Multiple sequence alignment - TraesCS3D01G515600

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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 TraesCS3D01G515600 chr3D 100.000 2969 0 0 1 2969 599055416 599052448 0.000000e+00 5483
1 TraesCS3D01G515600 chr3D 92.903 775 44 6 1 772 463677707 463676941 0.000000e+00 1116
2 TraesCS3D01G515600 chr3D 92.426 779 38 11 2 768 107064482 107065251 0.000000e+00 1092
3 TraesCS3D01G515600 chr3D 90.379 343 28 3 2172 2511 599005354 599005694 2.100000e-121 446
4 TraesCS3D01G515600 chr3D 86.164 318 22 1 2621 2938 599005692 599005987 1.030000e-84 324
5 TraesCS3D01G515600 chr3D 80.519 231 36 4 1751 1978 288099404 288099628 5.090000e-38 169
6 TraesCS3D01G515600 chr3D 91.667 84 7 0 963 1046 598995727 598995810 1.870000e-22 117
7 TraesCS3D01G515600 chr3A 88.486 2232 149 35 802 2969 729173866 729171679 0.000000e+00 2599
8 TraesCS3D01G515600 chr3B 84.696 1333 120 28 796 2066 806273849 806272539 0.000000e+00 1254
9 TraesCS3D01G515600 chr3B 85.087 1207 112 32 911 2066 807074204 807073015 0.000000e+00 1170
10 TraesCS3D01G515600 chr3B 85.274 292 32 7 2114 2400 807073020 807072735 1.040000e-74 291
11 TraesCS3D01G515600 chr2D 94.057 774 34 7 1 772 77120691 77121454 0.000000e+00 1164
12 TraesCS3D01G515600 chr2D 92.737 771 44 8 1 768 472502222 472501461 0.000000e+00 1103
13 TraesCS3D01G515600 chr2D 92.477 771 45 8 1 768 2911146 2911906 0.000000e+00 1090
14 TraesCS3D01G515600 chr7D 93.686 776 36 8 1 773 89869304 89870069 0.000000e+00 1149
15 TraesCS3D01G515600 chr7D 93.636 770 39 5 1 768 42198915 42198154 0.000000e+00 1142
16 TraesCS3D01G515600 chr5D 93.506 770 39 6 1 768 371016150 371016910 0.000000e+00 1134
17 TraesCS3D01G515600 chr5D 93.238 769 40 7 1 766 407015514 407014755 0.000000e+00 1122
18 TraesCS3D01G515600 chr7A 81.614 669 87 21 1660 2319 688857321 688857962 3.390000e-144 521


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 TraesCS3D01G515600 chr3D 599052448 599055416 2968 True 5483.0 5483 100.0000 1 2969 1 chr3D.!!$R2 2968
1 TraesCS3D01G515600 chr3D 463676941 463677707 766 True 1116.0 1116 92.9030 1 772 1 chr3D.!!$R1 771
2 TraesCS3D01G515600 chr3D 107064482 107065251 769 False 1092.0 1092 92.4260 2 768 1 chr3D.!!$F1 766
3 TraesCS3D01G515600 chr3D 599005354 599005987 633 False 385.0 446 88.2715 2172 2938 2 chr3D.!!$F4 766
4 TraesCS3D01G515600 chr3A 729171679 729173866 2187 True 2599.0 2599 88.4860 802 2969 1 chr3A.!!$R1 2167
5 TraesCS3D01G515600 chr3B 806272539 806273849 1310 True 1254.0 1254 84.6960 796 2066 1 chr3B.!!$R1 1270
6 TraesCS3D01G515600 chr3B 807072735 807074204 1469 True 730.5 1170 85.1805 911 2400 2 chr3B.!!$R2 1489
