Multiple sequence alignment - TraesCS1B01G226600

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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 TraesCS1B01G226600 chr1B 100.000 4724 0 0 1 4724 407305839 407301116 0.000000e+00 8724
1 TraesCS1B01G226600 chr1A 93.451 2443 91 24 1 2407 376513876 376511467 0.000000e+00 3561
2 TraesCS1B01G226600 chr1A 93.601 2313 93 20 2391 4678 376510766 376508484 0.000000e+00 3400
3 TraesCS1B01G226600 chr1D 97.029 1649 31 10 1 1649 301640823 301639193 0.000000e+00 2758
4 TraesCS1B01G226600 chr1D 92.247 1135 63 15 3544 4674 301636365 301635252 0.000000e+00 1585
5 TraesCS1B01G226600 chr1D 89.173 822 46 12 2698 3510 301637334 301636547 0.000000e+00 985
6 TraesCS1B01G226600 chr1D 84.573 363 51 4 1722 2081 301639177 301638817 5.810000e-94 355
7 TraesCS1B01G226600 chr1D 83.041 171 21 6 2082 2251 301637725 301637562 1.060000e-31 148


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 TraesCS1B01G226600 chr1B 407301116 407305839 4723 True 8724.0 8724 100.0000 1 4724 1 chr1B.!!$R1 4723
1 TraesCS1B01G226600 chr1A 376508484 376513876 5392 True 3480.5 3561 93.5260 1 4678 2 chr1A.!!$R1 4677
2 TraesCS1B01G226600 chr1D 301635252 301640823 5571 True 1166.2 2758 89.2126 1 4674 5 chr1D.!!$R1 4673

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
951 985 0.400594 CAAAACTCCCGACTCCCCTT 59.599 55.0 0.00 0.00 0.00 3.95 F
1161 1208 0.030195 TAGGGGATGCTGGTGGATGA 60.030 55.0 0.00 0.00 0.00 2.92 F
1877 1924 0.251073 ATGCAGCTGCCATTTTTCCC 59.749 50.0 34.64 4.94 41.18 3.97 F
3257 5194 0.591170 CTTCCGCGTTGTGGTTCAAT 59.409 50.0 4.92 0.00 38.38 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 4788 1.318576 GTTTTGGGTGTCCAGGTCAG 58.681 55.000 0.00 0.00 45.04 3.51 R
2959 4895 3.618150 GCAAACAAATGGTATCACATGGC 59.382 43.478 0.00 0.00 0.00 4.40 R
3586 5673 0.595825 GCAGAGCCAACAGTTTGCAC 60.596 55.000 11.72 5.49 0.00 4.57 R
4618 6723 0.032130 GAGGAATATGCCACGCGAGA 59.968 55.000 15.93 0.00 0.00 4.04 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
588 589 2.284190 GAATCAGCACCTACTTCCTGC 58.716 52.381 0.00 0.00 0.00 4.85
945 979 1.228154 GGGTGCAAAACTCCCGACT 60.228 57.895 0.00 0.00 42.12 4.18
951 985 0.400594 CAAAACTCCCGACTCCCCTT 59.599 55.000 0.00 0.00 0.00 3.95
1077 1111 3.813443 CGATTCCATCTCCAACTCCAAT 58.187 45.455 0.00 0.00 0.00 3.16
1152 1199 0.261991 TCTCCTTCGTAGGGGATGCT 59.738 55.000 6.56 0.00 46.52 3.79
