Multiple sequence alignment - TraesCS5D01G011900

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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 TraesCS5D01G011900 chr5D 100.000 7039 0 0 1 7039 6443975 6451013 0.000000e+00 12999.0
1 TraesCS5D01G011900 chr5D 96.094 1280 38 7 2992 4270 528583341 528584609 0.000000e+00 2076.0
2 TraesCS5D01G011900 chr5D 95.755 1272 53 1 2999 4270 363541833 363543103 0.000000e+00 2049.0
3 TraesCS5D01G011900 chr5D 95.302 298 12 1 4269 4566 8404627 8404922 8.260000e-129 472.0
4 TraesCS5D01G011900 chr5D 95.608 296 10 2 4269 4564 528585150 528585442 8.260000e-129 472.0
5 TraesCS5D01G011900 chr5D 95.270 296 12 1 4269 4564 231231096 231230803 1.070000e-127 468.0
6 TraesCS5D01G011900 chr5D 94.295 298 14 2 4269 4564 425844559 425844855 2.990000e-123 453.0
7 TraesCS5D01G011900 chr5D 77.365 835 138 37 5491 6299 5358026 5358835 1.390000e-121 448.0
8 TraesCS5D01G011900 chr5D 80.880 523 71 17 4827 5344 5357139 5357637 1.110000e-102 385.0
9 TraesCS5D01G011900 chr5D 82.500 360 50 11 2503 2860 328921762 328921414 3.190000e-78 303.0
10 TraesCS5D01G011900 chr5D 83.962 318 41 8 2545 2859 409571898 409571588 5.340000e-76 296.0
11 TraesCS5D01G011900 chr5D 86.466 266 22 8 2003 2258 5356347 5356608 5.380000e-71 279.0
12 TraesCS5D01G011900 chr5D 86.154 260 31 3 1020 1279 5355326 5355580 6.960000e-70 276.0
13 TraesCS5D01G011900 chr5D 85.845 219 19 4 1732 1949 5356022 5356229 9.190000e-54 222.0
14 TraesCS5D01G011900 chr5D 88.764 178 15 3 667 840 546677028 546676852 5.530000e-51 213.0
15 TraesCS5D01G011900 chr5D 77.823 248 36 16 6348 6586 5358973 5359210 1.230000e-27 135.0
16 TraesCS5D01G011900 chr5A 97.783 3022 48 8 1 3007 3219778 3216761 0.000000e+00 5192.0
17 TraesCS5D01G011900 chr5A 97.044 2503 42 10 4563 7039 3216775 3214279 0.000000e+00 4183.0
18 TraesCS5D01G011900 chr7D 96.247 1279 41 2 2999 4270 436839712 436840990 0.000000e+00 2089.0
19 TraesCS5D01G011900 chr7D 82.740 365 50 10 2502 2858 483478679 483478320 5.300000e-81 313.0
20 TraesCS5D01G011900 chr7D 90.323 186 17 1 656 841 638206232 638206416 7.050000e-60 243.0
21 TraesCS5D01G011900 chr7D 86.559 186 24 1 657 841 512000245 512000430 3.330000e-48 204.0
22 TraesCS5D01G011900 chr1D 96.019 1281 44 3 2995 4269 398094492 398095771 0.000000e+00 2076.0
23 TraesCS5D01G011900 chr1D 95.219 1276 58 3 2997 4270 491719189 491720463 0.000000e+00 2015.0
24 TraesCS5D01G011900 chr1D 94.595 296 12 3 4271 4566 338879082 338879373 8.320000e-124 455.0
25 TraesCS5D01G011900 chr1D 94.314 299 12 4 4269 4566 398096330 398096624 2.990000e-123 453.0
