Multiple sequence alignment - TraesCS5D01G430900

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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 TraesCS5D01G430900 chr5D 100.000 2803 0 0 1 2803 487995423 487992621 0.000000e+00 5177
1 TraesCS5D01G430900 chr5D 77.299 511 111 5 31 539 488163147 488162640 2.110000e-76 296
2 TraesCS5D01G430900 chr5D 93.277 119 8 0 3 121 488039620 488039502 2.870000e-40 176
3 TraesCS5D01G430900 chr5A 87.417 1804 127 31 1042 2803 608806908 608805163 0.000000e+00 1982
4 TraesCS5D01G430900 chr5A 92.542 952 54 9 1 951 608815157 608814222 0.000000e+00 1349
5 TraesCS5D01G430900 chr5A 86.158 708 90 8 942 1645 608814039 608813336 0.000000e+00 758
6 TraesCS5D01G430900 chr5A 81.713 607 98 9 1102 1703 608702109 608701511 6.970000e-136 494
7 TraesCS5D01G430900 chr3B 84.756 328 42 7 2080 2403 733898540 733898863 3.480000e-84 322
8 TraesCS5D01G430900 chr3B 76.615 325 62 12 2082 2399 545561542 545561225 1.730000e-37 167
9 TraesCS5D01G430900 chr7B 80.539 334 49 11 2080 2403 144109636 144109963 2.790000e-60 243
10 TraesCS5D01G430900 chr6A 78.638 323 60 9 2082 2399 598164117 598164435 3.660000e-49 206
11 TraesCS5D01G430900 chr7D 78.528 326 51 17 2084 2399 93031424 93031108 2.200000e-46 196
12 TraesCS5D01G430900 chr7A 77.846 325 59 13 2082 2399 690434299 690433981 3.690000e-44 189
13 TraesCS5D01G430900 chr1D 77.301 326 59 11 2079 2399 441544711 441545026 7.980000e-41 178
14 TraesCS5D01G430900 chr1D 77.580 281 53 9 2135 2409 462286924 462287200 8.030000e-36 161
15 TraesCS5D01G430900 chr6D 77.815 302 49 11 2081 2380 134340119 134339834 1.340000e-38 171


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 TraesCS5D01G430900 chr5D 487992621 487995423 2802 True 5177.0 5177 100.000 1 2803 1 chr5D.!!$R1 2802
1 TraesCS5D01G430900 chr5D 488162640 488163147 507 True 296.0 296 77.299 31 539 1 chr5D.!!$R3 508
2 TraesCS5D01G430900 chr5A 608805163 608806908 1745 True 1982.0 1982 87.417 1042 2803 1 chr5A.!!$R2 1761
3 TraesCS5D01G430900 chr5A 608813336 608815157 1821 True 1053.5 1349 89.350 1 1645 2 chr5A.!!$R3 1644
4 TraesCS5D01G430900 chr5A 608701511 608702109 598 True 494.0 494 81.713 1102 1703 1 chr5A.!!$R1 601

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
682 683 0.179275 TTCGTCTTCGTCGTCGTACG 60.179 55.0 9.53 9.53 44.19 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2474 2712 0.118346 ACATACACCCCTGACCCTGA 59.882 55.0 0.0 0.0 0.0 3.86 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
43 44 4.142381 GGGGAAACAGAGCACAAATGATAC 60.142 45.833 0.00 0.00 0.00 2.24
71 72 1.007118 GGGACAATGAAGGAACCCCAT 59.993 52.381 0.00 0.00 33.88 4.00
79 80 5.605540 ATGAAGGAACCCCATGCTAATAT 57.394 39.130 0.00 0.00 33.88 1.28
134 135 1.736645 CAGCAACGTAGTCACCGGG 60.737 63.158 6.32 0.00 45.00 5.73
150 151 1.342074 CGGGGGAAGCTCTATGATGA 58.658 55.000 0.00 0.00 0.00 2.92
174 175 3.508762 CGTGTGAGCGGATTTAGTAGTT 58.491 45.455 0.00 0.00 0.00 2.24
274 275 4.039004 CAGGAGATCCACTTCTATGGTCTG 59.961 50.000 0.92 0.00 40.95 3.51
394 395 2.262915 CCCTAGCGGATCGATGCC 59.737 66.667 11.64 7.49 0.00 4.40
399 400 1.391933 TAGCGGATCGATGCCACACT 61.392 55.000 11.64 6.50 0.00 3.55
410 411 3.663176 CCACACTGCCGCCAAGTG 61.663 66.667 8.85 8.85 39.26 3.16
