Multiple sequence alignment - TraesCS4D01G103600

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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 TraesCS4D01G103600 chr4D 100.000 5277 0 0 1 5277 82296369 82291093 0.000000e+00 9745.0
1 TraesCS4D01G103600 chr4D 89.411 1341 113 20 2990 4313 435063944 435062616 0.000000e+00 1663.0
2 TraesCS4D01G103600 chr4D 87.259 934 75 20 4345 5247 435062616 435061696 0.000000e+00 1026.0
3 TraesCS4D01G103600 chr4D 84.115 938 116 21 2017 2931 435064869 435063942 0.000000e+00 876.0
4 TraesCS4D01G103600 chr4D 87.015 747 73 15 526 1258 435066125 435065389 0.000000e+00 821.0
5 TraesCS4D01G103600 chr4D 87.387 222 20 3 1805 2019 435065384 435065164 1.130000e-61 248.0
6 TraesCS4D01G103600 chr4B 92.488 4686 212 66 1 4577 116217395 116212741 0.000000e+00 6575.0
7 TraesCS4D01G103600 chr4B 85.170 1497 141 43 3584 5029 535247770 535246304 0.000000e+00 1459.0
8 TraesCS4D01G103600 chr4B 87.394 825 80 11 2125 2931 535249335 535248517 0.000000e+00 926.0
9 TraesCS4D01G103600 chr4B 95.345 580 13 7 4702 5277 116212745 116212176 0.000000e+00 909.0
10 TraesCS4D01G103600 chr4B 91.000 600 45 8 2990 3585 535248519 535247925 0.000000e+00 800.0
11 TraesCS4D01G103600 chr4B 90.000 410 40 1 850 1258 535251590 535251181 3.620000e-146 529.0
12 TraesCS4D01G103600 chr4B 88.000 275 19 7 4979 5247 535226632 535226366 3.970000e-81 313.0
13 TraesCS4D01G103600 chr4B 82.184 348 43 14 526 868 535251940 535251607 1.120000e-71 281.0
14 TraesCS4D01G103600 chr4B 82.059 340 29 10 4675 4994 535237229 535236902 1.460000e-65 261.0
15 TraesCS4D01G103600 chr4B 89.474 76 6 1 2017 2092 535249481 535249408 1.560000e-15 95.3
16 TraesCS4D01G103600 chr4A 96.712 2281 55 7 3009 5277 492532432 492530160 0.000000e+00 3779.0
17 TraesCS4D01G103600 chr4A 94.103 1221 35 12 1733 2940 492533624 492532428 0.000000e+00 1821.0
18 TraesCS4D01G103600 chr4A 89.038 1341 108 23 2990 4308 36413091 36411768 0.000000e+00 1626.0
19 TraesCS4D01G103600 chr4A 92.152 892 42 15 781 1660 492534776 492533901 0.000000e+00 1234.0
20 TraesCS4D01G103600 chr4A 86.879 846 87 13 2106 2931 36413930 36413089 0.000000e+00 926.0
21 TraesCS4D01G103600 chr4A 88.774 775 42 24 51 784 492536493 492535723 0.000000e+00 907.0
22 TraesCS4D01G103600 chr4A 90.843 415 32 5 850 1258 36414917 36414503 7.720000e-153 551.0
23 TraesCS4D01G103600 chr4A 81.221 639 75 27 4345 4963 36411763 36411150 1.720000e-129 473.0