7 TraesCS3D01G515600 chr2D 77120691 77121454 763 False 1164.0 1164 94.0570 1 772 1 chr2D.!!$F2 771
8 TraesCS3D01G515600 chr2D 472501461 472502222 761 True 1103.0 1103 92.7370 1 768 1 chr2D.!!$R1 767
9 TraesCS3D01G515600 chr2D 2911146 2911906 760 False 1090.0 1090 92.4770 1 768 1 chr2D.!!$F1 767
10 TraesCS3D01G515600 chr7D 89869304 89870069 765 False 1149.0 1149 93.6860 1 773 1 chr7D.!!$F1 772
11 TraesCS3D01G515600 chr7D 42198154 42198915 761 True 1142.0 1142 93.6360 1 768 1 chr7D.!!$R1 767
12 TraesCS3D01G515600 chr5D 371016150 371016910 760 False 1134.0 1134 93.5060 1 768 1 chr5D.!!$F1 767
13 TraesCS3D01G515600 chr5D 407014755 407015514 759 True 1122.0 1122 93.2380 1 766 1 chr5D.!!$R1 765
14 TraesCS3D01G515600 chr7A 688857321 688857962 641 False 521.0 521 81.6140 1660 2319 1 chr7A.!!$F1 659

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
707 728 0.604578 AAAAGCACTGCATGGCGATT 59.395 45.0 3.3 2.1 34.54 3.34 F
1482 1534 0.393132 AGGAGACGCTGTCGATGAGA 60.393 55.0 0.0 0.0 37.67 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1839 0.037232 CACCCTCTTGTTCCCGTCTC 60.037 60.0 0.00 0.0 0.00 3.36 R
2389 2502 0.252057 TCAGCTAGGTGGTGTAGCCA 60.252 55.0 21.22 0.0 43.44 4.75 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
35 36 1.191489 TCAGGTCAAGTGCCGGATGA 61.191 55.000 5.05 0.00 0.00 2.92
111 113 7.060383 TGCCATGATTTGAAAACTTTAGGAA 57.940 32.000 0.00 0.00 0.00 3.36
128 130 4.862641 AGGAATTGCCACCTACTAACAT 57.137 40.909 0.00 0.00 40.02 2.71
197 209 2.484264 CAGGTAAAAAGAGAGTTGCCGG 59.516 50.000 0.00 0.00 34.94 6.13
244 257 1.668628 GCCATGTACCCTGCAAAAACG 60.669 52.381 0.00 0.00 0.00 3.60
289 302 3.462678 GGGAGAGGAGACGGGCAC 61.463 72.222 0.00 0.00 0.00 5.01
473 492 6.756299 AAAAACATGGCAAATGACAACTTT 57.244 29.167 5.69 0.00 36.16 2.66
500 519 1.549950 GGAGAGTGGGAAAATGGGCAA 60.550 52.381 0.00 0.00 0.00 4.52
633 653 2.203001 CCTCACACGCCACACACA 60.203 61.111 0.00 0.00 0.00 3.72
646 666 2.482316 CCACACACACGAGTTGTCCTAA 60.482 50.000 0.00 0.00 35.67 2.69
661 681 6.377146 AGTTGTCCTAAGTGACACACAAAATT 59.623 34.615 8.59 0.00 44.55 1.82
670 690 3.820467 TGACACACAAAATTAGCCCTCTG 59.180 43.478 0.00 0.00 0.00 3.35
691 712 2.468831 GTGCCAAGATTCGTGCAAAAA 58.531 42.857 0.00 0.00 35.16 1.94
707 728 0.604578 AAAAGCACTGCATGGCGATT 59.395 45.000 3.30 2.10 34.54 3.34
720 741 3.499737 CGATTGAGGCGTGTGGGC 61.500 66.667 0.00 0.00 42.69 5.36
800 821 5.177696 TCTCTCTTCGCTAAAAAGAAGCAAC 59.822 40.000 0.76 0.00 42.48 4.17
1033 1085 3.275617 AGGTGCTGAACAAACACTACA 57.724 42.857 0.00 0.00 34.70 2.74
