Multiple sequence alignment - TraesCS4D01G346200

Loading Multiple Alignment...

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 TraesCS4D01G346200 chr4D 100.000 5198 0 0 1 5198 500299954 500305151 0.000000e+00 9600.0
1 TraesCS4D01G346200 chr4D 87.064 4275 489 36 951 5197 500197148 500201386 0.000000e+00 4772.0
2 TraesCS4D01G346200 chr4D 82.262 389 39 13 4812 5197 500155372 500155733 5.060000e-80 309.0
3 TraesCS4D01G346200 chr5A 96.570 4636 149 8 62 4694 680980253 680984881 0.000000e+00 7672.0
4 TraesCS4D01G346200 chr5A 86.553 4291 480 51 907 5142 680865403 680869651 0.000000e+00 4638.0
5 TraesCS4D01G346200 chr5A 88.269 3640 401 11 908 4533 680921195 680924822 0.000000e+00 4333.0
6 TraesCS4D01G346200 chr5A 97.670 515 11 1 4685 5198 680985067 680985581 0.000000e+00 883.0
7 TraesCS4D01G346200 chr4B 93.363 5168 315 14 53 5198 643628149 643633310 0.000000e+00 7618.0
8 TraesCS4D01G346200 chr4B 87.107 4258 500 23 908 5142 643528096 643532327 0.000000e+00 4776.0
9 TraesCS4D01G346200 chr4B 87.279 3954 450 33 951 4876 643481808 643485736 0.000000e+00 4466.0
10 TraesCS4D01G346200 chr4B 91.211 2833 239 6 14 2843 643534513 643537338 0.000000e+00 3843.0
11 TraesCS4D01G346200 chrUn 87.509 4251 483 23 914 5142 60417293 60413069 0.000000e+00 4865.0
12 TraesCS4D01G346200 chrUn 87.309 4058 461 26 914 4950 16761265 16757241 0.000000e+00 4591.0
13 TraesCS4D01G346200 chrUn 87.647 3238 333 37 1986 5197 60473866 60470670 0.000000e+00 3701.0
14 TraesCS4D01G346200 chrUn 82.838 303 33 11 4581 4876 60493857 60493567 2.400000e-63 254.0
15 TraesCS4D01G346200 chrUn 82.524 309 35 11 4575 4876 318519288 318519584 2.400000e-63 254.0
16 TraesCS4D01G346200 chrUn 85.926 135 15 3 369 500 277589979 277589846 1.950000e-29 141.0
17 TraesCS4D01G346200 chrUn 100.000 47 0 0 72 118 277590257 277590211 2.580000e-13 87.9


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 TraesCS4D01G346200 chr4D 500299954 500305151 5197 False 9600.0 9600 100.000 1 5198 1 chr4D.!!$F3 5197
1 TraesCS4D01G346200 chr4D 500197148 500201386 4238 False 4772.0 4772 87.064 951 5197 1 chr4D.!!$F2 4246
2 TraesCS4D01G346200 chr5A 680865403 680869651 4248 False 4638.0 4638 86.553 907 5142 1 chr5A.!!$F1 4235
3 TraesCS4D01G346200 chr5A 680921195 680924822 3627 False 4333.0 4333 88.269 908 4533 1 chr5A.!!$F2 3625
4 TraesCS4D01G346200 chr5A 680980253 680985581 5328 False 4277.5 7672 97.120 62 5198 2 chr5A.!!$F3 5136
5 TraesCS4D01G346200 chr4B 643628149 643633310 5161 False 7618.0 7618 93.363 53 5198 1 chr4B.!!$F2 5145
6 TraesCS4D01G346200 chr4B 643481808 643485736 3928 False 4466.0 4466 87.279 951 4876 1 chr4B.!!$F1 3925
