Multiple sequence alignment - TraesCS5B01G234100

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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 TraesCS5B01G234100 chr5B 100.000 4184 0 0 1 4184 411933006 411928823 0.000000e+00 7727.0
1 TraesCS5B01G234100 chr5B 96.998 533 15 1 1 532 358026732 358027264 0.000000e+00 894.0
2 TraesCS5B01G234100 chr5B 95.238 462 16 6 1 460 706379050 706378593 0.000000e+00 726.0
3 TraesCS5B01G234100 chr5B 80.800 500 56 20 44 532 547398209 547398679 5.140000e-94 355.0
4 TraesCS5B01G234100 chr5B 86.076 79 11 0 997 1075 582891329 582891251 7.450000e-13 86.1
5 TraesCS5B01G234100 chr5D 93.305 3331 148 36 874 4170 351007496 351004207 0.000000e+00 4846.0
6 TraesCS5B01G234100 chr5D 90.223 358 17 5 536 877 351008215 351007860 6.380000e-123 451.0
7 TraesCS5B01G234100 chr5D 85.281 231 31 3 3624 3852 518917273 518917502 6.990000e-58 235.0
8 TraesCS5B01G234100 chr5D 74.053 528 105 25 1666 2187 475510582 475510081 1.990000e-43 187.0
9 TraesCS5B01G234100 chr5D 87.342 79 10 0 997 1075 475511503 475511425 1.600000e-14 91.6
10 TraesCS5B01G234100 chr5A 91.096 3167 153 47 532 3628 451481472 451478365 0.000000e+00 4167.0
11 TraesCS5B01G234100 chr5A 82.938 211 35 1 3624 3833 100066924 100067134 5.520000e-44 189.0
12 TraesCS5B01G234100 chr5A 74.102 529 106 25 1666 2187 594963386 594962882 5.520000e-44 189.0
13 TraesCS5B01G234100 chr5A 92.683 82 5 1 3919 4000 451478069 451477989 2.640000e-22 117.0
14 TraesCS5B01G234100 chr5A 87.342 79 10 0 997 1075 594964352 594964274 1.600000e-14 91.6
15 TraesCS5B01G234100 chr6B 97.948 536 10 1 1 535 566153587 566154122 0.000000e+00 928.0
16 TraesCS5B01G234100 chr1B 96.296 513 15 2 21 532 673998300 673998809 0.000000e+00 839.0
17 TraesCS5B01G234100 chr7B 93.996 533 16 3 1 532 564175296 564174779 0.000000e+00 793.0
18 TraesCS5B01G234100 chr4B 97.907 430 8 1 1 429 28266064 28265635 0.000000e+00 743.0
19 TraesCS5B01G234100 chr4B 96.380 442 11 3 1 441 640825964 640825527 0.000000e+00 723.0
20 TraesCS5B01G234100 chr2B 97.045 440 11 2 1 439 617149558 617149996 0.000000e+00 739.0
21 TraesCS5B01G234100 chr2B 96.818 440 12 2 1 439 752930816 752930378 0.000000e+00 734.0
22 TraesCS5B01G234100 chr2B 96.591 440 13 2 1 439 369806883 369807321 0.000000e+00 728.0
23 TraesCS5B01G234100 chr2B 93.983 349 19 2 190 536 595127608 595127956 1.030000e-145 527.0
