Multiple sequence alignment - TraesCS2D01G010000

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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 TraesCS2D01G010000 chr2D 100.000 3700 0 0 2466 6165 5182538 5178839 0.000000e+00 6833.0
1 TraesCS2D01G010000 chr2D 100.000 2066 0 0 1 2066 5185003 5182938 0.000000e+00 3816.0
2 TraesCS2D01G010000 chr2A 96.493 1768 57 5 296 2061 3608385 3610149 0.000000e+00 2916.0
3 TraesCS2D01G010000 chr2A 95.044 1695 43 15 2842 4510 3619365 3621044 0.000000e+00 2627.0
4 TraesCS2D01G010000 chr2A 92.027 1505 89 18 4511 6004 3621073 3622557 0.000000e+00 2085.0
5 TraesCS2D01G010000 chr2A 93.019 1146 74 5 4514 5653 3715664 3716809 0.000000e+00 1668.0
6 TraesCS2D01G010000 chr2A 92.323 977 58 10 2466 3434 3713812 3714779 0.000000e+00 1373.0
7 TraesCS2D01G010000 chr2A 91.667 996 61 12 1 976 3711651 3712644 0.000000e+00 1360.0
8 TraesCS2D01G010000 chr2A 89.242 818 57 11 3466 4263 3714772 3715578 0.000000e+00 994.0
9 TraesCS2D01G010000 chr2A 91.392 697 35 6 1006 1701 3712641 3713313 0.000000e+00 931.0
10 TraesCS2D01G010000 chr2A 97.486 358 7 2 2493 2850 3610374 3610729 1.470000e-170 610.0
11 TraesCS2D01G010000 chr2A 91.781 365 28 2 1698 2062 3713354 3713716 1.980000e-139 507.0
12 TraesCS2D01G010000 chr2A 86.710 459 42 8 5683 6136 3716804 3717248 5.550000e-135 492.0
13 TraesCS2D01G010000 chr2A 96.386 249 8 1 1 249 3608140 3608387 5.750000e-110 409.0
14 TraesCS2D01G010000 chr2A 96.216 185 6 1 4263 4447 66912296 66912113 1.000000e-77 302.0
15 TraesCS2D01G010000 chr2A 92.593 189 12 2 4263 4451 563202202 563202016 2.830000e-68 270.0
16 TraesCS2D01G010000 chr2B 92.865 1808 87 15 2466 4248 6297699 6295909 0.000000e+00 2586.0
17 TraesCS2D01G010000 chr2B 91.282 1732 112 20 1 1701 62208877 62210600 0.000000e+00 2326.0
18 TraesCS2D01G010000 chr2B 92.166 1085 69 5 4514 5596 6295807 6294737 0.000000e+00 1519.0
19 TraesCS2D01G010000 chr2B 91.265 1099 78 11 4677 5770 62213829 62214914 0.000000e+00 1482.0
20 TraesCS2D01G010000 chr2B 89.318 1011 83 10 1 990 6299783 6298777 0.000000e+00 1245.0
21 TraesCS2D01G010000 chr2B 93.165 790 26 16 1280 2066 6298554 6297790 0.000000e+00 1134.0
22 TraesCS2D01G010000 chr2B 89.976 838 61 9 3429 4247 62210979 62211812 0.000000e+00 1061.0
23 TraesCS2D01G010000 chr2B 93.496 246 15 1 1698 1943 62210641 62210885 1.260000e-96 364.0
24 TraesCS2D01G010000 chr2B 94.619 223 10 2 1020 1240 6298776 6298554 1.650000e-90 344.0
25 TraesCS2D01G010000 chr2B 83.924 367 29 6 5770 6136 62333412 62333748 2.140000e-84 324.0
