Multiple sequence alignment - TraesCS1D01G278100

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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 TraesCS1D01G278100 chr1D 100.000 3716 0 0 1 3716 375370894 375367179 0.000000e+00 6863.0
1 TraesCS1D01G278100 chr1D 91.820 489 35 4 3232 3716 233888768 233889255 0.000000e+00 676.0
2 TraesCS1D01G278100 chr1D 91.718 483 35 4 3238 3716 367673932 367673451 0.000000e+00 665.0
3 TraesCS1D01G278100 chr1B 94.290 2189 67 18 924 3090 500539094 500541246 0.000000e+00 3297.0
4 TraesCS1D01G278100 chr1B 90.067 594 46 7 310 895 500537921 500538509 0.000000e+00 758.0
5 TraesCS1D01G278100 chr1B 88.021 192 12 3 132 312 500537410 500537601 2.250000e-52 217.0
6 TraesCS1D01G278100 chr1B 98.718 78 1 0 2 79 500536824 500536901 5.000000e-29 139.0
7 TraesCS1D01G278100 chr1B 95.082 61 3 0 75 135 500536936 500536996 3.050000e-16 97.1
8 TraesCS1D01G278100 chr1A 95.899 2024 68 7 924 2940 474432623 474430608 0.000000e+00 3264.0
9 TraesCS1D01G278100 chr1A 89.776 401 35 4 501 898 474433353 474432956 3.310000e-140 508.0
10 TraesCS1D01G278100 chr1A 88.036 443 35 14 75 514 474433795 474433368 3.310000e-140 508.0
11 TraesCS1D01G278100 chr3A 82.159 1306 208 24 1403 2697 616726252 616724961 0.000000e+00 1098.0
12 TraesCS1D01G278100 chr3D 81.645 1313 211 27 1400 2697 474450869 474452166 0.000000e+00 1062.0
13 TraesCS1D01G278100 chr3B 81.541 1311 213 27 1400 2697 630869158 630870452 0.000000e+00 1053.0
14 TraesCS1D01G278100 chr2D 92.540 496 30 6 3227 3716 316140210 316140704 0.000000e+00 704.0
15 TraesCS1D01G278100 chr6B 90.909 528 38 7 3195 3716 465666203 465665680 0.000000e+00 701.0
16 TraesCS1D01G278100 chr7D 87.122 629 62 12 3097 3716 453146514 453145896 0.000000e+00 695.0
17 TraesCS1D01G278100 chr7D 92.387 486 32 4 3235 3716 367576883 367577367 0.000000e+00 688.0
18 TraesCS1D01G278100 chr7D 91.753 485 35 4 3236 3716 412013394 412013877 0.000000e+00 669.0
19 TraesCS1D01G278100 chr2B 91.581 487 35 5 3235 3716 536614443 536613958 0.000000e+00 667.0
20 TraesCS1D01G278100 chr5B 91.358 486 36 5 3235 3716 670435444 670435927 0.000000e+00 660.0
21 TraesCS1D01G278100 chr7B 100.000 29 0 0 293 321 455440626 455440598 2.000000e-03 54.7