1153 1200 0.390860 CTCCTTCGTAGGGGATGCTG 59.609 60.000 0.71 0.00 45.85 4.41
1155 1202 1.338136 CCTTCGTAGGGGATGCTGGT 61.338 60.000 0.00 0.00 37.94 4.00
1156 1203 0.179073 CTTCGTAGGGGATGCTGGTG 60.179 60.000 0.00 0.00 0.00 4.17
1158 1205 2.063979 CGTAGGGGATGCTGGTGGA 61.064 63.158 0.00 0.00 0.00 4.02
1159 1206 1.410850 CGTAGGGGATGCTGGTGGAT 61.411 60.000 0.00 0.00 0.00 3.41
1160 1207 0.109342 GTAGGGGATGCTGGTGGATG 59.891 60.000 0.00 0.00 0.00 3.51
1161 1208 0.030195 TAGGGGATGCTGGTGGATGA 60.030 55.000 0.00 0.00 0.00 2.92
1162 1209 0.700269 AGGGGATGCTGGTGGATGAT 60.700 55.000 0.00 0.00 0.00 2.45
1163 1210 0.538977 GGGGATGCTGGTGGATGATG 60.539 60.000 0.00 0.00 0.00 3.07
1164 1211 1.177256 GGGATGCTGGTGGATGATGC 61.177 60.000 0.00 0.00 0.00 3.91
1165 1212 1.512996 GGATGCTGGTGGATGATGCG 61.513 60.000 0.00 0.00 0.00 4.73
1166 1213 0.816825 GATGCTGGTGGATGATGCGT 60.817 55.000 0.00 0.00 0.00 5.24
1167 1214 1.099295 ATGCTGGTGGATGATGCGTG 61.099 55.000 0.00 0.00 0.00 5.34
1168 1215 3.104766 CTGGTGGATGATGCGTGC 58.895 61.111 0.00 0.00 0.00 5.34
1169 1216 1.450848 CTGGTGGATGATGCGTGCT 60.451 57.895 0.00 0.00 0.00 4.40
1183 1230 2.553602 TGCGTGCTGATTTGATTTGACT 59.446 40.909 0.00 0.00 0.00 3.41
1290 1337 2.609737 CGCTTCCAAACGTAACCTCTCT 60.610 50.000 0.00 0.00 0.00 3.10
1372 1419 8.918202 ATTGCCTTCTTCAAAATATATCCGTA 57.082 30.769 0.00 0.00 0.00 4.02
1410 1457 4.019174 GGAATGAGATTGACCATGGTTGT 58.981 43.478 20.85 8.13 0.00 3.32
1437 1484 8.375465 GTTTTAAGCTCAATGTTTGATGTATGC 58.625 33.333 0.00 0.00 39.30 3.14
1504 1551 7.229907 TCTCTTCCCAAAATAACAGGTTACAAC 59.770 37.037 0.00 0.00 0.00 3.32
1533 1580 4.466370 ACTCAAATCGGTCAGTATCTGGAA 59.534 41.667 0.00 0.00 31.51 3.53
1577 1624 1.780309 TGAAGGGTCCTGTGGTTGATT 59.220 47.619 0.00 0.00 0.00 2.57
1687 1734 8.559175 ACTCTTGTTCTACCTACTAATCCTAGT 58.441 37.037 0.00 0.00 41.43 2.57
1725 1772 5.339008 ACCAGACGAATGCTTTAGATACA 57.661 39.130 0.00 0.00 0.00 2.29
1783 1830 5.946942 TTTTCTAGCAGATGGAGTGAGAT 57.053 39.130 0.00 0.00 0.00 2.75
1807 1854 7.510549 TTGAAGAGGTTTTGATTAGAAGTGG 57.489 36.000 0.00 0.00 0.00 4.00
1815 1862 7.391833 AGGTTTTGATTAGAAGTGGTCATCTTC 59.608 37.037 0.00 0.00 40.83 2.87
1877 1924 0.251073 ATGCAGCTGCCATTTTTCCC 59.749 50.000 34.64 4.94 41.18 3.97
1957 2004 9.060347 GCTATGAATAATTTCTGAGGATTGACA 57.940 33.333 0.00 0.00 32.78 3.58
1985 2032 8.968242 GTAACTTCAACAAAAGTGAATCAATCC 58.032 33.333 0.00 0.00 39.40 3.01
