Multiple sequence alignment - TraesCS4D01G125600

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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 TraesCS4D01G125600 chr4D 100.000 4053 0 0 1 4053 109916338 109912286 0.000000e+00 7485.0
1 TraesCS4D01G125600 chr4A 89.818 3290 184 61 863 4053 466922462 466925699 0.000000e+00 4080.0
2 TraesCS4D01G125600 chr4A 80.181 883 102 38 18 863 715077570 715076724 9.700000e-166 593.0
3 TraesCS4D01G125600 chr4A 83.890 509 56 22 18 513 715080281 715079786 2.850000e-126 462.0
4 TraesCS4D01G125600 chr4A 82.175 561 76 19 18 564 39586615 39586065 1.030000e-125 460.0
5 TraesCS4D01G125600 chr4A 81.229 586 83 21 297 863 39586256 39585679 7.990000e-122 448.0
6 TraesCS4D01G125600 chr4B 89.375 2814 191 57 950 3711 171092527 171089770 0.000000e+00 3441.0
7 TraesCS4D01G125600 chr4B 82.206 562 77 19 15 564 624514558 624515108 2.850000e-126 462.0
8 TraesCS4D01G125600 chr4B 79.110 584 90 28 298 863 624514880 624515449 1.380000e-99 374.0
9 TraesCS4D01G125600 chr4B 86.957 230 17 6 3752 3973 171089699 171089475 3.130000e-61 246.0
10 TraesCS4D01G125600 chr7D 91.732 895 18 14 18 861 419373513 419372624 0.000000e+00 1192.0
11 TraesCS4D01G125600 chr7B 87.653 899 55 19 18 864 598900069 598900963 0.000000e+00 994.0
12 TraesCS4D01G125600 chr7B 81.831 732 98 25 17 722 641179966 641179244 2.100000e-162 582.0
13 TraesCS4D01G125600 chrUn 85.934 782 55 22 18 745 391494226 391493446 0.000000e+00 784.0
14 TraesCS4D01G125600 chrUn 97.647 85 1 1 779 863 391403608 391403525 1.170000e-30 145.0
15 TraesCS4D01G125600 chrUn 97.647 85 1 1 779 863 391493445 391493362 1.170000e-30 145.0
16 TraesCS4D01G125600 chr5D 79.428 909 112 45 17 863 515242099 515241204 1.260000e-159 573.0
17 TraesCS4D01G125600 chr5D 83.333 132 16 6 2425 2553 7500668 7500540 2.560000e-22 117.0
18 TraesCS4D01G125600 chr1B 82.168 572 71 25 7 566 645134114 645133562 2.850000e-126 462.0
19 TraesCS4D01G125600 chr1A 79.027 658 97 34 231 863 318507733 318507092 2.920000e-111 412.0
20 TraesCS4D01G125600 chr6B 77.891 588 91 31 297 863 714259019 714259588 3.020000e-86 329.0
21 TraesCS4D01G125600 chr6B 84.848 132 16 2 2423 2553 337236955 337236827 3.290000e-26 130.0
22 TraesCS4D01G125600 chr6D 84.091 132 17 2 2423 2553 249454364 249454236 1.530000e-24 124.0
23 TraesCS4D01G125600 chr6A 84.091 132 17 2 2423 2553 349512769 349512897 1.530000e-24 124.0
24 TraesCS4D01G125600 chr3A 77.982 218 33 11 636 852 553323384 553323587 5.500000e-24 122.0
