Multiple sequence alignment - TraesCS2D01G038000

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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 TraesCS2D01G038000 chr2D 100.000 4301 0 0 1 4301 14086147 14081847 0.000000e+00 7943.0
1 TraesCS2D01G038000 chr2D 88.564 411 33 5 941 1348 648652190 648652589 1.800000e-133 486.0
2 TraesCS2D01G038000 chr2D 84.270 89 4 1 771 859 648652051 648652129 1.280000e-10 78.7
3 TraesCS2D01G038000 chr2A 94.796 3017 85 22 743 3732 16129967 16132938 0.000000e+00 4636.0
4 TraesCS2D01G038000 chr2A 92.560 457 27 5 1 456 16129287 16129737 0.000000e+00 649.0
5 TraesCS2D01G038000 chr2A 81.743 482 41 16 882 1350 177981896 177982343 4.090000e-95 359.0
6 TraesCS2D01G038000 chr2A 89.634 164 16 1 441 603 16129754 16129917 1.570000e-49 207.0
7 TraesCS2D01G038000 chr2A 90.769 65 4 2 882 944 177870870 177870934 7.660000e-13 86.1
8 TraesCS2D01G038000 chr2B 95.413 1984 67 8 2337 4301 25580744 25578766 0.000000e+00 3138.0
9 TraesCS2D01G038000 chr2B 80.885 565 84 16 154 706 25586452 25585900 1.430000e-114 424.0
10 TraesCS2D01G038000 chr1B 86.412 2458 271 34 888 3305 100815173 100812739 0.000000e+00 2630.0
11 TraesCS2D01G038000 chr1B 87.395 476 42 9 887 1350 389003697 389004166 8.190000e-147 531.0
12 TraesCS2D01G038000 chr1B 86.902 481 42 9 882 1350 389086331 389086802 1.770000e-143 520.0
13 TraesCS2D01G038000 chr1B 85.000 80 2 1 777 856 389086212 389086281 5.970000e-09 73.1
14 TraesCS2D01G038000 chr1A 83.864 1853 243 34 1473 3303 51678703 51680521 0.000000e+00 1714.0
15 TraesCS2D01G038000 chr1A 82.988 482 35 15 882 1350 309695291 309695738 4.030000e-105 392.0
16 TraesCS2D01G038000 chr1A 89.583 48 3 2 778 825 555959994 555960039 4.640000e-05 60.2
17 TraesCS2D01G038000 chr1D 85.480 1522 165 29 892 2379 51993845 51995344 0.000000e+00 1535.0
18 TraesCS2D01G038000 chr1D 85.810 895 118 7 2417 3305 51995351 51996242 0.000000e+00 941.0
19 TraesCS2D01G038000 chr1D 90.395 177 17 0 3129 3305 52128607 52128431 2.590000e-57 233.0
20 TraesCS2D01G038000 chr6B 84.602 565 47 20 3740 4301 434413918 434414445 3.810000e-145 525.0
21 TraesCS2D01G038000 chr6A 86.583 477 37 16 3827 4301 390097256 390097707 6.420000e-138 501.0
22 TraesCS2D01G038000 chrUn 88.517 418 25 8 882 1287 312292653 312293059 6.470000e-133 484.0
23 TraesCS2D01G038000 chrUn 82.365 482 38 17 882 1350 13785668 13786115 4.060000e-100 375.0
24 TraesCS2D01G038000 chr6D 82.109 531 51 22 3771 4301 272864306 272864792 8.600000e-112 414.0
25 TraesCS2D01G038000 chr4A 82.438 484 40 16 882 1353 22876196 22875746 8.730000e-102 381.0
26 TraesCS2D01G038000 chr4A 83.908 87 2 3 778 862 22876316 22876240 5.970000e-09 73.1
