Multiple sequence alignment - TraesCS1B01G015900

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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 TraesCS1B01G015900 chr1B 100.000 4961 0 0 1 4961 7613445 7608485 0.000000e+00 9162.0
1 TraesCS1B01G015900 chr1B 89.108 762 77 6 4199 4959 411094867 411094111 0.000000e+00 942.0
2 TraesCS1B01G015900 chr1B 87.059 765 79 16 4200 4961 543389160 543389907 0.000000e+00 846.0
3 TraesCS1B01G015900 chrUn 94.518 2627 126 11 1576 4199 76524696 76522085 0.000000e+00 4037.0
4 TraesCS1B01G015900 chrUn 90.788 1346 96 14 256 1580 76526359 76525021 0.000000e+00 1773.0
5 TraesCS1B01G015900 chrUn 88.417 1295 124 18 208 1488 76580396 76579114 0.000000e+00 1537.0
6 TraesCS1B01G015900 chrUn 96.237 186 3 1 1 186 76528527 76528346 8.070000e-78 302.0
7 TraesCS1B01G015900 chrUn 88.889 189 8 7 1 184 76582941 76582761 2.320000e-53 220.0
8 TraesCS1B01G015900 chrUn 100.000 36 0 0 208 243 76527931 76527896 3.210000e-07 67.6
9 TraesCS1B01G015900 chr1D 91.420 2634 190 18 1583 4199 4607106 4604492 0.000000e+00 3579.0
10 TraesCS1B01G015900 chr1D 90.794 2607 199 27 1580 4173 3515622 3518200 0.000000e+00 3446.0
11 TraesCS1B01G015900 chr1D 94.344 937 51 2 586 1521 3514250 3515185 0.000000e+00 1435.0
12 TraesCS1B01G015900 chr1D 86.735 392 42 7 208 589 3512517 3512908 1.280000e-115 427.0
13 TraesCS1B01G015900 chr1D 93.333 165 7 1 1 165 3511967 3512127 1.780000e-59 241.0
14 TraesCS1B01G015900 chr2B 88.142 759 76 14 4206 4959 383923768 383923019 0.000000e+00 891.0
15 TraesCS1B01G015900 chr7D 87.795 762 82 10 4200 4959 208149511 208148759 0.000000e+00 881.0
16 TraesCS1B01G015900 chr7D 82.653 98 17 0 607 704 461395508 461395411 2.460000e-13 87.9
17 TraesCS1B01G015900 chr7D 86.667 75 10 0 607 681 411924426 411924500 3.180000e-12 84.2
18 TraesCS1B01G015900 chr6D 88.032 752 74 15 4199 4945 392906181 392906921 0.000000e+00 876.0
19 TraesCS1B01G015900 chr6B 87.467 766 83 13 4199 4961 295327076 295327831 0.000000e+00 870.0
20 TraesCS1B01G015900 chr6B 84.722 72 11 0 633 704 397554562 397554491 6.890000e-09 73.1
21 TraesCS1B01G015900 chr7B 87.715 757 78 13 4200 4952 517640126 517640871 0.000000e+00 869.0
22 TraesCS1B01G015900 chr7B 85.542 83 12 0 607 689 426308643 426308725 2.460000e-13 87.9
23 TraesCS1B01G015900 chr7B 80.612 98 19 0 607 704 483861744 483861647 5.330000e-10 76.8
24 TraesCS1B01G015900 chr2A 87.320 765 83 14 4199 4959 572242099 572241345 0.000000e+00 863.0
25 TraesCS1B01G015900 chr7A 87.320 765 81 14 4200 4959 404392287 404391534 0.000000e+00 861.0
