Multiple sequence alignment - TraesCS4A01G002300

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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 TraesCS4A01G002300 chr4A 100.000 3296 0 0 1 3296 1914926 1911631 0.000000e+00 6087.0
1 TraesCS4A01G002300 chr4B 91.059 2058 109 32 296 2299 590138059 590140095 0.000000e+00 2712.0
2 TraesCS4A01G002300 chr4B 86.965 537 57 9 2761 3292 590423300 590423828 2.830000e-165 592.0
3 TraesCS4A01G002300 chr4B 89.394 198 13 2 2438 2631 590140292 590140485 3.290000e-60 243.0
4 TraesCS4A01G002300 chr4B 86.425 221 21 8 1 219 590137761 590137974 1.980000e-57 233.0
5 TraesCS4A01G002300 chr4B 86.986 146 2 6 2296 2438 590140120 590140251 7.370000e-32 148.0
6 TraesCS4A01G002300 chr4B 88.462 52 5 1 2627 2678 590140494 590140544 9.880000e-06 62.1
7 TraesCS4A01G002300 chr4D 96.019 1482 48 8 819 2299 469562491 469563962 0.000000e+00 2399.0
8 TraesCS4A01G002300 chr4D 90.614 586 39 8 2709 3292 469567892 469568463 0.000000e+00 763.0
9 TraesCS4A01G002300 chr4D 92.268 194 11 1 2438 2631 469564162 469564351 4.190000e-69 272.0
10 TraesCS4A01G002300 chr4D 91.111 135 0 4 2306 2439 469564002 469564125 4.370000e-39 172.0
11 TraesCS4A01G002300 chr4D 80.814 172 9 6 46 215 469559922 469560071 2.690000e-21 113.0
12 TraesCS4A01G002300 chr4D 90.385 52 4 1 2627 2678 469564360 469564410 2.120000e-07 67.6
13 TraesCS4A01G002300 chr3A 71.550 703 157 32 1615 2291 719109268 719108583 2.050000e-32 150.0
14 TraesCS4A01G002300 chr3D 71.587 630 136 34 1685 2291 589218120 589218729 7.420000e-27 132.0
15 TraesCS4A01G002300 chr3B 88.312 77 9 0 1685 1761 787443254 787443178 3.500000e-15 93.5
16 TraesCS4A01G002300 chr7A 83.562 73 9 3 1894 1966 589238167 589238098 7.630000e-07 65.8
17 TraesCS4A01G002300 chr7B 91.304 46 1 3 1894 1939 546252221 546252179 3.550000e-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 TraesCS4A01G002300 chr4A 1911631 1914926 3295 True 6087.00 6087 100.000000 1 3296 1 chr4A.!!$R1 3295
1 TraesCS4A01G002300 chr4B 590137761 590140544 2783 False 679.62 2712 88.465200 1 2678 5 chr4B.!!$F2 2677
2 TraesCS4A01G002300 chr4B 590423300 590423828 528 False 592.00 592 86.965000 2761 3292 1 chr4B.!!$F1 531
3 TraesCS4A01G002300 chr4D 469559922 469568463 8541 False 631.10 2399 90.201833 46 3292 6 chr4D.!!$F1 3246

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
466 2057 0.112995 TTTCACTGGGGAGCAGCAAT 59.887 50.0 0.0 0.0 0.00 3.56 F
712 2326 0.322456 TTCAGGCCGTTGGATGAAGG 60.322 55.0 0.0 0.0 30.34 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 3665 1.093159 AGTACGACTTGTAGCTCGGG 58.907 55.000 0.00 0.0 34.07 5.14 R
2605 4651 1.071699 GGGCTGTCAGTACACTCCAAA 59.928 52.381 0.93 0.0 0.00 3.28 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
33 34 2.354109 GACAAGCTGTCGAGATGTGA 57.646 50.000 0.00 0.00 37.67 3.58
34 35 2.677199 GACAAGCTGTCGAGATGTGAA 58.323 47.619 0.00 0.00 37.67 3.18
