Multiple sequence alignment - TraesCS5D01G397300

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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 TraesCS5D01G397300 chr5D 100.000 5325 0 0 1 5325 464104925 464110249 0.000000e+00 9834
1 TraesCS5D01G397300 chr5D 88.813 3388 310 31 3 3350 474823396 474820038 0.000000e+00 4093
2 TraesCS5D01G397300 chr5D 86.585 1722 177 22 3392 5071 474820037 474818328 0.000000e+00 1851
3 TraesCS5D01G397300 chr5B 93.226 5152 271 39 135 5258 571200660 571205761 0.000000e+00 7509
4 TraesCS5D01G397300 chr5B 86.027 2011 201 36 3376 5325 582107196 582105205 0.000000e+00 2084
5 TraesCS5D01G397300 chr5B 87.981 1481 143 19 881 2339 582117196 582115729 0.000000e+00 1716
6 TraesCS5D01G397300 chr5A 91.503 3354 218 23 1 3338 584547967 584551269 0.000000e+00 4553
7 TraesCS5D01G397300 chr5A 92.111 1952 124 12 3386 5324 584551348 584553282 0.000000e+00 2724
8 TraesCS5D01G397300 chr2D 86.284 3084 342 39 1 3055 551823752 551820721 0.000000e+00 3277
9 TraesCS5D01G397300 chr2D 84.434 1317 134 31 1 1307 577356540 577355285 0.000000e+00 1230
10 TraesCS5D01G397300 chr2D 83.612 598 79 15 3726 4312 577342133 577341544 1.300000e-150 544
11 TraesCS5D01G397300 chr2D 85.000 440 39 11 4460 4895 551826585 551826169 6.380000e-114 422
12 TraesCS5D01G397300 chr2D 87.397 365 40 4 3460 3819 577349736 577349373 1.070000e-111 414
13 TraesCS5D01G397300 chr2D 83.827 439 47 11 4460 4895 551714273 551713856 3.860000e-106 396
14 TraesCS5D01G397300 chr2A 84.709 3283 399 50 1 3243 692359541 692356322 0.000000e+00 3186
15 TraesCS5D01G397300 chr2A 84.554 3276 389 61 1 3243 692273590 692270399 0.000000e+00 3138
16 TraesCS5D01G397300 chr2A 84.487 1560 213 17 1695 3238 692328250 692326704 0.000000e+00 1513
17 TraesCS5D01G397300 chr2A 80.241 1579 183 63 3365 4895 692356222 692354725 0.000000e+00 1068
18 TraesCS5D01G397300 chr2A 83.752 597 78 15 3726 4311 715422439 715421851 1.010000e-151 547
19 TraesCS5D01G397300 chr2A 77.104 297 23 22 5033 5320 715427287 715427027 4.330000e-26 130
20 TraesCS5D01G397300 chr7B 87.795 2327 244 17 1035 3340 626566820 626564513 0.000000e+00 2687
21 TraesCS5D01G397300 chr7B 85.812 2037 192 41 3360 5325 626564525 626562515 0.000000e+00 2071
22 TraesCS5D01G397300 chr7A 88.724 2155 174 33 3 2138 660067961 660070065 0.000000e+00 2569
23 TraesCS5D01G397300 chr7A 84.801 2033 177 55 3359 5325 660082211 660084177 0.000000e+00 1921
24 TraesCS5D01G397300 chr7A 87.295 1220 143 4 2134 3341 660081004 660082223 0.000000e+00 1384
25 TraesCS5D01G397300 chr2B 84.089 1942 220 52 1 1926 694486970 694485102 0.000000e+00 1792
