Multiple sequence alignment - TraesCS4A01G199400

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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 TraesCS4A01G199400 chr4A 100.000 4267 0 0 1 4267 486649440 486645174 0.000000e+00 7880
1 TraesCS4A01G199400 chr4D 96.148 3323 109 7 948 4267 94253274 94256580 0.000000e+00 5409
2 TraesCS4A01G199400 chr4B 95.529 2729 97 11 948 3674 132847703 132850408 0.000000e+00 4340
3 TraesCS4A01G199400 chr4B 89.624 559 25 10 3600 4156 132850482 132851009 0.000000e+00 680
4 TraesCS4A01G199400 chr4B 92.347 196 15 0 4072 4267 132851009 132851204 3.250000e-71 279
5 TraesCS4A01G199400 chr4B 93.333 75 5 0 3600 3674 132850408 132850482 1.250000e-20 111
6 TraesCS4A01G199400 chr7D 95.082 671 29 4 271 939 114467605 114468273 0.000000e+00 1053
7 TraesCS4A01G199400 chr7D 94.337 671 36 2 271 939 351641926 351641256 0.000000e+00 1027
8 TraesCS4A01G199400 chr7D 97.849 279 6 0 1 279 114467366 114467644 2.310000e-132 483
9 TraesCS4A01G199400 chr7D 97.491 279 7 0 1 279 151540164 151540442 1.070000e-130 477
10 TraesCS4A01G199400 chr7D 97.491 279 7 0 1 279 603599249 603598971 1.070000e-130 477
11 TraesCS4A01G199400 chr7D 97.473 277 7 0 3 279 351642163 351641887 1.390000e-129 473
12 TraesCS4A01G199400 chr6D 94.337 671 35 3 271 939 464214433 464213764 0.000000e+00 1026
13 TraesCS4A01G199400 chr6D 97.849 279 5 1 1 279 423491435 423491712 8.300000e-132 481
14 TraesCS4A01G199400 chr6D 97.491 279 7 0 1 279 379093363 379093085 1.070000e-130 477
15 TraesCS4A01G199400 chr3D 94.345 672 32 6 271 939 214958996 214959664 0.000000e+00 1026
16 TraesCS4A01G199400 chr3D 94.205 673 34 5 271 939 191558319 191557648 0.000000e+00 1022
17 TraesCS4A01G199400 chr3D 97.849 279 6 0 1 279 425153704 425153426 2.310000e-132 483
18 TraesCS4A01G199400 chr3D 97.491 279 7 0 1 279 65599421 65599699 1.070000e-130 477
19 TraesCS4A01G199400 chr3D 97.491 279 7 0 1 279 460502742 460502464 1.070000e-130 477
20 TraesCS4A01G199400 chr3A 94.337 671 35 3 271 939 660861518 660860849 0.000000e+00 1026
21 TraesCS4A01G199400 chr2D 94.311 668 35 2 271 937 70391213 70391878 0.000000e+00 1020
22 TraesCS4A01G199400 chr2D 93.899 672 37 4 271 939 484919816 484919146 0.000000e+00 1011
23 TraesCS4A01G199400 chr2D 93.899 672 35 5 271 939 486304022 486304690 0.000000e+00 1009


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 TraesCS4A01G199400 chr4A 486645174 486649440 4266 True 7880.0 7880 100.00000 1 4267 1 chr4A.!!$R1 4266
1 TraesCS4A01G199400 chr4D 94253274 94256580 3306 False 5409.0 5409 96.14800 948 4267 1 chr4D.!!$F1 3319
2 TraesCS4A01G199400 chr4B 132847703 132851204 3501 False 1352.5 4340 92.70825 948 4267 4 chr4B.!!$F1 3319
