Multiple sequence alignment - TraesCS2D01G084000

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 TraesCS2D01G084000 chr2D 100.000 5507 0 0 1 5507 36436382 36430876 0.000000e+00 10170.0
1 TraesCS2D01G084000 chr2D 77.487 2443 453 65 608 2990 19579902 19582307 0.000000e+00 1375.0
2 TraesCS2D01G084000 chr2D 78.825 2111 369 60 976 3029 19462191 19464280 0.000000e+00 1351.0
3 TraesCS2D01G084000 chr2D 79.022 1983 357 43 812 2751 10096751 10098717 0.000000e+00 1303.0
4 TraesCS2D01G084000 chr2D 77.599 2232 416 56 821 2990 10025062 10022853 0.000000e+00 1275.0
5 TraesCS2D01G084000 chr2D 83.108 148 13 8 3622 3764 72150944 72150804 2.080000e-24 124.0
6 TraesCS2D01G084000 chr2D 94.286 35 2 0 551 585 10025530 10025496 3.000000e-03 54.7
7 TraesCS2D01G084000 chr2A 94.014 5596 225 43 1 5507 40343253 40337679 0.000000e+00 8377.0
8 TraesCS2D01G084000 chr2A 89.288 1979 170 22 492 2450 9776818 9778774 0.000000e+00 2442.0
9 TraesCS2D01G084000 chr2A 77.605 2447 453 66 606 2990 10197977 10200390 0.000000e+00 1395.0
10 TraesCS2D01G084000 chr2A 87.551 1229 111 24 494 1705 10384208 10383005 0.000000e+00 1384.0
11 TraesCS2D01G084000 chr2A 77.956 2250 408 63 839 3029 20502494 20504714 0.000000e+00 1327.0
12 TraesCS2D01G084000 chr2A 79.506 1942 275 63 1587 3472 10374442 10376316 0.000000e+00 1267.0
13 TraesCS2D01G084000 chr2A 89.832 895 84 5 1547 2439 9201991 9201102 0.000000e+00 1142.0
14 TraesCS2D01G084000 chr2A 82.343 1178 166 30 2450 3610 9778900 9780052 0.000000e+00 985.0
15 TraesCS2D01G084000 chr2A 82.755 1096 155 24 2338 3419 9201003 9199928 0.000000e+00 946.0
16 TraesCS2D01G084000 chr2A 88.846 780 74 5 790 1561 9203464 9202690 0.000000e+00 946.0
17 TraesCS2D01G084000 chr2A 81.748 904 140 17 2338 3225 10382988 10382094 0.000000e+00 732.0
18 TraesCS2D01G084000 chr2B 78.013 2224 409 60 821 2990 31424220 31422023 0.000000e+00 1325.0
19 TraesCS2D01G084000 chr2B 77.996 2136 390 58 661 2751 13495192 13493092 0.000000e+00 1267.0
20 TraesCS2D01G084000 chr2B 78.673 1055 180 31 1730 2751 13735902 13736944 0.000000e+00 660.0
21 TraesCS2D01G084000 chr2B 91.787 207 16 1 3328 3533 59223585 59223791 2.510000e-73 287.0
22 TraesCS2D01G084000 chr2B 88.936 235 15 4 2973 3197 59218600 59218833 4.200000e-71 279.0
23 TraesCS2D01G084000 chr2B 75.962 520 90 20 2741 3253 13479739 13479248 9.220000e-58 235.0
24 TraesCS2D01G084000 chr2B 87.678 211 13 5 4328 4527 792213883 792214091 3.320000e-57 233.0
