Multiple sequence alignment - TraesCS3B01G536800

Loading Multiple Alignment...

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 TraesCS3B01G536800 chr3B 100.000 4075 0 0 1 4075 776862321 776866395 0.000000e+00 7526.0
1 TraesCS3B01G536800 chr3B 81.305 2268 358 37 901 3127 776996255 776998497 0.000000e+00 1779.0
2 TraesCS3B01G536800 chr3B 80.531 2147 345 51 996 3106 777033149 777035258 0.000000e+00 1581.0
3 TraesCS3B01G536800 chr3B 80.803 1594 257 28 1479 3050 777001555 777003121 0.000000e+00 1203.0
4 TraesCS3B01G536800 chr3B 80.516 698 73 32 3 662 31869005 31868333 1.020000e-130 477.0
5 TraesCS3B01G536800 chr3B 94.215 242 12 2 3835 4075 776555265 776555505 6.430000e-98 368.0
6 TraesCS3B01G536800 chr3B 80.549 437 45 19 1 411 19741414 19740992 2.380000e-77 300.0
7 TraesCS3B01G536800 chr3B 93.043 115 6 2 3962 4075 776584735 776584848 2.520000e-37 167.0
8 TraesCS3B01G536800 chr3B 75.785 446 43 30 1 406 741648540 741648960 9.060000e-37 165.0
9 TraesCS3B01G536800 chr3B 94.444 36 2 0 859 894 777032897 777032932 5.690000e-04 56.5
10 TraesCS3B01G536800 chr3B 100.000 28 0 0 3839 3866 776866120 776866147 7.000000e-03 52.8
11 TraesCS3B01G536800 chr3B 100.000 28 0 0 3800 3827 776866159 776866186 7.000000e-03 52.8
12 TraesCS3B01G536800 chr3D 94.914 2045 77 11 1115 3150 581458836 581456810 0.000000e+00 3175.0
13 TraesCS3B01G536800 chr3D 81.507 2071 340 29 994 3042 581507695 581505646 0.000000e+00 1663.0
14 TraesCS3B01G536800 chr3D 80.818 2127 352 34 996 3105 581514875 581512788 0.000000e+00 1616.0
15 TraesCS3B01G536800 chr3D 93.041 934 54 8 3149 4075 581456771 581455842 0.000000e+00 1354.0
16 TraesCS3B01G536800 chr3D 82.556 1244 193 14 1871 3105 581517684 581516456 0.000000e+00 1074.0
17 TraesCS3B01G536800 chr3D 94.895 333 14 3 679 1010 581459678 581459348 6.040000e-143 518.0
18 TraesCS3B01G536800 chr3D 92.975 242 15 2 3835 4075 581525938 581525698 6.480000e-93 351.0
19 TraesCS3B01G536800 chr3D 79.426 209 34 5 999 1207 581412801 581412602 5.490000e-29 139.0
20 TraesCS3B01G536800 chr3D 96.154 52 2 0 1077 1128 581458912 581458861 7.260000e-13 86.1
21 TraesCS3B01G536800 chr3D 100.000 28 0 0 3800 3827 581456077 581456050 7.000000e-03 52.8
22 TraesCS3B01G536800 chr3A 81.814 1985 320 28 1193 3150 716597810 716599780 0.000000e+00 1628.0
23 TraesCS3B01G536800 chr3A 80.272 2129 360 37 996 3105 716586855 716588942 0.000000e+00 1550.0
24 TraesCS3B01G536800 chr3A 75.888 1576 315 44 997 2541 716627661 716629202 0.000000e+00 745.0
25 TraesCS3B01G536800 chr3A 77.944 1070 196 25 956 2010 716563596 716564640 2.070000e-177 632.0
26 TraesCS3B01G536800 chr3A 83.258 663 86 20 13 663 489756287 489756936 1.630000e-163 586.0
27 TraesCS3B01G536800 chr3A 83.359 637 82 19 40 663 118452057 118452682 5.910000e-158 568.0