467 468 0.390603 CGTGGGCAAGGACGTAATCA 60.391 55.000 0.00 0.00 0.00 2.57
475 476 2.783828 AGGACGTAATCAGCGATCAG 57.216 50.000 0.00 0.00 0.00 2.90
476 477 2.025155 AGGACGTAATCAGCGATCAGT 58.975 47.619 0.00 0.00 0.00 3.41
485 486 1.227380 AGCGATCAGTCCAATCGGC 60.227 57.895 7.52 1.03 44.71 5.54
560 561 8.408601 AGACCGAAATCAGATAAATTTCATTGG 58.591 33.333 0.00 5.04 41.23 3.16
562 563 8.748412 ACCGAAATCAGATAAATTTCATTGGAA 58.252 29.630 0.00 0.00 41.23 3.53
564 565 9.023967 CGAAATCAGATAAATTTCATTGGAACC 57.976 33.333 0.00 0.00 41.23 3.62
565 566 9.874205 GAAATCAGATAAATTTCATTGGAACCA 57.126 29.630 0.00 0.00 40.97 3.67
566 567 9.657419 AAATCAGATAAATTTCATTGGAACCAC 57.343 29.630 0.00 0.00 31.35 4.16
567 568 6.851609 TCAGATAAATTTCATTGGAACCACG 58.148 36.000 0.00 0.00 31.35 4.94
568 569 6.432783 TCAGATAAATTTCATTGGAACCACGT 59.567 34.615 0.00 0.00 31.35 4.49
569 570 6.527722 CAGATAAATTTCATTGGAACCACGTG 59.472 38.462 9.08 9.08 31.35 4.49
570 571 4.927978 AAATTTCATTGGAACCACGTGA 57.072 36.364 19.30 0.00 31.35 4.35
571 572 4.927978 AATTTCATTGGAACCACGTGAA 57.072 36.364 19.30 2.61 32.56 3.18
572 573 3.701532 TTTCATTGGAACCACGTGAAC 57.298 42.857 19.30 7.57 33.48 3.18
573 574 2.333688 TCATTGGAACCACGTGAACA 57.666 45.000 19.30 7.23 0.00 3.18
574 575 2.644676 TCATTGGAACCACGTGAACAA 58.355 42.857 19.30 15.65 0.00 2.83
575 576 3.017442 TCATTGGAACCACGTGAACAAA 58.983 40.909 19.30 7.92 0.00 2.83
576 577 2.923605 TTGGAACCACGTGAACAAAC 57.076 45.000 19.30 2.56 0.00 2.93
578 579 1.008329 GGAACCACGTGAACAAACGA 58.992 50.000 19.30 0.00 46.49 3.85
579 580 1.600485 GGAACCACGTGAACAAACGAT 59.400 47.619 19.30 0.00 46.49 3.73
580 581 2.601266 GGAACCACGTGAACAAACGATG 60.601 50.000 19.30 0.00 46.49 3.84
581 582 0.306533 ACCACGTGAACAAACGATGC 59.693 50.000 19.30 0.00 46.49 3.91
595 596 0.301687 CGATGCACGTACCATTCAGC 59.698 55.000 0.00 0.00 37.22 4.26
682 683 0.179275 TTCGTCTTCGTCGTCGTACG 60.179 55.000 9.53 9.53 44.19 3.67
686 687 4.444024 TTCGTCGTCGTACGGGCG 62.444 66.667 16.52 19.27 42.81 6.13
729 730 1.823041 GAGAATGAGCAGCCCTGGC 60.823 63.158 0.00 0.00 42.33 4.85
778 779 3.112709 GCGCCCGTGAGACTGTTC 61.113 66.667 0.00 0.00 0.00 3.18
779 780 2.432628 CGCCCGTGAGACTGTTCC 60.433 66.667 0.00 0.00 0.00 3.62
808 809 2.280524 AGTGCGCACGCCTGTAAA 60.281 55.556 32.94 0.00 41.09 2.01
825 826 1.733385 AAACCGGGGGTAGTGTAAGT 58.267 50.000 6.32 0.00 33.12 2.24
831 832 1.558294 GGGGGTAGTGTAAGTTCCCTG 59.442 57.143 0.00 0.00 45.56 4.45
836 837 3.070590 GGTAGTGTAAGTTCCCTGTGTGT 59.929 47.826 0.00 0.00 0.00 3.72
839 840 3.454812 AGTGTAAGTTCCCTGTGTGTTCT 59.545 43.478 0.00 0.00 0.00 3.01
869 870 5.666462 TGTGCGTTTATATGCCCGATATAT 58.334 37.500 0.00 0.00 35.33 0.86
931 933 1.065928 CGTCTCCGTATCCAGCACC 59.934 63.158 0.00 0.00 0.00 5.01
936 938 2.203070 CGTATCCAGCACCAGGCC 60.203 66.667 0.00 0.00 46.50 5.19
937 939 2.998097 GTATCCAGCACCAGGCCA 59.002 61.111 5.01 0.00 46.50 5.36
941 943 1.207488 ATCCAGCACCAGGCCAAGTA 61.207 55.000 5.01 0.00 46.50 2.24
957 1149 3.251571 CAAGTAGGTTTAGAGTCCGTGC 58.748 50.000 0.00 0.00 0.00 5.34
964 1156 1.504359 TTAGAGTCCGTGCCGTTTTG 58.496 50.000 0.00 0.00 0.00 2.44
965 1157 0.320073 TAGAGTCCGTGCCGTTTTGG 60.320 55.000 0.00 0.00 42.50 3.28
984 1176 2.831284 GTTGCACCCACCCACGTT 60.831 61.111 0.00 0.00 0.00 3.99