26 TraesCS1B01G015900 chr3B 94.444 54 1 2 256 307 684049369 684049316 1.140000e-11 82.4
27 TraesCS1B01G015900 chr4D 100.000 28 0 0 630 657 394237692 394237665 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 TraesCS1B01G015900 chr1B 7608485 7613445 4960 True 9162.00 9162 100.00000 1 4961 1 chr1B.!!$R1 4960
1 TraesCS1B01G015900 chr1B 411094111 411094867 756 True 942.00 942 89.10800 4199 4959 1 chr1B.!!$R2 760
2 TraesCS1B01G015900 chr1B 543389160 543389907 747 False 846.00 846 87.05900 4200 4961 1 chr1B.!!$F1 761
3 TraesCS1B01G015900 chrUn 76522085 76528527 6442 True 1544.90 4037 95.38575 1 4199 4 chrUn.!!$R1 4198
4 TraesCS1B01G015900 chrUn 76579114 76582941 3827 True 878.50 1537 88.65300 1 1488 2 chrUn.!!$R2 1487
5 TraesCS1B01G015900 chr1D 4604492 4607106 2614 True 3579.00 3579 91.42000 1583 4199 1 chr1D.!!$R1 2616
6 TraesCS1B01G015900 chr1D 3511967 3518200 6233 False 1387.25 3446 91.30150 1 4173 4 chr1D.!!$F1 4172
7 TraesCS1B01G015900 chr2B 383923019 383923768 749 True 891.00 891 88.14200 4206 4959 1 chr2B.!!$R1 753
8 TraesCS1B01G015900 chr7D 208148759 208149511 752 True 881.00 881 87.79500 4200 4959 1 chr7D.!!$R1 759
9 TraesCS1B01G015900 chr6D 392906181 392906921 740 False 876.00 876 88.03200 4199 4945 1 chr6D.!!$F1 746
10 TraesCS1B01G015900 chr6B 295327076 295327831 755 False 870.00 870 87.46700 4199 4961 1 chr6B.!!$F1 762
11 TraesCS1B01G015900 chr7B 517640126 517640871 745 False 869.00 869 87.71500 4200 4952 1 chr7B.!!$F2 752
12 TraesCS1B01G015900 chr2A 572241345 572242099 754 True 863.00 863 87.32000 4199 4959 1 chr2A.!!$R1 760
13 TraesCS1B01G015900 chr7A 404391534 404392287 753 True 861.00 861 87.32000 4200 4959 1 chr7A.!!$R1 759

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
198 2146 0.108804 CACATCTGCTACGTCCCGTT 60.109 55.0 0.00 0.0 41.54 4.44 F
199 2147 0.108804 ACATCTGCTACGTCCCGTTG 60.109 55.0 0.00 0.0 41.54 4.10 F
1925 7621 0.464916 TACGCCCGATCTGACAGCTA 60.465 55.0 0.00 0.0 0.00 3.32 F
1932 7628 2.093973 CCGATCTGACAGCTAACAACCT 60.094 50.0 0.00 0.0 0.00 3.50 F
2148 7849 2.617250 TAATTGCTCGTGCTTTGCAG 57.383 45.0 11.19 0.0 40.08 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 7621 0.396556 AAAAGGTCCGCCAGGTTGTT 60.397 50.0 0.0 0.0 39.05 2.83 R
1932 7628 0.608035 GGATGTGAAAAGGTCCGCCA 60.608 55.0 0.0 0.0 37.19 5.69 R
2911 8620 0.251209 TCCTCCTAGCAGTCGTGTGT 60.251 55.0 0.0 0.0 0.00 3.72 R
2969 8681 0.546122 AGACAACCCACTTCAGCACA 59.454 50.0 0.0 0.0 0.00 4.57 R
4130 9842 0.322648 TGGGACATCAGCAGACACTG 59.677 55.0 0.0 0.0 39.12 3.66 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
