Multiple sequence alignment - TraesCS1B01G072500

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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 TraesCS1B01G072500 chr1B 100.000 3854 0 0 1 3854 57025451 57021598 0.000000e+00 7118.0
1 TraesCS1B01G072500 chr1B 98.992 1488 15 0 1 1488 57052121 57050634 0.000000e+00 2665.0
2 TraesCS1B01G072500 chr1B 90.378 1164 65 11 1291 2410 57070847 57069687 0.000000e+00 1485.0
3 TraesCS1B01G072500 chr1B 90.135 963 56 8 1484 2410 57045406 57044447 0.000000e+00 1216.0
4 TraesCS1B01G072500 chr1B 85.518 801 88 15 3 785 57071981 57071191 0.000000e+00 811.0
5 TraesCS1B01G072500 chr1B 97.778 225 5 0 2649 2873 57067909 57067685 4.670000e-104 388.0
6 TraesCS1B01G072500 chr1B 97.333 225 6 0 2649 2873 57042670 57042446 2.170000e-102 383.0
7 TraesCS1B01G072500 chr1B 87.550 249 14 2 2408 2651 57068284 57068048 4.910000e-69 272.0
8 TraesCS1B01G072500 chr1B 83.280 311 33 11 857 1150 57071152 57070844 6.350000e-68 268.0
9 TraesCS1B01G072500 chr1B 87.149 249 15 4 2408 2651 57043045 57042809 2.280000e-67 267.0
10 TraesCS1B01G072500 chr1D 93.089 1939 80 24 970 2873 37438802 37436883 0.000000e+00 2789.0
11 TraesCS1B01G072500 chr1D 81.755 433 45 22 3448 3852 37436266 37435840 7.980000e-87 331.0
12 TraesCS1B01G072500 chr1A 92.514 1937 85 24 970 2873 31894847 31896756 0.000000e+00 2719.0
13 TraesCS1B01G072500 chr1A 91.878 1933 94 21 987 2873 36621349 36619434 0.000000e+00 2641.0
14 TraesCS1B01G072500 chr1A 92.607 257 17 2 3370 3625 31898900 31899155 6.080000e-98 368.0
15 TraesCS1B01G072500 chr1A 89.121 239 19 4 3144 3380 31897042 31897275 1.350000e-74 291.0
16 TraesCS1B01G072500 chr1A 78.089 429 52 31 3451 3852 36618780 36618367 2.320000e-57 233.0
17 TraesCS1B01G072500 chr1A 91.667 84 6 1 2883 2965 31896859 31896942 8.750000e-22 115.0
18 TraesCS1B01G072500 chr6B 92.517 294 20 2 3144 3435 561143688 561143395 1.660000e-113 420.0
19 TraesCS1B01G072500 chr6B 92.177 294 21 2 3144 3435 561007924 561008217 7.700000e-112 414.0
20 TraesCS1B01G072500 chr6B 88.841 233 18 3 3144 3374 135132510 135132736 2.930000e-71 279.0
21 TraesCS1B01G072500 chr6B 95.122 82 3 1 3004 3085 135132431 135132511 1.120000e-25 128.0
22 TraesCS1B01G072500 chr6B 93.617 47 2 1 3100 3146 437482965 437483010 6.910000e-08 69.4
23 TraesCS1B01G072500 chr4B 91.837 294 22 2 3144 3435 665338915 665338622 3.580000e-110 409.0
24 TraesCS1B01G072500 chr4B 86.256 211 26 3 1 210 424746858 424746650 3.870000e-55 226.0
25 TraesCS1B01G072500 chr7B 91.497 294 23 2 3144 3435 154565896 154566189 1.670000e-108 403.0
26 TraesCS1B01G072500 chr7B 92.045 88 6 1 2998 3085 154565811 154565897 5.230000e-24 122.0
27 TraesCS1B01G072500 chr3D 92.893 197 12 2 14 210 462452962 462452768 6.300000e-73 285.0
28 TraesCS1B01G072500 chr3D 76.210 248 57 2 1784 2030 480969936 480970182 3.120000e-26 130.0
29 TraesCS1B01G072500 chr3D 100.000 31 0 0 1790 1820 578259650 578259620 1.500000e-04 58.4
30 TraesCS1B01G072500 chr3B 90.521 211 16 4 1 210 614249458 614249251 3.790000e-70 276.0
