Multiple sequence alignment - TraesCS3A01G528400

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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 TraesCS3A01G528400 chr3A 100.000 4265 0 0 1 4265 742440296 742436032 0.000000e+00 7877.0
1 TraesCS3A01G528400 chr3D 94.228 3985 191 19 35 4003 609085650 609081689 0.000000e+00 6048.0
2 TraesCS3A01G528400 chr3B 92.056 3298 181 36 1 3270 819788739 819785495 0.000000e+00 4564.0
3 TraesCS3A01G528400 chr3B 93.617 705 27 8 3576 4265 819785465 819784764 0.000000e+00 1037.0
4 TraesCS3A01G528400 chr3B 100.000 35 0 0 3291 3325 819785496 819785462 9.900000e-07 65.8
5 TraesCS3A01G528400 chr2D 88.031 259 14 12 977 1222 623474986 623474732 1.500000e-74 291.0
6 TraesCS3A01G528400 chr2D 77.876 226 38 10 1149 1370 598308983 598308766 3.460000e-26 130.0
7 TraesCS3A01G528400 chr2D 72.802 364 62 21 1016 1370 642203691 642203356 5.870000e-14 89.8
8 TraesCS3A01G528400 chr2B 88.889 207 18 5 274 479 765484586 765484384 2.550000e-62 250.0
9 TraesCS3A01G528400 chr2B 75.069 361 63 14 1016 1370 799614132 799614471 4.450000e-30 143.0
10 TraesCS3A01G528400 chr6B 86.667 120 11 3 127 242 701866517 701866635 1.240000e-25 128.0
11 TraesCS3A01G528400 chr6A 84.746 118 13 3 129 242 606965203 606965319 3.490000e-21 113.0
12 TraesCS3A01G528400 chr2A 77.143 210 36 9 1058 1261 766919390 766919187 1.250000e-20 111.0
13 TraesCS3A01G528400 chr2A 81.522 92 9 7 971 1055 766973932 766973842 7.650000e-08 69.4


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 TraesCS3A01G528400 chr3A 742436032 742440296 4264 True 7877.000000 7877 100.000000 1 4265 1 chr3A.!!$R1 4264
1 TraesCS3A01G528400 chr3D 609081689 609085650 3961 True 6048.000000 6048 94.228000 35 4003 1 chr3D.!!$R1 3968
2 TraesCS3A01G528400 chr3B 819784764 819788739 3975 True 1888.933333 4564 95.224333 1 4265 3 chr3B.!!$R1 4264

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
286 298 0.538057 CAGGCAAGGCTTCAGGACAA 60.538 55.000 0.0 0.0 0.00 3.18 F
954 983 1.202879 CCCAACAAGGTCCAGCACTTA 60.203 52.381 0.0 0.0 34.66 2.24 F
2169 2201 0.186873 AAGGATATGCAAGGCTGGGG 59.813 55.000 0.0 0.0 0.00 4.96 F
2511 2543 0.394565 AGCTCTTCAACCAGCTTCGT 59.605 50.000 0.0 0.0 43.80 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 1693 0.251165 GCCCTCTACAAACCCAAGCA 60.251 55.0 0.00 0.0 0.00 3.91 R
2628 2660 0.112412 AAACATGGGGGTCACTGTCC 59.888 55.0 0.00 0.0 0.00 4.02 R
