Multiple sequence alignment - TraesCS5D01G265900

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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 TraesCS5D01G265900 chr5D 100.000 3180 0 0 1 3180 370308292 370305113 0.000000e+00 5873.0
1 TraesCS5D01G265900 chr5D 79.383 1135 178 31 2089 3180 370138039 370136918 0.000000e+00 749.0
2 TraesCS5D01G265900 chr5D 79.167 1152 169 49 2066 3180 370135203 370134086 0.000000e+00 732.0
3 TraesCS5D01G265900 chr5D 82.456 114 18 2 752 863 564918913 564919026 7.260000e-17 99.0
4 TraesCS5D01G265900 chr5D 90.909 44 4 0 816 859 134728397 134728354 3.430000e-05 60.2
5 TraesCS5D01G265900 chr5A 90.267 1459 79 32 925 2370 472591132 472589724 0.000000e+00 1849.0
6 TraesCS5D01G265900 chr5A 88.229 875 76 12 2328 3180 472589735 472588866 0.000000e+00 1020.0
7 TraesCS5D01G265900 chr5A 80.505 990 125 32 2066 3013 472546204 472545241 0.000000e+00 697.0
8 TraesCS5D01G265900 chr5A 79.841 878 135 25 2222 3071 472553801 472552938 1.260000e-168 603.0
9 TraesCS5D01G265900 chr5A 79.089 593 104 16 2314 2892 689183932 689184518 1.070000e-104 390.0
10 TraesCS5D01G265900 chr7B 86.803 735 76 13 20 742 295508641 295509366 0.000000e+00 800.0
11 TraesCS5D01G265900 chr7B 85.970 727 81 13 28 742 609181426 609182143 0.000000e+00 758.0
12 TraesCS5D01G265900 chr7B 82.143 84 14 1 790 872 210430669 210430752 1.580000e-08 71.3
13 TraesCS5D01G265900 chr5B 86.126 728 81 14 1 719 666365076 666365792 0.000000e+00 767.0
14 TraesCS5D01G265900 chr5B 80.432 741 121 15 2378 3108 439355710 439354984 7.760000e-151 544.0
15 TraesCS5D01G265900 chr6D 82.751 887 112 25 1 858 456115468 456116342 0.000000e+00 752.0
16 TraesCS5D01G265900 chr7A 83.154 742 87 25 20 746 200068351 200069069 0.000000e+00 643.0
17 TraesCS5D01G265900 chr3B 83.456 677 92 11 1 672 757723027 757723688 2.100000e-171 612.0
18 TraesCS5D01G265900 chr3B 83.013 677 95 11 1 672 757720547 757721208 2.110000e-166 595.0
19 TraesCS5D01G265900 chr3B 82.032 679 101 12 1 674 757718040 757718702 2.770000e-155 558.0
20 TraesCS5D01G265900 chr3B 84.565 460 53 7 1 444 739834621 739835078 1.050000e-119 440.0
21 TraesCS5D01G265900 chr3B 83.200 250 37 4 2317 2563 57319810 57320057 1.150000e-54 224.0
22 TraesCS5D01G265900 chrUn 81.509 795 90 32 116 862 93027406 93026621 4.540000e-168 601.0
23 TraesCS5D01G265900 chrUn 79.422 588 99 18 2320 2892 377500874 377500294 2.300000e-106 396.0
24 TraesCS5D01G265900 chr6A 84.823 593 82 5 42 628 260487415 260486825 9.820000e-165 590.0
25 TraesCS5D01G265900 chr6A 80.120 332 51 14 2317 2642 586331439 586331761 1.910000e-57 233.0
26 TraesCS5D01G265900 chr3D 78.831 496 68 20 2316 2800 349793004 349793473 1.850000e-77 300.0
27 TraesCS5D01G265900 chr2D 79.560 455 57 26 465 898 60063298 60062859 3.100000e-75 292.0
28 TraesCS5D01G265900 chr2D 83.333 90 14 1 782 870 537335050 537334961 7.310000e-12 82.4
29 TraesCS5D01G265900 chr1B 85.484 62 7 2 782 843 256200341 256200400 2.650000e-06 63.9


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 TraesCS5D01G265900 chr5D 370305113 370308292 3179 True 5873.000000 5873 100.000000 1 3180 1 chr5D.!!$R2 3179
