Multiple sequence alignment - TraesCS1B01G080800

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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 TraesCS1B01G080800 chr1B 100.000 2750 0 0 1 2750 63201138 63203887 0.000000e+00 5079.0
1 TraesCS1B01G080800 chr1B 88.489 1390 128 23 433 1806 63888649 63890022 0.000000e+00 1652.0
2 TraesCS1B01G080800 chr1B 88.120 1372 127 21 433 1788 63479350 63480701 0.000000e+00 1598.0
3 TraesCS1B01G080800 chr1B 87.810 1370 136 20 433 1788 63613760 63615112 0.000000e+00 1576.0
4 TraesCS1B01G080800 chr1B 87.299 1370 144 19 433 1788 63808361 63809714 0.000000e+00 1539.0
5 TraesCS1B01G080800 chr1B 84.568 324 34 14 355 669 63201581 63201897 9.570000e-80 307.0
6 TraesCS1B01G080800 chr1A 91.069 2049 171 11 153 2193 42669809 42671853 0.000000e+00 2760.0
7 TraesCS1B01G080800 chr1A 91.416 1328 109 4 870 2193 42721111 42722437 0.000000e+00 1816.0
8 TraesCS1B01G080800 chr1A 91.039 1328 114 4 870 2193 42685948 42687274 0.000000e+00 1788.0
9 TraesCS1B01G080800 chr1A 91.905 840 68 0 870 1709 42695242 42696081 0.000000e+00 1175.0
10 TraesCS1B01G080800 chr1A 87.112 869 75 14 30 871 42683050 42683908 0.000000e+00 950.0
11 TraesCS1B01G080800 chr1A 86.552 870 73 18 30 871 42692400 42693253 0.000000e+00 918.0
12 TraesCS1B01G080800 chr1A 86.207 870 81 18 30 871 42718215 42719073 0.000000e+00 905.0
13 TraesCS1B01G080800 chr1A 89.788 519 48 4 1679 2193 42696080 42696597 0.000000e+00 660.0
14 TraesCS1B01G080800 chr1A 80.769 468 48 20 71 496 42801182 42801649 7.340000e-86 327.0
15 TraesCS1B01G080800 chr1A 90.196 51 2 3 3 53 283818452 283818405 2.290000e-06 63.9
16 TraesCS1B01G080800 chr1D 91.770 1944 150 10 257 2193 43305362 43307302 0.000000e+00 2695.0
17 TraesCS1B01G080800 chr1D 87.099 1248 127 24 563 1806 44628763 44629980 0.000000e+00 1382.0
18 TraesCS1B01G080800 chr1D 88.808 1099 99 14 717 1806 43823101 43824184 0.000000e+00 1327.0
19 TraesCS1B01G080800 chr1D 85.512 283 30 9 434 710 43822330 43822607 4.480000e-73 285.0
20 TraesCS1B01G080800 chr1D 80.663 362 48 12 1820 2176 44161448 44161792 7.550000e-66 261.0
21 TraesCS1B01G080800 chr1D 80.878 319 41 11 1820 2133 43825800 43826103 1.650000e-57 233.0
22 TraesCS1B01G080800 chr5A 79.502 1688 240 70 527 2171 608949799 608951423 0.000000e+00 1103.0
23 TraesCS1B01G080800 chr5D 81.177 1376 191 45 527 1873 488203313 488204649 0.000000e+00 1044.0
24 TraesCS1B01G080800 chr5B 98.743 557 7 0 2194 2750 503413522 503412966 0.000000e+00 990.0
25 TraesCS1B01G080800 chr3B 98.743 557 6 1 2194 2750 663848974 663849529 0.000000e+00 989.0
