Multiple sequence alignment - TraesCS4B01G223100

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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 TraesCS4B01G223100 chr4B 100.000 4476 0 0 1 4476 467795597 467800072 0.000000e+00 8266.0
1 TraesCS4B01G223100 chr4A 93.008 3132 147 25 594 3697 83406654 83403567 0.000000e+00 4505.0
2 TraesCS4B01G223100 chr4A 92.588 769 51 6 3705 4472 83398475 83397712 0.000000e+00 1099.0
3 TraesCS4B01G223100 chr4D 93.716 1655 74 15 1896 3541 380338246 380339879 0.000000e+00 2453.0
4 TraesCS4B01G223100 chr4D 92.830 1311 65 14 591 1894 380336196 380337484 0.000000e+00 1873.0
5 TraesCS4B01G223100 chr4D 92.883 829 54 5 3649 4476 380344053 380344877 0.000000e+00 1199.0
6 TraesCS4B01G223100 chr4D 95.413 109 5 0 3546 3654 380341236 380341344 1.660000e-39 174.0
7 TraesCS4B01G223100 chr2B 93.445 595 35 4 1 593 735408506 735407914 0.000000e+00 880.0
8 TraesCS4B01G223100 chr5B 93.423 593 32 7 1 590 496571887 496571299 0.000000e+00 872.0
9 TraesCS4B01G223100 chr5B 90.566 53 4 1 3160 3211 299680039 299680091 8.030000e-08 69.4
10 TraesCS4B01G223100 chr6B 91.371 591 42 9 4 590 158281688 158282273 0.000000e+00 800.0
11 TraesCS4B01G223100 chr5D 87.584 596 52 18 4 591 412616108 412616689 0.000000e+00 671.0
12 TraesCS4B01G223100 chr5D 85.714 595 65 17 4 590 73463380 73463962 1.060000e-170 610.0
13 TraesCS4B01G223100 chr5D 87.603 242 22 4 3001 3238 20094388 20094625 1.590000e-69 274.0
14 TraesCS4B01G223100 chr3B 86.877 602 56 19 4 592 556084147 556084738 0.000000e+00 652.0
15 TraesCS4B01G223100 chr3B 85.660 265 25 8 3282 3541 542403700 542403444 2.650000e-67 267.0
16 TraesCS4B01G223100 chr3B 86.008 243 25 5 3000 3238 542403938 542403701 7.430000e-63 252.0
17 TraesCS4B01G223100 chr3B 90.566 53 4 1 3160 3211 303333698 303333646 8.030000e-08 69.4
18 TraesCS4B01G223100 chr3B 91.837 49 4 0 3160 3208 554900672 554900720 8.030000e-08 69.4
19 TraesCS4B01G223100 chr3D 86.575 581 56 19 17 590 597280782 597281347 4.920000e-174 621.0
20 TraesCS4B01G223100 chr7A 85.833 600 60 19 4 592 654827626 654828211 8.230000e-172 614.0
21 TraesCS4B01G223100 chr7A 85.497 593 67 18 4 590 77730620 77731199 6.410000e-168 601.0
22 TraesCS4B01G223100 chr1A 78.947 114 22 2 3894 4007 560439203 560439092 4.800000e-10 76.8


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 TraesCS4B01G223100 chr4B 467795597 467800072 4475 False 8266.00 8266 100.0000 1 4476 1 chr4B.!!$F1 4475
1 TraesCS4B01G223100 chr4A 83403567 83406654 3087 True 4505.00 4505 93.0080 594 3697 1 chr4A.!!$R2 3103
