Multiple sequence alignment - TraesCS1B01G474200

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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 TraesCS1B01G474200 chr1B 100.000 3992 0 0 1 3992 683218313 683214322 0.000000e+00 7372
1 TraesCS1B01G474200 chr7B 96.007 2404 92 3 628 3030 156689765 156687365 0.000000e+00 3904
2 TraesCS1B01G474200 chr7B 83.065 248 35 7 2784 3027 708445409 708445165 6.720000e-53 219
3 TraesCS1B01G474200 chr2A 86.039 1977 244 14 1 1969 711725 713677 0.000000e+00 2093
4 TraesCS1B01G474200 chr2A 87.209 1587 191 9 1 1580 706154 707735 0.000000e+00 1796
5 TraesCS1B01G474200 chr2A 87.821 1092 127 5 1926 3015 778844605 778843518 0.000000e+00 1275
6 TraesCS1B01G474200 chr1A 80.377 2120 393 21 12 2119 560257119 560255011 0.000000e+00 1589
7 TraesCS1B01G474200 chr1A 92.369 498 27 2 3370 3858 588688531 588688036 0.000000e+00 699
8 TraesCS1B01G474200 chr1A 77.568 847 176 12 2175 3014 560254902 560254063 2.140000e-137 499
9 TraesCS1B01G474200 chr1A 87.773 229 23 4 3740 3968 588688082 588687859 3.060000e-66 263
10 TraesCS1B01G474200 chr1A 81.034 348 45 17 3029 3372 588688913 588688583 1.420000e-64 257
11 TraesCS1B01G474200 chr2D 82.880 1507 243 14 12 1510 305859011 305860510 0.000000e+00 1339
12 TraesCS1B01G474200 chr2D 83.333 282 47 0 2730 3011 305863638 305863919 1.100000e-65 261
13 TraesCS1B01G474200 chr5B 74.934 3040 697 61 9 3015 358801024 358804031 0.000000e+00 1332
14 TraesCS1B01G474200 chr3D 76.256 2409 535 32 11 2400 451103833 451106223 0.000000e+00 1245
15 TraesCS1B01G474200 chr7D 78.784 1744 344 22 1280 3015 94763318 94761593 0.000000e+00 1147
16 TraesCS1B01G474200 chr6D 74.409 2790 656 50 8 2768 221299637 221296877 0.000000e+00 1144
17 TraesCS1B01G474200 chr5A 77.677 1662 362 9 18 1674 399259019 399257362 0.000000e+00 1005
18 TraesCS1B01G474200 chr5A 84.795 171 16 8 2864 3031 658988774 658988937 3.190000e-36 163
19 TraesCS1B01G474200 chr1D 88.436 614 33 11 3370 3968 490490053 490489463 0.000000e+00 706
20 TraesCS1B01G474200 chr2B 85.437 412 54 5 2619 3027 646127892 646127484 1.330000e-114 424
21 TraesCS1B01G474200 chr7A 83.929 168 21 6 2864 3028 497617098 497617262 5.340000e-34 156


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 TraesCS1B01G474200 chr1B 683214322 683218313 3991 True 7372.000000 7372 100.000000 1 3992 1 chr1B.!!$R1 3991
1 TraesCS1B01G474200 chr7B 156687365 156689765 2400 True 3904.000000 3904 96.007000 628 3030 1 chr7B.!!$R1 2402
