Multiple sequence alignment - TraesCS7A01G303500

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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 TraesCS7A01G303500 chr7A 100.000 5803 0 0 1 5803 426807702 426801900 0.000000e+00 10717.0
1 TraesCS7A01G303500 chr7A 85.526 76 7 2 1547 1619 159599897 159599971 6.240000e-10 76.8
2 TraesCS7A01G303500 chr7A 94.000 50 3 0 1571 1620 285793637 285793686 6.240000e-10 76.8
3 TraesCS7A01G303500 chr7A 82.353 85 11 4 1542 1623 377428 377345 2.900000e-08 71.3
4 TraesCS7A01G303500 chr7B 95.187 5298 189 25 4 5267 373182393 373177128 0.000000e+00 8311.0
5 TraesCS7A01G303500 chr7D 96.383 3843 116 17 4 3840 378498071 378494246 0.000000e+00 6305.0
6 TraesCS7A01G303500 chr7D 97.681 733 12 4 4537 5267 378493703 378492974 0.000000e+00 1254.0
7 TraesCS7A01G303500 chr7D 96.948 557 11 1 3892 4448 378494248 378493698 0.000000e+00 929.0
8 TraesCS7A01G303500 chr7D 95.353 538 23 2 5265 5801 168499958 168499422 0.000000e+00 854.0
9 TraesCS7A01G303500 chr7D 94.953 535 27 0 5267 5801 136692660 136692126 0.000000e+00 839.0
10 TraesCS7A01G303500 chr7D 94.786 537 28 0 5265 5801 527732854 527732318 0.000000e+00 837.0
11 TraesCS7A01G303500 chr7D 94.340 53 2 1 1572 1623 263044785 263044837 4.820000e-11 80.5
12 TraesCS7A01G303500 chr2D 95.911 538 22 0 5264 5801 95504993 95504456 0.000000e+00 872.0
13 TraesCS7A01G303500 chr2D 95.531 537 24 0 5265 5801 35246590 35247126 0.000000e+00 859.0
14 TraesCS7A01G303500 chr2D 92.157 51 3 1 1570 1619 249895008 249894958 2.900000e-08 71.3
15 TraesCS7A01G303500 chr4D 95.701 535 23 0 5267 5801 66298013 66298547 0.000000e+00 861.0
16 TraesCS7A01G303500 chr4D 94.796 538 24 2 5267 5801 487284284 487284820 0.000000e+00 835.0
17 TraesCS7A01G303500 chr6D 94.834 542 24 1 5264 5801 107938742 107938201 0.000000e+00 843.0
18 TraesCS7A01G303500 chr6D 74.314 401 88 12 232 626 454997335 454996944 7.790000e-34 156.0
19 TraesCS7A01G303500 chr1D 94.953 535 26 1 5267 5801 30587758 30588291 0.000000e+00 837.0
20 TraesCS7A01G303500 chr2B 88.811 143 11 1 2771 2908 2619081 2618939 2.780000e-38 171.0
21 TraesCS7A01G303500 chr2B 92.000 50 3 1 1571 1619 338755750 338755701 1.040000e-07 69.4
22 TraesCS7A01G303500 chr3A 87.097 62 4 4 1568 1626 24207796 24207736 3.750000e-07 67.6
23 TraesCS7A01G303500 chrUn 82.500 80 8 3 1546 1619 90132032 90132111 1.350000e-06 65.8
