Multiple sequence alignment - TraesCS1B01G119400

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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 TraesCS1B01G119400 chr1B 100.000 3852 0 0 1 3852 141720771 141724622 0.000000e+00 7114.0
1 TraesCS1B01G119400 chr1B 86.522 690 85 6 1 688 403813019 403813702 0.000000e+00 752.0
2 TraesCS1B01G119400 chr1B 83.988 687 104 4 1 686 121253671 121252990 0.000000e+00 654.0
3 TraesCS1B01G119400 chr1B 83.697 687 99 10 1 686 558063562 558064236 1.510000e-178 636.0
4 TraesCS1B01G119400 chr1A 90.283 1307 67 22 1636 2920 84023008 84024276 0.000000e+00 1655.0
5 TraesCS1B01G119400 chr1A 87.391 920 69 25 686 1591 84022122 84023008 0.000000e+00 1013.0
6 TraesCS1B01G119400 chr1D 94.592 1054 27 7 1873 2902 87776812 87777859 0.000000e+00 1604.0
7 TraesCS1B01G119400 chr1D 88.137 961 55 27 686 1622 87775550 87776475 0.000000e+00 1088.0
8 TraesCS1B01G119400 chr1D 93.878 49 2 1 2917 2964 446802701 446802653 5.340000e-09 73.1
9 TraesCS1B01G119400 chr5B 87.565 957 97 12 2917 3852 674886948 674885993 0.000000e+00 1088.0
10 TraesCS1B01G119400 chr5B 82.717 920 134 16 2914 3811 450455883 450456799 0.000000e+00 795.0
11 TraesCS1B01G119400 chr2B 87.227 963 91 20 2917 3852 190056555 190057512 0.000000e+00 1068.0
12 TraesCS1B01G119400 chr2B 88.158 684 65 14 3172 3843 24851322 24852001 0.000000e+00 800.0
13 TraesCS1B01G119400 chr2B 91.379 58 5 0 1395 1452 100325945 100326002 3.190000e-11 80.5
14 TraesCS1B01G119400 chr3B 86.364 946 97 19 2919 3852 795811827 795810902 0.000000e+00 1003.0
15 TraesCS1B01G119400 chr6D 85.624 953 83 22 2919 3852 468259130 468260047 0.000000e+00 952.0
16 TraesCS1B01G119400 chr6B 90.217 736 62 6 3118 3843 142222378 142223113 0.000000e+00 952.0
17 TraesCS1B01G119400 chr6B 84.805 691 91 13 1 688 551911882 551911203 0.000000e+00 682.0
18 TraesCS1B01G119400 chr6B 84.454 669 92 11 35 699 533276894 533277554 0.000000e+00 649.0
19 TraesCS1B01G119400 chr6B 84.148 675 96 9 13 686 4548855 4548191 0.000000e+00 643.0
20 TraesCS1B01G119400 chrUn 82.999 947 134 20 2917 3852 91510107 91509177 0.000000e+00 832.0
21 TraesCS1B01G119400 chr5D 82.684 924 120 25 2913 3833 469479288 469478402 0.000000e+00 784.0
22 TraesCS1B01G119400 chr3D 82.938 885 131 17 2979 3852 28857158 28856283 0.000000e+00 780.0
23 TraesCS1B01G119400 chr3D 84.948 671 82 14 1 668 442508565 442509219 0.000000e+00 662.0
24 TraesCS1B01G119400 chr4B 81.435 948 144 22 2916 3843 291848918 291849853 0.000000e+00 747.0
25 TraesCS1B01G119400 chr2A 82.729 828 127 13 3030 3852 715901074 715901890 0.000000e+00 723.0
26 TraesCS1B01G119400 chr3A 84.783 690 95 9 1 686 519747870 519747187 0.000000e+00 684.0
27 TraesCS1B01G119400 chr4A 84.180 689 99 9 1 688 571991210 571991889 0.000000e+00 660.0


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 TraesCS1B01G119400 chr1B 141720771 141724622 3851 False 7114 7114 100.0000 1 3852 1 chr1B.!!$F1 3851
