Multiple sequence alignment - TraesCS1A01G209900

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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 TraesCS1A01G209900 chr1A 100.000 2525 0 0 1 2525 372317119 372314595 0.000000e+00 4663
1 TraesCS1A01G209900 chr1A 91.379 1218 72 23 452 1647 372288197 372286991 0.000000e+00 1637
2 TraesCS1A01G209900 chr1A 88.889 900 75 9 1648 2525 335548936 335548040 0.000000e+00 1085
3 TraesCS1A01G209900 chr1A 87.386 880 103 6 1648 2525 301146290 301145417 0.000000e+00 1003
4 TraesCS1A01G209900 chr1D 90.305 1671 98 27 1 1648 298605327 298603698 0.000000e+00 2130
5 TraesCS1A01G209900 chr1B 88.061 1315 105 24 350 1648 401764268 401762990 0.000000e+00 1511
6 TraesCS1A01G209900 chr1B 90.169 1007 72 16 652 1648 401992765 401991776 0.000000e+00 1286
7 TraesCS1A01G209900 chr1B 89.979 968 63 20 692 1648 402039923 402038979 0.000000e+00 1219
8 TraesCS1A01G209900 chr1B 90.675 311 24 4 1 310 402041381 402041075 2.340000e-110 409
9 TraesCS1A01G209900 chr1B 88.608 237 23 4 350 584 401993001 401992767 4.110000e-73 285
10 TraesCS1A01G209900 chr1B 83.150 273 18 7 302 573 402040168 402039923 9.090000e-55 224
11 TraesCS1A01G209900 chr3B 89.522 878 71 1 1663 2519 828541459 828542336 0.000000e+00 1092
12 TraesCS1A01G209900 chr3B 88.543 899 81 12 1648 2525 774691358 774690461 0.000000e+00 1070
13 TraesCS1A01G209900 chr3D 89.708 855 65 3 1692 2525 310694351 310695203 0.000000e+00 1070
14 TraesCS1A01G209900 chr3D 90.464 388 36 1 1658 2045 446110337 446110723 6.230000e-141 510
15 TraesCS1A01G209900 chr2D 88.690 893 79 5 1648 2519 448632451 448633342 0.000000e+00 1070
16 TraesCS1A01G209900 chr2B 88.320 899 82 5 1648 2525 529642316 529641420 0.000000e+00 1057
17 TraesCS1A01G209900 chr3A 88.124 901 85 5 1647 2525 119685433 119684533 0.000000e+00 1051
18 TraesCS1A01G209900 chr5B 88.994 845 72 4 1702 2525 592722596 592723440 0.000000e+00 1026
19 TraesCS1A01G209900 chr6D 88.889 846 72 6 1701 2525 97811138 97810294 0.000000e+00 1022
20 TraesCS1A01G209900 chr6D 89.932 586 38 4 1961 2525 34320321 34319736 0.000000e+00 736
21 TraesCS1A01G209900 chr7D 88.215 874 76 10 1649 2500 540409046 540408178 0.000000e+00 1018
22 TraesCS1A01G209900 chr7D 91.304 713 41 4 1834 2525 159740966 159741678 0.000000e+00 953
23 TraesCS1A01G209900 chr6B 88.757 845 73 5 1702 2525 182379721 182378878 0.000000e+00 1014
24 TraesCS1A01G209900 chr5D 89.099 688 54 6 1859 2525 509962319 509961632 0.000000e+00 835
