Multiple sequence alignment - TraesCS2D01G366000

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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 TraesCS2D01G366000 chr2D 100.000 3008 0 0 1 3008 470544283 470541276 0.000000e+00 5555.0
1 TraesCS2D01G366000 chr2D 96.779 621 18 2 2389 3008 127600655 127601274 0.000000e+00 1035.0
2 TraesCS2D01G366000 chr2A 92.065 2092 96 21 45 2080 612307584 612305507 0.000000e+00 2880.0
3 TraesCS2D01G366000 chr2A 82.988 241 12 10 2132 2360 612304209 612303986 1.100000e-44 191.0
4 TraesCS2D01G366000 chr2B 92.093 1252 50 16 866 2080 549539904 549538665 0.000000e+00 1718.0
5 TraesCS2D01G366000 chr2B 84.302 688 58 23 45 711 549551939 549551281 7.080000e-176 627.0
6 TraesCS2D01G366000 chr2B 96.178 157 5 1 703 858 549540513 549540357 3.850000e-64 255.0
7 TraesCS2D01G366000 chr6D 97.262 621 15 2 2389 3008 128805370 128804751 0.000000e+00 1051.0
8 TraesCS2D01G366000 chr6D 96.457 621 20 2 2389 3008 226262135 226261516 0.000000e+00 1024.0
9 TraesCS2D01G366000 chr3D 96.790 623 17 3 2388 3008 40687714 40687093 0.000000e+00 1037.0
10 TraesCS2D01G366000 chr3D 96.779 621 18 2 2389 3008 343726077 343725458 0.000000e+00 1035.0
11 TraesCS2D01G366000 chr3D 96.618 621 19 2 2389 3008 58502773 58502154 0.000000e+00 1029.0
12 TraesCS2D01G366000 chr3D 78.935 413 74 11 1313 1723 551207510 551207911 4.940000e-68 268.0
13 TraesCS2D01G366000 chr3D 77.540 374 51 24 1024 1375 511444272 511443910 8.510000e-46 195.0
14 TraesCS2D01G366000 chr7D 96.779 621 18 2 2389 3008 414408626 414408007 0.000000e+00 1035.0
15 TraesCS2D01G366000 chr1D 96.618 621 18 3 2389 3008 345195522 345196140 0.000000e+00 1027.0
16 TraesCS2D01G366000 chr1D 82.805 221 38 0 1200 1420 462298914 462299134 6.580000e-47 198.0
17 TraesCS2D01G366000 chr4D 96.314 624 21 2 2386 3008 448575261 448575883 0.000000e+00 1024.0
18 TraesCS2D01G366000 chr4D 84.302 172 25 2 1205 1375 477089284 477089114 1.850000e-37 167.0
19 TraesCS2D01G366000 chr3A 88.136 177 21 0 1199 1375 647499535 647499359 8.450000e-51 211.0
20 TraesCS2D01G366000 chr5D 87.719 171 21 0 1205 1375 554577217 554577047 1.830000e-47 200.0
21 TraesCS2D01G366000 chr3B 87.079 178 21 2 1199 1375 673097981 673097805 1.830000e-47 200.0
22 TraesCS2D01G366000 chr3B 78.310 355 45 25 1024 1375 673106491 673106166 1.830000e-47 200.0
23 TraesCS2D01G366000 chr5B 83.654 208 34 0 1208 1415 689646157 689646364 2.370000e-46 196.0
24 TraesCS2D01G366000 chr5B 86.782 174 23 0 1202 1375 696154660 696154833 8.510000e-46 195.0
25 TraesCS2D01G366000 chr5B 85.897 78 11 0 1020 1097 689646080 689646157 1.920000e-12 84.2
26 TraesCS2D01G366000 chr4A 86.207 174 24 0 1202 1375 614004689 614004862 3.960000e-44 189.0
27 TraesCS2D01G366000 chr4A 82.927 205 35 0 1211 1415 622441691 622441487 5.120000e-43 185.0
28 TraesCS2D01G366000 chr4A 82.927 205 35 0 1211 1415 622510758 622510554 5.120000e-43 185.0


