Multiple sequence alignment - TraesCS1A01G356400

Loading Multiple Alignment...

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 TraesCS1A01G356400 chr1A 100.000 3795 0 0 1 3795 539617592 539613798 0.000000e+00 7009.0
1 TraesCS1A01G356400 chr1A 88.741 2407 238 16 1057 3442 539428233 539425839 0.000000e+00 2913.0
2 TraesCS1A01G356400 chr1A 82.237 760 93 20 2019 2749 539721619 539722365 6.280000e-173 617.0
3 TraesCS1A01G356400 chr1A 100.000 182 0 0 4237 4418 539613356 539613175 1.970000e-88 337.0
4 TraesCS1A01G356400 chr1A 84.718 301 34 5 37 326 574917338 574917637 1.550000e-74 291.0
5 TraesCS1A01G356400 chr1B 93.158 3201 180 19 609 3793 603149849 603146672 0.000000e+00 4662.0
6 TraesCS1A01G356400 chr1B 87.773 2609 255 37 1057 3618 603093725 603091134 0.000000e+00 2992.0
7 TraesCS1A01G356400 chr1B 84.075 2449 328 27 1027 3438 603261334 603263757 0.000000e+00 2305.0
8 TraesCS1A01G356400 chr1B 91.837 98 5 1 4237 4334 603146611 603146517 2.770000e-27 134.0
9 TraesCS1A01G356400 chr1B 98.214 56 1 0 4360 4415 603146517 603146462 1.010000e-16 99.0
10 TraesCS1A01G356400 chr1B 96.970 33 1 0 7 39 10270794 10270762 6.170000e-04 56.5
11 TraesCS1A01G356400 chr1D 96.852 2764 77 3 774 3536 443552425 443555179 0.000000e+00 4614.0
12 TraesCS1A01G356400 chr1D 89.312 2414 217 16 1057 3442 443716375 443718775 0.000000e+00 2990.0
13 TraesCS1A01G356400 chr1D 84.124 2444 321 37 1030 3438 443467411 443465000 0.000000e+00 2302.0
14 TraesCS1A01G356400 chr1D 89.057 1718 145 23 1057 2746 443429569 443427867 0.000000e+00 2091.0
15 TraesCS1A01G356400 chr1D 90.110 728 53 8 37 755 443550889 443551606 0.000000e+00 928.0
16 TraesCS1A01G356400 chr1D 87.054 757 83 10 3036 3786 443556963 443557710 0.000000e+00 841.0
17 TraesCS1A01G356400 chr1D 88.433 268 20 3 3537 3793 443555218 443555485 3.320000e-81 313.0
18 TraesCS1A01G356400 chr1D 100.000 28 0 0 12 39 10537102 10537129 8.000000e-03 52.8
19 TraesCS1A01G356400 chr3D 85.744 2413 282 36 1070 3433 341493496 341495895 0.000000e+00 2494.0
20 TraesCS1A01G356400 chr3D 84.308 325 39 5 39 352 94822512 94822189 1.540000e-79 307.0
21 TraesCS1A01G356400 chr3D 87.149 249 30 2 37 283 173712326 173712574 9.360000e-72 281.0
22 TraesCS1A01G356400 chr3B 85.614 2412 284 31 1059 3421 440228921 440231318 0.000000e+00 2473.0
23 TraesCS1A01G356400 chr4B 84.232 2448 322 33 1017 3438 660197530 660195121 0.000000e+00 2324.0
24 TraesCS1A01G356400 chr7D 80.763 655 89 16 37 662 101389326 101389972 1.110000e-130 477.0