25 TraesCS2D01G084000 chr2B 97.015 67 1 1 3609 3674 792213817 792213883 1.620000e-20 111.0
26 TraesCS2D01G084000 chr2B 95.312 64 2 1 4050 4113 49494778 49494840 3.510000e-17 100.0
27 TraesCS2D01G084000 chr7B 89.697 990 69 10 3603 4573 25303809 25304784 0.000000e+00 1232.0
28 TraesCS2D01G084000 chr7B 81.844 347 28 11 4549 4893 25314688 25315001 5.470000e-65 259.0
29 TraesCS2D01G084000 chr7B 98.438 64 1 0 4050 4113 352534572 352534635 4.510000e-21 113.0
30 TraesCS2D01G084000 chr7B 88.060 67 5 1 4696 4762 25314694 25314757 5.920000e-10 76.8
31 TraesCS2D01G084000 chr1A 92.057 768 57 4 3607 4371 253306039 253306805 0.000000e+00 1077.0
32 TraesCS2D01G084000 chr1A 86.035 401 31 6 4769 5168 51717492 51717868 1.850000e-109 407.0
33 TraesCS2D01G084000 chr1A 82.883 111 12 6 3760 3869 574280068 574280172 5.870000e-15 93.5
34 TraesCS2D01G084000 chr1A 92.857 42 2 1 4543 4583 508962947 508962906 5.960000e-05 60.2
35 TraesCS2D01G084000 chr7A 88.803 777 63 11 3603 4377 104129362 104128608 0.000000e+00 931.0
36 TraesCS2D01G084000 chr7A 89.066 439 46 2 5070 5507 104128406 104127969 1.350000e-150 544.0
37 TraesCS2D01G084000 chr7A 95.349 43 1 1 4253 4294 38149505 38149547 3.560000e-07 67.6
38 TraesCS2D01G084000 chr5D 91.762 437 32 4 5072 5507 70872115 70871682 6.100000e-169 604.0
39 TraesCS2D01G084000 chr5D 87.500 344 24 9 4328 4657 70872509 70872171 4.030000e-101 379.0
40 TraesCS2D01G084000 chr5D 95.890 73 1 2 3603 3674 70872580 70872509 3.490000e-22 117.0
41 TraesCS2D01G084000 chr5D 85.000 120 7 7 4651 4769 70872283 70872174 1.620000e-20 111.0
42 TraesCS2D01G084000 chr5D 97.917 48 1 0 4846 4893 70872168 70872121 3.540000e-12 84.2
43 TraesCS2D01G084000 chr5D 100.000 33 0 0 4812 4844 69456410 69456378 1.660000e-05 62.1
44 TraesCS2D01G084000 chr4D 87.781 401 23 6 4769 5168 336602384 336602009 3.910000e-121 446.0
45 TraesCS2D01G084000 chr6A 87.958 382 28 3 4787 5168 108253463 108253100 8.470000e-118 435.0
46 TraesCS2D01G084000 chr6A 89.583 48 4 1 4543 4589 26329082 26329035 5.960000e-05 60.2
47 TraesCS2D01G084000 chr5A 87.958 382 24 5 4788 5168 675485917 675485557 1.100000e-116 431.0
48 TraesCS2D01G084000 chr5A 87.273 385 30 4 4784 5168 427081716 427082081 6.600000e-114 422.0
49 TraesCS2D01G084000 chr5A 98.438 64 1 0 4050 4113 647705445 647705382 4.510000e-21 113.0
50 TraesCS2D01G084000 chr5A 100.000 30 0 0 3759 3788 52496198 52496227 7.710000e-04 56.5
