Multiple sequence alignment - TraesCS2D01G576700

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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 TraesCS2D01G576700 chr2D 100.000 4554 0 0 1 4554 640173369 640177922 0.000000e+00 8410.0
1 TraesCS2D01G576700 chr2D 82.407 108 18 1 311 417 572642506 572642613 4.850000e-15 93.5
2 TraesCS2D01G576700 chr2A 96.115 1802 43 11 875 2674 765662958 765664734 0.000000e+00 2915.0
3 TraesCS2D01G576700 chr2A 98.541 754 11 0 2936 3689 765664975 765665728 0.000000e+00 1332.0
4 TraesCS2D01G576700 chr2A 90.859 722 58 5 1 714 765662235 765662956 0.000000e+00 961.0
5 TraesCS2D01G576700 chr2A 92.575 633 20 9 3930 4541 765676602 765677228 0.000000e+00 883.0
6 TraesCS2D01G576700 chr2A 97.788 226 5 0 2668 2893 765664760 765664985 1.540000e-104 390.0
7 TraesCS2D01G576700 chr2A 74.955 559 115 19 5 547 456752159 456752708 2.740000e-57 233.0
8 TraesCS2D01G576700 chr2A 97.015 134 4 0 3801 3934 765667395 765667528 4.580000e-55 226.0
9 TraesCS2D01G576700 chr2A 74.885 434 89 18 69 487 670667853 670668281 3.620000e-41 180.0
10 TraesCS2D01G576700 chr2A 98.039 102 2 0 3688 3789 765666099 765666200 1.300000e-40 178.0
11 TraesCS2D01G576700 chr2A 86.207 116 11 3 3322 3437 765605348 765605458 2.230000e-23 121.0
12 TraesCS2D01G576700 chr2A 83.495 103 17 0 306 408 203092384 203092282 3.750000e-16 97.1
13 TraesCS2D01G576700 chr2A 78.462 130 13 9 96 211 332510788 332510660 2.270000e-08 71.3
14 TraesCS2D01G576700 chr2B 95.308 1428 63 3 1248 2674 801255843 801254419 0.000000e+00 2263.0
15 TraesCS2D01G576700 chr2B 94.291 1051 40 6 2902 3936 801254104 801253058 0.000000e+00 1591.0
16 TraesCS2D01G576700 chr2B 89.150 682 60 6 397 1066 801256633 801255954 0.000000e+00 837.0
17 TraesCS2D01G576700 chr2B 91.463 328 17 6 3922 4240 801253026 801252701 1.500000e-119 440.0
18 TraesCS2D01G576700 chr2B 89.720 321 18 4 4241 4552 801251914 801251600 3.300000e-106 396.0
19 TraesCS2D01G576700 chr2B 93.200 250 8 3 2668 2910 801254393 801254146 4.330000e-95 359.0
20 TraesCS2D01G576700 chr2B 76.471 306 59 10 82 377 23004064 23004366 2.190000e-33 154.0
21 TraesCS2D01G576700 chr2B 79.365 126 22 3 324 446 764141403 764141527 8.120000e-13 86.1
22 TraesCS2D01G576700 chrUn 87.529 433 48 4 397 824 322968384 322967953 3.160000e-136 496.0
23 TraesCS2D01G576700 chrUn 87.529 433 48 4 397 824 322978056 322977625 3.160000e-136 496.0
24 TraesCS2D01G576700 chrUn 92.273 220 14 2 5 222 322968639 322968421 4.420000e-80 309.0
