Multiple sequence alignment - TraesCS7D01G463800

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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 TraesCS7D01G463800 chr7D 100.000 2324 0 0 1 2324 578811621 578809298 0.000000e+00 4292.0
1 TraesCS7D01G463800 chr7D 88.716 1223 75 25 336 1511 578913075 578911869 0.000000e+00 1435.0
2 TraesCS7D01G463800 chr7D 83.837 959 89 25 443 1381 579361867 579362779 0.000000e+00 852.0
3 TraesCS7D01G463800 chr7D 92.059 340 13 5 1 340 578914378 578914053 1.260000e-127 466.0
4 TraesCS7D01G463800 chr7A 87.867 1772 110 45 71 1798 670865775 670864065 0.000000e+00 1984.0
5 TraesCS7D01G463800 chr7A 83.881 943 84 32 443 1370 671200422 671201311 0.000000e+00 837.0
6 TraesCS7D01G463800 chr7A 81.675 382 37 19 1949 2323 670861238 670860883 1.050000e-73 287.0
7 TraesCS7D01G463800 chr7A 93.478 92 6 0 1856 1947 670862303 670862212 1.120000e-28 137.0
8 TraesCS7D01G463800 chr7A 87.500 64 5 3 127 189 671195485 671195546 1.150000e-08 71.3
9 TraesCS7D01G463800 chr7B 86.572 1415 104 36 276 1638 642832190 642830810 0.000000e+00 1482.0
10 TraesCS7D01G463800 chr7B 88.156 819 62 14 832 1633 642974186 642973386 0.000000e+00 942.0
11 TraesCS7D01G463800 chr7B 88.156 819 62 13 832 1633 643002555 643001755 0.000000e+00 942.0
12 TraesCS7D01G463800 chr7B 87.668 819 66 16 832 1633 642989259 642988459 0.000000e+00 920.0
13 TraesCS7D01G463800 chr7B 87.057 819 62 15 832 1633 643015513 643014722 0.000000e+00 885.0
14 TraesCS7D01G463800 chr7B 92.225 463 27 5 832 1288 645265709 645265250 0.000000e+00 647.0
15 TraesCS7D01G463800 chr7B 85.768 534 34 23 9 531 643017301 643016799 5.690000e-146 527.0
16 TraesCS7D01G463800 chr7B 85.581 534 35 24 9 531 642991047 642990545 2.650000e-144 521.0
17 TraesCS7D01G463800 chr7B 85.206 534 37 23 9 531 643004343 643003841 5.730000e-141 510.0
18 TraesCS7D01G463800 chr7B 84.457 534 40 24 9 531 642975973 642975472 9.650000e-134 486.0
19 TraesCS7D01G463800 chr7B 86.280 379 23 8 439 789 645266092 645265715 3.620000e-103 385.0
20 TraesCS7D01G463800 chr7B 86.719 256 19 9 35 288 642834524 642834282 1.060000e-68 270.0
21 TraesCS7D01G463800 chr7B 91.667 180 9 2 615 789 643015697 643015519 6.410000e-61 244.0
22 TraesCS7D01G463800 chr7B 91.111 180 10 2 615 789 642989443 642989265 2.980000e-59 239.0
23 TraesCS7D01G463800 chr7B 93.671 158 9 1 615 772 643002739 643002583 3.860000e-58 235.0
24 TraesCS7D01G463800 chr7B 90.556 180 11 2 615 789 642974370 642974192 1.390000e-57 233.0
25 TraesCS7D01G463800 chr7B 93.103 116 8 0 68 183 645266796 645266681 1.100000e-38 171.0


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 TraesCS7D01G463800 chr7D 578809298 578811621 2323 True 4292.000000 4292 100.000000 1 2324 1 chr7D.!!$R1 2323
