Multiple sequence alignment - TraesCS2B01G523800

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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 TraesCS2B01G523800 chr2B 100.000 2440 0 0 817 3256 718583566 718586005 0.000000e+00 4506.0
1 TraesCS2B01G523800 chr2B 100.000 255 0 0 1 255 718582750 718583004 3.800000e-129 472.0
2 TraesCS2B01G523800 chr2B 78.723 94 17 3 1299 1391 64323230 64323321 3.510000e-05 60.2
3 TraesCS2B01G523800 chr2D 93.187 1864 83 19 886 2716 592615728 592617580 0.000000e+00 2699.0
4 TraesCS2B01G523800 chr2D 90.070 574 24 14 2707 3256 592617841 592618405 0.000000e+00 713.0
5 TraesCS2B01G523800 chr2D 89.474 228 14 7 33 255 592615010 592615232 2.470000e-71 279.0
6 TraesCS2B01G523800 chr2D 86.000 100 14 0 1418 1517 634561365 634561266 1.240000e-19 108.0
7 TraesCS2B01G523800 chr2A 94.390 1319 40 11 1959 3256 727171419 727172724 0.000000e+00 1995.0
8 TraesCS2B01G523800 chr2A 92.673 505 31 3 886 1390 727165070 727165568 0.000000e+00 723.0
9 TraesCS2B01G523800 chr2A 90.643 342 16 10 1624 1955 727165891 727166226 1.070000e-119 440.0
10 TraesCS2B01G523800 chr2A 93.396 212 13 1 33 243 727164323 727164534 2.440000e-81 313.0
11 TraesCS2B01G523800 chr2A 88.843 242 18 3 1401 1633 727165609 727165850 4.110000e-74 289.0
12 TraesCS2B01G523800 chr7A 91.912 136 11 0 970 1105 179895995 179895860 1.190000e-44 191.0
13 TraesCS2B01G523800 chr1A 86.087 115 15 1 1401 1514 568021220 568021334 4.410000e-24 122.0
14 TraesCS2B01G523800 chr1A 89.655 87 7 2 1305 1390 9089190 9089275 3.430000e-20 110.0
15 TraesCS2B01G523800 chr4D 87.778 90 11 0 1301 1390 509278005 509277916 4.440000e-19 106.0
16 TraesCS2B01G523800 chr4B 86.458 96 10 2 952 1047 614431444 614431352 5.750000e-18 102.0
17 TraesCS2B01G523800 chr5D 82.105 95 17 0 1299 1393 443881018 443880924 7.490000e-12 82.4
18 TraesCS2B01G523800 chr7B 87.879 66 8 0 1308 1373 642267873 642267808 9.690000e-11 78.7
19 TraesCS2B01G523800 chr3D 77.670 103 19 4 1289 1391 415532721 415532819 3.510000e-05 60.2


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 TraesCS2B01G523800 chr2B 718582750 718586005 3255 False 2489.000000 4506 100.000000 1 3256 2 chr2B.!!$F2 3255
1 TraesCS2B01G523800 chr2D 592615010 592618405 3395 False 1230.333333 2699 90.910333 33 3256 3 chr2D.!!$F1 3223
