Multiple sequence alignment - TraesCS1B01G062100

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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 TraesCS1B01G062100 chr1B 100.000 3545 0 0 1 3545 47172030 47175574 0.000000e+00 6547.0
1 TraesCS1B01G062100 chr1B 91.892 185 9 5 360 543 47166989 47167168 1.630000e-63 254.0
2 TraesCS1B01G062100 chr1A 88.780 3173 199 64 360 3432 29786796 29789911 0.000000e+00 3742.0
3 TraesCS1B01G062100 chr1A 92.073 164 8 1 199 362 29786537 29786695 3.560000e-55 226.0
4 TraesCS1B01G062100 chr1A 91.150 113 9 1 3432 3544 29789956 29790067 6.130000e-33 152.0
5 TraesCS1B01G062100 chr1A 78.924 223 23 13 1 205 29786293 29786509 2.870000e-26 130.0
6 TraesCS1B01G062100 chr1D 90.720 2360 139 32 360 2677 28564198 28566519 0.000000e+00 3072.0
7 TraesCS1B01G062100 chr1D 86.364 704 38 13 2733 3432 28566609 28567258 0.000000e+00 715.0
8 TraesCS1B01G062100 chr1D 90.566 159 9 2 204 362 28563947 28564099 4.640000e-49 206.0
9 TraesCS1B01G062100 chr1D 85.052 194 3 4 1 168 28563649 28563842 1.310000e-39 174.0
10 TraesCS1B01G062100 chr1D 93.333 45 2 1 1092 1135 54927198 54927154 8.210000e-07 65.8
11 TraesCS1B01G062100 chr5D 75.956 549 108 18 1733 2275 469245439 469245969 9.760000e-66 261.0
12 TraesCS1B01G062100 chr5D 95.556 45 1 1 1092 1135 495290612 495290656 1.770000e-08 71.3
13 TraesCS1B01G062100 chr5B 75.862 551 105 21 1733 2275 576055149 576055679 4.540000e-64 255.0
14 TraesCS1B01G062100 chr5B 74.790 476 89 18 1849 2313 576260681 576261136 6.040000e-43 185.0
15 TraesCS1B01G062100 chr5B 75.972 283 63 3 1733 2014 576257393 576257671 1.330000e-29 141.0
16 TraesCS1B01G062100 chr5B 95.556 45 1 1 1092 1135 611868621 611868665 1.770000e-08 71.3
17 TraesCS1B01G062100 chr5A 75.862 551 105 21 1733 2275 589329025 589329555 4.540000e-64 255.0
18 TraesCS1B01G062100 chr5A 87.671 146 16 2 2098 2242 590453210 590453354 6.090000e-38 169.0
19 TraesCS1B01G062100 chr5A 87.671 146 16 2 2098 2242 590527395 590527539 6.090000e-38 169.0
20 TraesCS1B01G062100 chr5A 88.806 134 14 1 3298 3430 4705016 4704883 2.830000e-36 163.0
21 TraesCS1B01G062100 chr5A 81.633 196 34 2 2098 2292 589585149 589585343 1.020000e-35 161.0
22 TraesCS1B01G062100 chr5A 95.556 45 1 1 1092 1135 619359906 619359950 1.770000e-08 71.3
23 TraesCS1B01G062100 chr6D 89.542 153 14 2 3281 3432 470858580 470858429 3.610000e-45 193.0
24 TraesCS1B01G062100 chr2D 80.952 126 19 5 1013 1135 337923093 337923216 1.050000e-15 95.3
25 TraesCS1B01G062100 chr2B 85.106 94 12 2 3451 3544 47757529 47757620 1.050000e-15 95.3
26 TraesCS1B01G062100 chr2B 80.952 126 19 5 1013 1135 405262351 405262474 1.050000e-15 95.3
