Multiple sequence alignment - TraesCS2B01G302800

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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 TraesCS2B01G302800 chr2B 100.000 6396 0 0 1 6396 427947498 427953893 0.000000e+00 11812
1 TraesCS2B01G302800 chr2B 98.462 65 1 0 5762 5826 427953225 427953289 1.460000e-21 115
2 TraesCS2B01G302800 chr2B 98.462 65 1 0 5728 5792 427953259 427953323 1.460000e-21 115
3 TraesCS2B01G302800 chr2D 96.771 5792 137 24 1 5761 358461589 358455817 0.000000e+00 9614
4 TraesCS2B01G302800 chr2D 89.362 517 16 6 5919 6396 358455114 358454598 1.180000e-171 614
5 TraesCS2B01G302800 chr2D 82.699 289 41 8 6108 6391 306293801 306294085 1.380000e-61 248
6 TraesCS2B01G302800 chr2A 96.765 5070 104 23 724 5758 485043090 485048134 0.000000e+00 8399
7 TraesCS2B01G302800 chr2A 92.059 743 47 5 1 732 485040409 485041150 0.000000e+00 1035
8 TraesCS2B01G302800 chr2A 89.103 312 7 5 5984 6268 485048243 485048554 4.710000e-96 363
9 TraesCS2B01G302800 chr2A 93.846 130 8 0 6267 6396 485049083 485049212 5.060000e-46 196
10 TraesCS2B01G302800 chr2A 88.991 109 10 2 5796 5904 485048105 485048211 4.020000e-27 134
11 TraesCS2B01G302800 chr7D 87.066 518 22 13 5919 6396 572661635 572662147 1.570000e-150 544
12 TraesCS2B01G302800 chr7A 82.828 495 28 15 5919 6396 661830425 661830879 2.160000e-104 390
13 TraesCS2B01G302800 chr6D 80.464 517 55 29 5919 6394 452545851 452545340 2.840000e-93 353
14 TraesCS2B01G302800 chr7B 88.660 291 17 2 6116 6394 629403228 629402942 2.210000e-89 340
15 TraesCS2B01G302800 chr7B 86.942 291 23 4 6116 6394 629974534 629974821 4.810000e-81 313
16 TraesCS2B01G302800 chr7B 89.928 139 11 3 5919 6056 629409731 629409595 6.590000e-40 176
17 TraesCS2B01G302800 chr1D 77.451 510 60 29 5919 6391 121526678 121526187 2.960000e-63 254
18 TraesCS2B01G302800 chr1D 82.807 285 42 6 6110 6391 448740083 448740363 1.380000e-61 248
19 TraesCS2B01G302800 chr1D 82.979 282 41 6 6113 6391 449011471 449011194 1.380000e-61 248


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 TraesCS2B01G302800 chr2B 427947498 427953893 6395 False 4014.0 11812 98.974667 1 6396 3 chr2B.!!$F1 6395
1 TraesCS2B01G302800 chr2D 358454598 358461589 6991 True 5114.0 9614 93.066500 1 6396 2 chr2D.!!$R1 6395
2 TraesCS2B01G302800 chr2A 485040409 485049212 8803 False 2025.4 8399 92.152800 1 6396 5 chr2A.!!$F1 6395
3 TraesCS2B01G302800 chr7D 572661635 572662147 512 False 544.0 544 87.066000 5919 6396 1 chr7D.!!$F1 477
4 TraesCS2B01G302800 chr6D 452545340 452545851 511 True 353.0 353 80.464000 5919 6394 1 chr6D.!!$R1 475

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
848 2810 0.688487 TTCTTACCAACCCCAGTCCG 59.312 55.0 0.00 0.0 0.00 4.79 F
1747 3722 1.192428 CCTACTAGGCTGGTTTCCGT 58.808 55.0 9.37 0.0 0.00 4.69 F