31 TraesCS1B01G072500 chr3B 70.853 645 154 25 1394 2030 641804821 641805439 6.760000e-23 119.0
32 TraesCS1B01G072500 chr3B 97.368 38 1 0 346 383 486597332 486597295 8.940000e-07 65.8
33 TraesCS1B01G072500 chr3B 100.000 31 0 0 1790 1820 771558308 771558278 1.500000e-04 58.4
34 TraesCS1B01G072500 chr3B 87.500 48 4 2 1771 1818 773569338 773569383 2.000000e-03 54.7
35 TraesCS1B01G072500 chr2B 90.000 210 20 1 1 210 793384252 793384460 1.760000e-68 270.0
36 TraesCS1B01G072500 chr2B 92.593 54 3 1 2446 2498 731006497 731006550 4.130000e-10 76.8
37 TraesCS1B01G072500 chr7A 89.062 192 18 3 2207 2397 465753347 465753158 6.440000e-58 235.0
38 TraesCS1B01G072500 chr3A 92.593 135 10 0 76 210 54446609 54446475 1.090000e-45 195.0
39 TraesCS1B01G072500 chr3A 72.245 490 112 17 1544 2030 623777304 623777772 3.120000e-26 130.0
40 TraesCS1B01G072500 chr3A 93.182 44 2 1 349 391 522265506 522265463 3.210000e-06 63.9
41 TraesCS1B01G072500 chr6A 83.333 198 31 1 2109 2306 142076355 142076550 8.510000e-42 182.0
42 TraesCS1B01G072500 chr5A 87.500 64 7 1 349 411 378503240 378503303 5.340000e-09 73.1
43 TraesCS1B01G072500 chr5A 95.238 42 1 1 3104 3145 678203617 678203657 8.940000e-07 65.8


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 TraesCS1B01G072500 chr1B 57021598 57025451 3853 True 7118.00 7118 100.00000 1 3854 1 chr1B.!!$R1 3853
1 TraesCS1B01G072500 chr1B 57050634 57052121 1487 True 2665.00 2665 98.99200 1 1488 1 chr1B.!!$R2 1487
2 TraesCS1B01G072500 chr1B 57067685 57071981 4296 True 644.80 1485 88.90080 3 2873 5 chr1B.!!$R4 2870
3 TraesCS1B01G072500 chr1B 57042446 57045406 2960 True 622.00 1216 91.53900 1484 2873 3 chr1B.!!$R3 1389
4 TraesCS1B01G072500 chr1D 37435840 37438802 2962 True 1560.00 2789 87.42200 970 3852 2 chr1D.!!$R1 2882
5 TraesCS1B01G072500 chr1A 36618367 36621349 2982 True 1437.00 2641 84.98350 987 3852 2 chr1A.!!$R1 2865
6 TraesCS1B01G072500 chr1A 31894847 31899155 4308 False 873.25 2719 91.47725 970 3625 4 chr1A.!!$F1 2655

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
771 793 1.226802 CACCAGCGTCAGATCGGAG 60.227 63.158 0.0 0.0 0.0 4.63 F
2184 2422 0.593128 GCGCTCTTCTTTTTGCTCCA 59.407 50.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2566 1.133025 CTTGGGCTATCAAAAGGCACG 59.867 52.381 0.0 0.0 43.58 5.34 R
3091 5038 0.180171 TGGCACTATGATTGGGACGG 59.820 55.000 0.0 0.0 0.00 4.79 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
576 598 5.768317 CAAAAGTTTGGTTATGTCCACGAT 58.232 37.500 0.00 0.00 37.20 3.73
651 673 5.579384 AATTTCAACATTGTTGCGATGTG 57.421 34.783 22.02 0.70 38.36 3.21
771 793 1.226802 CACCAGCGTCAGATCGGAG 60.227 63.158 0.00 0.00 0.00 4.63
1611 1806 1.826442 GCCTACCCCTACTTCGCCTAT 60.826 57.143 0.00 0.00 0.00 2.57
2142 2377 3.463574 CTACTACAGCATCTCGGCG 57.536 57.895 0.00 0.00 39.27 6.46
2172 2410 1.664965 GAACGTGGTGAGCGCTCTT 60.665 57.895 35.27 21.47 0.00 2.85
2183 2421 0.877743 AGCGCTCTTCTTTTTGCTCC 59.122 50.000 2.64 0.00 0.00 4.70
2184 2422 0.593128 GCGCTCTTCTTTTTGCTCCA 59.407 50.000 0.00 0.00 0.00 3.86
