Multiple sequence alignment - TraesCS1D01G331100

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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 TraesCS1D01G331100 chr1D 100.000 2840 0 0 1 2840 421225250 421228089 0.000000e+00 5245.0
1 TraesCS1D01G331100 chr1D 88.708 1355 76 30 627 1976 421464496 421465778 0.000000e+00 1583.0
2 TraesCS1D01G331100 chr1D 89.594 567 51 6 2281 2840 300067924 300068489 0.000000e+00 713.0
3 TraesCS1D01G331100 chr1D 88.336 583 60 4 2265 2840 53821784 53822365 0.000000e+00 693.0
4 TraesCS1D01G331100 chr1D 88.165 583 60 6 2265 2840 300194545 300195125 0.000000e+00 686.0
5 TraesCS1D01G331100 chr1D 90.149 538 24 10 133 642 421463946 421464482 0.000000e+00 673.0
6 TraesCS1D01G331100 chr1D 89.224 232 19 4 1987 2213 421465838 421466068 4.630000e-73 285.0
7 TraesCS1D01G331100 chr1A 87.868 1632 91 37 394 1978 517519117 517520688 0.000000e+00 1818.0
8 TraesCS1D01G331100 chr1A 87.843 255 24 5 1987 2239 517520742 517520991 2.770000e-75 292.0
9 TraesCS1D01G331100 chr1A 85.612 278 17 4 1 263 517518801 517519070 1.300000e-68 270.0
10 TraesCS1D01G331100 chr1B 87.877 1361 96 32 634 1979 570525546 570526852 0.000000e+00 1535.0
11 TraesCS1D01G331100 chr1B 82.248 783 52 34 1481 2237 570831730 570832451 1.880000e-166 595.0
12 TraesCS1D01G331100 chr1B 83.808 562 29 20 1 522 570524896 570525435 7.120000e-131 477.0
13 TraesCS1D01G331100 chr1B 85.745 470 37 10 1029 1498 570825984 570826423 1.190000e-128 470.0
14 TraesCS1D01G331100 chr1B 79.859 566 55 30 1713 2226 570720196 570720754 2.690000e-95 359.0
15 TraesCS1D01G331100 chr1B 82.353 408 45 10 538 925 570718414 570718814 2.110000e-86 329.0
16 TraesCS1D01G331100 chr1B 89.615 260 17 8 1987 2239 570526905 570527161 3.530000e-84 322.0
17 TraesCS1D01G331100 chr1B 78.552 359 40 19 1804 2136 570718811 570719158 4.800000e-48 202.0
18 TraesCS1D01G331100 chr1B 91.729 133 9 1 900 1032 570824786 570824916 1.740000e-42 183.0
19 TraesCS1D01G331100 chr1B 89.189 148 8 3 765 908 570820643 570820786 8.080000e-41 178.0
20 TraesCS1D01G331100 chr1B 79.615 260 32 7 538 777 570814893 570815151 1.750000e-37 167.0
21 TraesCS1D01G331100 chr5D 90.223 583 50 4 2265 2840 207731607 207731025 0.000000e+00 754.0
22 TraesCS1D01G331100 chr5D 88.165 583 62 4 2265 2840 207687480 207686898 0.000000e+00 688.0
23 TraesCS1D01G331100 chr5D 79.265 844 113 38 1028 1846 556423346 556424152 1.500000e-147 532.0
24 TraesCS1D01G331100 chr5D 78.636 777 109 32 1043 1785 559979041 559978288 1.990000e-126 462.0
25 TraesCS1D01G331100 chr7D 89.880 583 49 7 2265 2840 229707410 229707989 0.000000e+00 741.0
26 TraesCS1D01G331100 chr7D 89.880 583 49 8 2265 2840 229762241 229762820 0.000000e+00 741.0
