Multiple sequence alignment - TraesCS3D01G392000

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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 TraesCS3D01G392000 chr3D 100.000 3806 0 0 1 3806 507045456 507041651 0.000000e+00 7029.0
1 TraesCS3D01G392000 chr3D 91.616 2314 152 19 1512 3806 507111070 507108780 0.000000e+00 3160.0
2 TraesCS3D01G392000 chr3D 82.528 269 37 6 3225 3486 507108292 507108027 1.060000e-55 228.0
3 TraesCS3D01G392000 chr3B 93.691 2774 121 14 950 3692 669445188 669442438 0.000000e+00 4104.0
4 TraesCS3D01G392000 chr3B 82.807 791 121 15 1 787 654053401 654052622 0.000000e+00 693.0
5 TraesCS3D01G392000 chr3A 96.029 2367 72 7 950 3296 645150235 645147871 0.000000e+00 3831.0
6 TraesCS3D01G392000 chr3A 90.460 2935 208 24 913 3806 645392897 645389994 0.000000e+00 3803.0
7 TraesCS3D01G392000 chr3A 89.286 532 29 12 3295 3806 645147767 645147244 3.210000e-180 641.0
8 TraesCS3D01G392000 chr3A 89.796 49 5 0 898 946 645392863 645392815 3.170000e-06 63.9
9 TraesCS3D01G392000 chr3A 96.875 32 0 1 851 882 645392933 645392903 7.000000e-03 52.8
10 TraesCS3D01G392000 chr5A 94.789 710 28 2 1774 2474 510160274 510160983 0.000000e+00 1098.0
11 TraesCS3D01G392000 chr5A 96.115 489 19 0 2524 3012 510160982 510161470 0.000000e+00 798.0
12 TraesCS3D01G392000 chr4A 87.666 827 96 5 10 834 603833264 603832442 0.000000e+00 957.0
13 TraesCS3D01G392000 chr4A 87.183 827 99 6 10 834 603762668 603761847 0.000000e+00 933.0
14 TraesCS3D01G392000 chr7D 87.700 813 94 6 18 828 501028105 501027297 0.000000e+00 942.0
15 TraesCS3D01G392000 chr6A 86.336 827 107 5 4 828 125250708 125251530 0.000000e+00 896.0
16 TraesCS3D01G392000 chr6A 84.116 831 123 9 1 828 18578138 18578962 0.000000e+00 795.0
17 TraesCS3D01G392000 chr6A 89.441 322 24 4 953 1270 606975081 606975396 7.660000e-107 398.0
18 TraesCS3D01G392000 chr6A 100.000 33 0 0 914 946 606975091 606975123 1.140000e-05 62.1
19 TraesCS3D01G392000 chr2D 86.199 826 111 3 1 826 450246844 450247666 0.000000e+00 891.0
20 TraesCS3D01G392000 chr5D 85.301 830 116 6 1 828 360908259 360909084 0.000000e+00 852.0
21 TraesCS3D01G392000 chr5B 84.764 827 119 7 4 828 660722860 660722039 0.000000e+00 822.0
22 TraesCS3D01G392000 chr6D 90.823 316 19 2 954 1265 460718092 460718401 7.610000e-112 414.0
23 TraesCS3D01G392000 chr6D 100.000 32 0 0 915 946 460718102 460718133 4.110000e-05 60.2
