Multiple sequence alignment - TraesCS1A01G314200

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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 TraesCS1A01G314200 chr1A 100.000 2567 0 0 1 2567 505682360 505679794 0.000000e+00 4741.0
1 TraesCS1A01G314200 chr1A 82.143 308 29 18 515 806 505733312 505733015 9.180000e-60 241.0
2 TraesCS1A01G314200 chr1A 83.523 176 27 2 1102 1276 505925847 505925673 2.040000e-36 163.0
3 TraesCS1A01G314200 chr1A 87.121 132 8 4 1354 1485 505732782 505732660 9.580000e-30 141.0
4 TraesCS1A01G314200 chr1A 90.654 107 6 2 222 328 505738833 505738731 3.440000e-29 139.0
5 TraesCS1A01G314200 chr1D 89.832 1426 80 29 843 2260 409799452 409798084 0.000000e+00 1770.0
6 TraesCS1A01G314200 chr1D 84.091 704 28 24 179 836 409800163 409799498 1.020000e-168 603.0
7 TraesCS1A01G314200 chr1D 93.431 137 7 1 2433 2567 409797584 409797448 4.330000e-48 202.0
8 TraesCS1A01G314200 chr1D 82.796 186 29 3 1102 1286 410072051 410071868 2.040000e-36 163.0
9 TraesCS1A01G314200 chr1D 98.718 78 1 0 2252 2329 409797929 409797852 3.440000e-29 139.0
10 TraesCS1A01G314200 chr1D 94.203 69 1 2 225 293 409986779 409986714 4.520000e-18 102.0
11 TraesCS1A01G314200 chr1B 92.361 1008 44 18 820 1824 551870450 551869473 0.000000e+00 1404.0
12 TraesCS1A01G314200 chr1B 83.140 860 43 39 38 836 551871286 551870468 0.000000e+00 691.0
13 TraesCS1A01G314200 chr1B 87.161 553 37 15 1813 2352 551869288 551868757 4.730000e-167 597.0
14 TraesCS1A01G314200 chr1B 76.285 506 56 37 194 673 552277812 552277345 7.200000e-51 211.0
15 TraesCS1A01G314200 chr1B 84.091 176 26 2 1102 1276 552474263 552474089 4.390000e-38 169.0
16 TraesCS1A01G314200 chr1B 87.879 132 7 4 1354 1485 552277090 552276968 2.060000e-31 147.0
17 TraesCS1A01G314200 chr1B 85.882 85 8 2 2433 2515 551868455 551868373 1.270000e-13 87.9
18 TraesCS1A01G314200 chr6D 82.041 245 31 11 1034 1273 139916256 139916492 2.010000e-46 196.0
19 TraesCS1A01G314200 chr6B 81.633 245 32 11 1034 1273 239729193 239729429 9.370000e-45 191.0
20 TraesCS1A01G314200 chr6A 81.633 245 32 11 1034 1273 183188119 183188355 9.370000e-45 191.0
21 TraesCS1A01G314200 chr2D 78.857 175 29 8 1106 1276 367089165 367089335 7.510000e-21 111.0
22 TraesCS1A01G314200 chr3D 100.000 30 0 0 963 992 359855997 359855968 3.570000e-04 56.5
23 TraesCS1A01G314200 chr5B 100.000 28 0 0 963 990 481046345 481046318 5.000000e-03 52.8


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 TraesCS1A01G314200 chr1A 505679794 505682360 2566 True 4741.000 4741 100.000 1 2567 1 chr1A.!!$R1 2566