24 TraesCS5B01G234100 chr6A 90.892 538 30 11 1 534 616893660 616893138 0.000000e+00 704.0
25 TraesCS5B01G234100 chr2A 87.135 171 21 1 3624 3794 142895187 142895356 4.270000e-45 193.0
26 TraesCS5B01G234100 chr2A 80.269 223 41 3 3618 3838 81014759 81014980 9.310000e-37 165.0
27 TraesCS5B01G234100 chr2A 82.258 186 29 4 3626 3809 452311823 452311640 1.560000e-34 158.0
28 TraesCS5B01G234100 chr1A 82.648 219 30 3 3629 3839 481503796 481504014 1.990000e-43 187.0
29 TraesCS5B01G234100 chrUn 83.708 178 23 6 3629 3803 35453766 35453940 3.350000e-36 163.0
30 TraesCS5B01G234100 chr3D 82.778 180 27 4 3632 3809 5607730 5607553 1.560000e-34 158.0


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 TraesCS5B01G234100 chr5B 411928823 411933006 4183 True 7727.0 7727 100.0000 1 4184 1 chr5B.!!$R1 4183
1 TraesCS5B01G234100 chr5B 358026732 358027264 532 False 894.0 894 96.9980 1 532 1 chr5B.!!$F1 531
2 TraesCS5B01G234100 chr5D 351004207 351008215 4008 True 2648.5 4846 91.7640 536 4170 2 chr5D.!!$R1 3634
3 TraesCS5B01G234100 chr5A 451477989 451481472 3483 True 2142.0 4167 91.8895 532 4000 2 chr5A.!!$R1 3468
4 TraesCS5B01G234100 chr6B 566153587 566154122 535 False 928.0 928 97.9480 1 535 1 chr6B.!!$F1 534
5 TraesCS5B01G234100 chr1B 673998300 673998809 509 False 839.0 839 96.2960 21 532 1 chr1B.!!$F1 511
6 TraesCS5B01G234100 chr7B 564174779 564175296 517 True 793.0 793 93.9960 1 532 1 chr7B.!!$R1 531
7 TraesCS5B01G234100 chr6A 616893138 616893660 522 True 704.0 704 90.8920 1 534 1 chr6A.!!$R1 533

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
903 1317 2.522436 CCCCGCCGGTATGGTCTA 60.522 66.667 1.9 0.0 41.21 2.59 F
1794 2214 0.107848 CGTCCAAGTCCATGTACCCC 60.108 60.000 0.0 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2647 3095 0.036732 AGGCTCCTTTTGTCATCGCA 59.963 50.0 0.0 0.0 0.0 5.10 R
3231 3683 0.254178 GAGGATTGAAGCTCAGCCCA 59.746 55.0 0.0 0.0 0.0 5.36 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
252 277 5.694231 TTGATGTGTCTTTCATGTCTTGG 57.306 39.130 0.00 0.00 0.00 3.61
284 309 5.798125 TTGCATTTGAACTTGGTTGGATA 57.202 34.783 0.00 0.00 0.00 2.59
555 582 9.507329 TCTAATAAGTTTGCTCATTTCTCACTT 57.493 29.630 0.00 0.00 0.00 3.16
566 593 6.876257 GCTCATTTCTCACTTCTTTTCCTCTA 59.124 38.462 0.00 0.00 0.00 2.43
