Multiple sequence alignment - TraesCS5D01G429800

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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 TraesCS5D01G429800 chr5D 100.000 2613 0 0 1 2613 487288305 487285693 0.000000e+00 4826
1 TraesCS5D01G429800 chr5D 79.921 508 72 15 1695 2179 550406564 550406064 1.930000e-91 346
2 TraesCS5D01G429800 chr5D 83.902 205 25 7 1693 1896 268692169 268691972 3.430000e-44 189
3 TraesCS5D01G429800 chr5B 90.656 1723 88 24 1 1695 599652965 599651288 0.000000e+00 2222
4 TraesCS5D01G429800 chr5B 75.587 979 152 51 1695 2611 485730700 485729747 1.130000e-108 403
5 TraesCS5D01G429800 chr5A 93.287 715 35 6 5 719 607680995 607680294 0.000000e+00 1042
6 TraesCS5D01G429800 chr5A 90.717 474 41 1 1225 1695 607679849 607679376 1.710000e-176 628
7 TraesCS5D01G429800 chr5A 81.757 444 46 14 767 1181 607680287 607679850 3.220000e-89 339
8 TraesCS5D01G429800 chr4A 81.040 654 79 23 1695 2311 84944454 84945099 1.820000e-131 479
9 TraesCS5D01G429800 chr3B 78.061 825 121 38 1815 2612 380867906 380867115 1.420000e-127 466
10 TraesCS5D01G429800 chr3B 75.944 715 115 41 1727 2418 762973651 762974331 5.430000e-82 315
11 TraesCS5D01G429800 chr3B 87.500 120 10 4 2457 2574 70091706 70091822 1.630000e-27 134
12 TraesCS5D01G429800 chr1B 78.849 695 111 27 1934 2610 623378710 623379386 1.110000e-118 436
13 TraesCS5D01G429800 chr2B 82.834 501 65 13 1695 2179 647332569 647333064 1.860000e-116 429
14 TraesCS5D01G429800 chr3A 76.271 944 135 43 1727 2612 377647949 377647037 1.120000e-113 420
15 TraesCS5D01G429800 chr3D 77.411 788 109 38 1815 2567 288047925 288047172 3.130000e-109 405
16 TraesCS5D01G429800 chr6B 79.281 584 95 20 1678 2242 77149737 77150313 4.080000e-103 385
17 TraesCS5D01G429800 chr2D 83.432 338 38 12 1857 2178 429922827 429922492 5.470000e-77 298
18 TraesCS5D01G429800 chr2D 82.336 351 42 12 1844 2179 109728225 109728570 1.180000e-73 287
19 TraesCS5D01G429800 chr2D 77.560 459 55 29 1695 2118 578936287 578935842 1.560000e-57 233
20 TraesCS5D01G429800 chr2D 77.337 353 55 16 2270 2612 338682050 338681713 4.440000e-43 185
21 TraesCS5D01G429800 chr1D 74.215 923 140 59 1763 2610 288794390 288793491 1.970000e-76 296
22 TraesCS5D01G429800 chr7D 73.145 849 140 54 1809 2610 400217887 400218694 9.410000e-55 224
23 TraesCS5D01G429800 chr7D 84.906 212 26 6 1697 1906 603341098 603341305 2.640000e-50 209