1 TraesCS1A01G314200 chr1D 409797448 409800163 2715 True 678.500 1770 91.518 179 2567 4 chr1D.!!$R3 2388
2 TraesCS1A01G314200 chr1B 551868373 551871286 2913 True 694.975 1404 87.136 38 2515 4 chr1B.!!$R2 2477

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
991 1127 0.108585 CGAGAGAGGGAGAGGGAGAG 59.891 65.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2186 2.031595 TCGCTTTTTACAGCATTTCGCA 60.032 40.909 0.0 0.0 46.13 5.1 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
17 18 2.577059 TTCCCGATGCGGTGTCTC 59.423 61.111 5.06 0.00 46.80 3.36
18 19 3.014085 TTCCCGATGCGGTGTCTCC 62.014 63.158 5.06 0.00 46.80 3.71
19 20 4.530857 CCCGATGCGGTGTCTCCC 62.531 72.222 5.06 0.00 46.80 4.30
20 21 4.530857 CCGATGCGGTGTCTCCCC 62.531 72.222 0.00 0.00 42.73 4.81
21 22 4.530857 CGATGCGGTGTCTCCCCC 62.531 72.222 0.00 0.00 0.00 5.40
22 23 4.530857 GATGCGGTGTCTCCCCCG 62.531 72.222 0.00 0.00 46.90 5.73
28 29 3.775654 GTGTCTCCCCCGCTCCTG 61.776 72.222 0.00 0.00 0.00 3.86
67 68 2.825836 GCCATGCCAGTTCCCGAG 60.826 66.667 0.00 0.00 0.00 4.63
83 84 1.782181 GAGAACGACTCGCCAAAGC 59.218 57.895 0.00 0.00 35.84 3.51
93 94 4.147449 GCCAAAGCGAATGCCCCC 62.147 66.667 0.00 0.00 44.31 5.40
94 95 3.825611 CCAAAGCGAATGCCCCCG 61.826 66.667 0.00 0.00 44.31 5.73
123 124 0.721718 CCACGAGAAACGAATCAGGC 59.278 55.000 0.00 0.00 45.77 4.85
125 126 1.798223 CACGAGAAACGAATCAGGCAA 59.202 47.619 0.00 0.00 45.77 4.52
278 334 2.348998 CACCTCCACCTGGTCTGC 59.651 66.667 0.00 0.00 35.28 4.26
279 335 2.930562 ACCTCCACCTGGTCTGCC 60.931 66.667 0.00 0.00 36.34 4.85
280 336 3.721706 CCTCCACCTGGTCTGCCC 61.722 72.222 0.00 0.00 36.34 5.36
281 337 4.087892 CTCCACCTGGTCTGCCCG 62.088 72.222 0.00 0.00 35.15 6.13
694 774 4.459089 GTCAGCGACAGCCTCCCC 62.459 72.222 4.20 0.00 46.67 4.81
926 1054 2.747855 GCCAGCCAGGGTTCTTCG 60.748 66.667 0.00 0.00 38.09 3.79
964 1100 1.709147 CGCCAGCCATACTGTGAAGC 61.709 60.000 0.00 0.00 45.68 3.86
972 1108 0.526524 ATACTGTGAAGCGAGCGAGC 60.527 55.000 0.00 0.00 37.41 5.03
978 1114 3.102107 GAAGCGAGCGAGCGAGAGA 62.102 63.158 1.41 0.00 43.00 3.10
980 1116 4.605967 GCGAGCGAGCGAGAGAGG 62.606 72.222 1.41 0.00 0.00 3.69
983 1119 2.515991 AGCGAGCGAGAGAGGGAG 60.516 66.667 0.00 0.00 0.00 4.30
984 1120 2.515057 GCGAGCGAGAGAGGGAGA 60.515 66.667 0.00 0.00 0.00 3.71
985 1121 2.542907 GCGAGCGAGAGAGGGAGAG 61.543 68.421 0.00 0.00 0.00 3.20
986 1122 1.891919 CGAGCGAGAGAGGGAGAGG 60.892 68.421 0.00 0.00 0.00 3.69
987 1123 1.528309 GAGCGAGAGAGGGAGAGGG 60.528 68.421 0.00 0.00 0.00 4.30
988 1124 1.990160 GAGCGAGAGAGGGAGAGGGA 61.990 65.000 0.00 0.00 0.00 4.20