26 TraesCS5D01G397300 chr2B 85.626 1621 194 28 314 1920 722379786 722378191 0.000000e+00 1666
27 TraesCS5D01G397300 chr2B 83.642 593 78 15 3726 4307 694420844 694420260 1.690000e-149 540
28 TraesCS5D01G397300 chr2B 85.399 363 48 3 3460 3818 694429089 694428728 6.510000e-99 372
29 TraesCS5D01G397300 chr2B 83.508 382 51 8 3442 3818 722377303 722376929 3.950000e-91 346
30 TraesCS5D01G397300 chr2B 78.521 284 21 20 5033 5308 694477562 694477311 3.320000e-32 150
31 TraesCS5D01G397300 chr2B 79.508 244 13 19 5033 5265 694425902 694425685 7.190000e-29 139
32 TraesCS5D01G397300 chr2B 79.098 244 14 19 5033 5265 694446679 694446462 3.350000e-27 134
33 TraesCS5D01G397300 chr7D 88.435 1444 127 21 3460 4867 570988194 570989633 0.000000e+00 1705
34 TraesCS5D01G397300 chr7D 87.164 483 37 12 4864 5325 570992321 570992799 4.720000e-145 525
35 TraesCS5D01G397300 chrUn 83.710 1240 131 31 1 1230 421373886 421372708 0.000000e+00 1105


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 TraesCS5D01G397300 chr5D 464104925 464110249 5324 False 9834.0 9834 100.0000 1 5325 1 chr5D.!!$F1 5324
1 TraesCS5D01G397300 chr5D 474818328 474823396 5068 True 2972.0 4093 87.6990 3 5071 2 chr5D.!!$R1 5068
2 TraesCS5D01G397300 chr5B 571200660 571205761 5101 False 7509.0 7509 93.2260 135 5258 1 chr5B.!!$F1 5123
3 TraesCS5D01G397300 chr5B 582105205 582107196 1991 True 2084.0 2084 86.0270 3376 5325 1 chr5B.!!$R1 1949
4 TraesCS5D01G397300 chr5B 582115729 582117196 1467 True 1716.0 1716 87.9810 881 2339 1 chr5B.!!$R2 1458
5 TraesCS5D01G397300 chr5A 584547967 584553282 5315 False 3638.5 4553 91.8070 1 5324 2 chr5A.!!$F1 5323
6 TraesCS5D01G397300 chr2D 551820721 551826585 5864 True 1849.5 3277 85.6420 1 4895 2 chr2D.!!$R5 4894
7 TraesCS5D01G397300 chr2D 577355285 577356540 1255 True 1230.0 1230 84.4340 1 1307 1 chr2D.!!$R4 1306
8 TraesCS5D01G397300 chr2D 577341544 577342133 589 True 544.0 544 83.6120 3726 4312 1 chr2D.!!$R2 586
9 TraesCS5D01G397300 chr2A 692270399 692273590 3191 True 3138.0 3138 84.5540 1 3243 1 chr2A.!!$R1 3242
10 TraesCS5D01G397300 chr2A 692354725 692359541 4816 True 2127.0 3186 82.4750 1 4895 2 chr2A.!!$R5 4894
11 TraesCS5D01G397300 chr2A 692326704 692328250 1546 True 1513.0 1513 84.4870 1695 3238 1 chr2A.!!$R2 1543
12 TraesCS5D01G397300 chr2A 715421851 715422439 588 True 547.0 547 83.7520 3726 4311 1 chr2A.!!$R3 585
13 TraesCS5D01G397300 chr7B 626562515 626566820 4305 True 2379.0 2687 86.8035 1035 5325 2 chr7B.!!$R1 4290
14 TraesCS5D01G397300 chr7A 660067961 660070065 2104 False 2569.0 2569 88.7240 3 2138 1 chr7A.!!$F1 2135
15 TraesCS5D01G397300 chr7A 660081004 660084177 3173 False 1652.5 1921 86.0480 2134 5325 2 chr7A.!!$F2 3191
