Multiple sequence alignment - TraesCS3D01G240000

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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 TraesCS3D01G240000 chr3D 100.000 4893 0 0 1 4893 332489842 332494734 0.000000e+00 9036.0
1 TraesCS3D01G240000 chr3D 98.083 887 15 2 1829 2714 338939114 338938229 0.000000e+00 1543.0
2 TraesCS3D01G240000 chr3D 98.180 879 15 1 1829 2706 338944481 338943603 0.000000e+00 1533.0
3 TraesCS3D01G240000 chr3D 85.075 737 64 15 4201 4893 445087241 445086507 0.000000e+00 710.0
4 TraesCS3D01G240000 chr3D 85.782 633 68 16 4278 4893 14806262 14805635 0.000000e+00 651.0
5 TraesCS3D01G240000 chr3D 82.861 741 69 25 4203 4887 339453113 339453851 3.240000e-171 612.0
6 TraesCS3D01G240000 chr3D 84.211 247 15 14 4196 4424 335200725 335200485 8.250000e-53 219.0
7 TraesCS3D01G240000 chr3A 92.937 1869 82 19 1 1829 449666122 449667980 0.000000e+00 2675.0
8 TraesCS3D01G240000 chr3A 91.359 1354 78 18 2707 4047 449667975 449669302 0.000000e+00 1816.0
9 TraesCS3D01G240000 chr3A 96.178 157 6 0 4052 4208 449679494 449679650 1.750000e-64 257.0
10 TraesCS3D01G240000 chr3B 89.174 1441 86 19 450 1829 431536608 431538039 0.000000e+00 1733.0
11 TraesCS3D01G240000 chr3B 92.843 992 54 8 2707 3697 431538034 431539009 0.000000e+00 1423.0
12 TraesCS3D01G240000 chr3B 95.793 523 12 3 3694 4208 431539186 431539706 0.000000e+00 835.0
13 TraesCS3D01G240000 chr3B 94.059 101 6 0 301 401 431536500 431536600 2.360000e-33 154.0
14 TraesCS3D01G240000 chr3B 96.774 31 1 0 3572 3602 431539222 431539252 9.000000e-03 52.8
15 TraesCS3D01G240000 chr6D 99.091 880 7 1 1829 2707 7699897 7699018 0.000000e+00 1580.0
16 TraesCS3D01G240000 chr6D 98.862 879 9 1 1829 2706 7713946 7713068 0.000000e+00 1567.0
17 TraesCS3D01G240000 chr6D 97.735 883 18 2 1826 2706 82954674 82953792 0.000000e+00 1519.0
18 TraesCS3D01G240000 chr6D 87.183 710 66 14 4204 4893 458391313 458392017 0.000000e+00 784.0
19 TraesCS3D01G240000 chr5D 98.407 879 13 1 1829 2706 56932387 56933265 0.000000e+00 1544.0
20 TraesCS3D01G240000 chr5D 98.407 879 13 1 1829 2706 56946323 56947201 0.000000e+00 1544.0
21 TraesCS3D01G240000 chr5D 80.345 290 34 17 4203 4474 429742376 429742092 1.070000e-46 198.0
22 TraesCS3D01G240000 chr5D 80.417 240 19 11 4204 4418 444279094 444278858 1.820000e-34 158.0
23 TraesCS3D01G240000 chr5D 84.663 163 10 7 4209 4357 237270667 237270506 1.100000e-31 148.0
24 TraesCS3D01G240000 chr4D 98.174 876 15 1 1832 2706 6082911 6082036 0.000000e+00 1528.0
25 TraesCS3D01G240000 chr4D 97.948 877 16 2 1832 2706 6080012 6079136 0.000000e+00 1519.0
