Multiple sequence alignment - TraesCS3D01G459200

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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 TraesCS3D01G459200 chr3D 100.000 2702 0 0 1 2702 564524687 564521986 0.000000e+00 4990.0
1 TraesCS3D01G459200 chr3D 81.484 1523 221 34 951 2445 564530986 564529497 0.000000e+00 1194.0
2 TraesCS3D01G459200 chr3D 80.273 512 96 3 1171 1681 564399408 564398901 5.460000e-102 381.0
3 TraesCS3D01G459200 chr3D 83.333 354 52 5 568 917 564531413 564531063 1.210000e-83 320.0
4 TraesCS3D01G459200 chr3D 83.513 279 39 5 537 808 564449126 564448848 1.240000e-63 254.0
5 TraesCS3D01G459200 chr3D 85.153 229 27 5 516 742 564457275 564457052 7.530000e-56 228.0
6 TraesCS3D01G459200 chr3D 76.218 349 35 32 1708 2023 564398811 564398478 1.010000e-29 141.0
7 TraesCS3D01G459200 chr3D 80.447 179 17 7 2472 2646 564529504 564529340 1.310000e-23 121.0
8 TraesCS3D01G459200 chr3D 73.262 374 78 14 1319 1678 567906793 567907158 1.700000e-22 117.0
9 TraesCS3D01G459200 chr3D 83.158 95 16 0 2499 2593 565606133 565606227 1.330000e-13 87.9
10 TraesCS3D01G459200 chr3B 93.270 1798 85 13 869 2634 752210848 752209055 0.000000e+00 2617.0
11 TraesCS3D01G459200 chr3B 83.990 812 51 38 131 876 752212009 752211211 0.000000e+00 706.0
12 TraesCS3D01G459200 chr3B 81.915 846 108 21 1632 2460 752225867 752225050 0.000000e+00 673.0
13 TraesCS3D01G459200 chr3B 78.632 702 119 21 951 1634 752232795 752232107 1.150000e-118 436.0
14 TraesCS3D01G459200 chr3B 83.616 354 51 5 568 917 752263836 752263486 2.590000e-85 326.0
15 TraesCS3D01G459200 chr3B 79.121 455 86 5 1236 1687 752972548 752972100 3.380000e-79 305.0
16 TraesCS3D01G459200 chr3B 77.189 434 67 17 2246 2677 752807267 752806864 9.740000e-55 224.0
17 TraesCS3D01G459200 chr3B 96.809 94 3 0 3 96 752212190 752212097 1.000000e-34 158.0
18 TraesCS3D01G459200 chr3B 95.652 46 2 0 2472 2517 752261934 752261889 1.040000e-09 75.0
19 TraesCS3D01G459200 chr3A 79.762 1512 231 43 951 2445 699317471 699316018 0.000000e+00 1027.0
20 TraesCS3D01G459200 chr3A 80.979 1083 154 22 516 1570 699081227 699080169 0.000000e+00 811.0
21 TraesCS3D01G459200 chr3A 80.908 1079 157 20 516 1569 699158641 699157587 0.000000e+00 806.0
22 TraesCS3D01G459200 chr3A 85.199 831 36 33 311 1073 699292079 699291268 0.000000e+00 773.0
23 TraesCS3D01G459200 chr3A 81.165 515 94 1 1171 1685 699108718 699108207 6.960000e-111 411.0
24 TraesCS3D01G459200 chr3A 79.707 478 78 12 1220 1686 699534036 699534505 7.210000e-86 327.0
25 TraesCS3D01G459200 chr3A 91.949 236 12 4 3 235 699308467 699308236 9.330000e-85 324.0
26 TraesCS3D01G459200 chr3A 85.981 214 25 4 587 796 699533372 699533584 9.740000e-55 224.0
27 TraesCS3D01G459200 chr3A 85.915 213 25 3 586 794 655920286 655920497 3.500000e-54 222.0
28 TraesCS3D01G459200 chr3A 77.364 349 31 31 1708 2023 699108144 699107811 2.150000e-36 163.0
29 TraesCS3D01G459200 chr3A 82.407 108 18 1 2487 2593 699765010 699765117 2.860000e-15 93.5
