Multiple sequence alignment - TraesCS3D01G343500

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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 TraesCS3D01G343500 chr3D 100.000 4558 0 0 1 4558 455867693 455863136 0.000000e+00 8418.0
1 TraesCS3D01G343500 chr3A 92.104 3850 181 54 4 3753 598552645 598548819 0.000000e+00 5312.0
2 TraesCS3D01G343500 chr3A 94.379 765 37 5 3795 4558 598548816 598548057 0.000000e+00 1170.0
3 TraesCS3D01G343500 chr3A 96.000 50 1 1 3755 3803 475279754 475279705 3.780000e-11 80.5
4 TraesCS3D01G343500 chr3B 93.669 2938 101 39 760 3637 602305318 602302406 0.000000e+00 4316.0
5 TraesCS3D01G343500 chr3B 95.170 559 22 3 3793 4347 602302279 602301722 0.000000e+00 878.0
6 TraesCS3D01G343500 chr3B 83.506 770 93 23 1 760 602350922 602350177 0.000000e+00 688.0
7 TraesCS3D01G343500 chr3B 91.667 120 6 1 4344 4459 70295864 70295983 3.650000e-36 163.0
8 TraesCS3D01G343500 chr3B 91.667 108 5 1 4455 4558 602301721 602301614 3.670000e-31 147.0
9 TraesCS3D01G343500 chr3B 85.000 80 11 1 639 718 685061276 685061354 3.780000e-11 80.5
10 TraesCS3D01G343500 chr3B 95.652 46 2 0 3714 3759 602302320 602302275 1.760000e-09 75.0
11 TraesCS3D01G343500 chr3B 87.302 63 8 0 1 63 602330487 602330425 6.330000e-09 73.1
12 TraesCS3D01G343500 chr5D 78.902 346 53 18 424 756 449650902 449650564 2.760000e-52 217.0
13 TraesCS3D01G343500 chr5D 89.844 128 8 5 4345 4467 461071761 461071634 4.720000e-35 159.0
14 TraesCS3D01G343500 chr5D 78.974 195 32 6 566 760 449693474 449693289 1.720000e-24 124.0
15 TraesCS3D01G343500 chr5D 94.231 52 2 1 3755 3805 528980831 528980780 1.360000e-10 78.7
16 TraesCS3D01G343500 chr5A 77.814 311 47 13 408 714 131569324 131569616 6.060000e-39 172.0
17 TraesCS3D01G343500 chr7A 92.500 120 5 4 4345 4460 375886610 375886491 7.840000e-38 169.0
18 TraesCS3D01G343500 chr7A 100.000 32 0 0 3646 3677 673029622 673029591 4.920000e-05 60.2
19 TraesCS3D01G343500 chr6B 89.764 127 9 1 4339 4461 248362100 248362226 4.720000e-35 159.0
20 TraesCS3D01G343500 chr4D 90.244 123 8 1 4344 4462 367720888 367720766 1.700000e-34 158.0
21 TraesCS3D01G343500 chr4B 89.600 125 9 3 4345 4465 411629803 411629679 6.110000e-34 156.0
22 TraesCS3D01G343500 chr4B 94.118 51 0 3 3749 3797 34029094 34029045 1.760000e-09 75.0
23 TraesCS3D01G343500 chr4B 94.000 50 1 2 3752 3800 612271443 612271491 1.760000e-09 75.0
24 TraesCS3D01G343500 chr4B 90.385 52 5 0 452 503 24734607 24734658 8.180000e-08 69.4
25 TraesCS3D01G343500 chr2B 89.600 125 9 2 4345 4465 643184735 643184611 6.110000e-34 156.0
26 TraesCS3D01G343500 chr2B 78.109 201 31 5 499 699 666656820 666656633 1.040000e-21 115.0
27 TraesCS3D01G343500 chr2B 95.833 48 1 1 3757 3803 417500805 417500758 4.890000e-10 76.8
28 TraesCS3D01G343500 chr7B 87.313 134 12 2 4337 4466 433515374 433515242 1.020000e-31 148.0
29 TraesCS3D01G343500 chr7B 96.000 50 0 2 3749 3796 684939968 684939919 3.780000e-11 80.5
30 TraesCS3D01G343500 chr7B 92.593 54 1 3 3755 3806 829786 829838 1.760000e-09 75.0
31 TraesCS3D01G343500 chr2A 77.682 233 35 6 502 730 698830527 698830308 4.790000e-25 126.0
