Multiple sequence alignment - TraesCS3B01G197100

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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 TraesCS3B01G197100 chr3B 100.000 3602 0 0 725 4326 224281914 224278313 0.000000e+00 6652.0
1 TraesCS3B01G197100 chr3B 96.762 3243 74 7 1086 4326 223663312 223660099 0.000000e+00 5378.0
2 TraesCS3B01G197100 chr3B 92.347 2718 149 29 888 3594 224317408 224314739 0.000000e+00 3812.0
3 TraesCS3B01G197100 chr3B 100.000 292 0 0 1 292 224282638 224282347 1.370000e-149 540.0
4 TraesCS3B01G197100 chr3B 96.552 290 10 0 3 292 828550747 828550458 8.410000e-132 481.0
5 TraesCS3B01G197100 chr3B 94.863 292 15 0 1 292 745711870 745712161 1.420000e-124 457.0
6 TraesCS3B01G197100 chr3B 94.521 292 16 0 1 292 761666690 761666981 6.600000e-123 451.0
7 TraesCS3B01G197100 chr3B 94.178 292 17 0 1 292 734988715 734988424 3.070000e-121 446.0
8 TraesCS3B01G197100 chr3B 93.590 234 15 0 888 1121 224155983 224155750 2.480000e-92 350.0
9 TraesCS3B01G197100 chr3B 97.041 169 5 0 922 1090 223669342 223669174 7.080000e-73 285.0
10 TraesCS3B01G197100 chr3B 100.000 41 0 0 888 928 223674686 223674646 4.640000e-10 76.8
11 TraesCS3B01G197100 chr3B 95.349 43 2 0 1115 1157 224150154 224150112 7.760000e-08 69.4
12 TraesCS3B01G197100 chr3D 96.633 1574 39 5 888 2459 152848777 152847216 0.000000e+00 2601.0
13 TraesCS3B01G197100 chr3D 93.224 1579 85 9 888 2458 153082013 153080449 0.000000e+00 2303.0
14 TraesCS3B01G197100 chr3D 91.175 1575 75 24 2484 4029 153080352 153078813 0.000000e+00 2080.0
15 TraesCS3B01G197100 chr3D 96.184 1022 24 3 2460 3475 152847186 152846174 0.000000e+00 1657.0
16 TraesCS3B01G197100 chr3D 84.892 556 47 13 3472 4008 152846072 152845535 1.070000e-145 527.0
17 TraesCS3B01G197100 chr3A 96.139 1580 46 3 882 2459 177673979 177675545 0.000000e+00 2566.0
18 TraesCS3B01G197100 chr3A 92.875 1586 84 12 882 2458 177107102 177108667 0.000000e+00 2276.0
19 TraesCS3B01G197100 chr3A 89.754 1181 75 11 2481 3654 177109062 177110203 0.000000e+00 1469.0
20 TraesCS3B01G197100 chr3A 94.553 716 21 4 2512 3209 177675569 177676284 0.000000e+00 1090.0
21 TraesCS3B01G197100 chr3A 84.091 792 55 31 3273 4005 177676286 177677065 0.000000e+00 699.0
22 TraesCS3B01G197100 chr3A 96.970 165 5 0 3865 4029 177110651 177110815 1.180000e-70 278.0
23 TraesCS3B01G197100 chr1B 96.564 291 10 0 1 291 565941161 565941451 2.340000e-132 483.0
24 TraesCS3B01G197100 chr1B 95.890 292 12 0 1 292 329301642 329301933 1.410000e-129 473.0
25 TraesCS3B01G197100 chr1B 94.464 289 16 0 1 289 66280836 66280548 3.070000e-121 446.0
26 TraesCS3B01G197100 chr4B 95.548 292 13 0 1 292 644327247 644327538 6.550000e-128 468.0
