Multiple sequence alignment - TraesCS5D01G413500

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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 TraesCS5D01G413500 chr5D 100.000 2924 0 0 1 2924 476465334 476462411 0.000000e+00 5400.0
1 TraesCS5D01G413500 chr5D 85.227 176 24 2 2642 2816 458632796 458632622 2.320000e-41 180.0
2 TraesCS5D01G413500 chr5B 94.498 2181 86 24 756 2924 583915389 583913231 0.000000e+00 3332.0
3 TraesCS5D01G413500 chr5B 85.795 176 23 2 2642 2816 562048493 562048319 4.980000e-43 185.0
4 TraesCS5D01G413500 chr5A 91.597 2166 95 20 773 2924 595898165 595896073 0.000000e+00 2911.0
5 TraesCS5D01G413500 chr5A 81.595 489 63 16 39 518 595939577 595940047 2.130000e-101 379.0
6 TraesCS5D01G413500 chr5A 78.274 336 46 21 164 486 12149670 12149349 1.070000e-44 191.0
7 TraesCS5D01G413500 chr7D 80.915 503 69 18 35 518 39528496 39528990 3.560000e-99 372.0
8 TraesCS5D01G413500 chr7D 85.030 334 34 8 405 734 39528919 39529240 2.810000e-85 326.0
9 TraesCS5D01G413500 chr7D 79.252 294 44 14 203 486 520327827 520328113 3.850000e-44 189.0
10 TraesCS5D01G413500 chr7D 84.091 176 26 2 2642 2816 332692924 332692750 5.010000e-38 169.0
11 TraesCS5D01G413500 chr7D 80.137 146 17 7 1404 1549 153314418 153314285 6.670000e-17 99.0
12 TraesCS5D01G413500 chr7B 85.570 298 34 6 405 697 611300249 611300542 1.320000e-78 303.0
13 TraesCS5D01G413500 chr7B 83.505 194 26 5 330 518 611300128 611300320 2.990000e-40 176.0
14 TraesCS5D01G413500 chr7B 76.471 323 54 16 181 493 597604495 597604185 3.900000e-34 156.0
15 TraesCS5D01G413500 chr1B 82.143 280 48 2 1646 1924 678259787 678259509 3.770000e-59 239.0
16 TraesCS5D01G413500 chr1B 75.117 426 77 22 74 489 594494433 594494839 3.870000e-39 172.0
17 TraesCS5D01G413500 chr1D 81.786 280 49 2 1646 1924 487168799 487168521 1.750000e-57 233.0
18 TraesCS5D01G413500 chr1A 81.786 280 49 2 1646 1924 584676321 584676043 1.750000e-57 233.0
19 TraesCS5D01G413500 chr3D 82.018 228 31 9 262 486 537339522 537339742 4.980000e-43 185.0
20 TraesCS5D01G413500 chr4A 84.659 176 25 2 2642 2816 532162172 532161998 1.080000e-39 174.0
21 TraesCS5D01G413500 chr4A 100.000 33 0 0 707 739 114806454 114806486 8.750000e-06 62.1
22 TraesCS5D01G413500 chr3A 83.422 187 25 5 336 518 108477072 108476888 5.010000e-38 169.0
