Multiple sequence alignment - TraesCS2A01G483500

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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 TraesCS2A01G483500 chr2A 100.000 3738 0 0 1 3738 719318166 719321903 0.000000e+00 6903.0
1 TraesCS2A01G483500 chr2A 92.355 968 39 8 2783 3738 89535145 89534201 0.000000e+00 1345.0
2 TraesCS2A01G483500 chr2A 91.106 877 45 13 2783 3626 688204075 688204951 0.000000e+00 1157.0
3 TraesCS2A01G483500 chr2A 80.892 1256 214 19 1444 2688 719305347 719306587 0.000000e+00 966.0
4 TraesCS2A01G483500 chr2A 94.798 346 12 4 3393 3738 738268329 738268668 5.500000e-148 534.0
5 TraesCS2A01G483500 chr2A 94.509 346 13 4 3393 3738 759116069 759115730 2.560000e-146 529.0
6 TraesCS2A01G483500 chr2A 93.931 346 21 0 1033 1378 719467947 719468292 1.190000e-144 523.0
7 TraesCS2A01G483500 chr2A 93.983 349 12 4 3393 3738 762240579 762240237 1.540000e-143 520.0
8 TraesCS2A01G483500 chr2A 92.174 345 27 0 1039 1383 719473906 719474250 4.340000e-134 488.0
9 TraesCS2A01G483500 chr2A 92.615 325 24 0 1058 1382 719302856 719303180 5.650000e-128 468.0
10 TraesCS2A01G483500 chr2A 76.439 747 159 14 1998 2736 719470122 719470859 4.530000e-104 388.0
11 TraesCS2A01G483500 chr2D 93.598 1359 66 5 1427 2773 585115449 585116798 0.000000e+00 2008.0
12 TraesCS2A01G483500 chr2D 88.589 1446 92 22 1 1381 585113535 585114972 0.000000e+00 1688.0
13 TraesCS2A01G483500 chr2D 80.778 1259 218 20 1444 2688 585107280 585108528 0.000000e+00 963.0
14 TraesCS2A01G483500 chr2D 91.365 359 28 2 1033 1388 585382715 585383073 4.340000e-134 488.0
15 TraesCS2A01G483500 chr2D 92.771 332 24 0 1047 1378 585368570 585368901 7.260000e-132 481.0
16 TraesCS2A01G483500 chr2D 92.615 325 24 0 1058 1382 585102716 585103040 5.650000e-128 468.0
17 TraesCS2A01G483500 chr2D 90.476 336 32 0 1047 1382 585344104 585344439 9.530000e-121 444.0
18 TraesCS2A01G483500 chr2D 87.792 385 38 5 1001 1382 585209096 585209474 3.430000e-120 442.0
19 TraesCS2A01G483500 chr2D 76.738 748 151 16 1998 2736 585376303 585377036 2.710000e-106 396.0
20 TraesCS2A01G483500 chr2D 74.118 425 90 16 369 782 546636834 546637249 1.390000e-34 158.0
21 TraesCS2A01G483500 chr2D 72.120 434 96 16 369 782 546732578 546733006 1.420000e-19 108.0
22 TraesCS2A01G483500 chr2D 79.245 159 23 9 108 262 11989451 11989603 6.610000e-18 102.0
23 TraesCS2A01G483500 chr7A 95.620 959 39 2 2783 3738 515738859 515739817 0.000000e+00 1535.0
24 TraesCS2A01G483500 chr3A 95.931 934 33 4 2810 3738 143018525 143019458 0.000000e+00 1509.0
25 TraesCS2A01G483500 chr3A 93.108 769 36 11 2783 3534 634126609 634127377 0.000000e+00 1110.0
26 TraesCS2A01G483500 chr3A 82.576 264 39 6 1 262 21776809 21777067 3.760000e-55 226.0