24 TraesCS4D01G103600 chr4A 89.655 116 9 2 1904 2019 36414446 36414334 1.530000e-30 145.0
25 TraesCS4D01G103600 chr4A 93.671 79 3 1 2941 3017 556767968 556768046 3.340000e-22 117.0
26 TraesCS4D01G103600 chr3D 94.872 78 2 1 2941 3016 546329970 546330047 2.580000e-23 121.0
27 TraesCS4D01G103600 chr3D 89.362 94 5 4 2923 3012 562507957 562507865 4.320000e-21 113.0
28 TraesCS4D01G103600 chr5D 95.890 73 3 0 2941 3013 438690508 438690580 9.280000e-23 119.0
29 TraesCS4D01G103600 chr7D 94.737 76 2 1 2939 3012 226690357 226690432 3.340000e-22 117.0
30 TraesCS4D01G103600 chr2D 93.671 79 3 1 2941 3017 53145798 53145720 3.340000e-22 117.0
31 TraesCS4D01G103600 chr2D 90.588 85 6 2 2942 3024 23143486 23143402 1.550000e-20 111.0
32 TraesCS4D01G103600 chr6D 92.593 81 4 1 2939 3017 462762751 462762831 1.200000e-21 115.0


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 TraesCS4D01G103600 chr4D 82291093 82296369 5276 True 9745.000000 9745 100.00000 1 5277 1 chr4D.!!$R1 5276
1 TraesCS4D01G103600 chr4D 435061696 435066125 4429 True 926.800000 1663 87.03740 526 5247 5 chr4D.!!$R2 4721
2 TraesCS4D01G103600 chr4B 116212176 116217395 5219 True 3742.000000 6575 93.91650 1 5277 2 chr4B.!!$R3 5276
3 TraesCS4D01G103600 chr4B 535246304 535251940 5636 True 681.716667 1459 87.53700 526 5029 6 chr4B.!!$R4 4503
4 TraesCS4D01G103600 chr4A 492530160 492536493 6333 True 1935.250000 3779 92.93525 51 5277 4 chr4A.!!$R2 5226
5 TraesCS4D01G103600 chr4A 36411150 36414917 3767 True 744.200000 1626 87.52720 850 4963 5 chr4A.!!$R1 4113

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
157 174 0.249073 ACATCATCTAGGACGCGTGC 60.249 55.000 24.26 24.26 0.0 5.34 F
1302 2378 0.109551 TCGTCTTCTTCTCTGCAGCG 60.110 55.000 9.47 2.08 0.0 5.18 F
1326 2414 0.250640 CTGCTCTTGGGCTGTCACTT 60.251 55.000 0.00 0.00 0.0 3.16 F
2472 5414 0.736053 TATTTGTTGAATCGCCCGCC 59.264 50.000 0.00 0.00 0.0 6.13 F
2578 5524 2.203209 CAGGATGCCGGTTAGCCC 60.203 66.667 1.90 0.00 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 2645 0.108281 GTCCTAACTCCCAACCGCTC 60.108 60.000 0.0 0.0 0.00 5.03 R
3301 6279 0.867753 GTCGTAGCTCCTGCATCACG 60.868 60.000 0.0 0.0 42.74 4.35 R
3356 6336 9.726232 CAAAGGTTCTGATGTAAATATCATGTG 57.274 33.333 0.0 0.0 36.55 3.21 R
4117 7288 4.525487 AGATTACCGTACTCTGTTGTCCAA 59.475 41.667 0.0 0.0 0.00 3.53 R
4443 7651 7.068716 AGGTTTTGAGGGATGCAATCTAATAAC 59.931 37.037 0.0 0.0 44.71 1.89 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
