Multiple sequence alignment - TraesCS4D01G323300

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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 TraesCS4D01G323300 chr4D 100.000 2375 0 0 1 2375 484722441 484720067 0.000000e+00 4386.0
1 TraesCS4D01G323300 chr4D 76.508 315 54 15 107 408 138259778 138260085 1.140000e-33 154.0
2 TraesCS4D01G323300 chr4B 88.521 1629 90 38 1 1556 617425432 617423828 0.000000e+00 1882.0
3 TraesCS4D01G323300 chr4B 89.482 1217 54 23 409 1556 617404769 617403558 0.000000e+00 1471.0
4 TraesCS4D01G323300 chr4B 94.293 368 19 2 4 370 617405142 617404776 1.590000e-156 562.0
5 TraesCS4D01G323300 chr4B 79.433 141 21 8 125 262 78660935 78661070 2.510000e-15 93.5
6 TraesCS4D01G323300 chr5A 89.491 1237 45 26 377 1554 665763186 665761976 0.000000e+00 1485.0
7 TraesCS4D01G323300 chr5A 92.375 341 17 4 1 335 665763522 665763185 5.940000e-131 477.0
8 TraesCS4D01G323300 chr3A 93.535 727 43 2 1652 2375 725923634 725924359 0.000000e+00 1079.0
9 TraesCS4D01G323300 chr3D 87.336 229 23 5 584 808 523814793 523815019 8.420000e-65 257.0
10 TraesCS4D01G323300 chr3D 75.000 348 61 22 75 405 512259117 512258779 1.140000e-28 137.0
11 TraesCS4D01G323300 chr3B 87.273 220 21 6 593 808 691275023 691275239 6.560000e-61 244.0
12 TraesCS4D01G323300 chr3B 85.263 95 11 2 2282 2375 780747167 780747259 6.990000e-16 95.3
13 TraesCS4D01G323300 chr5B 89.362 188 19 1 1655 1841 595141915 595142102 3.950000e-58 235.0
14 TraesCS4D01G323300 chr4A 82.671 277 37 8 539 805 743989688 743989413 3.950000e-58 235.0
15 TraesCS4D01G323300 chr1B 82.545 275 40 6 538 805 174963737 174963464 3.950000e-58 235.0
16 TraesCS4D01G323300 chr1B 81.884 276 40 8 538 805 174982397 174982124 8.540000e-55 224.0
17 TraesCS4D01G323300 chr1B 87.097 93 6 4 2285 2375 532661370 532661282 1.500000e-17 100.0
18 TraesCS4D01G323300 chr1B 100.000 28 0 0 1095 1122 133171320 133171347 4.000000e-03 52.8
19 TraesCS4D01G323300 chr2D 88.298 188 20 2 1656 1841 524270496 524270309 8.540000e-55 224.0
20 TraesCS4D01G323300 chr2D 87.302 189 21 3 1656 1842 524269083 524269270 1.850000e-51 213.0
21 TraesCS4D01G323300 chr2D 77.949 195 33 7 148 339 285350187 285350374 1.930000e-21 113.0
22 TraesCS4D01G323300 chr1D 76.905 420 77 16 4 414 398021315 398020907 1.110000e-53 220.0
23 TraesCS4D01G323300 chr1D 87.302 189 21 3 1654 1841 14148206 14148392 1.850000e-51 213.0
24 TraesCS4D01G323300 chr1D 87.571 177 17 4 628 800 268952514 268952689 1.440000e-47 200.0
25 TraesCS4D01G323300 chr1D 78.157 293 52 11 1656 1942 229879376 229879090 2.430000e-40 176.0
26 TraesCS4D01G323300 chr6D 87.701 187 23 0 1656 1842 454584676 454584862 3.970000e-53 219.0