993 1185 2.893404 ACCCACGTTCGTGTGTGC 60.893 61.111 20.93 0.00 38.20 4.57
996 1188 1.082821 CCACGTTCGTGTGTGCATG 60.083 57.895 20.93 3.48 38.20 4.06
998 1190 0.654184 CACGTTCGTGTGTGCATGTG 60.654 55.000 15.81 0.00 35.12 3.21
1006 1202 6.361214 CGTTCGTGTGTGCATGTGTATATATA 59.639 38.462 0.00 0.00 33.51 0.86
1007 1203 7.061789 CGTTCGTGTGTGCATGTGTATATATAT 59.938 37.037 0.00 0.00 33.51 0.86
1008 1204 7.810766 TCGTGTGTGCATGTGTATATATATG 57.189 36.000 5.44 2.39 33.51 1.78
1021 1217 7.831562 GTGTATATATATGCACATACAGCACG 58.168 38.462 28.68 0.00 45.95 5.34
1059 1255 1.141881 CCGTGAGATCGTGGGAAGG 59.858 63.158 0.00 0.00 0.00 3.46
1062 1258 1.469940 CGTGAGATCGTGGGAAGGAAG 60.470 57.143 0.00 0.00 0.00 3.46
1070 1266 1.152830 TGGGAAGGAAGCCAACACC 59.847 57.895 0.00 0.00 0.00 4.16
1166 1374 3.382832 CGCTGGAGGGAGTCGGTT 61.383 66.667 0.00 0.00 0.00 4.44
1167 1375 2.943978 CGCTGGAGGGAGTCGGTTT 61.944 63.158 0.00 0.00 0.00 3.27
1184 1392 4.680237 TTGCTCCGCCTCCACACG 62.680 66.667 0.00 0.00 0.00 4.49
1432 1640 0.830648 CCCTATGAGAAGGCCGTCAA 59.169 55.000 21.26 8.94 35.09 3.18
1503 1711 4.347453 GCTTGGCCACCAACGCAG 62.347 66.667 3.88 0.00 38.75 5.18
1508 1716 1.302192 GGCCACCAACGCAGAACTA 60.302 57.895 0.00 0.00 0.00 2.24
1509 1717 0.887387 GGCCACCAACGCAGAACTAA 60.887 55.000 0.00 0.00 0.00 2.24
1518 1726 4.024048 CCAACGCAGAACTAAATGACACTT 60.024 41.667 0.00 0.00 0.00 3.16
1539 1747 2.001812 CCTGTGTCTCATCGTGAAGG 57.998 55.000 0.00 0.00 0.00 3.46
1656 1864 1.754803 CCAGGGTAGAGTATGTTCGCA 59.245 52.381 0.00 0.00 0.00 5.10
1665 1873 1.094785 GTATGTTCGCAATGGCAGGT 58.905 50.000 0.00 0.00 41.24 4.00
1669 1877 2.395360 TTCGCAATGGCAGGTACGC 61.395 57.895 0.00 0.00 41.24 4.42
1687 1895 4.541482 TCCGCCGACGACATACGC 62.541 66.667 0.00 0.00 46.94 4.42
1706 1914 1.220477 GCAAGACAGCTCCTCCTCC 59.780 63.158 0.00 0.00 0.00 4.30
1707 1915 1.264045 GCAAGACAGCTCCTCCTCCT 61.264 60.000 0.00 0.00 0.00 3.69
1708 1916 0.823460 CAAGACAGCTCCTCCTCCTC 59.177 60.000 0.00 0.00 0.00 3.71
1709 1917 0.411452 AAGACAGCTCCTCCTCCTCA 59.589 55.000 0.00 0.00 0.00 3.86
1710 1918 0.033208 AGACAGCTCCTCCTCCTCAG 60.033 60.000 0.00 0.00 0.00 3.35
1711 1919 0.033601 GACAGCTCCTCCTCCTCAGA 60.034 60.000 0.00 0.00 0.00 3.27
1712 1920 0.636101 ACAGCTCCTCCTCCTCAGAT 59.364 55.000 0.00 0.00 0.00 2.90
1721 1929 3.512329 CCTCCTCCTCAGATGATGATGAG 59.488 52.174 11.04 11.04 45.37 2.90
1759 1967 2.126914 CGGAGGACGTGATTCAGATC 57.873 55.000 0.00 0.00 37.93 2.75
1760 1968 1.405463 CGGAGGACGTGATTCAGATCA 59.595 52.381 0.00 0.00 39.92 2.92
1790 1998 2.747855 GGCGAGCCTGTTGGAAGG 60.748 66.667 6.90 0.00 40.63 3.46
1838 2048 1.522668 TGAGTCTGGCGGAAACATTG 58.477 50.000 0.00 0.00 0.00 2.82
1840 2050 0.250901 AGTCTGGCGGAAACATTGCT 60.251 50.000 0.00 0.00 0.00 3.91
1841 2051 0.598065 GTCTGGCGGAAACATTGCTT 59.402 50.000 0.00 0.00 0.00 3.91
1842 2052 1.000274 GTCTGGCGGAAACATTGCTTT 60.000 47.619 0.00 0.00 0.00 3.51
1843 2053 1.686052 TCTGGCGGAAACATTGCTTTT 59.314 42.857 0.00 0.00 0.00 2.27
1844 2054 2.061028 CTGGCGGAAACATTGCTTTTC 58.939 47.619 0.00 0.00 33.00 2.29
1845 2055 1.059942 GGCGGAAACATTGCTTTTCG 58.940 50.000 7.58 7.58 35.55 3.46
1846 2056 1.335506 GGCGGAAACATTGCTTTTCGA 60.336 47.619 13.21 0.00 34.53 3.71
