Multiple sequence alignment - TraesCS7B01G310100

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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 TraesCS7B01G310100 chr7B 100.000 5928 0 0 1 5928 554194609 554188682 0.000000e+00 10948.0
1 TraesCS7B01G310100 chr7B 90.635 929 57 10 801 1710 554339914 554338997 0.000000e+00 1206.0
2 TraesCS7B01G310100 chr7B 94.177 790 40 5 1 787 554340685 554339899 0.000000e+00 1199.0
3 TraesCS7B01G310100 chr7B 90.244 369 26 6 916 1282 554355500 554355140 1.930000e-129 473.0
4 TraesCS7B01G310100 chr7A 96.728 4920 132 18 914 5814 598354343 598349434 0.000000e+00 8167.0
5 TraesCS7B01G310100 chr7A 80.446 808 122 22 1 783 305688 306484 8.560000e-163 584.0
6 TraesCS7B01G310100 chr7A 98.485 66 1 0 5863 5928 598349436 598349371 3.750000e-22 117.0
7 TraesCS7B01G310100 chr7A 91.667 48 3 1 5374 5421 474730850 474730804 1.380000e-06 65.8
8 TraesCS7B01G310100 chr7D 96.548 4722 142 14 1214 5927 520865159 520860451 0.000000e+00 7797.0
9 TraesCS7B01G310100 chr7D 90.095 525 44 3 913 1437 520872287 520871771 0.000000e+00 675.0
10 TraesCS7B01G310100 chr7D 92.929 99 6 1 913 1010 520865699 520865601 6.190000e-30 143.0
11 TraesCS7B01G310100 chr1B 80.952 756 104 20 1 725 671214086 671213340 4.010000e-156 562.0
12 TraesCS7B01G310100 chr3D 82.740 365 41 10 1 346 24096322 24096683 7.460000e-79 305.0
13 TraesCS7B01G310100 chrUn 86.232 138 19 0 2309 2446 22142955 22142818 3.700000e-32 150.0
14 TraesCS7B01G310100 chrUn 91.919 99 8 0 3763 3861 22160198 22160296 8.010000e-29 139.0
15 TraesCS7B01G310100 chrUn 98.438 64 1 0 2443 2506 22142269 22142206 4.860000e-21 113.0
16 TraesCS7B01G310100 chr2A 86.232 138 19 0 2309 2446 681091991 681092128 3.700000e-32 150.0
17 TraesCS7B01G310100 chr2A 91.919 99 8 0 3763 3861 681100313 681100411 8.010000e-29 139.0
18 TraesCS7B01G310100 chr2A 91.667 48 2 2 5374 5421 297253189 297253234 1.380000e-06 65.8
19 TraesCS7B01G310100 chr2A 91.489 47 4 0 9 55 726777124 726777078 1.380000e-06 65.8
20 TraesCS7B01G310100 chr2D 91.919 99 8 0 3763 3861 538676350 538676448 8.010000e-29 139.0
21 TraesCS7B01G310100 chr2D 98.438 64 1 0 2443 2506 538669336 538669399 4.860000e-21 113.0
22 TraesCS7B01G310100 chr2D 91.667 48 2 2 5374 5421 247098429 247098474 1.380000e-06 65.8
23 TraesCS7B01G310100 chr1D 88.000 100 10 2 102 199 157721885 157721786 3.750000e-22 117.0
24 TraesCS7B01G310100 chr1A 93.750 48 3 0 5374 5421 60355426 60355379 8.240000e-09 73.1
