Multiple sequence alignment - TraesCS2A01G075600

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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 TraesCS2A01G075600 chr2A 100.000 4681 0 0 1 4681 33579336 33574656 0.000000e+00 8645.0
1 TraesCS2A01G075600 chr2A 92.593 621 30 9 4068 4681 33707910 33708521 0.000000e+00 878.0
2 TraesCS2A01G075600 chr2A 92.063 63 3 2 103 164 33579187 33579126 2.320000e-13 87.9
3 TraesCS2A01G075600 chr2A 92.063 63 3 2 150 211 33579234 33579173 2.320000e-13 87.9
4 TraesCS2A01G075600 chr6A 92.628 3988 137 30 25 3936 15883178 15887084 0.000000e+00 5590.0
5 TraesCS2A01G075600 chr6A 86.754 536 61 6 2630 3162 501229253 501228725 5.220000e-164 588.0
6 TraesCS2A01G075600 chr6A 94.565 92 5 0 3932 4023 15887163 15887254 4.880000e-30 143.0
7 TraesCS2A01G075600 chr6A 100.000 53 0 0 150 202 15883256 15883308 1.070000e-16 99.0
8 TraesCS2A01G075600 chr7A 97.418 2788 61 6 1253 4036 696711255 696714035 0.000000e+00 4739.0
9 TraesCS2A01G075600 chr7A 94.386 1140 26 6 150 1254 696710036 696711172 0.000000e+00 1716.0
10 TraesCS2A01G075600 chr7A 88.398 1336 87 20 2724 4023 316028460 316029763 0.000000e+00 1546.0
11 TraesCS2A01G075600 chr7A 93.537 820 43 3 1697 2508 316027063 316027880 0.000000e+00 1212.0
12 TraesCS2A01G075600 chr7A 92.317 846 54 6 845 1684 316025745 316026585 0.000000e+00 1192.0
13 TraesCS2A01G075600 chr7A 87.575 837 66 15 1697 2530 130083052 130082251 0.000000e+00 935.0
14 TraesCS2A01G075600 chr7A 84.412 680 72 19 150 804 316025077 316025747 5.110000e-179 638.0
15 TraesCS2A01G075600 chr7A 88.302 530 45 9 1697 2224 33512173 33512687 1.850000e-173 619.0
16 TraesCS2A01G075600 chr7A 93.548 155 9 1 1 155 696709935 696710088 3.640000e-56 230.0
17 TraesCS2A01G075600 chr7A 92.308 156 12 0 2525 2680 316028306 316028461 6.100000e-54 222.0
18 TraesCS2A01G075600 chr6D 93.702 2191 71 15 92 2233 436650133 436652305 0.000000e+00 3219.0
19 TraesCS2A01G075600 chr6D 96.898 1483 44 2 2230 3710 436664894 436666376 0.000000e+00 2483.0
20 TraesCS2A01G075600 chr6D 95.595 227 8 1 3797 4023 436666373 436666597 3.440000e-96 363.0
21 TraesCS2A01G075600 chr6D 98.113 53 1 0 150 202 436650144 436650196 4.990000e-15 93.5
22 TraesCS2A01G075600 chr7D 89.254 1582 107 24 150 1684 279737713 279736148 0.000000e+00 1921.0
23 TraesCS2A01G075600 chr7D 89.347 1333 77 23 2727 4023 279734299 279732996 0.000000e+00 1615.0
24 TraesCS2A01G075600 chr7D 93.873 816 38 5 1697 2508 279735670 279734863 0.000000e+00 1219.0