1847 2057 2.595386 GCGGAAACATTGCTTTTCGAT 58.405 42.857 13.21 0.00 34.53 3.59
1848 2058 2.594214 GCGGAAACATTGCTTTTCGATC 59.406 45.455 13.21 0.00 34.53 3.69
1849 2059 2.840176 CGGAAACATTGCTTTTCGATCG 59.160 45.455 9.36 9.36 34.53 3.69
1850 2060 3.666902 CGGAAACATTGCTTTTCGATCGT 60.667 43.478 15.94 0.00 34.53 3.73
1851 2061 3.603770 GGAAACATTGCTTTTCGATCGTG 59.396 43.478 15.94 5.77 34.34 4.35
1852 2062 2.247311 ACATTGCTTTTCGATCGTGC 57.753 45.000 15.94 14.98 0.00 5.34
1853 2063 1.535028 ACATTGCTTTTCGATCGTGCA 59.465 42.857 15.94 17.21 0.00 4.57
1885 2095 1.672356 ATGCCAAGTCAGTCCGTGC 60.672 57.895 0.00 0.00 0.00 5.34
1927 2137 1.746615 AACGTAGCCGAGCCGAGTA 60.747 57.895 0.00 0.00 37.88 2.59
1946 2156 5.645624 GAGTAACGGAGTAAGGTTTAGGAC 58.354 45.833 0.00 0.00 45.00 3.85
1958 2168 4.525912 GGTTTAGGACCGAGTTTGAGTA 57.474 45.455 0.00 0.00 39.00 2.59
2004 2239 9.672086 TCCAAAGAAATAATGAAAACAACGTAG 57.328 29.630 0.00 0.00 0.00 3.51
2048 2283 2.721274 TGGTTCGATTGTTTGGCATG 57.279 45.000 0.00 0.00 0.00 4.06
2053 2288 1.543802 TCGATTGTTTGGCATGGGTTC 59.456 47.619 0.00 0.00 0.00 3.62
2055 2290 2.687370 GATTGTTTGGCATGGGTTCAC 58.313 47.619 0.00 0.00 0.00 3.18
2107 2343 3.478857 TCTCCAACAGAGGCGTAAAAA 57.521 42.857 0.00 0.00 43.44 1.94
2116 2352 3.802139 CAGAGGCGTAAAAATATCGAGCA 59.198 43.478 0.00 0.00 0.00 4.26
2118 2354 3.793559 AGGCGTAAAAATATCGAGCACT 58.206 40.909 0.00 0.00 0.00 4.40
2155 2391 1.128692 GCCACTGTAGCACTTTTAGCG 59.871 52.381 0.00 0.00 37.01 4.26
2158 2394 1.336517 ACTGTAGCACTTTTAGCGCGA 60.337 47.619 12.10 0.00 37.01 5.87
2159 2395 1.927174 CTGTAGCACTTTTAGCGCGAT 59.073 47.619 12.10 5.99 37.01 4.58
2172 2408 4.365287 GCGATGCGGTCAACAATG 57.635 55.556 0.00 0.00 0.00 2.82
2179 2416 3.296322 TGCGGTCAACAATGATTTTCC 57.704 42.857 0.00 0.00 38.01 3.13
2180 2417 2.625314 TGCGGTCAACAATGATTTTCCA 59.375 40.909 0.00 0.00 38.01 3.53
2182 2419 3.057596 GCGGTCAACAATGATTTTCCAGA 60.058 43.478 0.00 0.00 38.01 3.86
2183 2420 4.380867 GCGGTCAACAATGATTTTCCAGAT 60.381 41.667 0.00 0.00 38.01 2.90
2193 2430 6.684897 ATGATTTTCCAGATCCCAAAAACA 57.315 33.333 6.72 6.72 0.00 2.83
2200 2437 2.136196 GATCCCAAAAACACGCGCCA 62.136 55.000 5.73 0.00 0.00 5.69
2230 2468 2.228582 TGCAGTGCAAATTATGAAGCGT 59.771 40.909 17.26 0.00 34.76 5.07
2287 2525 2.559330 CTTTTTAGCGCGGGCGTT 59.441 55.556 19.46 11.38 46.35 4.84
2290 2528 1.593933 CTTTTTAGCGCGGGCGTTATA 59.406 47.619 19.46 5.50 46.35 0.98
2335 2573 0.108424 AACATCTGCTGGAGCGTCTC 60.108 55.000 0.00 0.00 45.83 3.36
2355 2593 1.206831 GGCGCTCAAAAAGGACGAC 59.793 57.895 7.64 0.00 0.00 4.34
2387 2625 2.356194 GCAGTTTTTGGGCGCCTG 60.356 61.111 28.56 16.05 0.00 4.85
2399 2637 2.042831 GCGCCTGTTGGAGATGCTT 61.043 57.895 0.00 0.00 34.95 3.91
2407 2645 4.142093 CCTGTTGGAGATGCTTTTAATGGG 60.142 45.833 0.00 0.00 34.57 4.00
2410 2648 4.314522 TGGAGATGCTTTTAATGGGTCA 57.685 40.909 0.00 0.00 0.00 4.02
2413 2651 4.889409 GGAGATGCTTTTAATGGGTCATCA 59.111 41.667 0.00 0.00 34.42 3.07
2415 2653 6.212888 AGATGCTTTTAATGGGTCATCAAC 57.787 37.500 0.00 0.00 34.42 3.18
2421 2659 7.043565 GCTTTTAATGGGTCATCAACAATGAT 58.956 34.615 0.00 0.00 45.94 2.45
2457 2695 4.193090 TCTAGGAGAGAAGTGATGACGAC 58.807 47.826 0.00 0.00 0.00 4.34
2517 2755 1.303236 TTGTTGATGGCCAGGTCGG 60.303 57.895 13.05 0.00 38.11 4.79