574 601 6.390721 TCACTTCTTTTCCTCTATCGTTGAG 58.609 40.000 0.00 0.00 0.00 3.02
590 621 4.097741 TCGTTGAGCCCATTTCCAATATTG 59.902 41.667 8.58 8.58 0.00 1.90
611 642 5.730296 TGCCGGGAAAATTCTCAAAAATA 57.270 34.783 2.18 0.00 0.00 1.40
625 664 3.269381 TCAAAAATAGCCAGGGGATGTCT 59.731 43.478 0.00 0.00 0.00 3.41
903 1317 2.522436 CCCCGCCGGTATGGTCTA 60.522 66.667 1.90 0.00 41.21 2.59
1159 1573 2.681778 CCTCCTCTCGCCACCAGT 60.682 66.667 0.00 0.00 0.00 4.00
1272 1689 0.967887 TCTCCGGAAGCCACTCTCTG 60.968 60.000 5.23 0.00 0.00 3.35
1794 2214 0.107848 CGTCCAAGTCCATGTACCCC 60.108 60.000 0.00 0.00 0.00 4.95
1803 2223 0.837272 CCATGTACCCCACCTTCGAT 59.163 55.000 0.00 0.00 0.00 3.59
1806 2226 1.354101 TGTACCCCACCTTCGATGTT 58.646 50.000 0.00 0.00 0.00 2.71
1824 2244 0.824109 TTGGTGATCGGATTCTCGCT 59.176 50.000 0.00 0.00 0.00 4.93
1843 2263 5.757886 TCGCTGAGAAGGTAAAACATTTTG 58.242 37.500 0.00 0.00 0.00 2.44
1846 2266 5.010617 GCTGAGAAGGTAAAACATTTTGGGA 59.989 40.000 0.00 0.00 0.00 4.37
1847 2267 6.648879 TGAGAAGGTAAAACATTTTGGGAG 57.351 37.500 0.00 0.00 0.00 4.30
1849 2269 5.711698 AGAAGGTAAAACATTTTGGGAGGA 58.288 37.500 0.00 0.00 0.00 3.71
1850 2270 6.322931 AGAAGGTAAAACATTTTGGGAGGAT 58.677 36.000 0.00 0.00 0.00 3.24
1852 2272 6.358974 AGGTAAAACATTTTGGGAGGATTG 57.641 37.500 0.00 0.00 0.00 2.67
1853 2273 4.935205 GGTAAAACATTTTGGGAGGATTGC 59.065 41.667 0.00 0.00 0.00 3.56
1872 2292 9.021807 AGGATTGCTATCTGATGATTAATTTGG 57.978 33.333 8.06 0.00 34.32 3.28
1873 2293 8.800332 GGATTGCTATCTGATGATTAATTTGGT 58.200 33.333 8.06 0.00 34.32 3.67
1874 2294 9.622004 GATTGCTATCTGATGATTAATTTGGTG 57.378 33.333 0.00 0.00 34.32 4.17
1884 2310 7.816995 TGATGATTAATTTGGTGTTTTGCTACC 59.183 33.333 0.00 0.00 37.48 3.18
1901 2327 3.127721 GCTACCTGGTTTCTGATCTTTGC 59.872 47.826 3.84 0.00 0.00 3.68
1905 2331 3.057736 CCTGGTTTCTGATCTTTGCTGTG 60.058 47.826 0.00 0.00 0.00 3.66
1933 2359 7.839680 ATGTGATCTGTAGGTGTCATATGTA 57.160 36.000 1.90 0.00 0.00 2.29
1963 2389 5.335976 GGAACCAGAAATCTTGGACATTGTC 60.336 44.000 8.34 8.34 0.00 3.18
2062 2494 7.669427 ACTGGTGAATTTGATGCTAATTTGAA 58.331 30.769 0.00 0.00 0.00 2.69
2069 2501 9.646336 GAATTTGATGCTAATTTGAATGCAATC 57.354 29.630 0.00 0.00 38.96 2.67
2154 2586 1.202234 GGGACTACGTCGAAGTAAGCC 60.202 57.143 12.28 14.46 32.65 4.35
2177 2609 5.398581 CCTTTATCCCAATGGTAGTGCCTTA 60.399 44.000 0.00 0.00 38.35 2.69
