Multiple sequence alignment - TraesCS6A01G031600

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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 TraesCS6A01G031600 chr6A 100.000 3161 0 0 1 3161 15874188 15871028 0.000000e+00 5838.0
1 TraesCS6A01G031600 chr6A 82.717 1244 203 10 979 2217 15925256 15924020 0.000000e+00 1096.0
2 TraesCS6A01G031600 chr6A 80.412 1164 213 14 1058 2213 15914091 15912935 0.000000e+00 872.0
3 TraesCS6A01G031600 chr6A 86.973 522 40 17 2639 3156 15718983 15719480 2.130000e-156 562.0
4 TraesCS6A01G031600 chr6A 91.803 61 2 1 2409 2466 15871550 15871490 7.270000e-12 82.4
5 TraesCS6A01G031600 chr6A 91.803 61 2 1 2639 2699 15871780 15871723 7.270000e-12 82.4
6 TraesCS6A01G031600 chr6D 93.956 1671 74 15 742 2388 14689524 14687857 0.000000e+00 2501.0
7 TraesCS6A01G031600 chr6D 93.555 993 62 1 1395 2385 14518038 14519030 0.000000e+00 1478.0
8 TraesCS6A01G031600 chr6D 91.988 1011 66 9 2154 3156 14519237 14520240 0.000000e+00 1404.0
9 TraesCS6A01G031600 chr6D 81.197 1420 229 19 979 2385 14941177 14939783 0.000000e+00 1109.0
10 TraesCS6A01G031600 chr6D 79.450 1455 256 27 945 2385 14503303 14504728 0.000000e+00 990.0
11 TraesCS6A01G031600 chr6D 93.846 585 35 1 1 585 14719789 14719206 0.000000e+00 880.0
12 TraesCS6A01G031600 chr6D 89.318 337 33 3 251 587 427085252 427084919 1.360000e-113 420.0
13 TraesCS6A01G031600 chr6D 93.706 143 8 1 599 741 14691462 14691321 2.470000e-51 213.0
14 TraesCS6A01G031600 chr6D 92.000 75 5 1 703 776 14511696 14511770 1.550000e-18 104.0
15 TraesCS6A01G031600 chr6B 83.890 1347 202 8 1041 2385 26291365 26292698 0.000000e+00 1271.0
16 TraesCS6A01G031600 chr6B 79.684 1265 232 18 1138 2388 28730858 28729605 0.000000e+00 889.0
17 TraesCS6A01G031600 chr5D 80.198 1414 223 40 979 2379 27979315 27977946 0.000000e+00 1007.0
18 TraesCS6A01G031600 chr5B 86.405 331 39 6 261 587 691775173 691774845 1.080000e-94 357.0
19 TraesCS6A01G031600 chr5B 86.093 302 34 7 225 523 72250042 72250338 5.090000e-83 318.0
20 TraesCS6A01G031600 chr1D 86.711 301 33 6 225 523 238937250 238936955 8.450000e-86 327.0
21 TraesCS6A01G031600 chr1B 86.333 300 35 5 225 522 650493015 650493310 3.930000e-84 322.0
22 TraesCS6A01G031600 chr1B 82.063 223 15 10 366 587 658462129 658462327 1.950000e-37 167.0
23 TraesCS6A01G031600 chr3B 87.085 271 30 4 225 495 661794355 661794620 5.120000e-78 302.0
24 TraesCS6A01G031600 chr5A 86.989 269 30 5 225 492 24409104 24408840 6.630000e-77 298.0
25 TraesCS6A01G031600 chr5A 83.553 152 24 1 599 749 74938646 74938797 1.180000e-29 141.0
26 TraesCS6A01G031600 chr3D 86.813 273 26 9 225 495 500511444 500511708 2.380000e-76 296.0
27 TraesCS6A01G031600 chr4B 81.303 353 40 9 225 577 66156572 66156246 2.420000e-66 263.0