27 TraesCS1D01G331100 chr6D 88.527 584 59 5 2265 2840 143596032 143595449 0.000000e+00 701.0
28 TraesCS1D01G331100 chr2D 88.165 583 60 6 2265 2840 98209572 98208992 0.000000e+00 686.0
29 TraesCS1D01G331100 chr2D 85.177 479 51 11 1367 1841 498532623 498532161 9.210000e-130 473.0
30 TraesCS1D01G331100 chr4A 78.041 970 139 48 862 1785 613544513 613543572 6.920000e-151 544.0
31 TraesCS1D01G331100 chr4A 79.016 772 115 28 1036 1785 604940680 604941426 4.250000e-133 484.0
32 TraesCS1D01G331100 chr5B 79.501 761 101 34 1051 1785 710314394 710313663 9.140000e-135 490.0
33 TraesCS1D01G331100 chr2A 85.294 476 54 10 1368 1841 643230802 643230341 7.120000e-131 477.0
34 TraesCS1D01G331100 chr2A 80.065 306 28 16 994 1298 643231190 643230917 2.230000e-46 196.0
35 TraesCS1D01G331100 chr2B 83.613 476 57 11 1368 1840 585757061 585756604 7.270000e-116 427.0
36 TraesCS1D01G331100 chr2B 80.392 306 27 18 994 1298 585757449 585757176 4.800000e-48 202.0
37 TraesCS1D01G331100 chr4B 86.957 69 9 0 574 642 76818025 76817957 8.440000e-11 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 TraesCS1D01G331100 chr1D 421225250 421228089 2839 False 5245.000000 5245 100.000000 1 2840 1 chr1D.!!$F4 2839
1 TraesCS1D01G331100 chr1D 421463946 421466068 2122 False 847.000000 1583 89.360333 133 2213 3 chr1D.!!$F5 2080
2 TraesCS1D01G331100 chr1D 300067924 300068489 565 False 713.000000 713 89.594000 2281 2840 1 chr1D.!!$F2 559
3 TraesCS1D01G331100 chr1D 53821784 53822365 581 False 693.000000 693 88.336000 2265 2840 1 chr1D.!!$F1 575
4 TraesCS1D01G331100 chr1D 300194545 300195125 580 False 686.000000 686 88.165000 2265 2840 1 chr1D.!!$F3 575
5 TraesCS1D01G331100 chr1A 517518801 517520991 2190 False 793.333333 1818 87.107667 1 2239 3 chr1A.!!$F1 2238
6 TraesCS1D01G331100 chr1B 570524896 570527161 2265 False 778.000000 1535 87.100000 1 2239 3 chr1B.!!$F4 2238
7 TraesCS1D01G331100 chr1B 570831730 570832451 721 False 595.000000 595 82.248000 1481 2237 1 chr1B.!!$F3 756
8 TraesCS1D01G331100 chr1B 570824786 570826423 1637 False 326.500000 470 88.737000 900 1498 2 chr1B.!!$F6 598
9 TraesCS1D01G331100 chr1B 570718414 570720754 2340 False 296.666667 359 80.254667 538 2226 3 chr1B.!!$F5 1688
10 TraesCS1D01G331100 chr5D 207731025 207731607 582 True 754.000000 754 90.223000 2265 2840 1 chr5D.!!$R2 575
11 TraesCS1D01G331100 chr5D 207686898 207687480 582 True 688.000000 688 88.165000 2265 2840 1 chr5D.!!$R1 575
12 TraesCS1D01G331100 chr5D 556423346 556424152 806 False 532.000000 532 79.265000 1028 1846 1 chr5D.!!$F1 818
13 TraesCS1D01G331100 chr5D 559978288 559979041 753 True 462.000000 462 78.636000 1043 1785 1 chr5D.!!$R3 742
