Multiple sequence alignment - TraesCS3B01G075000

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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 TraesCS3B01G075000 chr3B 100.000 2669 0 0 1 2669 46034340 46031672 0.000000e+00 4929.0
1 TraesCS3B01G075000 chr3B 87.133 1158 103 11 678 1813 46903767 46904900 0.000000e+00 1271.0
2 TraesCS3B01G075000 chr3B 87.084 782 81 3 1014 1795 46932191 46932952 0.000000e+00 867.0
3 TraesCS3B01G075000 chr3B 88.397 474 39 3 711 1184 46793172 46793629 8.350000e-155 556.0
4 TraesCS3B01G075000 chr3D 94.494 1998 89 6 648 2627 27551546 27549552 0.000000e+00 3061.0
5 TraesCS3B01G075000 chr3D 91.201 966 69 5 711 1664 27943792 27944753 0.000000e+00 1299.0
6 TraesCS3B01G075000 chr3D 87.742 465 44 8 1942 2399 27944969 27945427 5.060000e-147 531.0
7 TraesCS3B01G075000 chr3D 90.845 142 12 1 507 648 27551761 27551621 3.510000e-44 189.0
8 TraesCS3B01G075000 chr3D 94.444 90 1 3 87 174 27552122 27552035 4.630000e-28 135.0
9 TraesCS3B01G075000 chr3D 75.884 311 49 17 170 464 28208118 28208418 4.630000e-28 135.0
10 TraesCS3B01G075000 chr3D 98.039 51 1 0 2619 2669 26652407 26652357 3.660000e-14 89.8
11 TraesCS3B01G075000 chr3A 91.287 2238 123 24 54 2267 37652133 37649944 0.000000e+00 2987.0
12 TraesCS3B01G075000 chr3A 91.624 967 67 3 712 1667 37827696 37826733 0.000000e+00 1325.0
13 TraesCS3B01G075000 chr3A 82.797 1087 106 31 805 1841 38124779 38125834 0.000000e+00 896.0
14 TraesCS3B01G075000 chr3A 89.107 459 44 5 1942 2399 37826520 37826067 1.390000e-157 566.0
15 TraesCS3B01G075000 chr3A 96.716 335 11 0 2289 2623 37649010 37648676 2.320000e-155 558.0
16 TraesCS3B01G075000 chr3A 86.612 366 42 7 1883 2241 38125900 38126265 5.350000e-107 398.0
17 TraesCS3B01G075000 chr3A 89.175 194 20 1 2435 2627 37826073 37825880 9.550000e-60 241.0
18 TraesCS3B01G075000 chrUn 89.280 653 56 1 1020 1672 287642991 287642353 0.000000e+00 806.0
19 TraesCS3B01G075000 chrUn 87.156 109 14 0 860 968 287643115 287643007 1.000000e-24 124.0
20 TraesCS3B01G075000 chrUn 78.621 145 20 6 2091 2224 347229041 347229185 4.730000e-13 86.1
21 TraesCS3B01G075000 chr6B 100.000 50 0 0 2620 2669 245047886 245047837 2.830000e-15 93.5
22 TraesCS3B01G075000 chr6B 98.039 51 1 0 2619 2669 8238787 8238737 3.660000e-14 89.8
