Multiple sequence alignment - TraesCS5B01G144200

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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 TraesCS5B01G144200 chr5B 100.000 2356 0 0 1 2356 271577619 271575264 0.000000e+00 4351.0
1 TraesCS5B01G144200 chr5D 88.854 1588 105 32 208 1746 233488132 233489696 0.000000e+00 1886.0
2 TraesCS5B01G144200 chr5D 88.787 544 59 2 1811 2354 61484869 61485410 0.000000e+00 665.0
3 TraesCS5B01G144200 chr5D 89.431 123 10 2 25 147 233487996 233488115 4.060000e-33 152.0
4 TraesCS5B01G144200 chr5A 91.131 654 36 9 918 1553 321713111 321713760 0.000000e+00 867.0
5 TraesCS5B01G144200 chr5A 89.482 618 37 14 176 783 321712460 321713059 0.000000e+00 756.0
6 TraesCS5B01G144200 chr5A 87.543 578 62 5 1784 2354 340812293 340811719 0.000000e+00 660.0
7 TraesCS5B01G144200 chr5A 96.522 115 3 1 1633 1746 321713763 321713877 3.090000e-44 189.0
8 TraesCS5B01G144200 chr5A 91.057 123 9 2 25 147 321712339 321712459 5.210000e-37 165.0
9 TraesCS5B01G144200 chr3D 87.583 604 58 6 1765 2354 401012361 401011761 0.000000e+00 684.0
10 TraesCS5B01G144200 chr3D 87.542 594 59 7 1770 2356 514644682 514645267 0.000000e+00 673.0
11 TraesCS5B01G144200 chr3D 89.011 546 56 4 1810 2354 553333668 553334210 0.000000e+00 673.0
12 TraesCS5B01G144200 chr3D 87.205 594 66 7 1768 2354 452573702 452573112 0.000000e+00 667.0
13 TraesCS5B01G144200 chr3D 78.899 109 19 3 1199 1306 323246319 323246424 1.170000e-08 71.3
14 TraesCS5B01G144200 chr1B 88.807 545 58 3 1811 2354 40601334 40600792 0.000000e+00 665.0
15 TraesCS5B01G144200 chr1B 80.385 831 123 21 935 1740 436930413 436929598 1.560000e-166 595.0
16 TraesCS5B01G144200 chr7D 88.645 546 58 4 1810 2354 182613055 182613597 0.000000e+00 662.0
17 TraesCS5B01G144200 chr7B 86.913 596 68 6 1766 2355 451365714 451365123 0.000000e+00 660.0
18 TraesCS5B01G144200 chr1D 81.437 835 116 21 935 1740 324623027 324622203 0.000000e+00 647.0
19 TraesCS5B01G144200 chr1A 79.880 830 115 32 936 1734 420382084 420382892 5.690000e-156 560.0


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 TraesCS5B01G144200 chr5B 271575264 271577619 2355 True 4351.00 4351 100.0000 1 2356 1 chr5B.!!$R1 2355
1 TraesCS5B01G144200 chr5D 233487996 233489696 1700 False 1019.00 1886 89.1425 25 1746 2 chr5D.!!$F2 1721
2 TraesCS5B01G144200 chr5D 61484869 61485410 541 False 665.00 665 88.7870 1811 2354 1 chr5D.!!$F1 543
3 TraesCS5B01G144200 chr5A 340811719 340812293 574 True 660.00 660 87.5430 1784 2354 1 chr5A.!!$R1 570
4 TraesCS5B01G144200 chr5A 321712339 321713877 1538 False 494.25 867 92.0480 25 1746 4 chr5A.!!$F1 1721
5 TraesCS5B01G144200 chr3D 401011761 401012361 600 True 684.00 684 87.5830 1765 2354 1 chr3D.!!$R1 589
6 TraesCS5B01G144200 chr3D 514644682 514645267 585 False 673.00 673 87.5420 1770 2356 1 chr3D.!!$F2 586
7 TraesCS5B01G144200 chr3D 553333668 553334210 542 False 673.00 673 89.0110 1810 2354 1 chr3D.!!$F3 544
8 TraesCS5B01G144200 chr3D 452573112 452573702 590 True 667.00 667 87.2050 1768 2354 1 chr3D.!!$R2 586
9 TraesCS5B01G144200 chr1B 40600792 40601334 542 True 665.00 665 88.8070 1811 2354 1 chr1B.!!$R1 543
