Multiple sequence alignment - TraesCS7A01G298200

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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 TraesCS7A01G298200 chr7A 100.000 5000 0 0 1 5000 403195103 403190104 0.000000e+00 9234.0
1 TraesCS7A01G298200 chr7A 89.855 69 4 3 4931 4999 365077257 365077192 8.920000e-13 86.1
2 TraesCS7A01G298200 chr7B 95.196 4996 146 30 1 4946 321340119 321345070 0.000000e+00 7810.0
3 TraesCS7A01G298200 chr7D 95.052 2607 93 15 2326 4913 365316516 365313927 0.000000e+00 4067.0
4 TraesCS7A01G298200 chr7D 93.855 1367 60 10 1 1355 365319022 365317668 0.000000e+00 2037.0
5 TraesCS7A01G298200 chr7D 96.552 986 22 5 1345 2328 365317632 365316657 0.000000e+00 1622.0
6 TraesCS7A01G298200 chr7D 90.909 66 4 2 4930 4994 478082393 478082457 2.480000e-13 87.9
7 TraesCS7A01G298200 chr2A 98.148 54 0 1 4941 4994 691214580 691214528 5.330000e-15 93.5
8 TraesCS7A01G298200 chr1D 96.429 56 1 1 4939 4994 472517773 472517827 1.920000e-14 91.6
9 TraesCS7A01G298200 chr1B 93.651 63 1 3 4932 4994 476030745 476030804 1.920000e-14 91.6
10 TraesCS7A01G298200 chr2D 94.828 58 2 1 4937 4994 121720738 121720682 6.890000e-14 89.8
11 TraesCS7A01G298200 chr6D 90.909 66 2 4 4935 4999 431311751 431311813 8.920000e-13 86.1
12 TraesCS7A01G298200 chr5A 90.769 65 4 2 4930 4994 618475129 618475191 8.920000e-13 86.1
13 TraesCS7A01G298200 chr2B 88.889 72 5 3 4925 4994 654952689 654952759 8.920000e-13 86.1


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 TraesCS7A01G298200 chr7A 403190104 403195103 4999 True 9234.000000 9234 100.000 1 5000 1 chr7A.!!$R2 4999
1 TraesCS7A01G298200 chr7B 321340119 321345070 4951 False 7810.000000 7810 95.196 1 4946 1 chr7B.!!$F1 4945
2 TraesCS7A01G298200 chr7D 365313927 365319022 5095 True 2575.333333 4067 95.153 1 4913 3 chr7D.!!$R1 4912


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
899 908 0.322098 TATTGACCGGTGCCAAGGTG 60.322 55.000 14.63 0.0 41.51 4.00 F
1743 1815 0.530650 ATGACGCCACCATCGACATC 60.531 55.000 0.00 0.0 37.68 3.06 F
3564 3806 2.821969 ACAACTTTCCTGCATGGCTTAG 59.178 45.455 0.00 0.0 35.26 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 2568 0.322975 AGAGCAGCCGATGAACAAGT 59.677 50.0 0.00 0.0 0.00 3.16 R
3607 3849 0.096454 GTGCCCTCGAAAATACACGC 59.904 55.0 0.00 0.0 0.00 5.34 R
4631 4875 0.253044 CGAATTCAGGAGGGGCTCAA 59.747 55.0 6.22 0.0 31.08 3.02 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
21 22 2.556622 CCCACCTTTACACATTGTCACC 59.443 50.000 0.00 0.00 0.00 4.02
22 23 3.218453 CCACCTTTACACATTGTCACCA 58.782 45.455 0.00 0.00 0.00 4.17
71 72 5.809051 TGCGAATGCTGATATACTCATGATC 59.191 40.000 0.00 0.00 43.34 2.92