23 TraesCS3B01G075000 chr7B 100.000 49 0 0 2621 2669 649279430 649279478 1.020000e-14 91.6
24 TraesCS3B01G075000 chr7B 100.000 49 0 0 2621 2669 696910925 696910877 1.020000e-14 91.6
25 TraesCS3B01G075000 chr5B 100.000 49 0 0 2621 2669 67011339 67011387 1.020000e-14 91.6
26 TraesCS3B01G075000 chr7A 98.039 51 1 0 2619 2669 40439944 40439894 3.660000e-14 89.8
27 TraesCS3B01G075000 chr6D 96.364 55 1 1 2616 2669 191393972 191394026 3.660000e-14 89.8
28 TraesCS3B01G075000 chr5A 98.039 51 1 0 2619 2669 357164201 357164151 3.660000e-14 89.8


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 TraesCS3B01G075000 chr3B 46031672 46034340 2668 True 4929.000000 4929 100.000000 1 2669 1 chr3B.!!$R1 2668
1 TraesCS3B01G075000 chr3B 46903767 46904900 1133 False 1271.000000 1271 87.133000 678 1813 1 chr3B.!!$F2 1135
2 TraesCS3B01G075000 chr3B 46932191 46932952 761 False 867.000000 867 87.084000 1014 1795 1 chr3B.!!$F3 781
3 TraesCS3B01G075000 chr3D 27549552 27552122 2570 True 1128.333333 3061 93.261000 87 2627 3 chr3D.!!$R2 2540
4 TraesCS3B01G075000 chr3D 27943792 27945427 1635 False 915.000000 1299 89.471500 711 2399 2 chr3D.!!$F2 1688
5 TraesCS3B01G075000 chr3A 37648676 37652133 3457 True 1772.500000 2987 94.001500 54 2623 2 chr3A.!!$R1 2569
6 TraesCS3B01G075000 chr3A 37825880 37827696 1816 True 710.666667 1325 89.968667 712 2627 3 chr3A.!!$R2 1915
7 TraesCS3B01G075000 chr3A 38124779 38126265 1486 False 647.000000 896 84.704500 805 2241 2 chr3A.!!$F1 1436
8 TraesCS3B01G075000 chrUn 287642353 287643115 762 True 465.000000 806 88.218000 860 1672 2 chrUn.!!$R1 812

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
464 660 0.036732 TGTTGCCGATTCTCCAGCTT 59.963 50.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2597 0.110486 GGGACCTCCTCAACAGCAAA 59.89 55.0 0.0 0.0 35.95 3.68 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
31 32 4.644103 TTTTCTATTACGGACCCTCTCG 57.356 45.455 0.00 0.00 0.00 4.04
32 33 1.602311 TCTATTACGGACCCTCTCGC 58.398 55.000 0.00 0.00 0.00 5.03
33 34 1.142465 TCTATTACGGACCCTCTCGCT 59.858 52.381 0.00 0.00 0.00 4.93
34 35 1.536331 CTATTACGGACCCTCTCGCTC 59.464 57.143 0.00 0.00 0.00 5.03
35 36 0.395311 ATTACGGACCCTCTCGCTCA 60.395 55.000 0.00 0.00 0.00 4.26
36 37 0.395311 TTACGGACCCTCTCGCTCAT 60.395 55.000 0.00 0.00 0.00 2.90
37 38 0.395311 TACGGACCCTCTCGCTCATT 60.395 55.000 0.00 0.00 0.00 2.57