28 TraesCS3B01G536800 chr2B 79.543 2234 378 45 901 3087 26574091 26571890 0.000000e+00 1520.0
29 TraesCS3B01G536800 chr5A 83.140 688 85 18 1 666 30859901 30859223 2.100000e-167 599.0
30 TraesCS3B01G536800 chr6D 83.871 651 70 23 40 663 147646934 147647576 4.540000e-164 588.0
31 TraesCS3B01G536800 chr4D 83.901 646 70 20 46 665 347508294 347507657 1.630000e-163 586.0
32 TraesCS3B01G536800 chr2D 84.080 647 62 24 46 665 567084002 567083370 1.630000e-163 586.0
33 TraesCS3B01G536800 chr6B 83.994 631 78 18 46 663 19904550 19903930 5.870000e-163 584.0
34 TraesCS3B01G536800 chrUn 83.856 638 75 14 46 663 260712403 260713032 2.110000e-162 582.0
35 TraesCS3B01G536800 chrUn 83.518 631 80 19 46 663 225327172 225326553 5.910000e-158 568.0


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 TraesCS3B01G536800 chr3B 776862321 776866395 4074 False 2543.866667 7526 100.0000 1 4075 3 chr3B.!!$F4 4074
1 TraesCS3B01G536800 chr3B 776996255 777003121 6866 False 1491.000000 1779 81.0540 901 3127 2 chr3B.!!$F5 2226
2 TraesCS3B01G536800 chr3B 777032897 777035258 2361 False 818.750000 1581 87.4875 859 3106 2 chr3B.!!$F6 2247
3 TraesCS3B01G536800 chr3B 31868333 31869005 672 True 477.000000 477 80.5160 3 662 1 chr3B.!!$R2 659
4 TraesCS3B01G536800 chr3D 581505646 581507695 2049 True 1663.000000 1663 81.5070 994 3042 1 chr3D.!!$R2 2048
5 TraesCS3B01G536800 chr3D 581512788 581517684 4896 True 1345.000000 1616 81.6870 996 3105 2 chr3D.!!$R5 2109
6 TraesCS3B01G536800 chr3D 581455842 581459678 3836 True 1037.180000 3175 95.8008 679 4075 5 chr3D.!!$R4 3396
7 TraesCS3B01G536800 chr3A 716597810 716599780 1970 False 1628.000000 1628 81.8140 1193 3150 1 chr3A.!!$F5 1957
8 TraesCS3B01G536800 chr3A 716586855 716588942 2087 False 1550.000000 1550 80.2720 996 3105 1 chr3A.!!$F4 2109
9 TraesCS3B01G536800 chr3A 716627661 716629202 1541 False 745.000000 745 75.8880 997 2541 1 chr3A.!!$F6 1544
10 TraesCS3B01G536800 chr3A 716563596 716564640 1044 False 632.000000 632 77.9440 956 2010 1 chr3A.!!$F3 1054
11 TraesCS3B01G536800 chr3A 489756287 489756936 649 False 586.000000 586 83.2580 13 663 1 chr3A.!!$F2 650
12 TraesCS3B01G536800 chr3A 118452057 118452682 625 False 568.000000 568 83.3590 40 663 1 chr3A.!!$F1 623
13 TraesCS3B01G536800 chr2B 26571890 26574091 2201 True 1520.000000 1520 79.5430 901 3087 1 chr2B.!!$R1 2186
14 TraesCS3B01G536800 chr5A 30859223 30859901 678 True 599.000000 599 83.1400 1 666 1 chr5A.!!$R1 665
15 TraesCS3B01G536800 chr6D 147646934 147647576 642 False 588.000000 588 83.8710 40 663 1 chr6D.!!$F1 623
16 TraesCS3B01G536800 chr4D 347507657 347508294 637 True 586.000000 586 83.9010 46 665 1 chr4D.!!$R1 619
17 TraesCS3B01G536800 chr2D 567083370 567084002 632 True 586.000000 586 84.0800 46 665 1 chr2D.!!$R1 619