25 TraesCS7B01G310100 chr6D 95.349 43 0 2 5386 5426 56277770 56277728 3.830000e-07 67.6
26 TraesCS7B01G310100 chr4A 95.349 43 0 2 5387 5428 35175888 35175847 3.830000e-07 67.6
27 TraesCS7B01G310100 chr3A 89.091 55 2 3 5379 5429 728992445 728992499 1.380000e-06 65.8


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 TraesCS7B01G310100 chr7B 554188682 554194609 5927 True 10948.0 10948 100.0000 1 5928 1 chr7B.!!$R1 5927
1 TraesCS7B01G310100 chr7B 554338997 554340685 1688 True 1202.5 1206 92.4060 1 1710 2 chr7B.!!$R3 1709
2 TraesCS7B01G310100 chr7A 598349371 598354343 4972 True 4142.0 8167 97.6065 914 5928 2 chr7A.!!$R2 5014
3 TraesCS7B01G310100 chr7A 305688 306484 796 False 584.0 584 80.4460 1 783 1 chr7A.!!$F1 782
4 TraesCS7B01G310100 chr7D 520860451 520865699 5248 True 3970.0 7797 94.7385 913 5927 2 chr7D.!!$R2 5014
5 TraesCS7B01G310100 chr7D 520871771 520872287 516 True 675.0 675 90.0950 913 1437 1 chr7D.!!$R1 524
6 TraesCS7B01G310100 chr1B 671213340 671214086 746 True 562.0 562 80.9520 1 725 1 chr1B.!!$R1 724

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
878 916 0.108186 AATTCATGCTCGCAGACCGA 60.108 50.0 0.00 0.0 45.15 4.69 F
958 1015 0.251341 ACCCTCCTGCGAGCAAAAAT 60.251 50.0 0.00 0.0 34.49 1.82 F
2571 2880 0.037303 ATGTTGTGGAGGCACCTCTG 59.963 55.0 16.08 0.0 42.38 3.35 F
2649 2958 0.179073 TTGAGCTCCTATCGGCAAGC 60.179 55.0 12.15 0.0 0.00 4.01 F
4502 4816 0.723981 GCTAGCGTTTGAAGGCTCAG 59.276 55.0 13.49 10.7 46.10 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2688 0.743345 GACCAAGCCGGACCATGTAC 60.743 60.000 5.05 0.0 38.63 2.90 R
2671 2980 2.228343 GCCATATCTGAGCTGAATTGCC 59.772 50.000 0.00 0.0 0.00 4.52 R
4291 4605 0.242825 CGTGAACTGTCTTAGGCGGA 59.757 55.000 0.00 0.0 0.00 5.54 R
4618 4932 1.143684 TCATATTCTTCCTGCCAGCCC 59.856 52.381 0.00 0.0 0.00 5.19 R
5577 5895 2.158549 GGAAGAAAGATAGGCTGGGCAT 60.159 50.000 0.00 0.0 0.00 4.40 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
195 200 5.064707 TGGATGCGAGTACATAAGCTTTTTC 59.935 40.000 3.20 0.00 0.00 2.29
595 630 4.074526 GAGCAGCGGGAGAGTGCA 62.075 66.667 0.00 0.00 42.01 4.57
597 632 4.385405 GCAGCGGGAGAGTGCAGT 62.385 66.667 0.00 0.00 40.06 4.40
643 678 3.462169 CGGGTGCCGTGGGATATA 58.538 61.111 0.00 0.00 42.73 0.86
644 679 1.980052 CGGGTGCCGTGGGATATAT 59.020 57.895 0.00 0.00 42.73 0.86
653 688 3.505723 CCGTGGGATATATGCGGAAAGC 61.506 54.545 8.19 0.00 44.57 3.51