27 TraesCS2A01G483500 chr6A 96.351 877 29 2 2865 3738 598045514 598044638 0.000000e+00 1439.0
28 TraesCS2A01G483500 chr6A 93.667 979 32 5 2785 3735 601150338 601151314 0.000000e+00 1437.0
29 TraesCS2A01G483500 chr6A 94.737 779 34 5 2783 3554 596681185 596680407 0.000000e+00 1205.0
30 TraesCS2A01G483500 chr6A 83.459 266 34 6 1 262 237561249 237561508 4.830000e-59 239.0
31 TraesCS2A01G483500 chr5A 94.069 961 22 7 2783 3738 599375004 599374074 0.000000e+00 1426.0
32 TraesCS2A01G483500 chr5A 83.146 178 29 1 267 443 686504831 686504654 1.070000e-35 161.0
33 TraesCS2A01G483500 chr5A 75.097 257 33 21 10 252 454323246 454323007 1.430000e-14 91.6
34 TraesCS2A01G483500 chr5B 90.744 994 50 19 2780 3738 704413999 704414985 0.000000e+00 1288.0
35 TraesCS2A01G483500 chr1A 96.467 736 26 0 3003 3738 566360448 566361183 0.000000e+00 1216.0
36 TraesCS2A01G483500 chr1A 94.156 770 36 6 2783 3543 589670742 589671511 0.000000e+00 1164.0
37 TraesCS2A01G483500 chr6B 92.098 772 41 15 2783 3543 98509574 98510336 0.000000e+00 1070.0
38 TraesCS2A01G483500 chr6B 92.098 772 41 15 2783 3543 98652084 98652846 0.000000e+00 1070.0
39 TraesCS2A01G483500 chr6B 77.970 463 76 14 267 713 52393188 52392736 2.210000e-67 267.0
40 TraesCS2A01G483500 chr2B 82.271 863 147 5 1444 2306 705727245 705728101 0.000000e+00 741.0
41 TraesCS2A01G483500 chr2B 91.494 482 30 5 2302 2773 705876306 705876786 0.000000e+00 652.0
42 TraesCS2A01G483500 chr2B 92.470 332 25 0 1047 1378 706267882 706268213 3.380000e-130 475.0
43 TraesCS2A01G483500 chr2B 92.615 325 24 0 1058 1382 705724644 705724968 5.650000e-128 468.0
44 TraesCS2A01G483500 chr2B 87.273 385 40 6 1001 1382 706115374 706115752 7.420000e-117 431.0
45 TraesCS2A01G483500 chr2B 83.175 315 49 4 2376 2688 705728179 705728491 6.110000e-73 285.0
46 TraesCS2A01G483500 chr2B 72.622 431 91 22 365 782 653402976 653403392 2.360000e-22 117.0
47 TraesCS2A01G483500 chr2B 72.727 374 79 17 380 742 653414936 653415297 1.840000e-18 104.0
48 TraesCS2A01G483500 chr2B 74.729 277 42 20 1 262 136477346 136477083 8.540000e-17 99.0
49 TraesCS2A01G483500 chr2B 94.444 54 3 0 350 403 349605255 349605308 2.390000e-12 84.2
50 TraesCS2A01G483500 chr5D 77.022 544 90 23 268 782 442917725 442917188 2.840000e-71 279.0
51 TraesCS2A01G483500 chr5D 74.402 418 76 24 271 675 327987623 327987224 2.330000e-32 150.0
52 TraesCS2A01G483500 chr5D 85.455 55 6 2 382 435 358795648 358795595 5.220000e-04 56.5
53 TraesCS2A01G483500 chr6D 83.459 266 34 6 1 262 175642890 175643149 4.830000e-59 239.0
54 TraesCS2A01G483500 chr7B 83.936 249 29 6 13 259 240027205 240026966 1.040000e-55 228.0
55 TraesCS2A01G483500 chr7B 79.781 183 29 6 63 240 11462371 11462550 3.920000e-25 126.0
