Multiple sequence alignment - TraesCS2A01G455100

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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 TraesCS2A01G455100 chr2A 100.000 8594 0 0 1 8594 703868014 703876607 0.000000e+00 15871.0
1 TraesCS2A01G455100 chr2D 94.723 4662 162 34 3994 8594 563789779 563794417 0.000000e+00 7169.0
2 TraesCS2A01G455100 chr2D 96.400 3556 98 20 1 3533 563785745 563789293 0.000000e+00 5830.0
3 TraesCS2A01G455100 chr2D 98.073 467 7 2 3529 3994 563789352 563789817 0.000000e+00 811.0
4 TraesCS2A01G455100 chr2B 94.729 3282 115 27 727 3994 674029903 674033140 0.000000e+00 5049.0
5 TraesCS2A01G455100 chr2B 92.555 1867 92 18 6742 8594 674035389 674037222 0.000000e+00 2634.0
6 TraesCS2A01G455100 chr2B 92.547 738 38 10 1 731 674029134 674029861 0.000000e+00 1042.0
7 TraesCS2A01G455100 chr2B 91.581 677 22 6 4763 5429 674034038 674034689 0.000000e+00 902.0
8 TraesCS2A01G455100 chr2B 93.502 554 24 6 4214 4764 674033400 674033944 0.000000e+00 813.0
9 TraesCS2A01G455100 chr2B 95.516 223 9 1 3994 4215 674033102 674033324 1.060000e-93 355.0
10 TraesCS2A01G455100 chr2B 93.989 183 8 2 5980 6159 674035211 674035393 3.060000e-69 274.0
11 TraesCS2A01G455100 chr2B 87.156 109 11 3 5897 6004 674035104 674035210 4.210000e-23 121.0
12 TraesCS2A01G455100 chr3B 90.690 580 38 10 1843 2411 133770988 133771562 0.000000e+00 758.0
13 TraesCS2A01G455100 chr3B 91.619 525 33 4 3419 3939 133773267 133773784 0.000000e+00 715.0
14 TraesCS2A01G455100 chr3B 87.559 635 56 16 6063 6685 133774532 133775155 0.000000e+00 713.0
15 TraesCS2A01G455100 chr3B 92.553 470 20 9 2969 3432 133772575 133773035 0.000000e+00 660.0
16 TraesCS2A01G455100 chr3B 90.541 222 17 2 2685 2903 133771711 133771931 3.030000e-74 291.0
17 TraesCS2A01G455100 chr3B 88.235 102 8 2 5141 5241 133773784 133773882 1.520000e-22 119.0
18 TraesCS2A01G455100 chr3B 100.000 35 0 0 6676 6710 133775167 133775201 2.000000e-06 65.8


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 TraesCS2A01G455100 chr2A 703868014 703876607 8593 False 15871.000000 15871 100.000000 1 8594 1 chr2A.!!$F1 8593
1 TraesCS2A01G455100 chr2D 563785745 563794417 8672 False 4603.333333 7169 96.398667 1 8594 3 chr2D.!!$F1 8593
2 TraesCS2A01G455100 chr2B 674029134 674037222 8088 False 1398.750000 5049 92.696875 1 8594 8 chr2B.!!$F1 8593
3 TraesCS2A01G455100 chr3B 133770988 133775201 4213 False 474.542857 758 91.599571 1843 6710 7 chr3B.!!$F1 4867


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
810 872 0.530870 GCTTCCTAGCACGGTCCATC 60.531 60.000 0.00 0.00 46.95 3.51 F
1403 1467 0.460987 GAGGCGATCAGGGTGAGTTG 60.461 60.000 0.00 0.00 0.00 3.16 F
1971 2038 0.687354 AAGATCGCCAACAGTCTGGT 59.313 50.000 4.53 0.00 38.86 4.00 F
