Multiple sequence alignment - TraesCS5D01G304700

Loading Multiple Alignment...

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 TraesCS5D01G304700 chr5D 100.000 4863 0 0 1 4863 399945236 399950098 0.000000e+00 8981
1 TraesCS5D01G304700 chr5D 86.000 100 14 0 3709 3808 546906678 546906579 1.850000e-19 108
2 TraesCS5D01G304700 chr5B 91.432 4482 198 61 12 4421 479825569 479829936 0.000000e+00 5978
3 TraesCS5D01G304700 chr5B 85.783 415 12 25 4452 4853 479830351 479830731 3.530000e-106 396
4 TraesCS5D01G304700 chr5A 92.735 2808 98 42 12 2765 505502005 505504760 0.000000e+00 3958
5 TraesCS5D01G304700 chr5A 88.284 1451 87 28 3458 4853 505505913 505507335 0.000000e+00 1661
6 TraesCS5D01G304700 chr5A 93.031 617 20 7 2871 3464 505504921 505505537 0.000000e+00 880
7 TraesCS5D01G304700 chr5A 98.795 83 1 0 2763 2845 505504841 505504923 1.090000e-31 148
8 TraesCS5D01G304700 chr7D 86.063 287 40 0 2385 2671 250670893 250671179 4.730000e-80 309
9 TraesCS5D01G304700 chr7B 85.714 287 41 0 2385 2671 227282175 227282461 2.200000e-78 303
10 TraesCS5D01G304700 chr7B 84.106 151 24 0 2117 2267 227281894 227282044 3.920000e-31 147
11 TraesCS5D01G304700 chr7A 85.714 287 41 0 2385 2671 270763544 270763258 2.200000e-78 303


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 TraesCS5D01G304700 chr5D 399945236 399950098 4862 False 8981.00 8981 100.00000 1 4863 1 chr5D.!!$F1 4862
1 TraesCS5D01G304700 chr5B 479825569 479830731 5162 False 3187.00 5978 88.60750 12 4853 2 chr5B.!!$F1 4841
2 TraesCS5D01G304700 chr5A 505502005 505507335 5330 False 1661.75 3958 93.21125 12 4853 4 chr5A.!!$F1 4841
3 TraesCS5D01G304700 chr7B 227281894 227282461 567 False 225.00 303 84.91000 2117 2671 2 chr7B.!!$F1 554

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
153 155 0.178990 GCCCAACTTGGTCTCTGGTT 60.179 55.000 7.06 0.00 35.17 3.67 F
278 301 0.588252 AACGCAGACAATGTGCACTC 59.412 50.000 19.41 7.08 43.57 3.51 F
712 762 0.968393 ACCAAAAGGCACAACACGGT 60.968 50.000 0.00 0.00 0.00 4.83 F
732 782 1.226746 GCTGAGTGTTTACTTGCGGT 58.773 50.000 0.00 0.00 37.25 5.68 F
1603 1658 1.831736 TCTTACCTAGCAGCTGAACCC 59.168 52.381 20.43 0.00 0.00 4.11 F
1604 1659 1.834263 CTTACCTAGCAGCTGAACCCT 59.166 52.381 20.43 7.41 0.00 4.34 F
3286 3443 1.903860 AGTAGGGCATTAACACCGACA 59.096 47.619 7.54 0.00 33.07 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1647 0.902531 TACAGGTAGGGTTCAGCTGC 59.097 55.000 9.47 0.0 43.65 5.25 R
1710 1766 1.671556 GGCCCCAATAACAAAAGCACG 60.672 52.381 0.00 0.0 0.00 5.34 R
1797 1853 3.053619 GGTATTTCAATGGGAGGAGGTGT 60.054 47.826 0.00 0.0 0.00 4.16 R
2059 2115 3.682592 AGTACTAGCAGATACCCCACA 57.317 47.619 0.00 0.0 0.00 4.17 R
3406 3584 1.069906 GTACAGGAACACAAAGCAGCG 60.070 52.381 0.00 0.0 0.00 5.18 R
3480 4043 3.838317 TGTCCACAGAAGGTAGTAGCAAT 59.162 43.478 1.58 0.0 0.00 3.56 R
4098 4670 0.034337 TCAAGCCACGGACCAACTAC 59.966 55.000 0.00 0.0 0.00 2.73 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