18 TraesCS3B01G536800 chr6B 19903930 19904550 620 True 584.000000 584 83.9940 46 663 1 chr6B.!!$R1 617
19 TraesCS3B01G536800 chrUn 260712403 260713032 629 False 582.000000 582 83.8560 46 663 1 chrUn.!!$F1 617
20 TraesCS3B01G536800 chrUn 225326553 225327172 619 True 568.000000 568 83.5180 46 663 1 chrUn.!!$R1 617

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
304 345 0.303493 GCAAAACAGTGACTCGCGAA 59.697 50.0 11.33 0.0 0.0 4.70 F
1422 3676 0.178947 ATCCCCTTGAAAACGGCCAA 60.179 50.0 2.24 0.0 0.0 4.52 F
1567 3824 0.526211 CGTCAACTCCATCGTCTCCA 59.474 55.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 4308 0.103755 TGCGAATTTGTTGGCTGCAA 59.896 45.0 0.50 0.0 0.00 4.08 R
2650 4946 0.679960 GGTGGTATGTGCCCCAGTTC 60.680 60.0 0.00 0.0 0.00 3.01 R
3155 10202 1.183676 ACCGTCGTGGCCTTTCTAGT 61.184 55.0 3.32 0.0 43.94 2.57 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
44 68 4.261888 TCTTCGAAAGAGGCACGC 57.738 55.556 0.00 0.00 43.69 5.34
292 333 1.593196 CCTCTCACGGAAGCAAAACA 58.407 50.000 0.00 0.00 0.00 2.83
300 341 1.070577 CGGAAGCAAAACAGTGACTCG 60.071 52.381 0.00 0.00 0.00 4.18
303 344 0.529773 AGCAAAACAGTGACTCGCGA 60.530 50.000 9.26 9.26 0.00 5.87
304 345 0.303493 GCAAAACAGTGACTCGCGAA 59.697 50.000 11.33 0.00 0.00 4.70
306 347 2.629022 CAAAACAGTGACTCGCGAAAG 58.371 47.619 11.33 1.10 0.00 2.62
308 349 2.218953 AACAGTGACTCGCGAAAGAA 57.781 45.000 11.33 0.00 0.00 2.52
481 567 1.349067 AAGCTAGGAAAGACCGGTGT 58.651 50.000 14.63 4.35 44.74 4.16
538 633 2.855660 AAAAGCCAAAAACGCGTACT 57.144 40.000 14.46 0.00 0.00 2.73
548 643 6.129035 GCCAAAAACGCGTACTGAAAAATAAT 60.129 34.615 14.46 0.00 0.00 1.28
595 695 1.502990 CGCAACACGTGGTGAATGGA 61.503 55.000 36.68 0.00 36.96 3.41
667 769 5.163854 CGGTTGTTAATTAGTTGCTCTCAGG 60.164 44.000 0.00 0.00 0.00 3.86
668 770 5.705905 GGTTGTTAATTAGTTGCTCTCAGGT 59.294 40.000 0.00 0.00 0.00 4.00
669 771 6.206829 GGTTGTTAATTAGTTGCTCTCAGGTT 59.793 38.462 0.00 0.00 0.00 3.50
670 772 7.255486 GGTTGTTAATTAGTTGCTCTCAGGTTT 60.255 37.037 0.00 0.00 0.00 3.27
671 773 7.202016 TGTTAATTAGTTGCTCTCAGGTTTG 57.798 36.000 0.00 0.00 0.00 2.93
672 774 6.995686 TGTTAATTAGTTGCTCTCAGGTTTGA 59.004 34.615 0.00 0.00 0.00 2.69
673 775 7.500892 TGTTAATTAGTTGCTCTCAGGTTTGAA 59.499 33.333 0.00 0.00 31.69 2.69
674 776 5.948992 ATTAGTTGCTCTCAGGTTTGAAC 57.051 39.130 0.00 0.00 31.69 3.18
686 788 2.793278 GTTTGAACCTGCCAAACGAT 57.207 45.000 0.00 0.00 42.32 3.73
687 789 3.907894 GTTTGAACCTGCCAAACGATA 57.092 42.857 0.00 0.00 42.32 2.92
688 790 3.821841 GTTTGAACCTGCCAAACGATAG 58.178 45.455 0.00 0.00 42.32 2.08
689 791 1.448985 TGAACCTGCCAAACGATAGC 58.551 50.000 0.00 0.00 42.67 2.97
724 826 0.888285 AGCAGACAGGAGCAGCAAAC 60.888 55.000 0.00 0.00 0.00 2.93
728 830 4.093952 CAGGAGCAGCAAACGCCG 62.094 66.667 0.00 0.00 31.44 6.46