2187 2619 6.664428 ATGGTAGTGCCTTATGTTTGTTTT 57.336 33.333 0.00 0.00 38.35 2.43
2189 2621 6.508777 TGGTAGTGCCTTATGTTTGTTTTTC 58.491 36.000 0.00 0.00 38.35 2.29
2191 2623 7.502895 TGGTAGTGCCTTATGTTTGTTTTTCTA 59.497 33.333 0.00 0.00 38.35 2.10
2219 2658 3.057969 ACTAGTAATTGCTGTGCTGCA 57.942 42.857 6.28 0.00 41.65 4.41
2383 2822 8.553153 TGGAACCATTGGTATGTTTATCTTCTA 58.447 33.333 9.20 0.00 33.12 2.10
2423 2862 7.483059 GTGTCTCTACCACTACGTATTTTGTAC 59.517 40.741 0.00 0.00 0.00 2.90
2520 2960 0.622665 AGCTGAATTCTGGGACCTGG 59.377 55.000 13.50 0.00 0.00 4.45
2522 2962 1.004745 GCTGAATTCTGGGACCTGGAA 59.995 52.381 13.50 0.00 0.00 3.53
2533 2973 4.641868 TGGGACCTGGAATTAGTTAGGAT 58.358 43.478 0.00 0.00 34.42 3.24
2608 3055 6.001460 TCTTCCAAACCAACTGTTATACCTG 58.999 40.000 0.00 0.00 35.67 4.00
2621 3068 5.396484 TGTTATACCTGCGAGCGAATATAC 58.604 41.667 0.00 0.00 0.00 1.47
2631 3078 7.275779 CCTGCGAGCGAATATACATAAATAAGT 59.724 37.037 0.00 0.00 0.00 2.24
2870 3318 1.438651 TGTCAGCCTTTCCGATTTCG 58.561 50.000 0.00 0.00 39.44 3.46
2893 3341 4.361926 CGAACTAATCGCTGCTGTTATC 57.638 45.455 0.00 0.00 45.89 1.75
2997 3446 1.804151 CGAACCGAGCTCCATTTTCAA 59.196 47.619 8.47 0.00 0.00 2.69
3000 3449 1.202879 ACCGAGCTCCATTTTCAACCA 60.203 47.619 8.47 0.00 0.00 3.67
3030 3481 8.721133 TTCAGCTACATATTAGAATCCAGGTA 57.279 34.615 0.00 0.00 0.00 3.08
3206 3658 4.457496 CGTGCCTCCGGTGATGCT 62.457 66.667 4.76 0.00 33.73 3.79
3220 3672 3.898509 TGCTGTGGCAACCAACGC 61.899 61.111 0.00 0.00 46.36 4.84
3221 3673 4.980903 GCTGTGGCAACCAACGCG 62.981 66.667 3.53 3.53 34.18 6.01
3222 3674 4.980903 CTGTGGCAACCAACGCGC 62.981 66.667 5.73 0.00 34.18 6.86
3224 3676 4.683334 GTGGCAACCAACGCGCTC 62.683 66.667 5.73 0.00 34.18 5.03
3335 3815 1.915614 CTACTGGCAGGCGCTTGTTG 61.916 60.000 21.36 13.14 38.60 3.33
3338 3818 1.870055 CTGGCAGGCGCTTGTTGAAT 61.870 55.000 21.36 0.00 38.60 2.57
3352 3833 4.902443 TGTTGAATAACCACGAAAAGCA 57.098 36.364 0.00 0.00 35.92 3.91
3369 3850 6.237942 CGAAAAGCATGGTTATGTGTAGAGAG 60.238 42.308 11.15 0.00 36.65 3.20
3370 3851 5.939764 AAGCATGGTTATGTGTAGAGAGA 57.060 39.130 8.73 0.00 36.65 3.10
3371 3852 5.528043 AGCATGGTTATGTGTAGAGAGAG 57.472 43.478 0.00 0.00 36.65 3.20
3735 4226 2.354510 TCCGAAGCTGACTGTTTGTTTG 59.645 45.455 0.00 0.00 0.00 2.93
