Multiple sequence alignment - TraesCS5D01G466300

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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 TraesCS5D01G466300 chr5D 100.000 4732 0 0 1 4732 508625087 508629818 0.000000e+00 8739.0
1 TraesCS5D01G466300 chr5D 100.000 165 0 0 3946 4110 397324157 397324321 5.950000e-79 305.0
2 TraesCS5D01G466300 chr5D 96.629 178 5 1 3942 4119 56451750 56451574 1.290000e-75 294.0
3 TraesCS5D01G466300 chr5A 96.392 2966 70 23 1020 3949 635961814 635964778 0.000000e+00 4850.0
4 TraesCS5D01G466300 chr5A 94.533 1061 18 18 1 1024 635960522 635961579 0.000000e+00 1602.0
5 TraesCS5D01G466300 chr5A 97.448 627 10 3 4109 4732 635964776 635965399 0.000000e+00 1064.0
6 TraesCS5D01G466300 chr5B 95.685 672 24 5 1394 2063 638468672 638468004 0.000000e+00 1075.0
7 TraesCS5D01G466300 chr5B 90.000 500 25 13 7 488 638469265 638468773 1.450000e-174 623.0
8 TraesCS5D01G466300 chr5B 94.565 92 4 1 4641 4732 638464219 638464129 1.780000e-29 141.0
9 TraesCS5D01G466300 chr5B 81.395 86 4 6 4647 4732 639417825 639417898 5.110000e-05 60.2
10 TraesCS5D01G466300 chr2D 98.837 172 2 0 3945 4116 155759902 155759731 1.650000e-79 307.0
11 TraesCS5D01G466300 chr2D 98.830 171 2 0 3944 4114 286465042 286464872 5.950000e-79 305.0
12 TraesCS5D01G466300 chr7D 97.175 177 5 0 3941 4117 14654515 14654691 2.770000e-77 300.0
13 TraesCS5D01G466300 chr7D 95.161 186 7 2 3943 4128 611391077 611390894 4.630000e-75 292.0
14 TraesCS5D01G466300 chr4D 97.688 173 4 0 3945 4117 10770525 10770697 9.960000e-77 298.0
15 TraesCS5D01G466300 chr3D 95.604 182 6 2 3931 4110 317205686 317205867 1.670000e-74 291.0
16 TraesCS5D01G466300 chr1D 93.467 199 6 5 3912 4110 439752895 439753086 5.990000e-74 289.0
17 TraesCS5D01G466300 chr3A 90.476 84 6 2 4650 4732 427213259 427213341 5.010000e-20 110.0


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 TraesCS5D01G466300 chr5D 508625087 508629818 4731 False 8739.000000 8739 100.000000 1 4732 1 chr5D.!!$F2 4731
1 TraesCS5D01G466300 chr5A 635960522 635965399 4877 False 2505.333333 4850 96.124333 1 4732 3 chr5A.!!$F1 4731
2 TraesCS5D01G466300 chr5B 638464129 638469265 5136 True 613.000000 1075 93.416667 7 4732 3 chr5B.!!$R1 4725

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
40 41 0.875059 GAAACGAAGGCCAACTGGAG 59.125 55.0 5.01 0.00 37.39 3.86 F
516 561 0.941463 CAGGTGAGGATATGCGACGC 60.941 60.0 14.19 14.19 0.00 5.19 F
2210 2524 0.461961 GTCAAGTCGCAGGGATAGCT 59.538 55.0 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1570 3.374058 CCACAATTACTCGGTGATGGTTC 59.626 47.826 0.00 0.0 34.52 3.62 R
2363 2677 0.692476 AGTCAATGGCACTGCACCTA 59.308 50.000 2.82 0.0 0.00 3.08 R
4138 6403 1.016627 GCAGCACTGTGTCAGAAACA 58.983 50.000 9.86 0.0 35.18 2.83 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
40 41 0.875059 GAAACGAAGGCCAACTGGAG 59.125 55.000 5.01 0.00 37.39 3.86
83 84 3.115554 GGGCGATATTGCATTTTCACAC 58.884 45.455 16.83 0.00 36.28 3.82
479 524 3.532155 GCCAGCCTCTCCGTCGAT 61.532 66.667 0.00 0.00 0.00 3.59
516 561 0.941463 CAGGTGAGGATATGCGACGC 60.941 60.000 14.19 14.19 0.00 5.19
582 627 2.178273 GTGTGATTTTCCGGCGGC 59.822 61.111 23.83 7.39 0.00 6.53
862 910 5.069648 TGGCTATCCATCTCACTGTAAGAAG 59.930 44.000 0.00 0.00 37.47 2.85
866 914 5.016051 TCCATCTCACTGTAAGAAGATGC 57.984 43.478 13.89 0.00 46.51 3.91
904 952 3.519579 CACAAAGCCACAAACACATTCA 58.480 40.909 0.00 0.00 0.00 2.57