3 TraesCS4A01G199400 chr7D 114467366 114468273 907 False 768.0 1053 96.46550 1 939 2 chr7D.!!$F2 938
4 TraesCS4A01G199400 chr7D 351641256 351642163 907 True 750.0 1027 95.90500 3 939 2 chr7D.!!$R2 936
5 TraesCS4A01G199400 chr6D 464213764 464214433 669 True 1026.0 1026 94.33700 271 939 1 chr6D.!!$R2 668
6 TraesCS4A01G199400 chr3D 214958996 214959664 668 False 1026.0 1026 94.34500 271 939 1 chr3D.!!$F2 668
7 TraesCS4A01G199400 chr3D 191557648 191558319 671 True 1022.0 1022 94.20500 271 939 1 chr3D.!!$R1 668
8 TraesCS4A01G199400 chr3A 660860849 660861518 669 True 1026.0 1026 94.33700 271 939 1 chr3A.!!$R1 668
9 TraesCS4A01G199400 chr2D 70391213 70391878 665 False 1020.0 1020 94.31100 271 937 1 chr2D.!!$F1 666
10 TraesCS4A01G199400 chr2D 484919146 484919816 670 True 1011.0 1011 93.89900 271 939 1 chr2D.!!$R1 668
11 TraesCS4A01G199400 chr2D 486304022 486304690 668 False 1009.0 1009 93.89900 271 939 1 chr2D.!!$F2 668

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
249 250 0.109597 GCAGTGTACATGGCAACTGC 60.110 55.0 24.01 24.01 42.64 4.40 F
267 268 0.453390 GCCCTAGTGTGATTGCAAGC 59.547 55.0 7.99 7.99 0.00 4.01 F
440 444 0.608130 TGTCCTAGCGTGCTTGTGAT 59.392 50.0 0.00 0.00 0.00 3.06 F
646 654 1.059098 TGACCTGAGATGGCAACTGT 58.941 50.0 0.51 0.00 37.61 3.55 F
2491 2505 0.108186 TTAGTGCATGCCGAGTCCAG 60.108 55.0 16.68 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1425 0.252927 AGGGGTCAGAGGGAAAGAGG 60.253 60.000 0.0 0.0 0.00 3.69 R
1894 1908 0.950116 GCATCTTGCCATACAGCTCC 59.050 55.000 0.0 0.0 37.42 4.70 R
2392 2406 0.321564 CCTCATCAAGACAACCGGCA 60.322 55.000 0.0 0.0 0.00 5.69 R
2539 2553 1.003355 CCCACTGTTGGTCGCATCT 60.003 57.895 0.0 0.0 42.10 2.90 R
4092 4262 0.449388 GCTTGAATCACTTCCAGGCG 59.551 55.000 0.0 0.0 0.00 5.52 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
62 63 1.040646 GTGGTGTGTGAGAGAGGTCA 58.959 55.000 0.00 0.00 0.00 4.02
73 74 1.203237 AGAGAGGTCACCCACACATCT 60.203 52.381 0.00 0.00 37.60 2.90
242 243 1.685302 GCGTTTTGCAGTGTACATGG 58.315 50.000 0.00 0.00 45.45 3.66
243 244 1.685302 CGTTTTGCAGTGTACATGGC 58.315 50.000 13.09 13.09 0.00 4.40
244 245 1.001924 CGTTTTGCAGTGTACATGGCA 60.002 47.619 17.30 17.30 0.00 4.92
245 246 2.542618 CGTTTTGCAGTGTACATGGCAA 60.543 45.455 24.54 24.54 43.79 4.52
246 247 2.791383 TTTGCAGTGTACATGGCAAC 57.209 45.000 26.78 4.07 44.99 4.17
247 248 1.979855 TTGCAGTGTACATGGCAACT 58.020 45.000 24.54 4.62 40.94 3.16
248 249 1.237533 TGCAGTGTACATGGCAACTG 58.762 50.000 18.49 15.65 32.54 3.16
249 250 0.109597 GCAGTGTACATGGCAACTGC 60.110 55.000 24.01 24.01 42.64 4.40