67 69 1.153549 CTCAGCCTACCGCCTTCAC 60.154 63.158 0.00 0.00 38.78 3.18
68 70 2.125106 CAGCCTACCGCCTTCACC 60.125 66.667 0.00 0.00 38.78 4.02
69 71 2.284699 AGCCTACCGCCTTCACCT 60.285 61.111 0.00 0.00 38.78 4.00
70 72 2.125106 GCCTACCGCCTTCACCTG 60.125 66.667 0.00 0.00 0.00 4.00
71 73 2.125106 CCTACCGCCTTCACCTGC 60.125 66.667 0.00 0.00 0.00 4.85
72 74 2.660064 CCTACCGCCTTCACCTGCT 61.660 63.158 0.00 0.00 0.00 4.24
119 121 2.175811 GGGCGTCGTCATTTGCAC 59.824 61.111 0.00 0.00 0.00 4.57
122 124 1.017177 GGCGTCGTCATTTGCACCTA 61.017 55.000 0.00 0.00 0.00 3.08
149 151 1.352622 TGGTGCCCAACTTGGTCTCT 61.353 55.000 7.06 0.00 35.17 3.10
150 152 0.890996 GGTGCCCAACTTGGTCTCTG 60.891 60.000 7.06 0.00 35.17 3.35
151 153 0.890996 GTGCCCAACTTGGTCTCTGG 60.891 60.000 7.06 0.00 35.17 3.86
153 155 0.178990 GCCCAACTTGGTCTCTGGTT 60.179 55.000 7.06 0.00 35.17 3.67
154 156 1.897560 CCCAACTTGGTCTCTGGTTC 58.102 55.000 7.06 0.00 35.17 3.62
155 157 1.142870 CCCAACTTGGTCTCTGGTTCA 59.857 52.381 7.06 0.00 35.17 3.18
157 159 2.498167 CAACTTGGTCTCTGGTTCAGG 58.502 52.381 0.00 0.00 31.51 3.86
168 189 3.723348 GTTCAGGCCCGCGTTCAC 61.723 66.667 4.92 0.00 0.00 3.18
180 201 0.784778 GCGTTCACTTCAGACTTCCG 59.215 55.000 0.00 0.00 0.00 4.30
194 215 1.553704 ACTTCCGGTCTGGGATTGTAC 59.446 52.381 0.00 0.00 38.76 2.90
196 217 1.191535 TCCGGTCTGGGATTGTACAG 58.808 55.000 0.00 0.00 38.76 2.74
212 233 8.880750 GGATTGTACAGTAGTAATTGAGGTTTC 58.119 37.037 0.00 0.00 30.67 2.78
221 242 1.620822 ATTGAGGTTTCTGCACCACC 58.379 50.000 0.00 0.00 39.62 4.61
224 245 3.670377 GGTTTCTGCACCACCGGC 61.670 66.667 0.00 0.00 36.73 6.13
225 246 2.904866 GTTTCTGCACCACCGGCA 60.905 61.111 0.00 0.00 39.32 5.69
250 273 7.129457 TCATCATCAGCTTATGGTAGAAACT 57.871 36.000 8.01 0.00 0.00 2.66
257 280 6.599244 TCAGCTTATGGTAGAAACTGAAATGG 59.401 38.462 0.00 0.00 30.24 3.16
278 301 0.588252 AACGCAGACAATGTGCACTC 59.412 50.000 19.41 7.08 43.57 3.51
282 305 2.222886 CGCAGACAATGTGCACTCATAC 60.223 50.000 19.41 7.07 41.26 2.39
286 309 5.563475 GCAGACAATGTGCACTCATACTTTT 60.563 40.000 19.41 0.00 40.86 2.27
287 310 6.082338 CAGACAATGTGCACTCATACTTTTC 58.918 40.000 19.41 5.00 0.00 2.29
288 311 5.034554 ACAATGTGCACTCATACTTTTCG 57.965 39.130 19.41 0.00 0.00 3.46
384 418 1.664306 GCTGGCTTGCTCTGCTTTT 59.336 52.632 0.00 0.00 0.00 2.27
415 465 2.303022 TCTGGCTACCCTGTTTCTCTTG 59.697 50.000 0.00 0.00 0.00 3.02
564 614 2.905075 CACTCATGGTTTGGCTATCGA 58.095 47.619 0.00 0.00 0.00 3.59
583 633 5.009854 TCGACATGAGATTGCACATAGAA 57.990 39.130 0.00 0.00 0.00 2.10
619 669 3.947910 AAAAGAGCATGACCCATGTTG 57.052 42.857 0.00 0.00 43.10 3.33
712 762 0.968393 ACCAAAAGGCACAACACGGT 60.968 50.000 0.00 0.00 0.00 4.83
732 782 1.226746 GCTGAGTGTTTACTTGCGGT 58.773 50.000 0.00 0.00 37.25 5.68
755 805 5.779529 ACTGATTGTCAAAACTTGATGCT 57.220 34.783 0.00 0.00 42.47 3.79
1104 1158 3.061369 AGAAGGTACCCCTCCTTTTTGT 58.939 45.455 8.74 0.00 44.19 2.83
