Multiple sequence alignment - TraesCS5D01G208800

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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 TraesCS5D01G208800 chr5D 100.000 5309 0 0 1 5309 315381893 315376585 0.000000e+00 9804.0
1 TraesCS5D01G208800 chr5D 100.000 321 0 0 5563 5883 315376331 315376011 1.410000e-165 593.0
2 TraesCS5D01G208800 chr5D 80.088 683 119 14 225 895 163999127 163998450 5.300000e-135 492.0
3 TraesCS5D01G208800 chr5D 94.512 164 9 0 4033 4196 172296285 172296448 2.720000e-63 254.0
4 TraesCS5D01G208800 chr5D 92.683 164 12 0 4033 4196 368502031 368501868 2.740000e-58 237.0
5 TraesCS5D01G208800 chr5D 75.556 225 45 7 5663 5879 558871977 558872199 1.040000e-17 102.0
6 TraesCS5D01G208800 chr5A 96.294 4425 119 21 908 5301 409819142 409814732 0.000000e+00 7221.0
7 TraesCS5D01G208800 chr5A 90.370 893 78 7 8 895 409824168 409823279 0.000000e+00 1166.0
8 TraesCS5D01G208800 chr5A 92.835 321 17 3 5563 5883 409814312 409813998 1.490000e-125 460.0
9 TraesCS5D01G208800 chr5A 97.959 49 1 0 5261 5309 409814728 409814680 1.050000e-12 86.1
10 TraesCS5D01G208800 chr5B 95.313 3990 136 21 898 4872 363574399 363570446 0.000000e+00 6285.0
11 TraesCS5D01G208800 chr5B 92.227 862 46 15 3596 4454 239385921 239385078 0.000000e+00 1201.0
12 TraesCS5D01G208800 chr5B 87.915 331 27 7 5563 5882 363568913 363568585 1.550000e-100 377.0
13 TraesCS5D01G208800 chr5B 83.212 274 23 9 4873 5145 363570265 363570014 4.590000e-56 230.0
14 TraesCS5D01G208800 chr5B 93.750 48 2 1 4836 4882 363570449 363570402 2.940000e-08 71.3
15 TraesCS5D01G208800 chr4A 93.717 1337 63 9 3122 4454 689221795 689220476 0.000000e+00 1984.0
16 TraesCS5D01G208800 chr4A 95.740 493 16 4 2638 3130 689222761 689222274 0.000000e+00 789.0
17 TraesCS5D01G208800 chr4A 95.122 164 7 1 4033 4196 95707174 95707012 2.100000e-64 257.0
18 TraesCS5D01G208800 chr6B 90.347 1295 82 18 3051 4342 629834050 629832796 0.000000e+00 1659.0
19 TraesCS5D01G208800 chr6B 77.171 714 138 18 23 719 277120070 277120775 5.530000e-105 392.0
20 TraesCS5D01G208800 chr6D 87.515 833 95 7 4 834 382566494 382565669 0.000000e+00 953.0
21 TraesCS5D01G208800 chr6D 77.419 713 135 19 23 719 153162507 153163209 9.180000e-108 401.0
22 TraesCS5D01G208800 chr1B 83.408 892 133 12 1 883 242237115 242238000 0.000000e+00 813.0
23 TraesCS5D01G208800 chr3D 80.642 904 159 13 1 895 333990976 333991872 0.000000e+00 686.0
24 TraesCS5D01G208800 chr3D 95.122 164 8 0 4033 4196 575152238 575152075 5.850000e-65 259.0
25 TraesCS5D01G208800 chr3B 80.642 904 159 14 1 895 433107189 433108085 0.000000e+00 686.0
26 TraesCS5D01G208800 chr3B 84.892 139 15 5 2459 2595 511167332 511167466 1.030000e-27 135.0