7 TraesCS4D01G346200 chr4B 643528096 643537338 9242 False 4309.5 4776 89.159 14 5142 2 chr4B.!!$F3 5128
8 TraesCS4D01G346200 chrUn 60413069 60417293 4224 True 4865.0 4865 87.509 914 5142 1 chrUn.!!$R2 4228
9 TraesCS4D01G346200 chrUn 16757241 16761265 4024 True 4591.0 4591 87.309 914 4950 1 chrUn.!!$R1 4036
10 TraesCS4D01G346200 chrUn 60470670 60473866 3196 True 3701.0 3701 87.647 1986 5197 1 chrUn.!!$R3 3211

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
46 47 0.106819 CTGCTATGGCTTGGGCTCTT 60.107 55.000 1.68 0.0 39.59 2.85 F
51 52 0.114954 ATGGCTTGGGCTCTTTGGAA 59.885 50.000 0.00 0.0 38.73 3.53 F
52 53 0.114954 TGGCTTGGGCTCTTTGGAAT 59.885 50.000 0.00 0.0 38.73 3.01 F
1404 1434 0.178990 GGCTCACCAACCTCAACCTT 60.179 55.000 0.00 0.0 35.26 3.50 F
1440 1470 0.541863 AAGGTAACATCCCGCCTGAG 59.458 55.000 0.00 0.0 41.41 3.35 F
2172 2209 1.338674 CCCTTCGACATTGGCTACACA 60.339 52.381 0.00 0.0 0.00 3.72 F
2908 2945 2.353889 CCAGATGAAGTTGGCAATCTCG 59.646 50.000 1.92 0.0 0.00 4.04 F
3657 3715 1.132453 GCCCTAAGAAATGTTCGCCAC 59.868 52.381 0.00 0.0 34.02 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1470 0.390998 GCTGGGAACACTCAGAGAGC 60.391 60.000 3.79 0.00 35.60 4.09 R
1448 1478 1.272147 GGATTTGGAGCTGGGAACACT 60.272 52.381 0.00 0.00 35.60 3.55 R
1785 1815 3.909995 TGAGAAGATCCTTTGGGAGTTCA 59.090 43.478 10.53 0.52 45.86 3.18 R
2631 2668 2.228822 CCTGTTTTGCGCAAAGGATAGT 59.771 45.455 31.88 0.00 0.00 2.12 R
3258 3295 2.289002 CACTGCTGAACAAAGAGACACC 59.711 50.000 0.00 0.00 0.00 4.16 R
3259 3296 2.289002 CCACTGCTGAACAAAGAGACAC 59.711 50.000 0.00 0.00 0.00 3.67 R
3711 3769 2.808906 ACACTAGGGCCTTGAAATCC 57.191 50.000 21.96 0.00 0.00 3.01 R
4908 5212 1.677217 GGGGAGATCTGTGTGCTGAAC 60.677 57.143 0.00 0.00 0.00 3.18 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
24 25 3.393426 AAGACATGCTTGGATGGGATT 57.607 42.857 4.44 0.00 34.93 3.01
25 26 3.393426 AGACATGCTTGGATGGGATTT 57.607 42.857 4.44 0.00 0.00 2.17
26 27 3.028850 AGACATGCTTGGATGGGATTTG 58.971 45.455 4.44 0.00 0.00 2.32
27 28 1.483415 ACATGCTTGGATGGGATTTGC 59.517 47.619 4.44 0.00 0.00 3.68
28 29 1.760613 CATGCTTGGATGGGATTTGCT 59.239 47.619 0.00 0.00 0.00 3.91
29 30 1.187974 TGCTTGGATGGGATTTGCTG 58.812 50.000 0.00 0.00 0.00 4.41
30 31 0.179092 GCTTGGATGGGATTTGCTGC 60.179 55.000 0.00 0.00 0.00 5.25
31 32 1.481871 CTTGGATGGGATTTGCTGCT 58.518 50.000 0.00 0.00 0.00 4.24
32 33 2.658285 CTTGGATGGGATTTGCTGCTA 58.342 47.619 0.00 0.00 0.00 3.49
33 34 3.228453 CTTGGATGGGATTTGCTGCTAT 58.772 45.455 0.00 0.00 0.00 2.97
34 35 2.589720 TGGATGGGATTTGCTGCTATG 58.410 47.619 0.00 0.00 0.00 2.23
35 36 1.891150 GGATGGGATTTGCTGCTATGG 59.109 52.381 0.00 0.00 0.00 2.74