1 TraesCS5D01G265900 chr5D 370134086 370138039 3953 True 740.500000 749 79.275000 2066 3180 2 chr5D.!!$R3 1114
2 TraesCS5D01G265900 chr5A 472588866 472591132 2266 True 1434.500000 1849 89.248000 925 3180 2 chr5A.!!$R3 2255
3 TraesCS5D01G265900 chr5A 472545241 472546204 963 True 697.000000 697 80.505000 2066 3013 1 chr5A.!!$R1 947
4 TraesCS5D01G265900 chr5A 472552938 472553801 863 True 603.000000 603 79.841000 2222 3071 1 chr5A.!!$R2 849
5 TraesCS5D01G265900 chr5A 689183932 689184518 586 False 390.000000 390 79.089000 2314 2892 1 chr5A.!!$F1 578
6 TraesCS5D01G265900 chr7B 295508641 295509366 725 False 800.000000 800 86.803000 20 742 1 chr7B.!!$F2 722
7 TraesCS5D01G265900 chr7B 609181426 609182143 717 False 758.000000 758 85.970000 28 742 1 chr7B.!!$F3 714
8 TraesCS5D01G265900 chr5B 666365076 666365792 716 False 767.000000 767 86.126000 1 719 1 chr5B.!!$F1 718
9 TraesCS5D01G265900 chr5B 439354984 439355710 726 True 544.000000 544 80.432000 2378 3108 1 chr5B.!!$R1 730
10 TraesCS5D01G265900 chr6D 456115468 456116342 874 False 752.000000 752 82.751000 1 858 1 chr6D.!!$F1 857
11 TraesCS5D01G265900 chr7A 200068351 200069069 718 False 643.000000 643 83.154000 20 746 1 chr7A.!!$F1 726
12 TraesCS5D01G265900 chr3B 757718040 757723688 5648 False 588.333333 612 82.833667 1 674 3 chr3B.!!$F3 673
13 TraesCS5D01G265900 chrUn 93026621 93027406 785 True 601.000000 601 81.509000 116 862 1 chrUn.!!$R1 746
14 TraesCS5D01G265900 chrUn 377500294 377500874 580 True 396.000000 396 79.422000 2320 2892 1 chrUn.!!$R2 572
15 TraesCS5D01G265900 chr6A 260486825 260487415 590 True 590.000000 590 84.823000 42 628 1 chr6A.!!$R1 586

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
618 3163 0.037303 AGGAGGACGACGAGGTGTAA 59.963 55.0 0.0 0.0 0.0 2.41 F
1177 3800 0.251916 TCACATGACCACCGATTCCC 59.748 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 4474 0.109086 AACTCACGGTCATCTCGCTG 60.109 55.0 0.0 0.0 0.0 5.18 R
2849 9074 0.250124 TAGGAGTTTGGCCGTGTGTG 60.250 55.0 0.0 0.0 0.0 3.82 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
323 2859 3.444805 GTCGTCTCAGCCTCGCCT 61.445 66.667 0.00 0.00 0.00 5.52
329 2865 0.183731 TCTCAGCCTCGCCTAGATGA 59.816 55.000 0.00 0.00 0.00 2.92
332 2868 0.461548 CAGCCTCGCCTAGATGAACA 59.538 55.000 0.00 0.00 0.00 3.18
338 2874 3.190874 CTCGCCTAGATGAACAAGGAAC 58.809 50.000 0.00 0.00 31.64 3.62
405 2941 1.821336 CAACAGTTCTTCGCGCAAAA 58.179 45.000 8.75 0.00 0.00 2.44
412 2948 1.966451 CTTCGCGCAAAAGGAGGGT 60.966 57.895 8.75 0.00 0.00 4.34
545 3081 2.539142 CGAAGACGATCGGTACCTTGAG 60.539 54.545 20.98 9.03 42.66 3.02
549 3085 1.392710 CGATCGGTACCTTGAGGCCT 61.393 60.000 3.86 3.86 39.32 5.19
614 3159 2.045143 GGAGGAGGACGACGAGGT 60.045 66.667 0.00 0.00 0.00 3.85
618 3163 0.037303 AGGAGGACGACGAGGTGTAA 59.963 55.000 0.00 0.00 0.00 2.41
650 3199 4.100707 TGTCGTTTTGTCTATCGTAGGG 57.899 45.455 0.00 0.00 0.00 3.53
652 3201 3.129287 GTCGTTTTGTCTATCGTAGGGGA 59.871 47.826 0.00 0.00 0.00 4.81
771 3375 8.358148 TGGCTTTATCTATCGTAGTAGAAAAGG 58.642 37.037 17.55 7.38 34.59 3.11