38 39 1.066587 CGGACCCTCTCGCTCATTC 59.933 63.158 0.00 0.00 0.00 2.67
39 40 1.388065 CGGACCCTCTCGCTCATTCT 61.388 60.000 0.00 0.00 0.00 2.40
40 41 0.387565 GGACCCTCTCGCTCATTCTC 59.612 60.000 0.00 0.00 0.00 2.87
41 42 0.387565 GACCCTCTCGCTCATTCTCC 59.612 60.000 0.00 0.00 0.00 3.71
42 43 1.361993 CCCTCTCGCTCATTCTCCG 59.638 63.158 0.00 0.00 0.00 4.63
43 44 1.361993 CCTCTCGCTCATTCTCCGG 59.638 63.158 0.00 0.00 0.00 5.14
44 45 1.299773 CTCTCGCTCATTCTCCGGC 60.300 63.158 0.00 0.00 0.00 6.13
48 49 2.964389 GCTCATTCTCCGGCGAGC 60.964 66.667 9.30 3.04 43.60 5.03
49 50 2.811101 CTCATTCTCCGGCGAGCT 59.189 61.111 9.30 0.00 35.94 4.09
50 51 1.591059 CTCATTCTCCGGCGAGCTG 60.591 63.158 9.30 0.00 35.94 4.24
51 52 2.185350 CATTCTCCGGCGAGCTGT 59.815 61.111 9.30 0.00 35.94 4.40
52 53 2.169789 CATTCTCCGGCGAGCTGTG 61.170 63.158 9.30 0.00 35.94 3.66
61 62 2.360350 CGAGCTGTGGCCCATTGT 60.360 61.111 0.00 0.00 39.73 2.71
80 81 3.782443 GGAGTGTACCCGGGCAGG 61.782 72.222 24.08 0.00 40.63 4.85
154 156 2.303175 GTGGTGTTGGGCTTACTTTCA 58.697 47.619 0.00 0.00 0.00 2.69
229 407 3.518998 CGGCGATGTCGACCCTCT 61.519 66.667 14.12 0.00 46.52 3.69
260 439 4.374702 GTTCGCACGCCACTGCTG 62.375 66.667 0.00 0.00 34.77 4.41
269 448 1.377333 GCCACTGCTGTTCCCTACC 60.377 63.158 0.00 0.00 33.53 3.18
282 461 2.774799 CCTACCTGCGCATTTGCCC 61.775 63.158 12.24 0.00 37.91 5.36
314 493 4.200283 GCTCCCGTCTCCAGCGAG 62.200 72.222 0.00 0.00 37.48 5.03
315 494 2.752238 CTCCCGTCTCCAGCGAGT 60.752 66.667 0.00 0.00 37.40 4.18
316 495 2.750637 TCCCGTCTCCAGCGAGTC 60.751 66.667 0.00 0.00 37.40 3.36
317 496 3.827898 CCCGTCTCCAGCGAGTCC 61.828 72.222 0.00 0.00 37.40 3.85
318 497 3.827898 CCGTCTCCAGCGAGTCCC 61.828 72.222 0.00 0.00 37.40 4.46
319 498 3.827898 CGTCTCCAGCGAGTCCCC 61.828 72.222 0.00 0.00 37.40 4.81
320 499 3.827898 GTCTCCAGCGAGTCCCCG 61.828 72.222 0.00 0.00 37.40 5.73
340 519 1.918800 GGGGTGGTACCTCACTGCT 60.919 63.158 15.56 0.00 39.07 4.24
348 544 4.504916 CCTCACTGCTCCTCCGCG 62.505 72.222 0.00 0.00 0.00 6.46
370 566 4.195416 GTCCAGATTCCAGAAGGTGAATC 58.805 47.826 4.48 4.48 44.58 2.52
403 599 4.155733 CGGTGATGGCGGCCAGTA 62.156 66.667 27.62 15.47 36.75 2.74
423 619 6.183360 CCAGTAGATGCGTAAATTGTAGCAAA 60.183 38.462 6.15 0.00 43.19 3.68
424 620 7.409697 CAGTAGATGCGTAAATTGTAGCAAAT 58.590 34.615 6.15 2.05 43.19 2.32
