Multiple sequence alignment - TraesCS2B01G627100

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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 TraesCS2B01G627100 chr2B 100.000 3141 0 0 1 3141 799028231 799031371 0.000000e+00 5801.0
1 TraesCS2B01G627100 chr2B 81.636 1993 200 85 194 2096 798956900 798958816 0.000000e+00 1500.0
2 TraesCS2B01G627100 chr2B 93.929 873 29 10 1 871 799108625 799107775 0.000000e+00 1297.0
3 TraesCS2B01G627100 chr2B 80.176 1251 139 60 1246 2405 799047323 799046091 0.000000e+00 835.0
4 TraesCS2B01G627100 chr2B 90.551 635 48 2 1016 1641 799107582 799106951 0.000000e+00 830.0
5 TraesCS2B01G627100 chr2B 78.233 634 63 34 40 610 799048522 799047901 1.400000e-88 337.0
6 TraesCS2B01G627100 chr2B 75.789 665 97 36 2492 3141 799046095 799045480 8.580000e-71 278.0
7 TraesCS2B01G627100 chr2B 92.593 189 7 1 675 863 799047886 799047705 6.680000e-67 265.0
8 TraesCS2B01G627100 chr2B 88.043 184 17 4 2219 2398 798958949 798959131 2.450000e-51 213.0
9 TraesCS2B01G627100 chr2D 86.546 1717 152 26 580 2247 639732800 639734486 0.000000e+00 1818.0
10 TraesCS2B01G627100 chr2D 82.410 2166 192 85 40 2096 639822822 639820737 0.000000e+00 1714.0
11 TraesCS2B01G627100 chr2D 81.915 1222 125 46 1247 2398 639746496 639745301 0.000000e+00 944.0
12 TraesCS2B01G627100 chr2D 86.076 474 38 9 2518 2986 639734541 639734991 4.710000e-133 484.0
13 TraesCS2B01G627100 chr2D 84.830 501 46 10 728 1223 639747034 639746559 7.880000e-131 477.0
14 TraesCS2B01G627100 chr2D 80.465 645 86 28 856 1496 639872366 639871758 1.030000e-124 457.0
15 TraesCS2B01G627100 chr2D 81.413 538 72 18 2492 3017 639820432 639819911 6.270000e-112 414.0
16 TraesCS2B01G627100 chr2D 77.348 724 71 47 1 666 639747740 639747052 3.000000e-90 342.0
17 TraesCS2B01G627100 chr2D 79.426 418 43 27 1 404 639732072 639732460 4.020000e-64 255.0
18 TraesCS2B01G627100 chr2D 82.712 295 34 4 196 475 639891677 639891385 2.420000e-61 246.0
19 TraesCS2B01G627100 chr2D 78.933 356 60 12 2462 2808 639745197 639744848 8.760000e-56 228.0
20 TraesCS2B01G627100 chr2D 77.247 356 36 20 319 650 639872790 639872456 1.940000e-37 167.0
21 TraesCS2B01G627100 chr2D 86.395 147 19 1 1672 1817 639890194 639890048 3.240000e-35 159.0
22 TraesCS2B01G627100 chr2A 87.106 1047 88 24 774 1777 765373507 765374549 0.000000e+00 1142.0
23 TraesCS2B01G627100 chr2A 84.249 1238 110 45 925 2096 765442334 765441116 0.000000e+00 1127.0
24 TraesCS2B01G627100 chr2A 83.333 984 110 26 1248 2198 765393348 765392386 0.000000e+00 859.0
25 TraesCS2B01G627100 chr2A 85.278 720 69 17 2286 2969 765374982 765375700 0.000000e+00 708.0
26 TraesCS2B01G627100 chr2A 82.189 859 64 46 40 835 765394585 765393753 0.000000e+00 656.0
27 TraesCS2B01G627100 chr2A 79.250 853 101 32 1319 2107 765278135 765278975 2.780000e-145 525.0
28 TraesCS2B01G627100 chr2A 84.645 521 45 16 1799 2305 765374544 765375043 1.310000e-133 486.0