14 TraesCS1D01G331100 chr7D 229707410 229707989 579 False 741.000000 741 89.880000 2265 2840 1 chr7D.!!$F1 575
15 TraesCS1D01G331100 chr7D 229762241 229762820 579 False 741.000000 741 89.880000 2265 2840 1 chr7D.!!$F2 575
16 TraesCS1D01G331100 chr6D 143595449 143596032 583 True 701.000000 701 88.527000 2265 2840 1 chr6D.!!$R1 575
17 TraesCS1D01G331100 chr2D 98208992 98209572 580 True 686.000000 686 88.165000 2265 2840 1 chr2D.!!$R1 575
18 TraesCS1D01G331100 chr4A 613543572 613544513 941 True 544.000000 544 78.041000 862 1785 1 chr4A.!!$R1 923
19 TraesCS1D01G331100 chr4A 604940680 604941426 746 False 484.000000 484 79.016000 1036 1785 1 chr4A.!!$F1 749
20 TraesCS1D01G331100 chr5B 710313663 710314394 731 True 490.000000 490 79.501000 1051 1785 1 chr5B.!!$R1 734
21 TraesCS1D01G331100 chr2A 643230341 643231190 849 True 336.500000 477 82.679500 994 1841 2 chr2A.!!$R1 847
22 TraesCS1D01G331100 chr2B 585756604 585757449 845 True 314.500000 427 82.002500 994 1840 2 chr2B.!!$R1 846

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
242 261 0.109781 CACGTACCACCATTTGCAGC 60.11 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 4024 0.178533 TCGATCAGGACATGCATGCA 59.821 50.0 26.53 25.04 0.0 3.96 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
30 31 8.163408 TCTAAATGATGGAACCAAGAAAGAAGA 58.837 33.333 0.00 0.00 0.00 2.87
42 43 5.594317 CCAAGAAAGAAGAAGGAAGGAACAA 59.406 40.000 0.00 0.00 0.00 2.83
59 60 3.753294 ACAAGCGAAAGAAGGAGAGAA 57.247 42.857 0.00 0.00 0.00 2.87
164 180 3.549070 GCTATGCTTGCTTGGAAATTTCG 59.451 43.478 11.95 0.00 0.00 3.46
178 194 9.862585 CTTGGAAATTTCGGACAAATTAAAAAG 57.137 29.630 11.95 0.00 30.38 2.27
180 196 8.204836 TGGAAATTTCGGACAAATTAAAAAGGA 58.795 29.630 11.95 0.00 30.38 3.36
242 261 0.109781 CACGTACCACCATTTGCAGC 60.110 55.000 0.00 0.00 0.00 5.25
304 342 4.218417 GTGGAGTGTGTTATGCTTGGAAAT 59.782 41.667 0.00 0.00 0.00 2.17
448 506 2.583593 GGCTAAGCTCGCTCACCG 60.584 66.667 7.74 0.00 38.61 4.94
469 535 2.526304 TTGAGTGCAGTGGAGTGTAC 57.474 50.000 0.00 0.00 33.57 2.90
486 552 1.549170 GTACACCACTACCACCCTCTG 59.451 57.143 0.00 0.00 0.00 3.35
572 639 6.264744 ACCATGATTTTCCATGATCACAGATC 59.735 38.462 0.00 0.15 44.98 2.75
638 749 6.422776 TTCGAGCCAGATTCAATCTAAAAC 57.577 37.500 0.00 0.00 37.58 2.43
668 779 7.381744 GAGTTTTGAAAACTCAAAATCCGAG 57.618 36.000 33.85 0.00 46.81 4.63
874 994 6.670695 AACCAGGAAACAGAGCATTTTTAT 57.329 33.333 0.00 0.00 0.00 1.40
877 998 7.775120 ACCAGGAAACAGAGCATTTTTATATG 58.225 34.615 0.00 0.00 0.00 1.78
886 1007 9.812347 ACAGAGCATTTTTATATGATCCCAATA 57.188 29.630 0.00 0.00 40.82 1.90
942 1075 3.118519 ACTCCTGTCGCCGGTATAAAAAT 60.119 43.478 1.90 0.00 0.00 1.82
989 1127 5.499139 TCAACTTTCAACTCCACATCAAC 57.501 39.130 0.00 0.00 0.00 3.18
