Multiple sequence alignment - TraesCS4D01G142900

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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 TraesCS4D01G142900 chr4D 100.000 2319 0 0 964 3282 129776337 129778655 0.000000e+00 4283.0
1 TraesCS4D01G142900 chr4D 100.000 697 0 0 1 697 129775374 129776070 0.000000e+00 1288.0
2 TraesCS4D01G142900 chr4D 79.130 230 41 5 2974 3197 38342423 38342651 5.670000e-33 152.0
3 TraesCS4D01G142900 chr4A 93.316 1900 56 22 964 2849 437484117 437482275 0.000000e+00 2739.0
4 TraesCS4D01G142900 chr4A 91.566 664 30 6 2 640 437485118 437484456 0.000000e+00 893.0
5 TraesCS4D01G142900 chr4A 85.100 349 44 6 2941 3282 437482262 437481915 1.870000e-92 350.0
6 TraesCS4D01G142900 chr4A 80.088 226 40 3 2982 3202 570453696 570453471 2.620000e-36 163.0
7 TraesCS4D01G142900 chrUn 94.951 1624 42 15 964 2584 58871032 58869446 0.000000e+00 2508.0
8 TraesCS4D01G142900 chrUn 98.212 671 10 2 1 670 319831908 319831239 0.000000e+00 1171.0
9 TraesCS4D01G142900 chrUn 98.212 671 10 2 1 670 332180561 332181230 0.000000e+00 1171.0
10 TraesCS4D01G142900 chrUn 98.212 671 10 2 1 670 380953793 380954462 0.000000e+00 1171.0
11 TraesCS4D01G142900 chrUn 99.197 249 2 0 964 1212 319831199 319830951 1.800000e-122 449.0
12 TraesCS4D01G142900 chrUn 99.197 249 2 0 964 1212 332181270 332181518 1.800000e-122 449.0
13 TraesCS4D01G142900 chrUn 93.525 278 10 2 2580 2849 58869382 58869105 1.100000e-109 407.0
14 TraesCS4D01G142900 chrUn 85.484 124 12 6 2848 2970 339555144 339555026 1.240000e-24 124.0
15 TraesCS4D01G142900 chr3D 82.114 246 40 4 1053 1296 525917798 525917555 1.190000e-49 207.0
16 TraesCS4D01G142900 chr3D 82.105 190 32 2 1698 1886 525917553 525917365 9.420000e-36 161.0
17 TraesCS4D01G142900 chr5D 92.908 141 10 0 1163 1303 110794092 110794232 4.290000e-49 206.0
18 TraesCS4D01G142900 chr5B 94.074 135 8 0 1169 1303 122101437 122101303 4.290000e-49 206.0
19 TraesCS4D01G142900 chr5A 93.846 130 8 0 1174 1303 116034549 116034420 2.580000e-46 196.0
20 TraesCS4D01G142900 chr3B 81.148 244 42 4 1055 1296 694263459 694263700 3.340000e-45 193.0
21 TraesCS4D01G142900 chr3B 80.087 231 37 7 2979 3202 704570063 704570291 2.620000e-36 163.0
22 TraesCS4D01G142900 chr6B 79.913 229 41 4 2979 3202 161595502 161595730 2.620000e-36 163.0
23 TraesCS4D01G142900 chr6B 93.684 95 5 1 2847 2941 506874096 506874003 1.230000e-29 141.0
24 TraesCS4D01G142900 chr6B 89.189 74 5 3 1691 1762 457216782 457216710 4.510000e-14 89.8
25 TraesCS4D01G142900 chr1A 88.806 134 13 2 1166 1298 58946920 58947052 2.620000e-36 163.0
26 TraesCS4D01G142900 chr3A 82.011 189 32 2 1698 1885 660196184 660196371 3.390000e-35 159.0
27 TraesCS4D01G142900 chr3A 94.737 95 4 1 2848 2942 550433963 550433870 2.640000e-31 147.0
28 TraesCS4D01G142900 chr3A 89.189 111 6 4 2828 2934 646126807 646126915 2.050000e-27 134.0