27 TraesCS4D01G323300 chr6D 87.701 187 22 1 1656 1841 454586088 454585902 1.430000e-52 217.0
28 TraesCS4D01G323300 chr6D 95.000 40 2 0 1087 1126 115331920 115331881 1.970000e-06 63.9
29 TraesCS4D01G323300 chr7B 87.368 190 22 2 1653 1841 5040813 5041001 1.430000e-52 217.0
30 TraesCS4D01G323300 chr7B 73.134 335 67 17 77 397 528769084 528769409 5.400000e-17 99.0
31 TraesCS4D01G323300 chr7B 100.000 28 0 0 1096 1123 708918099 708918072 4.000000e-03 52.8
32 TraesCS4D01G323300 chr2A 79.916 239 43 4 538 771 527782033 527781795 1.130000e-38 171.0
33 TraesCS4D01G323300 chr7A 74.481 337 61 20 78 399 671225713 671225387 3.210000e-24 122.0
34 TraesCS4D01G323300 chr7A 94.872 39 2 0 1087 1125 660173389 660173427 7.090000e-06 62.1
35 TraesCS4D01G323300 chr6A 86.538 52 5 2 132 182 13748861 13748811 3.300000e-04 56.5


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 TraesCS4D01G323300 chr4D 484720067 484722441 2374 True 4386.0 4386 100.0000 1 2375 1 chr4D.!!$R1 2374
1 TraesCS4D01G323300 chr4B 617423828 617425432 1604 True 1882.0 1882 88.5210 1 1556 1 chr4B.!!$R1 1555
2 TraesCS4D01G323300 chr4B 617403558 617405142 1584 True 1016.5 1471 91.8875 4 1556 2 chr4B.!!$R2 1552
3 TraesCS4D01G323300 chr5A 665761976 665763522 1546 True 981.0 1485 90.9330 1 1554 2 chr5A.!!$R1 1553
4 TraesCS4D01G323300 chr3A 725923634 725924359 725 False 1079.0 1079 93.5350 1652 2375 1 chr3A.!!$F1 723

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
926 1013 0.042581 TCCTGGACATACTCTGCCCA 59.957 55.0 0.0 0.0 34.6 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 2076 0.9337 AGGGGAGGAGAGAAGAGGAG 59.066 60.0 0.0 0.0 0.0 3.69 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
24 25 2.533266 TAATTCATCTCTGAGCCCGC 57.467 50.000 0.00 0.00 31.68 6.13
70 71 8.305441 AGTAAAATCATTAAAACCCGCAAAAG 57.695 30.769 0.00 0.00 0.00 2.27
143 145 3.316588 TGCTCGTGCTAAATTTGGTGAAA 59.683 39.130 11.19 0.00 40.48 2.69
172 175 1.338107 TCGAGGAGCCTGTGAGAAAA 58.662 50.000 0.00 0.00 0.00 2.29
266 274 5.009410 AGAGCTTCTCAAATGTCCAAACTTG 59.991 40.000 0.00 0.00 32.06 3.16
298 306 0.667487 ACGGACATCACGCACTCAAG 60.667 55.000 0.00 0.00 34.00 3.02
408 418 4.130281 CGAAAACGTCGCTCCCGC 62.130 66.667 0.00 0.00 44.14 6.13
409 419 2.737376 GAAAACGTCGCTCCCGCT 60.737 61.111 0.00 0.00 0.00 5.52
610 645 5.068855 TCAACAAATCTCAGCCATCAAACAA 59.931 36.000 0.00 0.00 0.00 2.83
621 656 3.670055 GCCATCAAACAACGTCAATTCAG 59.330 43.478 0.00 0.00 0.00 3.02
926 1013 0.042581 TCCTGGACATACTCTGCCCA 59.957 55.000 0.00 0.00 34.60 5.36
927 1014 1.135094 CCTGGACATACTCTGCCCAT 58.865 55.000 0.00 0.00 36.72 4.00
928 1015 1.071385 CCTGGACATACTCTGCCCATC 59.929 57.143 0.00 0.00 36.72 3.51