23 TraesCS5D01G413500 chr3A 86.777 121 6 6 625 738 108475783 108475666 3.060000e-25 126.0
24 TraesCS5D01G413500 chr3A 100.000 33 0 0 707 739 219164688 219164656 8.750000e-06 62.1
25 TraesCS5D01G413500 chr3A 100.000 32 0 0 707 738 656971090 656971059 3.150000e-05 60.2
26 TraesCS5D01G413500 chr2D 84.393 173 25 2 2642 2813 601056086 601056257 5.010000e-38 169.0
27 TraesCS5D01G413500 chr2D 83.893 149 22 2 2651 2798 616634913 616635060 1.090000e-29 141.0
28 TraesCS5D01G413500 chr6D 90.833 120 10 1 39 157 397259343 397259462 3.020000e-35 159.0
29 TraesCS5D01G413500 chr2A 83.893 149 22 2 2651 2798 746852013 746852160 1.090000e-29 141.0
30 TraesCS5D01G413500 chr3B 91.000 100 8 1 59 157 145418610 145418511 1.830000e-27 134.0


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 TraesCS5D01G413500 chr5D 476462411 476465334 2923 True 5400 5400 100.0000 1 2924 1 chr5D.!!$R2 2923
1 TraesCS5D01G413500 chr5B 583913231 583915389 2158 True 3332 3332 94.4980 756 2924 1 chr5B.!!$R2 2168
2 TraesCS5D01G413500 chr5A 595896073 595898165 2092 True 2911 2911 91.5970 773 2924 1 chr5A.!!$R2 2151
3 TraesCS5D01G413500 chr7D 39528496 39529240 744 False 349 372 82.9725 35 734 2 chr7D.!!$F2 699

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
144 145 0.035458 CGGTGGGCTTCACTCTTTCT 59.965 55.0 9.77 0.0 45.38 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2194 1.800586 CGTTGTAGCAGTGCACAATCT 59.199 47.619 25.38 14.4 34.33 2.4 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
57 58 1.269166 GGCGAATCCTATATGACGCG 58.731 55.000 3.53 3.53 45.50 6.01
61 62 0.736325 AATCCTATATGACGCGCGCC 60.736 55.000 32.58 21.99 0.00 6.53
139 140 2.358737 CCACGGTGGGCTTCACTC 60.359 66.667 19.63 1.74 45.38 3.51
144 145 0.035458 CGGTGGGCTTCACTCTTTCT 59.965 55.000 9.77 0.00 45.38 2.52
152 153 4.824537 GGGCTTCACTCTTTCTTTCTCTTT 59.175 41.667 0.00 0.00 0.00 2.52
157 158 7.536964 GCTTCACTCTTTCTTTCTCTTTTATGC 59.463 37.037 0.00 0.00 0.00 3.14
177 178 9.750125 TTTATGCTTCTTTTCTTCTTCTTTTCC 57.250 29.630 0.00 0.00 0.00 3.13
179 180 6.799512 TGCTTCTTTTCTTCTTCTTTTCCTG 58.200 36.000 0.00 0.00 0.00 3.86
180 181 6.378280 TGCTTCTTTTCTTCTTCTTTTCCTGT 59.622 34.615 0.00 0.00 0.00 4.00
183 192 9.295214 CTTCTTTTCTTCTTCTTTTCCTGTTTC 57.705 33.333 0.00 0.00 0.00 2.78