27 TraesCS5D01G208800 chr2D 80.000 890 159 17 15 893 282694307 282693426 1.790000e-179 640.0
28 TraesCS5D01G208800 chr1A 83.488 648 91 13 246 883 175171365 175172006 1.830000e-164 590.0
29 TraesCS5D01G208800 chr4D 81.110 757 97 24 1862 2606 486107534 486106812 1.110000e-156 564.0
30 TraesCS5D01G208800 chr4D 94.595 37 2 0 5783 5819 429489506 429489542 2.290000e-04 58.4
31 TraesCS5D01G208800 chrUn 83.570 493 73 8 410 895 88210565 88211056 6.950000e-124 455.0
32 TraesCS5D01G208800 chr7A 91.463 164 13 1 4033 4196 578546889 578546727 2.130000e-54 224.0
33 TraesCS5D01G208800 chr7A 75.692 506 89 28 2165 2649 217767332 217767824 7.670000e-54 222.0
34 TraesCS5D01G208800 chr7B 79.018 224 37 10 5663 5882 715722578 715722361 1.710000e-30 145.0
35 TraesCS5D01G208800 chr7B 87.302 63 8 0 5760 5822 715723289 715723227 8.180000e-09 73.1
36 TraesCS5D01G208800 chr4B 83.453 139 17 5 2459 2595 357394823 357394689 2.230000e-24 124.0
37 TraesCS5D01G208800 chr4B 83.212 137 18 4 2459 2593 357293452 357293319 2.880000e-23 121.0


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 TraesCS5D01G208800 chr5D 315376011 315381893 5882 True 5198.500000 9804 100.0000 1 5883 2 chr5D.!!$R3 5882
1 TraesCS5D01G208800 chr5D 163998450 163999127 677 True 492.000000 492 80.0880 225 895 1 chr5D.!!$R1 670
2 TraesCS5D01G208800 chr5A 409813998 409819142 5144 True 2589.033333 7221 95.6960 908 5883 3 chr5A.!!$R2 4975
3 TraesCS5D01G208800 chr5A 409823279 409824168 889 True 1166.000000 1166 90.3700 8 895 1 chr5A.!!$R1 887
4 TraesCS5D01G208800 chr5B 363568585 363574399 5814 True 1740.825000 6285 90.0475 898 5882 4 chr5B.!!$R2 4984
5 TraesCS5D01G208800 chr5B 239385078 239385921 843 True 1201.000000 1201 92.2270 3596 4454 1 chr5B.!!$R1 858
6 TraesCS5D01G208800 chr4A 689220476 689222761 2285 True 1386.500000 1984 94.7285 2638 4454 2 chr4A.!!$R2 1816
7 TraesCS5D01G208800 chr6B 629832796 629834050 1254 True 1659.000000 1659 90.3470 3051 4342 1 chr6B.!!$R1 1291
8 TraesCS5D01G208800 chr6B 277120070 277120775 705 False 392.000000 392 77.1710 23 719 1 chr6B.!!$F1 696
9 TraesCS5D01G208800 chr6D 382565669 382566494 825 True 953.000000 953 87.5150 4 834 1 chr6D.!!$R1 830
10 TraesCS5D01G208800 chr6D 153162507 153163209 702 False 401.000000 401 77.4190 23 719 1 chr6D.!!$F1 696
11 TraesCS5D01G208800 chr1B 242237115 242238000 885 False 813.000000 813 83.4080 1 883 1 chr1B.!!$F1 882
12 TraesCS5D01G208800 chr3D 333990976 333991872 896 False 686.000000 686 80.6420 1 895 1 chr3D.!!$F1 894
13 TraesCS5D01G208800 chr3B 433107189 433108085 896 False 686.000000 686 80.6420 1 895 1 chr3B.!!$F1 894
