Multiple sequence alignment - TraesCS1D01G434500

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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 TraesCS1D01G434500 chr1D 100.000 2784 0 0 1 2784 483679714 483682497 0.000000e+00 5142.0
1 TraesCS1D01G434500 chr1D 90.265 2188 109 41 98 2225 483864258 483866401 0.000000e+00 2765.0
2 TraesCS1D01G434500 chr1D 82.238 822 106 22 985 1776 483901995 483902806 0.000000e+00 673.0
3 TraesCS1D01G434500 chr1D 83.413 627 64 15 1169 1776 483895754 483896359 1.890000e-151 545.0
4 TraesCS1D01G434500 chr1D 84.834 422 37 16 814 1231 483895333 483895731 1.550000e-107 399.0
5 TraesCS1D01G434500 chr1B 86.169 1916 121 61 405 2223 673854902 673856770 0.000000e+00 1938.0
6 TraesCS1D01G434500 chr1B 84.127 819 96 21 985 1776 673893200 673894011 0.000000e+00 761.0
7 TraesCS1D01G434500 chr1B 80.710 902 127 26 906 1776 673889168 673890053 0.000000e+00 658.0
8 TraesCS1D01G434500 chr1B 81.784 807 108 25 985 1776 673925947 673926729 8.410000e-180 640.0
9 TraesCS1D01G434500 chr1B 90.598 117 4 4 2112 2225 673858936 673859048 6.210000e-32 148.0
10 TraesCS1D01G434500 chr1A 83.496 818 99 23 985 1776 580925427 580926234 0.000000e+00 730.0
11 TraesCS1D01G434500 chr1A 87.852 568 30 16 1640 2170 580511402 580511967 5.060000e-177 630.0
12 TraesCS1D01G434500 chr1A 83.784 592 68 11 1169 1741 580893649 580894231 1.130000e-148 536.0
13 TraesCS1D01G434500 chr1A 86.760 287 22 9 374 650 580509882 580510162 3.480000e-79 305.0
14 TraesCS1D01G434500 chr1A 86.760 287 22 9 374 650 580525399 580525679 3.480000e-79 305.0
15 TraesCS1D01G434500 chr1A 82.988 241 25 8 143 377 580509543 580509773 1.310000e-48 204.0
16 TraesCS1D01G434500 chr1A 82.988 241 25 8 143 377 580525060 580525290 1.310000e-48 204.0
17 TraesCS1D01G434500 chr1A 94.340 106 3 1 39 141 580509225 580509330 2.870000e-35 159.0
18 TraesCS1D01G434500 chr1A 94.340 106 3 1 39 141 580524762 580524867 2.870000e-35 159.0
19 TraesCS1D01G434500 chr1A 79.091 110 6 8 662 760 580893135 580893238 2.990000e-05 60.2
20 TraesCS1D01G434500 chrUn 97.436 312 8 0 2473 2784 108901889 108901578 1.470000e-147 532.0
21 TraesCS1D01G434500 chrUn 94.882 254 11 1 2226 2477 108902432 108902179 2.010000e-106 396.0
22 TraesCS1D01G434500 chr2B 97.115 312 9 0 2473 2784 173304842 173304531 6.830000e-146 527.0
23 TraesCS1D01G434500 chr3D 97.115 312 8 1 2473 2784 99747451 99747761 2.460000e-145 525.0
24 TraesCS1D01G434500 chr3D 96.474 312 11 0 2473 2784 416574270 416574581 1.480000e-142 516.0
