Multiple sequence alignment - TraesCS2A01G184300

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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 TraesCS2A01G184300 chr2A 100.000 1478 0 0 898 2375 144657939 144659416 0.000000e+00 2730.0
1 TraesCS2A01G184300 chr2A 100.000 563 0 0 1 563 144657042 144657604 0.000000e+00 1040.0
2 TraesCS2A01G184300 chr2D 92.902 789 26 15 963 1728 155506914 155506133 0.000000e+00 1120.0
3 TraesCS2A01G184300 chr2D 83.384 662 91 16 1726 2375 155505598 155504944 1.570000e-166 595.0
4 TraesCS2A01G184300 chr2D 84.337 332 18 8 218 519 155507678 155507351 6.420000e-76 294.0
5 TraesCS2A01G184300 chr2D 83.420 193 14 6 7 191 155507856 155507674 1.890000e-36 163.0
6 TraesCS2A01G184300 chr2B 90.921 771 36 13 898 1643 212931415 212930654 0.000000e+00 1005.0
7 TraesCS2A01G184300 chr2B 82.443 655 98 11 1726 2375 212929247 212928605 7.420000e-155 556.0
8 TraesCS2A01G184300 chr2B 83.982 437 24 23 139 532 212932001 212931568 6.200000e-101 377.0
9 TraesCS2A01G184300 chr2B 97.059 34 0 1 1634 1667 212930632 212930600 3.300000e-04 56.5
10 TraesCS2A01G184300 chr7B 76.518 247 50 8 1984 2225 634759830 634760073 6.890000e-26 128.0


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 TraesCS2A01G184300 chr2A 144657042 144659416 2374 False 1885.000 2730 100.00000 1 2375 2 chr2A.!!$F1 2374
1 TraesCS2A01G184300 chr2D 155504944 155507856 2912 True 543.000 1120 86.01075 7 2375 4 chr2D.!!$R1 2368
2 TraesCS2A01G184300 chr2B 212928605 212932001 3396 True 498.625 1005 88.60125 139 2375 4 chr2B.!!$R1 2236

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
443 502 0.028374 ACGCGGAAAAACCAACGAAG 59.972 50.0 12.47 0.0 39.31 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 3703 0.037326 GAGTTGGTGATCCAGTGCGA 60.037 55.0 0.0 0.0 45.22 5.1 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 3.181367 CTCGCAATGCCAGGACAC 58.819 61.111 0.00 0.00 0.00 3.67
18 19 1.672030 CTCGCAATGCCAGGACACA 60.672 57.895 0.00 0.00 0.00 3.72
19 20 1.002257 TCGCAATGCCAGGACACAT 60.002 52.632 0.00 0.00 0.00 3.21
22 24 1.743431 CGCAATGCCAGGACACATAGA 60.743 52.381 0.00 0.00 0.00 1.98
24 26 2.940971 GCAATGCCAGGACACATAGACA 60.941 50.000 0.00 0.00 0.00 3.41
43 45 5.892348 AGACAATACAATTCACCTTTCCCT 58.108 37.500 0.00 0.00 0.00 4.20
46 48 5.476945 ACAATACAATTCACCTTTCCCTCAC 59.523 40.000 0.00 0.00 0.00 3.51
47 49 2.504367 ACAATTCACCTTTCCCTCACG 58.496 47.619 0.00 0.00 0.00 4.35
49 51 2.744202 CAATTCACCTTTCCCTCACGAG 59.256 50.000 0.00 0.00 0.00 4.18
52 54 2.043992 TCACCTTTCCCTCACGAGAAA 58.956 47.619 0.00 0.00 0.00 2.52
