Multiple sequence alignment - TraesCS2D01G446500

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 TraesCS2D01G446500 chr2D 100.000 3394 0 0 1 3394 556641287 556644680 0.000000e+00 6268.0
1 TraesCS2D01G446500 chr2D 91.604 798 46 10 1111 1904 556365491 556366271 0.000000e+00 1083.0
2 TraesCS2D01G446500 chr2D 81.931 1212 155 34 1111 2304 556350547 556351712 0.000000e+00 966.0
3 TraesCS2D01G446500 chr2D 95.270 592 28 0 2802 3393 556676156 556676747 0.000000e+00 939.0
4 TraesCS2D01G446500 chr2D 95.270 592 26 2 2802 3393 383221410 383220821 0.000000e+00 937.0
5 TraesCS2D01G446500 chr2D 86.463 820 66 25 1111 1904 556619139 556619939 0.000000e+00 857.0
6 TraesCS2D01G446500 chr2D 86.403 809 68 27 1111 1902 556408039 556408822 0.000000e+00 846.0
7 TraesCS2D01G446500 chr2D 79.172 845 117 24 1488 2303 556339276 556340090 6.450000e-147 531.0
8 TraesCS2D01G446500 chr2D 76.380 326 43 17 591 906 556317940 556318241 9.820000e-31 145.0
9 TraesCS2D01G446500 chr2D 78.333 180 21 11 548 720 556265746 556265914 2.150000e-17 100.0
10 TraesCS2D01G446500 chr2D 93.939 66 4 0 2358 2423 556351714 556351779 2.150000e-17 100.0
11 TraesCS2D01G446500 chr2D 93.878 49 2 1 2520 2568 556643707 556643754 4.700000e-09 73.1
12 TraesCS2D01G446500 chr2D 93.878 49 2 1 2421 2468 556643806 556643854 4.700000e-09 73.1
13 TraesCS2D01G446500 chr2D 78.788 99 18 3 64 161 394558135 394558231 2.830000e-06 63.9
14 TraesCS2D01G446500 chr2B 93.769 2006 96 9 483 2468 663898120 663900116 0.000000e+00 2985.0
15 TraesCS2D01G446500 chr2B 82.459 1220 139 36 1111 2303 663828972 663830143 0.000000e+00 998.0
16 TraesCS2D01G446500 chr2B 82.540 1197 140 38 1111 2303 663838018 663839149 0.000000e+00 989.0
17 TraesCS2D01G446500 chr2B 95.270 592 28 0 2802 3393 139229943 139229352 0.000000e+00 939.0
18 TraesCS2D01G446500 chr2B 84.720 805 76 34 1111 1904 663886031 663886799 0.000000e+00 761.0
19 TraesCS2D01G446500 chr2B 89.347 291 27 2 2514 2800 663900062 663900352 2.490000e-96 363.0
20 TraesCS2D01G446500 chr2B 88.070 285 17 12 167 438 663897738 663898018 4.220000e-84 322.0
21 TraesCS2D01G446500 chr2B 87.421 159 14 3 747 905 663837643 663837795 9.680000e-41 178.0
22 TraesCS2D01G446500 chr2B 93.902 82 5 0 1717 1798 53059466 53059385 1.280000e-24 124.0
23 TraesCS2D01G446500 chr2B 92.857 70 5 0 2354 2423 663180041 663179972 5.990000e-18 102.0
24 TraesCS2D01G446500 chr2A 89.857 2021 149 25 464 2464 696314967 696316951 0.000000e+00 2545.0
25 TraesCS2D01G446500 chr2A 89.994 1569 103 25 923 2468 696825069 696826606 0.000000e+00 1978.0
26 TraesCS2D01G446500 chr2A 84.254 1213 142 18 1111 2303 695999116 696000299 0.000000e+00 1136.0
