Multiple sequence alignment - TraesCS2B01G298900

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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 TraesCS2B01G298900 chr2B 100.000 4049 0 0 1 4049 418947064 418951112 0.000000e+00 7478.0
1 TraesCS2B01G298900 chr2D 94.134 3597 102 29 191 3756 352703393 352706911 0.000000e+00 5373.0
2 TraesCS2B01G298900 chr2D 89.338 272 23 4 3782 4049 352706969 352707238 1.800000e-88 337.0
3 TraesCS2B01G298900 chr2D 93.299 194 7 2 1 188 352703005 352703198 8.570000e-72 281.0
4 TraesCS2B01G298900 chr2D 82.727 110 12 7 3938 4044 363977833 363977938 1.550000e-14 91.6
5 TraesCS2B01G298900 chr2A 93.933 3544 132 38 542 4049 470638630 470642126 0.000000e+00 5276.0
6 TraesCS2B01G298900 chr2A 86.481 503 25 17 1 481 470638138 470638619 2.790000e-141 512.0
7 TraesCS2B01G298900 chr7D 77.863 2096 372 61 991 3052 84986118 84988155 0.000000e+00 1216.0
8 TraesCS2B01G298900 chr7A 77.663 2131 378 65 991 3083 86048189 86050259 0.000000e+00 1208.0
9 TraesCS2B01G298900 chr7A 83.908 87 14 0 3936 4022 202995087 202995001 2.590000e-12 84.2
10 TraesCS2B01G298900 chr7B 77.422 2095 373 59 991 3052 34610041 34612068 0.000000e+00 1157.0
11 TraesCS2B01G298900 chr5D 76.316 342 29 20 3617 3945 468159013 468159315 7.060000e-28 135.0
12 TraesCS2B01G298900 chr5D 93.878 49 3 0 3942 3990 482103362 482103314 1.560000e-09 75.0
13 TraesCS2B01G298900 chr5A 97.917 48 1 0 3945 3992 436352521 436352474 2.590000e-12 84.2
14 TraesCS2B01G298900 chr1B 96.000 50 2 0 3946 3995 110618687 110618638 9.330000e-12 82.4
15 TraesCS2B01G298900 chr6D 91.525 59 4 1 3937 3995 437685906 437685849 3.350000e-11 80.5
16 TraesCS2B01G298900 chr1A 90.909 55 3 2 3946 3999 568391287 568391234 5.610000e-09 73.1


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 TraesCS2B01G298900 chr2B 418947064 418951112 4048 False 7478 7478 100.000 1 4049 1 chr2B.!!$F1 4048
1 TraesCS2B01G298900 chr2D 352703005 352707238 4233 False 1997 5373 92.257 1 4049 3 chr2D.!!$F2 4048
2 TraesCS2B01G298900 chr2A 470638138 470642126 3988 False 2894 5276 90.207 1 4049 2 chr2A.!!$F1 4048
3 TraesCS2B01G298900 chr7D 84986118 84988155 2037 False 1216 1216 77.863 991 3052 1 chr7D.!!$F1 2061
4 TraesCS2B01G298900 chr7A 86048189 86050259 2070 False 1208 1208 77.663 991 3083 1 chr7A.!!$F1 2092
5 TraesCS2B01G298900 chr7B 34610041 34612068 2027 False 1157 1157 77.422 991 3052 1 chr7B.!!$F1 2061

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
657 891 0.033504 AGATGAAACACGTGAGCGGT 59.966 50.0 25.01 4.82 43.45 5.68 F
