Multiple sequence alignment - TraesCS2A01G479600

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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 TraesCS2A01G479600 chr2A 100.000 3817 0 0 1 3817 717859489 717855673 0 7049
1 TraesCS2A01G479600 chr2B 92.194 2037 91 21 939 2961 698296814 698294832 0 2819
2 TraesCS2A01G479600 chr2B 91.180 907 58 16 45 947 698297895 698297007 0 1212
3 TraesCS2A01G479600 chr2D 93.313 1645 78 9 1317 2961 579996216 579994604 0 2399
4 TraesCS2A01G479600 chr2D 92.428 1215 64 13 45 1239 579997442 579996236 0 1709
5 TraesCS2A01G479600 chr2D 92.882 857 58 3 2962 3817 650828609 650829463 0 1242
6 TraesCS2A01G479600 chr2D 92.326 860 64 2 2959 3817 39418597 39417739 0 1221
7 TraesCS2A01G479600 chr1A 94.614 854 42 3 2962 3814 563825097 563825947 0 1319
8 TraesCS2A01G479600 chr3A 93.816 857 51 2 2962 3817 374981940 374981085 0 1288
9 TraesCS2A01G479600 chr1D 92.666 859 54 6 2962 3817 52330641 52331493 0 1229
10 TraesCS2A01G479600 chr4D 92.415 857 60 2 2962 3817 334646394 334645542 0 1218
11 TraesCS2A01G479600 chr7D 92.299 857 64 2 2962 3817 631613001 631612146 0 1216
12 TraesCS2A01G479600 chr5D 92.218 861 60 3 2960 3817 482694952 482695808 0 1212
13 TraesCS2A01G479600 chr3D 92.308 858 59 4 2961 3817 573668986 573669837 0 1212


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 TraesCS2A01G479600 chr2A 717855673 717859489 3816 True 7049.0 7049 100.0000 1 3817 1 chr2A.!!$R1 3816
1 TraesCS2A01G479600 chr2B 698294832 698297895 3063 True 2015.5 2819 91.6870 45 2961 2 chr2B.!!$R1 2916
2 TraesCS2A01G479600 chr2D 579994604 579997442 2838 True 2054.0 2399 92.8705 45 2961 2 chr2D.!!$R2 2916
3 TraesCS2A01G479600 chr2D 650828609 650829463 854 False 1242.0 1242 92.8820 2962 3817 1 chr2D.!!$F1 855
4 TraesCS2A01G479600 chr2D 39417739 39418597 858 True 1221.0 1221 92.3260 2959 3817 1 chr2D.!!$R1 858
5 TraesCS2A01G479600 chr1A 563825097 563825947 850 False 1319.0 1319 94.6140 2962 3814 1 chr1A.!!$F1 852
6 TraesCS2A01G479600 chr3A 374981085 374981940 855 True 1288.0 1288 93.8160 2962 3817 1 chr3A.!!$R1 855
7 TraesCS2A01G479600 chr1D 52330641 52331493 852 False 1229.0 1229 92.6660 2962 3817 1 chr1D.!!$F1 855
8 TraesCS2A01G479600 chr4D 334645542 334646394 852 True 1218.0 1218 92.4150 2962 3817 1 chr4D.!!$R1 855
9 TraesCS2A01G479600 chr7D 631612146 631613001 855 True 1216.0 1216 92.2990 2962 3817 1 chr7D.!!$R1 855
10 TraesCS2A01G479600 chr5D 482694952 482695808 856 False 1212.0 1212 92.2180 2960 3817 1 chr5D.!!$F1 857