25 TraesCS1A01G356400 chr7D 78.035 692 94 27 37 711 589449461 589450111 2.490000e-102 383.0
26 TraesCS1A01G356400 chr5A 76.791 642 103 28 34 658 662967887 662968499 7.130000e-83 318.0
27 TraesCS1A01G356400 chr7B 78.237 556 78 16 37 566 454821257 454820719 2.560000e-82 316.0
28 TraesCS1A01G356400 chr7B 80.612 98 16 3 494 590 130107679 130107774 6.130000e-09 73.1
29 TraesCS1A01G356400 chrUn 84.036 332 39 6 37 354 290724 291055 1.540000e-79 307.0
30 TraesCS1A01G356400 chrUn 82.875 327 44 4 37 352 346316762 346317087 2.600000e-72 283.0
31 TraesCS1A01G356400 chrUn 82.569 327 45 4 37 352 362225667 362225992 1.210000e-70 278.0
32 TraesCS1A01G356400 chrUn 94.595 37 1 1 4 39 147926113 147926077 6.170000e-04 56.5
33 TraesCS1A01G356400 chr3A 83.180 327 43 4 37 352 738645561 738645886 5.590000e-74 289.0
34 TraesCS1A01G356400 chr3A 82.875 327 44 4 37 352 738567053 738567378 2.600000e-72 283.0
35 TraesCS1A01G356400 chr3A 83.784 296 42 2 37 326 702566542 702566837 4.350000e-70 276.0
36 TraesCS1A01G356400 chr4A 82.515 326 54 3 37 359 666016463 666016138 2.600000e-72 283.0
37 TraesCS1A01G356400 chr4A 100.000 29 0 0 493 521 192728289 192728261 2.000000e-03 54.7
38 TraesCS1A01G356400 chr2A 81.437 334 51 5 37 360 694867000 694867332 3.390000e-66 263.0
39 TraesCS1A01G356400 chr2A 92.857 42 1 2 3616 3656 771545932 771545892 4.770000e-05 60.2
40 TraesCS1A01G356400 chr2A 94.595 37 1 1 4 39 98900718 98900682 6.170000e-04 56.5
41 TraesCS1A01G356400 chr5B 75.174 576 102 27 37 590 598320266 598320822 2.660000e-57 233.0
42 TraesCS1A01G356400 chr5B 74.483 580 95 36 37 590 598290007 598289455 7.490000e-48 202.0
43 TraesCS1A01G356400 chr7A 77.143 245 32 18 366 591 104778959 104779198 2.160000e-23 121.0
44 TraesCS1A01G356400 chr5D 84.848 99 13 2 493 590 430092309 430092406 1.010000e-16 99.0
45 TraesCS1A01G356400 chr5D 79.231 130 19 6 478 607 325965919 325965798 2.830000e-12 84.2
46 TraesCS1A01G356400 chr6D 94.595 37 1 1 4 39 5695503 5695467 6.170000e-04 56.5


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 TraesCS1A01G356400 chr1A 539613175 539617592 4417 True 3673.000000 7009 100.00000 1 4418 2 chr1A.!!$R2 4417
1 TraesCS1A01G356400 chr1A 539425839 539428233 2394 True 2913.000000 2913 88.74100 1057 3442 1 chr1A.!!$R1 2385
2 TraesCS1A01G356400 chr1A 539721619 539722365 746 False 617.000000 617 82.23700 2019 2749 1 chr1A.!!$F1 730
3 TraesCS1A01G356400 chr1B 603091134 603093725 2591 True 2992.000000 2992 87.77300 1057 3618 1 chr1B.!!$R2 2561