3020 3052 0.254178 AGCTGGTTCAATCGGCATCT 59.746 50.0 3.76 0.0 38.87 2.90 R
3668 3704 0.601576 ACAGTGAACATGCGCGGTAA 60.602 50.0 8.83 0.0 0.00 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
157 169 1.148273 GAAGACCCTGGTGCACACA 59.852 57.895 20.43 13.12 0.00 3.72
286 298 0.538057 CAGGCAAGGCTTCAGGACAA 60.538 55.000 0.00 0.00 0.00 3.18
288 300 1.583477 GCAAGGCTTCAGGACAAGC 59.417 57.895 0.00 0.00 46.99 4.01
317 329 2.308570 TCCAGCTGCTAAAGGAAATCCA 59.691 45.455 8.66 0.00 38.89 3.41
326 338 2.744352 AAGGAAATCCATCTCTGCCC 57.256 50.000 1.67 0.00 38.89 5.36
364 379 9.495572 AGAGGAAAACTGATACTCTGTAAAAAG 57.504 33.333 0.00 0.00 37.16 2.27
417 432 9.567776 TTCTGTATTTATTCCAAAACTCACAGA 57.432 29.630 0.00 0.00 35.44 3.41
493 514 7.342284 TCTTTCCTCTGTCGGTTAATAAGAGAT 59.658 37.037 0.00 0.00 37.20 2.75
654 675 6.500684 AGTAATTACACTGTCTTGCATTGG 57.499 37.500 17.65 0.00 32.74 3.16
746 769 3.643792 CCCTTGTGGTTGGATTTGGTAAA 59.356 43.478 0.00 0.00 0.00 2.01
854 882 3.655615 AGGTGTTAAACTGTCCCAACA 57.344 42.857 0.00 0.00 0.00 3.33
943 972 2.201927 GCCCATTAGCCCAACAAGG 58.798 57.895 0.00 0.00 37.03 3.61
951 980 2.564721 GCCCAACAAGGTCCAGCAC 61.565 63.158 0.00 0.00 34.66 4.40
954 983 1.202879 CCCAACAAGGTCCAGCACTTA 60.203 52.381 0.00 0.00 34.66 2.24
955 984 1.880027 CCAACAAGGTCCAGCACTTAC 59.120 52.381 0.00 0.00 0.00 2.34
1194 1223 1.375396 CCTGTTCGACCGAATGCCA 60.375 57.895 8.14 1.56 36.45 4.92
1503 1535 1.341802 GATGCTTGTCTTCGACGCG 59.658 57.895 3.53 3.53 34.95 6.01
1506 1538 2.765785 CTTGTCTTCGACGCGCTG 59.234 61.111 5.73 0.00 34.95 5.18
1542 1574 3.319198 ACCTGGACCGCGGTGATT 61.319 61.111 39.65 11.74 30.90 2.57
1545 1577 1.515954 CTGGACCGCGGTGATTACT 59.484 57.895 39.65 9.27 0.00 2.24
1555 1587 2.954318 GCGGTGATTACTGGGTACTCTA 59.046 50.000 0.00 0.00 33.62 2.43
1661 1693 1.600076 CTGCCAGTGCTTGCTCTGT 60.600 57.895 19.03 0.00 38.71 3.41
1695 1727 2.111878 GGCGGCAGGCAGATACAT 59.888 61.111 3.07 0.00 46.16 2.29
1710 1742 1.320507 TACATGGCTATGCGTACCGA 58.679 50.000 10.37 0.00 37.85 4.69
1845 1877 2.750712 TGTGTCTTGGACGACGATGATA 59.249 45.455 0.00 0.00 36.71 2.15
1851 1883 0.669077 GGACGACGATGATAGCTGGT 59.331 55.000 0.00 0.00 0.00 4.00
1932 1964 0.681175 GGTGGCAGCCTGATGTTTTT 59.319 50.000 14.15 0.00 0.00 1.94
1979 2011 0.871057 GGCTCTTTGGCAGCGATATC 59.129 55.000 0.00 0.00 41.37 1.63
