Multiple sequence alignment - TraesCS7A01G436400

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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 TraesCS7A01G436400 chr7A 100.000 2846 0 0 1 2846 630868691 630871536 0.000000e+00 5256.0
1 TraesCS7A01G436400 chr7D 91.913 2708 101 41 182 2846 547682219 547679587 0.000000e+00 3679.0
2 TraesCS7A01G436400 chr7D 89.815 108 10 1 53 160 547682847 547682741 1.380000e-28 137.0
3 TraesCS7A01G436400 chr7B 88.873 2741 170 60 157 2846 590843571 590840915 0.000000e+00 3247.0
4 TraesCS7A01G436400 chr2D 95.122 41 2 0 53 93 175305477 175305517 6.580000e-07 65.8
5 TraesCS7A01G436400 chr2B 95.122 41 2 0 53 93 223096434 223096474 6.580000e-07 65.8


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 TraesCS7A01G436400 chr7A 630868691 630871536 2845 False 5256 5256 100.000 1 2846 1 chr7A.!!$F1 2845
1 TraesCS7A01G436400 chr7D 547679587 547682847 3260 True 1908 3679 90.864 53 2846 2 chr7D.!!$R1 2793
2 TraesCS7A01G436400 chr7B 590840915 590843571 2656 True 3247 3247 88.873 157 2846 1 chr7B.!!$R1 2689

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
42 43 0.106167 CGGTAGACAGAGGGGATCCA 60.106 60.0 15.23 0.00 34.83 3.41 F
46 47 0.396417 AGACAGAGGGGATCCACGAG 60.396 60.0 15.23 7.97 34.83 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2233 0.974383 TCTCGTTCCTTTCCCCAGTC 59.026 55.000 0.0 0.0 0.00 3.51 R
1985 2555 1.430632 CAATCACCGGCAGCATGTC 59.569 57.895 0.0 0.0 39.31 3.06 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
18 19 2.892305 CTCCTCGACATTGGCGATC 58.108 57.895 16.20 0.00 37.13 3.69
19 20 0.936764 CTCCTCGACATTGGCGATCG 60.937 60.000 16.20 11.69 37.13 3.69
20 21 1.951130 CCTCGACATTGGCGATCGG 60.951 63.158 16.20 10.49 37.13 4.18
21 22 1.065764 CTCGACATTGGCGATCGGA 59.934 57.895 16.20 1.67 37.13 4.55
22 23 0.936764 CTCGACATTGGCGATCGGAG 60.937 60.000 16.20 8.22 37.13 4.63
23 24 2.589492 CGACATTGGCGATCGGAGC 61.589 63.158 18.30 0.00 32.22 4.70
24 25 2.586079 ACATTGGCGATCGGAGCG 60.586 61.111 18.30 11.86 35.00 5.03
25 26 3.341043 CATTGGCGATCGGAGCGG 61.341 66.667 18.30 0.00 35.00 5.52
26 27 3.849951 ATTGGCGATCGGAGCGGT 61.850 61.111 18.30 0.00 35.00 5.68
27 28 2.495409 ATTGGCGATCGGAGCGGTA 61.495 57.895 18.30 0.00 35.00 4.02
28 29 2.421877 ATTGGCGATCGGAGCGGTAG 62.422 60.000 18.30 0.00 35.00 3.18