25 TraesCS1A01G209900 chr5D 90.273 586 36 4 1961 2525 226455195 226454610 0.000000e+00 747
26 TraesCS1A01G209900 chr5D 92.547 483 36 0 2043 2525 486992387 486992869 0.000000e+00 693
27 TraesCS1A01G209900 chr4B 82.394 994 123 38 679 1644 603037677 603038646 0.000000e+00 819
28 TraesCS1A01G209900 chr4B 81.256 1003 107 40 680 1648 602874006 602873051 0.000000e+00 736
29 TraesCS1A01G209900 chr4B 81.200 1000 109 38 680 1648 602893924 602892973 0.000000e+00 732
30 TraesCS1A01G209900 chr4D 83.191 934 103 33 720 1624 477543850 477542942 0.000000e+00 806
31 TraesCS1A01G209900 chr4D 83.657 875 81 37 679 1521 477558662 477559506 0.000000e+00 767


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 TraesCS1A01G209900 chr1A 372314595 372317119 2524 True 4663.000000 4663 100.000000 1 2525 1 chr1A.!!$R4 2524
1 TraesCS1A01G209900 chr1A 372286991 372288197 1206 True 1637.000000 1637 91.379000 452 1647 1 chr1A.!!$R3 1195
2 TraesCS1A01G209900 chr1A 335548040 335548936 896 True 1085.000000 1085 88.889000 1648 2525 1 chr1A.!!$R2 877
3 TraesCS1A01G209900 chr1A 301145417 301146290 873 True 1003.000000 1003 87.386000 1648 2525 1 chr1A.!!$R1 877
4 TraesCS1A01G209900 chr1D 298603698 298605327 1629 True 2130.000000 2130 90.305000 1 1648 1 chr1D.!!$R1 1647
5 TraesCS1A01G209900 chr1B 401762990 401764268 1278 True 1511.000000 1511 88.061000 350 1648 1 chr1B.!!$R1 1298
6 TraesCS1A01G209900 chr1B 401991776 401993001 1225 True 785.500000 1286 89.388500 350 1648 2 chr1B.!!$R2 1298
7 TraesCS1A01G209900 chr1B 402038979 402041381 2402 True 617.333333 1219 87.934667 1 1648 3 chr1B.!!$R3 1647
8 TraesCS1A01G209900 chr3B 828541459 828542336 877 False 1092.000000 1092 89.522000 1663 2519 1 chr3B.!!$F1 856
9 TraesCS1A01G209900 chr3B 774690461 774691358 897 True 1070.000000 1070 88.543000 1648 2525 1 chr3B.!!$R1 877
10 TraesCS1A01G209900 chr3D 310694351 310695203 852 False 1070.000000 1070 89.708000 1692 2525 1 chr3D.!!$F1 833
11 TraesCS1A01G209900 chr2D 448632451 448633342 891 False 1070.000000 1070 88.690000 1648 2519 1 chr2D.!!$F1 871
12 TraesCS1A01G209900 chr2B 529641420 529642316 896 True 1057.000000 1057 88.320000 1648 2525 1 chr2B.!!$R1 877
13 TraesCS1A01G209900 chr3A 119684533 119685433 900 True 1051.000000 1051 88.124000 1647 2525 1 chr3A.!!$R1 878
14 TraesCS1A01G209900 chr5B 592722596 592723440 844 False 1026.000000 1026 88.994000 1702 2525 1 chr5B.!!$F1 823
15 TraesCS1A01G209900 chr6D 97810294 97811138 844 True 1022.000000 1022 88.889000 1701 2525 1 chr6D.!!$R2 824