186 195 7.718334 TTTCTTCTTCTTTTCCTGTTTCCTT 57.282 32.000 0.00 0.00 0.00 3.36
191 200 9.302345 CTTCTTCTTTTCCTGTTTCCTTTTTAC 57.698 33.333 0.00 0.00 0.00 2.01
316 333 8.887264 ATGGTATATTACAAAAAGGTTCACCA 57.113 30.769 0.00 0.00 38.89 4.17
328 345 9.165035 CAAAAAGGTTCACCATGCATTATAAAT 57.835 29.630 0.00 0.00 38.89 1.40
331 348 9.985730 AAAGGTTCACCATGCATTATAAATATG 57.014 29.630 0.00 0.00 38.89 1.78
333 350 8.796475 AGGTTCACCATGCATTATAAATATGTC 58.204 33.333 0.00 0.00 38.89 3.06
378 395 9.796062 TTTTCGACGAATACTACAAATGTTTAC 57.204 29.630 11.71 0.00 0.00 2.01
380 397 8.746922 TCGACGAATACTACAAATGTTTACTT 57.253 30.769 0.00 0.00 0.00 2.24
420 437 9.814899 TTTAGGGCATATTACACAAAATCAATG 57.185 29.630 0.00 0.00 0.00 2.82
421 438 7.422465 AGGGCATATTACACAAAATCAATGT 57.578 32.000 0.00 0.00 0.00 2.71
472 492 6.874297 ACACAAATGTTCAATGCATATTCG 57.126 33.333 0.00 0.00 34.46 3.34
484 504 8.754230 TCAATGCATATTCGAAAATTGTTCAA 57.246 26.923 0.00 0.00 0.00 2.69
494 514 9.834628 ATTCGAAAATTGTTCAACGTACATTAT 57.165 25.926 0.00 0.00 0.00 1.28
524 544 8.754230 TGTTCAATGCATATTCGAATTTTTCA 57.246 26.923 17.19 9.80 0.00 2.69
527 591 6.196910 TCAATGCATATTCGAATTTTTCAGCG 59.803 34.615 17.19 5.53 0.00 5.18
537 601 9.741168 ATTCGAATTTTTCAGCGTATATATTCG 57.259 29.630 4.39 7.33 42.43 3.34
570 634 9.670180 CAAAATATTCGAAAATAAAAACCGAGC 57.330 29.630 0.00 0.00 31.28 5.03
571 635 9.634163 AAAATATTCGAAAATAAAAACCGAGCT 57.366 25.926 0.00 0.00 31.28 4.09
572 636 9.634163 AAATATTCGAAAATAAAAACCGAGCTT 57.366 25.926 0.00 0.00 31.28 3.74
573 637 8.836959 ATATTCGAAAATAAAAACCGAGCTTC 57.163 30.769 0.00 0.00 31.28 3.86
574 638 5.676532 TCGAAAATAAAAACCGAGCTTCA 57.323 34.783 0.00 0.00 0.00 3.02
575 639 6.062434 TCGAAAATAAAAACCGAGCTTCAA 57.938 33.333 0.00 0.00 0.00 2.69
576 640 6.496571 TCGAAAATAAAAACCGAGCTTCAAA 58.503 32.000 0.00 0.00 0.00 2.69
579 643 6.505039 AAATAAAAACCGAGCTTCAAAACG 57.495 33.333 0.00 0.00 0.00 3.60
583 647 2.499732 CGAGCTTCAAAACGCGGC 60.500 61.111 12.47 1.26 0.00 6.53
598 662 2.813908 GGCGCTACAGTGAACCGG 60.814 66.667 7.64 0.00 0.00 5.28
618 682 4.319133 GGTACAGTACCGTCCCGA 57.681 61.111 14.25 0.00 39.39 5.14
619 683 2.566824 GGTACAGTACCGTCCCGAA 58.433 57.895 14.25 0.00 39.39 4.30
622 686 1.541588 GTACAGTACCGTCCCGAAACT 59.458 52.381 0.00 0.00 0.00 2.66
636 700 2.034558 CCGAAACTGTGTTCCAGCATTT 59.965 45.455 0.00 0.00 45.68 2.32