2065 2115 4.612259 CGAACTGTCATTTTTGCCTCTCAG 60.612 45.833 0.00 0.00 0.00 3.35
2071 2121 8.049117 ACTGTCATTTTTGCCTCTCAGATTATA 58.951 33.333 0.00 0.00 0.00 0.98
2130 3271 3.701542 AGCCAAAAGGAAATTAGCTAGGC 59.298 43.478 5.43 5.43 38.65 3.93
2161 3302 5.354513 GTGGTTTCTTAGTTCTTATCCTGGC 59.645 44.000 0.00 0.00 0.00 4.85
2284 3426 8.999431 TCAAAACCTCAGAGTTATTTACATGTC 58.001 33.333 0.00 0.00 0.00 3.06
2438 4298 2.202987 GCTGGGAGAGGTGCATCG 60.203 66.667 0.00 0.00 0.00 3.84
2445 4305 1.646189 GAGAGGTGCATCGGTTTCTC 58.354 55.000 0.00 0.00 0.00 2.87
2460 4320 6.157211 TCGGTTTCTCACTTTCTCTTATGAC 58.843 40.000 0.00 0.00 0.00 3.06
2554 4415 5.515797 AGTTTGCTAACTTTGGTTCCTTC 57.484 39.130 7.78 0.00 41.85 3.46
2608 4469 6.909550 ATACAATTGGCAAGAGTAACCAAA 57.090 33.333 10.83 0.00 46.01 3.28
2692 4554 6.054941 TCTCTTGTTATGCTTTCAGTTGTGA 58.945 36.000 0.00 0.00 0.00 3.58
2710 4638 8.066595 CAGTTGTGAGTAGTTCTGAAGAAAATG 58.933 37.037 0.00 0.00 35.58 2.32
2738 4666 9.186323 CATTCTACTATCTCATTTAGTTCCGTG 57.814 37.037 0.00 0.00 32.35 4.94
2852 4788 8.331742 GCTTGCTGATAGTAGAAAACAAGATAC 58.668 37.037 0.00 0.00 36.28 2.24
2903 4839 6.017026 GGATATAACTGCTGAAAGGTAAAGGC 60.017 42.308 0.00 0.00 0.00 4.35
2916 4852 5.174037 AGGTAAAGGCTTGCACAGTAATA 57.826 39.130 0.00 0.00 0.00 0.98
2927 4863 6.091441 GCTTGCACAGTAATATACTATCTGCC 59.909 42.308 0.00 0.00 37.23 4.85
2959 4895 6.577103 TGTCTTGAGCAATGACTCTATTAGG 58.423 40.000 6.33 0.00 37.58 2.69
3223 5159 5.849357 TGTTTACGCGTTCAAGATATTGT 57.151 34.783 20.78 0.00 0.00 2.71
3227 5163 3.071479 ACGCGTTCAAGATATTGTGGTT 58.929 40.909 5.58 0.00 0.00 3.67
3257 5194 0.591170 CTTCCGCGTTGTGGTTCAAT 59.409 50.000 4.92 0.00 38.38 2.57
3334 5272 2.938798 CCCAGGGGTGGGCAGTTA 60.939 66.667 0.00 0.00 42.99 2.24
3510 5448 1.499049 GAGGCCATCGATTCGGTAAC 58.501 55.000 5.01 0.00 0.00 2.50
3538 5624 3.208747 CCCCCTCCATGTACAACATAC 57.791 52.381 0.00 0.00 36.53 2.39
3548 5634 5.690409 CCATGTACAACATACCGTCTATGTC 59.310 44.000 0.00 0.00 36.53 3.06
3576 5663 8.702163 AAATCTCAATTCGAAACACAAACTTT 57.298 26.923 0.00 0.00 0.00 2.66
3586 5673 5.681105 CGAAACACAAACTTTGATACTGTGG 59.319 40.000 8.55 0.00 41.32 4.17
3598 5685 3.314913 TGATACTGTGGTGCAAACTGTTG 59.685 43.478 15.47 0.00 37.83 3.33
3607 5694 0.102844 GCAAACTGTTGGCTCTGCAA 59.897 50.000 12.62 0.00 35.10 4.08
3625 5712 2.029649 GCAAGTGCATAATGGCCCATAG 60.030 50.000 0.00 0.00 41.59 2.23
3708 5795 3.119096 GCCGCAGTCCTTCCGTTC 61.119 66.667 0.00 0.00 0.00 3.95
