Multiple sequence alignment - TraesCS4B01G179300

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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 TraesCS4B01G179300 chr4B 100.000 3291 0 0 1 3291 392660263 392656973 0.000000e+00 6078
1 TraesCS4B01G179300 chr4D 93.808 2035 70 21 641 2648 314679086 314677081 0.000000e+00 3009
2 TraesCS4B01G179300 chr4D 92.226 656 32 8 2 644 314679793 314679144 0.000000e+00 911
3 TraesCS4B01G179300 chr4D 94.172 429 17 3 2868 3291 314676865 314676440 0.000000e+00 647
4 TraesCS4B01G179300 chr4A 92.433 2141 82 31 641 2729 161279919 161282031 0.000000e+00 2983
5 TraesCS4B01G179300 chr4A 89.583 576 33 14 2726 3290 161284222 161284781 0.000000e+00 706
6 TraesCS4B01G179300 chr4A 93.578 327 15 4 175 500 161279089 161279410 1.780000e-132 483
7 TraesCS4B01G179300 chr4A 93.919 148 8 1 498 644 161279714 161279861 4.270000e-54 222
8 TraesCS4B01G179300 chr2D 80.802 698 94 28 1069 1754 44470142 44469473 8.150000e-141 510
9 TraesCS4B01G179300 chr2D 80.603 696 104 24 1069 1754 48028291 48027617 2.930000e-140 508
10 TraesCS4B01G179300 chr2D 80.113 709 112 23 1056 1754 44339765 44340454 4.900000e-138 501
11 TraesCS4B01G179300 chr2B 80.664 693 105 24 1069 1754 71293664 71292994 8.150000e-141 510
12 TraesCS4B01G179300 chr2B 80.398 704 107 26 1069 1754 75990592 75991282 1.050000e-139 507
13 TraesCS4B01G179300 chr2B 80.172 696 101 28 1069 1754 71244283 71243615 1.370000e-133 486
14 TraesCS4B01G179300 chr2B 84.731 334 40 8 1428 1754 70837292 70837621 1.140000e-84 324
15 TraesCS4B01G179300 chr2A 80.316 696 101 26 1069 1754 48347446 48346777 8.200000e-136 494
16 TraesCS4B01G179300 chr2A 85.714 336 37 9 1426 1754 48246382 48246713 8.740000e-91 344
17 TraesCS4B01G179300 chr2A 84.478 335 43 8 1426 1754 48250315 48250646 4.100000e-84 322
18 TraesCS4B01G179300 chr2A 86.641 262 35 0 1069 1330 51040893 51041154 1.160000e-74 291
19 TraesCS4B01G179300 chr2A 84.151 265 36 2 1069 1330 48249983 48250244 5.450000e-63 252


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 TraesCS4B01G179300 chr4B 392656973 392660263 3290 True 6078.000000 6078 100.00000 1 3291 1 chr4B.!!$R1 3290
1 TraesCS4B01G179300 chr4D 314676440 314679793 3353 True 1522.333333 3009 93.40200 2 3291 3 chr4D.!!$R1 3289
2 TraesCS4B01G179300 chr4A 161279089 161284781 5692 False 1098.500000 2983 92.37825 175 3290 4 chr4A.!!$F1 3115