24 TraesCS5D01G429800 chr4D 75.855 468 75 27 2156 2610 215168455 215168897 1.230000e-48 204
25 TraesCS5D01G429800 chr2A 81.991 211 32 6 1686 1896 673548516 673548312 9.610000e-40 174
26 TraesCS5D01G429800 chr4B 78.571 224 36 8 2077 2292 619959444 619959225 1.260000e-28 137


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 TraesCS5D01G429800 chr5D 487285693 487288305 2612 True 4826.000000 4826 100.000 1 2613 1 chr5D.!!$R2 2612
1 TraesCS5D01G429800 chr5D 550406064 550406564 500 True 346.000000 346 79.921 1695 2179 1 chr5D.!!$R3 484
2 TraesCS5D01G429800 chr5B 599651288 599652965 1677 True 2222.000000 2222 90.656 1 1695 1 chr5B.!!$R2 1694
3 TraesCS5D01G429800 chr5B 485729747 485730700 953 True 403.000000 403 75.587 1695 2611 1 chr5B.!!$R1 916
4 TraesCS5D01G429800 chr5A 607679376 607680995 1619 True 669.666667 1042 88.587 5 1695 3 chr5A.!!$R1 1690
5 TraesCS5D01G429800 chr4A 84944454 84945099 645 False 479.000000 479 81.040 1695 2311 1 chr4A.!!$F1 616
6 TraesCS5D01G429800 chr3B 380867115 380867906 791 True 466.000000 466 78.061 1815 2612 1 chr3B.!!$R1 797
7 TraesCS5D01G429800 chr3B 762973651 762974331 680 False 315.000000 315 75.944 1727 2418 1 chr3B.!!$F2 691
8 TraesCS5D01G429800 chr1B 623378710 623379386 676 False 436.000000 436 78.849 1934 2610 1 chr1B.!!$F1 676
9 TraesCS5D01G429800 chr3A 377647037 377647949 912 True 420.000000 420 76.271 1727 2612 1 chr3A.!!$R1 885
10 TraesCS5D01G429800 chr3D 288047172 288047925 753 True 405.000000 405 77.411 1815 2567 1 chr3D.!!$R1 752
11 TraesCS5D01G429800 chr6B 77149737 77150313 576 False 385.000000 385 79.281 1678 2242 1 chr6B.!!$F1 564
12 TraesCS5D01G429800 chr1D 288793491 288794390 899 True 296.000000 296 74.215 1763 2610 1 chr1D.!!$R1 847
13 TraesCS5D01G429800 chr7D 400217887 400218694 807 False 224.000000 224 73.145 1809 2610 1 chr7D.!!$F1 801

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
921 946 1.0695 CGACAACGACACCCCAAAATC 60.069 52.381 0.0 0.0 42.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 2772 1.220749 GCCGATGCAGTAGGAACCA 59.779 57.895 8.82 0.0 37.47 3.67 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
110 111 2.800544 CGGTGTCTTCAGTTTGTACCAG 59.199 50.000 0.00 0.00 0.00 4.00
183 184 7.660617 ACTTGTTGGCTGATATTATCTGATCTG 59.339 37.037 13.09 0.00 0.00 2.90
184 185 7.307131 TGTTGGCTGATATTATCTGATCTGA 57.693 36.000 13.09 4.63 0.00 3.27