14 TraesCS5D01G208800 chr2D 282693426 282694307 881 True 640.000000 640 80.0000 15 893 1 chr2D.!!$R1 878
15 TraesCS5D01G208800 chr1A 175171365 175172006 641 False 590.000000 590 83.4880 246 883 1 chr1A.!!$F1 637
16 TraesCS5D01G208800 chr4D 486106812 486107534 722 True 564.000000 564 81.1100 1862 2606 1 chr4D.!!$R1 744

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
393 406 0.107017 CCATCCTGCGGAACCTCAAT 60.107 55.000 0.00 0.00 34.34 2.57 F
466 481 0.909623 CATCTAAGGTCAACCCGGGT 59.090 55.000 24.16 24.16 38.74 5.28 F
1044 1076 1.597461 GTCCTCTCCAAACCTCCCG 59.403 63.158 0.00 0.00 0.00 5.14 F
1319 1351 2.892425 GCTCCACGCCTCAATCGG 60.892 66.667 0.00 0.00 0.00 4.18 F
1746 1778 3.318313 CTGATACTGGGGACATTAGGGT 58.682 50.000 0.00 0.00 41.51 4.34 F
2692 2744 4.508662 GGAAGTATTGTGCTAGCTTGAGT 58.491 43.478 17.23 1.02 0.00 3.41 F
3943 4503 0.606401 ATGCTTGTCCCAGAACCACG 60.606 55.000 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1778 0.539986 GGGGACATCTCGGTTAAGCA 59.460 55.000 5.38 0.0 0.00 3.91 R
2263 2309 2.230992 TCAAACATGTGCAGGCAATACC 59.769 45.455 0.00 0.0 39.61 2.73 R
2692 2744 0.669619 TCGTAGGTGCGAGTTTGTCA 59.330 50.000 0.00 0.0 35.83 3.58 R
2772 2824 2.238942 TGTCAATGACACGCTTGAGT 57.761 45.000 12.63 0.0 37.67 3.41 R
2817 2869 6.062749 TCGAGATATTAGAAGCAGTACCTGT 58.937 40.000 0.00 0.0 33.43 4.00 R
4103 4681 0.693622 TGGTCGGCCATCCAGTTTAA 59.306 50.000 3.51 0.0 40.46 1.52 R
5630 7421 0.900647 AACTCCCCTCTCGACACCAG 60.901 60.000 0.00 0.0 0.00 4.00 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
79 80 4.644685 GCAAGCCTCATAAATTTAGACCCA 59.355 41.667 3.94 0.00 0.00 4.51
174 175 2.014128 CGCCACTCGGATTTTTATGGT 58.986 47.619 0.00 0.00 33.78 3.55
238 240 5.301551 ACACATGAATGCCACTAAGTTTTGA 59.698 36.000 0.00 0.00 0.00 2.69
287 290 5.627135 TCGGAAAACCTTTAGTCCAGAATT 58.373 37.500 0.00 0.00 0.00 2.17
320 331 7.093771 GGTTTCACTCAAGGATAACCAATTGAT 60.094 37.037 7.12 0.00 38.94 2.57
393 406 0.107017 CCATCCTGCGGAACCTCAAT 60.107 55.000 0.00 0.00 34.34 2.57
466 481 0.909623 CATCTAAGGTCAACCCGGGT 59.090 55.000 24.16 24.16 38.74 5.28
579 595 2.286121 TTCCCTCCAATCGGCCCT 60.286 61.111 0.00 0.00 0.00 5.19
756 779 4.083164 CCATTAAACCACCCTTGTAACGTC 60.083 45.833 0.00 0.00 0.00 4.34
821 845 3.131850 CCTTGGCAAGGGTTCAACT 57.868 52.632 34.03 0.00 45.27 3.16
822 846 2.286365 CCTTGGCAAGGGTTCAACTA 57.714 50.000 34.03 0.00 45.27 2.24
825 849 2.969821 TGGCAAGGGTTCAACTACAT 57.030 45.000 0.00 0.00 0.00 2.29
835 861 5.944007 AGGGTTCAACTACATTGTAATCACC 59.056 40.000 0.00 1.05 39.54 4.02
837 863 5.944007 GGTTCAACTACATTGTAATCACCCT 59.056 40.000 0.00 0.00 39.54 4.34