103 112 2.715532 AATACGATGGGCGCTCGCAT 62.716 55.000 16.33 5.87 46.81 4.73
106 115 4.916293 GATGGGCGCTCGCATGGA 62.916 66.667 11.32 0.00 44.59 3.41
107 116 4.488136 ATGGGCGCTCGCATGGAA 62.488 61.111 16.36 0.00 43.20 3.53
108 117 3.779850 ATGGGCGCTCGCATGGAAT 62.780 57.895 16.36 0.00 43.20 3.01
109 118 2.280797 GGGCGCTCGCATGGAATA 60.281 61.111 16.36 0.00 44.11 1.75
110 119 1.672356 GGGCGCTCGCATGGAATAT 60.672 57.895 16.36 0.00 44.11 1.28
111 120 1.499056 GGCGCTCGCATGGAATATG 59.501 57.895 16.36 0.00 44.11 1.78
157 166 3.947834 GACCCTGGAATGGTAAACTGATG 59.052 47.826 0.00 0.00 33.82 3.07
158 167 3.591527 ACCCTGGAATGGTAAACTGATGA 59.408 43.478 0.00 0.00 30.92 2.92
178 187 1.740025 AGCAGCCAATTCTTAACTCGC 59.260 47.619 0.00 0.00 0.00 5.03
273 295 0.742281 TCCTTCTCCGTCTCCGTACG 60.742 60.000 8.69 8.69 42.49 3.67
280 302 1.580845 CCGTCTCCGTACGTGAACCT 61.581 60.000 15.21 0.00 41.27 3.50
313 335 2.260434 GCACTTGGCCACAGCATG 59.740 61.111 3.88 0.03 42.56 4.06
319 341 3.446570 GGCCACAGCATGCTCCAC 61.447 66.667 19.68 7.62 42.53 4.02
344 366 2.250841 GAAGAGACGACCGACCGGAC 62.251 65.000 16.07 8.18 38.96 4.79
345 367 3.808656 GAGACGACCGACCGGACC 61.809 72.222 16.07 5.60 38.96 4.46
346 368 4.648626 AGACGACCGACCGGACCA 62.649 66.667 16.07 0.00 38.96 4.02
347 369 3.446570 GACGACCGACCGGACCAT 61.447 66.667 16.07 0.00 38.96 3.55
348 370 2.045045 ACGACCGACCGGACCATA 60.045 61.111 16.07 0.00 38.96 2.74
359 410 0.099259 CGGACCATACACGCGTTCTA 59.901 55.000 10.22 1.68 0.00 2.10
423 482 2.297033 CCATTCAAAACACAGACCCAGG 59.703 50.000 0.00 0.00 0.00 4.45
443 502 0.028374 ACGCGGAAAAACCAACGAAG 59.972 50.000 12.47 0.00 39.31 3.79
453 512 2.464459 CCAACGAAGCATCCTCGGC 61.464 63.158 0.00 0.00 0.00 5.54
527 598 0.604511 CGTACTCACAAACCCACCCC 60.605 60.000 0.00 0.00 0.00 4.95
991 1062 1.640428 CGCGAGGAAGCAATAACAGA 58.360 50.000 0.00 0.00 36.85 3.41
992 1063 1.590238 CGCGAGGAAGCAATAACAGAG 59.410 52.381 0.00 0.00 36.85 3.35
994 1065 2.555199 CGAGGAAGCAATAACAGAGGG 58.445 52.381 0.00 0.00 0.00 4.30
996 1067 3.536570 GAGGAAGCAATAACAGAGGGAC 58.463 50.000 0.00 0.00 0.00 4.46
1355 1435 3.382832 CGACGAGGAGGGGCTGTT 61.383 66.667 0.00 0.00 0.00 3.16
1356 1436 2.266055 GACGAGGAGGGGCTGTTG 59.734 66.667 0.00 0.00 0.00 3.33
1357 1437 2.526873 ACGAGGAGGGGCTGTTGT 60.527 61.111 0.00 0.00 0.00 3.32
1403 1483 2.887337 CCGTGATGTGCATGTGTACTA 58.113 47.619 0.00 0.00 0.00 1.82
1471 1551 3.071479 TGTCCGTTCCATTCTTTGTAGC 58.929 45.455 0.00 0.00 0.00 3.58
1498 1578 7.270047 ACTGTATAAACGCTGTACATATTGGT 58.730 34.615 0.00 0.00 0.00 3.67
1508 1588 5.416326 GCTGTACATATTGGTTTGGTTGGTA 59.584 40.000 0.00 0.00 0.00 3.25