27 TraesCS2D01G038000 chr3B 78.673 211 33 5 454 653 144213298 144213089 3.490000e-26 130.0
28 TraesCS2D01G038000 chr3B 74.320 331 54 20 35 342 144213798 144213476 1.260000e-20 111.0


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 TraesCS2D01G038000 chr2D 14081847 14086147 4300 True 7943.000000 7943 100.000 1 4301 1 chr2D.!!$R1 4300
1 TraesCS2D01G038000 chr2D 648652051 648652589 538 False 282.350000 486 86.417 771 1348 2 chr2D.!!$F1 577
2 TraesCS2D01G038000 chr2A 16129287 16132938 3651 False 1830.666667 4636 92.330 1 3732 3 chr2A.!!$F3 3731
3 TraesCS2D01G038000 chr2B 25578766 25580744 1978 True 3138.000000 3138 95.413 2337 4301 1 chr2B.!!$R1 1964
4 TraesCS2D01G038000 chr2B 25585900 25586452 552 True 424.000000 424 80.885 154 706 1 chr2B.!!$R2 552
5 TraesCS2D01G038000 chr1B 100812739 100815173 2434 True 2630.000000 2630 86.412 888 3305 1 chr1B.!!$R1 2417
6 TraesCS2D01G038000 chr1B 389086212 389086802 590 False 296.550000 520 85.951 777 1350 2 chr1B.!!$F2 573
7 TraesCS2D01G038000 chr1A 51678703 51680521 1818 False 1714.000000 1714 83.864 1473 3303 1 chr1A.!!$F1 1830
8 TraesCS2D01G038000 chr1D 51993845 51996242 2397 False 1238.000000 1535 85.645 892 3305 2 chr1D.!!$F1 2413
9 TraesCS2D01G038000 chr6B 434413918 434414445 527 False 525.000000 525 84.602 3740 4301 1 chr6B.!!$F1 561
10 TraesCS2D01G038000 chr4A 22875746 22876316 570 True 227.050000 381 83.173 778 1353 2 chr4A.!!$R1 575

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
595 631 0.383590 CGCTGAGATGTGACCGATCT 59.616 55.0 0.00 0.00 32.63 2.75 F
1007 1112 0.250038 CAAGGATCATCGATGGCGGT 60.250 55.0 24.61 9.11 38.28 5.68 F
2172 2319 0.320771 ATGATGATTACCCGGCGCTC 60.321 55.0 7.64 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2098 0.250467 ACCTCGATTGCAGCTGTGTT 60.250 50.0 16.64 0.0 0.0 3.32 R
2982 3135 0.313043 TCTTGTCCTCGTCGAACCAC 59.687 55.0 0.00 0.0 0.0 4.16 R
3659 3834 0.106708 TGAGGAAGGACAGCACACAC 59.893 55.0 0.00 0.0 0.0 3.82 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
46 47 2.276282 GCGACTTTGCATTAAATCGTGC 59.724 45.455 4.20 0.00 41.61 5.34
113 114 2.176546 CATTGAACTGCGTGGCGG 59.823 61.111 0.00 0.00 41.29 6.13
133 134 3.241995 CGGCGCTACTCTAAAACATTGTC 60.242 47.826 7.64 0.00 0.00 3.18
136 137 3.924686 CGCTACTCTAAAACATTGTCGGT 59.075 43.478 0.00 0.00 0.00 4.69
144 145 0.941542 AACATTGTCGGTGACCAACG 59.058 50.000 1.11 0.30 44.11 4.10
145 146 0.882927 ACATTGTCGGTGACCAACGG 60.883 55.000 7.65 0.00 42.74 4.44
174 175 1.078848 GGAGCACCGATTGAGCAGT 60.079 57.895 0.00 0.00 0.00 4.40
225 226 0.539438 ACCACCGATGCAACACCATT 60.539 50.000 0.00 0.00 0.00 3.16
227 228 0.597568 CACCGATGCAACACCATTGT 59.402 50.000 0.00 0.00 37.67 2.71
