Multiple sequence alignment - TraesCS3D01G105900

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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 TraesCS3D01G105900 chr3D 100.000 4259 0 0 1 4259 58114754 58110496 0.000000e+00 7866.0
1 TraesCS3D01G105900 chr3B 93.694 2474 119 28 1301 3744 91429032 91426566 0.000000e+00 3670.0
2 TraesCS3D01G105900 chr3B 91.801 1305 65 15 2 1285 91430367 91429084 0.000000e+00 1779.0
3 TraesCS3D01G105900 chr3B 94.643 336 18 0 3747 4082 91426396 91426061 4.880000e-144 521.0
4 TraesCS3D01G105900 chr3B 93.220 59 3 1 4200 4257 91425949 91425891 7.590000e-13 86.1
5 TraesCS3D01G105900 chr3A 93.846 1300 46 12 1 1285 67152716 67151436 0.000000e+00 1927.0
6 TraesCS3D01G105900 chr3A 95.290 1189 53 3 2471 3656 67150121 67148933 0.000000e+00 1882.0
7 TraesCS3D01G105900 chr3A 94.461 1029 44 7 1454 2472 67151269 67150244 0.000000e+00 1572.0
8 TraesCS3D01G105900 chr3A 85.027 187 26 2 3878 4063 67125296 67125111 5.620000e-44 189.0
9 TraesCS3D01G105900 chr3A 97.500 40 1 0 3744 3783 67125638 67125599 7.640000e-08 69.4
10 TraesCS3D01G105900 chr4D 82.927 123 20 1 3749 3870 455620394 455620516 4.500000e-20 110.0
11 TraesCS3D01G105900 chr4D 90.698 43 3 1 4089 4131 19297789 19297748 5.950000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G105900 chr3D 58110496 58114754 4258 True 7866.000000 7866 100.000000 1 4259 1 chr3D.!!$R1 4258
1 TraesCS3D01G105900 chr3B 91425891 91430367 4476 True 1514.025000 3670 93.339500 2 4257 4 chr3B.!!$R1 4255
2 TraesCS3D01G105900 chr3A 67148933 67152716 3783 True 1793.666667 1927 94.532333 1 3656 3 chr3A.!!$R2 3655

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
137 138 0.100861 GAGAGAAGGGGCTACGAACG 59.899 60.0 0.00 0.0 0.00 3.95 F
138 139 0.323178 AGAGAAGGGGCTACGAACGA 60.323 55.0 0.14 0.0 0.00 3.85 F
139 140 0.529378 GAGAAGGGGCTACGAACGAA 59.471 55.0 0.14 0.0 0.00 3.85 F
445 447 0.745468 GTAACCAGCCGGACCTAGAG 59.255 60.0 5.05 0.0 35.59 2.43 F
2367 2475 0.821517 TTCTTCTTCCGCCGCTGATA 59.178 50.0 0.00 0.0 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1655 2.125766 AACGGGGCTTCTTCACCTCC 62.126 60.000 0.0 0.0 0.00 4.30 R
1716 1817 4.038402 CCAGAGCAAATGAAGGTCAAAAGT 59.962 41.667 0.0 0.0 36.03 2.66 R
2076 2178 8.970691 AAACCTATTGATATATGCGAAAATGC 57.029 30.769 0.0 0.0 0.00 3.56 R
2406 2514 3.141398 TCGAGAACATGCAAGAAAGCTT 58.859 40.909 0.0 0.0 34.99 3.74 R
4109 4512 0.035725 CTCACATGCAAGCCAGGAGA 60.036 55.000 0.0 0.0 0.00 3.71 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