3 TraesCS4B01G179300 chr2D 44469473 44470142 669 True 510.000000 510 80.80200 1069 1754 1 chr2D.!!$R1 685
4 TraesCS4B01G179300 chr2D 48027617 48028291 674 True 508.000000 508 80.60300 1069 1754 1 chr2D.!!$R2 685
5 TraesCS4B01G179300 chr2D 44339765 44340454 689 False 501.000000 501 80.11300 1056 1754 1 chr2D.!!$F1 698
6 TraesCS4B01G179300 chr2B 71292994 71293664 670 True 510.000000 510 80.66400 1069 1754 1 chr2B.!!$R2 685
7 TraesCS4B01G179300 chr2B 75990592 75991282 690 False 507.000000 507 80.39800 1069 1754 1 chr2B.!!$F2 685
8 TraesCS4B01G179300 chr2B 71243615 71244283 668 True 486.000000 486 80.17200 1069 1754 1 chr2B.!!$R1 685
9 TraesCS4B01G179300 chr2A 48346777 48347446 669 True 494.000000 494 80.31600 1069 1754 1 chr2A.!!$R1 685
10 TraesCS4B01G179300 chr2A 48246382 48250646 4264 False 306.000000 344 84.78100 1069 1754 3 chr2A.!!$F2 685

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
450 464 0.107017 CTAAGGTAGGACGTCGGGGA 60.107 60.0 9.92 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 5000 1.064357 GGAACCGAACAGACGCAAAAA 59.936 47.619 0.0 0.0 0.0 1.94 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
36 37 2.796593 AGAAAACGACCGGAAAACTACG 59.203 45.455 9.46 4.58 0.00 3.51
72 73 0.315544 CGCGCACGTGTTACACTTTT 60.316 50.000 18.38 0.00 31.34 2.27
92 93 0.380378 GGTTTGTTCAGCAACAGCGA 59.620 50.000 0.00 0.00 43.54 4.93
99 100 3.194861 GTTCAGCAACAGCGATGGTATA 58.805 45.455 5.32 0.00 32.14 1.47
119 120 9.890629 TGGTATATGATGCATATTTTAGTCCTC 57.109 33.333 0.00 0.00 38.00 3.71
123 124 6.000246 TGATGCATATTTTAGTCCTCCACA 58.000 37.500 0.00 0.00 0.00 4.17
161 162 5.450171 ACGTAGTACGATCAATATGAGCAC 58.550 41.667 28.47 0.00 46.05 4.40
252 258 3.992427 GGAAGGACGACGTAAAACTTGAT 59.008 43.478 0.00 0.00 0.00 2.57
450 464 0.107017 CTAAGGTAGGACGTCGGGGA 60.107 60.000 9.92 0.00 0.00 4.81
453 467 1.152798 GGTAGGACGTCGGGGAGAT 60.153 63.158 9.92 0.00 0.00 2.75
456 470 0.256752 TAGGACGTCGGGGAGATGAA 59.743 55.000 9.92 0.00 39.17 2.57
471 485 3.748083 AGATGAATGTCCATTGATCCGG 58.252 45.455 13.55 0.00 40.69 5.14
504 825 4.094830 TCCACCCAAGAAAGTAAACTCC 57.905 45.455 0.00 0.00 0.00 3.85
544 865 1.039856 TGCCTTCAACCTTTGCCTTC 58.960 50.000 0.00 0.00 0.00 3.46
586 908 2.606725 GCAACGATCACTCCAGAGATTG 59.393 50.000 0.70 0.00 34.15 2.67
592 914 1.827344 TCACTCCAGAGATTGTGCGAT 59.173 47.619 0.70 0.00 0.00 4.58