27 TraesCS2D01G446500 chr2A 83.609 1208 129 41 1111 2303 696040431 696041584 0.000000e+00 1070.0
28 TraesCS2D01G446500 chr2A 87.053 811 66 26 1111 1904 696219212 696220000 0.000000e+00 880.0
29 TraesCS2D01G446500 chr2A 91.858 479 23 9 1 467 696314442 696314916 0.000000e+00 654.0
30 TraesCS2D01G446500 chr2A 90.244 287 22 4 2511 2795 696316899 696317181 1.490000e-98 370.0
31 TraesCS2D01G446500 chr2A 85.517 290 34 7 2514 2800 696826552 696826836 2.560000e-76 296.0
32 TraesCS2D01G446500 chr2A 94.286 70 4 0 2354 2423 696000298 696000367 1.290000e-19 108.0
33 TraesCS2D01G446500 chr2A 94.203 69 4 0 2355 2423 696001276 696001344 4.630000e-19 106.0
34 TraesCS2D01G446500 chr2A 80.000 140 12 11 586 720 695998619 695998747 4.660000e-14 89.8
35 TraesCS2D01G446500 chr2A 100.000 33 0 0 694 726 696040072 696040104 1.020000e-05 62.1
36 TraesCS2D01G446500 chr7D 95.608 592 25 1 2802 3393 504777343 504776753 0.000000e+00 948.0
37 TraesCS2D01G446500 chr7D 95.101 592 27 2 2802 3393 504798490 504797901 0.000000e+00 931.0
38 TraesCS2D01G446500 chr5D 95.439 592 27 0 2802 3393 270472091 270472682 0.000000e+00 944.0
39 TraesCS2D01G446500 chr5D 94.807 597 27 3 2799 3394 51835932 51835339 0.000000e+00 928.0
40 TraesCS2D01G446500 chr3D 95.439 592 26 1 2802 3393 488393871 488394461 0.000000e+00 942.0
41 TraesCS2D01G446500 chr1D 95.101 592 29 0 2802 3393 299614101 299614692 0.000000e+00 933.0
42 TraesCS2D01G446500 chr6D 83.636 165 26 1 2 165 9967068 9967232 1.630000e-33 154.0


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 TraesCS2D01G446500 chr2D 556641287 556644680 3393 False 2138.066667 6268 95.918667 1 3394 3 chr2D.!!$F10 3393
1 TraesCS2D01G446500 chr2D 556365491 556366271 780 False 1083.000000 1083 91.604000 1111 1904 1 chr2D.!!$F5 793
2 TraesCS2D01G446500 chr2D 556676156 556676747 591 False 939.000000 939 95.270000 2802 3393 1 chr2D.!!$F8 591
3 TraesCS2D01G446500 chr2D 383220821 383221410 589 True 937.000000 937 95.270000 2802 3393 1 chr2D.!!$R1 591
4 TraesCS2D01G446500 chr2D 556619139 556619939 800 False 857.000000 857 86.463000 1111 1904 1 chr2D.!!$F7 793
5 TraesCS2D01G446500 chr2D 556408039 556408822 783 False 846.000000 846 86.403000 1111 1902 1 chr2D.!!$F6 791
6 TraesCS2D01G446500 chr2D 556350547 556351779 1232 False 533.000000 966 87.935000 1111 2423 2 chr2D.!!$F9 1312
7 TraesCS2D01G446500 chr2D 556339276 556340090 814 False 531.000000 531 79.172000 1488 2303 1 chr2D.!!$F4 815
8 TraesCS2D01G446500 chr2B 663897738 663900352 2614 False 1223.333333 2985 90.395333 167 2800 3 chr2B.!!$F4 2633
9 TraesCS2D01G446500 chr2B 663828972 663830143 1171 False 998.000000 998 82.459000 1111 2303 1 chr2B.!!$F1 1192
