Multiple sequence alignment - TraesCS1A01G346200

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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 TraesCS1A01G346200 chr1A 100.000 8101 0 0 1 8101 532822638 532814538 0.000000e+00 14960.0
1 TraesCS1A01G346200 chr1A 94.097 288 17 0 2759 3046 518697353 518697640 9.650000e-119 438.0
2 TraesCS1A01G346200 chr1A 95.139 144 6 1 3055 3198 518726190 518726332 8.180000e-55 226.0
3 TraesCS1A01G346200 chr1A 100.000 29 0 0 213 241 185525697 185525669 4.000000e-03 54.7
4 TraesCS1A01G346200 chr1D 96.964 6127 116 20 215 6327 435316338 435310268 0.000000e+00 10220.0
5 TraesCS1A01G346200 chr1D 93.377 1827 65 11 6310 8101 435308068 435306263 0.000000e+00 2652.0
6 TraesCS1A01G346200 chr1D 85.325 477 45 12 6538 6991 452524627 452525101 3.420000e-128 470.0
7 TraesCS1A01G346200 chr1D 83.713 307 30 9 7008 7295 452525304 452525609 1.040000e-68 272.0
8 TraesCS1A01G346200 chr1D 90.854 164 13 2 56 218 73725589 73725751 1.370000e-52 219.0
9 TraesCS1A01G346200 chr1B 96.498 5397 157 18 292 5676 588635056 588629680 0.000000e+00 8890.0
10 TraesCS1A01G346200 chr1B 93.857 2458 104 21 5663 8087 588629463 588627020 0.000000e+00 3659.0
11 TraesCS1A01G346200 chr1B 93.617 329 20 1 1 328 588635382 588635054 2.630000e-134 490.0
12 TraesCS1A01G346200 chr2A 89.540 239 25 0 1385 1623 43916505 43916267 3.670000e-78 303.0
13 TraesCS1A01G346200 chr3D 92.121 165 12 1 53 216 87925997 87926161 1.760000e-56 231.0
14 TraesCS1A01G346200 chr2D 91.411 163 12 2 55 216 296364210 296364049 1.060000e-53 222.0
15 TraesCS1A01G346200 chr2B 90.964 166 13 2 52 216 366017515 366017679 1.060000e-53 222.0
16 TraesCS1A01G346200 chr4D 91.358 162 13 1 56 216 117421191 117421352 3.810000e-53 220.0
17 TraesCS1A01G346200 chr4D 90.058 171 16 1 48 217 386984660 386984830 3.810000e-53 220.0
18 TraesCS1A01G346200 chr4D 88.636 44 5 0 213 256 481171029 481170986 4.000000e-03 54.7
19 TraesCS1A01G346200 chr5A 89.143 175 17 2 44 216 569179329 569179155 4.920000e-52 217.0
20 TraesCS1A01G346200 chr5A 79.439 107 21 1 7551 7657 52174515 52174620 3.140000e-09 75.0
21 TraesCS1A01G346200 chrUn 89.820 167 15 2 52 216 141680912 141680746 6.370000e-51 213.0
22 TraesCS1A01G346200 chr7D 92.857 70 4 1 7819 7888 557077831 557077899 5.170000e-17 100.0