27 TraesCS1B01G062100 chr2A 81.102 127 17 7 1013 1135 448153121 448153244 1.050000e-15 95.3


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 TraesCS1B01G062100 chr1B 47172030 47175574 3544 False 6547.00 6547 100.00000 1 3545 1 chr1B.!!$F2 3544
1 TraesCS1B01G062100 chr1A 29786293 29790067 3774 False 1062.50 3742 87.73175 1 3544 4 chr1A.!!$F1 3543
2 TraesCS1B01G062100 chr1D 28563649 28567258 3609 False 1041.75 3072 88.17550 1 3432 4 chr1D.!!$F1 3431
3 TraesCS1B01G062100 chr5D 469245439 469245969 530 False 261.00 261 75.95600 1733 2275 1 chr5D.!!$F1 542
4 TraesCS1B01G062100 chr5B 576055149 576055679 530 False 255.00 255 75.86200 1733 2275 1 chr5B.!!$F1 542
5 TraesCS1B01G062100 chr5A 589329025 589329555 530 False 255.00 255 75.86200 1733 2275 1 chr5A.!!$F1 542

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
211 314 0.108615 AGAACCATCGCCTTGAGACG 60.109 55.0 0.0 0.0 0.00 4.18 F
793 1019 0.530431 GCTGTGCAAACCCCAACAAG 60.530 55.0 0.0 0.0 0.00 3.16 F
1590 1870 0.246635 CTACAGTGGGTGAGGGAACG 59.753 60.0 0.0 0.0 0.00 3.95 F
2412 2692 0.622665 ACCAGAGCATTCAGGAAGGG 59.377 55.0 0.0 0.0 34.29 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 1348 1.070786 GACGTTGAAGCCCCTGTCA 59.929 57.895 0.0 0.0 0.0 3.58 R
2469 2749 0.034059 CCTGAACGCTCACTTCCTGT 59.966 55.000 0.0 0.0 0.0 4.00 R
2470 2750 0.318441 TCCTGAACGCTCACTTCCTG 59.682 55.000 0.0 0.0 0.0 3.86 R
3472 3876 0.612453 GCCCCGACCTCCCTATAGAG 60.612 65.000 0.0 0.0 0.0 2.43 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
42 43 2.642171 TCCATTAGGGTGGTCTCACT 57.358 50.000 0.00 0.00 43.17 3.41
89 116 7.282224 GTGAATCCAACATAAGTATACCAGCAA 59.718 37.037 0.00 0.00 0.00 3.91
120 147 1.580942 GTCAAAGCTCGCATTGGCA 59.419 52.632 6.59 0.00 41.24 4.92
162 189 5.979288 TTTCAGAACAGAGGGAGTAGTAC 57.021 43.478 0.00 0.00 0.00 2.73
168 195 5.839606 AGAACAGAGGGAGTAGTACTGTTTT 59.160 40.000 7.76 0.00 46.81 2.43
169 196 5.725325 ACAGAGGGAGTAGTACTGTTTTC 57.275 43.478 7.76 0.53 38.41 2.29
170 197 5.145564 ACAGAGGGAGTAGTACTGTTTTCA 58.854 41.667 7.76 0.00 38.41 2.69
171 198 5.601313 ACAGAGGGAGTAGTACTGTTTTCAA 59.399 40.000 7.76 0.00 38.41 2.69
172 199 6.159988 CAGAGGGAGTAGTACTGTTTTCAAG 58.840 44.000 7.76 0.00 0.00 3.02
173 200 4.895961 AGGGAGTAGTACTGTTTTCAAGC 58.104 43.478 7.76 0.00 0.00 4.01
178 205 6.292919 GGAGTAGTACTGTTTTCAAGCAAGTG 60.293 42.308 7.76 0.00 0.00 3.16
198 225 0.473694 TGGAGGGAGCAGAAGAACCA 60.474 55.000 0.00 0.00 0.00 3.67
211 314 0.108615 AGAACCATCGCCTTGAGACG 60.109 55.000 0.00 0.00 0.00 4.18
218 321 3.185188 CCATCGCCTTGAGACGATAAATG 59.815 47.826 1.95 0.00 46.63 2.32
233 336 8.132995 AGACGATAAATGATGATACACGTAACA 58.867 33.333 0.00 0.00 0.00 2.41
