Multiple sequence alignment - TraesCS1D01G289800

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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 TraesCS1D01G289800 chr1D 100.000 5195 0 0 1 5195 387899132 387893938 0.000000e+00 9594.0
1 TraesCS1D01G289800 chr1D 84.970 998 95 26 1673 2662 387800153 387799203 0.000000e+00 961.0
2 TraesCS1D01G289800 chr1D 81.338 852 75 44 681 1512 387801089 387800302 2.660000e-172 616.0
3 TraesCS1D01G289800 chr1D 84.658 365 42 8 2853 3204 387798726 387798363 8.280000e-93 351.0
4 TraesCS1D01G289800 chr1D 94.839 155 8 0 4048 4202 387797019 387796865 5.200000e-60 243.0
5 TraesCS1D01G289800 chr1D 91.275 149 13 0 1028 1176 387898066 387897918 2.450000e-48 204.0
6 TraesCS1D01G289800 chr1D 91.275 149 13 0 1067 1215 387898105 387897957 2.450000e-48 204.0
7 TraesCS1D01G289800 chr1D 87.117 163 10 6 1017 1178 387800737 387800585 1.920000e-39 174.0
8 TraesCS1D01G289800 chr1D 82.857 140 21 3 4245 4383 387796643 387796506 7.060000e-24 122.0
9 TraesCS1D01G289800 chr1D 88.298 94 9 2 1018 1110 387800667 387800575 1.530000e-20 111.0
10 TraesCS1D01G289800 chr1D 82.946 129 13 4 1028 1156 387800687 387800568 1.980000e-19 108.0
11 TraesCS1D01G289800 chr1A 95.020 2048 78 15 2746 4775 487464689 487462648 0.000000e+00 3195.0
12 TraesCS1D01G289800 chr1A 94.583 1569 62 15 1106 2661 487466249 487464691 0.000000e+00 2405.0
13 TraesCS1D01G289800 chr1A 86.114 857 88 18 1673 2519 487332943 487332108 0.000000e+00 894.0
14 TraesCS1D01G289800 chr1A 93.709 461 25 2 699 1156 487466580 487466121 0.000000e+00 688.0
15 TraesCS1D01G289800 chr1A 92.145 331 19 3 358 681 487469652 487469322 1.320000e-125 460.0
16 TraesCS1D01G289800 chr1A 87.306 386 25 6 1127 1512 487333848 487333487 2.240000e-113 420.0
17 TraesCS1D01G289800 chr1A 94.717 265 13 1 4931 5195 487462631 487462368 1.350000e-110 411.0
18 TraesCS1D01G289800 chr1A 81.453 523 64 17 3501 4005 487331380 487330873 1.050000e-106 398.0
19 TraesCS1D01G289800 chr1A 82.365 499 48 23 2743 3204 487332037 487331542 1.050000e-106 398.0
20 TraesCS1D01G289800 chr1A 88.179 313 27 5 51 359 487469924 487469618 1.060000e-96 364.0
21 TraesCS1D01G289800 chr1A 95.062 162 7 1 4041 4202 487330784 487330624 2.400000e-63 254.0
22 TraesCS1D01G289800 chr1A 82.192 146 24 2 4239 4383 487330403 487330259 1.960000e-24 124.0
23 TraesCS1D01G289800 chr1A 88.060 67 8 0 4192 4258 487330619 487330553 4.310000e-11 80.5
24 TraesCS1D01G289800 chr1A 90.566 53 3 2 1017 1068 487333811 487333760 9.330000e-08 69.4
25 TraesCS1D01G289800 chr1B 92.893 1801 97 16 2742 4521 521000540 520998750 0.000000e+00 2588.0
26 TraesCS1D01G289800 chr1B 92.067 1311 48 19 358 1628 521002824 521001530 0.000000e+00 1794.0