26 TraesCS5D01G011900 chr1D 94.295 298 14 2 4269 4566 470554342 470554636 2.990000e-123 453.0
27 TraesCS5D01G011900 chr1D 83.425 362 48 11 2502 2857 47331087 47330732 6.810000e-85 326.0
28 TraesCS5D01G011900 chr1D 82.507 343 46 10 2503 2837 381308237 381308573 8.930000e-74 289.0
29 TraesCS5D01G011900 chr1D 81.115 323 48 10 2546 2863 361382488 361382174 5.450000e-61 246.0
30 TraesCS5D01G011900 chr1D 87.701 187 22 1 655 841 126588831 126588646 4.280000e-52 217.0
31 TraesCS5D01G011900 chr1D 82.470 251 34 8 2578 2827 326292049 326292290 1.990000e-50 211.0
32 TraesCS5D01G011900 chr1D 92.982 114 8 0 728 841 140527038 140526925 4.370000e-37 167.0
33 TraesCS5D01G011900 chr1D 91.089 101 7 2 656 754 140543805 140543705 1.230000e-27 135.0
34 TraesCS5D01G011900 chr3D 95.859 1280 44 8 2993 4270 575541386 575542658 0.000000e+00 2061.0
35 TraesCS5D01G011900 chr3D 81.742 356 56 8 2502 2855 3016730 3017078 8.930000e-74 289.0
36 TraesCS5D01G011900 chr6D 95.380 1277 57 2 2995 4270 469208181 469209456 0.000000e+00 2030.0
37 TraesCS5D01G011900 chr6D 79.834 362 63 9 2504 2862 340842735 340843089 9.060000e-64 255.0
38 TraesCS5D01G011900 chr6D 81.726 197 26 6 653 848 31830441 31830628 9.450000e-34 156.0
39 TraesCS5D01G011900 chr2D 95.074 1279 59 4 2995 4270 79276815 79278092 0.000000e+00 2010.0
40 TraesCS5D01G011900 chr2D 95.286 297 10 4 4269 4564 86069202 86069495 1.070000e-127 468.0
41 TraesCS5D01G011900 chr2D 93.960 298 16 1 4269 4566 413283903 413283608 3.870000e-122 449.0
42 TraesCS5D01G011900 chr3A 94.639 1287 66 2 2987 4270 447005617 447006903 0.000000e+00 1991.0
43 TraesCS5D01G011900 chr3A 83.008 359 53 7 2502 2858 40522 40170 1.140000e-82 318.0
44 TraesCS5D01G011900 chr3A 83.008 359 53 7 2502 2858 63439 63087 1.140000e-82 318.0
45 TraesCS5D01G011900 chr7B 77.453 856 149 34 5504 6342 717199717 717198889 8.260000e-129 472.0
46 TraesCS5D01G011900 chr7B 87.613 331 38 3 5015 5344 717200315 717199987 1.430000e-101 381.0
47 TraesCS5D01G011900 chr7B 86.970 330 40 2 5015 5344 716724571 716724897 1.120000e-97 368.0
48 TraesCS5D01G011900 chr7B 77.185 675 124 26 5504 6170 716725177 716725829 4.010000e-97 366.0
49 TraesCS5D01G011900 chr7B 81.841 391 50 11 1554 1941 717201869 717201497 6.860000e-80 309.0
50 TraesCS5D01G011900 chr7B 81.000 400 55 10 1545 1941 716723050 716723431 1.480000e-76 298.0
51 TraesCS5D01G011900 chr7B 91.005 189 15 1 656 842 588900011 588899823 3.260000e-63 254.0
52 TraesCS5D01G011900 chr7B 88.889 144 14 1 656 797 747458278 747458135 7.260000e-40 176.0
53 TraesCS5D01G011900 chr7A 86.179 369 46 4 4977 5344 715766426 715766062 1.840000e-105 394.0
