Multiple sequence alignment - TraesCS5A01G372800

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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 TraesCS5A01G372800 chr5A 100.000 2487 0 0 1 2487 570936140 570938626 0.000000e+00 4593.0
1 TraesCS5A01G372800 chr5A 75.844 563 113 21 1939 2487 611341847 611341294 5.270000e-67 265.0
2 TraesCS5A01G372800 chr5D 89.390 2083 138 37 461 2485 452216042 452218099 0.000000e+00 2545.0
3 TraesCS5A01G372800 chr5D 84.194 968 84 29 1 938 451978185 451979113 0.000000e+00 876.0
4 TraesCS5A01G372800 chr5D 80.046 431 57 23 1 424 452215633 452216041 2.420000e-75 292.0
5 TraesCS5A01G372800 chr5D 75.666 563 107 26 1939 2485 489777052 489776504 1.140000e-63 254.0
6 TraesCS5A01G372800 chr5D 95.455 44 1 1 922 964 451979316 451979359 4.440000e-08 69.4
7 TraesCS5A01G372800 chr5B 86.648 2112 149 65 461 2485 552292570 552294635 0.000000e+00 2215.0
8 TraesCS5A01G372800 chr5B 84.990 1006 94 34 1 964 551807279 551808269 0.000000e+00 968.0
9 TraesCS5A01G372800 chrUn 87.709 179 20 2 1 177 62126616 62126794 9.010000e-50 207.0
10 TraesCS5A01G372800 chr7A 87.709 179 20 2 1 177 315704518 315704696 9.010000e-50 207.0
11 TraesCS5A01G372800 chr7B 87.151 179 21 2 1 177 614366058 614365880 4.190000e-48 202.0
12 TraesCS5A01G372800 chr4B 86.813 182 22 2 1 180 509510930 509510749 4.190000e-48 202.0
13 TraesCS5A01G372800 chr4A 87.151 179 21 2 1 177 216408540 216408718 4.190000e-48 202.0
14 TraesCS5A01G372800 chr6A 86.034 179 23 2 1 177 204398483 204398305 9.080000e-45 191.0


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 TraesCS5A01G372800 chr5A 570936140 570938626 2486 False 4593.0 4593 100.0000 1 2487 1 chr5A.!!$F1 2486
1 TraesCS5A01G372800 chr5A 611341294 611341847 553 True 265.0 265 75.8440 1939 2487 1 chr5A.!!$R1 548
2 TraesCS5A01G372800 chr5D 452215633 452218099 2466 False 1418.5 2545 84.7180 1 2485 2 chr5D.!!$F2 2484
3 TraesCS5A01G372800 chr5D 451978185 451979359 1174 False 472.7 876 89.8245 1 964 2 chr5D.!!$F1 963
4 TraesCS5A01G372800 chr5D 489776504 489777052 548 True 254.0 254 75.6660 1939 2485 1 chr5D.!!$R1 546
5 TraesCS5A01G372800 chr5B 552292570 552294635 2065 False 2215.0 2215 86.6480 461 2485 1 chr5B.!!$F2 2024
6 TraesCS5A01G372800 chr5B 551807279 551808269 990 False 968.0 968 84.9900 1 964 1 chr5B.!!$F1 963

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
556 580 0.179119 ATCGAAAACCTAGGCGACGG 60.179 55.0 9.3 0.0 35.44 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2293 0.469494 AGGGTTGGGCAAGCTTTTTG 59.531 50.0 0.0 0.0 38.72 2.44 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
42 43 8.718102 ATGTACACCTACAAGACATATCAAAC 57.282 34.615 0.00 0.00 36.43 2.93
