Multiple sequence alignment - TraesCS1D01G091300

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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 TraesCS1D01G091300 chr1D 100.000 3896 0 0 1 3896 77393924 77390029 0.000000e+00 7195
1 TraesCS1D01G091300 chr1B 92.166 3255 163 50 682 3896 121011421 121008219 0.000000e+00 4514
2 TraesCS1D01G091300 chr1B 89.574 681 69 2 1 680 512445930 512446609 0.000000e+00 863
3 TraesCS1D01G091300 chr1B 76.453 688 145 15 2 680 305304784 305305463 1.330000e-94 357
4 TraesCS1D01G091300 chr1A 94.654 2806 99 22 1111 3896 108775698 108772924 0.000000e+00 4303
5 TraesCS1D01G091300 chr1A 78.545 275 18 17 732 990 108775987 108775738 4.060000e-30 143
6 TraesCS1D01G091300 chr6B 91.362 683 55 3 1 680 212622775 212623456 0.000000e+00 931
7 TraesCS1D01G091300 chr2D 91.189 681 59 1 1 680 512911719 512912399 0.000000e+00 924
8 TraesCS1D01G091300 chr6D 90.602 681 63 1 1 680 344219443 344220123 0.000000e+00 902
9 TraesCS1D01G091300 chr5A 88.743 684 76 1 1 683 27775907 27775224 0.000000e+00 835
10 TraesCS1D01G091300 chr7A 86.911 764 68 18 1916 2659 477173440 477172689 0.000000e+00 828
11 TraesCS1D01G091300 chr7A 85.127 316 22 9 1593 1899 477182080 477181781 2.280000e-77 300
12 TraesCS1D01G091300 chr5D 91.219 558 48 1 124 680 105092378 105092935 0.000000e+00 758
13 TraesCS1D01G091300 chr5D 90.625 128 12 0 1 128 105068287 105068414 1.860000e-38 171
14 TraesCS1D01G091300 chr6A 88.462 598 66 2 1 597 158915374 158914779 0.000000e+00 719
15 TraesCS1D01G091300 chr4B 76.556 691 146 14 2 683 393408866 393408183 7.960000e-97 364


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 TraesCS1D01G091300 chr1D 77390029 77393924 3895 True 7195 7195 100.0000 1 3896 1 chr1D.!!$R1 3895
1 TraesCS1D01G091300 chr1B 121008219 121011421 3202 True 4514 4514 92.1660 682 3896 1 chr1B.!!$R1 3214
2 TraesCS1D01G091300 chr1B 512445930 512446609 679 False 863 863 89.5740 1 680 1 chr1B.!!$F2 679
3 TraesCS1D01G091300 chr1B 305304784 305305463 679 False 357 357 76.4530 2 680 1 chr1B.!!$F1 678
4 TraesCS1D01G091300 chr1A 108772924 108775987 3063 True 2223 4303 86.5995 732 3896 2 chr1A.!!$R1 3164
5 TraesCS1D01G091300 chr6B 212622775 212623456 681 False 931 931 91.3620 1 680 1 chr6B.!!$F1 679
6 TraesCS1D01G091300 chr2D 512911719 512912399 680 False 924 924 91.1890 1 680 1 chr2D.!!$F1 679
