Multiple sequence alignment - TraesCS7B01G496600

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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 TraesCS7B01G496600 chr7B 100.000 2363 0 0 1 2363 747289718 747292080 0.000000e+00 4364
1 TraesCS7B01G496600 chr7B 86.660 1057 137 4 859 1913 745102808 745103862 0.000000e+00 1168
2 TraesCS7B01G496600 chr7B 84.006 619 71 15 4 612 745102198 745102798 9.480000e-159 569
3 TraesCS7B01G496600 chr7B 90.102 394 34 5 1965 2357 745104067 745104456 7.540000e-140 507
4 TraesCS7B01G496600 chr7B 75.427 586 116 21 814 1385 31795144 31794573 2.330000e-65 259
5 TraesCS7B01G496600 chr7D 87.700 1626 158 13 4 1622 633150789 633152379 0.000000e+00 1857
6 TraesCS7B01G496600 chr7D 87.700 1626 158 13 4 1622 633202998 633201408 0.000000e+00 1857
7 TraesCS7B01G496600 chr7D 88.186 1566 152 12 1 1545 633030977 633029424 0.000000e+00 1836
8 TraesCS7B01G496600 chr7D 79.741 617 48 25 1655 2241 633152377 633152946 2.220000e-100 375
9 TraesCS7B01G496600 chr7D 79.741 617 48 25 1655 2241 633201410 633200841 2.220000e-100 375
10 TraesCS7B01G496600 chr7D 91.176 204 16 1 2037 2240 633029028 633028827 2.310000e-70 276
11 TraesCS7B01G496600 chr7D 82.397 267 17 12 1779 2017 633029280 633029016 3.080000e-49 206
12 TraesCS7B01G496600 chr7D 97.647 85 2 0 2279 2363 633028834 633028750 1.890000e-31 147
13 TraesCS7B01G496600 chr7D 95.238 84 4 0 2280 2363 633152939 633153022 1.470000e-27 134
14 TraesCS7B01G496600 chr7D 95.238 84 4 0 2280 2363 633200848 633200765 1.470000e-27 134
15 TraesCS7B01G496600 chrUn 73.427 286 68 7 1074 1355 15778652 15778933 1.490000e-17 100
16 TraesCS7B01G496600 chrUn 73.427 286 68 7 1074 1355 439690791 439691072 1.490000e-17 100


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 TraesCS7B01G496600 chr7B 747289718 747292080 2362 False 4364.000000 4364 100.000000 1 2363 1 chr7B.!!$F1 2362
1 TraesCS7B01G496600 chr7B 745102198 745104456 2258 False 748.000000 1168 86.922667 4 2357 3 chr7B.!!$F2 2353
2 TraesCS7B01G496600 chr7B 31794573 31795144 571 True 259.000000 259 75.427000 814 1385 1 chr7B.!!$R1 571
3 TraesCS7B01G496600 chr7D 633150789 633153022 2233 False 788.666667 1857 87.559667 4 2363 3 chr7D.!!$F1 2359
4 TraesCS7B01G496600 chr7D 633200765 633202998 2233 True 788.666667 1857 87.559667 4 2363 3 chr7D.!!$R2 2359
5 TraesCS7B01G496600 chr7D 633028750 633030977 2227 True 616.250000 1836 89.851500 1 2363 4 chr7D.!!$R1 2362

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
784 811 0.03601 ATCCTCCCTGCAACAACTCG 60.036 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1821 0.318107 CCTGCGCAGAAAACCAACAG 60.318 55.0 38.06 13.63 0.0 3.16 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
61 62 1.081892 CCATGGACTGAAACTCTGCG 58.918 55.000 5.56 0.00 0.00 5.18
71 72 3.990092 TGAAACTCTGCGTAGTGTGAAT 58.010 40.909 8.99 0.00 31.47 2.57