16 TraesCS1A01G209900 chr6D 34319736 34320321 585 True 736.000000 736 89.932000 1961 2525 1 chr6D.!!$R1 564
17 TraesCS1A01G209900 chr7D 540408178 540409046 868 True 1018.000000 1018 88.215000 1649 2500 1 chr7D.!!$R1 851
18 TraesCS1A01G209900 chr7D 159740966 159741678 712 False 953.000000 953 91.304000 1834 2525 1 chr7D.!!$F1 691
19 TraesCS1A01G209900 chr6B 182378878 182379721 843 True 1014.000000 1014 88.757000 1702 2525 1 chr6B.!!$R1 823
20 TraesCS1A01G209900 chr5D 509961632 509962319 687 True 835.000000 835 89.099000 1859 2525 1 chr5D.!!$R2 666
21 TraesCS1A01G209900 chr5D 226454610 226455195 585 True 747.000000 747 90.273000 1961 2525 1 chr5D.!!$R1 564
22 TraesCS1A01G209900 chr4B 603037677 603038646 969 False 819.000000 819 82.394000 679 1644 1 chr4B.!!$F1 965
23 TraesCS1A01G209900 chr4B 602873051 602874006 955 True 736.000000 736 81.256000 680 1648 1 chr4B.!!$R1 968
24 TraesCS1A01G209900 chr4B 602892973 602893924 951 True 732.000000 732 81.200000 680 1648 1 chr4B.!!$R2 968
25 TraesCS1A01G209900 chr4D 477542942 477543850 908 True 806.000000 806 83.191000 720 1624 1 chr4D.!!$R1 904
26 TraesCS1A01G209900 chr4D 477558662 477559506 844 False 767.000000 767 83.657000 679 1521 1 chr4D.!!$F1 842

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
191 192 0.541296 AAGAGCAGCCCAGCAACATT 60.541 50.0 0.0 0.0 36.85 2.71 F
1011 1977 0.392336 TGCATCCCAAACCAAAGCAC 59.608 50.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 2010 0.971959 ATGCCATTGCGATTGTGGGT 60.972 50.000 0.0 0.0 41.78 4.51 R
2246 3290 2.107366 TGTGAAGACCATATCCGAGCA 58.893 47.619 0.0 0.0 0.00 4.26 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
36 37 3.300667 GAGTTGCTTGCGGTCGCTG 62.301 63.158 16.36 10.08 42.51 5.18
48 49 0.673644 GGTCGCTGCTGGCTCTAAAA 60.674 55.000 0.00 0.00 39.13 1.52
49 50 1.156736 GTCGCTGCTGGCTCTAAAAA 58.843 50.000 0.00 0.00 39.13 1.94
76 77 2.990967 CACCGCTGGCCACCAATT 60.991 61.111 0.00 0.00 30.80 2.32
128 129 0.902531 TGTGGAGCCTAAGTGGTAGC 59.097 55.000 0.00 0.00 38.35 3.58
137 138 3.506067 GCCTAAGTGGTAGCAACACATTT 59.494 43.478 0.00 0.00 41.21 2.32
138 139 4.615912 GCCTAAGTGGTAGCAACACATTTG 60.616 45.833 0.00 0.00 41.21 2.32
139 140 4.518970 CCTAAGTGGTAGCAACACATTTGT 59.481 41.667 0.00 0.00 41.21 2.83
140 141 5.703592 CCTAAGTGGTAGCAACACATTTGTA 59.296 40.000 0.00 0.00 41.21 2.41
142 143 6.458232 AAGTGGTAGCAACACATTTGTAAA 57.542 33.333 0.00 0.00 41.21 2.01
