Multiple sequence alignment - TraesCS2D01G388200

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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 TraesCS2D01G388200 chr2D 100.000 6457 0 0 1 6457 493527254 493520798 0.000000e+00 11924.0
1 TraesCS2D01G388200 chr2D 83.234 334 33 16 444 765 548899575 548899253 1.060000e-72 285.0
2 TraesCS2D01G388200 chr2D 91.667 168 14 0 1 168 548900288 548900121 3.890000e-57 233.0
3 TraesCS2D01G388200 chr2A 95.598 4998 154 29 755 5716 640081437 640086404 0.000000e+00 7950.0
4 TraesCS2D01G388200 chr2A 89.647 850 44 14 5641 6457 640086383 640087221 0.000000e+00 1042.0
5 TraesCS2D01G388200 chr2A 96.875 160 5 0 1 160 640078672 640078831 1.070000e-67 268.0
6 TraesCS2D01G388200 chr2B 94.306 3565 133 23 2135 5672 581712558 581709037 0.000000e+00 5395.0
7 TraesCS2D01G388200 chr2B 96.092 1177 32 6 770 1939 581714898 581713729 0.000000e+00 1906.0
8 TraesCS2D01G388200 chr2B 92.418 699 48 4 5759 6457 581708984 581708291 0.000000e+00 992.0
9 TraesCS2D01G388200 chr2B 76.908 498 67 27 206 659 679695384 679694891 8.370000e-59 239.0
10 TraesCS2D01G388200 chr7A 85.256 624 52 22 175 767 332448675 332449289 1.990000e-169 606.0
11 TraesCS2D01G388200 chr7A 84.236 628 64 24 166 765 125920021 125919401 4.340000e-161 579.0
12 TraesCS2D01G388200 chr7A 94.643 168 9 0 1 168 125920223 125920056 1.790000e-65 261.0
13 TraesCS2D01G388200 chr7A 82.292 96 11 6 682 775 39237497 39237406 1.930000e-10 78.7
14 TraesCS2D01G388200 chr3B 83.677 631 68 24 166 768 593931189 593931812 4.370000e-156 562.0
15 TraesCS2D01G388200 chr3B 84.768 453 35 21 166 594 520612794 520612352 2.150000e-114 424.0
16 TraesCS2D01G388200 chr3B 94.643 168 9 0 1 168 593930987 593931154 1.790000e-65 261.0
17 TraesCS2D01G388200 chr4B 83.438 634 62 21 166 766 73658294 73658917 3.400000e-152 549.0
18 TraesCS2D01G388200 chr4B 92.857 168 12 0 1 168 73658092 73658259 1.800000e-60 244.0
19 TraesCS2D01G388200 chr1A 85.246 427 34 20 166 568 343423480 343423901 4.660000e-111 412.0
20 TraesCS2D01G388200 chr1A 86.190 210 29 0 2925 3134 381307195 381306986 1.810000e-55 228.0
21 TraesCS2D01G388200 chr6D 87.115 357 23 12 166 501 140223051 140223405 3.650000e-102 383.0
22 TraesCS2D01G388200 chr5A 87.500 344 23 12 166 491 53462534 53462193 4.730000e-101 379.0
23 TraesCS2D01G388200 chr5A 95.395 152 7 0 12 163 53462725 53462574 6.470000e-60 243.0
24 TraesCS2D01G388200 chr5A 84.884 86 9 4 682 765 456626054 456625971 4.150000e-12 84.2
25 TraesCS2D01G388200 chr5D 88.644 317 17 11 166 465 385962567 385962253 1.020000e-97 368.0
26 TraesCS2D01G388200 chr5D 93.452 168 11 0 1 168 385962769 385962602 3.870000e-62 250.0
27 TraesCS2D01G388200 chr5D 85.849 106 4 4 520 620 385961993 385961894 1.150000e-17 102.0