7 TraesCS1D01G091300 chr6D 344219443 344220123 680 False 902 902 90.6020 1 680 1 chr6D.!!$F1 679
8 TraesCS1D01G091300 chr5A 27775224 27775907 683 True 835 835 88.7430 1 683 1 chr5A.!!$R1 682
9 TraesCS1D01G091300 chr7A 477172689 477173440 751 True 828 828 86.9110 1916 2659 1 chr7A.!!$R1 743
10 TraesCS1D01G091300 chr5D 105092378 105092935 557 False 758 758 91.2190 124 680 1 chr5D.!!$F2 556
11 TraesCS1D01G091300 chr6A 158914779 158915374 595 True 719 719 88.4620 1 597 1 chr6A.!!$R1 596
12 TraesCS1D01G091300 chr4B 393408183 393408866 683 True 364 364 76.5560 2 683 1 chr4B.!!$R1 681

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
563 567 1.229984 AGGAGGCCCAGCTTTAGGT 60.230 57.895 0.00 0.00 33.88 3.08 F
1105 1134 0.322546 ATTCGTTTCAGGTCTGGGGC 60.323 55.000 0.00 0.00 0.00 5.80 F
1390 1433 1.162698 GCTTCAGAGTCTGCATGCAA 58.837 50.000 22.88 10.06 0.00 4.08 F
1926 1977 1.241990 ACTCTTGCTGCATGTGCTGG 61.242 55.000 14.21 4.55 42.66 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1626 0.750850 GGCCGAAGAGCAGGTACATA 59.249 55.0 0.0 0.0 0.00 2.29 R
2663 2752 0.101219 ACGTCTTTACCCGTATCGCC 59.899 55.0 0.0 0.0 35.16 5.54 R
2840 2929 0.394352 ATCGGTCCATGAACCTTGCC 60.394 55.0 0.0 0.0 37.15 4.52 R
3701 3800 0.179073 AACTTCATCTCCCGATGCCG 60.179 55.0 0.0 0.0 45.32 5.69 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
63 64 1.270550 GTTGACTTCCAGTGGCCAATG 59.729 52.381 26.11 26.11 0.00 2.82
115 116 1.679032 GCGGGGCTTGTTCTCAGTAAT 60.679 52.381 0.00 0.00 0.00 1.89
248 249 3.099141 CCAAATTGTGGTCTATGCCCTT 58.901 45.455 0.00 0.00 43.20 3.95
256 257 2.968574 TGGTCTATGCCCTTTTTGCAAA 59.031 40.909 8.05 8.05 42.92 3.68
271 272 1.294659 GCAAACAGGCCTCAGAGACG 61.295 60.000 0.00 0.00 0.00 4.18
330 331 4.036262 CCGAGTTTGGAATGAAGTTGTCAA 59.964 41.667 0.00 0.00 40.50 3.18
348 351 2.515290 CTGGCTCGGCATGCATGA 60.515 61.111 30.64 15.46 0.00 3.07
355 358 1.746239 CGGCATGCATGACCACTCA 60.746 57.895 30.64 0.00 29.87 3.41
421 424 2.822643 ATTCGGTGGAGGCTGGAGGA 62.823 60.000 0.00 0.00 0.00 3.71
485 488 2.104792 TGGGAAATATGGAAGGAGCGAG 59.895 50.000 0.00 0.00 0.00 5.03
508 512 4.006319 AGCCAGAATCTTTAGCAACACTC 58.994 43.478 0.45 0.00 0.00 3.51
518 522 4.096003 CAACACTCCCGCCCCGAT 62.096 66.667 0.00 0.00 0.00 4.18
543 547 3.495193 CATTGTTGTTGCGAGGATCAAG 58.505 45.455 0.00 0.00 33.17 3.02
563 567 1.229984 AGGAGGCCCAGCTTTAGGT 60.230 57.895 0.00 0.00 33.88 3.08
660 668 7.280428 GGCTTATGTCTAAACCTTCTCCTTAAC 59.720 40.741 0.00 0.00 0.00 2.01