2 TraesCS1B01G474200 chr2A 706154 713677 7523 False 1944.500000 2093 86.624000 1 1969 2 chr2A.!!$F1 1968
3 TraesCS1B01G474200 chr2A 778843518 778844605 1087 True 1275.000000 1275 87.821000 1926 3015 1 chr2A.!!$R1 1089
4 TraesCS1B01G474200 chr1A 560254063 560257119 3056 True 1044.000000 1589 78.972500 12 3014 2 chr1A.!!$R1 3002
5 TraesCS1B01G474200 chr1A 588687859 588688913 1054 True 406.333333 699 87.058667 3029 3968 3 chr1A.!!$R2 939
6 TraesCS1B01G474200 chr2D 305859011 305863919 4908 False 800.000000 1339 83.106500 12 3011 2 chr2D.!!$F1 2999
7 TraesCS1B01G474200 chr5B 358801024 358804031 3007 False 1332.000000 1332 74.934000 9 3015 1 chr5B.!!$F1 3006
8 TraesCS1B01G474200 chr3D 451103833 451106223 2390 False 1245.000000 1245 76.256000 11 2400 1 chr3D.!!$F1 2389
9 TraesCS1B01G474200 chr7D 94761593 94763318 1725 True 1147.000000 1147 78.784000 1280 3015 1 chr7D.!!$R1 1735
10 TraesCS1B01G474200 chr6D 221296877 221299637 2760 True 1144.000000 1144 74.409000 8 2768 1 chr6D.!!$R1 2760
11 TraesCS1B01G474200 chr5A 399257362 399259019 1657 True 1005.000000 1005 77.677000 18 1674 1 chr5A.!!$R1 1656
12 TraesCS1B01G474200 chr1D 490489463 490490053 590 True 706.000000 706 88.436000 3370 3968 1 chr1D.!!$R1 598

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
472 478 0.178975 TGGCCAATCGGTTGAAGGTT 60.179 50.0 10.75 0.00 37.53 3.50 F
571 577 0.443869 ACGAATGCTTGCACACGATC 59.556 50.0 22.13 7.01 0.00 3.69 F
2331 8055 0.319900 GCTCTGACAAGGAAGCGACA 60.320 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1403 0.038166 ATGACCAGGAACGCCATTGT 59.962 50.0 0.0 0.0 36.29 2.71 R
2567 8291 0.332972 ACCAGATTTCTGCCCTTCCC 59.667 55.0 1.9 0.0 42.47 3.97 R
3205 10749 0.338120 ACAGGAGGAGAAGGAGGAGG 59.662 60.0 0.0 0.0 0.00 4.30 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
53 54 1.381735 CAGGGGGAAATCAAGGGCC 60.382 63.158 0.00 0.00 0.00 5.80
63 64 1.075601 ATCAAGGGCCTGGTTCAAGA 58.924 50.000 6.92 0.00 0.00 3.02
77 78 7.201652 GCCTGGTTCAAGACTTCTATGATAAAC 60.202 40.741 0.00 0.00 0.00 2.01
79 80 9.442047 CTGGTTCAAGACTTCTATGATAAACTT 57.558 33.333 0.00 0.00 0.00 2.66
101 102 3.586470 TTACCTCTGAACCTTGCCAAA 57.414 42.857 0.00 0.00 0.00 3.28
128 129 3.327757 GGACAGGGTCATAGATGCCATTA 59.672 47.826 0.00 0.00 33.68 1.90
129 130 4.202461 GGACAGGGTCATAGATGCCATTAA 60.202 45.833 0.00 0.00 33.68 1.40
132 133 5.311649 ACAGGGTCATAGATGCCATTAATCT 59.688 40.000 5.66 0.00 38.03 2.40
154 155 0.387202 AGATCACGCCGGAGATGAAG 59.613 55.000 13.83 0.00 0.00 3.02