69 70 2.550277 TCCTACTCCCTGCTGATTCA 57.450 50.000 0.00 0.00 0.00 2.57
92 93 4.891627 TCAAATTTGTGCGTCTGAAAGA 57.108 36.364 17.47 0.00 43.69 2.52
127 128 4.148825 CGCACGGGGAGAGAAGGG 62.149 72.222 0.00 0.00 0.00 3.95
136 137 0.460722 GGAGAGAAGGGGCTACGAAC 59.539 60.000 0.00 0.00 0.00 3.95
137 138 0.100861 GAGAGAAGGGGCTACGAACG 59.899 60.000 0.00 0.00 0.00 3.95
138 139 0.323178 AGAGAAGGGGCTACGAACGA 60.323 55.000 0.14 0.00 0.00 3.85
139 140 0.529378 GAGAAGGGGCTACGAACGAA 59.471 55.000 0.14 0.00 0.00 3.85
433 435 2.422127 CACGGGCAAAATAGGTAACCAG 59.578 50.000 0.00 0.00 37.17 4.00
445 447 0.745468 GTAACCAGCCGGACCTAGAG 59.255 60.000 5.05 0.00 35.59 2.43
455 457 2.530701 CGGACCTAGAGCCAGGATTAT 58.469 52.381 3.73 0.00 39.18 1.28
461 463 3.777522 CCTAGAGCCAGGATTATTAGGGG 59.222 52.174 0.00 0.00 38.00 4.79
585 593 1.883084 CAGCTAGGGTTTAGCGGCG 60.883 63.158 0.51 0.51 44.73 6.46
791 816 3.634910 AGAGCTCGAGAGATTTTACCCTC 59.365 47.826 18.75 8.85 40.84 4.30
828 853 2.738314 ACAAATACGCAACCCGACTTAC 59.262 45.455 0.00 0.00 41.02 2.34
866 891 2.297033 TCTAACGGAAGCGTAAACTGGT 59.703 45.455 0.00 0.00 0.00 4.00
872 897 3.306166 CGGAAGCGTAAACTGGTAATGAG 59.694 47.826 0.00 0.00 0.00 2.90
880 905 2.479566 ACTGGTAATGAGTGCACTGG 57.520 50.000 27.27 6.16 0.00 4.00
917 942 0.954452 GCCACAAACAGAACAGAGGG 59.046 55.000 0.00 0.00 0.00 4.30
1357 1427 5.726980 AAAAAGCAGGTGCAATAGAATGA 57.273 34.783 4.48 0.00 45.16 2.57
1368 1438 6.183360 GGTGCAATAGAATGATTGTGTCATCA 60.183 38.462 0.00 0.00 46.80 3.07
1456 1554 2.732412 GCTCTAGTGTTCAGTGAGCA 57.268 50.000 5.45 5.45 46.41 4.26
1493 1591 9.260002 GTAATTCTGTCAATTGATTGTTGGTTT 57.740 29.630 12.12 2.01 38.84 3.27
1635 1733 6.593382 GGGACTGCATATATGAAGTGAGAATC 59.407 42.308 27.98 13.69 46.59 2.52
1636 1734 6.593382 GGACTGCATATATGAAGTGAGAATCC 59.407 42.308 27.98 18.15 46.59 3.01
1767 1868 6.030548 ACTATATGATGTTCCTGACGATGG 57.969 41.667 0.00 0.00 0.00 3.51
1818 1919 5.126061 ACTTCAAGCTTGTTTGTTGTGAGAT 59.874 36.000 25.19 0.00 0.00 2.75
1840 1942 7.563020 AGATGATCTGATTCTTGCTCTTTGTA 58.437 34.615 0.00 0.00 0.00 2.41
2024 2126 6.091577 TGGTATGTTCGTTGATTGTGATGTAC 59.908 38.462 0.00 0.00 0.00 2.90
2076 2178 8.270030 TCCATTGGATCATAGCCTTCATATTAG 58.730 37.037 0.00 0.00 0.00 1.73
2167 2271 6.767902 TGTAGTTCAATTTCTGAAGAGCACTT 59.232 34.615 0.00 0.00 44.83 3.16
2189 2293 4.899502 TGTTTTGTTTGCCTTTTCTCCAA 58.100 34.783 0.00 0.00 0.00 3.53
2257 2361 6.477688 GTCAGGCATATTTTCACATCAATTGG 59.522 38.462 5.42 0.00 0.00 3.16