260 261 3.558674 GCAACTGCCCTAGTGTGAT 57.441 52.632 0.00 0.00 40.26 3.06
261 262 1.826385 GCAACTGCCCTAGTGTGATT 58.174 50.000 0.00 0.00 40.26 2.57
262 263 1.470098 GCAACTGCCCTAGTGTGATTG 59.530 52.381 0.00 0.00 40.26 2.67
263 264 1.470098 CAACTGCCCTAGTGTGATTGC 59.530 52.381 0.00 0.00 40.26 3.56
264 265 0.692476 ACTGCCCTAGTGTGATTGCA 59.308 50.000 0.00 0.00 38.49 4.08
265 266 1.073763 ACTGCCCTAGTGTGATTGCAA 59.926 47.619 0.00 0.00 38.49 4.08
266 267 1.741706 CTGCCCTAGTGTGATTGCAAG 59.258 52.381 4.94 0.00 0.00 4.01
267 268 0.453390 GCCCTAGTGTGATTGCAAGC 59.547 55.000 7.99 7.99 0.00 4.01
268 269 1.825090 CCCTAGTGTGATTGCAAGCA 58.175 50.000 14.49 14.49 0.00 3.91
269 270 1.741706 CCCTAGTGTGATTGCAAGCAG 59.258 52.381 19.34 5.73 0.00 4.24
440 444 0.608130 TGTCCTAGCGTGCTTGTGAT 59.392 50.000 0.00 0.00 0.00 3.06
465 469 4.042187 ACATGGCAACTCTCTCTTTTACCT 59.958 41.667 0.00 0.00 37.61 3.08
558 565 7.359514 GCAACTCCTAAAGTTTTGAAATCATGC 60.360 37.037 0.00 0.00 46.26 4.06
577 584 1.065854 GCCAACTGCAGTAGACCAGAT 60.066 52.381 22.01 0.00 40.77 2.90
646 654 1.059098 TGACCTGAGATGGCAACTGT 58.941 50.000 0.51 0.00 37.61 3.55
691 699 3.799755 GTCCGACATGGCAACCGC 61.800 66.667 0.00 0.00 37.80 5.68
693 701 3.361158 CCGACATGGCAACCGCAA 61.361 61.111 0.00 0.00 41.24 4.85
812 823 2.270205 CGAGGTGCAAGGCCTGAT 59.730 61.111 5.69 0.00 36.29 2.90
870 881 1.904865 ACGCGTGTAAGAGGGACCA 60.905 57.895 12.93 0.00 0.00 4.02
875 887 1.616187 CGTGTAAGAGGGACCAGGAGA 60.616 57.143 0.00 0.00 0.00 3.71
908 921 9.461312 AGAAACATATGGATGCTAGTTGTTTTA 57.539 29.630 7.80 0.00 36.33 1.52
939 952 2.665603 GTGTGGGCTGGTCCTCTC 59.334 66.667 0.00 0.00 34.39 3.20
940 953 1.915769 GTGTGGGCTGGTCCTCTCT 60.916 63.158 0.00 0.00 34.39 3.10
941 954 1.915266 TGTGGGCTGGTCCTCTCTG 60.915 63.158 0.00 0.00 34.39 3.35
942 955 3.005539 TGGGCTGGTCCTCTCTGC 61.006 66.667 0.00 0.00 34.39 4.26
943 956 4.154347 GGGCTGGTCCTCTCTGCG 62.154 72.222 0.00 0.00 34.39 5.18
944 957 3.386237 GGCTGGTCCTCTCTGCGT 61.386 66.667 0.00 0.00 0.00 5.24
945 958 2.659610 GCTGGTCCTCTCTGCGTT 59.340 61.111 0.00 0.00 0.00 4.84
946 959 1.446966 GCTGGTCCTCTCTGCGTTC 60.447 63.158 0.00 0.00 0.00 3.95
1033 1047 3.730761 GCTCCTGGCTGCGTTGTG 61.731 66.667 0.00 0.00 38.06 3.33
1053 1067 2.124983 CACCACCGGCATCTCAGG 60.125 66.667 0.00 0.00 36.01 3.86
1161 1175 2.821366 GAGCACGCCCATCCACAG 60.821 66.667 0.00 0.00 0.00 3.66
1426 1440 1.219393 CGGCCTCTTTCCCTCTGAC 59.781 63.158 0.00 0.00 0.00 3.51
1460 1474 1.204704 CCGCTCTTCTCCACATGTACA 59.795 52.381 0.00 0.00 0.00 2.90
1534 1548 1.295792 CCAACCCCGTCATTATCACG 58.704 55.000 0.00 0.00 36.99 4.35
1583 1597 2.822707 TCTAGTCTACCCCTCGCTTT 57.177 50.000 0.00 0.00 0.00 3.51