82 86 0.389296 TCACCAAGTACGGCATCACG 60.389 55.000 0.00 0.00 40.31 4.35
106 112 3.490348 GAATATGGTGCACCCTAATGCT 58.510 45.455 32.62 13.12 46.28 3.79
107 113 4.506625 GGAATATGGTGCACCCTAATGCTA 60.507 45.833 32.62 12.24 46.28 3.49
108 114 4.934797 ATATGGTGCACCCTAATGCTAT 57.065 40.909 32.62 18.52 46.28 2.97
109 115 6.387192 AATATGGTGCACCCTAATGCTATA 57.613 37.500 32.62 20.03 46.28 1.31
186 2134 0.738762 ACGCTACTGCTGCACATCTG 60.739 55.000 0.00 0.00 36.97 2.90
187 2135 1.720301 GCTACTGCTGCACATCTGC 59.280 57.895 0.00 0.00 44.52 4.26
188 2136 0.743701 GCTACTGCTGCACATCTGCT 60.744 55.000 0.00 0.00 44.57 4.24
189 2137 1.472201 GCTACTGCTGCACATCTGCTA 60.472 52.381 0.00 0.00 44.57 3.49
192 2140 0.738762 CTGCTGCACATCTGCTACGT 60.739 55.000 0.00 0.00 44.57 3.57
193 2141 0.737367 TGCTGCACATCTGCTACGTC 60.737 55.000 0.00 0.00 44.57 4.34
196 2144 1.878522 GCACATCTGCTACGTCCCG 60.879 63.158 0.00 0.00 40.63 5.14
197 2145 1.511305 CACATCTGCTACGTCCCGT 59.489 57.895 0.00 0.00 44.35 5.28
198 2146 0.108804 CACATCTGCTACGTCCCGTT 60.109 55.000 0.00 0.00 41.54 4.44
199 2147 0.108804 ACATCTGCTACGTCCCGTTG 60.109 55.000 0.00 0.00 41.54 4.10
204 2152 2.813908 CTACGTCCCGTTGCCTGC 60.814 66.667 0.00 0.00 41.54 4.85
205 2153 3.583276 CTACGTCCCGTTGCCTGCA 62.583 63.158 0.00 0.00 41.54 4.41
248 2595 9.793259 ACTTACAAATATCATGGTAAATCCGAT 57.207 29.630 0.00 0.00 39.52 4.18
260 2607 6.616947 TGGTAAATCCGATGCACTTAAAAAG 58.383 36.000 0.00 0.00 39.52 2.27
275 2622 9.946165 GCACTTAAAAAGTAGTTGAAACATACT 57.054 29.630 0.00 0.00 40.46 2.12
298 4168 4.066490 CGGTAACCTCATTGTAAACACCA 58.934 43.478 0.00 0.00 0.00 4.17
332 4202 9.667107 TTATGTAGATTGGAACTTTTGACCTAG 57.333 33.333 0.00 0.00 0.00 3.02
350 4220 5.283060 CCTAGAAAGGTCGTGAAAACATG 57.717 43.478 0.00 0.00 38.19 3.21
351 4221 4.994852 CCTAGAAAGGTCGTGAAAACATGA 59.005 41.667 0.00 0.00 38.19 3.07
352 4222 5.120830 CCTAGAAAGGTCGTGAAAACATGAG 59.879 44.000 0.00 0.00 38.19 2.90
354 4224 5.308825 AGAAAGGTCGTGAAAACATGAGAT 58.691 37.500 0.00 0.00 0.00 2.75
356 4226 6.263168 AGAAAGGTCGTGAAAACATGAGATTT 59.737 34.615 0.00 0.00 0.00 2.17
357 4227 7.444183 AGAAAGGTCGTGAAAACATGAGATTTA 59.556 33.333 0.00 0.00 0.00 1.40
589 5815 3.827876 TGTTACTAACCACCGATCACTCA 59.172 43.478 0.00 0.00 0.00 3.41
602 5828 4.398358 CCGATCACTCAGTAGTTAGTCCAA 59.602 45.833 0.00 0.00 31.97 3.53
604 5830 6.262496 CCGATCACTCAGTAGTTAGTCCAATA 59.738 42.308 0.00 0.00 31.97 1.90
773 5999 7.758820 TCCTATAGAAAAAGGGGTGTGATTA 57.241 36.000 0.00 0.00 33.40 1.75
873 6107 4.876107 CACAACAAGTTGAAGACTAGTGGT 59.124 41.667 18.90 0.00 42.93 4.16