11 TraesCS2A01G479600 chr3D 573668986 573669837 851 False 1212.0 1212 92.3080 2961 3817 1 chr3D.!!$F1 856

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
33 34 0.181587 AATCACGGTGTTGGTGACCA 59.818 50.0 0.0 0.0 46.22 4.02 F
1312 1542 0.107897 CCATTCCCGTCAACCGATGA 60.108 55.0 0.0 0.0 39.56 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1682 0.040692 GCTCGTCGGTGTATCGCATA 60.041 55.0 0.00 0.00 0.00 3.14 R
3296 3531 0.107312 AGATGAGCATTGCGCCTCTT 60.107 50.0 12.94 1.87 44.04 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
19 20 1.571919 CCGATCGTGAAGGGAATCAC 58.428 55.000 15.09 0.00 44.96 3.06
24 25 3.625745 GTGAAGGGAATCACGGTGT 57.374 52.632 8.17 0.00 40.23 4.16
25 26 1.892209 GTGAAGGGAATCACGGTGTT 58.108 50.000 8.17 1.99 40.23 3.32
26 27 1.535462 GTGAAGGGAATCACGGTGTTG 59.465 52.381 8.17 0.00 40.23 3.33
27 28 1.165270 GAAGGGAATCACGGTGTTGG 58.835 55.000 8.17 0.00 0.00 3.77
28 29 0.476771 AAGGGAATCACGGTGTTGGT 59.523 50.000 8.17 0.00 0.00 3.67
29 30 0.250727 AGGGAATCACGGTGTTGGTG 60.251 55.000 8.17 0.00 36.74 4.17
31 32 0.872388 GGAATCACGGTGTTGGTGAC 59.128 55.000 8.17 0.00 46.22 3.67
32 33 0.872388 GAATCACGGTGTTGGTGACC 59.128 55.000 8.17 0.00 46.22 4.02
33 34 0.181587 AATCACGGTGTTGGTGACCA 59.818 50.000 0.00 0.00 46.22 4.02
34 35 0.400213 ATCACGGTGTTGGTGACCAT 59.600 50.000 4.56 0.00 46.22 3.55
35 36 1.049402 TCACGGTGTTGGTGACCATA 58.951 50.000 4.56 0.00 39.36 2.74
36 37 1.626321 TCACGGTGTTGGTGACCATAT 59.374 47.619 4.56 0.00 39.36 1.78
37 38 2.039216 TCACGGTGTTGGTGACCATATT 59.961 45.455 4.56 0.00 39.36 1.28
38 39 2.161410 CACGGTGTTGGTGACCATATTG 59.839 50.000 4.56 0.00 37.60 1.90
39 40 1.742831 CGGTGTTGGTGACCATATTGG 59.257 52.381 4.56 0.00 45.02 3.16
40 41 1.476488 GGTGTTGGTGACCATATTGGC 59.524 52.381 4.56 0.00 42.67 4.52
41 42 2.166829 GTGTTGGTGACCATATTGGCA 58.833 47.619 4.56 0.00 42.67 4.92
42 43 2.094752 GTGTTGGTGACCATATTGGCAC 60.095 50.000 4.56 4.13 42.67 5.01
53 54 4.227300 ACCATATTGGCACCTTACAGAGAA 59.773 41.667 0.00 0.00 42.67 2.87
130 131 5.975693 TTTTGGGCCTAAGTGATGTAAAG 57.024 39.130 4.53 0.00 0.00 1.85
264 265 3.462982 TGTATGGTTCATACGATGTGGC 58.537 45.455 11.81 0.00 46.69 5.01
766 772 2.813779 GGCACGCTGACTCTTATTTG 57.186 50.000 0.00 0.00 0.00 2.32
779 785 5.953571 ACTCTTATTTGTTTTGAGGGGTCT 58.046 37.500 0.00 0.00 0.00 3.85
812 818 2.601504 GGAAAAGAAACGCGGAAGTGAC 60.602 50.000 12.47 0.00 46.66 3.67
839 845 0.247736 CAGCCCAAGTAGCTCTCGTT 59.752 55.000 0.00 0.00 38.95 3.85