794 3398 2.128035 ACAAATATAGCGCGTCTGCTC 58.872 47.619 8.43 0.00 45.87 4.26
811 3415 2.716244 CGAGTGGCTCGCGTATCT 59.284 61.111 5.77 0.00 46.75 1.98
814 3418 1.730612 CGAGTGGCTCGCGTATCTATA 59.269 52.381 5.77 0.00 46.75 1.31
819 3423 6.263516 AGTGGCTCGCGTATCTATATTTTA 57.736 37.500 5.77 0.00 0.00 1.52
820 3424 6.091437 AGTGGCTCGCGTATCTATATTTTAC 58.909 40.000 5.77 0.00 0.00 2.01
821 3425 5.003214 GTGGCTCGCGTATCTATATTTTACG 59.997 44.000 5.77 7.18 41.12 3.18
869 3482 2.681152 ACGCAAAAACTCGTGATTCC 57.319 45.000 0.00 0.00 37.55 3.01
871 3484 1.724654 CGCAAAAACTCGTGATTCCGG 60.725 52.381 0.00 0.00 0.00 5.14
915 3538 4.548991 GCATTTGGAGATGCTCTAACTG 57.451 45.455 2.79 6.54 46.85 3.16
917 3540 4.034975 GCATTTGGAGATGCTCTAACTGAC 59.965 45.833 12.65 3.71 46.85 3.51
918 3541 4.890158 TTTGGAGATGCTCTAACTGACA 57.110 40.909 0.00 0.00 30.99 3.58
920 3543 4.462508 TGGAGATGCTCTAACTGACAAG 57.537 45.455 0.00 0.00 0.00 3.16
925 3548 6.449635 AGATGCTCTAACTGACAAGTCTAG 57.550 41.667 1.53 0.81 34.77 2.43
926 3549 6.184068 AGATGCTCTAACTGACAAGTCTAGA 58.816 40.000 1.53 0.00 34.77 2.43
927 3550 5.630661 TGCTCTAACTGACAAGTCTAGAC 57.369 43.478 15.41 15.41 34.77 2.59
928 3551 5.317808 TGCTCTAACTGACAAGTCTAGACT 58.682 41.667 20.00 20.00 44.94 3.24
1059 3682 0.980423 GCAAGACCCTCCTCAAGAGT 59.020 55.000 0.00 0.00 41.47 3.24
1085 3708 4.884164 GCAGCTCTACCAGGTAAATCAAAT 59.116 41.667 0.00 0.00 0.00 2.32
1099 3722 6.836007 GGTAAATCAAATCCTCCCTCTTGATT 59.164 38.462 3.64 3.64 45.72 2.57
1103 3726 4.479796 TCAAATCCTCCCTCTTGATTCCAT 59.520 41.667 0.00 0.00 0.00 3.41
1152 3775 3.118592 ACTTCCTCGATCCATTTCCTCAC 60.119 47.826 0.00 0.00 0.00 3.51
1171 3794 3.118454 GCCGTCACATGACCACCG 61.118 66.667 0.00 0.00 41.86 4.94
1175 3798 0.999406 CGTCACATGACCACCGATTC 59.001 55.000 0.00 0.00 41.86 2.52
1176 3799 1.369625 GTCACATGACCACCGATTCC 58.630 55.000 0.00 0.00 39.07 3.01
1177 3800 0.251916 TCACATGACCACCGATTCCC 59.748 55.000 0.00 0.00 0.00 3.97
1180 3803 1.618143 ATGACCACCGATTCCCCCA 60.618 57.895 0.00 0.00 0.00 4.96
1184 3807 2.349755 CACCGATTCCCCCAACGT 59.650 61.111 0.00 0.00 0.00 3.99
1282 3908 2.672295 GCGACCCACCCCATGTAA 59.328 61.111 0.00 0.00 0.00 2.41
1285 3911 1.268992 CGACCCACCCCATGTAAGGA 61.269 60.000 0.98 0.00 0.00 3.36
1289 3915 0.478507 CCACCCCATGTAAGGATCCC 59.521 60.000 8.55 0.00 0.00 3.85
1301 3927 1.150081 GGATCCCGTCCGACTCCTA 59.850 63.158 0.00 0.00 37.23 2.94
1310 3936 0.841961 TCCGACTCCTAGGATTCCGA 59.158 55.000 20.32 16.88 0.00 4.55
1311 3937 1.424302 TCCGACTCCTAGGATTCCGAT 59.576 52.381 20.32 0.37 0.00 4.18
1312 3938 1.813786 CCGACTCCTAGGATTCCGATC 59.186 57.143 20.32 7.97 0.00 3.69
1313 3939 2.553466 CCGACTCCTAGGATTCCGATCT 60.553 54.545 20.32 0.00 32.66 2.75
1314 3940 2.745281 CGACTCCTAGGATTCCGATCTC 59.255 54.545 20.32 0.45 32.66 2.75
1315 3941 3.086282 GACTCCTAGGATTCCGATCTCC 58.914 54.545 13.12 0.00 32.66 3.71
1316 3942 2.088423 CTCCTAGGATTCCGATCTCCG 58.912 57.143 13.12 0.00 36.62 4.63
1327 3953 4.832608 ATCTCCGGCGGCGGTTTC 62.833 66.667 43.56 0.00 0.00 2.78
1329 3955 4.137872 CTCCGGCGGCGGTTTCTA 62.138 66.667 43.56 26.89 0.00 2.10
