Multiple sequence alignment - TraesCS4D01G288200

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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 TraesCS4D01G288200 chr4D 100.000 4019 0 0 1 4019 459382336 459386354 0.000000e+00 7422.0
1 TraesCS4D01G288200 chr4D 84.151 713 82 23 3322 4019 17969774 17970470 0.000000e+00 662.0
2 TraesCS4D01G288200 chr4D 84.579 214 25 7 93 303 354037793 354037585 5.270000e-49 206.0
3 TraesCS4D01G288200 chr4D 89.583 48 3 2 2277 2323 417608630 417608584 4.340000e-05 60.2
4 TraesCS4D01G288200 chr4B 93.281 2307 85 30 833 3103 574169212 574171484 0.000000e+00 3338.0
5 TraesCS4D01G288200 chr4B 93.144 773 33 9 1 762 574168409 574169172 0.000000e+00 1116.0
6 TraesCS4D01G288200 chr7D 92.019 2080 132 17 973 3021 117463211 117465287 0.000000e+00 2891.0
7 TraesCS4D01G288200 chr7A 91.377 2099 135 16 967 3022 121844340 121846435 0.000000e+00 2832.0
8 TraesCS4D01G288200 chr7A 84.291 783 101 16 3249 4018 322544 323317 0.000000e+00 745.0
9 TraesCS4D01G288200 chr7A 83.857 223 27 6 454 674 121843574 121843789 1.890000e-48 204.0
10 TraesCS4D01G288200 chr4A 93.611 1127 53 6 2127 3247 9400851 9399738 0.000000e+00 1664.0
11 TraesCS4D01G288200 chr4A 91.529 1027 49 25 840 1850 9402132 9401128 0.000000e+00 1380.0
12 TraesCS4D01G288200 chr4A 92.483 439 19 5 1 430 9405269 9404836 2.050000e-172 616.0
13 TraesCS4D01G288200 chr4A 88.756 418 21 6 449 847 9404584 9404174 4.670000e-134 488.0
14 TraesCS4D01G288200 chr4A 97.059 272 8 0 1863 2134 9401145 9400874 3.660000e-125 459.0
15 TraesCS4D01G288200 chr4A 81.532 222 35 5 84 303 110909199 110909416 1.150000e-40 178.0
16 TraesCS4D01G288200 chr6D 85.152 788 86 20 3247 4019 404615812 404615041 0.000000e+00 778.0
17 TraesCS4D01G288200 chr5D 84.000 700 86 14 3247 3937 538104254 538104936 0.000000e+00 649.0
18 TraesCS4D01G288200 chr5D 76.775 521 98 21 2184 2688 98228654 98229167 1.840000e-68 270.0
19 TraesCS4D01G288200 chr1A 83.333 708 86 20 3324 4019 535789151 535788464 3.410000e-175 625.0
20 TraesCS4D01G288200 chr1A 75.984 1270 248 38 1078 2329 334446747 334447977 1.600000e-168 603.0
21 TraesCS4D01G288200 chr1A 83.406 229 36 2 94 320 321187632 321187404 1.130000e-50 211.0
22 TraesCS4D01G288200 chr1A 80.645 93 18 0 1421 1513 238678391 238678483 5.570000e-09 73.1
23 TraesCS4D01G288200 chrUn 82.739 701 95 16 3247 3937 12347709 12348393 5.750000e-168 601.0
24 TraesCS4D01G288200 chrUn 83.359 661 86 16 3247 3898 12327857 12328502 1.240000e-164 590.0
