Multiple sequence alignment - TraesCS5A01G131800

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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 TraesCS5A01G131800 chr5A 100.000 3683 0 0 2022 5704 296726853 296723171 0.000000e+00 6802.0
1 TraesCS5A01G131800 chr5A 100.000 1365 0 0 1 1365 296728874 296727510 0.000000e+00 2521.0
2 TraesCS5A01G131800 chr5A 88.337 523 44 10 224 745 9209798 9210304 3.780000e-171 612.0
3 TraesCS5A01G131800 chr1B 94.651 1664 86 3 2033 3694 256628287 256626625 0.000000e+00 2577.0
4 TraesCS5A01G131800 chr1B 93.219 929 50 6 2037 2960 620724791 620725711 0.000000e+00 1354.0
5 TraesCS5A01G131800 chr1B 93.750 688 39 3 1 684 376489163 376488476 0.000000e+00 1029.0
6 TraesCS5A01G131800 chr1B 84.721 949 109 11 231 1174 335682784 335683701 0.000000e+00 917.0
7 TraesCS5A01G131800 chr1B 91.351 659 53 2 710 1365 376488485 376487828 0.000000e+00 898.0
8 TraesCS5A01G131800 chr1B 86.233 523 55 9 224 745 201444826 201444320 8.350000e-153 551.0
9 TraesCS5A01G131800 chr1B 86.111 216 26 2 5492 5704 484053084 484052870 4.450000e-56 230.0
10 TraesCS5A01G131800 chr1B 95.082 61 2 1 5347 5406 468215980 468216040 1.690000e-15 95.3
11 TraesCS5A01G131800 chr2B 95.225 1445 65 4 2252 3694 460566462 460567904 0.000000e+00 2283.0
12 TraesCS5A01G131800 chr2B 92.969 1081 64 6 4275 5353 458187668 458188738 0.000000e+00 1565.0
13 TraesCS5A01G131800 chr2B 92.222 1080 75 3 4275 5353 458145589 458144518 0.000000e+00 1520.0
14 TraesCS5A01G131800 chr2B 84.467 676 76 22 1 669 456977731 456977078 1.730000e-179 640.0
15 TraesCS5A01G131800 chrUn 94.948 1445 70 3 2252 3694 4554102 4552659 0.000000e+00 2261.0
16 TraesCS5A01G131800 chrUn 94.948 1445 69 4 2252 3694 124164170 124162728 0.000000e+00 2261.0
17 TraesCS5A01G131800 chrUn 95.808 1145 32 4 4275 5403 48739292 48740436 0.000000e+00 1834.0
18 TraesCS5A01G131800 chrUn 95.604 1001 43 1 2252 3252 131619455 131620454 0.000000e+00 1604.0
19 TraesCS5A01G131800 chrUn 94.295 596 30 4 3366 3960 48737367 48737959 0.000000e+00 909.0
20 TraesCS5A01G131800 chrUn 93.367 392 25 1 3886 4277 261371530 261371920 3.830000e-161 579.0
21 TraesCS5A01G131800 chrUn 93.538 325 18 3 3373 3694 131620448 131620772 1.110000e-131 481.0
22 TraesCS5A01G131800 chrUn 94.044 319 14 3 5388 5704 48740449 48740764 4.000000e-131 479.0
23 TraesCS5A01G131800 chrUn 94.613 297 16 0 3981 4277 48737948 48738244 1.450000e-125 460.0
24 TraesCS5A01G131800 chr1D 92.841 1369 77 5 1 1365 165410213 165411564 0.000000e+00 1965.0