843 872 9.226606 CAACTACATTGTAATCACCCTTAAGAA 57.773 33.333 3.36 0.00 33.20 2.52
872 901 2.619147 CCTCTGAGAACGAGACGTAGA 58.381 52.381 6.17 0.00 39.99 2.59
874 903 3.513662 CTCTGAGAACGAGACGTAGAGA 58.486 50.000 13.14 5.61 39.63 3.10
883 912 4.260170 ACGAGACGTAGAGATGTTACCTT 58.740 43.478 0.00 0.00 38.73 3.50
884 913 4.332268 ACGAGACGTAGAGATGTTACCTTC 59.668 45.833 0.00 0.00 38.73 3.46
885 914 4.571580 CGAGACGTAGAGATGTTACCTTCT 59.428 45.833 0.00 0.00 0.00 2.85
886 915 5.752472 CGAGACGTAGAGATGTTACCTTCTA 59.248 44.000 0.00 0.00 0.00 2.10
887 916 6.257411 CGAGACGTAGAGATGTTACCTTCTAA 59.743 42.308 0.00 0.00 0.00 2.10
888 917 7.517101 CGAGACGTAGAGATGTTACCTTCTAAG 60.517 44.444 0.00 0.00 0.00 2.18
889 918 7.337167 AGACGTAGAGATGTTACCTTCTAAGA 58.663 38.462 0.00 0.00 0.00 2.10
890 919 7.496591 AGACGTAGAGATGTTACCTTCTAAGAG 59.503 40.741 0.00 0.00 0.00 2.85
891 920 7.337167 ACGTAGAGATGTTACCTTCTAAGAGA 58.663 38.462 0.00 0.00 0.00 3.10
892 921 7.496591 ACGTAGAGATGTTACCTTCTAAGAGAG 59.503 40.741 0.00 0.00 0.00 3.20
893 922 7.041644 CGTAGAGATGTTACCTTCTAAGAGAGG 60.042 44.444 0.00 0.00 0.00 3.69
894 923 6.133356 AGAGATGTTACCTTCTAAGAGAGGG 58.867 44.000 3.24 3.24 46.03 4.30
895 924 6.068735 AGAGATGTTACCTTCTAAGAGAGGGA 60.069 42.308 11.29 0.53 43.58 4.20
896 925 5.894964 AGATGTTACCTTCTAAGAGAGGGAC 59.105 44.000 11.29 1.40 43.58 4.46
906 935 6.384342 TCTAAGAGAGGGACTGTACACTTA 57.616 41.667 0.00 0.00 41.55 2.24
1044 1076 1.597461 GTCCTCTCCAAACCTCCCG 59.403 63.158 0.00 0.00 0.00 5.14
1319 1351 2.892425 GCTCCACGCCTCAATCGG 60.892 66.667 0.00 0.00 0.00 4.18
1746 1778 3.318313 CTGATACTGGGGACATTAGGGT 58.682 50.000 0.00 0.00 41.51 4.34
2014 2056 5.984926 TGGTTTTGCTGATGATTTTGTTCTC 59.015 36.000 0.00 0.00 0.00 2.87
2015 2057 6.183360 TGGTTTTGCTGATGATTTTGTTCTCT 60.183 34.615 0.00 0.00 0.00 3.10
2247 2293 8.786826 TGTTGTACCAAGAGTTGATATTTAGG 57.213 34.615 0.00 0.00 0.00 2.69
2263 2309 8.839343 TGATATTTAGGTTGCACAATATCAGTG 58.161 33.333 14.53 4.37 40.92 3.66
2369 2416 8.214364 AGTTTCTAGGATGATGGTTTTAGATCC 58.786 37.037 0.00 0.00 33.97 3.36
2383 2433 7.886446 TGGTTTTAGATCCCTTAGTAACTTTGG 59.114 37.037 0.00 0.00 0.00 3.28
2479 2529 5.904984 ATGGCCACATCTATACAGGTTAA 57.095 39.130 8.16 0.00 29.20 2.01
2692 2744 4.508662 GGAAGTATTGTGCTAGCTTGAGT 58.491 43.478 17.23 1.02 0.00 3.41
2772 2824 9.053472 TCAGGTATTAATCTGGGAAAGTTTCTA 57.947 33.333 15.05 4.56 0.00 2.10
2817 2869 5.607939 TGAGAAAAGATATGCCTTCCGTA 57.392 39.130 0.00 0.00 0.00 4.02
2898 2950 3.093814 TCTCTGGGTGTAGCGTCAATTA 58.906 45.455 0.00 0.00 0.00 1.40
2905 2957 5.008217 TGGGTGTAGCGTCAATTATAAATGC 59.992 40.000 0.00 0.00 0.00 3.56
3111 3163 3.026694 GGGCAATTTGATAGAAGGTGCT 58.973 45.455 0.00 0.00 0.00 4.40