29 30 3.285215 GGCGATCGGAGCGGTAGA 61.285 66.667 18.30 0.00 35.00 2.59
30 31 2.051166 GCGATCGGAGCGGTAGAC 60.051 66.667 18.30 0.00 0.00 2.59
31 32 2.831366 GCGATCGGAGCGGTAGACA 61.831 63.158 18.30 0.00 0.00 3.41
32 33 1.280142 CGATCGGAGCGGTAGACAG 59.720 63.158 7.38 0.00 0.00 3.51
33 34 1.158484 CGATCGGAGCGGTAGACAGA 61.158 60.000 7.38 0.00 0.00 3.41
34 35 0.589223 GATCGGAGCGGTAGACAGAG 59.411 60.000 0.00 0.00 0.00 3.35
35 36 0.820074 ATCGGAGCGGTAGACAGAGG 60.820 60.000 0.00 0.00 0.00 3.69
36 37 2.482333 CGGAGCGGTAGACAGAGGG 61.482 68.421 0.00 0.00 0.00 4.30
37 38 2.128507 GGAGCGGTAGACAGAGGGG 61.129 68.421 0.00 0.00 0.00 4.79
38 39 1.076923 GAGCGGTAGACAGAGGGGA 60.077 63.158 0.00 0.00 0.00 4.81
39 40 0.468400 GAGCGGTAGACAGAGGGGAT 60.468 60.000 0.00 0.00 0.00 3.85
40 41 0.468400 AGCGGTAGACAGAGGGGATC 60.468 60.000 0.00 0.00 0.00 3.36
41 42 1.465200 GCGGTAGACAGAGGGGATCC 61.465 65.000 1.92 1.92 0.00 3.36
42 43 0.106167 CGGTAGACAGAGGGGATCCA 60.106 60.000 15.23 0.00 34.83 3.41
43 44 1.415200 GGTAGACAGAGGGGATCCAC 58.585 60.000 15.23 10.87 34.83 4.02
44 45 1.033574 GTAGACAGAGGGGATCCACG 58.966 60.000 15.23 0.00 34.83 4.94
45 46 0.924090 TAGACAGAGGGGATCCACGA 59.076 55.000 15.23 0.00 34.83 4.35
46 47 0.396417 AGACAGAGGGGATCCACGAG 60.396 60.000 15.23 7.97 34.83 4.18
47 48 2.022240 GACAGAGGGGATCCACGAGC 62.022 65.000 15.23 5.22 34.83 5.03
48 49 1.760086 CAGAGGGGATCCACGAGCT 60.760 63.158 15.23 7.68 34.83 4.09
49 50 1.002274 AGAGGGGATCCACGAGCTT 59.998 57.895 15.23 0.00 34.83 3.74
50 51 1.144936 GAGGGGATCCACGAGCTTG 59.855 63.158 15.23 0.00 34.83 4.01
51 52 2.514824 GGGGATCCACGAGCTTGC 60.515 66.667 15.23 0.00 0.00 4.01
90 91 3.019564 CCTTGCAAGAGGGGAAATACAG 58.980 50.000 28.05 2.04 32.94 2.74
102 103 4.825085 GGGGAAATACAGACTTCAAACACA 59.175 41.667 0.00 0.00 0.00 3.72
103 104 5.476945 GGGGAAATACAGACTTCAAACACAT 59.523 40.000 0.00 0.00 0.00 3.21
114 115 7.012610 CAGACTTCAAACACATATATGCATGGA 59.987 37.037 10.16 0.00 0.00 3.41
130 131 4.100035 TGCATGGAAGACTCGATAACAGAT 59.900 41.667 0.00 0.00 0.00 2.90
132 133 6.015095 TGCATGGAAGACTCGATAACAGATAT 60.015 38.462 0.00 0.00 0.00 1.63
140 141 9.877178 AAGACTCGATAACAGATATGAGTTTTT 57.123 29.630 0.00 0.00 34.93 1.94
143 144 7.711339 ACTCGATAACAGATATGAGTTTTTCCC 59.289 37.037 0.00 0.00 32.88 3.97
147 148 6.683974 AACAGATATGAGTTTTTCCCGATG 57.316 37.500 0.00 0.00 0.00 3.84