869 1117 0.105964 GGCACCGGCACACATATCTA 59.894 55.0 0.00 0.00 43.71 1.98 F
1872 2164 0.179234 TTCAGCGTGTGGAGTGGAAA 59.821 50.0 0.00 0.00 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2616 2908 1.152963 CCCCCGTGTCCAATGATCC 60.153 63.158 0.00 0.00 0.0 3.36 R
2632 2924 2.750237 AATCTTTCCACGGCGCCC 60.750 61.111 23.46 2.84 0.0 6.13 R
3491 3812 2.354821 GTCGGATTTTGCACTATGGTCC 59.645 50.000 0.00 0.00 0.0 4.46 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
22 23 0.318955 CGGAGCCTTTTGGTTTGCAG 60.319 55.000 0.00 0.00 42.99 4.41
104 111 3.531538 ACCCATGACATGATCGTTACAC 58.468 45.455 17.24 0.00 0.00 2.90
122 137 2.875933 ACACACACGGATAAACCTGTTG 59.124 45.455 0.00 0.00 36.31 3.33
208 425 5.068460 TGGAAAGACGTTTTTGAACATCCAT 59.932 36.000 9.02 0.00 0.00 3.41
209 426 5.629435 GGAAAGACGTTTTTGAACATCCATC 59.371 40.000 9.02 0.00 0.00 3.51
210 427 4.766404 AGACGTTTTTGAACATCCATCC 57.234 40.909 0.00 0.00 0.00 3.51
211 428 4.141287 AGACGTTTTTGAACATCCATCCA 58.859 39.130 0.00 0.00 0.00 3.41
212 429 4.766891 AGACGTTTTTGAACATCCATCCAT 59.233 37.500 0.00 0.00 0.00 3.41
224 441 1.417517 TCCATCCATGCTAAGTGCGAT 59.582 47.619 0.00 0.00 46.63 4.58
225 442 1.802960 CCATCCATGCTAAGTGCGATC 59.197 52.381 0.00 0.00 46.63 3.69
238 455 0.535335 TGCGATCTACCCCAAGTGAC 59.465 55.000 0.00 0.00 0.00 3.67
246 463 1.671054 CCCCAAGTGACGCGAATGT 60.671 57.895 15.93 0.00 0.00 2.71
268 485 4.023536 GTCGTGCTTTTCAAGATTTACCCA 60.024 41.667 0.00 0.00 35.71 4.51
269 486 4.215399 TCGTGCTTTTCAAGATTTACCCAG 59.785 41.667 0.00 0.00 0.00 4.45
272 489 5.241728 GTGCTTTTCAAGATTTACCCAGAGT 59.758 40.000 0.00 0.00 0.00 3.24
273 490 5.833131 TGCTTTTCAAGATTTACCCAGAGTT 59.167 36.000 0.00 0.00 0.00 3.01
274 491 6.323739 TGCTTTTCAAGATTTACCCAGAGTTT 59.676 34.615 0.00 0.00 0.00 2.66
275 492 7.147742 TGCTTTTCAAGATTTACCCAGAGTTTT 60.148 33.333 0.00 0.00 0.00 2.43
276 493 7.710907 GCTTTTCAAGATTTACCCAGAGTTTTT 59.289 33.333 0.00 0.00 0.00 1.94
315 536 3.194542 AGATTTCAGGAAGACGTCTCTGG 59.805 47.826 25.62 14.51 0.00 3.86
324 545 3.372660 AGACGTCTCTGGTCAAGTTTC 57.627 47.619 13.58 0.00 36.87 2.78
438 659 0.874390 GCAAAAGATGACAGCGACCA 59.126 50.000 0.00 0.00 0.00 4.02
448 669 0.108585 ACAGCGACCACCAAGAACAT 59.891 50.000 0.00 0.00 0.00 2.71
462 683 7.754924 CCACCAAGAACATTGTACATAATTGTC 59.245 37.037 0.00 0.00 37.28 3.18
470 691 6.377996 ACATTGTACATAATTGTCCAGTGCAT 59.622 34.615 0.00 0.00 34.20 3.96
471 692 6.832520 TTGTACATAATTGTCCAGTGCATT 57.167 33.333 0.00 0.00 37.28 3.56
472 693 6.435430 TGTACATAATTGTCCAGTGCATTC 57.565 37.500 0.00 0.00 37.28 2.67