1237 1289 5.005779 CGAATACACAGGTTCTACATCAAGC 59.994 44.000 0.00 0.00 0.00 4.01
1355 1407 4.729918 GGCTGAGGCTGTGGTGGG 62.730 72.222 0.00 0.00 38.73 4.61
1374 1426 0.799393 GCAAGGAGAAGAGGAAACGC 59.201 55.000 0.00 0.00 0.00 4.84
1377 1429 1.374252 GGAGAAGAGGAAACGCGCA 60.374 57.895 5.73 0.00 34.13 6.09
1378 1430 0.949105 GGAGAAGAGGAAACGCGCAA 60.949 55.000 5.73 0.00 34.13 4.85
1380 1432 1.206831 GAAGAGGAAACGCGCAACC 59.793 57.895 5.73 7.02 34.13 3.77
1396 1448 1.749334 AACCGAGGAGATGGGCGATC 61.749 60.000 0.65 0.65 0.00 3.69
1448 1500 1.301716 CCAAGCGGGATATGGACGG 60.302 63.158 0.00 0.00 40.01 4.79
1482 1534 0.393132 AGGAGACGCTGTCGATGAGA 60.393 55.000 0.00 0.00 37.67 3.27
1549 1601 5.869579 TGAACCATTCTTCTTCTACTGCTT 58.130 37.500 0.00 0.00 0.00 3.91
1604 1686 4.021104 ACTCGTGAGATCAATCACTTTCCA 60.021 41.667 11.93 0.00 46.04 3.53
1616 1698 3.596214 TCACTTTCCATAACTCGGAAGC 58.404 45.455 0.00 0.00 43.29 3.86
1620 1702 5.817816 CACTTTCCATAACTCGGAAGCTTAT 59.182 40.000 0.00 0.00 43.29 1.73
1626 1708 7.506114 TCCATAACTCGGAAGCTTATGTTAAT 58.494 34.615 0.00 0.00 31.54 1.40
1627 1709 7.990886 TCCATAACTCGGAAGCTTATGTTAATT 59.009 33.333 0.00 0.00 31.54 1.40
1633 1715 6.353323 TCGGAAGCTTATGTTAATTGGATCA 58.647 36.000 0.00 0.00 0.00 2.92
1642 1724 8.554835 TTATGTTAATTGGATCAAAGACGACA 57.445 30.769 0.00 0.00 0.00 4.35
1644 1726 6.664515 TGTTAATTGGATCAAAGACGACAAC 58.335 36.000 0.00 0.00 0.00 3.32
1678 1772 5.163784 CGGTCAGACATTAACGAGTCTTCTA 60.164 44.000 2.17 0.00 42.87 2.10
1687 1781 6.946229 TTAACGAGTCTTCTAAATCAGTGC 57.054 37.500 0.00 0.00 0.00 4.40
1691 1785 5.416326 ACGAGTCTTCTAAATCAGTGCTAGT 59.584 40.000 0.00 0.00 0.00 2.57
1694 1788 7.475137 AGTCTTCTAAATCAGTGCTAGTTCT 57.525 36.000 0.00 0.00 0.00 3.01
1695 1789 7.902087 AGTCTTCTAAATCAGTGCTAGTTCTT 58.098 34.615 0.00 0.00 0.00 2.52
1696 1790 8.032451 AGTCTTCTAAATCAGTGCTAGTTCTTC 58.968 37.037 0.00 0.00 0.00 2.87
1697 1791 7.276878 GTCTTCTAAATCAGTGCTAGTTCTTCC 59.723 40.741 0.00 0.00 0.00 3.46
1728 1822 3.419793 CTTGACCAAAGCCAGTGGA 57.580 52.632 15.20 0.00 39.62 4.02
1730 1824 0.550914 TTGACCAAAGCCAGTGGACT 59.449 50.000 15.20 6.84 39.62 3.85
1743 1837 1.202698 AGTGGACTTGAGAGTGCCAAC 60.203 52.381 0.00 0.00 42.97 3.77
1745 1839 1.202687 TGGACTTGAGAGTGCCAACAG 60.203 52.381 0.00 0.00 42.97 3.16
1749 1846 2.224161 ACTTGAGAGTGCCAACAGAGAC 60.224 50.000 0.00 0.00 33.99 3.36
1752 1849 1.374758 GAGTGCCAACAGAGACGGG 60.375 63.158 0.00 0.00 0.00 5.28
1755 1852 1.070786 TGCCAACAGAGACGGGAAC 59.929 57.895 0.00 0.00 0.00 3.62
1761 1858 0.969894 ACAGAGACGGGAACAAGAGG 59.030 55.000 0.00 0.00 0.00 3.69
1762 1859 0.247736 CAGAGACGGGAACAAGAGGG 59.752 60.000 0.00 0.00 0.00 4.30