155 156 1.874872 GTTTTTCCCGATGTCCGACAA 59.125 47.619 5.07 0.00 41.76 3.18
162 212 1.871039 CCGATGTCCGACAAAACTGTT 59.129 47.619 5.07 0.00 41.76 3.16
168 218 3.128349 GTCCGACAAAACTGTTCTAGCA 58.872 45.455 0.00 0.00 0.00 3.49
169 219 3.184581 GTCCGACAAAACTGTTCTAGCAG 59.815 47.826 0.00 0.00 41.92 4.24
195 696 5.585390 GACATTGCCAAGATACAATTCCAG 58.415 41.667 0.00 0.00 34.32 3.86
226 727 4.801330 TTCCATACCCGCATACTATCAG 57.199 45.455 0.00 0.00 0.00 2.90
229 730 1.263356 TACCCGCATACTATCAGCCC 58.737 55.000 0.00 0.00 0.00 5.19
233 734 1.202639 CCGCATACTATCAGCCCAACA 60.203 52.381 0.00 0.00 0.00 3.33
260 761 1.423845 CATCCAAACGGCGTGCTAC 59.576 57.895 15.70 0.00 0.00 3.58
275 776 6.265577 GGCGTGCTACTGAAAATTTGAATAT 58.734 36.000 0.00 0.00 0.00 1.28
329 838 3.644805 TTAAGCTCGCCGAAATTAACG 57.355 42.857 0.00 0.00 0.00 3.18
330 839 1.435577 AAGCTCGCCGAAATTAACGT 58.564 45.000 0.00 0.00 0.00 3.99
333 842 2.224784 AGCTCGCCGAAATTAACGTTTT 59.775 40.909 5.91 0.00 0.00 2.43
334 843 2.975193 GCTCGCCGAAATTAACGTTTTT 59.025 40.909 5.91 1.06 0.00 1.94
362 871 4.853276 TCTTAACCCCAAATCCTTCCTACA 59.147 41.667 0.00 0.00 0.00 2.74
371 886 5.875359 CCAAATCCTTCCTACACAGTAGTTC 59.125 44.000 3.76 0.00 0.00 3.01
376 891 3.955650 TCCTACACAGTAGTTCCTTGC 57.044 47.619 3.76 0.00 0.00 4.01
395 910 1.566563 CAGAGCAGAACACACGCAC 59.433 57.895 0.00 0.00 0.00 5.34
417 932 0.448197 CGCTCGAGTCTCTACAAGCA 59.552 55.000 15.13 0.00 31.76 3.91
424 939 1.694150 AGTCTCTACAAGCAAGCCACA 59.306 47.619 0.00 0.00 0.00 4.17
473 988 5.566469 CCCCAAAATTACTCTCCACTAACA 58.434 41.667 0.00 0.00 0.00 2.41
475 990 6.238648 CCCAAAATTACTCTCCACTAACACT 58.761 40.000 0.00 0.00 0.00 3.55
695 1234 1.783979 ACCCAACCAAACCAGACCATA 59.216 47.619 0.00 0.00 0.00 2.74
696 1235 2.167662 CCCAACCAAACCAGACCATAC 58.832 52.381 0.00 0.00 0.00 2.39
697 1236 2.167662 CCAACCAAACCAGACCATACC 58.832 52.381 0.00 0.00 0.00 2.73
698 1237 2.489985 CCAACCAAACCAGACCATACCA 60.490 50.000 0.00 0.00 0.00 3.25
699 1238 3.430453 CAACCAAACCAGACCATACCAT 58.570 45.455 0.00 0.00 0.00 3.55
724 1273 0.537188 AATCGTAGTGGTGGAGCAGG 59.463 55.000 0.00 0.00 0.00 4.85
796 1345 3.170672 ACCACCAGACCAGCAGCA 61.171 61.111 0.00 0.00 0.00 4.41
797 1346 2.359602 CCACCAGACCAGCAGCAG 60.360 66.667 0.00 0.00 0.00 4.24
876 1427 3.726517 CCAAAGCAGGCGTCCGTG 61.727 66.667 0.00 0.00 0.00 4.94