28 TraesCS6A01G031600 chr2B 88.050 159 15 3 337 495 44111177 44111331 5.380000e-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 TraesCS6A01G031600 chr6A 15871028 15874188 3160 True 2000.933333 5838 94.535333 1 3161 3 chr6A.!!$R3 3160
1 TraesCS6A01G031600 chr6A 15924020 15925256 1236 True 1096.000000 1096 82.717000 979 2217 1 chr6A.!!$R2 1238
2 TraesCS6A01G031600 chr6A 15912935 15914091 1156 True 872.000000 872 80.412000 1058 2213 1 chr6A.!!$R1 1155
3 TraesCS6A01G031600 chr6D 14518038 14520240 2202 False 1441.000000 1478 92.771500 1395 3156 2 chr6D.!!$F3 1761
4 TraesCS6A01G031600 chr6D 14687857 14691462 3605 True 1357.000000 2501 93.831000 599 2388 2 chr6D.!!$R4 1789
5 TraesCS6A01G031600 chr6D 14939783 14941177 1394 True 1109.000000 1109 81.197000 979 2385 1 chr6D.!!$R2 1406
6 TraesCS6A01G031600 chr6D 14503303 14504728 1425 False 990.000000 990 79.450000 945 2385 1 chr6D.!!$F1 1440
7 TraesCS6A01G031600 chr6D 14719206 14719789 583 True 880.000000 880 93.846000 1 585 1 chr6D.!!$R1 584
8 TraesCS6A01G031600 chr6B 26291365 26292698 1333 False 1271.000000 1271 83.890000 1041 2385 1 chr6B.!!$F1 1344
9 TraesCS6A01G031600 chr6B 28729605 28730858 1253 True 889.000000 889 79.684000 1138 2388 1 chr6B.!!$R1 1250
10 TraesCS6A01G031600 chr5D 27977946 27979315 1369 True 1007.000000 1007 80.198000 979 2379 1 chr5D.!!$R1 1400

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
915 2716 0.249699 CCCACACGCACTCACTGTTA 60.25 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 4899 0.114954 AATTTCCCCTCTGCAAGCCA 59.885 50.0 0.0 0.0 0.0 4.75 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
31 32 5.698089 TCAGAGTGTTTGAATGATGTCAGTC 59.302 40.000 3.68 3.68 40.94 3.51
71 72 7.774134 TGATAAATGGGATGATGTTGTTTCTG 58.226 34.615 0.00 0.00 0.00 3.02
86 87 8.682128 TGTTGTTTCTGTTAATGTGAAACTTC 57.318 30.769 20.74 16.26 45.51 3.01
117 118 6.239396 TCGATGGGGTGTAAGTTTGAATTAA 58.761 36.000 0.00 0.00 0.00 1.40
122 123 6.042093 TGGGGTGTAAGTTTGAATTAATGCAA 59.958 34.615 4.62 4.62 0.00 4.08
166 167 5.244402 ACCATTGACAATGCTCAAGATTTGA 59.756 36.000 20.69 0.00 37.57 2.69
181 182 1.266178 TTTGACGAGGGCTCTGATGA 58.734 50.000 0.00 0.00 0.00 2.92
217 218 8.253113 GGGAAATATTAATAACCATCAGGCATG 58.747 37.037 0.00 0.00 39.06 4.06
228 229 1.140161 CAGGCATGACCGGCAAATG 59.860 57.895 0.00 4.07 46.52 2.32
230 231 0.899717 AGGCATGACCGGCAAATGTT 60.900 50.000 0.00 0.00 46.52 2.71
244 245 6.346518 CCGGCAAATGTTGAGTTAAATTTGTC 60.347 38.462 0.00 6.34 40.50 3.18
274 275 4.149922 CACGAGCGTAATCTGTTTTCTGAA 59.850 41.667 0.00 0.00 0.00 3.02
275 276 4.150098 ACGAGCGTAATCTGTTTTCTGAAC 59.850 41.667 0.00 0.00 0.00 3.18
277 278 5.333035 CGAGCGTAATCTGTTTTCTGAACAA 60.333 40.000 0.00 0.00 0.00 2.83
304 305 8.024285 AGTGAAATTGTTTTTGTAAACGAGTGA 58.976 29.630 0.00 0.00 45.29 3.41
316 317 7.124347 TGTAAACGAGTGAAATATGTGTTCC 57.876 36.000 0.00 0.00 0.00 3.62
330 331 3.921677 TGTGTTCCGGAATAAGTGAGAC 58.078 45.455 22.04 5.21 0.00 3.36
