Multiple sequence alignment - TraesCS4A01G080800

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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 TraesCS4A01G080800 chr4A 100.000 6654 0 0 1 6654 83404442 83397789 0.000000e+00 12288.0
1 TraesCS4A01G080800 chr4A 93.722 3823 212 14 874 4678 438694287 438690475 0.000000e+00 5705.0
2 TraesCS4A01G080800 chr4A 88.921 3827 379 22 874 4678 668645676 668641873 0.000000e+00 4676.0
3 TraesCS4A01G080800 chr4A 93.415 1306 83 3 4664 5968 438690456 438689153 0.000000e+00 1932.0
4 TraesCS4A01G080800 chr4A 87.234 1316 155 11 4664 5972 668641854 668640545 0.000000e+00 1487.0
5 TraesCS4A01G080800 chr5A 92.779 3836 242 14 875 4678 602236849 602240681 0.000000e+00 5517.0
6 TraesCS4A01G080800 chr5A 92.414 1305 95 3 4664 5968 602240700 602242000 0.000000e+00 1858.0
7 TraesCS4A01G080800 chr1B 88.970 3826 374 26 874 4678 410050701 410046903 0.000000e+00 4684.0
8 TraesCS4A01G080800 chr1B 89.190 2803 277 16 1890 4678 24198719 24201509 0.000000e+00 3474.0
9 TraesCS4A01G080800 chr1B 88.244 1310 142 10 4664 5967 410046884 410045581 0.000000e+00 1555.0
10 TraesCS4A01G080800 chr1B 87.414 1311 152 11 4664 5968 24201528 24202831 0.000000e+00 1495.0
11 TraesCS4A01G080800 chr4D 86.129 3828 489 30 875 4678 82942478 82938669 0.000000e+00 4089.0
12 TraesCS4A01G080800 chr4D 95.297 723 27 4 1 720 380339161 380339879 0.000000e+00 1140.0
13 TraesCS4A01G080800 chr4D 95.640 688 29 1 5968 6654 380344109 380344796 0.000000e+00 1103.0
14 TraesCS4A01G080800 chr4D 97.248 109 3 0 725 833 380341236 380341344 1.140000e-42 185.0
15 TraesCS4A01G080800 chr6A 86.002 3822 500 25 875 4678 503930886 503934690 0.000000e+00 4061.0
16 TraesCS4A01G080800 chr6A 92.706 2591 168 11 1448 4020 133814937 133817524 0.000000e+00 3718.0
17 TraesCS4A01G080800 chr6A 89.414 1313 135 3 4664 5972 133819922 133821234 0.000000e+00 1652.0
18 TraesCS4A01G080800 chr6B 89.728 2979 288 13 1712 4678 59936439 59939411 0.000000e+00 3790.0
19 TraesCS4A01G080800 chr6B 87.691 1308 155 6 4664 5968 59939430 59940734 0.000000e+00 1519.0
20 TraesCS4A01G080800 chr6B 88.956 824 79 4 874 1688 59935623 59936443 0.000000e+00 1007.0
21 TraesCS4A01G080800 chr3D 83.969 3830 575 28 875 4678 136732985 136729169 0.000000e+00 3635.0
22 TraesCS4A01G080800 chr2A 84.119 3671 540 28 1040 4680 591998026 592001683 0.000000e+00 3509.0
