Multiple sequence alignment - TraesCS1B01G326100

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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 TraesCS1B01G326100 chr1B 100.000 5030 0 0 1 5030 551720629 551725658 0.000000e+00 9289
1 TraesCS1B01G326100 chr1D 94.094 4470 174 37 29 4437 409534959 409539399 0.000000e+00 6709
2 TraesCS1B01G326100 chr1D 95.109 368 17 1 4493 4860 409539398 409539764 3.380000e-161 579
3 TraesCS1B01G326100 chr1D 91.603 131 10 1 4901 5030 409539949 409540079 4.000000e-41 180
4 TraesCS1B01G326100 chr1A 93.375 3698 153 36 175 3838 505536954 505540593 0.000000e+00 5387
5 TraesCS1B01G326100 chr1A 90.339 1180 60 10 3861 5017 505540872 505542020 0.000000e+00 1498
6 TraesCS1B01G326100 chr5B 84.624 1756 182 52 2492 4212 582834178 582835880 0.000000e+00 1666
7 TraesCS1B01G326100 chr5B 86.412 942 97 19 23 945 692786562 692785633 0.000000e+00 1002
8 TraesCS1B01G326100 chr5B 84.326 957 109 31 22 943 12860603 12859653 0.000000e+00 898
9 TraesCS1B01G326100 chr5B 82.312 995 113 31 1525 2473 582833213 582834190 0.000000e+00 804
10 TraesCS1B01G326100 chr5B 87.080 565 56 11 972 1520 582832611 582833174 1.540000e-174 623
11 TraesCS1B01G326100 chr5A 84.379 1626 171 39 2607 4212 594954759 594956321 0.000000e+00 1519
12 TraesCS1B01G326100 chr5A 83.646 960 109 28 23 943 9856882 9855932 0.000000e+00 859
13 TraesCS1B01G326100 chr5A 81.809 995 117 35 1525 2477 594953722 594954694 0.000000e+00 776
14 TraesCS1B01G326100 chr5A 86.562 573 60 7 972 1528 594953120 594953691 2.570000e-172 616
15 TraesCS1B01G326100 chr5A 88.538 253 23 6 8 257 658008565 658008316 8.180000e-78 302
16 TraesCS1B01G326100 chr5A 88.446 251 22 6 25 273 13983443 13983198 3.810000e-76 296
17 TraesCS1B01G326100 chr5A 88.034 234 21 5 8 238 272387585 272387356 2.310000e-68 270
18 TraesCS1B01G326100 chr5A 77.907 172 32 5 2154 2324 594978189 594978355 8.910000e-18 102
19 TraesCS1B01G326100 chr5D 87.638 1181 106 25 3046 4212 475501802 475502956 0.000000e+00 1336
20 TraesCS1B01G326100 chr5D 80.556 1440 174 64 1620 3013 475500421 475501800 0.000000e+00 1011
21 TraesCS1B01G326100 chr5D 85.057 957 102 24 23 943 12992747 12991796 0.000000e+00 937
22 TraesCS1B01G326100 chr5D 83.613 952 97 27 32 953 114628119 114627197 0.000000e+00 839
23 TraesCS1B01G326100 chr5D 86.287 649 66 14 313 942 486900302 486899658 0.000000e+00 684
24 TraesCS1B01G326100 chr5D 86.092 568 58 5 972 1528 475499757 475500314 4.340000e-165 592