29 TraesCS2B01G627100 chr2A 89.426 331 25 6 901 1223 765393749 765393421 2.920000e-110 409.0
30 TraesCS2B01G627100 chr2A 79.070 602 57 40 164 709 765372919 765373507 1.790000e-92 350.0
31 TraesCS2B01G627100 chr2A 78.125 512 61 28 313 802 765548536 765548054 8.580000e-71 278.0
32 TraesCS2B01G627100 chr2A 82.051 351 27 17 1 324 765443251 765442910 1.860000e-67 267.0
33 TraesCS2B01G627100 chr2A 91.525 59 3 2 587 643 765516642 765516584 2.600000e-11 80.5
34 TraesCS2B01G627100 chr2A 94.444 36 2 0 2311 2346 765279504 765279539 4.380000e-04 56.5


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 TraesCS2B01G627100 chr2B 799028231 799031371 3140 False 5801.000000 5801 100.000000 1 3141 1 chr2B.!!$F1 3140
1 TraesCS2B01G627100 chr2B 799106951 799108625 1674 True 1063.500000 1297 92.240000 1 1641 2 chr2B.!!$R2 1640
2 TraesCS2B01G627100 chr2B 798956900 798959131 2231 False 856.500000 1500 84.839500 194 2398 2 chr2B.!!$F2 2204
3 TraesCS2B01G627100 chr2B 799045480 799048522 3042 True 428.750000 835 81.697750 40 3141 4 chr2B.!!$R1 3101
4 TraesCS2B01G627100 chr2D 639819911 639822822 2911 True 1064.000000 1714 81.911500 40 3017 2 chr2D.!!$R2 2977
5 TraesCS2B01G627100 chr2D 639732072 639734991 2919 False 852.333333 1818 84.016000 1 2986 3 chr2D.!!$F1 2985
6 TraesCS2B01G627100 chr2D 639744848 639747740 2892 True 497.750000 944 80.756500 1 2808 4 chr2D.!!$R1 2807
7 TraesCS2B01G627100 chr2D 639871758 639872790 1032 True 312.000000 457 78.856000 319 1496 2 chr2D.!!$R3 1177
8 TraesCS2B01G627100 chr2D 639890048 639891677 1629 True 202.500000 246 84.553500 196 1817 2 chr2D.!!$R4 1621
9 TraesCS2B01G627100 chr2A 765441116 765443251 2135 True 697.000000 1127 83.150000 1 2096 2 chr2A.!!$R4 2095
10 TraesCS2B01G627100 chr2A 765372919 765375700 2781 False 671.500000 1142 84.024750 164 2969 4 chr2A.!!$F2 2805
11 TraesCS2B01G627100 chr2A 765392386 765394585 2199 True 641.333333 859 84.982667 40 2198 3 chr2A.!!$R3 2158
12 TraesCS2B01G627100 chr2A 765278135 765279539 1404 False 290.750000 525 86.847000 1319 2346 2 chr2A.!!$F1 1027

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
244 279 0.101399 CCGGAGACCAGATGTTCTCG 59.899 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 3113 0.536006 AAATCGATGCTGCTAGGGCC 60.536 55.0 0.0 0.0 37.74 5.8 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
86 89 3.218398 GTTGAAATTCGTCTCTGCAACG 58.782 45.455 3.00 3.00 41.39 4.10
107 116 2.256117 TAGTCCTGCTCGATCGATCA 57.744 50.000 24.40 19.63 0.00 2.92
109 118 1.751351 AGTCCTGCTCGATCGATCAAA 59.249 47.619 24.40 8.80 0.00 2.69
121 130 4.675114 CGATCGATCAAATGATGTACGTCA 59.325 41.667 24.40 19.73 34.37 4.35
227 262 1.953686 AGTCCACCACAAAATTGACCG 59.046 47.619 0.00 0.00 0.00 4.79
244 279 0.101399 CCGGAGACCAGATGTTCTCG 59.899 60.000 0.00 0.00 0.00 4.04
258 293 4.160642 TGTTCTCGCTCTACCCATAGTA 57.839 45.455 0.00 0.00 0.00 1.82
266 306 4.880696 CGCTCTACCCATAGTATAGGTACC 59.119 50.000 2.73 2.73 35.02 3.34