3149 3806 1.758440 TTCGAGTGTTGCAGGGCTCT 61.758 55.000 10.34 0.00 0.00 4.09 F
3972 4950 7.777440 TGGTTACACTATGAATGAATATTGCCA 59.223 33.333 0.00 0.00 0.00 4.92 F
5471 6807 1.428718 GGGGTGGGGGTGTCTTGTTA 61.429 60.000 0.00 0.00 0.00 2.41 F
5695 7320 1.696884 TGACTTGTGGGTAGCATCACA 59.303 47.619 0.57 0.57 41.47 3.58 F
7521 9190 0.179004 AAGGAAATGCGGTCCACACA 60.179 50.000 3.28 0.00 37.65 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2366 0.973632 TCAGTATTGGGTGAGCACGT 59.026 50.000 0.00 0.00 0.00 4.49 R
2374 2450 3.901222 TGGAACTGTAGTCTGGAACATCA 59.099 43.478 0.00 0.00 38.20 3.07 R
3559 4534 5.392767 ACAAACTGTCACTCGAGATACAT 57.607 39.130 21.68 5.88 0.00 2.29 R
4053 5031 0.615331 GGATGACTGGCAGTCCTTCA 59.385 55.000 37.12 23.81 44.44 3.02 R
5711 7336 1.680522 ATGTGCAGGCTCCGGACTAG 61.681 60.000 0.00 0.00 0.00 2.57 R
7137 8806 0.323957 GGTGTGGTGAAGACCTACCC 59.676 60.000 0.00 0.00 43.58 3.69 R
7560 9229 0.826715 GCCCTACTGAGATCTGCACA 59.173 55.000 0.00 0.00 0.00 4.57 R
8456 10143 0.240145 TGTGCGTACCTGTCGAGAAG 59.760 55.000 0.00 0.00 0.00 2.85 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
303 305 7.451255 TGGATGAAACATAACTTCCTTGAATGT 59.549 33.333 0.00 0.00 33.41 2.71
356 362 1.413445 GCCTGCTGAGATGAGAGACAT 59.587 52.381 0.00 0.00 42.47 3.06
396 403 5.692654 TCGTTTTTCTGTGTATTGTCATCGA 59.307 36.000 0.00 0.00 0.00 3.59
476 485 4.148825 CTTCCCGGCGACCCTCAG 62.149 72.222 9.30 0.00 0.00 3.35
671 681 9.787532 TTCTTAGCAAAATTACATTCTGCATAC 57.212 29.630 0.00 0.00 35.44 2.39
721 733 0.542805 GCCCATACTGGACCGGTTTA 59.457 55.000 12.24 0.00 40.96 2.01
798 860 4.907875 AGCTCTGTAATATTGGGCTTCCTA 59.092 41.667 0.00 0.00 0.00 2.94
810 872 0.530870 GCTTCCTAGCACGGTCCATC 60.531 60.000 0.00 0.00 46.95 3.51
815 877 2.650813 CTAGCACGGTCCATCCAGCC 62.651 65.000 0.00 0.00 37.52 4.85
820 882 2.668632 GGTCCATCCAGCCGAACA 59.331 61.111 0.00 0.00 35.97 3.18
869 933 2.260869 CCCTCGGCCTTGTTGTGTG 61.261 63.158 0.00 0.00 0.00 3.82
1403 1467 0.460987 GAGGCGATCAGGGTGAGTTG 60.461 60.000 0.00 0.00 0.00 3.16
1405 1469 1.296715 GCGATCAGGGTGAGTTGGT 59.703 57.895 0.00 0.00 0.00 3.67
1413 1478 0.755327 GGGTGAGTTGGTGGCAGTTT 60.755 55.000 0.00 0.00 0.00 2.66
1679 1745 3.186909 TCAGGTTCATGCTACGAATTCG 58.813 45.455 25.64 25.64 46.33 3.34
1730 1796 6.267070 GTCCAAGTACTCTAAGTATGCTGAC 58.733 44.000 0.00 0.00 32.65 3.51
1859 1925 3.202906 GGCGATATTGCTAACTTGGTGA 58.797 45.455 14.65 0.00 34.52 4.02
1971 2038 0.687354 AAGATCGCCAACAGTCTGGT 59.313 50.000 4.53 0.00 38.86 4.00
2139 2207 6.772716 AGGTATACTTCAGGTTTTATGCATGG 59.227 38.462 10.16 0.00 0.00 3.66
2185 2253 7.757526 TGATATAAGCGTGTTAATGCAACTTT 58.242 30.769 0.00 0.00 41.09 2.66
2211 2279 7.012515 TGTGAACCAACTACGATTGTATTGTTT 59.987 33.333 0.00 0.00 0.00 2.83