27 TraesCS3B01G197100 chr4B 88.525 61 6 1 2441 2500 665610791 665610851 6.000000e-09 73.1
28 TraesCS3B01G197100 chr7B 94.178 292 17 0 1 292 673588413 673588704 3.070000e-121 446.0
29 TraesCS3B01G197100 chr5B 89.310 290 31 0 4037 4326 138555377 138555088 8.840000e-97 364.0
30 TraesCS3B01G197100 chr5B 100.000 50 0 0 801 850 670800081 670800130 4.610000e-15 93.5
31 TraesCS3B01G197100 chr5B 96.078 51 1 1 801 851 377343912 377343961 9.970000e-12 82.4
32 TraesCS3B01G197100 chr5B 97.872 47 1 0 2460 2506 440022866 440022912 9.970000e-12 82.4
33 TraesCS3B01G197100 chr5D 88.112 286 34 0 4037 4322 125775360 125775075 1.490000e-89 340.0
34 TraesCS3B01G197100 chr2D 91.071 56 3 2 2458 2513 647818464 647818411 1.670000e-09 75.0
35 TraesCS3B01G197100 chr5A 88.525 61 6 1 2441 2500 705592547 705592607 6.000000e-09 73.1


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 TraesCS3B01G197100 chr3B 224278313 224282638 4325 True 3596.000000 6652 100.000000 1 4326 2 chr3B.!!$R9 4325
1 TraesCS3B01G197100 chr3B 223660099 223663312 3213 True 5378.000000 5378 96.762000 1086 4326 1 chr3B.!!$R1 3240
2 TraesCS3B01G197100 chr3B 224314739 224317408 2669 True 3812.000000 3812 92.347000 888 3594 1 chr3B.!!$R6 2706
3 TraesCS3B01G197100 chr3D 153078813 153082013 3200 True 2191.500000 2303 92.199500 888 4029 2 chr3D.!!$R2 3141
4 TraesCS3B01G197100 chr3D 152845535 152848777 3242 True 1595.000000 2601 92.569667 888 4008 3 chr3D.!!$R1 3120
5 TraesCS3B01G197100 chr3A 177673979 177677065 3086 False 1451.666667 2566 91.594333 882 4005 3 chr3A.!!$F2 3123
6 TraesCS3B01G197100 chr3A 177107102 177110815 3713 False 1341.000000 2276 93.199667 882 4029 3 chr3A.!!$F1 3147

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
864 865 0.455815 GCGGGGTGCCAAAGATTAAG 59.544 55.0 0.00 0.00 37.76 1.85 F
2184 2211 0.745128 TTGGGGCGTAATTGGCTACG 60.745 55.0 0.89 0.89 45.89 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2838 3271 1.804748 GAAGAATTTCCTCCGTTGCGT 59.195 47.619 0.0 0.0 0.0 5.24 R
4125 4908 0.035881 CCTCTTCAGCACCTTGAGCA 59.964 55.000 0.0 0.0 0.0 4.26 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
111 112 4.293648 CACGCACCACCGGAGTCA 62.294 66.667 9.46 0.00 0.00 3.41
112 113 3.991051 ACGCACCACCGGAGTCAG 61.991 66.667 9.46 3.83 0.00 3.51
113 114 4.742201 CGCACCACCGGAGTCAGG 62.742 72.222 9.46 7.88 0.00 3.86
115 116 4.742201 CACCACCGGAGTCAGGCG 62.742 72.222 9.46 0.00 0.00 5.52
122 123 4.767255 GGAGTCAGGCGCCACTGG 62.767 72.222 31.54 15.18 38.98 4.00
239 240 4.593864 GAGGATCGCCGGAGTGCC 62.594 72.222 5.05 8.44 39.96 5.01
750 751 3.707189 GGGGGAGGAGAGGGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
751 752 2.040359 GGGGAGGAGAGGGGGAAG 60.040 72.222 0.00 0.00 0.00 3.46