2 TraesCS2B01G523800 chr2A 727171419 727172724 1305 False 1995.000000 1995 94.390000 1959 3256 1 chr2A.!!$F1 1297
3 TraesCS2B01G523800 chr2A 727164323 727166226 1903 False 441.250000 723 91.388750 33 1955 4 chr2A.!!$F2 1922

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
29 30 0.962855 GAGGCAGGGCAGGAAAGAAC 60.963 60.0 0.0 0.00 0.00 3.01 F
1077 1141 0.382158 TCGAGATGACGGACATGCTC 59.618 55.0 0.0 4.32 39.56 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1408 0.109365 CATGCCGCCGAAAATGTTCA 60.109 50.0 0.00 0.0 32.89 3.18 R
2933 3381 0.878523 TTGTTTCGTCAGCTCCGTGG 60.879 55.0 2.55 0.0 0.00 4.94 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
18 19 2.936823 AGTATGGAAGGAGGCAGGG 58.063 57.895 0.00 0.00 0.00 4.45
19 20 1.149401 GTATGGAAGGAGGCAGGGC 59.851 63.158 0.00 0.00 0.00 5.19
20 21 1.307778 TATGGAAGGAGGCAGGGCA 60.308 57.895 0.00 0.00 0.00 5.36
21 22 1.348008 TATGGAAGGAGGCAGGGCAG 61.348 60.000 0.00 0.00 0.00 4.85
22 23 4.120755 GGAAGGAGGCAGGGCAGG 62.121 72.222 0.00 0.00 0.00 4.85
23 24 3.011517 GAAGGAGGCAGGGCAGGA 61.012 66.667 0.00 0.00 0.00 3.86
24 25 2.532715 AAGGAGGCAGGGCAGGAA 60.533 61.111 0.00 0.00 0.00 3.36
25 26 2.142292 GAAGGAGGCAGGGCAGGAAA 62.142 60.000 0.00 0.00 0.00 3.13
26 27 2.044551 GGAGGCAGGGCAGGAAAG 60.045 66.667 0.00 0.00 0.00 2.62
27 28 2.606587 GGAGGCAGGGCAGGAAAGA 61.607 63.158 0.00 0.00 0.00 2.52
28 29 1.380302 GAGGCAGGGCAGGAAAGAA 59.620 57.895 0.00 0.00 0.00 2.52
29 30 0.962855 GAGGCAGGGCAGGAAAGAAC 60.963 60.000 0.00 0.00 0.00 3.01
30 31 1.979155 GGCAGGGCAGGAAAGAACC 60.979 63.158 0.00 0.00 0.00 3.62
31 32 1.075659 GCAGGGCAGGAAAGAACCT 59.924 57.895 0.00 0.00 41.43 3.50
49 50 1.891060 CTGACGCCGCAGAAGTCAAC 61.891 60.000 2.97 0.00 41.33 3.18
65 66 1.228459 AACGGGAGGAGCAAAACCC 60.228 57.895 0.00 0.00 39.02 4.11
95 96 1.942712 CGATAGGAACGGTTCGCGG 60.943 63.158 14.23 0.00 0.00 6.46
203 204 1.278985 CTGGAGTGCACACCATCCTTA 59.721 52.381 32.16 11.90 36.07 2.69
227 286 5.490139 TTTTTGAAGAGAGAACAGTGCAG 57.510 39.130 0.00 0.00 0.00 4.41
233 292 3.435275 AGAGAGAACAGTGCAGACCATA 58.565 45.455 0.00 0.00 0.00 2.74
238 297 4.067896 AGAACAGTGCAGACCATACTTTG 58.932 43.478 0.00 0.00 0.00 2.77