32 TraesCS3D01G343500 chr2A 80.263 152 23 5 580 727 717391910 717392058 1.730000e-19 108.0
33 TraesCS3D01G343500 chr2A 97.826 46 0 1 3754 3798 689711958 689711913 1.360000e-10 78.7
34 TraesCS3D01G343500 chr1A 95.918 49 0 2 3755 3802 241319965 241320012 1.360000e-10 78.7


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 TraesCS3D01G343500 chr3D 455863136 455867693 4557 True 8418 8418 100.0000 1 4558 1 chr3D.!!$R1 4557
1 TraesCS3D01G343500 chr3A 598548057 598552645 4588 True 3241 5312 93.2415 4 4558 2 chr3A.!!$R2 4554
2 TraesCS3D01G343500 chr3B 602301614 602305318 3704 True 1354 4316 94.0395 760 4558 4 chr3B.!!$R3 3798
3 TraesCS3D01G343500 chr3B 602350177 602350922 745 True 688 688 83.5060 1 760 1 chr3B.!!$R2 759

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
291 299 0.178990 GGAGGGCCTTTGTTGAGTGT 60.179 55.0 7.89 0.0 0.00 3.55 F
1640 1720 0.041926 AAAACTTGAACCGTACGCGC 60.042 50.0 10.49 0.0 36.67 6.86 F
1975 2071 0.039165 GTGCCTGGGAAGCTTTTTCG 60.039 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1778 0.038343 GTCTACACGTTAACCGGCCA 60.038 55.000 0.00 0.0 42.24 5.36 R
3224 3328 4.308458 TTGTAGTGCACCGCCGCT 62.308 61.111 14.63 0.0 0.00 5.52 R
3780 3938 0.116342 TTGCTACTCCCTCTGTCCCA 59.884 55.000 0.00 0.0 0.00 4.37 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
44 45 6.128929 GCGGTTTAAATGTGGATCAAAAGTTC 60.129 38.462 0.00 0.00 0.00 3.01
48 49 4.766404 AATGTGGATCAAAAGTTCGTCC 57.234 40.909 0.00 0.00 0.00 4.79
49 50 2.500229 TGTGGATCAAAAGTTCGTCCC 58.500 47.619 0.00 0.00 0.00 4.46
50 51 1.810755 GTGGATCAAAAGTTCGTCCCC 59.189 52.381 0.00 0.00 0.00 4.81
94 95 8.873215 ATATCTGAGTTTCGTATGTAAACCAG 57.127 34.615 0.00 0.00 37.51 4.00
105 106 3.034721 TGTAAACCAGCTTGTACCGAG 57.965 47.619 0.00 0.00 0.00 4.63
118 119 0.514255 TACCGAGAGACACGACAACG 59.486 55.000 0.00 0.00 45.75 4.10
131 132 1.583054 GACAACGTTGGCAACTCTCT 58.417 50.000 29.05 5.56 35.83 3.10
135 136 0.597637 ACGTTGGCAACTCTCTGTCG 60.598 55.000 26.26 13.94 37.61 4.35
149 156 2.257676 GTCGACCGTCAGGGACAC 59.742 66.667 3.51 0.00 43.47 3.67
153 160 4.295119 ACCGTCAGGGACACGTGC 62.295 66.667 17.22 8.51 43.47 5.34
186 193 0.392461 GAGTGCCCGGCTCATTGTAA 60.392 55.000 11.61 0.00 33.45 2.41
206 213 7.421530 TGTAATGTTTTCTAGTCTGCACTTC 57.578 36.000 0.00 0.00 33.62 3.01
291 299 0.178990 GGAGGGCCTTTGTTGAGTGT 60.179 55.000 7.89 0.00 0.00 3.55
293 301 0.846693 AGGGCCTTTGTTGAGTGTCT 59.153 50.000 0.00 0.00 0.00 3.41
298 306 2.682856 GCCTTTGTTGAGTGTCTGACAA 59.317 45.455 12.81 0.00 0.00 3.18
305 313 3.969117 TGAGTGTCTGACAAAATGCAC 57.031 42.857 12.81 0.00 0.00 4.57
308 316 2.032054 AGTGTCTGACAAAATGCACACG 59.968 45.455 12.81 0.00 39.30 4.49
342 350 0.739561 GGATACTCCGCAGTCTCGTT 59.260 55.000 0.00 0.00 33.62 3.85
351 359 1.126846 CGCAGTCTCGTTGATTTGGAC 59.873 52.381 0.00 0.00 0.00 4.02
353 361 2.548057 GCAGTCTCGTTGATTTGGACAA 59.452 45.455 0.00 0.00 0.00 3.18
369 377 5.265350 TGGACAATGCCATGTTATGATTG 57.735 39.130 0.00 0.00 33.28 2.67
394 402 9.317936 TGTTTTTCATTACAACAACAATGCATA 57.682 25.926 0.00 0.00 33.14 3.14
