Multiple sequence alignment - TraesCS3D01G324200

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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 TraesCS3D01G324200 chr3D 100.000 2808 0 0 1 2808 437474511 437477318 0.000000e+00 5186.0
1 TraesCS3D01G324200 chr3A 95.262 1984 78 10 1 1974 575483541 575485518 0.000000e+00 3129.0
2 TraesCS3D01G324200 chr3A 92.537 804 57 3 2007 2808 575485519 575486321 0.000000e+00 1149.0
3 TraesCS3D01G324200 chr3B 92.130 2033 111 23 1 1998 572678198 572680216 0.000000e+00 2822.0
4 TraesCS3D01G324200 chr4D 92.483 439 25 5 2313 2748 123299948 123300381 3.070000e-174 621.0
5 TraesCS3D01G324200 chrUn 92.255 439 26 5 2313 2748 36545921 36546354 1.430000e-172 616.0
6 TraesCS3D01G324200 chrUn 92.255 439 26 5 2316 2751 275330201 275329768 1.430000e-172 616.0
7 TraesCS3D01G324200 chr7B 92.255 439 26 5 2313 2748 644467502 644467935 1.430000e-172 616.0
8 TraesCS3D01G324200 chr7A 92.431 436 25 5 2316 2748 60148226 60147796 1.430000e-172 616.0
9 TraesCS3D01G324200 chr7A 92.593 54 2 1 834 887 26030899 26030848 3.000000e-10 76.8
10 TraesCS3D01G324200 chr7A 88.333 60 5 2 820 878 717413053 717412995 1.400000e-08 71.3
11 TraesCS3D01G324200 chr6B 92.255 439 26 5 2316 2751 306995929 306995496 1.430000e-172 616.0
12 TraesCS3D01G324200 chr1D 92.027 439 27 5 2316 2751 141313075 141312642 6.650000e-171 610.0
13 TraesCS3D01G324200 chr1D 85.328 259 36 2 1323 1580 407878354 407878097 1.660000e-67 267.0
14 TraesCS3D01G324200 chr1D 92.308 52 4 0 828 879 141705967 141706018 1.080000e-09 75.0
15 TraesCS3D01G324200 chr1A 92.027 439 27 5 2313 2748 415656100 415656533 6.650000e-171 610.0
16 TraesCS3D01G324200 chr5A 95.833 48 2 0 832 879 490326156 490326109 8.340000e-11 78.7
17 TraesCS3D01G324200 chr5A 95.833 48 2 0 832 879 490416186 490416139 8.340000e-11 78.7
18 TraesCS3D01G324200 chr2D 92.453 53 2 2 827 878 649145955 649145904 1.080000e-09 75.0
19 TraesCS3D01G324200 chr1B 92.308 52 4 0 828 879 195591191 195591242 1.080000e-09 75.0


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 TraesCS3D01G324200 chr3D 437474511 437477318 2807 False 5186 5186 100.0000 1 2808 1 chr3D.!!$F1 2807
1 TraesCS3D01G324200 chr3A 575483541 575486321 2780 False 2139 3129 93.8995 1 2808 2 chr3A.!!$F1 2807