151 152 4.787135 TGGCCATCCAATTGAGTACATA 57.213 40.909 0.00 0.00 39.99 2.29
310 311 5.106197 ACAATGTATGCCAATGTACTGTGTG 60.106 40.000 0.00 0.00 35.40 3.82
325 331 5.528043 ACTGTGTGTTTGATGGCAAAATA 57.472 34.783 0.00 0.00 44.91 1.40
355 361 6.618287 TTGACTGTCATCCTACTTTTTGTG 57.382 37.500 11.86 0.00 0.00 3.33
426 432 4.695217 TGTCGGCATTTCCTGAATTAAC 57.305 40.909 0.00 0.00 0.00 2.01
569 576 2.363306 TGATGTTCCTTTGTGCTGGT 57.637 45.000 0.00 0.00 0.00 4.00
610 617 3.531538 TCTCCGTATGATGTTCCTTTGC 58.468 45.455 0.00 0.00 0.00 3.68
617 624 2.571212 TGATGTTCCTTTGCGTTGTCT 58.429 42.857 0.00 0.00 0.00 3.41
624 631 1.403679 CCTTTGCGTTGTCTTGACCAA 59.596 47.619 0.00 0.00 0.00 3.67
634 642 5.469479 GTTGTCTTGACCAATGTTTATGGG 58.531 41.667 0.00 0.00 42.48 4.00
673 682 5.123227 TGCGGATATAGGAAGAACAAAAGG 58.877 41.667 0.00 0.00 0.00 3.11
674 683 4.023963 GCGGATATAGGAAGAACAAAAGGC 60.024 45.833 0.00 0.00 0.00 4.35
675 684 4.515567 CGGATATAGGAAGAACAAAAGGCC 59.484 45.833 0.00 0.00 0.00 5.19
679 688 7.124298 GGATATAGGAAGAACAAAAGGCCTTTT 59.876 37.037 33.27 33.27 42.91 2.27
680 689 6.747414 ATAGGAAGAACAAAAGGCCTTTTT 57.253 33.333 35.67 24.88 40.45 1.94
720 729 0.526096 CGTGCATGCCATAAACTGCC 60.526 55.000 16.68 0.00 33.70 4.85
743 752 1.066454 GAAGGACAAAACCAACCACCG 59.934 52.381 0.00 0.00 0.00 4.94
780 789 3.441572 CGCTGGATTTTCCTGAATTCTGT 59.558 43.478 7.05 0.00 37.65 3.41
799 808 6.545504 TCTGTGTGAATTAGTTTCTTCTGC 57.454 37.500 0.00 0.00 35.23 4.26
825 834 2.459060 TGCATTTGCCACATTGAAGG 57.541 45.000 0.00 0.00 41.18 3.46
836 845 4.321974 GCCACATTGAAGGGTAAAAGAAGG 60.322 45.833 0.00 0.00 0.00 3.46
837 846 5.076873 CCACATTGAAGGGTAAAAGAAGGA 58.923 41.667 0.00 0.00 0.00 3.36
856 865 2.163412 GGAAAATATGTGAAGCACGCCA 59.837 45.455 0.00 0.00 37.14 5.69
858 867 1.382522 AATATGTGAAGCACGCCAGG 58.617 50.000 0.00 0.00 37.14 4.45
899 908 0.322098 TATTGACCGGTGCCAAGGTG 60.322 55.000 14.63 0.00 41.51 4.00
900 909 4.947147 TGACCGGTGCCAAGGTGC 62.947 66.667 14.63 0.00 41.51 5.01
904 913 3.673484 CGGTGCCAAGGTGCCAAG 61.673 66.667 0.00 0.00 0.00 3.61
905 914 3.305516 GGTGCCAAGGTGCCAAGG 61.306 66.667 0.00 0.00 0.00 3.61
906 915 2.521708 GTGCCAAGGTGCCAAGGT 60.522 61.111 0.00 0.00 0.00 3.50
969 978 7.066163 TGGTCATGCACAACTTAGAATAGATTG 59.934 37.037 0.00 0.00 0.00 2.67
973 986 6.237901 TGCACAACTTAGAATAGATTGTGGT 58.762 36.000 15.06 0.00 46.53 4.16
988 1001 0.541764 GTGGTCCATCCCAAAGGCAA 60.542 55.000 0.00 0.00 35.92 4.52
1134 1147 5.964958 TCAGGTTTTGATGAGACATTTCC 57.035 39.130 0.00 0.00 0.00 3.13
1216 1229 9.382275 GCCTTTTCCAATGATATTGTATTTTGT 57.618 29.630 0.00 0.00 0.00 2.83