847 853 0.714439 GTAGCTCTCGTTGCCGTTTC 59.286 55.000 0.00 0.00 35.01 2.78
860 866 2.682856 TGCCGTTTCCTCATTATTCAGC 59.317 45.455 0.00 0.00 0.00 4.26
866 872 5.502606 GTTTCCTCATTATTCAGCGCTTAC 58.497 41.667 7.50 0.00 0.00 2.34
927 934 1.231641 CTCCCTCTCCACCGGATCT 59.768 63.158 9.46 0.00 0.00 2.75
1047 1274 1.153147 GGGGAATCAAGGCGAGGAC 60.153 63.158 0.00 0.00 0.00 3.85
1270 1500 3.071580 GCCCCACGATCTTCTTCTG 57.928 57.895 0.00 0.00 0.00 3.02
1276 1506 1.227380 CGATCTTCTTCTGGCCCCG 60.227 63.158 0.00 0.00 0.00 5.73
1305 1535 1.065491 CATCTCCACCATTCCCGTCAA 60.065 52.381 0.00 0.00 0.00 3.18
1308 1538 2.038269 CCACCATTCCCGTCAACCG 61.038 63.158 0.00 0.00 0.00 4.44
1309 1539 1.004320 CACCATTCCCGTCAACCGA 60.004 57.895 0.00 0.00 39.56 4.69
1310 1540 0.392461 CACCATTCCCGTCAACCGAT 60.392 55.000 0.00 0.00 39.56 4.18
1311 1541 0.392461 ACCATTCCCGTCAACCGATG 60.392 55.000 0.00 0.00 39.56 3.84
1312 1542 0.107897 CCATTCCCGTCAACCGATGA 60.108 55.000 0.00 0.00 39.56 2.92
1313 1543 1.677518 CCATTCCCGTCAACCGATGAA 60.678 52.381 0.00 0.00 40.50 2.57
1314 1544 1.396996 CATTCCCGTCAACCGATGAAC 59.603 52.381 0.00 0.00 40.50 3.18
1315 1545 0.668096 TTCCCGTCAACCGATGAACG 60.668 55.000 0.00 0.00 40.50 3.95
1403 1633 2.118679 TCGTCAGATCATGGATGGGTT 58.881 47.619 0.00 0.00 0.00 4.11
1427 1660 8.507249 GTTACTAAACTGAATCTTGATTGTGCT 58.493 33.333 0.09 0.00 32.54 4.40
1428 1661 6.906659 ACTAAACTGAATCTTGATTGTGCTG 58.093 36.000 0.09 0.00 0.00 4.41
1429 1662 3.844577 ACTGAATCTTGATTGTGCTGC 57.155 42.857 0.09 0.00 0.00 5.25
1449 1682 0.460311 GTGCAGCGTCTATACCACCT 59.540 55.000 0.00 0.00 0.00 4.00
1578 1811 1.740296 GCTGGATGTGTACGGCGTT 60.740 57.895 21.24 0.00 29.03 4.84
1596 1829 4.162690 GTCGCTGCCCGGGATTCT 62.163 66.667 29.31 0.00 36.91 2.40
1632 1865 1.738099 CCTCCTCTTCAACCGCACG 60.738 63.158 0.00 0.00 0.00 5.34
1674 1907 1.521457 CGCAGAGGTGTGTGTGTGT 60.521 57.895 0.00 0.00 0.00 3.72
1675 1908 1.765161 CGCAGAGGTGTGTGTGTGTG 61.765 60.000 0.00 0.00 0.00 3.82
1676 1909 0.744414 GCAGAGGTGTGTGTGTGTGT 60.744 55.000 0.00 0.00 0.00 3.72
1677 1910 1.009078 CAGAGGTGTGTGTGTGTGTG 58.991 55.000 0.00 0.00 0.00 3.82
1678 1911 0.744414 AGAGGTGTGTGTGTGTGTGC 60.744 55.000 0.00 0.00 0.00 4.57
1679 1912 1.002746 AGGTGTGTGTGTGTGTGCA 60.003 52.632 0.00 0.00 0.00 4.57
1680 1913 0.394216 AGGTGTGTGTGTGTGTGCAT 60.394 50.000 0.00 0.00 0.00 3.96
1681 1914 0.029300 GGTGTGTGTGTGTGTGCATC 59.971 55.000 0.00 0.00 0.00 3.91
1682 1915 0.316114 GTGTGTGTGTGTGTGCATCG 60.316 55.000 0.00 0.00 0.00 3.84
