Multiple sequence alignment - TraesCS3D01G523200

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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 TraesCS3D01G523200 chr3D 100.000 4849 0 0 1 4849 603972192 603977040 0.000000e+00 8955
1 TraesCS3D01G523200 chr3D 94.039 671 38 2 4180 4849 610887154 610886485 0.000000e+00 1016
2 TraesCS3D01G523200 chr3D 86.165 571 67 5 1916 2481 7591904 7592467 1.490000e-169 606
3 TraesCS3D01G523200 chr3A 96.517 3273 95 10 1580 4849 733491754 733495010 0.000000e+00 5395
4 TraesCS3D01G523200 chr3A 89.573 1055 48 18 3 1008 733489998 733491039 0.000000e+00 1282
5 TraesCS3D01G523200 chr3A 89.312 552 30 15 1058 1584 733491059 733491606 0.000000e+00 665
6 TraesCS3D01G523200 chr3A 84.853 614 78 7 1880 2481 12813858 12813248 5.370000e-169 604
7 TraesCS3D01G523200 chr3B 96.091 2277 74 8 1580 3845 811094276 811096548 0.000000e+00 3698
8 TraesCS3D01G523200 chr3B 89.150 894 41 22 580 1461 811093114 811093963 0.000000e+00 1062
9 TraesCS3D01G523200 chr3B 82.818 1164 139 38 1917 3048 9915868 9917002 0.000000e+00 985
10 TraesCS3D01G523200 chr3B 81.473 421 52 17 1038 1453 9914370 9914769 6.050000e-84 322
11 TraesCS3D01G523200 chr3B 87.747 253 23 4 83 333 811090337 811090583 6.140000e-74 289
12 TraesCS3D01G523200 chr3B 81.639 305 31 14 3890 4180 811096560 811096853 3.770000e-56 230
13 TraesCS3D01G523200 chr3B 89.781 137 10 3 380 515 811092973 811093106 6.450000e-39 172
14 TraesCS3D01G523200 chr3B 92.157 102 6 1 1483 1582 811094025 811094126 5.060000e-30 143
15 TraesCS3D01G523200 chr1D 95.827 671 27 1 4180 4849 319517715 319517045 0.000000e+00 1083
16 TraesCS3D01G523200 chr5D 94.627 670 35 1 4181 4849 389374131 389374800 0.000000e+00 1037
17 TraesCS3D01G523200 chr4D 94.039 671 39 1 4180 4849 455275781 455276451 0.000000e+00 1016
18 TraesCS3D01G523200 chr4D 94.393 214 12 0 1241 1454 393635964 393636177 3.620000e-86 329
19 TraesCS3D01G523200 chr4D 93.810 210 13 0 1241 1450 28837078 28837287 2.820000e-82 316
20 TraesCS3D01G523200 chr7D 94.039 671 37 2 4180 4849 117521635 117520967 0.000000e+00 1014
21 TraesCS3D01G523200 chr7D 93.890 671 40 1 4180 4849 635693011 635692341 0.000000e+00 1011
22 TraesCS3D01G523200 chr7D 94.030 670 33 4 4182 4849 379328638 379327974 0.000000e+00 1009
23 TraesCS3D01G523200 chr2D 93.658 678 42 1 4173 4849 394919683 394919006 0.000000e+00 1013
24 TraesCS3D01G523200 chr4A 95.714 210 9 0 1241 1450 75215127 75214918 6.010000e-89 339
25 TraesCS3D01G523200 chr4A 94.762 210 11 0 1241 1450 574872618 574872409 1.300000e-85 327