989 1125 1.528309 GCGAGAGAGGGAGAGGGAG 60.528 68.421 0.00 0.00 0.00 4.30
990 1126 1.990160 GCGAGAGAGGGAGAGGGAGA 61.990 65.000 0.00 0.00 0.00 3.71
991 1127 0.108585 CGAGAGAGGGAGAGGGAGAG 59.891 65.000 0.00 0.00 0.00 3.20
992 1128 0.478507 GAGAGAGGGAGAGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
993 1129 1.152546 GAGAGGGAGAGGGAGAGGC 60.153 68.421 0.00 0.00 0.00 4.70
1548 1684 4.717629 CTCAACGAGCCGCCGTCA 62.718 66.667 7.25 0.00 42.54 4.35
1573 1709 3.485463 TGTTTGGGTCGTGATCTCTTT 57.515 42.857 0.00 0.00 0.00 2.52
1656 1792 4.335874 ACGTAGTGAGCATGTAGAGGTAAG 59.664 45.833 0.00 0.00 42.51 2.34
1669 1805 0.252375 AGGTAAGTTAGCGGGGTGGA 60.252 55.000 6.45 0.00 0.00 4.02
1708 1844 4.504461 GTGTGCTGTGTACATATACTGCTC 59.496 45.833 15.22 12.85 40.84 4.26
1709 1845 4.402474 TGTGCTGTGTACATATACTGCTCT 59.598 41.667 15.22 0.00 40.84 4.09
1710 1846 4.742167 GTGCTGTGTACATATACTGCTCTG 59.258 45.833 15.22 0.00 40.84 3.35
1739 1875 3.705604 AGCAAAATTTCACCTTGTGTCG 58.294 40.909 0.00 0.00 34.79 4.35
1740 1876 2.218530 GCAAAATTTCACCTTGTGTCGC 59.781 45.455 0.00 0.00 34.79 5.19
1742 1878 1.981256 AATTTCACCTTGTGTCGCCT 58.019 45.000 0.00 0.00 34.79 5.52
1744 1880 1.021202 TTTCACCTTGTGTCGCCTTG 58.979 50.000 0.00 0.00 34.79 3.61
1746 1882 2.594592 ACCTTGTGTCGCCTTGGC 60.595 61.111 0.75 0.75 0.00 4.52
1758 1895 1.949257 CCTTGGCTGGTGTTCGTTC 59.051 57.895 0.00 0.00 0.00 3.95
1785 1922 0.322975 TCTCTTGCAGTTCTGGCCTC 59.677 55.000 3.32 0.00 0.00 4.70
1827 2186 4.377897 CAAGACACTTTAACCCGAGACTT 58.622 43.478 0.00 0.00 0.00 3.01
1829 2188 2.479275 GACACTTTAACCCGAGACTTGC 59.521 50.000 0.00 0.00 0.00 4.01
1830 2189 1.459592 CACTTTAACCCGAGACTTGCG 59.540 52.381 0.00 0.00 0.00 4.85
1831 2190 1.342174 ACTTTAACCCGAGACTTGCGA 59.658 47.619 0.00 0.00 0.00 5.10
1832 2191 2.224113 ACTTTAACCCGAGACTTGCGAA 60.224 45.455 0.00 0.00 0.00 4.70
1833 2192 2.529780 TTAACCCGAGACTTGCGAAA 57.470 45.000 0.00 0.00 0.00 3.46
1835 2194 1.156736 AACCCGAGACTTGCGAAATG 58.843 50.000 0.00 0.00 0.00 2.32
1836 2195 1.298859 ACCCGAGACTTGCGAAATGC 61.299 55.000 0.00 0.00 46.70 3.56
1837 2196 1.021390 CCCGAGACTTGCGAAATGCT 61.021 55.000 0.00 0.00 46.63 3.79
1838 2197 0.095935 CCGAGACTTGCGAAATGCTG 59.904 55.000 0.00 0.00 46.63 4.41
1839 2198 0.792640 CGAGACTTGCGAAATGCTGT 59.207 50.000 0.00 0.00 46.63 4.40
1840 2199 1.992667 CGAGACTTGCGAAATGCTGTA 59.007 47.619 0.00 0.00 46.63 2.74
1841 2200 2.411748 CGAGACTTGCGAAATGCTGTAA 59.588 45.455 0.00 0.00 46.63 2.41
1842 2201 3.120683 CGAGACTTGCGAAATGCTGTAAA 60.121 43.478 0.00 0.00 46.63 2.01