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 TraesCS2D01G366000 chr2D 470541276 470544283 3007 True 5555.0 5555 100.0000 1 3008 1 chr2D.!!$R1 3007
1 TraesCS2D01G366000 chr2D 127600655 127601274 619 False 1035.0 1035 96.7790 2389 3008 1 chr2D.!!$F1 619
2 TraesCS2D01G366000 chr2A 612303986 612307584 3598 True 1535.5 2880 87.5265 45 2360 2 chr2A.!!$R1 2315
3 TraesCS2D01G366000 chr2B 549538665 549540513 1848 True 986.5 1718 94.1355 703 2080 2 chr2B.!!$R2 1377
4 TraesCS2D01G366000 chr2B 549551281 549551939 658 True 627.0 627 84.3020 45 711 1 chr2B.!!$R1 666
5 TraesCS2D01G366000 chr6D 128804751 128805370 619 True 1051.0 1051 97.2620 2389 3008 1 chr6D.!!$R1 619
6 TraesCS2D01G366000 chr6D 226261516 226262135 619 True 1024.0 1024 96.4570 2389 3008 1 chr6D.!!$R2 619
7 TraesCS2D01G366000 chr3D 40687093 40687714 621 True 1037.0 1037 96.7900 2388 3008 1 chr3D.!!$R1 620
8 TraesCS2D01G366000 chr3D 343725458 343726077 619 True 1035.0 1035 96.7790 2389 3008 1 chr3D.!!$R3 619
9 TraesCS2D01G366000 chr3D 58502154 58502773 619 True 1029.0 1029 96.6180 2389 3008 1 chr3D.!!$R2 619
10 TraesCS2D01G366000 chr7D 414408007 414408626 619 True 1035.0 1035 96.7790 2389 3008 1 chr7D.!!$R1 619
11 TraesCS2D01G366000 chr1D 345195522 345196140 618 False 1027.0 1027 96.6180 2389 3008 1 chr1D.!!$F1 619
12 TraesCS2D01G366000 chr4D 448575261 448575883 622 False 1024.0 1024 96.3140 2386 3008 1 chr4D.!!$F1 622

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
746 799 0.459899 TGTAGTGCTGCGTATCCCTG 59.540 55.0 0.00 0.0 0.0 4.45 F
1632 2138 0.461516 TCGCCGTCTACTCGATGACT 60.462 55.0 10.25 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 2368 0.030908 CCCTCGTTATCTGCTCGACC 59.969 60.0 0.00 0.0 0.00 4.79 R
2758 4560 0.599204 TTGAAGACTTCGTCCCGTGC 60.599 55.0 10.56 0.0 32.18 5.34 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
26 27 8.617290 AGGTCAAATCTATTTACAAAACGACT 57.383 30.769 0.00 0.00 0.00 4.18
27 28 8.504005 AGGTCAAATCTATTTACAAAACGACTG 58.496 33.333 0.00 0.00 0.00 3.51
28 29 8.500773 GGTCAAATCTATTTACAAAACGACTGA 58.499 33.333 0.00 0.00 0.00 3.41
66 67 3.577649 ACGTGTCCTGAACATGACTAG 57.422 47.619 0.00 0.00 46.13 2.57
195 212 1.837439 AGCTGTGGACATTATTCGGGA 59.163 47.619 0.00 0.00 0.00 5.14
242 266 1.518102 GCAATGTGCAAGACAACAACG 59.482 47.619 0.00 0.00 44.26 4.10
253 277 6.150307 TGCAAGACAACAACGGTTATGAATAT 59.850 34.615 11.43 0.00 34.87 1.28
262 286 7.974675 ACAACGGTTATGAATATGAAGAAGTG 58.025 34.615 0.00 0.00 0.00 3.16
486 515 8.530804 TCTACCCTTAATAGAGAACTACCAAC 57.469 38.462 0.00 0.00 0.00 3.77
505 534 4.874966 CCAACATGTCTTTTGAGCCAAAAA 59.125 37.500 0.00 4.75 41.77 1.94
513 542 4.462483 TCTTTTGAGCCAAAAACTGACTGT 59.538 37.500 12.25 0.00 41.77 3.55
631 684 1.487300 CATGGACAATGGCCAATGGA 58.513 50.000 24.49 8.67 39.21 3.41
682 735 1.872388 TCATCGCTTCGAACAAACCA 58.128 45.000 0.00 0.00 39.99 3.67