2361 2469 1.639298 CTGCCTTTCTTCTTCCGCCG 61.639 60.000 0.00 0.00 0.00 6.46
2367 2475 0.821517 TTCTTCTTCCGCCGCTGATA 59.178 50.000 0.00 0.00 0.00 2.15
2378 2486 2.009774 GCCGCTGATATGTGTCTTGTT 58.990 47.619 0.00 0.00 0.00 2.83
2515 2747 6.239543 CCTCTATACACATGATTGAGCTTCCT 60.240 42.308 0.00 0.00 0.00 3.36
2541 2773 4.629634 CGGTGTTAGTGCATCAGTATTCAA 59.370 41.667 0.00 0.00 0.00 2.69
2606 2838 6.364165 CACCACATTTGTTTTCTCTGCATTAG 59.636 38.462 0.00 0.00 0.00 1.73
2726 2958 2.158519 ACTTCGTTGGGGAAGGAACATT 60.159 45.455 7.18 0.00 46.06 2.71
2900 3132 5.684704 TCTCCCTTCCATTATAAGTTGCAG 58.315 41.667 0.00 0.00 0.00 4.41
2903 3135 4.202050 CCCTTCCATTATAAGTTGCAGTGC 60.202 45.833 8.58 8.58 0.00 4.40
2972 3205 8.697507 AAGACTAATCCTCACATTGTTTCTTT 57.302 30.769 0.00 0.00 0.00 2.52
2976 3209 9.082313 ACTAATCCTCACATTGTTTCTTTGAAT 57.918 29.630 0.00 0.00 0.00 2.57
3099 3332 1.013596 CAAGTGGTGCTTCGTCACAA 58.986 50.000 0.00 0.00 38.66 3.33
3178 3411 5.941647 CCTCTGGTTCCGGTTTTTAATCTAA 59.058 40.000 0.00 0.00 0.00 2.10
3186 3419 4.142469 CCGGTTTTTAATCTAAGGCTGTGG 60.142 45.833 0.00 0.00 0.00 4.17
3303 3536 4.651778 TGAACCGGAGTTTCTTTGATGAT 58.348 39.130 9.46 0.00 35.94 2.45
3441 3675 8.191446 GGAACATATATGATCGTGCATACTAGT 58.809 37.037 19.63 0.00 33.88 2.57
3580 3815 2.351726 GTGTGGATTCCGTGTAAGATGC 59.648 50.000 0.00 0.00 0.00 3.91
3583 3818 2.093921 TGGATTCCGTGTAAGATGCGAA 60.094 45.455 0.00 0.00 0.00 4.70
3661 3897 8.141909 GGTATATTTCCCATTCTTGTTAAAGGC 58.858 37.037 0.00 0.00 33.90 4.35
3673 3909 6.205784 TCTTGTTAAAGGCGAGTCAAATTTG 58.794 36.000 12.15 12.15 33.90 2.32
3744 3980 3.117776 TCCGGATTGCCTAGTGACTACTA 60.118 47.826 0.00 0.00 38.36 1.82
3745 3981 3.827302 CCGGATTGCCTAGTGACTACTAT 59.173 47.826 0.00 0.00 38.65 2.12
3817 4220 5.743026 ACTATCATATAGATCACGGAGCG 57.257 43.478 0.00 0.00 38.19 5.03
3822 4225 1.858091 ATAGATCACGGAGCGCAAAG 58.142 50.000 11.47 1.66 0.00 2.77
3833 4236 1.433534 AGCGCAAAGAACAGCTCTAC 58.566 50.000 11.47 0.00 34.48 2.59
3851 4254 5.105716 GCTCTACTAGAGTTGTCATTCACCA 60.106 44.000 13.60 0.00 44.12 4.17
3898 4301 3.922171 ATTTGGAGACCATGGAGACTC 57.078 47.619 21.47 21.17 31.53 3.36
3928 4331 1.228245 GCTCTGAACCCAACTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
3929 4332 1.239968 GCTCTGAACCCAACTGCCAG 61.240 60.000 0.00 0.00 0.00 4.85
3945 4348 0.955919 CCAGCGTGGGAGGAAAGTTC 60.956 60.000 0.00 0.00 32.67 3.01
3969 4372 1.118965 TTCTTCCTCCTCGTGCCACA 61.119 55.000 0.00 0.00 0.00 4.17