30 TraesCS3D01G459200 chrUn 72.703 370 81 15 1319 1678 314515552 314515193 3.680000e-19 106.0
31 TraesCS3D01G459200 chr6D 84.259 108 15 2 2488 2593 380450917 380450810 1.320000e-18 104.0
32 TraesCS3D01G459200 chr6B 82.243 107 18 1 2488 2593 565400645 565400751 1.030000e-14 91.6


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 TraesCS3D01G459200 chr3D 564521986 564524687 2701 True 4990.000000 4990 100.000000 1 2702 1 chr3D.!!$R3 2701
1 TraesCS3D01G459200 chr3D 564529340 564531413 2073 True 545.000000 1194 81.754667 568 2646 3 chr3D.!!$R5 2078
2 TraesCS3D01G459200 chr3D 564398478 564399408 930 True 261.000000 381 78.245500 1171 2023 2 chr3D.!!$R4 852
3 TraesCS3D01G459200 chr3B 752209055 752212190 3135 True 1160.333333 2617 91.356333 3 2634 3 chr3B.!!$R5 2631
4 TraesCS3D01G459200 chr3B 752225050 752225867 817 True 673.000000 673 81.915000 1632 2460 1 chr3B.!!$R1 828
5 TraesCS3D01G459200 chr3B 752232107 752232795 688 True 436.000000 436 78.632000 951 1634 1 chr3B.!!$R2 683
6 TraesCS3D01G459200 chr3B 752261889 752263836 1947 True 200.500000 326 89.634000 568 2517 2 chr3B.!!$R6 1949
7 TraesCS3D01G459200 chr3A 699316018 699317471 1453 True 1027.000000 1027 79.762000 951 2445 1 chr3A.!!$R5 1494
8 TraesCS3D01G459200 chr3A 699080169 699081227 1058 True 811.000000 811 80.979000 516 1570 1 chr3A.!!$R1 1054
9 TraesCS3D01G459200 chr3A 699157587 699158641 1054 True 806.000000 806 80.908000 516 1569 1 chr3A.!!$R2 1053
10 TraesCS3D01G459200 chr3A 699291268 699292079 811 True 773.000000 773 85.199000 311 1073 1 chr3A.!!$R3 762
11 TraesCS3D01G459200 chr3A 699107811 699108718 907 True 287.000000 411 79.264500 1171 2023 2 chr3A.!!$R6 852
12 TraesCS3D01G459200 chr3A 699533372 699534505 1133 False 275.500000 327 82.844000 587 1686 2 chr3A.!!$F3 1099

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
326 397 0.316196 GAACCTTACATCGCGCATGC 60.316 55.0 7.91 7.91 35.65 4.06 F
355 434 0.318441 TGATCCGGCGAGATGGAATC 59.682 55.0 9.30 0.00 46.04 2.52 F
903 1437 0.533308 CGGGTCCGGTTTGAAGACAA 60.533 55.0 0.00 0.00 35.56 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 2145 0.611618 TGGACCACCACATGCCAATC 60.612 55.000 0.00 0.0 41.77 2.67 R
1528 2187 1.466167 CTCGCCAAATCTGACCAACAG 59.534 52.381 0.00 0.0 46.97 3.16 R
2656 3429 0.327924 TGGACCCATGGTGCTAAGTG 59.672 55.000 11.73 0.0 44.53 3.16 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
32 33 3.149981 TCGAGTCTGGCGATTCTATCAT 58.850 45.455 0.00 0.00 32.09 2.45
83 84 3.070018 CCTGCAGTCCTGTTGTAGAAAG 58.930 50.000 13.81 0.00 30.91 2.62
129 180 8.673711 GGAAGAGCAATACAAATATGTGTGTTA 58.326 33.333 8.91 0.00 40.84 2.41
175 238 4.998671 TGAAATCAGTGAAAAAGTGGCA 57.001 36.364 0.00 0.00 0.00 4.92
182 245 3.003689 CAGTGAAAAAGTGGCATCGTTCT 59.996 43.478 0.00 0.00 0.00 3.01
188 251 0.321919 AGTGGCATCGTTCTGTGCAT 60.322 50.000 0.00 0.00 43.00 3.96
202 265 9.562583 TCGTTCTGTGCATTTTATATAAAAACC 57.437 29.630 21.33 15.74 38.50 3.27
