Multiple sequence alignment - TraesCS7A01G483100

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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 TraesCS7A01G483100 chr7A 100.000 4183 0 0 1 4183 674817552 674813370 0.000000e+00 7725.0
1 TraesCS7A01G483100 chr7B 95.852 1832 50 12 1947 3763 650612883 650611063 0.000000e+00 2939.0
2 TraesCS7A01G483100 chr7B 90.771 1972 107 38 11 1953 650614838 650612913 0.000000e+00 2564.0
3 TraesCS7A01G483100 chr7B 91.258 469 39 2 3716 4183 650611077 650610610 4.560000e-179 638.0
4 TraesCS7A01G483100 chr7D 96.058 1801 42 12 1947 3727 583065288 583063497 0.000000e+00 2905.0
5 TraesCS7A01G483100 chr7D 94.484 1251 41 9 715 1953 583066553 583065319 0.000000e+00 1903.0
6 TraesCS7A01G483100 chr7D 94.986 738 23 6 3 731 583067218 583066486 0.000000e+00 1146.0
7 TraesCS7A01G483100 chr7D 89.316 468 32 4 3717 4183 583063171 583062721 4.690000e-159 571.0
8 TraesCS7A01G483100 chr6A 77.320 291 45 16 1086 1367 144247521 144247799 7.240000e-33 152.0
9 TraesCS7A01G483100 chr6A 80.128 156 23 3 2595 2750 144248656 144248803 4.420000e-20 110.0
10 TraesCS7A01G483100 chr6D 76.976 291 47 16 1086 1367 115772127 115772406 9.370000e-32 148.0
11 TraesCS7A01G483100 chr6D 79.394 165 24 4 2595 2757 115773257 115773413 1.590000e-19 108.0
12 TraesCS7A01G483100 chr6B 90.000 110 11 0 1086 1195 205234733 205234842 4.360000e-30 143.0
13 TraesCS7A01G483100 chr6B 91.026 78 7 0 2595 2672 205235863 205235940 5.720000e-19 106.0
14 TraesCS7A01G483100 chr2A 92.857 56 2 1 1320 1375 24909547 24909600 3.470000e-11 80.5
15 TraesCS7A01G483100 chr2A 94.340 53 1 1 1323 1375 25099422 25099372 3.470000e-11 80.5


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 TraesCS7A01G483100 chr7A 674813370 674817552 4182 True 7725.00 7725 100.000 1 4183 1 chr7A.!!$R1 4182
1 TraesCS7A01G483100 chr7B 650610610 650614838 4228 True 2047.00 2939 92.627 11 4183 3 chr7B.!!$R1 4172
2 TraesCS7A01G483100 chr7D 583062721 583067218 4497 True 1631.25 2905 93.711 3 4183 4 chr7D.!!$R1 4180

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
839 869 0.659957 CCACTACCGCGTCTACTACC 59.340 60.0 4.92 0.0 0.00 3.18 F
1327 1360 0.106669 GGGTTATGGGAGTCAAGGGC 60.107 60.0 0.00 0.0 0.00 5.19 F
2100 2211 0.763652 CCATGAGCAGCTGGAGGTAT 59.236 55.0 17.12 0.0 34.24 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2456 1.475280 CAAGCATGGAGGTTCACATGG 59.525 52.381 0.00 0.00 43.5 3.66 R
3098 3217 1.451927 GCTGATGATTGGGCCGTCA 60.452 57.895 12.98 12.98 0.0 4.35 R
3904 4382 0.896923 GTCATGCAAATCAAGGGGCA 59.103 50.000 0.00 0.00 41.0 5.36 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
108 109 9.578576 AGCTAATCAATGTGGATTATTGTATGT 57.421 29.630 0.00 0.00 38.64 2.29
119 120 6.985645 TGGATTATTGTATGTTGGTACGTACC 59.014 38.462 33.42 33.42 43.24 3.34
176 177 1.129917 CTCCAGATGATGTGGGAGCT 58.870 55.000 8.90 0.00 40.37 4.09
181 182 4.907269 TCCAGATGATGTGGGAGCTATTTA 59.093 41.667 8.90 0.00 35.58 1.40
355 360 5.123979 ACTGTCTGGAAAACACTCTTTTGAC 59.876 40.000 0.00 0.00 0.00 3.18
415 421 3.634397 TGCTTTAGCCAGTCAATAGCT 57.366 42.857 0.00 0.00 41.18 3.32
420 426 7.279615 TGCTTTAGCCAGTCAATAGCTTATTA 58.720 34.615 0.00 0.00 41.18 0.98
427 433 4.049186 AGTCAATAGCTTATTACACGCGG 58.951 43.478 12.47 1.27 0.00 6.46
434 440 2.348218 GCTTATTACACGCGGCATGTAC 60.348 50.000 12.47 0.00 32.30 2.90
435 441 1.855513 TATTACACGCGGCATGTACC 58.144 50.000 12.47 0.00 32.30 3.34