36 37 1.271656 GATGGGATTTGCTGCTATGGC 59.728 52.381 0.00 0.00 39.26 4.40
37 38 0.259647 TGGGATTTGCTGCTATGGCT 59.740 50.000 1.68 0.00 39.59 4.75
38 39 1.342275 TGGGATTTGCTGCTATGGCTT 60.342 47.619 1.68 0.00 39.59 4.35
39 40 1.068127 GGGATTTGCTGCTATGGCTTG 59.932 52.381 1.68 0.00 39.59 4.01
40 41 1.068127 GGATTTGCTGCTATGGCTTGG 59.932 52.381 1.68 0.00 39.59 3.61
41 42 1.068127 GATTTGCTGCTATGGCTTGGG 59.932 52.381 1.68 0.00 39.59 4.12
42 43 1.606885 TTTGCTGCTATGGCTTGGGC 61.607 55.000 1.68 2.57 39.59 5.36
43 44 2.123982 GCTGCTATGGCTTGGGCT 60.124 61.111 1.68 0.00 39.59 5.19
44 45 2.192187 GCTGCTATGGCTTGGGCTC 61.192 63.158 1.68 0.00 39.59 4.70
45 46 1.530771 CTGCTATGGCTTGGGCTCT 59.469 57.895 1.68 0.00 39.59 4.09
46 47 0.106819 CTGCTATGGCTTGGGCTCTT 60.107 55.000 1.68 0.00 39.59 2.85
47 48 0.332632 TGCTATGGCTTGGGCTCTTT 59.667 50.000 1.68 0.00 39.59 2.52
48 49 0.743097 GCTATGGCTTGGGCTCTTTG 59.257 55.000 0.00 0.00 38.73 2.77
49 50 1.396653 CTATGGCTTGGGCTCTTTGG 58.603 55.000 0.00 0.00 38.73 3.28
50 51 0.998928 TATGGCTTGGGCTCTTTGGA 59.001 50.000 0.00 0.00 38.73 3.53
51 52 0.114954 ATGGCTTGGGCTCTTTGGAA 59.885 50.000 0.00 0.00 38.73 3.53
52 53 0.114954 TGGCTTGGGCTCTTTGGAAT 59.885 50.000 0.00 0.00 38.73 3.01
53 54 0.533951 GGCTTGGGCTCTTTGGAATG 59.466 55.000 0.00 0.00 38.73 2.67
54 55 1.260544 GCTTGGGCTCTTTGGAATGT 58.739 50.000 0.00 0.00 35.22 2.71
55 56 1.620323 GCTTGGGCTCTTTGGAATGTT 59.380 47.619 0.00 0.00 35.22 2.71
56 57 2.825532 GCTTGGGCTCTTTGGAATGTTA 59.174 45.455 0.00 0.00 35.22 2.41
57 58 3.119352 GCTTGGGCTCTTTGGAATGTTAG 60.119 47.826 0.00 0.00 35.22 2.34
58 59 4.335416 CTTGGGCTCTTTGGAATGTTAGA 58.665 43.478 0.00 0.00 0.00 2.10
59 60 4.380843 TGGGCTCTTTGGAATGTTAGAA 57.619 40.909 0.00 0.00 0.00 2.10
60 61 4.735369 TGGGCTCTTTGGAATGTTAGAAA 58.265 39.130 0.00 0.00 0.00 2.52
187 190 8.861086 AGTATCTGTTACTTTCTCAGTCTGAAA 58.139 33.333 3.67 0.00 37.96 2.69
201 204 4.210120 CAGTCTGAAACCTCGAGTCAAAAG 59.790 45.833 12.31 3.65 0.00 2.27
207 210 1.619332 ACCTCGAGTCAAAAGGAGTCC 59.381 52.381 12.31 0.00 42.05 3.85
208 211 1.618837 CCTCGAGTCAAAAGGAGTCCA 59.381 52.381 12.86 0.00 42.05 4.02
210 213 3.447586 CCTCGAGTCAAAAGGAGTCCATA 59.552 47.826 12.86 0.00 42.05 2.74
211 214 4.440802 CCTCGAGTCAAAAGGAGTCCATAG 60.441 50.000 12.86 0.00 42.05 2.23
212 215 3.447586 TCGAGTCAAAAGGAGTCCATAGG 59.552 47.826 12.86 0.00 42.05 2.57
215 218 2.093658 GTCAAAAGGAGTCCATAGGCGA 60.094 50.000 12.86 0.00 0.00 5.54
217 220 3.199946 TCAAAAGGAGTCCATAGGCGATT 59.800 43.478 12.86 0.00 0.00 3.34
279 282 3.365064 CGCGTTTCTCTAGTTGACTCTGA 60.365 47.826 0.00 0.00 0.00 3.27