308 348 3.745458 GGCGCAGAAAAATGATGGAAAAA 59.255 39.130 10.83 0.00 0.00 1.94
422 514 4.883585 CAGCTATATGCAGGTCCTTTTCAA 59.116 41.667 0.00 0.00 45.94 2.69
459 551 5.316987 TCCATCTTCTTCCTTTCCAACTTC 58.683 41.667 0.00 0.00 0.00 3.01
658 932 1.418373 TCATATGAGCGTGCGCATAC 58.582 50.000 15.91 9.26 40.43 2.39
660 934 1.728425 CATATGAGCGTGCGCATACAT 59.272 47.619 15.91 18.17 40.43 2.29
661 935 1.139163 TATGAGCGTGCGCATACATG 58.861 50.000 15.91 2.50 44.88 3.21
662 936 0.811219 ATGAGCGTGCGCATACATGT 60.811 50.000 15.91 2.69 44.88 3.21
663 937 1.011904 GAGCGTGCGCATACATGTG 60.012 57.895 15.91 0.00 44.88 3.21
664 938 1.695893 GAGCGTGCGCATACATGTGT 61.696 55.000 15.91 0.00 44.88 3.72
669 943 1.398041 GTGCGCATACATGTGTCATGT 59.602 47.619 15.91 17.37 40.29 3.21
673 947 2.672381 CGCATACATGTGTCATGTGTGA 59.328 45.455 29.43 12.63 41.64 3.58
709 1041 2.402305 CTGTCAAGAGTCTGTGCTCAC 58.598 52.381 0.00 0.00 37.94 3.51
710 1042 2.034878 TGTCAAGAGTCTGTGCTCACT 58.965 47.619 0.00 0.00 37.94 3.41
711 1043 2.223900 TGTCAAGAGTCTGTGCTCACTG 60.224 50.000 0.00 1.29 37.94 3.66
712 1044 1.146637 CAAGAGTCTGTGCTCACTGC 58.853 55.000 0.00 0.00 43.25 4.40
713 1045 1.047002 AAGAGTCTGTGCTCACTGCT 58.953 50.000 0.00 3.31 43.37 4.24
714 1046 0.602562 AGAGTCTGTGCTCACTGCTC 59.397 55.000 15.87 15.87 43.37 4.26
715 1047 0.316522 GAGTCTGTGCTCACTGCTCA 59.683 55.000 17.35 0.00 42.06 4.26
836 1183 7.875554 TGTTCCACACGCATACAACATATATAT 59.124 33.333 0.00 0.00 0.00 0.86
920 1329 2.616510 GCCTCCACACATGCTTCTACTT 60.617 50.000 0.00 0.00 0.00 2.24
923 1364 3.861840 TCCACACATGCTTCTACTTAGC 58.138 45.455 0.00 0.00 39.10 3.09
938 1382 7.653767 TCTACTTAGCAGTAAGTTGAAAAGC 57.346 36.000 3.93 0.00 45.62 3.51
945 1389 4.671377 CAGTAAGTTGAAAAGCTTGTGCA 58.329 39.130 0.00 0.00 42.74 4.57
1212 1745 8.537223 CATCTGAATTTTGAAAGTTGTCTTGTG 58.463 33.333 0.00 0.00 33.79 3.33
1243 1788 5.008316 ACTCCAAAATACTTGTCGTGGTTTC 59.992 40.000 0.00 0.00 0.00 2.78
1256 1836 5.693104 TGTCGTGGTTTCAATAGTGTTCTAC 59.307 40.000 0.00 0.00 0.00 2.59
1258 1838 6.089150 GTCGTGGTTTCAATAGTGTTCTACTC 59.911 42.308 0.00 0.00 40.89 2.59
1287 1885 9.289303 GTGGTGATTCACATTGAATATTAACAC 57.711 33.333 18.09 8.29 46.20 3.32
1358 1956 2.525629 TGTCAGGTGGCGGAGGAA 60.526 61.111 0.00 0.00 0.00 3.36
1361 1959 1.306141 TCAGGTGGCGGAGGAAGAT 60.306 57.895 0.00 0.00 0.00 2.40
1369 1967 0.173708 GCGGAGGAAGATCAGTCGTT 59.826 55.000 0.00 0.00 0.00 3.85
1646 2372 5.149977 CGCAATTCTTCAGTTCTTCTTTCC 58.850 41.667 0.00 0.00 0.00 3.13
1670 2396 4.749245 TCTTCTTGAGAATTTGGCGTTC 57.251 40.909 0.00 0.00 33.01 3.95
1693 2596 0.250901 ATCAAGGTGGTGTGCAGGAC 60.251 55.000 0.00 0.00 0.00 3.85
1765 2671 1.067582 GTCCTACATCTTCCCCGCG 59.932 63.158 0.00 0.00 0.00 6.46
1795 2701 2.113139 CCGGATTTGGGCGGCTAT 59.887 61.111 9.56 0.00 0.00 2.97
1960 2896 3.197766 TCTTCGACAATATCCCACAGCTT 59.802 43.478 0.00 0.00 0.00 3.74
1974 2910 2.066393 AGCTTATCCAGAGCCCGCA 61.066 57.895 0.00 0.00 41.03 5.69
2042 2987 2.048127 GACAGGGACAGACGGTGC 60.048 66.667 0.00 0.00 37.06 5.01