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 TraesCS1D01G278100 chr1D 375367179 375370894 3715 True 6863.000000 6863 100.0000 1 3716 1 chr1D.!!$R2 3715
1 TraesCS1D01G278100 chr1B 500536824 500541246 4422 False 901.620000 3297 93.2356 2 3090 5 chr1B.!!$F1 3088
2 TraesCS1D01G278100 chr1A 474430608 474433795 3187 True 1426.666667 3264 91.2370 75 2940 3 chr1A.!!$R1 2865
3 TraesCS1D01G278100 chr3A 616724961 616726252 1291 True 1098.000000 1098 82.1590 1403 2697 1 chr3A.!!$R1 1294
4 TraesCS1D01G278100 chr3D 474450869 474452166 1297 False 1062.000000 1062 81.6450 1400 2697 1 chr3D.!!$F1 1297
5 TraesCS1D01G278100 chr3B 630869158 630870452 1294 False 1053.000000 1053 81.5410 1400 2697 1 chr3B.!!$F1 1297
6 TraesCS1D01G278100 chr6B 465665680 465666203 523 True 701.000000 701 90.9090 3195 3716 1 chr6B.!!$R1 521
7 TraesCS1D01G278100 chr7D 453145896 453146514 618 True 695.000000 695 87.1220 3097 3716 1 chr7D.!!$R1 619

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
902 1730 0.108585 AGAAAAGCGTTGCTGGAGGA 59.891 50.0 0.00 0.00 39.62 3.71 F
1029 2495 0.326264 GCTTTCTCTGGCCAGGAAGA 59.674 55.0 31.23 25.79 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 4142 1.154016 CAGGAACTCGTCGTCGCAT 60.154 57.895 0.0 0.0 34.6 4.73 R
2981 4461 0.536460 GTGGTTTTGGCCCTCTTCGA 60.536 55.000 0.0 0.0 0.0 3.71 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
92 132 4.338400 GTCTTTCCACCTATAACCATTGCC 59.662 45.833 0.00 0.00 0.00 4.52
207 666 6.946340 AGAAGTTTGTTCTGGTTGGAAAAAT 58.054 32.000 0.00 0.00 0.00 1.82
211 670 7.791029 AGTTTGTTCTGGTTGGAAAAATATGT 58.209 30.769 0.00 0.00 0.00 2.29
249 708 8.950210 TCTGATCAGGTGATTTTAAGTTTGATC 58.050 33.333 22.42 4.63 39.84 2.92
381 1172 3.990469 AGTCGATCTAGTTGTGCACAAAG 59.010 43.478 32.61 25.92 37.63 2.77
428 1219 9.860898 AGTAAATTCTGCTGAAAATAAATCACC 57.139 29.630 10.27 0.00 35.63 4.02
429 1220 9.638239 GTAAATTCTGCTGAAAATAAATCACCA 57.362 29.630 10.27 0.00 35.63 4.17
430 1221 8.538409 AAATTCTGCTGAAAATAAATCACCAC 57.462 30.769 10.27 0.00 35.63 4.16
432 1223 6.899393 TCTGCTGAAAATAAATCACCACTT 57.101 33.333 0.00 0.00 0.00 3.16
433 1224 6.680810 TCTGCTGAAAATAAATCACCACTTG 58.319 36.000 0.00 0.00 0.00 3.16
553 1372 9.979578 TTTAATGTAATTCATTGTCAAAGTGCT 57.020 25.926 11.20 0.00 45.14 4.40
563 1382 2.878406 TGTCAAAGTGCTACTTTCCAGC 59.122 45.455 10.19 0.00 44.47 4.85