10 TraesCS2D01G446500 chr2B 139229352 139229943 591 True 939.000000 939 95.270000 2802 3393 1 chr2B.!!$R2 591
11 TraesCS2D01G446500 chr2B 663886031 663886799 768 False 761.000000 761 84.720000 1111 1904 1 chr2B.!!$F2 793
12 TraesCS2D01G446500 chr2B 663837643 663839149 1506 False 583.500000 989 84.980500 747 2303 2 chr2B.!!$F3 1556
13 TraesCS2D01G446500 chr2A 696314442 696317181 2739 False 1189.666667 2545 90.653000 1 2795 3 chr2A.!!$F4 2794
14 TraesCS2D01G446500 chr2A 696825069 696826836 1767 False 1137.000000 1978 87.755500 923 2800 2 chr2A.!!$F5 1877
15 TraesCS2D01G446500 chr2A 696219212 696220000 788 False 880.000000 880 87.053000 1111 1904 1 chr2A.!!$F1 793
16 TraesCS2D01G446500 chr2A 696040072 696041584 1512 False 566.050000 1070 91.804500 694 2303 2 chr2A.!!$F3 1609
17 TraesCS2D01G446500 chr2A 695998619 696001344 2725 False 359.950000 1136 88.185750 586 2423 4 chr2A.!!$F2 1837
18 TraesCS2D01G446500 chr7D 504776753 504777343 590 True 948.000000 948 95.608000 2802 3393 1 chr7D.!!$R1 591
19 TraesCS2D01G446500 chr7D 504797901 504798490 589 True 931.000000 931 95.101000 2802 3393 1 chr7D.!!$R2 591
20 TraesCS2D01G446500 chr5D 270472091 270472682 591 False 944.000000 944 95.439000 2802 3393 1 chr5D.!!$F1 591
21 TraesCS2D01G446500 chr5D 51835339 51835932 593 True 928.000000 928 94.807000 2799 3394 1 chr5D.!!$R1 595
22 TraesCS2D01G446500 chr3D 488393871 488394461 590 False 942.000000 942 95.439000 2802 3393 1 chr3D.!!$F1 591
23 TraesCS2D01G446500 chr1D 299614101 299614692 591 False 933.000000 933 95.101000 2802 3393 1 chr1D.!!$F1 591

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
98 99 0.104120 GGACCAACTGTTGCCCAAAC 59.896 55.0 14.94 2.57 39.41 2.93 F
1432 1675 0.034896 CTACTCCACACACCACCACC 59.965 60.0 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2376 0.102844 TGGTTCAGCTGTTGCAAAGC 59.897 50.0 14.67 19.56 42.74 3.51 R
3300 4158 0.105453 GGCCCAGAGATACCTCTCCA 60.105 60.0 0.00 0.00 46.38 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
37 38 3.370978 CACGTGGCCAGTTTTATACTCAG 59.629 47.826 5.11 0.00 33.85 3.35
40 41 4.271049 CGTGGCCAGTTTTATACTCAGATG 59.729 45.833 5.11 0.00 33.85 2.90
61 62 9.439500 CAGATGTGGTTTTGGATGAAATTTATT 57.561 29.630 0.00 0.00 0.00 1.40
63 64 7.881643 TGTGGTTTTGGATGAAATTTATTCG 57.118 32.000 0.00 0.00 0.00 3.34
64 65 6.870965 TGTGGTTTTGGATGAAATTTATTCGG 59.129 34.615 0.00 0.00 0.00 4.30
65 66 6.871492 GTGGTTTTGGATGAAATTTATTCGGT 59.129 34.615 0.00 0.00 0.00 4.69
68 69 8.227119 GGTTTTGGATGAAATTTATTCGGTTTG 58.773 33.333 0.00 0.00 0.00 2.93
74 75 7.148069 GGATGAAATTTATTCGGTTTGGAGTCT 60.148 37.037 0.00 0.00 0.00 3.24
86 87 1.056660 TGGAGTCTTGAGGGACCAAC 58.943 55.000 0.00 0.00 36.95 3.77
