Multiple sequence alignment - TraesCS3D01G544300

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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 TraesCS3D01G544300 chr3D 100.000 4392 0 0 1 4392 613899308 613903699 0.000000e+00 8111.0
1 TraesCS3D01G544300 chr3D 84.965 858 105 15 3545 4392 355998078 355998921 0.000000e+00 848.0
2 TraesCS3D01G544300 chr3D 74.111 506 116 6 1004 1494 569207970 569208475 1.250000e-45 195.0
3 TraesCS3D01G544300 chr3D 87.356 87 4 3 675 754 284323662 284323748 4.680000e-15 93.5
4 TraesCS3D01G544300 chr3D 93.617 47 2 1 2432 2477 3372373 3372419 7.880000e-08 69.4
5 TraesCS3D01G544300 chr3B 95.076 3615 150 12 783 4392 823554230 823550639 0.000000e+00 5664.0
6 TraesCS3D01G544300 chr3B 94.055 471 18 4 293 755 823554861 823554393 0.000000e+00 706.0
7 TraesCS3D01G544300 chr3B 95.956 272 11 0 1 272 823555729 823555458 4.030000e-120 442.0
8 TraesCS3D01G544300 chr3B 92.308 65 1 4 782 845 554486402 554486341 6.050000e-14 89.8
9 TraesCS3D01G544300 chr4D 85.698 860 102 13 3542 4392 63901525 63902372 0.000000e+00 887.0
10 TraesCS3D01G544300 chr4D 84.988 866 111 13 3538 4392 119918116 119917259 0.000000e+00 861.0
11 TraesCS3D01G544300 chr4D 100.000 52 0 0 782 833 329425283 329425334 3.620000e-16 97.1
12 TraesCS3D01G544300 chr2D 85.181 857 103 14 3545 4392 22281512 22280671 0.000000e+00 857.0
13 TraesCS3D01G544300 chr2D 84.848 858 110 15 3545 4392 6161074 6160227 0.000000e+00 846.0
14 TraesCS3D01G544300 chr2D 79.412 272 56 0 1223 1494 60202665 60202394 4.480000e-45 193.0
15 TraesCS3D01G544300 chr2D 89.552 67 5 2 767 833 59462651 59462587 2.810000e-12 84.2
16 TraesCS3D01G544300 chr7B 85.099 859 102 19 3545 4392 323725428 323726271 0.000000e+00 854.0
17 TraesCS3D01G544300 chr5A 84.884 860 103 19 3545 4392 349618432 349619276 0.000000e+00 843.0
18 TraesCS3D01G544300 chr5B 84.669 861 108 18 3545 4392 295664611 295663762 0.000000e+00 837.0
19 TraesCS3D01G544300 chr2A 81.575 749 118 13 1547 2289 754610335 754611069 6.290000e-168 601.0
20 TraesCS3D01G544300 chr2A 90.323 62 6 0 675 736 99128682 99128743 1.010000e-11 82.4
21 TraesCS3D01G544300 chr2B 76.102 431 99 4 1054 1482 794621579 794622007 5.720000e-54 222.0
22 TraesCS3D01G544300 chr2B 76.471 323 72 4 1052 1372 797080064 797080384 5.840000e-39 172.0
23 TraesCS3D01G544300 chr2B 98.077 52 1 0 782 833 575883639 575883588 1.680000e-14 91.6
24 TraesCS3D01G544300 chr7D 75.168 447 109 2 1037 1482 622271372 622271817 4.450000e-50 209.0
25 TraesCS3D01G544300 chr6D 78.676 272 58 0 1223 1494 97569999 97569728 9.700000e-42 182.0
26 TraesCS3D01G544300 chrUn 98.077 52 1 0 782 833 353135691 353135640 1.680000e-14 91.6
27 TraesCS3D01G544300 chrUn 93.443 61 2 2 773 833 87230012 87229954 6.050000e-14 89.8
28 TraesCS3D01G544300 chr3A 92.063 63 3 2 771 833 742329497 742329557 2.180000e-13 87.9
29 TraesCS3D01G544300 chr3A 87.302 63 8 0 2413 2475 541981 542043 6.090000e-09 73.1