120 121 5.385198 AGCTTTCCTACTCAACAAATTCCA 58.615 37.500 0.00 0.00 0.00 3.53
124 125 7.627300 GCTTTCCTACTCAACAAATTCCATCTC 60.627 40.741 0.00 0.00 0.00 2.75
127 128 6.213397 TCCTACTCAACAAATTCCATCTCTGA 59.787 38.462 0.00 0.00 0.00 3.27
129 130 7.555554 CCTACTCAACAAATTCCATCTCTGAAT 59.444 37.037 0.00 0.00 33.97 2.57
139 143 3.087031 CCATCTCTGAATGCTGTTTGGT 58.913 45.455 0.00 0.00 0.00 3.67
146 150 3.573598 TGAATGCTGTTTGGTAATTGCG 58.426 40.909 0.00 0.00 0.00 4.85
152 156 3.800604 GCTGTTTGGTAATTGCGGGAAAA 60.801 43.478 0.00 0.00 0.00 2.29
165 169 2.736400 GCGGGAAAAGATGATTTGCAGG 60.736 50.000 0.00 0.00 32.86 4.85
193 197 6.445451 AGATGAGGTGGTAGCATTCAATAT 57.555 37.500 13.70 1.50 0.00 1.28
194 198 6.471146 AGATGAGGTGGTAGCATTCAATATC 58.529 40.000 13.70 8.76 0.00 1.63
195 199 4.973168 TGAGGTGGTAGCATTCAATATCC 58.027 43.478 0.00 0.00 0.00 2.59
196 200 4.660303 TGAGGTGGTAGCATTCAATATCCT 59.340 41.667 0.00 0.00 0.00 3.24
197 201 4.978099 AGGTGGTAGCATTCAATATCCTG 58.022 43.478 0.00 0.00 0.00 3.86
198 202 4.660303 AGGTGGTAGCATTCAATATCCTGA 59.340 41.667 0.00 0.00 0.00 3.86
199 203 4.757149 GGTGGTAGCATTCAATATCCTGAC 59.243 45.833 0.00 0.00 0.00 3.51
200 204 5.368145 GTGGTAGCATTCAATATCCTGACA 58.632 41.667 0.00 0.00 0.00 3.58
201 205 6.000219 GTGGTAGCATTCAATATCCTGACAT 59.000 40.000 0.00 0.00 0.00 3.06
202 206 7.161404 GTGGTAGCATTCAATATCCTGACATA 58.839 38.462 0.00 0.00 0.00 2.29
203 207 7.826252 GTGGTAGCATTCAATATCCTGACATAT 59.174 37.037 0.00 0.00 0.00 1.78
220 224 6.154203 GACATATCCTGACATGTCTTGAGA 57.846 41.667 25.55 18.34 44.94 3.27
225 229 5.752036 TCCTGACATGTCTTGAGAATCTT 57.248 39.130 25.55 0.00 34.92 2.40
232 236 7.039434 TGACATGTCTTGAGAATCTTGTACTCT 60.039 37.037 25.55 0.00 34.92 3.24
233 237 7.095910 ACATGTCTTGAGAATCTTGTACTCTG 58.904 38.462 0.00 0.00 34.92 3.35
238 242 4.825422 TGAGAATCTTGTACTCTGCAAGG 58.175 43.478 5.39 0.00 42.44 3.61
293 297 4.054671 CTGACCTCACTGAAGAAGTTGAC 58.945 47.826 0.00 0.00 36.83 3.18
309 315 3.709653 AGTTGACTGTACTGGGTTCAGAA 59.290 43.478 10.39 0.00 43.49 3.02
335 341 3.515901 GTGATTGTAGAGGGTTCAGAGGT 59.484 47.826 0.00 0.00 0.00 3.85
382 388 2.933287 ATCTTGTGGTCCGGGGCA 60.933 61.111 0.00 0.00 0.00 5.36
431 437 1.073319 TCCTCACCCACCTCCCAAA 60.073 57.895 0.00 0.00 0.00 3.28
439 445 1.685820 CACCTCCCAAACCTCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
454 460 5.699143 ACCTCTCCCAATTGGAAATCATAG 58.301 41.667 26.60 11.86 44.57 2.23
514 520 1.746760 GCAACAAGCAACGTCAGAAG 58.253 50.000 0.00 0.00 44.79 2.85
515 521 1.746760 CAACAAGCAACGTCAGAAGC 58.253 50.000 0.00 0.00 0.00 3.86
517 523 0.940126 ACAAGCAACGTCAGAAGCAG 59.060 50.000 0.00 0.00 0.00 4.24
557 572 6.114767 AGGAGAAAGAAGAAGATGATTCAGC 58.885 40.000 0.00 0.00 0.00 4.26
588 603 0.693430 TGCCTGCCCATCTCTCTGAT 60.693 55.000 0.00 0.00 35.40 2.90