2 TraesCS4B01G223100 chr4A 83397712 83398475 763 True 1099.00 1099 92.5880 3705 4472 1 chr4A.!!$R1 767
3 TraesCS4B01G223100 chr4D 380336196 380344877 8681 False 1424.75 2453 93.7105 591 4476 4 chr4D.!!$F1 3885
4 TraesCS4B01G223100 chr2B 735407914 735408506 592 True 880.00 880 93.4450 1 593 1 chr2B.!!$R1 592
5 TraesCS4B01G223100 chr5B 496571299 496571887 588 True 872.00 872 93.4230 1 590 1 chr5B.!!$R1 589
6 TraesCS4B01G223100 chr6B 158281688 158282273 585 False 800.00 800 91.3710 4 590 1 chr6B.!!$F1 586
7 TraesCS4B01G223100 chr5D 412616108 412616689 581 False 671.00 671 87.5840 4 591 1 chr5D.!!$F3 587
8 TraesCS4B01G223100 chr5D 73463380 73463962 582 False 610.00 610 85.7140 4 590 1 chr5D.!!$F2 586
9 TraesCS4B01G223100 chr3B 556084147 556084738 591 False 652.00 652 86.8770 4 592 1 chr3B.!!$F2 588
10 TraesCS4B01G223100 chr3D 597280782 597281347 565 False 621.00 621 86.5750 17 590 1 chr3D.!!$F1 573
11 TraesCS4B01G223100 chr7A 654827626 654828211 585 False 614.00 614 85.8330 4 592 1 chr7A.!!$F2 588
12 TraesCS4B01G223100 chr7A 77730620 77731199 579 False 601.00 601 85.4970 4 590 1 chr7A.!!$F1 586

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
886 921 0.377554 ACATTAGAGCTCGGTCGTCG 59.622 55.0 8.37 0.0 40.90 5.12 F
1574 1616 0.038599 ACTGTGCCCTGCATTGATGA 59.961 50.0 0.00 0.0 41.91 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 3472 0.250513 CAGTAACAGTCCCTGCTCCC 59.749 60.0 0.00 0.0 34.37 4.30 R
3490 4304 0.247460 ACGCAATGCAGAGTCAGCTA 59.753 50.0 5.91 0.0 0.00 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
113 114 2.163509 CTTGGTGAGGAGAGACTCGAA 58.836 52.381 0.00 0.00 40.39 3.71
364 369 2.400158 CGAACGCGAGAGAGAGGGT 61.400 63.158 15.93 0.00 40.82 4.34
375 380 1.700739 GAGAGAGGGTATCGGGAGAGA 59.299 57.143 0.00 0.00 45.48 3.10
433 451 6.846988 AGGAAGAAGGACTTTTCTTTCAGAT 58.153 36.000 8.92 0.00 45.00 2.90
613 639 7.093814 ACAATTGCTATATTGAGCCACTTCAAA 60.094 33.333 5.05 0.00 42.11 2.69
624 650 2.094545 GCCACTTCAAATTCGGAATGCT 60.095 45.455 3.59 0.00 0.00 3.79
629 655 3.071874 TCAAATTCGGAATGCTGAGGT 57.928 42.857 3.59 0.00 0.00 3.85
635 661 0.824109 CGGAATGCTGAGGTCACCTA 59.176 55.000 0.00 0.00 31.76 3.08
660 686 1.756538 CTTTGGGGTGCAAACTGAGTT 59.243 47.619 0.00 0.00 0.00 3.01
682 708 1.870402 CACACTACCGTGCATTGTTCA 59.130 47.619 0.00 0.00 45.10 3.18
760 786 4.142182 CCCCAATTATACAGCTGTTGTTGG 60.142 45.833 27.06 27.51 41.29 3.77
784 810 6.650390 GGAGATGCTCTTAGATTGATCTTTCC 59.350 42.308 0.00 0.00 38.32 3.13