348 349 5.296780 GTGAGACCAGTGTTTCAAAATGAGA 59.703 40.000 0.00 0.00 37.35 3.27
357 358 9.956720 CAGTGTTTCAAAATGAGAGAATTTAGT 57.043 29.630 0.00 0.00 0.00 2.24
408 409 3.423645 CGAAATGAGCGAAACCAGTTCTC 60.424 47.826 0.00 0.00 35.85 2.87
419 420 5.107298 CGAAACCAGTTCTCTGAAATGACTC 60.107 44.000 8.96 2.85 43.76 3.36
420 421 3.919216 ACCAGTTCTCTGAAATGACTCG 58.081 45.455 8.96 0.00 43.76 4.18
422 423 4.172505 CCAGTTCTCTGAAATGACTCGAG 58.827 47.826 11.84 11.84 43.76 4.04
434 435 6.704050 TGAAATGACTCGAGTATGTGTTTTGA 59.296 34.615 20.09 4.06 0.00 2.69
441 442 4.796830 TCGAGTATGTGTTTTGATACGAGC 59.203 41.667 0.00 0.00 31.46 5.03
459 460 8.958175 ATACGAGCGAAATCAATGTTTTAAAA 57.042 26.923 0.00 0.00 0.00 1.52
585 586 5.570234 TTTTAAACAAAGTGGAGCGAGTT 57.430 34.783 0.00 0.00 0.00 3.01
586 587 5.570234 TTTAAACAAAGTGGAGCGAGTTT 57.430 34.783 0.00 0.00 34.11 2.66
587 588 6.680874 TTTAAACAAAGTGGAGCGAGTTTA 57.319 33.333 0.00 0.00 32.23 2.01
588 589 4.547406 AAACAAAGTGGAGCGAGTTTAC 57.453 40.909 0.00 0.00 0.00 2.01
589 590 3.188159 ACAAAGTGGAGCGAGTTTACA 57.812 42.857 0.00 0.00 0.00 2.41
590 591 3.537580 ACAAAGTGGAGCGAGTTTACAA 58.462 40.909 0.00 0.00 0.00 2.41
591 592 3.942748 ACAAAGTGGAGCGAGTTTACAAA 59.057 39.130 0.00 0.00 0.00 2.83
592 593 4.396790 ACAAAGTGGAGCGAGTTTACAAAA 59.603 37.500 0.00 0.00 0.00 2.44
593 594 4.813296 AAGTGGAGCGAGTTTACAAAAG 57.187 40.909 0.00 0.00 0.00 2.27
594 595 4.067972 AGTGGAGCGAGTTTACAAAAGA 57.932 40.909 0.00 0.00 0.00 2.52
595 596 4.642429 AGTGGAGCGAGTTTACAAAAGAT 58.358 39.130 0.00 0.00 0.00 2.40
596 597 4.452455 AGTGGAGCGAGTTTACAAAAGATG 59.548 41.667 0.00 0.00 0.00 2.90
597 598 4.451096 GTGGAGCGAGTTTACAAAAGATGA 59.549 41.667 0.00 0.00 0.00 2.92
611 612 0.254178 AGATGATGGTCAGGTGGTGC 59.746 55.000 0.00 0.00 0.00 5.01
614 615 1.377725 GATGGTCAGGTGGTGCCAG 60.378 63.158 0.00 0.00 40.61 4.85
688 689 1.726853 AGGACAGCGTGCATCTTAAC 58.273 50.000 0.00 0.00 0.00 2.01
700 701 4.851558 GTGCATCTTAACGTTGAAATGGAC 59.148 41.667 13.67 13.67 0.00 4.02
704 705 1.880271 TAACGTTGAAATGGACGGCA 58.120 45.000 11.99 0.00 43.16 5.69
748 787 8.146479 ACCGGTTCCGATAAATTTACTTATTC 57.854 34.615 13.08 0.00 0.00 1.75
799 2600 3.224324 GGCCGGGCATACGAGAGA 61.224 66.667 25.33 0.00 35.47 3.10
801 2602 1.367840 GCCGGGCATACGAGAGATT 59.632 57.895 15.62 0.00 35.47 2.40
817 2618 8.287439 ACGAGAGATTAAAATTGAGAGAGAGA 57.713 34.615 0.00 0.00 0.00 3.10
819 2620 8.620416 CGAGAGATTAAAATTGAGAGAGAGAGA 58.380 37.037 0.00 0.00 0.00 3.10
820 2621 9.956720 GAGAGATTAAAATTGAGAGAGAGAGAG 57.043 37.037 0.00 0.00 0.00 3.20
821 2622 8.917088 AGAGATTAAAATTGAGAGAGAGAGAGG 58.083 37.037 0.00 0.00 0.00 3.69
822 2623 8.837099 AGATTAAAATTGAGAGAGAGAGAGGA 57.163 34.615 0.00 0.00 0.00 3.71
824 2625 4.981806 AAATTGAGAGAGAGAGAGGACG 57.018 45.455 0.00 0.00 0.00 4.79