185 186 7.914859 TGTTGGCTGATATTATCTGATCTGAT 58.085 34.615 17.88 17.88 0.00 2.90
186 187 8.380867 TGTTGGCTGATATTATCTGATCTGATT 58.619 33.333 18.83 6.27 0.00 2.57
187 188 9.881649 GTTGGCTGATATTATCTGATCTGATTA 57.118 33.333 18.83 11.43 0.00 1.75
378 379 2.417924 CCCTCGTGTTCCTGAGAAGATG 60.418 54.545 0.00 0.00 34.38 2.90
508 510 3.991773 TCGTTGCAAGTACACATTAGACC 59.008 43.478 0.00 0.00 0.00 3.85
537 539 3.117888 AGAGAACTGAAGAACCAAGCCAA 60.118 43.478 0.00 0.00 0.00 4.52
550 552 4.469657 ACCAAGCCAATGACAAACTAGAA 58.530 39.130 0.00 0.00 0.00 2.10
551 553 4.520492 ACCAAGCCAATGACAAACTAGAAG 59.480 41.667 0.00 0.00 0.00 2.85
552 554 4.761739 CCAAGCCAATGACAAACTAGAAGA 59.238 41.667 0.00 0.00 0.00 2.87
625 632 6.223138 TGTTCGTGCTGTATTCTTGTTTAG 57.777 37.500 0.00 0.00 0.00 1.85
634 641 8.462811 TGCTGTATTCTTGTTTAGTTTTGTTCA 58.537 29.630 0.00 0.00 0.00 3.18
724 731 7.964604 AACATACTAGGAACAGTTTTGAGTC 57.035 36.000 0.00 0.00 0.00 3.36
725 732 7.304497 ACATACTAGGAACAGTTTTGAGTCT 57.696 36.000 0.00 0.00 0.00 3.24
726 733 7.736893 ACATACTAGGAACAGTTTTGAGTCTT 58.263 34.615 0.00 0.00 0.00 3.01
727 734 7.657761 ACATACTAGGAACAGTTTTGAGTCTTG 59.342 37.037 0.00 0.00 0.00 3.02
728 735 4.816925 ACTAGGAACAGTTTTGAGTCTTGC 59.183 41.667 0.00 0.00 0.00 4.01
729 736 3.891049 AGGAACAGTTTTGAGTCTTGCT 58.109 40.909 0.00 0.00 0.00 3.91
730 737 3.879892 AGGAACAGTTTTGAGTCTTGCTC 59.120 43.478 0.00 0.00 44.36 4.26
735 742 1.333619 GTTTTGAGTCTTGCTCGGCAA 59.666 47.619 10.28 10.28 46.80 4.52
769 776 6.843069 AAAGAAATGTGCATTGTTGTTACC 57.157 33.333 0.00 0.00 0.00 2.85
818 826 4.335647 CGCTGCCCTCCACCTGTT 62.336 66.667 0.00 0.00 0.00 3.16
850 858 1.623811 CCAGCGGCCAGGTAGTAATAT 59.376 52.381 2.24 0.00 0.00 1.28
905 930 3.706373 GGAGGCTCCAAGGCGACA 61.706 66.667 28.55 0.00 46.58 4.35
919 944 1.716826 GCGACAACGACACCCCAAAA 61.717 55.000 0.00 0.00 42.66 2.44
921 946 1.069500 CGACAACGACACCCCAAAATC 60.069 52.381 0.00 0.00 42.66 2.17
923 948 2.359531 GACAACGACACCCCAAAATCAA 59.640 45.455 0.00 0.00 0.00 2.57
924 949 2.761208 ACAACGACACCCCAAAATCAAA 59.239 40.909 0.00 0.00 0.00 2.69
1119 1160 1.688735 ACTACAACTCTGCAGCACTCA 59.311 47.619 9.47 0.00 0.00 3.41
1121 1162 1.805869 ACAACTCTGCAGCACTCATC 58.194 50.000 9.47 0.00 0.00 2.92
1124 1165 2.096220 ACTCTGCAGCACTCATCTTG 57.904 50.000 9.47 0.00 0.00 3.02