2792 4768 0.835941 CTGCTATTCTGTCTGCCCCT 59.164 55.0 0.00 0.0 0.00 4.79 F
3214 5199 1.332144 TACGGTCATACCCCCTGTGC 61.332 60.0 0.00 0.0 33.75 4.57 F
5140 7130 0.901580 CCAATGCACAGGGAAGCCTT 60.902 55.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 3814 1.265095 CCCTGCACATATTCACATCGC 59.735 52.381 0.00 0.0 0.0 4.58 R
3115 5100 3.620374 GCACTCACCACAGATCACTAATG 59.380 47.826 0.00 0.0 0.0 1.90 R
4583 6573 1.956477 CTACTTGCAAACTGTGGCCTT 59.044 47.619 3.32 0.0 0.0 4.35 R
5182 7172 1.532868 CAGAGAGAAAACACAAGGCCG 59.467 52.381 0.00 0.0 0.0 6.13 R
6114 8759 3.543680 ACTAGCTGTGTGAGTTGTGTT 57.456 42.857 0.00 0.0 0.0 3.32 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
51 53 3.897141 TCCAGTGTAATGGTTATCGCA 57.103 42.857 0.00 0.00 41.43 5.10
166 168 5.114764 TGGAAAATGCTATCATGTCTCCA 57.885 39.130 0.00 2.11 35.17 3.86
187 189 4.260743 CCAACAATGCACACCGTATGATAG 60.261 45.833 0.00 0.00 0.00 2.08
201 203 6.588756 ACCGTATGATAGTTTAATGCATACCG 59.411 38.462 0.00 0.00 38.54 4.02
269 271 9.295825 TGCTTCCTAGAAAAATAGAAAATGACA 57.704 29.630 0.00 0.00 0.00 3.58
278 280 7.692908 AAAATAGAAAATGACACAACCGTTG 57.307 32.000 9.80 9.80 0.00 4.10
334 336 5.163713 GCAGTTATCTTCACACCATCTTTCC 60.164 44.000 0.00 0.00 0.00 3.13
348 350 8.566109 ACACCATCTTTCCCTACCTTTTATATT 58.434 33.333 0.00 0.00 0.00 1.28
404 406 4.041723 CGAGAACAAAATCCAACAACCAC 58.958 43.478 0.00 0.00 0.00 4.16
406 408 3.445805 AGAACAAAATCCAACAACCACGT 59.554 39.130 0.00 0.00 0.00 4.49
437 439 6.695278 TCACGTGGAAAAGTGAATTTGAATTC 59.305 34.615 17.00 9.05 43.47 2.17
614 626 3.880490 TCAAACCTTTCAGTTGTATGCGT 59.120 39.130 0.00 0.00 0.00 5.24
630 642 6.985013 TGTATGCGTATTCTGAAAGTAAACG 58.015 36.000 0.00 1.80 33.76 3.60
699 711 8.200792 CACTATAGAGCCACTCAAATAAAGACT 58.799 37.037 6.78 0.00 32.06 3.24
805 2767 5.071788 TGAAAATGACAGTGAGGTCCTAACT 59.928 40.000 2.53 2.53 36.97 2.24
848 2810 0.688487 TTCTTACCAACCCCAGTCCG 59.312 55.000 0.00 0.00 0.00 4.79
1070 3036 2.513897 GGGAATGCGGGGAGTTCG 60.514 66.667 0.00 0.00 0.00 3.95
1584 3559 1.200948 GGTTTGATGCTCTCTGTTGGC 59.799 52.381 0.00 0.00 0.00 4.52
1675 3650 4.216411 TGAGGGAAAAGACGGGAATAAG 57.784 45.455 0.00 0.00 0.00 1.73
1747 3722 1.192428 CCTACTAGGCTGGTTTCCGT 58.808 55.000 9.37 0.00 0.00 4.69
1839 3814 5.333875 CGTGATTGTATCTTCATCTGCATGG 60.334 44.000 0.00 0.00 0.00 3.66
2353 4329 6.092944 ACATGAAACAATTAATGCTTGCCATG 59.907 34.615 0.00 0.00 31.35 3.66
2482 4458 3.006859 GGGATGGAAACCAAGGAAACAAG 59.993 47.826 0.00 0.00 36.95 3.16
2792 4768 0.835941 CTGCTATTCTGTCTGCCCCT 59.164 55.000 0.00 0.00 0.00 4.79
2973 4954 9.985730 TTATACCTAATTATAGTTGGGTGAACG 57.014 33.333 21.58 0.00 42.17 3.95
3137 5122 3.319137 TTAGTGATCTGTGGTGAGTGC 57.681 47.619 0.00 0.00 0.00 4.40