78 79 1.551430 TGAAACCCGCGGATTCTAGAA 59.449 47.619 30.58 7.82 35.83 2.10
89 90 4.931661 GGATTCTAGAATACGGTGGTCA 57.068 45.455 17.94 0.00 0.00 4.02
115 116 3.939066 ACTTCCTTGCGCTGTAGTAAAT 58.061 40.909 9.73 0.00 0.00 1.40
120 121 0.533491 TGCGCTGTAGTAAATCCGGT 59.467 50.000 9.73 0.00 0.00 5.28
126 127 3.551454 GCTGTAGTAAATCCGGTCGCATA 60.551 47.826 0.00 0.00 0.00 3.14
144 145 7.115095 GGTCGCATAAATCATCAACTAGACTAC 59.885 40.741 0.00 0.00 0.00 2.73
145 146 6.856426 TCGCATAAATCATCAACTAGACTACG 59.144 38.462 0.00 0.00 0.00 3.51
146 147 6.088217 CGCATAAATCATCAACTAGACTACGG 59.912 42.308 0.00 0.00 0.00 4.02
147 148 7.145985 GCATAAATCATCAACTAGACTACGGA 58.854 38.462 0.00 0.00 0.00 4.69
148 149 7.327275 GCATAAATCATCAACTAGACTACGGAG 59.673 40.741 0.00 0.00 0.00 4.63
150 151 7.876936 AAATCATCAACTAGACTACGGAGTA 57.123 36.000 0.00 0.00 45.11 2.59
193 194 1.694844 TATACGCGGTGGATTCCAGA 58.305 50.000 12.47 0.00 32.34 3.86
205 206 3.596046 TGGATTCCAGATTACCAGGGTTT 59.404 43.478 0.00 0.00 0.00 3.27
206 207 4.791334 TGGATTCCAGATTACCAGGGTTTA 59.209 41.667 0.00 0.00 0.00 2.01
207 208 5.131067 GGATTCCAGATTACCAGGGTTTAC 58.869 45.833 0.00 0.00 0.00 2.01
208 209 4.579647 TTCCAGATTACCAGGGTTTACC 57.420 45.455 0.00 0.00 40.67 2.85
209 210 3.533146 TCCAGATTACCAGGGTTTACCA 58.467 45.455 0.00 0.00 43.89 3.25
210 211 4.116113 TCCAGATTACCAGGGTTTACCAT 58.884 43.478 0.00 0.00 43.89 3.55
211 212 5.290335 TCCAGATTACCAGGGTTTACCATA 58.710 41.667 0.00 0.00 43.89 2.74
212 213 5.368523 TCCAGATTACCAGGGTTTACCATAG 59.631 44.000 0.00 0.00 43.89 2.23
254 1589 9.979578 ATGCATAGTTAAAAAGTCAATTGAACA 57.020 25.926 10.35 0.00 0.00 3.18
255 1590 9.243637 TGCATAGTTAAAAAGTCAATTGAACAC 57.756 29.630 10.35 0.00 0.00 3.32
256 1591 9.243637 GCATAGTTAAAAAGTCAATTGAACACA 57.756 29.630 10.35 0.00 0.00 3.72
260 1595 9.139174 AGTTAAAAAGTCAATTGAACACAGTTG 57.861 29.630 10.35 0.00 34.22 3.16
261 1596 6.966435 AAAAAGTCAATTGAACACAGTTGG 57.034 33.333 10.35 0.00 33.90 3.77
262 1597 5.659440 AAAGTCAATTGAACACAGTTGGT 57.341 34.783 10.35 0.00 33.90 3.67
263 1598 6.767524 AAAGTCAATTGAACACAGTTGGTA 57.232 33.333 10.35 0.00 33.90 3.25
264 1599 6.377327 AAGTCAATTGAACACAGTTGGTAG 57.623 37.500 10.35 0.00 33.90 3.18
265 1600 4.275936 AGTCAATTGAACACAGTTGGTAGC 59.724 41.667 10.35 0.00 33.90 3.58
266 1601 4.275936 GTCAATTGAACACAGTTGGTAGCT 59.724 41.667 10.35 0.00 33.90 3.32
267 1602 5.468746 GTCAATTGAACACAGTTGGTAGCTA 59.531 40.000 10.35 0.00 33.90 3.32
268 1603 5.700832 TCAATTGAACACAGTTGGTAGCTAG 59.299 40.000 5.45 0.00 33.90 3.42
269 1604 3.040147 TGAACACAGTTGGTAGCTAGC 57.960 47.619 16.08 16.08 0.00 3.42
270 1605 2.632996 TGAACACAGTTGGTAGCTAGCT 59.367 45.455 23.12 23.12 0.00 3.32
271 1606 3.071023 TGAACACAGTTGGTAGCTAGCTT 59.929 43.478 24.88 7.25 0.00 3.74
272 1607 3.320673 ACACAGTTGGTAGCTAGCTTC 57.679 47.619 24.88 18.24 0.00 3.86
273 1608 2.632996 ACACAGTTGGTAGCTAGCTTCA 59.367 45.455 24.88 18.43 0.00 3.02
274 1609 3.261897 ACACAGTTGGTAGCTAGCTTCAT 59.738 43.478 24.88 0.00 0.00 2.57