24 TraesCS3D01G392000 chr6D 100.000 31 0 0 2882 2912 460722729 460722759 1.480000e-04 58.4
25 TraesCS3D01G392000 chr6B 90.759 303 21 2 954 1249 701886587 701886889 7.660000e-107 398.0
26 TraesCS3D01G392000 chr6B 100.000 33 0 0 914 946 701886596 701886628 1.140000e-05 62.1


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 TraesCS3D01G392000 chr3D 507041651 507045456 3805 True 7029.000000 7029 100.0000 1 3806 1 chr3D.!!$R1 3805
1 TraesCS3D01G392000 chr3D 507108027 507111070 3043 True 1694.000000 3160 87.0720 1512 3806 2 chr3D.!!$R2 2294
2 TraesCS3D01G392000 chr3B 669442438 669445188 2750 True 4104.000000 4104 93.6910 950 3692 1 chr3B.!!$R2 2742
3 TraesCS3D01G392000 chr3B 654052622 654053401 779 True 693.000000 693 82.8070 1 787 1 chr3B.!!$R1 786
4 TraesCS3D01G392000 chr3A 645147244 645150235 2991 True 2236.000000 3831 92.6575 950 3806 2 chr3A.!!$R1 2856
5 TraesCS3D01G392000 chr3A 645389994 645392933 2939 True 1306.566667 3803 92.3770 851 3806 3 chr3A.!!$R2 2955
6 TraesCS3D01G392000 chr5A 510160274 510161470 1196 False 948.000000 1098 95.4520 1774 3012 2 chr5A.!!$F1 1238
7 TraesCS3D01G392000 chr4A 603832442 603833264 822 True 957.000000 957 87.6660 10 834 1 chr4A.!!$R2 824
8 TraesCS3D01G392000 chr4A 603761847 603762668 821 True 933.000000 933 87.1830 10 834 1 chr4A.!!$R1 824
9 TraesCS3D01G392000 chr7D 501027297 501028105 808 True 942.000000 942 87.7000 18 828 1 chr7D.!!$R1 810
10 TraesCS3D01G392000 chr6A 125250708 125251530 822 False 896.000000 896 86.3360 4 828 1 chr6A.!!$F2 824
11 TraesCS3D01G392000 chr6A 18578138 18578962 824 False 795.000000 795 84.1160 1 828 1 chr6A.!!$F1 827
12 TraesCS3D01G392000 chr2D 450246844 450247666 822 False 891.000000 891 86.1990 1 826 1 chr2D.!!$F1 825
13 TraesCS3D01G392000 chr5D 360908259 360909084 825 False 852.000000 852 85.3010 1 828 1 chr5D.!!$F1 827
14 TraesCS3D01G392000 chr5B 660722039 660722860 821 True 822.000000 822 84.7640 4 828 1 chr5B.!!$R1 824

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
781 784 0.179111 GGATCGCAATCTCCACGTCA 60.179 55.0 0.0 0.0 32.12 4.35 F
1315 1350 0.601311 GGATGATCCCTTCGCCTTCG 60.601 60.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1902 2.108514 CGCCGTCCGGAGTACAGTA 61.109 63.158 3.06 0.0 37.5 2.74 R
2871 2915 1.039785 TCACCAGAGATGCGGAGAGG 61.040 60.000 0.00 0.0 0.0 3.69 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
