Multiple sequence alignment - TraesCS3A01G163600

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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 TraesCS3A01G163600 chr3A 100.000 3186 0 0 1 3186 166922329 166925514 0.000000e+00 5884.0
1 TraesCS3A01G163600 chr3A 95.261 211 10 0 2976 3186 181107338 181107548 5.090000e-88 335.0
2 TraesCS3A01G163600 chr3A 90.066 151 8 2 848 998 177859727 177859870 4.200000e-44 189.0
3 TraesCS3A01G163600 chr3A 88.333 60 5 2 2363 2421 166924661 166924719 1.590000e-08 71.3
4 TraesCS3A01G163600 chr3A 88.333 60 5 2 2333 2391 166924691 166924749 1.590000e-08 71.3
5 TraesCS3A01G163600 chr3D 92.526 1512 59 7 926 2391 149544036 149545539 0.000000e+00 2117.0
6 TraesCS3A01G163600 chr3D 92.571 1373 65 10 926 2262 149204875 149206246 0.000000e+00 1936.0
7 TraesCS3A01G163600 chr3D 93.812 1115 40 11 926 2011 147336227 147335113 0.000000e+00 1650.0
8 TraesCS3A01G163600 chr3D 93.599 828 38 6 2363 3186 149545480 149546296 0.000000e+00 1221.0
9 TraesCS3A01G163600 chr3D 91.768 826 56 8 1099 1918 141410595 141411414 0.000000e+00 1138.0
10 TraesCS3A01G163600 chr3D 84.921 1008 120 15 1150 2139 360691527 360692520 0.000000e+00 990.0
11 TraesCS3A01G163600 chr3D 87.561 820 87 12 6 818 147425232 147424421 0.000000e+00 935.0
12 TraesCS3A01G163600 chr3D 96.209 211 8 0 2976 3186 149767523 149767313 2.350000e-91 346.0
13 TraesCS3A01G163600 chr3D 87.448 239 14 2 2043 2265 147334799 147334561 8.770000e-66 261.0
14 TraesCS3A01G163600 chr3D 87.736 212 13 6 2976 3186 149207004 149207203 5.310000e-58 235.0
15 TraesCS3A01G163600 chr3B 90.521 1287 72 24 1000 2269 221912358 221913611 0.000000e+00 1655.0
16 TraesCS3A01G163600 chr3B 89.821 1287 71 25 1000 2269 221979838 221981081 0.000000e+00 1596.0
17 TraesCS3A01G163600 chr3B 89.677 1269 72 20 1004 2259 215572008 215573230 0.000000e+00 1563.0
18 TraesCS3A01G163600 chr3B 93.678 1044 58 1 1000 2035 215104678 215105721 0.000000e+00 1555.0
19 TraesCS3A01G163600 chr3B 88.846 1291 90 27 1000 2269 215385072 215386329 0.000000e+00 1537.0
20 TraesCS3A01G163600 chr3B 88.259 1252 95 23 1000 2237 215310446 215311659 0.000000e+00 1450.0
21 TraesCS3A01G163600 chr3B 92.719 879 34 9 1534 2391 221749621 221750490 0.000000e+00 1242.0
22 TraesCS3A01G163600 chr3B 89.689 708 46 14 2506 3186 221981527 221982234 0.000000e+00 878.0
23 TraesCS3A01G163600 chr3B 89.548 708 46 14 2506 3186 221914043 221914749 0.000000e+00 872.0
24 TraesCS3A01G163600 chr3B 87.553 707 58 15 2505 3186 215386788 215387489 0.000000e+00 791.0