51 TraesCS2D01G084000 chr6D 86.816 402 27 5 4769 5168 122515739 122515362 5.100000e-115 425.0
52 TraesCS2D01G084000 chr6D 92.096 291 19 2 4878 5168 428628601 428628315 1.850000e-109 407.0
53 TraesCS2D01G084000 chr3B 85.974 385 30 7 4784 5168 81525362 81525722 1.860000e-104 390.0
54 TraesCS2D01G084000 chr1B 91.519 283 19 3 4887 5168 567469910 567470188 8.650000e-103 385.0
55 TraesCS2D01G084000 chr1B 92.593 81 6 0 4777 4857 30507150 30507230 3.490000e-22 117.0
56 TraesCS2D01G084000 chr1B 90.217 92 5 3 4766 4857 567469825 567469912 3.490000e-22 117.0
57 TraesCS2D01G084000 chr1B 92.683 41 2 1 4543 4582 167562654 167562694 2.140000e-04 58.4
58 TraesCS2D01G084000 chr7D 98.020 101 2 0 4050 4150 114141646 114141746 5.670000e-40 176.0
59 TraesCS2D01G084000 chr6B 96.875 64 1 1 4050 4113 666785555 666785617 7.540000e-19 106.0
60 TraesCS2D01G084000 chr6B 90.667 75 7 0 5365 5439 720408253 720408327 3.510000e-17 100.0
61 TraesCS2D01G084000 chr6B 95.122 41 2 0 5256 5296 720408162 720408202 1.280000e-06 65.8
62 TraesCS2D01G084000 chr6B 100.000 33 0 0 4812 4844 720408108 720408076 1.660000e-05 62.1
63 TraesCS2D01G084000 chr6B 92.857 42 2 1 4543 4583 423092654 423092695 5.960000e-05 60.2
64 TraesCS2D01G084000 chrUn 82.883 111 12 6 3760 3869 341585794 341585898 5.870000e-15 93.5
65 TraesCS2D01G084000 chrUn 82.883 111 12 6 3760 3869 453615554 453615450 5.870000e-15 93.5
66 TraesCS2D01G084000 chr4B 81.982 111 13 6 3760 3869 410811658 410811554 2.730000e-13 87.9
67 TraesCS2D01G084000 chr4B 95.349 43 1 1 4253 4294 198260150 198260108 3.560000e-07 67.6
68 TraesCS2D01G084000 chr4B 95.349 43 1 1 4253 4294 341438137 341438179 3.560000e-07 67.6
69 TraesCS2D01G084000 chr4A 95.349 43 1 1 4253 4294 719330876 719330834 3.560000e-07 67.6
70 TraesCS2D01G084000 chr4A 95.349 43 1 1 4253 4294 720665150 720665192 3.560000e-07 67.6
71 TraesCS2D01G084000 chr3A 89.583 48 4 1 4543 4589 411271115 411271068 5.960000e-05 60.2
72 TraesCS2D01G084000 chr1D 92.857 42 2 1 4543 4583 493748065 493748106 5.960000e-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 TraesCS2D01G084000 chr2D 36430876 36436382 5506 True 10170.000000 10170 100.000000 1 5507 1 chr2D.!!$R1 5506
1 TraesCS2D01G084000 chr2D 19579902 19582307 2405 False 1375.000000 1375 77.487000 608 2990 1 chr2D.!!$F3 2382
2 TraesCS2D01G084000 chr2D 19462191 19464280 2089 False 1351.000000 1351 78.825000 976 3029 1 chr2D.!!$F2 2053
