Multiple sequence alignment - TraesCS4D01G046900

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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 TraesCS4D01G046900 chr4D 100.000 3890 0 0 970 4859 22236347 22232458 0.000000e+00 7184.0
1 TraesCS4D01G046900 chr4D 100.000 644 0 0 1 644 22237316 22236673 0.000000e+00 1190.0
2 TraesCS4D01G046900 chr4D 88.889 63 7 0 2589 2651 487405707 487405645 1.450000e-10 78.7
3 TraesCS4D01G046900 chr4A 93.516 3871 159 48 988 4801 579609641 579613476 0.000000e+00 5674.0
4 TraesCS4D01G046900 chr4A 82.258 434 30 24 185 594 579607603 579608013 1.010000e-86 331.0
5 TraesCS4D01G046900 chr4A 97.315 149 4 0 4065 4213 481920544 481920692 2.240000e-63 254.0
6 TraesCS4D01G046900 chr4A 89.256 121 8 2 4742 4857 481921110 481921230 3.920000e-31 147.0
7 TraesCS4D01G046900 chr4A 91.579 95 5 2 1 92 579609109 579609203 1.420000e-25 128.0
8 TraesCS4D01G046900 chr4A 84.348 115 4 3 498 610 579609455 579609557 3.090000e-17 100.0
9 TraesCS4D01G046900 chr4A 95.082 61 3 0 2597 2657 673443022 673443082 4.000000e-16 97.1
10 TraesCS4D01G046900 chr4B 93.516 3717 150 36 970 4647 34278595 34274931 0.000000e+00 5445.0
11 TraesCS4D01G046900 chr4B 91.317 357 17 10 240 594 34279358 34279014 4.400000e-130 475.0
12 TraesCS4D01G046900 chr4B 88.068 176 12 5 16 186 34279547 34279376 2.970000e-47 200.0
13 TraesCS4D01G046900 chr6A 97.315 149 4 0 4065 4213 8884312 8884460 2.240000e-63 254.0
14 TraesCS4D01G046900 chr6A 96.644 149 5 0 4065 4213 616697957 616698105 1.040000e-61 248.0
15 TraesCS4D01G046900 chr6A 90.909 121 6 2 4742 4857 268259510 268259630 1.810000e-34 158.0
16 TraesCS4D01G046900 chr3A 96.711 152 5 0 4065 4216 142731839 142731688 2.240000e-63 254.0
17 TraesCS4D01G046900 chr3A 89.256 121 8 2 4742 4857 723962154 723962274 3.920000e-31 147.0
18 TraesCS4D01G046900 chr2A 96.711 152 5 0 4065 4216 693627418 693627267 2.240000e-63 254.0
19 TraesCS4D01G046900 chr2A 90.909 121 6 2 4742 4857 292395061 292395181 1.810000e-34 158.0
20 TraesCS4D01G046900 chr2A 90.411 73 7 0 2584 2656 583834065 583833993 4.000000e-16 97.1
21 TraesCS4D01G046900 chr3B 96.053 152 6 0 4065 4216 807024564 807024413 1.040000e-61 248.0
22 TraesCS4D01G046900 chr1A 96.644 149 5 0 4065 4213 96086447 96086595 1.040000e-61 248.0
23 TraesCS4D01G046900 chr1A 90.083 121 7 2 4742 4857 31510025 31510145 8.420000e-33 152.0
24 TraesCS4D01G046900 chr1A 90.083 121 7 2 4742 4857 96087226 96087346 8.420000e-33 152.0
25 TraesCS4D01G046900 chr2B 90.083 121 7 2 4742 4857 8841048 8840928 8.420000e-33 152.0
26 TraesCS4D01G046900 chr2B 89.041 73 7 1 2584 2656 518042384 518042313 6.700000e-14 89.8
27 TraesCS4D01G046900 chr7A 89.256 121 8 2 4742 4857 466904828 466904948 3.920000e-31 147.0
28 TraesCS4D01G046900 chr2D 88.095 84 10 0 2584 2667 440317313 440317230 3.090000e-17 100.0
29 TraesCS4D01G046900 chr5D 80.208 96 15 3 2571 2666 319256336 319256427 8.730000e-08 69.4