30 TraesCS3D01G544300 chr5D 88.406 69 6 2 765 833 527893202 527893136 1.010000e-11 82.4
31 TraesCS3D01G544300 chr1B 90.909 55 5 0 675 729 177066948 177066894 1.690000e-09 75.0
32 TraesCS3D01G544300 chr6A 100.000 35 0 0 2441 2475 35149375 35149341 1.020000e-06 65.8


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 TraesCS3D01G544300 chr3D 613899308 613903699 4391 False 8111.000000 8111 100.000 1 4392 1 chr3D.!!$F5 4391
1 TraesCS3D01G544300 chr3D 355998078 355998921 843 False 848.000000 848 84.965 3545 4392 1 chr3D.!!$F3 847
2 TraesCS3D01G544300 chr3B 823550639 823555729 5090 True 2270.666667 5664 95.029 1 4392 3 chr3B.!!$R2 4391
3 TraesCS3D01G544300 chr4D 63901525 63902372 847 False 887.000000 887 85.698 3542 4392 1 chr4D.!!$F1 850
4 TraesCS3D01G544300 chr4D 119917259 119918116 857 True 861.000000 861 84.988 3538 4392 1 chr4D.!!$R1 854
5 TraesCS3D01G544300 chr2D 22280671 22281512 841 True 857.000000 857 85.181 3545 4392 1 chr2D.!!$R2 847
6 TraesCS3D01G544300 chr2D 6160227 6161074 847 True 846.000000 846 84.848 3545 4392 1 chr2D.!!$R1 847
7 TraesCS3D01G544300 chr7B 323725428 323726271 843 False 854.000000 854 85.099 3545 4392 1 chr7B.!!$F1 847
8 TraesCS3D01G544300 chr5A 349618432 349619276 844 False 843.000000 843 84.884 3545 4392 1 chr5A.!!$F1 847
9 TraesCS3D01G544300 chr5B 295663762 295664611 849 True 837.000000 837 84.669 3545 4392 1 chr5B.!!$R1 847
10 TraesCS3D01G544300 chr2A 754610335 754611069 734 False 601.000000 601 81.575 1547 2289 1 chr2A.!!$F2 742

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
769 1354 0.035317 GAGACCAGTGGCACATCACA 59.965 55.0 21.41 0.0 44.52 3.58 F
1591 2312 0.393537 GGAGGGAGATGGTGTGCAAG 60.394 60.0 0.00 0.0 0.00 4.01 F
2445 3170 0.250338 GTGTGGAGTTGGACCTGGAC 60.250 60.0 0.00 0.0 0.00 4.02 F
3224 3949 0.833949 TGTCAACTACCAGGCACACA 59.166 50.0 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 3151 0.250338 GTCCAGGTCCAACTCCACAC 60.250 60.000 0.00 0.0 0.0 3.82 R
3347 4072 0.327924 ACAATGAAGCCCGTGATGGA 59.672 50.000 0.00 0.0 42.0 3.41 R
3354 4079 1.139163 GCAAAACACAATGAAGCCCG 58.861 50.000 0.00 0.0 0.0 6.13 R
4139 4887 2.412325 CGGCAAATCTCTTTACGCGTTT 60.412 45.455 20.78 0.0 0.0 3.60 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
27 28 0.677731 ATCCACCTGCAATGTCACGG 60.678 55.000 0.00 0.00 0.00 4.94
37 38 0.035439 AATGTCACGGTGATCCCCAC 60.035 55.000 14.78 1.21 44.95 4.61
81 82 1.533033 CCCCAGACCACCCAAAACC 60.533 63.158 0.00 0.00 0.00 3.27
82 83 1.901464 CCCAGACCACCCAAAACCG 60.901 63.158 0.00 0.00 0.00 4.44
128 129 1.264749 TGACCCCCTCGACCATCTTG 61.265 60.000 0.00 0.00 0.00 3.02
131 132 1.141881 CCCCTCGACCATCTTGACG 59.858 63.158 0.00 0.00 0.00 4.35
133 134 1.141881 CCTCGACCATCTTGACGGG 59.858 63.158 0.00 0.00 0.00 5.28
216 217 3.403038 AGCAAACTACACTAAGTGGCAG 58.597 45.455 0.00 0.00 37.94 4.85
272 273 0.892755 TCACTAACCCCTGCTACGTG 59.107 55.000 0.00 0.00 0.00 4.49
273 274 0.108329 CACTAACCCCTGCTACGTGG 60.108 60.000 0.00 0.00 0.00 4.94
