61.523 63.158 0.00 0.00 0.00 6.86
845 848 2.856346 CGAATACTGGTTCCGCGCG 61.856 63.158 25.67 25.67 0.00 6.86
846 849 3.151673 GAATACTGGTTCCGCGCGC 62.152 63.158 27.36 23.91 0.00 6.86
847 850 3.943479 AATACTGGTTCCGCGCGCA 62.943 57.895 32.61 16.27 0.00 6.09
865 868 1.115467 CAGCTCCTATCCCGACAGTT 58.885 55.000 0.00 0.00 0.00 3.16
886 890 2.703536 TGCTGCTTTATAGGGATCCGAA 59.296 45.455 5.45 0.00 0.00 4.30
895 899 4.886121 GGATCCGAACGACCCGGC 62.886 72.222 0.00 0.00 46.10 6.13
907 911 4.939368 CCCGGCCCGAACACAACA 62.939 66.667 3.71 0.00 0.00 3.33
945 950 1.131638 TCCCAAGACTGACAGCAACT 58.868 50.000 1.25 0.00 0.00 3.16
979 993 0.444651 CGCCGCCAACGAAAAAGATA 59.555 50.000 0.00 0.00 43.93 1.98
980 994 1.529010 CGCCGCCAACGAAAAAGATAG 60.529 52.381 0.00 0.00 43.93 2.08
981 995 1.202143 GCCGCCAACGAAAAAGATAGG 60.202 52.381 0.00 0.00 43.93 2.57
982 996 1.400494 CCGCCAACGAAAAAGATAGGG 59.600 52.381 0.00 0.00 43.93 3.53
983 997 1.202143 CGCCAACGAAAAAGATAGGGC 60.202 52.381 0.00 0.00 43.93 5.19
984 998 1.816224 GCCAACGAAAAAGATAGGGCA 59.184 47.619 0.00 0.00 39.88 5.36
985 999 2.159379 GCCAACGAAAAAGATAGGGCAG 60.159 50.000 0.00 0.00 39.88 4.85
986 1000 3.343617 CCAACGAAAAAGATAGGGCAGA 58.656 45.455 0.00 0.00 0.00 4.26
987 1001 3.375299 CCAACGAAAAAGATAGGGCAGAG 59.625 47.826 0.00 0.00 0.00 3.35
988 1002 4.253685 CAACGAAAAAGATAGGGCAGAGA 58.746 43.478 0.00 0.00 0.00 3.10
989 1003 4.130286 ACGAAAAAGATAGGGCAGAGAG 57.870 45.455 0.00 0.00 0.00 3.20
990 1004 3.515901 ACGAAAAAGATAGGGCAGAGAGT 59.484 43.478 0.00 0.00 0.00 3.24
991 1005 4.710375 ACGAAAAAGATAGGGCAGAGAGTA 59.290 41.667 0.00 0.00 0.00 2.59
992 1006 5.163499 ACGAAAAAGATAGGGCAGAGAGTAG 60.163 44.000 0.00 0.00 0.00 2.57
993 1007 5.067936 CGAAAAAGATAGGGCAGAGAGTAGA 59.932 44.000 0.00 0.00 0.00 2.59
994 1008 6.478512 AAAAAGATAGGGCAGAGAGTAGAG 57.521 41.667 0.00 0.00 0.00 2.43
1021 1051 0.109272 GCAGACCGATGTCGACAGAA 60.109 55.000 24.41 0.00 46.51 3.02
1024 1054 1.611977 AGACCGATGTCGACAGAACAA 59.388 47.619 24.41 0.00 46.51 2.83
1113 1146 0.970427 TCCACTACAGCATCCTCGCA 60.970 55.000 0.00 0.00 0.00 5.10
1392 1426 1.374758 CACGAGCGGCCTTCTTCTT 60.375 57.895 0.00 0.00 0.00 2.52
2290 5698 3.710677 CTCTCCATCTCCATCTCAAGGTT 59.289 47.826 0.00 0.00 0.00 3.50
2334 5742 1.604755 ACTCGATCATCGCAGGTACTC 59.395 52.381 0.80 0.00 40.21 2.59
2337 5745 2.030805 TCGATCATCGCAGGTACTCATG 60.031 50.000 0.80 0.00 40.21 3.07
2380 5788 7.174253 ACTTTTCAGCTATCTATCTACCTCTCG 59.826 40.741 0.00 0.00 0.00 4.04