90 91 2.104963 GAGTCTTGAGGGACCAACTGTT 59.895 50.000 0.00 0.00 36.95 3.16
98 99 0.104120 GGACCAACTGTTGCCCAAAC 59.896 55.000 14.94 2.57 39.41 2.93
106 107 2.906691 TGTTGCCCAAACATTCTTGG 57.093 45.000 0.00 0.00 43.96 3.61
114 115 2.490718 CCAAACATTCTTGGGGGACTCA 60.491 50.000 0.00 0.00 41.96 3.41
131 132 5.341617 GGACTCAATGTAGACTTTCGGTAG 58.658 45.833 0.00 0.00 0.00 3.18
154 155 6.784031 AGACTTGAGGGATGAAAAACATACT 58.216 36.000 0.00 0.00 39.63 2.12
401 420 0.179056 GCCGCCAGCAGGATTAGTTA 60.179 55.000 0.00 0.00 42.97 2.24
522 643 2.482142 CCTTTGACGATAGCTCCAGGTC 60.482 54.545 0.00 0.00 42.67 3.85
624 745 8.935614 ATTACAGGTGCTACACTACATAGATA 57.064 34.615 0.00 0.00 34.40 1.98
641 762 8.402798 ACATAGATAGTCCTCATAGACAAGTG 57.597 38.462 0.00 0.00 39.34 3.16
674 795 1.965930 CGCAGCCTGCCACTTGTTA 60.966 57.895 11.83 0.00 41.12 2.41
729 854 0.808125 GCGACATGCATACACCCAAA 59.192 50.000 0.00 0.00 45.45 3.28
960 1133 3.991051 CCGTCTGCACCACGACCT 61.991 66.667 13.80 0.00 39.75 3.85
1069 1272 2.029221 GCCCGATCGAACCTAGCC 59.971 66.667 18.66 0.00 0.00 3.93
1072 1275 0.464452 CCCGATCGAACCTAGCCTTT 59.536 55.000 18.66 0.00 0.00 3.11
1303 1517 0.472352 TCCGGTGGACCAACTACCTT 60.472 55.000 8.18 0.00 46.07 3.50
1432 1675 0.034896 CTACTCCACACACCACCACC 59.965 60.000 0.00 0.00 0.00 4.61
1465 1735 3.490759 CCGCCATGCACTGTCGTC 61.491 66.667 0.00 0.00 0.00 4.20
1466 1736 2.433145 CGCCATGCACTGTCGTCT 60.433 61.111 0.00 0.00 0.00 4.18
1467 1737 2.733671 CGCCATGCACTGTCGTCTG 61.734 63.158 0.00 0.00 0.00 3.51
1468 1738 1.669115 GCCATGCACTGTCGTCTGT 60.669 57.895 0.00 0.00 0.00 3.41
1469 1739 1.630244 GCCATGCACTGTCGTCTGTC 61.630 60.000 0.00 0.00 0.00 3.51
1513 1808 8.445275 TTTTGCATAGTTGTTAGTCTTGAAGA 57.555 30.769 0.00 0.00 0.00 2.87
1817 2135 2.583520 CAGCAGCTCCTCCAGACC 59.416 66.667 0.00 0.00 0.00 3.85
1818 2136 2.121385 AGCAGCTCCTCCAGACCA 59.879 61.111 0.00 0.00 0.00 4.02
1819 2137 1.306825 AGCAGCTCCTCCAGACCAT 60.307 57.895 0.00 0.00 0.00 3.55
1936 2263 2.976185 TCCAGGACCAACTGAACATGTA 59.024 45.455 0.00 0.00 40.97 2.29
1937 2264 3.587061 TCCAGGACCAACTGAACATGTAT 59.413 43.478 0.00 0.00 40.97 2.29
1994 2321 3.555586 GCAACACCTCCAATTTTGCAGAT 60.556 43.478 4.33 0.00 41.77 2.90
2047 2376 0.534412 ATGTCTCCTGGAACGAGCTG 59.466 55.000 0.00 0.00 0.00 4.24
2055 2384 1.100463 TGGAACGAGCTGCTTTGCAA 61.100 50.000 2.53 0.00 38.41 4.08
2164 2517 2.746277 GTTCGCCGGCTTGATGGT 60.746 61.111 26.68 0.00 0.00 3.55
2177 2530 0.323633 TGATGGTGCCCATGGAACTG 60.324 55.000 15.22 0.00 45.26 3.16
2201 2557 3.243724 ACTACCCAATCTATGCTCCCTC 58.756 50.000 0.00 0.00 0.00 4.30
2323 2682 9.357652 TGTACATAACCTATAACGTTTGAACTC 57.642 33.333 5.91 0.00 0.00 3.01