743 845 0.996462 CGCCGAAACGAAGAATGCTA 59.004 50.000 0.00 0.00 34.06 3.49
783 885 1.649390 AAACAAACGTGCTGGCGTGA 61.649 50.000 0.00 0.00 45.00 4.35
810 912 1.682854 TGACGGGTACTTGAACTTCGT 59.317 47.619 0.00 0.00 34.11 3.85
840 943 5.667172 TGGATAGATGGAAGATTTGGTCTGA 59.333 40.000 0.00 0.00 37.23 3.27
841 944 5.994668 GGATAGATGGAAGATTTGGTCTGAC 59.005 44.000 0.00 0.00 37.23 3.51
845 948 4.008074 TGGAAGATTTGGTCTGACAGAC 57.992 45.455 24.76 24.76 44.32 3.51
846 949 3.390967 TGGAAGATTTGGTCTGACAGACA 59.609 43.478 31.35 17.73 46.79 3.41
860 963 3.193479 TGACAGACAGCACATAGTACCTG 59.807 47.826 0.00 0.00 0.00 4.00
1062 2889 2.975732 TGCTCCTCTGCTACTTGATG 57.024 50.000 0.00 0.00 0.00 3.07
1154 3382 2.158871 ACAACGCCCAAGACTTCAGTTA 60.159 45.455 0.00 0.00 0.00 2.24
1244 3472 1.956629 ATCCGGAACAGTGTAGGCCG 61.957 60.000 9.01 19.50 41.53 6.13
1245 3473 2.125673 CGGAACAGTGTAGGCCGG 60.126 66.667 18.97 0.00 38.40 6.13
1246 3474 2.267961 GGAACAGTGTAGGCCGGG 59.732 66.667 2.18 0.00 0.00 5.73
1247 3475 2.436115 GAACAGTGTAGGCCGGGC 60.436 66.667 22.67 22.67 0.00 6.13
1248 3476 4.388499 AACAGTGTAGGCCGGGCG 62.388 66.667 23.81 9.72 0.00 6.13
1422 3676 0.178947 ATCCCCTTGAAAACGGCCAA 60.179 50.000 2.24 0.00 0.00 4.52
1567 3824 0.526211 CGTCAACTCCATCGTCTCCA 59.474 55.000 0.00 0.00 0.00 3.86
1629 3886 2.990479 GGCCTCCCGATGACTTGT 59.010 61.111 0.00 0.00 0.00 3.16
1659 3916 3.064820 CCTACAGCAACGAAACACAAACT 59.935 43.478 0.00 0.00 0.00 2.66
1876 4154 2.618816 CCTGCACCAAAGATCCTGCTAA 60.619 50.000 0.00 0.00 0.00 3.09
1986 4270 1.095600 AGCGTTACAGATCTCTCGCA 58.904 50.000 22.68 0.00 44.83 5.10
2011 4295 4.592778 GGGGCATTGGACATATTGGTTATT 59.407 41.667 0.00 0.00 0.00 1.40
2024 4308 2.785562 TGGTTATTGTAAGTTGGCGCT 58.214 42.857 7.64 0.00 0.00 5.92
2650 4946 0.954452 GCAAGGTCTGTTCACCAAGG 59.046 55.000 0.00 0.00 39.16 3.61
2663 4959 4.850193 CAAGGAACTGGGGCACAT 57.150 55.556 0.00 0.00 40.86 3.21
2669 4965 0.679960 GAACTGGGGCACATACCACC 60.680 60.000 0.00 0.00 32.33 4.61
2839 5135 4.535781 CCTCCATTGACATCATGGGTAAA 58.464 43.478 6.36 0.00 36.18 2.01
2933 5229 0.867746 GACAACAGATGAAGCGTGCA 59.132 50.000 0.00 0.00 0.00 4.57
3050 5346 2.041922 ATCACTCCCCTAGCGCCA 60.042 61.111 2.29 0.00 0.00 5.69
3051 5347 1.689233 ATCACTCCCCTAGCGCCAA 60.689 57.895 2.29 0.00 0.00 4.52
3155 10202 6.551227 ACATGTTGAGCCTAGATGTACTCATA 59.449 38.462 0.00 0.00 38.84 2.15
3159 10206 7.445707 TGTTGAGCCTAGATGTACTCATACTAG 59.554 40.741 0.00 0.00 38.84 2.57
3189 10236 1.019278 ACGGTGGCAGCGACATAAAG 61.019 55.000 41.06 13.76 42.41 1.85
3210 10257 7.454260 AAAGTAATTCTCAGGTTGGTTCATC 57.546 36.000 0.00 0.00 0.00 2.92
3223 10270 7.554118 CAGGTTGGTTCATCTAAATCAGTATGT 59.446 37.037 0.00 0.00 37.40 2.29
3224 10271 8.109634 AGGTTGGTTCATCTAAATCAGTATGTT 58.890 33.333 0.00 0.00 37.40 2.71