251 256 1.207329 GTCCTGACGGTTATCCAGCTT 59.793 52.381 0.00 0.00 0.00 3.74
253 258 3.101437 TCCTGACGGTTATCCAGCTTTA 58.899 45.455 0.00 0.00 0.00 1.85
286 291 4.151883 CTCATTGGAGTTTTCTTGGGGAA 58.848 43.478 0.00 0.00 36.36 3.97
295 300 6.207614 GGAGTTTTCTTGGGGAAGATATATGC 59.792 42.308 0.00 0.00 35.16 3.14
302 307 1.635487 GGGAAGATATATGCCAGGCCA 59.365 52.381 9.64 0.00 0.00 5.36
355 360 2.147150 GAGGGCTTTTGTGACTCTGTC 58.853 52.381 0.00 0.00 0.00 3.51
373 378 6.553100 ACTCTGTCATTGTTTTAATCCCCAAA 59.447 34.615 0.00 0.00 0.00 3.28
377 382 7.569240 TGTCATTGTTTTAATCCCCAAAACTT 58.431 30.769 10.86 0.00 43.25 2.66
379 384 7.931407 GTCATTGTTTTAATCCCCAAAACTTCT 59.069 33.333 10.86 0.00 43.25 2.85
380 385 8.490311 TCATTGTTTTAATCCCCAAAACTTCTT 58.510 29.630 10.86 0.00 43.25 2.52
415 420 1.106285 AGAATTTCCGCCCAATCAGC 58.894 50.000 0.00 0.00 0.00 4.26
472 478 0.178975 TGGCCAATCGGTTGAAGGTT 60.179 50.000 10.75 0.00 37.53 3.50
531 537 3.576078 TGTGCCGGGAAGATTAATCAT 57.424 42.857 17.56 5.50 0.00 2.45
553 559 7.684670 TCATCGACAATACTTTGATTGCTTAC 58.315 34.615 0.00 0.00 39.94 2.34
571 577 0.443869 ACGAATGCTTGCACACGATC 59.556 50.000 22.13 7.01 0.00 3.69
590 596 1.686587 TCAGAAGGCAACGAGTGAAGA 59.313 47.619 0.00 0.00 46.39 2.87
715 722 6.108687 TGGATTGACACTGTTATGAGATGTC 58.891 40.000 0.00 0.00 40.08 3.06
831 838 4.562963 CCCTACTTGTTCCTCTTGTGTACC 60.563 50.000 0.00 0.00 0.00 3.34
889 896 0.829990 TGGCGAGCTACATGGAATCA 59.170 50.000 0.00 0.00 0.00 2.57
976 984 1.810755 AGAGCGATCAACGTAGTGTGA 59.189 47.619 2.38 0.00 45.00 3.58
1235 1243 1.488705 TTTGGGTGGTCAGATCGGCT 61.489 55.000 0.00 0.00 0.00 5.52
1395 1403 5.276440 AGAGAGGATGGAAAGAAGAAGCTA 58.724 41.667 0.00 0.00 0.00 3.32
1398 1406 5.249393 AGAGGATGGAAAGAAGAAGCTACAA 59.751 40.000 0.00 0.00 0.00 2.41
1433 1441 1.145571 TGGTTGACAGCCCCTAAGTT 58.854 50.000 5.81 0.00 0.00 2.66
1511 7181 3.532641 ACAAGGATGGAGGCTTCTTTT 57.467 42.857 0.00 0.00 0.00 2.27
1715 7386 2.558795 CGGATCACTGGATTCCGTCTAT 59.441 50.000 2.55 0.00 38.39 1.98
1813 7484 2.338015 GAGTGGGACGCGGACACTA 61.338 63.158 25.24 3.51 44.79 2.74
2122 7793 3.339547 CCGTCTGGGGAACAATTGT 57.660 52.632 4.92 4.92 0.00 2.71
2331 8055 0.319900 GCTCTGACAAGGAAGCGACA 60.320 55.000 0.00 0.00 0.00 4.35
2346 8070 1.129809 GACAATTGTCACCGTCGCG 59.870 57.895 29.43 0.00 44.18 5.87
2361 8085 2.921121 CGTCGCGTTATGGCATATATGT 59.079 45.455 14.14 0.00 0.00 2.29
2414 8138 3.470888 ACCTGCGCCGGCTTCTAT 61.471 61.111 26.68 3.94 40.82 1.98