2043 2988 2.524394 ACAGGGACAGACGGTGCT 60.524 61.111 0.00 0.00 38.05 4.40
2047 2992 3.371063 GGACAGACGGTGCTCGGA 61.371 66.667 0.00 0.00 44.45 4.55
2075 3023 0.398318 GAACTTCCTGGACAGCCTGT 59.602 55.000 0.00 0.00 34.31 4.00
2119 3067 4.687215 TCTGCCACTGCTGCGTCC 62.687 66.667 0.00 0.00 38.71 4.79
2153 3105 3.127895 AGAGCAGTGAAGTAGAGTTAGCG 59.872 47.826 0.00 0.00 0.00 4.26
2161 3113 4.034858 TGAAGTAGAGTTAGCGGACATACG 59.965 45.833 0.00 0.00 0.00 3.06
2163 3115 0.384669 AGAGTTAGCGGACATACGGC 59.615 55.000 0.00 0.00 43.63 5.68
2164 3116 0.596859 GAGTTAGCGGACATACGGCC 60.597 60.000 0.00 0.00 44.22 6.13
2165 3117 1.593479 GTTAGCGGACATACGGCCC 60.593 63.158 0.00 0.00 44.22 5.80
2190 3153 8.671921 CCTAGCAGCATCGATTTCATTTTATAT 58.328 33.333 0.00 0.00 0.00 0.86
2265 3321 5.883673 AGCTAGACTAGTCTGTTCCACTTAG 59.116 44.000 31.47 19.26 40.71 2.18
2268 3324 4.218852 AGACTAGTCTGTTCCACTTAGTGC 59.781 45.833 24.62 0.00 38.75 4.40
2280 3337 3.363970 CCACTTAGTGCGTCATGTGTTTC 60.364 47.826 6.88 0.00 31.34 2.78
2281 3338 2.806244 ACTTAGTGCGTCATGTGTTTCC 59.194 45.455 0.00 0.00 0.00 3.13
2315 3642 8.258007 CCACTCTGTTCCACTTACTGAATATAA 58.742 37.037 0.00 0.00 0.00 0.98
2346 3673 6.205076 TCACTGTAGACTACTCTGTTTCACTC 59.795 42.308 13.67 0.00 0.00 3.51
2449 3911 6.912591 GCTAATAATAGTCCATGTGTTTGTGC 59.087 38.462 0.00 0.00 0.00 4.57
2454 3916 1.000060 GTCCATGTGTTTGTGCTGCAT 60.000 47.619 5.27 0.00 0.00 3.96
2457 3919 2.288579 CCATGTGTTTGTGCTGCATCTT 60.289 45.455 5.27 0.00 0.00 2.40
2458 3920 3.386486 CATGTGTTTGTGCTGCATCTTT 58.614 40.909 5.27 0.00 0.00 2.52
2459 3921 2.811855 TGTGTTTGTGCTGCATCTTTG 58.188 42.857 5.27 0.00 0.00 2.77
2464 3950 0.669619 TGTGCTGCATCTTTGTGTGG 59.330 50.000 5.27 0.00 0.00 4.17
2475 3961 5.472137 GCATCTTTGTGTGGGTTCTAGTTTA 59.528 40.000 0.00 0.00 0.00 2.01
2478 3964 6.053005 TCTTTGTGTGGGTTCTAGTTTACAG 58.947 40.000 0.00 0.00 0.00 2.74
2482 3968 3.244422 TGTGGGTTCTAGTTTACAGCAGG 60.244 47.826 0.00 0.00 0.00 4.85
2483 3969 2.290071 TGGGTTCTAGTTTACAGCAGGC 60.290 50.000 0.00 0.00 0.00 4.85
2485 3971 3.003480 GGTTCTAGTTTACAGCAGGCAG 58.997 50.000 0.00 0.00 0.00 4.85
2486 3972 3.003480 GTTCTAGTTTACAGCAGGCAGG 58.997 50.000 0.00 0.00 0.00 4.85
2489 3975 0.038744 AGTTTACAGCAGGCAGGCAT 59.961 50.000 0.00 0.00 35.83 4.40
2491 3977 1.401905 GTTTACAGCAGGCAGGCATAC 59.598 52.381 0.00 0.00 35.83 2.39
2528 4023 6.257411 ACTCACTGAATTTTAGCTGATCATCG 59.743 38.462 0.00 0.00 0.00 3.84
2539 4034 3.131755 AGCTGATCATCGTCACTCATCAA 59.868 43.478 0.00 0.00 0.00 2.57
2556 4051 9.249457 CACTCATCAATGTACGTATATGTTTCT 57.751 33.333 5.52 0.00 0.00 2.52
2566 4061 9.297586 TGTACGTATATGTTTCTCTCAATGAAC 57.702 33.333 2.23 0.00 0.00 3.18
2595 4090 7.833682 TCTTTAATTTGACCATAGGCATGAGAA 59.166 33.333 0.00 0.00 33.67 2.87
2626 4121 0.398696 ATTTGTCTGGGCCGTACACA 59.601 50.000 10.02 4.97 0.00 3.72
2677 4173 5.592688 CCACGGGGATTAGTTAACATCAATT 59.407 40.000 0.00 0.00 35.59 2.32