30 TraesCS4D01G046900 chr1D 79.310 87 16 2 2571 2656 60405062 60405147 5.250000e-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 TraesCS4D01G046900 chr4D 22232458 22237316 4858 True 4187.00 7184 100.00000 1 4859 2 chr4D.!!$R2 4858
1 TraesCS4D01G046900 chr4A 579607603 579613476 5873 False 1558.25 5674 87.92525 1 4801 4 chr4A.!!$F3 4800
2 TraesCS4D01G046900 chr4A 481920544 481921230 686 False 200.50 254 93.28550 4065 4857 2 chr4A.!!$F2 792
3 TraesCS4D01G046900 chr4B 34274931 34279547 4616 True 2040.00 5445 90.96700 16 4647 3 chr4B.!!$R1 4631

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
550 2077 0.107557 GGAATAAAACCCGGCCGAGA 60.108 55.0 30.73 4.76 0.00 4.04 F
604 2131 0.331954 GGTTTTTCCCTCCCTCCCTC 59.668 60.0 0.00 0.00 0.00 4.30 F
605 2132 0.331954 GTTTTTCCCTCCCTCCCTCC 59.668 60.0 0.00 0.00 0.00 4.30 F
606 2133 0.849540 TTTTTCCCTCCCTCCCTCCC 60.850 60.0 0.00 0.00 0.00 4.30 F
2464 4345 1.024046 TGTTGTGCTCGTGCTTGTGT 61.024 50.0 11.19 0.00 40.48 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 4155 1.185618 AGTAAGCACGGAGAGGCACA 61.186 55.000 0.0 0.0 34.24 4.57 R
2491 4372 1.687123 GTACCACTCTACCATCGCCAT 59.313 52.381 0.0 0.0 0.00 4.40 R
2663 4544 7.512130 AGATAATCAAGCCATGACAGATGTAA 58.488 34.615 0.0 0.0 41.93 2.41 R
2697 4578 1.557443 CGCCTTCGACAAGACACACC 61.557 60.000 0.0 0.0 38.10 4.16 R
4346 6645 0.099613 CCGGATCGAGACAGACACAG 59.900 60.000 0.0 0.0 0.00 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
60 1567 3.208884 GACAGACGGACGCTGTGGT 62.209 63.158 20.38 1.76 45.94 4.16
94 1604 1.003233 GAGGCCGCTCTGACCTTTT 60.003 57.895 0.00 0.00 32.67 2.27
111 1621 2.559698 TTTCAGGCGACCTTTCATCA 57.440 45.000 0.00 0.00 0.00 3.07
154 1664 4.245054 CGATCGATCGCCGGAAAT 57.755 55.556 32.34 0.00 43.84 2.17
155 1665 2.517598 CGATCGATCGCCGGAAATT 58.482 52.632 32.34 0.00 43.84 1.82
157 1667 1.784525 GATCGATCGCCGGAAATTCT 58.215 50.000 11.09 0.00 39.14 2.40
194 1706 8.506168 TGGAAGAGCAGTAAATATTAACCAAG 57.494 34.615 0.00 0.00 0.00 3.61
195 1707 8.107095 TGGAAGAGCAGTAAATATTAACCAAGT 58.893 33.333 0.00 0.00 0.00 3.16
201 1713 8.985805 AGCAGTAAATATTAACCAAGTATACGC 58.014 33.333 0.00 0.00 0.00 4.42
202 1714 8.985805 GCAGTAAATATTAACCAAGTATACGCT 58.014 33.333 0.00 0.00 0.00 5.07
204 1716 9.702494 AGTAAATATTAACCAAGTATACGCTCC 57.298 33.333 0.00 0.00 0.00 4.70
205 1717 9.480053 GTAAATATTAACCAAGTATACGCTCCA 57.520 33.333 0.00 0.00 0.00 3.86
206 1718 8.603242 AAATATTAACCAAGTATACGCTCCAG 57.397 34.615 0.00 0.00 0.00 3.86
210 1722 4.755266 ACCAAGTATACGCTCCAGAATT 57.245 40.909 0.00 0.00 0.00 2.17
211 1723 4.442706 ACCAAGTATACGCTCCAGAATTG 58.557 43.478 0.00 0.00 0.00 2.32
212 1724 3.809832 CCAAGTATACGCTCCAGAATTGG 59.190 47.826 0.00 0.00 46.49 3.16
213 1725 3.113260 AGTATACGCTCCAGAATTGGC 57.887 47.619 0.00 0.00 44.63 4.52
214 1726 2.434336 AGTATACGCTCCAGAATTGGCA 59.566 45.455 0.00 0.00 44.63 4.92
217 1729 2.753966 CGCTCCAGAATTGGCACGG 61.754 63.158 0.00 0.00 44.63 4.94
221 1733 1.002134 CCAGAATTGGCACGGAGGT 60.002 57.895 0.00 0.00 37.73 3.85
223 1735 1.339631 CCAGAATTGGCACGGAGGTAA 60.340 52.381 0.00 0.00 37.73 2.85
