Multiple sequence alignment - TraesCS7B01G004800

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 TraesCS7B01G004800 chr7B 100.000 3440 0 0 1 3440 2748130 2751569 0.000000e+00 6353.0
1 TraesCS7B01G004800 chr7B 91.040 1317 96 3 1127 2443 2663086 2664380 0.000000e+00 1759.0
2 TraesCS7B01G004800 chr7B 97.059 170 4 1 2702 2870 2756197 2756028 5.620000e-73 285.0
3 TraesCS7B01G004800 chr7B 86.449 214 14 3 924 1128 2660858 2661065 1.610000e-53 220.0
4 TraesCS7B01G004800 chr7B 80.505 277 27 13 594 870 2660500 2660749 1.630000e-43 187.0
5 TraesCS7B01G004800 chr7B 85.294 68 9 1 535 602 741799176 741799242 6.160000e-08 69.4
6 TraesCS7B01G004800 chr7A 92.617 1788 101 17 925 2701 64591004 64592771 0.000000e+00 2542.0
7 TraesCS7B01G004800 chr7A 92.553 1786 100 17 925 2701 64531943 64530182 0.000000e+00 2531.0
8 TraesCS7B01G004800 chr7A 72.617 1238 269 58 1038 2243 63502961 63501762 9.140000e-91 344.0
9 TraesCS7B01G004800 chr7D 94.402 1554 72 3 924 2468 60148168 60146621 0.000000e+00 2374.0
10 TraesCS7B01G004800 chr7D 90.738 637 58 1 1829 2465 60234619 60235254 0.000000e+00 848.0
11 TraesCS7B01G004800 chr4B 98.111 741 12 2 2702 3440 602889305 602888565 0.000000e+00 1290.0
12 TraesCS7B01G004800 chr4B 95.269 761 18 7 2698 3440 183673231 183673991 0.000000e+00 1190.0
13 TraesCS7B01G004800 chr4B 97.059 170 3 2 2702 2870 183675891 183675723 5.620000e-73 285.0
14 TraesCS7B01G004800 chr4B 97.059 170 4 1 2702 2870 602883933 602884102 5.620000e-73 285.0
15 TraesCS7B01G004800 chr5A 95.894 755 15 7 2702 3440 423046850 423046096 0.000000e+00 1208.0
16 TraesCS7B01G004800 chr5A 94.152 171 7 2 2702 2870 423044194 423044363 1.220000e-64 257.0
17 TraesCS7B01G004800 chr2A 95.503 756 19 6 2700 3440 757960597 757959842 0.000000e+00 1194.0
18 TraesCS7B01G004800 chr2A 96.491 171 3 2 2702 2870 757957940 757958109 2.610000e-71 279.0
19 TraesCS7B01G004800 chr5B 90.170 529 42 7 74 598 513378939 513378417 0.000000e+00 680.0
20 TraesCS7B01G004800 chr5B 84.497 587 82 8 16 597 301564244 301563662 3.850000e-159 571.0
21 TraesCS7B01G004800 chr5B 97.436 78 2 0 1 78 513394635 513394558 2.150000e-27 134.0
22 TraesCS7B01G004800 chr3D 84.590 597 84 7 6 598 282931684 282931092 1.380000e-163 586.0
23 TraesCS7B01G004800 chr3D 89.420 293 26 2 1297 1589 376810571 376810858 7.020000e-97 364.0
24 TraesCS7B01G004800 chr3A 80.431 603 110 7 1 598 466038701 466039300 1.460000e-123 453.0
25 TraesCS7B01G004800 chr5D 78.405 602 123 5 1 598 164638502 164639100 5.390000e-103 385.0
26 TraesCS7B01G004800 chr5D 77.483 604 124 10 1 598 432982369 432981772 5.460000e-93 351.0
27 TraesCS7B01G004800 chr1D 77.265 607 127 9 1 602 478022537 478023137 2.540000e-91 346.0
28 TraesCS7B01G004800 chr4A 77.025 605 125 10 1 598 39919098 39918501 5.500000e-88 335.0
29 TraesCS7B01G004800 chr4A 92.157 51 4 0 1330 1380 709623994 709623944 4.760000e-09 73.1