3759 4250 5.010282 CCCTGCTATAGAAAAACCACAAGT 58.990 41.667 3.21 0.00 0.00 3.16
3782 4273 2.166829 TGTGTAATGTCCACAATGCCC 58.833 47.619 0.00 0.00 39.73 5.36
3791 4282 2.423538 GTCCACAATGCCCAGAATACAC 59.576 50.000 0.00 0.00 0.00 2.90
3800 4291 3.088532 GCCCAGAATACACAAATGGTCA 58.911 45.455 0.00 0.00 0.00 4.02
3876 4367 4.945246 TCCAAGTGTAGTGAAGTCTGAAC 58.055 43.478 0.00 0.00 0.00 3.18
3974 4698 8.025445 GGAGTTACGTTCTCTTTTAGTATCACA 58.975 37.037 16.16 0.00 33.06 3.58
4025 4749 8.742777 AGTTGCAAATATGATAACTTGTGATGT 58.257 29.630 0.00 0.00 34.09 3.06
4040 4764 4.130857 TGTGATGTTAACGTGTTCATGGT 58.869 39.130 4.71 0.00 0.00 3.55
4054 4778 7.822334 ACGTGTTCATGGTAGAAATAGAAATGA 59.178 33.333 0.00 0.00 0.00 2.57
4055 4779 8.331022 CGTGTTCATGGTAGAAATAGAAATGAG 58.669 37.037 0.00 0.00 0.00 2.90
4056 4780 8.616076 GTGTTCATGGTAGAAATAGAAATGAGG 58.384 37.037 0.00 0.00 0.00 3.86
4057 4781 7.775093 TGTTCATGGTAGAAATAGAAATGAGGG 59.225 37.037 0.00 0.00 0.00 4.30
4061 4785 7.510675 TGGTAGAAATAGAAATGAGGGTTCT 57.489 36.000 0.00 0.00 38.80 3.01
4080 4804 9.267071 AGGGTTCTTATATGCCTTGTTTTTATT 57.733 29.630 0.00 0.00 0.00 1.40
4114 4840 7.187824 ACTCTTGACATCCTAGAATGCTAAA 57.812 36.000 0.00 0.00 0.00 1.85
4117 4843 9.118300 CTCTTGACATCCTAGAATGCTAAAAAT 57.882 33.333 0.00 0.00 0.00 1.82
4118 4844 9.466497 TCTTGACATCCTAGAATGCTAAAAATT 57.534 29.630 0.00 0.00 0.00 1.82
4170 4900 8.983702 AAAATGTTGTTGTTTACTACTCCCTA 57.016 30.769 0.00 0.00 34.20 3.53
4171 4901 9.582648 AAAATGTTGTTGTTTACTACTCCCTAT 57.417 29.630 0.00 0.00 34.20 2.57
4172 4902 9.582648 AAATGTTGTTGTTTACTACTCCCTATT 57.417 29.630 0.00 0.00 34.20 1.73
4173 4903 9.582648 AATGTTGTTGTTTACTACTCCCTATTT 57.417 29.630 0.00 0.00 34.20 1.40
4174 4904 8.611654 TGTTGTTGTTTACTACTCCCTATTTC 57.388 34.615 0.00 0.00 34.20 2.17
4175 4905 7.662669 TGTTGTTGTTTACTACTCCCTATTTCC 59.337 37.037 0.00 0.00 34.20 3.13
4176 4906 6.400568 TGTTGTTTACTACTCCCTATTTCCG 58.599 40.000 0.00 0.00 0.00 4.30
4177 4907 6.014327 TGTTGTTTACTACTCCCTATTTCCGT 60.014 38.462 0.00 0.00 0.00 4.69
4178 4908 5.969423 TGTTTACTACTCCCTATTTCCGTG 58.031 41.667 0.00 0.00 0.00 4.94
4179 4909 5.716228 TGTTTACTACTCCCTATTTCCGTGA 59.284 40.000 0.00 0.00 0.00 4.35
4180 4910 6.127535 TGTTTACTACTCCCTATTTCCGTGAG 60.128 42.308 0.00 0.00 0.00 3.51
4181 4911 3.978610 ACTACTCCCTATTTCCGTGAGT 58.021 45.455 0.00 0.00 39.47 3.41