261 332 1.000955 ACTCAATTCGAACTGCTCCGT 59.999 47.619 0.00 0.00 0.00 4.69
262 333 1.656095 CTCAATTCGAACTGCTCCGTC 59.344 52.381 0.00 0.00 0.00 4.79
282 353 2.202440 CAGCAGCGCAACAGCATC 60.202 61.111 11.47 0.00 40.15 3.91
284 355 4.824166 GCAGCGCAACAGCATCGG 62.824 66.667 11.47 0.00 40.15 4.18
309 380 8.517878 GGACAGAAATCAGATGAGAAAATTGAA 58.482 33.333 0.00 0.00 0.00 2.69
324 395 1.732941 TTGAACCTTACATCGCGCAT 58.267 45.000 8.75 0.00 0.00 4.73
325 396 1.006086 TGAACCTTACATCGCGCATG 58.994 50.000 8.75 12.98 38.64 4.06
326 397 0.316196 GAACCTTACATCGCGCATGC 60.316 55.000 7.91 7.91 35.65 4.06
327 398 1.024046 AACCTTACATCGCGCATGCA 61.024 50.000 19.57 0.00 42.97 3.96
355 434 0.318441 TGATCCGGCGAGATGGAATC 59.682 55.000 9.30 0.00 46.04 2.52
367 446 2.541466 GATGGAATCGGGGGATCTAGT 58.459 52.381 0.00 0.00 31.13 2.57
368 447 2.011122 TGGAATCGGGGGATCTAGTC 57.989 55.000 0.00 0.00 0.00 2.59
369 448 1.503784 TGGAATCGGGGGATCTAGTCT 59.496 52.381 0.00 0.00 0.00 3.24
370 449 2.720254 TGGAATCGGGGGATCTAGTCTA 59.280 50.000 0.00 0.00 0.00 2.59
371 450 3.245300 TGGAATCGGGGGATCTAGTCTAG 60.245 52.174 0.00 0.00 0.00 2.43
411 490 2.405143 GGCGGAGACAAATTAGGGC 58.595 57.895 0.00 0.00 31.66 5.19
464 564 4.394712 AGGGCCGCCTCGACTTTG 62.395 66.667 9.86 0.00 0.00 2.77
511 625 3.005791 AGCTTGCCAAACCAGTTTATGTC 59.994 43.478 0.00 0.00 0.00 3.06
513 627 2.577700 TGCCAAACCAGTTTATGTCGT 58.422 42.857 0.00 0.00 0.00 4.34
518 652 4.320202 CCAAACCAGTTTATGTCGTTCCAG 60.320 45.833 0.00 0.00 0.00 3.86
532 666 5.642491 TGTCGTTCCAGATATATCTCTACGG 59.358 44.000 25.31 18.76 34.99 4.02
534 668 5.046087 TCGTTCCAGATATATCTCTACGGGA 60.046 44.000 25.31 19.89 34.99 5.14
559 702 2.823147 CCGACCTACCGACGCTCT 60.823 66.667 0.00 0.00 0.00 4.09
903 1437 0.533308 CGGGTCCGGTTTGAAGACAA 60.533 55.000 0.00 0.00 35.56 3.18
915 1449 0.966920 GAAGACAAGGTCCGTCTGGA 59.033 55.000 0.63 0.00 42.90 3.86
948 1504 5.013568 TCCTTTTCACTGACACGACTAAA 57.986 39.130 0.00 0.00 0.00 1.85
1137 1735 2.350514 GGCTCAGTTCAGCTGCCT 59.649 61.111 9.47 4.20 44.66 4.75
1363 2012 3.181507 CGGCATGTCCAACTTTAGTGATG 60.182 47.826 6.92 0.00 34.01 3.07
1364 2013 4.009675 GGCATGTCCAACTTTAGTGATGA 58.990 43.478 0.00 0.00 34.01 2.92
1445 2100 5.357032 CCTTAAACTATCGGGTTGAATTGCT 59.643 40.000 0.00 0.00 0.00 3.91
1450 2105 1.698506 TCGGGTTGAATTGCTGGTTT 58.301 45.000 0.00 0.00 0.00 3.27
1486 2145 3.366679 GCAGTTTGGTCAGATTGTCCATG 60.367 47.826 0.00 0.00 35.61 3.66
1528 2187 4.063689 CTCTTGTGATGGTGATATGCTCC 58.936 47.826 0.00 0.00 0.00 4.70
1552 2211 0.321653 GGTCAGATTTGGCGAGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
1601 2260 2.244510 TGGTGGCCTATTTCCATCATGT 59.755 45.455 3.32 0.00 39.63 3.21
1703 2415 2.750166 TGAACCGTCAGTGCTTTTGAAA 59.250 40.909 0.00 0.00 0.00 2.69
1705 2417 3.145212 ACCGTCAGTGCTTTTGAAAAC 57.855 42.857 0.00 0.00 0.00 2.43
1717 2439 9.005777 AGTGCTTTTGAAAACCGTATCTTTATA 57.994 29.630 0.00 0.00 0.00 0.98