54 TraesCS5D01G011900 chr7A 82.750 400 48 10 1545 1941 715768418 715768037 3.150000e-88 337.0
55 TraesCS5D01G011900 chr7A 89.305 187 19 1 656 841 127006211 127006025 4.250000e-57 233.0
56 TraesCS5D01G011900 chrUn 87.311 331 39 3 5015 5344 383782941 383782613 6.670000e-100 375.0
57 TraesCS5D01G011900 chrUn 83.871 310 36 12 2559 2860 90130833 90131136 4.160000e-72 283.0
58 TraesCS5D01G011900 chrUn 85.887 248 32 3 5098 5344 456773174 456773419 1.950000e-65 261.0
59 TraesCS5D01G011900 chrUn 83.784 148 24 0 2711 2858 32151014 32150867 2.650000e-29 141.0
60 TraesCS5D01G011900 chrUn 74.862 362 59 23 2503 2857 46260787 46260451 1.230000e-27 135.0
61 TraesCS5D01G011900 chrUn 86.842 114 13 2 2745 2858 1496786 1496675 7.410000e-25 126.0
62 TraesCS5D01G011900 chrUn 87.805 82 10 0 2772 2853 339339623 339339542 5.810000e-16 97.1
63 TraesCS5D01G011900 chr1B 84.110 365 41 14 2502 2857 67055289 67054933 3.150000e-88 337.0
64 TraesCS5D01G011900 chr1B 84.366 339 45 7 2502 2837 511445463 511445796 6.810000e-85 326.0
65 TraesCS5D01G011900 chr1B 90.055 181 17 1 656 836 12996034 12996213 4.250000e-57 233.0
66 TraesCS5D01G011900 chr1B 87.709 179 21 1 658 836 12410722 12410899 2.570000e-49 207.0
67 TraesCS5D01G011900 chr1B 90.840 131 11 1 706 836 13450317 13450446 2.610000e-39 174.0
68 TraesCS5D01G011900 chr3B 83.747 363 48 10 2504 2862 404620022 404620377 4.070000e-87 333.0
69 TraesCS5D01G011900 chr3B 90.286 175 16 1 667 841 795999022 795999195 1.980000e-55 228.0
70 TraesCS5D01G011900 chr1A 83.657 361 40 14 2502 2853 47213010 47212660 8.810000e-84 322.0
71 TraesCS5D01G011900 chr1A 83.577 274 37 7 2506 2776 481925545 481925813 4.220000e-62 250.0
72 TraesCS5D01G011900 chr1A 82.857 280 37 10 2578 2855 412466812 412467082 2.540000e-59 241.0
73 TraesCS5D01G011900 chr5B 86.047 301 32 8 2559 2858 139410806 139411097 1.470000e-81 315.0
74 TraesCS5D01G011900 chr5B 81.163 361 54 10 2501 2859 491367753 491367405 1.930000e-70 278.0
75 TraesCS5D01G011900 chr5B 88.587 184 20 1 656 839 689864135 689863953 9.190000e-54 222.0
76 TraesCS5D01G011900 chr5B 85.027 187 27 1 656 842 419990163 419990348 9.320000e-44 189.0
77 TraesCS5D01G011900 chr4D 82.909 275 38 7 2503 2773 67319378 67319109 9.130000e-59 239.0
78 TraesCS5D01G011900 chr4D 82.042 284 40 10 2578 2857 211388060 211388336 1.530000e-56 231.0
79 TraesCS5D01G011900 chr4D 78.592 355 57 16 2506 2857 152917032 152916694 4.280000e-52 217.0
80 TraesCS5D01G011900 chr4D 80.565 283 45 9 2579 2857 75046568 75046292 7.150000e-50 209.0
81 TraesCS5D01G011900 chr4D 79.371 286 45 13 2582 2860 427611195 427610917 9.320000e-44 189.0
82 TraesCS5D01G011900 chr4D 84.302 172 21 4 2501 2671 477416372 477416538 5.650000e-36 163.0