2546 2784 2.748605 CCCTATCTCATGAGCGTGTTC 58.251 52.381 18.36 0.00 0.00 3.18
2586 2824 7.271539 CGTATATCTCGTTCCAAAAACATACG 58.728 38.462 0.00 0.00 33.88 3.06
2624 2862 1.339055 ACATTAGTGTGCGGCTGTGAT 60.339 47.619 0.00 0.00 37.14 3.06
2627 2865 2.557059 TAGTGTGCGGCTGTGATCGG 62.557 60.000 0.00 0.00 0.00 4.18
2663 2901 4.171005 TCTCGTATCGTGTTCACCATTTC 58.829 43.478 0.00 0.00 0.00 2.17
2670 2908 2.218603 GTGTTCACCATTTCCACGTCT 58.781 47.619 0.00 0.00 0.00 4.18
2712 2950 1.333308 TGCAAATTGAGTCACACACGG 59.667 47.619 0.00 0.00 0.00 4.94
2769 3007 2.034254 GTCTTGCGATGATGTGTGATCG 60.034 50.000 0.00 0.00 43.14 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.609610 TGTTTCCCCTCCCTCGGG 60.610 66.667 0.00 0.00 44.27 5.14
43 44 2.507058 TCCTTCATTGTCCCTGATCCTG 59.493 50.000 0.00 0.00 0.00 3.86
52 53 2.102578 CATGGGGTTCCTTCATTGTCC 58.897 52.381 0.00 0.00 0.00 4.02
71 72 9.762933 GATCTTTTTAATGGCCAAATATTAGCA 57.237 29.630 10.96 0.00 0.00 3.49
79 80 8.359875 TCACTATGATCTTTTTAATGGCCAAA 57.640 30.769 10.96 0.00 0.00 3.28
115 116 1.006571 CCGGTGACTACGTTGCTGT 60.007 57.895 0.00 0.00 0.00 4.40
134 135 1.337635 CGCCTCATCATAGAGCTTCCC 60.338 57.143 0.00 0.00 34.26 3.97
150 151 0.460284 CTAAATCCGCTCACACGCCT 60.460 55.000 0.00 0.00 0.00 5.52
174 175 4.494484 CTCGATGAGTACAACCACATTCA 58.506 43.478 0.00 0.00 0.00 2.57
274 275 1.194781 TCTCAACCTCTCCACTGGCC 61.195 60.000 0.00 0.00 0.00 5.36
376 377 2.262915 GCATCGATCCGCTAGGGG 59.737 66.667 19.63 19.63 38.33 4.79
394 395 4.332637 GCACTTGGCGGCAGTGTG 62.333 66.667 29.29 29.29 43.21 3.82
416 417 4.148825 ATCCGCCTCCGTGCTGTC 62.149 66.667 0.00 0.00 0.00 3.51
467 468 1.227380 GCCGATTGGACTGATCGCT 60.227 57.895 1.98 0.00 43.67 4.93
475 476 2.591715 CGATGGGGCCGATTGGAC 60.592 66.667 1.98 0.00 45.75 4.02
476 477 3.872603 CCGATGGGGCCGATTGGA 61.873 66.667 26.42 0.00 37.49 3.53
485 486 1.521681 GCGAGTCTTTCCGATGGGG 60.522 63.158 0.00 0.00 37.02 4.96
539 540 9.874205 TGGTTCCAATGAAATTTATCTGATTTC 57.126 29.630 0.00 3.33 41.59 2.17
546 547 6.616947 TCACGTGGTTCCAATGAAATTTATC 58.383 36.000 17.00 0.00 31.22 1.75
560 561 2.635444 CATCGTTTGTTCACGTGGTTC 58.365 47.619 17.00 7.12 41.16 3.62
562 563 0.306533 GCATCGTTTGTTCACGTGGT 59.693 50.000 17.00 0.00 41.16 4.16
564 565 1.385038 GTGCATCGTTTGTTCACGTG 58.615 50.000 9.94 9.94 41.16 4.49
565 566 0.042535 CGTGCATCGTTTGTTCACGT 60.043 50.000 5.09 0.00 43.58 4.49
566 567 2.683136 CGTGCATCGTTTGTTCACG 58.317 52.632 0.00 0.00 43.19 4.35
576 577 0.301687 GCTGAATGGTACGTGCATCG 59.698 55.000 5.86 7.07 46.00 3.84
577 578 0.657840 GGCTGAATGGTACGTGCATC 59.342 55.000 5.86 1.29 0.00 3.91
578 579 1.089481 CGGCTGAATGGTACGTGCAT 61.089 55.000 5.86 0.00 0.00 3.96
579 580 1.739929 CGGCTGAATGGTACGTGCA 60.740 57.895 5.86 0.00 0.00 4.57
580 581 0.458889 TACGGCTGAATGGTACGTGC 60.459 55.000 0.00 0.00 38.34 5.34
581 582 1.556564 CTACGGCTGAATGGTACGTG 58.443 55.000 0.00 0.00 38.34 4.49
672 673 4.527157 CCTCGCCCGTACGACGAC 62.527 72.222 23.37 7.72 46.05 4.34
682 683 2.438434 CAACCATCACCCTCGCCC 60.438 66.667 0.00 0.00 0.00 6.13
686 687 2.043953 GCCCCAACCATCACCCTC 60.044 66.667 0.00 0.00 0.00 4.30
687 688 4.047125 CGCCCCAACCATCACCCT 62.047 66.667 0.00 0.00 0.00 4.34
778 779 4.899239 GCACTCGGATGGCGGAGG 62.899 72.222 0.00 0.00 43.52 4.30