1 TraesCS7D01G463800 chr7D 578911869 578914378 2509 True 950.500000 1435 90.387500 1 1511 2 chr7D.!!$R2 1510
2 TraesCS7D01G463800 chr7D 579361867 579362779 912 False 852.000000 852 83.837000 443 1381 1 chr7D.!!$F1 938
3 TraesCS7D01G463800 chr7A 671200422 671201311 889 False 837.000000 837 83.881000 443 1370 1 chr7A.!!$F2 927
4 TraesCS7D01G463800 chr7A 670860883 670865775 4892 True 802.666667 1984 87.673333 71 2323 3 chr7A.!!$R1 2252
5 TraesCS7D01G463800 chr7B 642830810 642834524 3714 True 876.000000 1482 86.645500 35 1638 2 chr7B.!!$R1 1603
6 TraesCS7D01G463800 chr7B 643001755 643004343 2588 True 562.333333 942 89.011000 9 1633 3 chr7B.!!$R4 1624
7 TraesCS7D01G463800 chr7B 642988459 642991047 2588 True 560.000000 920 88.120000 9 1633 3 chr7B.!!$R3 1624
8 TraesCS7D01G463800 chr7B 642973386 642975973 2587 True 553.666667 942 87.723000 9 1633 3 chr7B.!!$R2 1624
9 TraesCS7D01G463800 chr7B 643014722 643017301 2579 True 552.000000 885 88.164000 9 1633 3 chr7B.!!$R5 1624
10 TraesCS7D01G463800 chr7B 645265250 645266796 1546 True 401.000000 647 90.536000 68 1288 3 chr7B.!!$R6 1220

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
480 3754 0.179062 CCCTTGATTCCTGGAGCTCG 60.179 60.0 7.83 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 6326 0.037697 AACAATCGCTGCGGTGACTA 60.038 50.0 25.76 7.4 34.6 2.59 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
179 186 2.730094 CCACTGCCACTTGCCAAC 59.270 61.111 0.00 0.00 40.16 3.77
180 187 2.332514 CACTGCCACTTGCCAACG 59.667 61.111 0.00 0.00 40.16 4.10
181 188 2.906897 ACTGCCACTTGCCAACGG 60.907 61.111 0.00 0.00 40.16 4.44
228 235 1.068741 ACGAGCAAAAGGTCGAAGAGT 59.931 47.619 21.62 0.00 39.53 3.24
229 236 2.135933 CGAGCAAAAGGTCGAAGAGTT 58.864 47.619 11.15 0.00 38.50 3.01
230 237 2.096713 CGAGCAAAAGGTCGAAGAGTTG 60.097 50.000 11.15 0.00 38.50 3.16
231 238 2.872858 GAGCAAAAGGTCGAAGAGTTGT 59.127 45.455 0.00 0.00 36.95 3.32
278 2541 0.740868 CGTCAAGTCCCATGCATCGT 60.741 55.000 0.00 0.00 0.00 3.73
350 3599 7.226523 TGTCTACGTACGCCTAGTTTATTCATA 59.773 37.037 16.72 0.00 0.00 2.15
357 3606 4.562963 CGCCTAGTTTATTCATAGGTCCCC 60.563 50.000 0.00 0.00 38.68 4.81
365 3614 3.849951 ATAGGTCCCCGCTGCGTG 61.850 66.667 21.59 9.77 0.00 5.34
383 3638 5.307204 TGCGTGTAGTAAAATGTAAACCCT 58.693 37.500 0.00 0.00 0.00 4.34
401 3656 3.506067 ACCCTTCTTTGTTAGGAAATGCG 59.494 43.478 0.00 0.00 33.13 4.73
411 3672 5.113383 TGTTAGGAAATGCGTAATCGATGT 58.887 37.500 0.00 0.00 39.71 3.06
480 3754 0.179062 CCCTTGATTCCTGGAGCTCG 60.179 60.000 7.83 0.00 0.00 5.03
574 4206 1.120437 GCAACCGAAAAAGCAACTCG 58.880 50.000 0.00 0.00 0.00 4.18
646 4977 2.467826 GCTCGTGGCTCATCCTTGC 61.468 63.158 0.00 0.00 38.06 4.01
772 5120 4.460683 TACGTCCGGGCCACATGC 62.461 66.667 4.39 0.00 40.16 4.06