1835 1935 6.433766 CAAATCCTCAGAAGAAACACAAGAC 58.566 40.000 0.00 0.00 0.00 3.01
1865 1965 1.948138 CAGCTGCACGAGATAGCGG 60.948 63.158 0.00 0.00 42.10 5.52
1891 1991 1.610522 CAACAGTTGCAGAAGGGGAAG 59.389 52.381 0.00 0.00 0.00 3.46
1904 2004 2.555664 AGGGGAAGATGAAGCTTCAGA 58.444 47.619 31.14 11.97 44.71 3.27
1905 2005 2.915604 AGGGGAAGATGAAGCTTCAGAA 59.084 45.455 31.14 11.22 44.71 3.02
1906 2006 3.331889 AGGGGAAGATGAAGCTTCAGAAA 59.668 43.478 31.14 10.85 44.71 2.52
1927 2027 7.646922 CAGAAAAAGAGAAGACCAATGTTCTTG 59.353 37.037 0.00 0.00 38.52 3.02
1949 2049 4.162320 TGATTCCCTCTTCCAGTATGACAC 59.838 45.833 0.00 0.00 39.69 3.67
1975 2075 6.400834 CGATGAAAGTGATGACTGAAGACAAG 60.401 42.308 0.00 0.00 30.61 3.16
2035 2142 4.447325 CCCCTGGAACAAGATCATCATCAT 60.447 45.833 0.00 0.00 38.70 2.45
2037 2144 4.451435 CCTGGAACAAGATCATCATCATCG 59.549 45.833 0.00 0.00 38.70 3.84
2039 2146 5.052481 TGGAACAAGATCATCATCATCGTC 58.948 41.667 0.00 0.00 31.92 4.20
2040 2147 5.052481 GGAACAAGATCATCATCATCGTCA 58.948 41.667 0.00 0.00 0.00 4.35
2041 2148 5.699915 GGAACAAGATCATCATCATCGTCAT 59.300 40.000 0.00 0.00 0.00 3.06
2042 2149 6.347483 GGAACAAGATCATCATCATCGTCATG 60.347 42.308 0.00 0.00 0.00 3.07
2043 2150 5.608449 ACAAGATCATCATCATCGTCATGT 58.392 37.500 0.00 0.00 0.00 3.21
2044 2151 6.752168 ACAAGATCATCATCATCGTCATGTA 58.248 36.000 0.00 0.00 0.00 2.29
2045 2152 6.867293 ACAAGATCATCATCATCGTCATGTAG 59.133 38.462 0.00 0.00 0.00 2.74
2046 2153 5.409211 AGATCATCATCATCGTCATGTAGC 58.591 41.667 0.00 0.00 0.00 3.58
2047 2154 4.861102 TCATCATCATCGTCATGTAGCT 57.139 40.909 0.00 0.00 0.00 3.32
2048 2155 4.802999 TCATCATCATCGTCATGTAGCTC 58.197 43.478 0.00 0.00 0.00 4.09
2140 2247 8.911247 AAACAGAGTTGTGTTTGAGATAAAAC 57.089 30.769 6.59 0.00 46.53 2.43
2165 2272 7.379529 ACTTTTAACATTGACAAATTCAGAGCG 59.620 33.333 0.00 0.00 34.94 5.03
2235 2342 5.527214 CAGGTCGGCACATTCAGATTTATTA 59.473 40.000 0.00 0.00 0.00 0.98
2349 2462 1.137675 TGCATGTCTAGGCTGTAGCTG 59.862 52.381 0.00 0.00 41.70 4.24
2389 2502 9.436957 AAGAATTGAGAAAATATCACTACGTGT 57.563 29.630 0.00 0.00 34.79 4.49
2525 2638 0.692476 CACCACCCCAGTCTTGATCA 59.308 55.000 0.00 0.00 0.00 2.92
2536 2649 6.385843 CCCAGTCTTGATCATAAGATAGACG 58.614 44.000 14.33 10.52 41.54 4.18
2548 2661 3.735237 AGATAGACGCGTTCATGGATT 57.265 42.857 15.53 0.00 0.00 3.01
2567 2680 1.154150 GCCTTGATGAGCAACGTGC 60.154 57.895 0.00 0.00 45.46 5.34
2569 2682 1.236616 CCTTGATGAGCAACGTGCCA 61.237 55.000 6.39 5.39 46.52 4.92
2574 2687 1.470098 GATGAGCAACGTGCCATTCTT 59.530 47.619 6.39 0.00 46.52 2.52
2575 2688 0.874390 TGAGCAACGTGCCATTCTTC 59.126 50.000 6.39 0.00 46.52 2.87