224 1736 2.432444 CAGAATTGGCACGGAGGTAAA 58.568 47.619 0.00 0.00 0.00 2.01
226 1738 2.304761 AGAATTGGCACGGAGGTAAAGA 59.695 45.455 0.00 0.00 0.00 2.52
227 1739 2.871096 ATTGGCACGGAGGTAAAGAA 57.129 45.000 0.00 0.00 0.00 2.52
228 1740 2.642154 TTGGCACGGAGGTAAAGAAA 57.358 45.000 0.00 0.00 0.00 2.52
229 1741 2.642154 TGGCACGGAGGTAAAGAAAA 57.358 45.000 0.00 0.00 0.00 2.29
230 1742 2.223745 TGGCACGGAGGTAAAGAAAAC 58.776 47.619 0.00 0.00 0.00 2.43
231 1743 1.538512 GGCACGGAGGTAAAGAAAACC 59.461 52.381 0.00 0.00 37.27 3.27
232 1744 1.196127 GCACGGAGGTAAAGAAAACCG 59.804 52.381 0.00 0.00 42.15 4.44
233 1745 1.196127 CACGGAGGTAAAGAAAACCGC 59.804 52.381 0.00 0.00 43.36 5.68
234 1746 1.202675 ACGGAGGTAAAGAAAACCGCA 60.203 47.619 0.00 0.00 43.36 5.69
235 1747 1.463444 CGGAGGTAAAGAAAACCGCAG 59.537 52.381 0.00 0.00 42.15 5.18
236 1748 2.501261 GGAGGTAAAGAAAACCGCAGT 58.499 47.619 0.00 0.00 42.15 4.40
247 1759 2.270352 AACCGCAGTGAAAATCAGGA 57.730 45.000 0.00 0.00 0.00 3.86
251 1763 2.813754 CCGCAGTGAAAATCAGGAAGAA 59.186 45.455 0.00 0.00 0.00 2.52
292 1805 1.556911 TCCAGCTCAGAACAATCCCTC 59.443 52.381 0.00 0.00 0.00 4.30
295 1808 0.915364 GCTCAGAACAATCCCTCCCT 59.085 55.000 0.00 0.00 0.00 4.20
300 1813 2.893682 GAACAATCCCTCCCTGCCCG 62.894 65.000 0.00 0.00 0.00 6.13
301 1814 4.195334 CAATCCCTCCCTGCCCGG 62.195 72.222 0.00 0.00 0.00 5.73
542 2069 2.122797 CCCCCGCGGAATAAAACCC 61.123 63.158 30.73 0.00 0.00 4.11
544 2071 2.474612 CCCGCGGAATAAAACCCGG 61.475 63.158 30.73 0.00 45.42 5.73
545 2072 2.405997 CGCGGAATAAAACCCGGC 59.594 61.111 0.00 0.00 45.42 6.13
546 2073 2.802792 GCGGAATAAAACCCGGCC 59.197 61.111 0.00 0.00 45.42 6.13
547 2074 3.103875 CGGAATAAAACCCGGCCG 58.896 61.111 21.04 21.04 41.89 6.13
548 2075 1.449956 CGGAATAAAACCCGGCCGA 60.450 57.895 30.73 5.29 41.89 5.54
549 2076 1.433837 CGGAATAAAACCCGGCCGAG 61.434 60.000 30.73 18.52 41.89 4.63
550 2077 0.107557 GGAATAAAACCCGGCCGAGA 60.108 55.000 30.73 4.76 0.00 4.04
551 2078 1.296727 GAATAAAACCCGGCCGAGAG 58.703 55.000 30.73 17.70 0.00 3.20
603 2130 2.487741 GGTTTTTCCCTCCCTCCCT 58.512 57.895 0.00 0.00 0.00 4.20
604 2131 0.331954 GGTTTTTCCCTCCCTCCCTC 59.668 60.000 0.00 0.00 0.00 4.30
605 2132 0.331954 GTTTTTCCCTCCCTCCCTCC 59.668 60.000 0.00 0.00 0.00 4.30
606 2133 0.849540 TTTTTCCCTCCCTCCCTCCC 60.850 60.000 0.00 0.00 0.00 4.30
1744 3619 4.657824 CCTCGCCGACAACACCGT 62.658 66.667 0.00 0.00 0.00 4.83
1884 3759 2.235898 GTTCCTTCTCATCTGCCTCTGT 59.764 50.000 0.00 0.00 0.00 3.41
1932 3807 3.531207 CTCGAGATGCCGCCTCCA 61.531 66.667 6.58 0.00 0.00 3.86
2277 4155 2.072298 GAGCTTCAGCACGAGTTCATT 58.928 47.619 0.75 0.00 45.16 2.57
2385 4263 2.009774 CACGGTGAGAATTCCACATCC 58.990 52.381 21.19 14.99 36.31 3.51
2390 4268 3.562176 GGTGAGAATTCCACATCCCAGTT 60.562 47.826 21.19 0.00 36.31 3.16
2400 4278 3.244911 CCACATCCCAGTTCCTTTACAGT 60.245 47.826 0.00 0.00 0.00 3.55
2464 4345 1.024046 TGTTGTGCTCGTGCTTGTGT 61.024 50.000 11.19 0.00 40.48 3.72
2491 4372 6.003234 TCTTATTTTCGCATTTTTCGTCCA 57.997 33.333 0.00 0.00 0.00 4.02