249 313 7.041372 TGCAGACCATACTTTGTTTTAAGAGAC 60.041 37.037 0.00 0.00 0.00 3.36
856 920 2.956964 GTTCGATCTCGCGGCTGG 60.957 66.667 6.13 0.00 39.60 4.85
857 921 4.207281 TTCGATCTCGCGGCTGGG 62.207 66.667 6.13 2.51 39.60 4.45
859 923 3.983494 CGATCTCGCGGCTGGGAT 61.983 66.667 13.33 6.86 36.36 3.85
860 924 2.423446 GATCTCGCGGCTGGGATT 59.577 61.111 13.33 3.82 36.36 3.01
861 925 1.227674 GATCTCGCGGCTGGGATTT 60.228 57.895 13.33 3.44 36.36 2.17
862 926 1.502163 GATCTCGCGGCTGGGATTTG 61.502 60.000 13.33 1.77 36.36 2.32
863 927 3.880846 CTCGCGGCTGGGATTTGC 61.881 66.667 13.33 0.00 36.36 3.68
864 928 4.408821 TCGCGGCTGGGATTTGCT 62.409 61.111 8.45 0.00 31.21 3.91
865 929 4.183686 CGCGGCTGGGATTTGCTG 62.184 66.667 2.84 0.00 38.49 4.41
866 930 2.751436 GCGGCTGGGATTTGCTGA 60.751 61.111 0.00 0.00 37.75 4.26
867 931 2.768492 GCGGCTGGGATTTGCTGAG 61.768 63.158 0.00 0.00 37.75 3.35
868 932 2.768492 CGGCTGGGATTTGCTGAGC 61.768 63.158 0.00 0.00 37.75 4.26
869 933 2.768492 GGCTGGGATTTGCTGAGCG 61.768 63.158 0.00 0.00 0.00 5.03
870 934 2.796651 CTGGGATTTGCTGAGCGC 59.203 61.111 0.00 0.00 39.77 5.92
871 935 3.104602 CTGGGATTTGCTGAGCGCG 62.105 63.158 0.00 0.00 43.27 6.86
872 936 4.543084 GGGATTTGCTGAGCGCGC 62.543 66.667 26.66 26.66 43.27 6.86
873 937 4.543084 GGATTTGCTGAGCGCGCC 62.543 66.667 30.33 19.97 43.27 6.53
874 938 4.876081 GATTTGCTGAGCGCGCCG 62.876 66.667 30.33 17.93 43.27 6.46
961 1025 5.282510 CCTGTAACTAATCGATCCTGTGAC 58.717 45.833 0.00 2.38 0.00 3.67
976 1040 1.880796 TGACTGTTGTGGTGTCGCG 60.881 57.895 0.00 0.00 33.81 5.87
1041 1105 4.321718 ACATCATAAAGCAGATGGATCCG 58.678 43.478 7.39 0.00 44.50 4.18
1077 1141 0.382158 TCGAGATGACGGACATGCTC 59.618 55.000 0.00 4.32 39.56 4.26
1186 1250 5.246883 TGTGAGGACTGTATATCCATCATGG 59.753 44.000 0.00 0.00 38.86 3.66
1356 1420 2.293122 TGGCAACTCTGAACATTTTCGG 59.707 45.455 0.00 0.00 39.24 4.30
1362 1426 0.171007 CTGAACATTTTCGGCGGCAT 59.829 50.000 10.53 0.00 34.04 4.40
1397 1483 1.666888 GGATGGCAACTTTCGTGCTTG 60.667 52.381 0.00 0.00 37.61 4.01
1398 1484 0.318955 ATGGCAACTTTCGTGCTTGC 60.319 50.000 0.00 0.00 39.70 4.01
1401 1487 1.531522 GCAACTTTCGTGCTTGCGTG 61.532 55.000 0.00 0.00 31.61 5.34
1402 1488 0.027455 CAACTTTCGTGCTTGCGTGA 59.973 50.000 0.00 0.00 0.00 4.35
1403 1489 0.027586 AACTTTCGTGCTTGCGTGAC 59.972 50.000 0.00 0.00 0.00 3.67