1 TraesCS1B01G119400 chr1B 403813019 403813702 683 False 752 752 86.5220 1 688 1 chr1B.!!$F2 687
2 TraesCS1B01G119400 chr1B 121252990 121253671 681 True 654 654 83.9880 1 686 1 chr1B.!!$R1 685
3 TraesCS1B01G119400 chr1B 558063562 558064236 674 False 636 636 83.6970 1 686 1 chr1B.!!$F3 685
4 TraesCS1B01G119400 chr1A 84022122 84024276 2154 False 1334 1655 88.8370 686 2920 2 chr1A.!!$F1 2234
5 TraesCS1B01G119400 chr1D 87775550 87777859 2309 False 1346 1604 91.3645 686 2902 2 chr1D.!!$F1 2216
6 TraesCS1B01G119400 chr5B 674885993 674886948 955 True 1088 1088 87.5650 2917 3852 1 chr5B.!!$R1 935
7 TraesCS1B01G119400 chr5B 450455883 450456799 916 False 795 795 82.7170 2914 3811 1 chr5B.!!$F1 897
8 TraesCS1B01G119400 chr2B 190056555 190057512 957 False 1068 1068 87.2270 2917 3852 1 chr2B.!!$F3 935
9 TraesCS1B01G119400 chr2B 24851322 24852001 679 False 800 800 88.1580 3172 3843 1 chr2B.!!$F1 671
10 TraesCS1B01G119400 chr3B 795810902 795811827 925 True 1003 1003 86.3640 2919 3852 1 chr3B.!!$R1 933
11 TraesCS1B01G119400 chr6D 468259130 468260047 917 False 952 952 85.6240 2919 3852 1 chr6D.!!$F1 933
12 TraesCS1B01G119400 chr6B 142222378 142223113 735 False 952 952 90.2170 3118 3843 1 chr6B.!!$F1 725
13 TraesCS1B01G119400 chr6B 551911203 551911882 679 True 682 682 84.8050 1 688 1 chr6B.!!$R2 687
14 TraesCS1B01G119400 chr6B 533276894 533277554 660 False 649 649 84.4540 35 699 1 chr6B.!!$F2 664
15 TraesCS1B01G119400 chr6B 4548191 4548855 664 True 643 643 84.1480 13 686 1 chr6B.!!$R1 673
16 TraesCS1B01G119400 chrUn 91509177 91510107 930 True 832 832 82.9990 2917 3852 1 chrUn.!!$R1 935
17 TraesCS1B01G119400 chr5D 469478402 469479288 886 True 784 784 82.6840 2913 3833 1 chr5D.!!$R1 920
18 TraesCS1B01G119400 chr3D 28856283 28857158 875 True 780 780 82.9380 2979 3852 1 chr3D.!!$R1 873
19 TraesCS1B01G119400 chr3D 442508565 442509219 654 False 662 662 84.9480 1 668 1 chr3D.!!$F1 667
20 TraesCS1B01G119400 chr4B 291848918 291849853 935 False 747 747 81.4350 2916 3843 1 chr4B.!!$F1 927
21 TraesCS1B01G119400 chr2A 715901074 715901890 816 False 723 723 82.7290 3030 3852 1 chr2A.!!$F1 822
22 TraesCS1B01G119400 chr3A 519747187 519747870 683 True 684 684 84.7830 1 686 1 chr3A.!!$R1 685
23 TraesCS1B01G119400 chr4A 571991210 571991889 679 False 660 660 84.1800 1 688 1 chr4A.!!$F1 687

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
656 681 0.677414 GGTTATTTTGCGGGTCGGGA 60.677 55.0 0.0 0.0 0.0 5.14 F
2234 2398 0.037697 CCCGAAGAATCACGACCACA 60.038 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 2720 0.037975 GTTCTGACCGGCGTTTCCTA 60.038 55.0 6.01 0.0 0.0 2.94 R
3386 3629 0.032130 AAGTTCAACTGCGCTCGAGA 59.968 50.0 18.75 0.0 0.0 4.04 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
31 32 1.066858 TCATCTTCGTGCTCCTTCACC 60.067 52.381 0.00 0.00 33.57 4.02
33 34 1.006102 CTTCGTGCTCCTTCACCGT 60.006 57.895 0.00 0.00 33.57 4.83
141 142 2.125350 CCTCTCGCAAGGGCTCAC 60.125 66.667 0.00 0.00 38.17 3.51