689 727 0.698818 GAGGAAGGAGCTTTTGGGGA 59.301 55.000 0.00 0.00 0.00 4.81
766 804 1.598685 GTCCGGCCGAAACTTTGGA 60.599 57.895 30.73 9.92 33.23 3.53
770 808 1.598685 GGCCGAAACTTTGGACCGA 60.599 57.895 0.00 0.00 33.19 4.69
771 809 0.958876 GGCCGAAACTTTGGACCGAT 60.959 55.000 0.00 0.00 33.19 4.18
772 810 0.168128 GCCGAAACTTTGGACCGATG 59.832 55.000 0.00 0.00 33.23 3.84
773 811 0.168128 CCGAAACTTTGGACCGATGC 59.832 55.000 0.00 0.00 33.23 3.91
774 812 0.871722 CGAAACTTTGGACCGATGCA 59.128 50.000 0.00 0.00 0.00 3.96
775 813 1.399727 CGAAACTTTGGACCGATGCAC 60.400 52.381 0.00 0.00 0.00 4.57
776 814 0.958822 AAACTTTGGACCGATGCACC 59.041 50.000 0.00 0.00 0.00 5.01
777 815 1.234615 AACTTTGGACCGATGCACCG 61.235 55.000 0.00 0.00 0.00 4.94
778 816 1.375396 CTTTGGACCGATGCACCGA 60.375 57.895 0.00 0.00 0.00 4.69
779 817 1.635663 CTTTGGACCGATGCACCGAC 61.636 60.000 0.00 0.00 0.00 4.79
780 818 3.925362 TTGGACCGATGCACCGACG 62.925 63.158 0.00 0.00 0.00 5.12
785 823 3.118454 CGATGCACCGACGCCTTT 61.118 61.111 0.00 0.00 0.00 3.11
786 824 2.677003 CGATGCACCGACGCCTTTT 61.677 57.895 0.00 0.00 0.00 2.27
787 825 1.579429 GATGCACCGACGCCTTTTT 59.421 52.632 0.00 0.00 0.00 1.94
878 916 0.108186 AATTCATGCTCGCAGACCGA 60.108 50.000 0.00 0.00 45.15 4.69
902 940 1.570857 TATGGCCAGGGTTGAGTGGG 61.571 60.000 13.05 0.00 34.06 4.61
907 945 2.936032 AGGGTTGAGTGGGAGGCC 60.936 66.667 0.00 0.00 0.00 5.19
908 946 4.048470 GGGTTGAGTGGGAGGCCC 62.048 72.222 0.00 0.00 45.71 5.80
958 1015 0.251341 ACCCTCCTGCGAGCAAAAAT 60.251 50.000 0.00 0.00 34.49 1.82
959 1016 1.004277 ACCCTCCTGCGAGCAAAAATA 59.996 47.619 0.00 0.00 34.49 1.40
960 1017 2.091541 CCCTCCTGCGAGCAAAAATAA 58.908 47.619 0.00 0.00 34.49 1.40
1194 1262 3.006728 CCCAAGGCGTCCCCTACA 61.007 66.667 0.00 0.00 45.62 2.74
1743 2052 2.984562 TCATCTTTATCAGCGGTGCAA 58.015 42.857 10.38 3.47 0.00 4.08
1933 2242 2.489751 GGCGTACAATTGCTGGGC 59.510 61.111 5.05 4.15 0.00 5.36
1971 2280 2.111878 CAGGGGAGGCATAAGGCG 59.888 66.667 0.00 0.00 46.16 5.52
2202 2511 2.179427 CTGGTAGAGTGGTGTGGATCA 58.821 52.381 0.00 0.00 0.00 2.92
2207 2516 2.614259 AGAGTGGTGTGGATCAGAGTT 58.386 47.619 0.00 0.00 0.00 3.01
2331 2640 2.678336 GGAAATGTTACCTGAAGCTCGG 59.322 50.000 0.00 0.00 0.00 4.63
2379 2688 1.762957 TCAGAGCCTCGGAATTTAGGG 59.237 52.381 0.00 0.00 33.17 3.53
2433 2742 6.207417 ACGGAACATCATTTCAGAGTTTTCAT 59.793 34.615 0.00 0.00 0.00 2.57
2571 2880 0.037303 ATGTTGTGGAGGCACCTCTG 59.963 55.000 16.08 0.00 42.38 3.35