30 TraesCS7B01G004800 chr2B 88.889 198 22 0 1245 1442 172889529 172889726 9.540000e-61 244.0
31 TraesCS7B01G004800 chr2D 93.333 90 6 0 1301 1390 35548415 35548326 2.150000e-27 134.0


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 TraesCS7B01G004800 chr7B 2748130 2751569 3439 False 6353 6353 100.000 1 3440 1 chr7B.!!$F1 3439
1 TraesCS7B01G004800 chr7B 2660500 2664380 3880 False 722 1759 85.998 594 2443 3 chr7B.!!$F3 1849
2 TraesCS7B01G004800 chr7A 64591004 64592771 1767 False 2542 2542 92.617 925 2701 1 chr7A.!!$F1 1776
3 TraesCS7B01G004800 chr7A 64530182 64531943 1761 True 2531 2531 92.553 925 2701 1 chr7A.!!$R2 1776
4 TraesCS7B01G004800 chr7A 63501762 63502961 1199 True 344 344 72.617 1038 2243 1 chr7A.!!$R1 1205
5 TraesCS7B01G004800 chr7D 60146621 60148168 1547 True 2374 2374 94.402 924 2468 1 chr7D.!!$R1 1544
6 TraesCS7B01G004800 chr7D 60234619 60235254 635 False 848 848 90.738 1829 2465 1 chr7D.!!$F1 636
7 TraesCS7B01G004800 chr4B 602888565 602889305 740 True 1290 1290 98.111 2702 3440 1 chr4B.!!$R2 738
8 TraesCS7B01G004800 chr4B 183673231 183673991 760 False 1190 1190 95.269 2698 3440 1 chr4B.!!$F1 742
9 TraesCS7B01G004800 chr5A 423046096 423046850 754 True 1208 1208 95.894 2702 3440 1 chr5A.!!$R1 738
10 TraesCS7B01G004800 chr2A 757959842 757960597 755 True 1194 1194 95.503 2700 3440 1 chr2A.!!$R1 740
11 TraesCS7B01G004800 chr5B 513378417 513378939 522 True 680 680 90.170 74 598 1 chr5B.!!$R2 524
12 TraesCS7B01G004800 chr5B 301563662 301564244 582 True 571 571 84.497 16 597 1 chr5B.!!$R1 581
13 TraesCS7B01G004800 chr3D 282931092 282931684 592 True 586 586 84.590 6 598 1 chr3D.!!$R1 592
14 TraesCS7B01G004800 chr3A 466038701 466039300 599 False 453 453 80.431 1 598 1 chr3A.!!$F1 597
15 TraesCS7B01G004800 chr5D 164638502 164639100 598 False 385 385 78.405 1 598 1 chr5D.!!$F1 597
16 TraesCS7B01G004800 chr5D 432981772 432982369 597 True 351 351 77.483 1 598 1 chr5D.!!$R1 597
17 TraesCS7B01G004800 chr1D 478022537 478023137 600 False 346 346 77.265 1 602 1 chr1D.!!$F1 601
18 TraesCS7B01G004800 chr4A 39918501 39919098 597 True 335 335 77.025 1 598 1 chr4A.!!$R1 597

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
840 845 0.248907 ACGGCTTGTCATATCGGTCG 60.249 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 4591 0.036164 ATTTGTACTGCAGCCGTCCA 59.964 50.0 15.27 0.12 0.0 4.02 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
37 38 2.716217 GTCTGGCTTGCCTTACAGAAT 58.284 47.619 13.18 0.00 41.17 2.40
86 87 2.501723 AGACACGGGCTACAAGATCATT 59.498 45.455 0.00 0.00 0.00 2.57
170 171 3.701542 CACTTATGCTCAGGAGGTGTAGA 59.298 47.826 0.00 0.00 0.00 2.59
208 209 7.177216 AGTCTTCTTCAAATTAATGTGCATGGA 59.823 33.333 0.22 0.00 0.00 3.41
211 212 4.734398 TCAAATTAATGTGCATGGACCC 57.266 40.909 15.34 0.00 0.00 4.46