80 81 6.783708 ACCACCAAAGAAACAACATTCTTA 57.216 33.333 3.00 0.00 46.25 2.10
83 84 7.123547 ACCACCAAAGAAACAACATTCTTAAGA 59.876 33.333 0.00 0.00 46.25 2.10
110 111 7.606456 GGTTTTGTAACATCCACTCTGATTCTA 59.394 37.037 0.00 0.00 35.92 2.10
170 171 4.356405 TTCAGCAAAGATGAACTCTCCA 57.644 40.909 0.00 0.00 32.88 3.86
181 182 2.965831 TGAACTCTCCAACAGTAGCAGT 59.034 45.455 0.00 0.00 0.00 4.40
208 209 4.074970 GACTTGATCAGGCCAAAGAAGAA 58.925 43.478 5.01 0.00 0.00 2.52
243 244 6.276091 TCGTGAATTTAGATCCACATCTCAG 58.724 40.000 0.00 0.00 40.18 3.35
253 254 6.064060 AGATCCACATCTCAGTTTTGTTCAA 58.936 36.000 0.00 0.00 33.71 2.69
254 255 5.756195 TCCACATCTCAGTTTTGTTCAAG 57.244 39.130 0.00 0.00 0.00 3.02
266 267 5.981315 AGTTTTGTTCAAGTCTATCGACGAA 59.019 36.000 0.00 0.00 44.93 3.85
269 270 3.504906 TGTTCAAGTCTATCGACGAAGGT 59.495 43.478 0.00 0.00 44.93 3.50
373 374 1.167851 CCGAGGCAAGAGAATTGCAA 58.832 50.000 13.94 0.00 46.58 4.08
380 381 3.255642 GGCAAGAGAATTGCAAGGTGTAA 59.744 43.478 13.94 0.00 46.58 2.41
389 390 4.394439 TTGCAAGGTGTAAAGGTTTTCC 57.606 40.909 0.00 0.00 41.05 3.13
461 462 6.986817 GCATATTGTGATAGAACCAGTACTGT 59.013 38.462 21.18 3.76 0.00 3.55
469 470 9.775854 GTGATAGAACCAGTACTGTCTATACTA 57.224 37.037 25.01 17.32 32.45 1.82
530 531 2.635229 CTTCCTCTGGGATGTCGCCG 62.635 65.000 0.00 0.00 41.87 6.46
545 546 0.319211 CGCCGTCTTCTACCACAACA 60.319 55.000 0.00 0.00 0.00 3.33
601 602 1.944709 CATCATTGCTTCCATCTCGCA 59.055 47.619 0.00 0.00 0.00 5.10
634 635 2.872001 CGCAGACGTCGAGCACTC 60.872 66.667 27.31 7.45 33.53 3.51
696 699 1.619160 GGAGGTTCCCTAAGTCGACCT 60.619 57.143 13.01 0.75 43.12 3.85
707 710 2.437449 TCGACCTCCCTTCGACCA 59.563 61.111 0.00 0.00 40.51 4.02
781 784 0.179111 GGATCGCAATCTCCACGTCA 60.179 55.000 0.00 0.00 32.12 4.35
789 792 2.198827 ATCTCCACGTCAATGCCAAA 57.801 45.000 0.00 0.00 0.00 3.28
796 799 1.286880 GTCAATGCCAAAGCGCTGT 59.713 52.632 12.58 0.14 44.31 4.40
834 838 3.150767 CCTAACTAGAGGGGATCACGAG 58.849 54.545 0.00 0.00 32.39 4.18
835 839 2.830651 AACTAGAGGGGATCACGAGT 57.169 50.000 0.00 0.00 0.00 4.18
836 840 2.830651 ACTAGAGGGGATCACGAGTT 57.169 50.000 0.00 0.00 0.00 3.01
837 841 3.103080 ACTAGAGGGGATCACGAGTTT 57.897 47.619 0.00 0.00 0.00 2.66
838 842 3.025262 ACTAGAGGGGATCACGAGTTTC 58.975 50.000 0.00 0.00 0.00 2.78
839 843 2.239681 AGAGGGGATCACGAGTTTCT 57.760 50.000 0.00 0.00 0.00 2.52