752 753 2.040359 GGGAGGAGAGGGGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
753 754 2.040359 GGAGGAGAGGGGGAAGGG 60.040 72.222 0.00 0.00 0.00 3.95
754 755 2.040359 GAGGAGAGGGGGAAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
755 756 2.543637 AGGAGAGGGGGAAGGGGA 60.544 66.667 0.00 0.00 0.00 4.81
756 757 2.040359 GGAGAGGGGGAAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
757 758 2.647949 GGAGAGGGGGAAGGGGAGA 61.648 68.421 0.00 0.00 0.00 3.71
758 759 1.074850 GAGAGGGGGAAGGGGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
759 760 2.040359 GAGGGGGAAGGGGAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
760 761 3.711782 AGGGGGAAGGGGAGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
761 762 4.845307 GGGGGAAGGGGAGAGGGG 62.845 77.778 0.00 0.00 0.00 4.79
762 763 4.845307 GGGGAAGGGGAGAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
763 764 3.707189 GGGAAGGGGAGAGGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
764 765 2.040359 GGAAGGGGAGAGGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
765 766 2.040359 GAAGGGGAGAGGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
766 767 3.711782 AAGGGGAGAGGGGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
769 770 4.179599 GGGAGAGGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
770 771 4.890306 GGAGAGGGGGAGGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
841 842 4.304432 CCTAGGGAGGGGAGCTTC 57.696 66.667 0.00 0.00 39.48 3.86
842 843 1.834822 CCTAGGGAGGGGAGCTTCG 60.835 68.421 0.00 0.00 39.48 3.79
843 844 2.444140 TAGGGAGGGGAGCTTCGC 60.444 66.667 0.00 0.00 0.00 4.70
861 862 3.061848 CGCGGGGTGCCAAAGATT 61.062 61.111 0.00 0.00 42.08 2.40
862 863 1.747367 CGCGGGGTGCCAAAGATTA 60.747 57.895 0.00 0.00 42.08 1.75
863 864 1.309499 CGCGGGGTGCCAAAGATTAA 61.309 55.000 0.00 0.00 42.08 1.40
864 865 0.455815 GCGGGGTGCCAAAGATTAAG 59.544 55.000 0.00 0.00 37.76 1.85
865 866 1.953311 GCGGGGTGCCAAAGATTAAGA 60.953 52.381 0.00 0.00 37.76 2.10
866 867 2.654863 CGGGGTGCCAAAGATTAAGAT 58.345 47.619 0.00 0.00 0.00 2.40
867 868 2.618709 CGGGGTGCCAAAGATTAAGATC 59.381 50.000 0.00 0.00 0.00 2.75
868 869 3.685550 CGGGGTGCCAAAGATTAAGATCT 60.686 47.826 0.00 0.00 44.51 2.75
930 931 2.715880 TCCATGGCTTATCATTGGGCTA 59.284 45.455 6.96 0.00 0.00 3.93
937 938 5.222192 TGGCTTATCATTGGGCTATCAGAAT 60.222 40.000 0.00 0.00 0.00 2.40
1003 1004 1.918262 AGAACTTGGGATCTGCCATGA 59.082 47.619 10.03 0.00 38.95 3.07
1064 1065 3.941483 CGATCAGCAGGGTGAGTAATTTT 59.059 43.478 7.30 0.00 0.00 1.82
1171 1172 5.804944 CTGGTGATCTCCAGTCATTATCT 57.195 43.478 28.32 0.00 46.92 1.98
1172 1173 6.172136 CTGGTGATCTCCAGTCATTATCTT 57.828 41.667 28.32 0.00 46.92 2.40
1173 1174 5.922053 TGGTGATCTCCAGTCATTATCTTG 58.078 41.667 12.50 0.00 33.19 3.02