2 TraesCS3D01G324200 chr3B 572678198 572680216 2018 False 2822 2822 92.1300 1 1998 1 chr3B.!!$F1 1997

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
316 321 0.526211 GGAAACGGAGAACATTGGCC 59.474 55.0 0.0 0.0 0.00 5.36 F
1517 1529 0.103208 ATGTCCGAGGCAAGATCGAC 59.897 55.0 0.0 0.0 42.76 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1587 0.319555 GTCGGTTCTGCAGCAGTACA 60.320 55.0 27.63 10.54 34.26 2.90 R
2760 2804 0.375803 ACGTTGTCAAAGGTCGTTGC 59.624 50.0 3.52 0.00 28.30 4.17 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
123 128 5.940470 AGCTAATCAACGGTTCAAAGAATCT 59.060 36.000 0.00 0.00 0.00 2.40
137 142 9.741647 GTTCAAAGAATCTATCCAAATTCCATC 57.258 33.333 0.00 0.00 33.29 3.51
289 294 6.430925 GTCCATGAATAGTGGCAAGCATAATA 59.569 38.462 0.00 0.00 36.66 0.98
290 295 7.003482 TCCATGAATAGTGGCAAGCATAATAA 58.997 34.615 0.00 0.00 36.66 1.40
316 321 0.526211 GGAAACGGAGAACATTGGCC 59.474 55.000 0.00 0.00 0.00 5.36
365 370 0.673985 TGTCCGCTCCGATCCAATAG 59.326 55.000 0.00 0.00 0.00 1.73
503 508 4.344968 AGCAAAAGGTGTAGGCAAAAAGAT 59.655 37.500 0.00 0.00 0.00 2.40
504 509 4.686091 GCAAAAGGTGTAGGCAAAAAGATC 59.314 41.667 0.00 0.00 0.00 2.75
531 536 4.103311 AGAGAGGCAACAGTAAGAGGTTTT 59.897 41.667 0.00 0.00 41.41 2.43
561 566 1.279840 GAGCAGCCGTTGTTGACAC 59.720 57.895 0.00 0.00 0.00 3.67
574 579 3.638484 TGTTGACACGTCTACACATCAG 58.362 45.455 9.86 0.00 39.63 2.90
575 580 3.316868 TGTTGACACGTCTACACATCAGA 59.683 43.478 9.86 0.00 39.63 3.27
577 582 4.096732 TGACACGTCTACACATCAGATG 57.903 45.455 9.03 9.03 35.54 2.90
578 583 3.756434 TGACACGTCTACACATCAGATGA 59.244 43.478 17.81 0.00 33.93 2.92
579 584 4.142600 TGACACGTCTACACATCAGATGAG 60.143 45.833 17.81 11.80 33.93 2.90
580 585 4.010349 ACACGTCTACACATCAGATGAGA 58.990 43.478 17.81 6.79 33.93 3.27
581 586 4.642437 ACACGTCTACACATCAGATGAGAT 59.358 41.667 17.81 4.45 33.93 2.75
656 667 5.022122 TGATTCAGTCTGACTCCTCATTCT 58.978 41.667 15.47 0.00 0.00 2.40
841 852 8.420374 ACCATTCAATCACTAATAAGTACACG 57.580 34.615 0.00 0.00 33.48 4.49
947 958 9.905171 GAATTGATTTTGCCTCTAATAAGATCC 57.095 33.333 0.00 0.00 0.00 3.36
1203 1215 1.119684 TACTCACACACACACCTGCT 58.880 50.000 0.00 0.00 0.00 4.24
1204 1216 0.462581 ACTCACACACACACCTGCTG 60.463 55.000 0.00 0.00 0.00 4.41