27 TraesCS1D01G289800 chr1B 94.701 1019 45 5 1645 2662 521001547 521000537 0.000000e+00 1574.0
28 TraesCS1D01G289800 chr1B 86.477 843 76 23 1673 2505 520928546 520927732 0.000000e+00 891.0
29 TraesCS1D01G289800 chr1B 80.697 803 80 48 722 1512 520929411 520928672 5.880000e-154 555.0
30 TraesCS1D01G289800 chr1B 78.836 756 124 27 3270 4005 520927047 520926308 1.310000e-130 477.0
31 TraesCS1D01G289800 chr1B 90.884 362 24 5 2 360 521003144 521002789 1.310000e-130 477.0
32 TraesCS1D01G289800 chr1B 83.128 486 57 12 2743 3204 520927560 520927076 2.240000e-113 420.0
33 TraesCS1D01G289800 chr1B 94.839 155 8 0 4048 4202 520926211 520926057 5.200000e-60 243.0
34 TraesCS1D01G289800 chr1B 86.471 170 12 6 1017 1185 520929104 520928945 5.350000e-40 176.0
35 TraesCS1D01G289800 chr1B 93.548 93 6 0 2661 2753 631232677 631232769 7.010000e-29 139.0
36 TraesCS1D01G289800 chr1B 90.000 90 7 2 1019 1107 520929033 520928945 1.180000e-21 115.0
37 TraesCS1D01G289800 chr1B 84.874 119 9 4 1028 1146 520929054 520928945 1.530000e-20 111.0
38 TraesCS1D01G289800 chr1B 95.122 41 2 0 1028 1068 520928985 520928945 1.210000e-06 65.8
39 TraesCS1D01G289800 chr3A 78.382 791 140 24 4413 5195 194677142 194677909 7.820000e-133 484.0
40 TraesCS1D01G289800 chr5D 76.542 746 143 22 4415 5152 117355137 117355858 3.800000e-101 379.0
41 TraesCS1D01G289800 chrUn 94.382 89 5 0 2657 2745 62663490 62663402 2.520000e-28 137.0
42 TraesCS1D01G289800 chrUn 92.391 92 7 0 2659 2750 224653395 224653304 1.170000e-26 132.0
43 TraesCS1D01G289800 chr7B 93.548 93 5 1 2661 2752 440325688 440325596 2.520000e-28 137.0
44 TraesCS1D01G289800 chr7B 79.532 171 29 5 147 314 178402344 178402177 3.290000e-22 117.0
45 TraesCS1D01G289800 chr7B 88.679 53 5 1 49 101 384383346 384383397 4.340000e-06 63.9
46 TraesCS1D01G289800 chr2D 93.548 93 5 1 2659 2750 25037970 25037878 2.520000e-28 137.0
47 TraesCS1D01G289800 chr7A 81.765 170 23 3 147 314 232756029 232756192 9.070000e-28 135.0
48 TraesCS1D01G289800 chr4A 89.899 99 10 0 2647 2745 614251416 614251514 1.520000e-25 128.0
49 TraesCS1D01G289800 chr5B 87.963 108 11 2 2640 2745 218214227 218214334 5.460000e-25 126.0
50 TraesCS1D01G289800 chr2B 87.156 109 14 0 2659 2767 10083550 10083442 1.960000e-24 124.0
51 TraesCS1D01G289800 chr4D 84.874 119 17 1 2650 2767 23884426 23884308 9.140000e-23 119.0
52 TraesCS1D01G289800 chr4D 100.000 32 0 0 214 245 399614125 399614156 5.620000e-05 60.2
53 TraesCS1D01G289800 chr7D 88.679 53 5 1 49 101 389190572 389190623 4.340000e-06 63.9


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 TraesCS1D01G289800 chr1D 387893938 387899132 5194 True 3334.000000 9594 94.183333 1 5195 3 chr1D.!!$R2 5194