2192 2430 6.925718 GCTCTTCTTTTTGCTCCAGTTAATTT 59.074 34.615 0.00 0.00 0.00 1.82
2193 2431 7.115520 GCTCTTCTTTTTGCTCCAGTTAATTTC 59.884 37.037 0.00 0.00 0.00 2.17
2267 2517 5.257082 TGGACTAGTTTGCAAAGTTTTCC 57.743 39.130 25.88 25.88 0.00 3.13
2279 2529 4.270084 GCAAAGTTTTCCTGGTAAAAGTGC 59.730 41.667 0.00 6.88 33.38 4.40
2363 2624 3.301794 TCATGGCATAAAGGAGCATGT 57.698 42.857 0.00 0.00 0.00 3.21
2383 2644 6.623486 CATGTCATTGCTTGATCCAAAACTA 58.377 36.000 0.00 0.00 36.54 2.24
2397 2658 8.243426 TGATCCAAAACTATGTTTCTGTAATGC 58.757 33.333 0.00 0.00 0.00 3.56
2415 4087 6.827762 TGTAATGCAAGACATCATAACCATGA 59.172 34.615 0.00 0.00 45.15 3.07
2493 4165 3.783943 GCGTTTTAGTGTGTTGTTCACTG 59.216 43.478 8.54 0.00 46.27 3.66
2496 4168 5.676744 CGTTTTAGTGTGTTGTTCACTGATG 59.323 40.000 8.54 0.00 46.27 3.07
2874 4710 4.889409 TGATTCTGAGCAACTTCCAAGTTT 59.111 37.500 1.76 0.00 46.52 2.66
2875 4711 4.900635 TTCTGAGCAACTTCCAAGTTTC 57.099 40.909 1.76 0.00 46.52 2.78
2876 4712 4.156455 TCTGAGCAACTTCCAAGTTTCT 57.844 40.909 4.29 4.29 46.52 2.52
2878 4714 4.576463 TCTGAGCAACTTCCAAGTTTCTTC 59.424 41.667 5.92 4.00 46.52 2.87
2879 4715 4.269183 TGAGCAACTTCCAAGTTTCTTCA 58.731 39.130 5.92 6.07 46.52 3.02
2880 4716 4.336433 TGAGCAACTTCCAAGTTTCTTCAG 59.664 41.667 5.92 0.00 46.52 3.02
2883 4814 3.229697 ACTTCCAAGTTTCTTCAGGGG 57.770 47.619 0.00 0.00 35.21 4.79
2924 4871 3.057315 CGCTCCAATCTTCCATGTTGTTT 60.057 43.478 0.00 0.00 0.00 2.83
2933 4880 6.713762 TCTTCCATGTTGTTTCAGTTGATT 57.286 33.333 0.00 0.00 0.00 2.57
2935 4882 8.231692 TCTTCCATGTTGTTTCAGTTGATTTA 57.768 30.769 0.00 0.00 0.00 1.40
2959 4906 4.217550 GTCTTGTAATTGGTGGCAAGCTAA 59.782 41.667 0.00 0.00 38.44 3.09
2960 4907 5.016173 TCTTGTAATTGGTGGCAAGCTAAT 58.984 37.500 0.00 0.00 38.44 1.73
2961 4908 4.717233 TGTAATTGGTGGCAAGCTAATG 57.283 40.909 0.00 0.00 0.00 1.90
2962 4909 3.446873 TGTAATTGGTGGCAAGCTAATGG 59.553 43.478 0.00 0.00 0.00 3.16
2963 4910 1.488390 ATTGGTGGCAAGCTAATGGG 58.512 50.000 0.00 0.00 0.00 4.00
2964 4911 0.114168 TTGGTGGCAAGCTAATGGGT 59.886 50.000 0.00 0.00 0.00 4.51
2965 4912 0.995803 TGGTGGCAAGCTAATGGGTA 59.004 50.000 0.00 0.00 0.00 3.69
2966 4913 1.356059 TGGTGGCAAGCTAATGGGTAA 59.644 47.619 0.00 0.00 0.00 2.85
2967 4914 2.024464 TGGTGGCAAGCTAATGGGTAAT 60.024 45.455 0.00 0.00 0.00 1.89
2982 4929 5.881923 TGGGTAATATGGGTTAGTCAGTC 57.118 43.478 0.00 0.00 0.00 3.51
2987 4934 7.453752 GGGTAATATGGGTTAGTCAGTCTCATA 59.546 40.741 0.00 0.00 0.00 2.15
2999 4946 2.749621 CAGTCTCATAAAACCAGGCACC 59.250 50.000 0.00 0.00 0.00 5.01
3000 4947 2.375174 AGTCTCATAAAACCAGGCACCA 59.625 45.455 0.00 0.00 0.00 4.17
3001 4948 3.010584 AGTCTCATAAAACCAGGCACCAT 59.989 43.478 0.00 0.00 0.00 3.55
3002 4949 3.763897 GTCTCATAAAACCAGGCACCATT 59.236 43.478 0.00 0.00 0.00 3.16
3003 4950 4.220602 GTCTCATAAAACCAGGCACCATTT 59.779 41.667 0.00 0.00 0.00 2.32
3006 4953 6.495181 TCTCATAAAACCAGGCACCATTTTTA 59.505 34.615 0.00 3.37 0.00 1.52
3016 4963 7.775561 ACCAGGCACCATTTTTATTTTTGTTTA 59.224 29.630 0.00 0.00 0.00 2.01