637 701 3.252215 CCGAAACTGTGTTCCAGCATTTA 59.748 43.478 0.00 0.00 45.68 1.40
638 702 4.219033 CGAAACTGTGTTCCAGCATTTAC 58.781 43.478 0.00 0.00 45.68 2.01
639 703 4.260990 CGAAACTGTGTTCCAGCATTTACA 60.261 41.667 0.00 0.00 45.68 2.41
644 708 6.581712 ACTGTGTTCCAGCATTTACATTTTT 58.418 32.000 0.00 0.00 45.68 1.94
748 812 1.604915 GGACTCTCCCTTGGAAGGC 59.395 63.158 0.00 0.00 45.10 4.35
749 813 1.201429 GGACTCTCCCTTGGAAGGCA 61.201 60.000 0.00 0.00 45.10 4.75
750 814 0.251634 GACTCTCCCTTGGAAGGCAG 59.748 60.000 0.00 0.00 45.10 4.85
751 815 1.077858 CTCTCCCTTGGAAGGCAGC 60.078 63.158 0.00 0.00 45.10 5.25
752 816 2.437359 CTCCCTTGGAAGGCAGCG 60.437 66.667 0.00 0.00 45.10 5.18
753 817 4.722700 TCCCTTGGAAGGCAGCGC 62.723 66.667 0.00 0.00 45.10 5.92
754 818 4.729918 CCCTTGGAAGGCAGCGCT 62.730 66.667 2.64 2.64 45.10 5.92
755 819 2.674380 CCTTGGAAGGCAGCGCTT 60.674 61.111 7.50 0.00 39.76 4.68
756 820 2.694760 CCTTGGAAGGCAGCGCTTC 61.695 63.158 7.50 1.16 39.76 3.86
757 821 1.673665 CTTGGAAGGCAGCGCTTCT 60.674 57.895 7.50 5.54 0.00 2.85
758 822 1.642952 CTTGGAAGGCAGCGCTTCTC 61.643 60.000 7.50 1.19 0.00 2.87
759 823 2.046892 GGAAGGCAGCGCTTCTCA 60.047 61.111 7.50 0.00 0.00 3.27
760 824 1.672356 GGAAGGCAGCGCTTCTCAA 60.672 57.895 7.50 0.00 0.00 3.02
761 825 1.028868 GGAAGGCAGCGCTTCTCAAT 61.029 55.000 7.50 0.00 0.00 2.57
762 826 0.807496 GAAGGCAGCGCTTCTCAATT 59.193 50.000 7.50 0.00 0.00 2.32
763 827 2.009774 GAAGGCAGCGCTTCTCAATTA 58.990 47.619 7.50 0.00 0.00 1.40
764 828 1.661341 AGGCAGCGCTTCTCAATTAG 58.339 50.000 7.50 0.00 0.00 1.73
765 829 1.065854 AGGCAGCGCTTCTCAATTAGT 60.066 47.619 7.50 0.00 0.00 2.24
766 830 1.740025 GGCAGCGCTTCTCAATTAGTT 59.260 47.619 7.50 0.00 0.00 2.24
767 831 2.162408 GGCAGCGCTTCTCAATTAGTTT 59.838 45.455 7.50 0.00 0.00 2.66
768 832 3.166657 GCAGCGCTTCTCAATTAGTTTG 58.833 45.455 7.50 0.00 36.61 2.93
769 833 3.166657 CAGCGCTTCTCAATTAGTTTGC 58.833 45.455 7.50 0.00 35.16 3.68
770 834 3.077359 AGCGCTTCTCAATTAGTTTGCT 58.923 40.909 2.64 0.00 35.16 3.91
771 835 3.126000 AGCGCTTCTCAATTAGTTTGCTC 59.874 43.478 2.64 0.00 35.16 4.26
840 907 1.312371 CCGGCCCAACACGAATTGAT 61.312 55.000 0.00 0.00 0.00 2.57
843 910 1.402720 GGCCCAACACGAATTGATGTG 60.403 52.381 0.00 0.00 41.81 3.21
888 967 0.874175 CGTCTTGTCCGCAACTGTGA 60.874 55.000 0.00 0.00 0.00 3.58