23 TraesCS4A01G080800 chr5B 85.848 2996 378 29 874 3852 462212623 462209657 0.000000e+00 3142.0
24 TraesCS4A01G080800 chr5B 86.113 2902 376 18 1794 4678 485735016 485732125 0.000000e+00 3101.0
25 TraesCS4A01G080800 chr5B 87.605 1307 156 6 4664 5967 80273750 80272447 0.000000e+00 1511.0
26 TraesCS4A01G080800 chr5B 86.839 889 101 11 874 1754 485735979 485735099 0.000000e+00 979.0
27 TraesCS4A01G080800 chr5B 90.566 53 4 1 339 390 299680039 299680091 1.200000e-07 69.4
28 TraesCS4A01G080800 chr7A 90.291 1308 122 3 4664 5967 12891686 12892992 0.000000e+00 1707.0
29 TraesCS4A01G080800 chr4B 94.457 884 34 8 1 876 467798417 467799293 0.000000e+00 1347.0
30 TraesCS4A01G080800 chr4B 92.486 692 46 6 5968 6654 467799301 467799991 0.000000e+00 985.0
31 TraesCS4A01G080800 chr5D 87.552 241 23 3 181 417 20094388 20094625 8.500000e-69 272.0
32 TraesCS4A01G080800 chr5D 82.784 273 33 7 452 721 20094620 20094881 1.440000e-56 231.0
33 TraesCS4A01G080800 chr2B 84.559 272 29 6 452 720 291851214 291851475 2.380000e-64 257.0
34 TraesCS4A01G080800 chr2B 83.088 272 32 7 452 720 532869461 532869201 1.120000e-57 235.0
35 TraesCS4A01G080800 chr3B 85.537 242 27 4 180 417 542403938 542403701 5.150000e-61 246.0
36 TraesCS4A01G080800 chr3B 83.150 273 32 8 452 720 542403706 542403444 3.100000e-58 237.0
37 TraesCS4A01G080800 chr3B 90.566 53 4 1 339 390 303333698 303333646 1.200000e-07 69.4
38 TraesCS4A01G080800 chr3B 91.837 49 4 0 339 387 554900672 554900720 1.200000e-07 69.4


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 TraesCS4A01G080800 chr4A 83397789 83404442 6653 True 12288.000000 12288 100.000000 1 6654 1 chr4A.!!$R1 6653
1 TraesCS4A01G080800 chr4A 438689153 438694287 5134 True 3818.500000 5705 93.568500 874 5968 2 chr4A.!!$R2 5094
2 TraesCS4A01G080800 chr4A 668640545 668645676 5131 True 3081.500000 4676 88.077500 874 5972 2 chr4A.!!$R3 5098
3 TraesCS4A01G080800 chr5A 602236849 602242000 5151 False 3687.500000 5517 92.596500 875 5968 2 chr5A.!!$F1 5093
4 TraesCS4A01G080800 chr1B 410045581 410050701 5120 True 3119.500000 4684 88.607000 874 5967 2 chr1B.!!$R1 5093
5 TraesCS4A01G080800 chr1B 24198719 24202831 4112 False 2484.500000 3474 88.302000 1890 5968 2 chr1B.!!$F1 4078
6 TraesCS4A01G080800 chr4D 82938669 82942478 3809 True 4089.000000 4089 86.129000 875 4678 1 chr4D.!!$R1 3803