3019 4966 8.835439 AGGCACCATTTTTATTTTTGTTTACTG 58.165 29.630 0.00 0.00 0.00 2.74
3040 4987 3.514706 TGGTAATCATGCAATGCAAGGTT 59.485 39.130 13.45 13.50 46.21 3.50
3046 4993 3.056678 TCATGCAATGCAAGGTTAGTTGG 60.057 43.478 13.45 0.00 46.21 3.77
3051 4998 5.421693 TGCAATGCAAGGTTAGTTGGATATT 59.578 36.000 5.01 0.00 37.49 1.28
3081 5028 0.618680 AGTCACTGGCTGGCTCCATA 60.619 55.000 2.00 0.00 35.22 2.74
3083 5030 0.618680 TCACTGGCTGGCTCCATACT 60.619 55.000 2.00 0.00 35.22 2.12
3084 5031 1.123077 CACTGGCTGGCTCCATACTA 58.877 55.000 2.00 0.00 35.22 1.82
3085 5032 1.123928 ACTGGCTGGCTCCATACTAC 58.876 55.000 2.00 0.00 35.22 2.73
3086 5033 1.343478 ACTGGCTGGCTCCATACTACT 60.343 52.381 2.00 0.00 35.22 2.57
3087 5034 1.342819 CTGGCTGGCTCCATACTACTC 59.657 57.143 2.00 0.00 35.22 2.59
3088 5035 0.682292 GGCTGGCTCCATACTACTCC 59.318 60.000 0.00 0.00 0.00 3.85
3090 5037 1.759562 GCTGGCTCCATACTACTCCCT 60.760 57.143 0.00 0.00 0.00 4.20
3091 5038 2.243810 CTGGCTCCATACTACTCCCTC 58.756 57.143 0.00 0.00 0.00 4.30
3092 5039 1.133136 TGGCTCCATACTACTCCCTCC 60.133 57.143 0.00 0.00 0.00 4.30
3093 5040 1.249407 GCTCCATACTACTCCCTCCG 58.751 60.000 0.00 0.00 0.00 4.63
3094 5041 1.479021 GCTCCATACTACTCCCTCCGT 60.479 57.143 0.00 0.00 0.00 4.69
3095 5042 2.506444 CTCCATACTACTCCCTCCGTC 58.494 57.143 0.00 0.00 0.00 4.79
3096 5043 1.144503 TCCATACTACTCCCTCCGTCC 59.855 57.143 0.00 0.00 0.00 4.79
3097 5044 1.618487 CATACTACTCCCTCCGTCCC 58.382 60.000 0.00 0.00 0.00 4.46
3098 5045 1.133575 CATACTACTCCCTCCGTCCCA 60.134 57.143 0.00 0.00 0.00 4.37
3099 5046 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3100 5047 0.338814 ACTACTCCCTCCGTCCCAAT 59.661 55.000 0.00 0.00 0.00 3.16
3101 5048 1.041437 CTACTCCCTCCGTCCCAATC 58.959 60.000 0.00 0.00 0.00 2.67
3102 5049 0.337082 TACTCCCTCCGTCCCAATCA 59.663 55.000 0.00 0.00 0.00 2.57
3103 5050 0.326618 ACTCCCTCCGTCCCAATCAT 60.327 55.000 0.00 0.00 0.00 2.45
3104 5051 1.062428 ACTCCCTCCGTCCCAATCATA 60.062 52.381 0.00 0.00 0.00 2.15
3105 5052 1.620819 CTCCCTCCGTCCCAATCATAG 59.379 57.143 0.00 0.00 0.00 2.23
3106 5053 1.062428 TCCCTCCGTCCCAATCATAGT 60.062 52.381 0.00 0.00 0.00 2.12
3107 5054 1.070758 CCCTCCGTCCCAATCATAGTG 59.929 57.143 0.00 0.00 0.00 2.74
3108 5055 1.541233 CCTCCGTCCCAATCATAGTGC 60.541 57.143 0.00 0.00 0.00 4.40
3109 5056 0.468226 TCCGTCCCAATCATAGTGCC 59.532 55.000 0.00 0.00 0.00 5.01
3110 5057 0.180171 CCGTCCCAATCATAGTGCCA 59.820 55.000 0.00 0.00 0.00 4.92
3111 5058 1.408127 CCGTCCCAATCATAGTGCCAA 60.408 52.381 0.00 0.00 0.00 4.52
3112 5059 2.364632 CGTCCCAATCATAGTGCCAAA 58.635 47.619 0.00 0.00 0.00 3.28
3113 5060 2.752354 CGTCCCAATCATAGTGCCAAAA 59.248 45.455 0.00 0.00 0.00 2.44
3114 5061 3.192422 CGTCCCAATCATAGTGCCAAAAA 59.808 43.478 0.00 0.00 0.00 1.94
3135 5082 6.799786 AAAAACGTCTTACATTTTGGAACG 57.200 33.333 0.00 0.00 0.00 3.95
3136 5083 4.477302 AACGTCTTACATTTTGGAACGG 57.523 40.909 0.00 0.00 0.00 4.44
3137 5084 3.731089 ACGTCTTACATTTTGGAACGGA 58.269 40.909 0.00 0.00 0.00 4.69