25 TraesCS1B01G326100 chr6A 85.285 931 94 24 31 943 579956388 579955483 0.000000e+00 920
26 TraesCS1B01G326100 chr6D 84.607 929 105 20 31 943 433769291 433768385 0.000000e+00 889
27 TraesCS1B01G326100 chr7B 83.192 946 105 25 15 937 26739144 26740058 0.000000e+00 817
28 TraesCS1B01G326100 chr6B 87.979 574 53 12 31 596 656034333 656033768 0.000000e+00 664


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 TraesCS1B01G326100 chr1B 551720629 551725658 5029 False 9289.000000 9289 100.000 1 5030 1 chr1B.!!$F1 5029
1 TraesCS1B01G326100 chr1D 409534959 409540079 5120 False 2489.333333 6709 93.602 29 5030 3 chr1D.!!$F1 5001
2 TraesCS1B01G326100 chr1A 505536954 505542020 5066 False 3442.500000 5387 91.857 175 5017 2 chr1A.!!$F1 4842
3 TraesCS1B01G326100 chr5B 582832611 582835880 3269 False 1031.000000 1666 84.672 972 4212 3 chr5B.!!$F1 3240
4 TraesCS1B01G326100 chr5B 692785633 692786562 929 True 1002.000000 1002 86.412 23 945 1 chr5B.!!$R2 922
5 TraesCS1B01G326100 chr5B 12859653 12860603 950 True 898.000000 898 84.326 22 943 1 chr5B.!!$R1 921
6 TraesCS1B01G326100 chr5A 594953120 594956321 3201 False 970.333333 1519 84.250 972 4212 3 chr5A.!!$F2 3240
7 TraesCS1B01G326100 chr5A 9855932 9856882 950 True 859.000000 859 83.646 23 943 1 chr5A.!!$R1 920
8 TraesCS1B01G326100 chr5D 475499757 475502956 3199 False 979.666667 1336 84.762 972 4212 3 chr5D.!!$F1 3240
9 TraesCS1B01G326100 chr5D 12991796 12992747 951 True 937.000000 937 85.057 23 943 1 chr5D.!!$R1 920
10 TraesCS1B01G326100 chr5D 114627197 114628119 922 True 839.000000 839 83.613 32 953 1 chr5D.!!$R2 921
11 TraesCS1B01G326100 chr5D 486899658 486900302 644 True 684.000000 684 86.287 313 942 1 chr5D.!!$R3 629
12 TraesCS1B01G326100 chr6A 579955483 579956388 905 True 920.000000 920 85.285 31 943 1 chr6A.!!$R1 912
13 TraesCS1B01G326100 chr6D 433768385 433769291 906 True 889.000000 889 84.607 31 943 1 chr6D.!!$R1 912
14 TraesCS1B01G326100 chr7B 26739144 26740058 914 False 817.000000 817 83.192 15 937 1 chr7B.!!$F1 922
15 TraesCS1B01G326100 chr6B 656033768 656034333 565 True 664.000000 664 87.979 31 596 1 chr6B.!!$R1 565

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
27 28 0.406361 ACTCACTCCTTCGTCCTCCT 59.594 55.0 0.00 0.0 0.0 3.69 F
1053 1145 0.824109 AGATCGGCAAGTTCATCGGA 59.176 50.0 0.00 0.0 0.0 4.55 F
1477 1586 0.036875 CTTTCCTGCCGTCTTTCCCT 59.963 55.0 0.00 0.0 0.0 4.20 F