589 1408 2.609002 GCAAGAAAAAGGTGCCACTTTG 59.391 45.455 0.00 0.00 40.36 2.77
591 1410 1.202405 AGAAAAAGGTGCCACTTTGCG 60.202 47.619 0.00 0.00 40.36 4.85
612 1431 1.741706 GATGCACATCACTGTCCAAGG 59.258 52.381 5.76 0.00 37.74 3.61
647 1468 7.028926 TGAGGATCAGAAAGAATACGTACTC 57.971 40.000 0.00 0.00 42.56 2.59
724 1545 2.731217 GTGCGCTCAAATGTGACTTTT 58.269 42.857 9.73 0.00 0.00 2.27
726 1547 2.618241 TGCGCTCAAATGTGACTTTTCT 59.382 40.909 9.73 0.00 0.00 2.52
754 1582 1.328279 TTCCTTGTGAGAGCGACAGA 58.672 50.000 0.00 0.00 0.00 3.41
756 1584 1.474478 TCCTTGTGAGAGCGACAGATC 59.526 52.381 0.00 0.00 0.00 2.75
759 1587 1.539157 TGTGAGAGCGACAGATCTGT 58.461 50.000 28.23 28.23 44.10 3.41
760 1588 1.200948 TGTGAGAGCGACAGATCTGTG 59.799 52.381 32.50 23.02 44.10 3.66
763 1591 2.163211 TGAGAGCGACAGATCTGTGAAG 59.837 50.000 32.50 22.13 44.10 3.02
830 1658 6.516718 TCCTATTCCTCGTCAATTGAAGATC 58.483 40.000 21.83 4.31 32.45 2.75
882 1710 3.261897 TGGAGAAGAAATGAGGTCTCACC 59.738 47.826 2.46 0.00 43.11 4.02
888 1716 5.310409 AGAAATGAGGTCTCACCAGAAAA 57.690 39.130 2.46 0.00 41.95 2.29
889 1717 5.312079 AGAAATGAGGTCTCACCAGAAAAG 58.688 41.667 2.46 0.00 41.95 2.27
895 1723 0.944386 TCTCACCAGAAAAGCGTTGC 59.056 50.000 0.00 0.00 0.00 4.17
897 1725 0.662619 TCACCAGAAAAGCGTTGCTG 59.337 50.000 13.04 13.04 39.62 4.41
900 1728 3.761481 CAGAAAAGCGTTGCTGGAG 57.239 52.632 12.23 0.00 39.62 3.86
901 1729 0.239347 CAGAAAAGCGTTGCTGGAGG 59.761 55.000 12.23 0.00 39.62 4.30
902 1730 0.108585 AGAAAAGCGTTGCTGGAGGA 59.891 50.000 0.00 0.00 39.62 3.71
903 1731 0.951558 GAAAAGCGTTGCTGGAGGAA 59.048 50.000 0.00 0.00 39.62 3.36
904 1732 1.541588 GAAAAGCGTTGCTGGAGGAAT 59.458 47.619 0.00 0.00 39.62 3.01
905 1733 0.883833 AAAGCGTTGCTGGAGGAATG 59.116 50.000 0.00 0.00 39.62 2.67
926 1754 2.159338 GGCGTATGGTTGACTAGTTCGA 60.159 50.000 0.00 0.00 0.00 3.71
927 1755 3.490419 GGCGTATGGTTGACTAGTTCGAT 60.490 47.826 0.00 0.00 0.00 3.59
931 1759 5.803461 CGTATGGTTGACTAGTTCGATTGAA 59.197 40.000 0.00 0.00 0.00 2.69
932 1760 6.309494 CGTATGGTTGACTAGTTCGATTGAAA 59.691 38.462 0.00 0.00 35.46 2.69
933 1761 5.917541 TGGTTGACTAGTTCGATTGAAAC 57.082 39.130 0.00 0.00 35.46 2.78
934 1762 5.607477 TGGTTGACTAGTTCGATTGAAACT 58.393 37.500 0.00 0.55 35.46 2.66
935 1763 6.751157 TGGTTGACTAGTTCGATTGAAACTA 58.249 36.000 0.00 1.67 35.46 2.24