1189 2823 3.129502 CCGACTCCGTGCCGTCTA 61.130 66.667 0.00 0.00 0.00 2.59
1206 2852 2.842394 CTACGTGGAGCACCTGCCAG 62.842 65.000 0.00 0.00 43.38 4.85
1699 3434 0.243636 GTGCCGCAAAATAGCCAAGT 59.756 50.000 0.00 0.00 0.00 3.16
1825 3566 2.815211 GTTCATGGCGCTCGAGCA 60.815 61.111 34.69 18.03 42.21 4.26
1896 3653 5.147162 GCCATTTGTGTAGTTCTTTCTTCG 58.853 41.667 0.00 0.00 0.00 3.79
1897 3654 5.689819 CCATTTGTGTAGTTCTTTCTTCGG 58.310 41.667 0.00 0.00 0.00 4.30
1898 3655 5.238650 CCATTTGTGTAGTTCTTTCTTCGGT 59.761 40.000 0.00 0.00 0.00 4.69
1899 3656 5.978934 TTTGTGTAGTTCTTTCTTCGGTC 57.021 39.130 0.00 0.00 0.00 4.79
1900 3657 4.931661 TGTGTAGTTCTTTCTTCGGTCT 57.068 40.909 0.00 0.00 0.00 3.85
1901 3658 4.868067 TGTGTAGTTCTTTCTTCGGTCTC 58.132 43.478 0.00 0.00 0.00 3.36
1902 3659 4.236147 GTGTAGTTCTTTCTTCGGTCTCC 58.764 47.826 0.00 0.00 0.00 3.71
1903 3660 3.257624 TGTAGTTCTTTCTTCGGTCTCCC 59.742 47.826 0.00 0.00 0.00 4.30
1981 3751 4.218312 AGGATTGAGAAAAGGTTTGCTGT 58.782 39.130 0.00 0.00 0.00 4.40
1982 3752 4.651045 AGGATTGAGAAAAGGTTTGCTGTT 59.349 37.500 0.00 0.00 0.00 3.16
1983 3753 5.129320 AGGATTGAGAAAAGGTTTGCTGTTT 59.871 36.000 0.00 0.00 0.00 2.83
1984 3754 5.817296 GGATTGAGAAAAGGTTTGCTGTTTT 59.183 36.000 0.00 0.00 0.00 2.43
1985 3755 6.316140 GGATTGAGAAAAGGTTTGCTGTTTTT 59.684 34.615 0.00 0.00 0.00 1.94
2156 4009 1.122632 TCCAGTGGCGGGTAAAGTGA 61.123 55.000 3.51 0.00 0.00 3.41
2161 4014 0.759959 TGGCGGGTAAAGTGAACTGA 59.240 50.000 0.00 0.00 0.00 3.41
2165 4019 3.549423 GGCGGGTAAAGTGAACTGAAAAC 60.549 47.826 0.00 0.00 0.00 2.43
2170 4024 6.238648 CGGGTAAAGTGAACTGAAAACAAGAT 60.239 38.462 0.00 0.00 0.00 2.40
2219 4077 1.000843 GTCCAAAGTCCAAACATGCCC 59.999 52.381 0.00 0.00 0.00 5.36
2226 4084 1.080569 CCAAACATGCCCGCAAGTC 60.081 57.895 0.00 0.00 0.00 3.01
2233 4091 0.960364 ATGCCCGCAAGTCGATGTTT 60.960 50.000 0.00 0.00 41.67 2.83
2235 4093 1.501741 CCCGCAAGTCGATGTTTGG 59.498 57.895 8.65 0.52 41.67 3.28
2236 4094 1.234615 CCCGCAAGTCGATGTTTGGT 61.235 55.000 8.65 0.00 41.67 3.67
2237 4095 0.110238 CCGCAAGTCGATGTTTGGTG 60.110 55.000 8.65 0.00 41.67 4.17
2238 4096 0.586319 CGCAAGTCGATGTTTGGTGT 59.414 50.000 8.65 0.00 41.67 4.16
2239 4097 1.398451 CGCAAGTCGATGTTTGGTGTC 60.398 52.381 8.65 0.00 41.67 3.67
2240 4098 1.601903 GCAAGTCGATGTTTGGTGTCA 59.398 47.619 8.65 0.00 0.00 3.58
2241 4099 2.032799 GCAAGTCGATGTTTGGTGTCAA 59.967 45.455 8.65 0.00 0.00 3.18
2242 4100 3.304659 GCAAGTCGATGTTTGGTGTCAAT 60.305 43.478 8.65 0.00 32.28 2.57
2243 4101 4.221342 CAAGTCGATGTTTGGTGTCAATG 58.779 43.478 0.00 0.00 32.28 2.82
2244 4102 3.476552 AGTCGATGTTTGGTGTCAATGT 58.523 40.909 0.00 0.00 32.28 2.71
2245 4103 3.882888 AGTCGATGTTTGGTGTCAATGTT 59.117 39.130 0.00 0.00 32.28 2.71