1539 1619 4.141680 CGAGAAATCAAGACGGTTTTTCG 58.858 43.478 0.00 0.00 34.63 3.46
1547 1627 1.950909 AGACGGTTTTTCGCATTTGGA 59.049 42.857 0.00 0.00 0.00 3.53
1554 1634 5.612276 CGGTTTTTCGCATTTGGATTCTTTG 60.612 40.000 0.00 0.00 0.00 2.77
1555 1635 5.334028 GGTTTTTCGCATTTGGATTCTTTGG 60.334 40.000 0.00 0.00 0.00 3.28
1556 1636 4.599047 TTTCGCATTTGGATTCTTTGGT 57.401 36.364 0.00 0.00 0.00 3.67
1557 1637 4.599047 TTCGCATTTGGATTCTTTGGTT 57.401 36.364 0.00 0.00 0.00 3.67
1558 1638 4.599047 TCGCATTTGGATTCTTTGGTTT 57.401 36.364 0.00 0.00 0.00 3.27
1559 1639 4.305769 TCGCATTTGGATTCTTTGGTTTG 58.694 39.130 0.00 0.00 0.00 2.93
1560 1640 4.038522 TCGCATTTGGATTCTTTGGTTTGA 59.961 37.500 0.00 0.00 0.00 2.69
1599 1696 4.216257 CAGATGGAAATTATGCCCGTTAGG 59.784 45.833 0.00 0.00 39.47 2.69
1661 1790 6.620429 TCTCCTGTCCTTGTCATGGTATATA 58.380 40.000 4.76 0.00 0.00 0.86
1662 1791 6.493802 TCTCCTGTCCTTGTCATGGTATATAC 59.506 42.308 4.14 4.14 0.00 1.47
1663 1792 6.140377 TCCTGTCCTTGTCATGGTATATACA 58.860 40.000 14.70 1.84 0.00 2.29
1669 2647 9.337396 GTCCTTGTCATGGTATATACAAAATCA 57.663 33.333 14.70 3.52 31.90 2.57
1720 2698 3.345508 AGACAAAACCGGGAGATAACC 57.654 47.619 6.32 0.00 0.00 2.85
1741 3288 5.440610 ACCTGATGTGTTGAAGTCTTCTTT 58.559 37.500 13.67 0.00 33.64 2.52
1751 3298 4.978099 TGAAGTCTTCTTTCTCCTGCATT 58.022 39.130 13.67 0.00 33.64 3.56
1752 3299 5.380043 TGAAGTCTTCTTTCTCCTGCATTT 58.620 37.500 13.67 0.00 33.64 2.32
1755 3308 5.249420 AGTCTTCTTTCTCCTGCATTTACC 58.751 41.667 0.00 0.00 0.00 2.85
1764 3317 4.530325 GCATTTACCGGCGGCGTG 62.530 66.667 30.09 21.26 0.00 5.34
1779 3332 1.281899 GCGTGTTGTGAGGATAGCTC 58.718 55.000 0.00 0.00 0.00 4.09
1790 3343 2.123854 ATAGCTCCACCTCGGCGA 60.124 61.111 10.14 10.14 33.14 5.54
1792 3345 1.327690 ATAGCTCCACCTCGGCGAAA 61.328 55.000 12.13 0.00 33.14 3.46
1795 3348 1.738099 CTCCACCTCGGCGAAACAG 60.738 63.158 12.13 2.53 33.14 3.16
1801 3356 0.790814 CCTCGGCGAAACAGACTTTC 59.209 55.000 12.13 0.00 0.00 2.62
1804 3359 2.132762 TCGGCGAAACAGACTTTCTTC 58.867 47.619 7.35 0.00 0.00 2.87
1824 3379 6.361433 TCTTCAACCCATGAACTTGTAGAAA 58.639 36.000 0.00 0.00 43.08 2.52
1827 3382 5.888724 TCAACCCATGAACTTGTAGAAACAA 59.111 36.000 0.00 0.00 37.98 2.83
1831 3386 5.507315 CCCATGAACTTGTAGAAACAACACC 60.507 44.000 0.00 0.00 40.69 4.16
1834 3389 2.567985 ACTTGTAGAAACAACACCCGG 58.432 47.619 0.00 0.00 40.69 5.73
1835 3390 2.092807 ACTTGTAGAAACAACACCCGGT 60.093 45.455 0.00 0.00 40.69 5.28
1838 3393 3.465871 TGTAGAAACAACACCCGGTAAC 58.534 45.455 0.00 0.00 30.91 2.50