929 1016 2.045524 CTGGACATACTCTGCCCATCT 58.954 52.381 0.00 0.00 36.72 2.90
930 1017 2.036992 CTGGACATACTCTGCCCATCTC 59.963 54.545 0.00 0.00 36.72 2.75
931 1018 2.324541 GGACATACTCTGCCCATCTCT 58.675 52.381 0.00 0.00 0.00 3.10
932 1019 2.036992 GGACATACTCTGCCCATCTCTG 59.963 54.545 0.00 0.00 0.00 3.35
933 1020 2.036992 GACATACTCTGCCCATCTCTGG 59.963 54.545 0.00 0.00 42.73 3.86
934 1021 2.045524 CATACTCTGCCCATCTCTGGT 58.954 52.381 0.00 0.00 41.37 4.00
935 1022 1.781786 TACTCTGCCCATCTCTGGTC 58.218 55.000 0.00 0.00 41.37 4.02
936 1023 0.980231 ACTCTGCCCATCTCTGGTCC 60.980 60.000 0.00 0.00 41.37 4.46
940 1027 0.636647 TGCCCATCTCTGGTCCTAGA 59.363 55.000 0.00 0.00 41.37 2.43
981 1068 4.223953 TCTACCCATCCTCGAGCTTTATT 58.776 43.478 6.99 0.00 0.00 1.40
1083 1172 3.708734 GTGGCCGGTTCGTGTTCG 61.709 66.667 1.90 0.00 38.55 3.95
1088 1177 1.663702 CCGGTTCGTGTTCGCTCTT 60.664 57.895 0.00 0.00 36.96 2.85
1089 1178 1.615107 CCGGTTCGTGTTCGCTCTTC 61.615 60.000 0.00 0.00 36.96 2.87
1092 1181 0.850856 GTTCGTGTTCGCTCTTCGTT 59.149 50.000 0.00 0.00 39.67 3.85
1107 1196 6.243649 CGCTCTTCGTTTTAAAATAAGTGTCG 59.756 38.462 18.18 17.68 0.00 4.35
1129 1218 9.729023 TGTCGCTGATTTAATACAAAATTATGG 57.271 29.630 0.00 0.00 0.00 2.74
1142 1231 6.365520 ACAAAATTATGGATGGAGGGAGTAC 58.634 40.000 0.00 0.00 0.00 2.73
1183 1273 7.252965 TGAACATTTTCGTGTGTTGAGATAA 57.747 32.000 0.00 0.00 38.57 1.75
1281 1371 4.254709 ACGCAGTGCTGGCTGGAA 62.255 61.111 14.33 0.00 42.51 3.53
1412 1509 1.227674 CTAGCGTCAAGGCCATCCC 60.228 63.158 5.01 0.00 0.00 3.85
1447 1563 5.127491 TCCTACCGAGTTGAATTGTTGTTT 58.873 37.500 0.00 0.00 0.00 2.83
1571 1688 3.883631 AAAGGTAAACGTTTGTAGCCG 57.116 42.857 23.46 0.00 33.32 5.52
1572 1689 1.799544 AGGTAAACGTTTGTAGCCGG 58.200 50.000 23.46 0.00 0.00 6.13
1573 1690 1.070601 AGGTAAACGTTTGTAGCCGGT 59.929 47.619 23.46 3.39 0.00 5.28
1574 1691 1.460743 GGTAAACGTTTGTAGCCGGTC 59.539 52.381 23.46 0.00 0.00 4.79
1575 1692 2.134346 GTAAACGTTTGTAGCCGGTCA 58.866 47.619 23.46 0.00 0.00 4.02
1576 1693 1.223187 AAACGTTTGTAGCCGGTCAG 58.777 50.000 13.81 0.00 0.00 3.51
1577 1694 1.226030 AACGTTTGTAGCCGGTCAGC 61.226 55.000 1.90 0.00 0.00 4.26
1578 1695 2.388232 CGTTTGTAGCCGGTCAGCC 61.388 63.158 1.90 0.00 0.00 4.85
1588 1705 2.597510 GGTCAGCCGGCCAAACTT 60.598 61.111 26.15 0.00 0.00 2.66
1589 1706 2.200337 GGTCAGCCGGCCAAACTTT 61.200 57.895 26.15 0.00 0.00 2.66
1590 1707 1.285950 GTCAGCCGGCCAAACTTTC 59.714 57.895 26.15 1.31 0.00 2.62
1591 1708 1.901464 TCAGCCGGCCAAACTTTCC 60.901 57.895 26.15 0.00 0.00 3.13
1592 1709 2.983592 AGCCGGCCAAACTTTCCG 60.984 61.111 26.15 0.00 42.58 4.30