2576 2689 1.160137 GAGCAACGTGCCATTCTTCT 58.840 50.000 6.39 0.00 46.52 2.85
2590 2703 4.333095 CCATTCTTCTCTCTCAAGCATGTG 59.667 45.833 0.00 0.00 0.00 3.21
2595 2708 6.800543 TCTTCTCTCTCAAGCATGTGTATAC 58.199 40.000 0.00 0.00 0.00 1.47
2600 2713 2.541346 CTCAAGCATGTGTATACCGCTG 59.459 50.000 0.00 0.00 35.48 5.18
2608 2721 4.394439 TGTGTATACCGCTGCTTCAATA 57.606 40.909 0.00 0.00 0.00 1.90
2620 2733 4.732938 GCTGCTTCAATATCCTTGTTCAGC 60.733 45.833 0.00 0.00 36.81 4.26
2672 2785 0.533308 TGTGTAAAGGTGTGCCGTCC 60.533 55.000 0.00 0.00 40.50 4.79
2847 2960 1.203187 AGACTGTAGAACCCTGAGGCA 60.203 52.381 0.00 0.00 36.11 4.75
2964 3077 1.369091 CGCACATGTTCCACCTAGGC 61.369 60.000 9.30 0.00 37.29 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.811176 GCTGCAGTTGCCCAAAAATGT 60.811 47.619 16.64 0.00 41.18 2.71
111 113 6.070194 ACTGTCTAATGTTAGTAGGTGGCAAT 60.070 38.462 0.00 0.00 32.61 3.56
128 130 3.007940 AGTGCTACATGGCAACTGTCTAA 59.992 43.478 0.00 0.00 44.18 2.10
176 187 2.484264 CCGGCAACTCTCTTTTTACCTG 59.516 50.000 0.00 0.00 0.00 4.00
177 188 2.779506 CCGGCAACTCTCTTTTTACCT 58.220 47.619 0.00 0.00 0.00 3.08
181 192 0.954452 CAGCCGGCAACTCTCTTTTT 59.046 50.000 31.54 0.00 0.00 1.94
244 257 3.184541 CAAAAGCTATCAGTTGCCATGC 58.815 45.455 0.00 0.00 0.00 4.06
385 400 4.287067 AGATGGCAACTCTCTTTTACTCCA 59.713 41.667 0.00 0.00 37.61 3.86
388 404 4.006319 GCAGATGGCAACTCTCTTTTACT 58.994 43.478 0.00 0.00 43.97 2.24
454 472 3.134442 ACCAAAGTTGTCATTTGCCATGT 59.866 39.130 0.00 0.00 36.52 3.21
473 492 0.696143 TTTCCCACTCTCCCACACCA 60.696 55.000 0.00 0.00 0.00 4.17
500 519 0.620410 TTGTCCCCATCTCCCACGAT 60.620 55.000 0.00 0.00 0.00 3.73
519 539 3.732892 CACGCCCCGCACGATTTT 61.733 61.111 0.00 0.00 0.00 1.82
549 569 4.382320 GGGCGTGCGGTGGAACTA 62.382 66.667 0.00 0.00 36.74 2.24
646 666 3.821033 GAGGGCTAATTTTGTGTGTCACT 59.179 43.478 4.27 0.00 35.11 3.41
661 681 0.621571 ATCTTGGCACCAGAGGGCTA 60.622 55.000 0.00 0.00 37.90 3.93
670 690 0.313672 TTTGCACGAATCTTGGCACC 59.686 50.000 0.00 0.00 35.74 5.01
691 712 1.374343 CTCAATCGCCATGCAGTGCT 61.374 55.000 17.60 0.00 0.00 4.40
698 719 2.108514 ACACGCCTCAATCGCCATG 61.109 57.895 0.00 0.00 0.00 3.66
720 741 2.047655 TTAGCCAACTCGCCCACG 60.048 61.111 0.00 0.00 42.01 4.94
721 742 2.388232 CGTTAGCCAACTCGCCCAC 61.388 63.158 0.00 0.00 32.09 4.61
722 743 2.047655 CGTTAGCCAACTCGCCCA 60.048 61.111 0.00 0.00 32.09 5.36
723 744 3.497031 GCGTTAGCCAACTCGCCC 61.497 66.667 0.00 0.00 42.33 6.13
773 794 6.428159 TGCTTCTTTTTAGCGAAGAGAGATTT 59.572 34.615 3.43 0.00 41.54 2.17
774 795 5.934625 TGCTTCTTTTTAGCGAAGAGAGATT 59.065 36.000 3.43 0.00 41.54 2.40