1180 1235 6.979238 GCCTATGTTCGATACTCATAATACCC 59.021 42.308 0.00 0.00 0.00 3.69
1226 1281 8.046294 TCTTGTGCAAACTCAAGTTTTAGTTA 57.954 30.769 12.84 0.00 45.07 2.24
1236 1291 8.166422 ACTCAAGTTTTAGTTACTGGATTTGG 57.834 34.615 0.00 0.00 0.00 3.28
1413 1468 5.155161 AGTATCTCCACCCAGCATGTATTA 58.845 41.667 0.00 0.00 0.00 0.98
1471 1526 5.242393 AGCATGAGCACCAAAATGGATATAC 59.758 40.000 2.85 0.00 45.49 1.47
1480 1535 9.691362 GCACCAAAATGGATATACGATTTTAAT 57.309 29.630 2.85 0.00 42.13 1.40
1592 1647 7.490000 ACACCGTTTCAGATTATCTTACCTAG 58.510 38.462 0.00 0.00 0.00 3.02
1602 1657 3.828875 ATCTTACCTAGCAGCTGAACC 57.171 47.619 20.43 0.00 0.00 3.62
1603 1658 1.831736 TCTTACCTAGCAGCTGAACCC 59.168 52.381 20.43 0.00 0.00 4.11
1604 1659 1.834263 CTTACCTAGCAGCTGAACCCT 59.166 52.381 20.43 7.41 0.00 4.34
1605 1660 2.840640 TACCTAGCAGCTGAACCCTA 57.159 50.000 20.43 8.26 0.00 3.53
1710 1766 7.171630 TCTAGTTATCCTCTGTTTTCCTGTC 57.828 40.000 0.00 0.00 0.00 3.51
1797 1853 7.334090 TGATTCCAAAAGTGATCCAACAAAAA 58.666 30.769 0.00 0.00 0.00 1.94
1928 1984 4.521130 TTATGCTATTCTAGACAGCGGG 57.479 45.455 16.81 0.00 38.15 6.13
2031 2087 9.665264 GTAATAACCATCTTTTGCTAGTTATGC 57.335 33.333 0.00 0.00 32.35 3.14
2048 2104 9.868277 CTAGTTATGCTAGCTTTATCTGCTATT 57.132 33.333 17.23 0.00 41.45 1.73
2050 2106 9.646427 AGTTATGCTAGCTTTATCTGCTATTAC 57.354 33.333 17.23 1.19 41.45 1.89
2051 2107 9.646427 GTTATGCTAGCTTTATCTGCTATTACT 57.354 33.333 17.23 0.00 41.45 2.24
2054 2110 8.964476 TGCTAGCTTTATCTGCTATTACTTTT 57.036 30.769 17.23 0.00 41.45 2.27
2055 2111 9.396022 TGCTAGCTTTATCTGCTATTACTTTTT 57.604 29.630 17.23 0.00 41.45 1.94
2093 2149 8.534333 TCTGCTAGTACTTTTTGTATGAACTG 57.466 34.615 0.00 0.00 33.23 3.16
2131 2187 8.630037 TCTTGAACTTATTTTCCTCTTTTGGTC 58.370 33.333 0.00 0.00 0.00 4.02
2374 2448 3.126831 ACTCTGACGTCTTTTCTGCTTG 58.873 45.455 17.92 0.00 0.00 4.01
2378 2452 5.113383 TCTGACGTCTTTTCTGCTTGTTTA 58.887 37.500 17.92 0.00 0.00 2.01
2379 2453 5.006358 TCTGACGTCTTTTCTGCTTGTTTAC 59.994 40.000 17.92 0.00 0.00 2.01
3149 3306 5.876460 GTCTGGTTACATGGGTACGTATTTT 59.124 40.000 0.00 0.00 0.00 1.82
3259 3416 3.641434 ACAAGGAGAGCATGCATTAGT 57.359 42.857 21.98 5.90 0.00 2.24
3286 3443 1.903860 AGTAGGGCATTAACACCGACA 59.096 47.619 7.54 0.00 33.07 4.35
3349 3506 7.549839 ACTGCAATATCATGTAAACAAGCATT 58.450 30.769 0.00 0.00 0.00 3.56
3369 3526 3.229276 TGAAAATGCGCGGAATTTGAT 57.771 38.095 18.64 0.00 0.00 2.57
3406 3584 8.873215 TGTTCAGAGTGCTTACTATATTTAGC 57.127 34.615 0.00 0.00 0.00 3.09
3480 4043 6.350906 TGTCTGATGTGCATATTCTGATTGA 58.649 36.000 0.00 0.00 0.00 2.57
3645 4208 0.888619 CGCACTCCCTCTCTTACACA 59.111 55.000 0.00 0.00 0.00 3.72
3674 4237 4.319177 AGCTAAGAAACAGCTCGAAACAT 58.681 39.130 0.00 0.00 46.37 2.71
3826 4390 0.035458 AGAAACCTCAAGCTCCACCG 59.965 55.000 0.00 0.00 0.00 4.94
3856 4420 4.810790 CTCCTAACACAACGACTTCAGAT 58.189 43.478 0.00 0.00 0.00 2.90