680 688 2.489329 ACCAATGAAATCGGCAAGTCTG 59.511 45.455 0.00 0.00 0.00 3.51
685 693 5.957842 ATGAAATCGGCAAGTCTGTTAAA 57.042 34.783 0.00 0.00 0.00 1.52
706 714 2.470983 AAATGGGCAAAATTGGGTCG 57.529 45.000 0.00 0.00 0.00 4.79
707 715 1.347062 AATGGGCAAAATTGGGTCGT 58.653 45.000 0.00 0.00 0.00 4.34
710 718 1.889829 TGGGCAAAATTGGGTCGTAAG 59.110 47.619 0.00 0.00 0.00 2.34
866 882 4.895297 TCTATTTTTGGGGCATCAGATTCC 59.105 41.667 0.00 0.00 0.00 3.01
978 1007 1.533625 CCTCAATTCCACCTCGCAAA 58.466 50.000 0.00 0.00 0.00 3.68
1000 1029 1.669779 GCAGCACAGGAATCATCTGTC 59.330 52.381 0.00 0.00 42.87 3.51
1001 1030 2.680221 GCAGCACAGGAATCATCTGTCT 60.680 50.000 0.00 0.00 42.87 3.41
1002 1031 2.937149 CAGCACAGGAATCATCTGTCTG 59.063 50.000 0.00 0.00 42.87 3.51
1003 1032 1.669779 GCACAGGAATCATCTGTCTGC 59.330 52.381 0.00 0.00 42.87 4.26
1004 1033 2.938314 GCACAGGAATCATCTGTCTGCA 60.938 50.000 0.00 0.00 42.87 4.41
1054 1083 2.303022 ACGACATGTGAACCTCCATTCT 59.697 45.455 1.15 0.00 0.00 2.40
1105 1134 0.322546 ATTCGTTTCAGGTCTGGGGC 60.323 55.000 0.00 0.00 0.00 5.80
1349 1392 2.362120 AGCAGAAGCCACCATGCC 60.362 61.111 0.00 0.00 43.56 4.40
1352 1395 1.818959 GCAGAAGCCACCATGCCAAA 61.819 55.000 0.00 0.00 32.49 3.28
1364 1407 3.518705 ACCATGCCAAATTTAGCATCCAA 59.481 39.130 19.35 0.00 46.58 3.53
1365 1408 4.019501 ACCATGCCAAATTTAGCATCCAAA 60.020 37.500 19.35 0.00 46.58 3.28
1366 1409 4.942483 CCATGCCAAATTTAGCATCCAAAA 59.058 37.500 19.35 0.00 46.58 2.44
1381 1424 3.679389 TCCAAAATGGAGCTTCAGAGTC 58.321 45.455 0.00 0.00 42.67 3.36
1390 1433 1.162698 GCTTCAGAGTCTGCATGCAA 58.837 50.000 22.88 10.06 0.00 4.08
1393 1436 3.564644 GCTTCAGAGTCTGCATGCAATAT 59.435 43.478 22.88 9.91 0.00 1.28
1394 1437 4.753610 GCTTCAGAGTCTGCATGCAATATA 59.246 41.667 22.88 4.70 0.00 0.86
1399 1442 5.913514 CAGAGTCTGCATGCAATATAAAAGC 59.086 40.000 22.88 4.51 0.00 3.51
1577 1620 2.014857 CAGGAGTTCGTCGTCCTCATA 58.985 52.381 13.27 0.00 41.57 2.15
1583 1626 1.399714 TCGTCGTCCTCATATGCCTT 58.600 50.000 0.00 0.00 0.00 4.35
1613 1656 3.818121 CTTCGGCCCCAACGTCACA 62.818 63.158 0.00 0.00 0.00 3.58
1628 1671 2.757099 ACACGCCGGGTAGGGTAG 60.757 66.667 2.18 0.00 41.48 3.18
1678 1722 3.688673 GTCTGCAGGAGAATTCTTCTTGG 59.311 47.826 14.01 5.18 40.87 3.61
1685 1729 4.764308 AGGAGAATTCTTCTTGGCTTCAAC 59.236 41.667 10.75 0.00 40.87 3.18
1884 1935 2.285069 AGGACGCCCACCCACATA 60.285 61.111 0.00 0.00 33.88 2.29