808 809 1.269958 GAACTTACACTACCCCCGGT 58.730 55.000 0.00 0.00 40.16 5.28
825 826 0.396435 ATCGCAGAACACACAGGGAA 59.604 50.000 0.00 0.00 43.58 3.97
831 832 0.164647 GCACAGATCGCAGAACACAC 59.835 55.000 0.00 0.00 43.58 3.82
836 837 2.073117 TAAACGCACAGATCGCAGAA 57.927 45.000 0.00 0.00 43.58 3.02
839 840 2.220824 GCATATAAACGCACAGATCGCA 59.779 45.455 0.00 0.00 0.00 5.10
869 870 5.943416 TCGGCCTTCTTATTTTTGAGATTCA 59.057 36.000 0.00 0.00 0.00 2.57
919 920 2.203070 GGCCTGGTGCTGGATACG 60.203 66.667 0.00 0.00 40.92 3.06
926 928 1.427072 AACCTACTTGGCCTGGTGCT 61.427 55.000 3.32 0.00 40.92 4.40
931 933 3.369576 GGACTCTAAACCTACTTGGCCTG 60.370 52.174 3.32 0.00 40.22 4.85
936 938 3.251571 GCACGGACTCTAAACCTACTTG 58.748 50.000 0.00 0.00 0.00 3.16
937 939 2.233186 GGCACGGACTCTAAACCTACTT 59.767 50.000 0.00 0.00 0.00 2.24
965 1157 3.591835 CGTGGGTGGGTGCAACAC 61.592 66.667 3.06 9.28 44.11 3.32
984 1176 6.310224 GCATATATATACACATGCACACACGA 59.690 38.462 15.74 0.00 42.61 4.35
993 1185 9.316730 TGCTGTATGTGCATATATATACACATG 57.683 33.333 33.29 24.01 45.46 3.21
996 1188 7.488150 ACGTGCTGTATGTGCATATATATACAC 59.512 37.037 16.29 16.29 42.69 2.90
998 1190 7.097006 CGACGTGCTGTATGTGCATATATATAC 60.097 40.741 6.43 5.78 42.69 1.47
1006 1202 1.695893 GCGACGTGCTGTATGTGCAT 61.696 55.000 0.00 0.00 42.69 3.96
1007 1203 2.379634 GCGACGTGCTGTATGTGCA 61.380 57.895 0.00 0.00 41.73 4.57
1008 1204 2.395690 GCGACGTGCTGTATGTGC 59.604 61.111 0.00 0.00 41.73 4.57
1021 1217 1.562575 CCTGGTACCACAAACGCGAC 61.563 60.000 15.93 0.00 0.00 5.19
1027 1223 1.228003 CACGGCCTGGTACCACAAA 60.228 57.895 11.60 0.00 0.00 2.83
1029 1225 2.524640 TCACGGCCTGGTACCACA 60.525 61.111 11.60 0.00 0.00 4.17
1030 1226 1.614241 ATCTCACGGCCTGGTACCAC 61.614 60.000 11.60 1.57 0.00 4.16
1032 1228 1.442148 GATCTCACGGCCTGGTACC 59.558 63.158 4.43 4.43 0.00 3.34
1059 1255 3.365265 CCTGGCGGTGTTGGCTTC 61.365 66.667 0.00 0.00 35.06 3.86
1128 1336 2.409651 GTAGCCGCTCTCTCCGTG 59.590 66.667 0.00 0.00 0.00 4.94
1401 1609 1.069204 CTCATAGGGCACGCTGTATGT 59.931 52.381 0.00 0.00 0.00 2.29
1402 1610 1.341209 TCTCATAGGGCACGCTGTATG 59.659 52.381 0.00 5.37 0.00 2.39
1503 1711 4.787598 CACAGGCAAGTGTCATTTAGTTC 58.212 43.478 2.37 0.00 34.83 3.01
1518 1726 0.678950 TTCACGATGAGACACAGGCA 59.321 50.000 0.00 0.00 0.00 4.75
1527 1735 3.452474 GGAACTGATCCTTCACGATGAG 58.548 50.000 0.00 0.00 45.56 2.90
1578 1786 1.673009 CCACGCCCACACGGTATTT 60.673 57.895 0.00 0.00 37.37 1.40
1580 1788 2.998480 TCCACGCCCACACGGTAT 60.998 61.111 0.00 0.00 37.37 2.73
1656 1864 2.186903 CGGAGCGTACCTGCCATT 59.813 61.111 0.00 0.00 34.65 3.16
1669 1877 2.352001 CGTATGTCGTCGGCGGAG 60.352 66.667 10.62 0.91 38.89 4.63
1675 1883 1.866059 TCTTGCGCGTATGTCGTCG 60.866 57.895 8.43 0.00 42.13 5.12
1683 1891 2.126071 GGAGCTGTCTTGCGCGTA 60.126 61.111 8.43 0.00 38.13 4.42
1687 1895 1.153667 GAGGAGGAGCTGTCTTGCG 60.154 63.158 0.00 0.00 38.13 4.85
1706 1914 2.405172 CACCGCTCATCATCATCTGAG 58.595 52.381 0.00 0.00 41.47 3.35
1707 1915 1.539712 GCACCGCTCATCATCATCTGA 60.540 52.381 0.00 0.00 38.53 3.27
1708 1916 0.866427 GCACCGCTCATCATCATCTG 59.134 55.000 0.00 0.00 0.00 2.90
1709 1917 0.250209 GGCACCGCTCATCATCATCT 60.250 55.000 0.00 0.00 0.00 2.90