295 296 5.650703 TGACAGTAGAGGATTTGACACGATA 59.349 40.000 0.00 0.00 0.00 2.92
296 297 6.152154 TGACAGTAGAGGATTTGACACGATAA 59.848 38.462 0.00 0.00 0.00 1.75
302 303 7.348080 AGAGGATTTGACACGATAATGACTA 57.652 36.000 0.00 0.00 0.00 2.59
309 310 6.020971 TGACACGATAATGACTACAGTTGT 57.979 37.500 0.00 0.00 0.00 3.32
322 323 0.327924 CAGTTGTGTGGGCCCTATGA 59.672 55.000 25.70 0.00 0.00 2.15
338 339 3.308323 CCTATGAAAGCAGAGAAACGCTC 59.692 47.826 0.00 0.00 44.29 5.03
507 509 0.391597 GTCGAGTGGGGTGTTTCTCA 59.608 55.000 0.00 0.00 0.00 3.27
614 619 2.951457 AAACGAGGAGAAGCTAGCTC 57.049 50.000 19.65 11.66 0.00 4.09
616 621 0.393267 ACGAGGAGAAGCTAGCTCGT 60.393 55.000 19.65 18.88 41.73 4.18
653 658 1.152247 ACTGGAGTGACCTCAGCCA 60.152 57.895 3.24 0.00 39.64 4.75
662 667 2.125753 CCTCAGCCAGCGTGTCTC 60.126 66.667 0.00 0.00 0.00 3.36
665 670 4.056125 CAGCCAGCGTGTCTCCGA 62.056 66.667 0.00 0.00 0.00 4.55
675 680 1.719780 CGTGTCTCCGAGCTAAACAAC 59.280 52.381 0.00 0.00 0.00 3.32
677 682 1.610038 TGTCTCCGAGCTAAACAACGA 59.390 47.619 0.00 0.00 0.00 3.85
690 695 1.220206 CAACGAGCTCTCCCTGCAT 59.780 57.895 12.85 0.00 0.00 3.96
692 697 0.975040 AACGAGCTCTCCCTGCATCT 60.975 55.000 12.85 0.00 0.00 2.90
696 701 1.340889 GAGCTCTCCCTGCATCTGTAG 59.659 57.143 6.43 0.00 0.00 2.74
700 705 0.387202 CTCCCTGCATCTGTAGTCGG 59.613 60.000 0.00 0.00 0.00 4.79
702 707 1.227380 CCTGCATCTGTAGTCGGCC 60.227 63.158 0.00 0.00 0.00 6.13
703 708 1.589993 CTGCATCTGTAGTCGGCCG 60.590 63.158 22.12 22.12 0.00 6.13
704 709 2.284798 CTGCATCTGTAGTCGGCCGT 62.285 60.000 27.15 9.68 0.00 5.68
705 710 1.033202 TGCATCTGTAGTCGGCCGTA 61.033 55.000 27.15 8.44 0.00 4.02
706 711 0.317938 GCATCTGTAGTCGGCCGTAG 60.318 60.000 27.15 16.02 0.00 3.51
707 712 0.317938 CATCTGTAGTCGGCCGTAGC 60.318 60.000 27.15 16.47 38.76 3.58
714 719 1.661821 GTCGGCCGTAGCTAGCATG 60.662 63.158 27.15 8.32 39.73 4.06
733 738 4.439700 GCATGTGGAGTTTAGCTCGTAGTA 60.440 45.833 0.00 0.00 45.03 1.82
737 742 6.118170 TGTGGAGTTTAGCTCGTAGTAGTAT 58.882 40.000 0.00 0.00 45.03 2.12
739 744 7.131565 GTGGAGTTTAGCTCGTAGTAGTATTC 58.868 42.308 0.00 0.00 45.03 1.75
740 745 7.012232 GTGGAGTTTAGCTCGTAGTAGTATTCT 59.988 40.741 0.00 0.00 45.03 2.40
743 748 8.503458 AGTTTAGCTCGTAGTAGTATTCTTCA 57.497 34.615 0.00 0.00 0.00 3.02
744 749 9.122779 AGTTTAGCTCGTAGTAGTATTCTTCAT 57.877 33.333 0.00 0.00 0.00 2.57
745 750 9.384682 GTTTAGCTCGTAGTAGTATTCTTCATC 57.615 37.037 0.00 0.00 0.00 2.92
746 751 6.230849 AGCTCGTAGTAGTATTCTTCATCG 57.769 41.667 0.00 0.00 0.00 3.84
747 752 5.990386 AGCTCGTAGTAGTATTCTTCATCGA 59.010 40.000 0.00 0.00 0.00 3.59
748 753 6.072733 GCTCGTAGTAGTATTCTTCATCGAC 58.927 44.000 0.00 0.00 0.00 4.20
749 754 6.207864 TCGTAGTAGTATTCTTCATCGACG 57.792 41.667 0.00 0.00 0.00 5.12
750 755 5.750547 TCGTAGTAGTATTCTTCATCGACGT 59.249 40.000 0.00 0.00 0.00 4.34