1843 2202 4.610456 CGAGACTTGCGAAATGCTGTAAAA 60.610 41.667 0.00 0.00 46.63 1.52
1844 2203 5.181690 AGACTTGCGAAATGCTGTAAAAA 57.818 34.783 0.00 0.00 46.63 1.94
1845 2204 5.215160 AGACTTGCGAAATGCTGTAAAAAG 58.785 37.500 0.00 0.00 46.63 2.27
1846 2205 3.735746 ACTTGCGAAATGCTGTAAAAAGC 59.264 39.130 0.00 0.00 46.63 3.51
1847 2206 2.315011 TGCGAAATGCTGTAAAAAGCG 58.685 42.857 0.00 0.00 46.65 4.68
1848 2207 2.031595 TGCGAAATGCTGTAAAAAGCGA 60.032 40.909 0.00 0.00 46.65 4.93
1851 2210 3.840763 CGAAATGCTGTAAAAAGCGACTC 59.159 43.478 0.00 0.00 46.65 3.36
1853 2212 3.813529 ATGCTGTAAAAAGCGACTCAC 57.186 42.857 0.00 0.00 46.65 3.51
1854 2213 2.833794 TGCTGTAAAAAGCGACTCACT 58.166 42.857 0.00 0.00 46.65 3.41
1855 2214 3.202906 TGCTGTAAAAAGCGACTCACTT 58.797 40.909 0.00 0.00 46.65 3.16
1856 2215 3.002246 TGCTGTAAAAAGCGACTCACTTG 59.998 43.478 0.00 0.00 46.65 3.16
1857 2216 3.247648 GCTGTAAAAAGCGACTCACTTGA 59.752 43.478 0.00 0.00 32.56 3.02
1858 2217 4.609336 GCTGTAAAAAGCGACTCACTTGAG 60.609 45.833 4.63 4.63 39.61 3.02
1859 2218 6.976627 GCTGTAAAAAGCGACTCACTTGAGT 61.977 44.000 11.75 11.75 44.71 3.41
1860 2219 8.364504 GCTGTAAAAAGCGACTCACTTGAGTT 62.365 42.308 13.08 0.00 43.35 3.01
1861 2220 9.724410 GCTGTAAAAAGCGACTCACTTGAGTTT 62.724 40.741 13.08 5.37 43.35 2.66
1876 2235 2.285756 TGAGTTTTTAGTGTTCGTGCGG 59.714 45.455 0.00 0.00 0.00 5.69
1904 2263 3.085952 TGGAATGGACATGGTTTCCTC 57.914 47.619 15.03 2.27 38.73 3.71
1952 2311 4.308458 AGCCCAAGCGTACGTGCA 62.308 61.111 17.90 0.00 46.67 4.57
1953 2312 4.084888 GCCCAAGCGTACGTGCAC 62.085 66.667 17.90 6.82 37.31 4.57
1954 2313 3.773630 CCCAAGCGTACGTGCACG 61.774 66.667 35.99 35.99 44.71 5.34
1955 2314 2.731721 CCAAGCGTACGTGCACGA 60.732 61.111 42.94 24.54 44.69 4.35
1956 2315 2.304401 CCAAGCGTACGTGCACGAA 61.304 57.895 42.94 0.00 44.69 3.85
1957 2316 1.623081 CCAAGCGTACGTGCACGAAT 61.623 55.000 42.94 25.58 44.69 3.34
2033 2392 1.265635 TGTTAACCACAGCGTCATTGC 59.734 47.619 2.48 0.00 0.00 3.56
2052 2411 6.529829 TCATTGCGTTTATAAATTGTTCCTGC 59.470 34.615 0.31 0.00 0.00 4.85
2060 2419 1.165270 AATTGTTCCTGCCGCAGTAC 58.835 50.000 18.98 15.75 0.00 2.73
2078 2437 2.124736 GCCCTAATGGAGCACGCA 60.125 61.111 0.00 0.00 35.39 5.24
2087 2446 1.635844 TGGAGCACGCAACGTATAAG 58.364 50.000 0.00 0.00 38.32 1.73
2136 2495 4.156556 TCAAGTTAATGATCCTTGTGCTGC 59.843 41.667 8.06 0.00 37.45 5.25
2225 2587 8.308931 ACTGTTATTGTTATTCGGTTGTCTAGA 58.691 33.333 0.00 0.00 0.00 2.43
2331 2858 5.245075 AGCTTCCTAGTGCAGAAGGATATAC 59.755 44.000 15.90 7.63 41.50 1.47
2342 2869 9.109393 GTGCAGAAGGATATACACAAAGAATTA 57.891 33.333 0.00 0.00 0.00 1.40