825 2626 1.745232 TTGAGAGAGAGAGAGGACGC 58.255 55.000 0.00 0.00 0.00 5.19
826 2627 0.615850 TGAGAGAGAGAGAGGACGCA 59.384 55.000 0.00 0.00 0.00 5.24
827 2628 1.003696 TGAGAGAGAGAGAGGACGCAA 59.996 52.381 0.00 0.00 0.00 4.85
912 2713 3.349006 GCCCACACGCACTCACTG 61.349 66.667 0.00 0.00 0.00 3.66
915 2716 0.249699 CCCACACGCACTCACTGTTA 60.250 55.000 0.00 0.00 0.00 2.41
916 2717 1.139989 CCACACGCACTCACTGTTAG 58.860 55.000 0.00 0.00 0.00 2.34
917 2718 1.139989 CACACGCACTCACTGTTAGG 58.860 55.000 0.00 0.00 0.00 2.69
918 2719 0.750850 ACACGCACTCACTGTTAGGT 59.249 50.000 0.00 0.00 0.00 3.08
919 2720 1.139989 CACGCACTCACTGTTAGGTG 58.860 55.000 0.00 0.00 38.44 4.00
920 2721 0.750850 ACGCACTCACTGTTAGGTGT 59.249 50.000 0.00 0.00 38.28 4.16
928 2736 0.462375 ACTGTTAGGTGTGACACGCA 59.538 50.000 20.15 5.35 34.83 5.24
1086 2913 2.043450 CTCCACCGGCTCCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
1089 2916 4.504916 CACCGGCTCCTCTCTGCG 62.505 72.222 0.00 0.00 0.00 5.18
1153 2992 4.198625 AGGACTACCTCGTCGACG 57.801 61.111 31.30 31.30 44.13 5.12
1621 3463 1.683707 TGCATCTCTGAGCCGAGGT 60.684 57.895 0.00 0.00 0.00 3.85
1714 3556 0.608035 GGGGATGTTCAAGGTTGCGA 60.608 55.000 0.00 0.00 0.00 5.10
1783 3625 3.490399 GACTACCTGAAGAAGACGTTCG 58.510 50.000 0.00 0.00 37.79 3.95
1839 3681 1.246056 TGGCTCCAATGCTGCTCAAC 61.246 55.000 0.00 0.00 0.00 3.18
1897 3739 1.376553 GTCTCTGAGGTGGGCTTGC 60.377 63.158 4.59 0.00 0.00 4.01
2058 3900 6.839134 TCACTAGGCCTGAGAAGTATTTCATA 59.161 38.462 17.99 0.00 35.70 2.15
2090 3932 8.559464 TGCATATGCCCTTACAAGGAATCTGT 62.559 42.308 24.54 0.00 46.11 3.41
2109 3951 2.224281 TGTACCACACCTTGCTGAAGAG 60.224 50.000 0.00 0.00 0.00 2.85
2183 4025 4.344978 ACCAGAAAAGGGCTAAGGAAATC 58.655 43.478 0.00 0.00 0.00 2.17
2207 4053 0.454957 GCTTGTGTATGGCGCAACAG 60.455 55.000 10.83 0.09 42.05 3.16
2249 4101 2.105821 CTGGTACTCCCTGTTTTGGTGA 59.894 50.000 0.00 0.00 0.00 4.02
2300 4592 5.276461 TCTGTAGTATGCCTGTTACATGG 57.724 43.478 0.00 0.00 0.00 3.66
2376 4682 4.398988 TGAACCCTGATATGTTGATGTTGC 59.601 41.667 0.00 0.00 0.00 4.17
2385 4691 3.663995 TGTTGATGTTGCCATTCCTTG 57.336 42.857 0.00 0.00 0.00 3.61
2410 4716 7.662669 TGGATCATATGATGTGTTTAGTGATGG 59.337 37.037 22.86 0.00 34.37 3.51
2429 4735 0.802494 GCATTGACACCTTACACCCG 59.198 55.000 0.00 0.00 0.00 5.28
2441 4747 4.162698 ACCTTACACCCGCTGTTCATTATA 59.837 41.667 0.00 0.00 33.91 0.98
2442 4748 5.120399 CCTTACACCCGCTGTTCATTATAA 58.880 41.667 0.00 0.00 33.91 0.98
2444 4750 6.094325 CCTTACACCCGCTGTTCATTATAAAA 59.906 38.462 0.00 0.00 33.91 1.52
2468 4780 1.340088 AGTGGCAAATTGATGTGGCA 58.660 45.000 6.33 6.33 46.84 4.92
2495 4807 0.314302 CGGTCCTCCAGGCTATAACG 59.686 60.000 0.00 0.00 34.44 3.18
2501 4813 5.048507 GTCCTCCAGGCTATAACGTAAAAG 58.951 45.833 0.00 0.00 34.44 2.27
2505 4817 4.467082 TCCAGGCTATAACGTAAAAGTGGA 59.533 41.667 0.00 0.00 0.00 4.02