26 TraesCS1B01G080800 chr3B 98.571 560 7 1 2192 2750 690714303 690713744 0.000000e+00 989.0
27 TraesCS1B01G080800 chr6B 98.566 558 7 1 2194 2750 599949687 599949130 0.000000e+00 985.0
28 TraesCS1B01G080800 chr6B 98.214 560 10 0 2191 2750 541991416 541991975 0.000000e+00 979.0
29 TraesCS1B01G080800 chr2B 98.566 558 6 2 2194 2750 24611278 24611834 0.000000e+00 985.0
30 TraesCS1B01G080800 chr2B 98.564 557 8 0 2194 2750 465525182 465524626 0.000000e+00 985.0
31 TraesCS1B01G080800 chr2B 98.566 558 7 1 2194 2750 771276316 771276873 0.000000e+00 985.0
32 TraesCS1B01G080800 chr2B 98.393 560 8 1 2192 2750 600834860 600834301 0.000000e+00 983.0
33 TraesCS1B01G080800 chr7D 97.297 37 1 0 4 40 500269069 500269033 2.290000e-06 63.9
34 TraesCS1B01G080800 chr7B 97.297 37 1 0 4 40 144749485 144749449 2.290000e-06 63.9
35 TraesCS1B01G080800 chr4B 89.583 48 3 2 3 49 599434864 599434818 2.960000e-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 TraesCS1B01G080800 chr1B 63201138 63203887 2749 False 2693.000000 5079 92.2840 1 2750 2 chr1B.!!$F5 2749
1 TraesCS1B01G080800 chr1B 63888649 63890022 1373 False 1652.000000 1652 88.4890 433 1806 1 chr1B.!!$F4 1373
2 TraesCS1B01G080800 chr1B 63479350 63480701 1351 False 1598.000000 1598 88.1200 433 1788 1 chr1B.!!$F1 1355
3 TraesCS1B01G080800 chr1B 63613760 63615112 1352 False 1576.000000 1576 87.8100 433 1788 1 chr1B.!!$F2 1355
4 TraesCS1B01G080800 chr1B 63808361 63809714 1353 False 1539.000000 1539 87.2990 433 1788 1 chr1B.!!$F3 1355
5 TraesCS1B01G080800 chr1A 42669809 42671853 2044 False 2760.000000 2760 91.0690 153 2193 1 chr1A.!!$F1 2040
6 TraesCS1B01G080800 chr1A 42683050 42687274 4224 False 1369.000000 1788 89.0755 30 2193 2 chr1A.!!$F3 2163
7 TraesCS1B01G080800 chr1A 42718215 42722437 4222 False 1360.500000 1816 88.8115 30 2193 2 chr1A.!!$F5 2163
8 TraesCS1B01G080800 chr1A 42692400 42696597 4197 False 917.666667 1175 89.4150 30 2193 3 chr1A.!!$F4 2163
9 TraesCS1B01G080800 chr1D 43305362 43307302 1940 False 2695.000000 2695 91.7700 257 2193 1 chr1D.!!$F1 1936
10 TraesCS1B01G080800 chr1D 44628763 44629980 1217 False 1382.000000 1382 87.0990 563 1806 1 chr1D.!!$F3 1243
11 TraesCS1B01G080800 chr1D 43822330 43826103 3773 False 615.000000 1327 85.0660 434 2133 3 chr1D.!!$F4 1699
12 TraesCS1B01G080800 chr5A 608949799 608951423 1624 False 1103.000000 1103 79.5020 527 2171 1 chr5A.!!$F1 1644
13 TraesCS1B01G080800 chr5D 488203313 488204649 1336 False 1044.000000 1044 81.1770 527 1873 1 chr5D.!!$F1 1346
14 TraesCS1B01G080800 chr5B 503412966 503413522 556 True 990.000000 990 98.7430 2194 2750 1 chr5B.!!$R1 556