29 TraesCS4D01G142900 chr2B 80.000 225 37 6 2979 3197 505930418 505930196 3.390000e-35 159.0
30 TraesCS4D01G142900 chr2B 79.464 224 41 3 2982 3200 162860810 162860587 1.580000e-33 154.0
31 TraesCS4D01G142900 chr2B 87.179 117 10 5 2819 2934 677852906 677853018 9.560000e-26 128.0
32 TraesCS4D01G142900 chr2B 88.571 70 6 2 1694 1762 545366056 545365988 2.100000e-12 84.2
33 TraesCS4D01G142900 chr7A 79.204 226 42 3 2982 3202 140745891 140745666 5.670000e-33 152.0
34 TraesCS4D01G142900 chr7A 79.204 226 42 3 2982 3202 141294350 141294125 5.670000e-33 152.0
35 TraesCS4D01G142900 chr7A 94.505 91 3 2 2844 2934 643550142 643550230 4.420000e-29 139.0
36 TraesCS4D01G142900 chr1D 87.121 132 15 2 1166 1296 60317506 60317636 7.340000e-32 148.0
37 TraesCS4D01G142900 chr6A 93.548 93 5 1 2848 2940 23628289 23628380 1.590000e-28 137.0
38 TraesCS4D01G142900 chr6A 87.838 74 6 3 1691 1762 428426484 428426556 2.100000e-12 84.2
39 TraesCS4D01G142900 chr1B 91.837 98 7 1 2840 2937 632863272 632863368 5.710000e-28 135.0
40 TraesCS4D01G142900 chr7B 86.777 121 9 6 2848 2964 29827088 29826971 9.560000e-26 128.0
41 TraesCS4D01G142900 chr6D 89.189 74 5 3 1691 1762 292737755 292737683 4.510000e-14 89.8
42 TraesCS4D01G142900 chr2D 88.571 70 6 2 1694 1762 466723987 466723919 2.100000e-12 84.2


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 TraesCS4D01G142900 chr4D 129775374 129778655 3281 False 2785.500000 4283 100.0000 1 3282 2 chr4D.!!$F2 3281
1 TraesCS4D01G142900 chr4A 437481915 437485118 3203 True 1327.333333 2739 89.9940 2 3282 3 chr4A.!!$R2 3280
2 TraesCS4D01G142900 chrUn 58869105 58871032 1927 True 1457.500000 2508 94.2380 964 2849 2 chrUn.!!$R2 1885
3 TraesCS4D01G142900 chrUn 380953793 380954462 669 False 1171.000000 1171 98.2120 1 670 1 chrUn.!!$F1 669
4 TraesCS4D01G142900 chrUn 319830951 319831908 957 True 810.000000 1171 98.7045 1 1212 2 chrUn.!!$R3 1211
5 TraesCS4D01G142900 chrUn 332180561 332181518 957 False 810.000000 1171 98.7045 1 1212 2 chrUn.!!$F2 1211

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
668 994 0.106217 CCCAGTCTCTCTCTCTCCCC 60.106 65.0 0.0 0.0 0.0 4.81 F
1275 1601 0.847373 AGCTCCTCATCCTCGACCTA 59.153 55.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1888 0.178944 CCATGCACCCATCCCATCAT 60.179 55.0 0.0 0.0 0.0 2.45 R
3092 3535 0.036388 GCAAGGAAGGGTGATGACGA 60.036 55.0 0.0 0.0 0.0 4.20 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
41 42 8.462016 GTGATAGCCTGAAACAAGACAAATAAT 58.538 33.333 0.00 0.00 0.00 1.28
246 256 0.179054 GCCTCCGGCCTTTAAGTAGG 60.179 60.000 0.00 0.00 44.06 3.18
446 457 9.986833 TCGAAAATCATGTTATGTTGATACAAG 57.013 29.630 0.00 0.00 37.91 3.16
663 989 1.381165 GGCGTCCCAGTCTCTCTCTC 61.381 65.000 0.00 0.00 0.00 3.20
664 990 0.393808 GCGTCCCAGTCTCTCTCTCT 60.394 60.000 0.00 0.00 0.00 3.10