917 965 4.959596 ACACATTCAGAACATGCAGATC 57.040 40.909 0.00 0.00 0.00 2.75
938 986 1.120530 AGTCACACTTGAGGTCGGTT 58.879 50.000 0.00 0.00 30.10 4.44
963 1011 2.986479 CCTTTACACGCCAAATTTGCTC 59.014 45.455 12.92 5.73 0.00 4.26
994 1042 2.201830 TGGGGGATCCGTGTAAGAAAT 58.798 47.619 5.45 0.00 38.76 2.17
1283 1570 4.963276 TCATTCCAAAAACGAGCTATGG 57.037 40.909 0.00 0.00 0.00 2.74
1670 1961 6.393990 GCACACCATTTGTAAATCATTACCA 58.606 36.000 0.00 0.00 40.61 3.25
1724 2015 9.901172 ATATGCATCATGATATACACAACTCAT 57.099 29.630 8.15 2.69 0.00 2.90
1789 2081 5.193099 ACCATACTGCCCTTTTGTAATCT 57.807 39.130 0.00 0.00 0.00 2.40
2085 2377 1.069838 CGATACACGAGATGGAGGACG 60.070 57.143 0.00 0.00 45.77 4.79
2139 2453 1.061131 CCGCGACAATGTTAGAAGCTG 59.939 52.381 8.23 0.00 0.00 4.24
2171 2485 0.674895 CCCTTTCAACTAGCGCTGCT 60.675 55.000 22.90 0.47 43.41 4.24
2186 2500 3.238232 TGCTCACTTGGTGCAGATC 57.762 52.632 0.00 0.00 40.80 2.75
2210 2524 0.461961 GTCAAGTCGCAGGGATAGCT 59.538 55.000 0.00 0.00 0.00 3.32
2284 2598 5.255710 TCTCGAATAGAAGCTTCTGGAAG 57.744 43.478 34.26 23.01 38.19 3.46
2327 2641 1.812686 TACTTGAGTCCGCCGCACTT 61.813 55.000 0.00 0.00 0.00 3.16
2342 2656 0.788995 CACTTGCACGAGAAGCTGAG 59.211 55.000 0.00 0.00 0.00 3.35
2363 2677 5.488919 TGAGAATGTAGGAAACCAGATCCTT 59.511 40.000 0.00 0.00 45.06 3.36
2399 2713 3.360956 CTTGGGAAATGCTGGGCGC 62.361 63.158 0.00 0.00 39.77 6.53
2606 4490 3.012502 TCAGGGACAATACCTCTACCACT 59.987 47.826 0.00 0.00 35.78 4.00
2664 4548 7.228706 CCATTTAGTATCCATTGGTGAGGTTAC 59.771 40.741 1.86 0.00 32.66 2.50
2774 4682 7.890515 TCTGCTTCTATCCTCATGTAGTAATG 58.109 38.462 0.00 0.00 0.00 1.90
2864 4772 7.937942 TCATGGTTGACAATTGAAAATTGGAAT 59.062 29.630 13.59 0.00 33.56 3.01
3220 5128 7.195646 CACTTGGCAATACTTGGTATGTTATG 58.804 38.462 0.00 0.00 0.00 1.90
3272 5212 3.753272 GCTTTCTCACAGCTTCCAATACA 59.247 43.478 0.00 0.00 34.15 2.29
3273 5213 4.397417 GCTTTCTCACAGCTTCCAATACAT 59.603 41.667 0.00 0.00 34.15 2.29
3274 5214 5.675575 GCTTTCTCACAGCTTCCAATACATG 60.676 44.000 0.00 0.00 34.15 3.21
3276 5216 4.763073 TCTCACAGCTTCCAATACATGAG 58.237 43.478 0.00 0.00 34.87 2.90
3277 5217 4.223700 TCTCACAGCTTCCAATACATGAGT 59.776 41.667 0.00 0.00 35.07 3.41
3354 5469 6.094061 AGAAGTACGACAATCTAACTCTTGC 58.906 40.000 0.00 0.00 0.00 4.01
3442 5701 4.875544 TTATGCGCCTTGTATTTCTGAC 57.124 40.909 4.18 0.00 0.00 3.51
3467 5726 5.455326 GGAGTGAGTATTAATGGATGCTGGT 60.455 44.000 0.00 0.00 0.00 4.00
3543 5802 6.041409 TGTTCTCTCATTGGATACTGGAGATC 59.959 42.308 0.00 0.00 37.20 2.75
3559 5818 3.506059 ATCGAGGCGATTGAGGCGG 62.506 63.158 0.00 0.00 44.59 6.13
3638 5898 7.340122 TCATAGCTTATGATTCTATCCCTCG 57.660 40.000 0.00 0.00 40.09 4.63
3645 5905 2.292569 TGATTCTATCCCTCGTGCGTAC 59.707 50.000 0.00 0.00 0.00 3.67
3745 6005 3.631453 GGTGACCTGTGATGCTTCA 57.369 52.632 0.00 0.00 0.00 3.02
3878 6138 3.793797 ACAACTGTGGGTTTTACTTGC 57.206 42.857 0.00 0.00 35.74 4.01
3911 6171 3.823873 CTGTATGATTCTAGCCCTCGTCT 59.176 47.826 0.00 0.00 0.00 4.18
3912 6172 4.981812 TGTATGATTCTAGCCCTCGTCTA 58.018 43.478 0.00 0.00 0.00 2.59
3918 6180 6.304624 TGATTCTAGCCCTCGTCTATCTTTA 58.695 40.000 0.00 0.00 0.00 1.85
3946 6208 6.640518 TCACTTTCTGTTCTGACTTTGTACT 58.359 36.000 0.00 0.00 0.00 2.73
3947 6209 7.778083 TCACTTTCTGTTCTGACTTTGTACTA 58.222 34.615 0.00 0.00 0.00 1.82
3948 6210 7.705325 TCACTTTCTGTTCTGACTTTGTACTAC 59.295 37.037 0.00 0.00 0.00 2.73
