Multiple sequence alignment - TraesCS1B01G266400

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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 TraesCS1B01G266400 chr1B 100.000 5189 0 0 1 5189 468501657 468506845 0.000000e+00 9583.0
1 TraesCS1B01G266400 chr7B 96.590 3138 74 9 1550 4679 126777323 126780435 0.000000e+00 5171.0
2 TraesCS1B01G266400 chrUn 96.240 3138 91 7 1550 4679 16578556 16581674 0.000000e+00 5116.0
3 TraesCS1B01G266400 chr1D 94.046 3275 134 27 1963 5182 347396253 347399521 0.000000e+00 4911.0
4 TraesCS1B01G266400 chr1D 96.210 1029 31 1 907 1927 347395230 347396258 0.000000e+00 1677.0
5 TraesCS1B01G266400 chr1A 94.088 1607 63 6 1745 3349 448009330 448010906 0.000000e+00 2412.0
6 TraesCS1B01G266400 chr1A 94.793 845 39 4 907 1748 448007879 448008721 0.000000e+00 1312.0
7 TraesCS1B01G266400 chr1A 84.459 296 26 6 3931 4209 448017228 448017520 1.840000e-69 274.0
8 TraesCS1B01G266400 chr6A 87.851 1531 135 24 1975 3497 23888307 23889794 0.000000e+00 1749.0
9 TraesCS1B01G266400 chr6D 86.805 1546 136 39 1975 3497 25782036 25783536 0.000000e+00 1663.0
10 TraesCS1B01G266400 chr6D 90.759 909 64 10 1 894 439489320 439488417 0.000000e+00 1195.0
11 TraesCS1B01G266400 chr6D 85.848 643 80 6 958 1599 25781042 25781674 0.000000e+00 673.0
12 TraesCS1B01G266400 chr6B 86.537 1545 142 29 1975 3496 41992290 41993791 0.000000e+00 1640.0
13 TraesCS1B01G266400 chr6B 87.091 581 67 6 1020 1599 41991359 41991932 0.000000e+00 651.0
14 TraesCS1B01G266400 chr2D 91.695 879 51 10 1 859 92867543 92868419 0.000000e+00 1199.0
15 TraesCS1B01G266400 chr2B 90.731 917 57 14 1 894 781116209 781117120 0.000000e+00 1197.0
16 TraesCS1B01G266400 chr2B 89.462 873 77 7 2 859 757191683 757192555 0.000000e+00 1088.0
17 TraesCS1B01G266400 chr2B 90.493 831 47 14 1 822 681944470 681945277 0.000000e+00 1068.0
18 TraesCS1B01G266400 chr2B 86.579 909 101 12 1 894 75909509 75910411 0.000000e+00 983.0
19 TraesCS1B01G266400 chr2B 86.359 909 103 16 1 894 798666191 798665289 0.000000e+00 972.0
20 TraesCS1B01G266400 chr2B 86.123 908 103 17 1 894 111305520 111306418 0.000000e+00 957.0
21 TraesCS1B01G266400 chr5B 89.716 914 72 14 1 894 659761132 659760221 0.000000e+00 1147.0
22 TraesCS1B01G266400 chr5B 85.576 929 96 17 1 909 362773779 362774689 0.000000e+00 939.0
23 TraesCS1B01G266400 chr5B 84.930 929 104 13 1 909 362805641 362806553 0.000000e+00 907.0
24 TraesCS1B01G266400 chr3B 83.721 258 42 0 2053 2310 463112486 463112229 1.440000e-60 244.0
25 TraesCS1B01G266400 chr3B 78.676 408 56 18 2946 3346 463111511 463111128 5.190000e-60 243.0
26 TraesCS1B01G266400 chr3B 82.564 195 31 3 1395 1588 463113303 463113111 8.940000e-38 169.0