3185 5170 8.773645 CATGTGTATGTGGTTTAATATCGATGT 58.226 33.333 8.54 0.00 0.00 3.06
3186 5171 8.137210 TGTGTATGTGGTTTAATATCGATGTG 57.863 34.615 8.54 0.00 0.00 3.21
3187 5172 7.766738 TGTGTATGTGGTTTAATATCGATGTGT 59.233 33.333 8.54 0.00 0.00 3.72
3188 5173 9.251792 GTGTATGTGGTTTAATATCGATGTGTA 57.748 33.333 8.54 0.00 0.00 2.90
3189 5174 9.990360 TGTATGTGGTTTAATATCGATGTGTAT 57.010 29.630 8.54 0.00 0.00 2.29
3214 5199 1.332144 TACGGTCATACCCCCTGTGC 61.332 60.000 0.00 0.00 33.75 4.57
3356 5341 4.933330 TGTGACGGTAGAATTGCTAGATC 58.067 43.478 0.00 0.00 0.00 2.75
3499 5484 6.548622 ACCTAGCATGAAAACATATTGCTGAT 59.451 34.615 0.00 0.00 43.12 2.90
4017 6003 8.314751 GCACAACCACCAGTTATATATAGAGAT 58.685 37.037 0.00 0.00 36.18 2.75
4583 6573 7.453752 ACAAGTAGTAGAAAGTATGTTGGGAGA 59.546 37.037 0.00 0.00 0.00 3.71
4760 6750 2.614969 ATCCAGGGCTGCAGGGAA 60.615 61.111 17.12 0.00 32.25 3.97
5134 7124 2.677524 GCTGCCAATGCACAGGGA 60.678 61.111 8.23 4.49 44.23 4.20
5140 7130 0.901580 CCAATGCACAGGGAAGCCTT 60.902 55.000 0.00 0.00 0.00 4.35
5173 7163 1.614241 AAACCGGATAGCGGCAGTCT 61.614 55.000 9.46 0.00 0.00 3.24
5182 7172 2.970974 GCGGCAGTCTTCAACCTGC 61.971 63.158 3.12 3.12 41.60 4.85
5266 7256 1.154197 GCTTTCCGGTGGTGTTAGAC 58.846 55.000 0.00 0.00 0.00 2.59
5412 7407 1.843851 TGTCTGTTGTCCCTGTTCCTT 59.156 47.619 0.00 0.00 0.00 3.36
5532 7530 1.700955 GCTGGATTGGATGGCTCAAT 58.299 50.000 0.00 0.00 37.52 2.57
5568 7569 2.065899 TTTGTGCTTGCTAGGTGGTT 57.934 45.000 0.00 0.00 0.00 3.67
5581 7582 0.034337 GGTGGTTAGTGCTCGGTTCA 59.966 55.000 0.00 0.00 0.00 3.18
5605 7606 1.497161 TAGCTAAAGTGGAGGCCCTC 58.503 55.000 0.73 0.73 0.00 4.30
5649 7650 4.614993 CGGCTGGTGTTTATTTGATCGTTT 60.615 41.667 0.00 0.00 0.00 3.60
5650 7651 4.621034 GGCTGGTGTTTATTTGATCGTTTG 59.379 41.667 0.00 0.00 0.00 2.93
5651 7652 5.219633 GCTGGTGTTTATTTGATCGTTTGT 58.780 37.500 0.00 0.00 0.00 2.83
5672 7673 2.742116 TTGATGCGAGGGGCCCTAC 61.742 63.158 28.92 21.66 42.61 3.18
5727 7729 3.802948 ACTTGACTAGTAAGATGCCCG 57.197 47.619 14.93 0.00 34.56 6.13
5728 7730 3.097614 ACTTGACTAGTAAGATGCCCGT 58.902 45.455 14.93 0.00 34.56 5.28
5729 7731 3.119101 ACTTGACTAGTAAGATGCCCGTG 60.119 47.826 14.93 0.00 34.56 4.94
5730 7732 1.136305 TGACTAGTAAGATGCCCGTGC 59.864 52.381 0.00 0.00 38.26 5.34
5731 7733 1.409427 GACTAGTAAGATGCCCGTGCT 59.591 52.381 0.00 0.00 38.71 4.40
5732 7734 2.621998 GACTAGTAAGATGCCCGTGCTA 59.378 50.000 0.00 0.00 38.71 3.49
5733 7735 3.231818 ACTAGTAAGATGCCCGTGCTAT 58.768 45.455 0.00 0.00 38.71 2.97
5734 7736 2.533266 AGTAAGATGCCCGTGCTATG 57.467 50.000 0.00 0.00 38.71 2.23
5735 7737 1.762957 AGTAAGATGCCCGTGCTATGT 59.237 47.619 0.00 0.00 38.71 2.29
5736 7738 2.170607 AGTAAGATGCCCGTGCTATGTT 59.829 45.455 0.00 0.00 38.71 2.71
5737 7739 3.386726 AGTAAGATGCCCGTGCTATGTTA 59.613 43.478 0.00 0.00 38.71 2.41