333 344 2.043604 AATCGCTCGATGCCCATCCA 62.044 55.000 5.47 0.00 38.78 3.41
346 357 2.404215 CCCATCCATGTAACGACGATC 58.596 52.381 0.00 0.00 0.00 3.69
352 363 4.295870 TCCATGTAACGACGATCATTAGC 58.704 43.478 0.00 0.00 0.00 3.09
502 513 0.674581 CAGCTGATTCAAGGGTCGCA 60.675 55.000 8.42 0.00 0.00 5.10
540 551 5.929415 TCCAAATTAATCACGCGCTCATATA 59.071 36.000 5.73 0.00 0.00 0.86
609 620 8.109705 TGTGTGCTAATATATTAATTGCCAGG 57.890 34.615 6.63 0.00 0.00 4.45
623 634 1.007842 TGCCAGGGATAGTACACTCCA 59.992 52.381 13.81 0.00 32.90 3.86
641 652 6.098838 ACACTCCAAGTTGCAGATATCATCTA 59.901 38.462 0.00 0.00 37.58 1.98
681 693 5.020132 CCCCAACCAAACCATTGTTCTATA 58.980 41.667 0.00 0.00 34.60 1.31
717 729 4.720090 CTCATGACTTGCAACAATGACTC 58.280 43.478 0.00 0.00 0.00 3.36
737 749 4.001652 CTCGCAGATATCATTGCTGGAAT 58.998 43.478 13.32 0.00 38.16 3.01
762 774 5.359009 CCTGGAACAATGACTTGCAGATATT 59.641 40.000 6.67 0.00 38.70 1.28
763 775 6.198650 TGGAACAATGACTTGCAGATATTG 57.801 37.500 11.21 11.21 35.69 1.90
772 784 7.558161 TGACTTGCAGATATTGTTATTGAGG 57.442 36.000 0.00 0.00 0.00 3.86
790 802 2.489722 GAGGTTCAGGCAGATTTTCCAC 59.510 50.000 0.00 0.00 0.00 4.02
809 821 4.770010 TCCACAAGGTCCAAAATCCATTAC 59.230 41.667 0.00 0.00 35.89 1.89
814 826 4.014406 AGGTCCAAAATCCATTACGTTCC 58.986 43.478 0.00 0.00 0.00 3.62
822 834 1.070445 TCCATTACGTTCCGGTGTTGT 59.930 47.619 0.00 0.00 0.00 3.32
823 835 1.195900 CCATTACGTTCCGGTGTTGTG 59.804 52.381 0.00 2.09 0.00 3.33
912 924 1.367346 TGTTGCTCCAATCCCCTACA 58.633 50.000 0.00 0.00 0.00 2.74
957 983 6.468543 TGCTACACACCATACTTAAACATCA 58.531 36.000 0.00 0.00 0.00 3.07
998 1028 3.056962 TCCATCAATCTCGATAGCTGAGC 60.057 47.826 0.00 0.00 33.41 4.26
1040 1070 1.701031 TTGTTTCCGGGCCTCTGTCA 61.701 55.000 0.84 0.00 0.00 3.58
1148 1178 1.003233 GCTTCAAGTCCGGGCTCTT 60.003 57.895 10.20 5.27 0.00 2.85
1193 1223 3.499737 GAGCAACGCGTCCATGGG 61.500 66.667 14.44 0.00 0.00 4.00
1245 1275 3.767630 GACACCACCCAGGCGTGTT 62.768 63.158 10.53 0.00 40.70 3.32
1267 1297 2.464459 GCGCTGGACCTTGAATCCG 61.464 63.158 0.00 0.00 39.30 4.18
1359 1389 3.003173 AGCTTCAGTGGCGGCCTA 61.003 61.111 21.46 3.65 34.52 3.93
1362 1392 2.925706 TTCAGTGGCGGCCTACCA 60.926 61.111 21.46 10.19 34.57 3.25
1404 1434 0.178990 GGCTCACCAACCTCAACCTT 60.179 55.000 0.00 0.00 35.26 3.50
1440 1470 0.541863 AAGGTAACATCCCGCCTGAG 59.458 55.000 0.00 0.00 41.41 3.35
1448 1478 2.580155 ATCCCGCCTGAGCTCTCTGA 62.580 60.000 16.19 3.56 36.60 3.27
1910 1940 6.942576 TCCCCTATTAAGCATCTTGATTTAGC 59.057 38.462 0.00 0.00 0.00 3.09
2172 2209 1.338674 CCCTTCGACATTGGCTACACA 60.339 52.381 0.00 0.00 0.00 3.72
2408 2445 6.040278 TCACTATCTAATTGCTCCAGACTGAG 59.960 42.308 3.32 0.89 35.40 3.35