746 799 0.459899 TGTAGTGCTGCGTATCCCTG 59.540 55.000 0.00 0.00 0.00 4.45
748 801 2.349969 TAGTGCTGCGTATCCCTGCG 62.350 60.000 0.00 0.00 0.00 5.18
772 825 1.652012 GGCCGTCAGAGATCTCGAG 59.348 63.158 16.97 5.93 34.09 4.04
786 839 1.909141 CTCGAGCAGGCAAACAGCTG 61.909 60.000 13.48 13.48 44.79 4.24
804 857 7.439108 ACAGCTGGGTCTTAGTTAATTATCT 57.561 36.000 19.93 1.81 0.00 1.98
863 917 5.050499 CACGTACACGCTAGCTAAGTACTAT 60.050 44.000 25.23 16.78 44.43 2.12
866 920 3.884091 ACACGCTAGCTAAGTACTATGCT 59.116 43.478 21.13 21.13 39.30 3.79
867 921 5.061853 ACACGCTAGCTAAGTACTATGCTA 58.938 41.667 21.11 21.11 37.02 3.49
868 922 5.706369 ACACGCTAGCTAAGTACTATGCTAT 59.294 40.000 22.06 10.92 37.39 2.97
869 923 6.877855 ACACGCTAGCTAAGTACTATGCTATA 59.122 38.462 22.06 9.83 37.39 1.31
870 924 7.389884 ACACGCTAGCTAAGTACTATGCTATAA 59.610 37.037 22.06 9.30 37.39 0.98
887 1384 5.105877 TGCTATAAGTATAAGCTAGCACGGG 60.106 44.000 18.83 0.00 39.72 5.28
925 1422 3.623906 ATCAGTAGCAGCTGTCAACAT 57.376 42.857 16.64 0.00 37.70 2.71
926 1423 4.743057 ATCAGTAGCAGCTGTCAACATA 57.257 40.909 16.64 4.18 37.70 2.29
927 1424 4.115401 TCAGTAGCAGCTGTCAACATAG 57.885 45.455 16.64 5.95 37.70 2.23
968 1469 1.880675 ACACGTGGAGCTAGATATCGG 59.119 52.381 21.57 0.00 0.00 4.18
975 1476 3.271729 GGAGCTAGATATCGGTCGATCA 58.728 50.000 9.25 0.00 36.17 2.92
1111 1612 3.486542 CGGGTACGTACTTTACTCTGAGC 60.487 52.174 24.07 3.91 34.81 4.26
1112 1613 3.693578 GGGTACGTACTTTACTCTGAGCT 59.306 47.826 24.07 0.00 0.00 4.09
1113 1614 4.878397 GGGTACGTACTTTACTCTGAGCTA 59.122 45.833 24.07 0.00 0.00 3.32
1114 1615 5.530543 GGGTACGTACTTTACTCTGAGCTAT 59.469 44.000 24.07 0.00 0.00 2.97
1115 1616 6.039159 GGGTACGTACTTTACTCTGAGCTATT 59.961 42.308 24.07 0.00 0.00 1.73
1172 1678 5.584003 CGTTACAGAATTAACGCGCTATAC 58.416 41.667 5.73 0.00 45.54 1.47
1229 1735 3.842923 CGTGGAGGAGCTGGCGAT 61.843 66.667 0.00 0.00 0.00 4.58
1375 1881 1.086634 GGAGAAGCTCATGGACACGC 61.087 60.000 0.00 0.00 31.08 5.34
1383 1889 2.104859 CATGGACACGCTGAGGCAG 61.105 63.158 0.00 0.00 38.60 4.85
1632 2138 0.461516 TCGCCGTCTACTCGATGACT 60.462 55.000 10.25 0.00 0.00 3.41
1751 2257 3.206150 ACATCGCCAAAGACATGGTATC 58.794 45.455 0.00 0.00 42.75 2.24
1790 2326 5.934781 ACTGTGATCTTCTTGGAGAAACTT 58.065 37.500 0.00 0.00 33.19 2.66
1830 2368 4.532276 TCGATTTCGTTTTTGTGATGTGG 58.468 39.130 0.00 0.00 40.80 4.17
2059 2602 2.802816 AGTCACACATCGTTCAAAGCTC 59.197 45.455 0.00 0.00 0.00 4.09
2063 2606 2.549754 ACACATCGTTCAAAGCTCTTGG 59.450 45.455 8.23 0.00 0.00 3.61
2075 2618 5.181245 TCAAAGCTCTTGGACGGATAAAAAG 59.819 40.000 8.23 0.00 0.00 2.27
2080 2623 5.560966 TCTTGGACGGATAAAAAGATTGC 57.439 39.130 0.00 0.00 0.00 3.56
2081 2624 5.007034 TCTTGGACGGATAAAAAGATTGCA 58.993 37.500 0.00 0.00 0.00 4.08
2082 2625 4.695217 TGGACGGATAAAAAGATTGCAC 57.305 40.909 0.00 0.00 0.00 4.57