4021 4424 4.419921 ACCGGCGATGGGGGAAAC 62.420 66.667 9.30 0.00 0.00 2.78
4033 4436 1.009335 GGGAAACGCGGTTGTCAAC 60.009 57.895 17.39 7.20 0.00 3.18
4053 4456 3.180507 ACCATTTGGCCATTAACACCAT 58.819 40.909 6.09 0.00 39.32 3.55
4078 4481 2.225467 GCTCACTCCAATTCCTATGGC 58.775 52.381 0.00 0.00 37.88 4.40
4082 4485 2.119495 ACTCCAATTCCTATGGCGACT 58.881 47.619 0.00 0.00 37.88 4.18
4084 4487 1.068588 TCCAATTCCTATGGCGACTCG 59.931 52.381 0.00 0.00 37.88 4.18
4085 4488 1.202533 CCAATTCCTATGGCGACTCGT 60.203 52.381 0.00 0.00 0.00 4.18
4088 4491 0.738975 TTCCTATGGCGACTCGTCAG 59.261 55.000 11.97 0.00 46.78 3.51
4089 4492 0.107361 TCCTATGGCGACTCGTCAGA 60.107 55.000 11.97 6.02 46.78 3.27
4090 4493 0.955178 CCTATGGCGACTCGTCAGAT 59.045 55.000 11.97 0.00 46.78 2.90
4092 4495 0.668535 TATGGCGACTCGTCAGATGG 59.331 55.000 11.97 0.00 46.78 3.51
4093 4496 2.583593 GGCGACTCGTCAGATGGC 60.584 66.667 0.00 0.00 0.00 4.40
4094 4497 2.583593 GCGACTCGTCAGATGGCC 60.584 66.667 0.00 0.00 0.00 5.36
4095 4498 2.278206 CGACTCGTCAGATGGCCG 60.278 66.667 0.00 0.00 0.00 6.13
4096 4499 2.583593 GACTCGTCAGATGGCCGC 60.584 66.667 0.00 0.00 0.00 6.53
4097 4500 4.148825 ACTCGTCAGATGGCCGCC 62.149 66.667 1.04 1.04 0.00 6.13
4098 4501 4.147449 CTCGTCAGATGGCCGCCA 62.147 66.667 16.17 16.17 38.19 5.69
4099 4502 4.451150 TCGTCAGATGGCCGCCAC 62.451 66.667 16.16 9.05 35.80 5.01
4113 4516 2.969238 CCACGCGGCATCATCTCC 60.969 66.667 12.47 0.00 0.00 3.71
4114 4517 2.107750 CACGCGGCATCATCTCCT 59.892 61.111 12.47 0.00 0.00 3.69
4115 4518 2.107750 ACGCGGCATCATCTCCTG 59.892 61.111 12.47 0.00 0.00 3.86
4116 4519 2.664185 CGCGGCATCATCTCCTGG 60.664 66.667 0.00 0.00 0.00 4.45
4117 4520 2.976903 GCGGCATCATCTCCTGGC 60.977 66.667 0.00 0.00 34.81 4.85
4118 4521 2.827423 CGGCATCATCTCCTGGCT 59.173 61.111 0.00 0.00 35.91 4.75
4119 4522 1.147824 CGGCATCATCTCCTGGCTT 59.852 57.895 0.00 0.00 35.91 4.35
4120 4523 1.164662 CGGCATCATCTCCTGGCTTG 61.165 60.000 0.00 0.00 35.91 4.01
4121 4524 1.453762 GGCATCATCTCCTGGCTTGC 61.454 60.000 0.00 0.00 35.25 4.01
4122 4525 0.750546 GCATCATCTCCTGGCTTGCA 60.751 55.000 0.00 0.00 0.00 4.08
4123 4526 1.982660 CATCATCTCCTGGCTTGCAT 58.017 50.000 0.00 0.00 0.00 3.96
4124 4527 1.609072 CATCATCTCCTGGCTTGCATG 59.391 52.381 0.00 0.00 0.00 4.06
4125 4528 0.622136 TCATCTCCTGGCTTGCATGT 59.378 50.000 1.14 0.00 0.00 3.21
4126 4529 0.738975 CATCTCCTGGCTTGCATGTG 59.261 55.000 1.14 0.00 0.00 3.21
4127 4530 0.622136 ATCTCCTGGCTTGCATGTGA 59.378 50.000 1.14 0.00 0.00 3.58