635 957 5.679734 ACTAAACACAATCACAAGAGCAG 57.320 39.130 0.00 0.00 0.00 4.24
830 1214 4.415332 CTGACCGACGACGTGGGG 62.415 72.222 29.17 20.55 35.71 4.96
831 1215 4.953010 TGACCGACGACGTGGGGA 62.953 66.667 29.17 14.99 35.71 4.81
835 1219 3.812019 CGACGACGTGGGGAGGAG 61.812 72.222 4.58 0.00 34.56 3.69
906 1292 2.517402 GCCACCCACCGTGAAACA 60.517 61.111 0.00 0.00 46.20 2.83
907 1293 2.841160 GCCACCCACCGTGAAACAC 61.841 63.158 0.00 0.00 46.20 3.32
908 1294 2.190841 CCACCCACCGTGAAACACC 61.191 63.158 0.00 0.00 46.20 4.16
948 1356 4.378046 CCAAAAACCACTCTAAATCCGACG 60.378 45.833 0.00 0.00 0.00 5.12
958 1366 2.309898 AAATCCGACGCAAAAACTCG 57.690 45.000 0.00 0.00 0.00 4.18
1402 3985 5.894964 TGGTAGTAGTAATGGTGTGCTGATA 59.105 40.000 0.00 0.00 0.00 2.15
1412 4006 4.847198 TGGTGTGCTGATATGTTCTTGAT 58.153 39.130 0.00 0.00 0.00 2.57
1413 4007 5.255687 TGGTGTGCTGATATGTTCTTGATT 58.744 37.500 0.00 0.00 0.00 2.57
1414 4008 5.711506 TGGTGTGCTGATATGTTCTTGATTT 59.288 36.000 0.00 0.00 0.00 2.17
1415 4009 6.032094 GGTGTGCTGATATGTTCTTGATTTG 58.968 40.000 0.00 0.00 0.00 2.32
1416 4010 6.032094 GTGTGCTGATATGTTCTTGATTTGG 58.968 40.000 0.00 0.00 0.00 3.28
1417 4011 5.711506 TGTGCTGATATGTTCTTGATTTGGT 59.288 36.000 0.00 0.00 0.00 3.67
1418 4012 6.209192 TGTGCTGATATGTTCTTGATTTGGTT 59.791 34.615 0.00 0.00 0.00 3.67
1419 4013 7.092716 GTGCTGATATGTTCTTGATTTGGTTT 58.907 34.615 0.00 0.00 0.00 3.27
1420 4014 7.599998 GTGCTGATATGTTCTTGATTTGGTTTT 59.400 33.333 0.00 0.00 0.00 2.43
1421 4015 7.599621 TGCTGATATGTTCTTGATTTGGTTTTG 59.400 33.333 0.00 0.00 0.00 2.44
1422 4016 7.814107 GCTGATATGTTCTTGATTTGGTTTTGA 59.186 33.333 0.00 0.00 0.00 2.69
1423 4017 9.350357 CTGATATGTTCTTGATTTGGTTTTGAG 57.650 33.333 0.00 0.00 0.00 3.02
1424 4018 7.814107 TGATATGTTCTTGATTTGGTTTTGAGC 59.186 33.333 0.00 0.00 0.00 4.26
1605 4204 3.535629 CTGCCAGCAGTGTCCCGAA 62.536 63.158 11.55 0.00 39.10 4.30
1791 4394 7.659799 TGATTTTGTTTCGAGTCTCCAGATTTA 59.340 33.333 0.00 0.00 0.00 1.40
1797 4400 3.129462 TCGAGTCTCCAGATTTAGCAGTG 59.871 47.826 0.00 0.00 0.00 3.66
1918 4521 2.483745 CTTGTGCTGGCGATGCTG 59.516 61.111 0.00 0.00 0.00 4.41
2021 4624 1.668751 CCGGTGGTATGAATTCCGTTG 59.331 52.381 2.27 0.00 39.62 4.10
2302 4928 4.517815 GCGTAATCCCCGGTCGCA 62.518 66.667 0.00 0.00 45.01 5.10
2374 5000 7.927629 CACCTATAAGCATTTGCATTTTGGTAT 59.072 33.333 5.20 0.00 45.16 2.73