2649 2958 0.179073 TTGAGCTCCTATCGGCAAGC 60.179 55.000 12.15 0.00 0.00 4.01
2671 2980 4.355437 CGAGTACTATGCAGAAGACAAGG 58.645 47.826 0.00 0.00 0.00 3.61
2679 2988 1.888512 GCAGAAGACAAGGGCAATTCA 59.111 47.619 0.00 0.00 0.00 2.57
2874 3183 7.377398 TCACAAAATATGGTGTTGAAATGGAG 58.623 34.615 0.00 0.00 36.43 3.86
2880 3189 3.909732 TGGTGTTGAAATGGAGGACTTT 58.090 40.909 0.00 0.00 0.00 2.66
3076 3385 7.458806 TGGAAGATAGTGATGATGGAATGGATA 59.541 37.037 0.00 0.00 0.00 2.59
3150 3459 3.875134 TGCATATGTGTCAGATCTGCAAG 59.125 43.478 18.36 6.43 35.42 4.01
3287 3596 4.758674 TGCATGCAAGGAGATAATAGAAGC 59.241 41.667 20.30 0.00 0.00 3.86
3341 3650 7.712639 GGCTGAACTATCAAAGAGATATGACAA 59.287 37.037 0.00 0.00 38.50 3.18
3381 3690 7.475840 AGTCAAAGATTTTAGAAATCATCCGC 58.524 34.615 13.92 3.84 0.00 5.54
3898 4207 7.900782 TCACTTAGTGCTTTTAACTATGACC 57.099 36.000 7.61 0.00 32.98 4.02
3904 4218 6.357367 AGTGCTTTTAACTATGACCTATGGG 58.643 40.000 0.00 0.00 38.88 4.00
4102 4416 4.202274 GGAGGAAAGCTTACTGGTAGGATC 60.202 50.000 0.00 0.00 0.00 3.36
4208 4522 3.759086 TCTCTTCACAAGCATACTCGACT 59.241 43.478 0.00 0.00 0.00 4.18
4291 4605 6.594744 AGCAAAAAGGGTTGAAATGAAAGAT 58.405 32.000 0.00 0.00 0.00 2.40
4297 4611 2.755103 GGTTGAAATGAAAGATCCGCCT 59.245 45.455 0.00 0.00 0.00 5.52
4381 4695 1.616865 CGTGGAGTTACTTGGGAGTCA 59.383 52.381 0.00 0.00 37.33 3.41
4384 4698 1.066071 GGAGTTACTTGGGAGTCAGCC 60.066 57.143 0.00 0.00 37.33 4.85
4420 4734 1.888512 GAAAGGCAGAAAGATGGTGCA 59.111 47.619 0.00 0.00 39.05 4.57
4428 4742 4.482386 CAGAAAGATGGTGCATGTTCTTG 58.518 43.478 8.25 0.00 28.48 3.02
4502 4816 0.723981 GCTAGCGTTTGAAGGCTCAG 59.276 55.000 13.49 10.70 46.10 3.35
4549 4863 2.282180 GCCGTTGGGGAAGCTTCA 60.282 61.111 27.02 5.46 38.47 3.02
4579 4893 2.716217 CCTTTGGCTGAACTAGAAGGG 58.284 52.381 0.00 0.00 32.08 3.95
4593 4907 5.404395 ACTAGAAGGGAAGTACAAGAAGGT 58.596 41.667 0.00 0.00 0.00 3.50
4606 4920 1.786937 AGAAGGTCTCATCGGCTGAT 58.213 50.000 0.90 0.90 32.10 2.90
4618 4932 1.209504 TCGGCTGATAAAACTGGGGAG 59.790 52.381 0.00 0.00 0.00 4.30
4816 5130 2.161012 TCACAAGAGGATACGTGTCGTC 59.839 50.000 22.59 22.59 41.54 4.20
4823 5137 3.695022 ATACGTGTCGTCCGCCTGC 62.695 63.158 0.00 0.00 41.54 4.85
5054 5368 0.621571 TCTTCATGGGGTGGGAGAGG 60.622 60.000 0.00 0.00 0.00 3.69
5119 5433 9.220767 AGGAAAGTAAATACAACATCTTCTGTC 57.779 33.333 0.00 0.00 36.98 3.51