2083 2626 4.075682 TGGACGGATAAAAAGATTGCACA 58.924 39.130 0.00 0.00 0.00 4.57
2085 2628 4.096732 ACGGATAAAAAGATTGCACAGC 57.903 40.909 0.00 0.00 0.00 4.40
2086 2629 3.758554 ACGGATAAAAAGATTGCACAGCT 59.241 39.130 0.00 0.00 0.00 4.24
2087 2630 4.941263 ACGGATAAAAAGATTGCACAGCTA 59.059 37.500 0.00 0.00 0.00 3.32
2088 2631 5.590259 ACGGATAAAAAGATTGCACAGCTAT 59.410 36.000 0.00 0.00 0.00 2.97
2089 2632 5.911280 CGGATAAAAAGATTGCACAGCTATG 59.089 40.000 0.00 0.00 0.00 2.23
2107 3644 6.706716 CAGCTATGTGTCATTCTCATTCTCAT 59.293 38.462 0.00 0.00 33.23 2.90
2109 3646 8.427276 AGCTATGTGTCATTCTCATTCTCATAA 58.573 33.333 0.00 0.00 33.23 1.90
2110 3647 8.494347 GCTATGTGTCATTCTCATTCTCATAAC 58.506 37.037 0.00 0.00 33.23 1.89
2112 3649 6.710278 TGTGTCATTCTCATTCTCATAACCA 58.290 36.000 0.00 0.00 0.00 3.67
2113 3650 7.341030 TGTGTCATTCTCATTCTCATAACCAT 58.659 34.615 0.00 0.00 0.00 3.55
2116 3653 9.498176 TGTCATTCTCATTCTCATAACCATATG 57.502 33.333 0.00 0.00 40.29 1.78
2117 3654 9.499479 GTCATTCTCATTCTCATAACCATATGT 57.501 33.333 1.24 0.00 39.94 2.29
2118 3655 9.498176 TCATTCTCATTCTCATAACCATATGTG 57.502 33.333 1.24 0.00 39.94 3.21
2123 3660 9.933723 CTCATTCTCATAACCATATGTGTCATA 57.066 33.333 1.24 0.00 39.94 2.15
2124 3661 9.933723 TCATTCTCATAACCATATGTGTCATAG 57.066 33.333 1.24 0.00 39.94 2.23
2125 3662 9.933723 CATTCTCATAACCATATGTGTCATAGA 57.066 33.333 1.24 0.00 39.94 1.98
2167 3956 7.554835 TGTGTCATTCTCATTCATGAATCATCA 59.445 33.333 18.16 8.61 40.57 3.07
2184 3973 8.745590 TGAATCATCAATGATGTGAATTTGTCT 58.254 29.630 21.13 0.00 46.22 3.41
2186 3975 6.327154 TCATCAATGATGTGAATTTGTCTGC 58.673 36.000 21.13 0.00 40.55 4.26
2229 4025 4.899239 CACATCCTCCGAGCGGGC 62.899 72.222 9.29 0.00 34.94 6.13
2235 4031 3.764466 CTCCGAGCGGGCTGTCTT 61.764 66.667 9.29 0.00 34.94 3.01
2236 4032 3.708220 CTCCGAGCGGGCTGTCTTC 62.708 68.421 9.29 0.00 34.94 2.87
2238 4034 4.421479 CGAGCGGGCTGTCTTCGT 62.421 66.667 0.00 0.00 0.00 3.85
2239 4035 2.048127 GAGCGGGCTGTCTTCGTT 60.048 61.111 0.00 0.00 0.00 3.85
2240 4036 1.668151 GAGCGGGCTGTCTTCGTTT 60.668 57.895 0.00 0.00 0.00 3.60
2248 4044 4.042398 GGGCTGTCTTCGTTTTCTTTTTC 58.958 43.478 0.00 0.00 0.00 2.29
2261 4057 3.982576 TCTTTTTCTTTTGAGCGGGAC 57.017 42.857 0.00 0.00 0.00 4.46
2262 4058 3.283751 TCTTTTTCTTTTGAGCGGGACA 58.716 40.909 0.00 0.00 0.00 4.02
2267 4063 0.447801 CTTTTGAGCGGGACATTCGG 59.552 55.000 0.00 0.00 0.00 4.30
2292 4093 5.982465 TTTTGTTATTTCTGTTTGGCTGC 57.018 34.783 0.00 0.00 0.00 5.25
2348 4149 3.036429 GCTGGACCTGGCCTAGTGG 62.036 68.421 3.32 3.56 0.00 4.00
2363 4164 5.344207 CCTAGTGGCTTTTCGTATTATGC 57.656 43.478 0.00 0.00 0.00 3.14
2364 4165 3.944422 AGTGGCTTTTCGTATTATGCG 57.056 42.857 0.00 0.00 0.00 4.73
2365 4166 2.612212 AGTGGCTTTTCGTATTATGCGG 59.388 45.455 2.53 0.00 0.00 5.69
2366 4167 1.332375 TGGCTTTTCGTATTATGCGGC 59.668 47.619 2.53 0.00 0.00 6.53