1127 1168 2.415857 CTCTGCAGCACTCATCTTGTTC 59.584 50.000 9.47 0.00 0.00 3.18
1132 1173 3.979495 GCAGCACTCATCTTGTTCTTTTG 59.021 43.478 0.00 0.00 0.00 2.44
1133 1174 4.498682 GCAGCACTCATCTTGTTCTTTTGT 60.499 41.667 0.00 0.00 0.00 2.83
1135 1176 6.038356 CAGCACTCATCTTGTTCTTTTGTTT 58.962 36.000 0.00 0.00 0.00 2.83
1136 1177 6.197842 CAGCACTCATCTTGTTCTTTTGTTTC 59.802 38.462 0.00 0.00 0.00 2.78
1137 1178 5.172053 GCACTCATCTTGTTCTTTTGTTTCG 59.828 40.000 0.00 0.00 0.00 3.46
1138 1179 5.172053 CACTCATCTTGTTCTTTTGTTTCGC 59.828 40.000 0.00 0.00 0.00 4.70
1146 1187 1.337703 TCTTTTGTTTCGCAGCAGCAT 59.662 42.857 0.82 0.00 42.27 3.79
1156 1197 5.497635 TTCGCAGCAGCATTCATAATTTA 57.502 34.783 0.82 0.00 42.27 1.40
1183 1224 6.128117 GCATACACTTGTAAATTTCCTCCGAA 60.128 38.462 0.00 0.00 33.76 4.30
1193 1234 4.680171 ATTTCCTCCGAACGAACAATTC 57.320 40.909 0.00 0.00 0.00 2.17
1200 1241 3.431912 TCCGAACGAACAATTCATGACTG 59.568 43.478 0.00 0.00 0.00 3.51
1201 1242 3.431912 CCGAACGAACAATTCATGACTGA 59.568 43.478 10.31 0.00 0.00 3.41
1203 1244 4.386230 GAACGAACAATTCATGACTGACG 58.614 43.478 10.31 14.65 0.00 4.35
1208 1249 2.289631 ACAATTCATGACTGACGCCTCA 60.290 45.455 10.31 0.00 0.00 3.86
1215 1256 0.249489 GACTGACGCCTCAACTGTGT 60.249 55.000 0.00 0.00 0.00 3.72
1216 1257 0.530650 ACTGACGCCTCAACTGTGTG 60.531 55.000 0.00 0.00 0.00 3.82
1229 1270 6.293407 CCTCAACTGTGTGGTTTGTAAGTATG 60.293 42.308 0.00 0.00 34.30 2.39
1281 1325 2.264005 TGCCGCTTTTGAGGAACTTA 57.736 45.000 0.00 0.00 41.55 2.24
1289 1333 5.617087 CGCTTTTGAGGAACTTAAGCCTAAC 60.617 44.000 1.29 0.00 41.55 2.34
1296 1347 8.370266 TGAGGAACTTAAGCCTAACTATTGTA 57.630 34.615 1.29 0.00 41.55 2.41
1297 1348 8.818860 TGAGGAACTTAAGCCTAACTATTGTAA 58.181 33.333 1.29 0.00 41.55 2.41
1298 1349 9.096160 GAGGAACTTAAGCCTAACTATTGTAAC 57.904 37.037 1.29 0.00 41.55 2.50
1299 1350 8.823794 AGGAACTTAAGCCTAACTATTGTAACT 58.176 33.333 1.29 0.00 27.25 2.24
1329 1380 5.913137 AGTCTTTGTCCATGTGTTTGAAA 57.087 34.783 0.00 0.00 0.00 2.69
1332 1383 7.425606 AGTCTTTGTCCATGTGTTTGAAATAC 58.574 34.615 0.00 0.00 0.00 1.89
1335 1386 7.920151 TCTTTGTCCATGTGTTTGAAATACTTG 59.080 33.333 11.84 11.84 0.00 3.16
1342 1396 5.587289 TGTGTTTGAAATACTTGAGCCAAC 58.413 37.500 6.38 0.00 0.00 3.77
1385 1442 4.962362 TCTCTCAATTAGGATGCTGTGGTA 59.038 41.667 0.00 0.00 0.00 3.25
1427 1484 4.046462 CGAAAACAAGACTAGAACCGTCA 58.954 43.478 0.00 0.00 33.89 4.35