1683 1916 0.460987 TGTGTGTGTGTGTGCATCGA 60.461 50.000 0.00 0.00 0.00 3.59
1684 1917 0.867746 GTGTGTGTGTGTGCATCGAT 59.132 50.000 0.00 0.00 0.00 3.59
1685 1918 0.867086 TGTGTGTGTGTGCATCGATG 59.133 50.000 21.27 21.27 0.00 3.84
1722 1955 4.321750 CCATGCTATTTTGCCTGATCCATC 60.322 45.833 0.00 0.00 31.71 3.51
1764 1997 4.927782 GCATGGCCGCGTGGGATA 62.928 66.667 18.41 0.00 38.47 2.59
1771 2004 2.026641 GGCCGCGTGGGATATATACTA 58.973 52.381 18.41 0.00 38.47 1.82
1792 2025 2.024464 AGCAGGGTTTATGGCATGGTTA 60.024 45.455 10.98 0.00 0.00 2.85
1798 2031 2.680841 GTTTATGGCATGGTTACGCTGA 59.319 45.455 10.98 0.00 0.00 4.26
1858 2091 6.399639 TTCTATGAGTGTGTCACAGTTACA 57.600 37.500 14.49 9.33 38.28 2.41
1886 2119 7.093992 TGCCGTCGATATGTGATATTTTCATA 58.906 34.615 0.00 0.00 36.54 2.15
1927 2160 2.221169 CTAGTTGAGCCTGTGCAAACA 58.779 47.619 0.00 0.00 41.13 2.83
1928 2161 5.681351 GCTAGTTGAGCCTGTGCAAACAC 62.681 52.174 0.00 0.00 46.41 3.32
1949 2182 9.865321 AAACACATGAAGAATGGAATTAAGATG 57.135 29.630 0.00 0.00 40.94 2.90
2054 2287 4.594491 AGCAAGGGTTTGAGGATTTGAAAT 59.406 37.500 0.00 0.00 36.36 2.17
2242 2475 1.122632 TTGTTGACCGGTCCTAGCCA 61.123 55.000 31.19 16.74 0.00 4.75
2250 2483 2.731571 GGTCCTAGCCACGCCATCA 61.732 63.158 0.00 0.00 0.00 3.07
2290 2523 7.148639 TGTCGACTATGATGTTGAACTAAAAGC 60.149 37.037 17.92 0.00 32.72 3.51
2436 2669 0.899720 GGTGATGGTCGGACACCTTA 59.100 55.000 10.76 0.00 46.98 2.69
2471 2704 2.205074 GCTACCATGACAATCCGAGTG 58.795 52.381 0.00 0.00 0.00 3.51
2553 2786 3.523157 TGATGACAGGGACATGGTATTGT 59.477 43.478 0.00 0.00 0.00 2.71
2609 2842 1.370810 TGGCACAATCGAGCTCACA 59.629 52.632 15.40 0.00 31.92 3.58
2617 2850 3.461982 CGAGCTCACACGTCGTGC 61.462 66.667 24.80 11.20 45.92 5.34
2631 2864 0.462225 TCGTGCTGTTTCGGTGGAAA 60.462 50.000 0.00 0.00 39.77 3.13
2671 2904 2.359850 GGTGGACGCATGGCTTGA 60.360 61.111 4.32 0.00 0.00 3.02
2688 2921 3.243670 GCTTGATGATGGTGATCTCGAGA 60.244 47.826 19.19 19.19 0.00 4.04
2692 2925 1.406898 TGATGGTGATCTCGAGACTGC 59.593 52.381 19.30 10.90 0.00 4.40
2976 3209 9.832445 ACATGAGAAAACACTAGTAGAAAAAGA 57.168 29.630 3.59 0.00 0.00 2.52
3223 3458 8.859236 TGTACTAGAGTTTCTTAGTAAGCTGA 57.141 34.615 4.93 0.00 0.00 4.26
3296 3531 3.371285 CGTGAGTACAGAGACGATGAAGA 59.629 47.826 0.00 0.00 0.00 2.87
3393 3628 4.245660 GCAGTGCAGTCTACACTATTTCA 58.754 43.478 11.09 0.00 46.44 2.69
3414 3649 9.948964 ATTTCAAAAGGCTTGAAGCTAATTAAT 57.051 25.926 17.59 6.02 41.99 1.40
3473 3710 2.696707 ACAACTCCGGACTTCTTGTGTA 59.303 45.455 0.00 0.00 0.00 2.90