801 827 6.928979 TCTTTCCGTTGTTTGTCAAATCTA 57.071 33.333 0.40 0.00 37.81 1.98
841 875 4.202080 CCACCATGTGCCATATTTTCTGAG 60.202 45.833 0.00 0.00 31.34 3.35
873 907 2.677836 CACCGTTGGATGGTCACATTAG 59.322 50.000 0.00 0.00 34.66 1.73
883 918 1.534175 GGTCACATTAGAGCTCGGTCG 60.534 57.143 8.37 1.28 33.41 4.79
886 921 0.377554 ACATTAGAGCTCGGTCGTCG 59.622 55.000 8.37 0.00 40.90 5.12
922 958 2.270986 CCAACTGCCTGCCTCCAAC 61.271 63.158 0.00 0.00 0.00 3.77
959 995 0.884704 TGAGGCTCGCAAACTTCCAC 60.885 55.000 10.42 0.00 0.00 4.02
1065 1104 2.916502 TACCCATGATCACCGTGCGC 62.917 60.000 0.00 0.00 0.00 6.09
1124 1163 2.203195 GCGTCTATGGCCATGGCA 60.203 61.111 36.56 23.14 44.11 4.92
1289 1328 3.397317 GTGCGCGCAAAAAGGCTG 61.397 61.111 38.24 0.00 0.00 4.85
1304 1343 4.389576 CTGCAACGCCCGTTCTGC 62.390 66.667 9.76 9.76 36.00 4.26
1323 1362 2.007608 GCGGAGGTTACCACTTGATTC 58.992 52.381 3.51 0.00 0.00 2.52
1452 1491 8.110860 AGAATCAAATTGACAATTCCGTAAGT 57.889 30.769 13.68 0.00 0.00 2.24
1453 1492 8.576442 AGAATCAAATTGACAATTCCGTAAGTT 58.424 29.630 13.68 3.43 0.00 2.66
1510 1549 9.959721 TTAAGTTTGCTGAAGTAAGATTAGGAT 57.040 29.630 0.00 0.00 0.00 3.24
1549 1590 4.883585 ACATGCTGACTGAAACTGAAAGAA 59.116 37.500 0.00 0.00 37.43 2.52
1574 1616 0.038599 ACTGTGCCCTGCATTGATGA 59.961 50.000 0.00 0.00 41.91 2.92
1695 1737 5.590259 CCCTTCGATTGATGTCCTAATTTGT 59.410 40.000 0.00 0.00 0.00 2.83
1697 1739 7.362920 CCCTTCGATTGATGTCCTAATTTGTTT 60.363 37.037 0.00 0.00 0.00 2.83
1703 1745 6.817765 TGATGTCCTAATTTGTTTCACTCC 57.182 37.500 0.00 0.00 0.00 3.85
1740 1782 1.434555 TCGTTTCAATGGCACGGTAG 58.565 50.000 0.00 0.00 34.61 3.18
1764 1806 7.441836 AGACACACTACATGTAAAATGAGACA 58.558 34.615 7.06 0.00 40.64 3.41
1769 1811 9.120538 ACACTACATGTAAAATGAGACAAACTT 57.879 29.630 7.06 0.00 40.88 2.66
1784 1827 6.314917 AGACAAACTTATGGGATTTGGAAGT 58.685 36.000 0.00 0.00 37.59 3.01
1854 1898 5.457140 CGGTTAGTTTAGCTTGCATTTTGA 58.543 37.500 0.00 0.00 0.00 2.69
1908 2713 7.776030 TCTCCATGTTTGGTAGTCTTGTTTTAA 59.224 33.333 0.00 0.00 44.06 1.52
1919 2724 7.444487 GGTAGTCTTGTTTTAACTGGAATGACT 59.556 37.037 0.00 0.00 35.59 3.41
1999 2805 9.606631 TTAACTGAATAATTTTGTTTTGCACCT 57.393 25.926 0.00 0.00 0.00 4.00
2001 2807 8.816640 ACTGAATAATTTTGTTTTGCACCTAG 57.183 30.769 0.00 0.00 0.00 3.02
2066 2872 1.076841 TCAGTGAAATGGGATTGGGCA 59.923 47.619 0.00 0.00 0.00 5.36
2084 2890 1.293924 CAGCGGCCTGTATCTTGAAG 58.706 55.000 0.00 0.00 34.31 3.02
2276 3082 1.202099 TGGCAATAGAACCGGGTGGA 61.202 55.000 6.32 0.00 39.21 4.02