3 TraesCS2D01G084000 chr2D 10096751 10098717 1966 False 1303.000000 1303 79.022000 812 2751 1 chr2D.!!$F1 1939
4 TraesCS2D01G084000 chr2D 10022853 10025530 2677 True 664.850000 1275 85.942500 551 2990 2 chr2D.!!$R3 2439
5 TraesCS2D01G084000 chr2A 40337679 40343253 5574 True 8377.000000 8377 94.014000 1 5507 1 chr2A.!!$R1 5506
6 TraesCS2D01G084000 chr2A 9776818 9780052 3234 False 1713.500000 2442 85.815500 492 3610 2 chr2A.!!$F4 3118
7 TraesCS2D01G084000 chr2A 10197977 10200390 2413 False 1395.000000 1395 77.605000 606 2990 1 chr2A.!!$F1 2384
8 TraesCS2D01G084000 chr2A 20502494 20504714 2220 False 1327.000000 1327 77.956000 839 3029 1 chr2A.!!$F3 2190
9 TraesCS2D01G084000 chr2A 10374442 10376316 1874 False 1267.000000 1267 79.506000 1587 3472 1 chr2A.!!$F2 1885
10 TraesCS2D01G084000 chr2A 10382094 10384208 2114 True 1058.000000 1384 84.649500 494 3225 2 chr2A.!!$R3 2731
11 TraesCS2D01G084000 chr2A 9199928 9203464 3536 True 1011.333333 1142 87.144333 790 3419 3 chr2A.!!$R2 2629
12 TraesCS2D01G084000 chr2B 31422023 31424220 2197 True 1325.000000 1325 78.013000 821 2990 1 chr2B.!!$R3 2169
13 TraesCS2D01G084000 chr2B 13493092 13495192 2100 True 1267.000000 1267 77.996000 661 2751 1 chr2B.!!$R2 2090
14 TraesCS2D01G084000 chr2B 13735902 13736944 1042 False 660.000000 660 78.673000 1730 2751 1 chr2B.!!$F1 1021
15 TraesCS2D01G084000 chr7B 25303809 25304784 975 False 1232.000000 1232 89.697000 3603 4573 1 chr7B.!!$F1 970
16 TraesCS2D01G084000 chr1A 253306039 253306805 766 False 1077.000000 1077 92.057000 3607 4371 1 chr1A.!!$F2 764
17 TraesCS2D01G084000 chr7A 104127969 104129362 1393 True 737.500000 931 88.934500 3603 5507 2 chr7A.!!$R1 1904
18 TraesCS2D01G084000 chr5D 70871682 70872580 898 True 259.040000 604 91.613800 3603 5507 5 chr5D.!!$R2 1904

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
654 671 0.798771 CCTCGCTGAGTCGCTGTTAC 60.799 60.000 5.63 0.0 0.0 2.50 F
1461 1782 1.134068 GCAAAGTATGGGGAGAGGACC 60.134 57.143 0.00 0.0 0.0 4.46 F
3310 4755 1.258445 CGGAGGTCTTAGCTGTGGGT 61.258 60.000 0.00 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 4032 0.110056 CACGAGAACCAGCAACATGC 60.110 55.000 0.0 0.0 45.46 4.06 R
3352 4811 1.208706 TCACAGAACACCAACTGGGA 58.791 50.000 0.0 0.0 43.05 4.37 R
5260 6788 1.200020 GTAATGCACAACCAGGCAGTC 59.800 52.381 0.0 0.0 44.24 3.51 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
30 31 1.186200 GGAAACTCCCCAAATCTGGC 58.814 55.000 0.00 0.00 41.99 4.85