2070 2102 5.756833 TGCTCTGATTGACATGTATGCTAAG 59.243 40.000 0.00 0.00 0.00 2.18
2125 2157 3.200605 TGAAGCCTTGGCAGAAGATGATA 59.799 43.478 14.54 0.00 0.00 2.15
2169 2201 0.186873 AAGGATATGCAAGGCTGGGG 59.813 55.000 0.00 0.00 0.00 4.96
2187 2219 0.984995 GGGACCTTACAGGAGCAGTT 59.015 55.000 0.00 0.00 37.67 3.16
2350 2382 3.060479 TGGACCTATATGCAGGGAGTT 57.940 47.619 0.00 0.00 40.29 3.01
2436 2468 2.825532 GCACAACAGGGACATGGTAATT 59.174 45.455 0.00 0.00 0.00 1.40
2499 2531 2.345876 GAAGAGGCTGTGAAGCTCTTC 58.654 52.381 16.65 16.65 39.41 2.87
2511 2543 0.394565 AGCTCTTCAACCAGCTTCGT 59.605 50.000 0.00 0.00 43.80 3.85
2553 2585 3.263261 TGAGTTCACGTTTGTTGCACTA 58.737 40.909 0.00 0.00 0.00 2.74
2589 2621 2.064014 GCTCTGGCAAGCATTTTTCAC 58.936 47.619 14.15 0.00 42.05 3.18
2592 2624 0.749649 TGGCAAGCATTTTTCACGGT 59.250 45.000 0.00 0.00 0.00 4.83
2621 2653 3.211865 TCCATGCTCAGATCATCAAAGC 58.788 45.455 4.68 4.68 0.00 3.51
2702 2734 0.895530 TTCATCGAAGAAGGACGGCT 59.104 50.000 0.00 0.00 43.58 5.52
2719 2751 2.791158 CGGCTGTTGTTTGAGTCAACAC 60.791 50.000 4.68 7.97 46.35 3.32
2720 2752 2.423538 GGCTGTTGTTTGAGTCAACACT 59.576 45.455 4.68 0.00 46.35 3.55
2757 2789 5.152623 TCTGTTGGAACTCGATGATTTCT 57.847 39.130 0.00 0.00 0.00 2.52
2902 2934 5.240713 CCTTGTGAATGAAGGCTTACATC 57.759 43.478 0.00 0.00 33.84 3.06
2910 2942 9.807649 GTGAATGAAGGCTTACATCATTTTAAT 57.192 29.630 12.15 0.00 42.26 1.40
3020 3052 4.343526 TGCTGCCAAGGAGTTTATTGAAAA 59.656 37.500 0.00 0.00 0.00 2.29
3100 3132 4.021894 TGTTTGGTAATGTTGAAATCGGGG 60.022 41.667 0.00 0.00 0.00 5.73
3141 3173 1.905215 CTCTTGGCGGATCCTATGGAT 59.095 52.381 10.75 0.00 46.28 3.41
3227 3259 1.208293 GTTGAGACAGGGGATGGACTC 59.792 57.143 0.00 0.00 37.14 3.36
3268 3300 2.634940 GCAGGATATAGCTGGTGAAGGA 59.365 50.000 0.00 0.00 0.00 3.36
3274 3306 2.024176 TAGCTGGTGAAGGAGGTTCA 57.976 50.000 0.00 0.00 43.26 3.18
3275 3307 1.366319 AGCTGGTGAAGGAGGTTCAT 58.634 50.000 0.00 0.00 46.99 2.57
3349 3381 3.056250 CAGTACTGGATGAGCTGACAAGT 60.056 47.826 15.49 0.00 0.00 3.16
3433 3465 5.496556 TGGTTGATGGTACTTACTGAATGG 58.503 41.667 0.00 0.00 0.00 3.16
3438 3470 7.490657 TGATGGTACTTACTGAATGGTAACT 57.509 36.000 0.00 0.00 37.61 2.24
3481 3513 3.937706 GACAGATGGTCTTGGATGAACTG 59.062 47.826 0.00 0.00 43.46 3.16
3486 3518 3.743521 TGGTCTTGGATGAACTGTTCTG 58.256 45.455 20.18 5.36 0.00 3.02
3489 3521 2.373169 TCTTGGATGAACTGTTCTGGCT 59.627 45.455 20.18 4.06 0.00 4.75