2567 8291 2.821366 GGATGCTGCGGTGTCTGG 60.821 66.667 0.00 0.00 0.00 3.86
2590 8314 3.444034 GGAAGGGCAGAAATCTGGTTTAC 59.556 47.826 12.09 0.00 43.94 2.01
2604 8328 1.228003 TTTACGGGTGGTGGTGCTG 60.228 57.895 0.00 0.00 0.00 4.41
2812 10356 3.141398 CATTCGGTGGTAGGATCCATTG 58.859 50.000 15.82 0.00 39.81 2.82
3016 10560 0.244178 AAAGCCCGACGTTCTCTCTC 59.756 55.000 0.00 0.00 0.00 3.20
3017 10561 0.609681 AAGCCCGACGTTCTCTCTCT 60.610 55.000 0.00 0.00 0.00 3.10
3018 10562 1.027792 AGCCCGACGTTCTCTCTCTC 61.028 60.000 0.00 0.00 0.00 3.20
3077 10621 6.454795 GTCAAACTAGGGCAAAATTCATTCA 58.545 36.000 0.00 0.00 0.00 2.57
3082 10626 7.066307 ACTAGGGCAAAATTCATTCAAACTT 57.934 32.000 0.00 0.00 0.00 2.66
3085 10629 9.487790 CTAGGGCAAAATTCATTCAAACTTAAA 57.512 29.630 0.00 0.00 0.00 1.52
3190 10734 2.086869 AGATGTTTCAATGGCGGTCTG 58.913 47.619 0.00 0.00 0.00 3.51
3205 10749 3.755628 CTGCATGCTGGGCCACAC 61.756 66.667 20.33 0.00 0.00 3.82
3208 10752 2.753043 CATGCTGGGCCACACCTC 60.753 66.667 0.00 0.00 39.10 3.85
3209 10753 4.052518 ATGCTGGGCCACACCTCC 62.053 66.667 0.00 0.00 39.10 4.30
3211 10755 4.416738 GCTGGGCCACACCTCCTC 62.417 72.222 0.00 0.00 39.10 3.71
3212 10756 3.721706 CTGGGCCACACCTCCTCC 61.722 72.222 0.00 0.00 39.10 4.30
3213 10757 4.270153 TGGGCCACACCTCCTCCT 62.270 66.667 0.00 0.00 39.10 3.69
3214 10758 2.936032 GGGCCACACCTCCTCCTT 60.936 66.667 4.39 0.00 39.10 3.36
3215 10759 2.671682 GGCCACACCTCCTCCTTC 59.328 66.667 0.00 0.00 34.51 3.46
3216 10760 1.920835 GGCCACACCTCCTCCTTCT 60.921 63.158 0.00 0.00 34.51 2.85
3217 10761 1.599576 GCCACACCTCCTCCTTCTC 59.400 63.158 0.00 0.00 0.00 2.87
3218 10762 1.904990 GCCACACCTCCTCCTTCTCC 61.905 65.000 0.00 0.00 0.00 3.71
3219 10763 0.252467 CCACACCTCCTCCTTCTCCT 60.252 60.000 0.00 0.00 0.00 3.69
3220 10764 1.190643 CACACCTCCTCCTTCTCCTC 58.809 60.000 0.00 0.00 0.00 3.71
3221 10765 0.041982 ACACCTCCTCCTTCTCCTCC 59.958 60.000 0.00 0.00 0.00 4.30
3222 10766 0.338120 CACCTCCTCCTTCTCCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
3223 10767 0.338120 ACCTCCTCCTTCTCCTCCTG 59.662 60.000 0.00 0.00 0.00 3.86
3224 10768 0.338120 CCTCCTCCTTCTCCTCCTGT 59.662 60.000 0.00 0.00 0.00 4.00
3225 10769 1.571457 CCTCCTCCTTCTCCTCCTGTA 59.429 57.143 0.00 0.00 0.00 2.74
3230 10774 2.000803 TCCTTCTCCTCCTGTACCAGA 58.999 52.381 0.00 0.00 32.44 3.86
3232 10776 2.383855 CTTCTCCTCCTGTACCAGAGG 58.616 57.143 18.12 18.12 32.44 3.69
3241 10785 1.320344 TGTACCAGAGGTAGGCTGCG 61.320 60.000 0.00 0.00 39.02 5.18