1205 1217 1.779025 CTCACACACACACCTGCTGC 61.779 60.000 0.00 0.00 0.00 5.25
1280 1292 0.541863 CCCAAGTCATAGCTTCCGGT 59.458 55.000 0.00 0.00 0.00 5.28
1517 1529 0.103208 ATGTCCGAGGCAAGATCGAC 59.897 55.000 0.00 0.00 42.76 4.20
1575 1587 2.569134 GCTTCGGCTCTGTCGTCT 59.431 61.111 0.00 0.00 38.08 4.18
1577 1589 1.581954 CTTCGGCTCTGTCGTCTGT 59.418 57.895 0.00 0.00 30.45 3.41
1595 1607 1.080772 TACTGCTGCAGAACCGACG 60.081 57.895 34.28 8.18 35.18 5.12
1607 1622 1.852067 AACCGACGCCATGCTTTGAC 61.852 55.000 0.00 0.00 0.00 3.18
1608 1623 2.096406 CGACGCCATGCTTTGACG 59.904 61.111 0.00 0.00 0.00 4.35
1614 1629 2.202388 CATGCTTTGACGCTGGCG 60.202 61.111 13.56 13.56 46.03 5.69
1626 1641 2.185350 CTGGCGGTGCTGAGGTAG 59.815 66.667 0.00 0.00 0.00 3.18
1635 1650 2.496817 CTGAGGTAGCAGCGGTCC 59.503 66.667 0.00 0.00 0.00 4.46
1657 1672 2.106938 GGCTGGCGATGTCGATGA 59.893 61.111 6.60 0.00 43.02 2.92
1661 1676 3.330853 GGCGATGTCGATGACGGC 61.331 66.667 15.42 15.42 44.90 5.68
1682 1697 0.248702 GCATCGTCTCGGGAGAACTC 60.249 60.000 0.00 0.00 39.48 3.01
1728 1743 0.601046 TGCCAGCTTCGTGAACTCTG 60.601 55.000 0.00 0.00 0.00 3.35
1739 1754 4.002982 TCGTGAACTCTGCTGCATAATTT 58.997 39.130 1.31 0.00 0.00 1.82
1742 1757 5.091431 GTGAACTCTGCTGCATAATTTGAC 58.909 41.667 1.31 0.00 0.00 3.18
1779 1794 9.694137 GTACCCAAATACAGTATCAGATAGAAC 57.306 37.037 0.00 0.00 0.00 3.01
1785 1800 5.876651 ACAGTATCAGATAGAACATGGCA 57.123 39.130 0.00 0.00 0.00 4.92
1849 1891 0.389391 AGTGTGGAAGTGAGACACCG 59.611 55.000 0.00 0.00 40.78 4.94
1866 1908 1.009829 CCGTATCAAGGTCTTGCTGC 58.990 55.000 5.88 0.00 40.24 5.25
1929 1971 5.136828 TGTTGTGTTTGTATTGGATGGAGT 58.863 37.500 0.00 0.00 0.00 3.85
1980 2022 1.202452 GCTTTCCAAAGTGCTGCAACT 60.202 47.619 2.77 1.01 38.28 3.16
1988 2030 1.590932 AGTGCTGCAACTGTGAAGAG 58.409 50.000 2.77 0.00 30.87 2.85
1989 2031 1.139654 AGTGCTGCAACTGTGAAGAGA 59.860 47.619 2.77 0.00 30.87 3.10
1990 2032 2.149578 GTGCTGCAACTGTGAAGAGAT 58.850 47.619 2.77 0.00 30.87 2.75
1992 2034 2.224354 TGCTGCAACTGTGAAGAGATGA 60.224 45.455 0.00 0.00 30.87 2.92
1993 2035 2.415857 GCTGCAACTGTGAAGAGATGAG 59.584 50.000 0.00 0.00 30.87 2.90
1994 2036 2.415857 CTGCAACTGTGAAGAGATGAGC 59.584 50.000 0.00 0.00 30.87 4.26