25 TraesCS4D01G288200 chrUn 83.206 655 86 16 3253 3898 12611450 12610811 2.690000e-161 579.0
26 TraesCS4D01G288200 chr6A 80.605 794 114 24 3247 4019 309869327 309870101 9.690000e-161 577.0
27 TraesCS4D01G288200 chr6A 82.479 234 35 6 95 325 591887465 591887695 2.450000e-47 200.0
28 TraesCS4D01G288200 chr1D 74.022 1074 224 45 1409 2445 268000666 267999611 1.750000e-103 387.0
29 TraesCS4D01G288200 chr1D 84.456 193 24 5 2140 2329 294227201 294227390 6.860000e-43 185.0
30 TraesCS4D01G288200 chr1D 83.770 191 29 2 2140 2329 382917956 382917767 3.190000e-41 180.0
31 TraesCS4D01G288200 chr1D 82.796 93 16 0 1421 1513 192569738 192569830 2.570000e-12 84.2
32 TraesCS4D01G288200 chr5A 76.538 520 101 18 2184 2688 105416187 105415674 8.560000e-67 265.0
33 TraesCS4D01G288200 chr5A 80.349 229 39 5 95 320 84163651 84163876 6.910000e-38 169.0
34 TraesCS4D01G288200 chr5B 76.726 507 97 19 2184 2676 107370402 107370901 3.080000e-66 263.0
35 TraesCS4D01G288200 chr7B 81.967 244 40 4 83 324 602639144 602638903 1.890000e-48 204.0
36 TraesCS4D01G288200 chr7B 83.007 153 15 4 522 674 77800134 77800275 1.170000e-25 128.0
37 TraesCS4D01G288200 chr3D 81.545 233 37 6 101 330 170066281 170066052 1.910000e-43 187.0
38 TraesCS4D01G288200 chr3A 81.675 191 33 2 2140 2329 63469639 63469828 1.500000e-34 158.0
39 TraesCS4D01G288200 chr2D 80.000 135 23 4 1381 1513 472470806 472470938 3.310000e-16 97.1
40 TraesCS4D01G288200 chr2A 79.845 129 22 4 1381 1507 613991806 613991932 1.540000e-14 91.6


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 TraesCS4D01G288200 chr4D 459382336 459386354 4018 False 7422.0 7422 100.0000 1 4019 1 chr4D.!!$F2 4018
1 TraesCS4D01G288200 chr4D 17969774 17970470 696 False 662.0 662 84.1510 3322 4019 1 chr4D.!!$F1 697
2 TraesCS4D01G288200 chr4B 574168409 574171484 3075 False 2227.0 3338 93.2125 1 3103 2 chr4B.!!$F1 3102
3 TraesCS4D01G288200 chr7D 117463211 117465287 2076 False 2891.0 2891 92.0190 973 3021 1 chr7D.!!$F1 2048
4 TraesCS4D01G288200 chr7A 121843574 121846435 2861 False 1518.0 2832 87.6170 454 3022 2 chr7A.!!$F2 2568
5 TraesCS4D01G288200 chr7A 322544 323317 773 False 745.0 745 84.2910 3249 4018 1 chr7A.!!$F1 769
6 TraesCS4D01G288200 chr4A 9399738 9405269 5531 True 921.4 1664 92.6876 1 3247 5 chr4A.!!$R1 3246
7 TraesCS4D01G288200 chr6D 404615041 404615812 771 True 778.0 778 85.1520 3247 4019 1 chr6D.!!$R1 772
8 TraesCS4D01G288200 chr5D 538104254 538104936 682 False 649.0 649 84.0000 3247 3937 1 chr5D.!!$F2 690