25 TraesCS4D01G125600 chr3A 81.395 129 23 1 2423 2550 90297714 90297842 1.990000e-18 104.0
26 TraesCS4D01G125600 chr5A 75.481 208 39 7 2357 2553 324391582 324391376 1.550000e-14 91.6


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 TraesCS4D01G125600 chr4D 109912286 109916338 4052 True 7485.0 7485 100.0000 1 4053 1 chr4D.!!$R1 4052
1 TraesCS4D01G125600 chr4A 466922462 466925699 3237 False 4080.0 4080 89.8180 863 4053 1 chr4A.!!$F1 3190
2 TraesCS4D01G125600 chr4A 715076724 715080281 3557 True 527.5 593 82.0355 18 863 2 chr4A.!!$R2 845
3 TraesCS4D01G125600 chr4A 39585679 39586615 936 True 454.0 460 81.7020 18 863 2 chr4A.!!$R1 845
4 TraesCS4D01G125600 chr4B 171089475 171092527 3052 True 1843.5 3441 88.1660 950 3973 2 chr4B.!!$R1 3023
5 TraesCS4D01G125600 chr4B 624514558 624515449 891 False 418.0 462 80.6580 15 863 2 chr4B.!!$F1 848
6 TraesCS4D01G125600 chr7D 419372624 419373513 889 True 1192.0 1192 91.7320 18 861 1 chr7D.!!$R1 843
7 TraesCS4D01G125600 chr7B 598900069 598900963 894 False 994.0 994 87.6530 18 864 1 chr7B.!!$F1 846
8 TraesCS4D01G125600 chr7B 641179244 641179966 722 True 582.0 582 81.8310 17 722 1 chr7B.!!$R1 705
9 TraesCS4D01G125600 chrUn 391493362 391494226 864 True 464.5 784 91.7905 18 863 2 chrUn.!!$R2 845
10 TraesCS4D01G125600 chr5D 515241204 515242099 895 True 573.0 573 79.4280 17 863 1 chr5D.!!$R2 846
11 TraesCS4D01G125600 chr1B 645133562 645134114 552 True 462.0 462 82.1680 7 566 1 chr1B.!!$R1 559
12 TraesCS4D01G125600 chr1A 318507092 318507733 641 True 412.0 412 79.0270 231 863 1 chr1A.!!$R1 632
13 TraesCS4D01G125600 chr6B 714259019 714259588 569 False 329.0 329 77.8910 297 863 1 chr6B.!!$F1 566

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
891 3754 0.666577 GGTGGGAGACTTTGTCGTCG 60.667 60.0 0.0 0.0 38.90 5.12 F
1270 4136 0.181350 ACCATGCCCTTCGGAGATTC 59.819 55.0 0.0 0.0 35.04 2.52 F
1908 4829 0.037326 GGAGATGTGGTTGAGCGTCA 60.037 55.0 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 4810 0.037326 TGACGCTCAACCACATCTCC 60.037 55.0 0.0 0.0 0.0 3.71 R
2615 5557 0.896923 GATGCAGCCCAAATCCAACA 59.103 50.0 0.0 0.0 0.0 3.33 R
3412 6405 0.323302 TGCAGCTCCCATCGTAAACA 59.677 50.0 0.0 0.0 0.0 2.83 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
454 3277 8.572855 TTTGGAAAAAGTTCATCAAATTTGGT 57.427 26.923 17.90 8.39 35.25 3.67
704 3554 4.019950 ACCGTGGTTTACTATTAAGCAGGT 60.020 41.667 0.00 0.00 37.24 4.00
731 3582 4.440250 CCCGAGTTCGATTCTCAGTACAAT 60.440 45.833 15.16 0.00 43.02 2.71