151 152 2.619646 ACACATTTGTAAACCGGGTGTC 59.380 45.455 6.32 0.00 33.10 3.67
174 175 3.268013 ACCAAAATTCGCGTGAGAAAG 57.732 42.857 5.77 0.00 33.43 2.62
191 192 0.541296 AAGAGCAGCCCAGCAACATT 60.541 50.000 0.00 0.00 36.85 2.71
214 218 2.750637 GACCGTCTCCTCCTGCGA 60.751 66.667 0.00 0.00 0.00 5.10
216 220 1.874345 GACCGTCTCCTCCTGCGAAA 61.874 60.000 0.00 0.00 0.00 3.46
252 259 2.410469 GATGTTGCAGATGCCGCC 59.590 61.111 1.72 0.00 41.18 6.13
280 287 2.433145 ATCGGCAGTGCACAGTCG 60.433 61.111 27.71 27.71 0.00 4.18
346 1268 1.079543 CGGAAGACCAGGTCTGCTG 60.080 63.158 25.07 22.98 42.59 4.41
368 1290 6.261826 GCTGTGCTGATTAATCTCTACCATTT 59.738 38.462 16.24 0.00 0.00 2.32
370 1292 6.479990 TGTGCTGATTAATCTCTACCATTTCG 59.520 38.462 16.24 0.00 0.00 3.46
413 1335 8.503428 ACTATCAAAGGATGGATCTGTAGAAT 57.497 34.615 0.00 0.00 35.70 2.40
421 1348 8.676397 AGGATGGATCTGTAGAATCATCATAA 57.324 34.615 19.67 0.00 38.30 1.90
450 1377 7.770801 TGTATGATACCATCAAAGAAGAACG 57.229 36.000 0.00 0.00 43.50 3.95
485 1413 5.684704 TGTTCATTATTGATCTCCTCACCC 58.315 41.667 0.00 0.00 32.17 4.61
530 1458 7.722795 CATATGAATGGATGTAACGTAACCA 57.277 36.000 0.00 0.00 35.09 3.67
538 1466 6.751157 TGGATGTAACGTAACCATCGATATT 58.249 36.000 0.00 0.00 36.65 1.28
780 1716 4.858850 TGTTGCCATATCTCCAGAATTGT 58.141 39.130 0.00 0.00 0.00 2.71
786 1722 7.118723 TGCCATATCTCCAGAATTGTTAAACT 58.881 34.615 0.00 0.00 0.00 2.66
901 1857 4.368315 GCCACGTCTGATCATACATACAA 58.632 43.478 11.35 0.00 0.00 2.41
902 1858 4.808895 GCCACGTCTGATCATACATACAAA 59.191 41.667 11.35 0.00 0.00 2.83
937 1897 2.797156 CGTCAAACATCTCGATCCCATC 59.203 50.000 0.00 0.00 0.00 3.51
1008 1974 2.827322 TCTCATGCATCCCAAACCAAAG 59.173 45.455 0.00 0.00 0.00 2.77
1009 1975 1.275856 TCATGCATCCCAAACCAAAGC 59.724 47.619 0.00 0.00 0.00 3.51
1010 1976 1.002201 CATGCATCCCAAACCAAAGCA 59.998 47.619 0.00 0.00 34.78 3.91
1011 1977 0.392336 TGCATCCCAAACCAAAGCAC 59.608 50.000 0.00 0.00 0.00 4.40
1012 1978 0.681175 GCATCCCAAACCAAAGCACT 59.319 50.000 0.00 0.00 0.00 4.40
1013 1979 1.892474 GCATCCCAAACCAAAGCACTA 59.108 47.619 0.00 0.00 0.00 2.74
1014 1980 2.352715 GCATCCCAAACCAAAGCACTAC 60.353 50.000 0.00 0.00 0.00 2.73
1029 2010 5.100344 AGCACTACTACTACTCTAGCACA 57.900 43.478 0.00 0.00 0.00 4.57
1039 2020 1.066858 ACTCTAGCACACCCACAATCG 60.067 52.381 0.00 0.00 0.00 3.34
1228 2221 2.401766 GGGCAGTGCTCCATCAACG 61.402 63.158 16.11 0.00 0.00 4.10
1229 2222 1.672356 GGCAGTGCTCCATCAACGT 60.672 57.895 16.11 0.00 0.00 3.99
1289 2282 3.082579 GCTCGGCCTCAAGATCGGT 62.083 63.158 0.00 0.00 0.00 4.69