2681 4177 8.050930 ACGGGGATTAGTTAACATCAATTTAGT 58.949 33.333 8.61 0.00 0.00 2.24
2715 4212 8.160765 TGAGTTGATTAATTGAGTTTCCCTGTA 58.839 33.333 0.00 0.00 0.00 2.74
2725 4222 4.712337 TGAGTTTCCCTGTAGATCCTCTTC 59.288 45.833 0.00 0.00 0.00 2.87
2808 4305 2.750814 TGCAGACAGATAGATGGGTCA 58.249 47.619 0.00 0.00 32.79 4.02
2822 4319 0.179081 GGGTCACCTACTCGCCATTC 60.179 60.000 0.00 0.00 0.00 2.67
2882 4379 2.832129 CAGGGACTTGCACTACCTAGAA 59.168 50.000 0.00 0.00 34.60 2.10
2898 4396 9.054922 ACTACCTAGAAAAGTATGTATCTCGAC 57.945 37.037 0.00 0.00 0.00 4.20
2986 4490 3.872511 TGGTTGGTGAATACGTACGAT 57.127 42.857 24.41 8.32 0.00 3.73
2994 4498 5.409214 TGGTGAATACGTACGATATCGATGA 59.591 40.000 30.75 12.87 43.02 2.92
3019 4528 9.901172 GAAATACCTACTAAAAGGAAAGGATGA 57.099 33.333 0.00 0.00 39.15 2.92
3035 4544 4.911390 AGGATGAGATTTTTCGAACCTGT 58.089 39.130 0.00 0.00 0.00 4.00
3038 4547 6.940298 AGGATGAGATTTTTCGAACCTGTTAA 59.060 34.615 0.00 0.00 0.00 2.01
3043 4552 9.443323 TGAGATTTTTCGAACCTGTTAATATCA 57.557 29.630 0.00 2.13 0.00 2.15
3050 4559 7.384439 TCGAACCTGTTAATATCAAATTGCA 57.616 32.000 0.00 0.00 0.00 4.08
3072 4581 8.519492 TGCACTTCATAAACTAAGCAAAAATC 57.481 30.769 0.00 0.00 0.00 2.17
3073 4582 8.140628 TGCACTTCATAAACTAAGCAAAAATCA 58.859 29.630 0.00 0.00 0.00 2.57
3082 4591 8.702163 AAACTAAGCAAAAATCATATTTCCGG 57.298 30.769 0.00 0.00 0.00 5.14
3085 4594 8.137437 ACTAAGCAAAAATCATATTTCCGGATG 58.863 33.333 4.15 0.00 0.00 3.51
3087 4596 6.507023 AGCAAAAATCATATTTCCGGATGTC 58.493 36.000 4.15 0.00 0.00 3.06
3088 4597 6.096705 AGCAAAAATCATATTTCCGGATGTCA 59.903 34.615 4.15 0.00 0.00 3.58
3089 4598 6.925165 GCAAAAATCATATTTCCGGATGTCAT 59.075 34.615 4.15 0.00 0.00 3.06
3096 4606 9.745018 ATCATATTTCCGGATGTCATAAATTCT 57.255 29.630 4.15 0.00 0.00 2.40
3102 4612 4.516698 CCGGATGTCATAAATTCTGGGAAG 59.483 45.833 0.00 0.00 32.06 3.46
3107 4617 8.966868 GGATGTCATAAATTCTGGGAAGTAAAA 58.033 33.333 0.00 0.00 0.00 1.52
3109 4619 8.934023 TGTCATAAATTCTGGGAAGTAAAACT 57.066 30.769 0.00 0.00 0.00 2.66
3115 4625 6.796705 ATTCTGGGAAGTAAAACTAACACG 57.203 37.500 0.00 0.00 0.00 4.49
3117 4627 5.916318 TCTGGGAAGTAAAACTAACACGAA 58.084 37.500 0.00 0.00 0.00 3.85
3119 4629 4.512571 TGGGAAGTAAAACTAACACGAAGC 59.487 41.667 0.00 0.00 0.00 3.86
3124 4634 6.854496 AGTAAAACTAACACGAAGCATTGA 57.146 33.333 0.00 0.00 0.00 2.57
3132 4642 7.370383 ACTAACACGAAGCATTGATTTGAAAT 58.630 30.769 8.84 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 89 2.744741 TGATCGATCGAGCAGGACTATC 59.255 50.000 30.45 16.04 35.47 2.08
107 116 8.506168 AATATGGTTTCTGACGTACATCATTT 57.494 30.769 0.00 0.00 0.00 2.32
109 118 6.706270 GGAATATGGTTTCTGACGTACATCAT 59.294 38.462 0.00 0.00 0.00 2.45
121 130 3.525199 ACCAGCAGAGGAATATGGTTTCT 59.475 43.478 0.00 0.00 41.44 2.52
244 279 5.887035 CAGGTACCTATACTATGGGTAGAGC 59.113 48.000 15.80 4.12 45.50 4.09
266 306 0.824759 GGCCTACTGGTACTGGACAG 59.175 60.000 0.00 0.00 40.48 3.51