751 756 5.839753 CGTAGTAGTATTCTTCATCGACGTG 59.160 44.000 0.00 0.00 0.00 4.49
752 757 4.599047 AGTAGTATTCTTCATCGACGTGC 58.401 43.478 0.00 0.00 0.00 5.34
753 758 2.810650 AGTATTCTTCATCGACGTGCC 58.189 47.619 0.00 0.00 0.00 5.01
754 759 2.165641 AGTATTCTTCATCGACGTGCCA 59.834 45.455 0.00 0.00 0.00 4.92
755 760 1.645034 ATTCTTCATCGACGTGCCAG 58.355 50.000 0.00 0.00 0.00 4.85
756 761 0.601057 TTCTTCATCGACGTGCCAGA 59.399 50.000 0.00 0.00 0.00 3.86
757 762 0.601057 TCTTCATCGACGTGCCAGAA 59.399 50.000 0.00 0.00 0.00 3.02
758 763 0.716108 CTTCATCGACGTGCCAGAAC 59.284 55.000 0.00 0.00 0.00 3.01
759 764 0.317160 TTCATCGACGTGCCAGAACT 59.683 50.000 0.00 0.00 0.00 3.01
760 765 1.170442 TCATCGACGTGCCAGAACTA 58.830 50.000 0.00 0.00 0.00 2.24
761 766 1.132453 TCATCGACGTGCCAGAACTAG 59.868 52.381 0.00 0.00 0.00 2.57
762 767 0.456221 ATCGACGTGCCAGAACTAGG 59.544 55.000 0.00 0.00 0.00 3.02
763 768 0.892358 TCGACGTGCCAGAACTAGGT 60.892 55.000 0.00 0.00 0.00 3.08
764 769 0.732880 CGACGTGCCAGAACTAGGTG 60.733 60.000 0.00 0.00 0.00 4.00
770 775 2.103042 CCAGAACTAGGTGCTGCGC 61.103 63.158 0.00 0.00 37.86 6.09
786 791 4.752879 GCACTTGGCCCGCGTCTA 62.753 66.667 4.92 0.00 36.11 2.59
797 802 1.670811 CCCGCGTCTAATTCTGCATTT 59.329 47.619 4.92 0.00 0.00 2.32
839 844 3.661745 ACGGCTTGTCATATCGGTC 57.338 52.632 0.00 0.00 0.00 4.79
840 845 0.248907 ACGGCTTGTCATATCGGTCG 60.249 55.000 0.00 0.00 0.00 4.79
847 852 3.204306 TGTCATATCGGTCGGTCTACT 57.796 47.619 0.00 0.00 0.00 2.57
850 855 4.400251 TGTCATATCGGTCGGTCTACTTTT 59.600 41.667 0.00 0.00 0.00 2.27
853 858 0.387622 TCGGTCGGTCTACTTTTGCG 60.388 55.000 0.00 0.00 0.00 4.85
859 864 2.540931 TCGGTCTACTTTTGCGTTGAAC 59.459 45.455 0.00 0.00 0.00 3.18
866 871 1.189884 CTTTTGCGTTGAACAATGGCG 59.810 47.619 8.51 1.33 0.00 5.69
894 916 3.120060 CGTGCCCATTTTCTCTTCTTCTG 60.120 47.826 0.00 0.00 0.00 3.02
895 917 3.192212 GTGCCCATTTTCTCTTCTTCTGG 59.808 47.826 0.00 0.00 0.00 3.86
896 918 3.074390 TGCCCATTTTCTCTTCTTCTGGA 59.926 43.478 0.00 0.00 0.00 3.86
897 919 4.082125 GCCCATTTTCTCTTCTTCTGGAA 58.918 43.478 0.00 0.00 0.00 3.53
898 920 4.524328 GCCCATTTTCTCTTCTTCTGGAAA 59.476 41.667 0.00 0.00 33.07 3.13
899 921 5.336293 GCCCATTTTCTCTTCTTCTGGAAAG 60.336 44.000 0.00 0.00 33.07 2.62
900 922 5.184671 CCCATTTTCTCTTCTTCTGGAAAGG 59.815 44.000 0.00 0.00 33.07 3.11
901 923 5.184671 CCATTTTCTCTTCTTCTGGAAAGGG 59.815 44.000 0.00 0.00 33.07 3.95
902 924 5.388599 TTTTCTCTTCTTCTGGAAAGGGT 57.611 39.130 0.00 0.00 33.07 4.34
905 927 3.073062 TCTCTTCTTCTGGAAAGGGTTGG 59.927 47.826 0.00 0.00 33.07 3.77
906 928 2.783510 TCTTCTTCTGGAAAGGGTTGGT 59.216 45.455 0.00 0.00 33.07 3.67
907 929 3.204382 TCTTCTTCTGGAAAGGGTTGGTT 59.796 43.478 0.00 0.00 33.07 3.67
908 930 2.944129 TCTTCTGGAAAGGGTTGGTTG 58.056 47.619 0.00 0.00 0.00 3.77
909 931 2.512056 TCTTCTGGAAAGGGTTGGTTGA 59.488 45.455 0.00 0.00 0.00 3.18