3258 3814 6.203723 GGCTTCTATACATGTAGCCTTTTCTG 59.796 42.308 23.62 5.38 46.14 3.02
3262 3818 9.905713 TTCTATACATGTAGCCTTTTCTGAAAT 57.094 29.630 11.91 0.00 0.00 2.17
3318 3874 7.363268 GCCCATGATCTTTGTACTTTCTTTCAT 60.363 37.037 0.00 0.00 0.00 2.57
3466 4024 2.766313 ACTGTTACTGCAGCGATCAAA 58.234 42.857 15.27 0.00 39.96 2.69
3707 4266 2.104451 AGCTGACAGCCTTCTCATATGG 59.896 50.000 23.74 0.00 43.77 2.74
3826 4385 6.183360 TGTCACCCCATTCAGTTTTAACTTTC 60.183 38.462 0.00 0.00 37.08 2.62
3851 4410 8.663167 TCAATATTGATCCTGAGTATTGGATGT 58.337 33.333 14.23 0.00 42.56 3.06
3943 4503 0.606401 ATGCTTGTCCCAGAACCACG 60.606 55.000 0.00 0.00 0.00 4.94
3987 4565 1.873698 TGTACTGTTGCGTTTCTCCC 58.126 50.000 0.00 0.00 0.00 4.30
4084 4662 6.042143 ACAGCTGAACACCACTTTTATTTTG 58.958 36.000 23.35 0.00 0.00 2.44
4103 4681 5.762179 TTTGTGGTAGATGGTTGAGAGAT 57.238 39.130 0.00 0.00 0.00 2.75
4328 4906 1.254026 TCGGCTACAGGGATTATCCG 58.746 55.000 5.03 0.00 37.43 4.18
4395 4977 5.449177 GCTTGGCTGGTATGAGATTTTACAC 60.449 44.000 0.00 0.00 0.00 2.90
4550 5136 2.642995 CAGTTGCTTCACATCAACACG 58.357 47.619 7.68 0.00 43.55 4.49
4590 5176 9.034544 TGATACACTCAATGAAGATGATTTACG 57.965 33.333 0.00 0.00 0.00 3.18
4807 5393 3.985279 CACATGAACATGCAAAGGAACAG 59.015 43.478 13.71 0.00 42.39 3.16
4926 5691 4.373156 AGTGGTTGACCTTATTCTTGCT 57.627 40.909 1.34 0.00 36.82 3.91
4927 5692 5.499004 AGTGGTTGACCTTATTCTTGCTA 57.501 39.130 1.34 0.00 36.82 3.49
4934 5699 7.201705 GGTTGACCTTATTCTTGCTATGTAACC 60.202 40.741 0.00 0.00 0.00 2.85
4943 5708 1.338674 TGCTATGTAACCGCACAAGCT 60.339 47.619 0.00 0.00 39.10 3.74
4961 5726 7.182089 CACAAGCTGTTTTCTTTTTGGAATTC 58.818 34.615 0.00 0.00 0.00 2.17
4962 5727 7.064966 CACAAGCTGTTTTCTTTTTGGAATTCT 59.935 33.333 5.23 0.00 0.00 2.40
4963 5728 8.257306 ACAAGCTGTTTTCTTTTTGGAATTCTA 58.743 29.630 5.23 0.00 0.00 2.10
4964 5729 8.758715 CAAGCTGTTTTCTTTTTGGAATTCTAG 58.241 33.333 5.23 0.00 0.00 2.43
4966 5731 8.864087 AGCTGTTTTCTTTTTGGAATTCTAGAT 58.136 29.630 5.23 0.00 0.00 1.98
5228 6449 3.507411 TGCCTTCTACCACTAGACAAGT 58.493 45.455 0.00 0.00 39.81 3.16
5301 6522 0.178970 TAGGAGTCGGGATAGGGTGC 60.179 60.000 0.00 0.00 0.00 5.01
5303 6524 1.826921 GAGTCGGGATAGGGTGCGA 60.827 63.158 0.00 0.00 0.00 5.10
5304 6525 1.380785 AGTCGGGATAGGGTGCGAA 60.381 57.895 0.00 0.00 0.00 4.70
5305 6526 1.227176 GTCGGGATAGGGTGCGAAC 60.227 63.158 0.00 0.00 0.00 3.95
5307 6528 1.067582 CGGGATAGGGTGCGAACTC 59.932 63.158 0.00 0.00 0.00 3.01
5308 6529 1.672854 CGGGATAGGGTGCGAACTCA 61.673 60.000 0.00 0.00 0.00 3.41
5674 7476 0.743345 GGCCGATTGTCCACCACTAC 60.743 60.000 0.00 0.00 0.00 2.73