2586 4467 7.273598 CGATTGTCTTGTACTATATCCATTCCG 59.726 40.741 0.00 0.00 0.00 4.30
2663 4544 8.548880 TTAGAAACAGAGGGTGTAGCTATTAT 57.451 34.615 0.00 0.00 39.03 1.28
2697 4578 8.243426 GTCATGGCTTGATTATCTCTAGTCTAG 58.757 40.741 6.35 0.00 36.54 2.43
2715 4596 0.249911 AGGTGTGTCTTGTCGAAGGC 60.250 55.000 0.00 0.00 34.08 4.35
2872 4755 6.451393 GTCTGAGACTATGTTTATGGCTAGG 58.549 44.000 5.12 0.00 0.00 3.02
2930 4813 1.408822 GGGGTTACCAATCTGCTCCAG 60.409 57.143 2.98 0.00 39.85 3.86
2935 4818 4.321230 GGTTACCAATCTGCTCCAGTTTTG 60.321 45.833 0.00 0.00 32.61 2.44
3097 4982 2.706723 TGGGAAGCTGTTGTAGTTGGTA 59.293 45.455 0.00 0.00 0.00 3.25
3158 5043 4.143986 TGTGTCACTTGACCATGTAACA 57.856 40.909 6.91 1.00 44.15 2.41
3187 5072 4.177026 CCTTGAACTCTAATCTCACACGG 58.823 47.826 0.00 0.00 0.00 4.94
3190 5075 3.572682 TGAACTCTAATCTCACACGGTGT 59.427 43.478 8.21 8.21 34.79 4.16
3361 5246 3.643237 TCCAATATCCTCCTGTCGAAGT 58.357 45.455 0.00 0.00 0.00 3.01
3417 5302 2.162208 CACCCTTGTTGGTTCATCATCG 59.838 50.000 0.00 0.00 36.12 3.84
3437 5322 3.997064 CTGGACCTTCTCGCGCCAG 62.997 68.421 11.41 11.41 40.03 4.85
3514 5399 2.033424 GTGTTCAGCTTTGGTGTTCTCC 59.967 50.000 0.00 0.00 32.43 3.71
3796 5681 2.549349 GGTGGAAGCACCGAAGAAACTA 60.549 50.000 0.00 0.00 42.61 2.24
3811 5699 6.292865 CGAAGAAACTAATCAACAACAGAGCA 60.293 38.462 0.00 0.00 0.00 4.26
3870 5758 0.394192 CGCCCTGATCTCTAATGGCA 59.606 55.000 0.00 0.00 38.81 4.92
3906 5797 2.034066 TGCCTGTTGCTGTAGCCC 59.966 61.111 0.80 0.00 42.00 5.19
4165 6077 3.906720 TCTTTAGCTGTCCCCATGTAC 57.093 47.619 0.00 0.00 0.00 2.90
4224 6523 4.261447 GCGAAAACCATTGGTGAGTTTACT 60.261 41.667 9.62 0.00 35.34 2.24
4256 6555 1.272490 TGTCCTGTGGATCGAGTTGTC 59.728 52.381 0.00 0.00 32.73 3.18
4301 6600 1.891449 TGTGTGTGTGGGTCATGCG 60.891 57.895 0.00 0.00 0.00 4.73
4346 6645 0.586319 TGTTGAAAGCTACTGCGTGC 59.414 50.000 0.00 0.00 45.42 5.34
4427 6726 0.675633 CTGTTTTGAACTGGCAGGGG 59.324 55.000 20.34 0.00 0.00 4.79
4429 6728 2.199652 TTTTGAACTGGCAGGGGCG 61.200 57.895 20.34 0.00 42.47 6.13
4493 6804 0.913924 TGCCTGCTCCTCATCATTGA 59.086 50.000 0.00 0.00 0.00 2.57
4584 6896 1.402984 CCAGAGGTTCTGTACACGCTC 60.403 57.143 5.46 0.00 42.80 5.03
4606 6918 6.741811 GCTCGATGATGATTATGATTCAAAGC 59.258 38.462 0.00 0.00 0.00 3.51
4634 6946 5.984233 TCTTAGTTGTTGTAGTTGCTGTG 57.016 39.130 0.00 0.00 0.00 3.66
4636 6948 5.293324 TCTTAGTTGTTGTAGTTGCTGTGTG 59.707 40.000 0.00 0.00 0.00 3.82
4642 6954 3.701205 TGTAGTTGCTGTGTGGATGAT 57.299 42.857 0.00 0.00 0.00 2.45
4652 6964 4.545929 TGGATGATCCAAGCGCTG 57.454 55.556 12.58 5.12 45.00 5.18
4653 6965 1.906995 TGGATGATCCAAGCGCTGA 59.093 52.632 12.58 4.96 45.00 4.26
4660 6972 0.176680 ATCCAAGCGCTGAATCTCGT 59.823 50.000 12.58 0.00 0.00 4.18
4661 6973 0.815095 TCCAAGCGCTGAATCTCGTA 59.185 50.000 12.58 0.00 0.00 3.43
4662 6974 1.202302 TCCAAGCGCTGAATCTCGTAG 60.202 52.381 12.58 0.00 0.00 3.51
4663 6975 0.574454 CAAGCGCTGAATCTCGTAGC 59.426 55.000 12.58 0.00 0.00 3.58
4668 6980 2.980962 GCTGAATCTCGTAGCGTTTC 57.019 50.000 0.00 0.00 0.00 2.78