28 TraesCS2D01G388200 chr6B 94.083 169 9 1 1 168 459386751 459386583 8.310000e-64 255.0
29 TraesCS2D01G388200 chr3D 92.262 168 11 2 1 167 5370973 5370807 3.010000e-58 237.0
30 TraesCS2D01G388200 chr3D 98.000 50 0 1 718 767 582541014 582541062 1.150000e-12 86.1
31 TraesCS2D01G388200 chr3D 97.959 49 0 1 718 766 559264019 559264066 4.150000e-12 84.2
32 TraesCS2D01G388200 chr3D 82.609 92 14 2 676 766 28986556 28986646 5.370000e-11 80.5
33 TraesCS2D01G388200 chrUn 85.238 210 31 0 2925 3134 11032037 11031828 3.920000e-52 217.0
34 TraesCS2D01G388200 chr1B 85.238 210 31 0 2925 3134 411570178 411569969 3.920000e-52 217.0
35 TraesCS2D01G388200 chr4D 98.039 51 0 1 718 768 483117582 483117533 3.210000e-13 87.9
36 TraesCS2D01G388200 chr7D 84.884 86 9 4 682 765 583330326 583330243 4.150000e-12 84.2
37 TraesCS2D01G388200 chr7D 87.324 71 7 2 694 763 515476108 515476039 5.370000e-11 80.5


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 TraesCS2D01G388200 chr2D 493520798 493527254 6456 True 11924.000000 11924 100.0000 1 6457 1 chr2D.!!$R1 6456
1 TraesCS2D01G388200 chr2D 548899253 548900288 1035 True 259.000000 285 87.4505 1 765 2 chr2D.!!$R2 764
2 TraesCS2D01G388200 chr2A 640078672 640087221 8549 False 3086.666667 7950 94.0400 1 6457 3 chr2A.!!$F1 6456
3 TraesCS2D01G388200 chr2B 581708291 581714898 6607 True 2764.333333 5395 94.2720 770 6457 3 chr2B.!!$R2 5687
4 TraesCS2D01G388200 chr7A 332448675 332449289 614 False 606.000000 606 85.2560 175 767 1 chr7A.!!$F1 592
5 TraesCS2D01G388200 chr7A 125919401 125920223 822 True 420.000000 579 89.4395 1 765 2 chr7A.!!$R2 764
6 TraesCS2D01G388200 chr3B 593930987 593931812 825 False 411.500000 562 89.1600 1 768 2 chr3B.!!$F1 767
7 TraesCS2D01G388200 chr4B 73658092 73658917 825 False 396.500000 549 88.1475 1 766 2 chr4B.!!$F1 765
8 TraesCS2D01G388200 chr5A 53462193 53462725 532 True 311.000000 379 91.4475 12 491 2 chr5A.!!$R2 479
9 TraesCS2D01G388200 chr5D 385961894 385962769 875 True 240.000000 368 89.3150 1 620 3 chr5D.!!$R1 619

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
705 1206 0.546122 TCTAATTGGCTGCATCGGGT 59.454 50.000 0.50 0.0 0.00 5.28 F
1955 4280 0.187361 AGCCAGTGGTTTTAAGGGCA 59.813 50.000 11.74 0.0 43.72 5.36 F
3374 6675 1.134848 TGAGCTTTTTGGGTGTGTTGC 60.135 47.619 0.00 0.0 0.00 4.17 F
4913 8231 0.615850 GGGTTGCCTAGCTCTGTTCT 59.384 55.000 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 5962 0.745845 ACGGATGCAGTGCAGATTCC 60.746 55.000 24.20 22.67 43.65 3.01 R
3796 7100 0.250901 AATGAGGTGAGTGGTGGCAC 60.251 55.000 9.70 9.70 0.00 5.01 R
4952 8270 0.249741 AGTGAGGAAACGTTGTCCCG 60.250 55.000 19.44 0.00 35.59 5.14 R
5956 9377 1.202486 TCGCTAAGGGCTTATTCGGTG 60.202 52.381 0.00 0.00 39.13 4.94 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