436 438 3.594775 CCGCTGTTGTTGCTGCCA 61.595 61.111 0.00 0.00 0.00 4.92
475 510 0.461548 CTATCACAAGCGAGAGGCCA 59.538 55.000 5.01 0.00 45.17 5.36
537 573 1.066605 TGTAAAGGTCTATCGCGAGCC 59.933 52.381 16.66 13.86 32.00 4.70
565 601 2.117156 GCGTGGCTCAGATGGCATT 61.117 57.895 0.00 0.00 44.18 3.56
588 624 1.683385 CATCCTACCGCTGAGATGTGA 59.317 52.381 0.00 0.00 33.09 3.58
595 631 0.383590 CGCTGAGATGTGACCGATCT 59.616 55.000 0.00 0.00 32.63 2.75
598 634 2.035704 GCTGAGATGTGACCGATCTGAT 59.964 50.000 0.00 0.00 29.97 2.90
603 639 1.775385 TGTGACCGATCTGATGGCTA 58.225 50.000 0.00 0.00 0.00 3.93
604 640 1.683385 TGTGACCGATCTGATGGCTAG 59.317 52.381 0.00 0.00 0.00 3.42
632 672 6.095440 ACCTTAATTCTGGATCAAATCAACCG 59.905 38.462 0.00 0.00 0.00 4.44
634 674 7.148086 CCTTAATTCTGGATCAAATCAACCGAA 60.148 37.037 0.00 0.00 0.00 4.30
635 675 6.780457 AATTCTGGATCAAATCAACCGAAT 57.220 33.333 0.00 0.00 32.15 3.34
651 691 1.595489 CGAATGATTTGTAGCAGCCGC 60.595 52.381 0.00 0.00 38.99 6.53
688 728 7.351952 TGTACATGACCAATCCTAGTACTACT 58.648 38.462 0.00 0.00 33.45 2.57
690 730 9.001542 GTACATGACCAATCCTAGTACTACTAG 57.998 40.741 14.28 14.28 45.93 2.57
707 747 3.913509 ACTAGGACTAGGAGTTTAGGGC 58.086 50.000 10.81 0.00 37.49 5.19
708 748 2.942604 AGGACTAGGAGTTTAGGGCA 57.057 50.000 0.00 0.00 0.00 5.36
709 749 2.468915 AGGACTAGGAGTTTAGGGCAC 58.531 52.381 0.00 0.00 0.00 5.01
710 750 1.136500 GGACTAGGAGTTTAGGGCACG 59.864 57.143 0.00 0.00 0.00 5.34
711 751 2.097825 GACTAGGAGTTTAGGGCACGA 58.902 52.381 0.00 0.00 0.00 4.35
712 752 1.823610 ACTAGGAGTTTAGGGCACGAC 59.176 52.381 0.00 0.00 0.00 4.34
713 753 1.136500 CTAGGAGTTTAGGGCACGACC 59.864 57.143 0.00 0.00 37.93 4.79
714 754 0.544595 AGGAGTTTAGGGCACGACCT 60.545 55.000 0.00 0.00 44.75 3.85
727 767 1.822990 CACGACCTGGCTCTACCTTAA 59.177 52.381 0.00 0.00 40.22 1.85
728 768 1.823610 ACGACCTGGCTCTACCTTAAC 59.176 52.381 0.00 0.00 40.22 2.01
730 770 2.416972 CGACCTGGCTCTACCTTAACAC 60.417 54.545 0.00 0.00 40.22 3.32
731 771 1.549170 ACCTGGCTCTACCTTAACACG 59.451 52.381 0.00 0.00 40.22 4.49
734 774 3.181489 CCTGGCTCTACCTTAACACGTAG 60.181 52.174 0.00 0.00 40.22 3.51
735 775 3.689347 TGGCTCTACCTTAACACGTAGA 58.311 45.455 0.00 0.00 38.86 2.59
739 779 4.660105 CTCTACCTTAACACGTAGAGCAC 58.340 47.826 10.39 0.00 46.91 4.40
740 780 4.330250 TCTACCTTAACACGTAGAGCACT 58.670 43.478 0.00 0.00 36.82 4.40
741 781 5.491070 TCTACCTTAACACGTAGAGCACTA 58.509 41.667 0.00 0.00 36.82 2.74
762 812 4.234530 ACTCAAACACGTAGACACTACC 57.765 45.455 0.00 0.00 0.00 3.18
772 822 4.874966 ACGTAGACACTACCTAGCTAACAG 59.125 45.833 0.00 0.00 0.00 3.16
812 862 5.583854 CACGTAGACACTAGCTAGGAAACTA 59.416 44.000 24.35 17.02 43.67 2.24