3491 3523 4.225942 TCTTGGATGAACTGTTCTGGCTAT 59.774 41.667 20.18 6.11 0.00 2.97
3495 3527 3.334583 TGAACTGTTCTGGCTATGTCC 57.665 47.619 20.18 0.00 0.00 4.02
3503 3535 0.548031 CTGGCTATGTCCCCACACAT 59.452 55.000 0.00 0.00 40.28 3.21
3550 3582 7.069455 TGCTTTGATATAGTAGTTCTGGCTGTA 59.931 37.037 0.00 0.00 0.00 2.74
3566 3598 8.635765 TCTGGCTGTATTCTTTGATAACTTTT 57.364 30.769 0.00 0.00 0.00 2.27
3592 3624 4.561213 GTGTTTTACAACAGCTTGTCCAAC 59.439 41.667 0.00 0.96 43.83 3.77
3606 3642 3.296854 TGTCCAACGACTATCTGGCTAT 58.703 45.455 0.00 0.00 39.94 2.97
3651 3687 5.485620 CAGAGTTGGAATGACTTGATCAGA 58.514 41.667 0.00 0.00 41.91 3.27
3668 3704 8.515695 TTGATCAGATCAAATGCAAAGTATCT 57.484 30.769 21.52 0.00 45.57 1.98
3669 3705 8.515695 TGATCAGATCAAATGCAAAGTATCTT 57.484 30.769 10.93 0.00 36.11 2.40
3704 3740 1.274167 CTGTGGGCTTGACAAATGCAT 59.726 47.619 0.00 0.00 0.00 3.96
3932 3973 2.900122 TTAGCGTGCTTTGATTCAGC 57.100 45.000 0.00 0.00 37.82 4.26
3938 3979 2.666619 CGTGCTTTGATTCAGCTGAACC 60.667 50.000 30.66 22.93 38.19 3.62
4004 4048 3.628646 GATGGCGTGCTGGAGGGTT 62.629 63.158 0.00 0.00 0.00 4.11
4015 4059 0.544357 TGGAGGGTTCGACATGGTCT 60.544 55.000 0.00 0.00 0.00 3.85
4016 4060 0.613777 GGAGGGTTCGACATGGTCTT 59.386 55.000 0.00 0.00 0.00 3.01
4065 4109 2.430921 GAGTGCCACGTCGTCTGG 60.431 66.667 0.00 0.00 0.00 3.86
4118 4162 1.407299 CGATGGCTGGATGGACTTTGA 60.407 52.381 0.00 0.00 0.00 2.69
4144 4188 3.807538 GCCTCGTCGACGGCTACA 61.808 66.667 35.05 16.53 42.98 2.74
4153 4197 1.376683 GACGGCTACAACATGCCCA 60.377 57.895 0.00 0.00 45.90 5.36
4162 4206 0.250793 CAACATGCCCATGCCATGTT 59.749 50.000 25.10 25.10 43.53 2.71
4164 4208 1.145156 CATGCCCATGCCATGTTGG 59.855 57.895 3.63 0.00 41.55 3.77
4166 4210 0.910566 ATGCCCATGCCATGTTGGTT 60.911 50.000 3.63 0.00 40.46 3.67
4167 4211 1.218854 GCCCATGCCATGTTGGTTC 59.781 57.895 3.63 0.00 40.46 3.62
4168 4212 1.543065 GCCCATGCCATGTTGGTTCA 61.543 55.000 3.63 0.00 40.46 3.18
4169 4213 0.247185 CCCATGCCATGTTGGTTCAC 59.753 55.000 3.63 0.00 40.46 3.18
4221 4267 0.541998 ACGAGGACACCATCTCCACA 60.542 55.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.325150 CAGAAAGAAATAAAAAGCAATGCAATG 57.675 29.630 8.35 0.00 0.00 2.82
123 135 1.070134 TCTTCCACTTGTCCTGGTTCG 59.930 52.381 0.00 0.00 0.00 3.95
306 318 2.584498 AGGGCAGAGATGGATTTCCTTT 59.416 45.455 0.00 0.00 36.82 3.11