1593 1710 4.717629 GCCGGCCAAACTTTCCGC 62.718 66.667 18.11 0.00 41.68 5.54
1594 1711 2.983592 CCGGCCAAACTTTCCGCT 60.984 61.111 2.24 0.00 41.68 5.52
1595 1712 2.255252 CGGCCAAACTTTCCGCTG 59.745 61.111 2.24 0.00 36.53 5.18
1596 1713 2.650778 GGCCAAACTTTCCGCTGG 59.349 61.111 0.00 0.00 0.00 4.85
1597 1714 2.049156 GCCAAACTTTCCGCTGGC 60.049 61.111 0.00 0.00 46.95 4.85
1598 1715 3.763671 CCAAACTTTCCGCTGGCT 58.236 55.556 0.00 0.00 0.00 4.75
1599 1716 2.041153 CCAAACTTTCCGCTGGCTT 58.959 52.632 0.00 0.00 0.00 4.35
1600 1717 0.318955 CCAAACTTTCCGCTGGCTTG 60.319 55.000 0.00 0.00 0.00 4.01
1601 1718 0.940991 CAAACTTTCCGCTGGCTTGC 60.941 55.000 0.00 0.00 0.00 4.01
1625 1742 4.717629 CTGGTTCGCTCGCCACGA 62.718 66.667 0.00 0.00 37.86 4.35
1626 1743 3.989698 CTGGTTCGCTCGCCACGAT 62.990 63.158 0.00 0.00 39.65 3.73
1627 1744 2.813908 GGTTCGCTCGCCACGATT 60.814 61.111 0.00 0.00 39.65 3.34
1628 1745 2.695646 GTTCGCTCGCCACGATTC 59.304 61.111 0.00 0.00 39.65 2.52
1629 1746 1.805945 GTTCGCTCGCCACGATTCT 60.806 57.895 0.00 0.00 39.65 2.40
1630 1747 1.080093 TTCGCTCGCCACGATTCTT 60.080 52.632 0.00 0.00 39.65 2.52
1631 1748 1.076533 TTCGCTCGCCACGATTCTTC 61.077 55.000 0.00 0.00 39.65 2.87
1632 1749 2.517450 CGCTCGCCACGATTCTTCC 61.517 63.158 0.00 0.00 34.61 3.46
1633 1750 2.174319 GCTCGCCACGATTCTTCCC 61.174 63.158 0.00 0.00 34.61 3.97
1634 1751 1.218047 CTCGCCACGATTCTTCCCA 59.782 57.895 0.00 0.00 34.61 4.37
1635 1752 0.391130 CTCGCCACGATTCTTCCCAA 60.391 55.000 0.00 0.00 34.61 4.12
1636 1753 0.672401 TCGCCACGATTCTTCCCAAC 60.672 55.000 0.00 0.00 0.00 3.77
1637 1754 0.673644 CGCCACGATTCTTCCCAACT 60.674 55.000 0.00 0.00 0.00 3.16
1638 1755 1.087501 GCCACGATTCTTCCCAACTC 58.912 55.000 0.00 0.00 0.00 3.01
1639 1756 1.610624 GCCACGATTCTTCCCAACTCA 60.611 52.381 0.00 0.00 0.00 3.41
1640 1757 2.076863 CCACGATTCTTCCCAACTCAC 58.923 52.381 0.00 0.00 0.00 3.51
1641 1758 1.726791 CACGATTCTTCCCAACTCACG 59.273 52.381 0.00 0.00 0.00 4.35
1642 1759 0.721718 CGATTCTTCCCAACTCACGC 59.278 55.000 0.00 0.00 0.00 5.34
1643 1760 0.721718 GATTCTTCCCAACTCACGCG 59.278 55.000 3.53 3.53 0.00 6.01
1644 1761 0.320374 ATTCTTCCCAACTCACGCGA 59.680 50.000 15.93 0.00 0.00 5.87
1645 1762 0.599204 TTCTTCCCAACTCACGCGAC 60.599 55.000 15.93 0.00 0.00 5.19
1646 1763 2.355363 TTCCCAACTCACGCGACG 60.355 61.111 15.93 2.89 0.00 5.12
1647 1764 3.851845 TTCCCAACTCACGCGACGG 62.852 63.158 15.93 4.06 0.00 4.79
1649 1766 4.657824 CCAACTCACGCGACGGGT 62.658 66.667 15.93 12.27 0.00 5.28
1650 1767 3.403057 CAACTCACGCGACGGGTG 61.403 66.667 32.20 32.20 45.77 4.61
1656 1773 3.598715 ACGCGACGGGTGAACAGA 61.599 61.111 15.93 0.00 0.00 3.41
1696 1813 2.223805 CCAGTTTGAAGGTCAGGTTTGC 60.224 50.000 0.00 0.00 0.00 3.68