105 108 5.632034 ACCCAGGAAATCCTAGTAATCAC 57.368 43.478 0.70 0.00 46.65 3.06
109 112 6.284459 CCAGGAAATCCTAGTAATCACTCAC 58.716 44.000 0.70 0.00 46.65 3.51
129 132 1.331854 CGCGGCACAAACAAAACATTG 60.332 47.619 0.00 0.00 0.00 2.82
185 191 3.533606 ATGACGAGAAACCTCATGGAG 57.466 47.619 0.00 0.00 37.04 3.86
187 193 0.976641 ACGAGAAACCTCATGGAGCA 59.023 50.000 0.00 0.00 37.04 4.26
213 219 6.884295 TCCCAAGTTAGGAATAATCACAACTG 59.116 38.462 0.00 0.00 33.73 3.16
234 240 4.528920 TGGTAATTCCTAAATGAACCCCG 58.471 43.478 0.00 0.00 33.63 5.73
263 270 1.098869 TGCGAGCAGAAACAAAACCA 58.901 45.000 0.00 0.00 0.00 3.67
292 300 0.830648 TCATCCCTCGTCAATCCACC 59.169 55.000 0.00 0.00 0.00 4.61
333 341 6.311690 GTCTAAGAAATGGGAACTTCTTCTCG 59.688 42.308 0.57 0.00 40.27 4.04
343 351 3.393089 ACTTCTTCTCGCATCAGTTGT 57.607 42.857 0.00 0.00 0.00 3.32
344 352 3.733337 ACTTCTTCTCGCATCAGTTGTT 58.267 40.909 0.00 0.00 0.00 2.83
346 354 5.297547 ACTTCTTCTCGCATCAGTTGTTAA 58.702 37.500 0.00 0.00 0.00 2.01
347 355 5.758296 ACTTCTTCTCGCATCAGTTGTTAAA 59.242 36.000 0.00 0.00 0.00 1.52
349 357 4.149922 TCTTCTCGCATCAGTTGTTAAACG 59.850 41.667 0.00 0.00 41.45 3.60
355 363 4.723862 CGCATCAGTTGTTAAACGATTAGC 59.276 41.667 0.00 0.00 41.45 3.09
373 386 1.129326 GCGCAGGCAATACTACTACG 58.871 55.000 0.30 0.00 39.62 3.51
395 408 2.789208 CATGATTCGCGAGCAACAAAT 58.211 42.857 9.59 0.00 0.00 2.32
425 438 4.339872 AGCAGCAGAAATCCAGATCTAG 57.660 45.455 0.00 0.00 0.00 2.43
440 453 4.455533 CAGATCTAGCAGATTCTACGAGCT 59.544 45.833 0.00 0.00 34.53 4.09
449 462 1.978712 TTCTACGAGCTGCGAGGACG 61.979 60.000 11.64 0.13 44.57 4.79
453 466 1.355563 CGAGCTGCGAGGACGATTA 59.644 57.895 0.00 0.00 44.57 1.75
458 471 0.317103 CTGCGAGGACGATTACTCCG 60.317 60.000 0.00 0.00 42.66 4.63
495 508 1.336440 CACCGCAGATCTGACTAGGAG 59.664 57.143 27.04 16.09 0.00 3.69
517 531 0.750546 GCTAAACCCTAAAGCCCCGG 60.751 60.000 0.00 0.00 0.00 5.73
556 580 0.179119 ATCGAAAACCTAGGCGACGG 60.179 55.000 9.30 0.00 35.44 4.79
623 661 1.679977 GCAGCAGCCATGGAGGAAA 60.680 57.895 18.40 0.00 41.22 3.13
629 667 1.283029 CAGCCATGGAGGAAAAGGAGA 59.717 52.381 18.40 0.00 41.22 3.71
630 668 1.563410 AGCCATGGAGGAAAAGGAGAG 59.437 52.381 18.40 0.00 41.22 3.20
631 669 2.021208 GCCATGGAGGAAAAGGAGAGC 61.021 57.143 18.40 0.00 41.22 4.09
634 672 2.030027 TGGAGGAAAAGGAGAGCAGA 57.970 50.000 0.00 0.00 0.00 4.26
639 677 1.209261 GGAAAAGGAGAGCAGAGGAGG 59.791 57.143 0.00 0.00 0.00 4.30
654 692 0.750911 GGAGGTCGGACGTACCATCT 60.751 60.000 8.64 0.00 39.64 2.90
837 904 2.436824 GGCCTCTTTCGGTCTGCC 60.437 66.667 0.00 0.00 0.00 4.85
867 934 0.517316 ATGAGCTGCGTTTCGGTTTC 59.483 50.000 0.00 0.00 0.00 2.78