951 6188 6.313519 AGAGTTGGCTGGTAGATGATAAAA 57.686 37.500 0.00 0.00 0.00 1.52
1080 6320 3.324846 TGCTCTTCTTCCTCTTTGTGCTA 59.675 43.478 0.00 0.00 0.00 3.49
1083 6323 5.140747 TCTTCTTCCTCTTTGTGCTAGTC 57.859 43.478 0.00 0.00 0.00 2.59
1630 7324 4.275508 CTGTGTGTGGCCTGGGCT 62.276 66.667 21.72 0.00 41.60 5.19
1862 7556 3.002965 GTGTTACAAAAGGGAACTCACGG 59.997 47.826 0.00 0.00 42.68 4.94
1877 7571 3.067106 CTCACGGCATGACTTTAGTTGT 58.933 45.455 0.00 0.00 32.37 3.32
1884 7578 7.381139 CACGGCATGACTTTAGTTGTAAAAATT 59.619 33.333 0.00 0.00 0.00 1.82
1925 7621 0.464916 TACGCCCGATCTGACAGCTA 60.465 55.000 0.00 0.00 0.00 3.32
1932 7628 2.093973 CCGATCTGACAGCTAACAACCT 60.094 50.000 0.00 0.00 0.00 3.50
1996 7692 5.447624 AAACTAACCATTTCTTTGACGGG 57.552 39.130 0.00 0.00 0.00 5.28
2087 7788 2.842394 ATCCGTCGTGCTCCAGCTTG 62.842 60.000 0.00 0.00 42.66 4.01
2148 7849 2.617250 TAATTGCTCGTGCTTTGCAG 57.383 45.000 11.19 0.00 40.08 4.41
2575 8283 7.362660 GGGGACTTAGGTCATTGTAATTGTTTC 60.363 40.741 7.35 0.00 43.77 2.78
2724 8433 3.538634 AATTAGCTAACCCTGACGTCC 57.461 47.619 14.12 0.00 0.00 4.79
2911 8620 5.191522 TGTTCCAGGACCTGATCAATGATAA 59.808 40.000 23.77 0.00 32.44 1.75
2950 8662 4.372656 GGATTCATCCTTGAGTACTTCCG 58.627 47.826 0.00 0.00 43.73 4.30
2989 8701 1.765904 TGTGCTGAAGTGGGTTGTCTA 59.234 47.619 0.00 0.00 0.00 2.59
2991 8703 3.181445 TGTGCTGAAGTGGGTTGTCTATT 60.181 43.478 0.00 0.00 0.00 1.73
3012 8724 3.338249 TCAAAAGCCGAGAGAATGAAGG 58.662 45.455 0.00 0.00 0.00 3.46
3091 8803 5.655488 CGTGATGTCTGATAAGAAAGAGGT 58.345 41.667 0.00 0.00 0.00 3.85
3143 8855 8.585018 TCTGTTCAACAAGAGTATGATCTAACA 58.415 33.333 0.00 0.00 0.00 2.41
3168 8880 3.001414 GAGCACATCATAGCTATGCTGG 58.999 50.000 30.87 22.94 46.33 4.85
3422 9134 2.438411 AGACGAGGTCAGGAGTAACAG 58.562 52.381 0.00 0.00 34.60 3.16
3480 9192 6.206634 TCAACCAGAACAACATGATTTACCTC 59.793 38.462 0.00 0.00 0.00 3.85
3687 9399 5.067936 TGAAAGGTTTTTAGATGACGGCAAA 59.932 36.000 0.00 0.00 0.00 3.68
3695 9407 1.855213 GATGACGGCAAAGCAGCACA 61.855 55.000 0.00 0.00 35.83 4.57
3786 9498 1.032014 ACTTTGCGGTTGACAGCATT 58.968 45.000 9.63 0.00 45.71 3.56
3885 9597 0.250553 CGGAGGTGTTTGGGCTAACA 60.251 55.000 2.38 2.38 35.75 2.41
3971 9683 1.226746 GCACCGTAATAGCACCATCC 58.773 55.000 0.00 0.00 0.00 3.51
3984 9696 5.966742 AGCACCATCCTCTTTTCTTAAAC 57.033 39.130 0.00 0.00 0.00 2.01
4109 9821 7.614124 GATGCAAACATCCCAACAATAAAAT 57.386 32.000 0.00 0.00 45.94 1.82
4125 9837 9.979578 AACAATAAAATTTGTTGTCATCTAGCA 57.020 25.926 18.54 0.00 45.55 3.49
4126 9838 9.630098 ACAATAAAATTTGTTGTCATCTAGCAG 57.370 29.630 13.79 0.00 40.33 4.24