910 932 3.053245 TCTTCTGGAAAGGGTTGGTTGAA 60.053 43.478 0.00 0.00 0.00 2.69
911 933 3.390175 TCTGGAAAGGGTTGGTTGAAA 57.610 42.857 0.00 0.00 0.00 2.69
912 934 3.295973 TCTGGAAAGGGTTGGTTGAAAG 58.704 45.455 0.00 0.00 0.00 2.62
913 935 3.031013 CTGGAAAGGGTTGGTTGAAAGT 58.969 45.455 0.00 0.00 0.00 2.66
914 936 3.445987 TGGAAAGGGTTGGTTGAAAGTT 58.554 40.909 0.00 0.00 0.00 2.66
918 940 6.013639 TGGAAAGGGTTGGTTGAAAGTTAAAA 60.014 34.615 0.00 0.00 0.00 1.52
919 941 6.314400 GGAAAGGGTTGGTTGAAAGTTAAAAC 59.686 38.462 0.00 0.00 0.00 2.43
921 943 6.361768 AGGGTTGGTTGAAAGTTAAAACAA 57.638 33.333 0.00 0.00 30.72 2.83
966 1035 1.028330 CGCTCCTACCTACGTGTCCA 61.028 60.000 0.00 0.00 0.00 4.02
1044 1113 4.176851 GCCGTCGAGGTCGTCTCC 62.177 72.222 4.18 0.00 43.70 3.71
1150 3241 0.389817 CCACGTCTTCTTCATCGCCA 60.390 55.000 0.00 0.00 0.00 5.69
2049 4147 3.023949 GCACGAGGAGCTGGTGGAT 62.024 63.158 0.00 0.00 39.87 3.41
2178 4276 2.747686 GTGGAGGGCGACTTTGGA 59.252 61.111 0.00 0.00 0.00 3.53
2486 4584 6.677781 TGCTGTTAAAATAGATGTACTGCC 57.322 37.500 0.00 0.00 31.92 4.85
2490 4588 1.865865 AAATAGATGTACTGCCGCCG 58.134 50.000 0.00 0.00 0.00 6.46
2491 4589 0.600255 AATAGATGTACTGCCGCCGC 60.600 55.000 0.00 0.00 0.00 6.53
2492 4590 2.749110 ATAGATGTACTGCCGCCGCG 62.749 60.000 5.59 5.59 38.08 6.46
2520 4618 3.809832 GGCTGCAGTACAAATATCGTCAT 59.190 43.478 16.64 0.00 0.00 3.06
2533 4631 3.500448 ATCGTCATAGCCTCTCTCTCA 57.500 47.619 0.00 0.00 0.00 3.27
2640 4754 4.455533 TCATTTTTCTCATGAACCGTCTGG 59.544 41.667 0.00 0.00 42.84 3.86
2641 4755 3.762407 TTTTCTCATGAACCGTCTGGA 57.238 42.857 0.00 0.00 39.21 3.86
2648 4762 2.455674 TGAACCGTCTGGACTTGATG 57.544 50.000 0.00 0.00 39.21 3.07
2673 4787 0.109597 GCCCAAAACAGATCGCACTG 60.110 55.000 7.04 7.04 42.78 3.66
3000 5129 0.252513 TTTCCCTCTCACCGGATGGA 60.253 55.000 9.46 1.08 39.21 3.41
3226 5356 1.669049 CGTACCCGTACATGGAGGCA 61.669 60.000 5.47 0.00 35.87 4.75
3296 5426 1.686325 GAAGGCGGCAGACCTGGATA 61.686 60.000 13.08 0.00 37.67 2.59
3350 5480 1.352753 GCCGTTCGTTTGTCCGTTT 59.647 52.632 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.019249 CTATCCGACGTCCACAACCTA 58.981 52.381 10.58 0.00 0.00 3.08
86 87 4.111016 CGTGTAGCAGGCCGACGA 62.111 66.667 0.00 0.00 31.71 4.20
170 171 5.344743 TGAAGAAGACTGAACACTCTGTT 57.655 39.130 0.00 0.00 44.37 3.16
211 212 2.736719 CGTGAACTCATCAGCCACTAGG 60.737 54.545 0.00 0.00 39.19 3.02
267 268 4.284490 TGTCAAATCCTCTACTGTCAGCTT 59.716 41.667 0.00 0.00 0.00 3.74
275 276 7.068839 AGTCATTATCGTGTCAAATCCTCTACT 59.931 37.037 0.00 0.00 0.00 2.57
295 296 2.504367 GCCCACACAACTGTAGTCATT 58.496 47.619 0.00 0.00 0.00 2.57
296 297 1.271379 GGCCCACACAACTGTAGTCAT 60.271 52.381 0.00 0.00 0.00 3.06
302 303 0.038166 CATAGGGCCCACACAACTGT 59.962 55.000 27.56 1.16 0.00 3.55
309 310 0.034186 CTGCTTTCATAGGGCCCACA 60.034 55.000 27.56 12.31 0.00 4.17