26 TraesCS3D01G240000 chr4D 77.670 206 41 5 526 729 455708316 455708114 2.390000e-23 121.0
27 TraesCS3D01G240000 chr2D 86.299 708 74 13 4204 4893 329146412 329145710 0.000000e+00 749.0
28 TraesCS3D01G240000 chr2D 84.497 716 75 24 4208 4893 314358598 314359307 0.000000e+00 675.0
29 TraesCS3D01G240000 chr2D 83.082 331 31 7 4203 4510 509745242 509744914 1.340000e-70 278.0
30 TraesCS3D01G240000 chr2D 89.055 201 9 1 4201 4388 127941957 127942157 2.280000e-58 237.0
31 TraesCS3D01G240000 chr5A 84.734 714 78 15 4208 4893 559505211 559504501 0.000000e+00 686.0
32 TraesCS3D01G240000 chr1A 84.755 715 76 15 4208 4893 557121034 557121744 0.000000e+00 686.0
33 TraesCS3D01G240000 chr7A 83.799 716 74 24 4208 4893 133350 134053 4.130000e-180 641.0
34 TraesCS3D01G240000 chr7A 83.264 723 81 24 4204 4893 149421967 149422682 3.210000e-176 628.0
35 TraesCS3D01G240000 chr7A 82.476 719 89 17 4208 4893 694135247 694134533 3.260000e-166 595.0
36 TraesCS3D01G240000 chr7A 74.242 264 61 7 449 707 126937846 126937585 2.410000e-18 104.0
37 TraesCS3D01G240000 chr1B 82.051 234 25 7 4201 4418 142529155 142529387 3.010000e-42 183.0
38 TraesCS3D01G240000 chr1B 78.070 114 19 3 3621 3730 596321980 596322091 3.160000e-07 67.6
39 TraesCS3D01G240000 chr4A 78.333 180 29 8 534 706 572709760 572709936 1.860000e-19 108.0
40 TraesCS3D01G240000 chr4A 80.612 98 19 0 609 706 676455526 676455623 5.250000e-10 76.8
41 TraesCS3D01G240000 chr7B 77.852 149 26 6 505 651 595162631 595162488 8.730000e-13 86.1
42 TraesCS3D01G240000 chr6B 88.462 52 5 1 3683 3734 133437460 133437510 1.470000e-05 62.1
43 TraesCS3D01G240000 chr6A 83.824 68 7 4 3666 3731 9191256 9191191 1.470000e-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 TraesCS3D01G240000 chr3D 332489842 332494734 4892 False 9036.00 9036 100.0000 1 4893 1 chr3D.!!$F1 4892
1 TraesCS3D01G240000 chr3D 338938229 338939114 885 True 1543.00 1543 98.0830 1829 2714 1 chr3D.!!$R3 885
2 TraesCS3D01G240000 chr3D 338943603 338944481 878 True 1533.00 1533 98.1800 1829 2706 1 chr3D.!!$R4 877
3 TraesCS3D01G240000 chr3D 445086507 445087241 734 True 710.00 710 85.0750 4201 4893 1 chr3D.!!$R5 692
4 TraesCS3D01G240000 chr3D 14805635 14806262 627 True 651.00 651 85.7820 4278 4893 1 chr3D.!!$R1 615
5 TraesCS3D01G240000 chr3D 339453113 339453851 738 False 612.00 612 82.8610 4203 4887 1 chr3D.!!$F2 684
6 TraesCS3D01G240000 chr3A 449666122 449669302 3180 False 2245.50 2675 92.1480 1 4047 2 chr3A.!!$F2 4046
7 TraesCS3D01G240000 chr3B 431536500 431539706 3206 False 839.56 1733 93.7286 301 4208 5 chr3B.!!$F1 3907
8 TraesCS3D01G240000 chr6D 7699018 7699897 879 True 1580.00 1580 99.0910 1829 2707 1 chr6D.!!$R1 878