9 TraesCS4D01G288200 chr5D 98228654 98229167 513 False 270.0 270 76.7750 2184 2688 1 chr5D.!!$F1 504
10 TraesCS4D01G288200 chr1A 535788464 535789151 687 True 625.0 625 83.3330 3324 4019 1 chr1A.!!$R2 695
11 TraesCS4D01G288200 chr1A 334446747 334447977 1230 False 603.0 603 75.9840 1078 2329 1 chr1A.!!$F2 1251
12 TraesCS4D01G288200 chrUn 12347709 12348393 684 False 601.0 601 82.7390 3247 3937 1 chrUn.!!$F2 690
13 TraesCS4D01G288200 chrUn 12327857 12328502 645 False 590.0 590 83.3590 3247 3898 1 chrUn.!!$F1 651
14 TraesCS4D01G288200 chrUn 12610811 12611450 639 True 579.0 579 83.2060 3253 3898 1 chrUn.!!$R1 645
15 TraesCS4D01G288200 chr6A 309869327 309870101 774 False 577.0 577 80.6050 3247 4019 1 chr6A.!!$F1 772
16 TraesCS4D01G288200 chr1D 267999611 268000666 1055 True 387.0 387 74.0220 1409 2445 1 chr1D.!!$R1 1036
17 TraesCS4D01G288200 chr5A 105415674 105416187 513 True 265.0 265 76.5380 2184 2688 1 chr5A.!!$R1 504

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
820 1093 0.110238 GCGCAAGTCGATGCTCAAAA 60.110 50.0 0.3 0.0 44.21 2.44 F
1932 4636 0.307760 GAACACTCACCTTGGTTGCG 59.692 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 5013 1.751924 GTAGACGAGGAGCAGGTCATT 59.248 52.381 1.2 0.0 33.18 2.57 R
3516 6301 0.106469 ATCAGTCTAGCTCAGGCGGA 60.106 55.000 0.0 0.0 44.37 5.54 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
91 92 4.806286 GCACCCAACAATACCTACTGTCTT 60.806 45.833 0.00 0.00 0.00 3.01
115 116 4.610333 GTCCTGATTTATTGGTCCCCTTT 58.390 43.478 0.00 0.00 0.00 3.11
171 173 2.634982 AAAATGTTGATGCGCGTCAT 57.365 40.000 31.37 15.49 38.32 3.06
288 297 7.001674 TGATCAAAATATGGCCCTAAATACGT 58.998 34.615 0.00 0.00 0.00 3.57
441 450 3.621268 GTGTCTTACAGCACAGTTCAACA 59.379 43.478 0.00 0.00 35.81 3.33
451 697 3.003689 GCACAGTTCAACAATGCTGTAGT 59.996 43.478 8.43 0.00 39.82 2.73
468 714 6.373216 TGCTGTAGTGTACCAATTAATTGACC 59.627 38.462 26.32 14.70 40.14 4.02
632 878 4.318021 GGCACACGCACAGCACAG 62.318 66.667 0.00 0.00 41.24 3.66
655 907 3.332919 GCAGTGATGTTGTGATCAGTCT 58.667 45.455 0.00 0.00 34.37 3.24
789 1060 3.566351 TCCTCTTCTCTTGTCACTCACA 58.434 45.455 0.00 0.00 0.00 3.58
795 1066 2.558795 TCTCTTGTCACTCACACTAGCC 59.441 50.000 0.00 0.00 33.41 3.93
796 1067 1.618837 TCTTGTCACTCACACTAGCCC 59.381 52.381 0.00 0.00 33.41 5.19
797 1068 1.620819 CTTGTCACTCACACTAGCCCT 59.379 52.381 0.00 0.00 33.41 5.19
819 1092 0.950555 AGCGCAAGTCGATGCTCAAA 60.951 50.000 11.47 0.00 44.21 2.69