27 TraesCS1B01G266400 chr3A 83.721 258 42 0 2053 2310 477589633 477589376 1.440000e-60 244.0
28 TraesCS1B01G266400 chr3A 78.431 408 57 18 2946 3346 477586465 477586082 2.420000e-58 237.0
29 TraesCS1B01G266400 chr5D 92.683 41 3 0 4633 4673 370727625 370727585 5.610000e-05 60.2


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 TraesCS1B01G266400 chr1B 468501657 468506845 5188 False 9583.000000 9583 100.000000 1 5189 1 chr1B.!!$F1 5188
1 TraesCS1B01G266400 chr7B 126777323 126780435 3112 False 5171.000000 5171 96.590000 1550 4679 1 chr7B.!!$F1 3129
2 TraesCS1B01G266400 chrUn 16578556 16581674 3118 False 5116.000000 5116 96.240000 1550 4679 1 chrUn.!!$F1 3129
3 TraesCS1B01G266400 chr1D 347395230 347399521 4291 False 3294.000000 4911 95.128000 907 5182 2 chr1D.!!$F1 4275
4 TraesCS1B01G266400 chr1A 448007879 448010906 3027 False 1862.000000 2412 94.440500 907 3349 2 chr1A.!!$F2 2442
5 TraesCS1B01G266400 chr6A 23888307 23889794 1487 False 1749.000000 1749 87.851000 1975 3497 1 chr6A.!!$F1 1522
6 TraesCS1B01G266400 chr6D 439488417 439489320 903 True 1195.000000 1195 90.759000 1 894 1 chr6D.!!$R1 893
7 TraesCS1B01G266400 chr6D 25781042 25783536 2494 False 1168.000000 1663 86.326500 958 3497 2 chr6D.!!$F1 2539
8 TraesCS1B01G266400 chr6B 41991359 41993791 2432 False 1145.500000 1640 86.814000 1020 3496 2 chr6B.!!$F1 2476
9 TraesCS1B01G266400 chr2D 92867543 92868419 876 False 1199.000000 1199 91.695000 1 859 1 chr2D.!!$F1 858
10 TraesCS1B01G266400 chr2B 781116209 781117120 911 False 1197.000000 1197 90.731000 1 894 1 chr2B.!!$F5 893
11 TraesCS1B01G266400 chr2B 757191683 757192555 872 False 1088.000000 1088 89.462000 2 859 1 chr2B.!!$F4 857
12 TraesCS1B01G266400 chr2B 681944470 681945277 807 False 1068.000000 1068 90.493000 1 822 1 chr2B.!!$F3 821
13 TraesCS1B01G266400 chr2B 75909509 75910411 902 False 983.000000 983 86.579000 1 894 1 chr2B.!!$F1 893
14 TraesCS1B01G266400 chr2B 798665289 798666191 902 True 972.000000 972 86.359000 1 894 1 chr2B.!!$R1 893
15 TraesCS1B01G266400 chr2B 111305520 111306418 898 False 957.000000 957 86.123000 1 894 1 chr2B.!!$F2 893
16 TraesCS1B01G266400 chr5B 659760221 659761132 911 True 1147.000000 1147 89.716000 1 894 1 chr5B.!!$R1 893
17 TraesCS1B01G266400 chr5B 362773779 362774689 910 False 939.000000 939 85.576000 1 909 1 chr5B.!!$F1 908
18 TraesCS1B01G266400 chr5B 362805641 362806553 912 False 907.000000 907 84.930000 1 909 1 chr5B.!!$F2 908
19 TraesCS1B01G266400 chr3B 463111128 463113303 2175 True 218.666667 244 81.653667 1395 3346 3 chr3B.!!$R1 1951
20 TraesCS1B01G266400 chr3A 477586082 477589633 3551 True 240.500000 244 81.076000 2053 3346 2 chr3A.!!$R1 1293