2535 4847 1.058428 AGCATATGAGCTGGCCCTCA 61.058 55.000 13.34 13.34 44.66 3.86
2538 4850 1.419012 CATATGAGCTGGCCCTCAAGA 59.581 52.381 14.72 7.43 44.34 3.02
2564 4876 9.651913 ACTATAATAAAACAGTTTTGGCATTGG 57.348 29.630 19.77 9.61 34.19 3.16
2577 4889 1.892474 GGCATTGGCACCTTACTGAAA 59.108 47.619 5.17 0.00 43.71 2.69
2587 4899 4.000988 CACCTTACTGAAAACTATGCGGT 58.999 43.478 0.00 0.00 0.00 5.68
2588 4900 4.000988 ACCTTACTGAAAACTATGCGGTG 58.999 43.478 0.00 0.00 0.00 4.94
2595 4907 0.893270 AAACTATGCGGTGGCTTGCA 60.893 50.000 1.69 1.69 46.51 4.08
2636 4948 1.353804 TGCCGTCGCAAAAACAGTC 59.646 52.632 0.00 0.00 43.74 3.51
2654 4966 3.189287 CAGTCTTGGCATTGACACCTTAC 59.811 47.826 18.76 0.00 35.81 2.34
2655 4967 3.146066 GTCTTGGCATTGACACCTTACA 58.854 45.455 13.82 0.00 33.75 2.41
2659 4971 0.802494 GCATTGACACCTTACACCCG 59.198 55.000 0.00 0.00 0.00 5.28
2678 4990 6.600032 ACACCCGCTGTTCATTATAACATAAA 59.400 34.615 0.00 0.00 38.61 1.40
2679 4991 7.121463 ACACCCGCTGTTCATTATAACATAAAA 59.879 33.333 0.00 0.00 38.61 1.52
2680 4992 8.134895 CACCCGCTGTTCATTATAACATAAAAT 58.865 33.333 0.00 0.00 38.61 1.82
2745 5057 6.673154 TGATTGTGTCTAATGATGCAAGAG 57.327 37.500 0.00 0.00 0.00 2.85
2776 5089 1.280457 CCCCTCTACTGTTCCTTGCT 58.720 55.000 0.00 0.00 0.00 3.91
2811 5125 5.964958 TTTCTGGAGATCAATGGTCAAAC 57.035 39.130 0.00 0.00 0.00 2.93
2813 5127 5.183530 TCTGGAGATCAATGGTCAAACAT 57.816 39.130 0.00 0.00 0.00 2.71
2814 5128 5.573219 TCTGGAGATCAATGGTCAAACATT 58.427 37.500 0.00 0.00 41.51 2.71
2818 5132 6.267242 TGGAGATCAATGGTCAAACATTTTCA 59.733 34.615 0.00 0.00 38.94 2.69
2846 5160 2.391616 TCGCATGAAAGATCACTGCT 57.608 45.000 0.00 0.00 38.69 4.24
2884 5198 6.579666 ATGAAGAGAAAACTGCAGCAATTA 57.420 33.333 15.27 0.00 0.00 1.40
2956 5270 8.587950 GCAAGATGAACAATATAGTATACGCTC 58.412 37.037 0.00 0.00 0.00 5.03
2965 5279 9.204570 ACAATATAGTATACGCTCATTGGAAAC 57.795 33.333 18.34 0.00 31.09 2.78
2999 5313 7.124573 ACACTAATGTTCATGAGTGGCTATA 57.875 36.000 25.21 0.00 42.93 1.31
3000 5314 7.739825 ACACTAATGTTCATGAGTGGCTATAT 58.260 34.615 25.21 8.40 42.93 0.86
3022 5336 1.593196 TTCCTGAAGGTTGCTTCACG 58.407 50.000 0.00 0.00 38.30 4.35
3042 5356 6.504398 TCACGTTAATCTCAGGACATGATAC 58.496 40.000 0.00 0.00 37.28 2.24
3057 5371 6.072838 GGACATGATACGATGAAAGCAATGAT 60.073 38.462 0.00 0.00 0.00 2.45
3082 5396 6.810911 TCACTAGAGCAGATAGATTTGGTTC 58.189 40.000 0.00 0.00 0.00 3.62
3100 5414 3.477530 GTTCCAAGCAAGTAGTGAGGTT 58.522 45.455 0.00 0.00 0.00 3.50
3141 5455 4.661993 TGCTTTTAAGTAGTGCATGACG 57.338 40.909 0.00 0.00 0.00 4.35
3156 5470 0.107703 TGACGCAGATAAAGGCCAGG 60.108 55.000 5.01 0.00 0.00 4.45
3157 5471 0.107654 GACGCAGATAAAGGCCAGGT 60.108 55.000 5.01 0.00 0.00 4.00
3158 5472 1.138266 GACGCAGATAAAGGCCAGGTA 59.862 52.381 5.01 0.00 0.00 3.08