3737 5825 3.839293 ACTCTTAATCACGTCAGCAGAC 58.161 45.455 0.00 0.00 41.46 3.51
3745 5833 2.946762 GTCAGCAGACCGGTTTGC 59.053 61.111 36.02 36.02 40.56 3.68
3764 5852 1.734465 GCGTTCTCCTTGAAGTCCATG 59.266 52.381 0.00 0.00 35.01 3.66
3796 5884 1.104630 GACCTCTCTTGTACCTCGGG 58.895 60.000 0.00 0.00 0.00 5.14
3836 5924 1.826054 TGGCAAGTGTTGTTCCCCG 60.826 57.895 0.00 0.00 0.00 5.73
3972 6060 0.883370 GAGCCGAACGGTGTTTTCCT 60.883 55.000 14.63 1.41 37.65 3.36
3975 6063 1.069703 GCCGAACGGTGTTTTCCTTAC 60.070 52.381 14.63 0.00 37.65 2.34
3979 6067 3.676646 CGAACGGTGTTTTCCTTACTAGG 59.323 47.826 0.00 0.00 43.46 3.02
3994 6082 8.109560 TCCTTACTAGGCAGGGTTTATTTATT 57.890 34.615 9.11 0.00 41.69 1.40
4026 6114 1.706866 CCCTGGGATTCATCTGCCATA 59.293 52.381 7.01 0.00 0.00 2.74
4150 6244 0.251634 TGTGGTGGCGCAGAATGATA 59.748 50.000 10.83 0.00 39.69 2.15
4160 6254 2.049228 GCAGAATGATATTGCGCTTGC 58.951 47.619 9.73 0.00 39.69 4.01
4199 6293 0.884704 AATTGCCGTGCGTGTTCTCT 60.885 50.000 0.00 0.00 0.00 3.10
4215 6309 2.010582 CTCTAGGCGTGAGAGGCACC 62.011 65.000 4.20 0.00 44.85 5.01
4238 6333 2.328099 CGACTTGGGCAGGCAGTTC 61.328 63.158 0.00 0.00 0.00 3.01
4286 6381 2.194388 TACGCCTGGACTCGAGAGGT 62.194 60.000 21.68 3.30 0.00 3.85
4307 6402 4.287067 GGTTGAGATATATCCTGCTTCCCA 59.713 45.833 9.18 0.00 0.00 4.37
4425 6523 2.678580 TCCGTCCACATCGCCTCA 60.679 61.111 0.00 0.00 0.00 3.86
4593 6698 4.016706 CCCGCGAAGTCCCCAACT 62.017 66.667 8.23 0.00 41.10 3.16
4618 6723 3.087065 CCCCCAAACAGGATCCGT 58.913 61.111 5.98 4.69 41.22 4.69
4642 6747 0.389391 CGTGGCATATTCCTCTCCGT 59.611 55.000 0.00 0.00 0.00 4.69
4674 6779 4.314440 TGAGTGCACCGGCCAGTC 62.314 66.667 14.63 18.77 40.13 3.51
4686 6791 2.734723 CCAGTCGGCACACTCGTG 60.735 66.667 0.00 0.00 46.56 4.35
4687 6792 2.027605 CAGTCGGCACACTCGTGT 59.972 61.111 0.00 0.00 45.50 4.49
4697 6802 2.653742 CACTCGTGTGTGATAGCCG 58.346 57.895 9.42 0.00 40.12 5.52
4698 6803 0.109272 CACTCGTGTGTGATAGCCGT 60.109 55.000 9.42 0.00 40.12 5.68
4699 6804 0.109272 ACTCGTGTGTGATAGCCGTG 60.109 55.000 0.00 0.00 0.00 4.94
4700 6805 1.413767 CTCGTGTGTGATAGCCGTGC 61.414 60.000 0.00 0.00 0.00 5.34
4701 6806 2.788176 CGTGTGTGATAGCCGTGCG 61.788 63.158 0.00 0.00 0.00 5.34
4702 6807 1.736645 GTGTGTGATAGCCGTGCGT 60.737 57.895 0.00 0.00 0.00 5.24
4703 6808 1.005512 TGTGTGATAGCCGTGCGTT 60.006 52.632 0.00 0.00 0.00 4.84
4704 6809 1.288419 TGTGTGATAGCCGTGCGTTG 61.288 55.000 0.00 0.00 0.00 4.10