56 TraesCS2A01G483500 chr3D 82.657 271 34 10 1 262 459520935 459520669 1.040000e-55 228.0
57 TraesCS2A01G483500 chr3D 76.617 201 32 14 69 262 231806786 231806594 3.070000e-16 97.1
58 TraesCS2A01G483500 chr3D 75.369 203 34 14 69 264 175749433 175749240 2.390000e-12 84.2
59 TraesCS2A01G483500 chr3D 78.030 132 24 4 283 412 274346283 274346411 1.110000e-10 78.7
60 TraesCS2A01G483500 chr1D 81.028 253 40 6 11 260 262155806 262156053 1.060000e-45 195.0
61 TraesCS2A01G483500 chrUn 84.066 182 28 1 263 443 297433393 297433212 1.380000e-39 174.0
62 TraesCS2A01G483500 chrUn 83.516 182 29 1 263 443 297428441 297428260 6.420000e-38 169.0
63 TraesCS2A01G483500 chrUn 86.598 97 13 0 347 443 358392417 358392321 1.420000e-19 108.0
64 TraesCS2A01G483500 chrUn 86.598 97 13 0 347 443 358434776 358434680 1.420000e-19 108.0
65 TraesCS2A01G483500 chr4B 75.090 277 41 20 1 262 412780791 412781054 1.840000e-18 104.0
66 TraesCS2A01G483500 chr4D 75.180 278 38 21 1 263 166935623 166935884 6.610000e-18 102.0
67 TraesCS2A01G483500 chr4A 90.667 75 7 0 1 75 352468456 352468530 2.380000e-17 100.0
68 TraesCS2A01G483500 chr1B 75.814 215 29 16 1 203 201044470 201044673 1.850000e-13 87.9
69 TraesCS2A01G483500 chr1B 72.348 264 48 18 1 251 103548249 103547998 4.030000e-05 60.2


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 TraesCS2A01G483500 chr2A 719318166 719321903 3737 False 6903.000000 6903 100.000000 1 3738 1 chr2A.!!$F2 3737
1 TraesCS2A01G483500 chr2A 89534201 89535145 944 True 1345.000000 1345 92.355000 2783 3738 1 chr2A.!!$R1 955
2 TraesCS2A01G483500 chr2A 688204075 688204951 876 False 1157.000000 1157 91.106000 2783 3626 1 chr2A.!!$F1 843
3 TraesCS2A01G483500 chr2A 719302856 719306587 3731 False 717.000000 966 86.753500 1058 2688 2 chr2A.!!$F4 1630
4 TraesCS2A01G483500 chr2A 719467947 719474250 6303 False 466.333333 523 87.514667 1033 2736 3 chr2A.!!$F5 1703
5 TraesCS2A01G483500 chr2D 585113535 585116798 3263 False 1848.000000 2008 91.093500 1 2773 2 chr2D.!!$F11 2772
6 TraesCS2A01G483500 chr2D 585107280 585108528 1248 False 963.000000 963 80.778000 1444 2688 1 chr2D.!!$F5 1244
7 TraesCS2A01G483500 chr2D 585376303 585377036 733 False 396.000000 396 76.738000 1998 2736 1 chr2D.!!$F9 738
8 TraesCS2A01G483500 chr7A 515738859 515739817 958 False 1535.000000 1535 95.620000 2783 3738 1 chr7A.!!$F1 955
9 TraesCS2A01G483500 chr3A 143018525 143019458 933 False 1509.000000 1509 95.931000 2810 3738 1 chr3A.!!$F2 928
10 TraesCS2A01G483500 chr3A 634126609 634127377 768 False 1110.000000 1110 93.108000 2783 3534 1 chr3A.!!$F3 751
11 TraesCS2A01G483500 chr6A 598044638 598045514 876 True 1439.000000 1439 96.351000 2865 3738 1 chr6A.!!$R2 873
12 TraesCS2A01G483500 chr6A 601150338 601151314 976 False 1437.000000 1437 93.667000 2785 3735 1 chr6A.!!$F2 950