775 796 5.482908 TGCTTCTTTTTAGCGAAGAGAGAT 58.517 37.500 3.43 0.00 41.54 2.75
776 797 4.883083 TGCTTCTTTTTAGCGAAGAGAGA 58.117 39.130 3.43 0.00 41.54 3.10
777 798 5.050091 TGTTGCTTCTTTTTAGCGAAGAGAG 60.050 40.000 3.43 2.42 41.54 3.20
778 799 4.814234 TGTTGCTTCTTTTTAGCGAAGAGA 59.186 37.500 3.43 0.00 41.54 3.10
779 800 5.095691 TGTTGCTTCTTTTTAGCGAAGAG 57.904 39.130 3.43 0.00 41.54 2.85
780 801 5.493133 TTGTTGCTTCTTTTTAGCGAAGA 57.507 34.783 3.43 0.00 41.54 2.87
781 802 5.331830 GCTTTGTTGCTTCTTTTTAGCGAAG 60.332 40.000 0.00 0.00 41.54 3.79
782 803 4.502645 GCTTTGTTGCTTCTTTTTAGCGAA 59.497 37.500 0.00 0.00 41.54 4.70
783 804 4.041723 GCTTTGTTGCTTCTTTTTAGCGA 58.958 39.130 0.00 0.00 41.54 4.93
784 805 4.044426 AGCTTTGTTGCTTCTTTTTAGCG 58.956 39.130 0.00 0.00 40.93 4.26
785 806 5.284864 AGAGCTTTGTTGCTTCTTTTTAGC 58.715 37.500 0.00 0.00 44.17 3.09
786 807 7.761651 AAAGAGCTTTGTTGCTTCTTTTTAG 57.238 32.000 0.00 0.00 44.17 1.85
787 808 8.546597 AAAAAGAGCTTTGTTGCTTCTTTTTA 57.453 26.923 22.11 0.00 45.13 1.52
788 809 7.439157 AAAAAGAGCTTTGTTGCTTCTTTTT 57.561 28.000 20.14 20.14 44.06 1.94
866 887 4.275689 TCGACGAAGGCGGTTAATATTAGA 59.724 41.667 0.00 0.00 43.17 2.10
902 923 2.135933 GGATCGCGTGGGATTCTTAAG 58.864 52.381 5.77 0.00 0.00 1.85
957 1009 2.192187 GGAGCCCTAGGTCGTACGG 61.192 68.421 16.52 0.00 41.62 4.02
1033 1085 3.730761 CGGGTCGAAGTCGTCCGT 61.731 66.667 20.98 0.00 45.99 4.69
1281 1333 3.703052 ACTCCACCGTATAATCCGAGTTT 59.297 43.478 0.00 0.00 0.00 2.66
1313 1365 2.034879 CATGGCTCGAAGTTGCGGT 61.035 57.895 0.00 0.00 0.00 5.68
1355 1407 0.799393 GCGTTTCCTCTTCTCCTTGC 59.201 55.000 0.00 0.00 0.00 4.01
1374 1426 2.202932 CCCATCTCCTCGGTTGCG 60.203 66.667 0.00 0.00 0.00 4.85
1377 1429 1.749334 GATCGCCCATCTCCTCGGTT 61.749 60.000 0.00 0.00 0.00 4.44
1378 1430 2.123251 ATCGCCCATCTCCTCGGT 60.123 61.111 0.00 0.00 0.00 4.69
1380 1432 1.175347 TCTGATCGCCCATCTCCTCG 61.175 60.000 0.00 0.00 31.92 4.63
1396 1448 0.459078 TTCTCCAGCGCTCTCATCTG 59.541 55.000 7.13 0.00 0.00 2.90
1448 1500 0.248702 CTCCTCTAAAGCGGCGAGTC 60.249 60.000 12.98 0.00 0.00 3.36
1482 1534 2.180276 GAGACCCGGGCATGTATAGAT 58.820 52.381 24.08 0.00 0.00 1.98
1549 1601 9.408648 GTCTCCCTCCTTTAAATTTTGATGATA 57.591 33.333 0.00 0.00 0.00 2.15
1587 1669 6.201806 CCGAGTTATGGAAAGTGATTGATCTC 59.798 42.308 0.00 0.00 0.00 2.75
1604 1686 7.990886 TCCAATTAACATAAGCTTCCGAGTTAT 59.009 33.333 0.00 0.00 0.00 1.89
1616 1698 8.664798 TGTCGTCTTTGATCCAATTAACATAAG 58.335 33.333 0.00 0.00 0.00 1.73
1620 1702 6.565060 CGTTGTCGTCTTTGATCCAATTAACA 60.565 38.462 0.00 0.00 0.00 2.41