25 TraesCS2A01G075600 chr7B 88.486 1598 108 24 150 1684 253702743 253704327 0.000000e+00 1862.0
26 TraesCS2A01G075600 chr7B 88.545 1196 76 20 2844 4001 253704879 253706051 0.000000e+00 1393.0
27 TraesCS2A01G075600 chr7B 82.440 336 41 13 3305 3625 711517528 711517860 1.280000e-70 278.0
28 TraesCS2A01G075600 chr7B 96.703 91 3 0 2233 2323 253704793 253704883 8.110000e-33 152.0
29 TraesCS2A01G075600 chr2B 88.564 1233 86 28 2829 4023 69359368 69360583 0.000000e+00 1445.0
30 TraesCS2A01G075600 chr2B 89.474 608 52 8 4069 4676 51863508 51862913 0.000000e+00 758.0
31 TraesCS2A01G075600 chr2B 89.327 609 56 5 4068 4676 52096228 52096827 0.000000e+00 756.0
32 TraesCS2A01G075600 chr2B 88.418 613 57 5 4068 4676 51859512 51858910 0.000000e+00 726.0
33 TraesCS2A01G075600 chr2B 94.079 152 8 1 2527 2678 69351838 69351988 3.640000e-56 230.0
34 TraesCS2A01G075600 chr3D 95.760 849 34 2 2486 3333 495792466 495793313 0.000000e+00 1367.0
35 TraesCS2A01G075600 chr3D 96.006 651 25 1 2672 3321 495793477 495794127 0.000000e+00 1057.0
36 TraesCS2A01G075600 chr3D 95.023 663 29 2 2672 3333 495794303 495794962 0.000000e+00 1038.0
37 TraesCS2A01G075600 chr3D 90.034 582 24 8 3317 3879 495798498 495799064 0.000000e+00 723.0
38 TraesCS2A01G075600 chr3D 93.798 129 8 0 3895 4023 495804086 495804214 1.330000e-45 195.0
39 TraesCS2A01G075600 chr3D 81.667 180 20 5 813 979 546332745 546332566 2.270000e-28 137.0
40 TraesCS2A01G075600 chr1B 86.414 1001 85 24 3058 4017 589511285 589512275 0.000000e+00 1048.0
41 TraesCS2A01G075600 chr1B 93.913 115 7 0 2527 2641 589508027 589508141 1.730000e-39 174.0
42 TraesCS2A01G075600 chr5A 87.455 837 64 16 1697 2530 353160705 353159907 0.000000e+00 926.0
43 TraesCS2A01G075600 chr4A 92.926 622 34 5 1697 2315 740771527 740772141 0.000000e+00 896.0
44 TraesCS2A01G075600 chr4A 92.063 189 15 0 2313 2501 740774559 740774747 2.780000e-67 267.0
45 TraesCS2A01G075600 chr4A 95.455 66 3 0 1619 1684 740771011 740771076 6.410000e-19 106.0
46 TraesCS2A01G075600 chr4A 96.491 57 2 0 2261 2317 740772143 740772199 1.390000e-15 95.3
47 TraesCS2A01G075600 chr6B 85.934 519 55 9 2630 3145 678292045 678291542 5.330000e-149 538.0
48 TraesCS2A01G075600 chr6B 81.337 359 47 10 3308 3649 211692939 211692584 1.660000e-69 274.0
49 TraesCS2A01G075600 chr5B 84.423 520 48 15 1697 2215 123406805 123407292 9.110000e-132 481.0
50 TraesCS2A01G075600 chr5B 84.190 525 50 17 1697 2220 123206471 123206963 3.280000e-131 479.0