2325 2684 6.532657 ACATAACCTATAACGTTTGAACTCCG 59.467 38.462 5.91 0.00 0.00 4.63
2331 2690 1.305201 ACGTTTGAACTCCGTGCAAT 58.695 45.000 0.00 0.00 30.44 3.56
2408 2767 9.878667 TGAGATGATAAAACATGCATTGATTTT 57.121 25.926 14.33 14.33 33.04 1.82
2423 2783 9.755804 TGCATTGATTTTTCTGTGTGTTTATTA 57.244 25.926 0.00 0.00 0.00 0.98
2428 2788 9.755804 TGATTTTTCTGTGTGTTTATTATTGCA 57.244 25.926 0.00 0.00 0.00 4.08
2461 2821 8.918202 TGATTTTTGTCACTATAGTTGAAGGT 57.082 30.769 1.56 0.00 0.00 3.50
2462 2822 9.349713 TGATTTTTGTCACTATAGTTGAAGGTT 57.650 29.630 1.56 0.00 0.00 3.50
2463 2823 9.612620 GATTTTTGTCACTATAGTTGAAGGTTG 57.387 33.333 1.56 0.00 0.00 3.77
2464 2824 6.554334 TTTGTCACTATAGTTGAAGGTTGC 57.446 37.500 1.56 0.00 0.00 4.17
2465 2825 5.222079 TGTCACTATAGTTGAAGGTTGCA 57.778 39.130 1.56 0.00 0.00 4.08
2466 2826 5.616270 TGTCACTATAGTTGAAGGTTGCAA 58.384 37.500 1.56 0.00 0.00 4.08
2467 2827 6.237901 TGTCACTATAGTTGAAGGTTGCAAT 58.762 36.000 0.59 0.00 0.00 3.56
2468 2828 7.390823 TGTCACTATAGTTGAAGGTTGCAATA 58.609 34.615 0.59 0.00 0.00 1.90
2469 2829 7.549134 TGTCACTATAGTTGAAGGTTGCAATAG 59.451 37.037 0.59 0.00 0.00 1.73
2470 2830 7.764443 GTCACTATAGTTGAAGGTTGCAATAGA 59.236 37.037 0.59 0.00 0.00 1.98
2471 2831 8.486210 TCACTATAGTTGAAGGTTGCAATAGAT 58.514 33.333 0.59 0.00 0.00 1.98
2472 2832 9.113838 CACTATAGTTGAAGGTTGCAATAGATT 57.886 33.333 0.59 0.00 0.00 2.40
2473 2833 9.686683 ACTATAGTTGAAGGTTGCAATAGATTT 57.313 29.630 0.59 0.00 0.00 2.17
2474 2834 9.941664 CTATAGTTGAAGGTTGCAATAGATTTG 57.058 33.333 0.59 0.00 0.00 2.32
2475 2835 6.899393 AGTTGAAGGTTGCAATAGATTTGA 57.101 33.333 0.59 0.00 0.00 2.69
2476 2836 7.472334 AGTTGAAGGTTGCAATAGATTTGAT 57.528 32.000 0.59 0.00 0.00 2.57
2477 2837 7.899973 AGTTGAAGGTTGCAATAGATTTGATT 58.100 30.769 0.59 0.00 0.00 2.57
2478 2838 8.370182 AGTTGAAGGTTGCAATAGATTTGATTT 58.630 29.630 0.59 0.00 0.00 2.17
2479 2839 8.992073 GTTGAAGGTTGCAATAGATTTGATTTT 58.008 29.630 0.59 0.00 0.00 1.82
2480 2840 8.537049 TGAAGGTTGCAATAGATTTGATTTTG 57.463 30.769 0.59 0.00 0.00 2.44
2481 2841 8.149647 TGAAGGTTGCAATAGATTTGATTTTGT 58.850 29.630 0.59 0.00 0.00 2.83
2482 2842 8.538409 AAGGTTGCAATAGATTTGATTTTGTC 57.462 30.769 0.59 0.00 0.00 3.18
2483 2843 7.669427 AGGTTGCAATAGATTTGATTTTGTCA 58.331 30.769 0.59 0.00 34.25 3.58
2484 2844 7.599998 AGGTTGCAATAGATTTGATTTTGTCAC 59.400 33.333 0.59 0.00 36.32 3.67
2485 2845 7.599998 GGTTGCAATAGATTTGATTTTGTCACT 59.400 33.333 0.59 0.00 36.32 3.41
2486 2846 9.624697 GTTGCAATAGATTTGATTTTGTCACTA 57.375 29.630 0.59 0.00 36.32 2.74
2645 3011 5.995565 TCAAAAAGGAGGATTACTCTCGA 57.004 39.130 0.00 0.00 45.83 4.04
2655 3021 6.436738 AGGATTACTCTCGACCTCTACATA 57.563 41.667 0.00 0.00 0.00 2.29