44 45 1.227089 CATCGGGGAGAGTTGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
168 169 0.940991 CAAAAGCTTCAACCCGCAGC 60.941 55.000 0.00 0.00 0.00 5.25
169 170 2.087462 AAAAGCTTCAACCCGCAGCC 62.087 55.000 0.00 0.00 33.73 4.85
172 173 3.726517 CTTCAACCCGCAGCCGTG 61.727 66.667 0.00 0.00 0.00 4.94
174 175 4.680237 TCAACCCGCAGCCGTGAG 62.680 66.667 0.00 0.00 0.00 3.51
290 331 3.360758 GCGGAAAGTTTTAATGTGCGAAG 59.639 43.478 0.00 0.00 0.00 3.79
295 336 6.345803 GGAAAGTTTTAATGTGCGAAGAAAGC 60.346 38.462 0.00 0.00 0.00 3.51
318 360 5.643379 TTCAATCGGCATAGAAAAAGCTT 57.357 34.783 0.00 0.00 0.00 3.74
338 380 6.173339 AGCTTCAACCGATGATAGAAAAAGA 58.827 36.000 0.00 0.00 38.03 2.52
351 393 6.940298 TGATAGAAAAAGATTCAACCCGACTT 59.060 34.615 0.00 0.00 0.00 3.01
386 428 2.429236 ACGACGTTGAGAGCTGCG 60.429 61.111 10.51 0.00 0.00 5.18
387 429 2.429236 CGACGTTGAGAGCTGCGT 60.429 61.111 0.00 0.00 40.44 5.24
435 492 1.073897 GTGCTGACAGAGGGGCTTT 59.926 57.895 6.65 0.00 0.00 3.51
438 495 1.763770 CTGACAGAGGGGCTTTGGT 59.236 57.895 0.00 0.00 0.00 3.67
454 726 2.980233 GTGTGCTTCAAGGCGGCT 60.980 61.111 5.25 5.25 34.52 5.52
568 1046 3.319198 GTGGAACTGCGAGGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
570 1048 3.787001 GGAACTGCGAGGGGGAGG 61.787 72.222 0.00 0.00 38.63 4.30
571 1049 3.787001 GAACTGCGAGGGGGAGGG 61.787 72.222 0.00 0.00 38.63 4.30
661 1162 4.580995 AGAAGAAGAGAGAAGTCAACGTGA 59.419 41.667 0.00 0.00 0.00 4.35
690 1191 0.747255 GGCAGATCAGACGGCTCTAA 59.253 55.000 0.00 0.00 0.00 2.10
705 1206 0.546122 TCTAATTGGCTGCATCGGGT 59.454 50.000 0.50 0.00 0.00 5.28
797 3116 0.995024 AATTGAGGGGTAGTGCTGCT 59.005 50.000 0.00 0.00 0.00 4.24
821 3140 2.356069 GGCCAATTCTTTCTAGCCTTCG 59.644 50.000 0.00 0.00 37.42 3.79
845 3164 2.335712 GGCAAGTTCCAAGCCTCCG 61.336 63.158 0.00 0.00 44.92 4.63
1403 3722 3.382546 TGTACTACGGGTCTATGGCTTTC 59.617 47.826 0.00 0.00 0.00 2.62
1459 3778 4.570926 TCCATCTGGATGAGACCCTAATT 58.429 43.478 11.66 0.00 41.20 1.40
1760 4085 6.163135 AGATTTCTAGTTATGGTTCCCTCG 57.837 41.667 0.00 0.00 0.00 4.63
1837 4162 0.464373 GTGATCATGGGATGCGGTGT 60.464 55.000 0.00 0.00 32.67 4.16
1849 4174 0.584396 TGCGGTGTCGACATGAAAAC 59.416 50.000 23.12 7.31 39.00 2.43
1939 4264 3.672295 AAGGCACTAGCAGCGAGCC 62.672 63.158 1.81 7.34 41.88 4.70
1944 4269 3.011635 ACTAGCAGCGAGCCAGTGG 62.012 63.158 4.20 4.20 43.73 4.00
1955 4280 0.187361 AGCCAGTGGTTTTAAGGGCA 59.813 50.000 11.74 0.00 43.72 5.36
1957 4282 1.623311 GCCAGTGGTTTTAAGGGCAAT 59.377 47.619 11.74 0.00 41.02 3.56
1964 4289 5.782845 AGTGGTTTTAAGGGCAATCCATTTA 59.217 36.000 0.00 0.00 37.56 1.40
1977 4302 6.105333 GCAATCCATTTACTTTGGCATGTTA 58.895 36.000 0.00 0.00 34.06 2.41
1983 4308 7.816995 TCCATTTACTTTGGCATGTTATCAAAC 59.183 33.333 0.00 0.00 34.06 2.93