429 625 5.157781 TGCGTAAATTGTAGCAAATGAACC 58.842 37.500 0.32 0.00 36.60 3.62
440 636 1.962807 CAAATGAACCCTTCTGCACCA 59.037 47.619 0.00 0.00 0.00 4.17
444 640 1.168714 GAACCCTTCTGCACCATGAC 58.831 55.000 0.00 0.00 0.00 3.06
454 650 1.308069 GCACCATGACTGTTGCCGAT 61.308 55.000 0.00 0.00 0.00 4.18
457 653 1.003580 ACCATGACTGTTGCCGATTCT 59.996 47.619 0.00 0.00 0.00 2.40
464 660 0.036732 TGTTGCCGATTCTCCAGCTT 59.963 50.000 0.00 0.00 0.00 3.74
504 700 2.354510 TGCCTTCGTTATAGCATTGCAC 59.645 45.455 11.91 0.00 0.00 4.57
505 701 2.599848 GCCTTCGTTATAGCATTGCACG 60.600 50.000 11.91 11.78 0.00 5.34
506 702 2.607635 CCTTCGTTATAGCATTGCACGT 59.392 45.455 11.91 0.00 32.65 4.49
507 703 3.063452 CCTTCGTTATAGCATTGCACGTT 59.937 43.478 11.91 0.00 32.65 3.99
508 704 3.918258 TCGTTATAGCATTGCACGTTC 57.082 42.857 11.91 0.00 32.65 3.95
509 705 3.254892 TCGTTATAGCATTGCACGTTCA 58.745 40.909 11.91 0.00 32.65 3.18
510 706 3.305897 TCGTTATAGCATTGCACGTTCAG 59.694 43.478 11.91 0.00 32.65 3.02
511 707 3.305897 CGTTATAGCATTGCACGTTCAGA 59.694 43.478 11.91 0.00 0.00 3.27
512 708 4.201676 CGTTATAGCATTGCACGTTCAGAA 60.202 41.667 11.91 0.00 0.00 3.02
513 709 5.258622 GTTATAGCATTGCACGTTCAGAAG 58.741 41.667 11.91 0.00 0.00 2.85
514 710 0.239347 AGCATTGCACGTTCAGAAGC 59.761 50.000 11.91 0.00 0.00 3.86
515 711 0.040157 GCATTGCACGTTCAGAAGCA 60.040 50.000 3.15 0.00 34.00 3.91
516 712 1.959747 CATTGCACGTTCAGAAGCAG 58.040 50.000 0.00 0.00 36.28 4.24
517 713 0.239347 ATTGCACGTTCAGAAGCAGC 59.761 50.000 0.00 0.00 36.28 5.25
518 714 1.094650 TTGCACGTTCAGAAGCAGCA 61.095 50.000 0.00 0.41 36.28 4.41
519 715 1.206072 GCACGTTCAGAAGCAGCAG 59.794 57.895 0.00 0.00 0.00 4.24
520 716 1.224069 GCACGTTCAGAAGCAGCAGA 61.224 55.000 0.00 0.00 0.00 4.26
521 717 0.788995 CACGTTCAGAAGCAGCAGAG 59.211 55.000 0.00 0.00 0.00 3.35
522 718 0.948141 ACGTTCAGAAGCAGCAGAGC 60.948 55.000 0.00 0.00 0.00 4.09
553 749 3.370366 CCAGACTTTGCTTGATCTCTTCG 59.630 47.826 0.00 0.00 0.00 3.79
616 814 2.801421 GCGATGAGCGTCTCCTCA 59.199 61.111 0.00 3.67 45.16 3.86
617 815 1.139734 GCGATGAGCGTCTCCTCAA 59.860 57.895 0.00 0.00 44.34 3.02
622 820 3.489229 CGATGAGCGTCTCCTCAAATACA 60.489 47.826 10.77 0.00 44.34 2.29
738 1024 5.055642 CTGAAGCATTTTCAGAATCAGCA 57.944 39.130 10.58 0.00 46.57 4.41