733 3584 5.449314 CCGAGTTCGATTCTCAGTACAATCT 60.449 44.000 15.16 0.00 43.02 2.40
871 3734 4.708177 GAATAGGATTCAGCCTGCTTGTA 58.292 43.478 0.00 0.00 39.08 2.41
877 3740 1.377725 CAGCCTGCTTGTAGGTGGG 60.378 63.158 6.62 0.00 40.11 4.61
884 3747 2.039084 CTGCTTGTAGGTGGGAGACTTT 59.961 50.000 0.00 0.00 0.00 2.66
890 3753 0.680061 AGGTGGGAGACTTTGTCGTC 59.320 55.000 0.00 0.00 37.67 4.20
891 3754 0.666577 GGTGGGAGACTTTGTCGTCG 60.667 60.000 0.00 0.00 38.90 5.12
1198 4062 4.281182 TCTTAACTATGCCCTTCGGAGATC 59.719 45.833 0.00 0.00 35.04 2.75
1222 4088 5.519927 CGATAAGAAAAACCCATGGAATTGC 59.480 40.000 15.22 3.59 0.00 3.56
1248 4114 4.021456 GGGTTGAATTCGAATCAAAACCCT 60.021 41.667 34.58 14.76 41.57 4.34
1253 4119 6.683715 TGAATTCGAATCAAAACCCTTAACC 58.316 36.000 11.83 0.00 0.00 2.85
1270 4136 0.181350 ACCATGCCCTTCGGAGATTC 59.819 55.000 0.00 0.00 35.04 2.52
1324 4208 2.048127 ACAGGAAACGAGCGCTCC 60.048 61.111 30.66 17.91 0.00 4.70
1394 4278 6.677552 TCCCATTCCACCAAATTCACATATA 58.322 36.000 0.00 0.00 0.00 0.86
1456 4340 6.389091 CCTGTTCAATCAATTTCATTCCGAA 58.611 36.000 0.00 0.00 0.00 4.30
1484 4368 8.434392 TCACTACAACAACTCTTTACCCTTTAT 58.566 33.333 0.00 0.00 0.00 1.40
1503 4387 9.099454 CCCTTTATTTACTCTCAACTACATCAC 57.901 37.037 0.00 0.00 0.00 3.06
1530 4414 5.295431 TGAAATGAGCATTTGTTAGGTCG 57.705 39.130 12.73 0.00 40.77 4.79
1571 4455 5.102953 TGGATCACCCTCTGATTAAGTTG 57.897 43.478 0.00 0.00 39.96 3.16
1575 4459 7.567250 TGGATCACCCTCTGATTAAGTTGTATA 59.433 37.037 0.00 0.00 39.96 1.47
1579 4463 5.368816 ACCCTCTGATTAAGTTGTATACCCC 59.631 44.000 0.00 0.00 0.00 4.95
1767 4651 4.400120 AGAACTTCTCTTCGTACCTCACT 58.600 43.478 0.00 0.00 0.00 3.41
1769 4653 2.820787 ACTTCTCTTCGTACCTCACTGG 59.179 50.000 0.00 0.00 42.93 4.00
1904 4825 1.667724 CATTCGGAGATGTGGTTGAGC 59.332 52.381 0.00 0.00 35.04 4.26
1908 4829 0.037326 GGAGATGTGGTTGAGCGTCA 60.037 55.000 0.00 0.00 0.00 4.35
1910 4831 0.969149 AGATGTGGTTGAGCGTCAGA 59.031 50.000 0.00 0.00 0.00 3.27
1911 4832 1.344438 AGATGTGGTTGAGCGTCAGAA 59.656 47.619 0.00 0.00 0.00 3.02
1922 4843 1.284198 AGCGTCAGAACCTCTACCCTA 59.716 52.381 0.00 0.00 0.00 3.53
1924 4845 2.494870 GCGTCAGAACCTCTACCCTAAA 59.505 50.000 0.00 0.00 0.00 1.85
1937 4858 7.511028 ACCTCTACCCTAAAGGATAATTCAGAG 59.489 40.741 0.00 0.00 39.89 3.35
1965 4886 6.992664 ATGAGCTAGTTCTAGAATCACCAT 57.007 37.500 8.75 5.54 0.00 3.55
2053 4975 4.028131 CCAAGTACCTGTACTCCCATGTA 58.972 47.826 10.22 0.00 44.96 2.29