101 106 0.533755 AGGTGATTCGCTATGCTGCC 60.534 55.000 0.00 0.00 0.00 4.85
102 107 0.815213 GGTGATTCGCTATGCTGCCA 60.815 55.000 0.00 0.00 0.00 4.92
139 156 4.312443 TGTCGACATAGGAAAGGAACAAC 58.688 43.478 15.76 0.00 0.00 3.32
157 174 0.249073 ACATCATCTAGGACGCGTGC 60.249 55.000 24.26 24.26 0.00 5.34
175 192 2.289547 GTGCGTTTGCCATCCGTAATAT 59.710 45.455 0.00 0.00 41.78 1.28
270 290 2.996631 AGTGGTTTCTCATGCTGGATC 58.003 47.619 0.00 0.00 0.00 3.36
394 415 0.378962 CGGCGGAAAAACAAGTCACA 59.621 50.000 0.00 0.00 0.00 3.58
453 476 1.494721 GTGCCAGAAGAATATCCCCCA 59.505 52.381 0.00 0.00 0.00 4.96
589 625 4.554723 GCCATAACGAAATCACCTATGCAC 60.555 45.833 0.00 0.00 0.00 4.57
604 641 2.433145 CACTGGCATCGCAGACGT 60.433 61.111 0.00 0.00 42.51 4.34
608 645 1.690283 CTGGCATCGCAGACGTCAAG 61.690 60.000 19.50 11.01 42.51 3.02
618 655 2.095718 GCAGACGTCAAGAAATTGGACC 60.096 50.000 19.50 0.00 0.00 4.46
622 660 2.139917 CGTCAAGAAATTGGACCGTCA 58.860 47.619 0.00 0.00 0.00 4.35
629 667 3.502211 AGAAATTGGACCGTCACAACATC 59.498 43.478 0.00 5.15 0.00 3.06
705 757 5.661056 ACATGTACCATATACATCCTCCG 57.339 43.478 0.00 0.00 36.13 4.63
727 779 6.265649 TCCGAAATCACAAATAAGGGTTCAAA 59.734 34.615 0.00 0.00 0.00 2.69
737 794 8.743714 ACAAATAAGGGTTCAAATCAAGAGATC 58.256 33.333 0.00 0.00 31.90 2.75
739 796 8.517062 AATAAGGGTTCAAATCAAGAGATCAG 57.483 34.615 0.00 0.00 31.90 2.90
742 799 6.355747 AGGGTTCAAATCAAGAGATCAGATC 58.644 40.000 1.64 1.64 31.90 2.75
960 2032 4.382852 CCCCCTCCTACCTCACTG 57.617 66.667 0.00 0.00 0.00 3.66
1200 2272 0.393402 TCTACTACTTCGCGGAGGCA 60.393 55.000 20.69 4.97 39.92 4.75
1269 2341 1.777941 AGTACCTACTGGCTGGCTAC 58.222 55.000 2.00 0.00 34.72 3.58
1272 2348 2.107141 CTACTGGCTGGCTACCGC 59.893 66.667 2.00 0.00 0.00 5.68
1274 2350 1.076559 TACTGGCTGGCTACCGCTA 60.077 57.895 2.00 0.00 36.09 4.26
1282 2358 0.970937 TGGCTACCGCTACTGCTTCT 60.971 55.000 0.00 0.00 36.97 2.85
1291 2367 2.414824 CGCTACTGCTTCTTCGTCTTCT 60.415 50.000 0.00 0.00 36.97 2.85
1293 2369 3.610677 GCTACTGCTTCTTCGTCTTCTTC 59.389 47.826 0.00 0.00 36.03 2.87
1295 2371 3.908213 ACTGCTTCTTCGTCTTCTTCTC 58.092 45.455 0.00 0.00 0.00 2.87
1296 2372 3.572255 ACTGCTTCTTCGTCTTCTTCTCT 59.428 43.478 0.00 0.00 0.00 3.10
1297 2373 3.906998 TGCTTCTTCGTCTTCTTCTCTG 58.093 45.455 0.00 0.00 0.00 3.35
1298 2374 2.666022 GCTTCTTCGTCTTCTTCTCTGC 59.334 50.000 0.00 0.00 0.00 4.26