1447 1504 5.235616 CGTCATACTTGCGGTTATGGTAATT 59.764 40.000 0.00 0.00 0.00 1.40
1451 1508 2.130272 TGCGGTTATGGTAATTGGCA 57.870 45.000 0.00 0.00 0.00 4.92
1570 1627 2.040412 GGTTCTGGAGGGTCTTCATGTT 59.960 50.000 0.00 0.00 0.00 2.71
1618 1675 2.803492 GCCCTCGTGGAGATGATTGTAC 60.803 54.545 4.76 0.00 35.39 2.90
1641 1698 4.995487 CCGCCTTCTATGTTTACCTAATCC 59.005 45.833 0.00 0.00 0.00 3.01
1701 1758 7.932491 TGGTGTGTTATTTAGTGTTACTAGCAA 59.068 33.333 0.00 0.00 31.47 3.91
1717 1774 1.657181 CAAAACAGCCCGTGCGTTC 60.657 57.895 1.45 0.00 44.33 3.95
1760 1817 4.971939 TCATAATCTCCAATCGCCATGAA 58.028 39.130 0.00 0.00 0.00 2.57
1820 1896 5.811588 TCATTTTCGTGAAATCGTGAACAA 58.188 33.333 0.00 0.00 35.79 2.83
2007 2118 8.989767 CATTTCTAGAATCGACGAACATTTTTC 58.010 33.333 5.89 0.00 0.00 2.29
2008 2119 7.646446 TTCTAGAATCGACGAACATTTTTCA 57.354 32.000 0.00 0.00 0.00 2.69
2013 2124 8.574196 AGAATCGACGAACATTTTTCAAAAAT 57.426 26.923 0.00 1.98 0.00 1.82
2014 2125 9.030301 AGAATCGACGAACATTTTTCAAAAATT 57.970 25.926 5.29 0.00 0.00 1.82
2015 2126 8.970529 AATCGACGAACATTTTTCAAAAATTG 57.029 26.923 5.29 7.94 36.10 2.32
2017 2128 6.019479 TCGACGAACATTTTTCAAAAATTGGG 60.019 34.615 5.29 0.00 34.98 4.12
2019 2130 5.298026 ACGAACATTTTTCAAAAATTGGGGG 59.702 36.000 5.29 0.00 34.98 5.40
2023 2143 7.724490 ACATTTTTCAAAAATTGGGGGAAAA 57.276 28.000 5.29 0.00 36.13 2.29
2027 2147 9.610705 ATTTTTCAAAAATTGGGGGAAAATTTG 57.389 25.926 1.98 0.00 37.32 2.32
2412 2660 6.648879 AAATGAAGACGGAAAAGGAATTCA 57.351 33.333 7.93 0.00 0.00 2.57
2413 2661 6.648879 AATGAAGACGGAAAAGGAATTCAA 57.351 33.333 7.93 0.00 0.00 2.69
2492 2740 1.668294 CGCTGTGTCTTCTCCCAGT 59.332 57.895 0.00 0.00 0.00 4.00
2493 2741 0.034059 CGCTGTGTCTTCTCCCAGTT 59.966 55.000 0.00 0.00 0.00 3.16
2523 2783 3.366070 CGCGGTATAGATGGTTCCTACTG 60.366 52.174 0.00 0.00 0.00 2.74
2527 2787 5.622460 CGGTATAGATGGTTCCTACTGCATC 60.622 48.000 0.00 0.00 0.00 3.91
2532 2792 1.220749 GTTCCTACTGCATCGGCCA 59.779 57.895 2.24 0.00 40.13 5.36
2567 2827 6.208599 GGGATTCCTCTGTGTGAAATGTTTTA 59.791 38.462 2.01 0.00 0.00 1.52
2605 2874 4.892934 ACATCGGTGGGTAATATTTTGCAT 59.107 37.500 0.00 0.00 0.00 3.96
2612 2881 7.327214 GGTGGGTAATATTTTGCATCTTTGAA 58.673 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.130298 TCACACCTGTAACAAGAACAAATG 57.870 37.500 0.00 0.00 0.00 2.32
110 111 6.072112 TGGTCTTTCAATGCTTACTTGTTC 57.928 37.500 0.00 0.00 0.00 3.18