820 1093 0.110238 GCGCAAGTCGATGCTCAAAA 60.110 50.000 0.30 0.00 44.21 2.44
830 1103 2.165998 GATGCTCAAAAGTCAAGCCCT 58.834 47.619 0.00 0.00 35.12 5.19
831 1104 1.321474 TGCTCAAAAGTCAAGCCCTG 58.679 50.000 0.00 0.00 35.12 4.45
882 3553 1.721487 GATGGCGACCAACCAATCG 59.279 57.895 2.68 0.00 41.49 3.34
917 3588 7.229306 ACCCAACACATTCTGCATATACATAAG 59.771 37.037 0.00 0.00 0.00 1.73
919 3590 8.285394 CCAACACATTCTGCATATACATAAGAC 58.715 37.037 0.00 0.00 0.00 3.01
922 3593 7.169813 ACACATTCTGCATATACATAAGACGTG 59.830 37.037 0.00 0.00 31.52 4.49
923 3594 6.646653 ACATTCTGCATATACATAAGACGTGG 59.353 38.462 0.00 0.00 0.00 4.94
924 3595 6.399639 TTCTGCATATACATAAGACGTGGA 57.600 37.500 0.00 0.00 0.00 4.02
925 3596 6.590234 TCTGCATATACATAAGACGTGGAT 57.410 37.500 0.00 0.00 0.00 3.41
926 3597 6.993079 TCTGCATATACATAAGACGTGGATT 58.007 36.000 0.00 0.00 0.00 3.01
927 3598 7.090808 TCTGCATATACATAAGACGTGGATTC 58.909 38.462 0.00 0.00 0.00 2.52
931 3602 8.459635 GCATATACATAAGACGTGGATTCTCTA 58.540 37.037 0.00 0.00 0.00 2.43
935 3606 7.818997 ACATAAGACGTGGATTCTCTATACA 57.181 36.000 0.00 0.00 0.00 2.29
936 3607 8.410673 ACATAAGACGTGGATTCTCTATACAT 57.589 34.615 0.00 0.00 27.31 2.29
937 3608 9.516546 ACATAAGACGTGGATTCTCTATACATA 57.483 33.333 0.00 0.00 27.31 2.29
940 3611 7.818997 AGACGTGGATTCTCTATACATAACA 57.181 36.000 0.00 0.00 27.31 2.41
941 3612 8.410673 AGACGTGGATTCTCTATACATAACAT 57.589 34.615 0.00 0.00 27.31 2.71
942 3613 9.516546 AGACGTGGATTCTCTATACATAACATA 57.483 33.333 0.00 0.00 27.31 2.29
1033 3710 2.658064 GCTGCTCTGTGCCTCTCCT 61.658 63.158 0.00 0.00 42.00 3.69
1299 3976 0.869730 TCGTCTTCGACATCGTGACA 59.130 50.000 20.58 11.18 41.35 3.58
1311 3988 2.561956 CGTGACAGTCGGGACAGGT 61.562 63.158 1.17 0.00 0.00 4.00
1437 4114 2.107546 AACCACGTCTTCGCCGTT 59.892 55.556 0.00 0.00 41.18 4.44
1713 4408 1.339151 ACAAAGCTTGATCTCCGGTCC 60.339 52.381 0.00 0.00 0.00 4.46
1752 4447 2.509561 GTCGGCTTCTCTTCGGCC 60.510 66.667 0.00 0.00 42.18 6.13
1801 4496 1.750399 CTGGCATGGAGTTTCCGGG 60.750 63.158 0.00 0.00 40.17 5.73
1932 4636 0.307760 GAACACTCACCTTGGTTGCG 59.692 55.000 0.00 0.00 0.00 4.85
1953 4657 0.723414 CAGCGATGGTTACTGTGCTG 59.277 55.000 0.00 0.00 43.08 4.41
3017 5785 4.830765 GCTGCATGGCGGTCGGTA 62.831 66.667 0.00 0.00 37.24 4.02
3034 5802 0.388294 GTAAGCTGCGGGGTACTAGG 59.612 60.000 0.00 0.00 0.00 3.02
3054 5822 7.650660 ACTAGGAGGTTAACTAACTGGTCTAT 58.349 38.462 5.42 0.00 36.47 1.98