2367 4168 1.332375 GGCTTTTCGTATTATGCGGCA 59.668 47.619 4.58 4.58 0.00 5.69
2368 4169 2.602217 GGCTTTTCGTATTATGCGGCAG 60.602 50.000 9.25 0.00 0.00 4.85
2369 4170 2.602217 GCTTTTCGTATTATGCGGCAGG 60.602 50.000 9.25 0.00 0.00 4.85
2370 4171 2.605837 TTTCGTATTATGCGGCAGGA 57.394 45.000 9.25 0.00 0.00 3.86
2371 4172 1.860676 TTCGTATTATGCGGCAGGAC 58.139 50.000 9.25 2.71 0.00 3.85
2372 4173 0.318360 TCGTATTATGCGGCAGGACG 60.318 55.000 9.25 14.39 0.00 4.79
2380 4181 4.069232 CGGCAGGACGCTTGAGGA 62.069 66.667 0.00 0.00 41.91 3.71
2381 4182 2.125350 GGCAGGACGCTTGAGGAG 60.125 66.667 0.00 0.00 41.91 3.69
2382 4183 2.650116 GGCAGGACGCTTGAGGAGA 61.650 63.158 0.00 0.00 41.91 3.71
2383 4184 1.293498 GCAGGACGCTTGAGGAGAA 59.707 57.895 0.00 0.00 37.77 2.87
2384 4185 1.016653 GCAGGACGCTTGAGGAGAAC 61.017 60.000 0.00 0.00 37.77 3.01
2385 4186 0.605589 CAGGACGCTTGAGGAGAACT 59.394 55.000 0.00 0.00 0.00 3.01
2386 4187 1.819288 CAGGACGCTTGAGGAGAACTA 59.181 52.381 0.00 0.00 0.00 2.24
2420 4221 2.593725 CGGCGGATCTCGGGTAGA 60.594 66.667 0.00 0.00 39.69 2.59
2466 4267 2.203877 TGGTAACAGGAGGCGGGT 60.204 61.111 0.00 0.00 46.17 5.28
2503 4304 2.043349 TTCGGGCCCTCTCGATGA 60.043 61.111 22.43 4.41 35.25 2.92
2717 4518 4.883006 GGGAGGAGATCTACATATCCGTAC 59.117 50.000 7.93 0.00 44.22 3.67
2733 4535 0.961753 GTACTGCCAAGCTTGCCTTT 59.038 50.000 21.43 7.44 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.063615 AGTCGTTTTGTAAATAGATTTGACCTT 57.936 29.630 0.00 0.00 0.00 3.50
22 23 9.199184 CGTTTCTTATGTTAATTTGATCAGTCG 57.801 33.333 0.00 0.00 0.00 4.18
24 25 9.825972 CACGTTTCTTATGTTAATTTGATCAGT 57.174 29.630 0.00 0.00 0.00 3.41
25 26 9.825972 ACACGTTTCTTATGTTAATTTGATCAG 57.174 29.630 0.00 0.00 0.00 2.90
26 27 9.820229 GACACGTTTCTTATGTTAATTTGATCA 57.180 29.630 0.00 0.00 0.00 2.92
27 28 9.274065 GGACACGTTTCTTATGTTAATTTGATC 57.726 33.333 1.13 0.00 0.00 2.92
28 29 9.010029 AGGACACGTTTCTTATGTTAATTTGAT 57.990 29.630 1.13 0.00 0.00 2.57
29 30 8.286800 CAGGACACGTTTCTTATGTTAATTTGA 58.713 33.333 1.13 0.00 0.00 2.69
30 31 8.286800 TCAGGACACGTTTCTTATGTTAATTTG 58.713 33.333 1.13 0.00 0.00 2.32
31 32 8.385898 TCAGGACACGTTTCTTATGTTAATTT 57.614 30.769 1.13 0.00 0.00 1.82
32 33 7.972832 TCAGGACACGTTTCTTATGTTAATT 57.027 32.000 1.13 0.00 0.00 1.40
33 34 7.442969 TGTTCAGGACACGTTTCTTATGTTAAT 59.557 33.333 1.13 0.00 32.00 1.40
34 35 6.762187 TGTTCAGGACACGTTTCTTATGTTAA 59.238 34.615 1.13 0.00 32.00 2.01
35 36 6.282167 TGTTCAGGACACGTTTCTTATGTTA 58.718 36.000 1.13 0.00 32.00 2.41
36 37 5.120399 TGTTCAGGACACGTTTCTTATGTT 58.880 37.500 1.13 0.00 32.00 2.71
37 38 4.699637 TGTTCAGGACACGTTTCTTATGT 58.300 39.130 1.13 0.00 32.00 2.29
38 39 5.408299 TCATGTTCAGGACACGTTTCTTATG 59.592 40.000 1.13 0.00 42.04 1.90
39 40 5.408604 GTCATGTTCAGGACACGTTTCTTAT 59.591 40.000 11.79 0.00 42.04 1.73
40 41 4.748102 GTCATGTTCAGGACACGTTTCTTA 59.252 41.667 11.79 0.00 42.04 2.10