1280 1297 3.785486 CGCAGTTCATCCTACATTCTCA 58.215 45.455 0.00 0.00 0.00 3.27
1413 1485 2.959030 GTCTGGCTTCAGGGTTTCTTTT 59.041 45.455 0.00 0.00 38.96 2.27
1497 1569 9.613428 TGGTCGTATCTGATTTGATAATTTCTT 57.387 29.630 0.00 0.00 31.61 2.52
1743 1815 0.530650 ATGACGCCACCATCGACATC 60.531 55.000 0.00 0.00 37.68 3.06
2019 2094 8.856490 TGCTCAAAAGTGACTCTTAAAAATTC 57.144 30.769 0.00 0.00 35.02 2.17
2032 2107 9.267084 ACTCTTAAAAATTCTCTCAGAAGTGTC 57.733 33.333 0.00 0.00 37.69 3.67
2110 2185 5.713792 ACTAGATCACCATTACATCTCCG 57.286 43.478 0.00 0.00 0.00 4.63
2146 2221 5.179368 TGTTTTGACCGCATTTTGAAAAACA 59.821 32.000 6.69 6.69 41.27 2.83
2264 2339 4.382254 CCATGCTCACCAGTTGCAATATTT 60.382 41.667 0.59 0.00 40.24 1.40
2339 2557 8.677148 TTACTTGGGATTTATTGCTGATAGTC 57.323 34.615 0.00 0.00 0.00 2.59
2346 2564 6.701841 GGATTTATTGCTGATAGTCTTCACGA 59.298 38.462 0.00 0.00 0.00 4.35
2347 2565 7.386299 GGATTTATTGCTGATAGTCTTCACGAT 59.614 37.037 0.00 0.00 0.00 3.73
2348 2566 7.468922 TTTATTGCTGATAGTCTTCACGATG 57.531 36.000 0.00 0.00 0.00 3.84
2349 2567 4.718940 TTGCTGATAGTCTTCACGATGA 57.281 40.909 0.00 0.00 0.00 2.92
2350 2568 4.718940 TGCTGATAGTCTTCACGATGAA 57.281 40.909 0.00 0.00 34.79 2.57
2407 2626 6.873605 TGTTGTATGTCTCAGTTGGAATGTAG 59.126 38.462 0.00 0.00 0.00 2.74
2544 2765 2.977580 TCTCCTTGCCATCATCTATGCT 59.022 45.455 0.00 0.00 33.92 3.79
2912 3136 3.256383 TGTGTTATTGCTGCAATTGCTCT 59.744 39.130 30.35 10.88 42.66 4.09
3046 3270 3.134458 GGGAATTCTTGTGGCTATCGAG 58.866 50.000 5.23 0.00 0.00 4.04
3211 3437 3.149981 TGGATTTGTATTGTTCACGGCA 58.850 40.909 0.00 0.00 0.00 5.69
3271 3497 5.124936 TGCACATTTCATCTCCTCATTTCTG 59.875 40.000 0.00 0.00 0.00 3.02
3321 3547 5.508280 TTGGCCTGGTTGTTACTACTATT 57.492 39.130 3.32 0.00 0.00 1.73
3328 3554 6.313905 CCTGGTTGTTACTACTATTGCTCTTG 59.686 42.308 0.00 0.00 0.00 3.02
3405 3646 6.432162 ACTTGCATTCATTCATGTTAGTGACT 59.568 34.615 0.00 0.00 0.00 3.41
3563 3805 2.875296 ACAACTTTCCTGCATGGCTTA 58.125 42.857 0.00 0.00 35.26 3.09
3564 3806 2.821969 ACAACTTTCCTGCATGGCTTAG 59.178 45.455 0.00 0.00 35.26 2.18
3602 3844 8.738645 AATTTACTCCTACTATTTTGCAGAGG 57.261 34.615 0.00 0.00 0.00 3.69
3607 3849 6.174720 TCCTACTATTTTGCAGAGGGTATG 57.825 41.667 0.00 0.00 0.00 2.39
3609 3851 3.206150 ACTATTTTGCAGAGGGTATGCG 58.794 45.455 0.00 0.00 46.87 4.73
3649 3891 2.093235 GGTGAAGCCTAGCAATGAGACT 60.093 50.000 0.00 0.00 0.00 3.24
3724 3966 3.181501 ACACAAAGTTGACGGTGAATGTG 60.182 43.478 9.86 9.86 41.86 3.21
3735 3977 0.598065 GTGAATGTGGGTGAACTGCC 59.402 55.000 0.00 0.00 0.00 4.85
3741 3983 2.149383 TGGGTGAACTGCCTCTGCT 61.149 57.895 0.00 0.00 38.71 4.24
3870 4112 0.398318 GGTACCAGATCCCATGCCTC 59.602 60.000 7.15 0.00 0.00 4.70