16 TraesCS5D01G397300 chr2B 694485102 694486970 1868 True 1792.0 1792 84.0890 1 1926 1 chr2B.!!$R4 1925
17 TraesCS5D01G397300 chr2B 722376929 722379786 2857 True 1006.0 1666 84.5670 314 3818 2 chr2B.!!$R6 3504
18 TraesCS5D01G397300 chr2B 694420260 694420844 584 True 540.0 540 83.6420 3726 4307 1 chr2B.!!$R1 581
19 TraesCS5D01G397300 chr2B 694425685 694429089 3404 True 255.5 372 82.4535 3460 5265 2 chr2B.!!$R5 1805
20 TraesCS5D01G397300 chr7D 570988194 570992799 4605 False 1115.0 1705 87.7995 3460 5325 2 chr7D.!!$F1 1865
21 TraesCS5D01G397300 chrUn 421372708 421373886 1178 True 1105.0 1105 83.7100 1 1230 1 chrUn.!!$R1 1229

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
88 2924 1.070134 TCCCCGTCTTCTCACTTTGTG 59.930 52.381 0.0 0.0 34.45 3.33 F
89 2925 1.202651 CCCCGTCTTCTCACTTTGTGT 60.203 52.381 0.0 0.0 34.79 3.72 F
1982 4926 0.675633 GCATGTTTGGGTTGTGCTCT 59.324 50.000 0.0 0.0 33.25 4.09 F
2598 5557 0.110373 GACCGACGATGGTTTTGTGC 60.110 55.000 0.0 0.0 44.01 4.57 F
3345 6348 0.111310 CACATACACACACACGCACG 60.111 55.000 0.0 0.0 0.00 5.34 F
3346 6349 1.154672 CATACACACACACGCACGC 60.155 57.895 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 4437 2.436911 AGAAAACCTACCACGTGTTCCT 59.563 45.455 15.65 0.54 29.09 3.36 R
2013 4959 3.197265 TGGTCTGCAACATATGTCATCG 58.803 45.455 9.23 0.00 0.00 3.84 R
3358 6361 0.098552 AATGTGTGTGTGTGCGTGTG 59.901 50.000 0.00 0.00 0.00 3.82 R
3802 7085 0.099968 CTCTGCGACGTTAATCCCGA 59.900 55.000 0.00 0.00 0.00 5.14 R
4196 9183 0.105964 CACACGTCCCACTTCTCCAA 59.894 55.000 0.00 0.00 0.00 3.53 R
4819 9937 1.771854 TCTTGTGGTGGGAAGCAGTAA 59.228 47.619 0.00 0.00 0.00 2.24 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
88 2924 1.070134 TCCCCGTCTTCTCACTTTGTG 59.930 52.381 0.00 0.00 34.45 3.33
89 2925 1.202651 CCCCGTCTTCTCACTTTGTGT 60.203 52.381 0.00 0.00 34.79 3.72
91 2927 2.550978 CCGTCTTCTCACTTTGTGTGT 58.449 47.619 0.00 0.00 46.27 3.72
92 2928 2.285220 CCGTCTTCTCACTTTGTGTGTG 59.715 50.000 0.00 0.00 46.27 3.82
93 2929 2.930040 CGTCTTCTCACTTTGTGTGTGT 59.070 45.455 0.00 0.00 46.27 3.72
94 2930 3.242091 CGTCTTCTCACTTTGTGTGTGTG 60.242 47.826 0.00 0.00 46.27 3.82
95 2931 3.684788 GTCTTCTCACTTTGTGTGTGTGT 59.315 43.478 0.00 0.00 46.27 3.72
96 2932 3.684305 TCTTCTCACTTTGTGTGTGTGTG 59.316 43.478 0.00 0.00 46.27 3.82
97 2933 2.355197 TCTCACTTTGTGTGTGTGTGG 58.645 47.619 0.00 0.00 46.27 4.17
178 3031 3.506844 GCATTGGAAATTTGGCCATGTTT 59.493 39.130 6.09 11.17 33.46 2.83
493 3360 8.401709 GTTTGGCAAATTCTCTAGAAGGATAAG 58.598 37.037 16.74 0.00 37.48 1.73
632 3506 5.183014 TGCGGCCACTCTATATATATTCG 57.817 43.478 2.24 0.00 0.00 3.34