1915 1966 3.056891 GCTCTTCAGTCAGTACTCTTGCT 60.057 47.826 0.00 0.00 31.97 3.91
1916 1967 4.484236 CTCTTCAGTCAGTACTCTTGCTG 58.516 47.826 0.00 0.00 36.82 4.41
1917 1968 2.732412 TCAGTCAGTACTCTTGCTGC 57.268 50.000 0.00 0.00 35.52 5.25
1918 1969 1.963515 TCAGTCAGTACTCTTGCTGCA 59.036 47.619 0.00 0.00 35.52 4.41
1926 1977 1.241990 ACTCTTGCTGCATGTGCTGG 61.242 55.000 14.21 4.55 42.66 4.85
1996 2052 9.743057 TGTAATTCAAAATAGAACCAAAGTGTG 57.257 29.630 0.00 0.00 0.00 3.82
2092 2154 2.113807 TCTCCATGATCAGATGGGCT 57.886 50.000 14.11 0.00 42.95 5.19
2137 2199 1.531578 GAAAGCAACGACACTTCTCCC 59.468 52.381 0.00 0.00 0.00 4.30
2142 2204 2.671632 GCAACGACACTTCTCCCTAGTC 60.672 54.545 0.00 0.00 0.00 2.59
2145 2207 4.506937 ACGACACTTCTCCCTAGTCTAT 57.493 45.455 0.00 0.00 0.00 1.98
2148 2212 5.125739 ACGACACTTCTCCCTAGTCTATTTG 59.874 44.000 0.00 0.00 0.00 2.32
2153 2217 3.577919 TCTCCCTAGTCTATTTGAGGCC 58.422 50.000 0.00 0.00 0.00 5.19
2159 2223 4.898861 CCTAGTCTATTTGAGGCCTCTTCT 59.101 45.833 32.28 18.48 0.00 2.85
2179 2243 7.000472 TCTTCTCCTCATCAGTTTGTCAAAAT 59.000 34.615 0.00 0.00 0.00 1.82
2180 2244 8.156820 TCTTCTCCTCATCAGTTTGTCAAAATA 58.843 33.333 0.00 0.00 0.00 1.40
2181 2245 7.912056 TCTCCTCATCAGTTTGTCAAAATAG 57.088 36.000 0.00 0.00 0.00 1.73
2184 2248 8.272545 TCCTCATCAGTTTGTCAAAATAGATG 57.727 34.615 20.24 20.24 38.94 2.90
2186 2250 8.733458 CCTCATCAGTTTGTCAAAATAGATGAA 58.267 33.333 24.35 16.13 42.02 2.57
2196 2260 8.175925 TGTCAAAATAGATGAACAATCACCAA 57.824 30.769 0.00 0.00 38.69 3.67
2216 2280 5.475564 ACCAATTGCAAGTTAATCCTACGTT 59.524 36.000 4.94 0.00 0.00 3.99
2223 2289 7.970384 TGCAAGTTAATCCTACGTTTTATGAG 58.030 34.615 0.00 0.00 0.00 2.90
2229 2296 8.601476 GTTAATCCTACGTTTTATGAGAAGGTG 58.399 37.037 0.00 0.00 0.00 4.00
2232 2299 3.134574 ACGTTTTATGAGAAGGTGCCA 57.865 42.857 0.00 0.00 0.00 4.92
2260 2327 7.995289 TGTTATGGCATCATTAGTTAACCTTG 58.005 34.615 1.65 0.00 34.96 3.61
2284 2352 2.642311 TGTTCAGGGCAGATGGAACTTA 59.358 45.455 0.00 0.00 40.12 2.24
2345 2419 7.549488 ACTGCATCTCCAAAGTTTGTATAGTAC 59.451 37.037 14.36 0.00 0.00 2.73
2410 2488 7.064134 TGCATCATCAATTCAAAGAAAGCATTC 59.936 33.333 0.00 0.00 35.70 2.67
2417 2495 7.597369 TCAATTCAAAGAAAGCATTCTCATGTG 59.403 33.333 4.40 2.12 45.19 3.21
2419 2497 4.828939 TCAAAGAAAGCATTCTCATGTGGT 59.171 37.500 4.40 0.00 45.19 4.16
2436 2514 2.032426 GTGGTGTACAAAAACGACCTGG 59.968 50.000 0.00 0.00 0.00 4.45
