Multiple sequence alignment - TraesCS7D01G274800

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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 TraesCS7D01G274800 chr7D 100.000 2378 0 0 1 2378 264324066 264326443 0.000000e+00 4392
1 TraesCS7D01G274800 chr7D 89.574 1525 89 29 240 1710 264359223 264360731 0.000000e+00 1871
2 TraesCS7D01G274800 chr7D 89.122 1526 87 30 240 1710 264369103 264370604 0.000000e+00 1825
3 TraesCS7D01G274800 chr7D 88.060 1206 72 30 569 1710 264337504 264338701 0.000000e+00 1363
4 TraesCS7D01G274800 chr7D 85.817 557 53 22 1835 2378 264370608 264371151 3.430000e-158 568
5 TraesCS7D01G274800 chr7D 83.333 558 65 24 1837 2378 264360737 264361282 7.640000e-135 490
6 TraesCS7D01G274800 chr7D 84.583 480 56 15 1907 2378 264338749 264339218 5.990000e-126 460
7 TraesCS7D01G274800 chr7D 95.604 91 4 0 1707 1797 528060317 528060407 1.900000e-31 147
8 TraesCS7D01G274800 chr7A 93.142 1531 65 13 185 1713 287861050 287862542 0.000000e+00 2209
9 TraesCS7D01G274800 chr7A 87.638 1181 92 19 540 1687 287888315 287889474 0.000000e+00 1323
10 TraesCS7D01G274800 chr7A 93.220 531 19 5 1865 2378 287889480 287890010 0.000000e+00 765
11 TraesCS7D01G274800 chr7A 87.052 363 31 5 253 613 287913023 287913371 1.710000e-106 396
12 TraesCS7D01G274800 chr7A 95.580 181 8 0 6 186 287860712 287860892 8.320000e-75 291
13 TraesCS7D01G274800 chr7B 87.696 1528 101 32 240 1710 244691244 244692741 0.000000e+00 1700
14 TraesCS7D01G274800 chr7B 87.185 1506 114 31 240 1710 244714754 244716215 0.000000e+00 1639
15 TraesCS7D01G274800 chr7B 88.659 1208 89 24 540 1712 244650201 244651395 0.000000e+00 1428
16 TraesCS7D01G274800 chr7B 93.699 857 46 4 240 1096 244643180 244644028 0.000000e+00 1277
17 TraesCS7D01G274800 chr7B 85.740 554 54 21 1837 2378 244716221 244716761 1.600000e-156 562
18 TraesCS7D01G274800 chr7B 84.919 557 57 25 1835 2378 244644943 244645485 2.690000e-149 538
19 TraesCS7D01G274800 chr7B 83.789 549 61 23 1837 2378 244692747 244693274 1.640000e-136 496
20 TraesCS7D01G274800 chr7B 81.208 596 45 24 1128 1671 244644027 244644607 3.660000e-113 418
21 TraesCS7D01G274800 chr7B 97.863 234 5 0 2145 2378 244651643 244651876 2.850000e-109 405
22 TraesCS7D01G274800 chr7B 93.651 252 15 1 1832 2083 244651394 244651644 2.230000e-100 375
23 TraesCS7D01G274800 chr7B 94.355 124 6 1 54 176 244640913 244641036 3.120000e-44 189
24 TraesCS7D01G274800 chr7B 93.878 98 6 0 1700 1797 744290794 744290697 5.300000e-32 148
25 TraesCS7D01G274800 chr7B 94.624 93 5 0 1705 1797 217312257 217312349 6.850000e-31 145
26 TraesCS7D01G274800 chrUn 91.657 875 51 10 240 1113 284874376 284875229 0.000000e+00 1192
27 TraesCS7D01G274800 chr5D 98.851 87 1 0 1711 1797 262838791 262838705 3.160000e-34 156
28 TraesCS7D01G274800 chr4B 96.591 88 3 0 1710 1797 99581209 99581296 1.900000e-31 147
29 TraesCS7D01G274800 chr4B 94.681 94 4 1 1704 1797 216815100 216815008 6.850000e-31 145
30 TraesCS7D01G274800 chr2D 96.591 88 3 0 1710 1797 488233729 488233642 1.900000e-31 147