10 TraesCS5B01G144200 chr1B 436929598 436930413 815 True 595.00 595 80.3850 935 1740 1 chr1B.!!$R2 805
11 TraesCS5B01G144200 chr7D 182613055 182613597 542 False 662.00 662 88.6450 1810 2354 1 chr7D.!!$F1 544
12 TraesCS5B01G144200 chr7B 451365123 451365714 591 True 660.00 660 86.9130 1766 2355 1 chr7B.!!$R1 589
13 TraesCS5B01G144200 chr1D 324622203 324623027 824 True 647.00 647 81.4370 935 1740 1 chr1D.!!$R1 805
14 TraesCS5B01G144200 chr1A 420382084 420382892 808 False 560.00 560 79.8800 936 1734 1 chr1A.!!$F1 798

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
316 324 0.17576 CTCATGGACTGGTACCACCG 59.824 60.0 11.6 4.87 42.58 4.94 F
317 325 0.54341 TCATGGACTGGTACCACCGT 60.543 55.0 11.6 10.60 42.58 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 1209 0.036952 CAACATCTCGCTCCACCTGT 60.037 55.0 0.00 0.00 0.00 4.00 R
1757 1832 0.179161 CGACTGGCTAGGTCAAGTCG 60.179 60.0 11.41 11.41 41.99 4.18 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
22 23 4.950479 CAGATGGTGGAGGTGAGC 57.050 61.111 0.00 0.00 0.00 4.26
23 24 1.222936 CAGATGGTGGAGGTGAGCC 59.777 63.158 0.00 0.00 0.00 4.70
80 81 3.131478 CGGCGTGGGATTTGGGAC 61.131 66.667 0.00 0.00 0.00 4.46
86 87 0.676782 GTGGGATTTGGGACGGTGAG 60.677 60.000 0.00 0.00 0.00 3.51
97 98 1.204231 GGACGGTGAGGACCTAGTTTC 59.796 57.143 0.00 0.00 40.58 2.78
101 102 3.390311 ACGGTGAGGACCTAGTTTCTTTT 59.610 43.478 0.00 0.00 40.58 2.27
102 103 4.141551 ACGGTGAGGACCTAGTTTCTTTTT 60.142 41.667 0.00 0.00 40.58 1.94
151 152 4.192000 CGTGGATCGCTTTGCTCT 57.808 55.556 0.00 0.00 0.00 4.09
152 153 1.712081 CGTGGATCGCTTTGCTCTG 59.288 57.895 0.00 0.00 0.00 3.35
153 154 0.737367 CGTGGATCGCTTTGCTCTGA 60.737 55.000 0.00 0.00 0.00 3.27
154 155 1.661341 GTGGATCGCTTTGCTCTGAT 58.339 50.000 0.00 0.00 0.00 2.90
155 156 1.329906 GTGGATCGCTTTGCTCTGATG 59.670 52.381 0.00 0.00 0.00 3.07
156 157 1.207811 TGGATCGCTTTGCTCTGATGA 59.792 47.619 0.00 0.00 0.00 2.92
157 158 2.158856 TGGATCGCTTTGCTCTGATGAT 60.159 45.455 0.00 0.00 0.00 2.45
158 159 2.479656 GGATCGCTTTGCTCTGATGATC 59.520 50.000 0.00 0.00 0.00 2.92
159 160 2.975732 TCGCTTTGCTCTGATGATCT 57.024 45.000 0.00 0.00 0.00 2.75
160 161 3.257469 TCGCTTTGCTCTGATGATCTT 57.743 42.857 0.00 0.00 0.00 2.40
161 162 3.603532 TCGCTTTGCTCTGATGATCTTT 58.396 40.909 0.00 0.00 0.00 2.52
162 163 4.005650 TCGCTTTGCTCTGATGATCTTTT 58.994 39.130 0.00 0.00 0.00 2.27
163 164 4.096311 CGCTTTGCTCTGATGATCTTTTG 58.904 43.478 0.00 0.00 0.00 2.44
164 165 4.379186 CGCTTTGCTCTGATGATCTTTTGT 60.379 41.667 0.00 0.00 0.00 2.83
165 166 5.467705 GCTTTGCTCTGATGATCTTTTGTT 58.532 37.500 0.00 0.00 0.00 2.83
166 167 5.572126 GCTTTGCTCTGATGATCTTTTGTTC 59.428 40.000 0.00 0.00 0.00 3.18
167 168 6.569994 GCTTTGCTCTGATGATCTTTTGTTCT 60.570 38.462 0.00 0.00 0.00 3.01
168 169 5.874895 TGCTCTGATGATCTTTTGTTCTG 57.125 39.130 0.00 0.00 0.00 3.02
169 170 4.698780 TGCTCTGATGATCTTTTGTTCTGG 59.301 41.667 0.00 0.00 0.00 3.86
170 171 4.940046 GCTCTGATGATCTTTTGTTCTGGA 59.060 41.667 0.00 0.00 0.00 3.86
171 172 5.064962 GCTCTGATGATCTTTTGTTCTGGAG 59.935 44.000 0.00 0.00 0.00 3.86