4669 6981 2.531206 GCTGAATCTCGTAGCGTTTCT 58.469 47.619 0.00 0.00 0.00 2.52
4670 6982 3.692576 GCTGAATCTCGTAGCGTTTCTA 58.307 45.455 0.00 0.00 0.00 2.10
4671 6983 3.726730 GCTGAATCTCGTAGCGTTTCTAG 59.273 47.826 0.00 0.00 0.00 2.43
4673 6985 3.693085 TGAATCTCGTAGCGTTTCTAGGT 59.307 43.478 0.00 0.00 35.32 3.08
4674 6986 3.967203 ATCTCGTAGCGTTTCTAGGTC 57.033 47.619 0.00 0.00 35.32 3.85
4675 6987 2.012673 TCTCGTAGCGTTTCTAGGTCC 58.987 52.381 0.00 0.00 35.32 4.46
4717 7043 1.396653 GAACAAGCATCATCCCTGGG 58.603 55.000 6.33 6.33 0.00 4.45
4718 7044 0.032813 AACAAGCATCATCCCTGGGG 60.033 55.000 14.00 2.42 0.00 4.96
4727 7053 3.916184 TCCCTGGGGACTTGGTTC 58.084 61.111 14.00 0.00 39.76 3.62
4728 7054 1.241929 TCCCTGGGGACTTGGTTCT 59.758 57.895 14.00 0.00 39.76 3.01
4732 7058 0.890996 CTGGGGACTTGGTTCTGTGC 60.891 60.000 0.00 0.00 0.00 4.57
4817 7148 2.435410 CGGGGCGGGTTTCACTAC 60.435 66.667 0.00 0.00 0.00 2.73
4837 7168 2.812011 ACGTTTCAATGGTTCTGGTAGC 59.188 45.455 0.00 0.00 0.00 3.58
4839 7170 3.421844 GTTTCAATGGTTCTGGTAGCCT 58.578 45.455 0.00 0.00 0.00 4.58
4841 7172 1.281867 TCAATGGTTCTGGTAGCCTGG 59.718 52.381 0.00 0.00 0.00 4.45
4849 7180 2.366435 GGTAGCCTGGGCCACCTA 60.366 66.667 19.26 3.30 46.72 3.08
4857 7188 1.550072 CCTGGGCCACCTACAATTTTG 59.450 52.381 0.00 0.00 37.76 2.44
4858 7189 1.550072 CTGGGCCACCTACAATTTTGG 59.450 52.381 0.00 0.00 37.76 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.825160 ATTGTCGTGCGGCAGTGGT 62.825 57.895 1.18 0.00 0.00 4.16
1 2 3.027170 GATTGTCGTGCGGCAGTGG 62.027 63.158 1.18 0.00 0.00 4.00
2 3 2.476051 GATTGTCGTGCGGCAGTG 59.524 61.111 1.18 0.00 0.00 3.66
3 4 2.742372 GGATTGTCGTGCGGCAGT 60.742 61.111 1.18 0.00 0.00 4.40
4 5 1.647545 ATTGGATTGTCGTGCGGCAG 61.648 55.000 1.18 0.00 0.00 4.85
5 6 1.643868 GATTGGATTGTCGTGCGGCA 61.644 55.000 0.00 0.00 0.00 5.69
6 7 1.062525 GATTGGATTGTCGTGCGGC 59.937 57.895 0.00 0.00 0.00 6.53
8 9 0.801872 TTGGATTGGATTGTCGTGCG 59.198 50.000 0.00 0.00 0.00 5.34
9 10 1.468054 GCTTGGATTGGATTGTCGTGC 60.468 52.381 0.00 0.00 0.00 5.34
10 11 1.202065 CGCTTGGATTGGATTGTCGTG 60.202 52.381 0.00 0.00 0.00 4.35
11 12 1.086696 CGCTTGGATTGGATTGTCGT 58.913 50.000 0.00 0.00 0.00 4.34
12 13 1.062587 GACGCTTGGATTGGATTGTCG 59.937 52.381 0.00 0.00 0.00 4.35
13 14 1.401905 GGACGCTTGGATTGGATTGTC 59.598 52.381 0.00 0.00 0.00 3.18
60 1567 1.254026 CCTCTCCGTGTTGACTGGTA 58.746 55.000 0.00 0.00 0.00 3.25
94 1604 0.391661 GCTGATGAAAGGTCGCCTGA 60.392 55.000 0.00 0.00 32.13 3.86
140 1650 0.458260 TGAGAATTTCCGGCGATCGA 59.542 50.000 21.57 0.00 42.43 3.59
154 1664 0.179032 TTCCAGCGTTTGCCTGAGAA 60.179 50.000 0.00 0.00 44.31 2.87
155 1665 0.603707 CTTCCAGCGTTTGCCTGAGA 60.604 55.000 0.00 0.00 44.31 3.27
157 1667 0.603707 CTCTTCCAGCGTTTGCCTGA 60.604 55.000 0.00 0.00 44.31 3.86
186 1698 5.664294 TTCTGGAGCGTATACTTGGTTAA 57.336 39.130 0.56 0.00 0.00 2.01
187 1699 5.864418 ATTCTGGAGCGTATACTTGGTTA 57.136 39.130 0.56 0.00 0.00 2.85
188 1700 4.755266 ATTCTGGAGCGTATACTTGGTT 57.245 40.909 0.56 0.00 0.00 3.67