275 276 0.108329 CTAACCCCTGCTACGTGGTG 60.108 60.000 0.00 0.00 0.00 4.17
276 277 2.175035 TAACCCCTGCTACGTGGTGC 62.175 60.000 0.00 0.06 0.00 5.01
277 278 4.778143 CCCCTGCTACGTGGTGCC 62.778 72.222 0.00 0.00 0.00 5.01
278 279 3.706373 CCCTGCTACGTGGTGCCT 61.706 66.667 0.00 0.00 0.00 4.75
279 280 2.125512 CCTGCTACGTGGTGCCTC 60.126 66.667 0.00 0.00 0.00 4.70
280 281 2.125512 CTGCTACGTGGTGCCTCC 60.126 66.667 0.00 0.00 0.00 4.30
290 291 2.597510 GTGCCTCCACCCACCAAC 60.598 66.667 0.00 0.00 35.92 3.77
291 292 3.099841 TGCCTCCACCCACCAACA 61.100 61.111 0.00 0.00 0.00 3.33
308 885 1.692411 ACAAGGAACAAAGGAGTGGC 58.308 50.000 0.00 0.00 0.00 5.01
325 902 2.485814 GTGGCTTTGTCTCAACTCCATC 59.514 50.000 5.61 0.00 0.00 3.51
386 965 4.168101 AGACCTGGTTATGAAGGAGAACA 58.832 43.478 0.00 0.00 37.01 3.18
391 970 5.187967 CCTGGTTATGAAGGAGAACACTACT 59.812 44.000 0.00 0.00 35.40 2.57
422 1001 1.265236 TTGGATGCACATGGGGAAAC 58.735 50.000 0.00 0.00 0.00 2.78
585 1164 2.171448 GGGTCCATGCTTCTCACACTAT 59.829 50.000 0.00 0.00 0.00 2.12
591 1170 4.880120 CCATGCTTCTCACACTATGATTGT 59.120 41.667 0.00 0.00 36.48 2.71
622 1201 1.679680 CCACCACATGATTCATCAGCC 59.320 52.381 0.00 0.00 40.64 4.85
692 1271 1.539065 CGAGGCTGGCCATAGTGTTAG 60.539 57.143 5.51 0.00 38.92 2.34
719 1298 2.860009 AGCTGATATCATGCACTTGGG 58.140 47.619 21.46 4.74 0.00 4.12
732 1311 2.295909 GCACTTGGGAATAGCAAACACA 59.704 45.455 0.00 0.00 0.00 3.72
755 1340 8.713271 CACACTGTAGAGAATTAAAAAGAGACC 58.287 37.037 0.00 0.00 0.00 3.85
756 1341 8.429641 ACACTGTAGAGAATTAAAAAGAGACCA 58.570 33.333 0.00 0.00 0.00 4.02
757 1342 8.930760 CACTGTAGAGAATTAAAAAGAGACCAG 58.069 37.037 0.00 0.00 0.00 4.00
758 1343 8.652290 ACTGTAGAGAATTAAAAAGAGACCAGT 58.348 33.333 0.00 0.00 0.00 4.00
759 1344 8.833231 TGTAGAGAATTAAAAAGAGACCAGTG 57.167 34.615 0.00 0.00 0.00 3.66
760 1345 7.878127 TGTAGAGAATTAAAAAGAGACCAGTGG 59.122 37.037 7.91 7.91 0.00 4.00
761 1346 5.707764 AGAGAATTAAAAAGAGACCAGTGGC 59.292 40.000 9.78 1.85 0.00 5.01
762 1347 5.385198 AGAATTAAAAAGAGACCAGTGGCA 58.615 37.500 9.78 0.00 0.00 4.92
763 1348 5.241728 AGAATTAAAAAGAGACCAGTGGCAC 59.758 40.000 10.29 10.29 0.00 5.01
764 1349 2.435372 AAAAAGAGACCAGTGGCACA 57.565 45.000 21.41 0.00 0.00 4.57
766 1351 2.191128 AAAGAGACCAGTGGCACATC 57.809 50.000 21.41 13.85 44.52 3.06
767 1352 1.059098 AAGAGACCAGTGGCACATCA 58.941 50.000 21.41 0.00 44.52 3.07
768 1353 0.322975 AGAGACCAGTGGCACATCAC 59.677 55.000 21.41 12.33 44.52 3.06
769 1354 0.035317 GAGACCAGTGGCACATCACA 59.965 55.000 21.41 0.00 44.52 3.58
771 1356 0.806868 GACCAGTGGCACATCACATG 59.193 55.000 21.41 7.87 44.52 3.21
847 1567 7.833786 TGGTACTAGTAGTTAATGAACACCAG 58.166 38.462 8.40 0.00 38.10 4.00
849 1569 7.758528 GGTACTAGTAGTTAATGAACACCAGTG 59.241 40.741 8.40 0.00 38.10 3.66
899 1619 1.203050 ACCCCCATTCTTCACAACCTG 60.203 52.381 0.00 0.00 0.00 4.00
948 1669 4.804665 GTCGGTGACTCCTAGCTTAATTTC 59.195 45.833 0.00 0.00 0.00 2.17