813 863 6.093219 CACGTAGACACTAGCTAGGAAACTAA 59.907 42.308 24.35 1.48 43.83 2.24
814 864 6.827762 ACGTAGACACTAGCTAGGAAACTAAT 59.172 38.462 24.35 10.58 43.83 1.73
815 865 7.012232 ACGTAGACACTAGCTAGGAAACTAATC 59.988 40.741 24.35 9.48 43.83 1.75
816 866 6.718522 AGACACTAGCTAGGAAACTAATCC 57.281 41.667 24.35 2.40 43.83 3.01
859 911 5.238650 CCAAACCGAATCTAACTCAAACACT 59.761 40.000 0.00 0.00 0.00 3.55
862 914 8.504005 CAAACCGAATCTAACTCAAACACTAAT 58.496 33.333 0.00 0.00 0.00 1.73
863 915 7.829378 ACCGAATCTAACTCAAACACTAATC 57.171 36.000 0.00 0.00 0.00 1.75
867 919 7.276658 CGAATCTAACTCAAACACTAATCTGCT 59.723 37.037 0.00 0.00 0.00 4.24
869 921 9.593134 AATCTAACTCAAACACTAATCTGCTAG 57.407 33.333 0.00 0.00 0.00 3.42
870 922 8.349568 TCTAACTCAAACACTAATCTGCTAGA 57.650 34.615 0.00 0.00 0.00 2.43
872 924 6.346477 ACTCAAACACTAATCTGCTAGACA 57.654 37.500 0.00 0.00 0.00 3.41
873 925 6.759272 ACTCAAACACTAATCTGCTAGACAA 58.241 36.000 0.00 0.00 0.00 3.18
874 926 6.870965 ACTCAAACACTAATCTGCTAGACAAG 59.129 38.462 0.00 0.00 0.00 3.16
875 927 6.993079 TCAAACACTAATCTGCTAGACAAGA 58.007 36.000 0.00 0.00 0.00 3.02
876 928 7.615403 TCAAACACTAATCTGCTAGACAAGAT 58.385 34.615 0.00 0.00 0.00 2.40
880 932 8.299990 ACACTAATCTGCTAGACAAGATTACT 57.700 34.615 14.30 7.30 32.20 2.24
881 933 8.194104 ACACTAATCTGCTAGACAAGATTACTG 58.806 37.037 14.30 15.88 32.20 2.74
882 934 7.168972 CACTAATCTGCTAGACAAGATTACTGC 59.831 40.741 14.30 0.00 32.20 4.40
883 935 4.392921 TCTGCTAGACAAGATTACTGCC 57.607 45.455 0.00 0.00 0.00 4.85
956 1050 1.410850 AAGGATCGGGGCATCATCGT 61.411 55.000 0.00 0.00 0.00 3.73
971 1076 2.536997 ATCGTAAGCCACCACAGCCC 62.537 60.000 0.00 0.00 37.18 5.19
988 1093 2.558359 AGCCCAGAACAATTAAGCACAC 59.442 45.455 0.00 0.00 0.00 3.82
989 1094 2.295909 GCCCAGAACAATTAAGCACACA 59.704 45.455 0.00 0.00 0.00 3.72
991 1096 4.549458 CCCAGAACAATTAAGCACACAAG 58.451 43.478 0.00 0.00 0.00 3.16
992 1097 4.549458 CCAGAACAATTAAGCACACAAGG 58.451 43.478 0.00 0.00 0.00 3.61
993 1098 4.278170 CCAGAACAATTAAGCACACAAGGA 59.722 41.667 0.00 0.00 0.00 3.36
994 1099 5.047802 CCAGAACAATTAAGCACACAAGGAT 60.048 40.000 0.00 0.00 0.00 3.24
995 1100 6.088824 CAGAACAATTAAGCACACAAGGATC 58.911 40.000 0.00 0.00 0.00 3.36
1007 1112 0.250038 CAAGGATCATCGATGGCGGT 60.250 55.000 24.61 9.11 38.28 5.68
1032 1137 1.449956 GCAGGAGAAGCAGCAGGAG 60.450 63.158 0.00 0.00 0.00 3.69
1033 1138 1.221293 CAGGAGAAGCAGCAGGAGG 59.779 63.158 0.00 0.00 0.00 4.30
1034 1139 1.079987 AGGAGAAGCAGCAGGAGGA 59.920 57.895 0.00 0.00 0.00 3.71
1045 1150 1.070445 CAGGAGGACGATGATGCCC 59.930 63.158 0.00 0.00 0.00 5.36
1089 1194 2.940410 ACACAAAGTCGTCACGGAAATT 59.060 40.909 0.00 0.00 0.00 1.82