2370 2446 7.955864 GGAAAGTCAAGCTTTTATAGTTGTACG 59.044 37.037 0.00 0.00 46.54 3.67
2374 2450 9.649167 AGTCAAGCTTTTATAGTTGTACGTTAT 57.351 29.630 0.00 0.00 0.00 1.89
2388 2464 6.762702 TGTACGTTATGATGTTCCAGACTA 57.237 37.500 0.00 0.00 0.00 2.59
2486 2562 2.162319 TGCGTTTCTGCAGTGATACA 57.838 45.000 14.67 5.53 40.62 2.29
2546 2623 6.014327 ACCTTTATCCATGCAAAGTCATTTGT 60.014 34.615 0.00 0.99 46.26 2.83
2553 2630 6.939730 TCCATGCAAAGTCATTTGTAGAGTTA 59.060 34.615 0.00 0.00 46.26 2.24
2650 2727 8.577939 CAAGCGATTGTTTTTAGTATGTTGATG 58.422 33.333 4.96 0.00 0.00 3.07
2766 2843 8.489559 GCAATGTATACAATATTTTGGTGCATG 58.510 33.333 10.14 0.00 37.15 4.06
2982 3639 6.872020 TGTTAGTTCACTTGCCTCTTATGTAC 59.128 38.462 0.00 0.00 0.00 2.90
2986 3643 7.852263 AGTTCACTTGCCTCTTATGTACTTAT 58.148 34.615 0.00 0.00 0.00 1.73
3149 3806 1.758440 TTCGAGTGTTGCAGGGCTCT 61.758 55.000 10.34 0.00 0.00 4.09
3559 4534 8.500753 AATGCTTGAATTACCGATGTTAGTTA 57.499 30.769 0.00 0.00 0.00 2.24
3971 4949 8.165239 TGGTTACACTATGAATGAATATTGCC 57.835 34.615 0.00 0.00 0.00 4.52
3972 4950 7.777440 TGGTTACACTATGAATGAATATTGCCA 59.223 33.333 0.00 0.00 0.00 4.92
3973 4951 8.796475 GGTTACACTATGAATGAATATTGCCAT 58.204 33.333 0.00 0.00 0.00 4.40
3977 4955 9.578576 ACACTATGAATGAATATTGCCATACTT 57.421 29.630 0.00 0.00 0.00 2.24
4053 5031 8.777578 AGTTCTATGAACTAAAAGGGGTTTTT 57.222 30.769 10.76 0.00 41.68 1.94
4198 5177 3.319405 TCCAGCAAAGCCAATTTCGTTAA 59.681 39.130 0.00 0.00 0.00 2.01
4516 5580 7.178451 TGAAGACAAGTCCATAACAGTAGATGA 59.822 37.037 0.00 0.00 0.00 2.92
4669 5735 7.932491 CCATGGATCTGGATATGATATCAACTC 59.068 40.741 5.56 9.16 38.69 3.01
4670 5736 8.706521 CATGGATCTGGATATGATATCAACTCT 58.293 37.037 9.99 0.00 0.00 3.24
4953 6114 4.100084 CTGCGGAGGCACCCATCA 62.100 66.667 0.00 0.00 46.21 3.07
5049 6212 7.725844 TGATCCAGTGTGTATATATCTCTGTGT 59.274 37.037 13.59 6.62 0.00 3.72
5167 6337 6.536224 GTCCATAAGCTAATTGCAATGCTTTT 59.464 34.615 30.53 23.44 42.22 2.27
5234 6404 2.171448 ACCTAAGAAGATTGGCGCTGAT 59.829 45.455 7.64 0.71 0.00 2.90
5267 6601 2.172505 TGAAGAGACAGACCCTGCAAAA 59.827 45.455 0.00 0.00 34.37 2.44
5324 6658 5.819825 ACAGACTTTGTTTTCTCACTTCC 57.180 39.130 0.00 0.00 36.31 3.46
5469 6805 3.182996 GGGGTGGGGGTGTCTTGT 61.183 66.667 0.00 0.00 0.00 3.16
5471 6807 1.428718 GGGGTGGGGGTGTCTTGTTA 61.429 60.000 0.00 0.00 0.00 2.41
5638 7261 3.629398 TCGGAGTAGAACTAACCGGATTC 59.371 47.826 9.46 6.43 43.14 2.52
5695 7320 1.696884 TGACTTGTGGGTAGCATCACA 59.303 47.619 0.57 0.57 41.47 3.58
5793 7418 2.612285 TTTGCCCCCACATAACATCA 57.388 45.000 0.00 0.00 0.00 3.07
5802 7427 6.881602 GCCCCCACATAACATCAAAATAAAAA 59.118 34.615 0.00 0.00 0.00 1.94
5848 7473 3.342377 TTGTTCATCCCGAAGCATACA 57.658 42.857 0.00 0.00 33.09 2.29