3138 5085 3.744426 ACGTCTTACATTTTGGAACGGAG 59.256 43.478 0.00 0.00 0.00 4.63
3139 5086 3.124636 CGTCTTACATTTTGGAACGGAGG 59.875 47.826 0.00 0.00 0.00 4.30
3140 5087 3.439129 GTCTTACATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
3141 5088 3.328343 TCTTACATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
3142 5089 2.200373 ACATTTTGGAACGGAGGGAG 57.800 50.000 0.00 0.00 0.00 4.30
3420 7124 2.308275 AGAGAGGCTGCCTTCTTCAATT 59.692 45.455 24.26 0.00 31.76 2.32
3445 7149 5.949354 CCCATTAATAGAAACCAAGGTCACA 59.051 40.000 0.00 0.00 0.00 3.58
3525 7241 7.915293 TGTGTATGGTATCTAAAAACTGGTG 57.085 36.000 0.00 0.00 0.00 4.17
3530 7246 9.116067 GTATGGTATCTAAAAACTGGTGCATAA 57.884 33.333 0.00 0.00 0.00 1.90
3583 7305 7.039644 ACTCCATACACTACTGCTATGTATTCC 60.040 40.741 0.00 0.00 37.42 3.01
3589 7312 7.338710 ACACTACTGCTATGTATTCCACATTT 58.661 34.615 0.00 0.00 46.01 2.32
3608 7331 7.537306 CCACATTTGTAGTACTGAAAATTTCCG 59.463 37.037 5.39 0.00 0.00 4.30
3610 7333 5.616488 TTGTAGTACTGAAAATTTCCGGC 57.384 39.130 5.39 0.00 0.00 6.13
3654 7377 9.541884 AGTCCCACATAACAAACCTAATTAATT 57.458 29.630 5.89 5.89 0.00 1.40
3655 7378 9.797556 GTCCCACATAACAAACCTAATTAATTC 57.202 33.333 3.39 0.00 0.00 2.17
3696 7421 1.453015 GGGCACACACCACACAGAA 60.453 57.895 0.00 0.00 0.00 3.02
3754 7480 2.926778 AGCATAGAGATGGGCTGAAC 57.073 50.000 0.00 0.00 34.83 3.18
3762 7488 1.899437 GATGGGCTGAACTGGACCGA 61.899 60.000 0.00 0.00 33.80 4.69
3780 7508 2.286872 CGAAGGAGCATGCTCTGATTT 58.713 47.619 38.84 28.18 33.13 2.17
3783 7511 4.421948 GAAGGAGCATGCTCTGATTTTTG 58.578 43.478 38.84 0.00 33.13 2.44
3784 7512 3.428532 AGGAGCATGCTCTGATTTTTGT 58.571 40.909 38.84 15.17 42.38 2.83
3795 7524 4.792068 TCTGATTTTTGTGTCCTCAAGGT 58.208 39.130 0.00 0.00 36.34 3.50
3827 7556 2.865492 CTGCAAGGGAAGAAGGCTC 58.135 57.895 0.00 0.00 0.00 4.70
3828 7557 1.003355 TGCAAGGGAAGAAGGCTCG 60.003 57.895 0.00 0.00 0.00 5.03
3831 7560 0.035458 CAAGGGAAGAAGGCTCGTGT 59.965 55.000 0.00 0.00 0.00 4.49
3849 7578 0.383860 GTAACGGTGTGTGCGCTTTC 60.384 55.000 9.73 0.00 0.00 2.62
3852 7581 2.542907 CGGTGTGTGCGCTTTCCTT 61.543 57.895 9.73 0.00 0.00 3.36
3853 7582 1.733526 GGTGTGTGCGCTTTCCTTT 59.266 52.632 9.73 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
576 598 3.988976 AGCACTTGAGAGAGCCAAATA 57.011 42.857 0.00 0.00 39.93 1.40
651 673 0.671163 TCGTGGTATTTGTGCCGACC 60.671 55.000 0.00 0.00 0.00 4.79
771 793 2.736826 GGAGGTGTCTAGCCAGCCC 61.737 68.421 0.00 0.00 33.34 5.19
2166 2404 1.876156 ACTGGAGCAAAAAGAAGAGCG 59.124 47.619 0.00 0.00 0.00 5.03
2172 2410 6.723298 TGGAAATTAACTGGAGCAAAAAGA 57.277 33.333 0.00 0.00 0.00 2.52
2183 2421 3.425404 CGCGGACAATGGAAATTAACTG 58.575 45.455 0.00 0.00 0.00 3.16
2184 2422 2.159435 GCGCGGACAATGGAAATTAACT 60.159 45.455 8.83 0.00 0.00 2.24
2192 2430 2.976840 GCAAAGCGCGGACAATGGA 61.977 57.895 8.83 0.00 0.00 3.41
2193 2431 2.504681 GCAAAGCGCGGACAATGG 60.505 61.111 8.83 0.00 0.00 3.16
2267 2517 1.956477 ACTTGCCTGCACTTTTACCAG 59.044 47.619 0.00 0.00 0.00 4.00