51 TraesCS2A01G075600 chr2D 79.558 543 74 17 4068 4604 31750316 31749805 2.070000e-93 353.0
52 TraesCS2A01G075600 chr3A 100.000 34 0 0 4035 4068 235675 235708 3.910000e-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 TraesCS2A01G075600 chr2A 33574656 33579336 4680 True 2940.266667 8645 94.708667 1 4681 3 chr2A.!!$R1 4680
1 TraesCS2A01G075600 chr2A 33707910 33708521 611 False 878.000000 878 92.593000 4068 4681 1 chr2A.!!$F1 613
2 TraesCS2A01G075600 chr6A 15883178 15887254 4076 False 1944.000000 5590 95.731000 25 4023 3 chr6A.!!$F1 3998
3 TraesCS2A01G075600 chr6A 501228725 501229253 528 True 588.000000 588 86.754000 2630 3162 1 chr6A.!!$R1 532
4 TraesCS2A01G075600 chr7A 696709935 696714035 4100 False 2228.333333 4739 95.117333 1 4036 3 chr7A.!!$F3 4035
5 TraesCS2A01G075600 chr7A 316025077 316029763 4686 False 962.000000 1546 90.194400 150 4023 5 chr7A.!!$F2 3873
6 TraesCS2A01G075600 chr7A 130082251 130083052 801 True 935.000000 935 87.575000 1697 2530 1 chr7A.!!$R1 833
7 TraesCS2A01G075600 chr7A 33512173 33512687 514 False 619.000000 619 88.302000 1697 2224 1 chr7A.!!$F1 527
8 TraesCS2A01G075600 chr6D 436650133 436652305 2172 False 1656.250000 3219 95.907500 92 2233 2 chr6D.!!$F1 2141
9 TraesCS2A01G075600 chr6D 436664894 436666597 1703 False 1423.000000 2483 96.246500 2230 4023 2 chr6D.!!$F2 1793
10 TraesCS2A01G075600 chr7D 279732996 279737713 4717 True 1585.000000 1921 90.824667 150 4023 3 chr7D.!!$R1 3873
11 TraesCS2A01G075600 chr7B 253702743 253706051 3308 False 1135.666667 1862 91.244667 150 4001 3 chr7B.!!$F2 3851
12 TraesCS2A01G075600 chr2B 69359368 69360583 1215 False 1445.000000 1445 88.564000 2829 4023 1 chr2B.!!$F3 1194
13 TraesCS2A01G075600 chr2B 52096228 52096827 599 False 756.000000 756 89.327000 4068 4676 1 chr2B.!!$F1 608
14 TraesCS2A01G075600 chr2B 51858910 51863508 4598 True 742.000000 758 88.946000 4068 4676 2 chr2B.!!$R1 608
15 TraesCS2A01G075600 chr3D 495792466 495799064 6598 False 1046.250000 1367 94.205750 2486 3879 4 chr3D.!!$F2 1393
16 TraesCS2A01G075600 chr1B 589508027 589512275 4248 False 611.000000 1048 90.163500 2527 4017 2 chr1B.!!$F1 1490
17 TraesCS2A01G075600 chr5A 353159907 353160705 798 True 926.000000 926 87.455000 1697 2530 1 chr5A.!!$R1 833
18 TraesCS2A01G075600 chr4A 740771011 740774747 3736 False 341.075000 896 94.233750 1619 2501 4 chr4A.!!$F1 882
19 TraesCS2A01G075600 chr6B 678291542 678292045 503 True 538.000000 538 85.934000 2630 3145 1 chr6B.!!$R2 515