2449 2527 1.473434 CGACCTGGCTACATTTCCTCC 60.473 57.143 0.00 0.00 0.00 4.30
2578 2667 2.479049 CGATCTTGAATTTGCCAGCCAG 60.479 50.000 0.00 0.00 0.00 4.85
2720 2809 2.964740 TCTTTCTGCATCAAGGTCTCG 58.035 47.619 5.43 0.00 0.00 4.04
2806 2895 3.420606 CAGTGCTGCCAGCGACAG 61.421 66.667 12.80 4.90 46.26 3.51
3315 3411 3.995048 TGACACACGTACACACAGAAAAA 59.005 39.130 0.00 0.00 0.00 1.94
3699 3798 2.693074 GGAAAAGGTTTCTGTTCAGGCA 59.307 45.455 0.00 0.00 38.65 4.75
3700 3799 3.321968 GGAAAAGGTTTCTGTTCAGGCAT 59.678 43.478 0.00 0.00 38.65 4.40
3701 3800 4.550422 GAAAAGGTTTCTGTTCAGGCATC 58.450 43.478 0.00 0.00 37.23 3.91
3702 3801 1.813513 AGGTTTCTGTTCAGGCATCG 58.186 50.000 0.00 0.00 0.00 3.84
3703 3802 0.804989 GGTTTCTGTTCAGGCATCGG 59.195 55.000 0.00 0.00 0.00 4.18
3704 3803 0.169009 GTTTCTGTTCAGGCATCGGC 59.831 55.000 0.00 0.00 40.13 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.619654 CTGAACATTGGCCACTGGAA 58.380 50.000 25.24 10.50 0.00 3.53
115 116 1.391577 TCCACGTTATAGCAGCGGTA 58.608 50.000 0.00 0.00 34.79 4.02
248 249 1.682854 CTCTGAGGCCTGTTTGCAAAA 59.317 47.619 12.00 3.77 0.00 2.44
271 272 2.949705 GAAAGAGGAGATGGGCGGCC 62.950 65.000 23.42 23.42 0.00 6.13
330 331 2.827190 CATGCATGCCGAGCCAGT 60.827 61.111 14.93 0.00 0.00 4.00
348 351 1.003355 CAAGCCATCGGTGAGTGGT 60.003 57.895 0.00 0.00 37.81 4.16
355 358 3.286694 ATGGTGCCAAGCCATCGGT 62.287 57.895 0.00 0.00 42.62 4.69
421 424 1.069049 GCAGTGGCCTTTTTGATGTGT 59.931 47.619 3.32 0.00 0.00 3.72
485 488 4.006319 AGTGTTGCTAAAGATTCTGGCTC 58.994 43.478 7.65 3.52 0.00 4.70
508 512 4.189580 AATGGTGATCGGGGCGGG 62.190 66.667 0.00 0.00 0.00 6.13
543 547 1.529309 CTAAAGCTGGGCCTCCTCC 59.471 63.158 4.53 0.00 0.00 4.30
563 567 2.975799 GTTTCGCTCCCGCCAACA 60.976 61.111 0.00 0.00 31.56 3.33
585 589 5.244785 ACTCTCGCGACATAAGACAAATA 57.755 39.130 3.71 0.00 0.00 1.40
587 591 3.570926 ACTCTCGCGACATAAGACAAA 57.429 42.857 3.71 0.00 0.00 2.83
589 593 3.528532 TCTACTCTCGCGACATAAGACA 58.471 45.455 3.71 0.00 0.00 3.41
660 668 2.489329 ACAGACTTGCCGATTTCATTGG 59.511 45.455 0.00 0.00 36.85 3.16
685 693 3.145286 CGACCCAATTTTGCCCATTTTT 58.855 40.909 0.00 0.00 0.00 1.94
690 698 1.889829 CTTACGACCCAATTTTGCCCA 59.110 47.619 0.00 0.00 0.00 5.36
729 737 2.003301 GTCCTTTCATCTCCTTGTCGC 58.997 52.381 0.00 0.00 0.00 5.19
978 1007 0.917533 AGATGATTCCTGTGCTGCCT 59.082 50.000 0.00 0.00 0.00 4.75