5738 7740 2.240493 AGATGCCCGTGCTATGTTAC 57.760 50.000 0.00 0.00 38.71 2.50
5739 7741 0.859232 GATGCCCGTGCTATGTTACG 59.141 55.000 0.00 0.00 39.83 3.18
5740 7742 0.177141 ATGCCCGTGCTATGTTACGT 59.823 50.000 0.00 0.00 38.56 3.57
5741 7743 0.738063 TGCCCGTGCTATGTTACGTG 60.738 55.000 0.00 0.00 38.56 4.49
5742 7744 0.458889 GCCCGTGCTATGTTACGTGA 60.459 55.000 0.00 0.00 38.56 4.35
5743 7745 1.999048 CCCGTGCTATGTTACGTGAA 58.001 50.000 0.00 0.00 38.56 3.18
5744 7746 1.657094 CCCGTGCTATGTTACGTGAAC 59.343 52.381 0.00 0.00 38.56 3.18
5756 7758 6.519353 TGTTACGTGAACACACAAGATTAG 57.481 37.500 0.00 0.00 43.30 1.73
5757 7759 6.274579 TGTTACGTGAACACACAAGATTAGA 58.725 36.000 0.00 0.00 43.30 2.10
5758 7760 6.199531 TGTTACGTGAACACACAAGATTAGAC 59.800 38.462 0.00 0.00 43.30 2.59
5759 7761 3.734231 ACGTGAACACACAAGATTAGACG 59.266 43.478 5.80 0.00 34.59 4.18
5760 7762 3.121279 CGTGAACACACAAGATTAGACGG 59.879 47.826 5.80 0.00 34.59 4.79
5761 7763 3.432252 GTGAACACACAAGATTAGACGGG 59.568 47.826 0.00 0.00 34.98 5.28
5762 7764 3.070446 TGAACACACAAGATTAGACGGGT 59.930 43.478 0.00 0.00 0.00 5.28
5763 7765 3.040147 ACACACAAGATTAGACGGGTG 57.960 47.619 0.00 0.00 0.00 4.61
5764 7766 1.732259 CACACAAGATTAGACGGGTGC 59.268 52.381 0.00 0.00 0.00 5.01
5765 7767 1.623811 ACACAAGATTAGACGGGTGCT 59.376 47.619 0.00 0.00 0.00 4.40
5766 7768 2.829720 ACACAAGATTAGACGGGTGCTA 59.170 45.455 0.00 0.00 0.00 3.49
5767 7769 3.451178 ACACAAGATTAGACGGGTGCTAT 59.549 43.478 0.00 0.00 0.00 2.97
5768 7770 3.804325 CACAAGATTAGACGGGTGCTATG 59.196 47.826 0.00 0.00 0.00 2.23
5769 7771 3.451178 ACAAGATTAGACGGGTGCTATGT 59.549 43.478 0.00 0.00 0.00 2.29
5770 7772 4.081087 ACAAGATTAGACGGGTGCTATGTT 60.081 41.667 0.00 0.00 0.00 2.71
5771 7773 5.128171 ACAAGATTAGACGGGTGCTATGTTA 59.872 40.000 0.00 0.00 0.00 2.41
5772 7774 5.197682 AGATTAGACGGGTGCTATGTTAC 57.802 43.478 0.00 0.00 0.00 2.50
5773 7775 3.425577 TTAGACGGGTGCTATGTTACG 57.574 47.619 0.00 0.00 0.00 3.18
5774 7776 0.458669 AGACGGGTGCTATGTTACGG 59.541 55.000 0.00 0.00 0.00 4.02
5775 7777 0.529119 GACGGGTGCTATGTTACGGG 60.529 60.000 0.00 0.00 0.00 5.28
5776 7778 0.971959 ACGGGTGCTATGTTACGGGA 60.972 55.000 0.00 0.00 0.00 5.14
5777 7779 0.176219 CGGGTGCTATGTTACGGGAA 59.824 55.000 0.00 0.00 0.00 3.97
5778 7780 1.660167 GGGTGCTATGTTACGGGAAC 58.340 55.000 0.00 0.00 38.65 3.62
5786 7788 2.983907 TGTTACGGGAACACACAAGA 57.016 45.000 0.55 0.00 43.30 3.02
5787 7789 3.478857 TGTTACGGGAACACACAAGAT 57.521 42.857 0.55 0.00 43.30 2.40
5788 7790 3.811083 TGTTACGGGAACACACAAGATT 58.189 40.909 0.55 0.00 43.30 2.40
5789 7791 4.958509 TGTTACGGGAACACACAAGATTA 58.041 39.130 0.55 0.00 43.30 1.75
5790 7792 4.992319 TGTTACGGGAACACACAAGATTAG 59.008 41.667 0.55 0.00 43.30 1.73