23 TraesCS1A01G346200 chr7B 91.667 72 5 1 7817 7888 604660300 604660370 1.860000e-16 99.0
24 TraesCS1A01G346200 chr4B 89.583 48 5 0 213 260 609499537 609499490 2.440000e-05 62.1


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 TraesCS1A01G346200 chr1A 532814538 532822638 8100 True 14960.000000 14960 100.000000 1 8101 1 chr1A.!!$R2 8100
1 TraesCS1A01G346200 chr1D 435306263 435316338 10075 True 6436.000000 10220 95.170500 215 8101 2 chr1D.!!$R1 7886
2 TraesCS1A01G346200 chr1D 452524627 452525609 982 False 371.000000 470 84.519000 6538 7295 2 chr1D.!!$F2 757
3 TraesCS1A01G346200 chr1B 588627020 588635382 8362 True 4346.333333 8890 94.657333 1 8087 3 chr1B.!!$R1 8086

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
120 121 0.727398 GGACTGCATACCGAGCAAAC 59.273 55.000 0.00 0.0 42.17 2.93 F
123 124 0.729116 CTGCATACCGAGCAAACTGG 59.271 55.000 0.00 0.0 42.17 4.00 F
1021 1063 1.071605 GCAGCTCCTCAGTAAACACG 58.928 55.000 0.00 0.0 0.00 4.49 F
1671 1716 0.988832 ATGCCTTTTGTCCTCCGGTA 59.011 50.000 0.00 0.0 0.00 4.02 F
2296 2342 2.416296 GCTTTAATAACGTGTTGCCCCC 60.416 50.000 0.00 0.0 0.00 5.40 F
2668 2716 2.426522 CCAGACGATGTGGTGATTTGT 58.573 47.619 0.00 0.0 0.00 2.83 F
2872 2920 4.023980 ACGATCACCCTATTCACTCAGAA 58.976 43.478 0.00 0.0 41.28 3.02 F
4884 4936 2.353109 CCATGTCTCAGTTCGAGCAAGA 60.353 50.000 1.01 1.1 41.98 3.02 F
5676 5963 0.033504 TCACACGGCTTCCACTTCTC 59.966 55.000 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 1108 0.178068 AGAACCGTGGGATTCCGATG 59.822 55.000 0.12 0.12 35.24 3.84 R
1107 1149 1.888512 TGGCAACCATTCTTCTCTTGC 59.111 47.619 0.00 0.00 37.16 4.01 R
2872 2920 3.081804 CTGCTCCCTCGTTAAATTTGGT 58.918 45.455 0.00 0.00 0.00 3.67 R
3515 3563 2.171448 AGGAGTCTTCAAACAGCAGTGT 59.829 45.455 0.00 0.00 39.19 3.55 R
4060 4110 5.221422 GGGAGTTGTTTGATCACCAAATCAA 60.221 40.000 24.51 9.56 45.48 2.57 R
4884 4936 7.624549 TGTTAAGAGAGATGACCTTGCTATTT 58.375 34.615 0.00 0.00 0.00 1.40 R
5045 5097 2.767505 AGTGAAAGTACCTTGCCTTCG 58.232 47.619 0.00 0.00 0.00 3.79 R
7046 9763 0.991920 TTCCATCCTTCACCACTCCC 59.008 55.000 0.00 0.00 0.00 4.30 R
7629 10364 0.323451 AGAAAAACCCGAGGCCATCC 60.323 55.000 5.01 0.00 0.00 3.51 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