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
889 941 0.874607 ACTAGAATTTAGCGCGCCGG 60.875 55.000 30.33 11.73 0.00 6.13 F
1924 2928 1.202675 TCACACTGATCACAGCTTGCA 60.203 47.619 0.00 0.00 46.95 4.08 F
1925 2929 1.810755 CACACTGATCACAGCTTGCAT 59.189 47.619 0.00 0.00 46.95 3.96 F
3818 7429 1.075212 TGATGCCCTTTGTCCATGTGA 59.925 47.619 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 3278 2.385013 TCACATGTTCATCAGTCCCG 57.615 50.000 0.00 0.0 0.00 5.14 R
3400 6990 5.279708 GCCATCTAGTGCACCATTAGAGTAT 60.280 44.000 14.63 0.0 36.44 2.12 R
3863 7474 6.951198 AGAGGAAGAGAGAGAACACATTTCTA 59.049 38.462 0.00 0.0 0.00 2.10 R
5011 8669 0.039527 GGGTCACCGCATTGTTGAAC 60.040 55.000 0.00 0.0 0.00 3.18 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
529 533 1.067212 GCTCGATACCTCGGACAACAT 59.933 52.381 0.00 0.00 45.10 2.71
767 809 1.593196 ATATTGTGGCATTAGCGCGT 58.407 45.000 8.43 0.00 43.41 6.01
866 918 2.805353 CTGGCGAAGGACGTGTCG 60.805 66.667 0.00 0.00 44.60 4.35
889 941 0.874607 ACTAGAATTTAGCGCGCCGG 60.875 55.000 30.33 11.73 0.00 6.13
890 942 2.159272 CTAGAATTTAGCGCGCCGGC 62.159 60.000 30.33 19.07 0.00 6.13
944 996 2.295885 CCAAAGAGCTCATGGGTCATC 58.704 52.381 23.97 2.24 44.16 2.92
974 1029 1.670059 AACCCCAAACCCAAAAACCA 58.330 45.000 0.00 0.00 0.00 3.67
1065 1128 1.339151 GGCGAGAACTTGGTCCTCATT 60.339 52.381 0.00 0.00 0.00 2.57
1669 1848 5.344665 TGCTAATAAGTTCAATTGCGTTTGC 59.655 36.000 0.00 3.02 43.20 3.68
1851 2847 1.205820 GCGGGTTGTGTCTTTACGC 59.794 57.895 0.00 0.00 38.70 4.42
1923 2927 1.516161 TCACACTGATCACAGCTTGC 58.484 50.000 0.00 0.00 46.95 4.01
1924 2928 1.202675 TCACACTGATCACAGCTTGCA 60.203 47.619 0.00 0.00 46.95 4.08
1925 2929 1.810755 CACACTGATCACAGCTTGCAT 59.189 47.619 0.00 0.00 46.95 3.96
1926 2930 3.004862 CACACTGATCACAGCTTGCATA 58.995 45.455 0.00 0.00 46.95 3.14
1927 2931 3.626217 CACACTGATCACAGCTTGCATAT 59.374 43.478 0.00 0.00 46.95 1.78
1928 2932 4.095932 CACACTGATCACAGCTTGCATATT 59.904 41.667 0.00 0.00 46.95 1.28
1929 2933 4.095932 ACACTGATCACAGCTTGCATATTG 59.904 41.667 0.00 0.00 46.95 1.90
1930 2934 3.066342 ACTGATCACAGCTTGCATATTGC 59.934 43.478 0.00 0.00 46.95 3.56
1931 2935 3.284617 TGATCACAGCTTGCATATTGCT 58.715 40.909 0.00 0.00 45.31 3.91
1939 2943 5.080969 AGCTTGCATATTGCTGATTGTTT 57.919 34.783 0.75 0.00 45.31 2.83
1940 2944 6.211587 AGCTTGCATATTGCTGATTGTTTA 57.788 33.333 0.75 0.00 45.31 2.01
1942 2946 7.270047 AGCTTGCATATTGCTGATTGTTTATT 58.730 30.769 0.75 0.00 45.31 1.40
1944 2948 9.033481 GCTTGCATATTGCTGATTGTTTATTTA 57.967 29.630 0.75 0.00 45.31 1.40
1953 2957 9.906660 TTGCTGATTGTTTATTTACTAGTTTGG 57.093 29.630 0.00 0.00 0.00 3.28