41 42 3.560068 GTCATGTTCAGGACACGTTTCTT 59.440 43.478 11.79 0.00 42.04 2.52
42 43 3.131396 GTCATGTTCAGGACACGTTTCT 58.869 45.455 11.79 0.00 42.04 2.52
43 44 3.131396 AGTCATGTTCAGGACACGTTTC 58.869 45.455 17.49 0.00 42.04 2.78
201 218 4.202493 TGCCATTGTCTGATGCATATACCT 60.202 41.667 0.00 0.00 0.00 3.08
202 219 4.074259 TGCCATTGTCTGATGCATATACC 58.926 43.478 0.00 0.00 0.00 2.73
449 478 6.793505 ATTAAGGGTAGATTTGTCGTCTCT 57.206 37.500 0.00 0.00 0.00 3.10
486 515 5.232838 GTCAGTTTTTGGCTCAAAAGACATG 59.767 40.000 16.98 0.00 41.30 3.21
505 534 6.992123 TCAGTGATTTGTATGAAACAGTCAGT 59.008 34.615 0.00 0.00 40.43 3.41
553 582 7.597288 TGCTGTACATCCTACTACACAATAT 57.403 36.000 0.00 0.00 0.00 1.28
556 585 5.731957 TTGCTGTACATCCTACTACACAA 57.268 39.130 0.00 0.00 0.00 3.33
557 586 5.731957 TTTGCTGTACATCCTACTACACA 57.268 39.130 0.00 0.00 0.00 3.72
631 684 2.616960 CATGCAATTTCATGCTGCTGT 58.383 42.857 5.12 0.00 46.54 4.40
682 735 0.738389 CGTCCAGCCAACAAACTGTT 59.262 50.000 0.00 0.00 42.08 3.16
748 801 0.241481 GATCTCTGACGGCCGGATAC 59.759 60.000 31.76 17.58 0.00 2.24
772 825 2.914097 ACCCAGCTGTTTGCCTGC 60.914 61.111 13.81 0.00 44.23 4.85
786 839 5.401674 CGTCGCAGATAATTAACTAAGACCC 59.598 44.000 16.70 2.97 40.67 4.46
804 857 2.355837 GGTGCAGAAGTCGTCGCA 60.356 61.111 0.00 2.38 34.73 5.10
863 917 5.105877 CCCGTGCTAGCTTATACTTATAGCA 60.106 44.000 17.23 0.00 44.77 3.49
866 920 5.573219 TCCCCGTGCTAGCTTATACTTATA 58.427 41.667 17.23 0.00 0.00 0.98
867 921 4.413760 TCCCCGTGCTAGCTTATACTTAT 58.586 43.478 17.23 0.00 0.00 1.73
868 922 3.836146 TCCCCGTGCTAGCTTATACTTA 58.164 45.455 17.23 0.00 0.00 2.24
869 923 2.674420 TCCCCGTGCTAGCTTATACTT 58.326 47.619 17.23 0.00 0.00 2.24
870 924 2.376695 TCCCCGTGCTAGCTTATACT 57.623 50.000 17.23 0.00 0.00 2.12
887 1384 5.837437 ACTGATACGAATTGAGAGACATCC 58.163 41.667 0.00 0.00 0.00 3.51
968 1469 1.065928 CGGCCTACTGGTGATCGAC 59.934 63.158 0.00 0.00 35.27 4.20
975 1476 2.042843 CCTCTCCGGCCTACTGGT 60.043 66.667 0.00 0.00 43.58 4.00
1114 1615 8.758829 CCCATGTAATAGCATAGATGGTACTAA 58.241 37.037 14.89 0.00 42.38 2.24
1115 1616 7.899172 ACCCATGTAATAGCATAGATGGTACTA 59.101 37.037 14.89 0.00 42.38 1.82
1172 1678 0.738063 TACCGCACCATGCAAGTACG 60.738 55.000 6.01 6.01 45.36 3.67
1292 1798 0.325272 GAGGTTCTTGTCCTCCCACC 59.675 60.000 0.98 0.00 43.90 4.61
1375 1881 4.106925 GCCCAGGGTCTGCCTCAG 62.107 72.222 7.55 0.00 34.45 3.35
1395 1901 0.615331 TCACCAGGATGTCCAGCTTC 59.385 55.000 0.00 0.00 38.89 3.86
1560 2066 1.738099 GATGTGGACGACGCTGCTT 60.738 57.895 0.00 0.00 0.00 3.91
1632 2138 1.912220 CTGGTTCATCGCCCCCTTA 59.088 57.895 0.00 0.00 0.00 2.69
1751 2257 7.504403 AGATCACAGTTACATAAAGGGATCAG 58.496 38.462 14.90 0.00 33.01 2.90
1790 2326 7.043854 CGAAATCGAAGTTAGCCGTTATTAAGA 60.044 37.037 0.00 0.00 43.02 2.10
1830 2368 0.030908 CCCTCGTTATCTGCTCGACC 59.969 60.000 0.00 0.00 0.00 4.79