840 844 2.541466 AGAGGGGATCACGAGTTTCTT 58.459 47.619 0.00 0.00 0.00 2.52
841 845 3.709587 AGAGGGGATCACGAGTTTCTTA 58.290 45.455 0.00 0.00 0.00 2.10
842 846 4.290942 AGAGGGGATCACGAGTTTCTTAT 58.709 43.478 0.00 0.00 0.00 1.73
843 847 5.455872 AGAGGGGATCACGAGTTTCTTATA 58.544 41.667 0.00 0.00 0.00 0.98
844 848 6.078664 AGAGGGGATCACGAGTTTCTTATAT 58.921 40.000 0.00 0.00 0.00 0.86
845 849 6.555360 AGAGGGGATCACGAGTTTCTTATATT 59.445 38.462 0.00 0.00 0.00 1.28
846 850 7.728981 AGAGGGGATCACGAGTTTCTTATATTA 59.271 37.037 0.00 0.00 0.00 0.98
847 851 8.258850 AGGGGATCACGAGTTTCTTATATTAA 57.741 34.615 0.00 0.00 0.00 1.40
848 852 8.368668 AGGGGATCACGAGTTTCTTATATTAAG 58.631 37.037 0.00 0.00 0.00 1.85
849 853 8.148999 GGGGATCACGAGTTTCTTATATTAAGT 58.851 37.037 0.00 0.00 0.00 2.24
886 890 9.332502 TCAACTACTTAGCACAAATAAGTTTGA 57.667 29.630 7.79 6.36 46.03 2.69
889 893 8.730680 ACTACTTAGCACAAATAAGTTTGATGG 58.269 33.333 7.79 0.00 46.03 3.51
890 894 6.924111 ACTTAGCACAAATAAGTTTGATGGG 58.076 36.000 7.79 0.00 46.03 4.00
891 895 4.192429 AGCACAAATAAGTTTGATGGGC 57.808 40.909 7.79 0.00 46.03 5.36
892 896 3.577848 AGCACAAATAAGTTTGATGGGCA 59.422 39.130 7.79 0.00 46.03 5.36
893 897 4.223477 AGCACAAATAAGTTTGATGGGCAT 59.777 37.500 7.79 0.00 46.03 4.40
894 898 4.567959 GCACAAATAAGTTTGATGGGCATC 59.432 41.667 7.79 0.00 46.03 3.91
895 899 5.722263 CACAAATAAGTTTGATGGGCATCA 58.278 37.500 7.79 0.00 46.03 3.07
896 900 6.342906 CACAAATAAGTTTGATGGGCATCAT 58.657 36.000 7.79 0.00 46.12 2.45
897 901 6.256975 CACAAATAAGTTTGATGGGCATCATG 59.743 38.462 7.79 0.00 46.12 3.07
898 902 5.540400 AATAAGTTTGATGGGCATCATGG 57.460 39.130 0.00 0.00 46.12 3.66
899 903 1.117150 AGTTTGATGGGCATCATGGC 58.883 50.000 1.56 1.56 46.12 4.40
909 913 2.105006 GCATCATGGCCATCGATACT 57.895 50.000 17.61 0.00 0.00 2.12
910 914 3.251479 GCATCATGGCCATCGATACTA 57.749 47.619 17.61 0.00 0.00 1.82
911 915 3.801698 GCATCATGGCCATCGATACTAT 58.198 45.455 17.61 0.00 0.00 2.12
1113 1136 3.964221 GACGACGATGTGGCGCTCA 62.964 63.158 7.64 7.90 33.86 4.26
1302 1337 2.527875 GAGGCCCTCCCGGATGAT 60.528 66.667 0.73 0.00 39.21 2.45
1315 1350 0.601311 GGATGATCCCTTCGCCTTCG 60.601 60.000 0.00 0.00 0.00 3.79
1398 1433 4.088351 TGGGAGGAGGATGCGGGA 62.088 66.667 0.00 0.00 0.00 5.14
1867 1902 4.458989 TGCTTGACAAGTTCAGTGAGTTTT 59.541 37.500 16.39 0.00 34.94 2.43
1868 1903 5.645929 TGCTTGACAAGTTCAGTGAGTTTTA 59.354 36.000 16.39 0.00 34.94 1.52