5195 5510 0.535102 ACAAGTTGAAGGGCCGTCAG 60.535 55.000 21.18 12.75 0.00 3.51
5223 5538 4.141937 TGAAGAATAGTGATTCCCCTGTCG 60.142 45.833 0.00 0.00 42.25 4.35
5225 5540 4.227197 AGAATAGTGATTCCCCTGTCGAT 58.773 43.478 0.00 0.00 42.25 3.59
5235 5550 1.597742 CCCTGTCGATGGCATTTAGG 58.402 55.000 0.00 7.30 0.00 2.69
5239 5554 3.885297 CCTGTCGATGGCATTTAGGAAAT 59.115 43.478 0.00 0.00 0.00 2.17
5295 5611 5.163447 GGTTTGGAAATTCCCCATTAGCTAC 60.163 44.000 9.87 0.00 35.03 3.58
5446 5763 9.668497 GTACCTTTCTGATAACCTTTTCAGTAT 57.332 33.333 5.68 0.00 40.22 2.12
5447 5764 8.567285 ACCTTTCTGATAACCTTTTCAGTATG 57.433 34.615 5.68 0.72 40.22 2.39
5483 5801 4.284490 TGGTATGATCCTGAGTCAATAGCC 59.716 45.833 7.97 2.84 0.00 3.93
5511 5829 4.457466 TGGTTTACTTGGAACAGGAAGAC 58.543 43.478 0.00 0.00 42.39 3.01
5516 5834 4.344359 ACTTGGAACAGGAAGACTCTTC 57.656 45.455 9.99 9.99 42.39 2.87
5527 5845 5.296283 CAGGAAGACTCTTCAATTATGGCAG 59.704 44.000 18.56 0.00 0.00 4.85
5549 5867 4.593634 AGTATGAATCTAAGGGGGTGTAGC 59.406 45.833 0.00 0.00 0.00 3.58
5559 5877 0.893727 GGGGTGTAGCCTTTGTGTGG 60.894 60.000 0.00 0.00 37.43 4.17
5577 5895 7.517614 TGTGTGGCATTGTTAATTTTAGAGA 57.482 32.000 0.00 0.00 0.00 3.10
5580 5898 7.009540 GTGTGGCATTGTTAATTTTAGAGATGC 59.990 37.037 0.00 0.00 38.26 3.91
5584 5902 6.698766 GCATTGTTAATTTTAGAGATGCCCAG 59.301 38.462 0.00 0.00 34.21 4.45
5661 5979 2.507407 TTTGTGGCCTCTATCCCAAC 57.493 50.000 3.32 0.00 31.90 3.77
5673 5991 6.431234 GCCTCTATCCCAACATAAAGTAATGG 59.569 42.308 0.00 0.00 0.00 3.16
5698 6016 6.402550 GCATATGACATTATGGCTAAACCTCG 60.403 42.308 6.97 0.00 40.22 4.63
5745 6063 6.441093 TTGAATCAATATGTCCTCTGTTGC 57.559 37.500 0.00 0.00 0.00 4.17
5762 6084 2.780065 TGCTTGAGTGCATTGTTGTC 57.220 45.000 0.00 0.00 38.12 3.18
5792 6114 6.150976 CAGTTTGGGATGATGTTAAGCAAGTA 59.849 38.462 0.00 0.00 0.00 2.24
5793 6115 6.719370 AGTTTGGGATGATGTTAAGCAAGTAA 59.281 34.615 0.00 0.00 0.00 2.24
5794 6116 7.232534 AGTTTGGGATGATGTTAAGCAAGTAAA 59.767 33.333 0.00 0.00 0.00 2.01
5826 6148 5.053145 TGCCATTGTTGATTGTAAAACACC 58.947 37.500 0.00 0.00 36.08 4.16
5831 6153 4.930963 TGTTGATTGTAAAACACCTGCTG 58.069 39.130 0.00 0.00 31.52 4.41
5832 6154 3.641437 TGATTGTAAAACACCTGCTGC 57.359 42.857 0.00 0.00 0.00 5.25
5839 6161 0.316204 AAACACCTGCTGCTCATTGC 59.684 50.000 0.00 0.00 43.25 3.56
5842 6164 3.197614 CCTGCTGCTCATTGCTGG 58.802 61.111 0.00 0.00 43.37 4.85
5843 6165 1.677966 CCTGCTGCTCATTGCTGGT 60.678 57.895 0.00 0.00 41.41 4.00