508 510 2.613730 TCTTCAGTTCTCTACACGCG 57.386 50.000 3.53 3.53 0.00 6.01
725 732 7.773213 CTTTAACAAGAGCATTGCCGAGCAA 62.773 44.000 12.63 12.63 41.72 3.91
726 733 0.890542 AACAAGAGCATTGCCGAGCA 60.891 50.000 4.70 0.00 36.47 4.26
727 734 1.086696 TAACAAGAGCATTGCCGAGC 58.913 50.000 4.70 0.00 0.00 5.03
728 735 3.436704 TCTTTAACAAGAGCATTGCCGAG 59.563 43.478 4.70 0.00 33.80 4.63
729 736 3.407698 TCTTTAACAAGAGCATTGCCGA 58.592 40.909 4.70 0.00 33.80 5.54
730 737 3.829886 TCTTTAACAAGAGCATTGCCG 57.170 42.857 4.70 0.00 33.80 5.69
731 738 5.928264 ACATTTCTTTAACAAGAGCATTGCC 59.072 36.000 4.70 0.00 40.28 4.52
732 739 6.617105 GCACATTTCTTTAACAAGAGCATTGC 60.617 38.462 0.00 0.00 40.28 3.56
733 740 6.421501 TGCACATTTCTTTAACAAGAGCATTG 59.578 34.615 0.51 0.51 40.28 2.82
734 741 6.514947 TGCACATTTCTTTAACAAGAGCATT 58.485 32.000 0.00 0.00 40.28 3.56
735 742 6.088016 TGCACATTTCTTTAACAAGAGCAT 57.912 33.333 0.00 0.00 40.28 3.79
736 743 5.512753 TGCACATTTCTTTAACAAGAGCA 57.487 34.783 0.00 0.00 40.28 4.26
737 744 6.421801 ACAATGCACATTTCTTTAACAAGAGC 59.578 34.615 0.00 0.00 40.28 4.09
738 745 7.935338 ACAATGCACATTTCTTTAACAAGAG 57.065 32.000 0.00 0.00 40.28 2.85
769 776 0.243095 GCTGCTGCTTCTCCAAAAGG 59.757 55.000 8.53 0.00 36.03 3.11
850 858 3.394274 CCCATGGGTGATGTCCACTATAA 59.606 47.826 23.93 0.00 45.03 0.98
897 922 2.280592 GGGTGTCGTTGTCGCCTT 60.281 61.111 0.00 0.00 35.96 4.35
905 930 4.681074 ATTTTGATTTTGGGGTGTCGTT 57.319 36.364 0.00 0.00 0.00 3.85
915 940 7.020602 GGGGCGTATCAAAAATTTTGATTTTG 58.979 34.615 30.98 22.65 44.97 2.44
919 944 5.413309 TGGGGCGTATCAAAAATTTTGAT 57.587 34.783 29.42 29.42 41.54 2.57
921 946 3.932089 CCTGGGGCGTATCAAAAATTTTG 59.068 43.478 11.92 11.92 0.00 2.44
923 948 2.093711 GCCTGGGGCGTATCAAAAATTT 60.094 45.455 0.00 0.00 39.62 1.82
924 949 1.480545 GCCTGGGGCGTATCAAAAATT 59.519 47.619 0.00 0.00 39.62 1.82
1083 1124 7.556996 AGAGTTGTAGTAGTACCTATGTCTTGG 59.443 40.741 5.26 0.00 0.00 3.61
1099 1140 1.688735 TGAGTGCTGCAGAGTTGTAGT 59.311 47.619 20.43 0.00 39.03 2.73
1102 1143 1.347050 AGATGAGTGCTGCAGAGTTGT 59.653 47.619 20.43 0.00 0.00 3.32
1105 1146 1.347050 ACAAGATGAGTGCTGCAGAGT 59.653 47.619 20.43 5.50 0.00 3.24
1119 1160 4.044426 GCTGCGAAACAAAAGAACAAGAT 58.956 39.130 0.00 0.00 0.00 2.40
1121 1162 3.178267 TGCTGCGAAACAAAAGAACAAG 58.822 40.909 0.00 0.00 0.00 3.16