1713 1830 6.861055 CAGGTTTGCGAAAAACACTACAATAT 59.139 34.615 6.70 0.00 32.04 1.28
1742 1859 6.497785 TTTTTCAGAAAACACCACGTCTTA 57.502 33.333 7.89 0.00 30.07 2.10
1743 1860 6.687081 TTTTCAGAAAACACCACGTCTTAT 57.313 33.333 4.06 0.00 0.00 1.73
1749 1866 7.117236 TCAGAAAACACCACGTCTTATGTAATC 59.883 37.037 0.00 0.00 0.00 1.75
1814 1931 2.552315 GTGTTTATGACATATGGGCCCG 59.448 50.000 19.37 4.81 41.10 6.13
1816 1933 3.073798 TGTTTATGACATATGGGCCCGAT 59.926 43.478 19.37 14.37 32.00 4.18
1836 1953 4.266029 CGATTTTTGCTGATGTGGCATAAC 59.734 41.667 0.00 0.00 39.54 1.89
1863 1980 6.381481 TCACAAGTAACGACTTTAGACAGA 57.619 37.500 0.00 0.00 43.70 3.41
1868 1985 7.222224 ACAAGTAACGACTTTAGACAGAGTTTG 59.778 37.037 0.00 0.00 43.70 2.93
1905 2022 9.020731 ACAAAATAGTCCCTGGTATTTTACAAG 57.979 33.333 11.13 4.84 36.93 3.16
1917 2034 8.918202 TGGTATTTTACAAGAACACTCTTCAT 57.082 30.769 0.00 0.00 40.05 2.57
1959 2076 2.484062 CCCCATCTTGATGCGTGCC 61.484 63.158 5.16 0.00 0.00 5.01
1978 2095 0.933700 CTCCTCTTCTCTCCTCCCCT 59.066 60.000 0.00 0.00 0.00 4.79
2055 2172 0.898320 AGCTAGAAGAAGGCGAGCAA 59.102 50.000 0.00 0.00 35.55 3.91
2162 2282 1.096416 GACTGGTCCACTCCTACTCG 58.904 60.000 0.00 0.00 0.00 4.18
2167 2287 0.109226 GTCCACTCCTACTCGTGTGC 60.109 60.000 0.00 0.00 0.00 4.57
2169 2289 1.801913 CACTCCTACTCGTGTGCGC 60.802 63.158 0.00 0.00 38.14 6.09
2170 2290 2.265904 ACTCCTACTCGTGTGCGCA 61.266 57.895 5.66 5.66 38.14 6.09
2171 2291 1.801913 CTCCTACTCGTGTGCGCAC 60.802 63.158 33.11 33.11 41.97 5.34
2212 2332 3.449227 CCGGCAGTGTAGAGCGGA 61.449 66.667 0.00 0.00 33.49 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.240549 ACTATTCACCAAGGTTAGATGAGG 57.759 41.667 4.00 0.00 0.00 3.86
143 145 1.561542 AGGCTCCTCGAATGTCCAAAT 59.438 47.619 0.00 0.00 0.00 2.32
404 414 0.468648 CCTTTAGGTTAGGGAGCGGG 59.531 60.000 0.00 0.00 0.00 6.13
568 603 2.964740 TGAATCTGCTCCTTTGAGTCG 58.035 47.619 0.00 0.00 40.95 4.18
610 645 5.523916 GCAATATAGGTCACTGAATTGACGT 59.476 40.000 0.00 0.00 45.95 4.34
621 656 4.511454 TCGCATTGAAGCAATATAGGTCAC 59.489 41.667 0.00 0.00 32.35 3.67
770 813 8.359642 GCAGGTTGATATGGCAGAAAATTAATA 58.640 33.333 0.00 0.00 0.00 0.98
926 1013 5.480205 GTTTCGTTTTCTAGGACCAGAGAT 58.520 41.667 0.00 0.00 0.00 2.75
927 1014 4.262335 GGTTTCGTTTTCTAGGACCAGAGA 60.262 45.833 0.00 0.00 0.00 3.10
928 1015 3.995048 GGTTTCGTTTTCTAGGACCAGAG 59.005 47.826 0.00 0.00 0.00 3.35
929 1016 3.244318 GGGTTTCGTTTTCTAGGACCAGA 60.244 47.826 0.00 0.00 0.00 3.86
930 1017 3.072211 GGGTTTCGTTTTCTAGGACCAG 58.928 50.000 0.00 0.00 0.00 4.00
931 1018 2.438763 TGGGTTTCGTTTTCTAGGACCA 59.561 45.455 0.00 0.00 0.00 4.02