5875 7500 3.861840 ACATAACTGGTTCGATGACAGG 58.138 45.455 13.73 1.99 36.57 4.00
5969 7594 4.227754 TGGCCTACAGAGTAGAGACTAACT 59.772 45.833 3.32 0.00 35.45 2.24
6193 7823 7.119387 AGCATACCTTTTAAGATAACTGGCTT 58.881 34.615 0.00 0.00 0.00 4.35
6310 7941 4.664150 ATAGTTGGGTGTTGTTTTGTGG 57.336 40.909 0.00 0.00 0.00 4.17
6493 8131 4.963628 ACTAGGGAGGAACTGATAACCTTC 59.036 45.833 0.00 0.00 41.55 3.46
6498 8136 4.500035 GGAGGAACTGATAACCTTCGCTAG 60.500 50.000 0.00 0.00 41.55 3.42
6592 8230 3.030291 CTGGACTAGATGGAAGTCTGCT 58.970 50.000 0.00 0.00 42.48 4.24
6602 8240 3.405831 TGGAAGTCTGCTTGATGAACAG 58.594 45.455 0.00 0.00 34.61 3.16
6637 8276 5.648092 ACAATGATAGTGGTTTACTTGCCTC 59.352 40.000 0.00 0.00 40.89 4.70
6750 8408 9.851686 ATGGACAATTGCTATTATTTGTCTAGA 57.148 29.630 5.05 0.00 44.57 2.43
6777 8435 6.100279 TCTCATGGACAGTTTATTGCCTATCT 59.900 38.462 0.00 0.00 0.00 1.98
6901 8559 7.724061 ACAACTTAGTGTCCTTATTTCAATGGT 59.276 33.333 0.00 0.00 0.00 3.55
6943 8601 7.034685 TGATTATTCAGCTCATTTCATGTGG 57.965 36.000 0.00 0.00 0.00 4.17
6948 8606 3.008923 TCAGCTCATTTCATGTGGTACCA 59.991 43.478 11.60 11.60 33.72 3.25
7137 8806 8.709646 GTTTACTTATATAGTTTGCCGAGATGG 58.290 37.037 0.00 0.00 38.33 3.51
7173 8842 5.104485 ACCACACCTTCCACTAGATATTTCC 60.104 44.000 0.00 0.00 0.00 3.13
7233 8902 3.620488 CAGCTTTGCCACCCTCTTATTA 58.380 45.455 0.00 0.00 0.00 0.98
7234 8903 4.210331 CAGCTTTGCCACCCTCTTATTAT 58.790 43.478 0.00 0.00 0.00 1.28
7264 8933 7.826260 ACTGTTTAAATGTTTGTGTTCAAGG 57.174 32.000 0.00 0.00 34.88 3.61
7288 8957 0.613777 GCCGGGTCCTTATCATAGGG 59.386 60.000 2.18 0.00 35.90 3.53
7310 8979 3.643792 GGTCCTATCTACTGCCACTTGAT 59.356 47.826 0.00 0.00 0.00 2.57
7481 9150 2.009774 CTTTGGGTGCCAGTCGAATAG 58.990 52.381 0.00 0.00 33.81 1.73
7521 9190 0.179004 AAGGAAATGCGGTCCACACA 60.179 50.000 3.28 0.00 37.65 3.72
7532 9201 1.607251 GGTCCACACACTAGAAACCGG 60.607 57.143 0.00 0.00 0.00 5.28
7564 9241 0.941542 TGCTAAAAGGTCACGTGTGC 59.058 50.000 16.51 9.75 0.00 4.57
7580 9257 0.249238 GTGCAGATCTCAGTAGGGCG 60.249 60.000 0.00 0.00 0.00 6.13
7808 9485 2.422276 ACAAATGCCGTTTCAGCTTC 57.578 45.000 0.00 0.00 0.00 3.86
7938 9615 1.595794 CGTCAGCCACGTTGTTTAACT 59.404 47.619 0.00 0.00 44.07 2.24
7939 9616 2.031191 CGTCAGCCACGTTGTTTAACTT 59.969 45.455 0.00 0.00 44.07 2.66
7940 9617 3.359654 GTCAGCCACGTTGTTTAACTTG 58.640 45.455 0.00 0.00 36.22 3.16
7943 9620 2.098443 AGCCACGTTGTTTAACTTGTGG 59.902 45.455 20.88 20.88 44.45 4.17
7947 9624 1.331138 CGTTGTTTAACTTGTGGGCGA 59.669 47.619 0.00 0.00 34.60 5.54
7953 9630 1.847798 TAACTTGTGGGCGAGGGCAT 61.848 55.000 0.00 0.00 42.47 4.40
7975 9652 6.374333 GCATTGTGACCTGATTTAGAAGGTTA 59.626 38.462 0.00 0.00 46.97 2.85
7978 9655 6.698380 TGTGACCTGATTTAGAAGGTTAGAC 58.302 40.000 0.00 0.00 46.97 2.59