7 TraesCS4A01G080800 chr4D 380339161 380344796 5635 False 809.333333 1140 96.061667 1 6654 3 chr4D.!!$F1 6653
8 TraesCS4A01G080800 chr6A 503930886 503934690 3804 False 4061.000000 4061 86.002000 875 4678 1 chr6A.!!$F1 3803
9 TraesCS4A01G080800 chr6A 133814937 133821234 6297 False 2685.000000 3718 91.060000 1448 5972 2 chr6A.!!$F2 4524
10 TraesCS4A01G080800 chr6B 59935623 59940734 5111 False 2105.333333 3790 88.791667 874 5968 3 chr6B.!!$F1 5094
11 TraesCS4A01G080800 chr3D 136729169 136732985 3816 True 3635.000000 3635 83.969000 875 4678 1 chr3D.!!$R1 3803
12 TraesCS4A01G080800 chr2A 591998026 592001683 3657 False 3509.000000 3509 84.119000 1040 4680 1 chr2A.!!$F1 3640
13 TraesCS4A01G080800 chr5B 462209657 462212623 2966 True 3142.000000 3142 85.848000 874 3852 1 chr5B.!!$R2 2978
14 TraesCS4A01G080800 chr5B 485732125 485735979 3854 True 2040.000000 3101 86.476000 874 4678 2 chr5B.!!$R3 3804
15 TraesCS4A01G080800 chr5B 80272447 80273750 1303 True 1511.000000 1511 87.605000 4664 5967 1 chr5B.!!$R1 1303
16 TraesCS4A01G080800 chr7A 12891686 12892992 1306 False 1707.000000 1707 90.291000 4664 5967 1 chr7A.!!$F1 1303
17 TraesCS4A01G080800 chr4B 467798417 467799991 1574 False 1166.000000 1347 93.471500 1 6654 2 chr4B.!!$F1 6653

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
708 719 3.242739 CGTTGGTGCTTATATTGTGGAGC 60.243 47.826 0.00 0.0 35.74 4.70 F
1212 5292 0.105760 AAACCATGGTTGTGGAGGCA 60.106 50.000 30.44 0.0 42.02 4.75 F
2002 6140 0.253160 ATACCAGGGCCACCAGAAGA 60.253 55.000 6.18 0.0 40.13 2.87 F
3458 7633 1.759445 TGCTGGGAGATAGTGAAGAGC 59.241 52.381 0.00 0.0 0.00 4.09 F
4859 10794 1.078567 CCCTCTGGCTGAGCAGTTC 60.079 63.158 15.25 0.0 41.35 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 6342 0.033208 TGCCAATTGAGGGGATCCAC 60.033 55.000 15.23 10.87 34.83 4.02 R
3178 7350 1.137086 CCTCAATCACCGTACTCCCAG 59.863 57.143 0.00 0.00 0.00 4.45 R
3551 7727 0.954452 GCTGAATCTTATTGGCCCCG 59.046 55.000 0.00 0.00 0.00 5.73 R
5123 11058 0.620556 GAGGGATTCTGGCACTCCAA 59.379 55.000 7.95 0.00 42.91 3.53 R
5778 11717 0.335019 TCTGCAGCTAGGGACCAGTA 59.665 55.000 9.47 0.00 0.00 2.74 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
40 41 4.572389 GTCTGTGGAATAACACCATGCTAG 59.428 45.833 0.00 0.00 40.62 3.42
170 171 9.587772 GAGATGACAAAATTACTTAGCTACAGA 57.412 33.333 0.00 0.00 0.00 3.41