1299 2375 3.858877 GCTTCTTCGTCTTCTTCTCTGCA 60.859 47.826 0.00 0.00 0.00 4.41
1300 2376 3.567576 TCTTCGTCTTCTTCTCTGCAG 57.432 47.619 7.63 7.63 0.00 4.41
1301 2377 1.991965 CTTCGTCTTCTTCTCTGCAGC 59.008 52.381 9.47 0.00 0.00 5.25
1302 2378 0.109551 TCGTCTTCTTCTCTGCAGCG 60.110 55.000 9.47 2.08 0.00 5.18
1303 2379 1.681945 CGTCTTCTTCTCTGCAGCGC 61.682 60.000 9.47 0.00 0.00 5.92
1304 2380 0.668706 GTCTTCTTCTCTGCAGCGCA 60.669 55.000 11.47 0.00 36.92 6.09
1326 2414 0.250640 CTGCTCTTGGGCTGTCACTT 60.251 55.000 0.00 0.00 0.00 3.16
1336 2424 2.235898 GGGCTGTCACTTTCTGATCTCT 59.764 50.000 0.00 0.00 0.00 3.10
1337 2425 3.260740 GGCTGTCACTTTCTGATCTCTG 58.739 50.000 0.00 0.00 0.00 3.35
1339 2427 3.306641 GCTGTCACTTTCTGATCTCTGGT 60.307 47.826 0.00 0.00 0.00 4.00
1340 2428 4.802248 GCTGTCACTTTCTGATCTCTGGTT 60.802 45.833 0.00 0.00 0.00 3.67
1341 2429 5.567623 GCTGTCACTTTCTGATCTCTGGTTA 60.568 44.000 0.00 0.00 0.00 2.85
1342 2430 6.611613 TGTCACTTTCTGATCTCTGGTTAT 57.388 37.500 0.00 0.00 0.00 1.89
1344 2432 6.875726 TGTCACTTTCTGATCTCTGGTTATTG 59.124 38.462 0.00 0.00 0.00 1.90
1345 2433 6.876257 GTCACTTTCTGATCTCTGGTTATTGT 59.124 38.462 0.00 0.00 0.00 2.71
1346 2434 7.064016 GTCACTTTCTGATCTCTGGTTATTGTC 59.936 40.741 0.00 0.00 0.00 3.18
1348 2436 4.046938 TCTGATCTCTGGTTATTGTCGC 57.953 45.455 0.00 0.00 0.00 5.19
1351 2439 3.195610 TGATCTCTGGTTATTGTCGCTGT 59.804 43.478 0.00 0.00 0.00 4.40
1352 2440 3.678056 TCTCTGGTTATTGTCGCTGTT 57.322 42.857 0.00 0.00 0.00 3.16
1448 2543 3.745975 TGTTCGCATCTGAATTTTCTCGT 59.254 39.130 0.00 0.00 0.00 4.18
1547 2645 2.854777 CGGTTGATTAGCTCTCGACTTG 59.145 50.000 13.54 6.05 0.00 3.16
1585 2683 1.287425 CGACGCAGGAATTTCTACCC 58.713 55.000 0.00 0.00 0.00 3.69
1599 2697 1.066430 TCTACCCGGTCTGCATTTCAC 60.066 52.381 0.00 0.00 0.00 3.18
1661 2759 2.100584 CTGGATCTCGAGAGTTTCTGGG 59.899 54.545 21.52 4.81 0.00 4.45
1664 2762 3.429684 GGATCTCGAGAGTTTCTGGGAAC 60.430 52.174 21.52 0.00 0.00 3.62
1665 2763 2.877866 TCTCGAGAGTTTCTGGGAACT 58.122 47.619 12.08 0.00 42.31 3.01
1677 2775 6.041637 AGTTTCTGGGAACTATTTTGGTTTCC 59.958 38.462 0.00 0.00 41.45 3.13
1679 2777 3.512496 TGGGAACTATTTTGGTTTCCCC 58.488 45.455 14.32 5.16 40.62 4.81
1693 2791 6.123045 TGGTTTCCCCAAACAGTTTTAAAA 57.877 33.333 0.00 0.00 43.41 1.52
2036 4889 1.550869 CCTTGGACCCTTGCCTCATTT 60.551 52.381 0.00 0.00 0.00 2.32
2037 4890 2.250924 CTTGGACCCTTGCCTCATTTT 58.749 47.619 0.00 0.00 0.00 1.82
2129 5061 6.728200 TGCTTCTTTCTTTGATGTAACAGTG 58.272 36.000 0.00 0.00 0.00 3.66