982 1703 7.081526 TGTACCTAAAGTCGTCTATGTCTTC 57.918 40.000 0.00 0.00 0.00 2.87
1018 1739 9.512588 AGAGAAATATATAAATGGCTGGTGAAG 57.487 33.333 0.00 0.00 0.00 3.02
1030 1751 4.160439 TGGCTGGTGAAGTAGAGATACTTG 59.840 45.833 5.44 0.00 40.09 3.16
1042 1763 1.915489 AGATACTTGTGGTGGCATGGA 59.085 47.619 0.00 0.00 0.00 3.41
1182 1903 0.462581 CATACATGCTGGCCGACACT 60.463 55.000 0.00 0.00 0.00 3.55
1221 1942 0.674895 GACACATGTCCCTGGTGAGC 60.675 60.000 0.00 0.00 39.07 4.26
1236 1957 3.240134 GAGCAGGTCACCGGAGCAA 62.240 63.158 9.46 0.00 43.97 3.91
1449 2170 2.964464 TGCCATTCTCATGTTTGTGGTT 59.036 40.909 10.17 0.00 0.00 3.67
1464 2185 2.158726 TGTGGTTGGGGTTCTCAAGTAC 60.159 50.000 0.00 0.00 0.00 2.73
1485 2206 2.693591 CGAGGAAAGAGTATGGGCACTA 59.306 50.000 0.00 0.00 0.00 2.74
1591 2312 0.393537 GGAGGGAGATGGTGTGCAAG 60.394 60.000 0.00 0.00 0.00 4.01
1594 2315 1.064906 AGGGAGATGGTGTGCAAGATG 60.065 52.381 0.00 0.00 0.00 2.90
1661 2386 2.060383 CAGACGGAGCCCATCAGGA 61.060 63.158 0.00 0.00 38.24 3.86
1722 2447 2.223947 GGACGTTCCCAAGCAATTGTTT 60.224 45.455 7.40 4.26 0.00 2.83
1761 2486 7.812191 CGTTTTGTGAAAATCAATAGGGATCAA 59.188 33.333 0.00 0.00 32.22 2.57
1842 2567 1.600636 GCTGTACACCAAGGCTGCA 60.601 57.895 0.50 0.00 0.00 4.41
1910 2635 3.225272 CCACAGTCACGGCATTACA 57.775 52.632 0.00 0.00 0.00 2.41
2160 2885 1.603802 CATGAGTTGTTTCGCCTGTGT 59.396 47.619 0.00 0.00 0.00 3.72
2281 3006 4.548991 CAGCTTATCATTCAGAAGGTGC 57.451 45.455 0.00 0.00 40.56 5.01
2300 3025 5.183522 AGGTGCTGAAACTAGTGTCTACTAC 59.816 44.000 14.23 7.86 38.36 2.73
2305 3030 5.798132 TGAAACTAGTGTCTACTACGGAGA 58.202 41.667 14.23 0.00 38.36 3.71
2354 3079 1.226262 GCCGGAATGCCCTAAGGAA 59.774 57.895 5.05 0.00 33.47 3.36
2356 3081 0.819666 CCGGAATGCCCTAAGGAAGC 60.820 60.000 0.00 0.00 33.47 3.86
2368 3093 2.134789 AAGGAAGCATAGTGCCTTGG 57.865 50.000 0.00 0.00 46.52 3.61
2426 3151 5.940617 TGTATTATTGGACCTGGAATGGAG 58.059 41.667 0.00 0.00 0.00 3.86
2445 3170 0.250338 GTGTGGAGTTGGACCTGGAC 60.250 60.000 0.00 0.00 0.00 4.02
2484 3209 3.717294 ATCGCCACCCGCCTCTTT 61.717 61.111 0.00 0.00 36.73 2.52
2502 3227 2.819984 TTCTCGGCTGGTTGGATGCC 62.820 60.000 0.00 0.00 42.94 4.40
2506 3231 2.353610 GGCTGGTTGGATGCCAAGG 61.354 63.158 0.00 0.00 44.82 3.61
2570 3295 2.286365 AATCTTTTCCTGGCAACCGA 57.714 45.000 0.00 0.00 0.00 4.69
2668 3393 6.520272 AGGTATGTTCAACTCTGCTATGATC 58.480 40.000 0.00 0.00 0.00 2.92
2686 3411 5.762825 TGATCTGATAAATTGCTTGGAGC 57.237 39.130 0.00 0.00 42.82 4.70
2710 3435 1.303309 CGGGAATTGTGATCTGCTCC 58.697 55.000 0.00 0.00 0.00 4.70
2988 3713 4.885426 CACCTGAGCAGTGGTGTT 57.115 55.556 0.00 0.00 46.18 3.32
3074 3799 2.746277 GTCCCATGCACCGGACAC 60.746 66.667 23.14 8.98 46.59 3.67
3144 3869 7.264221 ACTGATGTGATGTGAGTATTCTCTTC 58.736 38.462 0.77 0.00 40.98 2.87
3224 3949 0.833949 TGTCAACTACCAGGCACACA 59.166 50.000 0.00 0.00 0.00 3.72
3247 3972 4.823157 TCCATGAATCATTTGCTTGTTGG 58.177 39.130 0.00 0.00 0.00 3.77