3949 6211 7.707035 CACTTTCTGTTCTGACTTTGTACTACT 59.293 37.037 0.00 0.00 0.00 2.57
3950 6212 7.921745 ACTTTCTGTTCTGACTTTGTACTACTC 59.078 37.037 0.00 0.00 0.00 2.59
3951 6213 6.328641 TCTGTTCTGACTTTGTACTACTCC 57.671 41.667 0.00 0.00 0.00 3.85
3952 6214 5.243283 TCTGTTCTGACTTTGTACTACTCCC 59.757 44.000 0.00 0.00 0.00 4.30
3953 6215 5.145564 TGTTCTGACTTTGTACTACTCCCT 58.854 41.667 0.00 0.00 0.00 4.20
3954 6216 5.243283 TGTTCTGACTTTGTACTACTCCCTC 59.757 44.000 0.00 0.00 0.00 4.30
3955 6217 4.342359 TCTGACTTTGTACTACTCCCTCC 58.658 47.826 0.00 0.00 0.00 4.30
3956 6218 3.087031 TGACTTTGTACTACTCCCTCCG 58.913 50.000 0.00 0.00 0.00 4.63
3957 6219 3.087781 GACTTTGTACTACTCCCTCCGT 58.912 50.000 0.00 0.00 0.00 4.69
3958 6220 3.504375 ACTTTGTACTACTCCCTCCGTT 58.496 45.455 0.00 0.00 0.00 4.44
3959 6221 3.509184 ACTTTGTACTACTCCCTCCGTTC 59.491 47.826 0.00 0.00 0.00 3.95
3960 6222 2.134789 TGTACTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
3961 6223 1.637553 TGTACTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
3962 6224 2.846206 TGTACTACTCCCTCCGTTCCTA 59.154 50.000 0.00 0.00 0.00 2.94
3963 6225 3.266772 TGTACTACTCCCTCCGTTCCTAA 59.733 47.826 0.00 0.00 0.00 2.69
3964 6226 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3965 6227 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3966 6228 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3967 6229 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
3968 6230 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
3969 6231 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
3970 6232 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
3971 6233 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
3972 6234 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
3973 6235 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
3974 6236 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3975 6237 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3976 6238 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
3977 6239 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
3978 6240 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
3979 6241 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
3980 6242 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
3981 6243 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
3982 6244 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
3983 6245 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
3984 6246 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
3985 6247 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
3987 6249 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
3988 6250 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
3989 6251 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
3990 6252 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
3991 6253 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
3992 6254 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
3993 6255 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
3994 6256 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
3995 6257 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
3996 6258 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
3997 6259 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
3998 6260 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