26 TraesCS3D01G523200 chr4B 93.925 214 13 0 1241 1454 483335245 483335032 1.680000e-84 324
27 TraesCS3D01G523200 chr4B 94.286 210 12 0 1241 1450 41010038 41010247 6.050000e-84 322


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 TraesCS3D01G523200 chr3D 603972192 603977040 4848 False 8955.000000 8955 100.000000 1 4849 1 chr3D.!!$F2 4848
1 TraesCS3D01G523200 chr3D 610886485 610887154 669 True 1016.000000 1016 94.039000 4180 4849 1 chr3D.!!$R1 669
2 TraesCS3D01G523200 chr3D 7591904 7592467 563 False 606.000000 606 86.165000 1916 2481 1 chr3D.!!$F1 565
3 TraesCS3D01G523200 chr3A 733489998 733495010 5012 False 2447.333333 5395 91.800667 3 4849 3 chr3A.!!$F1 4846
4 TraesCS3D01G523200 chr3A 12813248 12813858 610 True 604.000000 604 84.853000 1880 2481 1 chr3A.!!$R1 601
5 TraesCS3D01G523200 chr3B 811090337 811096853 6516 False 932.333333 3698 89.427500 83 4180 6 chr3B.!!$F2 4097
6 TraesCS3D01G523200 chr3B 9914370 9917002 2632 False 653.500000 985 82.145500 1038 3048 2 chr3B.!!$F1 2010
7 TraesCS3D01G523200 chr1D 319517045 319517715 670 True 1083.000000 1083 95.827000 4180 4849 1 chr1D.!!$R1 669
8 TraesCS3D01G523200 chr5D 389374131 389374800 669 False 1037.000000 1037 94.627000 4181 4849 1 chr5D.!!$F1 668
9 TraesCS3D01G523200 chr4D 455275781 455276451 670 False 1016.000000 1016 94.039000 4180 4849 1 chr4D.!!$F3 669
10 TraesCS3D01G523200 chr7D 117520967 117521635 668 True 1014.000000 1014 94.039000 4180 4849 1 chr7D.!!$R1 669
11 TraesCS3D01G523200 chr7D 635692341 635693011 670 True 1011.000000 1011 93.890000 4180 4849 1 chr7D.!!$R3 669
12 TraesCS3D01G523200 chr7D 379327974 379328638 664 True 1009.000000 1009 94.030000 4182 4849 1 chr7D.!!$R2 667
13 TraesCS3D01G523200 chr2D 394919006 394919683 677 True 1013.000000 1013 93.658000 4173 4849 1 chr2D.!!$R1 676

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
446 2806 0.439985 CTTTGATGAGTGCACCGTCG 59.560 55.000 14.63 0.61 0.00 5.12 F
1429 3839 0.034767 TCGACATGGACGAGTACCCT 60.035 55.000 11.96 0.00 34.85 4.34 F
1464 3874 1.270839 CCAGGTCCGTGATCACAGTTT 60.271 52.381 24.93 4.06 0.00 2.66 F
3562 6810 0.528470 GTCCTGGACACCGAGAAGAG 59.472 60.000 21.70 0.00 32.09 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 3878 0.608130 CTACTACTGCTGGTGGTGCA 59.392 55.000 8.94 0.0 39.92 4.57 R
2705 5938 2.158986 CCACTCAAGCTCAGGATGTAGG 60.159 54.545 0.00 0.0 37.40 3.18 R
3693 6941 1.072159 GCAAGCTGACAGGGAGTGT 59.928 57.895 4.26 0.0 44.49 3.55 R
4414 7683 0.469331 CATACCCGGCAGGAGTCCTA 60.469 60.000 12.53 0.0 41.02 2.94 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