1626 1708 3.100658 TCGTTGTCGTCTTTGATCCAA 57.899 42.857 0.00 0.00 38.33 3.53
1627 1709 2.804697 TCGTTGTCGTCTTTGATCCA 57.195 45.000 0.00 0.00 38.33 3.41
1662 1753 7.276658 AGCACTGATTTAGAAGACTCGTTAATG 59.723 37.037 0.00 0.00 0.00 1.90
1665 1756 6.268825 AGCACTGATTTAGAAGACTCGTTA 57.731 37.500 0.00 0.00 0.00 3.18
1678 1772 4.287067 TGGAGGAAGAACTAGCACTGATTT 59.713 41.667 0.00 0.00 0.00 2.17
1714 1808 0.550914 TCAAGTCCACTGGCTTTGGT 59.449 50.000 9.98 0.00 35.42 3.67
1722 1816 0.394192 TGGCACTCTCAAGTCCACTG 59.606 55.000 0.00 0.00 31.71 3.66
1724 1818 1.230324 GTTGGCACTCTCAAGTCCAC 58.770 55.000 0.00 0.00 34.49 4.02
1727 1821 2.036475 TCTCTGTTGGCACTCTCAAGTC 59.964 50.000 0.00 0.00 31.71 3.01
1728 1822 2.042464 TCTCTGTTGGCACTCTCAAGT 58.958 47.619 0.00 0.00 35.60 3.16
1730 1824 1.269778 CGTCTCTGTTGGCACTCTCAA 60.270 52.381 0.00 0.00 0.00 3.02
1743 1837 0.247736 CCCTCTTGTTCCCGTCTCTG 59.752 60.000 0.00 0.00 0.00 3.35
1745 1839 0.037232 CACCCTCTTGTTCCCGTCTC 60.037 60.000 0.00 0.00 0.00 3.36
1749 1846 2.359975 GCCACCCTCTTGTTCCCG 60.360 66.667 0.00 0.00 0.00 5.14
1752 1849 3.055094 TCTTAGATGCCACCCTCTTGTTC 60.055 47.826 0.00 0.00 0.00 3.18
1755 1852 3.474600 CATCTTAGATGCCACCCTCTTG 58.525 50.000 9.43 0.00 0.00 3.02
1779 1876 4.686091 GGCTTTGCCTTTACAATGAACTTC 59.314 41.667 0.73 0.00 46.69 3.01
1853 1953 2.203800 TGCTTTACCGCTATCTCGTG 57.796 50.000 0.00 0.00 0.00 4.35
1856 1956 3.522553 ACTGTTGCTTTACCGCTATCTC 58.477 45.455 0.00 0.00 0.00 2.75
1884 1984 2.555664 TCTGAAGCTTCATCTTCCCCT 58.444 47.619 28.57 0.00 41.23 4.79
1886 1986 5.474876 TCTTTTTCTGAAGCTTCATCTTCCC 59.525 40.000 28.57 0.00 41.23 3.97
1888 1988 7.432350 TCTCTTTTTCTGAAGCTTCATCTTC 57.568 36.000 28.57 1.24 42.04 2.87
1891 1991 7.297391 GTCTTCTCTTTTTCTGAAGCTTCATC 58.703 38.462 28.57 2.90 37.63 2.92
1904 2004 7.645058 TCAAGAACATTGGTCTTCTCTTTTT 57.355 32.000 14.05 0.00 0.00 1.94
1905 2005 7.830099 ATCAAGAACATTGGTCTTCTCTTTT 57.170 32.000 14.05 0.00 0.00 2.27
1906 2006 7.040132 GGAATCAAGAACATTGGTCTTCTCTTT 60.040 37.037 14.05 5.84 0.00 2.52
1927 2027 4.443598 GGTGTCATACTGGAAGAGGGAATC 60.444 50.000 0.00 0.00 37.43 2.52
1949 2049 4.328440 GTCTTCAGTCATCACTTTCATCGG 59.672 45.833 0.00 0.00 0.00 4.18
1975 2075 2.605366 GCAGTTATGACTCGAAGAAGCC 59.395 50.000 0.00 0.00 34.09 4.35
2035 2142 3.696548 AGACTTGATGAGCTACATGACGA 59.303 43.478 0.00 0.00 39.56 4.20
2037 2144 4.753233 ACAGACTTGATGAGCTACATGAC 58.247 43.478 0.00 0.00 39.56 3.06
2039 2146 7.601073 TTTTACAGACTTGATGAGCTACATG 57.399 36.000 3.76 0.00 39.56 3.21
2040 2147 8.263640 AGATTTTACAGACTTGATGAGCTACAT 58.736 33.333 0.00 0.00 42.47 2.29
2041 2148 7.615403 AGATTTTACAGACTTGATGAGCTACA 58.385 34.615 0.00 0.00 0.00 2.74