36 37 1.220518 TCCCCAAATCTGGCCATCCA 61.221 55.000 5.51 0.00 41.99 3.41
48 55 1.718757 GCCATCCAAATCGCGCTCTT 61.719 55.000 5.56 0.00 0.00 2.85
113 120 3.217743 GCCTCCTCCCGTCCGTAG 61.218 72.222 0.00 0.00 0.00 3.51
161 168 2.202932 CGCGCCATGTAGCTTCCT 60.203 61.111 0.00 0.00 0.00 3.36
163 170 1.153369 GCGCCATGTAGCTTCCTCA 60.153 57.895 0.00 0.00 0.00 3.86
165 172 1.506493 CGCCATGTAGCTTCCTCATC 58.494 55.000 0.00 0.00 0.00 2.92
246 253 4.592936 CTAGACCGACCGCGAGCG 62.593 72.222 8.23 11.00 40.82 5.03
265 272 1.023513 GCATCAGTCAAGCGCCTCTT 61.024 55.000 2.29 0.00 34.78 2.85
354 361 6.072728 CCGTGTTTCCTTATCAACATCTGAAA 60.073 38.462 0.00 0.00 37.67 2.69
462 469 8.378565 CCATAACATGGTCTGGAAATAGAGTAT 58.621 37.037 9.56 0.00 45.54 2.12
479 486 5.794894 AGAGTATTGTTGGTCGACTGAATT 58.205 37.500 16.46 0.00 0.00 2.17
505 512 5.367937 AGCTTCTATACAACCATGGTCTCAT 59.632 40.000 20.07 13.41 0.00 2.90
654 671 0.798771 CCTCGCTGAGTCGCTGTTAC 60.799 60.000 5.63 0.00 0.00 2.50
690 708 2.554032 TCTTGCTTCTTTGGCTACTTGC 59.446 45.455 0.00 0.00 41.94 4.01
773 809 8.503458 AATAGATAGCATATTCATTCACCAGC 57.497 34.615 0.00 0.00 0.00 4.85
779 990 4.261072 GCATATTCATTCACCAGCAGACTG 60.261 45.833 0.00 0.00 44.05 3.51
910 1214 4.740902 TGCCATCTCCTAGCTCACTATAA 58.259 43.478 0.00 0.00 0.00 0.98
918 1222 7.887381 TCTCCTAGCTCACTATAAGCAATTAC 58.113 38.462 0.00 0.00 42.35 1.89
1353 1674 1.492993 GCCTTCTGGTCCAGGTCCTT 61.493 60.000 19.11 0.00 35.27 3.36
1461 1782 1.134068 GCAAAGTATGGGGAGAGGACC 60.134 57.143 0.00 0.00 0.00 4.46
1516 1837 1.465794 GAGCTCTCTCAAGGTACGGT 58.534 55.000 6.43 0.00 39.16 4.83
1689 2728 4.102838 CAGAATGAGGTGGATTCTCTGGAT 59.897 45.833 0.00 0.00 37.95 3.41
2296 3338 4.712337 TCCCTGAGAAGGTCAAGAAGTATC 59.288 45.833 0.00 0.00 33.60 2.24
2314 3356 6.753913 AGTATCCATGGAGTAATGTCACAT 57.246 37.500 21.33 0.66 0.00 3.21
2358 3412 2.914289 CTCAGGACTGGATGGGGC 59.086 66.667 0.00 0.00 0.00 5.80
2564 3953 2.291346 TGATGTTCCTCCTCGTGGACTA 60.291 50.000 1.10 0.00 37.46 2.59
2570 3959 3.145551 CCTCGTGGACTACCCCGG 61.146 72.222 0.00 0.00 34.57 5.73
2635 4024 4.761739 CCTGCAAACAACTGGAGAAGATAA 59.238 41.667 0.00 0.00 36.94 1.75
2643 4032 6.402222 ACAACTGGAGAAGATAAGCAGTAAG 58.598 40.000 0.00 0.00 0.00 2.34
3210 4652 2.009774 CCTAGCAATGTTCCGGTGAAG 58.990 52.381 0.00 0.00 0.00 3.02
3253 4697 1.474017 GTTGCAATGATGATCTGCGC 58.526 50.000 0.59 0.00 38.97 6.09
3310 4755 1.258445 CGGAGGTCTTAGCTGTGGGT 61.258 60.000 0.00 0.00 0.00 4.51