275 1610 3.868077 CACAGTTGGTAGCTAGCTTCATC 59.132 47.826 24.88 18.71 0.00 2.92
276 1611 3.118592 ACAGTTGGTAGCTAGCTTCATCC 60.119 47.826 24.88 19.20 0.00 3.51
277 1612 2.101582 AGTTGGTAGCTAGCTTCATCCG 59.898 50.000 24.88 0.00 0.00 4.18
278 1613 2.067365 TGGTAGCTAGCTTCATCCGA 57.933 50.000 24.88 0.00 0.00 4.55
279 1614 2.384828 TGGTAGCTAGCTTCATCCGAA 58.615 47.619 24.88 0.00 0.00 4.30
280 1615 2.764010 TGGTAGCTAGCTTCATCCGAAA 59.236 45.455 24.88 0.00 0.00 3.46
281 1616 3.181475 TGGTAGCTAGCTTCATCCGAAAG 60.181 47.826 24.88 0.00 0.00 2.62
282 1617 3.181474 GGTAGCTAGCTTCATCCGAAAGT 60.181 47.826 24.88 0.00 0.00 2.66
283 1618 3.172229 AGCTAGCTTCATCCGAAAGTC 57.828 47.619 12.68 0.00 0.00 3.01
284 1619 2.763448 AGCTAGCTTCATCCGAAAGTCT 59.237 45.455 12.68 0.00 0.00 3.24
285 1620 3.196685 AGCTAGCTTCATCCGAAAGTCTT 59.803 43.478 12.68 0.00 0.00 3.01
286 1621 3.935828 GCTAGCTTCATCCGAAAGTCTTT 59.064 43.478 7.70 0.00 0.00 2.52
287 1622 4.393371 GCTAGCTTCATCCGAAAGTCTTTT 59.607 41.667 7.70 0.00 0.00 2.27
288 1623 5.106515 GCTAGCTTCATCCGAAAGTCTTTTT 60.107 40.000 7.70 0.00 0.00 1.94
340 1898 9.138596 GGTTTTGCTATTTATAGGGTATCCAAA 57.861 33.333 0.00 0.00 34.83 3.28
354 1912 5.507650 GGGTATCCAAACTTTTTGTTGCGTA 60.508 40.000 0.00 0.00 39.13 4.42
385 1956 6.861065 TTTTCTTCTTCTTCATAAGCGTGT 57.139 33.333 0.00 0.00 0.00 4.49
387 1958 5.134202 TCTTCTTCTTCATAAGCGTGTGA 57.866 39.130 0.00 0.00 0.00 3.58
395 1966 6.986250 TCTTCATAAGCGTGTGATATCTCAT 58.014 36.000 10.47 0.00 32.98 2.90
400 1991 4.926140 AGCGTGTGATATCTCATCAGAA 57.074 40.909 10.47 0.00 32.98 3.02
415 2006 3.243359 TCAGAAAAGAAGCAACCCCAT 57.757 42.857 0.00 0.00 0.00 4.00
426 2017 6.915786 AGAAGCAACCCCATTATCTATCTTT 58.084 36.000 0.00 0.00 0.00 2.52
451 2042 0.396435 ATGACGAGGGTGCAGTTTCA 59.604 50.000 0.00 0.00 0.00 2.69
452 2043 0.531974 TGACGAGGGTGCAGTTTCAC 60.532 55.000 0.00 0.00 36.28 3.18
466 2057 0.112995 TTTCACTGGGGAGCAGCAAT 59.887 50.000 0.00 0.00 0.00 3.56
474 2065 1.474143 GGGGAGCAGCAATCTCACTAC 60.474 57.143 0.00 0.00 34.50 2.73
494 2092 0.765510 CTATCTTAGGGGTGTGGGGC 59.234 60.000 0.00 0.00 0.00 5.80
528 2141 1.227973 CGGGGCTTAGAGGAATGGC 60.228 63.158 0.00 0.00 0.00 4.40
531 2144 1.696097 GGGCTTAGAGGAATGGCCGA 61.696 60.000 0.00 0.00 43.27 5.54
570 2183 0.787084 AGTGAGAGGAGGTTGAGGGA 59.213 55.000 0.00 0.00 0.00 4.20
572 2185 2.192263 GTGAGAGGAGGTTGAGGGAAT 58.808 52.381 0.00 0.00 0.00 3.01
585 2199 1.142688 AGGGAATGGTGGAGCAAGGT 61.143 55.000 0.00 0.00 0.00 3.50
591 2205 1.966451 GGTGGAGCAAGGTGGTTCG 60.966 63.158 0.00 0.00 0.00 3.95
598 2212 0.602905 GCAAGGTGGTTCGCAGTAGT 60.603 55.000 0.00 0.00 0.00 2.73
599 2213 1.148310 CAAGGTGGTTCGCAGTAGTG 58.852 55.000 0.00 0.00 0.00 2.74
626 2240 3.569210 CACTGGTGGTGGAGGCCA 61.569 66.667 5.01 0.00 41.90 5.36
643 2257 4.195334 AGCTATTGGGGCTGGGCG 62.195 66.667 0.00 0.00 38.73 6.13
712 2326 0.322456 TTCAGGCCGTTGGATGAAGG 60.322 55.000 0.00 0.00 30.34 3.46