3881 4123 0.680618 CCATGCCTCCAAAACTTGCA 59.319 50.000 0.00 0.00 36.23 4.08
3903 4145 2.887568 GTCTCCTGCCGATGTGCG 60.888 66.667 0.00 0.00 40.47 5.34
3906 4148 1.522355 CTCCTGCCGATGTGCGAAT 60.522 57.895 0.00 0.00 44.57 3.34
3972 4214 6.325596 GGTCAAAGATGAAAGCATTTAGGAC 58.674 40.000 0.00 0.00 39.27 3.85
4130 4372 1.961277 CACCTGGTGCACCGACTTC 60.961 63.158 30.07 6.48 39.43 3.01
4140 4382 1.734465 GCACCGACTTCAATCTTCAGG 59.266 52.381 0.00 0.00 0.00 3.86
4388 4632 3.126171 TCGTGCAAATCCAAGTTTATCCG 59.874 43.478 0.00 0.00 0.00 4.18
4399 4643 5.296780 TCCAAGTTTATCCGAGCAATTCATC 59.703 40.000 0.00 0.00 0.00 2.92
4429 4673 2.949447 AGGTCCAAAATGAGCAACTGT 58.051 42.857 0.00 0.00 35.23 3.55
4505 4749 8.196378 ACACAATCCCCTACTCTAAATAGATC 57.804 38.462 0.00 0.00 0.00 2.75
4560 4804 7.320399 TCATTGTACTACACACTACAGGAATG 58.680 38.462 0.00 0.00 36.69 2.67
4573 4817 4.164822 ACAGGAATGCAAAACATCTTCG 57.835 40.909 0.00 0.00 38.34 3.79
4629 4873 1.919956 CTTGGCTTGCCTCTTGAGCG 61.920 60.000 13.18 0.00 37.29 5.03
4630 4874 3.130160 GGCTTGCCTCTTGAGCGG 61.130 66.667 4.11 0.00 37.29 5.52
4631 4875 2.359230 GCTTGCCTCTTGAGCGGT 60.359 61.111 0.00 0.00 0.00 5.68
4632 4876 1.968540 GCTTGCCTCTTGAGCGGTT 60.969 57.895 0.00 0.00 0.00 4.44
4633 4877 1.871772 CTTGCCTCTTGAGCGGTTG 59.128 57.895 0.00 0.00 0.00 3.77
4634 4878 0.603707 CTTGCCTCTTGAGCGGTTGA 60.604 55.000 0.00 0.00 0.00 3.18
4635 4879 0.603707 TTGCCTCTTGAGCGGTTGAG 60.604 55.000 0.00 0.00 0.00 3.02
4636 4880 2.394563 GCCTCTTGAGCGGTTGAGC 61.395 63.158 0.00 0.00 37.41 4.26
4690 4934 4.582656 TCCTGTCAAATGAACAAACCGAAT 59.417 37.500 0.00 0.00 0.00 3.34
4814 5058 1.211969 CGACGATCCAACGGTCAGT 59.788 57.895 0.00 0.00 37.61 3.41
4844 5088 1.271597 ACACTCCACAGGATTGCTTCC 60.272 52.381 3.61 0.00 45.85 3.46
4886 5130 7.329438 CTGTGAAACTGCATATGTCAAAAAG 57.671 36.000 4.29 0.00 38.04 2.27
4888 5132 6.917477 TGTGAAACTGCATATGTCAAAAAGTC 59.083 34.615 4.29 0.00 38.04 3.01
4890 5134 7.434897 GTGAAACTGCATATGTCAAAAAGTCAA 59.565 33.333 4.29 0.00 0.00 3.18
4892 5136 7.878477 AACTGCATATGTCAAAAAGTCAATG 57.122 32.000 4.29 0.00 0.00 2.82
4893 5137 5.865552 ACTGCATATGTCAAAAAGTCAATGC 59.134 36.000 4.29 0.00 39.08 3.56
4894 5138 5.170021 TGCATATGTCAAAAAGTCAATGCC 58.830 37.500 4.29 0.00 38.11 4.40
4895 5139 5.170021 GCATATGTCAAAAAGTCAATGCCA 58.830 37.500 4.29 0.00 33.96 4.92
4906 5150 5.643379 AAGTCAATGCCATAAAATCACGT 57.357 34.783 0.00 0.00 0.00 4.49
4946 5190 2.294074 TGGGTGTGCTTTGTCAAGTAC 58.706 47.619 0.00 0.00 43.88 2.73
4947 5191 2.092646 TGGGTGTGCTTTGTCAAGTACT 60.093 45.455 5.06 0.00 43.93 2.73
4948 5192 2.548480 GGGTGTGCTTTGTCAAGTACTC 59.452 50.000 0.00 1.82 43.93 2.59