13 TraesCS2A01G483500 chr6A 596680407 596681185 778 True 1205.000000 1205 94.737000 2783 3554 1 chr6A.!!$R1 771
14 TraesCS2A01G483500 chr5A 599374074 599375004 930 True 1426.000000 1426 94.069000 2783 3738 1 chr5A.!!$R2 955
15 TraesCS2A01G483500 chr5B 704413999 704414985 986 False 1288.000000 1288 90.744000 2780 3738 1 chr5B.!!$F1 958
16 TraesCS2A01G483500 chr1A 566360448 566361183 735 False 1216.000000 1216 96.467000 3003 3738 1 chr1A.!!$F1 735
17 TraesCS2A01G483500 chr1A 589670742 589671511 769 False 1164.000000 1164 94.156000 2783 3543 1 chr1A.!!$F2 760
18 TraesCS2A01G483500 chr6B 98509574 98510336 762 False 1070.000000 1070 92.098000 2783 3543 1 chr6B.!!$F1 760
19 TraesCS2A01G483500 chr6B 98652084 98652846 762 False 1070.000000 1070 92.098000 2783 3543 1 chr6B.!!$F2 760
20 TraesCS2A01G483500 chr2B 705724644 705728491 3847 False 498.000000 741 86.020333 1058 2688 3 chr2B.!!$F7 1630
21 TraesCS2A01G483500 chr5D 442917188 442917725 537 True 279.000000 279 77.022000 268 782 1 chr5D.!!$R3 514

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
488 530 0.037882 CACCAGCAGTCATCGACACT 60.038 55.000 0.0 0.0 34.60 3.55 F
1404 1501 1.079819 CATTCGTCTCCGGTGCTGT 60.080 57.895 0.0 0.0 33.95 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 4997 0.388649 GAGACGAACGGCATGACAGT 60.389 55.0 0.00 0.0 0.00 3.55 R
2780 6049 0.251354 GGCTGTTGGAGATGCTCTCA 59.749 55.0 13.06 0.0 45.12 3.27 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
76 77 6.817140 GGGTTTAGAAGACAACATACGATCTT 59.183 38.462 0.00 0.00 34.11 2.40
80 81 6.516739 AGAAGACAACATACGATCTTGAGA 57.483 37.500 0.00 0.00 31.58 3.27
106 108 2.753452 TCAACCTGTACTCGATCTCCAC 59.247 50.000 0.00 0.00 0.00 4.02
124 126 5.934043 TCTCCACCATCAATATAATCAAGCG 59.066 40.000 0.00 0.00 0.00 4.68
125 127 5.003160 TCCACCATCAATATAATCAAGCGG 58.997 41.667 0.00 0.00 0.00 5.52
155 157 9.583765 GTAGTGTTTTAATTACCTCTTCGAGAT 57.416 33.333 0.00 0.00 0.00 2.75
163 165 1.676678 CCTCTTCGAGATGGCCCGAA 61.677 60.000 12.95 12.95 41.71 4.30
178 180 1.668751 CCCGAACATGGGTAAACATCG 59.331 52.381 0.00 0.00 44.76 3.84
207 209 3.738982 TGTCTCATGTTCACCATCGTTT 58.261 40.909 0.00 0.00 0.00 3.60
219 221 3.501828 CACCATCGTTTGAAGATCCACAA 59.498 43.478 0.00 0.00 0.00 3.33
222 224 4.142816 CCATCGTTTGAAGATCCACAACTC 60.143 45.833 2.33 0.14 0.00 3.01
230 232 1.229529 ATCCACAACTCGGGACCCT 60.230 57.895 9.41 0.00 35.67 4.34
286 291 1.668101 GGAGAAGATGCGGTCGAGGT 61.668 60.000 0.00 0.00 0.00 3.85
290 295 4.451150 GATGCGGTCGAGGTGGCA 62.451 66.667 2.65 2.65 40.06 4.92
423 429 1.336517 CGTCGTGGCAGTTCTTAAGGA 60.337 52.381 1.85 0.00 0.00 3.36
474 516 4.994756 GGCCACCCCAACCACCAG 62.995 72.222 0.00 0.00 0.00 4.00