713 2327 1.750399 CAGGCCGTTGGATGAAGGG 60.750 63.158 0.00 0.00 41.80 3.95
714 2328 2.231380 AGGCCGTTGGATGAAGGGT 61.231 57.895 0.00 0.00 41.08 4.34
716 2330 1.313091 GGCCGTTGGATGAAGGGTTC 61.313 60.000 0.00 0.00 41.08 3.62
719 2333 2.235016 CCGTTGGATGAAGGGTTCAAA 58.765 47.619 0.00 0.00 43.95 2.69
720 2334 2.030274 CCGTTGGATGAAGGGTTCAAAC 60.030 50.000 0.00 0.00 43.95 2.93
729 2353 3.203716 GAAGGGTTCAAACGAGAACTGT 58.796 45.455 15.61 5.23 45.52 3.55
741 2365 2.156504 CGAGAACTGTCTGATGCAACAC 59.843 50.000 0.00 0.00 32.80 3.32
767 2391 3.297134 TCAAGTGCACTCTCCCTTTTT 57.703 42.857 21.95 0.00 0.00 1.94
846 2809 8.573035 TGTTTGTAGATTTTGGAATCCAACTAC 58.427 33.333 23.52 23.52 43.82 2.73
867 2830 8.336801 ACTACTATCAAAATTTCAACAGGGAC 57.663 34.615 0.00 0.00 0.00 4.46
879 2842 4.148838 TCAACAGGGACGGAAATGAAAAT 58.851 39.130 0.00 0.00 0.00 1.82
889 2853 3.123959 CGGAAATGAAAATGCAAGCAAGG 59.876 43.478 0.00 0.00 0.00 3.61
936 2900 4.342951 GCCAAAACCCCTATATAAACCCAC 59.657 45.833 0.00 0.00 0.00 4.61
1036 3000 1.541672 CCTCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1037 3001 0.998945 CCTCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1038 3002 0.478507 CTCTCCTCCTCCTCCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
1094 3058 0.759812 TACCACAACGTCCACCCTCA 60.760 55.000 0.00 0.00 0.00 3.86
1095 3059 1.374947 CCACAACGTCCACCCTCAT 59.625 57.895 0.00 0.00 0.00 2.90
1488 3452 4.722700 TGCGCCTTCTCCAAGCCC 62.723 66.667 4.18 0.00 0.00 5.19
1701 3665 0.101579 GCGTCTTCTCCTACTGCCTC 59.898 60.000 0.00 0.00 0.00 4.70
1704 3668 0.395862 TCTTCTCCTACTGCCTCCCG 60.396 60.000 0.00 0.00 0.00 5.14
1797 3761 2.202932 CCGATGCTGAGGAACCCG 60.203 66.667 0.00 0.00 0.00 5.28
2145 4109 3.200593 CTGATCCACAGCAGCGCC 61.201 66.667 2.29 0.00 39.86 6.53
2194 4158 4.409588 CGCCGCAGAACGTGAACG 62.410 66.667 0.40 0.40 46.33 3.95
2299 4263 2.353704 CGGGAGTCATGCAACTAGTTCA 60.354 50.000 4.77 7.61 0.00 3.18
2300 4264 3.679917 CGGGAGTCATGCAACTAGTTCAT 60.680 47.826 4.77 9.56 0.00 2.57
2301 4265 3.624861 GGGAGTCATGCAACTAGTTCATG 59.375 47.826 25.97 25.97 39.02 3.07
2303 4267 2.674852 AGTCATGCAACTAGTTCATGCG 59.325 45.455 26.53 12.07 42.91 4.73
2304 4268 2.009051 TCATGCAACTAGTTCATGCGG 58.991 47.619 26.53 16.90 42.91 5.69
2456 4498 8.704234 GTTTGTCAGAACTAGAGAATTACTGTG 58.296 37.037 0.00 0.00 0.00 3.66
2468 4510 0.318360 TTACTGTGCTGGTCGTCGTG 60.318 55.000 0.00 0.00 0.00 4.35
2492 4534 4.695455 ACTATTTACTGGTGTGATGTGTGC 59.305 41.667 0.00 0.00 0.00 4.57
2504 4546 6.092092 GTGTGATGTGTGCTGCATTTAATTA 58.908 36.000 5.27 0.00 0.00 1.40
2505 4547 6.585702 GTGTGATGTGTGCTGCATTTAATTAA 59.414 34.615 5.27 0.00 0.00 1.40
2506 4548 6.807720 TGTGATGTGTGCTGCATTTAATTAAG 59.192 34.615 5.27 0.00 0.00 1.85
2507 4549 6.254157 GTGATGTGTGCTGCATTTAATTAAGG 59.746 38.462 5.27 0.00 0.00 2.69
2577 4623 1.064582 CACGCTGCACATACGTACAA 58.935 50.000 0.00 0.00 38.09 2.41