31 TraesCS7D01G274800 chr1B 93.684 95 6 0 1703 1797 636267268 636267362 2.460000e-30 143
32 TraesCS7D01G274800 chr6A 88.793 116 9 4 1682 1797 507082123 507082012 3.190000e-29 139


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 TraesCS7D01G274800 chr7D 264324066 264326443 2377 False 4392.0 4392 100.00000 1 2378 1 chr7D.!!$F1 2377
1 TraesCS7D01G274800 chr7D 264369103 264371151 2048 False 1196.5 1825 87.46950 240 2378 2 chr7D.!!$F5 2138
2 TraesCS7D01G274800 chr7D 264359223 264361282 2059 False 1180.5 1871 86.45350 240 2378 2 chr7D.!!$F4 2138
3 TraesCS7D01G274800 chr7D 264337504 264339218 1714 False 911.5 1363 86.32150 569 2378 2 chr7D.!!$F3 1809
4 TraesCS7D01G274800 chr7A 287860712 287862542 1830 False 1250.0 2209 94.36100 6 1713 2 chr7A.!!$F2 1707
5 TraesCS7D01G274800 chr7A 287888315 287890010 1695 False 1044.0 1323 90.42900 540 2378 2 chr7A.!!$F3 1838
6 TraesCS7D01G274800 chr7B 244714754 244716761 2007 False 1100.5 1639 86.46250 240 2378 2 chr7B.!!$F5 2138
7 TraesCS7D01G274800 chr7B 244691244 244693274 2030 False 1098.0 1700 85.74250 240 2378 2 chr7B.!!$F4 2138
8 TraesCS7D01G274800 chr7B 244650201 244651876 1675 False 736.0 1428 93.39100 540 2378 3 chr7B.!!$F3 1838
9 TraesCS7D01G274800 chr7B 244640913 244645485 4572 False 605.5 1277 88.54525 54 2378 4 chr7B.!!$F2 2324
10 TraesCS7D01G274800 chrUn 284874376 284875229 853 False 1192.0 1192 91.65700 240 1113 1 chrUn.!!$F1 873

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
784 3029 0.823356 TTCCTGTTGTCTGCAAGGCC 60.823 55.0 0.0 0.0 38.23 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 4631 0.4546 CCCATGCTACTTGCTTGCTG 59.545 55.0 0.0 0.0 43.09 4.41 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
55 56 7.894708 TGGCAAATTCACTCAGAATATTTTCA 58.105 30.769 0.00 0.00 46.09 2.69
472 2714 3.127589 CACCAGACAAACACATCGTGTA 58.872 45.455 0.00 0.00 46.79 2.90
739 2983 2.934932 TGGAGATGGGTGGCAGCA 60.935 61.111 19.48 5.16 0.00 4.41
758 3003 4.146058 CGCAGCATCCCATTAGCA 57.854 55.556 0.00 0.00 0.00 3.49
777 3022 2.158449 GCAACGAGATTCCTGTTGTCTG 59.842 50.000 15.78 0.00 43.66 3.51
782 3027 2.746362 GAGATTCCTGTTGTCTGCAAGG 59.254 50.000 0.00 0.00 34.94 3.61
783 3028 1.200948 GATTCCTGTTGTCTGCAAGGC 59.799 52.381 0.00 0.00 40.66 4.35
784 3029 0.823356 TTCCTGTTGTCTGCAAGGCC 60.823 55.000 0.00 0.00 38.23 5.19
785 3030 1.529010 CCTGTTGTCTGCAAGGCCA 60.529 57.895 5.01 0.00 38.23 5.36
954 3204 4.037327 GCCAGCAAAACTTCTTTTCTCTCT 59.963 41.667 0.00 0.00 0.00 3.10
1187 3453 4.276678 TCAAGACAAGCACTCAGGAAATTG 59.723 41.667 0.00 0.00 0.00 2.32
1252 3528 2.490993 GATGGCGCCAAAACAGTGGG 62.491 60.000 36.33 0.00 39.26 4.61
1382 3666 3.309954 CGGCTCCTACTGAAGTAAATTGC 59.690 47.826 0.00 0.00 0.00 3.56
1388 3672 4.572389 CCTACTGAAGTAAATTGCGATGCT 59.428 41.667 0.00 0.00 0.00 3.79
1433 3732 6.625362 TGTCTCTAAGTTCACTTCTATGCAG 58.375 40.000 0.00 0.00 37.40 4.41
1518 3823 4.099881 AGGAGATTGATCAGAGCAGAGTTC 59.900 45.833 0.00 0.00 0.00 3.01