665 991 1.663695 CGTCCCAGTCTCTCTCTCTC 58.336 60.000 0.00 0.00 0.00 3.20
666 992 1.745827 CGTCCCAGTCTCTCTCTCTCC 60.746 61.905 0.00 0.00 0.00 3.71
667 993 0.923358 TCCCAGTCTCTCTCTCTCCC 59.077 60.000 0.00 0.00 0.00 4.30
668 994 0.106217 CCCAGTCTCTCTCTCTCCCC 60.106 65.000 0.00 0.00 0.00 4.81
669 995 0.106217 CCAGTCTCTCTCTCTCCCCC 60.106 65.000 0.00 0.00 0.00 5.40
1275 1601 0.847373 AGCTCCTCATCCTCGACCTA 59.153 55.000 0.00 0.00 0.00 3.08
1445 1771 4.141876 ATTGGGCCGGTGATGGGG 62.142 66.667 1.90 0.00 0.00 4.96
1480 1806 1.937223 GTGTGAACACGTCCATGTCAA 59.063 47.619 0.00 0.00 37.10 3.18
1554 1883 3.636231 CGGCTCTTCACCCACCCA 61.636 66.667 0.00 0.00 0.00 4.51
1558 1887 2.122769 TCTTCACCCACCCACCGA 60.123 61.111 0.00 0.00 0.00 4.69
1559 1888 1.764571 CTCTTCACCCACCCACCGAA 61.765 60.000 0.00 0.00 0.00 4.30
1562 1891 1.419720 TTCACCCACCCACCGAATGA 61.420 55.000 0.00 0.00 0.00 2.57
1563 1892 1.204786 TCACCCACCCACCGAATGAT 61.205 55.000 0.00 0.00 0.00 2.45
1564 1893 1.031571 CACCCACCCACCGAATGATG 61.032 60.000 0.00 0.00 0.00 3.07
1565 1894 1.453745 CCCACCCACCGAATGATGG 60.454 63.158 0.00 0.00 35.59 3.51
1626 1967 2.563427 GCACGCCTTCTTCCTTGC 59.437 61.111 0.00 0.00 0.00 4.01
1627 1968 1.968540 GCACGCCTTCTTCCTTGCT 60.969 57.895 0.00 0.00 0.00 3.91
1641 1982 1.416813 CTTGCTGACCTCATCGTCGC 61.417 60.000 0.00 0.00 35.40 5.19
1672 2013 7.963532 TCTGTAATCTCCATGGGTAGTTAATC 58.036 38.462 13.02 0.00 0.00 1.75
1834 2175 3.181436 CCTTCAAGGATGCCATGAGGTAT 60.181 47.826 0.00 0.00 43.54 2.73
1943 2305 4.077184 GGGTCACGTCGATGGCCA 62.077 66.667 8.56 8.56 46.96 5.36
1944 2306 2.813908 GGTCACGTCGATGGCCAC 60.814 66.667 8.16 0.47 44.34 5.01
1945 2307 2.813908 GTCACGTCGATGGCCACC 60.814 66.667 8.16 0.00 0.00 4.61
1946 2308 3.307108 TCACGTCGATGGCCACCA 61.307 61.111 8.16 0.00 38.19 4.17
1947 2309 3.118454 CACGTCGATGGCCACCAC 61.118 66.667 8.16 3.66 35.80 4.16
1948 2310 4.388499 ACGTCGATGGCCACCACC 62.388 66.667 8.16 0.00 35.80 4.61
2167 2529 0.468648 TGCAGATCCAGCCTGATGAG 59.531 55.000 0.00 0.00 33.65 2.90
2564 2928 5.297278 AGGAGAGACGATGACAGTGTTATAC 59.703 44.000 0.00 0.00 0.00 1.47
2565 2929 5.297278 GGAGAGACGATGACAGTGTTATACT 59.703 44.000 0.00 1.70 41.36 2.12
2566 2930 6.366315 AGAGACGATGACAGTGTTATACTC 57.634 41.667 15.17 15.17 37.60 2.59
2567 2931 5.297278 AGAGACGATGACAGTGTTATACTCC 59.703 44.000 17.40 1.94 37.60 3.85
2570 2934 4.705507 ACGATGACAGTGTTATACTCCTGT 59.294 41.667 0.00 0.00 37.60 4.00
2572 2936 6.100004 CGATGACAGTGTTATACTCCTGTTT 58.900 40.000 0.00 0.00 37.60 2.83
2573 2937 6.035005 CGATGACAGTGTTATACTCCTGTTTG 59.965 42.308 0.00 0.00 37.60 2.93
2576 2940 6.873605 TGACAGTGTTATACTCCTGTTTGATG 59.126 38.462 0.00 0.00 37.60 3.07
2578 2942 5.643348 CAGTGTTATACTCCTGTTTGATGCA 59.357 40.000 0.00 0.00 37.60 3.96
2663 3092 8.241497 TGCATCTCTTATCCTTGCATATTTTT 57.759 30.769 0.00 0.00 38.32 1.94