9 TraesCS3D01G240000 chr6D 7713068 7713946 878 True 1567.00 1567 98.8620 1829 2706 1 chr6D.!!$R2 877
10 TraesCS3D01G240000 chr6D 82953792 82954674 882 True 1519.00 1519 97.7350 1826 2706 1 chr6D.!!$R3 880
11 TraesCS3D01G240000 chr6D 458391313 458392017 704 False 784.00 784 87.1830 4204 4893 1 chr6D.!!$F1 689
12 TraesCS3D01G240000 chr5D 56932387 56933265 878 False 1544.00 1544 98.4070 1829 2706 1 chr5D.!!$F1 877
13 TraesCS3D01G240000 chr5D 56946323 56947201 878 False 1544.00 1544 98.4070 1829 2706 1 chr5D.!!$F2 877
14 TraesCS3D01G240000 chr4D 6079136 6082911 3775 True 1523.50 1528 98.0610 1832 2706 2 chr4D.!!$R2 874
15 TraesCS3D01G240000 chr2D 329145710 329146412 702 True 749.00 749 86.2990 4204 4893 1 chr2D.!!$R1 689
16 TraesCS3D01G240000 chr2D 314358598 314359307 709 False 675.00 675 84.4970 4208 4893 1 chr2D.!!$F2 685
17 TraesCS3D01G240000 chr5A 559504501 559505211 710 True 686.00 686 84.7340 4208 4893 1 chr5A.!!$R1 685
18 TraesCS3D01G240000 chr1A 557121034 557121744 710 False 686.00 686 84.7550 4208 4893 1 chr1A.!!$F1 685
19 TraesCS3D01G240000 chr7A 133350 134053 703 False 641.00 641 83.7990 4208 4893 1 chr7A.!!$F1 685
20 TraesCS3D01G240000 chr7A 149421967 149422682 715 False 628.00 628 83.2640 4204 4893 1 chr7A.!!$F2 689
21 TraesCS3D01G240000 chr7A 694134533 694135247 714 True 595.00 595 82.4760 4208 4893 1 chr7A.!!$R2 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
110 114 0.248296 GACAGAAAAACCGTGCGCAA 60.248 50.000 14.00 0.0 0.0 4.85 F
872 909 1.007734 TCGTTGTCTGCTGTCCGTC 60.008 57.895 0.00 0.0 0.0 4.79 F
2499 2576 0.091344 CGAGCGCACTAAAACTCACG 59.909 55.000 11.47 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1246 1.003718 GAAGTAGCGGTTGGCCAGT 60.004 57.895 5.11 0.0 45.17 4.00 R
2741 5718 0.449388 CCTTCGTGGCAAGCAGAATC 59.551 55.000 1.26 0.0 0.00 2.52 R
4263 7430 1.001520 GTTTGGGCCGCCTTTTATGTT 59.998 47.619 9.86 0.0 0.00 2.71 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
23 24 6.552445 ACAAAGTGAGCTAGAGACCAATAT 57.448 37.500 0.00 0.00 0.00 1.28
27 28 7.847711 AAGTGAGCTAGAGACCAATATACAT 57.152 36.000 0.00 0.00 0.00 2.29
110 114 0.248296 GACAGAAAAACCGTGCGCAA 60.248 50.000 14.00 0.00 0.00 4.85
149 153 7.281324 CGTATCCCTCTAGTAATGACCTATCTG 59.719 44.444 0.00 0.00 0.00 2.90
186 190 8.602472 ATTTTAGCCATAACTATTTGTGGGAA 57.398 30.769 10.05 0.00 42.81 3.97
205 209 7.996644 TGTGGGAAAGAAATTACAGACTACTTT 59.003 33.333 0.00 0.00 0.00 2.66
228 232 4.636648 TGATACGGTGACAACAACAAAACT 59.363 37.500 0.00 0.00 32.53 2.66
286 290 3.041946 GCCTCTTTCTCTCTCCCCATTA 58.958 50.000 0.00 0.00 0.00 1.90