899 978 0.997226 CAACTGTGACCTCGTCGTCG 60.997 60.000 0.00 0.00 34.95 5.12
900 979 1.162181 AACTGTGACCTCGTCGTCGA 61.162 55.000 4.42 4.42 44.12 4.20
936 1015 1.827399 CTCTGCGTGTGGTTACCCCT 61.827 60.000 0.00 0.00 0.00 4.79
965 1044 0.454620 GCGTACCAGACAGACACTCG 60.455 60.000 0.00 0.00 0.00 4.18
1139 1218 1.517257 CGAAGACCCGCTGCTACAG 60.517 63.158 0.00 0.00 34.12 2.74
1214 1293 2.279517 GGGCAGCGTATCGACCAG 60.280 66.667 0.00 0.00 0.00 4.00
1228 1307 0.941463 GACCAGTGACACTCAGTGCG 60.941 60.000 4.13 0.00 44.38 5.34
1462 1541 3.974757 GGTACTCCGGGATCGCCG 61.975 72.222 13.78 13.78 33.83 6.46
1611 1690 0.041386 AGGAGGCCTACGAGAAGGTT 59.959 55.000 10.07 0.00 39.02 3.50
1898 1977 1.674322 ACCATTTCAAGGACGGCGG 60.674 57.895 13.24 0.00 0.00 6.13
1986 2075 2.088423 AGCCTAGTTCAGTGTCTCGAG 58.912 52.381 5.93 5.93 0.00 4.04
2091 2180 3.301794 TGATGCATTACCCAGCAAGAT 57.698 42.857 0.00 0.00 44.88 2.40
2094 2183 2.368439 TGCATTACCCAGCAAGATGAC 58.632 47.619 0.00 0.00 37.90 3.06
2097 2186 3.614092 CATTACCCAGCAAGATGACACT 58.386 45.455 0.00 0.00 0.00 3.55
2098 2187 2.768253 TACCCAGCAAGATGACACTG 57.232 50.000 0.00 0.00 0.00 3.66
2104 2193 3.256558 CAGCAAGATGACACTGATCGAA 58.743 45.455 0.00 0.00 31.67 3.71
2105 2194 3.681417 CAGCAAGATGACACTGATCGAAA 59.319 43.478 0.00 0.00 31.67 3.46
2187 2276 4.162888 TCCTAGGAAAACCCCTCGTATTTC 59.837 45.833 9.71 0.00 37.74 2.17
2578 2673 4.854924 CATGTCCGGCCGCCATCA 62.855 66.667 22.85 15.45 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.837272 TAGGATTCGCCCTTCCAAGG 59.163 55.000 0.00 0.00 46.06 3.61
30 31 2.938956 ATAGGATTCGCCCTTCCAAG 57.061 50.000 0.00 0.00 37.74 3.61
31 32 3.907474 TCATATAGGATTCGCCCTTCCAA 59.093 43.478 0.00 0.00 37.74 3.53
32 33 3.260884 GTCATATAGGATTCGCCCTTCCA 59.739 47.826 0.00 0.00 37.74 3.53
33 34 3.676324 CGTCATATAGGATTCGCCCTTCC 60.676 52.174 0.00 0.00 37.74 3.46
36 37 1.204941 GCGTCATATAGGATTCGCCCT 59.795 52.381 10.28 0.00 40.29 5.19
61 62 2.050895 CTCGCCTCTATGACGCCG 60.051 66.667 0.00 0.00 0.00 6.46
125 126 0.035458 AGAAAGAGTGAAGCCCACCG 59.965 55.000 3.51 0.00 46.87 4.94
129 130 4.014569 AGAGAAAGAAAGAGTGAAGCCC 57.985 45.455 0.00 0.00 0.00 5.19
131 132 7.536964 GCATAAAAGAGAAAGAAAGAGTGAAGC 59.463 37.037 0.00 0.00 0.00 3.86
152 153 9.136323 AGGAAAAGAAGAAGAAAAGAAGCATAA 57.864 29.630 0.00 0.00 0.00 1.90