25 TraesCS5A01G131800 chr1D 78.378 296 39 18 885 1170 237419979 237419699 9.830000e-38 169.0
26 TraesCS5A01G131800 chr3A 92.482 1370 68 16 1 1365 6685845 6687184 0.000000e+00 1927.0
27 TraesCS5A01G131800 chr3A 94.619 223 11 1 3855 4077 198241516 198241295 1.520000e-90 344.0
28 TraesCS5A01G131800 chr3A 85.185 216 24 5 5492 5704 328661817 328661607 1.240000e-51 215.0
29 TraesCS5A01G131800 chr3A 96.364 55 2 0 5349 5403 541796493 541796547 2.190000e-14 91.6
30 TraesCS5A01G131800 chr3B 95.546 1145 27 8 4275 5402 531496956 531495819 0.000000e+00 1810.0
31 TraesCS5A01G131800 chr3B 95.309 1002 45 2 3277 4277 531499061 531498061 0.000000e+00 1589.0
32 TraesCS5A01G131800 chr3B 93.691 317 17 3 5388 5704 531495804 531495491 6.690000e-129 472.0
33 TraesCS5A01G131800 chr3B 92.258 155 9 1 2832 2983 341338582 341338736 3.460000e-52 217.0
34 TraesCS5A01G131800 chr3B 78.049 328 38 21 859 1168 40047327 40047016 5.870000e-40 176.0
35 TraesCS5A01G131800 chr6B 95.212 1107 48 3 4275 5380 381168429 381167327 0.000000e+00 1746.0
36 TraesCS5A01G131800 chr6B 93.713 1002 61 2 3277 4277 381170664 381169664 0.000000e+00 1500.0
37 TraesCS5A01G131800 chr6B 94.799 423 22 0 3855 4277 253546952 253547374 0.000000e+00 660.0
38 TraesCS5A01G131800 chr6B 93.651 315 19 1 3855 4169 267743941 267744254 2.410000e-128 470.0
39 TraesCS5A01G131800 chr6B 92.063 315 20 4 5388 5702 381167276 381166967 6.780000e-119 438.0
40 TraesCS5A01G131800 chr6B 82.883 444 51 15 32 469 355980197 355980621 5.400000e-100 375.0
41 TraesCS5A01G131800 chr6B 95.625 160 7 0 3693 3852 691695510 691695351 2.040000e-64 257.0
42 TraesCS5A01G131800 chr6B 95.000 160 8 0 3693 3852 591328648 591328489 9.490000e-63 252.0
43 TraesCS5A01G131800 chr6B 87.500 216 23 2 5492 5704 691689507 691689293 4.410000e-61 246.0
44 TraesCS5A01G131800 chr6B 93.220 59 3 1 5349 5406 691689936 691689878 1.020000e-12 86.1
45 TraesCS5A01G131800 chr3D 93.739 1102 61 6 4280 5380 145293691 145292597 0.000000e+00 1646.0
46 TraesCS5A01G131800 chr3D 93.013 1145 52 10 4275 5403 146087714 146088846 0.000000e+00 1646.0
47 TraesCS5A01G131800 chr4A 91.384 1149 80 7 4275 5406 398484925 398486071 0.000000e+00 1555.0
48 TraesCS5A01G131800 chr4A 94.079 152 6 1 2835 2983 295023443 295023292 1.600000e-55 228.0
49 TraesCS5A01G131800 chr4A 90.816 98 5 3 5396 5492 398486269 398486363 1.670000e-25 128.0
50 TraesCS5A01G131800 chr4D 93.605 860 52 2 4494 5353 195708142 195707286 0.000000e+00 1280.0
51 TraesCS5A01G131800 chr4D 96.774 31 1 0 2973 3003 37439180 37439210 1.000000e-02 52.8