25 TraesCS1D01G434500 chr3D 94.841 252 13 0 2226 2477 29859255 29859506 7.230000e-106 394.0
26 TraesCS1D01G434500 chr2D 96.795 312 10 0 2473 2784 651599179 651598868 3.180000e-144 521.0
27 TraesCS1D01G434500 chr2D 95.238 252 12 0 2226 2477 651599719 651599468 1.550000e-107 399.0
28 TraesCS1D01G434500 chr5B 96.474 312 11 0 2473 2784 19664756 19664445 1.480000e-142 516.0
29 TraesCS1D01G434500 chr7D 95.833 312 13 0 2473 2784 46408359 46408048 3.200000e-139 505.0
30 TraesCS1D01G434500 chr7D 94.444 252 14 0 2226 2477 3826570 3826821 3.360000e-104 388.0
31 TraesCS1D01G434500 chr5D 95.833 312 13 0 2473 2784 450669042 450669353 3.200000e-139 505.0
32 TraesCS1D01G434500 chr5D 94.841 252 13 0 2226 2477 37144595 37144846 7.230000e-106 394.0
33 TraesCS1D01G434500 chr2A 95.833 312 13 0 2473 2784 613075859 613075548 3.200000e-139 505.0
34 TraesCS1D01G434500 chr6A 94.841 252 13 0 2226 2477 13595984 13595733 7.230000e-106 394.0
35 TraesCS1D01G434500 chr6D 94.444 252 14 0 2226 2477 51472073 51471822 3.360000e-104 388.0
36 TraesCS1D01G434500 chr3B 94.444 252 14 0 2226 2477 520368190 520367939 3.360000e-104 388.0
37 TraesCS1D01G434500 chr4B 94.094 254 15 0 2226 2479 187630630 187630377 1.210000e-103 387.0


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 TraesCS1D01G434500 chr1D 483679714 483682497 2783 False 5142.000000 5142 100.000000 1 2784 1 chr1D.!!$F1 2783
1 TraesCS1D01G434500 chr1D 483864258 483866401 2143 False 2765.000000 2765 90.265000 98 2225 1 chr1D.!!$F2 2127
2 TraesCS1D01G434500 chr1D 483901995 483902806 811 False 673.000000 673 82.238000 985 1776 1 chr1D.!!$F3 791
3 TraesCS1D01G434500 chr1D 483895333 483896359 1026 False 472.000000 545 84.123500 814 1776 2 chr1D.!!$F4 962
4 TraesCS1D01G434500 chr1B 673854902 673859048 4146 False 1043.000000 1938 88.383500 405 2225 2 chr1B.!!$F2 1820
5 TraesCS1D01G434500 chr1B 673889168 673894011 4843 False 709.500000 761 82.418500 906 1776 2 chr1B.!!$F3 870
6 TraesCS1D01G434500 chr1B 673925947 673926729 782 False 640.000000 640 81.784000 985 1776 1 chr1B.!!$F1 791
7 TraesCS1D01G434500 chr1A 580925427 580926234 807 False 730.000000 730 83.496000 985 1776 1 chr1A.!!$F1 791
8 TraesCS1D01G434500 chr1A 580509225 580511967 2742 False 324.500000 630 87.985000 39 2170 4 chr1A.!!$F2 2131
9 TraesCS1D01G434500 chr1A 580893135 580894231 1096 False 298.100000 536 81.437500 662 1741 2 chr1A.!!$F4 1079
10 TraesCS1D01G434500 chr1A 580524762 580525679 917 False 222.666667 305 88.029333 39 650 3 chr1A.!!$F3 611