438 470 5.181748 AGAAAAGCTATTCTACTGTGCAGG 58.818 41.667 4.11 0.00 37.88 4.85
439 471 4.826274 AAAGCTATTCTACTGTGCAGGA 57.174 40.909 4.11 0.00 0.00 3.86
459 491 3.323115 GGAGATACTCTGTGCATGGATCA 59.677 47.826 0.00 0.00 0.00 2.92
461 493 4.958509 AGATACTCTGTGCATGGATCAAG 58.041 43.478 0.00 0.00 0.00 3.02
463 495 1.003928 ACTCTGTGCATGGATCAAGCA 59.996 47.619 0.00 0.00 35.71 3.91
492 524 5.884232 TGATTGCTTTGAGATTCATGCTACT 59.116 36.000 0.00 0.00 30.95 2.57
564 596 9.459640 GGTTTTTCTTCCAGTTTCAAAGTATAC 57.540 33.333 0.00 0.00 0.00 1.47
609 641 2.418628 CGTGTATCAGCAAACCCGATTT 59.581 45.455 0.00 0.00 0.00 2.17
611 643 4.260212 CGTGTATCAGCAAACCCGATTTAG 60.260 45.833 0.00 0.00 0.00 1.85
625 657 4.438744 CCCGATTTAGAACAAGTGCATTCC 60.439 45.833 0.00 0.00 0.00 3.01
678 711 7.306213 TGATACACGTTGAAACAAGACAAAAA 58.694 30.769 0.00 0.00 0.00 1.94
695 728 6.034150 AGACAAAAACCGAACGAAACATTTTC 59.966 34.615 0.00 0.00 0.00 2.29
734 767 2.089201 CAACCTAAAAAGTAGCCCGGG 58.911 52.381 19.09 19.09 0.00 5.73
783 816 2.569404 CCACTCTCTATATTGCTCCCCC 59.431 54.545 0.00 0.00 0.00 5.40
849 890 3.619900 TGGACAGGCCACTCTCTATAT 57.380 47.619 5.01 0.00 43.33 0.86
851 892 3.117131 TGGACAGGCCACTCTCTATATCA 60.117 47.826 5.01 0.00 43.33 2.15
886 935 1.138266 ACCCAAACGATGTATCCCTCG 59.862 52.381 0.00 0.00 40.62 4.63
923 972 5.116084 TCCTCCATTCCCAAATAGTCAAG 57.884 43.478 0.00 0.00 0.00 3.02
972 1023 2.028190 CGATAGAGGCCGGCACTG 59.972 66.667 30.85 11.12 39.76 3.66
1373 1453 1.411977 CATGAATCTCCTCTGCTCGGT 59.588 52.381 0.00 0.00 0.00 4.69
1374 1454 1.107114 TGAATCTCCTCTGCTCGGTC 58.893 55.000 0.00 0.00 0.00 4.79
1416 1496 0.841356 GTGTTTGCGGCGTTGTTAAC 59.159 50.000 9.37 0.00 0.00 2.01
1596 1676 0.419865 TCCCCATGAGGAAGGTACCA 59.580 55.000 15.94 0.00 38.24 3.25
1638 1718 4.386652 TGAGATAAAACTTGAACCGTACGC 59.613 41.667 10.49 0.00 0.00 4.42
1639 1719 3.365820 AGATAAAACTTGAACCGTACGCG 59.634 43.478 10.49 3.53 37.95 6.01
1640 1720 0.041926 AAAACTTGAACCGTACGCGC 60.042 50.000 10.49 0.00 36.67 6.86
1641 1721 1.152989 AAACTTGAACCGTACGCGCA 61.153 50.000 10.49 4.24 36.67 6.09
1642 1722 1.824272 AACTTGAACCGTACGCGCAC 61.824 55.000 10.49 1.24 36.67 5.34
1643 1723 2.019951 CTTGAACCGTACGCGCACT 61.020 57.895 10.49 0.00 36.67 4.40
1644 1724 2.210524 CTTGAACCGTACGCGCACTG 62.211 60.000 10.49 1.67 36.67 3.66
1645 1725 4.130281 GAACCGTACGCGCACTGC 62.130 66.667 10.49 0.00 41.47 4.40
1646 1726 4.953868 AACCGTACGCGCACTGCA 62.954 61.111 10.49 0.00 46.97 4.41
1651 1731 1.735198 GTACGCGCACTGCACCTAA 60.735 57.895 5.73 0.00 46.97 2.69
1652 1732 1.082117 GTACGCGCACTGCACCTAAT 61.082 55.000 5.73 0.00 46.97 1.73
1654 1734 0.390603 ACGCGCACTGCACCTAATTA 60.391 50.000 5.73 0.00 46.97 1.40
1655 1735 0.937304 CGCGCACTGCACCTAATTAT 59.063 50.000 8.75 0.00 46.97 1.28
1657 1737 2.155732 CGCGCACTGCACCTAATTATAG 59.844 50.000 8.75 0.00 46.97 1.31
1658 1738 2.096218 GCGCACTGCACCTAATTATAGC 60.096 50.000 0.30 0.00 45.45 2.97
1660 1740 3.430218 CGCACTGCACCTAATTATAGCTC 59.570 47.826 1.11 0.00 0.00 4.09
1662 1742 4.450419 GCACTGCACCTAATTATAGCTCTG 59.550 45.833 0.00 3.12 0.00 3.35