954 2420 9.444600 TGAAACTAGTAACATATTTTCAGGGTC 57.555 33.333 0.00 0.00 32.55 4.46
1029 2495 0.326264 GCTTTCTCTGGCCAGGAAGA 59.674 55.000 31.23 25.79 0.00 2.87
1139 2611 1.442526 GCGAGATGCATGAACCCAGG 61.443 60.000 2.46 0.00 45.45 4.45
1410 2882 1.671379 GCCGGTTGGAGACCTCAAC 60.671 63.158 1.90 0.00 46.92 3.18
1461 2933 1.985159 TGCCACTACATTCAGAAGGGT 59.015 47.619 0.00 0.00 0.00 4.34
2136 3611 3.319198 GTCCAGGGAGGTTGCGGA 61.319 66.667 0.00 0.00 39.02 5.54
2667 4142 4.815973 ACCATGGGCCGCCTCCTA 62.816 66.667 18.09 0.00 0.00 2.94
2712 4187 2.040544 GTCCCATGCACCTTCACCG 61.041 63.158 0.00 0.00 0.00 4.94
2837 4312 6.121613 CATGTCACATGCATGTATGTAACA 57.878 37.500 28.28 28.28 41.92 2.41
2838 4313 5.544136 TGTCACATGCATGTATGTAACAC 57.456 39.130 30.92 20.82 42.09 3.32
2840 4315 5.647225 TGTCACATGCATGTATGTAACACAT 59.353 36.000 30.92 1.90 42.09 3.21
2846 4324 7.523544 ACATGCATGTATGTAACACATGTTTGT 60.524 33.333 30.50 14.49 46.02 2.83
2873 4351 7.622256 GCAGCAGATACGTAATGGATTTGTATC 60.622 40.741 0.00 12.28 40.91 2.24
2879 4357 4.200827 CGTAATGGATTTGTATCGTTGCG 58.799 43.478 0.00 0.00 33.08 4.85
2884 4362 4.939271 TGGATTTGTATCGTTGCGAGATA 58.061 39.130 0.00 0.00 39.91 1.98
2885 4363 5.538118 TGGATTTGTATCGTTGCGAGATAT 58.462 37.500 0.00 0.00 39.91 1.63
2886 4364 5.633601 TGGATTTGTATCGTTGCGAGATATC 59.366 40.000 0.00 0.00 39.91 1.63
2887 4365 5.633601 GGATTTGTATCGTTGCGAGATATCA 59.366 40.000 5.32 0.00 39.91 2.15
2921 4399 2.615986 TGGACTGGTTGGCTACTCTA 57.384 50.000 0.00 0.00 0.00 2.43
2929 4409 4.816126 TGGTTGGCTACTCTATATCCAGT 58.184 43.478 0.00 0.00 0.00 4.00
2981 4461 1.802337 TACTGGCGCTCAAGTCGTGT 61.802 55.000 7.64 0.00 0.00 4.49
3004 4484 0.261696 AGAGGGCCAAAACCACTGTT 59.738 50.000 6.18 0.00 35.82 3.16
3063 4555 7.024340 AGCGAAGTTAAGTATGATCTCGTTA 57.976 36.000 0.00 0.00 0.00 3.18
3073 4565 7.507672 AGTATGATCTCGTTACGAAACTTTG 57.492 36.000 9.23 0.00 34.74 2.77
3082 4574 2.793278 ACGAAACTTTGGCATGAACC 57.207 45.000 0.00 0.00 0.00 3.62
3083 4575 2.028130 ACGAAACTTTGGCATGAACCA 58.972 42.857 0.00 0.00 38.16 3.67
3090 4582 1.337118 TTGGCATGAACCAACCTTCC 58.663 50.000 0.00 0.00 44.80 3.46
3091 4583 0.893270 TGGCATGAACCAACCTTCCG 60.893 55.000 0.00 0.00 36.55 4.30
3092 4584 0.608035 GGCATGAACCAACCTTCCGA 60.608 55.000 0.00 0.00 0.00 4.55