478 520 3.103213 ACCCCAACCACCAGCAGT 61.103 61.111 0.00 0.00 0.00 4.40
480 522 2.515398 CCCAACCACCAGCAGTCA 59.485 61.111 0.00 0.00 0.00 3.41
487 529 1.016130 CCACCAGCAGTCATCGACAC 61.016 60.000 0.00 0.00 34.60 3.67
488 530 0.037882 CACCAGCAGTCATCGACACT 60.038 55.000 0.00 0.00 34.60 3.55
501 544 2.899976 TCGACACTTCTGCAAGTTTGA 58.100 42.857 0.00 0.00 41.24 2.69
511 554 1.515521 GCAAGTTTGAGTGGGGGACG 61.516 60.000 0.00 0.00 0.00 4.79
549 595 1.860641 TGAGTAGGGATTTCTCGCCA 58.139 50.000 0.00 0.00 34.99 5.69
572 618 2.434359 GAGGTTTCGCGGTGGAGG 60.434 66.667 6.13 0.00 0.00 4.30
578 624 2.796483 TTTCGCGGTGGAGGTGGATG 62.796 60.000 6.13 0.00 0.00 3.51
659 705 1.302993 GGCAGTTTACGGGCTTCCA 60.303 57.895 0.00 0.00 34.08 3.53
765 813 5.287752 GTGCGTTTCATCGAAGTTATACAGA 59.712 40.000 0.00 0.00 0.00 3.41
782 830 8.735315 GTTATACAGAATCTGCTAGAGATGCTA 58.265 37.037 10.62 0.00 44.56 3.49
783 831 7.959658 ATACAGAATCTGCTAGAGATGCTAT 57.040 36.000 10.62 4.95 44.56 2.97
785 833 7.773489 ACAGAATCTGCTAGAGATGCTATTA 57.227 36.000 10.62 0.00 44.56 0.98
790 838 6.324561 TCTGCTAGAGATGCTATTACACTG 57.675 41.667 0.00 0.00 0.00 3.66
793 841 6.276091 TGCTAGAGATGCTATTACACTGTTG 58.724 40.000 0.00 0.00 0.00 3.33
850 898 4.927782 TGTGAAGCCGTGCGCCTT 62.928 61.111 4.18 0.00 38.78 4.35
853 901 4.090057 GAAGCCGTGCGCCTTCAC 62.090 66.667 16.25 2.69 38.78 3.18
866 930 1.471119 CCTTCACGCTCCCACTACTA 58.529 55.000 0.00 0.00 0.00 1.82
900 964 4.404394 TCTCCCGTGATTAATTAGCTGTGA 59.596 41.667 0.00 0.00 0.00 3.58
969 1054 2.049526 CGAGCACCTACACGCACA 60.050 61.111 0.00 0.00 0.00 4.57
1031 1116 1.153086 AGGCGCTCCTTGCTAATGG 60.153 57.895 7.64 0.00 40.66 3.16
1402 1499 2.579201 CCATTCGTCTCCGGTGCT 59.421 61.111 0.00 0.00 33.95 4.40
1404 1501 1.079819 CATTCGTCTCCGGTGCTGT 60.080 57.895 0.00 0.00 33.95 4.40
1418 1515 4.142491 CCGGTGCTGTTTTATTTGCTCATA 60.142 41.667 0.00 0.00 0.00 2.15
1424 1621 9.013490 GTGCTGTTTTATTTGCTCATATAAGTG 57.987 33.333 0.00 0.00 0.00 3.16
1532 4729 1.228657 GCTTCCTCAACGCCGTCTTT 61.229 55.000 0.00 0.00 0.00 2.52
1796 4993 2.183555 CCCTCCCTTGCGTACGTC 59.816 66.667 17.90 9.82 0.00 4.34
1800 4997 0.242825 CTCCCTTGCGTACGTCTTCA 59.757 55.000 17.90 2.92 0.00 3.02
1985 5182 1.956802 GGTTGGCACCGGAGAAAAG 59.043 57.895 9.46 0.00 31.60 2.27
1988 5185 2.034221 GGCACCGGAGAAAAGGCT 59.966 61.111 9.46 0.00 0.00 4.58
2083 5292 2.939103 CGGTGATCATCCACTTCCTTTC 59.061 50.000 0.00 0.00 37.24 2.62
2087 5296 0.690192 TCATCCACTTCCTTTCCGCA 59.310 50.000 0.00 0.00 0.00 5.69
2196 5405 1.934220 CTCTTACCTGCTCACCGCGA 61.934 60.000 8.23 0.00 43.27 5.87
2322 5571 2.543635 GGTAGTTGACCCCTTCCTGTA 58.456 52.381 0.00 0.00 43.25 2.74
2327 5576 4.172807 AGTTGACCCCTTCCTGTATGTTA 58.827 43.478 0.00 0.00 0.00 2.41