11 TraesCS1D01G434500 chrUn 108901578 108902432 854 True 464.000000 532 96.159000 2226 2784 2 chrUn.!!$R1 558
12 TraesCS1D01G434500 chr2D 651598868 651599719 851 True 460.000000 521 96.016500 2226 2784 2 chr2D.!!$R1 558

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
24 25 0.171455 GACACTGCCCTACGAGACAG 59.829 60.0 0.0 0.0 36.22 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 6376 0.448197 TTCTGCAACACGAAAACGCA 59.552 45.0 0.0 0.0 0.0 5.24 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
18 19 1.596934 ATGTGGACACTGCCCTACG 59.403 57.895 3.91 0.00 0.00 3.51
19 20 0.902984 ATGTGGACACTGCCCTACGA 60.903 55.000 3.91 0.00 0.00 3.43
20 21 1.215647 GTGGACACTGCCCTACGAG 59.784 63.158 0.00 0.00 0.00 4.18
21 22 1.076014 TGGACACTGCCCTACGAGA 59.924 57.895 0.00 0.00 0.00 4.04
22 23 1.248785 TGGACACTGCCCTACGAGAC 61.249 60.000 0.00 0.00 0.00 3.36
23 24 1.248785 GGACACTGCCCTACGAGACA 61.249 60.000 0.00 0.00 0.00 3.41
24 25 0.171455 GACACTGCCCTACGAGACAG 59.829 60.000 0.00 0.00 36.22 3.51
25 26 1.251527 ACACTGCCCTACGAGACAGG 61.252 60.000 0.00 0.00 34.40 4.00
33 34 3.651803 CCTACGAGACAGGGATTCATC 57.348 52.381 0.00 0.00 0.00 2.92
34 35 2.959030 CCTACGAGACAGGGATTCATCA 59.041 50.000 0.00 0.00 0.00 3.07
35 36 3.576118 CCTACGAGACAGGGATTCATCAT 59.424 47.826 0.00 0.00 0.00 2.45
36 37 3.465742 ACGAGACAGGGATTCATCATG 57.534 47.619 0.00 0.00 0.00 3.07
37 38 2.768527 ACGAGACAGGGATTCATCATGT 59.231 45.455 0.00 0.00 32.93 3.21
146 361 4.880696 TGCACGATCATGTATTGGATTTGA 59.119 37.500 0.00 0.00 0.00 2.69
210 425 6.170506 TGTAGTAAAAGGAGCTTGTATGGTG 58.829 40.000 0.00 0.00 0.00 4.17
211 426 4.589908 AGTAAAAGGAGCTTGTATGGTGG 58.410 43.478 0.00 0.00 0.00 4.61
212 427 3.525800 AAAAGGAGCTTGTATGGTGGT 57.474 42.857 0.00 0.00 0.00 4.16
245 463 9.702726 ATTATGAACGAGATAATGAAAAACGTG 57.297 29.630 0.00 0.00 33.05 4.49
316 534 6.472680 CAGTCATACATCTTTGACAACATCG 58.527 40.000 5.91 0.00 43.72 3.84
317 535 5.582269 AGTCATACATCTTTGACAACATCGG 59.418 40.000 5.91 0.00 43.72 4.18
326 544 0.960364 GACAACATCGGCACCACCAT 60.960 55.000 0.00 0.00 39.03 3.55
332 550 3.361158 CGGCACCACCATTTCGCA 61.361 61.111 0.00 0.00 39.03 5.10
341 559 1.291877 ACCATTTCGCACGCAGACTC 61.292 55.000 0.00 0.00 0.00 3.36
378 596 1.064611 AGCAGAGCCGAGTCCTACTTA 60.065 52.381 0.00 0.00 0.00 2.24
388 717 6.039605 AGCCGAGTCCTACTTAGTTAATCTTC 59.960 42.308 0.00 0.00 0.00 2.87
401 730 6.385649 AGTTAATCTTCGCACCTTTTCAAA 57.614 33.333 0.00 0.00 0.00 2.69
406 735 3.629855 TCTTCGCACCTTTTCAAACATGA 59.370 39.130 0.00 0.00 0.00 3.07
425 754 4.119442 TGAAGGGAGTACTATTCAACGC 57.881 45.455 12.75 1.66 0.00 4.84