20 TraesCS2A01G075600 chr2D 31749805 31750316 511 True 353.000000 353 79.558000 4068 4604 1 chr2D.!!$R1 536

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
72 73 1.228521 CATCAAGGTGTGGGTGCCA 60.229 57.895 0.00 0.00 0.00 4.92 F
373 425 1.679305 AGGACACCGTCGCAGATCT 60.679 57.895 0.00 0.00 40.67 2.75 F
1220 1351 0.807496 GCAGGCACTCTCATTTGTCC 59.193 55.000 0.00 0.00 34.60 4.02 F
2136 2861 3.939592 GAGTACCTTTTCCTTGGAATCGG 59.060 47.826 2.65 8.93 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1351 0.912486 AGAAAGGATCGGAAGGGTGG 59.088 55.0 0.00 0.0 0.00 4.61 R
2336 5497 0.829333 AGCATCATCTCTTGACCGCT 59.171 50.0 0.00 0.0 40.11 5.52 R
3152 11012 0.906066 TGCAGGTATTGAGCGGGTAA 59.094 50.0 0.00 0.0 0.00 2.85 R
4054 15620 0.027324 GTAGTCGGTCTTCGTAGCGG 59.973 60.0 6.86 0.0 40.61 5.52 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
23 24 1.913762 CCCGTCCACTGGAGAAGGT 60.914 63.158 0.00 0.00 29.39 3.50
56 57 2.512515 GCTTCTCGCCCTTCGCAT 60.513 61.111 0.00 0.00 37.30 4.73
72 73 1.228521 CATCAAGGTGTGGGTGCCA 60.229 57.895 0.00 0.00 0.00 4.92
82 83 3.325753 GGGTGCCAGAGGAGCAGT 61.326 66.667 0.00 0.00 41.87 4.40
83 84 2.046507 GGTGCCAGAGGAGCAGTG 60.047 66.667 0.00 0.00 41.87 3.66
120 121 3.108289 CAGCGACGACCAGCAGTG 61.108 66.667 0.00 0.00 35.48 3.66
121 122 3.295273 AGCGACGACCAGCAGTGA 61.295 61.111 0.00 0.00 35.48 3.41
122 123 2.807045 GCGACGACCAGCAGTGAG 60.807 66.667 0.00 0.00 0.00 3.51
123 124 2.807045 CGACGACCAGCAGTGAGC 60.807 66.667 0.00 0.00 46.19 4.26
146 147 4.504916 CGGCTCGCAGTGGAGGAG 62.505 72.222 9.72 0.00 34.56 3.69
373 425 1.679305 AGGACACCGTCGCAGATCT 60.679 57.895 0.00 0.00 40.67 2.75
448 528 3.371063 GACGGAGGTGCTGGACGA 61.371 66.667 0.00 0.00 0.00 4.20
581 661 2.362503 TCGCACTCCAGATCCCGT 60.363 61.111 0.00 0.00 0.00 5.28
675 765 8.774546 ACTCTGTTTCCAATCTAGAGATGATA 57.225 34.615 9.34 0.00 38.53 2.15
793 916 7.011950 TGTCTGCTACCCGTGATAAAATTAATG 59.988 37.037 0.00 0.00 0.00 1.90
915 1038 6.978338 TGTACTTAGTTCTCATCACGTTTCT 58.022 36.000 0.00 0.00 0.00 2.52
1020 1151 2.035442 GGGAAGCAGAGACAACCGC 61.035 63.158 0.00 0.00 0.00 5.68
1054 1185 4.470170 CATCGCCGTCCGTCGACA 62.470 66.667 17.16 0.00 42.86 4.35
1220 1351 0.807496 GCAGGCACTCTCATTTGTCC 59.193 55.000 0.00 0.00 34.60 4.02
1912 2635 7.108841 ACTTAGAATGCATCATTTTGCTCAT 57.891 32.000 0.00 0.00 43.18 2.90
2136 2861 3.939592 GAGTACCTTTTCCTTGGAATCGG 59.060 47.826 2.65 8.93 0.00 4.18
2262 2997 4.076394 GGCTACAGGTAAAACAATGTGGA 58.924 43.478 0.00 0.00 0.00 4.02