2849 3286 4.641989 ACATGTGGAAGGAATGAAGCATAC 59.358 41.667 0.00 0.00 0.00 2.39
2850 3287 4.574674 TGTGGAAGGAATGAAGCATACT 57.425 40.909 0.00 0.00 0.00 2.12
2851 3288 4.517285 TGTGGAAGGAATGAAGCATACTC 58.483 43.478 0.00 0.00 0.00 2.59
2854 3291 3.117888 GGAAGGAATGAAGCATACTCCCA 60.118 47.826 0.00 0.00 0.00 4.37
2856 3293 4.363991 AGGAATGAAGCATACTCCCATC 57.636 45.455 0.00 0.00 0.00 3.51
2857 3294 3.073650 AGGAATGAAGCATACTCCCATCC 59.926 47.826 0.00 0.00 0.00 3.51
2858 3295 2.847327 ATGAAGCATACTCCCATCCG 57.153 50.000 0.00 0.00 0.00 4.18
2859 3296 1.496060 TGAAGCATACTCCCATCCGT 58.504 50.000 0.00 0.00 0.00 4.69
2860 3297 1.837439 TGAAGCATACTCCCATCCGTT 59.163 47.619 0.00 0.00 0.00 4.44
2861 3298 2.238646 TGAAGCATACTCCCATCCGTTT 59.761 45.455 0.00 0.00 0.00 3.60
2862 3299 2.622064 AGCATACTCCCATCCGTTTC 57.378 50.000 0.00 0.00 0.00 2.78
2863 3300 1.837439 AGCATACTCCCATCCGTTTCA 59.163 47.619 0.00 0.00 0.00 2.69
2864 3301 2.238646 AGCATACTCCCATCCGTTTCAA 59.761 45.455 0.00 0.00 0.00 2.69
2865 3302 3.013921 GCATACTCCCATCCGTTTCAAA 58.986 45.455 0.00 0.00 0.00 2.69
2866 3303 3.442273 GCATACTCCCATCCGTTTCAAAA 59.558 43.478 0.00 0.00 0.00 2.44
2867 3304 4.097892 GCATACTCCCATCCGTTTCAAAAT 59.902 41.667 0.00 0.00 0.00 1.82
2868 3305 5.298276 GCATACTCCCATCCGTTTCAAAATA 59.702 40.000 0.00 0.00 0.00 1.40
2869 3306 6.513393 GCATACTCCCATCCGTTTCAAAATAG 60.513 42.308 0.00 0.00 0.00 1.73
2870 3307 5.174037 ACTCCCATCCGTTTCAAAATAGA 57.826 39.130 0.00 0.00 0.00 1.98
2871 3308 5.755849 ACTCCCATCCGTTTCAAAATAGAT 58.244 37.500 0.00 0.00 0.00 1.98
2872 3309 5.590259 ACTCCCATCCGTTTCAAAATAGATG 59.410 40.000 9.20 9.20 33.56 2.90
2873 3310 5.750524 TCCCATCCGTTTCAAAATAGATGA 58.249 37.500 14.42 0.00 34.68 2.92
2874 3311 5.588648 TCCCATCCGTTTCAAAATAGATGAC 59.411 40.000 14.42 0.00 34.68 3.06
2875 3312 5.221048 CCCATCCGTTTCAAAATAGATGACC 60.221 44.000 14.42 0.00 34.68 4.02
2876 3313 5.221048 CCATCCGTTTCAAAATAGATGACCC 60.221 44.000 14.42 0.00 34.68 4.46
2877 3314 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
2878 3315 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
2879 3316 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
2880 3317 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
2881 3318 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
2882 3319 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
2883 3320 8.293867 CGTTTCAAAATAGATGACCCAACTTTA 58.706 33.333 0.00 0.00 0.00 1.85
2920 3357 8.680903 AGCATAAAGTTGAGTCATCTATTTTGG 58.319 33.333 4.14 0.00 0.00 3.28
2921 3358 8.677300 GCATAAAGTTGAGTCATCTATTTTGGA 58.323 33.333 4.14 0.00 0.00 3.53