819 5177 4.699522 GTCACCACCACCCCGCTC 62.700 72.222 0.00 0.00 0.00 5.03
824 5182 3.000819 CACCACCCCGCTCCAGTA 61.001 66.667 0.00 0.00 0.00 2.74
825 5183 2.683933 ACCACCCCGCTCCAGTAG 60.684 66.667 0.00 0.00 0.00 2.57
826 5184 2.683933 CCACCCCGCTCCAGTAGT 60.684 66.667 0.00 0.00 0.00 2.73
827 5185 2.722201 CCACCCCGCTCCAGTAGTC 61.722 68.421 0.00 0.00 0.00 2.59
828 5186 1.682684 CACCCCGCTCCAGTAGTCT 60.683 63.158 0.00 0.00 0.00 3.24
829 5187 1.380112 ACCCCGCTCCAGTAGTCTC 60.380 63.158 0.00 0.00 0.00 3.36
1035 5430 1.377366 ATGCATCCTCGTCGTCGTCT 61.377 55.000 1.33 0.00 38.33 4.18
1303 5720 2.955246 TGCTCCCCTCCTCCTCCT 60.955 66.667 0.00 0.00 0.00 3.69
1363 5800 1.630244 GCTGGTCGCAAGTAGCACTG 61.630 60.000 0.00 0.00 46.13 3.66
1426 5872 1.520342 GGCTTCAGCTAGCGGAGTG 60.520 63.158 17.10 14.66 42.15 3.51
1461 5921 2.675603 CGTGTTCATATGTGGGGTCGAA 60.676 50.000 1.90 0.00 0.00 3.71
1502 5962 5.690865 TCTGTCCTAAAATTTGTGACCACT 58.309 37.500 10.66 0.00 0.00 4.00
1544 6005 4.525912 AGCCAAGTGGATGAAATGTTTC 57.474 40.909 0.18 0.00 37.39 2.78
1550 6011 5.712152 AGTGGATGAAATGTTTCCAAGAC 57.288 39.130 3.26 0.00 41.05 3.01
1584 6045 4.039124 ACATTTCTTGAATTTGTCGGCCTT 59.961 37.500 0.00 0.00 0.00 4.35
1585 6046 4.664150 TTTCTTGAATTTGTCGGCCTTT 57.336 36.364 0.00 0.00 0.00 3.11
1616 6083 6.487331 CCGTCTCTAATGTTCCTGATAGTACT 59.513 42.308 0.00 0.00 0.00 2.73
1627 6094 9.647918 TGTTCCTGATAGTACTAATCATCTCTT 57.352 33.333 6.70 0.00 0.00 2.85
1641 6108 2.024176 TCTCTTCATACGCCCTTTGC 57.976 50.000 0.00 0.00 0.00 3.68
1643 6110 0.742990 TCTTCATACGCCCTTTGCCG 60.743 55.000 0.00 0.00 36.24 5.69
1646 6113 4.499633 ATACGCCCTTTGCCGGGG 62.500 66.667 2.18 0.00 44.83 5.73
1710 6180 1.383803 GGAGGCATCTCTGGGACCT 60.384 63.158 0.00 0.00 39.86 3.85
1735 6205 2.437359 AGACGAGGCTGGCATTGC 60.437 61.111 3.38 0.00 0.00 3.56
1747 6217 1.402613 TGGCATTGCATCAAGTGATCG 59.597 47.619 11.39 0.00 31.21 3.69
1751 6221 3.545624 GCATTGCATCAAGTGATCGAGAC 60.546 47.826 3.15 0.00 31.21 3.36
1780 6250 5.130311 TGGAGGAGTACAATAATTGCTGCTA 59.870 40.000 0.00 0.00 0.00 3.49
1798 6268 3.769300 TGCTACTGAGGATGCAGTTTAGA 59.231 43.478 2.09 0.00 46.42 2.10
1799 6269 4.222810 TGCTACTGAGGATGCAGTTTAGAA 59.777 41.667 2.09 0.00 46.42 2.10
1800 6270 5.178797 GCTACTGAGGATGCAGTTTAGAAA 58.821 41.667 2.09 0.00 46.42 2.52
1802 6272 6.317391 GCTACTGAGGATGCAGTTTAGAAAAT 59.683 38.462 2.09 0.00 46.42 1.82
1803 6273 7.148171 GCTACTGAGGATGCAGTTTAGAAAATT 60.148 37.037 2.09 0.00 46.42 1.82
1804 6274 7.150783 ACTGAGGATGCAGTTTAGAAAATTC 57.849 36.000 0.00 0.00 46.42 2.17
1805 6275 6.944862 ACTGAGGATGCAGTTTAGAAAATTCT 59.055 34.615 0.77 0.77 46.42 2.40
1806 6276 8.103305 ACTGAGGATGCAGTTTAGAAAATTCTA 58.897 33.333 0.00 0.00 46.42 2.10
1817 6287 6.490566 TTAGAAAATTCTAAACTCACGGGC 57.509 37.500 12.07 0.00 44.36 6.13