5736 7538 1.648116 AGCAATTGCAAATGGGGTCT 58.352 45.000 30.89 4.40 45.16 3.85
5763 7565 0.258774 AGTTATCGGGGCCAATTGCT 59.741 50.000 4.39 0.00 40.92 3.91
5862 7664 1.185618 CGGGAGTGGAGTTGTCAGGA 61.186 60.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.858135 CCTTGGAGCCTAGTAATAGGGA 58.142 50.000 17.58 0.00 37.69 4.20
238 240 1.804151 CGGACAATGTTGATCGTTGGT 59.196 47.619 0.00 0.00 44.64 3.67
287 290 1.537348 CCTTGAGTGAAACCACGACGA 60.537 52.381 0.00 0.00 39.45 4.20
320 331 1.327690 GGGTCACTCGGCATCCAGTA 61.328 60.000 0.00 0.00 0.00 2.74
393 406 1.001974 CATCATTAGCCCCCGAATCGA 59.998 52.381 3.36 0.00 0.00 3.59
466 481 3.527253 ACCTATCAATGATGGTGTGGGAA 59.473 43.478 13.79 0.00 0.00 3.97
579 595 2.355412 CCTTGTCTGAGTGATGATGGCA 60.355 50.000 0.00 0.00 0.00 4.92
706 724 3.128349 ACTACGGCAGTTACAAGTGTTG 58.872 45.455 0.00 0.00 31.59 3.33
732 750 3.822167 CGTTACAAGGGTGGTTTAATGGT 59.178 43.478 0.00 0.00 0.00 3.55
738 760 1.585297 CGACGTTACAAGGGTGGTTT 58.415 50.000 0.00 0.00 0.00 3.27
756 779 2.582498 CGCGGCCTCTTTACTCCG 60.582 66.667 0.00 0.00 44.29 4.63
843 872 3.541632 TCGTTCTCAGAGGCTTGTTTTT 58.458 40.909 0.00 0.00 0.00 1.94
856 885 3.597255 ACATCTCTACGTCTCGTTCTCA 58.403 45.455 0.00 0.00 41.54 3.27
858 887 4.332268 GGTAACATCTCTACGTCTCGTTCT 59.668 45.833 0.00 0.00 41.54 3.01
874 903 5.659079 CAGTCCCTCTCTTAGAAGGTAACAT 59.341 44.000 8.75 0.00 41.41 2.71
883 912 4.931027 AGTGTACAGTCCCTCTCTTAGA 57.069 45.455 0.00 0.00 0.00 2.10
884 913 7.648039 AATAAGTGTACAGTCCCTCTCTTAG 57.352 40.000 3.07 0.00 0.00 2.18
885 914 9.710818 AATAATAAGTGTACAGTCCCTCTCTTA 57.289 33.333 3.07 2.46 0.00 2.10
886 915 8.611051 AATAATAAGTGTACAGTCCCTCTCTT 57.389 34.615 3.07 0.12 0.00 2.85
887 916 8.478877 CAAATAATAAGTGTACAGTCCCTCTCT 58.521 37.037 3.07 0.00 0.00 3.10
888 917 8.258708 ACAAATAATAAGTGTACAGTCCCTCTC 58.741 37.037 3.07 0.00 0.00 3.20
889 918 8.147244 ACAAATAATAAGTGTACAGTCCCTCT 57.853 34.615 3.07 0.00 0.00 3.69
890 919 8.665685 CAACAAATAATAAGTGTACAGTCCCTC 58.334 37.037 3.07 0.00 0.00 4.30
891 920 8.161425 ACAACAAATAATAAGTGTACAGTCCCT 58.839 33.333 3.07 0.00 0.00 4.20
892 921 8.331730 ACAACAAATAATAAGTGTACAGTCCC 57.668 34.615 3.07 0.00 0.00 4.46
893 922 9.607285 CAACAACAAATAATAAGTGTACAGTCC 57.393 33.333 3.07 0.00 0.00 3.85
906 935 6.173427 AGGGCAACTTCAACAACAAATAAT 57.827 33.333 0.00 0.00 0.00 1.28
920 949 1.077005 TGAGGGCATTTAGGGCAACTT 59.923 47.619 0.00 0.00 34.52 2.66
1662 1694 3.393970 CCCAGCAAGGCGAGGAGA 61.394 66.667 4.65 0.00 35.39 3.71
1746 1778 0.539986 GGGGACATCTCGGTTAAGCA 59.460 55.000 5.38 0.00 0.00 3.91
2247 2293 5.036737 GCAATACCACTGATATTGTGCAAC 58.963 41.667 5.23 0.00 40.62 4.17
2263 2309 2.230992 TCAAACATGTGCAGGCAATACC 59.769 45.455 0.00 0.00 39.61 2.73