1332 3958 2.510691 CGGCGGCGGTTTCTATGT 60.511 61.111 25.36 0.00 0.00 2.29
1335 3961 1.808390 GCGGCGGTTTCTATGTCGT 60.808 57.895 9.78 0.00 0.00 4.34
1337 3963 1.469126 CGGCGGTTTCTATGTCGTCG 61.469 60.000 0.00 0.00 43.73 5.12
1355 3981 2.929960 TCGTTGCTCGAGTAGTTCTTG 58.070 47.619 15.13 0.00 44.01 3.02
1356 3982 2.292569 TCGTTGCTCGAGTAGTTCTTGT 59.707 45.455 15.13 0.00 44.01 3.16
1357 3983 3.499537 TCGTTGCTCGAGTAGTTCTTGTA 59.500 43.478 15.13 0.00 44.01 2.41
1358 3984 3.602915 CGTTGCTCGAGTAGTTCTTGTAC 59.397 47.826 15.13 0.94 42.86 2.90
1359 3985 3.466712 TGCTCGAGTAGTTCTTGTACG 57.533 47.619 15.13 0.00 0.00 3.67
1360 3986 2.161012 TGCTCGAGTAGTTCTTGTACGG 59.839 50.000 15.13 0.00 0.00 4.02
1361 3987 2.161211 GCTCGAGTAGTTCTTGTACGGT 59.839 50.000 15.13 0.00 0.00 4.83
1373 3999 1.288350 TGTACGGTTGGTGTTTGACG 58.712 50.000 0.00 0.00 0.00 4.35
1524 4150 3.450115 ACCGGGTACTCGCTGCTC 61.450 66.667 10.40 0.00 0.00 4.26
1564 4190 1.444553 GACGACGGCAAGGTCAGAG 60.445 63.158 0.00 0.00 36.73 3.35
1565 4191 2.811317 CGACGGCAAGGTCAGAGC 60.811 66.667 0.00 0.00 36.73 4.09
1569 4195 2.125350 GGCAAGGTCAGAGCTCCG 60.125 66.667 10.93 0.00 0.00 4.63
1587 4213 2.815647 CCGTTCGCTGGCTTCCTC 60.816 66.667 0.00 0.00 0.00 3.71
1588 4214 2.815647 CGTTCGCTGGCTTCCTCC 60.816 66.667 0.00 0.00 0.00 4.30
1589 4215 2.665603 GTTCGCTGGCTTCCTCCT 59.334 61.111 0.00 0.00 0.00 3.69
1635 4261 4.821805 CCATTGTCTTTGACCTGTGTTACT 59.178 41.667 0.00 0.00 0.00 2.24
1648 4274 5.047590 ACCTGTGTTACTATGTCGTTGATGA 60.048 40.000 0.00 0.00 0.00 2.92
1663 4289 0.392998 GATGACAGGTCGTGGCCATT 60.393 55.000 9.72 0.00 29.87 3.16
1671 4297 1.369625 GTCGTGGCCATTGACCTTAG 58.630 55.000 23.62 3.61 0.00 2.18
1789 4415 3.449227 CAGCTGGTCGCCGAGGTA 61.449 66.667 5.57 0.00 40.39 3.08
1843 4470 4.424566 GCGCCCCTGTGTTGCATG 62.425 66.667 0.00 0.00 0.00 4.06
1845 4472 3.304721 GCCCCTGTGTTGCATGCA 61.305 61.111 18.46 18.46 0.00 3.96
1846 4473 2.967397 CCCCTGTGTTGCATGCAG 59.033 61.111 21.50 8.75 0.00 4.41
1847 4474 2.260434 CCCTGTGTTGCATGCAGC 59.740 61.111 25.78 25.78 45.96 5.25
1856 4483 2.328289 GCATGCAGCAGCGAGATG 59.672 61.111 14.21 0.00 46.23 2.90
1859 4486 1.523258 ATGCAGCAGCGAGATGACC 60.523 57.895 0.00 0.00 46.23 4.02
1860 4487 3.260483 GCAGCAGCGAGATGACCG 61.260 66.667 1.59 0.00 35.00 4.79
1861 4488 2.182791 CAGCAGCGAGATGACCGT 59.817 61.111 0.00 0.00 35.00 4.83
1862 4489 2.163390 CAGCAGCGAGATGACCGTG 61.163 63.158 0.00 0.00 35.00 4.94
1863 4490 2.181777 GCAGCGAGATGACCGTGA 59.818 61.111 0.00 0.00 0.00 4.35
1864 4491 1.875813 GCAGCGAGATGACCGTGAG 60.876 63.158 0.00 0.00 0.00 3.51
1865 4492 1.508545 CAGCGAGATGACCGTGAGT 59.491 57.895 0.00 0.00 0.00 3.41
1866 4493 0.109086 CAGCGAGATGACCGTGAGTT 60.109 55.000 0.00 0.00 0.00 3.01
1915 4566 1.082104 GGGCAAGTTTGACTTCGCG 60.082 57.895 0.00 0.00 36.03 5.87
2011 4662 2.716828 CGCCTACGACAACACGCTG 61.717 63.158 0.00 0.00 43.93 5.18
2220 4880 1.131126 CGATGTTGATGTTGGTGCTCC 59.869 52.381 0.00 0.00 0.00 4.70
2226 4886 0.605319 GATGTTGGTGCTCCGTTGGA 60.605 55.000 0.00 0.00 36.30 3.53