874 3776 7.426929 GAAAGCGTTCCATATGTAGATTCAT 57.573 36.000 0.30 0.00 0.00 2.57
907 3809 6.542370 GTGGAACTTGTGTGGTATTATATGCT 59.458 38.462 0.00 0.00 0.00 3.79
988 3898 4.404073 AGAGAGAAGTACCTGCCATAAGTG 59.596 45.833 0.00 0.00 0.00 3.16
994 3904 2.496899 ACCTGCCATAAGTGAAGGTG 57.503 50.000 0.00 0.00 39.38 4.00
998 3908 1.885887 TGCCATAAGTGAAGGTGCAAC 59.114 47.619 0.00 0.00 0.00 4.17
1087 3997 9.237187 AGGTAAAAGAAGAGGAAGATGAAAATC 57.763 33.333 0.00 0.00 0.00 2.17
1184 4095 5.982516 CGAAGAGGAAGATGGATAAGAACAG 59.017 44.000 0.00 0.00 0.00 3.16
1511 4437 5.880332 GGGCGCTCATATCCTATTCATTTAA 59.120 40.000 7.64 0.00 0.00 1.52
1635 4564 7.162761 TGTGAAGGTTATCTTTTCCATTACGA 58.837 34.615 0.00 0.00 35.50 3.43
1982 4926 0.675633 GCATGTTTGGGTTGTGCTCT 59.324 50.000 0.00 0.00 33.25 4.09
2045 4991 0.911769 TGCAGACCATTCCAGTAGGG 59.088 55.000 0.00 0.00 34.83 3.53
2198 5144 0.756294 ACAATCGCATCGGGTATGGA 59.244 50.000 0.00 0.00 35.99 3.41
2284 5230 1.072159 GCGAGGCTCCCTATGCATT 59.928 57.895 3.54 0.00 35.83 3.56
2291 5237 1.143305 CTCCCTATGCATTTCTCGCG 58.857 55.000 3.54 0.00 0.00 5.87
2377 5324 4.466370 TGTAGATGGTACTGTCCTTCAAGG 59.534 45.833 0.00 0.00 35.11 3.61
2566 5525 3.289834 AGCGCAACAACAGCAGGG 61.290 61.111 11.47 0.00 0.00 4.45
2598 5557 0.110373 GACCGACGATGGTTTTGTGC 60.110 55.000 0.00 0.00 44.01 4.57
2760 5720 6.293735 CGACAGTTTGGCAGGTAATTAAGAAA 60.294 38.462 0.00 0.00 0.00 2.52
2828 5788 9.585099 TGTAGTACTTTTTACGTGTATATTGGG 57.415 33.333 0.00 0.00 0.00 4.12
2937 5898 1.450312 GAGCATCGTCCACCCAAGG 60.450 63.158 0.00 0.00 0.00 3.61
2970 5931 5.389520 CTGAGGTGATAAGGTCTCCATCTA 58.610 45.833 0.00 0.00 41.88 1.98
3025 5986 5.634859 GTGACAATTTTGCAGGTAATTCAGG 59.365 40.000 0.00 0.00 0.00 3.86
3080 6045 8.425577 AACTATATATCGTGATGGCTAAATGC 57.574 34.615 0.00 0.00 41.94 3.56
3215 6185 5.356190 GGTCCTTTAGTTGTTTATACCAGGC 59.644 44.000 0.00 0.00 0.00 4.85
3330 6325 8.902540 TCAAAATGAGTAGTACTTGTTCACAT 57.097 30.769 0.00 0.00 0.00 3.21
3341 6344 3.308595 ACTTGTTCACATACACACACACG 59.691 43.478 0.00 0.00 0.00 4.49
3342 6345 1.595328 TGTTCACATACACACACACGC 59.405 47.619 0.00 0.00 0.00 5.34
3343 6346 1.595328 GTTCACATACACACACACGCA 59.405 47.619 0.00 0.00 0.00 5.24
3344 6347 1.213491 TCACATACACACACACGCAC 58.787 50.000 0.00 0.00 0.00 5.34
3345 6348 0.111310 CACATACACACACACGCACG 60.111 55.000 0.00 0.00 0.00 5.34
3346 6349 1.154672 CATACACACACACGCACGC 60.155 57.895 0.00 0.00 0.00 5.34
3347 6350 1.592939 ATACACACACACGCACGCA 60.593 52.632 0.00 0.00 0.00 5.24
3348 6351 1.827315 ATACACACACACGCACGCAC 61.827 55.000 0.00 0.00 0.00 5.34
3349 6352 3.858989 CACACACACGCACGCACA 61.859 61.111 0.00 0.00 0.00 4.57