2168 5100 7.432059 TGATGCAGATAAAGATCTCAGTACTG 58.568 38.462 17.17 17.17 40.68 2.74
2169 5101 5.595885 TGCAGATAAAGATCTCAGTACTGC 58.404 41.667 18.45 22.77 40.68 4.40
2170 5102 5.362143 TGCAGATAAAGATCTCAGTACTGCT 59.638 40.000 26.20 6.46 45.22 4.24
2176 5108 4.243793 AGATCTCAGTACTGCTACCACT 57.756 45.455 18.45 9.15 0.00 4.00
2259 5191 2.513259 TTCTTCGGTTGGAGGCGGT 61.513 57.895 0.00 0.00 0.00 5.68
2277 5209 2.126189 GCGTTTACGGAGCTCGGT 60.126 61.111 27.35 27.35 44.45 4.69
2345 5277 4.884668 AGTCGTGGAATAAAGGTTGAGA 57.115 40.909 0.00 0.00 0.00 3.27
2391 5324 5.766150 TCACATGTTTCGGTGAAAGAAAT 57.234 34.783 0.00 0.00 40.80 2.17
2472 5414 0.736053 TATTTGTTGAATCGCCCGCC 59.264 50.000 0.00 0.00 0.00 6.13
2517 5459 4.720090 ACACTTCGTCAGACTACAATACG 58.280 43.478 0.00 0.00 34.99 3.06
2578 5524 2.203209 CAGGATGCCGGTTAGCCC 60.203 66.667 1.90 0.00 0.00 5.19
2596 5542 3.055094 AGCCCGAACACATCAATCTAACT 60.055 43.478 0.00 0.00 0.00 2.24
2748 5700 9.965902 ATTTCAAGTTCTACTTCAGGAATATGT 57.034 29.630 0.00 0.00 36.03 2.29
2824 5779 4.315803 GGCATTATATACCGCAACTCACT 58.684 43.478 5.24 0.00 0.00 3.41
2911 5873 2.752030 AGTAGTCAAGCATAGCCTGGA 58.248 47.619 0.00 0.00 0.00 3.86
2955 5925 9.862371 ATGTTCTACTTCCATAATATAAGAGCG 57.138 33.333 0.00 0.00 0.00 5.03
2956 5926 8.857098 TGTTCTACTTCCATAATATAAGAGCGT 58.143 33.333 0.00 0.00 0.00 5.07
2972 5942 6.512342 AAGAGCGTATTTGACACTAGTAGT 57.488 37.500 0.00 0.00 0.00 2.73
2989 5960 5.646577 AGTAGTGTCAGAAACGCTCTTAT 57.353 39.130 0.00 0.00 45.69 1.73
3130 6108 5.028678 TCTGGTCCCATGGTATGATATCT 57.971 43.478 11.73 0.00 0.00 1.98
3301 6279 2.728922 GACGTCTGTTACCCATCGATC 58.271 52.381 8.70 0.00 0.00 3.69
3340 6318 3.205338 ACTGCGCAAATATGTATGCTCA 58.795 40.909 13.05 4.56 40.39 4.26
3753 6894 5.106555 ACATCAACATCTTGCCTTTACTTCG 60.107 40.000 0.00 0.00 0.00 3.79
4117 7288 5.208121 TCTTTGATTTTCAAGGTTGGAGGT 58.792 37.500 0.21 0.00 37.70 3.85
4303 7474 4.202441 ACCTACAAAAGCAGCTGGATATG 58.798 43.478 17.12 1.37 0.00 1.78
4443 7651 6.593382 GCTAGCAAGTATGATCTTTATCAGGG 59.407 42.308 10.63 0.00 45.17 4.45
4659 7880 2.177394 TGTTGCTAACGGAATGCTGA 57.823 45.000 0.00 0.00 0.00 4.26
4981 8231 5.475564 GCAATGGTAGTTTAAGACCTGGAAA 59.524 40.000 0.00 0.00 36.62 3.13
4982 8232 6.015772 GCAATGGTAGTTTAAGACCTGGAAAA 60.016 38.462 0.00 0.00 36.62 2.29
4983 8233 7.368059 CAATGGTAGTTTAAGACCTGGAAAAC 58.632 38.462 0.00 5.74 36.62 2.43