2246 4104 4.338118 AGTCGATGTTTGGTGTCAATGTTT 59.662 37.500 0.00 0.00 32.28 2.83
2247 4105 5.040635 GTCGATGTTTGGTGTCAATGTTTT 58.959 37.500 0.00 0.00 32.28 2.43
2248 4106 5.039984 TCGATGTTTGGTGTCAATGTTTTG 58.960 37.500 0.00 0.00 32.28 2.44
2249 4107 4.803088 CGATGTTTGGTGTCAATGTTTTGT 59.197 37.500 0.00 0.00 34.32 2.83
2250 4108 5.276301 CGATGTTTGGTGTCAATGTTTTGTG 60.276 40.000 0.00 0.00 34.32 3.33
2251 4109 4.887748 TGTTTGGTGTCAATGTTTTGTGT 58.112 34.783 0.00 0.00 34.32 3.72
2252 4110 5.300752 TGTTTGGTGTCAATGTTTTGTGTT 58.699 33.333 0.00 0.00 34.32 3.32
2253 4111 5.178252 TGTTTGGTGTCAATGTTTTGTGTTG 59.822 36.000 0.00 0.00 34.32 3.33
2254 4112 3.854666 TGGTGTCAATGTTTTGTGTTGG 58.145 40.909 0.00 0.00 34.32 3.77
2255 4113 3.259374 TGGTGTCAATGTTTTGTGTTGGT 59.741 39.130 0.00 0.00 34.32 3.67
2256 4114 4.462834 TGGTGTCAATGTTTTGTGTTGGTA 59.537 37.500 0.00 0.00 34.32 3.25
2257 4115 5.040635 GGTGTCAATGTTTTGTGTTGGTAG 58.959 41.667 0.00 0.00 34.32 3.18
2258 4116 4.502645 GTGTCAATGTTTTGTGTTGGTAGC 59.497 41.667 0.00 0.00 34.32 3.58
2259 4117 4.158579 TGTCAATGTTTTGTGTTGGTAGCA 59.841 37.500 0.00 0.00 34.32 3.49
2260 4118 4.739716 GTCAATGTTTTGTGTTGGTAGCAG 59.260 41.667 0.00 0.00 34.32 4.24
2261 4119 4.400884 TCAATGTTTTGTGTTGGTAGCAGT 59.599 37.500 0.00 0.00 34.32 4.40
2262 4120 4.568152 ATGTTTTGTGTTGGTAGCAGTC 57.432 40.909 0.00 0.00 0.00 3.51
2263 4121 2.685897 TGTTTTGTGTTGGTAGCAGTCC 59.314 45.455 0.00 0.00 0.00 3.85
2271 4129 2.939103 GTTGGTAGCAGTCCATGACATC 59.061 50.000 0.00 0.00 34.60 3.06
2274 4132 4.226384 TGGTAGCAGTCCATGACATCTAT 58.774 43.478 0.00 0.00 34.60 1.98
2279 4137 5.639139 AGCAGTCCATGACATCTATCTAGA 58.361 41.667 0.00 0.00 34.60 2.43
2316 4175 5.221722 GCCTGACCTAGACATCATATCCAAA 60.222 44.000 0.00 0.00 0.00 3.28
2318 4177 6.042552 CCTGACCTAGACATCATATCCAAAGT 59.957 42.308 0.00 0.00 0.00 2.66
2324 4184 9.303116 CCTAGACATCATATCCAAAGTACTACT 57.697 37.037 0.00 0.00 0.00 2.57
2333 4193 9.787435 CATATCCAAAGTACTACTCTAGAGTCT 57.213 37.037 28.42 16.37 42.54 3.24
2365 4225 5.178797 CAAGGTTCAACAGAAGATACCGAT 58.821 41.667 0.00 0.00 0.00 4.18
2386 4246 2.722094 TGAAATCGCCCTAAAGTGCAT 58.278 42.857 0.00 0.00 0.00 3.96
2441 4301 5.065914 CCAATTCCACTCGACCATGATAAT 58.934 41.667 0.00 0.00 0.00 1.28
2472 4332 2.027561 CCATACAAGAACCCACTCGGAA 60.028 50.000 0.00 0.00 34.64 4.30
2473 4333 2.825861 TACAAGAACCCACTCGGAAC 57.174 50.000 0.00 0.00 34.64 3.62
2552 4412 1.846007 AAGACCATTTATTGCGGGCA 58.154 45.000 0.00 0.00 0.00 5.36
2554 4414 1.956477 AGACCATTTATTGCGGGCATC 59.044 47.619 0.00 0.00 0.00 3.91
2634 4494 2.094649 GGGCCAGACGCACTCTATATAC 60.095 54.545 4.39 0.00 38.16 1.47