4182 4912 3.952967 ACTACTCCCTATTTCCGTGAGTC 59.047 47.826 0.00 0.00 37.47 3.36
4183 4913 1.749634 ACTCCCTATTTCCGTGAGTCG 59.250 52.381 0.00 0.00 30.81 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 277 7.277760 ACCAAGTTCAAATGCAAACTAAAAGTC 59.722 33.333 2.05 0.00 34.71 3.01
284 309 4.686191 TCAAAATCATGCCCACAAGTTT 57.314 36.364 0.00 0.00 0.00 2.66
390 417 1.812093 CGACTCGCCGGGCATTTTA 60.812 57.895 20.71 0.00 0.00 1.52
555 582 3.118738 GGGCTCAACGATAGAGGAAAAGA 60.119 47.826 0.00 0.00 41.38 2.52
566 593 2.214376 TTGGAAATGGGCTCAACGAT 57.786 45.000 0.00 0.00 0.00 3.73
574 601 1.270252 CCGGCAATATTGGAAATGGGC 60.270 52.381 17.02 0.00 0.00 5.36
590 621 4.566759 GCTATTTTTGAGAATTTTCCCGGC 59.433 41.667 0.00 0.00 0.00 6.13
657 696 0.680618 CGGGCGGGTGGTGTATATAA 59.319 55.000 0.00 0.00 0.00 0.98
903 1317 0.595053 CGCGATCGGCTACTGATTGT 60.595 55.000 18.30 0.00 40.44 2.71
1008 1422 0.393944 AGTAGGAGACGGTGATGCGA 60.394 55.000 0.00 0.00 0.00 5.10
1253 1670 0.967887 CAGAGAGTGGCTTCCGGAGA 60.968 60.000 3.34 0.00 0.00 3.71
1272 1689 0.976590 AGTAGGGCCTCGAAGGGAAC 60.977 60.000 10.74 0.00 35.37 3.62
1329 1749 3.121030 GCGAGCACCGACAGCAAT 61.121 61.111 2.63 0.00 41.76 3.56
1737 2157 1.962402 GCAAGGGAGGAGCTGTAGAGA 60.962 57.143 0.00 0.00 0.00 3.10
1803 2223 1.739035 GCGAGAATCCGATCACCAACA 60.739 52.381 0.00 0.00 0.00 3.33
1806 2226 0.103026 CAGCGAGAATCCGATCACCA 59.897 55.000 0.00 0.00 0.00 4.17
1812 2232 0.741326 CCTTCTCAGCGAGAATCCGA 59.259 55.000 17.30 0.87 45.84 4.55
1824 2244 5.538433 CCTCCCAAAATGTTTTACCTTCTCA 59.462 40.000 0.00 0.00 0.00 3.27
1843 2263 4.840716 ATCATCAGATAGCAATCCTCCC 57.159 45.455 0.00 0.00 31.98 4.30
1846 2266 9.021807 CCAAATTAATCATCAGATAGCAATCCT 57.978 33.333 0.00 0.00 33.08 3.24
1847 2267 8.800332 ACCAAATTAATCATCAGATAGCAATCC 58.200 33.333 0.00 0.00 33.08 3.01
1849 2269 9.139734 ACACCAAATTAATCATCAGATAGCAAT 57.860 29.630 0.00 0.00 33.08 3.56
1850 2270 8.523915 ACACCAAATTAATCATCAGATAGCAA 57.476 30.769 0.00 0.00 33.08 3.91
1852 2272 9.807649 AAAACACCAAATTAATCATCAGATAGC 57.192 29.630 0.00 0.00 33.08 2.97
1872 2292 3.630312 TCAGAAACCAGGTAGCAAAACAC 59.370 43.478 0.00 0.00 0.00 3.32
1873 2293 3.892284 TCAGAAACCAGGTAGCAAAACA 58.108 40.909 0.00 0.00 0.00 2.83
1874 2294 4.762251 AGATCAGAAACCAGGTAGCAAAAC 59.238 41.667 0.00 0.00 0.00 2.43