3475 3712 4.202326 ACAACTCCGGACTTCTTGTGTAAT 60.202 41.667 0.00 0.00 0.00 1.89
3529 3766 6.702329 ACTGGACAATCTCTTTCGAAGTATT 58.298 36.000 0.00 0.00 0.00 1.89
3532 3769 7.837863 TGGACAATCTCTTTCGAAGTATTAGT 58.162 34.615 0.00 0.00 0.00 2.24
3542 3783 3.056678 TCGAAGTATTAGTGCCGGTTTCA 60.057 43.478 1.90 0.00 0.00 2.69
3567 3808 3.739300 CGAAAACTCATCTGTTACACCGT 59.261 43.478 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.571919 GTGATTCCCTTCACGATCGG 58.428 55.000 20.98 8.65 36.93 4.18
6 7 1.535462 CAACACCGTGATTCCCTTCAC 59.465 52.381 5.28 0.00 42.10 3.18
7 8 1.544537 CCAACACCGTGATTCCCTTCA 60.545 52.381 5.28 0.00 0.00 3.02
8 9 1.165270 CCAACACCGTGATTCCCTTC 58.835 55.000 5.28 0.00 0.00 3.46
9 10 0.476771 ACCAACACCGTGATTCCCTT 59.523 50.000 5.28 0.00 0.00 3.95
10 11 0.250727 CACCAACACCGTGATTCCCT 60.251 55.000 5.28 0.00 32.77 4.20
11 12 0.250553 TCACCAACACCGTGATTCCC 60.251 55.000 5.28 0.00 35.35 3.97
12 13 0.872388 GTCACCAACACCGTGATTCC 59.128 55.000 5.28 0.00 41.99 3.01
13 14 0.872388 GGTCACCAACACCGTGATTC 59.128 55.000 5.28 0.00 41.99 2.52
14 15 0.181587 TGGTCACCAACACCGTGATT 59.818 50.000 5.28 0.00 41.99 2.57
15 16 0.400213 ATGGTCACCAACACCGTGAT 59.600 50.000 0.00 0.00 41.99 3.06
16 17 1.049402 TATGGTCACCAACACCGTGA 58.951 50.000 0.00 0.00 36.95 4.35
17 18 2.107950 ATATGGTCACCAACACCGTG 57.892 50.000 0.00 0.00 36.95 4.94
18 19 2.432444 CAATATGGTCACCAACACCGT 58.568 47.619 0.00 0.00 36.95 4.83
19 20 1.742831 CCAATATGGTCACCAACACCG 59.257 52.381 0.00 0.00 36.95 4.94
20 21 1.476488 GCCAATATGGTCACCAACACC 59.524 52.381 0.00 0.00 40.46 4.16
21 22 2.094752 GTGCCAATATGGTCACCAACAC 60.095 50.000 0.00 0.00 40.46 3.32
22 23 2.166829 GTGCCAATATGGTCACCAACA 58.833 47.619 0.00 0.00 40.46 3.33
23 24 2.939460 GTGCCAATATGGTCACCAAC 57.061 50.000 0.00 0.00 40.46 3.77
27 28 3.616219 TGTAAGGTGCCAATATGGTCAC 58.384 45.455 12.53 12.53 40.46 3.67
28 29 3.521531 TCTGTAAGGTGCCAATATGGTCA 59.478 43.478 0.00 0.00 40.46 4.02
29 30 4.130118 CTCTGTAAGGTGCCAATATGGTC 58.870 47.826 0.00 0.00 40.46 4.02
30 31 3.780294 TCTCTGTAAGGTGCCAATATGGT 59.220 43.478 0.00 0.00 40.46 3.55
31 32 4.422073 TCTCTGTAAGGTGCCAATATGG 57.578 45.455 0.00 0.00 41.55 2.74
32 33 5.674525 TCTTCTCTGTAAGGTGCCAATATG 58.325 41.667 0.00 0.00 0.00 1.78
33 34 5.957771 TCTTCTCTGTAAGGTGCCAATAT 57.042 39.130 0.00 0.00 0.00 1.28
34 35 5.957771 ATCTTCTCTGTAAGGTGCCAATA 57.042 39.130 0.00 0.00 0.00 1.90
35 36 4.851639 ATCTTCTCTGTAAGGTGCCAAT 57.148 40.909 0.00 0.00 0.00 3.16