24 TraesCS7A01G303500 chr5D 88.462 52 5 1 1518 1568 416183309 416183258 1.750000e-05 62.1
25 TraesCS7A01G303500 chr5A 100.000 30 0 0 1536 1565 593453349 593453378 8.120000e-04 56.5


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 TraesCS7A01G303500 chr7A 426801900 426807702 5802 True 10717.000000 10717 100.000 1 5803 1 chr7A.!!$R2 5802
1 TraesCS7A01G303500 chr7B 373177128 373182393 5265 True 8311.000000 8311 95.187 4 5267 1 chr7B.!!$R1 5263
2 TraesCS7A01G303500 chr7D 378492974 378498071 5097 True 2829.333333 6305 97.004 4 5267 3 chr7D.!!$R4 5263
3 TraesCS7A01G303500 chr7D 168499422 168499958 536 True 854.000000 854 95.353 5265 5801 1 chr7D.!!$R2 536
4 TraesCS7A01G303500 chr7D 136692126 136692660 534 True 839.000000 839 94.953 5267 5801 1 chr7D.!!$R1 534
5 TraesCS7A01G303500 chr7D 527732318 527732854 536 True 837.000000 837 94.786 5265 5801 1 chr7D.!!$R3 536
6 TraesCS7A01G303500 chr2D 95504456 95504993 537 True 872.000000 872 95.911 5264 5801 1 chr2D.!!$R1 537
7 TraesCS7A01G303500 chr2D 35246590 35247126 536 False 859.000000 859 95.531 5265 5801 1 chr2D.!!$F1 536
8 TraesCS7A01G303500 chr4D 66298013 66298547 534 False 861.000000 861 95.701 5267 5801 1 chr4D.!!$F1 534
9 TraesCS7A01G303500 chr4D 487284284 487284820 536 False 835.000000 835 94.796 5267 5801 1 chr4D.!!$F2 534
10 TraesCS7A01G303500 chr6D 107938201 107938742 541 True 843.000000 843 94.834 5264 5801 1 chr6D.!!$R1 537
11 TraesCS7A01G303500 chr1D 30587758 30588291 533 False 837.000000 837 94.953 5267 5801 1 chr1D.!!$F1 534

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
208 210 0.037605 CGCCTAGTCTTTGTTCCGGT 60.038 55.000 0.00 0.0 0.00 5.28 F
270 272 0.179073 CAGCGGATCTCGTGGGATTT 60.179 55.000 5.66 0.0 41.72 2.17 F
330 333 0.240678 TGGTGCGTATACGTTCGTGT 59.759 50.000 25.04 4.0 42.22 4.49 F
599 602 0.389817 CCACGAGGATTGACGAGCAA 60.390 55.000 0.00 0.0 41.53 3.91 F
2545 2573 0.179000 GACCTCAGTACATGCCCTGG 59.821 60.000 11.17 0.0 0.00 4.45 F
4269 4307 2.735151 CCCAGGGGTTATTTTCTCCAC 58.265 52.381 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1169 1.228429 CTTCCCCCGTTCTTGGCAA 60.228 57.895 0.00 0.00 0.00 4.52 R
1384 1387 2.479566 ACACGACAATGATCCAGCTT 57.520 45.000 0.00 0.00 0.00 3.74 R
1857 1884 3.107601 ACTGATAGTAGCTTCTTGGGCA 58.892 45.455 0.00 0.00 0.00 5.36 R