2555 2592 6.725364 AGATTGGAAATCTTAAGAGCCTCAA 58.275 36.000 11.53 12.43 0.00 3.02
2626 2663 2.727123 TGGGAAACTGCAGAACTTGA 57.273 45.000 23.35 0.00 0.00 3.02
2630 2667 3.823304 GGGAAACTGCAGAACTTGATCTT 59.177 43.478 23.35 0.00 0.00 2.40
2631 2668 5.003804 GGGAAACTGCAGAACTTGATCTTA 58.996 41.667 23.35 0.00 0.00 2.10
2908 2945 2.353889 CCAGATGAAGTTGGCAATCTCG 59.646 50.000 1.92 0.00 0.00 4.04
3258 3295 2.242043 ACAAGCATTCCAACAAGAGGG 58.758 47.619 0.00 0.00 0.00 4.30
3259 3296 1.547372 CAAGCATTCCAACAAGAGGGG 59.453 52.381 0.00 0.00 0.00 4.79
3657 3715 1.132453 GCCCTAAGAAATGTTCGCCAC 59.868 52.381 0.00 0.00 34.02 5.01
3675 3733 4.095185 CGCCACCGGAATCTTGTAAAAATA 59.905 41.667 9.46 0.00 0.00 1.40
3711 3769 0.250038 CAGTGGATCATACTGGGGCG 60.250 60.000 17.19 0.00 41.36 6.13
3942 4000 0.184692 TGGGTCTTGACATGGTTGCA 59.815 50.000 0.00 0.00 0.00 4.08
3987 4045 4.153835 GCAAGATTCTTGTTCAGGACAGAG 59.846 45.833 23.66 0.00 39.94 3.35
4041 4099 3.881220 CCGCTTAAAAGGAACCATAGGA 58.119 45.455 0.00 0.00 0.00 2.94
4880 5184 2.355756 CAGTGTTCCAAACCTGACTGTG 59.644 50.000 0.00 0.00 33.97 3.66
4908 5212 7.031226 TGAATTTCTGAAACAAGGACTTCAG 57.969 36.000 4.73 5.63 46.56 3.02
5131 5437 2.096565 CCTCACATAATCGCAAGCATCG 60.097 50.000 0.00 0.00 37.18 3.84
5134 5440 2.284952 CACATAATCGCAAGCATCGTCA 59.715 45.455 0.00 0.00 37.18 4.35
5145 5451 0.659957 GCATCGTCAATTCTCCCAGC 59.340 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.028850 CAAATCCCATCCAAGCATGTCT 58.971 45.455 0.00 0.00 0.00 3.41
6 7 2.482490 GCAAATCCCATCCAAGCATGTC 60.482 50.000 0.00 0.00 0.00 3.06
7 8 1.483415 GCAAATCCCATCCAAGCATGT 59.517 47.619 0.00 0.00 0.00 3.21
8 9 1.760613 AGCAAATCCCATCCAAGCATG 59.239 47.619 0.00 0.00 0.00 4.06
9 10 1.760613 CAGCAAATCCCATCCAAGCAT 59.239 47.619 0.00 0.00 0.00 3.79
10 11 1.187974 CAGCAAATCCCATCCAAGCA 58.812 50.000 0.00 0.00 0.00 3.91
11 12 0.179092 GCAGCAAATCCCATCCAAGC 60.179 55.000 0.00 0.00 0.00 4.01
12 13 1.481871 AGCAGCAAATCCCATCCAAG 58.518 50.000 0.00 0.00 0.00 3.61
13 14 2.824689 TAGCAGCAAATCCCATCCAA 57.175 45.000 0.00 0.00 0.00 3.53
14 15 2.589720 CATAGCAGCAAATCCCATCCA 58.410 47.619 0.00 0.00 0.00 3.41
15 16 1.891150 CCATAGCAGCAAATCCCATCC 59.109 52.381 0.00 0.00 0.00 3.51
16 17 1.271656 GCCATAGCAGCAAATCCCATC 59.728 52.381 0.00 0.00 39.53 3.51
17 18 1.133262 AGCCATAGCAGCAAATCCCAT 60.133 47.619 0.00 0.00 43.56 4.00
18 19 0.259647 AGCCATAGCAGCAAATCCCA 59.740 50.000 0.00 0.00 43.56 4.37
19 20 1.068127 CAAGCCATAGCAGCAAATCCC 59.932 52.381 0.00 0.00 43.56 3.85
20 21 1.068127 CCAAGCCATAGCAGCAAATCC 59.932 52.381 0.00 0.00 43.56 3.01
21 22 1.068127 CCCAAGCCATAGCAGCAAATC 59.932 52.381 0.00 0.00 43.56 2.17