244 249 4.402155 TGCCTTTTATGCCCTTGATAACAG 59.598 41.667 0.00 0.00 0.00 3.16
318 324 6.590357 CGACATTCCGAATAAATGGATGTAC 58.410 40.000 0.00 0.00 38.23 2.90
347 353 4.190001 CAAAGGAGATGTCTGATGGTCTG 58.810 47.826 0.00 0.00 0.00 3.51
656 667 4.072131 ACATAGCGTGTTCTTTCCAATGT 58.928 39.130 0.00 0.00 38.01 2.71
657 668 5.121611 CACATAGCGTGTTCTTTCCAATGTA 59.878 40.000 0.00 0.00 39.62 2.29
658 669 5.121768 ACATAGCGTGTTCTTTCCAATGTAC 59.878 40.000 0.00 0.00 38.01 2.90
702 713 3.486841 GCATTGCGTTGGTGCTTATATTG 59.513 43.478 0.00 0.00 36.02 1.90
708 719 3.242739 CGTTGGTGCTTATATTGTGGAGC 60.243 47.826 0.00 0.00 35.74 4.70
1162 5242 5.965033 AGAAGGAGAAAGCATGGAATCTA 57.035 39.130 0.00 0.00 0.00 1.98
1212 5292 0.105760 AAACCATGGTTGTGGAGGCA 60.106 50.000 30.44 0.00 42.02 4.75
1277 5357 4.766373 TGTTGATGACACCAAGCATAATGT 59.234 37.500 0.00 0.00 32.00 2.71
1460 5544 1.203440 AGTTTCCTGCCTCCCCTTCTA 60.203 52.381 0.00 0.00 0.00 2.10
1594 5678 6.829849 TGCCATTTCCAAGAAGAGAAATTTT 58.170 32.000 0.00 0.00 39.97 1.82
1914 6050 2.747989 GCCCTAAAGTGAAAGTGGCTAC 59.252 50.000 0.00 0.00 34.61 3.58
2002 6140 0.253160 ATACCAGGGCCACCAGAAGA 60.253 55.000 6.18 0.00 40.13 2.87
2008 6146 3.706373 GCCACCAGAAGAGGGCGA 61.706 66.667 0.00 0.00 36.58 5.54
2108 6249 6.332635 TGTCCCATATGATTAAGGACCATTCT 59.667 38.462 19.41 0.00 45.26 2.40
2200 6342 3.278574 TCACAACTTGTTTGAGTGGGAG 58.721 45.455 0.00 0.00 38.73 4.30
2401 6545 6.272822 AGTGATTTTCTTAGTGAATTGGCC 57.727 37.500 0.00 0.00 34.24 5.36
2409 6553 5.984725 TCTTAGTGAATTGGCCGATTTCTA 58.015 37.500 19.61 19.37 0.00 2.10
2473 6617 7.069344 TCAATATCCTCAGACATAGTGGAGAA 58.931 38.462 0.00 0.00 32.74 2.87
3013 7167 5.308825 AGACCATGAACTGTTTTGTAGGAG 58.691 41.667 0.00 0.00 0.00 3.69
3019 7173 3.771577 ACTGTTTTGTAGGAGGACTGG 57.228 47.619 0.00 0.00 0.00 4.00
3178 7350 7.816945 AAAACACTATACATTTGCTTCATGC 57.183 32.000 0.00 0.00 43.25 4.06
3284 7457 2.710096 ACATATTCCACCTTGACCCG 57.290 50.000 0.00 0.00 0.00 5.28
3340 7515 6.640518 AGCTGGACAACGAGATTCTTAATAA 58.359 36.000 0.00 0.00 0.00 1.40
3458 7633 1.759445 TGCTGGGAGATAGTGAAGAGC 59.241 52.381 0.00 0.00 0.00 4.09
3575 7751 3.067320 GGGCCAATAAGATTCAGCAGTTC 59.933 47.826 4.39 0.00 0.00 3.01
3605 7781 2.636893 CTGCCTGCTTAGATGTCCCTAT 59.363 50.000 0.00 0.00 0.00 2.57
3612 7788 6.174720 TGCTTAGATGTCCCTATAAGTTGG 57.825 41.667 0.00 0.00 0.00 3.77