1 TraesCS1D01G289800 chr1D 387796506 387801089 4583 True 335.750000 961 85.877875 681 4383 8 chr1D.!!$R1 3702
2 TraesCS1D01G289800 chr1A 487462368 487469924 7556 True 1253.833333 3195 93.058833 51 5195 6 chr1A.!!$R2 5144
3 TraesCS1D01G289800 chr1A 487330259 487333848 3589 True 329.737500 894 86.639750 1017 4383 8 chr1A.!!$R1 3366
4 TraesCS1D01G289800 chr1B 520998750 521003144 4394 True 1608.250000 2588 92.636250 2 4521 4 chr1B.!!$R2 4519
5 TraesCS1D01G289800 chr1B 520926057 520929411 3354 True 339.311111 891 86.716000 722 4202 9 chr1B.!!$R1 3480
6 TraesCS1D01G289800 chr3A 194677142 194677909 767 False 484.000000 484 78.382000 4413 5195 1 chr3A.!!$F1 782
7 TraesCS1D01G289800 chr5D 117355137 117355858 721 False 379.000000 379 76.542000 4415 5152 1 chr5D.!!$F1 737

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
648 659 1.679898 CTGCTCCCGGTCCTTTTCT 59.320 57.895 0.00 0.00 0.00 2.52 F
1260 4125 0.109532 TGGTGGAGTGGAATTTCGCA 59.890 50.000 0.00 0.00 0.00 5.10 F
2053 5356 0.036306 CCTTTGCCTTACTGTCCGGT 59.964 55.000 0.00 0.00 0.00 5.28 F
2225 5536 0.548989 CCCGTTCATCCCAATGGGTA 59.451 55.000 19.28 5.53 44.84 3.69 F
2675 6024 1.646912 TTTGTACTCCATCCGTCCCA 58.353 50.000 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 5351 0.320374 ATTCAAACAGAGCGACCGGA 59.680 50.00 9.46 0.0 0.00 5.14 R
2724 6073 0.192566 ACTCCCTCCGCCCCATAATA 59.807 55.00 0.00 0.0 0.00 0.98 R
2996 6735 5.824904 ATCAATAACTGAGGCATGTGAAC 57.175 39.13 0.00 0.0 37.52 3.18 R
3223 6967 5.944007 GCTTATTGACACTCCCTAAGGAAAA 59.056 40.00 0.00 0.0 43.40 2.29 R
4618 9165 1.122019 ACTGCCTTCAACCTCCGTCT 61.122 55.00 0.00 0.0 0.00 4.18 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
31 32 9.707957 ACATAATTAATCTTGGGACCAACATTA 57.292 29.630 7.45 7.45 29.77 1.90
42 43 8.722622 TTGGGACCAACATTAATTAAGGTAAA 57.277 30.769 15.28 4.82 29.18 2.01
48 49 9.869757 ACCAACATTAATTAAGGTAAATCTTGC 57.130 29.630 15.28 0.00 29.18 4.01
96 97 2.986141 CGTGCACGCACACAATTAG 58.014 52.632 28.16 0.00 46.47 1.73
116 117 8.564574 CAATTAGTAGTCTTTGGTAAGCAACAA 58.435 33.333 0.00 0.00 0.00 2.83
120 121 4.270008 AGTCTTTGGTAAGCAACAAGTGT 58.730 39.130 0.00 0.00 0.00 3.55
276 283 5.804692 ATCACGGTGATTGCGTATAAAAA 57.195 34.783 17.62 0.00 32.13 1.94
314 321 3.611517 CAACGCACTGCAATTATCTAGC 58.388 45.455 1.11 0.00 0.00 3.42
351 358 6.824305 GAGATCAACTCATTCCCTCAAAAA 57.176 37.500 0.00 0.00 44.36 1.94
544 551 1.922447 AGGGTTCATCCAGCCACATAA 59.078 47.619 0.00 0.00 36.72 1.90
648 659 1.679898 CTGCTCCCGGTCCTTTTCT 59.320 57.895 0.00 0.00 0.00 2.52
697 3435 6.300703 AGAGATAAGTGTAGCCAGTAGTAGG 58.699 44.000 0.00 0.00 0.00 3.18
1139 3971 4.980903 CAACAGCAACGGCCACGC 62.981 66.667 2.24 0.80 46.04 5.34