5791 7793 5.221481 TGTTACGGGAACACACAAGATTAGA 60.221 40.000 0.55 0.00 43.30 2.10
5792 7794 3.660865 ACGGGAACACACAAGATTAGAC 58.339 45.455 0.00 0.00 0.00 2.59
5793 7795 2.666508 CGGGAACACACAAGATTAGACG 59.333 50.000 0.00 0.00 0.00 4.18
5794 7796 3.000727 GGGAACACACAAGATTAGACGG 58.999 50.000 0.00 0.00 0.00 4.79
5801 7803 3.451178 ACACAAGATTAGACGGGTGCTAT 59.549 43.478 0.00 0.00 0.00 2.97
5811 7813 0.176219 CGGGTGCTATGTTACGGGAA 59.824 55.000 0.00 0.00 0.00 3.97
5812 7814 1.660167 GGGTGCTATGTTACGGGAAC 58.340 55.000 0.00 0.00 38.65 3.62
5833 7835 7.093771 GGGAACACACAAGATTAGATGGATTTT 60.094 37.037 0.00 0.00 0.00 1.82
5853 7855 6.973229 TTTTAAGTTATAGTCAGGAACCGC 57.027 37.500 0.00 0.00 0.00 5.68
5856 7858 4.060038 AGTTATAGTCAGGAACCGCATG 57.940 45.455 0.00 0.00 0.00 4.06
5904 7906 4.092529 CGGAGATATTGATCGAAGCAATGG 59.907 45.833 20.64 5.61 36.68 3.16
5905 7907 4.142730 GGAGATATTGATCGAAGCAATGGC 60.143 45.833 20.64 14.25 36.68 4.40
5908 7910 3.637998 ATTGATCGAAGCAATGGCATC 57.362 42.857 13.93 0.00 44.61 3.91
5909 7911 1.311859 TGATCGAAGCAATGGCATCC 58.688 50.000 0.00 0.00 44.61 3.51
5910 7912 0.236711 GATCGAAGCAATGGCATCCG 59.763 55.000 0.00 0.00 44.61 4.18
5911 7913 0.464373 ATCGAAGCAATGGCATCCGT 60.464 50.000 0.00 0.00 44.61 4.69
5912 7914 0.176910 TCGAAGCAATGGCATCCGTA 59.823 50.000 0.00 0.00 44.61 4.02
5913 7915 0.304705 CGAAGCAATGGCATCCGTAC 59.695 55.000 0.00 0.00 44.61 3.67
5914 7916 1.378531 GAAGCAATGGCATCCGTACA 58.621 50.000 0.00 0.00 44.61 2.90
5915 7917 1.949525 GAAGCAATGGCATCCGTACAT 59.050 47.619 0.00 0.00 44.61 2.29
5916 7918 2.928801 AGCAATGGCATCCGTACATA 57.071 45.000 0.00 0.00 44.61 2.29
5917 7919 2.771089 AGCAATGGCATCCGTACATAG 58.229 47.619 0.00 0.00 44.61 2.23
5952 8568 5.755375 CAGTATATTAGCCACACCAGACTTG 59.245 44.000 0.00 0.00 0.00 3.16
6087 8705 3.449737 ACTGATGCTTTGCCAAATATGCT 59.550 39.130 0.00 0.00 0.00 3.79
6188 8833 1.758280 TCAGGCCATGGAATCATTTGC 59.242 47.619 18.40 0.00 0.00 3.68
6318 9493 9.618890 AATCACTACTGCATACATAATTGTCTT 57.381 29.630 0.00 0.00 37.28 3.01
6355 9531 6.691508 ACAAAGGAAAAAGAATGTGCCTATC 58.308 36.000 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 101 7.284489 GTGAAATGCCATATAGTACCAAGGAAA 59.716 37.037 0.00 0.00 0.00 3.13
166 168 4.513442 ACTATCATACGGTGTGCATTGTT 58.487 39.130 0.00 0.00 0.00 2.83
201 203 5.389935 CCTTTATGAGAAAGAACTGTCGTGC 60.390 44.000 0.38 0.00 0.00 5.34
269 271 0.963355 AACTGTGGTGCAACGGTTGT 60.963 50.000 20.92 0.00 45.70 3.32
278 280 1.128692 GACGCATAGAAACTGTGGTGC 59.871 52.381 0.00 0.00 0.00 5.01
312 314 5.251700 AGGGAAAGATGGTGTGAAGATAACT 59.748 40.000 0.00 0.00 0.00 2.24
334 336 8.463930 TTGCAATCAGGAATATAAAAGGTAGG 57.536 34.615 0.00 0.00 0.00 3.18
348 350 4.022068 GGTTGTCAGATTTTGCAATCAGGA 60.022 41.667 0.00 0.00 41.37 3.86