3659 7835 2.172717 GACCCCCTTTGCTGATAAGCTA 59.827 50.000 3.06 0.00 35.49 3.32
3664 7840 5.833131 CCCCCTTTGCTGATAAGCTATTTAA 59.167 40.000 3.06 0.00 35.49 1.52
3781 7957 2.094078 TGGGCATTGTCATTAAGCTTGC 60.094 45.455 9.86 0.23 0.00 4.01
3829 8005 6.646653 GTGAATTGGGACTTTCTTTTGGAATC 59.353 38.462 0.00 0.00 33.53 2.52
3921 8097 7.582679 CAGTTAGTGTGAAGTTGAATAACGTTG 59.417 37.037 11.99 0.00 41.71 4.10
3980 8157 1.683441 GGATCCGGTGTCACCCTTT 59.317 57.895 16.60 0.63 33.75 3.11
3989 8166 4.279922 CCGGTGTCACCCTTTCTTTTTAAT 59.720 41.667 16.60 0.00 33.75 1.40
4337 10236 7.229506 CCAGTGACCTTTTCTTCTTTATGAGTT 59.770 37.037 0.00 0.00 0.00 3.01
4435 10334 2.594529 CGTTTAACGCTGCTCAATGT 57.405 45.000 4.11 0.00 33.65 2.71
4439 10338 4.317291 CGTTTAACGCTGCTCAATGTTAAC 59.683 41.667 4.11 0.00 36.74 2.01
4743 10678 1.651240 CTCACCATGCTGGAAAGCGG 61.651 60.000 8.91 0.00 40.96 5.52
4790 10725 2.239907 GGCAGGGAGGAGAGTAATTGTT 59.760 50.000 0.00 0.00 0.00 2.83
4859 10794 1.078567 CCCTCTGGCTGAGCAGTTC 60.079 63.158 15.25 0.00 41.35 3.01
4879 10814 3.882444 TCCCTCGTCTTTTCTCGATCTA 58.118 45.455 0.00 0.00 35.57 1.98
4902 10837 5.804639 ACAATTATCCTGAGTGCACTGTTA 58.195 37.500 27.27 9.50 0.00 2.41
4907 10842 8.668510 ATTATCCTGAGTGCACTGTTAATAAG 57.331 34.615 27.27 9.42 0.00 1.73
4959 10894 7.674348 TCTTTAGAAGGAGACTAAATGGTGAGA 59.326 37.037 0.00 0.00 42.68 3.27
4976 10911 5.185635 TGGTGAGATTTTTGATCAATGGGTC 59.814 40.000 9.40 5.85 0.00 4.46
5123 11058 2.700371 TGGATGCGACTACAGATGGATT 59.300 45.455 0.00 0.00 0.00 3.01
5151 11086 4.221482 GTGCCAGAATCCCTCTCAAAATTT 59.779 41.667 0.00 0.00 29.07 1.82
5279 11214 0.040958 CCGCACAGCACTTGTTCTTC 60.041 55.000 0.00 0.00 38.16 2.87
5414 11351 4.595986 GGGGGAAAAGTTCTATACAGCAA 58.404 43.478 0.00 0.00 0.00 3.91
5416 11353 5.497474 GGGGAAAAGTTCTATACAGCAAGA 58.503 41.667 0.00 0.00 0.00 3.02
5421 11358 7.064728 GGAAAAGTTCTATACAGCAAGAATCGT 59.935 37.037 0.00 0.00 34.43 3.73
5558 11495 3.201487 AGGAATGATGAAGCAGGATGACA 59.799 43.478 0.00 0.00 39.69 3.58
5596 11533 1.361668 GCGCGAAGATGCTGAAGGAA 61.362 55.000 12.10 0.00 0.00 3.36
5690 11627 3.585289 TGTCCCTGTGGTTTAGCTTGATA 59.415 43.478 0.00 0.00 0.00 2.15
5709 11646 1.885049 ATTTGAGCTGCTCTCCCCTA 58.115 50.000 28.04 6.12 41.18 3.53
5710 11647 1.885049 TTTGAGCTGCTCTCCCCTAT 58.115 50.000 28.04 0.00 41.18 2.57
5778 11717 1.413118 CTCTTTTGGGGCTGTTTGGT 58.587 50.000 0.00 0.00 0.00 3.67