2555 2583 2.239201 GCAAAAACAGATACGCGGTTC 58.761 47.619 12.47 6.77 33.67 3.62 R
4490 4528 2.356535 GGTCCAGATTCAAGATGCCTGT 60.357 50.000 0.00 0.00 0.00 4.00 R
5719 5767 1.000171 CAAGGCTTTCAGTTTCAGGGC 60.000 52.381 0.00 0.00 0.00 5.19 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
29 30 1.079057 GGGTCTTCGCCTTGTCTCC 60.079 63.158 0.00 0.00 0.00 3.71
48 49 1.622607 CGGTGGCCTTAGGTCCATGA 61.623 60.000 15.37 0.00 33.13 3.07
63 64 2.224159 ATGAAGGCACGGTGGACCT 61.224 57.895 10.60 5.88 34.45 3.85
66 67 2.391724 GAAGGCACGGTGGACCTCAA 62.392 60.000 10.60 0.00 31.86 3.02
105 106 4.130857 GGCTCCTGCTCTATTTTTAGGTC 58.869 47.826 0.00 0.00 39.59 3.85
109 110 6.037720 GCTCCTGCTCTATTTTTAGGTCTTTC 59.962 42.308 0.00 0.00 36.03 2.62
160 161 1.471119 AGGAAAGCGAGACGATGGTA 58.529 50.000 0.00 0.00 0.00 3.25
174 175 4.080687 ACGATGGTAGCTCCCTATAGTTC 58.919 47.826 0.00 0.00 34.77 3.01
184 185 9.478768 GTAGCTCCCTATAGTTCAAATAAAGTC 57.521 37.037 0.00 0.00 0.00 3.01
185 186 8.090788 AGCTCCCTATAGTTCAAATAAAGTCA 57.909 34.615 0.00 0.00 0.00 3.41
200 202 0.544595 AGTCACCCCGCCTAGTCTTT 60.545 55.000 0.00 0.00 0.00 2.52
208 210 0.037605 CGCCTAGTCTTTGTTCCGGT 60.038 55.000 0.00 0.00 0.00 5.28
212 214 3.868754 GCCTAGTCTTTGTTCCGGTGATT 60.869 47.826 0.00 0.00 0.00 2.57
221 223 2.223994 TGTTCCGGTGATTCGTACAACA 60.224 45.455 0.00 0.00 0.00 3.33
227 229 3.247442 GGTGATTCGTACAACATCGTCA 58.753 45.455 0.00 0.00 0.00 4.35
239 241 1.276138 ACATCGTCAGAAGGCATGTGA 59.724 47.619 0.00 0.00 0.00 3.58
270 272 0.179073 CAGCGGATCTCGTGGGATTT 60.179 55.000 5.66 0.00 41.72 2.17
319 322 1.252215 TGGATCCGTCTTGGTGCGTA 61.252 55.000 7.39 0.00 39.52 4.42
330 333 0.240678 TGGTGCGTATACGTTCGTGT 59.759 50.000 25.04 4.00 42.22 4.49
338 341 4.030529 GCGTATACGTTCGTGTGTTTACAT 59.969 41.667 25.04 0.00 39.34 2.29
343 346 3.242478 ACGTTCGTGTGTTTACATGTTGG 60.242 43.478 2.30 0.00 42.99 3.77
360 363 5.873179 TGTTGGATTTTTCCGATCTACAC 57.127 39.130 0.00 0.00 0.00 2.90
363 366 6.488683 TGTTGGATTTTTCCGATCTACACTTT 59.511 34.615 0.00 0.00 0.00 2.66
365 368 7.141100 TGGATTTTTCCGATCTACACTTTTC 57.859 36.000 0.00 0.00 0.00 2.29
390 393 3.599412 GGTGACGGTTGCTGTTCTA 57.401 52.632 0.00 0.00 0.00 2.10
402 405 2.009042 GCTGTTCTAATGCGCTGGTCT 61.009 52.381 9.73 0.00 0.00 3.85
413 416 0.396435 CGCTGGTCTTATGGGGCATA 59.604 55.000 0.00 0.00 0.00 3.14
427 430 1.130561 GGGCATAAGCACGACAACTTC 59.869 52.381 0.00 0.00 44.61 3.01