2582 4628 2.858344 GCTGCACATACGTACAAGTAGG 59.142 50.000 0.00 0.00 34.88 3.18
2605 4651 0.675633 AATGCAAAAGCTGGCTCGTT 59.324 45.000 0.00 0.00 0.00 3.85
2619 4665 2.547218 GGCTCGTTTTGGAGTGTACTGA 60.547 50.000 0.00 0.00 36.41 3.41
2657 4716 1.604593 GCACAGTGCCCAGACCAAT 60.605 57.895 15.27 0.00 37.42 3.16
2711 8220 9.435688 AAAATTTTGAAGCTTGAAGTTACTTGT 57.564 25.926 2.10 0.00 0.00 3.16
2744 8253 7.036996 TGTTAAGTCTTTCATCAATGTGCAA 57.963 32.000 0.00 0.00 0.00 4.08
2759 8268 6.643360 TCAATGTGCAAAAGTTTCATGATGAG 59.357 34.615 0.00 0.00 0.00 2.90
2839 8352 5.064962 TGAAAGCATTTTGGAGCACTTTTTG 59.935 36.000 0.00 0.00 39.27 2.44
2847 8360 2.165437 TGGAGCACTTTTTGGTTGTCAC 59.835 45.455 0.00 0.00 35.52 3.67
2848 8361 2.165437 GGAGCACTTTTTGGTTGTCACA 59.835 45.455 0.00 0.00 35.52 3.58
2865 8378 2.672874 TCACACGCATTCTATCAAGTGC 59.327 45.455 0.00 0.00 33.36 4.40
2875 8388 6.966632 GCATTCTATCAAGTGCGTGAAAATAA 59.033 34.615 0.00 0.00 0.00 1.40
2876 8389 7.164826 GCATTCTATCAAGTGCGTGAAAATAAG 59.835 37.037 0.00 0.00 0.00 1.73
2907 8420 3.513662 AGTAAACGTGTTGCCAAAAACC 58.486 40.909 0.00 0.00 0.00 3.27
2923 8436 9.190317 TGCCAAAAACCCAGTAATTTTTATTTT 57.810 25.926 0.00 0.00 36.18 1.82
2956 8469 2.967599 TCGCTGTTCATATCAGTGCT 57.032 45.000 0.00 0.00 41.42 4.40
2964 8477 6.092670 GCTGTTCATATCAGTGCTGTCTTTTA 59.907 38.462 0.00 0.00 35.60 1.52
3021 8535 9.709495 ACAACATAAAACATAGTGAAATTGCAT 57.291 25.926 0.00 0.00 0.00 3.96
3139 8653 0.373716 GACAGCAGCCGTAATTTCCG 59.626 55.000 0.00 0.00 0.00 4.30
3141 8655 0.373716 CAGCAGCCGTAATTTCCGAC 59.626 55.000 0.00 0.00 0.00 4.79
3144 8658 1.073177 CAGCCGTAATTTCCGACGTT 58.927 50.000 0.00 0.00 37.36 3.99
3205 8719 6.850752 TTTTGGAGTGGAGGGAAATAATTC 57.149 37.500 0.00 0.00 34.66 2.17
3219 8733 9.822727 AGGGAAATAATTCTTTTCAGGAGTTTA 57.177 29.630 13.02 0.00 35.29 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.067565 TCACATCTCGACAGCTTGTCC 60.068 52.381 9.71 0.00 44.20 4.02
31 32 2.532186 GCAGACAGCGTGACATTCA 58.468 52.632 0.00 0.00 0.00 2.57
42 43 2.084610 TTCATGGAACTCGCAGACAG 57.915 50.000 0.00 0.00 0.00 3.51
78 79 5.431179 AGGAAGTAAAATGACCACCGTAT 57.569 39.130 0.00 0.00 0.00 3.06
89 90 4.324267 ACTACAGCGCAAGGAAGTAAAAT 58.676 39.130 11.47 0.00 38.28 1.82
115 116 2.869801 GTTGATGATTTATGCGACCGGA 59.130 45.455 9.46 0.00 0.00 5.14
120 121 6.856426 CGTAGTCTAGTTGATGATTTATGCGA 59.144 38.462 0.00 0.00 0.00 5.10
126 127 6.777213 ACTCCGTAGTCTAGTTGATGATTT 57.223 37.500 0.00 0.00 0.00 2.17
144 145 9.186323 CATGAGTTTTTCTACATATCTACTCCG 57.814 37.037 0.00 0.00 31.99 4.63
145 146 8.983724 GCATGAGTTTTTCTACATATCTACTCC 58.016 37.037 0.00 0.00 31.99 3.85
146 147 9.534565 TGCATGAGTTTTTCTACATATCTACTC 57.465 33.333 0.00 0.00 33.25 2.59
147 148 9.890629 TTGCATGAGTTTTTCTACATATCTACT 57.109 29.630 0.00 0.00 0.00 2.57
175 176 1.048601 ATCTGGAATCCACCGCGTAT 58.951 50.000 4.92 0.00 0.00 3.06
193 194 3.725267 CCCCTATGGTAAACCCTGGTAAT 59.275 47.826 0.00 0.00 34.29 1.89