818 1115 7.585573 GCATCGTTAGAATCTAAAAGCTTCATG 59.414 37.037 4.04 3.89 0.00 3.07
922 1232 4.697352 AGAAATCTGATACAGGTTGCACAC 59.303 41.667 5.67 0.00 34.77 3.82
937 1247 1.407258 GCACACACTTGGCTTTGGTTA 59.593 47.619 0.00 0.00 0.00 2.85
950 1260 3.186613 GCTTTGGTTACACTCCTTTCTCG 59.813 47.826 0.00 0.00 0.00 4.04
969 1297 6.730960 TCTCGTCACATTATTTAAACCCAC 57.269 37.500 0.00 0.00 0.00 4.61
970 1298 6.231951 TCTCGTCACATTATTTAAACCCACA 58.768 36.000 0.00 0.00 0.00 4.17
994 1323 4.853468 TCTCTACTCCATCTCTGTGTCT 57.147 45.455 0.00 0.00 0.00 3.41
1025 1354 5.357878 TGAAGCTCTTCACTGTCATGTTTTT 59.642 36.000 8.14 0.00 43.90 1.94
1045 1380 0.970937 CTACGTCCTCCTCCTTGGCA 60.971 60.000 0.00 0.00 35.26 4.92
1062 1397 2.843730 TGGCATCTATACACCACCAAGT 59.156 45.455 0.00 0.00 0.00 3.16
1080 1415 1.471119 GTCTATCAGACGGTCCACCA 58.529 55.000 4.14 0.00 35.28 4.17
1233 1568 0.690192 ACAACATGGTCCGGTCATCA 59.310 50.000 0.00 0.00 0.00 3.07
1735 2079 4.898829 TTTACCCGCAGATGATGATTTG 57.101 40.909 0.00 0.00 0.00 2.32
1787 2132 8.904834 GGACAGAATCTCAGTCTAGTAATGTTA 58.095 37.037 1.59 0.00 33.96 2.41
1836 2181 9.836864 ATGTGATGTAGCTGATTAATTTCTGTA 57.163 29.630 0.00 0.00 0.00 2.74
1837 2182 9.317936 TGTGATGTAGCTGATTAATTTCTGTAG 57.682 33.333 0.00 0.00 0.00 2.74
1838 2183 8.768955 GTGATGTAGCTGATTAATTTCTGTAGG 58.231 37.037 0.00 0.00 0.00 3.18
1839 2184 8.704668 TGATGTAGCTGATTAATTTCTGTAGGA 58.295 33.333 0.00 0.00 0.00 2.94
1840 2185 9.547753 GATGTAGCTGATTAATTTCTGTAGGAA 57.452 33.333 0.00 0.00 0.00 3.36
1841 2186 9.905713 ATGTAGCTGATTAATTTCTGTAGGAAA 57.094 29.630 0.00 0.00 46.33 3.13
1842 2187 9.162764 TGTAGCTGATTAATTTCTGTAGGAAAC 57.837 33.333 0.00 0.00 45.29 2.78
1843 2188 9.384764 GTAGCTGATTAATTTCTGTAGGAAACT 57.615 33.333 0.00 0.00 45.29 2.66
1869 2251 6.649557 AGGAATTATAAAGATAAGAACCGCGG 59.350 38.462 26.86 26.86 31.02 6.46
2207 2602 8.115490 AGTATTGTTATCTTTTGCTCTTTGCT 57.885 30.769 0.00 0.00 43.37 3.91
2323 3634 2.240493 ACCTATGATGCCACTTACGC 57.760 50.000 0.00 0.00 0.00 4.42
2530 3846 7.862372 TCTGACTAGATTTGCAAAAATGTTGTC 59.138 33.333 17.19 14.95 38.05 3.18
2588 3904 1.072173 ACATGGTCACAGCAGTAGCAA 59.928 47.619 0.00 0.00 45.49 3.91
2620 3936 1.178276 CAGACTTGACGCCCTCTAGT 58.822 55.000 0.00 0.00 37.64 2.57
2623 3939 1.133407 GACTTGACGCCCTCTAGTCAG 59.867 57.143 12.75 2.34 45.81 3.51