4984 8234 6.003859 TGGTAGTTTAAGACCTGGAAAACA 57.996 37.500 0.00 0.00 36.62 2.83
4985 8235 6.424883 TGGTAGTTTAAGACCTGGAAAACAA 58.575 36.000 0.00 0.00 36.62 2.83
5222 8483 6.127730 GGGTGACAAAGTATTACCATTCAAGG 60.128 42.308 0.00 0.00 33.10 3.61
5265 8527 7.610305 TGGAAACAATAAGAGTTGTATCTTCCC 59.390 37.037 14.35 0.00 41.46 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.822350 GGTGATAAGAAGCCATTTACTCCC 59.178 45.833 0.00 0.00 0.00 4.30
101 106 2.093500 TCGACATGGAAGAGGGTCAATG 60.093 50.000 0.00 0.00 35.38 2.82
102 107 2.093447 GTCGACATGGAAGAGGGTCAAT 60.093 50.000 11.55 0.00 0.00 2.57
139 156 1.271446 CGCACGCGTCCTAGATGATG 61.271 60.000 9.86 0.00 34.35 3.07
157 174 5.917541 AGTAATATTACGGATGGCAAACG 57.082 39.130 17.77 11.81 38.65 3.60
175 192 6.520272 CCTCGTCCTAGCTTAGTACTAGTAA 58.480 44.000 3.61 0.00 36.23 2.24
349 369 1.241315 TTGCTGTTTTCCTAGCCGGC 61.241 55.000 21.89 21.89 39.15 6.13
354 374 2.814336 GGTCTGGTTGCTGTTTTCCTAG 59.186 50.000 0.00 0.00 0.00 3.02
394 415 0.464036 TGCGGCCGAGTCAAGAATAT 59.536 50.000 33.48 0.00 0.00 1.28
453 476 1.610522 GCTTGCAGTCAAACATCCAGT 59.389 47.619 0.00 0.00 0.00 4.00
589 625 1.690283 CTTGACGTCTGCGATGCCAG 61.690 60.000 17.92 0.00 42.00 4.85
604 641 3.201353 TGTGACGGTCCAATTTCTTGA 57.799 42.857 5.55 0.00 34.04 3.02
608 645 3.502211 AGATGTTGTGACGGTCCAATTTC 59.498 43.478 5.55 9.80 0.00 2.17
618 655 3.786576 GTCTCATCGTAGATGTTGTGACG 59.213 47.826 9.50 0.00 45.12 4.35
622 660 5.573282 CGAAAAGTCTCATCGTAGATGTTGT 59.427 40.000 9.50 0.00 45.12 3.32
629 667 4.971008 TGAGTCGAAAAGTCTCATCGTAG 58.029 43.478 0.00 0.00 39.46 3.51
705 757 9.487790 TTGATTTGAACCCTTATTTGTGATTTC 57.512 29.630 0.00 0.00 0.00 2.17
727 779 5.554437 ATGCTGTGATCTGATCTCTTGAT 57.446 39.130 17.82 5.88 35.26 2.57
737 794 2.490509 TGCTGGAAAATGCTGTGATCTG 59.509 45.455 0.00 0.00 0.00 2.90
739 796 2.416431 GGTGCTGGAAAATGCTGTGATC 60.416 50.000 0.00 0.00 0.00 2.92
742 799 0.387622 CGGTGCTGGAAAATGCTGTG 60.388 55.000 0.00 0.00 0.00 3.66
960 2032 0.913924 TAACGGGAATTGGGAGGACC 59.086 55.000 0.00 0.00 40.81 4.46
1272 2348 5.054390 AGAAGAAGACGAAGAAGCAGTAG 57.946 43.478 0.00 0.00 0.00 2.57
1274 2350 3.572255 AGAGAAGAAGACGAAGAAGCAGT 59.428 43.478 0.00 0.00 0.00 4.40
1282 2358 1.667177 CGCTGCAGAGAAGAAGACGAA 60.667 52.381 20.43 0.00 0.00 3.85
1291 2367 1.373873 CAGAGTGCGCTGCAGAGAA 60.374 57.895 22.55 8.12 40.08 2.87
1302 2378 2.039405 CAGCCCAAGAGCAGAGTGC 61.039 63.158 0.00 0.00 45.46 4.40