1549 3875 8.375506 TCTGAATGATACATTACCTATGGTTCC 58.624 37.037 0.00 0.00 38.64 3.62
1550 3876 8.040002 TGAATGATACATTACCTATGGTTCCA 57.960 34.615 0.00 0.00 38.64 3.53
1551 3877 8.156820 TGAATGATACATTACCTATGGTTCCAG 58.843 37.037 0.00 0.00 38.64 3.86
1552 3878 7.872061 ATGATACATTACCTATGGTTCCAGA 57.128 36.000 0.00 0.00 38.64 3.86
1557 3890 5.011738 ACATTACCTATGGTTCCAGATACCG 59.988 44.000 0.00 0.00 38.64 4.02
1559 3892 3.858135 ACCTATGGTTCCAGATACCGAT 58.142 45.455 0.00 0.00 38.55 4.18
1714 4359 3.988517 GGCCGTCATACAAGCTAATACTC 59.011 47.826 0.00 0.00 0.00 2.59
1715 4360 3.988517 GCCGTCATACAAGCTAATACTCC 59.011 47.826 0.00 0.00 0.00 3.85
1716 4361 4.557205 CCGTCATACAAGCTAATACTCCC 58.443 47.826 0.00 0.00 0.00 4.30
1717 4362 4.281182 CCGTCATACAAGCTAATACTCCCT 59.719 45.833 0.00 0.00 0.00 4.20
1718 4363 5.462405 CGTCATACAAGCTAATACTCCCTC 58.538 45.833 0.00 0.00 0.00 4.30
1719 4364 5.565045 CGTCATACAAGCTAATACTCCCTCC 60.565 48.000 0.00 0.00 0.00 4.30
1720 4365 4.523173 TCATACAAGCTAATACTCCCTCCG 59.477 45.833 0.00 0.00 0.00 4.63
1721 4366 2.748388 ACAAGCTAATACTCCCTCCGT 58.252 47.619 0.00 0.00 0.00 4.69
1722 4367 3.105283 ACAAGCTAATACTCCCTCCGTT 58.895 45.455 0.00 0.00 0.00 4.44
1723 4368 3.132467 ACAAGCTAATACTCCCTCCGTTC 59.868 47.826 0.00 0.00 0.00 3.95
1724 4369 2.317973 AGCTAATACTCCCTCCGTTCC 58.682 52.381 0.00 0.00 0.00 3.62
1725 4370 2.037144 GCTAATACTCCCTCCGTTCCA 58.963 52.381 0.00 0.00 0.00 3.53
1726 4371 2.433239 GCTAATACTCCCTCCGTTCCAA 59.567 50.000 0.00 0.00 0.00 3.53
1727 4372 3.118519 GCTAATACTCCCTCCGTTCCAAA 60.119 47.826 0.00 0.00 0.00 3.28
1728 4373 4.624604 GCTAATACTCCCTCCGTTCCAAAA 60.625 45.833 0.00 0.00 0.00 2.44
1729 4374 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1730 4375 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1731 4376 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1732 4377 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1733 4378 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1734 4379 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1735 4380 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1736 4381 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1737 4382 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1738 4383 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1739 4384 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1740 4385 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1741 4386 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1742 4387 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1743 4388 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1744 4389 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1745 4390 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1746 4391 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1747 4392 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1748 4393 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1749 4394 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