23 24 1.067071 CACCAGTTCGGGACTCCTTAC 60.067 57.143 0.00 0.00 40.22 2.34
24 25 1.203149 ACCAGTTCGGGACTCCTTACT 60.203 52.381 0.00 0.00 40.22 2.24
25 26 2.042162 ACCAGTTCGGGACTCCTTACTA 59.958 50.000 0.00 0.00 40.22 1.82
62 63 1.610554 GCTCCGGCAAGTACCTACCA 61.611 60.000 0.00 0.00 38.54 3.25
70 71 3.043418 GCAAGTACCTACCATCCCCTTA 58.957 50.000 0.00 0.00 0.00 2.69
72 73 4.080186 GCAAGTACCTACCATCCCCTTAAA 60.080 45.833 0.00 0.00 0.00 1.52
73 74 5.681639 CAAGTACCTACCATCCCCTTAAAG 58.318 45.833 0.00 0.00 0.00 1.85
132 133 5.581126 TGCTTTGAAATAGCGATTCCAAT 57.419 34.783 0.00 0.00 41.54 3.16
138 139 7.579589 TTGAAATAGCGATTCCAATTGTTTG 57.420 32.000 4.43 0.00 0.00 2.93
143 144 8.600449 AATAGCGATTCCAATTGTTTGAAAAA 57.400 26.923 4.43 0.00 34.60 1.94
190 192 1.672356 GGCATTCACGAGTGCACCT 60.672 57.895 14.63 0.04 44.58 4.00
230 244 6.508030 TGGTCCATAAACCTAGCAATCATA 57.492 37.500 0.00 0.00 40.20 2.15
295 309 2.876581 AGGTGGTTTGTGGGAATCTTC 58.123 47.619 0.00 0.00 0.00 2.87
306 320 2.202566 GGGAATCTTCTAGGCGAAACG 58.797 52.381 0.00 0.00 0.00 3.60
310 324 1.542492 TCTTCTAGGCGAAACGGTCT 58.458 50.000 0.00 0.00 0.00 3.85
327 341 1.078426 CTGTGGGATTGGTCGGGTC 60.078 63.158 0.00 0.00 0.00 4.46
340 1676 3.327172 TGGTCGGGTCCTGTTGTTAAATA 59.673 43.478 0.00 0.00 0.00 1.40
341 1677 4.202440 TGGTCGGGTCCTGTTGTTAAATAA 60.202 41.667 0.00 0.00 0.00 1.40
342 1678 4.945543 GGTCGGGTCCTGTTGTTAAATAAT 59.054 41.667 0.00 0.00 0.00 1.28
415 2775 4.890158 AAAATCTTCCATGTGTTTCCCC 57.110 40.909 0.00 0.00 0.00 4.81
416 2776 2.532250 ATCTTCCATGTGTTTCCCCC 57.468 50.000 0.00 0.00 0.00 5.40
417 2777 1.153539 TCTTCCATGTGTTTCCCCCA 58.846 50.000 0.00 0.00 0.00 4.96
446 2806 0.439985 CTTTGATGAGTGCACCGTCG 59.560 55.000 14.63 0.61 0.00 5.12
543 2910 3.825328 ACAAGATGAGAAGTTGGCTTGT 58.175 40.909 0.00 0.00 40.55 3.16
578 2952 1.864669 TTTAGGTACGATCGGGGGTT 58.135 50.000 20.98 0.00 0.00 4.11
588 2962 1.411612 GATCGGGGGTTGGTAGTGTAG 59.588 57.143 0.00 0.00 0.00 2.74
589 2963 1.219935 CGGGGGTTGGTAGTGTAGC 59.780 63.158 0.00 0.00 0.00 3.58
595 2986 1.135170 GGTTGGTAGTGTAGCGGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
612 3003 2.670414 GAGACGATGCTCTTTTGGTGAG 59.330 50.000 0.00 0.00 34.87 3.51
799 3190 2.091541 CCTTGCTTCCTTTTGGCGATA 58.908 47.619 0.00 0.00 40.12 2.92
916 3315 1.326245 CACGTACACATGCCGGTAATG 59.674 52.381 15.30 15.30 0.00 1.90
945 3344 2.667470 AGCTAATCCGGCTCTCTGTTA 58.333 47.619 0.00 0.00 34.70 2.41
946 3345 3.031736 AGCTAATCCGGCTCTCTGTTAA 58.968 45.455 0.00 0.00 34.70 2.01