2429 5837 9.932207 TTAGAGATTTCAATACGGACTACAAAA 57.068 29.630 0.00 0.00 0.00 2.44
2611 6032 7.663905 TGATTTTACGGAATCTCAAAGAGGAAA 59.336 33.333 9.01 0.00 37.04 3.13
2629 6051 3.011369 GGAAAGGGTTATTTCAGGGGAGT 59.989 47.826 2.05 0.00 40.29 3.85
2689 6234 9.060347 CCTGCAGAATCTAATGTACATGTTTAT 57.940 33.333 17.39 0.00 0.00 1.40
2792 6486 1.077787 CTGCTGGCCCGATGGTTTA 60.078 57.895 0.00 0.00 0.00 2.01
2793 6487 1.077787 TGCTGGCCCGATGGTTTAG 60.078 57.895 0.00 0.00 0.00 1.85
2794 6488 2.481471 GCTGGCCCGATGGTTTAGC 61.481 63.158 0.00 0.00 0.00 3.09
2830 6524 1.616872 CTGCGTTTTTGGCCATTCGC 61.617 55.000 25.88 25.88 43.14 4.70
2844 6538 2.958355 CCATTCGCTTATGGGGATTTGT 59.042 45.455 6.15 0.00 41.18 2.83
2845 6539 4.141287 CCATTCGCTTATGGGGATTTGTA 58.859 43.478 6.15 0.00 41.18 2.41
2889 6592 4.349048 TCATGGTAGGCTTGATCTTGCTAT 59.651 41.667 0.00 3.45 0.00 2.97
2948 6652 7.645058 AAGGGTACATGAGGTGATAAAATTG 57.355 36.000 0.00 0.00 0.00 2.32
3178 6888 5.032846 AGATTGTACTTGAATGAGGAGGGA 58.967 41.667 0.00 0.00 0.00 4.20
3181 6892 1.589414 ACTTGAATGAGGAGGGAGGG 58.411 55.000 0.00 0.00 0.00 4.30
3182 6893 1.203492 ACTTGAATGAGGAGGGAGGGT 60.203 52.381 0.00 0.00 0.00 4.34
3183 6894 1.211457 CTTGAATGAGGAGGGAGGGTG 59.789 57.143 0.00 0.00 0.00 4.61
3184 6895 0.621571 TGAATGAGGAGGGAGGGTGG 60.622 60.000 0.00 0.00 0.00 4.61
3185 6896 1.308216 AATGAGGAGGGAGGGTGGG 60.308 63.158 0.00 0.00 0.00 4.61
3186 6897 1.837533 AATGAGGAGGGAGGGTGGGA 61.838 60.000 0.00 0.00 0.00 4.37
3226 6937 1.807165 GCTCTCGCAAGCGACATCA 60.807 57.895 13.74 0.00 44.01 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.003580 TGTTTCTGGGTGGAGATCAGC 59.996 52.381 0.00 0.00 42.74 4.26
50 51 2.032808 GGTCGCAAAGAATATCCTTCGC 60.033 50.000 0.00 0.00 0.00 4.70
86 87 2.531522 ACAATTTTTGCCCTGTCAGC 57.468 45.000 0.00 0.00 0.00 4.26
91 92 4.942852 TCACAGTAACAATTTTTGCCCTG 58.057 39.130 0.00 0.00 0.00 4.45
140 141 7.280876 TGAGCTTTCCTTATCATGTGTTATGTC 59.719 37.037 0.00 0.00 0.00 3.06
168 169 3.619038 CGATCTCAAAAACTGGACTAGGC 59.381 47.826 0.00 0.00 0.00 3.93
171 172 6.280855 TGATCGATCTCAAAAACTGGACTA 57.719 37.500 25.02 0.00 0.00 2.59
182 185 3.616956 AGCAACCTTGATCGATCTCAA 57.383 42.857 25.02 13.44 34.14 3.02
183 186 3.616956 AAGCAACCTTGATCGATCTCA 57.383 42.857 25.02 11.64 0.00 3.27
198 201 0.536233 TTCTAGCACCGCCAAAGCAA 60.536 50.000 0.00 0.00 39.83 3.91
245 248 1.523938 GTCTCCAACCATAGCCGGC 60.524 63.158 21.89 21.89 0.00 6.13