1750 4395 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
1751 4396 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1752 4397 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
1753 4398 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
1754 4399 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
1755 4400 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
1756 4401 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
1757 4402 6.181908 TGACCCAACTTTGTACTAACTTTGT 58.818 36.000 0.00 0.00 0.00 2.83
1758 4403 7.337167 TGACCCAACTTTGTACTAACTTTGTA 58.663 34.615 0.00 0.00 0.00 2.41
1759 4404 7.280652 TGACCCAACTTTGTACTAACTTTGTAC 59.719 37.037 6.58 6.58 40.27 2.90
1760 4405 7.341030 ACCCAACTTTGTACTAACTTTGTACT 58.659 34.615 12.73 0.00 40.44 2.73
1761 4406 8.485392 ACCCAACTTTGTACTAACTTTGTACTA 58.515 33.333 12.73 4.86 40.44 1.82
1762 4407 8.768019 CCCAACTTTGTACTAACTTTGTACTAC 58.232 37.037 12.73 0.00 40.44 2.73
1763 4408 9.316730 CCAACTTTGTACTAACTTTGTACTACA 57.683 33.333 12.73 0.00 40.44 2.74
1798 4443 9.793259 AAAGTTGAGTCATCTATTTTAGAACCA 57.207 29.630 4.14 0.00 38.50 3.67
1799 4444 9.965902 AAGTTGAGTCATCTATTTTAGAACCAT 57.034 29.630 4.14 0.00 38.50 3.55
1812 4457 7.883391 TTTTAGAACCATACTGTTCAAACCA 57.117 32.000 6.67 0.00 45.62 3.67
1813 4458 8.472007 TTTTAGAACCATACTGTTCAAACCAT 57.528 30.769 6.67 0.00 45.62 3.55
1814 4459 9.575868 TTTTAGAACCATACTGTTCAAACCATA 57.424 29.630 6.67 0.00 45.62 2.74
1815 4460 8.786826 TTAGAACCATACTGTTCAAACCATAG 57.213 34.615 6.67 0.00 45.62 2.23
1816 4461 6.180472 AGAACCATACTGTTCAAACCATAGG 58.820 40.000 6.67 0.00 45.62 2.57
1817 4462 5.514500 ACCATACTGTTCAAACCATAGGT 57.486 39.130 0.00 0.00 37.65 3.08
1818 4463 6.630203 ACCATACTGTTCAAACCATAGGTA 57.370 37.500 0.00 0.00 33.12 3.08
1819 4464 7.023171 ACCATACTGTTCAAACCATAGGTAA 57.977 36.000 0.00 0.00 33.12 2.85
1820 4465 7.639378 ACCATACTGTTCAAACCATAGGTAAT 58.361 34.615 0.00 0.00 33.12 1.89
1821 4466 8.774183 ACCATACTGTTCAAACCATAGGTAATA 58.226 33.333 0.00 0.00 33.12 0.98
1822 4467 9.793259 CCATACTGTTCAAACCATAGGTAATAT 57.207 33.333 0.00 0.00 33.12 1.28
1863 4508 4.993029 TCAAACCGAGTTTTGGAATGTT 57.007 36.364 0.03 0.00 37.13 2.71
1930 4576 3.255642 GCAACAAGCAAAGGATCCTTGTA 59.744 43.478 27.71 0.00 45.95 2.41
1935 4581 3.679389 AGCAAAGGATCCTTGTACAGTG 58.321 45.455 27.71 20.34 36.26 3.66
1984 4631 3.312697 GCCAACTCGAATATCCAAGGTTC 59.687 47.826 0.00 0.00 0.00 3.62
2010 4657 0.168788 CAAGTAGCATGGGTTGTGCG 59.831 55.000 0.00 0.00 46.86 5.34
2034 4684 6.128309 CGACACATCACACCTATTCAAATCAA 60.128 38.462 0.00 0.00 0.00 2.57
2086 4739 1.835531 ACCAACCCATACTCGGTTAGG 59.164 52.381 0.00 0.00 41.78 2.69
2094 4747 3.492656 CCATACTCGGTTAGGACACCATG 60.493 52.174 0.00 0.00 36.49 3.66
2097 4769 0.687920 TCGGTTAGGACACCATGCAA 59.312 50.000 0.00 0.00 36.49 4.08
2315 4989 5.762179 TGATTCCTTGTGTCTACCATTCT 57.238 39.130 0.00 0.00 0.00 2.40
2357 5031 6.226787 CAGTTCCTCTGTATAAATAGGCCTG 58.773 44.000 17.99 0.00 39.17 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.893124 ATATTCTGAGTGAATTTGCCAGATT 57.107 32.000 0.00 0.00 42.28 2.40