2163 3262 5.569355 TGTGCTGGATGAGGAAATTAAGAA 58.431 37.500 0.00 0.00 0.00 2.52
3108 6694 8.458052 GTTTGATCTTTTTCAACCATTGGTTTT 58.542 29.630 18.52 0.00 44.33 2.43
3568 7177 7.916450 CCTGCTAGAGTAGTTTGTGAATACTAC 59.084 40.741 0.00 0.00 44.44 2.73
3818 7429 1.075212 TGATGCCCTTTGTCCATGTGA 59.925 47.619 0.00 0.00 0.00 3.58
3905 7516 5.356882 TCCTCTCATTTTGTTAACAAGCG 57.643 39.130 19.72 12.73 37.15 4.68
4418 8031 1.291033 TCCCTGCCTTTCTAGAGCCTA 59.709 52.381 0.00 0.00 0.00 3.93
4426 8039 3.637229 CCTTTCTAGAGCCTATTGGACGA 59.363 47.826 0.00 0.00 34.57 4.20
4601 8214 0.251653 ACTCCTAACAGACGCTGGGA 60.252 55.000 10.80 7.24 35.51 4.37
4684 8298 5.532406 TGGAGATATGGCTTTAGCATGTTTC 59.468 40.000 3.88 0.21 44.36 2.78
4692 8306 3.181516 GCTTTAGCATGTTTCTCTCCACG 60.182 47.826 0.00 0.00 41.59 4.94
4706 8320 6.665992 TCTCTCCACGGTATAATTAATGCT 57.334 37.500 0.00 0.00 0.00 3.79
4709 8323 5.305902 TCTCCACGGTATAATTAATGCTCCA 59.694 40.000 0.00 0.00 0.00 3.86
4714 8328 7.148407 CCACGGTATAATTAATGCTCCAATCTC 60.148 40.741 0.00 0.00 0.00 2.75
4715 8329 7.387673 CACGGTATAATTAATGCTCCAATCTCA 59.612 37.037 0.00 0.00 0.00 3.27
4762 8397 4.702612 TCACTTCTCTCTACAACTAGCCTG 59.297 45.833 0.00 0.00 0.00 4.85
4768 8403 3.963374 TCTCTACAACTAGCCTGCATGAT 59.037 43.478 0.00 0.00 0.00 2.45
4790 8425 6.259387 TGATGATGCACATGTGATCTCTAAAC 59.741 38.462 29.80 8.59 39.56 2.01
4794 8429 4.455533 TGCACATGTGATCTCTAAACCAAC 59.544 41.667 29.80 6.70 0.00 3.77
4817 8452 5.463061 ACTGCATGCAACATCACTTAAAAAC 59.537 36.000 22.88 0.00 0.00 2.43
4828 8463 8.920509 ACATCACTTAAAAACAACACCTAAAC 57.079 30.769 0.00 0.00 0.00 2.01
4841 8476 2.916716 CACCTAAACGACAATGCATTGC 59.083 45.455 33.94 25.29 41.38 3.56
4846 8481 3.913548 AACGACAATGCATTGCAGTTA 57.086 38.095 33.15 0.00 43.65 2.24
4847 8482 4.439305 AACGACAATGCATTGCAGTTAT 57.561 36.364 33.15 19.70 43.65 1.89
4848 8483 4.439305 ACGACAATGCATTGCAGTTATT 57.561 36.364 33.94 16.50 43.65 1.40
4889 8524 3.910627 AGGTCTAAGGACAACTCCAATGT 59.089 43.478 0.00 0.00 43.77 2.71
4890 8525 4.351111 AGGTCTAAGGACAACTCCAATGTT 59.649 41.667 0.00 0.00 43.77 2.71
4908 8543 6.399880 CCAATGTTGTGCATTAAATCGAACAC 60.400 38.462 0.00 0.00 45.33 3.32
4917 8552 5.460419 GCATTAAATCGAACACACCAAACAA 59.540 36.000 0.00 0.00 0.00 2.83
4918 8553 6.019479 GCATTAAATCGAACACACCAAACAAA 60.019 34.615 0.00 0.00 0.00 2.83
4919 8554 6.872670 TTAAATCGAACACACCAAACAAAC 57.127 33.333 0.00 0.00 0.00 2.93
4920 8555 4.442375 AATCGAACACACCAAACAAACA 57.558 36.364 0.00 0.00 0.00 2.83
4938 8574 2.925170 CGGATAGGGAGGGGGCAG 60.925 72.222 0.00 0.00 0.00 4.85
4957 8593 0.386731 GCAAACGTCCGACCCATTTG 60.387 55.000 10.92 10.92 34.17 2.32