2408 5034 5.047164 TGTTCGGTTCCAAGTTAGCAGTATA 60.047 40.000 0.00 0.00 0.00 1.47
2409 5035 5.864418 TCGGTTCCAAGTTAGCAGTATAT 57.136 39.130 0.00 0.00 0.00 0.86
2434 5067 9.981460 ATCATTTCAAGTTTAAGATAGGAGGTT 57.019 29.630 0.00 0.00 0.00 3.50
2435 5068 9.807921 TCATTTCAAGTTTAAGATAGGAGGTTT 57.192 29.630 0.00 0.00 0.00 3.27
2436 5069 9.846248 CATTTCAAGTTTAAGATAGGAGGTTTG 57.154 33.333 0.00 0.00 0.00 2.93
2437 5070 9.807921 ATTTCAAGTTTAAGATAGGAGGTTTGA 57.192 29.630 0.00 0.00 0.00 2.69
2444 5077 8.388853 GTTTAAGATAGGAGGTTTGATCGAAAC 58.611 37.037 2.11 2.11 42.97 2.78
2449 5082 3.325135 AGGAGGTTTGATCGAAACAGTCT 59.675 43.478 13.33 4.42 45.15 3.24
2463 5096 6.963242 TCGAAACAGTCTACGTATGTGAATAC 59.037 38.462 0.00 0.00 0.00 1.89
2468 5103 5.298527 CAGTCTACGTATGTGAATACCCTCA 59.701 44.000 0.00 0.00 0.00 3.86
2483 5118 1.528129 CCTCAGACCCTTTGTGAAGC 58.472 55.000 0.00 0.00 0.00 3.86
2556 5191 7.656948 GGAAGCTGCAAAAATTATGGCATATAA 59.343 33.333 8.24 0.00 35.45 0.98
2602 5238 1.221414 ACGTTTGTCAGCTCTGCTTC 58.779 50.000 0.00 0.00 36.40 3.86
2652 5288 1.227002 GCGTCATTCTCGGGGAGAC 60.227 63.158 0.00 0.00 38.51 3.36
2653 5289 1.945354 GCGTCATTCTCGGGGAGACA 61.945 60.000 0.00 0.00 38.51 3.41
2654 5290 0.530744 CGTCATTCTCGGGGAGACAA 59.469 55.000 0.00 0.00 38.51 3.18
2681 5317 0.530431 TGCTGCGATGCGTGATACAT 60.530 50.000 0.00 0.00 35.36 2.29
2703 5343 0.620556 GCAATCCTTCTCCCTGACCA 59.379 55.000 0.00 0.00 0.00 4.02
2717 5357 3.403038 CCTGACCATCTTCACGTTTCTT 58.597 45.455 0.00 0.00 0.00 2.52
2823 7673 4.148825 CGGAAGAGCCAGGTCCCG 62.149 72.222 1.18 1.18 35.94 5.14
2826 7676 1.375326 GAAGAGCCAGGTCCCGTTT 59.625 57.895 0.00 0.00 0.00 3.60
2828 7678 0.185175 AAGAGCCAGGTCCCGTTTTT 59.815 50.000 0.00 0.00 0.00 1.94
2829 7679 0.250770 AGAGCCAGGTCCCGTTTTTC 60.251 55.000 0.00 0.00 0.00 2.29
2830 7680 0.250770 GAGCCAGGTCCCGTTTTTCT 60.251 55.000 0.00 0.00 0.00 2.52
2831 7681 0.250770 AGCCAGGTCCCGTTTTTCTC 60.251 55.000 0.00 0.00 0.00 2.87
2833 7683 0.109723 CCAGGTCCCGTTTTTCTCCA 59.890 55.000 0.00 0.00 0.00 3.86
2834 7684 1.271926 CCAGGTCCCGTTTTTCTCCAT 60.272 52.381 0.00 0.00 0.00 3.41
2835 7685 2.084546 CAGGTCCCGTTTTTCTCCATC 58.915 52.381 0.00 0.00 0.00 3.51
2836 7686 1.985895 AGGTCCCGTTTTTCTCCATCT 59.014 47.619 0.00 0.00 0.00 2.90
2837 7687 3.055385 CAGGTCCCGTTTTTCTCCATCTA 60.055 47.826 0.00 0.00 0.00 1.98