25 TraesCS2D01G576700 chrUn 91.364 220 16 2 5 222 322978311 322978093 9.580000e-77 298.0
26 TraesCS2D01G576700 chrUn 77.889 199 35 9 682 875 345756797 345756991 1.040000e-21 115.0
27 TraesCS2D01G576700 chrUn 95.238 63 2 1 5 67 338435778 338435839 1.040000e-16 99.0
28 TraesCS2D01G576700 chr7D 84.656 189 18 10 1 183 206698964 206698781 1.300000e-40 178.0
29 TraesCS2D01G576700 chr7D 74.398 332 69 14 161 480 614413892 614413565 1.330000e-25 128.0
30 TraesCS2D01G576700 chr6D 81.053 190 32 4 688 875 390481425 390481238 1.020000e-31 148.0
31 TraesCS2D01G576700 chr6D 85.556 90 11 2 319 407 312802970 312802882 4.850000e-15 93.5
32 TraesCS2D01G576700 chr6D 97.059 34 0 1 69 102 263479652 263479620 6.360000e-04 56.5
33 TraesCS2D01G576700 chr3B 81.421 183 29 5 702 881 663947043 663946863 1.320000e-30 145.0
34 TraesCS2D01G576700 chr1D 80.108 186 30 5 692 875 342174406 342174586 1.030000e-26 132.0
35 TraesCS2D01G576700 chr1D 78.378 148 26 5 366 509 214605584 214605439 1.740000e-14 91.6
36 TraesCS2D01G576700 chr7A 78.680 197 34 8 682 875 27398473 27398664 1.720000e-24 124.0
37 TraesCS2D01G576700 chr1A 78.283 198 37 6 681 875 459096800 459096994 6.190000e-24 122.0
38 TraesCS2D01G576700 chr4A 80.769 78 13 2 473 549 702059600 702059676 4.920000e-05 60.2


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 TraesCS2D01G576700 chr2D 640173369 640177922 4553 False 8410.000000 8410 100.000000 1 4554 1 chr2D.!!$F2 4553
1 TraesCS2D01G576700 chr2A 765662235 765667528 5293 False 1000.333333 2915 96.392833 1 3934 6 chr2A.!!$F5 3933
2 TraesCS2D01G576700 chr2A 765676602 765677228 626 False 883.000000 883 92.575000 3930 4541 1 chr2A.!!$F4 611
3 TraesCS2D01G576700 chr2A 456752159 456752708 549 False 233.000000 233 74.955000 5 547 1 chr2A.!!$F1 542
4 TraesCS2D01G576700 chr2B 801251600 801256633 5033 True 981.000000 2263 92.188667 397 4552 6 chr2B.!!$R1 4155
5 TraesCS2D01G576700 chrUn 322967953 322968639 686 True 402.500000 496 89.901000 5 824 2 chrUn.!!$R1 819
6 TraesCS2D01G576700 chrUn 322977625 322978311 686 True 397.000000 496 89.446500 5 824 2 chrUn.!!$R2 819

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
239 243 0.109319 GGTGTGCCACTTTAATGCCG 60.109 55.000 0.0 0.0 34.40 5.69 F
1065 1089 0.472471 TTCCTCCGGCACATATTCCC 59.528 55.000 0.0 0.0 0.00 3.97 F
1790 1819 0.664166 GCGTCGAAGGGTTTACGTCA 60.664 55.000 0.0 0.0 37.64 4.35 F