3242 10786 2.423898 TACCAGAGGTAGGCTGCGC 61.424 63.158 0.00 0.00 37.09 6.09
3265 10809 3.800863 CTTGCTCGGCTGCTGCTG 61.801 66.667 17.69 17.69 46.48 4.41
3279 10832 1.888215 CTGCTGGCAAGAGTTCTTCA 58.112 50.000 0.00 0.00 33.11 3.02
3280 10833 2.434428 CTGCTGGCAAGAGTTCTTCAT 58.566 47.619 0.00 0.00 33.11 2.57
3291 10845 5.651387 AGAGTTCTTCATCTTCGTCATCA 57.349 39.130 0.00 0.00 0.00 3.07
3296 10850 8.103948 AGTTCTTCATCTTCGTCATCAAATTT 57.896 30.769 0.00 0.00 0.00 1.82
3306 10860 6.182039 TCGTCATCAAATTTGAAGTCATCC 57.818 37.500 23.91 7.82 41.13 3.51
3312 10866 6.486253 TCAAATTTGAAGTCATCCTCTTCG 57.514 37.500 18.45 0.00 42.68 3.79
3325 10879 3.082548 TCCTCTTCGTCTTCTTCATCGT 58.917 45.455 0.00 0.00 0.00 3.73
3357 10911 0.391661 GCGCATGGGAGAGAAAGTCA 60.392 55.000 14.90 0.00 0.00 3.41
3368 10976 1.825474 GAGAAAGTCATCCGAGGACCA 59.175 52.381 9.52 0.00 35.89 4.02
3408 11016 3.772025 CCACTTCTCTGTCCCAGTAAGAT 59.228 47.826 12.63 0.00 33.39 2.40
3411 11019 5.128499 CACTTCTCTGTCCCAGTAAGATGAT 59.872 44.000 12.63 0.00 33.39 2.45
3435 11043 1.004200 CCGTGTGTACTTGGGGTCC 60.004 63.158 0.00 0.00 0.00 4.46
3437 11045 1.760479 CGTGTGTACTTGGGGTCCCA 61.760 60.000 10.98 7.91 45.63 4.37
3458 11066 1.376609 CGTAGCTCCAATGGCAACCC 61.377 60.000 0.00 0.00 0.00 4.11
3538 11146 2.026445 CGTGGACGACGTTGGTCA 59.974 61.111 18.54 9.04 43.61 4.02
3598 11206 1.772063 GAGTTGTCGCGCAGGTGTTT 61.772 55.000 8.75 0.00 0.00 2.83
3609 11217 3.423154 GGTGTTTGAGCGCCTCCG 61.423 66.667 2.29 0.00 36.19 4.63
3737 11360 0.839946 GATACATGGTGGTGGCCTCT 59.160 55.000 3.32 0.00 0.00 3.69
3844 11467 1.300931 GCTGCGAGGACAACTCACA 60.301 57.895 0.00 0.00 46.98 3.58
3872 11567 0.447801 GAAACATGGTGGTAGCAGCG 59.552 55.000 18.30 8.33 0.00 5.18
3873 11568 0.960364 AAACATGGTGGTAGCAGCGG 60.960 55.000 18.30 15.04 0.00 5.52
3895 11590 2.203640 AGACGGTCTGGTCTGGCA 60.204 61.111 10.41 0.00 45.24 4.92
3934 11629 1.268899 GGAGACGAGAGGAAACGTGAA 59.731 52.381 0.00 0.00 42.74 3.18
3944 11639 2.480419 AGGAAACGTGAAAATGCGAGAG 59.520 45.455 0.00 0.00 0.00 3.20
3959 11654 2.015227 GAGAGAGAAGAGGCAGGCGG 62.015 65.000 0.00 0.00 0.00 6.13
3982 11677 2.357760 GGCACGGGCGAGTTGTTA 60.358 61.111 2.17 0.00 42.47 2.41
3983 11678 1.962306 GGCACGGGCGAGTTGTTAA 60.962 57.895 2.17 0.00 42.47 2.01
3984 11679 1.303091 GGCACGGGCGAGTTGTTAAT 61.303 55.000 2.17 0.00 42.47 1.40
3985 11680 1.361793 GCACGGGCGAGTTGTTAATA 58.638 50.000 0.00 0.00 0.00 0.98
3986 11681 1.733360 GCACGGGCGAGTTGTTAATAA 59.267 47.619 0.00 0.00 0.00 1.40