234 337 8.812147 ACGATAAATGATGATACACGTAACAT 57.188 30.769 0.10 0.10 32.31 2.71
235 338 9.902196 ACGATAAATGATGATACACGTAACATA 57.098 29.630 0.51 0.00 30.21 2.29
318 421 1.084370 GGTCGAATGTTCCGAGCTGG 61.084 60.000 0.00 0.00 46.92 4.85
319 422 3.426126 GGTCGAATGTTCCGAGCTGGA 62.426 57.143 0.00 0.00 46.92 3.86
338 441 5.386924 CTGGATAGGCTAGGTAGTGTTACT 58.613 45.833 0.00 0.00 0.00 2.24
462 668 7.065120 TGTCAAAAATGACAAAAGATGGGAT 57.935 32.000 9.07 0.00 44.73 3.85
518 734 1.607225 TGGGAGCCAGGTTCCATTAT 58.393 50.000 23.14 0.00 34.53 1.28
537 753 3.627395 ATGTCATCTTGGGCGAAGTTA 57.373 42.857 9.15 0.00 32.90 2.24
664 890 6.375455 CCAAGTGTGTTTATCTCCTATGCTTT 59.625 38.462 0.00 0.00 0.00 3.51
745 971 8.297470 ACAATGCCTGATCATAAAATACAAGT 57.703 30.769 0.00 0.00 0.00 3.16
759 985 5.435686 AATACAAGTAGAATGCCAGACCA 57.564 39.130 0.00 0.00 0.00 4.02
789 1015 4.040645 TTGCTGTGCAAACCCCAA 57.959 50.000 2.24 0.00 45.96 4.12
790 1016 1.519719 TTGCTGTGCAAACCCCAAC 59.480 52.632 2.24 0.00 45.96 3.77
791 1017 1.260538 TTGCTGTGCAAACCCCAACA 61.261 50.000 2.24 0.00 45.96 3.33
792 1018 1.260538 TGCTGTGCAAACCCCAACAA 61.261 50.000 0.00 0.00 34.76 2.83
793 1019 0.530431 GCTGTGCAAACCCCAACAAG 60.530 55.000 0.00 0.00 0.00 3.16
794 1020 1.110442 CTGTGCAAACCCCAACAAGA 58.890 50.000 0.00 0.00 0.00 3.02
795 1021 1.480137 CTGTGCAAACCCCAACAAGAA 59.520 47.619 0.00 0.00 0.00 2.52
796 1022 1.902508 TGTGCAAACCCCAACAAGAAA 59.097 42.857 0.00 0.00 0.00 2.52
797 1023 2.276201 GTGCAAACCCCAACAAGAAAC 58.724 47.619 0.00 0.00 0.00 2.78
798 1024 1.208293 TGCAAACCCCAACAAGAAACC 59.792 47.619 0.00 0.00 0.00 3.27
799 1025 1.474320 GCAAACCCCAACAAGAAACCC 60.474 52.381 0.00 0.00 0.00 4.11
800 1026 1.140052 CAAACCCCAACAAGAAACCCC 59.860 52.381 0.00 0.00 0.00 4.95
846 1072 5.740290 AGAAGGTCCAAGAACGAGATTAA 57.260 39.130 0.00 0.00 0.00 1.40
849 1075 3.581332 AGGTCCAAGAACGAGATTAACCA 59.419 43.478 0.00 0.00 0.00 3.67
878 1104 7.554476 GGAGCAACAAGAATTATACCTTCTTCT 59.446 37.037 6.53 2.78 40.16 2.85
913 1142 2.520069 TGTCTCCACACTCTCTTCTCC 58.480 52.381 0.00 0.00 0.00 3.71
972 1230 2.785562 CTACTAGCTAGGATCACCGCT 58.214 52.381 24.35 2.98 41.83 5.52
976 1234 3.094062 GCTAGGATCACCGCTGCCA 62.094 63.158 0.00 0.00 41.83 4.92
991 1253 4.371786 CGCTGCCAAGATCTCAGTTATAA 58.628 43.478 10.62 0.00 0.00 0.98
994 1256 6.646653 CGCTGCCAAGATCTCAGTTATAATTA 59.353 38.462 10.62 0.00 0.00 1.40
1059 1321 3.009275 CAGGGCCATGTCATCCCA 58.991 61.111 9.85 0.00 42.52 4.37
1395 1669 2.032634 GGACATTGCGCGAAGGACA 61.033 57.895 12.10 0.00 0.00 4.02
1458 1732 1.376553 GGTCACCCTGCTGAGCTTC 60.377 63.158 5.83 0.00 36.04 3.86
1508 1783 2.695359 TGCGGAAGATGGTAAACTGAC 58.305 47.619 0.00 0.00 0.00 3.51
