Multiple sequence alignment - TraesCS1B01G467400

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 TraesCS1B01G467400 chr1B 100.000 5178 0 0 1 5178 677253102 677258279 0.000000e+00 9563.0
1 TraesCS1B01G467400 chr1B 82.497 857 131 16 1 847 670876603 670877450 0.000000e+00 734.0
2 TraesCS1B01G467400 chr1D 94.890 3718 143 24 672 4362 486239527 486243224 0.000000e+00 5770.0
3 TraesCS1B01G467400 chr1D 94.684 1091 56 2 1676 2766 486210662 486211750 0.000000e+00 1692.0
4 TraesCS1B01G467400 chr1D 81.073 1268 186 25 1780 3036 408626179 408627403 0.000000e+00 963.0
5 TraesCS1B01G467400 chr1D 93.993 283 12 2 1105 1387 486202118 486202395 1.720000e-114 424.0
6 TraesCS1B01G467400 chr1D 86.957 391 21 15 4335 4722 486245106 486245469 3.730000e-111 412.0
7 TraesCS1B01G467400 chr1D 92.334 287 18 1 4763 5049 486245466 486245748 6.240000e-109 405.0
8 TraesCS1B01G467400 chr1D 89.641 251 17 4 4367 4612 486157947 486158193 1.400000e-80 311.0
9 TraesCS1B01G467400 chr1D 84.642 293 17 5 1399 1689 486202458 486202724 3.070000e-67 267.0
10 TraesCS1B01G467400 chr1D 87.162 148 16 1 5034 5178 486245762 486245909 1.150000e-36 165.0
11 TraesCS1B01G467400 chr1A 93.125 3462 163 40 921 4362 583923805 583927211 0.000000e+00 5005.0
12 TraesCS1B01G467400 chr1A 87.217 618 43 17 4362 4973 583935887 583936474 0.000000e+00 671.0
13 TraesCS1B01G467400 chr1A 90.038 261 22 2 4362 4622 583894995 583895251 8.310000e-88 335.0
14 TraesCS1B01G467400 chr1A 86.408 206 20 3 4976 5178 583936511 583936711 8.730000e-53 219.0
15 TraesCS1B01G467400 chr7A 79.406 2190 332 67 1780 3925 709755483 709757597 0.000000e+00 1435.0
16 TraesCS1B01G467400 chr7A 78.559 1721 288 52 1625 3296 709285675 709283987 0.000000e+00 1059.0
17 TraesCS1B01G467400 chr7A 76.404 1496 282 42 1780 3228 709265468 709263997 0.000000e+00 741.0
18 TraesCS1B01G467400 chr7A 72.871 505 101 23 1630 2103 62752727 62752228 1.940000e-29 141.0
19 TraesCS1B01G467400 chr7D 78.613 2235 359 77 1780 3971 616276221 616274063 0.000000e+00 1369.0
20 TraesCS1B01G467400 chr7D 79.171 1954 292 58 1780 3682 617028012 617029901 0.000000e+00 1247.0
21 TraesCS1B01G467400 chr7D 78.242 1650 279 46 1837 3441 616331565 616329951 0.000000e+00 985.0
22 TraesCS1B01G467400 chr7D 76.600 1500 288 32 1777 3228 616220143 616221627 0.000000e+00 767.0
23 TraesCS1B01G467400 chr7D 75.534 1312 238 58 1500 2758 617009849 617011130 7.520000e-158 568.0
24 TraesCS1B01G467400 chr7D 75.779 867 173 26 1804 2649 616412108 616411258 2.250000e-108 403.0
25 TraesCS1B01G467400 chr7D 74.286 560 112 23 2222 2760 588073266 588072718 1.890000e-49 207.0
26 TraesCS1B01G467400 chr7D 82.412 199 28 4 4032 4229 616274038 616273846 3.210000e-37 167.0
27 TraesCS1B01G467400 chr7B 77.530 2154 339 84 1596 3682 709530609 709528534 0.000000e+00 1162.0