875 948 1.776897 GCGTTTCGGTTTCTTTTTCCG 59.223 47.619 0.00 0.00 44.76 4.30
877 957 2.779471 CGTTTCGGTTTCTTTTTCCGTG 59.221 45.455 0.00 0.00 43.94 4.94
915 1222 2.046314 ATAACGCCCGCTGTTGCT 60.046 55.556 7.02 0.00 36.97 3.91
929 1243 2.108771 TGCTGTCGCAGTTGCAGA 59.891 55.556 4.84 0.21 42.25 4.26
1116 1454 2.300967 GCTCTGGTCCATCCCCACA 61.301 63.158 0.00 0.00 34.77 4.17
1126 1464 2.596851 ATCCCCACAAGCAGCGACT 61.597 57.895 0.00 0.00 0.00 4.18
1132 1470 1.630148 CACAAGCAGCGACTACTACC 58.370 55.000 0.00 0.00 0.00 3.18
1151 1489 3.977244 CAACTGGGCGGGCAACAC 61.977 66.667 3.27 0.00 39.74 3.32
1185 1523 2.741092 GACAACCTCGGTGAGCCA 59.259 61.111 0.00 0.00 34.09 4.75
1186 1524 1.668151 GACAACCTCGGTGAGCCAC 60.668 63.158 0.00 0.00 34.09 5.01
1197 1538 2.351276 GAGCCACCCATCACCGTT 59.649 61.111 0.00 0.00 0.00 4.44
1204 1545 0.544357 ACCCATCACCGTTCCTCTCA 60.544 55.000 0.00 0.00 0.00 3.27
1205 1546 0.613260 CCCATCACCGTTCCTCTCAA 59.387 55.000 0.00 0.00 0.00 3.02
1206 1547 1.406069 CCCATCACCGTTCCTCTCAAG 60.406 57.143 0.00 0.00 0.00 3.02
1207 1548 1.363744 CATCACCGTTCCTCTCAAGC 58.636 55.000 0.00 0.00 0.00 4.01
1208 1549 0.108615 ATCACCGTTCCTCTCAAGCG 60.109 55.000 0.00 0.00 0.00 4.68
1209 1550 2.048127 ACCGTTCCTCTCAAGCGC 60.048 61.111 0.00 0.00 0.00 5.92
1210 1551 3.181967 CCGTTCCTCTCAAGCGCG 61.182 66.667 0.00 0.00 0.00 6.86
1211 1552 2.126463 CGTTCCTCTCAAGCGCGA 60.126 61.111 12.10 0.00 0.00 5.87
1212 1553 2.155194 CGTTCCTCTCAAGCGCGAG 61.155 63.158 12.10 3.46 0.00 5.03
1241 1582 1.934463 CACGAGTGCAGTTGGTGTC 59.066 57.895 13.47 0.00 0.00 3.67
1244 1585 0.530650 CGAGTGCAGTTGGTGTCTGT 60.531 55.000 0.20 0.00 35.60 3.41
1250 1591 1.869767 GCAGTTGGTGTCTGTTCTCTG 59.130 52.381 0.00 0.00 35.60 3.35
1255 1596 1.609072 TGGTGTCTGTTCTCTGACGAG 59.391 52.381 0.00 0.00 42.70 4.18
1256 1597 1.880675 GGTGTCTGTTCTCTGACGAGA 59.119 52.381 0.00 0.00 44.32 4.04
1310 1659 1.153706 GGGATGTACGACGTGGTGG 60.154 63.158 13.96 0.00 0.00 4.61
1333 1682 2.998949 GGGGGCTGGGAGTACAAG 59.001 66.667 0.00 0.00 0.00 3.16
1334 1683 2.680370 GGGGGCTGGGAGTACAAGG 61.680 68.421 0.00 0.00 0.00 3.61
1335 1684 2.272471 GGGCTGGGAGTACAAGGC 59.728 66.667 0.00 0.00 0.00 4.35
1347 1696 4.335647 CAAGGCCTGCTCGTGGGT 62.336 66.667 5.69 0.00 0.00 4.51
1367 1716 1.192428 GGACCAATACTCGGACACCT 58.808 55.000 0.00 0.00 0.00 4.00
1369 1718 2.618053 GACCAATACTCGGACACCTTG 58.382 52.381 0.00 0.00 0.00 3.61
1407 1756 4.796231 CCACCTCGACTTCGCCGG 62.796 72.222 0.00 0.00 39.60 6.13
1464 1813 1.227089 CCCTCGGCGTCAAGATCTG 60.227 63.158 6.85 0.00 0.00 2.90
1465 1814 1.227089 CCTCGGCGTCAAGATCTGG 60.227 63.158 6.85 0.00 0.00 3.86
1469 1818 1.901085 GGCGTCAAGATCTGGGTCT 59.099 57.895 0.00 0.00 0.00 3.85