4127 9839 9.079833 CAATAAAATTTGTTGTCATCTAGCAGG 57.920 33.333 6.98 0.00 0.00 4.85
4128 9840 4.708726 AATTTGTTGTCATCTAGCAGGC 57.291 40.909 0.00 0.00 0.00 4.85
4129 9841 3.423539 TTTGTTGTCATCTAGCAGGCT 57.576 42.857 0.00 0.00 0.00 4.58
4130 9842 2.680312 TGTTGTCATCTAGCAGGCTC 57.320 50.000 0.00 0.00 0.00 4.70
4131 9843 1.901833 TGTTGTCATCTAGCAGGCTCA 59.098 47.619 0.00 0.00 0.00 4.26
4151 9873 0.035317 GTGTCTGCTGATGTCCCACA 59.965 55.000 0.00 0.00 0.00 4.17
4203 9925 0.955428 GTCGGCCAACTTCTGCATGA 60.955 55.000 2.24 0.00 0.00 3.07
4219 9941 6.463360 TCTGCATGAAAATACCGCATATAGA 58.537 36.000 0.00 0.00 31.10 1.98
4228 9950 8.888579 AAAATACCGCATATAGATAGGTATGC 57.111 34.615 13.96 7.17 44.63 3.14
4230 9952 8.935614 AATACCGCATATAGATAGGTATGCTA 57.064 34.615 13.96 3.37 46.82 3.49
4239 9961 5.913137 AGATAGGTATGCTAGACTCATGC 57.087 43.478 0.00 0.00 0.00 4.06
4259 9981 2.930682 GCGGCACAACTTTGGTTTTAAA 59.069 40.909 0.00 0.00 32.73 1.52
4266 9988 6.672118 GCACAACTTTGGTTTTAAAGAGTTGC 60.672 38.462 19.20 10.99 39.46 4.17
4277 9999 1.325355 AAGAGTTGCATGCACAAGCT 58.675 45.000 22.58 15.80 42.74 3.74
4283 10005 3.006110 AGTTGCATGCACAAGCTGTATTT 59.994 39.130 22.58 0.00 42.74 1.40
4310 10033 2.434336 TCGTACAAATGGAGGCTAGCAT 59.566 45.455 18.24 10.08 0.00 3.79
4351 10074 5.005299 CCAACCAAGAAACAAAAACGATCAC 59.995 40.000 0.00 0.00 0.00 3.06
4359 10082 7.257722 AGAAACAAAAACGATCACAAATGAGT 58.742 30.769 0.00 0.00 38.57 3.41
4389 10112 7.801716 ACATAACTAACACCGAATAATGCAT 57.198 32.000 0.00 0.00 0.00 3.96
4468 10191 7.033185 GGAATCACAAACCATAACACCAATAC 58.967 38.462 0.00 0.00 0.00 1.89
4475 10198 8.915036 ACAAACCATAACACCAATACTTTTACA 58.085 29.630 0.00 0.00 0.00 2.41
4496 10220 9.906660 TTTACAAAAGCATAATTACTCACCAAG 57.093 29.630 0.00 0.00 0.00 3.61
4677 10404 7.951530 AACATGCTCTCAAACAAATTTAAGG 57.048 32.000 0.00 0.00 0.00 2.69
4678 10405 7.288810 ACATGCTCTCAAACAAATTTAAGGA 57.711 32.000 0.00 0.00 0.00 3.36
4680 10407 8.370182 ACATGCTCTCAAACAAATTTAAGGAAT 58.630 29.630 0.00 0.00 0.00 3.01
4762 10490 8.223177 AGCATGAGAGGATATTTCTTCAAAAG 57.777 34.615 0.00 0.00 30.59 2.27
4929 10664 8.882415 AATTCTAACAAATCATGGCATCATTC 57.118 30.769 0.00 0.00 0.00 2.67
4932 10667 5.670792 AACAAATCATGGCATCATTCTGT 57.329 34.783 0.00 2.07 0.00 3.41
4939 10674 4.163649 TCATGGCATCATTCTGTCTCTCTT 59.836 41.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 86 3.290948 TTAGGGTGCACCATATTCCAC 57.709 47.619 35.78 16.64 43.89 4.02
192 2140 0.392461 GTCTATTGCAGGCAACGGGA 60.392 55.000 9.13 5.24 46.39 5.14
193 2141 1.376609 GGTCTATTGCAGGCAACGGG 61.377 60.000 9.13 2.98 46.39 5.28