1260 4125 0.109532 TGGTGGAGTGGAATTTCGCA 59.890 50.000 0.00 0.00 0.00 5.10
1606 4902 2.239907 ACTGTTCCTCTTTCCCTATGCC 59.760 50.000 0.00 0.00 0.00 4.40
1659 4959 7.423844 AAAGGAACAAGAAATTTGACCTTCT 57.576 32.000 16.33 0.00 38.04 2.85
1661 4961 7.043961 AGGAACAAGAAATTTGACCTTCTTC 57.956 36.000 0.00 0.00 39.34 2.87
1916 5216 2.034048 GAAGGGCTGGGAGATCGACC 62.034 65.000 0.00 2.15 0.00 4.79
1996 5296 1.138036 CAATCCATGTGGCAGCGTG 59.862 57.895 0.00 0.00 34.44 5.34
2029 5329 3.181459 ACCATTTGGCCAAGGTTTTACAC 60.181 43.478 20.91 0.00 39.32 2.90
2044 5347 4.390129 TTTACACCCATCCTTTGCCTTA 57.610 40.909 0.00 0.00 0.00 2.69
2047 5350 2.094675 CACCCATCCTTTGCCTTACTG 58.905 52.381 0.00 0.00 0.00 2.74
2048 5351 1.710809 ACCCATCCTTTGCCTTACTGT 59.289 47.619 0.00 0.00 0.00 3.55
2049 5352 2.290960 ACCCATCCTTTGCCTTACTGTC 60.291 50.000 0.00 0.00 0.00 3.51
2050 5353 2.369394 CCATCCTTTGCCTTACTGTCC 58.631 52.381 0.00 0.00 0.00 4.02
2051 5354 2.009774 CATCCTTTGCCTTACTGTCCG 58.990 52.381 0.00 0.00 0.00 4.79
2052 5355 0.323629 TCCTTTGCCTTACTGTCCGG 59.676 55.000 0.00 0.00 0.00 5.14
2053 5356 0.036306 CCTTTGCCTTACTGTCCGGT 59.964 55.000 0.00 0.00 0.00 5.28
2054 5357 1.439679 CTTTGCCTTACTGTCCGGTC 58.560 55.000 0.00 0.00 0.00 4.79
2225 5536 0.548989 CCCGTTCATCCCAATGGGTA 59.451 55.000 19.28 5.53 44.84 3.69
2371 5686 6.621613 GGTAACTCCCAATCATTCTTTTCAC 58.378 40.000 0.00 0.00 0.00 3.18
2673 6022 9.886132 ATAAATATATTTGTACTCCATCCGTCC 57.114 33.333 18.98 0.00 0.00 4.79
2674 6023 4.618920 ATATTTGTACTCCATCCGTCCC 57.381 45.455 0.00 0.00 0.00 4.46
2675 6024 1.646912 TTTGTACTCCATCCGTCCCA 58.353 50.000 0.00 0.00 0.00 4.37
2676 6025 1.874129 TTGTACTCCATCCGTCCCAT 58.126 50.000 0.00 0.00 0.00 4.00
2677 6026 2.759839 TGTACTCCATCCGTCCCATA 57.240 50.000 0.00 0.00 0.00 2.74
2678 6027 3.035055 TGTACTCCATCCGTCCCATAA 57.965 47.619 0.00 0.00 0.00 1.90
2679 6028 3.583228 TGTACTCCATCCGTCCCATAAT 58.417 45.455 0.00 0.00 0.00 1.28
2680 6029 3.323691 TGTACTCCATCCGTCCCATAATG 59.676 47.826 0.00 0.00 0.00 1.90
2681 6030 2.408565 ACTCCATCCGTCCCATAATGT 58.591 47.619 0.00 0.00 0.00 2.71
2682 6031 3.583228 ACTCCATCCGTCCCATAATGTA 58.417 45.455 0.00 0.00 0.00 2.29
2683 6032 3.971305 ACTCCATCCGTCCCATAATGTAA 59.029 43.478 0.00 0.00 0.00 2.41
2684 6033 4.410883 ACTCCATCCGTCCCATAATGTAAA 59.589 41.667 0.00 0.00 0.00 2.01
2685 6034 5.104277 ACTCCATCCGTCCCATAATGTAAAA 60.104 40.000 0.00 0.00 0.00 1.52
2686 6035 5.947663 TCCATCCGTCCCATAATGTAAAAT 58.052 37.500 0.00 0.00 0.00 1.82
2687 6036 5.767665 TCCATCCGTCCCATAATGTAAAATG 59.232 40.000 0.00 0.00 0.00 2.32
2688 6037 5.534654 CCATCCGTCCCATAATGTAAAATGT 59.465 40.000 0.00 0.00 0.00 2.71
2689 6038 6.040391 CCATCCGTCCCATAATGTAAAATGTT 59.960 38.462 0.00 0.00 0.00 2.71