3350 6353 3.860125 ACACACACGCACGCACAC 61.860 61.111 0.00 0.00 0.00 3.82
3363 6366 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
3458 6683 7.980099 ACATAGCACTGGTCTTATACTGTAAAC 59.020 37.037 0.00 0.00 0.00 2.01
3459 6684 6.607004 AGCACTGGTCTTATACTGTAAACT 57.393 37.500 0.00 0.00 0.00 2.66
3460 6685 7.713734 AGCACTGGTCTTATACTGTAAACTA 57.286 36.000 0.00 0.00 0.00 2.24
3461 6686 8.130671 AGCACTGGTCTTATACTGTAAACTAA 57.869 34.615 0.00 0.00 0.00 2.24
3462 6687 8.591072 AGCACTGGTCTTATACTGTAAACTAAA 58.409 33.333 0.00 0.00 0.00 1.85
3463 6688 8.654215 GCACTGGTCTTATACTGTAAACTAAAC 58.346 37.037 0.00 0.00 0.00 2.01
3577 6802 2.030274 GGACTTAACCATGTGGCACAAC 60.030 50.000 25.95 7.36 44.16 3.32
3668 6926 4.227864 CCTGGCAGAGGTAAATCTCTTT 57.772 45.455 17.94 0.00 41.76 2.52
3669 6927 4.195416 CCTGGCAGAGGTAAATCTCTTTC 58.805 47.826 17.94 0.00 41.76 2.62
3670 6928 4.080638 CCTGGCAGAGGTAAATCTCTTTCT 60.081 45.833 17.94 0.00 41.76 2.52
3671 6929 5.495640 CTGGCAGAGGTAAATCTCTTTCTT 58.504 41.667 9.42 0.00 41.76 2.52
3672 6930 5.880901 TGGCAGAGGTAAATCTCTTTCTTT 58.119 37.500 0.00 0.00 41.76 2.52
3676 6938 7.175816 GGCAGAGGTAAATCTCTTTCTTTCTTT 59.824 37.037 0.00 0.00 41.76 2.52
3711 6981 2.352342 TGTAAGCGCGCCCTTTTATTAC 59.648 45.455 30.33 25.51 0.00 1.89
3736 7006 9.991906 ACACTGCTAGTACTAATTAGAACAAAA 57.008 29.630 19.38 0.00 0.00 2.44
4196 9183 0.674895 GCTCGCCATGGAGAACAACT 60.675 55.000 19.39 0.00 36.08 3.16
4264 9251 1.229428 ACATCAAGTTGCACGTCCAG 58.771 50.000 0.00 0.00 0.00 3.86
4297 9286 1.002069 TGATCACCCCTTGCATCCTT 58.998 50.000 0.00 0.00 0.00 3.36
4502 9530 4.167307 GTCCCAATCCCCTTCATAACCTAA 59.833 45.833 0.00 0.00 0.00 2.69
4556 9603 2.094752 ACCCGAAAATCCTGCAAAATCG 60.095 45.455 0.00 0.00 0.00 3.34
4623 9735 9.449719 GGATTTCTTATCTTGTCCTCTTGTTTA 57.550 33.333 0.00 0.00 0.00 2.01
4714 9832 3.660865 CTTGGTAAGCCTACGTTCTGTT 58.339 45.455 0.00 0.00 35.27 3.16
4756 9874 5.052481 GCAATTGAATCTTTAGCCCATTCC 58.948 41.667 10.34 0.00 0.00 3.01
4794 9912 6.948886 TCTCAATCGGCTTAGGATTCTATACT 59.051 38.462 0.00 0.00 31.98 2.12
4819 9937 2.633967 TCCATGGTGCATCTTGCTTTTT 59.366 40.909 12.58 0.00 45.31 1.94
4931 12745 4.636249 ACTAGAGGTTTCAGCAAGTTGAG 58.364 43.478 7.16 0.00 0.00 3.02
4945 12759 7.118825 TCAGCAAGTTGAGAAGATTGACTTATG 59.881 37.037 7.16 0.00 39.13 1.90
4979 12793 0.822164 GTGGGCCTCTTAGACGCTTA 59.178 55.000 4.53 0.00 0.00 3.09
5077 12903 4.342665 AGTCCATAGGTTGCTAGCTAGTTC 59.657 45.833 21.62 11.87 37.74 3.01
5183 13018 4.355437 TGGTTTACTGAATTTGCACAACG 58.645 39.130 0.00 0.00 0.00 4.10