430 433 2.422597 CATAAGCACGACAACTTCCCA 58.577 47.619 0.00 0.00 0.00 4.37
432 435 1.981256 AAGCACGACAACTTCCCAAT 58.019 45.000 0.00 0.00 0.00 3.16
454 457 4.267357 TGTCTACGACAACAAGTTTTGC 57.733 40.909 0.00 0.00 39.78 3.68
496 499 0.802494 GATGACGCCGGTGTGATTTT 59.198 50.000 28.44 1.05 0.00 1.82
499 502 0.589223 GACGCCGGTGTGATTTTTGA 59.411 50.000 28.44 0.00 0.00 2.69
517 520 3.251479 TGATCGCTTCAGTGCTTGTAT 57.749 42.857 0.00 0.00 0.00 2.29
528 531 3.926527 CAGTGCTTGTATTTGTCGCTAGA 59.073 43.478 0.00 0.00 0.00 2.43
537 540 6.811954 TGTATTTGTCGCTAGATGGTCAATA 58.188 36.000 0.00 0.00 0.00 1.90
588 591 3.890756 TGTTCTTTGTACTACCACGAGGA 59.109 43.478 5.68 0.00 38.69 3.71
599 602 0.389817 CCACGAGGATTGACGAGCAA 60.390 55.000 0.00 0.00 41.53 3.91
612 615 3.882888 TGACGAGCAAATTGGAAGTTCTT 59.117 39.130 2.25 0.00 0.00 2.52
619 622 7.515684 CGAGCAAATTGGAAGTTCTTGAAAAAG 60.516 37.037 2.25 0.00 0.00 2.27
622 625 8.615211 GCAAATTGGAAGTTCTTGAAAAAGAAT 58.385 29.630 2.25 0.00 40.50 2.40
941 944 1.207329 CCTCCCTCCGTTAACTTGAGG 59.793 57.143 24.03 24.03 44.34 3.86
1166 1169 1.048601 TGTCCTTGCTTTCTCGAGGT 58.951 50.000 13.56 0.00 38.52 3.85
1210 1213 3.981375 AGGAGGGGTAGTTCAAGTTTTCT 59.019 43.478 0.00 0.00 0.00 2.52
1355 1358 2.104792 TGTGTCTAGTTGCTGGCTTTCT 59.895 45.455 0.00 0.00 0.00 2.52
1365 1368 1.952839 GCTGGCTTTCTTTCCTCTCCC 60.953 57.143 0.00 0.00 0.00 4.30
1384 1387 7.278724 TCTCCCTGGGTTAAATCTTAAATGA 57.721 36.000 13.56 0.00 0.00 2.57
1445 1448 8.912988 AGTTTTCATTACAAATGGAGAGTTTGA 58.087 29.630 5.69 0.00 38.51 2.69
1502 1505 6.258160 ACATTGTTTTTCTATGCATCGTAGC 58.742 36.000 0.19 0.00 33.75 3.58
1609 1625 4.634004 AGTCGCGTCAATTAATTTGGATCA 59.366 37.500 5.77 0.00 35.92 2.92
1736 1762 6.585695 AAGTTTTCATCTTGACATGAGCAT 57.414 33.333 0.00 0.00 34.22 3.79
1857 1884 3.146066 TGCTTTTCCTACAATTCACGCT 58.854 40.909 0.00 0.00 0.00 5.07
2050 2077 3.879892 GAGCAACTTCCCAGCTATTTAGG 59.120 47.826 0.00 0.00 39.02 2.69
2147 2174 0.318275 CTGGATTCCGTAGCTCTCGC 60.318 60.000 0.00 0.00 0.00 5.03
2265 2292 5.397142 AAAGATCCCTTTCAGTTTCATGC 57.603 39.130 0.00 0.00 38.13 4.06
2545 2573 0.179000 GACCTCAGTACATGCCCTGG 59.821 60.000 11.17 0.00 0.00 4.45
2555 2583 3.228188 ACATGCCCTGGTGGTAATATG 57.772 47.619 0.00 0.00 36.04 1.78
2597 2625 5.886715 CAATTGTGCTTTCGTTTCATTGA 57.113 34.783 0.00 0.00 0.00 2.57