3103 5871 2.027192 GGATGCCCACTTGTTCTCTGTA 60.027 50.000 0.00 0.00 0.00 2.74
3104 5872 3.370953 GGATGCCCACTTGTTCTCTGTAT 60.371 47.826 0.00 0.00 0.00 2.29
3126 5896 8.695456 TGTATGAGTAAGAGTAGAATGCATTGA 58.305 33.333 18.59 1.04 0.00 2.57
3129 5899 7.840931 TGAGTAAGAGTAGAATGCATTGAAGA 58.159 34.615 18.59 0.00 0.00 2.87
3132 5902 6.841443 AAGAGTAGAATGCATTGAAGATCG 57.159 37.500 18.59 0.00 0.00 3.69
3143 5913 6.112734 TGCATTGAAGATCGTAAACCTACAT 58.887 36.000 0.00 0.00 0.00 2.29
3153 5923 3.120616 CGTAAACCTACATCGTGTGTGTG 59.879 47.826 6.49 1.32 42.24 3.82
3154 5924 3.462483 AAACCTACATCGTGTGTGTGA 57.538 42.857 6.49 0.00 42.24 3.58
3155 5925 2.724977 ACCTACATCGTGTGTGTGAG 57.275 50.000 6.49 0.00 42.24 3.51
3156 5926 1.336887 ACCTACATCGTGTGTGTGAGC 60.337 52.381 6.49 0.00 42.24 4.26
3157 5927 1.067565 CCTACATCGTGTGTGTGAGCT 60.068 52.381 6.49 0.00 42.24 4.09
3158 5928 2.163613 CCTACATCGTGTGTGTGAGCTA 59.836 50.000 6.49 0.00 42.24 3.32
3159 5929 2.354109 ACATCGTGTGTGTGAGCTAG 57.646 50.000 0.00 0.00 40.28 3.42
3160 5930 1.067565 ACATCGTGTGTGTGAGCTAGG 60.068 52.381 0.00 0.00 40.28 3.02
3161 5931 1.067565 CATCGTGTGTGTGAGCTAGGT 60.068 52.381 0.00 0.00 0.00 3.08
3162 5932 0.596577 TCGTGTGTGTGAGCTAGGTC 59.403 55.000 15.12 15.12 0.00 3.85
3163 5933 0.313987 CGTGTGTGTGAGCTAGGTCA 59.686 55.000 20.43 20.43 0.00 4.02
3164 5934 1.784525 GTGTGTGTGAGCTAGGTCAC 58.215 55.000 36.73 36.73 46.08 3.67
3196 5966 7.496346 TGAAAAGAGAATGTACATCCTAGGT 57.504 36.000 9.23 0.00 0.00 3.08
3197 5967 8.603898 TGAAAAGAGAATGTACATCCTAGGTA 57.396 34.615 9.23 0.00 0.00 3.08
3231 6002 1.598130 GTATGGGGCGATGGCTGAC 60.598 63.158 0.00 0.00 39.81 3.51
3301 6076 7.885399 AGAGAAAAACTAGATTATGCAGGTGTT 59.115 33.333 0.00 0.00 0.00 3.32
3307 6086 7.366847 ACTAGATTATGCAGGTGTTGTAGAT 57.633 36.000 0.00 0.00 0.00 1.98
3308 6087 8.478775 ACTAGATTATGCAGGTGTTGTAGATA 57.521 34.615 0.00 0.00 0.00 1.98
3309 6088 9.094578 ACTAGATTATGCAGGTGTTGTAGATAT 57.905 33.333 0.00 0.00 0.00 1.63
3483 6268 0.110373 CTAAGGCGCCACAACGAAAC 60.110 55.000 31.54 0.00 34.06 2.78
3490 6275 2.596343 GCGCCACAACGAAACATTTTTG 60.596 45.455 0.00 0.00 34.06 2.44
3516 6301 2.649331 GCAAACTGCATTGATGAGCT 57.351 45.000 4.21 0.00 44.26 4.09
3518 6303 2.734492 GCAAACTGCATTGATGAGCTCC 60.734 50.000 12.15 0.00 44.26 4.70
3536 6322 1.143073 TCCGCCTGAGCTAGACTGATA 59.857 52.381 0.00 0.00 36.60 2.15
3593 6392 7.101054 GGTGTTTATCATAACCAGTACTGTGA 58.899 38.462 21.18 17.39 32.69 3.58