157 158 9.295214 GAAACAGGAAAAGAAGAAGAAAAGAAG 57.705 33.333 0.00 0.00 0.00 2.85
168 169 9.653287 AAAGTAAAAAGGAAACAGGAAAAGAAG 57.347 29.630 0.00 0.00 0.00 2.85
290 307 9.315363 TGGTGAACCTTTTTGTAATATACCATT 57.685 29.630 0.37 0.00 36.82 3.16
300 317 5.543507 AATGCATGGTGAACCTTTTTGTA 57.456 34.783 0.00 0.00 36.82 2.41
353 370 9.195411 AGTAAACATTTGTAGTATTCGTCGAAA 57.805 29.630 12.40 0.00 0.00 3.46
396 413 8.412456 CACATTGATTTTGTGTAATATGCCCTA 58.588 33.333 0.00 0.00 39.66 3.53
455 475 8.706492 ACAATTTTCGAATATGCATTGAACAT 57.294 26.923 3.54 0.90 0.00 2.71
466 486 9.834628 AATGTACGTTGAACAATTTTCGAATAT 57.165 25.926 0.00 0.00 0.00 1.28
506 526 4.980590 ACGCTGAAAAATTCGAATATGCA 58.019 34.783 11.83 7.65 0.00 3.96
507 527 8.880768 ATATACGCTGAAAAATTCGAATATGC 57.119 30.769 11.83 8.58 0.00 3.14
519 539 9.465985 TGAACATACGAATATATACGCTGAAAA 57.534 29.630 0.00 0.00 0.00 2.29
522 542 9.465985 TTTTGAACATACGAATATATACGCTGA 57.534 29.630 0.00 0.00 0.00 4.26
549 613 7.808672 TGAAGCTCGGTTTTTATTTTCGAATA 58.191 30.769 0.00 0.00 0.00 1.75
551 615 6.062434 TGAAGCTCGGTTTTTATTTTCGAA 57.938 33.333 0.00 0.00 0.00 3.71
565 629 2.173382 CCGCGTTTTGAAGCTCGG 59.827 61.111 4.92 0.00 0.00 4.63
570 634 1.509162 GTAGCGCCGCGTTTTGAAG 60.509 57.895 15.34 0.00 0.00 3.02
571 635 2.165362 CTGTAGCGCCGCGTTTTGAA 62.165 55.000 15.34 0.00 0.00 2.69
572 636 2.662196 TGTAGCGCCGCGTTTTGA 60.662 55.556 15.34 0.00 0.00 2.69
573 637 2.202171 CTGTAGCGCCGCGTTTTG 60.202 61.111 15.34 0.00 0.00 2.44
574 638 2.663852 ACTGTAGCGCCGCGTTTT 60.664 55.556 15.34 3.31 0.00 2.43
575 639 3.411351 CACTGTAGCGCCGCGTTT 61.411 61.111 15.34 5.91 0.00 3.60
576 640 3.851845 TTCACTGTAGCGCCGCGTT 62.852 57.895 15.34 11.43 0.00 4.84
579 643 3.488090 GGTTCACTGTAGCGCCGC 61.488 66.667 2.29 0.00 0.00 6.53
583 647 0.806102 CCATCCGGTTCACTGTAGCG 60.806 60.000 0.00 0.68 36.35 4.26
612 676 1.226746 CTGGAACACAGTTTCGGGAC 58.773 55.000 0.00 0.00 42.42 4.46
650 714 0.680618 CCAGCCCATTTGCAGTTCAA 59.319 50.000 0.00 0.00 0.00 2.69
651 715 1.818959 GCCAGCCCATTTGCAGTTCA 61.819 55.000 0.00 0.00 0.00 3.18
652 716 1.079612 GCCAGCCCATTTGCAGTTC 60.080 57.895 0.00 0.00 0.00 3.01
653 717 2.586293 GGCCAGCCCATTTGCAGTT 61.586 57.895 0.00 0.00 0.00 3.16
699 763 1.278637 CGTGTGCGTCAAGAAACCC 59.721 57.895 0.00 0.00 0.00 4.11