265 268 7.781056 TGATTTTAATCAAATAACCCTCAGGC 58.219 34.615 2.77 0.00 42.11 4.85
279 282 6.209192 ACCTGCATCAGTGTTGATTTTAATCA 59.791 34.615 5.35 1.12 42.12 2.57
320 323 1.497309 CCTCCTGCACCCCCTTTACA 61.497 60.000 0.00 0.00 0.00 2.41
425 428 0.681733 AGAACACCATCACGCAGAGT 59.318 50.000 0.00 0.00 0.00 3.24
475 478 0.836606 TGCAGTCAACCTCCAGAACA 59.163 50.000 0.00 0.00 0.00 3.18
499 502 0.830444 AAGCCCACAGGTCGTCTACA 60.830 55.000 0.00 0.00 34.57 2.74
542 545 1.948145 CTCCAGTAGAACGGACGCTAT 59.052 52.381 0.00 0.00 0.00 2.97
548 551 5.369409 TCTTCTATCTCCAGTAGAACGGA 57.631 43.478 0.00 0.00 37.89 4.69
557 560 9.023962 AGATAATGCTAGTTCTTCTATCTCCAG 57.976 37.037 0.00 0.00 0.00 3.86
606 609 9.330063 TGAAGTATTGGCTTTTCTAGATACATG 57.670 33.333 0.00 0.00 0.00 3.21
662 665 2.817844 CCAGCAACTTGTAACCCCTAAC 59.182 50.000 0.00 0.00 0.00 2.34
705 708 5.294734 TGAGCCATAATGCTAGTCATGAA 57.705 39.130 0.00 0.00 42.95 2.57
726 729 3.258622 TCATCTCTAGCTCCTGCATGATG 59.741 47.826 0.00 0.00 42.74 3.07
784 787 1.885887 TGTGTTTTGGCATGGCTAGAC 59.114 47.619 21.08 17.85 0.00 2.59
786 789 2.035704 TGTTGTGTTTTGGCATGGCTAG 59.964 45.455 21.08 0.00 0.00 3.42
787 790 2.034878 TGTTGTGTTTTGGCATGGCTA 58.965 42.857 21.08 10.42 0.00 3.93
788 791 0.829333 TGTTGTGTTTTGGCATGGCT 59.171 45.000 21.08 0.00 0.00 4.75
789 792 0.936600 GTGTTGTGTTTTGGCATGGC 59.063 50.000 13.29 13.29 0.00 4.40
790 793 1.207390 CGTGTTGTGTTTTGGCATGG 58.793 50.000 0.00 0.00 0.00 3.66
791 794 0.576328 GCGTGTTGTGTTTTGGCATG 59.424 50.000 0.00 0.00 0.00 4.06
792 795 0.529555 GGCGTGTTGTGTTTTGGCAT 60.530 50.000 0.00 0.00 0.00 4.40
793 796 1.153745 GGCGTGTTGTGTTTTGGCA 60.154 52.632 0.00 0.00 0.00 4.92
794 797 2.227568 CGGCGTGTTGTGTTTTGGC 61.228 57.895 0.00 0.00 0.00 4.52
795 798 2.227568 GCGGCGTGTTGTGTTTTGG 61.228 57.895 9.37 0.00 0.00 3.28
796 799 1.515088 TGCGGCGTGTTGTGTTTTG 60.515 52.632 9.37 0.00 0.00 2.44
797 800 1.515304 GTGCGGCGTGTTGTGTTTT 60.515 52.632 9.37 0.00 0.00 2.43
798 801 2.101380 GTGCGGCGTGTTGTGTTT 59.899 55.556 9.37 0.00 0.00 2.83
799 802 3.883180 GGTGCGGCGTGTTGTGTT 61.883 61.111 9.37 0.00 0.00 3.32
803 806 3.893763 TTTGGGTGCGGCGTGTTG 61.894 61.111 9.37 0.00 0.00 3.33
804 807 3.894947 GTTTGGGTGCGGCGTGTT 61.895 61.111 9.37 0.00 0.00 3.32
805 808 4.868116 AGTTTGGGTGCGGCGTGT 62.868 61.111 9.37 0.00 0.00 4.49
806 809 4.326766 CAGTTTGGGTGCGGCGTG 62.327 66.667 9.37 0.00 0.00 5.34
807 810 4.555709 TCAGTTTGGGTGCGGCGT 62.556 61.111 9.37 0.00 0.00 5.68