317 329 2.903871 TAGGCAGGCAGGGCAGAGAT 62.904 60.000 0.00 0.00 35.46 2.75
326 338 1.198713 TTTCCTCTCTAGGCAGGCAG 58.801 55.000 0.00 0.00 43.31 4.85
443 464 1.681327 CCTGGCCTGAGCAGCAAAT 60.681 57.895 11.88 0.00 42.56 2.32
493 514 1.470098 GTCGAGACCAGGCGTTTAGTA 59.530 52.381 0.00 0.00 0.00 1.82
632 653 6.149474 ACTCCAATGCAAGACAGTGTAATTAC 59.851 38.462 8.75 8.75 42.83 1.89
634 655 5.072741 ACTCCAATGCAAGACAGTGTAATT 58.927 37.500 0.00 0.00 42.83 1.40
637 658 3.769739 ACTCCAATGCAAGACAGTGTA 57.230 42.857 0.00 0.00 42.83 2.90
668 689 5.897377 AAACAATAATCCGGTTTCTCTGG 57.103 39.130 0.00 0.00 43.70 3.86
719 740 4.384647 CCAAATCCAACCACAAGGGAAAAA 60.385 41.667 0.00 0.00 41.15 1.94
724 745 1.715785 ACCAAATCCAACCACAAGGG 58.284 50.000 0.00 0.00 44.81 3.95
769 792 7.722285 AGCAACTACTGTACCATTTCCTAAAAA 59.278 33.333 0.00 0.00 0.00 1.94
770 793 7.228590 AGCAACTACTGTACCATTTCCTAAAA 58.771 34.615 0.00 0.00 0.00 1.52
771 794 6.775708 AGCAACTACTGTACCATTTCCTAAA 58.224 36.000 0.00 0.00 0.00 1.85
834 862 3.655615 TGTTGGGACAGTTTAACACCT 57.344 42.857 0.00 0.00 42.39 4.00
835 863 4.929819 ATTGTTGGGACAGTTTAACACC 57.070 40.909 0.00 0.00 42.39 4.16
942 971 2.614734 GGTAACTGGTAAGTGCTGGACC 60.615 54.545 0.00 0.00 36.51 4.46
943 972 2.038033 TGGTAACTGGTAAGTGCTGGAC 59.962 50.000 0.00 0.00 36.51 4.02
951 980 3.368531 GCAGAGGAGTGGTAACTGGTAAG 60.369 52.174 0.00 0.00 36.52 2.34
954 983 0.977395 GCAGAGGAGTGGTAACTGGT 59.023 55.000 0.00 0.00 36.52 4.00
955 984 0.250513 GGCAGAGGAGTGGTAACTGG 59.749 60.000 0.00 0.00 36.52 4.00
1020 1049 1.674764 CGAGGCATGAGAGGAGCAGT 61.675 60.000 0.00 0.00 0.00 4.40
1188 1217 4.684134 AGGTTGCGGCCTGGCATT 62.684 61.111 22.05 0.00 43.52 3.56
1194 1223 4.070552 GAGACGAGGTTGCGGCCT 62.071 66.667 0.00 0.00 41.12 5.19
1200 1229 2.982130 CCCCAGGAGACGAGGTTG 59.018 66.667 0.00 0.00 0.00 3.77
1289 1318 3.853330 CATCGTTGTCGGCGGCAG 61.853 66.667 15.90 3.97 37.69 4.85
1297 1329 3.084579 CAGCTCGCCATCGTTGTC 58.915 61.111 0.00 0.00 36.96 3.18
1313 1345 2.281484 GCAGGAACTCGTTGGGCA 60.281 61.111 0.00 0.00 34.60 5.36
1542 1574 2.358932 CCCAGCCTTAGAGTACCCAGTA 60.359 54.545 0.00 0.00 0.00 2.74
1545 1577 0.981277 GCCCAGCCTTAGAGTACCCA 60.981 60.000 0.00 0.00 0.00 4.51
1661 1693 0.251165 GCCCTCTACAAACCCAAGCA 60.251 55.000 0.00 0.00 0.00 3.91
1781 1813 3.772853 AACAGCCTGCGAGCCAACA 62.773 57.895 0.00 0.00 0.00 3.33