2924 3361 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2925 3362 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2926 3363 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2927 3364 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2928 3365 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2929 3366 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2930 3367 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2931 3368 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2932 3369 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2933 3370 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2934 3371 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
2935 3372 6.138263 TCTATTTTGGAACGGAGGGAGTATA 58.862 40.000 0.00 0.00 0.00 1.47
2936 3373 5.906772 ATTTTGGAACGGAGGGAGTATAT 57.093 39.130 0.00 0.00 0.00 0.86
2962 3399 7.394359 TCCTTAAGTGAATGCTATGCTCTTTTT 59.606 33.333 0.97 0.00 0.00 1.94
3013 3453 1.196808 CCGTGGCAGTACAATCAACAC 59.803 52.381 0.00 0.00 0.00 3.32
3053 3496 9.640963 AATTACATCTAAATCCATAGACGTAGC 57.359 33.333 0.00 0.00 33.59 3.58
3056 3499 5.354054 TCTAAATCCATAGACGTAGCGAC 57.646 43.478 0.00 0.00 0.00 5.19
3057 3500 4.818005 TCTAAATCCATAGACGTAGCGACA 59.182 41.667 0.00 0.00 0.00 4.35
3078 3521 1.354040 CTACAAGCACTGAAGCGAGG 58.646 55.000 0.00 0.00 40.15 4.63
3080 3523 2.740055 AAGCACTGAAGCGAGGCG 60.740 61.111 0.00 0.00 40.15 5.52
3107 3550 0.815615 GCCATCGTCATCACCCTTCC 60.816 60.000 0.00 0.00 0.00 3.46
3114 3557 1.198094 TCATCACCCTTCCTTGCCGA 61.198 55.000 0.00 0.00 0.00 5.54
3117 3560 2.034221 ACCCTTCCTTGCCGAAGC 59.966 61.111 0.00 0.00 38.35 3.86
3128 3571 0.749818 TGCCGAAGCAGGACAAAACA 60.750 50.000 0.00 0.00 46.52 2.83
3133 3576 3.751175 CCGAAGCAGGACAAAACAGATTA 59.249 43.478 0.00 0.00 0.00 1.75
3136 3579 6.093495 CCGAAGCAGGACAAAACAGATTATAA 59.907 38.462 0.00 0.00 0.00 0.98
3140 3583 9.461312 AAGCAGGACAAAACAGATTATAATACA 57.539 29.630 0.00 0.00 0.00 2.29
3144 3587 9.959721 AGGACAAAACAGATTATAATACACAGT 57.040 29.630 0.00 0.00 0.00 3.55
3164 3607 2.901264 GTCGAGAAGTCGTCGTGTTAAG 59.099 50.000 0.00 0.00 46.85 1.85
3166 3609 1.984297 GAGAAGTCGTCGTGTTAAGGC 59.016 52.381 0.00 0.00 0.00 4.35
3167 3610 1.066136 GAAGTCGTCGTGTTAAGGCC 58.934 55.000 0.00 0.00 0.00 5.19
3168 3611 0.320160 AAGTCGTCGTGTTAAGGCCC 60.320 55.000 0.00 0.00 0.00 5.80
3173 3616 3.023119 TCGTCGTGTTAAGGCCCTATAA 58.977 45.455 0.00 0.00 0.00 0.98
3174 3617 3.446873 TCGTCGTGTTAAGGCCCTATAAA 59.553 43.478 0.00 0.00 0.00 1.40
3177 3620 4.333649 GTCGTGTTAAGGCCCTATAAAACC 59.666 45.833 0.00 0.00 0.00 3.27
3191 3634 0.466555 AAAACCAGCGCACCCTAACA 60.467 50.000 11.47 0.00 0.00 2.41
3197 3640 1.082366 GCGCACCCTAACAACAACG 60.082 57.895 0.30 0.00 0.00 4.10
3209 3652 1.072505 AACAACGGCCGAATGACCT 59.927 52.632 35.90 16.08 0.00 3.85
3211 3654 2.125673 AACGGCCGAATGACCTCG 60.126 61.111 35.90 0.02 38.58 4.63
3222 3665 4.299155 CGAATGACCTCGTATTGCTACAT 58.701 43.478 0.00 0.00 34.08 2.29
3269 3712 9.243637 CAATGGGTGTAATTAATATTTGTTCCG 57.756 33.333 0.00 0.00 0.00 4.30