1470 1819 0.179097 GGCGTCAAGATCTGGGTCTC 60.179 60.000 0.00 0.00 0.00 3.36
1495 1844 2.816958 CAGGCCTAGCACAGCACG 60.817 66.667 3.98 0.00 0.00 5.34
1496 1845 4.087892 AGGCCTAGCACAGCACGG 62.088 66.667 1.29 0.00 0.00 4.94
1497 1846 4.394712 GGCCTAGCACAGCACGGT 62.395 66.667 0.00 0.00 0.00 4.83
1551 1900 3.007398 ACTCCTTTCAACTGCTACTCCTG 59.993 47.826 0.00 0.00 0.00 3.86
1552 1901 2.972713 TCCTTTCAACTGCTACTCCTGT 59.027 45.455 0.00 0.00 0.00 4.00
1554 1903 4.137543 CCTTTCAACTGCTACTCCTGTTT 58.862 43.478 0.00 0.00 0.00 2.83
1556 1905 5.278022 CCTTTCAACTGCTACTCCTGTTTTC 60.278 44.000 0.00 0.00 0.00 2.29
1561 1910 6.041637 TCAACTGCTACTCCTGTTTTCTTCTA 59.958 38.462 0.00 0.00 0.00 2.10
1563 1912 4.806330 TGCTACTCCTGTTTTCTTCTACG 58.194 43.478 0.00 0.00 0.00 3.51
1600 1949 8.408043 TCCAATATAATGGAATTGTGCTTAGG 57.592 34.615 7.08 0.00 46.36 2.69
1613 1962 4.188462 TGTGCTTAGGTCGACAATAATGG 58.812 43.478 18.91 6.32 0.00 3.16
1616 1965 5.353123 GTGCTTAGGTCGACAATAATGGAAA 59.647 40.000 18.91 0.00 0.00 3.13
1622 1971 5.765182 AGGTCGACAATAATGGAAATGGATC 59.235 40.000 18.91 0.00 0.00 3.36
1635 1984 5.011227 TGGAAATGGATCATAATGTGCATGG 59.989 40.000 0.00 0.00 0.00 3.66
1643 1992 5.952526 TCATAATGTGCATGGTGATGATC 57.047 39.130 0.00 0.00 0.00 2.92
1649 1998 3.568007 TGTGCATGGTGATGATCATGATG 59.432 43.478 14.30 10.43 42.60 3.07
1650 1999 2.556622 TGCATGGTGATGATCATGATGC 59.443 45.455 23.80 23.80 42.60 3.91
1652 2001 3.153919 CATGGTGATGATCATGATGCCA 58.846 45.455 14.30 14.86 42.60 4.92
1653 2002 2.858745 TGGTGATGATCATGATGCCAG 58.141 47.619 14.30 0.00 0.00 4.85
1654 2003 1.540267 GGTGATGATCATGATGCCAGC 59.460 52.381 14.30 12.90 0.00 4.85
1655 2004 1.540267 GTGATGATCATGATGCCAGCC 59.460 52.381 14.30 0.00 0.00 4.85
1656 2005 1.423921 TGATGATCATGATGCCAGCCT 59.576 47.619 14.30 0.00 0.00 4.58
1657 2006 1.813178 GATGATCATGATGCCAGCCTG 59.187 52.381 14.30 0.00 0.00 4.85
1659 2008 1.423921 TGATCATGATGCCAGCCTGAT 59.576 47.619 14.30 0.16 0.00 2.90
1660 2009 2.158519 TGATCATGATGCCAGCCTGATT 60.159 45.455 14.30 0.00 0.00 2.57
1661 2010 3.073356 TGATCATGATGCCAGCCTGATTA 59.927 43.478 14.30 0.00 0.00 1.75
1672 2023 4.440663 GCCAGCCTGATTAAAAACCTGATC 60.441 45.833 0.00 0.00 0.00 2.92
1710 2061 2.969628 TTGCAAAATTGTCCACGGTT 57.030 40.000 0.00 0.00 0.00 4.44
1733 2084 5.399858 TCTGCTTAGACAACGTATTCAGAC 58.600 41.667 0.00 0.00 0.00 3.51
1739 2102 2.729882 GACAACGTATTCAGACAGCGTT 59.270 45.455 0.00 0.00 44.91 4.84
1820 2185 5.277825 CCACGTAGCATTTTTCAAAAGACA 58.722 37.500 0.00 0.00 0.00 3.41
1821 2186 5.920273 CCACGTAGCATTTTTCAAAAGACAT 59.080 36.000 0.00 0.00 0.00 3.06
1822 2187 6.129115 CCACGTAGCATTTTTCAAAAGACATG 60.129 38.462 0.00 0.00 0.00 3.21