26 TraesCS2D01G010000 chr2B 96.196 184 6 1 4263 4446 63059160 63058978 3.610000e-77 300.0
27 TraesCS2D01G010000 chr2B 95.266 169 8 0 4514 4682 62211915 62212083 1.020000e-67 268.0
28 TraesCS2D01G010000 chr4A 93.782 193 10 2 4260 4451 415467321 415467512 7.820000e-74 289.0
29 TraesCS2D01G010000 chr4A 93.264 193 10 3 4260 4451 733663898 733663708 1.310000e-71 281.0
30 TraesCS2D01G010000 chr7D 93.158 190 11 2 4260 4448 6579899 6580087 1.690000e-70 278.0
31 TraesCS2D01G010000 chr7A 93.122 189 11 2 4260 4448 7666355 7666541 6.090000e-70 276.0
32 TraesCS2D01G010000 chr5A 92.593 189 13 1 4263 4451 431654391 431654204 2.830000e-68 270.0
33 TraesCS2D01G010000 chrUn 88.406 69 8 0 3710 3778 45118860 45118792 3.960000e-12 84.2
34 TraesCS2D01G010000 chr4D 89.394 66 7 0 3710 3775 6759764 6759829 3.960000e-12 84.2
35 TraesCS2D01G010000 chr4D 89.394 66 7 0 3710 3775 123305539 123305604 3.960000e-12 84.2
36 TraesCS2D01G010000 chr4D 89.394 66 7 0 3710 3775 123308681 123308746 3.960000e-12 84.2
37 TraesCS2D01G010000 chr4D 88.406 69 8 0 3710 3778 123459748 123459680 3.960000e-12 84.2


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 TraesCS2D01G010000 chr2D 5178839 5185003 6164 True 5324.500000 6833 100.000000 1 6165 2 chr2D.!!$R1 6164
1 TraesCS2D01G010000 chr2A 3619365 3622557 3192 False 2356.000000 2627 93.535500 2842 6004 2 chr2A.!!$F2 3162
2 TraesCS2D01G010000 chr2A 3608140 3610729 2589 False 1311.666667 2916 96.788333 1 2850 3 chr2A.!!$F1 2849
3 TraesCS2D01G010000 chr2A 3711651 3717248 5597 False 1046.428571 1668 90.876286 1 6136 7 chr2A.!!$F3 6135
4 TraesCS2D01G010000 chr2B 6294737 6299783 5046 True 1365.600000 2586 92.426600 1 5596 5 chr2B.!!$R2 5595
5 TraesCS2D01G010000 chr2B 62208877 62214914 6037 False 1100.200000 2326 92.257000 1 5770 5 chr2B.!!$F2 5769

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
651 679 2.364970 CCCACATTTGTGTCATGGTTGT 59.635 45.455 9.66 0.00 44.21 3.32 F
1489 1531 2.158608 AGCTGAGGTTTGCCAAAGTAGT 60.159 45.455 0.00 0.00 37.19 2.73 F
1781 1867 3.248125 GTCAAACAAATTGCACCCATGTG 59.752 43.478 0.00 0.00 45.65 3.21 F
2682 2772 4.891168 TGTGTGGAGACTACTGTTCAAGTA 59.109 41.667 0.00 0.00 40.56 2.24 F
3950 4109 0.386985 GTGGGAGACGACGTTCTCAC 60.387 60.000 19.87 19.87 45.12 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2107 7.172703 GTGCTACTTTTAGTAGGTGTTGACAAT 59.827 37.037 13.95 0.00 46.31 2.71 R
3065 3160 0.179145 ATACCGGACAAGCGTCTTCG 60.179 55.000 9.46 0.00 42.21 3.79 R