2631 3947 3.691820 CCTCTAGTCAGGGTGGACA 57.308 57.895 0.00 0.00 40.29 4.02
2632 3948 1.187087 CCTCTAGTCAGGGTGGACAC 58.813 60.000 0.00 0.00 40.29 3.67
2633 3949 0.811915 CTCTAGTCAGGGTGGACACG 59.188 60.000 0.00 0.00 40.29 4.49
2634 3950 0.611062 TCTAGTCAGGGTGGACACGG 60.611 60.000 0.00 0.00 40.29 4.94
2635 3951 0.898789 CTAGTCAGGGTGGACACGGT 60.899 60.000 0.00 0.00 40.29 4.83
2636 3952 0.896940 TAGTCAGGGTGGACACGGTC 60.897 60.000 0.00 0.00 40.29 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.678840 GCGAGAGGGTCCGTAATAGAAAAA 60.679 45.833 0.00 0.00 0.00 1.94
10 11 3.181483 GCGAGAGGGTCCGTAATAGAAAA 60.181 47.826 0.00 0.00 0.00 2.29
11 12 2.360165 GCGAGAGGGTCCGTAATAGAAA 59.640 50.000 0.00 0.00 0.00 2.52
12 13 1.952296 GCGAGAGGGTCCGTAATAGAA 59.048 52.381 0.00 0.00 0.00 2.10
13 14 1.142465 AGCGAGAGGGTCCGTAATAGA 59.858 52.381 0.00 0.00 0.00 1.98
14 15 1.536331 GAGCGAGAGGGTCCGTAATAG 59.464 57.143 0.00 0.00 37.18 1.73
15 16 1.134007 TGAGCGAGAGGGTCCGTAATA 60.134 52.381 0.00 0.00 42.55 0.98
16 17 0.395311 TGAGCGAGAGGGTCCGTAAT 60.395 55.000 0.00 0.00 42.55 1.89
17 18 0.395311 ATGAGCGAGAGGGTCCGTAA 60.395 55.000 0.00 0.00 42.55 3.18
18 19 0.395311 AATGAGCGAGAGGGTCCGTA 60.395 55.000 0.00 0.00 42.55 4.02
19 20 1.668101 GAATGAGCGAGAGGGTCCGT 61.668 60.000 0.00 0.00 42.55 4.69
20 21 1.066587 GAATGAGCGAGAGGGTCCG 59.933 63.158 0.00 0.00 42.55 4.79
21 22 0.387565 GAGAATGAGCGAGAGGGTCC 59.612 60.000 0.00 0.00 42.55 4.46
22 23 0.387565 GGAGAATGAGCGAGAGGGTC 59.612 60.000 0.00 0.00 43.52 4.46
23 24 1.388065 CGGAGAATGAGCGAGAGGGT 61.388 60.000 0.00 0.00 0.00 4.34
24 25 1.361993 CGGAGAATGAGCGAGAGGG 59.638 63.158 0.00 0.00 0.00 4.30
25 26 1.361993 CCGGAGAATGAGCGAGAGG 59.638 63.158 0.00 0.00 0.00 3.69
26 27 1.299773 GCCGGAGAATGAGCGAGAG 60.300 63.158 5.05 0.00 0.00 3.20
27 28 2.808315 GCCGGAGAATGAGCGAGA 59.192 61.111 5.05 0.00 0.00 4.04
31 32 2.964389 GCTCGCCGGAGAATGAGC 60.964 66.667 9.83 12.62 45.95 4.26
32 33 1.591059 CAGCTCGCCGGAGAATGAG 60.591 63.158 9.83 6.54 43.27 2.90
33 34 2.351244 ACAGCTCGCCGGAGAATGA 61.351 57.895 21.76 4.29 43.27 2.57
34 35 2.169789 CACAGCTCGCCGGAGAATG 61.170 63.158 9.83 13.37 43.27 2.67
35 36 2.185350 CACAGCTCGCCGGAGAAT 59.815 61.111 9.83 0.00 43.27 2.40
36 37 4.069232 CCACAGCTCGCCGGAGAA 62.069 66.667 9.83 0.00 43.27 2.87
43 44 3.818787 CAATGGGCCACAGCTCGC 61.819 66.667 9.28 0.00 45.33 5.03