2013 4338 6.586868 TGTTTGCATGTTCACTGAATTTTC 57.413 33.333 0.00 0.00 0.00 2.29
2030 4355 6.873076 TGAATTTTCTTTCAGTTTGCACTTGT 59.127 30.769 0.00 0.00 32.07 3.16
2061 4386 1.299541 CAGCAGTCACCGAAGTGTTT 58.700 50.000 0.00 0.00 44.83 2.83
2338 5638 5.089970 TGACTCATATCAGTTGAACAGGG 57.910 43.478 0.00 0.00 0.00 4.45
2416 5716 7.341445 ACTTTGCTATGTTTCTTTAACCACA 57.659 32.000 0.00 0.00 35.81 4.17
2490 5790 6.098409 GTCTTCATCACTTCCCTATTCTACCA 59.902 42.308 0.00 0.00 0.00 3.25
2539 5839 2.362397 TCTCTTGCGACTGAAGTCTGTT 59.638 45.455 8.73 0.00 42.66 3.16
2545 5845 2.612212 GCGACTGAAGTCTGTTCCAAAA 59.388 45.455 8.73 0.00 42.66 2.44
2621 5921 3.116096 AGGGGCACTAACTCTGATACA 57.884 47.619 0.00 0.00 0.00 2.29
2662 5962 2.159184 TGAAGCTAGAGATGAGGTTGCG 60.159 50.000 0.00 0.00 34.87 4.85
2879 6179 5.234752 GTTGTTCTTGGTGTTTCCTGTTTT 58.765 37.500 0.00 0.00 37.07 2.43
3184 6484 8.652810 ATTTCAATTTGGAGAGAAAAGTGTTG 57.347 30.769 0.00 0.00 34.94 3.33
3187 6487 4.981806 TTTGGAGAGAAAAGTGTTGTGG 57.018 40.909 0.00 0.00 0.00 4.17
3300 6601 6.697019 AGCAGTAAATTGCAAGTTTACAACTG 59.303 34.615 25.09 25.09 46.47 3.16
3303 6604 4.670896 AATTGCAAGTTTACAACTGCCT 57.329 36.364 4.94 0.00 41.91 4.75
3374 6675 1.134848 TGAGCTTTTTGGGTGTGTTGC 60.135 47.619 0.00 0.00 0.00 4.17
3380 6681 4.497984 TGGGTGTGTTGCGCCTGT 62.498 61.111 4.18 0.00 46.69 4.00
3398 6699 3.108144 CTGTTTTGACAAAGCTTGACCG 58.892 45.455 14.74 0.00 0.00 4.79
3453 6754 6.084925 CAGAAGTTGATTGATCAGCTGTTTC 58.915 40.000 14.67 12.51 45.75 2.78
3542 6846 2.479566 TGGAGAACACCTGAATCTGC 57.520 50.000 0.00 0.00 32.78 4.26
3770 7074 6.278172 TGCAATCAAACCAAGCATGTATAA 57.722 33.333 0.00 0.00 0.00 0.98
3771 7075 6.695429 TGCAATCAAACCAAGCATGTATAAA 58.305 32.000 0.00 0.00 0.00 1.40
3970 7274 7.832187 CCAGTTAGGTTTCATATTGTTAGGGAA 59.168 37.037 0.00 0.00 0.00 3.97
4040 7352 9.344772 TCTTCTACCAACTGTTTTTGCTTAATA 57.655 29.630 0.00 0.00 0.00 0.98
4405 7720 2.124695 GGCCAGTCGGACATTCCC 60.125 66.667 11.27 1.45 41.77 3.97
4408 7723 2.511600 CAGTCGGACATTCCCCGC 60.512 66.667 11.27 0.00 46.10 6.13
4420 7735 3.069729 ACATTCCCCGCTCTAGTAATGTC 59.930 47.826 0.00 0.00 33.50 3.06
4561 7878 6.037786 TCTCCTGTTGGTAGATAAACTGTG 57.962 41.667 0.00 0.00 34.23 3.66
4593 7911 8.478066 TCAGCATACTTTACAGTCATCTTGTAT 58.522 33.333 0.00 0.00 34.06 2.29
4606 7924 4.694982 TCATCTTGTATCTTTCGCTTGCAA 59.305 37.500 0.00 0.00 0.00 4.08
4662 7980 6.068010 TCAATTACACTGAATTGACACCCTT 58.932 36.000 7.33 0.00 46.12 3.95
4758 8076 8.261522 TGTTTTTGCTTTTATTGGAACTAACCT 58.738 29.630 0.00 0.00 0.00 3.50
4774 8092 6.936968 ACTAACCTCAACCAGAAGATAGTT 57.063 37.500 0.00 0.00 0.00 2.24
4846 8164 9.337396 TGATAGACAAGAAAACTGCTTCTTTTA 57.663 29.630 3.34 0.00 41.81 1.52