7991 9668 7.997773 AGAAGGTTAGACTTTGGATTTTACC 57.002 36.000 0.00 0.00 0.00 2.85
8098 9776 0.462937 TATGCCATGTGGTACGGTGC 60.463 55.000 0.35 0.00 37.57 5.01
8139 9817 6.867550 TCTCATTCGTCTGATGTTGTATCTT 58.132 36.000 0.00 0.00 0.00 2.40
8269 9947 1.760613 TCGGGATTGCCGAACTATCTT 59.239 47.619 17.54 0.00 36.73 2.40
8285 9963 0.104120 TCTTGTCCATCCATACGCCG 59.896 55.000 0.00 0.00 0.00 6.46
8288 9966 0.756294 TGTCCATCCATACGCCGAAT 59.244 50.000 0.00 0.00 0.00 3.34
8296 9974 2.066262 CCATACGCCGAATCCACATAC 58.934 52.381 0.00 0.00 0.00 2.39
8397 10084 0.471211 TCTTGGGAACTCCGTCCTGT 60.471 55.000 0.00 0.00 37.85 4.00
8399 10086 1.052124 TTGGGAACTCCGTCCTGTGT 61.052 55.000 0.00 0.00 37.85 3.72
8436 10123 4.447342 CGGATGGGGCCCTTGCTT 62.447 66.667 25.93 2.71 37.74 3.91
8456 10143 2.343758 TCAGCCGACCTGACAAGC 59.656 61.111 2.18 0.00 45.44 4.01
8542 10237 5.299028 GCATCCCATATTCACATGTGTACAA 59.701 40.000 24.63 12.85 0.00 2.41
8543 10238 6.016024 GCATCCCATATTCACATGTGTACAAT 60.016 38.462 24.63 18.52 0.00 2.71
8545 10240 6.899089 TCCCATATTCACATGTGTACAATCT 58.101 36.000 24.63 8.05 0.00 2.40
8552 10247 7.977789 TTCACATGTGTACAATCTATGTTGT 57.022 32.000 24.63 0.00 43.63 3.32
8553 10248 9.665719 ATTCACATGTGTACAATCTATGTTGTA 57.334 29.630 24.63 0.00 43.63 2.41
8562 10257 5.730550 ACAATCTATGTTGTACGTGGATGT 58.269 37.500 0.00 0.00 40.06 3.06
8586 10281 1.946768 CCAGTTCGTTCCTCTTGCAAA 59.053 47.619 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.369904 ACAATTAAAATGATTAGATGCAACACC 57.630 29.630 0.00 0.00 0.00 4.16
52 53 1.890876 TTAGCGAAGAAAGGCTGCAA 58.109 45.000 0.50 0.00 40.32 4.08
253 255 1.683917 AGAGGTCAGCACATATCCGAC 59.316 52.381 0.00 0.00 0.00 4.79
411 419 6.538381 TGAGAAGCGCATATACATCTTTTCAA 59.462 34.615 11.47 0.00 28.99 2.69
476 485 8.515414 AGTTCAAAATAGGAAAGTAACTGCATC 58.485 33.333 0.00 0.00 0.00 3.91
798 860 4.101448 GGCTGGATGGACCGTGCT 62.101 66.667 6.77 0.00 42.61 4.40
810 872 2.813908 GCCTACGTGTTCGGCTGG 60.814 66.667 0.00 0.00 40.62 4.85
815 877 1.226491 CCTACCGCCTACGTGTTCG 60.226 63.158 0.00 0.00 43.34 3.95
816 878 1.517913 GCCTACCGCCTACGTGTTC 60.518 63.158 0.00 0.00 37.70 3.18
854 916 1.821759 CCACACACAACAAGGCCGA 60.822 57.895 0.00 0.00 0.00 5.54
856 918 3.128375 CCCACACACAACAAGGCC 58.872 61.111 0.00 0.00 0.00 5.19
869 933 1.227853 ACTTGTCAGTTCGGCCCAC 60.228 57.895 0.00 0.00 0.00 4.61
1107 1171 3.947841 CGCGAGGAGAGGAGCTCG 61.948 72.222 7.83 0.00 44.91 5.03
1377 1441 2.543802 CCTGATCGCCTCGTCGCTA 61.544 63.158 0.00 0.00 0.00 4.26
1403 1467 7.116233 CACAAATGAATAGTTAAAACTGCCACC 59.884 37.037 5.62 0.00 40.07 4.61
1405 1469 7.651304 CACACAAATGAATAGTTAAAACTGCCA 59.349 33.333 5.62 1.80 40.07 4.92
1413 1478 6.451393 GCCCAACACACAAATGAATAGTTAA 58.549 36.000 0.00 0.00 0.00 2.01