2059 4981 5.934402 ACCTGTACTCCCATGTACTAAAG 57.066 43.478 6.41 0.00 42.22 1.85
2060 4982 4.161754 ACCTGTACTCCCATGTACTAAAGC 59.838 45.833 6.41 0.00 42.22 3.51
2075 4997 9.784531 ATGTACTAAAGCTTATCATTACTGCAT 57.215 29.630 0.00 0.00 0.00 3.96
2182 5105 4.574599 ATCTCTGAGTTTTGCCAACAAC 57.425 40.909 4.32 0.00 34.87 3.32
2199 5124 5.458779 CCAACAACGTGAAAGGAGATTTTTC 59.541 40.000 0.00 0.00 35.59 2.29
2200 5125 6.265577 CAACAACGTGAAAGGAGATTTTTCT 58.734 36.000 0.00 0.00 35.94 2.52
2201 5126 6.451064 ACAACGTGAAAGGAGATTTTTCTT 57.549 33.333 0.00 0.00 35.94 2.52
2204 5129 7.913821 ACAACGTGAAAGGAGATTTTTCTTTAC 59.086 33.333 0.00 0.00 35.94 2.01
2205 5130 7.803279 ACGTGAAAGGAGATTTTTCTTTACT 57.197 32.000 0.00 0.00 35.94 2.24
2206 5131 7.639945 ACGTGAAAGGAGATTTTTCTTTACTG 58.360 34.615 0.00 0.00 35.94 2.74
2207 5132 7.078228 CGTGAAAGGAGATTTTTCTTTACTGG 58.922 38.462 0.00 0.00 35.94 4.00
2208 5133 7.255139 CGTGAAAGGAGATTTTTCTTTACTGGT 60.255 37.037 0.00 0.00 35.94 4.00
2209 5134 7.862873 GTGAAAGGAGATTTTTCTTTACTGGTG 59.137 37.037 0.00 0.00 35.94 4.17
2210 5135 7.559897 TGAAAGGAGATTTTTCTTTACTGGTGT 59.440 33.333 0.00 0.00 35.94 4.16
2212 5137 7.898014 AGGAGATTTTTCTTTACTGGTGTTT 57.102 32.000 0.00 0.00 0.00 2.83
2213 5138 8.306313 AGGAGATTTTTCTTTACTGGTGTTTT 57.694 30.769 0.00 0.00 0.00 2.43
2267 5197 1.901591 AGGATGTGGTTGTTCTGCTG 58.098 50.000 0.00 0.00 0.00 4.41
2287 5217 7.929245 TCTGCTGTTGTAAGAAGTGTATGTTAA 59.071 33.333 0.00 0.00 0.00 2.01
2354 5288 9.988350 CTGCATAGTATAAATTGTTCGTCTTTT 57.012 29.630 0.00 0.00 0.00 2.27
2457 5391 3.589288 ACATACTGGCCTTCTTCTTCCTT 59.411 43.478 3.32 0.00 0.00 3.36
2497 5439 2.283617 CGGAGATTGAAATCGCACTGAG 59.716 50.000 8.69 0.00 40.35 3.35
2498 5440 3.265791 GGAGATTGAAATCGCACTGAGT 58.734 45.455 8.69 0.00 40.35 3.41
2950 5911 4.201628 GCTATACACAGCTTCAAGACAACG 60.202 45.833 0.00 0.00 38.57 4.10
2974 5935 5.042463 TGTCTAATGTGGTTGTTGAGGAA 57.958 39.130 0.00 0.00 0.00 3.36
3104 6065 4.045104 CAGTAACATACGAGTGCAGGATC 58.955 47.826 0.00 0.00 0.00 3.36
3106 6067 2.586258 ACATACGAGTGCAGGATCAC 57.414 50.000 0.00 0.00 37.24 3.06
3149 6110 3.632145 AGGCTTATTAATTCCCAGTTGCG 59.368 43.478 0.00 0.00 0.00 4.85
3221 6186 8.038351 TGTCAAATAAGTGGATTACATCGAAGA 58.962 33.333 0.00 0.00 45.75 2.87
3299 6291 7.066307 AGCCAATTTTTATTCAGAACAAGGT 57.934 32.000 0.00 0.00 0.00 3.50
3341 6333 3.004106 GCTTTTGCGCAGGATGATCTATT 59.996 43.478 11.31 0.00 34.25 1.73
3404 6397 5.913137 TTTGGAAGGGTTTACATGCTATG 57.087 39.130 0.00 0.00 0.00 2.23