1995 2037 2.038164 TGCAACTGTGAAGAGATGAGCT 59.962 45.455 0.00 0.00 0.00 4.09
1996 2038 3.259123 TGCAACTGTGAAGAGATGAGCTA 59.741 43.478 0.00 0.00 0.00 3.32
1997 2039 4.248859 GCAACTGTGAAGAGATGAGCTAA 58.751 43.478 0.00 0.00 0.00 3.09
1998 2040 4.692625 GCAACTGTGAAGAGATGAGCTAAA 59.307 41.667 0.00 0.00 0.00 1.85
1999 2041 5.390356 GCAACTGTGAAGAGATGAGCTAAAC 60.390 44.000 0.00 0.00 0.00 2.01
2000 2042 5.736951 ACTGTGAAGAGATGAGCTAAACT 57.263 39.130 0.00 0.00 0.00 2.66
2001 2043 6.107901 ACTGTGAAGAGATGAGCTAAACTT 57.892 37.500 0.00 0.00 0.00 2.66
2002 2044 5.931146 ACTGTGAAGAGATGAGCTAAACTTG 59.069 40.000 0.00 0.00 0.00 3.16
2003 2045 5.240891 TGTGAAGAGATGAGCTAAACTTGG 58.759 41.667 0.00 0.00 0.00 3.61
2004 2046 5.221722 TGTGAAGAGATGAGCTAAACTTGGT 60.222 40.000 0.00 0.00 0.00 3.67
2005 2047 5.703130 GTGAAGAGATGAGCTAAACTTGGTT 59.297 40.000 0.00 0.00 0.00 3.67
2054 2096 7.708752 AGAATTGACCGCTGTTTAAAAATTCAA 59.291 29.630 15.09 8.43 35.98 2.69
2080 2122 8.821686 TTGTGTTCTGTAATGGGATAATGATT 57.178 30.769 0.00 0.00 0.00 2.57
2113 2155 6.371548 TGTGTTATCTTCAGTTAGATGCAACC 59.628 38.462 0.00 0.00 36.34 3.77
2238 2281 4.202182 ACTGTCTAAACGTTTACTCCTGCA 60.202 41.667 16.59 8.34 0.00 4.41
2250 2293 6.307800 CGTTTACTCCTGCAAATTTATGTTGG 59.692 38.462 0.00 0.00 0.00 3.77
2256 2299 4.063689 CTGCAAATTTATGTTGGCAACCA 58.936 39.130 26.31 15.17 0.00 3.67
2260 2303 5.412286 GCAAATTTATGTTGGCAACCATCTT 59.588 36.000 26.31 11.29 31.53 2.40
2267 2310 3.444742 TGTTGGCAACCATCTTCATCATC 59.555 43.478 26.31 0.00 31.53 2.92
2307 2350 5.509771 TGAAGAAACATCGTCACACAAATG 58.490 37.500 0.00 0.00 0.00 2.32
2326 2369 1.224722 GGGAGTGCGCTAGCTAATGC 61.225 60.000 13.93 9.29 45.42 3.56
2414 2457 1.689575 GGCCTGAGAGTGATGGGACTA 60.690 57.143 0.00 0.00 0.00 2.59
2434 2477 6.935208 GGACTACTTCTTTAAAGAGCCTTTCA 59.065 38.462 17.05 1.13 36.22 2.69
2441 2484 1.269958 AAAGAGCCTTTCATTGGGGC 58.730 50.000 0.00 0.00 45.57 5.80
2467 2510 4.103153 CAGGTGGAGCCCTAATCTATCAAA 59.897 45.833 0.00 0.00 38.26 2.69
2468 2511 4.103311 AGGTGGAGCCCTAATCTATCAAAC 59.897 45.833 0.00 0.00 38.26 2.93
2506 2549 0.540597 GTCTGCTTTGCTCCCCCTTT 60.541 55.000 0.00 0.00 0.00 3.11
2530 2574 6.635030 TTTAGTGAAGAAAGAAAGAAGGGC 57.365 37.500 0.00 0.00 0.00 5.19
2541 2585 4.316645 AGAAAGAAGGGCGAAGTTTAGAC 58.683 43.478 0.00 0.00 0.00 2.59