894 1445 4.928520 CCCCATCCCCTCCCTCCC 62.929 77.778 0.00 0.00 0.00 4.30
895 1446 3.795924 CCCATCCCCTCCCTCCCT 61.796 72.222 0.00 0.00 0.00 4.20
1462 2027 3.151022 AGCTACTGCGGCTCCTCC 61.151 66.667 0.00 0.00 45.42 4.30
1546 2111 4.738998 CTGAACATGCCGCCCCCA 62.739 66.667 0.00 0.00 0.00 4.96
1631 2196 1.820056 CTCCGCCTCTAGCTCGACA 60.820 63.158 0.00 0.00 40.39 4.35
1632 2197 1.377366 CTCCGCCTCTAGCTCGACAA 61.377 60.000 0.00 0.00 40.39 3.18
1633 2198 1.226717 CCGCCTCTAGCTCGACAAC 60.227 63.158 0.00 0.00 40.39 3.32
1766 2332 6.348868 GGTGTTCTCTTTTGCTAGAAATGGAG 60.349 42.308 0.00 0.37 33.70 3.86
1877 2447 0.807496 GCTGCGAGCAAGGAAATCTT 59.193 50.000 0.00 0.00 41.89 2.40
1971 2541 5.693769 AGGGTAATCGAAGGAATGAAGAA 57.306 39.130 0.00 0.00 0.00 2.52
1985 2555 9.971922 AAGGAATGAAGAAAAAGTATTTGACAG 57.028 29.630 0.00 0.00 39.02 3.51
2087 2657 7.446013 TCATATGTAGCAAGCATCATGAATTGA 59.554 33.333 17.91 2.95 39.12 2.57
2143 2716 7.062605 GCTGAAATGCAAATTATCATTATCCGG 59.937 37.037 0.00 0.00 33.05 5.14
2150 2723 7.448161 TGCAAATTATCATTATCCGGATGTCTT 59.552 33.333 27.55 10.18 0.00 3.01
2265 2842 7.210174 AGCTAAACGAAGAATACATAGCATGA 58.790 34.615 0.00 0.00 37.37 3.07
2286 2863 3.713858 TCACAAGTGCCTGAATTGTTG 57.286 42.857 0.00 0.00 35.04 3.33
2338 2916 9.412460 AGTTTGATGGATAGCATTATCTGAAAA 57.588 29.630 0.00 0.00 36.67 2.29
2495 3073 1.399440 CCATTGCTTCACTGGATCACG 59.601 52.381 0.00 0.00 36.47 4.35
2516 3094 4.202111 ACGTTTTGTAGGCTTGAAGCAATT 60.202 37.500 19.89 6.42 44.75 2.32
2600 3186 6.183360 GCATATAGTTTTGGCTGTCACATTCT 60.183 38.462 0.00 0.00 0.00 2.40
2641 3227 1.072806 TGCTCATCCTTGTGCTTGACT 59.927 47.619 2.29 0.00 41.73 3.41
2642 3228 1.467734 GCTCATCCTTGTGCTTGACTG 59.532 52.381 0.00 0.00 38.89 3.51
2670 3256 9.223099 CATTCTCCTCATATGCACAAATACATA 57.777 33.333 0.00 0.00 33.52 2.29
2722 3311 4.637091 CCTCATGATGTGATTTGTGCACTA 59.363 41.667 19.41 7.83 35.97 2.74
2734 3323 1.140852 TGTGCACTACAAAGCAGGAGT 59.859 47.619 19.41 0.00 42.14 3.85
2749 3338 4.889409 AGCAGGAGTTTGAAGTGAAATTGA 59.111 37.500 0.00 0.00 0.00 2.57
2753 3342 5.893824 AGGAGTTTGAAGTGAAATTGAGGTT 59.106 36.000 0.00 0.00 0.00 3.50
2765 3354 6.151817 GTGAAATTGAGGTTTCCTAGCTGATT 59.848 38.462 0.00 0.00 37.31 2.57
2766 3355 6.151648 TGAAATTGAGGTTTCCTAGCTGATTG 59.848 38.462 0.00 0.00 37.31 2.67