3999 6261 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
4000 6262 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
4001 6263 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
4002 6264 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
4003 6265 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
4004 6266 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
4005 6267 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
4006 6268 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
4007 6269 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
4008 6270 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
4009 6271 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
4010 6272 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
4025 6287 5.903810 ACGGAGTAAAATGAGTGGATCTAC 58.096 41.667 0.00 0.00 41.94 2.59
4026 6288 5.421056 ACGGAGTAAAATGAGTGGATCTACA 59.579 40.000 12.16 0.00 41.94 2.74
4027 6289 5.749109 CGGAGTAAAATGAGTGGATCTACAC 59.251 44.000 12.16 5.82 41.63 2.90
4068 6330 8.763049 CATACATCCGTATGTGATAGTCATTT 57.237 34.615 3.56 0.00 46.70 2.32
4073 6335 8.777413 CATCCGTATGTGATAGTCATTTGAAAT 58.223 33.333 0.00 0.00 0.00 2.17
4074 6336 8.141835 TCCGTATGTGATAGTCATTTGAAATG 57.858 34.615 11.54 11.54 0.00 2.32
4075 6337 6.852853 CCGTATGTGATAGTCATTTGAAATGC 59.147 38.462 12.86 8.33 0.00 3.56
4076 6338 6.852853 CGTATGTGATAGTCATTTGAAATGCC 59.147 38.462 12.86 1.61 0.00 4.40
4077 6339 7.254898 CGTATGTGATAGTCATTTGAAATGCCT 60.255 37.037 12.86 9.73 0.00 4.75
4079 6341 7.558161 TGTGATAGTCATTTGAAATGCCTAG 57.442 36.000 13.20 0.00 0.00 3.02
4083 6345 8.896744 TGATAGTCATTTGAAATGCCTAGAAAG 58.103 33.333 13.20 0.00 0.00 2.62
4084 6346 9.113838 GATAGTCATTTGAAATGCCTAGAAAGA 57.886 33.333 13.20 0.00 0.00 2.52
4088 6350 7.540055 GTCATTTGAAATGCCTAGAAAGACAAG 59.460 37.037 12.86 0.00 0.00 3.16
4089 6351 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
4096 6358 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
4098 6360 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
4102 6364 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
4103 6365 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
4106 6368 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4138 6403 4.494091 AGCACTAATAACCTCTGCACAT 57.506 40.909 0.00 0.00 0.00 3.21
4147 6412 2.498167 ACCTCTGCACATGTTTCTGAC 58.502 47.619 0.00 0.00 0.00 3.51
4369 6634 2.038557 GGTACATATCGCCATGGAAGGT 59.961 50.000 18.40 7.34 0.00 3.50
4466 6731 2.290323 ACTAGGTGAATTGGTGCTCCAC 60.290 50.000 7.09 0.00 44.22 4.02
4467 6732 0.478072 AGGTGAATTGGTGCTCCACA 59.522 50.000 7.09 0.00 44.22 4.17
4481 6746 3.435327 TGCTCCACAGTGTTAATAAAGCG 59.565 43.478 0.00 0.00 0.00 4.68
4620 6885 3.726517 CAAACGTCTGCTGGGGCG 61.727 66.667 0.00 0.00 42.25 6.13
4648 6913 2.375345 CCCTGTACCCGCCCAGATT 61.375 63.158 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 3.787476 GCGCTGTGGGTACGAAATATTTG 60.787 47.826 5.17 1.06 0.00 2.32
479 524 4.735132 CTTCTTCCGCCGTCCGCA 62.735 66.667 0.00 0.00 37.30 5.69
516 561 4.175516 CCATTCCCATCAACGAAACAATG 58.824 43.478 0.00 0.00 0.00 2.82
582 627 2.420022 CGGGCTGGAGAAAAATACACAG 59.580 50.000 0.00 0.00 0.00 3.66
904 952 3.750130 GTGTGACTTGATCTGCATGTTCT 59.250 43.478 0.00 0.00 35.27 3.01
929 977 1.001633 TGTAAAGGCTGAACCGACCTC 59.998 52.381 0.00 0.00 46.52 3.85
938 986 1.904287 ATTTGGCGTGTAAAGGCTGA 58.096 45.000 0.00 0.00 42.44 4.26