308 348 8.830915 TTAATCTCCTCTCTCTCTGTTGTATT 57.169 34.615 0.00 0.00 0.00 1.89
422 514 6.889595 AGAAGATGGAAGAGAAAAGAGGAT 57.110 37.500 0.00 0.00 0.00 3.24
459 551 6.741992 TGGAATTGTCTAGCTTGTAATGTG 57.258 37.500 0.00 0.00 0.00 3.21
658 932 2.415512 CAGAGCTCACACATGACACATG 59.584 50.000 17.77 9.72 0.00 3.21
660 934 1.875157 GCAGAGCTCACACATGACACA 60.875 52.381 17.77 0.00 0.00 3.72
661 935 0.795085 GCAGAGCTCACACATGACAC 59.205 55.000 17.77 0.00 0.00 3.67
662 936 0.683412 AGCAGAGCTCACACATGACA 59.317 50.000 17.77 0.00 30.62 3.58
663 937 3.529252 AGCAGAGCTCACACATGAC 57.471 52.632 17.77 1.81 30.62 3.06
673 947 1.376166 CAGCAAGCAGAGCAGAGCT 60.376 57.895 0.00 0.00 43.88 4.09
709 1041 1.370609 CTGCAATGAGAGGTGAGCAG 58.629 55.000 0.00 0.00 42.69 4.24
710 1042 0.689055 ACTGCAATGAGAGGTGAGCA 59.311 50.000 0.00 0.00 0.00 4.26
711 1043 1.085091 CACTGCAATGAGAGGTGAGC 58.915 55.000 0.00 0.00 0.00 4.26
712 1044 2.469274 ACACTGCAATGAGAGGTGAG 57.531 50.000 0.26 0.00 0.00 3.51
713 1045 2.497138 CAACACTGCAATGAGAGGTGA 58.503 47.619 0.26 0.00 0.00 4.02
714 1046 2.983402 CAACACTGCAATGAGAGGTG 57.017 50.000 0.26 0.00 0.00 4.00
791 1123 5.301805 GGAACAAAGAAGGTGAAAAGGATCA 59.698 40.000 0.00 0.00 0.00 2.92
854 1201 0.458543 ACAATGGTGCTAGCTCGTCG 60.459 55.000 17.23 1.95 0.00 5.12
858 1205 1.745653 GGGAAACAATGGTGCTAGCTC 59.254 52.381 17.23 12.62 0.00 4.09
913 1322 7.931948 AGCTTTTCAACTTACTGCTAAGTAGAA 59.068 33.333 0.00 0.00 41.58 2.10
920 1329 5.505654 GCACAAGCTTTTCAACTTACTGCTA 60.506 40.000 0.00 0.00 37.91 3.49
923 1364 4.500477 GTGCACAAGCTTTTCAACTTACTG 59.500 41.667 13.17 0.00 42.74 2.74
938 1382 4.736793 GTGAACTGAAATCAAGTGCACAAG 59.263 41.667 21.04 11.01 40.75 3.16
945 1389 6.293081 CGATGTCTTGTGAACTGAAATCAAGT 60.293 38.462 0.00 0.00 37.39 3.16
1212 1745 8.169268 CACGACAAGTATTTTGGAGTAGAAATC 58.831 37.037 0.00 0.00 0.00 2.17
1243 1788 5.047306 TCACCACCTGAGTAGAACACTATTG 60.047 44.000 0.00 0.00 37.72 1.90
1256 1836 3.678289 TCAATGTGAATCACCACCTGAG 58.322 45.455 11.24 0.00 36.26 3.35
1258 1838 6.704289 ATATTCAATGTGAATCACCACCTG 57.296 37.500 11.24 3.22 43.03 4.00
1287 1885 2.022195 CCTCTCTGCACCATCCATTTG 58.978 52.381 0.00 0.00 0.00 2.32
1341 1939 2.525629 TTCCTCCGCCACCTGACA 60.526 61.111 0.00 0.00 0.00 3.58
1358 1956 1.200252 CACTCCGACAACGACTGATCT 59.800 52.381 0.00 0.00 42.66 2.75
1361 1959 1.105167 ACCACTCCGACAACGACTGA 61.105 55.000 0.00 0.00 42.66 3.41
1369 1967 2.557056 CTGAAGAAGTACCACTCCGACA 59.443 50.000 0.00 0.00 0.00 4.35
1556 2178 1.186200 TGATCCAGTCGGTCTTCCTG 58.814 55.000 0.00 0.00 0.00 3.86
1646 2372 3.503748 ACGCCAAATTCTCAAGAAGAAGG 59.496 43.478 0.00 1.67 46.95 3.46
1670 2396 1.471287 CTGCACACCACCTTGATCATG 59.529 52.381 0.00 0.00 0.00 3.07
1693 2596 2.551912 GCACACCACCCAACCTTCG 61.552 63.158 0.00 0.00 0.00 3.79
1786 2692 3.034343 GCGTCGTAATAGCCGCCC 61.034 66.667 0.00 0.00 40.25 6.13
1960 2896 2.490148 CGTCTGCGGGCTCTGGATA 61.490 63.158 0.00 0.00 0.00 2.59
1974 2910 1.753463 CCTAGAAGGGCGGTCGTCT 60.753 63.158 0.00 0.00 0.00 4.18