4949 5193 2.548480 GGTGTGCTTTGTCAAGTACTCC 59.452 50.000 0.00 8.05 45.83 3.85
4950 5194 2.548480 GTGTGCTTTGTCAAGTACTCCC 59.452 50.000 0.00 0.00 43.93 4.30
4951 5195 2.438021 TGTGCTTTGTCAAGTACTCCCT 59.562 45.455 0.00 0.00 43.93 4.20
4952 5196 3.067833 GTGCTTTGTCAAGTACTCCCTC 58.932 50.000 0.00 0.00 41.22 4.30
4953 5197 2.038557 TGCTTTGTCAAGTACTCCCTCC 59.961 50.000 0.00 0.00 31.86 4.30
4954 5198 2.931320 GCTTTGTCAAGTACTCCCTCCG 60.931 54.545 0.00 0.00 31.86 4.63
4955 5199 2.005370 TTGTCAAGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
4956 5200 2.005370 TGTCAAGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
4957 5201 1.891150 TGTCAAGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
4958 5202 1.204231 GTCAAGTACTCCCTCCGTTCC 59.796 57.143 0.00 0.00 0.00 3.62
4959 5203 1.203087 TCAAGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
4960 5204 1.621814 CAAGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
4961 5205 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4962 5206 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
4963 5207 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
4964 5208 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
4965 5209 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
4966 5210 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
4967 5211 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
4968 5212 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
4969 5213 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
4970 5214 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
4971 5215 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
4972 5216 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
4973 5217 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
4974 5218 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
4975 5219 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
4976 5220 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
4977 5221 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
4978 5222 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
4979 5223 8.076178 CGTTCCAAAATAGATGACTCAACTTTT 58.924 33.333 0.00 0.00 0.00 2.27
4980 5224 9.185192 GTTCCAAAATAGATGACTCAACTTTTG 57.815 33.333 0.00 1.40 0.00 2.44
4981 5225 8.463930 TCCAAAATAGATGACTCAACTTTTGT 57.536 30.769 10.34 0.00 0.00 2.83
4982 5226 9.567776 TCCAAAATAGATGACTCAACTTTTGTA 57.432 29.630 10.34 0.00 0.00 2.41
4983 5227 9.612620 CCAAAATAGATGACTCAACTTTTGTAC 57.387 33.333 10.34 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.892755 AGTGTGGCCAAAGCATGATG 59.107 50.000 7.24 0.00 42.56 3.07