52 TraesCS5A01G131800 chr7D 91.991 874 54 8 1 871 300550114 300550974 0.000000e+00 1212.0
53 TraesCS5A01G131800 chr6A 91.733 750 55 5 4276 5023 526173637 526172893 0.000000e+00 1035.0
54 TraesCS5A01G131800 chr6A 94.326 423 24 0 3855 4277 533017765 533017343 0.000000e+00 649.0
55 TraesCS5A01G131800 chr6A 91.202 341 23 5 3356 3694 581495754 581495419 1.870000e-124 457.0
56 TraesCS5A01G131800 chr6A 95.000 160 8 0 3693 3852 581494623 581494464 9.490000e-63 252.0
57 TraesCS5A01G131800 chr6A 93.750 48 3 0 775 822 365553999 365554046 7.930000e-09 73.1
58 TraesCS5A01G131800 chr6A 93.750 48 3 0 775 822 365561190 365561237 7.930000e-09 73.1
59 TraesCS5A01G131800 chr7B 90.413 751 65 5 4275 5023 624546890 624547635 0.000000e+00 981.0
60 TraesCS5A01G131800 chr7B 80.438 731 87 24 32 749 631779802 631779115 1.830000e-139 507.0
61 TraesCS5A01G131800 chr7B 86.891 267 35 0 1099 1365 244356896 244356630 3.340000e-77 300.0
62 TraesCS5A01G131800 chr7B 89.062 192 17 2 5492 5680 277975718 277975528 9.550000e-58 235.0
63 TraesCS5A01G131800 chr7B 81.743 241 36 7 509 745 143235358 143235594 1.620000e-45 195.0
64 TraesCS5A01G131800 chr2A 89.943 527 44 7 4834 5357 356873914 356873394 0.000000e+00 671.0
65 TraesCS5A01G131800 chr2A 93.381 423 28 0 3855 4277 331192363 331191941 1.350000e-175 627.0
66 TraesCS5A01G131800 chr2A 92.435 423 32 0 3855 4277 522922263 522922685 6.320000e-169 604.0
67 TraesCS5A01G131800 chr2A 83.228 316 40 8 766 1069 275906041 275905727 1.570000e-70 278.0
68 TraesCS5A01G131800 chr2A 93.750 48 3 0 775 822 667586022 667585975 7.930000e-09 73.1
69 TraesCS5A01G131800 chr7A 88.372 516 44 9 224 738 683295053 683295553 1.760000e-169 606.0
70 TraesCS5A01G131800 chr7A 94.375 160 9 0 3693 3852 233813286 233813127 4.410000e-61 246.0
71 TraesCS5A01G131800 chr7A 100.000 28 0 0 2976 3003 332930030 332930003 1.000000e-02 52.8
72 TraesCS5A01G131800 chr2D 88.479 217 20 3 5492 5704 220708481 220708266 2.040000e-64 257.0
73 TraesCS5A01G131800 chr1A 95.000 160 8 0 3693 3852 534661697 534661856 9.490000e-63 252.0
74 TraesCS5A01G131800 chr1A 94.375 160 9 0 3693 3852 347069187 347069028 4.410000e-61 246.0
75 TraesCS5A01G131800 chr1A 91.912 136 8 1 3001 3133 489150791 489150926 2.710000e-43 187.0
76 TraesCS5A01G131800 chr4B 86.301 219 26 2 5489 5704 560906066 560906283 9.550000e-58 235.0
77 TraesCS5A01G131800 chr5D 91.824 159 6 2 2832 2983 193547486 193547644 1.240000e-51 215.0
78 TraesCS5A01G131800 chr6D 90.977 133 10 2 3001 3133 245569153 245569283 1.630000e-40 178.0