2046 2076 2.426738 TGTTCCTGCTTGTTTCAGTTGG 59.573 45.455 0.0 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1393 0.466189 AAGTTCCCGCATGCCCTATG 60.466 55.0 13.15 0.00 39.88 2.23 R
2937 3109 0.183014 TGACTTGGCCCGGTTACAAA 59.817 50.0 0.00 0.00 0.00 2.83 R
2938 3110 0.402504 ATGACTTGGCCCGGTTACAA 59.597 50.0 0.00 1.32 0.00 2.41 R
3633 3805 0.892063 AGTCTGGACTCTTCCGAAGC 59.108 55.0 3.00 0.00 46.37 3.86 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
239 243 0.109319 GGTGTGCCACTTTAATGCCG 60.109 55.000 0.00 0.00 34.40 5.69
311 321 1.469423 GCTCTAGAGTAGCGCCGTTTT 60.469 52.381 20.75 0.00 30.57 2.43
315 325 1.375013 GAGTAGCGCCGTTTTGGGA 60.375 57.895 2.29 0.00 38.63 4.37
388 399 4.487412 GGACGTGGTAGCGGTCCG 62.487 72.222 16.22 6.99 35.98 4.79
417 433 2.876581 CAAAGCCCCCTAGTTTGTCTT 58.123 47.619 0.00 0.00 0.00 3.01
424 441 4.813133 GCCCCCTAGTTTGTCTTGGTTTAT 60.813 45.833 0.00 0.00 37.36 1.40
436 453 6.126409 TGTCTTGGTTTATGAGGAAAAGTGT 58.874 36.000 0.00 0.00 0.00 3.55
451 468 1.183030 AGTGTGTCCGGACCATCGAA 61.183 55.000 31.19 9.20 0.00 3.71
464 481 1.542328 CCATCGAATGGGCCGATACAA 60.542 52.381 0.00 0.00 46.86 2.41
515 532 1.651987 CGCATGGTCCGAACAGTTAT 58.348 50.000 0.00 0.00 0.00 1.89
525 542 6.154877 TGGTCCGAACAGTTATAGATGGTTTA 59.845 38.462 0.00 0.00 0.00 2.01
571 588 6.083487 TCCTAGTAGGAGTAAGTTGGCTAA 57.917 41.667 15.33 0.00 40.06 3.09
575 592 7.288158 CCTAGTAGGAGTAAGTTGGCTAAAGAT 59.712 40.741 11.09 0.00 37.67 2.40
621 638 3.971245 AACAATCAGACTGTCCTCTCC 57.029 47.619 3.76 0.00 0.00 3.71
641 658 5.713389 TCTCCGATGGAAAGACAAACTACTA 59.287 40.000 0.00 0.00 0.00 1.82
656 673 8.876275 ACAAACTACTATTCGTAAAGTGAACA 57.124 30.769 0.00 0.00 0.00 3.18
694 711 7.107542 ACGCTTATGGAGTATAACTTTTTGGA 58.892 34.615 0.00 0.00 0.00 3.53
726 743 4.493547 GACATATCTAGATGTGCTCCTGC 58.506 47.826 24.68 7.89 40.18 4.85
728 745 5.328565 ACATATCTAGATGTGCTCCTGCTA 58.671 41.667 24.68 0.00 38.64 3.49
737 754 1.671979 TGCTCCTGCTATTGCACATC 58.328 50.000 0.00 0.00 45.31 3.06
751 768 7.802251 GCTATTGCACATCTAAATGACTCAATC 59.198 37.037 0.00 0.00 39.41 2.67
754 771 7.451501 TGCACATCTAAATGACTCAATCAAA 57.548 32.000 0.00 0.00 41.93 2.69
791 808 9.997172 ATGGGAAGAGAATAAAGAAAAATACCT 57.003 29.630 0.00 0.00 0.00 3.08
805 822 8.986477 AGAAAAATACCTACATGAATTGTTGC 57.014 30.769 0.00 0.00 39.87 4.17
811 828 5.242434 ACCTACATGAATTGTTGCGTAAGA 58.758 37.500 0.00 0.00 39.87 2.10
813 830 6.037172 ACCTACATGAATTGTTGCGTAAGATC 59.963 38.462 0.00 0.00 39.87 2.75