2042 2149 7.978975 AGAGATTTTACAGACTTGATGAGCTAC 59.021 37.037 0.00 0.00 0.00 3.58
2043 2150 7.978414 CAGAGATTTTACAGACTTGATGAGCTA 59.022 37.037 0.00 0.00 0.00 3.32
2044 2151 6.817641 CAGAGATTTTACAGACTTGATGAGCT 59.182 38.462 0.00 0.00 0.00 4.09
2045 2152 6.456718 GCAGAGATTTTACAGACTTGATGAGC 60.457 42.308 0.00 0.00 0.00 4.26
2046 2153 6.817641 AGCAGAGATTTTACAGACTTGATGAG 59.182 38.462 0.00 0.00 0.00 2.90
2047 2154 6.592994 CAGCAGAGATTTTACAGACTTGATGA 59.407 38.462 0.00 0.00 0.00 2.92
2048 2155 6.370994 ACAGCAGAGATTTTACAGACTTGATG 59.629 38.462 0.00 0.00 0.00 3.07
2140 2247 7.591057 TCGCTCTGAATTTGTCAATGTTAAAAG 59.409 33.333 0.00 0.00 35.22 2.27
2209 2316 0.247460 TCTGAATGTGCCGACCTGAG 59.753 55.000 0.00 0.00 0.00 3.35
2260 2368 9.878667 TCTCGTCCATGTTAAAATCAATAGTAA 57.121 29.630 0.00 0.00 0.00 2.24
2274 2382 5.833667 TCCTCATATTACTCTCGTCCATGTT 59.166 40.000 0.00 0.00 0.00 2.71
2292 2400 9.558396 GTAGATGAAAATCAGAGAATTCCTCAT 57.442 33.333 0.65 0.00 44.40 2.90
2301 2409 7.962995 ACAGTAGGTAGATGAAAATCAGAGA 57.037 36.000 0.00 0.00 0.00 3.10
2349 2462 6.959361 TCTCAATTCTTTAGTTTGCACTGTC 58.041 36.000 0.00 0.00 34.06 3.51
2389 2502 0.252057 TCAGCTAGGTGGTGTAGCCA 60.252 55.000 21.22 0.00 43.44 4.75
2390 2503 0.461961 CTCAGCTAGGTGGTGTAGCC 59.538 60.000 21.22 0.00 43.44 3.93
2525 2638 4.848562 TCCATGAACGCGTCTATCTTAT 57.151 40.909 14.44 0.00 0.00 1.73
2536 2649 0.810648 TCAAGGCAATCCATGAACGC 59.189 50.000 0.00 0.00 37.16 4.84
2548 2661 1.855213 GCACGTTGCTCATCAAGGCA 61.855 55.000 0.00 0.00 42.58 4.75
2567 2680 4.333095 CACATGCTTGAGAGAGAAGAATGG 59.667 45.833 6.60 0.00 39.83 3.16
2569 2682 5.163281 ACACATGCTTGAGAGAGAAGAAT 57.837 39.130 6.60 0.00 0.00 2.40
2574 2687 4.036852 CGGTATACACATGCTTGAGAGAGA 59.963 45.833 6.60 0.00 0.00 3.10
2575 2688 4.294232 CGGTATACACATGCTTGAGAGAG 58.706 47.826 6.60 0.00 0.00 3.20
2576 2689 3.490933 GCGGTATACACATGCTTGAGAGA 60.491 47.826 6.60 0.00 0.00 3.10
2590 2703 4.822026 AGGATATTGAAGCAGCGGTATAC 58.178 43.478 0.00 0.00 0.00 1.47
2595 2708 2.292267 ACAAGGATATTGAAGCAGCGG 58.708 47.619 0.00 0.00 0.00 5.52
2600 2713 3.696051 TGGCTGAACAAGGATATTGAAGC 59.304 43.478 0.00 1.42 0.00 3.86
2608 2721 6.400568 CAAACATATTTGGCTGAACAAGGAT 58.599 36.000 0.00 0.00 41.39 3.24
2672 2785 4.970860 AGAGATGTGGATATGGAACCAG 57.029 45.455 0.00 0.00 36.82 4.00
2705 2818 3.127548 CAGTGCTCAACCTGCGAATAAAT 59.872 43.478 0.00 0.00 0.00 1.40
2745 2858 7.700656 CCGTTTATACCTTAAGCTTGAATTTGG 59.299 37.037 9.86 0.60 0.00 3.28
2847 2960 0.540830 TGCGCAGGTTATTTTGGGGT 60.541 50.000 5.66 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.