3943 4508 1.515304 GGCGTGTGCGTTGTTTTGT 60.515 52.632 0.00 0.00 44.10 2.83
3961 4526 2.676076 TGTTTTTACCGAGAGTACCGC 58.324 47.619 0.00 0.00 0.00 5.68
3962 4527 1.995484 GTTTTTACCGAGAGTACCGCC 59.005 52.381 0.00 0.00 0.00 6.13
3979 4544 1.205064 CCGTCGCTTTGCTGAGTTG 59.795 57.895 0.00 0.00 0.00 3.16
4021 4586 0.671781 GCCGAGTGATGTGCTCTTGT 60.672 55.000 0.00 0.00 0.00 3.16
4046 4616 4.083271 GCATTCCGATCACCTTAATAAGCC 60.083 45.833 0.00 0.00 0.00 4.35
4048 4618 1.798813 CCGATCACCTTAATAAGCCGC 59.201 52.381 0.00 0.00 0.00 6.53
4061 4631 4.424566 GCCGCGTTCTGGGTCGTA 62.425 66.667 4.92 0.00 0.00 3.43
4097 4669 0.930726 TGGGAACTTGGGAAGGTTGT 59.069 50.000 0.00 0.00 0.00 3.32
4098 4670 1.328279 GGGAACTTGGGAAGGTTGTG 58.672 55.000 0.00 0.00 0.00 3.33
4132 4704 2.289010 GGCTTGATGTTTCTGGGTTTGG 60.289 50.000 0.00 0.00 0.00 3.28
4191 4763 0.514691 CTGCTGAACTCGAAGTTGGC 59.485 55.000 5.20 9.03 38.80 4.52
4203 4782 0.598065 AAGTTGGCGTGAGAAATGGC 59.402 50.000 0.00 0.00 40.77 4.40
4204 4783 1.154225 GTTGGCGTGAGAAATGGCG 60.154 57.895 0.00 0.00 43.29 5.69
4246 4825 3.302365 TTTTGTTATCTGCTTGCCTGC 57.698 42.857 0.00 0.00 0.00 4.85
4249 4828 1.020437 GTTATCTGCTTGCCTGCTCC 58.980 55.000 0.00 0.00 0.00 4.70
4250 4829 0.914644 TTATCTGCTTGCCTGCTCCT 59.085 50.000 0.00 0.00 0.00 3.69
4263 4842 4.164030 TGCCTGCTCCTAATTATGTGAGAA 59.836 41.667 9.70 1.05 0.00 2.87
4265 4844 5.180868 GCCTGCTCCTAATTATGTGAGAATG 59.819 44.000 9.70 0.81 0.00 2.67
4279 4861 4.286032 TGTGAGAATGGGTACTACTGCTTT 59.714 41.667 0.00 0.00 0.00 3.51
4281 4863 5.122396 GTGAGAATGGGTACTACTGCTTTTG 59.878 44.000 0.00 0.00 0.00 2.44
4283 4865 2.194201 TGGGTACTACTGCTTTTGGC 57.806 50.000 0.00 0.00 42.22 4.52
4285 4867 1.004394 GGGTACTACTGCTTTTGGCCT 59.996 52.381 3.32 0.00 40.92 5.19
4286 4868 2.357075 GGTACTACTGCTTTTGGCCTC 58.643 52.381 3.32 0.00 40.92 4.70
4287 4869 2.027100 GGTACTACTGCTTTTGGCCTCT 60.027 50.000 3.32 0.00 40.92 3.69
4288 4870 2.481289 ACTACTGCTTTTGGCCTCTC 57.519 50.000 3.32 0.00 40.92 3.20
4306 4889 0.614294 TCGGGTAGGCAATTTTCCGA 59.386 50.000 0.00 0.00 43.29 4.55
4313 4896 5.340803 GGTAGGCAATTTTCCGAAGAAATC 58.659 41.667 0.00 0.00 41.55 2.17
4327 4910 4.956184 CGAAGAAATCGCCGAGAATTTTAC 59.044 41.667 0.00 0.00 45.89 2.01
4338 4922 6.540205 GCCGAGAATTTTACGTTTTGTATCT 58.460 36.000 0.00 0.00 31.81 1.98
4354 4938 6.819397 TTGTATCTATCTCGTGTAGATGGG 57.181 41.667 14.42 2.53 44.95 4.00
4362 4946 4.755411 TCTCGTGTAGATGGGTTGAATTC 58.245 43.478 0.00 0.00 0.00 2.17
4371 4955 0.098728 GGGTTGAATTCATCCGTGCG 59.901 55.000 23.23 0.00 36.75 5.34
4401 4985 0.168128 GTTGTAATGCCGGTGTCTGC 59.832 55.000 1.90 0.00 0.00 4.26
4421 5005 5.303845 TCTGCTGAGATGATAGTGCAATACT 59.696 40.000 0.00 0.00 43.56 2.12
4422 5006 6.491403 TCTGCTGAGATGATAGTGCAATACTA 59.509 38.462 0.00 0.00 45.50 1.82
4423 5007 6.450545 TGCTGAGATGATAGTGCAATACTAC 58.549 40.000 0.00 0.00 44.30 2.73
4512 5505 3.455990 GCCTACTGCCTACTTTAGTCC 57.544 52.381 0.00 0.00 0.00 3.85