83 TraesCS5D01G011900 chr4D 78.279 244 45 8 2615 2853 220346782 220347022 4.400000e-32 150.0
84 TraesCS5D01G011900 chr4D 85.586 111 10 5 2577 2685 102386699 102386805 2.080000e-20 111.0
85 TraesCS5D01G011900 chr4B 78.947 361 61 13 2501 2857 568628290 568628639 1.530000e-56 231.0
86 TraesCS5D01G011900 chr2B 88.172 186 22 0 656 841 157678721 157678536 9.190000e-54 222.0
87 TraesCS5D01G011900 chr2B 87.978 183 20 2 658 840 244870067 244870247 1.540000e-51 215.0


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 TraesCS5D01G011900 chr5D 6443975 6451013 7038 False 12999.000000 12999 100.000000 1 7039 1 chr5D.!!$F1 7038
1 TraesCS5D01G011900 chr5D 363541833 363543103 1270 False 2049.000000 2049 95.755000 2999 4270 1 chr5D.!!$F3 1271
2 TraesCS5D01G011900 chr5D 528583341 528585442 2101 False 1274.000000 2076 95.851000 2992 4564 2 chr5D.!!$F6 1572
3 TraesCS5D01G011900 chr5D 5355326 5359210 3884 False 290.833333 448 82.422167 1020 6586 6 chr5D.!!$F5 5566
4 TraesCS5D01G011900 chr5A 3214279 3219778 5499 True 4687.500000 5192 97.413500 1 7039 2 chr5A.!!$R1 7038
5 TraesCS5D01G011900 chr7D 436839712 436840990 1278 False 2089.000000 2089 96.247000 2999 4270 1 chr7D.!!$F1 1271
6 TraesCS5D01G011900 chr1D 491719189 491720463 1274 False 2015.000000 2015 95.219000 2997 4270 1 chr1D.!!$F5 1273
7 TraesCS5D01G011900 chr1D 398094492 398096624 2132 False 1264.500000 2076 95.166500 2995 4566 2 chr1D.!!$F6 1571
8 TraesCS5D01G011900 chr3D 575541386 575542658 1272 False 2061.000000 2061 95.859000 2993 4270 1 chr3D.!!$F2 1277
9 TraesCS5D01G011900 chr6D 469208181 469209456 1275 False 2030.000000 2030 95.380000 2995 4270 1 chr6D.!!$F3 1275
10 TraesCS5D01G011900 chr2D 79276815 79278092 1277 False 2010.000000 2010 95.074000 2995 4270 1 chr2D.!!$F1 1275
11 TraesCS5D01G011900 chr3A 447005617 447006903 1286 False 1991.000000 1991 94.639000 2987 4270 1 chr3A.!!$F1 1283
12 TraesCS5D01G011900 chr7B 717198889 717201869 2980 True 387.333333 472 82.302333 1554 6342 3 chr7B.!!$R3 4788
13 TraesCS5D01G011900 chr7B 716723050 716725829 2779 False 344.000000 368 81.718333 1545 6170 3 chr7B.!!$F1 4625
14 TraesCS5D01G011900 chr7A 715766062 715768418 2356 True 365.500000 394 84.464500 1545 5344 2 chr7A.!!$R2 3799

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
870 876 2.157279 GCGAGCAGCTCTTATATTGCAG 59.843 50.0 20.39 1.75 44.04 4.41 F
2728 2918 1.175654 CATGGTTGCATGTGCTGGTA 58.824 50.0 6.55 0.00 42.66 3.25 F
3435 3644 0.558220 TGGGTCTCGGATCTCCTGAT 59.442 55.0 0.00 0.00 35.26 2.90 F