172 173 6.364568 TCTGATGATCTTTTGTTCTGGAGA 57.635 37.500 0.00 0.00 0.00 3.71
173 174 6.169094 TCTGATGATCTTTTGTTCTGGAGAC 58.831 40.000 0.00 0.00 0.00 3.36
174 175 4.931601 TGATGATCTTTTGTTCTGGAGACG 59.068 41.667 0.00 0.00 0.00 4.18
195 196 2.434702 GACAATGGAACCCCGACTAGAT 59.565 50.000 0.00 0.00 34.29 1.98
205 206 4.409187 ACCCCGACTAGATTATCCTTCTC 58.591 47.826 0.00 0.00 0.00 2.87
206 207 4.106663 ACCCCGACTAGATTATCCTTCTCT 59.893 45.833 0.00 0.00 0.00 3.10
210 211 5.465935 CGACTAGATTATCCTTCTCTTGCC 58.534 45.833 0.00 0.00 0.00 4.52
251 259 3.318275 CCCAATCTTTCTGGCTCATCATG 59.682 47.826 0.00 0.00 32.10 3.07
267 275 2.045143 TGCGATGGCAGGAATGCA 60.045 55.556 0.00 0.00 46.21 3.96
298 306 3.134623 TCCATGTATCTCGGTGCAATTCT 59.865 43.478 0.00 0.00 0.00 2.40
305 313 1.667724 CTCGGTGCAATTCTCATGGAC 59.332 52.381 0.00 0.00 38.28 4.02
306 314 1.278985 TCGGTGCAATTCTCATGGACT 59.721 47.619 0.00 0.00 38.92 3.85
308 316 1.747355 GGTGCAATTCTCATGGACTGG 59.253 52.381 0.00 0.00 38.92 4.00
309 317 2.440409 GTGCAATTCTCATGGACTGGT 58.560 47.619 0.00 0.00 36.35 4.00
310 318 3.609853 GTGCAATTCTCATGGACTGGTA 58.390 45.455 0.00 0.00 36.35 3.25
312 320 2.945668 GCAATTCTCATGGACTGGTACC 59.054 50.000 4.43 4.43 0.00 3.34
313 321 3.622206 GCAATTCTCATGGACTGGTACCA 60.622 47.826 15.39 15.39 41.83 3.25
315 323 1.568504 TCTCATGGACTGGTACCACC 58.431 55.000 11.60 12.75 40.36 4.61
316 324 0.175760 CTCATGGACTGGTACCACCG 59.824 60.000 11.60 4.87 42.58 4.94
317 325 0.543410 TCATGGACTGGTACCACCGT 60.543 55.000 11.60 10.60 42.58 4.83
319 327 0.834687 ATGGACTGGTACCACCGTGT 60.835 55.000 11.60 7.44 42.58 4.49
320 328 1.049855 TGGACTGGTACCACCGTGTT 61.050 55.000 11.60 0.00 42.58 3.32
349 358 9.899661 AGTTTATATTTAAAGAAAATTGGGGCC 57.100 29.630 0.00 0.00 38.71 5.80
370 379 1.613630 AGCCGAACCCTCATCCACT 60.614 57.895 0.00 0.00 0.00 4.00
412 422 3.354948 TTGTTCATATGAGCTGGCACT 57.645 42.857 18.83 0.00 0.00 4.40
423 433 1.173913 GCTGGCACTACGGGATTTTT 58.826 50.000 0.00 0.00 0.00 1.94
530 543 2.028112 TGCTAAGGTACCAGCTGTCTTG 60.028 50.000 21.29 0.00 37.72 3.02
635 648 7.050970 TCTTTCATATAGTATGGCTGTTCGT 57.949 36.000 0.00 0.00 0.00 3.85
658 671 8.402472 TCGTTTGATGACAACTTATTTTGTTCT 58.598 29.630 0.00 0.00 39.88 3.01
659 672 9.658475 CGTTTGATGACAACTTATTTTGTTCTA 57.342 29.630 0.00 0.00 39.88 2.10
745 758 0.854218 TGCCCAAGGACAAACCCTTA 59.146 50.000 0.00 0.00 44.30 2.69
754 767 4.270008 AGGACAAACCCTTAATGGATTCG 58.730 43.478 3.52 0.00 40.05 3.34
774 787 8.373220 GGATTCGGATAAGAAAAATCTAGGGTA 58.627 37.037 0.00 0.00 33.43 3.69
787 825 4.100707 TCTAGGGTACGATGTGTTTTCG 57.899 45.455 0.00 0.00 42.20 3.46
841 879 7.673641 AGTCAATTCTGAGGATTCACTCTAT 57.326 36.000 0.00 0.00 38.32 1.98
845 883 7.502561 TCAATTCTGAGGATTCACTCTATCGTA 59.497 37.037 0.00 0.00 38.32 3.43
884 923 3.137176 CCTGGACAGGTCACATATGGATT 59.863 47.826 10.22 0.00 43.61 3.01
886 925 3.779738 TGGACAGGTCACATATGGATTGA 59.220 43.478 7.80 0.00 0.00 2.57
902 941 6.160576 TGGATTGATTCGTATGTCTCATCA 57.839 37.500 0.00 0.00 0.00 3.07
916 955 3.029570 TCTCATCAGCATGCTACTCTGT 58.970 45.455 22.19 0.00 34.76 3.41
944 986 9.996554 TCATGTAATCTTTCTTCTTGTGAACTA 57.003 29.630 0.00 0.00 0.00 2.24