3159 5473 1.134491 ACGCAGATAAAGGCCAGGTAC 60.134 52.381 5.01 0.00 0.00 3.34
3160 5474 1.134521 CGCAGATAAAGGCCAGGTACA 60.135 52.381 5.01 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 7.592938 TCACATTAACAGAAACAACATCATCC 58.407 34.615 0.00 0.00 0.00 3.51
117 118 9.372369 GTTTTAAGACAGACTAGATAGTTGCAT 57.628 33.333 0.00 0.00 36.50 3.96
122 123 9.877178 CAATGGTTTTAAGACAGACTAGATAGT 57.123 33.333 0.00 0.00 39.71 2.12
166 167 0.976641 TTGTTCATCAGAGCCCTCGT 59.023 50.000 0.00 0.00 34.09 4.18
181 182 7.977293 GGTTATTAATATTTCCCTTGCGTTGTT 59.023 33.333 0.00 0.00 0.00 2.83
217 218 3.907894 TTAACTCAACATTTGCCGGTC 57.092 42.857 1.90 0.00 0.00 4.79
228 229 8.311120 CGTGTCAAAAGACAAATTTAACTCAAC 58.689 33.333 0.00 0.00 36.77 3.18
230 231 7.753659 TCGTGTCAAAAGACAAATTTAACTCA 58.246 30.769 0.00 0.00 36.77 3.41
244 245 3.428870 ACAGATTACGCTCGTGTCAAAAG 59.571 43.478 5.05 0.00 0.00 2.27
274 275 8.979574 TCGTTTACAAAAACAATTTCACTTTGT 58.020 25.926 4.18 4.18 44.37 2.83
275 276 9.459276 CTCGTTTACAAAAACAATTTCACTTTG 57.541 29.630 2.33 0.00 44.37 2.77
277 278 8.643752 CACTCGTTTACAAAAACAATTTCACTT 58.356 29.630 2.33 0.00 44.37 3.16
304 305 7.280205 GTCTCACTTATTCCGGAACACATATTT 59.720 37.037 21.56 3.11 0.00 1.40
316 317 3.594603 ACACTGGTCTCACTTATTCCG 57.405 47.619 0.00 0.00 0.00 4.30
330 331 9.403110 CTAAATTCTCTCATTTTGAAACACTGG 57.597 33.333 0.00 0.00 0.00 4.00
408 409 6.712241 AAACACATACTCGAGTCATTTCAG 57.288 37.500 23.89 9.29 0.00 3.02
419 420 4.316446 CGCTCGTATCAAAACACATACTCG 60.316 45.833 0.00 0.00 0.00 4.18
420 421 4.796830 TCGCTCGTATCAAAACACATACTC 59.203 41.667 0.00 0.00 0.00 2.59
422 423 5.444586 TTCGCTCGTATCAAAACACATAC 57.555 39.130 0.00 0.00 0.00 2.39
434 435 8.958175 TTTTAAAACATTGATTTCGCTCGTAT 57.042 26.923 0.00 0.00 0.00 3.06
504 505 8.995906 GTCATTCGGAAATACAAATTTAACTCG 58.004 33.333 0.00 0.00 35.41 4.18
516 517 8.742554 AACAAATTTGAGTCATTCGGAAATAC 57.257 30.769 24.64 0.00 0.00 1.89
566 567 5.117584 TGTAAACTCGCTCCACTTTGTTTA 58.882 37.500 0.00 0.00 0.00 2.01
579 580 5.106712 TGACCATCATCTTTTGTAAACTCGC 60.107 40.000 0.00 0.00 0.00 5.03
585 586 5.009631 CCACCTGACCATCATCTTTTGTAA 58.990 41.667 0.00 0.00 0.00 2.41
586 587 4.042809 ACCACCTGACCATCATCTTTTGTA 59.957 41.667 0.00 0.00 0.00 2.41
587 588 3.181429 ACCACCTGACCATCATCTTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
588 589 3.192001 CACCACCTGACCATCATCTTTTG 59.808 47.826 0.00 0.00 0.00 2.44
589 590 3.424703 CACCACCTGACCATCATCTTTT 58.575 45.455 0.00 0.00 0.00 2.27
590 591 2.881403 GCACCACCTGACCATCATCTTT 60.881 50.000 0.00 0.00 0.00 2.52
591 592 1.340405 GCACCACCTGACCATCATCTT 60.340 52.381 0.00 0.00 0.00 2.40
592 593 0.254178 GCACCACCTGACCATCATCT 59.746 55.000 0.00 0.00 0.00 2.90
593 594 0.749454 GGCACCACCTGACCATCATC 60.749 60.000 0.00 0.00 34.51 2.92
594 595 1.304282 GGCACCACCTGACCATCAT 59.696 57.895 0.00 0.00 34.51 2.45