1845 3400 0.390735 AACACCCGGTAACTCATCGC 60.391 55.000 0.00 0.00 0.00 4.58
1856 3411 0.035317 ACTCATCGCTGCAGACCAAA 59.965 50.000 20.43 0.00 0.00 3.28
1858 3413 1.536766 CTCATCGCTGCAGACCAAAAA 59.463 47.619 20.43 0.00 0.00 1.94
1880 3435 1.369321 GAAACAAATTGCCGCCCCA 59.631 52.632 0.00 0.00 0.00 4.96
1902 3457 5.522460 CCAAAGAAGGCAATGCTGATAAATG 59.478 40.000 4.82 0.00 0.00 2.32
1908 3464 3.378339 GCAATGCTGATAAATGCCTGTC 58.622 45.455 0.00 0.00 0.00 3.51
1912 3468 5.664294 ATGCTGATAAATGCCTGTCAAAA 57.336 34.783 0.00 0.00 0.00 2.44
1913 3469 4.808558 TGCTGATAAATGCCTGTCAAAAC 58.191 39.130 0.00 0.00 0.00 2.43
1914 3470 4.523943 TGCTGATAAATGCCTGTCAAAACT 59.476 37.500 0.00 0.00 0.00 2.66
1916 3472 5.643379 TGATAAATGCCTGTCAAAACTCC 57.357 39.130 0.00 0.00 0.00 3.85
1917 3473 5.076182 TGATAAATGCCTGTCAAAACTCCA 58.924 37.500 0.00 0.00 0.00 3.86
1925 3481 5.127845 TGCCTGTCAAAACTCCAAATACAAA 59.872 36.000 0.00 0.00 0.00 2.83
1942 3498 1.815003 CAAAGAAAGCTGGCCGAATCT 59.185 47.619 0.00 0.00 0.00 2.40
1958 3514 5.798132 CCGAATCTAGATGGATCCATTTGA 58.202 41.667 27.93 23.25 36.70 2.69
1970 3526 1.528292 CCATTTGAAAACCGGCGGGA 61.528 55.000 31.78 5.26 36.97 5.14
1990 3546 3.509967 GGACATTGGAAACCTAAACCCAG 59.490 47.826 0.00 0.00 0.00 4.45
2003 3559 1.996798 AACCCAGACTCGAAGACTCA 58.003 50.000 0.00 0.00 0.00 3.41
2059 3616 2.837031 TACACGACGGGTAGGGGTCC 62.837 65.000 5.70 0.00 0.00 4.46
2074 3631 1.541588 GGGTCCAATGTTGAGCTTGTC 59.458 52.381 0.00 0.00 0.00 3.18
2099 3656 0.180171 CCAGGACCATGCACCGATTA 59.820 55.000 0.00 0.00 0.00 1.75
2111 3668 2.093658 GCACCGATTACCTCTTCTCCAA 60.094 50.000 0.00 0.00 0.00 3.53
2146 3703 1.964373 GGCCACCGTTGACGATTGT 60.964 57.895 4.91 0.00 43.02 2.71
2164 3721 0.320771 GTCGCACTGGATCACCAACT 60.321 55.000 0.00 0.00 46.32 3.16
2166 3723 0.320683 CGCACTGGATCACCAACTCA 60.321 55.000 0.00 0.00 46.32 3.41
2171 3728 0.037326 TGGATCACCAACTCAGTCGC 60.037 55.000 0.00 0.00 43.91 5.19
2180 3737 1.241990 AACTCAGTCGCCGAGCACTA 61.242 55.000 0.00 0.00 33.58 2.74
2185 3742 3.449227 TCGCCGAGCACTACCTGG 61.449 66.667 0.00 0.00 0.00 4.45
2186 3743 3.449227 CGCCGAGCACTACCTGGA 61.449 66.667 0.00 0.00 0.00 3.86
2223 3780 1.293924 CACACATCTCCTTCGCCATC 58.706 55.000 0.00 0.00 0.00 3.51
2225 3782 0.178767 CACATCTCCTTCGCCATCCA 59.821 55.000 0.00 0.00 0.00 3.41
2230 3787 1.073125 TCTCCTTCGCCATCCAACAAA 59.927 47.619 0.00 0.00 0.00 2.83
2231 3788 1.885887 CTCCTTCGCCATCCAACAAAA 59.114 47.619 0.00 0.00 0.00 2.44
2263 3820 0.606401 CCTCCACAAACATGTCGCCT 60.606 55.000 0.00 0.00 0.00 5.52
2279 3837 1.834822 CCTCGATCTGGACCTCCCC 60.835 68.421 0.00 0.00 34.29 4.81