1855 1872 6.038356 TCTACAACCGCTACTTAAAGCATAC 58.962 40.000 0.38 0.00 42.91 2.39
2059 2080 8.746922 TGATTTGAATGAGTTGCACTAAATTC 57.253 30.769 0.00 2.19 34.47 2.17
2184 2211 0.745128 TTGGGGCGTAATTGGCTACG 60.745 55.000 0.89 0.89 45.89 3.51
2838 3271 9.719355 TGCTTTAGATCACTGTATGTTCTTTTA 57.281 29.630 0.00 0.00 38.20 1.52
3194 3628 1.136147 CTTGGAGCTGCATTGACGC 59.864 57.895 9.39 0.00 0.00 5.19
3259 3693 0.878086 GCCTAGCTGTTCGGCTGATC 60.878 60.000 15.35 0.00 43.01 2.92
3442 3877 1.621672 GCCAGCAGGAAGGTAGCTCT 61.622 60.000 0.00 0.00 36.26 4.09
3443 3878 0.463620 CCAGCAGGAAGGTAGCTCTC 59.536 60.000 0.00 0.00 36.26 3.20
3486 3921 7.071069 ACATGCATATACTTGAATGAGAGGA 57.929 36.000 0.00 0.00 36.33 3.71
3488 3923 7.660617 ACATGCATATACTTGAATGAGAGGAAG 59.339 37.037 0.00 0.00 36.33 3.46
3489 3924 7.365497 TGCATATACTTGAATGAGAGGAAGA 57.635 36.000 0.00 0.00 0.00 2.87
3490 3925 7.440198 TGCATATACTTGAATGAGAGGAAGAG 58.560 38.462 0.00 0.00 0.00 2.85
3491 3926 7.070447 TGCATATACTTGAATGAGAGGAAGAGT 59.930 37.037 0.00 0.00 0.00 3.24
3492 3927 7.384660 GCATATACTTGAATGAGAGGAAGAGTG 59.615 40.741 0.00 0.00 0.00 3.51
3493 3928 3.936564 ACTTGAATGAGAGGAAGAGTGC 58.063 45.455 0.00 0.00 0.00 4.40
3494 3929 3.326006 ACTTGAATGAGAGGAAGAGTGCA 59.674 43.478 0.00 0.00 0.00 4.57
3495 3930 4.202398 ACTTGAATGAGAGGAAGAGTGCAA 60.202 41.667 0.00 0.00 0.00 4.08
3509 4050 4.446371 AGAGTGCAATAGCTGACATTACC 58.554 43.478 0.00 0.00 42.74 2.85
3538 4079 4.605640 AAGCAATGGCAAAACTGTGTAT 57.394 36.364 0.00 0.00 44.61 2.29
3974 4756 4.340617 TCTTTCCAACCAAACACAAGAGT 58.659 39.130 0.00 0.00 0.00 3.24
4029 4812 3.255642 ACCAAACAGATGAATGAAACCGG 59.744 43.478 0.00 0.00 0.00 5.28
4032 4815 2.711542 ACAGATGAATGAAACCGGTCC 58.288 47.619 8.04 3.33 0.00 4.46
4063 4846 4.347583 TGGAAGGGCAAGTTGATGAATTTT 59.652 37.500 7.16 0.00 0.00 1.82
4072 4855 1.543607 TGATGAATTTTGCAGGCCGA 58.456 45.000 0.00 0.00 0.00 5.54
4073 4856 2.101783 TGATGAATTTTGCAGGCCGAT 58.898 42.857 0.00 0.00 0.00 4.18
4100 4883 1.664965 GTGCGAACGGTGCTCTCTT 60.665 57.895 0.00 0.00 0.00 2.85
4101 4884 1.372997 TGCGAACGGTGCTCTCTTC 60.373 57.895 0.00 0.00 0.00 2.87
4117 4900 0.890996 CTTCCCTGCCAACTTTCGCT 60.891 55.000 0.00 0.00 0.00 4.93
4118 4901 0.467290 TTCCCTGCCAACTTTCGCTT 60.467 50.000 0.00 0.00 0.00 4.68
4119 4902 0.467290 TCCCTGCCAACTTTCGCTTT 60.467 50.000 0.00 0.00 0.00 3.51
4120 4903 0.318955 CCCTGCCAACTTTCGCTTTG 60.319 55.000 0.00 0.00 0.00 2.77
4121 4904 0.667993 CCTGCCAACTTTCGCTTTGA 59.332 50.000 0.00 0.00 0.00 2.69
4122 4905 1.600413 CCTGCCAACTTTCGCTTTGAC 60.600 52.381 0.00 0.00 0.00 3.18
4123 4906 1.065401 CTGCCAACTTTCGCTTTGACA 59.935 47.619 0.00 0.00 0.00 3.58
4124 4907 1.065401 TGCCAACTTTCGCTTTGACAG 59.935 47.619 0.00 0.00 0.00 3.51