5311 13150 1.385528 GACAGGGTGTCAAAACCGTT 58.614 50.000 2.12 0.00 46.22 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 2905 1.202651 ACACAAAGTGAGAAGACGGGG 60.203 52.381 3.88 0.00 36.96 5.73
70 2906 2.240493 ACACAAAGTGAGAAGACGGG 57.760 50.000 3.88 0.00 36.96 5.28
341 3203 5.938125 GTCTTAAGACAAGAAAGGTATGGCA 59.062 40.000 27.12 0.00 44.18 4.92
493 3360 1.389609 CCTTCATGTGCTCCCCATGC 61.390 60.000 0.00 0.00 39.60 4.06
584 3452 5.417811 CATAATATTTTGGCAAGGCACACA 58.582 37.500 0.00 0.00 0.00 3.72
632 3506 7.953158 AGTACACATCATACATGAATGCTAC 57.047 36.000 0.00 2.20 40.69 3.58
859 3761 8.134261 CCACTCGAGATATGAATCTACATATGG 58.866 40.741 21.68 5.89 42.73 2.74
874 3776 3.056821 CCACACAAGTTCCACTCGAGATA 60.057 47.826 21.68 0.19 0.00 1.98
988 3898 1.904287 TGTACCATGGTTGCACCTTC 58.096 50.000 25.38 4.64 39.58 3.46
1087 3997 8.154649 TGCTTCCTTTTCTCTTTTGTACTAAG 57.845 34.615 0.00 0.00 0.00 2.18
1091 4001 8.648557 ATTTTGCTTCCTTTTCTCTTTTGTAC 57.351 30.769 0.00 0.00 0.00 2.90
1184 4095 3.997681 CGTTTTCTTCTCTTTCTCCTCCC 59.002 47.826 0.00 0.00 0.00 4.30
1295 4206 2.846827 TCATTCTCCTCCTTCCTTTCCC 59.153 50.000 0.00 0.00 0.00 3.97
1302 4213 5.867903 TCTCATTCTCATTCTCCTCCTTC 57.132 43.478 0.00 0.00 0.00 3.46
1511 4437 2.436911 AGAAAACCTACCACGTGTTCCT 59.563 45.455 15.65 0.54 29.09 3.36
1635 4564 5.574188 AGAGCACCATTCCTAAAAGTGAAT 58.426 37.500 0.00 0.00 0.00 2.57
1749 4689 7.816640 TCTCAAAGGCAGAAAACATTGTATAC 58.183 34.615 0.00 0.00 0.00 1.47
1982 4926 8.951787 ATTAATTAGTAATGGCTGAACACGTA 57.048 30.769 0.00 0.00 30.83 3.57
2013 4959 3.197265 TGGTCTGCAACATATGTCATCG 58.803 45.455 9.23 0.00 0.00 3.84
2045 4991 6.981722 ACAATCTTCCAAGTATTTGTGGAAC 58.018 36.000 1.01 0.00 46.58 3.62
2198 5144 8.809324 CGTCGTAACGGAATACCAACAGGTAT 62.809 46.154 1.42 1.42 45.44 2.73
2377 5324 1.140816 GCCAGTGTGAACGTCTTCTC 58.859 55.000 0.00 0.00 0.00 2.87
2461 5420 4.537135 AATGCGTCTTCAACTTCCTCTA 57.463 40.909 0.00 0.00 0.00 2.43
2566 5525 0.248949 GTCGGTCTTGCGTAGATCCC 60.249 60.000 0.00 0.00 34.79 3.85
2598 5557 1.290134 AACCTAGCCCTCTTCCCAAG 58.710 55.000 0.00 0.00 0.00 3.61
2760 5720 3.384789 TCAATCGATCGATCAGAGGGTTT 59.615 43.478 29.48 9.87 33.08 3.27
2828 5788 8.937634 ATTTTACAAAATGAAGCCATCTCATC 57.062 30.769 0.00 0.00 37.24 2.92
2937 5898 0.908198 ATCACCTCAGCCTTGGACTC 59.092 55.000 0.00 0.00 0.00 3.36
3080 6045 7.160049 AGATAAGCCTATGAATCATGTGACAG 58.840 38.462 5.91 0.00 0.00 3.51
3215 6185 7.327214 AGTCTTTTAGATGCTGAAGTAGAAGG 58.673 38.462 0.00 0.00 0.00 3.46
3326 6321 0.111310 CGTGCGTGTGTGTGTATGTG 60.111 55.000 0.00 0.00 0.00 3.21
3330 6325 2.202756 TGCGTGCGTGTGTGTGTA 60.203 55.556 0.00 0.00 0.00 2.90
3357 6360 2.277247 GTGTGTGTGTGCGTGTGC 60.277 61.111 0.00 0.00 43.20 4.57