36 37 4.640771 AATCTTCTCTGTAAGGTGCCAA 57.359 40.909 0.00 0.00 0.00 4.52
37 38 5.163301 GGATAATCTTCTCTGTAAGGTGCCA 60.163 44.000 0.00 0.00 0.00 4.92
38 39 5.301555 GGATAATCTTCTCTGTAAGGTGCC 58.698 45.833 0.00 0.00 0.00 5.01
39 40 5.071115 AGGGATAATCTTCTCTGTAAGGTGC 59.929 44.000 0.00 0.00 0.00 5.01
40 41 6.739331 AGGGATAATCTTCTCTGTAAGGTG 57.261 41.667 0.00 0.00 0.00 4.00
41 42 8.855804 TTAAGGGATAATCTTCTCTGTAAGGT 57.144 34.615 0.00 0.00 0.00 3.50
159 160 6.931840 CCTATAGGTCTAAAAGCATCTCCAAC 59.068 42.308 10.96 0.00 0.00 3.77
300 302 7.619050 ACATGACATGAGACTGTTAGAAAGAT 58.381 34.615 22.19 0.00 0.00 2.40
552 558 6.158598 ACGCAATTTAAAGAAATGCTCACAT 58.841 32.000 12.98 0.00 35.38 3.21
755 761 6.004574 AGACCCCTCAAAACAAATAAGAGTC 58.995 40.000 0.00 0.00 0.00 3.36
762 768 5.953571 AGTAAGAGACCCCTCAAAACAAAT 58.046 37.500 0.00 0.00 41.87 2.32
766 772 4.283722 TGAGAGTAAGAGACCCCTCAAAAC 59.716 45.833 0.00 0.00 41.87 2.43
779 785 5.465724 GCGTTTCTTTTCCTTGAGAGTAAGA 59.534 40.000 0.00 0.00 0.00 2.10
839 845 2.682856 GCTGAATAATGAGGAAACGGCA 59.317 45.455 0.00 0.00 0.00 5.69
847 853 4.722203 CTGTAAGCGCTGAATAATGAGG 57.278 45.455 12.58 0.00 0.00 3.86
887 894 1.375326 GCCTCTTTCGGTCCAAGGT 59.625 57.895 0.00 0.00 0.00 3.50
927 934 3.994392 GTCGGAGAAGATGCAACAGTTAA 59.006 43.478 0.00 0.00 39.69 2.01
1031 1258 1.339151 ACTTGTCCTCGCCTTGATTCC 60.339 52.381 0.00 0.00 0.00 3.01
1035 1262 1.118965 TCCACTTGTCCTCGCCTTGA 61.119 55.000 0.00 0.00 0.00 3.02
1037 1264 1.371558 GTCCACTTGTCCTCGCCTT 59.628 57.895 0.00 0.00 0.00 4.35
1047 1274 2.742372 CGCTTCCCCGTCCACTTG 60.742 66.667 0.00 0.00 0.00 3.16
1119 1346 0.689412 CTGGTTCCTCCTCCTCCTCC 60.689 65.000 0.00 0.00 37.07 4.30
1120 1347 0.041982 ACTGGTTCCTCCTCCTCCTC 59.958 60.000 0.00 0.00 37.07 3.71
1121 1348 0.252467 CACTGGTTCCTCCTCCTCCT 60.252 60.000 0.00 0.00 37.07 3.69
1210 1437 0.813184 TTACTTGCGTCCTCGTAGGG 59.187 55.000 1.76 0.00 35.59 3.53
1253 1483 0.462759 GCCAGAAGAAGATCGTGGGG 60.463 60.000 0.00 0.00 0.00 4.96
1254 1484 0.462759 GGCCAGAAGAAGATCGTGGG 60.463 60.000 0.00 0.00 0.00 4.61
1257 1487 1.908483 GGGGCCAGAAGAAGATCGT 59.092 57.895 4.39 0.00 0.00 3.73
1276 1506 1.227674 GGTGGAGATGGTGATCGCC 60.228 63.158 18.84 18.84 46.17 5.54
1329 1559 7.272978 CCCTGTTTAGAATCGGAGAAAGAATA 58.727 38.462 0.00 0.00 43.58 1.75
1346 1576 2.351706 ACAAAACCTCGCCCTGTTTA 57.648 45.000 0.00 0.00 33.76 2.01
1401 1631 8.507249 AGCACAATCAAGATTCAGTTTAGTAAC 58.493 33.333 0.00 0.00 34.36 2.50
1403 1633 7.361201 GCAGCACAATCAAGATTCAGTTTAGTA 60.361 37.037 0.00 0.00 0.00 1.82