2336 5497 6.497624 TTAGGTTGGTTAGAACAAGGTGTA 57.502 37.500 0.00 0.00 0.00 2.90
2513 5684 6.509418 TTTCATAGTTTGGCAAGTATCACC 57.491 37.500 0.00 0.00 0.00 4.02
2821 8924 4.842574 TGTTGACAAGCAAGCCAGATATA 58.157 39.130 0.00 0.00 37.12 0.86
3220 11081 3.111939 CTTCTCGGCCTCGACGAT 58.888 61.111 0.00 0.00 44.17 3.73
3337 14762 6.770746 AGTACTTTAGTTATGCTTCTCGGA 57.229 37.500 0.00 0.00 0.00 4.55
3603 15043 3.812609 TCATTGCATTGTTGAGTACGTGT 59.187 39.130 8.36 0.00 0.00 4.49
3651 15130 1.828595 TGCATACTTCACGGAAGCCTA 59.171 47.619 11.97 1.65 42.79 3.93
3865 15345 9.679661 TTGTGTCATTGGTGATGTAAACTATAT 57.320 29.630 0.00 0.00 36.60 0.86
3917 15398 8.233349 TCCTAAGGCTATTCTCTTATCTCCTA 57.767 38.462 0.00 0.00 0.00 2.94
4036 15602 1.297364 GCGCCCCAACCACTAGTAA 59.703 57.895 0.00 0.00 0.00 2.24
4037 15603 0.107361 GCGCCCCAACCACTAGTAAT 60.107 55.000 0.00 0.00 0.00 1.89
4038 15604 1.949465 CGCCCCAACCACTAGTAATC 58.051 55.000 0.00 0.00 0.00 1.75
4039 15605 1.474498 CGCCCCAACCACTAGTAATCC 60.474 57.143 0.00 0.00 0.00 3.01
4040 15606 1.844497 GCCCCAACCACTAGTAATCCT 59.156 52.381 0.00 0.00 0.00 3.24
4041 15607 3.043418 GCCCCAACCACTAGTAATCCTA 58.957 50.000 0.00 0.00 0.00 2.94
4042 15608 3.181457 GCCCCAACCACTAGTAATCCTAC 60.181 52.174 0.00 0.00 0.00 3.18
4043 15609 4.035112 CCCCAACCACTAGTAATCCTACA 58.965 47.826 0.00 0.00 0.00 2.74
4044 15610 4.658901 CCCCAACCACTAGTAATCCTACAT 59.341 45.833 0.00 0.00 0.00 2.29
4045 15611 5.221661 CCCCAACCACTAGTAATCCTACATC 60.222 48.000 0.00 0.00 0.00 3.06
4046 15612 5.602978 CCCAACCACTAGTAATCCTACATCT 59.397 44.000 0.00 0.00 0.00 2.90
4047 15613 6.781014 CCCAACCACTAGTAATCCTACATCTA 59.219 42.308 0.00 0.00 0.00 1.98
4048 15614 7.255871 CCCAACCACTAGTAATCCTACATCTAC 60.256 44.444 0.00 0.00 0.00 2.59
4049 15615 7.361127 CAACCACTAGTAATCCTACATCTACG 58.639 42.308 0.00 0.00 0.00 3.51
4050 15616 6.599445 ACCACTAGTAATCCTACATCTACGT 58.401 40.000 0.00 0.00 0.00 3.57
4051 15617 7.739825 ACCACTAGTAATCCTACATCTACGTA 58.260 38.462 0.00 0.00 0.00 3.57
4052 15618 8.213679 ACCACTAGTAATCCTACATCTACGTAA 58.786 37.037 0.00 0.00 0.00 3.18
4053 15619 8.502387 CCACTAGTAATCCTACATCTACGTAAC 58.498 40.741 0.00 0.00 0.00 2.50
4054 15620 8.502387 CACTAGTAATCCTACATCTACGTAACC 58.498 40.741 0.00 0.00 0.00 2.85
4055 15621 6.890979 AGTAATCCTACATCTACGTAACCC 57.109 41.667 0.00 0.00 0.00 4.11
4056 15622 4.843220 AATCCTACATCTACGTAACCCG 57.157 45.455 0.00 0.00 44.03 5.28
4057 15623 1.949525 TCCTACATCTACGTAACCCGC 59.050 52.381 0.00 0.00 41.42 6.13