1024 1066 3.579151 GTCCTTCCTGAGACTGTTACCTT 59.421 47.826 0.00 0.00 0.00 3.50
1042 1084 3.502356 CCTTAAAGGTTGCCCCAGTTTA 58.498 45.455 0.00 0.00 34.66 2.01
1056 1100 4.638865 CCCCAGTTTATTAGGTACTTGCAC 59.361 45.833 0.00 0.00 41.75 4.57
1057 1101 5.250200 CCCAGTTTATTAGGTACTTGCACA 58.750 41.667 0.00 0.00 41.75 4.57
1060 1104 6.238103 CCAGTTTATTAGGTACTTGCACATCG 60.238 42.308 0.00 0.00 41.75 3.84
1074 1118 4.823130 GCACATCGCACCTTTAAAATTC 57.177 40.909 0.00 0.00 41.79 2.17
1118 1163 6.015504 CGTAAATATTCCAGCATTATCGTGC 58.984 40.000 0.00 0.00 45.38 5.34
1163 1209 0.173255 TCTTGATGATCGCGCACAGA 59.827 50.000 8.75 0.00 0.00 3.41
1254 1300 3.834489 AATTCACCGATGCAGAGATCT 57.166 42.857 0.00 0.00 0.00 2.75
1269 1315 1.416813 GATCTGCGAGACACAAGGCG 61.417 60.000 0.00 0.00 0.00 5.52
1370 1417 4.158579 TCGAAGTAACTCTCTGCATCATGT 59.841 41.667 0.00 0.00 0.00 3.21
1417 1479 2.093921 TGAAAGTGTGTCGTGGTCTTGA 60.094 45.455 0.00 0.00 0.00 3.02
1464 1526 2.100252 GTGGACCCATGCAATTGATGAG 59.900 50.000 10.34 3.98 0.00 2.90
1508 1576 2.739292 TCAGTGAAAGTACACGCTGTC 58.261 47.619 19.59 0.00 44.35 3.51
1559 1627 5.446860 TCTGACGTTCTCAGTAATATCCCT 58.553 41.667 3.02 0.00 46.09 4.20
1560 1628 6.598503 TCTGACGTTCTCAGTAATATCCCTA 58.401 40.000 3.02 0.00 46.09 3.53
1567 1635 6.835819 TCTCAGTAATATCCCTACAATCCG 57.164 41.667 0.00 0.00 0.00 4.18
1568 1636 6.312529 TCTCAGTAATATCCCTACAATCCGT 58.687 40.000 0.00 0.00 0.00 4.69
1575 1643 4.602340 ATCCCTACAATCCGTATGTGAC 57.398 45.455 0.00 0.00 32.27 3.67
1594 1662 1.610522 ACTTGCAGCACTTTGTGGATC 59.389 47.619 0.00 0.00 33.64 3.36
1595 1663 1.610038 CTTGCAGCACTTTGTGGATCA 59.390 47.619 0.00 0.00 33.64 2.92
1596 1664 1.689984 TGCAGCACTTTGTGGATCAA 58.310 45.000 0.00 0.00 33.64 2.57
1597 1665 1.610038 TGCAGCACTTTGTGGATCAAG 59.390 47.619 0.00 0.00 37.35 3.02
1599 1667 2.813754 GCAGCACTTTGTGGATCAAGTA 59.186 45.455 0.00 0.00 37.35 2.24
1602 1670 5.396484 CAGCACTTTGTGGATCAAGTATTG 58.604 41.667 0.00 0.00 39.86 1.90
1717 1792 4.342772 GCAGTTTGCACCTGTTTATATCG 58.657 43.478 12.75 0.00 44.26 2.92
1746 1821 5.461737 TGAATTCCGTTTGTTGAAAATGAGC 59.538 36.000 2.27 0.00 0.00 4.26
1747 1822 3.363341 TCCGTTTGTTGAAAATGAGCC 57.637 42.857 0.00 0.00 0.00 4.70
1748 1823 2.955660 TCCGTTTGTTGAAAATGAGCCT 59.044 40.909 0.00 0.00 0.00 4.58
1749 1824 4.138290 TCCGTTTGTTGAAAATGAGCCTA 58.862 39.130 0.00 0.00 0.00 3.93
1750 1825 4.764823 TCCGTTTGTTGAAAATGAGCCTAT 59.235 37.500 0.00 0.00 0.00 2.57
1751 1826 4.858692 CCGTTTGTTGAAAATGAGCCTATG 59.141 41.667 0.00 0.00 0.00 2.23
1752 1827 4.324402 CGTTTGTTGAAAATGAGCCTATGC 59.676 41.667 0.00 0.00 37.95 3.14
1753 1828 3.763097 TGTTGAAAATGAGCCTATGCG 57.237 42.857 0.00 0.00 44.33 4.73
1754 1829 3.342719 TGTTGAAAATGAGCCTATGCGA 58.657 40.909 0.00 0.00 44.33 5.10
1755 1830 3.126858 TGTTGAAAATGAGCCTATGCGAC 59.873 43.478 0.00 0.00 44.33 5.19
1756 1831 1.933181 TGAAAATGAGCCTATGCGACG 59.067 47.619 0.00 0.00 44.33 5.12
1757 1832 0.657840 AAAATGAGCCTATGCGACGC 59.342 50.000 14.19 14.19 44.33 5.19
1758 1833 1.490693 AAATGAGCCTATGCGACGCG 61.491 55.000 16.14 3.53 44.33 6.01