28 TraesCS1B01G467400 chr7B 89.202 852 88 4 1 850 720486696 720485847 0.000000e+00 1061.0
29 TraesCS1B01G467400 chr7B 79.795 1559 232 48 1780 3296 709591701 709590184 0.000000e+00 1057.0
30 TraesCS1B01G467400 chr7B 79.269 1013 181 22 1780 2779 709515484 709514488 0.000000e+00 680.0
31 TraesCS1B01G467400 chr7B 75.979 945 166 36 3051 3976 711206644 711207546 1.030000e-116 431.0
32 TraesCS1B01G467400 chr7B 78.441 603 87 23 2755 3339 709514438 709513861 2.290000e-93 353.0
33 TraesCS1B01G467400 chr7B 77.508 329 41 23 980 1296 709531247 709530940 3.210000e-37 167.0
34 TraesCS1B01G467400 chr7B 76.077 209 22 11 984 1177 709516801 709516606 3.320000e-12 84.2
35 TraesCS1B01G467400 chr6B 88.836 842 88 5 1 841 476734018 476734854 0.000000e+00 1029.0
36 TraesCS1B01G467400 chr6B 88.042 853 90 10 1 849 673021936 673021092 0.000000e+00 1000.0
37 TraesCS1B01G467400 chr2B 88.862 817 84 6 1 814 25795439 25796251 0.000000e+00 998.0
38 TraesCS1B01G467400 chr2B 86.030 859 99 10 1 849 775132099 775131252 0.000000e+00 902.0
39 TraesCS1B01G467400 chr2B 84.660 867 112 11 1 851 260763526 260762665 0.000000e+00 845.0
40 TraesCS1B01G467400 chrUn 85.380 855 107 10 3 849 15867829 15866985 0.000000e+00 870.0
41 TraesCS1B01G467400 chr5B 85.190 844 117 7 1 840 659734994 659734155 0.000000e+00 859.0
42 TraesCS1B01G467400 chr3B 84.929 491 46 12 360 847 188234096 188233631 6.070000e-129 472.0


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 TraesCS1B01G467400 chr1B 677253102 677258279 5177 False 9563.0 9563 100.00000 1 5178 1 chr1B.!!$F2 5177
1 TraesCS1B01G467400 chr1B 670876603 670877450 847 False 734.0 734 82.49700 1 847 1 chr1B.!!$F1 846
2 TraesCS1B01G467400 chr1D 486210662 486211750 1088 False 1692.0 1692 94.68400 1676 2766 1 chr1D.!!$F3 1090
3 TraesCS1B01G467400 chr1D 486239527 486245909 6382 False 1688.0 5770 90.33575 672 5178 4 chr1D.!!$F5 4506
4 TraesCS1B01G467400 chr1D 408626179 408627403 1224 False 963.0 963 81.07300 1780 3036 1 chr1D.!!$F1 1256
5 TraesCS1B01G467400 chr1D 486202118 486202724 606 False 345.5 424 89.31750 1105 1689 2 chr1D.!!$F4 584
6 TraesCS1B01G467400 chr1A 583923805 583927211 3406 False 5005.0 5005 93.12500 921 4362 1 chr1A.!!$F2 3441
7 TraesCS1B01G467400 chr1A 583935887 583936711 824 False 445.0 671 86.81250 4362 5178 2 chr1A.!!$F3 816
8 TraesCS1B01G467400 chr7A 709755483 709757597 2114 False 1435.0 1435 79.40600 1780 3925 1 chr7A.!!$F1 2145
9 TraesCS1B01G467400 chr7A 709283987 709285675 1688 True 1059.0 1059 78.55900 1625 3296 1 chr7A.!!$R3 1671
10 TraesCS1B01G467400 chr7A 709263997 709265468 1471 True 741.0 741 76.40400 1780 3228 1 chr7A.!!$R2 1448
11 TraesCS1B01G467400 chr7D 617028012 617029901 1889 False 1247.0 1247 79.17100 1780 3682 1 chr7D.!!$F3 1902
12 TraesCS1B01G467400 chr7D 616329951 616331565 1614 True 985.0 985 78.24200 1837 3441 1 chr7D.!!$R2 1604