2351 3159 8.394893 AACTATTCGTTTGATTGCACAAGGCA 62.395 38.462 0.00 0.00 41.63 4.75
2527 3336 2.738587 TCGGAAGAGGATGACTAGCT 57.261 50.000 0.00 0.00 34.84 3.32
2545 3354 9.049523 TGACTAGCTATAGCAAAATCAAATGAG 57.950 33.333 26.07 7.94 45.16 2.90
2550 3359 7.228308 AGCTATAGCAAAATCAAATGAGGACTC 59.772 37.037 26.07 0.00 45.16 3.36
2559 3368 0.257039 AATGAGGACTCCATGGTGCC 59.743 55.000 12.58 14.35 0.00 5.01
2563 3372 2.673523 GACTCCATGGTGCCTGCT 59.326 61.111 12.58 0.00 0.00 4.24
2598 3407 7.461182 TTCTTTTCCTTTTTCTCTGTGTCAA 57.539 32.000 0.00 0.00 0.00 3.18
2714 3523 4.024556 GGCAATGGTGAATCTGAAGTATCG 60.025 45.833 0.00 0.00 0.00 2.92
2759 3568 0.179181 GCTCATTGACATGCACCACG 60.179 55.000 0.00 0.00 0.00 4.94
2954 3763 5.895534 ACTTGAAGCCATCATAATGTGGATT 59.104 36.000 0.00 3.14 45.96 3.01
2958 3767 7.042950 TGAAGCCATCATAATGTGGATTTTTG 58.957 34.615 4.69 0.00 43.57 2.44
3010 3819 2.352715 GCTGGCCCATAGTGTTTTTCAC 60.353 50.000 0.00 0.00 46.46 3.18
3033 3842 5.104360 ACATTGTATAGGAACCTGTCATGCT 60.104 40.000 3.36 0.00 0.00 3.79
3053 3862 1.077005 TGGGACCTTGCCTTTTATGCT 59.923 47.619 0.00 0.00 0.00 3.79
3054 3863 2.179427 GGGACCTTGCCTTTTATGCTT 58.821 47.619 0.00 0.00 0.00 3.91
3057 3866 4.245660 GGACCTTGCCTTTTATGCTTTTC 58.754 43.478 0.00 0.00 0.00 2.29
3058 3867 4.245660 GACCTTGCCTTTTATGCTTTTCC 58.754 43.478 0.00 0.00 0.00 3.13
3060 3869 4.347876 ACCTTGCCTTTTATGCTTTTCCTT 59.652 37.500 0.00 0.00 0.00 3.36
3061 3870 4.692155 CCTTGCCTTTTATGCTTTTCCTTG 59.308 41.667 0.00 0.00 0.00 3.61
3062 3871 5.511202 CCTTGCCTTTTATGCTTTTCCTTGA 60.511 40.000 0.00 0.00 0.00 3.02
3063 3872 5.743636 TGCCTTTTATGCTTTTCCTTGAT 57.256 34.783 0.00 0.00 0.00 2.57
3065 3874 7.238486 TGCCTTTTATGCTTTTCCTTGATAA 57.762 32.000 0.00 0.00 0.00 1.75
3094 3903 8.995027 ATTGAATATACCTGTTTCTTATGCCA 57.005 30.769 0.00 0.00 0.00 4.92
3163 3972 5.877012 GCTTGAACAAAGGAGATGTCTGATA 59.123 40.000 0.00 0.00 36.30 2.15
3261 4072 4.543689 ACGGTAAGGTGAGGAATCTGATA 58.456 43.478 0.00 0.00 0.00 2.15
3262 4073 5.148502 ACGGTAAGGTGAGGAATCTGATAT 58.851 41.667 0.00 0.00 0.00 1.63
3267 4078 9.041354 GGTAAGGTGAGGAATCTGATATCTAAT 57.959 37.037 3.98 0.00 0.00 1.73
3441 4252 9.206870 GGCAAAGATGATATTTTCTTGTTGAAA 57.793 29.630 2.82 0.00 42.33 2.69
3486 4300 4.213482 GCGTGTTCTTTCCAATGTAGAAGT 59.787 41.667 0.00 0.00 0.00 3.01
3490 4304 7.170998 CGTGTTCTTTCCAATGTAGAAGTTAGT 59.829 37.037 0.00 0.00 0.00 2.24
3577 5743 3.960102 AGGATGTCAACTTTTCAGCCAAA 59.040 39.130 0.00 0.00 39.69 3.28
3661 8541 2.965831 ACTGTTGACCTAAGAGCACAGA 59.034 45.455 4.19 0.00 33.14 3.41