1759 1834 2.349969 AATGAGCCTATGCGACGCGA 62.350 55.000 15.93 4.61 44.33 5.87
1760 1835 3.025176 GAGCCTATGCGACGCGAC 61.025 66.667 15.93 5.54 44.33 5.19
1761 1836 3.471244 GAGCCTATGCGACGCGACT 62.471 63.158 15.93 7.45 44.33 4.18
1762 1837 2.582498 GCCTATGCGACGCGACTT 60.582 61.111 15.93 2.50 0.00 3.01
1763 1838 2.860628 GCCTATGCGACGCGACTTG 61.861 63.158 15.93 3.64 0.00 3.16
1830 1917 2.360852 GGTCCGTCCCGTCTCTGA 60.361 66.667 0.00 0.00 0.00 3.27
1867 1954 3.532155 GCGGAGTGGATCTCGCCT 61.532 66.667 0.00 0.00 43.60 5.52
1897 1984 2.714250 TGGGAGGCCTCTGTTTTTAGAA 59.286 45.455 31.36 3.39 0.00 2.10
1960 2048 2.404995 CGAGACGGCGGTAGTTCCT 61.405 63.158 13.24 0.00 0.00 3.36
1962 2050 0.179142 GAGACGGCGGTAGTTCCTTC 60.179 60.000 13.24 0.00 0.00 3.46
1969 2057 2.093658 GGCGGTAGTTCCTTCAAGATGA 60.094 50.000 0.00 0.00 0.00 2.92
2037 2125 2.750814 TCATCAGTAGGCATGTGGAGA 58.249 47.619 0.00 0.00 0.00 3.71
2063 2151 1.205655 CTCCAGCGGATCTGTCTTTGA 59.794 52.381 2.89 0.42 41.25 2.69
2086 2174 2.540515 GATTTGCTCGGATCTGTTCGA 58.459 47.619 0.42 0.00 0.00 3.71
2087 2175 2.672961 TTTGCTCGGATCTGTTCGAT 57.327 45.000 0.42 0.00 34.77 3.59
2146 2235 7.038729 TCCTTTTGATCTACACTCTTCATCTGT 60.039 37.037 0.00 0.00 0.00 3.41
2149 2238 5.019470 TGATCTACACTCTTCATCTGTGGT 58.981 41.667 0.00 0.00 36.16 4.16
2162 2251 0.947244 CTGTGGTGGTTGCTGTTCTC 59.053 55.000 0.00 0.00 0.00 2.87
2183 2272 1.077716 GCGTTGGTTCTATGGGGCT 60.078 57.895 0.00 0.00 0.00 5.19
2184 2273 1.095807 GCGTTGGTTCTATGGGGCTC 61.096 60.000 0.00 0.00 0.00 4.70
2225 2314 5.751990 CGACTGTCTACTACAACAAGGTTTT 59.248 40.000 6.21 0.00 37.74 2.43
2260 2349 2.276116 GGAGGGGCGATGATAGCGA 61.276 63.158 0.00 0.00 35.00 4.93
2265 2354 1.299165 GGCGATGATAGCGACACGT 60.299 57.895 0.00 0.00 36.61 4.49
2270 2359 2.538939 CGATGATAGCGACACGTCTTCA 60.539 50.000 0.00 0.00 0.00 3.02
2274 2363 0.596577 TAGCGACACGTCTTCAGCTT 59.403 50.000 14.06 4.47 36.30 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.402681 CCTCCACCATCTGGCCGT 61.403 66.667 0.00 0.00 40.39 5.68
1 2 3.402681 ACCTCCACCATCTGGCCG 61.403 66.667 0.00 0.00 40.39 6.13
2 3 2.262774 CTCACCTCCACCATCTGGCC 62.263 65.000 0.00 0.00 40.39 5.36
3 4 1.222936 CTCACCTCCACCATCTGGC 59.777 63.158 0.00 0.00 40.39 4.85
4 5 1.222936 GCTCACCTCCACCATCTGG 59.777 63.158 0.00 0.00 42.29 3.86
5 6 1.222936 GGCTCACCTCCACCATCTG 59.777 63.158 0.00 0.00 0.00 2.90
6 7 2.362369 CGGCTCACCTCCACCATCT 61.362 63.158 0.00 0.00 0.00 2.90
7 8 2.187946 CGGCTCACCTCCACCATC 59.812 66.667 0.00 0.00 0.00 3.51
8 9 2.607750 ACGGCTCACCTCCACCAT 60.608 61.111 0.00 0.00 0.00 3.55
9 10 3.625897 CACGGCTCACCTCCACCA 61.626 66.667 0.00 0.00 0.00 4.17
10 11 3.302347 CTCACGGCTCACCTCCACC 62.302 68.421 0.00 0.00 0.00 4.61
11 12 2.262915 CTCACGGCTCACCTCCAC 59.737 66.667 0.00 0.00 0.00 4.02
12 13 3.695606 GCTCACGGCTCACCTCCA 61.696 66.667 0.00 0.00 38.06 3.86
13 14 4.803426 CGCTCACGGCTCACCTCC 62.803 72.222 0.00 0.00 39.13 4.30
101 102 5.125739 GTCTTATGGTCTCGAGAGGAAGAAA 59.874 44.000 17.22 5.15 0.00 2.52
102 103 4.641094 GTCTTATGGTCTCGAGAGGAAGAA 59.359 45.833 17.22 7.07 0.00 2.52
103 104 4.200874 GTCTTATGGTCTCGAGAGGAAGA 58.799 47.826 17.22 17.55 0.00 2.87