454 461 1.870064 CCCCCTTGCAAAATCTCCAT 58.130 50.000 0.00 0.00 0.00 3.41
572 579 4.568760 GTCTCATCTTTAGAAAAGAGGCGG 59.431 45.833 8.72 5.35 0.00 6.13
626 633 1.842381 CGGTGGCTTTTCCTCTCCCT 61.842 60.000 0.00 0.00 35.26 4.20
658 665 1.026718 CACCCGTCCATGAGCTTTCC 61.027 60.000 0.00 0.00 0.00 3.13
716 725 4.207165 AGAAACAAAGCCACTAAAGCAGA 58.793 39.130 0.00 0.00 0.00 4.26
717 726 4.276926 AGAAACAAAGCCACTAAAGCAGAG 59.723 41.667 0.00 0.00 0.00 3.35
718 727 3.492102 ACAAAGCCACTAAAGCAGAGA 57.508 42.857 0.00 0.00 0.00 3.10
719 728 3.406764 ACAAAGCCACTAAAGCAGAGAG 58.593 45.455 0.00 0.00 0.00 3.20
720 729 3.071602 ACAAAGCCACTAAAGCAGAGAGA 59.928 43.478 0.00 0.00 0.00 3.10
721 730 3.608316 AAGCCACTAAAGCAGAGAGAG 57.392 47.619 0.00 0.00 0.00 3.20
722 731 2.813907 AGCCACTAAAGCAGAGAGAGA 58.186 47.619 0.00 0.00 0.00 3.10
723 732 2.760092 AGCCACTAAAGCAGAGAGAGAG 59.240 50.000 0.00 0.00 0.00 3.20
724 733 2.159114 GCCACTAAAGCAGAGAGAGAGG 60.159 54.545 0.00 0.00 0.00 3.69
725 734 2.430332 CCACTAAAGCAGAGAGAGAGGG 59.570 54.545 0.00 0.00 0.00 4.30
726 735 3.360867 CACTAAAGCAGAGAGAGAGGGA 58.639 50.000 0.00 0.00 0.00 4.20
727 736 3.381272 CACTAAAGCAGAGAGAGAGGGAG 59.619 52.174 0.00 0.00 0.00 4.30
728 737 2.917713 AAAGCAGAGAGAGAGGGAGA 57.082 50.000 0.00 0.00 0.00 3.71
729 738 2.442236 AAGCAGAGAGAGAGGGAGAG 57.558 55.000 0.00 0.00 0.00 3.20
730 739 1.595311 AGCAGAGAGAGAGGGAGAGA 58.405 55.000 0.00 0.00 0.00 3.10
731 740 1.492176 AGCAGAGAGAGAGGGAGAGAG 59.508 57.143 0.00 0.00 0.00 3.20
732 741 1.490490 GCAGAGAGAGAGGGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
733 742 2.486191 GCAGAGAGAGAGGGAGAGAGAG 60.486 59.091 0.00 0.00 0.00 3.20
734 743 3.041211 CAGAGAGAGAGGGAGAGAGAGA 58.959 54.545 0.00 0.00 0.00 3.10
735 744 3.070734 CAGAGAGAGAGGGAGAGAGAGAG 59.929 56.522 0.00 0.00 0.00 3.20
736 745 3.051803 AGAGAGAGAGGGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
737 746 3.312890 AGAGAGAGGGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
738 747 3.051803 AGAGAGAGGGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
739 748 3.312890 AGAGAGGGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
740 749 3.051803 AGAGAGGGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
741 750 3.312890 AGAGGGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
742 751 3.051803 AGAGGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
743 752 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
744 753 3.051803 AGGGAGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
745 754 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
746 755 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
747 756 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
748 757 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
749 758 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
750 759 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
751 760 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
752 761 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
753 762 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
754 763 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
755 764 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
756 765 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
757 766 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