30 31 6.631016 ACATGAGAAAGCGTCAAAGATAGTA 58.369 36.000 0.00 0.00 0.00 1.82
120 121 0.727398 GGACTGCATACCGAGCAAAC 59.273 55.000 0.00 0.00 42.17 2.93
123 124 0.729116 CTGCATACCGAGCAAACTGG 59.271 55.000 0.00 0.00 42.17 4.00
136 137 3.007635 GCAAACTGGGTAAATCTACGCT 58.992 45.455 0.00 0.00 40.68 5.07
390 426 8.787852 GTTGTCTCACATTCTCCTTCTTAATTT 58.212 33.333 0.00 0.00 0.00 1.82
498 536 7.429340 GTCATATTTTTGCGAATAGTGGAAGTG 59.571 37.037 0.00 0.00 0.00 3.16
1021 1063 1.071605 GCAGCTCCTCAGTAAACACG 58.928 55.000 0.00 0.00 0.00 4.49
1036 1078 1.302431 CACGCATCCAGTTCCACCA 60.302 57.895 0.00 0.00 0.00 4.17
1060 1102 4.154195 ACGTAAATAAGGCAACAGAAGCTG 59.846 41.667 0.00 0.00 41.41 4.24
1066 1108 1.578423 GCAACAGAAGCTGCTCCAC 59.422 57.895 1.00 0.00 34.08 4.02
1107 1149 6.404708 TCTTGATCTCTTCCTGAAGTCATTG 58.595 40.000 6.78 1.80 39.38 2.82
1344 1389 2.237392 ACTTATTCTCCACTGGGCACTC 59.763 50.000 0.00 0.00 0.00 3.51
1356 1401 2.563427 GCACTCGCAAAGAAGGCC 59.437 61.111 0.00 0.00 38.36 5.19
1383 1428 5.940470 AGAGTGGAAGGTAAAATCATCACAC 59.060 40.000 0.00 0.00 0.00 3.82
1485 1530 1.337447 ACATTGCTTGAACTGGCATGC 60.337 47.619 9.90 9.90 38.30 4.06
1528 1573 5.123820 GCTGAACTAGATGGTTTGCATTACA 59.876 40.000 0.00 0.00 33.07 2.41
1566 1611 5.639757 TCATCATTGCAGTATTTGTTTCCG 58.360 37.500 0.00 0.00 0.00 4.30
1671 1716 0.988832 ATGCCTTTTGTCCTCCGGTA 59.011 50.000 0.00 0.00 0.00 4.02
1829 1874 7.068716 AGAGTTCCTTCAAAAGTGCTAACAAAT 59.931 33.333 0.00 0.00 0.00 2.32
1831 1876 8.691797 AGTTCCTTCAAAAGTGCTAACAAATTA 58.308 29.630 0.00 0.00 0.00 1.40
2203 2249 4.641989 CCCTCATTTCATCAACCCTACAAG 59.358 45.833 0.00 0.00 0.00 3.16
2296 2342 2.416296 GCTTTAATAACGTGTTGCCCCC 60.416 50.000 0.00 0.00 0.00 5.40
2668 2716 2.426522 CCAGACGATGTGGTGATTTGT 58.573 47.619 0.00 0.00 0.00 2.83
2854 2902 5.283457 AGGAAAGATTAGCAAGCTACGAT 57.717 39.130 0.40 0.00 0.00 3.73
2872 2920 4.023980 ACGATCACCCTATTCACTCAGAA 58.976 43.478 0.00 0.00 41.28 3.02
3069 3117 6.367161 TCATCTCCATATGGAAGAAAATGCA 58.633 36.000 24.54 10.48 44.91 3.96
3514 3562 5.358298 GTGGAATCACTTGTTGAGGTAAC 57.642 43.478 0.00 0.00 40.58 2.50
3515 3563 4.819630 GTGGAATCACTTGTTGAGGTAACA 59.180 41.667 0.00 0.00 42.28 2.41
3874 3924 5.299279 TGCGTACTGTCTCATAATCATCTCA 59.701 40.000 0.00 0.00 0.00 3.27