3987 11682 2.160022 GCACGGGCGAGTTGTTAATAAA 59.840 45.455 0.00 0.00 0.00 1.40
3988 11683 3.726782 GCACGGGCGAGTTGTTAATAAAG 60.727 47.826 0.00 0.00 0.00 1.85
3989 11684 3.680937 CACGGGCGAGTTGTTAATAAAGA 59.319 43.478 0.00 0.00 0.00 2.52
3990 11685 4.331717 CACGGGCGAGTTGTTAATAAAGAT 59.668 41.667 0.00 0.00 0.00 2.40
3991 11686 4.331717 ACGGGCGAGTTGTTAATAAAGATG 59.668 41.667 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 9.442047 AAGTTTATCATAGAAGTCTTGAACCAG 57.558 33.333 0.00 0.00 0.00 4.00
77 78 3.888930 TGGCAAGGTTCAGAGGTAAAAAG 59.111 43.478 0.00 0.00 0.00 2.27
79 80 3.586470 TGGCAAGGTTCAGAGGTAAAA 57.414 42.857 0.00 0.00 0.00 1.52
101 102 0.324368 TCTATGACCCTGTCCGCAGT 60.324 55.000 0.00 0.00 41.02 4.40
128 129 2.693591 TCTCCGGCGTGATCTTAAGATT 59.306 45.455 18.88 3.47 34.37 2.40
129 130 2.307768 TCTCCGGCGTGATCTTAAGAT 58.692 47.619 17.96 17.96 37.51 2.40
132 133 2.028876 TCATCTCCGGCGTGATCTTAA 58.971 47.619 6.01 0.00 0.00 1.85
154 155 1.227497 CGGCTTGCAGAGATCCTCC 60.227 63.158 0.00 0.00 0.00 4.30
232 237 1.568504 AAGCTGGATAACCGTCAGGA 58.431 50.000 0.00 0.00 41.02 3.86
243 248 9.638176 AATGAGTTTGATAGAATAAAGCTGGAT 57.362 29.630 0.00 0.00 0.00 3.41
286 291 1.407851 CGCATGGCCTGGCATATATCT 60.408 52.381 22.05 0.00 0.00 1.98
302 307 1.247567 CCTTCAAGGAAACCACGCAT 58.752 50.000 0.00 0.00 37.67 4.73
355 360 8.558700 CAAGAAGTTTTGGGGATTAAAACAATG 58.441 33.333 13.68 5.32 45.67 2.82
373 378 2.689983 CAAGTGCTTGGGTCAAGAAGTT 59.310 45.455 11.35 7.26 41.76 2.66
377 382 2.172505 TCTTCAAGTGCTTGGGTCAAGA 59.827 45.455 11.35 9.89 43.42 3.02
379 384 2.727123 TCTTCAAGTGCTTGGGTCAA 57.273 45.000 11.47 0.00 40.78 3.18
380 385 2.727123 TTCTTCAAGTGCTTGGGTCA 57.273 45.000 11.47 0.00 40.78 4.02
472 478 1.345415 GAAACCACAACCGGTAGGAGA 59.655 52.381 23.03 0.00 38.76 3.71
531 537 5.865013 TCGTAAGCAATCAAAGTATTGTCGA 59.135 36.000 0.00 0.00 38.78 4.20
553 559 0.443478 TGATCGTGTGCAAGCATTCG 59.557 50.000 12.86 12.86 0.00 3.34
571 577 2.154854 TCTTCACTCGTTGCCTTCTG 57.845 50.000 0.00 0.00 0.00 3.02
590 596 6.322201 TCAATCTTGAGAGCAAAGAAAGGTTT 59.678 34.615 0.00 0.00 32.73 3.27
715 722 1.066143 AGCATAACGGACCTTGGTGAG 60.066 52.381 0.00 0.00 0.00 3.51
831 838 3.305398 AGCAGACTAGACAAACCTTCG 57.695 47.619 0.00 0.00 0.00 3.79
942 950 3.610040 TCGCTCTTGGCAAAGAAGATA 57.390 42.857 4.77 0.00 41.89 1.98
976 984 5.104527 TGGATAAGACCGAATCCAATGAGTT 60.105 40.000 1.60 0.00 46.74 3.01
1235 1243 0.482446 ATTCCCAGCCCTTGACAACA 59.518 50.000 0.00 0.00 0.00 3.33