818 835 6.493449 TGAATTGTTGCGTAAGATCAATGA 57.507 33.333 0.00 0.00 43.02 2.57
820 837 6.968335 TGAATTGTTGCGTAAGATCAATGATG 59.032 34.615 0.00 0.00 43.02 3.07
824 841 5.411053 TGTTGCGTAAGATCAATGATGTTGA 59.589 36.000 14.84 0.00 43.02 3.18
921 945 4.392921 AGCTAAGCGAGATACACAACAT 57.607 40.909 0.00 0.00 0.00 2.71
1065 1089 0.472471 TTCCTCCGGCACATATTCCC 59.528 55.000 0.00 0.00 0.00 3.97
1067 1091 1.445942 CTCCGGCACATATTCCCGT 59.554 57.895 0.00 0.00 40.38 5.28
1232 1260 1.727511 CTTGCACCGGGCCACATATG 61.728 60.000 6.32 0.00 43.89 1.78
1729 1758 4.889995 AGTGGCTTCTTAATTTAGGCATCC 59.110 41.667 9.87 1.60 44.69 3.51
1749 1778 3.004315 TCCGCTTGTTGAAATCTTGTTCC 59.996 43.478 0.00 0.00 0.00 3.62
1790 1819 0.664166 GCGTCGAAGGGTTTACGTCA 60.664 55.000 0.00 0.00 37.64 4.35
2044 2074 3.701040 ACATGTTCCTGCTTGTTTCAGTT 59.299 39.130 0.00 0.00 0.00 3.16
2045 2075 3.781079 TGTTCCTGCTTGTTTCAGTTG 57.219 42.857 0.00 0.00 0.00 3.16
2046 2076 2.426738 TGTTCCTGCTTGTTTCAGTTGG 59.573 45.455 0.00 0.00 0.00 3.77
2088 2118 6.069684 AGATAATTCATTGCAGCTGCTAAC 57.930 37.500 36.61 18.34 42.66 2.34
2094 2124 5.084818 TCATTGCAGCTGCTAACTAACTA 57.915 39.130 36.61 12.87 42.66 2.24
2132 2162 6.873605 CGTGATGATCCATGCTAGGTAAATAA 59.126 38.462 0.00 0.00 0.00 1.40
2419 2449 6.127869 TGTGGATTGGTATGTTCGTTTATTGG 60.128 38.462 0.00 0.00 0.00 3.16
2423 2453 7.700656 GGATTGGTATGTTCGTTTATTGGAAAG 59.299 37.037 0.00 0.00 0.00 2.62
2424 2454 5.945155 TGGTATGTTCGTTTATTGGAAAGC 58.055 37.500 0.00 0.00 0.00 3.51
2431 2461 7.247728 TGTTCGTTTATTGGAAAGCATACATC 58.752 34.615 0.00 0.00 0.00 3.06
2616 2646 6.038382 GTGCATGATTCAACTGATCAGAGATT 59.962 38.462 29.27 19.60 0.00 2.40
2773 2835 4.097286 ACACCACACATTTAGTCAACAACC 59.903 41.667 0.00 0.00 0.00 3.77
2784 2853 3.970842 AGTCAACAACCTAAAACCCACA 58.029 40.909 0.00 0.00 0.00 4.17
2912 3084 9.772973 TGTGACCTACATATACAACATATTTCC 57.227 33.333 0.00 0.00 33.42 3.13
2913 3085 9.998106 GTGACCTACATATACAACATATTTCCT 57.002 33.333 0.00 0.00 0.00 3.36
2926 3098 9.174166 ACAACATATTTCCTACTTGTGATTACC 57.826 33.333 0.00 0.00 0.00 2.85
2927 3099 9.173021 CAACATATTTCCTACTTGTGATTACCA 57.827 33.333 0.00 0.00 0.00 3.25
2928 3100 8.732746 ACATATTTCCTACTTGTGATTACCAC 57.267 34.615 0.00 0.00 45.88 4.16
2929 3101 7.773690 ACATATTTCCTACTTGTGATTACCACC 59.226 37.037 0.00 0.00 45.09 4.61
2930 3102 5.570205 TTTCCTACTTGTGATTACCACCA 57.430 39.130 0.00 0.00 45.09 4.17
2931 3103 5.772393 TTCCTACTTGTGATTACCACCAT 57.228 39.130 0.00 0.00 45.09 3.55