3273 3716 9.857957 GGGTGTAATTAATATTTGTTCCGAAAA 57.142 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.277779 CGTCACAAGCCTTGTTCTTTTATCA 60.278 40.000 7.51 0.00 43.23 2.15
246 256 5.250200 TGTGTTACCTGGAATACATGGTTC 58.750 41.667 0.00 0.90 34.11 3.62
614 640 2.434336 GGTTTTGAGAAGGCAAAAGGGT 59.566 45.455 0.00 0.00 45.33 4.34
1275 1601 3.241530 TTGCCCCAGCGAGAGTGT 61.242 61.111 0.00 0.00 44.31 3.55
1445 1771 5.003590 GTGTTCACACGAGTCTAATCGATTC 59.996 44.000 15.25 0.00 45.56 2.52
1480 1806 1.912043 AGTTGATCAAGCTAGTGGGCT 59.088 47.619 8.80 0.00 45.30 5.19
1554 1883 0.183492 CACCCATCCCATCATTCGGT 59.817 55.000 0.00 0.00 0.00 4.69
1558 1887 1.712056 CATGCACCCATCCCATCATT 58.288 50.000 0.00 0.00 0.00 2.57
1559 1888 0.178944 CCATGCACCCATCCCATCAT 60.179 55.000 0.00 0.00 0.00 2.45
1562 1891 2.123164 GCCATGCACCCATCCCAT 60.123 61.111 0.00 0.00 0.00 4.00
1563 1892 3.670319 TGCCATGCACCCATCCCA 61.670 61.111 0.00 0.00 31.71 4.37
1641 1982 3.493350 CCCATGGAGATTACAGAAGACGG 60.493 52.174 15.22 0.00 0.00 4.79
1672 2013 3.055963 TGCAGCCATTAATCCCAAAAGTG 60.056 43.478 0.00 0.00 0.00 3.16
1723 2064 3.940975 CTCGTTGTCCGTCCGACCG 62.941 68.421 0.00 0.00 41.18 4.79
1786 2127 2.050351 CCGACGTCGCAGTTGAGT 60.050 61.111 31.73 0.00 38.18 3.41
1834 2175 2.042537 AGGCGAGGCATCCAGAGA 60.043 61.111 0.00 0.00 0.00 3.10
1891 2244 3.315140 TCGCCGATTGTGGGGTCA 61.315 61.111 0.00 0.00 42.29 4.02
1927 2280 2.813908 GTGGCCATCGACGTGACC 60.814 66.667 9.72 0.00 0.00 4.02
1951 2313 4.769063 TATGTGGTGGCGGTGGCG 62.769 66.667 0.00 0.00 41.24 5.69
2350 2712 9.922477 TCCTTACTCGGATGTATATGATCTAAT 57.078 33.333 0.00 0.00 0.00 1.73
2351 2713 9.922477 ATCCTTACTCGGATGTATATGATCTAA 57.078 33.333 0.00 0.00 42.13 2.10
2367 2729 0.742990 TTTGCCGCCATCCTTACTCG 60.743 55.000 0.00 0.00 0.00 4.18
2548 2912 5.250235 ACAGGAGTATAACACTGTCATCG 57.750 43.478 0.00 0.00 39.84 3.84
2564 2928 7.930325 TCTTCTTAGATATGCATCAAACAGGAG 59.070 37.037 0.19 0.00 33.21 3.69
2565 2929 7.795047 TCTTCTTAGATATGCATCAAACAGGA 58.205 34.615 0.19 0.00 33.21 3.86
2566 2930 8.341173 GTTCTTCTTAGATATGCATCAAACAGG 58.659 37.037 0.19 0.00 33.21 4.00
2567 2931 9.107177 AGTTCTTCTTAGATATGCATCAAACAG 57.893 33.333 0.19 0.00 33.21 3.16
2570 2934 7.553760 TGCAGTTCTTCTTAGATATGCATCAAA 59.446 33.333 0.19 0.00 42.52 2.69
2572 2936 6.481313 GTGCAGTTCTTCTTAGATATGCATCA 59.519 38.462 0.19 0.00 45.78 3.07
2573 2937 6.481313 TGTGCAGTTCTTCTTAGATATGCATC 59.519 38.462 0.19 0.00 45.78 3.91
2576 2940 6.668541 TTGTGCAGTTCTTCTTAGATATGC 57.331 37.500 0.00 0.00 40.21 3.14
2578 2942 9.624373 ATCAATTGTGCAGTTCTTCTTAGATAT 57.376 29.630 5.13 0.00 0.00 1.63
2849 3286 5.822519 TCATCTATTTTGAAACGGATGGGAG 59.177 40.000 14.63 0.00 34.20 4.30
2850 3287 5.588648 GTCATCTATTTTGAAACGGATGGGA 59.411 40.000 14.63 0.00 34.20 4.37
2851 3288 5.221048 GGTCATCTATTTTGAAACGGATGGG 60.221 44.000 14.63 0.00 34.20 4.00