1710 1918 1.233285 GGGCACCGCTCATCATCATC 61.233 60.000 0.00 0.00 40.86 2.92
1711 1919 1.228063 GGGCACCGCTCATCATCAT 60.228 57.895 0.00 0.00 40.86 2.45
1712 1920 2.190313 GGGCACCGCTCATCATCA 59.810 61.111 0.00 0.00 40.86 3.07
1753 1961 2.413837 CGCATGCATCTGATGATCTGA 58.586 47.619 21.30 4.47 0.00 3.27
1754 1962 1.464997 CCGCATGCATCTGATGATCTG 59.535 52.381 21.30 14.10 0.00 2.90
1755 1963 1.809684 CCGCATGCATCTGATGATCT 58.190 50.000 21.30 1.84 0.00 2.75
1756 1964 0.168348 GCCGCATGCATCTGATGATC 59.832 55.000 21.30 5.16 40.77 2.92
1757 1965 1.574702 CGCCGCATGCATCTGATGAT 61.575 55.000 21.30 8.90 41.33 2.45
1758 1966 2.248835 CGCCGCATGCATCTGATGA 61.249 57.895 21.30 7.00 41.33 2.92
1759 1967 2.171489 CTCGCCGCATGCATCTGATG 62.171 60.000 19.57 13.26 41.33 3.07
1760 1968 1.959738 CTCGCCGCATGCATCTGAT 60.960 57.895 19.57 0.00 41.33 2.90
1784 1992 6.550108 AGCTTATTACGAGTAGATTCCTTCCA 59.450 38.462 0.00 0.00 0.00 3.53
1787 1995 7.707035 CACAAGCTTATTACGAGTAGATTCCTT 59.293 37.037 0.00 0.00 0.00 3.36
1790 1998 7.988904 ACACAAGCTTATTACGAGTAGATTC 57.011 36.000 0.00 0.00 0.00 2.52
1838 2048 1.135972 ACACATGCACGATCGAAAAGC 60.136 47.619 24.34 18.91 0.00 3.51
1840 2050 1.125930 CGACACATGCACGATCGAAAA 59.874 47.619 24.34 6.47 34.77 2.29
1841 2051 0.713329 CGACACATGCACGATCGAAA 59.287 50.000 24.34 6.87 34.77 3.46
1842 2052 1.075979 CCGACACATGCACGATCGAA 61.076 55.000 24.34 7.26 34.77 3.71
1843 2053 1.516169 CCGACACATGCACGATCGA 60.516 57.895 24.34 0.00 34.77 3.59
1844 2054 2.997869 CCGACACATGCACGATCG 59.002 61.111 14.88 14.88 0.00 3.69
1845 2055 1.361668 AAGCCGACACATGCACGATC 61.362 55.000 8.04 0.00 0.00 3.69
1846 2056 1.375908 AAGCCGACACATGCACGAT 60.376 52.632 8.04 0.00 0.00 3.73
1847 2057 2.030412 AAGCCGACACATGCACGA 59.970 55.556 8.04 0.00 0.00 4.35
1848 2058 2.174107 CAAGCCGACACATGCACG 59.826 61.111 0.00 0.00 0.00 5.34
1849 2059 2.126734 GCAAGCCGACACATGCAC 60.127 61.111 0.00 0.00 38.63 4.57
1850 2060 2.594013 TGCAAGCCGACACATGCA 60.594 55.556 0.00 0.00 45.75 3.96
1851 2061 1.515519 CATGCAAGCCGACACATGC 60.516 57.895 0.00 0.00 39.22 4.06
1852 2062 1.515519 GCATGCAAGCCGACACATG 60.516 57.895 14.21 0.00 42.20 3.21
1853 2063 2.703798 GGCATGCAAGCCGACACAT 61.704 57.895 18.44 0.00 46.12 3.21
1885 2095 1.891150 AGCACCCAAGCAGAATTCAAG 59.109 47.619 8.44 0.69 36.85 3.02
1927 2137 2.232208 CGGTCCTAAACCTTACTCCGTT 59.768 50.000 0.00 0.00 46.87 4.44
1946 2156 3.235195 CGTCTTGACTACTCAAACTCGG 58.765 50.000 0.00 0.00 35.92 4.63
1958 2168 1.060713 CGCGATCAAACGTCTTGACT 58.939 50.000 0.00 5.67 35.59 3.41
2004 2239 3.191078 AGAGGCATGCATCTCAAGTAC 57.809 47.619 28.17 1.94 30.72 2.73
2005 2240 3.243535 CGTAGAGGCATGCATCTCAAGTA 60.244 47.826 35.70 17.35 38.16 2.24
2006 2241 2.482664 CGTAGAGGCATGCATCTCAAGT 60.483 50.000 35.70 16.48 38.16 3.16
2048 2283 0.179158 AAAACAACGCACGTGAACCC 60.179 50.000 22.23 0.00 0.00 4.11
2053 2288 0.565679 GCAGAAAAACAACGCACGTG 59.434 50.000 12.28 12.28 0.00 4.49
2055 2290 1.263776 TTGCAGAAAAACAACGCACG 58.736 45.000 0.00 0.00 31.10 5.34
2116 2352 5.704053 AGTGGCGCTGTAAAACTATTTTAGT 59.296 36.000 7.64 0.00 41.73 2.24
2118 2354 5.933790 CAGTGGCGCTGTAAAACTATTTTA 58.066 37.500 19.69 0.00 40.27 1.52
2155 2391 0.378257 ATCATTGTTGACCGCATCGC 59.622 50.000 0.00 0.00 33.85 4.58