973 3372 1.602311 ATAGTAGTACTCCACGGCCG 58.398 55.000 26.86 26.86 0.00 6.13
982 3381 2.738521 CCACGGCCGACACTTCAG 60.739 66.667 35.90 10.12 0.00 3.02
1031 3440 1.159713 TCGTTGTGACAGCAAGCAGG 61.160 55.000 0.00 0.00 0.00 4.85
1032 3441 1.008079 GTTGTGACAGCAAGCAGGC 60.008 57.895 0.00 0.00 0.00 4.85
1033 3442 2.195567 TTGTGACAGCAAGCAGGCC 61.196 57.895 0.00 0.00 0.00 5.19
1034 3443 2.595463 GTGACAGCAAGCAGGCCA 60.595 61.111 5.01 0.00 0.00 5.36
1035 3444 2.195411 TGACAGCAAGCAGGCCAA 59.805 55.556 5.01 0.00 0.00 4.52
1036 3445 1.900016 TGACAGCAAGCAGGCCAAG 60.900 57.895 5.01 0.00 0.00 3.61
1221 3631 2.811317 GGCGAGCCGTCTGACAAG 60.811 66.667 8.73 0.00 0.00 3.16
1222 3632 2.258591 GCGAGCCGTCTGACAAGA 59.741 61.111 8.73 0.00 0.00 3.02
1297 3707 0.934901 CGGCGTACCAGATGATCACG 60.935 60.000 0.00 0.00 34.57 4.35
1429 3839 0.034767 TCGACATGGACGAGTACCCT 60.035 55.000 11.96 0.00 34.85 4.34
1464 3874 1.270839 CCAGGTCCGTGATCACAGTTT 60.271 52.381 24.93 4.06 0.00 2.66
1467 3877 4.253685 CAGGTCCGTGATCACAGTTTATT 58.746 43.478 24.93 1.97 0.00 1.40
1468 3878 4.695455 CAGGTCCGTGATCACAGTTTATTT 59.305 41.667 24.93 0.52 0.00 1.40
1469 3879 4.695455 AGGTCCGTGATCACAGTTTATTTG 59.305 41.667 24.93 5.71 0.00 2.32
1470 3880 4.403453 GTCCGTGATCACAGTTTATTTGC 58.597 43.478 24.93 0.00 0.00 3.68
1471 3881 4.068599 TCCGTGATCACAGTTTATTTGCA 58.931 39.130 24.93 0.00 0.00 4.08
1472 3882 4.083537 TCCGTGATCACAGTTTATTTGCAC 60.084 41.667 24.93 0.00 0.00 4.57
1473 3883 4.158384 CGTGATCACAGTTTATTTGCACC 58.842 43.478 24.93 0.00 0.00 5.01
1474 3884 4.320129 CGTGATCACAGTTTATTTGCACCA 60.320 41.667 24.93 0.00 0.00 4.17
1476 3886 4.022416 TGATCACAGTTTATTTGCACCACC 60.022 41.667 0.00 0.00 0.00 4.61
1478 3888 3.317711 TCACAGTTTATTTGCACCACCAG 59.682 43.478 0.00 0.00 0.00 4.00
1479 3889 2.035832 ACAGTTTATTTGCACCACCAGC 59.964 45.455 0.00 0.00 0.00 4.85
1480 3890 2.035704 CAGTTTATTTGCACCACCAGCA 59.964 45.455 0.00 0.00 40.85 4.41
1481 3891 2.297033 AGTTTATTTGCACCACCAGCAG 59.703 45.455 0.00 0.00 43.75 4.24
1554 4577 8.246180 ACTCAAAATTGATGCCACAATTAGTAG 58.754 33.333 15.16 14.00 45.71 2.57
1596 4775 3.423539 TTGATGTCCCTTGGTTGAGAG 57.576 47.619 0.00 0.00 0.00 3.20
1598 4777 2.303022 TGATGTCCCTTGGTTGAGAGTC 59.697 50.000 0.00 0.00 0.00 3.36
1657 4836 5.003804 ACCGTAGATATTTGATTGGGATGC 58.996 41.667 0.00 0.00 0.00 3.91
1730 4927 5.303078 ACACATATACCGCATTCTCTCTTCT 59.697 40.000 0.00 0.00 0.00 2.85
2158 5363 4.202419 ACTGGTGCAAATGTTCAGGTACTA 60.202 41.667 0.00 0.00 36.02 1.82