190 1702 3.809832 CCAATTCTGGAGCGTATACTTGG 59.190 47.826 0.56 1.23 46.92 3.61
191 1703 3.248602 GCCAATTCTGGAGCGTATACTTG 59.751 47.826 0.56 0.00 46.92 3.16
194 1706 2.544267 GTGCCAATTCTGGAGCGTATAC 59.456 50.000 0.00 0.00 46.92 1.47
195 1707 2.801699 CGTGCCAATTCTGGAGCGTATA 60.802 50.000 0.00 0.00 46.92 1.47
198 1710 2.034879 CGTGCCAATTCTGGAGCGT 61.035 57.895 0.00 0.00 46.92 5.07
200 1712 1.372087 CTCCGTGCCAATTCTGGAGC 61.372 60.000 0.00 0.00 46.92 4.70
201 1713 0.745845 CCTCCGTGCCAATTCTGGAG 60.746 60.000 0.00 0.00 46.92 3.86
202 1714 1.299648 CCTCCGTGCCAATTCTGGA 59.700 57.895 0.00 0.00 46.92 3.86
203 1715 0.251916 TACCTCCGTGCCAATTCTGG 59.748 55.000 0.00 0.00 46.65 3.86
204 1716 2.107950 TTACCTCCGTGCCAATTCTG 57.892 50.000 0.00 0.00 0.00 3.02
205 1717 2.304761 TCTTTACCTCCGTGCCAATTCT 59.695 45.455 0.00 0.00 0.00 2.40
206 1718 2.706890 TCTTTACCTCCGTGCCAATTC 58.293 47.619 0.00 0.00 0.00 2.17
210 1722 2.223745 GTTTTCTTTACCTCCGTGCCA 58.776 47.619 0.00 0.00 0.00 4.92
211 1723 1.538512 GGTTTTCTTTACCTCCGTGCC 59.461 52.381 0.00 0.00 32.75 5.01
212 1724 1.196127 CGGTTTTCTTTACCTCCGTGC 59.804 52.381 0.00 0.00 33.35 5.34
213 1725 1.196127 GCGGTTTTCTTTACCTCCGTG 59.804 52.381 0.00 0.00 40.05 4.94
214 1726 1.202675 TGCGGTTTTCTTTACCTCCGT 60.203 47.619 0.00 0.00 40.05 4.69
217 1729 3.135994 TCACTGCGGTTTTCTTTACCTC 58.864 45.455 0.00 0.00 33.35 3.85
221 1733 6.137794 TGATTTTCACTGCGGTTTTCTTTA 57.862 33.333 0.00 0.00 0.00 1.85
223 1735 4.499696 CCTGATTTTCACTGCGGTTTTCTT 60.500 41.667 0.00 0.00 0.00 2.52
224 1736 3.004734 CCTGATTTTCACTGCGGTTTTCT 59.995 43.478 0.00 0.00 0.00 2.52
226 1738 2.955660 TCCTGATTTTCACTGCGGTTTT 59.044 40.909 0.00 0.00 0.00 2.43
227 1739 2.582052 TCCTGATTTTCACTGCGGTTT 58.418 42.857 0.00 0.00 0.00 3.27
228 1740 2.270352 TCCTGATTTTCACTGCGGTT 57.730 45.000 0.00 0.00 0.00 4.44
229 1741 2.154462 CTTCCTGATTTTCACTGCGGT 58.846 47.619 0.00 0.00 0.00 5.68
230 1742 2.426522 TCTTCCTGATTTTCACTGCGG 58.573 47.619 0.00 0.00 0.00 5.69
231 1743 4.023707 ACTTTCTTCCTGATTTTCACTGCG 60.024 41.667 0.00 0.00 0.00 5.18
232 1744 5.009010 TCACTTTCTTCCTGATTTTCACTGC 59.991 40.000 0.00 0.00 0.00 4.40
233 1745 6.624352 TCACTTTCTTCCTGATTTTCACTG 57.376 37.500 0.00 0.00 0.00 3.66
234 1746 7.340487 AGTTTCACTTTCTTCCTGATTTTCACT 59.660 33.333 0.00 0.00 0.00 3.41
235 1747 7.433425 CAGTTTCACTTTCTTCCTGATTTTCAC 59.567 37.037 0.00 0.00 0.00 3.18
236 1748 7.339212 TCAGTTTCACTTTCTTCCTGATTTTCA 59.661 33.333 0.00 0.00 0.00 2.69
247 1759 1.597663 CCGCGTCAGTTTCACTTTCTT 59.402 47.619 4.92 0.00 0.00 2.52
251 1763 1.227556 AGCCGCGTCAGTTTCACTT 60.228 52.632 4.92 0.00 0.00 3.16
331 1844 2.255252 GCCGAACAAATGCGTGCT 59.745 55.556 0.00 0.00 0.00 4.40
363 1876 2.264794 GGATTGCGACACCGGACT 59.735 61.111 9.46 0.00 35.37 3.85
365 1878 4.444838 CGGGATTGCGACACCGGA 62.445 66.667 9.46 0.00 42.48 5.14
376 1889 3.081409 CTGGGGGACGACGGGATT 61.081 66.667 0.00 0.00 0.00 3.01
437 1952 2.047213 TTTGGTTCGCTCGGTTCCCT 62.047 55.000 0.00 0.00 0.00 4.20
451 1966 1.157870 CGTTGGCTCGTCTGTTTGGT 61.158 55.000 0.00 0.00 0.00 3.67