2225 2268 1.326548 GTCCTTTGCTGCCGTTATACG 59.673 52.381 0.00 0.00 42.11 3.06
2251 2294 2.439409 TGTGCAGGATGAAGAATGTGG 58.561 47.619 0.00 0.00 39.69 4.17
2253 2296 3.285484 GTGCAGGATGAAGAATGTGGAT 58.715 45.455 0.00 0.00 39.69 3.41
2516 2560 7.995463 AGAAGATCTATCGAAAACTAAGCAC 57.005 36.000 0.00 0.00 0.00 4.40
2750 2794 1.070758 CATTACCCGCAGCCTCATAGT 59.929 52.381 0.00 0.00 0.00 2.12
2782 2826 3.448660 GGAATTGGAAATGGAAGAGGTGG 59.551 47.826 0.00 0.00 0.00 4.61
2870 2914 2.768253 GGGGAATTTGCCCTCTTTTG 57.232 50.000 18.15 0.00 45.75 2.44
2871 2915 1.339055 GGGGAATTTGCCCTCTTTTGC 60.339 52.381 18.15 0.00 45.75 3.68
3221 3270 1.596934 GCAGCAGCAGGTACCTGTA 59.403 57.895 36.31 0.00 45.24 2.74
3239 3288 0.882927 TAGGTGCTTTGGTGCGTGAC 60.883 55.000 0.00 0.00 35.36 3.67
3268 3317 7.503566 ACAAGAACATGCCTATATGCTGTTATT 59.496 33.333 13.51 13.62 35.86 1.40
3338 3499 6.653320 TCATAGATTTGTTGACACTGGTAACC 59.347 38.462 0.00 0.00 0.00 2.85
3344 3505 1.991121 TGACACTGGTAACCGACTCT 58.009 50.000 0.00 0.00 0.00 3.24
3358 3519 2.351447 CCGACTCTGCGAAGACACTTTA 60.351 50.000 0.00 0.00 0.00 1.85
3457 3630 8.458843 GCACTTGATGGTTTATTACTAATGTGT 58.541 33.333 0.00 0.00 0.00 3.72
3478 3651 6.043411 GTGTATTCACTGATAACACTCTCCC 58.957 44.000 13.47 0.00 40.98 4.30
3508 3681 0.746063 CTGCTGGGTCTTTTGTGCAA 59.254 50.000 0.00 0.00 0.00 4.08
3517 3690 5.248020 TGGGTCTTTTGTGCAATATTTGGAT 59.752 36.000 0.00 0.00 32.24 3.41
3536 3710 6.908870 TGGATCATGATTTGACGAGTTTAG 57.091 37.500 10.14 0.00 37.11 1.85
3537 3711 6.406370 TGGATCATGATTTGACGAGTTTAGT 58.594 36.000 10.14 0.00 37.11 2.24
3538 3712 6.313658 TGGATCATGATTTGACGAGTTTAGTG 59.686 38.462 10.14 0.00 37.11 2.74
3539 3713 6.313905 GGATCATGATTTGACGAGTTTAGTGT 59.686 38.462 10.14 0.00 37.11 3.55
3571 3745 7.652909 TGACTATTCAGCTTTTCATTTGGTTTG 59.347 33.333 0.00 0.00 0.00 2.93
3634 3818 2.756207 TGTGTAATCACCGCACTAGCTA 59.244 45.455 0.00 0.00 43.26 3.32
3651 3835 1.468565 GCTACGGTTACTGCGATCACA 60.469 52.381 0.00 0.00 0.00 3.58
3734 3922 6.988580 ACATGAAATCTCAGCTGAATCGAATA 59.011 34.615 18.85 2.37 34.23 1.75
3775 3967 1.497716 TCGGGCCTAATCAGGAGTAGA 59.502 52.381 0.84 0.00 45.91 2.59
3776 3968 2.110188 TCGGGCCTAATCAGGAGTAGAT 59.890 50.000 0.84 0.00 45.91 1.98
3777 3969 2.232452 CGGGCCTAATCAGGAGTAGATG 59.768 54.545 0.84 0.00 45.91 2.90