4705 6810 1.011968 GTGTGATAGCCGTGCGTTGA 61.012 55.000 0.00 0.00 0.00 3.18
4706 6811 1.011968 TGTGATAGCCGTGCGTTGAC 61.012 55.000 0.00 0.00 0.00 3.18
4707 6812 1.803922 TGATAGCCGTGCGTTGACG 60.804 57.895 0.00 0.00 43.27 4.35
4716 6821 2.951360 CGTGCGTTGACGGTATTATTG 58.049 47.619 5.62 0.00 40.23 1.90
4717 6822 2.700694 GTGCGTTGACGGTATTATTGC 58.299 47.619 5.62 0.00 40.23 3.56
4718 6823 1.325037 TGCGTTGACGGTATTATTGCG 59.675 47.619 5.62 0.00 40.23 4.85
4719 6824 1.914257 GCGTTGACGGTATTATTGCGC 60.914 52.381 0.00 0.00 40.23 6.09
4720 6825 1.591158 CGTTGACGGTATTATTGCGCT 59.409 47.619 9.73 0.00 35.37 5.92
4721 6826 2.029970 CGTTGACGGTATTATTGCGCTT 59.970 45.455 9.73 0.00 35.37 4.68
4722 6827 3.350912 GTTGACGGTATTATTGCGCTTG 58.649 45.455 9.73 0.00 0.00 4.01
4723 6828 1.329292 TGACGGTATTATTGCGCTTGC 59.671 47.619 9.73 0.00 39.78 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
588 589 4.888326 TGTCAAATCTGGGGAATTTTGG 57.112 40.909 0.00 0.00 31.57 3.28
779 804 3.790437 CCAGGAGATGGCTGCGGT 61.790 66.667 0.00 0.00 43.83 5.68
945 979 2.029964 GCGTCGTGTTCAAGGGGA 59.970 61.111 0.00 0.00 0.00 4.81
1017 1051 3.660111 GTCGCCAGCGCCTTTTGT 61.660 61.111 2.29 0.00 39.59 2.83
1152 1199 1.746239 CAGCACGCATCATCCACCA 60.746 57.895 0.00 0.00 0.00 4.17
1153 1200 0.816825 ATCAGCACGCATCATCCACC 60.817 55.000 0.00 0.00 0.00 4.61
1155 1202 1.402613 CAAATCAGCACGCATCATCCA 59.597 47.619 0.00 0.00 0.00 3.41
1156 1203 1.672363 TCAAATCAGCACGCATCATCC 59.328 47.619 0.00 0.00 0.00 3.51
1158 1205 4.109766 CAAATCAAATCAGCACGCATCAT 58.890 39.130 0.00 0.00 0.00 2.45
1159 1206 3.190953 TCAAATCAAATCAGCACGCATCA 59.809 39.130 0.00 0.00 0.00 3.07
1160 1207 3.545078 GTCAAATCAAATCAGCACGCATC 59.455 43.478 0.00 0.00 0.00 3.91
1161 1208 3.192001 AGTCAAATCAAATCAGCACGCAT 59.808 39.130 0.00 0.00 0.00 4.73
1162 1209 2.553602 AGTCAAATCAAATCAGCACGCA 59.446 40.909 0.00 0.00 0.00 5.24
1163 1210 2.912967 CAGTCAAATCAAATCAGCACGC 59.087 45.455 0.00 0.00 0.00 5.34
1164 1211 3.495193 CCAGTCAAATCAAATCAGCACG 58.505 45.455 0.00 0.00 0.00 5.34
1165 1212 3.507233 TCCCAGTCAAATCAAATCAGCAC 59.493 43.478 0.00 0.00 0.00 4.40
1166 1213 3.507233 GTCCCAGTCAAATCAAATCAGCA 59.493 43.478 0.00 0.00 0.00 4.41
1167 1214 3.426695 CGTCCCAGTCAAATCAAATCAGC 60.427 47.826 0.00 0.00 0.00 4.26
1168 1215 3.753272 ACGTCCCAGTCAAATCAAATCAG 59.247 43.478 0.00 0.00 0.00 2.90
1169 1216 3.501828 CACGTCCCAGTCAAATCAAATCA 59.498 43.478 0.00 0.00 0.00 2.57