3252 3977 5.299148 TGAATCATTTGCTTGTTGGAAAGG 58.701 37.500 0.00 0.00 39.29 3.11
3270 3995 5.809051 GGAAAGGATCAATCATTTGCTTGTC 59.191 40.000 12.46 0.00 42.79 3.18
3287 4012 4.377431 GCTTGTCGTGGTTGATAGTTCAAG 60.377 45.833 0.00 0.00 42.41 3.02
3324 4049 1.158484 TCTACGCCGGAGAGTCATCG 61.158 60.000 13.83 1.58 0.00 3.84
3347 4072 6.887545 TCGATAATTCCATTTTGTACCTGGTT 59.112 34.615 3.84 0.00 0.00 3.67
3354 4079 4.082245 CCATTTTGTACCTGGTTCCATCAC 60.082 45.833 3.84 0.00 0.00 3.06
3367 4092 0.452987 CCATCACGGGCTTCATTGTG 59.547 55.000 0.00 0.00 0.00 3.33
3509 4235 4.829064 TGCCGGCATATGTTCTTTATTC 57.171 40.909 29.03 0.00 0.00 1.75
3537 4263 8.515414 CCTTTGATTCTTTTTCTCCGTTAGAAT 58.485 33.333 0.00 0.00 43.75 2.40
3610 4343 4.454728 TTTCCCTGTTCATGCTAAATGC 57.545 40.909 0.00 0.00 43.25 3.56
3611 4344 2.378038 TCCCTGTTCATGCTAAATGCC 58.622 47.619 0.00 0.00 42.00 4.40
3612 4345 2.101783 CCCTGTTCATGCTAAATGCCA 58.898 47.619 0.00 0.00 42.00 4.92
3615 4348 4.116961 CCTGTTCATGCTAAATGCCAATG 58.883 43.478 0.00 0.00 42.00 2.82
3616 4349 4.382254 CCTGTTCATGCTAAATGCCAATGT 60.382 41.667 0.00 0.00 42.00 2.71
3618 4351 5.549347 TGTTCATGCTAAATGCCAATGTTT 58.451 33.333 0.00 0.00 42.00 2.83
3619 4352 6.695429 TGTTCATGCTAAATGCCAATGTTTA 58.305 32.000 0.00 0.00 42.00 2.01
3620 4353 7.329499 TGTTCATGCTAAATGCCAATGTTTAT 58.671 30.769 0.00 0.00 42.00 1.40
3621 4354 7.823310 TGTTCATGCTAAATGCCAATGTTTATT 59.177 29.630 0.00 0.00 42.00 1.40
3622 4355 9.311916 GTTCATGCTAAATGCCAATGTTTATTA 57.688 29.630 0.00 0.00 42.00 0.98
3659 4392 7.293402 TGTATTGACCGGAAACTTAAATACG 57.707 36.000 9.46 0.00 33.68 3.06
3761 4496 7.975750 GTTTCCTAACCATAGACATGAGTTTC 58.024 38.462 0.00 0.00 33.67 2.78
3838 4577 5.275927 CGTAAACTTAGCATCTCATCGTGTG 60.276 44.000 0.00 0.00 0.00 3.82
3843 4582 2.886081 AGCATCTCATCGTGTGACTTC 58.114 47.619 0.00 0.00 32.22 3.01
3941 4683 5.523916 CGGAAGAATACTTTGTGGGTATCAG 59.476 44.000 0.00 0.00 36.39 2.90
3952 4694 1.822990 TGGGTATCAGACGTCACTTCC 59.177 52.381 19.50 12.48 0.00 3.46
3957 4699 4.157289 GGTATCAGACGTCACTTCCTAACA 59.843 45.833 19.50 0.00 0.00 2.41
3958 4700 4.866508 ATCAGACGTCACTTCCTAACAA 57.133 40.909 19.50 0.00 0.00 2.83
4139 4887 8.853345 GTTTAGTCACGAGATTTTGTATTACGA 58.147 33.333 0.00 0.00 0.00 3.43
4166 4915 3.930848 CGTAAAGAGATTTGCCGGTAACT 59.069 43.478 3.74 0.00 0.00 2.24
4301 5054 6.088217 CGATAACGATCTTCGCTGAATATGTT 59.912 38.462 0.00 0.00 45.12 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.376609 GGGGATCACCGTGACATTGC 61.377 60.000 0.00 0.00 41.60 3.56
27 28 1.218316 GAGGTGACGTGGGGATCAC 59.782 63.158 0.00 0.00 43.75 3.06
37 38 1.381872 AGATGGGGAGGAGGTGACG 60.382 63.158 0.00 0.00 0.00 4.35
81 82 1.361668 CCTCTCAAACATGGCGACCG 61.362 60.000 0.00 0.00 0.00 4.79
82 83 1.026718 CCCTCTCAAACATGGCGACC 61.027 60.000 0.00 0.00 0.00 4.79
128 129 1.098712 TGCAACCACTTGAACCCGTC 61.099 55.000 0.00 0.00 0.00 4.79
131 132 0.240945 CGATGCAACCACTTGAACCC 59.759 55.000 0.00 0.00 0.00 4.11