3778 3970 2.569404 GGGCCTAATCAGGAGTAGATGG 59.431 54.545 0.84 0.00 45.91 3.51
3783 3975 4.081198 CCTAATCAGGAGTAGATGGATGCC 60.081 50.000 5.41 0.00 45.91 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.115467 AGTATGAGAGGTTGCCCGAG 58.885 55.000 0.00 0.00 35.12 4.63
80 81 5.765182 CAGAGTGGATGTTACAAAACCTCTT 59.235 40.000 10.48 2.69 31.10 2.85
83 84 5.304686 TCAGAGTGGATGTTACAAAACCT 57.695 39.130 0.00 0.00 34.49 3.50
170 171 2.016905 AGTCCCTGACTGCTACTGTT 57.983 50.000 0.00 0.00 41.76 3.16
181 182 0.547471 TGGCCTGATCAAGTCCCTGA 60.547 55.000 3.32 0.00 0.00 3.86
208 209 6.485830 TCTAAATTCACGATCTCCCAGAAT 57.514 37.500 0.00 0.00 0.00 2.40
373 374 4.562963 CGCTAGAGGAAAACCTTTACACCT 60.563 45.833 0.00 0.00 0.00 4.00
380 381 1.067071 CGACCGCTAGAGGAAAACCTT 60.067 52.381 20.46 0.00 34.73 3.50
389 390 4.430908 AGGTAAAATTTCGACCGCTAGAG 58.569 43.478 13.74 0.00 38.35 2.43
392 393 4.460948 AGAGGTAAAATTTCGACCGCTA 57.539 40.909 20.16 0.00 41.02 4.26
461 462 7.430211 CGCGTAAACACTGACAAATAGTATAGA 59.570 37.037 0.00 0.00 0.00 1.98
469 470 2.096417 GCTCGCGTAAACACTGACAAAT 60.096 45.455 5.77 0.00 0.00 2.32
505 506 2.123632 TCCCAGAGGAAGCTGCCT 59.876 61.111 15.29 15.29 40.08 4.75
530 531 4.385825 TGGTTGATGTTGTGGTAGAAGAC 58.614 43.478 0.00 0.00 0.00 3.01
545 546 4.042884 TGAAGGAGGATGATCTGGTTGAT 58.957 43.478 0.00 0.00 38.27 2.57
631 632 1.767681 GGGCAAGAGATCTGATGGAGT 59.232 52.381 0.00 0.00 0.00 3.85
633 634 0.755079 CGGGCAAGAGATCTGATGGA 59.245 55.000 0.00 0.00 0.00 3.41
634 635 0.755079 TCGGGCAAGAGATCTGATGG 59.245 55.000 0.00 0.00 0.00 3.51
690 693 1.975407 GTGGTCGAAGGGAGGTCGA 60.975 63.158 0.00 0.00 44.82 4.20
696 699 1.592400 CTAGCGTGTGGTCGAAGGGA 61.592 60.000 0.00 0.00 0.00 4.20
769 772 2.198827 TTGGCATTGACGTGGAGATT 57.801 45.000 0.00 0.00 0.00 2.40
781 784 2.562912 CGACAGCGCTTTGGCATT 59.437 55.556 7.50 0.00 38.60 3.56
796 799 0.475048 AGGGTTTTTCCTCCTCCCGA 60.475 55.000 0.00 0.00 42.57 5.14
847 851 9.944376 TGCTAAGTAGTTGAATTTCAAGATACT 57.056 29.630 20.81 20.81 39.66 2.12
848 852 9.974750 GTGCTAAGTAGTTGAATTTCAAGATAC 57.025 33.333 12.02 15.95 37.00 2.24
849 853 9.719355 TGTGCTAAGTAGTTGAATTTCAAGATA 57.281 29.630 12.02 6.08 37.00 1.98
850 854 8.621532 TGTGCTAAGTAGTTGAATTTCAAGAT 57.378 30.769 12.02 6.98 37.00 2.40
851 855 8.445275 TTGTGCTAAGTAGTTGAATTTCAAGA 57.555 30.769 12.02 1.26 37.00 3.02
852 856 9.683069 ATTTGTGCTAAGTAGTTGAATTTCAAG 57.317 29.630 12.02 0.36 37.00 3.02