508 838 1.069823 CTGTATGGCTGCGATTCTCCT 59.930 52.381 1.63 0.00 0.00 3.69
531 861 3.334691 CCTGTGTCCGTGTCATAATGTT 58.665 45.455 0.00 0.00 0.00 2.71
574 904 2.095213 GCGTTTTGACGAGCAATATCCA 59.905 45.455 2.79 0.00 36.15 3.41
640 979 8.794335 AGGAGTATAAGAAAAATCACACTTCC 57.206 34.615 0.00 0.00 0.00 3.46
687 1027 2.225491 GACAATCTTGTAAACCGCAGCA 59.775 45.455 0.00 0.00 42.43 4.41
703 1043 2.097142 GCAGCAAGCTCACCAATAGAAG 59.903 50.000 0.00 0.00 41.15 2.85
704 1044 3.603532 CAGCAAGCTCACCAATAGAAGA 58.396 45.455 0.00 0.00 0.00 2.87
705 1045 3.622163 CAGCAAGCTCACCAATAGAAGAG 59.378 47.826 0.00 0.00 0.00 2.85
760 1111 1.186200 ACGTCCAGCTCTATCTGCAA 58.814 50.000 0.00 0.00 32.87 4.08
761 1112 1.759445 ACGTCCAGCTCTATCTGCAAT 59.241 47.619 0.00 0.00 32.87 3.56
762 1113 2.169352 ACGTCCAGCTCTATCTGCAATT 59.831 45.455 0.00 0.00 32.87 2.32
763 1114 2.799412 CGTCCAGCTCTATCTGCAATTC 59.201 50.000 0.00 0.00 32.87 2.17
764 1115 3.492309 CGTCCAGCTCTATCTGCAATTCT 60.492 47.826 0.00 0.00 32.87 2.40
807 1159 5.421056 GGGACTGTATTCCATCCATATACGA 59.579 44.000 0.00 0.00 37.40 3.43
808 1160 6.098409 GGGACTGTATTCCATCCATATACGAT 59.902 42.308 0.00 0.00 37.40 3.73
857 1237 8.628281 AGATTCTAGATTCAGATAGGTATCCCA 58.372 37.037 15.21 0.00 33.17 4.37
858 1238 9.261035 GATTCTAGATTCAGATAGGTATCCCAA 57.739 37.037 9.30 0.00 33.17 4.12
859 1239 9.621239 ATTCTAGATTCAGATAGGTATCCCAAA 57.379 33.333 0.00 0.00 33.17 3.28
860 1240 9.621239 TTCTAGATTCAGATAGGTATCCCAAAT 57.379 33.333 0.00 0.00 33.17 2.32
895 1287 8.211116 TCAAACTTCTCTATCTCTAACGTAGG 57.789 38.462 0.00 0.00 0.00 3.18
896 1288 8.045507 TCAAACTTCTCTATCTCTAACGTAGGA 58.954 37.037 0.00 0.00 0.00 2.94
897 1289 8.339714 CAAACTTCTCTATCTCTAACGTAGGAG 58.660 40.741 10.33 10.33 0.00 3.69
898 1290 7.128234 ACTTCTCTATCTCTAACGTAGGAGT 57.872 40.000 14.52 1.78 0.00 3.85
899 1291 8.248904 ACTTCTCTATCTCTAACGTAGGAGTA 57.751 38.462 14.52 7.96 0.00 2.59
900 1292 8.143835 ACTTCTCTATCTCTAACGTAGGAGTAC 58.856 40.741 14.52 0.00 0.00 2.73
951 1348 2.196742 TAGTTGGGCATCCTCTCCAT 57.803 50.000 0.00 0.00 0.00 3.41
1114 5472 0.039165 CGCAAACCAAGAAGAAGCCC 60.039 55.000 0.00 0.00 0.00 5.19
1200 5648 1.451936 CATGCCTAGCCTACCACCC 59.548 63.158 0.00 0.00 0.00 4.61
1820 6319 6.816140 TCTCTCATATATGCGTTGAACAACAA 59.184 34.615 16.13 5.71 41.20 2.83
1876 6376 4.142381 GCCTCTGACATTAATTTCGCCTTT 60.142 41.667 0.00 0.00 0.00 3.11
1932 6436 0.928505 AAGGATGGATGCATGGACCA 59.071 50.000 2.46 5.89 38.09 4.02
2030 6571 1.067212 CGATCAGCTAGCGTTTAGGGT 59.933 52.381 9.55 0.00 30.71 4.34