2543 2587 1.975680 AGAAGGGCGAAGTTTAGACCA 59.024 47.619 6.90 0.00 38.23 4.02
2563 2607 5.778542 ACCACTCATAGTAGTTCTACCCAT 58.221 41.667 6.39 0.00 0.00 4.00
2583 2627 7.865820 ACCCATAGAAAAGATCATGAAAGAGA 58.134 34.615 0.00 0.00 0.00 3.10
2585 2629 7.042187 CCCATAGAAAAGATCATGAAAGAGACG 60.042 40.741 0.00 0.00 0.00 4.18
2606 2650 3.005897 CGATCAGAATGGTACCCGAATCT 59.994 47.826 10.07 4.79 36.16 2.40
2608 2652 5.620205 CGATCAGAATGGTACCCGAATCTAG 60.620 48.000 10.07 3.69 36.16 2.43
2626 2670 6.793505 ATCTAGTTACAATCCCGAGTTTCT 57.206 37.500 0.00 0.00 0.00 2.52
2628 2672 7.330900 TCTAGTTACAATCCCGAGTTTCTAG 57.669 40.000 0.00 0.00 0.00 2.43
2642 2686 4.632153 AGTTTCTAGACACATCGCACTTT 58.368 39.130 11.48 0.00 0.00 2.66
2643 2687 5.057149 AGTTTCTAGACACATCGCACTTTT 58.943 37.500 11.48 0.00 0.00 2.27
2666 2710 2.268920 GGTCGAGGCTGCCATTCA 59.731 61.111 22.65 0.00 0.00 2.57
2760 2804 7.433708 TTTCACACCATCAACTATTGTACAG 57.566 36.000 0.00 0.00 0.00 2.74
2762 2806 4.694982 CACACCATCAACTATTGTACAGCA 59.305 41.667 0.00 0.00 0.00 4.41
2766 2810 4.629634 CCATCAACTATTGTACAGCAACGA 59.370 41.667 0.00 0.00 40.28 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 295 3.021177 TGTTCTCCGTTTCCCCTTTTT 57.979 42.857 0.00 0.00 0.00 1.94
503 508 3.572682 TCTTACTGTTGCCTCTCTTTCGA 59.427 43.478 0.00 0.00 0.00 3.71
504 509 3.914312 TCTTACTGTTGCCTCTCTTTCG 58.086 45.455 0.00 0.00 0.00 3.46
548 553 0.505655 GTAGACGTGTCAACAACGGC 59.494 55.000 0.00 0.00 34.70 5.68
561 566 5.687770 AGATCTCATCTGATGTGTAGACG 57.312 43.478 16.66 0.00 38.44 4.18
574 579 3.493877 CCGAAGTGCATCAAGATCTCATC 59.506 47.826 0.00 0.00 0.00 2.92
575 580 3.118482 ACCGAAGTGCATCAAGATCTCAT 60.118 43.478 0.00 0.00 0.00 2.90
577 582 2.898705 ACCGAAGTGCATCAAGATCTC 58.101 47.619 0.00 0.00 0.00 2.75
578 583 3.449018 ACTACCGAAGTGCATCAAGATCT 59.551 43.478 0.00 0.00 36.93 2.75
579 584 3.786635 ACTACCGAAGTGCATCAAGATC 58.213 45.455 0.00 0.00 36.93 2.75
580 585 3.449018 AGACTACCGAAGTGCATCAAGAT 59.551 43.478 0.00 0.00 39.07 2.40
581 586 2.826128 AGACTACCGAAGTGCATCAAGA 59.174 45.455 0.00 0.00 39.07 3.02
841 852 8.421673 AAACGTCTTATATTTAGGAACAGAGC 57.578 34.615 0.00 0.00 0.00 4.09
947 958 5.741388 AAAGCTTATTACCGATTCAGCAG 57.259 39.130 0.00 0.00 0.00 4.24