1303 2379 0.673022 GACAGCCCAAGAGCAGAGTG 60.673 60.000 0.00 0.00 34.23 3.51
1304 2380 1.123861 TGACAGCCCAAGAGCAGAGT 61.124 55.000 0.00 0.00 34.23 3.24
1326 2414 4.160439 AGCGACAATAACCAGAGATCAGAA 59.840 41.667 0.00 0.00 0.00 3.02
1336 2424 3.880490 AGAAACAACAGCGACAATAACCA 59.120 39.130 0.00 0.00 0.00 3.67
1337 2425 4.483476 AGAAACAACAGCGACAATAACC 57.517 40.909 0.00 0.00 0.00 2.85
1339 2427 4.319190 CCGAAGAAACAACAGCGACAATAA 60.319 41.667 0.00 0.00 0.00 1.40
1340 2428 3.185594 CCGAAGAAACAACAGCGACAATA 59.814 43.478 0.00 0.00 0.00 1.90
1341 2429 2.032030 CCGAAGAAACAACAGCGACAAT 60.032 45.455 0.00 0.00 0.00 2.71
1342 2430 1.329292 CCGAAGAAACAACAGCGACAA 59.671 47.619 0.00 0.00 0.00 3.18
1344 2432 0.384353 GCCGAAGAAACAACAGCGAC 60.384 55.000 0.00 0.00 0.00 5.19
1345 2433 1.503818 GGCCGAAGAAACAACAGCGA 61.504 55.000 0.00 0.00 0.00 4.93
1346 2434 1.082104 GGCCGAAGAAACAACAGCG 60.082 57.895 0.00 0.00 0.00 5.18
1348 2436 1.308998 ACTGGCCGAAGAAACAACAG 58.691 50.000 0.00 0.00 0.00 3.16
1351 2439 1.202359 GCAAACTGGCCGAAGAAACAA 60.202 47.619 0.00 0.00 0.00 2.83
1352 2440 0.383949 GCAAACTGGCCGAAGAAACA 59.616 50.000 0.00 0.00 0.00 2.83
1448 2543 1.347707 ACTGTTGCCTCTCGAATCCAA 59.652 47.619 0.00 0.00 0.00 3.53
1516 2614 2.287915 GCTAATCAACCGTGCACATAGG 59.712 50.000 18.64 12.67 0.00 2.57
1547 2645 0.108281 GTCCTAACTCCCAACCGCTC 60.108 60.000 0.00 0.00 0.00 5.03
1585 2683 2.159627 GTGTAAGGTGAAATGCAGACCG 59.840 50.000 0.00 0.00 34.72 4.79
1599 2697 3.935203 CTGTGAAGGCTGTATGTGTAAGG 59.065 47.826 0.00 0.00 0.00 2.69
1726 2824 7.825331 TGACAATTCCAACACCATAGTAAAA 57.175 32.000 0.00 0.00 0.00 1.52
1727 2825 7.093988 CCATGACAATTCCAACACCATAGTAAA 60.094 37.037 0.00 0.00 0.00 2.01
1729 2827 5.885352 CCATGACAATTCCAACACCATAGTA 59.115 40.000 0.00 0.00 0.00 1.82
1731 2829 4.440525 GCCATGACAATTCCAACACCATAG 60.441 45.833 0.00 0.00 0.00 2.23
2036 4889 0.534412 CCACAACACACAAAGCCCAA 59.466 50.000 0.00 0.00 0.00 4.12
2037 4890 0.613292 ACCACAACACACAAAGCCCA 60.613 50.000 0.00 0.00 0.00 5.36
2129 5061 2.547211 CTGCATCATAGTGTAGCAAGGC 59.453 50.000 0.00 0.00 34.45 4.35
2176 5108 6.237901 ACAGTTAGCAATCACACTTCCATAA 58.762 36.000 0.00 0.00 0.00 1.90
2184 5116 5.088739 GCAACATACAGTTAGCAATCACAC 58.911 41.667 0.00 0.00 38.74 3.82
2259 5191 2.126228 CCGAGCTCCGTAAACGCA 60.126 61.111 8.47 0.00 38.18 5.24
2277 5209 3.110293 TCTCCTCTGGGATAAAACGGA 57.890 47.619 0.00 0.00 41.36 4.69
2345 5277 4.537688 TCAGAGAGATGGTTCCCAAAATCT 59.462 41.667 0.00 0.00 36.95 2.40