4060 4110 8.776470 CAAGGTGCATTCAAAGAAAACAATTAT 58.224 29.630 0.00 0.00 0.00 1.28
4222 4274 9.350357 CCTTGAAATGTCAAACAAATCTGATAG 57.650 33.333 0.00 0.00 43.18 2.08
4884 4936 2.353109 CCATGTCTCAGTTCGAGCAAGA 60.353 50.000 1.01 1.10 41.98 3.02
5176 5228 6.554982 TGATATGCCTAACATCTACCTGTCTT 59.445 38.462 0.00 0.00 40.38 3.01
5266 5321 1.480137 AGCACCATCTCTGTCACTAGC 59.520 52.381 0.00 0.00 0.00 3.42
5280 5335 4.152402 TGTCACTAGCGAAGAAGCAATTTC 59.848 41.667 0.00 0.00 40.15 2.17
5355 5410 5.587388 TCCAATGCCATTCTGAATTTCTC 57.413 39.130 0.00 0.00 0.00 2.87
5358 5413 6.155565 TCCAATGCCATTCTGAATTTCTCATT 59.844 34.615 0.00 5.52 32.14 2.57
5424 5479 5.869579 ACCACGGAGCATATTCATATTCTT 58.130 37.500 0.00 0.00 0.00 2.52
5430 5485 8.774586 ACGGAGCATATTCATATTCTTTTACAC 58.225 33.333 0.00 0.00 0.00 2.90
5579 5636 3.308530 CATTTGGAACCTTCGAAACAGC 58.691 45.455 0.00 0.00 37.64 4.40
5592 5649 5.591643 TCGAAACAGCTTTGTCTGATAAC 57.408 39.130 0.00 0.00 37.51 1.89
5653 5710 4.987285 ACTCTCGCAAATGCATCATACTAG 59.013 41.667 0.00 0.00 42.21 2.57
5654 5711 3.742882 TCTCGCAAATGCATCATACTAGC 59.257 43.478 0.00 0.00 42.21 3.42
5662 5719 3.732212 TGCATCATACTAGCCATCACAC 58.268 45.455 0.00 0.00 0.00 3.82
5676 5963 0.033504 TCACACGGCTTCCACTTCTC 59.966 55.000 0.00 0.00 0.00 2.87
5686 5973 3.997681 GCTTCCACTTCTCAAACTCTACC 59.002 47.826 0.00 0.00 0.00 3.18
5784 6071 6.114187 TGGTGAAATGTCAGATGTCTACTT 57.886 37.500 0.00 0.00 33.27 2.24
5792 6079 6.037786 TGTCAGATGTCTACTTACCAAAGG 57.962 41.667 0.00 0.00 37.01 3.11
5808 6095 8.880991 TTACCAAAGGCCATGTTAAGTTATAA 57.119 30.769 5.01 0.00 0.00 0.98
5899 6186 1.547901 GGCAGGAAGTAGCCCAAAAGT 60.548 52.381 0.00 0.00 45.18 2.66
6102 6389 3.905416 GCAACAGTTTGTTTTTGCAACAC 59.095 39.130 0.00 0.00 43.16 3.32
6755 9286 2.520979 GTCATCTTCCGTTCTGACTCG 58.479 52.381 0.00 0.00 36.07 4.18
6975 9506 3.472652 ACAGATTGCAGTTTCCGTAACA 58.527 40.909 0.00 0.00 39.30 2.41
6999 9530 6.090763 CACAATACTCTCAAACATTGCTCGTA 59.909 38.462 0.00 0.00 32.76 3.43
7046 9763 3.041211 TGGGTCTCCACAGGATATTGAG 58.959 50.000 0.00 0.00 38.32 3.02
7164 9887 3.731216 CGTGCATCTTATAGAGTTCCACG 59.269 47.826 0.00 0.00 36.00 4.94
7230 9954 7.055667 TGGTATAAGATGGCAAACTAGAGAG 57.944 40.000 0.00 0.00 0.00 3.20
7245 9975 7.678207 AACTAGAGAGTAATAAAAGGAGGGG 57.322 40.000 0.00 0.00 33.58 4.79