1834 1848 4.694760 TGATACCATGGAGAAGGATGTG 57.305 45.455 21.47 0.00 0.00 3.21
1978 1992 1.506309 CTGTGTTACTGGCTTGCGCA 61.506 55.000 5.66 5.66 38.10 6.09
2005 2019 2.901192 TGGGACGATACAGACTGGAAAA 59.099 45.455 7.51 0.00 0.00 2.29
2132 2146 2.959516 AGGCTTTCGGCAAAATTAAGC 58.040 42.857 0.00 0.00 44.01 3.09
2146 2160 6.309737 GCAAAATTAAGCAGAAGAATGTCCTG 59.690 38.462 0.00 0.00 0.00 3.86
2392 2406 1.299976 GGTGGATCTTCTTGGCCGT 59.700 57.895 0.00 0.00 0.00 5.68
2482 2496 1.939255 GGAGCTCTTCTTAGTGCATGC 59.061 52.381 14.64 11.82 42.04 4.06
2491 2505 0.108186 TTAGTGCATGCCGAGTCCAG 60.108 55.000 16.68 0.00 0.00 3.86
2539 2553 6.612247 TCTGCGAAAAGATTGTTTGAGTTA 57.388 33.333 0.00 0.00 0.00 2.24
2545 2559 6.247165 CGAAAAGATTGTTTGAGTTAGATGCG 59.753 38.462 0.00 0.00 0.00 4.73
2604 2618 0.807496 GCAGAAGCTGGAATGTGGAC 59.193 55.000 0.00 0.00 37.91 4.02
2750 2764 7.665690 TCAGCACAAGGAGATCTATTCTTATC 58.334 38.462 0.00 0.00 33.74 1.75
2767 2781 2.503895 ATCTGGGGAAACTGCTTGAG 57.496 50.000 0.00 0.00 0.00 3.02
2779 2793 2.813754 ACTGCTTGAGATAGCGCAAAAA 59.186 40.909 11.47 0.00 44.18 1.94
2872 2886 2.057137 TCCACAGTGAAAAGCTTGCT 57.943 45.000 0.00 0.00 0.00 3.91
3028 3042 6.624423 AGATTTACAGCGCTTTCATCATTTT 58.376 32.000 7.50 0.00 0.00 1.82
3123 3137 0.038067 CGTTGTCCGTCATACCACCA 60.038 55.000 0.00 0.00 0.00 4.17
3138 3152 9.502091 GTCATACCACCATTGTATTATGTACAT 57.498 33.333 13.93 13.93 0.00 2.29
3140 3154 6.633500 ACCACCATTGTATTATGTACATGC 57.367 37.500 18.81 6.61 0.00 4.06
3142 3156 5.534278 CCACCATTGTATTATGTACATGCCA 59.466 40.000 18.81 6.55 0.00 4.92
3195 3211 6.625362 TCATCTCGATTAGGCTAATGACATC 58.375 40.000 23.78 9.35 0.00 3.06
3212 3228 2.563013 ATCGCCTTGCTGCCCTGAAT 62.563 55.000 0.00 0.00 0.00 2.57
3405 3421 2.026641 CATGTCCCCAGCAAGGTATTG 58.973 52.381 0.00 0.00 39.57 1.90
3524 3541 3.435026 GGGAGCCAAGGATATAAAGCACA 60.435 47.826 0.00 0.00 0.00 4.57
3538 3555 0.324614 AGCACATGATGTTCACGGGA 59.675 50.000 0.00 0.00 0.00 5.14
3641 3806 2.485814 GGTCAGTGATGCTTGAGGAAAC 59.514 50.000 0.00 0.00 0.00 2.78
3645 3810 4.276678 TCAGTGATGCTTGAGGAAACTTTG 59.723 41.667 0.00 0.00 44.43 2.77
3646 3811 4.276678 CAGTGATGCTTGAGGAAACTTTGA 59.723 41.667 0.00 0.00 44.43 2.69
3647 3812 4.518211 AGTGATGCTTGAGGAAACTTTGAG 59.482 41.667 0.00 0.00 44.43 3.02
3670 3838 3.728845 AGTACTGTCAAACATTCAGCGT 58.271 40.909 0.00 0.00 33.12 5.07
3684 3852 1.758280 TCAGCGTTTATGGGTCGGTAT 59.242 47.619 0.00 0.00 34.09 2.73
3705 3873 0.248539 GTGTACAGGAGACGATCGCC 60.249 60.000 16.60 8.70 36.52 5.54
3724 3892 2.981859 CGTAGGGGCATGGTATATCC 57.018 55.000 0.00 0.00 0.00 2.59