4128 4531 0.035725 TCTCCTGGCTTGCATGTGAG 60.036 55.000 1.14 3.56 0.00 3.51
4129 4532 1.654954 CTCCTGGCTTGCATGTGAGC 61.655 60.000 12.32 12.32 38.17 4.26
4130 4533 1.974875 CCTGGCTTGCATGTGAGCA 60.975 57.895 19.44 0.00 43.99 4.26
4136 4539 4.084265 TGCATGTGAGCAACCCAG 57.916 55.556 0.00 0.00 42.46 4.45
4137 4540 1.604308 TGCATGTGAGCAACCCAGG 60.604 57.895 0.00 0.00 42.46 4.45
4138 4541 1.604593 GCATGTGAGCAACCCAGGT 60.605 57.895 0.00 0.00 0.00 4.00
4139 4542 1.870055 GCATGTGAGCAACCCAGGTG 61.870 60.000 0.00 0.00 0.00 4.00
4140 4543 1.075482 ATGTGAGCAACCCAGGTGG 59.925 57.895 0.00 0.00 41.37 4.61
4189 4592 0.530870 GGTCGTCTATTGCTCCTGCC 60.531 60.000 0.00 0.00 38.71 4.85
4228 4671 4.175962 TCCCACCCTCTCTCTTATGTTTT 58.824 43.478 0.00 0.00 0.00 2.43
4231 4674 4.019321 CCACCCTCTCTCTTATGTTTTCCA 60.019 45.833 0.00 0.00 0.00 3.53
4245 4689 0.319555 TTTCCACTCTTCGTGCCTCG 60.320 55.000 0.00 0.00 42.42 4.63
4257 4701 1.908299 TGCCTCGCACTCTCCTCAA 60.908 57.895 0.00 0.00 31.71 3.02
4258 4702 1.446966 GCCTCGCACTCTCCTCAAC 60.447 63.158 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.300388 TCAGCAGGGAGTAGGATAAGTG 58.700 50.000 0.00 0.00 0.00 3.16
69 70 5.687285 GTCTTTCAGACGCACAAATTTGATT 59.313 36.000 24.64 0.00 35.28 2.57
92 93 0.937304 CGCTACTGTTGTGTTGCAGT 59.063 50.000 0.00 0.00 46.33 4.40
96 97 0.383002 CGTGCGCTACTGTTGTGTTG 60.383 55.000 9.73 0.00 0.00 3.33
127 128 1.681025 GGCGTTCTTCGTTCGTAGCC 61.681 60.000 0.00 0.00 42.13 3.93
136 137 0.742990 TTAGGCCATGGCGTTCTTCG 60.743 55.000 34.72 0.00 43.06 3.79
137 138 0.733150 GTTAGGCCATGGCGTTCTTC 59.267 55.000 34.72 18.05 43.06 2.87
138 139 0.679960 GGTTAGGCCATGGCGTTCTT 60.680 55.000 34.72 17.42 43.06 2.52
139 140 1.077716 GGTTAGGCCATGGCGTTCT 60.078 57.895 34.72 25.20 43.06 3.01
420 421 1.211212 GGTCCGGCTGGTTACCTATTT 59.789 52.381 12.43 0.00 36.30 1.40
433 435 3.541713 CCTGGCTCTAGGTCCGGC 61.542 72.222 0.00 0.00 32.99 6.13
445 447 3.651423 ACAGTACCCCTAATAATCCTGGC 59.349 47.826 0.00 0.00 0.00 4.85
455 457 3.588396 CCAAACCCTAACAGTACCCCTAA 59.412 47.826 0.00 0.00 0.00 2.69
461 463 2.344025 CGCTCCAAACCCTAACAGTAC 58.656 52.381 0.00 0.00 0.00 2.73
632 641 3.564027 GGCCTGCCGAATCGAACG 61.564 66.667 3.36 8.11 0.00 3.95
733 757 2.035442 GGAGCTCGCCTGTTGAACC 61.035 63.158 7.83 0.00 0.00 3.62
828 853 2.080286 AGACATGGGAAGACGTTTCG 57.920 50.000 0.00 0.00 0.00 3.46
866 891 0.692476 ACCTGCCAGTGCACTCATTA 59.308 50.000 18.64 2.85 44.23 1.90
894 919 1.077357 TGTTCTGTTTGTGGCCCGT 60.077 52.632 0.00 0.00 0.00 5.28