1054 1083 4.518590 CGTCAATGGGGTAATATGCATCAA 59.481 41.667 0.19 0.00 0.00 2.57
1360 1403 3.328931 AGACTCTGAAGCTCCATTTTGGA 59.671 43.478 0.00 0.00 45.98 3.53
1364 1407 2.039480 TGCAGACTCTGAAGCTCCATTT 59.961 45.455 10.45 0.00 32.44 2.32
1365 1408 1.627329 TGCAGACTCTGAAGCTCCATT 59.373 47.619 10.45 0.00 32.44 3.16
1366 1409 1.273759 TGCAGACTCTGAAGCTCCAT 58.726 50.000 10.45 0.00 32.44 3.41
1381 1424 4.600032 TCACGCTTTTATATTGCATGCAG 58.400 39.130 21.50 7.72 0.00 4.41
1399 1442 1.221466 TGAAAGTCGCAAGCCTCACG 61.221 55.000 0.00 0.00 37.18 4.35
1411 1454 1.340248 TGGAGTCCGTGTCTGAAAGTC 59.660 52.381 4.30 0.00 33.76 3.01
1577 1620 3.493350 CGAAGAGCAGGTACATAAGGCAT 60.493 47.826 0.00 0.00 0.00 4.40
1583 1626 0.750850 GGCCGAAGAGCAGGTACATA 59.249 55.000 0.00 0.00 0.00 2.29
1628 1671 1.598701 GGAAGATGTGGCTGGTTGGC 61.599 60.000 0.00 0.00 42.18 4.52
1636 1679 1.452833 GCCAGGAGGAAGATGTGGC 60.453 63.158 0.00 0.00 46.49 5.01
1678 1722 3.188048 CCTCATCAGTGAACTGTTGAAGC 59.812 47.826 19.52 0.00 46.15 3.86
1685 1729 2.775890 ACAAGCCTCATCAGTGAACTG 58.224 47.619 3.98 3.98 45.08 3.16
1699 1743 4.213482 ACGACAAACAAGATAGAACAAGCC 59.787 41.667 0.00 0.00 0.00 4.35
1746 1797 3.544285 CGTCGAAGATGTAGTTGAGCTTC 59.456 47.826 0.00 0.00 40.67 3.86
1884 1935 1.486310 TGACTGAAGAGCTGTGTGGTT 59.514 47.619 0.00 0.00 0.00 3.67
1915 1966 2.438074 TAAAGGGGCCAGCACATGCA 62.438 55.000 4.39 0.00 45.16 3.96
1916 1967 1.044790 ATAAAGGGGCCAGCACATGC 61.045 55.000 4.39 0.00 42.49 4.06
1917 1968 1.488390 AATAAAGGGGCCAGCACATG 58.512 50.000 4.39 0.00 0.00 3.21
1918 1969 2.110578 GAAATAAAGGGGCCAGCACAT 58.889 47.619 4.39 0.00 0.00 3.21
1926 1977 2.760092 TGTGCATGAGAAATAAAGGGGC 59.240 45.455 0.00 0.00 0.00 5.80
1963 2019 9.295825 TGGTTCTATTTTGAATTACACATGACT 57.704 29.630 0.00 0.00 0.00 3.41
1982 2038 5.872617 CGGAACATATCACACTTTGGTTCTA 59.127 40.000 0.00 0.00 34.96 2.10
1996 2052 4.201783 GCAACAAGGTACACGGAACATATC 60.202 45.833 0.00 0.00 0.00 1.63
2004 2060 1.148310 CTCTGCAACAAGGTACACGG 58.852 55.000 0.00 0.00 0.00 4.94
2137 2199 5.010617 GGAGAAGAGGCCTCAAATAGACTAG 59.989 48.000 33.90 0.00 32.48 2.57
2153 2217 5.144692 TGACAAACTGATGAGGAGAAGAG 57.855 43.478 0.00 0.00 0.00 2.85
2159 2223 8.102676 TCATCTATTTTGACAAACTGATGAGGA 58.897 33.333 22.40 13.35 38.13 3.71
2179 2243 6.209192 ACTTGCAATTGGTGATTGTTCATCTA 59.791 34.615 7.72 0.00 45.62 1.98
2180 2244 5.011329 ACTTGCAATTGGTGATTGTTCATCT 59.989 36.000 7.72 0.00 45.62 2.90