22 23 0.892755 CAGTGTGGCCAAAGCATGAT 59.107 50.000 7.24 0.00 42.56 2.45
151 152 1.688772 GTGCATCCAGATCAAGGCAT 58.311 50.000 5.59 0.00 33.43 4.40
310 311 8.223100 GTCAAAGACAATATTTTGCCATCAAAC 58.777 33.333 0.00 0.00 35.95 2.93
325 331 6.365970 AGTAGGATGACAGTCAAAGACAAT 57.634 37.500 7.50 0.00 34.60 2.71
355 361 9.929722 TCGAAGTTAATGCAACATTATTATGTC 57.070 29.630 0.00 0.00 44.14 3.06
393 399 2.401583 TGCCGACAAATGTCAGCTAT 57.598 45.000 19.28 0.00 45.88 2.97
426 432 2.093783 GGAGTTTGATACGGAAAGTGCG 59.906 50.000 0.00 0.00 37.19 5.34
569 576 5.453903 GGAGAAAGGGAAATGATCTCGATGA 60.454 44.000 0.00 0.00 37.89 2.92
610 617 5.153513 CCATAAACATTGGTCAAGACAACG 58.846 41.667 2.29 0.00 0.00 4.10
617 624 6.924913 TGATTTCCCATAAACATTGGTCAA 57.075 33.333 0.00 0.00 31.99 3.18
647 655 5.353394 TTGTTCTTCCTATATCCGCAACT 57.647 39.130 0.00 0.00 0.00 3.16
679 688 0.187361 ACAGGCAGCAAGGGGTTAAA 59.813 50.000 0.00 0.00 0.00 1.52
680 689 0.539438 CACAGGCAGCAAGGGGTTAA 60.539 55.000 0.00 0.00 0.00 2.01
694 703 0.744057 TATGGCATGCACGTCACAGG 60.744 55.000 21.36 0.00 0.00 4.00
720 729 3.568430 GGTGGTTGGTTTTGTCCTTCTAG 59.432 47.826 0.00 0.00 0.00 2.43
743 752 1.212616 CAGCGTTCCGATTCCAGATC 58.787 55.000 0.00 0.00 0.00 2.75
758 767 3.441572 ACAGAATTCAGGAAAATCCAGCG 59.558 43.478 8.44 0.00 39.61 5.18
760 769 5.474532 TCACACAGAATTCAGGAAAATCCAG 59.525 40.000 8.44 0.00 39.61 3.86
761 770 5.384336 TCACACAGAATTCAGGAAAATCCA 58.616 37.500 8.44 0.00 39.61 3.41
780 789 7.939782 TGAATTGCAGAAGAAACTAATTCACA 58.060 30.769 0.00 0.00 38.72 3.58
799 808 4.393371 TCAATGTGGCAAATGCATGAATTG 59.607 37.500 0.00 2.14 44.36 2.32
825 834 8.303876 TGCTTCACATATTTTCCTTCTTTTACC 58.696 33.333 0.00 0.00 0.00 2.85
836 845 3.429085 CTGGCGTGCTTCACATATTTTC 58.571 45.455 0.00 0.00 33.40 2.29
837 846 2.164219 CCTGGCGTGCTTCACATATTTT 59.836 45.455 0.00 0.00 33.40 1.82
969 978 0.541764 TTGCCTTTGGGATGGACCAC 60.542 55.000 0.00 0.00 41.03 4.16
973 986 1.691434 GTTGTTTGCCTTTGGGATGGA 59.309 47.619 0.00 0.00 33.58 3.41
988 1001 4.677779 GCATGAATAAATCCCTGCGTTGTT 60.678 41.667 0.00 0.00 0.00 2.83
1134 1147 4.744137 TGAAAACTCGAATGTTTGCAATGG 59.256 37.500 8.17 0.00 41.11 3.16
1280 1297 2.893489 GAGCAAGTTCTTGATTTGGGGT 59.107 45.455 15.52 0.00 0.00 4.95
1413 1485 6.373216 CGACTAAAATTTCAACCTATCCACCA 59.627 38.462 0.00 0.00 0.00 4.17
2019 2094 5.333952 GCAAAGAATGTGACACTTCTGAGAG 60.334 44.000 16.17 10.25 32.20 3.20
2032 2107 7.443272 TCTGTATGATATCCTGCAAAGAATGTG 59.557 37.037 0.00 0.00 0.00 3.21
2110 2185 4.384547 GCGGTCAAAACATTAAACCATGAC 59.615 41.667 0.00 0.00 36.01 3.06
2321 2396 6.701841 TCGTGAAGACTATCAGCAATAAATCC 59.298 38.462 0.00 0.00 0.00 3.01