1434 1499 0.465460 TAGCCAATTCACCATCGCCC 60.465 55.000 0.00 0.00 0.00 6.13
1679 1745 7.408123 CAAGCAACTCTAGAACATCATCAATC 58.592 38.462 0.00 0.00 0.00 2.67
1730 1796 1.804151 CCAGTCACCACATACCAAACG 59.196 52.381 0.00 0.00 0.00 3.60
1791 1857 5.917462 AGGGAAACAAGTTTTTCAAGGATG 58.083 37.500 0.00 0.00 37.24 3.51
1902 1969 4.572909 GCAGGAGCAATTGGAGAAAAATT 58.427 39.130 7.72 0.00 41.58 1.82
1971 2038 6.440647 AGAGATATTACCAGTGGTTTGACTGA 59.559 38.462 22.49 0.00 45.39 3.41
2155 2223 8.371770 TGCATTAACACGCTTATATCAATGTA 57.628 30.769 0.00 0.00 0.00 2.29
2185 2253 5.992829 ACAATACAATCGTAGTTGGTTCACA 59.007 36.000 0.00 0.00 33.40 3.58
2211 2279 1.609580 GGTGTGCCTACGGAAATGTCA 60.610 52.381 0.00 0.00 0.00 3.58
2240 2309 6.703165 TGCAGAATAGCATGTGTACTTCATAG 59.297 38.462 0.00 0.00 40.11 2.23
2241 2310 6.581712 TGCAGAATAGCATGTGTACTTCATA 58.418 36.000 0.00 0.00 40.11 2.15
2242 2311 5.430886 TGCAGAATAGCATGTGTACTTCAT 58.569 37.500 0.00 0.00 40.11 2.57
2243 2312 4.831107 TGCAGAATAGCATGTGTACTTCA 58.169 39.130 0.00 0.00 40.11 3.02
2291 2366 0.973632 TCAGTATTGGGTGAGCACGT 59.026 50.000 0.00 0.00 0.00 4.49
2370 2446 6.535508 GGAACTGTAGTCTGGAACATCATAAC 59.464 42.308 0.00 0.00 38.20 1.89
2374 2450 3.901222 TGGAACTGTAGTCTGGAACATCA 59.099 43.478 0.00 0.00 38.20 3.07
2388 2464 6.879458 GTCTATAATCAAGGTGTTGGAACTGT 59.121 38.462 0.00 0.00 34.09 3.55
2553 2630 8.593945 ATTCACACCATTTATAATCCAACTGT 57.406 30.769 0.00 0.00 0.00 3.55
2567 2644 9.920946 ACTATGACCTAAATAATTCACACCATT 57.079 29.630 0.00 0.00 0.00 3.16
2637 2714 7.759489 AAACTTGAAGGCATCAACATACTAA 57.241 32.000 0.22 0.00 43.08 2.24
2674 2751 9.231297 AGCATAAGAAACAGAACTAAAATAGCA 57.769 29.630 0.00 0.00 0.00 3.49
2766 2843 4.712122 TCTTAAAATCCAATGCGGGAAC 57.288 40.909 0.00 0.00 41.12 3.62
3004 3661 7.438564 ACACAAAAGGTTAGAACAAAAACACT 58.561 30.769 0.00 0.00 0.00 3.55
3559 4534 5.392767 ACAAACTGTCACTCGAGATACAT 57.607 39.130 21.68 5.88 0.00 2.29
3994 4972 9.081204 TGCTAAAGTATGGCAATATTCATTCAT 57.919 29.630 0.00 0.00 32.79 2.57
3995 4973 8.462589 TGCTAAAGTATGGCAATATTCATTCA 57.537 30.769 0.00 0.00 32.79 2.57
4053 5031 0.615331 GGATGACTGGCAGTCCTTCA 59.385 55.000 37.12 23.81 44.44 3.02
4220 5276 0.749091 CATTCCTCAGCATTCCGCCA 60.749 55.000 0.00 0.00 44.04 5.69
4272 5328 2.621055 TCAACGGCATGCTAAACTTGTT 59.379 40.909 18.92 8.23 0.00 2.83
4678 5744 4.442375 ACACGTTTGTTTGTTCAATCCA 57.558 36.364 0.00 0.00 28.43 3.41
4766 5927 9.651913 AAACAAGTCAAACACAAAGTCATAATT 57.348 25.926 0.00 0.00 0.00 1.40
5167 6337 4.526970 AGCAACTTCCTGAAAGAGAAACA 58.473 39.130 0.00 0.00 38.44 2.83
5234 6404 6.710744 GGTCTGTCTCTTCATTGTTAAAAGGA 59.289 38.462 0.00 0.00 0.00 3.36
5313 6647 7.561356 AGGATTGAAAGAAAAGGAAGTGAGAAA 59.439 33.333 0.00 0.00 0.00 2.52
5324 6658 7.176340 AGGACAGATTGAGGATTGAAAGAAAAG 59.824 37.037 0.00 0.00 0.00 2.27