25 TraesCS3A01G163600 chr3B 90.000 450 41 4 2367 2813 215115108 215115556 2.130000e-161 579.0
26 TraesCS3A01G163600 chr3B 85.817 557 44 16 2505 3036 221467325 221467871 2.780000e-155 558.0
27 TraesCS3A01G163600 chr3B 93.503 354 20 3 2835 3186 221753057 221753409 1.010000e-144 523.0
28 TraesCS3A01G163600 chr3B 86.242 487 43 12 1533 2004 469631613 469632090 1.020000e-139 507.0
29 TraesCS3A01G163600 chr3B 92.330 352 23 1 2835 3186 215115615 215115962 6.140000e-137 497.0
30 TraesCS3A01G163600 chr3B 87.147 389 28 8 2355 2738 221750419 221750790 3.800000e-114 422.0
31 TraesCS3A01G163600 chr3B 85.752 379 23 13 2031 2391 215114800 215115165 3.880000e-99 372.0
32 TraesCS3A01G163600 chr3B 79.331 508 61 21 441 937 221911886 221912360 1.840000e-82 316.0
33 TraesCS3A01G163600 chr3B 79.331 508 61 22 441 937 221979366 221979840 1.840000e-82 316.0
34 TraesCS3A01G163600 chr3B 87.245 196 18 5 744 937 215104490 215104680 1.920000e-52 217.0
35 TraesCS3A01G163600 chr3B 96.063 127 5 0 3060 3186 221467864 221467990 1.160000e-49 207.0
36 TraesCS3A01G163600 chr3B 93.893 131 6 1 2139 2269 221466846 221466974 2.510000e-46 196.0
37 TraesCS3A01G163600 chr3B 92.453 106 8 0 2732 2837 221752849 221752954 5.500000e-33 152.0
38 TraesCS3A01G163600 chr6A 85.103 1168 118 32 1000 2141 146441722 146440585 0.000000e+00 1142.0
39 TraesCS3A01G163600 chr1D 76.136 176 25 9 133 307 440750414 440750573 3.410000e-10 76.8


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 TraesCS3A01G163600 chr3A 166922329 166925514 3185 False 2008.866667 5884 92.222000 1 3186 3 chr3A.!!$F3 3185
1 TraesCS3A01G163600 chr3D 149544036 149546296 2260 False 1669.000000 2117 93.062500 926 3186 2 chr3D.!!$F4 2260
2 TraesCS3A01G163600 chr3D 141410595 141411414 819 False 1138.000000 1138 91.768000 1099 1918 1 chr3D.!!$F1 819
3 TraesCS3A01G163600 chr3D 149204875 149207203 2328 False 1085.500000 1936 90.153500 926 3186 2 chr3D.!!$F3 2260
4 TraesCS3A01G163600 chr3D 360691527 360692520 993 False 990.000000 990 84.921000 1150 2139 1 chr3D.!!$F2 989
5 TraesCS3A01G163600 chr3D 147334561 147336227 1666 True 955.500000 1650 90.630000 926 2265 2 chr3D.!!$R3 1339
6 TraesCS3A01G163600 chr3D 147424421 147425232 811 True 935.000000 935 87.561000 6 818 1 chr3D.!!$R1 812
7 TraesCS3A01G163600 chr3B 215572008 215573230 1222 False 1563.000000 1563 89.677000 1004 2259 1 chr3B.!!$F2 1255
8 TraesCS3A01G163600 chr3B 215310446 215311659 1213 False 1450.000000 1450 88.259000 1000 2237 1 chr3B.!!$F1 1237