362 366 9.169468 CACTGTTGTTGTACATGTCTTAAAATC 57.831 33.333 0.00 0.00 0.00 2.17
441 445 8.634475 ACATAAAAAGTTTTCTTCAGCAGAAC 57.366 30.769 0.32 0.00 41.56 3.01
442 446 7.706607 ACATAAAAAGTTTTCTTCAGCAGAACC 59.293 33.333 0.32 0.00 41.56 3.62
448 452 7.845042 AAGTTTTCTTCAGCAGAACCAGTCTG 61.845 42.308 0.00 0.00 45.62 3.51
459 463 3.584406 AGAACCAGTCTGTGATTGGATGA 59.416 43.478 14.56 0.00 41.15 2.92
479 483 6.183361 GGATGATAAGGAGGACAGTGGTATTT 60.183 42.308 0.00 0.00 0.00 1.40
545 550 9.334947 GATCACATTTCCTAGATTCATTTCAGA 57.665 33.333 0.00 0.00 0.00 3.27
573 578 3.324846 AGCTAATGTGTGTTCAGTGGAGA 59.675 43.478 0.00 0.00 0.00 3.71
597 603 1.403780 CGTTCCCCTCAACTACGAAGG 60.404 57.143 0.00 0.00 34.36 3.46
604 611 4.142790 CCCTCAACTACGAAGGCTCTATA 58.857 47.826 0.00 0.00 0.00 1.31
633 640 2.034254 CGTCAATGTCGAGATGATGTGC 60.034 50.000 0.00 0.00 0.00 4.57
655 662 2.790433 GACTCAGTCTCTCAGAGGTGT 58.210 52.381 0.57 0.00 34.58 4.16
704 711 3.677121 CGTTCATAGGAGTGAGCATATGC 59.323 47.826 20.36 20.36 42.49 3.14
722 738 4.627611 ATGCTGCATCTGTATTGTGTTC 57.372 40.909 9.81 0.00 0.00 3.18
860 897 2.029073 CCCGCACAGAGTCGTTGT 59.971 61.111 0.00 0.00 0.00 3.32
872 909 1.007734 TCGTTGTCTGCTGTCCGTC 60.008 57.895 0.00 0.00 0.00 4.79
994 1037 3.854669 CTCGCTCCTCCGGGCATT 61.855 66.667 0.00 0.00 0.00 3.56
1131 1186 2.989253 TCAGCGTCGCCTCTTCCA 60.989 61.111 14.86 0.00 0.00 3.53
1672 1744 7.764443 CCAAGCTAAATTCTACTAGCACTTACA 59.236 37.037 9.05 0.00 42.51 2.41
1673 1745 9.151471 CAAGCTAAATTCTACTAGCACTTACAA 57.849 33.333 9.05 0.00 42.51 2.41
1685 1761 7.695820 ACTAGCACTTACAACGAGTATTAGAG 58.304 38.462 0.00 0.00 31.53 2.43
1752 1828 5.673514 TGAAGACGTTGGTACCTTAGTTTT 58.326 37.500 14.36 10.91 0.00 2.43
1963 2039 6.278363 AGTCATGCAATCAAAATCATAAGCC 58.722 36.000 0.00 0.00 0.00 4.35
2499 2576 0.091344 CGAGCGCACTAAAACTCACG 59.909 55.000 11.47 0.00 0.00 4.35
2596 2673 3.129871 CACGTGGCATTGGTCAATTTTT 58.870 40.909 7.95 0.00 0.00 1.94
2646 2723 3.181436 CCACATGAGCCTCTGGGATTTAT 60.181 47.826 0.00 0.00 33.58 1.40
2707 5684 2.969821 TGGCCAATAACTCCAACAGT 57.030 45.000 0.61 0.00 36.64 3.55
2709 5686 3.681593 TGGCCAATAACTCCAACAGTAC 58.318 45.455 0.61 0.00 32.30 2.73
2710 5687 3.073209 TGGCCAATAACTCCAACAGTACA 59.927 43.478 0.61 0.00 32.30 2.90
2736 5713 6.148948 TGCAAAACTGAAATACGAAGGATTG 58.851 36.000 0.00 0.00 0.00 2.67
2741 5718 5.178797 ACTGAAATACGAAGGATTGGTGAG 58.821 41.667 0.00 0.00 37.67 3.51
2755 5732 0.807496 GGTGAGATTCTGCTTGCCAC 59.193 55.000 0.00 0.00 0.00 5.01
2786 5763 4.499183 CAACAGTCACTGGTTCTAGATCC 58.501 47.826 10.28 12.29 35.51 3.36
2799 5776 7.179966 TGGTTCTAGATCCGCCTAATAGAATA 58.820 38.462 13.93 0.00 35.56 1.75