4959 8595 1.604755 CAAACGTCCGACCCATTTGAA 59.395 47.619 10.15 0.00 33.08 2.69
4965 8601 1.003812 TCCGACCCATTTGAAACGGAT 59.996 47.619 0.00 0.00 43.30 4.18
4969 8605 3.023832 GACCCATTTGAAACGGATGGAT 58.976 45.455 0.00 0.00 42.31 3.41
5033 8692 0.109179 CAACAATGCGGTGACCCATG 60.109 55.000 6.39 0.00 0.00 3.66
5041 8700 0.976073 CGGTGACCCATGGTAGAGGT 60.976 60.000 11.73 0.00 35.25 3.85
5051 8710 1.668826 TGGTAGAGGTTGATTGGCCT 58.331 50.000 3.32 0.00 37.91 5.19
5058 8717 0.744771 GGTTGATTGGCCTCGGAGTC 60.745 60.000 3.32 0.00 0.00 3.36
5065 8725 1.522580 GGCCTCGGAGTCTTGATGC 60.523 63.158 4.02 0.00 0.00 3.91
5072 8732 1.067283 CGGAGTCTTGATGCAGTCTGT 60.067 52.381 0.93 0.00 0.00 3.41
5082 8742 1.953559 TGCAGTCTGTGTTCTTCACC 58.046 50.000 0.93 0.00 45.61 4.02
5094 8754 5.066593 GTGTTCTTCACCTTCAGGATTTCT 58.933 41.667 0.00 0.00 40.84 2.52
5118 8778 9.581099 TCTCATTTGAAAAGGTTAAAACTTCAC 57.419 29.630 0.00 0.00 0.00 3.18
5120 8780 9.581099 TCATTTGAAAAGGTTAAAACTTCACTC 57.419 29.630 0.00 0.00 0.00 3.51
5154 8814 6.998074 GTCATCAACATCCTCCCAATAATGTA 59.002 38.462 0.00 0.00 32.28 2.29
5183 8844 7.448748 AAACATCCTCCCAATAATAATACGC 57.551 36.000 0.00 0.00 0.00 4.42
5184 8845 6.374417 ACATCCTCCCAATAATAATACGCT 57.626 37.500 0.00 0.00 0.00 5.07
5185 8846 6.173339 ACATCCTCCCAATAATAATACGCTG 58.827 40.000 0.00 0.00 0.00 5.18
5186 8847 4.575885 TCCTCCCAATAATAATACGCTGC 58.424 43.478 0.00 0.00 0.00 5.25
5187 8848 3.689649 CCTCCCAATAATAATACGCTGCC 59.310 47.826 0.00 0.00 0.00 4.85
5188 8849 4.323417 CTCCCAATAATAATACGCTGCCA 58.677 43.478 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
426 430 4.147701 GCACTGCGATAAGGCCAT 57.852 55.556 5.01 0.00 0.00 4.40
476 480 2.267642 CGCAGATCGTTGGGGGAA 59.732 61.111 0.00 0.00 0.00 3.97
529 533 1.413812 CACCATCATCATCCTCGGTGA 59.586 52.381 0.00 0.00 45.41 4.02
750 788 0.179166 CAACGCGCTAATGCCACAAT 60.179 50.000 5.73 0.00 35.36 2.71
755 793 0.801836 AAATGCAACGCGCTAATGCC 60.802 50.000 21.03 8.28 43.06 4.40
760 800 1.872029 CGTTAAAATGCAACGCGCTA 58.128 45.000 5.73 0.00 41.84 4.26
761 803 2.707192 CGTTAAAATGCAACGCGCT 58.293 47.368 5.73 0.00 41.84 5.92
767 809 1.006314 GCAGGCGCGTTAAAATGCAA 61.006 50.000 8.43 0.00 40.94 4.08
793 835 0.295470 GCTAAAATGCAATGCGCGTG 59.705 50.000 8.43 4.39 46.97 5.34
842 893 0.673644 CGTCCTTCGCCAGGTTTGAT 60.674 55.000 0.85 0.00 44.37 2.57
843 894 1.301401 CGTCCTTCGCCAGGTTTGA 60.301 57.895 0.85 0.00 44.37 2.69
866 918 3.600909 CGGCGCGCTAAATTCTAGTTTAC 60.601 47.826 32.29 6.92 0.00 2.01
890 942 3.965701 GAGCATCTCGAACGCGCG 61.966 66.667 30.96 30.96 37.46 6.86
944 996 2.948801 TTTGGGGTTTTGGGGTCGGG 62.949 60.000 0.00 0.00 0.00 5.14
974 1029 2.741878 TAGGCGGCGGAGGGGAATAT 62.742 60.000 9.78 0.00 0.00 1.28