1663 1743 4.993584 CACTGCACCTAATTATAGCTCTGG 59.006 45.833 0.00 0.00 0.00 3.86
1664 1744 3.999663 CTGCACCTAATTATAGCTCTGGC 59.000 47.826 0.00 0.00 39.06 4.85
1666 1746 4.141505 TGCACCTAATTATAGCTCTGGCAA 60.142 41.667 0.00 0.00 41.70 4.52
1667 1747 4.821805 GCACCTAATTATAGCTCTGGCAAA 59.178 41.667 0.00 0.00 41.70 3.68
1668 1748 5.049129 GCACCTAATTATAGCTCTGGCAAAG 60.049 44.000 0.00 0.00 41.70 2.77
1669 1749 6.058183 CACCTAATTATAGCTCTGGCAAAGT 58.942 40.000 0.00 0.00 41.70 2.66
1670 1750 6.543831 CACCTAATTATAGCTCTGGCAAAGTT 59.456 38.462 0.00 0.00 41.70 2.66
1673 1753 7.500559 CCTAATTATAGCTCTGGCAAAGTTCTT 59.499 37.037 0.00 0.00 41.70 2.52
1695 1778 2.502947 TCTGATGCATTCCTACTGTGCT 59.497 45.455 0.00 0.00 39.52 4.40
1784 1867 1.808945 CACCTCATCAACAGCTTCCAC 59.191 52.381 0.00 0.00 0.00 4.02
1820 1903 0.317770 TGCAAGCAAAGTAAGCACGC 60.318 50.000 0.00 0.00 33.63 5.34
1838 1921 2.094390 ACGCACGGAGCTACTAAATCAA 60.094 45.455 0.00 0.00 42.61 2.57
1839 1922 3.123804 CGCACGGAGCTACTAAATCAAT 58.876 45.455 0.00 0.00 42.61 2.57
1840 1923 3.182572 CGCACGGAGCTACTAAATCAATC 59.817 47.826 0.00 0.00 42.61 2.67
1841 1924 4.119862 GCACGGAGCTACTAAATCAATCA 58.880 43.478 0.00 0.00 41.15 2.57
1855 1941 8.486210 ACTAAATCAATCACATCAACCTAGCTA 58.514 33.333 0.00 0.00 0.00 3.32
1975 2071 0.039165 GTGCCTGGGAAGCTTTTTCG 60.039 55.000 0.00 0.00 0.00 3.46
2046 2142 2.999185 TCTTCCCTTCATTTGGGCTT 57.001 45.000 0.00 0.00 44.23 4.35
2048 2144 0.975887 TTCCCTTCATTTGGGCTTGC 59.024 50.000 0.00 0.00 44.23 4.01
2082 2182 3.868754 GCGGGTAACTTATCCATCCATCC 60.869 52.174 0.00 0.00 0.00 3.51
2098 2198 3.118445 TCCATCCATTCTACATGTCGCAA 60.118 43.478 0.00 0.00 0.00 4.85
2118 2218 4.315803 CAATCCAACCGAGAACTACTTGT 58.684 43.478 0.00 0.00 0.00 3.16
2147 2247 3.748048 TGATCAGTGAAAGCTACTTGTGC 59.252 43.478 0.00 0.00 0.00 4.57
2156 2256 2.420642 AGCTACTTGTGCTGTGTGATG 58.579 47.619 0.00 0.00 39.56 3.07
2158 2258 1.127397 CTACTTGTGCTGTGTGATGCG 59.873 52.381 0.00 0.00 0.00 4.73
2160 2260 0.308684 CTTGTGCTGTGTGATGCGTT 59.691 50.000 0.00 0.00 0.00 4.84
2329 2433 1.227497 CGATCTCCAGGAAGGCAGC 60.227 63.158 0.00 0.00 37.29 5.25
2384 2488 5.180117 AGTTTCTGATCGACCAACAGATTTG 59.820 40.000 12.00 0.00 39.78 2.32
2389 2493 1.508632 CGACCAACAGATTTGGACGT 58.491 50.000 16.36 0.00 46.81 4.34
3512 3616 2.435059 GCCAGGGAGCAGAACGAC 60.435 66.667 0.00 0.00 0.00 4.34
3690 3847 7.351414 TGATGTAGAATGAACAGACTTTTCG 57.649 36.000 0.00 0.00 0.00 3.46
3692 3849 6.764877 TGTAGAATGAACAGACTTTTCGAC 57.235 37.500 0.00 0.00 0.00 4.20
3699 3856 3.469008 ACAGACTTTTCGACCATGTCA 57.531 42.857 10.71 0.00 32.09 3.58
3707 3864 3.394674 TTCGACCATGTCAGCAGTTTA 57.605 42.857 0.00 0.00 32.09 2.01
3747 3905 8.964420 ATGTAGTGCAAATGTACAATACAAAC 57.036 30.769 0.00 0.00 46.48 2.93
3755 3913 9.550811 GCAAATGTACAATACAAACCTAACTAC 57.449 33.333 0.00 0.00 42.76 2.73
3840 3998 6.940867 CCATAGTGGATCAGATGAATCAACAT 59.059 38.462 0.00 0.00 40.96 2.71
3846 4004 8.288208 GTGGATCAGATGAATCAACATATCAAC 58.712 37.037 0.00 0.00 0.00 3.18
3877 4035 0.825425 TGCATTTGAGGTGCGGGAAA 60.825 50.000 0.00 0.00 45.37 3.13