3569 3709 2.236893 TGATGGTGATGCTAGCTTGTCA 59.763 45.455 17.23 14.15 0.00 3.58 R
4020 4179 0.036483 TCACCCACATCATCACCACG 60.036 55.000 0.00 0.00 0.00 4.94 R
5567 7524 0.171007 CAAATCAAGCCCATTCGCGT 59.829 50.000 5.77 0.00 0.00 6.01 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
267 270 3.876914 GACATGTGTCACTTTCCTTGTCA 59.123 43.478 1.15 0.00 44.18 3.58
269 272 4.276678 ACATGTGTCACTTTCCTTGTCATG 59.723 41.667 0.00 0.00 36.99 3.07
389 394 5.977725 GTCAAAACTTTCCCTCTTGTAAAGC 59.022 40.000 0.00 0.00 45.70 3.51
559 584 7.882791 TGAAACATACTCTCTTTCTTGCCATTA 59.117 33.333 0.00 0.00 0.00 1.90
651 679 2.364970 CCCACATTTGTGTCATGGTTGT 59.635 45.455 9.66 0.00 44.21 3.32
821 851 7.277174 TCTGCATATATGTATAGTCATCCGG 57.723 40.000 14.14 0.00 0.00 5.14
1035 1074 4.996758 TCAAGATCTTCATCAAAACGAGCA 59.003 37.500 4.57 0.00 0.00 4.26
1245 1286 6.164408 TGTTGTTATGTAGTCTTGATTGCG 57.836 37.500 0.00 0.00 0.00 4.85
1489 1531 2.158608 AGCTGAGGTTTGCCAAAGTAGT 60.159 45.455 0.00 0.00 37.19 2.73
1504 1546 6.151144 GCCAAAGTAGTTCCAAGACATACAAT 59.849 38.462 0.00 0.00 0.00 2.71
1651 1693 7.201548 CCAATGGCTAAAATTCTTGCATTGTAC 60.202 37.037 0.00 0.00 0.00 2.90
1701 1743 6.161381 GTGAAAGAAAATCTGCCAACATGAT 58.839 36.000 0.00 0.00 0.00 2.45
1781 1867 3.248125 GTCAAACAAATTGCACCCATGTG 59.752 43.478 0.00 0.00 45.65 3.21
2046 2135 5.070714 TCAACACCTACTAAAAGTAGCACCA 59.929 40.000 8.32 0.00 45.21 4.17
2682 2772 4.891168 TGTGTGGAGACTACTGTTCAAGTA 59.109 41.667 0.00 0.00 40.56 2.24
3065 3160 5.382618 AGTCCAATCAAACAATGAAGAGC 57.617 39.130 0.00 0.00 42.54 4.09
3458 3556 8.996651 AGGAAATTCAATATACCTTGTTAGGG 57.003 34.615 0.00 0.00 46.58 3.53
3459 3557 8.787818 AGGAAATTCAATATACCTTGTTAGGGA 58.212 33.333 0.00 0.00 46.58 4.20
3462 3560 9.936329 AAATTCAATATACCTTGTTAGGGATGT 57.064 29.630 0.00 0.00 45.30 3.06
3463 3561 8.924511 ATTCAATATACCTTGTTAGGGATGTG 57.075 34.615 0.00 0.00 45.30 3.21
3464 3562 7.446106 TCAATATACCTTGTTAGGGATGTGT 57.554 36.000 0.00 0.00 45.30 3.72
3465 3563 7.867921 TCAATATACCTTGTTAGGGATGTGTT 58.132 34.615 0.00 0.00 45.30 3.32
3466 3564 8.333235 TCAATATACCTTGTTAGGGATGTGTTT 58.667 33.333 0.00 0.00 45.30 2.83
3467 3565 8.966868 CAATATACCTTGTTAGGGATGTGTTTT 58.033 33.333 0.00 0.00 45.30 2.43
3468 3566 9.541884 AATATACCTTGTTAGGGATGTGTTTTT 57.458 29.630 0.00 0.00 45.30 1.94
3569 3709 7.667219 ACCAAAGATAGAACATGTTGAGTCATT 59.333 33.333 17.58 7.02 0.00 2.57
3828 3969 6.190346 TGGTGTAGGTGTACCATAAAAACT 57.810 37.500 3.56 0.00 41.80 2.66