79 TraesCS5A01G131800 chr6D 90.441 136 9 2 3001 3133 245496419 245496553 5.870000e-40 176.0
80 TraesCS5A01G131800 chr6D 96.364 55 2 0 5349 5403 201585753 201585699 2.190000e-14 91.6
81 TraesCS5A01G131800 chr5B 85.143 175 24 2 1151 1325 11190937 11191109 1.630000e-40 178.0


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 TraesCS5A01G131800 chr5A 296723171 296728874 5703 True 4661.500000 6802 100.000000 1 5704 2 chr5A.!!$R1 5703
1 TraesCS5A01G131800 chr5A 9209798 9210304 506 False 612.000000 612 88.337000 224 745 1 chr5A.!!$F1 521
2 TraesCS5A01G131800 chr1B 256626625 256628287 1662 True 2577.000000 2577 94.651000 2033 3694 1 chr1B.!!$R2 1661
3 TraesCS5A01G131800 chr1B 620724791 620725711 920 False 1354.000000 1354 93.219000 2037 2960 1 chr1B.!!$F3 923
4 TraesCS5A01G131800 chr1B 376487828 376489163 1335 True 963.500000 1029 92.550500 1 1365 2 chr1B.!!$R4 1364
5 TraesCS5A01G131800 chr1B 335682784 335683701 917 False 917.000000 917 84.721000 231 1174 1 chr1B.!!$F1 943
6 TraesCS5A01G131800 chr1B 201444320 201444826 506 True 551.000000 551 86.233000 224 745 1 chr1B.!!$R1 521
7 TraesCS5A01G131800 chr2B 460566462 460567904 1442 False 2283.000000 2283 95.225000 2252 3694 1 chr2B.!!$F2 1442
8 TraesCS5A01G131800 chr2B 458187668 458188738 1070 False 1565.000000 1565 92.969000 4275 5353 1 chr2B.!!$F1 1078
9 TraesCS5A01G131800 chr2B 458144518 458145589 1071 True 1520.000000 1520 92.222000 4275 5353 1 chr2B.!!$R2 1078
10 TraesCS5A01G131800 chr2B 456977078 456977731 653 True 640.000000 640 84.467000 1 669 1 chr2B.!!$R1 668
11 TraesCS5A01G131800 chrUn 4552659 4554102 1443 True 2261.000000 2261 94.948000 2252 3694 1 chrUn.!!$R1 1442
12 TraesCS5A01G131800 chrUn 124162728 124164170 1442 True 2261.000000 2261 94.948000 2252 3694 1 chrUn.!!$R2 1442
13 TraesCS5A01G131800 chrUn 131619455 131620772 1317 False 1042.500000 1604 94.571000 2252 3694 2 chrUn.!!$F3 1442
14 TraesCS5A01G131800 chrUn 48737367 48740764 3397 False 920.500000 1834 94.690000 3366 5704 4 chrUn.!!$F2 2338
15 TraesCS5A01G131800 chr1D 165410213 165411564 1351 False 1965.000000 1965 92.841000 1 1365 1 chr1D.!!$F1 1364
16 TraesCS5A01G131800 chr3A 6685845 6687184 1339 False 1927.000000 1927 92.482000 1 1365 1 chr3A.!!$F1 1364
17 TraesCS5A01G131800 chr3B 531495491 531499061 3570 True 1290.333333 1810 94.848667 3277 5704 3 chr3B.!!$R2 2427
18 TraesCS5A01G131800 chr6B 381166967 381170664 3697 True 1228.000000 1746 93.662667 3277 5702 3 chr6B.!!$R3 2425