2032 6573 2.667473 TCAGCTAGCGTTTAGGGTTC 57.333 50.000 9.55 0.00 0.00 3.62
2033 6574 1.897133 TCAGCTAGCGTTTAGGGTTCA 59.103 47.619 9.55 0.00 0.00 3.18
2034 6575 2.094182 TCAGCTAGCGTTTAGGGTTCAG 60.094 50.000 9.55 0.00 0.00 3.02
2035 6576 2.094182 CAGCTAGCGTTTAGGGTTCAGA 60.094 50.000 9.55 0.00 0.00 3.27
2063 6606 4.599047 GTCATACGTAGTTCCTAGTGCTG 58.401 47.826 0.08 0.00 37.78 4.41
2077 6620 6.806751 TCCTAGTGCTGCTTAGTTACATTAG 58.193 40.000 0.00 0.00 0.00 1.73
2079 6622 7.558807 TCCTAGTGCTGCTTAGTTACATTAGTA 59.441 37.037 0.00 0.00 0.00 1.82
2080 6623 7.863375 CCTAGTGCTGCTTAGTTACATTAGTAG 59.137 40.741 0.00 0.00 0.00 2.57
2081 6624 7.406031 AGTGCTGCTTAGTTACATTAGTAGA 57.594 36.000 0.00 0.00 0.00 2.59
2082 6625 7.484975 AGTGCTGCTTAGTTACATTAGTAGAG 58.515 38.462 0.00 0.00 0.00 2.43
2083 6626 7.122948 AGTGCTGCTTAGTTACATTAGTAGAGT 59.877 37.037 0.00 0.00 0.00 3.24
2084 6627 7.760340 GTGCTGCTTAGTTACATTAGTAGAGTT 59.240 37.037 0.00 0.00 0.00 3.01
2183 9016 3.245229 TGTGTGATGGCCCAGAGTTAATT 60.245 43.478 0.00 0.00 0.00 1.40
2184 9017 4.018870 TGTGTGATGGCCCAGAGTTAATTA 60.019 41.667 0.00 0.00 0.00 1.40
2185 9018 4.947388 GTGTGATGGCCCAGAGTTAATTAA 59.053 41.667 0.00 0.00 0.00 1.40
2186 9019 5.066505 GTGTGATGGCCCAGAGTTAATTAAG 59.933 44.000 0.00 0.00 0.00 1.85
2197 9033 5.355350 CAGAGTTAATTAAGGCTGGGTTGAG 59.645 44.000 14.92 0.00 0.00 3.02
2217 9053 4.459337 TGAGGTGATCTACTGTATATGCGG 59.541 45.833 0.00 0.00 0.00 5.69
2292 9128 4.835615 ACAGATGTCTTCTCAGTAAGTGGT 59.164 41.667 0.00 0.00 29.93 4.16
2326 9162 3.470645 AGTTAAGACTGAGGCAACGTT 57.529 42.857 0.00 0.00 36.65 3.99
2339 9175 0.238289 CAACGTTGGCGCAGATTCTT 59.762 50.000 20.71 0.00 42.83 2.52
2341 9177 0.602638 ACGTTGGCGCAGATTCTTCA 60.603 50.000 10.83 0.00 42.83 3.02
2371 9207 3.281727 TCTGCAGTCCAAGACTTTGTT 57.718 42.857 14.67 0.00 41.37 2.83
2372 9208 3.620488 TCTGCAGTCCAAGACTTTGTTT 58.380 40.909 14.67 0.00 41.37 2.83
2614 9746 3.130516 CGCAACTGGACAGGATCTACTAA 59.869 47.826 4.14 0.00 0.00 2.24
2713 9845 2.474735 CGGTGCAAATTGCCTTTAACAC 59.525 45.455 15.98 4.70 44.23 3.32
2728 9860 6.171213 CCTTTAACACTACTCCTCCGAATTT 58.829 40.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.532078 TCGTAGGGCAGTGTCCACA 60.532 57.895 17.90 0.00 0.00 4.17
2 3 1.215647 CTCGTAGGGCAGTGTCCAC 59.784 63.158 17.90 11.10 0.00 4.02
3 4 1.076014 TCTCGTAGGGCAGTGTCCA 59.924 57.895 17.90 0.00 0.00 4.02
4 5 1.248785 TGTCTCGTAGGGCAGTGTCC 61.249 60.000 5.33 5.33 0.00 4.02
5 6 0.171455 CTGTCTCGTAGGGCAGTGTC 59.829 60.000 0.00 0.00 0.00 3.67