133 134 2.143122 TCTCGATGCAACCACTTGAAC 58.857 47.619 0.00 0.00 0.00 3.18
166 167 2.378208 TGTTGAGGGTGATGGGAATGAA 59.622 45.455 0.00 0.00 0.00 2.57
169 170 2.582172 TGATGTTGAGGGTGATGGGAAT 59.418 45.455 0.00 0.00 0.00 3.01
272 273 3.897122 TTGGTGGGTGGAGGCACC 61.897 66.667 0.00 0.00 44.27 5.01
273 274 2.597510 GTTGGTGGGTGGAGGCAC 60.598 66.667 0.00 0.00 0.00 5.01
275 276 1.903404 CTTGTTGGTGGGTGGAGGC 60.903 63.158 0.00 0.00 0.00 4.70
276 277 1.228552 CCTTGTTGGTGGGTGGAGG 60.229 63.158 0.00 0.00 0.00 4.30
277 278 0.184933 TTCCTTGTTGGTGGGTGGAG 59.815 55.000 0.00 0.00 37.07 3.86
278 279 0.106419 GTTCCTTGTTGGTGGGTGGA 60.106 55.000 0.00 0.00 37.07 4.02
279 280 0.396417 TGTTCCTTGTTGGTGGGTGG 60.396 55.000 0.00 0.00 37.07 4.61
280 281 1.479709 TTGTTCCTTGTTGGTGGGTG 58.520 50.000 0.00 0.00 37.07 4.61
282 283 1.412343 CCTTTGTTCCTTGTTGGTGGG 59.588 52.381 0.00 0.00 37.07 4.61
283 284 2.362077 CTCCTTTGTTCCTTGTTGGTGG 59.638 50.000 0.00 0.00 37.07 4.61
284 285 3.023832 ACTCCTTTGTTCCTTGTTGGTG 58.976 45.455 0.00 0.00 37.07 4.17
285 286 3.023832 CACTCCTTTGTTCCTTGTTGGT 58.976 45.455 0.00 0.00 37.07 3.67
286 287 2.362077 CCACTCCTTTGTTCCTTGTTGG 59.638 50.000 0.00 0.00 37.10 3.77
287 288 2.223805 GCCACTCCTTTGTTCCTTGTTG 60.224 50.000 0.00 0.00 0.00 3.33
288 289 2.031870 GCCACTCCTTTGTTCCTTGTT 58.968 47.619 0.00 0.00 0.00 2.83
289 290 1.215423 AGCCACTCCTTTGTTCCTTGT 59.785 47.619 0.00 0.00 0.00 3.16
290 291 1.986882 AGCCACTCCTTTGTTCCTTG 58.013 50.000 0.00 0.00 0.00 3.61
291 292 2.695147 CAAAGCCACTCCTTTGTTCCTT 59.305 45.455 6.50 0.00 44.08 3.36
308 885 4.008330 AGCATGATGGAGTTGAGACAAAG 58.992 43.478 0.00 0.00 0.00 2.77
325 902 6.126854 TGGATCCATAGATCTATTGGAGCATG 60.127 42.308 29.79 16.20 46.96 4.06
386 965 5.106157 GCATCCAAACATGTTTAGCAGTAGT 60.106 40.000 22.87 0.00 0.00 2.73
391 970 3.320256 TGTGCATCCAAACATGTTTAGCA 59.680 39.130 22.87 23.57 0.00 3.49
422 1001 2.555199 CTTTGGGCTATCGTGGAAGAG 58.445 52.381 0.00 0.00 0.00 2.85
500 1079 0.833949 GCCTAGGAGGGGTCAAAGAG 59.166 60.000 14.75 0.00 35.37 2.85
585 1164 2.570365 GGGCAGATGCACACAATCA 58.430 52.632 7.19 0.00 45.57 2.57
597 1176 0.697658 TGAATCATGTGGTGGGCAGA 59.302 50.000 0.00 0.00 0.00 4.26
650 1229 2.182842 CATTGCCCTGCTAGACGGC 61.183 63.158 7.93 7.93 43.32 5.68
651 1230 2.182842 GCATTGCCCTGCTAGACGG 61.183 63.158 0.00 0.00 39.12 4.79
652 1231 2.182842 GGCATTGCCCTGCTAGACG 61.183 63.158 17.28 0.00 44.06 4.18
653 1232 3.833304 GGCATTGCCCTGCTAGAC 58.167 61.111 17.28 0.00 44.06 2.59
672 1251 0.464036 TAACACTATGGCCAGCCTCG 59.536 55.000 13.05 0.45 36.94 4.63
692 1271 7.064371 CCAAGTGCATGATATCAGCTAAGATAC 59.936 40.741 20.51 12.88 33.61 2.24
719 1298 7.602517 ATTCTCTACAGTGTGTTTGCTATTC 57.397 36.000 5.88 0.00 0.00 1.75
732 1311 8.652290 ACTGGTCTCTTTTTAATTCTCTACAGT 58.348 33.333 0.00 0.00 0.00 3.55
762 1347 3.128068 GCATGATGTGTCACATGTGATGT 59.872 43.478 30.10 16.50 46.22 3.06
763 1348 3.127895 TGCATGATGTGTCACATGTGATG 59.872 43.478 30.10 22.07 43.67 3.07