1330 1338 4.549458 ACAATCTGCCTGAATTTTTCACG 58.451 39.130 0.00 0.00 35.46 4.35
1395 1403 0.038166 ATGACCAGGAACGCCATTGT 59.962 50.000 0.00 0.00 36.29 2.71
1398 1406 1.077501 CCATGACCAGGAACGCCAT 60.078 57.895 0.00 0.00 36.29 4.40
1433 1441 0.917333 AAAGCCCATACCCCCGAGAA 60.917 55.000 0.00 0.00 0.00 2.87
1511 7181 0.736053 GCACAACGAACCTGGTTCAA 59.264 50.000 32.35 0.00 42.05 2.69
1813 7484 0.991920 TCAGGGAAAAAGGCTCGGAT 59.008 50.000 0.00 0.00 0.00 4.18
2188 7912 0.764369 TGAGGACAGAACAGCAGGGT 60.764 55.000 0.00 0.00 0.00 4.34
2331 8055 1.392168 CATAACGCGACGGTGACAATT 59.608 47.619 15.93 0.00 0.00 2.32
2346 8070 4.503910 TCGCCTCACATATATGCCATAAC 58.496 43.478 12.79 0.00 0.00 1.89
2361 8085 3.760035 GCCTCGTTCCTCGCCTCA 61.760 66.667 0.00 0.00 39.67 3.86
2567 8291 0.332972 ACCAGATTTCTGCCCTTCCC 59.667 55.000 1.90 0.00 42.47 3.97
2590 8314 2.978010 GTTCAGCACCACCACCCG 60.978 66.667 0.00 0.00 0.00 5.28
2656 8380 3.181456 GCTTCAGCCACTTCAGGAGATAT 60.181 47.826 0.00 0.00 34.31 1.63
2777 10321 0.533755 CGAATGATCCCTGGCAGGAC 60.534 60.000 34.84 23.23 39.24 3.85
2812 10356 3.676646 GCCAAATCTTTGACATCTGCAAC 59.323 43.478 4.25 0.00 40.55 4.17
2918 10462 6.570692 AGAAAAACACAAAGACTAGACGAGA 58.429 36.000 0.00 0.00 0.00 4.04
2967 10511 9.846248 GATCAAGCAACAAATTTACATAGAGTT 57.154 29.630 0.00 0.00 0.00 3.01
3050 10594 4.651503 TGAATTTTGCCCTAGTTTGACCAA 59.348 37.500 0.00 0.00 0.00 3.67
3054 10598 6.662865 TGAATGAATTTTGCCCTAGTTTGA 57.337 33.333 0.00 0.00 0.00 2.69
3055 10599 7.442062 AGTTTGAATGAATTTTGCCCTAGTTTG 59.558 33.333 0.00 0.00 0.00 2.93
3057 10601 7.066307 AGTTTGAATGAATTTTGCCCTAGTT 57.934 32.000 0.00 0.00 0.00 2.24
3058 10602 6.670695 AGTTTGAATGAATTTTGCCCTAGT 57.329 33.333 0.00 0.00 0.00 2.57
3092 10636 9.996554 TCTCTTAGTTTCAATGAAGTTGTATCA 57.003 29.630 0.00 0.00 38.95 2.15
3116 10660 6.587273 GTGGTCTGCCTCTAAATTATCTTCT 58.413 40.000 0.00 0.00 35.27 2.85
3124 10668 1.066143 CACCGTGGTCTGCCTCTAAAT 60.066 52.381 0.00 0.00 35.27 1.40
3194 10738 4.416738 GAGGAGGTGTGGCCCAGC 62.417 72.222 13.60 13.60 42.00 4.85
3205 10749 0.338120 ACAGGAGGAGAAGGAGGAGG 59.662 60.000 0.00 0.00 0.00 4.30
3206 10750 2.661718 GTACAGGAGGAGAAGGAGGAG 58.338 57.143 0.00 0.00 0.00 3.69
3207 10751 1.288335 GGTACAGGAGGAGAAGGAGGA 59.712 57.143 0.00 0.00 0.00 3.71
3208 10752 1.007238 TGGTACAGGAGGAGAAGGAGG 59.993 57.143 0.00 0.00 0.00 4.30
3209 10753 2.534042 TGGTACAGGAGGAGAAGGAG 57.466 55.000 0.00 0.00 0.00 3.69
3222 10766 1.320344 CGCAGCCTACCTCTGGTACA 61.320 60.000 0.00 0.00 37.09 2.90