758 767 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
759 768 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
760 769 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
761 770 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
762 771 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
763 772 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
764 773 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
765 774 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
839 869 0.659957 CCACTACCGCGTCTACTACC 59.340 60.000 4.92 0.00 0.00 3.18
859 892 2.290514 CCACGACTATATACCCTCCCGA 60.291 54.545 0.00 0.00 0.00 5.14
1040 1073 1.983224 CTTCCTCCAAGAAGCCCGA 59.017 57.895 0.00 0.00 37.08 5.14
1235 1268 2.426738 TGCTTGTTTCAGTCCAGGTTTG 59.573 45.455 0.00 0.00 0.00 2.93
1265 1298 3.202829 TGGGGTTGTTAGTGACTTGTC 57.797 47.619 0.00 0.00 0.00 3.18
1280 1313 4.514816 TGACTTGTCGATTTTGCTTCATGA 59.485 37.500 0.00 0.00 0.00 3.07
1327 1360 0.106669 GGGTTATGGGAGTCAAGGGC 60.107 60.000 0.00 0.00 0.00 5.19
1408 1465 6.326323 AGGTTTTTGTTTCTCTCTCTCTCTCT 59.674 38.462 0.00 0.00 0.00 3.10
1409 1466 6.645003 GGTTTTTGTTTCTCTCTCTCTCTCTC 59.355 42.308 0.00 0.00 0.00 3.20
1410 1467 7.433680 GTTTTTGTTTCTCTCTCTCTCTCTCT 58.566 38.462 0.00 0.00 0.00 3.10
1411 1468 6.817765 TTTGTTTCTCTCTCTCTCTCTCTC 57.182 41.667 0.00 0.00 0.00 3.20
1412 1469 5.762179 TGTTTCTCTCTCTCTCTCTCTCT 57.238 43.478 0.00 0.00 0.00 3.10
1413 1470 5.734720 TGTTTCTCTCTCTCTCTCTCTCTC 58.265 45.833 0.00 0.00 0.00 3.20
1414 1471 5.485353 TGTTTCTCTCTCTCTCTCTCTCTCT 59.515 44.000 0.00 0.00 0.00 3.10
1415 1472 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
1416 1473 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1417 1474 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1418 1475 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1419 1476 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1420 1477 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1421 1478 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1451 1508 8.206126 TCTCTCTCTCTAGATCTCATATGTGT 57.794 38.462 0.00 0.00 0.00 3.72
1456 1513 8.637099 TCTCTCTAGATCTCATATGTGTTTTGG 58.363 37.037 0.00 0.00 0.00 3.28
1813 1879 5.763698 GGTCAAAAAGGCAAAGTAGTACTCT 59.236 40.000 2.58 0.00 0.00 3.24
1868 1942 2.821969 CACCTTCAAATTACCTGCAGCT 59.178 45.455 8.66 0.00 0.00 4.24
1944 2018 4.702392 CATGAACGAGTAAGCTTCACAAC 58.298 43.478 0.00 0.00 0.00 3.32
1949 2060 4.569943 ACGAGTAAGCTTCACAACATCAT 58.430 39.130 0.00 0.00 0.00 2.45
1982 2093 4.311816 ACAGTGCATTTCCAAAAGACTG 57.688 40.909 0.00 0.00 36.30 3.51
1995 2106 4.143094 CCAAAAGACTGCTAGCTAACGTTC 60.143 45.833 17.23 3.29 0.00 3.95
2100 2211 0.763652 CCATGAGCAGCTGGAGGTAT 59.236 55.000 17.12 0.00 34.24 2.73
2101 2212 1.973515 CCATGAGCAGCTGGAGGTATA 59.026 52.381 17.12 0.00 34.24 1.47
2102 2213 2.369860 CCATGAGCAGCTGGAGGTATAA 59.630 50.000 17.12 0.00 34.24 0.98
2103 2214 3.181451 CCATGAGCAGCTGGAGGTATAAA 60.181 47.826 17.12 0.00 34.24 1.40
2104 2215 4.506271 CCATGAGCAGCTGGAGGTATAAAT 60.506 45.833 17.12 0.00 34.24 1.40
2105 2216 4.778213 TGAGCAGCTGGAGGTATAAATT 57.222 40.909 17.12 0.00 0.00 1.82
2340 2456 3.505680 TCCTTTACACATGCATGTTGGTC 59.494 43.478 29.48 0.00 39.39 4.02
2439 2555 1.065854 GGTAGCACTCATGAGCTTGGT 60.066 52.381 22.83 20.31 40.45 3.67
2493 2609 6.815142 AGAAGAAATTATCACTTTGCATTGCC 59.185 34.615 6.12 0.00 0.00 4.52