2354 2881 7.219484 ACACAAAGAATTATCACCTTCAAGG 57.781 36.000 0.22 0.22 42.49 3.61
2355 2882 6.095377 CACAAAGAATTATCACCTTCAAGGC 58.905 40.000 2.20 0.00 39.63 4.35
2356 2883 6.012745 ACAAAGAATTATCACCTTCAAGGCT 58.987 36.000 2.20 0.00 39.63 4.58
2359 2886 7.631717 AAGAATTATCACCTTCAAGGCTAAC 57.368 36.000 2.20 0.00 39.63 2.34
2361 2888 7.175104 AGAATTATCACCTTCAAGGCTAACAA 58.825 34.615 2.20 0.00 39.63 2.83
2364 2891 4.911514 TCACCTTCAAGGCTAACAAAAC 57.088 40.909 2.20 0.00 39.63 2.43
2365 2892 3.314080 TCACCTTCAAGGCTAACAAAACG 59.686 43.478 2.20 0.00 39.63 3.60
2366 2893 3.314080 CACCTTCAAGGCTAACAAAACGA 59.686 43.478 2.20 0.00 39.63 3.85
2368 2895 5.180492 CACCTTCAAGGCTAACAAAACGATA 59.820 40.000 2.20 0.00 39.63 2.92
2369 2896 5.180680 ACCTTCAAGGCTAACAAAACGATAC 59.819 40.000 2.20 0.00 39.63 2.24
2370 2897 5.180492 CCTTCAAGGCTAACAAAACGATACA 59.820 40.000 0.00 0.00 0.00 2.29
2371 2898 6.293735 CCTTCAAGGCTAACAAAACGATACAA 60.294 38.462 0.00 0.00 0.00 2.41
2372 2899 6.236017 TCAAGGCTAACAAAACGATACAAG 57.764 37.500 0.00 0.00 0.00 3.16
2374 2901 6.261381 TCAAGGCTAACAAAACGATACAAGTT 59.739 34.615 0.00 0.00 0.00 2.66
2376 2903 7.360575 AGGCTAACAAAACGATACAAGTTAG 57.639 36.000 0.00 0.00 40.61 2.34
2405 3268 1.675483 TGAAAGTCACGCAAGCAACAT 59.325 42.857 0.00 0.00 45.62 2.71
2406 3269 2.098934 TGAAAGTCACGCAAGCAACATT 59.901 40.909 0.00 0.00 45.62 2.71
2408 3271 2.969443 AGTCACGCAAGCAACATTAC 57.031 45.000 0.00 0.00 45.62 1.89
2409 3272 2.217750 AGTCACGCAAGCAACATTACA 58.782 42.857 0.00 0.00 45.62 2.41
2410 3273 2.813754 AGTCACGCAAGCAACATTACAT 59.186 40.909 0.00 0.00 45.62 2.29
2412 3275 3.980775 GTCACGCAAGCAACATTACATTT 59.019 39.130 0.00 0.00 45.62 2.32
2413 3276 4.444056 GTCACGCAAGCAACATTACATTTT 59.556 37.500 0.00 0.00 45.62 1.82
2414 3277 5.046529 TCACGCAAGCAACATTACATTTTT 58.953 33.333 0.00 0.00 45.62 1.94
2490 3355 3.498927 AACGTGTCTAACCATACCTCG 57.501 47.619 0.00 0.00 0.00 4.63
2559 3424 4.709886 GGGCATACCAGGATTACAAAGTTT 59.290 41.667 0.00 0.00 39.85 2.66
2564 3429 5.453567 ACCAGGATTACAAAGTTTCTTGC 57.546 39.130 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.775654 CAGGAGCGGGGGAGACAC 61.776 72.222 0.00 0.00 0.00 3.67
42 43 4.790962 CTGGCATGGCGACCTGCT 62.791 66.667 18.38 0.00 45.43 4.24
97 98 3.047877 GTTTCTCGTGGGGTGCGG 61.048 66.667 0.00 0.00 0.00 5.69
98 99 3.411351 CGTTTCTCGTGGGGTGCG 61.411 66.667 0.00 0.00 34.52 5.34
101 102 0.682852 TGATTCGTTTCTCGTGGGGT 59.317 50.000 0.00 0.00 40.80 4.95
102 103 1.359848 CTGATTCGTTTCTCGTGGGG 58.640 55.000 0.00 0.00 40.80 4.96