4523 5516 0.601841 CTTTAGTCCGGTTGCCACGT 60.602 55.000 0.00 0.00 0.00 4.49
4566 5559 4.473520 CCGAGCCAACCTGCCGAT 62.474 66.667 0.00 0.00 0.00 4.18
4567 5560 2.892425 CGAGCCAACCTGCCGATC 60.892 66.667 0.00 0.00 0.00 3.69
4568 5561 2.514824 GAGCCAACCTGCCGATCC 60.515 66.667 0.00 0.00 0.00 3.36
4569 5562 4.473520 AGCCAACCTGCCGATCCG 62.474 66.667 0.00 0.00 0.00 4.18
4610 5615 3.093172 CTTCCCCTGGCCCTCCTC 61.093 72.222 0.00 0.00 0.00 3.71
4853 5884 4.459089 GGCCTCTGTGCGTCCTCC 62.459 72.222 0.00 0.00 0.00 4.30
4854 5885 3.386237 GCCTCTGTGCGTCCTCCT 61.386 66.667 0.00 0.00 0.00 3.69
4855 5886 2.888863 CCTCTGTGCGTCCTCCTC 59.111 66.667 0.00 0.00 0.00 3.71
4856 5887 1.680651 CCTCTGTGCGTCCTCCTCT 60.681 63.158 0.00 0.00 0.00 3.69
4857 5888 1.662438 CCTCTGTGCGTCCTCCTCTC 61.662 65.000 0.00 0.00 0.00 3.20
4858 5889 1.662438 CTCTGTGCGTCCTCCTCTCC 61.662 65.000 0.00 0.00 0.00 3.71
4859 5890 3.057547 CTGTGCGTCCTCCTCTCCG 62.058 68.421 0.00 0.00 0.00 4.63
4860 5891 4.500116 GTGCGTCCTCCTCTCCGC 62.500 72.222 0.00 0.00 45.92 5.54
4861 5892 4.742649 TGCGTCCTCCTCTCCGCT 62.743 66.667 0.00 0.00 45.90 5.52
4862 5893 3.894947 GCGTCCTCCTCTCCGCTC 61.895 72.222 0.00 0.00 42.66 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 1.587043 ATGACAAGCAGCAGCAGCAG 61.587 55.000 12.92 6.63 45.49 4.24
72 74 1.602605 ATGACAAGCAGCAGCAGCA 60.603 52.632 12.92 0.00 45.49 4.41
119 121 3.890674 GGCACCAAAGCGACTAGG 58.109 61.111 0.00 0.00 34.64 3.02
151 153 3.723348 GTGAACGCGGGCCTGAAC 61.723 66.667 18.31 3.20 0.00 3.18
153 155 3.876589 GAAGTGAACGCGGGCCTGA 62.877 63.158 18.31 0.00 0.00 3.86
154 156 3.423154 GAAGTGAACGCGGGCCTG 61.423 66.667 12.47 7.41 0.00 4.85
155 157 3.883744 CTGAAGTGAACGCGGGCCT 62.884 63.158 12.47 0.00 0.00 5.19
157 159 2.357034 TCTGAAGTGAACGCGGGC 60.357 61.111 12.47 1.50 0.00 6.13
163 184 2.405172 GACCGGAAGTCTGAAGTGAAC 58.595 52.381 9.46 0.00 42.69 3.18
180 201 5.927281 TTACTACTGTACAATCCCAGACC 57.073 43.478 0.00 0.00 32.93 3.85
185 206 6.885922 ACCTCAATTACTACTGTACAATCCC 58.114 40.000 0.00 0.00 0.00 3.85
194 215 5.122396 GGTGCAGAAACCTCAATTACTACTG 59.878 44.000 0.00 0.00 37.24 2.74
196 217 5.001232 TGGTGCAGAAACCTCAATTACTAC 58.999 41.667 0.00 0.00 41.16 2.73
212 233 2.438975 ATGATGCCGGTGGTGCAG 60.439 61.111 1.90 0.00 42.92 4.41
221 242 2.418976 CCATAAGCTGATGATGATGCCG 59.581 50.000 13.15 0.00 0.00 5.69
224 245 7.660617 AGTTTCTACCATAAGCTGATGATGATG 59.339 37.037 13.15 0.00 0.00 3.07
225 246 7.660617 CAGTTTCTACCATAAGCTGATGATGAT 59.339 37.037 13.15 0.00 37.35 2.45
250 273 1.028130 TTGTCTGCGTTGCCATTTCA 58.972 45.000 0.00 0.00 0.00 2.69
257 280 1.008652 TGCACATTGTCTGCGTTGC 60.009 52.632 0.00 0.00 37.46 4.17
278 301 5.008019 ACCTTATGCTGATGCGAAAAGTATG 59.992 40.000 0.00 0.00 43.34 2.39
282 305 4.100529 CAACCTTATGCTGATGCGAAAAG 58.899 43.478 0.00 0.00 43.34 2.27
286 309 1.016627 GCAACCTTATGCTGATGCGA 58.983 50.000 0.00 0.00 43.06 5.10
287 310 3.539253 GCAACCTTATGCTGATGCG 57.461 52.632 0.00 0.00 43.06 4.73