3829 3970 7.313740 TGGTGTAGGTGTACCATAAAAACTA 57.686 36.000 3.56 0.00 41.80 2.24
3830 3971 7.388437 TGGTGTAGGTGTACCATAAAAACTAG 58.612 38.462 3.56 0.00 41.80 2.57
3831 3972 6.314648 GGTGTAGGTGTACCATAAAAACTAGC 59.685 42.308 3.56 0.00 38.89 3.42
3832 3973 6.314648 GTGTAGGTGTACCATAAAAACTAGCC 59.685 42.308 3.56 0.00 38.89 3.93
3833 3974 5.774102 AGGTGTACCATAAAAACTAGCCT 57.226 39.130 3.56 0.00 38.89 4.58
3834 3975 6.879367 AGGTGTACCATAAAAACTAGCCTA 57.121 37.500 3.56 0.00 38.89 3.93
3835 3976 6.885922 AGGTGTACCATAAAAACTAGCCTAG 58.114 40.000 3.56 0.00 38.89 3.02
3850 4009 2.965831 AGCCTAGAGAATGGTTATGCGA 59.034 45.455 0.00 0.00 0.00 5.10
3895 4054 9.125026 CACCAGAGATTAAATGCTAGGTTTAAT 57.875 33.333 4.14 4.14 41.77 1.40
3950 4109 0.386985 GTGGGAGACGACGTTCTCAC 60.387 60.000 19.87 19.87 45.12 3.51
3999 4158 7.401484 TTCGTCAATCTTAAAATTTTGCACC 57.599 32.000 13.76 0.00 0.00 5.01
4020 4179 3.496870 CCATGGTATTCAGTAGGCCCTTC 60.497 52.174 2.57 0.00 0.00 3.46
4179 4338 3.259374 ACTCAGTCACTCACATTGGTAGG 59.741 47.826 0.00 0.00 0.00 3.18
4248 4408 5.559427 TGTCACATTTTGATATCAACGGG 57.441 39.130 17.76 10.54 36.32 5.28
4251 4411 6.207614 TGTCACATTTTGATATCAACGGGAAA 59.792 34.615 17.76 9.52 36.32 3.13
4363 4524 1.373435 CAAGTGGCGACCCTGGTTA 59.627 57.895 0.00 0.00 0.00 2.85
4384 4545 8.511465 GGTTAAGAGAAACCGAAAATTTAACC 57.489 34.615 6.97 6.97 39.62 2.85
4417 4578 4.023107 GCTTCTTTTGTTTCTGTCCCTACC 60.023 45.833 0.00 0.00 0.00 3.18
4421 4582 4.781775 TTTGTTTCTGTCCCTACCTTCA 57.218 40.909 0.00 0.00 0.00 3.02
4510 4671 1.369692 CTAGTGTGTGCCCCGAACA 59.630 57.895 0.00 0.00 0.00 3.18
4511 4672 0.670546 CTAGTGTGTGCCCCGAACAG 60.671 60.000 0.00 0.00 0.00 3.16
4512 4673 1.404479 TAGTGTGTGCCCCGAACAGT 61.404 55.000 0.00 0.00 0.00 3.55
4571 4760 2.264813 CATTTGCCAACATGCTGCTAC 58.735 47.619 0.00 0.00 0.00 3.58
4632 4821 8.514594 TCCAAGCTACATTCAGTTCTTTATTTG 58.485 33.333 0.00 0.00 0.00 2.32
4648 4837 6.823182 TCTTTATTTGCTGCTAAGATGCACTA 59.177 34.615 0.00 0.00 38.12 2.74
4825 6768 1.814394 TGCACCAAGCTGATTCATGTC 59.186 47.619 0.00 0.00 45.94 3.06
4851 6794 9.770503 CTCAAGAATCAATATATAGTTGCATGC 57.229 33.333 11.82 11.82 0.00 4.06
4852 6795 9.287373 TCAAGAATCAATATATAGTTGCATGCA 57.713 29.630 18.46 18.46 0.00 3.96
4902 6845 4.616604 CGATTTCTTCACATTGCACACCAT 60.617 41.667 0.00 0.00 0.00 3.55
4903 6846 3.646611 TTCTTCACATTGCACACCATG 57.353 42.857 0.00 0.00 0.00 3.66
4923 6866 3.401182 TGATTTTGCAAACATCAAGGCC 58.599 40.909 23.13 0.00 0.00 5.19