2838 7688 3.055312 AGGTCCCGTTTTTCTCCATCTAC 60.055 47.826 0.00 0.00 0.00 2.59
2839 7689 3.055312 GGTCCCGTTTTTCTCCATCTACT 60.055 47.826 0.00 0.00 0.00 2.57
2840 7690 4.161001 GGTCCCGTTTTTCTCCATCTACTA 59.839 45.833 0.00 0.00 0.00 1.82
2842 7692 4.120589 CCCGTTTTTCTCCATCTACTAGC 58.879 47.826 0.00 0.00 0.00 3.42
2843 7693 4.141914 CCCGTTTTTCTCCATCTACTAGCT 60.142 45.833 0.00 0.00 0.00 3.32
2844 7694 5.068723 CCCGTTTTTCTCCATCTACTAGCTA 59.931 44.000 0.00 0.00 0.00 3.32
2906 7780 0.602905 CAAAGGGTCCCGTCAGTGTC 60.603 60.000 0.99 0.00 0.00 3.67
3054 7931 2.094906 TCGTCGGTGAAATGGTAGTCTG 60.095 50.000 0.00 0.00 0.00 3.51
3128 8007 1.513586 GCAGCTGCGAAATGTGAGC 60.514 57.895 25.23 0.00 0.00 4.26
3173 8055 1.344942 CTCTGCCGTCGTGTTACTGC 61.345 60.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.242413 CGTTTTCTGAAGTGGACACTGTG 60.242 47.826 6.19 6.19 41.58 3.66
36 37 1.241990 GCGGGACCAAAAGGTTCTCC 61.242 60.000 0.00 0.00 0.00 3.71
54 55 1.109296 CAAAAGTGTAACACGTGCGC 58.891 50.000 17.22 0.00 41.43 6.09
55 56 1.062880 ACCAAAAGTGTAACACGTGCG 59.937 47.619 17.22 0.00 41.43 5.34
72 73 0.100325 CGCTGTTGCTGAACAAACCA 59.900 50.000 0.00 0.00 41.62 3.67
99 100 6.488006 GTGTGGAGGACTAAAATATGCATCAT 59.512 38.462 0.19 0.00 0.00 2.45
119 120 1.239296 TACCGTGAGAGTCCGTGTGG 61.239 60.000 0.00 0.00 0.00 4.17
123 124 0.037326 TACGTACCGTGAGAGTCCGT 60.037 55.000 0.00 0.00 41.39 4.69
143 144 3.362237 GCTCGTGCTCATATTGATCGTAC 59.638 47.826 1.41 0.00 36.03 3.67
161 162 4.929808 ACATTTCTACTGTACCAAAGCTCG 59.070 41.667 0.00 0.00 0.00 5.03
215 216 5.189342 TCGTCCTTCCTTCTTCTAGTCTAGA 59.811 44.000 5.41 5.41 0.00 2.43
297 303 9.868160 CCCTTCCTTTCCTTATTTGATTACTAT 57.132 33.333 0.00 0.00 0.00 2.12
310 319 6.391055 TCATGAATAGATCCCTTCCTTTCCTT 59.609 38.462 0.00 0.00 0.00 3.36
311 320 5.913534 TCATGAATAGATCCCTTCCTTTCCT 59.086 40.000 0.00 0.00 0.00 3.36
312 321 6.192970 TCATGAATAGATCCCTTCCTTTCC 57.807 41.667 0.00 0.00 0.00 3.13
313 322 8.525290 TTTTCATGAATAGATCCCTTCCTTTC 57.475 34.615 9.40 0.00 0.00 2.62
314 323 8.921205 CATTTTCATGAATAGATCCCTTCCTTT 58.079 33.333 9.40 0.00 31.07 3.11
367 376 8.924303 TGCTATACTTATGTTCTTGATACCACT 58.076 33.333 0.00 0.00 0.00 4.00
450 464 3.748083 CCGGATCAATGGACATTCATCT 58.252 45.455 8.47 0.00 30.36 2.90
453 467 1.679139 GCCGGATCAATGGACATTCA 58.321 50.000 5.05 0.00 0.00 2.57
456 470 0.532862 GTCGCCGGATCAATGGACAT 60.533 55.000 5.05 0.00 0.00 3.06