1449 1682 0.040692 GCTCGTCGGTGTATCGCATA 60.041 55.000 0.00 0.00 0.00 3.14
1578 1811 4.467084 GAATCCCGGGCAGCGACA 62.467 66.667 18.49 0.00 0.00 4.35
1632 1865 1.342819 AGTGTCTGGCAGTTGTCTCTC 59.657 52.381 15.27 1.53 0.00 3.20
1665 1898 0.867746 ATCGATGCACACACACACAC 59.132 50.000 0.00 0.00 0.00 3.82
1666 1899 0.867086 CATCGATGCACACACACACA 59.133 50.000 13.37 0.00 0.00 3.72
1676 1909 7.553760 ATGGAAAACATATATAGCATCGATGCA 59.446 33.333 42.35 30.71 46.74 3.96
1677 1910 7.854422 CATGGAAAACATATATAGCATCGATGC 59.146 37.037 37.29 37.29 45.66 3.91
1678 1911 7.854422 GCATGGAAAACATATATAGCATCGATG 59.146 37.037 21.27 21.27 37.84 3.84
1679 1912 7.772292 AGCATGGAAAACATATATAGCATCGAT 59.228 33.333 0.00 0.00 37.84 3.59
1680 1913 7.105588 AGCATGGAAAACATATATAGCATCGA 58.894 34.615 0.00 0.00 37.84 3.59
1681 1914 7.312657 AGCATGGAAAACATATATAGCATCG 57.687 36.000 0.00 0.00 37.84 3.84
1688 1921 8.873144 AGGCAAAATAGCATGGAAAACATATAT 58.127 29.630 0.00 0.00 37.84 0.86
1689 1922 8.143193 CAGGCAAAATAGCATGGAAAACATATA 58.857 33.333 0.00 0.00 42.15 0.86
1690 1923 6.987992 CAGGCAAAATAGCATGGAAAACATAT 59.012 34.615 0.00 0.00 42.15 1.78
1691 1924 6.154192 TCAGGCAAAATAGCATGGAAAACATA 59.846 34.615 0.66 0.00 45.56 2.29
1692 1925 5.046448 TCAGGCAAAATAGCATGGAAAACAT 60.046 36.000 0.66 0.00 45.56 2.71
1693 1926 4.282957 TCAGGCAAAATAGCATGGAAAACA 59.717 37.500 0.66 0.00 45.56 2.83
1694 1927 4.819769 TCAGGCAAAATAGCATGGAAAAC 58.180 39.130 0.66 0.00 45.56 2.43
1695 1928 5.395546 GGATCAGGCAAAATAGCATGGAAAA 60.396 40.000 0.66 0.00 45.56 2.29
1696 1929 4.099881 GGATCAGGCAAAATAGCATGGAAA 59.900 41.667 0.66 0.00 45.56 3.13
1697 1930 3.638160 GGATCAGGCAAAATAGCATGGAA 59.362 43.478 0.66 0.00 45.56 3.53
1698 1931 3.225104 GGATCAGGCAAAATAGCATGGA 58.775 45.455 0.66 0.00 45.56 3.41
1699 1932 2.960384 TGGATCAGGCAAAATAGCATGG 59.040 45.455 0.66 0.00 45.56 3.66
1700 1933 4.615223 CGATGGATCAGGCAAAATAGCATG 60.615 45.833 0.00 0.00 46.77 4.06
1722 1955 2.857748 TGCAAGTAAGTGATGATACGCG 59.142 45.455 3.53 3.53 0.00 6.01
1757 1990 6.622427 AAACCCTGCTAGTATATATCCCAC 57.378 41.667 0.00 0.00 0.00 4.61
1763 1996 7.365563 CCATGCCATAAACCCTGCTAGTATATA 60.366 40.741 0.00 0.00 0.00 0.86
1764 1997 6.418101 CATGCCATAAACCCTGCTAGTATAT 58.582 40.000 0.00 0.00 0.00 0.86
1771 2004 0.336048 ACCATGCCATAAACCCTGCT 59.664 50.000 0.00 0.00 0.00 4.24
1792 2025 9.424319 CTAATTAACCTATGAATACATCAGCGT 57.576 33.333 0.00 0.00 42.53 5.07
1831 2064 9.419297 GTAACTGTGACACACTCATAGAATTTA 57.581 33.333 3.56 0.00 39.88 1.40