1823 2188 5.920273 ACGTAGCATTTTTCAAAAGACATGG 59.080 36.000 0.00 0.00 0.00 3.66
1895 2267 0.178992 CACCAAAACCCCAGAGAGCA 60.179 55.000 0.00 0.00 0.00 4.26
1913 2285 1.202734 GCAGGCAGGCATCTTGATCTA 60.203 52.381 0.00 0.00 0.00 1.98
1921 2293 1.349357 GCATCTTGATCTAGGGTCCCC 59.651 57.143 3.51 0.00 0.00 4.81
1933 2305 1.371183 GGTCCCCAAAAAGCTTGCC 59.629 57.895 0.00 0.00 0.00 4.52
1934 2306 1.371183 GTCCCCAAAAAGCTTGCCC 59.629 57.895 0.00 0.00 0.00 5.36
1935 2307 1.074926 TCCCCAAAAAGCTTGCCCA 60.075 52.632 0.00 0.00 0.00 5.36
1936 2308 0.692419 TCCCCAAAAAGCTTGCCCAA 60.692 50.000 0.00 0.00 0.00 4.12
2091 2465 1.136774 CGTCTCCTCGCATTCGTCA 59.863 57.895 0.00 0.00 36.96 4.35
2181 2555 4.162690 GCCAGCGAGTCGGGGAAT 62.163 66.667 15.52 0.00 0.00 3.01
2187 2561 1.898154 CGAGTCGGGGAATTCCACT 59.102 57.895 24.21 18.89 37.25 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.325293 AGGTGTACTCATGTGCTTCTG 57.675 47.619 0.00 0.00 0.00 3.02
105 108 0.524392 TTTTGTTTGTGCCGCGTGAG 60.524 50.000 4.92 0.00 0.00 3.51
109 112 0.926846 AATGTTTTGTTTGTGCCGCG 59.073 45.000 0.00 0.00 0.00 6.46
163 169 4.256920 CTCCATGAGGTTTCTCGTCATTT 58.743 43.478 0.00 0.00 45.57 2.32
185 191 5.827797 TGTGATTATTCCTAACTTGGGATGC 59.172 40.000 0.00 0.00 32.41 3.91
187 193 7.557719 CAGTTGTGATTATTCCTAACTTGGGAT 59.442 37.037 0.00 0.00 32.41 3.85
195 201 9.403583 GGAATTACCAGTTGTGATTATTCCTAA 57.596 33.333 0.00 0.00 33.66 2.69
197 203 7.643123 AGGAATTACCAGTTGTGATTATTCCT 58.357 34.615 0.00 0.00 42.04 3.36
198 204 7.881775 AGGAATTACCAGTTGTGATTATTCC 57.118 36.000 0.00 0.00 42.04 3.01
213 219 4.784177 TCGGGGTTCATTTAGGAATTACC 58.216 43.478 0.00 0.00 39.35 2.85
227 233 0.108756 GCACAGTAGACTCGGGGTTC 60.109 60.000 0.00 0.00 0.00 3.62
234 240 0.805614 TCTGCTCGCACAGTAGACTC 59.194 55.000 4.71 0.00 38.83 3.36
263 270 0.321671 CGAGGGATGACTGTTGGTGT 59.678 55.000 0.00 0.00 0.00 4.16
292 300 7.854557 TTCTTAGACCAGATTCATCATTGTG 57.145 36.000 0.00 0.00 0.00 3.33
333 341 4.723862 CGCTAATCGTTTAACAACTGATGC 59.276 41.667 0.00 0.00 31.08 3.91
343 351 1.728068 TGCCTGCGCTAATCGTTTAA 58.272 45.000 9.73 0.00 41.07 1.52
344 352 1.728068 TTGCCTGCGCTAATCGTTTA 58.272 45.000 9.73 0.00 41.07 2.01
346 354 1.597663 GTATTGCCTGCGCTAATCGTT 59.402 47.619 9.73 0.00 41.07 3.85
347 355 1.202533 AGTATTGCCTGCGCTAATCGT 60.203 47.619 9.73 0.00 41.07 3.73
349 357 3.654414 AGTAGTATTGCCTGCGCTAATC 58.346 45.455 9.73 0.00 35.36 1.75
355 363 1.767289 CCGTAGTAGTATTGCCTGCG 58.233 55.000 0.00 0.00 34.68 5.18
373 386 1.297893 GTTGCTCGCGAATCATGCC 60.298 57.895 11.33 0.00 0.00 4.40
395 408 5.255687 TGGATTTCTGCTGCTTCATAAGAA 58.744 37.500 0.00 0.00 0.00 2.52