4200 4701 1.644509 ACACTCTATGCTGGTGGACA 58.355 50.0 0.00 0.00 35.53 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2785 2975 0.821517 AAGCATGCCACATCACCATG 59.178 50.000 15.66 0.0 39.38 3.66 R
4590 5651 1.072331 TGAAGGCTTGAGGTCAGGAAC 59.928 52.381 3.46 0.0 0.00 3.62 R
4603 5664 2.235402 CAGGCATTGGATTTTGAAGGCT 59.765 45.455 0.00 0.0 0.00 4.58 R
6088 7638 2.833794 TGCTTGGTGTAGACAGTTGAC 58.166 47.619 0.00 0.0 0.00 3.18 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
127 132 4.221703 CCTATGATGCCCTTACTACAGGAG 59.778 50.000 0.00 0.00 35.71 3.69
151 156 8.068892 AGGTCTTAGTAGTGGATTAGTTGAAG 57.931 38.462 0.00 0.00 0.00 3.02
256 261 4.080582 TGGTTGTGGGATTCTCAATCGTAT 60.081 41.667 0.00 0.00 38.82 3.06
281 286 8.282455 TGGTCTTGTTAAAACACATCTACAAA 57.718 30.769 0.00 0.00 38.92 2.83
646 652 8.198109 GGCTATTATATTCCTCGCATCTAGAAA 58.802 37.037 0.00 0.00 0.00 2.52
682 688 6.510879 TTAGATCGTGTCTATTATGCGGAT 57.489 37.500 0.00 0.00 39.14 4.18
712 718 2.903784 TCTGTATTGGTGCAGGTGTACT 59.096 45.455 0.00 0.00 38.45 2.73
727 733 3.553508 GGTGTACTGACTTTGTTCGCCTA 60.554 47.826 0.00 0.00 34.16 3.93
740 746 2.506472 GCCTAGAAGGGGGCTTCG 59.494 66.667 0.00 0.00 44.48 3.79
742 748 2.444256 CCTAGAAGGGGGCTTCGGG 61.444 68.421 0.00 0.00 38.31 5.14
767 773 9.573133 GGTTGATCCTTGTATTAATTTTGTCAG 57.427 33.333 0.00 0.00 0.00 3.51
870 876 2.157279 GCGAGCAGCTCTTATATTGCAG 59.843 50.000 20.39 1.75 44.04 4.41
965 971 3.007398 AGACAGAGGGAAGCAAGTACTTG 59.993 47.826 27.85 27.85 43.14 3.16
1658 1679 2.865343 AATGTCGAGGGTACGTCATC 57.135 50.000 0.00 0.00 44.35 2.92
1936 2002 3.138304 AGTCGATTTGCTTGTTACTGCA 58.862 40.909 0.00 0.32 37.42 4.41
2498 2688 6.094881 TGAACAAAAGTGGGTAGAAAGTCTTG 59.905 38.462 0.00 0.00 0.00 3.02
2728 2918 1.175654 CATGGTTGCATGTGCTGGTA 58.824 50.000 6.55 0.00 42.66 3.25
2968 3160 2.923020 GGCCATCAAAATTACAAGCACG 59.077 45.455 0.00 0.00 0.00 5.34
2971 3163 4.175516 CCATCAAAATTACAAGCACGCAT 58.824 39.130 0.00 0.00 0.00 4.73
3069 3276 4.157120 AGCCGGCGCTAAATCCGT 62.157 61.111 23.20 0.00 46.08 4.69
3182 3390 2.027192 GGCGAGAATAGGCCCATATTCA 60.027 50.000 20.92 0.00 42.28 2.57
3407 3616 0.593618 GATCATGCTGCAGCTGATGG 59.406 55.000 36.60 24.31 42.66 3.51
3435 3644 0.558220 TGGGTCTCGGATCTCCTGAT 59.442 55.000 0.00 0.00 35.26 2.90
3681 3890 2.892640 CCCGCTCGACATCCTTCA 59.107 61.111 0.00 0.00 0.00 3.02
3746 3955 1.823250 GCCACAGGGTTTGAGATGGTT 60.823 52.381 0.00 0.00 36.17 3.67
4169 4670 4.947147 GCCACCACTGCCCGACAA 62.947 66.667 0.00 0.00 0.00 3.18
4200 4701 1.644509 ACACTCTATGCTGGTGGACA 58.355 50.000 0.00 0.00 35.53 4.02
4434 5494 2.671070 CTGGGTTCGGCCTGTGAT 59.329 61.111 0.00 0.00 37.43 3.06
4603 5664 0.534203 GGCAACGTTCCTGACCTCAA 60.534 55.000 0.00 0.00 0.00 3.02