433 435 5.413309 TTTACAATGGCCCGAAATGAATT 57.587 34.783 0.00 0.00 0.00 2.17
437 439 4.151512 GTGTTTTTACAATGGCCCGAAATG 59.848 41.667 0.00 0.00 0.00 2.32
630 642 8.576442 TGTTGAGGGTGAGAGAATTTAAATTTC 58.424 33.333 14.45 12.86 0.00 2.17
732 744 1.216678 TCTTGGTTGCCTTCTTTCCCA 59.783 47.619 0.00 0.00 0.00 4.37
848 2810 4.851179 CTTAACGGGCGGCCCTCC 62.851 72.222 33.80 10.11 42.67 4.30
917 2880 1.906824 GGTGGTGGACTCCGTGAGA 60.907 63.158 7.76 0.00 33.32 3.27
1070 3036 1.819632 CCCATAGCGGCTCACCAAC 60.820 63.158 5.39 0.00 34.57 3.77
1259 3234 2.761195 CCGATCGGAGAGACGCACA 61.761 63.158 30.62 0.00 43.63 4.57
1584 3559 2.755655 TCTAGAGTCCAGCGAGAAAAGG 59.244 50.000 0.00 0.00 0.00 3.11
1642 3617 1.679981 TTCCCTCAATCCCATCCACA 58.320 50.000 0.00 0.00 0.00 4.17
1646 3621 2.945668 CGTCTTTTCCCTCAATCCCATC 59.054 50.000 0.00 0.00 0.00 3.51
1675 3650 4.718276 TCTTAGGGGATTACTAACCACACC 59.282 45.833 0.00 0.00 31.04 4.16
1713 3688 9.080097 CAGCCTAGTAGGTAAGATATTTGTACT 57.920 37.037 17.69 0.00 37.80 2.73
1839 3814 1.265095 CCCTGCACATATTCACATCGC 59.735 52.381 0.00 0.00 0.00 4.58
1937 3912 1.954146 GGTGAACGTCTGCGCAGAA 60.954 57.895 39.63 22.63 42.83 3.02
2066 4041 3.500343 AGACCTAGCTTTGCCAACAAAT 58.500 40.909 0.00 0.00 44.54 2.32
2353 4329 9.651718 CTTTAGGACATAAAATACTTCATTCGC 57.348 33.333 0.00 0.00 32.98 4.70
2482 4458 1.636003 AGGACCTCCACCAGAAATTCC 59.364 52.381 0.00 0.00 38.89 3.01
3115 5100 3.620374 GCACTCACCACAGATCACTAATG 59.380 47.826 0.00 0.00 0.00 1.90
3185 5170 5.422970 GGGGGTATGACCGTATGAATATACA 59.577 44.000 0.00 0.00 39.83 2.29
3186 5171 5.659971 AGGGGGTATGACCGTATGAATATAC 59.340 44.000 0.00 0.00 39.83 1.47
3187 5172 5.659525 CAGGGGGTATGACCGTATGAATATA 59.340 44.000 0.00 0.00 39.83 0.86
3188 5173 4.469945 CAGGGGGTATGACCGTATGAATAT 59.530 45.833 0.00 0.00 39.83 1.28
3189 5174 3.835978 CAGGGGGTATGACCGTATGAATA 59.164 47.826 0.00 0.00 39.83 1.75
3312 5297 7.175467 TCACAGTGATTGCTTTATTCACTTCAT 59.825 33.333 0.00 0.00 43.76 2.57
3313 5298 6.486320 TCACAGTGATTGCTTTATTCACTTCA 59.514 34.615 0.00 0.00 43.76 3.02
4456 6443 8.927059 ATAGCTTCTAAATATACCCCCACATA 57.073 34.615 0.00 0.00 0.00 2.29
4583 6573 1.956477 CTACTTGCAAACTGTGGCCTT 59.044 47.619 3.32 0.00 0.00 4.35
5134 7124 3.795688 TCAGTTGGAGAATCAAGGCTT 57.204 42.857 0.00 0.00 36.25 4.35
5140 7130 2.370519 TCCGGTTTCAGTTGGAGAATCA 59.629 45.455 0.00 0.00 36.25 2.57
5182 7172 1.532868 CAGAGAGAAAACACAAGGCCG 59.467 52.381 0.00 0.00 0.00 6.13
5266 7256 5.124138 TGTTTTGCCCCTATAAATGTACACG 59.876 40.000 0.00 0.00 0.00 4.49
5568 7569 3.447586 AGCTAAAGATGAACCGAGCACTA 59.552 43.478 0.00 0.00 32.28 2.74
5581 7582 3.117851 GGGCCTCCACTTTAGCTAAAGAT 60.118 47.826 39.86 25.93 44.07 2.40
5631 7632 7.221067 TCAACAACAAACGATCAAATAAACACC 59.779 33.333 0.00 0.00 0.00 4.16