5580 7202 5.265989 AGTAACACTTTCCCCTTTGAAACA 58.734 37.500 0.00 0.00 31.28 2.83
5695 7320 2.175284 GACTAGGGTAGCCTACTCAGGT 59.825 54.545 16.84 12.48 44.68 4.00
5711 7336 1.680522 ATGTGCAGGCTCCGGACTAG 61.681 60.000 0.00 0.00 0.00 2.57
5802 7427 6.274157 AGAAACTACAGTTGAGATCGTGAT 57.726 37.500 0.00 0.00 38.44 3.06
5806 7431 7.630924 ACAAAAAGAAACTACAGTTGAGATCG 58.369 34.615 0.00 0.00 38.44 3.69
5848 7473 8.330466 TGTCATCGAACCAGTTATGTTAAAAT 57.670 30.769 0.00 0.00 0.00 1.82
5875 7500 6.506500 AGGACTCATGTTCAAATCATCAAC 57.493 37.500 0.00 0.00 0.00 3.18
5969 7594 4.649674 GGACTAGTCAATGTCCTACATCCA 59.350 45.833 23.91 0.00 46.65 3.41
6069 7696 1.217779 GGACTCTGGCAGCTGACTC 59.782 63.158 22.80 9.76 0.00 3.36
6098 7725 7.822161 TGATTATGTTATGTGCTGGCTATTT 57.178 32.000 0.00 0.00 0.00 1.40
6193 7823 5.188434 GTTCAAATCCTCCATCTGACATCA 58.812 41.667 0.00 0.00 0.00 3.07
6279 7909 9.693739 AAACAACACCCAACTATATAATCATCA 57.306 29.630 0.00 0.00 0.00 3.07
6493 8131 1.140375 GTACCCACCGGTTCTAGCG 59.860 63.158 2.97 0.00 40.58 4.26
6498 8136 3.941573 TCATTTAAGTACCCACCGGTTC 58.058 45.455 2.97 0.00 40.58 3.62
6592 8230 2.437651 TCTCACCACCACTGTTCATCAA 59.562 45.455 0.00 0.00 0.00 2.57
6602 8240 3.935203 CACTATCATTGTCTCACCACCAC 59.065 47.826 0.00 0.00 0.00 4.16
6637 8276 5.860716 GCTTGAAGCTGTAATTTGGAAGAAG 59.139 40.000 10.44 0.00 38.45 2.85
6750 8408 5.513233 AGGCAATAAACTGTCCATGAGATT 58.487 37.500 0.00 0.00 0.00 2.40
6901 8559 8.477419 AATAATCAAACAGGAAAAAGGAGACA 57.523 30.769 0.00 0.00 0.00 3.41
6943 8601 2.351738 GCAACAAATCTGGCAGTGGTAC 60.352 50.000 15.27 0.00 0.00 3.34
6948 8606 0.593128 GACGCAACAAATCTGGCAGT 59.407 50.000 15.27 0.00 0.00 4.40
7076 8734 2.416972 GGTGAATGTAGTCAGACGGGTC 60.417 54.545 0.00 0.00 0.00 4.46
7137 8806 0.323957 GGTGTGGTGAAGACCTACCC 59.676 60.000 0.00 0.00 43.58 3.69
7173 8842 4.487714 TTAGGCTGACATAAACCAGAGG 57.512 45.455 0.00 0.00 32.37 3.69
7233 8902 8.940768 ACACAAACATTTAAACAGTTAAGCAT 57.059 26.923 7.94 0.00 30.92 3.79
7234 8903 8.764524 AACACAAACATTTAAACAGTTAAGCA 57.235 26.923 7.94 0.00 30.92 3.91
7251 8920 1.269257 GGCTCAGCCTTGAACACAAAC 60.269 52.381 9.09 0.00 46.69 2.93
7264 8933 1.069935 GATAAGGACCCGGCTCAGC 59.930 63.158 0.00 0.00 0.00 4.26
7277 8946 6.322712 GCAGTAGATAGGACCCCTATGATAAG 59.677 46.154 10.03 0.26 45.78 1.73
7288 8957 3.031736 TCAAGTGGCAGTAGATAGGACC 58.968 50.000 0.00 0.00 0.00 4.46
7310 8979 8.052748 ACCCTTAGTGATGTTTAATAATGAGCA 58.947 33.333 0.00 0.00 0.00 4.26
7521 9190 1.207329 GAGGCATCACCGGTTTCTAGT 59.793 52.381 2.97 0.00 46.52 2.57
7560 9229 0.826715 GCCCTACTGAGATCTGCACA 59.173 55.000 0.00 0.00 0.00 4.57
7564 9241 1.606668 GTCTCGCCCTACTGAGATCTG 59.393 57.143 0.00 0.00 42.73 2.90