1065 1128 3.040414 CTGCGAGCCGAAGTCGAGA 62.040 63.158 1.43 0.00 43.02 4.04
1669 1848 7.375280 CACAATCTCGCAAAATAAGCTAATCAG 59.625 37.037 0.00 0.00 0.00 2.90
1785 2781 5.977489 AGAAACCCAAGTAATTTGTAGCC 57.023 39.130 0.00 0.00 34.87 3.93
1927 2931 9.906660 CCAAACTAGTAAATAAACAATCAGCAA 57.093 29.630 0.00 0.00 0.00 3.91
1928 2932 8.519526 CCCAAACTAGTAAATAAACAATCAGCA 58.480 33.333 0.00 0.00 0.00 4.41
1929 2933 8.520351 ACCCAAACTAGTAAATAAACAATCAGC 58.480 33.333 0.00 0.00 0.00 4.26
1939 2943 7.937942 TGCACTACAAACCCAAACTAGTAAATA 59.062 33.333 0.00 0.00 0.00 1.40
1940 2944 6.773685 TGCACTACAAACCCAAACTAGTAAAT 59.226 34.615 0.00 0.00 0.00 1.40
1942 2946 5.682659 TGCACTACAAACCCAAACTAGTAA 58.317 37.500 0.00 0.00 0.00 2.24
1944 2948 4.159244 TGCACTACAAACCCAAACTAGT 57.841 40.909 0.00 0.00 0.00 2.57
1945 2949 5.123344 GGTATGCACTACAAACCCAAACTAG 59.877 44.000 0.00 0.00 31.44 2.57
1947 2951 3.824443 GGTATGCACTACAAACCCAAACT 59.176 43.478 0.00 0.00 31.44 2.66
1948 2952 3.570550 TGGTATGCACTACAAACCCAAAC 59.429 43.478 0.00 0.00 31.44 2.93
1949 2953 3.833732 TGGTATGCACTACAAACCCAAA 58.166 40.909 0.00 0.00 31.44 3.28
1950 2954 3.510531 TGGTATGCACTACAAACCCAA 57.489 42.857 0.00 0.00 31.44 4.12
1953 2957 3.936453 TCGATTGGTATGCACTACAAACC 59.064 43.478 0.00 0.00 31.44 3.27
1956 2960 4.827692 ACTTCGATTGGTATGCACTACAA 58.172 39.130 0.00 0.00 31.44 2.41
1958 2962 5.231568 GTGTACTTCGATTGGTATGCACTAC 59.768 44.000 0.00 0.00 0.00 2.73
1959 2963 5.105675 TGTGTACTTCGATTGGTATGCACTA 60.106 40.000 0.00 0.00 0.00 2.74
1961 2965 3.930229 TGTGTACTTCGATTGGTATGCAC 59.070 43.478 0.00 0.00 0.00 4.57
2163 3262 3.263425 AGTCCCGACCATACTTTTGATGT 59.737 43.478 0.00 0.00 0.00 3.06
2179 3278 2.385013 TCACATGTTCATCAGTCCCG 57.615 50.000 0.00 0.00 0.00 5.14
3400 6990 5.279708 GCCATCTAGTGCACCATTAGAGTAT 60.280 44.000 14.63 0.00 36.44 2.12
3568 7177 7.658179 TGCTGAATTGTCTAAGTCAAACTAG 57.342 36.000 0.00 0.00 40.01 2.57
3818 7429 7.255139 GCGCTAAAAACAATCCTATACCAAGAT 60.255 37.037 0.00 0.00 0.00 2.40
3863 7474 6.951198 AGAGGAAGAGAGAGAACACATTTCTA 59.049 38.462 0.00 0.00 0.00 2.10
3905 7516 9.061610 CAAATAACAGAAACATCGGTAATCAAC 57.938 33.333 0.00 0.00 0.00 3.18
4418 8031 3.452755 TGCAAGATACGATCGTCCAAT 57.547 42.857 26.48 13.28 0.00 3.16
4601 8214 2.190578 GGAGCGCCCTAAGCACAT 59.809 61.111 2.29 0.00 44.04 3.21
4684 8298 5.869888 GGAGCATTAATTATACCGTGGAGAG 59.130 44.000 0.00 0.00 0.00 3.20
4692 8306 8.854614 AGTGAGATTGGAGCATTAATTATACC 57.145 34.615 0.00 0.00 0.00 2.73
4732 8347 7.589958 AGTTGTAGAGAGAAGTGAAAGAGAA 57.410 36.000 0.00 0.00 0.00 2.87
4736 8351 6.071616 AGGCTAGTTGTAGAGAGAAGTGAAAG 60.072 42.308 0.00 0.00 0.00 2.62