9 TraesCS3A01G163600 chr3B 215385072 215387489 2417 False 1164.000000 1537 88.199500 1000 3186 2 chr3B.!!$F6 2186
10 TraesCS3A01G163600 chr3B 221911886 221914749 2863 False 947.666667 1655 86.466667 441 3186 3 chr3B.!!$F9 2745
11 TraesCS3A01G163600 chr3B 221979366 221982234 2868 False 930.000000 1596 86.280333 441 3186 3 chr3B.!!$F10 2745
12 TraesCS3A01G163600 chr3B 215104490 215105721 1231 False 886.000000 1555 90.461500 744 2035 2 chr3B.!!$F4 1291
13 TraesCS3A01G163600 chr3B 221749621 221753409 3788 False 584.750000 1242 91.455500 1534 3186 4 chr3B.!!$F8 1652
14 TraesCS3A01G163600 chr3B 215114800 215115962 1162 False 482.666667 579 89.360667 2031 3186 3 chr3B.!!$F5 1155
15 TraesCS3A01G163600 chr3B 221466846 221467990 1144 False 320.333333 558 91.924333 2139 3186 3 chr3B.!!$F7 1047
16 TraesCS3A01G163600 chr6A 146440585 146441722 1137 True 1142.000000 1142 85.103000 1000 2141 1 chr6A.!!$R1 1141


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
231 232 0.036388 TTTACGAGAAGCCTGGCCTG 60.036 55.0 16.57 2.54 0.0 4.85 F
1162 1227 0.411058 AGGGCCTGGAGCAAGATTTT 59.589 50.0 4.50 0.00 46.5 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1795 0.179000 AGCCGGTGATGGTGATCTTC 59.821 55.000 1.9 0.0 0.0 2.87 R
3037 6311 1.134965 CAGAGTAGCTTGTTCCCCTCG 60.135 57.143 0.0 0.0 0.0 4.63 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
26 27 2.772287 GGTCTGTGAAGCAGCTACTTT 58.228 47.619 0.00 0.00 44.66 2.66
27 28 2.481952 GGTCTGTGAAGCAGCTACTTTG 59.518 50.000 0.00 0.00 44.66 2.77
58 59 0.383231 AATACGTAACGAGGAGCGGG 59.617 55.000 0.00 0.00 46.49 6.13
75 76 1.066752 GGGTTTGCGTGTTTGGTCC 59.933 57.895 0.00 0.00 0.00 4.46
84 85 1.278127 CGTGTTTGGTCCCTATCCTGT 59.722 52.381 0.00 0.00 0.00 4.00
89 90 0.716591 TGGTCCCTATCCTGTGAGGT 59.283 55.000 0.00 0.00 36.53 3.85
97 98 1.693627 ATCCTGTGAGGTAGTAGCCG 58.306 55.000 0.00 0.00 36.53 5.52
100 101 0.377554 CTGTGAGGTAGTAGCCGACG 59.622 60.000 0.00 0.00 0.00 5.12
114 115 2.024868 CGACGTGGCATGAACGGAA 61.025 57.895 20.89 0.00 45.20 4.30
136 137 2.885266 CACTTGATAGGCCTAGCGTAGA 59.115 50.000 27.19 8.97 32.49 2.59
138 139 2.953284 TGATAGGCCTAGCGTAGACT 57.047 50.000 22.50 0.26 32.49 3.24
140 141 1.733360 GATAGGCCTAGCGTAGACTCG 59.267 57.143 19.33 0.00 32.49 4.18
153 154 1.745489 GACTCGGGCATGGACAACC 60.745 63.158 0.00 0.00 0.00 3.77
159 160 0.464554 GGGCATGGACAACCTAGCTC 60.465 60.000 0.00 0.00 37.05 4.09
160 161 0.253044 GGCATGGACAACCTAGCTCA 59.747 55.000 0.00 0.00 37.05 4.26