2181 2245 5.232463 ACTTGCAATTGGTGATTGTTCATC 58.768 37.500 7.72 0.00 45.62 2.92
2184 2248 7.148590 GGATTAACTTGCAATTGGTGATTGTTC 60.149 37.037 7.72 0.00 45.62 3.18
2186 2250 6.014327 AGGATTAACTTGCAATTGGTGATTGT 60.014 34.615 7.72 0.00 45.62 2.71
2196 2260 8.952278 TCATAAAACGTAGGATTAACTTGCAAT 58.048 29.630 0.00 0.00 0.00 3.56
2216 2280 4.574674 ACAGATGGCACCTTCTCATAAA 57.425 40.909 2.22 0.00 0.00 1.40
2232 2299 8.220559 AGGTTAACTAATGATGCCATAACAGAT 58.779 33.333 5.42 0.00 31.59 2.90
2260 2327 2.424956 GTTCCATCTGCCCTGAACATTC 59.575 50.000 0.00 0.00 37.60 2.67
2284 2352 4.206477 TGCTGTCTGCTGTGTATACATT 57.794 40.909 9.18 0.00 43.37 2.71
2405 2479 4.764679 TTTGTACACCACATGAGAATGC 57.235 40.909 0.00 0.00 36.90 3.56
2410 2488 4.523813 GTCGTTTTTGTACACCACATGAG 58.476 43.478 0.00 0.00 36.90 2.90
2411 2489 3.312973 GGTCGTTTTTGTACACCACATGA 59.687 43.478 0.00 0.00 36.90 3.07
2417 2495 1.002142 GCCAGGTCGTTTTTGTACACC 60.002 52.381 0.00 0.00 0.00 4.16
2419 2497 2.335316 AGCCAGGTCGTTTTTGTACA 57.665 45.000 0.00 0.00 0.00 2.90
2436 2514 3.057734 CGGTATTCGGAGGAAATGTAGC 58.942 50.000 0.00 0.00 35.40 3.58
2449 2527 4.434330 GCTCTCAGTTTTGTTCGGTATTCG 60.434 45.833 0.00 0.00 40.90 3.34
2578 2667 2.960688 AAGGACGCAGGGAAGGAGC 61.961 63.158 0.00 0.00 0.00 4.70
2663 2752 0.101219 ACGTCTTTACCCGTATCGCC 59.899 55.000 0.00 0.00 35.16 5.54
2765 2854 3.047877 GTCAACCTGGCGAACCCG 61.048 66.667 0.00 0.00 35.87 5.28
2794 2883 2.849120 CTTCTCCCTGTCGCTGGCAG 62.849 65.000 10.94 10.94 0.00 4.85
2840 2929 0.394352 ATCGGTCCATGAACCTTGCC 60.394 55.000 0.00 0.00 37.15 4.52
3052 3146 4.750098 TCACAAGTTAGTGCTTTACTGCTC 59.250 41.667 0.00 0.00 40.65 4.26
3217 3311 3.313249 TCATTGTTGACTGTTGTCTGCAG 59.687 43.478 7.63 7.63 43.29 4.41
3467 3566 2.107204 AGAGGCACAGAAACTGGTTCAT 59.893 45.455 8.34 0.00 38.86 2.57
3699 3798 0.319728 CTTCATCTCCCGATGCCGAT 59.680 55.000 0.00 0.00 45.32 4.18
3700 3799 1.043116 ACTTCATCTCCCGATGCCGA 61.043 55.000 0.00 0.00 45.32 5.54
3701 3800 0.179073 AACTTCATCTCCCGATGCCG 60.179 55.000 0.00 0.00 45.32 5.69
3702 3801 1.139853 AGAACTTCATCTCCCGATGCC 59.860 52.381 0.00 0.00 45.32 4.40
3703 3802 2.208431 CAGAACTTCATCTCCCGATGC 58.792 52.381 0.00 0.00 45.32 3.91
3704 3803 2.169352 ACCAGAACTTCATCTCCCGATG 59.831 50.000 0.00 0.00 46.73 3.84


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

AutoCloner maintained by Alex Coulton.