808 811 3.283684 TTCAGTTTGGGTGCGGCG 61.284 61.111 0.51 0.51 0.00 6.46
809 812 2.335011 GTTCAGTTTGGGTGCGGC 59.665 61.111 0.00 0.00 0.00 6.53
810 813 2.903547 CGGTTCAGTTTGGGTGCGG 61.904 63.158 0.00 0.00 0.00 5.69
811 814 1.440938 TTCGGTTCAGTTTGGGTGCG 61.441 55.000 0.00 0.00 0.00 5.34
812 815 0.958822 ATTCGGTTCAGTTTGGGTGC 59.041 50.000 0.00 0.00 0.00 5.01
813 816 3.188460 CAGTATTCGGTTCAGTTTGGGTG 59.812 47.826 0.00 0.00 0.00 4.61
814 817 3.408634 CAGTATTCGGTTCAGTTTGGGT 58.591 45.455 0.00 0.00 0.00 4.51
815 818 2.747446 CCAGTATTCGGTTCAGTTTGGG 59.253 50.000 0.00 0.00 0.00 4.12
816 819 3.408634 ACCAGTATTCGGTTCAGTTTGG 58.591 45.455 0.00 0.00 30.53 3.28
825 828 1.153706 CGCGGAACCAGTATTCGGT 60.154 57.895 0.00 0.00 38.85 4.69
826 829 2.522638 GCGCGGAACCAGTATTCGG 61.523 63.158 8.83 0.00 33.33 4.30
827 830 2.856346 CGCGCGGAACCAGTATTCG 61.856 63.158 24.84 0.00 0.00 3.34
828 831 3.003478 CGCGCGGAACCAGTATTC 58.997 61.111 24.84 0.00 0.00 1.75
829 832 3.192922 GCGCGCGGAACCAGTATT 61.193 61.111 33.06 0.00 0.00 1.89
830 833 4.444838 TGCGCGCGGAACCAGTAT 62.445 61.111 33.06 0.00 0.00 2.12
843 846 3.606662 TCGGGATAGGAGCTGCGC 61.607 66.667 0.00 0.00 0.00 6.09
844 847 2.336809 GTCGGGATAGGAGCTGCG 59.663 66.667 0.00 0.00 0.00 5.18
845 848 1.365633 CTGTCGGGATAGGAGCTGC 59.634 63.158 0.00 0.00 0.00 5.25
846 849 1.115467 AACTGTCGGGATAGGAGCTG 58.885 55.000 0.00 0.00 0.00 4.24
847 850 1.115467 CAACTGTCGGGATAGGAGCT 58.885 55.000 0.00 0.00 0.00 4.09
848 851 0.530870 GCAACTGTCGGGATAGGAGC 60.531 60.000 0.00 0.00 0.00 4.70
852 855 0.176680 AGCAGCAACTGTCGGGATAG 59.823 55.000 0.00 0.00 33.43 2.08
857 860 2.609459 CCTATAAAGCAGCAACTGTCGG 59.391 50.000 0.00 0.00 33.43 4.79
865 868 2.325484 TCGGATCCCTATAAAGCAGCA 58.675 47.619 6.06 0.00 0.00 4.41
894 898 1.003223 GTTGTACTGTTGTGTTCGGGC 60.003 52.381 0.00 0.00 0.00 6.13
895 899 1.600485 GGTTGTACTGTTGTGTTCGGG 59.400 52.381 0.00 0.00 0.00 5.14
900 904 5.906113 TTTTGATGGTTGTACTGTTGTGT 57.094 34.783 0.00 0.00 0.00 3.72
907 911 5.144100 TGGGACAATTTTGATGGTTGTACT 58.856 37.500 0.00 0.00 36.98 2.73
970 984 6.322712 TCTCTACTCTCTGCCCTATCTTTTTC 59.677 42.308 0.00 0.00 0.00 2.29
971 985 6.097696 GTCTCTACTCTCTGCCCTATCTTTTT 59.902 42.308 0.00 0.00 0.00 1.94
988 1002 2.294074 GGTCTGCATCGAGTCTCTACT 58.706 52.381 0.00 0.00 39.21 2.57
989 1003 1.003331 CGGTCTGCATCGAGTCTCTAC 60.003 57.143 0.00 0.00 0.00 2.59