2696 2725 9.958180 TGTTTCATCTCCTTTCATATGTTTCTA 57.042 29.630 1.90 0.00 0.00 2.10
2750 2780 5.481824 TCTGCTGATCTCCATCGGTTATTAT 59.518 40.000 0.00 0.00 37.68 1.28
2751 2781 6.014242 TCTGCTGATCTCCATCGGTTATTATT 60.014 38.462 0.00 0.00 37.68 1.40
2752 2782 6.533730 TGCTGATCTCCATCGGTTATTATTT 58.466 36.000 0.00 0.00 37.68 1.40
2753 2783 6.427853 TGCTGATCTCCATCGGTTATTATTTG 59.572 38.462 0.00 0.00 37.68 2.32
2754 2784 6.650807 GCTGATCTCCATCGGTTATTATTTGA 59.349 38.462 0.00 0.00 37.68 2.69
2755 2785 7.173218 GCTGATCTCCATCGGTTATTATTTGAA 59.827 37.037 0.00 0.00 37.68 2.69
2756 2786 8.607441 TGATCTCCATCGGTTATTATTTGAAG 57.393 34.615 0.00 0.00 0.00 3.02
3142 3179 8.902540 AGTTCTGTTGACAATTTGACATACTA 57.097 30.769 2.79 0.00 0.00 1.82
3331 3368 7.148557 GCTGATGGTAAGTTTACTTCTTCTGTC 60.149 40.741 0.00 0.00 37.40 3.51
3387 3424 6.824553 TGACTCTTATTGCATAGCTGATTCT 58.175 36.000 0.00 0.00 0.00 2.40
3890 3928 6.371548 TGCATCCTGTCTTCTGTTTTACATAC 59.628 38.462 0.00 0.00 0.00 2.39
3903 3941 8.148351 TCTGTTTTACATACCCATAGCTATGAC 58.852 37.037 31.14 18.25 35.75 3.06
4084 4122 3.895232 TCTGCCTTTATCACCAGAGAC 57.105 47.619 0.00 0.00 31.29 3.36
4087 4125 4.225942 TCTGCCTTTATCACCAGAGACAAT 59.774 41.667 0.00 0.00 31.29 2.71
4170 4208 9.091220 AGGTTAAGAGTGGTACTTATATGGATC 57.909 37.037 0.00 0.00 31.34 3.36
4177 4215 6.151312 AGTGGTACTTATATGGATCGTAGCAG 59.849 42.308 6.76 0.00 38.67 4.24
4269 4307 2.735151 CCCAGGGGTTATTTTCTCCAC 58.265 52.381 0.00 0.00 0.00 4.02
4355 4393 7.449704 AGTGGAAGACTCAGATTATTTTGCTTT 59.550 33.333 0.00 0.00 0.00 3.51
4476 4514 3.476552 CACCTCTTTCACTTGGCTTGTA 58.523 45.455 0.00 0.00 0.00 2.41
4490 4528 2.819608 GGCTTGTAATGGCTGTTTCAGA 59.180 45.455 0.66 0.00 32.44 3.27
4520 4558 5.136828 TCTTGAATCTGGACCTAGAGCTAG 58.863 45.833 0.00 0.00 0.00 3.42
4521 4559 4.528076 TGAATCTGGACCTAGAGCTAGT 57.472 45.455 4.02 0.00 0.00 2.57
4590 4628 1.745653 GGCCTCACTTTGTAGATTGCC 59.254 52.381 0.00 0.00 0.00 4.52
4594 4632 2.346803 TCACTTTGTAGATTGCCGAGC 58.653 47.619 0.00 0.00 0.00 5.03
4857 4896 3.762288 TGACAGTTCCGAGCAATACTACT 59.238 43.478 0.00 0.00 0.00 2.57
4990 5029 1.182667 GTTTGTAGGCCCCCATTGAC 58.817 55.000 0.00 0.00 0.00 3.18
5016 5055 5.450550 GGCAAGTGTATATTCCAGGAAAAGC 60.451 44.000 5.81 0.00 0.00 3.51
5332 5376 1.461559 TTTTTGTCCGTTTGGGTCGT 58.538 45.000 0.00 0.00 37.00 4.34
5367 5411 3.427503 CGTCCACCCTGTTTTTCATATGC 60.428 47.826 0.00 0.00 0.00 3.14