3352 4811 0.888285 GGCAGCAGCAGAAAGTCACT 60.888 55.000 2.65 0.00 44.61 3.41
3460 4934 1.734137 CGCTGGTATCGGCTACAGT 59.266 57.895 5.03 0.00 42.91 3.55
3504 4978 0.742281 CTGGACTGGCAAGATGACGG 60.742 60.000 0.00 0.00 37.91 4.79
3576 5050 2.620115 CTCTTTGTTGCCATGTCAGTGT 59.380 45.455 0.00 0.00 0.00 3.55
3690 5165 1.644786 GCTTGCGAGCCGTGGTAAAT 61.645 55.000 15.66 0.00 43.29 1.40
3843 5318 5.845985 TTCAGTCACTGCTTATTTCTTCG 57.154 39.130 0.00 0.00 0.00 3.79
3845 5320 3.372206 CAGTCACTGCTTATTTCTTCGGG 59.628 47.826 0.00 0.00 0.00 5.14
3846 5321 3.008049 AGTCACTGCTTATTTCTTCGGGT 59.992 43.478 0.00 0.00 0.00 5.28
3848 5323 4.567159 GTCACTGCTTATTTCTTCGGGTAG 59.433 45.833 0.00 0.00 0.00 3.18
3849 5324 3.309954 CACTGCTTATTTCTTCGGGTAGC 59.690 47.826 0.00 0.00 0.00 3.58
3850 5325 3.197983 ACTGCTTATTTCTTCGGGTAGCT 59.802 43.478 0.00 0.00 0.00 3.32
4209 5690 2.170187 GTGATGGAGCTCCTTGATCAGT 59.830 50.000 32.28 8.92 36.82 3.41
4372 5854 4.334203 CCAGCAGTTTTGTGTAGTTGTACA 59.666 41.667 0.00 0.00 36.78 2.90
4391 5873 5.932303 TGTACAGAAAAGTTGCAGGAGTATC 59.068 40.000 0.00 0.00 0.00 2.24
4472 5964 6.947903 GGAGTAGTTTTACTGCAGAAGTAC 57.052 41.667 23.35 19.72 44.84 2.73
4499 5995 4.549458 CCAATTGGCAAGTTTCAGTACTG 58.451 43.478 17.17 17.17 0.00 2.74
4541 6040 6.331061 AGCTACTCCTAAATGAAACTACACG 58.669 40.000 0.00 0.00 0.00 4.49
4927 6453 7.891498 AAGGAACAAGAAAAGCTTTAACCTA 57.109 32.000 13.10 0.00 33.60 3.08
4950 6476 7.284034 CCTATTCCAGCAAGTGATAACAGATTT 59.716 37.037 0.00 0.00 0.00 2.17
4976 6502 6.100004 TCTAATCGACACTCAAACAGGATTC 58.900 40.000 0.00 0.00 0.00 2.52
5068 6594 9.533831 AAAGATAAATGTTATCCAACCAGTTCT 57.466 29.630 4.71 0.00 33.41 3.01
5168 6696 3.251729 TGTTCAGTTGCAAGCTCATCTTC 59.748 43.478 0.00 0.00 31.27 2.87
5241 6769 7.765307 ACACATCAAAATCTACCACATCATTC 58.235 34.615 0.00 0.00 0.00 2.67
5342 6870 3.189080 TGCTGATGTTCAGGAAATTCACG 59.811 43.478 6.64 0.00 41.94 4.35
5448 6976 2.046507 AAAGAGGAGGCAGCAGCG 60.047 61.111 0.00 0.00 43.41 5.18
5484 7012 1.221840 GCAAAGAGGATGGAGGCGA 59.778 57.895 0.00 0.00 0.00 5.54
5489 7017 3.781770 GAGGATGGAGGCGACAGCG 62.782 68.421 0.00 0.00 46.35 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.468771 GGATGGCCAGATTTGGGGAG 60.469 60.000 13.05 0.00 45.16 4.30
30 31 0.305922 GAAGAGCGCGATTTGGATGG 59.694 55.000 12.10 0.00 0.00 3.51
36 37 1.086634 GGCTGAGAAGAGCGCGATTT 61.087 55.000 12.10 0.00 40.13 2.17