7580 9257 4.452455 CAGTGAAATGTTACACCCTGTCTC 59.548 45.833 0.00 0.00 37.69 3.36
7696 9373 9.710900 GAAGAATAATTTCCTCACATGGTTTTT 57.289 29.630 0.00 0.00 31.84 1.94
7779 9456 5.527951 TGAAACGGCATTTGTTACTCTACAA 59.472 36.000 0.00 0.00 36.30 2.41
7780 9457 5.057819 TGAAACGGCATTTGTTACTCTACA 58.942 37.500 0.00 0.00 0.00 2.74
7781 9458 5.600908 TGAAACGGCATTTGTTACTCTAC 57.399 39.130 0.00 0.00 0.00 2.59
7782 9459 4.153475 GCTGAAACGGCATTTGTTACTCTA 59.847 41.667 0.00 0.00 35.55 2.43
7783 9460 3.058224 GCTGAAACGGCATTTGTTACTCT 60.058 43.478 0.00 0.00 35.55 3.24
7784 9461 3.058224 AGCTGAAACGGCATTTGTTACTC 60.058 43.478 5.39 0.00 38.37 2.59
7785 9462 2.884639 AGCTGAAACGGCATTTGTTACT 59.115 40.909 5.39 0.00 38.37 2.24
7858 9535 3.135457 TCGTCGCACGATAGGCCA 61.135 61.111 5.01 0.00 46.73 5.36
7938 9615 2.676121 CAATGCCCTCGCCCACAA 60.676 61.111 0.00 0.00 0.00 3.33
7939 9616 3.965258 ACAATGCCCTCGCCCACA 61.965 61.111 0.00 0.00 0.00 4.17
7940 9617 3.443045 CACAATGCCCTCGCCCAC 61.443 66.667 0.00 0.00 0.00 4.61
7943 9620 3.134127 GGTCACAATGCCCTCGCC 61.134 66.667 0.00 0.00 0.00 5.54
7947 9624 2.610438 AAATCAGGTCACAATGCCCT 57.390 45.000 0.00 0.00 0.00 5.19
7953 9630 7.016268 AGTCTAACCTTCTAAATCAGGTCACAA 59.984 37.037 0.00 0.00 43.05 3.33
7960 9637 9.454859 AATCCAAAGTCTAACCTTCTAAATCAG 57.545 33.333 0.00 0.00 0.00 2.90
7961 9638 9.807921 AAATCCAAAGTCTAACCTTCTAAATCA 57.192 29.630 0.00 0.00 0.00 2.57
7966 9643 8.662255 TGGTAAAATCCAAAGTCTAACCTTCTA 58.338 33.333 0.00 0.00 34.24 2.10
7967 9644 7.523415 TGGTAAAATCCAAAGTCTAACCTTCT 58.477 34.615 0.00 0.00 34.24 2.85
7968 9645 7.754851 TGGTAAAATCCAAAGTCTAACCTTC 57.245 36.000 0.00 0.00 34.24 3.46
7991 9668 6.425114 ACTTGCCAATATCTTAGTAGCGATTG 59.575 38.462 0.00 0.00 0.00 2.67
7996 9673 5.611374 TGGACTTGCCAATATCTTAGTAGC 58.389 41.667 0.00 0.00 45.87 3.58
8098 9776 6.252015 CGAATGAGATATTTTGTGGCTGTTTG 59.748 38.462 0.00 0.00 0.00 2.93
8139 9817 2.333926 CAATGAAGACGACGTTAGGCA 58.666 47.619 0.13 0.00 0.00 4.75
8199 9877 1.961277 AGCAACAGCCTTCCGTTCG 60.961 57.895 0.00 0.00 0.00 3.95
8206 9884 2.203451 AGCAGCAGCAACAGCCTT 60.203 55.556 3.17 0.00 45.49 4.35
8269 9947 0.756294 ATTCGGCGTATGGATGGACA 59.244 50.000 6.85 0.00 0.00 4.02
8285 9963 2.746472 GCACCTGAGGGTATGTGGATTC 60.746 54.545 2.38 0.00 45.41 2.52
8288 9966 1.271840 GGCACCTGAGGGTATGTGGA 61.272 60.000 2.38 0.00 45.41 4.02
8456 10143 0.240145 TGTGCGTACCTGTCGAGAAG 59.760 55.000 0.00 0.00 0.00 2.85
8508 10195 2.277672 TATGGGATGCCAACCCCGTG 62.278 60.000 11.10 0.00 46.21 4.94
8523 10214 9.276590 ACATAGATTGTACACATGTGAATATGG 57.723 33.333 31.94 15.74 36.57 2.74
8562 10257 3.007506 TGCAAGAGGAACGAACTGGAATA 59.992 43.478 0.00 0.00 0.00 1.75



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

AutoCloner maintained by Alex Coulton.