Multiple sequence alignment - TraesCS5D01G027700

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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 TraesCS5D01G027700 chr5D 100.000 4871 0 0 1 4871 25312595 25307725 0.000000e+00 8996.0
1 TraesCS5D01G027700 chr5D 92.063 126 8 1 3894 4019 25308502 25308379 5.010000e-40 176.0
2 TraesCS5D01G027700 chr5D 92.063 126 8 1 4094 4217 25308702 25308577 5.010000e-40 176.0
3 TraesCS5D01G027700 chr5D 88.976 127 11 1 4233 4356 246865609 246865735 2.350000e-33 154.0
4 TraesCS5D01G027700 chr5A 94.289 4535 121 42 1 4466 17829268 17833733 0.000000e+00 6813.0
5 TraesCS5D01G027700 chr5A 91.270 126 9 1 4094 4217 17833150 17833275 2.330000e-38 171.0
6 TraesCS5D01G027700 chr5A 97.778 90 2 0 3651 3740 504543200 504543289 6.530000e-34 156.0
7 TraesCS5D01G027700 chr5A 90.196 102 10 0 3958 4059 17833396 17833497 3.060000e-27 134.0
8 TraesCS5D01G027700 chr5B 90.648 2160 104 49 497 2604 17970875 17972988 0.000000e+00 2780.0
9 TraesCS5D01G027700 chr5B 96.877 1441 42 3 2599 4037 17973021 17974460 0.000000e+00 2409.0
10 TraesCS5D01G027700 chr5B 90.625 512 41 4 1 506 17970278 17970788 0.000000e+00 673.0
11 TraesCS5D01G027700 chr5B 86.697 436 27 16 4438 4869 17974584 17974992 5.750000e-124 455.0
12 TraesCS5D01G027700 chr5B 91.824 318 20 4 3776 4090 69574319 69574005 5.790000e-119 438.0
13 TraesCS5D01G027700 chr5B 83.333 438 30 7 4232 4635 69573989 69573561 9.960000e-97 364.0
14 TraesCS5D01G027700 chr5B 90.551 127 9 2 4094 4217 17974315 17974441 1.080000e-36 165.0
15 TraesCS5D01G027700 chr5B 96.703 91 3 0 3650 3740 192087464 192087554 8.440000e-33 152.0
16 TraesCS5D01G027700 chr6B 91.304 161 11 1 4232 4392 642296835 642296678 2.950000e-52 217.0
17 TraesCS5D01G027700 chr6B 96.703 91 3 0 3650 3740 183060521 183060431 8.440000e-33 152.0
18 TraesCS5D01G027700 chr6B 93.407 91 6 0 3650 3740 635775273 635775363 8.500000e-28 135.0
19 TraesCS5D01G027700 chr6B 93.407 91 5 1 3650 3739 430964599 430964509 3.060000e-27 134.0
20 TraesCS5D01G027700 chr6B 96.154 78 3 0 3714 3791 642297155 642297078 1.420000e-25 128.0
21 TraesCS5D01G027700 chr3D 92.126 127 7 1 4233 4356 120527397 120527523 5.010000e-40 176.0
22 TraesCS5D01G027700 chrUn 89.764 127 9 2 4233 4356 379040833 379040708 5.050000e-35 159.0
23 TraesCS5D01G027700 chrUn 91.304 69 2 2 4324 4392 3908015 3908079 1.870000e-14 91.6
24 TraesCS5D01G027700 chr4A 89.764 127 9 2 4233 4356 635820928 635820803 5.050000e-35 159.0
25 TraesCS5D01G027700 chr2B 89.764 127 9 2 4233 4356 758940713 758940588 5.050000e-35 159.0