1405 1491 0.383491 CTTTCGTGCTTGCGTGACTG 60.383 55.000 0.00 0.00 0.00 3.51
1406 1492 1.771073 TTTCGTGCTTGCGTGACTGG 61.771 55.000 0.00 0.00 0.00 4.00
1407 1493 2.636778 TTCGTGCTTGCGTGACTGGA 62.637 55.000 0.00 0.00 0.00 3.86
1408 1494 2.243957 CGTGCTTGCGTGACTGGAA 61.244 57.895 0.00 0.00 0.00 3.53
1425 1520 0.385974 GAATTGCCGTGTGTCACTGC 60.386 55.000 4.27 8.82 43.15 4.40
1427 1522 2.894879 TGCCGTGTGTCACTGCAC 60.895 61.111 13.17 0.14 46.28 4.57
1441 1536 2.555325 CACTGCACATTGTCATCCTTGT 59.445 45.455 0.00 0.00 0.00 3.16
1518 1621 6.179756 TGTGTGGCACTTATCATTTGAGTAT 58.820 36.000 19.83 0.00 35.11 2.12
1596 1706 6.517529 GCATAAACCTCTCTGAGATTATCGGT 60.518 42.308 8.00 8.66 35.60 4.69
1610 1720 9.914131 TGAGATTATCGGTTTCTCATTATACTG 57.086 33.333 6.86 0.00 40.59 2.74
1648 1807 2.412870 CATGCTCGTGTTGGTTGAGTA 58.587 47.619 0.00 0.00 32.32 2.59
1720 1879 0.040067 GTTCTTGCTTGCCACTTCCG 60.040 55.000 0.00 0.00 0.00 4.30
1869 2028 2.665603 GCCTTCGCCAGGTCTCTT 59.334 61.111 2.76 0.00 46.07 2.85
1870 2029 1.003233 GCCTTCGCCAGGTCTCTTT 60.003 57.895 2.76 0.00 46.07 2.52
1871 2030 1.301677 GCCTTCGCCAGGTCTCTTTG 61.302 60.000 2.76 0.00 46.07 2.77
1893 2052 3.896272 GTCTCTCTCCCGGGTTATAACAT 59.104 47.826 22.86 0.00 0.00 2.71
1908 2073 7.201696 GGGTTATAACATTCTTTGATCGCTGAA 60.202 37.037 17.16 0.00 0.00 3.02
1909 2074 8.345565 GGTTATAACATTCTTTGATCGCTGAAT 58.654 33.333 17.16 2.38 0.00 2.57
1955 2124 9.135843 AGTTAATTTTAGAAAGCGTTTATTGCC 57.864 29.630 0.00 0.00 0.00 4.52
1957 2126 7.954788 AATTTTAGAAAGCGTTTATTGCCAA 57.045 28.000 0.00 0.00 0.00 4.52
1975 2144 3.128242 GCCAAGAATCACTCAATGACCTG 59.872 47.826 0.00 0.00 41.24 4.00
1980 2149 5.482908 AGAATCACTCAATGACCTGTGTAC 58.517 41.667 1.88 0.00 41.24 2.90
2168 2337 1.561542 GTGACCAGGAACATGGAGGAT 59.438 52.381 12.42 0.00 43.57 3.24
2256 2425 9.091220 TGGATGATTATGATGCCATGATTTAAA 57.909 29.630 0.00 0.00 34.31 1.52
2570 2742 4.337836 TGTTGCTAACAAATTGTGCTCTGA 59.662 37.500 0.00 0.00 38.72 3.27
2634 2813 6.923508 TGAATTGTATATGTAGCTGGACTTCG 59.076 38.462 0.00 0.00 0.00 3.79
2933 3381 8.340443 ACGTTCCTTGATGTAAAGAAAAGTTAC 58.660 33.333 0.00 0.00 33.00 2.50
2972 3420 9.358872 GAAACAAATCACTGGGAAATTCTTATC 57.641 33.333 0.00 0.00 0.00 1.75