103 104 1.359848 CCTGATTCGTTTCTCGTGGG 58.640 55.000 0.00 0.00 40.80 4.61
104 105 0.721718 GCCTGATTCGTTTCTCGTGG 59.278 55.000 0.00 0.00 40.80 4.94
211 246 1.579429 GTTCGGTGGTTCACATGGC 59.421 57.895 0.00 0.00 35.86 4.40
215 250 1.521906 CACGGTTCGGTGGTTCACA 60.522 57.895 0.38 0.00 35.86 3.58
262 318 2.930562 GGCAGACCAGGTGGAGGT 60.931 66.667 0.00 0.00 43.46 3.85
264 320 4.087892 CGGGCAGACCAGGTGGAG 62.088 72.222 0.00 0.00 40.22 3.86
310 370 3.062466 GCGAGGCCTTTTGACCCC 61.062 66.667 6.77 0.00 0.00 4.95
539 611 4.034258 CATCCATCATGCGCCCGC 62.034 66.667 4.18 5.60 42.35 6.13
540 612 3.359523 CCATCCATCATGCGCCCG 61.360 66.667 4.18 0.00 0.00 6.13
541 613 2.203394 ACCATCCATCATGCGCCC 60.203 61.111 4.18 0.00 0.00 6.13
542 614 0.534877 TACACCATCCATCATGCGCC 60.535 55.000 4.18 0.00 0.00 6.53
543 615 0.870393 CTACACCATCCATCATGCGC 59.130 55.000 0.00 0.00 0.00 6.09
806 891 4.676723 GCTGCCTACTCTATGCTATGCTAC 60.677 50.000 0.00 0.00 0.00 3.58
815 900 0.600557 CCCTCGCTGCCTACTCTATG 59.399 60.000 0.00 0.00 0.00 2.23
816 901 0.186386 ACCCTCGCTGCCTACTCTAT 59.814 55.000 0.00 0.00 0.00 1.98
818 903 2.055042 CACCCTCGCTGCCTACTCT 61.055 63.158 0.00 0.00 0.00 3.24
819 904 2.052690 TCACCCTCGCTGCCTACTC 61.053 63.158 0.00 0.00 0.00 2.59
879 1005 1.664965 CTTATACGGAGCGGCAGGC 60.665 63.158 1.45 0.00 44.05 4.85
950 1086 1.756375 CGCTCGCTTCACAGTATGGC 61.756 60.000 0.00 0.00 43.62 4.40
964 1100 3.947841 CCCTCTCTCGCTCGCTCG 61.948 72.222 0.00 0.00 0.00 5.03
972 1108 0.108585 CTCTCCCTCTCCCTCTCTCG 59.891 65.000 0.00 0.00 0.00 4.04
978 1114 4.150454 CCGCCTCTCCCTCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
985 1121 4.899239 CATGACGCCGCCTCTCCC 62.899 72.222 0.00 0.00 0.00 4.30
987 1123 4.819761 TGCATGACGCCGCCTCTC 62.820 66.667 0.00 0.00 41.33 3.20
988 1124 3.899981 TTTGCATGACGCCGCCTCT 62.900 57.895 0.00 0.00 41.33 3.69
989 1125 2.764314 ATTTGCATGACGCCGCCTC 61.764 57.895 0.00 0.00 41.33 4.70
990 1126 2.751436 ATTTGCATGACGCCGCCT 60.751 55.556 0.00 0.00 41.33 5.52
991 1127 2.580326 CATTTGCATGACGCCGCC 60.580 61.111 0.00 0.00 41.33 6.13
992 1128 3.249605 GCATTTGCATGACGCCGC 61.250 61.111 0.00 0.00 41.33 6.53
993 1129 1.870458 CAGCATTTGCATGACGCCG 60.870 57.895 5.20 0.00 45.16 6.46
1158 1294 2.257371 CGCGTCTTCTTCCACGGA 59.743 61.111 0.00 0.00 36.50 4.69
1486 1622 4.504916 CGTCCGGAGCTCCAGCAG 62.505 72.222 31.67 16.90 45.16 4.24
1548 1684 2.303022 AGATCACGACCCAAACATCAGT 59.697 45.455 0.00 0.00 0.00 3.41
1551 1687 3.252974 AGAGATCACGACCCAAACATC 57.747 47.619 0.00 0.00 0.00 3.06
1642 1778 3.381949 CCGCTAACTTACCTCTACATGC 58.618 50.000 0.00 0.00 0.00 4.06