700 764 1.278637 CCGTGTGCGTCAAGAAACC 59.721 57.895 0.00 0.00 36.15 3.27
702 766 2.539338 GCCCGTGTGCGTCAAGAAA 61.539 57.895 0.00 0.00 36.15 2.52
736 800 4.722700 GCGCTGCCTTCCAAGGGA 62.723 66.667 0.00 3.37 46.56 4.20
737 801 4.729918 AGCGCTGCCTTCCAAGGG 62.730 66.667 10.39 0.00 46.56 3.95
739 803 1.642952 GAGAAGCGCTGCCTTCCAAG 61.643 60.000 12.58 0.00 41.65 3.61
740 804 1.672356 GAGAAGCGCTGCCTTCCAA 60.672 57.895 12.58 0.00 41.65 3.53
741 805 2.046892 GAGAAGCGCTGCCTTCCA 60.047 61.111 12.58 0.00 41.65 3.53
742 806 1.028868 ATTGAGAAGCGCTGCCTTCC 61.029 55.000 12.58 14.60 41.65 3.46
743 807 0.807496 AATTGAGAAGCGCTGCCTTC 59.193 50.000 12.58 17.63 41.15 3.46
744 808 2.012673 CTAATTGAGAAGCGCTGCCTT 58.987 47.619 12.58 2.77 0.00 4.35
745 809 1.065854 ACTAATTGAGAAGCGCTGCCT 60.066 47.619 12.58 12.09 0.00 4.75
746 810 1.373570 ACTAATTGAGAAGCGCTGCC 58.626 50.000 12.58 6.27 0.00 4.85
747 811 3.166657 CAAACTAATTGAGAAGCGCTGC 58.833 45.455 12.58 9.98 41.85 5.25
748 812 3.120060 AGCAAACTAATTGAGAAGCGCTG 60.120 43.478 12.58 0.00 41.85 5.18
749 813 3.077359 AGCAAACTAATTGAGAAGCGCT 58.923 40.909 2.64 2.64 41.85 5.92
750 814 3.126000 AGAGCAAACTAATTGAGAAGCGC 59.874 43.478 0.00 0.00 41.85 5.92
751 815 4.201763 GGAGAGCAAACTAATTGAGAAGCG 60.202 45.833 0.00 0.00 41.85 4.68
752 816 4.095632 GGGAGAGCAAACTAATTGAGAAGC 59.904 45.833 0.00 0.00 41.85 3.86
753 817 4.637977 GGGGAGAGCAAACTAATTGAGAAG 59.362 45.833 0.00 0.00 41.85 2.85
754 818 4.289672 AGGGGAGAGCAAACTAATTGAGAA 59.710 41.667 0.00 0.00 41.85 2.87
755 819 3.846588 AGGGGAGAGCAAACTAATTGAGA 59.153 43.478 0.00 0.00 41.85 3.27
756 820 4.227864 AGGGGAGAGCAAACTAATTGAG 57.772 45.455 0.00 0.00 41.85 3.02
757 821 4.042809 TGAAGGGGAGAGCAAACTAATTGA 59.957 41.667 0.00 0.00 41.85 2.57
758 822 4.335416 TGAAGGGGAGAGCAAACTAATTG 58.665 43.478 0.00 0.00 42.21 2.32
759 823 4.289672 TCTGAAGGGGAGAGCAAACTAATT 59.710 41.667 0.00 0.00 0.00 1.40
760 824 3.846588 TCTGAAGGGGAGAGCAAACTAAT 59.153 43.478 0.00 0.00 0.00 1.73
761 825 3.248024 TCTGAAGGGGAGAGCAAACTAA 58.752 45.455 0.00 0.00 0.00 2.24
762 826 2.902608 TCTGAAGGGGAGAGCAAACTA 58.097 47.619 0.00 0.00 0.00 2.24
763 827 1.734655 TCTGAAGGGGAGAGCAAACT 58.265 50.000 0.00 0.00 0.00 2.66
764 828 2.039084 TCTTCTGAAGGGGAGAGCAAAC 59.961 50.000 16.83 0.00 0.00 2.93