3603 6402 6.374417 AACCAGTACTGTGATACCAGAATT 57.626 37.500 21.18 0.00 36.30 2.17
3613 6412 8.924303 ACTGTGATACCAGAATTAACATAGCTA 58.076 33.333 0.00 0.00 36.30 3.32
3614 6413 9.197694 CTGTGATACCAGAATTAACATAGCTAC 57.802 37.037 0.00 0.00 34.23 3.58
3635 6435 6.036735 GCTACGTATTGAGGCAAAATAGACAA 59.963 38.462 0.00 0.00 0.00 3.18
3675 6476 7.826918 TTGCTTACAAAAACTAACCCATAGT 57.173 32.000 0.00 0.00 38.54 2.12
3715 6519 1.165270 GGGCTCTGCGTTGTACAAAT 58.835 50.000 10.51 0.00 0.00 2.32
3785 6598 3.150767 CGACCTCTACAGATCCCCTAAG 58.849 54.545 0.00 0.00 0.00 2.18
3830 6644 9.535878 ACGGTTTGTTTTGTTCATTATTTATGT 57.464 25.926 0.00 0.00 35.64 2.29
3937 6756 9.672673 TTGGGTTTTTAAGAAAATCATGAACAA 57.327 25.926 0.00 0.00 37.55 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.552350 AGGTCCTAGAATACGTTATTGCCTAA 59.448 38.462 0.00 0.00 0.00 2.69
91 92 3.553828 GGGACCAATAAATCAGGACGA 57.446 47.619 0.00 0.00 0.00 4.20
288 297 5.190132 TCCGTCCTCATTTATTAGTTTCCCA 59.810 40.000 0.00 0.00 0.00 4.37
304 313 5.844004 ACATTTGATACTACATCCGTCCTC 58.156 41.667 0.00 0.00 0.00 3.71
441 450 8.458843 GTCAATTAATTGGTACACTACAGCATT 58.541 33.333 24.40 0.00 39.29 3.56
451 697 4.626604 GTCGTCGGTCAATTAATTGGTACA 59.373 41.667 24.40 5.86 38.30 2.90
468 714 2.448153 TTCCGTCCAAGTCGTCGTCG 62.448 60.000 0.00 0.00 38.55 5.12
628 874 0.594602 CACAACATCACTGCCCTGTG 59.405 55.000 0.00 0.00 39.15 3.66
629 875 0.473755 TCACAACATCACTGCCCTGT 59.526 50.000 0.00 0.00 0.00 4.00
630 876 1.741706 GATCACAACATCACTGCCCTG 59.258 52.381 0.00 0.00 0.00 4.45
631 877 1.352017 TGATCACAACATCACTGCCCT 59.648 47.619 0.00 0.00 0.00 5.19
632 878 1.741706 CTGATCACAACATCACTGCCC 59.258 52.381 0.00 0.00 0.00 5.36
670 922 4.545678 TGGCTGGCTGGTTGATTAATTAT 58.454 39.130 2.00 0.00 0.00 1.28
672 924 2.818921 TGGCTGGCTGGTTGATTAATT 58.181 42.857 2.00 0.00 0.00 1.40
673 925 2.530460 TGGCTGGCTGGTTGATTAAT 57.470 45.000 2.00 0.00 0.00 1.40
675 927 2.496871 CAATTGGCTGGCTGGTTGATTA 59.503 45.455 2.00 0.00 0.00 1.75
676 928 1.276989 CAATTGGCTGGCTGGTTGATT 59.723 47.619 2.00 0.00 0.00 2.57
677 929 0.899720 CAATTGGCTGGCTGGTTGAT 59.100 50.000 2.00 0.00 0.00 2.57
679 931 1.375013 GCAATTGGCTGGCTGGTTG 60.375 57.895 7.72 6.17 40.25 3.77
714 971 5.477607 TGATAGACAAAGAACGGGAAAGA 57.522 39.130 0.00 0.00 0.00 2.52
716 973 4.454504 GCTTGATAGACAAAGAACGGGAAA 59.545 41.667 0.00 0.00 38.08 3.13
795 1066 0.026803 GCATCGACTTGCGCTTTAGG 59.973 55.000 9.73 0.00 40.61 2.69
796 1067 3.498840 GCATCGACTTGCGCTTTAG 57.501 52.632 9.73 6.06 40.61 1.85