5154 7102 0.322816 GCAGGGAGCCAAGATGAACA 60.323 55.000 0.00 0.00 37.23 3.18
5258 7206 8.099364 ACTCGATGTGTTAGTCATTTCAATTT 57.901 30.769 0.00 0.00 0.00 1.82
5479 7428 8.109705 TGTTATTTATTGGATGCGATTGCTAT 57.890 30.769 6.47 0.00 43.34 2.97
5567 7524 2.988688 GCCGCGAAAAAGGATGGCA 61.989 57.895 8.23 0.00 42.03 4.92
5569 7526 1.511887 CGCGAAAAAGGATGGCACG 60.512 57.895 0.00 0.00 0.00 5.34
5571 7528 1.511887 CGAAAAAGGATGGCACGCG 60.512 57.895 3.53 3.53 0.00 6.01
5586 7543 0.171007 ACGCGAATGGGCTTGATTTG 59.829 50.000 15.93 0.00 0.00 2.32
5670 7629 5.446473 CGGTCAATCAGAAGCAATACACTTC 60.446 44.000 0.00 0.00 43.16 3.01
5748 7708 4.081030 CAAGTGCGCAGTGCTCCG 62.081 66.667 20.39 1.47 46.63 4.63
5771 7736 6.150474 CCGAAATTTCTGGTGGTACAAACTAT 59.850 38.462 15.92 0.00 44.16 2.12
5778 7743 8.556213 TTCTGGTGGTACAAACTATATTTCAC 57.444 34.615 0.00 0.00 44.16 3.18
5906 7871 6.183360 CCAATCTTTGAACAATGAATTCTGCG 60.183 38.462 7.05 0.00 0.00 5.18
5950 7915 4.583426 TCAAACAAACACGAGAATGTTCG 58.417 39.130 7.98 0.00 42.01 3.95
5955 7920 5.025826 ACAAACACGAGAATGTTCGAAAAC 58.974 37.500 0.00 0.00 42.01 2.43
6004 7969 2.196595 TCCTGGCTGCCAAATACTACT 58.803 47.619 23.51 0.00 30.80 2.57
6005 7970 3.380393 TCCTGGCTGCCAAATACTACTA 58.620 45.455 23.51 0.00 30.80 1.82
6006 7971 3.388024 TCCTGGCTGCCAAATACTACTAG 59.612 47.826 23.51 6.54 30.80 2.57
6008 7973 4.372656 CTGGCTGCCAAATACTACTAGAC 58.627 47.826 23.51 0.00 30.80 2.59
6010 7975 4.408921 TGGCTGCCAAATACTACTAGACAT 59.591 41.667 21.08 0.00 0.00 3.06
6011 7976 4.991687 GGCTGCCAAATACTACTAGACATC 59.008 45.833 15.17 0.00 0.00 3.06
6012 7977 4.991687 GCTGCCAAATACTACTAGACATCC 59.008 45.833 0.00 0.00 0.00 3.51
6013 7978 5.221541 GCTGCCAAATACTACTAGACATCCT 60.222 44.000 0.00 0.00 0.00 3.24
6014 7979 6.686632 GCTGCCAAATACTACTAGACATCCTT 60.687 42.308 0.00 0.00 0.00 3.36
6015 7980 6.817184 TGCCAAATACTACTAGACATCCTTC 58.183 40.000 0.00 0.00 0.00 3.46
6024 7989 7.863722 ACTACTAGACATCCTTCAGTCTTCTA 58.136 38.462 0.00 0.00 42.12 2.10
6056 8021 3.436704 TGTCAAAATCGAAGCATCCAGTC 59.563 43.478 0.00 0.00 0.00 3.51
6085 8050 6.655078 ACCTGCTGAATTTTTCTACATTGT 57.345 33.333 0.00 0.00 0.00 2.71
6102 8067 0.603065 TGTGTCTCATCGACCACCTG 59.397 55.000 0.00 0.00 42.13 4.00
6129 8094 4.364415 AAAACAAGCTACGCAAACTTCA 57.636 36.364 0.00 0.00 0.00 3.02
6136 8101 6.090898 ACAAGCTACGCAAACTTCAAGTATAG 59.909 38.462 0.00 0.00 0.00 1.31
6137 8102 5.109903 AGCTACGCAAACTTCAAGTATAGG 58.890 41.667 0.00 0.00 0.00 2.57
6138 8103 5.105473 AGCTACGCAAACTTCAAGTATAGGA 60.105 40.000 0.00 0.00 0.00 2.94