1931 2685 4.869297 TGCCACATGTCTTTGTTTTTCTTG 59.131 37.500 0.00 0.00 0.00 3.02
1939 2693 7.214467 TGTCTTTGTTTTTCTTGTCTGAAGT 57.786 32.000 0.00 0.00 0.00 3.01
1979 2737 6.817765 TCATGGTCTTCTACATTTTTGGAC 57.182 37.500 0.00 0.00 0.00 4.02
2054 2815 6.978674 TTGTTCCATGTTATTTTGTACCCA 57.021 33.333 0.00 0.00 0.00 4.51
2060 2821 6.071108 TCCATGTTATTTTGTACCCAACCATG 60.071 38.462 0.00 0.00 0.00 3.66
2140 2901 0.465705 ATCCACTGCACCTGGATACG 59.534 55.000 16.55 0.00 45.21 3.06
2146 2907 0.671796 TGCACCTGGATACGTATCGG 59.328 55.000 25.21 23.09 42.51 4.18
2162 2923 4.916249 CGTATCGGAACCTTCTGCTATAAC 59.084 45.833 0.00 0.00 33.56 1.89
2203 2964 4.400251 TCGTTAGGTGTTATCTCCGTCATT 59.600 41.667 0.00 0.00 33.02 2.57
2204 2965 5.105635 TCGTTAGGTGTTATCTCCGTCATTT 60.106 40.000 0.00 0.00 33.02 2.32
2205 2966 5.231568 CGTTAGGTGTTATCTCCGTCATTTC 59.768 44.000 0.00 0.00 33.02 2.17
2206 2967 6.338937 GTTAGGTGTTATCTCCGTCATTTCT 58.661 40.000 0.00 0.00 33.02 2.52
2209 2970 5.875359 AGGTGTTATCTCCGTCATTTCTTTC 59.125 40.000 0.00 0.00 33.02 2.62
2215 2980 4.324267 TCTCCGTCATTTCTTTCCCTTTC 58.676 43.478 0.00 0.00 0.00 2.62
2373 3138 1.007038 GCACTACCGTTGGTCGTCA 60.007 57.895 0.00 0.00 37.09 4.35
2410 3175 1.361204 TGCCTTGTCTCAATCAGGGA 58.639 50.000 0.00 0.00 34.59 4.20
2429 3194 3.356290 GGAACAGCACCAGGAATTATGT 58.644 45.455 0.00 0.00 0.00 2.29
2460 3225 6.017440 TGCAGTTGTAAAAGCGAATAGAAAGT 60.017 34.615 0.00 0.00 32.44 2.66
2461 3226 6.856426 GCAGTTGTAAAAGCGAATAGAAAGTT 59.144 34.615 0.00 0.00 0.00 2.66
2501 3266 2.257353 GCCGTTGAAAGATGGCTGT 58.743 52.632 0.99 0.00 46.12 4.40
2509 3274 4.524316 TGAAAGATGGCTGTTCATTTGG 57.476 40.909 0.00 0.00 0.00 3.28
2523 3292 7.552458 TGTTCATTTGGTAGTGCATATGTAG 57.448 36.000 4.29 0.00 0.00 2.74
2530 3299 4.641541 TGGTAGTGCATATGTAGTACGTGT 59.358 41.667 24.01 0.00 37.41 4.49
2635 3408 7.545265 TCAACAGCCAATTTTCTATTGCATAAC 59.455 33.333 0.00 0.00 0.00 1.89
2642 3415 7.823799 CCAATTTTCTATTGCATAACCCTTTGT 59.176 33.333 0.00 0.00 0.00 2.83
2646 3419 5.815581 TCTATTGCATAACCCTTTGTGAGT 58.184 37.500 0.00 0.00 0.00 3.41
2647 3420 4.789012 ATTGCATAACCCTTTGTGAGTG 57.211 40.909 0.00 0.00 0.00 3.51
2648 3421 1.885887 TGCATAACCCTTTGTGAGTGC 59.114 47.619 0.00 0.00 32.88 4.40
2649 3422 1.202348 GCATAACCCTTTGTGAGTGCC 59.798 52.381 0.00 0.00 0.00 5.01
2650 3423 2.795329 CATAACCCTTTGTGAGTGCCT 58.205 47.619 0.00 0.00 0.00 4.75
2651 3424 2.270352 TAACCCTTTGTGAGTGCCTG 57.730 50.000 0.00 0.00 0.00 4.85
2652 3425 0.468029 AACCCTTTGTGAGTGCCTGG 60.468 55.000 0.00 0.00 0.00 4.45
2653 3426 1.151450 CCCTTTGTGAGTGCCTGGT 59.849 57.895 0.00 0.00 0.00 4.00
2654 3427 0.468029 CCCTTTGTGAGTGCCTGGTT 60.468 55.000 0.00 0.00 0.00 3.67
2655 3428 1.202879 CCCTTTGTGAGTGCCTGGTTA 60.203 52.381 0.00 0.00 0.00 2.85
2656 3429 1.880027 CCTTTGTGAGTGCCTGGTTAC 59.120 52.381 0.00 0.00 0.00 2.50
2657 3430 2.571212 CTTTGTGAGTGCCTGGTTACA 58.429 47.619 0.00 0.00 0.00 2.41
2658 3431 1.961793 TTGTGAGTGCCTGGTTACAC 58.038 50.000 0.00 2.41 37.05 2.90