595 596 2.128290 CTGGCACCACCTGACCATCA 62.128 60.000 0.00 0.00 39.72 3.07
596 597 1.377725 CTGGCACCACCTGACCATC 60.378 63.158 0.00 0.00 39.72 3.51
597 598 1.847506 TCTGGCACCACCTGACCAT 60.848 57.895 0.00 0.00 41.17 3.55
676 677 3.845775 CCATTTCAACGTTAAGATGCACG 59.154 43.478 0.00 0.00 42.29 5.34
688 689 1.086696 ATCTGCCGTCCATTTCAACG 58.913 50.000 0.00 0.00 38.58 4.10
700 701 0.249447 TACCGATGAAGCATCTGCCG 60.249 55.000 5.94 0.00 43.38 5.69
704 705 4.258702 GGTATGTACCGATGAAGCATCT 57.741 45.455 5.94 0.00 38.59 2.90
727 766 7.073883 GGCCGAATAAGTAAATTTATCGGAAC 58.926 38.462 28.68 20.20 36.69 3.62
748 787 1.228429 TGAAGAGGGTTTTGGGCCG 60.228 57.895 0.00 0.00 0.00 6.13
780 2577 3.214250 CTCTCGTATGCCCGGCCTC 62.214 68.421 7.03 0.00 0.00 4.70
799 2600 7.488322 CGTCCTCTCTCTCTCTCAATTTTAAT 58.512 38.462 0.00 0.00 0.00 1.40
801 2602 5.163602 GCGTCCTCTCTCTCTCTCAATTTTA 60.164 44.000 0.00 0.00 0.00 1.52
920 2721 4.994201 GACGGCGAGTGCGTGTCA 62.994 66.667 16.62 0.00 44.10 3.58
928 2736 2.279918 AAGTTTGCGACGGCGAGT 60.280 55.556 18.90 0.00 44.10 4.18
950 2758 4.619394 CGAGGAAGATATTTCCGATGGGAG 60.619 50.000 0.00 0.00 44.98 4.30
1580 3422 2.679837 AGCTTGGTAATGTCGCAATCAG 59.320 45.455 0.00 0.00 0.00 2.90
1590 3432 3.064958 CAGAGATGCACAGCTTGGTAATG 59.935 47.826 0.00 0.00 0.00 1.90
1621 3463 0.749818 TCCAGTTTGTTGCCGAGCAA 60.750 50.000 7.15 7.15 46.80 3.91
1714 3556 0.833287 AGGAATGCGACAGCCTGTAT 59.167 50.000 0.00 0.00 44.33 2.29
1783 3625 1.450312 CCTCAGCATCCGACCAACC 60.450 63.158 0.00 0.00 0.00 3.77
1839 3681 1.271543 TGCAGGATGTCCTTTGACCTG 60.272 52.381 0.00 0.00 46.09 4.00
1897 3739 0.322098 TGAGCAATGTACCCCGGTTG 60.322 55.000 0.00 0.00 0.00 3.77
2090 3932 2.047061 ACTCTTCAGCAAGGTGTGGTA 58.953 47.619 0.00 0.00 35.75 3.25
2109 3951 2.044832 CTCTGCAAGCTGCCGCATAC 62.045 60.000 13.84 0.00 44.23 2.39
2183 4025 1.134487 CGCCATACACAAGCAACCG 59.866 57.895 0.00 0.00 0.00 4.44
2207 4053 5.582665 CCAGCTTGGTATAGAGTGAAAACTC 59.417 44.000 0.00 0.00 33.20 3.01
2223 4069 0.693049 AACAGGGAGTACCAGCTTGG 59.307 55.000 0.00 1.16 45.02 3.61
2224 4070 2.554032 CAAAACAGGGAGTACCAGCTTG 59.446 50.000 0.00 0.00 43.89 4.01
2236 4088 2.289010 GGCAAAGATCACCAAAACAGGG 60.289 50.000 0.00 0.00 0.00 4.45
2249 4101 5.079643 ACCAACATCTAGTTTGGCAAAGAT 58.920 37.500 13.94 9.94 38.74 2.40
2300 4592 3.368843 GCATTTAGCAATGACCAAACTGC 59.631 43.478 1.12 0.00 42.35 4.40
2385 4691 7.361542 GCCATCACTAAACACATCATATGATCC 60.362 40.741 15.49 0.00 31.21 3.36
2410 4716 0.802494 CGGGTGTAAGGTGTCAATGC 59.198 55.000 0.00 0.00 0.00 3.56
2429 4735 9.364989 TGCCACTTTTATTTTATAATGAACAGC 57.635 29.630 0.00 0.00 0.00 4.40
2441 4747 7.521910 GCCACATCAATTTGCCACTTTTATTTT 60.522 33.333 0.00 0.00 0.00 1.82
2442 4748 6.072563 GCCACATCAATTTGCCACTTTTATTT 60.073 34.615 0.00 0.00 0.00 1.40
2444 4750 4.937015 GCCACATCAATTTGCCACTTTTAT 59.063 37.500 0.00 0.00 0.00 1.40