174 175 1.589113 GCTCAGATAGCCTAGCCCG 59.411 63.158 0.00 0.00 46.25 6.13
180 181 0.320858 GATAGCCTAGCCCGAAAGCC 60.321 60.000 0.00 0.00 0.00 4.35
200 201 2.039624 ACATCTGGGTCGGGCTCT 59.960 61.111 0.00 0.00 0.00 4.09
201 202 2.022240 GACATCTGGGTCGGGCTCTC 62.022 65.000 0.00 0.00 0.00 3.20
213 214 0.957888 GGGCTCTCGCTCTGCTTTTT 60.958 55.000 0.00 0.00 32.44 1.94
230 231 0.690762 TTTTACGAGAAGCCTGGCCT 59.309 50.000 16.57 6.05 0.00 5.19
231 232 0.036388 TTTACGAGAAGCCTGGCCTG 60.036 55.000 16.57 2.54 0.00 4.85
234 235 1.003355 CGAGAAGCCTGGCCTGAAA 60.003 57.895 16.57 0.00 0.00 2.69
237 238 1.979155 GAAGCCTGGCCTGAAACCC 60.979 63.158 16.57 0.00 0.00 4.11
249 250 3.089284 CCTGAAACCCGAAAATAAGCCT 58.911 45.455 0.00 0.00 0.00 4.58
250 251 4.266714 CCTGAAACCCGAAAATAAGCCTA 58.733 43.478 0.00 0.00 0.00 3.93
256 257 6.408107 AACCCGAAAATAAGCCTAAACAAA 57.592 33.333 0.00 0.00 0.00 2.83
321 322 6.704289 ATTTTAAATACCGGCCCTAAAGAC 57.296 37.500 0.00 0.00 0.00 3.01
324 325 6.497624 TTAAATACCGGCCCTAAAGACATA 57.502 37.500 0.00 0.00 0.00 2.29
335 336 9.063615 CGGCCCTAAAGACATATTTTAAATACT 57.936 33.333 0.00 0.00 0.00 2.12
385 387 8.261492 AGTTACTGTTCATCTATTTTGAGCTG 57.739 34.615 0.00 0.00 32.27 4.24
420 422 4.565022 CAACGGCTTGGGATTTTAATGTT 58.435 39.130 0.00 0.00 0.00 2.71
445 447 2.188062 TTACAAAGCCCGACCGAAAT 57.812 45.000 0.00 0.00 0.00 2.17
454 456 1.641123 CCGACCGAAATCAAACCCGG 61.641 60.000 0.00 0.00 46.65 5.73
456 458 1.228306 ACCGAAATCAAACCCGGCA 60.228 52.632 0.00 0.00 45.29 5.69
457 459 0.610785 ACCGAAATCAAACCCGGCAT 60.611 50.000 0.00 0.00 45.29 4.40
487 489 4.126524 GGTTTAGCCTAGCCGCAG 57.873 61.111 0.00 0.00 0.00 5.18
529 531 9.528018 TGTCACTTTGATTTATTTTTCTTCACC 57.472 29.630 0.00 0.00 0.00 4.02
530 532 8.978539 GTCACTTTGATTTATTTTTCTTCACCC 58.021 33.333 0.00 0.00 0.00 4.61
714 727 3.776340 ACAAATGTTCCCGTGTTTCAAC 58.224 40.909 0.00 0.00 0.00 3.18
725 738 4.732923 CCCGTGTTTCAACAAATATATGCG 59.267 41.667 0.00 0.00 41.21 4.73
871 888 8.089115 AGATTAGATTAGAAAATTAGCGCCAC 57.911 34.615 2.29 0.00 0.00 5.01
878 895 1.356527 AAATTAGCGCCACCGACGTC 61.357 55.000 2.29 5.18 36.29 4.34
888 905 2.478200 GCCACCGACGTCAAAAAGAAAA 60.478 45.455 17.16 0.00 0.00 2.29
889 906 3.760537 CCACCGACGTCAAAAAGAAAAA 58.239 40.909 17.16 0.00 0.00 1.94
983 1000 5.034852 TGCGGATCCAAGAATCAGATTTA 57.965 39.130 13.41 0.00 0.00 1.40
1056 1100 5.908341 ACCCTAGTTTTCGATCTGATCTTC 58.092 41.667 15.16 2.27 0.00 2.87