322 323 1.269831 ACTCGAGCGTTTCTCTGCTTT 60.270 47.619 13.61 0.00 42.60 3.51
346 347 2.356553 CTTTCGTTGGTCCGGCGA 60.357 61.111 9.30 0.00 0.00 5.54
347 348 1.897398 CTTCTTTCGTTGGTCCGGCG 61.897 60.000 0.00 0.00 0.00 6.46
382 384 3.912496 TTCGTCCAGGATCATGAATGT 57.088 42.857 9.37 0.00 0.00 2.71
438 440 3.921677 TCTCACGAAATGTTGTAGTCCC 58.078 45.455 0.00 0.00 0.00 4.46
461 463 2.490115 CACCTCGCTATCCTAGGCTAAG 59.510 54.545 2.96 2.11 33.42 2.18
507 509 2.002586 CTTGATGCGAACACGAAGGAT 58.997 47.619 0.00 0.00 0.00 3.24
608 613 0.454620 CGGCGGCTATTACGAGCTAG 60.455 60.000 7.61 0.00 42.43 3.42
612 617 0.030369 AGAACGGCGGCTATTACGAG 59.970 55.000 13.24 0.00 0.00 4.18
614 619 0.575390 CAAGAACGGCGGCTATTACG 59.425 55.000 13.24 0.00 0.00 3.18
616 621 0.825410 TCCAAGAACGGCGGCTATTA 59.175 50.000 13.24 0.00 0.00 0.98
653 658 0.109226 GTTTAGCTCGGAGACACGCT 60.109 55.000 9.69 1.26 38.75 5.07
662 667 3.123674 AGCTCGTTGTTTAGCTCGG 57.876 52.632 0.00 0.00 45.92 4.63
675 680 1.067749 CAGATGCAGGGAGAGCTCG 59.932 63.158 8.37 0.00 0.00 5.03
677 682 1.342874 ACTACAGATGCAGGGAGAGCT 60.343 52.381 2.33 0.00 0.00 4.09
680 685 1.393603 CGACTACAGATGCAGGGAGA 58.606 55.000 2.33 0.00 0.00 3.71
690 695 0.178767 TAGCTACGGCCGACTACAGA 59.821 55.000 35.90 7.89 39.73 3.41
692 697 1.442526 GCTAGCTACGGCCGACTACA 61.443 60.000 35.90 12.75 39.73 2.74
696 701 1.661821 CATGCTAGCTACGGCCGAC 60.662 63.158 35.90 20.66 39.73 4.79
700 705 0.598680 CTCCACATGCTAGCTACGGC 60.599 60.000 17.23 0.00 39.06 5.68
702 707 2.586258 AACTCCACATGCTAGCTACG 57.414 50.000 17.23 6.67 0.00 3.51
703 708 3.804873 GCTAAACTCCACATGCTAGCTAC 59.195 47.826 17.23 0.00 31.23 3.58
704 709 3.706594 AGCTAAACTCCACATGCTAGCTA 59.293 43.478 17.23 2.58 40.12 3.32
705 710 2.503356 AGCTAAACTCCACATGCTAGCT 59.497 45.455 17.23 0.00 37.78 3.32
706 711 2.869192 GAGCTAAACTCCACATGCTAGC 59.131 50.000 8.10 8.10 39.75 3.42
707 712 3.119291 CGAGCTAAACTCCACATGCTAG 58.881 50.000 0.00 0.00 43.01 3.42
714 719 4.961435 ACTACTACGAGCTAAACTCCAC 57.039 45.455 0.00 0.00 43.01 4.02
733 738 2.165641 TGGCACGTCGATGAAGAATACT 59.834 45.455 12.58 0.00 0.00 2.12
737 742 0.601057 TCTGGCACGTCGATGAAGAA 59.399 50.000 12.58 0.00 0.00 2.52
739 744 0.716108 GTTCTGGCACGTCGATGAAG 59.284 55.000 12.58 4.57 0.00 3.02
740 745 0.317160 AGTTCTGGCACGTCGATGAA 59.683 50.000 12.58 0.00 0.00 2.57
743 748 0.456221 CCTAGTTCTGGCACGTCGAT 59.544 55.000 0.00 0.00 0.00 3.59
744 749 0.892358 ACCTAGTTCTGGCACGTCGA 60.892 55.000 0.00 0.00 0.00 4.20
745 750 0.732880 CACCTAGTTCTGGCACGTCG 60.733 60.000 0.00 0.00 0.00 5.12
746 751 1.014564 GCACCTAGTTCTGGCACGTC 61.015 60.000 0.00 0.00 0.00 4.34
747 752 1.004918 GCACCTAGTTCTGGCACGT 60.005 57.895 0.00 0.00 0.00 4.49
748 753 1.016130 CAGCACCTAGTTCTGGCACG 61.016 60.000 0.00 0.00 0.00 5.34
749 754 1.301677 GCAGCACCTAGTTCTGGCAC 61.302 60.000 0.00 0.00 28.18 5.01