764 1349 3.128068 GTGCATGATGTGTCACATGTGAT 59.872 43.478 30.10 15.36 43.67 3.06
766 1351 2.486592 AGTGCATGATGTGTCACATGTG 59.513 45.455 23.08 20.18 43.67 3.21
767 1352 2.786777 AGTGCATGATGTGTCACATGT 58.213 42.857 23.08 8.73 43.67 3.21
768 1353 4.573201 TCATAGTGCATGATGTGTCACATG 59.427 41.667 23.08 11.59 39.27 3.21
769 1354 4.773013 TCATAGTGCATGATGTGTCACAT 58.227 39.130 18.45 18.45 42.43 3.21
771 1356 4.034858 CCTTCATAGTGCATGATGTGTCAC 59.965 45.833 0.00 0.00 43.26 3.67
773 1358 4.194640 ACCTTCATAGTGCATGATGTGTC 58.805 43.478 0.00 0.00 43.26 3.67
775 1360 5.363101 ACTACCTTCATAGTGCATGATGTG 58.637 41.667 0.00 0.10 43.26 3.21
776 1361 5.620738 ACTACCTTCATAGTGCATGATGT 57.379 39.130 0.00 4.42 43.26 3.06
777 1362 7.381323 TGATACTACCTTCATAGTGCATGATG 58.619 38.462 0.00 0.00 43.26 3.07
780 1365 8.306761 TGTATGATACTACCTTCATAGTGCATG 58.693 37.037 4.03 0.00 35.94 4.06
781 1366 8.307483 GTGTATGATACTACCTTCATAGTGCAT 58.693 37.037 4.03 0.00 35.94 3.96
800 1520 8.366359 ACCATGCATATGATACTAGTGTATGA 57.634 34.615 6.97 0.00 39.29 2.15
916 1637 1.673033 GGAGTCACCGACCATCAACAG 60.673 57.143 0.00 0.00 32.18 3.16
948 1669 9.798994 AGACGACTTTAGGTACATTTACATAAG 57.201 33.333 0.00 0.00 36.20 1.73
957 1678 7.466996 CGAAGACATAGACGACTTTAGGTACAT 60.467 40.741 0.00 0.00 0.00 2.29
975 1696 4.944619 TCTCTGCCATAATCGAAGACAT 57.055 40.909 0.00 0.00 42.51 3.06
1018 1739 3.887621 TGCCACCACAAGTATCTCTAC 57.112 47.619 0.00 0.00 0.00 2.59
1030 1751 1.228862 ACCCTTTCCATGCCACCAC 60.229 57.895 0.00 0.00 0.00 4.16
1042 1763 0.780090 ACTTGGATCCCCCACCCTTT 60.780 55.000 9.90 0.00 46.62 3.11
1138 1859 6.860023 GCTGACCATATGATGAATTTAAGCAC 59.140 38.462 3.65 0.00 0.00 4.40
1221 1942 1.669115 CTGTTGCTCCGGTGACCTG 60.669 63.158 7.92 0.00 0.00 4.00
1236 1957 1.227764 CCATAGCGCCATGAGCTGT 60.228 57.895 17.76 14.04 45.60 4.40
1449 2170 1.203087 TCCTCGTACTTGAGAACCCCA 60.203 52.381 0.00 0.00 38.28 4.96
1464 2185 1.482593 AGTGCCCATACTCTTTCCTCG 59.517 52.381 0.00 0.00 0.00 4.63
1485 2206 1.794116 GCAGAATTGTTTGCGCACATT 59.206 42.857 11.12 6.27 0.00 2.71
1591 2312 3.181367 CGGTGCCAACTGCTCATC 58.819 61.111 0.00 0.00 42.00 2.92
1761 2486 3.181443 ACATCTCCCGTCCTTCAAAACTT 60.181 43.478 0.00 0.00 0.00 2.66
2160 2885 6.049149 GCTTGTATTATTCCTACTGTGAGCA 58.951 40.000 0.00 0.00 0.00 4.26
2262 2987 4.194640 TCAGCACCTTCTGAATGATAAGC 58.805 43.478 0.00 0.00 39.89 3.09
2281 3006 5.873712 TCTCCGTAGTAGACACTAGTTTCAG 59.126 44.000 11.48 0.00 37.94 3.02
2300 3025 1.879380 TGTCAAATTGGCTTGTCTCCG 59.121 47.619 0.00 0.00 0.00 4.63
2305 3030 2.964464 TGGTGATGTCAAATTGGCTTGT 59.036 40.909 0.00 0.00 0.00 3.16
2368 3093 3.571401 CCATGTTCCATTCCATTAGAGCC 59.429 47.826 0.00 0.00 0.00 4.70
2426 3151 0.250338 GTCCAGGTCCAACTCCACAC 60.250 60.000 0.00 0.00 0.00 3.82
2484 3209 2.268920 GCATCCAACCAGCCGAGA 59.731 61.111 0.00 0.00 0.00 4.04
2502 3227 1.946768 CGCCATACCACCATTACCTTG 59.053 52.381 0.00 0.00 0.00 3.61
2506 3231 2.210116 CTCACGCCATACCACCATTAC 58.790 52.381 0.00 0.00 0.00 1.89