819 1092 0.035458 CGAACCTCAGGGCTTGACTT 59.965 55.000 0.00 0.00 35.63 3.01
820 1093 1.122019 ACGAACCTCAGGGCTTGACT 61.122 55.000 0.00 0.00 35.63 3.41
830 1103 2.623878 TGGTAAAAGCACGAACCTCA 57.376 45.000 0.00 0.00 32.99 3.86
831 1104 4.023536 TGAATTGGTAAAAGCACGAACCTC 60.024 41.667 0.00 0.00 32.99 3.85
882 3553 3.502211 AGAATGTGTTGGGTTTCATCGTC 59.498 43.478 0.00 0.00 0.00 4.20
935 3606 9.688592 GGTTAAGTTCTGCTACGTATATGTTAT 57.311 33.333 2.23 0.00 0.00 1.89
936 3607 8.685427 TGGTTAAGTTCTGCTACGTATATGTTA 58.315 33.333 2.23 0.00 0.00 2.41
937 3608 7.549839 TGGTTAAGTTCTGCTACGTATATGTT 58.450 34.615 2.23 0.00 0.00 2.71
939 3610 7.997107 TTGGTTAAGTTCTGCTACGTATATG 57.003 36.000 0.00 0.00 0.00 1.78
940 3611 7.493645 GGTTTGGTTAAGTTCTGCTACGTATAT 59.506 37.037 0.00 0.00 0.00 0.86
941 3612 6.813152 GGTTTGGTTAAGTTCTGCTACGTATA 59.187 38.462 0.00 0.00 0.00 1.47
942 3613 5.640783 GGTTTGGTTAAGTTCTGCTACGTAT 59.359 40.000 0.00 0.00 0.00 3.06
945 3616 3.810941 TGGTTTGGTTAAGTTCTGCTACG 59.189 43.478 0.00 0.00 0.00 3.51
950 3621 3.697045 TGGTGTGGTTTGGTTAAGTTCTG 59.303 43.478 0.00 0.00 0.00 3.02
957 3628 1.005569 TGGTGTGGTGTGGTTTGGTTA 59.994 47.619 0.00 0.00 0.00 2.85
1033 3710 1.289066 CGACGAGGAGCAGGACAAA 59.711 57.895 0.00 0.00 0.00 2.83
1063 3740 0.879765 ATGAAGTCGACGTCGGAGTT 59.120 50.000 35.05 27.42 40.29 3.01
1064 3741 0.447011 GATGAAGTCGACGTCGGAGT 59.553 55.000 35.05 21.70 40.29 3.85
1218 3895 4.700365 CTGTCGTCGAGCGTGCCA 62.700 66.667 0.00 0.00 42.13 4.92
1251 3928 2.035940 AAGGAGGAGACCGCGAGT 59.964 61.111 8.23 3.14 34.73 4.18
1437 4114 1.361271 GGTCACCGTGTCGAACTCA 59.639 57.895 0.00 0.00 0.00 3.41
1550 4242 1.376037 GGCACCTTCCTGTTCTCGG 60.376 63.158 0.00 0.00 0.00 4.63
1713 4408 3.608506 CGTACATGTTCTCCTTGAAGACG 59.391 47.826 2.30 0.00 35.01 4.18
1811 4506 2.908940 GATCAATGGGCTGGGCGG 60.909 66.667 0.00 0.00 0.00 6.13
1932 4636 1.982073 GCACAGTAACCATCGCTGCC 61.982 60.000 0.00 0.00 33.87 4.85
2060 4770 4.214327 CGAGAAGCCCGCTCTCCC 62.214 72.222 9.23 0.00 0.00 4.30
2266 5013 1.751924 GTAGACGAGGAGCAGGTCATT 59.248 52.381 1.20 0.00 33.18 2.57
2858 5623 1.672356 CCGTTGAGGAACTGGCAGG 60.672 63.158 20.34 0.58 41.55 4.85
3017 5785 1.001248 TCCTAGTACCCCGCAGCTT 59.999 57.895 0.00 0.00 0.00 3.74
3103 5871 8.481314 TCTTCAATGCATTCTACTCTTACTCAT 58.519 33.333 9.53 0.00 0.00 2.90
3104 5872 7.840931 TCTTCAATGCATTCTACTCTTACTCA 58.159 34.615 9.53 0.00 0.00 3.41
3126 5896 5.100259 CACACGATGTAGGTTTACGATCTT 58.900 41.667 0.00 0.00 32.21 2.40