6139 8104 5.579511 GCTACGCAAACTTCAAGTATAGGAA 59.420 40.000 0.00 0.00 0.00 3.36
6140 8105 6.091713 GCTACGCAAACTTCAAGTATAGGAAA 59.908 38.462 0.00 0.00 0.00 3.13
6141 8106 6.870971 ACGCAAACTTCAAGTATAGGAAAA 57.129 33.333 0.00 0.00 0.00 2.29
6142 8107 7.266922 ACGCAAACTTCAAGTATAGGAAAAA 57.733 32.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 270 6.263842 TGAACTTTCATGTGAAAAGCTCTCAT 59.736 34.615 9.24 0.00 42.72 2.90
269 272 6.017605 TCTGAACTTTCATGTGAAAAGCTCTC 60.018 38.462 9.24 0.00 42.72 3.20
343 348 8.034313 TGACTAACTGAGCCATTTTAGGATAT 57.966 34.615 0.00 0.00 0.00 1.63
365 370 5.977725 GCTTTACAAGAGGGAAAGTTTTGAC 59.022 40.000 1.42 0.00 33.58 3.18
1035 1074 4.281688 CCCATCTTCATGACCAACAACTTT 59.718 41.667 0.00 0.00 30.57 2.66
1119 1159 5.983540 TGTTTGTTGGTGCCTAAAAGATTT 58.016 33.333 0.00 0.00 0.00 2.17
1651 1693 9.828220 CACATTTTTGTAATGTTTTCGTGTTAG 57.172 29.630 0.64 0.00 38.69 2.34
1781 1867 7.928706 ACTACTTCATAAACCATCTACATGCTC 59.071 37.037 0.00 0.00 0.00 4.26
2018 2107 7.172703 GTGCTACTTTTAGTAGGTGTTGACAAT 59.827 37.037 13.95 0.00 46.31 2.71
2853 2943 8.461222 TGGATTTATGTGCTGAATTCTAAGTTG 58.539 33.333 7.05 0.00 0.00 3.16
3065 3160 0.179145 ATACCGGACAAGCGTCTTCG 60.179 55.000 9.46 0.00 42.21 3.79
3249 3345 9.868277 AAAGTGATGTATCTTTGTTTTGACAAA 57.132 25.926 0.00 0.00 37.90 2.83
3432 3530 9.421399 CCCTAACAAGGTATATTGAATTTCCTT 57.579 33.333 0.00 0.00 35.97 3.36
3433 3531 8.787818 TCCCTAACAAGGTATATTGAATTTCCT 58.212 33.333 0.00 0.00 34.20 3.36
3434 3532 8.990163 TCCCTAACAAGGTATATTGAATTTCC 57.010 34.615 0.00 0.00 34.20 3.13
3436 3534 9.936329 ACATCCCTAACAAGGTATATTGAATTT 57.064 29.630 0.00 0.00 34.20 1.82
3437 3535 9.354673 CACATCCCTAACAAGGTATATTGAATT 57.645 33.333 0.00 0.00 34.20 2.17
3438 3536 8.502738 ACACATCCCTAACAAGGTATATTGAAT 58.497 33.333 0.00 0.00 34.20 2.57
3439 3537 7.867921 ACACATCCCTAACAAGGTATATTGAA 58.132 34.615 0.00 0.00 34.20 2.69
3440 3538 7.446106 ACACATCCCTAACAAGGTATATTGA 57.554 36.000 0.00 0.00 34.20 2.57
3441 3539 8.519799 AAACACATCCCTAACAAGGTATATTG 57.480 34.615 0.00 0.00 36.22 1.90
3442 3540 9.541884 AAAAACACATCCCTAACAAGGTATATT 57.458 29.630 0.00 0.00 0.00 1.28
3466 3564 5.685520 AGGTTTTGCCTCTGGTTTAAAAA 57.314 34.783 0.00 0.00 46.96 1.94
3493 3631 7.581213 TGTTGGTCTCAATTAGTGAAACAAT 57.419 32.000 0.00 0.00 35.42 2.71
3569 3709 2.236893 TGATGGTGATGCTAGCTTGTCA 59.763 45.455 17.23 14.15 0.00 3.58
3828 3969 4.149598 TCGCATAACCATTCTCTAGGCTA 58.850 43.478 0.00 0.00 0.00 3.93