932 1019 3.130280 TGGGTTTCGTTTTCTAGGACC 57.870 47.619 0.00 0.00 0.00 4.46
933 1020 3.878699 TGTTGGGTTTCGTTTTCTAGGAC 59.121 43.478 0.00 0.00 0.00 3.85
934 1021 3.878699 GTGTTGGGTTTCGTTTTCTAGGA 59.121 43.478 0.00 0.00 0.00 2.94
935 1022 3.881089 AGTGTTGGGTTTCGTTTTCTAGG 59.119 43.478 0.00 0.00 0.00 3.02
936 1023 6.649557 AGATAGTGTTGGGTTTCGTTTTCTAG 59.350 38.462 0.00 0.00 0.00 2.43
940 1027 5.471116 GGTAGATAGTGTTGGGTTTCGTTTT 59.529 40.000 0.00 0.00 0.00 2.43
981 1068 6.119536 GTCCATGGTATGTGATGGTTTCTTA 58.880 40.000 12.58 0.00 40.21 2.10
1083 1172 6.031107 GCGACACTTATTTTAAAACGAAGAGC 59.969 38.462 22.32 17.93 0.00 4.09
1088 1177 6.528014 TCAGCGACACTTATTTTAAAACGA 57.472 33.333 1.97 0.00 0.00 3.85
1089 1178 7.775729 AATCAGCGACACTTATTTTAAAACG 57.224 32.000 1.97 1.83 0.00 3.60
1116 1205 7.166758 ACTCCCTCCATCCATAATTTTGTAT 57.833 36.000 0.00 0.00 0.00 2.29
1129 1218 3.941483 CACAACAATGTACTCCCTCCATC 59.059 47.826 0.00 0.00 37.82 3.51
1183 1273 6.203915 TCTGCACGAAAACAACACATAAGTAT 59.796 34.615 0.00 0.00 0.00 2.12
1412 1509 4.128643 ACTCGGTAGGATTTCGTCTCTAG 58.871 47.826 0.00 0.00 0.00 2.43
1447 1563 6.151648 ACACTACTGGCTAGTACACGATTTTA 59.848 38.462 5.74 0.00 38.36 1.52
1516 1632 2.164338 TGATTTCCTACCCCGCAAAAC 58.836 47.619 0.00 0.00 0.00 2.43
1522 1638 2.747446 CACTGTTTGATTTCCTACCCCG 59.253 50.000 0.00 0.00 0.00 5.73
1556 1673 2.406130 CTGACCGGCTACAAACGTTTA 58.594 47.619 14.20 0.00 0.00 2.01
1557 1674 1.223187 CTGACCGGCTACAAACGTTT 58.777 50.000 7.96 7.96 0.00 3.60
1558 1675 1.226030 GCTGACCGGCTACAAACGTT 61.226 55.000 0.00 0.00 0.00 3.99
1559 1676 1.666872 GCTGACCGGCTACAAACGT 60.667 57.895 0.00 0.00 0.00 3.99
1560 1677 2.388232 GGCTGACCGGCTACAAACG 61.388 63.158 0.00 0.00 34.85 3.60
1561 1678 3.574780 GGCTGACCGGCTACAAAC 58.425 61.111 0.00 0.00 34.85 2.93
1571 1688 2.142357 GAAAGTTTGGCCGGCTGACC 62.142 60.000 28.56 10.32 0.00 4.02
1572 1689 1.285950 GAAAGTTTGGCCGGCTGAC 59.714 57.895 28.56 21.17 0.00 3.51
1573 1690 1.901464 GGAAAGTTTGGCCGGCTGA 60.901 57.895 28.56 12.69 0.00 4.26
1574 1691 2.650778 GGAAAGTTTGGCCGGCTG 59.349 61.111 28.56 0.00 0.00 4.85
1575 1692 2.983592 CGGAAAGTTTGGCCGGCT 60.984 61.111 28.56 3.45 41.29 5.52
1576 1693 4.717629 GCGGAAAGTTTGGCCGGC 62.718 66.667 21.18 21.18 44.92 6.13
1577 1694 2.983592 AGCGGAAAGTTTGGCCGG 60.984 61.111 15.28 0.00 44.92 6.13
1579 1696 2.650778 CCAGCGGAAAGTTTGGCC 59.349 61.111 0.00 0.00 0.00 5.36
1581 1698 0.318955 CAAGCCAGCGGAAAGTTTGG 60.319 55.000 0.00 0.00 0.00 3.28
1582 1699 0.940991 GCAAGCCAGCGGAAAGTTTG 60.941 55.000 0.00 0.00 0.00 2.93
1583 1700 1.363807 GCAAGCCAGCGGAAAGTTT 59.636 52.632 0.00 0.00 0.00 2.66