1519 1794 2.223377 GGTAAACTGACCGAGCAACTTG 59.777 50.000 0.00 0.00 0.00 3.16
1569 1849 0.874390 GTTCGTCTTTGCATGCAGGA 59.126 50.000 21.50 19.18 0.00 3.86
1590 1870 0.246635 CTACAGTGGGTGAGGGAACG 59.753 60.000 0.00 0.00 0.00 3.95
1615 1895 4.100084 TGAGCCCCGACATGCCTG 62.100 66.667 0.00 0.00 0.00 4.85
1690 1970 1.677637 GACCCTCTACCGGCTCCTTG 61.678 65.000 0.00 0.00 0.00 3.61
1691 1971 1.686110 CCCTCTACCGGCTCCTTGT 60.686 63.158 0.00 0.00 0.00 3.16
1692 1972 1.677637 CCCTCTACCGGCTCCTTGTC 61.678 65.000 0.00 0.00 0.00 3.18
1701 1981 2.049433 CTCCTTGTCGACGGCGTT 60.049 61.111 16.19 0.00 38.98 4.84
1788 2068 1.128188 AGCTCTTCCCCAACGTCCTT 61.128 55.000 0.00 0.00 0.00 3.36
1800 2080 3.961414 GTCCTTCCCGTTGGCCCA 61.961 66.667 0.00 0.00 0.00 5.36
1801 2081 3.179339 TCCTTCCCGTTGGCCCAA 61.179 61.111 0.00 0.00 0.00 4.12
1803 2083 1.208844 TCCTTCCCGTTGGCCCAATA 61.209 55.000 0.00 0.00 0.00 1.90
1956 2236 4.735132 CGGCGCCAGTTCGAGGAA 62.735 66.667 28.98 0.00 0.00 3.36
2046 2326 2.758089 CGTCCACGACTACCCGGAG 61.758 68.421 0.73 0.00 43.02 4.63
2061 2341 2.110006 GAGGGCTTCCTGGATCGC 59.890 66.667 0.00 3.45 41.93 4.58
2064 2344 2.125106 GGCTTCCTGGATCGCGTT 60.125 61.111 5.77 0.00 0.00 4.84
2391 2671 3.880846 GCCATGAAGAAGGCCGCG 61.881 66.667 0.00 0.00 45.18 6.46
2412 2692 0.622665 ACCAGAGCATTCAGGAAGGG 59.377 55.000 0.00 0.00 34.29 3.95
2433 2713 1.228657 GCTCCTCGCACGGAAACTTT 61.229 55.000 0.00 0.00 38.92 2.66
2442 2722 2.726241 GCACGGAAACTTTGATGCTTTC 59.274 45.455 0.00 0.00 0.00 2.62
2469 2749 2.438254 ATGAAGAATGCGGCGCCA 60.438 55.556 30.82 19.01 0.00 5.69
2470 2750 2.764314 ATGAAGAATGCGGCGCCAC 61.764 57.895 30.82 19.07 0.00 5.01
2472 2752 3.386867 GAAGAATGCGGCGCCACAG 62.387 63.158 30.82 11.84 0.00 3.66
2565 2845 2.027385 TCATCTGCTGCTCGAGTGTAT 58.973 47.619 15.13 0.00 0.00 2.29
2587 2869 3.445450 TGTGTGGTAGTGTGCAATTTTGT 59.555 39.130 0.00 0.00 0.00 2.83
2588 2870 3.796178 GTGTGGTAGTGTGCAATTTTGTG 59.204 43.478 0.00 0.00 0.00 3.33
2592 2874 4.158579 TGGTAGTGTGCAATTTTGTGTTCA 59.841 37.500 0.00 0.00 0.00 3.18
2613 2895 9.442047 TGTTCACACAAAGAATAAAAATGGTTT 57.558 25.926 0.00 0.00 0.00 3.27
2646 2928 3.435105 TTGCCTTTATATTTGCCGCTG 57.565 42.857 0.00 0.00 0.00 5.18
2649 2931 3.115554 GCCTTTATATTTGCCGCTGTTG 58.884 45.455 0.00 0.00 0.00 3.33
2651 2933 4.351192 CCTTTATATTTGCCGCTGTTGTC 58.649 43.478 0.00 0.00 0.00 3.18
2656 2938 0.814457 TTTGCCGCTGTTGTCTTTGT 59.186 45.000 0.00 0.00 0.00 2.83
2661 2943 1.670811 CCGCTGTTGTCTTTGTGAGTT 59.329 47.619 0.00 0.00 0.00 3.01
2667 2949 5.712217 TGTTGTCTTTGTGAGTTACTTCG 57.288 39.130 0.00 0.00 0.00 3.79
2690 3027 2.684881 GACGGAGGGTAACATAAGACGA 59.315 50.000 0.00 0.00 39.74 4.20