1643 1779 3.243771 CCCCGCTAACTTACCTCTACATG 60.244 52.174 0.00 0.00 0.00 3.21
1644 1780 2.963782 CCCCGCTAACTTACCTCTACAT 59.036 50.000 0.00 0.00 0.00 2.29
1645 1781 2.291800 ACCCCGCTAACTTACCTCTACA 60.292 50.000 0.00 0.00 0.00 2.74
1656 1792 1.262640 TTCTCCTCCACCCCGCTAAC 61.263 60.000 0.00 0.00 0.00 2.34
1669 1805 0.250814 ACACGGACGAGTCTTCTCCT 60.251 55.000 0.00 0.00 37.40 3.69
1708 1844 5.702209 AGGTGAAATTTTGCTAAAATGGCAG 59.298 36.000 0.00 0.00 40.05 4.85
1709 1845 5.619220 AGGTGAAATTTTGCTAAAATGGCA 58.381 33.333 0.00 0.00 40.05 4.92
1710 1846 6.017192 ACAAGGTGAAATTTTGCTAAAATGGC 60.017 34.615 0.00 0.32 40.05 4.40
1739 1875 2.130073 GAACGAACACCAGCCAAGGC 62.130 60.000 2.02 2.02 42.33 4.35
1740 1876 0.535102 AGAACGAACACCAGCCAAGG 60.535 55.000 0.00 0.00 0.00 3.61
1742 1878 1.021202 CAAGAACGAACACCAGCCAA 58.979 50.000 0.00 0.00 0.00 4.52
1744 1880 1.166531 AGCAAGAACGAACACCAGCC 61.167 55.000 0.00 0.00 0.00 4.85
1746 1882 1.581934 TCAGCAAGAACGAACACCAG 58.418 50.000 0.00 0.00 0.00 4.00
1758 1895 3.125487 CAGAACTGCAAGAGATCAGCAAG 59.875 47.826 0.00 0.00 37.89 4.01
1785 1922 1.609208 CAAAGAGACACCACCAAGGG 58.391 55.000 0.00 0.00 43.89 3.95
1827 2186 2.031595 TCGCTTTTTACAGCATTTCGCA 60.032 40.909 0.00 0.00 46.13 5.10
1829 2188 3.810373 AGTCGCTTTTTACAGCATTTCG 58.190 40.909 0.00 0.00 40.09 3.46
1830 2189 4.613031 GTGAGTCGCTTTTTACAGCATTTC 59.387 41.667 0.00 0.00 40.09 2.17
1831 2190 4.275936 AGTGAGTCGCTTTTTACAGCATTT 59.724 37.500 0.00 0.00 40.09 2.32
1832 2191 3.815401 AGTGAGTCGCTTTTTACAGCATT 59.185 39.130 0.00 0.00 40.09 3.56
1833 2192 3.403038 AGTGAGTCGCTTTTTACAGCAT 58.597 40.909 0.00 0.00 40.09 3.79
1835 2194 3.247648 TCAAGTGAGTCGCTTTTTACAGC 59.752 43.478 16.28 0.00 31.36 4.40
1836 2195 5.011451 CTCAAGTGAGTCGCTTTTTACAG 57.989 43.478 16.28 4.69 37.40 2.74
1851 2210 4.728608 GCACGAACACTAAAAACTCAAGTG 59.271 41.667 0.00 0.37 44.89 3.16
1853 2212 3.960002 CGCACGAACACTAAAAACTCAAG 59.040 43.478 0.00 0.00 0.00 3.02
1854 2213 3.242478 CCGCACGAACACTAAAAACTCAA 60.242 43.478 0.00 0.00 0.00 3.02
1855 2214 2.285756 CCGCACGAACACTAAAAACTCA 59.714 45.455 0.00 0.00 0.00 3.41
1856 2215 2.286025 ACCGCACGAACACTAAAAACTC 59.714 45.455 0.00 0.00 0.00 3.01
1857 2216 2.282407 ACCGCACGAACACTAAAAACT 58.718 42.857 0.00 0.00 0.00 2.66
1858 2217 2.742954 ACCGCACGAACACTAAAAAC 57.257 45.000 0.00 0.00 0.00 2.43
1859 2218 3.432933 GGATACCGCACGAACACTAAAAA 59.567 43.478 0.00 0.00 0.00 1.94
1860 2219 2.995258 GGATACCGCACGAACACTAAAA 59.005 45.455 0.00 0.00 0.00 1.52