473 694 5.942826 TGTACATAATTGTCCAGTGCATTCA 59.057 36.000 0.00 0.00 37.28 2.57
474 695 5.981088 ACATAATTGTCCAGTGCATTCAA 57.019 34.783 0.00 0.00 0.00 2.69
475 696 5.957798 ACATAATTGTCCAGTGCATTCAAG 58.042 37.500 0.00 0.00 0.00 3.02
503 724 1.986631 TCCAACGGGGTTAGATTTGGA 59.013 47.619 0.00 0.00 42.73 3.53
526 748 4.576993 GCGAGGCCAAAACCAATG 57.423 55.556 5.01 0.00 0.00 2.82
527 749 1.665442 GCGAGGCCAAAACCAATGT 59.335 52.632 5.01 0.00 0.00 2.71
528 750 0.667184 GCGAGGCCAAAACCAATGTG 60.667 55.000 5.01 0.00 0.00 3.21
529 751 0.673437 CGAGGCCAAAACCAATGTGT 59.327 50.000 5.01 0.00 0.00 3.72
530 752 1.883275 CGAGGCCAAAACCAATGTGTA 59.117 47.619 5.01 0.00 0.00 2.90
531 753 2.294791 CGAGGCCAAAACCAATGTGTAA 59.705 45.455 5.01 0.00 0.00 2.41
532 754 3.056891 CGAGGCCAAAACCAATGTGTAAT 60.057 43.478 5.01 0.00 0.00 1.89
533 755 4.560513 CGAGGCCAAAACCAATGTGTAATT 60.561 41.667 5.01 0.00 0.00 1.40
534 756 4.640364 AGGCCAAAACCAATGTGTAATTG 58.360 39.130 5.01 0.00 0.00 2.32
535 757 3.188254 GGCCAAAACCAATGTGTAATTGC 59.812 43.478 0.00 0.00 0.00 3.56
536 758 3.120718 GCCAAAACCAATGTGTAATTGCG 60.121 43.478 0.00 0.00 0.00 4.85
537 759 3.431572 CCAAAACCAATGTGTAATTGCGG 59.568 43.478 0.00 0.00 0.00 5.69
561 783 5.006941 GCCAATTGCGCAATTTATTCTTCAT 59.993 36.000 38.50 16.93 38.84 2.57
570 792 7.579726 CGCAATTTATTCTTCATTAGGAGAGG 58.420 38.462 0.00 0.00 0.00 3.69
599 821 1.062148 TCGTCGTCAAGCTCGATACTG 59.938 52.381 0.00 0.00 39.45 2.74
607 829 0.460987 AGCTCGATACTGCTTGTGGC 60.461 55.000 0.00 0.00 35.86 5.01
627 861 2.622436 CAAGAGAGAGTAAAAGCGGGG 58.378 52.381 0.00 0.00 0.00 5.73
651 885 2.091277 GCGAGAGAAGATGAAACACGTG 59.909 50.000 15.48 15.48 0.00 4.49
652 886 3.565516 CGAGAGAAGATGAAACACGTGA 58.434 45.455 25.01 0.00 0.00 4.35
653 887 3.605916 CGAGAGAAGATGAAACACGTGAG 59.394 47.826 25.01 0.00 0.00 3.51
654 888 3.321497 AGAGAAGATGAAACACGTGAGC 58.679 45.455 25.01 11.15 0.00 4.26
655 889 2.061773 AGAAGATGAAACACGTGAGCG 58.938 47.619 25.01 0.00 44.93 5.03
656 890 1.126846 GAAGATGAAACACGTGAGCGG 59.873 52.381 25.01 0.00 43.45 5.52
657 891 0.033504 AGATGAAACACGTGAGCGGT 59.966 50.000 25.01 4.82 43.45 5.68
658 892 0.163788 GATGAAACACGTGAGCGGTG 59.836 55.000 25.01 0.00 43.45 4.94
659 893 1.841663 ATGAAACACGTGAGCGGTGC 61.842 55.000 25.01 4.59 43.45 5.01
671 905 2.105128 CGGTGCGAGGATGAGGTC 59.895 66.667 0.00 0.00 0.00 3.85
741 978 2.268076 ACCGTGAATTGCCAGCCAC 61.268 57.895 0.00 0.00 0.00 5.01
743 980 2.568090 GTGAATTGCCAGCCACCG 59.432 61.111 0.00 0.00 0.00 4.94