2468 4780 1.645710 CCTGGAGGACCGGCTAATAT 58.354 55.000 0.00 0.00 40.99 1.28
2479 4791 4.713321 ACTTTTACGTTATAGCCTGGAGGA 59.287 41.667 0.00 0.00 37.39 3.71
2495 4807 8.986477 ATGCTACATCAATTTTCCACTTTTAC 57.014 30.769 0.00 0.00 0.00 2.01
2501 4813 6.860023 GCTCATATGCTACATCAATTTTCCAC 59.140 38.462 0.00 0.00 0.00 4.02
2505 4817 6.516194 GCCAGCTCATATGCTACATCAATTTT 60.516 38.462 0.00 0.00 41.98 1.82
2514 4826 0.689623 AGGGCCAGCTCATATGCTAC 59.310 55.000 6.18 0.00 41.98 3.58
2516 4828 1.058428 TGAGGGCCAGCTCATATGCT 61.058 55.000 6.18 0.00 45.18 3.79
2527 4839 6.964464 TGTTTTATTATAGTCTTGAGGGCCA 58.036 36.000 6.18 0.00 0.00 5.36
2538 4850 9.651913 CCAATGCCAAAACTGTTTTATTATAGT 57.348 29.630 17.31 1.32 0.00 2.12
2564 4876 3.181510 CCGCATAGTTTTCAGTAAGGTGC 60.182 47.826 0.00 0.00 0.00 5.01
2577 4889 1.303236 TGCAAGCCACCGCATAGTT 60.303 52.632 0.00 0.00 37.52 2.24
2587 4899 0.114954 AATTTCCCCTCTGCAAGCCA 59.885 50.000 0.00 0.00 0.00 4.75
2588 4900 0.533951 CAATTTCCCCTCTGCAAGCC 59.466 55.000 0.00 0.00 0.00 4.35
2595 4907 1.358787 TGCCACATCAATTTCCCCTCT 59.641 47.619 0.00 0.00 0.00 3.69
2622 4934 1.202245 TGCCAAGACTGTTTTTGCGAC 60.202 47.619 3.31 0.00 0.00 5.19
2625 4937 3.245990 GTCAATGCCAAGACTGTTTTTGC 59.754 43.478 0.84 0.84 0.00 3.68
2636 4948 2.228822 GGTGTAAGGTGTCAATGCCAAG 59.771 50.000 0.00 0.00 0.00 3.61
2654 4966 6.612247 TTATGTTATAATGAACAGCGGGTG 57.388 37.500 5.50 5.50 42.38 4.61
2655 4967 7.633193 TTTTATGTTATAATGAACAGCGGGT 57.367 32.000 0.00 0.00 42.38 5.28
2679 4991 9.638239 CACTAAACACATAAATTTGCCACTTAT 57.362 29.630 0.00 0.00 0.00 1.73
2680 4992 8.851145 TCACTAAACACATAAATTTGCCACTTA 58.149 29.630 0.00 0.00 0.00 2.24
2726 5038 3.370846 CCCCTCTTGCATCATTAGACACA 60.371 47.826 0.00 0.00 0.00 3.72
2788 5101 5.832595 TGTTTGACCATTGATCTCCAGAAAA 59.167 36.000 0.00 0.00 0.00 2.29
2811 5125 9.467990 CTTTCATGCGATTTAACAATGAAAATG 57.532 29.630 9.59 0.00 36.51 2.32
2813 5127 8.809159 TCTTTCATGCGATTTAACAATGAAAA 57.191 26.923 9.59 0.00 36.51 2.29
2814 5128 8.984891 ATCTTTCATGCGATTTAACAATGAAA 57.015 26.923 8.38 8.38 35.88 2.69
2818 5132 7.699391 CAGTGATCTTTCATGCGATTTAACAAT 59.301 33.333 0.00 0.00 33.56 2.71
2884 5198 9.248291 CATTTGCAGTTTATACACAAAAGAAGT 57.752 29.630 8.01 0.00 36.67 3.01
2984 5298 8.206126 TCAGGAATTATATAGCCACTCATGAA 57.794 34.615 0.00 0.00 0.00 2.57
3022 5336 7.371159 TCATCGTATCATGTCCTGAGATTAAC 58.629 38.462 0.00 0.00 37.28 2.01
3042 5356 6.594284 TCTAGTGAATCATTGCTTTCATCG 57.406 37.500 5.52 0.00 34.60 3.84
3057 5371 6.798427 ACCAAATCTATCTGCTCTAGTGAA 57.202 37.500 0.00 0.00 0.00 3.18
3082 5396 4.002906 TGTAACCTCACTACTTGCTTGG 57.997 45.455 0.00 0.00 0.00 3.61
3134 5448 0.308993 GGCCTTTATCTGCGTCATGC 59.691 55.000 0.00 0.00 46.70 4.06
3141 5455 2.710096 TGTACCTGGCCTTTATCTGC 57.290 50.000 3.32 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.