2513 2629 2.223548 CCATGACGCCAACATTATGTGG 60.224 50.000 0.00 4.18 0.00 4.17
2819 2938 1.736586 GTCGTCGAGCCATCTGGAT 59.263 57.895 0.00 0.00 37.39 3.41
3098 3217 0.251787 CCTTGGGCAGTAAGGGCTTT 60.252 55.000 6.54 0.00 40.79 3.51
3119 3238 1.153107 CGGCCCAATCATCAGCTCA 60.153 57.895 0.00 0.00 0.00 4.26
3285 3404 6.647334 TGTCATGAAACAAGCTTAATTGGA 57.353 33.333 0.00 0.00 34.36 3.53
3375 3496 1.338107 ATGCTGATGATGCCCAATGG 58.662 50.000 0.00 0.00 0.00 3.16
3434 3556 7.159322 TGTATTTTAACATATTGGCGTTGGT 57.841 32.000 0.00 0.00 0.00 3.67
3605 3742 6.615264 ATGCATGTGATAATGTGTTCTCTC 57.385 37.500 0.00 0.00 0.00 3.20
3824 4302 6.695713 TCATATTTGTCCTGAATTACGAGTCG 59.304 38.462 11.85 11.85 0.00 4.18
3899 4377 3.306917 TCGCTTCATAAACACTTCGGA 57.693 42.857 0.00 0.00 0.00 4.55
3904 4382 5.116882 GCTTCATAAACACTTCGGATACCT 58.883 41.667 0.00 0.00 0.00 3.08
3913 4391 0.619255 TTCGGATACCTGCCCCTTGA 60.619 55.000 0.00 0.00 0.00 3.02
3948 4426 3.306710 GGATTCATTGGTTTGGTTCACCC 60.307 47.826 0.00 0.00 32.71 4.61
4027 4505 8.179615 GGGAATTACACACTATAAAAGGAAACG 58.820 37.037 0.00 0.00 0.00 3.60
4094 4572 1.202879 TCGCACAGGAATGGAGGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
4126 4604 6.826741 GGGGCTGTAAATATAAGTCAACAAGA 59.173 38.462 0.00 0.00 0.00 3.02
4144 4622 4.080863 ACAAGAAATCGTAGCCTTCCATCT 60.081 41.667 0.00 0.00 0.00 2.90
4154 4632 3.669949 AGCCTTCCATCTACTTATGGGT 58.330 45.455 3.18 0.00 45.57 4.51
4178 4656 8.884726 GGTTTTTCCTTATGTTTTGTGCTAAAA 58.115 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 8.537728 ACCAACATACAATAATCCACATTGAT 57.462 30.769 2.29 0.00 36.95 2.57
119 120 6.840292 CGAACACATTGTTAACTTGCATTTTG 59.160 34.615 7.22 2.13 41.28 2.44
181 182 6.829298 AGATGATGATTGCAGTCTGAAAATCT 59.171 34.615 20.62 12.02 31.66 2.40
246 248 7.320443 TGAAGTTCATGGCTCATTTGTATAC 57.680 36.000 0.08 0.00 0.00 1.47
304 307 4.854173 TGGTTGGCTGAGATGCTATTTAA 58.146 39.130 0.00 0.00 0.00 1.52
319 324 4.150897 TCCAGACAGTATTATGGTTGGC 57.849 45.455 0.00 0.00 34.32 4.52
320 325 6.432783 TGTTTTCCAGACAGTATTATGGTTGG 59.567 38.462 0.00 0.00 34.32 3.77
355 360 2.485426 CTGCTTGTGGGTGTCATACTTG 59.515 50.000 0.00 0.00 0.00 3.16
415 421 2.203401 GGTACATGCCGCGTGTAATAA 58.797 47.619 23.80 4.55 37.55 1.40
420 426 4.770874 GGGGTACATGCCGCGTGT 62.771 66.667 21.48 21.48 37.38 4.49
435 441 1.483415 CATGGAGATTTTGCAAGGGGG 59.517 52.381 0.00 0.00 0.00 5.40
454 461 1.679977 GGCCAGCTCCTTTGATGCA 60.680 57.895 0.00 0.00 0.00 3.96
586 593 2.520536 AACCACTGGAAGCCTCGCT 61.521 57.895 0.71 0.00 42.56 4.93
626 633 2.632996 GGACGGGTGATGATATTCTCCA 59.367 50.000 0.00 0.00 32.13 3.86
658 665 4.338400 TCTCTCTCTCTCTCTCTACTCGTG 59.662 50.000 0.00 0.00 0.00 4.35
716 725 3.051803 TCTCTCTCTCTCTCCCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
717 726 3.309296 TCTCTCTCTCTCTCCCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
718 727 3.051803 TCTCTCTCTCTCTCTCCCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
719 728 3.309296 TCTCTCTCTCTCTCTCCCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
720 729 3.051803 TCTCTCTCTCTCTCTCTCCCTCT 60.052 52.174 0.00 0.00 0.00 3.69
721 730 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
722 731 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
723 732 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
724 733 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