1584 1701 3.042560 GCAAGCCAGCGGAAAGTT 58.957 55.556 0.00 0.00 0.00 2.66
1608 1725 3.989698 ATCGTGGCGAGCGAACCAG 62.990 63.158 3.04 0.00 41.84 4.00
1609 1726 3.583276 AATCGTGGCGAGCGAACCA 62.583 57.895 3.04 0.00 41.84 3.67
1610 1727 2.799540 GAATCGTGGCGAGCGAACC 61.800 63.158 3.04 0.00 41.84 3.62
1611 1728 1.352156 AAGAATCGTGGCGAGCGAAC 61.352 55.000 3.04 1.97 41.84 3.95
1612 1729 1.076533 GAAGAATCGTGGCGAGCGAA 61.077 55.000 3.04 0.00 41.84 4.70
1613 1730 1.516386 GAAGAATCGTGGCGAGCGA 60.516 57.895 0.00 1.51 39.91 4.93
1614 1731 2.517450 GGAAGAATCGTGGCGAGCG 61.517 63.158 0.00 0.00 39.91 5.03
1615 1732 2.174319 GGGAAGAATCGTGGCGAGC 61.174 63.158 0.00 0.00 39.91 5.03
1616 1733 0.391130 TTGGGAAGAATCGTGGCGAG 60.391 55.000 0.00 0.00 39.91 5.03
1617 1734 0.672401 GTTGGGAAGAATCGTGGCGA 60.672 55.000 0.00 0.00 41.13 5.54
1618 1735 0.673644 AGTTGGGAAGAATCGTGGCG 60.674 55.000 0.00 0.00 0.00 5.69
1619 1736 1.087501 GAGTTGGGAAGAATCGTGGC 58.912 55.000 0.00 0.00 0.00 5.01
1620 1737 2.076863 GTGAGTTGGGAAGAATCGTGG 58.923 52.381 0.00 0.00 0.00 4.94
1621 1738 1.726791 CGTGAGTTGGGAAGAATCGTG 59.273 52.381 0.00 0.00 0.00 4.35
1622 1739 1.939838 GCGTGAGTTGGGAAGAATCGT 60.940 52.381 0.00 0.00 0.00 3.73
1623 1740 0.721718 GCGTGAGTTGGGAAGAATCG 59.278 55.000 0.00 0.00 0.00 3.34
1624 1741 0.721718 CGCGTGAGTTGGGAAGAATC 59.278 55.000 0.00 0.00 0.00 2.52
1625 1742 0.320374 TCGCGTGAGTTGGGAAGAAT 59.680 50.000 5.77 0.00 0.00 2.40
1626 1743 0.599204 GTCGCGTGAGTTGGGAAGAA 60.599 55.000 5.77 0.00 0.00 2.52
1627 1744 1.006571 GTCGCGTGAGTTGGGAAGA 60.007 57.895 5.77 0.00 0.00 2.87
1628 1745 2.372690 CGTCGCGTGAGTTGGGAAG 61.373 63.158 5.77 0.00 0.00 3.46
1629 1746 2.355363 CGTCGCGTGAGTTGGGAA 60.355 61.111 5.77 0.00 0.00 3.97
1630 1747 4.351938 CCGTCGCGTGAGTTGGGA 62.352 66.667 5.77 0.00 0.00 4.37
1632 1749 4.657824 ACCCGTCGCGTGAGTTGG 62.658 66.667 5.77 2.63 0.00 3.77
1633 1750 3.403057 CACCCGTCGCGTGAGTTG 61.403 66.667 5.77 0.00 32.77 3.16
1634 1751 3.141522 TTCACCCGTCGCGTGAGTT 62.142 57.895 12.15 0.00 41.10 3.01
1635 1752 3.598715 TTCACCCGTCGCGTGAGT 61.599 61.111 12.15 0.00 41.10 3.41
1636 1753 3.103911 GTTCACCCGTCGCGTGAG 61.104 66.667 12.15 0.00 41.10 3.51
1637 1754 3.834447 CTGTTCACCCGTCGCGTGA 62.834 63.158 8.62 8.62 38.46 4.35
1638 1755 3.403057 CTGTTCACCCGTCGCGTG 61.403 66.667 5.77 3.59 0.00 5.34
1639 1756 3.553437 CTCTGTTCACCCGTCGCGT 62.553 63.158 5.77 0.00 0.00 6.01
1640 1757 2.191354 TACTCTGTTCACCCGTCGCG 62.191 60.000 0.00 0.00 0.00 5.87
1641 1758 0.038892 TTACTCTGTTCACCCGTCGC 60.039 55.000 0.00 0.00 0.00 5.19
1642 1759 2.427232 TTTACTCTGTTCACCCGTCG 57.573 50.000 0.00 0.00 0.00 5.12
1643 1760 3.120304 GCAATTTACTCTGTTCACCCGTC 60.120 47.826 0.00 0.00 0.00 4.79