2189 5411 8.999431 TGTTGTTCTGTGGAGTAGAATATTTTC 58.001 33.333 0.00 0.00 36.63 2.29
2481 5714 3.569701 CGGGGTATGCATTTTATCTGCTT 59.430 43.478 3.54 0.00 40.34 3.91
2490 5723 6.380995 TGCATTTTATCTGCTTACAGTTGTG 58.619 36.000 0.00 0.00 44.77 3.33
2705 5938 3.810386 GTGGAGGATTTATCGCTCCTTTC 59.190 47.826 19.25 11.33 42.02 2.62
3080 6328 5.877564 CCCTCATTTTAGGACTTGAGAGAAC 59.122 44.000 0.00 0.00 39.15 3.01
3161 6409 0.749091 TCATGGAGAATTGCCAGGCG 60.749 55.000 7.03 0.00 39.11 5.52
3562 6810 0.528470 GTCCTGGACACCGAGAAGAG 59.472 60.000 21.70 0.00 32.09 2.85
3731 6980 0.389391 TAGAGATTAGTGCGCAGGGC 59.611 55.000 12.22 1.58 43.96 5.19
3734 6983 1.889573 GATTAGTGCGCAGGGCCTC 60.890 63.158 12.22 0.00 42.61 4.70
3752 7001 3.195825 GCCTCTGGTTCTGTACAGTACAT 59.804 47.826 27.39 0.00 38.15 2.29
3768 7017 1.561643 ACATGACACCTCTCGATGGT 58.438 50.000 0.00 4.62 38.53 3.55
3788 7044 7.413219 CGATGGTGGTTATGTACGTATTTGTTT 60.413 37.037 0.00 0.00 0.00 2.83
3840 7096 4.620982 GTGTTTGCTGCATCCTTTAGTTT 58.379 39.130 1.84 0.00 0.00 2.66
3924 7180 6.926826 ACGATATACAGAGAGGATAGCTATCG 59.073 42.308 24.05 14.24 40.51 2.92
3941 7197 0.984230 TCGGATTGGACTTGCTTCCT 59.016 50.000 1.95 0.00 36.51 3.36
4102 7367 6.446318 TCAACACAATAACTGGATGCTTTTC 58.554 36.000 0.00 0.00 0.00 2.29
4221 7489 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
4694 7963 1.961277 GAGAAGGCACACCACACCG 60.961 63.158 0.00 0.00 39.06 4.94
4708 7977 3.626924 ACCGCCTCACGCCTCTTT 61.627 61.111 0.00 0.00 41.76 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.175989 GGAGTCCCGAACTGGTGATC 59.824 60.000 0.00 0.00 38.74 2.92
1 2 0.252284 AGGAGTCCCGAACTGGTGAT 60.252 55.000 5.25 0.00 38.74 3.06
5 6 1.558233 AGTAAGGAGTCCCGAACTGG 58.442 55.000 5.25 0.00 38.74 4.00
8 9 3.883669 TCTCTAGTAAGGAGTCCCGAAC 58.116 50.000 5.25 1.58 37.58 3.95
17 18 2.442126 TCCGGCAGATCTCTAGTAAGGA 59.558 50.000 0.00 0.00 0.00 3.36
23 24 2.805099 GCAAAATCCGGCAGATCTCTAG 59.195 50.000 0.00 0.00 32.47 2.43
24 25 2.435805 AGCAAAATCCGGCAGATCTCTA 59.564 45.455 0.00 0.00 32.47 2.43
25 26 1.211457 AGCAAAATCCGGCAGATCTCT 59.789 47.619 0.00 0.00 32.47 3.10
143 144 6.872920 TCTGCTAAAAATGTGGTTTCAACTT 58.127 32.000 0.00 0.00 0.00 2.66
190 192 5.441500 TGGACCAAAATCTTACACACAGAA 58.558 37.500 0.00 0.00 0.00 3.02
208 222 7.398024 AGATATGATTGCTAGGTTTATGGACC 58.602 38.462 0.00 0.00 40.11 4.46
260 274 4.278975 ACCACCTTCTCATCTTCTTGAC 57.721 45.455 0.00 0.00 0.00 3.18
295 309 0.736325 CCACAGACCGTTTCGCCTAG 60.736 60.000 0.00 0.00 0.00 3.02
306 320 1.078426 CCGACCAATCCCACAGACC 60.078 63.158 0.00 0.00 0.00 3.85