3129 5899 4.171005 CACACACGATGTAGGTTTACGAT 58.829 43.478 0.00 0.00 40.64 3.73
3132 5902 4.300803 TCACACACACGATGTAGGTTTAC 58.699 43.478 0.00 0.00 40.64 2.01
3143 5913 0.596577 GACCTAGCTCACACACACGA 59.403 55.000 0.00 0.00 0.00 4.35
3153 5923 9.547753 TCTTTTCATATTTATGTGACCTAGCTC 57.452 33.333 0.00 0.00 35.26 4.09
3154 5924 9.553064 CTCTTTTCATATTTATGTGACCTAGCT 57.447 33.333 0.00 0.00 35.26 3.32
3155 5925 9.547753 TCTCTTTTCATATTTATGTGACCTAGC 57.452 33.333 0.00 0.00 35.26 3.42
3192 5962 7.147620 CCATACAGACATACCAAACCTTACCTA 60.148 40.741 0.00 0.00 0.00 3.08
3193 5963 6.352737 CCATACAGACATACCAAACCTTACCT 60.353 42.308 0.00 0.00 0.00 3.08
3194 5964 5.820947 CCATACAGACATACCAAACCTTACC 59.179 44.000 0.00 0.00 0.00 2.85
3195 5965 5.820947 CCCATACAGACATACCAAACCTTAC 59.179 44.000 0.00 0.00 0.00 2.34
3196 5966 5.104277 CCCCATACAGACATACCAAACCTTA 60.104 44.000 0.00 0.00 0.00 2.69
3197 5967 4.325030 CCCCATACAGACATACCAAACCTT 60.325 45.833 0.00 0.00 0.00 3.50
3273 6045 7.550551 CACCTGCATAATCTAGTTTTTCTCTCA 59.449 37.037 0.00 0.00 0.00 3.27
3275 6047 7.398024 ACACCTGCATAATCTAGTTTTTCTCT 58.602 34.615 0.00 0.00 0.00 3.10
3483 6268 3.002553 GCAGTTTGCTCAACCCAAAAATG 59.997 43.478 0.00 0.00 40.96 2.32
3490 6275 1.340889 TCAATGCAGTTTGCTCAACCC 59.659 47.619 2.48 0.00 45.31 4.11
3516 6301 0.106469 ATCAGTCTAGCTCAGGCGGA 60.106 55.000 0.00 0.00 44.37 5.54
3518 6303 3.717400 TTTATCAGTCTAGCTCAGGCG 57.283 47.619 0.00 0.00 44.37 5.52
3536 6322 2.744202 GTCAAGGCGAGACACATCATTT 59.256 45.455 7.36 0.00 36.06 2.32
3603 6402 5.777850 TGCCTCAATACGTAGCTATGTTA 57.222 39.130 23.14 10.16 0.00 2.41
3613 6412 7.391148 AATTGTCTATTTTGCCTCAATACGT 57.609 32.000 0.00 0.00 0.00 3.57
3614 6413 8.612619 ACTAATTGTCTATTTTGCCTCAATACG 58.387 33.333 0.00 0.00 0.00 3.06
3618 6417 7.994425 TGACTAATTGTCTATTTTGCCTCAA 57.006 32.000 8.73 0.00 45.54 3.02
3652 6453 8.921353 TTACTATGGGTTAGTTTTTGTAAGCA 57.079 30.769 0.00 0.00 41.49 3.91
3695 6499 0.107831 TTTGTACAACGCAGAGCCCT 59.892 50.000 8.07 0.00 0.00 5.19
3702 6506 4.519350 TGGTTTCCATATTTGTACAACGCA 59.481 37.500 8.07 0.00 0.00 5.24
3785 6598 2.591584 CGTCGCTTACGTAGAGGTTTTC 59.408 50.000 0.00 0.00 46.72 2.29
3880 6694 8.778358 CAAAACATATTCGGGAATTTGGAAAAA 58.222 29.630 13.77 0.00 35.14 1.94
3885 6699 9.762933 ATATTCAAAACATATTCGGGAATTTGG 57.237 29.630 13.77 2.45 35.14 3.28


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

AutoCloner maintained by Alex Coulton.