990 1004 1.134491 TCGGTCTGCATCGAGTCTCTA 60.134 52.381 0.00 0.00 0.00 2.43
991 1005 0.393132 TCGGTCTGCATCGAGTCTCT 60.393 55.000 0.00 0.00 0.00 3.10
992 1006 0.665835 ATCGGTCTGCATCGAGTCTC 59.334 55.000 11.46 0.00 38.83 3.36
993 1007 0.383590 CATCGGTCTGCATCGAGTCT 59.616 55.000 11.46 0.00 38.83 3.24
994 1008 0.101399 ACATCGGTCTGCATCGAGTC 59.899 55.000 11.46 0.00 38.83 3.36
1045 1075 2.721859 CGTGATCTGCCGATCCGA 59.278 61.111 14.66 0.00 44.40 4.55
1321 1355 2.434359 GACGACGGGCAAGAAGGG 60.434 66.667 0.00 0.00 0.00 3.95
1392 1426 4.927782 GTGCTGCCGGTGGTGACA 62.928 66.667 1.90 0.00 38.70 3.58
1511 1545 1.134965 CGAGGTGGTAGCTTTCCTGAG 60.135 57.143 0.00 1.11 0.00 3.35
1512 1546 0.895530 CGAGGTGGTAGCTTTCCTGA 59.104 55.000 0.00 0.00 0.00 3.86
1547 1581 1.985159 ACCTCCACAGCTCCATGTTTA 59.015 47.619 0.00 0.00 0.00 2.01
1668 1702 4.753662 TACGAGAGCCCGCCCAGT 62.754 66.667 0.00 0.00 0.00 4.00
1764 1801 2.291043 GGACGGCCTCTTCTTCCCA 61.291 63.158 0.00 0.00 0.00 4.37
1843 1880 1.439228 CTGACACCATCGCGATCCT 59.561 57.895 20.85 3.62 0.00 3.24
1925 1968 3.770040 CCATCTCCCACCGCGTCA 61.770 66.667 4.92 0.00 0.00 4.35
1927 1970 4.082523 CACCATCTCCCACCGCGT 62.083 66.667 4.92 0.00 0.00 6.01
2290 5698 8.912988 AGTTCCATCAAATTACTGTCAGAAAAA 58.087 29.630 6.91 0.00 0.00 1.94
2334 5742 9.956720 GAAAAGTGAAATATCCAGAATACCATG 57.043 33.333 0.00 0.00 0.00 3.66
2337 5745 8.131731 GCTGAAAAGTGAAATATCCAGAATACC 58.868 37.037 0.00 0.00 0.00 2.73
2611 6032 1.923148 CCACTCCCCTGAAATAACCCT 59.077 52.381 0.00 0.00 0.00 4.34
2629 6051 6.662865 TTCTGCAAAAATAAACATCTCCCA 57.337 33.333 0.00 0.00 0.00 4.37
2792 6486 4.272018 CGCAGATAAAATTCACTAGCAGCT 59.728 41.667 0.00 0.00 0.00 4.24
2793 6487 4.034510 ACGCAGATAAAATTCACTAGCAGC 59.965 41.667 0.00 0.00 0.00 5.25
2794 6488 5.725110 ACGCAGATAAAATTCACTAGCAG 57.275 39.130 0.00 0.00 0.00 4.24
2889 6592 7.121463 ACAAAGTTAACACACCATAGTTCAACA 59.879 33.333 8.61 0.00 0.00 3.33
2948 6652 4.708726 AGCAATGCAACCTAAACATCTC 57.291 40.909 8.35 0.00 0.00 2.75
3121 6831 9.799106 TTGAATCATCTCTTTTCTTTCTAACCT 57.201 29.630 0.00 0.00 0.00 3.50
3183 6894 4.475135 GAGAAGCGGTGCCCTCCC 62.475 72.222 0.00 0.00 0.00 4.30
3184 6895 4.475135 GGAGAAGCGGTGCCCTCC 62.475 72.222 12.96 12.96 40.01 4.30
3185 6896 4.475135 GGGAGAAGCGGTGCCCTC 62.475 72.222 11.87 7.94 37.59 4.30
3190 6901 2.432628 GACACGGGAGAAGCGGTG 60.433 66.667 0.00 0.00 36.50 4.94



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

AutoCloner maintained by Alex Coulton.