598 613 3.132467 CCATCTCTCTGATTCACTGCAGA 59.868 47.826 23.35 0.00 38.72 4.26
698 725 2.592993 CCCTGCCGTCCCTCAAGAA 61.593 63.158 0.00 0.00 0.00 2.52
699 726 1.078848 CCTGCCGTCCCTCAAGAAG 60.079 63.158 0.00 0.00 0.00 2.85
700 727 1.674057 CTGCCGTCCCTCAAGAAGT 59.326 57.895 0.00 0.00 0.00 3.01
710 737 6.142817 CGTCCCTCAAGAAGTTACAAATTTG 58.857 40.000 16.67 16.67 0.00 2.32
713 740 6.264518 TCCCTCAAGAAGTTACAAATTTGGTC 59.735 38.462 21.74 11.27 0.00 4.02
718 745 5.140454 AGAAGTTACAAATTTGGTCCTGCT 58.860 37.500 21.74 13.76 0.00 4.24
720 747 3.826729 AGTTACAAATTTGGTCCTGCTCC 59.173 43.478 21.74 0.40 0.00 4.70
736 763 2.297315 TGCTCCAAGATACTATCCGCAG 59.703 50.000 0.00 0.00 0.00 5.18
771 798 1.039785 GCTGCCCTTTTCCATCCTCC 61.040 60.000 0.00 0.00 0.00 4.30
780 807 0.776810 TTCCATCCTCCCTGCAACAA 59.223 50.000 0.00 0.00 0.00 2.83
784 811 0.036010 ATCCTCCCTGCAACAACTCG 60.036 55.000 0.00 0.00 0.00 4.18
785 812 1.071471 CCTCCCTGCAACAACTCGT 59.929 57.895 0.00 0.00 0.00 4.18
787 814 0.868406 CTCCCTGCAACAACTCGTTC 59.132 55.000 0.00 0.00 34.86 3.95
806 833 0.890996 CTTGAGGGTGTGGAAGGCAC 60.891 60.000 0.00 0.00 36.22 5.01
809 836 4.265056 GGGTGTGGAAGGCACGGT 62.265 66.667 0.00 0.00 37.70 4.83
816 843 2.047179 GAAGGCACGGTGACCCTC 60.047 66.667 11.09 4.02 0.00 4.30
831 858 1.075896 CCTCGGGCCTCTCCTTACT 60.076 63.158 0.84 0.00 34.39 2.24
841 868 0.118346 TCTCCTTACTGCTGGGGGAA 59.882 55.000 0.00 0.00 0.00 3.97
850 877 1.144503 CTGCTGGGGGAAAGCTCATAT 59.855 52.381 0.00 0.00 41.42 1.78
851 878 1.133699 TGCTGGGGGAAAGCTCATATG 60.134 52.381 0.00 0.00 41.42 1.78
856 883 3.138283 TGGGGGAAAGCTCATATGGTTAG 59.862 47.826 2.13 0.00 0.00 2.34
857 884 3.138468 GGGGGAAAGCTCATATGGTTAGT 59.862 47.826 2.13 0.00 0.00 2.24
900 927 3.333381 TCTTTGTTGGATGGGATCAGGAA 59.667 43.478 0.00 0.00 0.00 3.36
907 937 2.158564 GGATGGGATCAGGAATTGCAGA 60.159 50.000 0.00 0.00 0.00 4.26
912 942 3.434167 GGGATCAGGAATTGCAGAAGCTA 60.434 47.826 0.00 0.00 42.74 3.32
954 987 1.066002 GAACTGCAGCAGCTTGTTTCA 59.934 47.619 23.05 0.00 42.74 2.69
959 992 0.825010 CAGCAGCTTGTTTCACCCCT 60.825 55.000 0.00 0.00 0.00 4.79
976 1009 2.173519 CCCTGAATGGATGCAAACTGT 58.826 47.619 0.00 0.00 38.35 3.55
1013 1046 2.421725 TGATGCCATGGGACTCCTATT 58.578 47.619 15.13 0.00 0.00 1.73
1031 1064 0.758310 TTTGTGCCCATCTGCAACCA 60.758 50.000 0.00 0.00 44.11 3.67
1035 1068 2.048603 GCCCATCTGCAACCACCTC 61.049 63.158 0.00 0.00 0.00 3.85
1125 1158 2.050350 CGCCCTTCACCTCCTCGTA 61.050 63.158 0.00 0.00 0.00 3.43
1127 1160 1.700955 GCCCTTCACCTCCTCGTATA 58.299 55.000 0.00 0.00 0.00 1.47
1134 1167 2.242965 TCACCTCCTCGTATACCTCCAA 59.757 50.000 0.00 0.00 0.00 3.53
1142 1175 7.243604 TCCTCGTATACCTCCAAAAACTAAA 57.756 36.000 0.00 0.00 0.00 1.85
1155 1188 9.946165 CTCCAAAAACTAAAGTTTATCGACTTT 57.054 29.630 8.45 7.96 46.47 2.66
1167 1200 6.426937 AGTTTATCGACTTTAGCAAGCTTCAA 59.573 34.615 0.00 0.00 32.57 2.69