744 981 3.372730 TGAATTGCCAGCCACCGC 61.373 61.111 0.00 0.00 0.00 5.68
745 982 3.372730 GAATTGCCAGCCACCGCA 61.373 61.111 0.00 0.00 37.52 5.69
746 983 2.681064 AATTGCCAGCCACCGCAT 60.681 55.556 0.00 0.00 37.52 4.73
747 984 2.229690 GAATTGCCAGCCACCGCATT 62.230 55.000 0.00 0.00 37.52 3.56
762 1010 1.537776 CGCATTCCACCAAACAGCAAA 60.538 47.619 0.00 0.00 0.00 3.68
804 1052 1.379642 GCCATTTGCTTCCCTCCTCG 61.380 60.000 0.00 0.00 36.87 4.63
812 1060 1.999071 CTTCCCTCCTCGTCTCGCAG 61.999 65.000 0.00 0.00 0.00 5.18
813 1061 3.522731 CCCTCCTCGTCTCGCAGG 61.523 72.222 0.00 0.00 0.00 4.85
814 1062 3.522731 CCTCCTCGTCTCGCAGGG 61.523 72.222 0.00 0.00 0.00 4.45
815 1063 2.752238 CTCCTCGTCTCGCAGGGT 60.752 66.667 0.00 0.00 0.00 4.34
816 1064 1.451567 CTCCTCGTCTCGCAGGGTA 60.452 63.158 0.00 0.00 0.00 3.69
819 1067 1.655329 CTCGTCTCGCAGGGTATCC 59.345 63.158 0.00 0.00 0.00 2.59
868 1116 1.153168 GGCACCGGCACACATATCT 60.153 57.895 0.00 0.00 43.71 1.98
869 1117 0.105964 GGCACCGGCACACATATCTA 59.894 55.000 0.00 0.00 43.71 1.98
870 1118 1.270839 GGCACCGGCACACATATCTAT 60.271 52.381 0.00 0.00 43.71 1.98
871 1119 2.069273 GCACCGGCACACATATCTATC 58.931 52.381 0.00 0.00 40.72 2.08
872 1120 2.289072 GCACCGGCACACATATCTATCT 60.289 50.000 0.00 0.00 40.72 1.98
873 1121 3.579709 CACCGGCACACATATCTATCTC 58.420 50.000 0.00 0.00 0.00 2.75
874 1122 3.256879 CACCGGCACACATATCTATCTCT 59.743 47.826 0.00 0.00 0.00 3.10
875 1123 3.898123 ACCGGCACACATATCTATCTCTT 59.102 43.478 0.00 0.00 0.00 2.85
976 1244 1.078708 CAGTAAACCACCGCCGGAT 60.079 57.895 11.71 0.00 0.00 4.18
1210 1493 2.182030 CCGACCTCTTCCACTCGC 59.818 66.667 0.00 0.00 0.00 5.03
1276 1568 3.535962 CCGAGGGCCTCTCTCTGC 61.536 72.222 29.81 3.91 40.30 4.26
1277 1569 2.441901 CGAGGGCCTCTCTCTGCT 60.442 66.667 29.81 0.00 40.30 4.24
1596 1888 0.538977 TCGACACCTCCTCCGAGTTT 60.539 55.000 0.00 0.00 33.93 2.66
1872 2164 0.179234 TTCAGCGTGTGGAGTGGAAA 59.821 50.000 0.00 0.00 0.00 3.13
1990 2282 1.216444 GTGTCTGATGAGCTGCGGA 59.784 57.895 0.00 0.00 0.00 5.54
2082 2374 2.260434 CCTCGTTCGCCGGAGAAA 59.740 61.111 22.82 7.18 37.11 2.52
2145 2437 3.625649 ATTCCTGAGCTCAAGGAACTC 57.374 47.619 32.20 3.80 43.49 3.01
2616 2908 2.746472 CGAGCTTGGGAGGATTTTAGGG 60.746 54.545 0.00 0.00 0.00 3.53
2632 2924 1.152963 GGGGATCATTGGACACGGG 60.153 63.158 0.00 0.00 0.00 5.28
3060 3375 9.268282 AGAAGAAGGTTATAGTTCCTATGACAA 57.732 33.333 8.01 0.00 35.51 3.18
3092 3410 7.147426 GGTTACAGGTATATCTTTACAAGGGGT 60.147 40.741 0.00 0.00 0.00 4.95
3116 3434 4.637534 AGTATATTGCTGAACTGCTGGTTG 59.362 41.667 5.42 0.00 38.41 3.77