175 176 1.325037 CACAAATACGAACGCCGCATA 59.675 47.619 0.00 0.00 43.32 3.14
193 194 3.755378 GCATAAGCCAACTATGCATAGCT 59.245 43.478 29.60 20.31 44.21 3.32
194 195 4.379186 GCATAAGCCAACTATGCATAGCTG 60.379 45.833 29.60 26.76 44.21 4.24
195 196 7.823647 GCATAAGCCAACTATGCATAGCTGC 62.824 48.000 29.60 26.60 44.21 5.25
226 227 2.917933 AGCACAAGCACAAGTACTCAA 58.082 42.857 0.00 0.00 45.49 3.02
228 229 2.354510 GCACAAGCACAAGTACTCAACA 59.645 45.455 0.00 0.00 41.58 3.33
350 369 4.410400 GAACAGGGTGAGGGGCGG 62.410 72.222 0.00 0.00 0.00 6.13
366 385 4.476752 GGCCCCGCGGTGTGATTA 62.477 66.667 26.12 0.00 0.00 1.75
417 436 1.377202 GGCTGAGCGGAACCAATGA 60.377 57.895 0.00 0.00 0.00 2.57
421 440 2.746277 AGCGGAACCAATGACGGC 60.746 61.111 0.00 0.00 0.00 5.68
427 446 3.185299 AACCAATGACGGCCGACCA 62.185 57.895 35.90 27.90 34.57 4.02
599 623 2.993545 GCAACACGTTTGCATTGTCTA 58.006 42.857 22.20 0.00 44.34 2.59
606 630 2.675844 CGTTTGCATTGTCTAATCGGGA 59.324 45.455 0.00 0.00 0.00 5.14
656 681 0.677414 GGTTATTTTGCGGGTCGGGA 60.677 55.000 0.00 0.00 0.00 5.14
668 693 1.331214 GGTCGGGACATTATACGGGA 58.669 55.000 0.75 0.00 0.00 5.14
673 698 2.094182 CGGGACATTATACGGGATCTGG 60.094 54.545 0.00 0.00 0.00 3.86
689 714 4.083003 GGATCTGGTAGAGATGCTCTTACG 60.083 50.000 1.88 0.00 44.26 3.18
765 792 6.173339 CCATTTCTCTCCACTTGCTTACTTA 58.827 40.000 0.00 0.00 0.00 2.24
770 797 8.691661 TTCTCTCCACTTGCTTACTTATTTTT 57.308 30.769 0.00 0.00 0.00 1.94
899 932 2.483014 TGTGGGGAACAATTACCTCG 57.517 50.000 0.00 0.00 35.24 4.63
900 933 1.700739 TGTGGGGAACAATTACCTCGT 59.299 47.619 0.00 0.00 35.24 4.18
940 973 3.320826 CACCCGAAAAACAAAAGGAGGAT 59.679 43.478 0.00 0.00 0.00 3.24
942 975 4.765339 ACCCGAAAAACAAAAGGAGGATAG 59.235 41.667 0.00 0.00 0.00 2.08
945 978 6.015772 CCCGAAAAACAAAAGGAGGATAGAAA 60.016 38.462 0.00 0.00 0.00 2.52
975 1009 4.583871 AGGAAAACAAAACCAATGCAACA 58.416 34.783 0.00 0.00 0.00 3.33
1076 1110 1.001393 CCCCCTTTTGCTCGCCTTA 60.001 57.895 0.00 0.00 0.00 2.69
1079 1113 1.313091 CCCTTTTGCTCGCCTTACCC 61.313 60.000 0.00 0.00 0.00 3.69
1126 1160 1.765904 TCCTCACTTGCACCAACACTA 59.234 47.619 0.00 0.00 0.00 2.74
1174 1208 2.313041 TCTCTCCATTCTCCTCACTCCA 59.687 50.000 0.00 0.00 0.00 3.86
1225 1259 2.028658 CAGCCGCTCATGTATCAGGTAT 60.029 50.000 0.00 0.00 0.00 2.73
1232 1266 4.818546 GCTCATGTATCAGGTATGCAGTTT 59.181 41.667 0.00 0.00 33.37 2.66
1239 1273 7.217200 TGTATCAGGTATGCAGTTTAGGATTC 58.783 38.462 0.00 0.00 0.00 2.52
1242 1276 6.349300 TCAGGTATGCAGTTTAGGATTCTTC 58.651 40.000 0.00 0.00 0.00 2.87
1243 1277 6.156949 TCAGGTATGCAGTTTAGGATTCTTCT 59.843 38.462 0.00 0.00 0.00 2.85
1244 1278 6.825721 CAGGTATGCAGTTTAGGATTCTTCTT 59.174 38.462 0.00 0.00 0.00 2.52
1245 1279 6.825721 AGGTATGCAGTTTAGGATTCTTCTTG 59.174 38.462 0.00 0.00 0.00 3.02
1246 1280 6.823689 GGTATGCAGTTTAGGATTCTTCTTGA 59.176 38.462 0.00 0.00 0.00 3.02
1247 1281 7.500559 GGTATGCAGTTTAGGATTCTTCTTGAT 59.499 37.037 0.00 0.00 0.00 2.57