3737 3905 0.313987 TATATCCTGTGGCAGCGACG 59.686 55.000 2.81 0.00 0.00 5.12
3751 3919 1.004595 GCGACGGGAGGTTGTTAATC 58.995 55.000 0.00 0.00 32.16 1.75
3757 3925 2.481449 CGGGAGGTTGTTAATCGAGGAG 60.481 54.545 0.00 0.00 0.00 3.69
3802 3970 4.558178 TGTGTTTGCAATTCAGGCTATTG 58.442 39.130 0.00 5.77 36.34 1.90
3827 3995 3.120199 GCGAACTATGCAAAAGCTCTGAA 60.120 43.478 0.00 0.00 0.00 3.02
3850 4018 4.287067 ACAGTTCACAACCAGTCCTGATAT 59.713 41.667 0.00 0.00 0.00 1.63
3874 4043 3.122480 TGAGGGAAGCCTCATGGAATTA 58.878 45.455 0.00 0.00 41.27 1.40
3904 4073 4.519350 ACTGAATGTGGATGCATCATCATC 59.481 41.667 27.25 20.04 42.13 2.92
3905 4074 4.465886 TGAATGTGGATGCATCATCATCA 58.534 39.130 27.25 21.72 43.44 3.07
3906 4075 5.076873 TGAATGTGGATGCATCATCATCAT 58.923 37.500 27.25 18.31 43.44 2.45
3907 4076 6.242396 TGAATGTGGATGCATCATCATCATA 58.758 36.000 27.25 14.17 43.44 2.15
3908 4077 6.150474 TGAATGTGGATGCATCATCATCATAC 59.850 38.462 27.25 18.73 43.44 2.39
3909 4078 5.237236 TGTGGATGCATCATCATCATACT 57.763 39.130 27.25 0.00 43.44 2.12
3910 4079 5.627135 TGTGGATGCATCATCATCATACTT 58.373 37.500 27.25 0.00 43.44 2.24
4022 4191 4.509737 GGTGGAGGCGACCGCTAC 62.510 72.222 14.25 8.29 41.60 3.58
4092 4262 1.268794 CCATCATCGTCGAGTCTGACC 60.269 57.143 3.76 0.00 35.40 4.02
4118 4372 3.248266 GGAAGTGATTCAAGCATGCAAC 58.752 45.455 21.98 6.14 0.00 4.17
4139 4393 3.316868 ACGGTTTGTTTGGTCAAGGTATG 59.683 43.478 0.00 0.00 0.00 2.39
4140 4394 3.305064 CGGTTTGTTTGGTCAAGGTATGG 60.305 47.826 0.00 0.00 0.00 2.74
4148 4402 4.927267 TGGTCAAGGTATGGAAGTGATT 57.073 40.909 0.00 0.00 0.00 2.57
4208 4462 6.362248 TGAACCCCTTAGCTATGTTTTATCC 58.638 40.000 0.00 0.00 0.00 2.59
4227 4481 7.780008 TTATCCAATGATAAACGTGTACTGG 57.220 36.000 0.00 0.00 39.83 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.189231 GTCCTACGTGGCATACAAAATCT 58.811 43.478 0.00 0.00 35.26 2.40
62 63 3.219281 GTGGTAAAACAGATGTGTGGGT 58.781 45.455 0.00 0.00 36.84 4.51
73 74 0.108963 CCCCTCCGTGTGGTAAAACA 59.891 55.000 0.00 0.00 36.30 2.83
119 120 2.026729 TGACTGAAAACTGGTGTGTGGA 60.027 45.455 0.00 0.00 0.00 4.02
189 190 0.545309 CTTGGGTGTGGGAGAGGAGA 60.545 60.000 0.00 0.00 0.00 3.71
242 243 1.470098 CAATCACACTAGGGCAGTTGC 59.530 52.381 0.00 0.00 34.26 4.17
243 244 1.470098 GCAATCACACTAGGGCAGTTG 59.530 52.381 0.00 0.00 34.26 3.16
244 245 1.073763 TGCAATCACACTAGGGCAGTT 59.926 47.619 0.00 0.00 34.26 3.16
245 246 0.692476 TGCAATCACACTAGGGCAGT 59.308 50.000 0.00 0.00 38.32 4.40
246 247 1.741706 CTTGCAATCACACTAGGGCAG 59.258 52.381 0.00 0.00 32.31 4.85
247 248 1.825090 CTTGCAATCACACTAGGGCA 58.175 50.000 0.00 0.00 0.00 5.36
248 249 0.453390 GCTTGCAATCACACTAGGGC 59.547 55.000 0.00 0.00 0.00 5.19