3759 8639 3.644265 TCTGGTTTGTCCTAGCAAGTGTA 59.356 43.478 0.00 0.00 37.07 2.90
3819 8699 7.911651 TCTGATGAAGTAACAGAAGGATTTCT 58.088 34.615 0.00 0.00 44.45 2.52
3866 8746 1.001503 AGAGGGCTCTCCACCTGAG 59.998 63.158 10.85 0.00 40.83 3.35
3869 8749 0.907230 AGGGCTCTCCACCTGAGTTC 60.907 60.000 0.00 0.00 42.12 3.01
3879 8759 5.248248 TCTCCACCTGAGTTCACATCATTTA 59.752 40.000 0.00 0.00 42.12 1.40
3880 8760 5.875224 TCCACCTGAGTTCACATCATTTAA 58.125 37.500 0.00 0.00 0.00 1.52
3930 8810 5.881777 GGAGACCAGATTGAAAACCTAAC 57.118 43.478 0.00 0.00 0.00 2.34
3935 8815 6.043243 AGACCAGATTGAAAACCTAACAGAGA 59.957 38.462 0.00 0.00 0.00 3.10
3968 8848 3.370104 TGAGGAAAACCAGGCTGAAAAA 58.630 40.909 17.94 0.00 0.00 1.94
3988 8868 1.447317 CCACACAAGCAACGAAGCCT 61.447 55.000 0.00 0.00 34.23 4.58
3989 8869 0.381801 CACACAAGCAACGAAGCCTT 59.618 50.000 0.00 0.00 34.23 4.35
3990 8870 0.381801 ACACAAGCAACGAAGCCTTG 59.618 50.000 0.00 0.00 34.23 3.61
3995 8875 0.320771 AGCAACGAAGCCTTGTCGAT 60.321 50.000 0.18 0.00 41.02 3.59
4013 8893 3.321682 TCGATCATCTGACACATGCCATA 59.678 43.478 0.00 0.00 0.00 2.74
4019 8899 1.929169 CTGACACATGCCATAGTCACG 59.071 52.381 7.76 2.88 36.20 4.35
4022 8902 0.923403 CACATGCCATAGTCACGACG 59.077 55.000 0.00 0.00 36.20 5.12
4027 8907 1.000052 TGCCATAGTCACGACGAACAA 60.000 47.619 0.00 0.00 36.20 2.83
4060 8941 4.235079 TCAAGAGATTACAACATGGGGG 57.765 45.455 0.00 0.00 0.00 5.40
4061 8942 2.689983 CAAGAGATTACAACATGGGGGC 59.310 50.000 0.00 0.00 0.00 5.80
4062 8943 1.922447 AGAGATTACAACATGGGGGCA 59.078 47.619 0.00 0.00 0.00 5.36
4066 8947 2.685106 TTACAACATGGGGGCAGAAA 57.315 45.000 0.00 0.00 0.00 2.52
4067 8948 2.214376 TACAACATGGGGGCAGAAAG 57.786 50.000 0.00 0.00 0.00 2.62
4081 8962 2.230025 GCAGAAAGGAAAAGAGGGAAGC 59.770 50.000 0.00 0.00 0.00 3.86
4082 8963 3.490348 CAGAAAGGAAAAGAGGGAAGCA 58.510 45.455 0.00 0.00 0.00 3.91
4114 8995 2.902423 AAAGCACGACCCAGTTGGCA 62.902 55.000 0.00 0.00 37.83 4.92
4218 9099 1.038280 GTAGGTGTCGGTATCCCCAG 58.962 60.000 0.00 0.00 0.00 4.45
4221 9102 1.153429 GTGTCGGTATCCCCAGTGC 60.153 63.158 0.00 0.00 0.00 4.40
4277 9158 0.108138 GACCGCAAGCTCCACTACAT 60.108 55.000 0.00 0.00 0.00 2.29
4294 9175 6.018425 CCACTACATTGAGCATGATACAAGAC 60.018 42.308 0.00 0.00 36.24 3.01
4339 9220 1.606668 TGAACACGAACCTTGAATGGC 59.393 47.619 0.00 0.00 0.00 4.40
4383 9264 1.053264 ACATTTTGCAAGGTGGGGCA 61.053 50.000 14.99 0.00 38.46 5.36
4399 9280 1.303561 GCAAGCATCCTGGTCACCA 60.304 57.895 0.00 0.00 0.00 4.17
4432 9313 0.739561 AACCGAGATAGTGGCGAGAC 59.260 55.000 0.00 0.00 0.00 3.36