4913 8231 0.615850 GGGTTGCCTAGCTCTGTTCT 59.384 55.000 0.00 0.00 0.00 3.01
4940 8258 9.814899 CTTCTTGACTCTTATGTAGACATTGAT 57.185 33.333 0.00 0.00 37.76 2.57
4952 8270 6.341316 TGTAGACATTGATGGAGCTTACTTC 58.659 40.000 0.00 0.00 0.00 3.01
5120 8438 1.181001 GAGTTGTCTGATACGTCGCG 58.819 55.000 0.00 0.00 0.00 5.87
5153 8471 0.958876 CCAAGCTGCTCATCTGTGCA 60.959 55.000 1.00 6.74 41.53 4.57
5305 8628 8.654485 TTGTTTAGTGTAGTAGGTTCCTATCA 57.346 34.615 1.73 0.85 0.00 2.15
5362 8686 5.678616 GCAGTTGTTAAAAGAAGGCAGTTCA 60.679 40.000 1.32 0.00 37.67 3.18
5532 8856 2.643304 ACCCCCAGAGAAAGTTACCTTC 59.357 50.000 0.00 0.00 0.00 3.46
5597 8922 0.612732 TTGCTCAGAGCCCCAATTGG 60.613 55.000 20.16 18.21 41.51 3.16
5716 9106 3.230976 TGCAGAAGAGTCAGACCACTTA 58.769 45.455 9.66 0.00 0.00 2.24
5717 9107 3.834813 TGCAGAAGAGTCAGACCACTTAT 59.165 43.478 9.66 5.37 0.00 1.73
5722 9122 3.435275 AGAGTCAGACCACTTATGCAGA 58.565 45.455 0.00 0.00 0.00 4.26
5750 9166 2.617308 CTGCATTTCTCCAGCCATGTAG 59.383 50.000 0.00 0.00 0.00 2.74
5757 9173 1.227556 CCAGCCATGTAGGTACCGC 60.228 63.158 6.18 2.36 40.61 5.68
5852 9273 5.241403 TGTGTCCATATTGACCTGACTTT 57.759 39.130 4.59 0.00 34.25 2.66
5877 9298 1.860641 TTCTTGGCGAGACCCTCATA 58.139 50.000 3.27 0.00 37.83 2.15
5878 9299 2.088104 TCTTGGCGAGACCCTCATAT 57.912 50.000 0.00 0.00 37.83 1.78
5907 9328 3.455910 TCCAAGGATTAGAGTGGACATGG 59.544 47.826 0.00 0.00 35.22 3.66
5926 9347 7.553760 GGACATGGCATTTCAATCCTTTAATTT 59.446 33.333 15.00 0.00 0.00 1.82
5956 9377 6.737254 TTTCTATGATTTGAAGTCCCGTTC 57.263 37.500 0.00 0.00 0.00 3.95
5991 9412 2.185004 AGCGACATAAACACAAGGCT 57.815 45.000 0.00 0.00 0.00 4.58
6028 9449 4.060900 CGGAAGTGCGTCTATAGTAGGTA 58.939 47.826 0.00 0.00 0.00 3.08
6106 9527 4.455606 GTTAGGATCCAGCAAACTAGCAT 58.544 43.478 15.82 0.00 36.85 3.79
6175 9596 4.641645 TTGGTCAGGCGCACAGGG 62.642 66.667 10.83 0.00 0.00 4.45
6230 9651 0.463204 CTGGCACTGATCTCGTCCAT 59.537 55.000 0.00 0.00 0.00 3.41
6285 9706 0.107643 GCATGCTCCCTAGAACCTCC 59.892 60.000 11.37 0.00 0.00 4.30
6288 9709 0.395862 TGCTCCCTAGAACCTCCGAG 60.396 60.000 0.00 0.00 0.00 4.63
6295 9716 0.614979 TAGAACCTCCGAGGCAAGCT 60.615 55.000 14.86 8.90 39.63 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.557903 ATGCCGTGGTTGCAGCTCT 62.558 57.895 0.00 0.00 42.92 4.09
44 45 1.885887 TGTAGCATGGGAAAACACTGC 59.114 47.619 0.00 0.00 0.00 4.40
168 169 1.401018 GGTTGCGAAAAATCCTCACGG 60.401 52.381 0.00 0.00 0.00 4.94
169 170 1.265635 TGGTTGCGAAAAATCCTCACG 59.734 47.619 0.00 0.00 0.00 4.35
171 172 4.392921 TTTTGGTTGCGAAAAATCCTCA 57.607 36.364 0.00 0.00 0.00 3.86
172 173 4.749598 ACATTTTGGTTGCGAAAAATCCTC 59.250 37.500 0.00 0.00 34.55 3.71
174 175 5.204101 CAACATTTTGGTTGCGAAAAATCC 58.796 37.500 0.00 0.00 41.37 3.01