1884 2310 3.817084 TCACAGCAAAGATCAGAAACCAG 59.183 43.478 0.00 0.00 0.00 4.00
1901 2327 6.577103 ACACCTACAGATCACATTATCACAG 58.423 40.000 0.00 0.00 0.00 3.66
1905 2331 9.363763 CATATGACACCTACAGATCACATTATC 57.636 37.037 0.00 0.00 0.00 1.75
1933 2359 3.356290 CAAGATTTCTGGTTCCCGGAAT 58.644 45.455 0.73 0.00 46.71 3.01
1963 2389 2.190578 GGGGGAGCACGGAAGATG 59.809 66.667 0.00 0.00 0.00 2.90
2062 2494 4.954202 CCATATCCTGCCATAAGATTGCAT 59.046 41.667 0.00 0.00 33.97 3.96
2069 2501 3.264193 TGTAGCCCATATCCTGCCATAAG 59.736 47.826 0.00 0.00 0.00 1.73
2154 2586 4.170468 AGGCACTACCATTGGGATAAAG 57.830 45.455 7.78 0.00 43.14 1.85
2177 2609 7.023197 AGTAGCAACGTAGAAAAACAAACAT 57.977 32.000 0.00 0.00 0.00 2.71
2187 2619 6.750501 CAGCAATTACTAGTAGCAACGTAGAA 59.249 38.462 13.34 0.00 0.00 2.10
2189 2621 6.020599 CACAGCAATTACTAGTAGCAACGTAG 60.021 42.308 13.34 1.24 0.00 3.51
2191 2623 4.625742 CACAGCAATTACTAGTAGCAACGT 59.374 41.667 13.34 6.14 0.00 3.99
2383 2822 6.384595 TGGTAGAGACACTAGAGACTAGACAT 59.615 42.308 11.94 0.00 0.00 3.06
2545 2992 9.683069 ACATTAACAGAAAAATCTTACTTGCAG 57.317 29.630 0.00 0.00 0.00 4.41
2582 3029 7.827236 CAGGTATAACAGTTGGTTTGGAAGATA 59.173 37.037 0.00 0.00 40.96 1.98
2588 3035 3.119990 CGCAGGTATAACAGTTGGTTTGG 60.120 47.826 0.00 0.00 40.96 3.28
2590 3037 4.000988 CTCGCAGGTATAACAGTTGGTTT 58.999 43.478 0.00 0.00 40.96 3.27
2608 3055 6.895040 GCACTTATTTATGTATATTCGCTCGC 59.105 38.462 0.00 0.00 0.00 5.03
2647 3095 0.036732 AGGCTCCTTTTGTCATCGCA 59.963 50.000 0.00 0.00 0.00 5.10
2893 3341 0.605319 TTCCGGTACAAGCTGCAAGG 60.605 55.000 0.00 0.00 0.00 3.61
3017 3468 9.177608 CACAAAGAAATCATACCTGGATTCTAA 57.822 33.333 0.00 0.00 34.02 2.10
3030 3481 7.698506 ACATCACAGATCACAAAGAAATCAT 57.301 32.000 0.00 0.00 0.00 2.45
3227 3679 0.465097 ATTGAAGCTCAGCCCATCGG 60.465 55.000 0.00 0.00 0.00 4.18
3228 3680 0.942962 GATTGAAGCTCAGCCCATCG 59.057 55.000 0.00 0.00 0.00 3.84
3229 3681 1.133853 AGGATTGAAGCTCAGCCCATC 60.134 52.381 0.00 0.00 0.00 3.51
3230 3682 0.924823 AGGATTGAAGCTCAGCCCAT 59.075 50.000 0.00 0.00 0.00 4.00
3231 3683 0.254178 GAGGATTGAAGCTCAGCCCA 59.746 55.000 0.00 0.00 0.00 5.36
3232 3684 0.545646 AGAGGATTGAAGCTCAGCCC 59.454 55.000 0.00 0.00 0.00 5.19
3233 3685 2.015587 CAAGAGGATTGAAGCTCAGCC 58.984 52.381 0.00 0.00 0.00 4.85
3234 3686 2.709213 ACAAGAGGATTGAAGCTCAGC 58.291 47.619 0.00 0.00 0.00 4.26