5902 6224 8.210946 TCTCTAGTTTCTGATTGAAAAACCTGA 58.789 33.333 0.00 0.00 45.10 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.149196 CATGGTTGTAGCACTTCCTGTT 58.851 45.455 0.00 0.00 0.00 3.16
195 200 2.605580 GCGGTCCAGCAAAAAGAAGAAG 60.606 50.000 1.46 0.00 37.05 2.85
595 630 3.015293 CTCGTCAATTGCGCGCACT 62.015 57.895 36.72 27.66 0.00 4.40
597 632 4.444024 GCTCGTCAATTGCGCGCA 62.444 61.111 33.09 33.09 39.48 6.09
715 753 5.587844 GCCATCAGATGTCAGTTGTCTTATT 59.412 40.000 9.64 0.00 0.00 1.40
718 756 3.341823 GCCATCAGATGTCAGTTGTCTT 58.658 45.455 9.64 0.00 0.00 3.01
770 808 3.758172 AAAAAGGCGTCGGTGCAT 58.242 50.000 0.00 0.00 36.28 3.96
788 826 0.965439 CCGGTGCATTCCCTCAAAAA 59.035 50.000 0.00 0.00 0.00 1.94
789 827 1.531739 GCCGGTGCATTCCCTCAAAA 61.532 55.000 1.90 0.00 37.47 2.44
790 828 1.976474 GCCGGTGCATTCCCTCAAA 60.976 57.895 1.90 0.00 37.47 2.69
791 829 2.361104 GCCGGTGCATTCCCTCAA 60.361 61.111 1.90 0.00 37.47 3.02
792 830 4.776322 CGCCGGTGCATTCCCTCA 62.776 66.667 0.00 0.00 37.32 3.86
796 834 4.849310 TAGGCGCCGGTGCATTCC 62.849 66.667 38.40 22.56 37.32 3.01
797 835 0.882927 TAATAGGCGCCGGTGCATTC 60.883 55.000 38.40 22.93 37.32 2.67
798 836 0.884704 CTAATAGGCGCCGGTGCATT 60.885 55.000 38.40 30.34 37.32 3.56
799 837 1.301716 CTAATAGGCGCCGGTGCAT 60.302 57.895 38.40 34.95 37.32 3.96
803 841 2.726274 CGACTAATAGGCGCCGGT 59.274 61.111 23.20 15.66 41.27 5.28
838 876 0.249699 TTGTTCCGACACATGCGAGT 60.250 50.000 0.00 0.00 34.98 4.18
893 931 3.316573 CTCGGGCCTCCCACTCAAC 62.317 68.421 0.84 0.00 45.83 3.18
909 947 3.645268 AAATGGGGCCGTGGAGCTC 62.645 63.158 4.71 4.71 0.00 4.09
910 948 3.224007 AAAATGGGGCCGTGGAGCT 62.224 57.895 0.00 0.00 0.00 4.09
911 949 2.679996 AAAATGGGGCCGTGGAGC 60.680 61.111 0.00 0.00 0.00 4.70
960 1017 2.596338 CGGCCGTGGAGGGTTTTT 60.596 61.111 19.50 0.00 41.48 1.94
1212 1518 1.394151 CTGAGGAGGAAGGGGAGGT 59.606 63.158 0.00 0.00 0.00 3.85
1743 2052 3.581770 GGTTGTAAGTAGGTTCAGGAGGT 59.418 47.826 0.00 0.00 0.00 3.85
1933 2242 2.573369 CTGCCAATTCTCCCAGATCAG 58.427 52.381 0.00 0.00 0.00 2.90
2058 2367 6.604795 ACTTAGAATATGGCAGCTTGTTCAAT 59.395 34.615 0.00 0.00 0.00 2.57
2202 2511 1.971357 ACCACAAGACCATCGAACTCT 59.029 47.619 0.00 0.00 0.00 3.24
2207 2516 2.158885 TCAAACACCACAAGACCATCGA 60.159 45.455 0.00 0.00 0.00 3.59
2331 2640 1.266989 GTTGCTGAGCAGTAAACCACC 59.733 52.381 7.39 0.00 40.61 4.61
2379 2688 0.743345 GACCAAGCCGGACCATGTAC 60.743 60.000 5.05 0.00 38.63 2.90