2280 3838 1.075970 CTCGATCTGGACCTCCCCA 60.076 63.158 0.00 0.00 34.29 4.96
2368 3929 2.233305 AGATGGGACGACAACTAGGT 57.767 50.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.028330 ATGTGTCCTGGCATTGCGAG 61.028 55.000 13.18 13.18 34.22 5.03
1 2 0.251634 TATGTGTCCTGGCATTGCGA 59.748 50.000 1.91 0.00 0.00 5.10
2 3 0.659427 CTATGTGTCCTGGCATTGCG 59.341 55.000 1.91 0.00 0.00 4.85
3 4 1.672881 GTCTATGTGTCCTGGCATTGC 59.327 52.381 0.00 0.00 0.00 3.56
4 5 2.989909 TGTCTATGTGTCCTGGCATTG 58.010 47.619 0.00 0.00 0.00 2.82
5 6 3.719268 TTGTCTATGTGTCCTGGCATT 57.281 42.857 0.00 0.00 0.00 3.56
17 18 7.557719 AGGGAAAGGTGAATTGTATTGTCTATG 59.442 37.037 0.00 0.00 0.00 2.23
18 19 7.643123 AGGGAAAGGTGAATTGTATTGTCTAT 58.357 34.615 0.00 0.00 0.00 1.98
19 20 7.027874 AGGGAAAGGTGAATTGTATTGTCTA 57.972 36.000 0.00 0.00 0.00 2.59
22 24 5.476945 GTGAGGGAAAGGTGAATTGTATTGT 59.523 40.000 0.00 0.00 0.00 2.71
24 26 4.700213 CGTGAGGGAAAGGTGAATTGTATT 59.300 41.667 0.00 0.00 0.00 1.89
68 77 0.392461 TATTCCGTGGCCTGCTGAAC 60.392 55.000 3.32 0.00 0.00 3.18
95 104 0.514255 CCACATATTCCATGCGAGCG 59.486 55.000 0.00 0.00 0.00 5.03
97 106 3.005554 GGATCCACATATTCCATGCGAG 58.994 50.000 6.95 0.00 0.00 5.03
103 112 1.488393 TGTGCGGATCCACATATTCCA 59.512 47.619 13.41 0.00 40.55 3.53
104 113 1.873591 GTGTGCGGATCCACATATTCC 59.126 52.381 13.41 0.00 46.31 3.01
105 114 1.526887 CGTGTGCGGATCCACATATTC 59.473 52.381 13.41 0.00 46.31 1.75
106 115 1.581934 CGTGTGCGGATCCACATATT 58.418 50.000 13.41 0.00 46.31 1.28
107 116 3.289128 CGTGTGCGGATCCACATAT 57.711 52.632 13.41 0.00 46.31 1.78
108 117 4.825377 CGTGTGCGGATCCACATA 57.175 55.556 13.41 3.43 46.31 2.29
157 166 2.223135 GCGAGTTAAGAATTGGCTGCTC 60.223 50.000 0.00 0.00 0.00 4.26
158 167 1.740025 GCGAGTTAAGAATTGGCTGCT 59.260 47.619 0.00 0.00 0.00 4.24
167 176 3.306917 TCCAATGTCGCGAGTTAAGAA 57.693 42.857 10.24 0.00 0.00 2.52
178 187 4.160635 GCCGGCGTTCCAATGTCG 62.161 66.667 12.58 0.00 42.30 4.35
203 212 1.392589 CCGCTCAGCCATAACCATTT 58.607 50.000 0.00 0.00 0.00 2.32
204 213 0.466189 CCCGCTCAGCCATAACCATT 60.466 55.000 0.00 0.00 0.00 3.16
236 245 2.910977 AGGATTGACCCGGTAAAGAAGT 59.089 45.455 0.00 0.00 40.05 3.01
280 302 2.431260 GCCGTAGCCGTCGTGAAA 60.431 61.111 0.00 0.00 0.00 2.69
308 330 1.884075 TTCGTACGGTGGAGCATGCT 61.884 55.000 22.92 22.92 0.00 3.79
313 335 0.179169 GTCTCTTCGTACGGTGGAGC 60.179 60.000 16.52 11.76 0.00 4.70
319 341 1.059994 CGGTCGTCTCTTCGTACGG 59.940 63.158 16.52 0.00 39.52 4.02
344 366 3.961182 AGTGTATAGAACGCGTGTATGG 58.039 45.455 14.98 0.00 43.67 2.74
345 367 5.714272 CAAAGTGTATAGAACGCGTGTATG 58.286 41.667 14.98 0.00 43.67 2.39