2690 6039 7.417342 CCATCCGTCCCATAATGTAAAATGTTT 60.417 37.037 0.00 0.00 0.00 2.83
2691 6040 7.469537 TCCGTCCCATAATGTAAAATGTTTT 57.530 32.000 0.00 0.00 0.00 2.43
2692 6041 7.897864 TCCGTCCCATAATGTAAAATGTTTTT 58.102 30.769 0.00 0.00 0.00 1.94
2735 6084 5.934935 AAAACGTCTTATATTATGGGGCG 57.065 39.130 0.00 0.00 0.00 6.13
2736 6085 3.604875 ACGTCTTATATTATGGGGCGG 57.395 47.619 8.67 0.00 0.00 6.13
2737 6086 3.167485 ACGTCTTATATTATGGGGCGGA 58.833 45.455 8.67 0.00 0.00 5.54
2738 6087 3.194968 ACGTCTTATATTATGGGGCGGAG 59.805 47.826 8.67 0.00 0.00 4.63
2739 6088 3.430374 CGTCTTATATTATGGGGCGGAGG 60.430 52.174 0.00 0.00 0.00 4.30
2740 6089 3.112263 TCTTATATTATGGGGCGGAGGG 58.888 50.000 0.00 0.00 0.00 4.30
2820 6170 8.746530 ACTGAACCGACTATTGAATAGAACTAA 58.253 33.333 18.39 0.00 36.68 2.24
2996 6735 6.816640 TCCTTGACGTTATTGTTCTCTTATGG 59.183 38.462 0.00 0.00 0.00 2.74
3008 6747 4.142609 TCTCTTATGGTTCACATGCCTC 57.857 45.455 0.00 0.00 40.82 4.70
3206 6945 5.979993 TCGATGTTTGTAATGGTAAGCCTA 58.020 37.500 0.00 0.00 35.27 3.93
3651 7412 7.337942 AGGTAGGACTGCATTTTCTCATTTAAG 59.662 37.037 0.00 0.00 0.00 1.85
4031 8350 7.832503 ACTTTTGACAATTCTCAAAAACAGG 57.167 32.000 18.38 11.48 45.24 4.00
4324 8856 0.975040 TGTTATGGTTGCCATGGCCC 60.975 55.000 33.44 27.03 44.84 5.80
4438 8982 3.266510 AGAGAAAATGCATGTCGCCTA 57.733 42.857 0.00 0.00 41.33 3.93
4476 9020 3.181483 CCCAACAAGCCAAATCATAGAGC 60.181 47.826 0.00 0.00 0.00 4.09
4597 9144 2.771943 ACCAGAAGTCACACTCCAAAGA 59.228 45.455 0.00 0.00 0.00 2.52
4605 9152 0.475906 ACACTCCAAAGAGCTGGCTT 59.524 50.000 0.00 0.00 44.65 4.35
4770 9325 8.184192 GGACAGTTAGGAAATACATGTTCAATG 58.816 37.037 2.30 0.00 0.00 2.82
4788 9344 7.012894 TGTTCAATGTAAACTTGTTCCTAGTGG 59.987 37.037 0.00 0.00 0.00 4.00
4792 9348 4.657039 TGTAAACTTGTTCCTAGTGGTCCT 59.343 41.667 0.00 0.00 34.23 3.85
4794 9350 2.258109 ACTTGTTCCTAGTGGTCCTCC 58.742 52.381 0.00 0.00 34.23 4.30
4795 9351 2.257207 CTTGTTCCTAGTGGTCCTCCA 58.743 52.381 0.00 0.00 42.05 3.86
4796 9352 2.409064 TGTTCCTAGTGGTCCTCCAA 57.591 50.000 0.00 0.00 46.15 3.53
4837 9393 3.390135 CAAAGGCGAACTAGAAGACACA 58.610 45.455 0.00 0.00 0.00 3.72
4838 9394 3.746045 AAGGCGAACTAGAAGACACAA 57.254 42.857 0.00 0.00 0.00 3.33
4843 9399 2.351447 CGAACTAGAAGACACAAGCCGA 60.351 50.000 0.00 0.00 0.00 5.54
4845 9401 3.963428 ACTAGAAGACACAAGCCGATT 57.037 42.857 0.00 0.00 0.00 3.34
4890 9446 4.963318 TTCAAGAGATCCACACAACTCT 57.037 40.909 0.00 0.00 40.75 3.24
4896 9452 1.351017 GATCCACACAACTCTTGGGGA 59.649 52.381 0.00 0.00 38.76 4.81
4898 9454 0.890996 CCACACAACTCTTGGGGAGC 60.891 60.000 0.00 0.00 45.48 4.70
4899 9455 0.890996 CACACAACTCTTGGGGAGCC 60.891 60.000 0.00 0.00 45.48 4.70