26 TraesCS5D01G027700 chr2B 98.113 53 1 0 3651 3703 702038712 702038764 5.190000e-15 93.5
27 TraesCS5D01G027700 chr6D 88.550 131 11 2 4233 4360 430741275 430741146 6.530000e-34 156.0
28 TraesCS5D01G027700 chr1B 93.407 91 6 0 3650 3740 128745595 128745685 8.500000e-28 135.0
29 TraesCS5D01G027700 chr1B 89.855 69 3 2 4324 4392 90855434 90855498 8.690000e-13 86.1
30 TraesCS5D01G027700 chr1D 94.286 35 1 1 1 34 328862981 328863015 9.000000e-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 TraesCS5D01G027700 chr5D 25307725 25312595 4870 True 8996.000000 8996 100.000000 1 4871 1 chr5D.!!$R1 4870
1 TraesCS5D01G027700 chr5A 17829268 17833733 4465 False 2372.666667 6813 91.918333 1 4466 3 chr5A.!!$F2 4465
2 TraesCS5D01G027700 chr5B 17970278 17974992 4714 False 1296.400000 2780 91.079600 1 4869 5 chr5B.!!$F2 4868
3 TraesCS5D01G027700 chr5B 69573561 69574319 758 True 401.000000 438 87.578500 3776 4635 2 chr5B.!!$R1 859

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
183 184 0.393267 CGCTCCGGATGGGGTTTTTA 60.393 55.0 3.57 0.0 38.38 1.52 F
729 837 0.729140 GGCAACCGACGAAAGCATTG 60.729 55.0 0.00 0.0 0.00 2.82 F
1300 1439 0.603975 GTCTTCTGGGTTGCGCTTCT 60.604 55.0 9.73 0.0 0.00 2.85 F
1373 1530 1.232909 TGGGGGTTTAGGTTGGTTCA 58.767 50.0 0.00 0.0 0.00 3.18 F
2750 2989 1.323412 CATCCTACCCTGTCTCCGAG 58.677 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1300 1439 2.023673 CCCGCAAAATATTCCTCTGCA 58.976 47.619 10.53 0.00 33.19 4.41 R
2661 2900 1.534595 GCTGTCTTCACTTTCCTGCAG 59.465 52.381 6.78 6.78 0.00 4.41 R
3039 3278 3.056465 TGGTTGGAGTTGGACAAACAAAC 60.056 43.478 0.00 6.52 40.96 2.93 R
3320 3559 4.696877 TCCTCGTTCACATACGTCTTCTTA 59.303 41.667 0.00 0.00 42.01 2.10 R
4638 4993 0.106708 TGTCTGTGTCTGAACCTGCC 59.893 55.000 0.00 0.00 0.00 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 1.009222 GGGTGGTATAGCGACGACG 60.009 63.158 2.12 2.12 42.93 5.12
183 184 0.393267 CGCTCCGGATGGGGTTTTTA 60.393 55.000 3.57 0.00 38.38 1.52
195 196 1.258676 GGTTTTTATGGGGGTTGCGA 58.741 50.000 0.00 0.00 0.00 5.10
283 284 3.551551 AGTAGAATTTTGAAACACGCGC 58.448 40.909 5.73 0.00 0.00 6.86
327 329 1.135972 GCATGACGTTGGATGACACAC 60.136 52.381 0.00 0.00 0.00 3.82
451 459 3.615056 CGTATGAGATACAAAACCGCACA 59.385 43.478 0.00 0.00 35.48 4.57
453 461 5.220586 CGTATGAGATACAAAACCGCACAAT 60.221 40.000 0.00 0.00 35.48 2.71
544 648 7.202526 TCAACAAATTCTCTTTGCTTAACCTG 58.797 34.615 0.00 0.00 32.93 4.00
581 686 4.467795 TCTCCCTCAAGATAAACCTCACAG 59.532 45.833 0.00 0.00 0.00 3.66