3917 4075 7.436673 GCTTTTTCAAAACAAAACAAAAACCCT 59.563 29.630 0.00 0.00 0.00 4.34
4020 4178 3.281727 TTTCTTCAGACTTGCACCACT 57.718 42.857 0.00 0.00 0.00 4.00
4028 4186 2.434336 AGACTTGCACCACTCAACACTA 59.566 45.455 0.00 0.00 0.00 2.74
4123 4281 3.100111 GGGCCTCCCAACTCCATT 58.900 61.111 0.84 0.00 44.65 3.16
4149 4307 4.853924 AAAACTCCTGCCAACATAACAG 57.146 40.909 0.00 0.00 0.00 3.16
4357 4519 0.466007 GTCTCCTACTCCCTCCGTCC 60.466 65.000 0.00 0.00 0.00 4.79
4364 4526 0.966370 ACTCCCTCCGTCCGAGAAAG 60.966 60.000 0.00 0.00 41.63 2.62
4373 4535 0.034896 GTCCGAGAAAGCTTGTCCCA 59.965 55.000 0.00 0.00 0.00 4.37
4395 4557 5.279106 CCAAGCTTGTCTTTCAAATGGATGA 60.279 40.000 24.35 0.00 36.92 2.92
4396 4558 5.640189 AGCTTGTCTTTCAAATGGATGAG 57.360 39.130 0.00 0.00 35.48 2.90
4401 4563 7.094634 GCTTGTCTTTCAAATGGATGAGTCTAA 60.095 37.037 0.00 0.00 35.48 2.10
4548 4714 4.278170 CAGGTCAAAAATGTTGCTCCACTA 59.722 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 5.581085 GCTGGTTTACATACGAAACTCAGAT 59.419 40.000 15.06 0.00 37.31 2.90
82 83 4.497300 TCGGTACAAGCTGGTTTACATAC 58.503 43.478 0.00 0.00 0.00 2.39
83 84 4.463539 TCTCGGTACAAGCTGGTTTACATA 59.536 41.667 0.00 0.00 0.00 2.29
92 93 1.729472 CGTGTCTCTCGGTACAAGCTG 60.729 57.143 0.00 0.00 0.00 4.24
93 94 0.522180 CGTGTCTCTCGGTACAAGCT 59.478 55.000 0.00 0.00 0.00 3.74
94 95 0.520404 TCGTGTCTCTCGGTACAAGC 59.480 55.000 0.00 0.00 0.00 4.01
118 119 1.140816 GTCGACAGAGAGTTGCCAAC 58.859 55.000 11.55 0.00 0.00 3.77
122 123 0.729816 GACGGTCGACAGAGAGTTGC 60.730 60.000 22.71 0.00 0.00 4.17
127 128 1.674651 CCCTGACGGTCGACAGAGA 60.675 63.158 22.71 6.94 39.55 3.10
131 132 2.203379 TGTCCCTGACGGTCGACA 60.203 61.111 18.91 11.65 34.95 4.35
135 136 2.049433 CACGTGTCCCTGACGGTC 60.049 66.667 7.58 0.00 41.21 4.79
149 156 4.128388 GGCAAAATCGGGGGCACG 62.128 66.667 0.00 0.00 0.00 5.34
153 160 2.045340 ACTCGGCAAAATCGGGGG 60.045 61.111 0.00 0.00 31.46 5.40
180 187 7.986085 AGTGCAGACTAGAAAACATTACAAT 57.014 32.000 0.00 0.00 0.00 2.71
186 193 3.433615 GCGAAGTGCAGACTAGAAAACAT 59.566 43.478 0.00 0.00 45.45 2.71
206 213 1.665599 CCAAAGCCTTGCCTTTGCG 60.666 57.895 8.67 0.73 46.43 4.85
244 251 3.840437 TGCAGCGGAAAAGCACTT 58.160 50.000 0.00 0.00 40.15 3.16
291 299 1.264020 GAGCGTGTGCATTTTGTCAGA 59.736 47.619 0.00 0.00 46.23 3.27
293 301 1.020437 TGAGCGTGTGCATTTTGTCA 58.980 45.000 0.00 0.00 46.23 3.58
298 306 2.098934 TCTTTGTTGAGCGTGTGCATTT 59.901 40.909 0.00 0.00 46.23 2.32
326 334 1.460504 ATCAACGAGACTGCGGAGTA 58.539 50.000 10.47 0.00 35.12 2.59
331 339 1.126846 GTCCAAATCAACGAGACTGCG 59.873 52.381 0.00 0.00 37.29 5.18
335 343 3.492313 GCATTGTCCAAATCAACGAGAC 58.508 45.455 0.00 0.00 0.00 3.36
342 350 5.421374 TCATAACATGGCATTGTCCAAATCA 59.579 36.000 0.00 0.00 39.96 2.57
351 359 8.030744 TGAAAAACAATCATAACATGGCATTG 57.969 30.769 0.00 0.00 33.28 2.82
353 361 8.795842 AATGAAAAACAATCATAACATGGCAT 57.204 26.923 0.00 0.00 36.53 4.40
412 444 7.170393 TGCACAGTAGAATAGCTTTTCTCTA 57.830 36.000 20.81 4.22 37.20 2.43
438 470 6.532619 GCTTGATCCATGCACAGAGTATCTC 61.533 48.000 0.00 0.00 37.66 2.75