3244 10296 9.520204 GTATGTTTTGGTAATCAAGATCAATGG 57.480 33.333 0.00 0.00 36.62 3.16
3257 10309 6.834969 TCAAGATCAATGGAATATTGCCTTGA 59.165 34.615 22.95 22.95 40.93 3.02
3274 10326 5.412594 TGCCTTGACATTTGAGTATCTTCAC 59.587 40.000 0.00 0.00 34.92 3.18
3291 10343 4.704833 CCGGTGGCACCAGTCCAG 62.705 72.222 34.11 17.58 38.47 3.86
3310 10362 3.317430 CCAGCTAGGAAATTGCCATTCTC 59.683 47.826 4.92 0.00 41.22 2.87
3321 10373 3.228188 TGCCATTCTCAAACTGGACTT 57.772 42.857 0.00 0.00 31.38 3.01
3340 10392 7.607250 TGGACTTTGAAAAAGCTTTTGAACTA 58.393 30.769 24.50 12.93 0.00 2.24
3347 10399 8.460831 TGAAAAAGCTTTTGAACTAAGTGAAC 57.539 30.769 24.50 4.85 0.00 3.18
3355 10407 4.054780 TGAACTAAGTGAACGCAAGACT 57.945 40.909 0.00 0.00 43.62 3.24
3386 10438 2.479566 TCTGCCTGCTAGAGGTTTTG 57.520 50.000 0.00 0.00 44.97 2.44
3407 10459 9.620259 GTTTTGGATAGAGATGGATAAAAGACT 57.380 33.333 0.00 0.00 0.00 3.24
3425 10477 8.457238 AAAAGACTAAGATGATATTTGGCTCC 57.543 34.615 0.00 0.00 0.00 4.70
3464 10516 5.163612 GCTTCTGAATGGTATTCCTGGAAAC 60.164 44.000 14.03 12.21 34.23 2.78
3481 10533 4.574599 GAAACAATTCCACTGCAGAAGT 57.425 40.909 23.35 0.14 40.93 3.01
3538 10590 3.323979 TGACCTAGTTGTTGACTTCCTCC 59.676 47.826 0.00 0.00 39.86 4.30
3543 10595 4.713792 AGTTGTTGACTTCCTCCAATCT 57.286 40.909 0.00 0.00 33.92 2.40
3550 10602 8.146053 TGTTGACTTCCTCCAATCTATTCTAA 57.854 34.615 0.00 0.00 0.00 2.10
3566 10618 7.654568 TCTATTCTAAATGAAGCAATGCATGG 58.345 34.615 8.35 0.00 38.18 3.66
3586 10638 4.922206 TGGTCAATTCATACAAGCTCCTT 58.078 39.130 0.00 0.00 0.00 3.36
3594 10646 1.234821 TACAAGCTCCTTTGTTGGCG 58.765 50.000 0.00 0.00 41.31 5.69
3614 10666 3.381590 GCGGAATCTTGCCCTAATTTTCT 59.618 43.478 0.00 0.00 0.00 2.52
3646 10698 6.149973 ACAACATGCTGATGATATAATTCGGG 59.850 38.462 2.44 0.00 33.36 5.14
3669 10721 1.757118 CTCCTTACATCCGAGCCTCAA 59.243 52.381 0.00 0.00 0.00 3.02
3672 10724 2.093447 CCTTACATCCGAGCCTCAACTT 60.093 50.000 0.00 0.00 0.00 2.66
3717 10769 4.556592 ACATTTTTGCAGCCCATATTGT 57.443 36.364 0.00 0.00 0.00 2.71
3722 10774 1.667236 TGCAGCCCATATTGTTCTCG 58.333 50.000 0.00 0.00 0.00 4.04
3778 10830 8.668510 ATGCAAACTCTTATTGTATACTGGAG 57.331 34.615 4.17 6.93 32.40 3.86
3822 10874 9.360901 TGGGCAGTAAGATATTTATATGCAAAA 57.639 29.630 0.00 0.00 34.17 2.44
3903 10955 8.347004 TGCCAGAATGAACTATTAAAATGTGA 57.653 30.769 0.00 0.00 39.69 3.58
3946 10998 0.307760 GCTTTCACTGGACAACACGG 59.692 55.000 0.00 0.00 0.00 4.94
3963 11015 3.782632 GGGAGGCTTAGTGCTTACC 57.217 57.895 0.00 0.00 44.88 2.85
3967 11019 4.061357 GGAGGCTTAGTGCTTACCTAAG 57.939 50.000 0.00 0.00 42.72 2.18
4019 11071 6.776116 TCAGTAGTCGAATCCCAGTTATGTAT 59.224 38.462 0.00 0.00 0.00 2.29
4020 11072 6.863645 CAGTAGTCGAATCCCAGTTATGTATG 59.136 42.308 0.00 0.00 0.00 2.39