1819 6289 5.070685 AGAAAATTCTAAACTCACGGGCTT 58.929 37.500 0.00 0.00 35.34 4.35
1820 6290 5.535030 AGAAAATTCTAAACTCACGGGCTTT 59.465 36.000 0.00 0.00 35.34 3.51
1821 6291 5.784578 AAATTCTAAACTCACGGGCTTTT 57.215 34.783 0.00 0.00 0.00 2.27
1822 6292 6.887626 AAATTCTAAACTCACGGGCTTTTA 57.112 33.333 0.00 0.00 0.00 1.52
1823 6293 5.874895 ATTCTAAACTCACGGGCTTTTAC 57.125 39.130 0.00 0.00 0.00 2.01
1824 6294 3.319755 TCTAAACTCACGGGCTTTTACG 58.680 45.455 0.00 0.00 0.00 3.18
1825 6295 1.232119 AAACTCACGGGCTTTTACGG 58.768 50.000 0.00 0.00 0.00 4.02
1827 6297 1.743995 CTCACGGGCTTTTACGGGG 60.744 63.158 0.00 0.00 33.57 5.73
1828 6298 2.175035 CTCACGGGCTTTTACGGGGA 62.175 60.000 0.00 0.00 33.57 4.81
1830 6300 0.678684 CACGGGCTTTTACGGGGATT 60.679 55.000 0.00 0.00 0.00 3.01
1831 6301 0.038599 ACGGGCTTTTACGGGGATTT 59.961 50.000 0.00 0.00 0.00 2.17
1832 6302 1.179152 CGGGCTTTTACGGGGATTTT 58.821 50.000 0.00 0.00 0.00 1.82
1833 6303 1.133598 CGGGCTTTTACGGGGATTTTC 59.866 52.381 0.00 0.00 0.00 2.29
1835 6305 2.165641 GGGCTTTTACGGGGATTTTCTG 59.834 50.000 0.00 0.00 0.00 3.02
1837 6307 3.366985 GGCTTTTACGGGGATTTTCTGTG 60.367 47.826 0.00 0.00 0.00 3.66
1838 6308 3.366985 GCTTTTACGGGGATTTTCTGTGG 60.367 47.826 0.00 0.00 0.00 4.17
1839 6309 2.500392 TTACGGGGATTTTCTGTGGG 57.500 50.000 0.00 0.00 0.00 4.61
1840 6310 0.621609 TACGGGGATTTTCTGTGGGG 59.378 55.000 0.00 0.00 0.00 4.96
1841 6311 2.052104 CGGGGATTTTCTGTGGGGC 61.052 63.158 0.00 0.00 0.00 5.80
1843 6313 0.972471 GGGGATTTTCTGTGGGGCTG 60.972 60.000 0.00 0.00 0.00 4.85
1844 6314 0.972471 GGGATTTTCTGTGGGGCTGG 60.972 60.000 0.00 0.00 0.00 4.85
1847 6317 0.712380 ATTTTCTGTGGGGCTGGGAT 59.288 50.000 0.00 0.00 0.00 3.85
1848 6318 0.486879 TTTTCTGTGGGGCTGGGATT 59.513 50.000 0.00 0.00 0.00 3.01
1850 6320 1.434513 TTCTGTGGGGCTGGGATTGT 61.435 55.000 0.00 0.00 0.00 2.71
1851 6321 1.077265 CTGTGGGGCTGGGATTGTT 59.923 57.895 0.00 0.00 0.00 2.83
1852 6322 0.967380 CTGTGGGGCTGGGATTGTTC 60.967 60.000 0.00 0.00 0.00 3.18
1853 6323 2.046285 GTGGGGCTGGGATTGTTCG 61.046 63.158 0.00 0.00 0.00 3.95
1854 6324 2.227757 TGGGGCTGGGATTGTTCGA 61.228 57.895 0.00 0.00 0.00 3.71
1855 6325 1.749258 GGGGCTGGGATTGTTCGAC 60.749 63.158 0.00 0.00 0.00 4.20
1856 6326 1.299976 GGGCTGGGATTGTTCGACT 59.700 57.895 0.00 0.00 0.00 4.18
1857 6327 0.539986 GGGCTGGGATTGTTCGACTA 59.460 55.000 0.00 0.00 0.00 2.59
1860 6330 2.541556 GCTGGGATTGTTCGACTAGTC 58.458 52.381 13.18 13.18 0.00 2.59
1861 6331 2.094182 GCTGGGATTGTTCGACTAGTCA 60.094 50.000 22.37 7.25 0.00 3.41
1864 6334 2.527100 GGATTGTTCGACTAGTCACCG 58.473 52.381 22.37 9.76 0.00 4.94
1865 6335 1.918609 GATTGTTCGACTAGTCACCGC 59.081 52.381 22.37 9.67 0.00 5.68
1866 6336 0.669619 TTGTTCGACTAGTCACCGCA 59.330 50.000 22.37 11.96 0.00 5.69