15 TraesCS1B01G080800 chr3B 663848974 663849529 555 False 989.000000 989 98.7430 2194 2750 1 chr3B.!!$F1 556
16 TraesCS1B01G080800 chr3B 690713744 690714303 559 True 989.000000 989 98.5710 2192 2750 1 chr3B.!!$R1 558
17 TraesCS1B01G080800 chr6B 599949130 599949687 557 True 985.000000 985 98.5660 2194 2750 1 chr6B.!!$R1 556
18 TraesCS1B01G080800 chr6B 541991416 541991975 559 False 979.000000 979 98.2140 2191 2750 1 chr6B.!!$F1 559
19 TraesCS1B01G080800 chr2B 24611278 24611834 556 False 985.000000 985 98.5660 2194 2750 1 chr2B.!!$F1 556
20 TraesCS1B01G080800 chr2B 465524626 465525182 556 True 985.000000 985 98.5640 2194 2750 1 chr2B.!!$R1 556
21 TraesCS1B01G080800 chr2B 771276316 771276873 557 False 985.000000 985 98.5660 2194 2750 1 chr2B.!!$F2 556
22 TraesCS1B01G080800 chr2B 600834301 600834860 559 True 983.000000 983 98.3930 2192 2750 1 chr2B.!!$R2 558

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
225 251 0.251519 CCCCCAAAAAGCTCTGCTCT 60.252 55.0 0.0 0.0 38.25 4.09 F
1355 4149 0.107654 ATGGAGAAGGTTGGCTACGC 60.108 55.0 0.0 0.0 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 4402 0.755686 CTAATGCTTCTCCTCCCGCT 59.244 55.0 0.0 0.0 0.0 5.52 R
2218 6657 1.222567 AAATCGCCTATTCACCCCCT 58.777 50.0 0.0 0.0 0.0 4.79 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
17 18 4.719369 AGAGACGGGCGCGACAAC 62.719 66.667 30.98 19.84 0.00 3.32
31 32 2.945576 CAACGCGCGCCATCAATG 60.946 61.111 32.58 12.27 0.00 2.82
34 35 1.157257 AACGCGCGCCATCAATGATA 61.157 50.000 32.58 0.00 0.00 2.15
37 38 1.005662 CGCGCGCCATCAATGATATAG 60.006 52.381 27.72 1.36 0.00 1.31
60 61 7.613551 AGTAGTATACAAATAGGAACCCCAG 57.386 40.000 5.50 0.00 46.26 4.45
61 62 5.306114 AGTATACAAATAGGAACCCCAGC 57.694 43.478 5.50 0.00 33.88 4.85
63 64 2.990740 ACAAATAGGAACCCCAGCAA 57.009 45.000 0.00 0.00 33.88 3.91
64 65 3.252554 ACAAATAGGAACCCCAGCAAA 57.747 42.857 0.00 0.00 33.88 3.68
65 66 3.582164 ACAAATAGGAACCCCAGCAAAA 58.418 40.909 0.00 0.00 33.88 2.44
66 67 3.970640 ACAAATAGGAACCCCAGCAAAAA 59.029 39.130 0.00 0.00 33.88 1.94
106 107 1.407258 GCTCAATCAGTAGCGGAGAGT 59.593 52.381 0.00 0.00 0.00 3.24
108 109 2.685388 CTCAATCAGTAGCGGAGAGTGA 59.315 50.000 0.00 0.00 35.43 3.41
126 127 2.232941 GTGACATGGAAGTAAGACGGGA 59.767 50.000 0.00 0.00 0.00 5.14
141 142 1.318576 CGGGACCAATTGATAAGCCC 58.681 55.000 7.12 8.71 0.00 5.19
144 145 3.103742 GGGACCAATTGATAAGCCCAAA 58.896 45.455 7.12 0.00 34.25 3.28
145 146 3.132824 GGGACCAATTGATAAGCCCAAAG 59.867 47.826 7.12 0.00 34.25 2.77
146 147 3.769300 GGACCAATTGATAAGCCCAAAGT 59.231 43.478 7.12 0.00 0.00 2.66