196 2144 2.113860 TCAGGTCTATTGCAGGCAAC 57.886 50.000 9.13 0.00 38.88 4.17
197 2145 4.502105 TTATCAGGTCTATTGCAGGCAA 57.498 40.909 9.38 9.38 40.47 4.52
198 2146 4.712051 ATTATCAGGTCTATTGCAGGCA 57.288 40.909 0.00 0.00 0.00 4.75
199 2147 6.712547 AGTAAATTATCAGGTCTATTGCAGGC 59.287 38.462 0.00 0.00 0.00 4.85
243 2590 5.992829 TCAACTACTTTTTAAGTGCATCGGA 59.007 36.000 2.45 0.00 42.84 4.55
244 2591 6.236017 TCAACTACTTTTTAAGTGCATCGG 57.764 37.500 2.45 0.00 42.84 4.18
245 2592 7.642194 TGTTTCAACTACTTTTTAAGTGCATCG 59.358 33.333 2.45 0.00 42.84 3.84
248 2595 9.724839 GTATGTTTCAACTACTTTTTAAGTGCA 57.275 29.630 2.45 0.00 42.84 4.57
260 2607 6.393171 AGGTTACCGAGTATGTTTCAACTAC 58.607 40.000 0.00 0.00 0.00 2.73
275 2622 4.202336 TGGTGTTTACAATGAGGTTACCGA 60.202 41.667 0.00 0.00 0.00 4.69
276 2623 4.066490 TGGTGTTTACAATGAGGTTACCG 58.934 43.478 0.00 0.00 0.00 4.02
277 2624 5.708230 TCATGGTGTTTACAATGAGGTTACC 59.292 40.000 0.00 0.00 41.31 2.85
332 4202 5.613358 ATCTCATGTTTTCACGACCTTTC 57.387 39.130 0.00 0.00 0.00 2.62
342 4212 8.660373 AGATCGTCAACTAAATCTCATGTTTTC 58.340 33.333 0.00 0.00 0.00 2.29
350 4220 6.975197 TGTGATGAGATCGTCAACTAAATCTC 59.025 38.462 6.32 4.63 42.83 2.75
351 4221 6.867550 TGTGATGAGATCGTCAACTAAATCT 58.132 36.000 6.32 0.00 42.83 2.40
352 4222 6.292061 GCTGTGATGAGATCGTCAACTAAATC 60.292 42.308 6.32 0.00 42.83 2.17
354 4224 4.864806 GCTGTGATGAGATCGTCAACTAAA 59.135 41.667 6.32 0.00 42.83 1.85
356 4226 3.487544 CGCTGTGATGAGATCGTCAACTA 60.488 47.826 6.32 0.00 42.83 2.24
357 4227 2.733542 CGCTGTGATGAGATCGTCAACT 60.734 50.000 6.32 0.00 42.83 3.16
400 4281 6.511767 GCTCAAATCGTCGGTATGATTGAAAT 60.512 38.462 0.00 0.00 39.86 2.17
410 4291 3.853831 TTGTAGCTCAAATCGTCGGTA 57.146 42.857 0.00 0.00 32.64 4.02
555 4436 7.413657 CGGTGGTTAGTAACAAATCGAAATGAT 60.414 37.037 14.81 0.00 39.67 2.45
562 4443 4.865925 TGATCGGTGGTTAGTAACAAATCG 59.134 41.667 14.81 13.31 0.00 3.34
654 5880 8.487028 GGAAGAGGAAAGTCATAGGAAATTAGA 58.513 37.037 0.00 0.00 0.00 2.10
703 5929 9.831737 CACTTTGTATGATTTTCTTAGGTCTTG 57.168 33.333 0.00 0.00 0.00 3.02
763 5989 3.838244 TCTATGCACCTAATCACACCC 57.162 47.619 0.00 0.00 0.00 4.61
773 5999 9.391006 TCGTAAAAATTTCTATTCTATGCACCT 57.609 29.630 0.00 0.00 0.00 4.00
816 6042 5.207768 GCAGCAACAAACTATCATATTCCG 58.792 41.667 0.00 0.00 0.00 4.30
904 6140 2.093306 TGTGAATCGCAAGGGTACTG 57.907 50.000 0.00 0.00 38.47 2.74
912 6148 2.221169 ACTCTTGCTTGTGAATCGCAA 58.779 42.857 9.03 9.03 40.93 4.85
1080 6320 4.023365 GTCAACGAGTAGTGTACAAGGACT 60.023 45.833 0.00 0.73 0.00 3.85
1083 6323 4.500603 AGTCAACGAGTAGTGTACAAGG 57.499 45.455 0.00 0.00 0.00 3.61