1922 8096 4.082523 CGGGTGGTGCCGATCAGT 62.083 66.667 0.00 0.00 38.44 3.41
1944 8118 2.070783 GCGGTCTTCGTTATTTCACCA 58.929 47.619 0.00 0.00 41.72 4.17
1947 8121 4.330620 GCGGTCTTCGTTATTTCACCAATA 59.669 41.667 0.00 0.00 41.72 1.90
1950 9097 7.469260 CGGTCTTCGTTATTTCACCAATATTT 58.531 34.615 0.00 0.00 0.00 1.40
1995 9142 9.664332 TTTCAAATCCATAATTACCATGGTTTG 57.336 29.630 25.38 16.58 43.03 2.93
1996 9143 8.601047 TCAAATCCATAATTACCATGGTTTGA 57.399 30.769 25.38 18.61 42.78 2.69
1997 9144 9.211410 TCAAATCCATAATTACCATGGTTTGAT 57.789 29.630 25.38 12.23 41.76 2.57
1998 9145 9.263538 CAAATCCATAATTACCATGGTTTGATG 57.736 33.333 25.38 18.29 43.03 3.07
1999 9146 8.551682 AATCCATAATTACCATGGTTTGATGT 57.448 30.769 25.38 5.60 43.03 3.06
2000 9147 7.581213 TCCATAATTACCATGGTTTGATGTC 57.419 36.000 25.38 0.00 43.03 3.06
2001 9148 7.122048 TCCATAATTACCATGGTTTGATGTCA 58.878 34.615 25.38 0.00 43.03 3.58
2002 9149 7.617329 TCCATAATTACCATGGTTTGATGTCAA 59.383 33.333 25.38 8.94 43.03 3.18
2003 9150 7.706179 CCATAATTACCATGGTTTGATGTCAAC 59.294 37.037 25.38 0.00 38.53 3.18
2012 9159 6.030548 TGGTTTGATGTCAACTTGTTTTCA 57.969 33.333 0.00 0.00 35.28 2.69
2013 9160 5.866633 TGGTTTGATGTCAACTTGTTTTCAC 59.133 36.000 0.00 0.00 35.28 3.18
2017 9164 6.206395 TGATGTCAACTTGTTTTCACACAT 57.794 33.333 0.00 0.00 30.32 3.21
2028 9175 8.250332 ACTTGTTTTCACACATCTTGTACATTT 58.750 29.630 0.00 0.00 35.67 2.32
2031 9178 9.081997 TGTTTTCACACATCTTGTACATTTTTC 57.918 29.630 0.00 0.00 35.67 2.29
2037 9184 9.546909 CACACATCTTGTACATTTTTCTCATAC 57.453 33.333 0.00 0.00 35.67 2.39
2047 9194 6.392353 CATTTTTCTCATACAAAATGCGCA 57.608 33.333 14.96 14.96 41.23 6.09
2049 9196 7.457868 CATTTTTCTCATACAAAATGCGCATT 58.542 30.769 29.36 29.36 41.23 3.56
2051 9198 6.392353 TTTCTCATACAAAATGCGCATTTG 57.608 33.333 40.29 33.29 40.57 2.32
2057 9204 7.031975 TCATACAAAATGCGCATTTGTTCATA 58.968 30.769 40.29 27.92 40.57 2.15
2061 9208 5.954434 AAATGCGCATTTGTTCATACATC 57.046 34.783 39.54 0.00 39.36 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.019800 CGTCGGTCCGATCGATGA 58.980 61.111 18.75 2.87 43.83 2.92
184 191 2.579738 GTGGAGAAGGCGGGAGAC 59.420 66.667 0.00 0.00 39.17 3.36
185 192 2.683933 GGTGGAGAAGGCGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
186 193 2.685380 AGGTGGAGAAGGCGGGAG 60.685 66.667 0.00 0.00 0.00 4.30
187 194 2.683933 GAGGTGGAGAAGGCGGGA 60.684 66.667 0.00 0.00 0.00 5.14
188 195 4.148825 CGAGGTGGAGAAGGCGGG 62.149 72.222 0.00 0.00 0.00 6.13
228 235 8.369869 CGAAGACCGAGAAAATGGAACAACAA 62.370 42.308 0.00 0.00 41.73 2.83
229 236 6.981210 CGAAGACCGAGAAAATGGAACAACA 61.981 44.000 0.00 0.00 41.73 3.33
230 237 4.610680 CGAAGACCGAGAAAATGGAACAAC 60.611 45.833 0.00 0.00 41.73 3.32