2547 2791 0.251698 TTGGACCCATGCATTGCTGA 60.252 50.0 10.49 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1266 0.533308 AGTTTTCCGCCGTGTTAGCA 60.533 50.000 0.0 0.0 0.00 3.49 R
2826 3079 3.003897 GCCATAAGTTCCAAACACACGAA 59.996 43.478 0.0 0.0 0.00 3.85 R
3427 3700 0.247460 GGCCCTGCAAAGTGGAAATC 59.753 55.000 0.0 0.0 0.00 2.17 R
4431 5003 0.392998 AACATTGTAGCTCCCAGCCG 60.393 55.000 0.0 0.0 43.77 5.52 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
20 21 1.739562 GCCAGCACTCACTCCTTCG 60.740 63.158 0.00 0.00 0.00 3.79
27 28 0.406361 ACTCACTCCTTCGTCCTCCT 59.594 55.000 0.00 0.00 0.00 3.69
85 87 2.418471 CCTCTTGCATCCTCTGTCTGTC 60.418 54.545 0.00 0.00 0.00 3.51
93 98 3.703001 TCCTCTGTCTGTCCATTTTCC 57.297 47.619 0.00 0.00 0.00 3.13
97 102 1.355720 CTGTCTGTCCATTTTCCCCCT 59.644 52.381 0.00 0.00 0.00 4.79
105 110 4.293634 TGTCCATTTTCCCCCTCTGATTTA 59.706 41.667 0.00 0.00 0.00 1.40
126 131 1.795872 TGTATTGGACGAACACTTGCG 59.204 47.619 0.00 0.00 0.00 4.85
158 164 9.996554 TTGGATATTGTGAGAATATAACGATGT 57.003 29.630 0.00 0.00 0.00 3.06
160 166 9.088512 GGATATTGTGAGAATATAACGATGTCC 57.911 37.037 0.00 0.00 38.22 4.02
185 195 3.329386 TCTTGATGAGTACTTGCTGCAC 58.671 45.455 0.00 0.00 0.00 4.57
215 233 4.444536 TCCAGTGCGTGTTAAAGTTTACT 58.555 39.130 0.00 0.00 0.00 2.24
232 250 6.872920 AGTTTACTTGTGAAAGGATTTTGCA 58.127 32.000 0.00 0.00 39.27 4.08
467 505 3.844211 AGGAGCCTTGTCTTGGTTATACA 59.156 43.478 0.00 0.00 0.00 2.29
484 522 6.127675 GGTTATACAGGCCGAAATTGGTTAAA 60.128 38.462 0.00 0.00 0.00 1.52
584 637 6.127758 TGCTGTGTTGTTGATTTTAACAGTCT 60.128 34.615 0.00 0.00 41.18 3.24
744 812 7.994194 ACACTTACTAAAGTCTAACTATCCCG 58.006 38.462 0.00 0.00 44.28 5.14
752 820 3.450096 AGTCTAACTATCCCGTTGGAACC 59.550 47.826 0.00 0.00 45.98 3.62
769 837 2.155065 CCTGGAGTTGGAACAGGGT 58.845 57.895 0.00 0.00 46.24 4.34
1053 1145 0.824109 AGATCGGCAAGTTCATCGGA 59.176 50.000 0.00 0.00 0.00 4.55
1132 1224 1.381191 GGCCCCCGAACCATCAAAT 60.381 57.895 0.00 0.00 0.00 2.32
1143 1241 4.096382 CGAACCATCAAATTTCGATTCCCT 59.904 41.667 0.00 0.00 43.83 4.20
1194 1294 2.867472 CGGAAAACTGCGGCGATT 59.133 55.556 12.98 0.00 0.00 3.34
1326 1426 0.600255 CCAACGTGCTCCGACTCTTT 60.600 55.000 3.38 0.00 40.70 2.52
1452 1552 3.325753 GCCACAGTGAGCCCTCCT 61.326 66.667 0.62 0.00 0.00 3.69
1477 1586 0.036875 CTTTCCTGCCGTCTTTCCCT 59.963 55.000 0.00 0.00 0.00 4.20
1504 1614 1.061421 TGCGGCGTTTATTGATTCGAC 59.939 47.619 9.37 0.00 0.00 4.20
1550 1694 4.180057 TGCAATGAAGCTTGAACGTTTTT 58.820 34.783 2.10 0.00 34.99 1.94