1131 6371 2.358247 CGGCGGTTTACCTGCTGT 60.358 61.111 0.00 0.00 37.24 4.40
1330 6570 3.188786 GAGGATGTGGTCGTGCGC 61.189 66.667 0.00 0.00 0.00 6.09
1601 7295 2.027605 ACACAGGACACGCGTCAG 59.972 61.111 9.86 0.56 44.54 3.51
1630 7324 0.535335 GGAGAATAGTGTGGTGCGGA 59.465 55.000 0.00 0.00 0.00 5.54
1835 7529 5.104444 TGAGTTCCCTTTTGTAACACAGGTA 60.104 40.000 0.00 0.00 0.00 3.08
1862 7556 9.353999 CCCTAATTTTTACAACTAAAGTCATGC 57.646 33.333 0.00 0.00 0.00 4.06
1877 7571 3.827302 TGGCTGCGTTTCCCTAATTTTTA 59.173 39.130 0.00 0.00 0.00 1.52
1884 7578 2.047655 CGTGGCTGCGTTTCCCTA 60.048 61.111 0.00 0.00 0.00 3.53
1925 7621 0.396556 AAAAGGTCCGCCAGGTTGTT 60.397 50.000 0.00 0.00 39.05 2.83
1932 7628 0.608035 GGATGTGAAAAGGTCCGCCA 60.608 55.000 0.00 0.00 37.19 5.69
2057 7758 2.971261 GCACGACGGATGAAAAAGAAAC 59.029 45.455 0.00 0.00 0.00 2.78
2087 7788 3.826729 AGGGACCAGTAATTCAAAGTTGC 59.173 43.478 0.00 0.00 0.00 4.17
2148 7849 9.662947 AACATACTTATAGAATATTTACCCCGC 57.337 33.333 0.00 0.00 0.00 6.13
2328 8029 3.554129 CCCACCCGTTTTCCTTGAAAATC 60.554 47.826 5.40 0.39 42.31 2.17
2389 8091 0.543277 TAGCGTTCTCGGTCCCTCTA 59.457 55.000 0.00 0.00 46.53 2.43
2671 8380 9.343539 AGCTATTACCCTCTACAAAATGAAATC 57.656 33.333 0.00 0.00 0.00 2.17
2689 8398 9.717892 GGTTAGCTAATTTTTCACAGCTATTAC 57.282 33.333 9.88 3.59 43.94 1.89
2713 8422 3.638860 TCATATGTTAGGACGTCAGGGT 58.361 45.455 18.91 0.90 0.00 4.34
2724 8433 9.445878 AATGCTCACCTATCATTCATATGTTAG 57.554 33.333 1.90 0.00 35.33 2.34
2911 8620 0.251209 TCCTCCTAGCAGTCGTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
2969 8681 0.546122 AGACAACCCACTTCAGCACA 59.454 50.000 0.00 0.00 0.00 4.57
2989 8701 4.397417 CCTTCATTCTCTCGGCTTTTGAAT 59.603 41.667 0.00 0.00 0.00 2.57
2991 8703 3.007940 TCCTTCATTCTCTCGGCTTTTGA 59.992 43.478 0.00 0.00 0.00 2.69
3012 8724 3.894427 TCAAGTAGATCAGCCCATCTCTC 59.106 47.826 0.00 0.00 34.75 3.20
3081 8793 6.655003 TCGATAAAATCAGCAACCTCTTTCTT 59.345 34.615 0.00 0.00 0.00 2.52
3091 8803 5.355071 AGCAGAACATCGATAAAATCAGCAA 59.645 36.000 0.00 0.00 0.00 3.91
3143 8855 4.283978 AGCATAGCTATGATGTGCTCTCTT 59.716 41.667 33.10 3.81 41.97 2.85
3228 8940 2.221169 TCCGCTATGAAATGATGGTGC 58.779 47.619 0.00 0.00 0.00 5.01
3261 8973 5.116180 TGTTAGATCAACCTAGCCAAATCG 58.884 41.667 0.00 0.00 36.20 3.34
3422 9134 1.001406 CTCCTTCTCCCCGATGTATGC 59.999 57.143 0.00 0.00 0.00 3.14
3480 9192 5.634896 AGCGATTCTTTTATGACTGCTTTG 58.365 37.500 0.00 0.00 0.00 2.77
3678 9390 1.898094 ATGTGCTGCTTTGCCGTCA 60.898 52.632 0.00 0.00 0.00 4.35
3687 9399 3.305813 CCTTGAAATTGACATGTGCTGCT 60.306 43.478 1.15 0.00 0.00 4.24