175 176 5.204101 CCAACATTTTGGTTGCGAAAAATC 58.796 37.500 2.21 0.00 46.63 2.17
176 177 5.167218 CCAACATTTTGGTTGCGAAAAAT 57.833 34.783 2.21 0.00 46.63 1.82
266 306 1.982913 GCACATTAAAACTTTCCGCCG 59.017 47.619 0.00 0.00 0.00 6.46
272 312 6.273071 AGCTTTCTTCGCACATTAAAACTTT 58.727 32.000 0.00 0.00 0.00 2.66
290 331 4.882671 TTCTATGCCGATTGAAGCTTTC 57.117 40.909 0.00 0.00 0.00 2.62
295 336 5.240713 AGCTTTTTCTATGCCGATTGAAG 57.759 39.130 0.00 0.00 0.00 3.02
301 342 3.190535 GGTTGAAGCTTTTTCTATGCCGA 59.809 43.478 0.00 0.00 0.00 5.54
318 360 8.450964 GTTGAATCTTTTTCTATCATCGGTTGA 58.549 33.333 0.00 0.00 39.12 3.18
338 380 1.545582 CATTGGCAAGTCGGGTTGAAT 59.454 47.619 5.96 0.00 0.00 2.57
369 411 2.429236 CGCAGCTCTCAACGTCGT 60.429 61.111 0.00 0.00 0.00 4.34
413 465 1.965754 GCCCCTCTGTCAGCACCTAG 61.966 65.000 0.00 0.00 0.00 3.02
435 492 2.594303 CCGCCTTGAAGCACACCA 60.594 61.111 0.00 0.00 0.00 4.17
438 495 2.979676 CAGCCGCCTTGAAGCACA 60.980 61.111 0.00 0.00 0.00 4.57
466 738 1.152756 AGGAAGCCGTTGCCACTTT 60.153 52.632 0.00 0.00 38.69 2.66
551 1028 3.316573 CTCCCCCTCGCAGTTCCAC 62.317 68.421 0.00 0.00 0.00 4.02
570 1048 2.125225 ACCTGGACCTCTTCCCCC 59.875 66.667 0.00 0.00 45.17 5.40
571 1049 1.229529 TCACCTGGACCTCTTCCCC 60.230 63.158 0.00 0.00 45.17 4.81
661 1162 2.238395 GTCTGATCTGCCTTCTCCCTTT 59.762 50.000 0.00 0.00 0.00 3.11
690 1191 2.440796 CCACCCGATGCAGCCAAT 60.441 61.111 0.00 0.00 0.00 3.16
750 1251 1.446792 CATAGGGCGATGCTAGGCG 60.447 63.158 0.00 0.00 34.74 5.52
751 1252 4.606071 CATAGGGCGATGCTAGGC 57.394 61.111 0.00 0.00 0.00 3.93
777 3096 1.355720 AGCAGCACTACCCCTCAATTT 59.644 47.619 0.00 0.00 0.00 1.82
797 3116 4.862641 AGGCTAGAAAGAATTGGCCTTA 57.137 40.909 3.32 0.00 46.36 2.69
821 3140 1.578206 GCTTGGAACTTGCCGTCCTC 61.578 60.000 0.00 0.00 0.00 3.71
845 3164 0.108662 GGCCTTTGTATTGCAGTGCC 60.109 55.000 13.72 0.00 32.49 5.01
1403 3722 5.985530 TGATCTATGAACTTATCGCACCAAG 59.014 40.000 0.00 0.00 0.00 3.61
1459 3778 2.367202 GGAAGGGCACGATCTCCCA 61.367 63.158 14.51 0.00 45.07 4.37
1683 4003 1.945394 CCTAGCAGGCAAGCATAAGTG 59.055 52.381 4.78 0.00 36.85 3.16
1684 4004 1.561542 ACCTAGCAGGCAAGCATAAGT 59.438 47.619 4.78 0.00 39.63 2.24
1685 4005 2.338577 ACCTAGCAGGCAAGCATAAG 57.661 50.000 4.78 0.00 39.63 1.73
1760 4085 3.484407 ACATCCCATGCTTATCTGCTTC 58.516 45.455 0.00 0.00 0.00 3.86
1837 4162 6.201234 TCAACATTAGAACGTTTTCATGTCGA 59.799 34.615 16.26 10.00 30.70 4.20
1849 4174 8.809159 ATGATACTGATCTCAACATTAGAACG 57.191 34.615 0.00 0.00 32.79 3.95
1939 4264 2.896685 TGGATTGCCCTTAAAACCACTG 59.103 45.455 0.00 0.00 35.38 3.66
1944 4269 7.119116 CCAAAGTAAATGGATTGCCCTTAAAAC 59.881 37.037 0.00 0.00 40.56 2.43
1955 4280 8.076910 TGATAACATGCCAAAGTAAATGGATT 57.923 30.769 0.00 0.00 40.56 3.01