22 23 1.117150 CCCAAGCCATAGCAGCAAAT 58.883 50.000 0.00 0.00 43.56 2.32
23 24 1.606885 GCCCAAGCCATAGCAGCAAA 61.607 55.000 0.00 0.00 43.56 3.68
24 25 2.053865 GCCCAAGCCATAGCAGCAA 61.054 57.895 0.00 0.00 43.56 3.91
25 26 2.440796 GCCCAAGCCATAGCAGCA 60.441 61.111 0.00 0.00 43.56 4.41
26 27 2.123982 AGCCCAAGCCATAGCAGC 60.124 61.111 0.00 0.00 43.56 5.25
27 28 0.106819 AAGAGCCCAAGCCATAGCAG 60.107 55.000 0.00 0.00 43.56 4.24
28 29 0.332632 AAAGAGCCCAAGCCATAGCA 59.667 50.000 0.00 0.00 43.56 3.49
29 30 0.743097 CAAAGAGCCCAAGCCATAGC 59.257 55.000 0.00 0.00 41.25 2.97
30 31 1.064463 TCCAAAGAGCCCAAGCCATAG 60.064 52.381 0.00 0.00 41.25 2.23
31 32 0.998928 TCCAAAGAGCCCAAGCCATA 59.001 50.000 0.00 0.00 41.25 2.74
32 33 0.114954 TTCCAAAGAGCCCAAGCCAT 59.885 50.000 0.00 0.00 41.25 4.40
33 34 0.114954 ATTCCAAAGAGCCCAAGCCA 59.885 50.000 0.00 0.00 41.25 4.75
34 35 0.533951 CATTCCAAAGAGCCCAAGCC 59.466 55.000 0.00 0.00 41.25 4.35
35 36 1.260544 ACATTCCAAAGAGCCCAAGC 58.739 50.000 0.00 0.00 40.32 4.01
36 37 4.335416 TCTAACATTCCAAAGAGCCCAAG 58.665 43.478 0.00 0.00 0.00 3.61
37 38 4.380843 TCTAACATTCCAAAGAGCCCAA 57.619 40.909 0.00 0.00 0.00 4.12
38 39 4.380843 TTCTAACATTCCAAAGAGCCCA 57.619 40.909 0.00 0.00 0.00 5.36
39 40 4.522789 TGTTTCTAACATTCCAAAGAGCCC 59.477 41.667 0.00 0.00 36.25 5.19
40 41 5.705609 TGTTTCTAACATTCCAAAGAGCC 57.294 39.130 0.00 0.00 36.25 4.70
41 42 6.638468 CAGTTGTTTCTAACATTCCAAAGAGC 59.362 38.462 0.00 0.00 41.79 4.09
42 43 7.857885 GTCAGTTGTTTCTAACATTCCAAAGAG 59.142 37.037 0.00 0.00 41.79 2.85
43 44 7.338196 TGTCAGTTGTTTCTAACATTCCAAAGA 59.662 33.333 0.00 0.00 41.79 2.52
44 45 7.479980 TGTCAGTTGTTTCTAACATTCCAAAG 58.520 34.615 0.00 0.00 41.79 2.77
45 46 7.338196 TCTGTCAGTTGTTTCTAACATTCCAAA 59.662 33.333 0.00 0.00 41.79 3.28
46 47 6.826231 TCTGTCAGTTGTTTCTAACATTCCAA 59.174 34.615 0.00 0.00 41.79 3.53
47 48 6.353323 TCTGTCAGTTGTTTCTAACATTCCA 58.647 36.000 0.00 0.00 41.79 3.53
48 49 6.861065 TCTGTCAGTTGTTTCTAACATTCC 57.139 37.500 0.00 0.00 41.79 3.01
49 50 9.567848 TTTTTCTGTCAGTTGTTTCTAACATTC 57.432 29.630 0.00 0.00 41.79 2.67
50 51 9.353999 GTTTTTCTGTCAGTTGTTTCTAACATT 57.646 29.630 0.00 0.00 41.79 2.71
51 52 8.739972 AGTTTTTCTGTCAGTTGTTTCTAACAT 58.260 29.630 0.00 0.00 41.79 2.71
52 53 8.106247 AGTTTTTCTGTCAGTTGTTTCTAACA 57.894 30.769 0.00 0.00 40.21 2.41
55 56 9.391006 ACATAGTTTTTCTGTCAGTTGTTTCTA 57.609 29.630 0.00 0.00 0.00 2.10
56 57 8.281212 ACATAGTTTTTCTGTCAGTTGTTTCT 57.719 30.769 0.00 0.00 0.00 2.52
57 58 8.911247 AACATAGTTTTTCTGTCAGTTGTTTC 57.089 30.769 0.00 0.00 0.00 2.78
58 59 9.353999 GAAACATAGTTTTTCTGTCAGTTGTTT 57.646 29.630 0.00 0.00 36.57 2.83