1742 1918 6.363357 GTGTTTAGTCATGCCTTGTTGAAATC 59.637 38.462 0.00 0.00 0.00 2.17
1884 2060 0.746063 CACAAGGCAAAAGCCTCACA 59.254 50.000 9.77 0.00 39.63 3.58
2007 2184 2.158593 TCCAACCCGAAGATCCAAACAA 60.159 45.455 0.00 0.00 0.00 2.83
2012 2190 4.070009 ACCCGAAGATCCAAACAAAGTAC 58.930 43.478 0.00 0.00 0.00 2.73
2150 2332 6.017109 TGTTGCTTTTCTTCTGACTTACCATC 60.017 38.462 0.00 0.00 0.00 3.51
2330 2521 0.536687 CAGATGCTGCACCCCTATGG 60.537 60.000 3.57 0.00 41.37 2.74
2467 2667 9.793252 ATTCAACTACATCATTGCTGTAAATTC 57.207 29.630 2.34 0.00 0.00 2.17
2473 2673 5.887598 ACATCATTGCTGTAAATTCTGCCTA 59.112 36.000 0.00 0.00 0.00 3.93
2547 2791 0.251698 TTGGACCCATGCATTGCTGA 60.252 50.000 10.49 0.00 0.00 4.26
2826 3079 9.231297 ACATTTGTAACTGAAGCACTATACATT 57.769 29.630 0.00 0.00 0.00 2.71
2847 3101 4.822036 TTCGTGTGTTTGGAACTTATGG 57.178 40.909 0.00 0.00 0.00 2.74
2852 3106 3.900601 TGTGTTTGGAACTTATGGCCATT 59.099 39.130 26.37 6.21 0.00 3.16
2853 3107 4.244862 GTGTTTGGAACTTATGGCCATTG 58.755 43.478 26.37 19.23 0.00 2.82
2854 3108 3.260380 TGTTTGGAACTTATGGCCATTGG 59.740 43.478 26.37 18.76 0.00 3.16
2855 3109 2.917713 TGGAACTTATGGCCATTGGT 57.082 45.000 26.37 19.43 0.00 3.67
2856 3110 2.455557 TGGAACTTATGGCCATTGGTG 58.544 47.619 26.37 13.77 0.00 4.17
2857 3111 2.042297 TGGAACTTATGGCCATTGGTGA 59.958 45.455 26.37 1.26 0.00 4.02
2858 3112 3.096092 GGAACTTATGGCCATTGGTGAA 58.904 45.455 26.37 10.80 0.00 3.18
2884 3138 8.827832 TGGTGATTAATCCAATTGAAGAGAAT 57.172 30.769 12.90 1.34 0.00 2.40
3016 3270 5.356751 TGCAGTGTAATATTTGACATCCCAC 59.643 40.000 0.00 0.00 0.00 4.61
3062 3324 0.407528 ACCAATGTACATGGGTGCCA 59.592 50.000 30.60 0.00 43.42 4.92
3188 3450 6.112734 CACCTGGTTACTTTGTAGATGCATA 58.887 40.000 0.00 0.00 0.00 3.14
3239 3501 3.181485 GGAGCTACTTCTGTCGCAATAGT 60.181 47.826 0.00 0.00 37.35 2.12
3330 3596 6.299805 AGACTATCCTTTATTGTGCTGTCA 57.700 37.500 0.00 0.00 0.00 3.58
3731 4008 6.962182 TCCTTTGATACACATTCTCTGGAAT 58.038 36.000 0.00 0.00 42.29 3.01
3901 4440 7.111247 AGGAGATGAAGTTGAGAGTATGAAG 57.889 40.000 0.00 0.00 0.00 3.02
4067 4607 7.493320 AGTTCACGTATGTGTTTCACTAAAAGA 59.507 33.333 14.63 0.00 46.49 2.52
4211 4781 5.677319 ACGTTCTGGGATCAATTTCTAGA 57.323 39.130 0.00 0.00 0.00 2.43
4286 4856 3.126001 TCACTCGGAAATGCAAACTCT 57.874 42.857 0.00 0.00 0.00 3.24
4424 4996 8.897752 ACCTTAAATTCATACTGCAGATTTCTC 58.102 33.333 23.35 0.00 0.00 2.87
4425 4997 9.118300 CCTTAAATTCATACTGCAGATTTCTCT 57.882 33.333 23.35 0.00 0.00 3.10