7246 9976 5.603395 ACTAGAGAGTAATAAAAGGAGGGGC 59.397 44.000 0.00 0.00 32.65 5.80
7326 10061 9.628500 AACCTATCCATATAAGAAGTTCCAAAC 57.372 33.333 0.00 0.00 0.00 2.93
7333 10068 9.401058 CCATATAAGAAGTTCCAAACATCTCTT 57.599 33.333 0.00 3.62 38.39 2.85
7373 10108 5.105997 GCCTGCAAATGAAGATTAGAAGTGT 60.106 40.000 0.00 0.00 0.00 3.55
7468 10203 4.452114 CAGGCCATTAAAAGAAACAAAGGC 59.548 41.667 5.01 0.00 38.84 4.35
7530 10265 8.408601 CAGTTATTGGCTATTGCAGATAAGTTT 58.591 33.333 0.66 0.00 41.91 2.66
7585 10320 1.563879 TGGTCCATGGTCATAGGGTTG 59.436 52.381 12.58 0.00 0.00 3.77
7629 10364 1.538512 CTGTGAGGCAGGTTCAATGTG 59.461 52.381 0.00 0.00 41.42 3.21
7639 10374 0.734889 GTTCAATGTGGATGGCCTCG 59.265 55.000 3.32 0.00 34.31 4.63
7645 10380 1.304134 GTGGATGGCCTCGGGTTTT 60.304 57.895 3.32 0.00 34.31 2.43
7670 10405 7.780008 TCTTTCTTTTTGTGTAAGTCGATCA 57.220 32.000 0.00 0.00 0.00 2.92
7674 10409 6.943981 TCTTTTTGTGTAAGTCGATCAGTTG 58.056 36.000 0.00 0.00 0.00 3.16
7675 10410 6.537301 TCTTTTTGTGTAAGTCGATCAGTTGT 59.463 34.615 0.00 0.00 0.00 3.32
7684 10419 3.372206 AGTCGATCAGTTGTAATGCTTGC 59.628 43.478 0.00 0.00 0.00 4.01
7736 10471 1.753848 CAATTGATGCAGGGGCCGA 60.754 57.895 0.00 0.00 40.13 5.54
7758 10493 3.572642 GGGTTTCCCTCTTTTCCAGAAA 58.427 45.455 0.00 0.00 41.34 2.52
7759 10494 4.160329 GGGTTTCCCTCTTTTCCAGAAAT 58.840 43.478 0.00 0.00 41.34 2.17
7760 10495 5.330233 GGGTTTCCCTCTTTTCCAGAAATA 58.670 41.667 0.00 0.00 41.34 1.40
7795 10530 4.938226 CCACCTGTCCTTCTAATTCTTCAC 59.062 45.833 0.00 0.00 0.00 3.18
7801 10536 4.695928 GTCCTTCTAATTCTTCACCACCAC 59.304 45.833 0.00 0.00 0.00 4.16
7804 10539 4.286297 TCTAATTCTTCACCACCACAGG 57.714 45.455 0.00 0.00 0.00 4.00
7889 10624 2.827715 GACATCCCAGGGTCGAGAT 58.172 57.895 5.01 0.00 0.00 2.75
7890 10625 0.390860 GACATCCCAGGGTCGAGATG 59.609 60.000 5.01 3.82 41.50 2.90
7900 10635 6.272324 TCCCAGGGTCGAGATGAAATATATTT 59.728 38.462 10.51 10.51 0.00 1.40
7903 10638 8.292448 CCAGGGTCGAGATGAAATATATTTTTG 58.708 37.037 11.92 1.10 0.00 2.44
7957 10694 5.784578 AAGTTTTGAGCGGAAAAATACCT 57.215 34.783 0.00 0.00 0.00 3.08
8054 10796 3.244078 TGTTCAAACACGTGCCTAGATCT 60.244 43.478 17.22 0.00 33.17 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.707599 AAGTGTACTATCTTTGACGCTTTC 57.292 37.500 0.00 0.00 39.04 2.62