59 60 8.739972 AGAAACATAGTTTTTCTGTCAGTTGTT 58.260 29.630 0.00 0.00 40.93 2.83
60 61 8.281212 AGAAACATAGTTTTTCTGTCAGTTGT 57.719 30.769 0.00 0.00 40.93 3.32
187 190 1.619332 GGACTCCTTTTGACTCGAGGT 59.381 52.381 18.41 1.94 32.33 3.85
201 204 3.746045 TGTAAATCGCCTATGGACTCC 57.254 47.619 0.00 0.00 0.00 3.85
207 210 5.334414 GCTTCATCCTTGTAAATCGCCTATG 60.334 44.000 0.00 0.00 0.00 2.23
208 211 4.757149 GCTTCATCCTTGTAAATCGCCTAT 59.243 41.667 0.00 0.00 0.00 2.57
210 213 2.945668 GCTTCATCCTTGTAAATCGCCT 59.054 45.455 0.00 0.00 0.00 5.52
211 214 2.286418 CGCTTCATCCTTGTAAATCGCC 60.286 50.000 0.00 0.00 0.00 5.54
212 215 2.607635 TCGCTTCATCCTTGTAAATCGC 59.392 45.455 0.00 0.00 0.00 4.58
215 218 3.950397 TGGTCGCTTCATCCTTGTAAAT 58.050 40.909 0.00 0.00 0.00 1.40
217 220 3.627395 ATGGTCGCTTCATCCTTGTAA 57.373 42.857 0.00 0.00 0.00 2.41
279 282 6.360618 ACACTGAAAGGAGAAGATTGTTCTT 58.639 36.000 0.00 0.00 41.37 2.52
292 295 7.042051 CGATTTGAAAGAAGTACACTGAAAGGA 60.042 37.037 0.00 0.00 39.30 3.36
333 344 4.049186 GGTGCTAATGATCGTCGTTACAT 58.951 43.478 0.00 0.00 0.00 2.29
352 363 9.597170 CATTGGATGATAGTATATCTCAAGGTG 57.403 37.037 0.00 0.00 0.00 4.00
502 513 2.584835 TTTGGAGTATGTGCCTGCTT 57.415 45.000 0.00 0.00 0.00 3.91
540 551 1.620822 GAAATCAACAGGGCAGGTGT 58.379 50.000 0.00 0.00 0.00 4.16
609 620 4.081642 TCTGCAACTTGGAGTGTACTATCC 60.082 45.833 9.84 9.31 37.12 2.59
618 629 5.627182 AGATGATATCTGCAACTTGGAGT 57.373 39.130 9.84 1.48 38.44 3.85
623 634 6.261826 GCCAAAGTAGATGATATCTGCAACTT 59.738 38.462 3.98 6.33 43.41 2.66
641 652 1.456287 GGTCCTGTCCAGCCAAAGT 59.544 57.895 0.00 0.00 0.00 2.66
681 693 2.368221 GTCATGAGCTAGCTTCCAGGAT 59.632 50.000 20.42 1.88 0.00 3.24
717 729 3.126514 GGATTCCAGCAATGATATCTGCG 59.873 47.826 10.36 6.57 43.51 5.18
737 749 2.106338 TCTGCAAGTCATTGTTCCAGGA 59.894 45.455 0.00 0.00 38.76 3.86
762 774 4.574674 ATCTGCCTGAACCTCAATAACA 57.425 40.909 0.00 0.00 0.00 2.41
763 775 5.904362 AAATCTGCCTGAACCTCAATAAC 57.096 39.130 0.00 0.00 0.00 1.89
772 784 3.305608 CCTTGTGGAAAATCTGCCTGAAC 60.306 47.826 0.00 0.00 34.57 3.18
790 802 5.385509 AACGTAATGGATTTTGGACCTTG 57.614 39.130 0.00 0.00 0.00 3.61
814 826 2.409975 CAGGTAAGGTACACAACACCG 58.590 52.381 0.00 0.00 41.21 4.94
822 834 1.861982 GGAGGAGCAGGTAAGGTACA 58.138 55.000 0.00 0.00 0.00 2.90
823 835 0.745468 CGGAGGAGCAGGTAAGGTAC 59.255 60.000 0.00 0.00 0.00 3.34
912 924 4.765339 GCAGTACCTCACCCACTTTAAATT 59.235 41.667 0.00 0.00 0.00 1.82
957 983 3.547567 AGCTCTCGCTTTGCAAGAT 57.452 47.368 0.00 0.00 46.47 2.40
998 1028 1.586154 GGCACCCGAAGACACCATTG 61.586 60.000 0.00 0.00 0.00 2.82
1040 1070 3.075134 ACCCAAGAAGAGGCAGAGAAATT 59.925 43.478 0.00 0.00 0.00 1.82