113 120 4.874977 GAGGCGGCTGGTCGTAGC 62.875 72.222 19.63 0.00 42.94 3.58
161 168 4.559229 CGAGCAGAGCGGCGATGA 62.559 66.667 12.98 0.00 39.27 2.92
180 187 2.125350 GGCGACCAGAAGCTCCAG 60.125 66.667 0.00 0.00 0.00 3.86
218 225 3.217743 GGTCTAGCTAGGCGCCGT 61.218 66.667 23.20 12.38 40.39 5.68
246 253 1.023513 AAGAGGCGCTTGACTGATGC 61.024 55.000 7.64 0.00 34.93 3.91
354 361 4.915158 TTTTTCGACGGGTTAAAATGGT 57.085 36.364 0.00 0.00 0.00 3.55
411 418 1.472728 CCGGCTGCCGTCTACTAAAAT 60.473 52.381 35.82 0.00 46.80 1.82
415 422 3.524606 GCCGGCTGCCGTCTACTA 61.525 66.667 35.82 0.00 46.80 1.82
449 456 6.070995 AGTCGACCAACAATACTCTATTTCCA 60.071 38.462 13.01 0.00 0.00 3.53
452 459 6.931838 TCAGTCGACCAACAATACTCTATTT 58.068 36.000 13.01 0.00 0.00 1.40
462 469 2.548057 GCTGAATTCAGTCGACCAACAA 59.452 45.455 30.88 0.00 45.45 2.83
479 486 4.716784 AGACCATGGTTGTATAGAAGCTGA 59.283 41.667 20.85 0.00 0.00 4.26
537 544 0.107361 CATGTGCCTGCATCTGGAGA 60.107 55.000 0.00 0.00 35.31 3.71
538 545 0.393944 ACATGTGCCTGCATCTGGAG 60.394 55.000 0.00 0.00 0.00 3.86
654 671 6.974965 AGAAGCAAGAAATTAAGAACACTGG 58.025 36.000 0.00 0.00 0.00 4.00
690 708 3.761218 ACTAGACACATGTCCACTCTCAG 59.239 47.826 8.41 0.00 45.85 3.35
773 809 5.120399 AGTAGTAGCAGTAGTAGCAGTCTG 58.880 45.833 0.00 0.00 0.00 3.51
779 990 5.585445 TCAACTGAGTAGTAGCAGTAGTAGC 59.415 44.000 6.14 0.00 44.06 3.58
782 993 6.419791 AGATCAACTGAGTAGTAGCAGTAGT 58.580 40.000 6.14 0.00 44.06 2.73
1018 1336 0.034670 GCCCAGTCATTCCAGAAGCT 60.035 55.000 0.00 0.00 0.00 3.74
1516 1837 3.055240 TGCTGGTGATGTATGTCATGTGA 60.055 43.478 0.00 0.00 36.83 3.58
1689 2728 5.163561 CGAAAAGCCCTGGATTATTTTGCTA 60.164 40.000 0.00 0.00 0.00 3.49
2296 3338 6.319405 TCAATTGATGTGACATTACTCCATGG 59.681 38.462 4.97 4.97 0.00 3.66
2314 3356 5.657745 AGCCCATTGTGTTCATATCAATTGA 59.342 36.000 11.26 11.26 30.74 2.57
2358 3412 3.675228 GCTCTTCATCCAGTGCCATTTTG 60.675 47.826 0.00 0.00 0.00 2.44
2570 3959 1.825622 GGAAGGCCTGGTAGCATGC 60.826 63.158 5.69 10.51 0.00 4.06
2643 4032 0.110056 CACGAGAACCAGCAACATGC 60.110 55.000 0.00 0.00 45.46 4.06
2921 4334 1.748122 CCAAGCTTCCTCGCATGCT 60.748 57.895 17.13 0.00 37.37 3.79
3192 4634 3.410631 TTCTTCACCGGAACATTGCTA 57.589 42.857 9.46 0.00 0.00 3.49
3200 4642 2.293122 CAGCACAATTTCTTCACCGGAA 59.707 45.455 9.46 0.00 0.00 4.30
3204 4646 4.320494 CCTGTACAGCACAATTTCTTCACC 60.320 45.833 17.86 0.00 36.48 4.02
3210 4652 2.162681 AGCCCTGTACAGCACAATTTC 58.837 47.619 17.86 0.00 36.48 2.17