2479 5687 0.109723 AAAACCTAACGCCTGGAGCA 59.890 50.000 0.00 0.00 44.04 4.26
2529 5852 3.678072 GTCAACAACGCTTGCATAGACTA 59.322 43.478 0.00 0.00 0.00 2.59
2563 5886 1.364626 GCCCACTTGTCAGCATCTCG 61.365 60.000 0.00 0.00 0.00 4.04
2587 5910 3.641046 CCTCTCTTCATCCCTTCTCTGA 58.359 50.000 0.00 0.00 0.00 3.27
2622 8796 2.329678 CTGACGAGCTCGCCGAAGAT 62.330 60.000 34.83 14.67 44.43 2.40
2737 8962 2.890766 GCCGAGGTCCTGGTTCCAA 61.891 63.158 0.00 0.00 0.00 3.53
2757 8982 0.803117 CTCGGACGAGAAGTAGCACA 59.197 55.000 16.15 0.00 44.53 4.57
2827 9052 0.677288 TCCGTCGACACTCAATGGTT 59.323 50.000 17.16 0.00 0.00 3.67
2836 9061 1.266718 CACTCAATGGTTGTTGTCCCG 59.733 52.381 0.00 0.00 0.00 5.14
2837 9062 0.240945 CTCAATGGTTGTTGTCCCGC 59.759 55.000 0.00 0.00 0.00 6.13
2838 9063 0.466372 TCAATGGTTGTTGTCCCGCA 60.466 50.000 0.00 0.00 0.00 5.69
2839 9064 0.318614 CAATGGTTGTTGTCCCGCAC 60.319 55.000 0.00 0.00 0.00 5.34
2840 9065 1.791103 AATGGTTGTTGTCCCGCACG 61.791 55.000 0.00 0.00 0.00 5.34
2841 9066 3.656045 GGTTGTTGTCCCGCACGG 61.656 66.667 1.02 1.02 0.00 4.94
2842 9067 4.322385 GTTGTTGTCCCGCACGGC 62.322 66.667 2.83 0.00 0.00 5.68
2871 9112 0.981183 ACACGGCCAAACTCCTATCA 59.019 50.000 2.24 0.00 0.00 2.15
2926 9216 2.239654 CCTCATTCCCCTTCACAAGCTA 59.760 50.000 0.00 0.00 0.00 3.32
2931 9221 2.111384 TCCCCTTCACAAGCTAGCTAG 58.889 52.381 19.70 16.84 0.00 3.42
3053 9604 1.740296 CGGGTACAAGGCAGGTTCG 60.740 63.158 0.00 0.00 0.00 3.95
3063 9616 1.079819 GCAGGTTCGCTAGAGTGCA 60.080 57.895 0.00 0.00 32.77 4.57
3093 9677 1.200519 ATAAGGTAGGCTCGTTGGCA 58.799 50.000 0.00 0.00 44.55 4.92
3158 9750 8.277713 GTGATTTGGACTGATGATTTGTTTTTG 58.722 33.333 0.00 0.00 0.00 2.44
3176 9768 2.270352 TGATGAAACTTGAGCCGGTT 57.730 45.000 1.90 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 217 1.553248 CACCTCCGGGAAGTTCATGTA 59.447 52.381 0.00 0.00 36.25 2.29
323 2859 3.624707 GCCATGGGTTCCTTGTTCATCTA 60.625 47.826 15.13 0.00 0.00 1.98
329 2865 2.275380 GCGCCATGGGTTCCTTGTT 61.275 57.895 15.13 0.00 0.00 2.83
332 2868 2.361610 CAGCGCCATGGGTTCCTT 60.362 61.111 15.13 0.00 0.00 3.36
405 2941 3.700350 CCCCCTCTCCACCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
445 2981 3.285215 GCCGGTCCTCGCGATAGA 61.285 66.667 10.36 7.14 37.59 1.98
545 3081 1.672881 CCGATGTCTGAATGAAAGGCC 59.327 52.381 0.00 0.00 0.00 5.19
549 3085 3.118629 CCTCCTCCGATGTCTGAATGAAA 60.119 47.826 0.00 0.00 0.00 2.69
596 3141 3.203412 CCTCGTCGTCCTCCTCCG 61.203 72.222 0.00 0.00 0.00 4.63
630 3175 3.129287 TCCCCTACGATAGACAAAACGAC 59.871 47.826 0.00 0.00 41.38 4.34
638 3187 1.998222 AGCCTTCCCCTACGATAGAC 58.002 55.000 0.00 0.00 41.38 2.59
650 3199 5.872070 GTGCATAGATAGTTCATAGCCTTCC 59.128 44.000 0.00 0.00 0.00 3.46
652 3201 6.678568 AGTGCATAGATAGTTCATAGCCTT 57.321 37.500 0.00 0.00 0.00 4.35
746 3311 7.813627 CCCTTTTCTACTACGATAGATAAAGCC 59.186 40.741 0.00 0.00 41.38 4.35
771 3375 2.348591 GCAGACGCGCTATATTTGTTCC 60.349 50.000 5.73 0.00 0.00 3.62
807 3411 4.081862 AGCAGCCGCCGTAAAATATAGATA 60.082 41.667 0.00 0.00 39.83 1.98
808 3412 3.000727 GCAGCCGCCGTAAAATATAGAT 58.999 45.455 0.00 0.00 0.00 1.98