6 7 1.251527 CCTGTCTCGTAGGGCAGTGT 61.252 60.000 0.00 0.00 0.00 3.55
7 8 1.513158 CCTGTCTCGTAGGGCAGTG 59.487 63.158 6.65 0.00 0.00 3.66
8 9 4.019983 CCTGTCTCGTAGGGCAGT 57.980 61.111 6.65 0.00 0.00 4.40
13 14 2.959030 TGATGAATCCCTGTCTCGTAGG 59.041 50.000 0.00 0.00 35.01 3.18
14 15 4.038522 ACATGATGAATCCCTGTCTCGTAG 59.961 45.833 0.00 0.00 0.00 3.51
15 16 3.960755 ACATGATGAATCCCTGTCTCGTA 59.039 43.478 0.00 0.00 0.00 3.43
16 17 2.768527 ACATGATGAATCCCTGTCTCGT 59.231 45.455 0.00 0.00 0.00 4.18
17 18 3.465742 ACATGATGAATCCCTGTCTCG 57.534 47.619 0.00 0.00 0.00 4.04
18 19 5.923204 ACTTACATGATGAATCCCTGTCTC 58.077 41.667 0.00 0.00 0.00 3.36
19 20 5.965033 ACTTACATGATGAATCCCTGTCT 57.035 39.130 0.00 0.00 0.00 3.41
20 21 5.882557 ACAACTTACATGATGAATCCCTGTC 59.117 40.000 0.00 0.00 0.00 3.51
21 22 5.649395 CACAACTTACATGATGAATCCCTGT 59.351 40.000 0.00 0.00 0.00 4.00
22 23 5.066893 CCACAACTTACATGATGAATCCCTG 59.933 44.000 0.00 0.00 0.00 4.45
23 24 5.195940 CCACAACTTACATGATGAATCCCT 58.804 41.667 0.00 0.00 0.00 4.20
24 25 4.202050 GCCACAACTTACATGATGAATCCC 60.202 45.833 0.00 0.00 0.00 3.85
25 26 4.202050 GGCCACAACTTACATGATGAATCC 60.202 45.833 0.00 0.00 0.00 3.01
26 27 4.202050 GGGCCACAACTTACATGATGAATC 60.202 45.833 4.39 0.00 0.00 2.52
27 28 3.701040 GGGCCACAACTTACATGATGAAT 59.299 43.478 4.39 0.00 0.00 2.57
28 29 3.088532 GGGCCACAACTTACATGATGAA 58.911 45.455 4.39 0.00 0.00 2.57
29 30 2.620367 GGGGCCACAACTTACATGATGA 60.620 50.000 4.39 0.00 0.00 2.92
30 31 1.750778 GGGGCCACAACTTACATGATG 59.249 52.381 4.39 0.00 0.00 3.07
31 32 1.357420 TGGGGCCACAACTTACATGAT 59.643 47.619 4.31 0.00 0.00 2.45
32 33 0.774276 TGGGGCCACAACTTACATGA 59.226 50.000 4.31 0.00 0.00 3.07
33 34 0.887933 GTGGGGCCACAACTTACATG 59.112 55.000 10.80 0.00 45.53 3.21
34 35 0.608035 CGTGGGGCCACAACTTACAT 60.608 55.000 10.80 0.00 46.47 2.29
35 36 1.228003 CGTGGGGCCACAACTTACA 60.228 57.895 10.80 0.00 46.47 2.41
36 37 0.035176 TACGTGGGGCCACAACTTAC 59.965 55.000 10.80 0.00 46.47 2.34
37 38 0.985760 ATACGTGGGGCCACAACTTA 59.014 50.000 10.80 0.54 46.47 2.24
81 82 3.898123 CAGTATCCACCCTAGTAGCATGT 59.102 47.826 0.00 0.00 0.00 3.21
146 361 5.716228 TCTCATCCTTGGTTGCATTTGTTAT 59.284 36.000 0.00 0.00 0.00 1.89
245 463 1.553706 TCCCGGTGTAGACTTCCTTC 58.446 55.000 0.00 0.00 0.00 3.46
316 534 2.258286 GTGCGAAATGGTGGTGCC 59.742 61.111 0.00 0.00 37.90 5.01
317 535 2.126888 CGTGCGAAATGGTGGTGC 60.127 61.111 0.00 0.00 0.00 5.01
326 544 0.530744 ATAGGAGTCTGCGTGCGAAA 59.469 50.000 0.00 0.00 0.00 3.46