346 368 4.266976 GCAAAGTGTATAGAACGCGTGTAT 59.733 41.667 14.98 15.77 43.67 2.29
347 369 3.609373 GCAAAGTGTATAGAACGCGTGTA 59.391 43.478 14.98 8.49 43.67 2.90
348 370 2.410730 GCAAAGTGTATAGAACGCGTGT 59.589 45.455 14.98 5.97 43.67 4.49
359 410 0.881118 CGGGTGCAAGCAAAGTGTAT 59.119 50.000 0.00 0.00 34.77 2.29
423 482 0.027848 TTCGTTGGTTTTTCCGCGTC 59.972 50.000 4.92 0.00 39.52 5.19
929 1000 3.471244 TTTTGTTTGGCGCCGTCGG 62.471 57.895 23.90 6.99 35.95 4.79
931 1002 2.290082 CGTTTTGTTTGGCGCCGTC 61.290 57.895 23.90 14.89 0.00 4.79
984 1055 1.344087 ACCATCCGGTCCCTCTGTTAT 60.344 52.381 0.00 0.00 44.71 1.89
985 1056 0.042131 ACCATCCGGTCCCTCTGTTA 59.958 55.000 0.00 0.00 44.71 2.41
987 1058 1.990060 CACCATCCGGTCCCTCTGT 60.990 63.158 0.00 0.00 44.71 3.41
991 1062 1.537889 TGAACACCATCCGGTCCCT 60.538 57.895 0.00 0.00 44.71 4.20
992 1063 1.078426 CTGAACACCATCCGGTCCC 60.078 63.158 0.00 0.00 44.71 4.46
994 1065 2.100631 CGCTGAACACCATCCGGTC 61.101 63.158 0.00 0.00 44.71 4.79
996 1067 2.819595 CCGCTGAACACCATCCGG 60.820 66.667 0.00 0.00 34.69 5.14
1158 1238 2.733858 GCAGAAGAAGACGTAGAGGCAG 60.734 54.545 0.00 0.00 0.00 4.85
1279 1359 3.213402 GGAGAGCGAGAGGGACCG 61.213 72.222 0.00 0.00 0.00 4.79
1355 1435 4.406648 TCCTAGTCGTCCGAGTAATACA 57.593 45.455 5.81 0.00 30.61 2.29
1356 1436 5.741388 TTTCCTAGTCGTCCGAGTAATAC 57.259 43.478 5.81 0.00 30.61 1.89
1357 1437 4.274459 GCTTTCCTAGTCGTCCGAGTAATA 59.726 45.833 5.81 0.00 30.61 0.98
1403 1483 4.175489 CCCGACACGACGATCGCT 62.175 66.667 16.60 2.00 45.12 4.93
1471 1551 8.061857 CCAATATGTACAGCGTTTATACAGTTG 58.938 37.037 0.33 10.81 32.58 3.16
1498 1578 1.616159 GCTGAAGCCTACCAACCAAA 58.384 50.000 0.00 0.00 34.31 3.28
1508 1588 2.027745 TCTTGATTTCTCGCTGAAGCCT 60.028 45.455 0.00 0.00 37.91 4.58
1539 1619 5.933463 TCATCAAACCAAAGAATCCAAATGC 59.067 36.000 0.00 0.00 0.00 3.56
1547 1627 6.877236 ACAGTGTTTCATCAAACCAAAGAAT 58.123 32.000 0.00 0.00 41.25 2.40
1554 1634 8.094798 TCTGTTATACAGTGTTTCATCAAACC 57.905 34.615 0.00 0.00 46.03 3.27
1555 1635 9.546909 CATCTGTTATACAGTGTTTCATCAAAC 57.453 33.333 0.00 0.00 46.03 2.93
1556 1636 8.729756 CCATCTGTTATACAGTGTTTCATCAAA 58.270 33.333 0.00 0.00 46.03 2.69
1557 1637 8.100164 TCCATCTGTTATACAGTGTTTCATCAA 58.900 33.333 0.00 0.00 46.03 2.57
1558 1638 7.619965 TCCATCTGTTATACAGTGTTTCATCA 58.380 34.615 0.00 0.00 46.03 3.07
1559 1639 8.492673 TTCCATCTGTTATACAGTGTTTCATC 57.507 34.615 0.00 0.00 46.03 2.92
1560 1640 8.862325 TTTCCATCTGTTATACAGTGTTTCAT 57.138 30.769 0.00 0.00 46.03 2.57
1599 1696 6.734617 CGTTTACAACTTTGTTTCTTTTTGCC 59.265 34.615 0.00 0.00 42.35 4.52