975 2819 3.966543 GTGGGGTGTGGGTGGAGG 61.967 72.222 0.00 0.00 0.00 4.30
976 2820 3.966543 GGTGGGGTGTGGGTGGAG 61.967 72.222 0.00 0.00 0.00 3.86
1774 3649 3.096092 TGCCCTTCTTGTCAGTTTGTTT 58.904 40.909 0.00 0.00 0.00 2.83
1778 3653 2.689983 CTGTTGCCCTTCTTGTCAGTTT 59.310 45.455 0.00 0.00 0.00 2.66
1781 3656 1.242076 CCTGTTGCCCTTCTTGTCAG 58.758 55.000 0.00 0.00 0.00 3.51
1932 3807 4.880426 ACGGCGGGGGATGGAGAT 62.880 66.667 13.24 0.00 0.00 2.75
2277 4155 1.185618 AGTAAGCACGGAGAGGCACA 61.186 55.000 0.00 0.00 34.24 4.57
2464 4345 7.694784 GGACGAAAAATGCGAAAATAAGATACA 59.305 33.333 0.00 0.00 0.00 2.29
2491 4372 1.687123 GTACCACTCTACCATCGCCAT 59.313 52.381 0.00 0.00 0.00 4.40
2663 4544 7.512130 AGATAATCAAGCCATGACAGATGTAA 58.488 34.615 0.00 0.00 41.93 2.41
2697 4578 1.557443 CGCCTTCGACAAGACACACC 61.557 60.000 0.00 0.00 38.10 4.16
2715 4596 4.383774 TCAAAATTAGCTTGACGTGTCG 57.616 40.909 0.00 0.00 0.00 4.35
2930 4813 7.141363 ACAGTTCTATCAACATTCTGCAAAAC 58.859 34.615 0.00 0.00 0.00 2.43
2935 4818 6.486253 TCAACAGTTCTATCAACATTCTGC 57.514 37.500 0.00 0.00 0.00 4.26
3063 4948 3.983344 CAGCTTCCCAAGATTTTGTTTCG 59.017 43.478 0.00 0.00 32.21 3.46
3158 5043 7.038729 TGTGAGATTAGAGTTCAAGGTTCATCT 60.039 37.037 0.00 0.00 0.00 2.90
3361 5246 2.729360 CTGAAACACGTGCTTGATACGA 59.271 45.455 17.22 0.00 43.82 3.43
3417 5302 2.507324 GCGCGAGAAGGTCCAGAC 60.507 66.667 12.10 0.00 0.00 3.51
3437 5322 0.103208 CTCTGGAGCACGGTATCCAC 59.897 60.000 9.53 0.00 40.70 4.02
3514 5399 2.508887 GGTGAGCAGCTCGAGCAG 60.509 66.667 36.87 30.54 45.16 4.24
3747 5632 0.751643 TGATCTCCTCGATCCGCACA 60.752 55.000 0.00 0.00 46.52 4.57
3796 5681 2.158623 TCAGGGTGCTCTGTTGTTGATT 60.159 45.455 0.00 0.00 36.25 2.57
3855 5743 5.725325 TCTCTCATGCCATTAGAGATCAG 57.275 43.478 13.34 0.00 40.56 2.90
3870 5758 0.980231 AGCCGGCTCCTTTCTCTCAT 60.980 55.000 27.08 0.00 0.00 2.90
3896 5786 1.410083 GGAATGAATGGGGCTACAGCA 60.410 52.381 3.24 0.00 44.36 4.41
3906 5797 5.817296 TCAAGTCTATGAACGGAATGAATGG 59.183 40.000 0.00 0.00 0.00 3.16
4165 6077 3.242870 GCAATTTGATCGGGCTGAGTAAG 60.243 47.826 1.04 0.00 0.00 2.34
4224 6523 1.344953 ACAGGACAGACACCAGGCAA 61.345 55.000 0.00 0.00 0.00 4.52
4301 6600 1.598701 GGAGCCATCCAAAGCACCAC 61.599 60.000 0.00 0.00 45.87 4.16
4326 6625 1.398960 GCACGCAGTAGCTTTCAACAG 60.399 52.381 0.00 0.00 41.61 3.16
4346 6645 0.099613 CCGGATCGAGACAGACACAG 59.900 60.000 0.00 0.00 0.00 3.66
4427 6726 0.323451 AATTCAGTTTCCCTCCCCGC 60.323 55.000 0.00 0.00 0.00 6.13
4429 6728 2.899303 TCAATTCAGTTTCCCTCCCC 57.101 50.000 0.00 0.00 0.00 4.81
4493 6804 7.451255 TCCCAACTGTTAATCAACAATGAGAAT 59.549 33.333 0.00 0.00 43.92 2.40
4549 6861 2.333014 CTCTGGTTTTGCTCTCTCGAC 58.667 52.381 0.00 0.00 0.00 4.20
4584 6896 9.917872 GATAGCTTTGAATCATAATCATCATCG 57.082 33.333 0.00 0.00 0.00 3.84
4606 6918 8.598924 CAGCAACTACAACAACTAAGATGATAG 58.401 37.037 0.00 0.00 0.00 2.08
4611 6923 6.017934 CACACAGCAACTACAACAACTAAGAT 60.018 38.462 0.00 0.00 0.00 2.40
4612 6924 5.293324 CACACAGCAACTACAACAACTAAGA 59.707 40.000 0.00 0.00 0.00 2.10