725 734 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
726 735 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
727 736 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
728 737 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
729 738 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
730 739 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
731 740 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
732 741 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
733 742 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
734 743 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
735 744 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
736 745 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
737 746 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
738 747 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
739 748 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
740 749 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
741 750 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
742 751 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
743 752 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
744 753 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
745 754 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
746 755 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
747 756 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
748 757 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
749 758 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
750 759 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
751 760 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
752 761 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
753 762 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
754 763 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
755 764 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
756 765 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
757 766 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
758 767 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
759 768 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
760 769 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
761 770 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
762 771 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
763 772 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
764 773 5.337089 CGATATGCTCTCTCTCTCTCTCTCT 60.337 48.000 0.00 0.00 0.00 3.10
765 774 4.867047 CGATATGCTCTCTCTCTCTCTCTC 59.133 50.000 0.00 0.00 0.00 3.20
839 869 3.008330 CTCGGGAGGGTATATAGTCGTG 58.992 54.545 0.00 0.00 0.00 4.35
1235 1268 7.039293 AGTCACTAACAACCCCAAAAATTATCC 60.039 37.037 0.00 0.00 0.00 2.59
1265 1298 3.730061 GCCTCTGTCATGAAGCAAAATCG 60.730 47.826 0.00 0.00 0.00 3.34
1280 1313 0.318762 GTCTTCGGAGTTGCCTCTGT 59.681 55.000 0.00 0.00 43.46 3.41
1327 1360 2.672961 TGAGATGGTAAAGCGTGAGG 57.327 50.000 0.00 0.00 0.00 3.86
1408 1465 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1409 1466 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1410 1467 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1411 1468 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1412 1469 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1413 1470 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1414 1471 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1415 1472 6.303054 TCTAGAGAGAGAGAGAGAGAGAGAG 58.697 48.000 0.00 0.00 0.00 3.20