2658 3024 7.778853 AGGATTACTCTCGACCTCTACATAAAA 59.221 37.037 0.00 0.00 0.00 1.52
2683 3049 5.978919 CGATGCACATAGCCAAACAATTAAT 59.021 36.000 0.00 0.00 44.83 1.40
2795 3161 3.749609 GCTTTATCACAGTTACCACGGTT 59.250 43.478 0.00 0.00 0.00 4.44
2942 3439 9.114952 TGAATACATAGACAAAACAAAGTGTCA 57.885 29.630 6.57 0.00 45.40 3.58
2957 3454 6.381420 ACAAAGTGTCACTAGTATGCCTCTAT 59.619 38.462 5.77 0.00 0.00 1.98
3042 3541 4.753516 TGAACGGGATCACATCATTAGT 57.246 40.909 0.00 0.00 0.00 2.24
3144 3643 6.850752 TGACTTATACATGTTCCTCAGACA 57.149 37.500 2.30 0.00 0.00 3.41
3244 3743 2.020720 AGATGCTCTACAGGTGTCTCG 58.979 52.381 0.00 0.00 0.00 4.04
3269 4127 3.767131 AGGTATTTGTTGGGTTGGCATAC 59.233 43.478 0.00 0.00 0.00 2.39
3300 4158 3.551846 AGGATTTGTCACTCCGTGTTTT 58.448 40.909 0.00 0.00 36.62 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.857052 TCTGAGTATAAAACTGGCCACG 58.143 45.455 0.00 0.00 39.07 4.94
37 38 8.594687 CGAATAAATTTCATCCAAAACCACATC 58.405 33.333 0.00 0.00 0.00 3.06
40 41 6.871492 ACCGAATAAATTTCATCCAAAACCAC 59.129 34.615 0.00 0.00 0.00 4.16
61 62 0.685097 CCCTCAAGACTCCAAACCGA 59.315 55.000 0.00 0.00 0.00 4.69
63 64 1.271434 GGTCCCTCAAGACTCCAAACC 60.271 57.143 0.00 0.00 36.95 3.27
64 65 1.420138 TGGTCCCTCAAGACTCCAAAC 59.580 52.381 0.00 0.00 36.95 2.93
65 66 1.814429 TGGTCCCTCAAGACTCCAAA 58.186 50.000 0.00 0.00 36.95 3.28
68 69 1.002544 CAGTTGGTCCCTCAAGACTCC 59.997 57.143 0.00 0.00 36.95 3.85
74 75 0.467290 GGCAACAGTTGGTCCCTCAA 60.467 55.000 15.28 0.00 0.00 3.02
98 99 3.091633 ACATTGAGTCCCCCAAGAATG 57.908 47.619 0.00 0.00 0.00 2.67
106 107 3.522553 CGAAAGTCTACATTGAGTCCCC 58.477 50.000 0.00 0.00 0.00 4.81
114 115 6.350277 CCTCAAGTCTACCGAAAGTCTACATT 60.350 42.308 0.00 0.00 0.00 2.71
131 132 7.454260 AAGTATGTTTTTCATCCCTCAAGTC 57.546 36.000 0.00 0.00 37.91 3.01
401 420 7.185318 TGAGACACTACTACTAGCTACTCTT 57.815 40.000 0.00 0.00 0.00 2.85
433 456 5.294356 ACTCATGTCTGCGTTACTTGTTTA 58.706 37.500 0.00 0.00 0.00 2.01
474 551 1.112916 TTCCGAGTGCTGTCACCTGA 61.113 55.000 0.00 0.00 44.16 3.86
522 643 1.093972 TGCCACGGTAGAATGCAATG 58.906 50.000 0.00 0.00 0.00 2.82
624 745 4.029520 AGATGCACTTGTCTATGAGGACT 58.970 43.478 0.00 0.00 37.16 3.85
641 762 2.863137 GGCTGCGCTATATAGAAGATGC 59.137 50.000 14.16 12.22 0.00 3.91
729 854 0.884704 GCACTTCACACACGGTCCAT 60.885 55.000 0.00 0.00 0.00 3.41
757 882 5.946972 CCACGTAAGACCAGATATATCCTCT 59.053 44.000 9.18 4.53 43.62 3.69
960 1133 4.827835 GGGCTGCTGGTATATATAGATCGA 59.172 45.833 0.00 0.00 0.00 3.59
1069 1272 2.700722 GGGACCTCCTCTGCTAAAAG 57.299 55.000 0.00 0.00 35.95 2.27
1432 1675 2.870372 GGCTAAGCTGTTGTGCGG 59.130 61.111 0.00 0.00 38.13 5.69