2824 4690 3.555117 ACCCCCTACTCTTACTGTCAA 57.445 47.619 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.208747 TCTTTCGCTTGTTCCTTCCTT 57.791 42.857 0.00 0.00 0.00 3.36
42 43 2.530701 TCCTTCTCTCCTTCTTTCGCT 58.469 47.619 0.00 0.00 0.00 4.93
164 180 5.861787 CCATCACGTCCTTTTTAATTTGTCC 59.138 40.000 0.00 0.00 0.00 4.02
178 194 1.741770 GCACCTCACCATCACGTCC 60.742 63.158 0.00 0.00 0.00 4.79
180 196 0.179032 TTTGCACCTCACCATCACGT 60.179 50.000 0.00 0.00 0.00 4.49
242 261 6.511767 GCTGGGTGAGACGATTAATTATGTTG 60.512 42.308 0.00 0.00 0.00 3.33
304 342 1.618343 TCGTCTGGCATCACTCTGAAA 59.382 47.619 0.00 0.00 0.00 2.69
448 506 1.668419 ACACTCCACTGCACTCAAAC 58.332 50.000 0.00 0.00 0.00 2.93
469 535 1.983224 CCAGAGGGTGGTAGTGGTG 59.017 63.158 0.00 0.00 42.17 4.17
486 552 3.567478 ATGATCAAGTGGGAGTTAGCC 57.433 47.619 0.00 0.00 0.00 3.93
536 603 9.912634 CATGGAAAATCATGGTGGTAATATTAC 57.087 33.333 15.98 15.98 40.43 1.89
748 859 6.712095 ACTACAGCAATTGTGAAAGAAGATGA 59.288 34.615 7.40 0.00 41.10 2.92
824 940 1.215382 GTTTCCGGATGCCTTTGCC 59.785 57.895 4.15 0.00 36.33 4.52
825 941 0.109132 CTGTTTCCGGATGCCTTTGC 60.109 55.000 4.15 0.00 38.26 3.68
826 942 1.200020 GACTGTTTCCGGATGCCTTTG 59.800 52.381 4.15 0.00 0.00 2.77
827 943 1.534729 GACTGTTTCCGGATGCCTTT 58.465 50.000 4.15 0.00 0.00 3.11
828 944 0.673644 CGACTGTTTCCGGATGCCTT 60.674 55.000 4.15 0.00 0.00 4.35
860 977 8.716674 ATTGGGATCATATAAAAATGCTCTGT 57.283 30.769 0.00 0.00 0.00 3.41
874 994 5.043762 GGGGAGGGTAATATTGGGATCATA 58.956 45.833 0.00 0.00 0.00 2.15
877 998 3.267031 CAGGGGAGGGTAATATTGGGATC 59.733 52.174 0.00 0.00 0.00 3.36
886 1007 0.620700 ACGAAGCAGGGGAGGGTAAT 60.621 55.000 0.00 0.00 0.00 1.89
887 1008 0.838987 AACGAAGCAGGGGAGGGTAA 60.839 55.000 0.00 0.00 0.00 2.85
942 1075 4.838152 GGAAGCGCGCCTCCATGA 62.838 66.667 37.36 0.00 0.00 3.07
1123 2745 2.183555 GGGAAATGCTGCTGCTGC 59.816 61.111 22.51 22.51 40.48 5.25
1184 2818 1.154016 CAGGTGCTCCACGTAGACG 60.154 63.158 7.70 0.00 46.33 4.18
1185 2819 1.446272 GCAGGTGCTCCACGTAGAC 60.446 63.158 7.70 0.00 38.21 2.59
1186 2820 2.646175 GGCAGGTGCTCCACGTAGA 61.646 63.158 7.70 0.00 41.70 2.59
1187 2821 2.125512 GGCAGGTGCTCCACGTAG 60.126 66.667 7.70 0.00 41.70 3.51
1188 2822 2.920384 TGGCAGGTGCTCCACGTA 60.920 61.111 7.70 0.00 41.70 3.57
1189 2823 4.320456 CTGGCAGGTGCTCCACGT 62.320 66.667 6.61 0.00 41.70 4.49
1325 3004 4.093291 CCTCCTGCTTCAGCGGCT 62.093 66.667 0.00 0.00 45.75 5.52
1443 3158 4.351054 CCCAGCCACACCCTGACC 62.351 72.222 0.00 0.00 32.03 4.02
1727 3468 1.333636 AAGGTCCTCCAGCTCCATCG 61.334 60.000 0.00 0.00 35.89 3.84
1816 3557 1.194098 GATGGAATGATTGCTCGAGCG 59.806 52.381 30.75 0.00 45.83 5.03
1825 3566 6.127101 TCTTCTTGCATCAGATGGAATGATT 58.873 36.000 16.94 0.00 39.89 2.57
1897 3654 1.002011 GCAACAGGGAAGGGGAGAC 60.002 63.158 0.00 0.00 0.00 3.36