19 TraesCS5A01G131800 chr3D 145292597 145293691 1094 True 1646.000000 1646 93.739000 4280 5380 1 chr3D.!!$R1 1100
20 TraesCS5A01G131800 chr3D 146087714 146088846 1132 False 1646.000000 1646 93.013000 4275 5403 1 chr3D.!!$F1 1128
21 TraesCS5A01G131800 chr4A 398484925 398486363 1438 False 841.500000 1555 91.100000 4275 5492 2 chr4A.!!$F1 1217
22 TraesCS5A01G131800 chr4D 195707286 195708142 856 True 1280.000000 1280 93.605000 4494 5353 1 chr4D.!!$R1 859
23 TraesCS5A01G131800 chr7D 300550114 300550974 860 False 1212.000000 1212 91.991000 1 871 1 chr7D.!!$F1 870
24 TraesCS5A01G131800 chr6A 526172893 526173637 744 True 1035.000000 1035 91.733000 4276 5023 1 chr6A.!!$R1 747
25 TraesCS5A01G131800 chr6A 581494464 581495754 1290 True 354.500000 457 93.101000 3356 3852 2 chr6A.!!$R3 496
26 TraesCS5A01G131800 chr7B 624546890 624547635 745 False 981.000000 981 90.413000 4275 5023 1 chr7B.!!$F2 748
27 TraesCS5A01G131800 chr7B 631779115 631779802 687 True 507.000000 507 80.438000 32 749 1 chr7B.!!$R3 717
28 TraesCS5A01G131800 chr2A 356873394 356873914 520 True 671.000000 671 89.943000 4834 5357 1 chr2A.!!$R3 523
29 TraesCS5A01G131800 chr7A 683295053 683295553 500 False 606.000000 606 88.372000 224 738 1 chr7A.!!$F1 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
442 471 0.106708 ATCACACACGCACACCTTCT 59.893 50.0 0.00 0.0 0.00 2.85 F
936 977 0.250513 GACGAGGCAAGAGGTTGGAT 59.749 55.0 0.00 0.0 33.87 3.41 F
2262 2303 0.902984 TGCTTCCTCCCGACTGCTTA 60.903 55.0 0.00 0.0 0.00 3.09 F
2757 2800 0.674895 ATGCAGAAGGAACACCTCGC 60.675 55.0 0.00 0.0 32.98 5.03 F
4305 6392 0.595095 CCCAGACTGAGCAAAACAGC 59.405 55.0 3.32 0.0 38.74 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 2425 2.753452 AGACTCGAATTTGTAGCCTCGA 59.247 45.455 0.00 0.0 37.95 4.04 R
2730 2773 0.830648 TTCCTTCTGCATCCCTACCG 59.169 55.000 0.00 0.0 0.00 4.02 R
3908 4755 0.813610 TTTGTAGCAGCACACGCACT 60.814 50.000 0.00 0.0 42.27 4.40 R
4640 6729 1.481772 GGGCCAAGAAGCAATGCATAA 59.518 47.619 8.35 0.0 0.00 1.90 R
5591 7930 1.006813 TCCATGGTAGGTGGGCAAAT 58.993 50.000 12.58 0.0 37.34 2.32 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
442 471 0.106708 ATCACACACGCACACCTTCT 59.893 50.000 0.00 0.00 0.00 2.85
586 618 2.880890 GTGGATCTGTCAAACTGCTGTT 59.119 45.455 2.72 2.72 38.16 3.16
686 721 2.996621 GCTGCAAGAAGTATCGTTGTCT 59.003 45.455 0.00 0.00 34.07 3.41
688 723 4.434857 GCTGCAAGAAGTATCGTTGTCTTC 60.435 45.833 0.00 0.00 38.15 2.87
702 738 0.710567 GTCTTCACTGACGACGCATG 59.289 55.000 0.00 0.00 0.00 4.06