148 149 5.420739 GGACCAATTGATAAGCCCAAAGTAA 59.579 40.000 7.12 0.00 0.00 2.24
149 150 6.098266 GGACCAATTGATAAGCCCAAAGTAAT 59.902 38.462 7.12 0.00 0.00 1.89
150 151 7.286775 GGACCAATTGATAAGCCCAAAGTAATA 59.713 37.037 7.12 0.00 0.00 0.98
151 152 8.237811 ACCAATTGATAAGCCCAAAGTAATAG 57.762 34.615 7.12 0.00 0.00 1.73
152 153 7.147976 CCAATTGATAAGCCCAAAGTAATAGC 58.852 38.462 7.12 0.00 0.00 2.97
153 154 7.014615 CCAATTGATAAGCCCAAAGTAATAGCT 59.985 37.037 7.12 0.00 34.64 3.32
157 182 6.996282 TGATAAGCCCAAAGTAATAGCTTACC 59.004 38.462 5.01 0.00 45.75 2.85
160 185 4.473559 AGCCCAAAGTAATAGCTTACCTGA 59.526 41.667 0.00 0.00 38.40 3.86
169 194 2.656947 AGCTTACCTGAGCCAACAAA 57.343 45.000 0.00 0.00 43.74 2.83
187 212 7.011950 GCCAACAAATACAAATTTATTAGGCCC 59.988 37.037 0.00 0.00 33.85 5.80
193 218 5.840243 ACAAATTTATTAGGCCCCGTAAC 57.160 39.130 0.00 0.00 0.00 2.50
213 239 2.114411 GTTGCGTCCTCCCCCAAA 59.886 61.111 0.00 0.00 0.00 3.28
220 246 0.405973 GTCCTCCCCCAAAAAGCTCT 59.594 55.000 0.00 0.00 0.00 4.09
221 247 0.405585 TCCTCCCCCAAAAAGCTCTG 59.594 55.000 0.00 0.00 0.00 3.35
225 251 0.251519 CCCCCAAAAAGCTCTGCTCT 60.252 55.000 0.00 0.00 38.25 4.09
228 254 1.271656 CCCAAAAAGCTCTGCTCTTGG 59.728 52.381 18.63 18.63 38.25 3.61
314 341 8.783833 AGTGTGATATATAGGATTCAATGCAC 57.216 34.615 0.00 0.00 0.00 4.57
344 371 2.549754 AGTGCGATGCAATATTGTAGCC 59.450 45.455 16.61 9.61 41.47 3.93
371 398 4.755629 TGCGGTTAATGTTGTAGCTTGTAA 59.244 37.500 0.00 0.00 0.00 2.41
388 415 7.305474 AGCTTGTAAATGTGCAACTAATGTAC 58.695 34.615 0.00 0.00 44.10 2.90
425 452 8.523915 TTGATGCAGTACCATATCTTCAAAAT 57.476 30.769 0.00 0.00 0.00 1.82
490 691 9.646427 GCAATTAATGTACACATTCCCTTTTTA 57.354 29.630 10.74 0.00 44.67 1.52
737 1443 8.427012 TGTAAAACGTGTCGATATGAAGTTAAC 58.573 33.333 8.51 0.00 0.00 2.01
952 3732 4.083537 ACAACTGGTGTATGCGTTTGTATG 60.084 41.667 0.00 0.00 39.29 2.39
956 3736 4.765273 TGGTGTATGCGTTTGTATGATCT 58.235 39.130 0.00 0.00 0.00 2.75
963 3743 5.530519 TGCGTTTGTATGATCTTCTCAAC 57.469 39.130 0.00 0.00 37.44 3.18
1019 3799 4.225942 AGTCATGTATCCCACACATTCACT 59.774 41.667 0.00 0.00 40.86 3.41
1023 3805 4.323417 TGTATCCCACACATTCACTGAAC 58.677 43.478 0.00 0.00 30.04 3.18
1069 3863 6.099845 ACGATTCTAACACCAAAGGGATAGAT 59.900 38.462 0.00 0.00 38.05 1.98
1240 4034 0.323725 ATGGCCAGCAAATCCGAAGT 60.324 50.000 13.05 0.00 0.00 3.01
1355 4149 0.107654 ATGGAGAAGGTTGGCTACGC 60.108 55.000 0.00 0.00 0.00 4.42
1608 4402 6.825213 TCTGGCGTAGTGATTCTAGTTTAGTA 59.175 38.462 0.00 0.00 0.00 1.82
1626 4420 1.687123 GTAGCGGGAGGAGAAGCATTA 59.313 52.381 0.00 0.00 0.00 1.90