1162 1227 0.411058 AGGGCCTGGAGCAAGATTTT 59.589 50.000 4.50 0.00 46.50 1.82
1579 1644 3.037549 GTGGATCAATCTGAGAGTCCCT 58.962 50.000 0.00 0.00 0.00 4.20
2155 2565 5.821470 CAGTTGTTAGCCATCAGAATCAGAT 59.179 40.000 0.00 0.00 0.00 2.90
2337 2918 7.667043 TCACTGTAATTGGTGTCTGAATTAC 57.333 36.000 0.00 0.00 41.99 1.89
2461 3445 4.337060 GCAACGGGCCAACGGTTC 62.337 66.667 4.39 0.00 40.20 3.62
2462 3446 4.020378 CAACGGGCCAACGGTTCG 62.020 66.667 4.39 0.00 40.20 3.95
2467 3451 4.700365 GGCCAACGGTTCGCTTGC 62.700 66.667 10.22 0.00 0.00 4.01
2484 3468 6.389091 TCGCTTGCAAGTGAAATTGATAAAT 58.611 32.000 34.34 0.00 42.13 1.40
2485 3469 6.867816 TCGCTTGCAAGTGAAATTGATAAATT 59.132 30.769 34.34 0.00 42.13 1.82
2486 3470 7.384660 TCGCTTGCAAGTGAAATTGATAAATTT 59.615 29.630 34.34 0.00 42.13 1.82
2487 3471 7.685304 CGCTTGCAAGTGAAATTGATAAATTTC 59.315 33.333 31.64 18.16 44.99 2.17
2488 3472 8.715088 GCTTGCAAGTGAAATTGATAAATTTCT 58.285 29.630 26.55 6.93 45.01 2.52
2490 3474 9.761504 TTGCAAGTGAAATTGATAAATTTCTGA 57.238 25.926 23.18 6.93 45.01 3.27
2491 3475 9.932207 TGCAAGTGAAATTGATAAATTTCTGAT 57.068 25.926 23.18 10.60 45.01 2.90
2497 3481 9.590451 TGAAATTGATAAATTTCTGATGAAGGC 57.410 29.630 23.18 1.08 45.01 4.35
2498 3482 9.813446 GAAATTGATAAATTTCTGATGAAGGCT 57.187 29.630 17.83 0.00 42.75 4.58
2499 3483 9.595823 AAATTGATAAATTTCTGATGAAGGCTG 57.404 29.630 0.00 0.00 33.28 4.85
2500 3484 6.140303 TGATAAATTTCTGATGAAGGCTGC 57.860 37.500 0.00 0.00 33.28 5.25
2501 3485 5.653330 TGATAAATTTCTGATGAAGGCTGCA 59.347 36.000 0.00 0.00 33.28 4.41
2502 3486 4.877378 AAATTTCTGATGAAGGCTGCAA 57.123 36.364 0.00 0.00 33.28 4.08
2503 3487 4.877378 AATTTCTGATGAAGGCTGCAAA 57.123 36.364 0.00 0.00 33.28 3.68
2504 3488 4.877378 ATTTCTGATGAAGGCTGCAAAA 57.123 36.364 0.00 0.00 33.28 2.44
2505 3489 4.877378 TTTCTGATGAAGGCTGCAAAAT 57.123 36.364 0.00 0.00 33.28 1.82
2506 3490 4.877378 TTCTGATGAAGGCTGCAAAATT 57.123 36.364 0.00 0.00 0.00 1.82
2507 3491 4.182693 TCTGATGAAGGCTGCAAAATTG 57.817 40.909 0.00 0.00 0.00 2.32
2508 3492 3.827876 TCTGATGAAGGCTGCAAAATTGA 59.172 39.130 0.00 0.00 0.00 2.57
2509 3493 4.464951 TCTGATGAAGGCTGCAAAATTGAT 59.535 37.500 0.00 0.00 0.00 2.57
2510 3494 5.653330 TCTGATGAAGGCTGCAAAATTGATA 59.347 36.000 0.00 0.00 0.00 2.15
2511 3495 6.153170 TCTGATGAAGGCTGCAAAATTGATAA 59.847 34.615 0.00 0.00 0.00 1.75
2512 3496 6.699366 TGATGAAGGCTGCAAAATTGATAAA 58.301 32.000 0.00 0.00 0.00 1.40
2545 3558 4.331968 AGGCTACAATTCCAATCGACAAA 58.668 39.130 0.00 0.00 0.00 2.83