2995 3443 4.645535 TCTGAATTACAGCAAGAGCAGTT 58.354 39.130 0.00 0.00 45.38 3.16
3001 3461 3.492102 ACAGCAAGAGCAGTTTCCTTA 57.508 42.857 0.00 0.00 45.49 2.69
3002 3462 3.142174 ACAGCAAGAGCAGTTTCCTTAC 58.858 45.455 0.00 0.00 45.49 2.34
3010 3470 3.522553 AGCAGTTTCCTTACAGCGATAC 58.477 45.455 0.00 0.00 35.89 2.24
3043 3503 4.391523 GCCTTGTTTTGTTGTTGTTGATGT 59.608 37.500 0.00 0.00 0.00 3.06
3044 3504 5.578727 GCCTTGTTTTGTTGTTGTTGATGTA 59.421 36.000 0.00 0.00 0.00 2.29
3045 3505 6.454981 GCCTTGTTTTGTTGTTGTTGATGTAC 60.455 38.462 0.00 0.00 0.00 2.90
3046 3506 6.587990 CCTTGTTTTGTTGTTGTTGATGTACA 59.412 34.615 0.00 0.00 0.00 2.90
3047 3507 7.201427 CCTTGTTTTGTTGTTGTTGATGTACAG 60.201 37.037 0.33 0.00 0.00 2.74
3048 3508 6.914259 TGTTTTGTTGTTGTTGATGTACAGA 58.086 32.000 0.33 0.00 0.00 3.41
3049 3509 7.542890 TGTTTTGTTGTTGTTGATGTACAGAT 58.457 30.769 0.33 0.00 0.00 2.90
3050 3510 7.487509 TGTTTTGTTGTTGTTGATGTACAGATG 59.512 33.333 0.33 0.00 0.00 2.90
3051 3511 6.691754 TTGTTGTTGTTGATGTACAGATGT 57.308 33.333 0.33 0.00 0.00 3.06
3060 3520 7.390823 TGTTGATGTACAGATGTAGCCTAAAA 58.609 34.615 0.33 0.00 0.00 1.52
3085 3545 7.053316 TCAACTTGGTTTCATTGAACATGAT 57.947 32.000 0.00 0.00 0.00 2.45
3111 3571 7.031975 CAGCCATATTGTTTCCTTTTTCTCTC 58.968 38.462 0.00 0.00 0.00 3.20
3163 3623 3.020984 TGCTGTCATGCATGATGTGAAT 58.979 40.909 30.89 0.00 39.30 2.57
3167 3627 5.467735 GCTGTCATGCATGATGTGAATACTA 59.532 40.000 30.89 2.31 39.30 1.82
3169 3629 7.308408 GCTGTCATGCATGATGTGAATACTAAT 60.308 37.037 30.89 0.00 39.30 1.73
3170 3630 9.211485 CTGTCATGCATGATGTGAATACTAATA 57.789 33.333 30.89 0.93 39.30 0.98
3223 3694 3.151554 GGGTCGTACCAAATTGAAAGGT 58.848 45.455 0.00 0.00 41.02 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.348775 GCCCTGCCTCCTTCCATACT 61.349 60.000 0.00 0.00 0.00 2.12
1 2 1.149401 GCCCTGCCTCCTTCCATAC 59.851 63.158 0.00 0.00 0.00 2.39
2 3 1.307778 TGCCCTGCCTCCTTCCATA 60.308 57.895 0.00 0.00 0.00 2.74
3 4 2.614969 TGCCCTGCCTCCTTCCAT 60.615 61.111 0.00 0.00 0.00 3.41
4 5 3.333219 CTGCCCTGCCTCCTTCCA 61.333 66.667 0.00 0.00 0.00 3.53
5 6 4.120755 CCTGCCCTGCCTCCTTCC 62.121 72.222 0.00 0.00 0.00 3.46
6 7 2.142292 TTTCCTGCCCTGCCTCCTTC 62.142 60.000 0.00 0.00 0.00 3.46
7 8 2.147433 CTTTCCTGCCCTGCCTCCTT 62.147 60.000 0.00 0.00 0.00 3.36