3695 9407 8.782339 GAAATCATTTCCCTTGAAATTGACAT 57.218 30.769 0.00 0.00 46.57 3.06
3786 9498 1.276138 AGTGTCGCCAACATGATCTCA 59.724 47.619 0.00 0.00 40.80 3.27
3885 9597 1.294780 CTTCTCCCTTCTGCGCACT 59.705 57.895 5.66 0.00 0.00 4.40
3984 9696 9.564041 GTCGCACTTTATTTCACTTAATATACG 57.436 33.333 0.00 0.00 0.00 3.06
3997 9709 6.386654 CAAGGTTTATGGTCGCACTTTATTT 58.613 36.000 0.00 0.00 0.00 1.40
4109 9821 3.244526 TGAGCCTGCTAGATGACAACAAA 60.245 43.478 0.00 0.00 0.00 2.83
4121 9833 1.593787 GCAGACACTGAGCCTGCTA 59.406 57.895 12.70 0.00 46.96 3.49
4122 9834 2.346739 GCAGACACTGAGCCTGCT 59.653 61.111 12.70 0.00 46.96 4.24
4124 9836 1.670015 TCAGCAGACACTGAGCCTG 59.330 57.895 2.81 1.59 41.72 4.85
4125 9837 4.204970 TCAGCAGACACTGAGCCT 57.795 55.556 2.81 0.00 41.72 4.58
4130 9842 0.322648 TGGGACATCAGCAGACACTG 59.677 55.000 0.00 0.00 39.12 3.66
4131 9843 0.322975 GTGGGACATCAGCAGACACT 59.677 55.000 0.00 0.00 44.52 3.55
4140 9862 0.611618 GGCATGGTTGTGGGACATCA 60.612 55.000 0.00 0.00 44.52 3.07
4203 9925 8.888579 GCATACCTATCTATATGCGGTATTTT 57.111 34.615 0.84 0.00 43.01 1.82
4219 9941 3.445450 CCGCATGAGTCTAGCATACCTAT 59.555 47.826 0.00 0.00 0.00 2.57
4228 9950 1.002366 GTTGTGCCGCATGAGTCTAG 58.998 55.000 0.00 0.00 0.00 2.43
4230 9952 0.250467 AAGTTGTGCCGCATGAGTCT 60.250 50.000 0.00 0.00 0.00 3.24
4238 9960 2.211353 TAAAACCAAAGTTGTGCCGC 57.789 45.000 0.00 0.00 35.97 6.53
4239 9961 4.425520 TCTTTAAAACCAAAGTTGTGCCG 58.574 39.130 0.00 0.00 36.94 5.69
4259 9981 0.596577 CAGCTTGTGCATGCAACTCT 59.403 50.000 24.58 14.03 42.74 3.24
4266 9988 3.119602 AGCAGAAATACAGCTTGTGCATG 60.120 43.478 7.17 0.00 43.52 4.06
4277 9999 5.935206 TCCATTTGTACGAAGCAGAAATACA 59.065 36.000 1.30 0.00 0.00 2.29
4283 10005 2.935238 GCCTCCATTTGTACGAAGCAGA 60.935 50.000 1.30 0.00 0.00 4.26
4290 10013 2.309528 TGCTAGCCTCCATTTGTACG 57.690 50.000 13.29 0.00 0.00 3.67
4310 10033 4.404394 TGGTTGGTCGCTTCTCAATCTATA 59.596 41.667 0.00 0.00 0.00 1.31
4389 10112 7.875554 TGCAATGAAGTTACATACTACTTGTGA 59.124 33.333 0.00 0.00 35.54 3.58
4468 10191 9.906660 TGGTGAGTAATTATGCTTTTGTAAAAG 57.093 29.630 11.71 11.71 46.25 2.27
4475 10198 8.462016 GTCATCTTGGTGAGTAATTATGCTTTT 58.538 33.333 0.00 0.00 0.00 2.27
4612 10337 7.026631 TGCTTAAGATATGAAATTTGTCCCG 57.973 36.000 6.67 0.00 0.00 5.14
4657 10384 7.652909 CACATTCCTTAAATTTGTTTGAGAGCA 59.347 33.333 0.00 0.00 0.00 4.26
4677 10404 8.620533 AAAAATATTTAAGCTCTCGCACATTC 57.379 30.769 0.01 0.00 39.10 2.67


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

AutoCloner maintained by Alex Coulton.