97 98 1.970640 TGCTCGGTATGCAGTCCATAT 59.029 47.619 9.98 0.00 38.60 1.78
106 107 0.676782 ACCCAGTTTGCTCGGTATGC 60.677 55.000 0.00 0.00 34.37 3.14
120 121 8.926710 CATATTTTAGAGCGTAGATTTACCCAG 58.073 37.037 0.00 0.00 0.00 4.45
123 124 9.694137 AGACATATTTTAGAGCGTAGATTTACC 57.306 33.333 0.00 0.00 0.00 2.85
194 196 7.229581 GAGTACTCCATCCGTTCCTAAATAT 57.770 40.000 12.13 0.00 0.00 1.28
195 197 6.645790 GAGTACTCCATCCGTTCCTAAATA 57.354 41.667 12.13 0.00 0.00 1.40
498 536 6.268797 TCGTTCAGCATAATTTCGATGTAC 57.731 37.500 0.00 0.00 0.00 2.90
666 704 8.164070 ACTGGTATTCAGAAGACAAAATAGGTT 58.836 33.333 10.08 0.00 46.18 3.50
669 707 8.877779 CAGACTGGTATTCAGAAGACAAAATAG 58.122 37.037 10.08 2.99 46.18 1.73
702 740 7.164498 CGTCTATCTCGATTTTCAGTGTAGAAC 59.836 40.741 0.00 0.00 0.00 3.01
1021 1063 0.889186 ACGTTGGTGGAACTGGATGC 60.889 55.000 0.00 0.00 36.74 3.91
1036 1078 4.760204 AGCTTCTGTTGCCTTATTTACGTT 59.240 37.500 0.00 0.00 0.00 3.99
1066 1108 0.178068 AGAACCGTGGGATTCCGATG 59.822 55.000 0.12 0.12 35.24 3.84
1107 1149 1.888512 TGGCAACCATTCTTCTCTTGC 59.111 47.619 0.00 0.00 37.16 4.01
1344 1389 2.047274 TCTCCGGCCTTCTTTGCG 60.047 61.111 0.00 0.00 0.00 4.85
1356 1401 4.202245 TGATTTTACCTTCCACTCTCCG 57.798 45.455 0.00 0.00 0.00 4.63
1383 1428 5.808540 TCGTTGTTAATCTTACCTGGAATCG 59.191 40.000 0.00 0.00 0.00 3.34
1485 1530 3.797796 CAGCATCAGAGAATGAACTCTCG 59.202 47.826 0.00 0.00 45.53 4.04
1528 1573 9.590451 CTGCAATGATGAATTTATGTTTACCTT 57.410 29.630 0.00 0.00 0.00 3.50
1566 1611 6.908825 TCAAATGTAGACACCATTACAAAGC 58.091 36.000 0.00 0.00 33.85 3.51
2251 2297 3.947834 ACTTGAGTTCTGTTTGGTGGAAG 59.052 43.478 0.00 0.00 0.00 3.46
2296 2342 8.494347 GCTAATCTCACTGCATAATTGTAAGAG 58.506 37.037 0.00 0.00 0.00 2.85
2502 2548 6.200286 GTGTACTCTTTCGTCAACAAATCAGA 59.800 38.462 0.00 0.00 0.00 3.27
2515 2561 4.611310 TCCTGTATCGTGTACTCTTTCG 57.389 45.455 0.00 0.00 0.00 3.46
2556 2604 8.556194 TCTACAATGAAAACAACTGATGTACAC 58.444 33.333 0.00 0.00 42.99 2.90
2668 2716 6.012337 TCCAAATATGAATGCCTTACCTGA 57.988 37.500 0.00 0.00 0.00 3.86
2854 2902 3.516586 TGGTTCTGAGTGAATAGGGTGA 58.483 45.455 0.00 0.00 36.99 4.02
2872 2920 3.081804 CTGCTCCCTCGTTAAATTTGGT 58.918 45.455 0.00 0.00 0.00 3.67