1416 1473 6.267492 TCTAGAGAGAGAGAGAGAGAGAGA 57.733 45.833 0.00 0.00 0.00 3.10
1417 1474 6.947733 AGATCTAGAGAGAGAGAGAGAGAGAG 59.052 46.154 0.00 0.00 34.35 3.20
1418 1475 6.857848 AGATCTAGAGAGAGAGAGAGAGAGA 58.142 44.000 0.00 0.00 34.35 3.10
1419 1476 6.718912 TGAGATCTAGAGAGAGAGAGAGAGAG 59.281 46.154 0.00 0.00 34.35 3.20
1420 1477 6.614657 TGAGATCTAGAGAGAGAGAGAGAGA 58.385 44.000 0.00 0.00 34.35 3.10
1421 1478 6.907853 TGAGATCTAGAGAGAGAGAGAGAG 57.092 45.833 0.00 0.00 34.35 3.20
1451 1508 8.314751 TGAGAACAATAAAACCAGAAACCAAAA 58.685 29.630 0.00 0.00 0.00 2.44
1456 1513 9.750125 ATTTCTGAGAACAATAAAACCAGAAAC 57.250 29.630 14.32 0.00 45.68 2.78
1562 1622 4.097286 CAGAAACATGATCCATGCACATCA 59.903 41.667 0.00 7.16 44.80 3.07
1813 1879 6.596309 AGGCGATGATATGAACAAGAGATA 57.404 37.500 0.00 0.00 0.00 1.98
1828 1894 6.229936 AGGTGTAGTTTATTAAGGCGATGA 57.770 37.500 0.00 0.00 0.00 2.92
1868 1942 2.221169 GCATTCCGTTGCATCTCCATA 58.779 47.619 0.00 0.00 42.31 2.74
1966 2077 3.192212 AGCTAGCAGTCTTTTGGAAATGC 59.808 43.478 18.83 0.00 38.47 3.56
1973 2084 4.447724 TGAACGTTAGCTAGCAGTCTTTTG 59.552 41.667 18.83 0.53 0.00 2.44
1982 2093 3.435671 ACACCAAATGAACGTTAGCTAGC 59.564 43.478 6.62 6.62 0.00 3.42
1995 2106 4.915085 GTGGTTATTTGACGACACCAAATG 59.085 41.667 10.32 0.00 42.28 2.32
2340 2456 1.475280 CAAGCATGGAGGTTCACATGG 59.525 52.381 0.00 0.00 43.50 3.66
2493 2609 2.795681 GCCACATAATGTTGGCGTCATG 60.796 50.000 0.00 0.00 35.82 3.07
2513 2629 3.534056 GCACCTGCATGGGGATGC 61.534 66.667 8.45 5.69 43.63 3.91
2708 2827 3.845259 GATCTGTACCCGGCGGCA 61.845 66.667 23.20 12.80 0.00 5.69
3098 3217 1.451927 GCTGATGATTGGGCCGTCA 60.452 57.895 12.98 12.98 0.00 4.35
3137 3256 3.055530 CACTTCCTACTTGCTGTGGAGAT 60.056 47.826 0.00 0.00 31.18 2.75
3257 3376 3.360249 AGCTTGTTTCATGACAACAGC 57.640 42.857 20.86 20.86 35.57 4.40
3434 3556 9.804758 CTACACCAAAATGTACAAACCTTAAAA 57.195 29.630 0.00 0.00 33.85 1.52
3499 3626 8.445275 AATACATGCACCGAACAAGAATTATA 57.555 30.769 0.00 0.00 0.00 0.98
3551 3688 5.292834 ACAGCGTGACATCAATAAATCTCAG 59.707 40.000 0.00 0.00 0.00 3.35
3605 3742 8.891928 CAACTTAATTGACTCAAACATAACACG 58.108 33.333 0.00 0.00 41.23 4.49
3802 4280 4.802039 GCGACTCGTAATTCAGGACAAATA 59.198 41.667 0.00 0.00 0.00 1.40
3807 4285 1.189403 CGCGACTCGTAATTCAGGAC 58.811 55.000 0.00 0.00 0.00 3.85
3818 4296 1.744374 GGAAGACTAATCGCGACTCG 58.256 55.000 12.93 0.00 40.15 4.18
3824 4302 1.948145 TCCTCTCGGAAGACTAATCGC 59.052 52.381 0.00 0.00 36.03 4.58
3826 4304 6.811954 AGAAAATCCTCTCGGAAGACTAATC 58.188 40.000 0.00 0.00 44.02 1.75
3899 4377 1.006998 TGCAAATCAAGGGGCAGGTAT 59.993 47.619 0.00 0.00 0.00 2.73
3904 4382 0.896923 GTCATGCAAATCAAGGGGCA 59.103 50.000 0.00 0.00 41.00 5.36
3913 4391 5.104693 ACCAATGAATCCATGTCATGCAAAT 60.105 36.000 7.35 0.00 35.87 2.32
4000 4478 9.239551 GTTTCCTTTTATAGTGTGTAATTCCCT 57.760 33.333 0.00 0.00 0.00 4.20
4011 4489 6.113411 ACTCCATCCGTTTCCTTTTATAGTG 58.887 40.000 0.00 0.00 0.00 2.74
4027 4505 4.607293 TGTGATGCATACTACTCCATCC 57.393 45.455 0.00 0.00 34.61 3.51
4071 4549 1.811266 CTCCATTCCTGTGCGACCG 60.811 63.158 0.00 0.00 0.00 4.79
4126 4604 5.615925 AAGTAGATGGAAGGCTACGATTT 57.384 39.130 0.00 0.00 41.34 2.17


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

AutoCloner maintained by Alex Coulton.