890 894 2.105006 AGTATCGATGGCCATGATGC 57.895 50.000 26.56 25.44 0.00 3.91
891 895 5.014808 TCATAGTATCGATGGCCATGATG 57.985 43.478 26.56 13.03 0.00 3.07
892 896 4.713814 ACTCATAGTATCGATGGCCATGAT 59.286 41.667 26.56 25.28 0.00 2.45
893 897 4.082026 CACTCATAGTATCGATGGCCATGA 60.082 45.833 26.56 20.53 0.00 3.07
894 898 4.179298 CACTCATAGTATCGATGGCCATG 58.821 47.826 26.56 15.66 0.00 3.66
895 899 3.196469 CCACTCATAGTATCGATGGCCAT 59.804 47.826 20.96 20.96 0.00 4.40
896 900 2.562738 CCACTCATAGTATCGATGGCCA 59.437 50.000 8.56 8.56 0.00 5.36
897 901 2.675317 GCCACTCATAGTATCGATGGCC 60.675 54.545 8.54 0.00 44.34 5.36
898 902 2.611518 GCCACTCATAGTATCGATGGC 58.388 52.381 8.54 6.66 43.89 4.40
899 903 2.093973 GGGCCACTCATAGTATCGATGG 60.094 54.545 8.54 0.00 0.00 3.51
900 904 2.562738 TGGGCCACTCATAGTATCGATG 59.437 50.000 8.54 0.00 0.00 3.84
901 905 2.889512 TGGGCCACTCATAGTATCGAT 58.110 47.619 0.00 2.16 0.00 3.59
902 906 2.364324 GTTGGGCCACTCATAGTATCGA 59.636 50.000 5.23 0.00 0.00 3.59
903 907 2.102420 TGTTGGGCCACTCATAGTATCG 59.898 50.000 5.23 0.00 0.00 2.92
904 908 3.838244 TGTTGGGCCACTCATAGTATC 57.162 47.619 5.23 0.00 0.00 2.24
905 909 4.796110 ATTGTTGGGCCACTCATAGTAT 57.204 40.909 5.23 0.00 0.00 2.12
906 910 4.444306 GCTATTGTTGGGCCACTCATAGTA 60.444 45.833 5.23 2.51 0.00 1.82
907 911 3.685550 GCTATTGTTGGGCCACTCATAGT 60.686 47.826 5.23 1.44 0.00 2.12
908 912 2.880890 GCTATTGTTGGGCCACTCATAG 59.119 50.000 5.23 12.75 0.00 2.23
909 913 2.422803 GGCTATTGTTGGGCCACTCATA 60.423 50.000 5.23 1.36 44.69 2.15
910 914 1.686115 GGCTATTGTTGGGCCACTCAT 60.686 52.381 5.23 0.00 44.69 2.90
911 915 0.323360 GGCTATTGTTGGGCCACTCA 60.323 55.000 5.23 6.04 44.69 3.41
989 993 6.040616 TGAAAGGTTTCGCATTAGGGTTTAAA 59.959 34.615 0.00 0.00 40.01 1.52
1090 1113 2.175078 CCACATCGTCGTCGTCGT 59.825 61.111 11.41 0.00 38.33 4.34
1189 1212 3.407967 GGGTGGGGCTCGGATCAA 61.408 66.667 0.00 0.00 0.00 2.57
1220 1243 1.388837 GGAGAGGAAGCGGGAGAGAC 61.389 65.000 0.00 0.00 0.00 3.36
1398 1433 1.136984 GAAGATGTCGTCGGCGTCT 59.863 57.895 15.72 15.72 39.49 4.18
1569 1604 1.073373 CTCGGCGGAGAGGAGGATA 59.927 63.158 15.82 0.00 43.27 2.59
1867 1902 2.108514 CGCCGTCCGGAGTACAGTA 61.109 63.158 3.06 0.00 37.50 2.74
1868 1903 3.437795 CGCCGTCCGGAGTACAGT 61.438 66.667 3.06 0.00 37.50 3.55
2225 2268 5.182001 ACATTCTTCATCCTGCACAAACTAC 59.818 40.000 0.00 0.00 0.00 2.73