3093 4585 0.804989 GCATGAACCAACCTTCCGAG 59.195 55.000 0.00 0.00 0.00 4.63
3094 4586 1.610624 GCATGAACCAACCTTCCGAGA 60.611 52.381 0.00 0.00 0.00 4.04
3095 4587 2.076863 CATGAACCAACCTTCCGAGAC 58.923 52.381 0.00 0.00 0.00 3.36
3103 4595 2.217510 ACCTTCCGAGACTAAGAGCA 57.782 50.000 0.00 0.00 0.00 4.26
3135 4627 0.677842 GACCCCGTATAATGCCGACT 59.322 55.000 0.00 0.00 0.00 4.18
3167 4659 4.148891 CGTTTACAGATCGCAGAAAAACC 58.851 43.478 0.00 0.00 43.58 3.27
3173 4665 3.071479 AGATCGCAGAAAAACCGCTTTA 58.929 40.909 0.00 0.00 43.58 1.85
3174 4666 2.673976 TCGCAGAAAAACCGCTTTAC 57.326 45.000 0.00 0.00 0.00 2.01
3279 4786 9.703892 TTATTTCAATTTCGGACATGAAAACAT 57.296 25.926 0.00 0.00 42.89 2.71
3284 4791 9.703892 TCAATTTCGGACATGAAAACATATTTT 57.296 25.926 0.00 0.00 40.90 1.82
3320 4827 8.830915 TTATTTACTTCAAGGGCATTGGATAA 57.169 30.769 12.41 5.80 39.54 1.75
3440 4951 6.824305 CATTAGTTGGACCAACATCTTCTT 57.176 37.500 33.44 16.95 45.66 2.52
3580 5094 5.355350 GCCGCATTATTAGCCTCAATTCTAT 59.645 40.000 0.00 0.00 0.00 1.98
3599 5113 2.425578 TCAACGAGTGCACGAACATA 57.574 45.000 12.01 0.00 37.03 2.29
3673 5187 1.204146 TGAGCATCCACCTTCCTACC 58.796 55.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.814764 AGTCGGTAGTGCTATATATTCGG 57.185 43.478 0.00 0.00 0.00 4.30
207 666 9.295825 ACCTGATCAGACAAATTGTAAAACATA 57.704 29.630 24.62 0.00 0.00 2.29
211 670 7.815840 TCACCTGATCAGACAAATTGTAAAA 57.184 32.000 24.62 0.00 0.00 1.52
403 1194 9.638239 TGGTGATTTATTTTCAGCAGAATTTAC 57.362 29.630 1.76 0.00 44.23 2.01
424 1215 8.628630 TTACATGTTGATAATTCAAGTGGTGA 57.371 30.769 2.30 0.00 42.41 4.02
425 1216 9.859427 ATTTACATGTTGATAATTCAAGTGGTG 57.141 29.630 2.30 0.00 42.41 4.17
553 1372 2.478335 CTTGCGGGGGCTGGAAAGTA 62.478 60.000 0.00 0.00 0.00 2.24
563 1382 1.665442 CACCTTTTTCTTGCGGGGG 59.335 57.895 0.00 0.00 0.00 5.40
589 1408 1.709147 GGACAGTGATGTGCATCCGC 61.709 60.000 9.39 3.43 37.02 5.54
591 1410 1.741706 CTTGGACAGTGATGTGCATCC 59.258 52.381 9.39 0.00 39.75 3.51
612 1431 0.535335 TGATCCTCAACGTGGGTAGC 59.465 55.000 0.00 0.00 0.00 3.58
647 1468 4.261322 CGGATTGGCATAGAAATTCACAGG 60.261 45.833 0.00 0.00 0.00 4.00
724 1545 5.241403 TCTCACAAGGAAAAAGGCATAGA 57.759 39.130 0.00 0.00 0.00 1.98
726 1547 3.758554 GCTCTCACAAGGAAAAAGGCATA 59.241 43.478 0.00 0.00 0.00 3.14