2348 2566 1.129437 GAGCAGCCGATGAACAAGTTC 59.871 52.381 6.01 6.01 39.91 3.01
2349 2567 1.160137 GAGCAGCCGATGAACAAGTT 58.840 50.000 0.00 0.00 0.00 2.66
2350 2568 0.322975 AGAGCAGCCGATGAACAAGT 59.677 50.000 0.00 0.00 0.00 3.16
2407 2626 7.362662 TGAATTGATTCAACTAAGACAGCAAC 58.637 34.615 0.15 0.00 43.26 4.17
2544 2765 3.765381 TGAAAGAGGACATCCAAATGCA 58.235 40.909 0.00 0.00 38.89 3.96
2886 3110 4.905295 GCAATTGCAGCAATAACACAAAAC 59.095 37.500 25.36 0.23 41.59 2.43
2912 3136 4.649267 TTCCCCATGAATATTATCGGCA 57.351 40.909 0.00 0.00 0.00 5.69
3116 3342 4.611355 CGGCAAGTTACATCACTGAAGTTG 60.611 45.833 0.00 0.00 36.83 3.16
3211 3437 6.264067 GCACCCAAATGCTTATAAGAGATTCT 59.736 38.462 16.85 0.00 42.62 2.40
3321 3547 1.677576 CCAAGCAAGTTCACAAGAGCA 59.322 47.619 0.00 0.00 0.00 4.26
3328 3554 2.791158 CGTCACAACCAAGCAAGTTCAC 60.791 50.000 0.00 0.00 0.00 3.18
3405 3646 8.528643 TCTTATTGTTCTTCCTTCTATCACGAA 58.471 33.333 0.00 0.00 0.00 3.85
3542 3784 2.584835 AGCCATGCAGGAAAGTTGTA 57.415 45.000 0.00 0.00 41.22 2.41
3563 3805 9.668497 GTAGGAGTAAATTTTAAGGATGTCACT 57.332 33.333 0.00 0.00 0.00 3.41
3564 3806 9.668497 AGTAGGAGTAAATTTTAAGGATGTCAC 57.332 33.333 0.00 0.00 0.00 3.67
3602 3844 2.542595 CCCTCGAAAATACACGCATACC 59.457 50.000 0.00 0.00 0.00 2.73
3607 3849 0.096454 GTGCCCTCGAAAATACACGC 59.904 55.000 0.00 0.00 0.00 5.34
3609 3851 1.737793 CCTGTGCCCTCGAAAATACAC 59.262 52.381 0.00 0.00 0.00 2.90
3649 3891 6.660521 AGACAGTTGCCTTGAATGATTTCATA 59.339 34.615 0.00 0.00 41.38 2.15
3724 3966 1.673665 CAGCAGAGGCAGTTCACCC 60.674 63.158 0.00 0.00 44.61 4.61
3735 3977 6.373186 TGAATATGCAAGAATTCAGCAGAG 57.627 37.500 23.78 3.89 42.14 3.35
3741 3983 8.735692 TGTATGTCTGAATATGCAAGAATTCA 57.264 30.769 16.83 16.83 39.24 2.57
3870 4112 0.381801 AGACACGCTGCAAGTTTTGG 59.618 50.000 0.00 0.00 35.30 3.28
3881 4123 3.071206 ATCGGCAGGAGACACGCT 61.071 61.111 0.00 0.00 0.00 5.07
3903 4145 3.064207 TGTCTAACACGCTTCACCATTC 58.936 45.455 0.00 0.00 0.00 2.67
3906 4148 1.411246 ACTGTCTAACACGCTTCACCA 59.589 47.619 0.00 0.00 0.00 4.17
3972 4214 9.748708 TCAGATACAAATGAAAAACAAAAGAGG 57.251 29.630 0.00 0.00 0.00 3.69
4229 4471 9.483489 TTTCAGGTAGTACTGGATACTAATTGA 57.517 33.333 5.39 1.54 45.93 2.57
4292 4536 4.724279 AACCACCAGTTGTAATCTTCCT 57.276 40.909 0.00 0.00 37.29 3.36
4354 4598 3.332761 TTTGCACGACATGTTCTTCAC 57.667 42.857 0.00 0.00 0.00 3.18
4388 4632 6.529220 ACCTTACATCCTAGATGAATTGCTC 58.471 40.000 11.40 0.00 0.00 4.26
4399 4643 5.529060 GCTCATTTTGGACCTTACATCCTAG 59.471 44.000 0.00 0.00 37.13 3.02
4429 4673 8.826710 GGTGATTGATTAATCTTGTTCGATACA 58.173 33.333 16.24 0.00 42.56 2.29