5779 11718 2.593026 CTCTTTTGGGGCTGTTTGGTA 58.407 47.619 0.00 0.00 0.00 3.25
5991 11930 9.816354 AAATATTCTTTGCACAAAGTAAACTGT 57.184 25.926 19.61 1.74 45.88 3.55
6174 12114 5.482175 AGATAGATCCAATTTACGAGGGAGG 59.518 44.000 0.00 0.00 31.96 4.30
6176 12116 1.580059 TCCAATTTACGAGGGAGGCT 58.420 50.000 0.00 0.00 0.00 4.58
6230 12170 2.958355 TGAGGAAAACCAGGCTGAAAAG 59.042 45.455 17.94 0.84 0.00 2.27
6231 12171 2.959030 GAGGAAAACCAGGCTGAAAAGT 59.041 45.455 17.94 1.59 0.00 2.66
6233 12173 2.287608 GGAAAACCAGGCTGAAAAGTCG 60.288 50.000 17.94 0.00 0.00 4.18
6401 12344 2.130395 CCGATCATCACCACGAATGAG 58.870 52.381 0.00 0.00 0.00 2.90
6423 12366 1.758280 TGCACCGACGAAGGGTATTAT 59.242 47.619 0.00 0.00 35.58 1.28
6465 12408 0.615544 CCAGAACACCCGGGTAGGTA 60.616 60.000 29.72 0.00 38.39 3.08
6612 12556 0.694771 AATGGAAGCTCTGCCACAGA 59.305 50.000 0.00 0.00 38.25 3.41
6620 12564 2.526958 TCTGCCACAGAGACAACCA 58.473 52.632 0.00 0.00 35.39 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.874215 GTACCACTCTGAAGTTGTTAAATAAAC 57.126 33.333 0.00 0.00 33.67 2.01
170 171 6.383726 ACAATATGAAAAACACTATGGGCCAT 59.616 34.615 24.69 24.69 0.00 4.40
244 249 9.939802 ATAAGAAACGGGTATATTCAATACTCC 57.060 33.333 0.00 0.00 0.00 3.85
418 426 1.480954 TCAGATTCCTCACCTTACCGC 59.519 52.381 0.00 0.00 0.00 5.68
516 526 9.367160 CCATACATATTTACCAAAAAGGGAGAT 57.633 33.333 0.00 0.00 43.89 2.75
656 667 8.214364 TGCAGAGTCATCTTCTATCTTCTAGTA 58.786 37.037 0.00 0.00 31.64 1.82
657 668 7.059788 TGCAGAGTCATCTTCTATCTTCTAGT 58.940 38.462 0.00 0.00 31.64 2.57
658 669 7.509141 TGCAGAGTCATCTTCTATCTTCTAG 57.491 40.000 0.00 0.00 31.64 2.43
669 680 2.105006 ACGCAATGCAGAGTCATCTT 57.895 45.000 5.91 0.00 31.64 2.40
672 683 0.806868 CCAACGCAATGCAGAGTCAT 59.193 50.000 5.91 0.00 0.00 3.06
702 713 2.291741 GCATATAACTTGGCTGCTCCAC 59.708 50.000 0.00 0.00 46.55 4.02
708 719 4.581824 AGATTGTGGCATATAACTTGGCTG 59.418 41.667 0.00 0.00 40.12 4.85
1162 5242 6.773638 ACAGTGTGTTATCTTCTGATTCCTT 58.226 36.000 0.00 0.00 34.32 3.36
1212 5292 5.102313 GCCTGCGCTTTTTCTTTGTTATAT 58.898 37.500 9.73 0.00 0.00 0.86
1441 5525 1.286248 TAGAAGGGGAGGCAGGAAAC 58.714 55.000 0.00 0.00 0.00 2.78
1460 5544 2.277008 ATCACCTCTCCCACATCCTT 57.723 50.000 0.00 0.00 0.00 3.36
1594 5678 7.630082 AGTTATGGTTAGCTGAATTACCTTCA 58.370 34.615 0.00 0.00 41.61 3.02