4657 5718 3.703001 TTTTGTGGAAGCCAACCAAAA 57.297 38.095 9.54 9.54 37.24 2.44
5455 6975 2.124122 GGTTTTCCGAACAATGTGTGC 58.876 47.619 0.00 0.00 0.00 4.57
5657 7201 7.402811 TTTCTAACACGACAATAACAGACTG 57.597 36.000 0.00 0.00 0.00 3.51
6088 7638 3.502211 AGAGGGTGCACAATTAAGAAACG 59.498 43.478 20.43 0.00 0.00 3.60
6123 7682 6.286758 ACACCAAGCAATGTCTAGATATCTG 58.713 40.000 15.79 5.75 0.00 2.90
6154 7713 0.749649 GTGGTTGAAATGTGGTGGCA 59.250 50.000 0.00 0.00 0.00 4.92
6209 7768 6.558771 TGCACATATTACCATGAATAGTGC 57.441 37.500 20.25 20.25 41.15 4.40
6530 8181 5.594926 CTTCAACCATTTTGAAGTCTTGCT 58.405 37.500 15.58 0.00 46.17 3.91
6638 8291 1.406539 GCATCTTGTCATTCCGCCAAT 59.593 47.619 0.00 0.00 0.00 3.16
6672 8325 9.150348 CTTAGTTTTGGTGAAGTTGTTGAATTT 57.850 29.630 0.00 0.00 0.00 1.82
6681 8334 6.901357 GTGAAGTTGTTGAATTTTTCATGCAC 59.099 34.615 0.00 0.00 39.84 4.57
6734 8387 1.561542 AGCCACTTCAATGTCCTAGGG 59.438 52.381 9.46 0.00 0.00 3.53
6746 8399 7.867921 TCAATGTCCTAGGGTACATGTATTTT 58.132 34.615 15.03 0.35 36.47 1.82
6821 8474 4.104738 ACCCTCCAGATCTGAAACTCAAAA 59.895 41.667 24.62 0.00 0.00 2.44
6822 8475 5.072741 CCCTCCAGATCTGAAACTCAAAAA 58.927 41.667 24.62 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 132 7.838884 ACTTCAACTAATCCACTACTAAGACC 58.161 38.462 0.00 0.00 0.00 3.85
151 156 7.439655 CCTGAAATTCCATAGTGCTTCTACTAC 59.560 40.741 0.00 0.00 36.09 2.73
256 261 7.867305 TTGTAGATGTGTTTTAACAAGACCA 57.133 32.000 0.00 0.00 41.21 4.02
281 286 5.131142 AGACTTAGTGCAATACTTAGGGCAT 59.869 40.000 0.00 0.00 39.71 4.40
463 468 1.945354 TAGCTGGAGCCACGTGTAGC 61.945 60.000 15.65 11.80 43.38 3.58
646 652 7.500992 AGACACGATCTAATCCACATTAATGT 58.499 34.615 15.47 15.47 37.42 2.71
682 688 3.278574 GCACCAATACAGATGTGCCTTA 58.721 45.455 2.19 0.00 46.33 2.69
703 709 2.221055 GCGAACAAAGTCAGTACACCTG 59.779 50.000 0.00 0.00 42.97 4.00
712 718 2.289444 CCCTTCTAGGCGAACAAAGTCA 60.289 50.000 0.00 0.00 32.73 3.41
727 733 2.531942 AACCCGAAGCCCCCTTCT 60.532 61.111 2.44 0.00 44.24 2.85
740 746 8.527810 TGACAAAATTAATACAAGGATCAACCC 58.472 33.333 0.00 0.00 40.05 4.11
859 865 5.418840 AGGGAAAACACCACTGCAATATAAG 59.581 40.000 0.00 0.00 0.00 1.73
870 876 3.505835 TCCACAGGGAAAACACCAC 57.494 52.632 0.00 0.00 41.32 4.16
965 971 1.227002 GGCACTGCTAGCTACCGTC 60.227 63.158 17.23 0.00 0.00 4.79
1222 1235 1.206831 CGCAGACGTCGACAGAGAA 59.793 57.895 17.16 0.00 33.53 2.87
1325 1340 1.332375 CGAGTGGGCGTTCAAGAAAAA 59.668 47.619 0.00 0.00 0.00 1.94
1658 1679 8.948631 TGCTCAAAATAGGATTACTTCTACTG 57.051 34.615 0.00 0.00 0.00 2.74
2023 2164 1.545136 TGTGTATGCGTCGGGAAACTA 59.455 47.619 0.00 0.00 0.00 2.24