13 TraesCS1B01G467400 chr7D 616273846 616276221 2375 True 768.0 1369 80.51250 1780 4229 2 chr7D.!!$R4 2449
14 TraesCS1B01G467400 chr7D 616220143 616221627 1484 False 767.0 767 76.60000 1777 3228 1 chr7D.!!$F1 1451
15 TraesCS1B01G467400 chr7D 617009849 617011130 1281 False 568.0 568 75.53400 1500 2758 1 chr7D.!!$F2 1258
16 TraesCS1B01G467400 chr7D 616411258 616412108 850 True 403.0 403 75.77900 1804 2649 1 chr7D.!!$R3 845
17 TraesCS1B01G467400 chr7D 588072718 588073266 548 True 207.0 207 74.28600 2222 2760 1 chr7D.!!$R1 538
18 TraesCS1B01G467400 chr7B 720485847 720486696 849 True 1061.0 1061 89.20200 1 850 1 chr7B.!!$R2 849
19 TraesCS1B01G467400 chr7B 709590184 709591701 1517 True 1057.0 1057 79.79500 1780 3296 1 chr7B.!!$R1 1516
20 TraesCS1B01G467400 chr7B 709528534 709531247 2713 True 664.5 1162 77.51900 980 3682 2 chr7B.!!$R4 2702
21 TraesCS1B01G467400 chr7B 711206644 711207546 902 False 431.0 431 75.97900 3051 3976 1 chr7B.!!$F1 925
22 TraesCS1B01G467400 chr7B 709513861 709516801 2940 True 372.4 680 77.92900 984 3339 3 chr7B.!!$R3 2355
23 TraesCS1B01G467400 chr6B 476734018 476734854 836 False 1029.0 1029 88.83600 1 841 1 chr6B.!!$F1 840
24 TraesCS1B01G467400 chr6B 673021092 673021936 844 True 1000.0 1000 88.04200 1 849 1 chr6B.!!$R1 848
25 TraesCS1B01G467400 chr2B 25795439 25796251 812 False 998.0 998 88.86200 1 814 1 chr2B.!!$F1 813
26 TraesCS1B01G467400 chr2B 775131252 775132099 847 True 902.0 902 86.03000 1 849 1 chr2B.!!$R2 848
27 TraesCS1B01G467400 chr2B 260762665 260763526 861 True 845.0 845 84.66000 1 851 1 chr2B.!!$R1 850
28 TraesCS1B01G467400 chrUn 15866985 15867829 844 True 870.0 870 85.38000 3 849 1 chrUn.!!$R1 846
29 TraesCS1B01G467400 chr5B 659734155 659734994 839 True 859.0 859 85.19000 1 840 1 chr5B.!!$R1 839

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
882 919 0.396811 AGGTGTCCGCTAAAGTTGCT 59.603 50.0 0.00 0.0 0.00 3.91 F
883 920 0.796927 GGTGTCCGCTAAAGTTGCTC 59.203 55.0 0.00 0.0 0.00 4.26 F
1881 2654 1.180029 GCATCAGATGTGGCCTGTTT 58.820 50.0 12.18 0.0 33.57 2.83 F
2920 3862 2.484241 CCGGCATGATCATCTCAAGACA 60.484 50.0 4.86 0.0 37.44 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2823 3745 2.037381 TGCATTGGAAGCTTGCAATCAA 59.963 40.909 34.93 25.13 44.38 2.57 R
2920 3862 1.673033 CGAAACCCGCTCATGAAGACT 60.673 52.381 0.00 0.00 0.00 3.24 R
3586 4643 1.402968 CTGATGGGAAAGCCAACGATG 59.597 52.381 0.00 0.00 35.15 3.84 R
4529 7522 0.037590 GTACCCATCAGCCACCAACA 59.962 55.000 0.00 0.00 0.00 3.33 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
48 49 3.893763 CGATCTGCTCCTCGCGGT 61.894 66.667 6.13 0.00 45.50 5.68
65 66 0.676782 GGTGGCGCTGGAAGTACATT 60.677 55.000 7.64 0.00 35.30 2.71
98 99 4.430765 CTGTCGGGCGCGTACCTT 62.431 66.667 23.19 0.00 0.00 3.50