2932 3104 5.772393 TCCTACTTGTGATTACCACCATT 57.228 39.130 0.00 0.00 45.09 3.16
2933 3105 5.496556 TCCTACTTGTGATTACCACCATTG 58.503 41.667 0.00 0.00 45.09 2.82
2934 3106 5.013704 TCCTACTTGTGATTACCACCATTGT 59.986 40.000 0.00 0.00 45.09 2.71
2935 3107 6.213802 TCCTACTTGTGATTACCACCATTGTA 59.786 38.462 0.00 0.00 45.09 2.41
2936 3108 7.054124 CCTACTTGTGATTACCACCATTGTAT 58.946 38.462 0.00 0.00 45.09 2.29
2937 3109 7.556275 CCTACTTGTGATTACCACCATTGTATT 59.444 37.037 0.00 0.00 45.09 1.89
2938 3110 7.775053 ACTTGTGATTACCACCATTGTATTT 57.225 32.000 0.00 0.00 45.09 1.40
2939 3111 8.189119 ACTTGTGATTACCACCATTGTATTTT 57.811 30.769 0.00 0.00 45.09 1.82
2940 3112 8.087750 ACTTGTGATTACCACCATTGTATTTTG 58.912 33.333 0.00 0.00 45.09 2.44
2941 3113 7.531857 TGTGATTACCACCATTGTATTTTGT 57.468 32.000 0.00 0.00 45.09 2.83
2942 3114 8.637196 TGTGATTACCACCATTGTATTTTGTA 57.363 30.769 0.00 0.00 45.09 2.41
2943 3115 9.078990 TGTGATTACCACCATTGTATTTTGTAA 57.921 29.630 0.00 0.00 45.09 2.41
2944 3116 9.349145 GTGATTACCACCATTGTATTTTGTAAC 57.651 33.333 0.00 0.00 39.86 2.50
2945 3117 8.524487 TGATTACCACCATTGTATTTTGTAACC 58.476 33.333 0.00 0.00 0.00 2.85
3390 3562 3.741476 CTTGCTTGCGGGAGTGGC 61.741 66.667 0.00 0.00 0.00 5.01
3465 3637 2.751166 ACGAAGGTGATCCAAGACAG 57.249 50.000 0.00 0.00 35.89 3.51
3576 3748 1.534163 CACATGCATATTCCAGCCTCG 59.466 52.381 0.00 0.00 0.00 4.63
3625 3797 1.140852 CGATGGATTGGAGCTAACCCA 59.859 52.381 0.00 0.00 0.00 4.51
3633 3805 3.627395 TGGAGCTAACCCATTGTACTG 57.373 47.619 0.00 0.00 0.00 2.74
3638 3810 2.351726 GCTAACCCATTGTACTGCTTCG 59.648 50.000 0.00 0.00 0.00 3.79
3837 5580 6.978080 TCAAAAGGAAGAGTTAAAATGTGCAC 59.022 34.615 10.75 10.75 0.00 4.57
3987 5779 8.519526 TGTTGAAATAACATACCCTGATTTCAC 58.480 33.333 7.62 5.20 42.92 3.18
4116 5917 0.409876 AGTGTCTAGAGGAGTGCCCA 59.590 55.000 0.00 0.00 37.41 5.36
4174 5975 2.237751 GGCGCTGCGTGTATCGATT 61.238 57.895 24.04 0.00 42.86 3.34
4188 5989 1.227350 CGATTGATGCAGAGCCCGA 60.227 57.895 0.00 0.00 0.00 5.14
4232 6035 2.638480 AAAATAGGGCAGCGCAGATA 57.362 45.000 11.47 0.00 0.00 1.98
4362 6965 1.151777 ATCATAACGAACGGCCTGCG 61.152 55.000 0.00 3.98 0.00 5.18
4541 7144 1.463444 CCCGCTCTTTCACTTTAACCG 59.537 52.381 0.00 0.00 0.00 4.44
4552 7155 2.027561 CACTTTAACCGATCTGGACCCA 60.028 50.000 10.05 0.00 42.00 4.51
4553 7156 2.844348 ACTTTAACCGATCTGGACCCAT 59.156 45.455 10.05 0.00 42.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