901 926 3.555966 CCTTTCCCTCTGTTCTGTTTGT 58.444 45.455 0.00 0.00 0.00 2.83
903 928 2.158460 CCCCTTTCCCTCTGTTCTGTTT 60.158 50.000 0.00 0.00 0.00 2.83
904 929 1.425448 CCCCTTTCCCTCTGTTCTGTT 59.575 52.381 0.00 0.00 0.00 3.16
905 930 1.068121 CCCCTTTCCCTCTGTTCTGT 58.932 55.000 0.00 0.00 0.00 3.41
906 931 1.362224 TCCCCTTTCCCTCTGTTCTG 58.638 55.000 0.00 0.00 0.00 3.02
907 932 2.133858 TTCCCCTTTCCCTCTGTTCT 57.866 50.000 0.00 0.00 0.00 3.01
917 942 1.235724 CCGCGGATATTTCCCCTTTC 58.764 55.000 24.07 0.00 39.01 2.62
933 959 4.770874 TAAACAGCCTCCCGCCGC 62.771 66.667 0.00 0.00 38.78 6.53
1277 1306 4.898607 TCCAGTTGTTGTGGAGCC 57.101 55.556 0.00 0.00 39.28 4.70
1339 1409 4.097437 CACAATCATTCTATTGCACCTGCT 59.903 41.667 0.00 0.00 39.93 4.24
1343 1413 5.565592 TGACACAATCATTCTATTGCACC 57.434 39.130 0.00 0.00 39.93 5.01
1357 1427 7.698506 ATGTTCTCATTCTTGATGACACAAT 57.301 32.000 0.00 0.00 39.83 2.71
1456 1554 9.956720 CAATTGACAGAATTACAAACTTCTCTT 57.043 29.630 0.00 0.00 29.34 2.85
1493 1591 5.120208 GTGCTCTTCTTTGCTAATACGAACA 59.880 40.000 0.00 0.00 0.00 3.18
1557 1655 2.125766 AACGGGGCTTCTTCACCTCC 62.126 60.000 0.00 0.00 0.00 4.30
1635 1733 9.289303 CATAAAGACCAAAGAATAAAATGACGG 57.711 33.333 0.00 0.00 0.00 4.79
1636 1734 8.798153 GCATAAAGACCAAAGAATAAAATGACG 58.202 33.333 0.00 0.00 0.00 4.35
1716 1817 4.038402 CCAGAGCAAATGAAGGTCAAAAGT 59.962 41.667 0.00 0.00 36.03 2.66
1818 1919 9.102757 GTATTACAAAGAGCAAGAATCAGATCA 57.897 33.333 0.00 0.00 0.00 2.92
2076 2178 8.970691 AAACCTATTGATATATGCGAAAATGC 57.029 30.769 0.00 0.00 0.00 3.56
2167 2271 4.543590 TGGAGAAAAGGCAAACAAAACA 57.456 36.364 0.00 0.00 0.00 2.83
2189 2293 6.482641 CACTCTCTTATATGCAGCAAACAGAT 59.517 38.462 0.00 0.00 0.00 2.90
2229 2333 6.381481 TGATGTGAAAATATGCCTGACATC 57.619 37.500 0.00 0.00 40.38 3.06
2335 2443 4.695455 CGGAAGAAGAAAGGCAGATTAACA 59.305 41.667 0.00 0.00 0.00 2.41
2361 2469 5.665459 AGTAGGAACAAGACACATATCAGC 58.335 41.667 0.00 0.00 0.00 4.26
2367 2475 6.357367 AGAAACAAGTAGGAACAAGACACAT 58.643 36.000 0.00 0.00 0.00 3.21
2406 2514 3.141398 TCGAGAACATGCAAGAAAGCTT 58.859 40.909 0.00 0.00 34.99 3.74
2515 2747 1.155889 CTGATGCACTAACACCGCAA 58.844 50.000 0.00 0.00 39.48 4.85
2541 2773 7.504238 ACTCTAGGAAGATGAATTCATACGTCT 59.496 37.037 20.75 16.72 36.57 4.18
2726 2958 3.459145 TGTACGAGTTTTGCTGCTAACA 58.541 40.909 16.45 1.00 0.00 2.41
2867 3099 4.953781 ATGGAAGGGAGAGATCCAAAAA 57.046 40.909 0.00 0.00 45.75 1.94