288 311 0.593263 GCGCAACCTTATGCTGATGC 60.593 55.000 0.30 0.00 44.21 3.91
415 465 1.895131 TGAAAGCAGAAAATGGAGGCC 59.105 47.619 0.00 0.00 0.00 5.19
564 614 6.600427 TGTTGATTCTATGTGCAATCTCATGT 59.400 34.615 0.00 0.00 31.33 3.21
610 660 5.072600 TCCTAAACTCACTAACAACATGGGT 59.927 40.000 0.00 0.00 0.00 4.51
650 700 1.595109 CACGTGGTGAGCTGCAAGA 60.595 57.895 7.95 0.00 35.23 3.02
712 762 1.225855 CCGCAAGTAAACACTCAGCA 58.774 50.000 0.00 0.00 0.00 4.41
732 782 6.882610 AGCATCAAGTTTTGACAATCAGTA 57.117 33.333 0.00 0.00 43.48 2.74
755 805 4.175962 ACTGGGAAATGGAGAAGAGGTTA 58.824 43.478 0.00 0.00 0.00 2.85
1104 1158 6.863275 TGATTAATTACGAGACAGCAGAAGA 58.137 36.000 0.00 0.00 0.00 2.87
1226 1281 6.239289 CCAAAACAACTACATCCAAATCCAGT 60.239 38.462 0.00 0.00 0.00 4.00
1236 1291 4.825085 TGGAGAACCCAAAACAACTACATC 59.175 41.667 0.00 0.00 43.29 3.06
1413 1468 9.066892 TCTGTTACTCAATAGCAAAAGATTGTT 57.933 29.630 0.00 0.00 38.85 2.83
1471 1526 7.372451 TCCCTCACTTGTAACATTAAAATCG 57.628 36.000 0.00 0.00 0.00 3.34
1480 1535 4.141287 CCATGTTTCCCTCACTTGTAACA 58.859 43.478 0.00 0.00 0.00 2.41
1592 1647 0.902531 TACAGGTAGGGTTCAGCTGC 59.097 55.000 9.47 0.00 43.65 5.25
1602 1657 2.037144 AGCCCGTACATTACAGGTAGG 58.963 52.381 0.00 0.00 0.00 3.18
1603 1658 3.255149 CCTAGCCCGTACATTACAGGTAG 59.745 52.174 0.00 0.00 34.78 3.18
1604 1659 3.225104 CCTAGCCCGTACATTACAGGTA 58.775 50.000 0.00 0.00 0.00 3.08
1605 1660 2.037144 CCTAGCCCGTACATTACAGGT 58.963 52.381 0.00 0.00 0.00 4.00
1655 1710 2.229792 TGCACAACACAATCCCTTCTC 58.770 47.619 0.00 0.00 0.00 2.87
1710 1766 1.671556 GGCCCCAATAACAAAAGCACG 60.672 52.381 0.00 0.00 0.00 5.34
1797 1853 3.053619 GGTATTTCAATGGGAGGAGGTGT 60.054 47.826 0.00 0.00 0.00 4.16
1928 1984 7.222611 TCAAGCTTTTTAACAGCAAGATGTTTC 59.777 33.333 9.11 0.00 40.47 2.78
2055 2111 4.650972 ACTAGCAGATACCCCACAAAAA 57.349 40.909 0.00 0.00 0.00 1.94
2056 2112 4.781087 AGTACTAGCAGATACCCCACAAAA 59.219 41.667 0.00 0.00 0.00 2.44
2057 2113 4.359105 AGTACTAGCAGATACCCCACAAA 58.641 43.478 0.00 0.00 0.00 2.83
2058 2114 3.990369 AGTACTAGCAGATACCCCACAA 58.010 45.455 0.00 0.00 0.00 3.33
2059 2115 3.682592 AGTACTAGCAGATACCCCACA 57.317 47.619 0.00 0.00 0.00 4.17
2060 2116 5.354842 AAAAGTACTAGCAGATACCCCAC 57.645 43.478 0.00 0.00 0.00 4.61
2061 2117 5.249852 ACAAAAAGTACTAGCAGATACCCCA 59.750 40.000 0.00 0.00 0.00 4.96
2062 2118 5.742063 ACAAAAAGTACTAGCAGATACCCC 58.258 41.667 0.00 0.00 0.00 4.95
2063 2119 8.202137 TCATACAAAAAGTACTAGCAGATACCC 58.798 37.037 0.00 0.00 35.05 3.69
2064 2120 9.595823 TTCATACAAAAAGTACTAGCAGATACC 57.404 33.333 0.00 0.00 35.05 2.73
2374 2448 8.418662 ACCTTTTCTTCCTTTTGTATGGTAAAC 58.581 33.333 0.00 0.00 0.00 2.01
2378 2452 5.897250 ACACCTTTTCTTCCTTTTGTATGGT 59.103 36.000 0.00 0.00 0.00 3.55
2379 2453 6.405278 ACACCTTTTCTTCCTTTTGTATGG 57.595 37.500 0.00 0.00 0.00 2.74
3238 3395 3.960571 ACTAATGCATGCTCTCCTTGTT 58.039 40.909 20.33 3.77 0.00 2.83