1340 2333 4.722700 CAGGGGTTGGCCGACCTG 62.723 72.222 36.28 25.75 43.87 4.00
1479 2475 2.544721 TCATTTGCCCAGCCCATTAAA 58.455 42.857 0.00 0.00 0.00 1.52
1487 2485 0.446222 CAGCCCATTAAACGGACGTG 59.554 55.000 0.00 0.00 0.00 4.49
1503 2505 2.186826 GTGCTGTTTCACGGGCACT 61.187 57.895 13.83 0.00 42.63 4.40
1522 2524 5.105063 GCACTGAATAAGATTTGCTTTCCC 58.895 41.667 0.00 0.00 38.05 3.97
1534 2547 6.713450 AGATTTGCTTTCCCTACTTCGTTTTA 59.287 34.615 0.00 0.00 0.00 1.52
1535 2548 6.696441 TTTGCTTTCCCTACTTCGTTTTAA 57.304 33.333 0.00 0.00 0.00 1.52
1583 2597 5.925969 CCACTCCCACATTTTAATTGTTGTC 59.074 40.000 0.00 0.00 0.00 3.18
1587 2601 4.994217 CCCACATTTTAATTGTTGTCACCC 59.006 41.667 0.00 0.00 0.00 4.61
1597 2611 3.815856 TGTTGTCACCCGTACTACAAA 57.184 42.857 0.00 0.00 33.92 2.83
1602 2616 6.095160 TGTTGTCACCCGTACTACAAATTTTT 59.905 34.615 0.00 0.00 33.92 1.94
1632 2655 5.215160 GCAAAACAACCATGTACTCTTCAG 58.785 41.667 0.00 0.00 39.40 3.02
1728 2751 2.154462 GTCGGGCCCTCATATTTCATG 58.846 52.381 22.43 0.00 0.00 3.07
1752 2775 5.008019 GTCGTGCATCCACATATCTCAAATT 59.992 40.000 0.00 0.00 42.17 1.82
1756 2779 4.516698 GCATCCACATATCTCAAATTCGGT 59.483 41.667 0.00 0.00 0.00 4.69
1767 2790 4.864806 TCTCAAATTCGGTCTCTCAAATCG 59.135 41.667 0.00 0.00 0.00 3.34
1808 2831 3.780279 CGATTATGCAACACAATGTCACG 59.220 43.478 0.00 0.00 0.00 4.35
1844 2867 9.276590 CAATTGTTGGTATCAAGCATAGATAGA 57.723 33.333 0.00 0.00 32.92 1.98
2022 3045 2.208431 CGCATCTTGATCTTCCAGGAC 58.792 52.381 0.00 0.00 0.00 3.85
2075 3119 3.643320 AGCCTCATCCTCGACAATCATAA 59.357 43.478 0.00 0.00 0.00 1.90
2082 3126 4.512484 TCCTCGACAATCATAATGTGCAA 58.488 39.130 0.00 0.00 0.00 4.08
2210 3254 2.064581 TCCTTCCTAGCCGCTTCCC 61.065 63.158 0.00 0.00 0.00 3.97
2246 3290 1.539827 GGCTCTGTTTATTGCCACGTT 59.460 47.619 0.00 0.00 44.34 3.99
2278 3322 1.873591 GTCTTCACAAACACCGCTCAT 59.126 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.615912 GCAAGCAACTCAACTCTCTGTT 59.384 45.455 0.00 0.00 39.92 3.16
76 77 1.847506 AGTGGGGATGCACACTCCA 60.848 57.895 17.47 9.89 44.08 3.86
81 82 1.604308 CAAGCAGTGGGGATGCACA 60.604 57.895 0.00 0.00 46.31 4.57
83 84 2.036098 CCAAGCAGTGGGGATGCA 59.964 61.111 0.00 0.00 46.31 3.96
128 129 3.181485 ACACCCGGTTTACAAATGTGTTG 60.181 43.478 0.00 0.00 39.30 3.33
137 138 0.316841 GGTACGACACCCGGTTTACA 59.683 55.000 0.00 0.00 42.07 2.41
138 139 3.122150 GGTACGACACCCGGTTTAC 57.878 57.895 0.00 0.00 42.07 2.01
151 152 1.722464 TCTCACGCGAATTTTGGTACG 59.278 47.619 15.93 0.00 0.00 3.67