8 9 2.532715 TTTCCTGCCCTGCCTCCT 60.533 61.111 0.00 0.00 0.00 3.69
9 10 2.044551 CTTTCCTGCCCTGCCTCC 60.045 66.667 0.00 0.00 0.00 4.30
10 11 0.962855 GTTCTTTCCTGCCCTGCCTC 60.963 60.000 0.00 0.00 0.00 4.70
11 12 1.075659 GTTCTTTCCTGCCCTGCCT 59.924 57.895 0.00 0.00 0.00 4.75
12 13 1.979155 GGTTCTTTCCTGCCCTGCC 60.979 63.158 0.00 0.00 0.00 4.85
13 14 1.075659 AGGTTCTTTCCTGCCCTGC 59.924 57.895 0.00 0.00 36.35 4.85
14 15 2.952714 CAGGTTCTTTCCTGCCCTG 58.047 57.895 0.00 0.00 46.53 4.45
20 21 1.004918 CGGCGTCAGGTTCTTTCCT 60.005 57.895 0.00 0.00 38.51 3.36
21 22 2.677979 GCGGCGTCAGGTTCTTTCC 61.678 63.158 9.37 0.00 0.00 3.13
22 23 1.901650 CTGCGGCGTCAGGTTCTTTC 61.902 60.000 19.09 0.00 0.00 2.62
23 24 1.961277 CTGCGGCGTCAGGTTCTTT 60.961 57.895 19.09 0.00 0.00 2.52
24 25 2.357517 CTGCGGCGTCAGGTTCTT 60.358 61.111 19.09 0.00 0.00 2.52
25 26 2.771763 CTTCTGCGGCGTCAGGTTCT 62.772 60.000 23.88 0.00 34.91 3.01
26 27 2.357034 TTCTGCGGCGTCAGGTTC 60.357 61.111 23.88 1.98 34.91 3.62
27 28 2.357517 CTTCTGCGGCGTCAGGTT 60.358 61.111 23.88 0.00 34.91 3.50
28 29 3.575351 GACTTCTGCGGCGTCAGGT 62.575 63.158 23.88 17.26 34.91 4.00
29 30 2.811317 GACTTCTGCGGCGTCAGG 60.811 66.667 23.88 14.93 34.91 3.86
30 31 1.664649 TTGACTTCTGCGGCGTCAG 60.665 57.895 20.27 20.27 38.71 3.51
31 32 1.954146 GTTGACTTCTGCGGCGTCA 60.954 57.895 9.37 11.87 36.02 4.35
49 50 0.326927 TTAGGGTTTTGCTCCTCCCG 59.673 55.000 0.00 0.00 44.13 5.14
65 66 4.379603 CCGTTCCTATCGCTAGGTGATTAG 60.380 50.000 11.93 0.59 44.40 1.73
95 96 6.690194 AGACCAAGAGAATGTATTTGATGC 57.310 37.500 0.00 0.00 0.00 3.91
165 166 7.967303 GCACTCCAGATTTTCTCTCTATTTTTG 59.033 37.037 0.00 0.00 29.16 2.44
172 173 3.326006 TGTGCACTCCAGATTTTCTCTCT 59.674 43.478 19.41 0.00 29.16 3.10
220 279 4.836125 AAACAAAGTATGGTCTGCACTG 57.164 40.909 0.00 0.00 0.00 3.66
227 286 9.052759 TCTTGTCTCTTAAAACAAAGTATGGTC 57.947 33.333 0.00 0.00 35.13 4.02
880 944 2.419198 CTCAGCGAATCCCGGGAG 59.581 66.667 30.42 16.89 39.04 4.30
881 945 3.849951 GCTCAGCGAATCCCGGGA 61.850 66.667 29.18 29.18 39.04 5.14
905 969 3.598246 GCAAACGCTACGATTTCTTGAAC 59.402 43.478 0.00 0.00 0.00 3.18
961 1025 4.012895 GCCGCGACACCACAACAG 62.013 66.667 8.23 0.00 0.00 3.16
976 1040 0.808755 CAAATCCCGTTGTACCTGCC 59.191 55.000 0.00 0.00 0.00 4.85