4460 9341 2.172505 AGTCATCACAACACTTCCACCA 59.827 45.455 0.00 0.00 0.00 4.17
4462 9343 2.172505 TCATCACAACACTTCCACCACT 59.827 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 311 0.963355 AGCCAAATTTAGCCGCCGAA 60.963 50.000 4.91 0.00 0.00 4.30
314 318 4.261197 GGTAATCAGAGCCAAATTTAGCCG 60.261 45.833 4.91 0.00 0.00 5.52
364 369 0.478942 CTCACCCCTCTCTCCCGATA 59.521 60.000 0.00 0.00 0.00 2.92
375 380 4.988716 TCGTGCGTCCTCACCCCT 62.989 66.667 0.00 0.00 33.57 4.79
433 451 6.433847 TTCAAACTCTCACCTAATCCTTCA 57.566 37.500 0.00 0.00 0.00 3.02
613 639 1.407437 GGTGACCTCAGCATTCCGAAT 60.407 52.381 0.00 0.00 43.34 3.34
682 708 2.526873 AGAACACAGGCCTCCGGT 60.527 61.111 0.00 0.00 30.78 5.28
696 722 0.534203 GTTCCTTCGGTGTGCCAGAA 60.534 55.000 0.00 0.00 34.09 3.02
699 725 2.112297 GGTTCCTTCGGTGTGCCA 59.888 61.111 0.00 0.00 34.09 4.92
760 786 6.365789 CGGAAAGATCAATCTAAGAGCATCTC 59.634 42.308 0.00 0.00 40.01 2.75
801 827 2.562738 GGTGGCCAGCTCAATTAGTTTT 59.437 45.455 27.63 0.00 0.00 2.43
810 836 2.034532 CACATGGTGGCCAGCTCA 59.965 61.111 33.29 19.53 36.75 4.26
841 875 0.951040 CCAACGGTGAAGAGTGCTCC 60.951 60.000 0.00 0.00 0.00 4.70
873 907 4.838486 CTGCCGACGACCGAGCTC 62.838 72.222 2.73 2.73 41.76 4.09
922 958 2.234908 CTCACAACTCTCTACCCTTGGG 59.765 54.545 3.77 3.77 0.00 4.12
959 995 4.525996 TCGGATATGGGCATTATCCATTG 58.474 43.478 19.15 8.13 41.87 2.82
1124 1163 1.609794 GAGTCGGGAGGAGGTGGTT 60.610 63.158 0.00 0.00 0.00 3.67
1278 1317 2.930628 GCGTTGCAGCCTTTTTGC 59.069 55.556 0.00 0.00 41.86 3.68
1304 1343 2.629051 GGAATCAAGTGGTAACCTCCG 58.371 52.381 0.00 0.00 0.00 4.63
1323 1362 1.076332 CTCGTTAAAACTCGGCAGGG 58.924 55.000 0.00 0.00 0.00 4.45
1407 1446 0.859232 CGTAGAAAATCGGGATGCCG 59.141 55.000 21.08 21.08 0.00 5.69
1469 1508 7.116233 CAGCAAACTTAATTGTCCAAATACCAC 59.884 37.037 0.00 0.00 32.80 4.16
1531 1572 7.281100 AGTTTAGGTTCTTTCAGTTTCAGTCAG 59.719 37.037 0.00 0.00 0.00 3.51
1549 1590 0.405585 ATGCAGGGCACAGTTTAGGT 59.594 50.000 0.00 0.00 43.04 3.08
1668 1710 1.160329 GGACATCAATCGAAGGGGCG 61.160 60.000 0.00 0.00 0.00 6.13
1670 1712 3.838244 TTAGGACATCAATCGAAGGGG 57.162 47.619 0.00 0.00 0.00 4.79
1740 1782 7.652300 TGTCTCATTTTACATGTAGTGTGTC 57.348 36.000 5.56 6.53 42.24 3.67
1764 1806 6.994421 AACACTTCCAAATCCCATAAGTTT 57.006 33.333 0.00 0.00 0.00 2.66
1769 1811 7.726291 TCAACTTTAACACTTCCAAATCCCATA 59.274 33.333 0.00 0.00 0.00 2.74
1770 1812 6.553100 TCAACTTTAACACTTCCAAATCCCAT 59.447 34.615 0.00 0.00 0.00 4.00