332 550 1.828660 CCGGGATAGGAGTCTGCGT 60.829 63.158 0.00 0.00 0.00 5.24
378 596 6.183360 TGTTTGAAAAGGTGCGAAGATTAACT 60.183 34.615 0.00 0.00 0.00 2.24
388 717 3.052036 CCTTCATGTTTGAAAAGGTGCG 58.948 45.455 0.00 0.00 41.22 5.34
401 730 5.661458 CGTTGAATAGTACTCCCTTCATGT 58.339 41.667 0.00 0.00 0.00 3.21
406 735 2.159142 CCGCGTTGAATAGTACTCCCTT 60.159 50.000 4.92 0.00 0.00 3.95
425 754 0.098728 CCAAAAATAGAGCACGCCCG 59.901 55.000 0.00 0.00 0.00 6.13
508 838 0.682292 TTATGACACGGACACAGGCA 59.318 50.000 0.00 0.00 0.00 4.75
531 861 2.518312 CGACACAAACCGCACGACA 61.518 57.895 0.00 0.00 0.00 4.35
651 990 8.298729 ACAAGATTGTCTTTTTCCTTCTTCTT 57.701 30.769 0.00 0.00 36.50 2.52
652 991 7.888250 ACAAGATTGTCTTTTTCCTTCTTCT 57.112 32.000 0.00 0.00 36.50 2.85
656 995 7.378728 CGGTTTACAAGATTGTCTTTTTCCTTC 59.621 37.037 0.59 0.00 42.35 3.46
660 999 5.974751 TGCGGTTTACAAGATTGTCTTTTTC 59.025 36.000 0.59 0.00 42.35 2.29
661 1000 5.897050 TGCGGTTTACAAGATTGTCTTTTT 58.103 33.333 0.59 0.00 42.35 1.94
668 1008 2.987413 TGCTGCGGTTTACAAGATTG 57.013 45.000 0.00 0.00 0.00 2.67
687 1027 6.709846 GCATAATCTCTTCTATTGGTGAGCTT 59.290 38.462 0.00 0.00 0.00 3.74
703 1043 1.378531 TGCGGTTGGTGCATAATCTC 58.621 50.000 0.00 0.00 37.44 2.75
704 1044 3.568000 TGCGGTTGGTGCATAATCT 57.432 47.368 0.00 0.00 37.44 2.40
760 1111 5.766670 CCTGGACATGTGTATTATGCAGAAT 59.233 40.000 11.88 11.88 0.00 2.40
761 1112 5.125356 CCTGGACATGTGTATTATGCAGAA 58.875 41.667 1.15 0.00 0.00 3.02
762 1113 4.444733 CCCTGGACATGTGTATTATGCAGA 60.445 45.833 1.15 0.00 0.00 4.26
763 1114 3.817084 CCCTGGACATGTGTATTATGCAG 59.183 47.826 1.15 0.00 0.00 4.41
764 1115 3.457749 TCCCTGGACATGTGTATTATGCA 59.542 43.478 1.15 0.00 0.00 3.96
766 1117 5.059161 CAGTCCCTGGACATGTGTATTATG 58.941 45.833 18.12 0.44 46.76 1.90
767 1118 4.721776 ACAGTCCCTGGACATGTGTATTAT 59.278 41.667 18.12 0.00 46.76 1.28
768 1119 4.101114 ACAGTCCCTGGACATGTGTATTA 58.899 43.478 18.12 0.00 46.76 0.98
771 1122 2.024176 ACAGTCCCTGGACATGTGTA 57.976 50.000 18.12 0.00 46.76 2.90
772 1123 2.024176 TACAGTCCCTGGACATGTGT 57.976 50.000 18.12 14.99 46.76 3.72
773 1124 3.535561 GAATACAGTCCCTGGACATGTG 58.464 50.000 18.12 10.22 46.76 3.21
774 1125 2.505819 GGAATACAGTCCCTGGACATGT 59.494 50.000 18.12 18.47 46.76 3.21
777 1128 2.335681 TGGAATACAGTCCCTGGACA 57.664 50.000 18.12 0.00 46.76 4.02
807 1159 9.629878 TCTAGAAAAGATTCCTACGTCTAGAAT 57.370 33.333 0.00 0.00 39.23 2.40
808 1160 9.629878 ATCTAGAAAAGATTCCTACGTCTAGAA 57.370 33.333 10.56 0.00 42.62 2.10
853 1233 7.457535 AGAAGTTTGAATATTGGGAATTTGGGA 59.542 33.333 0.00 0.00 0.00 4.37