1208 1315 2.349755 GCGGGCAAACTACCAGGA 59.650 61.111 0.00 0.00 0.00 3.86
1237 1344 1.639298 CCGGCCAAAGCTCTTCTTCG 61.639 60.000 2.24 0.00 39.73 3.79
1290 1406 2.690653 TTTACGCTTGGCAGCCTGGT 62.691 55.000 14.15 7.67 44.06 4.00
1293 1409 4.982701 GCTTGGCAGCCTGGTGGT 62.983 66.667 14.15 0.00 40.61 4.16
1399 1518 2.412323 CGGAGTGGCGGCTACTACA 61.412 63.158 25.67 0.53 0.00 2.74
1855 1979 1.523938 GGGTGCCTATGCGTCTTCC 60.524 63.158 0.00 0.00 41.78 3.46
1856 1980 1.522569 GGTGCCTATGCGTCTTCCT 59.477 57.895 0.00 0.00 41.78 3.36
1858 1988 0.872021 GTGCCTATGCGTCTTCCTCG 60.872 60.000 0.00 0.00 41.78 4.63
1906 2036 0.392863 ATGGCTGCTGCGTGATTACA 60.393 50.000 9.65 0.29 40.82 2.41
1947 2077 3.834013 TTGTTGCATCGACCGGGCA 62.834 57.895 8.76 2.35 35.41 5.36
1971 2101 4.680237 CCGGAGCCACAGCGAACA 62.680 66.667 0.00 0.00 46.67 3.18
1992 2122 0.463295 AGCTGCAATCGAGGTGGATG 60.463 55.000 1.02 0.00 0.00 3.51
2028 2158 2.549754 GTCTAATGGTGCCAATGGATCG 59.450 50.000 2.05 0.00 0.00 3.69
2029 2159 2.437651 TCTAATGGTGCCAATGGATCGA 59.562 45.455 2.05 0.00 0.00 3.59
2046 2182 6.409704 TGGATCGAAGAAGAAGATCATGTTT 58.590 36.000 0.00 0.00 43.58 2.83
2121 2257 2.305927 AGAGATTCTTTTCCGGCCAGAA 59.694 45.455 2.24 3.93 0.00 3.02
2172 2319 0.320771 ATGATGATTACCCGGCGCTC 60.321 55.000 7.64 0.00 0.00 5.03
2802 2955 4.530857 GACGTGCCGCCAGCCTAT 62.531 66.667 0.00 0.00 42.71 2.57
2982 3135 1.665916 CGGTGCTATCTCCATGGCG 60.666 63.158 6.96 0.00 39.36 5.69
3020 3173 5.937540 ACAAGAATGTCATTGACGTATGGAA 59.062 36.000 11.80 0.00 33.41 3.53
3042 3195 2.325583 TCAAGGACATAATGGACGGC 57.674 50.000 0.00 0.00 0.00 5.68
3407 3582 9.896645 ATATTGCTGTTAGAATTTTCTCTCTCA 57.103 29.630 0.00 0.00 38.70 3.27
3607 3782 1.636148 AAGGGTAGTGTTAGACGCCA 58.364 50.000 0.00 0.00 0.00 5.69
3659 3834 1.263356 TTTCCACCCTAGTCGTCTGG 58.737 55.000 0.00 0.00 0.00 3.86
3666 3841 0.388649 CCTAGTCGTCTGGTGTGTGC 60.389 60.000 0.00 0.00 0.00 4.57
3817 3996 2.034812 GCCGTCGGATCAGAAGTAAGAT 59.965 50.000 17.49 0.00 0.00 2.40
3906 4085 6.261826 GCTGATCTGTAACTGCTTCCATAAAT 59.738 38.462 1.27 0.00 0.00 1.40
3911 4090 6.714810 TCTGTAACTGCTTCCATAAATGTTGT 59.285 34.615 0.00 0.00 0.00 3.32
3992 4172 3.006247 GTGAGTCTCCATTCTGGCTTTC 58.994 50.000 0.00 0.00 37.47 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 3.241995 CCGACAATGTTTTAGAGTAGCGC 60.242 47.826 0.00 0.00 0.00 5.92
121 122 4.533222 GTTGGTCACCGACAATGTTTTAG 58.467 43.478 9.66 0.00 37.82 1.85
133 134 1.373748 CACTACCCGTTGGTCACCG 60.374 63.158 0.00 0.00 43.06 4.94
136 137 1.001520 CATCACACTACCCGTTGGTCA 59.998 52.381 0.00 0.00 43.06 4.02
144 145 0.107654 GGTGCTCCATCACACTACCC 60.108 60.000 0.00 0.00 38.66 3.69
145 146 0.460284 CGGTGCTCCATCACACTACC 60.460 60.000 5.52 0.00 38.66 3.18