234 1569 9.139174 CAACTGTGTTCAATTGACTTTTTAACT 57.861 29.630 7.89 0.00 33.34 2.24
240 1575 5.659440 ACCAACTGTGTTCAATTGACTTT 57.341 34.783 7.89 0.00 33.34 2.66
241 1576 5.221048 GCTACCAACTGTGTTCAATTGACTT 60.221 40.000 7.89 0.00 33.34 3.01
242 1577 4.275936 GCTACCAACTGTGTTCAATTGACT 59.724 41.667 7.89 0.00 33.34 3.41
243 1578 4.275936 AGCTACCAACTGTGTTCAATTGAC 59.724 41.667 7.89 4.45 33.34 3.18
244 1579 4.460263 AGCTACCAACTGTGTTCAATTGA 58.540 39.130 3.38 3.38 33.34 2.57
245 1580 4.836125 AGCTACCAACTGTGTTCAATTG 57.164 40.909 0.00 0.00 31.64 2.32
246 1581 4.455877 GCTAGCTACCAACTGTGTTCAATT 59.544 41.667 7.70 0.00 0.00 2.32
247 1582 4.003648 GCTAGCTACCAACTGTGTTCAAT 58.996 43.478 7.70 0.00 0.00 2.57
248 1583 3.071023 AGCTAGCTACCAACTGTGTTCAA 59.929 43.478 17.69 0.00 0.00 2.69
249 1584 2.632996 AGCTAGCTACCAACTGTGTTCA 59.367 45.455 17.69 0.00 0.00 3.18
250 1585 3.320673 AGCTAGCTACCAACTGTGTTC 57.679 47.619 17.69 0.00 0.00 3.18
251 1586 3.071023 TGAAGCTAGCTACCAACTGTGTT 59.929 43.478 19.70 0.00 0.00 3.32
252 1587 2.632996 TGAAGCTAGCTACCAACTGTGT 59.367 45.455 19.70 0.00 0.00 3.72
253 1588 3.319137 TGAAGCTAGCTACCAACTGTG 57.681 47.619 19.70 0.00 0.00 3.66
254 1589 3.118592 GGATGAAGCTAGCTACCAACTGT 60.119 47.826 19.70 0.00 0.00 3.55
255 1590 3.462021 GGATGAAGCTAGCTACCAACTG 58.538 50.000 19.70 0.00 0.00 3.16
256 1591 2.101582 CGGATGAAGCTAGCTACCAACT 59.898 50.000 19.70 0.00 0.00 3.16
257 1592 2.100916 TCGGATGAAGCTAGCTACCAAC 59.899 50.000 19.70 16.57 0.00 3.77
258 1593 2.384828 TCGGATGAAGCTAGCTACCAA 58.615 47.619 19.70 4.29 0.00 3.67
259 1594 2.067365 TCGGATGAAGCTAGCTACCA 57.933 50.000 19.70 18.89 0.00 3.25
260 1595 3.181474 ACTTTCGGATGAAGCTAGCTACC 60.181 47.826 19.70 17.04 35.06 3.18
261 1596 4.045783 GACTTTCGGATGAAGCTAGCTAC 58.954 47.826 19.70 9.85 35.06 3.58
262 1597 3.954904 AGACTTTCGGATGAAGCTAGCTA 59.045 43.478 19.70 3.08 35.06 3.32
263 1598 2.763448 AGACTTTCGGATGAAGCTAGCT 59.237 45.455 12.68 12.68 35.06 3.32
264 1599 3.172229 AGACTTTCGGATGAAGCTAGC 57.828 47.619 6.62 6.62 35.06 3.42
265 1600 6.487689 AAAAAGACTTTCGGATGAAGCTAG 57.512 37.500 0.00 0.00 35.06 3.42
319 1876 9.930158 AAAAGTTTGGATACCCTATAAATAGCA 57.070 29.630 0.00 0.00 0.00 3.49
330 1887 3.738791 CGCAACAAAAAGTTTGGATACCC 59.261 43.478 5.76 0.00 38.74 3.69
337 1894 6.567769 ATGACTTACGCAACAAAAAGTTTG 57.432 33.333 0.00 0.00 38.74 2.93
340 1898 7.589574 AAAAATGACTTACGCAACAAAAAGT 57.410 28.000 0.00 0.00 34.96 2.66
366 1924 7.651304 AGATATCACACGCTTATGAAGAAGAAG 59.349 37.037 5.32 0.00 0.00 2.85
367 1925 7.492524 AGATATCACACGCTTATGAAGAAGAA 58.507 34.615 5.32 0.00 0.00 2.52
376 1934 6.581171 TCTGATGAGATATCACACGCTTAT 57.419 37.500 4.89 0.00 0.00 1.73
385 1956 7.281774 GGTTGCTTCTTTTCTGATGAGATATCA 59.718 37.037 5.32 0.00 0.00 2.15
387 1958 6.545298 GGGTTGCTTCTTTTCTGATGAGATAT 59.455 38.462 0.00 0.00 0.00 1.63
395 1966 2.746279 TGGGGTTGCTTCTTTTCTGA 57.254 45.000 0.00 0.00 0.00 3.27
400 1991 6.915786 AGATAGATAATGGGGTTGCTTCTTT 58.084 36.000 0.00 0.00 0.00 2.52