810 3414 2.157668 CAGCAGCCGCCGTAAAATATAG 59.842 50.000 0.00 0.00 39.83 1.31
811 3415 2.139917 CAGCAGCCGCCGTAAAATATA 58.860 47.619 0.00 0.00 39.83 0.86
814 3418 2.406616 CCAGCAGCCGCCGTAAAAT 61.407 57.895 0.00 0.00 39.83 1.82
850 3457 1.070175 CGGAATCACGAGTTTTTGCGT 60.070 47.619 0.00 0.00 42.11 5.24
863 3470 4.034742 GCTATAAAAGCGTTTCCGGAATCA 59.965 41.667 19.62 0.00 42.53 2.57
864 3471 4.524749 GCTATAAAAGCGTTTCCGGAATC 58.475 43.478 19.62 16.55 42.53 2.52
889 3502 2.764314 GCATCTCCAAATGCGCGGT 61.764 57.895 8.83 0.00 42.33 5.68
896 3509 8.274688 GACTTGTCAGTTAGAGCATCTCCAAAT 61.275 40.741 0.00 0.00 38.09 2.32
918 3541 9.765949 TGCTTCTTCGCAGAAAAGTCTAGACTT 62.766 40.741 28.73 28.73 45.90 3.01
920 3543 4.090786 GCTTCTTCGCAGAAAAGTCTAGAC 59.909 45.833 15.41 15.41 45.90 2.59
925 3548 3.248602 TCTTGCTTCTTCGCAGAAAAGTC 59.751 43.478 8.46 0.00 45.90 3.01
926 3549 3.206150 TCTTGCTTCTTCGCAGAAAAGT 58.794 40.909 8.46 0.00 45.90 2.66
927 3550 3.885484 TCTTGCTTCTTCGCAGAAAAG 57.115 42.857 0.00 1.31 45.90 2.27
928 3551 3.548818 GCTTCTTGCTTCTTCGCAGAAAA 60.549 43.478 0.00 0.00 41.55 2.29
930 3553 1.532868 GCTTCTTGCTTCTTCGCAGAA 59.467 47.619 0.00 0.00 41.55 3.02
932 3555 0.167689 GGCTTCTTGCTTCTTCGCAG 59.832 55.000 0.00 0.00 41.55 5.18
933 3556 0.250467 AGGCTTCTTGCTTCTTCGCA 60.250 50.000 0.00 0.00 42.39 5.10
934 3557 1.726853 TAGGCTTCTTGCTTCTTCGC 58.273 50.000 0.00 0.00 42.39 4.70
935 3558 4.954092 AAATAGGCTTCTTGCTTCTTCG 57.046 40.909 0.00 0.00 42.39 3.79
936 3559 6.259550 TGAAAATAGGCTTCTTGCTTCTTC 57.740 37.500 0.00 0.00 42.39 2.87
937 3560 5.184671 CCTGAAAATAGGCTTCTTGCTTCTT 59.815 40.000 0.00 0.00 42.39 2.52
1026 3649 0.979665 TCTTGCTGTAGAGGCTGCTT 59.020 50.000 0.00 0.00 34.93 3.91
1031 3654 0.176910 GAGGGTCTTGCTGTAGAGGC 59.823 60.000 0.00 0.00 0.00 4.70
1036 3659 1.902508 CTTGAGGAGGGTCTTGCTGTA 59.097 52.381 0.00 0.00 0.00 2.74
1059 3682 2.231716 TTACCTGGTAGAGCTGCTCA 57.768 50.000 29.49 14.02 32.06 4.26
1099 3722 3.682436 CGTGGTGATTTGATCTGGATGGA 60.682 47.826 0.00 0.00 0.00 3.41
1103 3726 1.737838 GCGTGGTGATTTGATCTGGA 58.262 50.000 0.00 0.00 0.00 3.86
1128 3751 3.873952 GAGGAAATGGATCGAGGAAGTTG 59.126 47.826 0.00 0.00 0.00 3.16
1129 3752 3.519510 TGAGGAAATGGATCGAGGAAGTT 59.480 43.478 0.00 0.00 0.00 2.66
1152 3775 2.034879 GGTGGTCATGTGACGGCTG 61.035 63.158 7.03 0.00 45.65 4.85
1171 3794 1.555533 AGAGAAGACGTTGGGGGAATC 59.444 52.381 0.00 0.00 0.00 2.52
1175 3798 1.376037 GCAGAGAAGACGTTGGGGG 60.376 63.158 0.00 0.00 0.00 5.40
1176 3799 1.376037 GGCAGAGAAGACGTTGGGG 60.376 63.158 0.00 0.00 0.00 4.96
1177 3800 1.738099 CGGCAGAGAAGACGTTGGG 60.738 63.158 0.00 0.00 34.68 4.12
1180 3803 1.373497 CTGCGGCAGAGAAGACGTT 60.373 57.895 25.33 0.00 43.41 3.99
1184 3807 1.186200 ATGTACTGCGGCAGAGAAGA 58.814 50.000 34.70 18.15 35.18 2.87
1268 3894 1.222567 GATCCTTACATGGGGTGGGT 58.777 55.000 0.00 0.00 0.00 4.51
1282 3908 1.351080 TAGGAGTCGGACGGGATCCT 61.351 60.000 17.56 17.56 46.69 3.24
1285 3911 1.150992 CCTAGGAGTCGGACGGGAT 59.849 63.158 1.05 0.00 0.00 3.85
1289 3915 0.953003 GGAATCCTAGGAGTCGGACG 59.047 60.000 27.99 0.00 39.77 4.79