4021 11073 6.776116 AGTAGTCGAATCCCAGTTATGTATGA 59.224 38.462 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.391389 GGGCGTGCCTCTTTCGAAG 61.391 63.158 11.25 0.00 36.10 3.79
30 31 4.735132 CGGGCGTGCCTCTTTCGA 62.735 66.667 11.25 0.00 36.10 3.71
44 68 1.079127 ATTTCGTCAGAGGCACGGG 60.079 57.895 0.00 0.00 37.85 5.28
548 643 4.504858 GACGCTCCCTCTGAATTCTTTTA 58.495 43.478 7.05 0.00 0.00 1.52
553 651 0.537188 TGGACGCTCCCTCTGAATTC 59.463 55.000 0.00 0.00 35.03 2.17
595 695 1.084370 GTCACTTGGCGCGCTCTTAT 61.084 55.000 32.29 10.39 0.00 1.73
645 747 6.803154 ACCTGAGAGCAACTAATTAACAAC 57.197 37.500 0.00 0.00 0.00 3.32
647 749 6.995686 TCAAACCTGAGAGCAACTAATTAACA 59.004 34.615 0.00 0.00 0.00 2.41
667 769 2.793278 ATCGTTTGGCAGGTTCAAAC 57.207 45.000 8.98 8.98 46.04 2.93
668 770 2.227865 GCTATCGTTTGGCAGGTTCAAA 59.772 45.455 0.00 0.00 0.00 2.69
669 771 1.810151 GCTATCGTTTGGCAGGTTCAA 59.190 47.619 0.00 0.00 0.00 2.69
670 772 1.271108 TGCTATCGTTTGGCAGGTTCA 60.271 47.619 0.00 0.00 0.00 3.18
671 773 1.398390 CTGCTATCGTTTGGCAGGTTC 59.602 52.381 15.11 0.00 46.51 3.62
672 774 1.453155 CTGCTATCGTTTGGCAGGTT 58.547 50.000 15.11 0.00 46.51 3.50
673 775 3.159298 CTGCTATCGTTTGGCAGGT 57.841 52.632 15.11 0.00 46.51 4.00
676 778 0.036483 TCTGCTGCTATCGTTTGGCA 60.036 50.000 0.00 0.00 34.66 4.92
677 779 0.375106 GTCTGCTGCTATCGTTTGGC 59.625 55.000 0.00 0.00 0.00 4.52
679 781 1.061711 GCTGTCTGCTGCTATCGTTTG 59.938 52.381 0.00 0.00 38.95 2.93
680 782 1.363744 GCTGTCTGCTGCTATCGTTT 58.636 50.000 0.00 0.00 38.95 3.60
682 784 1.226802 CGCTGTCTGCTGCTATCGT 60.227 57.895 0.00 0.00 40.11 3.73
683 785 1.948138 CCGCTGTCTGCTGCTATCG 60.948 63.158 0.00 0.00 40.11 2.92
684 786 0.179100 TTCCGCTGTCTGCTGCTATC 60.179 55.000 0.00 0.00 40.11 2.08
685 787 0.467384 ATTCCGCTGTCTGCTGCTAT 59.533 50.000 0.00 0.00 40.11 2.97
686 788 1.067669 CTATTCCGCTGTCTGCTGCTA 59.932 52.381 0.00 0.00 40.11 3.49
687 789 0.179089 CTATTCCGCTGTCTGCTGCT 60.179 55.000 0.00 0.00 40.11 4.24
688 790 1.770085 GCTATTCCGCTGTCTGCTGC 61.770 60.000 0.00 0.00 40.11 5.25
689 791 0.460811 TGCTATTCCGCTGTCTGCTG 60.461 55.000 0.00 0.00 40.11 4.41
724 826 0.996462 TAGCATTCTTCGTTTCGGCG 59.004 50.000 0.00 0.00 0.00 6.46
783 885 0.245539 CAAGTACCCGTCACCGTCAT 59.754 55.000 0.00 0.00 0.00 3.06
810 912 6.944290 CCAAATCTTCCATCTATCCAAGCATA 59.056 38.462 0.00 0.00 0.00 3.14
840 943 2.093973 GCAGGTACTATGTGCTGTCTGT 60.094 50.000 0.00 0.00 36.02 3.41
841 944 2.167281 AGCAGGTACTATGTGCTGTCTG 59.833 50.000 10.44 0.00 45.81 3.51
845 948 4.256920 AGAAAAGCAGGTACTATGTGCTG 58.743 43.478 11.53 2.63 46.86 4.41
860 963 3.625313 GCAATCTCCTAGGTGAGAAAAGC 59.375 47.826 17.98 12.73 44.16 3.51
1062 2889 0.533032 GAGGTAGGTGCAGAGACCAC 59.467 60.000 12.17 3.68 38.63 4.16
1154 3382 2.573609 GAAGTATGCGTCGCCCTGGT 62.574 60.000 15.88 0.00 0.00 4.00