5649 7650 1.971167 GCCCCTCGCATCAACAACA 60.971 57.895 0.00 0.00 37.47 3.33
5650 7651 2.700773 GGCCCCTCGCATCAACAAC 61.701 63.158 0.00 0.00 40.31 3.32
5651 7652 2.361104 GGCCCCTCGCATCAACAA 60.361 61.111 0.00 0.00 40.31 2.83
5672 7673 3.306166 CGTGCTAGAAAGTTACGGATTGG 59.694 47.826 0.00 0.00 34.17 3.16
5733 7735 6.199531 GTCTAATCTTGTGTGTTCACGTAACA 59.800 38.462 6.52 6.52 46.49 2.41
5734 7736 6.578691 GTCTAATCTTGTGTGTTCACGTAAC 58.421 40.000 0.00 0.00 46.49 2.50
5735 7737 5.400188 CGTCTAATCTTGTGTGTTCACGTAA 59.600 40.000 0.00 0.00 46.49 3.18
5736 7738 4.913345 CGTCTAATCTTGTGTGTTCACGTA 59.087 41.667 0.00 0.00 46.49 3.57
5737 7739 3.734231 CGTCTAATCTTGTGTGTTCACGT 59.266 43.478 0.00 0.00 46.49 4.49
5738 7740 3.121279 CCGTCTAATCTTGTGTGTTCACG 59.879 47.826 0.00 0.00 46.49 4.35
5739 7741 3.432252 CCCGTCTAATCTTGTGTGTTCAC 59.568 47.826 0.00 0.00 44.08 3.18
5740 7742 3.070446 ACCCGTCTAATCTTGTGTGTTCA 59.930 43.478 0.00 0.00 0.00 3.18
5741 7743 3.432252 CACCCGTCTAATCTTGTGTGTTC 59.568 47.826 0.00 0.00 0.00 3.18
5742 7744 3.399330 CACCCGTCTAATCTTGTGTGTT 58.601 45.455 0.00 0.00 0.00 3.32
5743 7745 2.870435 GCACCCGTCTAATCTTGTGTGT 60.870 50.000 0.00 0.00 0.00 3.72
5744 7746 1.732259 GCACCCGTCTAATCTTGTGTG 59.268 52.381 0.00 0.00 0.00 3.82
5745 7747 1.623811 AGCACCCGTCTAATCTTGTGT 59.376 47.619 0.00 0.00 0.00 3.72
5746 7748 2.386661 AGCACCCGTCTAATCTTGTG 57.613 50.000 0.00 0.00 0.00 3.33
5747 7749 3.451178 ACATAGCACCCGTCTAATCTTGT 59.549 43.478 0.00 0.00 0.00 3.16
5748 7750 4.060038 ACATAGCACCCGTCTAATCTTG 57.940 45.455 0.00 0.00 0.00 3.02
5749 7751 4.755266 AACATAGCACCCGTCTAATCTT 57.245 40.909 0.00 0.00 0.00 2.40
5750 7752 4.261489 CGTAACATAGCACCCGTCTAATCT 60.261 45.833 0.00 0.00 0.00 2.40
5751 7753 3.979495 CGTAACATAGCACCCGTCTAATC 59.021 47.826 0.00 0.00 0.00 1.75
5752 7754 3.243636 CCGTAACATAGCACCCGTCTAAT 60.244 47.826 0.00 0.00 0.00 1.73
5753 7755 2.099592 CCGTAACATAGCACCCGTCTAA 59.900 50.000 0.00 0.00 0.00 2.10
5754 7756 1.677576 CCGTAACATAGCACCCGTCTA 59.322 52.381 0.00 0.00 0.00 2.59
5755 7757 0.458669 CCGTAACATAGCACCCGTCT 59.541 55.000 0.00 0.00 0.00 4.18
5756 7758 0.529119 CCCGTAACATAGCACCCGTC 60.529 60.000 0.00 0.00 0.00 4.79
5757 7759 0.971959 TCCCGTAACATAGCACCCGT 60.972 55.000 0.00 0.00 0.00 5.28
5758 7760 0.176219 TTCCCGTAACATAGCACCCG 59.824 55.000 0.00 0.00 0.00 5.28
5759 7761 1.065998 TGTTCCCGTAACATAGCACCC 60.066 52.381 0.00 0.00 43.22 4.61
5760 7762 2.389962 TGTTCCCGTAACATAGCACC 57.610 50.000 0.00 0.00 43.22 5.01
5767 7769 2.983907 TCTTGTGTGTTCCCGTAACA 57.016 45.000 0.00 0.00 45.90 2.41
5768 7770 5.119743 GTCTAATCTTGTGTGTTCCCGTAAC 59.880 44.000 0.00 0.00 38.67 2.50
5769 7771 5.232463 GTCTAATCTTGTGTGTTCCCGTAA 58.768 41.667 0.00 0.00 0.00 3.18
5770 7772 4.616604 CGTCTAATCTTGTGTGTTCCCGTA 60.617 45.833 0.00 0.00 0.00 4.02