2767 3356 3.634397 TGAGGTTTCCTAGCTGATTGG 57.366 47.619 0.00 0.00 33.94 3.16
2774 3363 1.208052 TCCTAGCTGATTGGTGCACTC 59.792 52.381 17.98 7.24 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.936764 CGATCGCCAATGTCGAGGAG 60.937 60.000 0.26 0.00 39.47 3.69
1 2 1.065764 CGATCGCCAATGTCGAGGA 59.934 57.895 0.26 0.00 39.47 3.71
2 3 1.951130 CCGATCGCCAATGTCGAGG 60.951 63.158 10.32 0.00 39.47 4.63
3 4 0.936764 CTCCGATCGCCAATGTCGAG 60.937 60.000 10.32 4.47 39.47 4.04
4 5 1.065764 CTCCGATCGCCAATGTCGA 59.934 57.895 10.32 0.00 40.45 4.20
5 6 2.589492 GCTCCGATCGCCAATGTCG 61.589 63.158 10.32 0.00 35.29 4.35
6 7 2.589492 CGCTCCGATCGCCAATGTC 61.589 63.158 10.32 0.00 0.00 3.06
7 8 2.586079 CGCTCCGATCGCCAATGT 60.586 61.111 10.32 0.00 0.00 2.71
8 9 2.693250 TACCGCTCCGATCGCCAATG 62.693 60.000 10.32 0.00 0.00 2.82
9 10 2.421877 CTACCGCTCCGATCGCCAAT 62.422 60.000 10.32 0.00 0.00 3.16
10 11 3.133767 CTACCGCTCCGATCGCCAA 62.134 63.158 10.32 0.00 0.00 4.52
11 12 3.592814 CTACCGCTCCGATCGCCA 61.593 66.667 10.32 0.00 0.00 5.69
12 13 3.285215 TCTACCGCTCCGATCGCC 61.285 66.667 10.32 0.00 0.00 5.54
13 14 2.051166 GTCTACCGCTCCGATCGC 60.051 66.667 10.32 0.00 0.00 4.58
14 15 1.158484 TCTGTCTACCGCTCCGATCG 61.158 60.000 8.51 8.51 0.00 3.69
15 16 0.589223 CTCTGTCTACCGCTCCGATC 59.411 60.000 0.00 0.00 0.00 3.69
16 17 0.820074 CCTCTGTCTACCGCTCCGAT 60.820 60.000 0.00 0.00 0.00 4.18
17 18 1.451567 CCTCTGTCTACCGCTCCGA 60.452 63.158 0.00 0.00 0.00 4.55
18 19 2.482333 CCCTCTGTCTACCGCTCCG 61.482 68.421 0.00 0.00 0.00 4.63
19 20 2.128507 CCCCTCTGTCTACCGCTCC 61.129 68.421 0.00 0.00 0.00 4.70
20 21 0.468400 ATCCCCTCTGTCTACCGCTC 60.468 60.000 0.00 0.00 0.00 5.03
21 22 0.468400 GATCCCCTCTGTCTACCGCT 60.468 60.000 0.00 0.00 0.00 5.52
22 23 1.465200 GGATCCCCTCTGTCTACCGC 61.465 65.000 0.00 0.00 0.00 5.68
23 24 0.106167 TGGATCCCCTCTGTCTACCG 60.106 60.000 9.90 0.00 0.00 4.02
24 25 1.415200 GTGGATCCCCTCTGTCTACC 58.585 60.000 9.90 0.00 0.00 3.18
25 26 1.033574 CGTGGATCCCCTCTGTCTAC 58.966 60.000 9.90 0.00 0.00 2.59
26 27 0.924090 TCGTGGATCCCCTCTGTCTA 59.076 55.000 9.90 0.00 0.00 2.59
27 28 0.396417 CTCGTGGATCCCCTCTGTCT 60.396 60.000 9.90 0.00 0.00 3.41
28 29 2.022240 GCTCGTGGATCCCCTCTGTC 62.022 65.000 9.90 0.00 0.00 3.51
29 30 2.060980 GCTCGTGGATCCCCTCTGT 61.061 63.158 9.90 0.00 0.00 3.41