1249 3477 3.663176 CACGGGCTGCACCAACAG 61.663 66.667 0.50 0.00 42.05 3.16
1434 3688 2.306847 GTGCTGAGGTTTCCCTTGAAA 58.693 47.619 0.00 0.00 42.86 2.69
1567 3824 0.877213 GTCACGTTGGTGTACGCCTT 60.877 55.000 25.27 5.43 45.06 4.35
1629 3886 3.945981 TCGTTGCTGTAGGTGATGTTA 57.054 42.857 0.00 0.00 0.00 2.41
1659 3916 4.217334 CCGATCTTGAGAATAGCTGCTAGA 59.783 45.833 15.41 6.99 0.00 2.43
1841 4116 1.383803 GCAGGAGGGGGACTCTCAT 60.384 63.158 0.00 0.00 45.83 2.90
1876 4154 6.758806 AATTGGTCCGGTTATTACCTCTAT 57.241 37.500 10.37 0.05 42.66 1.98
1986 4270 1.133072 CCAATATGTCCAATGCCCCCT 60.133 52.381 0.00 0.00 0.00 4.79
2011 4295 1.948508 CTGCAAGCGCCAACTTACA 59.051 52.632 2.29 0.00 37.32 2.41
2024 4308 0.103755 TGCGAATTTGTTGGCTGCAA 59.896 45.000 0.50 0.00 0.00 4.08
2211 4495 4.935205 CACCAACCTATCAATTCGACAAGA 59.065 41.667 0.00 0.00 0.00 3.02
2650 4946 0.679960 GGTGGTATGTGCCCCAGTTC 60.680 60.000 0.00 0.00 0.00 3.01
2663 4959 1.661480 CTGGACAACGTCGGTGGTA 59.339 57.895 15.94 0.00 32.65 3.25
2669 4965 2.989055 AAGTGCCCTGGACAACGTCG 62.989 60.000 0.00 0.00 32.65 5.12
2795 5091 2.034179 CCTATCATTGAGACGCACCGTA 59.966 50.000 0.00 0.00 41.37 4.02
2933 5229 2.028020 GCACAAGAGCCCAACTAGTAGT 60.028 50.000 0.00 0.00 0.00 2.73
3005 5301 2.124109 AGCCTCTCCGATCGCAGA 60.124 61.111 8.76 8.76 45.75 4.26
3050 5346 4.508551 TGGCATCAAGAGTGGTATCATT 57.491 40.909 0.00 0.00 0.00 2.57
3051 5347 4.719026 ATGGCATCAAGAGTGGTATCAT 57.281 40.909 0.00 0.00 0.00 2.45
3108 5405 6.872920 TGTGGCCCTTGAATACATATTTTTC 58.127 36.000 0.00 0.00 0.00 2.29
3109 5406 6.865834 TGTGGCCCTTGAATACATATTTTT 57.134 33.333 0.00 0.00 0.00 1.94
3111 5408 5.898972 ACATGTGGCCCTTGAATACATATTT 59.101 36.000 0.00 0.00 31.34 1.40
3113 5410 5.065613 ACATGTGGCCCTTGAATACATAT 57.934 39.130 0.00 0.00 31.34 1.78
3114 5411 4.518278 ACATGTGGCCCTTGAATACATA 57.482 40.909 0.00 0.00 31.34 2.29
3155 10202 1.183676 ACCGTCGTGGCCTTTCTAGT 61.184 55.000 3.32 0.00 43.94 2.57
3179 10226 6.456988 CCAACCTGAGAATTACTTTATGTCGC 60.457 42.308 0.00 0.00 0.00 5.19
3189 10236 8.561738 TTTAGATGAACCAACCTGAGAATTAC 57.438 34.615 0.00 0.00 0.00 1.89
3244 10296 8.844244 AGATACTCAAATGTCAAGGCAATATTC 58.156 33.333 0.00 0.00 0.00 1.75
3257 10309 4.253685 CACCGGTGAAGATACTCAAATGT 58.746 43.478 31.31 0.00 0.00 2.71
3291 10343 4.989279 TTGAGAATGGCAATTTCCTAGC 57.011 40.909 0.00 0.00 0.00 3.42
3310 10362 6.726258 AAAGCTTTTTCAAAGTCCAGTTTG 57.274 33.333 5.69 1.01 38.55 2.93
3321 10373 8.921670 GTTCACTTAGTTCAAAAGCTTTTTCAA 58.078 29.630 21.70 14.18 0.00 2.69
3355 10407 2.573462 AGCAGGCAGAACTTCCAAGATA 59.427 45.455 0.00 0.00 0.00 1.98
3407 10459 3.072330 TGCCGGAGCCAAATATCATCTTA 59.928 43.478 5.05 0.00 38.69 2.10
3477 10529 1.194781 TCCCCTGTCTCAGCCACTTC 61.195 60.000 0.00 0.00 0.00 3.01