44 45 2.360350 ACAATGGGCCACAGCTCG 60.360 61.111 9.28 0.00 45.33 5.03
45 46 2.345760 CCACAATGGGCCACAGCTC 61.346 63.158 9.28 0.00 41.29 4.09
46 47 2.283388 CCACAATGGGCCACAGCT 60.283 61.111 9.28 0.00 39.73 4.24
66 67 0.179065 GATTACCTGCCCGGGTACAC 60.179 60.000 24.63 5.46 41.02 2.90
80 81 1.453928 GCCCCCAGTGCAGGATTAC 60.454 63.158 0.00 0.00 0.00 1.89
154 156 2.586792 GGAGGCCACTCGCAATCT 59.413 61.111 5.01 0.00 44.93 2.40
229 407 1.223417 GCGAACGGAAGGTTTCGGAA 61.223 55.000 5.93 0.00 39.50 4.30
260 439 0.451783 CAAATGCGCAGGTAGGGAAC 59.548 55.000 18.32 0.00 0.00 3.62
299 478 2.750637 GACTCGCTGGAGACGGGA 60.751 66.667 0.00 0.00 43.27 5.14
302 481 3.827898 GGGGACTCGCTGGAGACG 61.828 72.222 0.00 0.00 43.27 4.18
303 482 3.827898 CGGGGACTCGCTGGAGAC 61.828 72.222 0.00 0.00 43.27 3.36
319 498 4.446413 GTGAGGTACCACCCCGCG 62.446 72.222 15.94 0.00 39.75 6.46
320 499 3.001406 AGTGAGGTACCACCCCGC 61.001 66.667 15.94 6.85 39.75 6.13
321 500 2.978824 CAGTGAGGTACCACCCCG 59.021 66.667 15.94 0.00 39.75 5.73
322 501 1.900545 GAGCAGTGAGGTACCACCCC 61.901 65.000 15.94 1.20 39.75 4.95
323 502 1.597461 GAGCAGTGAGGTACCACCC 59.403 63.158 15.94 0.00 39.75 4.61
324 503 0.905337 AGGAGCAGTGAGGTACCACC 60.905 60.000 15.94 6.00 37.76 4.61
325 504 0.533032 GAGGAGCAGTGAGGTACCAC 59.467 60.000 15.94 8.81 37.32 4.16
340 519 2.423898 GGAATCTGGACGCGGAGGA 61.424 63.158 12.47 3.21 0.00 3.71
348 544 3.703001 TTCACCTTCTGGAATCTGGAC 57.297 47.619 0.00 0.00 37.04 4.02
399 595 5.966636 TGCTACAATTTACGCATCTACTG 57.033 39.130 0.00 0.00 0.00 2.74
403 599 6.435430 TCATTTGCTACAATTTACGCATCT 57.565 33.333 0.00 0.00 31.77 2.90
423 619 1.355381 TCATGGTGCAGAAGGGTTCAT 59.645 47.619 0.00 0.00 0.00 2.57
424 620 0.770499 TCATGGTGCAGAAGGGTTCA 59.230 50.000 0.00 0.00 0.00 3.18
429 625 1.538512 CAACAGTCATGGTGCAGAAGG 59.461 52.381 0.00 0.00 37.31 3.46
440 636 1.278985 TGGAGAATCGGCAACAGTCAT 59.721 47.619 0.00 0.00 34.37 3.06
444 640 0.392193 AGCTGGAGAATCGGCAACAG 60.392 55.000 0.00 0.00 37.07 3.16
454 650 6.550938 TCAGATTTCATAGAAGCTGGAGAA 57.449 37.500 3.45 0.00 41.92 2.87
457 653 6.490241 TCATCAGATTTCATAGAAGCTGGA 57.510 37.500 3.45 0.00 41.92 3.86
464 660 7.763071 CGAAGGCATATCATCAGATTTCATAGA 59.237 37.037 0.00 0.00 35.67 1.98
504 700 0.669932 AGCTCTGCTGCTTCTGAACG 60.670 55.000 0.00 0.00 40.93 3.95