3829 3970 2.965831 TCGCATAACCATTCTCTAGGCT 59.034 45.455 0.00 0.00 0.00 4.58
3830 3971 3.243907 ACTCGCATAACCATTCTCTAGGC 60.244 47.826 0.00 0.00 0.00 3.93
3831 3972 4.302455 CACTCGCATAACCATTCTCTAGG 58.698 47.826 0.00 0.00 0.00 3.02
3832 3973 4.202161 ACCACTCGCATAACCATTCTCTAG 60.202 45.833 0.00 0.00 0.00 2.43
3833 3974 3.704566 ACCACTCGCATAACCATTCTCTA 59.295 43.478 0.00 0.00 0.00 2.43
3834 3975 2.501723 ACCACTCGCATAACCATTCTCT 59.498 45.455 0.00 0.00 0.00 3.10
3835 3976 2.906354 ACCACTCGCATAACCATTCTC 58.094 47.619 0.00 0.00 0.00 2.87
3883 4042 4.286032 AGACACTGGACATTAAACCTAGCA 59.714 41.667 0.00 0.00 0.00 3.49
3884 4043 4.833390 AGACACTGGACATTAAACCTAGC 58.167 43.478 0.00 0.00 0.00 3.42
3895 4054 3.005472 CCTCTTTAACGAGACACTGGACA 59.995 47.826 10.40 0.00 32.74 4.02
3950 4109 2.159043 ACCACAGACGCCTCATTATCTG 60.159 50.000 0.00 0.00 43.47 2.90
3999 4158 3.744660 GAAGGGCCTACTGAATACCATG 58.255 50.000 6.41 0.00 0.00 3.66
4020 4179 0.036483 TCACCCACATCATCACCACG 60.036 55.000 0.00 0.00 0.00 4.94
4179 4338 1.002792 GAGAAGCCAAACCAACACGTC 60.003 52.381 0.00 0.00 0.00 4.34
4341 4502 3.168528 AGGGTCGCCACTTGTGGT 61.169 61.111 19.47 0.00 0.00 4.16
4363 4524 6.700081 GCTTGGTTAAATTTTCGGTTTCTCTT 59.300 34.615 0.00 0.00 0.00 2.85
4417 4578 7.927048 TGAAGCATGTGATATCATCTTTGAAG 58.073 34.615 9.02 0.00 34.96 3.02
4421 4582 9.582431 CTTTTTGAAGCATGTGATATCATCTTT 57.418 29.630 9.02 0.16 0.00 2.52
4510 4671 8.035984 GCTAGATACAAAAGGACTAGTTTGACT 58.964 37.037 11.14 9.33 37.98 3.41
4511 4672 7.009357 CGCTAGATACAAAAGGACTAGTTTGAC 59.991 40.741 11.14 3.87 37.98 3.18
4512 4673 7.033791 CGCTAGATACAAAAGGACTAGTTTGA 58.966 38.462 11.14 0.00 37.98 2.69
4632 4821 7.224362 CCATTAGATATAGTGCATCTTAGCAGC 59.776 40.741 0.00 0.00 46.69 5.25
4648 4837 7.465116 AGCCAATAGAACAAGCCATTAGATAT 58.535 34.615 0.00 0.00 0.00 1.63
4779 6721 6.731467 AGACCCCAATGAATTATGTACAGTT 58.269 36.000 0.33 0.00 0.00 3.16
4825 6768 9.770503 GCATGCAACTATATATTGATTCTTGAG 57.229 33.333 14.21 0.00 0.00 3.02
4851 6794 7.017055 GCAAAAATAATTAACAAAGCAGGCTG 58.983 34.615 10.94 10.94 0.00 4.85
4852 6795 6.149308 GGCAAAAATAATTAACAAAGCAGGCT 59.851 34.615 0.00 0.00 0.00 4.58
4902 6845 3.071312 AGGCCTTGATGTTTGCAAAATCA 59.929 39.130 22.25 22.25 0.00 2.57
4903 6846 3.667360 AGGCCTTGATGTTTGCAAAATC 58.333 40.909 14.67 17.62 0.00 2.17
5154 7102 1.084370 GCCAGCTGATTACTCGCGTT 61.084 55.000 17.39 0.00 0.00 4.84
5258 7206 6.413783 TGGACTTGTAGTGTCACTTATTGA 57.586 37.500 11.54 0.00 36.26 2.57