160 161 1.354040 CTGCTCTTTCTCACGCGAAT 58.646 50.000 15.93 0.00 0.00 3.34
174 175 0.389426 CAAATGTTGCTGGGCTGCTC 60.389 55.000 0.00 0.00 0.00 4.26
191 192 0.471211 AGGAGGAGACGGTCAACCAA 60.471 55.000 20.49 0.00 35.14 3.67
227 231 2.825075 ATCTGCAACATCCAGCGGCA 62.825 55.000 1.45 0.00 37.06 5.69
262 269 2.447887 CGACTGTGCACTGCCGATC 61.448 63.158 24.18 12.97 0.00 3.69
266 273 2.591715 AACCGACTGTGCACTGCC 60.592 61.111 22.15 11.64 0.00 4.85
272 279 0.861837 CTCTTCACAACCGACTGTGC 59.138 55.000 10.87 0.00 45.25 4.57
280 287 1.000938 CTTGGCTTGCTCTTCACAACC 60.001 52.381 0.00 0.00 0.00 3.77
328 1250 1.079543 CAGCAGACCTGGTCTTCCG 60.080 63.158 26.37 16.36 41.37 4.30
339 1261 4.440880 AGAGATTAATCAGCACAGCAGAC 58.559 43.478 17.56 0.00 0.00 3.51
346 1268 6.701841 TCGAAATGGTAGAGATTAATCAGCAC 59.298 38.462 17.56 10.61 0.00 4.40
368 1290 7.504574 TGATAGTCATCTGGGTTTAGTTATCGA 59.495 37.037 0.00 0.00 31.93 3.59
370 1292 9.832445 TTTGATAGTCATCTGGGTTTAGTTATC 57.168 33.333 0.00 0.00 31.93 1.75
427 1354 7.254455 CCACGTTCTTCTTTGATGGTATCATAC 60.254 40.741 0.00 0.00 39.39 2.39
428 1355 6.761242 CCACGTTCTTCTTTGATGGTATCATA 59.239 38.462 0.00 0.00 39.39 2.15
432 1359 3.689649 GCCACGTTCTTCTTTGATGGTAT 59.310 43.478 0.00 0.00 0.00 2.73
445 1372 1.302033 CAAGCTGGAGCCACGTTCT 60.302 57.895 0.00 0.00 43.38 3.01
447 1374 1.152963 AACAAGCTGGAGCCACGTT 60.153 52.632 0.00 0.00 43.38 3.99
450 1377 1.251251 AATGAACAAGCTGGAGCCAC 58.749 50.000 0.00 0.00 43.38 5.01
485 1413 1.136721 GCGTATTATAAGCGTGCGTGG 60.137 52.381 11.95 0.00 0.00 4.94
518 1446 4.746115 GCCAATATCGATGGTTACGTTACA 59.254 41.667 8.54 0.00 40.23 2.41
530 1458 3.589988 CGGAAGCTAAGCCAATATCGAT 58.410 45.455 2.16 2.16 0.00 3.59
538 1466 1.192146 AGACACCGGAAGCTAAGCCA 61.192 55.000 9.46 0.00 0.00 4.75
690 1619 2.183478 TACCTTGTCATGCCACACAG 57.817 50.000 0.00 0.00 0.00 3.66
925 1885 0.763986 TGCATGGGATGGGATCGAGA 60.764 55.000 0.00 0.00 0.00 4.04
937 1897 2.165641 GTGATATGGATGCATGCATGGG 59.834 50.000 35.62 4.09 39.29 4.00
1008 1974 4.035441 GGTGTGCTAGAGTAGTAGTAGTGC 59.965 50.000 0.00 0.00 0.00 4.40
1009 1975 4.575645 GGGTGTGCTAGAGTAGTAGTAGTG 59.424 50.000 0.00 0.00 0.00 2.74
1010 1976 4.226846 TGGGTGTGCTAGAGTAGTAGTAGT 59.773 45.833 0.00 0.00 0.00 2.73
1011 1977 4.575645 GTGGGTGTGCTAGAGTAGTAGTAG 59.424 50.000 0.00 0.00 0.00 2.57
1012 1978 4.019051 TGTGGGTGTGCTAGAGTAGTAGTA 60.019 45.833 0.00 0.00 0.00 1.82
1013 1979 3.245158 TGTGGGTGTGCTAGAGTAGTAGT 60.245 47.826 0.00 0.00 0.00 2.73