1248 1282 7.951347 ATGCAGTTTAGGATTCTTCTTGATT 57.049 32.000 0.00 0.00 0.00 2.57
1250 1284 8.498054 TGCAGTTTAGGATTCTTCTTGATTAG 57.502 34.615 0.00 0.00 0.00 1.73
1251 1285 7.066284 TGCAGTTTAGGATTCTTCTTGATTAGC 59.934 37.037 0.00 0.00 0.00 3.09
1252 1286 7.066284 GCAGTTTAGGATTCTTCTTGATTAGCA 59.934 37.037 0.00 0.00 0.00 3.49
1253 1287 8.610896 CAGTTTAGGATTCTTCTTGATTAGCAG 58.389 37.037 0.00 0.00 0.00 4.24
1254 1288 8.543774 AGTTTAGGATTCTTCTTGATTAGCAGA 58.456 33.333 0.00 0.00 0.00 4.26
1255 1289 9.336171 GTTTAGGATTCTTCTTGATTAGCAGAT 57.664 33.333 0.00 0.00 0.00 2.90
1257 1291 9.988815 TTAGGATTCTTCTTGATTAGCAGATAC 57.011 33.333 0.00 0.00 0.00 2.24
1258 1292 7.151308 AGGATTCTTCTTGATTAGCAGATACG 58.849 38.462 0.00 0.00 0.00 3.06
1259 1293 6.926272 GGATTCTTCTTGATTAGCAGATACGT 59.074 38.462 0.00 0.00 0.00 3.57
1260 1294 8.082852 GGATTCTTCTTGATTAGCAGATACGTA 58.917 37.037 0.00 0.00 0.00 3.57
1261 1295 9.123709 GATTCTTCTTGATTAGCAGATACGTAG 57.876 37.037 0.08 0.00 0.00 3.51
1329 1367 6.149973 TGGTTTCTTATCACTGCAAGATTCTG 59.850 38.462 6.63 0.00 37.43 3.02
1339 1377 5.645067 CACTGCAAGATTCTGATGAGGTTTA 59.355 40.000 0.00 0.00 37.43 2.01
1340 1378 6.149973 CACTGCAAGATTCTGATGAGGTTTAA 59.850 38.462 0.00 0.00 37.43 1.52
1341 1379 6.888632 ACTGCAAGATTCTGATGAGGTTTAAT 59.111 34.615 0.00 0.00 37.43 1.40
1342 1380 7.395489 ACTGCAAGATTCTGATGAGGTTTAATT 59.605 33.333 0.00 0.00 37.43 1.40
1363 1401 0.952010 CATGGTTTGGGCTTTGCTGC 60.952 55.000 0.00 0.00 0.00 5.25
1365 1403 1.005748 GGTTTGGGCTTTGCTGCTC 60.006 57.895 0.00 0.00 0.00 4.26
1436 1474 3.904339 AGAAGAAGGTCAAGAAGGTGCTA 59.096 43.478 0.00 0.00 0.00 3.49
1439 1477 3.007398 AGAAGGTCAAGAAGGTGCTACAG 59.993 47.826 0.00 0.00 0.00 2.74
1452 1490 3.430929 GGTGCTACAGACCATAGAAGGTG 60.431 52.174 0.00 0.00 43.38 4.00
1462 1500 4.763355 ACCATAGAAGGTGGGCATAGATA 58.237 43.478 0.00 0.00 41.30 1.98
1463 1501 5.162637 ACCATAGAAGGTGGGCATAGATAA 58.837 41.667 0.00 0.00 41.30 1.75
1464 1502 5.610982 ACCATAGAAGGTGGGCATAGATAAA 59.389 40.000 0.00 0.00 41.30 1.40
1465 1503 6.275618 ACCATAGAAGGTGGGCATAGATAAAT 59.724 38.462 0.00 0.00 41.30 1.40
1466 1504 7.461043 ACCATAGAAGGTGGGCATAGATAAATA 59.539 37.037 0.00 0.00 41.30 1.40
1539 1595 7.532571 CAGAAATGTTCAGCAAATCTGTATCA 58.467 34.615 0.00 0.00 43.32 2.15
1540 1596 7.696872 CAGAAATGTTCAGCAAATCTGTATCAG 59.303 37.037 0.00 0.00 43.32 2.90
1541 1597 7.392673 AGAAATGTTCAGCAAATCTGTATCAGT 59.607 33.333 0.00 0.00 43.32 3.41
1547 1603 8.887717 GTTCAGCAAATCTGTATCAGTAAATCT 58.112 33.333 0.00 0.00 43.32 2.40
1567 1623 7.458796 AATCTTAGGAAAGCTCCCTAGAAAT 57.541 36.000 12.80 7.23 43.64 2.17
1586 1642 5.643777 AGAAATGCAGTGGTAGTGTCATTAC 59.356 40.000 0.00 0.00 30.67 1.89
1599 1655 8.660373 GGTAGTGTCATTACATTTTTCTCTCTG 58.340 37.037 7.69 0.00 38.08 3.35
1652 1738 3.259064 TCCGTATTTCCTTCTTTCTGCG 58.741 45.455 0.00 0.00 0.00 5.18
1677 1763 4.861102 AGGCTTTGATTTCAACTTCAGG 57.139 40.909 0.00 0.00 35.28 3.86