1914 6050 3.456277 ACTTCTAGTAATGGGCCTGGAAG 59.544 47.826 4.53 9.60 46.07 3.46
2002 6140 0.704664 ATCTTTTCCCCTTTCGCCCT 59.295 50.000 0.00 0.00 0.00 5.19
2008 6146 8.122481 ACCTATCATTTGTATCTTTTCCCCTTT 58.878 33.333 0.00 0.00 0.00 3.11
2108 6249 6.266168 TCTTGCAAACAAAGAAAGTCAAGA 57.734 33.333 0.00 0.00 37.09 3.02
2200 6342 0.033208 TGCCAATTGAGGGGATCCAC 60.033 55.000 15.23 10.87 34.83 4.02
2401 6545 7.805071 GGAGTTTGAATATGGCAATAGAAATCG 59.195 37.037 0.00 0.00 0.00 3.34
2409 6553 8.980596 TCAATAAAGGAGTTTGAATATGGCAAT 58.019 29.630 0.00 0.00 0.00 3.56
2473 6617 5.180492 TGTTCGACGCCATCTTTTATTCTTT 59.820 36.000 0.00 0.00 0.00 2.52
3013 7167 2.759985 TCCACAAGGAGACCAGTCC 58.240 57.895 0.00 0.00 39.61 3.85
3109 7279 5.517322 TTTTTGGTAATAAGCGGTGTTGT 57.483 34.783 0.00 0.00 0.00 3.32
3178 7350 1.137086 CCTCAATCACCGTACTCCCAG 59.863 57.143 0.00 0.00 0.00 4.45
3340 7515 4.164221 TCACTTCTTCCTCTGTGAAAGGTT 59.836 41.667 0.00 0.00 36.64 3.50
3458 7633 6.765036 AGGCAGTAAACAGTCTCATGATATTG 59.235 38.462 0.00 0.00 0.00 1.90
3551 7727 0.954452 GCTGAATCTTATTGGCCCCG 59.046 55.000 0.00 0.00 0.00 5.73
3605 7781 4.594062 TCCAGCACCTTAGTTACCAACTTA 59.406 41.667 0.00 0.00 42.81 2.24
3612 7788 5.116882 CCTGTTATCCAGCACCTTAGTTAC 58.883 45.833 0.00 0.00 40.06 2.50
3639 7815 3.596362 GCTTATCAGCAAAGGGGGT 57.404 52.632 0.00 0.00 46.49 4.95
3659 7835 8.752187 ACAAATGCATTCTGGTGTCTATTAAAT 58.248 29.630 13.38 0.00 0.00 1.40
3664 7840 5.255687 TGACAAATGCATTCTGGTGTCTAT 58.744 37.500 28.84 5.56 37.02 1.98
3684 7860 7.609146 TCCATCCATGATATTTCTATGCTTGAC 59.391 37.037 0.00 0.00 0.00 3.18
3914 8090 2.810870 AATATGGCCCCACAACGTTA 57.189 45.000 0.00 0.00 0.00 3.18
3921 8097 1.683385 GCTCTTGAAATATGGCCCCAC 59.317 52.381 0.00 0.00 0.00 4.61
3980 8157 5.676079 GCACTCGGCAGCAATATTAAAAAGA 60.676 40.000 0.00 0.00 43.97 2.52
4106 10004 1.805943 TGATCAATGCACAAGACCGTG 59.194 47.619 0.00 0.00 40.00 4.94
4337 10236 3.391296 ACTCTAAAAAGTCCCAGTCAGCA 59.609 43.478 0.00 0.00 0.00 4.41
4481 10380 6.824958 ATCCTGGCCAGTATAGTTTTAGAA 57.175 37.500 30.63 0.00 0.00 2.10
4790 10725 3.278574 CCTAGCAATGTTTCCCGATTGA 58.721 45.455 0.00 0.00 32.24 2.57
4859 10794 3.377485 TGTAGATCGAGAAAAGACGAGGG 59.623 47.826 0.00 0.00 41.63 4.30
4879 10814 4.292186 ACAGTGCACTCAGGATAATTGT 57.708 40.909 18.64 5.76 0.00 2.71
4902 10837 7.449704 GGAGGGATCATCATTTAAGCACTTATT 59.550 37.037 0.00 0.00 0.00 1.40