55 56 9.745880 CATATTACTTCCGTAACAGTCAATAGT 57.254 33.333 0.00 0.00 38.35 2.12
153 154 4.569966 GTGTTGAGGTCTTGATGAGCATAG 59.430 45.833 0.42 0.00 44.98 2.23
274 2514 3.754955 CTTGTTCTCGTCATACGTGCTA 58.245 45.455 0.00 0.00 43.14 3.49
275 2515 2.596452 CTTGTTCTCGTCATACGTGCT 58.404 47.619 0.00 0.00 43.14 4.40
472 2714 0.886490 CACCTTTGAGCTCCAACGCT 60.886 55.000 12.15 0.00 44.33 5.07
698 2940 6.034898 CACGACAAGCTGATTTTTCTTTTGTT 59.965 34.615 0.00 0.00 0.00 2.83
739 2983 1.895707 GCTAATGGGATGCTGCGCT 60.896 57.895 9.73 0.00 0.00 5.92
748 2992 2.771943 AGGAATCTCGTTGCTAATGGGA 59.228 45.455 0.00 0.00 36.65 4.37
754 2999 3.258372 AGACAACAGGAATCTCGTTGCTA 59.742 43.478 12.75 0.00 42.98 3.49
758 3003 2.224281 TGCAGACAACAGGAATCTCGTT 60.224 45.455 0.00 0.00 0.00 3.85
1107 3373 1.863454 CGATCAGTGCAAGATAGTGCC 59.137 52.381 3.12 0.00 44.26 5.01
1187 3453 1.093159 CTTGGTCTGAGAGCCAATGC 58.907 55.000 9.40 0.00 43.00 3.56
1252 3528 7.605691 TGAAGGAGATTTCTTGTTGATCTTCTC 59.394 37.037 0.00 0.00 35.24 2.87
1382 3666 2.472861 CCGCTTGTTATACTCAGCATCG 59.527 50.000 0.00 0.00 0.00 3.84
1433 3732 4.479619 CAGTTTCAGTATTTGCTCCTTGC 58.520 43.478 0.00 0.00 43.25 4.01
1538 3864 3.323774 TCGGTATCTGGAACCATAGGT 57.676 47.619 0.00 0.00 36.78 3.08
1549 3875 8.153479 CTGATCCTCTAATAGATCGGTATCTG 57.847 42.308 0.00 0.00 42.60 2.90
1624 3976 5.393135 CGTCTGAGTTAAATGCTCCAGAGTA 60.393 44.000 0.00 0.00 32.31 2.59
1714 4359 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1715 4360 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1716 4361 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1717 4362 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1718 4363 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1719 4364 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1720 4365 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1721 4366 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1722 4367 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1723 4368 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1724 4369 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
1725 4370 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
1726 4371 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
1727 4372 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
1728 4373 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
1729 4374 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
1730 4375 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
1731 4376 7.012989 ACAAAGTTAGTACAAAGTTGGGTCATC 59.987 37.037 0.00 0.00 0.00 2.92
1732 4377 6.831868 ACAAAGTTAGTACAAAGTTGGGTCAT 59.168 34.615 0.00 0.00 0.00 3.06
1733 4378 6.181908 ACAAAGTTAGTACAAAGTTGGGTCA 58.818 36.000 0.00 0.00 0.00 4.02
1734 4379 6.688637 ACAAAGTTAGTACAAAGTTGGGTC 57.311 37.500 0.00 0.00 0.00 4.46
1735 4380 7.341030 AGTACAAAGTTAGTACAAAGTTGGGT 58.659 34.615 6.30 0.00 43.24 4.51