750 755 1.003355 GCAGCACCTAGTTCTGGCA 60.003 57.895 0.00 0.00 28.18 4.92
751 756 2.103042 CGCAGCACCTAGTTCTGGC 61.103 63.158 0.00 0.00 28.18 4.85
752 757 4.192000 CGCAGCACCTAGTTCTGG 57.808 61.111 0.00 0.00 28.18 3.86
770 775 1.024579 AATTAGACGCGGGCCAAGTG 61.025 55.000 12.47 7.34 0.00 3.16
774 779 1.153449 CAGAATTAGACGCGGGCCA 60.153 57.895 12.47 0.00 0.00 5.36
782 787 6.319658 TCATCTTCCCAAATGCAGAATTAGAC 59.680 38.462 0.00 0.00 0.00 2.59
786 791 4.161001 GGTCATCTTCCCAAATGCAGAATT 59.839 41.667 0.00 0.00 0.00 2.17
797 802 2.601240 TGCATTTGGTCATCTTCCCA 57.399 45.000 0.00 0.00 0.00 4.37
832 837 2.478370 CGCAAAAGTAGACCGACCGATA 60.478 50.000 0.00 0.00 0.00 2.92
839 844 2.285756 TGTTCAACGCAAAAGTAGACCG 59.714 45.455 0.00 0.00 0.00 4.79
840 845 3.955771 TGTTCAACGCAAAAGTAGACC 57.044 42.857 0.00 0.00 0.00 3.85
847 852 1.202302 TCGCCATTGTTCAACGCAAAA 60.202 42.857 7.06 0.00 0.00 2.44
850 855 0.382158 TTTCGCCATTGTTCAACGCA 59.618 45.000 7.06 0.00 0.00 5.24
853 858 1.386412 CGCATTTCGCCATTGTTCAAC 59.614 47.619 0.00 0.00 37.30 3.18
859 864 2.160221 GGCACGCATTTCGCCATTG 61.160 57.895 0.00 0.00 45.52 2.82
866 871 2.094545 AGAGAAAATGGGCACGCATTTC 60.095 45.455 21.36 15.64 37.91 2.17
873 895 3.192212 CCAGAAGAAGAGAAAATGGGCAC 59.808 47.826 0.00 0.00 0.00 5.01
878 900 5.772169 ACCCTTTCCAGAAGAAGAGAAAATG 59.228 40.000 0.00 0.00 35.40 2.32
894 916 5.601583 TTAACTTTCAACCAACCCTTTCC 57.398 39.130 0.00 0.00 0.00 3.13
895 917 6.874664 TGTTTTAACTTTCAACCAACCCTTTC 59.125 34.615 0.00 0.00 0.00 2.62
896 918 6.770542 TGTTTTAACTTTCAACCAACCCTTT 58.229 32.000 0.00 0.00 0.00 3.11
897 919 6.361768 TGTTTTAACTTTCAACCAACCCTT 57.638 33.333 0.00 0.00 0.00 3.95
898 920 6.361768 TTGTTTTAACTTTCAACCAACCCT 57.638 33.333 0.00 0.00 0.00 4.34
899 921 6.128227 GGTTTGTTTTAACTTTCAACCAACCC 60.128 38.462 10.01 0.00 39.01 4.11
900 922 6.401260 CGGTTTGTTTTAACTTTCAACCAACC 60.401 38.462 10.70 10.70 40.42 3.77
901 923 6.527089 CGGTTTGTTTTAACTTTCAACCAAC 58.473 36.000 0.00 0.00 0.00 3.77
902 924 5.120363 GCGGTTTGTTTTAACTTTCAACCAA 59.880 36.000 0.00 0.00 0.00 3.67
905 927 4.865925 AGGCGGTTTGTTTTAACTTTCAAC 59.134 37.500 0.00 0.00 0.00 3.18
906 928 5.074584 AGGCGGTTTGTTTTAACTTTCAA 57.925 34.783 0.00 0.00 0.00 2.69
907 929 4.674475 GAGGCGGTTTGTTTTAACTTTCA 58.326 39.130 0.00 0.00 0.00 2.69
908 930 3.727227 CGAGGCGGTTTGTTTTAACTTTC 59.273 43.478 0.00 0.00 0.00 2.62
909 931 3.129113 ACGAGGCGGTTTGTTTTAACTTT 59.871 39.130 0.00 0.00 0.00 2.66
910 932 2.684374 ACGAGGCGGTTTGTTTTAACTT 59.316 40.909 0.00 0.00 0.00 2.66
911 933 2.032426 CACGAGGCGGTTTGTTTTAACT 59.968 45.455 0.00 0.00 0.00 2.24
912 934 2.377880 CACGAGGCGGTTTGTTTTAAC 58.622 47.619 0.00 0.00 0.00 2.01
913 935 1.268640 GCACGAGGCGGTTTGTTTTAA 60.269 47.619 0.00 0.00 0.00 1.52
914 936 0.308376 GCACGAGGCGGTTTGTTTTA 59.692 50.000 0.00 0.00 0.00 1.52