2369 2416 3.437049 GCACTCAGCCAAAGTTACTAAGG 59.563 47.826 0.00 0.00 37.23 2.69
2383 2433 4.748892 TGAAGACAGTAATAGCACTCAGC 58.251 43.478 0.00 0.00 46.19 4.26
2692 2744 0.669619 TCGTAGGTGCGAGTTTGTCA 59.330 50.000 0.00 0.00 35.83 3.58
2772 2824 2.238942 TGTCAATGACACGCTTGAGT 57.761 45.000 12.63 0.00 37.67 3.41
2817 2869 6.062749 TCGAGATATTAGAAGCAGTACCTGT 58.937 40.000 0.00 0.00 33.43 4.00
2898 2950 8.517056 TCTTCGCATGATGAATTATGCATTTAT 58.483 29.630 17.15 0.00 46.46 1.40
2905 2957 8.624701 AAACTTTCTTCGCATGATGAATTATG 57.375 30.769 0.00 0.00 37.88 1.90
3111 3163 7.841729 AGGATGGATTCTCTGAAAGTAGAACTA 59.158 37.037 0.00 0.00 34.55 2.24
3318 3874 8.514594 CCACTTTCTTCAGCAATTCAAAGTATA 58.485 33.333 0.00 0.00 33.39 1.47
3466 4024 6.264518 AGTTCAATTCCTTGTTTACCGTTGAT 59.735 34.615 0.00 0.00 33.87 2.57
3826 4385 8.727910 CACATCCAATACTCAGGATCAATATTG 58.272 37.037 9.29 9.29 42.61 1.90
3851 4410 4.340246 CTGAGCCCAGCACAGCCA 62.340 66.667 1.14 0.00 39.93 4.75
4015 4593 5.751243 TTCAAACAGCTACTCCTTGAAAC 57.249 39.130 0.00 0.00 34.10 2.78
4084 4662 7.278868 CAGTTTAATCTCTCAACCATCTACCAC 59.721 40.741 0.00 0.00 0.00 4.16
4103 4681 0.693622 TGGTCGGCCATCCAGTTTAA 59.306 50.000 3.51 0.00 40.46 1.52
4328 4906 1.023502 GGAGAGGCTAGGTGACGTAC 58.976 60.000 0.00 0.00 0.00 3.67
4395 4977 5.991328 AAACGTCATGTCATAGCATAAGG 57.009 39.130 0.00 0.00 0.00 2.69
4590 5176 1.338655 GAGGAGTCAGATACTTCCGCC 59.661 57.143 0.00 0.00 39.07 6.13
4807 5393 6.908825 TGGTCTTACAATAATTTGCAGTGTC 58.091 36.000 0.00 0.00 36.22 3.67
4926 5691 2.465860 ACAGCTTGTGCGGTTACATA 57.534 45.000 0.00 0.00 44.77 2.29
4927 5692 3.322514 ACAGCTTGTGCGGTTACAT 57.677 47.368 0.00 0.00 44.77 2.29
4934 5699 3.242059 CCAAAAAGAAAACAGCTTGTGCG 60.242 43.478 0.00 0.00 45.42 5.34
5569 6790 1.825090 TGCATGTCTGATGGTTGACC 58.175 50.000 0.00 0.00 32.67 4.02
5629 7420 1.304547 CTCCCCTCTCGACACCAGT 60.305 63.158 0.00 0.00 0.00 4.00
5630 7421 0.900647 AACTCCCCTCTCGACACCAG 60.901 60.000 0.00 0.00 0.00 4.00
5631 7422 1.155390 AACTCCCCTCTCGACACCA 59.845 57.895 0.00 0.00 0.00 4.17
5632 7423 1.186267 ACAACTCCCCTCTCGACACC 61.186 60.000 0.00 0.00 0.00 4.16
5690 7492 2.571212 CCTTGCAGTCAGGTTACAACA 58.429 47.619 0.00 0.00 0.00 3.33
5691 7493 1.880027 CCCTTGCAGTCAGGTTACAAC 59.120 52.381 2.31 0.00 0.00 3.32
5722 7524 1.631405 CCTTCAGACCCCATTTGCAA 58.369 50.000 0.00 0.00 0.00 4.08
5736 7538 1.342672 GCCCCGATAACTCCCCTTCA 61.343 60.000 0.00 0.00 0.00 3.02
5763 7565 1.073603 TGCATGTCTCATGGTGGACAA 59.926 47.619 16.45 3.50 44.10 3.18
5862 7664 2.446435 GGTGGTGGACATGCAACTAAT 58.554 47.619 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.