1183 1230 0.893270 CAAGCCAAATCCACGTCCCA 60.893 55.000 0.00 0.00 0.00 4.37
1290 1337 4.946160 AATGGAACTGGGAGGATGTAAA 57.054 40.909 0.00 0.00 0.00 2.01
1383 1430 4.647853 CCATGGTCAATCTCATTCCACAAT 59.352 41.667 2.57 0.00 0.00 2.71
1410 1457 9.409312 CATACATCAAACATTGAGCTTAAAACA 57.591 29.630 0.00 0.00 43.98 2.83
1437 1484 4.500545 CCACTACCAGGATGATTCTTCGAG 60.501 50.000 0.00 0.00 39.69 4.04
1504 1551 7.328005 CAGATACTGACCGATTTGAGTGATATG 59.672 40.741 0.00 0.00 32.44 1.78
1577 1624 0.475044 AACCAAACTTCCGGGCACTA 59.525 50.000 0.00 0.00 0.00 2.74
1687 1734 6.289834 TCGTCTGGTTTAATCCTACAAACAA 58.710 36.000 4.25 0.00 36.56 2.83
1783 1830 7.060421 ACCACTTCTAATCAAAACCTCTTCAA 58.940 34.615 0.00 0.00 0.00 2.69
1807 1854 9.646427 GAGTTAACCATCCTATATGAAGATGAC 57.354 37.037 0.88 4.19 39.84 3.06
1883 1930 5.487488 TCAGATTCCTAGCAACTAAAGGGAA 59.513 40.000 0.00 0.00 37.28 3.97
1884 1931 5.030147 TCAGATTCCTAGCAACTAAAGGGA 58.970 41.667 0.00 0.00 0.00 4.20
2065 2115 9.628500 AGTGGTCTTCCTAAAACCAATATAATC 57.372 33.333 0.00 0.00 44.30 1.75
2071 2121 5.254115 GCTAGTGGTCTTCCTAAAACCAAT 58.746 41.667 0.00 0.00 44.30 3.16
2161 3302 4.596585 AACCTGCCCCCAACACCG 62.597 66.667 0.00 0.00 0.00 4.94
2309 3452 1.550524 ACAGCCTTACGCATCAGAAGA 59.449 47.619 0.00 0.00 41.38 2.87
2367 3510 5.129485 ACAAGGCTAAGTCATACTATGCAGT 59.871 40.000 0.00 0.00 38.91 4.40
2368 3511 5.605534 ACAAGGCTAAGTCATACTATGCAG 58.394 41.667 0.00 0.00 31.27 4.41
2438 4298 7.730364 TTGTCATAAGAGAAAGTGAGAAACC 57.270 36.000 0.00 0.00 0.00 3.27
2445 4305 7.536622 GCAAAGTGATTGTCATAAGAGAAAGTG 59.463 37.037 0.00 0.00 41.32 3.16
2460 4320 5.640783 TCATGACAGTAGAGCAAAGTGATTG 59.359 40.000 0.00 0.00 42.21 2.67
2608 4469 8.428063 TGTCCCAAATCACTATTTTTGACAATT 58.572 29.630 8.58 0.00 38.65 2.32
2628 4489 1.686052 GGCAAATTCAAGTGTGTCCCA 59.314 47.619 0.00 0.00 0.00 4.37
2710 4638 9.400638 CGGAACTAAATGAGATAGTAGAATGAC 57.599 37.037 0.00 0.00 33.36 3.06
2735 4663 5.408299 TCTGATCAAATACACAAGTTCCACG 59.592 40.000 0.00 0.00 0.00 4.94
2738 4666 7.335422 AGTCATCTGATCAAATACACAAGTTCC 59.665 37.037 0.00 0.00 0.00 3.62
2852 4788 1.318576 GTTTTGGGTGTCCAGGTCAG 58.681 55.000 0.00 0.00 45.04 3.51
2903 4839 6.309009 CGGCAGATAGTATATTACTGTGCAAG 59.691 42.308 14.83 0.00 40.32 4.01
2916 4852 9.628500 TCAAGACATATATACGGCAGATAGTAT 57.372 33.333 0.00 0.00 37.35 2.12
2927 4863 8.026026 AGAGTCATTGCTCAAGACATATATACG 58.974 37.037 9.67 0.00 37.94 3.06