4058 15624 1.952296 CCTACATCTACGTAACCCGCT 59.048 52.381 0.00 0.00 41.42 5.52
4059 15625 3.141398 CCTACATCTACGTAACCCGCTA 58.859 50.000 0.00 0.00 41.42 4.26
4060 15626 3.058639 CCTACATCTACGTAACCCGCTAC 60.059 52.174 0.00 0.00 41.42 3.58
4062 15628 1.599071 CATCTACGTAACCCGCTACGA 59.401 52.381 9.88 0.00 46.00 3.43
4063 15629 1.732941 TCTACGTAACCCGCTACGAA 58.267 50.000 9.88 0.00 46.00 3.85
4064 15630 1.665679 TCTACGTAACCCGCTACGAAG 59.334 52.381 9.88 0.00 46.00 3.79
4065 15631 1.665679 CTACGTAACCCGCTACGAAGA 59.334 52.381 9.88 0.00 46.00 2.87
4066 15632 0.169009 ACGTAACCCGCTACGAAGAC 59.831 55.000 9.88 0.00 46.00 3.01
4089 15655 0.250513 CTACACCTTCCACCTGGAGC 59.749 60.000 0.00 0.00 46.36 4.70
4097 15663 3.636231 CACCTGGAGCCCGTGGAA 61.636 66.667 0.00 0.00 0.00 3.53
4449 16023 2.380410 CCGTTCACGCTACCAGCAC 61.380 63.158 0.00 0.00 42.58 4.40
4611 20186 3.457625 CTCATCTCCTGCTGCCCGG 62.458 68.421 0.00 0.00 0.00 5.73
4650 20227 1.596934 GAGATGTGCGGGACTTCCA 59.403 57.895 11.08 0.00 37.91 3.53
4676 20253 1.444553 CGTCCTCGACAAGTGCCTC 60.445 63.158 0.00 0.00 39.71 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.005539 GCAGGTCTCAGGAGGGCA 61.006 66.667 0.00 0.00 0.00 5.36
56 57 2.055689 CTCTGGCACCCACACCTTGA 62.056 60.000 0.00 0.00 0.00 3.02
72 73 2.729479 CGGCCATCACTGCTCCTCT 61.729 63.158 2.24 0.00 0.00 3.69
103 104 3.108289 CACTGCTGGTCGTCGCTG 61.108 66.667 0.00 0.00 0.00 5.18
104 105 3.274455 CTCACTGCTGGTCGTCGCT 62.274 63.158 0.00 0.00 0.00 4.93
105 106 2.807045 CTCACTGCTGGTCGTCGC 60.807 66.667 0.00 0.00 0.00 5.19
106 107 2.807045 GCTCACTGCTGGTCGTCG 60.807 66.667 0.00 0.00 38.95 5.12
129 130 4.504916 CTCCTCCACTGCGAGCCG 62.505 72.222 0.00 0.00 0.00 5.52
130 131 4.828925 GCTCCTCCACTGCGAGCC 62.829 72.222 0.00 0.00 42.59 4.70
132 133 2.183811 CTGCTCCTCCACTGCGAG 59.816 66.667 0.00 0.00 0.00 5.03
133 134 4.074526 GCTGCTCCTCCACTGCGA 62.075 66.667 0.00 0.00 0.00 5.10
134 135 4.383861 TGCTGCTCCTCCACTGCG 62.384 66.667 0.00 0.00 33.87 5.18
135 136 2.436292 CTGCTGCTCCTCCACTGC 60.436 66.667 0.00 0.00 0.00 4.40
136 137 2.436292 GCTGCTGCTCCTCCACTG 60.436 66.667 8.53 0.00 36.03 3.66
137 138 4.079850 CGCTGCTGCTCCTCCACT 62.080 66.667 14.03 0.00 36.97 4.00
138 139 4.074526 TCGCTGCTGCTCCTCCAC 62.075 66.667 14.03 0.00 36.97 4.02
139 140 4.074526 GTCGCTGCTGCTCCTCCA 62.075 66.667 14.03 0.00 36.97 3.86
141 142 4.121669 TCGTCGCTGCTGCTCCTC 62.122 66.667 14.03 0.86 36.97 3.71
142 143 4.427661 GTCGTCGCTGCTGCTCCT 62.428 66.667 14.03 0.00 36.97 3.69