3400 3721 1.204467 CATGTTTAGGCCGCAAACCAT 59.796 47.619 24.53 17.51 35.46 3.55
3412 3733 3.181510 CCGCAAACCATAAGTAACAGAGC 60.182 47.826 0.00 0.00 0.00 4.09
3463 3784 6.917477 TGAAGTGAAACAAACATGTCTTATGC 59.083 34.615 0.00 0.00 41.43 3.14
3469 3790 4.985413 ACAAACATGTCTTATGCAATCCG 58.015 39.130 0.00 0.00 0.00 4.18
3491 3812 3.001365 GTGAAGCTACGGATCGTAAAACG 60.001 47.826 1.88 0.00 41.82 3.60
3578 3899 2.157863 GCGCAAAAGTCTAGACACTTCC 59.842 50.000 24.44 6.72 35.45 3.46
3582 3903 5.007724 CGCAAAAGTCTAGACACTTCCTTTT 59.992 40.000 24.44 16.66 35.45 2.27
3682 4003 3.128764 ACGCATTTATCGTCAGAGTCTGA 59.871 43.478 19.10 19.10 38.25 3.27
3722 4043 3.195610 CAGACTGTAGGGCATAGTGTCAA 59.804 47.826 11.98 0.00 0.00 3.18
3758 4079 0.908910 TGTAGGGCAGTGGTACATGG 59.091 55.000 0.00 0.00 44.52 3.66
3765 4086 3.881089 GGGCAGTGGTACATGGTAATAAC 59.119 47.826 0.00 0.00 44.52 1.89
3779 4134 4.161565 TGGTAATAACGATCTTCAGGCAGT 59.838 41.667 0.00 0.00 0.00 4.40
3780 4135 5.361571 TGGTAATAACGATCTTCAGGCAGTA 59.638 40.000 0.00 0.00 0.00 2.74
3808 4163 7.758528 ACGTACTAATTTAGAGGTGTCATTCAC 59.241 37.037 10.39 0.00 45.47 3.18
3845 4204 8.230486 ACTCTTGCTATTTTACTGACGAAAATG 58.770 33.333 0.00 0.00 37.16 2.32
3858 4217 6.481976 ACTGACGAAAATGTAAGTGTTGATGA 59.518 34.615 0.00 0.00 32.10 2.92
3892 4251 9.628746 TGGGCTATTTTCTTATTTAAAACGAAC 57.371 29.630 0.00 0.00 0.00 3.95
3893 4252 9.628746 GGGCTATTTTCTTATTTAAAACGAACA 57.371 29.630 0.00 0.00 0.00 3.18
3930 4289 5.368989 ACTGTTAGGACTCTTTTCTTGGTG 58.631 41.667 0.00 0.00 0.00 4.17
3941 4300 5.115480 TCTTTTCTTGGTGTTGGCAATTTC 58.885 37.500 1.92 0.00 0.00 2.17
4022 4381 7.190920 ACTTGTACTAAGTCAGCAACAATTC 57.809 36.000 0.00 0.00 34.61 2.17
4024 4383 7.282224 ACTTGTACTAAGTCAGCAACAATTCAA 59.718 33.333 0.00 0.00 34.61 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.374702 CGGCTCACGCACTGCAAC 62.375 66.667 1.11 0.00 38.10 4.17
104 111 1.199097 GCCAACAGGTTTATCCGTGTG 59.801 52.381 0.00 0.00 41.99 3.82
122 137 4.072131 TGTCACTAGGAATGTTTGAAGCC 58.928 43.478 0.00 0.00 0.00 4.35
176 201 5.062809 TCAAAAACGTCTTTCCAAACATTGC 59.937 36.000 0.00 0.00 0.00 3.56
208 425 2.035961 GGTAGATCGCACTTAGCATGGA 59.964 50.000 0.00 0.00 46.13 3.41
209 426 2.408050 GGTAGATCGCACTTAGCATGG 58.592 52.381 0.00 0.00 46.13 3.66
210 427 2.408050 GGGTAGATCGCACTTAGCATG 58.592 52.381 0.00 0.00 46.13 4.06
211 428 1.344763 GGGGTAGATCGCACTTAGCAT 59.655 52.381 0.00 0.00 46.13 3.79
212 429 0.750850 GGGGTAGATCGCACTTAGCA 59.249 55.000 0.00 0.00 46.13 3.49
224 441 1.180456 TTCGCGTCACTTGGGGTAGA 61.180 55.000 5.77 0.00 0.00 2.59