440 453 1.725665 CGGAGTAATCGTCCTCGCA 59.274 57.895 0.00 0.00 36.96 5.10
449 462 1.828832 CTCTGTGTCGCGGAGTAATC 58.171 55.000 13.26 0.00 43.83 1.75
458 471 2.246739 TGTGCTTGCTCTGTGTCGC 61.247 57.895 0.00 0.00 0.00 5.19
495 508 1.471119 GGGCTTTAGGGTTTAGCACC 58.529 55.000 0.00 0.00 46.46 5.01
508 522 2.115266 CTTGTGACCCGGGGCTTT 59.885 61.111 30.93 3.77 0.00 3.51
517 531 5.088739 CGATTTGTTTCATAGCTTGTGACC 58.911 41.667 0.00 0.00 0.00 4.02
623 661 0.682855 CGACCTCCTCTGCTCTCCTT 60.683 60.000 0.00 0.00 0.00 3.36
629 667 2.194388 TACGTCCGACCTCCTCTGCT 62.194 60.000 0.00 0.00 0.00 4.24
630 668 1.748122 TACGTCCGACCTCCTCTGC 60.748 63.158 0.00 0.00 0.00 4.26
631 669 1.375098 GGTACGTCCGACCTCCTCTG 61.375 65.000 0.00 0.00 33.86 3.35
634 672 0.750911 GATGGTACGTCCGACCTCCT 60.751 60.000 7.47 0.00 37.88 3.69
639 677 1.298190 GCGAGATGGTACGTCCGAC 60.298 63.158 0.00 0.00 39.52 4.79
711 773 4.157120 TAGCCCTTTCGCTCGCCC 62.157 66.667 0.00 0.00 40.39 6.13
712 774 2.586357 CTAGCCCTTTCGCTCGCC 60.586 66.667 0.00 0.00 40.39 5.54
713 775 2.586357 CCTAGCCCTTTCGCTCGC 60.586 66.667 0.00 0.00 40.39 5.03
714 776 1.749334 ATCCCTAGCCCTTTCGCTCG 61.749 60.000 0.00 0.00 40.39 5.03
715 777 0.250081 CATCCCTAGCCCTTTCGCTC 60.250 60.000 0.00 0.00 40.39 5.03
716 778 1.700042 CCATCCCTAGCCCTTTCGCT 61.700 60.000 0.00 0.00 43.09 4.93
717 779 1.227973 CCATCCCTAGCCCTTTCGC 60.228 63.158 0.00 0.00 0.00 4.70
718 780 1.054406 TCCCATCCCTAGCCCTTTCG 61.054 60.000 0.00 0.00 0.00 3.46
719 781 0.767998 CTCCCATCCCTAGCCCTTTC 59.232 60.000 0.00 0.00 0.00 2.62
720 782 1.356494 GCTCCCATCCCTAGCCCTTT 61.356 60.000 0.00 0.00 0.00 3.11
751 818 3.294214 CCGCCCCCTCGTATATATAAGT 58.706 50.000 5.71 0.00 0.00 2.24
837 904 0.534652 GCAGCTCATGGGCCTTAGAG 60.535 60.000 15.67 10.45 0.00 2.43
852 919 1.835121 AAAAGAAACCGAAACGCAGC 58.165 45.000 0.00 0.00 0.00 5.25
875 948 1.610673 TCCTCTCCAGTGAGCCCAC 60.611 63.158 0.00 0.00 43.50 4.61
877 957 1.000993 TCTCCTCTCCAGTGAGCCC 59.999 63.158 0.00 0.00 38.58 5.19
915 1222 2.031012 CCCTCTGCAACTGCGACA 59.969 61.111 0.00 0.00 45.83 4.35
918 1232 1.447489 CTCTCCCTCTGCAACTGCG 60.447 63.158 0.00 0.00 45.83 5.18
923 1237 0.543883 ACTGCTCTCTCCCTCTGCAA 60.544 55.000 0.00 0.00 33.07 4.08
924 1238 0.543883 AACTGCTCTCTCCCTCTGCA 60.544 55.000 0.00 0.00 0.00 4.41
925 1239 0.108233 CAACTGCTCTCTCCCTCTGC 60.108 60.000 0.00 0.00 0.00 4.26
926 1240 0.108233 GCAACTGCTCTCTCCCTCTG 60.108 60.000 0.00 0.00 38.21 3.35
927 1241 2.285824 GCAACTGCTCTCTCCCTCT 58.714 57.895 0.00 0.00 38.21 3.69
928 1242 4.930592 GCAACTGCTCTCTCCCTC 57.069 61.111 0.00 0.00 38.21 4.30
1105 1443 2.356278 GCTGCTTGTGGGGATGGA 59.644 61.111 0.00 0.00 0.00 3.41