4 TraesCS1A01G356400 chr1B 603261334 603263757 2423 False 2305.000000 2305 84.07500 1027 3438 1 chr1B.!!$F1 2411
5 TraesCS1A01G356400 chr1B 603146462 603149849 3387 True 1631.666667 4662 94.40300 609 4415 3 chr1B.!!$R3 3806
6 TraesCS1A01G356400 chr1D 443716375 443718775 2400 False 2990.000000 2990 89.31200 1057 3442 1 chr1D.!!$F2 2385
7 TraesCS1A01G356400 chr1D 443465000 443467411 2411 True 2302.000000 2302 84.12400 1030 3438 1 chr1D.!!$R2 2408
8 TraesCS1A01G356400 chr1D 443427867 443429569 1702 True 2091.000000 2091 89.05700 1057 2746 1 chr1D.!!$R1 1689
9 TraesCS1A01G356400 chr1D 443550889 443557710 6821 False 1674.000000 4614 90.61225 37 3793 4 chr1D.!!$F3 3756
10 TraesCS1A01G356400 chr3D 341493496 341495895 2399 False 2494.000000 2494 85.74400 1070 3433 1 chr3D.!!$F2 2363
11 TraesCS1A01G356400 chr3B 440228921 440231318 2397 False 2473.000000 2473 85.61400 1059 3421 1 chr3B.!!$F1 2362
12 TraesCS1A01G356400 chr4B 660195121 660197530 2409 True 2324.000000 2324 84.23200 1017 3438 1 chr4B.!!$R1 2421
13 TraesCS1A01G356400 chr7D 101389326 101389972 646 False 477.000000 477 80.76300 37 662 1 chr7D.!!$F1 625
14 TraesCS1A01G356400 chr7D 589449461 589450111 650 False 383.000000 383 78.03500 37 711 1 chr7D.!!$F2 674
15 TraesCS1A01G356400 chr5A 662967887 662968499 612 False 318.000000 318 76.79100 34 658 1 chr5A.!!$F1 624
16 TraesCS1A01G356400 chr7B 454820719 454821257 538 True 316.000000 316 78.23700 37 566 1 chr7B.!!$R1 529
17 TraesCS1A01G356400 chr5B 598320266 598320822 556 False 233.000000 233 75.17400 37 590 1 chr5B.!!$F1 553
18 TraesCS1A01G356400 chr5B 598289455 598290007 552 True 202.000000 202 74.48300 37 590 1 chr5B.!!$R1 553

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
20 21 0.034476 CTCTTCAGCACTGCTCCACA 59.966 55.000 0.0 0.0 36.40 4.17 F
26 27 0.250467 AGCACTGCTCCACAAACGAT 60.250 50.000 0.0 0.0 30.62 3.73 F
1125 1977 0.833287 CATCCCTGTCCGTGGAAGAT 59.167 55.000 0.0 0.0 33.54 2.40 F
2188 3127 1.133668 GTTGCTATCCCAAGGGCATCT 60.134 52.381 0.0 0.0 34.59 2.90 F
3336 4543 1.326213 CGTGCATGGAGGAGAGGAGT 61.326 60.000 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 2224 0.178992 AGTTGTTGCTGGCTGCCTTA 60.179 50.000 21.03 3.01 42.00 2.69 R
1380 2242 1.104630 GGAGGGAGACGGTGAAGTAG 58.895 60.000 0.00 0.00 0.00 2.57 R
2385 3481 0.103208 CGAGAAATCCTAGCACCGCT 59.897 55.000 0.00 0.00 43.41 5.52 R
3336 4543 2.364973 TCCATGGTCGGCCTGCTA 60.365 61.111 12.58 0.00 35.27 3.49 R