231 238 3.496884 CGAAGACCGAGAAAATGGAACAA 59.503 43.478 0.00 0.00 41.73 2.83
357 3606 4.571375 TTACATTTTACTACACGCAGCG 57.429 40.909 14.82 14.82 0.00 5.18
383 3638 6.369340 TCGATTACGCATTTCCTAACAAAGAA 59.631 34.615 0.00 0.00 39.58 2.52
401 3656 3.065371 CCCTCCAGCAAAACATCGATTAC 59.935 47.826 0.00 0.00 0.00 1.89
457 3723 1.492176 GCTCCAGGAATCAAGGGATGA 59.508 52.381 0.00 0.00 43.67 2.92
594 4229 5.163301 GCATCAATCCAACCTAGTTCCTAGA 60.163 44.000 0.00 0.00 36.26 2.43
687 5027 6.473758 AGTAGGTATGGTTCTTTCTTGGTTC 58.526 40.000 0.00 0.00 0.00 3.62
816 5174 0.757561 GGGGAGGAGACTACTGGAGC 60.758 65.000 0.00 0.00 42.84 4.70
818 5176 0.335361 GTGGGGAGGAGACTACTGGA 59.665 60.000 0.00 0.00 42.84 3.86
819 5177 0.041238 TGTGGGGAGGAGACTACTGG 59.959 60.000 0.00 0.00 42.84 4.00
820 5178 1.550976 GTTGTGGGGAGGAGACTACTG 59.449 57.143 0.00 0.00 42.84 2.74
821 5179 1.552719 GGTTGTGGGGAGGAGACTACT 60.553 57.143 0.00 0.00 42.84 2.57
822 5180 0.903236 GGTTGTGGGGAGGAGACTAC 59.097 60.000 0.00 0.00 44.43 2.73
823 5181 0.252558 GGGTTGTGGGGAGGAGACTA 60.253 60.000 0.00 0.00 44.43 2.59
825 5183 2.603652 GGGGTTGTGGGGAGGAGAC 61.604 68.421 0.00 0.00 0.00 3.36
826 5184 2.204090 GGGGTTGTGGGGAGGAGA 60.204 66.667 0.00 0.00 0.00 3.71
827 5185 3.717294 CGGGGTTGTGGGGAGGAG 61.717 72.222 0.00 0.00 0.00 3.69
982 5370 2.407440 ATCCCGATCGACCGCTCCTA 62.407 60.000 18.66 0.00 0.00 2.94
1249 5666 0.396811 GTGTAGTGGTGGCAGAGGTT 59.603 55.000 0.00 0.00 0.00 3.50
1426 5872 2.510238 CACGCAGACCAGCTAGCC 60.510 66.667 12.13 0.00 0.00 3.93
1480 5940 6.208644 CAAGTGGTCACAAATTTTAGGACAG 58.791 40.000 12.89 0.00 0.00 3.51
1502 5962 2.592102 ATTTTCCTGCAGCTCTCCAA 57.408 45.000 8.66 0.00 0.00 3.53
1544 6005 9.132521 CAAGAAATGTTAGCTTTTATGTCTTGG 57.867 33.333 19.20 8.68 0.00 3.61
1576 6037 2.350804 GAGACGGAAATAAAAGGCCGAC 59.649 50.000 7.16 0.70 46.29 4.79
1584 6045 7.617225 TCAGGAACATTAGAGACGGAAATAAA 58.383 34.615 0.00 0.00 0.00 1.40
1585 6046 7.177832 TCAGGAACATTAGAGACGGAAATAA 57.822 36.000 0.00 0.00 0.00 1.40
1616 6083 5.808366 AAGGGCGTATGAAGAGATGATTA 57.192 39.130 0.00 0.00 0.00 1.75
1619 6086 3.797039 CAAAGGGCGTATGAAGAGATGA 58.203 45.455 0.00 0.00 0.00 2.92
1645 6112 4.923415 TGAAGAGAGGATTTTCTTTCCCC 58.077 43.478 0.00 0.00 33.97 4.81
1646 6113 7.255416 GCATATGAAGAGAGGATTTTCTTTCCC 60.255 40.741 6.97 0.00 33.97 3.97
1647 6114 7.501892 AGCATATGAAGAGAGGATTTTCTTTCC 59.498 37.037 6.97 0.00 33.97 3.13
1652 6119 7.215789 TCAGAGCATATGAAGAGAGGATTTTC 58.784 38.462 6.97 0.00 0.00 2.29
1653 6120 7.134362 TCAGAGCATATGAAGAGAGGATTTT 57.866 36.000 6.97 0.00 0.00 1.82
1710 6180 1.979155 CAGCCTCGTCTCACCTCCA 60.979 63.158 0.00 0.00 0.00 3.86
1720 6190 2.044650 ATGCAATGCCAGCCTCGT 60.045 55.556 1.53 0.00 0.00 4.18
1722 6192 0.102481 CTTGATGCAATGCCAGCCTC 59.898 55.000 1.53 0.00 0.00 4.70