1124 1165 1.518515 GCTGCTGCGAAACAAAAGAAC 59.481 47.619 0.00 0.00 0.00 3.01
1127 1168 1.774639 ATGCTGCTGCGAAACAAAAG 58.225 45.000 11.21 0.00 43.34 2.27
1132 1173 2.830772 TATGAATGCTGCTGCGAAAC 57.169 45.000 11.21 3.43 43.34 2.78
1133 1174 4.374843 AATTATGAATGCTGCTGCGAAA 57.625 36.364 11.21 0.00 43.34 3.46
1135 1176 5.454520 CATAAATTATGAATGCTGCTGCGA 58.545 37.500 7.17 0.80 39.16 5.10
1136 1177 4.089493 GCATAAATTATGAATGCTGCTGCG 59.911 41.667 16.45 0.00 42.15 5.18
1137 1178 4.986034 TGCATAAATTATGAATGCTGCTGC 59.014 37.500 16.45 8.89 44.96 5.25
1138 1179 7.810759 TGTATGCATAAATTATGAATGCTGCTG 59.189 33.333 18.58 0.00 44.96 4.41
1156 1197 6.183360 CGGAGGAAATTTACAAGTGTATGCAT 60.183 38.462 3.79 3.79 0.00 3.96
1183 1224 2.157668 GCGTCAGTCATGAATTGTTCGT 59.842 45.455 0.00 0.00 37.14 3.85
1193 1234 1.073964 CAGTTGAGGCGTCAGTCATG 58.926 55.000 9.34 3.92 32.98 3.07
1200 1241 0.814010 AACCACACAGTTGAGGCGTC 60.814 55.000 0.00 0.00 36.98 5.19
1201 1242 0.393808 AAACCACACAGTTGAGGCGT 60.394 50.000 0.00 0.00 36.98 5.68
1203 1244 1.102978 ACAAACCACACAGTTGAGGC 58.897 50.000 0.00 0.00 36.98 4.70
1208 1249 9.953565 ATATACATACTTACAAACCACACAGTT 57.046 29.630 0.00 0.00 0.00 3.16
1229 1270 9.221775 CGTGCTGGATTTTTAGTCAAAATATAC 57.778 33.333 0.00 0.00 43.89 1.47
1241 1282 1.803334 ACGAGCGTGCTGGATTTTTA 58.197 45.000 10.94 0.00 0.00 1.52
1243 1284 1.665679 CATACGAGCGTGCTGGATTTT 59.334 47.619 10.94 0.00 0.00 1.82
1296 1347 8.950210 CACATGGACAAAGACTATCAAATAGTT 58.050 33.333 0.00 0.00 45.64 2.24
1298 1349 8.498054 ACACATGGACAAAGACTATCAAATAG 57.502 34.615 0.00 0.00 38.81 1.73
1299 1350 8.862325 AACACATGGACAAAGACTATCAAATA 57.138 30.769 0.00 0.00 0.00 1.40
1300 1351 7.765695 AACACATGGACAAAGACTATCAAAT 57.234 32.000 0.00 0.00 0.00 2.32
1301 1352 7.284261 TCAAACACATGGACAAAGACTATCAAA 59.716 33.333 0.00 0.00 0.00 2.69
1302 1353 6.770303 TCAAACACATGGACAAAGACTATCAA 59.230 34.615 0.00 0.00 0.00 2.57
1308 1359 7.425606 AGTATTTCAAACACATGGACAAAGAC 58.574 34.615 0.00 0.00 0.00 3.01
1318 1369 6.040842 AGTTGGCTCAAGTATTTCAAACACAT 59.959 34.615 0.00 0.00 0.00 3.21
1329 1380 5.749462 AGCTTGAATAGTTGGCTCAAGTAT 58.251 37.500 11.90 9.40 45.13 2.12
1332 1383 6.690194 ATTAGCTTGAATAGTTGGCTCAAG 57.310 37.500 7.37 7.37 45.78 3.02
1335 1386 8.383318 TGATAATTAGCTTGAATAGTTGGCTC 57.617 34.615 1.93 0.00 34.88 4.70
1385 1442 4.827087 CGCTGAGCTCCGTGCCAT 62.827 66.667 12.15 0.00 44.23 4.40