1814 1858 6.510536 ACTAACCGGCTGTTACATCTTATAC 58.489 40.000 0.00 0.00 38.42 1.47
1829 1873 1.161843 TGCAAGCTAAACTAACCGGC 58.838 50.000 0.00 0.00 0.00 6.13
1854 1898 9.153721 CAAATATAATGCAAGTGTGAAACCAAT 57.846 29.630 0.00 0.00 34.36 3.16
2066 2872 1.195115 TCTTCAAGATACAGGCCGCT 58.805 50.000 0.00 0.00 0.00 5.52
2227 3033 5.818678 TTAAGAACTAGCTGGAAAGTGGA 57.181 39.130 3.17 0.00 0.00 4.02
2276 3082 3.771577 AACGACTGAATTCTCCCAACT 57.228 42.857 7.05 0.00 0.00 3.16
2320 3128 7.023575 GTGCAATCAAACGAATAGTTGAAGAT 58.976 34.615 0.00 0.00 43.37 2.40
2326 3134 5.460646 CCTTGTGCAATCAAACGAATAGTT 58.539 37.500 0.00 0.00 46.76 2.24
2351 3159 6.710597 ACATCATCAGCTTCATTGCTTAAT 57.289 33.333 0.00 0.00 41.98 1.40
2360 3168 8.886719 CATACTCTTTTAACATCATCAGCTTCA 58.113 33.333 0.00 0.00 0.00 3.02
2527 3336 7.345691 TGGAGTCCTCATTTGATTTTGCTATA 58.654 34.615 11.33 0.00 0.00 1.31
2545 3354 2.439156 GCAGGCACCATGGAGTCC 60.439 66.667 21.47 15.90 0.00 3.85
2559 3368 4.860907 GGAAAAGAATAATGTGTGCAGCAG 59.139 41.667 0.00 0.00 0.00 4.24
2563 3372 8.203485 AGAAAAAGGAAAAGAATAATGTGTGCA 58.797 29.630 0.00 0.00 0.00 4.57
2663 3472 0.250513 CAGTAACAGTCCCTGCTCCC 59.749 60.000 0.00 0.00 34.37 4.30
2690 3499 2.086869 ACTTCAGATTCACCATTGCCG 58.913 47.619 0.00 0.00 0.00 5.69
2714 3523 1.195448 CCATCGCAGTTGACACACTTC 59.805 52.381 0.00 0.00 0.00 3.01
3010 3819 5.237996 CAGCATGACAGGTTCCTATACAATG 59.762 44.000 0.00 0.00 39.69 2.82
3033 3842 1.077005 AGCATAAAAGGCAAGGTCCCA 59.923 47.619 0.00 0.00 0.00 4.37
3081 3890 7.701445 CCAAAAATGTTTTGGCATAAGAAACA 58.299 30.769 17.12 15.28 44.45 2.83
3261 4072 8.888419 ACCAAGTATTCAGGATCATCATTAGAT 58.112 33.333 0.00 0.00 33.87 1.98
3262 4073 8.152898 CACCAAGTATTCAGGATCATCATTAGA 58.847 37.037 0.00 0.00 0.00 2.10
3267 4078 5.674525 GTCACCAAGTATTCAGGATCATCA 58.325 41.667 0.00 0.00 0.00 3.07
3274 4085 3.618594 CACATCGTCACCAAGTATTCAGG 59.381 47.826 0.00 0.00 0.00 3.86
3359 4170 4.191544 AGTGTGCATGTACATCCATACAC 58.808 43.478 23.62 22.59 38.85 2.90
3441 4252 7.661968 ACGCTATGTGACATATATTGAGAACT 58.338 34.615 5.65 0.00 0.00 3.01
3442 4253 7.875316 ACGCTATGTGACATATATTGAGAAC 57.125 36.000 5.65 0.00 0.00 3.01
3486 4300 3.525537 GCAATGCAGAGTCAGCTACTAA 58.474 45.455 9.11 0.00 39.07 2.24
3490 4304 0.247460 ACGCAATGCAGAGTCAGCTA 59.753 50.000 5.91 0.00 0.00 3.32
3577 5743 7.552687 CACTATTGTGTTACATCCACTAACCAT 59.447 37.037 0.00 0.00 39.24 3.55
3641 5807 3.667497 TCTGTGCTCTTAGGTCAACAG 57.333 47.619 0.00 0.00 0.00 3.16
3759 8639 9.190317 TCCTACGATGCATTACTAGATTATCAT 57.810 33.333 0.00 0.00 0.00 2.45