2279 2529 2.204237 GCAACCTTTTCAACTTGCCTG 58.796 47.619 0.00 0.00 34.21 4.85
2316 2566 1.133025 CTTGGGCTATCAAAAGGCACG 59.867 52.381 0.00 0.00 43.58 5.34
2317 2567 1.478105 CCTTGGGCTATCAAAAGGCAC 59.522 52.381 0.00 0.00 43.58 5.01
2363 2624 6.839124 ACATAGTTTTGGATCAAGCAATGA 57.161 33.333 0.00 0.00 43.67 2.57
2383 2644 6.822667 TGATGTCTTGCATTACAGAAACAT 57.177 33.333 7.59 0.24 38.06 2.71
2449 4121 4.476862 CGTCTATGTACATCCGATTCAGG 58.523 47.826 12.68 0.00 0.00 3.86
2493 4165 6.656632 TCAATATGGACTAGGACTGACATC 57.343 41.667 0.00 0.00 0.00 3.06
2496 4168 9.646427 GATATTTCAATATGGACTAGGACTGAC 57.354 37.037 0.00 0.00 31.96 3.51
2559 4236 3.356290 GGTCCAGTGGCATGTTCTTATT 58.644 45.455 3.51 0.00 0.00 1.40
2873 4709 6.266786 GGACAAAATAGTTTTCCCCTGAAGAA 59.733 38.462 5.91 0.00 0.00 2.52
2874 4710 5.773176 GGACAAAATAGTTTTCCCCTGAAGA 59.227 40.000 5.91 0.00 0.00 2.87
2875 4711 5.775195 AGGACAAAATAGTTTTCCCCTGAAG 59.225 40.000 10.98 0.00 33.09 3.02
2876 4712 5.711698 AGGACAAAATAGTTTTCCCCTGAA 58.288 37.500 10.98 0.00 33.09 3.02
2878 4714 5.047306 GGAAGGACAAAATAGTTTTCCCCTG 60.047 44.000 10.98 0.00 34.00 4.45
2879 4715 5.084519 GGAAGGACAAAATAGTTTTCCCCT 58.915 41.667 10.98 4.61 34.71 4.79
2880 4716 4.082408 CGGAAGGACAAAATAGTTTTCCCC 60.082 45.833 10.98 7.26 34.60 4.81
2883 4814 5.372547 AGCGGAAGGACAAAATAGTTTTC 57.627 39.130 0.00 0.00 0.00 2.29
2924 4871 8.783093 CACCAATTACAAGACTAAATCAACTGA 58.217 33.333 0.00 0.00 0.00 3.41
2933 4880 4.217550 GCTTGCCACCAATTACAAGACTAA 59.782 41.667 5.82 0.00 41.59 2.24
2935 4882 2.558359 GCTTGCCACCAATTACAAGACT 59.442 45.455 5.82 0.00 41.59 3.24
2959 4906 6.151049 AGACTGACTAACCCATATTACCCAT 58.849 40.000 0.00 0.00 0.00 4.00
2960 4907 5.535029 AGACTGACTAACCCATATTACCCA 58.465 41.667 0.00 0.00 0.00 4.51
2961 4908 5.601313 TGAGACTGACTAACCCATATTACCC 59.399 44.000 0.00 0.00 0.00 3.69
2962 4909 6.726490 TGAGACTGACTAACCCATATTACC 57.274 41.667 0.00 0.00 0.00 2.85
2965 4912 9.614792 GTTTTATGAGACTGACTAACCCATATT 57.385 33.333 0.00 0.00 0.00 1.28
2966 4913 8.211629 GGTTTTATGAGACTGACTAACCCATAT 58.788 37.037 0.00 0.00 30.32 1.78
2967 4914 7.181305 TGGTTTTATGAGACTGACTAACCCATA 59.819 37.037 0.00 0.00 33.61 2.74
2982 4929 4.806640 AAATGGTGCCTGGTTTTATGAG 57.193 40.909 0.00 0.00 0.00 2.90
2987 4934 7.123397 ACAAAAATAAAAATGGTGCCTGGTTTT 59.877 29.630 0.00 0.00 0.00 2.43
3006 4953 9.723601 ATTGCATGATTACCAGTAAACAAAAAT 57.276 25.926 0.00 3.61 32.81 1.82
3016 4963 3.131577 CCTTGCATTGCATGATTACCAGT 59.868 43.478 22.19 0.00 38.76 4.00
3019 4966 3.806625 ACCTTGCATTGCATGATTACC 57.193 42.857 22.19 0.00 38.76 2.85
3040 4987 9.513906 TGACTTGACAATCAAAATATCCAACTA 57.486 29.630 0.00 0.00 35.73 2.24
3046 4993 6.749118 GCCAGTGACTTGACAATCAAAATATC 59.251 38.462 0.00 0.00 35.73 1.63
3051 4998 3.316029 CAGCCAGTGACTTGACAATCAAA 59.684 43.478 0.00 0.00 35.73 2.69
3081 5028 0.338814 ATTGGGACGGAGGGAGTAGT 59.661 55.000 0.00 0.00 0.00 2.73
3083 5030 0.337082 TGATTGGGACGGAGGGAGTA 59.663 55.000 0.00 0.00 0.00 2.59
3084 5031 0.326618 ATGATTGGGACGGAGGGAGT 60.327 55.000 0.00 0.00 0.00 3.85