106 107 2.510382 AGGTCTTATGGTCTCGAGAGGA 59.490 50.000 17.22 5.49 0.00 3.71
107 108 2.938838 AGGTCTTATGGTCTCGAGAGG 58.061 52.381 17.22 2.52 0.00 3.69
113 114 3.723260 GCAAGCTAGGTCTTATGGTCTC 58.277 50.000 0.00 0.00 0.00 3.36
147 148 4.940046 TCCAGAACAAAAGATCATCAGAGC 59.060 41.667 0.00 0.00 0.00 4.09
148 149 6.313411 GTCTCCAGAACAAAAGATCATCAGAG 59.687 42.308 0.00 0.00 0.00 3.35
149 150 6.169094 GTCTCCAGAACAAAAGATCATCAGA 58.831 40.000 0.00 0.00 0.00 3.27
150 151 5.063186 CGTCTCCAGAACAAAAGATCATCAG 59.937 44.000 0.00 0.00 0.00 2.90
151 152 4.931601 CGTCTCCAGAACAAAAGATCATCA 59.068 41.667 0.00 0.00 0.00 3.07
152 153 5.062809 GTCGTCTCCAGAACAAAAGATCATC 59.937 44.000 0.00 0.00 0.00 2.92
153 154 4.932200 GTCGTCTCCAGAACAAAAGATCAT 59.068 41.667 0.00 0.00 0.00 2.45
154 155 4.202212 TGTCGTCTCCAGAACAAAAGATCA 60.202 41.667 0.00 0.00 0.00 2.92
155 156 4.307432 TGTCGTCTCCAGAACAAAAGATC 58.693 43.478 0.00 0.00 0.00 2.75
156 157 4.336889 TGTCGTCTCCAGAACAAAAGAT 57.663 40.909 0.00 0.00 0.00 2.40
157 158 3.812156 TGTCGTCTCCAGAACAAAAGA 57.188 42.857 0.00 0.00 0.00 2.52
158 159 4.319766 CCATTGTCGTCTCCAGAACAAAAG 60.320 45.833 0.00 0.00 0.00 2.27
159 160 3.563808 CCATTGTCGTCTCCAGAACAAAA 59.436 43.478 0.00 0.00 0.00 2.44
160 161 3.138304 CCATTGTCGTCTCCAGAACAAA 58.862 45.455 0.00 0.00 0.00 2.83
161 162 2.367241 TCCATTGTCGTCTCCAGAACAA 59.633 45.455 0.00 0.00 0.00 2.83
162 163 1.967779 TCCATTGTCGTCTCCAGAACA 59.032 47.619 0.00 0.00 0.00 3.18
163 164 2.737252 GTTCCATTGTCGTCTCCAGAAC 59.263 50.000 0.00 0.00 0.00 3.01
164 165 2.289444 GGTTCCATTGTCGTCTCCAGAA 60.289 50.000 0.00 0.00 0.00 3.02
165 166 1.275291 GGTTCCATTGTCGTCTCCAGA 59.725 52.381 0.00 0.00 0.00 3.86
166 167 1.676014 GGGTTCCATTGTCGTCTCCAG 60.676 57.143 0.00 0.00 0.00 3.86
167 168 0.323629 GGGTTCCATTGTCGTCTCCA 59.676 55.000 0.00 0.00 0.00 3.86
168 169 0.392595 GGGGTTCCATTGTCGTCTCC 60.393 60.000 0.00 0.00 0.00 3.71
169 170 0.739813 CGGGGTTCCATTGTCGTCTC 60.740 60.000 0.00 0.00 0.00 3.36
170 171 1.189524 TCGGGGTTCCATTGTCGTCT 61.190 55.000 0.00 0.00 0.00 4.18
171 172 1.017701 GTCGGGGTTCCATTGTCGTC 61.018 60.000 0.00 0.00 0.00 4.20
172 173 1.004200 GTCGGGGTTCCATTGTCGT 60.004 57.895 0.00 0.00 0.00 4.34
173 174 0.533491 TAGTCGGGGTTCCATTGTCG 59.467 55.000 0.00 0.00 0.00 4.35
174 175 1.829222 TCTAGTCGGGGTTCCATTGTC 59.171 52.381 0.00 0.00 0.00 3.18
195 196 6.438741 AGATCGATATGGCAAGAGAAGGATAA 59.561 38.462 0.00 0.00 0.00 1.75
205 206 4.447054 GTCAACTGAGATCGATATGGCAAG 59.553 45.833 0.00 0.00 0.00 4.01
206 207 4.371786 GTCAACTGAGATCGATATGGCAA 58.628 43.478 0.00 0.00 0.00 4.52
210 211 3.321968 TGGGGTCAACTGAGATCGATATG 59.678 47.826 0.00 0.00 0.00 1.78
267 275 4.244425 CGAGATACATGGAAATCGGAGT 57.756 45.455 7.15 0.00 0.00 3.85
298 306 0.543410 ACGGTGGTACCAGTCCATGA 60.543 55.000 16.93 0.00 38.47 3.07
305 313 1.342174 ACTACAACACGGTGGTACCAG 59.658 52.381 16.93 7.29 38.47 4.00
306 314 1.412079 ACTACAACACGGTGGTACCA 58.588 50.000 11.60 11.60 38.47 3.25
308 316 7.832503 AATATAAACTACAACACGGTGGTAC 57.167 36.000 13.48 0.00 31.75 3.34
309 317 9.935241 TTAAATATAAACTACAACACGGTGGTA 57.065 29.630 13.48 5.20 31.75 3.25