3412 6405 9.289782 GAAGGGTTTACATGCTATGATAATCTT 57.710 33.333 0.00 0.00 0.00 2.40
3423 6416 8.310406 TGCTATGATAATCTTGTTTACGATGG 57.690 34.615 0.00 0.00 0.00 3.51
3441 6434 4.499183 GATGGGAGCTGCATATACTGTAC 58.501 47.826 7.79 0.00 0.00 2.90
3459 6460 2.703798 CGCAAGTTGCCCCATGAGG 61.704 63.158 21.84 1.51 41.12 3.86
3466 6467 4.059773 AGTTGCCCCATGAGGAATTTTA 57.940 40.909 0.00 0.00 38.24 1.52
3469 6470 2.024080 TGCCCCATGAGGAATTTTAGCT 60.024 45.455 0.00 0.00 38.24 3.32
3508 6512 8.478066 TCAGTTCTCAACATAAGCACTGTATAT 58.522 33.333 3.52 0.00 38.59 0.86
3587 6591 3.643792 GCTTCCAGGTGATAGGATACAGT 59.356 47.826 0.00 0.00 41.41 3.55
3590 6594 4.215908 TCCAGGTGATAGGATACAGTCAC 58.784 47.826 4.56 4.56 46.37 3.67
3596 6600 3.891977 TGATAGGATACAGTCACCTGAGC 59.108 47.826 8.28 0.00 41.50 4.26
3605 6609 1.986757 TCACCTGAGCTCTGAGGCC 60.987 63.158 21.10 0.00 37.49 5.19
3610 6614 1.229304 TGAGCTCTGAGGCCTGGAA 60.229 57.895 12.00 0.00 0.00 3.53
3652 6658 8.890124 ATGTAGAGATGTTGAATCATCAGAAG 57.110 34.615 8.93 0.00 44.46 2.85
3654 6660 8.534496 TGTAGAGATGTTGAATCATCAGAAGAA 58.466 33.333 8.93 0.00 44.46 2.52
3658 6664 9.761504 GAGATGTTGAATCATCAGAAGAATAGA 57.238 33.333 8.93 0.00 44.46 1.98
3720 6727 7.064728 GTGTGTGTATAGAGATTGAAAAGTCCC 59.935 40.741 0.00 0.00 0.00 4.46
3724 6731 3.618690 AGAGATTGAAAAGTCCCGGAG 57.381 47.619 0.73 0.00 0.00 4.63
3738 6745 0.109342 CCGGAGCCTTATGGATGCTT 59.891 55.000 0.00 0.00 37.97 3.91
3742 6749 3.244215 CGGAGCCTTATGGATGCTTTAGA 60.244 47.826 3.02 0.00 37.97 2.10
3745 6752 6.112058 GGAGCCTTATGGATGCTTTAGATAG 58.888 44.000 0.00 0.00 37.11 2.08
3746 6753 6.070538 GGAGCCTTATGGATGCTTTAGATAGA 60.071 42.308 0.00 0.00 37.11 1.98
3747 6754 7.365473 GGAGCCTTATGGATGCTTTAGATAGAT 60.365 40.741 0.00 0.00 37.11 1.98
3748 6755 7.337167 AGCCTTATGGATGCTTTAGATAGATG 58.663 38.462 0.00 0.00 34.57 2.90
3766 6801 7.655328 AGATAGATGAGAAATGTTGAATCGACC 59.345 37.037 0.00 0.00 0.00 4.79
3780 6815 5.879237 TGAATCGACCTCAATTTTATGCAC 58.121 37.500 0.00 0.00 0.00 4.57
3929 6966 8.829612 GTGCATTTATCTTGGAAAAATAATGGG 58.170 33.333 0.00 0.00 0.00 4.00
3950 6987 4.270325 GGGCATACACTCGAAGAATTGTAC 59.730 45.833 0.00 0.00 37.73 2.90
4041 7087 1.952296 CAAGTGAGGAAGCAAGCAAGT 59.048 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.044946 CTACAAGCAGGGCCCACC 60.045 66.667 27.56 14.64 40.67 4.61
1 2 1.078143 CTCTACAAGCAGGGCCCAC 60.078 63.158 27.56 16.50 0.00 4.61
5 6 0.176910 GAGGACTCTACAAGCAGGGC 59.823 60.000 0.00 0.00 0.00 5.19