299 351 2.826738 GCGCCCGCCCAGATTTTA 60.827 61.111 0.00 0.00 34.56 1.52
373 425 2.682136 TCCCGACGGCAAGATGGA 60.682 61.111 8.86 0.00 0.00 3.41
448 528 2.350522 GCACCTTGACGATCTTCATGT 58.649 47.619 2.32 1.35 0.00 3.21
581 661 3.988525 GGTGCCATGCCGCAAACA 61.989 61.111 0.00 0.00 41.30 2.83
793 916 5.414454 TGGAACCAACTTAGATGTAATGTGC 59.586 40.000 0.00 0.00 0.00 4.57
915 1038 3.620488 CCTCCCTGAATTTCCATCGAAA 58.380 45.455 0.00 0.00 42.10 3.46
1020 1151 1.903877 ATGTTGGAGCAGGACGGAGG 61.904 60.000 0.00 0.00 0.00 4.30
1054 1185 2.353269 TGATGCGTTTCTTGTTCGTTGT 59.647 40.909 0.00 0.00 0.00 3.32
1170 1301 2.370519 TCCGTTGATGGTCCAAGAAGAA 59.629 45.455 0.00 0.00 0.00 2.52
1220 1351 0.912486 AGAAAGGATCGGAAGGGTGG 59.088 55.000 0.00 0.00 0.00 4.61
1323 1554 8.690203 TTGGAACATTGAACTTCAGAAGAATA 57.310 30.769 17.56 0.00 39.30 1.75
1404 1645 7.406916 TCTTAGGAAAATAATTACCAGTGCCA 58.593 34.615 0.00 0.00 0.00 4.92
1724 2446 6.681120 GCATGATGTGTAATGCACTTACCATT 60.681 38.462 2.75 0.00 46.75 3.16
1912 2635 3.281727 AAGCAAGTTCAGTCCAGTTCA 57.718 42.857 0.00 0.00 0.00 3.18
2136 2861 2.902343 GCCATTGCCCTACGCTCC 60.902 66.667 0.00 0.00 38.78 4.70
2262 2997 6.491403 ACAGAAACATGCCAATAAAAGAGACT 59.509 34.615 0.00 0.00 0.00 3.24
2336 5497 0.829333 AGCATCATCTCTTGACCGCT 59.171 50.000 0.00 0.00 40.11 5.52
2513 5684 8.870160 TCAGAAATGACTTAACCACAAATTTG 57.130 30.769 16.67 16.67 0.00 2.32
2913 9016 8.273557 GCATAAATCTTAATGCAGAGCAAAATG 58.726 33.333 0.00 0.00 46.19 2.32
3152 11012 0.906066 TGCAGGTATTGAGCGGGTAA 59.094 50.000 0.00 0.00 0.00 2.85
3220 11081 0.618981 TAGAGAGAGGCACGAGGACA 59.381 55.000 0.00 0.00 0.00 4.02
3337 14762 4.217118 GTCTGAGAACCATTCAAATGCTGT 59.783 41.667 0.00 0.00 35.08 4.40
3467 14892 2.279517 GCAGGCCTCGGTACATCG 60.280 66.667 0.00 0.00 0.00 3.84
3570 15010 5.971895 ACAATGCAATGACAGACAAAAAC 57.028 34.783 9.20 0.00 0.00 2.43
3603 15043 0.462581 CGCTGCTTTCCATCCTGCTA 60.463 55.000 0.00 0.00 0.00 3.49
3651 15130 1.048601 TCTTGGCGAGGAGAAACAGT 58.951 50.000 0.97 0.00 0.00 3.55
3917 15398 8.232913 AGTAACAAGTACACAACAATGGAAAT 57.767 30.769 0.00 0.00 34.88 2.17
4029 15595 7.663493 GGGTTACGTAGATGTAGGATTACTAGT 59.337 40.741 0.00 0.00 30.77 2.57
4036 15602 2.555757 GCGGGTTACGTAGATGTAGGAT 59.444 50.000 0.00 0.00 46.52 3.24
4037 15603 1.949525 GCGGGTTACGTAGATGTAGGA 59.050 52.381 0.00 0.00 46.52 2.94
4038 15604 1.952296 AGCGGGTTACGTAGATGTAGG 59.048 52.381 0.00 0.00 46.52 3.18
4039 15605 3.363378 CGTAGCGGGTTACGTAGATGTAG 60.363 52.174 6.88 0.00 46.52 2.74