5496 5544 5.198207 AGTAAAATAGTTTAGCCGCCCAAT 58.802 37.500 0.00 0.00 29.74 3.16
5497 5545 6.358991 AGTAAAATAGTTTAGCCGCCCAATA 58.641 36.000 0.00 0.00 29.74 1.90
5648 5696 1.812571 GCACGTGAGTTTCCCAATCAT 59.187 47.619 22.23 0.00 46.40 2.45
5719 5767 0.445436 GCTCAGGCACAACATTCTCG 59.555 55.000 0.00 0.00 38.54 4.04
5759 5807 2.956987 CGTACAGACGTTCCGGGT 59.043 61.111 0.00 0.00 44.31 5.28
5773 5821 1.313812 CCGGGTGCTCGTCTTCTACT 61.314 60.000 0.00 0.00 0.00 2.57
5780 5828 5.335035 GGGTGCTCGTCTTCTACTATCATAC 60.335 48.000 0.00 0.00 0.00 2.39
5801 5849 1.955080 TGTGCATGATCACACAAGCAA 59.045 42.857 14.82 3.12 43.48 3.91
5802 5850 2.559231 TGTGCATGATCACACAAGCAAT 59.441 40.909 14.82 0.00 43.48 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.153168 CATGGACCTAAGGCCACCG 60.153 63.158 5.01 0.00 33.27 4.94
48 49 2.448582 TTGAGGTCCACCGTGCCTT 61.449 57.895 0.00 0.00 42.08 4.35
63 64 1.533033 TCTCACCGGCAGAGGTTGA 60.533 57.895 20.65 6.59 43.00 3.18
114 115 8.353423 AGCATTACACAAATTCTAATCAACCT 57.647 30.769 0.00 0.00 0.00 3.50
154 155 6.420913 TTTGAACTATAGGGAGCTACCATC 57.579 41.667 19.90 5.89 41.20 3.51
160 161 7.988028 GTGACTTTATTTGAACTATAGGGAGCT 59.012 37.037 4.43 0.00 0.00 4.09
174 175 1.834188 AGGCGGGGTGACTTTATTTG 58.166 50.000 0.00 0.00 20.56 2.32
184 185 0.036306 AACAAAGACTAGGCGGGGTG 59.964 55.000 0.00 0.00 0.00 4.61
185 186 0.323957 GAACAAAGACTAGGCGGGGT 59.676 55.000 0.00 0.00 0.00 4.95
200 202 2.223994 TGTTGTACGAATCACCGGAACA 60.224 45.455 9.46 0.28 0.00 3.18
208 210 4.428615 TCTGACGATGTTGTACGAATCA 57.571 40.909 0.00 0.00 0.00 2.57
212 214 2.670229 GCCTTCTGACGATGTTGTACGA 60.670 50.000 0.00 0.00 0.00 3.43
221 223 2.625737 CTTCACATGCCTTCTGACGAT 58.374 47.619 0.00 0.00 0.00 3.73
227 229 1.701847 AGACACCTTCACATGCCTTCT 59.298 47.619 0.00 0.00 0.00 2.85
239 241 0.616111 ATCCGCTGGAGAGACACCTT 60.616 55.000 3.76 0.00 34.05 3.50
319 322 5.333492 CCAACATGTAAACACACGAACGTAT 60.333 40.000 0.00 0.00 0.00 3.06
330 333 6.392625 TCGGAAAAATCCAACATGTAAACA 57.607 33.333 0.00 0.00 0.00 2.83
338 341 5.556915 AGTGTAGATCGGAAAAATCCAACA 58.443 37.500 0.00 0.00 0.00 3.33
343 346 8.504005 TGAAGAAAAGTGTAGATCGGAAAAATC 58.496 33.333 0.00 0.00 0.00 2.17
360 363 2.413837 ACCGTCACCGATGAAGAAAAG 58.586 47.619 0.00 0.00 36.52 2.27
363 366 1.790755 CAACCGTCACCGATGAAGAA 58.209 50.000 0.00 0.00 36.52 2.52