2660 3433 1.488812 TGTGAGTGCCTGGTTACACTT 59.511 47.619 6.86 0.00 46.82 3.16
2661 3434 2.701423 TGTGAGTGCCTGGTTACACTTA 59.299 45.455 6.86 1.06 46.82 2.24
2662 3435 3.244078 TGTGAGTGCCTGGTTACACTTAG 60.244 47.826 6.86 0.00 46.82 2.18
2663 3436 2.289444 TGAGTGCCTGGTTACACTTAGC 60.289 50.000 6.86 0.00 46.82 3.09
2664 3437 1.697432 AGTGCCTGGTTACACTTAGCA 59.303 47.619 0.00 0.00 44.59 3.49
2665 3438 1.804748 GTGCCTGGTTACACTTAGCAC 59.195 52.381 0.00 0.00 41.86 4.40
2666 3439 1.271163 TGCCTGGTTACACTTAGCACC 60.271 52.381 0.00 0.00 0.00 5.01
2667 3440 1.271163 GCCTGGTTACACTTAGCACCA 60.271 52.381 0.00 0.00 36.94 4.17
2668 3441 2.618045 GCCTGGTTACACTTAGCACCAT 60.618 50.000 0.00 0.00 38.64 3.55
2669 3442 3.009723 CCTGGTTACACTTAGCACCATG 58.990 50.000 0.00 0.00 38.64 3.66
2670 3443 3.009723 CTGGTTACACTTAGCACCATGG 58.990 50.000 11.19 11.19 38.64 3.66
2671 3444 2.290641 TGGTTACACTTAGCACCATGGG 60.291 50.000 18.09 6.26 34.23 4.00
2672 3445 2.290705 GGTTACACTTAGCACCATGGGT 60.291 50.000 18.09 3.88 35.62 4.51
2673 3446 3.007635 GTTACACTTAGCACCATGGGTC 58.992 50.000 18.09 7.06 31.02 4.46
2674 3447 0.328258 ACACTTAGCACCATGGGTCC 59.672 55.000 18.09 3.43 31.02 4.46
2675 3448 0.327924 CACTTAGCACCATGGGTCCA 59.672 55.000 18.09 0.00 31.02 4.02
2676 3449 0.620556 ACTTAGCACCATGGGTCCAG 59.379 55.000 18.09 7.63 31.02 3.86
2677 3450 0.911769 CTTAGCACCATGGGTCCAGA 59.088 55.000 18.09 0.00 31.02 3.86
2678 3451 1.492176 CTTAGCACCATGGGTCCAGAT 59.508 52.381 18.09 1.57 31.02 2.90
2679 3452 1.595311 TAGCACCATGGGTCCAGATT 58.405 50.000 18.09 0.00 31.02 2.40
2680 3453 1.595311 AGCACCATGGGTCCAGATTA 58.405 50.000 18.09 0.00 31.02 1.75
2681 3454 2.138542 AGCACCATGGGTCCAGATTAT 58.861 47.619 18.09 0.00 31.02 1.28
2682 3455 2.515429 AGCACCATGGGTCCAGATTATT 59.485 45.455 18.09 0.00 31.02 1.40
2683 3456 3.721575 AGCACCATGGGTCCAGATTATTA 59.278 43.478 18.09 0.00 31.02 0.98
2684 3457 4.167892 AGCACCATGGGTCCAGATTATTAA 59.832 41.667 18.09 0.00 31.02 1.40
2685 3458 5.079643 GCACCATGGGTCCAGATTATTAAT 58.920 41.667 18.09 0.00 31.02 1.40
2686 3459 5.047802 GCACCATGGGTCCAGATTATTAATG 60.048 44.000 18.09 0.00 31.02 1.90
2687 3460 6.070656 CACCATGGGTCCAGATTATTAATGT 58.929 40.000 18.09 0.00 31.02 2.71
2688 3461 7.230747 CACCATGGGTCCAGATTATTAATGTA 58.769 38.462 18.09 0.00 31.02 2.29
2689 3462 7.890127 CACCATGGGTCCAGATTATTAATGTAT 59.110 37.037 18.09 0.00 31.02 2.29
2690 3463 8.456124 ACCATGGGTCCAGATTATTAATGTATT 58.544 33.333 18.09 0.00 0.00 1.89
2691 3464 8.960591 CCATGGGTCCAGATTATTAATGTATTC 58.039 37.037 2.85 0.00 0.00 1.75
2692 3465 8.960591 CATGGGTCCAGATTATTAATGTATTCC 58.039 37.037 0.00 0.00 0.00 3.01
2693 3466 8.051468 TGGGTCCAGATTATTAATGTATTCCA 57.949 34.615 0.00 0.00 0.00 3.53
2694 3467 8.506921 TGGGTCCAGATTATTAATGTATTCCAA 58.493 33.333 0.00 0.00 0.00 3.53
2695 3468 9.362151 GGGTCCAGATTATTAATGTATTCCAAA 57.638 33.333 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.228063 AACAGGACTGCAGGCACAG 60.228 57.895 23.90 12.82 43.59 3.66