209 210 0.597568 CACAATGGTGTTGCATCGGT 59.402 50.000 0.00 0.00 40.24 4.69
210 211 3.404978 CACAATGGTGTTGCATCGG 57.595 52.632 0.00 0.00 40.24 4.18
371 373 3.257561 CCGCCGACGATGCTTCAG 61.258 66.667 0.00 0.00 43.93 3.02
424 426 0.668401 GGCTTCATGGCAGCAACAAC 60.668 55.000 16.72 0.00 39.21 3.32
431 433 3.207669 GGCGAGGCTTCATGGCAG 61.208 66.667 0.00 0.00 44.55 4.85
461 496 2.437359 GCATGGCCTCTCGCTTGT 60.437 61.111 3.32 0.00 37.74 3.16
565 601 1.123077 ATCTCAGCGGTAGGATGCAA 58.877 50.000 0.00 0.00 30.27 4.08
588 624 0.760567 TGCCTAGCCATCAGATCGGT 60.761 55.000 0.00 0.00 0.00 4.69
595 631 3.459598 AGAATTAAGGTGCCTAGCCATCA 59.540 43.478 0.00 0.00 0.00 3.07
598 634 2.092429 CCAGAATTAAGGTGCCTAGCCA 60.092 50.000 0.00 0.00 0.00 4.75
603 639 4.591321 TTGATCCAGAATTAAGGTGCCT 57.409 40.909 0.00 0.00 0.00 4.75
604 640 5.360714 TGATTTGATCCAGAATTAAGGTGCC 59.639 40.000 0.00 0.00 0.00 5.01
632 672 1.268743 GGCGGCTGCTACAAATCATTC 60.269 52.381 18.85 0.00 42.25 2.67
634 674 0.107017 AGGCGGCTGCTACAAATCAT 60.107 50.000 18.85 0.00 42.25 2.45
635 675 0.322456 AAGGCGGCTGCTACAAATCA 60.322 50.000 18.85 0.00 42.25 2.57
664 704 7.820578 AGTAGTACTAGGATTGGTCATGTAC 57.179 40.000 1.87 0.00 0.00 2.90
688 728 3.639952 GTGCCCTAAACTCCTAGTCCTA 58.360 50.000 0.00 0.00 0.00 2.94
690 730 1.136500 CGTGCCCTAAACTCCTAGTCC 59.864 57.143 0.00 0.00 0.00 3.85
693 733 1.136500 GGTCGTGCCCTAAACTCCTAG 59.864 57.143 0.00 0.00 0.00 3.02
700 740 2.180159 GAGCCAGGTCGTGCCCTAAA 62.180 60.000 0.00 0.00 38.26 1.85
706 746 1.889530 AAGGTAGAGCCAGGTCGTGC 61.890 60.000 0.00 0.00 40.61 5.34
707 747 1.471119 TAAGGTAGAGCCAGGTCGTG 58.529 55.000 0.00 0.00 40.61 4.35
708 748 1.823610 GTTAAGGTAGAGCCAGGTCGT 59.176 52.381 0.00 0.00 40.61 4.34
709 749 1.822990 TGTTAAGGTAGAGCCAGGTCG 59.177 52.381 0.00 0.00 40.61 4.79
710 750 2.416972 CGTGTTAAGGTAGAGCCAGGTC 60.417 54.545 0.00 0.00 40.61 3.85
711 751 1.549170 CGTGTTAAGGTAGAGCCAGGT 59.451 52.381 0.00 0.00 40.61 4.00
712 752 1.549170 ACGTGTTAAGGTAGAGCCAGG 59.451 52.381 0.00 0.00 40.61 4.45
713 753 3.693085 TCTACGTGTTAAGGTAGAGCCAG 59.307 47.826 0.00 0.00 44.72 4.85
714 754 3.689347 TCTACGTGTTAAGGTAGAGCCA 58.311 45.455 0.00 0.00 44.72 4.75
731 771 3.898529 ACGTGTTTGAGTAGTGCTCTAC 58.101 45.455 16.42 16.42 44.41 2.59
734 774 3.913163 GTCTACGTGTTTGAGTAGTGCTC 59.087 47.826 0.00 0.56 44.36 4.26
735 775 3.317149 TGTCTACGTGTTTGAGTAGTGCT 59.683 43.478 0.00 0.00 40.69 4.40
736 776 3.424529 GTGTCTACGTGTTTGAGTAGTGC 59.575 47.826 0.00 0.00 40.69 4.40
739 779 5.180868 AGGTAGTGTCTACGTGTTTGAGTAG 59.819 44.000 0.00 0.00 41.08 2.57
740 780 5.065914 AGGTAGTGTCTACGTGTTTGAGTA 58.934 41.667 0.00 0.00 0.00 2.59