2847 5824 8.991026 CAGAGAGATAGGCTCATTTGAAAATAG 58.009 37.037 0.00 0.00 46.45 1.73
2856 5833 7.503902 AGGCTCATTTGAAAATAGGATAGGTTC 59.496 37.037 0.00 0.00 0.00 3.62
3045 6023 5.726397 TCATTGGTAAACATACGCTAGTGT 58.274 37.500 14.41 14.41 0.00 3.55
3106 6084 5.001237 TCGGTGTCAACATAATGTATCGT 57.999 39.130 0.00 0.00 0.00 3.73
3108 6086 5.041287 CGGTGTCAACATAATGTATCGTCT 58.959 41.667 0.00 0.00 0.00 4.18
3134 6112 8.264347 TGAGTTATGTTTATCAGGCTCAACATA 58.736 33.333 11.37 11.37 39.84 2.29
3168 6146 8.863049 GCAACAGATACAGATAATTTTGGTTTG 58.137 33.333 0.00 0.00 0.00 2.93
3169 6147 9.357652 CAACAGATACAGATAATTTTGGTTTGG 57.642 33.333 0.00 0.00 0.00 3.28
3201 6179 7.979444 TTTTCCTACAATGATCGAGTTTTCT 57.021 32.000 0.00 0.00 0.00 2.52
3203 6181 7.596749 TTCCTACAATGATCGAGTTTTCTTC 57.403 36.000 0.00 0.00 0.00 2.87
3209 6188 7.716738 CAATGATCGAGTTTTCTTCATTGTC 57.283 36.000 20.06 0.00 41.18 3.18
3229 6208 5.125356 TGTCATGGATTTAGGTGTATGCAG 58.875 41.667 0.00 0.00 0.00 4.41
3244 6223 6.147821 GGTGTATGCAGCTGATAATATTTCGT 59.852 38.462 20.43 0.00 39.79 3.85
3453 6432 5.391629 GCGGAGGTAAAAACTAATCCTTGTG 60.392 44.000 0.00 0.00 0.00 3.33
3485 6464 7.061905 CACTTCATTTTGCAAGCTTATCAGAAG 59.938 37.037 16.98 16.98 35.13 2.85
3488 6467 6.379133 TCATTTTGCAAGCTTATCAGAAGGAT 59.621 34.615 0.00 0.00 40.14 3.24
3526 6505 7.976135 ACTACTTGCATCAGATATTTGGATC 57.024 36.000 0.00 0.00 0.00 3.36
3559 6538 7.428020 CCTTTGATCCATAAACATACACCATG 58.572 38.462 0.00 0.00 40.78 3.66
3560 6539 6.957920 TTGATCCATAAACATACACCATGG 57.042 37.500 11.19 11.19 39.13 3.66
3567 6546 8.939932 TCCATAAACATACACCATGGATAGTTA 58.060 33.333 21.47 10.27 40.11 2.24
3597 6576 6.650120 TGAAGGGAAACATATCCTGACTAAC 58.350 40.000 0.00 0.00 39.57 2.34
3602 6581 6.049790 GGAAACATATCCTGACTAACTGACC 58.950 44.000 0.00 0.00 36.50 4.02
3732 6891 4.222588 CCCTCCTGCATGGTTCAAAAATAA 59.777 41.667 0.00 0.00 37.07 1.40
3736 6895 7.060383 TCCTGCATGGTTCAAAAATAAAAGA 57.940 32.000 0.00 0.00 37.07 2.52
3739 6898 7.820872 CCTGCATGGTTCAAAAATAAAAGAGAT 59.179 33.333 0.00 0.00 0.00 2.75
3943 7110 9.388506 CATATCCCCTGTACATGAAAGAATATC 57.611 37.037 0.00 0.00 0.00 1.63
4007 7174 1.441515 GCGTTCACTGCAGCACATG 60.442 57.895 15.27 4.46 0.00 3.21
4113 7280 8.956426 TCATGGTAGTAATGTTGAGATTTTTCC 58.044 33.333 0.00 0.00 0.00 3.13
4172 7339 7.642194 ACATGTAAACCATATAACGATTTTGCG 59.358 33.333 0.00 0.00 30.71 4.85
4239 7406 3.192922 GCGACCCATTTCGTCCGG 61.193 66.667 0.00 0.00 41.26 5.14
4267 7434 4.690719 TTGGGTCGGCGCGAACAT 62.691 61.111 12.10 0.00 46.28 2.71
4449 7643 0.542702 CCCATCCAACAGCAACCCTT 60.543 55.000 0.00 0.00 0.00 3.95
4536 7739 4.329545 ACATCCGCCCAGCAACGT 62.330 61.111 0.00 0.00 0.00 3.99