1463 1733 4.527564 CAACGGTGAAGAAATTGACAGAC 58.472 43.478 0.00 0.00 0.00 3.51
1464 1734 3.563808 CCAACGGTGAAGAAATTGACAGA 59.436 43.478 0.00 0.00 0.00 3.41
1465 1735 3.853307 GCCAACGGTGAAGAAATTGACAG 60.853 47.826 0.00 0.00 0.00 3.51
1466 1736 2.034053 GCCAACGGTGAAGAAATTGACA 59.966 45.455 0.00 0.00 0.00 3.58
1467 1737 2.293399 AGCCAACGGTGAAGAAATTGAC 59.707 45.455 0.00 0.00 0.00 3.18
1468 1738 2.582052 AGCCAACGGTGAAGAAATTGA 58.418 42.857 0.00 0.00 0.00 2.57
1469 1739 3.369546 AAGCCAACGGTGAAGAAATTG 57.630 42.857 0.00 0.00 0.00 2.32
1513 1808 4.492494 TTATCCATGCATGTCAGTGTCT 57.508 40.909 24.58 4.87 0.00 3.41
1817 2135 1.787847 GTCGTTGTTGGAGCCGATG 59.212 57.895 0.00 0.00 0.00 3.84
1818 2136 1.736645 CGTCGTTGTTGGAGCCGAT 60.737 57.895 0.00 0.00 0.00 4.18
1819 2137 2.355363 CGTCGTTGTTGGAGCCGA 60.355 61.111 0.00 0.00 0.00 5.54
1936 2263 1.033746 CATGCAGTTCGCCCCAGAAT 61.034 55.000 0.00 0.00 41.33 2.40
1937 2264 1.675310 CATGCAGTTCGCCCCAGAA 60.675 57.895 0.00 0.00 41.33 3.02
1994 2321 1.595109 CTGCTGCACCACGTCTTGA 60.595 57.895 0.00 0.00 0.00 3.02
2047 2376 0.102844 TGGTTCAGCTGTTGCAAAGC 59.897 50.000 14.67 19.56 42.74 3.51
2164 2517 0.403655 TAGTTGCAGTTCCATGGGCA 59.596 50.000 13.02 10.79 0.00 5.36
2177 2530 3.142174 GGAGCATAGATTGGGTAGTTGC 58.858 50.000 0.00 0.00 0.00 4.17
2201 2557 2.568696 TCCAGAAAGAATCGCTCTCG 57.431 50.000 0.00 0.00 31.02 4.04
2323 2682 2.535485 TACCAGGCCTGATTGCACGG 62.535 60.000 34.91 17.17 0.00 4.94
2325 2684 0.322456 TGTACCAGGCCTGATTGCAC 60.322 55.000 34.91 21.41 0.00 4.57
2331 2690 0.909133 TCTGCATGTACCAGGCCTGA 60.909 55.000 34.91 14.91 40.65 3.86
2435 2795 9.520515 ACCTTCAACTATAGTGACAAAAATCAT 57.479 29.630 6.06 0.00 0.00 2.45
2436 2796 8.918202 ACCTTCAACTATAGTGACAAAAATCA 57.082 30.769 6.06 0.00 0.00 2.57
2437 2797 9.612620 CAACCTTCAACTATAGTGACAAAAATC 57.387 33.333 6.06 0.00 0.00 2.17
2438 2798 8.082242 GCAACCTTCAACTATAGTGACAAAAAT 58.918 33.333 6.06 0.00 0.00 1.82
2439 2799 7.067615 TGCAACCTTCAACTATAGTGACAAAAA 59.932 33.333 6.06 0.00 0.00 1.94
2440 2800 6.544197 TGCAACCTTCAACTATAGTGACAAAA 59.456 34.615 6.06 0.00 0.00 2.44
2441 2801 6.058833 TGCAACCTTCAACTATAGTGACAAA 58.941 36.000 6.06 0.00 0.00 2.83
2442 2802 5.616270 TGCAACCTTCAACTATAGTGACAA 58.384 37.500 6.06 0.00 0.00 3.18
2443 2803 5.222079 TGCAACCTTCAACTATAGTGACA 57.778 39.130 6.06 0.00 0.00 3.58
2444 2804 6.743575 ATTGCAACCTTCAACTATAGTGAC 57.256 37.500 6.06 0.00 0.00 3.67
2445 2805 7.847096 TCTATTGCAACCTTCAACTATAGTGA 58.153 34.615 6.06 3.68 0.00 3.41
2446 2806 8.668510 ATCTATTGCAACCTTCAACTATAGTG 57.331 34.615 6.06 1.22 0.00 2.74
2447 2807 9.686683 AAATCTATTGCAACCTTCAACTATAGT 57.313 29.630 0.00 0.00 0.00 2.12