2333 5582 3.480470 CCCTTCCTGTATGTTAGCATGG 58.520 50.000 1.80 0.00 36.58 3.66
2344 5597 2.308570 TGTTAGCATGGGAATGACAGGT 59.691 45.455 0.00 0.00 0.00 4.00
2352 5609 2.627699 TGGGAATGACAGGTTTTTGCTC 59.372 45.455 0.00 0.00 0.00 4.26
2353 5610 2.029020 GGGAATGACAGGTTTTTGCTCC 60.029 50.000 0.00 0.00 0.00 4.70
2354 5611 2.627699 GGAATGACAGGTTTTTGCTCCA 59.372 45.455 0.00 0.00 0.00 3.86
2355 5612 3.069443 GGAATGACAGGTTTTTGCTCCAA 59.931 43.478 0.00 0.00 0.00 3.53
2362 5619 4.407296 ACAGGTTTTTGCTCCAATTAACCA 59.593 37.500 17.33 0.00 39.10 3.67
2539 5796 0.464373 CGCAGATGGGTGCCATACTT 60.464 55.000 0.00 0.00 45.26 2.24
2629 5886 1.474077 GGGCTGTTGTTCTTATGCCAG 59.526 52.381 0.00 0.00 41.86 4.85
2671 5928 1.284313 TGTATGACACCATGGCTGGA 58.716 50.000 13.04 1.59 46.37 3.86
2691 5948 1.356398 ACTCGAGAAAGGAGAGAGGGT 59.644 52.381 21.68 0.00 36.03 4.34
2697 5954 4.345854 GAGAAAGGAGAGAGGGTGTCTAA 58.654 47.826 0.00 0.00 34.71 2.10
2774 6043 1.284408 GGTGCGCCGAAAAATGTCA 59.716 52.632 4.18 0.00 0.00 3.58
2776 6045 1.482278 GTGCGCCGAAAAATGTCAAA 58.518 45.000 4.18 0.00 0.00 2.69
2777 6046 1.855360 GTGCGCCGAAAAATGTCAAAA 59.145 42.857 4.18 0.00 0.00 2.44
2778 6047 2.474735 GTGCGCCGAAAAATGTCAAAAT 59.525 40.909 4.18 0.00 0.00 1.82
2780 6049 4.326009 GTGCGCCGAAAAATGTCAAAATAT 59.674 37.500 4.18 0.00 0.00 1.28
2781 6050 4.325741 TGCGCCGAAAAATGTCAAAATATG 59.674 37.500 4.18 0.00 0.00 1.78
3086 6446 7.718753 TCCAACCAAATTCAAATGCAAACTAAT 59.281 29.630 0.00 0.00 0.00 1.73
3089 6453 8.086851 ACCAAATTCAAATGCAAACTAATGTC 57.913 30.769 0.00 0.00 0.00 3.06
3122 6487 8.400184 TGAAAGACACATCAATCTTCATCTTT 57.600 30.769 0.00 0.00 37.74 2.52
3159 6524 2.163815 GTCCTCATCTTCCGAAGACGAA 59.836 50.000 13.12 1.52 41.01 3.85
3262 6719 4.535526 TCTTCAACGACATCTTCATGGA 57.464 40.909 0.00 0.00 33.82 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.838986 TCTCTATGGACTAAACCCTATGGC 59.161 45.833 0.00 0.00 33.59 4.40
8 9 5.834460 TGTGTCTCTATGGACTAAACCCTA 58.166 41.667 0.00 0.00 37.16 3.53
76 77 5.681639 TCGAGTACAGGTTGATCTATCTCA 58.318 41.667 0.00 0.00 0.00 3.27
80 81 5.708230 GGAGATCGAGTACAGGTTGATCTAT 59.292 44.000 11.49 0.00 44.20 1.98
106 108 4.093408 CGTCCCGCTTGATTATATTGATGG 59.907 45.833 0.00 0.00 0.00 3.51
124 126 6.401394 AGAGGTAATTAAAACACTACGTCCC 58.599 40.000 0.00 0.00 32.28 4.46
125 127 7.201384 CGAAGAGGTAATTAAAACACTACGTCC 60.201 40.741 0.00 0.00 32.28 4.79
163 165 1.459450 GGCACGATGTTTACCCATGT 58.541 50.000 0.00 0.00 0.00 3.21
177 179 1.197721 GAACATGAGACAAAGGGCACG 59.802 52.381 0.00 0.00 0.00 5.34
178 180 2.030805 GTGAACATGAGACAAAGGGCAC 60.031 50.000 0.00 0.00 0.00 5.01
207 209 1.275291 GTCCCGAGTTGTGGATCTTCA 59.725 52.381 0.00 0.00 32.20 3.02
219 221 4.755507 GGGTCGAGGGTCCCGAGT 62.756 72.222 0.99 0.00 36.66 4.18