1686 1772 8.463930 TTGATTTCAACTTCAGGTCTGTAAAT 57.536 30.769 0.00 0.00 0.00 1.40
1692 1778 8.391075 TCAACTTCAGGTCTGTAAATAAAAGG 57.609 34.615 0.00 0.00 0.00 3.11
1697 1783 5.885912 TCAGGTCTGTAAATAAAAGGGCATC 59.114 40.000 0.00 0.00 0.00 3.91
1699 1785 5.888161 AGGTCTGTAAATAAAAGGGCATCTG 59.112 40.000 0.00 0.00 0.00 2.90
1712 1798 3.840078 AGGGCATCTGGCTGTTTAAAAAT 59.160 39.130 3.62 0.00 44.01 1.82
1737 1827 5.280164 TGCAAGTGATGTTTTATGTGTGTG 58.720 37.500 0.00 0.00 0.00 3.82
1773 1867 0.323816 GAAGGGGAAAAGCAGAGGGG 60.324 60.000 0.00 0.00 0.00 4.79
1794 1888 2.291605 GCCCCTGTTTCCCTCACTAAAT 60.292 50.000 0.00 0.00 0.00 1.40
1827 1931 6.272318 CCAAAGTTCTGCAATCTGTTACAAA 58.728 36.000 0.00 0.00 0.00 2.83
1830 1934 8.482429 CAAAGTTCTGCAATCTGTTACAAATTC 58.518 33.333 0.00 0.00 0.00 2.17
1837 1941 7.487484 TGCAATCTGTTACAAATTCTTCACAA 58.513 30.769 0.00 0.00 0.00 3.33
1862 1966 3.302365 AACGCATTGAATTGGTGGAAG 57.698 42.857 0.00 0.00 0.00 3.46
1865 1969 3.320541 ACGCATTGAATTGGTGGAAGAAA 59.679 39.130 0.00 0.00 0.00 2.52
1866 1970 4.021192 ACGCATTGAATTGGTGGAAGAAAT 60.021 37.500 0.00 0.00 0.00 2.17
1867 1971 4.327898 CGCATTGAATTGGTGGAAGAAATG 59.672 41.667 0.00 0.00 0.00 2.32
1868 1972 4.093850 GCATTGAATTGGTGGAAGAAATGC 59.906 41.667 0.00 0.00 41.06 3.56
1870 1974 5.549742 TTGAATTGGTGGAAGAAATGCTT 57.450 34.783 0.00 0.00 40.25 3.91
1871 1975 6.662865 TTGAATTGGTGGAAGAAATGCTTA 57.337 33.333 0.00 0.00 36.83 3.09
1890 2038 6.583562 TGCTTAGTAAGGGATTTAGAAGAGC 58.416 40.000 11.84 0.00 0.00 4.09
1893 2041 5.678955 AGTAAGGGATTTAGAAGAGCGTT 57.321 39.130 0.00 0.00 0.00 4.84
2219 2383 2.683933 GAGGCTCTGTTCCCCCGA 60.684 66.667 7.40 0.00 0.00 5.14
2234 2398 0.037697 CCCGAAGAATCACGACCACA 60.038 55.000 0.00 0.00 0.00 4.17
2561 2731 3.269347 CCGCCATAGGAAACGCCG 61.269 66.667 0.00 0.00 43.43 6.46
2972 3148 2.159226 CGCGGGTAAAATGCCCATTTAA 60.159 45.455 0.00 0.00 46.40 1.52
2977 3153 2.734276 AAAATGCCCATTTAACGCGT 57.266 40.000 5.58 5.58 39.88 6.01
3106 3300 0.859232 CTATAAAATGCGGCGCTCGT 59.141 50.000 33.26 16.05 41.72 4.18
3130 3329 1.371183 GCTCTACCACACTGCCACA 59.629 57.895 0.00 0.00 0.00 4.17
3175 3394 0.250295 CTTCCACCACTTTCTCGCCA 60.250 55.000 0.00 0.00 0.00 5.69
3386 3629 2.683933 CGTGGTGCCTAGGGAGGT 60.684 66.667 11.72 0.00 45.78 3.85
3391 3634 1.076923 GTGCCTAGGGAGGTCTCGA 60.077 63.158 11.72 0.00 45.78 4.04
3616 3859 1.519455 GAGCATAGCAAGACGCCGT 60.519 57.895 0.00 0.00 44.04 5.68
3784 4056 1.342496 GATGATGATGAGGACGGCTGA 59.658 52.381 0.00 0.00 0.00 4.26
3786 4058 0.033228 GATGATGAGGACGGCTGAGG 59.967 60.000 0.00 0.00 0.00 3.86
3791 4073 1.076923 GAGGACGGCTGAGGGTAGA 60.077 63.158 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.280524 TTGTCGTTGGCCCTCACG 60.281 61.111 11.93 11.93 0.00 4.35
33 34 0.605319 GATGTTGTCGTTGGCCCTCA 60.605 55.000 0.00 0.00 0.00 3.86
42 43 2.029288 CGGCAGCAGATGTTGTCGT 61.029 57.895 14.38 0.00 46.57 4.34
44 45 0.376152 CATCGGCAGCAGATGTTGTC 59.624 55.000 23.26 0.00 40.27 3.18