1296 3922 2.088423 CGGAGATCGGAATCCTAGGAG 58.912 57.143 18.34 3.33 33.12 3.69
1315 3941 2.510691 ACATAGAAACCGCCGCCG 60.511 61.111 0.00 0.00 0.00 6.46
1316 3942 2.522638 CGACATAGAAACCGCCGCC 61.523 63.158 0.00 0.00 0.00 6.13
1317 3943 1.749609 GACGACATAGAAACCGCCGC 61.750 60.000 0.00 0.00 0.00 6.53
1318 3944 1.469126 CGACGACATAGAAACCGCCG 61.469 60.000 0.00 0.00 0.00 6.46
1319 3945 0.457337 ACGACGACATAGAAACCGCC 60.457 55.000 0.00 0.00 0.00 6.13
1323 3949 2.026507 CGAGCAACGACGACATAGAAAC 59.973 50.000 0.00 0.00 45.77 2.78
1327 3953 1.202043 ACTCGAGCAACGACGACATAG 60.202 52.381 13.61 0.00 46.45 2.23
1329 3955 0.800631 TACTCGAGCAACGACGACAT 59.199 50.000 13.61 0.00 46.45 3.06
1332 3958 0.870393 AACTACTCGAGCAACGACGA 59.130 50.000 13.61 0.00 46.45 4.20
1337 3963 3.602915 CGTACAAGAACTACTCGAGCAAC 59.397 47.826 13.61 0.00 0.00 4.17
1346 3972 3.721035 ACACCAACCGTACAAGAACTAC 58.279 45.455 0.00 0.00 0.00 2.73
1347 3973 4.405116 AACACCAACCGTACAAGAACTA 57.595 40.909 0.00 0.00 0.00 2.24
1348 3974 2.994186 ACACCAACCGTACAAGAACT 57.006 45.000 0.00 0.00 0.00 3.01
1349 3975 3.374678 TCAAACACCAACCGTACAAGAAC 59.625 43.478 0.00 0.00 0.00 3.01
1350 3976 3.374678 GTCAAACACCAACCGTACAAGAA 59.625 43.478 0.00 0.00 0.00 2.52
1351 3977 2.937799 GTCAAACACCAACCGTACAAGA 59.062 45.455 0.00 0.00 0.00 3.02
1352 3978 2.285950 CGTCAAACACCAACCGTACAAG 60.286 50.000 0.00 0.00 0.00 3.16
1353 3979 1.664659 CGTCAAACACCAACCGTACAA 59.335 47.619 0.00 0.00 0.00 2.41
1354 3980 1.288350 CGTCAAACACCAACCGTACA 58.712 50.000 0.00 0.00 0.00 2.90
1355 3981 1.289276 ACGTCAAACACCAACCGTAC 58.711 50.000 0.00 0.00 0.00 3.67
1356 3982 2.021355 AACGTCAAACACCAACCGTA 57.979 45.000 0.00 0.00 0.00 4.02
1357 3983 1.166989 AAACGTCAAACACCAACCGT 58.833 45.000 0.00 0.00 0.00 4.83
1358 3984 1.914700 CAAAACGTCAAACACCAACCG 59.085 47.619 0.00 0.00 0.00 4.44
1359 3985 1.656594 GCAAAACGTCAAACACCAACC 59.343 47.619 0.00 0.00 0.00 3.77
1360 3986 1.656594 GGCAAAACGTCAAACACCAAC 59.343 47.619 0.00 0.00 0.00 3.77
1361 3987 1.404315 GGGCAAAACGTCAAACACCAA 60.404 47.619 0.00 0.00 0.00 3.67
1489 4115 2.181021 GAACACGCCGACCTCGAT 59.819 61.111 0.00 0.00 43.02 3.59
1611 4237 3.297134 ACACAGGTCAAAGACAATGGT 57.703 42.857 0.00 0.00 33.68 3.55
1635 4261 2.490509 ACGACCTGTCATCAACGACATA 59.509 45.455 0.00 0.00 44.61 2.29
1648 4274 1.302511 GTCAATGGCCACGACCTGT 60.303 57.895 21.53 0.00 0.00 4.00
1663 4289 3.064987 GCTCTCGCGGCTAAGGTCA 62.065 63.158 6.13 0.00 0.00 4.02
1828 4455 3.291101 CTGCATGCAACACAGGGGC 62.291 63.158 22.88 0.00 0.00 5.80
1829 4456 2.967397 CTGCATGCAACACAGGGG 59.033 61.111 22.88 3.14 0.00 4.79
1842 4469 2.125391 GGTCATCTCGCTGCTGCA 60.125 61.111 16.29 0.88 39.64 4.41
1843 4470 3.260483 CGGTCATCTCGCTGCTGC 61.260 66.667 5.34 5.34 0.00 5.25
1845 4472 2.182791 CACGGTCATCTCGCTGCT 59.817 61.111 0.00 0.00 0.00 4.24
1846 4473 1.875813 CTCACGGTCATCTCGCTGC 60.876 63.158 0.00 0.00 0.00 5.25
1847 4474 0.109086 AACTCACGGTCATCTCGCTG 60.109 55.000 0.00 0.00 0.00 5.18
1848 4475 0.171455 GAACTCACGGTCATCTCGCT 59.829 55.000 0.00 0.00 0.00 4.93