1629 4423 0.465705 CGGGAGGAGAAGCATTAGCA 59.534 55.000 0.00 0.00 45.49 3.49
1684 4510 9.348476 GAGCTTCCCTTTCAAATCTATAATTCT 57.652 33.333 0.00 0.00 0.00 2.40
1923 6355 2.310538 GGGTTCATTTATGCCCTGAGG 58.689 52.381 0.00 0.00 38.12 3.86
1943 6376 5.300792 TGAGGTCAACCAATTTTCACCTTAC 59.699 40.000 1.33 0.00 38.89 2.34
1971 6404 0.329596 ATTCTTGGACCCTGGCTGAC 59.670 55.000 0.00 0.00 0.00 3.51
1981 6414 1.670406 CTGGCTGACGCAAAGCTCT 60.670 57.895 4.80 0.00 40.64 4.09
1982 6415 1.909141 CTGGCTGACGCAAAGCTCTG 61.909 60.000 4.80 0.00 40.64 3.35
2002 6435 8.887717 AGCTCTGAATACAACTTAATTTGCTAG 58.112 33.333 5.53 0.00 0.00 3.42
2014 6450 7.856415 ACTTAATTTGCTAGAAGTGAGGAGAT 58.144 34.615 0.00 0.00 31.05 2.75
2031 6469 2.918266 GAGATTGATGGGAGGGGATGAT 59.082 50.000 0.00 0.00 0.00 2.45
2086 6524 6.757897 ATATGATTTCACACACAAATCCGT 57.242 33.333 3.35 0.00 38.84 4.69
2134 6573 3.243535 TGGATTTTGTAATGCGTGCAACA 60.244 39.130 0.00 0.00 35.07 3.33
2218 6657 3.268330 AGTGCGTTATGTCGACTAGAGA 58.732 45.455 17.92 0.00 0.00 3.10
2405 6844 5.023533 AGCGTAATCACAGGATAACACAT 57.976 39.130 0.00 0.00 32.09 3.21
2659 7099 1.000019 CCCGGACACCCAGTCTCTA 60.000 63.158 0.73 0.00 46.72 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.719369 GTTGTCGCGCCCGTCTCT 62.719 66.667 0.00 0.00 35.54 3.10
12 13 3.381169 ATTGATGGCGCGCGTTGTC 62.381 57.895 32.35 24.31 0.00 3.18
13 14 3.430862 ATTGATGGCGCGCGTTGT 61.431 55.556 32.35 17.09 0.00 3.32
14 15 2.651367 ATCATTGATGGCGCGCGTTG 62.651 55.000 32.35 15.09 0.00 4.10
15 16 1.157257 TATCATTGATGGCGCGCGTT 61.157 50.000 32.35 15.25 0.00 4.84
16 17 0.950555 ATATCATTGATGGCGCGCGT 60.951 50.000 32.35 16.88 0.00 6.01
17 18 0.998669 TATATCATTGATGGCGCGCG 59.001 50.000 28.44 28.44 0.00 6.86
18 19 2.002586 ACTATATCATTGATGGCGCGC 58.997 47.619 25.94 25.94 0.00 6.86
19 20 4.424626 ACTACTATATCATTGATGGCGCG 58.575 43.478 9.46 0.00 0.00 6.86
20 21 8.135529 TGTATACTACTATATCATTGATGGCGC 58.864 37.037 9.46 0.00 0.00 6.53
34 35 9.322769 CTGGGGTTCCTATTTGTATACTACTAT 57.677 37.037 4.17 0.00 0.00 2.12
37 38 6.183361 TGCTGGGGTTCCTATTTGTATACTAC 60.183 42.308 4.17 0.00 0.00 2.73
64 65 7.233348 TGAGCCCACATATCTTTCTTTCTTTTT 59.767 33.333 0.00 0.00 0.00 1.94
65 66 6.721208 TGAGCCCACATATCTTTCTTTCTTTT 59.279 34.615 0.00 0.00 0.00 2.27
66 67 6.248433 TGAGCCCACATATCTTTCTTTCTTT 58.752 36.000 0.00 0.00 0.00 2.52
67 68 5.819991 TGAGCCCACATATCTTTCTTTCTT 58.180 37.500 0.00 0.00 0.00 2.52
68 69 5.441718 TGAGCCCACATATCTTTCTTTCT 57.558 39.130 0.00 0.00 0.00 2.52
69 70 6.319658 TGATTGAGCCCACATATCTTTCTTTC 59.680 38.462 0.00 0.00 0.00 2.62