2433 2742 5.745312 TCTCAAGAGCACCTAGAAATTGA 57.255 39.130 0.00 0.00 0.00 2.57
2571 2880 7.445121 TGTACATATTCATCATTCTGTCCTCC 58.555 38.462 0.00 0.00 0.00 4.30
2649 2958 4.355437 CCTTGTCTTCTGCATAGTACTCG 58.645 47.826 0.00 0.00 0.00 4.18
2671 2980 2.228343 GCCATATCTGAGCTGAATTGCC 59.772 50.000 0.00 0.00 0.00 4.52
2679 2988 4.081972 CAGTATAACCGCCATATCTGAGCT 60.082 45.833 0.00 0.00 0.00 4.09
2874 3183 4.409247 TCTCTAGGGCCAGAAATAAAGTCC 59.591 45.833 6.18 0.00 0.00 3.85
2880 3189 3.134804 GCAACTCTCTAGGGCCAGAAATA 59.865 47.826 6.18 0.00 0.00 1.40
3150 3459 1.388837 GGCTCTTCTCCTCCTCGGTC 61.389 65.000 0.00 0.00 0.00 4.79
3244 3553 6.075762 TGCATAACATAACCAATCATCTGC 57.924 37.500 0.00 0.00 0.00 4.26
3287 3596 9.823647 TGTAAGCATCTCTCTCTTTAAAATAGG 57.176 33.333 0.00 0.00 0.00 2.57
3341 3650 1.059098 TGACTTCCTGTCCACTGCAT 58.941 50.000 0.00 0.00 44.75 3.96
3381 3690 7.389053 AGAGGATTATTAGGCAAATCTAAAGCG 59.611 37.037 0.00 0.00 33.54 4.68
3532 3841 5.404366 GCATATTGATCATGTCCAATGCAAC 59.596 40.000 18.64 0.00 36.25 4.17
3928 4242 4.288626 GCATCCTGTTCCATTATACCCCTA 59.711 45.833 0.00 0.00 0.00 3.53
4102 4416 6.077838 CACATCATGCATATCAGAATCAACG 58.922 40.000 0.00 0.00 0.00 4.10
4208 4522 6.871492 TCACTTCGTGCATTCTGAATTACTAA 59.129 34.615 0.00 1.73 32.98 2.24
4291 4605 0.242825 CGTGAACTGTCTTAGGCGGA 59.757 55.000 0.00 0.00 0.00 5.54
4297 4611 4.219944 AGGCTATCAACGTGAACTGTCTTA 59.780 41.667 0.00 0.00 0.00 2.10
4420 4734 7.392113 TCGTAAAACCCATCATTACAAGAACAT 59.608 33.333 0.00 0.00 31.45 2.71
4428 4742 4.573607 GGGACTCGTAAAACCCATCATTAC 59.426 45.833 0.00 0.00 41.72 1.89
4502 4816 2.674796 ACTCTGTACATTCCTTCCGC 57.325 50.000 0.00 0.00 0.00 5.54
4579 4893 4.425520 CCGATGAGACCTTCTTGTACTTC 58.574 47.826 0.00 0.00 0.00 3.01
4593 4907 3.432186 CCCAGTTTTATCAGCCGATGAGA 60.432 47.826 0.00 0.00 42.53 3.27
4606 4920 2.083715 CCAGCCCTCCCCAGTTTTA 58.916 57.895 0.00 0.00 0.00 1.52
4618 4932 1.143684 TCATATTCTTCCTGCCAGCCC 59.856 52.381 0.00 0.00 0.00 5.19
4816 5130 1.376424 ATCTGTTGTCTGCAGGCGG 60.376 57.895 14.71 7.33 34.89 6.13
4823 5137 4.675190 GATGGTTGTCATCTGTTGTCTG 57.325 45.455 0.00 0.00 46.59 3.51
5010 5324 7.881775 AAGAAGAAAGAAAGCTTAAACCTCA 57.118 32.000 0.00 0.00 32.98 3.86
5026 5340 4.151883 CCACCCCATGAAGAAAGAAGAAA 58.848 43.478 0.00 0.00 0.00 2.52
5054 5368 1.741706 CATCCATCACACCAAGCTGTC 59.258 52.381 0.00 0.00 0.00 3.51
5168 5483 1.133792 CCCTTCAACTTGTGGGTGACT 60.134 52.381 11.86 0.00 41.95 3.41