4560 4804 5.034554 TCAGATTCACGAAGATGTTTTGC 57.965 39.130 0.00 0.00 0.00 3.68
4573 4817 4.998671 TCTGGATCAGACTCAGATTCAC 57.001 45.455 0.00 0.00 35.39 3.18
4629 4873 0.332972 AATTCAGGAGGGGCTCAACC 59.667 55.000 0.00 0.00 37.93 3.77
4630 4874 1.756430 GAATTCAGGAGGGGCTCAAC 58.244 55.000 0.00 0.00 31.08 3.18
4631 4875 0.253044 CGAATTCAGGAGGGGCTCAA 59.747 55.000 6.22 0.00 31.08 3.02
4632 4876 0.617535 TCGAATTCAGGAGGGGCTCA 60.618 55.000 6.22 0.00 31.08 4.26
4633 4877 0.761802 ATCGAATTCAGGAGGGGCTC 59.238 55.000 6.22 0.00 0.00 4.70
4634 4878 0.761802 GATCGAATTCAGGAGGGGCT 59.238 55.000 6.22 0.00 0.00 5.19
4635 4879 0.761802 AGATCGAATTCAGGAGGGGC 59.238 55.000 6.22 0.00 0.00 5.80
4636 4880 3.567478 AAAGATCGAATTCAGGAGGGG 57.433 47.619 6.22 0.00 0.00 4.79
4690 4934 9.325198 ACTATTACTTTGCGATCATGAATTGTA 57.675 29.630 0.00 0.00 0.00 2.41
4814 5058 4.878968 TCCTGTGGAGTGTATGGAGAATA 58.121 43.478 0.00 0.00 0.00 1.75
4844 5088 3.017323 CGCCGCAAAGATAGCTGG 58.983 61.111 0.00 0.00 0.00 4.85
4880 5124 7.095691 ACGTGATTTTATGGCATTGACTTTTTG 60.096 33.333 4.78 0.00 0.00 2.44
4886 5130 4.980590 TCACGTGATTTTATGGCATTGAC 58.019 39.130 15.76 0.00 0.00 3.18
4888 5132 5.512788 GTCTTCACGTGATTTTATGGCATTG 59.487 40.000 20.80 0.00 0.00 2.82
4890 5134 4.943705 AGTCTTCACGTGATTTTATGGCAT 59.056 37.500 20.80 4.88 0.00 4.40
4892 5136 4.946784 AGTCTTCACGTGATTTTATGGC 57.053 40.909 20.80 7.30 0.00 4.40
4893 5137 6.590292 ACACTAGTCTTCACGTGATTTTATGG 59.410 38.462 20.80 9.27 0.00 2.74
4894 5138 7.201444 GGACACTAGTCTTCACGTGATTTTATG 60.201 40.741 20.80 13.85 44.36 1.90
4895 5139 6.812160 GGACACTAGTCTTCACGTGATTTTAT 59.188 38.462 20.80 7.50 44.36 1.40
4906 5150 3.515502 CCAATCTGGGACACTAGTCTTCA 59.484 47.826 0.00 0.00 44.36 3.02
4946 5190 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
4947 5191 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
4948 5192 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
4949 5193 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
4950 5194 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
4951 5195 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
4952 5196 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
4953 5197 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
4954 5198 9.185192 CAAAAGTTGAGTCATCTATTTTGGAAC 57.815 33.333 15.00 0.00 33.72 3.62
4955 5199 8.912988 ACAAAAGTTGAGTCATCTATTTTGGAA 58.087 29.630 21.47 0.00 37.26 3.53
4956 5200 8.463930 ACAAAAGTTGAGTCATCTATTTTGGA 57.536 30.769 21.47 0.00 37.26 3.53
4957 5201 9.612620 GTACAAAAGTTGAGTCATCTATTTTGG 57.387 33.333 21.47 8.90 37.26 3.28



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

AutoCloner maintained by Alex Coulton.