1858 2091 7.763985 TGAAAATATCACATATCGACGGCATAT 59.236 33.333 0.00 0.00 31.50 1.78
1886 2119 9.638176 AACTAGCTATCTTGGATTTCAATTCAT 57.362 29.630 0.00 0.00 34.45 2.57
1927 2160 7.123098 TGCACATCTTAATTCCATTCTTCATGT 59.877 33.333 0.00 0.00 0.00 3.21
1928 2161 7.485810 TGCACATCTTAATTCCATTCTTCATG 58.514 34.615 0.00 0.00 0.00 3.07
1949 2182 5.231568 GCAAATTCATCTTTCAGCTATGCAC 59.768 40.000 0.00 0.00 0.00 4.57
2054 2287 9.985730 AAATTGCTCTCATTTACTTCATCAAAA 57.014 25.926 0.00 0.00 0.00 2.44
2242 2475 2.643551 CCCTAACTTTCATGATGGCGT 58.356 47.619 0.00 0.00 0.00 5.68
2250 2483 2.567615 AGTCGACAGCCCTAACTTTCAT 59.432 45.455 19.50 0.00 0.00 2.57
2411 2644 1.535444 TCCGACCATCACCACCACT 60.535 57.895 0.00 0.00 0.00 4.00
2436 2669 1.601166 GTAGCCTCCACCGTTTGTTT 58.399 50.000 0.00 0.00 0.00 2.83
2471 2704 3.551407 GGCCAGGATCCCTCGGTC 61.551 72.222 8.55 4.55 0.00 4.79
2569 2802 5.008019 CCATTGCTCATAACAGTTATCGCTT 59.992 40.000 18.31 8.68 0.00 4.68
2597 2830 1.579932 ACGACGTGTGAGCTCGATT 59.420 52.632 9.64 0.00 35.78 3.34
2609 2842 2.105528 ACCGAAACAGCACGACGT 59.894 55.556 0.00 0.00 0.00 4.34
2631 2864 5.046807 CCAAAATCCTCAGCTCTCCATTTTT 60.047 40.000 0.00 0.00 0.00 1.94
2636 2869 1.988107 ACCAAAATCCTCAGCTCTCCA 59.012 47.619 0.00 0.00 0.00 3.86
2671 2904 2.035704 GCAGTCTCGAGATCACCATCAT 59.964 50.000 19.90 0.00 0.00 2.45
2688 2921 1.526575 CCATTGGCAACCGAAGCAGT 61.527 55.000 0.00 0.00 0.00 4.40
2692 2925 0.958091 TTCACCATTGGCAACCGAAG 59.042 50.000 0.00 0.00 0.00 3.79
2783 3016 2.883828 AAGGGACCAGGCGACAGTG 61.884 63.158 0.00 0.00 0.00 3.66
3041 3274 2.349755 GCCTAGCCGTTGGAACCA 59.650 61.111 0.00 0.00 0.00 3.67
3223 3458 1.276989 TCGCGAGGTGGGACTAAAAAT 59.723 47.619 3.71 0.00 34.10 1.82
3296 3531 0.107312 AGATGAGCATTGCGCCTCTT 60.107 50.000 12.94 1.87 44.04 2.85
3393 3628 7.038048 GCTCATTAATTAGCTTCAAGCCTTTT 58.962 34.615 13.31 0.00 43.77 2.27
3414 3649 0.961019 AAAAAGAGGCGCAATGCTCA 59.039 45.000 10.83 0.00 45.43 4.26
3449 3686 3.493503 CACAAGAAGTCCGGAGTTGTAAC 59.506 47.826 29.05 14.22 30.28 2.50
3473 3710 4.023726 AGTGCATCCAATTTTTGCCATT 57.976 36.364 0.00 0.00 35.51 3.16
3475 3712 3.401182 GAAGTGCATCCAATTTTTGCCA 58.599 40.909 0.00 0.00 35.51 4.92
3529 3766 0.675083 TTCGTCTGAAACCGGCACTA 59.325 50.000 0.00 0.00 0.00 2.74
3532 3769 0.658897 GTTTTCGTCTGAAACCGGCA 59.341 50.000 0.00 0.00 43.54 5.69
3696 3939 5.245531 TCACGGTCATTTAGCTCTCAAAAT 58.754 37.500 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.