505 701 3.230115 AGCTCTGCTGCTTCTGAAC 57.770 52.632 0.00 0.00 40.93 3.18
512 708 2.929830 CTGAACAAGCTCTGCTGCT 58.070 52.632 0.00 0.00 46.40 4.24
522 718 1.952296 AGCAAAGTCTGGCTGAACAAG 59.048 47.619 0.00 0.00 39.30 3.16
523 719 2.057137 AGCAAAGTCTGGCTGAACAA 57.943 45.000 0.00 0.00 39.30 2.83
617 815 9.899661 TGGCAATCTGTAGTTAGTAATTGTATT 57.100 29.630 0.00 0.00 0.00 1.89
622 820 9.601217 CTAGTTGGCAATCTGTAGTTAGTAATT 57.399 33.333 1.92 0.00 0.00 1.40
818 1115 3.491964 GGCAAAAGGGTGAAGGTGTTAAC 60.492 47.826 0.00 0.00 0.00 2.01
922 1232 2.293399 GGAGTGTAACCAAAGCCAAGTG 59.707 50.000 0.00 0.00 37.80 3.16
937 1247 3.753294 AATGTGACGAGAAAGGAGTGT 57.247 42.857 0.00 0.00 0.00 3.55
950 1260 9.353999 GAGAATTGTGGGTTTAAATAATGTGAC 57.646 33.333 0.00 0.00 0.00 3.67
969 1297 6.096705 AGACACAGAGATGGAGTAGAGAATTG 59.903 42.308 0.00 0.00 0.00 2.32
970 1298 6.194235 AGACACAGAGATGGAGTAGAGAATT 58.806 40.000 0.00 0.00 0.00 2.17
1025 1354 0.683504 GCCAAGGAGGAGGACGTAGA 60.684 60.000 0.00 0.00 41.22 2.59
1045 1380 7.231722 GTCTGATAGACTTGGTGGTGTATAGAT 59.768 40.741 1.86 0.00 41.88 1.98
1062 1397 1.005569 AGTGGTGGACCGTCTGATAGA 59.994 52.381 0.00 0.00 39.43 1.98
1080 1415 3.614092 CATAGGGCACACATCTTGAAGT 58.386 45.455 0.00 0.00 0.00 3.01
1233 1568 1.078709 CAGCGGTGATGATGTTCGTT 58.921 50.000 9.50 0.00 0.00 3.85
1787 2132 9.851686 ACATGGTATTTACATCATTGAGTACAT 57.148 29.630 0.00 0.00 0.00 2.29
1789 2134 9.325198 TCACATGGTATTTACATCATTGAGTAC 57.675 33.333 0.00 0.00 0.00 2.73
1841 2186 9.708092 GCGGTTCTTATCTTTATAATTCCTAGT 57.292 33.333 0.00 0.00 0.00 2.57
1842 2187 8.861101 CGCGGTTCTTATCTTTATAATTCCTAG 58.139 37.037 0.00 0.00 0.00 3.02
1843 2188 7.816031 CCGCGGTTCTTATCTTTATAATTCCTA 59.184 37.037 19.50 0.00 0.00 2.94
1859 2214 0.178068 ATCTATGTGCCGCGGTTCTT 59.822 50.000 28.70 18.85 0.00 2.52
1864 2219 2.253758 CCCAATCTATGTGCCGCGG 61.254 63.158 24.05 24.05 0.00 6.46
1869 2251 2.173569 AGAAGGGTCCCAATCTATGTGC 59.826 50.000 11.55 0.00 0.00 4.57
2202 2597 0.110486 GGGACCTCCTCAACAGCAAA 59.890 55.000 0.00 0.00 35.95 3.68
2264 2661 9.745018 AATCAAACTTTCCATGAAGAGAGAATA 57.255 29.630 0.00 0.00 0.00 1.75
2323 3634 5.593909 TGGTAGGATAATCCTTGCACAAATG 59.406 40.000 0.00 0.00 46.91 2.32
2530 3846 9.948964 TTATCAGGGTATATGACATCAGATTTG 57.051 33.333 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.