3085 5032 1.620819 CTATGATTGGGACGGAGGGAG 59.379 57.143 0.00 0.00 0.00 4.30
3086 5033 1.062428 ACTATGATTGGGACGGAGGGA 60.062 52.381 0.00 0.00 0.00 4.20
3087 5034 1.070758 CACTATGATTGGGACGGAGGG 59.929 57.143 0.00 0.00 0.00 4.30
3088 5035 1.541233 GCACTATGATTGGGACGGAGG 60.541 57.143 0.00 0.00 0.00 4.30
3090 5037 0.468226 GGCACTATGATTGGGACGGA 59.532 55.000 0.00 0.00 0.00 4.69
3091 5038 0.180171 TGGCACTATGATTGGGACGG 59.820 55.000 0.00 0.00 0.00 4.79
3092 5039 2.036958 TTGGCACTATGATTGGGACG 57.963 50.000 0.00 0.00 0.00 4.79
3093 5040 4.799564 TTTTTGGCACTATGATTGGGAC 57.200 40.909 0.00 0.00 0.00 4.46
3112 5059 5.744819 CCGTTCCAAAATGTAAGACGTTTTT 59.255 36.000 6.77 0.00 42.72 1.94
3113 5060 5.066246 TCCGTTCCAAAATGTAAGACGTTTT 59.934 36.000 4.14 4.14 45.25 2.43
3114 5061 4.575645 TCCGTTCCAAAATGTAAGACGTTT 59.424 37.500 0.00 0.00 38.84 3.60
3115 5062 4.128643 TCCGTTCCAAAATGTAAGACGTT 58.871 39.130 0.00 0.00 0.00 3.99
3116 5063 3.731089 TCCGTTCCAAAATGTAAGACGT 58.269 40.909 0.00 0.00 0.00 4.34
3117 5064 3.124636 CCTCCGTTCCAAAATGTAAGACG 59.875 47.826 0.00 0.00 0.00 4.18
3118 5065 3.439129 CCCTCCGTTCCAAAATGTAAGAC 59.561 47.826 0.00 0.00 0.00 3.01
3119 5066 3.328343 TCCCTCCGTTCCAAAATGTAAGA 59.672 43.478 0.00 0.00 0.00 2.10
3120 5067 3.681593 TCCCTCCGTTCCAAAATGTAAG 58.318 45.455 0.00 0.00 0.00 2.34
3121 5068 3.073356 ACTCCCTCCGTTCCAAAATGTAA 59.927 43.478 0.00 0.00 0.00 2.41
3122 5069 2.640826 ACTCCCTCCGTTCCAAAATGTA 59.359 45.455 0.00 0.00 0.00 2.29
3123 5070 1.423921 ACTCCCTCCGTTCCAAAATGT 59.576 47.619 0.00 0.00 0.00 2.71
3124 5071 2.200373 ACTCCCTCCGTTCCAAAATG 57.800 50.000 0.00 0.00 0.00 2.32
3125 5072 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
3126 5073 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
3127 5074 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
3128 5075 2.314071 TTCTACTCCCTCCGTTCCAA 57.686 50.000 0.00 0.00 0.00 3.53
3129 5076 2.176889 CTTTCTACTCCCTCCGTTCCA 58.823 52.381 0.00 0.00 0.00 3.53
3130 5077 1.134759 GCTTTCTACTCCCTCCGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
3131 5078 1.549170 TGCTTTCTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
3132 5079 1.275573 GTGCTTTCTACTCCCTCCGTT 59.724 52.381 0.00 0.00 0.00 4.44
3133 5080 0.896226 GTGCTTTCTACTCCCTCCGT 59.104 55.000 0.00 0.00 0.00 4.69
3134 5081 1.187087 AGTGCTTTCTACTCCCTCCG 58.813 55.000 0.00 0.00 0.00 4.63
3135 5082 2.567615 TGAAGTGCTTTCTACTCCCTCC 59.432 50.000 3.75 0.00 36.71 4.30
3136 5083 3.963428 TGAAGTGCTTTCTACTCCCTC 57.037 47.619 3.75 0.00 36.71 4.30
3137 5084 4.706842 TTTGAAGTGCTTTCTACTCCCT 57.293 40.909 3.75 0.00 36.71 4.20
3138 5085 5.966742 AATTTGAAGTGCTTTCTACTCCC 57.033 39.130 3.75 0.00 36.71 4.30
3139 5086 8.568794 ACTAAAATTTGAAGTGCTTTCTACTCC 58.431 33.333 5.82 0.00 36.71 3.85
3140 5087 9.387123 CACTAAAATTTGAAGTGCTTTCTACTC 57.613 33.333 16.64 0.00 36.71 2.59
3167 5114 2.240493 AGGTTTGTCTCGACTGTTGG 57.760 50.000 0.00 0.00 0.00 3.77
3171 5118 7.811236 TGTATTTTACTAGGTTTGTCTCGACTG 59.189 37.037 0.00 0.00 0.00 3.51