2766 5872 9.087424 GATTGGAAAATAAAATAGCCAACTGTC 57.913 33.333 0.00 0.00 38.12 3.51
2781 5887 5.525378 GCCAACTGTCGATTTCTGAGATAAT 59.475 40.000 0.00 0.00 0.00 1.28
2871 6119 6.869421 ACATTTTCAGTCACAAAACGAAAG 57.131 33.333 0.00 0.00 0.00 2.62
3037 6311 5.024785 ACTAGCAAAATCTACTGCCTACC 57.975 43.478 0.00 0.00 39.47 3.18
3059 6336 0.324943 GGGGAACAAGCTACTCTGCA 59.675 55.000 0.00 0.00 34.99 4.41
3119 6397 1.618861 CACCTAGAGAAGTTGTCGCG 58.381 55.000 0.00 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.184970 TTTGGGCAGGCCAAAGTAGC 61.185 55.000 32.21 5.62 37.98 3.58
26 27 0.540830 ACGTATTTTTGGGCAGGCCA 60.541 50.000 12.83 12.83 37.98 5.36
27 28 1.465794 TACGTATTTTTGGGCAGGCC 58.534 50.000 5.91 5.91 0.00 5.19
40 41 1.450531 CCCCGCTCCTCGTTACGTAT 61.451 60.000 4.24 0.00 36.19 3.06
58 59 1.066752 GGGACCAAACACGCAAACC 59.933 57.895 0.00 0.00 0.00 3.27
75 76 3.158676 GGCTACTACCTCACAGGATAGG 58.841 54.545 0.00 0.00 37.67 2.57
84 85 1.028330 CCACGTCGGCTACTACCTCA 61.028 60.000 0.00 0.00 0.00 3.86
97 98 1.225376 TGTTCCGTTCATGCCACGTC 61.225 55.000 14.00 6.84 35.81 4.34
100 101 0.951558 AAGTGTTCCGTTCATGCCAC 59.048 50.000 0.00 0.00 0.00 5.01
105 106 3.270877 GCCTATCAAGTGTTCCGTTCAT 58.729 45.455 0.00 0.00 0.00 2.57
110 111 2.803492 GCTAGGCCTATCAAGTGTTCCG 60.803 54.545 14.30 0.00 0.00 4.30
114 115 1.486211 ACGCTAGGCCTATCAAGTGT 58.514 50.000 14.30 13.39 0.00 3.55
136 137 0.907704 TAGGTTGTCCATGCCCGAGT 60.908 55.000 0.00 0.00 35.89 4.18
138 139 1.904771 CTAGGTTGTCCATGCCCGA 59.095 57.895 0.00 0.00 35.89 5.14
140 141 0.464554 GAGCTAGGTTGTCCATGCCC 60.465 60.000 0.00 0.00 35.78 5.36
159 160 1.606737 GCTTTCGGGCTAGGCTATCTG 60.607 57.143 16.80 5.63 0.00 2.90
160 161 0.682292 GCTTTCGGGCTAGGCTATCT 59.318 55.000 16.80 0.00 0.00 1.98
174 175 4.225497 CCCAGATGTCGGGCTTTC 57.775 61.111 0.00 0.00 36.72 2.62
213 214 0.902984 TCAGGCCAGGCTTCTCGTAA 60.903 55.000 12.43 0.00 0.00 3.18
230 231 5.535406 TGTTTAGGCTTATTTTCGGGTTTCA 59.465 36.000 0.00 0.00 0.00 2.69
231 232 6.016213 TGTTTAGGCTTATTTTCGGGTTTC 57.984 37.500 0.00 0.00 0.00 2.78
234 235 5.566032 GCTTTGTTTAGGCTTATTTTCGGGT 60.566 40.000 0.00 0.00 0.00 5.28
237 238 8.682128 TTATGCTTTGTTTAGGCTTATTTTCG 57.318 30.769 0.00 0.00 0.00 3.46
295 296 9.506018 GTCTTTAGGGCCGGTATTTAAAATATA 57.494 33.333 1.90 0.00 0.00 0.86
309 310 9.063615 AGTATTTAAAATATGTCTTTAGGGCCG 57.936 33.333 0.00 0.00 0.00 6.13
361 363 7.414540 CCCAGCTCAAAATAGATGAACAGTAAC 60.415 40.741 0.00 0.00 34.81 2.50
362 364 6.599244 CCCAGCTCAAAATAGATGAACAGTAA 59.401 38.462 0.00 0.00 34.81 2.24