1861 2220 2.609350 GGATACCGCACGAACACTAAA 58.391 47.619 0.00 0.00 0.00 1.85
1900 2259 2.265739 GGCACATGCGACTGAGGA 59.734 61.111 0.00 0.00 43.26 3.71
1904 2263 3.129502 CTGGGGCACATGCGACTG 61.130 66.667 0.00 0.00 43.26 3.51
1993 2352 2.271944 ACCTCTGTACAGCCAAAACC 57.728 50.000 18.45 0.00 0.00 3.27
2033 2392 3.789224 GCGGCAGGAACAATTTATAAACG 59.211 43.478 0.00 0.00 0.00 3.60
2060 2419 3.272334 GCGTGCTCCATTAGGGCG 61.272 66.667 0.00 0.00 34.84 6.13
2065 2424 2.303163 ATACGTTGCGTGCTCCATTA 57.697 45.000 0.00 0.00 41.39 1.90
2078 2437 8.173321 ACGTTTCGCTTATAAACTTATACGTT 57.827 30.769 0.00 0.00 35.20 3.99
2087 2446 5.273523 AGTTGGACGTTTCGCTTATAAAC 57.726 39.130 0.00 0.00 34.25 2.01
2193 2552 8.889717 CAACCGAATAACAATAACAGTAATCCT 58.110 33.333 0.00 0.00 0.00 3.24
2194 2553 8.671028 ACAACCGAATAACAATAACAGTAATCC 58.329 33.333 0.00 0.00 0.00 3.01
2225 2587 5.479124 ACCGGTCATAGTTTCTACAACTT 57.521 39.130 0.00 0.00 0.00 2.66
2331 2858 6.071728 AGCCTTGAAGGTGATAATTCTTTGTG 60.072 38.462 13.58 0.00 37.80 3.33
2342 2869 4.023193 CGTTTTGTTAGCCTTGAAGGTGAT 60.023 41.667 13.58 2.15 37.80 3.06
2352 2879 6.932960 ACTAACTTGTATCGTTTTGTTAGCCT 59.067 34.615 0.00 0.00 39.92 4.58
2353 2880 7.125536 ACTAACTTGTATCGTTTTGTTAGCC 57.874 36.000 0.00 0.00 39.92 3.93
2354 2881 8.919661 ACTACTAACTTGTATCGTTTTGTTAGC 58.080 33.333 0.00 0.00 39.92 3.09
2371 2898 6.640092 GCGTGACTTTCAAGTTACTACTAACT 59.360 38.462 11.56 0.00 43.87 2.24
2372 2899 6.418819 TGCGTGACTTTCAAGTTACTACTAAC 59.581 38.462 11.56 0.00 41.71 2.34
2374 2901 6.075762 TGCGTGACTTTCAAGTTACTACTA 57.924 37.500 11.56 0.00 41.71 1.82
2376 2903 5.646467 TTGCGTGACTTTCAAGTTACTAC 57.354 39.130 11.56 5.65 41.71 2.73
2416 3279 7.271511 AGAAATGTAATGTTGCCTGTCAAAAA 58.728 30.769 0.00 0.00 36.26 1.94
2417 3280 6.815089 AGAAATGTAATGTTGCCTGTCAAAA 58.185 32.000 0.00 0.00 36.26 2.44
2418 3281 6.403866 AGAAATGTAATGTTGCCTGTCAAA 57.596 33.333 0.00 0.00 36.26 2.69
2419 3282 7.517614 TTAGAAATGTAATGTTGCCTGTCAA 57.482 32.000 0.00 0.00 0.00 3.18
2420 3283 7.701539 ATTAGAAATGTAATGTTGCCTGTCA 57.298 32.000 0.00 0.00 0.00 3.58
2421 3284 8.893727 ACTATTAGAAATGTAATGTTGCCTGTC 58.106 33.333 0.00 0.00 0.00 3.51
2422 3285 8.677300 CACTATTAGAAATGTAATGTTGCCTGT 58.323 33.333 0.00 0.00 0.00 4.00
2423 3286 8.677300 ACACTATTAGAAATGTAATGTTGCCTG 58.323 33.333 0.00 0.00 0.00 4.85
2424 3287 8.807948 ACACTATTAGAAATGTAATGTTGCCT 57.192 30.769 0.00 0.00 0.00 4.75
2474 3337 6.776116 AGAATGATACGAGGTATGGTTAGACA 59.224 38.462 0.00 0.00 0.00 3.41
2534 3399 3.576078 TTGTAATCCTGGTATGCCCTG 57.424 47.619 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.