1849 4476 0.109272 TGAACTCACGGTCATCTCGC 60.109 55.000 0.00 0.00 0.00 5.03
1850 4477 2.188524 CATGAACTCACGGTCATCTCG 58.811 52.381 0.00 0.00 0.00 4.04
1851 4478 2.544685 CCATGAACTCACGGTCATCTC 58.455 52.381 0.00 0.00 0.00 2.75
1853 4480 1.009829 GCCATGAACTCACGGTCATC 58.990 55.000 0.00 0.00 30.68 2.92
1854 4481 0.324614 TGCCATGAACTCACGGTCAT 59.675 50.000 0.00 0.00 30.68 3.06
1855 4482 0.324614 ATGCCATGAACTCACGGTCA 59.675 50.000 0.00 0.00 30.68 4.02
1856 4483 0.729116 CATGCCATGAACTCACGGTC 59.271 55.000 0.00 0.00 30.68 4.79
1859 4486 1.430632 GCCATGCCATGAACTCACG 59.569 57.895 6.18 0.00 0.00 4.35
1871 4498 3.142838 ATCCTGCAACGGCCATGC 61.143 61.111 20.71 20.71 44.08 4.06
1915 4566 2.654912 CTTGTCCGCGTCCACGAAC 61.655 63.158 4.92 0.00 43.02 3.95
2088 4739 3.769358 TGAGCGCCGCGTTAAACG 61.769 61.111 15.34 1.60 45.88 3.60
2220 4880 2.158959 GTGCCGATCGACTCCAACG 61.159 63.158 18.66 0.00 0.00 4.10
2226 4886 1.428219 CAGTACGTGCCGATCGACT 59.572 57.895 18.66 7.95 0.00 4.18
2304 5380 3.067601 GCAATTTATTCCACCCTAACCCG 59.932 47.826 0.00 0.00 0.00 5.28
2367 5542 6.915349 TGAAGAAAAAGAAAACGAAAGGTGA 58.085 32.000 0.00 0.00 0.00 4.02
2432 5640 7.065085 ACTGAAACCACTCTAATTGATCAATCG 59.935 37.037 20.95 14.73 0.00 3.34
2439 5647 7.703328 GTTTTCACTGAAACCACTCTAATTGA 58.297 34.615 3.56 0.00 34.27 2.57
2467 5675 2.372040 TTACACGTGCTCCAGGCGTT 62.372 55.000 17.22 0.00 45.43 4.84
2479 5687 1.933500 GCCACGTCATCACTTACACGT 60.934 52.381 0.00 0.00 46.05 4.49
2529 5852 6.911308 ACAAGTGGGCCTATATCAACTTAAT 58.089 36.000 4.53 0.00 0.00 1.40
2563 5886 0.531753 GAAGGGATGAAGAGAGGCGC 60.532 60.000 0.00 0.00 0.00 6.53
2566 5889 3.384467 GTCAGAGAAGGGATGAAGAGAGG 59.616 52.174 0.00 0.00 0.00 3.69
2587 5910 2.132762 GTCAGTTGTTCGACGGAATGT 58.867 47.619 0.00 0.00 34.05 2.71
2720 8945 1.003718 GTTGGAACCAGGACCTCGG 60.004 63.158 0.00 8.07 0.00 4.63
2737 8962 0.803740 GTGCTACTTCTCGTCCGAGT 59.196 55.000 15.59 1.41 42.49 4.18
2817 9042 1.604604 CGGGACAACAACCATTGAGT 58.395 50.000 0.00 0.00 33.57 3.41
2847 9072 3.521308 GAGTTTGGCCGTGTGTGCG 62.521 63.158 0.00 0.00 0.00 5.34
2848 9073 2.331451 GAGTTTGGCCGTGTGTGC 59.669 61.111 0.00 0.00 0.00 4.57
2849 9074 0.250124 TAGGAGTTTGGCCGTGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
2850 9075 0.690762 ATAGGAGTTTGGCCGTGTGT 59.309 50.000 0.00 0.00 0.00 3.72
2851 9076 1.338674 TGATAGGAGTTTGGCCGTGTG 60.339 52.381 0.00 0.00 0.00 3.82
2926 9216 1.611851 ACTGCAGAGGTGGCTAGCT 60.612 57.895 23.35 0.00 37.35 3.32
2931 9221 2.046507 CAGGACTGCAGAGGTGGC 60.047 66.667 23.35 0.00 0.00 5.01
2933 9223 1.004080 CACCAGGACTGCAGAGGTG 60.004 63.158 23.35 24.84 43.14 4.00
2934 9224 2.888447 GCACCAGGACTGCAGAGGT 61.888 63.158 23.35 18.48 34.56 3.85
3031 9582 2.654877 CTGCCTTGTACCCGTCGT 59.345 61.111 0.00 0.00 0.00 4.34
3032 9583 2.125673 CCTGCCTTGTACCCGTCG 60.126 66.667 0.00 0.00 0.00 5.12
3063 9616 2.138656 CTACCTTATAGCGCCGCCGT 62.139 60.000 4.98 0.00 36.67 5.68
3131 9717 6.653526 AACAAATCATCAGTCCAAATCACA 57.346 33.333 0.00 0.00 0.00 3.58
3158 9750 4.759516 TTTAACCGGCTCAAGTTTCATC 57.240 40.909 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.