3396 3444 7.969536 ACATGCCTTCATATGTTACAGATAC 57.030 36.000 1.90 0.00 34.00 2.24
3514 3562 2.289002 GGAGTCTTCAAACAGCAGTGTG 59.711 50.000 0.00 0.00 36.84 3.82
3515 3563 2.171448 AGGAGTCTTCAAACAGCAGTGT 59.829 45.455 0.00 0.00 39.19 3.55
3874 3924 8.641498 AAGTACATGAGTTTCTGGATGAAAAT 57.359 30.769 0.00 0.00 45.10 1.82
4060 4110 5.221422 GGGAGTTGTTTGATCACCAAATCAA 60.221 40.000 24.51 9.56 45.48 2.57
4884 4936 7.624549 TGTTAAGAGAGATGACCTTGCTATTT 58.375 34.615 0.00 0.00 0.00 1.40
5045 5097 2.767505 AGTGAAAGTACCTTGCCTTCG 58.232 47.619 0.00 0.00 0.00 3.79
5176 5228 8.699130 TCTCTGCAATCTCTCTATTAAATGTGA 58.301 33.333 0.00 0.00 0.00 3.58
5332 5387 5.481122 TGAGAAATTCAGAATGGCATTGGAA 59.519 36.000 19.07 19.62 36.16 3.53
5478 5535 4.081087 GCTATATTCCGGGATTTAGCTCCA 60.081 45.833 28.53 0.00 37.01 3.86
5490 5547 4.235360 CGTTGAGGTAAGCTATATTCCGG 58.765 47.826 0.00 0.00 0.00 5.14
5579 5636 7.730364 ACCTTGTTAGTGTTATCAGACAAAG 57.270 36.000 0.00 0.00 0.00 2.77
5592 5649 6.315393 GTGATATGGTACCAACCTTGTTAGTG 59.685 42.308 20.76 0.00 46.91 2.74
5654 5711 0.606401 AAGTGGAAGCCGTGTGATGG 60.606 55.000 0.00 0.00 0.00 3.51
5662 5719 1.801178 GAGTTTGAGAAGTGGAAGCCG 59.199 52.381 0.00 0.00 0.00 5.52
5676 5963 6.402222 AGTATTGCTTCAGAGGTAGAGTTTG 58.598 40.000 0.00 0.00 0.00 2.93
5686 5973 8.281194 CAGTAAATGCATAGTATTGCTTCAGAG 58.719 37.037 0.00 0.00 43.18 3.35
5768 6055 6.644347 CCTTTGGTAAGTAGACATCTGACAT 58.356 40.000 0.00 0.00 0.00 3.06
5784 6071 8.908903 CATTATAACTTAACATGGCCTTTGGTA 58.091 33.333 3.32 1.57 0.00 3.25
5792 6079 8.996024 AAAACCACATTATAACTTAACATGGC 57.004 30.769 0.00 0.00 0.00 4.40
5808 6095 5.209818 TCAGTAGTTCTCGAAAACCACAT 57.790 39.130 3.09 0.00 0.00 3.21
6102 6389 7.228706 ACAAAGGAACTGTTACAAGTAGGATTG 59.771 37.037 5.41 0.66 40.86 2.67
6755 9286 2.716217 CCTTCCAAGTCCTCACCATTC 58.284 52.381 0.00 0.00 0.00 2.67
6810 9341 5.403766 ACAATCGCGTATCATGAAAGATCTC 59.596 40.000 5.77 0.00 0.00 2.75
6812 9343 5.582439 ACAATCGCGTATCATGAAAGATC 57.418 39.130 5.77 0.00 0.00 2.75
6975 9506 4.997395 ACGAGCAATGTTTGAGAGTATTGT 59.003 37.500 0.00 0.00 34.04 2.71
6999 9530 2.158842 GCTCCTCAATAGCATGACCAGT 60.159 50.000 0.00 0.00 39.83 4.00
7046 9763 0.991920 TTCCATCCTTCACCACTCCC 59.008 55.000 0.00 0.00 0.00 4.30
7164 9887 6.585702 TGCATGTTTTAGTACATTGCACAATC 59.414 34.615 0.00 0.00 37.49 2.67