963 1011 0.107654 GATCCCCCAACCGAGACTTG 60.108 60.000 0.00 0.00 0.00 3.16
994 1042 4.153475 GCTAAGTCAGCGTACCATTTTCAA 59.847 41.667 0.00 0.00 41.37 2.69
1283 1570 3.374058 CCACAATTACTCGGTGATGGTTC 59.626 47.826 0.00 0.00 34.52 3.62
1670 1961 5.046448 TGGCCAATCTGCATCTTATGTTTTT 60.046 36.000 0.61 0.00 0.00 1.94
1755 2046 7.246171 AGGGCAGTATGGTAATGTCTTATAG 57.754 40.000 0.00 0.00 35.86 1.31
1789 2081 5.843673 TGAGAACTGGTTGCAATGTTTTA 57.156 34.783 0.59 0.00 0.00 1.52
1947 2239 8.796475 TGAAGCAGCTATTTCAAAGAATAGTTT 58.204 29.630 9.04 0.00 40.26 2.66
2085 2377 2.610433 GGCTGCAGAATTTTTGTAGGC 58.390 47.619 20.43 13.77 43.93 3.93
2139 2453 0.884514 GAAAGGGCTGCCTTTGAGAC 59.115 55.000 17.33 5.79 39.72 3.36
2171 2485 1.737735 CGCGATCTGCACCAAGTGA 60.738 57.895 0.00 0.00 46.97 3.41
2210 2524 6.161855 ACCTTACTAGCAATCGAATCATCA 57.838 37.500 0.00 0.00 0.00 3.07
2284 2598 2.954868 CGCGTACGACATGAGCCC 60.955 66.667 21.65 0.00 43.93 5.19
2327 2641 1.001293 ACATTCTCAGCTTCTCGTGCA 59.999 47.619 0.00 0.00 0.00 4.57
2342 2656 6.126739 ACCTAAGGATCTGGTTTCCTACATTC 60.127 42.308 0.00 0.00 42.90 2.67
2363 2677 0.692476 AGTCAATGGCACTGCACCTA 59.308 50.000 2.82 0.00 0.00 3.08
2399 2713 1.996191 GCAGCGAGTTGTAGGAAAGAG 59.004 52.381 0.00 0.00 0.00 2.85
2426 2740 1.281867 TCCACCAGTCCATCCATGTTC 59.718 52.381 0.00 0.00 0.00 3.18
2664 4548 8.198109 AGTGACCAAATATTAGCTAGTGTGTAG 58.802 37.037 0.00 0.00 0.00 2.74
3253 5161 5.164620 TCATGTATTGGAAGCTGTGAGAA 57.835 39.130 0.00 0.00 0.00 2.87
3318 5258 8.882415 ATTGTCGTACTTCTCTTCAAAAAGTA 57.118 30.769 0.00 0.00 35.08 2.24
3320 5260 8.077836 AGATTGTCGTACTTCTCTTCAAAAAG 57.922 34.615 0.00 0.00 0.00 2.27
3442 5701 4.687948 CAGCATCCATTAATACTCACTCCG 59.312 45.833 0.00 0.00 0.00 4.63
3559 5818 7.359514 GCCAAGAAAAGATTTCAACAGTATTGC 60.360 37.037 5.71 0.00 0.00 3.56
3638 5898 5.840940 AGACAGTGAAAATAAGTACGCAC 57.159 39.130 0.00 0.00 0.00 5.34
3743 6003 2.436417 CCGAAATTCCTTTGCTCCTGA 58.564 47.619 0.00 0.00 0.00 3.86
3745 6005 1.354368 TCCCGAAATTCCTTTGCTCCT 59.646 47.619 0.00 0.00 0.00 3.69
3861 6121 3.361786 ACAAGCAAGTAAAACCCACAGT 58.638 40.909 0.00 0.00 0.00 3.55
3878 6138 7.117523 GGCTAGAATCATACAGCTATGAACAAG 59.882 40.741 3.33 1.65 41.73 3.16
3918 6180 7.830739 ACAAAGTCAGAACAGAAAGTGAAAAT 58.169 30.769 0.00 0.00 0.00 1.82
3946 6208 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
3947 6209 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
3948 6210 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3949 6211 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3950 6212 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3951 6213 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3952 6214 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
3953 6215 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
3954 6216 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
3955 6217 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
3956 6218 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
3957 6219 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
3958 6220 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
3959 6221 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
3961 6223 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
3962 6224 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
3963 6225 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