2251 2294 4.430137 TCAACAGCTTCTTTGCATCATC 57.570 40.909 0.00 0.00 34.99 2.92
2253 2296 3.822167 TCATCAACAGCTTCTTTGCATCA 59.178 39.130 0.00 0.00 34.99 3.07
2516 2560 5.402568 CGGATCAGTATGTGATAAGAAACCG 59.597 44.000 0.00 0.00 46.64 4.44
2750 2794 4.706476 CCATTTCCAATTCCTTGACTGCTA 59.294 41.667 0.00 0.00 34.04 3.49
2782 2826 1.067516 TGCTTCTTGGCTGTCTTTTGC 59.932 47.619 0.00 0.00 0.00 3.68
2870 2914 2.420890 CCAGAGATGCGGAGAGGC 59.579 66.667 0.00 0.00 0.00 4.70
2871 2915 1.039785 TCACCAGAGATGCGGAGAGG 61.040 60.000 0.00 0.00 0.00 3.69
2961 3005 1.873591 CTGCCGGTCCAGCATTTATAC 59.126 52.381 1.90 0.00 40.04 1.47
3035 3081 7.095691 GGATCAAAATTTGCGTGAAAATTCTCA 60.096 33.333 0.00 0.00 38.49 3.27
3180 3229 6.481644 TGCATCAACATGTTTTTCCTTTTACC 59.518 34.615 8.77 0.00 31.86 2.85
3221 3270 2.186826 GTCACGCACCAAAGCACCT 61.187 57.895 0.00 0.00 0.00 4.00
3239 3288 4.991056 AGCATATAGGCATGTTCTTGTACG 59.009 41.667 12.54 0.00 35.83 3.67
3268 3317 6.862608 GCATTGTCATTCTGATGTTTTACACA 59.137 34.615 0.00 0.00 40.71 3.72
3327 3481 0.317479 GCAGAGTCGGTTACCAGTGT 59.683 55.000 1.13 0.00 0.00 3.55
3338 3499 1.772182 AAAGTGTCTTCGCAGAGTCG 58.228 50.000 0.00 0.00 38.43 4.18
3344 3505 6.394809 TCATATCAGTTAAAGTGTCTTCGCA 58.605 36.000 0.00 0.00 0.00 5.10
3379 3540 5.755813 CAGCAGACTAATTGGCAATACATC 58.244 41.667 14.05 10.76 0.00 3.06
3457 3630 4.202121 GCGGGAGAGTGTTATCAGTGAATA 60.202 45.833 0.00 0.00 0.00 1.75
3508 3681 8.455903 AACTCGTCAAATCATGATCCAAATAT 57.544 30.769 9.06 0.00 40.97 1.28
3517 3690 5.989168 ACACACTAAACTCGTCAAATCATGA 59.011 36.000 0.00 0.00 35.05 3.07
3582 3756 2.687935 AGGCACTGTTTTGTGTTTCGAT 59.312 40.909 0.00 0.00 39.89 3.59
3584 3758 2.559998 AGGCACTGTTTTGTGTTTCG 57.440 45.000 0.00 0.00 39.89 3.46
3634 3818 0.736325 GCTGTGATCGCAGTAACCGT 60.736 55.000 31.23 0.00 38.65 4.83
3734 3922 4.443457 CGACCCACCAGATGACTATTCAAT 60.443 45.833 0.00 0.00 34.61 2.57
3775 3967 1.927487 TTCAACTGCAAGGCATCCAT 58.073 45.000 0.00 0.00 38.13 3.41
3776 3968 1.702182 TTTCAACTGCAAGGCATCCA 58.298 45.000 0.00 0.00 38.13 3.41
3777 3969 2.224018 TGTTTTCAACTGCAAGGCATCC 60.224 45.455 0.00 0.00 38.13 3.51
3778 3970 3.096489 TGTTTTCAACTGCAAGGCATC 57.904 42.857 0.00 0.00 38.13 3.91
3783 3975 2.861935 CTGCCTTGTTTTCAACTGCAAG 59.138 45.455 0.00 0.00 39.94 4.01


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

AutoCloner maintained by Alex Coulton.