3235 3687 4.758674 TGAAACAAGAGGATTGAAGCTCAG 59.241 41.667 0.00 0.00 0.00 3.35
3236 3688 4.717877 TGAAACAAGAGGATTGAAGCTCA 58.282 39.130 0.00 0.00 0.00 4.26
3237 3689 5.893897 ATGAAACAAGAGGATTGAAGCTC 57.106 39.130 0.00 0.00 0.00 4.09
3238 3690 5.771666 TCAATGAAACAAGAGGATTGAAGCT 59.228 36.000 0.00 0.00 31.68 3.74
3239 3691 6.017400 TCAATGAAACAAGAGGATTGAAGC 57.983 37.500 0.00 0.00 31.68 3.86
3240 3692 7.174599 ACTCTCAATGAAACAAGAGGATTGAAG 59.825 37.037 0.00 0.00 39.64 3.02
3241 3693 7.000472 ACTCTCAATGAAACAAGAGGATTGAA 59.000 34.615 0.00 0.00 39.64 2.69
3242 3694 6.537355 ACTCTCAATGAAACAAGAGGATTGA 58.463 36.000 3.55 0.00 39.64 2.57
3243 3695 6.814506 ACTCTCAATGAAACAAGAGGATTG 57.185 37.500 3.55 0.00 39.64 2.67
3352 3833 6.905736 TCTCTCTCTCTCTACACATAACCAT 58.094 40.000 0.00 0.00 0.00 3.55
3566 4056 5.637006 AAGCTGTTTCAGTACACACAAAA 57.363 34.783 0.00 0.00 33.43 2.44
3567 4057 5.637006 AAAGCTGTTTCAGTACACACAAA 57.363 34.783 0.00 0.00 33.43 2.83
3568 4058 5.637006 AAAAGCTGTTTCAGTACACACAA 57.363 34.783 0.00 0.00 33.43 3.33
3669 4160 4.039151 TGATTCTCAGAATCTCAGCGAC 57.961 45.455 24.80 0.79 0.00 5.19
3735 4226 3.352648 TGTGGTTTTTCTATAGCAGGGC 58.647 45.455 0.00 0.00 0.00 5.19
3780 4271 5.418524 TGATTGACCATTTGTGTATTCTGGG 59.581 40.000 0.00 0.00 0.00 4.45
3791 4282 7.655236 TTGCAAGTTTATGATTGACCATTTG 57.345 32.000 0.00 0.00 0.00 2.32
3845 4336 5.738619 TCACTACACTTGGAGCAAGATTA 57.261 39.130 0.00 0.00 43.42 1.75
3852 4343 3.005897 TCAGACTTCACTACACTTGGAGC 59.994 47.826 0.00 0.00 0.00 4.70
3876 4367 2.802256 TCGCTCGTGATTCAGATGAAG 58.198 47.619 1.32 0.00 37.48 3.02
3951 4675 9.350357 TCATGTGATACTAAAAGAGAACGTAAC 57.650 33.333 0.00 0.00 0.00 2.50
3956 4680 9.209175 ACAACTCATGTGATACTAAAAGAGAAC 57.791 33.333 0.94 0.00 41.93 3.01
4025 4749 9.491675 TTTCTATTTCTACCATGAACACGTTAA 57.508 29.630 0.00 0.00 0.00 2.01
4054 4778 8.838649 ATAAAAACAAGGCATATAAGAACCCT 57.161 30.769 0.00 0.00 0.00 4.34
4055 4779 9.884636 AAATAAAAACAAGGCATATAAGAACCC 57.115 29.630 0.00 0.00 0.00 4.11
4105 4831 8.736751 TTCAACGGTAGAAATTTTTAGCATTC 57.263 30.769 15.64 0.00 0.00 2.67
4117 4843 9.004717 TCAAATAACATCATTCAACGGTAGAAA 57.995 29.630 0.00 0.00 0.00 2.52
4118 4844 8.554835 TCAAATAACATCATTCAACGGTAGAA 57.445 30.769 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.