592 697 7.675062 AGATAAACCTCACAGTATCATCATCC 58.325 38.462 0.00 0.00 0.00 3.51
708 816 4.530553 ACTTTCCTTTTTGAACCCTGTTGT 59.469 37.500 0.00 0.00 0.00 3.32
710 818 2.763448 TCCTTTTTGAACCCTGTTGTGG 59.237 45.455 0.00 0.00 0.00 4.17
727 835 3.263941 GGCAACCGACGAAAGCAT 58.736 55.556 0.00 0.00 0.00 3.79
728 836 1.579429 GGCAACCGACGAAAGCATT 59.421 52.632 0.00 0.00 0.00 3.56
729 837 0.729140 GGCAACCGACGAAAGCATTG 60.729 55.000 0.00 0.00 0.00 2.82
778 891 1.821136 CCTCAGGGCTAAGCAAAAAGG 59.179 52.381 0.00 0.00 0.00 3.11
798 911 1.140852 GGGCAAAGAGGGCAACTTTTT 59.859 47.619 5.62 0.00 35.74 1.94
816 929 4.432741 GCTGGGCCTTGTCCTCCC 62.433 72.222 4.53 0.00 40.47 4.30
818 931 2.451493 TGGGCCTTGTCCTCCCAA 60.451 61.111 4.53 0.00 46.35 4.12
961 1087 4.150454 CTCCCTCCCCTCCGCTCT 62.150 72.222 0.00 0.00 0.00 4.09
962 1088 4.144727 TCCCTCCCCTCCGCTCTC 62.145 72.222 0.00 0.00 0.00 3.20
963 1089 4.150454 CCCTCCCCTCCGCTCTCT 62.150 72.222 0.00 0.00 0.00 3.10
964 1090 2.042435 CCTCCCCTCCGCTCTCTT 60.042 66.667 0.00 0.00 0.00 2.85
965 1091 2.131067 CCTCCCCTCCGCTCTCTTC 61.131 68.421 0.00 0.00 0.00 2.87
966 1092 2.042843 TCCCCTCCGCTCTCTTCC 60.043 66.667 0.00 0.00 0.00 3.46
983 1109 4.058731 TCTTCCCCTCTCTATCTCCTCTT 58.941 47.826 0.00 0.00 0.00 2.85
1287 1426 5.319453 TGAATGCTTTCTTGGATGTCTTCT 58.681 37.500 12.96 0.00 32.78 2.85
1299 1438 0.884704 TGTCTTCTGGGTTGCGCTTC 60.885 55.000 9.73 0.76 0.00 3.86
1300 1439 0.603975 GTCTTCTGGGTTGCGCTTCT 60.604 55.000 9.73 0.00 0.00 2.85
1373 1530 1.232909 TGGGGGTTTAGGTTGGTTCA 58.767 50.000 0.00 0.00 0.00 3.18
1457 1614 4.580167 TCCTCTTGAATGTTTGGAACACAG 59.420 41.667 0.00 0.00 45.50 3.66
1598 1764 5.080337 GGAGGGAAGAGGTTTTCAATTTCT 58.920 41.667 0.00 0.00 0.00 2.52
1599 1765 5.540337 GGAGGGAAGAGGTTTTCAATTTCTT 59.460 40.000 0.00 0.00 0.00 2.52
1600 1766 6.294787 GGAGGGAAGAGGTTTTCAATTTCTTC 60.295 42.308 5.57 5.57 41.74 2.87
1627 1793 3.987954 AATGGTAACTGCCGCCCGG 62.988 63.158 1.59 1.59 36.23 5.73
1676 1843 5.163457 CCGTGCAATAATTGTTTTATCCCCT 60.163 40.000 0.00 0.00 0.00 4.79
1751 1921 8.301720 GGAAAAGTATTTATGTTTCCCTTTCGT 58.698 33.333 3.16 0.00 42.07 3.85
1819 2004 4.273235 TCAATGTCGATGTGCATATGTTCC 59.727 41.667 0.00 0.00 0.00 3.62
1919 2104 6.093082 TGCAAGATTGTGACAGAGATATTGTG 59.907 38.462 5.38 0.00 0.00 3.33
2299 2492 1.899617 CGAATGCCCCCAAAGCAAT 59.100 52.632 0.00 0.00 44.83 3.56
2438 2638 7.321153 TGTTACTCCATACTTCTACTCTTTGC 58.679 38.462 0.00 0.00 0.00 3.68
2750 2989 1.323412 CATCCTACCCTGTCTCCGAG 58.677 60.000 0.00 0.00 0.00 4.63