3243 3400 5.118990 TCTTGTTACTAATGCATGCTCTCC 58.881 41.667 20.33 0.00 0.00 3.71
3259 3416 5.493809 GGTGTTAATGCCCTACTCTTGTTA 58.506 41.667 0.00 0.00 0.00 2.41
3286 3443 5.607477 TCTGAAGTTCAAACCGTTGACTAT 58.393 37.500 7.06 0.00 43.52 2.12
3349 3506 2.713895 TCAAATTCCGCGCATTTTCA 57.286 40.000 8.75 0.00 0.00 2.69
3357 3514 7.148820 ACAGTAAATTTTGAATCAAATTCCGCG 60.149 33.333 9.41 0.00 38.50 6.46
3369 3526 7.333528 AGCACTCTGAACAGTAAATTTTGAA 57.666 32.000 0.00 0.00 0.00 2.69
3406 3584 1.069906 GTACAGGAACACAAAGCAGCG 60.070 52.381 0.00 0.00 0.00 5.18
3464 3644 7.199541 AGTAGCAATCAATCAGAATATGCAC 57.800 36.000 0.00 0.00 37.06 4.57
3480 4043 3.838317 TGTCCACAGAAGGTAGTAGCAAT 59.162 43.478 1.58 0.00 0.00 3.56
3517 4080 5.541845 TGTTTCACTGTATCCTCAGTCAAG 58.458 41.667 0.00 0.00 45.37 3.02
3701 4264 2.202388 CGCAAGCTGCATTCCACG 60.202 61.111 1.02 0.00 45.36 4.94
3826 4390 2.820037 GTGTTAGGAGCAGCGGCC 60.820 66.667 4.82 0.00 42.56 6.13
3856 4420 0.764271 TGAACTGGACATGTCAGGCA 59.236 50.000 26.47 18.48 36.62 4.75
3864 4428 4.104383 ACATCCTTGTTGAACTGGACAT 57.896 40.909 11.48 2.69 29.55 3.06
3900 4465 1.025812 ATGCGTCTTACTAGCGCTCT 58.974 50.000 16.34 2.16 42.96 4.09
3901 4466 1.124462 CATGCGTCTTACTAGCGCTC 58.876 55.000 16.34 0.00 42.96 5.03
3902 4467 0.456221 ACATGCGTCTTACTAGCGCT 59.544 50.000 17.26 17.26 42.96 5.92
3903 4468 0.847035 GACATGCGTCTTACTAGCGC 59.153 55.000 0.00 0.00 42.89 5.92
3904 4469 1.065701 AGGACATGCGTCTTACTAGCG 59.934 52.381 0.00 0.00 42.21 4.26
3905 4470 2.464865 CAGGACATGCGTCTTACTAGC 58.535 52.381 0.00 0.00 42.21 3.42
3906 4471 2.799917 GCCAGGACATGCGTCTTACTAG 60.800 54.545 0.00 0.00 42.21 2.57
3907 4472 1.136305 GCCAGGACATGCGTCTTACTA 59.864 52.381 0.00 0.00 42.21 1.82
3908 4473 0.108138 GCCAGGACATGCGTCTTACT 60.108 55.000 0.00 0.00 42.21 2.24
3909 4474 1.421410 CGCCAGGACATGCGTCTTAC 61.421 60.000 0.00 0.00 45.43 2.34
3943 4508 1.402720 CGGCGGTACTCTCGGTAAAAA 60.403 52.381 0.00 0.00 31.56 1.94
3961 4526 1.205064 CAACTCAGCAAAGCGACGG 59.795 57.895 0.00 0.00 0.00 4.79
3962 4527 0.581529 TTCAACTCAGCAAAGCGACG 59.418 50.000 0.00 0.00 0.00 5.12
3979 4544 1.966451 CCACACAGCCCCGTTCTTC 60.966 63.158 0.00 0.00 0.00 2.87
4021 4586 5.008613 GCTTATTAAGGTGATCGGAATGCAA 59.991 40.000 5.61 0.00 0.00 4.08
4046 4616 2.975410 TATATACGACCCAGAACGCG 57.025 50.000 3.53 3.53 0.00 6.01
4048 4618 5.971792 CAGCATATATATACGACCCAGAACG 59.028 44.000 0.00 0.00 0.00 3.95
4061 4631 9.453572 CAAGTTCCCATGTTACAGCATATATAT 57.546 33.333 0.00 0.00 0.00 0.86
4097 4669 0.250124 CAAGCCACGGACCAACTACA 60.250 55.000 0.00 0.00 0.00 2.74
4098 4670 0.034337 TCAAGCCACGGACCAACTAC 59.966 55.000 0.00 0.00 0.00 2.73
4132 4704 3.671928 GTGTCAGCTCAAAATCACAATGC 59.328 43.478 0.00 0.00 0.00 3.56
4191 4763 4.201812 ACAATAATGTCGCCATTTCTCACG 60.202 41.667 0.00 0.00 41.50 4.35
4216 4795 7.622672 GCAAGCAGATAACAAAAATGGACATTG 60.623 37.037 0.00 0.00 0.00 2.82
4217 4796 6.369615 GCAAGCAGATAACAAAAATGGACATT 59.630 34.615 0.00 0.00 0.00 2.71