1203 1215 1.594194 GGCCATGATGGAACGTTGCA 61.594 55.000 25.00 25.00 40.96 4.08
1204 1216 1.139520 GGCCATGATGGAACGTTGC 59.860 57.895 17.22 13.47 40.96 4.17
1205 1217 1.429021 CGGCCATGATGGAACGTTG 59.571 57.895 17.22 0.00 40.96 4.10
1280 1292 1.517361 ATGCTCCGCGTGATCTTCA 59.483 52.632 4.92 0.00 0.00 3.02
1304 1316 0.827368 GCTTCCGGAGATTCCTCAGT 59.173 55.000 3.34 0.00 41.20 3.41
1534 1546 2.501610 GCTCCTCTAACGGCAGGG 59.498 66.667 0.00 0.00 0.00 4.45
1544 1556 3.308014 GAAGCTGCACCGCTCCTCT 62.308 63.158 1.02 0.00 39.86 3.69
1575 1587 0.319555 GTCGGTTCTGCAGCAGTACA 60.320 55.000 27.63 10.54 34.26 2.90
1577 1589 1.080772 CGTCGGTTCTGCAGCAGTA 60.081 57.895 22.10 10.23 32.61 2.74
1595 1607 2.180017 CCAGCGTCAAAGCATGGC 59.820 61.111 0.00 0.00 40.15 4.40
1608 1623 4.082523 TACCTCAGCACCGCCAGC 62.083 66.667 0.00 0.00 0.00 4.85
1635 1650 4.899239 GACATCGCCAGCCTCCCG 62.899 72.222 0.00 0.00 0.00 5.14
1644 1659 3.330853 GCCGTCATCGACATCGCC 61.331 66.667 0.00 0.00 39.71 5.54
1649 1664 4.141965 ATGCCGCCGTCATCGACA 62.142 61.111 0.00 0.00 39.71 4.35
1650 1665 3.330853 GATGCCGCCGTCATCGAC 61.331 66.667 0.00 0.00 39.71 4.20
1661 1676 2.771639 TTCTCCCGAGACGATGCCG 61.772 63.158 0.00 0.00 37.14 5.69
1670 1685 1.965219 AACACCGAGTTCTCCCGAG 59.035 57.895 0.00 0.00 34.74 4.63
1682 1697 0.884704 CCACCACTTCAGGAACACCG 60.885 60.000 0.00 0.00 0.00 4.94
1728 1743 4.974591 AGAACTTCGTCAAATTATGCAGC 58.025 39.130 0.00 0.00 0.00 5.25
1739 1754 3.823281 TGGGTACAAAGAACTTCGTCA 57.177 42.857 0.00 0.00 0.00 4.35
1779 1794 4.398358 CAGGCTATATGAAAGGATGCCATG 59.602 45.833 0.00 0.00 41.12 3.66
1785 1800 5.573380 TCAAGCAGGCTATATGAAAGGAT 57.427 39.130 0.00 0.00 0.00 3.24
1849 1891 6.284459 AGTATAAGCAGCAAGACCTTGATAC 58.716 40.000 13.44 10.20 42.93 2.24
1929 1971 5.748670 TGCTGGGTCACACTTACTATTAA 57.251 39.130 0.00 0.00 0.00 1.40
1980 2022 5.221722 ACCAAGTTTAGCTCATCTCTTCACA 60.222 40.000 0.00 0.00 0.00 3.58
1988 2030 5.586643 CCTAAGGAACCAAGTTTAGCTCATC 59.413 44.000 0.00 0.00 0.00 2.92
1989 2031 5.014228 ACCTAAGGAACCAAGTTTAGCTCAT 59.986 40.000 0.00 0.00 0.00 2.90
1990 2032 4.349930 ACCTAAGGAACCAAGTTTAGCTCA 59.650 41.667 0.00 0.00 0.00 4.26
1992 2034 4.995624 ACCTAAGGAACCAAGTTTAGCT 57.004 40.909 0.00 0.00 0.00 3.32