4657 7884 3.112205 GCCAGATCCTCACCGGCAT 62.112 63.158 0.00 0.00 42.50 4.40
4691 7937 2.735772 GCAGGGCAGCTAGCTGGTA 61.736 63.158 38.52 0.00 43.77 3.25
4693 7939 1.306141 AGGGCAGCTAGCTGGTACA 60.306 57.895 38.52 0.00 43.77 2.90
4747 7993 4.789075 GTCGACGCCCGCAAGCTA 62.789 66.667 0.00 0.00 38.37 3.32
4753 7999 2.589492 CGCCCGCAAGCTATTCGAG 61.589 63.158 4.09 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.700832 TCAGACTATTGTGTGTGAATGGAAC 59.299 40.000 4.48 0.00 37.31 3.62
48 49 5.863965 TCAGACTATTGTGTGTGAATGGAA 58.136 37.500 4.48 0.00 37.31 3.53
57 60 6.634436 GCTTCTTTGTTTCAGACTATTGTGTG 59.366 38.462 0.00 0.00 38.63 3.82
110 114 2.047274 ATACGTGCGCCTTGCTGT 60.047 55.556 4.18 0.00 46.63 4.40
123 127 7.281324 CAGATAGGTCATTACTAGAGGGATACG 59.719 44.444 0.00 0.00 37.60 3.06
186 190 9.367444 CCGTATCAAAGTAGTCTGTAATTTCTT 57.633 33.333 0.00 0.00 0.00 2.52
205 209 4.636648 AGTTTTGTTGTTGTCACCGTATCA 59.363 37.500 0.00 0.00 0.00 2.15
211 215 5.305139 ACAGTAGTTTTGTTGTTGTCACC 57.695 39.130 0.00 0.00 0.00 4.02
261 265 2.432874 GGGGAGAGAGAAAGAGGCTAAC 59.567 54.545 0.00 0.00 0.00 2.34
269 273 5.245977 GGAGAGATAATGGGGAGAGAGAAAG 59.754 48.000 0.00 0.00 0.00 2.62
362 366 5.745227 AGTGGGTGTATTACAATTCCTCAG 58.255 41.667 0.00 0.00 0.00 3.35
441 445 5.061853 CCTTATCATCCAATCACAGACTGG 58.938 45.833 7.51 0.00 0.00 4.00
442 446 5.922053 TCCTTATCATCCAATCACAGACTG 58.078 41.667 0.00 0.00 0.00 3.51
448 452 5.163258 ACTGTCCTCCTTATCATCCAATCAC 60.163 44.000 0.00 0.00 0.00 3.06
459 463 5.036916 TGGAAATACCACTGTCCTCCTTAT 58.963 41.667 0.00 0.00 44.64 1.73
505 509 8.051535 AGGAAATGTGATCATCTATGTCAAGTT 58.948 33.333 0.00 0.00 32.56 2.66
573 578 1.271656 CGTAGTTGAGGGGAACGTCTT 59.728 52.381 0.00 0.00 45.35 3.01
622 629 1.135915 ACTGAGTCGGCACATCATCTC 59.864 52.381 0.00 0.00 0.00 2.75
633 640 1.339631 ACCTCTGAGAGACTGAGTCGG 60.340 57.143 11.82 3.00 41.11 4.79
655 662 3.990959 TGCACACCATACCTGTATGAA 57.009 42.857 16.87 0.00 44.22 2.57
860 897 0.827925 AAGAGTGGACGGACAGCAGA 60.828 55.000 0.00 0.00 0.00 4.26
872 909 2.544685 CTCTCGCCAACATAAGAGTGG 58.455 52.381 0.00 0.00 32.41 4.00
959 999 2.805353 CACTCGTCGGACTTGCGG 60.805 66.667 6.57 0.00 0.00 5.69
992 1035 2.231235 GAGGTGGTTTGCATTTCCGAAT 59.769 45.455 0.00 0.00 0.00 3.34
994 1037 1.202879 AGAGGTGGTTTGCATTTCCGA 60.203 47.619 0.00 0.00 0.00 4.55
1191 1246 1.003718 GAAGTAGCGGTTGGCCAGT 60.004 57.895 5.11 0.00 45.17 4.00
1230 1285 4.143333 CCCTGCCCCTCGTACACG 62.143 72.222 0.00 0.00 41.45 4.49
1672 1744 6.208994 AGTCAGTTGTTCCTCTAATACTCGTT 59.791 38.462 0.00 0.00 0.00 3.85
1673 1745 5.711036 AGTCAGTTGTTCCTCTAATACTCGT 59.289 40.000 0.00 0.00 0.00 4.18