471 485 0.468226 TGGGTGGATATTCCTGTCGC 59.532 55.000 0.00 0.00 37.46 5.19
504 825 5.572896 GGCAATTGAAGATCCGTTTTAACTG 59.427 40.000 10.34 0.00 0.00 3.16
544 865 5.820131 TGCCGATTAGTCAAAATTATGCAG 58.180 37.500 0.00 0.00 0.00 4.41
586 908 0.098728 GTACATGGCAACCATCGCAC 59.901 55.000 0.00 0.00 43.15 5.34
592 914 1.015085 GCGTACGTACATGGCAACCA 61.015 55.000 24.50 0.00 38.19 3.67
635 957 3.876198 CCATGGCACGGCGCTAAC 61.876 66.667 6.90 0.00 41.91 2.34
790 1174 4.552365 ATGGCCTGTGCGATCGGG 62.552 66.667 18.30 10.52 38.85 5.14
830 1214 1.069935 GGATAACGCCAGGCTCCTC 59.930 63.158 10.54 0.75 0.00 3.71
831 1215 1.689233 TGGATAACGCCAGGCTCCT 60.689 57.895 16.53 1.09 33.10 3.69
906 1292 1.342374 GGCTTGGGATTTCTGATGGGT 60.342 52.381 0.00 0.00 0.00 4.51
907 1293 1.342275 TGGCTTGGGATTTCTGATGGG 60.342 52.381 0.00 0.00 0.00 4.00
908 1294 2.148446 TGGCTTGGGATTTCTGATGG 57.852 50.000 0.00 0.00 0.00 3.51
948 1356 0.385598 GTTCGGGCTCGAGTTTTTGC 60.386 55.000 9.49 0.00 46.75 3.68
958 1366 0.606673 AGCTTTCTTGGTTCGGGCTC 60.607 55.000 0.00 0.00 0.00 4.70
1402 3985 5.754890 GTGCTCAAAACCAAATCAAGAACAT 59.245 36.000 0.00 0.00 0.00 2.71
1412 4006 3.993081 CACAAACTGTGCTCAAAACCAAA 59.007 39.130 0.00 0.00 41.89 3.28
1413 4007 3.583806 CACAAACTGTGCTCAAAACCAA 58.416 40.909 0.00 0.00 41.89 3.67
1414 4008 2.094286 CCACAAACTGTGCTCAAAACCA 60.094 45.455 1.12 0.00 46.51 3.67
1415 4009 2.165437 TCCACAAACTGTGCTCAAAACC 59.835 45.455 1.12 0.00 46.51 3.27
1416 4010 3.119495 ACTCCACAAACTGTGCTCAAAAC 60.119 43.478 1.12 0.00 46.51 2.43
1417 4011 3.088532 ACTCCACAAACTGTGCTCAAAA 58.911 40.909 1.12 0.00 46.51 2.44
1418 4012 2.722094 ACTCCACAAACTGTGCTCAAA 58.278 42.857 1.12 0.00 46.51 2.69
1419 4013 2.418368 ACTCCACAAACTGTGCTCAA 57.582 45.000 1.12 0.00 46.51 3.02
1420 4014 2.801699 CGTACTCCACAAACTGTGCTCA 60.802 50.000 1.12 0.00 46.51 4.26
1421 4015 1.792949 CGTACTCCACAAACTGTGCTC 59.207 52.381 1.12 0.00 46.51 4.26
1422 4016 1.411246 TCGTACTCCACAAACTGTGCT 59.589 47.619 1.12 0.00 46.51 4.40
1423 4017 1.792949 CTCGTACTCCACAAACTGTGC 59.207 52.381 1.12 0.00 46.51 4.57
1761 4363 7.824289 TCTGGAGACTCGAAACAAAATCATTAT 59.176 33.333 0.00 0.00 0.00 1.28
1791 4394 1.076533 CGAACGCCGTTATCACTGCT 61.077 55.000 0.79 0.00 31.18 4.24
1819 4422 3.950395 GCAGATTAAGGGAGCAAGAACAT 59.050 43.478 0.00 0.00 0.00 2.71
1918 4521 3.319198 TTCTCCGGGTGCCTCCAC 61.319 66.667 0.00 0.00 41.32 4.02