365 368 0.670546 AGCAACCGTCACCGATGAAG 60.671 55.000 0.00 0.00 36.31 3.02
388 391 2.146342 CCCATAAGACCAGCGCATTAG 58.854 52.381 11.47 0.00 0.00 1.73
390 393 0.466189 CCCCATAAGACCAGCGCATT 60.466 55.000 11.47 0.00 0.00 3.56
402 405 1.210722 TGTCGTGCTTATGCCCCATAA 59.789 47.619 0.00 0.00 38.71 1.90
413 416 1.981256 ATTGGGAAGTTGTCGTGCTT 58.019 45.000 0.00 0.00 0.00 3.91
440 443 1.136891 AGCCTGGCAAAACTTGTTGTC 59.863 47.619 22.65 0.00 33.59 3.18
454 457 0.826715 TCTCCTTCATCGAAGCCTGG 59.173 55.000 0.00 0.00 38.24 4.45
484 487 1.468520 AGCGATCAAAAATCACACCGG 59.531 47.619 0.00 0.00 0.00 5.28
490 493 3.503363 AGCACTGAAGCGATCAAAAATCA 59.497 39.130 0.00 0.00 37.67 2.57
496 499 1.882912 ACAAGCACTGAAGCGATCAA 58.117 45.000 0.00 0.00 37.67 2.57
499 502 3.753272 ACAAATACAAGCACTGAAGCGAT 59.247 39.130 0.00 0.00 40.15 4.58
517 520 5.348986 GTCTATTGACCATCTAGCGACAAA 58.651 41.667 0.00 0.00 37.24 2.83
556 559 9.661563 TGGTAGTACAAAGAACACCATAAATAG 57.338 33.333 2.06 0.00 31.29 1.73
588 591 4.520492 AGAACTTCCAATTTGCTCGTCAAT 59.480 37.500 0.00 0.00 34.12 2.57
941 944 2.175878 TCAAGAAGCACCTCTCAAGC 57.824 50.000 0.00 0.00 0.00 4.01
976 979 2.449031 AATCTGGACGCGAGGCAACA 62.449 55.000 15.93 0.82 45.40 3.33
1118 1121 1.548357 ATCTGCACGCTCCAGTTCCT 61.548 55.000 0.00 0.00 0.00 3.36
1166 1169 1.228429 CTTCCCCCGTTCTTGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
1355 1358 4.183916 AGATTTAACCCAGGGAGAGGAAA 58.816 43.478 14.54 5.06 0.00 3.13
1365 1368 7.122650 TCCAGCTTCATTTAAGATTTAACCCAG 59.877 37.037 0.00 0.00 37.38 4.45
1384 1387 2.479566 ACACGACAATGATCCAGCTT 57.520 45.000 0.00 0.00 0.00 3.74
1445 1448 5.183904 GCAGGAGAAAAGTTTGTGACCATAT 59.816 40.000 0.00 0.00 0.00 1.78
1544 1547 4.398988 AGCTGCGTCAATTAATTTGGATCA 59.601 37.500 0.00 0.00 35.92 2.92
1609 1625 5.843421 AGCACTATGAATCAATACTCCCTCT 59.157 40.000 0.00 0.00 0.00 3.69
1857 1884 3.107601 ACTGATAGTAGCTTCTTGGGCA 58.892 45.455 0.00 0.00 0.00 5.36
2050 2077 6.922957 TGATTGGTCTTGCAAAACATTAAGTC 59.077 34.615 5.08 0.00 0.00 3.01
2147 2174 4.272504 TGCACTTTCTTGTAGAAAACCTCG 59.727 41.667 3.73 0.00 42.95 4.63
2246 2273 5.065731 CAGTAGCATGAAACTGAAAGGGATC 59.934 44.000 18.24 0.00 44.79 3.36
2265 2292 7.869016 TGACAGAAACTAAAACGATCAGTAG 57.131 36.000 0.00 0.00 0.00 2.57
2545 2573 4.384846 CAGATACGCGGTTCATATTACCAC 59.615 45.833 12.47 0.00 35.31 4.16
2555 2583 2.239201 GCAAAAACAGATACGCGGTTC 58.761 47.619 12.47 6.77 33.67 3.62