2695 3032 5.583457 CGGAGGGTAACATAAGACGATTTTT 59.417 40.000 0.00 0.00 39.74 1.94
2705 3042 4.452890 AAGACGATTTTTGACACTGTCG 57.547 40.909 4.71 0.00 34.95 4.35
2952 3303 4.175337 TAGTGAGCCGGCCCATGC 62.175 66.667 26.15 6.64 0.00 4.06
2994 3346 1.629043 GGAAGGTTCCCCCAGTTTTC 58.371 55.000 0.00 0.00 41.62 2.29
3030 3382 7.571080 TTTCTGTGGTTTATTTTAGAACGGT 57.429 32.000 0.00 0.00 0.00 4.83
3033 3385 7.641760 TCTGTGGTTTATTTTAGAACGGTTTC 58.358 34.615 0.00 0.00 0.00 2.78
3039 3391 9.481800 GGTTTATTTTAGAACGGTTTCTATTCG 57.518 33.333 0.00 0.00 42.71 3.34
3044 3396 7.495135 TTTAGAACGGTTTCTATTCGGTTTT 57.505 32.000 0.00 0.00 42.71 2.43
3064 3416 8.717821 CGGTTTTCCTTTTTCTTTTTCTTCTTT 58.282 29.630 0.00 0.00 37.95 2.52
3199 3554 4.823989 ACAACTCCTTTCCAAATCTGTGAG 59.176 41.667 0.00 0.00 0.00 3.51
3203 3558 6.410540 ACTCCTTTCCAAATCTGTGAGTATC 58.589 40.000 0.00 0.00 30.56 2.24
3348 3707 2.229543 TGAATCAATGTGAAGTGGCAGC 59.770 45.455 0.00 0.00 0.00 5.25
3397 3756 6.571605 TGATCAAGATTGCTTTTCACACAAA 58.428 32.000 0.00 0.00 30.14 2.83
3432 3791 1.083141 GAAGGAAGGAGGGGAGGGT 59.917 63.158 0.00 0.00 0.00 4.34
3433 3792 0.983905 GAAGGAAGGAGGGGAGGGTC 60.984 65.000 0.00 0.00 0.00 4.46
3434 3793 2.367107 GGAAGGAGGGGAGGGTCC 60.367 72.222 0.00 0.00 35.23 4.46
3472 3876 1.731720 CTACTGCAAGCTTCTGGTCC 58.268 55.000 0.00 0.00 37.60 4.46
3491 3895 0.612453 CTCTATAGGGAGGTCGGGGC 60.612 65.000 0.00 0.00 0.00 5.80
3537 3941 1.826921 GCAGGTGGAGCCCATGATG 60.827 63.158 0.00 0.00 35.28 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 7.815840 TCACATTTTTCTCACCTTGATACAA 57.184 32.000 0.00 0.00 0.00 2.41
59 60 9.693739 TGGTATACTTATGTTGGATTCACATTT 57.306 29.630 2.25 0.00 0.00 2.32
89 116 3.826729 GAGCTTTGACCAACAATTACCCT 59.173 43.478 0.00 0.00 38.36 4.34
120 147 3.560636 ATACCTTGCAGATTACGCCTT 57.439 42.857 0.00 0.00 0.00 4.35
162 189 3.489738 CCTCCACACTTGCTTGAAAACAG 60.490 47.826 0.00 0.00 0.00 3.16
168 195 0.397941 CTCCCTCCACACTTGCTTGA 59.602 55.000 0.00 0.00 0.00 3.02
169 196 1.239968 GCTCCCTCCACACTTGCTTG 61.240 60.000 0.00 0.00 0.00 4.01
170 197 1.073897 GCTCCCTCCACACTTGCTT 59.926 57.895 0.00 0.00 0.00 3.91
171 198 2.121992 CTGCTCCCTCCACACTTGCT 62.122 60.000 0.00 0.00 0.00 3.91
172 199 1.673665 CTGCTCCCTCCACACTTGC 60.674 63.158 0.00 0.00 0.00 4.01
173 200 0.397941 TTCTGCTCCCTCCACACTTG 59.602 55.000 0.00 0.00 0.00 3.16
178 205 0.035915 GGTTCTTCTGCTCCCTCCAC 60.036 60.000 0.00 0.00 0.00 4.02
218 321 9.244799 TCAAGATGTTATGTTACGTGTATCATC 57.755 33.333 0.00 6.67 30.62 2.92
233 336 6.822667 TCATGTGTTTGCTCAAGATGTTAT 57.177 33.333 0.00 0.00 0.00 1.89
234 337 6.822667 ATCATGTGTTTGCTCAAGATGTTA 57.177 33.333 0.00 0.00 29.17 2.41
235 338 5.717078 ATCATGTGTTTGCTCAAGATGTT 57.283 34.783 0.00 0.00 29.17 2.71