1992 4595 1.380785 ATACCACCGGCCGAGAAGA 60.381 57.895 30.73 9.33 0.00 2.87
1994 4597 1.259142 TTCATACCACCGGCCGAGAA 61.259 55.000 30.73 14.92 0.00 2.87
2021 4624 2.760092 TGCAAGCCATAATCAGAAACCC 59.240 45.455 0.00 0.00 0.00 4.11
2149 4763 2.871022 GAGGCTCTCGTCGTTGTAGATA 59.129 50.000 7.40 0.00 0.00 1.98
2215 4841 4.767255 CGGAGCGGCTTCTTGGCT 62.767 66.667 2.97 0.00 40.29 4.75
2374 5000 1.064357 GGAACCGAACAGACGCAAAAA 59.936 47.619 0.00 0.00 0.00 1.94
2408 5034 9.981460 AACCTCCTATCTTAAACTTGAAATGAT 57.019 29.630 0.00 0.00 0.00 2.45
2409 5035 9.807921 AAACCTCCTATCTTAAACTTGAAATGA 57.192 29.630 0.00 0.00 0.00 2.57
2431 5064 3.985925 ACGTAGACTGTTTCGATCAAACC 59.014 43.478 14.25 4.15 43.52 3.27
2432 5065 6.307318 ACATACGTAGACTGTTTCGATCAAAC 59.693 38.462 0.08 11.52 44.31 2.93
2433 5066 6.307077 CACATACGTAGACTGTTTCGATCAAA 59.693 38.462 0.08 0.00 0.00 2.69
2434 5067 5.798434 CACATACGTAGACTGTTTCGATCAA 59.202 40.000 0.08 0.00 0.00 2.57
2435 5068 5.122711 TCACATACGTAGACTGTTTCGATCA 59.877 40.000 0.08 0.00 0.00 2.92
2436 5069 5.566623 TCACATACGTAGACTGTTTCGATC 58.433 41.667 0.08 0.00 0.00 3.69
2437 5070 5.556355 TCACATACGTAGACTGTTTCGAT 57.444 39.130 0.08 0.00 0.00 3.59
2444 5077 5.298527 TGAGGGTATTCACATACGTAGACTG 59.701 44.000 0.08 0.00 36.81 3.51
2449 5082 4.581824 GGTCTGAGGGTATTCACATACGTA 59.418 45.833 0.00 0.00 36.81 3.57
2463 5096 1.884067 GCTTCACAAAGGGTCTGAGGG 60.884 57.143 0.00 0.00 32.79 4.30
2468 5103 1.771255 ACTCTGCTTCACAAAGGGTCT 59.229 47.619 0.00 0.00 32.79 3.85
2483 5118 0.109365 CAGGACGAGACAGCACTCTG 60.109 60.000 0.00 0.00 45.71 3.35
2556 5191 5.923684 GTGAGAGAGAAGTTGACGAGAAAAT 59.076 40.000 0.00 0.00 0.00 1.82
2562 5197 4.083961 CGTAAGTGAGAGAGAAGTTGACGA 60.084 45.833 0.00 0.00 0.00 4.20
2602 5238 3.936372 TTAGAGACAGAACGACAAGGG 57.064 47.619 0.00 0.00 0.00 3.95
2660 5296 0.583438 GTATCACGCATCGCAGCATT 59.417 50.000 0.00 0.00 0.00 3.56
2681 5317 0.549902 TCAGGGAGAAGGATTGCCCA 60.550 55.000 0.00 0.00 40.72 5.36
2703 5343 8.777865 TTAGAATCATCAAGAAACGTGAAGAT 57.222 30.769 0.00 0.00 35.52 2.40
2731 7565 4.458989 TGAAGCTCCGCTAAAAACATTCAT 59.541 37.500 0.00 0.00 38.25 2.57
2733 7567 4.419522 TGAAGCTCCGCTAAAAACATTC 57.580 40.909 0.00 0.00 38.25 2.67
2734 7568 6.318648 TCATATGAAGCTCCGCTAAAAACATT 59.681 34.615 1.98 0.00 38.25 2.71