1606 1704 6.739550 CGTTCTTCGTTTACAACTTTGTTTCT 59.260 34.615 0.00 0.00 37.40 2.52
1661 1790 5.680619 TCCCGATTAGTAGCATGATTTTGT 58.319 37.500 0.00 0.00 0.00 2.83
1662 1791 5.991606 TCTCCCGATTAGTAGCATGATTTTG 59.008 40.000 0.00 0.00 0.00 2.44
1663 1792 6.174720 TCTCCCGATTAGTAGCATGATTTT 57.825 37.500 0.00 0.00 0.00 1.82
1669 2647 8.596781 AATAGTTATCTCCCGATTAGTAGCAT 57.403 34.615 0.00 0.00 0.00 3.79
1708 2686 1.762957 ACACATCAGGTTATCTCCCGG 59.237 52.381 0.00 0.00 0.00 5.73
1720 2698 6.073331 GGAGAAAGAAGACTTCAACACATCAG 60.073 42.308 17.34 0.00 35.05 2.90
1741 3288 1.153449 CGCCGGTAAATGCAGGAGA 60.153 57.895 1.90 0.00 0.00 3.71
1751 3298 4.605634 ACAACACGCCGCCGGTAA 62.606 61.111 4.45 0.00 39.22 2.85
1763 3316 1.555075 GGTGGAGCTATCCTCACAACA 59.445 52.381 0.00 0.00 46.80 3.33
1764 3317 1.834263 AGGTGGAGCTATCCTCACAAC 59.166 52.381 0.00 0.00 46.80 3.32
1779 3332 2.027625 GTCTGTTTCGCCGAGGTGG 61.028 63.158 2.57 0.00 42.50 4.61
1790 3343 5.200483 TCATGGGTTGAAGAAAGTCTGTTT 58.800 37.500 0.00 0.00 0.00 2.83
1792 3345 4.437682 TCATGGGTTGAAGAAAGTCTGT 57.562 40.909 0.00 0.00 0.00 3.41
1795 3348 5.067805 ACAAGTTCATGGGTTGAAGAAAGTC 59.932 40.000 8.90 0.00 44.89 3.01
1801 3356 6.039270 TGTTTCTACAAGTTCATGGGTTGAAG 59.961 38.462 8.90 0.00 44.89 3.02
1804 3359 5.766150 TGTTTCTACAAGTTCATGGGTTG 57.234 39.130 0.00 0.00 0.00 3.77
1824 3379 1.337447 CGATGAGTTACCGGGTGTTGT 60.337 52.381 10.66 0.00 0.00 3.32
1827 3382 1.217244 GCGATGAGTTACCGGGTGT 59.783 57.895 10.66 0.00 0.00 4.16
1831 3386 1.148157 CTGCAGCGATGAGTTACCGG 61.148 60.000 4.02 0.00 0.00 5.28
1834 3389 1.281899 GGTCTGCAGCGATGAGTTAC 58.718 55.000 9.47 0.00 0.00 2.50
1835 3390 0.894835 TGGTCTGCAGCGATGAGTTA 59.105 50.000 9.47 0.00 0.00 2.24
1838 3393 1.159285 TTTTGGTCTGCAGCGATGAG 58.841 50.000 9.47 0.00 0.00 2.90
1856 3411 3.004210 GGGCGGCAATTTGTTTCATTTTT 59.996 39.130 12.47 0.00 0.00 1.94
1858 3413 2.150390 GGGCGGCAATTTGTTTCATTT 58.850 42.857 12.47 0.00 0.00 2.32
1865 3420 1.118356 TCTTTGGGGCGGCAATTTGT 61.118 50.000 12.47 0.00 0.00 2.83
1880 3435 5.114081 GCATTTATCAGCATTGCCTTCTTT 58.886 37.500 4.70 0.00 0.00 2.52
1891 3446 4.523943 AGTTTTGACAGGCATTTATCAGCA 59.476 37.500 0.00 0.00 0.00 4.41
1893 3448 5.183713 TGGAGTTTTGACAGGCATTTATCAG 59.816 40.000 0.00 0.00 0.00 2.90
1902 3457 4.846779 TGTATTTGGAGTTTTGACAGGC 57.153 40.909 0.00 0.00 0.00 4.85
1904 3459 8.925161 TTTCTTTGTATTTGGAGTTTTGACAG 57.075 30.769 0.00 0.00 0.00 3.51
1908 3464 7.042523 CCAGCTTTCTTTGTATTTGGAGTTTTG 60.043 37.037 0.00 0.00 0.00 2.44
1912 3468 4.021981 GCCAGCTTTCTTTGTATTTGGAGT 60.022 41.667 0.00 0.00 0.00 3.85