236 339 5.242171 TGAATCATGTGTTTGCTCAAGATGT 59.758 36.000 0.00 0.00 30.28 3.06
237 340 5.705902 TGAATCATGTGTTTGCTCAAGATG 58.294 37.500 0.00 0.00 30.28 2.90
318 421 6.016108 CCTTGAGTAACACTACCTAGCCTATC 60.016 46.154 0.00 0.00 0.00 2.08
319 422 5.834204 CCTTGAGTAACACTACCTAGCCTAT 59.166 44.000 0.00 0.00 0.00 2.57
419 625 4.018506 TGACAGGGATTGCCTCATTTAAGA 60.019 41.667 0.00 0.00 0.00 2.10
518 734 3.410631 TTAACTTCGCCCAAGATGACA 57.589 42.857 0.00 0.00 35.82 3.58
537 753 4.935352 TGCCAAGTAAGAAGCAACAATT 57.065 36.364 0.00 0.00 30.97 2.32
577 793 5.522824 AGTTCTTTTACCAAGTCTTCACGAC 59.477 40.000 0.00 0.00 43.17 4.34
745 971 7.618019 AGAATAGTTATGGTCTGGCATTCTA 57.382 36.000 0.00 0.00 31.52 2.10
788 1014 3.196901 GGTTCTTGTTGGGGTTTCTTGTT 59.803 43.478 0.00 0.00 0.00 2.83
789 1015 2.764010 GGTTCTTGTTGGGGTTTCTTGT 59.236 45.455 0.00 0.00 0.00 3.16
790 1016 2.763448 TGGTTCTTGTTGGGGTTTCTTG 59.237 45.455 0.00 0.00 0.00 3.02
791 1017 3.031013 CTGGTTCTTGTTGGGGTTTCTT 58.969 45.455 0.00 0.00 0.00 2.52
792 1018 2.666317 CTGGTTCTTGTTGGGGTTTCT 58.334 47.619 0.00 0.00 0.00 2.52
793 1019 1.068588 GCTGGTTCTTGTTGGGGTTTC 59.931 52.381 0.00 0.00 0.00 2.78
794 1020 1.119684 GCTGGTTCTTGTTGGGGTTT 58.880 50.000 0.00 0.00 0.00 3.27
795 1021 0.261696 AGCTGGTTCTTGTTGGGGTT 59.738 50.000 0.00 0.00 0.00 4.11
796 1022 0.178990 GAGCTGGTTCTTGTTGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
797 1023 0.178992 TGAGCTGGTTCTTGTTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
798 1024 1.691196 TTGAGCTGGTTCTTGTTGGG 58.309 50.000 0.00 0.00 0.00 4.12
799 1025 4.326504 AAATTGAGCTGGTTCTTGTTGG 57.673 40.909 0.00 0.00 0.00 3.77
829 1055 4.389077 CAGTGGTTAATCTCGTTCTTGGAC 59.611 45.833 0.00 0.00 0.00 4.02
846 1072 2.664402 ATTCTTGTTGCTCCAGTGGT 57.336 45.000 9.54 0.00 0.00 4.16
849 1075 6.067217 AGGTATAATTCTTGTTGCTCCAGT 57.933 37.500 0.00 0.00 0.00 4.00
878 1104 1.891919 GACACGCACCAAGAGCCAA 60.892 57.895 0.00 0.00 0.00 4.52
905 1131 5.994668 GGCAGAATTTATAGTGGGAGAAGAG 59.005 44.000 0.00 0.00 0.00 2.85
906 1132 5.453339 CGGCAGAATTTATAGTGGGAGAAGA 60.453 44.000 0.00 0.00 0.00 2.87
908 1134 4.444306 CCGGCAGAATTTATAGTGGGAGAA 60.444 45.833 0.00 0.00 0.00 2.87
913 1142 3.804036 TGACCGGCAGAATTTATAGTGG 58.196 45.455 0.00 0.00 0.00 4.00
972 1230 7.497595 ACGTAATTATAACTGAGATCTTGGCA 58.502 34.615 0.00 0.00 0.00 4.92
991 1253 1.338294 TGGACACGCCATTGACGTAAT 60.338 47.619 0.00 0.00 43.33 1.89
994 1256 2.423874 TGGACACGCCATTGACGT 59.576 55.556 0.00 0.00 43.33 4.34
1020 1282 1.666011 CGGGTAGGGGATGACGATG 59.334 63.158 0.00 0.00 0.00 3.84
1050 1312 1.206878 CCTCCATGAGTGGGATGACA 58.793 55.000 0.00 0.00 46.06 3.58