3358 6361 0.098552 AATGTGTGTGTGTGCGTGTG 59.901 50.000 0.00 0.00 0.00 3.82
3359 6362 0.098552 CAATGTGTGTGTGTGCGTGT 59.901 50.000 0.00 0.00 0.00 4.49
3360 6363 0.591994 CCAATGTGTGTGTGTGCGTG 60.592 55.000 0.00 0.00 0.00 5.34
3363 6366 1.133982 TCAACCAATGTGTGTGTGTGC 59.866 47.619 0.00 0.00 0.00 4.57
3458 6683 9.030452 AGAGCATATAGATAGGAACCAGTTTAG 57.970 37.037 0.00 0.00 0.00 1.85
3459 6684 8.958060 AGAGCATATAGATAGGAACCAGTTTA 57.042 34.615 0.00 0.00 0.00 2.01
3460 6685 7.863901 AGAGCATATAGATAGGAACCAGTTT 57.136 36.000 0.00 0.00 0.00 2.66
3461 6686 7.291182 ACAAGAGCATATAGATAGGAACCAGTT 59.709 37.037 0.00 0.00 0.00 3.16
3462 6687 6.784969 ACAAGAGCATATAGATAGGAACCAGT 59.215 38.462 0.00 0.00 0.00 4.00
3463 6688 7.039434 TGACAAGAGCATATAGATAGGAACCAG 60.039 40.741 0.00 0.00 0.00 4.00
3668 6926 6.663734 ACAAGAAGGAAGGAAGAAAGAAAGA 58.336 36.000 0.00 0.00 0.00 2.52
3669 6927 6.951062 ACAAGAAGGAAGGAAGAAAGAAAG 57.049 37.500 0.00 0.00 0.00 2.62
3670 6928 7.013369 GCTTACAAGAAGGAAGGAAGAAAGAAA 59.987 37.037 0.00 0.00 0.00 2.52
3671 6929 6.486993 GCTTACAAGAAGGAAGGAAGAAAGAA 59.513 38.462 0.00 0.00 0.00 2.52
3672 6930 5.998363 GCTTACAAGAAGGAAGGAAGAAAGA 59.002 40.000 0.00 0.00 0.00 2.52
3676 6938 3.864921 GCGCTTACAAGAAGGAAGGAAGA 60.865 47.826 0.00 0.00 0.00 2.87
3736 7006 7.714377 CAGACTATCAGGCTAGTTCAATTCAAT 59.286 37.037 0.00 0.00 26.27 2.57
3742 7012 3.769300 TGCAGACTATCAGGCTAGTTCAA 59.231 43.478 0.00 0.00 26.27 2.69
3802 7085 0.099968 CTCTGCGACGTTAATCCCGA 59.900 55.000 0.00 0.00 0.00 5.14
4196 9183 0.105964 CACACGTCCCACTTCTCCAA 59.894 55.000 0.00 0.00 0.00 3.53
4264 9251 1.929836 GTGATCATCAGCACGACCTTC 59.070 52.381 0.00 0.00 0.00 3.46
4297 9286 2.909965 GTGCGAGGTTTTGGGGCA 60.910 61.111 0.00 0.00 0.00 5.36
4329 9320 2.936498 AGATCAAAACGCCTATGAACGG 59.064 45.455 0.00 0.00 0.00 4.44
4623 9735 4.764143 CCAAGGGGGCTTCGATTT 57.236 55.556 0.00 0.00 0.00 2.17
4714 9832 7.872483 TCAATTGCGCTAACATAGATCTGATAA 59.128 33.333 9.73 0.00 0.00 1.75
4728 9846 4.202010 GGGCTAAAGATTCAATTGCGCTAA 60.202 41.667 9.73 1.22 0.00 3.09
4819 9937 1.771854 TCTTGTGGTGGGAAGCAGTAA 59.228 47.619 0.00 0.00 0.00 2.24
4874 12687 9.066892 ACAAGTTGATCTATGCTGAACTAAAAA 57.933 29.630 10.54 0.00 0.00 1.94
4931 12745 7.840342 TCAGAAGAAGCATAAGTCAATCTTC 57.160 36.000 5.43 5.43 41.79 2.87
4945 12759 2.353109 GGCCCACAAAATCAGAAGAAGC 60.353 50.000 0.00 0.00 0.00 3.86
5022 12844 7.775093 TGCAGAAGAGGTAGCATTACAATAATT 59.225 33.333 0.00 0.00 31.05 1.40
5077 12903 8.908786 TTGAGATAAGAAATGTATGGCCTAAG 57.091 34.615 3.32 0.00 0.00 2.18
5183 13018 9.657121 GAAGAGATTTACAAATTCGATCATTCC 57.343 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.