249 250 1.741706 CTGCTTGCAATCACACTAGGG 59.258 52.381 0.00 0.00 0.00 3.53
250 251 2.703416 TCTGCTTGCAATCACACTAGG 58.297 47.619 0.00 0.00 0.00 3.02
251 252 3.064958 CCATCTGCTTGCAATCACACTAG 59.935 47.826 0.00 0.00 0.00 2.57
252 253 3.011818 CCATCTGCTTGCAATCACACTA 58.988 45.455 0.00 0.00 0.00 2.74
253 254 1.816835 CCATCTGCTTGCAATCACACT 59.183 47.619 0.00 0.00 0.00 3.55
254 255 1.734707 GCCATCTGCTTGCAATCACAC 60.735 52.381 0.00 0.00 36.87 3.82
255 256 0.528924 GCCATCTGCTTGCAATCACA 59.471 50.000 0.00 0.00 36.87 3.58
256 257 0.528924 TGCCATCTGCTTGCAATCAC 59.471 50.000 0.00 0.00 42.00 3.06
257 258 1.067425 GTTGCCATCTGCTTGCAATCA 60.067 47.619 0.00 0.00 45.66 2.57
258 259 1.203994 AGTTGCCATCTGCTTGCAATC 59.796 47.619 0.00 0.00 45.66 2.67
259 260 1.067142 CAGTTGCCATCTGCTTGCAAT 60.067 47.619 0.00 0.00 45.66 3.56
260 261 0.315886 CAGTTGCCATCTGCTTGCAA 59.684 50.000 0.00 0.00 42.28 4.08
261 262 1.961378 CAGTTGCCATCTGCTTGCA 59.039 52.632 0.00 0.00 42.00 4.08
262 263 4.883026 CAGTTGCCATCTGCTTGC 57.117 55.556 0.00 0.00 42.00 4.01
333 336 4.804868 TGCAAAACATATGGCAACTGAT 57.195 36.364 7.80 0.00 32.54 2.90
423 427 0.894835 TGATCACAAGCACGCTAGGA 59.105 50.000 0.00 0.00 0.00 2.94
440 444 3.777106 AAAGAGAGAGTTGCCATGTGA 57.223 42.857 0.00 0.00 0.00 3.58
558 565 2.234661 TGATCTGGTCTACTGCAGTTGG 59.765 50.000 27.06 17.96 0.00 3.77
577 584 1.761449 ACAGTTGTTGCCATGTGTGA 58.239 45.000 0.00 0.00 0.00 3.58
618 626 3.077359 CCATCTCAGGTCAAAGTTCCAC 58.923 50.000 0.00 0.00 0.00 4.02
646 654 3.004629 CAGTTGCCATGTTTGCTCAACTA 59.995 43.478 5.73 0.00 40.24 2.24
691 699 3.728864 GCAGTTACCATGTCGCTGAATTG 60.729 47.826 7.64 0.00 0.00 2.32
693 701 2.009774 GCAGTTACCATGTCGCTGAAT 58.990 47.619 7.64 0.00 0.00 2.57
707 715 5.049954 GTCCATGTTCGTTTAAGTGCAGTTA 60.050 40.000 10.00 10.00 0.00 2.24
801 812 1.819632 CCGGTACATCAGGCCTTGC 60.820 63.158 0.00 0.00 0.00 4.01
812 823 4.418328 GCCCACATGCCCGGTACA 62.418 66.667 0.00 0.00 0.00 2.90
822 833 2.806244 GCGAAATAGATAACGCCCACAT 59.194 45.455 0.00 0.00 44.27 3.21
885 898 7.068226 GGGTAAAACAACTAGCATCCATATGTT 59.932 37.037 1.24 0.00 35.38 2.71
886 899 6.546034 GGGTAAAACAACTAGCATCCATATGT 59.454 38.462 1.24 0.00 35.38 2.29
890 903 4.705023 GTGGGTAAAACAACTAGCATCCAT 59.295 41.667 0.00 0.00 0.00 3.41
894 907 4.277423 GTGTGTGGGTAAAACAACTAGCAT 59.723 41.667 0.00 0.00 0.00 3.79
895 908 3.628487 GTGTGTGGGTAAAACAACTAGCA 59.372 43.478 0.00 0.00 0.00 3.49
939 952 3.359654 GTGTGTTTGGTTTAGAACGCAG 58.640 45.455 3.06 0.00 44.16 5.18
940 953 2.097791 GGTGTGTTTGGTTTAGAACGCA 59.902 45.455 0.00 0.00 42.14 5.24
941 954 2.542205 GGGTGTGTTTGGTTTAGAACGC 60.542 50.000 0.00 0.00 36.93 4.84