1230 1263 5.244178 GGAATTATCGGTCTACTCATGTCCT 59.756 44.000 0.00 0.00 0.00 3.85
1239 1272 1.048601 ACTCATGTCCTGTTGTCCGT 58.951 50.000 0.00 0.00 0.00 4.69
1303 1336 0.105964 TGTCAAGTACTGCGGCAACT 59.894 50.000 3.44 2.37 0.00 3.16
1340 1373 0.912487 TGCGAGGGGTTAGTGGGAAT 60.912 55.000 0.00 0.00 0.00 3.01
1359 1392 5.082425 GGAATCATCCCAAATATCAGGCTT 58.918 41.667 0.00 0.00 40.10 4.35
1411 1444 2.791655 CTACTTCCTTGTTTGTCCCCC 58.208 52.381 0.00 0.00 0.00 5.40
1412 1445 0.930726 ACTTCCTTGTTTGTCCCCCA 59.069 50.000 0.00 0.00 0.00 4.96
1413 1446 1.503347 ACTTCCTTGTTTGTCCCCCAT 59.497 47.619 0.00 0.00 0.00 4.00
1414 1447 2.090775 ACTTCCTTGTTTGTCCCCCATT 60.091 45.455 0.00 0.00 0.00 3.16
1415 1448 2.008242 TCCTTGTTTGTCCCCCATTG 57.992 50.000 0.00 0.00 0.00 2.82
1419 1452 1.799933 TGTTTGTCCCCCATTGCTTT 58.200 45.000 0.00 0.00 0.00 3.51
1420 1453 2.964209 TGTTTGTCCCCCATTGCTTTA 58.036 42.857 0.00 0.00 0.00 1.85
1515 1551 1.201429 TCTCAGCCTTGGAGTTCCCC 61.201 60.000 0.00 0.00 34.04 4.81
1568 1604 1.951209 TAGATGAGGGTCTTGTGGCA 58.049 50.000 0.00 0.00 0.00 4.92
1588 1624 5.125417 TGGCAAGCTTCTTGTACATAAATCC 59.875 40.000 0.00 0.00 0.00 3.01
1597 1633 9.760077 CTTCTTGTACATAAATCCGGTAAGTAT 57.240 33.333 0.00 0.00 0.00 2.12
1624 1663 9.185680 ACATCTAACTTAAAAGTTTGTTCCTGT 57.814 29.630 12.96 10.53 46.52 4.00
1640 1679 8.815141 TTGTTCCTGTTGTTTCATATCAATTG 57.185 30.769 0.00 0.00 0.00 2.32
1641 1680 6.867816 TGTTCCTGTTGTTTCATATCAATTGC 59.132 34.615 0.00 0.00 0.00 3.56
1648 1687 8.791675 TGTTGTTTCATATCAATTGCTAAGACA 58.208 29.630 0.00 0.00 0.00 3.41
1666 1705 4.631234 AGACATGTTATCCACTCCCCTTA 58.369 43.478 0.00 0.00 0.00 2.69
1667 1706 4.409247 AGACATGTTATCCACTCCCCTTAC 59.591 45.833 0.00 0.00 0.00 2.34
1682 1721 3.118592 CCCCTTACCTTCTCACTCACATC 60.119 52.174 0.00 0.00 0.00 3.06
1743 1783 8.932945 ATGAAGTTTCTTTGTTTTTCTTCCTC 57.067 30.769 0.00 0.00 31.90 3.71
1749 1789 6.119144 TCTTTGTTTTTCTTCCTCGACAAG 57.881 37.500 0.00 0.00 0.00 3.16
1753 1793 6.693315 TGTTTTTCTTCCTCGACAAGAATT 57.307 33.333 13.21 0.00 39.16 2.17
1773 1813 7.752695 AGAATTGTGAAATCGGTCTTGTATTC 58.247 34.615 0.00 0.00 0.00 1.75
1776 1816 4.693566 TGTGAAATCGGTCTTGTATTCACC 59.306 41.667 12.33 0.00 43.57 4.02
1777 1817 4.693566 GTGAAATCGGTCTTGTATTCACCA 59.306 41.667 5.40 0.00 40.25 4.17
1781 1821 6.436843 AATCGGTCTTGTATTCACCATTTC 57.563 37.500 0.00 0.00 0.00 2.17
1783 1823 4.935205 TCGGTCTTGTATTCACCATTTCTG 59.065 41.667 0.00 0.00 0.00 3.02
1784 1824 4.695455 CGGTCTTGTATTCACCATTTCTGT 59.305 41.667 0.00 0.00 0.00 3.41
1795 1835 3.803778 CACCATTTCTGTTGGTTTTCTGC 59.196 43.478 0.00 0.00 45.19 4.26
1820 1861 4.020218 CAGGTGTTCTTCTCATAGGGTTCA 60.020 45.833 0.00 0.00 0.00 3.18
1823 1864 5.305585 GTGTTCTTCTCATAGGGTTCAACA 58.694 41.667 0.00 0.00 0.00 3.33
1889 1930 7.994334 AGATTCGATGGTCTACTAAGTAGTTCT 59.006 37.037 0.00 0.00 37.41 3.01