310 324 2.598787 GGACCCGACCAATCCCACA 61.599 63.158 0.00 0.00 0.00 4.17
340 1676 9.454859 TTTTTCAAAACAGTTGGAACCATTATT 57.545 25.926 0.00 0.00 0.00 1.40
415 2775 4.508861 CACTCATCAAAGCCTTGTTTTTGG 59.491 41.667 0.00 0.00 35.52 3.28
416 2776 4.025480 GCACTCATCAAAGCCTTGTTTTTG 60.025 41.667 0.00 0.00 36.00 2.44
417 2777 4.122046 GCACTCATCAAAGCCTTGTTTTT 58.878 39.130 0.00 0.00 33.94 1.94
446 2806 0.957395 TAGACACCGACGTGGAGACC 60.957 60.000 10.46 0.00 44.86 3.85
543 2910 2.170166 CTAAAAGATGCCCACAAGCCA 58.830 47.619 0.00 0.00 0.00 4.75
578 2952 0.036105 TCGTCTCCGCTACACTACCA 60.036 55.000 0.00 0.00 0.00 3.25
588 2962 0.371645 CAAAAGAGCATCGTCTCCGC 59.628 55.000 0.00 0.00 42.67 5.54
589 2963 1.002366 CCAAAAGAGCATCGTCTCCG 58.998 55.000 0.00 0.00 42.67 4.63
612 3003 1.472276 CGTATCGGTCGTCAAGCTGC 61.472 60.000 0.00 0.00 0.00 5.25
799 3190 0.036010 CCTCGAAGGCACCAAGACAT 60.036 55.000 0.00 0.00 0.00 3.06
945 3344 9.702494 GCCGTGGAGTACTACTATAAATAATTT 57.298 33.333 6.66 0.00 0.00 1.82
946 3345 8.309656 GGCCGTGGAGTACTACTATAAATAATT 58.690 37.037 6.66 0.00 0.00 1.40
973 3372 0.308993 GCTTGTGGTGCTGAAGTGTC 59.691 55.000 0.00 0.00 0.00 3.67
982 3381 0.805711 GTGTTTGGTGCTTGTGGTGC 60.806 55.000 0.00 0.00 0.00 5.01
1023 3432 4.736896 GCTGCTTGGCCTGCTTGC 62.737 66.667 19.10 18.02 0.00 4.01
1032 3441 2.818714 CTGCTCTCCGCTGCTTGG 60.819 66.667 0.00 0.00 40.11 3.61
1033 3442 1.810441 CTCTGCTCTCCGCTGCTTG 60.810 63.158 0.00 0.00 40.11 4.01
1034 3443 2.578128 CTCTGCTCTCCGCTGCTT 59.422 61.111 0.00 0.00 40.11 3.91
1035 3444 3.459965 CCTCTGCTCTCCGCTGCT 61.460 66.667 0.00 0.00 40.11 4.24
1036 3445 3.456365 TCCTCTGCTCTCCGCTGC 61.456 66.667 0.00 0.00 40.11 5.25
1203 3613 4.373116 TTGTCAGACGGCTCGCCC 62.373 66.667 1.72 0.00 0.00 6.13
1221 3631 2.143122 TGATCGAGGCAACAAACACTC 58.857 47.619 0.00 0.00 41.41 3.51
1222 3632 2.146342 CTGATCGAGGCAACAAACACT 58.854 47.619 0.00 0.00 41.41 3.55
1429 3839 2.523168 TGGAGCTCGGTGGTGACA 60.523 61.111 7.83 0.00 38.70 3.58
1464 3874 2.039746 ACTACTGCTGGTGGTGCAAATA 59.960 45.455 0.00 0.00 38.23 1.40
1467 3877 1.001974 CTACTACTGCTGGTGGTGCAA 59.998 52.381 8.94 0.00 39.92 4.08
1468 3878 0.608130 CTACTACTGCTGGTGGTGCA 59.392 55.000 8.94 0.00 39.92 4.57
1469 3879 0.608640 ACTACTACTGCTGGTGGTGC 59.391 55.000 8.94 0.00 39.92 5.01
1470 3880 3.090037 ACTACTACTACTGCTGGTGGTG 58.910 50.000 8.94 3.61 39.92 4.17
1471 3881 3.453059 ACTACTACTACTGCTGGTGGT 57.547 47.619 0.00 0.32 42.30 4.16
1472 3882 5.191426 TCTTACTACTACTACTGCTGGTGG 58.809 45.833 0.00 0.00 0.00 4.61