754 1582 2.167281 AGCGATGCAGTACTTCACAGAT 59.833 45.455 0.00 0.00 0.00 2.90
756 1584 2.001812 AGCGATGCAGTACTTCACAG 57.998 50.000 0.00 0.00 0.00 3.66
759 1587 2.610433 CTCAAGCGATGCAGTACTTCA 58.390 47.619 0.00 0.00 0.00 3.02
760 1588 1.325943 GCTCAAGCGATGCAGTACTTC 59.674 52.381 0.00 0.00 0.00 3.01
800 1628 7.338710 TCAATTGACGAGGAATAGGAAAATCT 58.661 34.615 3.38 0.00 0.00 2.40
838 1666 6.263392 TCCACCAAAATCGTCTGAAACATTAA 59.737 34.615 0.00 0.00 0.00 1.40
840 1668 4.582656 TCCACCAAAATCGTCTGAAACATT 59.417 37.500 0.00 0.00 0.00 2.71
841 1669 4.141287 TCCACCAAAATCGTCTGAAACAT 58.859 39.130 0.00 0.00 0.00 2.71
842 1670 3.546724 TCCACCAAAATCGTCTGAAACA 58.453 40.909 0.00 0.00 0.00 2.83
843 1671 3.813166 TCTCCACCAAAATCGTCTGAAAC 59.187 43.478 0.00 0.00 0.00 2.78
882 1710 0.239347 CCTCCAGCAACGCTTTTCTG 59.761 55.000 0.00 0.00 36.40 3.02
888 1716 1.377725 CCATTCCTCCAGCAACGCT 60.378 57.895 0.00 0.00 40.77 5.07
889 1717 3.056313 GCCATTCCTCCAGCAACGC 62.056 63.158 0.00 0.00 0.00 4.84
895 1723 0.469917 ACCATACGCCATTCCTCCAG 59.530 55.000 0.00 0.00 0.00 3.86
897 1725 1.134220 TCAACCATACGCCATTCCTCC 60.134 52.381 0.00 0.00 0.00 4.30
898 1726 1.940613 GTCAACCATACGCCATTCCTC 59.059 52.381 0.00 0.00 0.00 3.71
899 1727 1.559682 AGTCAACCATACGCCATTCCT 59.440 47.619 0.00 0.00 0.00 3.36
900 1728 2.038387 AGTCAACCATACGCCATTCC 57.962 50.000 0.00 0.00 0.00 3.01
901 1729 3.793559 ACTAGTCAACCATACGCCATTC 58.206 45.455 0.00 0.00 0.00 2.67
902 1730 3.906720 ACTAGTCAACCATACGCCATT 57.093 42.857 0.00 0.00 0.00 3.16
903 1731 3.737047 CGAACTAGTCAACCATACGCCAT 60.737 47.826 0.00 0.00 0.00 4.40
904 1732 2.416296 CGAACTAGTCAACCATACGCCA 60.416 50.000 0.00 0.00 0.00 5.69
905 1733 2.159338 TCGAACTAGTCAACCATACGCC 60.159 50.000 0.00 0.00 0.00 5.68
927 1755 9.802039 ACCCTGAAAATATGTTACTAGTTTCAA 57.198 29.630 0.00 0.00 42.02 2.69
931 1759 7.548075 CACGACCCTGAAAATATGTTACTAGTT 59.452 37.037 0.00 0.00 0.00 2.24
932 1760 7.039882 CACGACCCTGAAAATATGTTACTAGT 58.960 38.462 0.00 0.00 0.00 2.57
933 1761 7.262772 TCACGACCCTGAAAATATGTTACTAG 58.737 38.462 0.00 0.00 0.00 2.57
934 1762 7.172868 TCACGACCCTGAAAATATGTTACTA 57.827 36.000 0.00 0.00 0.00 1.82
935 1763 6.045072 TCACGACCCTGAAAATATGTTACT 57.955 37.500 0.00 0.00 0.00 2.24
1029 2495 5.182001 GTGGATGTGCTGATAAGAAGTTGTT 59.818 40.000 0.00 0.00 0.00 2.83