7 8 1.754226 GAGGAGGACTCTACAAGCAGG 59.246 57.143 0.00 0.00 43.14 4.85
8 9 1.403679 CGAGGAGGACTCTACAAGCAG 59.596 57.143 0.00 0.00 44.33 4.24
9 10 1.271982 ACGAGGAGGACTCTACAAGCA 60.272 52.381 0.00 0.00 44.33 3.91
10 11 1.465794 ACGAGGAGGACTCTACAAGC 58.534 55.000 0.00 0.00 44.33 4.01
11 12 2.164624 CCAACGAGGAGGACTCTACAAG 59.835 54.545 0.00 0.00 44.33 3.16
12 13 2.168496 CCAACGAGGAGGACTCTACAA 58.832 52.381 0.00 0.00 44.33 2.41
13 14 1.835494 CCAACGAGGAGGACTCTACA 58.165 55.000 0.00 0.00 44.33 2.74
428 3208 9.187996 ACCAAATTTGATGAACTTTTTCCAAAT 57.812 25.926 19.86 0.00 36.20 2.32
429 3209 8.572855 ACCAAATTTGATGAACTTTTTCCAAA 57.427 26.923 19.86 0.00 31.51 3.28
430 3210 9.672673 TTACCAAATTTGATGAACTTTTTCCAA 57.327 25.926 19.86 0.00 0.00 3.53
431 3211 9.672673 TTTACCAAATTTGATGAACTTTTTCCA 57.327 25.926 19.86 0.00 0.00 3.53
685 3535 5.410355 ACGACCTGCTTAATAGTAAACCA 57.590 39.130 0.00 0.00 0.00 3.67
871 3734 0.680061 GACGACAAAGTCTCCCACCT 59.320 55.000 0.00 0.00 38.09 4.00
877 3740 1.053811 GAGTGCGACGACAAAGTCTC 58.946 55.000 0.00 0.00 38.90 3.36
884 3747 1.299850 CAAGTGGAGTGCGACGACA 60.300 57.895 0.00 0.00 0.00 4.35
890 3753 1.135257 CCTCTAGACAAGTGGAGTGCG 60.135 57.143 0.00 0.00 40.71 5.34
891 3754 1.896465 ACCTCTAGACAAGTGGAGTGC 59.104 52.381 2.14 0.00 40.71 4.40
1198 4062 5.519927 GCAATTCCATGGGTTTTTCTTATCG 59.480 40.000 13.02 0.00 0.00 2.92
1222 4088 6.322491 GGTTTTGATTCGAATTCAACCCTAG 58.678 40.000 23.75 0.00 0.00 3.02
1270 4136 1.978712 CTGCACCAGCGAGCAAGATG 61.979 60.000 0.00 0.00 46.23 2.90
1394 4278 1.814248 GCTTCCCTTCAGTTGTTCGGT 60.814 52.381 0.00 0.00 0.00 4.69
1456 4340 5.365895 AGGGTAAAGAGTTGTTGTAGTGACT 59.634 40.000 0.00 0.00 0.00 3.41
1484 4368 4.768448 TCCGGTGATGTAGTTGAGAGTAAA 59.232 41.667 0.00 0.00 0.00 2.01
1503 4387 3.788333 ACAAATGCTCATTTCATCCGG 57.212 42.857 0.00 0.00 38.84 5.14
1530 4414 5.762825 TCCATTGATTGCAGAAGCTATTC 57.237 39.130 0.00 0.00 42.74 1.75
1571 4455 4.130118 CTGCAAGAATGACAGGGGTATAC 58.870 47.826 0.00 0.00 34.07 1.47
1575 4459 0.038744 CCTGCAAGAATGACAGGGGT 59.961 55.000 0.19 0.00 42.38 4.95
1579 4463 3.377485 CCATTCTCCTGCAAGAATGACAG 59.623 47.826 30.09 16.85 39.66 3.51
1616 4500 4.264380 GCGACGTGTTGAAATTGAAGTTTT 59.736 37.500 0.00 0.00 0.00 2.43
1767 4651 1.303561 GCAGTTCCACTCATGGCCA 60.304 57.895 8.56 8.56 46.80 5.36
1769 4653 1.135199 CAATGCAGTTCCACTCATGGC 60.135 52.381 0.00 0.00 46.80 4.40
1803 4687 7.102346 AGAACTCTGTTAACATCTCAATGGAG 58.898 38.462 9.13 11.52 42.80 3.86