1957 4282 7.473735 TTGATAACATGCCAAAGTAAATGGA 57.526 32.000 0.00 0.00 40.56 3.41
1964 4289 3.900601 TGGGTTTGATAACATGCCAAAGT 59.099 39.130 0.00 0.00 35.92 2.66
1983 4308 2.865551 GTGAACATGCAAACAAAGTGGG 59.134 45.455 0.00 0.00 0.00 4.61
2013 4338 2.813061 CCCACAAGTGCAAACTGAAAG 58.187 47.619 0.00 0.00 42.29 2.62
2024 4349 2.758009 CTGGAAAATTGCCCACAAGTG 58.242 47.619 0.00 0.00 39.69 3.16
2030 4355 0.968405 GACTGCTGGAAAATTGCCCA 59.032 50.000 0.00 0.00 0.00 5.36
2061 4386 2.034048 TTGCCACACGACCAGCACTA 62.034 55.000 0.00 0.00 34.37 2.74
2416 5716 4.787551 TGTGGCGGTTCTTTATCCATAAT 58.212 39.130 0.00 0.00 0.00 1.28
2470 5770 7.578571 GCTCTATGGTAGAATAGGGAAGTGATG 60.579 44.444 0.00 0.00 33.09 3.07
2490 5790 1.109920 ACGATGAGGTGCGGCTCTAT 61.110 55.000 0.00 0.00 0.00 1.98
2662 5962 0.745845 ACGGATGCAGTGCAGATTCC 60.746 55.000 24.20 22.67 43.65 3.01
2879 6179 8.450964 GCAATCAGCAAACAAAGATTACTACTA 58.549 33.333 0.00 0.00 44.79 1.82
2965 6265 4.389374 ACCATGAAATCCACGATGTATCC 58.611 43.478 0.00 0.00 0.00 2.59
3184 6484 9.125026 AGGTATCATGATTGTTTAATCTTCCAC 57.875 33.333 14.65 0.22 42.56 4.02
3300 6601 2.024414 CCAGGGCATAGTAAACAAGGC 58.976 52.381 0.00 0.00 0.00 4.35
3303 6604 1.341581 GGGCCAGGGCATAGTAAACAA 60.342 52.381 16.36 0.00 44.11 2.83
3374 6675 1.854126 CAAGCTTTGTCAAAACAGGCG 59.146 47.619 0.00 0.00 39.39 5.52
3380 6681 3.692101 TCTTCGGTCAAGCTTTGTCAAAA 59.308 39.130 0.00 0.00 31.26 2.44
3398 6699 2.433970 ACTCATCCTAGCAGCCTTCTTC 59.566 50.000 0.00 0.00 0.00 2.87
3453 6754 0.392729 CTCCTCAGCCAAGCCAAGAG 60.393 60.000 0.00 0.00 0.00 2.85
3542 6846 6.827251 ACTTCTAGATATGGCCATATGCATTG 59.173 38.462 37.31 23.29 43.89 2.82
3604 6908 2.433239 TCTAATTAAGGCGTGTCCCCTC 59.567 50.000 0.00 0.00 34.51 4.30
3796 7100 0.250901 AATGAGGTGAGTGGTGGCAC 60.251 55.000 9.70 9.70 0.00 5.01
3970 7274 0.178929 AAGGTGGGAGACGGAAGACT 60.179 55.000 0.00 0.00 39.22 3.24
4040 7352 3.403038 AGCGTTGTAGAAAGTCAGCAAT 58.597 40.909 0.00 0.00 0.00 3.56
4405 7720 8.116753 CAGTAAATTTTGACATTACTAGAGCGG 58.883 37.037 0.00 0.00 37.68 5.52
4408 7723 8.398665 GGGCAGTAAATTTTGACATTACTAGAG 58.601 37.037 0.00 0.00 37.68 2.43
4420 7735 5.355596 TCACACTTTGGGCAGTAAATTTTG 58.644 37.500 0.00 0.00 0.00 2.44
4495 7810 6.799512 AGTTCAAAGGCACATGCTTATATTC 58.200 36.000 3.48 0.00 41.70 1.75
4561 7878 5.926542 TGACTGTAAAGTATGCTGACACTTC 59.073 40.000 0.00 0.00 33.92 3.01
4593 7911 2.546368 ACGTATTGTTGCAAGCGAAAGA 59.454 40.909 0.00 0.00 0.00 2.52
4598 7916 2.233355 CTGAACGTATTGTTGCAAGCG 58.767 47.619 0.00 2.57 42.09 4.68
4606 7924 8.832521 TCAAAACATTCTAACTGAACGTATTGT 58.167 29.630 0.00 0.00 37.52 2.71
4758 8076 7.990886 ACAGTGTTTTAACTATCTTCTGGTTGA 59.009 33.333 0.00 0.00 30.31 3.18
4774 8092 7.051623 ACCAGTCTAAATGTGACAGTGTTTTA 58.948 34.615 0.00 0.00 36.94 1.52