4738 8353 5.184096 CAGGCTAGTTGTAGAGAGAAGTGAA 59.816 44.000 0.00 0.00 0.00 3.18
4739 8354 4.702612 CAGGCTAGTTGTAGAGAGAAGTGA 59.297 45.833 0.00 0.00 0.00 3.41
4768 8403 4.877823 GGTTTAGAGATCACATGTGCATCA 59.122 41.667 26.20 12.35 0.00 3.07
4790 8425 1.271379 AGTGATGTTGCATGCAGTTGG 59.729 47.619 21.50 0.00 0.00 3.77
4794 8429 5.462729 TGTTTTTAAGTGATGTTGCATGCAG 59.537 36.000 21.50 0.00 0.00 4.41
4817 8452 3.617540 TGCATTGTCGTTTAGGTGTTG 57.382 42.857 0.00 0.00 0.00 3.33
4828 8463 5.766702 AAAATAACTGCAATGCATTGTCG 57.233 34.783 33.67 26.77 38.13 4.35
4889 8524 4.036852 TGGTGTGTTCGATTTAATGCACAA 59.963 37.500 0.00 0.00 38.35 3.33
4890 8525 3.565902 TGGTGTGTTCGATTTAATGCACA 59.434 39.130 0.00 0.00 34.95 4.57
4908 8543 2.227865 CCCTATCCGTGTTTGTTTGGTG 59.772 50.000 0.00 0.00 0.00 4.17
4917 8552 1.384082 CCCCCTCCCTATCCGTGTT 60.384 63.158 0.00 0.00 0.00 3.32
4918 8553 2.285868 CCCCCTCCCTATCCGTGT 59.714 66.667 0.00 0.00 0.00 4.49
4919 8554 3.242291 GCCCCCTCCCTATCCGTG 61.242 72.222 0.00 0.00 0.00 4.94
4920 8555 3.774336 TGCCCCCTCCCTATCCGT 61.774 66.667 0.00 0.00 0.00 4.69
4938 8574 0.386731 CAAATGGGTCGGACGTTTGC 60.387 55.000 14.74 0.00 37.82 3.68
4944 8580 0.519961 CCGTTTCAAATGGGTCGGAC 59.480 55.000 0.00 0.00 40.29 4.79
4948 8584 2.442413 TCCATCCGTTTCAAATGGGTC 58.558 47.619 8.61 0.00 40.34 4.46
4957 8593 5.413833 AGCATGAATATCATCCATCCGTTTC 59.586 40.000 0.00 0.00 34.28 2.78
4959 8595 4.914983 AGCATGAATATCATCCATCCGTT 58.085 39.130 0.00 0.00 34.28 4.44
4965 8601 4.020307 TCCGCTTAGCATGAATATCATCCA 60.020 41.667 4.70 0.00 34.28 3.41
4969 8605 5.151297 TCATCCGCTTAGCATGAATATCA 57.849 39.130 4.70 0.00 0.00 2.15
5007 8643 2.032799 GTCACCGCATTGTTGAACTTCA 59.967 45.455 0.00 0.00 0.00 3.02
5011 8669 0.039527 GGGTCACCGCATTGTTGAAC 60.040 55.000 0.00 0.00 0.00 3.18
5020 8678 1.610967 TCTACCATGGGTCACCGCA 60.611 57.895 18.09 0.00 40.75 5.69
5021 8679 1.144057 CTCTACCATGGGTCACCGC 59.856 63.158 18.09 0.00 40.75 5.68
5041 8700 0.984230 AAGACTCCGAGGCCAATCAA 59.016 50.000 5.01 0.00 0.00 2.57
5051 8710 1.203287 CAGACTGCATCAAGACTCCGA 59.797 52.381 0.00 0.00 0.00 4.55
5053 8712 2.289320 ACACAGACTGCATCAAGACTCC 60.289 50.000 1.25 0.00 0.00 3.85
5058 8717 3.811497 TGAAGAACACAGACTGCATCAAG 59.189 43.478 1.25 0.00 0.00 3.02
5072 8732 5.163205 TGAGAAATCCTGAAGGTGAAGAACA 60.163 40.000 0.00 0.00 36.34 3.18
5082 8742 7.664758 ACCTTTTCAAATGAGAAATCCTGAAG 58.335 34.615 0.00 0.00 37.35 3.02
5094 8754 9.581099 GAGTGAAGTTTTAACCTTTTCAAATGA 57.419 29.630 0.00 0.00 30.43 2.57
5116 8776 3.989817 TGTTGATGACAAGATCACGAGTG 59.010 43.478 0.00 0.00 41.24 3.51


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

AutoCloner maintained by Alex Coulton.