3039 3278 1.878522 GCGGTGATGAGGTGTAGCG 60.879 63.158 0.00 0.00 37.13 4.26
3320 3559 2.297129 GCAGGGCAAGAGGAGGACT 61.297 63.158 0.00 0.00 0.00 3.85
3763 4002 6.042208 AGTTGAAACTCCTTGTTAGCTCTAGT 59.958 38.462 0.00 0.00 38.03 2.57
3846 4085 6.493458 GGTTGGTTGATACAATATTATGCCCT 59.507 38.462 0.00 0.00 0.00 5.19
4096 4338 6.294731 GCATCTAAAAACACTGGATCAGGTTT 60.295 38.462 0.00 4.79 36.87 3.27
4142 4384 1.144969 CCTGCTGCATTGCTGTTTTG 58.855 50.000 15.71 5.26 0.00 2.44
4143 4385 0.511221 CTGCTGCATTGCTGTTTTGC 59.489 50.000 15.71 8.32 36.91 3.68
4144 4386 0.179081 TGCTGCATTGCTGTTTTGCA 60.179 45.000 15.71 10.38 43.63 4.08
4145 4387 1.153353 GCTGCATTGCTGTTTTGCAT 58.847 45.000 15.71 0.00 44.65 3.96
4146 4388 1.127951 GCTGCATTGCTGTTTTGCATC 59.872 47.619 15.71 0.00 44.65 3.91
4147 4389 2.409012 CTGCATTGCTGTTTTGCATCA 58.591 42.857 10.49 0.00 44.65 3.07
4148 4390 3.000041 CTGCATTGCTGTTTTGCATCAT 59.000 40.909 10.49 0.00 44.65 2.45
4152 4394 3.729862 TTGCTGTTTTGCATCATGTGA 57.270 38.095 0.00 0.00 42.96 3.58
4223 4465 7.215719 AGTTTAGTTGTTGGATTTTCTAGGC 57.784 36.000 0.00 0.00 0.00 3.93
4224 4466 7.004691 AGTTTAGTTGTTGGATTTTCTAGGCT 58.995 34.615 0.00 0.00 0.00 4.58
4225 4467 6.817765 TTAGTTGTTGGATTTTCTAGGCTG 57.182 37.500 0.00 0.00 0.00 4.85
4226 4468 3.507622 AGTTGTTGGATTTTCTAGGCTGC 59.492 43.478 0.00 0.00 0.00 5.25
4227 4469 3.153369 TGTTGGATTTTCTAGGCTGCA 57.847 42.857 0.50 0.00 0.00 4.41
4514 4866 2.421424 GAGTTGTGGCAGCAAATCTAGG 59.579 50.000 17.03 0.00 39.48 3.02
4565 4917 0.402121 GTTCTTGAGCTTCCTGGGGT 59.598 55.000 0.00 0.00 0.00 4.95
4602 4957 1.065928 CGGATGTACGGACTGGCTC 59.934 63.158 0.00 0.00 0.00 4.70
4607 4962 0.830444 TGTACGGACTGGCTCCAAGT 60.830 55.000 0.00 0.00 39.39 3.16
4608 4963 1.180029 GTACGGACTGGCTCCAAGTA 58.820 55.000 0.00 0.00 39.39 2.24
4609 4964 1.547372 GTACGGACTGGCTCCAAGTAA 59.453 52.381 0.00 0.00 39.39 2.24
4610 4965 0.320697 ACGGACTGGCTCCAAGTAAC 59.679 55.000 0.00 0.00 39.39 2.50
4641 4996 3.871850 TGCAAGCATCAGGCAGGCA 62.872 57.895 0.00 0.00 46.89 4.75
4645 5000 2.362120 GCATCAGGCAGGCAGGTT 60.362 61.111 0.00 0.00 43.97 3.50
4646 5001 2.413142 GCATCAGGCAGGCAGGTTC 61.413 63.158 0.00 0.00 43.97 3.62
4647 5002 1.001764 CATCAGGCAGGCAGGTTCA 60.002 57.895 0.00 0.00 0.00 3.18
4648 5003 1.030488 CATCAGGCAGGCAGGTTCAG 61.030 60.000 0.00 0.00 0.00 3.02
4649 5004 1.203441 ATCAGGCAGGCAGGTTCAGA 61.203 55.000 0.00 0.00 0.00 3.27
4650 5005 1.673665 CAGGCAGGCAGGTTCAGAC 60.674 63.158 0.00 0.00 0.00 3.51