306 311 2.978018 GCGCTTCCCTCCCAAAACG 61.978 63.158 0.00 0.00 0.00 3.60
357 368 1.006102 CGTCCGTTTCTGACTGCCT 60.006 57.895 0.00 0.00 0.00 4.75
417 433 4.825085 GGACACACTTTTCCTCATAAACCA 59.175 41.667 0.00 0.00 0.00 3.67
424 441 1.124780 TCCGGACACACTTTTCCTCA 58.875 50.000 0.00 0.00 0.00 3.86
436 453 1.520192 CCATTCGATGGTCCGGACA 59.480 57.895 34.40 21.15 45.54 4.02
451 468 0.034863 ACGGTTTTGTATCGGCCCAT 60.035 50.000 0.00 0.00 0.00 4.00
455 472 1.400500 CCAACACGGTTTTGTATCGGC 60.400 52.381 6.31 0.00 0.00 5.54
464 481 0.753479 TGTGCCATCCAACACGGTTT 60.753 50.000 0.00 0.00 39.71 3.27
510 527 6.592870 GCAGACCCTTAAACCATCTATAACT 58.407 40.000 0.00 0.00 0.00 2.24
515 532 2.835764 ACGCAGACCCTTAAACCATCTA 59.164 45.455 0.00 0.00 0.00 1.98
525 542 0.036010 CATCTCCAACGCAGACCCTT 60.036 55.000 0.00 0.00 0.00 3.95
621 638 6.530534 ACGAATAGTAGTTTGTCTTTCCATCG 59.469 38.462 0.00 0.00 0.00 3.84
641 658 3.243975 ACGGGACTGTTCACTTTACGAAT 60.244 43.478 0.00 0.00 0.00 3.34
694 711 8.310382 GCACATCTAGATATGTCCTAAACAGAT 58.690 37.037 12.47 0.00 42.43 2.90
705 722 4.158786 AGCAGGAGCACATCTAGATATGT 58.841 43.478 12.47 3.05 45.49 2.29
724 741 6.114767 TGAGTCATTTAGATGTGCAATAGCA 58.885 36.000 0.00 0.00 42.86 3.49
726 743 8.833493 TGATTGAGTCATTTAGATGTGCAATAG 58.167 33.333 0.00 0.00 33.74 1.73
728 745 7.634671 TGATTGAGTCATTTAGATGTGCAAT 57.365 32.000 0.00 9.14 34.91 3.56
781 798 7.540745 ACGCAACAATTCATGTAGGTATTTTTC 59.459 33.333 0.00 0.00 42.99 2.29
791 808 6.976636 TGATCTTACGCAACAATTCATGTA 57.023 33.333 0.00 0.00 42.99 2.29
794 811 7.087409 TCATTGATCTTACGCAACAATTCAT 57.913 32.000 0.00 0.00 0.00 2.57
795 812 6.493449 TCATTGATCTTACGCAACAATTCA 57.507 33.333 0.00 0.00 0.00 2.57
796 813 6.968904 ACATCATTGATCTTACGCAACAATTC 59.031 34.615 0.00 0.00 0.00 2.17
800 817 5.411053 TCAACATCATTGATCTTACGCAACA 59.589 36.000 0.00 0.00 0.00 3.33
835 852 9.411801 CACGTCTAGATGTGCTATAAATATTGT 57.588 33.333 27.60 0.00 40.88 2.71
921 945 7.977293 TCTCGTTTTGACGGAGATCAATTAATA 59.023 33.333 0.00 0.00 38.37 0.98
1065 1089 2.202676 GCCGAAGAGCAGGAGACG 60.203 66.667 0.00 0.00 0.00 4.18
1067 1091 3.011635 GCAGCCGAAGAGCAGGAGA 62.012 63.158 0.00 0.00 34.23 3.71
1154 1180 4.065088 CCTCCGTCTCAAAATGAGTTTCA 58.935 43.478 7.21 0.00 44.58 2.69
1155 1181 3.120165 GCCTCCGTCTCAAAATGAGTTTC 60.120 47.826 7.21 0.30 44.58 2.78
1156 1182 2.814336 GCCTCCGTCTCAAAATGAGTTT 59.186 45.455 7.21 0.00 44.58 2.66
1159 1185 2.005451 CTGCCTCCGTCTCAAAATGAG 58.995 52.381 0.88 0.88 45.59 2.90