846 886 2.045561 TTTTCCTCCGTTTCTGCACA 57.954 45.000 0.00 0.00 0.00 4.57
849 889 1.071471 CCTCCGTTTCTGCACAGGT 59.929 57.895 0.00 0.00 0.00 4.00
881 922 1.347707 CTGCACCTTCTGGTTCACCTA 59.652 52.381 0.00 0.00 46.05 3.08
883 924 1.939838 GCACCTTCTGGTTCACCTACG 60.940 57.143 0.00 0.00 46.05 3.51
889 930 2.803956 TCTGGTTCACCTACGAGATGT 58.196 47.619 0.00 0.00 36.82 3.06
936 977 0.250513 GACGAGGCAAGAGGTTGGAT 59.749 55.000 0.00 0.00 33.87 3.41
2175 2216 0.967887 CTTCCTCTCGACTGCCTCCA 60.968 60.000 0.00 0.00 0.00 3.86
2205 2246 1.595357 GGTACCCACCTCCACTTCG 59.405 63.158 0.00 0.00 42.11 3.79
2222 2263 4.322385 GCCGCCGTTCACCAACAC 62.322 66.667 0.00 0.00 32.14 3.32
2262 2303 0.902984 TGCTTCCTCCCGACTGCTTA 60.903 55.000 0.00 0.00 0.00 3.09
2364 2405 3.549433 TACCTCCCTTGCCCGTCCA 62.549 63.158 0.00 0.00 0.00 4.02
2384 2425 5.645497 GTCCAAGCTCAACAATTCTGACTAT 59.355 40.000 0.00 0.00 0.00 2.12
2637 2679 9.489084 AACTAAGAATTTGGGAAAACTAATTGC 57.511 29.630 0.00 0.00 0.00 3.56
2661 2703 7.551617 TGCATTACATATATCATCTCTTGCTGG 59.448 37.037 0.00 0.00 0.00 4.85
2757 2800 0.674895 ATGCAGAAGGAACACCTCGC 60.675 55.000 0.00 0.00 32.98 5.03
2830 2873 7.144661 CACCTACAATGTATTTTGTGCTGAAA 58.855 34.615 0.00 0.00 40.00 2.69
2845 2888 5.008613 TGTGCTGAAAGTGTTGTTCTAATCC 59.991 40.000 0.00 0.00 35.30 3.01
2950 2997 1.257936 CTTGTTGTCAGGTCGTGTTCG 59.742 52.381 0.00 0.00 38.55 3.95
2967 3014 8.219105 GTCGTGTTCGTCTTTTATAATCAGTTT 58.781 33.333 0.00 0.00 38.33 2.66
3197 3244 9.793252 AAAACATTTGCTATTGCTAGATAACAG 57.207 29.630 0.00 0.00 40.48 3.16
3345 3393 2.950673 GTTCAATGTCGCCGCCAA 59.049 55.556 0.00 0.00 0.00 4.52
3407 3455 3.520623 AAAAAGTGGAGCCTGCTGT 57.479 47.368 0.00 0.00 0.00 4.40
3444 3492 1.203187 AGGACCTCCAGCTCAACAGTA 60.203 52.381 0.00 0.00 38.89 2.74
3478 3526 4.162690 GGCCGGTCGCTCAAGGAT 62.163 66.667 1.90 0.00 37.74 3.24
3529 3577 2.176314 CTGCTGCACCTAGGACTGCA 62.176 60.000 26.63 26.63 41.13 4.41
3638 3688 9.772973 TTTCTATCTGAAGTTTAGTTTAGTGCA 57.227 29.630 0.00 0.00 35.89 4.57
4114 4961 2.318519 AATACATGGCACGGGCGCTA 62.319 55.000 7.64 0.00 42.47 4.26
4125 4972 0.874607 CGGGCGCTATTGGACAGTAC 60.875 60.000 7.64 0.00 0.00 2.73
4184 5031 6.772716 TGTGCTTCTTCAGTTCTAAAATTCCT 59.227 34.615 0.00 0.00 0.00 3.36
4305 6392 0.595095 CCCAGACTGAGCAAAACAGC 59.405 55.000 3.32 0.00 38.74 4.40
4457 6546 4.469657 ACAAGTGGAAAATGTTGAGGCTA 58.530 39.130 0.00 0.00 0.00 3.93
4458 6547 4.892934 ACAAGTGGAAAATGTTGAGGCTAA 59.107 37.500 0.00 0.00 0.00 3.09