1735 6205 3.516981 ACCAGTCTCGATCACTTGATG 57.483 47.619 0.00 0.00 34.37 3.07
1747 6217 2.526432 TGTACTCCTCCAACCAGTCTC 58.474 52.381 0.00 0.00 0.00 3.36
1751 6221 5.066505 GCAATTATTGTACTCCTCCAACCAG 59.933 44.000 6.81 0.00 0.00 4.00
1780 6250 6.944862 AGAATTTTCTAAACTGCATCCTCAGT 59.055 34.615 0.00 0.00 41.33 3.41
1798 6268 5.784578 AAAGCCCGTGAGTTTAGAATTTT 57.215 34.783 0.00 0.00 0.00 1.82
1799 6269 5.784578 AAAAGCCCGTGAGTTTAGAATTT 57.215 34.783 0.00 0.00 0.00 1.82
1800 6270 5.106830 CGTAAAAGCCCGTGAGTTTAGAATT 60.107 40.000 0.00 0.00 0.00 2.17
1802 6272 3.742369 CGTAAAAGCCCGTGAGTTTAGAA 59.258 43.478 0.00 0.00 0.00 2.10
1803 6273 3.319755 CGTAAAAGCCCGTGAGTTTAGA 58.680 45.455 0.00 0.00 0.00 2.10
1804 6274 2.414138 CCGTAAAAGCCCGTGAGTTTAG 59.586 50.000 0.00 0.00 0.00 1.85
1805 6275 2.415776 CCGTAAAAGCCCGTGAGTTTA 58.584 47.619 0.00 0.00 0.00 2.01
1806 6276 1.232119 CCGTAAAAGCCCGTGAGTTT 58.768 50.000 0.00 0.00 0.00 2.66
1810 6280 1.555477 ATCCCCGTAAAAGCCCGTGA 61.555 55.000 0.00 0.00 0.00 4.35
1815 6285 2.823747 ACAGAAAATCCCCGTAAAAGCC 59.176 45.455 0.00 0.00 0.00 4.35
1816 6286 3.366985 CCACAGAAAATCCCCGTAAAAGC 60.367 47.826 0.00 0.00 0.00 3.51
1817 6287 3.192633 CCCACAGAAAATCCCCGTAAAAG 59.807 47.826 0.00 0.00 0.00 2.27
1819 6289 2.555670 CCCCACAGAAAATCCCCGTAAA 60.556 50.000 0.00 0.00 0.00 2.01
1820 6290 1.004979 CCCCACAGAAAATCCCCGTAA 59.995 52.381 0.00 0.00 0.00 3.18
1821 6291 0.621609 CCCCACAGAAAATCCCCGTA 59.378 55.000 0.00 0.00 0.00 4.02
1822 6292 1.382629 CCCCACAGAAAATCCCCGT 59.617 57.895 0.00 0.00 0.00 5.28
1823 6293 2.052104 GCCCCACAGAAAATCCCCG 61.052 63.158 0.00 0.00 0.00 5.73
1824 6294 0.972471 CAGCCCCACAGAAAATCCCC 60.972 60.000 0.00 0.00 0.00 4.81
1825 6295 0.972471 CCAGCCCCACAGAAAATCCC 60.972 60.000 0.00 0.00 0.00 3.85
1827 6297 0.039618 TCCCAGCCCCACAGAAAATC 59.960 55.000 0.00 0.00 0.00 2.17
1828 6298 0.712380 ATCCCAGCCCCACAGAAAAT 59.288 50.000 0.00 0.00 0.00 1.82
1830 6300 0.251742 CAATCCCAGCCCCACAGAAA 60.252 55.000 0.00 0.00 0.00 2.52
1831 6301 1.383799 CAATCCCAGCCCCACAGAA 59.616 57.895 0.00 0.00 0.00 3.02
1832 6302 1.434513 AACAATCCCAGCCCCACAGA 61.435 55.000 0.00 0.00 0.00 3.41
1833 6303 0.967380 GAACAATCCCAGCCCCACAG 60.967 60.000 0.00 0.00 0.00 3.66
1835 6305 2.046285 CGAACAATCCCAGCCCCAC 61.046 63.158 0.00 0.00 0.00 4.61
1837 6307 1.749258 GTCGAACAATCCCAGCCCC 60.749 63.158 0.00 0.00 0.00 5.80
1838 6308 0.539986 TAGTCGAACAATCCCAGCCC 59.460 55.000 0.00 0.00 0.00 5.19
1839 6309 1.207329 ACTAGTCGAACAATCCCAGCC 59.793 52.381 0.00 0.00 0.00 4.85
1840 6310 2.094182 TGACTAGTCGAACAATCCCAGC 60.094 50.000 17.85 0.00 0.00 4.85
1841 6311 3.512680 GTGACTAGTCGAACAATCCCAG 58.487 50.000 17.85 0.00 0.00 4.45
1843 6313 2.734492 CGGTGACTAGTCGAACAATCCC 60.734 54.545 17.85 6.51 0.00 3.85