225 442 0.108329 ATTCGCGTCACTTGGGGTAG 60.108 55.000 5.77 0.00 0.00 3.18
238 455 0.110867 TGAAAAGCACGACATTCGCG 60.111 50.000 0.00 0.00 45.12 5.87
246 463 4.138290 TGGGTAAATCTTGAAAAGCACGA 58.862 39.130 0.00 0.00 45.70 4.35
302 523 3.372660 AACTTGACCAGAGACGTCTTC 57.627 47.619 21.08 13.61 0.00 2.87
306 527 1.679680 TCGAAACTTGACCAGAGACGT 59.320 47.619 0.00 0.00 0.00 4.34
315 536 2.165030 TCCCTATCCGTCGAAACTTGAC 59.835 50.000 0.00 0.00 0.00 3.18
324 545 1.470979 CCACAAAGTCCCTATCCGTCG 60.471 57.143 0.00 0.00 0.00 5.12
438 659 7.826690 GGACAATTATGTACAATGTTCTTGGT 58.173 34.615 0.00 0.00 40.39 3.67
462 683 2.233271 ACTGGAACTTGAATGCACTGG 58.767 47.619 0.00 0.00 0.00 4.00
470 691 2.294074 CCGTTGGAACTGGAACTTGAA 58.706 47.619 0.00 0.00 0.00 2.69
471 692 1.476110 CCCGTTGGAACTGGAACTTGA 60.476 52.381 0.00 0.00 35.55 3.02
472 693 0.951558 CCCGTTGGAACTGGAACTTG 59.048 55.000 0.00 0.00 35.55 3.16
473 694 0.179001 CCCCGTTGGAACTGGAACTT 60.179 55.000 1.79 0.00 35.55 2.66
474 695 1.350310 ACCCCGTTGGAACTGGAACT 61.350 55.000 1.79 0.00 35.55 3.01
475 696 0.466739 AACCCCGTTGGAACTGGAAC 60.467 55.000 1.79 0.00 35.55 3.62
520 742 0.530288 GGCCGCAATTACACATTGGT 59.470 50.000 0.00 0.00 0.00 3.67
521 743 0.529833 TGGCCGCAATTACACATTGG 59.470 50.000 0.00 0.00 0.00 3.16
522 744 2.360553 TTGGCCGCAATTACACATTG 57.639 45.000 0.00 0.00 0.00 2.82
523 745 3.260740 CAATTGGCCGCAATTACACATT 58.739 40.909 0.00 0.00 33.85 2.71
524 746 2.891112 CAATTGGCCGCAATTACACAT 58.109 42.857 0.00 0.00 33.85 3.21
525 747 1.671261 GCAATTGGCCGCAATTACACA 60.671 47.619 7.72 0.00 33.85 3.72
526 748 0.998669 GCAATTGGCCGCAATTACAC 59.001 50.000 7.72 0.00 33.85 2.90
527 749 0.457509 CGCAATTGGCCGCAATTACA 60.458 50.000 7.72 0.00 40.31 2.41
528 750 1.751536 GCGCAATTGGCCGCAATTAC 61.752 55.000 20.85 0.00 40.26 1.89
529 751 1.518133 GCGCAATTGGCCGCAATTA 60.518 52.632 20.85 0.00 40.26 1.40
530 752 2.814776 GCGCAATTGGCCGCAATT 60.815 55.556 20.85 0.00 40.26 2.32
531 753 4.066596 TGCGCAATTGGCCGCAAT 62.067 55.556 24.56 0.00 44.66 3.56
533 755 3.586461 AATTGCGCAATTGGCCGCA 62.586 52.632 39.54 23.46 45.46 5.69
534 756 1.080995 TAAATTGCGCAATTGGCCGC 61.081 50.000 40.29 19.52 40.57 6.53
535 757 1.569708 ATAAATTGCGCAATTGGCCG 58.430 45.000 40.29 4.30 40.57 6.13
536 758 3.197265 AGAATAAATTGCGCAATTGGCC 58.803 40.909 40.29 29.04 40.57 5.36
537 759 4.329528 TGAAGAATAAATTGCGCAATTGGC 59.670 37.500 40.29 29.10 40.57 4.52
561 783 4.617530 CGACGACATGTTTTCCTCTCCTAA 60.618 45.833 0.00 0.00 0.00 2.69