1898 3655 1.151810 AGCAACAGGGAAGGGGAGA 60.152 57.895 0.00 0.00 0.00 3.71
1899 3656 1.001641 CAGCAACAGGGAAGGGGAG 60.002 63.158 0.00 0.00 0.00 4.30
1900 3657 1.360393 AACAGCAACAGGGAAGGGGA 61.360 55.000 0.00 0.00 0.00 4.81
1901 3658 1.153756 AACAGCAACAGGGAAGGGG 59.846 57.895 0.00 0.00 0.00 4.79
1902 3659 1.809567 GCAACAGCAACAGGGAAGGG 61.810 60.000 0.00 0.00 0.00 3.95
1903 3660 0.825010 AGCAACAGCAACAGGGAAGG 60.825 55.000 0.00 0.00 0.00 3.46
1981 3751 6.486657 TCAAACCCAAACATTTGTCACAAAAA 59.513 30.769 7.14 0.00 37.16 1.94
1982 3752 5.997746 TCAAACCCAAACATTTGTCACAAAA 59.002 32.000 7.14 0.00 37.16 2.44
1983 3753 5.551233 TCAAACCCAAACATTTGTCACAAA 58.449 33.333 5.18 5.18 37.16 2.83
1984 3754 5.152623 TCAAACCCAAACATTTGTCACAA 57.847 34.783 3.79 0.00 37.16 3.33
1985 3755 4.808414 TCAAACCCAAACATTTGTCACA 57.192 36.364 3.79 0.00 37.16 3.58
2106 3956 5.467035 ACAACAATCCCATGTACCTTTTG 57.533 39.130 0.00 0.00 32.02 2.44
2140 3993 0.763035 AGTTCACTTTACCCGCCACT 59.237 50.000 0.00 0.00 0.00 4.00
2141 3994 0.872388 CAGTTCACTTTACCCGCCAC 59.128 55.000 0.00 0.00 0.00 5.01
2156 4009 4.325028 TGCATGCATCTTGTTTTCAGTT 57.675 36.364 18.46 0.00 0.00 3.16
2161 4014 3.259876 AGGACATGCATGCATCTTGTTTT 59.740 39.130 30.07 15.29 33.90 2.43
2165 4019 2.021457 TCAGGACATGCATGCATCTTG 58.979 47.619 30.07 24.98 33.90 3.02
2170 4024 0.178533 TCGATCAGGACATGCATGCA 59.821 50.000 26.53 25.04 0.00 3.96
2219 4077 0.586319 ACACCAAACATCGACTTGCG 59.414 50.000 0.00 0.00 42.69 4.85
2226 4084 4.803088 ACAAAACATTGACACCAAACATCG 59.197 37.500 0.00 0.00 35.67 3.84
2233 4091 3.259374 ACCAACACAAAACATTGACACCA 59.741 39.130 0.00 0.00 0.00 4.17
2235 4093 4.502645 GCTACCAACACAAAACATTGACAC 59.497 41.667 0.00 0.00 0.00 3.67
2236 4094 4.158579 TGCTACCAACACAAAACATTGACA 59.841 37.500 0.00 0.00 0.00 3.58
2237 4095 4.677584 TGCTACCAACACAAAACATTGAC 58.322 39.130 0.00 0.00 0.00 3.18
2238 4096 4.400884 ACTGCTACCAACACAAAACATTGA 59.599 37.500 0.00 0.00 0.00 2.57
2239 4097 4.681744 ACTGCTACCAACACAAAACATTG 58.318 39.130 0.00 0.00 0.00 2.82
2240 4098 4.202111 GGACTGCTACCAACACAAAACATT 60.202 41.667 0.00 0.00 0.00 2.71
2241 4099 3.317993 GGACTGCTACCAACACAAAACAT 59.682 43.478 0.00 0.00 0.00 2.71
2242 4100 2.685897 GGACTGCTACCAACACAAAACA 59.314 45.455 0.00 0.00 0.00 2.83
2243 4101 2.685897 TGGACTGCTACCAACACAAAAC 59.314 45.455 0.00 0.00 34.25 2.43
2244 4102 3.006112 TGGACTGCTACCAACACAAAA 57.994 42.857 0.00 0.00 34.25 2.44
2245 4103 2.719531 TGGACTGCTACCAACACAAA 57.280 45.000 0.00 0.00 34.25 2.83
2246 4104 2.105649 TCATGGACTGCTACCAACACAA 59.894 45.455 0.00 0.00 40.93 3.33
2247 4105 1.696884 TCATGGACTGCTACCAACACA 59.303 47.619 0.00 0.00 40.93 3.72
2248 4106 2.076863 GTCATGGACTGCTACCAACAC 58.923 52.381 0.00 0.00 40.93 3.32