4651 5006 2.149383 AGGCAGGCAGGTTCAGACA 61.149 57.895 0.00 0.00 0.00 3.41
4652 5007 1.968540 GGCAGGCAGGTTCAGACAC 60.969 63.158 0.00 0.00 0.00 3.67
4653 5008 1.227943 GCAGGCAGGTTCAGACACA 60.228 57.895 0.00 0.00 0.00 3.72
4654 5009 1.233285 GCAGGCAGGTTCAGACACAG 61.233 60.000 0.00 0.00 0.00 3.66
4665 5020 1.072159 AGACACAGACAGCAAGGGC 59.928 57.895 0.00 0.00 41.61 5.19
4679 5034 0.261696 AAGGGCCTCTCTCTCTCTCC 59.738 60.000 6.46 0.00 0.00 3.71
4680 5035 0.627469 AGGGCCTCTCTCTCTCTCCT 60.627 60.000 0.00 0.00 0.00 3.69
4687 5052 3.455910 CCTCTCTCTCTCTCCTTCTCTCA 59.544 52.174 0.00 0.00 0.00 3.27
4688 5053 4.103785 CCTCTCTCTCTCTCCTTCTCTCAT 59.896 50.000 0.00 0.00 0.00 2.90
4803 5172 4.444876 CCTTTCTTGTTTCCTCCTCACTCA 60.445 45.833 0.00 0.00 0.00 3.41
4829 5198 4.207165 CACAAGTGAAGGAAAGGAAAGGA 58.793 43.478 0.00 0.00 0.00 3.36
4869 5238 3.568430 TCCTCTTGCATCATCATTCATGC 59.432 43.478 0.00 0.00 44.87 4.06
4870 5239 3.570125 CCTCTTGCATCATCATTCATGCT 59.430 43.478 5.56 0.00 44.90 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 1.001888 TATACCACCCACTCCGCCA 59.998 57.895 0.00 0.00 0.00 5.69
105 106 4.874977 GCGTAGTCCGAGGCTGGC 62.875 72.222 0.00 0.00 39.56 4.85
177 178 1.890489 ACTCGCAACCCCCATAAAAAC 59.110 47.619 0.00 0.00 0.00 2.43
183 184 2.351276 GACACTCGCAACCCCCAT 59.649 61.111 0.00 0.00 0.00 4.00
195 196 3.437795 CGTAGGCGTCCCGACACT 61.438 66.667 0.00 0.00 37.34 3.55
219 220 1.144276 TCTGCAAACGTCCGGACAA 59.856 52.632 32.80 10.60 0.00 3.18
303 305 1.064505 GTCATCCAACGTCATGCATGG 59.935 52.381 25.97 13.66 0.00 3.66
327 329 1.680105 CGCTAAACGCCCGTACACTG 61.680 60.000 0.00 0.00 34.21 3.66
544 648 4.019174 TGAGGGAGAAAAGATTTCATGGC 58.981 43.478 5.71 0.00 0.00 4.40
581 686 7.980662 CCACATGAGAAGATAGGATGATGATAC 59.019 40.741 0.00 0.00 0.00 2.24
592 697 7.605691 GGTTTATCCATCCACATGAGAAGATAG 59.394 40.741 0.00 0.00 35.97 2.08
655 760 5.594725 TGTTTGGGTTTATGTGTGTATGTGT 59.405 36.000 0.00 0.00 0.00 3.72
686 791 4.869861 CACAACAGGGTTCAAAAAGGAAAG 59.130 41.667 0.00 0.00 0.00 2.62
687 792 4.323104 CCACAACAGGGTTCAAAAAGGAAA 60.323 41.667 0.00 0.00 0.00 3.13
708 816 2.975799 GCTTTCGTCGGTTGCCCA 60.976 61.111 0.00 0.00 0.00 5.36
710 818 0.729140 CAATGCTTTCGTCGGTTGCC 60.729 55.000 0.00 0.00 0.00 4.52
714 822 1.429463 GACTCAATGCTTTCGTCGGT 58.571 50.000 0.00 0.00 0.00 4.69
721 829 6.403866 TGTTTACAATGGACTCAATGCTTT 57.596 33.333 0.00 0.00 0.00 3.51
722 830 6.183360 TGTTGTTTACAATGGACTCAATGCTT 60.183 34.615 0.00 0.00 38.24 3.91
724 832 5.527951 TGTTGTTTACAATGGACTCAATGC 58.472 37.500 0.00 0.00 38.24 3.56