1873 4794 5.928264 CACATCTCCGAATGCTCATTATGTA 59.072 40.000 7.31 0.00 29.11 2.29
1875 4796 4.153655 CCACATCTCCGAATGCTCATTATG 59.846 45.833 0.00 0.00 0.00 1.90
1877 4798 3.134623 ACCACATCTCCGAATGCTCATTA 59.865 43.478 0.00 0.00 0.00 1.90
1881 4802 1.667724 CAACCACATCTCCGAATGCTC 59.332 52.381 0.00 0.00 0.00 4.26
1889 4810 0.037326 TGACGCTCAACCACATCTCC 60.037 55.000 0.00 0.00 0.00 3.71
1904 4825 3.130693 CCTTTAGGGTAGAGGTTCTGACG 59.869 52.174 0.00 0.00 0.00 4.35
1908 4829 7.849904 TGAATTATCCTTTAGGGTAGAGGTTCT 59.150 37.037 0.00 0.00 31.36 3.01
1910 4831 7.849904 TCTGAATTATCCTTTAGGGTAGAGGTT 59.150 37.037 0.00 0.00 31.36 3.50
1911 4832 7.371043 TCTGAATTATCCTTTAGGGTAGAGGT 58.629 38.462 0.00 0.00 31.36 3.85
1922 4843 7.292120 AGCTCATAGTCCTCTGAATTATCCTTT 59.708 37.037 0.00 0.00 0.00 3.11
1924 4845 6.322126 AGCTCATAGTCCTCTGAATTATCCT 58.678 40.000 0.00 0.00 0.00 3.24
1937 4858 7.308951 GGTGATTCTAGAACTAGCTCATAGTCC 60.309 44.444 7.48 1.58 44.26 3.85
1965 4886 5.643379 ACTCTTTTCTTGTGCTGTTTTCA 57.357 34.783 0.00 0.00 0.00 2.69
2053 4975 6.543465 TGCATGCAGTAATGATAAGCTTTAGT 59.457 34.615 18.46 0.00 0.00 2.24
2059 4981 5.179045 ACTTGCATGCAGTAATGATAAGC 57.821 39.130 21.50 0.00 31.65 3.09
2060 4982 6.788243 TGAACTTGCATGCAGTAATGATAAG 58.212 36.000 21.50 14.08 33.26 1.73
2075 4997 1.358725 GCGGCGTCTATGAACTTGCA 61.359 55.000 9.37 0.00 0.00 4.08
2168 5091 3.249917 CTTTCACGTTGTTGGCAAAACT 58.750 40.909 0.00 0.00 36.22 2.66
2182 5105 7.078228 CCAGTAAAGAAAAATCTCCTTTCACG 58.922 38.462 0.00 0.00 35.62 4.35
2215 5140 8.974408 GGTTTGAAGCGTACTTATTTCAAATTT 58.026 29.630 18.13 0.00 45.61 1.82
2259 5189 6.202954 ACATACACTTCTTACAACAGCAGAAC 59.797 38.462 0.00 0.00 0.00 3.01
2267 5197 8.084590 AGCTGTTAACATACACTTCTTACAAC 57.915 34.615 9.13 0.00 0.00 3.32
2287 5217 7.358770 AGATGATCTCAACTAACATAGCTGT 57.641 36.000 0.00 0.00 37.12 4.40
2406 5340 8.226819 TCAATGTAATGTACTGGTTGTTTTCA 57.773 30.769 0.00 0.00 0.00 2.69
2442 5376 2.680339 CAATCGAAGGAAGAAGAAGGCC 59.320 50.000 0.00 0.00 0.00 5.19
2457 5391 2.894879 CGGGCGGCAATCAATCGA 60.895 61.111 12.47 0.00 0.00 3.59
2497 5439 5.220989 GGTGTCCCTTTTCTTTACTGTTGAC 60.221 44.000 0.00 0.00 0.00 3.18
2498 5440 4.885325 GGTGTCCCTTTTCTTTACTGTTGA 59.115 41.667 0.00 0.00 0.00 3.18
2615 5557 0.896923 GATGCAGCCCAAATCCAACA 59.103 50.000 0.00 0.00 0.00 3.33
2950 5911 4.819630 TCCTCAACAACCACATTAGACAAC 59.180 41.667 0.00 0.00 0.00 3.32