4342 7852 0.106708 GACTGTTCAGTGCCTGTGGA 59.893 55.000 10.29 0.00 32.61 4.02 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
18 19 2.750665 TCTCTTCAGCACTGCTCCA 58.249 52.632 0.00 0.00 36.40 3.86
19 20 0.319728 TCTCTTCAGCACTGCTCCAC 59.680 55.000 0.00 0.00 36.40 4.02
20 21 0.034476 CTCTTCAGCACTGCTCCACA 59.966 55.000 0.00 0.00 36.40 4.17
21 22 0.469494 TCTTCAGCACTGCTCCACAA 59.531 50.000 0.00 0.00 36.40 3.33
22 23 1.134128 TCTTCAGCACTGCTCCACAAA 60.134 47.619 0.00 0.00 36.40 2.83
23 24 1.002033 CTTCAGCACTGCTCCACAAAC 60.002 52.381 0.00 0.00 36.40 2.93
24 25 1.159713 TCAGCACTGCTCCACAAACG 61.160 55.000 0.00 0.00 36.40 3.60
25 26 1.146041 AGCACTGCTCCACAAACGA 59.854 52.632 0.00 0.00 30.62 3.85
26 27 0.250467 AGCACTGCTCCACAAACGAT 60.250 50.000 0.00 0.00 30.62 3.73
27 28 1.001974 AGCACTGCTCCACAAACGATA 59.998 47.619 0.00 0.00 30.62 2.92
28 29 1.128692 GCACTGCTCCACAAACGATAC 59.871 52.381 0.00 0.00 0.00 2.24
29 30 2.688507 CACTGCTCCACAAACGATACT 58.311 47.619 0.00 0.00 0.00 2.12
30 31 2.668457 CACTGCTCCACAAACGATACTC 59.332 50.000 0.00 0.00 0.00 2.59
31 32 2.271800 CTGCTCCACAAACGATACTCC 58.728 52.381 0.00 0.00 0.00 3.85
32 33 1.066430 TGCTCCACAAACGATACTCCC 60.066 52.381 0.00 0.00 0.00 4.30
33 34 1.066430 GCTCCACAAACGATACTCCCA 60.066 52.381 0.00 0.00 0.00 4.37
34 35 2.614481 GCTCCACAAACGATACTCCCAA 60.614 50.000 0.00 0.00 0.00 4.12
35 36 3.670625 CTCCACAAACGATACTCCCAAA 58.329 45.455 0.00 0.00 0.00 3.28
53 54 3.632145 CCAAAAGATCCTATGGTTTCCCG 59.368 47.826 0.00 0.00 0.00 5.14
218 221 2.466846 TCTCGAGATCCAACCATCCAA 58.533 47.619 12.08 0.00 0.00 3.53
265 268 3.338250 ATGACCACCATGGCCGGT 61.338 61.111 23.24 23.24 42.67 5.28
397 416 2.514592 CATCGCTGCCACCCGAAT 60.515 61.111 0.00 0.00 37.00 3.34
491 525 1.675641 GCCGACCACAGCCATCTTT 60.676 57.895 0.00 0.00 0.00 2.52
513 547 2.011881 GCTTCGCTAGATCGGTCGC 61.012 63.158 0.00 0.00 0.00 5.19
553 588 3.625897 CGCACCACCCCTGAGACA 61.626 66.667 0.00 0.00 0.00 3.41
556 591 2.200370 ACCACCCCTGAGACACGA 59.800 61.111 0.00 0.00 0.00 4.35
582 617 4.035102 GAGTCCCCCACCACAGCC 62.035 72.222 0.00 0.00 0.00 4.85
700 735 4.899239 GCCATCCGAGTCGCCCTG 62.899 72.222 7.12 3.71 0.00 4.45
733 768 1.079336 GGGGACAGTTAGACGTGGC 60.079 63.158 0.00 0.00 0.00 5.01
796 1630 2.808543 GCACCGGATCCAATACAAGATC 59.191 50.000 9.46 0.00 38.54 2.75
943 1780 4.023878 GTGGCCTGACGTAAAACAAATACA 60.024 41.667 3.32 0.00 0.00 2.29
991 1828 4.211164 TCACATCCATCGCGACATTAATTC 59.789 41.667 12.93 0.00 0.00 2.17