1041 1105 1.831736 TCGATTCTGAAAGGGTCCCTC 59.168 52.381 12.07 0.00 30.89 4.30
1077 1141 2.726760 GGCGTCTTACAGCTTATCGATG 59.273 50.000 8.54 0.00 34.52 3.84
1152 1216 3.431415 ACAGTCCTCACAGTATGCAGTA 58.569 45.455 0.00 0.00 42.53 2.74
1163 1227 5.337894 CCCATGATGGATATACAGTCCTCAC 60.338 48.000 14.26 0.00 40.96 3.51
1186 1250 1.244019 ATTCTCACAAGGTTGCGGCC 61.244 55.000 0.00 0.00 0.00 6.13
1344 1408 0.109365 CATGCCGCCGAAAATGTTCA 60.109 50.000 0.00 0.00 32.89 3.18
1356 1420 0.179225 CACGTCACTAAACATGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
1362 1426 2.611971 GCCATCCTCACGTCACTAAACA 60.612 50.000 0.00 0.00 0.00 2.83
1397 1483 2.325082 ACGGCAATTCCAGTCACGC 61.325 57.895 0.00 0.00 34.01 5.34
1398 1484 1.227999 ACACGGCAATTCCAGTCACG 61.228 55.000 0.00 0.00 34.01 4.35
1401 1487 0.517316 GACACACGGCAATTCCAGTC 59.483 55.000 0.00 0.00 34.01 3.51
1402 1488 0.179032 TGACACACGGCAATTCCAGT 60.179 50.000 0.00 0.00 34.01 4.00
1403 1489 0.238289 GTGACACACGGCAATTCCAG 59.762 55.000 0.00 0.00 34.01 3.86
1405 1491 0.238289 CAGTGACACACGGCAATTCC 59.762 55.000 8.59 0.00 39.64 3.01
1406 1492 3.753774 CAGTGACACACGGCAATTC 57.246 52.632 8.59 0.00 39.64 2.17
1425 1520 3.817084 AGTCACACAAGGATGACAATGTG 59.183 43.478 7.10 10.61 46.34 3.21
1427 1522 3.189910 CCAGTCACACAAGGATGACAATG 59.810 47.826 7.10 0.00 46.34 2.82
1493 1596 4.456911 ACTCAAATGATAAGTGCCACACAG 59.543 41.667 0.00 0.00 36.74 3.66
1596 1706 9.890629 ACATAAGCAGAACAGTATAATGAGAAA 57.109 29.630 7.27 0.00 0.00 2.52
1608 1718 3.593096 TGCTCAGACATAAGCAGAACAG 58.407 45.455 0.00 0.00 43.30 3.16
1648 1807 5.643421 AGATGATTCTGGTAAGATGGCTT 57.357 39.130 0.00 0.00 38.15 4.35
1720 1879 5.163713 CCAGTGAAAGTAGCAAGGAATAAGC 60.164 44.000 0.00 0.00 0.00 3.09
1869 2028 2.544844 ATAACCCGGGAGAGAGACAA 57.455 50.000 32.02 0.96 0.00 3.18
1870 2029 3.294214 GTTATAACCCGGGAGAGAGACA 58.706 50.000 32.02 2.31 0.00 3.41
1871 2030 3.294214 TGTTATAACCCGGGAGAGAGAC 58.706 50.000 32.02 17.95 0.00 3.36
1893 2052 6.048509 TGCACTATATTCAGCGATCAAAGAA 58.951 36.000 0.00 0.00 0.00 2.52
1955 2124 4.758674 ACACAGGTCATTGAGTGATTCTTG 59.241 41.667 10.50 0.00 39.48 3.02
1957 2126 4.630644 ACACAGGTCATTGAGTGATTCT 57.369 40.909 10.50 0.00 39.48 2.40