1160 1186 1.347707 ACTGCCTCCGTCTCAAAATGA 59.652 47.619 0.00 0.00 0.00 2.57
1161 1187 1.813513 ACTGCCTCCGTCTCAAAATG 58.186 50.000 0.00 0.00 0.00 2.32
1206 1234 2.713967 GCCCGGTGCAAGCAATCAT 61.714 57.895 9.72 0.00 40.77 2.45
1207 1235 3.372730 GCCCGGTGCAAGCAATCA 61.373 61.111 9.72 0.00 40.77 2.57
1364 1393 0.466189 AAGTTCCCGCATGCCCTATG 60.466 55.000 13.15 0.00 39.88 2.23
1729 1758 4.222114 GAGGAACAAGATTTCAACAAGCG 58.778 43.478 0.00 0.00 0.00 4.68
1790 1819 1.142465 CCCTCTTGCTGCTACATCCAT 59.858 52.381 0.00 0.00 0.00 3.41
2132 2162 3.504906 CCCAATATCATGCAAAGCGAGAT 59.495 43.478 0.00 0.00 0.00 2.75
2340 2370 2.224499 TGCCAGCACAGTAACTCATGAA 60.224 45.455 0.00 0.00 0.00 2.57
2423 2453 8.693542 AAGCACAAATTTCTAAAGATGTATGC 57.306 30.769 0.00 0.00 0.00 3.14
2431 2461 6.149633 AGCGGTTAAGCACAAATTTCTAAAG 58.850 36.000 5.38 0.00 40.15 1.85
2616 2646 3.840124 TCTATGTAGAGGACGAGAGCA 57.160 47.619 0.00 0.00 0.00 4.26
2900 3072 9.174166 GGTAATCACAAGTAGGAAATATGTTGT 57.826 33.333 0.00 0.00 0.00 3.32
2901 3073 9.173021 TGGTAATCACAAGTAGGAAATATGTTG 57.827 33.333 0.00 0.00 0.00 3.33
2902 3074 9.174166 GTGGTAATCACAAGTAGGAAATATGTT 57.826 33.333 0.00 0.00 45.39 2.71
2903 3075 8.732746 GTGGTAATCACAAGTAGGAAATATGT 57.267 34.615 0.00 0.00 45.39 2.29
2918 3090 9.349145 GTTACAAAATACAATGGTGGTAATCAC 57.651 33.333 0.00 0.00 45.34 3.06
2919 3091 8.524487 GGTTACAAAATACAATGGTGGTAATCA 58.476 33.333 0.00 0.00 0.00 2.57
2920 3092 7.698970 CGGTTACAAAATACAATGGTGGTAATC 59.301 37.037 0.00 0.00 0.00 1.75
2921 3093 7.363094 CCGGTTACAAAATACAATGGTGGTAAT 60.363 37.037 0.00 0.00 0.00 1.89
2922 3094 6.072064 CCGGTTACAAAATACAATGGTGGTAA 60.072 38.462 0.00 0.00 0.00 2.85
2923 3095 5.415077 CCGGTTACAAAATACAATGGTGGTA 59.585 40.000 0.00 0.00 0.00 3.25
2924 3096 4.218852 CCGGTTACAAAATACAATGGTGGT 59.781 41.667 0.00 0.00 0.00 4.16
2925 3097 4.381079 CCCGGTTACAAAATACAATGGTGG 60.381 45.833 0.00 0.00 0.00 4.61
2926 3098 4.739195 CCCGGTTACAAAATACAATGGTG 58.261 43.478 0.00 0.00 0.00 4.17
2927 3099 3.193903 GCCCGGTTACAAAATACAATGGT 59.806 43.478 0.00 0.00 0.00 3.55
2928 3100 3.429684 GGCCCGGTTACAAAATACAATGG 60.430 47.826 0.00 0.00 0.00 3.16
2929 3101 3.193691 TGGCCCGGTTACAAAATACAATG 59.806 43.478 0.00 0.00 0.00 2.82
2930 3102 3.432378 TGGCCCGGTTACAAAATACAAT 58.568 40.909 0.00 0.00 0.00 2.71
2931 3103 2.872732 TGGCCCGGTTACAAAATACAA 58.127 42.857 0.00 0.00 0.00 2.41
2932 3104 2.581216 TGGCCCGGTTACAAAATACA 57.419 45.000 0.00 0.00 0.00 2.29