741 781 3.887716 AGGTAGTGTCTACGTGTTTGAGT 59.112 43.478 0.00 0.00 0.00 3.41
772 822 6.128445 TGTCTACGTGTTTGAGTAGTACTAGC 60.128 42.308 1.87 0.00 40.69 3.42
811 861 4.497300 CGTCCCGTGTCTTTTTAGGATTA 58.503 43.478 0.00 0.00 0.00 1.75
812 862 3.332034 CGTCCCGTGTCTTTTTAGGATT 58.668 45.455 0.00 0.00 0.00 3.01
813 863 2.933928 GCGTCCCGTGTCTTTTTAGGAT 60.934 50.000 0.00 0.00 0.00 3.24
814 864 1.606224 GCGTCCCGTGTCTTTTTAGGA 60.606 52.381 0.00 0.00 0.00 2.94
815 865 0.794473 GCGTCCCGTGTCTTTTTAGG 59.206 55.000 0.00 0.00 0.00 2.69
816 866 0.794473 GGCGTCCCGTGTCTTTTTAG 59.206 55.000 0.00 0.00 0.00 1.85
817 867 0.603439 GGGCGTCCCGTGTCTTTTTA 60.603 55.000 0.00 0.00 32.13 1.52
818 868 1.895231 GGGCGTCCCGTGTCTTTTT 60.895 57.895 0.00 0.00 32.13 1.94
819 869 2.281276 GGGCGTCCCGTGTCTTTT 60.281 61.111 0.00 0.00 32.13 2.27
859 911 6.098266 TGGCAGTAATCTTGTCTAGCAGATTA 59.902 38.462 11.78 11.78 33.63 1.75
862 914 3.769300 TGGCAGTAATCTTGTCTAGCAGA 59.231 43.478 0.00 0.00 0.00 4.26
863 915 3.868077 GTGGCAGTAATCTTGTCTAGCAG 59.132 47.826 0.00 0.00 0.00 4.24
867 919 3.197766 CCAGGTGGCAGTAATCTTGTCTA 59.802 47.826 0.00 0.00 0.00 2.59
869 921 2.027192 TCCAGGTGGCAGTAATCTTGTC 60.027 50.000 0.00 0.00 34.44 3.18
870 922 1.985159 TCCAGGTGGCAGTAATCTTGT 59.015 47.619 0.00 0.00 34.44 3.16
872 924 4.018050 AGAAATCCAGGTGGCAGTAATCTT 60.018 41.667 0.00 0.00 34.44 2.40
873 925 3.525199 AGAAATCCAGGTGGCAGTAATCT 59.475 43.478 0.00 0.00 34.44 2.40
874 926 3.879892 GAGAAATCCAGGTGGCAGTAATC 59.120 47.826 0.00 0.00 34.44 1.75
875 927 3.682718 CGAGAAATCCAGGTGGCAGTAAT 60.683 47.826 0.00 0.00 34.44 1.89
876 928 2.354704 CGAGAAATCCAGGTGGCAGTAA 60.355 50.000 0.00 0.00 34.44 2.24
880 932 1.377202 GCGAGAAATCCAGGTGGCA 60.377 57.895 0.00 0.00 34.44 4.92
881 933 2.115291 GGCGAGAAATCCAGGTGGC 61.115 63.158 0.00 0.00 34.44 5.01
882 934 1.815421 CGGCGAGAAATCCAGGTGG 60.815 63.158 0.00 0.00 0.00 4.61
883 935 0.673644 AACGGCGAGAAATCCAGGTG 60.674 55.000 16.62 0.00 0.00 4.00
956 1050 1.422977 TTCTGGGCTGTGGTGGCTTA 61.423 55.000 0.00 0.00 0.00 3.09
971 1076 5.437289 TCCTTGTGTGCTTAATTGTTCTG 57.563 39.130 0.00 0.00 0.00 3.02
988 1093 0.250038 ACCGCCATCGATGATCCTTG 60.250 55.000 26.86 9.71 38.10 3.61
989 1094 0.250038 CACCGCCATCGATGATCCTT 60.250 55.000 26.86 3.95 38.10 3.36
991 1096 2.320587 GCACCGCCATCGATGATCC 61.321 63.158 26.86 12.86 38.10 3.36
992 1097 1.595109 TGCACCGCCATCGATGATC 60.595 57.895 26.86 15.86 38.10 2.92
993 1098 1.889105 GTGCACCGCCATCGATGAT 60.889 57.895 26.86 6.31 38.10 2.45
994 1099 2.511373 GTGCACCGCCATCGATGA 60.511 61.111 26.86 1.43 38.10 2.92
995 1100 3.928769 CGTGCACCGCCATCGATG 61.929 66.667 18.76 18.76 38.10 3.84
1169 1274 0.968393 GAGGTGGAGCTCGAGGAAGT 60.968 60.000 15.58 0.00 0.00 3.01