1975 2144 6.587226 TGGTAAGTGAAATATGACACGTACAC 59.413 38.462 24.35 18.46 45.88 2.90
1980 2149 8.826710 ACAATATGGTAAGTGAAATATGACACG 58.173 33.333 0.00 0.00 41.22 4.49
2264 2433 8.877864 ATGTTCCCAAAATTTCTACTATCACA 57.122 30.769 0.00 0.00 0.00 3.58
2563 2733 3.058983 CACAACGTGCTTTTATCAGAGCA 60.059 43.478 0.00 0.00 45.91 4.26
2570 2742 5.475564 AGGGAATTACACAACGTGCTTTTAT 59.524 36.000 0.00 0.00 36.98 1.40
2579 2751 4.332819 GGAAGATCAGGGAATTACACAACG 59.667 45.833 0.00 0.00 0.00 4.10
2634 2813 8.557592 TGATACTTCATATCAGCAATTCATCC 57.442 34.615 0.00 0.00 43.99 3.51
2870 3318 5.055144 GTGATAAGAGCTGCATCATCAAGA 58.945 41.667 1.02 0.00 31.74 3.02
2883 3331 9.690434 CGTCTTTTATTAACTTGTGATAAGAGC 57.310 33.333 0.00 0.00 0.00 4.09
2912 3360 7.075741 CGTGGTAACTTTTCTTTACATCAAGG 58.924 38.462 0.00 0.00 32.01 3.61
2933 3381 0.878523 TTGTTTCGTCAGCTCCGTGG 60.879 55.000 2.55 0.00 0.00 4.94
2972 3420 4.252073 ACTGCTCTTGCTGTAATTCAGAG 58.748 43.478 8.52 0.00 46.92 3.35
2995 3443 4.630069 GCTTCTTTGTATCGCTGTAAGGAA 59.370 41.667 0.00 0.00 0.00 3.36
3001 3461 1.734465 GCTGCTTCTTTGTATCGCTGT 59.266 47.619 0.00 0.00 0.00 4.40
3002 3462 1.063174 GGCTGCTTCTTTGTATCGCTG 59.937 52.381 0.00 0.00 0.00 5.18
3010 3470 3.524541 ACAAAACAAGGCTGCTTCTTTG 58.475 40.909 0.00 6.07 0.00 2.77
3043 3503 7.552687 CCAAGTTGATTTTAGGCTACATCTGTA 59.447 37.037 3.87 0.00 0.00 2.74
3044 3504 6.375455 CCAAGTTGATTTTAGGCTACATCTGT 59.625 38.462 3.87 0.00 0.00 3.41
3045 3505 6.375455 ACCAAGTTGATTTTAGGCTACATCTG 59.625 38.462 3.87 4.61 0.00 2.90
3046 3506 6.485171 ACCAAGTTGATTTTAGGCTACATCT 58.515 36.000 3.87 2.38 0.00 2.90
3047 3507 6.759497 ACCAAGTTGATTTTAGGCTACATC 57.241 37.500 3.87 0.00 0.00 3.06
3048 3508 7.232534 TGAAACCAAGTTGATTTTAGGCTACAT 59.767 33.333 3.87 0.00 0.00 2.29
3049 3509 6.547880 TGAAACCAAGTTGATTTTAGGCTACA 59.452 34.615 3.87 0.00 0.00 2.74
3050 3510 6.977213 TGAAACCAAGTTGATTTTAGGCTAC 58.023 36.000 3.87 0.00 0.00 3.58
3051 3511 7.775053 ATGAAACCAAGTTGATTTTAGGCTA 57.225 32.000 3.87 0.00 0.00 3.93
3060 3520 7.053316 TCATGTTCAATGAAACCAAGTTGAT 57.947 32.000 3.87 0.00 31.39 2.57
3085 3545 6.721208 AGAGAAAAAGGAAACAATATGGCTGA 59.279 34.615 0.00 0.00 0.00 4.26
3175 3635 4.662468 ACTACATAGATGAGCACCTGTG 57.338 45.455 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.