2854 3291 5.505780 TGGGTCATCTATTTTGAAACGGAT 58.494 37.500 0.00 0.00 0.00 4.18
2856 3293 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
2857 3294 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
2894 3331 8.680903 CCAAAATAGATGACTCAACTTTATGCT 58.319 33.333 0.00 0.00 0.00 3.79
2895 3332 8.677300 TCCAAAATAGATGACTCAACTTTATGC 58.323 33.333 0.00 0.00 0.00 3.14
2898 3335 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
2899 3336 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2900 3337 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2901 3338 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2902 3339 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2903 3340 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2904 3341 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2905 3342 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2906 3343 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2907 3344 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2908 3345 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2909 3346 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2910 3347 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2911 3348 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2912 3349 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2913 3350 6.013984 GGATATACTCCCTCCGTTCCAAAATA 60.014 42.308 0.00 0.00 38.19 1.40
2914 3351 5.221864 GGATATACTCCCTCCGTTCCAAAAT 60.222 44.000 0.00 0.00 38.19 1.82
2915 3352 4.102054 GGATATACTCCCTCCGTTCCAAAA 59.898 45.833 0.00 0.00 38.19 2.44
2916 3353 3.644738 GGATATACTCCCTCCGTTCCAAA 59.355 47.826 0.00 0.00 38.19 3.28
2917 3354 3.116862 AGGATATACTCCCTCCGTTCCAA 60.117 47.826 0.00 0.00 46.27 3.53
2918 3355 2.449730 AGGATATACTCCCTCCGTTCCA 59.550 50.000 0.00 0.00 46.27 3.53
2919 3356 3.172471 AGGATATACTCCCTCCGTTCC 57.828 52.381 0.00 0.00 46.27 3.62
2920 3357 5.774184 ACTTAAGGATATACTCCCTCCGTTC 59.226 44.000 7.53 0.00 46.27 3.95
2921 3358 5.539193 CACTTAAGGATATACTCCCTCCGTT 59.461 44.000 7.53 0.00 46.27 4.44
2922 3359 5.078256 CACTTAAGGATATACTCCCTCCGT 58.922 45.833 7.53 0.00 46.27 4.69
2923 3360 5.322754 TCACTTAAGGATATACTCCCTCCG 58.677 45.833 7.53 0.00 46.27 4.63
2924 3361 7.616313 CATTCACTTAAGGATATACTCCCTCC 58.384 42.308 7.53 0.00 46.27 4.30
2925 3362 7.038658 AGCATTCACTTAAGGATATACTCCCTC 60.039 40.741 7.53 0.00 46.27 4.30
2926 3363 6.789959 AGCATTCACTTAAGGATATACTCCCT 59.210 38.462 7.53 0.00 46.27 4.20
2927 3364 7.010339 AGCATTCACTTAAGGATATACTCCC 57.990 40.000 7.53 0.00 46.27 4.30
2928 3365 9.593134 CATAGCATTCACTTAAGGATATACTCC 57.407 37.037 7.53 0.00 45.33 3.85
2929 3366 9.092876 GCATAGCATTCACTTAAGGATATACTC 57.907 37.037 7.53 0.00 29.29 2.59
2930 3367 8.820831 AGCATAGCATTCACTTAAGGATATACT 58.179 33.333 7.53 0.39 29.29 2.12