1059 1321 3.381983 TGCGCGACCTCCATGAGT 61.382 61.111 12.10 0.00 0.00 3.41
1086 1348 1.070786 GACGTTGAAGCCCCTGTCA 59.929 57.895 0.00 0.00 0.00 3.58
1147 1409 3.799755 GGCACCGTTCGACATGGC 61.800 66.667 0.00 0.00 34.31 4.40
1218 1480 4.257810 TGGTTCCGGTCCTCCCCA 62.258 66.667 16.54 6.29 0.00 4.96
1389 1663 1.995626 CACCCGGATCCCTGTCCTT 60.996 63.158 0.73 0.00 36.07 3.36
1447 1721 2.045131 GCTTGGGGAAGCTCAGCAG 61.045 63.158 0.00 0.00 42.32 4.24
1458 1732 1.144936 GTCCTCGATCAGCTTGGGG 59.855 63.158 0.00 0.00 0.00 4.96
1508 1783 2.614057 AGAAGTCAAACAAGTTGCTCGG 59.386 45.455 1.81 0.00 37.13 4.63
1548 1828 1.267806 CCTGCATGCAAAGACGAACTT 59.732 47.619 22.88 0.00 40.98 2.66
1569 1849 2.188817 GTTCCCTCACCCACTGTAGAT 58.811 52.381 0.00 0.00 0.00 1.98
1590 1870 3.706373 TCGGGGCTCAGCTGGAAC 61.706 66.667 15.13 3.32 0.00 3.62
1701 1981 2.327343 GCACTGCTCCATTGCACGA 61.327 57.895 3.14 0.00 39.34 4.35
1704 1984 2.032376 TCGCACTGCTCCATTGCA 59.968 55.556 8.03 0.00 39.47 4.08
1788 2068 1.202099 TGAGTATTGGGCCAACGGGA 61.202 55.000 23.59 4.38 35.59 5.14
1800 2080 2.104331 CGCTCGCCGGTGAGTATT 59.896 61.111 37.94 0.00 38.28 1.89
1801 2081 4.570663 GCGCTCGCCGGTGAGTAT 62.571 66.667 37.94 0.00 38.28 2.12
2028 2308 2.747460 TCCGGGTAGTCGTGGACG 60.747 66.667 0.00 0.00 37.67 4.79
2046 2326 3.682292 AACGCGATCCAGGAAGCCC 62.682 63.158 15.93 0.00 0.00 5.19
2292 2572 3.431486 GCTCCTTGGTTATGACTCCTGAG 60.431 52.174 0.00 0.00 0.00 3.35
2295 2575 2.237392 GTGCTCCTTGGTTATGACTCCT 59.763 50.000 0.00 0.00 0.00 3.69
2387 2667 3.869272 GAATGCTCTGGTGCGCGG 61.869 66.667 8.83 0.00 35.36 6.46
2391 2671 1.093159 CTTCCTGAATGCTCTGGTGC 58.907 55.000 0.00 0.00 40.64 5.01
2395 2675 0.106819 CCCCCTTCCTGAATGCTCTG 60.107 60.000 0.00 0.00 0.00 3.35
2442 2722 1.524621 ATTCTTCATGGCCTCCGCG 60.525 57.895 3.32 0.00 35.02 6.46
2469 2749 0.034059 CCTGAACGCTCACTTCCTGT 59.966 55.000 0.00 0.00 0.00 4.00
2470 2750 0.318441 TCCTGAACGCTCACTTCCTG 59.682 55.000 0.00 0.00 0.00 3.86
2472 2752 1.009389 CGTCCTGAACGCTCACTTCC 61.009 60.000 0.00 0.00 45.76 3.46
2473 2753 2.435741 CGTCCTGAACGCTCACTTC 58.564 57.895 0.00 0.00 45.76 3.01
2474 2754 4.655527 CGTCCTGAACGCTCACTT 57.344 55.556 0.00 0.00 45.76 3.16
2497 2777 1.674651 GGAAGTTTCCGGGTGAGGC 60.675 63.158 0.00 0.00 37.65 4.70
2504 2784 4.771134 CGCAAGAGTATGGAAGTTTCCGG 61.771 52.174 0.00 0.00 46.50 5.14
2505 2785 2.348666 CGCAAGAGTATGGAAGTTTCCG 59.651 50.000 6.43 0.00 46.50 4.30
2565 2845 3.445450 ACAAAATTGCACACTACCACACA 59.555 39.130 0.00 0.00 0.00 3.72
2587 2869 9.442047 AAACCATTTTTATTCTTTGTGTGAACA 57.558 25.926 0.00 0.00 0.00 3.18
2592 2874 9.892130 TGGTTAAACCATTTTTATTCTTTGTGT 57.108 25.926 0.00 0.00 44.79 3.72