2686 3411 1.739466 CAGATCACAATTCCCGGTGTG 59.261 52.381 15.01 15.01 45.29 3.82
2782 3507 9.336462 AGATCCTCTGTCCAATATAAGATTGAT 57.664 33.333 0.00 0.00 0.00 2.57
2988 3713 3.371917 GGGAAATGGTGGTCATGATCTCA 60.372 47.826 7.64 6.30 35.99 3.27
3074 3799 2.739784 CTCTAGGAGCCGCATGGG 59.260 66.667 2.06 2.06 39.58 4.00
3100 3825 8.846211 ACATCAGTATAATTAAACATTTCCGGG 58.154 33.333 0.00 0.00 0.00 5.73
3144 3869 4.997565 TGTATAGTTTCTCGGGTAAACGG 58.002 43.478 5.19 0.00 40.86 4.44
3224 3949 5.188163 TCCAACAAGCAAATGATTCATGGAT 59.812 36.000 9.43 0.00 33.18 3.41
3247 3972 5.514204 CGACAAGCAAATGATTGATCCTTTC 59.486 40.000 17.36 3.44 43.50 2.62
3252 3977 4.100529 CCACGACAAGCAAATGATTGATC 58.899 43.478 17.36 10.09 43.50 2.92
3270 3995 3.498397 ACTTGCTTGAACTATCAACCACG 59.502 43.478 0.00 0.00 40.59 4.94
3287 4012 2.953020 AGATCGTCACTGAAGACTTGC 58.047 47.619 0.00 0.00 36.38 4.01
3288 4013 4.092120 CGTAGATCGTCACTGAAGACTTG 58.908 47.826 0.00 0.00 36.38 3.16
3324 4049 7.123547 TGGAACCAGGTACAAAATGGAATTATC 59.876 37.037 11.31 3.72 33.67 1.75
3347 4072 0.327924 ACAATGAAGCCCGTGATGGA 59.672 50.000 0.00 0.00 42.00 3.41
3354 4079 1.139163 GCAAAACACAATGAAGCCCG 58.861 50.000 0.00 0.00 0.00 6.13
3367 4092 7.532682 TTAACAACTTGAGGAAATGCAAAAC 57.467 32.000 0.00 0.00 0.00 2.43
3487 4212 5.072741 AGAATAAAGAACATATGCCGGCAT 58.927 37.500 41.28 41.28 40.19 4.40
3509 4235 5.948992 ACGGAGAAAAAGAATCAAAGGAG 57.051 39.130 0.00 0.00 0.00 3.69
3537 4263 8.923270 CCTCTAGGGCATATTTCCAAAATTTTA 58.077 33.333 2.44 0.00 0.00 1.52
3539 4265 7.365497 CCTCTAGGGCATATTTCCAAAATTT 57.635 36.000 0.00 0.00 0.00 1.82
3619 4352 8.886719 CGGTCAATACAATGATAGCATGATAAT 58.113 33.333 0.00 0.00 34.26 1.28
3620 4353 7.334171 CCGGTCAATACAATGATAGCATGATAA 59.666 37.037 0.00 0.00 34.26 1.75
3621 4354 6.818142 CCGGTCAATACAATGATAGCATGATA 59.182 38.462 0.00 0.00 34.26 2.15
3622 4355 5.645067 CCGGTCAATACAATGATAGCATGAT 59.355 40.000 0.00 0.00 34.26 2.45
3659 4392 5.176958 GGTGTCTATTTATGTATCCACGCAC 59.823 44.000 0.00 0.00 0.00 5.34
3689 4424 6.612456 AGTTAGTCTAGTAGAGGCTCACTAGA 59.388 42.308 31.11 31.11 41.58 2.43
3838 4577 8.068380 AGAAAGTTGTAGCAATTAAACGAAGTC 58.932 33.333 0.00 0.00 45.00 3.01
3843 4582 8.728088 ATGAAGAAAGTTGTAGCAATTAAACG 57.272 30.769 0.00 0.00 0.00 3.60
3941 4683 3.057734 CACCTTGTTAGGAAGTGACGTC 58.942 50.000 9.11 9.11 45.05 4.34
3952 4694 5.938125 AGCACCTTTATGTACACCTTGTTAG 59.062 40.000 0.00 0.00 0.00 2.34
3957 4699 4.910458 AGAGCACCTTTATGTACACCTT 57.090 40.909 0.00 0.00 0.00 3.50
3958 4700 4.775780 TGTAGAGCACCTTTATGTACACCT 59.224 41.667 0.00 0.00 0.00 4.00
4139 4887 2.412325 CGGCAAATCTCTTTACGCGTTT 60.412 45.455 20.78 0.00 0.00 3.60
4256 5008 2.813754 CGGTTGAACCATGATGTCAAGT 59.186 45.455 15.58 0.00 38.47 3.16
4301 5054 3.435457 CCTGGATGCCCATATTGACTTCA 60.435 47.826 0.00 0.00 42.59 3.02


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

AutoCloner maintained by Alex Coulton.