70 71 6.189859 TGATTGAGCCCACATATCTTTCTTT 58.810 36.000 0.00 0.00 0.00 2.52
73 74 5.128919 ACTGATTGAGCCCACATATCTTTC 58.871 41.667 0.00 0.00 0.00 2.62
106 107 2.232941 GTCCCGTCTTACTTCCATGTCA 59.767 50.000 0.00 0.00 0.00 3.58
108 109 1.553704 GGTCCCGTCTTACTTCCATGT 59.446 52.381 0.00 0.00 0.00 3.21
126 127 7.201911 GCTATTACTTTGGGCTTATCAATTGGT 60.202 37.037 5.42 0.00 0.00 3.67
141 142 5.428253 TGGCTCAGGTAAGCTATTACTTTG 58.572 41.667 0.00 0.00 40.99 2.77
144 145 4.469945 TGTTGGCTCAGGTAAGCTATTACT 59.530 41.667 0.00 0.00 40.99 2.24
145 146 4.766375 TGTTGGCTCAGGTAAGCTATTAC 58.234 43.478 0.00 0.00 42.13 1.89
146 147 5.429681 TTGTTGGCTCAGGTAAGCTATTA 57.570 39.130 0.00 0.00 42.13 0.98
148 149 4.301072 TTTGTTGGCTCAGGTAAGCTAT 57.699 40.909 0.00 0.00 42.13 2.97
149 150 3.780804 TTTGTTGGCTCAGGTAAGCTA 57.219 42.857 0.00 0.00 42.13 3.32
150 151 2.656947 TTTGTTGGCTCAGGTAAGCT 57.343 45.000 0.00 0.00 42.13 3.74
151 152 3.756434 TGTATTTGTTGGCTCAGGTAAGC 59.244 43.478 0.00 0.00 41.73 3.09
152 153 5.957842 TTGTATTTGTTGGCTCAGGTAAG 57.042 39.130 0.00 0.00 0.00 2.34
153 154 6.909550 ATTTGTATTTGTTGGCTCAGGTAA 57.090 33.333 0.00 0.00 0.00 2.85
160 185 7.768582 GGCCTAATAAATTTGTATTTGTTGGCT 59.231 33.333 19.52 0.00 41.65 4.75
169 194 6.491062 GGTTACGGGGCCTAATAAATTTGTAT 59.509 38.462 0.84 0.00 0.00 2.29
202 228 0.405585 CAGAGCTTTTTGGGGGAGGA 59.594 55.000 0.00 0.00 0.00 3.71
204 230 0.251519 AGCAGAGCTTTTTGGGGGAG 60.252 55.000 0.00 0.00 33.89 4.30
210 236 1.959282 ACCCAAGAGCAGAGCTTTTTG 59.041 47.619 0.00 9.04 39.88 2.44
211 237 2.371658 ACCCAAGAGCAGAGCTTTTT 57.628 45.000 0.00 0.00 39.88 1.94
213 239 1.143684 TGAACCCAAGAGCAGAGCTTT 59.856 47.619 0.00 0.00 39.88 3.51
220 246 3.806949 ATAAGGTTGAACCCAAGAGCA 57.193 42.857 11.41 0.00 39.75 4.26
221 247 5.468540 AAAATAAGGTTGAACCCAAGAGC 57.531 39.130 11.41 0.00 39.75 4.09
259 285 6.170506 AGACATTGGACACGTACAATAATGT 58.829 36.000 7.30 13.59 41.96 2.71
265 291 6.032956 AGATAAGACATTGGACACGTACAA 57.967 37.500 0.00 0.00 37.88 2.41
271 297 6.631016 TCACACTAGATAAGACATTGGACAC 58.369 40.000 0.00 0.00 0.00 3.67
314 341 4.914312 ATTGCATCGCACTTTGAAAATG 57.086 36.364 0.00 0.00 38.71 2.32
319 346 4.700268 ACAATATTGCATCGCACTTTGA 57.300 36.364 15.48 0.00 38.71 2.69
344 371 4.732784 AGCTACAACATTAACCGCAAATG 58.267 39.130 0.00 0.00 39.68 2.32
442 469 6.749139 TGCACATCTATAGGCTACAACTTAG 58.251 40.000 0.00 0.00 0.00 2.18
528 738 5.163733 TGCACATCTACATGCTACAACATTG 60.164 40.000 0.00 0.00 42.55 2.82
540 751 7.102993 TGTGTACATTAGTTGCACATCTACAT 58.897 34.615 0.00 0.00 37.44 2.29
658 965 9.283768 TCGAATATATGGTACTGCATCAAAAAT 57.716 29.630 0.00 0.00 0.00 1.82