2437 5379 7.223584 TCAACAAATAGAAGATTGGACACTGA 58.776 34.615 0.00 0.00 0.00 3.41
2472 5414 1.409427 GAGTAGGACCATCCAACTCCG 59.591 57.143 0.00 0.00 39.61 4.63
2578 5524 7.525688 ACATACAGTTAGATTGATGTGTTCG 57.474 36.000 0.00 0.00 0.00 3.95
2748 5700 3.685139 AGAAGAGAGGCAATCGAAACA 57.315 42.857 0.00 0.00 0.00 2.83
2824 5779 3.836365 TTGTGTGTGAGAAGGACATCA 57.164 42.857 0.00 0.00 0.00 3.07
2911 5873 9.593134 GTAGAACATAGTTGATTCAAGAGATGT 57.407 33.333 11.97 11.97 0.00 3.06
2939 5901 9.419297 GTGTCAAATACGCTCTTATATTATGGA 57.581 33.333 0.00 0.00 35.62 3.41
2970 5940 7.653713 CCATAATATAAGAGCGTTTCTGACACT 59.346 37.037 0.00 0.00 35.91 3.55
2971 5941 7.095607 CCCATAATATAAGAGCGTTTCTGACAC 60.096 40.741 0.00 0.00 35.91 3.67
2972 5942 6.929049 CCCATAATATAAGAGCGTTTCTGACA 59.071 38.462 0.00 0.00 35.91 3.58
2975 5945 6.089551 CGTCCCATAATATAAGAGCGTTTCTG 59.910 42.308 0.00 0.00 35.91 3.02
2976 5946 6.157211 CGTCCCATAATATAAGAGCGTTTCT 58.843 40.000 0.00 0.00 37.93 2.52
2977 5947 5.347907 CCGTCCCATAATATAAGAGCGTTTC 59.652 44.000 0.00 0.00 0.00 2.78
2981 5952 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2989 5960 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3130 6108 7.289310 TGTTTATGGCCAGAAATATCTCATCA 58.711 34.615 27.10 15.17 32.03 3.07
3301 6279 0.867753 GTCGTAGCTCCTGCATCACG 60.868 60.000 0.00 0.00 42.74 4.35
3356 6336 9.726232 CAAAGGTTCTGATGTAAATATCATGTG 57.274 33.333 0.00 0.00 36.55 3.21
3753 6894 7.873505 GTGGTATCTTATGTTCCACTATTCTCC 59.126 40.741 0.00 0.00 43.34 3.71
4087 7256 6.165700 ACCTTGAAAATCAAAGAGCAACAT 57.834 33.333 0.00 0.00 35.73 2.71
4117 7288 4.525487 AGATTACCGTACTCTGTTGTCCAA 59.475 41.667 0.00 0.00 0.00 3.53
4317 7490 8.635765 TTGTAGCAAGACTGAAAAATCCTAAT 57.364 30.769 0.00 0.00 0.00 1.73
4443 7651 7.068716 AGGTTTTGAGGGATGCAATCTAATAAC 59.931 37.037 0.00 0.00 44.71 1.89
4981 8231 2.162681 GGGCAGCTTCTATGTGTTGTT 58.837 47.619 0.00 0.00 0.00 2.83
4982 8232 1.614317 GGGGCAGCTTCTATGTGTTGT 60.614 52.381 0.00 0.00 0.00 3.32
4983 8233 1.098050 GGGGCAGCTTCTATGTGTTG 58.902 55.000 0.00 0.00 0.00 3.33
4984 8234 0.698238 TGGGGCAGCTTCTATGTGTT 59.302 50.000 0.00 0.00 0.00 3.32
4985 8235 0.254178 CTGGGGCAGCTTCTATGTGT 59.746 55.000 0.00 0.00 0.00 3.72
5085 8346 3.383761 GACTGCCCAAGAACAACAAATG 58.616 45.455 0.00 0.00 0.00 2.32
5222 8483 6.744112 TGTTTCCATCCAAGTTAACATTGTC 58.256 36.000 8.61 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.