4125 4908 1.065551 GCCAACTTTCGCTTTGACAGT 59.934 47.619 0.00 0.00 39.28 3.55
4126 4909 2.719798 CCAACTTTCGCTTTGACAGTG 58.280 47.619 0.00 0.00 37.67 3.66
4127 4910 2.111756 CAACTTTCGCTTTGACAGTGC 58.888 47.619 0.00 0.00 37.67 4.40
4128 4911 1.668419 ACTTTCGCTTTGACAGTGCT 58.332 45.000 0.00 0.00 36.28 4.40
4129 4912 1.599542 ACTTTCGCTTTGACAGTGCTC 59.400 47.619 0.00 0.00 36.28 4.26
4130 4913 1.599071 CTTTCGCTTTGACAGTGCTCA 59.401 47.619 0.00 0.00 32.41 4.26
4131 4914 1.662517 TTCGCTTTGACAGTGCTCAA 58.337 45.000 4.62 4.62 32.41 3.02
4132 4915 1.220529 TCGCTTTGACAGTGCTCAAG 58.779 50.000 7.77 1.31 31.76 3.02
4133 4916 0.236711 CGCTTTGACAGTGCTCAAGG 59.763 55.000 10.91 10.91 31.76 3.61
4137 4920 0.181114 TTGACAGTGCTCAAGGTGCT 59.819 50.000 4.62 0.00 0.00 4.40
4206 4989 3.482783 GCAGGACGAAGCGCTGAC 61.483 66.667 12.58 7.85 0.00 3.51
4228 5011 0.459489 GTGGAAAGTGCAAAGTGGCA 59.541 50.000 0.00 0.00 42.53 4.92
4318 5101 2.565841 GCCCTAAGACTATGCTGGTTG 58.434 52.381 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 4.293648 TGACTCCGGTGGTGCGTG 62.294 66.667 8.63 0.00 0.00 5.34
95 96 3.991051 CTGACTCCGGTGGTGCGT 61.991 66.667 8.63 0.00 0.00 5.24
96 97 4.742201 CCTGACTCCGGTGGTGCG 62.742 72.222 8.63 0.00 0.00 5.34
98 99 4.742201 CGCCTGACTCCGGTGGTG 62.742 72.222 8.63 4.22 0.00 4.17
105 106 4.767255 CCAGTGGCGCCTGACTCC 62.767 72.222 29.70 8.28 34.23 3.85
220 221 4.271816 CACTCCGGCGATCCTCGG 62.272 72.222 9.30 13.39 46.89 4.63
221 222 4.933064 GCACTCCGGCGATCCTCG 62.933 72.222 9.30 0.00 43.89 4.63
222 223 4.593864 GGCACTCCGGCGATCCTC 62.594 72.222 9.30 0.00 33.57 3.71
733 734 3.707189 TTCCCCCTCTCCTCCCCC 61.707 72.222 0.00 0.00 0.00 5.40
734 735 2.040359 CTTCCCCCTCTCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
735 736 2.040359 CCTTCCCCCTCTCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
736 737 2.040359 CCCTTCCCCCTCTCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
737 738 2.040359 CCCCTTCCCCCTCTCCTC 60.040 72.222 0.00 0.00 0.00 3.71
738 739 2.543637 TCCCCTTCCCCCTCTCCT 60.544 66.667 0.00 0.00 0.00 3.69
739 740 2.040359 CTCCCCTTCCCCCTCTCC 60.040 72.222 0.00 0.00 0.00 3.71
740 741 1.074850 CTCTCCCCTTCCCCCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
741 742 2.652113 CCTCTCCCCTTCCCCCTCT 61.652 68.421 0.00 0.00 0.00 3.69
742 743 2.040359 CCTCTCCCCTTCCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
743 744 3.711782 CCCTCTCCCCTTCCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
744 745 4.845307 CCCCTCTCCCCTTCCCCC 62.845 77.778 0.00 0.00 0.00 5.40
745 746 4.845307 CCCCCTCTCCCCTTCCCC 62.845 77.778 0.00 0.00 0.00 4.81
746 747 3.707189 TCCCCCTCTCCCCTTCCC 61.707 72.222 0.00 0.00 0.00 3.97