1139 2611 0.622665 ATATAGGCATGGAGCTGGGC 59.377 55.000 0.00 0.00 44.79 5.36
1296 2768 0.963355 GGTTTAGCACGGCCATGGAA 60.963 55.000 18.40 0.00 0.00 3.53
1461 2933 3.771160 GCGGGCGGGAAGAAGAGA 61.771 66.667 0.00 0.00 0.00 3.10
2136 3611 2.422803 CGACTGGAAGGAGGAGATCTCT 60.423 54.545 21.81 8.41 42.10 3.10
2667 4142 1.154016 CAGGAACTCGTCGTCGCAT 60.154 57.895 0.00 0.00 34.60 4.73
2745 4220 3.829948 CTGGTACTGTAGTGGTACAACG 58.170 50.000 0.00 0.00 44.16 4.10
2835 4310 1.391577 TCTGCTGCACAAACATGTGT 58.608 45.000 0.00 0.00 41.53 3.72
2836 4311 2.717580 ATCTGCTGCACAAACATGTG 57.282 45.000 0.00 4.64 42.32 3.21
2837 4312 2.160219 CGTATCTGCTGCACAAACATGT 59.840 45.455 0.00 0.00 0.00 3.21
2838 4313 2.160219 ACGTATCTGCTGCACAAACATG 59.840 45.455 0.00 0.00 0.00 3.21
2840 4315 1.877637 ACGTATCTGCTGCACAAACA 58.122 45.000 0.00 0.00 0.00 2.83
2841 4316 4.334443 CATTACGTATCTGCTGCACAAAC 58.666 43.478 0.00 0.00 0.00 2.93
2842 4317 3.373748 CCATTACGTATCTGCTGCACAAA 59.626 43.478 0.00 0.00 0.00 2.83
2846 4324 3.751479 ATCCATTACGTATCTGCTGCA 57.249 42.857 0.88 0.88 0.00 4.41
2873 4351 5.641777 TTCTTGATTGATATCTCGCAACG 57.358 39.130 3.98 0.00 0.00 4.10
2884 4362 8.003044 ACCAGTCCATGATATTTCTTGATTGAT 58.997 33.333 0.00 0.00 30.49 2.57
2885 4363 7.348815 ACCAGTCCATGATATTTCTTGATTGA 58.651 34.615 0.00 0.00 30.49 2.57
2886 4364 7.578310 ACCAGTCCATGATATTTCTTGATTG 57.422 36.000 0.00 0.00 30.49 2.67
2887 4365 7.069085 CCAACCAGTCCATGATATTTCTTGATT 59.931 37.037 0.00 0.00 30.49 2.57
2921 4399 5.326283 TCTAGCTGGTCACTACTGGATAT 57.674 43.478 0.00 0.00 0.00 1.63
2929 4409 7.033782 ACATATCCTATCTAGCTGGTCACTA 57.966 40.000 0.00 0.00 0.00 2.74
2981 4461 0.536460 GTGGTTTTGGCCCTCTTCGA 60.536 55.000 0.00 0.00 0.00 3.71
3010 4490 8.586570 AAAATCATAACAATGTCTTCGCAAAA 57.413 26.923 0.00 0.00 0.00 2.44
3040 4527 6.129769 CGTAACGAGATCATACTTAACTTCGC 60.130 42.308 0.00 0.00 0.00 4.70
3051 4538 5.290158 GCCAAAGTTTCGTAACGAGATCATA 59.710 40.000 0.00 0.00 39.31 2.15
3059 4551 3.529634 TCATGCCAAAGTTTCGTAACG 57.470 42.857 0.00 0.00 39.31 3.18
3063 4555 2.028130 TGGTTCATGCCAAAGTTTCGT 58.972 42.857 0.00 0.00 35.25 3.85
3073 4565 0.608035 TCGGAAGGTTGGTTCATGCC 60.608 55.000 0.00 0.00 0.00 4.40
3082 4574 2.231478 TGCTCTTAGTCTCGGAAGGTTG 59.769 50.000 0.00 0.00 0.00 3.77