4613 6925 5.501715 CACACAGCAACTACAACAACTAAG 58.498 41.667 0.00 0.00 0.00 2.18
4614 6926 4.334203 CCACACAGCAACTACAACAACTAA 59.666 41.667 0.00 0.00 0.00 2.24
4615 6927 3.874543 CCACACAGCAACTACAACAACTA 59.125 43.478 0.00 0.00 0.00 2.24
4616 6928 2.682856 CCACACAGCAACTACAACAACT 59.317 45.455 0.00 0.00 0.00 3.16
4617 6929 2.680841 TCCACACAGCAACTACAACAAC 59.319 45.455 0.00 0.00 0.00 3.32
4618 6930 2.992593 TCCACACAGCAACTACAACAA 58.007 42.857 0.00 0.00 0.00 2.83
4619 6931 2.700722 TCCACACAGCAACTACAACA 57.299 45.000 0.00 0.00 0.00 3.33
4620 6932 3.138304 TCATCCACACAGCAACTACAAC 58.862 45.455 0.00 0.00 0.00 3.32
4636 6948 1.534595 GATTCAGCGCTTGGATCATCC 59.465 52.381 7.50 0.00 40.92 3.51
4642 6954 0.815095 TACGAGATTCAGCGCTTGGA 59.185 50.000 7.50 0.00 0.00 3.53
4649 6961 2.531206 AGAAACGCTACGAGATTCAGC 58.469 47.619 0.00 0.00 0.00 4.26
4651 6963 3.693085 ACCTAGAAACGCTACGAGATTCA 59.307 43.478 0.00 0.00 0.00 2.57
4652 6964 4.281264 GACCTAGAAACGCTACGAGATTC 58.719 47.826 0.00 0.00 0.00 2.52
4653 6965 3.066481 GGACCTAGAAACGCTACGAGATT 59.934 47.826 0.00 0.00 0.00 2.40
4660 6972 0.323725 ACCGGGACCTAGAAACGCTA 60.324 55.000 6.32 0.00 0.00 4.26
4661 6973 0.323725 TACCGGGACCTAGAAACGCT 60.324 55.000 6.32 0.00 0.00 5.07
4662 6974 0.101939 CTACCGGGACCTAGAAACGC 59.898 60.000 6.32 0.00 0.00 4.84
4663 6975 1.755179 TCTACCGGGACCTAGAAACG 58.245 55.000 6.32 0.00 0.00 3.60
4664 6976 2.364647 CCATCTACCGGGACCTAGAAAC 59.635 54.545 6.32 0.00 0.00 2.78
4665 6977 2.674420 CCATCTACCGGGACCTAGAAA 58.326 52.381 6.32 0.00 0.00 2.52
4666 6978 1.756690 GCCATCTACCGGGACCTAGAA 60.757 57.143 6.32 0.00 0.00 2.10
4667 6979 0.178970 GCCATCTACCGGGACCTAGA 60.179 60.000 6.32 3.90 0.00 2.43
4668 6980 0.469331 TGCCATCTACCGGGACCTAG 60.469 60.000 6.32 0.00 0.00 3.02
4669 6981 0.031917 TTGCCATCTACCGGGACCTA 60.032 55.000 6.32 0.00 0.00 3.08
4670 6982 1.306654 TTGCCATCTACCGGGACCT 60.307 57.895 6.32 0.00 0.00 3.85
4671 6983 1.146263 CTTGCCATCTACCGGGACC 59.854 63.158 6.32 0.00 0.00 4.46
4673 6985 2.908015 GCTTGCCATCTACCGGGA 59.092 61.111 6.32 0.00 0.00 5.14
4674 6986 2.588877 CGCTTGCCATCTACCGGG 60.589 66.667 6.32 0.00 0.00 5.73
4675 6987 3.272334 GCGCTTGCCATCTACCGG 61.272 66.667 0.00 0.00 0.00 5.28
4717 7043 1.941812 CGTGCACAGAACCAAGTCC 59.058 57.895 18.64 0.00 0.00 3.85
4718 7044 1.279840 GCGTGCACAGAACCAAGTC 59.720 57.895 18.64 0.00 0.00 3.01
4719 7045 2.534019 CGCGTGCACAGAACCAAGT 61.534 57.895 18.64 0.00 0.00 3.16
4720 7046 2.243957 TCGCGTGCACAGAACCAAG 61.244 57.895 18.64 0.00 0.00 3.61
4723 7049 2.943345 CTGTCGCGTGCACAGAACC 61.943 63.158 18.65 5.44 43.54 3.62
4724 7050 2.546321 CTGTCGCGTGCACAGAAC 59.454 61.111 18.65 11.26 43.54 3.01
4801 7132 2.435410 CGTAGTGAAACCCGCCCC 60.435 66.667 0.00 0.00 37.80 5.80
4817 7148 2.161609 GGCTACCAGAACCATTGAAACG 59.838 50.000 0.00 0.00 0.00 3.60
4837 7168 1.550072 CAAAATTGTAGGTGGCCCAGG 59.450 52.381 0.00 0.00 0.00 4.45
4839 7170 1.638529 CCAAAATTGTAGGTGGCCCA 58.361 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.