1895 1936 5.709164 TGGTCTACTAAGTAGTTCTGGTGTC 59.291 44.000 0.00 0.00 37.41 3.67
1942 2011 8.997323 CAGAAGCCTTATTGATATTACCAGAAG 58.003 37.037 0.00 0.00 0.00 2.85
1985 2181 8.318412 ACACAAATCTGGTATGTACATCTAACA 58.682 33.333 12.68 3.74 0.00 2.41
2023 2219 8.321353 CCTGATCTGCCATATACCAGTTATAAA 58.679 37.037 0.00 0.00 0.00 1.40
2039 2235 8.842280 CCAGTTATAAAAACTTCCACTTGTACA 58.158 33.333 0.00 0.00 0.00 2.90
2222 2418 7.605410 TTACTTCCTGGACGAAAATCATAAC 57.395 36.000 7.25 0.00 0.00 1.89
2225 2421 4.900684 TCCTGGACGAAAATCATAACACA 58.099 39.130 0.00 0.00 0.00 3.72
2226 2422 5.496556 TCCTGGACGAAAATCATAACACAT 58.503 37.500 0.00 0.00 0.00 3.21
2236 2432 9.986833 CGAAAATCATAACACATCTTTCATGTA 57.013 29.630 0.00 0.00 0.00 2.29
2252 2448 8.637099 TCTTTCATGTATTCACCATTTGTTTCA 58.363 29.630 0.00 0.00 0.00 2.69
2260 2456 9.313118 GTATTCACCATTTGTTTCAGTTTTCTT 57.687 29.630 0.00 0.00 0.00 2.52
2305 2501 7.770433 TGTACTCGTAGGCTTCTACATACTTTA 59.230 37.037 0.00 0.00 42.55 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 5.767816 TTGTTGAGTAGGAAAGCTTTTCC 57.232 39.130 14.05 15.10 38.86 3.13
95 96 6.323739 TGGAATTTGTTGAGTAGGAAAGCTTT 59.676 34.615 12.53 12.53 0.00 3.51
102 103 6.213397 TCAGAGATGGAATTTGTTGAGTAGGA 59.787 38.462 0.00 0.00 0.00 2.94
103 104 6.409704 TCAGAGATGGAATTTGTTGAGTAGG 58.590 40.000 0.00 0.00 0.00 3.18
104 105 7.912056 TTCAGAGATGGAATTTGTTGAGTAG 57.088 36.000 0.00 0.00 0.00 2.57
120 121 6.626623 GCAATTACCAAACAGCATTCAGAGAT 60.627 38.462 0.00 0.00 0.00 2.75
124 125 3.609373 CGCAATTACCAAACAGCATTCAG 59.391 43.478 0.00 0.00 0.00 3.02
127 128 2.353605 CCCGCAATTACCAAACAGCATT 60.354 45.455 0.00 0.00 0.00 3.56
129 130 0.600557 CCCGCAATTACCAAACAGCA 59.399 50.000 0.00 0.00 0.00 4.41
139 143 5.108517 GCAAATCATCTTTTCCCGCAATTA 58.891 37.500 0.00 0.00 0.00 1.40
146 150 2.419159 GCCCTGCAAATCATCTTTTCCC 60.419 50.000 0.00 0.00 0.00 3.97
152 156 3.939740 TCTAAGCCCTGCAAATCATCT 57.060 42.857 0.00 0.00 0.00 2.90
165 169 1.762957 TGCTACCACCTCATCTAAGCC 59.237 52.381 0.00 0.00 0.00 4.35
198 202 6.550938 TTCTCAAGACATGTCAGGATATGT 57.449 37.500 27.02 10.85 44.19 2.29
199 203 7.443477 AGATTCTCAAGACATGTCAGGATATG 58.557 38.462 27.02 14.78 36.22 1.78
200 204 7.615039 AGATTCTCAAGACATGTCAGGATAT 57.385 36.000 27.02 17.33 0.00 1.63
201 205 7.093156 ACAAGATTCTCAAGACATGTCAGGATA 60.093 37.037 27.02 13.35 0.00 2.59
202 206 5.954153 AGATTCTCAAGACATGTCAGGAT 57.046 39.130 27.02 15.78 0.00 3.24
203 207 5.012458 ACAAGATTCTCAAGACATGTCAGGA 59.988 40.000 27.02 20.75 0.00 3.86
220 224 2.619074 GGCCCTTGCAGAGTACAAGATT 60.619 50.000 5.12 0.00 45.99 2.40
225 229 1.841302 CTGGGCCCTTGCAGAGTACA 61.841 60.000 25.70 0.00 40.13 2.90
232 236 4.355720 CAGAGCTGGGCCCTTGCA 62.356 66.667 31.67 10.87 40.13 4.08
238 242 3.557903 TTGACTGCAGAGCTGGGCC 62.558 63.158 23.35 0.00 0.00 5.80