3083 4575 2.526432 TGCTCTTAGTCTCGGAAGGTT 58.474 47.619 0.00 0.00 0.00 3.50
3090 4582 5.989168 TCTTCTAGAGATGCTCTTAGTCTCG 59.011 44.000 1.88 0.00 41.50 4.04
3091 4583 7.715249 TCTTCTTCTAGAGATGCTCTTAGTCTC 59.285 40.741 1.88 0.00 41.50 3.36
3092 4584 7.499232 GTCTTCTTCTAGAGATGCTCTTAGTCT 59.501 40.741 1.88 0.00 41.50 3.24
3093 4585 7.255139 GGTCTTCTTCTAGAGATGCTCTTAGTC 60.255 44.444 1.88 0.00 41.50 2.59
3094 4586 6.546034 GGTCTTCTTCTAGAGATGCTCTTAGT 59.454 42.308 1.88 0.00 41.50 2.24
3095 4587 6.016276 GGGTCTTCTTCTAGAGATGCTCTTAG 60.016 46.154 1.88 0.00 41.50 2.18
3103 4595 3.673543 ACGGGGTCTTCTTCTAGAGAT 57.326 47.619 0.00 0.00 33.49 2.75
3109 4601 3.071167 GGCATTATACGGGGTCTTCTTCT 59.929 47.826 0.00 0.00 0.00 2.85
3110 4602 3.400255 GGCATTATACGGGGTCTTCTTC 58.600 50.000 0.00 0.00 0.00 2.87
3111 4603 2.224209 CGGCATTATACGGGGTCTTCTT 60.224 50.000 0.00 0.00 0.00 2.52
3151 4643 3.296516 GCGGTTTTTCTGCGATCTG 57.703 52.632 0.00 0.00 38.74 2.90
3235 4727 7.708998 TGAAATAAATTACTGATTTACGGGCC 58.291 34.615 0.00 0.00 41.64 5.80
3285 4792 9.320352 GCCCTTGAAGTAAATAAAGAAACAAAA 57.680 29.630 0.00 0.00 0.00 2.44
3290 4797 8.093927 CCAATGCCCTTGAAGTAAATAAAGAAA 58.906 33.333 0.00 0.00 36.97 2.52
3301 4808 7.919385 ATTATTTATCCAATGCCCTTGAAGT 57.081 32.000 0.00 0.00 36.97 3.01
3309 4816 9.995003 TTGGTGAATTATTATTTATCCAATGCC 57.005 29.630 0.00 0.00 30.63 4.40
3392 4903 8.271458 TGGAAGCAGTTATGAAAGTTGGATATA 58.729 33.333 0.00 0.00 0.00 0.86
3440 4951 3.129813 GCAGATCAACAATGAAGGCATGA 59.870 43.478 0.00 0.00 39.49 3.07
3509 5023 1.275573 GAGGGGAAGCAACGTCTACTT 59.724 52.381 0.00 0.00 0.00 2.24
3510 5024 0.896226 GAGGGGAAGCAACGTCTACT 59.104 55.000 0.00 0.00 0.00 2.57
3511 5025 0.896226 AGAGGGGAAGCAACGTCTAC 59.104 55.000 0.00 0.00 30.81 2.59
3516 5030 2.028020 AGAAACTAGAGGGGAAGCAACG 60.028 50.000 0.00 0.00 0.00 4.10
3563 5077 7.867909 CACTCGTTGATAGAATTGAGGCTAATA 59.132 37.037 0.00 0.00 0.00 0.98
3580 5094 2.425578 TATGTTCGTGCACTCGTTGA 57.574 45.000 16.19 0.73 0.00 3.18
3626 5140 7.206789 TGGTATTGGGAAGAAGAATACATCA 57.793 36.000 0.00 0.00 35.24 3.07
3638 5152 5.452356 GGATGCTCATTTTGGTATTGGGAAG 60.452 44.000 0.00 0.00 0.00 3.46
3673 5187 4.458397 AGCTTATTGAGATGGTCATGTGG 58.542 43.478 0.00 0.00 34.17 4.17


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

AutoCloner maintained by Alex Coulton.