7230 9954 3.555527 ACTCGCCCCTCCTTTTATTAC 57.444 47.619 0.00 0.00 0.00 1.89
7245 9975 2.543777 TATGCTTGGGGATAACTCGC 57.456 50.000 0.00 0.00 0.00 5.03
7246 9976 5.661056 TCTATATGCTTGGGGATAACTCG 57.339 43.478 0.00 0.00 29.93 4.18
7333 10068 2.489329 GCAGGCTGCATTCTTTTCTGTA 59.511 45.455 33.33 0.00 44.26 2.74
7482 10217 3.371166 GCCAGCCATTACCAGTTACCTTA 60.371 47.826 0.00 0.00 0.00 2.69
7530 10265 3.056536 CGAGGAATCAGAGGACTTTGTGA 60.057 47.826 0.00 0.00 0.00 3.58
7585 10320 2.548920 GCATCTCCACCATACTAGCACC 60.549 54.545 0.00 0.00 0.00 5.01
7629 10364 0.323451 AGAAAAACCCGAGGCCATCC 60.323 55.000 5.01 0.00 0.00 3.51
7639 10374 8.542497 ACTTACACAAAAAGAAAGAAAAACCC 57.458 30.769 0.00 0.00 0.00 4.11
7645 10380 8.203937 TGATCGACTTACACAAAAAGAAAGAA 57.796 30.769 0.00 0.00 0.00 2.52
7670 10405 3.321682 ACACAATGGCAAGCATTACAACT 59.678 39.130 0.00 0.00 0.00 3.16
7674 10409 6.966435 ATTAAACACAATGGCAAGCATTAC 57.034 33.333 0.00 0.00 0.00 1.89
7736 10471 4.140686 ATTTCTGGAAAAGAGGGAAACCCT 60.141 41.667 9.27 9.27 44.80 4.34
7743 10478 8.586879 AGAGAATTTATTTCTGGAAAAGAGGG 57.413 34.615 0.00 0.00 44.88 4.30
7751 10486 5.418840 GTGGCCAAGAGAATTTATTTCTGGA 59.581 40.000 7.24 0.00 44.88 3.86
7753 10488 5.420104 AGGTGGCCAAGAGAATTTATTTCTG 59.580 40.000 7.24 0.00 44.88 3.02
7755 10490 5.185828 ACAGGTGGCCAAGAGAATTTATTTC 59.814 40.000 7.24 0.00 34.31 2.17
7758 10493 4.273318 GACAGGTGGCCAAGAGAATTTAT 58.727 43.478 7.24 0.00 0.00 1.40
7759 10494 3.561313 GGACAGGTGGCCAAGAGAATTTA 60.561 47.826 7.24 0.00 44.76 1.40
7760 10495 2.519013 GACAGGTGGCCAAGAGAATTT 58.481 47.619 7.24 0.00 0.00 1.82
7804 10539 5.523438 TGTGAAAACATTTAGGTGGGAAC 57.477 39.130 0.00 0.00 0.00 3.62
7929 10666 4.712122 TTTCCGCTCAAAACTTTCAAGT 57.288 36.364 0.00 0.00 42.04 3.16
7930 10667 6.588348 ATTTTTCCGCTCAAAACTTTCAAG 57.412 33.333 0.00 0.00 0.00 3.02
7934 10671 6.156748 AGGTATTTTTCCGCTCAAAACTTT 57.843 33.333 0.00 0.00 0.00 2.66
7941 10678 9.849166 CTTAAAATTTAGGTATTTTTCCGCTCA 57.151 29.630 0.00 0.00 38.36 4.26
7977 10715 4.207955 GAGGGAACAAGAGAACCAGTTTT 58.792 43.478 0.00 0.00 0.00 2.43
8054 10796 4.314522 TTCCCATGCAAAGGATGACTTA 57.685 40.909 8.76 0.00 38.85 2.24


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

AutoCloner maintained by Alex Coulton.