2158 2394 3.257873 TGGAAAATCATTGTTGACCGCAT 59.742 39.130 0.00 0.00 33.85 4.73
2159 2395 2.625314 TGGAAAATCATTGTTGACCGCA 59.375 40.909 0.00 0.00 33.85 5.69
2164 2400 5.331906 TGGGATCTGGAAAATCATTGTTGA 58.668 37.500 0.00 0.00 36.00 3.18
2170 2406 6.466812 GTGTTTTTGGGATCTGGAAAATCAT 58.533 36.000 0.00 0.00 0.00 2.45
2171 2407 5.508825 CGTGTTTTTGGGATCTGGAAAATCA 60.509 40.000 0.00 0.00 0.00 2.57
2172 2408 4.923281 CGTGTTTTTGGGATCTGGAAAATC 59.077 41.667 0.00 0.00 0.00 2.17
2179 2416 0.729140 GCGCGTGTTTTTGGGATCTG 60.729 55.000 8.43 0.00 0.00 2.90
2180 2417 1.579429 GCGCGTGTTTTTGGGATCT 59.421 52.632 8.43 0.00 0.00 2.75
2182 2419 1.739338 TTGGCGCGTGTTTTTGGGAT 61.739 50.000 8.43 0.00 0.00 3.85
2183 2420 1.945354 TTTGGCGCGTGTTTTTGGGA 61.945 50.000 8.43 0.00 0.00 4.37
2209 2447 2.228582 ACGCTTCATAATTTGCACTGCA 59.771 40.909 0.00 0.00 36.47 4.41
2236 2474 1.288752 CAAATGTTGGTGGCCGGAC 59.711 57.895 5.05 0.56 0.00 4.79
2243 2481 1.550659 GCACGCTGCAAATGTTGGTG 61.551 55.000 0.00 0.00 44.26 4.17
2244 2482 1.300080 GCACGCTGCAAATGTTGGT 60.300 52.632 0.00 0.00 44.26 3.67
2298 2536 2.202298 GCAAAATAGTGCGCGCGT 60.202 55.556 32.35 18.96 34.21 6.01
2335 2573 2.561373 GTCCTTTTTGAGCGCCGG 59.439 61.111 2.29 0.00 0.00 6.13
2355 2593 0.512952 ACTGCTTCGCGTGCTAAAAG 59.487 50.000 22.18 12.22 0.00 2.27
2363 2601 1.358759 CCCAAAAACTGCTTCGCGT 59.641 52.632 5.77 0.00 0.00 6.01
2364 2602 2.016165 GCCCAAAAACTGCTTCGCG 61.016 57.895 0.00 0.00 0.00 5.87
2365 2603 2.016165 CGCCCAAAAACTGCTTCGC 61.016 57.895 0.00 0.00 0.00 4.70
2371 2609 0.875474 CAACAGGCGCCCAAAAACTG 60.875 55.000 26.15 15.88 35.40 3.16
2387 2625 4.462483 TGACCCATTAAAAGCATCTCCAAC 59.538 41.667 0.00 0.00 0.00 3.77
2410 2648 3.190079 CGACTCCGACATCATTGTTGAT 58.810 45.455 1.79 0.00 39.29 2.57
2413 2651 1.359848 GCGACTCCGACATCATTGTT 58.640 50.000 0.00 0.00 35.79 2.83
2415 2653 2.301505 GGCGACTCCGACATCATTG 58.698 57.895 0.00 0.00 44.91 2.82
2474 2712 0.118346 ACATACACCCCTGACCCTGA 59.882 55.000 0.00 0.00 0.00 3.86
2475 2713 0.253044 CACATACACCCCTGACCCTG 59.747 60.000 0.00 0.00 0.00 4.45
2476 2714 0.914417 CCACATACACCCCTGACCCT 60.914 60.000 0.00 0.00 0.00 4.34
2477 2715 1.607612 CCACATACACCCCTGACCC 59.392 63.158 0.00 0.00 0.00 4.46
2478 2716 1.205460 ACCCACATACACCCCTGACC 61.205 60.000 0.00 0.00 0.00 4.02
2479 2717 0.252197 GACCCACATACACCCCTGAC 59.748 60.000 0.00 0.00 0.00 3.51
2517 2755 2.568956 TCATGAGATAGGGCATACTGGC 59.431 50.000 0.00 0.00 42.88 4.85
2546 2784 7.094890 ACGAGATATACGGGTGAATACTGTTAG 60.095 40.741 0.00 0.00 34.93 2.34
2616 2854 2.554032 CCCATATTTTCCGATCACAGCC 59.446 50.000 0.00 0.00 0.00 4.85
2619 2857 3.136443 AGAGCCCATATTTTCCGATCACA 59.864 43.478 0.00 0.00 0.00 3.58
2624 2862 2.035961 CGAGAGAGCCCATATTTTCCGA 59.964 50.000 0.00 0.00 0.00 4.55
2627 2865 4.859798 CGATACGAGAGAGCCCATATTTTC 59.140 45.833 0.00 0.00 0.00 2.29
2663 2901 4.092968 GGAAACAAGTAGCATAAGACGTGG 59.907 45.833 0.00 0.00 30.45 4.94
2670 2908 5.642063 GCACTAGTGGAAACAAGTAGCATAA 59.358 40.000 23.95 0.00 46.06 1.90
2712 2950 8.999431 TCTCCATATGCGATAAGGATTTTTAAC 58.001 33.333 0.00 0.00 32.70 2.01
2769 3007 2.658285 TCTTAAGCGAAGACGTGTGAC 58.342 47.619 0.00 0.00 39.36 3.67


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

AutoCloner maintained by Alex Coulton.