5195 5510 6.261826 CAGGGGAATCACTATTCTTCATTCAC 59.738 42.308 0.00 0.00 41.18 3.18
5223 5538 8.872845 CAGTTTTACAATTTCCTAAATGCCATC 58.127 33.333 0.00 0.00 0.00 3.51
5225 5540 6.648725 GCAGTTTTACAATTTCCTAAATGCCA 59.351 34.615 0.00 0.00 0.00 4.92
5295 5611 1.420138 ACTACAGGTCCCCAAACTGTG 59.580 52.381 6.00 0.00 44.48 3.66
5446 5763 2.637382 TCATACCACAGACTCAAAGCCA 59.363 45.455 0.00 0.00 0.00 4.75
5447 5764 3.334583 TCATACCACAGACTCAAAGCC 57.665 47.619 0.00 0.00 0.00 4.35
5511 5829 8.618702 AGATTCATACTGCCATAATTGAAGAG 57.381 34.615 0.00 0.00 0.00 2.85
5516 5834 7.121759 CCCCTTAGATTCATACTGCCATAATTG 59.878 40.741 0.00 0.00 0.00 2.32
5527 5845 4.262938 GGCTACACCCCCTTAGATTCATAC 60.263 50.000 0.00 0.00 0.00 2.39
5549 5867 6.616774 AAAATTAACAATGCCACACAAAGG 57.383 33.333 0.00 0.00 0.00 3.11
5559 5877 6.572519 TGGGCATCTCTAAAATTAACAATGC 58.427 36.000 0.00 0.00 37.98 3.56
5577 5895 2.158549 GGAAGAAAGATAGGCTGGGCAT 60.159 50.000 0.00 0.00 0.00 4.40
5580 5898 2.507471 ACAGGAAGAAAGATAGGCTGGG 59.493 50.000 0.00 0.00 0.00 4.45
5584 5902 4.154918 CACACAACAGGAAGAAAGATAGGC 59.845 45.833 0.00 0.00 0.00 3.93
5673 5991 6.402550 CGAGGTTTAGCCATAATGTCATATGC 60.403 42.308 0.00 0.00 40.61 3.14
5698 6016 4.188247 TCAGTACAGTGGATGCACTAAC 57.812 45.455 20.32 19.31 32.90 2.34
5745 6063 2.880268 TCCTGACAACAATGCACTCAAG 59.120 45.455 0.00 0.00 0.00 3.02
5762 6084 3.077484 ACATCATCCCAAACTGTCCTG 57.923 47.619 0.00 0.00 0.00 3.86
5792 6114 8.901793 ACAATCAACAATGGCAACTTTAAATTT 58.098 25.926 0.00 0.00 37.61 1.82
5793 6115 8.449251 ACAATCAACAATGGCAACTTTAAATT 57.551 26.923 0.00 0.00 37.61 1.82
5794 6116 9.553064 TTACAATCAACAATGGCAACTTTAAAT 57.447 25.926 0.00 0.00 37.61 1.40
5817 6139 3.568538 CAATGAGCAGCAGGTGTTTTAC 58.431 45.455 0.66 0.00 0.00 2.01
5831 6153 2.945447 TGCATAAACCAGCAATGAGC 57.055 45.000 0.00 0.00 46.19 4.26
5839 6161 6.506500 AGAACTTCTCATTGCATAAACCAG 57.493 37.500 0.00 0.00 0.00 4.00
5842 6164 5.284660 CGCAAGAACTTCTCATTGCATAAAC 59.715 40.000 12.37 0.00 46.48 2.01
5843 6165 5.393124 CGCAAGAACTTCTCATTGCATAAA 58.607 37.500 12.37 0.00 46.48 1.40
5852 6174 3.874543 TGTTTAAGCGCAAGAACTTCTCA 59.125 39.130 11.47 0.00 43.02 3.27
5853 6175 4.468095 TGTTTAAGCGCAAGAACTTCTC 57.532 40.909 11.47 0.00 43.02 2.87
5902 6224 3.823304 GCCAAACCTGTTTCAGAGAGATT 59.177 43.478 0.00 0.00 32.44 2.40


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

AutoCloner maintained by Alex Coulton.