2696 2725 2.037772 CAGGTTACCAGCTCAGTCAAGT 59.962 50.000 3.51 0.00 0.00 3.16
2697 2726 2.037772 ACAGGTTACCAGCTCAGTCAAG 59.962 50.000 3.51 0.00 0.00 3.02
2698 2727 2.047061 ACAGGTTACCAGCTCAGTCAA 58.953 47.619 3.51 0.00 0.00 3.18
2756 2786 8.931012 ACGCAGTTCAAAGTTCAAACTTCAAAC 61.931 37.037 17.09 17.09 44.03 2.93
3142 3179 2.208132 TGACAACAACACACCACCTT 57.792 45.000 0.00 0.00 0.00 3.50
3331 3368 1.135373 CACCACTACAGAGCTACACGG 60.135 57.143 0.00 0.00 0.00 4.94
3387 3424 9.502091 AAGTTTTAACACAGACTAGCATCATTA 57.498 29.630 0.00 0.00 0.00 1.90
3771 3809 9.162764 GTAACTAGCATGAGTGGATCTTTAAAA 57.837 33.333 0.00 0.00 0.00 1.52
3872 3910 6.821665 GCTATGGGTATGTAAAACAGAAGACA 59.178 38.462 0.00 0.00 0.00 3.41
3890 3928 7.498900 TGACTAAAAACATGTCATAGCTATGGG 59.501 37.037 29.02 19.25 36.03 4.00
4084 4122 3.684788 CGGTGACTCCAAGTTAGGAATTG 59.315 47.826 0.00 0.00 37.20 2.32
4087 4125 2.600790 TCGGTGACTCCAAGTTAGGAA 58.399 47.619 0.00 0.00 37.20 3.36
4170 4208 3.181465 ACCCAATTATCTCCACTGCTACG 60.181 47.826 0.00 0.00 0.00 3.51
4177 4215 4.100498 TCCTCGTAACCCAATTATCTCCAC 59.900 45.833 0.00 0.00 0.00 4.02
4269 4307 2.466846 CTGAGCTTTTGGTGCAACAAG 58.533 47.619 18.10 8.28 39.98 3.16
4355 4393 5.275067 AGCAAAACTGATAGGCAACAAAA 57.725 34.783 0.00 0.00 41.41 2.44
4490 4528 2.356535 GGTCCAGATTCAAGATGCCTGT 60.357 50.000 0.00 0.00 0.00 4.00
4590 4628 7.306051 CGACAAAGGTAATTATTACTCAGCTCG 60.306 40.741 13.86 11.00 36.39 5.03
4594 4632 9.751542 AGATCGACAAAGGTAATTATTACTCAG 57.248 33.333 13.86 5.73 36.39 3.35
4990 5029 2.104111 TCCTGGAATATACACTTGCCCG 59.896 50.000 0.00 0.00 0.00 6.13
5016 5055 2.485814 CCAAGAAGAAAAGGAAGCCTCG 59.514 50.000 0.00 0.00 30.89 4.63
5028 5067 4.365514 TGTACTTCCATGCCAAGAAGAA 57.634 40.909 14.14 0.00 41.69 2.52
5250 5293 7.174107 AGTTGCTCTAATGGTGCATAAAAAT 57.826 32.000 0.00 0.00 42.78 1.82
5386 5430 2.203015 GCACATATGGGTCGGCGT 60.203 61.111 6.85 0.00 0.00 5.68
5585 5633 4.080975 TGAGCATATGTGGACTCATGTTGA 60.081 41.667 4.29 0.00 34.35 3.18
5667 5715 3.983344 GGCAACATTTAAGCAGTTCACTG 59.017 43.478 2.31 2.31 46.40 3.66
5719 5767 1.000171 CAAGGCTTTCAGTTTCAGGGC 60.000 52.381 0.00 0.00 0.00 5.19
5759 5807 6.017852 CACAGTATGATAGTAGAAGACGAGCA 60.018 42.308 0.00 0.00 39.69 4.26


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

AutoCloner maintained by Alex Coulton.