2609 2891 3.260632 AGGCAAATGGTGATGGTTAAACC 59.739 43.478 0.00 0.00 39.22 3.27
2613 2895 8.546083 AATATAAAGGCAAATGGTGATGGTTA 57.454 30.769 0.00 0.00 0.00 2.85
2614 2896 7.436320 AATATAAAGGCAAATGGTGATGGTT 57.564 32.000 0.00 0.00 0.00 3.67
2646 2928 4.025145 CCCGAAGTAACTCACAAAGACAAC 60.025 45.833 0.00 0.00 0.00 3.32
2649 2931 3.739810 GTCCCGAAGTAACTCACAAAGAC 59.260 47.826 0.00 0.00 0.00 3.01
2651 2933 2.729882 CGTCCCGAAGTAACTCACAAAG 59.270 50.000 0.00 0.00 0.00 2.77
2656 2938 1.171308 CTCCGTCCCGAAGTAACTCA 58.829 55.000 0.00 0.00 0.00 3.41
2661 2943 0.331278 TTACCCTCCGTCCCGAAGTA 59.669 55.000 0.00 0.00 0.00 2.24
2667 2949 2.102084 GTCTTATGTTACCCTCCGTCCC 59.898 54.545 0.00 0.00 0.00 4.46
2677 2959 8.280497 ACAGTGTCAAAAATCGTCTTATGTTAC 58.720 33.333 0.00 0.00 0.00 2.50
2678 2960 8.373048 ACAGTGTCAAAAATCGTCTTATGTTA 57.627 30.769 0.00 0.00 0.00 2.41
2679 2961 7.259290 ACAGTGTCAAAAATCGTCTTATGTT 57.741 32.000 0.00 0.00 0.00 2.71
2680 2962 6.346598 CGACAGTGTCAAAAATCGTCTTATGT 60.347 38.462 22.66 0.00 32.09 2.29
2681 2963 6.009474 CGACAGTGTCAAAAATCGTCTTATG 58.991 40.000 22.66 0.00 32.09 1.90
2690 3027 4.073293 AGAGTCCGACAGTGTCAAAAAT 57.927 40.909 22.66 6.64 32.09 1.82
2695 3032 2.953648 TGTTTAGAGTCCGACAGTGTCA 59.046 45.455 22.66 1.39 32.09 3.58
2705 3042 8.837389 ACTTTTTGTAAGATGTGTTTAGAGTCC 58.163 33.333 0.00 0.00 0.00 3.85
2818 3166 2.035442 GTTCCTGGCAAGTCCTCGC 61.035 63.158 0.00 0.00 35.26 5.03
2824 3172 1.418637 TCCGTTTAGTTCCTGGCAAGT 59.581 47.619 0.00 0.00 0.00 3.16
2829 3177 0.323629 TGCCTCCGTTTAGTTCCTGG 59.676 55.000 0.00 0.00 0.00 4.45
3030 3382 9.878667 AAAAGAAAAAGGAAAACCGAATAGAAA 57.121 25.926 0.00 0.00 0.00 2.52
3033 3385 9.529325 AGAAAAAGAAAAAGGAAAACCGAATAG 57.471 29.630 0.00 0.00 0.00 1.73
3281 3638 8.480501 TCTTTACTGTTTTAGTAGTTCACCACT 58.519 33.333 0.00 0.00 42.57 4.00
3282 3639 8.652810 TCTTTACTGTTTTAGTAGTTCACCAC 57.347 34.615 0.00 0.00 42.57 4.16
3313 3671 7.392953 TCACATTGATTCAACATGGCTAGTTTA 59.607 33.333 0.15 0.00 0.00 2.01
3373 3732 5.771153 TGTGTGAAAAGCAATCTTGATCA 57.229 34.783 0.00 0.00 31.78 2.92
3397 3756 2.158460 CCTTCCCCTTCCTGTCAAGTTT 60.158 50.000 0.00 0.00 0.00 2.66
3432 3791 2.498248 GAGCAGCAGCATCTCGGA 59.502 61.111 3.17 0.00 45.49 4.55
3433 3792 2.588314 GGAGCAGCAGCATCTCGG 60.588 66.667 3.17 0.00 45.49 4.63
3434 3793 1.883544 CAGGAGCAGCAGCATCTCG 60.884 63.158 3.17 0.00 45.49 4.04
3472 3876 0.612453 GCCCCGACCTCCCTATAGAG 60.612 65.000 0.00 0.00 0.00 2.43
3501 3905 2.907407 GCCCTATTGCCGGCCTTC 60.907 66.667 26.77 1.83 39.39 3.46
3502 3906 4.875713 CGCCCTATTGCCGGCCTT 62.876 66.667 26.77 14.16 42.53 4.35


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

AutoCloner maintained by Alex Coulton.