293 297 2.368875 ACACCTTCTGAACCCAGTACAG 59.631 50.000 0.00 0.00 41.16 2.74
309 315 3.248024 TGAACCCTCTACAATCACACCT 58.752 45.455 0.00 0.00 0.00 4.00
335 341 0.889994 GTGCTGCCATTCCACATCAA 59.110 50.000 0.00 0.00 0.00 2.57
377 383 2.046285 CCACGTGATTCCTTGCCCC 61.046 63.158 19.30 0.00 0.00 5.80
382 388 1.358152 TCCTTCCCACGTGATTCCTT 58.642 50.000 19.30 0.00 0.00 3.36
454 460 6.363357 GCCAGTTGTGTTATCTTTTCACATTC 59.637 38.462 0.00 0.00 40.85 2.67
502 508 1.206072 CTGCTGCTTCTGACGTTGC 59.794 57.895 0.00 0.00 0.00 4.17
514 520 2.510238 CACCTCCGTAGCTGCTGC 60.510 66.667 13.43 10.46 40.05 5.25
515 521 2.185350 CCACCTCCGTAGCTGCTG 59.815 66.667 13.43 0.00 0.00 4.41
517 523 2.496817 CTCCACCTCCGTAGCTGC 59.503 66.667 0.00 0.00 0.00 5.25
588 603 2.259266 TGCTCAACATCTGCAGTGAA 57.741 45.000 14.67 0.00 32.55 3.18
598 613 3.693085 GGACAACTCATGATGCTCAACAT 59.307 43.478 0.00 0.00 43.54 2.71
644 659 4.277476 TCTGGCAGGAAGAAAAGTTGAAA 58.723 39.130 15.73 0.00 0.00 2.69
686 713 5.941948 AATTTGTAACTTCTTGAGGGACG 57.058 39.130 0.00 0.00 0.00 4.79
698 725 3.826729 GGAGCAGGACCAAATTTGTAACT 59.173 43.478 16.73 8.38 0.00 2.24
699 726 3.572255 TGGAGCAGGACCAAATTTGTAAC 59.428 43.478 16.73 6.32 34.25 2.50
700 727 3.838565 TGGAGCAGGACCAAATTTGTAA 58.161 40.909 16.73 0.00 34.25 2.41
710 737 3.259625 GGATAGTATCTTGGAGCAGGACC 59.740 52.174 9.97 0.00 0.00 4.46
713 740 2.353208 GCGGATAGTATCTTGGAGCAGG 60.353 54.545 9.97 0.00 0.00 4.85
718 745 4.075682 CTCTCTGCGGATAGTATCTTGGA 58.924 47.826 9.97 4.00 0.00 3.53
720 747 5.240623 AGAACTCTCTGCGGATAGTATCTTG 59.759 44.000 13.48 4.64 30.31 3.02
736 763 1.473080 GCAGCAGGATGGAGAACTCTC 60.473 57.143 0.00 0.00 42.14 3.20
771 798 1.939934 TCAAGAACGAGTTGTTGCAGG 59.060 47.619 17.56 0.00 42.09 4.85
780 807 0.393077 CCACACCCTCAAGAACGAGT 59.607 55.000 0.00 0.00 0.00 4.18
784 811 1.897560 CCTTCCACACCCTCAAGAAC 58.102 55.000 0.00 0.00 0.00 3.01
785 812 0.110486 GCCTTCCACACCCTCAAGAA 59.890 55.000 0.00 0.00 0.00 2.52
787 814 0.890996 GTGCCTTCCACACCCTCAAG 60.891 60.000 0.00 0.00 44.06 3.02
809 836 4.779733 GGAGAGGCCCGAGGGTCA 62.780 72.222 15.96 0.00 43.56 4.02
816 843 2.060980 AGCAGTAAGGAGAGGCCCG 61.061 63.158 0.00 0.00 37.37 6.13
831 858 1.133699 CATATGAGCTTTCCCCCAGCA 60.134 52.381 0.00 0.00 39.99 4.41
841 868 5.824624 CACCAATGACTAACCATATGAGCTT 59.175 40.000 3.65 0.00 0.00 3.74
850 877 1.886222 GCAGCCACCAATGACTAACCA 60.886 52.381 0.00 0.00 0.00 3.67
851 878 0.811281 GCAGCCACCAATGACTAACC 59.189 55.000 0.00 0.00 0.00 2.85
856 883 2.036256 AGGGCAGCCACCAATGAC 59.964 61.111 15.19 0.00 0.00 3.06
857 884 2.036098 CAGGGCAGCCACCAATGA 59.964 61.111 15.19 0.00 0.00 2.57
900 927 4.197750 CTCCATTCTGTAGCTTCTGCAAT 58.802 43.478 0.00 0.00 42.74 3.56
907 937 5.495640 CTCTTTTCCTCCATTCTGTAGCTT 58.504 41.667 0.00 0.00 0.00 3.74
912 942 3.560882 CCTGCTCTTTTCCTCCATTCTGT 60.561 47.826 0.00 0.00 0.00 3.41