2974 5935 7.334090 TCTCTAGTGCAGCATAAAATTCTTCT 58.666 34.615 0.00 0.00 0.00 2.85
3075 6036 5.066764 TGCACTCGTATGTTACTGCACTATA 59.933 40.000 0.00 0.00 33.99 1.31
3136 6097 3.596214 CAGTAGTACGCAACTGGGAATT 58.404 45.455 14.62 0.00 39.55 2.17
3149 6110 6.341316 TCTTGATTCATTCCTGCAGTAGTAC 58.659 40.000 13.81 0.00 0.00 2.73
3188 6150 7.888021 TGTAATCCACTTATTTGACACCTTCAT 59.112 33.333 0.00 0.00 32.84 2.57
3234 6226 6.936279 ACATCGATCTTTCTAGTTTGAAGGA 58.064 36.000 0.00 0.00 36.68 3.36
3239 6231 6.703607 AGGCATACATCGATCTTTCTAGTTTG 59.296 38.462 0.00 0.00 0.00 2.93
3253 6245 5.615544 GCTTACATTTAGCAGGCATACATCG 60.616 44.000 0.00 0.00 38.51 3.84
3404 6397 5.992217 AGCTCCCATCGTAAACAAGATTATC 59.008 40.000 0.00 0.00 0.00 1.75
3412 6405 0.323302 TGCAGCTCCCATCGTAAACA 59.677 50.000 0.00 0.00 0.00 2.83
3423 6416 2.288213 TGCGTACAGTATATGCAGCTCC 60.288 50.000 0.00 0.00 34.84 4.70
3441 6434 2.703798 CCTCATGGGGCAACTTGCG 61.704 63.158 0.00 0.00 46.21 4.85
3450 6451 4.141158 ACCTAGCTAAAATTCCTCATGGGG 60.141 45.833 4.76 4.76 35.33 4.96
3457 6458 6.898521 ACTAGAGACACCTAGCTAAAATTCCT 59.101 38.462 0.00 0.00 39.71 3.36
3459 6460 7.773149 TGACTAGAGACACCTAGCTAAAATTC 58.227 38.462 0.00 0.00 39.71 2.17
3466 6467 4.018779 AGAACTGACTAGAGACACCTAGCT 60.019 45.833 0.00 0.00 39.71 3.32
3469 6470 5.500546 TGAGAACTGACTAGAGACACCTA 57.499 43.478 0.00 0.00 0.00 3.08
3508 6512 8.424918 CCTCTGAAACTCCAAATAAGATAGCTA 58.575 37.037 0.00 0.00 0.00 3.32
3587 6591 1.986757 GGCCTCAGAGCTCAGGTGA 60.987 63.158 17.77 10.20 31.65 4.02
3590 6594 2.733669 CCAGGCCTCAGAGCTCAGG 61.734 68.421 17.77 15.89 0.00 3.86
3596 6600 3.037549 AGTAATCTTCCAGGCCTCAGAG 58.962 50.000 0.00 0.00 0.00 3.35
3720 6727 1.972872 AAAGCATCCATAAGGCTCCG 58.027 50.000 0.00 0.00 36.76 4.63
3724 6731 7.334090 TCATCTATCTAAAGCATCCATAAGGC 58.666 38.462 0.00 0.00 33.74 4.35
3742 6749 7.504403 AGGTCGATTCAACATTTCTCATCTAT 58.496 34.615 0.00 0.00 0.00 1.98
3745 6752 5.582269 TGAGGTCGATTCAACATTTCTCATC 59.418 40.000 0.00 0.00 0.00 2.92
3746 6753 5.491070 TGAGGTCGATTCAACATTTCTCAT 58.509 37.500 0.00 0.00 0.00 2.90
3747 6754 4.893608 TGAGGTCGATTCAACATTTCTCA 58.106 39.130 0.00 0.00 0.00 3.27
3748 6755 5.862924 TTGAGGTCGATTCAACATTTCTC 57.137 39.130 10.24 0.00 30.03 2.87
3766 6801 2.684881 AGCCCTCGTGCATAAAATTGAG 59.315 45.455 0.00 0.00 0.00 3.02
3929 6966 7.932120 ATAGTACAATTCTTCGAGTGTATGC 57.068 36.000 0.00 0.00 0.00 3.14
3950 6987 6.370718 GGTACGCCCCATTTTGATACTAATAG 59.629 42.308 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.