4435 5007 2.693069 CAGATTTCTCTGTTGACGGCT 58.307 47.619 0.00 0.00 43.35 5.52
4438 5010 0.250295 TTTCTCTGTTGACGGCTGGG 60.250 55.000 0.00 0.00 0.00 4.45
4439 5011 1.118965 TTCTCTGTTGACGGCTGGGA 61.119 55.000 0.00 0.00 0.00 4.37
4440 5012 1.079543 CTCTGTTGACGGCTGGGAG 60.080 63.158 0.00 0.00 0.00 4.30
4441 5013 2.743928 CTGTTGACGGCTGGGAGC 60.744 66.667 0.00 0.00 41.46 4.70
4442 5014 3.241530 TGTTGACGGCTGGGAGCT 61.242 61.111 0.00 0.00 41.99 4.09
4443 5015 1.888436 CTGTTGACGGCTGGGAGCTA 61.888 60.000 0.00 0.00 41.99 3.32
4457 5029 2.290323 GGGAGCTACAATGTTCCTGTGT 60.290 50.000 0.00 0.00 37.47 3.72
4522 5094 7.657354 GCCTCCTCTTATTTGTTGTTTGAATTT 59.343 33.333 0.00 0.00 0.00 1.82
4575 5147 3.873952 GGAGAGAATTGAATCTTGTCCCG 59.126 47.826 0.00 0.00 31.36 5.14
4614 5186 1.001641 GGCCAGTCATGTTCTGCCT 60.002 57.895 0.00 0.00 0.00 4.75
4640 5212 7.686434 AGCTGTAAAACTCCCTAGTCATTTTA 58.314 34.615 0.00 0.00 33.75 1.52
4641 5213 8.161425 AGCTGTAAAACTCCCTAGTCATTTTAA 58.839 33.333 0.00 0.00 33.75 1.52
4642 5214 8.789762 GCTGTAAAACTCCCTAGTCATTTTAAA 58.210 33.333 0.00 0.00 33.75 1.52
4815 5387 2.308347 TGCGTTAGAATTGTGTTGCG 57.692 45.000 0.00 0.00 0.00 4.85
4836 5408 3.015383 GCCTTGGATTGGGCCCTA 58.985 61.111 25.70 17.71 42.30 3.53
4894 5629 8.340618 AGCTTGTCATTGATTGTTTATGTACT 57.659 30.769 0.00 0.00 0.00 2.73
4895 5630 9.448438 AGCTTGTCATTGATTGTTTATGTACTA 57.552 29.630 0.00 0.00 0.00 1.82
4896 5631 9.490663 GCTTGTCATTGATTGTTTATGTACTAC 57.509 33.333 0.00 0.00 0.00 2.73
4908 5643 8.942669 TGTTTATGTACTACAAAATTTCAGCG 57.057 30.769 0.00 0.00 0.00 5.18
4924 5659 1.448540 GCGATGGGTCAGGTCACTG 60.449 63.158 0.00 0.00 46.30 3.66
4991 5726 2.789409 AGGAAGTGCTGTATTGTCCC 57.211 50.000 0.00 0.00 0.00 4.46
4994 5729 2.504175 GGAAGTGCTGTATTGTCCCCTA 59.496 50.000 0.00 0.00 0.00 3.53
5020 5755 8.187913 TGAATGAATCTTTTTCCAACCATACA 57.812 30.769 0.00 0.00 0.00 2.29
5026 5761 6.024552 TCTTTTTCCAACCATACATGAAGC 57.975 37.500 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.676384 GAAGGAGTGAGTGCTGGCT 59.324 57.895 0.00 0.00 0.00 4.75
2 3 1.739562 CGAAGGAGTGAGTGCTGGC 60.740 63.158 0.00 0.00 0.00 4.85
5 6 0.540830 AGGACGAAGGAGTGAGTGCT 60.541 55.000 0.00 0.00 0.00 4.40
6 7 0.109039 GAGGACGAAGGAGTGAGTGC 60.109 60.000 0.00 0.00 0.00 4.40
8 9 0.406361 AGGAGGACGAAGGAGTGAGT 59.594 55.000 0.00 0.00 0.00 3.41
9 10 1.551452 AAGGAGGACGAAGGAGTGAG 58.449 55.000 0.00 0.00 0.00 3.51