747 748 2.040359 CTCCCCCTCTCCCCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
748 749 2.040359 CCTCCCCCTCTCCCCTTC 60.040 72.222 0.00 0.00 0.00 3.46
749 750 3.711782 CCCTCCCCCTCTCCCCTT 61.712 72.222 0.00 0.00 0.00 3.95
752 753 4.179599 CTCCCCTCCCCCTCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
753 754 4.890306 GCTCCCCTCCCCCTCTCC 62.890 77.778 0.00 0.00 0.00 3.71
815 816 1.693103 CCTCCCTAGGGTTCCCACC 60.693 68.421 27.58 0.00 43.37 4.61
816 817 4.068257 CCTCCCTAGGGTTCCCAC 57.932 66.667 27.58 0.00 39.48 4.61
824 825 1.834822 CGAAGCTCCCCTCCCTAGG 60.835 68.421 0.06 0.06 43.25 3.02
825 826 3.863606 CGAAGCTCCCCTCCCTAG 58.136 66.667 0.00 0.00 0.00 3.02
844 845 1.309499 TTAATCTTTGGCACCCCGCG 61.309 55.000 0.00 0.00 43.84 6.46
845 846 0.455815 CTTAATCTTTGGCACCCCGC 59.544 55.000 0.00 0.00 41.28 6.13
846 847 2.122783 TCTTAATCTTTGGCACCCCG 57.877 50.000 0.00 0.00 0.00 5.73
847 848 3.903467 AGATCTTAATCTTTGGCACCCC 58.097 45.455 0.00 0.00 39.27 4.95
862 863 9.579932 AAAGACCACTAGAAATGAAAAGATCTT 57.420 29.630 0.88 0.88 0.00 2.40
863 864 9.579932 AAAAGACCACTAGAAATGAAAAGATCT 57.420 29.630 0.00 0.00 0.00 2.75
864 865 9.833182 GAAAAGACCACTAGAAATGAAAAGATC 57.167 33.333 0.00 0.00 0.00 2.75
865 866 9.579932 AGAAAAGACCACTAGAAATGAAAAGAT 57.420 29.630 0.00 0.00 0.00 2.40
866 867 8.980481 AGAAAAGACCACTAGAAATGAAAAGA 57.020 30.769 0.00 0.00 0.00 2.52
868 869 9.847224 ACTAGAAAAGACCACTAGAAATGAAAA 57.153 29.630 0.00 0.00 37.58 2.29
869 870 9.273016 CACTAGAAAAGACCACTAGAAATGAAA 57.727 33.333 0.00 0.00 37.58 2.69
870 871 7.878127 CCACTAGAAAAGACCACTAGAAATGAA 59.122 37.037 0.00 0.00 37.58 2.57
871 872 7.016268 ACCACTAGAAAAGACCACTAGAAATGA 59.984 37.037 0.00 0.00 37.58 2.57
872 873 7.162082 ACCACTAGAAAAGACCACTAGAAATG 58.838 38.462 0.00 0.00 37.58 2.32
873 874 7.235812 AGACCACTAGAAAAGACCACTAGAAAT 59.764 37.037 0.00 0.00 37.58 2.17
874 875 6.553852 AGACCACTAGAAAAGACCACTAGAAA 59.446 38.462 0.00 0.00 37.58 2.52
875 876 6.075984 AGACCACTAGAAAAGACCACTAGAA 58.924 40.000 0.00 0.00 37.58 2.10
876 877 5.642165 AGACCACTAGAAAAGACCACTAGA 58.358 41.667 0.00 0.00 37.58 2.43
877 878 5.986501 AGACCACTAGAAAAGACCACTAG 57.013 43.478 0.00 0.00 39.32 2.57
878 879 6.553852 AGAAAGACCACTAGAAAAGACCACTA 59.446 38.462 0.00 0.00 0.00 2.74
879 880 5.367060 AGAAAGACCACTAGAAAAGACCACT 59.633 40.000 0.00 0.00 0.00 4.00
880 881 5.612351 AGAAAGACCACTAGAAAAGACCAC 58.388 41.667 0.00 0.00 0.00 4.16
881 882 5.602978 AGAGAAAGACCACTAGAAAAGACCA 59.397 40.000 0.00 0.00 0.00 4.02
882 883 6.104146 AGAGAAAGACCACTAGAAAAGACC 57.896 41.667 0.00 0.00 0.00 3.85
883 884 9.713713 AAATAGAGAAAGACCACTAGAAAAGAC 57.286 33.333 0.00 0.00 0.00 3.01
884 885 9.930693 GAAATAGAGAAAGACCACTAGAAAAGA 57.069 33.333 0.00 0.00 0.00 2.52