725 833 7.042791 GGTTTGTTGTTTACAATGGACTCAATG 60.043 37.037 0.00 0.00 45.72 2.82
726 834 6.983890 GGTTTGTTGTTTACAATGGACTCAAT 59.016 34.615 0.00 0.00 45.72 2.57
727 835 6.334202 GGTTTGTTGTTTACAATGGACTCAA 58.666 36.000 0.00 0.00 45.72 3.02
728 836 5.163499 GGGTTTGTTGTTTACAATGGACTCA 60.163 40.000 0.00 0.00 45.72 3.41
729 837 5.068591 AGGGTTTGTTGTTTACAATGGACTC 59.931 40.000 0.00 0.00 45.72 3.36
778 891 0.758734 AAAAGTTGCCCTCTTTGCCC 59.241 50.000 0.00 0.00 35.65 5.36
798 911 3.650950 GGAGGACAAGGCCCAGCA 61.651 66.667 0.00 0.00 0.00 4.41
957 1083 3.421844 GAGATAGAGAGGGGAAGAGAGC 58.578 54.545 0.00 0.00 0.00 4.09
958 1084 3.657727 AGGAGATAGAGAGGGGAAGAGAG 59.342 52.174 0.00 0.00 0.00 3.20
959 1085 3.655777 GAGGAGATAGAGAGGGGAAGAGA 59.344 52.174 0.00 0.00 0.00 3.10
960 1086 3.657727 AGAGGAGATAGAGAGGGGAAGAG 59.342 52.174 0.00 0.00 0.00 2.85
961 1087 3.687045 AGAGGAGATAGAGAGGGGAAGA 58.313 50.000 0.00 0.00 0.00 2.87
962 1088 4.469469 AAGAGGAGATAGAGAGGGGAAG 57.531 50.000 0.00 0.00 0.00 3.46
963 1089 4.388118 GGAAAGAGGAGATAGAGAGGGGAA 60.388 50.000 0.00 0.00 0.00 3.97
964 1090 3.141272 GGAAAGAGGAGATAGAGAGGGGA 59.859 52.174 0.00 0.00 0.00 4.81
965 1091 3.116939 TGGAAAGAGGAGATAGAGAGGGG 60.117 52.174 0.00 0.00 0.00 4.79
966 1092 3.895041 GTGGAAAGAGGAGATAGAGAGGG 59.105 52.174 0.00 0.00 0.00 4.30
1287 1426 2.979676 CTGCAGAAGCGCAACCCA 60.980 61.111 8.42 0.00 46.23 4.51
1299 1438 2.033801 CCCGCAAAATATTCCTCTGCAG 59.966 50.000 7.63 7.63 33.19 4.41
1300 1439 2.023673 CCCGCAAAATATTCCTCTGCA 58.976 47.619 10.53 0.00 33.19 4.41
1373 1530 2.893424 AGGGTTCAAGGAATTGCACAT 58.107 42.857 0.00 0.00 0.00 3.21
1598 1764 4.321899 GGCAGTTACCATTGAATTGCTGAA 60.322 41.667 5.84 0.00 38.97 3.02
1599 1765 3.193267 GGCAGTTACCATTGAATTGCTGA 59.807 43.478 5.84 0.00 38.97 4.26
1600 1766 3.514645 GGCAGTTACCATTGAATTGCTG 58.485 45.455 5.84 0.00 38.97 4.41
1650 1817 5.518487 GGGATAAAACAATTATTGCACGGTG 59.482 40.000 4.68 3.15 0.00 4.94
1676 1843 4.841813 TGAACCTGACATGAACCCTAGTAA 59.158 41.667 0.00 0.00 0.00 2.24
1734 1902 6.039941 ACATCACAACGAAAGGGAAACATAAA 59.960 34.615 0.00 0.00 0.00 1.40
1751 1921 4.058124 CTCTTTCTTCCGTGACATCACAA 58.942 43.478 12.32 0.00 46.75 3.33
1765 1939 3.319122 ACGCATTGCTTTTCCTCTTTCTT 59.681 39.130 7.12 0.00 0.00 2.52
1766 1940 2.887152 ACGCATTGCTTTTCCTCTTTCT 59.113 40.909 7.12 0.00 0.00 2.52
1767 1941 2.982470 CACGCATTGCTTTTCCTCTTTC 59.018 45.455 7.12 0.00 0.00 2.62
1768 1942 2.362077 ACACGCATTGCTTTTCCTCTTT 59.638 40.909 7.12 0.00 0.00 2.52