10 11 1.893801 GAAAGGAGGACGAAGGAGTGA 59.106 52.381 0.00 0.00 0.00 3.41
11 12 1.896465 AGAAAGGAGGACGAAGGAGTG 59.104 52.381 0.00 0.00 0.00 3.51
12 13 2.312424 AGAAAGGAGGACGAAGGAGT 57.688 50.000 0.00 0.00 0.00 3.85
13 14 2.093921 GGAAGAAAGGAGGACGAAGGAG 60.094 54.545 0.00 0.00 0.00 3.69
20 21 1.834896 GAGGGAGGAAGAAAGGAGGAC 59.165 57.143 0.00 0.00 0.00 3.85
27 28 2.158004 TGAGGGAAGAGGGAGGAAGAAA 60.158 50.000 0.00 0.00 0.00 2.52
85 87 5.211201 ACATAAATCAGAGGGGGAAAATGG 58.789 41.667 0.00 0.00 0.00 3.16
93 98 4.997395 CGTCCAATACATAAATCAGAGGGG 59.003 45.833 0.00 0.00 0.00 4.79
97 102 7.327975 AGTGTTCGTCCAATACATAAATCAGA 58.672 34.615 0.00 0.00 0.00 3.27
105 110 2.415168 CGCAAGTGTTCGTCCAATACAT 59.585 45.455 0.00 0.00 0.00 2.29
193 203 4.444536 AGTAAACTTTAACACGCACTGGA 58.555 39.130 0.00 0.00 0.00 3.86
201 211 9.797556 AATCCTTTCACAAGTAAACTTTAACAC 57.202 29.630 0.00 0.00 33.11 3.32
206 216 7.821846 TGCAAAATCCTTTCACAAGTAAACTTT 59.178 29.630 0.00 0.00 33.11 2.66
215 233 6.211184 ACCTATCATGCAAAATCCTTTCACAA 59.789 34.615 0.00 0.00 0.00 3.33
232 250 7.340232 ACAAGCATTATCACAAACACCTATCAT 59.660 33.333 0.00 0.00 0.00 2.45
376 405 4.024048 AGACGGTGCAGATAAAACAACTTG 60.024 41.667 0.00 0.00 0.00 3.16
467 505 4.882842 ATGTTTTAACCAATTTCGGCCT 57.117 36.364 0.00 0.00 0.00 5.19
484 522 8.044908 CCCAACAATACCACTAGTACTAATGTT 58.955 37.037 10.26 0.00 32.46 2.71
508 551 2.957402 TTGGGACATCTATCATGCCC 57.043 50.000 0.00 0.00 39.30 5.36
584 637 8.460428 CACTTTAAACGGTAATATTTTAGGGCA 58.540 33.333 0.00 0.00 0.00 5.36
744 812 1.954382 GTTCCAACTCCAGGTTCCAAC 59.046 52.381 0.00 0.00 35.74 3.77
752 820 2.571653 TGATACCCTGTTCCAACTCCAG 59.428 50.000 0.00 0.00 0.00 3.86
769 837 5.335897 GCAGCTCCAACTGAAAATGTTGATA 60.336 40.000 8.01 0.00 45.27 2.15
982 1074 2.648613 ATCAGAGGGGCGAGGACGAT 62.649 60.000 0.00 0.00 42.66 3.73
1053 1145 1.302832 CTTGCCGAACTTGCCCTCT 60.303 57.895 0.00 0.00 0.00 3.69
1102 1194 2.851045 GGGGCCAGGGTTTCAAGA 59.149 61.111 4.39 0.00 0.00 3.02
1166 1266 0.533308 AGTTTTCCGCCGTGTTAGCA 60.533 50.000 0.00 0.00 0.00 3.49
1194 1294 2.675423 ACCACGTAGCCGCTCTGA 60.675 61.111 0.00 0.00 37.70 3.27
1326 1426 4.980805 GCGTCGTGGAACCAGGCA 62.981 66.667 8.44 0.00 0.00 4.75
1411 1511 3.764466 CCGCTCCGAGAAGTGGCT 61.764 66.667 0.00 0.00 39.90 4.75
1440 1540 1.383803 GGGATGAGGAGGGCTCACT 60.384 63.158 0.00 0.00 33.29 3.41
1452 1552 0.909610 AGACGGCAGGAAAGGGATGA 60.910 55.000 0.00 0.00 0.00 2.92
1504 1614 3.742433 TGCAAATAACAACTGGGTTGG 57.258 42.857 13.75 0.00 46.50 3.77