439 471 4.743045 GCTTGATCCATGCACAGAGTATCT 60.743 45.833 0.00 0.00 39.11 1.98
461 493 1.739466 TCTCAAAGCAATCACGGATGC 59.261 47.619 0.00 0.00 0.00 3.91
463 495 4.264253 TGAATCTCAAAGCAATCACGGAT 58.736 39.130 0.00 0.00 0.00 4.18
467 499 4.995124 AGCATGAATCTCAAAGCAATCAC 58.005 39.130 0.00 0.00 35.02 3.06
470 502 6.770746 AAGTAGCATGAATCTCAAAGCAAT 57.229 33.333 0.00 0.00 35.02 3.56
527 559 7.064229 ACTGGAAGAAAAACCCAATGTAACTA 58.936 34.615 0.00 0.00 37.43 2.24
564 596 8.455682 ACGGTTATACACAATGAAACATTAAGG 58.544 33.333 0.00 0.00 0.00 2.69
609 641 8.087750 CCAATAAAAAGGAATGCACTTGTTCTA 58.912 33.333 0.00 0.00 0.00 2.10
611 643 6.705825 ACCAATAAAAAGGAATGCACTTGTTC 59.294 34.615 0.00 0.00 0.00 3.18
625 657 5.289675 TGTTTCGTTGTGCACCAATAAAAAG 59.710 36.000 15.69 3.16 35.02 2.27
678 711 4.106909 GGTTTGAAAATGTTTCGTTCGGT 58.893 39.130 0.00 0.00 0.00 4.69
695 728 6.345298 AGGTTGTCAAAATTTACCTGGTTTG 58.655 36.000 3.84 2.99 37.80 2.93
734 767 1.651138 CGTTCGTGATTGCTCTGAGAC 59.349 52.381 9.28 0.42 0.00 3.36
783 816 4.324267 ACTCCCGGAACAAAATTACAGAG 58.676 43.478 0.73 0.00 0.00 3.35
849 890 6.310956 CGTTTGGGTTACTATTATTGACGTGA 59.689 38.462 0.00 0.00 0.00 4.35
851 892 6.397272 TCGTTTGGGTTACTATTATTGACGT 58.603 36.000 0.00 0.00 0.00 4.34
886 935 0.388263 GAGGAGGGACGAACGAACAC 60.388 60.000 0.14 0.00 0.00 3.32
1351 1431 1.411977 CGAGCAGAGGAGATTCATGGT 59.588 52.381 0.00 0.00 0.00 3.55
1373 1453 2.530958 GAAATCAAGGGACCGGCCGA 62.531 60.000 30.73 3.37 37.63 5.54
1374 1454 2.045340 AAATCAAGGGACCGGCCG 60.045 61.111 21.04 21.04 37.63 6.13
1416 1496 1.413077 GACCCGAACCCTCCTAATCAG 59.587 57.143 0.00 0.00 0.00 2.90
1638 1718 3.393800 AGCTATAATTAGGTGCAGTGCG 58.606 45.455 11.20 0.00 34.90 5.34
1639 1719 4.450419 CAGAGCTATAATTAGGTGCAGTGC 59.550 45.833 8.58 8.58 36.32 4.40
1640 1720 4.993584 CCAGAGCTATAATTAGGTGCAGTG 59.006 45.833 0.00 0.00 36.32 3.66
1641 1721 4.503991 GCCAGAGCTATAATTAGGTGCAGT 60.504 45.833 0.00 0.00 36.32 4.40
1642 1722 3.999663 GCCAGAGCTATAATTAGGTGCAG 59.000 47.826 0.00 1.23 36.32 4.41
1643 1723 3.390967 TGCCAGAGCTATAATTAGGTGCA 59.609 43.478 8.96 0.00 40.80 4.57
1644 1724 4.008074 TGCCAGAGCTATAATTAGGTGC 57.992 45.455 0.00 0.00 40.80 5.01
1645 1725 6.058183 ACTTTGCCAGAGCTATAATTAGGTG 58.942 40.000 0.00 0.00 40.80 4.00
1646 1726 6.253946 ACTTTGCCAGAGCTATAATTAGGT 57.746 37.500 0.00 0.00 40.80 3.08
1647 1727 6.995091 AGAACTTTGCCAGAGCTATAATTAGG 59.005 38.462 0.00 0.00 40.80 2.69
1648 1728 8.443953 AAGAACTTTGCCAGAGCTATAATTAG 57.556 34.615 0.00 0.00 40.80 1.73
1649 1729 8.807948 AAAGAACTTTGCCAGAGCTATAATTA 57.192 30.769 0.00 0.00 40.80 1.40
1651 1731 7.066766 CAGAAAGAACTTTGCCAGAGCTATAAT 59.933 37.037 4.48 0.00 40.80 1.28
1652 1732 6.372659 CAGAAAGAACTTTGCCAGAGCTATAA 59.627 38.462 4.48 0.00 40.80 0.98
1654 1734 4.699257 CAGAAAGAACTTTGCCAGAGCTAT 59.301 41.667 4.48 0.00 40.80 2.97
1655 1735 4.067896 CAGAAAGAACTTTGCCAGAGCTA 58.932 43.478 4.48 0.00 40.80 3.32
1657 1737 2.880890 TCAGAAAGAACTTTGCCAGAGC 59.119 45.455 4.48 0.00 40.48 4.09
1658 1738 4.615452 GCATCAGAAAGAACTTTGCCAGAG 60.615 45.833 4.48 0.00 32.11 3.35