363 365 6.115446 CCCAGCTCAAAATAGATGAACAGTA 58.885 40.000 0.00 0.00 34.81 2.74
373 375 1.396653 CCCAGCCCAGCTCAAAATAG 58.603 55.000 0.00 0.00 36.40 1.73
375 377 1.986210 GCCCAGCCCAGCTCAAAAT 60.986 57.895 0.00 0.00 36.40 1.82
399 401 4.562552 CCAACATTAAAATCCCAAGCCGTT 60.563 41.667 0.00 0.00 0.00 4.44
400 402 3.056179 CCAACATTAAAATCCCAAGCCGT 60.056 43.478 0.00 0.00 0.00 5.68
401 403 3.520569 CCAACATTAAAATCCCAAGCCG 58.479 45.455 0.00 0.00 0.00 5.52
438 440 0.610785 ATGCCGGGTTTGATTTCGGT 60.611 50.000 2.18 0.00 43.87 4.69
439 441 0.179140 CATGCCGGGTTTGATTTCGG 60.179 55.000 2.18 0.00 44.70 4.30
445 447 0.331278 ATTCTCCATGCCGGGTTTGA 59.669 50.000 2.18 0.00 34.36 2.69
456 458 2.687914 GCTAAACCTGGGCATTCTCCAT 60.688 50.000 0.00 0.00 33.29 3.41
457 459 1.340991 GCTAAACCTGGGCATTCTCCA 60.341 52.381 0.00 0.00 0.00 3.86
483 485 2.893895 AGCATGATGACCGCTGCG 60.894 61.111 16.34 16.34 39.57 5.18
846 861 7.173390 GGTGGCGCTAATTTTCTAATCTAATCT 59.827 37.037 7.64 0.00 0.00 2.40
862 879 2.696409 TTTGACGTCGGTGGCGCTAA 62.696 55.000 11.62 0.00 0.00 3.09
889 906 1.018910 ACAACAGTAGGCGCGTTTTT 58.981 45.000 8.36 0.00 0.00 1.94
890 907 1.003223 GAACAACAGTAGGCGCGTTTT 60.003 47.619 8.36 0.65 0.00 2.43
900 917 3.185594 CGATGCTTTTCGGAACAACAGTA 59.814 43.478 0.00 0.00 35.50 2.74
983 1000 8.244113 CCCTTTAAATCTATCGAAGCAAAAACT 58.756 33.333 0.00 0.00 0.00 2.66
1147 1212 5.656213 AGAAATCAAAATCTTGCTCCAGG 57.344 39.130 0.00 0.00 32.14 4.45
1162 1227 1.341852 TCGACCACCACGAAGAAATCA 59.658 47.619 0.00 0.00 36.84 2.57
1483 1548 4.314440 GTGCGGCAGTCCCAGTCA 62.314 66.667 1.18 0.00 0.00 3.41
1729 1795 0.179000 AGCCGGTGATGGTGATCTTC 59.821 55.000 1.90 0.00 0.00 2.87
1783 1864 2.979676 CAAGGGCTTGTGCGAGCA 60.980 61.111 12.86 0.00 44.49 4.26
1949 2050 1.951130 ACAAGCACGTCGCAGAGTG 60.951 57.895 11.58 6.95 46.13 3.51
1950 2051 1.951130 CACAAGCACGTCGCAGAGT 60.951 57.895 11.58 5.00 46.13 3.24
2008 2109 1.699656 CGCATCCCGAGAAGCACTTG 61.700 60.000 0.00 0.00 36.50 3.16
2051 2437 2.348888 CGAAGTAGGGGCAGACGGT 61.349 63.158 0.00 0.00 0.00 4.83
2056 2442 2.509336 CACGCGAAGTAGGGGCAG 60.509 66.667 15.93 0.00 0.00 4.85
2057 2443 4.077184 CCACGCGAAGTAGGGGCA 62.077 66.667 15.93 0.00 0.00 5.36
2155 2565 7.514721 AGACCAAATTTACACCTAGACAAGAA 58.485 34.615 0.00 0.00 0.00 2.52
2159 2569 7.284074 TCAAAGACCAAATTTACACCTAGACA 58.716 34.615 0.00 0.00 0.00 3.41
2408 3164 8.120140 AGAAATCCAGAGAAAAAGGAATCTTG 57.880 34.615 0.00 0.00 34.62 3.02