1290 1406 3.923864 AGCTTCGTCACCGCACCA 61.924 61.111 0.00 0.00 0.00 4.17
1293 1409 1.737735 CATCAGCTTCGTCACCGCA 60.738 57.895 0.00 0.00 0.00 5.69
1298 1414 1.403647 CGTTACCCATCAGCTTCGTCA 60.404 52.381 0.00 0.00 0.00 4.35
1399 1518 1.077501 CGGTGGATGGGTTGCAGAT 60.078 57.895 0.00 0.00 0.00 2.90
1634 1753 2.281484 GCTTGGACGTGGCAGGAA 60.281 61.111 14.98 0.00 0.00 3.36
1635 1754 4.329545 GGCTTGGACGTGGCAGGA 62.330 66.667 14.98 0.00 0.00 3.86
1882 2012 1.518352 CACGCAGCAGCCATACGTA 60.518 57.895 0.00 0.00 37.52 3.57
1884 2014 1.431488 AATCACGCAGCAGCCATACG 61.431 55.000 0.00 0.00 37.52 3.06
1906 2036 2.113139 CTCCCACCGTTGTGCCTT 59.887 61.111 0.00 0.00 41.35 4.35
1968 2098 0.250467 ACCTCGATTGCAGCTGTGTT 60.250 50.000 16.64 0.00 0.00 3.32
1971 2101 1.376424 CCACCTCGATTGCAGCTGT 60.376 57.895 16.64 0.00 0.00 4.40
1992 2122 2.428544 TAGACAGACAGAGAGGAGCC 57.571 55.000 0.00 0.00 0.00 4.70
2028 2158 5.397326 GTGCCAAACATGATCTTCTTCTTC 58.603 41.667 0.00 0.00 0.00 2.87
2029 2159 4.083110 CGTGCCAAACATGATCTTCTTCTT 60.083 41.667 0.00 0.00 37.49 2.52
2172 2319 0.458716 GACTCTCCTCGAAAAGGCCG 60.459 60.000 0.00 0.00 45.78 6.13
2178 2325 1.000955 GGCACAAGACTCTCCTCGAAA 59.999 52.381 0.00 0.00 0.00 3.46
2601 2754 1.406539 GCGATTGATCTGCCCAACAAT 59.593 47.619 0.00 0.00 35.99 2.71
2802 2955 4.776837 ACCCAATAAATCTTGCCATTCACA 59.223 37.500 0.00 0.00 0.00 3.58
2982 3135 0.313043 TCTTGTCCTCGTCGAACCAC 59.687 55.000 0.00 0.00 0.00 4.16
3020 3173 3.495100 GCCGTCCATTATGTCCTTGATCT 60.495 47.826 0.00 0.00 0.00 2.75
3313 3487 7.565680 CACAATGAGGTAGGTAGGAAATTAGT 58.434 38.462 0.00 0.00 0.00 2.24
3314 3488 6.483640 GCACAATGAGGTAGGTAGGAAATTAG 59.516 42.308 0.00 0.00 0.00 1.73
3315 3489 6.157994 AGCACAATGAGGTAGGTAGGAAATTA 59.842 38.462 0.00 0.00 0.00 1.40
3317 3491 4.475016 AGCACAATGAGGTAGGTAGGAAAT 59.525 41.667 0.00 0.00 0.00 2.17
3319 3493 3.450904 AGCACAATGAGGTAGGTAGGAA 58.549 45.455 0.00 0.00 0.00 3.36
3320 3494 3.031736 GAGCACAATGAGGTAGGTAGGA 58.968 50.000 0.00 0.00 0.00 2.94
3607 3782 0.178973 AAAGTTTAGGCCGGCCAACT 60.179 50.000 45.13 39.06 34.91 3.16
3659 3834 0.106708 TGAGGAAGGACAGCACACAC 59.893 55.000 0.00 0.00 0.00 3.82
3666 3841 2.738846 CGTTTGTGATGAGGAAGGACAG 59.261 50.000 0.00 0.00 0.00 3.51
3781 3960 2.187946 GGCCATCGACTGGTCTGG 59.812 66.667 0.00 6.03 46.85 3.86
3817 3996 2.234168 TGATTACCAAATCGGACGGACA 59.766 45.455 0.00 0.00 43.84 4.02
3906 4085 5.656416 AGGAAACAAATGAGAGGAAACAACA 59.344 36.000 0.00 0.00 0.00 3.33
3911 4090 7.230712 GGAAGTTAGGAAACAAATGAGAGGAAA 59.769 37.037 0.00 0.00 38.12 3.13
3992 4172 2.673368 GGAAGCAAATACTCTGACGTGG 59.327 50.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.