765 829 2.039084 GTCTTCTGAAGGGGAGAGCAAA 59.961 50.000 16.83 0.00 0.00 3.68
766 830 1.625818 GTCTTCTGAAGGGGAGAGCAA 59.374 52.381 16.83 0.00 0.00 3.91
767 831 1.203237 AGTCTTCTGAAGGGGAGAGCA 60.203 52.381 16.83 0.00 0.00 4.26
768 832 1.567357 AGTCTTCTGAAGGGGAGAGC 58.433 55.000 16.83 0.78 0.00 4.09
769 833 4.243793 TCTAGTCTTCTGAAGGGGAGAG 57.756 50.000 16.83 8.07 0.00 3.20
770 834 4.676799 TTCTAGTCTTCTGAAGGGGAGA 57.323 45.455 16.83 12.94 0.00 3.71
771 835 4.161377 CCTTTCTAGTCTTCTGAAGGGGAG 59.839 50.000 16.83 11.10 34.57 4.30
815 879 2.030958 CGTGTTGGGCCGGTAAGTC 61.031 63.158 1.90 0.00 0.00 3.01
874 953 1.069090 GAGGTCACAGTTGCGGACA 59.931 57.895 0.00 0.00 33.26 4.02
883 962 3.250986 TCGACGACGAGGTCACAG 58.749 61.111 5.75 0.00 43.81 3.66
899 978 2.750637 TGCGAGGGAGGACGAGTC 60.751 66.667 0.00 0.00 0.00 3.36
900 979 3.063084 GTGCGAGGGAGGACGAGT 61.063 66.667 0.00 0.00 0.00 4.18
936 1015 1.068055 GTCTGGTACGCGAAGGAGAAA 60.068 52.381 15.93 0.00 0.00 2.52
965 1044 2.360475 GTGGCAGGGGAACTCAGC 60.360 66.667 0.00 0.00 0.00 4.26
1049 1128 3.976701 CTGGCGGCGGTGAGGAAAT 62.977 63.158 9.78 0.00 0.00 2.17
1186 1265 2.980233 GCTGCCCGCAACAGAAGT 60.980 61.111 2.03 0.00 37.32 3.01
1192 1271 3.925238 CGATACGCTGCCCGCAAC 61.925 66.667 0.00 0.00 41.76 4.17
1214 1293 3.044305 GGCCGCACTGAGTGTCAC 61.044 66.667 14.82 3.54 35.75 3.67
1252 1331 4.432741 GGGCTCTTGGCAGACCCC 62.433 72.222 5.21 3.94 44.01 4.95
1362 1441 2.037367 TAGCACTGGAGGACCGCT 59.963 61.111 0.00 0.00 39.42 5.52
1737 1816 2.743928 GTGCTCACCAGCCCGAAG 60.744 66.667 0.00 0.00 46.26 3.79
1961 2041 4.336993 CGAGACACTGAACTAGGCTAAGAT 59.663 45.833 0.00 0.00 0.00 2.40
2091 2180 3.433274 GCACAATCTTTCGATCAGTGTCA 59.567 43.478 0.00 0.00 37.64 3.58
2094 2183 3.434641 AGTGCACAATCTTTCGATCAGTG 59.565 43.478 21.04 0.00 38.02 3.66
2097 2186 2.160219 GCAGTGCACAATCTTTCGATCA 59.840 45.455 21.04 0.00 0.00 2.92
2098 2187 2.417933 AGCAGTGCACAATCTTTCGATC 59.582 45.455 21.04 0.00 0.00 3.69
2104 2193 2.224079 CGTTGTAGCAGTGCACAATCTT 59.776 45.455 25.38 6.27 34.33 2.40
2105 2194 1.800586 CGTTGTAGCAGTGCACAATCT 59.199 47.619 25.38 14.40 34.33 2.40
2187 2276 4.797471 TGATTCTTTGCTTCGATTTGTGG 58.203 39.130 0.00 0.00 0.00 4.17
2578 2673 1.587933 GAGAGGAAGACGGCGACAGT 61.588 60.000 16.62 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.