1913 3469 4.488879 GCCAGCTTTCTTTGTATTTGGAG 58.511 43.478 0.00 0.00 0.00 3.86
1914 3470 3.258123 GGCCAGCTTTCTTTGTATTTGGA 59.742 43.478 0.00 0.00 0.00 3.53
1916 3472 3.057596 TCGGCCAGCTTTCTTTGTATTTG 60.058 43.478 2.24 0.00 0.00 2.32
1917 3473 3.153919 TCGGCCAGCTTTCTTTGTATTT 58.846 40.909 2.24 0.00 0.00 1.40
1925 3481 2.111384 TCTAGATTCGGCCAGCTTTCT 58.889 47.619 2.24 0.00 0.00 2.52
1942 3498 4.887071 CCGGTTTTCAAATGGATCCATCTA 59.113 41.667 27.45 12.98 35.31 1.98
1958 3514 2.272447 CCAATGTCCCGCCGGTTTT 61.272 57.895 1.90 0.00 0.00 2.43
1970 3526 4.141018 AGTCTGGGTTTAGGTTTCCAATGT 60.141 41.667 0.00 0.00 0.00 2.71
1990 3546 5.343860 GCTTTCTTTAGTGAGTCTTCGAGTC 59.656 44.000 0.00 0.00 33.05 3.36
2038 3595 1.250840 ACCCCTACCCGTCGTGTAAC 61.251 60.000 0.00 0.00 0.00 2.50
2041 3598 2.677875 GACCCCTACCCGTCGTGT 60.678 66.667 0.00 0.00 0.00 4.49
2048 3605 0.996583 TCAACATTGGACCCCTACCC 59.003 55.000 0.00 0.00 0.00 3.69
2052 3609 0.779997 AAGCTCAACATTGGACCCCT 59.220 50.000 0.00 0.00 0.00 4.79
2053 3610 0.890683 CAAGCTCAACATTGGACCCC 59.109 55.000 0.00 0.00 0.00 4.95
2074 3631 2.821366 GCATGGTCCTGGACAGCG 60.821 66.667 26.94 15.16 33.68 5.18
2077 3634 2.756400 GGTGCATGGTCCTGGACA 59.244 61.111 26.94 14.17 39.04 4.02
2099 3656 2.769095 GCTAGGTCATTGGAGAAGAGGT 59.231 50.000 0.00 0.00 0.00 3.85
2132 3689 1.300311 TGCGACAATCGTCAACGGT 60.300 52.632 2.31 0.00 42.74 4.83
2146 3703 0.037326 GAGTTGGTGATCCAGTGCGA 60.037 55.000 0.00 0.00 45.22 5.10
2150 3707 1.273606 CGACTGAGTTGGTGATCCAGT 59.726 52.381 0.00 0.00 45.22 4.00
2164 3721 2.697761 GGTAGTGCTCGGCGACTGA 61.698 63.158 4.99 0.00 0.00 3.41
2166 3723 2.361357 AGGTAGTGCTCGGCGACT 60.361 61.111 4.99 5.04 0.00 4.18
2171 3728 0.457851 CTTCTCCAGGTAGTGCTCGG 59.542 60.000 0.00 0.00 0.00 4.63
2180 3737 2.232452 CGAGTGACAATCTTCTCCAGGT 59.768 50.000 0.92 0.00 0.00 4.00
2185 3742 2.920490 GTGCTCGAGTGACAATCTTCTC 59.080 50.000 15.13 0.00 0.00 2.87
2186 3743 2.297315 TGTGCTCGAGTGACAATCTTCT 59.703 45.455 15.13 0.00 0.00 2.85
2223 3780 1.762370 AGTTGGAGGGCTTTTTGTTGG 59.238 47.619 0.00 0.00 0.00 3.77
2225 3782 2.039418 GGAGTTGGAGGGCTTTTTGTT 58.961 47.619 0.00 0.00 0.00 2.83
2230 3787 0.772124 TGGAGGAGTTGGAGGGCTTT 60.772 55.000 0.00 0.00 0.00 3.51
2231 3788 1.151810 TGGAGGAGTTGGAGGGCTT 60.152 57.895 0.00 0.00 0.00 4.35
2263 3820 1.381327 GTGGGGAGGTCCAGATCGA 60.381 63.158 0.00 0.00 37.50 3.59
2306 3864 1.578926 CGCGTTGCCAGGAAAATCA 59.421 52.632 0.00 0.00 0.00 2.57
2332 3890 2.606519 TACACCCCTCTTGCCGCT 60.607 61.111 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.