5479 7428 6.442952 AGCGCATAAACATACTTCAAAAACA 58.557 32.000 11.47 0.00 0.00 2.83
5519 7474 8.778358 GTTCATGACCTTCTCAAATATATGGAC 58.222 37.037 0.00 0.00 30.60 4.02
5567 7524 0.171007 CAAATCAAGCCCATTCGCGT 59.829 50.000 5.77 0.00 0.00 6.01
5569 7526 0.817013 TCCAAATCAAGCCCATTCGC 59.183 50.000 0.00 0.00 0.00 4.70
5571 7528 3.515104 TCCTTTCCAAATCAAGCCCATTC 59.485 43.478 0.00 0.00 0.00 2.67
5599 7556 4.715527 AGAGTATAAACGGTGTGGAGTC 57.284 45.455 0.00 0.00 0.00 3.36
5601 7558 6.446781 TTCTAGAGTATAAACGGTGTGGAG 57.553 41.667 0.00 0.00 0.00 3.86
5602 7559 6.839124 TTTCTAGAGTATAAACGGTGTGGA 57.161 37.500 0.00 0.00 0.00 4.02
5670 7629 0.320946 CTTTGGCCTTGCATGGTTGG 60.321 55.000 19.05 3.55 0.00 3.77
5712 7671 7.147976 GCACTTGGATCAGTGTTTTTATTTCT 58.852 34.615 13.14 0.00 45.31 2.52
5716 7675 4.615912 GCGCACTTGGATCAGTGTTTTTAT 60.616 41.667 0.30 0.00 45.31 1.40
5717 7676 3.304391 GCGCACTTGGATCAGTGTTTTTA 60.304 43.478 0.30 0.00 45.31 1.52
5786 7751 7.995289 TCGTTAGAAATTTGGCATATGACAAT 58.005 30.769 24.42 10.25 43.55 2.71
5849 7814 7.453126 CCCTACTTCTCCATATATCTGAACTGT 59.547 40.741 0.00 0.00 0.00 3.55
5906 7871 6.494842 TGAACTTGTCAGTGCTTGTTAATTC 58.505 36.000 0.00 0.00 31.60 2.17
5950 7915 6.357240 GCTGTCGTTCTAGTGATTTTGTTTTC 59.643 38.462 0.00 0.00 0.00 2.29
5955 7920 6.893958 ATAGCTGTCGTTCTAGTGATTTTG 57.106 37.500 0.00 0.00 0.00 2.44
6004 7969 6.722328 TGTCTAGAAGACTGAAGGATGTCTA 58.278 40.000 8.42 0.00 45.27 2.59
6005 7970 5.575157 TGTCTAGAAGACTGAAGGATGTCT 58.425 41.667 8.42 0.00 45.27 3.41
6006 7971 5.906113 TGTCTAGAAGACTGAAGGATGTC 57.094 43.478 8.42 0.00 45.27 3.06
6008 7973 5.598005 AGGATGTCTAGAAGACTGAAGGATG 59.402 44.000 8.42 0.00 45.27 3.51
6010 7975 5.199982 AGGATGTCTAGAAGACTGAAGGA 57.800 43.478 8.42 0.00 45.27 3.36
6011 7976 5.930837 AAGGATGTCTAGAAGACTGAAGG 57.069 43.478 8.42 0.00 45.27 3.46
6012 7977 6.696411 ACAAAGGATGTCTAGAAGACTGAAG 58.304 40.000 8.42 0.00 45.27 3.02
6013 7978 6.672266 ACAAAGGATGTCTAGAAGACTGAA 57.328 37.500 8.42 0.00 45.27 3.02
6064 8029 7.365741 AGACACAATGTAGAAAAATTCAGCAG 58.634 34.615 0.00 0.00 0.00 4.24
6065 8030 7.013178 TGAGACACAATGTAGAAAAATTCAGCA 59.987 33.333 0.00 0.00 0.00 4.41
6066 8031 7.362662 TGAGACACAATGTAGAAAAATTCAGC 58.637 34.615 0.00 0.00 0.00 4.26
6067 8032 9.552114 GATGAGACACAATGTAGAAAAATTCAG 57.448 33.333 0.00 0.00 0.00 3.02
6068 8033 8.229811 CGATGAGACACAATGTAGAAAAATTCA 58.770 33.333 0.00 0.00 0.00 2.57
6070 8035 8.322906 TCGATGAGACACAATGTAGAAAAATT 57.677 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.