1993 2035 4.217767 CCAACCTAAGGAACCAAGTTTAGC 59.782 45.833 0.00 0.00 0.00 3.09
1994 2036 5.382616 ACCAACCTAAGGAACCAAGTTTAG 58.617 41.667 0.00 0.00 0.00 1.85
1995 2037 5.133153 AGACCAACCTAAGGAACCAAGTTTA 59.867 40.000 0.00 0.00 0.00 2.01
1996 2038 4.079385 AGACCAACCTAAGGAACCAAGTTT 60.079 41.667 0.00 0.00 0.00 2.66
1997 2039 3.462205 AGACCAACCTAAGGAACCAAGTT 59.538 43.478 0.00 0.00 0.00 2.66
1998 2040 3.053826 AGACCAACCTAAGGAACCAAGT 58.946 45.455 0.00 0.00 0.00 3.16
1999 2041 3.790089 AGACCAACCTAAGGAACCAAG 57.210 47.619 0.00 0.00 0.00 3.61
2000 2042 3.720002 AGAAGACCAACCTAAGGAACCAA 59.280 43.478 0.00 0.00 0.00 3.67
2001 2043 3.323775 AGAAGACCAACCTAAGGAACCA 58.676 45.455 0.00 0.00 0.00 3.67
2002 2044 3.583526 AGAGAAGACCAACCTAAGGAACC 59.416 47.826 0.00 0.00 0.00 3.62
2003 2045 4.563786 CCAGAGAAGACCAACCTAAGGAAC 60.564 50.000 0.00 0.00 0.00 3.62
2004 2046 3.583086 CCAGAGAAGACCAACCTAAGGAA 59.417 47.826 0.00 0.00 0.00 3.36
2005 2047 3.173965 CCAGAGAAGACCAACCTAAGGA 58.826 50.000 0.00 0.00 0.00 3.36
2029 2071 7.401484 TGAATTTTTAAACAGCGGTCAATTC 57.599 32.000 9.33 9.33 32.40 2.17
2034 2076 7.062848 CACAATTGAATTTTTAAACAGCGGTC 58.937 34.615 13.59 0.00 0.00 4.79
2038 2080 9.424659 CAGAACACAATTGAATTTTTAAACAGC 57.575 29.630 13.59 0.00 0.00 4.40
2054 2096 9.425248 AATCATTATCCCATTACAGAACACAAT 57.575 29.630 0.00 0.00 0.00 2.71
2105 2147 4.525912 AAAGACATTTCCAGGTTGCATC 57.474 40.909 0.00 0.00 0.00 3.91
2132 2175 3.198635 CCAGAGAGCCAAGTATTCAAGGA 59.801 47.826 0.00 0.00 0.00 3.36
2176 2219 7.072177 TCCTAATTCTGTAACAGCAAAATCG 57.928 36.000 0.00 0.00 0.00 3.34
2203 2246 8.821147 AACGTTTAGACAGTACATGTGATAAA 57.179 30.769 9.11 2.35 44.17 1.40
2204 2247 8.821147 AAACGTTTAGACAGTACATGTGATAA 57.179 30.769 12.83 0.00 44.17 1.75
2238 2281 6.767456 TGAAGATGGTTGCCAACATAAATTT 58.233 32.000 10.18 0.00 36.95 1.82
2250 2293 4.931661 AATGGATGATGAAGATGGTTGC 57.068 40.909 0.00 0.00 0.00 4.17
2260 2303 9.411189 TCATCAAGACATTTAAATGGATGATGA 57.589 29.630 35.89 35.89 46.63 2.92
2267 2310 9.695526 TGTTTCTTCATCAAGACATTTAAATGG 57.304 29.630 27.43 12.92 38.44 3.16
2281 2324 4.376146 TGTGTGACGATGTTTCTTCATCA 58.624 39.130 0.00 0.00 42.82 3.07
2284 2327 5.505489 CCATTTGTGTGACGATGTTTCTTCA 60.505 40.000 0.00 0.00 0.00 3.02
2307 2350 1.224722 GCATTAGCTAGCGCACTCCC 61.225 60.000 11.47 0.00 39.10 4.30