942 955 2.946990 AGGGTGTGTTTGGTTTAGAACG 59.053 45.455 0.00 0.00 0.00 3.95
943 956 4.024641 CGTAGGGTGTGTTTGGTTTAGAAC 60.025 45.833 0.00 0.00 0.00 3.01
944 957 4.128643 CGTAGGGTGTGTTTGGTTTAGAA 58.871 43.478 0.00 0.00 0.00 2.10
945 958 3.134442 ACGTAGGGTGTGTTTGGTTTAGA 59.866 43.478 0.00 0.00 0.00 2.10
946 959 3.469739 ACGTAGGGTGTGTTTGGTTTAG 58.530 45.455 0.00 0.00 0.00 1.85
1053 1067 2.042831 ACTCTTGCTGCCGCCATTC 61.043 57.895 0.00 0.00 34.43 2.67
1121 1135 0.538287 AGGCTTTGAGTGTTGGAGGC 60.538 55.000 0.00 0.00 0.00 4.70
1161 1175 2.350134 GGACGGAAGGGGTGGAAC 59.650 66.667 0.00 0.00 0.00 3.62
1411 1425 0.252927 AGGGGTCAGAGGGAAAGAGG 60.253 60.000 0.00 0.00 0.00 3.69
1489 1503 2.940410 GGGAATTTCATCGAACGCCTTA 59.060 45.455 0.00 0.00 0.00 2.69
1583 1597 1.213013 GCAAGTCGCGGAAGAGAGA 59.787 57.895 6.13 0.00 41.70 3.10
1641 1655 1.301716 GAGGAGAACGCCACAAGCA 60.302 57.895 0.00 0.00 44.04 3.91
1642 1656 2.383527 CGAGGAGAACGCCACAAGC 61.384 63.158 0.00 0.00 38.52 4.01
1645 1659 2.649034 GACGAGGAGAACGCCACA 59.351 61.111 0.00 0.00 0.00 4.17
1797 1811 2.270352 ATCAAACACCTTCCTCGCAA 57.730 45.000 0.00 0.00 0.00 4.85
1834 1848 3.753294 ATCATCGTATTCCAGGACACC 57.247 47.619 0.00 0.00 0.00 4.16
1894 1908 0.950116 GCATCTTGCCATACAGCTCC 59.050 55.000 0.00 0.00 37.42 4.70
1978 1992 1.137086 GTCTGTATCGTCCCAGCATGT 59.863 52.381 0.00 0.00 0.00 3.21
2005 2019 3.281727 ACCACCTGATTATGAATGCGT 57.718 42.857 0.00 0.00 0.00 5.24
2132 2146 3.937706 GACCATGACAGGACATTCTTCTG 59.062 47.826 0.00 0.00 34.91 3.02
2328 2342 5.105351 CCAGGTTCAATCCCAAACTTATTCC 60.105 44.000 0.00 0.00 0.00 3.01
2392 2406 0.321564 CCTCATCAAGACAACCGGCA 60.322 55.000 0.00 0.00 0.00 5.69
2482 2496 3.365364 GCTCAACATTTTTCTGGACTCGG 60.365 47.826 0.00 0.00 0.00 4.63
2491 2505 3.648339 TCTGCCAGCTCAACATTTTTC 57.352 42.857 0.00 0.00 0.00 2.29
2539 2553 1.003355 CCCACTGTTGGTCGCATCT 60.003 57.895 0.00 0.00 42.10 2.90
2545 2559 3.975168 ACATAGTACCCACTGTTGGTC 57.025 47.619 6.86 0.27 42.10 4.02
2604 2618 5.127519 AGAACTCTCATTCTCTCCACATCTG 59.872 44.000 0.00 0.00 33.50 2.90
2750 2764 2.503895 ATCTCAAGCAGTTTCCCCAG 57.496 50.000 0.00 0.00 0.00 4.45
2767 2781 0.453390 AGCCTGCTTTTTGCGCTATC 59.547 50.000 9.73 0.00 46.63 2.08
2779 2793 2.711542 GTGTTTGGTACATAGCCTGCT 58.288 47.619 0.00 0.00 39.39 4.24
2857 2871 1.856597 GCAACAGCAAGCTTTTCACTG 59.143 47.619 0.00 5.12 0.00 3.66
2872 2886 3.633525 AGTTCATCAGAGCAAAAGCAACA 59.366 39.130 0.00 0.00 0.00 3.33
3028 3042 4.445305 CCACAAGAGCATGATCCATCCTTA 60.445 45.833 7.49 0.00 0.00 2.69
3138 3152 8.538701 ACAATATGTCTTGGAAATAAATTGGCA 58.461 29.630 0.00 0.00 0.00 4.92