996 1833 3.365264 CCATCGCGACATTAATTCCATGG 60.365 47.826 12.93 4.97 0.00 3.66
1014 1851 1.138859 TGGACCATGGCTAGATTCGTG 59.861 52.381 13.04 0.00 0.00 4.35
1028 1865 8.732531 GGCTAGATTCGTGATTAGTCTTATAGT 58.267 37.037 0.00 0.00 0.00 2.12
1125 1977 0.833287 CATCCCTGTCCGTGGAAGAT 59.167 55.000 0.00 0.00 33.54 2.40
1170 2022 2.584391 GGACGCCACCTTCTCCTGT 61.584 63.158 0.00 0.00 0.00 4.00
1194 2055 4.821589 CTCCCAGCCGGCGAAGTC 62.822 72.222 23.20 0.00 0.00 3.01
1212 2074 2.035576 AGTCGACAACGCCTTCTACTTT 59.964 45.455 19.50 0.00 39.58 2.66
1372 2234 1.845664 TGGGACAGTAAGGCAGCCA 60.846 57.895 15.80 0.00 0.00 4.75
1982 2885 1.498176 AACCCCACCTTCAGCCTACC 61.498 60.000 0.00 0.00 0.00 3.18
1983 2886 2.680370 CCCCACCTTCAGCCTACCC 61.680 68.421 0.00 0.00 0.00 3.69
1984 2887 1.923395 CCCACCTTCAGCCTACCCA 60.923 63.158 0.00 0.00 0.00 4.51
1985 2888 1.299976 CCACCTTCAGCCTACCCAC 59.700 63.158 0.00 0.00 0.00 4.61
1986 2889 1.299976 CACCTTCAGCCTACCCACC 59.700 63.158 0.00 0.00 0.00 4.61
1987 2890 1.151899 ACCTTCAGCCTACCCACCA 60.152 57.895 0.00 0.00 0.00 4.17
1988 2891 1.299976 CCTTCAGCCTACCCACCAC 59.700 63.158 0.00 0.00 0.00 4.16
1989 2892 1.299976 CTTCAGCCTACCCACCACC 59.700 63.158 0.00 0.00 0.00 4.61
1990 2893 1.462432 TTCAGCCTACCCACCACCA 60.462 57.895 0.00 0.00 0.00 4.17
2108 3047 3.064207 TCACGTTCCAATACTGCAAGAC 58.936 45.455 0.00 0.00 37.43 3.01
2188 3127 1.133668 GTTGCTATCCCAAGGGCATCT 60.134 52.381 0.00 0.00 34.59 2.90
3336 4543 1.326213 CGTGCATGGAGGAGAGGAGT 61.326 60.000 0.00 0.00 0.00 3.85
3451 4658 9.607988 TCCTTGCTATATTAATTCGTCAAAAGA 57.392 29.630 0.00 0.00 0.00 2.52
3519 4744 6.684555 CGTGAAAAGATAAGATTGCAGTTAGC 59.315 38.462 0.00 0.00 45.96 3.09
3623 7133 1.909986 GAGACCAAGGAGTAAGGCCTT 59.090 52.381 24.18 24.18 46.36 4.35
3636 7146 5.070685 AGTAAGGCCTTCTTTGGTTTACAG 58.929 41.667 24.49 0.00 36.93 2.74
3752 7262 9.472361 CATGCTAGAAAATCTCATAAAAATGGG 57.528 33.333 0.00 0.00 0.00 4.00
3760 7270 6.937436 ATCTCATAAAAATGGGTAACGGTC 57.063 37.500 0.00 0.00 37.60 4.79
3787 7297 3.825585 TGGCATCTCATAAAAGCACAACA 59.174 39.130 0.00 0.00 0.00 3.33
3793 7303 7.221452 GCATCTCATAAAAGCACAACAATTAGG 59.779 37.037 0.00 0.00 0.00 2.69
3794 7304 6.620678 TCTCATAAAAGCACAACAATTAGGC 58.379 36.000 0.00 0.00 0.00 3.93
4272 7782 6.957631 TGTCATCCTCAAAGCCTAATTTAGA 58.042 36.000 4.96 0.00 0.00 2.10
4273 7783 7.402054 TGTCATCCTCAAAGCCTAATTTAGAA 58.598 34.615 4.96 0.00 0.00 2.10