45 46 1.028330 CCATCGGCAGCAGATGTTGT 61.028 55.000 27.43 0.00 42.78 3.32
141 142 9.490663 GTTCGTATTTGTGAATTTAGATGGAAG 57.509 33.333 0.00 0.00 0.00 3.46
193 194 1.742324 TTGTGCTTTTGGGATGCGCA 61.742 50.000 14.96 14.96 44.25 6.09
194 195 1.006337 TTGTGCTTTTGGGATGCGC 60.006 52.632 0.00 0.00 38.87 6.09
195 196 1.010419 GCTTGTGCTTTTGGGATGCG 61.010 55.000 0.00 0.00 36.03 4.73
245 247 4.148825 GATCCACCGCCGCAGAGT 62.149 66.667 0.00 0.00 0.00 3.24
312 331 1.448540 CCTAGCCACTTCACCGCTG 60.449 63.158 0.00 0.00 34.03 5.18
313 332 1.913762 ACCTAGCCACTTCACCGCT 60.914 57.895 0.00 0.00 36.63 5.52
314 333 1.741770 CACCTAGCCACTTCACCGC 60.742 63.158 0.00 0.00 0.00 5.68
350 369 3.199891 GTAATCACACCGCGGGGC 61.200 66.667 31.32 5.86 36.48 5.80
359 378 4.006989 CCAAATCCGTGGAAGTAATCACA 58.993 43.478 0.00 0.00 41.65 3.58
366 385 1.674322 CGGCCAAATCCGTGGAAGT 60.674 57.895 2.24 0.00 44.18 3.01
404 423 2.746277 GCCGTCATTGGTTCCGCT 60.746 61.111 0.00 0.00 0.00 5.52
427 446 1.229853 ATTCCCCACCCTCTTCCGT 60.230 57.895 0.00 0.00 0.00 4.69
434 453 2.610859 ACGCTCATTCCCCACCCT 60.611 61.111 0.00 0.00 0.00 4.34
579 603 1.838913 AGACAATGCAAACGTGTTGC 58.161 45.000 21.06 21.06 45.11 4.17
599 623 2.556622 ACGTGAAAAATGCTTCCCGATT 59.443 40.909 0.00 0.00 31.67 3.34
606 630 1.339929 GGGTCCACGTGAAAAATGCTT 59.660 47.619 19.30 0.00 0.00 3.91
656 681 5.888901 TCTCTACCAGATCCCGTATAATGT 58.111 41.667 0.00 0.00 0.00 2.71
689 714 4.895961 ACACTTACTTTGTCTAAGGCCTC 58.104 43.478 5.23 0.00 38.23 4.70
741 766 4.583871 AGTAAGCAAGTGGAGAGAAATGG 58.416 43.478 0.00 0.00 0.00 3.16
743 768 8.870075 AAATAAGTAAGCAAGTGGAGAGAAAT 57.130 30.769 0.00 0.00 0.00 2.17
744 769 8.691661 AAAATAAGTAAGCAAGTGGAGAGAAA 57.308 30.769 0.00 0.00 0.00 2.52
770 797 7.164230 TGCAGAAGGTTGTTTAGAAAAGAAA 57.836 32.000 0.00 0.00 0.00 2.52
771 798 6.767524 TGCAGAAGGTTGTTTAGAAAAGAA 57.232 33.333 0.00 0.00 0.00 2.52
773 800 7.826260 TTTTGCAGAAGGTTGTTTAGAAAAG 57.174 32.000 0.00 0.00 0.00 2.27
804 836 5.660864 TCTTGGGATTCTCCTGTTTTGTTTT 59.339 36.000 0.00 0.00 36.57 2.43
808 840 4.144297 TGTCTTGGGATTCTCCTGTTTTG 58.856 43.478 0.00 0.00 36.57 2.44
834 867 6.699575 ATATGCATGTAGACCAAGGAAAAC 57.300 37.500 10.16 0.00 0.00 2.43
899 932 3.689649 GGTGTGTAGTGGAATGAATGGAC 59.310 47.826 0.00 0.00 0.00 4.02
900 933 3.308117 GGGTGTGTAGTGGAATGAATGGA 60.308 47.826 0.00 0.00 0.00 3.41
940 973 4.817874 TGTTTTCCTTTCCCCCTTTCTA 57.182 40.909 0.00 0.00 0.00 2.10
942 975 4.764050 TTTGTTTTCCTTTCCCCCTTTC 57.236 40.909 0.00 0.00 0.00 2.62
945 978 2.775384 GGTTTTGTTTTCCTTTCCCCCT 59.225 45.455 0.00 0.00 0.00 4.79
1021 1055 1.761174 GCAGAGTTTGGTCCTGGGA 59.239 57.895 0.00 0.00 0.00 4.37
1126 1160 3.584848 ACAGGGAAGTGAGAGTGCTTATT 59.415 43.478 0.00 0.00 0.00 1.40
1174 1208 4.025858 AGCAGACGCCATGGCTGT 62.026 61.111 33.07 29.63 39.83 4.40
1186 1220 1.669115 GTGCGCCTTCTTCAGCAGA 60.669 57.895 4.18 0.00 40.53 4.26
1209 1243 4.000331 ACTGCATACCTGATACATGAGC 58.000 45.455 0.00 0.00 0.00 4.26