1758 1934 7.716799 ATAACTCATGCCAAAATCCTTAACA 57.283 32.000 0.00 0.00 0.00 2.41
1819 1995 7.426929 TCTTAAGAAGTTCTTCATCTTGCAC 57.573 36.000 21.25 0.00 37.89 4.57
1884 2060 3.517901 TCCATCGTTTATGAAGAGGGTGT 59.482 43.478 0.00 0.00 37.86 4.16
2150 2332 3.044986 CAACAGAAAATCCAGCACAACG 58.955 45.455 0.00 0.00 0.00 4.10
2483 2727 3.963383 AGGCATAATTTACTTTCCGCG 57.037 42.857 0.00 0.00 0.00 6.46
2517 2761 5.971763 TGCATGGGTCCAATTATTGTTTAC 58.028 37.500 4.15 0.00 0.00 2.01
2547 2791 8.417273 AGCACAAAATGGTACTAAAATTACCT 57.583 30.769 0.00 0.00 39.94 3.08
2826 3079 3.003897 GCCATAAGTTCCAAACACACGAA 59.996 43.478 0.00 0.00 0.00 3.85
2852 3106 6.666980 TCAATTGGATTAATCACCATTCACCA 59.333 34.615 17.07 0.47 36.02 4.17
2853 3107 7.111247 TCAATTGGATTAATCACCATTCACC 57.889 36.000 17.07 0.00 36.02 4.02
2854 3108 8.469200 TCTTCAATTGGATTAATCACCATTCAC 58.531 33.333 17.07 0.00 36.02 3.18
2855 3109 8.592529 TCTTCAATTGGATTAATCACCATTCA 57.407 30.769 17.07 2.09 36.02 2.57
2856 3110 8.906867 TCTCTTCAATTGGATTAATCACCATTC 58.093 33.333 17.07 0.00 36.02 2.67
2857 3111 8.827832 TCTCTTCAATTGGATTAATCACCATT 57.172 30.769 17.07 8.56 36.02 3.16
2858 3112 8.827832 TTCTCTTCAATTGGATTAATCACCAT 57.172 30.769 17.07 3.04 36.02 3.55
2884 3138 4.640201 GCTATGTCTGCCATAACCTCAAAA 59.360 41.667 0.00 0.00 35.62 2.44
2989 3243 6.458751 GGGATGTCAAATATTACACTGCACTG 60.459 42.308 0.00 0.00 0.00 3.66
3116 3378 5.838531 TGCAAATCAGCATAATCATGTGA 57.161 34.783 0.00 0.00 40.11 3.58
3188 3450 7.945664 AGTAATCTCGAGAAAGGTATACAGGAT 59.054 37.037 20.91 0.00 0.00 3.24
3239 3501 6.437477 AGGTGTCTGACAGTATTTGATAGTCA 59.563 38.462 11.41 0.00 37.61 3.41
3311 3577 7.362834 CCAATGTTGACAGCACAATAAAGGATA 60.363 37.037 0.00 0.00 32.36 2.59
3315 3581 5.531634 ACCAATGTTGACAGCACAATAAAG 58.468 37.500 0.00 0.00 32.36 1.85
3319 3585 4.523943 ACATACCAATGTTGACAGCACAAT 59.476 37.500 0.00 0.00 44.07 2.71
3330 3596 4.558226 TCAGCTCTCACATACCAATGTT 57.442 40.909 0.00 0.00 44.07 2.71
3427 3700 0.247460 GGCCCTGCAAAGTGGAAATC 59.753 55.000 0.00 0.00 0.00 2.17
3435 3708 1.243902 TTTAAGTCGGCCCTGCAAAG 58.756 50.000 0.00 0.00 0.00 2.77
3901 4440 5.356882 TTCACTAACAGCTGCATACAAAC 57.643 39.130 15.27 0.00 0.00 2.93
4081 4623 8.511321 TCAGTAATTCGACTGCAAAATAACATT 58.489 29.630 3.82 0.00 45.44 2.71
4095 4637 7.148787 GGATTATCGGTTGATCAGTAATTCGAC 60.149 40.741 0.00 0.00 35.99 4.20
4107 4650 4.252971 CCGTACAGGATTATCGGTTGAT 57.747 45.455 0.00 0.00 45.00 2.57