310 318 8.845413 TTAAATATAAACTACAACACGGTGGT 57.155 30.769 13.48 2.02 33.56 4.16
349 358 1.144936 GGATGAGGGTTCGGCTGAG 59.855 63.158 0.00 0.00 0.00 3.35
362 371 3.963733 CTTGAGGGCAAGTGGATGA 57.036 52.632 0.00 0.00 45.10 2.92
436 446 4.162888 TGCATCCACATCTGACATAGTCTT 59.837 41.667 0.00 0.00 33.15 3.01
437 447 3.708121 TGCATCCACATCTGACATAGTCT 59.292 43.478 0.00 0.00 33.15 3.24
659 672 9.702726 CGATTTGATTCGAACACAAACTTATAT 57.297 29.630 24.41 13.76 41.62 0.86
660 673 8.927721 TCGATTTGATTCGAACACAAACTTATA 58.072 29.630 24.41 10.15 44.56 0.98
674 687 4.565229 CGGTAAGTGTTCGATTTGATTCG 58.435 43.478 0.00 0.00 40.46 3.34
680 693 3.135994 AGTTGCGGTAAGTGTTCGATTT 58.864 40.909 0.00 0.00 0.00 2.17
681 694 2.762745 AGTTGCGGTAAGTGTTCGATT 58.237 42.857 0.00 0.00 0.00 3.34
695 708 4.708038 ACAAGGTTTGTTTGCAAGTTGCG 61.708 43.478 22.27 6.41 43.92 4.85
745 758 9.289782 CCTAGATTTTTCTTATCCGAATCCATT 57.710 33.333 0.00 0.00 0.00 3.16
754 767 8.148999 ACATCGTACCCTAGATTTTTCTTATCC 58.851 37.037 0.00 0.00 0.00 2.59
841 879 7.557358 TCCAGGTACAATTACTATTCACTACGA 59.443 37.037 0.00 0.00 0.00 3.43
845 883 7.364762 CCTGTCCAGGTACAATTACTATTCACT 60.365 40.741 5.11 0.00 43.61 3.41
864 902 3.779738 TCAATCCATATGTGACCTGTCCA 59.220 43.478 1.24 0.00 0.00 4.02
876 914 8.534496 TGATGAGACATACGAATCAATCCATAT 58.466 33.333 0.00 0.00 0.00 1.78
877 915 7.895759 TGATGAGACATACGAATCAATCCATA 58.104 34.615 0.00 0.00 0.00 2.74
884 923 4.654091 TGCTGATGAGACATACGAATCA 57.346 40.909 0.00 0.00 0.00 2.57
886 925 3.744942 GCATGCTGATGAGACATACGAAT 59.255 43.478 11.37 0.00 0.00 3.34
902 941 2.235650 ACATGACACAGAGTAGCATGCT 59.764 45.455 25.99 25.99 39.82 3.79
916 955 8.559536 GTTCACAAGAAGAAAGATTACATGACA 58.440 33.333 0.00 0.00 33.63 3.58
1056 1100 3.786048 GCTCGAATTTTAAAGGTGCGATG 59.214 43.478 6.30 3.65 0.00 3.84
1057 1101 3.438781 TGCTCGAATTTTAAAGGTGCGAT 59.561 39.130 6.30 0.00 0.00 4.58
1060 1104 3.364920 GCTTGCTCGAATTTTAAAGGTGC 59.635 43.478 0.00 0.00 0.00 5.01
1155 1201 2.740055 CTCCACCTGTCTGTGCGC 60.740 66.667 0.00 0.00 34.85 6.09
1163 1209 0.036952 CAACATCTCGCTCCACCTGT 60.037 55.000 0.00 0.00 0.00 4.00
1260 1306 0.320771 CTCCTTACTGCGCCTTGTGT 60.321 55.000 4.18 0.00 0.00 3.72
1262 1308 1.376037 GCTCCTTACTGCGCCTTGT 60.376 57.895 4.18 3.75 0.00 3.16
1269 1315 0.670546 TGAACTGCGCTCCTTACTGC 60.671 55.000 9.73 0.00 0.00 4.40
1379 1426 4.081752 ACTTTCATTTTCAGTGTTGGTGCA 60.082 37.500 0.00 0.00 0.00 4.57
1417 1479 7.450074 TGACAGAGAAAACATACCAACTACAT 58.550 34.615 0.00 0.00 0.00 2.29
1484 1549 5.294356 ACAGCGTGTACTTTCACTGATAAA 58.706 37.500 0.00 0.00 36.33 1.40
1508 1576 8.722394 GTTAGAGGAACAATTTAGGAAACTCAG 58.278 37.037 0.00 0.00 38.88 3.35
1541 1609 7.091443 GGATTGTAGGGATATTACTGAGAACG 58.909 42.308 0.00 0.00 0.00 3.95
1559 1627 4.180817 CTGCAAGTCACATACGGATTGTA 58.819 43.478 0.00 0.00 37.49 2.41
1560 1628 3.002791 CTGCAAGTCACATACGGATTGT 58.997 45.455 0.00 0.00 0.00 2.71
1567 1635 3.003689 ACAAAGTGCTGCAAGTCACATAC 59.996 43.478 2.77 0.00 41.38 2.39
1568 1636 3.003585 CACAAAGTGCTGCAAGTCACATA 59.996 43.478 2.77 0.00 41.38 2.29
1575 1643 1.610038 TGATCCACAAAGTGCTGCAAG 59.390 47.619 2.77 0.00 31.34 4.01