1473 3883 5.220892 GCTCTTACTACTACTACTGCTGGTG 60.221 48.000 0.00 0.00 0.00 4.17
1474 3884 4.883006 GCTCTTACTACTACTACTGCTGGT 59.117 45.833 0.00 0.00 0.00 4.00
1476 3886 5.504994 GCTGCTCTTACTACTACTACTGCTG 60.505 48.000 0.00 0.00 0.00 4.41
1478 3888 4.335874 TGCTGCTCTTACTACTACTACTGC 59.664 45.833 0.00 0.00 0.00 4.40
1479 3889 5.587043 ACTGCTGCTCTTACTACTACTACTG 59.413 44.000 0.00 0.00 0.00 2.74
1480 3890 5.747342 ACTGCTGCTCTTACTACTACTACT 58.253 41.667 0.00 0.00 0.00 2.57
1481 3891 6.762661 ACTACTGCTGCTCTTACTACTACTAC 59.237 42.308 0.00 0.00 0.00 2.73
1554 4577 6.639686 TCAATTGTGACGTCACTTACTAGAAC 59.360 38.462 39.62 17.32 46.55 3.01
1596 4775 0.680061 AACCGGTTCAGACAGGAGAC 59.320 55.000 15.86 0.00 42.97 3.36
1598 4777 1.344763 AGAAACCGGTTCAGACAGGAG 59.655 52.381 22.53 0.00 42.97 3.69
1657 4836 7.208080 ACTACTACAAGAATAATACGGGCAAG 58.792 38.462 0.00 0.00 0.00 4.01
1829 5029 3.197333 ACATATATAGGAGCAGCAGCAGG 59.803 47.826 3.17 0.00 45.49 4.85
2158 5363 5.680619 TCTACTCCACAGAACAACAACAAT 58.319 37.500 0.00 0.00 0.00 2.71
2189 5411 5.473796 AAGTACACACTGTGGTAAAAACG 57.526 39.130 13.77 0.00 37.94 3.60
2481 5714 3.073209 TGCCTAATTGGGACACAACTGTA 59.927 43.478 12.81 0.00 42.94 2.74
2510 5743 8.665643 ATGCATCTTTTCTGAACAATTTCAAA 57.334 26.923 0.00 0.00 41.34 2.69
2705 5938 2.158986 CCACTCAAGCTCAGGATGTAGG 60.159 54.545 0.00 0.00 37.40 3.18
3693 6941 1.072159 GCAAGCTGACAGGGAGTGT 59.928 57.895 4.26 0.00 44.49 3.55
3698 6946 1.189752 TCTCTAGCAAGCTGACAGGG 58.810 55.000 4.53 0.00 0.00 4.45
3731 6980 4.462834 TCATGTACTGTACAGAACCAGAGG 59.537 45.833 29.30 10.97 42.77 3.69
3734 6983 4.923871 GTGTCATGTACTGTACAGAACCAG 59.076 45.833 29.30 14.87 42.77 4.00
3788 7044 7.930865 ACATTTCAAGGCATAACTAAAGCAAAA 59.069 29.630 0.00 0.00 0.00 2.44
3840 7096 6.818142 CCACATGTACAATCATCTCAGTACAA 59.182 38.462 0.00 0.00 46.63 2.41
3924 7180 2.795329 TGAAGGAAGCAAGTCCAATCC 58.205 47.619 4.18 0.00 40.48 3.01
3941 7197 0.881118 GGCAACCGAATCTGCTTGAA 59.119 50.000 0.00 0.00 38.65 2.69
4117 7382 9.048446 GGTTTTACATTTTCCCTTTTTAGGAAC 57.952 33.333 0.00 0.00 43.08 3.62
4221 7489 0.734889 AAAGTGGCTACATGCATCGC 59.265 50.000 2.02 0.00 45.15 4.58
4409 7678 0.970937 CCGGCAGGAGTCCTAGTTGA 60.971 60.000 12.53 0.00 41.02 3.18
4414 7683 0.469331 CATACCCGGCAGGAGTCCTA 60.469 60.000 12.53 0.00 41.02 2.94
4581 7850 4.265056 AGGGTGGTGGCGTTGTCC 62.265 66.667 0.00 0.00 0.00 4.02
4595 7864 1.442526 GATGATGGACAAGCGCAGGG 61.443 60.000 11.47 0.00 0.00 4.45
4808 8078 1.544691 ACTATCGTCAACCTGCTCGTT 59.455 47.619 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.