1685 1761 2.930826 TCCCTCAAGTCAGTTGTTCC 57.069 50.000 0.00 0.00 37.43 3.62
1771 1847 8.894409 TCTAAAGTTCATTCGTTGCAATAATG 57.106 30.769 22.21 22.21 32.96 1.90
1963 2039 6.090763 GCAATTGACATGGATATGATGCATTG 59.909 38.462 10.34 0.00 39.45 2.82
2499 2576 4.083961 GGGAGAAGAAACTAAACACTTCGC 60.084 45.833 0.00 0.00 0.00 4.70
2596 2673 2.049888 TGCATGACAAGGTTGTGTGA 57.950 45.000 0.00 0.00 42.43 3.58
2707 5684 7.041030 TCCTTCGTATTTCAGTTTTGCAATGTA 60.041 33.333 0.00 0.00 0.00 2.29
2709 5686 6.148948 TCCTTCGTATTTCAGTTTTGCAATG 58.851 36.000 0.00 0.00 0.00 2.82
2710 5687 6.325919 TCCTTCGTATTTCAGTTTTGCAAT 57.674 33.333 0.00 0.00 0.00 3.56
2736 5713 0.807496 GTGGCAAGCAGAATCTCACC 59.193 55.000 0.00 0.00 0.00 4.02
2741 5718 0.449388 CCTTCGTGGCAAGCAGAATC 59.551 55.000 1.26 0.00 0.00 2.52
2755 5732 0.882042 AGTGACTGTTGCTGCCTTCG 60.882 55.000 0.00 0.00 0.00 3.79
2825 5802 8.860780 ATCCTATTTTCAAATGAGCCTATCTC 57.139 34.615 0.00 0.00 42.23 2.75
2830 5807 6.915786 ACCTATCCTATTTTCAAATGAGCCT 58.084 36.000 0.00 0.00 0.00 4.58
2884 5861 6.918067 TTAGTTCTCAGAATTCACAGAGGA 57.082 37.500 17.22 9.87 0.00 3.71
3026 6004 3.255725 GCACACTAGCGTATGTTTACCA 58.744 45.455 0.00 0.00 0.00 3.25
3030 6008 4.454161 TCATTTGCACACTAGCGTATGTTT 59.546 37.500 0.00 0.00 37.31 2.83
3031 6009 4.000325 TCATTTGCACACTAGCGTATGTT 59.000 39.130 0.00 0.00 37.31 2.71
3078 6056 4.566759 ACATTATGTTGACACCGAGATTCG 59.433 41.667 0.00 0.00 40.07 3.34
3079 6057 7.358435 CGATACATTATGTTGACACCGAGATTC 60.358 40.741 2.23 0.00 0.00 2.52
3080 6058 6.420903 CGATACATTATGTTGACACCGAGATT 59.579 38.462 2.23 0.00 0.00 2.40
3081 6059 5.920840 CGATACATTATGTTGACACCGAGAT 59.079 40.000 2.23 0.00 0.00 2.75
3082 6060 5.163591 ACGATACATTATGTTGACACCGAGA 60.164 40.000 2.23 0.00 0.00 4.04
3083 6061 5.041287 ACGATACATTATGTTGACACCGAG 58.959 41.667 2.23 0.00 0.00 4.63
3084 6062 5.001237 ACGATACATTATGTTGACACCGA 57.999 39.130 2.23 0.00 0.00 4.69
3089 6067 7.757097 AACTCAGACGATACATTATGTTGAC 57.243 36.000 2.23 0.00 0.00 3.18
3091 6069 9.249457 ACATAACTCAGACGATACATTATGTTG 57.751 33.333 2.23 0.00 38.14 3.33
3106 6084 6.544928 TGAGCCTGATAAACATAACTCAGA 57.455 37.500 0.00 0.00 37.85 3.27
3108 6086 6.472016 TGTTGAGCCTGATAAACATAACTCA 58.528 36.000 0.00 0.00 33.20 3.41
3120 6098 3.879295 CACCGAATTATGTTGAGCCTGAT 59.121 43.478 0.00 0.00 0.00 2.90
3121 6099 3.270027 CACCGAATTATGTTGAGCCTGA 58.730 45.455 0.00 0.00 0.00 3.86
3134 6112 3.937814 TCTGTATCTGTTGCACCGAATT 58.062 40.909 0.00 0.00 0.00 2.17
3137 6115 4.729227 TTATCTGTATCTGTTGCACCGA 57.271 40.909 0.00 0.00 0.00 4.69
3178 6156 7.659799 TGAAGAAAACTCGATCATTGTAGGAAA 59.340 33.333 0.00 0.00 0.00 3.13