30 31 1.333636 AAGCTCGTGGATCCCCTCTG 61.334 60.000 9.90 0.00 0.00 3.35
31 32 1.002274 AAGCTCGTGGATCCCCTCT 59.998 57.895 9.90 0.00 0.00 3.69
32 33 1.144936 CAAGCTCGTGGATCCCCTC 59.855 63.158 9.90 0.00 0.00 4.30
33 34 3.036429 GCAAGCTCGTGGATCCCCT 62.036 63.158 9.90 0.00 0.00 4.79
34 35 2.514824 GCAAGCTCGTGGATCCCC 60.515 66.667 9.90 0.00 0.00 4.81
35 36 1.817099 CTGCAAGCTCGTGGATCCC 60.817 63.158 9.90 0.00 0.00 3.85
36 37 1.817099 CCTGCAAGCTCGTGGATCC 60.817 63.158 4.20 4.20 0.00 3.36
37 38 2.467826 GCCTGCAAGCTCGTGGATC 61.468 63.158 0.00 0.00 0.00 3.36
38 39 2.437359 GCCTGCAAGCTCGTGGAT 60.437 61.111 0.00 0.00 0.00 3.41
39 40 2.680974 AAAGCCTGCAAGCTCGTGGA 62.681 55.000 10.92 0.00 44.11 4.02
40 41 2.263741 AAAGCCTGCAAGCTCGTGG 61.264 57.895 10.92 0.00 44.11 4.94
41 42 1.081641 CAAAGCCTGCAAGCTCGTG 60.082 57.895 10.92 8.33 44.11 4.35
42 43 3.348236 CAAAGCCTGCAAGCTCGT 58.652 55.556 10.92 0.00 44.11 4.18
90 91 7.263100 TCCATGCATATATGTGTTTGAAGTC 57.737 36.000 14.14 0.00 0.00 3.01
102 103 7.840931 TGTTATCGAGTCTTCCATGCATATAT 58.159 34.615 0.00 0.00 0.00 0.86
103 104 7.176690 TCTGTTATCGAGTCTTCCATGCATATA 59.823 37.037 0.00 0.00 0.00 0.86
114 115 9.877178 AAAAACTCATATCTGTTATCGAGTCTT 57.123 29.630 0.00 0.00 32.36 3.01
130 131 3.196039 TCGGACATCGGGAAAAACTCATA 59.804 43.478 0.00 0.00 39.77 2.15
132 133 1.345089 TCGGACATCGGGAAAAACTCA 59.655 47.619 0.00 0.00 39.77 3.41
140 141 0.682852 AGTTTTGTCGGACATCGGGA 59.317 50.000 12.26 0.00 39.77 5.14
143 144 2.800544 AGAACAGTTTTGTCGGACATCG 59.199 45.455 12.26 1.91 36.23 3.84
147 148 3.128349 TGCTAGAACAGTTTTGTCGGAC 58.872 45.455 0.00 0.00 36.23 4.79
155 156 1.070134 TGTCGGCTGCTAGAACAGTTT 59.930 47.619 0.00 0.00 39.96 2.66
162 212 1.153369 GGCAATGTCGGCTGCTAGA 60.153 57.895 0.00 0.00 38.65 2.43
168 218 1.065491 TGTATCTTGGCAATGTCGGCT 60.065 47.619 0.00 0.00 0.00 5.52
169 219 1.378531 TGTATCTTGGCAATGTCGGC 58.621 50.000 0.00 0.00 0.00 5.54
195 696 3.380004 TGCGGGTATGGAATTTCATGAAC 59.620 43.478 7.89 0.27 0.00 3.18
226 727 0.387239 GATGCTTCACGTTGTTGGGC 60.387 55.000 0.00 0.00 0.00 5.36
229 730 2.772568 TTGGATGCTTCACGTTGTTG 57.227 45.000 1.64 0.00 0.00 3.33
233 734 0.591170 CCGTTTGGATGCTTCACGTT 59.409 50.000 1.64 0.00 37.49 3.99
335 844 6.147473 AGGAAGGATTTGGGGTTAAGAAAAA 58.853 36.000 0.00 0.00 0.00 1.94
336 845 5.722290 AGGAAGGATTTGGGGTTAAGAAAA 58.278 37.500 0.00 0.00 0.00 2.29