2959 4895 3.618150 GCAAACAAATGGTATCACATGGC 59.382 43.478 0.00 0.00 0.00 4.40
3198 5134 6.740905 ACAATATCTTGAACGCGTAAACAATG 59.259 34.615 14.46 15.28 36.20 2.82
3244 5181 4.083324 AGAGCAACATATTGAACCACAACG 60.083 41.667 0.00 0.00 41.52 4.10
3257 5194 8.978472 ACTTGGATAAACTACTAGAGCAACATA 58.022 33.333 0.00 0.00 0.00 2.29
3328 5266 6.827641 TCAGAAATACGAACAACATAACTGC 58.172 36.000 0.00 0.00 0.00 4.40
3334 5272 6.627395 TTGGTTCAGAAATACGAACAACAT 57.373 33.333 0.00 0.00 42.67 2.71
3392 5330 5.752036 ATCAGAATCTCTGGAGAAACACA 57.248 39.130 4.34 0.00 44.39 3.72
3527 5473 4.635324 TCGACATAGACGGTATGTTGTACA 59.365 41.667 19.38 0.00 39.30 2.90
3538 5624 6.560433 CGAATTGAGATTTTCGACATAGACGG 60.560 42.308 0.00 0.00 45.68 4.79
3548 5634 6.968004 TTGTGTTTCGAATTGAGATTTTCG 57.032 33.333 0.00 0.00 44.53 3.46
3576 5663 3.207265 ACAGTTTGCACCACAGTATCA 57.793 42.857 0.00 0.00 0.00 2.15
3586 5673 0.595825 GCAGAGCCAACAGTTTGCAC 60.596 55.000 11.72 5.49 0.00 4.57
3607 5694 3.225104 CAACTATGGGCCATTATGCACT 58.775 45.455 26.58 0.00 35.05 4.40
3625 5712 1.666888 CGCATTCCTCTGCCAAACAAC 60.667 52.381 0.00 0.00 39.00 3.32
3699 5786 3.271014 TCGACTCCGAACGGAAGG 58.729 61.111 16.56 8.86 44.66 3.46
3708 5795 2.095532 ACGTGATTAAGAGTCGACTCCG 59.904 50.000 35.83 30.29 43.88 4.63
3737 5825 0.882927 TCAAGGAGAACGCAAACCGG 60.883 55.000 0.00 0.00 42.52 5.28
3745 5833 2.028112 TCCATGGACTTCAAGGAGAACG 60.028 50.000 11.44 0.00 38.22 3.95
3764 5852 1.408702 GAGAGGTCTCATGTCAGCTCC 59.591 57.143 17.00 9.03 42.42 4.70
3796 5884 1.916000 CGATCGTTACAGGTTTCGACC 59.084 52.381 7.03 0.00 35.24 4.79
3836 5924 2.587522 AGGGACAACAGAAAAAGGAGC 58.412 47.619 0.00 0.00 0.00 4.70
3972 6060 7.645002 ACCAATAAATAAACCCTGCCTAGTAA 58.355 34.615 0.00 0.00 0.00 2.24
3975 6063 6.365520 AGACCAATAAATAAACCCTGCCTAG 58.634 40.000 0.00 0.00 0.00 3.02
3979 6067 6.280855 ACAAGACCAATAAATAAACCCTGC 57.719 37.500 0.00 0.00 0.00 4.85
3994 6082 3.636231 CCAGGGCCGACAAGACCA 61.636 66.667 0.00 0.00 0.00 4.02
4026 6114 1.094785 CGGTTCATCGATTTGGCCTT 58.905 50.000 3.32 0.00 0.00 4.35
4114 6202 5.180492 CCACCACAATTTACTGTATCGTGTT 59.820 40.000 0.00 0.00 0.00 3.32
4157 6251 4.380843 TTCTCCTCCCAGTAATTTGCAA 57.619 40.909 0.00 0.00 0.00 4.08
4158 6252 4.380843 TTTCTCCTCCCAGTAATTTGCA 57.619 40.909 0.00 0.00 0.00 4.08
4160 6254 6.591448 GCAATTTTTCTCCTCCCAGTAATTTG 59.409 38.462 0.00 0.00 0.00 2.32
4167 6261 1.474077 CGGCAATTTTTCTCCTCCCAG 59.526 52.381 0.00 0.00 0.00 4.45