4274 7784 7.888021 TGTCATCCTCAAAGCCTAATTTAGAAA 59.112 33.333 4.96 0.00 0.00 2.52
4309 7819 0.026803 GCAGCTACGGCAAATTCGAG 59.973 55.000 0.00 0.00 41.70 4.04
4406 7916 1.661463 ATGGACCTCATATCCGGCAT 58.339 50.000 0.00 0.00 39.30 4.40
4415 7925 4.835056 CCTCATATCCGGCATCCTATATCA 59.165 45.833 0.00 0.00 0.00 2.15
4416 7926 5.305386 CCTCATATCCGGCATCCTATATCAA 59.695 44.000 0.00 0.00 0.00 2.57
4417 7927 6.013898 CCTCATATCCGGCATCCTATATCAAT 60.014 42.308 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.034476 TGTGGAGCAGTGCTGAAGAG 59.966 55.000 25.35 0.00 39.88 2.85
2 3 0.469494 TTGTGGAGCAGTGCTGAAGA 59.531 50.000 25.35 5.82 39.88 2.87
3 4 1.002033 GTTTGTGGAGCAGTGCTGAAG 60.002 52.381 25.35 0.00 39.88 3.02
5 6 1.159713 CGTTTGTGGAGCAGTGCTGA 61.160 55.000 25.35 5.76 39.88 4.26
7 8 0.250467 ATCGTTTGTGGAGCAGTGCT 60.250 50.000 19.86 19.86 43.88 4.40
8 9 1.128692 GTATCGTTTGTGGAGCAGTGC 59.871 52.381 7.13 7.13 0.00 4.40
9 10 2.668457 GAGTATCGTTTGTGGAGCAGTG 59.332 50.000 0.00 0.00 0.00 3.66
10 11 2.353803 GGAGTATCGTTTGTGGAGCAGT 60.354 50.000 0.00 0.00 34.37 4.40
11 12 2.271800 GGAGTATCGTTTGTGGAGCAG 58.728 52.381 0.00 0.00 34.37 4.24
12 13 1.066430 GGGAGTATCGTTTGTGGAGCA 60.066 52.381 0.00 0.00 34.37 4.26
13 14 1.066430 TGGGAGTATCGTTTGTGGAGC 60.066 52.381 0.00 0.00 34.37 4.70
14 15 3.328382 TTGGGAGTATCGTTTGTGGAG 57.672 47.619 0.00 0.00 34.37 3.86
15 16 3.773418 TTTGGGAGTATCGTTTGTGGA 57.227 42.857 0.00 0.00 34.37 4.02
16 17 4.069304 TCTTTTGGGAGTATCGTTTGTGG 58.931 43.478 0.00 0.00 34.37 4.17
17 18 5.163754 GGATCTTTTGGGAGTATCGTTTGTG 60.164 44.000 0.00 0.00 34.37 3.33
18 19 4.941873 GGATCTTTTGGGAGTATCGTTTGT 59.058 41.667 0.00 0.00 34.37 2.83
19 20 5.186198 AGGATCTTTTGGGAGTATCGTTTG 58.814 41.667 0.00 0.00 34.37 2.93
20 21 5.437191 AGGATCTTTTGGGAGTATCGTTT 57.563 39.130 0.00 0.00 34.37 3.60
21 22 6.464465 CCATAGGATCTTTTGGGAGTATCGTT 60.464 42.308 6.44 0.00 34.37 3.85
22 23 5.012148 CCATAGGATCTTTTGGGAGTATCGT 59.988 44.000 6.44 0.00 34.37 3.73
23 24 5.012148 ACCATAGGATCTTTTGGGAGTATCG 59.988 44.000 16.75 0.00 34.37 2.92
24 25 6.441088 ACCATAGGATCTTTTGGGAGTATC 57.559 41.667 16.75 0.00 33.39 2.24
25 26 6.848562 AACCATAGGATCTTTTGGGAGTAT 57.151 37.500 16.75 0.00 33.39 2.12
26 27 6.353602 GGAAACCATAGGATCTTTTGGGAGTA 60.354 42.308 16.75 0.00 33.39 2.59
27 28 5.510430 GAAACCATAGGATCTTTTGGGAGT 58.490 41.667 16.75 3.53 33.39 3.85
28 29 4.889995 GGAAACCATAGGATCTTTTGGGAG 59.110 45.833 16.75 0.00 33.39 4.30
29 30 4.867086 GGAAACCATAGGATCTTTTGGGA 58.133 43.478 16.75 0.00 33.39 4.37