2870 3102 6.851836 ACTTATAATGGAAGGGAGAGATCCAA 59.148 38.462 0.00 0.00 45.75 3.53
2881 3113 4.641989 AGCACTGCAACTTATAATGGAAGG 59.358 41.667 3.30 0.00 0.00 3.46
2972 3205 9.295825 ACCAACAATGTGAGAATTTAGTATTCA 57.704 29.630 0.00 0.00 0.00 2.57
2976 3209 8.729756 CATCACCAACAATGTGAGAATTTAGTA 58.270 33.333 0.00 0.00 45.20 1.82
3178 3411 3.523564 ACATCCATTAGTAACCACAGCCT 59.476 43.478 0.00 0.00 0.00 4.58
3186 3419 7.103641 TCCTGACAGAAACATCCATTAGTAAC 58.896 38.462 3.32 0.00 0.00 2.50
3303 3536 0.037419 TGCTTGTATCAGTCGCTGCA 60.037 50.000 0.00 0.00 0.00 4.41
3580 3815 9.177304 CAACATCAATTCATTCCATAGATTTCG 57.823 33.333 0.00 0.00 0.00 3.46
3653 3889 5.278604 ACACAAATTTGACTCGCCTTTAAC 58.721 37.500 24.64 0.00 0.00 2.01
3661 3897 4.562394 ACAAAGCAACACAAATTTGACTCG 59.438 37.500 24.64 11.63 36.41 4.18
3673 3909 1.472480 AGGACACACACAAAGCAACAC 59.528 47.619 0.00 0.00 0.00 3.32
3718 3954 0.249657 CACTAGGCAATCCGGAGCTC 60.250 60.000 11.34 4.71 37.47 4.09
3817 4220 5.066968 ACTCTAGTAGAGCTGTTCTTTGC 57.933 43.478 24.37 0.00 46.12 3.68
3833 4236 7.009631 CGATTTAGTGGTGAATGACAACTCTAG 59.990 40.741 0.00 0.00 41.30 2.43
3876 4279 4.698575 GAGTCTCCATGGTCTCCAAATAC 58.301 47.826 12.58 0.00 36.95 1.89
3893 4296 0.394565 AGCAAGCTCCAAACGAGTCT 59.605 50.000 0.00 0.00 41.10 3.24
3898 4301 1.069636 GTTCAGAGCAAGCTCCAAACG 60.070 52.381 17.81 3.13 43.70 3.60
3909 4312 1.228245 GGCAGTTGGGTTCAGAGCA 60.228 57.895 0.00 0.00 0.00 4.26
3928 4331 1.375326 GGAACTTTCCTCCCACGCT 59.625 57.895 0.34 0.00 44.11 5.07
3929 4332 3.982829 GGAACTTTCCTCCCACGC 58.017 61.111 0.34 0.00 44.11 5.34
3945 4348 0.108424 CACGAGGAGGAAGAAGCTGG 60.108 60.000 0.00 0.00 0.00 4.85
3969 4372 0.482446 TGCCACTTCAAATCCCACCT 59.518 50.000 0.00 0.00 0.00 4.00
4017 4420 4.601315 GGTTGACAACCGCGTTTC 57.399 55.556 21.24 0.00 42.62 2.78
4033 4436 3.533547 CATGGTGTTAATGGCCAAATGG 58.466 45.455 10.96 0.00 35.74 3.16
4053 4456 1.377202 GAATTGGAGTGAGCGGCCA 60.377 57.895 2.24 0.00 0.00 5.36
4078 4481 2.278206 CGGCCATCTGACGAGTCG 60.278 66.667 11.85 11.85 0.00 4.18
4082 4485 4.451150 GTGGCGGCCATCTGACGA 62.451 66.667 26.68 0.00 35.28 4.20
4096 4499 2.969238 GGAGATGATGCCGCGTGG 60.969 66.667 11.67 11.67 38.77 4.94
4097 4500 2.107750 AGGAGATGATGCCGCGTG 59.892 61.111 4.92 0.00 0.00 5.34
4098 4501 2.107750 CAGGAGATGATGCCGCGT 59.892 61.111 4.92 0.00 0.00 6.01
4099 4502 2.664185 CCAGGAGATGATGCCGCG 60.664 66.667 0.00 0.00 0.00 6.46
4100 4503 2.955022 AAGCCAGGAGATGATGCCGC 62.955 60.000 0.00 0.00 0.00 6.53