4914 9470 2.501316 GGGAGCCCAATTGCAATTAAGT 59.499 45.455 23.69 9.43 35.81 2.24
4918 9474 3.196254 AGCCCAATTGCAATTAAGTCAGG 59.804 43.478 23.69 18.27 0.00 3.86
4919 9475 3.195396 GCCCAATTGCAATTAAGTCAGGA 59.805 43.478 23.69 0.00 0.00 3.86
4956 9513 2.531055 CCAAACTTGGCCAAATGCG 58.469 52.632 20.91 10.38 42.21 4.73
5142 9699 2.555325 CCTTAAAAAGGTTGTCCCGACC 59.445 50.000 0.00 0.00 43.95 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.868277 TGCAAGATTTACCTTAATTAATGTTGG 57.132 29.630 10.80 5.72 34.01 3.77
91 92 8.685838 TTGTTGCTTACCAAAGACTACTAATT 57.314 30.769 0.00 0.00 34.68 1.40
96 97 5.296035 ACACTTGTTGCTTACCAAAGACTAC 59.704 40.000 0.00 0.00 34.68 2.73
116 117 9.034544 GCACTTTCTTCAAAAATAATCAACACT 57.965 29.630 0.00 0.00 0.00 3.55
120 121 7.429633 TCGGCACTTTCTTCAAAAATAATCAA 58.570 30.769 0.00 0.00 0.00 2.57
141 144 4.181309 TGGTTTCATTTGGTAAATCGGC 57.819 40.909 0.00 0.00 0.00 5.54
314 321 6.039717 TGAGTTGATCTCTTTCTTTTGTTGGG 59.960 38.462 0.00 0.00 43.13 4.12
419 426 2.877300 GCCAGTGAGGAATGACACACAT 60.877 50.000 0.00 0.00 41.22 3.21
514 521 4.227197 CTGGATGAACCCTCCTACTACAT 58.773 47.826 0.00 0.00 38.00 2.29
515 522 3.643237 CTGGATGAACCCTCCTACTACA 58.357 50.000 0.00 0.00 38.00 2.74
544 551 2.099098 CCAGTTCCGCTCAAAGTGTTTT 59.901 45.455 0.00 0.00 0.00 2.43
697 3435 1.377333 GGCAGCACCAAGGAGTACC 60.377 63.158 0.00 0.00 38.86 3.34
1234 4093 3.706373 CCACTCCACCACCTCCGG 61.706 72.222 0.00 0.00 0.00 5.14
1241 4106 0.109532 TGCGAAATTCCACTCCACCA 59.890 50.000 0.00 0.00 0.00 4.17
1606 4902 7.269477 ACTGAAGAAGGTCAAATTTCTGAAG 57.731 36.000 0.00 0.00 34.09 3.02
1642 4942 5.302823 AGGTGGAAGAAGGTCAAATTTCTTG 59.697 40.000 4.38 0.00 42.13 3.02
1659 4959 3.131400 GGCACTGTTTTTACAAGGTGGAA 59.869 43.478 0.00 0.00 0.00 3.53
1661 4961 2.542824 CGGCACTGTTTTTACAAGGTGG 60.543 50.000 0.00 0.00 0.00 4.61
1916 5216 0.387202 ATGGATTCCAGCGAGTCGAG 59.613 55.000 18.61 7.62 36.75 4.04
1996 5296 2.547826 GCCAAATGGTCGTAGGAGTAC 58.452 52.381 0.71 0.00 37.57 2.73
2029 5329 2.369394 GACAGTAAGGCAAAGGATGGG 58.631 52.381 0.00 0.00 0.00 4.00
2044 5347 1.745320 AAACAGAGCGACCGGACAGT 61.745 55.000 9.46 0.00 0.00 3.55
2047 5350 0.599204 TTCAAACAGAGCGACCGGAC 60.599 55.000 9.46 0.00 0.00 4.79
2048 5351 0.320374 ATTCAAACAGAGCGACCGGA 59.680 50.000 9.46 0.00 0.00 5.14
2049 5352 2.004583 TATTCAAACAGAGCGACCGG 57.995 50.000 0.00 0.00 0.00 5.28
2050 5353 2.285220 CCATATTCAAACAGAGCGACCG 59.715 50.000 0.00 0.00 0.00 4.79
2051 5354 3.531538 TCCATATTCAAACAGAGCGACC 58.468 45.455 0.00 0.00 0.00 4.79
2052 5355 5.294306 TGAATCCATATTCAAACAGAGCGAC 59.706 40.000 0.00 0.00 46.64 5.19
2053 5356 5.427378 TGAATCCATATTCAAACAGAGCGA 58.573 37.500 0.00 0.00 46.64 4.93
2054 5357 5.739752 TGAATCCATATTCAAACAGAGCG 57.260 39.130 0.00 0.00 46.64 5.03