1660 1740 3.005050 TGCATCAGAAAGAACTTTGCCAG 59.995 43.478 4.48 0.00 32.11 4.85
1662 1742 3.648339 TGCATCAGAAAGAACTTTGCC 57.352 42.857 4.48 0.00 32.11 4.52
1663 1743 4.624452 GGAATGCATCAGAAAGAACTTTGC 59.376 41.667 0.00 3.33 32.11 3.68
1664 1744 6.022163 AGGAATGCATCAGAAAGAACTTTG 57.978 37.500 0.00 0.00 32.11 2.77
1666 1746 6.373774 CAGTAGGAATGCATCAGAAAGAACTT 59.626 38.462 0.00 0.00 0.00 2.66
1667 1747 5.879223 CAGTAGGAATGCATCAGAAAGAACT 59.121 40.000 0.00 0.00 0.00 3.01
1668 1748 5.645497 ACAGTAGGAATGCATCAGAAAGAAC 59.355 40.000 0.00 0.00 0.00 3.01
1669 1749 5.645067 CACAGTAGGAATGCATCAGAAAGAA 59.355 40.000 0.00 0.00 0.00 2.52
1670 1750 5.181009 CACAGTAGGAATGCATCAGAAAGA 58.819 41.667 0.00 0.00 0.00 2.52
1673 1753 3.054875 AGCACAGTAGGAATGCATCAGAA 60.055 43.478 0.00 0.00 41.97 3.02
1695 1778 0.038343 GTCTACACGTTAACCGGCCA 60.038 55.000 0.00 0.00 42.24 5.36
1742 1825 4.577246 GTAGCTGAGCCGCTCGGG 62.577 72.222 26.93 17.37 41.30 5.14
1820 1903 5.109210 TGTGATTGATTTAGTAGCTCCGTG 58.891 41.667 0.00 0.00 0.00 4.94
1838 1921 4.065321 GCAGTAGCTAGGTTGATGTGAT 57.935 45.455 0.00 0.00 37.91 3.06
1839 1922 3.526931 GCAGTAGCTAGGTTGATGTGA 57.473 47.619 0.00 0.00 37.91 3.58
1855 1941 1.185618 TGCTACCGGAGTTGAGCAGT 61.186 55.000 9.46 0.00 39.93 4.40
2082 2182 4.496341 GGTTGGATTGCGACATGTAGAATG 60.496 45.833 10.44 0.00 0.00 2.67
2098 2198 4.618920 AACAAGTAGTTCTCGGTTGGAT 57.381 40.909 0.00 0.00 34.74 3.41
2118 2218 7.652524 AGTAGCTTTCACTGATCATCTCTAA 57.347 36.000 0.00 0.00 0.00 2.10
2147 2247 0.870393 AAGCTGAACGCATCACACAG 59.130 50.000 0.00 0.00 42.61 3.66
2156 2256 2.080286 TTGAGGTAGAAGCTGAACGC 57.920 50.000 0.00 0.00 39.57 4.84
2158 2258 6.374578 GTTCAAATTGAGGTAGAAGCTGAAC 58.625 40.000 0.00 0.00 35.04 3.18
2160 2260 4.690748 CGTTCAAATTGAGGTAGAAGCTGA 59.309 41.667 0.00 0.00 0.00 4.26
2329 2433 2.176546 CCGTTGATGCCACGCAAG 59.823 61.111 0.00 0.00 43.62 4.01
2384 2488 2.358615 TGCATGTGCTCCACGTCC 60.359 61.111 6.55 0.00 42.66 4.79
2389 2493 3.356267 GTGCGTGCATGTGCTCCA 61.356 61.111 7.93 0.00 42.66 3.86
3224 3328 4.308458 TTGTAGTGCACCGCCGCT 62.308 61.111 14.63 0.00 0.00 5.52
3656 3813 6.429692 TGTTCATTCTACATCAAACGACCAAT 59.570 34.615 0.00 0.00 0.00 3.16
3690 3847 2.484264 GTGGTAAACTGCTGACATGGTC 59.516 50.000 0.00 0.00 0.00 4.02
3692 3849 2.503331 TGTGGTAAACTGCTGACATGG 58.497 47.619 0.00 0.00 0.00 3.66
3699 3856 4.655963 AGTTGATCATGTGGTAAACTGCT 58.344 39.130 0.00 0.00 0.00 4.24
3707 3864 5.118990 GCACTACATAGTTGATCATGTGGT 58.881 41.667 9.60 9.60 44.64 4.16
3762 3920 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
3763 3921 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
3764 3922 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
3765 3923 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
3766 3924 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
3767 3925 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
3768 3926 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
3769 3927 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
3770 3928 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3771 3929 7.147811 GCTACTCCCTCTGTCCCATAATATAAG 60.148 44.444 0.00 0.00 0.00 1.73