3223 10767 1.437986 CGCAGCCTACCTCTGGTAC 59.562 63.158 0.00 0.00 37.09 3.34
3224 10768 3.935024 CGCAGCCTACCTCTGGTA 58.065 61.111 0.00 0.00 37.09 3.25
3246 10790 2.823147 GCAGCAGCCGAGCAAGAT 60.823 61.111 0.00 0.00 36.85 2.40
3265 10809 3.330267 ACGAAGATGAAGAACTCTTGCC 58.670 45.455 0.00 0.00 36.11 4.52
3269 10822 5.651387 TGATGACGAAGATGAAGAACTCT 57.349 39.130 0.00 0.00 0.00 3.24
3275 10828 8.019669 ACTTCAAATTTGATGACGAAGATGAAG 58.980 33.333 30.30 18.57 43.03 3.02
3279 10832 7.439157 TGACTTCAAATTTGATGACGAAGAT 57.561 32.000 30.30 13.43 37.00 2.40
3280 10833 6.859420 TGACTTCAAATTTGATGACGAAGA 57.141 33.333 30.30 11.56 37.00 2.87
3291 10845 6.234177 AGACGAAGAGGATGACTTCAAATTT 58.766 36.000 0.00 0.00 42.39 1.82
3296 10850 4.082845 AGAAGACGAAGAGGATGACTTCA 58.917 43.478 0.00 0.00 42.39 3.02
3306 10860 5.224562 ACTACGATGAAGAAGACGAAGAG 57.775 43.478 0.00 0.00 0.00 2.85
3312 10866 3.408288 AGCGACTACGATGAAGAAGAC 57.592 47.619 0.00 0.00 42.66 3.01
3342 10896 2.697751 CTCGGATGACTTTCTCTCCCAT 59.302 50.000 0.00 0.00 0.00 4.00
3343 10897 2.103373 CTCGGATGACTTTCTCTCCCA 58.897 52.381 0.00 0.00 0.00 4.37
3357 10911 0.991920 ACAATTGGTGGTCCTCGGAT 59.008 50.000 10.83 0.00 34.23 4.18
3368 10976 3.910627 AGTGGAGAAGGAGTACAATTGGT 59.089 43.478 10.83 0.00 0.00 3.67
3408 11016 3.584834 CAAGTACACACGGTCATCATCA 58.415 45.455 0.00 0.00 0.00 3.07
3411 11019 1.001520 CCCAAGTACACACGGTCATCA 59.998 52.381 0.00 0.00 0.00 3.07
3435 11043 2.182842 GCCATTGGAGCTACGCTGG 61.183 63.158 6.95 11.44 39.88 4.85
3437 11045 1.026718 GTTGCCATTGGAGCTACGCT 61.027 55.000 6.95 0.00 43.88 5.07
3538 11146 3.765257 CTCTCCCCGAGGGCTGGAT 62.765 68.421 1.76 0.00 43.94 3.41
3552 11160 2.435059 GGCTGGTTGCGTCCTCTC 60.435 66.667 0.00 0.00 44.05 3.20
3553 11161 4.379243 CGGCTGGTTGCGTCCTCT 62.379 66.667 0.00 0.00 44.05 3.69
3586 11194 4.724697 CGCTCAAACACCTGCGCG 62.725 66.667 0.00 0.00 43.19 6.86
3720 11343 1.613317 CGAGAGGCCACCACCATGTA 61.613 60.000 5.01 0.00 0.00 2.29
3838 11461 0.874607 GTTTCGCCGTGAGTGTGAGT 60.875 55.000 0.00 0.00 0.00 3.41
3844 11467 1.070786 ACCATGTTTCGCCGTGAGT 59.929 52.632 0.00 0.00 0.00 3.41
3873 11568 3.075641 GACCAGACCGTCTCCCCC 61.076 72.222 0.00 0.00 0.00 5.40
3934 11629 1.552337 TGCCTCTTCTCTCTCGCATTT 59.448 47.619 0.00 0.00 0.00 2.32
3968 11663 3.929094 TCTTTATTAACAACTCGCCCGT 58.071 40.909 0.00 0.00 0.00 5.28
3969 11664 4.833126 CATCTTTATTAACAACTCGCCCG 58.167 43.478 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.