2249 4107 1.696884 TGTCATGGACTGCTACCAACA 59.303 47.619 0.00 0.00 40.93 3.33
2250 4108 2.472695 TGTCATGGACTGCTACCAAC 57.527 50.000 0.00 0.00 40.93 3.77
2251 4109 2.840038 AGATGTCATGGACTGCTACCAA 59.160 45.455 0.00 0.00 40.93 3.67
2252 4110 2.470990 AGATGTCATGGACTGCTACCA 58.529 47.619 0.00 0.00 41.83 3.25
2253 4111 4.526262 AGATAGATGTCATGGACTGCTACC 59.474 45.833 0.00 0.00 33.15 3.18
2254 4112 5.720371 AGATAGATGTCATGGACTGCTAC 57.280 43.478 0.00 0.00 33.15 3.58
2255 4113 6.784031 TCTAGATAGATGTCATGGACTGCTA 58.216 40.000 0.00 0.71 33.15 3.49
2256 4114 5.639139 TCTAGATAGATGTCATGGACTGCT 58.361 41.667 0.00 0.00 33.15 4.24
2257 4115 5.476599 ACTCTAGATAGATGTCATGGACTGC 59.523 44.000 0.00 0.00 33.15 4.40
2258 4116 7.336679 CCTACTCTAGATAGATGTCATGGACTG 59.663 44.444 0.00 0.00 33.15 3.51
2259 4117 7.402054 CCTACTCTAGATAGATGTCATGGACT 58.598 42.308 0.00 0.00 33.15 3.85
2260 4118 6.601613 CCCTACTCTAGATAGATGTCATGGAC 59.398 46.154 0.00 0.00 0.00 4.02
2261 4119 6.275855 ACCCTACTCTAGATAGATGTCATGGA 59.724 42.308 0.00 0.00 0.00 3.41
2262 4120 6.489603 ACCCTACTCTAGATAGATGTCATGG 58.510 44.000 0.00 0.00 0.00 3.66
2263 4121 8.415950 AAACCCTACTCTAGATAGATGTCATG 57.584 38.462 0.00 0.00 0.00 3.07
2271 4129 6.209788 CAGGCCTAAAACCCTACTCTAGATAG 59.790 46.154 3.98 0.00 0.00 2.08
2274 4132 4.016851 TCAGGCCTAAAACCCTACTCTAGA 60.017 45.833 3.98 0.00 0.00 2.43
2279 4137 1.914108 GGTCAGGCCTAAAACCCTACT 59.086 52.381 3.98 0.00 0.00 2.57
2306 4165 9.781633 GACTCTAGAGTAGTACTTTGGATATGA 57.218 37.037 25.23 0.00 42.66 2.15
2311 4170 8.266473 CCTTAGACTCTAGAGTAGTACTTTGGA 58.734 40.741 25.23 5.52 42.66 3.53
2316 4175 5.907079 AGGCCTTAGACTCTAGAGTAGTACT 59.093 44.000 25.23 18.97 42.66 2.73
2318 4177 6.843333 TGTAGGCCTTAGACTCTAGAGTAGTA 59.157 42.308 25.23 16.31 42.66 1.82
2324 4184 4.230041 ACCTTGTAGGCCTTAGACTCTAGA 59.770 45.833 12.58 0.00 39.63 2.43
2333 4193 3.649023 TCTGTTGAACCTTGTAGGCCTTA 59.351 43.478 12.58 0.00 39.63 2.69
2365 4225 2.509569 TGCACTTTAGGGCGATTTCAA 58.490 42.857 0.00 0.00 0.00 2.69
2378 4238 1.577328 CGGCGAGTGGAATGCACTTT 61.577 55.000 9.18 0.00 32.33 2.66
2386 4246 0.108329 GAATCTTCCGGCGAGTGGAA 60.108 55.000 9.30 1.75 43.07 3.53
2441 4301 4.312443 GGTTCTTGTATGGTCGAGTGAAA 58.688 43.478 0.00 0.00 0.00 2.69
2472 4332 2.224548 GGTGACTTTAGGCCTTCTGTGT 60.225 50.000 12.58 3.13 0.00 3.72
2473 4333 2.427506 GGTGACTTTAGGCCTTCTGTG 58.572 52.381 12.58 0.00 0.00 3.66
2552 4412 8.268850 GTTATGTCTTGAACATTACTGGTGAT 57.731 34.615 0.00 0.00 46.73 3.06
2585 4445 1.423921 CCCTCAGTTACACAGGGGTTT 59.576 52.381 10.00 0.00 43.12 3.27
2620 4480 1.268899 GGTGGCGTATATAGAGTGCGT 59.731 52.381 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.