1644 1761 2.812011 GCAATTTACTCTGTTCACCCGT 59.188 45.455 0.00 0.00 0.00 5.28
1645 1762 2.811431 TGCAATTTACTCTGTTCACCCG 59.189 45.455 0.00 0.00 0.00 5.28
1646 1763 3.568007 TGTGCAATTTACTCTGTTCACCC 59.432 43.478 0.00 0.00 0.00 4.61
1647 1764 4.829064 TGTGCAATTTACTCTGTTCACC 57.171 40.909 0.00 0.00 0.00 4.02
1648 1765 6.019881 GGTTTTGTGCAATTTACTCTGTTCAC 60.020 38.462 0.00 0.00 0.00 3.18
1649 1766 6.039616 GGTTTTGTGCAATTTACTCTGTTCA 58.960 36.000 0.00 0.00 0.00 3.18
1650 1767 6.019881 GTGGTTTTGTGCAATTTACTCTGTTC 60.020 38.462 0.00 0.00 0.00 3.18
1651 1768 5.810074 GTGGTTTTGTGCAATTTACTCTGTT 59.190 36.000 0.00 0.00 0.00 3.16
1652 1769 5.348164 GTGGTTTTGTGCAATTTACTCTGT 58.652 37.500 0.00 0.00 0.00 3.41
1653 1770 4.744631 GGTGGTTTTGTGCAATTTACTCTG 59.255 41.667 0.00 0.00 0.00 3.35
1654 1771 4.404073 TGGTGGTTTTGTGCAATTTACTCT 59.596 37.500 0.00 0.00 0.00 3.24
1655 1772 4.688021 TGGTGGTTTTGTGCAATTTACTC 58.312 39.130 0.00 0.00 0.00 2.59
1656 1773 4.161377 ACTGGTGGTTTTGTGCAATTTACT 59.839 37.500 0.00 0.00 0.00 2.24
1682 1799 3.113322 GTTTTTCGCAAACCTGACCTTC 58.887 45.455 0.00 0.00 0.00 3.46
1685 1802 2.159296 AGTGTTTTTCGCAAACCTGACC 60.159 45.455 7.37 0.00 0.00 4.02
1688 1805 4.022464 TGTAGTGTTTTTCGCAAACCTG 57.978 40.909 7.37 0.00 0.00 4.00
1723 1840 4.699637 ACATAAGACGTGGTGTTTTCTGA 58.300 39.130 0.00 0.00 0.00 3.27
1742 1859 9.545105 TCAGTGATTTTTGCAAAAAGATTACAT 57.455 25.926 33.47 20.07 40.78 2.29
1743 1860 8.939201 TCAGTGATTTTTGCAAAAAGATTACA 57.061 26.923 33.47 24.74 40.78 2.41
1749 1866 5.613142 GCCGATCAGTGATTTTTGCAAAAAG 60.613 40.000 33.47 22.84 40.78 2.27
1814 1931 4.266029 CGTTATGCCACATCAGCAAAAATC 59.734 41.667 0.00 0.00 44.83 2.17
1816 1933 3.573598 CGTTATGCCACATCAGCAAAAA 58.426 40.909 0.00 0.00 44.83 1.94
1836 1953 4.977963 TCTAAAGTCGTTACTTGTGAACCG 59.022 41.667 0.00 0.00 45.37 4.44
1868 1985 8.244113 CCAGGGACTATTTTGTGAATTTAGAAC 58.756 37.037 0.00 0.00 36.02 3.01
1905 2022 8.687824 TCTTTTGTTTTGAATGAAGAGTGTTC 57.312 30.769 0.00 0.00 0.00 3.18
1917 2034 6.238429 GGCTGATTGCATTCTTTTGTTTTGAA 60.238 34.615 9.81 0.00 45.15 2.69
1959 2076 0.933700 AGGGGAGGAGAGAAGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
2017 2134 1.592400 GCACCTGTTGTTGCTTGCC 60.592 57.895 0.00 0.00 0.00 4.52
2028 2145 1.277557 CCTTCTTCTAGCTGCACCTGT 59.722 52.381 1.02 0.00 0.00 4.00
2075 2192 3.437795 GCTTCAGCGCCTGCACAT 61.438 61.111 2.29 0.00 46.23 3.21
2198 2318 2.580867 CGCTCCGCTCTACACTGC 60.581 66.667 0.00 0.00 0.00 4.40
2332 2452 4.157120 ATGGAGGGGCGCACGTAC 62.157 66.667 7.86 7.86 0.00 3.67


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

AutoCloner maintained by Alex Coulton.