1736 4381 7.797038 AGTACAAAGTTAGTACAAAGTTGGG 57.203 36.000 6.30 0.00 43.24 4.12
1737 4382 9.316730 TGTAGTACAAAGTTAGTACAAAGTTGG 57.683 33.333 0.00 0.00 43.24 3.77
1772 4417 9.793259 TGGTTCTAAAATAGATGACTCAACTTT 57.207 29.630 0.00 0.00 34.22 2.66
1773 4418 9.965902 ATGGTTCTAAAATAGATGACTCAACTT 57.034 29.630 0.00 0.00 34.22 2.66
1786 4431 9.575868 TGGTTTGAACAGTATGGTTCTAAAATA 57.424 29.630 7.47 0.00 33.00 1.40
1787 4432 8.472007 TGGTTTGAACAGTATGGTTCTAAAAT 57.528 30.769 7.47 0.00 33.00 1.82
1788 4433 7.883391 TGGTTTGAACAGTATGGTTCTAAAA 57.117 32.000 7.47 0.00 33.00 1.52
1789 4434 9.226606 CTATGGTTTGAACAGTATGGTTCTAAA 57.773 33.333 7.47 4.38 33.00 1.85
1790 4435 7.827236 CCTATGGTTTGAACAGTATGGTTCTAA 59.173 37.037 7.47 3.74 33.00 2.10
1791 4436 7.037873 ACCTATGGTTTGAACAGTATGGTTCTA 60.038 37.037 7.47 0.00 39.55 2.10
1792 4437 6.180472 CCTATGGTTTGAACAGTATGGTTCT 58.820 40.000 7.47 0.00 33.00 3.01
1793 4438 5.944007 ACCTATGGTTTGAACAGTATGGTTC 59.056 40.000 0.00 0.00 39.40 3.62
1794 4439 5.887754 ACCTATGGTTTGAACAGTATGGTT 58.112 37.500 0.00 0.00 32.96 3.67
1795 4440 5.514500 ACCTATGGTTTGAACAGTATGGT 57.486 39.130 0.00 0.00 32.96 3.55
1796 4441 9.793259 ATATTACCTATGGTTTGAACAGTATGG 57.207 33.333 0.00 0.00 37.55 2.74
1809 4454 9.228077 TGGTACCAAGTTTATATTACCTATGGT 57.772 33.333 13.60 0.00 41.27 3.55
1821 4466 8.789762 GTTTGAACAGTATGGTACCAAGTTTAT 58.210 33.333 20.76 3.33 33.00 1.40
1822 4467 7.229106 GGTTTGAACAGTATGGTACCAAGTTTA 59.771 37.037 20.76 14.47 33.00 2.01
1823 4468 6.040054 GGTTTGAACAGTATGGTACCAAGTTT 59.960 38.462 20.76 4.60 33.00 2.66
1824 4469 5.533528 GGTTTGAACAGTATGGTACCAAGTT 59.466 40.000 20.76 19.72 33.00 2.66
1825 4470 5.067954 GGTTTGAACAGTATGGTACCAAGT 58.932 41.667 20.76 12.40 33.00 3.16
1826 4471 4.153475 CGGTTTGAACAGTATGGTACCAAG 59.847 45.833 20.76 11.74 33.00 3.61
1827 4472 4.066490 CGGTTTGAACAGTATGGTACCAA 58.934 43.478 20.76 5.65 33.00 3.67
1828 4473 3.324268 TCGGTTTGAACAGTATGGTACCA 59.676 43.478 18.99 18.99 33.00 3.25
1829 4474 3.929094 TCGGTTTGAACAGTATGGTACC 58.071 45.455 4.43 4.43 33.00 3.34
1830 4475 4.563061 ACTCGGTTTGAACAGTATGGTAC 58.437 43.478 0.00 0.00 33.00 3.34
1831 4476 4.877378 ACTCGGTTTGAACAGTATGGTA 57.123 40.909 0.00 0.00 33.00 3.25
1832 4477 3.764237 ACTCGGTTTGAACAGTATGGT 57.236 42.857 0.00 0.00 42.46 3.55
1833 4478 5.212194 CAAAACTCGGTTTGAACAGTATGG 58.788 41.667 1.24 0.00 39.69 2.74
1838 4483 4.364415 TTCCAAAACTCGGTTTGAACAG 57.636 40.909 8.90 0.00 40.29 3.16
1863 4508 4.574674 AACATGGCCATCTTGTAGAGAA 57.425 40.909 17.61 0.00 38.06 2.87
1935 4581 1.074405 TGGCCATGGATAGCAAGATCC 59.926 52.381 18.40 3.07 45.06 3.36
1984 4631 0.454600 CCCATGCTACTTGCTTGCTG 59.545 55.000 0.00 0.00 43.09 4.41
2010 4657 6.741992 TGATTTGAATAGGTGTGATGTGTC 57.258 37.500 0.00 0.00 0.00 3.67
2086 4739 6.389091 TCTTGACATAATTTTGCATGGTGTC 58.611 36.000 0.00 0.00 36.09 3.67
2094 4747 5.964758 TGGTGGATCTTGACATAATTTTGC 58.035 37.500 0.00 0.00 0.00 3.68
2097 4769 9.347240 CTCTATTGGTGGATCTTGACATAATTT 57.653 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.