3481 10533 1.690633 GGATCCCCTGTCTCAGCCA 60.691 63.158 0.00 0.00 0.00 4.75
3483 10535 3.235369 GGGATCCCCTGTCTCAGC 58.765 66.667 21.42 0.00 41.34 4.26
3505 10557 6.271391 TCAACAACTAGGTCAAAGATTAGGGA 59.729 38.462 0.00 0.00 0.00 4.20
3508 10560 8.608844 AAGTCAACAACTAGGTCAAAGATTAG 57.391 34.615 0.00 0.00 37.17 1.73
3510 10562 6.486993 GGAAGTCAACAACTAGGTCAAAGATT 59.513 38.462 0.00 0.00 37.17 2.40
3538 10590 9.692749 ATGCATTGCTTCATTTAGAATAGATTG 57.307 29.630 10.49 0.00 35.25 2.67
3543 10595 7.068470 TGACCATGCATTGCTTCATTTAGAATA 59.932 33.333 10.49 0.00 35.25 1.75
3550 10602 3.965379 TTGACCATGCATTGCTTCATT 57.035 38.095 10.49 0.00 0.00 2.57
3566 10618 6.259550 ACAAAGGAGCTTGTATGAATTGAC 57.740 37.500 0.00 0.00 37.76 3.18
3594 10646 8.747538 TTACTAGAAAATTAGGGCAAGATTCC 57.252 34.615 0.00 0.00 0.00 3.01
3625 10677 6.596888 AGAACCCGAATTATATCATCAGCATG 59.403 38.462 0.00 0.00 37.54 4.06
3643 10695 1.067212 CTCGGATGTAAGGAGAACCCG 59.933 57.143 0.00 0.00 40.87 5.28
3646 10698 1.757699 AGGCTCGGATGTAAGGAGAAC 59.242 52.381 0.00 0.00 0.00 3.01
3669 10721 5.053978 ACAGGTTCTTGATTTGGAGAAGT 57.946 39.130 0.00 0.00 32.91 3.01
3672 10724 4.792068 ACAACAGGTTCTTGATTTGGAGA 58.208 39.130 0.00 0.00 0.00 3.71
3717 10769 5.209818 ACATTCACACTTTACCTCGAGAA 57.790 39.130 15.71 0.00 0.00 2.87
3722 10774 8.788325 AACCTAATACATTCACACTTTACCTC 57.212 34.615 0.00 0.00 0.00 3.85
3773 10825 3.672767 AACGTAAACCCAGTACTCCAG 57.327 47.619 0.00 0.00 0.00 3.86
3778 10830 3.550639 GCCCAAAAACGTAAACCCAGTAC 60.551 47.826 0.00 0.00 0.00 2.73
3816 10868 4.513442 CAGTAGGCCAGTATACTTTTGCA 58.487 43.478 5.01 0.00 29.77 4.08
3822 10874 3.033659 ACTGCAGTAGGCCAGTATACT 57.966 47.619 20.16 0.00 43.89 2.12
3879 10931 8.462016 AGTCACATTTTAATAGTTCATTCTGGC 58.538 33.333 0.00 0.00 0.00 4.85
3903 10955 3.891366 GCATATATGACTGCCCCAAAAGT 59.109 43.478 17.10 0.00 32.15 2.66
3909 10961 1.457346 GCAGCATATATGACTGCCCC 58.543 55.000 31.10 16.86 44.51 5.80
3987 11039 7.232188 ACTGGGATTCGACTACTGAATATAGA 58.768 38.462 0.00 0.00 36.24 1.98
3988 11040 7.455641 ACTGGGATTCGACTACTGAATATAG 57.544 40.000 0.00 0.00 36.24 1.31
3989 11041 7.834881 AACTGGGATTCGACTACTGAATATA 57.165 36.000 0.00 0.00 36.24 0.86
3990 11042 6.732896 AACTGGGATTCGACTACTGAATAT 57.267 37.500 0.00 0.00 36.24 1.28
4002 11054 8.777865 ATATTGTCATACATAACTGGGATTCG 57.222 34.615 0.00 0.00 0.00 3.34
4003 11055 9.167311 GGATATTGTCATACATAACTGGGATTC 57.833 37.037 0.00 0.00 0.00 2.52
4019 11071 8.801299 TCAAGCAAAAATACAAGGATATTGTCA 58.199 29.630 0.00 0.00 34.11 3.58
4020 11072 9.807649 ATCAAGCAAAAATACAAGGATATTGTC 57.192 29.630 0.00 0.00 34.11 3.18
4021 11073 9.590451 CATCAAGCAAAAATACAAGGATATTGT 57.410 29.630 0.00 0.00 36.49 2.71
4035 11087 9.606631 AATAAAACTAACACCATCAAGCAAAAA 57.393 25.926 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.