2077 5388 2.915738 GAAGAATTCAGCAGGTGCAG 57.084 50.000 8.44 0.00 46.62 4.41
2352 5663 5.105473 AGCATGTGAAAAGAATGATTGGGAG 60.105 40.000 0.00 0.00 0.00 4.30
2371 5686 7.660208 AGTTTAATTAATCCCCGTAGTAGCATG 59.340 37.037 0.00 0.00 0.00 4.06
2503 5821 4.202131 GGACAAGGAGGAGTAAATACCGAG 60.202 50.000 0.00 0.00 0.00 4.63
2609 5958 4.772046 TTGACTTCGACTTTCAAACTCG 57.228 40.909 1.05 0.00 0.00 4.18
2650 5999 6.271391 TGGGACGGATGGAGTACAAATATATT 59.729 38.462 0.00 0.00 0.00 1.28
2661 6010 2.408565 ACATTATGGGACGGATGGAGT 58.591 47.619 0.00 0.00 0.00 3.85
2662 6011 4.617253 TTACATTATGGGACGGATGGAG 57.383 45.455 0.00 0.00 0.00 3.86
2663 6012 5.375283 TTTTACATTATGGGACGGATGGA 57.625 39.130 0.00 0.00 0.00 3.41
2664 6013 5.534654 ACATTTTACATTATGGGACGGATGG 59.465 40.000 0.00 0.00 0.00 3.51
2665 6014 6.633500 ACATTTTACATTATGGGACGGATG 57.367 37.500 0.00 0.00 0.00 3.51
2666 6015 7.654022 AAACATTTTACATTATGGGACGGAT 57.346 32.000 0.00 0.00 0.00 4.18
2667 6016 7.469537 AAAACATTTTACATTATGGGACGGA 57.530 32.000 0.00 0.00 0.00 4.69
2712 6061 5.239963 CCGCCCCATAATATAAGACGTTTTT 59.760 40.000 0.00 0.00 0.00 1.94
2713 6062 4.758165 CCGCCCCATAATATAAGACGTTTT 59.242 41.667 0.00 0.00 0.00 2.43
2714 6063 4.040706 TCCGCCCCATAATATAAGACGTTT 59.959 41.667 0.00 0.00 0.00 3.60
2715 6064 3.579586 TCCGCCCCATAATATAAGACGTT 59.420 43.478 0.00 0.00 0.00 3.99
2716 6065 3.167485 TCCGCCCCATAATATAAGACGT 58.833 45.455 0.00 0.00 0.00 4.34
2717 6066 3.430374 CCTCCGCCCCATAATATAAGACG 60.430 52.174 0.00 0.00 0.00 4.18
2718 6067 3.118371 CCCTCCGCCCCATAATATAAGAC 60.118 52.174 0.00 0.00 0.00 3.01
2719 6068 3.112263 CCCTCCGCCCCATAATATAAGA 58.888 50.000 0.00 0.00 0.00 2.10
2720 6069 3.112263 TCCCTCCGCCCCATAATATAAG 58.888 50.000 0.00 0.00 0.00 1.73
2721 6070 3.112263 CTCCCTCCGCCCCATAATATAA 58.888 50.000 0.00 0.00 0.00 0.98
2722 6071 2.045326 ACTCCCTCCGCCCCATAATATA 59.955 50.000 0.00 0.00 0.00 0.86
2723 6072 1.203440 ACTCCCTCCGCCCCATAATAT 60.203 52.381 0.00 0.00 0.00 1.28
2724 6073 0.192566 ACTCCCTCCGCCCCATAATA 59.807 55.000 0.00 0.00 0.00 0.98
2725 6074 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
2726 6075 0.471211 CTACTCCCTCCGCCCCATAA 60.471 60.000 0.00 0.00 0.00 1.90
2727 6076 1.155390 CTACTCCCTCCGCCCCATA 59.845 63.158 0.00 0.00 0.00 2.74
2728 6077 2.122813 CTACTCCCTCCGCCCCAT 60.123 66.667 0.00 0.00 0.00 4.00
2729 6078 1.877672 TAACTACTCCCTCCGCCCCA 61.878 60.000 0.00 0.00 0.00 4.96
2730 6079 0.471401 ATAACTACTCCCTCCGCCCC 60.471 60.000 0.00 0.00 0.00 5.80
2731 6080 1.421480 AATAACTACTCCCTCCGCCC 58.579 55.000 0.00 0.00 0.00 6.13
2732 6081 3.244009 GGTAAATAACTACTCCCTCCGCC 60.244 52.174 0.00 0.00 0.00 6.13