97 98 9.632638 ACATATTTGTATTGCTCTTCCAAGTAT 57.367 29.630 0.00 0.00 33.16 2.12
99 100 7.394359 ACACATATTTGTATTGCTCTTCCAAGT 59.606 33.333 0.00 0.00 33.76 3.16
100 101 7.699391 CACACATATTTGTATTGCTCTTCCAAG 59.301 37.037 0.00 0.00 33.76 3.61
101 102 7.176515 ACACACATATTTGTATTGCTCTTCCAA 59.823 33.333 0.00 0.00 33.76 3.53
102 103 6.658816 ACACACATATTTGTATTGCTCTTCCA 59.341 34.615 0.00 0.00 33.76 3.53
103 104 7.088589 ACACACATATTTGTATTGCTCTTCC 57.911 36.000 0.00 0.00 33.76 3.46
152 212 6.647334 TGCCACTTTTTCACTGATTTCATA 57.353 33.333 0.00 0.00 0.00 2.15
153 213 5.534207 TGCCACTTTTTCACTGATTTCAT 57.466 34.783 0.00 0.00 0.00 2.57
162 225 3.243068 ACAGAACGATGCCACTTTTTCAC 60.243 43.478 0.00 0.00 0.00 3.18
173 236 8.781067 TTTATATAAAATGCACAGAACGATGC 57.219 30.769 5.41 0.00 42.40 3.91
202 265 5.723672 TCTACCTGGACTTGACTAGTTTG 57.276 43.478 0.00 0.00 37.17 2.93
244 315 1.391485 CTGACGGAGCAGTTCGAATTG 59.609 52.381 15.68 15.68 0.00 2.32
245 316 1.714794 CTGACGGAGCAGTTCGAATT 58.285 50.000 0.00 0.00 0.00 2.17
246 317 3.425578 CTGACGGAGCAGTTCGAAT 57.574 52.632 0.00 0.00 0.00 3.34
247 318 4.966005 CTGACGGAGCAGTTCGAA 57.034 55.556 0.00 0.00 0.00 3.71
261 332 3.351416 CTGTTGCGCTGCTGCTGA 61.351 61.111 9.73 0.00 36.97 4.26
272 343 0.874390 TTTCTGTCCGATGCTGTTGC 59.126 50.000 0.00 0.00 40.20 4.17
273 344 2.743664 TGATTTCTGTCCGATGCTGTTG 59.256 45.455 0.00 0.00 0.00 3.33
274 345 3.005554 CTGATTTCTGTCCGATGCTGTT 58.994 45.455 0.00 0.00 0.00 3.16
276 347 2.897436 TCTGATTTCTGTCCGATGCTG 58.103 47.619 0.00 0.00 0.00 4.41
277 348 3.133542 TCATCTGATTTCTGTCCGATGCT 59.866 43.478 4.17 0.00 38.76 3.79
278 349 3.461061 TCATCTGATTTCTGTCCGATGC 58.539 45.455 4.17 0.00 38.76 3.91
279 350 4.941657 TCTCATCTGATTTCTGTCCGATG 58.058 43.478 2.99 2.99 39.65 3.84
280 351 5.604758 TTCTCATCTGATTTCTGTCCGAT 57.395 39.130 0.00 0.00 0.00 4.18
282 353 6.674694 ATTTTCTCATCTGATTTCTGTCCG 57.325 37.500 0.00 0.00 0.00 4.79
284 355 9.339492 GTTCAATTTTCTCATCTGATTTCTGTC 57.661 33.333 0.00 0.00 0.00 3.51
298 369 5.022021 CGCGATGTAAGGTTCAATTTTCTC 58.978 41.667 0.00 0.00 0.00 2.87
309 380 1.449423 TGCATGCGCGATGTAAGGT 60.449 52.632 12.10 0.00 42.97 3.50
325 396 1.430632 CCGGATCAGTTGCATGTGC 59.569 57.895 0.00 0.00 42.50 4.57
326 397 1.430632 GCCGGATCAGTTGCATGTG 59.569 57.895 5.05 0.00 0.00 3.21
327 398 2.108514 CGCCGGATCAGTTGCATGT 61.109 57.895 5.05 0.00 0.00 3.21
355 434 0.778720 ACCCTAGACTAGATCCCCCG 59.221 60.000 11.27 0.00 0.00 5.73
367 446 6.011981 ACAAATGATACCCTTCAAACCCTAGA 60.012 38.462 0.00 0.00 0.00 2.43
368 447 6.095440 CACAAATGATACCCTTCAAACCCTAG 59.905 42.308 0.00 0.00 0.00 3.02
369 448 5.949354 CACAAATGATACCCTTCAAACCCTA 59.051 40.000 0.00 0.00 0.00 3.53
370 449 4.772100 CACAAATGATACCCTTCAAACCCT 59.228 41.667 0.00 0.00 0.00 4.34
371 450 4.081697 CCACAAATGATACCCTTCAAACCC 60.082 45.833 0.00 0.00 0.00 4.11
427 527 5.567823 GCCCTCTGCTCAAGTTATATACTCC 60.568 48.000 0.00 0.00 34.43 3.85