3219 5282 7.112779 ACTGGGAAAAGGAGTATATTGTCAAG 58.887 38.462 0.00 0.00 0.00 3.02
3298 5368 8.726988 CACCCCGGTTGTATGATATATTTTTAG 58.273 37.037 0.00 0.00 0.00 1.85
3307 5377 3.913509 TCTACACCCCGGTTGTATGATA 58.086 45.455 12.33 0.00 0.00 2.15
3311 5381 3.645434 TGTATCTACACCCCGGTTGTAT 58.355 45.455 12.33 4.37 0.00 2.29
3396 7100 2.906389 TGAAGAAGGCAGCCTCTCTTTA 59.094 45.455 26.63 22.68 34.06 1.85
3420 7124 6.184789 GTGACCTTGGTTTCTATTAATGGGA 58.815 40.000 0.00 0.00 0.00 4.37
3504 7212 6.995511 TGCACCAGTTTTTAGATACCATAC 57.004 37.500 0.00 0.00 0.00 2.39
3583 7305 7.537306 CCGGAAATTTTCAGTACTACAAATGTG 59.463 37.037 11.09 0.00 0.00 3.21
3589 7312 3.680937 CGCCGGAAATTTTCAGTACTACA 59.319 43.478 5.05 0.00 0.00 2.74
3604 7327 0.676466 AAATGCATCTGTCGCCGGAA 60.676 50.000 5.05 0.00 0.00 4.30
3608 7331 5.292101 GGACTATATAAATGCATCTGTCGCC 59.708 44.000 0.00 0.00 0.00 5.54
3610 7333 6.311445 GTGGGACTATATAAATGCATCTGTCG 59.689 42.308 0.00 0.00 0.00 4.35
3653 7376 8.635328 CCAAGCTTTTACTACTTAAAAAGGGAA 58.365 33.333 0.00 0.00 41.10 3.97
3654 7377 7.231925 CCCAAGCTTTTACTACTTAAAAAGGGA 59.768 37.037 0.00 0.00 41.10 4.20
3655 7378 7.375834 CCCAAGCTTTTACTACTTAAAAAGGG 58.624 38.462 0.00 0.00 41.10 3.95
3660 7385 5.828859 TGTGCCCAAGCTTTTACTACTTAAA 59.171 36.000 0.00 0.00 40.80 1.52
3668 7393 1.269569 GGTGTGTGCCCAAGCTTTTAC 60.270 52.381 0.00 0.00 40.80 2.01
3670 7395 0.975040 TGGTGTGTGCCCAAGCTTTT 60.975 50.000 0.00 0.00 40.80 2.27
3675 7400 1.727511 CTGTGTGGTGTGTGCCCAAG 61.728 60.000 0.00 0.00 32.72 3.61
3696 7421 5.754782 TCATTTTGGATGCAGTACCTATGT 58.245 37.500 0.00 0.00 0.00 2.29
3748 7474 0.390472 CTCCTTCGGTCCAGTTCAGC 60.390 60.000 0.00 0.00 0.00 4.26
3754 7480 1.817099 GCATGCTCCTTCGGTCCAG 60.817 63.158 11.37 0.00 0.00 3.86
3762 7488 3.830755 ACAAAAATCAGAGCATGCTCCTT 59.169 39.130 37.79 26.80 43.70 3.36
3767 7493 3.057033 AGGACACAAAAATCAGAGCATGC 60.057 43.478 10.51 10.51 0.00 4.06
3768 7494 4.216902 TGAGGACACAAAAATCAGAGCATG 59.783 41.667 0.00 0.00 0.00 4.06
3777 7505 6.365520 AGTTCTACCTTGAGGACACAAAAAT 58.634 36.000 3.59 0.00 38.94 1.82
3780 7508 5.367945 AAGTTCTACCTTGAGGACACAAA 57.632 39.130 3.59 0.00 38.94 2.83
3783 7511 5.216614 AGAAAGTTCTACCTTGAGGACAC 57.783 43.478 3.59 0.00 38.94 3.67
3784 7512 4.283722 GGAGAAAGTTCTACCTTGAGGACA 59.716 45.833 3.59 0.00 37.73 4.02
3795 7524 2.305927 CCTTGCAGGGGAGAAAGTTCTA 59.694 50.000 7.05 0.00 37.73 2.10
3820 7549 0.319297 ACACCGTTACACGAGCCTTC 60.319 55.000 0.00 0.00 46.05 3.46
3822 7551 1.006571 CACACCGTTACACGAGCCT 60.007 57.895 0.00 0.00 46.05 4.58
3824 7553 1.850640 CACACACCGTTACACGAGC 59.149 57.895 0.00 0.00 46.05 5.03
3825 7554 1.850640 GCACACACCGTTACACGAG 59.149 57.895 0.00 0.00 46.05 4.18
3826 7555 1.945169 CGCACACACCGTTACACGA 60.945 57.895 0.00 0.00 46.05 4.35
3827 7556 2.542409 CGCACACACCGTTACACG 59.458 61.111 0.00 0.00 42.11 4.49
3828 7557 1.768112 AAGCGCACACACCGTTACAC 61.768 55.000 11.47 0.00 0.00 2.90
3831 7560 1.500512 GGAAAGCGCACACACCGTTA 61.501 55.000 11.47 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.