4691 6780 7.168905 AGAGAACCCTCATGTTAAAAAGTAGG 58.831 38.462 0.00 0.00 41.87 3.18
4988 7088 2.031870 GTGCAATGGTTATCCCCCTTC 58.968 52.381 0.00 0.00 0.00 3.46
5200 7308 7.513371 TGGTAAAAATGTAAGTCCGTTCAAT 57.487 32.000 0.00 0.00 0.00 2.57
5381 7506 4.623595 GGAAAAAGTTCAAGTCGCAAAACA 59.376 37.500 0.00 0.00 35.25 2.83
5606 7945 5.046950 GTGAAATTTATTTGCCCACCTACCA 60.047 40.000 0.00 0.00 0.00 3.25
5607 7946 5.723887 TGAAATTTATTTGCCCACCTACCAT 59.276 36.000 0.00 0.00 0.00 3.55
5609 7948 2.746279 TATTTGCCCACCTACCATGG 57.254 50.000 11.19 11.19 36.94 3.66
5635 7974 0.378257 CGCAAAATACGAGCTGCCAT 59.622 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 5.515270 CGTATGCTAAAGTTCAGATGTTCGA 59.485 40.000 0.00 0.00 0.00 3.71
505 536 1.484653 CATCGACCATGTTCCCAGGTA 59.515 52.381 0.00 0.00 35.36 3.08
576 608 9.083080 GTTCAACAAAATAACTAACAGCAGTTT 57.917 29.630 0.00 0.00 39.45 2.66
640 673 8.183830 CAAAAACTGCAACATTTCTTCAGTAA 57.816 30.769 0.00 0.00 37.04 2.24
677 712 2.662700 GTCGTCAGTGAAGACAACGAT 58.337 47.619 27.64 0.00 41.57 3.73
686 721 2.027073 GGCATGCGTCGTCAGTGAA 61.027 57.895 12.44 0.00 0.00 3.18
688 723 3.490759 GGGCATGCGTCGTCAGTG 61.491 66.667 12.44 0.00 0.00 3.66
702 738 2.591715 CCAACGATCCATCCGGGC 60.592 66.667 0.00 0.00 36.21 6.13
846 886 1.298014 GCAGGTGCAGAGCTAACCT 59.702 57.895 4.46 4.46 45.32 3.50
881 922 1.763968 TGCTAGCCAGTACATCTCGT 58.236 50.000 13.29 0.00 0.00 4.18
883 924 3.243704 CCTCTTGCTAGCCAGTACATCTC 60.244 52.174 13.29 0.00 0.00 2.75
889 930 1.476891 CGTTCCTCTTGCTAGCCAGTA 59.523 52.381 13.29 0.30 0.00 2.74
936 977 4.332683 TCCCTCTTCTGCCTAGAACTTA 57.667 45.455 0.00 0.00 37.99 2.24
1065 1106 2.184322 CACACACCCCTCGATCCG 59.816 66.667 0.00 0.00 0.00 4.18
1233 1274 3.406595 GATTCCCTCCCGTGGCCAG 62.407 68.421 5.11 0.00 0.00 4.85
2105 2146 3.255379 GCGCTCGAATCCGTGGAC 61.255 66.667 0.00 0.00 37.05 4.02
2133 2174 3.081409 CGTCCCTCCAATCCGGGT 61.081 66.667 0.00 0.00 41.40 5.28
2163 2204 3.680786 CACGGTGGAGGCAGTCGA 61.681 66.667 0.00 0.00 0.00 4.20
2175 2216 4.108673 GGTACCTGGAGTCACGGT 57.891 61.111 4.06 7.61 34.86 4.83
2205 2246 4.322385 GTGTTGGTGAACGGCGGC 62.322 66.667 13.24 0.00 34.49 6.53
2364 2405 5.724328 TCGATAGTCAGAATTGTTGAGCTT 58.276 37.500 0.00 0.00 37.40 3.74
2384 2425 2.753452 AGACTCGAATTTGTAGCCTCGA 59.247 45.455 0.00 0.00 37.95 4.04
2501 2542 9.787532 CTGATGTGAGTTTTTCTTTTGAACTTA 57.212 29.630 0.00 0.00 38.30 2.24
2637 2679 9.833917 ATCCAGCAAGAGATGATATATGTAATG 57.166 33.333 0.00 0.00 31.30 1.90