4114 4657 6.630444 TTCTGAGTACCGTACAGGATTATC 57.370 41.667 11.26 0.00 45.00 1.75
4245 4815 8.451908 AGTGATTATTCTGGTATAGCAAAACC 57.548 34.615 6.04 0.00 36.24 3.27
4286 4856 5.505819 GCGACATACTTGCTGATACACTCTA 60.506 44.000 0.00 0.00 0.00 2.43
4378 4948 6.131972 AGGTGGCATTAGAGCATGTTATAT 57.868 37.500 0.00 0.00 35.83 0.86
4379 4949 5.567037 AGGTGGCATTAGAGCATGTTATA 57.433 39.130 0.00 0.00 35.83 0.98
4424 4996 1.888436 TAGCTCCCAGCCGTCAACAG 61.888 60.000 0.00 0.00 43.77 3.16
4425 4997 1.911269 TAGCTCCCAGCCGTCAACA 60.911 57.895 0.00 0.00 43.77 3.33
4426 4998 1.448013 GTAGCTCCCAGCCGTCAAC 60.448 63.158 0.00 0.00 43.77 3.18
4428 5000 1.264749 ATTGTAGCTCCCAGCCGTCA 61.265 55.000 0.00 0.00 43.77 4.35
4429 5001 0.811616 CATTGTAGCTCCCAGCCGTC 60.812 60.000 0.00 0.00 43.77 4.79
4430 5002 1.221840 CATTGTAGCTCCCAGCCGT 59.778 57.895 0.00 0.00 43.77 5.68
4431 5003 0.392998 AACATTGTAGCTCCCAGCCG 60.393 55.000 0.00 0.00 43.77 5.52
4433 5005 1.065126 AGGAACATTGTAGCTCCCAGC 60.065 52.381 0.00 0.00 42.84 4.85
4434 5006 2.026822 ACAGGAACATTGTAGCTCCCAG 60.027 50.000 0.00 0.21 0.00 4.45
4435 5007 1.985159 ACAGGAACATTGTAGCTCCCA 59.015 47.619 0.00 0.00 0.00 4.37
4438 5010 4.184629 CCTACACAGGAACATTGTAGCTC 58.815 47.826 0.00 0.00 45.91 4.09
4439 5011 4.207891 CCTACACAGGAACATTGTAGCT 57.792 45.455 0.00 0.00 45.91 3.32
4457 5029 7.334171 CACAGTAACATCAAATGACATGTCCTA 59.666 37.037 22.85 5.83 31.79 2.94
4462 5034 6.088173 CCACACAGTAACATCAAATGACATG 58.912 40.000 0.00 0.00 0.00 3.21
4551 5123 3.873952 GGACAAGATTCAATTCTCTCCCG 59.126 47.826 0.00 0.00 0.00 5.14
4575 5147 0.246635 TAGCAGCAAGGTTCGGAGTC 59.753 55.000 0.00 0.00 0.00 3.36
4614 5186 6.869206 AATGACTAGGGAGTTTTACAGCTA 57.131 37.500 0.00 0.00 35.45 3.32
4860 5432 9.577110 AACAATCAATGACAAGCTTGTTATATG 57.423 29.630 30.34 26.79 42.43 1.78
4894 5629 4.075682 TGACCCATCGCTGAAATTTTGTA 58.924 39.130 0.00 0.00 0.00 2.41
4895 5630 2.890311 TGACCCATCGCTGAAATTTTGT 59.110 40.909 0.00 0.00 0.00 2.83
4896 5631 3.504863 CTGACCCATCGCTGAAATTTTG 58.495 45.455 0.00 0.00 0.00 2.44
4908 5643 2.180276 ACTACAGTGACCTGACCCATC 58.820 52.381 0.00 0.00 41.50 3.51
4924 5659 1.226746 ACTGTTTCGCTGGCAACTAC 58.773 50.000 0.00 0.00 37.61 2.73
4978 5713 4.411869 TCATTCATAGGGGACAATACAGCA 59.588 41.667 0.00 0.00 0.00 4.41
4991 5726 7.839907 TGGTTGGAAAAAGATTCATTCATAGG 58.160 34.615 0.00 0.00 0.00 2.57
4994 5729 8.814931 TGTATGGTTGGAAAAAGATTCATTCAT 58.185 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.