3772 3930 6.668283 GCTACTCCCTCTGTCCCATAATATAA 59.332 42.308 0.00 0.00 0.00 0.98
3773 3931 6.195700 GCTACTCCCTCTGTCCCATAATATA 58.804 44.000 0.00 0.00 0.00 0.86
3774 3932 5.026790 GCTACTCCCTCTGTCCCATAATAT 58.973 45.833 0.00 0.00 0.00 1.28
3775 3933 4.140782 TGCTACTCCCTCTGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
3776 3934 3.243724 GCTACTCCCTCTGTCCCATAAT 58.756 50.000 0.00 0.00 0.00 1.28
3777 3935 2.023404 TGCTACTCCCTCTGTCCCATAA 60.023 50.000 0.00 0.00 0.00 1.90
3778 3936 1.573857 TGCTACTCCCTCTGTCCCATA 59.426 52.381 0.00 0.00 0.00 2.74
3779 3937 0.339859 TGCTACTCCCTCTGTCCCAT 59.660 55.000 0.00 0.00 0.00 4.00
3780 3938 0.116342 TTGCTACTCCCTCTGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
3781 3939 1.066071 GTTTGCTACTCCCTCTGTCCC 60.066 57.143 0.00 0.00 0.00 4.46
3782 3940 1.623811 TGTTTGCTACTCCCTCTGTCC 59.376 52.381 0.00 0.00 0.00 4.02
3783 3941 2.563179 TCTGTTTGCTACTCCCTCTGTC 59.437 50.000 0.00 0.00 0.00 3.51
3784 3942 2.564947 CTCTGTTTGCTACTCCCTCTGT 59.435 50.000 0.00 0.00 0.00 3.41
3785 3943 2.564947 ACTCTGTTTGCTACTCCCTCTG 59.435 50.000 0.00 0.00 0.00 3.35
3786 3944 2.564947 CACTCTGTTTGCTACTCCCTCT 59.435 50.000 0.00 0.00 0.00 3.69
3787 3945 2.563179 TCACTCTGTTTGCTACTCCCTC 59.437 50.000 0.00 0.00 0.00 4.30
3788 3946 2.300437 GTCACTCTGTTTGCTACTCCCT 59.700 50.000 0.00 0.00 0.00 4.20
3789 3947 2.613223 GGTCACTCTGTTTGCTACTCCC 60.613 54.545 0.00 0.00 0.00 4.30
3790 3948 2.037251 TGGTCACTCTGTTTGCTACTCC 59.963 50.000 0.00 0.00 0.00 3.85
3791 3949 3.386768 TGGTCACTCTGTTTGCTACTC 57.613 47.619 0.00 0.00 0.00 2.59
3840 3998 2.279741 GCACATGAAGCCTCGTTGATA 58.720 47.619 0.00 0.00 0.00 2.15
3846 4004 1.469703 TCAAATGCACATGAAGCCTCG 59.530 47.619 0.00 0.00 0.00 4.63
3877 4035 9.087424 GTTTTGAAAAAGCTATCTGTTTCTTGT 57.913 29.630 9.94 0.00 43.69 3.16
3917 4075 3.943671 TCAGGGTTCTTTGGTTTCTCA 57.056 42.857 0.00 0.00 0.00 3.27
3983 4141 0.475906 AAAAGCTCCAGTGTCAGGCT 59.524 50.000 0.00 0.00 34.52 4.58
4011 4169 1.593196 GCTAGTGTTGAGTGGTGCAA 58.407 50.000 0.00 0.00 0.00 4.08
4013 4171 0.250295 TGGCTAGTGTTGAGTGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
4020 4178 0.179070 TGCGTGTTGGCTAGTGTTGA 60.179 50.000 0.00 0.00 0.00 3.18
4028 4186 3.543680 ATAGAATAGTGCGTGTTGGCT 57.456 42.857 0.00 0.00 0.00 4.75
4123 4281 3.006112 TGTTGGCAGGAGTTTTACACA 57.994 42.857 0.00 0.00 0.00 3.72
4149 4307 8.936864 GTTGGTACTGGATAGAATATTACATGC 58.063 37.037 0.00 0.00 0.00 4.06
4171 4332 5.757320 TGTTGCTTTAAATTGTGATGGTTGG 59.243 36.000 0.00 0.00 0.00 3.77
4364 4526 6.232513 TTGAAAGACAAGCTTGGGACAAGC 62.233 45.833 29.18 22.54 43.31 4.01
4373 4535 5.537674 ACTCATCCATTTGAAAGACAAGCTT 59.462 36.000 0.00 0.00 39.77 3.74
4395 4557 7.534723 TGTATCACCAAGTTAGTGTTAGACT 57.465 36.000 1.30 0.00 38.88 3.24
4396 4558 7.491696 GGATGTATCACCAAGTTAGTGTTAGAC 59.508 40.741 1.30 0.00 36.58 2.59
4401 4563 5.755409 TGGATGTATCACCAAGTTAGTGT 57.245 39.130 1.30 0.00 36.58 3.55


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

AutoCloner maintained by Alex Coulton.