3819 8699 6.349280 CGGCCTGACAGATTCAAAAAGAATAA 60.349 38.462 3.32 0.00 46.76 1.40
3887 8767 9.315363 GTCTCCCTCTTAAATTGGATCTATCTA 57.685 37.037 0.00 0.00 0.00 1.98
3904 8784 3.009584 GGTTTTCAATCTGGTCTCCCTCT 59.990 47.826 0.00 0.00 0.00 3.69
3930 8810 6.985653 TTCCTCATAAATAGGGTCTCTCTG 57.014 41.667 0.00 0.00 34.66 3.35
3935 8815 6.353951 CCTGGTTTTCCTCATAAATAGGGTCT 60.354 42.308 0.00 0.00 41.38 3.85
3968 8848 1.724582 GGCTTCGTTGCTTGTGTGGT 61.725 55.000 2.92 0.00 0.00 4.16
3988 8868 2.931969 GCATGTGTCAGATGATCGACAA 59.068 45.455 13.91 10.75 43.40 3.18
3989 8869 2.543641 GCATGTGTCAGATGATCGACA 58.456 47.619 13.91 13.35 39.77 4.35
3990 8870 1.863454 GGCATGTGTCAGATGATCGAC 59.137 52.381 13.91 9.42 0.00 4.20
3995 8875 3.451902 TGACTATGGCATGTGTCAGATGA 59.548 43.478 24.28 9.72 34.94 2.92
4013 8893 3.191669 TCATTGTTTGTTCGTCGTGACT 58.808 40.909 0.00 0.00 0.00 3.41
4019 8899 5.356882 TGATTCCTCATTGTTTGTTCGTC 57.643 39.130 0.00 0.00 0.00 4.20
4022 8902 7.206981 TCTCTTGATTCCTCATTGTTTGTTC 57.793 36.000 0.00 0.00 0.00 3.18
4027 8907 8.734386 GTTGTAATCTCTTGATTCCTCATTGTT 58.266 33.333 0.00 0.00 41.55 2.83
4060 8941 2.230025 GCTTCCCTCTTTTCCTTTCTGC 59.770 50.000 0.00 0.00 0.00 4.26
4061 8942 3.490348 TGCTTCCCTCTTTTCCTTTCTG 58.510 45.455 0.00 0.00 0.00 3.02
4062 8943 3.499382 CCTGCTTCCCTCTTTTCCTTTCT 60.499 47.826 0.00 0.00 0.00 2.52
4066 8947 1.074566 CACCTGCTTCCCTCTTTTCCT 59.925 52.381 0.00 0.00 0.00 3.36
4067 8948 1.539157 CACCTGCTTCCCTCTTTTCC 58.461 55.000 0.00 0.00 0.00 3.13
4081 8962 0.675083 TGCTTTGTCATTGGCACCTG 59.325 50.000 0.00 0.00 0.00 4.00
4082 8963 0.675633 GTGCTTTGTCATTGGCACCT 59.324 50.000 11.73 0.00 46.17 4.00
4114 8995 2.481276 CGTGGTGATGATCGGTGTGTAT 60.481 50.000 0.00 0.00 0.00 2.29
4175 9056 3.739519 CGGGTGTTCTGGAAATTTGCAAA 60.740 43.478 15.44 15.44 0.00 3.68
4218 9099 3.666374 GCATCTGCTCATTTATAGCGCAC 60.666 47.826 11.47 0.00 43.11 5.34
4277 9158 5.111989 GCACTAGTCTTGTATCATGCTCAA 58.888 41.667 0.00 0.00 0.00 3.02
4339 9220 1.888436 TTGTCCCGGTAGCAGAGCTG 61.888 60.000 0.00 0.00 40.10 4.24
4363 9244 0.972883 GCCCCACCTTGCAAAATGTA 59.027 50.000 0.00 0.00 0.00 2.29
4370 9251 3.831727 ATGCTTGCCCCACCTTGCA 62.832 57.895 0.00 0.00 35.27 4.08
4383 9264 1.548582 CCTTTGGTGACCAGGATGCTT 60.549 52.381 3.77 0.00 33.81 3.91
4399 9280 2.162681 CTCGGTTGATCTTTGCCCTTT 58.837 47.619 0.00 0.00 0.00 3.11
4432 9313 5.443185 AAGTGTTGTGATGACTTTCATGG 57.557 39.130 0.00 0.00 37.20 3.66


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

AutoCloner maintained by Alex Coulton.