2042 2987 2.531206 GAAGTTCCAGTCGATTCCGAG 58.469 52.381 0.00 0.00 46.52 4.63
2043 2988 1.203994 GGAAGTTCCAGTCGATTCCGA 59.796 52.381 17.44 0.00 38.36 4.55
2047 2992 2.028020 GTCCAGGAAGTTCCAGTCGATT 60.028 50.000 23.87 0.00 39.61 3.34
2075 3023 2.661537 CAGCTGCGACGTGGACAA 60.662 61.111 0.00 0.00 0.00 3.18
2153 3105 1.367840 CTGCTAGGGCCGTATGTCC 59.632 63.158 5.45 0.00 37.74 4.02
2161 3113 0.536006 AAATCGATGCTGCTAGGGCC 60.536 55.000 0.00 0.00 37.74 5.80
2163 3115 2.245159 TGAAATCGATGCTGCTAGGG 57.755 50.000 0.00 0.00 0.00 3.53
2164 3116 4.825546 AAATGAAATCGATGCTGCTAGG 57.174 40.909 0.00 0.00 0.00 3.02
2214 3242 1.213296 AGTGTCAACCAAGTGTCCCT 58.787 50.000 0.00 0.00 0.00 4.20
2265 3321 0.238289 CAGGGAAACACATGACGCAC 59.762 55.000 0.00 0.00 0.00 5.34
2268 3324 2.993899 GTCTACAGGGAAACACATGACG 59.006 50.000 0.00 0.00 0.00 4.35
2280 3337 1.550976 GGAACAGAGTGGTCTACAGGG 59.449 57.143 0.00 0.00 33.75 4.45
2281 3338 2.028930 GTGGAACAGAGTGGTCTACAGG 60.029 54.545 3.79 0.00 43.87 4.00
2315 3642 5.828859 ACAGAGTAGTCTACAGTGAAACACT 59.171 40.000 12.54 0.00 46.51 3.55
2346 3673 6.824305 ATCAACTGTCCCTGAAATTTAGTG 57.176 37.500 0.00 0.00 0.00 2.74
2418 3864 8.978874 ACACATGGACTATTATTAGCAAATCA 57.021 30.769 0.00 0.00 0.00 2.57
2421 3867 9.019656 ACAAACACATGGACTATTATTAGCAAA 57.980 29.630 0.00 0.00 0.00 3.68
2422 3868 8.458052 CACAAACACATGGACTATTATTAGCAA 58.542 33.333 0.00 0.00 0.00 3.91
2424 3870 6.912591 GCACAAACACATGGACTATTATTAGC 59.087 38.462 0.00 0.00 0.00 3.09
2425 3871 8.124823 CAGCACAAACACATGGACTATTATTAG 58.875 37.037 0.00 0.00 0.00 1.73
2426 3872 7.415095 GCAGCACAAACACATGGACTATTATTA 60.415 37.037 0.00 0.00 0.00 0.98
2427 3873 6.625740 GCAGCACAAACACATGGACTATTATT 60.626 38.462 0.00 0.00 0.00 1.40
2429 3875 4.155826 GCAGCACAAACACATGGACTATTA 59.844 41.667 0.00 0.00 0.00 0.98
2430 3876 3.057315 GCAGCACAAACACATGGACTATT 60.057 43.478 0.00 0.00 0.00 1.73
2431 3877 2.489329 GCAGCACAAACACATGGACTAT 59.511 45.455 0.00 0.00 0.00 2.12
2449 3911 2.233271 AGAACCCACACAAAGATGCAG 58.767 47.619 0.00 0.00 0.00 4.41
2454 3916 5.991861 TGTAAACTAGAACCCACACAAAGA 58.008 37.500 0.00 0.00 0.00 2.52
2457 3919 4.131596 GCTGTAAACTAGAACCCACACAA 58.868 43.478 0.00 0.00 0.00 3.33
2458 3920 3.134985 TGCTGTAAACTAGAACCCACACA 59.865 43.478 0.00 0.00 0.00 3.72
2459 3921 3.735591 TGCTGTAAACTAGAACCCACAC 58.264 45.455 0.00 0.00 0.00 3.82
2464 3950 3.003480 CTGCCTGCTGTAAACTAGAACC 58.997 50.000 0.00 0.00 0.00 3.62
2475 3961 2.273449 GGTATGCCTGCCTGCTGT 59.727 61.111 0.00 0.00 0.00 4.40
2478 3964 1.821332 GAGTGGTATGCCTGCCTGC 60.821 63.158 0.16 0.00 35.27 4.85
2482 3968 1.740025 GAAACAGAGTGGTATGCCTGC 59.260 52.381 0.16 0.00 35.27 4.85
2483 3969 2.744202 GTGAAACAGAGTGGTATGCCTG 59.256 50.000 0.16 0.00 36.32 4.85
2485 3971 3.003480 GAGTGAAACAGAGTGGTATGCC 58.997 50.000 0.00 0.00 41.43 4.40
2486 3972 3.433615 GTGAGTGAAACAGAGTGGTATGC 59.566 47.826 0.00 0.00 41.43 3.14