2059 2602 5.095490 GTGCAATCTTTTTATCCGTCCAAG 58.905 41.667 0.00 0.00 0.00 3.61
2063 2606 4.098416 GCTGTGCAATCTTTTTATCCGTC 58.902 43.478 0.00 0.00 0.00 4.79
2081 2624 5.987098 AGAATGAGAATGACACATAGCTGT 58.013 37.500 0.00 0.00 35.44 4.40
2082 2625 6.047231 TGAGAATGAGAATGACACATAGCTG 58.953 40.000 0.00 0.00 0.00 4.24
2083 2626 6.231258 TGAGAATGAGAATGACACATAGCT 57.769 37.500 0.00 0.00 0.00 3.32
2085 2628 8.986847 GGTTATGAGAATGAGAATGACACATAG 58.013 37.037 0.00 0.00 0.00 2.23
2086 2629 8.485392 TGGTTATGAGAATGAGAATGACACATA 58.515 33.333 0.00 0.00 0.00 2.29
2087 2630 7.341030 TGGTTATGAGAATGAGAATGACACAT 58.659 34.615 0.00 0.00 0.00 3.21
2088 2631 6.710278 TGGTTATGAGAATGAGAATGACACA 58.290 36.000 0.00 0.00 0.00 3.72
2089 2632 7.798596 ATGGTTATGAGAATGAGAATGACAC 57.201 36.000 0.00 0.00 0.00 3.67
2091 2634 9.499479 ACATATGGTTATGAGAATGAGAATGAC 57.501 33.333 7.80 0.00 37.94 3.06
2092 2635 9.498176 CACATATGGTTATGAGAATGAGAATGA 57.502 33.333 7.80 0.00 37.94 2.57
2123 3660 9.466497 AATGACACATATGGTTATGTCTTTTCT 57.534 29.630 19.26 3.01 45.27 2.52
2124 3661 9.722056 GAATGACACATATGGTTATGTCTTTTC 57.278 33.333 19.26 17.34 45.27 2.29
2125 3662 9.466497 AGAATGACACATATGGTTATGTCTTTT 57.534 29.630 19.26 14.41 45.27 2.27
2126 3663 9.113838 GAGAATGACACATATGGTTATGTCTTT 57.886 33.333 19.26 18.49 45.27 2.52
2127 3664 8.267183 TGAGAATGACACATATGGTTATGTCTT 58.733 33.333 19.26 13.14 45.27 3.01
2128 3665 7.795047 TGAGAATGACACATATGGTTATGTCT 58.205 34.615 19.26 14.01 45.27 3.41
2129 3666 8.613060 ATGAGAATGACACATATGGTTATGTC 57.387 34.615 14.28 14.28 45.27 3.06
2135 3924 7.284820 TCATGAATGAGAATGACACATATGGT 58.715 34.615 7.80 2.03 32.11 3.55
2167 3956 3.674138 GCGGCAGACAAATTCACATCATT 60.674 43.478 0.00 0.00 0.00 2.57
2184 3973 3.157252 GATGGGAGAGGAGCGGCA 61.157 66.667 1.45 0.00 0.00 5.69
2186 3975 1.333636 AACAGATGGGAGAGGAGCGG 61.334 60.000 0.00 0.00 0.00 5.52
2224 4020 1.206831 GAAAACGAAGACAGCCCGC 59.793 57.895 0.00 0.00 0.00 6.13
2229 4025 8.447787 TCAAAAGAAAAAGAAAACGAAGACAG 57.552 30.769 0.00 0.00 0.00 3.51
2230 4026 7.061789 GCTCAAAAGAAAAAGAAAACGAAGACA 59.938 33.333 0.00 0.00 0.00 3.41
2232 4028 6.250527 CGCTCAAAAGAAAAAGAAAACGAAGA 59.749 34.615 0.00 0.00 0.00 2.87
2233 4029 6.394867 CGCTCAAAAGAAAAAGAAAACGAAG 58.605 36.000 0.00 0.00 0.00 3.79
2234 4030 5.287513 CCGCTCAAAAGAAAAAGAAAACGAA 59.712 36.000 0.00 0.00 0.00 3.85
2235 4031 4.796312 CCGCTCAAAAGAAAAAGAAAACGA 59.204 37.500 0.00 0.00 0.00 3.85
2236 4032 4.026886 CCCGCTCAAAAGAAAAAGAAAACG 60.027 41.667 0.00 0.00 0.00 3.60
2237 4033 5.005394 GTCCCGCTCAAAAGAAAAAGAAAAC 59.995 40.000 0.00 0.00 0.00 2.43
2238 4034 5.106442 GTCCCGCTCAAAAGAAAAAGAAAA 58.894 37.500 0.00 0.00 0.00 2.29
2239 4035 4.158764 TGTCCCGCTCAAAAGAAAAAGAAA 59.841 37.500 0.00 0.00 0.00 2.52
2240 4036 3.697045 TGTCCCGCTCAAAAGAAAAAGAA 59.303 39.130 0.00 0.00 0.00 2.52
2248 4044 0.447801 CCGAATGTCCCGCTCAAAAG 59.552 55.000 0.00 0.00 0.00 2.27