4101 4504 1.147824 AAGCCAGGAGATGATGCCG 59.852 57.895 0.00 0.00 0.00 5.69
4102 4505 1.453762 GCAAGCCAGGAGATGATGCC 61.454 60.000 0.00 0.00 30.95 4.40
4103 4506 0.750546 TGCAAGCCAGGAGATGATGC 60.751 55.000 0.00 0.00 35.00 3.91
4104 4507 1.609072 CATGCAAGCCAGGAGATGATG 59.391 52.381 0.00 0.00 0.00 3.07
4105 4508 1.214673 ACATGCAAGCCAGGAGATGAT 59.785 47.619 0.00 0.00 0.00 2.45
4106 4509 0.622136 ACATGCAAGCCAGGAGATGA 59.378 50.000 0.00 0.00 0.00 2.92
4107 4510 0.738975 CACATGCAAGCCAGGAGATG 59.261 55.000 0.00 0.00 0.00 2.90
4108 4511 0.622136 TCACATGCAAGCCAGGAGAT 59.378 50.000 0.00 0.00 0.00 2.75
4109 4512 0.035725 CTCACATGCAAGCCAGGAGA 60.036 55.000 0.00 0.00 0.00 3.71
4110 4513 1.654954 GCTCACATGCAAGCCAGGAG 61.655 60.000 8.39 0.00 32.22 3.69
4111 4514 1.676635 GCTCACATGCAAGCCAGGA 60.677 57.895 8.39 0.00 32.22 3.86
4112 4515 1.529152 TTGCTCACATGCAAGCCAGG 61.529 55.000 15.20 0.00 46.43 4.45
4113 4516 1.961378 TTGCTCACATGCAAGCCAG 59.039 52.632 15.20 0.00 46.43 4.85
4114 4517 4.177673 TTGCTCACATGCAAGCCA 57.822 50.000 15.20 3.96 46.43 4.75
4119 4522 1.604308 CCTGGGTTGCTCACATGCA 60.604 57.895 0.00 0.00 41.65 3.96
4120 4523 1.604593 ACCTGGGTTGCTCACATGC 60.605 57.895 0.00 0.00 0.00 4.06
4121 4524 1.246056 CCACCTGGGTTGCTCACATG 61.246 60.000 0.00 0.00 0.00 3.21
4122 4525 1.075482 CCACCTGGGTTGCTCACAT 59.925 57.895 0.00 0.00 0.00 3.21
4123 4526 2.055689 CTCCACCTGGGTTGCTCACA 62.056 60.000 0.00 0.00 38.11 3.58
4124 4527 1.302832 CTCCACCTGGGTTGCTCAC 60.303 63.158 0.00 0.00 38.11 3.51
4125 4528 2.528818 CCTCCACCTGGGTTGCTCA 61.529 63.158 0.00 0.00 38.11 4.26
4126 4529 2.352805 CCTCCACCTGGGTTGCTC 59.647 66.667 0.00 0.00 38.11 4.26
4127 4530 3.971702 GCCTCCACCTGGGTTGCT 61.972 66.667 0.00 0.00 38.11 3.91
4129 4532 3.953775 ACGCCTCCACCTGGGTTG 61.954 66.667 0.00 0.00 38.11 3.77
4130 4533 3.953775 CACGCCTCCACCTGGGTT 61.954 66.667 0.00 0.00 38.11 4.11
4132 4535 4.704833 CACACGCCTCCACCTGGG 62.705 72.222 0.00 0.00 35.41 4.45
4133 4536 3.596066 CTCACACGCCTCCACCTGG 62.596 68.421 0.00 0.00 0.00 4.45
4134 4537 2.047844 CTCACACGCCTCCACCTG 60.048 66.667 0.00 0.00 0.00 4.00
4135 4538 4.008933 GCTCACACGCCTCCACCT 62.009 66.667 0.00 0.00 0.00 4.00
4165 4568 1.476891 GGAGCAATAGACGACCACAGA 59.523 52.381 0.00 0.00 0.00 3.41
4166 4569 1.478510 AGGAGCAATAGACGACCACAG 59.521 52.381 0.00 0.00 0.00 3.66
4194 4597 3.365265 GTGGGAAGGGCGCAGTTG 61.365 66.667 10.83 0.00 40.43 3.16


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

AutoCloner maintained by Alex Coulton.