1819 2004 3.641434 ATGACAATGACAGGAGGGAAG 57.359 47.619 0.00 0.00 0.00 3.46
2001 2186 4.036852 CAGACCAAAACTGAAGAACCCTTC 59.963 45.833 0.00 0.00 46.89 3.46
2015 2200 5.104277 TCCTTCAAGGAGTTACAGACCAAAA 60.104 40.000 0.34 0.00 40.06 2.44
2062 2247 9.346005 ACTGATGCATTTCATAATAAGTGATGA 57.654 29.630 0.00 0.00 35.05 2.92
2063 2248 9.961265 AACTGATGCATTTCATAATAAGTGATG 57.039 29.630 0.00 0.00 35.05 3.07
2280 2473 2.242797 ATTGCTTTGGGGGCATTCGC 62.243 55.000 0.00 0.00 39.54 4.70
2299 2492 7.451255 AGTCCACACCATCAATCAATAGAAAAA 59.549 33.333 0.00 0.00 0.00 1.94
2438 2638 3.742013 GCATTGGCAATATGGTTCCCAAG 60.742 47.826 13.23 0.00 38.78 3.61
2657 2896 3.071457 TGTCTTCACTTTCCTGCAGATCA 59.929 43.478 17.39 0.00 0.00 2.92
2661 2900 1.534595 GCTGTCTTCACTTTCCTGCAG 59.465 52.381 6.78 6.78 0.00 4.41
2750 2989 3.153919 TGGGTTTACAGATGCTTGTTCC 58.846 45.455 0.00 0.00 32.56 3.62
3039 3278 3.056465 TGGTTGGAGTTGGACAAACAAAC 60.056 43.478 0.00 6.52 40.96 2.93
3320 3559 4.696877 TCCTCGTTCACATACGTCTTCTTA 59.303 41.667 0.00 0.00 42.01 2.10
3763 4002 4.072839 TCTCTCAAGCGAAAGACTGACTA 58.927 43.478 0.00 0.00 0.00 2.59
3846 4085 5.660460 AGCATAACATCGCGATATAATGGA 58.340 37.500 23.22 3.66 0.00 3.41
4051 4293 3.197434 CATGTCAATGCTGTGTGTGAG 57.803 47.619 0.00 0.00 0.00 3.51
4096 4338 0.396974 AACTCCAGCCCTGCAAACAA 60.397 50.000 0.00 0.00 0.00 2.83
4142 4384 1.617322 ATGCCAGGATCACATGATGC 58.383 50.000 0.00 5.30 42.32 3.91
4143 4385 2.288213 GCAATGCCAGGATCACATGATG 60.288 50.000 0.00 0.00 34.37 3.07
4144 4386 1.961394 GCAATGCCAGGATCACATGAT 59.039 47.619 0.00 0.00 37.51 2.45
4145 4387 1.064240 AGCAATGCCAGGATCACATGA 60.064 47.619 0.00 0.00 0.00 3.07
4146 4388 1.067060 CAGCAATGCCAGGATCACATG 59.933 52.381 0.00 0.00 0.00 3.21
4147 4389 1.064240 TCAGCAATGCCAGGATCACAT 60.064 47.619 0.00 0.00 0.00 3.21
4148 4390 0.328926 TCAGCAATGCCAGGATCACA 59.671 50.000 0.00 0.00 0.00 3.58
4152 4394 2.226962 AAAGTCAGCAATGCCAGGAT 57.773 45.000 0.00 0.00 0.00 3.24
4217 4459 2.028112 CAGTAACCTGTTGCAGCCTAGA 60.028 50.000 0.00 0.00 33.80 2.43
4222 4464 1.160137 CTCCAGTAACCTGTTGCAGC 58.840 55.000 0.00 0.00 36.95 5.25
4223 4465 2.417719 GACTCCAGTAACCTGTTGCAG 58.582 52.381 1.08 0.00 36.95 4.41
4224 4466 1.071699 GGACTCCAGTAACCTGTTGCA 59.928 52.381 1.08 0.00 36.95 4.08
4225 4467 1.071699 TGGACTCCAGTAACCTGTTGC 59.928 52.381 0.00 0.00 36.95 4.17
4226 4468 3.244561 ACATGGACTCCAGTAACCTGTTG 60.245 47.826 3.62 0.00 36.75 3.33
4227 4469 2.979678 ACATGGACTCCAGTAACCTGTT 59.020 45.455 3.62 0.00 36.75 3.16