2448 2808 9.941664 CAAATCTATTGCAACCTTCAACTATAG 57.058 33.333 0.00 0.00 0.00 1.31
2449 2809 9.679661 TCAAATCTATTGCAACCTTCAACTATA 57.320 29.630 0.00 0.00 0.00 1.31
2450 2810 8.579850 TCAAATCTATTGCAACCTTCAACTAT 57.420 30.769 0.00 0.00 0.00 2.12
2451 2811 7.994425 TCAAATCTATTGCAACCTTCAACTA 57.006 32.000 0.00 0.00 0.00 2.24
2452 2812 6.899393 TCAAATCTATTGCAACCTTCAACT 57.101 33.333 0.00 0.00 0.00 3.16
2453 2813 8.538409 AAATCAAATCTATTGCAACCTTCAAC 57.462 30.769 0.00 0.00 0.00 3.18
2454 2814 8.991026 CAAAATCAAATCTATTGCAACCTTCAA 58.009 29.630 0.00 0.00 0.00 2.69
2455 2815 8.149647 ACAAAATCAAATCTATTGCAACCTTCA 58.850 29.630 0.00 0.00 0.00 3.02
2456 2816 8.538409 ACAAAATCAAATCTATTGCAACCTTC 57.462 30.769 0.00 0.00 0.00 3.46
2457 2817 8.149647 TGACAAAATCAAATCTATTGCAACCTT 58.850 29.630 0.00 0.00 33.02 3.50
2458 2818 7.599998 GTGACAAAATCAAATCTATTGCAACCT 59.400 33.333 0.00 0.00 39.72 3.50
2459 2819 7.599998 AGTGACAAAATCAAATCTATTGCAACC 59.400 33.333 0.00 0.00 39.72 3.77
2460 2820 8.524870 AGTGACAAAATCAAATCTATTGCAAC 57.475 30.769 0.00 0.00 39.72 4.17
2501 2861 9.836864 TGCAAGAATCATAATGTACAGAACTAT 57.163 29.630 0.33 0.00 0.00 2.12
2502 2862 9.665719 TTGCAAGAATCATAATGTACAGAACTA 57.334 29.630 0.33 0.00 0.00 2.24
2503 2863 8.565896 TTGCAAGAATCATAATGTACAGAACT 57.434 30.769 0.33 0.00 0.00 3.01
2645 3011 4.827692 TGTGCATCGTTTTATGTAGAGGT 58.172 39.130 0.00 0.00 0.00 3.85
2655 3021 3.005261 TGTTTGGCTATGTGCATCGTTTT 59.995 39.130 0.00 0.00 45.15 2.43
2658 3024 1.819928 TGTTTGGCTATGTGCATCGT 58.180 45.000 0.00 0.00 45.15 3.73
2706 3072 5.428496 TTTTGAGTTGTCTGCAATCTCAG 57.572 39.130 0.00 0.00 40.35 3.35
2784 3150 3.992427 CCTTCACTAAGAACCGTGGTAAC 59.008 47.826 0.00 0.00 34.37 2.50
2795 3161 5.975988 AGGGCATATTTCCTTCACTAAGA 57.024 39.130 0.00 0.00 34.37 2.10
2911 3408 9.169468 CTTTGTTTTGTCTATGTATTCACACAC 57.831 33.333 0.00 0.00 37.54 3.82
2942 3439 7.007723 AGCTAGTCAAATAGAGGCATACTAGT 58.992 38.462 0.00 0.00 38.02 2.57
2957 3454 7.064609 CCATCTTTGATTAACGAGCTAGTCAAA 59.935 37.037 0.00 5.76 36.02 2.69
3042 3541 6.115446 GGGTCTTGTCAATCACATCATTCTA 58.885 40.000 0.00 0.00 33.90 2.10
3056 3555 2.301870 AGCTAACGAATGGGTCTTGTCA 59.698 45.455 0.00 0.00 0.00 3.58
3112 3611 9.739276 AGGAACATGTATAAGTCATGAAGAAAA 57.261 29.630 0.00 0.00 43.47 2.29
3144 3643 7.446625 GGTATTCAGGAGTTGCATAATCTCATT 59.553 37.037 0.00 0.00 0.00 2.57
3244 3743 2.028476 GCCAACCCAACAAATACCTTCC 60.028 50.000 0.00 0.00 0.00 3.46
3269 4127 5.694006 GGAGTGACAAATCCTAATCTCGATG 59.306 44.000 1.45 0.00 32.51 3.84
3300 4158 0.105453 GGCCCAGAGATACCTCTCCA 60.105 60.000 0.00 0.00 46.38 3.86


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

AutoCloner maintained by Alex Coulton.