3964 6226 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
3965 6227 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
3966 6228 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
3967 6229 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
3968 6230 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
3969 6231 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
3970 6232 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
3971 6233 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
3972 6234 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
3973 6235 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
3974 6236 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
3975 6237 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
3976 6238 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
3977 6239 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
3978 6240 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
3979 6241 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
3980 6242 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
3981 6243 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
3982 6244 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3983 6245 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3984 6246 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
3985 6247 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
3986 6248 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
3987 6249 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
3988 6250 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
3989 6251 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
3990 6252 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
3991 6253 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
3992 6254 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
3993 6255 7.255569 CACTCATTTTACTCCGTATGTAGTCA 58.744 38.462 0.00 0.00 0.00 3.41
3994 6256 6.696148 CCACTCATTTTACTCCGTATGTAGTC 59.304 42.308 0.00 0.00 0.00 2.59
3995 6257 6.379133 TCCACTCATTTTACTCCGTATGTAGT 59.621 38.462 0.00 0.00 0.00 2.73
3996 6258 6.802608 TCCACTCATTTTACTCCGTATGTAG 58.197 40.000 0.00 0.00 0.00 2.74
3997 6259 6.778834 TCCACTCATTTTACTCCGTATGTA 57.221 37.500 0.00 0.00 0.00 2.29
3998 6260 5.670792 TCCACTCATTTTACTCCGTATGT 57.329 39.130 0.00 0.00 0.00 2.29
3999 6261 6.516718 AGATCCACTCATTTTACTCCGTATG 58.483 40.000 0.00 0.00 0.00 2.39
4000 6262 6.732896 AGATCCACTCATTTTACTCCGTAT 57.267 37.500 0.00 0.00 0.00 3.06
4001 6263 6.604396 TGTAGATCCACTCATTTTACTCCGTA 59.396 38.462 0.00 0.00 0.00 4.02
4002 6264 5.421056 TGTAGATCCACTCATTTTACTCCGT 59.579 40.000 0.00 0.00 0.00 4.69
4003 6265 5.749109 GTGTAGATCCACTCATTTTACTCCG 59.251 44.000 0.00 0.00 32.50 4.63
4004 6266 6.879400 AGTGTAGATCCACTCATTTTACTCC 58.121 40.000 0.00 0.00 41.84 3.85
4005 6267 8.779354 AAAGTGTAGATCCACTCATTTTACTC 57.221 34.615 5.25 0.00 44.74 2.59
4044 6306 8.585018 TCAAATGACTATCACATACGGATGTAT 58.415 33.333 14.23 10.02 44.82 2.29
4045 6307 7.947282 TCAAATGACTATCACATACGGATGTA 58.053 34.615 14.23 2.61 44.82 2.29
4047 6309 7.713764 TTCAAATGACTATCACATACGGATG 57.286 36.000 5.94 5.94 39.16 3.51
4048 6310 8.777413 CATTTCAAATGACTATCACATACGGAT 58.223 33.333 3.82 0.00 0.00 4.18
4049 6311 7.254761 GCATTTCAAATGACTATCACATACGGA 60.255 37.037 14.65 0.00 0.00 4.69
4050 6312 6.852853 GCATTTCAAATGACTATCACATACGG 59.147 38.462 14.65 0.00 0.00 4.02