2489 3975 3.958147 TCAGTGAGTGAAACAGAGTGGTA 59.042 43.478 0.00 0.00 41.43 3.25
2491 3977 3.459232 TCAGTGAGTGAAACAGAGTGG 57.541 47.619 0.00 0.00 41.43 4.00
2528 4023 8.575565 AACATATACGTACATTGATGAGTGAC 57.424 34.615 0.00 0.00 0.00 3.67
2556 4051 9.912634 GGTCAAATTAAAGATTGTTCATTGAGA 57.087 29.630 0.00 0.00 0.00 3.27
2566 4061 8.415553 TCATGCCTATGGTCAAATTAAAGATTG 58.584 33.333 0.00 0.00 34.97 2.67
2574 4069 7.427989 AATTTCTCATGCCTATGGTCAAATT 57.572 32.000 0.00 0.00 34.97 1.82
2595 4090 4.821260 GCCCAGACAAATCAACCAAAAATT 59.179 37.500 0.00 0.00 0.00 1.82
2626 4121 6.306837 CACATCACGCATTTAATTAACCGTTT 59.693 34.615 12.41 4.45 0.00 3.60
2681 4177 8.394971 ACTCAATTAATCAACTCAACATCACA 57.605 30.769 0.00 0.00 0.00 3.58
2688 4184 7.505585 ACAGGGAAACTCAATTAATCAACTCAA 59.494 33.333 0.00 0.00 0.00 3.02
2725 4222 9.577003 GACGCGTAAAATTAAATTACATAGGAG 57.423 33.333 13.97 3.90 33.78 3.69
2808 4305 2.165845 GTGTACTGAATGGCGAGTAGGT 59.834 50.000 0.00 0.00 0.00 3.08
2822 4319 6.707599 TCGATAGATACTCGATGTGTACTG 57.292 41.667 0.00 0.00 42.67 2.74
2882 4379 7.142021 CAGTATGCAGTCGAGATACATACTTT 58.858 38.462 19.72 5.98 46.94 2.66
2946 4449 4.022329 ACCAATTGATCCCGTCAGAAAAAC 60.022 41.667 7.12 0.00 38.29 2.43
2994 4498 9.907229 CTCATCCTTTCCTTTTAGTAGGTATTT 57.093 33.333 0.00 0.00 36.63 1.40
3017 4526 9.443323 TGATATTAACAGGTTCGAAAAATCTCA 57.557 29.630 0.00 0.18 0.00 3.27
3027 4536 7.250569 AGTGCAATTTGATATTAACAGGTTCG 58.749 34.615 0.00 0.00 0.00 3.95
3042 4551 7.872163 TGCTTAGTTTATGAAGTGCAATTTG 57.128 32.000 0.00 0.00 0.00 2.32
3043 4552 8.885494 TTTGCTTAGTTTATGAAGTGCAATTT 57.115 26.923 0.00 0.00 38.64 1.82
3044 4553 8.885494 TTTTGCTTAGTTTATGAAGTGCAATT 57.115 26.923 0.00 0.00 38.64 2.32
3048 4557 8.519492 TGATTTTTGCTTAGTTTATGAAGTGC 57.481 30.769 0.00 0.00 0.00 4.40
3062 4571 6.877236 ACATCCGGAAATATGATTTTTGCTT 58.123 32.000 9.01 0.00 0.00 3.91
3072 4581 8.239314 CCAGAATTTATGACATCCGGAAATATG 58.761 37.037 9.01 4.36 0.00 1.78
3073 4582 7.394359 CCCAGAATTTATGACATCCGGAAATAT 59.606 37.037 9.01 3.55 0.00 1.28
3080 4589 5.126067 ACTTCCCAGAATTTATGACATCCG 58.874 41.667 0.00 0.00 0.00 4.18
3082 4591 9.788960 GTTTTACTTCCCAGAATTTATGACATC 57.211 33.333 0.00 0.00 0.00 3.06
3089 4598 8.776470 CGTGTTAGTTTTACTTCCCAGAATTTA 58.224 33.333 0.00 0.00 0.00 1.40
3096 4606 4.512571 GCTTCGTGTTAGTTTTACTTCCCA 59.487 41.667 0.00 0.00 0.00 4.37
3102 4612 8.417176 CAAATCAATGCTTCGTGTTAGTTTTAC 58.583 33.333 0.00 0.00 0.00 2.01
3107 4617 5.940192 TCAAATCAATGCTTCGTGTTAGT 57.060 34.783 0.00 0.00 0.00 2.24
3109 4619 8.586570 AAATTTCAAATCAATGCTTCGTGTTA 57.413 26.923 0.00 0.00 0.00 2.41
3111 4621 7.867403 AGTAAATTTCAAATCAATGCTTCGTGT 59.133 29.630 0.00 0.00 0.00 4.49
3112 4622 8.231304 AGTAAATTTCAAATCAATGCTTCGTG 57.769 30.769 0.00 0.00 0.00 4.35
3113 4623 8.081633 TGAGTAAATTTCAAATCAATGCTTCGT 58.918 29.630 0.00 0.00 0.00 3.85
3114 4624 8.451687 TGAGTAAATTTCAAATCAATGCTTCG 57.548 30.769 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.