426 2017 4.481368 ACTGCACCCTCGTCATATTTTA 57.519 40.909 0.00 0.00 0.00 1.52
432 2023 0.396435 TGAAACTGCACCCTCGTCAT 59.604 50.000 0.00 0.00 0.00 3.06
434 2025 2.235546 GTGAAACTGCACCCTCGTC 58.764 57.895 0.00 0.00 32.68 4.20
435 2026 4.456806 GTGAAACTGCACCCTCGT 57.543 55.556 0.00 0.00 32.68 4.18
451 2042 1.203441 TGAGATTGCTGCTCCCCAGT 61.203 55.000 0.00 0.00 43.71 4.00
452 2043 0.747283 GTGAGATTGCTGCTCCCCAG 60.747 60.000 0.00 0.00 44.67 4.45
466 2057 4.481280 ACACCCCTAAGATAGGTAGTGAGA 59.519 45.833 21.39 0.00 44.71 3.27
474 2065 1.435256 CCCCACACCCCTAAGATAGG 58.565 60.000 0.00 0.00 45.81 2.57
551 2164 0.787084 TCCCTCAACCTCCTCTCACT 59.213 55.000 0.00 0.00 0.00 3.41
555 2168 1.203492 ACCATTCCCTCAACCTCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
570 2183 0.188342 AACCACCTTGCTCCACCATT 59.812 50.000 0.00 0.00 0.00 3.16
572 2185 1.150536 GAACCACCTTGCTCCACCA 59.849 57.895 0.00 0.00 0.00 4.17
585 2199 2.345991 GGGCACTACTGCGAACCA 59.654 61.111 0.00 0.00 45.31 3.67
610 2224 3.252284 CTGGCCTCCACCACCAGT 61.252 66.667 3.32 0.00 44.91 4.00
612 2226 3.863114 TAGCTGGCCTCCACCACCA 62.863 63.158 3.32 0.00 35.33 4.17
626 2240 4.195334 CGCCCAGCCCCAATAGCT 62.195 66.667 0.00 0.00 42.70 3.32
712 2326 3.454375 TCAGACAGTTCTCGTTTGAACC 58.546 45.455 12.38 2.30 45.25 3.62
713 2327 4.609336 GCATCAGACAGTTCTCGTTTGAAC 60.609 45.833 9.45 9.45 44.67 3.18
714 2328 3.494626 GCATCAGACAGTTCTCGTTTGAA 59.505 43.478 0.00 0.00 32.02 2.69
716 2330 2.802247 TGCATCAGACAGTTCTCGTTTG 59.198 45.455 0.00 0.00 0.00 2.93
719 2333 2.224042 TGTTGCATCAGACAGTTCTCGT 60.224 45.455 0.00 0.00 0.00 4.18
720 2334 2.156504 GTGTTGCATCAGACAGTTCTCG 59.843 50.000 0.00 0.00 0.00 4.04
846 2809 5.414454 TCCGTCCCTGTTGAAATTTTGATAG 59.586 40.000 0.00 0.00 0.00 2.08
854 2817 3.761897 TCATTTCCGTCCCTGTTGAAAT 58.238 40.909 0.00 0.00 37.79 2.17
867 2830 3.123959 CCTTGCTTGCATTTTCATTTCCG 59.876 43.478 0.00 0.00 0.00 4.30
879 2842 1.417288 ATTTTGGGGCCTTGCTTGCA 61.417 50.000 0.84 0.00 0.00 4.08
889 2853 5.220951 CCTTTTTGTTTGTACATTTTGGGGC 60.221 40.000 0.00 0.00 33.44 5.80
936 2900 2.262915 GGAGTGAGGAGTGTGGCG 59.737 66.667 0.00 0.00 0.00 5.69
1488 3452 4.436998 AAGGAGGCGTCGGCGAAG 62.437 66.667 16.53 18.47 41.24 3.79
1599 3563 1.446272 CTGCTTCGGGAGGTTCGAC 60.446 63.158 0.00 0.00 36.30 4.20
1701 3665 1.093159 AGTACGACTTGTAGCTCGGG 58.907 55.000 0.00 0.00 34.07 5.14
1704 3668 5.220643 GGAGAAGTAGTACGACTTGTAGCTC 60.221 48.000 23.77 20.81 39.79 4.09
2286 4250 2.113860 ACCGCATGAACTAGTTGCAT 57.886 45.000 14.14 12.87 36.15 3.96
2299 4263 4.154195 GGCTAATGATTCGATTAACCGCAT 59.846 41.667 0.00 0.00 0.00 4.73
2300 4264 3.496884 GGCTAATGATTCGATTAACCGCA 59.503 43.478 0.00 0.00 0.00 5.69
2301 4265 3.496884 TGGCTAATGATTCGATTAACCGC 59.503 43.478 0.00 0.00 29.78 5.68
2303 4267 5.048782 TGCATGGCTAATGATTCGATTAACC 60.049 40.000 0.00 0.00 38.72 2.85
2304 4268 6.000891 TGCATGGCTAATGATTCGATTAAC 57.999 37.500 0.00 0.00 38.72 2.01