954 987 1.077663 AGTTTGCATCCATTCAGGGGT 59.922 47.619 0.00 0.00 38.24 4.95
959 992 4.264253 CTCCTACAGTTTGCATCCATTCA 58.736 43.478 0.00 0.00 0.00 2.57
976 1009 3.513119 GCATCATCTGTATGGAGCTCCTA 59.487 47.826 32.28 19.38 36.82 2.94
1013 1046 1.152589 TGGTTGCAGATGGGCACAA 60.153 52.632 0.00 0.00 44.86 3.33
1031 1064 0.041982 GGTGAGGGAGGAAGAGAGGT 59.958 60.000 0.00 0.00 0.00 3.85
1035 1068 0.689412 GGAGGGTGAGGGAGGAAGAG 60.689 65.000 0.00 0.00 0.00 2.85
1125 1158 9.729281 TCGATAAACTTTAGTTTTTGGAGGTAT 57.271 29.630 12.62 0.00 45.07 2.73
1127 1160 7.718314 AGTCGATAAACTTTAGTTTTTGGAGGT 59.282 33.333 12.62 1.62 45.07 3.85
1142 1175 5.932303 TGAAGCTTGCTAAAGTCGATAAACT 59.068 36.000 2.10 0.00 35.69 2.66
1197 1230 5.437191 AGACCGATAATTCCTTGAGGTTT 57.563 39.130 0.00 0.00 36.34 3.27
1230 1263 2.970324 GGCAGCGAACGGACAACA 60.970 61.111 0.00 0.00 0.00 3.33
1239 1272 2.586245 CCATCCTCTGGCAGCGAA 59.414 61.111 10.34 0.00 38.47 4.70
1289 1322 2.214181 CTCCGAGTTGCCGCAGTACT 62.214 60.000 0.00 0.00 0.00 2.73
1340 1373 5.833131 GGTTAAAGCCTGATATTTGGGATGA 59.167 40.000 0.00 0.00 0.00 2.92
1350 1383 3.767673 AGTCTCACGGTTAAAGCCTGATA 59.232 43.478 0.00 0.00 0.00 2.15
1355 1388 2.450609 TCAGTCTCACGGTTAAAGCC 57.549 50.000 0.00 0.00 0.00 4.35
1356 1389 2.930682 GGATCAGTCTCACGGTTAAAGC 59.069 50.000 0.00 0.00 0.00 3.51
1359 1392 3.056107 CCTTGGATCAGTCTCACGGTTAA 60.056 47.826 0.00 0.00 0.00 2.01
1411 1444 4.380867 GGTTGTGGGATCTGTAAAGCAATG 60.381 45.833 0.00 0.00 0.00 2.82
1412 1445 3.763897 GGTTGTGGGATCTGTAAAGCAAT 59.236 43.478 0.00 0.00 0.00 3.56
1413 1446 3.153919 GGTTGTGGGATCTGTAAAGCAA 58.846 45.455 0.00 0.00 0.00 3.91
1414 1447 2.107378 TGGTTGTGGGATCTGTAAAGCA 59.893 45.455 0.00 0.00 0.00 3.91
1415 1448 2.488153 GTGGTTGTGGGATCTGTAAAGC 59.512 50.000 0.00 0.00 0.00 3.51
1419 1452 0.988832 GGGTGGTTGTGGGATCTGTA 59.011 55.000 0.00 0.00 0.00 2.74
1420 1453 0.772124 AGGGTGGTTGTGGGATCTGT 60.772 55.000 0.00 0.00 0.00 3.41
1500 1535 0.178873 TACAGGGGAACTCCAAGGCT 60.179 55.000 0.00 0.00 37.91 4.58
1515 1551 6.631016 TGTACAAGGCTAGAAGAATGTACAG 58.369 40.000 17.58 0.00 44.64 2.74
1568 1604 5.497474 ACCGGATTTATGTACAAGAAGCTT 58.503 37.500 9.46 0.00 0.00 3.74
1613 1652 8.816640 ATTGATATGAAACAACAGGAACAAAC 57.183 30.769 0.00 0.00 0.00 2.93
1618 1657 7.230849 AGCAATTGATATGAAACAACAGGAA 57.769 32.000 10.34 0.00 0.00 3.36
1624 1663 9.791820 CATGTCTTAGCAATTGATATGAAACAA 57.208 29.630 17.74 7.56 33.22 2.83
1640 1679 4.381411 GGGAGTGGATAACATGTCTTAGC 58.619 47.826 0.00 0.00 0.00 3.09
1641 1680 4.656112 AGGGGAGTGGATAACATGTCTTAG 59.344 45.833 0.00 0.00 0.00 2.18
1648 1687 4.022359 AGGTAAGGGGAGTGGATAACAT 57.978 45.455 0.00 0.00 0.00 2.71
1653 1692 2.045885 TGAGAAGGTAAGGGGAGTGGAT 59.954 50.000 0.00 0.00 0.00 3.41
1682 1721 8.517878 ACTGATAATCACACCATTTTTCTCAAG 58.482 33.333 0.00 0.00 0.00 3.02