4846 8164 6.391227 ACTCCTCGAACATGTGAAAATTTT 57.609 33.333 2.28 2.28 0.00 1.82
4892 8210 0.615850 AACAGAGCTAGGCAACCCTC 59.384 55.000 0.00 0.00 41.75 4.30
4913 8231 9.025041 TCAATGTCTACATAAGAGTCAAGAAGA 57.975 33.333 0.00 0.00 35.10 2.87
4940 8258 1.001633 GTTGTCCCGAAGTAAGCTCCA 59.998 52.381 0.00 0.00 0.00 3.86
4952 8270 0.249741 AGTGAGGAAACGTTGTCCCG 60.250 55.000 19.44 0.00 35.59 5.14
5120 8438 1.656441 CTTGGAAGTGCTGTGTGGC 59.344 57.895 0.00 0.00 0.00 5.01
5153 8471 0.306533 CAAGTTAAACTGCGCCACGT 59.693 50.000 4.18 0.00 0.00 4.49
5362 8686 5.871524 CACAGCAGAGACATAACACTGTTAT 59.128 40.000 8.41 8.41 34.84 1.89
5532 8856 2.361789 TCACATCCATGACAGCACATG 58.638 47.619 0.00 10.24 44.78 3.21
5617 8944 0.400594 AGCTACGGACTGCCCTTTTT 59.599 50.000 0.00 0.00 0.00 1.94
5622 8949 3.851128 GGGAGCTACGGACTGCCC 61.851 72.222 0.00 0.00 39.59 5.36
5625 8952 1.726853 CAAAAGGGAGCTACGGACTG 58.273 55.000 0.00 0.00 0.00 3.51
5626 8953 0.036294 GCAAAAGGGAGCTACGGACT 60.036 55.000 0.00 0.00 0.00 3.85
5627 8954 1.359459 CGCAAAAGGGAGCTACGGAC 61.359 60.000 0.00 0.00 0.00 4.79
5628 8955 1.079405 CGCAAAAGGGAGCTACGGA 60.079 57.895 0.00 0.00 0.00 4.69
5629 8956 0.672401 TTCGCAAAAGGGAGCTACGG 60.672 55.000 0.00 0.00 0.00 4.02
5669 9004 4.364415 TGCAGGAAAAAGTTGTGTACAC 57.636 40.909 19.36 19.36 0.00 2.90
5707 9097 4.018050 AGGGAAAATCTGCATAAGTGGTCT 60.018 41.667 0.00 0.00 0.00 3.85
5722 9122 2.498885 GCTGGAGAAATGCAGGGAAAAT 59.501 45.455 0.00 0.00 0.00 1.82
5739 9139 1.227556 GCGGTACCTACATGGCTGG 60.228 63.158 10.90 0.00 40.22 4.85
5750 9166 3.735181 CTGACCTAACAGCGGTACC 57.265 57.895 0.16 0.16 34.19 3.34
5757 9173 5.163814 GCTTTATCTTGTGCTGACCTAACAG 60.164 44.000 0.00 0.00 40.43 3.16
5852 9273 4.407621 TGAGGGTCTCGCCAAGAATATTAA 59.592 41.667 0.00 0.00 39.65 1.40
5877 9298 9.190317 GTCCACTCTAATCCTTGGAAAATTTAT 57.810 33.333 0.00 0.00 39.86 1.40
5878 9299 8.167392 TGTCCACTCTAATCCTTGGAAAATTTA 58.833 33.333 0.00 0.00 39.86 1.40
5907 9328 8.334263 TGGGAAAAATTAAAGGATTGAAATGC 57.666 30.769 0.00 0.00 0.00 3.56
5926 9347 7.124147 GGGACTTCAAATCATAGAAATGGGAAA 59.876 37.037 0.00 0.00 33.61 3.13
5956 9377 1.202486 TCGCTAAGGGCTTATTCGGTG 60.202 52.381 0.00 0.00 39.13 4.94
5991 9412 4.570772 GCACTTCCGTCAATATTGCTCTTA 59.429 41.667 10.76 0.00 0.00 2.10
6025 9446 3.889520 AGCTGCTACTACCAAGTTACC 57.110 47.619 0.00 0.00 37.15 2.85
6028 9449 4.527038 TCACTTAGCTGCTACTACCAAGTT 59.473 41.667 9.27 0.00 37.15 2.66
6106 9527 4.701765 AGTAGATCCGTAGCGTCTTCTTA 58.298 43.478 0.00 0.00 0.00 2.10
6158 9579 4.641645 CCCTGTGCGCCTGACCAA 62.642 66.667 4.18 0.00 0.00 3.67
6285 9706 1.581447 GGACCAAAAGCTTGCCTCG 59.419 57.895 0.00 0.00 0.00 4.63
6288 9709 1.285950 GTCGGACCAAAAGCTTGCC 59.714 57.895 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.