1014 1980 3.353557 TGTGGGTGTGCTAGAGTAGTAG 58.646 50.000 0.00 0.00 0.00 2.57
1029 2010 0.971959 ATGCCATTGCGATTGTGGGT 60.972 50.000 0.00 0.00 41.78 4.51
1039 2020 3.059603 CAGCTTTGGATGCCATTGC 57.940 52.632 0.00 0.00 34.17 3.56
1228 2221 4.386413 CCCTCAGGTTGAGCACAC 57.614 61.111 0.54 0.00 42.98 3.82
1446 2442 1.627879 CAAATGAAATTGGACGGGCG 58.372 50.000 0.00 0.00 36.10 6.13
1455 2451 1.360185 TGGGCTGGGCAAATGAAATT 58.640 45.000 0.00 0.00 38.98 1.82
1479 2475 3.713963 GTGAAACAGCACGTCCGT 58.286 55.556 0.00 0.00 36.32 4.69
1487 2485 1.444119 TTCAGTGCCCGTGAAACAGC 61.444 55.000 0.00 0.00 35.74 4.40
1493 2491 3.627395 AATCTTATTCAGTGCCCGTGA 57.373 42.857 0.00 0.00 0.00 4.35
1501 2503 7.406104 AGTAGGGAAAGCAAATCTTATTCAGT 58.594 34.615 0.00 0.00 33.88 3.41
1503 2505 7.065803 CGAAGTAGGGAAAGCAAATCTTATTCA 59.934 37.037 0.00 0.00 33.88 2.57
1534 2547 8.822652 GAAGAGTTCCACATTTCATGAAATTT 57.177 30.769 27.30 20.17 38.84 1.82
1556 2570 6.345096 ACAATTAAAATGTGGGAGTGGAAG 57.655 37.500 0.00 0.00 0.00 3.46
1604 2627 5.810074 AGAGTACATGGTTGTTTTGCAAAAC 59.190 36.000 36.78 36.78 46.40 2.43
1610 2633 6.618287 TCTGAAGAGTACATGGTTGTTTTG 57.382 37.500 0.00 0.00 37.28 2.44
1611 2634 7.502226 TCAATCTGAAGAGTACATGGTTGTTTT 59.498 33.333 0.00 0.00 37.28 2.43
1650 2673 3.380320 GCCAAGTCCGGTTATAAATGCTT 59.620 43.478 0.00 0.00 0.00 3.91
1659 2682 1.828979 GGATTTGCCAAGTCCGGTTA 58.171 50.000 2.98 0.00 36.34 2.85
1709 2732 1.774254 ACATGAAATATGAGGGCCCGA 59.226 47.619 18.44 7.74 0.00 5.14
1728 2751 3.097877 TGAGATATGTGGATGCACGAC 57.902 47.619 13.03 4.12 0.00 4.34
1752 2775 1.476488 TGCATCGATTTGAGAGACCGA 59.524 47.619 0.00 0.00 0.00 4.69
1756 2779 6.512253 GCATGTATTTGCATCGATTTGAGAGA 60.512 38.462 0.00 0.00 42.31 3.10
1783 2806 4.142708 TGACATTGTGTTGCATAATCGACC 60.143 41.667 0.00 0.00 0.00 4.79
1808 2831 6.491394 TGATACCAACAATTGCTATTTACGC 58.509 36.000 5.05 0.00 0.00 4.42
1864 2887 2.798283 CAATGCTTGAGTTTGGCACTTG 59.202 45.455 0.00 0.00 38.83 3.16
2022 3045 2.291741 GCACCTGGAGAACAAGTTGAAG 59.708 50.000 10.54 0.00 0.00 3.02
2054 3098 2.540265 ATGATTGTCGAGGATGAGGC 57.460 50.000 0.00 0.00 0.00 4.70
2075 3119 6.279123 TGACATGTTGTGTTATTTTGCACAT 58.721 32.000 0.00 0.00 43.89 3.21
2082 3126 6.384224 CAGCTGATGACATGTTGTGTTATTT 58.616 36.000 8.42 0.00 42.36 1.40
2246 3290 2.107366 TGTGAAGACCATATCCGAGCA 58.893 47.619 0.00 0.00 0.00 4.26
2278 3322 6.068670 TCTTGTCGATGGTATCTATCCTCAA 58.931 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.