1692 1731 5.994250 AGCACTAACTGATAATCACACCAT 58.006 37.500 0.00 0.00 0.00 3.55
1693 1732 5.420725 AGCACTAACTGATAATCACACCA 57.579 39.130 0.00 0.00 0.00 4.17
1743 1783 4.152402 AGACCGATTTCACAATTCTTGTCG 59.848 41.667 0.00 0.00 43.23 4.35
1749 1789 7.481798 GTGAATACAAGACCGATTTCACAATTC 59.518 37.037 8.32 0.00 41.44 2.17
1753 1793 4.693566 GGTGAATACAAGACCGATTTCACA 59.306 41.667 13.61 0.00 42.81 3.58
1761 1801 4.695455 ACAGAAATGGTGAATACAAGACCG 59.305 41.667 0.00 0.00 0.00 4.79
1776 1816 2.472488 GCGCAGAAAACCAACAGAAATG 59.528 45.455 0.30 0.00 0.00 2.32
1777 1817 2.100584 TGCGCAGAAAACCAACAGAAAT 59.899 40.909 5.66 0.00 0.00 2.17
1781 1821 0.318107 CCTGCGCAGAAAACCAACAG 60.318 55.000 38.06 13.63 0.00 3.16
1783 1823 0.594796 CACCTGCGCAGAAAACCAAC 60.595 55.000 38.06 0.00 0.00 3.77
1784 1824 1.034838 ACACCTGCGCAGAAAACCAA 61.035 50.000 38.06 0.00 0.00 3.67
1795 1835 2.544685 CCTATGAGAAGAACACCTGCG 58.455 52.381 0.00 0.00 0.00 5.18
1823 1864 5.149973 TCCAAATGTACATGCAAAAGCAT 57.850 34.783 9.63 0.00 0.00 3.79
1911 1952 8.376270 GGTAATATCAATAAGGCTTCTGGTAGT 58.624 37.037 1.30 5.42 0.00 2.73
1913 1954 8.270137 TGGTAATATCAATAAGGCTTCTGGTA 57.730 34.615 1.30 3.76 0.00 3.25
1914 1955 7.072454 TCTGGTAATATCAATAAGGCTTCTGGT 59.928 37.037 1.30 1.24 0.00 4.00
1915 1956 7.453393 TCTGGTAATATCAATAAGGCTTCTGG 58.547 38.462 1.30 0.00 0.00 3.86
1916 1957 8.908786 TTCTGGTAATATCAATAAGGCTTCTG 57.091 34.615 1.30 2.67 0.00 3.02
1917 1958 7.663493 GCTTCTGGTAATATCAATAAGGCTTCT 59.337 37.037 1.30 0.00 0.00 2.85
1918 1959 7.094592 GGCTTCTGGTAATATCAATAAGGCTTC 60.095 40.741 1.30 0.00 35.92 3.86
1919 1960 6.717084 GGCTTCTGGTAATATCAATAAGGCTT 59.283 38.462 4.58 4.58 35.92 4.35
1942 2011 2.565834 TGTGTACAGGAAGGTAGAAGGC 59.434 50.000 0.00 0.00 0.00 4.35
2005 2201 9.127277 TGGAAGTTTTTATAACTGGTATATGGC 57.873 33.333 0.00 0.00 0.00 4.40
2122 2318 3.845178 TGTATGTACGAAGACAAGGCAG 58.155 45.455 0.00 0.00 31.83 4.85
2166 2362 9.686683 AGAAACTCACATAAGGCATTAACTAAT 57.313 29.630 0.00 0.00 0.00 1.73
2168 2364 9.515226 AAAGAAACTCACATAAGGCATTAACTA 57.485 29.630 0.00 0.00 0.00 2.24
2184 2380 6.887545 TCCAGGAAGTAAAACAAAGAAACTCA 59.112 34.615 0.00 0.00 0.00 3.41
2222 2418 8.030692 ACAAATGGTGAATACATGAAAGATGTG 58.969 33.333 0.00 0.00 33.76 3.21
2225 2421 9.643693 GAAACAAATGGTGAATACATGAAAGAT 57.356 29.630 0.00 0.00 0.00 2.40
2226 2422 8.637099 TGAAACAAATGGTGAATACATGAAAGA 58.363 29.630 0.00 0.00 0.00 2.52
2236 2432 8.667463 CAAAGAAAACTGAAACAAATGGTGAAT 58.333 29.630 0.00 0.00 0.00 2.57
2237 2433 7.360776 GCAAAGAAAACTGAAACAAATGGTGAA 60.361 33.333 0.00 0.00 0.00 3.18
2252 2448 6.096846 ACATAAGAACACCTGCAAAGAAAACT 59.903 34.615 0.00 0.00 0.00 2.66
2260 2456 5.825679 AGTACAAACATAAGAACACCTGCAA 59.174 36.000 0.00 0.00 0.00 4.08
2305 2501 6.377146 AGTGATGGCTACCGAAATTTAAATGT 59.623 34.615 0.39 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.