1225 1259 7.066284 GCTAATCAAGAAGAATCCTAAACTGCA 59.934 37.037 0.00 0.00 0.00 4.41
1232 1266 8.300286 CGTATCTGCTAATCAAGAAGAATCCTA 58.700 37.037 0.00 0.00 43.57 2.94
1239 1273 8.343366 TGTACTACGTATCTGCTAATCAAGAAG 58.657 37.037 0.00 0.00 31.00 2.85
1242 1276 8.343366 TCTTGTACTACGTATCTGCTAATCAAG 58.657 37.037 0.00 0.00 0.00 3.02
1243 1277 8.217131 TCTTGTACTACGTATCTGCTAATCAA 57.783 34.615 0.00 0.00 0.00 2.57
1244 1278 7.797038 TCTTGTACTACGTATCTGCTAATCA 57.203 36.000 0.00 0.00 0.00 2.57
1247 1281 9.498176 TGATATCTTGTACTACGTATCTGCTAA 57.502 33.333 3.98 0.00 0.00 3.09
1248 1282 9.668497 ATGATATCTTGTACTACGTATCTGCTA 57.332 33.333 3.98 0.00 0.00 3.49
1249 1283 7.981102 TGATATCTTGTACTACGTATCTGCT 57.019 36.000 3.98 0.00 0.00 4.24
1250 1284 8.451748 TGATGATATCTTGTACTACGTATCTGC 58.548 37.037 3.98 0.00 0.00 4.26
1256 1290 9.684448 CAAAGATGATGATATCTTGTACTACGT 57.316 33.333 3.98 0.00 44.43 3.57
1257 1291 9.684448 ACAAAGATGATGATATCTTGTACTACG 57.316 33.333 3.98 0.00 44.43 3.51
1263 1297 9.458727 AGACAAACAAAGATGATGATATCTTGT 57.541 29.630 3.98 1.62 44.43 3.16
1281 1315 7.661847 ACCAAAACCAAACAAAATAGACAAACA 59.338 29.630 0.00 0.00 0.00 2.83
1290 1324 9.454859 TGATAAGAAACCAAAACCAAACAAAAT 57.545 25.926 0.00 0.00 0.00 1.82
1291 1325 8.722394 GTGATAAGAAACCAAAACCAAACAAAA 58.278 29.630 0.00 0.00 0.00 2.44
1293 1327 7.547370 CAGTGATAAGAAACCAAAACCAAACAA 59.453 33.333 0.00 0.00 0.00 2.83
1363 1401 2.562298 AGAGCCACAGTCTGAAGAAGAG 59.438 50.000 6.91 0.00 34.84 2.85
1365 1403 2.298446 TCAGAGCCACAGTCTGAAGAAG 59.702 50.000 6.91 0.00 45.93 2.85
1436 1474 0.912486 GCCCACCTTCTATGGTCTGT 59.088 55.000 0.00 0.00 38.45 3.41
1439 1477 2.972713 TCTATGCCCACCTTCTATGGTC 59.027 50.000 0.00 0.00 38.45 4.02
1488 1526 8.945057 GCTTTGTATTTCTCTTCTTCTTCATCT 58.055 33.333 0.00 0.00 0.00 2.90
1491 1535 7.933577 TCTGCTTTGTATTTCTCTTCTTCTTCA 59.066 33.333 0.00 0.00 0.00 3.02
1539 1595 7.133483 TCTAGGGAGCTTTCCTAAGATTTACT 58.867 38.462 14.97 0.00 36.54 2.24
1540 1596 7.362802 TCTAGGGAGCTTTCCTAAGATTTAC 57.637 40.000 14.97 0.00 36.54 2.01
1541 1597 7.989947 TTCTAGGGAGCTTTCCTAAGATTTA 57.010 36.000 14.97 0.00 36.54 1.40
1547 1603 4.227300 TGCATTTCTAGGGAGCTTTCCTAA 59.773 41.667 14.97 5.95 36.54 2.69
1549 1605 2.578021 TGCATTTCTAGGGAGCTTTCCT 59.422 45.455 13.14 13.14 38.36 3.36
1550 1606 2.948315 CTGCATTTCTAGGGAGCTTTCC 59.052 50.000 0.00 0.00 0.00 3.13
1567 1623 4.551702 ATGTAATGACACTACCACTGCA 57.448 40.909 0.00 0.00 38.76 4.41
1622 1678 9.770503 GAAAGAAGGAAATACGGAGAAATAAAC 57.229 33.333 0.00 0.00 0.00 2.01
1626 1712 6.094186 GCAGAAAGAAGGAAATACGGAGAAAT 59.906 38.462 0.00 0.00 0.00 2.17
1633 1719 4.921470 TTCGCAGAAAGAAGGAAATACG 57.079 40.909 0.00 0.00 45.90 3.06
1640 1726 1.882623 AGCCTTTTCGCAGAAAGAAGG 59.117 47.619 9.66 11.65 45.90 3.46
1652 1738 6.201615 CCTGAAGTTGAAATCAAAGCCTTTTC 59.798 38.462 0.00 0.00 37.63 2.29
1677 1763 5.450550 GCCAGATGCCCTTTTATTTACAGAC 60.451 44.000 0.00 0.00 0.00 3.51