3186 6164 7.439157 TGACAATGAAGAAAACTCGATCATT 57.561 32.000 3.00 3.00 40.37 2.57
3201 6179 7.201812 GCATACACCTAAATCCATGACAATGAA 60.202 37.037 0.00 0.00 35.67 2.57
3203 6181 6.039605 TGCATACACCTAAATCCATGACAATG 59.960 38.462 0.00 0.00 0.00 2.82
3209 6188 4.023450 CAGCTGCATACACCTAAATCCATG 60.023 45.833 0.00 0.00 0.00 3.66
3229 6208 7.643528 TGATGTCTGACGAAATATTATCAGC 57.356 36.000 14.94 11.89 38.77 4.26
3244 6223 2.338809 AGGAGGTGGTTTGATGTCTGA 58.661 47.619 0.00 0.00 0.00 3.27
3453 6432 3.737774 GCTTGCAAAATGAAGTGGAGTTC 59.262 43.478 0.00 0.00 0.00 3.01
3485 6464 3.446516 AGTAGTACGTCCACAGGAAATCC 59.553 47.826 0.00 0.00 31.38 3.01
3488 6467 3.553508 GCAAGTAGTACGTCCACAGGAAA 60.554 47.826 0.00 0.00 31.38 3.13
3500 6479 8.839310 ATCCAAATATCTGATGCAAGTAGTAC 57.161 34.615 0.00 0.00 0.00 2.73
3526 6505 2.717639 ATGGATCAAAGGGAACGGAG 57.282 50.000 0.00 0.00 0.00 4.63
3559 6538 7.110155 TGTTTCCCTTCAATCAGTAACTATCC 58.890 38.462 0.00 0.00 0.00 2.59
3560 6539 8.738645 ATGTTTCCCTTCAATCAGTAACTATC 57.261 34.615 0.00 0.00 0.00 2.08
3567 6546 6.069440 TCAGGATATGTTTCCCTTCAATCAGT 60.069 38.462 0.00 0.00 36.35 3.41
3618 6597 3.580731 CAACCAAACGACCACAAAACTT 58.419 40.909 0.00 0.00 0.00 2.66
3739 6898 9.797642 AAGTTGCATCATTAATCAGGATATGTA 57.202 29.630 0.00 0.00 0.00 2.29
3943 7110 6.151648 CCATTAAGCTATACAATGTCATGGGG 59.848 42.308 0.00 0.00 0.00 4.96
4007 7174 1.527034 TCAGATTTGCTGGCTGTCAC 58.473 50.000 0.00 0.00 44.98 3.67
4113 7280 3.934457 ACAAAGGTAAATTCCCTTGCG 57.066 42.857 9.47 7.29 41.47 4.85
4156 7323 9.811655 AAAGATGTATCGCAAAATCGTTATATG 57.188 29.630 0.00 0.00 0.00 1.78
4172 7339 6.853362 GCTTTCGCCTATTTCAAAGATGTATC 59.147 38.462 0.00 0.00 0.00 2.24
4239 7406 3.351416 GACCCAAACGGACGCCAC 61.351 66.667 0.00 0.00 34.64 5.01
4263 7430 1.001520 GTTTGGGCCGCCTTTTATGTT 59.998 47.619 9.86 0.00 0.00 2.71
4267 7434 2.269529 CCGTTTGGGCCGCCTTTTA 61.270 57.895 9.86 0.00 0.00 1.52
4384 7565 4.798682 GCCCGGGGGAGGAGAAGA 62.799 72.222 25.28 0.00 37.50 2.87
4490 7689 1.744741 GCAGCTGGCAGAGTCTTCC 60.745 63.158 20.86 1.25 43.97 3.46
4513 7716 3.402681 CTGGGCGGATGTGGAGGT 61.403 66.667 0.00 0.00 0.00 3.85
4588 7808 3.570212 GCTGTGTGGTGGGAGGGT 61.570 66.667 0.00 0.00 0.00 4.34
4657 7884 4.175489 GCTAGCGTCCGACGAGCA 62.175 66.667 24.78 7.19 46.05 4.26
4671 7917 2.438249 CCAGCTAGCTGCCCTGCTA 61.438 63.158 34.82 6.69 43.74 3.49
4747 7993 2.568623 ACCTTGGCAAACTCTCGAAT 57.431 45.000 0.00 0.00 0.00 3.34
4753 7999 4.038642 TCCATTTTGTACCTTGGCAAACTC 59.961 41.667 0.00 0.00 34.77 3.01


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

AutoCloner maintained by Alex Coulton.