1844 6314 2.527100 CGGTGACTAGTCGAACAATCC 58.473 52.381 17.85 9.80 0.00 3.01
1847 6317 0.669619 TGCGGTGACTAGTCGAACAA 59.330 50.000 17.85 1.11 0.00 2.83
1848 6318 0.240145 CTGCGGTGACTAGTCGAACA 59.760 55.000 17.85 11.86 0.00 3.18
1850 6320 1.211969 GCTGCGGTGACTAGTCGAA 59.788 57.895 17.85 0.58 0.00 3.71
1851 6321 2.875485 GCTGCGGTGACTAGTCGA 59.125 61.111 17.85 4.78 0.00 4.20
1852 6322 2.324332 ATCGCTGCGGTGACTAGTCG 62.324 60.000 23.03 8.18 34.60 4.18
1853 6323 0.179134 AATCGCTGCGGTGACTAGTC 60.179 55.000 23.03 16.32 34.60 2.59
1854 6324 0.458543 CAATCGCTGCGGTGACTAGT 60.459 55.000 23.03 0.00 34.60 2.57
1855 6325 0.458543 ACAATCGCTGCGGTGACTAG 60.459 55.000 25.76 6.82 34.60 2.57
1856 6326 0.037697 AACAATCGCTGCGGTGACTA 60.038 50.000 25.76 7.40 34.60 2.59
1857 6327 1.291877 GAACAATCGCTGCGGTGACT 61.292 55.000 25.76 15.54 34.60 3.41
1860 6330 2.096406 CGAACAATCGCTGCGGTG 59.904 61.111 23.03 21.25 42.96 4.94
1922 8096 2.070783 GTGAAATAACGAAGACCGCCA 58.929 47.619 0.00 0.00 43.32 5.69
1979 9126 8.593945 AGTTGACATCAAACCATGGTAATTAT 57.406 30.769 20.12 6.96 37.63 1.28
1988 9135 6.534793 GTGAAAACAAGTTGACATCAAACCAT 59.465 34.615 10.54 0.00 37.63 3.55
1993 9140 6.018589 TGTGTGAAAACAAGTTGACATCAA 57.981 33.333 10.54 0.00 0.00 2.57
1994 9141 5.635417 TGTGTGAAAACAAGTTGACATCA 57.365 34.783 10.54 7.42 0.00 3.07
1995 9142 6.498304 AGATGTGTGAAAACAAGTTGACATC 58.502 36.000 17.49 17.49 39.04 3.06
1996 9143 6.455360 AGATGTGTGAAAACAAGTTGACAT 57.545 33.333 10.54 6.83 32.81 3.06
1997 9144 5.895636 AGATGTGTGAAAACAAGTTGACA 57.104 34.783 10.54 1.64 32.81 3.58
1998 9145 6.092748 ACAAGATGTGTGAAAACAAGTTGAC 58.907 36.000 10.54 0.00 39.72 3.18
1999 9146 6.266168 ACAAGATGTGTGAAAACAAGTTGA 57.734 33.333 10.54 0.00 39.72 3.18
2000 9147 7.026562 TGTACAAGATGTGTGAAAACAAGTTG 58.973 34.615 0.00 0.00 41.89 3.16
2001 9148 7.151999 TGTACAAGATGTGTGAAAACAAGTT 57.848 32.000 0.00 0.00 41.89 2.66
2002 9149 6.751514 TGTACAAGATGTGTGAAAACAAGT 57.248 33.333 0.00 0.00 41.89 3.16
2003 9150 8.633075 AAATGTACAAGATGTGTGAAAACAAG 57.367 30.769 0.00 0.00 41.89 3.16
2012 9159 9.283768 TGTATGAGAAAAATGTACAAGATGTGT 57.716 29.630 0.00 0.00 44.82 3.72
2028 9175 5.925397 ACAAATGCGCATTTTGTATGAGAAA 59.075 32.000 38.50 0.00 38.84 2.52
2031 9178 5.345472 TGAACAAATGCGCATTTTGTATGAG 59.655 36.000 38.50 28.17 38.84 2.90
2037 9184 5.512573 TGTATGAACAAATGCGCATTTTG 57.487 34.783 38.50 32.45 38.84 2.44
2041 9188 4.906065 AGATGTATGAACAAATGCGCAT 57.094 36.364 19.28 19.28 39.58 4.73
2042 9189 4.700268 AAGATGTATGAACAAATGCGCA 57.300 36.364 14.96 14.96 39.58 6.09
2043 9190 7.684062 ATTAAAGATGTATGAACAAATGCGC 57.316 32.000 0.00 0.00 39.58 6.09


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

AutoCloner maintained by Alex Coulton.