108 109 1.003718 GCGTACCTTGGCTGGTTCT 60.004 57.895 7.94 0.00 41.22 3.01
122 123 1.004440 GTTCTGCTGCTCCTCCGTT 60.004 57.895 0.00 0.00 0.00 4.44
139 140 0.833287 GTTAGGGAGGAGCAGATGCA 59.167 55.000 7.68 0.00 45.16 3.96
140 141 1.419387 GTTAGGGAGGAGCAGATGCAT 59.581 52.381 0.00 0.00 45.16 3.96
364 369 4.656117 TGCTTTGCTCGTCGGCGA 62.656 61.111 13.29 13.29 45.79 5.54
590 606 2.270923 CCTTGACATTGATTCTCGCGA 58.729 47.619 9.26 9.26 0.00 5.87
606 622 2.771639 CGAGAACCGAGGCGATGGA 61.772 63.158 0.00 0.00 41.76 3.41
607 623 1.515954 GAGAACCGAGGCGATGGAA 59.484 57.895 0.00 0.00 0.00 3.53
742 775 2.342650 GCTGATTTCGGCCCAAGCA 61.343 57.895 0.00 0.00 42.27 3.91
830 867 1.802337 GAAAAGTCGTGTTGGGGGCC 61.802 60.000 0.00 0.00 0.00 5.80
841 878 4.191015 GGGGGCCCGAATGGAGAC 62.191 72.222 17.79 0.00 37.49 3.36
868 905 1.666054 TTGTCGCGGTTTTAAGGTGT 58.334 45.000 6.13 0.00 0.00 4.16
870 907 0.514255 GTCGCGGTTTTAAGGTGTCC 59.486 55.000 6.13 0.00 0.00 4.02
875 912 2.415776 CGGTTTTAAGGTGTCCGCTAA 58.584 47.619 0.00 0.00 35.01 3.09
876 913 2.807392 CGGTTTTAAGGTGTCCGCTAAA 59.193 45.455 0.00 0.00 35.01 1.85
877 914 3.120442 CGGTTTTAAGGTGTCCGCTAAAG 60.120 47.826 0.00 0.00 35.01 1.85
878 915 3.817084 GGTTTTAAGGTGTCCGCTAAAGT 59.183 43.478 0.00 0.00 0.00 2.66
879 916 4.276678 GGTTTTAAGGTGTCCGCTAAAGTT 59.723 41.667 0.00 0.00 0.00 2.66
880 917 5.209977 GTTTTAAGGTGTCCGCTAAAGTTG 58.790 41.667 0.00 0.00 0.00 3.16
881 918 1.235724 AAGGTGTCCGCTAAAGTTGC 58.764 50.000 0.00 0.00 0.00 4.17
882 919 0.396811 AGGTGTCCGCTAAAGTTGCT 59.603 50.000 0.00 0.00 0.00 3.91
883 920 0.796927 GGTGTCCGCTAAAGTTGCTC 59.203 55.000 0.00 0.00 0.00 4.26
884 921 1.608283 GGTGTCCGCTAAAGTTGCTCT 60.608 52.381 0.00 0.00 0.00 4.09
947 984 3.568538 CGCTTTCAGTAATTGCAAAGCT 58.431 40.909 20.89 0.00 41.96 3.74
951 988 5.463061 GCTTTCAGTAATTGCAAAGCTTTGA 59.537 36.000 37.14 21.11 41.49 2.69
1067 1110 5.519808 TCCTGTAGATCCACAAGTGAGTAT 58.480 41.667 0.94 0.00 0.00 2.12
1134 1191 3.173965 TCTGAGGAATCCCTTTTCTCGT 58.826 45.455 0.00 0.00 44.53 4.18
1368 1951 4.280677 TCTGCAACTTTGGGACATAAAAGG 59.719 41.667 0.00 0.00 39.30 3.11
1539 2190 6.498304 TGCAGTTTGTTTCAGATTTCTCTTC 58.502 36.000 0.00 0.00 0.00 2.87
1636 2381 7.397221 TGAAAATACATGTCCTCTCTTGTCAT 58.603 34.615 0.00 0.00 0.00 3.06
1881 2654 1.180029 GCATCAGATGTGGCCTGTTT 58.820 50.000 12.18 0.00 33.57 2.83
2748 3589 5.186215 TGGAGACATTGCAATTGAATGTGAT 59.814 36.000 26.68 19.37 42.74 3.06
2801 3723 2.879026 GCGGACCTTGAAGAAAGAACTT 59.121 45.455 0.00 0.00 38.24 2.66
2920 3862 2.484241 CCGGCATGATCATCTCAAGACA 60.484 50.000 4.86 0.00 37.44 3.41
3224 4194 4.390909 GGTAGTGTAAAGTACGCAGCATTT 59.609 41.667 0.00 0.00 41.48 2.32
3308 4284 3.119637 GGTTACTATTTGTGGCATTGCGT 60.120 43.478 1.91 0.00 0.00 5.24
3737 4811 7.541091 GTGAGAACAAATACTTCGTAGACATGA 59.459 37.037 0.00 0.00 34.32 3.07