4218 4797 5.870978 GCAAGCAGATAACAAAAATGGACAT 59.129 36.000 0.00 0.00 0.00 3.06
4219 4798 5.229423 GCAAGCAGATAACAAAAATGGACA 58.771 37.500 0.00 0.00 0.00 4.02
4220 4799 4.627035 GGCAAGCAGATAACAAAAATGGAC 59.373 41.667 0.00 0.00 0.00 4.02
4221 4800 4.527816 AGGCAAGCAGATAACAAAAATGGA 59.472 37.500 0.00 0.00 0.00 3.41
4222 4801 4.628333 CAGGCAAGCAGATAACAAAAATGG 59.372 41.667 0.00 0.00 0.00 3.16
4234 4813 0.914644 ATTAGGAGCAGGCAAGCAGA 59.085 50.000 4.78 0.00 36.85 4.26
4246 4825 7.967908 AGTACCCATTCTCACATAATTAGGAG 58.032 38.462 3.76 4.89 0.00 3.69
4249 4828 9.698309 CAGTAGTACCCATTCTCACATAATTAG 57.302 37.037 0.00 0.00 0.00 1.73
4250 4829 8.148351 GCAGTAGTACCCATTCTCACATAATTA 58.852 37.037 0.00 0.00 0.00 1.40
4263 4842 2.620627 GGCCAAAAGCAGTAGTACCCAT 60.621 50.000 0.00 0.00 46.50 4.00
4265 4844 1.004394 AGGCCAAAAGCAGTAGTACCC 59.996 52.381 5.01 0.00 46.50 3.69
4285 4867 1.406341 CGGAAAATTGCCTACCCGAGA 60.406 52.381 0.00 0.00 39.31 4.04
4286 4868 1.014352 CGGAAAATTGCCTACCCGAG 58.986 55.000 0.00 0.00 39.31 4.63
4287 4869 0.614294 TCGGAAAATTGCCTACCCGA 59.386 50.000 0.00 0.00 42.92 5.14
4288 4870 1.400494 CTTCGGAAAATTGCCTACCCG 59.600 52.381 0.00 0.00 38.41 5.28
4306 4889 4.390909 ACGTAAAATTCTCGGCGATTTCTT 59.609 37.500 11.27 3.37 0.00 2.52
4313 4896 3.547601 ACAAAACGTAAAATTCTCGGCG 58.452 40.909 0.00 0.00 0.00 6.46
4327 4910 7.323895 CCATCTACACGAGATAGATACAAAACG 59.676 40.741 0.00 0.00 43.52 3.60
4338 4922 6.097696 TGAATTCAACCCATCTACACGAGATA 59.902 38.462 5.45 0.00 43.52 1.98
4354 4938 0.523335 GGCGCACGGATGAATTCAAC 60.523 55.000 13.09 9.88 0.00 3.18
4362 4946 2.512286 ATCACAGGCGCACGGATG 60.512 61.111 10.83 1.70 0.00 3.51
4371 4955 1.795162 GCATTACAACGCATCACAGGC 60.795 52.381 0.00 0.00 0.00 4.85
4401 4985 7.063191 GCATGTAGTATTGCACTATCATCTCAG 59.937 40.741 0.00 0.00 41.77 3.35
4421 5005 6.254589 GCTGCCAAATTAAATTTACGCATGTA 59.745 34.615 0.00 0.00 36.63 2.29
4422 5006 5.063312 GCTGCCAAATTAAATTTACGCATGT 59.937 36.000 0.00 0.00 36.63 3.21
4423 5007 5.291614 AGCTGCCAAATTAAATTTACGCATG 59.708 36.000 0.00 0.00 36.63 4.06
4508 5501 2.590575 CAACGTGGCAACCGGACT 60.591 61.111 9.46 0.00 35.02 3.85
4512 5505 1.298041 GTTCACAACGTGGCAACCG 60.298 57.895 0.00 0.00 33.87 4.44
4523 5516 2.646117 TAGCGGCGTGGTGTTCACAA 62.646 55.000 9.37 0.00 46.36 3.33
4536 5529 4.849329 CTCGGTCGGTGTAGCGGC 62.849 72.222 3.51 1.17 40.61 6.53
4687 5718 2.725008 CGACCCTCATCTCGCCTC 59.275 66.667 0.00 0.00 0.00 4.70
4688 5719 2.835431 CCGACCCTCATCTCGCCT 60.835 66.667 0.00 0.00 0.00 5.52
4689 5720 4.593864 GCCGACCCTCATCTCGCC 62.594 72.222 0.00 0.00 0.00 5.54
4690 5721 4.933064 CGCCGACCCTCATCTCGC 62.933 72.222 0.00 0.00 0.00 5.03
4691 5722 3.471244 GACGCCGACCCTCATCTCG 62.471 68.421 0.00 0.00 0.00 4.04
4692 5723 2.413765 GACGCCGACCCTCATCTC 59.586 66.667 0.00 0.00 0.00 2.75
4726 5757 0.319211 CTTGTCCGCGTAGAACACCA 60.319 55.000 4.92 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.