4168 6262 1.203001 ACGGCAATTTTTCTCCTCCCA 60.203 47.619 0.00 0.00 0.00 4.37
4169 6263 1.202348 CACGGCAATTTTTCTCCTCCC 59.798 52.381 0.00 0.00 0.00 4.30
4238 6333 1.272781 GAGTTTCGGCGTGAGATCTG 58.727 55.000 6.85 0.00 0.00 2.90
4286 6381 6.708885 AATGGGAAGCAGGATATATCTCAA 57.291 37.500 12.42 0.00 0.00 3.02
4362 6457 1.081892 CTTTCGTGCCTCCATCACTG 58.918 55.000 0.00 0.00 32.54 3.66
4363 6458 0.036010 CCTTTCGTGCCTCCATCACT 60.036 55.000 0.00 0.00 32.54 3.41
4484 6587 3.365472 AGAAAACAAGGACAAGTTGGCT 58.635 40.909 9.01 0.00 0.00 4.75
4517 6622 1.673920 GAACAAACTGGCTGGAACGAA 59.326 47.619 0.00 0.00 0.00 3.85
4521 6626 2.687935 GACAAGAACAAACTGGCTGGAA 59.312 45.455 0.00 0.00 0.00 3.53
4618 6723 0.032130 GAGGAATATGCCACGCGAGA 59.968 55.000 15.93 0.00 0.00 4.04
4680 6785 0.109272 CACGGCTATCACACACGAGT 60.109 55.000 0.00 0.00 0.00 4.18
4681 6786 1.413767 GCACGGCTATCACACACGAG 61.414 60.000 0.00 0.00 0.00 4.18
4682 6787 1.445410 GCACGGCTATCACACACGA 60.445 57.895 0.00 0.00 0.00 4.35
4683 6788 2.788176 CGCACGGCTATCACACACG 61.788 63.158 0.00 0.00 0.00 4.49
4684 6789 1.289109 AACGCACGGCTATCACACAC 61.289 55.000 0.00 0.00 0.00 3.82
4685 6790 1.005512 AACGCACGGCTATCACACA 60.006 52.632 0.00 0.00 0.00 3.72
4686 6791 1.011968 TCAACGCACGGCTATCACAC 61.012 55.000 0.00 0.00 0.00 3.82
4687 6792 1.011968 GTCAACGCACGGCTATCACA 61.012 55.000 0.00 0.00 0.00 3.58
4688 6793 1.708027 GTCAACGCACGGCTATCAC 59.292 57.895 0.00 0.00 0.00 3.06
4689 6794 1.803922 CGTCAACGCACGGCTATCA 60.804 57.895 0.00 0.00 36.07 2.15
4690 6795 2.995482 CGTCAACGCACGGCTATC 59.005 61.111 0.00 0.00 36.07 2.08
4696 6801 2.844281 GCAATAATACCGTCAACGCACG 60.844 50.000 0.00 0.00 39.61 5.34
4697 6802 2.700694 GCAATAATACCGTCAACGCAC 58.299 47.619 0.00 0.00 38.18 5.34
4698 6803 1.325037 CGCAATAATACCGTCAACGCA 59.675 47.619 0.00 0.00 38.18 5.24
4699 6804 1.914257 GCGCAATAATACCGTCAACGC 60.914 52.381 0.30 0.00 38.18 4.84
4700 6805 1.591158 AGCGCAATAATACCGTCAACG 59.409 47.619 11.47 0.00 39.44 4.10
4701 6806 3.350912 CAAGCGCAATAATACCGTCAAC 58.649 45.455 11.47 0.00 0.00 3.18
4702 6807 2.223157 GCAAGCGCAATAATACCGTCAA 60.223 45.455 11.47 0.00 38.36 3.18
4703 6808 1.329292 GCAAGCGCAATAATACCGTCA 59.671 47.619 11.47 0.00 38.36 4.35
4704 6809 2.018717 GCAAGCGCAATAATACCGTC 57.981 50.000 11.47 0.00 38.36 4.79


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

AutoCloner maintained by Alex Coulton.