1185 1523 0.544357 TGAGAGGAACGGTGATGGGT 60.544 55.000 0.00 0.00 0.00 4.51
1186 1524 0.613260 TTGAGAGGAACGGTGATGGG 59.387 55.000 0.00 0.00 0.00 4.00
1189 1527 0.108615 CGCTTGAGAGGAACGGTGAT 60.109 55.000 0.00 0.00 0.00 3.06
1190 1528 1.289066 CGCTTGAGAGGAACGGTGA 59.711 57.895 0.00 0.00 0.00 4.02
1197 1538 4.482684 CGCTCGCGCTTGAGAGGA 62.483 66.667 15.42 0.00 39.63 3.71
1223 1564 0.530650 AGACACCAACTGCACTCGTG 60.531 55.000 0.00 0.00 0.00 4.35
1224 1565 0.530650 CAGACACCAACTGCACTCGT 60.531 55.000 0.00 0.00 0.00 4.18
1232 1573 2.223829 CGTCAGAGAACAGACACCAACT 60.224 50.000 0.00 0.00 33.15 3.16
1250 1591 2.391821 CACGCACGCATTCTCGTC 59.608 61.111 0.00 0.00 41.21 4.20
1319 1668 2.272471 GGCCTTGTACTCCCAGCC 59.728 66.667 0.00 0.00 0.00 4.85
1320 1669 1.078143 CAGGCCTTGTACTCCCAGC 60.078 63.158 0.00 0.00 0.00 4.85
1321 1670 1.078143 GCAGGCCTTGTACTCCCAG 60.078 63.158 0.00 0.00 0.00 4.45
1335 1684 4.394712 GGTCCACCCACGAGCAGG 62.395 72.222 0.00 0.00 0.00 4.85
1347 1696 0.899720 GGTGTCCGAGTATTGGTCCA 59.100 55.000 0.00 0.00 41.84 4.02
1353 1702 3.368531 GCTCTTCAAGGTGTCCGAGTATT 60.369 47.826 0.00 0.00 0.00 1.89
1354 1703 2.166664 GCTCTTCAAGGTGTCCGAGTAT 59.833 50.000 0.00 0.00 0.00 2.12
1367 1716 4.722700 GGCGGGGCTGCTCTTCAA 62.723 66.667 0.00 0.00 34.52 2.69
1464 1813 3.775654 CCTGCTGGACCGAGACCC 61.776 72.222 2.92 0.00 34.57 4.46
1465 1814 4.459089 GCCTGCTGGACCGAGACC 62.459 72.222 14.77 0.00 34.57 3.85
1469 1818 2.759973 CTAGGCCTGCTGGACCGA 60.760 66.667 17.99 8.55 44.45 4.69
1470 1819 4.537433 GCTAGGCCTGCTGGACCG 62.537 72.222 17.99 4.89 44.45 4.79
1580 1929 6.704493 GTCGACCTAAGCACAATTCCATTATA 59.296 38.462 3.51 0.00 0.00 0.98
1581 1930 5.527582 GTCGACCTAAGCACAATTCCATTAT 59.472 40.000 3.51 0.00 0.00 1.28
1600 1949 6.618287 TGATCCATTTCCATTATTGTCGAC 57.382 37.500 9.11 9.11 0.00 4.20
1613 1962 5.924254 CACCATGCACATTATGATCCATTTC 59.076 40.000 0.00 0.00 0.00 2.17
1616 1965 4.732065 TCACCATGCACATTATGATCCAT 58.268 39.130 0.00 0.00 0.00 3.41
1622 1971 5.699097 TGATCATCACCATGCACATTATG 57.301 39.130 0.00 0.00 0.00 1.90
1635 1984 1.540267 GGCTGGCATCATGATCATCAC 59.460 52.381 4.86 0.00 0.00 3.06
1643 1992 4.659111 TTTTAATCAGGCTGGCATCATG 57.341 40.909 15.73 0.00 0.00 3.07
1649 1998 2.825532 TCAGGTTTTTAATCAGGCTGGC 59.174 45.455 15.73 0.00 0.00 4.85
1650 1999 4.706476 TGATCAGGTTTTTAATCAGGCTGG 59.294 41.667 15.73 0.00 0.00 4.85
1652 2001 6.916360 TTTGATCAGGTTTTTAATCAGGCT 57.084 33.333 0.00 0.00 30.39 4.58
1653 2002 7.095229 GGTTTTTGATCAGGTTTTTAATCAGGC 60.095 37.037 0.00 0.00 30.39 4.85
1654 2003 7.930865 TGGTTTTTGATCAGGTTTTTAATCAGG 59.069 33.333 0.00 0.00 30.39 3.86
1655 2004 8.764287 GTGGTTTTTGATCAGGTTTTTAATCAG 58.236 33.333 0.00 0.00 30.39 2.90