3783 4859 0.951558 CGGGGAAACTGAACAACTGG 59.048 55.000 0.00 0.00 0.00 4.00
3792 4868 5.757850 AACTGAACAACTGGTCATCTTTC 57.242 39.130 0.00 0.00 41.51 2.62
3977 5055 3.626670 GGCTCTCTGGAACATCTGAAATG 59.373 47.826 0.00 0.00 38.20 2.32
3978 5056 3.626670 GCTCTCTGGAACATCTGAAATGG 59.373 47.826 0.00 0.00 38.20 3.16
4123 5201 2.125512 GAGTGCCGTCATCGCCTT 60.126 61.111 0.00 0.00 35.54 4.35
4137 5215 5.763204 GTCATCGCCTTTGGATTATTAGGAA 59.237 40.000 0.00 0.00 0.00 3.36
4198 5277 1.707989 TCCCTGGCATCTGTTTTACCA 59.292 47.619 0.00 0.00 0.00 3.25
4200 5279 2.513753 CCTGGCATCTGTTTTACCACA 58.486 47.619 0.00 0.00 0.00 4.17
4201 5280 3.091545 CCTGGCATCTGTTTTACCACAT 58.908 45.455 0.00 0.00 0.00 3.21
4238 5317 4.547671 CTGGAGGGAGTTATGGTTCTCTA 58.452 47.826 0.00 0.00 0.00 2.43
4255 5334 5.099042 TCTCTATTAGGGAGTTTTGCACC 57.901 43.478 0.00 0.00 33.06 5.01
4388 7374 5.047021 TCAAGGACTTCTGTGGATTCTAGTG 60.047 44.000 0.00 0.00 0.00 2.74
4405 7391 1.134965 AGTGCTGCTAGCTACCTTTCG 60.135 52.381 17.23 0.00 42.97 3.46
4438 7430 0.034896 ACAAAGGTAGGTCAGCCACG 59.965 55.000 0.00 0.00 37.19 4.94
4467 7459 9.674824 GCCTAATTTTCATTGAGATTGTGATAG 57.325 33.333 7.30 0.00 0.00 2.08
4476 7468 8.927411 TCATTGAGATTGTGATAGAGTTCCATA 58.073 33.333 0.00 0.00 0.00 2.74
4510 7503 9.121517 GTATATATTTGAATCACATTGCAGTGC 57.878 33.333 8.58 8.58 39.35 4.40
4511 7504 3.729862 TTTGAATCACATTGCAGTGCA 57.270 38.095 15.37 15.37 39.35 4.57
4512 7505 3.945981 TTGAATCACATTGCAGTGCAT 57.054 38.095 20.50 6.43 38.76 3.96
4513 7506 3.224884 TGAATCACATTGCAGTGCATG 57.775 42.857 20.50 19.89 38.76 4.06
4516 7509 0.518195 TCACATTGCAGTGCATGACG 59.482 50.000 20.50 14.45 38.76 4.35
4529 7522 1.730501 CATGACGCACTTGTCCTGAT 58.269 50.000 0.00 0.00 36.85 2.90
4530 7523 1.395954 CATGACGCACTTGTCCTGATG 59.604 52.381 0.00 0.00 36.85 3.07
4531 7524 0.392706 TGACGCACTTGTCCTGATGT 59.607 50.000 0.00 0.00 38.11 3.06
4646 7639 8.223177 TGGTTTTCTTAGTCCGATTGTTAAAA 57.777 30.769 0.00 0.00 0.00 1.52
4676 7669 7.591006 TTTACATCTTCTACAATTGACCGAC 57.409 36.000 13.59 0.00 0.00 4.79
4813 7806 7.439381 AGTGATTTCTGCAACAAATTCTGAAT 58.561 30.769 0.00 0.00 0.00 2.57
4836 7829 5.665916 TCTACTCTGCATTCTGAACATCA 57.334 39.130 0.00 0.00 0.00 3.07
4849 7842 9.734620 CATTCTGAACATCAAAGAGTAACAAAA 57.265 29.630 0.00 0.00 0.00 2.44
4888 7881 2.094854 GGAGCACCAGAAGCAAAATCTG 60.095 50.000 0.00 0.00 43.15 2.90
4903 7896 1.830486 ATCTGGCTGGGGAATCTCAT 58.170 50.000 0.00 0.00 0.00 2.90
4916 7909 6.380846 TGGGGAATCTCATAGAAAACCAAATG 59.619 38.462 0.00 0.00 0.00 2.32
4955 7948 7.700505 TCATCATACTGAAATTGAATGCACTC 58.299 34.615 0.00 0.00 0.00 3.51
4981 8008 3.769739 TTCTGTTGTGATGCCAGTACT 57.230 42.857 0.00 0.00 0.00 2.73
5014 8041 0.601558 TAAGAGACCGTTTGCTCGCT 59.398 50.000 0.00 0.00 36.29 4.93
5015 8042 0.667792 AAGAGACCGTTTGCTCGCTC 60.668 55.000 0.00 0.00 36.29 5.03