230 232 2.183300 CGGCAAATCTCGGGTCGA 59.817 61.111 0.00 0.00 0.00 4.20
265 270 1.379977 TCGACCGCATCTTCTCCCT 60.380 57.895 0.00 0.00 0.00 4.20
286 291 1.444119 GCGTGGACAAACTTCTGCCA 61.444 55.000 0.00 0.00 0.00 4.92
290 295 1.597027 CGGGCGTGGACAAACTTCT 60.597 57.895 0.00 0.00 0.00 2.85
376 382 4.851214 GGAGCTCCTCCCTCCGCT 62.851 72.222 26.25 0.00 44.36 5.52
414 420 0.611714 GGCGACCCACTCCTTAAGAA 59.388 55.000 3.36 0.00 0.00 2.52
415 421 1.601419 CGGCGACCCACTCCTTAAGA 61.601 60.000 0.00 0.00 0.00 2.10
470 512 0.681733 AAGTGTCGATGACTGCTGGT 59.318 50.000 1.16 0.00 33.15 4.00
474 516 0.718343 GCAGAAGTGTCGATGACTGC 59.282 55.000 13.69 13.69 42.44 4.40
478 520 2.820059 ACTTGCAGAAGTGTCGATGA 57.180 45.000 0.00 0.00 41.12 2.92
480 522 3.466836 TCAAACTTGCAGAAGTGTCGAT 58.533 40.909 0.00 0.00 41.87 3.59
487 529 1.610522 CCCCACTCAAACTTGCAGAAG 59.389 52.381 0.00 0.00 35.07 2.85
488 530 1.691196 CCCCACTCAAACTTGCAGAA 58.309 50.000 0.00 0.00 0.00 3.02
511 554 1.644786 AAGCTACGATTTGCGGCACC 61.645 55.000 0.05 0.00 46.49 5.01
549 595 1.606889 ACCGCGAAACCTCTCCTCT 60.607 57.895 8.23 0.00 0.00 3.69
659 705 2.025898 CCCGGCCCGTAAATTGTTTAT 58.974 47.619 0.85 0.00 0.00 1.40
723 771 4.244862 CGCACTTTTTCCAGCCATTTTAT 58.755 39.130 0.00 0.00 0.00 1.40
729 777 0.820871 AAACGCACTTTTTCCAGCCA 59.179 45.000 0.00 0.00 0.00 4.75
733 781 2.614520 TCGATGAAACGCACTTTTTCCA 59.385 40.909 0.00 0.00 32.83 3.53
741 789 5.287752 TCTGTATAACTTCGATGAAACGCAC 59.712 40.000 5.16 0.00 0.00 5.34
742 790 5.404096 TCTGTATAACTTCGATGAAACGCA 58.596 37.500 5.16 0.00 0.00 5.24
765 813 7.015098 ACAGTGTAATAGCATCTCTAGCAGATT 59.985 37.037 0.00 0.00 40.20 2.40
782 830 5.364778 TGACTTGCAGTACAACAGTGTAAT 58.635 37.500 0.00 0.00 41.89 1.89
783 831 4.760878 TGACTTGCAGTACAACAGTGTAA 58.239 39.130 0.00 0.00 41.89 2.41
785 833 3.260475 TGACTTGCAGTACAACAGTGT 57.740 42.857 0.00 0.00 42.09 3.55
790 838 6.898041 TCACATATTTGACTTGCAGTACAAC 58.102 36.000 0.00 0.00 33.68 3.32
793 841 7.535258 CAGTTTCACATATTTGACTTGCAGTAC 59.465 37.037 0.00 0.00 0.00 2.73
850 898 1.171308 GTGTAGTAGTGGGAGCGTGA 58.829 55.000 0.00 0.00 0.00 4.35
853 901 0.377554 CTCGTGTAGTAGTGGGAGCG 59.622 60.000 0.00 0.00 0.00 5.03
900 964 1.163420 TGCGCATGTCAACGGTTCTT 61.163 50.000 5.66 0.00 0.00 2.52
983 1068 4.437930 CGGACATTTGATTCCTGCTTTCTC 60.438 45.833 0.00 0.00 0.00 2.87
989 1074 0.101219 GGCGGACATTTGATTCCTGC 59.899 55.000 0.00 0.00 33.41 4.85
1158 1243 1.465794 TCATGACCATGGTGTGCATG 58.534 50.000 27.55 27.55 39.24 4.06
1418 1515 3.381335 ACCCACGGGATAAGTCACTTAT 58.619 45.455 9.99 9.99 39.09 1.73
1424 1621 3.357504 CGAACCCACGGGATAAGTC 57.642 57.895 9.72 0.00 38.96 3.01
1796 4993 0.439985 CGAACGGCATGACAGTGAAG 59.560 55.000 0.00 0.00 0.00 3.02