2352 2395 1.202867 GGGGCTCTCTCCAATCATTCC 60.203 57.143 0.00 0.00 0.00 3.01
2399 2442 5.669164 AAAGAAGTAGTCCCATCACTCTC 57.331 43.478 0.00 0.00 0.00 3.20
2414 2457 6.015095 CCCAATGAAAGGCTCTTTAAAGAAGT 60.015 38.462 18.25 3.92 34.03 3.01
2451 2494 4.349342 CCCTCAGTTTGATAGATTAGGGCT 59.651 45.833 0.00 0.00 36.30 5.19
2455 2498 6.166984 TGCTCCCTCAGTTTGATAGATTAG 57.833 41.667 0.00 0.00 0.00 1.73
2457 2500 5.441718 TTGCTCCCTCAGTTTGATAGATT 57.558 39.130 0.00 0.00 0.00 2.40
2490 2533 3.238987 AAAAAGGGGGAGCAAAGCA 57.761 47.368 0.00 0.00 0.00 3.91
2506 2549 6.238648 CGCCCTTCTTTCTTTCTTCACTAAAA 60.239 38.462 0.00 0.00 0.00 1.52
2511 2554 3.139077 TCGCCCTTCTTTCTTTCTTCAC 58.861 45.455 0.00 0.00 0.00 3.18
2512 2555 3.485463 TCGCCCTTCTTTCTTTCTTCA 57.515 42.857 0.00 0.00 0.00 3.02
2520 2564 3.436015 GGTCTAAACTTCGCCCTTCTTTC 59.564 47.826 0.00 0.00 0.00 2.62
2527 2571 1.001633 TGAGTGGTCTAAACTTCGCCC 59.998 52.381 0.00 0.00 0.00 6.13
2530 2574 7.086230 ACTACTATGAGTGGTCTAAACTTCG 57.914 40.000 0.00 0.00 34.71 3.79
2541 2585 7.232188 TCTATGGGTAGAACTACTATGAGTGG 58.768 42.308 11.04 0.00 34.06 4.00
2543 2587 9.710818 TTTTCTATGGGTAGAACTACTATGAGT 57.289 33.333 11.04 0.00 44.47 3.41
2563 2607 8.470002 TGATCGTCTCTTTCATGATCTTTTCTA 58.530 33.333 0.00 0.00 37.25 2.10
2606 2650 6.660521 TGTCTAGAAACTCGGGATTGTAACTA 59.339 38.462 0.00 0.00 0.00 2.24
2608 2652 5.575995 GTGTCTAGAAACTCGGGATTGTAAC 59.424 44.000 5.75 0.00 0.00 2.50
2663 2707 1.883678 TGATCCATCTGAGGGCTGAA 58.116 50.000 2.89 0.00 0.00 3.02
2666 2710 2.485659 TCTTTGATCCATCTGAGGGCT 58.514 47.619 2.89 0.00 0.00 5.19
2701 2745 3.735746 GTCGAATTCCAAAAACCAGCAAG 59.264 43.478 0.00 0.00 0.00 4.01
2707 2751 5.768317 TCTTGATGTCGAATTCCAAAAACC 58.232 37.500 0.00 0.00 0.00 3.27
2708 2752 6.918022 ACTTCTTGATGTCGAATTCCAAAAAC 59.082 34.615 0.00 0.00 0.00 2.43
2748 2792 4.267349 AGGTCGTTGCTGTACAATAGTT 57.733 40.909 0.00 0.00 41.27 2.24
2760 2804 0.375803 ACGTTGTCAAAGGTCGTTGC 59.624 50.000 3.52 0.00 28.30 4.17
2762 2806 2.286025 GCTTACGTTGTCAAAGGTCGTT 59.714 45.455 0.00 0.00 35.98 3.85
2766 2810 2.634600 TGTGCTTACGTTGTCAAAGGT 58.365 42.857 0.00 0.21 38.01 3.50


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

AutoCloner maintained by Alex Coulton.