5016 8043 2.430921 AGACCGTTTGCTCGCTCG 60.431 61.111 0.00 0.00 0.00 5.03
5017 8044 4.135493 GACCGTTTGCTCGCTCGC 62.135 66.667 0.00 0.00 0.00 5.03
5040 8097 2.383855 GGGCTCCATATCTCGCTAGAT 58.616 52.381 5.98 5.98 44.80 1.98
5090 8150 4.393155 TCTGGCTTGCCATCGCGT 62.393 61.111 15.21 0.00 38.08 6.01
5113 8173 6.910433 CGTAGCTAATTTGCCGTTTCAATAAT 59.090 34.615 8.30 0.00 0.00 1.28
5119 8179 3.435105 TGCCGTTTCAATAATGGATGC 57.565 42.857 0.00 0.00 0.00 3.91
5128 8188 4.598022 TCAATAATGGATGCACACCTTCA 58.402 39.130 12.09 0.00 0.00 3.02
5133 8193 3.940209 TGGATGCACACCTTCAATTTC 57.060 42.857 12.09 0.00 0.00 2.17
5134 8194 3.499338 TGGATGCACACCTTCAATTTCT 58.501 40.909 12.09 0.00 0.00 2.52
5148 8208 7.817478 ACCTTCAATTTCTTGTTCGTTTCTTTT 59.183 29.630 0.00 0.00 33.87 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.036164 ACAATGTACTTCCAGCGCCA 59.964 50.000 2.29 0.00 0.00 5.69
65 66 0.107897 ACAGCGAAACACTGTGGACA 60.108 50.000 13.09 0.00 46.38 4.02
98 99 2.033141 GAGCAGCAGAACCAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
122 123 1.054231 CATGCATCTGCTCCTCCCTA 58.946 55.000 0.00 0.00 42.66 3.53
198 199 4.008933 GGCGTGGAGGCTGAGTGT 62.009 66.667 0.00 0.00 42.90 3.55
339 344 0.314935 ACGAGCAAAGCAAACATGGG 59.685 50.000 0.00 0.00 0.00 4.00
364 369 0.957888 GCTCGCAAAAGCCTTCTCCT 60.958 55.000 0.00 0.00 36.22 3.69
457 471 4.796231 GTCGTCCCGCATGTCGCT 62.796 66.667 0.00 0.00 39.08 4.93
505 519 4.280494 ACGCAGTGAAGACGCCGT 62.280 61.111 0.00 0.00 42.51 5.68
568 584 1.739466 GCGAGAATCAATGTCAAGGCA 59.261 47.619 0.00 0.00 33.17 4.75
575 591 3.301776 CGGTTCTCGCGAGAATCAATGT 61.302 50.000 43.83 0.00 46.27 2.71
590 606 1.517832 CTTCCATCGCCTCGGTTCT 59.482 57.895 0.00 0.00 0.00 3.01
742 775 0.890996 CAGGAGCCTGTTTTTCGCCT 60.891 55.000 8.38 0.00 39.10 5.52
807 843 1.675552 CCCAACACGACTTTTCCAGT 58.324 50.000 0.00 0.00 39.07 4.00
814 851 4.280019 GGGCCCCCAACACGACTT 62.280 66.667 12.23 0.00 35.81 3.01
830 867 2.797156 CAATTAGAGCGTCTCCATTCGG 59.203 50.000 3.66 0.00 0.00 4.30
833 870 3.448686 CGACAATTAGAGCGTCTCCATT 58.551 45.455 3.66 1.28 0.00 3.16
875 912 9.578439 GCATAAGATTTCAATAAAGAGCAACTT 57.422 29.630 0.00 0.00 40.98 2.66
876 913 8.742777 TGCATAAGATTTCAATAAAGAGCAACT 58.257 29.630 0.00 0.00 0.00 3.16
877 914 8.915871 TGCATAAGATTTCAATAAAGAGCAAC 57.084 30.769 0.00 0.00 0.00 4.17
878 915 9.577110 CTTGCATAAGATTTCAATAAAGAGCAA 57.423 29.630 0.00 0.00 35.92 3.91
879 916 7.703621 GCTTGCATAAGATTTCAATAAAGAGCA 59.296 33.333 0.00 0.00 35.92 4.26
880 917 7.168804 GGCTTGCATAAGATTTCAATAAAGAGC 59.831 37.037 0.00 0.00 35.92 4.09
881 918 8.411683 AGGCTTGCATAAGATTTCAATAAAGAG 58.588 33.333 0.00 0.00 35.92 2.85
882 919 8.192774 CAGGCTTGCATAAGATTTCAATAAAGA 58.807 33.333 0.00 0.00 35.92 2.52
883 920 8.348983 CAGGCTTGCATAAGATTTCAATAAAG 57.651 34.615 0.00 0.00 35.92 1.85