1800 4997 0.388649 GAGACGAACGGCATGACAGT 60.389 55.000 0.00 0.00 0.00 3.55
1964 5161 1.701031 TTTCTCCGGTGCCAACCTGA 61.701 55.000 0.00 0.00 45.17 3.86
1965 5162 0.821711 TTTTCTCCGGTGCCAACCTG 60.822 55.000 0.00 0.00 45.17 4.00
1974 5171 0.836400 TCCTCAGCCTTTTCTCCGGT 60.836 55.000 0.00 0.00 0.00 5.28
1988 5185 2.677979 CGACGACGACAGCTCCTCA 61.678 63.158 0.00 0.00 42.66 3.86
2087 5296 0.830444 TCAGCCCGAAGTACACCACT 60.830 55.000 0.00 0.00 40.05 4.00
2306 5515 3.434940 AACATACAGGAAGGGGTCAAC 57.565 47.619 0.00 0.00 0.00 3.18
2311 5520 3.480470 CATGCTAACATACAGGAAGGGG 58.520 50.000 0.00 0.00 33.67 4.79
2318 5567 5.125356 TGTCATTCCCATGCTAACATACAG 58.875 41.667 0.00 0.00 33.67 2.74
2322 5571 3.053395 ACCTGTCATTCCCATGCTAACAT 60.053 43.478 0.00 0.00 36.79 2.71
2327 5576 2.610438 AAACCTGTCATTCCCATGCT 57.390 45.000 0.00 0.00 0.00 3.79
2333 5582 2.627699 TGGAGCAAAAACCTGTCATTCC 59.372 45.455 0.00 0.00 0.00 3.01
2344 5597 4.754114 GCATGTGGTTAATTGGAGCAAAAA 59.246 37.500 0.00 0.00 0.00 1.94
2352 5609 2.995258 GCAACTGCATGTGGTTAATTGG 59.005 45.455 0.00 0.00 41.59 3.16
2629 5886 1.696832 GCTTGTTCATCGTCTCGGGC 61.697 60.000 0.00 0.00 0.00 6.13
2671 5928 1.356398 ACCCTCTCTCCTTTCTCGAGT 59.644 52.381 13.13 0.00 0.00 4.18
2691 5948 5.047847 CACCTTCGTCTTCACTTTTAGACA 58.952 41.667 0.00 0.00 40.59 3.41
2697 5954 2.213499 CTGCACCTTCGTCTTCACTTT 58.787 47.619 0.00 0.00 0.00 2.66
2763 6032 8.624701 ATGCTCTCATATTTTGACATTTTTCG 57.375 30.769 0.00 0.00 0.00 3.46
2764 6033 9.798994 AGATGCTCTCATATTTTGACATTTTTC 57.201 29.630 0.00 0.00 31.96 2.29
2774 6043 5.298777 GCTGTTGGAGATGCTCTCATATTTT 59.701 40.000 13.06 0.00 45.12 1.82
2776 6045 4.387598 GCTGTTGGAGATGCTCTCATATT 58.612 43.478 13.06 0.00 45.12 1.28
2777 6046 3.244491 GGCTGTTGGAGATGCTCTCATAT 60.244 47.826 13.06 0.00 45.12 1.78
2778 6047 2.103771 GGCTGTTGGAGATGCTCTCATA 59.896 50.000 13.06 2.07 45.12 2.15
2780 6049 0.251354 GGCTGTTGGAGATGCTCTCA 59.749 55.000 13.06 0.00 45.12 3.27
2781 6050 0.809241 CGGCTGTTGGAGATGCTCTC 60.809 60.000 5.01 5.01 42.66 3.20
2910 6237 0.961019 ATTTTTGCGCTCTGCTGGAA 59.039 45.000 9.73 0.00 46.63 3.53
3086 6446 4.149511 TGTGTCTTTCATGTCTTGGACA 57.850 40.909 2.80 2.80 46.90 4.02
3089 6453 5.694231 TTGATGTGTCTTTCATGTCTTGG 57.306 39.130 0.00 0.00 0.00 3.61
3122 6487 0.795085 GGACGAAGACGAAGACGAGA 59.205 55.000 0.00 0.00 42.66 4.04
3159 6524 4.356979 TCTTCGGAGGCGGAAGAT 57.643 55.556 11.76 0.00 42.16 2.40
3262 6719 2.653726 TGTGCCTTCTCACACACATTT 58.346 42.857 0.00 0.00 41.67 2.32
3284 6741 1.894466 CCATGGGTGCAATGTCTTTCA 59.106 47.619 2.85 0.00 0.00 2.69
3320 6777 1.767088 CTTCTCTCATGGGAGGCATGA 59.233 52.381 22.52 0.00 41.69 3.07


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

AutoCloner maintained by Alex Coulton.