2933 3105 2.821378 ACTTGGCCCGGTTACAAAATAC 59.179 45.455 0.00 0.00 0.00 1.89
2934 3106 3.083293 GACTTGGCCCGGTTACAAAATA 58.917 45.455 0.00 0.00 0.00 1.40
2935 3107 1.890489 GACTTGGCCCGGTTACAAAAT 59.110 47.619 0.00 0.00 0.00 1.82
2936 3108 1.320507 GACTTGGCCCGGTTACAAAA 58.679 50.000 0.00 0.00 0.00 2.44
2937 3109 0.183014 TGACTTGGCCCGGTTACAAA 59.817 50.000 0.00 0.00 0.00 2.83
2938 3110 0.402504 ATGACTTGGCCCGGTTACAA 59.597 50.000 0.00 1.32 0.00 2.41
2939 3111 0.402504 AATGACTTGGCCCGGTTACA 59.597 50.000 0.00 0.00 0.00 2.41
2940 3112 2.406596 TAATGACTTGGCCCGGTTAC 57.593 50.000 0.00 0.00 0.00 2.50
2941 3113 2.572556 TCTTAATGACTTGGCCCGGTTA 59.427 45.455 0.00 0.00 0.00 2.85
2942 3114 1.353022 TCTTAATGACTTGGCCCGGTT 59.647 47.619 0.00 0.00 0.00 4.44
2943 3115 0.988832 TCTTAATGACTTGGCCCGGT 59.011 50.000 0.00 0.00 0.00 5.28
2944 3116 1.949525 CATCTTAATGACTTGGCCCGG 59.050 52.381 0.00 0.00 34.61 5.73
2945 3117 1.949525 CCATCTTAATGACTTGGCCCG 59.050 52.381 0.00 0.00 34.61 6.13
3390 3562 3.066064 TGGACCGACAAAACATTCAACAG 59.934 43.478 0.00 0.00 0.00 3.16
3576 3748 5.800438 GTCTCACCAAAACAAGTCAACTTTC 59.200 40.000 0.00 0.00 33.11 2.62
3625 3797 3.368531 GGACTCTTCCGAAGCAGTACAAT 60.369 47.826 13.75 0.00 29.98 2.71
3633 3805 0.892063 AGTCTGGACTCTTCCGAAGC 59.108 55.000 3.00 0.00 46.37 3.86
3638 3810 6.969993 ATCATAAGTAGTCTGGACTCTTCC 57.030 41.667 6.52 0.00 42.54 3.46
3973 5765 4.014406 GTTTTCGGGTGAAATCAGGGTAT 58.986 43.478 0.00 0.00 43.32 2.73
3987 5779 7.553881 AACACATAGATCTAATGTTTTCGGG 57.446 36.000 21.57 10.67 29.53 5.14
4068 5863 3.548415 CCGCAAATGCAAGCAATTTGTTT 60.548 39.130 20.36 7.78 42.21 2.83
4174 5975 1.044790 TCATCTCGGGCTCTGCATCA 61.045 55.000 0.00 0.00 0.00 3.07
4206 6009 2.094752 GCGCTGCCCTATTTTTCTTTCA 60.095 45.455 0.00 0.00 0.00 2.69
4232 6035 5.010820 GGGTATTTCCGCTTAGAGTAGTCAT 59.989 44.000 0.00 0.00 37.00 3.06
4301 6890 3.154710 TGTAATGTCGGCGGATAGAGAT 58.845 45.455 7.21 0.00 0.00 2.75
4342 6945 1.014352 GCAGGCCGTTCGTTATGATT 58.986 50.000 0.00 0.00 0.00 2.57
4343 6946 1.151777 CGCAGGCCGTTCGTTATGAT 61.152 55.000 0.00 0.00 0.00 2.45
4344 6947 1.807981 CGCAGGCCGTTCGTTATGA 60.808 57.895 0.00 0.00 0.00 2.15
4362 6965 0.529992 GATAGCCTACGTGTGTGCCC 60.530 60.000 0.00 0.00 0.00 5.36
4431 7034 1.067495 GCCGTCTGAAGTAGTGAAGCT 60.067 52.381 0.00 0.00 0.00 3.74
4435 7038 1.174783 GAGGCCGTCTGAAGTAGTGA 58.825 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.