464 564 1.973812 GCCCAGGCTCTCAACAACC 60.974 63.158 0.08 0.00 38.26 3.77
499 613 4.553330 ATCTGGAACGACATAAACTGGT 57.447 40.909 0.00 0.00 0.00 4.00
511 625 5.183969 TCCCGTAGAGATATATCTGGAACG 58.816 45.833 20.05 21.52 37.25 3.95
513 627 5.491439 TCCTCCCGTAGAGATATATCTGGAA 59.509 44.000 20.05 3.63 46.50 3.53
518 652 6.127675 GGTGTTTCCTCCCGTAGAGATATATC 60.128 46.154 4.42 4.42 46.50 1.63
532 666 0.248565 GGTAGGTCGGTGTTTCCTCC 59.751 60.000 0.00 0.00 33.34 4.30
534 668 0.540365 TCGGTAGGTCGGTGTTTCCT 60.540 55.000 0.00 0.00 35.60 3.36
559 702 1.379977 AGCTCTCGATCCGTCCCAA 60.380 57.895 0.00 0.00 0.00 4.12
802 951 2.938956 ATATGCCTCTGTAGTTGGGC 57.061 50.000 0.00 0.00 44.31 5.36
903 1437 0.263172 ATCCAGATCCAGACGGACCT 59.737 55.000 0.00 0.00 46.79 3.85
923 1457 0.868406 CGTGTCAGTGAAAAGGAGGC 59.132 55.000 0.00 0.00 0.00 4.70
948 1504 0.841961 TGCATATGGAGAAGCAGGCT 59.158 50.000 4.56 0.00 32.48 4.58
1137 1735 2.361119 CGTTGACCATCCGATCTTCCTA 59.639 50.000 0.00 0.00 0.00 2.94
1231 1874 3.951037 ACCATTATAATGTTGCTTCCGCA 59.049 39.130 21.20 0.00 38.05 5.69
1363 2012 7.307632 CCAGATATCAATGATTTCCACTTCGTC 60.308 40.741 0.00 0.00 0.00 4.20
1364 2013 6.484643 CCAGATATCAATGATTTCCACTTCGT 59.515 38.462 0.00 0.00 0.00 3.85
1445 2100 5.255687 ACTGCACATTGAGATATGAAACCA 58.744 37.500 0.00 0.00 0.00 3.67
1450 2105 5.255687 ACCAAACTGCACATTGAGATATGA 58.744 37.500 8.02 0.00 0.00 2.15
1486 2145 0.611618 TGGACCACCACATGCCAATC 60.612 55.000 0.00 0.00 41.77 2.67
1528 2187 1.466167 CTCGCCAAATCTGACCAACAG 59.534 52.381 0.00 0.00 46.97 3.16
1552 2211 7.665559 ACTGCCTTCAATATCAAAGTGAAGTAA 59.334 33.333 12.50 2.24 44.40 2.24
1588 2247 4.899457 ACGGAGACCTACATGATGGAAATA 59.101 41.667 13.89 0.00 0.00 1.40
1601 2260 5.220989 CGATGTTGAGAAATACGGAGACCTA 60.221 44.000 0.00 0.00 0.00 3.08
1717 2439 9.082313 GGATCCACTCCATACATATTGAAAAAT 57.918 33.333 6.95 0.00 44.26 1.82
1931 2685 9.508567 GATAAAAGCCAAATCAATACTTCAGAC 57.491 33.333 0.00 0.00 0.00 3.51
1939 2693 8.537728 AGACCATGATAAAAGCCAAATCAATA 57.462 30.769 0.00 0.00 33.60 1.90
1979 2737 8.883731 CAGTACTAAGAAAACCACTGGATAATG 58.116 37.037 0.71 0.00 31.83 1.90
2039 2800 6.978674 TTCATGGTTGGGTACAAAATAACA 57.021 33.333 0.00 0.00 38.54 2.41
2054 2815 6.294731 GGACACTCTGCTTTAATTTCATGGTT 60.295 38.462 0.00 0.00 0.00 3.67
2140 2901 6.086785 AGTTATAGCAGAAGGTTCCGATAC 57.913 41.667 0.00 0.00 0.00 2.24
2146 2907 8.950208 AAAGACATAGTTATAGCAGAAGGTTC 57.050 34.615 0.00 0.00 0.00 3.62
2162 2923 7.545965 ACCTAACGATTCAACAGAAAGACATAG 59.454 37.037 0.00 0.00 0.00 2.23
2203 2964 4.906618 AGTTATCAGCGAAAGGGAAAGAA 58.093 39.130 0.00 0.00 0.00 2.52
2204 2965 4.553330 AGTTATCAGCGAAAGGGAAAGA 57.447 40.909 0.00 0.00 0.00 2.52
2205 2966 6.927294 AATAGTTATCAGCGAAAGGGAAAG 57.073 37.500 0.00 0.00 0.00 2.62
2206 2967 8.795842 TTAAATAGTTATCAGCGAAAGGGAAA 57.204 30.769 0.00 0.00 0.00 3.13
2209 2970 7.444183 TCCATTAAATAGTTATCAGCGAAAGGG 59.556 37.037 0.00 0.00 0.00 3.95