354 863 4.246458 GCAAGGAACTACTGTGTAGGAAG 58.754 47.826 9.20 0.00 38.49 3.46
362 871 1.002544 GCTCTGGCAAGGAACTACTGT 59.997 52.381 0.00 0.00 38.49 3.55
376 891 1.595109 TGCGTGTGTTCTGCTCTGG 60.595 57.895 0.00 0.00 0.00 3.86
395 910 0.448197 TTGTAGAGACTCGAGCGCAG 59.552 55.000 13.61 2.69 0.00 5.18
404 919 1.694150 TGTGGCTTGCTTGTAGAGACT 59.306 47.619 0.00 0.00 0.00 3.24
417 932 1.299541 CGGCGATATTCTTGTGGCTT 58.700 50.000 0.00 0.00 0.00 4.35
424 939 2.029290 ACGATTAGGCGGCGATATTCTT 60.029 45.455 12.98 0.00 35.12 2.52
473 988 2.376518 TCTCGTCCCGGGGTATATTAGT 59.623 50.000 23.50 0.00 0.00 2.24
475 990 3.359033 CATCTCGTCCCGGGGTATATTA 58.641 50.000 23.50 0.00 0.00 0.98
492 1008 2.438975 TACCGTCCCGTCGCATCT 60.439 61.111 0.00 0.00 0.00 2.90
493 1009 2.278401 GTACCGTCCCGTCGCATC 60.278 66.667 0.00 0.00 0.00 3.91
494 1010 4.183686 CGTACCGTCCCGTCGCAT 62.184 66.667 0.00 0.00 0.00 4.73
498 1014 4.120331 CACCCGTACCGTCCCGTC 62.120 72.222 0.00 0.00 0.00 4.79
508 1024 3.463585 GGATGCGACCCACCCGTA 61.464 66.667 0.00 0.00 0.00 4.02
540 1056 3.000322 CGTTGCTCTAATTTCTACGGCAG 60.000 47.826 0.00 0.00 0.00 4.85
640 1172 9.626045 CGTGCCTTTTTCTTTCTATTAAAATCT 57.374 29.630 0.00 0.00 0.00 2.40
695 1234 1.202486 CCACTACGATTGCGGTATGGT 60.202 52.381 0.00 0.00 43.17 3.55
696 1235 1.202486 ACCACTACGATTGCGGTATGG 60.202 52.381 0.00 0.00 43.17 2.74
697 1236 1.858458 CACCACTACGATTGCGGTATG 59.142 52.381 0.00 0.00 43.17 2.39
698 1237 1.202486 CCACCACTACGATTGCGGTAT 60.202 52.381 0.00 0.00 43.17 2.73
699 1238 0.173935 CCACCACTACGATTGCGGTA 59.826 55.000 0.00 0.00 43.17 4.02
838 1387 3.522731 CTCCTCCTCCTCACGCGG 61.523 72.222 12.47 0.00 0.00 6.46
888 1439 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
894 1445 2.040359 GAAGGGGGAGGGAGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
895 1446 3.707189 GGAAGGGGGAGGGAGGGA 61.707 72.222 0.00 0.00 0.00 4.20
1331 1896 4.341783 GGTGCTGCTCTGGCTGGT 62.342 66.667 0.00 0.00 39.59 4.00
1426 1991 4.787280 CGGCAGTCCTCCTCCCCT 62.787 72.222 0.00 0.00 0.00 4.79
1462 2027 2.124693 GCAGAGGAGGACGGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
1546 2111 4.974438 TCAAGGGCCCCGTCCTGT 62.974 66.667 21.43 0.00 36.17 4.00
1582 2147 1.144716 GCGGCAGGTCATCTGATCA 59.855 57.895 0.00 0.00 46.18 2.92