4051 6313 6.852853 GGCATTTCAAATGACTATCACATACG 59.147 38.462 14.65 0.00 0.00 3.06
4052 6314 7.934457 AGGCATTTCAAATGACTATCACATAC 58.066 34.615 17.52 0.00 35.20 2.39
4053 6315 9.276590 CTAGGCATTTCAAATGACTATCACATA 57.723 33.333 23.50 4.36 38.80 2.29
4054 6316 7.994911 TCTAGGCATTTCAAATGACTATCACAT 59.005 33.333 23.50 1.77 38.80 3.21
4055 6317 7.337938 TCTAGGCATTTCAAATGACTATCACA 58.662 34.615 23.50 5.75 38.80 3.58
4056 6318 7.792374 TCTAGGCATTTCAAATGACTATCAC 57.208 36.000 23.50 0.15 38.80 3.06
4057 6319 8.806429 TTTCTAGGCATTTCAAATGACTATCA 57.194 30.769 23.50 12.23 38.80 2.15
4058 6320 9.113838 TCTTTCTAGGCATTTCAAATGACTATC 57.886 33.333 23.50 1.52 38.80 2.08
4059 6321 8.897752 GTCTTTCTAGGCATTTCAAATGACTAT 58.102 33.333 23.50 4.64 38.80 2.12
4060 6322 7.882791 TGTCTTTCTAGGCATTTCAAATGACTA 59.117 33.333 22.19 22.19 38.54 2.59
4061 6323 6.716628 TGTCTTTCTAGGCATTTCAAATGACT 59.283 34.615 22.35 22.35 41.04 3.41
4062 6324 6.913170 TGTCTTTCTAGGCATTTCAAATGAC 58.087 36.000 14.65 11.48 29.10 3.06
4063 6325 7.231317 ACTTGTCTTTCTAGGCATTTCAAATGA 59.769 33.333 14.65 0.00 35.56 2.57
4064 6326 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
4065 6327 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
4066 6328 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
4067 6329 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
4068 6330 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
4073 6335 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
4074 6336 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
4075 6337 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
4076 6338 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
4077 6339 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
4079 6341 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
4083 6345 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
4084 6346 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
4088 6350 4.646492 TGTACTCCCTCCGTTCCTAAATAC 59.354 45.833 0.00 0.00 0.00 1.89
4089 6351 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
4096 6358 4.737055 GCTTATCTTGTACTCCCTCCGTTC 60.737 50.000 0.00 0.00 0.00 3.95
4098 6360 2.694109 GCTTATCTTGTACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
4102 6364 8.422566 GTTATTAGTGCTTATCTTGTACTCCCT 58.577 37.037 0.00 0.00 32.86 4.20
4103 6365 7.656542 GGTTATTAGTGCTTATCTTGTACTCCC 59.343 40.741 0.00 0.00 32.86 4.30
4106 6368 9.203163 AGAGGTTATTAGTGCTTATCTTGTACT 57.797 33.333 0.00 0.00 34.85 2.73
4138 6403 1.016627 GCAGCACTGTGTCAGAAACA 58.983 50.000 9.86 0.00 35.18 2.83
4369 6634 2.225255 CACGGTATTGCACATCACACAA 59.775 45.455 0.00 0.00 0.00 3.33
4409 6674 5.370679 AGTTAGACGGGCTAAAGTCAAAAA 58.629 37.500 4.55 0.00 40.60 1.94
4420 6685 2.617774 GACTATCGAAGTTAGACGGGCT 59.382 50.000 0.00 0.00 39.07 5.19
4427 6692 6.967767 CACCTAGTGTTGACTATCGAAGTTAG 59.032 42.308 0.00 0.00 39.07 2.34
4466 6731 5.277828 GGGGATTAGCGCTTTATTAACACTG 60.278 44.000 18.68 0.00 0.00 3.66
4467 6732 4.820173 GGGGATTAGCGCTTTATTAACACT 59.180 41.667 18.68 0.00 0.00 3.55
4481 6746 9.750125 CAAATAACATCTAAAAAGGGGATTAGC 57.250 33.333 0.00 0.00 0.00 3.09
4620 6885 2.368011 GGTACAGGGAGGACTGGGC 61.368 68.421 0.00 0.00 42.75 5.36
4672 6937 4.795268 TGTAATCGCCATAGATCGAAGAC 58.205 43.478 0.00 0.00 42.51 3.01


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

AutoCloner maintained by Alex Coulton.