5771 7773 3.660865 GTCTAATCTTGTGTGTTCCCGT 58.339 45.455 0.00 0.00 0.00 5.28
5772 7774 2.666508 CGTCTAATCTTGTGTGTTCCCG 59.333 50.000 0.00 0.00 0.00 5.14
5773 7775 3.000727 CCGTCTAATCTTGTGTGTTCCC 58.999 50.000 0.00 0.00 0.00 3.97
5774 7776 3.000727 CCCGTCTAATCTTGTGTGTTCC 58.999 50.000 0.00 0.00 0.00 3.62
5775 7777 3.432252 CACCCGTCTAATCTTGTGTGTTC 59.568 47.826 0.00 0.00 0.00 3.18
5776 7778 3.399330 CACCCGTCTAATCTTGTGTGTT 58.601 45.455 0.00 0.00 0.00 3.32
5777 7779 2.870435 GCACCCGTCTAATCTTGTGTGT 60.870 50.000 0.00 0.00 0.00 3.72
5778 7780 1.732259 GCACCCGTCTAATCTTGTGTG 59.268 52.381 0.00 0.00 0.00 3.82
5779 7781 1.623811 AGCACCCGTCTAATCTTGTGT 59.376 47.619 0.00 0.00 0.00 3.72
5780 7782 2.386661 AGCACCCGTCTAATCTTGTG 57.613 50.000 0.00 0.00 0.00 3.33
5781 7783 3.451178 ACATAGCACCCGTCTAATCTTGT 59.549 43.478 0.00 0.00 0.00 3.16
5782 7784 4.060038 ACATAGCACCCGTCTAATCTTG 57.940 45.455 0.00 0.00 0.00 3.02
5783 7785 4.755266 AACATAGCACCCGTCTAATCTT 57.245 40.909 0.00 0.00 0.00 2.40
5784 7786 4.261489 CGTAACATAGCACCCGTCTAATCT 60.261 45.833 0.00 0.00 0.00 2.40
5785 7787 3.979495 CGTAACATAGCACCCGTCTAATC 59.021 47.826 0.00 0.00 0.00 1.75
5786 7788 3.243636 CCGTAACATAGCACCCGTCTAAT 60.244 47.826 0.00 0.00 0.00 1.73
5787 7789 2.099592 CCGTAACATAGCACCCGTCTAA 59.900 50.000 0.00 0.00 0.00 2.10
5788 7790 1.677576 CCGTAACATAGCACCCGTCTA 59.322 52.381 0.00 0.00 0.00 2.59
5789 7791 0.458669 CCGTAACATAGCACCCGTCT 59.541 55.000 0.00 0.00 0.00 4.18
5790 7792 0.529119 CCCGTAACATAGCACCCGTC 60.529 60.000 0.00 0.00 0.00 4.79
5791 7793 0.971959 TCCCGTAACATAGCACCCGT 60.972 55.000 0.00 0.00 0.00 5.28
5792 7794 0.176219 TTCCCGTAACATAGCACCCG 59.824 55.000 0.00 0.00 0.00 5.28
5793 7795 1.065998 TGTTCCCGTAACATAGCACCC 60.066 52.381 0.00 0.00 43.22 4.61
5794 7796 2.389962 TGTTCCCGTAACATAGCACC 57.610 50.000 0.00 0.00 43.22 5.01
5801 7803 2.983907 TCTTGTGTGTTCCCGTAACA 57.016 45.000 0.00 0.00 45.90 2.41
5811 7813 9.520515 ACTTAAAATCCATCTAATCTTGTGTGT 57.479 29.630 0.00 0.00 0.00 3.72
5833 7835 5.128171 ACATGCGGTTCCTGACTATAACTTA 59.872 40.000 0.00 0.00 0.00 2.24
5904 7906 1.726791 CGGAATGCTATGTACGGATGC 59.273 52.381 0.00 0.00 0.00 3.91
5905 7907 2.731451 CACGGAATGCTATGTACGGATG 59.269 50.000 0.00 0.00 0.00 3.51
5952 8568 7.467557 TTTTCTGCATTTGTCTTCACATTTC 57.532 32.000 0.00 0.00 30.55 2.17
6106 8724 5.391523 GCTGTGTGAGTTGTGTTTGAAACTA 60.392 40.000 9.69 0.00 36.77 2.24
6107 8725 4.615912 GCTGTGTGAGTTGTGTTTGAAACT 60.616 41.667 9.69 0.00 39.31 2.66
6108 8726 3.608073 GCTGTGTGAGTTGTGTTTGAAAC 59.392 43.478 0.14 0.14 0.00 2.78
6114 8759 3.543680 ACTAGCTGTGTGAGTTGTGTT 57.456 42.857 0.00 0.00 0.00 3.32
6188 8833 7.881775 AAAAAGAAGGGTATACTATGCTTGG 57.118 36.000 2.25 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.