737 1443 5.393124 AGCATCAAACAATGAATGTGTACG 58.607 37.500 0.00 0.00 42.99 3.67
805 1534 7.306341 CGATATTGCATCAAACAATGAATGTGG 60.306 37.037 0.00 0.00 42.99 4.17
956 3736 4.933400 GGTTTATGTAGCCTTCGTTGAGAA 59.067 41.667 0.00 0.00 37.31 2.87
963 3743 3.675467 GCTTGGTTTATGTAGCCTTCG 57.325 47.619 0.00 0.00 0.00 3.79
993 3773 4.842531 ATGTGTGGGATACATGACTTCA 57.157 40.909 0.00 0.00 42.24 3.02
1019 3799 6.489603 ACAATATAGGATTTGTGTGGGTTCA 58.510 36.000 0.00 0.00 34.87 3.18
1023 3805 6.285224 TCGTACAATATAGGATTTGTGTGGG 58.715 40.000 0.00 0.00 36.75 4.61
1056 3850 5.782845 ACTAGAGCCTTATCTATCCCTTTGG 59.217 44.000 0.00 0.00 31.50 3.28
1069 3863 5.691896 TGTATCTGCTACACTAGAGCCTTA 58.308 41.667 0.00 0.00 39.30 2.69
1240 4034 1.686587 ACATGCGTCCGATGGATCTAA 59.313 47.619 0.00 0.00 32.73 2.10
1355 4149 2.334838 GCTTCTTGCAGAAATTGGCAG 58.665 47.619 0.00 0.00 41.68 4.85
1377 4171 2.086869 CACTTGTAGCCATGTGGGAAG 58.913 52.381 0.54 0.00 40.96 3.46
1468 4262 4.970662 AACCATGTGAATCCGAAGAATG 57.029 40.909 0.00 0.00 0.00 2.67
1608 4402 0.755686 CTAATGCTTCTCCTCCCGCT 59.244 55.000 0.00 0.00 0.00 5.52
1626 4420 6.239008 GGCCACACACATATAATGTAAATGCT 60.239 38.462 0.00 0.00 42.70 3.79
1629 4423 7.013274 GTGAGGCCACACACATATAATGTAAAT 59.987 37.037 26.18 0.00 41.30 1.40
1714 4540 7.556844 TCACAAACCTTCTCATAGATAGTTCC 58.443 38.462 0.00 0.00 0.00 3.62
1716 4542 9.220767 GTTTCACAAACCTTCTCATAGATAGTT 57.779 33.333 0.00 0.00 35.35 2.24
1731 4557 9.880064 GAGAAGACTTTATTAGTTTCACAAACC 57.120 33.333 0.00 0.00 42.34 3.27
1892 6324 6.037062 GGCATAAATGAACCCATTAACTTTGC 59.963 38.462 0.00 0.00 41.84 3.68
1923 6355 7.937649 AGTTAGTAAGGTGAAAATTGGTTGAC 58.062 34.615 0.00 0.00 0.00 3.18
1943 6376 5.675538 CCAGGGTCCAAGAATAAGAGTTAG 58.324 45.833 0.00 0.00 0.00 2.34
1956 6389 4.329545 GCGTCAGCCAGGGTCCAA 62.330 66.667 0.00 0.00 37.42 3.53
1971 6404 4.410492 AAGTTGTATTCAGAGCTTTGCG 57.590 40.909 0.00 0.00 0.00 4.85
2002 6435 3.181456 CCTCCCATCAATCTCCTCACTTC 60.181 52.174 0.00 0.00 0.00 3.01
2014 6450 4.315115 TCTTTATCATCCCCTCCCATCAA 58.685 43.478 0.00 0.00 0.00 2.57
2103 6541 6.153067 CGCATTACAAAATCCAAGTAAACCA 58.847 36.000 0.00 0.00 32.18 3.67
2134 6573 7.321717 AGTGTATATAATGGACAAGGCAGAT 57.678 36.000 0.00 0.00 0.00 2.90
2218 6657 1.222567 AAATCGCCTATTCACCCCCT 58.777 50.000 0.00 0.00 0.00 4.79
2405 6844 5.917462 TCTTCAGTCTGTTTGTCTTCATCA 58.083 37.500 0.00 0.00 0.00 3.07
2586 7026 2.431419 TCCAACCAGACGTACAACTGAA 59.569 45.455 15.06 0.00 36.38 3.02


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

AutoCloner maintained by Alex Coulton.