570 792 2.221055 AGCTTGACGACGACATGTTTTC 59.779 45.455 0.00 0.00 0.00 2.29
599 821 2.751166 TACTCTCTCTTGCCACAAGC 57.249 50.000 2.41 0.00 44.14 4.01
602 824 3.403038 GCTTTTACTCTCTCTTGCCACA 58.597 45.455 0.00 0.00 0.00 4.17
605 827 2.003301 CCGCTTTTACTCTCTCTTGCC 58.997 52.381 0.00 0.00 0.00 4.52
607 829 2.622436 CCCCGCTTTTACTCTCTCTTG 58.378 52.381 0.00 0.00 0.00 3.02
627 861 2.926838 GTGTTTCATCTTCTCTCGCTCC 59.073 50.000 0.00 0.00 0.00 4.70
651 885 2.279120 CTCATCCTCGCACCGCTC 60.279 66.667 0.00 0.00 0.00 5.03
652 886 3.842923 CCTCATCCTCGCACCGCT 61.843 66.667 0.00 0.00 0.00 5.52
653 887 4.148825 ACCTCATCCTCGCACCGC 62.149 66.667 0.00 0.00 0.00 5.68
654 888 2.105128 GACCTCATCCTCGCACCG 59.895 66.667 0.00 0.00 0.00 4.94
655 889 2.105128 CGACCTCATCCTCGCACC 59.895 66.667 0.00 0.00 0.00 5.01
656 890 2.105128 CCGACCTCATCCTCGCAC 59.895 66.667 0.00 0.00 0.00 5.34
657 891 3.838271 GCCGACCTCATCCTCGCA 61.838 66.667 0.00 0.00 0.00 5.10
658 892 3.371097 TTGCCGACCTCATCCTCGC 62.371 63.158 0.00 0.00 0.00 5.03
659 893 1.227089 CTTGCCGACCTCATCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
671 905 0.593128 CTCCAAAGTCCAACTTGCCG 59.407 55.000 0.00 0.00 38.66 5.69
741 978 1.080569 GCTGTTTGGTGGAATGCGG 60.081 57.895 0.00 0.00 0.00 5.69
743 980 1.866601 GTTTGCTGTTTGGTGGAATGC 59.133 47.619 0.00 0.00 0.00 3.56
744 981 2.126467 CGTTTGCTGTTTGGTGGAATG 58.874 47.619 0.00 0.00 0.00 2.67
745 982 2.028130 TCGTTTGCTGTTTGGTGGAAT 58.972 42.857 0.00 0.00 0.00 3.01
746 983 1.464734 TCGTTTGCTGTTTGGTGGAA 58.535 45.000 0.00 0.00 0.00 3.53
747 984 1.464734 TTCGTTTGCTGTTTGGTGGA 58.535 45.000 0.00 0.00 0.00 4.02
814 1062 2.357361 CGGATAGAGGGAGAGGGGATAC 60.357 59.091 0.00 0.00 0.00 2.24
815 1063 1.923850 CGGATAGAGGGAGAGGGGATA 59.076 57.143 0.00 0.00 0.00 2.59
816 1064 0.707616 CGGATAGAGGGAGAGGGGAT 59.292 60.000 0.00 0.00 0.00 3.85
819 1067 0.251430 GGACGGATAGAGGGAGAGGG 60.251 65.000 0.00 0.00 0.00 4.30
868 1116 6.351711 TCGTAGCAGTAGTGGTAAAGAGATA 58.648 40.000 10.96 0.00 38.37 1.98
869 1117 5.191426 TCGTAGCAGTAGTGGTAAAGAGAT 58.809 41.667 10.96 0.00 38.37 2.75
870 1118 4.582869 TCGTAGCAGTAGTGGTAAAGAGA 58.417 43.478 10.96 6.30 38.37 3.10
871 1119 4.395542 ACTCGTAGCAGTAGTGGTAAAGAG 59.604 45.833 25.90 25.90 42.93 2.85
872 1120 4.155462 CACTCGTAGCAGTAGTGGTAAAGA 59.845 45.833 19.62 16.19 38.37 2.52
873 1121 4.413087 CACTCGTAGCAGTAGTGGTAAAG 58.587 47.826 10.96 13.07 38.37 1.85
874 1122 3.366679 GCACTCGTAGCAGTAGTGGTAAA 60.367 47.826 10.96 2.61 40.76 2.01
875 1123 2.163010 GCACTCGTAGCAGTAGTGGTAA 59.837 50.000 10.96 0.00 40.76 2.85