1631 2196 2.516923 CTTGCTATTCTCGTCGTCGTT 58.483 47.619 1.33 0.00 38.33 3.85
1632 2197 1.202154 CCTTGCTATTCTCGTCGTCGT 60.202 52.381 1.33 0.00 38.33 4.34
1633 2198 1.063616 TCCTTGCTATTCTCGTCGTCG 59.936 52.381 0.00 0.00 38.55 5.12
1668 2233 0.974383 TCTCGTTCCTTTCCCCAGTC 59.026 55.000 0.00 0.00 0.00 3.51
1877 2447 7.106239 CCACAGAGAAAGATAAGGAAAAGCTA 58.894 38.462 0.00 0.00 0.00 3.32
1971 2541 5.464168 GCAGCATGTCTGTCAAATACTTTT 58.536 37.500 15.48 0.00 44.66 2.27
1985 2555 1.430632 CAATCACCGGCAGCATGTC 59.569 57.895 0.00 0.00 39.31 3.06
2087 2657 9.066892 TGTGCATCTTAAAACTTTGAGATAACT 57.933 29.630 8.62 0.00 40.29 2.24
2265 2842 3.890756 TCAACAATTCAGGCACTTGTGAT 59.109 39.130 4.79 0.00 34.60 3.06
2286 2863 3.574284 TTGCAATGCACACATACCTTC 57.426 42.857 7.72 0.00 38.71 3.46
2362 2940 4.103365 TGAAAGAAGAAACGCTGCAAAA 57.897 36.364 0.00 0.00 0.00 2.44
2363 2941 3.773860 TGAAAGAAGAAACGCTGCAAA 57.226 38.095 0.00 0.00 0.00 3.68
2364 2942 3.694734 CTTGAAAGAAGAAACGCTGCAA 58.305 40.909 0.00 0.00 0.00 4.08
2365 2943 2.541588 GCTTGAAAGAAGAAACGCTGCA 60.542 45.455 0.00 0.00 0.00 4.41
2495 3073 5.177511 GGAAATTGCTTCAAGCCTACAAAAC 59.822 40.000 7.01 0.00 41.51 2.43
2516 3094 3.626222 CCCATCCCGGTTATTCAAAGGAA 60.626 47.826 0.00 0.00 37.45 3.36
2600 3186 3.051210 CACGTCTGTGGCTCCTCA 58.949 61.111 0.00 0.00 42.59 3.86
2641 3227 2.173143 TGTGCATATGAGGAGAATGGCA 59.827 45.455 6.97 0.00 0.00 4.92
2642 3228 2.854963 TGTGCATATGAGGAGAATGGC 58.145 47.619 6.97 0.00 0.00 4.40
2670 3256 4.142227 GCACAATGAGAAGGAGAAATGCAT 60.142 41.667 0.00 0.00 0.00 3.96
2672 3258 3.442977 AGCACAATGAGAAGGAGAAATGC 59.557 43.478 0.00 0.00 0.00 3.56
2722 3311 3.620488 TCACTTCAAACTCCTGCTTTGT 58.380 40.909 0.00 0.00 31.63 2.83
2734 3323 6.790232 AGGAAACCTCAATTTCACTTCAAA 57.210 33.333 1.11 0.00 39.85 2.69
2749 3338 2.619074 GCACCAATCAGCTAGGAAACCT 60.619 50.000 0.00 0.00 37.71 3.50
2753 3342 1.630369 AGTGCACCAATCAGCTAGGAA 59.370 47.619 14.63 0.00 0.00 3.36
2765 3354 1.278985 CATCCACCTTAGAGTGCACCA 59.721 52.381 14.63 0.00 36.38 4.17
2766 3355 2.014068 GCATCCACCTTAGAGTGCACC 61.014 57.143 14.63 5.12 36.38 5.01
2767 3356 1.339055 TGCATCCACCTTAGAGTGCAC 60.339 52.381 9.40 9.40 37.63 4.57
2774 3363 2.749621 GGAACAGTTGCATCCACCTTAG 59.250 50.000 0.00 0.00 33.30 2.18


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

AutoCloner maintained by Alex Coulton.