2733 6082 3.640498 AGGTAAATAACTACTCCCTCCGC 59.360 47.826 0.00 0.00 0.00 5.54
2734 6083 5.866159 AAGGTAAATAACTACTCCCTCCG 57.134 43.478 0.00 0.00 0.00 4.63
2735 6084 6.955364 ACAAAGGTAAATAACTACTCCCTCC 58.045 40.000 0.00 0.00 0.00 4.30
2736 6085 8.727910 CAAACAAAGGTAAATAACTACTCCCTC 58.272 37.037 0.00 0.00 0.00 4.30
2737 6086 7.176165 GCAAACAAAGGTAAATAACTACTCCCT 59.824 37.037 0.00 0.00 0.00 4.20
2738 6087 7.176165 AGCAAACAAAGGTAAATAACTACTCCC 59.824 37.037 0.00 0.00 0.00 4.30
2739 6088 8.107399 AGCAAACAAAGGTAAATAACTACTCC 57.893 34.615 0.00 0.00 0.00 3.85
2740 6089 9.961265 AAAGCAAACAAAGGTAAATAACTACTC 57.039 29.630 0.00 0.00 0.00 2.59
2836 6547 8.041323 ACATACTTGACCGAGAAGAATACAATT 58.959 33.333 0.00 0.00 0.00 2.32
2996 6735 5.824904 ATCAATAACTGAGGCATGTGAAC 57.175 39.130 0.00 0.00 37.52 3.18
3223 6967 5.944007 GCTTATTGACACTCCCTAAGGAAAA 59.056 40.000 0.00 0.00 43.40 2.29
3337 7083 6.741992 TTCTTCGAATACATGCATCTTTGT 57.258 33.333 0.00 0.00 0.00 2.83
4350 8883 5.171476 AGATCTTCGACACCAATGTAACTG 58.829 41.667 0.00 0.00 39.95 3.16
4388 8921 7.981102 AAGAGAATGTGTACTTAAAGTTCCC 57.019 36.000 0.00 0.00 0.00 3.97
4431 8975 6.368243 GGGCTTTATCTATAAAGTTAGGCGAC 59.632 42.308 18.85 0.00 46.78 5.19
4438 8982 7.147897 GGCTTGTTGGGCTTTATCTATAAAGTT 60.148 37.037 18.85 0.00 46.78 2.66
4476 9020 2.752354 TGTGAACTGGTCCTGTTTGTTG 59.248 45.455 14.68 0.00 0.00 3.33
4618 9165 1.122019 ACTGCCTTCAACCTCCGTCT 61.122 55.000 0.00 0.00 0.00 4.18
4770 9325 5.224821 AGGACCACTAGGAACAAGTTTAC 57.775 43.478 0.00 0.00 38.69 2.01
4781 9337 3.146847 GTGTTTTTGGAGGACCACTAGG 58.853 50.000 0.00 0.00 46.80 3.02
4788 9344 1.754226 TGCTTGGTGTTTTTGGAGGAC 59.246 47.619 0.00 0.00 0.00 3.85
4792 9348 3.006247 GCTTTTGCTTGGTGTTTTTGGA 58.994 40.909 0.00 0.00 43.35 3.53
4827 9383 2.972625 CCAATCGGCTTGTGTCTTCTA 58.027 47.619 0.00 0.00 32.61 2.10
4843 9399 6.603940 TTGCAAATTCTTTAGTAGGCCAAT 57.396 33.333 5.01 0.00 0.00 3.16
4845 9401 7.896383 ATATTGCAAATTCTTTAGTAGGCCA 57.104 32.000 5.01 0.00 0.00 5.36
4855 9411 8.974238 TGGATCTCTTGAATATTGCAAATTCTT 58.026 29.630 22.99 9.58 34.95 2.52
4874 9430 2.616510 CCCCAAGAGTTGTGTGGATCTC 60.617 54.545 0.00 0.00 34.05 2.75
4896 9452 3.196254 CCTGACTTAATTGCAATTGGGCT 59.804 43.478 30.43 12.75 34.04 5.19
4898 9454 4.706476 TCTCCTGACTTAATTGCAATTGGG 59.294 41.667 30.43 23.58 0.00 4.12
4899 9455 5.678107 GCTCTCCTGACTTAATTGCAATTGG 60.678 44.000 30.43 23.87 0.00 3.16
4905 9461 2.893637 TCGCTCTCCTGACTTAATTGC 58.106 47.619 0.00 0.00 0.00 3.56
4914 9470 1.181741 AGCTGTGTTCGCTCTCCTGA 61.182 55.000 0.00 0.00 30.49 3.86
5142 9699 4.087892 CCCGTCTCTGTGCTGGGG 62.088 72.222 0.00 0.00 36.16 4.96


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

AutoCloner maintained by Alex Coulton.