885 886 9.157104 GGAAATAGAGAAAGACCACTAGAAAAG 57.843 37.037 0.00 0.00 0.00 2.27
886 887 8.656806 TGGAAATAGAGAAAGACCACTAGAAAA 58.343 33.333 0.00 0.00 0.00 2.29
1003 1004 8.687292 ATCATTGCATCTATAACAACATCTGT 57.313 30.769 0.00 0.00 41.27 3.41
1064 1065 2.158769 ACAAGGTGAGACAAGATGCACA 60.159 45.455 0.00 0.00 33.09 4.57
1162 1163 5.533903 AGCCATTGATGACCAAGATAATGAC 59.466 40.000 0.00 0.00 38.31 3.06
1163 1164 5.533528 CAGCCATTGATGACCAAGATAATGA 59.466 40.000 0.00 0.00 38.31 2.57
1164 1165 5.301045 ACAGCCATTGATGACCAAGATAATG 59.699 40.000 0.00 0.00 38.31 1.90
1165 1166 5.452255 ACAGCCATTGATGACCAAGATAAT 58.548 37.500 0.00 0.00 38.31 1.28
1166 1167 4.858850 ACAGCCATTGATGACCAAGATAA 58.141 39.130 0.00 0.00 38.31 1.75
1167 1168 4.508551 ACAGCCATTGATGACCAAGATA 57.491 40.909 0.00 0.00 38.31 1.98
1168 1169 3.377253 ACAGCCATTGATGACCAAGAT 57.623 42.857 0.00 0.00 38.31 2.40
1169 1170 2.885135 ACAGCCATTGATGACCAAGA 57.115 45.000 0.00 0.00 38.31 3.02
1170 1171 2.947652 CCTACAGCCATTGATGACCAAG 59.052 50.000 0.00 0.00 38.31 3.61
1171 1172 2.357050 CCCTACAGCCATTGATGACCAA 60.357 50.000 0.00 0.00 39.41 3.67
1172 1173 1.212688 CCCTACAGCCATTGATGACCA 59.787 52.381 0.00 0.00 0.00 4.02
1173 1174 1.477558 CCCCTACAGCCATTGATGACC 60.478 57.143 0.00 0.00 0.00 4.02
1362 1375 7.512130 AGCACTATCAATATTCTGACCATCAA 58.488 34.615 0.00 0.00 0.00 2.57
1750 1763 2.752030 CCTCCAGATGTAGAACCTCCA 58.248 52.381 0.00 0.00 0.00 3.86
1891 1908 6.016024 ACATTTGCAGAAGATAAACAGCTTGA 60.016 34.615 0.00 0.00 0.00 3.02
2059 2080 8.352942 GGCTTATACCAAAAATACCAAGATGAG 58.647 37.037 0.00 0.00 0.00 2.90
2838 3271 1.804748 GAAGAATTTCCTCCGTTGCGT 59.195 47.619 0.00 0.00 0.00 5.24
3194 3628 1.391485 CGACGAGATGTTCAAAGCTGG 59.609 52.381 0.00 0.00 0.00 4.85
3465 3900 7.070447 ACTCTTCCTCTCATTCAAGTATATGCA 59.930 37.037 0.00 0.00 0.00 3.96
3475 3910 4.564782 ATTGCACTCTTCCTCTCATTCA 57.435 40.909 0.00 0.00 0.00 2.57
3476 3911 4.511082 GCTATTGCACTCTTCCTCTCATTC 59.489 45.833 0.00 0.00 39.41 2.67
3477 3912 4.163839 AGCTATTGCACTCTTCCTCTCATT 59.836 41.667 1.12 0.00 42.74 2.57
3478 3913 3.710677 AGCTATTGCACTCTTCCTCTCAT 59.289 43.478 1.12 0.00 42.74 2.90
3480 3915 3.131933 TCAGCTATTGCACTCTTCCTCTC 59.868 47.826 1.12 0.00 42.74 3.20
3481 3916 3.102972 TCAGCTATTGCACTCTTCCTCT 58.897 45.455 1.12 0.00 42.74 3.69
3482 3917 3.194062 GTCAGCTATTGCACTCTTCCTC 58.806 50.000 1.12 0.00 42.74 3.71
3483 3918 2.568956 TGTCAGCTATTGCACTCTTCCT 59.431 45.455 1.12 0.00 42.74 3.36
3484 3919 2.977914 TGTCAGCTATTGCACTCTTCC 58.022 47.619 1.12 0.00 42.74 3.46
3485 3920 5.007136 GGTAATGTCAGCTATTGCACTCTTC 59.993 44.000 1.12 0.00 42.74 2.87
3486 3921 4.878397 GGTAATGTCAGCTATTGCACTCTT 59.122 41.667 1.12 0.00 42.74 2.85
3488 3923 4.191544 TGGTAATGTCAGCTATTGCACTC 58.808 43.478 1.12 0.00 42.74 3.51