854 1234 7.623630 AGAAGTTTGAATATTGGGAATTTGGG 58.376 34.615 0.00 0.00 0.00 4.12
855 1235 8.534496 AGAGAAGTTTGAATATTGGGAATTTGG 58.466 33.333 0.00 0.00 0.00 3.28
860 1240 9.838339 GAGATAGAGAAGTTTGAATATTGGGAA 57.162 33.333 0.00 0.00 0.00 3.97
895 1287 1.379642 GGCTGGCTGGCAATGTACTC 61.380 60.000 13.06 0.00 41.37 2.59
896 1288 1.379044 GGCTGGCTGGCAATGTACT 60.379 57.895 13.06 0.00 41.37 2.73
897 1289 2.764314 CGGCTGGCTGGCAATGTAC 61.764 63.158 17.63 0.00 41.89 2.90
898 1290 2.438254 CGGCTGGCTGGCAATGTA 60.438 61.111 17.63 0.00 41.89 2.29
951 1348 3.144701 TGGAGAGGAGGATGGGATAATCA 59.855 47.826 0.00 0.00 0.00 2.57
1021 5376 2.332654 GGGCAAAGAACACGGCGAT 61.333 57.895 16.62 0.00 0.00 4.58
1200 5648 2.230660 GGGAAAAGGGAGCGGAATATG 58.769 52.381 0.00 0.00 0.00 1.78
1796 6295 6.588348 TGTTGTTCAACGCATATATGAGAG 57.412 37.500 21.48 13.47 0.00 3.20
1876 6376 0.448197 TTCTGCAACACGAAAACGCA 59.552 45.000 0.00 0.00 0.00 5.24
1884 6384 2.002586 CTAGGGTGATTCTGCAACACG 58.997 52.381 0.00 0.00 35.68 4.49
2080 6623 9.817365 CCAATATCGATTACATGATTGAAACTC 57.183 33.333 14.90 0.00 0.00 3.01
2081 6624 9.559732 TCCAATATCGATTACATGATTGAAACT 57.440 29.630 14.90 0.00 0.00 2.66
2119 8949 8.461222 GGCAGCAATAACATAATATGCATCTAA 58.539 33.333 0.19 0.00 34.17 2.10
2183 9016 1.559682 GATCACCTCAACCCAGCCTTA 59.440 52.381 0.00 0.00 0.00 2.69
2184 9017 0.329596 GATCACCTCAACCCAGCCTT 59.670 55.000 0.00 0.00 0.00 4.35
2185 9018 0.548682 AGATCACCTCAACCCAGCCT 60.549 55.000 0.00 0.00 0.00 4.58
2186 9019 1.134371 GTAGATCACCTCAACCCAGCC 60.134 57.143 0.00 0.00 0.00 4.85
2197 9033 3.676324 GCCCGCATATACAGTAGATCACC 60.676 52.174 0.00 0.00 0.00 4.02
2217 9053 1.474330 CCCTGGTCCTTTAACATGCC 58.526 55.000 0.00 0.00 0.00 4.40
2310 9146 1.166531 GCCAACGTTGCCTCAGTCTT 61.167 55.000 22.93 0.00 0.00 3.01
2326 9162 2.988010 ACTATGAAGAATCTGCGCCA 57.012 45.000 4.18 0.00 0.00 5.69
2339 9175 8.144478 GTCTTGGACTGCAGATATTTACTATGA 58.856 37.037 23.35 5.55 0.00 2.15
2341 9177 8.256356 AGTCTTGGACTGCAGATATTTACTAT 57.744 34.615 23.35 0.00 41.76 2.12
2371 9207 0.673985 CGGTCTCACTGTCACCTGAA 59.326 55.000 0.00 0.00 0.00 3.02
2372 9208 0.179001 TCGGTCTCACTGTCACCTGA 60.179 55.000 0.00 0.00 0.00 3.86
2614 9746 4.062991 GTCCCGATCACAAAAACTACACT 58.937 43.478 0.00 0.00 0.00 3.55
2713 9845 3.195825 ACTGACCAAATTCGGAGGAGTAG 59.804 47.826 0.00 0.00 0.00 2.57
2728 9860 4.958509 TGTTCCAAATAACGTACTGACCA 58.041 39.130 0.00 0.00 31.76 4.02


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

AutoCloner maintained by Alex Coulton.