1686 1772 2.603075 AACAGCCAGATGCCCTTTTA 57.397 45.000 0.00 0.00 42.71 1.52
1692 1778 5.617529 GCAAATTTTTAAACAGCCAGATGCC 60.618 40.000 0.00 0.00 42.71 4.40
1697 1783 6.036953 TCACTTGCAAATTTTTAAACAGCCAG 59.963 34.615 0.00 0.00 0.00 4.85
1699 1785 6.356757 TCACTTGCAAATTTTTAAACAGCC 57.643 33.333 0.00 0.00 0.00 4.85
1712 1798 6.255237 CACACACATAAAACATCACTTGCAAA 59.745 34.615 0.00 0.00 0.00 3.68
1737 1827 4.506802 CCCCTTCATAGTAAATACAGGGGC 60.507 50.000 15.35 0.00 45.86 5.80
1773 1867 0.696501 TTAGTGAGGGAAACAGGGGC 59.303 55.000 0.00 0.00 0.00 5.80
1794 1888 0.178964 CAGAACTTTGGGGCAAGGGA 60.179 55.000 0.00 0.00 0.00 4.20
1862 1966 9.614792 TCTTCTAAATCCCTTACTAAGCATTTC 57.385 33.333 7.01 0.00 0.00 2.17
1865 1969 7.220740 GCTCTTCTAAATCCCTTACTAAGCAT 58.779 38.462 0.00 0.00 0.00 3.79
1866 1970 6.583562 GCTCTTCTAAATCCCTTACTAAGCA 58.416 40.000 0.00 0.00 0.00 3.91
1867 1971 5.692654 CGCTCTTCTAAATCCCTTACTAAGC 59.307 44.000 0.00 0.00 0.00 3.09
1868 1972 6.807789 ACGCTCTTCTAAATCCCTTACTAAG 58.192 40.000 0.00 0.00 0.00 2.18
1870 1974 6.786967 AACGCTCTTCTAAATCCCTTACTA 57.213 37.500 0.00 0.00 0.00 1.82
1871 1975 5.678955 AACGCTCTTCTAAATCCCTTACT 57.321 39.130 0.00 0.00 0.00 2.24
1890 2038 2.468390 GCGCAACGAAATTAGCAAAACG 60.468 45.455 0.30 0.00 0.00 3.60
1893 2041 2.287308 ACAGCGCAACGAAATTAGCAAA 60.287 40.909 11.47 0.00 0.00 3.68
2200 2364 2.610859 GGGGGAACAGAGCCTCCA 60.611 66.667 0.00 0.00 45.96 3.86
2219 2383 0.320421 CCCGTGTGGTCGTGATTCTT 60.320 55.000 0.00 0.00 0.00 2.52
2261 2425 1.521010 CCTGATGAGGCTGCTCGTG 60.521 63.158 0.00 0.00 30.52 4.35
2550 2720 0.037975 GTTCTGACCGGCGTTTCCTA 60.038 55.000 6.01 0.00 0.00 2.94
2992 3182 2.551912 CGGTTGTTTTCCGCCAGCT 61.552 57.895 0.00 0.00 41.48 4.24
3011 3201 1.565591 CGCAAACGTTTACCGCTCA 59.434 52.632 14.20 0.00 41.42 4.26
3013 3203 2.250190 GCGCAAACGTTTACCGCT 59.750 55.556 32.80 6.55 42.83 5.52
3106 3300 0.313987 CAGTGTGGTAGAGCACGTGA 59.686 55.000 22.23 0.00 40.26 4.35
3111 3305 1.371183 GTGGCAGTGTGGTAGAGCA 59.629 57.895 0.00 0.00 0.00 4.26
3116 3310 2.280524 GCGTGTGGCAGTGTGGTA 60.281 61.111 0.00 0.00 42.87 3.25
3175 3394 4.443266 GCTGAGCGGCGAGGAAGT 62.443 66.667 12.98 0.00 0.00 3.01
3386 3629 0.032130 AAGTTCAACTGCGCTCGAGA 59.968 50.000 18.75 0.00 0.00 4.04
3391 3634 1.498865 CGTGGAAGTTCAACTGCGCT 61.499 55.000 9.73 0.00 0.00 5.92
3576 3819 1.671742 GCCCAGAAGACGTTCCAGA 59.328 57.895 0.00 0.00 32.48 3.86
3579 3822 2.434359 CCGCCCAGAAGACGTTCC 60.434 66.667 0.00 0.00 32.48 3.62
3585 3828 0.397114 TATGCTCTCCGCCCAGAAGA 60.397 55.000 0.00 0.00 38.05 2.87
3601 3844 2.703409 GCACGGCGTCTTGCTATG 59.297 61.111 10.85 0.00 45.43 2.23
3784 4056 2.431057 CGGTGCAACTAGAATCTACCCT 59.569 50.000 0.00 0.00 36.74 4.34
3786 4058 3.521947 ACGGTGCAACTAGAATCTACC 57.478 47.619 0.00 0.00 36.74 3.18
3791 4073 7.328737 AGATAAAACTACGGTGCAACTAGAAT 58.671 34.615 13.15 2.08 36.74 2.40


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

AutoCloner maintained by Alex Coulton.