3352 4811 1.208706 TCACAGAACACCAACTGGGA 58.791 50.000 0.00 0.00 43.05 4.37
3460 4934 2.099592 CAGCCAAGAGAAAAAGTGTGCA 59.900 45.455 0.00 0.00 0.00 4.57
3504 4978 0.172352 CTCCTCGAGCTTCCTGTCAC 59.828 60.000 6.99 0.00 0.00 3.67
3576 5050 5.366477 TGAGAGATTATGTGGGTGCTCATTA 59.634 40.000 0.00 0.00 0.00 1.90
3690 5165 4.647424 AAGCAAACGACCAAATTCAGAA 57.353 36.364 0.00 0.00 0.00 3.02
3843 5318 6.641474 ACTAAACTGAACTGATTAGCTACCC 58.359 40.000 0.00 0.00 0.00 3.69
3845 5320 8.535690 ACAACTAAACTGAACTGATTAGCTAC 57.464 34.615 0.00 0.00 0.00 3.58
3846 5321 9.204570 GAACAACTAAACTGAACTGATTAGCTA 57.795 33.333 0.00 0.00 0.00 3.32
3848 5323 8.012241 CAGAACAACTAAACTGAACTGATTAGC 58.988 37.037 0.00 0.00 32.90 3.09
3849 5324 8.012241 GCAGAACAACTAAACTGAACTGATTAG 58.988 37.037 0.00 0.00 32.90 1.73
3850 5325 7.497579 TGCAGAACAACTAAACTGAACTGATTA 59.502 33.333 0.00 0.00 32.90 1.75
3921 5396 4.995124 TCTAGACCTCTGAAATACGCAAC 58.005 43.478 0.00 0.00 0.00 4.17
3985 5460 9.533253 AGTACAAACTCTTTGATTTTGATTTGG 57.467 29.630 14.33 0.00 43.26 3.28
4209 5690 5.303589 ACTTGCACAACTACTCCAACTACTA 59.696 40.000 0.00 0.00 0.00 1.82
4372 5854 6.016777 CACAAAGATACTCCTGCAACTTTTCT 60.017 38.462 0.00 0.00 0.00 2.52
4391 5873 6.089820 CCATATGCAAGCAAAACTACACAAAG 59.910 38.462 0.00 0.00 0.00 2.77
4514 6010 7.705752 GTGTAGTTTCATTTAGGAGTAGCTACC 59.294 40.741 20.31 11.50 0.00 3.18
4775 6301 6.806739 GCAACCTGAAACTGTCATAATTAACC 59.193 38.462 0.00 0.00 35.07 2.85
4895 6421 7.404671 AGCTTTTCTTGTTCCTTTTCTGTTA 57.595 32.000 0.00 0.00 0.00 2.41
4927 6453 7.472334 AAAATCTGTTATCACTTGCTGGAAT 57.528 32.000 0.00 0.00 0.00 3.01
4950 6476 5.849510 TCCTGTTTGAGTGTCGATTAGAAA 58.150 37.500 0.00 0.00 0.00 2.52
4976 6502 5.605534 CCAGATCATGGTTCCTACTAACAG 58.394 45.833 0.00 0.00 44.91 3.16
5043 6569 9.178758 GAGAACTGGTTGGATAACATTTATCTT 57.821 33.333 6.02 0.00 38.58 2.40
5168 6696 8.612619 ACTGTACTGTGAAAAACAATTAGAGTG 58.387 33.333 4.39 0.00 38.67 3.51
5216 6744 7.613022 AGAATGATGTGGTAGATTTTGATGTGT 59.387 33.333 0.00 0.00 0.00 3.72
5260 6788 1.200020 GTAATGCACAACCAGGCAGTC 59.800 52.381 0.00 0.00 44.24 3.51
5301 6829 7.451501 TCAGCAGACATGAAAAACAATGATA 57.548 32.000 0.00 0.00 0.00 2.15
5363 6891 0.106066 CCTGCCAGGGCCAATATCAA 60.106 55.000 6.18 0.00 41.09 2.57
5448 6976 1.066587 CTGCTGCTCGCCTAGTACC 59.933 63.158 0.00 0.00 38.05 3.34


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

AutoCloner maintained by Alex Coulton.