4468 4820 3.808728 TCAGTGGTTTGGAAGTTCAGAG 58.191 45.455 5.01 0.00 0.00 3.35
4514 4866 2.025418 GCATTGTTGCCAGCAGTGC 61.025 57.895 12.77 12.77 43.38 4.40
4565 4917 6.776116 ACATCCGATGGAGTACTATTTGACTA 59.224 38.462 13.00 0.00 34.05 2.59
4602 4957 4.549458 CAGCAGGATTGTTTGTTACTTGG 58.451 43.478 0.00 0.00 0.00 3.61
4607 4962 3.552684 GCTTGCAGCAGGATTGTTTGTTA 60.553 43.478 9.09 0.00 41.89 2.41
4608 4963 2.804212 GCTTGCAGCAGGATTGTTTGTT 60.804 45.455 9.09 0.00 41.89 2.83
4609 4964 1.269936 GCTTGCAGCAGGATTGTTTGT 60.270 47.619 9.09 0.00 41.89 2.83
4610 4965 1.425412 GCTTGCAGCAGGATTGTTTG 58.575 50.000 9.09 0.00 41.89 2.93
4635 4990 1.227943 TGTGTCTGAACCTGCCTGC 60.228 57.895 0.00 0.00 0.00 4.85
4636 4991 0.394192 TCTGTGTCTGAACCTGCCTG 59.606 55.000 0.00 0.00 0.00 4.85
4637 4992 0.394565 GTCTGTGTCTGAACCTGCCT 59.605 55.000 0.00 0.00 0.00 4.75
4638 4993 0.106708 TGTCTGTGTCTGAACCTGCC 59.893 55.000 0.00 0.00 0.00 4.85
4639 4994 1.506493 CTGTCTGTGTCTGAACCTGC 58.494 55.000 0.00 0.00 0.00 4.85
4640 4995 1.202568 TGCTGTCTGTGTCTGAACCTG 60.203 52.381 0.00 0.00 0.00 4.00
4641 4996 1.123077 TGCTGTCTGTGTCTGAACCT 58.877 50.000 0.00 0.00 0.00 3.50
4642 4997 1.869767 CTTGCTGTCTGTGTCTGAACC 59.130 52.381 0.00 0.00 0.00 3.62
4643 4998 1.869767 CCTTGCTGTCTGTGTCTGAAC 59.130 52.381 0.00 0.00 0.00 3.18
4644 4999 1.202687 CCCTTGCTGTCTGTGTCTGAA 60.203 52.381 0.00 0.00 0.00 3.02
4645 5000 0.394192 CCCTTGCTGTCTGTGTCTGA 59.606 55.000 0.00 0.00 0.00 3.27
4646 5001 1.233285 GCCCTTGCTGTCTGTGTCTG 61.233 60.000 0.00 0.00 33.53 3.51
4647 5002 1.072159 GCCCTTGCTGTCTGTGTCT 59.928 57.895 0.00 0.00 33.53 3.41
4648 5003 1.968540 GGCCCTTGCTGTCTGTGTC 60.969 63.158 0.00 0.00 37.74 3.67
4649 5004 2.113986 GGCCCTTGCTGTCTGTGT 59.886 61.111 0.00 0.00 37.74 3.72
4650 5005 1.673665 GAGGCCCTTGCTGTCTGTG 60.674 63.158 0.00 0.00 37.74 3.66
4651 5006 1.835927 GAGAGGCCCTTGCTGTCTGT 61.836 60.000 0.00 0.00 37.74 3.41
4652 5007 1.078567 GAGAGGCCCTTGCTGTCTG 60.079 63.158 0.00 0.00 37.74 3.51
4653 5008 1.229464 AGAGAGGCCCTTGCTGTCT 60.229 57.895 0.00 0.00 37.74 3.41
4654 5009 1.220477 GAGAGAGGCCCTTGCTGTC 59.780 63.158 0.00 0.00 37.74 3.51
4665 5020 3.455910 TGAGAGAAGGAGAGAGAGAGAGG 59.544 52.174 0.00 0.00 0.00 3.69
4697 5062 6.266786 TGAGTGAGTGATACAAAAGGTGTCTA 59.733 38.462 0.00 0.00 41.98 2.59
4698 5063 5.070446 TGAGTGAGTGATACAAAAGGTGTCT 59.930 40.000 0.00 0.00 41.98 3.41
4803 5172 2.777692 TCCTTTCCTTCACTTGTGGAGT 59.222 45.455 8.11 0.00 39.89 3.85


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

AutoCloner maintained by Alex Coulton.