1427 1484 4.277423 GCCAATTACCATAACCGCAAGTAT 59.723 41.667 0.00 0.00 0.00 2.12
1447 1504 4.721776 AGGTAGAAGAAGGAACATATGCCA 59.278 41.667 1.58 0.00 0.00 4.92
1451 1508 6.100424 CCCAAGAGGTAGAAGAAGGAACATAT 59.900 42.308 0.00 0.00 0.00 1.78
1516 1573 3.072915 TCTCCTCAATCAACCTTCTTGCA 59.927 43.478 0.00 0.00 0.00 4.08
1570 1627 3.057245 CACCGAGAACAAGATGAGTCTCA 60.057 47.826 4.68 4.68 34.24 3.27
1618 1675 4.995487 GGATTAGGTAAACATAGAAGGCGG 59.005 45.833 0.00 0.00 0.00 6.13
1665 1722 6.767902 ACTAAATAACACACCATAGGAGCATG 59.232 38.462 0.00 0.00 0.00 4.06
1701 1758 3.284449 GGAACGCACGGGCTGTTT 61.284 61.111 18.24 4.67 37.06 2.83
1731 1788 8.408043 TGGCGATTGGAGATTATGATATTTTT 57.592 30.769 0.00 0.00 0.00 1.94
1732 1789 8.464404 CATGGCGATTGGAGATTATGATATTTT 58.536 33.333 0.00 0.00 0.00 1.82
1736 1793 6.298441 TCATGGCGATTGGAGATTATGATA 57.702 37.500 0.00 0.00 0.00 2.15
1760 1817 2.360483 TCGGTGATGCAACAAAATGTGT 59.640 40.909 0.00 0.00 44.64 3.72
1954 2062 7.122055 TCCGCCTATTCAAGAACAATGTTTTAT 59.878 33.333 0.00 0.00 0.00 1.40
1964 2072 4.636206 AGAAATGTCCGCCTATTCAAGAAC 59.364 41.667 0.00 0.00 0.00 3.01
2007 2118 6.721704 TTCCAAATTTTCCCCCAATTTTTG 57.278 33.333 0.00 0.00 32.57 2.44
2008 2119 7.927683 ATTTCCAAATTTTCCCCCAATTTTT 57.072 28.000 0.00 0.00 32.57 1.94
2013 2124 5.103940 TGTGAATTTCCAAATTTTCCCCCAA 60.104 36.000 0.00 0.00 38.64 4.12
2014 2125 4.413520 TGTGAATTTCCAAATTTTCCCCCA 59.586 37.500 0.00 0.00 38.64 4.96
2015 2126 4.979335 TGTGAATTTCCAAATTTTCCCCC 58.021 39.130 0.00 0.00 38.64 5.40
2017 2128 7.326968 TGTTTGTGAATTTCCAAATTTTCCC 57.673 32.000 12.88 4.31 38.64 3.97
2278 2486 8.948853 TTGTCGATTTAGAAAATGTTTGCTAG 57.051 30.769 0.00 0.00 30.25 3.42
2392 2624 6.458232 TTTTGAATTCCTTTTCCGTCTTCA 57.542 33.333 2.27 0.00 0.00 3.02
2421 2669 9.393249 GCCAGCCAAGTTTTTAAATTTATTTTC 57.607 29.630 0.00 0.00 0.00 2.29
2423 2671 7.308288 CGGCCAGCCAAGTTTTTAAATTTATTT 60.308 33.333 9.78 0.00 35.37 1.40
2426 2674 4.991687 CGGCCAGCCAAGTTTTTAAATTTA 59.008 37.500 9.78 0.00 35.37 1.40
2438 2686 3.136123 CATGTCCGGCCAGCCAAG 61.136 66.667 9.78 0.00 35.37 3.61
2504 2764 5.622460 CGATGCAGTAGGAACCATCTATACC 60.622 48.000 0.00 0.00 33.64 2.73
2512 2772 1.220749 GCCGATGCAGTAGGAACCA 59.779 57.895 8.82 0.00 37.47 3.67
2567 2827 6.459066 CCACCGATGTCATCTATAAGTGATT 58.541 40.000 11.04 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.