1656 2005 8.260818 TGTGGTTTTTGATCAGGTTTTTAATCA 58.739 29.630 0.00 0.00 0.00 2.57
1657 2006 8.655651 TGTGGTTTTTGATCAGGTTTTTAATC 57.344 30.769 0.00 0.00 0.00 1.75
1659 2008 8.722394 GTTTGTGGTTTTTGATCAGGTTTTTAA 58.278 29.630 0.00 0.00 0.00 1.52
1660 2009 7.878127 TGTTTGTGGTTTTTGATCAGGTTTTTA 59.122 29.630 0.00 0.00 0.00 1.52
1661 2010 6.712547 TGTTTGTGGTTTTTGATCAGGTTTTT 59.287 30.769 0.00 0.00 0.00 1.94
1672 2023 4.097012 GCAAAGCATGTTTGTGGTTTTTG 58.903 39.130 16.72 3.37 44.68 2.44
1710 2061 5.048294 TGTCTGAATACGTTGTCTAAGCAGA 60.048 40.000 0.00 0.00 0.00 4.26
1733 2084 3.579147 TGTGAAAACTAACGAACGCTG 57.421 42.857 0.00 0.00 0.00 5.18
1739 2102 5.968848 GCAATCTGTTTGTGAAAACTAACGA 59.031 36.000 0.00 0.00 37.65 3.85
1820 2185 1.492133 CCGGGGCTGTATCCATCCAT 61.492 60.000 0.00 0.00 0.00 3.41
1821 2186 2.146724 CCGGGGCTGTATCCATCCA 61.147 63.158 0.00 0.00 0.00 3.41
1822 2187 2.750350 CCGGGGCTGTATCCATCC 59.250 66.667 0.00 0.00 0.00 3.51
1823 2188 2.032681 GCCGGGGCTGTATCCATC 59.967 66.667 2.18 0.00 38.26 3.51
1845 2214 1.686052 TGAAGCTGATTTTTGCCCGTT 59.314 42.857 0.00 0.00 0.00 4.44
1895 2267 1.698532 CCTAGATCAAGATGCCTGCCT 59.301 52.381 0.00 0.00 0.00 4.75
1921 2293 0.469494 AGGGTTGGGCAAGCTTTTTG 59.531 50.000 0.00 0.00 38.72 2.44
1933 2305 3.074412 CACAACAGTAAGCTAGGGTTGG 58.926 50.000 18.60 8.73 42.23 3.77
1934 2306 2.484264 GCACAACAGTAAGCTAGGGTTG 59.516 50.000 14.96 14.96 43.24 3.77
1935 2307 2.779506 GCACAACAGTAAGCTAGGGTT 58.220 47.619 0.00 0.00 0.00 4.11
1936 2308 1.337823 CGCACAACAGTAAGCTAGGGT 60.338 52.381 0.00 0.00 0.00 4.34
2037 2411 1.301558 CATGGAGGAGGAGATGCGC 60.302 63.158 0.00 0.00 0.00 6.09
2091 2465 1.078848 GCTGACCGACATGGAGCTT 60.079 57.895 0.00 0.00 42.00 3.74
2181 2555 5.412594 GCTCTACATTCATTTCACAGTGGAA 59.587 40.000 0.00 0.00 0.00 3.53
2187 2561 4.156556 GGCAAGCTCTACATTCATTTCACA 59.843 41.667 0.00 0.00 0.00 3.58
2241 2615 2.184322 GCAATCAGCGACGAGGGA 59.816 61.111 0.00 0.00 0.00 4.20
2314 2688 3.126686 CGACCAATGTGTATGTTCATGCA 59.873 43.478 0.00 0.00 0.00 3.96
2315 2689 3.683989 CGACCAATGTGTATGTTCATGC 58.316 45.455 0.00 0.00 0.00 4.06
2316 2690 3.374988 AGCGACCAATGTGTATGTTCATG 59.625 43.478 0.00 0.00 0.00 3.07
2317 2691 3.374988 CAGCGACCAATGTGTATGTTCAT 59.625 43.478 0.00 0.00 0.00 2.57
2318 2692 2.741517 CAGCGACCAATGTGTATGTTCA 59.258 45.455 0.00 0.00 0.00 3.18
2319 2693 3.000041 TCAGCGACCAATGTGTATGTTC 59.000 45.455 0.00 0.00 0.00 3.18
2322 2696 2.892374 TCTCAGCGACCAATGTGTATG 58.108 47.619 0.00 0.00 0.00 2.39
2323 2697 3.386078 AGATCTCAGCGACCAATGTGTAT 59.614 43.478 0.00 0.00 0.00 2.29
2324 2698 2.760650 AGATCTCAGCGACCAATGTGTA 59.239 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.