956 1224 1.078708 CCGGCGGTGGTTTACTGAT 60.079 57.895 19.97 0.00 37.93 2.90
976 1244 4.090588 CGGGCCGCTAGGGTTTGA 62.091 66.667 15.42 0.00 38.44 2.69
1223 1506 4.716977 GGGTCGGGGAGTGGGAGT 62.717 72.222 0.00 0.00 0.00 3.85
1272 1564 0.456142 CGTCGTCGAAATCCAGCAGA 60.456 55.000 0.00 0.00 39.71 4.26
1276 1568 2.505498 CCGCGTCGTCGAAATCCAG 61.505 63.158 4.92 0.00 39.71 3.86
1277 1569 2.505337 CCGCGTCGTCGAAATCCA 60.505 61.111 4.92 0.00 39.71 3.41
1872 2164 4.903054 TCTTCATCTTGTCATTCAGCTGT 58.097 39.130 14.67 0.00 0.00 4.40
1990 2282 2.948979 TGGATTCAACAAAGCACTCGTT 59.051 40.909 0.00 0.00 0.00 3.85
2076 2368 1.555533 AGAATCCGGGACACTTTCTCC 59.444 52.381 0.00 0.00 0.00 3.71
2082 2374 3.711704 ACATATCAAGAATCCGGGACACT 59.288 43.478 0.00 0.00 0.00 3.55
2145 2437 1.503784 TCCCCAGGAGTCCCATAGTAG 59.496 57.143 5.25 0.00 33.88 2.57
2616 2908 1.152963 CCCCCGTGTCCAATGATCC 60.153 63.158 0.00 0.00 0.00 3.36
2632 2924 2.750237 AATCTTTCCACGGCGCCC 60.750 61.111 23.46 2.84 0.00 6.13
3092 3410 5.614324 ACCAGCAGTTCAGCAATATACTA 57.386 39.130 0.00 0.00 36.85 1.82
3116 3434 3.181473 ACATGCACCAATCCAATACATGC 60.181 43.478 0.00 0.00 37.52 4.06
3400 3721 4.082787 GCAAATGGCAAGCTCTGTTACTTA 60.083 41.667 0.00 0.00 43.97 2.24
3469 3790 3.001365 CGTTTTACGATCCGTAGCTTCAC 60.001 47.826 0.00 0.00 46.05 3.18
3491 3812 2.354821 GTCGGATTTTGCACTATGGTCC 59.645 50.000 0.00 0.00 0.00 4.46
3646 3967 8.444715 ACGATAAATGCGTTTAGTTCATACAAA 58.555 29.630 15.88 0.00 39.18 2.83
3662 3983 5.348724 TGTTTCAGACTCTGACGATAAATGC 59.651 40.000 8.35 0.00 40.46 3.56
3682 4003 8.747538 ACAGTCTGATTAAGTAACCTTTGTTT 57.252 30.769 6.91 0.00 35.87 2.83
3756 4077 4.161565 ACTGCCTGAAGATCGTTATTACCA 59.838 41.667 0.00 0.00 0.00 3.25
3758 4079 7.270793 CGTATACTGCCTGAAGATCGTTATTAC 59.729 40.741 0.56 0.00 0.00 1.89
3765 4086 3.627732 ACGTATACTGCCTGAAGATCG 57.372 47.619 0.56 0.00 0.00 3.69
3780 4135 9.962783 GAATGACACCTCTAAATTAGTACGTAT 57.037 33.333 0.00 0.00 0.00 3.06
3808 4163 6.851222 AAATAGCAAGAGTATTCCGATGTG 57.149 37.500 0.00 0.00 0.00 3.21
3845 4204 7.499232 AGCCCAATATAACTCATCAACACTTAC 59.501 37.037 0.00 0.00 0.00 2.34
3930 4289 5.299531 GGAGGGAGTATAAGAAATTGCCAAC 59.700 44.000 0.00 0.00 0.00 3.77
3941 4300 8.534954 TTAATATGGATCGGAGGGAGTATAAG 57.465 38.462 0.00 0.00 0.00 1.73
4015 4374 4.018779 TCCCTCCTATCCGTTTGAATTGTT 60.019 41.667 0.00 0.00 0.00 2.83
4022 4381 3.705072 AGTTACTCCCTCCTATCCGTTTG 59.295 47.826 0.00 0.00 0.00 2.93
4024 4383 3.684408 AGTTACTCCCTCCTATCCGTT 57.316 47.619 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.