1024 1093 4.808238 GACGACCTCGACGGCGAC 62.808 72.222 10.67 6.59 42.51 5.19
1596 3691 3.830192 GACGGGGTGTATCGCGGT 61.830 66.667 6.13 0.00 45.42 5.68
1602 3697 2.363276 TCCAGCGACGGGGTGTAT 60.363 61.111 0.00 0.00 42.62 2.29
2032 4130 0.742281 CAATCCACCAGCTCCTCGTG 60.742 60.000 0.00 0.00 0.00 4.35
2049 4147 1.675310 CTTGTGCGCCTCCATCCAA 60.675 57.895 4.18 0.00 0.00 3.53
2235 4333 0.977627 TCCGGATCACTGTCATGGCT 60.978 55.000 0.00 0.00 0.00 4.75
2490 4588 4.735132 TACTGCAGCCGTCCACGC 62.735 66.667 15.27 0.00 38.18 5.34
2491 4589 2.809601 GTACTGCAGCCGTCCACG 60.810 66.667 15.27 0.00 39.44 4.94
2492 4590 0.882927 TTTGTACTGCAGCCGTCCAC 60.883 55.000 15.27 3.05 0.00 4.02
2493 4591 0.036164 ATTTGTACTGCAGCCGTCCA 59.964 50.000 15.27 0.12 0.00 4.02
2494 4592 2.018542 TATTTGTACTGCAGCCGTCC 57.981 50.000 15.27 0.00 0.00 4.79
2495 4593 2.218759 CGATATTTGTACTGCAGCCGTC 59.781 50.000 15.27 2.30 0.00 4.79
2496 4594 2.201732 CGATATTTGTACTGCAGCCGT 58.798 47.619 15.27 0.00 0.00 5.68
2497 4595 2.201732 ACGATATTTGTACTGCAGCCG 58.798 47.619 15.27 6.13 0.00 5.52
2498 4596 3.194861 TGACGATATTTGTACTGCAGCC 58.805 45.455 15.27 5.21 0.00 4.85
2499 4597 5.388890 GCTATGACGATATTTGTACTGCAGC 60.389 44.000 15.27 0.00 0.00 5.25
2500 4598 5.119279 GGCTATGACGATATTTGTACTGCAG 59.881 44.000 13.48 13.48 0.00 4.41
2501 4599 4.988540 GGCTATGACGATATTTGTACTGCA 59.011 41.667 0.00 0.00 0.00 4.41
2502 4600 5.230942 AGGCTATGACGATATTTGTACTGC 58.769 41.667 0.00 0.00 0.00 4.40
2503 4601 6.682746 AGAGGCTATGACGATATTTGTACTG 58.317 40.000 0.00 0.00 0.00 2.74
2504 4602 6.717540 AGAGAGGCTATGACGATATTTGTACT 59.282 38.462 0.00 0.00 0.00 2.73
2505 4603 6.915349 AGAGAGGCTATGACGATATTTGTAC 58.085 40.000 0.00 0.00 0.00 2.90
2520 4618 5.213519 ACTCTAGTAGTGAGAGAGAGGCTA 58.786 45.833 6.67 0.00 42.69 3.93
2591 4705 3.358700 CGTTTTCACGCATCTGACAAATG 59.641 43.478 0.00 0.00 40.18 2.32
2620 4734 3.813166 GTCCAGACGGTTCATGAGAAAAA 59.187 43.478 0.00 0.00 35.08 1.94
2624 4738 1.924731 AGTCCAGACGGTTCATGAGA 58.075 50.000 0.00 0.00 36.20 3.27
2631 4745 3.139077 GTTTCATCAAGTCCAGACGGTT 58.861 45.455 0.00 0.00 36.20 4.44
2640 4754 1.243902 TTGGGCCGTTTCATCAAGTC 58.756 50.000 0.00 0.00 0.00 3.01
2641 4755 1.698506 TTTGGGCCGTTTCATCAAGT 58.301 45.000 0.00 0.00 0.00 3.16
2648 4762 1.401018 CGATCTGTTTTGGGCCGTTTC 60.401 52.381 0.00 0.00 0.00 2.78
2673 4787 6.937392 AGAGAGGTGTAGGTTGAAGATAAAC 58.063 40.000 0.00 0.00 0.00 2.01
2676 4790 6.378564 CAGAAGAGAGGTGTAGGTTGAAGATA 59.621 42.308 0.00 0.00 0.00 1.98
2809 4923 0.756903 AGTCGATGGGTATTTCCGGG 59.243 55.000 0.00 0.00 37.00 5.73
2980 5108 0.618458 CCATCCGGTGAGAGGGAAAA 59.382 55.000 0.00 0.00 40.19 2.29
3278 5408 1.689233 TATCCAGGTCTGCCGCCTT 60.689 57.895 0.00 0.00 40.50 4.35
3350 5480 4.820775 AGGTAGAGCTGAATATCCTTCCA 58.179 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.