2461 3445 6.636666 ATTTATCAATTTCACTTGCAAGCG 57.363 33.333 26.27 17.45 0.00 4.68
2484 3468 4.877378 ATTTTGCAGCCTTCATCAGAAA 57.123 36.364 0.00 0.00 32.35 2.52
2485 3469 4.281435 TCAATTTTGCAGCCTTCATCAGAA 59.719 37.500 0.00 0.00 0.00 3.02
2486 3470 3.827876 TCAATTTTGCAGCCTTCATCAGA 59.172 39.130 0.00 0.00 0.00 3.27
2487 3471 4.182693 TCAATTTTGCAGCCTTCATCAG 57.817 40.909 0.00 0.00 0.00 2.90
2488 3472 4.811969 ATCAATTTTGCAGCCTTCATCA 57.188 36.364 0.00 0.00 0.00 3.07
2489 3473 7.781548 ATTTATCAATTTTGCAGCCTTCATC 57.218 32.000 0.00 0.00 0.00 2.92
2490 3474 8.570068 AAATTTATCAATTTTGCAGCCTTCAT 57.430 26.923 0.00 0.00 39.19 2.57
2491 3475 7.879160 AGAAATTTATCAATTTTGCAGCCTTCA 59.121 29.630 0.00 0.00 41.79 3.02
2492 3476 8.173130 CAGAAATTTATCAATTTTGCAGCCTTC 58.827 33.333 0.00 0.00 41.79 3.46
2493 3477 7.879160 TCAGAAATTTATCAATTTTGCAGCCTT 59.121 29.630 0.00 0.00 41.79 4.35
2494 3478 7.388437 TCAGAAATTTATCAATTTTGCAGCCT 58.612 30.769 0.00 0.00 41.79 4.58
2495 3479 7.599630 TCAGAAATTTATCAATTTTGCAGCC 57.400 32.000 0.00 0.00 41.79 4.85
2496 3480 8.875803 TCATCAGAAATTTATCAATTTTGCAGC 58.124 29.630 0.00 0.00 41.79 5.25
2504 3488 9.412460 TGTAGCCTTCATCAGAAATTTATCAAT 57.588 29.630 0.00 0.00 32.35 2.57
2505 3489 8.806429 TGTAGCCTTCATCAGAAATTTATCAA 57.194 30.769 0.00 0.00 32.35 2.57
2506 3490 8.806429 TTGTAGCCTTCATCAGAAATTTATCA 57.194 30.769 0.00 0.00 32.35 2.15
2509 3493 8.686334 GGAATTGTAGCCTTCATCAGAAATTTA 58.314 33.333 0.00 0.00 32.35 1.40
2510 3494 7.178983 TGGAATTGTAGCCTTCATCAGAAATTT 59.821 33.333 0.00 0.00 32.35 1.82
2511 3495 6.664816 TGGAATTGTAGCCTTCATCAGAAATT 59.335 34.615 0.00 0.00 32.35 1.82
2512 3496 6.189859 TGGAATTGTAGCCTTCATCAGAAAT 58.810 36.000 0.00 0.00 32.35 2.17
2545 3558 3.935203 CGGATGATGACTTACAGTTTGCT 59.065 43.478 0.00 0.00 0.00 3.91
2745 5851 8.911247 AATCGACAGTTGGCTATTTTATTTTC 57.089 30.769 0.00 0.00 0.00 2.29
2755 5861 3.509967 TCTCAGAAATCGACAGTTGGCTA 59.490 43.478 0.00 0.00 0.00 3.93
2766 5872 9.684448 TTGAGTTAGCTATTATCTCAGAAATCG 57.316 33.333 13.80 0.00 38.61 3.34
2781 5887 8.458843 GTTGGAGCAAATTATTTGAGTTAGCTA 58.541 33.333 20.37 0.00 43.26 3.32
2795 5901 3.140623 GGCATTTGTGTTGGAGCAAATT 58.859 40.909 0.00 0.00 41.62 1.82
3037 6311 1.134965 CAGAGTAGCTTGTTCCCCTCG 60.135 57.143 0.00 0.00 0.00 4.63
3059 6336 2.917205 AGAAACCAAGGGCTAGGTAGT 58.083 47.619 0.00 0.00 37.07 2.73
3119 6397 1.600916 GGTGCACTTCAGGTGGTCC 60.601 63.158 17.98 0.00 45.44 4.46



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

AutoCloner maintained by Alex Coulton.