1845 1877 2.679837 CGAATTCTGCATGTAACCAGCT 59.320 45.455 3.52 0.00 0.00 4.24
1851 1883 2.887337 TCGAGCGAATTCTGCATGTAA 58.113 42.857 19.45 3.36 33.85 2.41
1923 1955 2.823984 CTTGTGCAGGCAAAAACATCA 58.176 42.857 0.00 0.00 0.00 3.07
1979 2011 0.392998 ATGTACCTGCCTTCCTTGCG 60.393 55.000 0.00 0.00 0.00 4.85
2070 2102 1.325943 GCTTCTGTTAGATGCTCGCAC 59.674 52.381 8.84 0.00 40.85 5.34
2097 2129 3.153369 TCTGCCAAGGCTTCAAATACA 57.847 42.857 12.96 0.00 42.51 2.29
2125 2157 6.037062 TCGATCATTGCATTGTAAGAAATCGT 59.963 34.615 19.02 0.00 35.19 3.73
2213 2245 2.237392 AGTAGGCTTGGCTTTAGTGAGG 59.763 50.000 1.22 0.00 0.00 3.86
2350 2382 7.340122 ACTTTGAATAGACATCGATCAGAGA 57.660 36.000 0.00 0.00 0.00 3.10
2436 2468 4.470664 AGGCCAAAAATCATAGCATTCCAA 59.529 37.500 5.01 0.00 0.00 3.53
2499 2531 1.671261 CCAGAGAGACGAAGCTGGTTG 60.671 57.143 0.00 0.00 42.26 3.77
2501 2533 1.254284 CCCAGAGAGACGAAGCTGGT 61.254 60.000 0.00 0.00 44.99 4.00
2511 2543 3.468071 TTAGGTGTTAGCCCAGAGAGA 57.532 47.619 0.00 0.00 0.00 3.10
2553 2585 0.533755 GAGCACTTGCCACAGTCACT 60.534 55.000 0.00 0.00 43.38 3.41
2583 2615 1.305201 GGAACTGCTGACCGTGAAAA 58.695 50.000 0.00 0.00 0.00 2.29
2585 2617 0.396435 ATGGAACTGCTGACCGTGAA 59.604 50.000 0.00 0.00 0.00 3.18
2589 2621 3.181367 GCATGGAACTGCTGACCG 58.819 61.111 0.00 0.00 39.12 4.79
2607 2639 2.362736 GCACCTGCTTTGATGATCTGA 58.637 47.619 0.00 0.00 38.21 3.27
2621 2653 2.357517 GGTCACTGTCCGCACCTG 60.358 66.667 0.00 0.00 0.00 4.00
2628 2660 0.112412 AAACATGGGGGTCACTGTCC 59.888 55.000 0.00 0.00 0.00 4.02
2719 2751 1.276421 ACAGATGACGTCCTTTCCCAG 59.724 52.381 14.12 3.80 0.00 4.45
2720 2752 1.348064 ACAGATGACGTCCTTTCCCA 58.652 50.000 14.12 0.00 0.00 4.37
2757 2789 0.874175 GACCGTGCTGCGCATATGTA 60.874 55.000 12.24 0.00 41.91 2.29
2913 2945 9.202273 GGTTCAACTGCATATTTTGTTTTCATA 57.798 29.630 0.00 0.00 0.00 2.15
2919 2951 5.540911 CCTGGTTCAACTGCATATTTTGTT 58.459 37.500 0.00 0.00 0.00 2.83
2928 2960 1.827789 GGTGCCTGGTTCAACTGCA 60.828 57.895 0.00 0.00 0.00 4.41
2931 2963 1.071471 CTCGGTGCCTGGTTCAACT 59.929 57.895 0.00 0.00 0.00 3.16
2983 3015 1.961378 CAGCATGCAGTTTGCCTGA 59.039 52.632 21.98 0.00 44.23 3.86
3020 3052 0.254178 AGCTGGTTCAATCGGCATCT 59.746 50.000 3.76 0.00 38.87 2.90
3141 3173 2.634639 TAAGAACAGAGGGGCCACTA 57.365 50.000 8.04 0.00 0.00 2.74
3227 3259 4.093952 CCTTCGCAACGCCAGCAG 62.094 66.667 0.00 0.00 0.00 4.24