2744 7578 5.445142 CGTCATAAATCATATGAAGCTCCGC 60.445 44.000 9.99 0.00 35.92 5.54
2752 7586 6.020971 AGCCGTACGTCATAAATCATATGA 57.979 37.500 15.21 8.10 0.00 2.15
2753 7587 7.488150 ACATAGCCGTACGTCATAAATCATATG 59.512 37.037 15.21 5.57 0.00 1.78
2816 7666 1.985895 AGATGGAGAAAAACGGGACCT 59.014 47.619 0.00 0.00 0.00 3.85
2819 7669 4.142004 GCTAGTAGATGGAGAAAAACGGGA 60.142 45.833 0.00 0.00 0.00 5.14
2823 7673 7.863877 GCTAGTAGCTAGTAGATGGAGAAAAAC 59.136 40.741 31.35 11.23 38.45 2.43
2826 7676 6.602278 TGCTAGTAGCTAGTAGATGGAGAAA 58.398 40.000 31.35 9.15 42.97 2.52
2828 7678 5.800296 CTGCTAGTAGCTAGTAGATGGAGA 58.200 45.833 31.35 11.58 45.32 3.71
2829 7679 4.394920 GCTGCTAGTAGCTAGTAGATGGAG 59.605 50.000 31.35 21.69 45.32 3.86
2830 7680 4.328536 GCTGCTAGTAGCTAGTAGATGGA 58.671 47.826 31.35 14.87 45.32 3.41
2831 7681 3.442273 GGCTGCTAGTAGCTAGTAGATGG 59.558 52.174 31.35 21.52 45.32 3.51
2833 7683 4.331968 CAGGCTGCTAGTAGCTAGTAGAT 58.668 47.826 31.35 13.26 45.32 1.98
2834 7684 3.497048 CCAGGCTGCTAGTAGCTAGTAGA 60.497 52.174 31.35 18.45 45.32 2.59
2835 7685 2.817258 CCAGGCTGCTAGTAGCTAGTAG 59.183 54.545 28.53 25.44 45.28 2.57
2836 7686 2.865079 CCAGGCTGCTAGTAGCTAGTA 58.135 52.381 28.53 8.04 42.97 1.82
2837 7687 1.698506 CCAGGCTGCTAGTAGCTAGT 58.301 55.000 28.53 13.52 42.97 2.57
2838 7688 0.316841 GCCAGGCTGCTAGTAGCTAG 59.683 60.000 28.53 20.93 42.97 3.42
2839 7689 0.397114 TGCCAGGCTGCTAGTAGCTA 60.397 55.000 28.53 10.48 42.97 3.32
2840 7690 1.053264 ATGCCAGGCTGCTAGTAGCT 61.053 55.000 28.53 14.32 42.97 3.32
2842 7692 1.967066 AGTATGCCAGGCTGCTAGTAG 59.033 52.381 14.15 3.05 0.00 2.57
2843 7693 2.088104 AGTATGCCAGGCTGCTAGTA 57.912 50.000 14.15 0.00 0.00 1.82
2844 7694 2.088104 TAGTATGCCAGGCTGCTAGT 57.912 50.000 14.15 7.33 0.00 2.57
2897 7771 2.221749 CCACACAATCAAGACACTGACG 59.778 50.000 0.00 0.00 0.00 4.35
2906 7780 3.058016 AGCACGAAATCCACACAATCAAG 60.058 43.478 0.00 0.00 0.00 3.02
3021 7898 1.732259 CACCGACGAAATTTCCCTCTG 59.268 52.381 12.54 6.52 0.00 3.35
3022 7899 1.621814 TCACCGACGAAATTTCCCTCT 59.378 47.619 12.54 0.00 0.00 3.69
3079 7957 4.999311 AGGGTACGTGGATTTGTTAAGTTC 59.001 41.667 0.00 0.00 0.00 3.01
3143 8022 2.796651 GGCAGAGCAAGCAATCGG 59.203 61.111 0.00 0.00 0.00 4.18
3173 8055 7.765360 TGTAAAAATACACTACGTAATCCAGGG 59.235 37.037 0.00 0.00 32.59 4.45


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

AutoCloner maintained by Alex Coulton.