2274 4070 2.562738 AGGGCAGCCAAACAGAAATAAC 59.437 45.455 15.19 0.00 0.00 1.89
2292 4093 1.523758 AACAAGAAAGCGCACTAGGG 58.476 50.000 11.47 0.00 0.00 3.53
2318 4119 3.506743 TCCAGCCCAAGTGCCCAA 61.507 61.111 0.00 0.00 0.00 4.12
2319 4120 4.284550 GTCCAGCCCAAGTGCCCA 62.285 66.667 0.00 0.00 0.00 5.36
2321 4122 3.971702 AGGTCCAGCCCAAGTGCC 61.972 66.667 0.00 0.00 38.26 5.01
2322 4123 2.674380 CAGGTCCAGCCCAAGTGC 60.674 66.667 0.00 0.00 38.26 4.40
2323 4124 2.034687 CCAGGTCCAGCCCAAGTG 59.965 66.667 0.00 0.00 38.26 3.16
2324 4125 3.971702 GCCAGGTCCAGCCCAAGT 61.972 66.667 0.00 0.00 38.26 3.16
2325 4126 4.748144 GGCCAGGTCCAGCCCAAG 62.748 72.222 11.15 0.00 43.76 3.61
2348 4149 2.602217 CCTGCCGCATAATACGAAAAGC 60.602 50.000 0.00 0.00 0.00 3.51
2365 4166 1.016653 GTTCTCCTCAAGCGTCCTGC 61.017 60.000 0.00 0.00 46.98 4.85
2366 4167 0.605589 AGTTCTCCTCAAGCGTCCTG 59.394 55.000 0.00 0.00 0.00 3.86
2367 4168 2.217510 TAGTTCTCCTCAAGCGTCCT 57.782 50.000 0.00 0.00 0.00 3.85
2368 4169 3.190874 CAATAGTTCTCCTCAAGCGTCC 58.809 50.000 0.00 0.00 0.00 4.79
2369 4170 3.851098 ACAATAGTTCTCCTCAAGCGTC 58.149 45.455 0.00 0.00 0.00 5.19
2370 4171 3.673594 CGACAATAGTTCTCCTCAAGCGT 60.674 47.826 0.00 0.00 0.00 5.07
2371 4172 2.854777 CGACAATAGTTCTCCTCAAGCG 59.145 50.000 0.00 0.00 0.00 4.68
2372 4173 3.190874 CCGACAATAGTTCTCCTCAAGC 58.809 50.000 0.00 0.00 0.00 4.01
2373 4174 4.177026 CACCGACAATAGTTCTCCTCAAG 58.823 47.826 0.00 0.00 0.00 3.02
2374 4175 3.576982 ACACCGACAATAGTTCTCCTCAA 59.423 43.478 0.00 0.00 0.00 3.02
2375 4176 3.162666 ACACCGACAATAGTTCTCCTCA 58.837 45.455 0.00 0.00 0.00 3.86
2376 4177 3.192844 TGACACCGACAATAGTTCTCCTC 59.807 47.826 0.00 0.00 0.00 3.71
2377 4178 3.162666 TGACACCGACAATAGTTCTCCT 58.837 45.455 0.00 0.00 0.00 3.69
2378 4179 3.587797 TGACACCGACAATAGTTCTCC 57.412 47.619 0.00 0.00 0.00 3.71
2379 4180 5.333875 GGTTTTGACACCGACAATAGTTCTC 60.334 44.000 0.00 0.00 0.00 2.87
2380 4181 4.514066 GGTTTTGACACCGACAATAGTTCT 59.486 41.667 0.00 0.00 0.00 3.01
2381 4182 4.779987 GGTTTTGACACCGACAATAGTTC 58.220 43.478 0.00 0.00 0.00 3.01
2382 4183 4.823790 GGTTTTGACACCGACAATAGTT 57.176 40.909 0.00 0.00 0.00 2.24
2420 4221 4.003788 CGCACAGTTCGGGACCCT 62.004 66.667 9.41 0.00 0.00 4.34
2466 4267 1.695242 ACCTGGGTAAACATCGTGTCA 59.305 47.619 0.00 0.00 0.00 3.58
2503 4304 4.632292 AGCAGGAAGTAGGGTATTACCTT 58.368 43.478 12.54 7.74 42.09 3.50
2733 4535 2.283529 GGGACTCTCCTTGGCGTGA 61.284 63.158 0.00 0.00 36.57 4.35
2758 4560 0.599204 TTGAAGACTTCGTCCCGTGC 60.599 55.000 10.56 0.00 32.18 5.34
2789 4591 1.754803 CAGCCGGACTGTTGGACTATA 59.245 52.381 5.05 0.00 41.86 1.31
2832 4634 2.041405 AGGGGCTACTGAGGGAGC 60.041 66.667 0.44 0.44 38.00 4.70
2878 4680 2.390599 GCCGAAGACAATCTGCGCA 61.391 57.895 10.98 10.98 44.09 6.09


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

AutoCloner maintained by Alex Coulton.