2477 2663 4.338118 TGCAAGACTTTCTACCCACTTTTG 59.662 41.667 0.00 0.00 0.00 2.44
2498 2688 2.548480 GCGGGGTATCATCTAGTTTTGC 59.452 50.000 0.00 0.00 0.00 3.68
2785 2975 0.821517 AAGCATGCCACATCACCATG 59.178 50.000 15.66 0.00 39.38 3.66
2860 3051 4.946160 TGACTGGGTCCTTCCAATTAAT 57.054 40.909 0.00 0.00 36.21 1.40
2968 3160 2.041620 TCCATCCAAATAGCCCCTATGC 59.958 50.000 0.00 0.00 0.00 3.14
2971 3163 2.979678 GACTCCATCCAAATAGCCCCTA 59.020 50.000 0.00 0.00 0.00 3.53
3017 3214 1.602377 GATTTTTATGCGTCCCGAGGG 59.398 52.381 0.65 0.65 0.00 4.30
3021 3218 0.375454 TGCGATTTTTATGCGTCCCG 59.625 50.000 0.00 0.00 0.00 5.14
3022 3219 1.533129 GGTGCGATTTTTATGCGTCCC 60.533 52.381 0.00 0.00 0.00 4.46
3435 3644 1.757118 GACTGCCTACCTCAGTATGCA 59.243 52.381 0.00 0.00 44.64 3.96
3501 3710 5.756347 TGTTTGACACTGAACCATACTACAC 59.244 40.000 0.00 0.00 0.00 2.90
3681 3890 2.652590 GAAGATTCAGGAGGCTTGCAT 58.347 47.619 0.00 0.00 0.00 3.96
4169 4670 6.428159 CCAGCATAGAGTGTTTCTACAAGTTT 59.572 38.462 0.00 0.00 41.10 2.66
4200 4701 2.896854 CTATGTGCGCATGGCCGT 60.897 61.111 22.84 4.24 42.61 5.68
4212 4713 3.181499 GGTGATTCACTCGACGACTATGT 60.181 47.826 16.02 0.00 34.40 2.29
4418 5478 2.668632 GATCACAGGCCGAACCCA 59.331 61.111 0.00 0.00 40.58 4.51
4463 5523 2.668212 CCAGGACGCCGAAAAGCA 60.668 61.111 0.00 0.00 0.00 3.91
4507 5567 2.429069 CACTTTTTCGGCGCTGGC 60.429 61.111 17.88 0.00 38.90 4.85
4583 5644 1.671379 GAGGTCAGGAACGTTGCCC 60.671 63.158 16.78 10.66 0.00 5.36
4590 5651 1.072331 TGAAGGCTTGAGGTCAGGAAC 59.928 52.381 3.46 0.00 0.00 3.62
4603 5664 2.235402 CAGGCATTGGATTTTGAAGGCT 59.765 45.455 0.00 0.00 0.00 4.58
4632 5693 2.364002 GGTTGGCTTCCACAAAAAGCTA 59.636 45.455 7.68 0.00 46.59 3.32
4657 5718 4.295201 TGTATCTAAGTGTGTATGGGGCT 58.705 43.478 0.00 0.00 0.00 5.19
5657 7201 6.668541 TGTCATGAACTTAGCTTTCTATGC 57.331 37.500 0.00 0.00 0.00 3.14
6088 7638 2.833794 TGCTTGGTGTAGACAGTTGAC 58.166 47.619 0.00 0.00 0.00 3.18
6123 7682 8.237267 CCACATTTCAACCACTAATAGAAAGAC 58.763 37.037 0.00 0.00 32.45 3.01
6209 7768 4.481930 TGTATGTGTTCTTTTCTTGGCG 57.518 40.909 0.00 0.00 0.00 5.69
6530 8181 6.697019 GTGCAAAATAAAGCTTGACTTCTTGA 59.303 34.615 0.00 0.00 37.75 3.02
6638 8291 4.139859 TCACCAAAACTAAGTGTCGGAA 57.860 40.909 0.00 0.00 33.21 4.30
6672 8325 3.508402 AGCTGTGAATGATGTGCATGAAA 59.492 39.130 0.00 0.00 37.28 2.69
6681 8334 3.806380 AGCCTAAGAGCTGTGAATGATG 58.194 45.455 0.00 0.00 42.95 3.07
6734 8387 9.979270 CACTCTTTCTCATCAAAATACATGTAC 57.021 33.333 7.96 0.00 0.00 2.90
6746 8399 4.141505 TGGGTTCAACACTCTTTCTCATCA 60.142 41.667 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.