2647 2689 3.952323 CCAACAATCCAGCAAGAGATGAT 59.048 43.478 0.00 0.00 31.30 2.45
2661 2703 2.565841 CTAGGCCTAGCACCAACAATC 58.434 52.381 26.62 0.00 0.00 2.67
2730 2773 0.830648 TTCCTTCTGCATCCCTACCG 59.169 55.000 0.00 0.00 0.00 4.02
2757 2800 2.132996 TGTGCTTGCCCACCAAAGG 61.133 57.895 0.00 0.00 34.85 3.11
2790 2833 4.980573 TGTAGGTGTGTATTGGAGCTTTT 58.019 39.130 0.00 0.00 0.00 2.27
2802 2845 5.534654 AGCACAAAATACATTGTAGGTGTGT 59.465 36.000 23.91 14.76 41.44 3.72
2830 2873 3.244078 TGACAGCGGATTAGAACAACACT 60.244 43.478 0.00 0.00 0.00 3.55
2845 2888 2.398429 CAGCTTGCGATGACAGCG 59.602 61.111 9.11 9.11 37.44 5.18
2967 3014 5.645929 ACTGAAAAGAACACACATGTACACA 59.354 36.000 0.00 0.00 38.45 3.72
3116 3163 7.865706 AAACTTGATACAGATTGTATGGACC 57.134 36.000 6.46 0.00 43.08 4.46
3282 3330 4.382320 GTACGCGGTGGCAGGGAA 62.382 66.667 12.47 0.00 39.92 3.97
3407 3455 4.100084 TCGACCCCGCGACTCCTA 62.100 66.667 8.23 0.00 35.01 2.94
3444 3492 1.065126 GGCCATAGAGGAAGCAGTTGT 60.065 52.381 0.00 0.00 41.22 3.32
3529 3577 2.731691 AAAGGATGCGGCTGTGTCGT 62.732 55.000 0.00 0.00 31.29 4.34
3638 3688 3.511934 CCTCTGTACCTTTGCTAGTCACT 59.488 47.826 0.00 0.00 0.00 3.41
3908 4755 0.813610 TTTGTAGCAGCACACGCACT 60.814 50.000 0.00 0.00 42.27 4.40
4082 4929 5.357878 GTGCCATGTATTCAGAATTTCCTCA 59.642 40.000 0.00 0.00 0.00 3.86
4184 5031 1.883926 TGTAGTTGCACTGACGCTCTA 59.116 47.619 0.00 0.00 0.00 2.43
4305 6392 4.338118 ACCACAAACCAAGACTAACATGTG 59.662 41.667 0.00 0.00 37.31 3.21
4640 6729 1.481772 GGGCCAAGAAGCAATGCATAA 59.518 47.619 8.35 0.00 0.00 1.90
4691 6780 3.742882 GGGAATTGCTTCAAAACTGCTTC 59.257 43.478 0.00 0.00 32.70 3.86
4988 7088 9.267096 GAAACAAAATACGAATCTTAGAAGCAG 57.733 33.333 0.00 0.00 0.00 4.24
5311 7420 9.122779 GTACTGATGGTACTAGAGAGTTTGTAT 57.877 37.037 0.00 0.00 45.25 2.29
5360 7485 4.089351 CGTGTTTTGCGACTTGAACTTTTT 59.911 37.500 0.00 0.00 0.00 1.94
5381 7506 3.107642 ACGATGTTTTGGACTTCTCGT 57.892 42.857 0.00 0.00 35.41 4.18
5448 7787 4.020485 GTGGTGTTTGTACTGAGGAGGTAT 60.020 45.833 0.00 0.00 0.00 2.73
5591 7930 1.006813 TCCATGGTAGGTGGGCAAAT 58.993 50.000 12.58 0.00 37.34 2.32
5606 7945 4.671766 GCTCGTATTTTGCGAAACTTCCAT 60.672 41.667 0.00 0.00 37.93 3.41
5607 7946 3.364565 GCTCGTATTTTGCGAAACTTCCA 60.365 43.478 0.00 0.00 37.93 3.53
5609 7948 3.840763 CAGCTCGTATTTTGCGAAACTTC 59.159 43.478 0.00 0.00 37.93 3.01
5635 7974 7.282585 ACTGAGCACCATATGAGCTATAAAAA 58.717 34.615 18.61 4.71 39.02 1.94
5647 7986 3.708121 TGACATGAGACTGAGCACCATAT 59.292 43.478 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.