3489 3924 4.220693 TGGTAATGTCAGCTATTGCACT 57.779 40.909 1.12 0.00 42.74 4.40
3490 3925 4.731773 GCTTGGTAATGTCAGCTATTGCAC 60.732 45.833 1.12 0.00 42.74 4.57
3491 3926 3.378112 GCTTGGTAATGTCAGCTATTGCA 59.622 43.478 1.12 0.00 42.74 4.08
3492 3927 3.546815 CGCTTGGTAATGTCAGCTATTGC 60.547 47.826 0.00 0.00 40.05 3.56
3493 3928 3.623060 ACGCTTGGTAATGTCAGCTATTG 59.377 43.478 0.00 0.00 0.00 1.90
3494 3929 3.873910 ACGCTTGGTAATGTCAGCTATT 58.126 40.909 0.00 0.00 0.00 1.73
3495 3930 3.543680 ACGCTTGGTAATGTCAGCTAT 57.456 42.857 0.00 0.00 0.00 2.97
3509 4050 2.063156 TTGCCATTGCTTAACGCTTG 57.937 45.000 0.00 0.00 40.11 4.01
3538 4079 6.183360 ACACATGTTCTTGCAAGTACATTTGA 60.183 34.615 41.31 24.39 42.28 2.69
4032 4815 0.682209 CTTGCCCTTCCATCCCACAG 60.682 60.000 0.00 0.00 0.00 3.66
4063 4846 2.983030 AAAACGCATCGGCCTGCA 60.983 55.556 16.45 0.00 42.40 4.41
4072 4855 1.369930 CGTTCGCACCAAAACGCAT 60.370 52.632 0.00 0.00 41.34 4.73
4073 4856 2.023461 CGTTCGCACCAAAACGCA 59.977 55.556 0.00 0.00 41.34 5.24
4079 4862 2.970324 GAGCACCGTTCGCACCAA 60.970 61.111 0.00 0.00 0.00 3.67
4100 4883 0.467290 AAAGCGAAAGTTGGCAGGGA 60.467 50.000 0.82 0.00 34.07 4.20
4101 4884 0.318955 CAAAGCGAAAGTTGGCAGGG 60.319 55.000 0.82 0.00 34.07 4.45
4117 4900 1.024271 GCACCTTGAGCACTGTCAAA 58.976 50.000 0.00 0.00 36.01 2.69
4118 4901 0.181114 AGCACCTTGAGCACTGTCAA 59.819 50.000 0.00 0.00 35.16 3.18
4119 4902 0.533531 CAGCACCTTGAGCACTGTCA 60.534 55.000 0.00 0.00 0.00 3.58
4120 4903 0.250038 TCAGCACCTTGAGCACTGTC 60.250 55.000 0.00 0.00 0.00 3.51
4121 4904 0.181114 TTCAGCACCTTGAGCACTGT 59.819 50.000 0.00 0.00 0.00 3.55
4122 4905 0.873054 CTTCAGCACCTTGAGCACTG 59.127 55.000 0.00 0.00 0.00 3.66
4123 4906 0.761187 TCTTCAGCACCTTGAGCACT 59.239 50.000 0.00 0.00 0.00 4.40
4124 4907 1.155042 CTCTTCAGCACCTTGAGCAC 58.845 55.000 0.00 0.00 0.00 4.40
4125 4908 0.035881 CCTCTTCAGCACCTTGAGCA 59.964 55.000 0.00 0.00 0.00 4.26
4126 4909 0.676151 CCCTCTTCAGCACCTTGAGC 60.676 60.000 0.00 0.00 0.00 4.26
4127 4910 0.689623 ACCCTCTTCAGCACCTTGAG 59.310 55.000 0.00 0.00 0.00 3.02
4128 4911 1.623811 GTACCCTCTTCAGCACCTTGA 59.376 52.381 0.00 0.00 0.00 3.02
4129 4912 1.625818 AGTACCCTCTTCAGCACCTTG 59.374 52.381 0.00 0.00 0.00 3.61
4130 4913 1.625818 CAGTACCCTCTTCAGCACCTT 59.374 52.381 0.00 0.00 0.00 3.50
4131 4914 1.203187 TCAGTACCCTCTTCAGCACCT 60.203 52.381 0.00 0.00 0.00 4.00
4132 4915 1.267121 TCAGTACCCTCTTCAGCACC 58.733 55.000 0.00 0.00 0.00 5.01
4133 4916 2.354203 CCTTCAGTACCCTCTTCAGCAC 60.354 54.545 0.00 0.00 0.00 4.40
4137 4920 4.081642 CGATTTCCTTCAGTACCCTCTTCA 60.082 45.833 0.00 0.00 0.00 3.02
4206 4989 0.030638 CACTTTGCACTTTCCACCCG 59.969 55.000 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.