1594 1662 6.695292 GGCAACTCAATTTGTCAATACTTG 57.305 37.500 0.00 0.00 31.03 3.16
1678 1753 2.092429 ACTGCTCCCTGAAACACTTGAA 60.092 45.455 0.00 0.00 0.00 2.69
1717 1792 3.701241 TCAACAAACGGAATTCAACTGC 58.299 40.909 7.93 0.00 0.00 4.40
1746 1821 1.226575 TCAAGTCGCGTCGCATAGG 60.227 57.895 18.75 0.21 0.00 2.57
1747 1822 1.472276 GGTCAAGTCGCGTCGCATAG 61.472 60.000 18.75 0.62 0.00 2.23
1748 1823 1.515519 GGTCAAGTCGCGTCGCATA 60.516 57.895 18.75 1.00 0.00 3.14
1749 1824 1.929806 TAGGTCAAGTCGCGTCGCAT 61.930 55.000 18.75 0.00 0.00 4.73
1750 1825 2.523184 CTAGGTCAAGTCGCGTCGCA 62.523 60.000 18.75 1.36 0.00 5.10
1751 1826 1.868251 CTAGGTCAAGTCGCGTCGC 60.868 63.158 7.29 7.29 0.00 5.19
1752 1827 1.868251 GCTAGGTCAAGTCGCGTCG 60.868 63.158 5.77 0.00 0.00 5.12
1753 1828 1.516603 GGCTAGGTCAAGTCGCGTC 60.517 63.158 5.77 0.00 0.00 5.19
1754 1829 2.214181 CTGGCTAGGTCAAGTCGCGT 62.214 60.000 5.77 0.00 0.00 6.01
1755 1830 1.517257 CTGGCTAGGTCAAGTCGCG 60.517 63.158 0.00 0.00 0.00 5.87
1756 1831 0.458716 GACTGGCTAGGTCAAGTCGC 60.459 60.000 0.85 0.00 34.23 5.19
1757 1832 0.179161 CGACTGGCTAGGTCAAGTCG 60.179 60.000 11.41 11.41 41.99 4.18
1758 1833 0.458716 GCGACTGGCTAGGTCAAGTC 60.459 60.000 0.85 0.00 39.11 3.01
1759 1834 1.592223 GCGACTGGCTAGGTCAAGT 59.408 57.895 0.85 0.00 39.11 3.16
1760 1835 1.153549 GGCGACTGGCTAGGTCAAG 60.154 63.158 0.85 0.00 42.94 3.02
1761 1836 2.978824 GGCGACTGGCTAGGTCAA 59.021 61.111 0.85 0.00 42.94 3.18
1762 1837 3.449227 CGGCGACTGGCTAGGTCA 61.449 66.667 0.00 0.00 42.94 4.02
1763 1838 4.874977 GCGGCGACTGGCTAGGTC 62.875 72.222 12.98 0.00 42.94 3.85
1847 1934 3.082579 GCGAGATCCACTCCGCCTT 62.083 63.158 0.00 0.00 42.18 4.35
1913 2001 0.872388 GCAGGACACAAACCCTAACG 59.128 55.000 0.00 0.00 0.00 3.18
1953 2041 9.449719 GACCTTTATTTCATCTTGAAGGAACTA 57.550 33.333 6.92 0.00 38.49 2.24
1956 2044 7.611855 GGAGACCTTTATTTCATCTTGAAGGAA 59.388 37.037 6.92 0.00 37.70 3.36
2025 2113 1.209019 GAGACACATCTCCACATGCCT 59.791 52.381 0.00 0.00 45.06 4.75
2037 2125 0.463204 CAGATCCGCTGGAGACACAT 59.537 55.000 3.76 0.00 41.07 3.21
2047 2135 1.833630 TCCATCAAAGACAGATCCGCT 59.166 47.619 0.00 0.00 0.00 5.52
2063 2151 3.209410 GAACAGATCCGAGCAAATCCAT 58.791 45.455 0.00 0.00 0.00 3.41
2086 2174 1.784856 CACACGAACGAAGACGAACAT 59.215 47.619 0.14 0.00 42.66 2.71
2087 2175 1.193644 CACACGAACGAAGACGAACA 58.806 50.000 0.14 0.00 42.66 3.18
2146 2235 0.813610 CACGAGAACAGCAACCACCA 60.814 55.000 0.00 0.00 0.00 4.17
2149 2238 2.243957 CGCACGAGAACAGCAACCA 61.244 57.895 0.00 0.00 0.00 3.67
2162 2251 1.366111 CCCCATAGAACCAACGCACG 61.366 60.000 0.00 0.00 0.00 5.34
2183 2272 0.738975 CGGGAAGTCATCGTGCTAGA 59.261 55.000 0.00 0.00 0.00 2.43
2184 2273 0.738975 TCGGGAAGTCATCGTGCTAG 59.261 55.000 0.00 0.00 0.00 3.42
2260 2349 1.221414 GAAGCAAGCTGAAGACGTGT 58.779 50.000 0.00 0.00 0.00 4.49
2265 2354 2.627515 ACACTGAAGCAAGCTGAAGA 57.372 45.000 10.24 0.00 0.00 2.87
2270 2359 3.545703 ACTACAAACACTGAAGCAAGCT 58.454 40.909 0.00 0.00 0.00 3.74
2274 2363 3.120792 GACGACTACAAACACTGAAGCA 58.879 45.455 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.