1193 1223 1.065199 TCCCATGCCAGTCACAGAATC 60.065 52.381 0.00 0.00 0.00 2.52
1245 1275 0.537143 ATTCAAGGTCCAGCGCAACA 60.537 50.000 11.47 0.00 0.00 3.33
1267 1297 2.049627 ATGGAGCCCGAGATGCCTTC 62.050 60.000 0.00 0.00 0.00 3.46
1291 1321 0.955428 GTGAGGTTGGCGATGCAAGA 60.955 55.000 0.00 0.00 0.00 3.02
1363 1393 4.479993 CAGGAGGCCAAGCTCCGG 62.480 72.222 5.01 0.00 44.09 5.14
1404 1434 2.083774 CCTTCCAAAGCGTTGATGCTA 58.916 47.619 14.32 0.00 46.60 3.49
1440 1470 0.390998 GCTGGGAACACTCAGAGAGC 60.391 60.000 3.79 0.00 35.60 4.09
1448 1478 1.272147 GGATTTGGAGCTGGGAACACT 60.272 52.381 0.00 0.00 35.60 3.55
1785 1815 3.909995 TGAGAAGATCCTTTGGGAGTTCA 59.090 43.478 10.53 0.52 45.86 3.18
1910 1940 9.922305 GTATTCTTCCTGAAAGATTGTTATTCG 57.078 33.333 0.00 0.00 43.50 3.34
2172 2209 3.151542 AGGTTCTGGATATTGGGGAGT 57.848 47.619 0.00 0.00 0.00 3.85
2408 2445 3.224324 CATCCAGGGCCAGCATGC 61.224 66.667 10.51 10.51 31.97 4.06
2538 2575 7.115414 ACAAGCTATTGAGGCTCTTAAGATTT 58.885 34.615 16.72 5.73 39.30 2.17
2614 2651 6.815089 AGGATAGTAAGATCAAGTTCTGCAG 58.185 40.000 7.63 7.63 0.00 4.41
2626 2663 5.414454 TGTTTTGCGCAAAGGATAGTAAGAT 59.586 36.000 31.88 0.00 0.00 2.40
2630 2667 3.438781 CCTGTTTTGCGCAAAGGATAGTA 59.561 43.478 31.88 15.58 0.00 1.82
2631 2668 2.228822 CCTGTTTTGCGCAAAGGATAGT 59.771 45.455 31.88 0.00 0.00 2.12
2908 2945 6.154445 ACATGTTGATTTTCTGCAGATGAAC 58.846 36.000 19.04 13.73 0.00 3.18
3258 3295 2.289002 CACTGCTGAACAAAGAGACACC 59.711 50.000 0.00 0.00 0.00 4.16
3259 3296 2.289002 CCACTGCTGAACAAAGAGACAC 59.711 50.000 0.00 0.00 0.00 3.67
3675 3733 6.313519 TCCACTGAAGAGCATAAGGTAATT 57.686 37.500 0.00 0.00 0.00 1.40
3711 3769 2.808906 ACACTAGGGCCTTGAAATCC 57.191 50.000 21.96 0.00 0.00 3.01
3942 4000 3.350219 AGGCCAAAGTCAATGACGTAT 57.650 42.857 5.01 0.00 37.67 3.06
3987 4045 5.065602 TGCTGAACTATCTTGATGTGCATTC 59.934 40.000 0.00 0.00 0.00 2.67
4041 4099 2.845659 TCTCACCTGGTGGGATGTATT 58.154 47.619 25.26 0.00 38.21 1.89
4299 4362 8.616076 CCTCGTGAATATTCTTTCTAAATGCTT 58.384 33.333 16.24 0.00 0.00 3.91
4308 4371 7.015877 GTCAACAACCTCGTGAATATTCTTTC 58.984 38.462 16.24 6.44 0.00 2.62
4594 4681 6.377327 TGACTCAAACTGGATTCAGAAAAC 57.623 37.500 8.39 0.00 43.49 2.43
4880 5184 6.218746 AGTCCTTGTTTCAGAAATTCATTGC 58.781 36.000 0.00 0.00 0.00 3.56
4908 5212 1.677217 GGGGAGATCTGTGTGCTGAAC 60.677 57.143 0.00 0.00 0.00 3.18
5131 5437 4.775236 ACTTCTATGCTGGGAGAATTGAC 58.225 43.478 0.00 0.00 31.45 3.18
5134 5440 4.103311 GGGTACTTCTATGCTGGGAGAATT 59.897 45.833 0.00 0.00 31.45 2.17


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

AutoCloner maintained by Alex Coulton.