947 984 2.200092 GGTGCCAAGGGGGTCAAA 59.800 61.111 0.00 0.00 39.65 2.69
971 1008 2.995574 CCCTCCGACCCACGTTCT 60.996 66.667 0.00 0.00 40.78 3.01
1067 1110 1.775459 AGAGGGGAGAGCGTGATAGTA 59.225 52.381 0.00 0.00 0.00 1.82
1368 1951 1.273327 CCAATCCCAGAAAACACCAGC 59.727 52.381 0.00 0.00 0.00 4.85
1539 2190 6.319658 AGTGACCTGAAACTGCATATATTTGG 59.680 38.462 0.00 0.00 0.00 3.28
1636 2381 7.438160 CGACATTATAACAGCTTGAACATCCTA 59.562 37.037 0.00 0.00 0.00 2.94
1830 2602 4.092279 TGATCCCTATCTGACTATGCTGG 58.908 47.826 0.00 0.00 32.93 4.85
1881 2654 3.360867 GAGATGAACAGAGTCCTCCTCA 58.639 50.000 0.00 0.00 43.12 3.86
2823 3745 2.037381 TGCATTGGAAGCTTGCAATCAA 59.963 40.909 34.93 25.13 44.38 2.57
2920 3862 1.673033 CGAAACCCGCTCATGAAGACT 60.673 52.381 0.00 0.00 0.00 3.24
3224 4194 6.017192 ACTTCTCCCATCTACACTGAAACTA 58.983 40.000 0.00 0.00 0.00 2.24
3345 4325 8.377799 AGATGCATTGGACACACATAGATTATA 58.622 33.333 0.00 0.00 0.00 0.98
3575 4632 3.743899 AAGCCAACGATGCATTGGTTTTT 60.744 39.130 18.31 8.16 45.22 1.94
3586 4643 1.402968 CTGATGGGAAAGCCAACGATG 59.597 52.381 0.00 0.00 35.15 3.84
3610 4667 2.092646 TCACCGATTATGGGGTTTGGAG 60.093 50.000 0.00 0.00 33.23 3.86
3737 4811 3.525537 CGTCATGTTTCATCTGTAGGCT 58.474 45.455 0.00 0.00 0.00 4.58
3783 4859 3.057245 GGGACAGCAAAAGGAAAGATGAC 60.057 47.826 0.00 0.00 0.00 3.06
4137 5215 7.174599 GCAAGATAGCATTCCACAAAGATCTAT 59.825 37.037 0.00 0.00 0.00 1.98
4200 5279 2.905085 CTCCAGGATCAGGATACAGCAT 59.095 50.000 6.59 0.00 41.41 3.79
4201 5280 2.323599 CTCCAGGATCAGGATACAGCA 58.676 52.381 6.59 0.00 41.41 4.41
4238 5317 2.159382 CACGGTGCAAAACTCCCTAAT 58.841 47.619 0.00 0.00 0.00 1.73
4255 5334 7.548075 AGGAATAACCACAGTTAAGATAACACG 59.452 37.037 3.37 0.00 41.68 4.49
4388 7374 1.135333 ACTCGAAAGGTAGCTAGCAGC 59.865 52.381 24.01 12.38 42.84 5.25
4438 7430 6.976925 CACAATCTCAATGAAAATTAGGCCTC 59.023 38.462 9.68 0.00 0.00 4.70
4490 7482 4.260139 TGCACTGCAATGTGATTCAAAT 57.740 36.364 10.09 0.00 40.12 2.32
4494 7487 3.176708 GTCATGCACTGCAATGTGATTC 58.823 45.455 8.03 0.00 43.62 2.52
4495 7488 2.414957 CGTCATGCACTGCAATGTGATT 60.415 45.455 8.03 0.00 43.62 2.57
4496 7489 1.131693 CGTCATGCACTGCAATGTGAT 59.868 47.619 8.03 0.00 43.62 3.06
4497 7490 0.518195 CGTCATGCACTGCAATGTGA 59.482 50.000 8.03 4.73 43.62 3.58
4498 7491 1.068832 GCGTCATGCACTGCAATGTG 61.069 55.000 8.03 2.13 43.62 3.21
4499 7492 1.210931 GCGTCATGCACTGCAATGT 59.789 52.632 8.03 0.00 43.62 2.71
4500 7493 4.066769 GCGTCATGCACTGCAATG 57.933 55.556 8.03 7.36 43.62 2.82
4509 7502 0.950555 TCAGGACAAGTGCGTCATGC 60.951 55.000 1.11 0.00 45.05 4.06
4510 7503 1.395954 CATCAGGACAAGTGCGTCATG 59.604 52.381 0.00 0.00 46.39 3.07
4511 7504 1.002430 ACATCAGGACAAGTGCGTCAT 59.998 47.619 0.00 0.00 37.66 3.06
4512 7505 0.392706 ACATCAGGACAAGTGCGTCA 59.607 50.000 0.00 0.00 37.66 4.35