53 54 3.414700 CCACTCGTGTTGCTCCGC 61.415 66.667 0.00 0.00 0.00 5.54
145 146 2.812011 GACATAGTTGCCGGTGAAAACT 59.188 45.455 1.90 10.88 37.82 2.66
214 217 2.081787 TGGTTGGCCTGAGGTTGGA 61.082 57.895 3.32 0.00 35.27 3.53
218 221 2.450502 AGGTGGTTGGCCTGAGGT 60.451 61.111 3.32 0.00 34.56 3.85
265 268 0.674581 CTCTGTTCTGGCCGATGCAA 60.675 55.000 0.00 0.00 40.13 4.08
326 343 1.004277 CGCGCCATCTAGATTCGGAC 61.004 60.000 19.71 8.53 0.00 4.79
513 547 1.154016 CTCTACACGTGTGGAGGCG 60.154 63.158 39.54 24.15 46.05 5.52
553 588 1.610873 GGGACTCCCTCTCTCTCGT 59.389 63.158 6.90 0.00 41.34 4.18
664 699 1.228737 GCCCAAACCTTAGCCACCA 60.229 57.895 0.00 0.00 0.00 4.17
667 702 2.675075 GCGCCCAAACCTTAGCCA 60.675 61.111 0.00 0.00 0.00 4.75
714 749 1.595357 CCACGTCTAACTGTCCCCC 59.405 63.158 0.00 0.00 0.00 5.40
796 1630 1.810151 CCATACCAACTTGTTGGACGG 59.190 52.381 31.71 23.89 44.82 4.79
832 1666 2.217750 TGTGGAATTGGACTTGTGACG 58.782 47.619 0.00 0.00 0.00 4.35
996 1833 2.890808 TCACGAATCTAGCCATGGTC 57.109 50.000 14.67 5.80 0.00 4.02
1014 1851 7.726738 AGTGGAAGGAGGACTATAAGACTAATC 59.273 40.741 0.00 0.00 0.00 1.75
1028 1865 2.584965 AGAGAGATGAGTGGAAGGAGGA 59.415 50.000 0.00 0.00 0.00 3.71
1192 2053 2.061740 AAGTAGAAGGCGTTGTCGAC 57.938 50.000 9.11 9.11 46.75 4.20
1193 2054 2.806608 AAAGTAGAAGGCGTTGTCGA 57.193 45.000 0.00 0.00 39.71 4.20
1194 2055 2.157085 GGAAAAGTAGAAGGCGTTGTCG 59.843 50.000 0.00 0.00 40.37 4.35
1212 2074 2.029964 GCGGTGAACCAGACGGAA 59.970 61.111 0.00 0.00 35.59 4.30
1362 2224 0.178992 AGTTGTTGCTGGCTGCCTTA 60.179 50.000 21.03 3.01 42.00 2.69
1372 2234 2.102588 AGACGGTGAAGTAGTTGTTGCT 59.897 45.455 0.00 0.00 0.00 3.91
1380 2242 1.104630 GGAGGGAGACGGTGAAGTAG 58.895 60.000 0.00 0.00 0.00 2.57
1743 2646 1.449778 GGTTAGCCGCCTCTTGACC 60.450 63.158 0.00 0.00 0.00 4.02
1927 2830 4.096003 CCGGCGGTCCACCATCTT 62.096 66.667 19.97 0.00 35.14 2.40
1983 2886 4.885270 TTGGTGGCGGTGGTGGTG 62.885 66.667 0.00 0.00 0.00 4.17
1984 2887 4.887190 GTTGGTGGCGGTGGTGGT 62.887 66.667 0.00 0.00 0.00 4.16
1985 2888 4.579384 AGTTGGTGGCGGTGGTGG 62.579 66.667 0.00 0.00 0.00 4.61
1986 2889 3.286751 CAGTTGGTGGCGGTGGTG 61.287 66.667 0.00 0.00 0.00 4.17
1989 2892 3.663176 CTGCAGTTGGTGGCGGTG 61.663 66.667 5.25 0.00 0.00 4.94
2108 3047 2.871022 GAGCACATACTCAAGCAGATGG 59.129 50.000 0.00 0.00 36.65 3.51
2188 3127 1.587490 CGACGTGTAACCGTTGAACAA 59.413 47.619 0.00 0.00 43.42 2.83
2320 3416 2.561894 CGTACGTGTCCGCGTATGC 61.562 63.158 16.68 0.00 46.81 3.14