4040 15606 2.543848 CGTAGCGGGTTACGTAGATGTA 59.456 50.000 6.88 0.00 46.52 2.29
4041 15607 1.331756 CGTAGCGGGTTACGTAGATGT 59.668 52.381 6.88 0.00 46.52 3.06
4042 15608 1.599071 TCGTAGCGGGTTACGTAGATG 59.401 52.381 13.40 0.00 44.95 2.90
4043 15609 1.953559 TCGTAGCGGGTTACGTAGAT 58.046 50.000 13.40 0.00 44.95 1.98
4044 15610 1.665679 CTTCGTAGCGGGTTACGTAGA 59.334 52.381 13.55 3.41 43.04 2.59
4045 15611 1.665679 TCTTCGTAGCGGGTTACGTAG 59.334 52.381 13.40 13.13 44.95 3.51
4046 15612 1.396996 GTCTTCGTAGCGGGTTACGTA 59.603 52.381 13.40 4.94 44.95 3.57
4047 15613 0.169009 GTCTTCGTAGCGGGTTACGT 59.831 55.000 13.40 0.00 44.95 3.57
4048 15614 0.524180 GGTCTTCGTAGCGGGTTACG 60.524 60.000 8.52 8.52 45.79 3.18
4049 15615 0.524180 CGGTCTTCGTAGCGGGTTAC 60.524 60.000 0.00 0.00 36.75 2.50
4050 15616 0.676466 TCGGTCTTCGTAGCGGGTTA 60.676 55.000 6.86 0.00 40.61 2.85
4051 15617 1.973281 TCGGTCTTCGTAGCGGGTT 60.973 57.895 6.86 0.00 40.61 4.11
4052 15618 2.360350 TCGGTCTTCGTAGCGGGT 60.360 61.111 6.86 0.00 40.61 5.28
4053 15619 1.091771 TAGTCGGTCTTCGTAGCGGG 61.092 60.000 6.86 0.00 40.61 6.13
4054 15620 0.027324 GTAGTCGGTCTTCGTAGCGG 59.973 60.000 6.86 0.00 40.61 5.52
4055 15621 0.723414 TGTAGTCGGTCTTCGTAGCG 59.277 55.000 0.00 0.00 41.54 4.26
4056 15622 1.202121 GGTGTAGTCGGTCTTCGTAGC 60.202 57.143 0.00 0.00 40.32 3.58
4057 15623 2.354259 AGGTGTAGTCGGTCTTCGTAG 58.646 52.381 0.00 0.00 40.32 3.51
4058 15624 2.479566 AGGTGTAGTCGGTCTTCGTA 57.520 50.000 0.00 0.00 40.32 3.43
4059 15625 1.538950 GAAGGTGTAGTCGGTCTTCGT 59.461 52.381 0.00 0.00 40.32 3.85
4060 15626 1.135460 GGAAGGTGTAGTCGGTCTTCG 60.135 57.143 0.00 0.00 35.86 3.79
4061 15627 1.891150 TGGAAGGTGTAGTCGGTCTTC 59.109 52.381 0.00 0.00 34.69 2.87
4062 15628 1.617357 GTGGAAGGTGTAGTCGGTCTT 59.383 52.381 0.00 0.00 0.00 3.01
4063 15629 1.254954 GTGGAAGGTGTAGTCGGTCT 58.745 55.000 0.00 0.00 0.00 3.85
4064 15630 0.245813 GGTGGAAGGTGTAGTCGGTC 59.754 60.000 0.00 0.00 0.00 4.79
4065 15631 0.178941 AGGTGGAAGGTGTAGTCGGT 60.179 55.000 0.00 0.00 0.00 4.69
4066 15632 0.246635 CAGGTGGAAGGTGTAGTCGG 59.753 60.000 0.00 0.00 0.00 4.79
4089 15655 3.423154 GCTTCGCTGTTCCACGGG 61.423 66.667 0.00 0.00 0.00 5.28
4097 15663 2.357517 CCGTTCCTGCTTCGCTGT 60.358 61.111 0.00 0.00 0.00 4.40
4449 16023 0.869454 GATGCGCAGGAGAAGAGACG 60.869 60.000 18.32 0.00 0.00 4.18
4611 20186 2.799371 CGTCAGGTCTACGAGGCC 59.201 66.667 0.00 0.00 41.32 5.19


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

AutoCloner maintained by Alex Coulton.