3195 3211 1.451927 TATTCAGGGCAGCAAGGCG 60.452 57.895 0.00 0.00 45.36 5.52
3256 3272 5.294552 GCAGATCTTACAGAAAAGGCGTAAT 59.705 40.000 0.00 0.00 0.00 1.89
3524 3541 1.153369 CGCCTCCCGTGAACATCAT 60.153 57.895 0.00 0.00 0.00 2.45
3601 3618 1.538849 CCCGTGATCGATCAATCTGCA 60.539 52.381 28.83 2.95 38.75 4.41
3641 3806 6.483307 TGAATGTTTGACAGTACTCCTCAAAG 59.517 38.462 19.16 0.15 35.18 2.77
3645 3810 4.390297 GCTGAATGTTTGACAGTACTCCTC 59.610 45.833 0.00 0.00 34.60 3.71
3646 3811 4.319177 GCTGAATGTTTGACAGTACTCCT 58.681 43.478 0.00 0.00 34.60 3.69
3647 3812 3.123621 CGCTGAATGTTTGACAGTACTCC 59.876 47.826 0.00 0.00 34.60 3.85
3670 3838 3.773667 TGTACACCATACCGACCCATAAA 59.226 43.478 0.00 0.00 0.00 1.40
3684 3852 1.092348 CGATCGTCTCCTGTACACCA 58.908 55.000 7.03 0.00 0.00 4.17
3705 3873 2.168521 CAGGATATACCATGCCCCTACG 59.831 54.545 0.00 0.00 42.04 3.51
3737 3905 2.764572 TCTCCTCGATTAACAACCTCCC 59.235 50.000 0.00 0.00 0.00 4.30
3802 3970 1.133946 GCTTTTGCATAGTTCGCGCC 61.134 55.000 0.00 0.00 46.58 6.53
3827 3995 1.837439 TCAGGACTGGTTGTGAACTGT 59.163 47.619 0.00 0.00 0.00 3.55
3874 4043 8.467963 TGATGCATCCACATTCAGTTTATAAT 57.532 30.769 23.67 0.00 0.00 1.28
3904 4073 6.650390 CCCCTGTTCCATTTTCAAAAAGTATG 59.350 38.462 0.00 0.00 0.00 2.39
3905 4074 6.744056 GCCCCTGTTCCATTTTCAAAAAGTAT 60.744 38.462 0.00 0.00 0.00 2.12
3906 4075 5.454045 GCCCCTGTTCCATTTTCAAAAAGTA 60.454 40.000 0.00 0.00 0.00 2.24
3907 4076 4.685848 GCCCCTGTTCCATTTTCAAAAAGT 60.686 41.667 0.00 0.00 0.00 2.66
3908 4077 3.814842 GCCCCTGTTCCATTTTCAAAAAG 59.185 43.478 0.00 0.00 0.00 2.27
3909 4078 3.200825 TGCCCCTGTTCCATTTTCAAAAA 59.799 39.130 0.00 0.00 0.00 1.94
3910 4079 2.774234 TGCCCCTGTTCCATTTTCAAAA 59.226 40.909 0.00 0.00 0.00 2.44
4035 4204 3.647771 AACCAGTTCCGGGGCTCC 61.648 66.667 0.00 0.00 0.00 4.70
4036 4205 2.359975 CAACCAGTTCCGGGGCTC 60.360 66.667 0.00 0.00 0.00 4.70
4037 4206 2.002018 TTTCAACCAGTTCCGGGGCT 62.002 55.000 0.00 0.00 0.00 5.19
4038 4207 1.110518 TTTTCAACCAGTTCCGGGGC 61.111 55.000 0.00 0.00 0.00 5.80
4039 4208 0.671796 GTTTTCAACCAGTTCCGGGG 59.328 55.000 0.00 0.00 0.00 5.73
4092 4262 0.449388 GCTTGAATCACTTCCAGGCG 59.551 55.000 0.00 0.00 0.00 5.52
4118 4372 3.305064 CCATACCTTGACCAAACAAACCG 60.305 47.826 0.00 0.00 0.00 4.44
4161 4415 5.862678 TCGTCCCAATACACATGAGAATA 57.137 39.130 0.00 0.00 0.00 1.75
4168 4422 3.541632 GGTTCATCGTCCCAATACACAT 58.458 45.455 0.00 0.00 0.00 3.21
4208 4462 6.035650 CAGGTACCAGTACACGTTTATCATTG 59.964 42.308 15.94 0.00 37.78 2.82
4227 4481 2.753452 TGGACTTCAGTCGATCAGGTAC 59.247 50.000 0.83 0.00 45.65 3.34


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

AutoCloner maintained by Alex Coulton.