4513 7506 1.195448 CAACATCAGGACAAGTGCGTC 59.805 52.381 0.00 0.00 35.03 5.19
4516 7509 1.267806 CACCAACATCAGGACAAGTGC 59.732 52.381 0.00 0.00 0.00 4.40
4529 7522 0.037590 GTACCCATCAGCCACCAACA 59.962 55.000 0.00 0.00 0.00 3.33
4530 7523 0.037590 TGTACCCATCAGCCACCAAC 59.962 55.000 0.00 0.00 0.00 3.77
4531 7524 0.998928 ATGTACCCATCAGCCACCAA 59.001 50.000 0.00 0.00 0.00 3.67
4614 7607 9.685828 CAATCGGACTAAGAAAACCAAAAATTA 57.314 29.630 0.00 0.00 0.00 1.40
4616 7609 7.722363 ACAATCGGACTAAGAAAACCAAAAAT 58.278 30.769 0.00 0.00 0.00 1.82
4668 7661 1.752498 ACATATACGGCAGTCGGTCAA 59.248 47.619 0.00 0.00 44.45 3.18
4673 7666 2.218953 AACCACATATACGGCAGTCG 57.781 50.000 0.00 0.00 45.88 4.18
4676 7669 5.520288 GCAGATATAACCACATATACGGCAG 59.480 44.000 0.00 0.00 0.00 4.85
4719 7712 8.188139 ACAAAGTGTATGTCGTTGAGAATTTTT 58.812 29.630 0.00 0.00 0.00 1.94
4724 7717 5.900339 GACAAAGTGTATGTCGTTGAGAA 57.100 39.130 0.00 0.00 37.98 2.87
4735 7728 3.857157 ACACCAGGTGACAAAGTGTAT 57.143 42.857 27.39 0.00 38.02 2.29
4780 7773 6.732531 TGTTGCAGAAATCACTAGATCTTG 57.267 37.500 0.00 0.36 31.90 3.02
4813 7806 6.041423 TGATGTTCAGAATGCAGAGTAGAA 57.959 37.500 0.00 0.00 34.76 2.10
4836 7829 9.543783 AGAGTCGAAATAGTTTTGTTACTCTTT 57.456 29.630 0.00 0.00 34.40 2.52
4849 7842 2.428890 CTCCAGCCAGAGTCGAAATAGT 59.571 50.000 0.00 0.00 0.00 2.12
4888 7881 3.864789 TTTCTATGAGATTCCCCAGCC 57.135 47.619 0.00 0.00 0.00 4.85
4903 7896 3.976169 GCACTGTGCATTTGGTTTTCTA 58.024 40.909 26.70 0.00 44.26 2.10
4916 7909 1.445871 TGATGATCAGTGCACTGTGC 58.554 50.000 38.41 30.87 44.12 4.57
4955 7948 4.044336 TGGCATCACAACAGAAAAACAG 57.956 40.909 0.00 0.00 0.00 3.16
5014 8041 3.311110 GATATGGAGCCCCCGCGA 61.311 66.667 8.23 0.00 41.18 5.87
5015 8042 3.302347 GAGATATGGAGCCCCCGCG 62.302 68.421 0.00 0.00 41.18 6.46
5016 8043 2.665603 GAGATATGGAGCCCCCGC 59.334 66.667 0.00 0.00 37.93 6.13
5017 8044 2.973899 CGAGATATGGAGCCCCCG 59.026 66.667 0.00 0.00 37.93 5.73
5018 8045 0.614979 TAGCGAGATATGGAGCCCCC 60.615 60.000 0.00 0.00 0.00 5.40
5090 8150 7.067615 TCCATTATTGAAACGGCAAATTAGCTA 59.932 33.333 0.00 0.00 34.17 3.32
5098 8158 3.194329 TGCATCCATTATTGAAACGGCAA 59.806 39.130 0.00 0.00 0.00 4.52
5099 8159 2.757314 TGCATCCATTATTGAAACGGCA 59.243 40.909 0.00 0.00 0.00 5.69
5113 8173 3.499338 AGAAATTGAAGGTGTGCATCCA 58.501 40.909 12.29 0.00 0.00 3.41
5119 8179 4.920376 ACGAACAAGAAATTGAAGGTGTG 58.080 39.130 0.00 0.00 0.00 3.82
5128 8188 7.275560 CAGACCAAAAGAAACGAACAAGAAATT 59.724 33.333 0.00 0.00 0.00 1.82
5133 8193 3.791353 GCAGACCAAAAGAAACGAACAAG 59.209 43.478 0.00 0.00 0.00 3.16
5134 8194 3.442273 AGCAGACCAAAAGAAACGAACAA 59.558 39.130 0.00 0.00 0.00 2.83
5148 8208 4.156455 AGAAAACTGAAGAAGCAGACCA 57.844 40.909 0.00 0.00 39.20 4.02


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

AutoCloner maintained by Alex Coulton.