2385 3481 0.103208 CGAGAAATCCTAGCACCGCT 59.897 55.000 0.00 0.00 43.41 5.52
2776 3896 4.008933 GTGCCTGTCCAGCGACCT 62.009 66.667 0.00 0.00 38.32 3.85
3336 4543 2.364973 TCCATGGTCGGCCTGCTA 60.365 61.111 12.58 0.00 35.27 3.49
3451 4658 7.739498 ACGTCTCACTACATTTTTGGTAAAT 57.261 32.000 0.00 0.00 0.00 1.40
3519 4744 4.018649 TCAATTGTAATCGCATGCACAG 57.981 40.909 19.57 0.99 0.00 3.66
3726 7236 9.472361 CCCATTTTTATGAGATTTTCTAGCATG 57.528 33.333 0.00 0.00 0.00 4.06
3751 7261 2.752903 AGATGCCAAATTGACCGTTACC 59.247 45.455 0.00 0.00 0.00 2.85
3752 7262 3.438781 TGAGATGCCAAATTGACCGTTAC 59.561 43.478 0.00 0.00 0.00 2.50
3760 7270 5.870433 TGTGCTTTTATGAGATGCCAAATTG 59.130 36.000 0.00 0.00 0.00 2.32
4239 7749 4.925646 GCTTTGAGGATGACAATGTTTTCC 59.074 41.667 7.27 7.27 0.00 3.13
4338 7848 4.662961 TCAGTGCCTGTGGACGCG 62.663 66.667 3.53 3.53 32.61 6.01
4339 7849 2.280797 TTCAGTGCCTGTGGACGC 60.281 61.111 2.68 0.00 32.61 5.19
4340 7850 1.224069 CTGTTCAGTGCCTGTGGACG 61.224 60.000 2.68 0.00 32.61 4.79
4341 7851 0.179045 ACTGTTCAGTGCCTGTGGAC 60.179 55.000 4.58 0.00 32.61 4.02
4342 7852 0.106708 GACTGTTCAGTGCCTGTGGA 59.893 55.000 10.29 0.00 32.61 4.02
4343 7853 0.179048 TGACTGTTCAGTGCCTGTGG 60.179 55.000 10.29 0.00 32.61 4.17
4344 7854 0.940126 GTGACTGTTCAGTGCCTGTG 59.060 55.000 10.29 0.00 32.61 3.66
4345 7855 0.530650 CGTGACTGTTCAGTGCCTGT 60.531 55.000 10.29 0.00 32.61 4.00
4346 7856 1.835483 GCGTGACTGTTCAGTGCCTG 61.835 60.000 10.29 0.00 31.07 4.85
4347 7857 1.595382 GCGTGACTGTTCAGTGCCT 60.595 57.895 10.29 0.00 31.07 4.75
4348 7858 2.607892 GGCGTGACTGTTCAGTGCC 61.608 63.158 10.29 12.50 43.62 5.01
4349 7859 1.160329 AAGGCGTGACTGTTCAGTGC 61.160 55.000 10.29 7.56 34.79 4.40
4350 7860 2.148916 TAAGGCGTGACTGTTCAGTG 57.851 50.000 10.29 0.00 30.10 3.66
4351 7861 2.902705 TTAAGGCGTGACTGTTCAGT 57.097 45.000 5.08 5.08 30.10 3.41
4352 7862 4.749245 AATTTAAGGCGTGACTGTTCAG 57.251 40.909 0.00 0.00 30.10 3.02
4353 7863 5.506649 GGAAAATTTAAGGCGTGACTGTTCA 60.507 40.000 0.00 0.00 0.00 3.18
4354 7864 4.915667 GGAAAATTTAAGGCGTGACTGTTC 59.084 41.667 0.00 0.00 0.00 3.18
4355 7865 4.583073 AGGAAAATTTAAGGCGTGACTGTT 59.417 37.500 0.00 0.00 0.00 3.16
4356 7866 4.142038 AGGAAAATTTAAGGCGTGACTGT 58.858 39.130 0.00 0.00 0.00 3.55
4357 7867 4.379499 GGAGGAAAATTTAAGGCGTGACTG 60.379 45.833 0.00 0.00 0.00 3.51
4358 7868 3.756963 GGAGGAAAATTTAAGGCGTGACT 59.243 43.478 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.