3268 3300 6.582636 TCTTGCGAAGAATGTATATGAACCT 58.417 36.000 0.00 0.00 33.83 3.50
3274 3306 5.009710 TCGTCCTCTTGCGAAGAATGTATAT 59.990 40.000 0.00 0.00 37.02 0.86
3275 3307 4.337274 TCGTCCTCTTGCGAAGAATGTATA 59.663 41.667 0.00 0.00 37.02 1.47
3438 3470 8.635328 TCTGTCTACACACTGAAAACTATGTAA 58.365 33.333 0.00 0.00 0.00 2.41
3473 3505 3.873952 GGACATAGCCAGAACAGTTCATC 59.126 47.826 15.85 4.01 0.00 2.92
3481 3513 0.618458 TGTGGGGACATAGCCAGAAC 59.382 55.000 0.00 0.00 46.14 3.01
3486 3518 2.172717 AGTTATGTGTGGGGACATAGCC 59.827 50.000 0.00 0.00 46.14 3.93
3489 3521 7.202056 CCAGTATTAGTTATGTGTGGGGACATA 60.202 40.741 0.00 0.00 46.14 2.29
3491 3523 5.104693 CCAGTATTAGTTATGTGTGGGGACA 60.105 44.000 0.00 0.00 38.70 4.02
3495 3527 5.454755 CCTCCCAGTATTAGTTATGTGTGGG 60.455 48.000 0.00 0.00 44.20 4.61
3503 3535 6.084738 AGCATCATCCTCCCAGTATTAGTTA 58.915 40.000 0.00 0.00 0.00 2.24
3566 3598 4.775058 ACAAGCTGTTGTAAAACACACA 57.225 36.364 0.00 0.00 45.48 3.72
3592 3624 6.804770 AAGTAGTACATAGCCAGATAGTCG 57.195 41.667 2.52 0.00 0.00 4.18
3606 3642 7.229308 TCTGGTCTCTTTCAGTAAGTAGTACA 58.771 38.462 2.52 0.00 34.88 2.90
3651 3687 5.504010 CGCGGTAAGATACTTTGCATTTGAT 60.504 40.000 0.00 0.00 0.00 2.57
3663 3699 2.034001 GTGAACATGCGCGGTAAGATAC 60.034 50.000 8.83 0.00 0.00 2.24
3668 3704 0.601576 ACAGTGAACATGCGCGGTAA 60.602 50.000 8.83 0.00 0.00 2.85
3669 3705 1.005512 ACAGTGAACATGCGCGGTA 60.006 52.632 8.83 0.00 0.00 4.02
3704 3740 4.129757 CATGGCTATGCGCAGTGA 57.870 55.556 18.32 2.30 41.67 3.41
3786 3827 6.521151 AGAAGATTCAAATTACTGCAAGGG 57.479 37.500 0.00 0.00 39.30 3.95
3932 3973 4.640201 TCACTTTTTCAGGAACAGGTTCAG 59.360 41.667 13.62 6.10 41.20 3.02
3938 3979 8.624776 ACTTCTAATTCACTTTTTCAGGAACAG 58.375 33.333 0.00 0.00 0.00 3.16
3993 4037 1.296392 CATGTCGAACCCTCCAGCA 59.704 57.895 0.00 0.00 0.00 4.41
4016 4060 4.283467 TGGAGCTGCAGTCTAGTAGAAAAA 59.717 41.667 16.64 0.00 0.00 1.94
4033 4077 3.137459 CTCGACCTCGCTGGAGCT 61.137 66.667 0.00 0.00 39.06 4.09
4065 4109 2.045634 TCTGTGAGCATGCTGGCC 60.046 61.111 28.27 11.81 0.00 5.36
4153 4197 1.001181 GCTTGTGAACCAACATGGCAT 59.999 47.619 0.00 0.00 42.67 4.40
4162 4206 3.286751 GGCAGCGCTTGTGAACCA 61.287 61.111 7.50 0.00 0.00 3.67
4164 4208 4.043200 GGGGCAGCGCTTGTGAAC 62.043 66.667 7.50 0.00 0.00 3.18
4221 4267 1.106351 TGGTGTGGTTGCAAGCGAAT 61.106 50.000 22.55 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.