2931 3368 9.092876 GAGCATAGCATTCACTTAAGGATATAC 57.907 37.037 7.53 0.00 29.29 1.47
2932 3369 9.040259 AGAGCATAGCATTCACTTAAGGATATA 57.960 33.333 7.53 0.00 29.29 0.86
2933 3370 7.915930 AGAGCATAGCATTCACTTAAGGATAT 58.084 34.615 7.53 0.00 31.03 1.63
2934 3371 7.308450 AGAGCATAGCATTCACTTAAGGATA 57.692 36.000 7.53 0.00 0.00 2.59
2935 3372 6.185114 AGAGCATAGCATTCACTTAAGGAT 57.815 37.500 7.53 0.00 0.00 3.24
2936 3373 5.620738 AGAGCATAGCATTCACTTAAGGA 57.379 39.130 7.53 0.00 0.00 3.36
2988 3428 0.673644 ATTGTACTGCCACGGCTGAC 60.674 55.000 20.34 13.84 41.63 3.51
2992 3432 0.168128 GTTGATTGTACTGCCACGGC 59.832 55.000 0.00 0.00 42.35 5.68
2995 3435 2.226330 TGGTGTTGATTGTACTGCCAC 58.774 47.619 0.00 0.00 0.00 5.01
3027 3467 9.640963 GCTACGTCTATGGATTTAGATGTAATT 57.359 33.333 12.26 0.00 44.30 1.40
3032 3472 5.795939 GTCGCTACGTCTATGGATTTAGATG 59.204 44.000 0.00 0.00 39.89 2.90
3038 3478 2.287668 GCTGTCGCTACGTCTATGGATT 60.288 50.000 0.00 0.00 0.00 3.01
3053 3496 1.723542 CTTCAGTGCTTGTAGCTGTCG 59.276 52.381 0.00 0.00 42.97 4.35
3056 3499 0.441533 CGCTTCAGTGCTTGTAGCTG 59.558 55.000 14.69 7.72 45.11 4.24
3057 3500 0.318441 TCGCTTCAGTGCTTGTAGCT 59.682 50.000 14.69 0.00 45.11 3.32
3066 3509 2.097038 CCTTCGCCTCGCTTCAGTG 61.097 63.158 0.00 0.00 0.00 3.66
3092 3535 0.036388 GCAAGGAAGGGTGATGACGA 60.036 55.000 0.00 0.00 0.00 4.20
3114 3557 9.461312 TGTATTATAATCTGTTTTGTCCTGCTT 57.539 29.630 0.00 0.00 0.00 3.91
3125 3568 9.737427 CTTCTCGACTGTGTATTATAATCTGTT 57.263 33.333 0.00 0.00 0.00 3.16
3128 3571 8.283992 CGACTTCTCGACTGTGTATTATAATCT 58.716 37.037 0.00 0.00 43.06 2.40
3133 3576 5.502058 CGACGACTTCTCGACTGTGTATTAT 60.502 44.000 0.00 0.00 43.06 1.28
3136 3579 2.093941 CGACGACTTCTCGACTGTGTAT 59.906 50.000 0.00 0.00 43.06 2.29
3140 3583 0.235144 CACGACGACTTCTCGACTGT 59.765 55.000 0.00 0.00 43.06 3.55
3144 3587 2.096069 CCTTAACACGACGACTTCTCGA 60.096 50.000 0.00 0.00 43.06 4.04
3164 3607 2.030551 GCGCTGGTTTTATAGGGCC 58.969 57.895 0.00 0.00 44.29 5.80
3166 3609 1.021968 GGTGCGCTGGTTTTATAGGG 58.978 55.000 9.73 0.00 0.00 3.53
3167 3610 1.021968 GGGTGCGCTGGTTTTATAGG 58.978 55.000 9.73 0.00 0.00 2.57
3168 3611 2.038387 AGGGTGCGCTGGTTTTATAG 57.962 50.000 9.73 0.00 0.00 1.31
3173 3616 0.466555 TTGTTAGGGTGCGCTGGTTT 60.467 50.000 9.73 0.00 0.00 3.27
3174 3617 1.149627 TTGTTAGGGTGCGCTGGTT 59.850 52.632 9.73 0.00 0.00 3.67
3177 3620 0.040425 GTTGTTGTTAGGGTGCGCTG 60.040 55.000 9.73 0.00 0.00 5.18
3191 3634 0.953960 GAGGTCATTCGGCCGTTGTT 60.954 55.000 27.15 13.45 0.00 2.83
3197 3640 1.217882 CAATACGAGGTCATTCGGCC 58.782 55.000 0.00 0.00 44.57 6.13
3209 3652 7.892778 TTCTTTGTACAATGTAGCAATACGA 57.107 32.000 18.04 0.00 0.00 3.43
3222 3665 5.843673 TGTGCCATCTTTTCTTTGTACAA 57.156 34.783 3.59 3.59 0.00 2.41


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

AutoCloner maintained by Alex Coulton.