2354 4355 3.181492 ACAATCACAAATTCACACGCACA 60.181 39.130 0.00 0.00 0.00 4.57
2355 4356 3.371168 ACAATCACAAATTCACACGCAC 58.629 40.909 0.00 0.00 0.00 5.34
2356 4357 3.706802 ACAATCACAAATTCACACGCA 57.293 38.095 0.00 0.00 0.00 5.24
2357 4358 6.689178 ATTAACAATCACAAATTCACACGC 57.311 33.333 0.00 0.00 0.00 5.34
2358 4359 7.526850 GCAAATTAACAATCACAAATTCACACG 59.473 33.333 0.00 0.00 0.00 4.49
2359 4360 7.526850 CGCAAATTAACAATCACAAATTCACAC 59.473 33.333 0.00 0.00 0.00 3.82
2360 4361 7.307042 CCGCAAATTAACAATCACAAATTCACA 60.307 33.333 0.00 0.00 0.00 3.58
2361 4362 7.008859 CCGCAAATTAACAATCACAAATTCAC 58.991 34.615 0.00 0.00 0.00 3.18
2362 4363 6.347240 GCCGCAAATTAACAATCACAAATTCA 60.347 34.615 0.00 0.00 0.00 2.57
2363 4364 6.014898 GCCGCAAATTAACAATCACAAATTC 58.985 36.000 0.00 0.00 0.00 2.17
2364 4365 5.700373 AGCCGCAAATTAACAATCACAAATT 59.300 32.000 0.00 0.00 0.00 1.82
2365 4366 5.237048 AGCCGCAAATTAACAATCACAAAT 58.763 33.333 0.00 0.00 0.00 2.32
2366 4367 4.626042 AGCCGCAAATTAACAATCACAAA 58.374 34.783 0.00 0.00 0.00 2.83
2367 4368 4.250116 AGCCGCAAATTAACAATCACAA 57.750 36.364 0.00 0.00 0.00 3.33
2456 4498 1.992170 AAATAGTCACGACGACCAGC 58.008 50.000 0.00 0.00 46.69 4.85
2468 4510 5.163854 GCACACATCACACCAGTAAATAGTC 60.164 44.000 0.00 0.00 0.00 2.59
2492 4534 9.260002 ACAAACAAGTTCCTTAATTAAATGCAG 57.740 29.630 0.00 0.00 0.00 4.41
2504 4546 4.926832 CCAAACGAAACAAACAAGTTCCTT 59.073 37.500 0.00 0.00 0.00 3.36
2505 4547 4.490743 CCAAACGAAACAAACAAGTTCCT 58.509 39.130 0.00 0.00 0.00 3.36
2506 4548 3.061563 GCCAAACGAAACAAACAAGTTCC 59.938 43.478 0.00 0.00 0.00 3.62
2507 4549 3.924073 AGCCAAACGAAACAAACAAGTTC 59.076 39.130 0.00 0.00 0.00 3.01
2605 4651 1.071699 GGGCTGTCAGTACACTCCAAA 59.928 52.381 0.93 0.00 0.00 3.28
2744 8253 8.137437 ACGATTGTTTTCTCATCATGAAACTTT 58.863 29.630 0.00 0.00 33.77 2.66
2759 8268 5.458452 TGCTCAAAACATCACGATTGTTTTC 59.542 36.000 18.09 11.71 41.85 2.29
2839 8352 3.000041 TGATAGAATGCGTGTGACAACC 59.000 45.455 0.00 0.00 0.00 3.77
2875 8388 6.201615 GGCAACACGTTTACTAGTTTTCTACT 59.798 38.462 0.00 0.00 41.04 2.57
2876 8389 6.018832 TGGCAACACGTTTACTAGTTTTCTAC 60.019 38.462 0.00 0.00 46.17 2.59
2907 8420 9.487790 TCTGAAGGCAAAAATAAAAATTACTGG 57.512 29.630 0.00 0.00 0.00 4.00
2923 8436 2.229792 ACAGCGAAAATCTGAAGGCAA 58.770 42.857 0.00 0.00 35.61 4.52
2938 8451 2.274437 ACAGCACTGATATGAACAGCG 58.726 47.619 4.31 0.00 38.74 5.18
2939 8452 3.529533 AGACAGCACTGATATGAACAGC 58.470 45.455 4.31 0.00 38.74 4.40
2974 8487 8.424918 TGTTGTGACAAATACAATTTTACCCAT 58.575 29.630 0.00 0.00 39.88 4.00
2994 8507 8.976471 TGCAATTTCACTATGTTTTATGTTGTG 58.024 29.630 0.00 0.00 0.00 3.33
3170 8684 9.025041 CCCTCCACTCCAAAATATATATTTTCC 57.975 37.037 24.32 0.00 42.26 3.13
3219 8733 7.734942 TCAACCTCCTCAAAATTTGCTAAAAT 58.265 30.769 0.00 0.00 37.61 1.82


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

AutoCloner maintained by Alex Coulton.