4907 10842 4.723309 AGGAGGGATCATCATTTAAGCAC 58.277 43.478 0.00 0.00 0.00 4.40
4918 10853 6.044171 CCTTCTAAAGAATGAGGAGGGATCAT 59.956 42.308 0.00 0.00 39.06 2.45
4946 10881 9.865321 CATTGATCAAAAATCTCACCATTTAGT 57.135 29.630 13.09 0.00 0.00 2.24
4949 10884 7.107542 CCCATTGATCAAAAATCTCACCATTT 58.892 34.615 13.09 0.00 0.00 2.32
4959 10894 3.831911 ACCACGACCCATTGATCAAAAAT 59.168 39.130 13.09 0.00 0.00 1.82
4976 10911 1.946768 CTGGCCATATTACCAACCACG 59.053 52.381 5.51 0.00 34.96 4.94
5022 10957 2.502538 CCAAGCCCCATTTGATCACATT 59.497 45.455 0.00 0.00 0.00 2.71
5123 11058 0.620556 GAGGGATTCTGGCACTCCAA 59.379 55.000 7.95 0.00 42.91 3.53
5310 11245 1.736696 GCCAAACATACATGCCACTGC 60.737 52.381 0.00 0.00 38.26 4.40
5558 11495 2.982130 GTCCCTCATGGCAGTCGT 59.018 61.111 0.00 0.00 0.00 4.34
5596 11533 2.804527 CCTCATCATCATCGACGCATTT 59.195 45.455 0.00 0.00 0.00 2.32
5690 11627 1.885049 TAGGGGAGAGCAGCTCAAAT 58.115 50.000 24.64 3.49 45.81 2.32
5709 11646 4.018960 AGCAGAATAAGTTCAGTCCCACAT 60.019 41.667 0.00 0.00 36.79 3.21
5710 11647 3.327757 AGCAGAATAAGTTCAGTCCCACA 59.672 43.478 0.00 0.00 36.79 4.17
5778 11717 0.335019 TCTGCAGCTAGGGACCAGTA 59.665 55.000 9.47 0.00 0.00 2.74
5779 11718 0.975040 CTCTGCAGCTAGGGACCAGT 60.975 60.000 9.47 0.00 0.00 4.00
5991 11930 3.248024 AGGACAAACCAGATGTACCAGA 58.752 45.455 0.00 0.00 42.04 3.86
6174 12114 6.052360 CCCTCTCTTAGGTTTTCAATCTAGC 58.948 44.000 0.00 0.00 44.90 3.42
6176 12116 6.156429 GGTCCCTCTCTTAGGTTTTCAATCTA 59.844 42.308 0.00 0.00 44.90 1.98
6231 12171 2.631428 GCTTCGTTGCTTGTGCGA 59.369 55.556 0.00 0.00 43.34 5.10
6233 12173 2.050077 GGGCTTCGTTGCTTGTGC 60.050 61.111 2.92 0.00 40.20 4.57
6401 12344 2.234913 ATACCCTTCGTCGGTGCACC 62.235 60.000 26.78 26.78 34.66 5.01
6423 12366 8.713708 TGGAAATTTGGAAGTTCTTGGTATTA 57.286 30.769 2.25 0.00 35.90 0.98
6434 12377 3.641436 GGGTGTTCTGGAAATTTGGAAGT 59.359 43.478 0.00 0.00 0.00 3.01
6438 12381 1.272212 CCGGGTGTTCTGGAAATTTGG 59.728 52.381 0.00 0.00 44.90 3.28
6546 12490 3.434641 CCATGACTTGCACTACTCTTGTG 59.565 47.826 0.00 0.00 38.36 3.33
6584 12528 3.415212 CAGAGCTTCCATTCAAGGTTCA 58.585 45.455 0.00 0.00 34.21 3.18
6612 12556 3.902881 TGCCAAATGTTTTGGTTGTCT 57.097 38.095 17.72 0.00 41.53 3.41
6620 12564 1.142667 CCCCACCTTGCCAAATGTTTT 59.857 47.619 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.