2373 3138 3.119137 AGGCAAGCAGAAAACTCGTTTTT 60.119 39.130 8.94 0.00 42.26 1.94
2379 3144 2.620585 AGACAAGGCAAGCAGAAAACTC 59.379 45.455 0.00 0.00 0.00 3.01
2410 3175 3.091545 CCACATAATTCCTGGTGCTGTT 58.908 45.455 0.00 0.00 0.00 3.16
2429 3194 1.068610 GCTTTTACAACTGCATCGCCA 60.069 47.619 0.00 0.00 0.00 5.69
2460 3225 6.291377 GCATAATACAACTGATGAGAGGGAA 58.709 40.000 0.00 0.00 0.00 3.97
2461 3226 5.221722 GGCATAATACAACTGATGAGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
2501 3266 7.436970 CGTACTACATATGCACTACCAAATGAA 59.563 37.037 1.58 0.00 0.00 2.57
2509 3274 5.813717 TGACACGTACTACATATGCACTAC 58.186 41.667 1.58 0.00 0.00 2.73
2523 3292 2.372690 CCGCTGCACTGACACGTAC 61.373 63.158 0.00 0.00 0.00 3.67
2590 3360 5.183140 TGTTGAGTAGCCTAAATTTTCCAGC 59.817 40.000 0.00 0.00 0.00 4.85
2591 3361 6.623767 GCTGTTGAGTAGCCTAAATTTTCCAG 60.624 42.308 0.00 0.00 35.15 3.86
2635 3408 0.468029 AACCAGGCACTCACAAAGGG 60.468 55.000 0.00 0.00 34.60 3.95
2642 3415 2.289444 GCTAAGTGTAACCAGGCACTCA 60.289 50.000 0.00 0.00 44.21 3.41
2646 3419 1.271163 GGTGCTAAGTGTAACCAGGCA 60.271 52.381 0.00 0.00 37.80 4.75
2647 3420 1.271163 TGGTGCTAAGTGTAACCAGGC 60.271 52.381 0.00 0.00 37.77 4.85
2648 3421 2.851263 TGGTGCTAAGTGTAACCAGG 57.149 50.000 0.00 0.00 37.77 4.45
2649 3422 3.009723 CCATGGTGCTAAGTGTAACCAG 58.990 50.000 2.57 0.00 45.46 4.00
2650 3423 2.290641 CCCATGGTGCTAAGTGTAACCA 60.291 50.000 11.73 0.00 46.26 3.67
2651 3424 2.290705 ACCCATGGTGCTAAGTGTAACC 60.291 50.000 11.73 0.00 32.49 2.85
2652 3425 3.007635 GACCCATGGTGCTAAGTGTAAC 58.992 50.000 11.73 0.00 35.25 2.50
2653 3426 2.026636 GGACCCATGGTGCTAAGTGTAA 60.027 50.000 11.73 0.00 40.95 2.41
2654 3427 1.557832 GGACCCATGGTGCTAAGTGTA 59.442 52.381 11.73 0.00 40.95 2.90
2655 3428 0.328258 GGACCCATGGTGCTAAGTGT 59.672 55.000 11.73 0.00 40.95 3.55
2656 3429 0.327924 TGGACCCATGGTGCTAAGTG 59.672 55.000 11.73 0.00 44.53 3.16
2657 3430 0.620556 CTGGACCCATGGTGCTAAGT 59.379 55.000 11.73 0.00 44.53 2.24
2658 3431 0.911769 TCTGGACCCATGGTGCTAAG 59.088 55.000 11.73 1.76 44.53 2.18
2659 3432 1.595311 ATCTGGACCCATGGTGCTAA 58.405 50.000 11.73 0.00 44.53 3.09
2660 3433 1.595311 AATCTGGACCCATGGTGCTA 58.405 50.000 11.73 0.00 44.53 3.49
2661 3434 1.595311 TAATCTGGACCCATGGTGCT 58.405 50.000 11.73 0.00 44.53 4.40
2662 3435 2.664402 ATAATCTGGACCCATGGTGC 57.336 50.000 11.73 4.96 44.48 5.01
2663 3436 6.070656 ACATTAATAATCTGGACCCATGGTG 58.929 40.000 11.73 4.77 35.25 4.17
2664 3437 6.279813 ACATTAATAATCTGGACCCATGGT 57.720 37.500 11.73 0.00 39.44 3.55
2665 3438 8.884124 AATACATTAATAATCTGGACCCATGG 57.116 34.615 4.14 4.14 0.00 3.66
2666 3439 8.960591 GGAATACATTAATAATCTGGACCCATG 58.039 37.037 0.00 0.00 0.00 3.66
2667 3440 8.677871 TGGAATACATTAATAATCTGGACCCAT 58.322 33.333 0.00 0.00 0.00 4.00
2668 3441 8.051468 TGGAATACATTAATAATCTGGACCCA 57.949 34.615 0.00 0.00 0.00 4.51
2669 3442 8.934023 TTGGAATACATTAATAATCTGGACCC 57.066 34.615 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.